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 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 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 4 TMT Channel Ratio 5 TMT Channel Ratio 6 TMT Channel Ratio 7 TMT Channel Ratio 8 TMT Channel Ratio 9 TMT Channel Ratio 10 Curve signal Log EC50 Curve slope Curve top Curve bottom R2 Curve RMSE Log EC50 error Curve slope error Curve top error Curve bottom error EC50 pEC50 Curve effect size Regulation (ac)AAAAAAAGDS(ph)DSWDADAFSVEDPVRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AAAAAAAGDSDSWDADAFSVEDPVRK 26 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 AAAAAAAGDS(0.817)DS(0.183)WDADAFSVEDPVRK;AAAAAAAGDS(0.915)DS(0.085)WDADAFSVEDPVRK;AAAAAAAGDS(0.957)DS(0.043)WDADAFSVEDPVRK;AAAAAAAGDS(0.899)DS(0.101)WDADAFSVEDPVRK 134.15 5.80E-62 2592640000 1634270 1505670 1436840 1451930 1543040 1075350 1765270 1361040 1726690 TRUE FALSE 1531983.958 1617151.373 1470922.523 1489188.982 1421855.863 1385786.088 1500584.151 1530968.84 1438494.284 1.064991342 1.124197288 1.022543182 1.035241501 0.988433446 0.963358773 1.043163096 1.064285661 1 20.45612806 3.787505961 2.924512627 1.015550426 1.095814619 0.511541905 0.031646075 0.197131266 3.348377715 0.008508922 0.016464746 6130.642073 -3.787505961 0.080264193 (ac)AAAITDMADLEELSRLS(ph)PLPPGS(ph)PGSAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAAITDMADLEELSRLSPLPPGSPGSAAR 29 1 Q6ZN18-2;Q6ZN18 Q6ZN18-2 AEBP2 Zinc finger protein AEBP2 2 AAAITDMADLEELS(0.005)RLS(0.986)PLPPGS(0.817)PGS(0.192)AAR;AAAIT(0.001)DMADLEELS(0.005)RLS(0.99)PLPPGS(0.871)PGS(0.133)AAR 56.231 1.29E-05 14342200 3365.1 3375.6 3492.6 2974 4879.5 3098 3706.5 2676.4 4177.14 TRUE FALSE 3154.484398 3625.532936 3575.446121 3050.317875 4496.283753 3992.342308 3150.744734 3010.554431 3479.948349 0.906474488 1.041835273 1.027442296 0.876541135 1.292054738 1.147241829 0.905399856 0.865114688 1 11.76485018 1.636670982 8.906631864 0.913395385 1.047758612 0.192702709 0.119868195 0.172498269 28.5657318 0.057788991 0.030041588 43.31825784 -1.636670982 0.134363227 (ac)AAAITDMADLEELSRLS(ph)PLPPGSPGSAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAAITDMADLEELSRLSPLPPGSPGSAAR 29 1 Q6ZN18-2;Q6ZN18 Q6ZN18-2 AEBP2 Zinc finger protein AEBP2 1 AAAITDMADLEELS(0.029)RLS(0.929)PLPPGS(0.029)PGS(0.013)AAR;AAAITDMADLEELS(0.015)RLS(0.98)PLPPGS(0.004)PGS(0.001)AAR 70.983 4.21E-05 17869800 1108.9 909.63 2100.72 979.66 829.51 2082.54 1638.55 1381.9 0 TRUE FALSE 1039.495928 976.9799517 2150.55007 1004.799734 764.3636307 2683.735491 1392.864639 1554.433257 0 0 (ac)AAASVT(ph)PPGSLELLQPGFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AAASVTPPGSLELLQPGFSK 20 0 Q12933-4;Q12933-3;Q12933;Q12933-2;B1AMX7;B1AMX8;B1AMY1 Q12933-4 TRAF2 TNF receptor-associated factor 2 1 AAAS(0.196)VT(0.782)PPGS(0.023)LELLQPGFSK;AAAS(0.22)VT(0.74)PPGS(0.04)LELLQPGFSK;AAAS(0.166)VT(0.764)PPGS(0.07)LELLQPGFSK 70.26 3.20E-07 117252000 268686 252808 228370 228478 273698 223994 316119 248455 314337 TRUE FALSE 251869.4229 271526.1674 233787.0442 234341.1323 252202.8631 288657.4316 268719.8907 279475.1537 261872.124 0.961803108 1.036865487 0.892752694 0.894868567 0.963076403 1.102283921 1.026149277 1.067219945 1 17.99850297 2.345752333 7.235405427 1.049938031 0.950477637 0.520883711 0.047321319 0.190040591 11.57109342 0.016921729 0.014108441 221.6931799 -2.345752333 -0.099460394 (ac)AADVSVTHRPPLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AADVSVTHRPPLSPK 15 1 A0A087WZ13;Q8IY67-2;Q8IY67;Q8IY67-3 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 AADVSVTHRPPLS(1)PK;AADVSVTHRPPLS(1)PK;AADVSVTHRPPLS(1)PK;AADVSVT(0.005)HRPPLS(0.995)PK;AADVSVTHRPPLS(1)PK;AADVSVT(0.017)HRPPLS(0.983)PK 117.84 3.37E-12 12077820000 7235480 5210730 5650210 5505320 6528040 4100500 7198510 5650670 7707620 TRUE FALSE 6782624.223 5596537.871 5784235.649 5646595.832 6015354.071 5284247.784 6119160.253 6356168.588 6421168.429 1.056291281 0.871576246 0.90080734 0.879372017 0.936800543 0.822941781 0.952966788 0.989877257 1 22.61440441 1.49538708 6.657016937 0.987976922 0.904143575 0.242728109 0.060231002 0.158675095 16.77999329 0.030819949 0.013842993 31.28866838 -1.49538708 -0.083833347 (ac)AAHEWDWFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAHEWDWFQR 10 0 Q96JQ2;G3V3D8 Q96JQ2 CLMN Calmin 0 ; 47.823 0.013477 39175000 12815.9 13493.4 19592.5 17896.3 13559.7 15679.5 19027.7 11431.9 19523.3 FALSE TRUE 12013.7757 14492.46538 20057.24335 18355.54936 12494.77586 20205.91711 16174.67303 12859.19788 16264.7351 0.738639493 0.891036053 1.233173687 1.128548927 0.768212687 1.242314553 0.99446274 0.790618341 1 13.98945971 4.494314401 2.94285449 1.037307519 0.744569443 0.253744347 0.158335122 0.361766244 5.847047868 0.037377858 0.189164312 31211.48272 -4.494314401 -0.292738076 (ac)AALGHLAGEAAAAPGPGT(ph)PCASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AALGHLAGEAAAAPGPGTPCASR 23 0 A0A3B3IT54;Q9H7E9;Q9H7E9-2;A0A3B3IRR6;A0A3B3ITA3 A0A3B3IT54 C8orf33 UPF0488 protein C8orf33 1 AALGHLAGEAAAAPGPGT(0.906)PCAS(0.094)R;AALGHLAGEAAAAPGPGT(0.858)PCAS(0.142)R 112.85 3.56E-32 178739000 12637.4 17098.2 11729.7 18115.2 16133.9 19555.5 18608.2 12026.7 21623 TRUE FALSE 11846.44769 18364.16852 12007.93402 18580.0667 14866.80858 25200.85539 15818.07316 13528.25997 18013.98161 0.657625169 1.019439728 0.666589668 1.031424762 0.825292759 1.39896087 0.878099773 0.750986665 1 14.13682947 3.213419283 24.98589846 0.989694487 0.815890065 0.175700664 0.198488807 408.7104232 406182.5576 0.054447076 0.065101395 1634.629314 -3.213419283 -0.173804422 (ac)AALHTTPDS(ph)PAAQLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AALHTTPDSPAAQLER 16 0 A6NFI3 A6NFI3 ZNF316 Zinc finger protein 316 1 AALHTT(0.011)PDS(0.989)PAAQLER;AALHTTPDS(1)PAAQLER;AALHTTPDS(1)PAAQLER;AALHTT(0.001)PDS(0.999)PAAQLER;AALHTTPDS(1)PAAQLER;AALHTTPDS(1)PAAQLER 171.15 1.29E-71 4710650000 144529 346978.7 270795.1 302987 343636 442304.5 222407 228379 222211.2 TRUE FALSE 135483.1879 372669.364 277218.4877 310762.1594 316648.2147 569990.6289 189059.1351 256892.6209 185122.7152 0.731856097 2.013093659 1.497484992 1.678681944 1.710477369 3.078988056 1.021263841 1.387688273 1 17.4981224 3.119174738 5.646946286 1.707788685 1.554946112 0.006743679 0.653689709 1.501444087 68.47979609 0.182434588 0.219758537 1315.754118 -3.119174738 -0.152842573 (ac)AARDS(ph)DS(ph)EEDLVSYGTGLEPLEEGERPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AARDSDSEEDLVSYGTGLEPLEEGERPK 28 2 Q9BRR8;K7EQ19 Q9BRR8 GPATCH1 G patch domain-containing protein 1 2 AARDS(0.999)DS(0.985)EEDLVS(0.016)YGTGLEPLEEGERPK;AARDS(1)DS(1)EEDLVSYGTGLEPLEEGERPK 103.63 3.37E-12 151700000 120144 96402 101858 96955 109128 86261 118081 91719 131485 TRUE FALSE 112624.4015 103539.7044 104274.1199 99443.02944 100557.5271 111163.1504 100375.8503 103170.319 109539.3041 1.028164296 0.945228795 0.951933379 0.907829662 0.918004071 1.014824325 0.916345517 0.941856623 1 16.74108909 (ac)AASAAAASAAAASAASGS(ph)PGPGEGSAGGEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AASAAAASAAAASAASGSPGPGEGSAGGEKR 31 1 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 AASAAAASAAAASAASGS(0.996)PGPGEGS(0.003)AGGEKR;AASAAAASAAAASAAS(0.001)GS(0.998)PGPGEGS(0.001)AGGEKR;AASAAAASAAAASAASGS(1)PGPGEGSAGGEKR;AASAAAASAAAASAASGS(0.998)PGPGEGS(0.002)AGGEKR;AASAAAASAAAASAAS(0.02)GS(0.971)PGPGEGS(0.009)AGGEKR;AASAAAASAAAASAASGS(1)PGPGEGSAGGEKR 209.56 5.43E-175 6925750000 6738960 5960430 6147100 5949410 7042120 5483920 8315800 6047470 9911590 TRUE FALSE 6317180.523 6401746.439 6292912.115 6102081.933 6489060.302 7067038.68 7068922.99 6802509.942 8257281.598 0.76504361 0.775284985 0.762104579 0.738994046 0.78585915 0.855855356 0.856083556 0.823819542 1 22.97723548 0.706497053 0.39187969 1.018173514 0.751705532 0.879786397 0.026117749 0.616457359 0.217010577 0.053429826 0.021918121 5.087413677 -0.706497053 -0.266467982 (ac)AATDLERFS(ph)NAEPEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AATDLERFSNAEPEPR 16 1 A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599 A0A087X142 8-Sep Septin-8 1 AAT(0.277)DLERFS(0.723)NAEPEPR 59.57 3.23E-06 46559000 8460.7 9448.9 8274 6275.1 8140.5 9773.8 9949.4 7044 8934.7 TRUE FALSE 7931.15989 10148.50639 8470.263187 6436.12969 7501.177967 12595.3374 8457.579836 7923.458906 7443.44085 1.065523331 1.363416005 1.137949956 0.864671302 1.007756778 1.692139113 1.136245992 1.064488731 1 12.86175397 1.262820248 4.755185642 1.025560138 1.202103073 0.070395923 0.222281161 0.476187634 24.46507983 0.175426872 0.054924688 18.31556197 -1.262820248 0.176542935 (ac)AATLGAGT(ph)PPRPQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AATLGAGTPPRPQAR 15 1 A0A075B730 A0A075B730 EPPK1 1 AAT(0.001)LGAGT(0.999)PPRPQAR 45.207 0.00036332 0 24283 21459 20714 23592 29283 18122 35661 18348 32371 TRUE FALSE 22763.17038 23047.84669 21205.34586 24197.41066 26983.2313 23353.52721 30313.96411 20638.78819 26968.07098 0.844078555 0.854634605 0.78631304 0.897261457 1.000562158 0.86596951 1.124068686 0.765304578 1 14.71896471 2.998709756 4.737065499 0.964632728 0.828469571 0.254203717 0.094416133 0.213374926 13.00570633 0.026016041 0.029750764 997.0335129 -2.998709756 -0.136163157 (ac)ACPLDQAIGLLVAIFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ACPLDQAIGLLVAIFHK 17 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ; 144.65 8.96E-20 8070300000 5516600 7795900 7250900 8656900 8135900 6297400 10174600 7102200 7758400 FALSE TRUE 5171325.853 8373116.548 7422894.772 8879050.71 7496939.233 8115357.15 8649013.186 7988925.304 6463472.919 0.80008471 1.295451633 1.148437514 1.373727533 1.159893346 1.255572237 1.338137143 1.23601126 1 22.62387812 4.742859196 24.67970871 1.241771472 0.800084498 0.605557571 0.107327463 218.4960056 1254408.749 0.022410266 0.175208827 55317.07351 -4.742859196 -0.441686974 (ac)ACRPRS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ACRPRSPPR 9 2 F8W8D3;Q14493;E7EUV9;Q14493-2 F8W8D3 SLBP Histone RNA hairpin-binding protein 1 ACRPRS(1)PPR 67.456 0.0020051 169390000 38290 25127 21649 24796 20802 23546 34465 19418 15902 TRUE FALSE 35893.49725 26987.42922 22162.5245 25432.30734 19168.29483 30343.34796 29297.29321 21842.38004 13247.85347 2.709382115 2.037117129 1.672914375 1.919730423 1.446898162 2.290435053 2.211474733 1.648748614 1 13.693471 4.752342232 2.279016727 1.838267937 2.946624158 0.380673383 0.375662704 0.714904555 4.256132144 0.087978033 1.611568922 56538.23312 -4.752342232 1.108356221 (ac)ACS(ph)PDAVVSPSSAFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ACSPDAVVSPSSAFLR 16 0 Q93100-4;Q93100-2;I3L3F2;H3BV13;H3BQ89 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 1 ACS(1)PDAVVSPSSAFLR 73.624 5.89E-09 116480000 12406 7624.3 8044.2 5080.6 8486.3 6720.7 6702.3 6961 5711.2 TRUE FALSE 11629.53061 8188.811105 8235.012223 5210.976797 7819.82023 8660.856989 5697.352336 7830.096173 4757.963824 2.44422426 1.721074688 1.730784959 1.095211521 1.643522422 1.820286431 1.197434984 1.645682158 1 12.21612859 7.999999984 0.626491614 1.433284271 74.94621188 0.56479313 0.275772014 140.9877313 0.986101523 0.102133433 14295.01641 99999996.41 -7.999999984 73.51292761 (ac)ADDKVAILT(ph)DDEEEQKRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADDKVAILTDDEEEQKRK 18 3 C9JAZ7;C9J134;C9JJH2;Q6ZSS7 C9JAZ7 MFSD6 Major facilitator superfamily domain-containing protein 6 1 ADDKVAILT(1)DDEEEQKRK;ADDKVAILT(1)DDEEEQKRK 94.201 2.95E-08 162929000 347160 146886 197179 212630 239620 117609 309120 174852 322710 TRUE FALSE 325431.8753 157761.5923 201856.179 218086.4458 220801.2118 151560.8091 262770.3257 196682.6571 268847.6162 1.210469633 0.586806736 0.750820044 0.811189807 0.821287594 0.563742432 0.977395037 0.731576719 1 18.03642915 0.255533061 0.753051444 1.003039278 0.776318437 0.070794848 0.187846857 6.204076499 4.518395506 0.228237452 0.059332351 1.801080236 -0.255533061 -0.226720841 (ac)ADEAALALQPGGS(ph)PSAAGADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ADEAALALQPGGSPSAAGADR 21 0 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 ADEAALALQPGGS(0.924)PS(0.076)AAGADR;ADEAALALQPGGS(0.749)PS(0.251)AAGADR;ADEAALALQPGGS(0.752)PS(0.248)AAGADR;ADEAALALQPGGS(0.959)PS(0.041)AAGADR;ADEAALALQPGGS(0.951)PS(0.049)AAGADR 121.44 4.80E-30 602670000 17483.2 27387.4 34097.9 35475.9 28692.1 21368.7 34831.4 27971 31239.1 TRUE FALSE 16388.95772 29415.19159 34906.71829 36386.27165 26438.7382 27537.4968 29608.75493 31463.24092 26025.0924 0.629736774 1.130262715 1.341271637 1.398122669 1.015894115 1.058113315 1.137700281 1.208957895 1 14.66761567 4.735931878 4.177836767 1.179479266 0.586594435 0.625365182 0.12923468 0.14406514 5.674584039 0.03160807 0.2555283 54441.72503 -4.735931878 -0.592884831 (ac)ADEELEALRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ADEELEALRR 10 1 O14737;O14737-2;Q3HM38;X6R2P6;K7ESJ4 O14737 PDCD5 Programmed cell death protein 5 0 ;;; 93.143 9.65E-06 3640880000 691676 727349 718404 685295 844299 547937 800689 683574 855370 FALSE TRUE 648385.2338 781202.6768 735444.8821 702880.8299 777991.1623 706117.5169 680633.1177 768919.7186 712603.2211 0.909882547 1.096265992 1.032053828 0.986356515 1.091759256 0.990898576 0.955136179 1.079029249 1 19.44273948 (ac)ADESETAVKPPAPPLPQMMEGNGNGHEHCSDCENEEDNS(ph)YNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADESETAVKPPAPPLPQMMEGNGNGHEHCSDCENEEDNSYNR 42 1 P30419;B7Z8J4 P30419 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 1 ADESETAVKPPAPPLPQMMEGNGNGHEHCS(0.366)DCENEEDNS(0.598)Y(0.036)NR 42.579 6.92E-05 159730000 12705 13332 11903 11624 12320 13648 23855 13141 14488 TRUE FALSE 11909.81673 14319.11515 12185.34478 11922.29152 11352.4369 17587.95604 20278.16421 14781.68278 12069.8592 0.98674032 1.186353122 1.009568096 0.987773869 0.940560839 1.457179885 1.680066343 1.224677316 1 13.55912123 2.231934905 24.99911124 1.42960911 1.04129664 0.368585339 0.190929585 125.4999293 473512.4829 0.066521111 0.0502641 170.5826688 -2.231934905 -0.38831247 (ac)ADGDS(ph)GS(ph)ERGGGGGPCGFQPASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 129.02 1.20E-08 2450120000 12529.2 19603.8 20377.4 21263.5 17683.6 16566.7 16817.6 18496.6 21730.2 TRUE FALSE 11745.01974 21055.28575 20860.76155 21809.15741 16294.80139 21349.23735 14295.95701 20805.94123 18103.28924 0.648778218 1.163064097 1.152318856 1.204706897 0.900101698 1.179301566 0.789688372 1.149290659 1 14.14396423 (ac)ADGDS(ph)GSERGGGGGPCGFQPASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADGDSGSERGGGGGPCGFQPASR 23 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 ADGDS(0.993)GS(0.007)ERGGGGGPCGFQPASR 194.51 2.96E-24 263570000 5103.9 4712.1 7230.3 10297 7171.6 4002.8 3865.6 7053 4363.6 TRUE FALSE 4784.45601 5060.988787 7401.80613 10561.23845 6608.371465 5158.34338 3285.989166 7933.582576 3635.28697 1.316115082 1.392184119 2.036099541 2.905200756 1.817840385 1.418964561 0.903914655 2.182381375 1 11.82785354 2.22168903 4.775710858 1.311813702 1.893593334 0.181547995 0.543228544 0.320155471 18.45763276 0.207410767 0.157737245 166.6053834 -2.22168903 0.581779632 (ac)ADHS(ph)FSDGVPSDSVEAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADHSFSDGVPSDSVEAAK 18 0 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;E9PKT8;E9PS34;E9PNW0;E9PJJ2;E9PP22;E9PKI2;C9J1B1 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 ADHS(0.998)FS(0.002)DGVPSDSVEAAK;ADHS(0.999)FS(0.001)DGVPSDSVEAAK 108.59 3.68E-191 377650000 1195900 986140 1086330 1081050 1064590 823250 1480170 933790 1278340 TRUE FALSE 1121050.754 1059154.832 1112098.261 1108791.573 980981.3957 1060908.911 1258232.25 1050375.737 1064976.796 1.052652751 0.994533248 1.044246471 1.041141533 0.921129361 0.996180306 1.181464474 0.986289787 1 20.02239057 (ac)ADILSQSETLASQDLSGDFKKPALPVS(ph)PAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADILSQSETLASQDLSGDFKKPALPVSPAAR 31 2 A0A087X0M4;A0A087WWF4 A0A087X0M4 SLC4A1AP 1 ADILSQSETLASQDLSGDFKKPALPVS(1)PAAR 217.8 3.51E-155 175910000 119260 140340 126170 127930 193990 114720 215740 109190 388270 TRUE FALSE 111795.7295 150730.9196 129162.812 131212.9004 178754.8079 147837.8017 183391.7898 122822.6119 323465.2287 0.345619002 0.465988014 0.399309726 0.405647621 0.552624493 0.457043875 0.566959826 0.379708856 1 18.30325111 -5 0.257010352 4.460425261 0.407962297 0.858688446 0.070551015 62.10905148 0.612257722 113.2826755 0.086684426 1.00E-05 5 -4.052462964 (ac)ADLEEQLS(ph)DEEKVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADLEEQLSDEEKVR 14 1 P47755;F8W9N7;C9JUG7;P47755-2 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 1 ADLEEQLS(1)DEEKVR;ADLEEQLS(1)DEEKVR 110.51 7.82E-06 242290000 493760 379820 390650 406280 428970 312810 522510 414770 566220 TRUE FALSE 462856.443 407942.268 399916.4025 416705.8326 395280.4266 403113.169 444164.4762 466554.9475 471714.2241 0.981222145 0.864808071 0.847793817 0.883386193 0.837965884 0.85457073 0.941596529 0.989062707 1 18.84755358 1.512420353 2.879839644 0.993174396 0.871990313 0.591826454 0.040006936 0.154572742 2.678420221 0.028167177 0.010140866 32.54021009 -1.512420353 -0.121184083 (ac)ADSRDPASDQMQHWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADSRDPASDQMQHWK 15 1 P04040 P04040 CAT Catalase 0 62.287 8.01E-05 363220000 137540 159100 113040 149100 209290 108390 188930 157640 189910 FALSE TRUE 128931.6169 170879.9295 115721.3622 152926.1584 192853.2076 139680.4334 160601.7004 177321.701 158212.7941 0.814925352 1.080063913 0.731428598 0.966585283 1.218948244 0.882864336 1.015099324 1.120779783 1 17.27150674 3.000625122 24.99998767 1.038032675 0.892519771 0.290751697 0.121459288 30.37860438 1214805.96 0.033649351 0.03988627 1001.440433 -3.000625122 -0.145512904 (ac)ADVLDLHEAGGEDFAMDEDGDES(ph)IHKLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ADVLDLHEAGGEDFAMDEDGDESIHKLK 28 1 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 1 ADVLDLHEAGGEDFAMDEDGDES(1)IHKLK;ADVLDLHEAGGEDFAMDEDGDES(1)IHKLK;ADVLDLHEAGGEDFAMDEDGDES(1)IHKLK 259.78 3.13E-146 188188000 285230 181558 233306 233903 270352 188239 358415 234694 409540 TRUE FALSE 267377.9635 195000.7432 238840.1285 239905.347 249119.6445 242580.5435 304673.9981 263996.0625 341185.1283 0.783674144 0.571539399 0.700030889 0.703153001 0.73015974 0.710993896 0.892987334 0.773761928 1 18.38019524 1.332274635 0.479636818 1.000507181 0.650112606 0.662152681 0.067561382 0.460865586 0.286436496 0.069104596 0.040727482 21.49189127 -1.332274635 -0.350394574 (ac)ADVLDLHEAGGEDFAMDEDGDESIHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ADVLDLHEAGGEDFAMDEDGDESIHK 26 0 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ;;; 155.05 1.94E-61 477757000 211985 192324 219130 204616 221576 158804 245143 174237 283623 FALSE TRUE 198717.2373 206563.8691 224327.8671 209866.793 204174.3148 204648.1368 208386.0829 195990.873 236284.489 0.841008388 0.874216797 0.949397347 0.888195386 0.864103757 0.866109061 0.881928745 0.829469906 1 17.8501654 -1.017778282 4.469768221 1.000004322 0.880844866 0.58998079 0.032527457 0.01105707 20187699.05 221.4631689 0.007931507 0.095989055 1.017778282 -0.119159456 (ac)AEPPS(ph)PVHCVAAAAPTATVSEKEPFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AEPPSPVHCVAAAAPTATVSEKEPFGK 27 1 Q6PCB5 Q6PCB5 RSBN1L Round spermatid basic protein 1-like protein 1 AEPPS(1)PVHCVAAAAPTATVSEKEPFGK;AEPPS(0.999)PVHCVAAAAPT(0.001)ATVSEKEPFGK;AEPPS(1)PVHCVAAAAPTATVSEKEPFGK 81.683 0.003249 3453050000 3596700 2674260 2953860 2884870 3366490 2334470 3985890 2864530 4349150 TRUE FALSE 3371588.967 2872264.993 3023926.954 2958900.648 3102099.455 3008393.592 3388242.798 3222172.876 3623248.768 0.930543052 0.792731931 0.834589935 0.816642974 0.856165186 0.830302798 0.935139433 0.889304898 1 21.78885243 1.209349653 0.788955233 0.994540138 0.831833174 0.55911299 0.042388506 0.372212905 0.526086853 0.036394236 0.014078126 16.19383287 -1.209349653 -0.162706964 (ac)AESSESFTMASS(ph)PAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AESSESFTMASSPAQR 16 0 P49736;F8WDM3 P49736 MCM2 DNA replication licensing factor MCM2 1 AESSESFT(0.002)MAS(0.37)S(0.627)PAQR 85.469 4.66E-58 149280000 17248 17692 17876 16063 19323 13697 17449 10103 14766 TRUE FALSE 16168.47847 19001.93409 18300.02716 16475.20377 17805.44953 17651.10155 14832.68444 11364.38179 12301.45921 1.314354516 1.544689436 1.487630602 1.339288575 1.447425807 1.43487868 1.205766258 0.923823881 1 13.58654184 1.507545303 2.457168627 0.960238116 1.447570913 0.876061137 0.07206679 0.082977307 1.021109716 0.056340651 0.019364939 32.17698164 -1.507545303 0.487332796 (ac)AGS(ph)PELVVLDPPWDKELAAGTESQALVSATPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGSPELVVLDPPWDKELAAGTESQALVSATPR 32 1 Q5SY74;Q96IY1-2;Q96IY1 Q5SY74 NSL1 Kinetochore-associated protein NSL1 homolog 1 AGS(1)PELVVLDPPWDKELAAGTESQALVSATPR 84.641 9.82E-27 28255000 20610 26727 22991 25660 35304 21400 31537 21557 54941 TRUE FALSE 19320.05689 28705.89489 23536.35738 26318.47904 32531.36625 27577.8326 26808.31963 24248.4389 45770.99217 0.422102646 0.627163483 0.514219952 0.575003464 0.710741994 0.602517693 0.585705451 0.529777437 1 15.48214594 -5 0.351985389 5.930705065 0.563736779 0.760210526 0.075626862 208.5464691 1.699654783 776.7879667 0.053567607 1.00E-05 5 -5.366968286 (ac)AHS(ph)PVAVQVPGMQNNIADPEELFTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AHSPVAVQVPGMQNNIADPEELFTK 25 0 Q8NBY1;B4E0Y9;Q9P289-3;Q9P289 Q8NBY1 STK26 Serine/threonine-protein kinase 26 1 AHS(1)PVAVQVPGMQNNIADPEELFTK;AHS(1)PVAVQVPGMQNNIADPEELFTK 42.806 2.12E-06 24959000 46198 40530 43095 42678 46658 34286 43896 38236 72101 TRUE FALSE 43306.54965 43530.88337 44117.23375 43773.18973 42993.66889 44183.81161 37314.20231 43009.84877 60066.87731 0.720972216 0.724706949 0.734468574 0.728740892 0.715763343 0.73557697 0.621210957 0.716032707 1 15.87428204 0.92940851 23.65969447 1 0.709964007 0.881921227 0.033096392 13825.33307 4633752.897 0.035007204 0.008751801 8.49979615 -0.92940851 -0.290035993 (ac)AHS(ph)PVQSGLPGMQNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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(0.999)PVQS(0.001)GLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(0.878)PVQS(0.122)GLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(0.998)PVQS(0.002)GLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(0.998)PVQS(0.002)GLPGMQNLK 129.82 1.03E-58 3436729000 2027355 1939777 1928232 1863442 2134836 1637853 2273190 1689288 2620246 TRUE FALSE 1900466.469 2083400.107 1973970.574 1911261.077 1967174.592 2110674.573 1932346.263 1900199.325 2182910.015 0.870611457 0.954414105 0.904283988 0.875556511 0.901170721 0.966908649 0.885215721 0.870489078 1 21.05782123 (ac)ALVTVSRS(ph)PPGSGASTPVGPWDQAVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALVTVSRSPPGSGASTPVGPWDQAVQR 27 1 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 ALVTVS(0.015)RS(0.908)PPGS(0.053)GAS(0.016)T(0.008)PVGPWDQAVQR;ALVT(0.009)VS(0.056)RS(0.556)PPGS(0.215)GAS(0.077)T(0.087)PVGPWDQAVQR 89.793 8.03E-61 330770000 5043.2 10817.9 9325.3 10544.2 11798.3 5034.8 10802.1 5317.6 13736.8 TRUE FALSE 4727.555114 11618.86857 9546.50052 10814.78202 10871.70911 6488.265027 9182.425387 5981.514065 11444.03934 0.413101963 1.015276882 0.834189768 0.945014405 0.949988792 0.566955848 0.802376252 0.52267507 1 13.48230874 2.252422931 24.99968276 0.711817112 0.862096797 0.051264544 0.207752404 490.162273 883971.2331 0.064817234 0.053971379 178.8228165 -2.252422931 0.150279685 (ac)ALVTVSRSPPGS(ph)GASTPVGPWDQAVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALVTVSRSPPGSGASTPVGPWDQAVQR 27 1 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 ALVT(0.028)VS(0.064)RS(0.289)PPGS(0.342)GAS(0.237)T(0.04)PVGPWDQAVQR 48.831 4.66E-35 201780000 5818.3 5888.9 4871.1 4492.9 7092.3 5425.2 4192.7 0 7326.6 TRUE FALSE 5454.142989 6324.920283 4986.644792 4608.19542 6535.299367 6991.367169 3564.043558 0 6103.743128 0.89357348 1.036236314 0.81698143 0.754978597 1.070703539 1.145422902 0.583911132 0 1 12.57547853 1.578073311 5.653833712 0.437287304 0.942261252 0.360145795 0.26463152 0.122733318 8.216867513 0.130840516 0.060467302 37.8506473 -1.578073311 0.504973948 (ac)AMFEDTVEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AMFEDTVEER 10 0 C9JAJ9 C9JAJ9 RBBP7 0 56.432 0.00084704 0 23044 24729 25620 25120 32188 22997 28154 30682 32321 FALSE TRUE 21601.71717 26559.96089 26227.7185 25764.62173 29660.08432 29635.86057 23932.56907 34512.71524 26926.4163 0.802249989 0.986390487 0.974051586 0.956852982 1.101523648 1.100624021 0.888813751 1.281741872 1 14.71673461 6.20392072 0.50345752 1.049437814 9.93E-13 0.341355634 0.105833936 22.15450263 1.350313708 0.052473746 18.92946815 1599266.059 -6.20392072 -1.049437814 (ac)AS(ph)ESDTEEFYDAPEDVHLGGGYPVGSPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASESDTEEFYDAPEDVHLGGGYPVGSPGK 29 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 AS(0.369)ES(0.311)DT(0.311)EEFY(0.01)DAPEDVHLGGGYPVGSPGK;AS(0.332)ES(0.332)DT(0.332)EEFY(0.003)DAPEDVHLGGGYPVGSPGK 80.139 7.84E-13 147348000 195948 180834 198098 181246 189588 170067 250598 192787 283780 TRUE FALSE 183683.9645 194223.1375 202796.9781 185897.0792 174698.5232 219162.5821 213023.1563 216856.8813 236415.2847 0.776954691 0.821533759 0.857799775 0.786315823 0.738947668 0.927023743 0.901054924 0.917270986 1 17.85096379 2.215987189 24.86941398 0.925157079 0.807680531 0.737809501 0.040928995 134.2922225 147950.312 0.015379904 0.011367189 164.4323216 -2.215987189 -0.117476548 (ac)AS(ph)GVAVSDGVIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 15 ASGVAVSDGVIK 12 0 P23528;E9PP50;E9PS23 P23528 CFL1 Cofilin-1 1 AS(1)GVAVSDGVIK;AS(0.997)GVAVS(0.003)DGVIK;AS(1)GVAVSDGVIK;AS(0.999)GVAVS(0.001)DGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(0.999)GVAVS(0.001)DGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(0.999)GVAVS(0.001)DGVIK 72.325 1.50E-21 57902746100 32759716.5 31900506.2 30708649.2 28484115.5 38206709 24096374.3 38375913.7 33248879.5 44559493 TRUE FALSE 30709344.32 34262452.87 31437072.86 29215066.13 35206108.19 31052606.39 32621801.71 37400075.3 37122225.75 0.827249544 0.922963324 0.846853124 0.786996618 0.948383549 0.836496351 0.878767397 1.007484722 1 25.14577988 1.257234039 5.791050456 1.005462577 0.866947181 0.613411944 0.0461431 0.097657181 10.20527184 0.032662972 0.01053079 18.08148264 -1.257234039 -0.138515396 (ac)AS(ph)GVQVADEVCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 78.098 1.07E-11 17878350000 595244.6 451311 498855.5 499359.9 560764.8 417822.3 577481.3 417871.3 598689.4 TRUE FALSE 557989.303 484726.536 510688.588 512174.3204 516724.5946 538440.8152 490893.3401 470043.4517 498764.2715 1.118743533 0.97185497 1.02390772 1.026886547 1.036009643 1.079549691 0.984219136 0.942416044 1 18.9279986 1.563890776 6.974252365 0.968974567 1.031738046 0.355673873 0.041131765 0.146644208 13.85351848 0.021457075 0.009999751 36.63454279 -1.563890776 0.062763479 (ac)AS(ph)GVTVNDEVIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASGVTVNDEVIK 12 0 Q9Y281;G3V2U0;F8WDN3 Q9Y281 CFL2 Cofilin-2 1 AS(0.872)GVT(0.128)VNDEVIK;AS(0.937)GVT(0.063)VNDEVIK 61.65 2.82E-05 394420000 518560 416010 534340 465510 614510 373520 578910 551960 816610 TRUE FALSE 486104.2553 446811.8133 547014.7971 477455.7747 566248.8634 481349.1604 492107.8198 620873.421 680312.5155 0.714530814 0.656774355 0.804063992 0.701818302 0.83233639 0.707541239 0.723355529 0.912629721 1 19.3758381 -5 0.151641421 1.958934772 0.665712213 0.658717546 0.062565881 81.39481022 0.729656477 23.23919436 0.293363678 1.00E-05 5 -1.29322256 (ac)AS(ph)LSLAPVNIFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASLSLAPVNIFK 12 0 P78371;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 1 AS(0.903)LS(0.097)LAPVNIFK;AS(0.5)LS(0.5)LAPVNIFK 56.563 5.15E-05 39945000 159446 171764 157939 172641 199841 97966 231010 167317 224590 TRUE FALSE 149466.5595 184481.5853 161685.3877 177071.2603 184146.294 126247.1939 196372.1951 188206.8958 187104.4781 0.798840097 0.985981667 0.864144938 0.946376389 0.984189667 0.674741701 1.04953231 1.00589199 1 17.51348456 1.607615358 25 1.020793882 0.89171318 0.333443099 0.093317238 0.053125023 2920.552074 0.042509128 0.021589295 40.51495476 -1.607615358 -0.129080702 (ac)AS(ph)PGKDNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASPGKDNYR 9 1 O15131;Q5TD90 O15131 KPNA5 Importin subunit alpha-6 1 AS(1)PGKDNYR;AS(1)PGKDNYR 53.751 0.015728 602370000 849540 640000 686420 679970 983610 667580 959850 728900 1179200 TRUE FALSE 796368.8079 687386.2659 702702.2066 697419.1814 906361.2383 860299.5087 815929.4033 819904.7695 982383.9021 0.810649285 0.699712469 0.715303055 0.709925295 0.922614099 0.875726391 0.830560641 0.834607293 1 19.90592739 2.745709021 24.98808492 0.87669536 0.725100932 0.648584176 0.057254519 337.4518757 1179602.814 0.016435927 0.017101663 556.8125579 -2.745709021 -0.151594428 (ac)AS(ph)PSSFTYYCPPSSSPVWSEPLYSLRPEHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASPSSFTYYCPPSSSPVWSEPLYSLRPEHAR 31 1 P49356 P49356 FNTB Protein farnesyltransferase subunit beta 1 AS(0.851)PS(0.119)S(0.018)FT(0.011)YYCPPSSSPVWSEPLYSLRPEHAR;AS(0.993)PS(0.006)S(0.001)FTYYCPPSSSPVWSEPLYSLRPEHAR;AS(0.997)PS(0.003)SFTYYCPPSSSPVWSEPLYSLRPEHAR 193.14 4.85E-93 1838270000 15837 9824 17950 14537.2 9936.9 22186.1 10557 14235 15471.1 TRUE FALSE 14845.79044 10551.37918 18375.78248 14910.24916 9156.495958 28590.86691 8974.075856 16012.27109 12888.87346 1.151829947 0.818642468 1.425708967 1.156831061 0.71041864 2.21825957 0.696265339 1.242332864 1 13.65383855 3.986144852 23.5955595 1.208308443 0.981529324 0.043574473 0.432059806 548.6724626 1434681.156 0.097373134 0.205282646 9686.008648 -3.986144852 -0.226779119 (ac)AS(ph)PTDGTDLEASLLSFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASPTDGTDLEASLLSFEK 18 0 G3V5T8 G3V5T8 LIN52 1 AS(0.889)PT(0.099)DGT(0.011)DLEASLLSFEK;AS(0.852)PT(0.128)DGT(0.02)DLEASLLSFEK;AS(0.471)PT(0.471)DGT(0.058)DLEASLLSFEK;AS(0.874)PT(0.11)DGT(0.016)DLEASLLSFEK 98.531 1.34E-15 139171000 298064 261061 280989 261944 293565 256286 323427 254993 357710 TRUE FALSE 279408.7063 280390.2281 287654.1918 268665.9265 270509.5891 330271.6077 274932.1239 286829.4374 298005.8901 0.937594576 0.940888209 0.965263444 0.901545692 0.907732357 1.10827208 0.922572785 0.962495866 1 18.18498132 (ac)ASAVS(ph)PANLPAVLLQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASAVSPANLPAVLLQPR 17 0 P51610-2;P51610;A6NEM2;P51610-4;P51610-3 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 1 AS(0.013)AVS(0.987)PANLPAVLLQPR;AS(0.131)AVS(0.869)PANLPAVLLQPR;AS(0.131)AVS(0.869)PANLPAVLLQPR 78.653 2.39E-10 178852000 148597 143600 130934 151795 172939 109907 167447 117583 214369 TRUE FALSE 139296.579 154232.2934 134039.8163 155690.3167 159357.0685 141635.3667 142339.8769 132263.4964 178589.429 0.779982218 0.863613789 0.750547314 0.871777896 0.892309637 0.793078109 0.797022968 0.740600925 1 17.44628716 -1.007278406 4.338572979 1.000008537 0.812654 0.577562065 0.050751499 0.054940557 28182979.3 595.2316502 0.011407588 0.098338051 1.007278406 -0.187354537 (ac)ASCAS(ph)IDIEDATQHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASCASIDIEDATQHLR 16 0 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 AS(0.016)CAS(0.984)IDIEDATQHLR;AS(0.005)CAS(0.995)IDIEDATQHLR;AS(0.009)CAS(0.991)IDIEDATQHLR 106.14 4.59E-21 293661000 93196 60753.2 79071.9 71875.5 91417 64253.7 89413 72919 109897 TRUE FALSE 87363.02872 65251.43014 80947.52281 73719.94701 84237.47758 82802.70012 76006.35072 82023.09766 91554.48074 0.95421904 0.712706026 0.884145944 0.805203049 0.920080338 0.904409041 0.830176198 0.895893866 1 16.48234287 -4.691507883 0.143348261 1.490327708 0.796419435 0.280777771 0.068330022 135.5335771 1.280322277 19.00635462 0.368149977 2.03E-05 4.691507883 -0.693908273 (ac)ASEDNRVPS(ph)PPPTGDDGGGGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASEDNRVPSPPPTGDDGGGGGR 22 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 AS(0.002)EDNRVPS(0.958)PPPT(0.04)GDDGGGGGR;ASEDNRVPS(0.978)PPPT(0.022)GDDGGGGGR 104.03 1.45E-11 724480000 24858 32644 35387 29052 36388 34102 32684 26851 28140 TRUE FALSE 23302.18215 35060.99573 36226.39635 29797.5235 33530.23326 43946.6938 27783.33762 30203.40646 23443.25221 0.993982488 1.495568764 1.545280323 1.271049052 1.430272258 1.874598857 1.185131541 1.288362476 1 14.5168851 1.098429342 1.775713456 1.02255084 1.442884278 0.228660802 0.231803194 0.43458935 2.68451513 0.201794852 0.058314042 12.54380639 -1.098429342 0.420333438 (ac)ASEDNRVPS(ph)PPPTGDDGGGGGREETPTEGGALSLKPGLPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASEDNRVPSPPPTGDDGGGGGREETPTEGGALSLKPGLPIR 41 3 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 AS(0.005)EDNRVPS(0.907)PPPT(0.078)GDDGGGGGREET(0.004)PT(0.004)EGGALS(0.001)LKPGLPIR;AS(0.003)EDNRVPS(0.945)PPPT(0.052)GDDGGGGGREETPTEGGALSLKPGLPIR;ASEDNRVPS(0.963)PPPT(0.037)GDDGGGGGREETPTEGGALSLKPGLPIR;AS(0.003)EDNRVPS(0.773)PPPT(0.213)GDDGGGGGREET(0.005)PT(0.005)EGGALSLKPGLPIR 124 1.04E-44 5659670000 1024756 1269759 1137383 1257481 1354159 969719 1434902 1069782 1511180 TRUE FALSE 960618.3512 1363773.278 1164362.262 1289750.091 1247808.815 1249661.133 1219751.766 1203346.638 1258954.295 0.763028773 1.083258767 0.924864601 1.024461409 0.991147033 0.992618348 0.968861039 0.955830281 1 20.26379448 4.753546468 24.9183634 0.990909538 0.763028604 0.747528658 0.041923675 1286.391586 2138965.234 0.009399142 0.215632067 56695.22296 -4.753546468 -0.227880934 (ac)ASEFKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASEFKK 6 1 P29972 P29972 AQP1 Aquaporin-1 0 58.577 0.067421 267510000 233060 969900 685550 780970 847150 1003300 648530 825200 503930 FALSE TRUE 218473.1906 1041712.405 701811.5697 801011.0124 780618.2562 1292936.423 551288.9472 928228.0365 419820.8275 0.520396265 2.481326168 1.671693074 1.907983025 1.859408122 3.079733872 1.313152924 2.211009973 1 18.67941422 3.067560074 5.4153856 1.953955195 1.771931102 0.01480482 0.725944438 1.301865613 72.02922713 0.195590535 0.234238551 1168.315326 -3.067560074 -0.182024093 (ac)ASGEHS(ph)PGSGAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASGEHSPGSGAAR 13 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 1 AS(0.008)GEHS(0.93)PGS(0.062)GAAR 42.317 0.0036114 47214000 1257 1439.3 1436.3 1281.2 1685.7 2186.4 1992.7 1366.2 1380.4 TRUE FALSE 1178.326614 1545.86727 1470.369714 1314.077761 1553.311922 2817.578187 1693.913134 1536.773077 1150.002322 1.024629769 1.344229694 1.278579778 1.142674006 1.350703291 2.450063041 1.472964968 1.336321717 1 10.16742106 2.460058392 24.99959938 1.655391154 1.236607076 0.15501861 0.37464468 345.8169015 506669.5896 0.119688351 0.100158933 288.4419294 -2.460058392 -0.418784078 (ac)ASGRPEELWEAVVGAAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASGRPEELWEAVVGAAER 18 1 Q96B36;H9KV91;M0R2V8 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 0 63.181 4.84E-05 17522000 2259.2 925.57 0 792.91 917.97 1726.9 984.72 731.92 1312.8 FALSE TRUE 2117.800705 994.1001659 0 813.257413 845.8763391 2225.427996 837.0703777 823.3018232 1093.685199 1.936389655 0.908945432 0 0.74359369 0.773418475 2.03479758 0.765366834 0.752777695 1 10.09498182 2.428549114 24.99999874 1.149865864 0.750524327 0.025903165 0.587441824 286.5863497 147503.8628 0.203581176 0.170328268 268.255796 -2.428549114 -0.399341536 (ac)ASLEVS(ph)RSPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASLEVSRSPRR 11 2 Q5QPJ9;Q5QPK2;O60762 Q5QPJ9 DPM1 Dolichol-phosphate mannosyltransferase subunit 1 1 ASLEVS(0.5)RS(0.5)PRR 58.268 0.010783 187910000 35801 42764 47889 40269 53527 43586 56904 49917 62976 TRUE FALSE 33560.27932 45930.29106 49024.94969 41302.37072 49323.20534 56168.57064 48371.77347 56149.24733 52464.89876 0.639671096 0.875448007 0.934433323 0.787238167 0.940118184 1.070593329 0.921983547 1.07022502 1 15.6790649 6.071265405 0.375280087 1.002224275 1.04E-22 0.634896337 0.078078904 11.66897259 0.596233213 0.061233177 6.457381683 1178325.849 -6.071265405 -1.002224275 (ac)ASLEVSRS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASLEVSRSPR 10 1 Q5QPJ9;Q5QPK2;O60762 Q5QPJ9 DPM1 Dolichol-phosphate mannosyltransferase subunit 1 1 ASLEVS(0.009)RS(0.991)PR;ASLEVS(0.002)RS(0.998)PR;ASLEVSRS(1)PR;ASLEVSRS(1)PR 117.94 9.59E-09 2968050000 189721 160992 182746 192353 183051 139324.1 214138 173334 191631 TRUE FALSE 177846.7013 172912.0152 187080.8214 197289.1036 168674.9129 179544.7059 182029.9949 194975.1315 159646.5481 1.114002798 1.083092727 1.171843824 1.235786843 1.056552208 1.124638823 1.140206268 1.221292497 1 17.28452183 -0.709294693 7.83274327 1.000001231 1.139913071 0.394481525 0.055693886 0 0 0.051230271 0.01207509 0.195301378 0.709294693 0.13991184 (ac)ASPTDGT(ph)DLEASLLSFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASPTDGTDLEASLLSFEK 18 0 G3V5T8 G3V5T8 LIN52 1 AS(0.301)PT(0.301)DGT(0.394)DLEAS(0.004)LLSFEK 61.038 0.0017403 0 9271.5 11306 8644.6 9039.6 9219.5 6911.2 10947 9522.6 10007 TRUE FALSE 8691.213365 12143.108 8849.653994 9271.57144 8495.43766 8906.351246 9305.598977 10711.51757 8336.767052 1.042516039 1.456572785 1.061521084 1.112130324 1.019032631 1.068321951 1.116211946 1.28485269 1 13.02527231 3.758346131 8.470267819 1.096561591 1.273687267 0.204595868 0.124891678 0.325009525 79.61385354 0.029072118 0.051838122 5732.527292 -3.758346131 0.177125677 (ac)AT(ph)PPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATPPKR 6 1 D6RCP9;D6RFG8;P27707;D6R9C6;D6RG38;Q9UBK9 D6RCP9 DCK;UXT Deoxycytidine kinase;Protein UXT 1 AT(1)PPKR;AT(1)PPKR 50.966 0.045934 3087540000 473280 619280 587910 540660 593990 607560 569850 638000 609050 TRUE FALSE 443658.2496 665132.1356 601855.5028 554534.2509 547340.4214 782952.7091 484406.2827 717655.7044 507395.6204 0.874383286 1.310874806 1.186166137 1.092903109 1.078725159 1.543081331 0.954691494 1.414390814 1 18.95275154 4.751446426 23.94629964 1.199874279 0.874382907 0.2348009 0.183333861 1611.768631 2995126.896 0.038339556 0.673444804 56421.73355 -4.751446426 -0.325491372 (ac)AT(ph)TGTPTADRGDAAATDDPAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATTGTPTADRGDAAATDDPAAR 22 1 Q86TI2;Q86TI2-4 Q86TI2 DPP9 Dipeptidyl peptidase 9 1 AT(0.331)T(0.331)GT(0.331)PT(0.008)ADRGDAAATDDPAAR 45.33 0.0066025 95407000 26549 26025 31190 22640 23285 25970 37227 29638 18755 TRUE FALSE 24887.34548 27951.91808 31929.84153 23220.98073 21456.29003 33467.11741 31645.15695 33338.36954 15624.66934 1.592823819 1.788960616 2.043553104 1.486174218 1.373231623 2.141940843 2.025332906 2.133700805 1 13.93153804 4.721174174 4.24633946 1.819720562 1.578581603 0 0.376746946 0.836198546 34.39083497 0.084409706 0.592154423 52622.82687 -4.721174174 -0.241138959 (ac)AYHSFLVEPISCHAWNK ddPTM_SK-BR-3_Pertuzumab_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 ; 148.03 4.62E-72 1585810000 1043180 2119600 1820550 1797480 2149400 1529560 2180900 2055680 2150300 FALSE TRUE 977889.2259 2276537.389 1863734.306 1843606.38 1980594.794 1971119.142 1853894.291 2312336.173 1791401.039 0.545879569 1.270813927 1.040378042 1.029142186 1.105612173 1.100322652 1.034885127 1.290797607 1 20.77265692 4.748974437 24.99894945 1.107384361 0.545879257 0.76247022 0.098771287 701.2163414 1683275.519 0.021995888 0.314545972 56101.49528 -4.748974437 -0.561505104 (ac)DDDIAALVVDNGSGMCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 DDDIAALVVDNGSGMCK 17 0 C9JTX5;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7 C9JTX5;P60709 ACTB "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed" 0 ;;;;;;;;; 163.46 1.68E-121 1982423000 3198363 3003528 2994307 2997915 3382186 2656729 3790734 2860999 3556514 FALSE TRUE 2998183.169 3225912.338 3065333.376 3074846.574 3116562.755 3423683.534 3222348.628 3218201.023 2962908.837 1.011905304 1.088765303 1.034568913 1.037779676 1.051859144 1.155514301 1.087562529 1.086162687 1 21.49858281 2.431109583 24.99998991 1.09323476 1.048934726 0.137905889 0.042087363 182.6853779 99259.28227 0.013113547 0.010971584 269.8420221 -2.431109583 -0.044300034 (ac)GDKKS(ph)PTRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDKKSPTRPK 10 3 Q8IY57;Q8IY57-5;G3V1X5;A0A0B4J255;F8VRE5;G3V219;G3V212;Q8IY57-4 Q8IY57 YAF2 YY1-associated factor 2 1 GDKKS(0.823)PT(0.177)RPK;GDKKS(0.931)PT(0.069)RPK 47.261 0.0049223 1937260000 4979900 2311560 3235800 3236800 3663500 2093800 4193700 2802180 4810900 TRUE FALSE 4668216.948 2482710.308 3312554.704 3319861.768 3375783.488 2698246.07 3564893.617 3152038.341 4007929.71 1.164745214 0.619449563 0.826500199 0.828323351 0.842276121 0.673226894 0.889460114 0.786450504 1 21.93442578 -0.556245921 0.949872146 1.008140119 0.808286996 0.106078445 0.145315443 63.72055403 33.81739283 2.053242869 0.04015124 0.277813969 0.556245921 -0.199853123 (ac)GDREQLLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDREQLLQR 9 1 Q04917;F8WEB6;A2IDB1 Q04917 YWHAH 14-3-3 protein eta 0 ; 102.72 0.00027971 477890000 129507 123671 102951 105753 129709 102237 126123 131196 192640 FALSE TRUE 121401.388 132827.7295 105393.0463 108466.801 119522.1784 131751.1622 107212.027 147576.1094 160487.1395 0.756455554 0.827653418 0.656707115 0.675859769 0.744746144 0.820945296 0.668041236 0.919550999 1 17.29209817 1.086390442 4.785022795 0.997582443 0.736730464 0.721576034 0.058842525 0.098632912 3.642877348 0.055978259 0.014217563 12.20085996 -1.086390442 -0.260851979 (ac)GDS(ph)DDEYDRR ddPTM_SK-BR-3_Pertuzumab_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 72.23 9.01E-07 5943950000 12944 14660 15820 18279 28162 31276 11208 10461 16696 TRUE FALSE 12133.85815 15745.44165 16195.25787 18748.07009 25950.27012 40304.87348 9527.46445 11767.07888 13909.32974 0.872353907 1.132005779 1.164344952 1.34787732 1.86567366 2.897686246 0.684969343 0.845984609 1 13.76376528 3.200942448 3.128858497 1.503209569 1.076672542 0.077640657 0.622194262 0.668694867 13.40429982 0.189188333 0.244440455 1588.336251 -3.200942448 -0.426537027 (ac)GS(ph)ASPGLSSVS(ph)PSHLLLPPDTVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GSASPGLSSVSPSHLLLPPDTVSR 24 0 O95238-2;O95238 O95238-2 SPDEF SAM pointed domain-containing Ets transcription factor 2 GS(0.315)AS(0.315)PGLS(0.315)S(0.121)VS(0.742)PS(0.193)HLLLPPDTVSR;GS(0.492)AS(0.492)PGLS(0.107)S(0.107)VS(0.703)PS(0.1)HLLLPPDTVSR;GS(0.498)AS(0.498)PGLS(0.131)S(0.128)VS(0.619)PS(0.127)HLLLPPDTVSR 87.519 0.00068131 147164000 21667.8 26527.1 22861.1 28000.3 27398.4 23859.6 26420.9 21851.5 26446.7 TRUE FALSE 20311.65108 28491.19409 23403.37609 28718.8351 25246.64018 30747.47919 22459.33132 24579.70788 22032.57492 0.921891842 1.293139553 1.062217021 1.303471574 1.145877878 1.395546336 1.019369339 1.115607593 1 14.42735049 1.611103254 25 1.050608477 1.189175119 0.197271399 0.13484995 0.473601025 3625.312143 0.058197556 0.030576451 40.84164758 -1.611103254 0.138566642 (ac)GS(ph)ASPGLSSVSPSHLLLPPDTVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GSASPGLSSVSPSHLLLPPDTVSR 24 0 O95238-2;O95238 O95238-2 SPDEF SAM pointed domain-containing Ets transcription factor 1 GS(0.424)AS(0.424)PGLS(0.057)S(0.079)VS(0.015)PS(0.002)HLLLPPDTVSR;GS(0.5)AS(0.5)PGLSSVSPSHLLLPPDTVSR;GS(0.5)AS(0.5)PGLSSVSPSHLLLPPDTVSR 136.81 7.08E-62 310750000 8251.2 9260.3 11362.9 10738.9 11449.6 7821.4 12034.4 8367.6 10208.4 TRUE FALSE 7734.772121 9945.942247 11632.43335 11014.47835 10550.3946 10079.31121 10229.95344 9412.313279 8504.552091 0.909486124 1.169484547 1.367789065 1.29512739 1.240558525 1.185166615 1.202879744 1.106738271 1 13.05401954 1.002609112 1.708228256 0.999742678 1.217760619 0.21105056 0.118994366 0.539832114 3.249156401 0.111718407 0.032196025 10.06025785 -1.002609112 0.218017942 (ac)GS(ph)PEDDLIGIPFPDHSSELLSCLNEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSPEDDLIGIPFPDHSSELLSCLNEQR 27 0 O15156 O15156 ZBTB7B Zinc finger and BTB domain-containing protein 7B 1 GS(1)PEDDLIGIPFPDHSSELLSCLNEQR 81.341 1.19E-05 17533000 2114.8 2379.5 2313.1 1923.8 2198 1005.7 2858.6 1563.2 1915.9 TRUE FALSE 1982.438443 2555.680656 2367.967824 1973.167965 2025.377946 1296.029264 2429.979468 1758.368961 1596.123913 1.242032919 1.601179354 1.483573929 1.2362248 1.268935281 0.811985369 1.522425326 1.101649406 1 10.64035694 3.164807486 3.263070211 1.179398675 1.48513722 0.296886103 0.203299231 0.276087509 5.900966898 0.057381565 0.072380569 1461.529166 -3.164807486 0.305738545 (ac)GSAS(ph)PGLSSVS(ph)PSHLLLPPDTVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSASPGLSSVSPSHLLLPPDTVSR 24 0 O95238-2;O95238 O95238-2 SPDEF SAM pointed domain-containing Ets transcription factor 2 GS(0.107)AS(0.713)PGLS(0.296)S(0.261)VS(0.531)PS(0.091)HLLLPPDTVSR 94.461 7.03E-12 27835000 13583 11118 13850 15230 12994 11454 15898 10338 14647 TRUE FALSE 12732.86428 11941.18829 14178.52854 15620.82758 11973.50366 14760.58386 13514.24249 11628.72206 12202.32108 1.043478876 0.978599745 1.161953406 1.280152152 0.981248041 1.209653784 1.107514087 0.95299263 1 13.57486798 -1.991861732 7.752326931 0.918010829 1.094808436 0.063583611 0.106122831 0.084810486 8.90E-05 0.057948913 0.02287703 0.010189157 1.991861732 0.176797607 (ac)GSAS(ph)PGLSSVSPSHLLLPPDTVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSASPGLSSVSPSHLLLPPDTVSR 24 0 O95238-2;O95238 O95238-2 SPDEF SAM pointed domain-containing Ets transcription factor 1 GS(0.009)AS(0.987)PGLS(0.003)S(0.001)VSPSHLLLPPDTVSR;GS(0.073)AS(0.903)PGLS(0.006)S(0.008)VS(0.008)PS(0.001)HLLLPPDTVSR 146.13 2.62E-87 197376000 40015.3 42170.4 39527 45982.6 44033.4 33267.9 56833.2 32702.8 65443.7 TRUE FALSE 37510.8138 45292.74029 40464.59911 47162.59136 40575.19439 42871.80267 48311.58927 36785.81657 54520.72369 0.688010196 0.830743564 0.742187491 0.865039717 0.744215991 0.786339575 0.886114233 0.674712551 1 15.73451709 -2.274069326 2.432290725 1.983135135 0.788192605 0.493660073 0.070137005 2188409.96 735376.0109 11867708.9 0.0159488 0.005320233 2.274069326 -1.194942529 (ac)GTRDDEYDYLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GTRDDEYDYLFK 12 1 H3BMH2;H3BSC1;P62491-2;Q15907-2;P62491;Q15907;B4DQU5 H3BMH2 RAB11A;RAB11B Ras-related protein Rab-11A;Ras-related protein Rab-11B 0 ;;; 94.692 2.15E-10 1247800000 1596570 1520580 1488410 1491990 1675270 1188660 1997680 1523830 1887430 FALSE TRUE 1496643.534 1633165.325 1523715.788 1530276.989 1543701.052 1531806.846 1698146.43 1714083.53 1572405.74 0.951817648 1.038641162 0.969034741 0.973207456 0.981744732 0.974180396 1.079967076 1.090102565 1 20.5845421 1.742359489 8.996114442 1.062811727 0.986299824 0.535923965 0.032608838 0.076332648 24.97262176 0.014652342 0.00789394 55.25346129 -1.742359489 -0.076511903 (ac)MATQQVDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MATQQVDSR 9 0 A0A1X7SBS2;A6NLE4 A0A1X7SBS2 SMIM23 Small integral membrane protein 23 0 49.358 0.057918 598730000 24159 8370.8 25376 17852 23039 17087 20289 22811 19135 FALSE TRUE 22646.93132 8990.582742 25977.9307 18310.11254 21229.60987 22019.73952 17246.8528 25659.00356 15941.24488 1.420650111 0.563982475 1.629604896 1.148599917 1.33174103 1.381306145 1.081901252 1.609598482 1 13.96047668 3.970849323 24.97227842 1.304703836 0.951834231 0.172913074 0.287168463 332.3341498 1323227.494 0.063878128 0.118875226 9350.811942 -3.970849323 -0.352869605 (ac)MDDREDLVYQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 MDDREDLVYQAK 12 1 P62258;B4DJF2;I3L3T1;I3L0W5 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;;; 142.92 1.11E-20 2028630000 5028500 4709420 4843240 4693990 5280900 3703830 6021310 4538320 6993500 FALSE TRUE 4713775.161 5058110.357 4958123.94 4814445.73 4866159.416 4773065.594 5118470.465 5104939.242 5826239.67 0.809059604 0.868160365 0.850998967 0.826338428 0.835214425 0.819236054 0.87852041 0.876197948 1 22.47413362 0.635382307 1.069888148 0.999831239 0.841118727 0.871135373 0.019403406 0.411368204 0.7544811 0.018426473 0.005802715 4.318991075 -0.635382307 -0.158712512 (ac)MDEET(ph)RHSLECIQANQIFPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MDEETRHSLECIQANQIFPR 20 1 Q13615-3;Q13615-2;Q13615;C9JLU3 Q13615-3 MTMR3 Myotubularin-related protein 3 1 MDEET(0.5)RHS(0.5)LECIQANQIFPR;MDEET(0.5)RHS(0.5)LECIQANQIFPR 79.311 1.62E-22 105030000 10425.9 8840.4 11915.6 11786.8 12070.6 11030.1 12857.3 11344.1 12398.2 TRUE FALSE 9773.36153 9494.952414 12198.24366 12089.26924 11122.62377 14214.31081 10929.46723 12760.43586 10328.86032 0.946218772 0.919264286 1.180986409 1.17043593 1.076849083 1.376174173 1.058148419 1.235415666 1 13.33439346 3.98625638 2.868264143 1.163414609 0.932565521 0.442949955 0.103861283 0.209264965 3.458148265 0.024160343 0.056204086 9688.49634 -3.98625638 -0.230849088 (ac)MDFEDDYTHSACR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MDFEDDYTHSACR 13 0 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-2;E2QRN4 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 0 ;; 119.53 1.85E-11 345050000 110190 100622 99114 105821 115269 95892 120127 94321 140764 FALSE TRUE 103293.4046 108072.1576 101465.0309 108536.546 106216.2377 123574.4637 102115.0716 106097.1845 117269.579 0.880820119 0.92157027 0.865228917 0.925530277 0.905744172 1.053764026 0.870772048 0.904728962 1 16.83946929 2.782658922 2.567260577 0.943659547 0.894054689 0.19195042 0.053149271 0.534350965 6.960533728 0.017192128 0.017632707 606.2600091 -2.782658922 -0.049604858 (ac)MDFQHRPGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MDFQHRPGGK 10 1 Q15428;K7EMT0 Q15428 SF3A2 Splicing factor 3A subunit 2 0 ;;; 87.913 0.0024287 1566750000 1777580 1847460 1889430 1758860 1944060 1538450 2082180 1720330 2199540 FALSE TRUE 1666324.441 1984247.861 1934248.172 1803995.325 1791381.37 1982575.54 1769976.439 1935116.987 1832422.564 0.909355993 1.082854959 1.055568846 0.984486526 0.977602767 1.081942331 0.965921547 1.056042981 1 20.8053208 3.24605452 24.99632926 1.009695845 1.035931564 0 0.057399275 605.8818791 2020936.417 0.014955279 0.019843354 1762.197255 -3.24605452 0.026235719 (ac)MDLAAAAEPGAGS(ph)QHLEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MDLAAAAEPGAGSQHLEVR 19 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 1 MDLAAAAEPGAGS(1)QHLEVR;MDLAAAAEPGAGS(1)QHLEVR 150.13 1.85E-49 238040000 24280.9 28299 29887 23961.7 35669 29140 35833 17771.2 31762 TRUE FALSE 22761.20181 30394.28741 30595.93375 24576.59779 32867.70062 37552.24495 30460.17431 19989.97344 26460.71701 0.860188399 1.148656984 1.156277577 0.92879561 1.242131897 1.419169592 1.151146974 0.755458495 1 14.69156453 1.254838756 24.9219464 0.877729294 1.145634645 0.285059627 0.164210203 236.4973338 362082.0933 0.106488965 0.038627425 17.98203159 -1.254838756 0.267905352 (ac)MDLFGDLPEPERS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 MDLFGDLPEPERSPR 15 1 Q9H0C8;E9PC05;F8SNU7;F8SNU6 Q9H0C8 ILKAP;ILKAP3;ILKAP2 Integrin-linked kinase-associated serine/threonine phosphatase 2C 1 MDLFGDLPEPERS(1)PR;MDLFGDLPEPERS(1)PR;MDLFGDLPEPERS(1)PR;MDLFGDLPEPERS(1)PR;MDLFGDLPEPERS(1)PR;MDLFGDLPEPERS(1)PR 133.86 7.57E-12 353709000 48745.3 53137.9 61724.3 56958.4 61392 52041.1 59136 49677.1 70293.9 TRUE FALSE 45694.41869 57072.28541 63188.42954 58420.04897 56570.51996 67064.52075 50269.10579 55879.39529 58561.39397 0.780282292 0.974571839 1.079011705 0.997586379 0.966003644 1.145200211 0.858400089 0.954201932 1 15.83766227 -0.316918322 6.841609739 0.999994706 0.979275429 0.000569188 0.101570835 0 0 0.092709718 0.02185189 0.482038446 0.316918322 -0.020719277 (ac)MDLFGDLPEPERS(ph)PRPAAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 MDLFGDLPEPERSPRPAAGK 20 2 Q9H0C8;E9PC05;F8SNU7;F8SNU6 Q9H0C8 ILKAP;ILKAP3;ILKAP2 Integrin-linked kinase-associated serine/threonine phosphatase 2C 1 MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK 161.04 9.71E-30 2677863000 2276618 2090405 2324904 2282029 2755961 2076006 3103916 2342992 3122887 TRUE FALSE 2134128.543 2245180.761 2380051.821 2340589.728 2539518.94 2675315.231 2638512.611 2635519.709 2601656.985 0.820295894 0.862981082 0.914821529 0.899653467 0.976115973 1.028312051 1.014166213 1.013015829 1 21.31099933 3.060571563 0.754734521 1.024080027 0.840720097 0.915333352 0.020694404 0.185781978 0.235326839 0.012894447 0.01835778 1149.665671 -3.060571563 -0.18335993 (ac)MDNYADLSDT(ph)ELTTLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MDNYADLSDTELTTLLR 17 0 P50402;Q5HY57;F8WEQ1 P50402 EMD Emerin 1 MDNYADLS(0.422)DT(0.575)ELT(0.002)TLLR;MDNYADLS(0.434)DT(0.563)ELT(0.003)T(0.001)LLR;MDNYADLS(0.421)DT(0.559)ELT(0.017)T(0.003)LLR 66.335 2.20E-06 86890000 29756.9 38834.7 24174.6 30531.5 46181.4 28442.6 31338.6 26493.6 33975.9 TRUE FALSE 27894.46875 41710.0616 24748.03293 31314.98998 42554.49913 36653.51689 26639.66786 29801.38428 28305.1028 0.985492579 1.473588063 0.874331145 1.106337264 1.503421466 1.294943783 0.941161318 1.052862605 1 14.78877454 1.722245734 9.547051394 1.000449921 1.20637003 0.201594578 0.195217626 0.175712302 47.56775776 0.092699824 0.049952016 52.75282651 -1.722245734 0.205920109 (ac)MDPQRS(ph)PLLEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 MDPQRSPLLEVK 12 1 Q9BW19;A2AB20;A0A140T9E6 Q9BW19 KIFC1 Kinesin-like protein KIFC1 1 MDPQRS(1)PLLEVK;MDPQRS(1)PLLEVK;MDPQRS(1)PLLEVK;MDPQRS(1)PLLEVK;MDPQRS(1)PLLEVK;MDPQRS(1)PLLEVK;MDPQRS(1)PLLEVK 72.089 0.00056212 2093870000 4646680 4089050 4521740 4213200 4513170 3538500 5246630 3973600 5852480 TRUE FALSE 4355852.593 4391807.517 4628997.808 4321317.845 4158723.833 4560007.507 4459946.539 4469712.707 4875663.28 0.893386672 0.900761038 0.949408838 0.886303585 0.852955505 0.935258906 0.914736372 0.916739416 1 22.21716706 0.154988838 0.837030163 1.001384687 0.906354992 0.565536827 0.026128131 3.145296413 2.453339537 0.037495112 0.008728315 1.428857234 -0.154988838 -0.095029695 (ac)MDRGEQGLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MDRGEQGLLR 10 1 P55327-2;P55327-4;E5RFR7 P55327-2 TPD52 0 ; 77.072 9.49E-05 613250000 92920 164938 150279 163862 172235 155761 158670 159759 177741 FALSE TRUE 87104.30307 177150.1811 153843.6888 168066.9763 158708.3579 200726.6721 134878.9065 179705.2628 148074.8788 0.588244973 1.196355402 1.038958735 1.135013431 1.071811499 1.355575461 0.910883112 1.213610737 1 17.17596738 4.74425499 24.93007955 1.11157671 0.588244739 0.642590129 0.123497631 355.006924 1554180.153 0.026019863 0.230866306 55495.14497 -4.74425499 -0.523331971 (ac)MDRNPS(ph)PPPPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 MDRNPSPPPPGR 12 1 J3KND1;E9PRZ1;Q96ER3;E9PL53;E9PMD2 J3KND1 SAAL1 Protein SAAL1 1 MDRNPS(1)PPPPGR;MDRNPS(1)PPPPGR;MDRNPS(1)PPPPGR;MDRNPS(1)PPPPGR;MDRNPS(1)PPPPGR;MDRNPS(1)PPPPGR;MDRNPS(1)PPPPGR;MDRNPS(1)PPPPGR 81.92 4.39E-05 3220481000 125501.6 185362.8 186707.5 176623.2 191833.2 173399.4 173740.6 166626.4 167366.8 TRUE FALSE 117646.6789 199087.2546 191136.2901 181155.6503 176767.3943 223456.9919 147689.81 187430.0728 139432.1998 0.843755453 1.427842742 1.370818866 1.299238272 1.267765943 1.602621146 1.059223121 1.344238082 1 17.08920424 -1.164432964 9.511199656 0.999999997 1.296152484 0.146236473 0.20568762 1.37E-08 1.12E-09 0.178916911 0.04217112 0.068480518 1.164432964 0.296152488 (ac)MDS(ph)AGQDINLNSPNKGLLSDSMTDVPVDTGVAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MDSAGQDINLNSPNKGLLSDSMTDVPVDTGVAAR 34 1 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;A0A087WZ51;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 1 MDS(0.495)AGQDINLNS(0.495)PNKGLLS(0.004)DS(0.004)MT(0.001)DVPVDTGVAAR 41.476 7.42E-10 252410000 145530 117490 116500 115990 128830 77736 130970 100470 137920 TRUE FALSE 136421.5371 126189.0818 119263.435 118966.4998 118712.2115 100177.1213 111332.2644 113013.9007 114900.261 1.187303979 1.09824887 1.037973578 1.035389291 1.033176169 0.871861564 0.96894701 0.983582628 1 16.81002255 4.533354597 0.49049061 0.954723791 1.296557741 0.72461426 0.043194809 1.950203386 0.419499788 0.027574616 0.377631027 34147.16061 -4.533354597 0.34183395 (ac)MDSAGQDINLNS(ph)PNKGLLSDSMTDVPVDTGVAAR ddPTM_SK-BR-3_Pertuzumab_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 MDSAGQDINLNS(0.992)PNKGLLS(0.004)DS(0.003)MTDVPVDTGVAAR;MDSAGQDINLNS(0.999)PNKGLLS(0.001)DSMTDVPVDTGVAAR 146.26 4.55E-117 278167000 203900 148880 168426 171848 203937 122846 200577 148182 202451 TRUE FALSE 191138.263 159903.2301 172421.1443 176257.9106 187920.6107 158309.646 170502.3409 166682.8489 168660.6202 1.133271434 0.948076853 1.022296396 1.045044839 1.11419376 0.938628387 1.010919684 0.988273663 1 17.36376364 2.209365366 24.99883313 0.986434235 1.033855329 0.240197903 0.054799599 413.3023759 353893.3387 0.020359484 0.01503884 161.944188 -2.209365366 0.047421095 (ac)MEDLDQS(ph)PLVSSSDS(ph)PPRPQPAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MEDLDQSPLVSSSDSPPRPQPAFK 24 1 Q9NQC3-5;Q9NQC3;Q9NQC3-4;Q9NQC3-2 Q9NQC3-5;Q9NQC3-2 RTN4 Reticulon-4 2 MEDLDQS(0.998)PLVS(0.002)S(0.019)S(0.073)DS(0.907)PPRPQPAFK;MEDLDQS(0.995)PLVS(0.004)S(0.002)S(0.005)DS(0.994)PPRPQPAFK 123.89 1.81E-17 51550000 110502 93519 102666 104409 113043 81736 108378 85288 114814 TRUE FALSE 103585.8771 100443.2441 105101.286 107088.3117 104165.0588 105331.8563 92127.72503 95936.39454 95650.80167 1.082958797 1.050103526 1.098801935 1.119575684 1.089013965 1.101212478 0.963167307 1.002985786 1 16.54548944 1.747669144 9.824527503 0.988423999 1.087710949 0.845340012 0.0204484 0.041463391 18.81997936 0.010143528 0.005506312 55.93313274 -1.747669144 0.099286951 (ac)MEDLDQSPLVSSSDS(ph)PPRPQPAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 MEDLDQSPLVSSSDSPPRPQPAFK 24 1 Q9NQC3-5;Q9NQC3;Q9NQC3-4;Q9NQC3-2 Q9NQC3-5;Q9NQC3-2 RTN4 Reticulon-4 1 MEDLDQSPLVSSS(0.001)DS(0.998)PPRPQPAFK;MEDLDQSPLVSSS(0.001)DS(0.999)PPRPQPAFK;MEDLDQSPLVSSS(0.001)DS(0.999)PPRPQPAFK;MEDLDQSPLVSSS(0.004)DS(0.996)PPRPQPAFK;MEDLDQSPLVSS(0.002)S(0.04)DS(0.958)PPRPQPAFK;MEDLDQSPLVSSSDS(0.999)PPRPQPAFK;MEDLDQSPLVSSSDS(1)PPRPQPAFK;MEDLDQSPLVSSS(0.001)DS(0.999)PPRPQPAFK;MEDLDQSPLVSSS(0.001)DS(0.999)PPRPQPAFK;MEDLDQSPLVSS(0.001)S(0.01)DS(0.989)PPRPQPAFK;MEDLDQSPLVSSSDS(1)PPRPQPAFK 172.18 2.63E-62 4749090000 5065280 4375380 4492830 4178860 5156800 4302320 5803270 4502440 6030170 TRUE FALSE 4748253.167 4699337.688 4599402.049 4286096.622 4751805.73 5544329.942 4933123.538 5064579.545 5023695.671 0.94517134 0.935434389 0.915541536 0.853176009 0.945878501 1.103635711 0.981971015 1.008138207 1 22.26031764 2.46165358 24.99492613 1.021093433 0.914997602 0.639907542 0.039590801 146.4489718 236652.2162 0.012923965 0.01081614 289.5033412 -2.46165358 -0.10609583 (ac)MEDS(ph)MDMDMSPLRPQNYLFGCELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 34 MEDSMDMDMSPLRPQNYLFGCELK 24 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 MEDS(0.495)MDMDMS(0.495)PLRPQNY(0.009)LFGCELK;MEDS(0.5)MDMDMS(0.5)PLRPQNYLFGCELK;MEDS(0.914)MDMDMS(0.086)PLRPQNYLFGCELK;MEDS(0.963)MDMDMS(0.037)PLRPQNYLFGCELK;MEDS(0.496)MDMDMS(0.501)PLRPQNY(0.003)LFGCELK;MEDS(0.953)MDMDMS(0.047)PLRPQNYLFGCELK;MEDS(0.934)MDMDMS(0.066)PLRPQNYLFGCELK;MEDS(0.95)MDMDMS(0.05)PLRPQNYLFGCELK;MEDS(0.923)MDMDMS(0.077)PLRPQNYLFGCELK;MEDS(0.969)MDMDMS(0.031)PLRPQNYLFGCELK;MEDS(0.527)MDMDMS(0.462)PLRPQNY(0.011)LFGCELK;MEDS(0.429)MDMDMS(0.571)PLRPQNYLFGCELK;MEDS(0.945)MDMDMS(0.054)PLRPQNYLFGCELK;MEDS(0.783)MDMDMS(0.217)PLRPQNYLFGCELK;MEDS(0.946)MDMDMS(0.054)PLRPQNYLFGCELK;MEDS(0.953)MDMDMS(0.047)PLRPQNYLFGCELK;MEDS(0.844)MDMDMS(0.153)PLRPQNY(0.003)LFGCELK;MEDS(0.897)MDMDMS(0.103)PLRPQNYLFGCELK;MEDS(0.494)MDMDMS(0.494)PLRPQNY(0.012)LFGCELK;MEDS(0.973)MDMDMS(0.027)PLRPQNYLFGCELK;MEDS(0.951)MDMDMS(0.049)PLRPQNYLFGCELK;MEDS(0.986)MDMDMS(0.014)PLRPQNYLFGCELK;MEDS(0.826)MDMDMS(0.174)PLRPQNYLFGCELK;MEDS(0.959)MDMDMS(0.041)PLRPQNYLFGCELK;MEDS(0.996)MDMDMS(0.004)PLRPQNYLFGCELK;MEDS(0.994)MDMDMS(0.006)PLRPQNYLFGCELK;MEDS(0.964)MDMDMS(0.036)PLRPQNY(0.001)LFGCELK;MEDS(0.989)MDMDMS(0.011)PLRPQNYLFGCELK;MEDS(0.994)MDMDMS(0.006)PLRPQNYLFGCELK;MEDS(0.957)MDMDMS(0.042)PLRPQNY(0.001)LFGCELK;MEDS(0.999)MDMDMS(0.001)PLRPQNYLFGCELK;MEDS(0.856)MDMDMS(0.144)PLRPQNYLFGCELK;MEDS(0.98)MDMDMS(0.02)PLRPQNYLFGCELK;MEDS(0.998)MDMDMS(0.002)PLRPQNYLFGCELK 98.121 4.18E-38 3669992000 3444022 2999576 3178129 2995599 3381758 2451995 3936896 2851119 4486539 TRUE FALSE 3228466.811 3221667.728 3253515.721 3072471.142 3116168.368 3159846.152 3346594.993 3207087.483 3737706.657 0.863756069 0.861937018 0.870457748 0.822020406 0.833711325 0.845397042 0.895360525 0.858036164 1 21.83372192 0.012216585 0.728510603 1.004791041 0.853865081 0.842037429 0.01963556 1.913242305 1.077763083 0.045955596 0.007216838 1.028529103 -0.012216585 -0.15092596 (ac)MEDSMDMDMS(ph)PLRPQNYLFGCELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 22 MEDSMDMDMSPLRPQNYLFGCELK 24 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 MEDS(0.195)MDMDMS(0.804)PLRPQNY(0.001)LFGCELK;MEDS(0.076)MDMDMS(0.919)PLRPQNY(0.004)LFGCELK;MEDS(0.414)MDMDMS(0.579)PLRPQNY(0.006)LFGCELK;MEDS(0.108)MDMDMS(0.892)PLRPQNYLFGCELK;MEDS(0.037)MDMDMS(0.963)PLRPQNYLFGCELK;MEDS(0.487)MDMDMS(0.513)PLRPQNYLFGCELK;MEDS(0.098)MDMDMS(0.901)PLRPQNY(0.001)LFGCELK;MEDS(0.044)MDMDMS(0.956)PLRPQNYLFGCELK;MEDS(0.005)MDMDMS(0.995)PLRPQNYLFGCELK;MEDSMDMDMS(1)PLRPQNYLFGCELK;MEDS(0.215)MDMDMS(0.783)PLRPQNY(0.002)LFGCELK;MEDS(0.009)MDMDMS(0.991)PLRPQNYLFGCELK;MEDS(0.037)MDMDMS(0.96)PLRPQNY(0.003)LFGCELK;MEDS(0.033)MDMDMS(0.963)PLRPQNY(0.004)LFGCELK;MEDS(0.128)MDMDMS(0.872)PLRPQNYLFGCELK;MEDS(0.044)MDMDMS(0.955)PLRPQNY(0.001)LFGCELK;MEDS(0.008)MDMDMS(0.98)PLRPQNY(0.012)LFGCELK;MEDS(0.101)MDMDMS(0.899)PLRPQNYLFGCELK;MEDS(0.012)MDMDMS(0.988)PLRPQNYLFGCELK;MEDS(0.481)MDMDMS(0.519)PLRPQNYLFGCELK;MEDS(0.462)MDMDMS(0.536)PLRPQNY(0.002)LFGCELK;MEDS(0.016)MDMDMS(0.982)PLRPQNY(0.002)LFGCELK 115.48 1.16E-44 3860374000 3038463 2673247 2852857 2677706 3065397 2286142 3444332 2635538 3870798 TRUE FALSE 2848291.025 2871176.989 2920528.115 2746420.469 2824653.085 2946114.083 2927886.392 2964590.721 3224736.807 0.883263099 0.890360101 0.905664025 0.851672751 0.875932907 0.913598305 0.907945847 0.919327963 1 21.62074999 0.611297419 0.727872558 1.000993563 0.885784273 0.835343284 0.015824809 0.542161614 0.51327657 0.017055778 0.005929405 4.08599113 -0.611297419 -0.11520929 (ac)MEFDLGAALEPTSQKPGVGAGHGGDPKLS(ph)PHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MEFDLGAALEPTSQKPGVGAGHGGDPKLSPHK 32 2 Q9GZP8-2;Q9GZP8 Q9GZP8-2 IMUP Immortalization up-regulated protein 1 MEFDLGAALEPTS(0.001)QKPGVGAGHGGDPKLS(0.998)PHK;MEFDLGAALEPT(0.01)S(0.01)QKPGVGAGHGGDPKLS(0.979)PHK;MEFDLGAALEPT(0.001)S(0.002)QKPGVGAGHGGDPKLS(0.998)PHK;MEFDLGAALEPT(0.001)S(0.002)QKPGVGAGHGGDPKLS(0.997)PHK 153.65 5.47E-47 1184790000 2399220 1171080 1595970 1566020 1654100 1138220 2191140 1408870 2279790 TRUE FALSE 2249057.103 1257787.982 1633827.162 1606206.724 1524193.658 1466805.637 1862598.899 1584770.521 1899278.321 1.184164047 0.662245216 0.860235777 0.845693181 0.802512008 0.772296309 0.980687705 0.834406681 1 20.8570199 1.011421012 0.876056391 0.991475301 0.835343176 0.044711188 0.140382569 1.390589942 2.342159329 0.121107332 0.042717485 10.26646692 -1.011421012 -0.156132125 (ac)MEFDLGAALEPTSQKPGVGAGHGGDPKLS(ph)PHKVQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MEFDLGAALEPTSQKPGVGAGHGGDPKLSPHKVQGR 36 3 Q9GZP8-2;Q9GZP8 Q9GZP8-2 IMUP Immortalization up-regulated protein 1 MEFDLGAALEPTSQKPGVGAGHGGDPKLS(1)PHKVQGR;MEFDLGAALEPTSQKPGVGAGHGGDPKLS(0.999)PHKVQGR;MEFDLGAALEPT(0.001)S(0.003)QKPGVGAGHGGDPKLS(0.996)PHKVQGR;MEFDLGAALEPTS(0.001)QKPGVGAGHGGDPKLS(0.999)PHKVQGR 92.486 6.42E-18 3294730000 2101930 1337470 1604680 1689500 1915290 1164994 2295140 1355620 3436410 TRUE FALSE 1970373.953 1436497.67 1642743.767 1732855.43 1764870.849 1501308.856 1951005.064 1524872.141 2862850.971 0.688255859 0.501771725 0.57381393 0.605290128 0.616473183 0.524410411 0.681490264 0.532641118 1 21.44902114 -5 0.38057135 6.86335384 0.57631264 0.799786904 0.063915869 236.3043576 1.763699003 1143.698174 0.038986569 1.00E-05 5 -6.2870412 (ac)MEGSGEQPGPQPQHPGDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MEGSGEQPGPQPQHPGDHR 19 0 Q9UJA5;Q9UJA5-2;Q9UJA5-3 Q9UJA5 TRMT6 tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 0 ; 73.11 2.47E-08 148330000 46839 60542 65607 59574 59794.5 54123 69272 53184 56856 FALSE TRUE 43907.4306 65024.59267 67163.22902 61102.7697 55098.48117 69747.43149 58885.30669 59824.13947 47366.3663 0.926974856 1.372800951 1.417951899 1.290003318 1.163240617 1.472509651 1.24318818 1.263008843 1 15.53157538 -1.088462911 4.489182362 0.999976199 1.29420201 0.220195164 0.152346522 3.33E-05 6.77E-06 0.135450054 0.031923303 0.081571245 1.088462911 0.29422581 (ac)MELDLS(ph)PPHLSSSPEDLCPAPGT(ph)PPGTPRPPDTPLPEEVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR 41 2 Q14451;Q14451-4;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 MELDLS(0.3)PPHLS(0.225)S(0.233)S(0.242)PEDLCPAPGT(0.805)PPGT(0.165)PRPPDT(0.029)PLPEEVKR;MELDLS(0.943)PPHLS(0.018)S(0.019)S(0.021)PEDLCPAPGT(0.977)PPGT(0.022)PRPPDTPLPEEVKR;MELDLS(0.689)PPHLS(0.143)S(0.143)S(0.144)PEDLCPAPGT(0.824)PPGT(0.054)PRPPDT(0.003)PLPEEVKR;MELDLS(0.553)PPHLS(0.248)S(0.101)S(0.108)PEDLCPAPGT(0.893)PPGT(0.093)PRPPDT(0.005)PLPEEVKR 80.053 1.40E-06 189684000 60902.6 96468 91239 98098 107949 91272 116223 86299 101188 TRUE FALSE 57090.81498 103610.5911 93403.23217 100615.3608 99471.12099 117620.7447 98796.44011 97073.62012 84299.0691 0.677241345 1.229083455 1.107998382 1.193552454 1.179978878 1.395279283 1.171975458 1.151538459 1 16.36322908 4.741205009 24.94701428 1.190199125 0.677241157 0.715502839 0.099132341 120.064014 1132610.317 0.021765345 0.150151808 55106.77672 -4.741205009 -0.512957968 (ac)MELDLS(ph)PPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR 41 2 Q14451;Q14451-4;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 MELDLS(0.928)PPHLS(0.024)S(0.024)S(0.024)PEDLCPAPGTPPGTPRPPDTPLPEEVKR 57.14 5.31E-05 3212700000 30316 71353 54984 55424 63110 56737 70827 50294 56600 TRUE FALSE 28418.57568 76636.05036 56288.24645 56846.27367 58153.59517 73116.05085 60207.14888 56573.31661 47153.09435 0.602687397 1.62526026 1.193733884 1.205568255 1.233293297 1.550609814 1.276844069 1.199779514 1 15.52506483 0.899816854 3.194788635 1.000453647 1.286607259 0.051651488 0.272901518 0.944915406 21.10094792 0.232730972 0.060643481 7.939933307 -0.899816854 0.286153612 (ac)MELDLSPPHLSSS(ph)PEDLCPAPGT(ph)PPGTPRPPDTPLPEEVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR 41 2 Q14451;Q14451-4;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 MELDLS(0.001)PPHLS(0.302)S(0.332)S(0.365)PEDLCPAPGT(0.988)PPGT(0.012)PRPPDTPLPEEVKR;MELDLS(0.062)PPHLS(0.299)S(0.313)S(0.328)PEDLCPAPGT(0.833)PPGT(0.163)PRPPDT(0.001)PLPEEVKR;MELDLS(0.006)PPHLS(0.138)S(0.177)S(0.679)PEDLCPAPGT(0.991)PPGT(0.009)PRPPDTPLPEEVKR 120.25 1.44E-44 416172000 110216 158778 143660 168453 185805 142648 220132 147052 160896 TRUE FALSE 103317.7773 170534.0883 147067.683 172775.7892 171212.6248 183828.1619 187125.2502 165411.7659 134041.4182 0.770789945 1.27224921 1.097180894 1.288973151 1.27731135 1.371428059 1.396025592 1.234034735 1 17.03231933 4.739627199 24.37467318 1.257680617 0.77078972 0.607460502 0.118496713 43.44525829 992667.7481 0.028291483 0.173117943 54906.93466 -4.739627199 -0.486890897 (ac)MELDLSPPHLSSSPEDLCPAPGT(ph)PPGT(ph)PRPPDTPLPEEVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR 41 2 Q14451;Q14451-4;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 MELDLS(0.001)PPHLS(0.003)S(0.003)S(0.004)PEDLCPAPGT(0.991)PPGT(0.993)PRPPDT(0.004)PLPEEVKR;MELDLS(0.005)PPHLS(0.018)S(0.019)S(0.02)PEDLCPAPGT(0.951)PPGT(0.972)PRPPDT(0.015)PLPEEVKR 69.969 1.28E-07 617470000 23386 62933 60644 83621 92930 45484 55042 42376 43832 TRUE FALSE 21922.31201 67592.6248 62082.50432 85766.85643 85631.65266 58614.49243 46788.96308 47666.73688 36516.15603 0.600345556 1.851033409 1.700137995 2.348737264 2.34503469 1.605166009 1.281322247 1.305360204 1 15.15624728 1.780740575 3.23171829 1.203406965 1.8063119 0.221788747 0.485127484 0.348378658 7.023018984 0.261536465 0.129563983 60.35879697 -1.780740575 0.602904934 (ac)MELDLSPPHLSSSPEDLCPAPGT(ph)PPGTPRPPDTPLPEEVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR 41 2 Q14451;Q14451-4;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 MELDLSPPHLSSSPEDLCPAPGT(0.993)PPGT(0.007)PRPPDTPLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(1)PPGTPRPPDTPLPEEVKR;MELDLSPPHLS(0.002)S(0.002)S(0.002)PEDLCPAPGT(0.919)PPGT(0.074)PRPPDT(0.003)PLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.984)PPGT(0.015)PRPPDTPLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.932)PPGT(0.066)PRPPDT(0.002)PLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.759)PPGT(0.217)PRPPDT(0.024)PLPEEVKR;MELDLS(0.004)PPHLS(0.059)S(0.059)S(0.012)PEDLCPAPGT(0.654)PPGT(0.2)PRPPDT(0.01)PLPEEVKR;MELDLSPPHLS(0.001)S(0.002)S(0.002)PEDLCPAPGT(0.93)PPGT(0.063)PRPPDT(0.002)PLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.752)PPGT(0.245)PRPPDT(0.002)PLPEEVKR 171.19 1.38E-96 10614330000 1410056 3646945 2963472 3350729 3391360 3011676 4783196 3181619 2916130 TRUE FALSE 1321803.112 3916968.602 3033766.955 3436714.379 3125016.266 3881097.971 4066000.165 3578851.136 2429409.064 0.54408421 1.612313324 1.248767447 1.414629767 1.286327738 1.597548156 1.673658103 1.473136488 1 21.212174 4.745053458 24.91383149 1.446220505 0.544083785 0.643282194 0.202101019 429.9332939 1649661.239 0.045763717 0.438669839 55597.26889 -4.745053458 -0.90213672 (ac)MENGYTYEDYKNTAEWLLSHTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MENGYTYEDYKNTAEWLLSHTK 22 1 P00491;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 ; 133.38 5.29E-55 430300000 630900 659930 512010 453840 835260 452940 636790 691870 578530 FALSE TRUE 591413.0952 708791.9039 524155.119 465486.3027 769662.0489 583696.4251 541309.2512 778251.4925 481969.6056 1.227075501 1.470615358 1.087527331 0.96580012 1.59690993 1.211064802 1.123119062 1.614731476 1 18.87858264 -1.460668147 3.166457781 0.994713572 1.270890659 0.145355144 0.21562383 24584045.63 30817622.61 1148548.39 0.049743474 0.034620382 1.460668147 0.276177087 (ac)MESYHKPDQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 16 MESYHKPDQQK 11 1 P29401;P29401-2;E9PFF2;F8W888;F8WAX4 P29401 TKT Transketolase 0 ;;;;;;;;;;;;;;; 118.28 2.28E-07 22943815000 13201388 16450305 14287025 13036177 21234080 11186818 19159493 18360690 26408982 FALSE TRUE 12375136.69 17668302.7 14625919.98 13370707.37 19566441.01 14416270.75 16286704.89 20653062.56 22001152.3 0.562476752 0.803062606 0.664779725 0.607727595 0.889337101 0.655250714 0.740265995 0.938726403 1 24.39107575 1.203520653 3.28040778 0.996519067 0.708301418 0.591155325 0.093076193 0.154945711 2.970888359 0.076839008 0.021292626 15.97793511 -1.203520653 -0.288217648 (ac)METMAS(ph)PGKDNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 METMASPGKDNYR 13 1 O60684;S4R3E5 O60684 KPNA6 Importin subunit alpha-7 1 MET(0.003)MAS(0.997)PGKDNYR;MET(0.191)MAS(0.809)PGKDNYR;MET(0.061)MAS(0.939)PGKDNYR 72.496 1.59E-05 1159340000 1598800 1169470 1320490 1270160 1494500 1103860 1763880 1265260 1739690 TRUE FALSE 1498733.962 1256058.776 1351812.646 1302754.456 1377127.999 1422526.462 1499402.569 1423230.496 1449324.5 1.034091373 0.866651171 0.932719102 0.898870098 0.950186103 0.981509981 1.034552696 0.981995748 1 20.46694922 2.249315441 2.531994583 1.008839726 0.922232828 0.324806643 0.044757906 0.24944856 3.279205033 0.01769824 0.012581546 177.5478594 -2.249315441 -0.086606898 (ac)MEVAEPS(ph)SPTEEEEEEEEHSAEPRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.452)S(0.452)PT(0.095)EEEEEEEEHSAEPRPR 68.733 0.001131 1066100000 0 0 0 0 0 0 0 0 0 TRUE FALSE 0 0 0 0 0 0 0 0 0 0 (ac)MEVAEPSS(ph)PTEEEEEEEEHSAEPRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MEVAEPSSPTEEEEEEEEHSAEPRPR 26 1 M0R3H9;M0QXG9;M0R3F4;M0R2A4;M0R2K3;M0R193;M0R0I0;J3KQS6;Q9NWV8-3;Q9NWV8 M0R3H9 BABAM1 BRISC and BRCA1-A complex member 1 1 MEVAEPS(0.023)S(0.84)PT(0.137)EEEEEEEEHSAEPRPR;MEVAEPS(0.158)S(0.644)PT(0.197)EEEEEEEEHSAEPRPR;MEVAEPS(0.008)S(0.834)PT(0.158)EEEEEEEEHSAEPRPR 82.492 0.00017379 5030500000 0 0 0 0 0 0 0 0 0 TRUE FALSE 0 0 0 0 0 0 0 0 0 0 (ac)MEVKPPPGRPQPDS(ph)GR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MEVKPPPGRPQPDSGR 16 2 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 MEVKPPPGRPQPDS(1)GR;MEVKPPPGRPQPDS(1)GR;MEVKPPPGRPQPDS(1)GR;MEVKPPPGRPQPDS(1)GR 76.704 0.00041286 1323950000 919410 775190 864110 848760 917370 759570 1064580 798080 1052950 TRUE FALSE 861865.7693 832585.8742 884607.0973 870540.6185 845323.4607 978845.5284 904956.1121 897722.0448 877205.8427 0.982512573 0.949133982 1.008437307 0.992401756 0.963654617 1.115867543 1.031634843 1.023388128 1 19.7425559 2.276796083 24.99999826 1.046406793 0.979706167 0.473169001 0.033188554 126.7302412 82861.22567 0.010745834 0.008990424 189.1455302 -2.276796083 -0.066700626 (ac)MEVKPPPGRPQPDS(ph)GRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MEVKPPPGRPQPDSGRR 17 3 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 MEVKPPPGRPQPDS(1)GRR;MEVKPPPGRPQPDS(1)GRR 43.955 0.0077336 623730000 432020 380640 450680 410940 470670 384640 517660 427490 579210 TRUE FALSE 404980.6394 408822.9817 461370.3424 421485.4161 433705.4768 495679.3239 440041.6887 480863.0675 482536.1092 0.839275303 0.847238111 0.956136409 0.873479535 0.89880419 1.027237785 0.911935253 0.996532816 1 18.88027738 7.999999999 0.174272719 1.011680784 0.260542739 0.593264999 0.041981197 40.294606 0.443115911 0.09529025 7.953725345 99999999.72 -7.999999999 -0.751138045 (ac)MEVKPPPGRPQPDSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MEVKPPPGRPQPDSGR 16 2 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 74.296 9.99E-06 1953010000 1028264 983749 1011161 964797 1077349 842298 1164525 872302 1130141 FALSE TRUE 963906.7917 1056586.8 1035146.216 989555.3244 992738.3554 1085455.759 989915.2872 981210.8249 941513.1661 1.023784719 1.122222012 1.099449539 1.051026539 1.0544073 1.152884312 1.051408863 1.042163679 1 19.84462174 1.165017729 2.075311307 1.003953337 1.087790044 0.324237893 0.037874919 0.309003597 2.41797968 0.033279359 0.0094862 14.62236865 -1.165017729 0.083836707 (ac)MEVKPPPGRPQPDSGRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MEVKPPPGRPQPDSGRR 17 3 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 41.554 0.00098517 401920000 147179 161911 154802 138425 165907 126619 169772 138288 201772 FALSE TRUE 137967.3291 173899.0589 158473.9765 141977.2199 152877.3335 163171.8498 144316.2647 155553.5612 168094.9497 0.820770222 1.034528754 0.942764651 0.844625137 0.909470116 0.970712387 0.858540158 0.925391045 1 17.35891685 3.463544917 24.76937221 0.90939564 0.958148112 0 0.06969213 465.0125876 848390.7823 0.017670654 0.02396665 2907.668669 -3.463544917 0.048752472 (ac)MEVS(ph)PLQPVNENMQVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 MEVSPLQPVNENMQVNK 17 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 MEVS(1)PLQPVNENMQVNK;MEVS(1)PLQPVNENMQVNK;MEVS(1)PLQPVNENMQVNK;MEVS(1)PLQPVNENMQVNK;MEVS(1)PLQPVNENMQVNK;MEVS(1)PLQPVNENMQVNK;MEVS(1)PLQPVNENMQVNK 176.32 8.95E-21 937500000 1588531 1390504 1551773 1420238 1655880 1257054 1968410 1384242 2306800 TRUE FALSE 1489107.68 1493458.363 1588581.788 1456683.712 1525833.864 1619945.083 1673265.194 1557067.661 1921780.178 0.774858487 0.777122368 0.826619926 0.757986646 0.793968989 0.842939844 0.870685011 0.810221522 1 20.87401189 -4.999999998 0.154090407 1.719986333 0.750646633 0.845193123 0.027328398 50.04396952 0.452224547 10.92910837 0.12903711 1.00E-05 4.999999998 -0.9693397 (ac)MFCVT(ph)PPELETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MFCVTPPELETK 12 0 O60256;O60256-2;O60256-3;E7EPA1;C9K0K7;C9JJS3;C9JDU5;I3L1T1;I3L275;E7EW35;I3L164;I3L331;I3L2J4;I3L3B8;C9JDH0 O60256 PRPSAP2 Phosphoribosyl pyrophosphate synthase-associated protein 2 1 MFCVT(0.999)PPELET(0.001)K 50.108 0.0062641 6301600 31051 25575 29176 29188 28941 28538 35820 24708 44264 TRUE FALSE 29107.57334 27468.59961 29868.0685 29937.0135 26668.0906 36776.45732 30449.12354 27792.84819 36876.05244 0.789335393 0.744889916 0.809958402 0.811828043 0.723181817 0.997299192 0.825715377 0.753682847 1 15.1703966 2.265132484 24.99999746 0.87807375 0.777906996 0.358931576 0.077236135 264.9580773 249283.4684 0.02479843 0.020742378 184.1333623 -2.265132484 -0.100166754 (ac)MFSFNMFDHPIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MFSFNMFDHPIPR 13 0 Q92890;Q92890-1;Q92890-3;C9IZG3 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 0 67.776 0.0011258 38655000 59573 58547 68729 58669 74502 48268 66189 48534 89698 FALSE TRUE 55844.43227 62881.8808 70359.28434 60174.54587 68650.91345 62202.18803 56264.57392 54593.57674 74726.82433 0.747314405 0.841490072 0.94155325 0.805260312 0.918691702 0.832394372 0.752936772 0.730575362 1 16.18933859 1.997128699 24.8852671 0.798455819 0.861183567 0 0.09039893 250.2552229 2168946.641 0.031369429 0.02274134 99.34103915 -1.997128699 0.062727747 (ac)MLSLQYPDVYRDETAVQDYHGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MLSLQYPDVYRDETAVQDYHGHK 23 1 P48147 P48147 PREP Prolyl endopeptidase 0 ; 86.557 2.10E-06 385600000 293390 377870 335410 358670 445080 246800 408050 330710 545650 FALSE TRUE 275027.2436 405847.888 343366.0836 367874.0794 410125.2122 318047.1535 346866.6907 371999.8715 454577.49 0.605017296 0.892802431 0.755352148 0.809265939 0.902211881 0.699654428 0.763052941 0.818342042 1 18.79416672 0.866870433 5.573110964 0.999997494 0.785571346 0.394100024 0.086326632 1.900733883 78.97816518 0.075196944 0.018943154 7.359874912 -0.866870433 -0.214426148 (ac)MLTAVCGSLGS(ph)QHTEAPHASPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MLTAVCGSLGSQHTEAPHASPPR 23 0 Q3SY56 Q3SY56 SP6 Transcription factor Sp6 1 MLTAVCGS(0.006)LGS(0.43)QHT(0.366)EAPHAS(0.198)PPR 46.66 3.71E-05 0 10207 11738 10217 10349 12205 7842.3 12205 12418 15494 TRUE FALSE 9568.16209 12607.09373 10459.35206 10614.57286 11246.46853 10106.2447 10374.97356 13968.41464 12907.9513 0.741261093 0.976692074 0.810303031 0.822328239 0.871282225 0.782947229 0.80376609 1.082155821 1 13.65597242 1.239500766 24.99999992 1.041077971 0.839387669 0.641388261 0.065374792 15.58222278 414454.7714 0.049111039 0.015573504 17.35804326 -1.239500766 -0.201690302 (ac)MLTAVCGSLGSQHTEAPHAS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MLTAVCGSLGSQHTEAPHASPPR 23 0 Q3SY56 Q3SY56 SP6 Transcription factor Sp6 1 MLTAVCGSLGS(0.002)QHT(0.022)EAPHAS(0.976)PPR 64.583 4.19E-08 106480000 16735 17044 16527 17218 17629 16425 17399 18873 18346 TRUE FALSE 15687.58622 18305.95549 16919.02824 17659.84303 16244.48945 21166.63086 14790.18147 21229.33559 15283.93408 1.026410225 1.197725363 1.106981236 1.1554514 1.06284739 1.384894148 0.967694665 1.388996804 1 13.89972832 (ac)MNGQLNGFHEAFIEEGTFLFTSESVGEGHPDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MNGQLNGFHEAFIEEGTFLFTSESVGEGHPDK 32 0 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ; 107.91 1.14E-46 62911000 26094 26999 29405 25951 30549 24237 34460 28090 28492 FALSE TRUE 24460.82312 28998.03405 30102.50049 26616.94659 28149.80477 31233.82845 29293.04291 31597.09833 23736.50113 1.030515112 1.221664216 1.268194513 1.121350887 1.185928988 1.315856464 1.234092706 1.331160737 1 14.53481967 4.738307861 6.856977147 1.225158682 1.027393132 0.240214675 0.09684237 0.135215772 45.70848195 0.020380776 0.12440368 54740.38674 -4.738307861 -0.19776555 (ac)MNLLPNIES(ph)PVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MNLLPNIESPVTR 13 0 P17980;E9PM69 P17980 PSMC3 26S protease regulatory subunit 6A 1 MNLLPNIES(0.84)PVT(0.16)R;MNLLPNIES(0.957)PVT(0.043)R 46.706 0.0060486 30499000 55133.6 35899.6 44462 47217 52919.3 29524.1 52855.9 39497.3 45778.1 TRUE FALSE 51682.88639 38557.64374 45516.65964 48428.66816 48763.23164 38047.22839 44930.64849 44428.62485 38137.43937 1.355174528 1.011018159 1.193490187 1.269845825 1.278618398 0.997634582 1.178124416 1.164960878 1 15.21892036 -0.717209127 0.407861502 0.947499626 1.177413076 0.214023814 0.110514757 19.45929929 2.681690341 1.413352725 0.068424264 0.191774506 0.717209127 0.229913449 (ac)MNTAPS(ph)RPSPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MNTAPSRPSPTR 12 1 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 MNT(0.001)APS(0.478)RPS(0.337)PT(0.185)R 49.978 0.00057724 338290000 277720 191130 246770 232250 252020 179950 315330 222890 322980 TRUE FALSE 260338.0009 205281.4641 252623.5009 238209.9282 232227.3658 231898.6438 268049.1939 250718.3071 269072.5515 0.967538307 0.762922353 0.938867601 0.885299994 0.863065982 0.861844296 0.996196722 0.931787006 1 18.0376357 1.749384685 9.610274522 0.971902914 0.87277061 0.385724439 0.056564701 0.108397194 45.05477062 0.02508112 0.013609874 56.15451557 -1.749384685 -0.099132305 (ac)MNTAPSRPS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 MNTAPSRPSPTR 12 1 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 MNTAPS(0.08)RPS(0.84)PT(0.08)R;MNTAPS(0.017)RPS(0.928)PT(0.056)R;MNTAPS(0.105)RPS(0.828)PT(0.067)R;MNT(0.003)APS(0.1)RPS(0.884)PT(0.013)R;MNTAPS(0.019)RPS(0.824)PT(0.158)R;MNTAPS(0.032)RPS(0.904)PT(0.064)R 96.313 2.55E-07 11954070000 409134 341505 395639 335463 391277 306386 386987 333040 428637 TRUE FALSE 383527.0333 366790.3855 405023.7439 344071.5485 360547.6828 394834.6644 328961.892 374620.7771 357094.7156 1.074020467 1.027151536 1.134219372 0.963530216 1.009669611 1.105686103 0.921217474 1.049079588 1 18.44594726 3.229998971 24.99888398 1.005399615 1.075433395 0.268930922 0.054407239 235.6932687 688192.6872 0.014928744 0.018109441 1698.239628 -3.229998971 0.07003378 (ac)MNTAPSRPS(ph)PTRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MNTAPSRPSPTRR 13 2 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 MNTAPS(0.032)RPS(0.484)PT(0.484)RR;MNT(0.001)APS(0.123)RPS(0.438)PT(0.438)RR 72.315 0.00075153 1857890000 40936 53991 56724.8 49231.9 57119.2 40192.8 58146.4 41855.2 66565 TRUE FALSE 38373.88883 57988.54982 58070.33904 50495.2739 52633.28844 51795.80888 49427.88712 47080.91385 55454.87147 0.691984091 1.045689013 1.047163892 0.91056516 0.949119294 0.934017292 0.891317315 0.848995095 1 15.75902658 2.2899731 1.634926562 0.904158761 0.964287103 0 0.106980519 1.268821563 6.805312942 0.054382519 0.035120098 194.9723831 -2.2899731 0.060128341 (ac)MNTAPSRPSPT(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MNTAPSRPSPTR 12 1 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 MNTAPS(0.017)RPS(0.289)PT(0.694)R 57.583 0.0011338 520280000 117330 78865 95819 112190 116660 77189 136940 104440 149170 TRUE FALSE 109986.5247 84704.24666 98091.87193 115068.9853 107497.9942 99472.21124 116407.1183 117479.5639 124272.5633 0.885042698 0.681600543 0.789328467 0.925940387 0.86501792 0.800435821 0.936708113 0.945337899 1 16.92314829 2.082222403 0.407554155 1.005006519 0.748202868 0.470773953 0.067397195 0.888442155 0.356960813 0.074364259 0.077008022 120.8432518 -2.082222403 -0.256803651 (ac)MNTAPSRPSPT(ph)RR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MNTAPSRPSPTRR 13 2 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 MNTAPS(0.012)RPS(0.392)PT(0.596)RR 61.165 0.0021676 973140000 36479 25572 33867 39810 46054 23279 48180 31271 39226 TRUE FALSE 34195.84451 27465.37749 34670.34123 40831.592 42437.10461 29999.2694 40955.85628 35175.25319 32678.92719 1.046418822 0.840461418 1.060938783 1.249477737 1.298607643 0.918000436 1.253280319 1.076389472 1 14.996073 3.594319046 3.541494826 1.145797042 0.934840481 0.262405633 0.127386498 0.244298093 5.698460122 0.032029334 0.051861775 3929.334907 -3.594319046 -0.210956561 (ac)MNVDHEVNLLVEEIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 MNVDHEVNLLVEEIHR 16 0 Q9P1F3;Q5SZC9 Q9P1F3 ABRACL Costars family protein ABRACL 0 ;;;;;;;;;;; 139.6 7.72E-36 2169486000 18361.01 35728.4 29423.4 32061.7 39230.51 35237.89 26382.6 28398.2 19998.77 FALSE TRUE 17211.82716 38373.76791 30121.33694 32884.4575 36149.50399 45410.4968 22426.77405 31943.77778 16660.84609 1.033070413 2.303230442 1.807911602 1.973756754 2.169727984 2.725581676 1.34607654 1.917296253 1 14.02417405 0.73103406 1.161878366 1.012281956 1.984093521 0.262805133 0.472380147 1.12591738 2.635478572 0.408101761 0.126334896 5.383119982 -0.73103406 0.971811565 (ac)MQPQSVLHSGYFHPLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MQPQSVLHSGYFHPLLR 17 0 P13716 P13716 ALAD Delta-aminolevulinic acid dehydratase 0 92.977 3.61E-05 198160000 11089 12150 11514 12680 10787 11540 12500 8666.7 14210 FALSE TRUE 10394.95928 13049.59864 11787.11752 13005.39027 9939.832533 14871.41066 10625.74104 9748.756573 11838.2592 0.878081744 1.102324119 0.995679966 1.098589754 0.839636332 1.256216004 0.897576313 0.823495787 1 13.53116933 1.595335192 25 0.895361352 1.032056475 0.17381472 0.123732174 1.23032827 2448.088233 0.057167955 0.026750199 39.38539381 -1.595335192 0.136695122 (ac)MS(ph)PTPPLFSLPEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MSPTPPLFSLPEAR 14 0 A0A087WWS1;Q96FV9;Q96FV9-2;J3KRD7;J3QQZ3;J3KT14 A0A087WWS1 THOC1 THO complex subunit 1 1 MS(0.892)PT(0.108)PPLFSLPEAR 58.676 0.0093602 6783200 3405.9 6490 7250.7 4986.7 10845 8918.6 6786.3 6013.1 7495.5 TRUE FALSE 3192.730799 6970.526353 7422.690028 5114.667164 9993.277447 11493.25504 5768.757316 6763.848771 6244.452627 0.511290739 1.116274999 1.188685458 0.819073739 1.600344825 1.840554445 0.923821135 1.083177209 1 12.6083594 4.92295132 1.79871111 1.22063237 6.41E-14 0.330864545 0.307280654 1.91350994 4.230982076 0.078468842 4.611546675 83743.54096 -4.92295132 -1.22063237 (ac)MTTS(ph)QKHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MTTSQKHR 8 1 O75531;E9PJJ8 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 1 MT(0.001)T(0.02)S(0.979)QKHR 83.397 0.0041666 63011000 35736 60202 41297 49169 75876 25578 35857 41743 169190 TRUE FALSE 33499.34755 64659.41872 42276.58434 50430.75978 69917.00503 32961.95338 30480.57573 46954.70544 140951.096 0.237666457 0.458736545 0.299937961 0.357789057 0.496037328 0.233853828 0.216249299 0.333127636 1 17.10483517 -1.220232135 3.706266665 1.000838905 0.33115134 0.839336851 0.092232695 58578925.89 93261281.39 574849.1186 0.022996841 0.06022376 1.220232135 -0.669687565 (ac)MVDYSVWDHIEVS(ph)DDEDETHPNIDTASLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 MVDYSVWDHIEVSDDEDETHPNIDTASLFR 30 0 Q16543;K7EKQ2;K7EQA9;K7EJ06 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 1 MVDY(0.035)S(0.038)VWDHIEVS(0.92)DDEDET(0.007)HPNIDTASLFR;MVDY(0.007)S(0.008)VWDHIEVS(0.975)DDEDET(0.008)HPNIDTASLFR;MVDY(0.075)S(0.079)VWDHIEVS(0.842)DDEDET(0.005)HPNIDTASLFR;MVDYSVWDHIEVS(0.998)DDEDET(0.001)HPNIDTASLFR;MVDY(0.003)S(0.003)VWDHIEVS(0.989)DDEDET(0.004)HPNIDTASLFR 81.068 7.07E-05 100968500 11930.79 10695.01 12462.37 18142.1 16061.55 12761.5 14666.5 10863.7 19100.2 TRUE FALSE 11184.06315 11486.87967 12757.9833 18607.657 14800.14065 16445.53788 12467.39448 12220.05686 15912.25323 0.702858545 0.721888943 0.801771007 1.169391709 0.930109673 1.033514088 0.783509055 0.767965208 1 13.95785052 3.464436291 24.99922704 0.93599107 0.737101804 0.419848962 0.115952969 231.4631447 456161.1717 0.032666851 0.044319486 2913.642683 -3.464436291 -0.198889267 (ac)S(ph)DAAVDTSSEITTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDAAVDTSSEITTK 14 0 B8ZZQ6;P06454-2;P06454 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 1 S(0.521)DAAVDT(0.215)S(0.193)S(0.063)EIT(0.004)T(0.004)K;S(0.979)DAAVDT(0.009)S(0.009)S(0.003)EITTK 72.289 1.83E-43 1010910000 1414780 1226950 1283980 1222050 1292210 1093090 1622610 1091890 1141680 TRUE FALSE 1326231.445 1317794.655 1314436.612 1253409.872 1190725.039 1408647.338 1379314.694 1228214.87 951126.2325 1.394380052 1.385509735 1.381979139 1.317816531 1.251910628 1.481030898 1.450190991 1.29132688 1 19.8592773 0.914510913 5.875674935 1.000013404 1.3826282 0.7820002 0.062988518 0.376735654 25.36544828 0.062857602 0.015814168 8.213171913 -0.914510913 0.382614796 (ac)S(ph)DCYTELEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDCYTELEK 9 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 1 S(0.823)DCY(0.137)T(0.04)ELEK 44.349 0.00056321 131140000 347100 211440 241680 231050 307020 236090 332740 228540 398750 TRUE FALSE 325375.6306 227095.2376 247412.7637 236979.1342 282907.8877 304245.3504 282848.726 257073.7221 332196.049 0.979468695 0.683618117 0.744779369 0.713371321 0.851629297 0.915860834 0.851451204 0.773861468 1 18.34167539 2.609898161 5.597344779 0.873338608 0.758672884 0.189223231 0.097150874 0.317079331 13.15482062 0.029499447 0.027691134 407.2847611 -2.609898161 -0.114665724 (ac)S(ph)DLEDDETPQLSAHALAALQEFYAEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDLEDDETPQLSAHALAALQEFYAEQK 27 0 Q8WVE0 Q8WVE0 N6AMT2 Protein-lysine N-methyltransferase N6AMT2 1 S(0.634)DLEDDET(0.362)PQLS(0.004)AHALAALQEFYAEQK 55.526 9.98E-08 6970300 3962.5 5496.7 4794.5 3472.8 6688 4693.2 6190.6 3296.1 7206 TRUE FALSE 3714.494198 5903.681387 4908.227804 3561.917927 6162.751458 6048.050652 5262.377001 3707.625341 6003.272047 0.618744939 0.983410604 0.817592101 0.593329421 1.026565415 1.007459033 0.876584796 0.617600754 1 12.55153333 2.694719557 24.99891221 0.904848856 0.802346013 0.155350774 0.15920708 1190.413927 678793.0223 0.050721334 0.047820804 495.1303605 -2.694719557 -0.102502842 (ac)S(ph)DNDDIEVES(ph)DADKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDNDDIEVESDADKR 15 1 Q6V3B1;G3V563;G3V2R5;P61244-2;A0A494C130 Q6V3B1 MAX Protein max 2 S(1)DNDDIEVES(1)DADKR;S(1)DNDDIEVES(1)DADKR 120.24 8.97E-13 544110000 1167600 849680 935010 926950 1154760 676490 1255670 964840 1475940 TRUE FALSE 1094522 912591.1913 957188.8787 950737.1063 1064069.808 871781.6811 1067393.941 1085302.398 1229596.079 0.890147601 0.742187786 0.778457979 0.773210913 0.865381588 0.708998423 0.868085023 0.882649527 1 20.22975304 1.059204296 1.380336679 0.997127593 0.787654134 0.573635752 0.05594034 0.261818277 1.014524087 0.046964207 0.014228553 11.46051927 -1.059204296 -0.209473459 (ac)S(ph)DNDDIEVES(ph)DEEQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDNDDIEVESDEEQPR 16 0 P61244-3;P61244-4;P61244;G3V5L1;P61244-6;P61244-5 P61244-3 MAX Protein max 2 S(1)DNDDIEVES(1)DEEQPR;S(1)DNDDIEVES(1)DEEQPR 71.176 1.05E-09 142206000 13812.2 15324.6 14609.9 17309.4 14087.4 12494.9 14195.9 12396 17126.3 TRUE FALSE 12947.71906 16459.24933 14956.45373 17753.58851 12981.03243 16101.97479 12067.35658 13943.66789 14267.80989 0.907477683 1.15359326 1.04826556 1.2443107 0.909812545 1.128552659 0.845774977 0.977281587 1 13.80047628 1.745986284 25 0.930204126 1.074451664 0.217839276 0.109509263 1.957220825 6607.966762 0.045124966 0.02502409 55.71681514 -1.745986284 0.144247538 (ac)S(ph)DNDDIEVESDADKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDNDDIEVESDADKR 15 1 Q6V3B1;G3V563;G3V2R5;P61244-2;A0A494C130 Q6V3B1 MAX Protein max 1 S(1)DNDDIEVESDADKR;S(1)DNDDIEVESDADKR 149.38 4.64E-44 2308500000 3881700 2738100 3047700 2967600 3136100 2339300 3555600 2575200 3376400 TRUE FALSE 3638751.326 2940831.773 3119992.883 3043753.64 2889803.356 3014617.935 3022470.789 2896719.389 2812857.028 1.293614034 1.045496356 1.109189999 1.082086153 1.027355222 1.071728106 1.074519877 1.029813944 1 21.42360479 4.741207647 24.97465421 1.063013671 1.293614117 0.842616978 0.032241579 89.16322754 841205.9288 0.007109295 0.049125162 55107.11148 -4.741207647 0.230600446 (ac)S(ph)DNGELEDKPPAPPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDNGELEDKPPAPPVR 16 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 S(1)DNGELEDKPPAPPVR;S(1)DNGELEDKPPAPPVR 61.344 0.0015169 443534000 306770 268470 267550 245770 288450 221490 352590 236640 276360 TRUE FALSE 287569.8133 288347.7981 273896.4123 252076.8743 265796.3006 285430.5674 299722.4028 266185.0249 230233.7306 1.249034242 1.252413351 1.189645025 1.094873777 1.154462901 1.239742616 1.301817948 1.156151291 1 17.81273969 -2.469221944 1.31711506 0.12346732 1.211228282 0.532706433 0.060002865 66398.49693 5401.991452 171399.9682 0.018129771 0.003394518 2.469221944 1.087760962 (ac)S(ph)DQDHSMDEMTAVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDQDHSMDEMTAVVK 15 0 P08047;H3BUU5;P08047-3 P08047 SP1 Transcription factor Sp1 1 S(0.841)DQDHS(0.159)MDEMTAVVK;S(1)DQDHSMDEMTAVVK 102.4 2.71E-11 196330000 259559 250370 291220 233870 253480 242230 318540 206978 288220 TRUE FALSE 243313.6655 268907.6553 298127.8759 239871.5001 233572.7033 312157.8687 270777.8842 232819.6589 240114.22 1.013324681 1.119915577 1.241608581 0.998989148 0.972756646 1.300039076 1.127704491 0.969620453 1 17.87336132 1.241860262 24.62446041 0.984810182 1.125654646 0.192903723 0.103491178 96.02854635 716694.115 0.074967914 0.024817259 17.45260509 -1.241860262 0.140844464 (ac)S(ph)DQEAKPSTEDLGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDQEAKPSTEDLGDK 15 1 B8ZZN6;P63165;B8ZZJ0;B9A032 B8ZZN6 SUMO1 Small ubiquitin-related modifier 1 1 S(1)DQEAKPSTEDLGDK;S(1)DQEAKPSTEDLGDK 164.81 1.48E-24 530000000 3079300 1264350 1898980 1806960 1751940 1383330 2368890 1456350 1550200 TRUE FALSE 2886572.11 1357963.79 1944024.702 1853329.653 1614349.699 1782674.915 2013696.936 1638178.503 1291461.605 2.235120346 1.051493737 1.505290358 1.435063687 1.250017571 1.380354559 1.559238717 1.268468607 1 20.30057332 7.999983828 0.033115389 3.80E-08 3.51337334 0.268140699 0.293029027 2125.57037 5.385237311 173.6443904 461.9852973 99996276.26 -7.999983828 3.513373302 (ac)S(ph)DQEAKPSTEDLGDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SDQEAKPSTEDLGDKK 16 2 B8ZZN6;P63165;B8ZZJ0;B9A032 B8ZZN6 SUMO1 Small ubiquitin-related modifier 1 1 S(0.943)DQEAKPS(0.026)T(0.031)EDLGDKK;S(1)DQEAKPSTEDLGDKK;S(0.996)DQEAKPS(0.003)T(0.001)EDLGDKK;S(1)DQEAKPSTEDLGDKK;S(1)DQEAKPSTEDLGDKK;S(0.907)DQEAKPS(0.042)T(0.05)EDLGDKK;S(1)DQEAKPSTEDLGDKK;S(1)DQEAKPSTEDLGDKK 99.747 4.90E-11 23387850000 23723520 7763860 12407150 11517610 11667210 8082160 17243820 8947120 14721680 TRUE FALSE 22238707.23 8338704.273 12701453.46 11813171.37 10750914.39 10415348.39 14658269.27 10064187.63 12264536.5 1.813252969 0.679903743 1.035624416 0.963197539 0.876585461 0.849224786 1.195175152 0.820592578 1 23.54798938 4.749083743 24.83812352 0.936151467 1.813253508 0.802086453 0.138209764 618.9759994 1460960.722 0.032794697 0.470690956 56115.6171 -4.749083743 0.877102042 (ac)S(ph)DQEAKPSTEDLGDKKEGEYIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SDQEAKPSTEDLGDKKEGEYIK 22 3 B8ZZN6;P63165;B8ZZJ0;B9A032 B8ZZN6 SUMO1 Small ubiquitin-related modifier 1 1 S(0.981)DQEAKPS(0.018)T(0.001)EDLGDKKEGEYIK;S(1)DQEAKPSTEDLGDKKEGEYIK;S(1)DQEAKPSTEDLGDKKEGEYIK;S(1)DQEAKPSTEDLGDKKEGEYIK;S(0.998)DQEAKPS(0.001)T(0.001)EDLGDKKEGEYIK 119.79 1.79E-17 3929593000 2543640 1352995 1588840 2118560 2937960 946853 2602330 1215369 7585760 TRUE FALSE 2384438.113 1453172.158 1626528.035 2172925.836 2707224.473 1220194.09 2212134.775 1367110.495 6319647.65 0.377305547 0.229945123 0.25737638 0.343836549 0.428382186 0.19307945 0.350040841 0.216327012 1 22.59141269 -1.9849574 3.0963094 1.634107278 0.294105105 0.892915259 0.076212997 44161311.71 43194861.25 200562916 0.017222705 0.010352437 1.9849574 -1.340002173 (ac)S(ph)DVEENNFEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDVEENNFEGR 11 0 Q13595;F8WEH2 Q13595 TRA2A Transformer-2 protein homolog alpha 1 S(1)DVEENNFEGR 68.893 3.89E-05 102760000 34843 83076 65377 63831 73076 26325 53020 47203 87663 TRUE FALSE 32662.23883 89227.03348 66927.77331 65469.01153 67336.90573 33924.60015 45070.14321 53096.39846 73031.47898 0.447235073 1.221761283 0.916423633 0.896449209 0.922025771 0.46452024 0.617133103 0.727034413 1 16.15623083 2.323626202 10.05205561 0.657453096 0.93357253 0.092241546 0.231505265 0.468655464 51.57154248 0.074436355 0.062225163 210.6814031 -2.323626202 0.276119433 (ac)S(ph)DVEENNFEGRES(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDVEENNFEGRESR 14 1 Q13595 Q13595 TRA2A Transformer-2 protein homolog alpha 2 S(1)DVEENNFEGRES(1)R 43.794 0.00010664 2353000000 28292 19826 28141 44143 30812 33393 43053 26706 42781 TRUE FALSE 26521.25422 21293.93767 28808.51781 45275.78411 28392.14981 43033.01701 36597.60233 30040.30289 35640.57472 0.744130936 0.597463364 0.808306769 1.270343828 0.796624354 1.207416472 1.026852194 0.842868083 1 15.12123298 3.449456495 8.94620779 1.028890153 0.686454055 0.512886363 0.145612539 0.172558909 51.13884749 0.036202229 0.04952779 2814.858026 -3.449456495 -0.342436098 (ac)S(ph)ESGHSQPGLYGIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SESGHSQPGLYGIER 15 0 Q9H0W8-2;Q9H0W8;M0R2N0;M0QZC7;M0QZH1;M0QX70;M0QYR7 Q9H0W8-2 SMG9 Protein SMG9 1 S(0.488)ES(0.488)GHS(0.024)QPGLYGIER;S(0.484)ES(0.484)GHS(0.031)QPGLYGIER;S(0.448)ES(0.448)GHS(0.104)QPGLYGIER 75.78 1.46E-24 281690000 128776 89715 105321 93221 115921 89204 124279 98748 122440 TRUE FALSE 120716.14 96357.59195 107819.2639 95613.20868 106817.0323 114955.7467 105644.5177 111076.9052 102003.973 1.183445472 0.944645479 1.057010435 0.937347888 1.047185018 1.126973228 1.035690224 1.088946851 1 16.63826582 2.483450585 24.86859696 1.067606333 1.017842424 0.026004942 0.074806986 641.6632809 2521175.791 0.022834316 0.019739297 304.4041615 -2.483450585 -0.049763909 (ac)S(ph)GDEMIFDPTMSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 18 SGDEMIFDPTMSK 13 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(0.999)GDEMIFDPT(0.001)MSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(0.998)GDEMIFDPT(0.002)MSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK 102.53 3.63E-52 9452850000 16247440 14535000 15151180 14425620 16072340 12629680 17856730 12941980 16213870 TRUE FALSE 15230541.73 15611186.52 15510573.14 14795805.83 14810083.25 16275663.59 15179279.11 14557814.69 13507670.35 1.127547633 1.155727532 1.148278922 1.09536326 1.096420246 1.204920106 1.123752558 1.077744297 1 23.68727554 0.990722945 2.453899352 1.000876895 1.139675704 0.670112416 0.031123086 0.164049949 2.22888078 0.02880556 0.007808578 9.788653263 -0.990722945 0.138798808 (ac)S(ph)GDEMIFDPTMSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 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(0.999)GDEMIFDPT(0.001)MS(0.001)KK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK 120.96 3.26E-08 2932110000 6062350 5876860 5532080 5570190 7681840 4168880 7821480 4908490 12773510 TRUE FALSE 5682918.335 6311988.829 5663303.55 5713130.506 7078539.273 5372367.98 6648721.685 5521325.781 10641528.66 0.534032141 0.593146815 0.532188911 0.536871223 0.66518068 0.50484927 0.624790093 0.518847053 1 23.34320207 -1.613668903 3.064454342 1.028320743 0.56741741 0.879913053 0.050633574 14510332.12 16591815.32 3316464.953 0.010879237 0.02434059 1.613668903 -0.460903332 (ac)S(ph)GEDEQQEQTIAEDLVVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 SGEDEQQEQTIAEDLVVTK 19 0 Q9UQ80;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 1 S(1)GEDEQQEQTIAEDLVVTK;S(0.963)GEDEQQEQT(0.037)IAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(0.997)GEDEQQEQT(0.003)IAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(0.911)GEDEQQEQT(0.089)IAEDLVVTK 147.73 4.96E-191 5229851000 3481455 2953996 3205605 3104603 3176825 2701681 3879405 2820508 3768944 TRUE FALSE 3263556.946 3172712.937 3281643.464 3184272.369 2927329.979 3481612.447 3297724.235 3172654.633 3139882.898 1.039388108 1.010455816 1.045148361 1.014137301 0.932305463 1.108835125 1.050269816 1.010437247 1 21.58227932 2.213327303 24.99999769 1.049194126 1.01387513 0.124450771 0.041865768 442.2720459 438179.6261 0.014923972 0.011026183 163.428315 -2.213327303 -0.035318997 (ac)S(ph)KGPAVGIDLGTTYSCVGVFQHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKGPAVGIDLGTTYSCVGVFQHGK 24 1 P11142;E9PKE3;E9PNE6;P11142-2;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 1 S(0.821)KGPAVGIDLGT(0.058)T(0.058)Y(0.055)S(0.009)CVGVFQHGK 46.178 0.030444 56342000 41747 26778 32776 29787 37522 20645 43718 33599 49742 TRUE FALSE 39134.12979 28760.67098 33553.4622 30551.38485 34575.17348 26604.87636 37162.89176 37793.90911 41439.73885 0.944362365 0.694036009 0.809692897 0.737248489 0.834348247 0.64201361 0.89679358 0.912020929 1 15.33872729 1.556444306 6.360971714 0.939341538 0.771266547 0.450634925 0.084156631 0.109330985 8.813845318 0.041101347 0.01898057 36.01175659 -1.556444306 -0.168074991 (ac)S(ph)KS(ph)ESPKEPEQLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSESPKEPEQLRK 14 3 F8W6I7;P09651-2;P09651;P09651-3;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 2 S(0.973)KS(0.846)ES(0.181)PKEPEQLRK 48.112 0.0021338 140220000 571780 155480 235390 248170 290050 164410 340040 173040 346870 TRUE FALSE 535993.3105 166991.901 240973.562 254538.4624 267270.643 211872.498 289054.1588 194644.4249 288975.1561 1.854807581 0.577876324 0.833890239 0.880831646 0.924891422 0.733185859 1.000273389 0.673568024 1 18.14058594 4.746938475 24.93646895 0.821681157 1.854808115 0.848540555 0.136301465 376.9943227 1122087.624 0.031510975 0.364026465 55839.10841 -4.746938475 1.033126958 (ac)S(ph)LDIQSLDIQCEELSDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLDIQSLDIQCEELSDAR 18 0 P13489;E9PMJ3;E9PLZ3;E9PIM9;E9PMN0;E9PIK5;E9PMA9;E9PR82;E9PMI1 P13489 RNH1 Ribonuclease inhibitor 1 S(0.879)LDIQS(0.121)LDIQCEELSDAR;S(0.972)LDIQS(0.028)LDIQCEELSDAR 59.185 0.00042835 38505000 7071.2 32080 8031.9 8988.8 9631.6 7092.8 10923.1 9736.5 11703.9 TRUE FALSE 6628.626214 34455.23658 8222.420461 9219.467826 8875.172988 9140.376218 9285.28256 10952.12346 9750.44348 0.679828177 3.533709687 0.843286818 0.945543436 0.910232751 0.937431845 0.952293358 1.123243623 1 13.25125212 3.744001514 8.265964703 0.952665279 2.277647324 0.322548122 0.681335768 0.157316887 60.73948024 0.154901441 0.270399874 5546.276459 -3.744001514 1.324982045 (ac)S(ph)LPLNPKPFLNGLTGKPVMVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLPLNPKPFLNGLTGKPVMVK 21 2 P62306;A0A0B4J254;F8W0W6 P62306 SNRPF Small nuclear ribonucleoprotein F 1 S(1)LPLNPKPFLNGLTGKPVMVK;S(1)LPLNPKPFLNGLTGKPVMVK;S(1)LPLNPKPFLNGLTGKPVMVK 112.74 6.26E-08 746110000 1425220 1445250 1129970 1117390 1711330 814210 1676910 1476310 1923860 TRUE FALSE 1336018.024 1552257.814 1156773.422 1146064.119 1576929.045 1049259.209 1425472.913 1660630.553 1602755.337 0.833575776 0.968493305 0.72174049 0.715058682 0.983886316 0.654659626 0.889388967 1.036109826 1 20.61212278 1.381611883 4.724502718 1.013882217 0.819809068 0.389713529 0.104532761 0.217327025 7.30151716 0.070985377 0.024993508 24.07752723 -1.381611883 -0.194073149 (ac)S(ph)MEDPFFVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SMEDPFFVVK 10 0 O43752 O43752 STX6 Syntaxin-6 1 S(1)MEDPFFVVK 41.029 0.0004208 21961000 41912 33150 33897 33027 27309 22511 45461 23793 40948 TRUE FALSE 39288.80274 35604.46049 34701.05285 33874.52873 25164.2613 29009.56026 38644.54509 26763.60842 34113.51427 1.151707867 1.043705442 1.017223045 0.992994403 0.737662532 0.850383225 1.132822165 0.784545627 1 15.05805576 3.882880631 1.063652788 0.92654739 1.121992563 0.30487419 0.115011529 0.933683035 1.854349202 0.039525017 0.149934882 7636.258671 -3.882880631 0.195445173 (ac)S(ph)QERPTFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQERPTFYR 9 1 Q16539-2;Q16539;Q16539-5;Q16539-3;Q16539-4;B5TY33 Q16539-2 MAPK14 Mitogen-activated protein kinase 14 1 S(0.999)QERPT(0.001)FYR;S(0.995)QERPT(0.005)FYR 61.962 0.00033235 707100000 60050 66376 59256 56582 67035 50213 68669 59850 102259 TRUE FALSE 56291.57769 71290.5481 60661.5803 58033.98991 61770.34151 64708.67796 58372.72094 67322.40425 85191.31228 0.660766646 0.836828853 0.712062987 0.681219579 0.725077943 0.759568977 0.685195701 0.790249645 1 16.37841869 0.910242764 6.149758842 0.999995395 0.73153631 0.754508762 0.049428935 0.51416192 34.82983991 0.046736212 0.011746397 8.132850037 -0.910242764 -0.268459085 (ac)S(ph)QGDSNPAAIPHAAEDIQGDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQGDSNPAAIPHAAEDIQGDDR 22 0 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 1 S(0.999)QGDS(0.001)NPAAIPHAAEDIQGDDR;S(0.5)QGDS(0.5)NPAAIPHAAEDIQGDDR 128.06 3.30E-47 750510000 3822.8 0 5930.2 2816.2 4589.2 0 0 0 0 TRUE FALSE 3583.537772 0 6070.867144 2888.46846 4228.782744 0 0 0 0 0 (ac)S(ph)QGDSNPAAIPHAAEDIQGDDRWMSQHNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SQGDSNPAAIPHAAEDIQGDDRWMSQHNR 29 1 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 1 S(0.884)QGDS(0.116)NPAAIPHAAEDIQGDDRWMSQHNR;S(0.815)QGDS(0.185)NPAAIPHAAEDIQGDDRWMSQHNR;S(1)QGDSNPAAIPHAAEDIQGDDRWMSQHNR;S(0.998)QGDS(0.002)NPAAIPHAAEDIQGDDRWMSQHNR 119.36 4.61E-18 825120000 16395.5 16207.4 25554.3 20401 21502 10403.3 11472.8 12091.9 25608.7 TRUE FALSE 15369.33492 17407.41276 26160.46006 20924.5242 19813.31965 13406.56383 9752.560148 13601.60033 21334.44253 0.720400118 0.81593005 1.22620781 0.980786077 0.928701072 0.628400007 0.457127489 0.637541867 1 14.38089679 2.252155168 5.102960306 0.613837243 0.962572927 0.273804722 0.189843213 0.169937343 12.1699793 0.068294096 0.053850007 178.712598 -2.252155168 0.348735684 (ac)S(ph)REMQDVDLAEVKPLVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SREMQDVDLAEVKPLVEK 18 2 Q92597;E5RI76;E5RIR1;E5RGM5;E5RIM2;E5RJ98 Q92597 NDRG1 Protein NDRG1 1 S(1)REMQDVDLAEVKPLVEK;S(1)REMQDVDLAEVKPLVEK;S(1)REMQDVDLAEVKPLVEK;S(1)REMQDVDLAEVKPLVEK;S(1)REMQDVDLAEVKPLVEK;S(1)REMQDVDLAEVKPLVEK 81.144 1.38E-05 678151000 1017213 1109693 902817 1111060 1526291 440751 980398 899941 1482083 TRUE FALSE 953547.4541 1191855.824 924232.2456 1139571.681 1406422.262 567988.6587 833396.4215 1012300.615 1234713.773 0.772282188 0.965289163 0.748539675 0.92294401 1.139067444 0.46001646 0.67497135 0.819866626 1 20.23574521 2.237764775 24.99999847 0.698714327 0.895854427 0.178640495 0.171487245 29.84098782 937354.903 0.057889456 0.045292544 172.8879699 -2.237764775 0.1971401 (ac)S(ph)SSPLSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSPLSKK 8 1 P22314;Q5JRR9 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 S(0.333)S(0.333)S(0.333)PLS(0.001)KK;S(0.333)S(0.333)S(0.333)PLS(0.001)KK 47.849 0.023509 2949400000 6613100 4872200 5585200 5013500 6164400 4141800 7845500 5113200 9933900 TRUE FALSE 6199197.876 5232942.758 5717683.582 5142154.898 5680272.89 5337470.423 6669140.109 5751594.276 8275867.915 0.749069214 0.63231347 0.690886278 0.621343278 0.686365823 0.644943887 0.805853861 0.694983817 1 22.98047919 0.202800719 0.548905598 1.019189123 0.664890427 0.77570455 0.052842353 1.247733792 0.525710652 0.102703519 0.021838849 1.595147029 -0.202800719 -0.354298696 (ac)S(ph)SSPVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSPVKR 7 1 P37837;F2Z393;E9PM01;E9PKI8 P37837 TALDO1 Transaldolase 1 S(0.333)S(0.333)S(0.333)PVKR 40.921 0.071949 38086000000 24744000 20005000 22020000 20000000 24430000 17933000 28535000 19160000 24952000 TRUE FALSE 23195317.21 21486191.02 22542324.8 20513233.86 22511366.35 23109965.98 24256441.66 21552168.18 20787350 1.115838104 1.033618571 1.084425133 0.986813319 1.08293584 1.111732182 1.166884747 1.036792481 1 24.30920252 2.485435282 24.43499764 1.100873398 1.054298284 0 0.056207814 570.1153765 1675585.297 0.017621376 0.015403575 305.7984517 -2.485435282 -0.046575114 (ac)S(ph)SSPVNVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSPVNVKK 9 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(0.333)S(0.333)S(0.333)PVNVKK 41.984 0.063362 1208100000 3118900 2504000 2751400 2644600 3113300 2142900 3653700 2373100 4194900 TRUE FALSE 2923693.616 2689398.765 2816664.507 2712464.913 2868793.976 2761520.443 3105861.604 2669386.759 3494744.09 0.836597342 0.76955528 0.805971606 0.776155519 0.82088814 0.790192464 0.888723616 0.763828964 1 21.73675538 -5 0.2430386 2.128731018 0.788430183 0.710199859 0.03829012 86.70791292 0.863822668 48.37978314 0.053236043 1.00E-05 5 -1.340300835 (ac)S(ph)TGGDFGNPLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STGGDFGNPLRK 12 1 P20340-2;P20340;P20340-3;F5H3K7;F5GX61 P20340-2;F5GX61 RAB6A Ras-related protein Rab-6A 1 S(0.972)T(0.028)GGDFGNPLRK 93.598 8.16E-05 110590000 283610 251730 254330 267620 293040 214680 334680 261560 325930 TRUE FALSE 265859.3564 270368.3511 260362.8277 274487.5823 270025.8205 276654.631 284497.841 294216.3418 271530.1774 0.979115319 0.995721189 0.958872528 1.010891625 0.994459706 1.018872501 1.047757725 1.08354933 1 18.05075302 2.137083663 1.596128705 1.049306223 0.983218545 0.533451974 0.023909622 0.253787486 1.244463734 0.012976149 0.007143885 137.1145879 -2.137083663 -0.066087678 (ac)S(ph)YGRPPPDVEGMTSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SYGRPPPDVEGMTSLK 16 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 S(0.57)Y(0.43)GRPPPDVEGMTSLK;S(0.59)Y(0.41)GRPPPDVEGMTSLK 115.57 2.37E-08 244180000 583450 479830 525850 497180 532000 419450 644010 551940 758720 TRUE FALSE 546932.906 515357.1125 538323.4103 509938.4805 490218.866 540538.4058 547446.6792 620850.924 632084.7305 0.865284161 0.81532916 0.851663368 0.806756525 0.775558786 0.855167638 0.866096985 0.982227372 1 19.26975844 1.301736649 2.107117697 1.004704506 0.826488951 0.865970768 0.026167742 0.099698031 0.751889528 0.022910524 0.006780936 20.03256907 -1.301736649 -0.178215555 (ac)SAADEVDGLGVARPHYGSVLDNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SAADEVDGLGVARPHYGSVLDNER 24 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;;; 156.36 7.15E-73 2063230000 56435.7 25650.8 48195.7 37190 47853.4 40053.5 46974.2 42071.5 41665.3 FALSE TRUE 52903.49028 27550.01192 49338.92476 38144.35836 44095.187 51616.29524 39930.8548 47324.21939 34711.09226 1.524109062 0.793694757 1.421416658 1.098909769 1.270348587 1.487025958 1.150377363 1.363374538 1 15.08310914 2.641819362 10.46921286 1.273532063 1.175576658 0 0.230281586 1.898057929 195.6610255 0.068532417 0.064592357 438.3483362 -2.641819362 -0.097955405 (ac)SAEVPEAASAEEQKEMEDKVT(ph)SPEKAEEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAEVPEAASAEEQKEMEDKVTSPEKAEEAK 30 3 P56211 P56211 ARPP19 cAMP-regulated phosphoprotein 19 1 SAEVPEAAS(0.038)AEEQKEMEDKVT(0.481)S(0.481)PEKAEEAK 65.758 0.00031731 100800000 381210 70043 146410 138660 153690 86180 182860 87344 229060 TRUE FALSE 357350.7466 75229.0566 149882.9143 142218.2504 141619.8074 111058.767 155441.8406 98249.09067 190828.4062 1.872628681 0.394223575 0.785432931 0.745267715 0.742131689 0.581982364 0.814563427 0.51485569 1 17.54191642 4.747229304 24.9980767 0.684614694 1.872629283 0.826670486 0.169044542 414.8671712 1196335.242 0.036487734 0.435982931 55876.51402 -4.747229304 1.188014589 (ac)SAHLQWMVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SAHLQWMVVR 10 0 P46779;H0YKD8;P46779-2;P46779-3;H0YLP6;H0YMF4;P46779-4;P46779-5 P46779 RPL28 60S ribosomal protein L28 0 ;; 80.229 3.52E-05 136610000 281874 267324 270082 286949 302222 215244 279873 248735 324333 FALSE TRUE 264232.0095 287116.9471 276488.4726 294312.5971 278486.7032 277381.4486 237908.6419 279790.1123 270199.727 0.97791368 1.062610056 1.023274433 1.089240912 1.030669817 1.026579307 0.880491792 1.03549369 1 18.04366669 1.969281425 23.38840739 0.957421192 1.03980294 0.259551826 0.048278781 287.1146351 218601.3447 0.017885874 0.01156211 93.1711433 -1.969281425 0.082381748 (ac)SAIQNLHSFDPFADASKGDDLLPAGTEDYIHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SAIQNLHSFDPFADASKGDDLLPAGTEDYIHIR 33 1 K7EM18;P41567 K7EM18 EIF1 Eukaryotic translation initiation factor 1 0 ; 113.17 9.07E-89 1349750000 582880 631710 624400 609680 714790 418440 721100 501320 857450 FALSE TRUE 546398.5813 678482.4657 639211.0629 625325.421 658653.2767 539236.8352 612977.7494 563910.9055 714336.0557 0.764904105 0.949808511 0.894832422 0.875393893 0.922049603 0.754878367 0.858108371 0.789419631 1 19.44624342 (ac)SCINLPTVLPGS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SCINLPTVLPGSPSK 15 0 P04183;K7ERV3;K7ES52;K7ERJ1;K7ENW5 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 1 SCINLPTVLPGS(0.847)PS(0.153)K;SCINLPTVLPGS(0.614)PS(0.386)K;SCINLPTVLPGS(0.856)PS(0.144)K;SCINLPTVLPGS(0.796)PS(0.204)K;SCINLPTVLPGS(0.754)PS(0.246)K;SCINLPTVLPGS(0.799)PS(0.201)K;SCINLPTVLPGS(0.789)PS(0.211)K;SCINLPTVLPGS(0.834)PS(0.166)K 96.64 2.60E-12 4782790000 10937980 7018420 9163950 7605100 9331740 8008690 11205470 8779040 15591960 TRUE FALSE 10253391.36 7538071.119 9381323.222 7800259.741 8598862.783 10320668.79 9525313.8 9875122.469 12989561.15 0.789356256 0.580317613 0.722220182 0.600502177 0.661982548 0.794535602 0.733305282 0.760235266 1 23.63084935 0.411048995 0.476442949 1.022204744 0.659203556 0.676950306 0.066927623 1.210178239 0.475045004 0.119572749 0.034174888 2.576611822 -0.411048995 -0.363001188 (ac)SCINLPTVLPGS(ph)PSKTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SCINLPTVLPGSPSKTR 17 1 P04183;K7ERV3;K7ES52;K7ERJ1;K7ENW5 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 1 SCINLPTVLPGS(0.445)PS(0.445)KT(0.111)R 87.388 3.38E-10 167920000 90580 129690 93474 96504 214850 60221 130560 92019 759680 TRUE FALSE 84910.75949 139292.3825 95691.24742 98980.45602 197976.5477 77605.82509 110983.7401 103507.7747 632884.5003 0.134164701 0.220091316 0.151198595 0.156395766 0.312816237 0.122622414 0.17536176 0.163549233 1 19.27158271 -1.586363191 2.67840665 1.063885783 0.180944988 0.957845816 0.054092184 3575325.677 3392367.002 1615121.989 0.012543171 0.025920108 1.586363191 -0.882940796 (ac)SCINLPTVLPGSPSKT(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SCINLPTVLPGSPSKTR 17 1 P04183;K7ERV3;K7ES52;K7ERJ1;K7ENW5 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 1 SCINLPTVLPGS(0.292)PS(0.313)KT(0.394)R 88.385 1.42E-10 184330000 64884 84155 70410 71608 157620 49924 99570 68912 546210 TRUE FALSE 60823.02626 90385.92376 72080.15845 73445.58251 145241.161 64336.24835 84640.40286 77515.81489 455044.0223 0.133664048 0.198631164 0.158402605 0.161403247 0.319180461 0.141384669 0.186004867 0.170347947 1 18.7956466 -1.600924685 2.597196173 1.074993748 0.184328633 0.960758261 0.051850928 2324236.57 2088737.883 1186317.521 0.012007996 0.025065439 1.600924685 -0.890665115 (ac)SDEFSLADALPEHS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_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 183.74 4.70E-122 3011100000 3175040 2126430 2519410 2333170 2767140 2310750 3586120 2582820 3348110 TRUE FALSE 2976319.914 2283873.09 2579171.595 2393043.092 2549819.987 2977826.013 3048414.598 2905290.762 2789288.811 1.06705333 0.818801223 0.924669968 0.857940233 0.914146995 1.067593288 1.092900307 1.041588361 1 21.41146589 2.257224155 6.295818797 1.062718907 0.900972018 0.47517911 0.068443625 0.108454698 15.3612981 0.022408186 0.01800798 180.8107113 -2.257224155 -0.161746889 (ac)SDQDHS(ph)MDEMTAVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDQDHSMDEMTAVVK 15 0 P08047;H3BUU5;P08047-3 P08047 SP1 Transcription factor Sp1 1 S(0.001)DQDHS(0.999)MDEMTAVVK 111.64 1.28E-24 114590000 115600 105610 117470 115380 127040 90357 141420 104020 164770 TRUE FALSE 108364.8024 113429.4743 120256.4439 118340.8461 117062.7909 116441.5991 120215.3839 117007.126 137268.8225 0.789434923 0.826330934 0.876065239 0.862110157 0.852799556 0.848274189 0.875766118 0.852394038 1 17.06664446 -5 0.184420845 1.622240071 0.820889984 0.840493819 0.021574948 54.09979253 0.525170908 12.35197129 0.064146644 1.00E-05 5 -0.801350087 (ac)SDSGEQNYGERES(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SDSGEQNYGERESR 14 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 1 SDSGEQNYGERES(1)R;SDSGEQNYGERES(1)R;SDSGEQNYGERES(1)R;SDSGEQNYGERES(1)R;SDSGEQNYGERES(1)R;SDSGEQNYGERES(1)R 89.466 6.57E-08 3864076000 38132.04 46747.3 46539.2 43215.9 28047.1 21993.6 47354.8 31037.5 40493 TRUE FALSE 35745.42368 50208.51873 47643.1318 44324.89316 25844.3939 28342.79528 40254.38736 34912.6002 33734.45671 1.05961166 1.48834526 1.412298773 1.31393529 0.766112646 0.840173462 1.19327214 1.034924039 1 15.04193531 2.87527876 6.605277683 0.986889073 1.368316133 0.538580968 0.158955154 0.178843172 8.891608401 0.049084679 0.052211429 750.3756967 -2.87527876 0.38142706 (ac)SES(ph)GHS(ph)QPGLYGIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SESGHSQPGLYGIER 15 0 Q9H0W8-2;Q9H0W8;M0R2N0;M0QZC7;M0QZH1;M0QX70;M0QYR7 Q9H0W8-2 SMG9 Protein SMG9 2 S(0.448)ES(0.596)GHS(0.954)QPGLY(0.002)GIER 52.026 3.86E-05 96574000 24275 22810 21181 25731 27191 17048 31959 20532 32200 TRUE FALSE 22755.67108 24498.87613 21683.42332 26391.30102 25055.52854 21969.48085 27167.04464 23095.4654 26825.61198 0.848281527 0.913264389 0.808310481 0.98380984 0.93401517 0.818974078 1.012727861 0.860948314 1 14.71132346 -5 0.050635434 1.438796393 0.684467654 0.211185517 0.065880188 745.1145435 2.788860453 43.40519297 9.539866202 1.00E-05 5 -0.75432874 (ac)SESGHS(ph)QPGLYGIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SESGHSQPGLYGIER 15 0 Q9H0W8-2;Q9H0W8;M0R2N0;M0QZC7;M0QZH1;M0QX70;M0QYR7 Q9H0W8-2 SMG9 Protein SMG9 1 S(0.042)ES(0.048)GHS(0.91)QPGLYGIER 78.508 5.91E-25 123650000 23078 21430 23053 21840 29059 17803 25063 22643 30565 TRUE FALSE 21633.58918 23016.6995 23599.82805 22400.45138 26776.82336 22942.43709 21305.03582 25470.02839 25463.50404 0.849591994 0.903909354 0.926809916 0.879708124 1.051576535 0.900992929 0.836689082 1.000256224 1 14.63614334 -2.008591761 0.011422928 1.957407933 3.30E-06 0.214494333 0.061831719 10945.1056 17.37324542 1633.094069 1353.922252 0.009804111 2.008591761 -1.957404635 (ac)SESSSKSS(ph)QPLASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SESSSKSSQPLASK 14 1 P17096;P17096-3;A0A669KAX1;A0A1W2PRV2;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 1 S(0.11)ES(0.11)S(0.126)S(0.126)KS(0.126)S(0.401)QPLASK 62.166 5.28E-07 148580000 492940 367050 394460 350480 509040 285280 526330 399070 1131100 TRUE FALSE 462087.7653 394226.7639 403816.7775 359473.9102 469062.0518 367635.7049 447411.7027 448894.768 942312.1028 0.490376558 0.418361138 0.428538248 0.381480731 0.497777807 0.390142187 0.474802034 0.476375891 1 19.84584545 -0.164143604 0.855614548 1.015245122 0.431706595 0.954264278 0.038309771 1.503324589 0.926441983 0.109981601 0.010760154 0.6852616 0.164143604 -0.583538526 (ac)SETAPAAPAAPAPAEKT(ph)PVK ddPTM_SK-BR-3_Pertuzumab_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 163.79 2.17E-54 2530660000 4926590 2530280 3367510 2903990 3435870 2174540 4758580 2284470 3886470 TRUE FALSE 4618243.526 2717624.564 3447388.927 2978511.3 3166030.63 2802294.397 4045075.105 2569691.108 3237793.049 1.426355377 0.83934474 1.06473418 0.919920222 0.977836008 0.865495217 1.249330962 0.793655144 1 21.62657934 4.750056434 24.67111679 0.980093175 1.426355695 0.55404327 0.129690753 1121.063116 2405853.78 0.029036186 0.455823712 56241.44024 -4.750056434 0.44626252 (ac)SETAPAAPAAPAPAEKT(ph)PVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SETAPAAPAAPAPAEKTPVKK 21 2 P10412 P10412 HIST1H1E Histone H1.4 1 SETAPAAPAAPAPAEKT(1)PVKK;SETAPAAPAAPAPAEKT(1)PVKK 98.491 2.24E-12 1187940000 2180360 961950 1404070 1262460 1538440 922230 2054500 922740 1727920 TRUE FALSE 2043895.16 1033173.779 1437375.203 1294856.861 1417617.128 1188462.83 1746446.798 1037946.12 1439518.989 1.419845917 0.717721535 0.998510762 0.89950662 0.984785292 0.825597188 1.213215533 0.721036769 1 20.45715539 (ac)SETAPAETATPAPVEKS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SETAPAETATPAPVEKSPAK 20 1 P16401 P16401 HIST1H1B Histone H1.5 1 S(0.001)ET(0.001)APAET(0.004)AT(0.103)PAPVEKS(0.892)PAK;SETAPAETAT(0.117)PAPVEKS(0.883)PAK;SETAPAETAT(0.001)PAPVEKS(0.999)PAK;SETAPAETATPAPVEKS(1)PAK;SETAPAETATPAPVEKS(1)PAK;SETAPAETATPAPVEKS(1)PAK 202.07 8.77E-66 5788730000 13177800 5842950 7864490 6988050 8268360 5725040 11137300 5453230 9651770 TRUE FALSE 12353025.02 6275568.098 8051039.417 7167375.194 7618996.359 7377766.11 9467365.259 6134077.77 8040827.234 1.53628783 0.780462994 1.001270041 0.891372863 0.947538871 0.917538195 1.177411849 0.762866505 1 22.9389125 4.74856133 24.9961612 0.94584908 1.536288151 0.720724384 0.117488701 772.9282514 1931847.371 0.027305493 0.373159763 56048.1561 -4.74856133 0.590439071 (ac)SETAPAETATPAPVEKS(ph)PAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SETAPAETATPAPVEKSPAKK 21 2 P16401 P16401 HIST1H1B Histone H1.5 1 SETAPAETATPAPVEKS(1)PAKK;SETAPAETAT(0.001)PAPVEKS(0.999)PAKK;SETAPAETATPAPVEKS(1)PAKK;SETAPAETATPAPVEKS(1)PAKK 176.14 1.65E-36 4268670000 8565200 2980990 4820900 4147760 4985700 3281180 6707500 2954040 5749400 TRUE FALSE 8029119.421 3201705.601 4935254.025 4254198.544 4594143.233 4228403.4 5701772.644 3322858.397 4789787.997 1.676299541 0.668444115 1.030370035 0.888180969 0.959153774 0.882795523 1.190401882 0.693738094 1 22.19153037 4.75112121 24.86961021 0.926905422 1.676300045 0.709255038 0.153163913 1053.09084 2085049.27 0.034982028 0.62354114 56379.49869 -4.75112121 0.749394623 (ac)SETAPLAPTIPAPAEKT(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SETAPLAPTIPAPAEKTPVK 20 1 P16402 P16402 HIST1H1D Histone H1.3 1 S(0.002)ET(0.002)APLAPT(0.003)IPAPAEKT(0.993)PVK;S(0.015)ET(0.07)APLAPT(0.086)IPAPAEKT(0.829)PVK;S(0.017)ET(0.017)APLAPT(0.023)IPAPAEKT(0.943)PVK 51.942 3.36E-06 0 1581290 875080 1080590 966960 1128820 677420 1487150 690680 1062360 TRUE FALSE 1482319.882 939871.8337 1106222.105 991773.8307 1040167.031 872980.157 1264165.664 776912.9184 885045.2529 1.674852079 1.061947771 1.249904569 1.120591097 1.175269883 0.98636782 1.428362741 0.877822818 1 19.7553917 4.744091338 24.72563924 1.144727317 1.674852343 0.556781131 0.155327942 379.3736252 1695967.238 0.033017635 0.28697359 55474.23707 -4.744091338 0.530125025 (ac)SETAPLAPTIPAPAEKT(ph)PVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SETAPLAPTIPAPAEKTPVKK 21 2 P16402 P16402 HIST1H1D Histone H1.3 1 SETAPLAPTIPAPAEKT(1)PVKK 66.853 5.00E-07 214670000 637390 271680 381410 350310 479790 235120 574530 272670 453190 TRUE FALSE 597496.8977 291795.4699 390457.2253 359299.5477 442109.2288 302995.3271 488384.5602 306713.4497 377549.6613 1.582565048 0.772866459 1.034187725 0.951661687 1.170996227 0.802531053 1.293563762 0.812379089 1 18.5263069 4.752211009 24.76975066 0.991859356 1.582565494 0.570169613 0.164183394 1507.274144 2735018.278 0.036418643 0.723116969 56521.15246 -4.752211009 0.590706138 (ac)SFDPNLLHNNGHNGYPNGTSAALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFDPNLLHNNGHNGYPNGTSAALR 24 0 O75534-2;O75534;E9PLD4;E9PKN4 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ; 119.76 9.14E-25 162436000 50892 49991 53103 54968 53894 45896 53962 43971 59873 FALSE TRUE 47706.76056 53692.38566 54362.62824 56378.57194 49661.38264 59145.43014 45870.89906 49460.87614 49879.80951 0.956434298 1.076435259 1.089872411 1.130288437 0.995620936 1.185758942 0.919628593 0.991601143 1 15.60616833 1.680481864 11.32762267 0.967564932 1.074048301 0.341856608 0.06655522 0.11729119 20.13658668 0.028018415 0.015249965 47.91614425 -1.680481864 0.106483369 (ac)SGDHLHNDS(ph)QIEADFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGDHLHNDSQIEADFR 16 0 P11387 P11387 TOP1 DNA topoisomerase 1 1 S(0.001)GDHLHNDS(0.999)QIEADFR;S(0.001)GDHLHNDS(0.999)QIEADFR 68.458 3.35E-20 972140000 65510 44119 43959 47718 54487 36960 47898 31224.5 63534 TRUE FALSE 61409.84604 47385.61667 45001.72824 48942.52467 50207.81081 47629.752 40716.13956 35122.94756 52929.76495 1.160213844 0.895254621 0.850215909 0.924669224 0.948574226 0.899867061 0.769248448 0.663576488 1 15.69179163 1.841517789 4.294066311 0.787982566 0.931038317 0.220798773 0.116274562 0.316051381 9.13999486 0.052584298 0.029282306 69.42530375 -1.841517789 0.143055751 (ac)SGEDEQQEQT(ph)IAEDLVVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGEDEQQEQTIAEDLVVTK 19 0 Q9UQ80;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 1 S(0.392)GEDEQQEQT(0.607)IAEDLVVTK 41.644 0.00079329 0 11342 14411 14591 12807 12616 10862 13986 10519 14255 TRUE FALSE 10632.12447 15478.00543 14937.10541 13135.6493 11625.19025 13997.68307 11888.92914 11832.32031 11875.74841 0.895280373 1.303328843 1.257782238 1.106090231 0.978901695 1.178677974 1.001109886 0.996343127 1 13.53573081 3.028669508 5.831275894 1.040778563 1.198671899 0.136371504 0.122296805 0.228713968 23.0758658 0.034339361 0.040517447 1068.241654 -3.028669508 0.157893336 (ac)SHVAVENALGLDQQFAGLDLNS(ph)SDNQSGGSTASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHVAVENALGLDQQFAGLDLNSSDNQSGGSTASK 34 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;F6S8Q4;A0A2R8YDH3;A0A2R8Y650;A0A2R8YCU0;A0A087WX09;A0A2R8Y770;A0A2R8YFS5;A0A2R8Y4A4 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 1 SHVAVENALGLDQQFAGLDLNS(0.365)S(0.304)DNQS(0.304)GGS(0.018)T(0.008)AS(0.002)K 45.748 8.03E-07 23014000 7226 6323.7 6363.3 6902.4 7017.8 6854.3 9359.8 5335.2 9450.3 TRUE FALSE 6773.737559 6791.913328 6514.240481 7079.52727 6466.650296 8833.02514 7956.384882 6001.311464 7872.983879 0.86037742 0.862686045 0.827416972 0.899217803 0.821372226 1.12194122 1.010593316 0.762266449 1 12.94269481 2.27817809 24.99998068 0.983704519 0.85376077 0.300075268 0.090102191 172.413148 108797.9385 0.029747929 0.024888565 189.7483857 -2.27817809 -0.129943749 GANLKDYYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GANLKDYYSR 10 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 99.343 0.004341 178400000 132070 197960 158110 174050 248690 113950 192120 160710 426110 FALSE TRUE 123803.9745 212617.1644 161860.4439 178516.4177 229158.8906 146845.5152 163313.3896 180774.9973 354989.4882 0.348753917 0.598939325 0.455958414 0.502878039 0.645537116 0.413661587 0.460051339 0.509240423 1 18.43741678 -1.670990902 2.160588931 1.097897857 0.496910738 0.780185863 0.084724271 591089.7282 390310.7833 316828.5694 0.020309724 0.021330896 1.670990902 -0.600987119 (ac)SKPHSEAGTAFIQTQQLHAAMADTFLEHMCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 SKPHSEAGTAFIQTQQLHAAMADTFLEHMCR 31 1 P14618;B4DNK4;H3BUW1;H3BTJ2;H3BT25;H3BN34;H3BQZ3;P14618-2;H3BTN5;H3BR70;H3BQ34;H3BU13 P14618;P14618-2;H3BU13 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;; 149.52 1.49E-271 12519486000 2438698 2611090.5 2510116.8 2441340.5 3083416 2251364 3107486 2344985.8 3009355 FALSE TRUE 2286064.245 2804418.357 2569657.956 2503989.43 2841256.945 2901296.239 2641547.323 2637762.439 2507074.209 0.911845464 1.118602053 1.024962862 0.99876957 1.133295909 1.157243861 1.053637468 1.052127787 1 21.25757327 2.746832079 24.93147959 1.086604142 1.032957479 0.162909164 0.066817855 1251.028998 3770787.637 0.019689359 0.020582737 558.254303 -2.746832079 -0.053646662 (ac)SKS(ph)ES(ph)PKEPEQLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSESPKEPEQLRK 14 3 F8W6I7;P09651-2;P09651;P09651-3;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 2 S(0.329)KS(0.718)ES(0.953)PKEPEQLRK 43.794 0.0020004 211650000 854150 263310 416000 449220 520300 291830 540860 313990 601380 TRUE FALSE 800690.2762 282805.7464 425867.7164 460747.7457 479437.7368 376076.5835 459763.0641 353192.3427 501005.7929 1.598165705 0.564476001 0.850025534 0.919645545 0.956950486 0.750643184 0.917680136 0.704966585 1 18.93446776 4.750583438 24.99888339 0.822616242 1.598166174 0.77091435 0.130967252 893.1987167 1857181.48 0.030674341 0.519454685 56309.72913 -4.750583438 0.775549932 (ac)SLHQFLLEPITCHAWNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLHQFLLEPITCHAWNR 17 0 A0A1W2PNV4;E9PF58;F8WFD3;Q92747 A0A1W2PNV4;Q92747 ARPC1A Actin-related protein 2/3 complex subunit 1A 0 65.105 0.00064255 137910000 26023 28934 29285 28994 40966 23315 31255 29080 40417 FALSE TRUE 24394.26688 31076.30347 29979.65403 29738.03513 37748.69561 30045.66201 26568.60291 32710.70201 33671.1416 0.724485887 0.922935843 0.890366427 0.883190582 1.121099369 0.892326799 0.789061542 0.971475883 1 15.03922502 4.73931177 23.7626734 0.918934543 0.724485787 0.347241783 0.088120855 39.57122154 1251336.389 0.020874652 0.125466583 54867.07021 -4.73931177 -0.194448756 (ac)SLICSISNEVPEHPCVSPVSNHVYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLICSISNEVPEHPCVSPVSNHVYER 26 0 Q9UMS4;F5GY56 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ; 102.69 7.91E-26 1085350000 11358 11773 0 15174 22132.4 0 17120 0 0 FALSE TRUE 10647.12305 12644.68517 0 15563.39053 20394.21058 0 14553.01493 0 0 0 (ac)SNGYEDHMAEDCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNGYEDHMAEDCR 13 0 Q15717;M0QZR9 Q15717 ELAVL1 ELAV-like protein 1 0 78.488 1.87E-07 0 7080.8 8200.9 8851.3 9723.1 8563.1 8688.8 8360.8 7763.4 8284.1 FALSE TRUE 6637.625368 8808.103169 9061.257016 9972.611207 7890.588668 11197.11551 7107.175658 8732.677579 6901.430193 0.96177534 1.276272153 1.312953513 1.445006459 1.143326593 1.622434075 1.029812004 1.265343173 1 12.75267965 0.93899176 1.239482113 1.011081797 1.283094858 0.147015978 0.190502818 0.909870463 2.830660272 0.160827234 0.049573885 8.689439414 -0.93899176 0.272013062 (ac)SQGDSNPAAIPHAAEDIQGDDRWMSQHNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQGDSNPAAIPHAAEDIQGDDRWMSQHNR 29 1 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 ; 80.359 9.84E-06 859290000 13096.8 5779.8 5774.9 12616 19660.8 19353.3 10210.4 9580.8 21882 FALSE TRUE 12277.09467 6207.742406 5911.883355 12939.74792 18116.72008 24940.28354 8679.445309 10776.98397 18229.75284 0.67346468 0.340528062 0.324298602 0.709814776 0.993799545 1.368108704 0.476114261 0.59117554 1 14.15400738 3.082081762 4.42015783 0.862387242 0.408287294 0.371451424 0.257894948 0.22022368 8.022650201 0.077925991 0.093780658 1208.041246 -3.082081762 -0.454099947 (ac)SQPGQKPAAS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SQPGQKPAASPR 12 1 P20810-6;P20810-10;P20810-7;P20810-9;P20810-5;F8W7E0;E9PSG1 P20810-6;P20810-5 CAST Calpastatin 1 SQPGQKPAAS(1)PR;SQPGQKPAAS(1)PR;SQPGQKPAAS(1)PR;SQPGQKPAAS(1)PR;SQPGQKPAAS(1)PR 103.97 4.93E-05 1624985000 1152543 952202 1036162 933524 1008421 964961 1182986 977215 1021419 TRUE FALSE 1080407.391 1022704.027 1060740.252 957479.8063 929223.6824 1243529.576 1005608.232 1099222.444 850937.5703 1.269667046 1.201855533 1.246554729 1.125205702 1.09199983 1.461364052 1.181764993 1.291778013 1 19.69869377 -1.443475509 2.79680113 0.993626517 1.231096239 0.344601393 0.101259528 12879644.28 14329344.67 649868.7901 0.02371283 0.036018406 1.443475509 0.237469722 (ac)SQPGQKPAAS(ph)PRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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;S(0.006)QPGQKPAAS(0.994)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR 113.88 1.88E-06 67195900000 7967049 7924839 8052488 7403835 8898829 6632178 9161942 7244999 10082693 TRUE FALSE 7468405.625 8511602.325 8243496.818 7593829.941 8199950.866 8546780.124 7788193.852 8149553.073 8399826.402 0.889114283 1.013306933 0.981388951 0.904046057 0.976204802 1.017494852 0.927185096 0.97020494 1 23.00192808 (ac)SQPGQKPAASPRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQPGQKPAASPRPR 14 2 P20810-6;P20810-10;P20810-7;P20810-9;P20810-5;F8W7E0;E9PSG1 P20810-6;P20810-5 CAST Calpastatin 0 59.248 0.046273 45976000 23314 25568 21875 24383 26034 23722 28433 23472 35345 FALSE TRUE 21854.81836 27461.08132 22393.88533 25008.70906 23989.39466 30570.15631 24169.73561 26402.53087 29445.69116 0.742207688 0.93260101 0.760514848 0.849316422 0.814699663 1.038187765 0.82082419 0.896651762 1 14.84576892 (ac)SQQHTLPVTLSPALS(ph)QELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SQQHTLPVTLSPALSQELLK 20 0 P07476 P07476 IVL Involucrin 1 SQQHTLPVT(0.005)LS(0.094)PALS(0.902)QELLK;SQQHTLPVTLS(0.005)PALS(0.995)QELLK;SQQHTLPVTLSPALS(1)QELLK 170.22 1.21E-55 142624000 232469 188191 239778 200155 256152 193419 249350 184473 379075 TRUE FALSE 217919.1803 202124.8575 245465.6474 205291.3162 236034.8552 249255.9254 211962.2824 207504.8601 315804.9336 0.690043622 0.640030715 0.777269831 0.650057343 0.747407118 0.789271791 0.671181036 0.657066556 1 18.26867418 -2.156786248 2.503990652 1.728629178 0.704950289 0.758219273 0.052732053 7790724.282 1642558.542 32321992.04 0.012386091 0.006969695 2.156786248 -1.023678889 (ac)SS(ph)SPVNVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSPVNVKK 9 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(0.128)S(0.503)S(0.37)PVNVKK;S(0.113)S(0.444)S(0.444)PVNVKK;S(0.036)S(0.594)S(0.37)PVNVKK 65.347 0.004716 51960700000 84596200 61975200 68469500 63112100 76150300 55901500 91211000 59420000 103667100 TRUE FALSE 79301474.85 66563908.29 70093628.87 64731663.33 70169762.61 72039355.56 77534757.31 66838717.8 86364391.29 0.918219577 0.770733254 0.811603345 0.749517971 0.812484886 0.834132615 0.897763027 0.773915231 1 26.36393326 -0.922544038 0.392955225 1.071768979 0.806914915 0.495745595 0.055003278 10.97915085 1.263687537 0.962040734 0.03507259 0.119524232 0.922544038 -0.264854064 (ac)SSILPFT(ph)PPVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSILPFTPPVVK 12 0 Q15796-2;Q15796;B7Z5N5;K7EJX0;K7ESI8;K7EL92;K7ERC7 Q15796-2 SMAD2 Mothers against decapentaplegic homolog 2;Mothers against decapentaplegic homolog 1 SS(0.002)ILPFT(0.998)PPVVK;S(0.005)S(0.005)ILPFT(0.989)PPVVK;S(0.001)S(0.001)ILPFT(0.998)PPVVK;S(0.006)S(0.006)ILPFT(0.987)PPVVK 65.347 0.0018181 131378000 476963 474564 478022 463401 513140 390622 584180 472836 501605 TRUE FALSE 447110.7372 509701.2123 489360.9076 475292.6542 472840.0543 503388.2302 496587.6323 531870.6154 417883.885 1.069940128 1.219719713 1.171045176 1.137379715 1.131510621 1.204612688 1.188338795 1.2727713 1 18.6727426 4.754576134 23.99106438 1.175746038 1.069939987 0.135795162 0.072016174 2941.185114 4405731.481 0.015009682 0.369214571 56829.80088 -4.754576134 -0.105806051 (ac)SSS(ph)PLSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSPLSKK 8 1 P22314;Q5JRR9 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 S(0.084)S(0.137)S(0.769)PLS(0.01)KK 64.04 0.00076614 1257500000 3624600 2731900 2872400 2815600 3296800 2123800 4286700 2605000 5389300 TRUE FALSE 3397742.756 2934172.719 2940534.684 2887853.063 3037882.627 2736906.583 3643949.131 2930239.984 4489791.014 0.756770804 0.653521001 0.654937986 0.643204339 0.676620051 0.609584405 0.811607738 0.652645073 1 22.09821686 -0.314923014 0.527383863 1.042378777 0.66594926 0.729140086 0.060408844 3.401280793 0.909138472 0.337945093 0.025720181 0.484258203 0.314923014 -0.376429517 (ac)SSS(ph)PVNVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSPVNVK 8 0 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(0.119)S(0.166)S(0.715)PVNVK;S(0.034)S(0.034)S(0.932)PVNVK;S(0.014)S(0.042)S(0.944)PVNVK 72.607 0.00044372 6197870000 8524100 7417100 7603400 7002200 7550700 6921400 9633700 7271500 8654400 TRUE FALSE 7990591.797 7966269.801 7783756.239 7181888.307 6957698.48 8919495.82 8189216.12 8179362.782 7209924.73 1.108276729 1.104903324 1.079589112 0.996111412 0.965016798 1.237113584 1.135825466 1.134458831 1 22.78155277 2.239017268 25 1.141450991 1.059603686 0.198054153 0.072294746 18.01292193 986198.2998 0.025150741 0.019853329 173.3872936 -2.239017268 -0.081847305 (ac)SSS(ph)PVNVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSPVNVKK 9 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(0.051)S(0.2)S(0.75)PVNVKK;S(0.313)S(0.313)S(0.373)PVNVKK;S(0.002)S(0.024)S(0.974)PVNVKK 60.398 0.01272 40880500000 32497800 24348500 26818900 24134100 29053700 21564200 35874800 22319200 40053600 TRUE FALSE 30463820.71 26151288.27 27455056.97 24753421.86 26771939.6 27789434.47 30495706.79 25105801.25 33368395.4 0.912954319 0.783714289 0.822786251 0.741822361 0.802314264 0.832807036 0.913909896 0.752382635 1 24.99197898 -2.139106472 0.363436956 1.209274028 0.812987668 0.462927493 0.059153182 39.95451672 2.062838426 6.915728522 0.041616695 0.00725928 2.139106472 -0.39628636 (ac)SVCTLSVPVS(ph)SLSPGRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVCTLSVPVSSLSPGRR 17 1 P86452 P86452 ZBED6 Zinc finger BED domain-containing protein 6 1 SVCTLSVPVS(0.377)S(0.287)LS(0.335)PGRR 46.319 0.0015383 0 20268 21892 21135 21077 22956 19850 25981 17447 27907 TRUE FALSE 18999.46206 23512.90646 21636.33218 21617.8715 21153.12836 25580.37276 22085.39025 19625.29636 23249.14141 0.817211342 1.011345152 0.930629299 0.929835262 0.909845572 1.100271718 0.949944338 0.84412994 1 14.50488982 (ac)SVCTLSVPVSSLS(ph)PGRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SVCTLSVPVSSLSPGRR 17 1 P86452 P86452 ZBED6 Zinc finger BED domain-containing protein 6 1 SVCTLSVPVS(0.052)S(0.042)LS(0.905)PGRR;SVCTLSVPVS(0.167)S(0.167)LS(0.666)PGRR;SVCTLS(0.002)VPVS(0.257)S(0.201)LS(0.54)PGRR 57.595 0.00021583 224524000 94617 95798 105892 100512 97944 80894 118965 90355 118918 TRUE FALSE 88695.09087 102890.9836 108403.8082 103091.3081 90251.87333 104246.7846 101127.3027 101636.0206 99069.81756 0.895278633 1.038570436 1.09421629 1.040592489 0.910992627 1.052255744 1.020768032 1.025902976 1 16.59615797 -0.850427641 4.243478755 0.999999737 1.019888352 0 0.062158205 1.44862E+12 3.90726E+11 4006109.718 0.014115841 0.141114733 0.850427641 0.019888615 (ac)T(ph)T(ph)SQKHRDFVAEPMGEKPVGSLAGIGEVLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TTSQKHRDFVAEPMGEKPVGSLAGIGEVLGK 31 3 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 2 T(0.665)T(0.665)S(0.665)QKHRDFVAEPMGEKPVGS(0.006)LAGIGEVLGK;T(0.877)T(0.889)S(0.234)QKHRDFVAEPMGEKPVGSLAGIGEVLGK;T(0.665)T(0.665)S(0.665)QKHRDFVAEPMGEKPVGS(0.005)LAGIGEVLGK 85 8.81E-09 752460000 565125 460113 581663 651875 853300 383431 710470 444180 1273880 TRUE FALSE 529754.835 494180.2453 595460.321 668603.2161 786285.26 494121.3052 603941.6192 499636.8508 1061261.198 0.499174789 0.465653739 0.561087433 0.630008161 0.740897021 0.465598201 0.569079149 0.470795363 1 20.01734835 -1.477036584 3.683084459 1.005340456 0.549419595 0.730173431 0.085913272 12161.52294 41827086.48 268477.1803 0.019943428 0.033339833 1.477036584 -0.455920861 (ac)T(ph)TS(ph)QKHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TTSQKHR 7 1 O75531;E9PJJ8 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 2 T(0.653)T(0.386)S(0.961)QKHR;T(0.653)T(0.386)S(0.961)QKHR 45.997 0.054903 531400000 345090 201382 286400 285910 231020 232730 266920 204169 251440 TRUE FALSE 323491.4329 216292.5328 293193.5432 293246.9346 212876.6211 299915.3729 226897.824 229659.9491 209473.0396 1.544310587 1.03255547 1.399671976 1.39992686 1.016248303 1.431761211 1.0831839 1.096369965 1 17.67640505 1.605937679 7.902504585 1.062426867 1.276292804 0.307810251 0.169524514 0.149194035 21.83726016 0.081196811 0.039611943 40.35874741 -1.605937679 0.213865937 (ac)TDRYTIHSQLEHLQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDRYTIHSQLEHLQSK 16 1 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 66.387 6.76E-08 74184000 62126 97123 76551 81015 108640 54441 93047 77225 153690 FALSE TRUE 58237.64456 104314.088 78366.82587 83093.98206 100107.8526 70157.23292 79095.46616 86866.71124 128038.1461 0.454846046 0.814711015 0.612058424 0.648978329 0.781859592 0.547940087 0.61774923 0.678443994 1 16.96621417 0.942813348 19.15289597 1.000000001 0.652655897 0.539604546 0.10324176 678.921323 227385.3278 0.091163544 0.022790886 8.766239831 -0.942813348 -0.347344104 (ac)TECFLPPTS(ph)SPSEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TECFLPPTSSPSEHR 15 0 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TECFLPPT(0.029)S(0.482)S(0.393)PS(0.096)EHR 59.68 0.00011881 287580000 63667 62075 63740 62397 61409 42931 73193 53119 72048 TRUE FALSE 59682.19612 66671.09759 65251.9429 63998.21266 56586.18485 55324.48277 62218.38914 59751.02408 60022.72335 0.994326695 1.110764288 1.087120665 1.066233071 0.942746042 0.921725635 1.036580576 0.995473393 1 15.87322116 2.828806996 6.355164747 0.981497958 1.076953348 0.481801293 0.043173506 0.189287744 11.08639933 0.01320528 0.014022128 674.2283283 -2.828806996 0.095455389 (ac)TECFLPPTSS(ph)PSEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TECFLPPTSSPSEHR 15 0 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TECFLPPT(0.002)S(0.09)S(0.819)PS(0.09)EHR;TECFLPPT(0.012)S(0.199)S(0.567)PS(0.223)EHR 83.499 8.32E-05 514794000 91230 95161 106627 89343 113174 80953 115438 85953 109312 TRUE FALSE 85520.07715 102206.8195 109156.2428 91635.69264 104285.7706 104322.8169 98129.14357 96684.42126 91067.12102 0.939088402 1.122324043 1.198635046 1.006243435 1.145152821 1.145559624 1.077547445 1.061683077 1 16.47464266 1.007358095 1.782412596 1.001359804 1.106578257 0.107462724 0.074776936 0.644800123 4.244241258 0.067376799 0.019275171 10.17086979 -1.007358095 0.105218453 (ac)TT(ph)S(ph)QKHRDFVAEPMGEKPVGSLAGIGEVLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTSQKHRDFVAEPMGEKPVGSLAGIGEVLGK 31 3 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 2 T(0.52)T(0.758)S(0.719)QKHRDFVAEPMGEKPVGS(0.003)LAGIGEVLGK 49.767 1.10E-08 566360000 219170 163590 204260 231620 301310 144870 242000 176490 500290 TRUE FALSE 205452.5409 175702.3738 209105.1437 237563.7613 277646.328 186691.6172 205714.3466 198525.165 416788.367 0.492942119 0.421562567 0.501705806 0.569986545 0.666156616 0.44792905 0.493570269 0.476321272 1 18.66895549 -1.196217367 3.457610934 1.000823983 0.503396951 0.837280851 0.068019815 15989787.12 24624163.58 142722.746 0.018083811 0.063647688 1.196217367 -0.497427032 (ac)VDYSVWDHIEVS(ph)DDEDETHPNIDTASLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 19 VDYSVWDHIEVSDDEDETHPNIDTASLFR 29 0 Q16543;K7EKQ2;K7EQA9;K7EJ06 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 1 VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDY(0.297)S(0.332)VWDHIEVS(0.371)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDY(0.001)S(0.001)VWDHIEVS(0.994)DDEDET(0.005)HPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDY(0.002)S(0.002)VWDHIEVS(0.995)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYS(0.001)VWDHIEVS(0.948)DDEDET(0.05)HPNIDTASLFR;VDY(0.004)S(0.006)VWDHIEVS(0.958)DDEDET(0.031)HPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDY(0.001)S(0.001)VWDHIEVS(0.965)DDEDET(0.031)HPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(0.996)DDEDET(0.003)HPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDY(0.02)S(0.065)VWDHIEVS(0.911)DDEDET(0.003)HPNIDTASLFR 224.78 4.30E-155 2271694600 136167.8 131388.4 141595.14 144100.63 156432.5 127287.19 164967.4 109972 148029.8 TRUE FALSE 127645.3005 141116.5338 144953.8436 147798.4961 144146.9225 164032.9354 140232.0699 123702.2463 123322.6701 1.035051385 1.144287046 1.175403059 1.198469803 1.168859889 1.330111774 1.137115096 1.003077911 1 16.91207851 1.286644038 4.674806367 0.998644686 1.176732533 0.496299349 0.071179725 0.153838145 6.564518812 0.053302213 0.017336061 19.34835459 -1.286644038 0.178087847 (ac)VEADRPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEADRPGK 8 1 P38159;P38159-2;H3BT71;H3BR27;P38159-3;H3BNC1;O75526;Q96E39;A0A1B0GUK8 P38159;Q96E39 RBMX;RBMXL2;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA-binding motif protein, X-linked-like-2;RNA binding motif protein, X-linked-like-1" 0 63.48 0.021663 293510000 279030 202930 206620 201550 221920 179300 278780 196170 289380 FALSE TRUE 261566.0104 217955.1483 211521.124 206722.1142 204491.2984 231060.9993 236979.5271 220662.2563 241080.6085 1.084973246 0.904075818 0.877387548 0.857481303 0.8482279 0.958438759 0.982988754 0.915304875 1 17.87915609 2.035806106 23.93932548 0.965834276 0.905207247 0.107216717 0.068823635 204.6060589 136794.7248 0.024926692 0.018409497 108.5940689 -2.035806106 -0.060627029 (ac)VSVINTVDTSHEDMIHDAQMDYYGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VSVINTVDTSHEDMIHDAQMDYYGTR 26 0 P55735 P55735 SEC13 Protein SEC13 homolog 0 ;;;;; 154.14 6.23E-61 1309689000 51704.57 79233.9 71245.2 59736.1 72261.4 54096.1 77916.1 68280.8 74607.9 FALSE TRUE 48468.47326 85100.4604 72935.16979 61269.02946 66586.28113 69712.76589 66233.30414 76805.80818 62155.3595 0.779795558 1.369157239 1.173433319 0.985740087 1.071287845 1.121588974 1.065608898 1.235706925 1 15.92359118 3.374342628 24.62338561 1.084024692 1.173000805 0 0.161495838 27.78523568 6594.954793 0.04163448 0.056373351 2367.78698 -3.374342628 0.088976113 AAAAAATAPPS(ph)PGPAQPGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AAAAAATAPPSPGPAQPGPR 20 0 Q6SPF0 Q6SPF0 SAMD1 Atherin 1 AAAAAATAPPS(1)PGPAQPGPR;AAAAAATAPPS(1)PGPAQPGPR;AAAAAATAPPS(1)PGPAQPGPR 224.41 6.09E-25 3969660000 915580 900420 919730 920770 975210 868250 1018220 838970 1016240 TRUE FALSE 858275.4822 967088.0337 941546.4299 944398.5171 898620.9404 1118899.68 865547.3637 943717.2513 846622.9788 1.013763509 1.142288903 1.112120098 1.115488878 1.061418084 1.32160325 1.022352789 1.114684192 1 19.69136012 -0.448089049 7.462708269 0.999997095 1.11637722 0.147152351 0.085115341 0 0 0.072718746 0.017139973 0.356378053 0.448089049 0.116380126 AAAAPGAS(ph)PSPGGDAAWSEAGPGPRPLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAAAPGASPSPGGDAAWSEAGPGPRPLAR 29 1 P52701;P52701-3;P52701-2;F8WAX8;F8W7G9 P52701 MSH6 DNA mismatch repair protein Msh6 1 AAAAPGAS(0.885)PS(0.115)PGGDAAWS(0.001)EAGPGPRPLAR 79.843 0.0022409 219490000 58927 116220 90392 93039 125800 90599 119770 117260 153970 TRUE FALSE 55238.86426 124825.0497 92536.14093 95426.53825 115920.1755 116753.4605 101811.6004 131900.1691 128271.4123 0.430640493 0.973132263 0.721408919 0.743942368 0.903710136 0.910206401 0.793720117 1.028289677 1 16.96884015 6.981665359 0.166176175 1.009213609 1.80E-17 0.40779547 0.135841575 55.35184971 0.792601346 0.3666204 12.96142046 9586616.6 -6.981665359 -1.009213609 AAAAPGASPS(ph)PGGDAAWSEAGPGPRPLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAAAPGASPSPGGDAAWSEAGPGPRPLAR 29 1 P52701;P52701-3;P52701-2;F8WAX8;F8W7G9 P52701 MSH6 DNA mismatch repair protein Msh6 1 AAAAPGAS(0.032)PS(0.968)PGGDAAWSEAGPGPRPLAR;AAAAPGAS(0.031)PS(0.969)PGGDAAWSEAGPGPRPLAR 291.21 6.93E-81 1465500000 381080 424260 443400 406210 479080 397620 488700 407610 595020 TRUE FALSE 357228.883 455672.6518 453917.6574 416634.0363 441454.9893 512406.4392 415423.9719 458501.0058 495707.318 0.720644764 0.91923729 0.915696906 0.840483933 0.890555724 1.033687461 0.838042847 0.924942984 1 18.91912903 4.739671462 24.34247085 0.91324073 0.720644677 0.509935321 0.061170439 52.94324621 1159951.941 0.013204246 0.08147634 54912.53111 -4.739671462 -0.192596053 AAAEEGHIIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAAEEGHIIPR 11 0 X6R5A3;O95551-3;O95551;O95551-2 X6R5A3 TDP2 Tyrosyl-DNA phosphodiesterase 2 0 140.3 3.87E-05 163170000 157830 208930 176200 203070 208070 147720 215490 172680 171360 FALSE TRUE 147951.702 224399.3946 180379.5472 208281.12 191729.0215 190364.366 183179.275 194239.4781 142758.909 1.036374564 1.571876643 1.263525678 1.458971083 1.343026666 1.333467504 1.283137258 1.360611954 1 17.12322126 -0.968205862 0.477139075 0.884616961 1.359712037 0.347389568 0.13905963 17.10708726 2.531135617 2.886873129 0.062643467 0.107595507 0.968205862 0.475095076 AAAFQVAPHSHGEEAVAQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAAFQVAPHSHGEEAVAQDR 20 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 ; 175.33 1.21E-12 885190000 435320 427820 452690 456440 483950 384940 472420 423150 357860 FALSE TRUE 408074.0983 459496.2379 463428.0206 468153.0232 445942.5192 496065.929 401585.0067 475981.209 298130.8541 1.368775129 1.541256906 1.554445017 1.570293771 1.495794591 1.663920128 1.347009211 1.596551321 1 18.18558616 -1.969707794 0.543968697 0.496318487 1.523266584 0.732866402 0.097744988 44.76802104 3.930700551 28.41040701 0.038428954 0.010722405 1.969707794 1.026948097 AAAIGIDLGTTYSCVGVFQHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AAAIGIDLGTTYSCVGVFQHGK 22 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ;; 336.3 5.86E-81 375869000 809594 843244 685659 660439 996365 518506 929710 898204 1099190 FALSE TRUE 758922.9567 905678.6632 701923.1553 677386.9829 918114.512 668190.265 790308.6165 1010346.747 915728.088 0.828764528 0.989025755 0.766519193 0.739725025 1.00260604 0.729681959 0.863038523 1.103326151 1 19.80455975 1.262083586 12.57671608 1.051636692 0.848598491 0.445528075 0.095515558 0.732780523 392.4664416 0.060962566 0.02188697 18.28452095 -1.262083586 -0.203038201 AAALEFLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAALEFLNR 9 0 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 118.06 0.0040738 0 149170 173890 155340 159080 200180 119110 165560 178120 192050 FALSE TRUE 139833.716 186764.9965 159024.7382 163162.2621 184458.6703 153495.1234 140735.815 200358.6741 159995.6143 0.873984681 1.167313225 0.993931858 1.019792091 1.152898291 0.959370818 0.879622955 1.252276039 1 17.28767283 AAALEFLNRFEEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAALEFLNRFEEAK 14 1 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 86.944 0.0065105 104670000 48691 47025 47538 47727 63264 42581 49502 55617 53311 FALSE TRUE 45643.51723 50506.77993 48665.62381 48951.75562 58295.50063 54873.44346 42079.63465 62560.90488 44413.0497 1.02770509 1.13720585 1.095750554 1.102193071 1.312575944 1.23552523 0.947461049 1.40861538 1 15.43869602 6.342262625 0.714629926 1.15340155 1.20E-15 0.076663923 0.13729415 74.9474447 4.575727599 0.046696504 114.771162 2199189.355 -6.342262625 -1.15340155 AAAPRPPVSAASGRPQDDTDSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AAAPRPPVSAASGRPQDDTDSSR 23 2 Q8TF74 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 0 ;;; 190.91 7.76E-18 2498630000 313860 375406 382418 337437 371788 357838 375970 325159 412610 FALSE TRUE 294216.0629 403201.4508 391489.1356 346096.2047 342589.2702 461140.0216 319596.7888 365755.8169 343742.7254 0.855919387 1.172974498 1.138901587 1.00684663 0.996644423 1.341526634 0.929755789 1.06403944 1 18.39096966 1.618645668 24.99999992 0.997667395 1.098174031 0.085847235 0.130314675 1.595242165 3690.405551 0.056339068 0.030846735 41.55714157 -1.618645668 0.100506635 AAARPLLTDLYQATMALGYWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAARPLLTDLYQATMALGYWR 21 1 Q6XQN6-3;Q6XQN6;Q6XQN6-2;C9J8U2;G5E977 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 0 161.02 1.86E-11 40398000 34052 88077 41357 37975 83533 30166 40827 74444 24986 FALSE TRUE 31920.7461 94598.31272 42338.00757 38949.50279 76972.65514 38874.4345 34705.37037 83738.49727 20815.67518 1.53349559 4.544570949 2.03394832 1.871162114 3.697821687 1.86755578 1.667270942 4.022857608 1 14.34538273 -1.101973247 0.204744737 2.97E-14 3.105236578 0.124108414 1.116844955 36.55325536 1.608279568 27.32149472 2.972542813 0.079072734 1.101973247 3.105236578 AAAT(ph)PAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AAATPAKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AAAT(1)PAKK;AAAT(1)PAKK;AAAT(1)PAKK;AAAT(1)PAKK 76.228 0.021298 1545260000 8272060 4668910 6974670 5513190 6500110 2999430 8509040 5020380 12571800 TRUE FALSE 7754326.531 5014600.954 7140112.466 5654667.789 5989617.581 3865316.749 7233188.446 5647185.494 10473485.36 0.740376891 0.478790086 0.681732224 0.539903155 0.571883893 0.36905735 0.690619044 0.539188751 1 23.32023829 -1.316728054 3.97036753 1.000821826 0.575226161 0.600013897 0.10867735 0.000702096 0.000120826 0.093332732 0.021957481 0.048224968 1.316728054 -0.425595665 AAAT(ph)PESQEPQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAATPESQEPQAK 13 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 AAAT(1)PESQEPQAK;AAAT(1)PESQEPQAK 256.96 7.77E-23 377250000 604750 502520 503260 467210 590320 379150 561350 439230 782040 TRUE FALSE 566899.777 539727.1037 515197.5649 479199.3996 543958.6484 488604.45 477180.7788 494068.8324 651512.4718 0.870128818 0.828421752 0.790771608 0.735518383 0.834916708 0.749954101 0.732420022 0.758341327 1 19.31343327 4.454895028 1.293329819 0.782189393 0.883055733 0.037860447 0.07933371 1.783159755 3.731988771 0.020018411 0.20812788 28503.29241 -4.454895028 0.10086634 AAATGNAS(ph)PGKLEHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AAATGNASPGKLEHSK 16 1 H0Y6H0;Q8NB78 H0Y6H0 KDM1B Lysine-specific histone demethylase 1B 1 AAATGNAS(1)PGKLEHSK;AAATGNAS(1)PGKLEHSK;AAAT(0.001)GNAS(0.999)PGKLEHSK 184.56 1.09E-09 1008000000 2230640 1415130 1654620 1678740 1792400 1218340 2166570 1533760 2012500 TRUE FALSE 2091028.224 1519907.698 1693868.368 1721819.311 1651632.134 1570054.98 1841712.942 1725253.312 1676600.749 1.247183163 0.906541226 1.010299184 1.026970381 0.985107597 0.936451317 1.098480329 1.029018574 1 20.67710775 1.723593816 24.99999997 1.049850958 1.00385417 0 0.093946326 3.026376227 5034.550175 0.039726453 0.022030354 52.91682956 -1.723593816 -0.045996788 AAAYDIS(ph)EDEED ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAAYDISEDEED 12 0 P49585 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 AAAYDIS(1)EDEED;AAAYDIS(1)EDEED 351.11 1.63E-71 1101730000 1521000 1663830 1650860 1564370 1724160 1538610 1826280 1547920 2038600 TRUE FALSE 1425803.325 1787021.704 1690019.179 1604514.383 1588751.429 1982781.73 1552446.268 1741181.219 1698344.49 0.839525393 1.052213915 0.995097984 0.944752017 0.935470653 1.167479119 0.914093859 1.025222639 1 20.69569769 AADAEAEVASLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AADAEAEVASLNR 13 0 J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753 J3KN67 TPM3 Tropomyosin alpha-3 chain 0 83.081 0.024657 145420000 216150 360330 401280 328720 336750 416900 453350 399490 295790 FALSE TRUE 202621.5573 387009.2081 410798.5511 337155.5117 310303.0134 537252.2622 385374.3762 449367.2059 246420.7381 0.822258544 1.570522072 1.667061605 1.368210786 1.259240662 2.180223411 1.56388776 1.823577063 1 17.91076415 AADAEAEVASLNRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AADAEAEVASLNRR 14 1 J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753 J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ; 254.4 4.76E-24 1975630000 1351090 2002960 1572500 1827700 2052060 1314340 2074180 1536730 2559100 FALSE TRUE 1266527.689 2151261.242 1609800.443 1874601.876 1890899.485 1693768.621 1763175.965 1728594.123 2131969.678 0.594064588 1.009048705 0.755076613 0.879281678 0.886926069 0.794461872 0.827017374 0.810796768 1 21.02375549 -2.128821253 2.27575714 1.328070824 0.83299558 0.213609821 0.106049445 9155858.789 2461470.243 15502075.12 0.023926284 0.00743325 2.128821253 -0.495075244 AADCEVEQWDSDEPIPAKELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AADCEVEQWDSDEPIPAKELER 22 1 U3KQ56;Q9UBQ7 U3KQ56 GRHPR Glyoxylate reductase/hydroxypyruvate reductase 0 132.83 9.12E-06 55102000 35186 55703 42499 46935 79703 28748 51219 45507 162240 FALSE TRUE 32983.77107 59827.30808 43507.09635 48139.43156 73443.44789 37047.08092 43539.18644 51188.64912 135161.0959 0.244033025 0.442637045 0.321890675 0.356163371 0.543377126 0.274095742 0.322128096 0.378723247 1 17.04432043 -1.494917777 2.042410642 1.059240563 0.362742092 0.84918119 0.084708078 89986.91051 65787.3017 29607.23843 0.020625436 0.031995008 1.494917777 -0.696498471 AADEEAFEDNSEEYIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AADEEAFEDNSEEYIR 16 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;;; 401.62 2.35E-139 774030000 607709 656198 677920 662799 634792 588263 779930 640554 546156 FALSE TRUE 569673.5785 704783.5827 694000.5825 679807.5445 584937.9969 758084.9784 662986.737 720528.5769 454999.0353 1.252032497 1.548978191 1.52527924 1.494085683 1.285580741 1.666124364 1.457116797 1.583582648 1 18.79550396 -1.648800553 6.650336533 0.997744775 1.488409937 0.582873193 0.12635645 0.00375097 0.000198086 0.108616115 0.025513856 0.022449126 1.648800553 0.490665163 AADEEAFEDNSEEYIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AADEEAFEDNSEEYIRR 17 1 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;;; 339.58 3.32E-72 3730930000 903680 1218390 993350 1134070 1342600 793520 1308430 1052240 1582860 FALSE TRUE 847120.2819 1308600.863 1016912.731 1163172.156 1237157.612 1022596.342 1112243.068 1183614.48 1318670.44 0.642404847 0.992363841 0.771165183 0.882079495 0.938185595 0.77547529 0.843457952 0.897581719 1 20.33065262 -4.999999968 0.293443506 2.199319081 0.841540235 0.218212037 0.096763515 412.7288355 3.865995195 303.3588881 0.091057464 1.00E-05 4.999999968 -1.357778847 AADESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AADESER 7 0 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;H0YL80;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5;H0YKP3;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2 TPM3;TPM1;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain 0 ; 133.81 0.0075265 767640000 787380 829110 923280 897500 907410 702250 813380 719620 707400 FALSE TRUE 738099.2913 890498.1671 945180.6376 920531.3695 836145.6789 904978.1749 691421.22 809466.1411 589330.37 1.252437222 1.511033899 1.603821364 1.561995472 1.418806363 1.535604172 1.173231951 1.373535426 1 19.16871709 1.185096665 0.784295847 1.020808775 1.509132465 0.563681514 0.126400544 0.393486405 0.552178863 0.113481817 0.043818619 15.31428288 -1.185096665 0.488323691 AADGGERPLAAS(ph)PPGTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AADGGERPLAASPPGTVK 18 1 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785;O95785-2 M0QXA7 WIZ Protein Wiz 1 AADGGERPLAAS(0.775)PPGT(0.225)VK;AADGGERPLAAS(1)PPGTVK 101.3 0.00041865 290790000 380220 278710 345150 330870 367800 264420 400080 302330 476500 TRUE FALSE 356422.7089 299345.9784 353337.121 339360.6844 338914.4716 340753.7615 340091.7182 340076.566 396969.0717 0.897860147 0.754078843 0.890087279 0.854879406 0.853755357 0.85838869 0.856720945 0.856682775 1 18.59866708 -5 0.231010601 1.826408957 0.830684887 0.585134655 0.038700912 106.8866185 1.069652993 41.28160863 0.06222733 1.00E-05 5 -0.99572407 AADIS(ph)LDNLVEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AADISLDNLVEGK 13 0 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 AADIS(1)LDNLVEGK;AADIS(1)LDNLVEGK;AADIS(1)LDNLVEGK;AADIS(1)LDNLVEGK;AADIS(1)LDNLVEGK 216.99 2.79E-11 195482000 510104 383316 443436 417565 470943 339943 585119 425404 628066 TRUE FALSE 478177.5012 411697.1155 453954.5113 428280.4248 433957.0365 438079.0256 497385.8379 478516.6258 523237.7271 0.913881925 0.786826129 0.867587499 0.818519771 0.829368782 0.837246634 0.950592459 0.914530052 1 18.99710704 1.729347643 4.91144878 0.950303201 0.837031329 0.649501763 0.038836977 0.09553519 5.503940373 0.01806979 0.009134764 53.62257223 -1.729347643 -0.113271872 AADKLIQNLDANHDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AADKLIQNLDANHDGR 16 1 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;; 274.17 1.91E-35 3505740000 2161120 2899320 2651940 2660300 4036040 2274630 3407940 2639580 6996000 FALSE TRUE 2025859.357 3113988.67 2714845.269 2728567.802 3719065.699 2931278.755 2896951.035 2969137.373 5828322.404 0.34758876 0.534285589 0.465802178 0.468156635 0.63810226 0.502936961 0.497047149 0.509432589 1 22.47464925 -5 0.316537133 5.63326682 0.476929527 0.843855175 0.068684145 111.9530312 1.000033199 346.8955307 0.058015949 1.00E-05 5 -5.156337293 AADPPAENSS(ph)APEAEQGGAE ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AADPPAENSSAPEAEQGGAE 20 0 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 AADPPAENS(0.015)S(0.985)APEAEQGGAE;AADPPAENS(0.097)S(0.903)APEAEQGGAE 270.37 2.36E-44 958310000 684870 787670 761220 730350 762190 663040 854550 687900 741770 TRUE FALSE 642005.2092 845989.9064 779276.4979 749092.0175 702330.6719 854448.8844 726418.1608 773785.8293 617963.795 1.038904244 1.368995908 1.261039084 1.212194021 1.13652398 1.382684376 1.175502783 1.252153986 1 19.23716279 -0.959861953 0.661090736 0.949599685 1.245563614 0.317260929 0.102694578 33.29424404 7.966538809 3.517380028 0.034904613 0.109682678 0.959861953 0.295963928 AADRLPNLS(ph)SPSAEGPPGPPSGPAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AADRLPNLSSPSAEGPPGPPSGPAPR 26 1 O60784;O60784-4;O60784-2;O60784-3 O60784 TOM1 Target of Myb protein 1 1 AADRLPNLS(0.669)S(0.318)PS(0.013)AEGPPGPPSGPAPR 128.22 5.41E-05 332010000 105330 111000 116570 132370 130870 89319 108100 84825 136330 TRUE FALSE 98737.58332 119218.5555 119335.0954 135766.8383 120591.9981 115103.9453 91891.40855 95415.58797 113575.6423 0.869355271 1.049684185 1.050710285 1.19538693 1.061776942 1.013456257 0.809076724 0.840106083 1 16.79329394 1.876418396 5.113860002 0.86724954 1.05226261 0.391750551 0.091891906 0.19674082 7.126938995 0.040179856 0.023613034 75.234735 -1.876418396 0.18501307 AADRLPNLSS(ph)PSAEGPPGPPSGPAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AADRLPNLSSPSAEGPPGPPSGPAPR 26 1 O60784;O60784-4;O60784-2;O60784-3 O60784 TOM1 Target of Myb protein 1 1 AADRLPNLS(0.074)S(0.915)PS(0.011)AEGPPGPPSGPAPR;AADRLPNLS(0.052)S(0.94)PS(0.008)AEGPPGPPSGPAPR;AADRLPNLS(0.063)S(0.841)PS(0.096)AEGPPGPPSGPAPR;AADRLPNLS(0.19)S(0.804)PS(0.005)AEGPPGPPSGPAPR 209.72 1.05E-25 2742270000 476699 621294 549657 705875 781128 511660 576108 481923 668463 TRUE FALSE 446863.2605 667295.2542 562695.1236 723988.9475 719781.3578 659367.9359 489725.9537 542092.1474 556892.2069 0.802423261 1.198248505 1.010420179 1.300052216 1.292496733 1.184013581 0.879390926 0.973423834 1 19.08703858 1.745589568 12.78924436 0.946231848 1.137748726 0.251218068 0.146387312 0.124553118 151.0743644 0.065930575 0.036210054 55.66594273 -1.745589568 0.191516878 AADS(ph)DDGAVSAPAASDGGVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AADSDDGAVSAPAASDGGVSK 21 0 Q96GM8 Q96GM8 TOE1 Target of EGR1 protein 1 1 AADS(0.997)DDGAVS(0.003)APAASDGGVSK;AADS(1)DDGAVSAPAASDGGVSK 481.28 1.96E-249 716650000 1489470 1137790 1329200 1261810 1342610 1051860 1729990 1183050 1628710 TRUE FALSE 1396246.731 1222033.155 1360729.252 1294190.181 1237166.826 1355514.906 1470594.06 1330756.397 1356867.779 1.029021953 0.90062803 1.002845872 0.953807144 0.911781417 0.999002944 1.083815301 0.980756133 1 20.37184871 2.00344678 24.72056444 1.03347975 0.95705276 0.268477933 0.045892015 85.5546458 613599.0683 0.015819823 0.011624308 100.7968082 -2.00344678 -0.076426991 AAEACARPHGPPPDLAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAEACARPHGPPPDLAAR 18 1 Q3KQV9;A0A087X226 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 110.44 0.00020032 537870000 153600 196930 188650 211050 212280 151170 199350 178070 166450 FALSE TRUE 143986.4502 211510.9021 193124.8671 216465.9003 195608.3851 194810.325 169459.3182 200302.4315 138668.4197 1.038350697 1.525299723 1.3927098 1.561032431 1.410619559 1.404864391 1.222046942 1.444470428 1 17.08127974 -0.112503024 0.571576143 0.967992569 1.405828825 0.357367332 0.152610952 5.211996583 1.833273524 0.5255572 0.060017349 0.771786141 0.112503024 0.437836256 AAEAHVDAHYYEQNEQPTGTCAACITGDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AAEAHVDAHYYEQNEQPTGTCAACITGDNR 30 0 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZHJ1;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZGZ8 P55263-3 ADK Adenosine kinase 0 ;;;;; 312.64 1.58E-92 1291377000 500488 492746 494453 486812 571113 427255 596573 456291 625563 FALSE TRUE 469163.3495 529229.4265 506181.6587 499304.4201 526260.0887 550596.5826 507122.417 513259.9358 521152.494 0.900241973 1.015498213 0.971273599 0.958077388 1.009800576 1.056498029 0.973078749 0.984855569 1 18.99134605 2.728474498 24.37370634 1.005007929 0.971977164 0.248740899 0.035525559 894.896483 2162565.233 0.011084779 0.010581109 535.1487288 -2.728474498 -0.033030764 AAEDDEDDDVDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 AAEDDEDDDVDTK 13 0 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;;; 346.01 1.89E-75 14970150000 11599350 6728235 7784880 7570069 7845070 5778361 10047920 6651572 9219620 FALSE TRUE 10873367.39 7226400.52 7969541.03 7764329.787 7228949.848 7446480.017 8541327.676 7482035.406 7680805.861 1.415654501 0.940838846 1.037591781 1.01087437 0.941170755 0.969492024 1.112035356 0.974121146 1 22.87282625 4.743962536 24.91071263 1.004094039 1.415654684 0.871012068 0.050434121 195.6587592 902242.8277 0.012313708 0.105843139 55457.78711 -4.743962536 0.411560645 AAEDDEDDDVDTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 AAEDDEDDDVDTKK 14 1 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;;;;;;; 324.78 6.79E-43 67728200000 31617369 12983425 17941019 16545290 16449200 11726474 23617507 13389348 21386176 FALSE TRUE 29638494.31 13944731.3 18366588.44 16969870.15 15157346.18 15111716.68 20076281.08 15061037.57 17816685.07 1.663524623 0.782678217 1.030864517 0.952470681 0.850738851 0.848177797 1.126824715 0.845333322 1 24.0867256 4.746064412 24.98984157 0.93711036 1.66352497 0.831951341 0.103609211 357.3589379 1190081.675 0.024009075 0.253429742 55726.83933 -4.746064412 0.72641461 AAEEAEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 144.9 0.00022904 374830000 291760 394240 399560 388580 424890 354650 462800 382970 361310 FALSE TRUE 273499.2624 423429.9398 409037.7519 398551.6207 391520.8533 457031.6977 393407.4364 430784.6475 301005.0268 0.908620249 1.406720493 1.358906714 1.32406965 1.300712009 1.518352376 1.306979623 1.43115433 1 18.19942805 4.742840839 24.67404464 1.352959004 0.908620036 0.481194363 0.136077457 262.6055084 1513764.376 0.027268932 0.213118783 55314.73541 -4.742840839 -0.444338968 AAEEEDEADPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AAEEEDEADPKR 12 1 P20962 P20962 PTMS Parathymosin 0 ;; 176.42 4.01E-05 3918420000 3093690 2151700 2431870 2539120 2746170 1822170 3077430 2265890 3492170 FALSE TRUE 2900061.465 2311014.107 2489555.105 2604278.118 2530496.886 2348200.899 2615997.941 2548791.354 2909304.267 0.99682302 0.79435284 0.855721807 0.895154951 0.869794512 0.807134862 0.899183345 0.876082775 1 21.47224276 0.432254856 1.149000193 1.000067311 0.861990102 0.319846466 0.055925686 2.494213052 4.0444862 0.049247159 0.014979014 2.705545587 -0.432254856 -0.138077209 AAEEPSKVEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAEEPSKVEEK 11 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 0 ; 123.95 0.0003277 748690000 1089130 648200 780490 780420 862120 569940 896860 611870 760680 FALSE TRUE 1020963.297 696193.4025 799003.5914 800446.8984 794412.5728 734472.4258 762384.169 688263.3164 633717.5938 1.611069832 1.098586199 1.260819645 1.263097169 1.253575063 1.158990113 1.203034564 1.086072603 1 19.27348054 7.999999998 0.070460392 0.77443772 2.247226539 0.470107082 0.119477341 264.1003614 1.372420213 4.97091328 38.53878158 99999999.65 -7.999999998 1.472788819 AAEEQGDDQDS(ph)EK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAEEQGDDQDSEK 13 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 AAEEQGDDQDS(1)EK;AAEEQGDDQDS(1)EK 263.15 3.91E-24 396000000 1153250 504440 773810 685960 555920 626750 934910 633400 492390 TRUE FALSE 1081070.141 541789.2625 792165.1386 703562.8949 512260.2857 807682.5506 794728.9248 712481.3843 410206.928 2.635426335 1.320770629 1.931135445 1.715141425 1.248785066 1.968963699 1.937385428 1.736882865 1 18.64599233 4.752019774 24.42959732 1.669793443 2.635427211 0.480080802 0.330597733 1483.261219 2692189.368 0.073106499 1.39869281 56496.26975 -4.752019774 0.965633767 AAEEQGDDQDS(ph)EKSKPAGSDGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AAEEQGDDQDSEKSKPAGSDGER 23 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 AAEEQGDDQDS(1)EKSKPAGSDGER;AAEEQGDDQDS(0.996)EKS(0.004)KPAGSDGER;AAEEQGDDQDS(1)EKSKPAGSDGER;AAEEQGDDQDS(1)EKSKPAGSDGER 252.77 9.28E-44 1080690000 1616730 596629 813740 868020 938430 538028 1008130 691654 1071590 TRUE FALSE 1515541.755 640804.032 833042.2971 890294.8628 864729.4932 693347.9494 856970.2655 778008.5244 892734.7063 1.697639561 0.717798947 0.933135333 0.997267 0.96862986 0.776656205 0.959938333 0.871489054 1 19.76787199 4.746376776 24.99946626 0.895308089 1.697639949 0.877185566 0.093390001 312.5132574 999529.8942 0.021747038 0.237015161 55766.93496 -4.746376776 0.80233186 AAEINGEVDDDDAGGEWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAEINGEVDDDDAGGEWR 18 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 346.5 1.04E-63 149630000 193078 216620 228962 194547 247530 183007 216833 193877 245630 FALSE TRUE 180993.5926 232658.7702 234393.0868 199539.4054 228089.9923 235838.15 184320.9046 218082.9702 204632.7662 0.884480018 1.136957558 1.145432822 0.97510975 1.114630841 1.152494561 0.900739936 1.065728497 1 17.64267764 1.742986906 25 0.982673077 1.083240026 0.125304765 0.0928824 1.258639527 7140.97869 0.040401542 0.022404659 55.33334255 -1.742986906 0.100566949 AAELEMELNEHSLVIDTLKEVDETRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAELEMELNEHSLVIDTLKEVDETRK 26 2 Q9UHV9 Q9UHV9 PFDN2 Prefoldin subunit 2 0 121.35 8.67E-05 26897000 17433 18095 15658 20158 31117 12591 22895 17363 64498 FALSE TRUE 16341.89965 19434.77263 16029.41515 20675.28841 28673.19634 16225.8173 19462.1073 19530.80877 53732.86713 0.304132285 0.361692455 0.298316766 0.384779177 0.533624909 0.301971925 0.362201169 0.363479744 1 15.7135172 -4.236398294 0.512215768 10 0.355861205 0.897592868 0.067528787 337.86956 3.475160034 3426.647639 0.030264967 5.80E-05 4.236398294 -9.644138795 AAEMHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAEMHK 6 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;P78347-5;C9J6M0 A0A494C1K3 GTF2I General transcription factor II-I 0 67.055 0.075688 15416000 41555 50020 36538 33526 49307 33584 43557 50241 47354 FALSE TRUE 38954.14673 53723.53285 37404.69861 34386.33392 45434.62711 43279.15561 37026.03221 56513.69944 39450.31148 0.987423046 1.361802501 0.948147105 0.871636563 1.151692481 1.097054852 0.938548539 1.432528599 1 15.26774907 3.959755394 23.44399921 1.05132957 1.195556714 0.057984226 0.178488712 394.5275262 532615.507 0.041882563 0.075787484 9114.973149 -3.959755394 0.144227144 AAESETPGKS(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AAESETPGKSPEK 13 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 AAESETPGKS(1)PEK;AAESETPGKS(1)PEK;AAESET(0.005)PGKS(0.995)PEK;AAESET(0.003)PGKS(0.997)PEK;AAES(0.005)ET(0.182)PGKS(0.812)PEK 310.36 3.76E-50 2287980000 4511430 1460320 2448930 2110200 1964870 1685790 3066400 1607140 1561128 TRUE FALSE 4229067.649 1568443.612 2507019.776 2164351.305 1810557.036 2172450.206 2606621.787 1807794.967 1300565.652 3.251714086 1.205970349 1.927638004 1.664161515 1.392130443 1.67038873 2.004221612 1.390006698 1 20.3107078 4.747125722 24.97882287 1.603848111 3.251714927 0.744803809 0.313881826 552.4781367 1611182.52 0.069744572 0.820033514 55863.18876 -4.747125722 1.647866816 AAESETPGKS(ph)PEKKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAESETPGKSPEKKPK 16 3 O76021;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 AAESET(0.075)PGKS(0.924)PEKKPK;AAESET(0.005)PGKS(0.995)PEKKPK 125.28 5.56E-05 1174340000 3929300 934890 1903600 1625350 1756650 1069120 2575500 1162460 2080430 TRUE FALSE 3683372.127 1004110.228 1948754.291 1667059.233 1618689.795 1377757.588 2189327.685 1307595.69 1733192.793 2.125194694 0.579341336 1.124372487 0.961842929 0.933935222 0.7949246 1.263176084 0.7544433 1 20.72500071 4.749547222 24.99738832 0.941588628 2.125195373 0.79520188 0.191039866 718.6041415 1634980.395 0.043782207 0.662497201 56175.53564 -4.749547222 1.183606746 AAESLTAIPEPAS(ph)PQLLETPIHASQIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AAESLTAIPEPASPQLLETPIHASQIQK 28 0 Q14676;Q14676-3;Q14676-2 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AAESLTAIPEPAS(1)PQLLETPIHASQIQK;AAESLTAIPEPAS(1)PQLLETPIHASQIQK;AAESLTAIPEPAS(1)PQLLETPIHASQIQK;AAESLTAIPEPAS(1)PQLLETPIHASQIQK 323.77 1.26E-83 784640000 520615 1332510 1265370 1357270 1499700 1295690 1689870 1368570 1339040 TRUE FALSE 488030.6365 1431170.427 1295385.174 1392099.846 1381919.611 1669734.669 1436489.681 1539438.977 1115545.573 0.437481577 1.282933177 1.16121224 1.247909435 1.238783645 1.496787499 1.287701476 1.379987527 1 20.08931802 4.738969423 24.91103951 1.273134605 0.437481317 0.800104539 0.129396806 12.84217532 782278.2934 0.028668687 0.168613155 54823.83644 -4.738969423 -0.835653287 AAEWQLDQPSWSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAEWQLDQPSWSGR 14 0 Q9NVZ3;Q9NVZ3-2;D6RAN6;F6SKB8;Q9NVZ3-3;H0Y970 Q9NVZ3 NECAP2 Adaptin ear-binding coat-associated protein 2 0 114.24 0.0011377 54817000 74880 80039 88366 75866 98352 72772 82574 69645 95301 FALSE TRUE 70193.39446 85965.17084 90462.08325 77812.85 90627.83065 93780.09505 70192.79528 78340.33156 79394.64743 0.884107389 1.082757763 1.139397758 0.980076775 1.141485397 1.181189137 0.884099842 0.986720567 1 16.27675413 1.720375849 14.15002569 0.952261083 1.077493956 0.246741849 0.090503105 0.15050647 96.63716908 0.03992542 0.021988265 52.5261838 -1.720375849 0.125232873 AAFDDAIAELDTLSEESYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAFDDAIAELDTLSEESYK 19 0 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ; 203.85 1.13E-15 32832000 177950 128747 143178 140259 137572 119453 172053 132142 141797 FALSE TRUE 166812.4271 138279.5618 146574.2498 143858.2834 126767.6501 153937.1419 146255.2499 148640.2196 118130.1647 1.412106955 1.17056945 1.24078596 1.217794657 1.073118373 1.303114597 1.23808555 1.258274887 1 16.85001788 -2.340364648 1.869641877 3.23E-05 1.231011619 0.426638246 0.086693256 1211207.698 138665.782 5106100.492 0.019264062 0.004567046 2.340364648 1.230979357 AAFGISDSYVDGSSFDPQRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAFGISDSYVDGSSFDPQRR 20 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1;I3L1C0 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 82.747 0.0056191 141500000 47286 56321 54989 56196 51686 41850 61475 48422 59013 FALSE TRUE 44326.45367 60491.06544 56293.36505 57638.0845 47626.79005 53931.41562 52257.39446 54467.59329 49163.34906 0.901615828 1.230409779 1.14502706 1.172379132 0.968745843 1.096984169 1.062933983 1.107890214 1 15.58529558 2.765477201 24.88209783 1.056248522 1.137478106 0.074289356 0.094712404 1290.162344 1192644.12 0.02680395 0.0284229 582.743182 -2.765477201 0.081229584 AAFNSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AAFNSGK 7 0 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;; 139.31 0.0062827 4599000000 6643200 7013820 6250630 6308430 6957880 4989170 7259000 6270750 5912920 FALSE TRUE 6227413.97 7533130.531 6398897.895 6470314.994 6411436.172 6429462.387 6170580.339 7053666.941 4926015.453 1.264188882 1.529254344 1.299000776 1.31349872 1.301546094 1.305205485 1.252651438 1.431921399 1 22.23198972 -4.066882586 0.201798573 6.17E-12 1.400849138 0.573607969 0.088065063 63.21282694 0.880680335 26.05245517 0.200392164 8.57E-05 4.066882586 1.400849138 AAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTVK 41 2 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 172.51 1.32E-20 295950000 255160 302210 351470 486030 431080 274550 239460 236050 136960 FALSE TRUE 239189.9911 324585.9428 359807.0344 498502.3526 397224.7157 353808.1281 203555.196 265521.3621 114100.4912 2.096309915 2.844737472 3.153422309 4.368976394 3.481358507 3.100846669 1.783999296 2.327083427 1 16.79994548 1.744330724 4.246471368 1.771488456 3.200334214 0.537909603 0.641436302 0.16117165 6.399226325 0.340375821 0.171806036 55.50482331 -1.744330724 1.428845757 AAFVLPEFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAFVLPEFAR 10 0 P19623;K7EL89 P19623 SRM Spermidine synthase 0 ; 112.84 0.003646 133139000 208774 321400 210009 227130 327920 186607 237830 260720 311820 FALSE TRUE 195707.208 345196.7904 214990.5127 232958.5403 302166.486 240477.4116 202169.5994 293271.4659 259775.2276 0.753371327 1.328828748 0.827602057 0.896769652 1.163184376 0.925713409 0.778248185 1.128943159 1 17.98690433 3.829781411 11.72104333 0.944468675 1.081517496 0.017303779 0.181876104 1.168158911 126.7324884 0.043194191 0.07790093 6757.427754 -3.829781411 0.137048822 AAGALGSASSGS(ph)MPNLAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AAGALGSASSGSMPNLAAR 19 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 AAGALGSAS(0.06)S(0.245)GS(0.695)MPNLAAR;AAGALGSAS(0.018)S(0.382)GS(0.6)MPNLAAR;AAGALGSAS(0.035)S(0.058)GS(0.907)MPNLAAR;AAGALGSASS(0.006)GS(0.994)MPNLAAR;AAGALGSASS(0.001)GS(0.999)MPNLAAR;AAGALGSASS(0.005)GS(0.994)MPNLAAR 279.5 1.43E-39 1740341000 968580 1232420 988820 1020970 1317380 697951 1439670 1084860 1568260 TRUE FALSE 907958.3068 1323669.659 1012275.277 1047169.819 1213918.289 899438.1234 1223804.849 1220307.159 1306507.275 0.694950824 1.01313608 0.77479498 0.801503244 0.929132438 0.68842948 0.936699605 0.934022476 1 20.31728373 1.565646649 9.866766184 0.955400683 0.836713351 0.293739731 0.099607328 0.163710975 27.34756265 0.049898194 0.023308907 36.78295783 -1.565646649 -0.118687332 AAGDGDCGTTHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AAGDGDCGTTHSR 13 0 H0YCY6;Q3LXA3-2;Q3LXA3;I3L252 H0YCY6 TKFC;DAK Bifunctional ATP-dependent dihydroxyacetone kinase/FAD-AMP lyase (cyclizing);ATP-dependent dihydroxyacetone kinase;FAD-AMP lyase (cyclizing) 0 ;; 181.98 1.16E-05 981699000 596575 578182 639070 575310 624203 556464 672685 514510 752593 FALSE TRUE 559236.4357 620991.1969 654229.0422 590073.4286 575180.6143 717106.1234 571822.1292 578747.7061 626980.3664 0.89195207 0.990447596 1.043460174 0.941135417 0.917382178 1.14374574 0.912025575 0.923071498 1 19.25806074 4.844555013 0.004987011 1.211992693 0.742381369 1.19E-05 0.076037593 590615.9121 443.2124268 20091.17918 21666.2169 69912.52904 -4.844555013 -0.469611324 AAGGAPS(ph)PPPPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AAGGAPSPPPPVR 13 0 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 AAGGAPS(1)PPPPVR;AAGGAPS(1)PPPPVR;AAGGAPS(1)PPPPVR;AAGGAPS(1)PPPPVR;AAGGAPS(1)PPPPVR;AAGGAPS(1)PPPPVR 183.89 1.05E-05 3217440000 1722610 1709810 1706960 1721020 1854980 1415330 1968190 1606420 2004400 TRUE FALSE 1614794.915 1836406.111 1747449.897 1765184.287 1709297.353 1823912.795 1673078.181 1806985.073 1669852.691 0.967028363 1.099741385 1.046469492 1.057089824 1.023621642 1.092259697 1.001931602 1.082122443 1 20.67128941 -2.092598006 2.23934986 0.920599767 1.049259889 0.107589757 0.041103822 10162799.45 2888674.235 4112308.274 0.009524346 0.008079826 2.092598006 0.128660122 AAGGAPS(ph)PPPPVRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AAGGAPSPPPPVRR 14 1 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 AAGGAPS(1)PPPPVRR;AAGGAPS(1)PPPPVRR;AAGGAPS(1)PPPPVRR;AAGGAPS(1)PPPPVRR 79.317 0.011897 1454810000 2568510 1760450 2117670 2141910 2149120 1749770 2438880 1625380 2104380 TRUE FALSE 2407751.544 1890795.55 2167902.132 2196875.037 1980336.784 2254900.194 2073192.585 1828312.271 1753145.383 1.373389547 1.078516116 1.236578639 1.253104881 1.129590736 1.286202625 1.182555996 1.042875445 1 20.74151421 1.213996875 3.548634492 1.004656793 1.20977094 0.512611803 0.080988682 0.181228786 4.194585019 0.066831126 0.018644445 16.36804742 -1.213996875 0.205114147 AAGGGAGS(ph)S(ph)EDDAQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAGGGAGSSEDDAQSR 16 0 Q9H4A6;D6REM1 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 2 AAGGGAGS(1)S(1)EDDAQSR;AAGGGAGS(1)S(1)EDDAQSR 201.18 4.92E-11 127276000 483940 512830 492890 498710 500130 404210 566320 405910 468210 TRUE FALSE 453651.0593 550800.4668 504581.5836 511507.7429 460851.8072 520898.8652 481405.5735 456588.757 390062.7262 1.163020788 1.412081775 1.293590876 1.311347403 1.181481275 1.335423331 1.234174765 1.170552135 1 18.57334662 0.670282896 0.617435367 0.991796502 1.309512146 0.590973323 0.073265025 0.811033575 0.608751502 0.077135041 0.028523713 4.680399198 -0.670282896 0.317715645 AAGGIILTAS(ph)HCPGGPGGEFGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AAGGIILTASHCPGGPGGEFGVK 23 0 Q15124;Q15124-2;Q5JTY7 Q15124 PGM5 Phosphoglucomutase-like protein 5 1 AAGGIILT(0.006)AS(0.994)HCPGGPGGEFGVK;AAGGIILT(0.001)AS(0.999)HCPGGPGGEFGVK;AAGGIILTAS(1)HCPGGPGGEFGVK;AAGGIILTAS(1)HCPGGPGGEFGVK;AAGGIILTAS(1)HCPGGPGGEFGVK;AAGGIILTAS(1)HCPGGPGGEFGVK 283.43 2.64E-52 7387270000 9276270 8766200 7778180 8073430 9888540 5484660 12677800 8959480 13830000 TRUE FALSE 8695684.819 9415258.569 7962682.103 8280607.882 9111933.957 7067992.306 10776881.58 10078090.8 11521683.65 0.754723448 0.81717732 0.691104038 0.718697729 0.790850906 0.613451343 0.93535649 0.874706432 1 23.45784822 1.639699139 8.011221584 0.930089246 0.738632998 0.701461952 0.062985557 0.064417653 8.349647604 0.02936507 0.015050779 43.62135375 -1.639699139 -0.191456247 AAGIDEQENWHEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAGIDEQENWHEGK 14 0 P28838-2;P28838 P28838-2 LAP3 Cytosol aminopeptidase 0 184.76 1.26E-06 470580000 541410 421680 471730 450150 474140 374170 546740 433430 525380 FALSE TRUE 507524.1145 452901.626 482919.6584 461701.6111 436902.957 482186.8049 464761.4127 487544.6896 437690.6839 1.15954973 1.034752721 1.103335474 1.054858209 0.998200266 1.10166111 1.061848995 1.113902369 1 18.73955215 4.749399202 24.26643181 1.06309888 1.159549814 0.376264651 0.04048772 1135.522981 2542241.558 0.008720581 0.127042227 56156.39263 -4.749399202 0.096450934 AAGISLIVPGKS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAGISLIVPGKSPTR 15 1 J3KPC5;P47736-3;P47736;P47736-4;F2Z357 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 AAGISLIVPGKS(0.864)PT(0.136)R;AAGISLIVPGKS(0.715)PT(0.285)R 179.46 1.76E-06 2916000000 3259040 2649960 3180270 3175970 3602890 2152980 2677210 2130580 3399280 TRUE FALSE 3055062.504 2846165.796 3255707.506 3257470.767 3319933.553 2774510.375 2275787.214 2396587.603 2831918.208 1.078796166 1.005031073 1.149647436 1.150270074 1.17232678 0.979728287 0.80362039 0.846277126 1 21.43334817 2.008219196 4.990031546 0.866769409 1.102912728 0.700865254 0.068136717 0.093996334 6.707560002 0.028042529 0.018830285 101.9105619 -2.008219196 0.236143318 AAGLATMISTMRPDIDNMDEYVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAGLATMISTMRPDIDNMDEYVR 23 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 223.07 1.39E-32 434070000 326930 390480 374440 381470 404980 327010 454810 391500 406150 FALSE TRUE 306468.0349 419391.5455 383321.8936 391259.166 373174.5044 421412.4784 386615.4627 440379.6368 338360.9412 0.905742944 1.239479782 1.132878672 1.156336676 1.102888836 1.245452495 1.142612565 1.301508488 1 18.36820351 4.747847875 24.54963243 1.171323641 0.905742763 0.48317899 0.084096844 739.5849459 1954941.038 0.017235336 0.213221979 55956.15638 -4.747847875 -0.265580878 AAGQPYEQHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAGQPYEQHAK 11 0 O14976-2;O14976;A0A087X1U9;H0Y8H5 O14976-2 GAK Cyclin-G-associated kinase 0 96.334 0.0070897 69026000 59803 87994 79147 91111 90292 69694 83531 73795 71202 FALSE TRUE 56060.03698 94509.16732 81024.40422 93449.06251 83200.83054 89813.52641 71006.30201 83008.46819 59317.92622 0.945077493 1.593264858 1.365934539 1.575393283 1.402625409 1.514104288 1.197046265 1.399382505 1 15.85618054 0.526204048 0.784313532 0.999541688 1.416373421 0.256902561 0.192645539 1.853968052 1.841214853 0.179030986 0.059319202 3.358953938 -0.526204048 0.416831733 AAGTDGSDFQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAGTDGSDFQHR 12 0 A0A3B3ITE9;Q8N5M9 A0A3B3ITE9 JAGN1 Protein jagunal homolog 1 0 95.401 0.0020397 0 84518 163430 125700 142350 157610 148800 155570 149510 148860 FALSE TRUE 79228.16925 175530.5272 128681.6634 146002.942 145231.9464 191756.1444 132243.7227 168176.6526 124014.3043 0.638863151 1.415405491 1.037635651 1.177307269 1.17109028 1.546242149 1.066358623 1.35610689 1 16.92014701 4.75054781 24.75965511 1.223171007 0.638862743 0.525119234 0.174048436 1242.48821 2566317.133 0.037252632 0.61954379 56305.10986 -4.75054781 -0.584308264 AAGVNVEPFWPGLFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAGVNVEPFWPGLFAK 16 0 P05386 P05386 RPLP1 60S acidic ribosomal protein P1 0 ; 228.07 1.03E-14 159125000 463710 496890 477200 463390 492230 371450 525350 439340 506520 FALSE TRUE 434687.2188 533680.2526 488519.4094 475281.3719 453572.2414 478681.585 446578.6446 494192.5661 421978.5398 1.030116885 1.264709463 1.157687805 1.126316452 1.074870399 1.134374239 1.058297052 1.171131988 1 18.68681011 3.146099145 2.504633984 1.092598116 1.17830693 0.103375597 0.07274059 0.401843527 5.125913193 0.020546146 0.026221441 1399.906871 -3.146099145 0.085708814 AAHSEGNTTAGLDMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 AAHSEGNTTAGLDMR 15 0 P78371;P78371-2 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;;;;;;; 254.18 1.09E-24 8540050000 3109000 3866910 3500310 3477090 3984350 3129990 3772620 3429480 4056290 FALSE TRUE 2914413.24 4153220.04 3583339.006 3566318.016 3671435.223 4033567.302 3206950.654 3857658.127 3379268.994 0.862438961 1.229029132 1.060388804 1.055351918 1.086458411 1.193621256 0.949007214 1.141565863 1 21.68827976 0.422374909 0.57586929 0.998727904 1.088047567 0.013403588 0.109105077 6.813152826 3.717999054 0.147848963 0.043811881 2.644690828 -0.422374909 0.089319663 AAHVFFTDSCPDALFNELVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAHVFFTDSCPDALFNELVK 20 0 A0A1B0GWF2;A0A1B0GVQ5;A0A2R8Y5D4;A0A0D9SG72;A0A1B0GTP9;P61764;P61764-2;A0A1B0GW76;A0A0D9SEP9;A0A0D9SFQ7;A0A0D9SFW6 A0A1B0GWF2 STXBP1 Syntaxin-binding protein 1 0 160.55 2.39E-11 64866000 68433 67310 69880 69565 87246 66458 89085 76301 83556 FALSE TRUE 64149.90069 72293.70244 71537.5866 71350.15567 80394.05109 85643.34574 75727.53127 85827.34781 69609.96381 0.921562046 1.038553944 1.027691765 1.024999178 1.154921605 1.230331709 1.087883503 1.232975039 1 16.0870062 2.765949847 5.454750933 1.149341794 1.01224868 0.460530484 0.073716536 0.157440234 14.39829291 0.020618591 0.021313485 583.3777317 -2.765949847 -0.137093113 AAHVPENS(ph)DTEQDVLTVKPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AAHVPENSDTEQDVLTVKPVR 21 1 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2;H3BS99 H3BSS6 ZNF106 Zinc finger protein 106 1 AAHVPENS(1)DTEQDVLTVKPVR;AAHVPENS(0.998)DT(0.002)EQDVLTVKPVR;AAHVPENS(1)DTEQDVLTVKPVR;AAHVPENS(1)DTEQDVLTVKPVR;AAHVPENS(1)DTEQDVLTVKPVR;AAHVPENS(0.998)DT(0.002)EQDVLTVKPVR 243.35 2.59E-30 4236680000 5284470 4459100 4873880 4631260 4882820 4010790 5576880 4191337 5065480 TRUE FALSE 4953724.456 4789256.404 4989490.735 4750105.972 4499343.014 5168639.963 4740678.617 4714634.651 4220018.664 1.173863163 1.134889863 1.182338547 1.125612551 1.066190311 1.224790783 1.12337859 1.117207061 1 22.00881795 0.738089465 1.769701794 1.000210424 1.149284515 0.552678547 0.041600012 0.686487316 3.394552742 0.036443694 0.01028289 5.471286608 -0.738089465 0.149074091 AAHVPENS(ph)DTEQDVLTVKPVRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAHVPENSDTEQDVLTVKPVRK 22 2 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2;H3BS99 H3BSS6 ZNF106 Zinc finger protein 106 1 AAHVPENS(1)DTEQDVLTVKPVRK 179.38 2.71E-17 212880000 161400 136870 153400 156820 189010 118580 205830 140820 332290 TRUE FALSE 151298.2621 147003.9972 157038.7204 160844.2667 174165.917 152812.121 174967.7023 158401.687 276828.6523 0.546541194 0.531028837 0.567277697 0.581024635 0.629147003 0.552009771 0.632043327 0.5722012 1 18.07863375 -5 0.274978496 4.017099595 0.546181729 0.951731335 0.030109521 39.62788185 0.382439145 68.02696057 0.032744205 1.00E-05 5 -3.470917865 AAHVTLLTSLVEGEAVHLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AAHVTLLTSLVEGEAVHLAR 20 0 Q92754;Q92754-2 Q92754 TFAP2C Transcription factor AP-2 gamma 0 ;; 255.19 2.18E-36 100029800 68810.2 95438.1 92172.1 89218.7 97890.9 78164.4 96699.1 88283.5 83353.6 FALSE TRUE 64503.49241 102504.4362 94358.46574 91508.20289 90202.94359 100729.1934 82199.96767 99305.88931 69441.34568 0.92889174 1.47612975 1.35882254 1.317776924 1.298980351 1.450565112 1.183732355 1.430068619 1 16.08350728 -1.195158428 3.672071216 0.999649516 1.321991524 0.262263775 0.158995897 5767003.008 5631053.026 13674.00906 0.033105466 0.063803069 1.195158428 0.322342008 AAIDWFDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAIDWFDGK 9 0 Q92804-2;Q92804;A0A075B7D9;P35637-2;P35637;H3BPE7 Q92804-2;P35637-2 TAF15;FUS TATA-binding protein-associated factor 2N;RNA-binding protein FUS 0 ; 171.75 0.00013194 1429510000 3664100 2967100 3203400 3053200 3063300 2682000 3825900 2812300 3144600 FALSE TRUE 3434770.522 3186787.171 3279386.161 3131550.281 2822720.775 3456249.861 3252241.813 3163421.846 2619745.945 1.31110825 1.216448937 1.251795491 1.19536411 1.077478822 1.319307266 1.241434048 1.207530009 1 21.32099548 0.801918446 4.883338069 1.000001407 1.22971935 0.538649052 0.066509076 2.765045364 67.70810553 0.060256043 0.015244152 6.337506908 -0.801918446 0.229717942 AAIDWFDGKEFSGNPIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAIDWFDGKEFSGNPIK 17 1 P35637-2;P35637;H3BPE7 P35637-2 FUS RNA-binding protein FUS 0 ; 166.76 2.10E-09 1172480000 1094910 1087200 1084010 1146140 1353560 771890 1464170 984730 2423410 FALSE TRUE 1026381.538 1167697.419 1109723.229 1175551.893 1247256.858 994722.1124 1244631.301 1107675.708 2018927.215 0.508379663 0.578375194 0.549659849 0.582265613 0.617781983 0.492698352 0.616481511 0.548645687 1 20.94515747 -4.803913962 0.4677008 10 0.560402015 0.919902069 0.040627143 304.6523104 1.997294058 2837.720342 0.018056919 1.57E-05 4.803913962 -9.439597985 AAIELPSLEVLS(ph)DQEEDREQCGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAIELPSLEVLSDQEEDREQCGVK 24 1 Q9BQI3-2;Q9BQI3 Q9BQI3-2 EIF2AK1 Eukaryotic translation initiation factor 2-alpha kinase 1 1 AAIELPSLEVLS(1)DQEEDREQCGVK 120.31 0.00011355 68642000 85669 58019 74447 74982 76661 63725 91578 68680 75346 TRUE FALSE 80307.13021 62314.78713 76212.918 76906.16506 70640.3543 82121.37301 77846.72907 77254.84918 62770.26585 1.279381713 0.992743719 1.214156368 1.225200563 1.125379244 1.308284614 1.240184792 1.230755488 1 15.9377937 3.725743039 24.41154558 1.209436617 1.111947006 0.014818863 0.107814034 84.83039346 1502598.052 0.025196778 0.041532856 5317.935178 -3.725743039 -0.097489611 AAIPPPVYEEQDRPRS(ph)PTGPSNSFLANMGGTVAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AAIPPPVYEEQDRPRSPTGPSNSFLANMGGTVAHK 35 2 H0Y6J6;Q5W012;Q96I25 H0Y6J6 RBM17 Splicing factor 45 1 AAIPPPVYEEQDRPRS(0.986)PT(0.014)GPSNSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.94)PT(0.06)GPSNSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.989)PT(0.011)GPSNSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.966)PT(0.033)GPS(0.001)NSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.988)PT(0.012)GPSNSFLANMGGTVAHK;AAIPPPVY(0.015)EEQDRPRS(0.962)PT(0.023)GPS(0.001)NSFLANMGGTVAHK 293.73 2.05E-90 2344810000 844842 1186998 1016557 1210833 1569098 680604 1187641 1015982 2091792 TRUE FALSE 791964.8473 1274884.567 1040670.212 1241905.025 1445867.373 877083.3261 1009565.258 1142829.589 1742658.402 0.454457883 0.731574568 0.597173956 0.712649722 0.829690645 0.503301924 0.579324816 0.655796677 1 20.73285837 0.941628714 21.10605752 1.000000001 0.635652005 0.526976142 0.10943387 2621.065674 947735.0643 0.099640091 0.024910023 8.742360557 -0.941628714 -0.364347995 AAISQLRS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAISQLRSPR 10 1 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 AAIS(0.007)QLRS(0.993)PR;AAIS(0.071)QLRS(0.929)PR 67.519 0.03799 883060000 622550 906630 715520 697920 1164540 520820 593510 844570 1218900 TRUE FALSE 583585.7068 973757.8285 732492.4723 715829.8088 1073081.726 671172.2792 504518.6854 950016.4236 1015457.716 0.574702125 0.958934886 0.72134217 0.704933153 1.056746834 0.660955418 0.496838694 0.935554882 1 19.95369874 AAKNS(ph)EEEEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAKNSEEEEEEK 12 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 AAKNS(1)EEEEEEK;AAKNS(1)EEEEEEK 250.52 1.94E-17 1619210000 2494200 724200 1242080 1170790 959750 913160 1635990 900130 1077590 TRUE FALSE 2338092.474 777820.5215 1271542.724 1200834.454 884375.1064 1176774.468 1390688.487 1012513.212 897733.2675 2.604440048 0.8664272 1.416392564 1.337629446 0.985120122 1.310828629 1.549111008 1.127855287 1 19.77592733 4.748111653 24.91807763 1.233055732 2.604440812 0.809188648 0.213894691 551.8857364 1439805.798 0.050971302 0.661335819 55990.15278 -4.748111653 1.371385079 AAKNS(ph)EEEEEEKKK ddPTM_SK-BR-3_Pertuzumab_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 181.4 6.33E-06 4149190000 8596300 1473960 3155910 2986970 3128520 1765660 4124390 1839200 4836750 TRUE FALSE 8058272.928 1583093.532 3230769.676 3063620.707 2882818.659 2275377.379 3505976.008 2068828.169 4029465.178 1.999836845 0.392879318 0.801786225 0.760304549 0.715434563 0.564684711 0.870084702 0.513425002 1 21.94215694 4.746671272 24.987419 0.692496835 1.999837491 0.841682245 0.17680413 354.9344766 1093462.102 0.038347358 0.430673428 55804.76353 -4.746671272 1.307340656 AAKPGPAEAPS(ph)PTASPSGDAS(ph)PPATAPYDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAKPGPAEAPSPTASPSGDASPPATAPYDPR 31 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 2 AAKPGPAEAPS(0.949)PT(0.049)AS(0.004)PS(0.003)GDAS(0.994)PPATAPYDPR;AAKPGPAEAPS(0.995)PT(0.005)ASPS(0.003)GDAS(0.996)PPAT(0.001)APYDPR 147.37 8.77E-09 863060000 380720 334900 374460 354430 417910 288120 456270 337890 534030 TRUE FALSE 356891.4148 359696.3445 383342.368 363525.2738 385089.0344 371295.5668 387856.5493 380076.3103 444896.943 0.802188957 0.80849363 0.86164307 0.817099959 0.865569073 0.834565336 0.871789648 0.854301915 1 18.76311166 -5 0.171708159 1.636729175 0.802329689 0.893876034 0.018242182 37.61359146 0.356410593 8.132980656 0.05949696 1.00E-05 5 -0.834399485 AAKPGPAEAPS(ph)PTASPSGDASPPATAPYDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAKPGPAEAPSPTASPSGDASPPATAPYDPR 31 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 AAKPGPAEAPS(0.681)PT(0.202)AS(0.095)PS(0.017)GDAS(0.006)PPATAPYDPR 127.37 3.41E-06 1255200000 89195 77563 86424 82657 89397 71660 104930 83188 116490 TRUE FALSE 83612.44417 83305.84522 88474.01809 84778.11856 82376.12023 92347.0787 89196.72062 93574.20492 97047.06645 0.861565911 0.85840663 0.911660922 0.873577344 0.848826484 0.951570017 0.91910785 0.964214668 1 16.56639698 1.47455229 0.725780936 0.99970788 0.872361472 0.756576012 0.024903307 0.299804125 0.341975474 0.022576235 0.009900881 29.82306603 -1.47455229 -0.127346408 AAKPGPAEAPSPTAS(ph)PSGDASPPATAPYDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAKPGPAEAPSPTASPSGDASPPATAPYDPR 31 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 AAKPGPAEAPS(0.001)PT(0.004)AS(0.565)PS(0.404)GDAS(0.027)PPATAPYDPR 139.75 1.60E-08 1573500000 632030 606610 605520 595880 715230 511210 771410 606430 806380 TRUE FALSE 592472.3705 651524.0356 619883.2203 611171.2896 659058.7209 658788.0282 655744.2319 682144.1204 671789.9686 0.881930958 0.969832933 0.922733666 0.90976543 0.981048768 0.980645825 0.97611495 1.015412781 1 19.35765073 2.651694385 5.835347507 0.987917407 0.929578418 0.657363374 0.024605374 0.163932789 8.770340934 0.007759886 0.007310832 448.4297167 -2.651694385 -0.058338988 AAKPGPAEAPSPTASPSGDAS(ph)PPATAPYDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AAKPGPAEAPSPTASPSGDASPPATAPYDPR 31 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 AAKPGPAEAPSPTASPS(0.009)GDAS(0.991)PPATAPYDPR;AAKPGPAEAPSPTASPS(0.003)GDAS(0.994)PPAT(0.003)APYDPR;AAKPGPAEAPSPTASPS(0.001)GDAS(0.995)PPAT(0.003)APYDPR;AAKPGPAEAPSPTAS(0.001)PS(0.009)GDAS(0.99)PPATAPYDPR 173.64 2.36E-13 1631670000 847560 792670 825940 828270 866630 694815 1000530 788380 1074670 TRUE FALSE 794512.7325 851360.1116 845531.6868 849524.8105 798568.3756 895396.8111 850509.815 886810.9784 895300.6344 0.887425633 0.95092093 0.94441091 0.948871002 0.891955557 1.000107424 0.949971197 0.990517536 1 19.77201268 1.621765155 0.85738272 0.998862744 0.932622348 0.438937138 0.029487833 0.553857974 0.798389641 0.024517323 0.010167807 41.85671639 -1.621765155 -0.066240396 AALAPAKES(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 AALAPAKESPR 11 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 AALAPAKES(1)PR;AALAPAKES(1)PR;AALAPAKES(1)PR;AALAPAKES(1)PR;AALAPAKES(1)PR;AALAPAKES(1)PR;AALAPAKES(1)PR;AALAPAKES(1)PR;AALAPAKES(1)PR;AALAPAKES(1)PR;AALAPAKES(1)PR 130.58 0.00013391 92849920000 61394030 47859070 51399000 45718140 57977360 41092880 61888030 52359770 64836960 TRUE FALSE 57551487.25 51402605.34 52618208.55 46891344.87 53424052.02 52955727.37 52608494.44 58897002.54 54015252.51 1.065467337 0.951631307 0.974136121 0.868113036 0.989054934 0.980384704 0.973956281 1.090377251 1 25.68686351 1.341701155 7.587756159 1.044610024 0.967469684 0.252187132 0.052181327 0.269168634 17.03806947 0.032431909 0.011785614 21.96348011 -1.341701155 -0.077140339 AALAPAKES(ph)PRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AALAPAKESPRK 12 2 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 AALAPAKES(1)PRK;AALAPAKES(1)PRK;AALAPAKES(1)PRK;AALAPAKES(1)PRK 134.25 7.76E-05 2296300000 5168860 2895750 3780870 3458250 4037020 2929810 4953170 3489750 5014930 TRUE FALSE 4845350.279 3110154.343 3870554.022 3546994.55 3719968.734 3775598.586 4210488.141 3925452.969 4177905.785 1.159755755 0.744429028 0.926434013 0.84898864 0.890390766 0.903706014 1.007798729 0.939574316 1 21.99434853 1.837436181 5.565961657 0.980819768 0.890382704 0.066290971 0.105268814 0.433737316 18.77596849 0.043805073 0.025726658 68.77588392 -1.837436181 -0.090437064 AALDGGVASAAS(ph)PESKPSPGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AALDGGVASAASPESKPSPGTK 22 1 A0A0J9YWL0;Q9Y4K1;A0A494C1M5 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 AALDGGVASAAS(1)PESKPSPGTK;AALDGGVASAAS(1)PESKPSPGTK 234.39 1.18E-30 777160000 1092200 617780 832910 700270 845720 653000 1045780 755220 1210950 TRUE FALSE 1023841.152 663521.074 852667.0185 718240.1138 779300.5627 841510.4994 888974.9975 849510.8794 1008834.622 1.014875114 0.657710451 0.845199996 0.711950302 0.772476029 0.834141177 0.881190017 0.842071496 1 19.94425826 0.976639744 0.72789364 0.995837503 0.784207388 0.258351927 0.096125176 0.852834225 1.025177492 0.084472552 0.032578198 9.476320566 -0.976639744 -0.211630115 AALEAIDELDLFGAHGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AALEAIDELDLFGAHGGR 18 0 P46019 P46019 PHKA2 "Phosphorylase b kinase regulatory subunit alpha, liver isoform" 0 152.68 3.88E-08 22177000 15246 18702 17736 17535 18154 15128 20040 19549 19348 FALSE TRUE 14291.78007 20086.71554 18156.7063 17984.97779 16728.25807 19495.20802 17035.18804 21989.73568 16118.69381 0.886658699 1.246175142 1.126437819 1.115783822 1.037817225 1.209478153 1.056859088 1.364238067 1 13.97644722 AALEEVYPDLTPEETRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AALEEVYPDLTPEETRR 17 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ;;;; 240.2 4.17E-20 1019752000 550698 639060 601354 567885 628529 550721 699941 554471 814550 FALSE TRUE 516230.7952 686376.6673 615618.4009 582457.8905 579166.8677 709705.2125 594991.345 623697.9249 678596.3428 0.760733241 1.01146532 0.907193809 0.858327482 0.853477732 1.045842967 0.876797158 0.919100039 1 19.37219413 AALLELWELRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AALLELWELRR 11 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 196.88 9.46E-08 294890000 179770 198200 190580 144270 179990 140950 215690 185780 289220 FALSE TRUE 168518.5166 212874.9342 195100.6476 147972.2124 165854.3114 181639.9769 183349.2869 208975.042 240947.3136 0.699399857 0.883491628 0.809723274 0.614126841 0.688342646 0.753857655 0.760951779 0.867305964 1 17.87835819 0.979357175 2.503336298 0.999436904 0.757945515 0.570544208 0.072682891 0.254493453 3.641703441 0.076562591 0.020672354 9.535800907 -0.979357175 -0.241491389 AALLKAS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AALLKASPK 9 1 P50914 P50914 RPL14 60S ribosomal protein L14 1 AALLKAS(1)PK;AALLKAS(1)PK 94.767 0.0051471 12351400000 15159100 9069700 11217600 11102100 13860300 8727400 13856600 8622700 14188100 TRUE FALSE 14210318.99 9741230.025 11483686.77 11386998.68 12771767.95 11246858.7 11778931.47 9699263.076 11820014.45 1.202225179 0.824130128 0.971545916 0.963365885 1.080520502 0.951509725 0.996524287 0.820579629 1 23.49472846 AALLNQHYQVNFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AALLNQHYQVNFK 13 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 290.07 1.63E-40 448690000 1264900 1252100 1230000 1270000 1471900 1002300 1496700 1325000 1536200 FALSE TRUE 1185732.167 1344806.787 1259176.181 1302590.35 1356302.911 1291647.739 1272283.73 1490429.167 1279798.296 0.926499254 1.050795888 0.983886434 1.017809099 1.059778651 1.009258837 0.99412832 1.164581303 1 20.28748502 4.746470999 24.3225378 1.028551867 0.926499181 0.292976917 0.052128832 877.2245315 2697163.445 0.01128099 0.121190984 55779.03527 -4.746470999 -0.102052686 AALPSHVVTMLDNFPTNLHPMSQLSAAVTALNSESNFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AALPSHVVTMLDNFPTNLHPMSQLSAAVTALNSESNFAR 39 0 O75390;B4DJV2;A0A0C4DGI3;F8VPA1;F8VX68;F8VPF9;F8VRI6;F8VR34;F8W1S4;H0YH82;F8VRP1 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ; 437.77 3.71E-222 676940000 119240 179376 133759 115935 211966 101216 125428 147086 135179 FALSE TRUE 111776.9812 192657.1857 136931.8266 118910.0884 195319.0454 130435.4161 106621.2358 165450.0109 112616.7516 0.992543113 1.710732932 1.215909931 1.055882777 1.734369378 1.158223925 0.946761776 1.469142099 1 16.78106192 2.026614276 24.99611738 1.112662363 1.369029996 0.107518197 0.275030641 367.6537488 345298.692 0.095734967 0.070703232 106.3198307 -2.026614276 0.256367634 AALQEELQLCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AALQEELQLCK 11 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 190.86 4.85E-06 174034000 302120 303750 280870 269080 316060 245260 387020 292570 394410 FALSE TRUE 283210.8485 326239.9661 287532.369 275985.0484 291237.9225 316062.5805 328989.9439 329098.0085 328580.423 0.861922466 0.992877065 0.87507456 0.839931502 0.886352023 0.961903261 1.001246334 1.001575217 1 18.325887 2.050121543 3.482687021 0.998528026 0.90074849 0.607590776 0.040409484 0.193972493 4.786991107 0.019098569 0.012417962 112.2332509 -2.050121543 -0.097779537 AALQELLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AALQELLSK 9 0 P62851 P62851 RPS25 40S ribosomal protein S25 0 ; 142.92 0.00024002 152544000 319810 333100 332080 316620 377930 275360 385510 308610 403840 FALSE TRUE 299793.663 357763.0706 339957.0944 324745.0052 348248.9023 354851.9619 327706.3544 347140.6378 336436.4951 0.891085442 1.063389602 1.01046438 0.965249044 1.035110362 1.054736829 0.974051148 1.031816235 1 18.35997469 AALS(ph)SSELLELGDSLMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AALSSSELLELGDSLMR 17 0 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 AALS(0.77)S(0.115)S(0.115)ELLELGDSLMR;AALS(0.947)S(0.052)S(0.001)ELLELGDSLMR 106.36 0.00079403 23774000 14507.8 17214.6 17434.8 18519.4 22053.3 20674.7 24273 17369.1 24923 TRUE FALSE 13599.7827 18489.1869 17848.36169 18994.63916 20321.32278 26643.15026 20633.48899 19537.67037 20763.19029 0.654994849 0.890479095 0.859615572 0.914822765 0.978718708 1.283191547 0.993753306 0.940976319 1 14.34174051 2.898239842 1.929665013 1.058795805 0.825803651 0.492063606 0.11045913 0.290781034 2.154454082 0.037848652 0.041740068 791.1154057 -2.898239842 -0.232992154 AALSEEELEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AALSEEELEKK 11 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;; 208.42 3.15E-08 1714210000 2908230 1704950 2102550 1989640 2031470 1536640 3700290 2099260 4266480 FALSE TRUE 2726209.076 1831186.272 2152423.479 2040697.531 1871926.541 1980243.023 3145465.866 2361357.232 3554376.925 0.767000555 0.51519192 0.605569844 0.574136501 0.52665392 0.557128032 0.884955629 0.664351947 1 21.76116525 1.215151976 0.861367021 0.974732581 0.579090142 0.553975477 0.107842302 0.367656141 0.6036589 0.094298969 0.034767751 16.41163978 -1.215151976 -0.395642439 AALSEMVEYITHNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 240.18 2.18E-17 43675000 60045 75020 76773 75201 79965 68000 80500 66390 86892 FALSE TRUE 56286.89063 80574.55886 78594.09181 77130.78497 73684.87146 87630.49611 68429.77233 74678.93764 72389.16386 0.777559619 1.113074866 1.085716254 1.065501808 1.017899193 1.210547152 0.945304085 1.031631444 1 16.14348613 1.622444238 25 0.991344594 1.058806553 0.038208884 0.111221295 2.225997392 3808.417862 0.047361196 0.026117276 41.92221667 -1.622444238 0.067461959 AALSRDEILRYS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AALSRDEILRYSR 13 2 O95396 O95396 MOCS3 Adenylyltransferase and sulfurtransferase MOCS3;Molybdopterin-synthase adenylyltransferase;Molybdopterin-synthase sulfurtransferase 1 AALSRDEILRY(0.44)S(0.56)R;AALSRDEILRY(0.448)S(0.552)R;AALSRDEILRY(0.442)S(0.558)R;AALSRDEILRY(0.447)S(0.553)R 63.181 0.055923 3546260000 412773 1542220 1138277 1269010 1237070 1364641 964240 1052730 1052476 TRUE FALSE 386938.2748 1656407.573 1165277.468 1301574.945 1139915.512 1758590.704 819661.1636 1184165.658 876810.9563 0.441301824 1.889127367 1.328995104 1.484441926 1.300069877 2.00566689 0.93482085 1.350537022 1 19.7419063 1.624714845 25 1.107017143 1.454610098 0.099177854 0.429501631 1.665011147 2464.656773 0.178586468 0.09869892 42.14197114 -1.624714845 0.347592955 AALSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AALSSPR 7 0 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 AALS(0.072)S(0.928)PR 86.833 0.032852 0 469420 586390 527060 448870 634490 454420 593920 658380 713340 TRUE FALSE 440039.8401 629806.9257 539562.1121 460388.7641 584659.7148 585603.6771 504867.2097 740580.1923 594278.9456 0.740460088 1.05978334 0.907927356 0.774701455 0.98381361 0.985402026 0.849545846 1.246182786 1 19.18078074 1.248282376 24.99887928 1.123091425 0.91621781 0.394774093 0.113382986 177.7681349 457127.3101 0.071461249 0.025370498 17.71260247 -1.248282376 -0.206873615 AALTGLLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AALTGLLHR 9 0 P55084-2;P55084;B5MD38;C9JEY0;C9JE81 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ; 164.96 6.19E-05 974140000 940550 1259430 936030 919490 1741950 947300 1063480 1323920 1713060 FALSE TRUE 881682.6544 1352679.508 958233.0736 943085.6701 1605144.274 1220770.132 904021.0469 1489214.326 1427139.219 0.617797229 0.947825895 0.671436298 0.660822474 1.124728584 0.855396667 0.633449796 1.043496182 1 20.44469465 AAMIWIVGEYAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAMIWIVGEYAER 13 0 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1;K7EJ01;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7;H7C034 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ; 194.54 2.16E-06 48670000 202565 220063 218879 244150 230130 204509 224390 191640 206535 FALSE TRUE 189886.8182 236356.6935 224070.9132 250415.3023 212056.5181 263547.4284 190744.8026 215566.6759 172062.9742 1.103589073 1.373663884 1.302261072 1.455370067 1.232435502 1.531691693 1.108575529 1.252835927 1 17.39257716 1.0344947 1.165248213 1.012036591 1.328984078 0.347783864 0.132551752 0.479939267 1.357293733 0.10957076 0.034694591 10.82666503 -1.0344947 0.316947487 AAMYDIIS(ph)SPSKDSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAMYDIISSPSKDSTK 16 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 AAMYDIIS(0.629)S(0.371)PSKDSTK 159.8 5.45E-09 315440000 943820 484810 627300 630310 724710 442910 920000 613060 847930 TRUE FALSE 884747.991 520705.8368 642179.8522 646484.8217 667794.1999 570770.927 782054.5409 689601.8905 706405.0052 1.252465632 0.73712082 0.909081685 0.915175879 0.945341829 0.807993888 1.107090883 0.9762132 1 19.43013604 1.732998752 24.99999367 1.031473119 0.903871635 0.088238658 0.137498741 1.024095532 4566.65561 0.058224773 0.032288507 54.07527695 -1.732998752 -0.127601484 AAMYDIISS(ph)PSKDSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AAMYDIISSPSKDSTK 16 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 AAMYDIIS(0.024)S(0.974)PS(0.003)KDSTK;AAMYDIIS(0.138)S(0.86)PS(0.002)KDSTK;AAMYDIIS(0.123)S(0.876)PS(0.001)KDSTK 155.11 1.76E-07 387768000 1538670 855630 1023110 1053590 1130580 725040 1516770 925440 1387060 TRUE FALSE 1442367.391 918981.7355 1047378.652 1080626.903 1041788.807 934347.278 1289344.42 1040983.221 1155550.725 1.248207768 0.79527598 0.906389161 0.935161806 0.901551775 0.80857314 1.115783489 0.90085463 1 20.14014916 -0.909357032 3.947185187 1.000002827 0.938317241 0.004182278 0.136871898 34317636.21 66629950.43 1454.421866 0.030503359 0.123209152 0.909357032 -0.061685586 AANCNLHVPGPMAVNQFS(ph)PSLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 AANCNLHVPGPMAVNQFSPSLAR 23 0 Q99990;H0Y5G3 Q99990 VGLL1 Transcription cofactor vestigial-like protein 1 1 AANCNLHVPGPMAVNQFS(0.989)PS(0.011)LAR;AANCNLHVPGPMAVNQFS(0.995)PS(0.005)LAR;AANCNLHVPGPMAVNQFS(1)PSLAR;AANCNLHVPGPMAVNQFS(0.793)PS(0.207)LAR;AANCNLHVPGPMAVNQFS(0.997)PS(0.003)LAR;AANCNLHVPGPMAVNQFS(0.979)PS(0.021)LAR;AANCNLHVPGPMAVNQFS(0.988)PS(0.012)LAR 252.44 1.17E-43 2754520000 1698969 2036649 1984422 1767979 2187192 1703782 2082689 1849485 2250757 TRUE FALSE 1592633.563 2187444.611 2031493.427 1813348.334 2015418.763 2195636.205 1770409.119 2080397.273 1875091.116 0.849363292 1.166580436 1.083410512 0.967072116 1.074837775 1.170949073 0.944172315 1.109491296 1 20.83852927 -0.168799702 0.578829656 0.995467266 1.058343998 0.000745579 0.101908264 27.34091151 9.403285522 0.398901204 0.039959629 0.67795411 0.168799702 0.062876732 AAPAQVRPPS(ph)PGNIRPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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;AAPAQVRPPS(1)PGNIRPVK 199.28 8.56E-16 10250820000 3401670 2830940 3330320 2986190 3480950 3027480 3434480 3118210 3218520 TRUE FALSE 3188765.547 3040545.743 3409316.763 3062820.691 3207570.228 3901464.329 2919511.608 3507525.383 2681328.22 1.189248494 1.133969993 1.271502958 1.142277424 1.19626169 1.455049143 1.088830374 1.308129813 1 21.3545164 -1.019563405 4.591799186 0.999993166 1.217094925 0.309640884 0.104370308 6.54E-06 1.40E-06 0.090548928 0.021341915 0.095595312 1.019563405 0.217101759 AAPAQVRPPS(ph)PGNIRPVKR ddPTM_SK-BR-3_Pertuzumab_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 125.04 2.01E-05 1094900000 362400 369970 410890 375540 438910 334190 465170 355530 580940 TRUE FALSE 339718.0309 397362.9638 420636.5048 385176.9922 404439.7791 430665.2279 395422.0769 399918.7031 483977.361 0.701929591 0.821036263 0.869124341 0.795857458 0.835658466 0.889845812 0.817025978 0.826316963 1 18.88458004 -5 0.163126368 1.637641765 0.781322113 0.63255604 0.045647574 94.68787931 0.878620137 19.65223687 0.181415264 1.00E-05 5 -0.856319652 AAPEAS(ph)SPPAS(ph)PLQHLLPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 2 AAPEAS(0.5)S(0.5)PPAS(1)PLQHLLPGK 167.72 7.03E-12 1051400000 529220 493610 575430 705780 661740 365350 432840 316120 444360 TRUE FALSE 496097.0649 530157.398 589079.4713 723891.5097 609769.6097 470820.614 367939.6603 355588.2779 370193.4453 1.340102239 1.43210909 1.591274721 1.955441186 1.647164793 1.271823205 0.993911872 0.960547201 1 18.49791983 1.982328526 2.854737921 0.988342248 1.586165612 0.75138008 0.160007586 0.146718722 2.264086135 0.087247717 0.049498504 96.0126654 -1.982328526 0.597823364 AAPEAS(ph)SPPASPLQHLLPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 AAPEAS(0.5)S(0.5)PPASPLQHLLPGK;AAPEAS(0.893)S(0.107)PPASPLQHLLPGK 282.86 4.78E-45 1277410000 831060 900740 987070 1243290 1121600 610730 695280 503300 671790 TRUE FALSE 779045.4381 967431.7268 1010483.767 1275194.926 1033514.06 787037.8366 591029.2187 566138.1129 559663.9091 1.391987987 1.728594092 1.805518902 2.278501268 1.846669123 1.406268698 1.056043116 1.011568021 1 19.09420119 1.977564158 2.554574452 1.025362347 1.819013972 0.739561881 0.213682448 0.150969514 1.834298679 0.116041159 0.06351921 94.96512809 -1.977564158 0.793651626 AAPEASS(ph)PPAS(ph)PLQHLLPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 2 AAPEAS(0.079)S(0.921)PPAS(1)PLQHLLPGK;AAPEAS(0.451)S(0.549)PPAS(1)PLQHLLPGK;AAPEAS(0.094)S(0.906)PPAS(1)PLQHLLPGK;AAPEAS(0.109)S(0.891)PPAS(1)PLQHLLPGK;AAPEAS(0.082)S(0.918)PPAS(1)PLQHLLPGK;AAPEAS(0.098)S(0.902)PPAS(1)PLQHLLPGK;AAPEAS(0.444)S(0.557)PPAS(0.999)PLQHLLPGK;AAPEAS(0.088)S(0.912)PPAS(1)PLQHLLPGK 198.73 8.06E-22 3476670000 3520680 3377565 3771820 4980120 4779090 2614741 3121402 2166664 3107300 TRUE FALSE 3300326.923 3627643.427 3861289.352 5107918.311 4403759.549 3369574.28 2653376.748 2437176.77 2588671.556 1.274911418 1.4013533 1.491610375 1.973181302 1.701165812 1.301661569 1.02499552 0.941477788 1 21.3037805 1.890609869 2.839039405 0.983988961 1.55185036 0.665861227 0.186532307 0.180105047 2.582143022 0.108340932 0.056554143 77.73379463 -1.890609869 0.567861399 AAPEASS(ph)PPASPLQHLLPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 AAPEAS(0.431)S(0.569)PPASPLQHLLPGK;AAPEAS(0.417)S(0.583)PPASPLQHLLPGK;AAPEAS(0.381)S(0.619)PPASPLQHLLPGK;AAPEAS(0.416)S(0.584)PPASPLQHLLPGK 253.13 2.76E-36 7427460000 1802780 1954010 2056370 2478570 2369800 1322940 1472910 1048870 1508760 TRUE FALSE 1689947.218 2098686.934 2105148.067 2542174.302 2183685.467 1704851.302 1252060.819 1179823.728 1256938.209 1.344495064 1.669681865 1.674822241 2.022513346 1.737305344 1.356352516 0.996119627 0.938648949 1 20.2614823 1.947552339 2.554065831 0.971609993 1.699238828 0.797047847 0.163698105 0.12369894 1.479316057 0.089039925 0.047406049 88.62420232 -1.947552339 0.727628835 AAPFSLEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AAPFSLEYR 9 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;; 129.56 0.00089739 569680000 230851 844410 179558 188828 877030 167601 237959 716660 715840 FALSE TRUE 216402.448 906930.995 183817.2006 193673.6462 808151.6016 215984.6879 202279.2571 806136.5786 596361.6795 0.362871149 1.520773427 0.308231073 0.324758704 1.355136705 0.362170635 0.339188892 1.351757845 1 19.18582803 -1.540548194 0.01184404 0.721496684 0.767101401 0 0.498064354 2834613.695 5336.472378 11169.58622 9429.01187 0.028803934 1.540548194 0.045604718 AAPGAEFAPNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AAPGAEFAPNKR 12 1 Q15233;Q15233-2 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;; 137.16 0.00015579 2307180000 1300230 1496880 1318710 1325070 1695300 1096930 1522860 1356930 1858180 FALSE TRUE 1218850.925 1607710.553 1349990.424 1359073.54 1562157.977 1413595.884 1294521.281 1526345.697 1548037.754 0.787352196 1.03854738 0.872065569 0.877933071 1.009121369 0.913153365 0.836233663 0.985987386 1 20.56200923 1.029748336 23.93443331 1.000000155 0.913776857 0.189511039 0.074296253 181.1178256 145719.9472 0.067273369 0.016818342 10.70898563 -1.029748336 -0.086223299 AAPLDSIHSLAAYYIDCIR ddPTM_SK-BR-3_Pertuzumab_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 ;; 417.5 6.00E-148 10870374000 2674008 4095213 3889396 3735251 4562031 3558306 5027407 4416927 4135514 FALSE TRUE 2506646.613 4398426.832 3981654.31 3831103.864 4203747.488 4585531.178 4273593.993 4968390.059 3445269.997 0.727561734 1.276656644 1.155687163 1.111989443 1.220150378 1.330964244 1.240423536 1.442090188 1 21.71618562 4.741898678 24.84009057 1.228938376 0.727561529 0.625924405 0.120085492 182.6589853 1359184.312 0.026162433 0.190678695 55194.86532 -4.741898678 -0.501376847 AAPQS(ph)PSVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AAPQSPSVPK 10 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 1 AAPQS(0.903)PS(0.097)VPK;AAPQS(0.999)PS(0.001)VPK;AAPQS(0.935)PS(0.065)VPK;AAPQS(0.999)PS(0.001)VPK;AAPQS(0.997)PS(0.003)VPK 233.46 4.80E-12 7450680000 7737340 6777330 7038180 7683200 7136280 4736140 7532510 5374360 6182510 TRUE FALSE 7253073.701 7279130.565 7205128.953 7880363.92 6575825.355 6103386.733 6403080.054 6045360.676 5150609.14 1.408197264 1.413256251 1.398888706 1.529986785 1.276708284 1.184983478 1.243169474 1.173717615 1 22.29631163 1.642644182 0.57471504 1.015569505 1.438980565 0.817271122 0.06523354 0.310428333 0.231816358 0.06349201 0.036049378 43.91816463 -1.642644182 0.42341106 AAPTRGS(ph)PTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAPTRGSPTK 10 1 Q8IYH5-2;Q8IYH5;Q8IYH5-4 Q8IYH5-2 ZZZ3 ZZ-type zinc finger-containing protein 3 1 AAPTRGS(0.799)PT(0.2)K;AAPTRGS(0.971)PT(0.029)K 87.155 0.0079148 249560000 519270 461430 445420 514040 601870 332270 581000 462100 738300 TRUE FALSE 486769.8176 495594.7573 455985.5727 527231.1367 554601.558 428190.955 493884.4437 519794.2022 615072.9604 0.791401751 0.805749544 0.741352006 0.857184709 0.90168418 0.696162866 0.802968876 0.845093567 1 19.23039803 0.835113315 2.753645319 0.999843363 0.795265845 0.557994516 0.055842286 0.496824944 6.64978546 0.051568661 0.013645315 6.840901158 -0.835113315 -0.204577519 AAPTT(ph)PPPPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.085)T(0.915)PPPPVK;AAPT(0.021)T(0.979)PPPPVK 100.93 0.0069578 0 1019530 893510 959040 963880 987630 786510 1180740 912080 1042450 TRUE FALSE 955719.4372 959666.4101 981788.8817 988614.7926 910065.5237 1013562.669 1003698.998 1025955.196 868458.3605 1.100478135 1.105022939 1.130496206 1.138356008 1.047909221 1.167082632 1.155724954 1.181352201 1 19.72809715 AAQDRDQIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 AAQDRDQIYR 10 1 P62995;P62995-3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 ;;;;;; 212.28 3.97E-08 14178570000 4037974 5217260 4457454 4711822 5362720 3714025 5169555 4622640 5950850 FALSE TRUE 3785244.415 5603551.359 4563186.914 4832735.33 4941553.603 4786203.725 4394428.22 5199786.78 4957614.691 0.7635213 1.130291825 0.92044001 0.974810596 0.996760319 0.96542471 0.886399709 1.04884851 1 22.24121472 2.003265841 24.18129274 0.955823424 0.976944304 0 0.09892741 488.981411 3620518.366 0.03445673 0.025299514 100.7548221 -2.003265841 0.02112088 AAQEEYVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AAQEEYVK 8 0 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;; 156.51 0.00091155 1061750000 1348870 1652570 1123390 1123610 1571470 771370 1317130 1444980 1240980 FALSE TRUE 1264446.635 1774928.002 1150037.341 1152443.735 1448053.085 994051.9969 1119638.584 1625388.934 1033852.421 1.223043646 1.716809833 1.112380566 1.114708165 1.400638095 0.961502799 1.082977185 1.572167266 1 19.97959883 3.83156585 4.963531912 1.169706871 1.490208583 0.235365233 0.217246198 0.248278143 9.612682496 0.051506242 0.095062652 6785.249946 -3.83156585 0.320501712 AAQEEYVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 AAQEEYVKR 9 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;;;;; 178.95 8.08E-05 1.05336E+11 18851680 20175260 18326010 19042120 19483160 14285890 22610500 15155550 20316320 FALSE TRUE 17671787 21669057.24 18760711.61 19530773.04 17953031.2 18409994.53 19220265.43 17047753.78 16925394.94 1.044098945 1.280268928 1.108435678 1.153933075 1.060715644 1.087714325 1.135587411 1.007229305 1 24.01268616 1.803106689 0.376957277 0.994544586 1.185323826 0.321331456 0.06732849 1.202505316 0.482737803 0.079501469 0.075617231 63.54870273 -1.803106689 0.19077924 AAQHHTEEQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAQHHTEEQSK 11 0 Q9NW13;Q9NW13-2 Q9NW13 RBM28 RNA-binding protein 28 0 ; 91.313 0.0062652 95184000 98013 106927 97477 98364 130968 85709 89222 96901 110315 FALSE TRUE 91878.54129 114843.9863 99789.20047 100888.1868 120682.3016 110451.7969 75843.9894 108999.3032 91902.71384 0.999736977 1.249625626 1.085813425 1.097771573 1.313152752 1.201833899 0.825263871 1.186029211 1 16.48781984 1.76890173 25 0.987275694 1.163886415 0.257243394 0.122200195 27.99376425 23078.29331 0.051641251 0.028643279 58.73564341 -1.76890173 0.176610721 AAQLQHSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAQLQHSEK 9 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 94.692 0.0085499 235700000 157209 246181 132912 133994.3 274162 108379.8 168623 235027 288327 FALSE TRUE 147369.5693 264408.4974 136064.7354 137432.8206 252630.4224 139667.2889 143339.5466 264370.6383 240203.361 0.613520014 1.100769349 0.566456418 0.572151947 1.051735585 0.581454349 0.596742468 1.100611737 1 17.87389681 1.228015366 24.99835293 1.050306073 0.738792199 0.315582789 0.197798308 298.8818243 708499.4122 0.178167072 0.0464337 16.90500742 -1.228015366 -0.311513874 AAQMHSGYQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AAQMHSGYQR 10 0 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ;;; 108.43 0.0021521 306859000 215395 425326 263732.8 283457 437777 165138.4 229980 393480 394167 FALSE TRUE 201913.8114 456817.5796 269988.6666 290730.9865 403395.7603 212811.1753 195496.634 442606.8442 328377.9813 0.614882309 1.391133406 0.822188703 0.885354692 1.22844948 0.648067737 0.595340264 1.347857863 1 18.32499787 2.232409774 24.96460463 0.827584492 1.015970306 0 0.295889128 373.9910731 1517913.656 0.103463297 0.078339385 170.7692906 -2.232409774 0.188385814 AAQQAASSSGQGQQAQT(ph)PTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAQQAASSSGQGQQAQTPTGK 21 0 P48729-2;U3KPX3;A0A590UJ43;P48729;H0Y9X2;U3KQK7 P48729-2 CSNK1A1 Casein kinase I isoform alpha 1 AAQQAASSSGQGQQAQT(1)PTGK;AAQQAASSSGQGQQAQT(1)PTGK 343.21 6.66E-80 105220000 96594 77085 85556 92424 96825 73767 96487 72127 108070 TRUE FALSE 90548.35397 82792.45361 87585.42872 94795.75631 89220.75507 95062.33539 82019.67009 81132.21472 90032.41884 1.005730548 0.919584908 0.972821011 1.052906914 0.990984761 1.055867838 0.911001516 0.901144452 1 16.45815696 -1.066832535 5.134472903 1.000000443 0.972570579 0.014580293 0.054294476 2.74E-07 4.97E-08 0.052218194 0.012307747 0.085736838 1.066832535 -0.027429865 AAQQDS(ph)DS(ph)DGEALGGNPMVAGFQDDVDLEDQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAQQDSDSDGEALGGNPMVAGFQDDVDLEDQPR 33 0 Q3YEC7;Q3YEC7-2;G3V154 Q3YEC7 RABL6 Rab-like protein 6 2 AAQQDS(1)DS(1)DGEALGGNPMVAGFQDDVDLEDQPR;AAQQDS(1)DS(1)DGEALGGNPMVAGFQDDVDLEDQPR 173.83 9.33E-15 145447000 45209 46731 45252 44540 45394 40024 53788 39408 50254 TRUE FALSE 42379.44939 50191.01186 46325.39881 45682.97181 41828.93835 51578.27906 45722.98874 44328.17555 41866.28275 1.012257277 1.198840895 1.106508526 1.091163791 0.999108008 1.231976562 1.092119619 1.058803711 1 15.35350121 1.046731915 2.678331887 1.001888191 1.115620644 0.176510418 0.07133807 0.365572026 5.614778107 0.062666481 0.016866178 11.13606905 -1.046731915 0.113732454 AAQSPFSIPNSSSGPYGS(ph)QDSVHSSPEDGGGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAQSPFSIPNSSSGPYGSQDSVHSSPEDGGGGR 33 0 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 AAQSPFSIPNSSSGPYGS(0.993)QDS(0.007)VHSSPEDGGGGR;AAQSPFSIPNSSSGPYGS(0.998)QDS(0.002)VHSSPEDGGGGR 259.57 1.28E-59 518570000 94649 229843 188172 194363 238420 237638 273340 192806 291410 TRUE FALSE 88725.08804 246860.8149 192635.5287 199350.6836 219695.4549 306240.2329 232355.2046 216878.2535 242771.7884 0.365467045 1.016843087 0.793483996 0.821144355 0.904946396 1.261432537 0.957093104 0.893342076 1 17.88924126 2.472414078 24.98464784 1.032839458 0.807394353 0.308634631 0.187995666 179.4121603 952267.3722 0.060799473 0.051043996 296.7659558 -2.472414078 -0.225445105 AARPEIADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AARPEIADR 9 1 Q96GM8;Q96GM8-2 Q96GM8 TOE1 Target of EGR1 protein 1 0 ;; 125.74 0.00044979 383110000 562370 689260 668710 632530 671840 583810 721300 643340 696140 FALSE TRUE 527172.2656 740293.5276 684572.117 648761.7907 619076.3965 752346.4696 613147.7612 723662.4152 579949.7368 0.908996474 1.276478772 1.180399048 1.118651755 1.067465605 1.297261507 1.057242934 1.247801955 1 19.14556834 -1.12520136 4.417075474 0.999978694 1.155795682 0.123820586 0.117119044 2.17E-05 4.31E-06 0.100363552 0.023652683 0.07495466 1.12520136 0.155816988 AAS(ph)ALLLR ddPTM_SK-BR-3_Pertuzumab_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 129.38 0.0011466 802098000 1304399 1317929 1363924 1330145 1358551 1165662 1510567 1230724 1471226 TRUE FALSE 1222758.995 1415509.834 1396276.921 1364278.773 1251855.885 1502169.696 1284071.502 1384382.601 1225668.876 0.997625883 1.154887639 1.13919587 1.113089187 1.021365484 1.225591777 1.047649595 1.129491519 1 20.22513785 -1.138110566 0.660069013 0.970037297 1.111095098 0.179632555 0.067648913 66.25229992 13.93080957 3.846899703 0.022517708 0.072759454 1.138110566 0.141057801 AAS(ph)DDGSLK ddPTM_SK-BR-3_Pertuzumab_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(1)DDGSLK 168.69 6.19E-05 347750000 784440 487490 657320 584520 574760 507350 690970 537460 715440 TRUE FALSE 735343.3007 523584.2668 672911.9408 599519.7728 529620.6681 653813.7089 587365.4632 604563.0641 596028.4421 1.233738608 0.878455171 1.128993003 1.005857658 0.888582877 1.096950519 0.985465494 1.014319152 1 19.18502165 3.028713735 24.98244624 0.997974146 1.046985159 0.09887249 0.101212096 683.5398079 594710.4598 0.027187057 0.032494147 1068.350444 -3.028713735 0.049011013 AAS(ph)LDSVATSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AASLDSVATSR 11 0 Q9Y2J4;Q9Y2J4-2;Q9Y2J4-4;Q9Y2J4-3 Q9Y2J4 AMOTL2 Angiomotin-like protein 2 1 AAS(1)LDSVATSR 147.96 3.68E-05 182970000 140470 204690 189340 178980 188370 186370 168890 149870 210000 TRUE FALSE 131678.2334 219845.4606 193831.2342 183572.9298 173576.18 240171.9935 143566.5124 168581.5994 174949.6433 0.752663629 1.25662137 1.107925861 1.049290106 0.992149379 1.37280642 0.820616205 0.963600703 1 17.4165802 1.63207279 23.54426529 0.919125816 1.104433569 0.164469185 0.16760368 0.874647474 846.832194 0.07059309 0.039103817 42.86203538 -1.63207279 0.185307753 AAS(ph)LNYLNQPSAAPLQVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 282.72 9.47E-40 1220510000 823060 1009800 935970 894020 966550 603920 1141760 809840 1324110 TRUE FALSE 771546.1438 1084566.643 958171.6504 916962.0668 890641.0619 778261.9002 970563.6876 910950.3067 1103107.487 0.699429705 0.983192169 0.86861132 0.831253597 0.807392818 0.705517739 0.879845073 0.825803757 1 20.07314194 -1.474416566 2.898257962 1.004776538 0.840419019 0.289244327 0.083131806 22663848.24 25762148.12 872358.2887 0.021226957 0.033541574 1.474416566 -0.164357519 AAS(ph)LRGGVGAPGSPSTPPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AASLRGGVGAPGSPSTPPTR 20 1 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 AAS(0.999)LRGGVGAPGS(0.001)PSTPPTR 50.626 0.083393 757610000 336310 309290 353940 334240 373140 306000 453140 337670 436250 TRUE FALSE 315260.9574 332190.1534 362335.6239 342817.1643 343835.0896 394337.2325 385195.8637 379828.8428 363437.0567 0.867443073 0.914023893 0.996969399 0.943264199 0.946065029 1.085022084 1.059869533 1.045102132 1 18.471346 2.250492607 24.17080644 1.05444043 0.939979089 0.682334024 0.038364553 84.56387999 171302.1212 0.013397 0.011118405 178.0297604 -2.250492607 -0.114461341 AAS(ph)LTEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.996)LT(0.004)EDR;AAS(0.983)LT(0.017)EDR;AAS(0.934)LT(0.066)EDR 163.91 0.00034946 1064570000 2231190 1814110 2167150 1724120 1514370 1860420 2217720 1790550 1467430 TRUE FALSE 2091543.801 1948428.592 2218555.821 1768363.838 1395437.489 2397493.053 1885193.474 2014104.109 1222506.453 1.710865244 1.593798206 1.814760009 1.446506752 1.141456133 1.961129159 1.542072412 1.647520227 1 20.22141065 -1.745130458 2.476812488 0.855961681 1.616245473 0.432923366 0.218206189 14802236.43 10562437 13052337.71 0.049744488 0.017983306 1.745130458 0.760283793 AAS(ph)LTEDRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AASLTEDRDR 10 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 AAS(1)LTEDRDR;AAS(1)LTEDRDR;AAS(1)LTEDRDR;AAS(0.998)LT(0.002)EDRDR 198.55 1.79E-07 14179000000 8707900 7865900 8401360 6676620 7219800 6106430 8144230 7383940 10630270 TRUE FALSE 8162888.083 8448299.42 8600644.227 6847953.373 6652786.031 7869257.211 6923078.319 8305841.163 8856009.263 0.921734366 0.953962351 0.971164773 0.773254992 0.751217149 0.88857825 0.781737927 0.937876296 1 23.0782253 3.253543429 24.99683872 0.838019233 0.953200104 0.22117552 0.078156133 253.3313983 422647.4862 0.019562345 0.026383881 1792.847825 -3.253543429 0.115180872 AAS(ph)PAGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AASPAGPR 8 0 Q6NV74 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 AAS(1)PAGPR 89.08 0.01489 0 181240 177440 186740 170580 201550 145810 187420 171490 195040 TRUE FALSE 169896.5119 190577.8422 191169.561 174957.3716 185721.076 187902.98 159318.1109 192900.904 162486.564 1.04560345 1.172883699 1.176525346 1.076749777 1.142993436 1.156421647 0.980500215 1.187180646 1 17.3099609 0.993000399 0.430954623 1.00056923 1.145044471 0.163336488 0.069133461 1.718913488 0.847452856 0.091742899 0.047340799 9.840120097 -0.993000399 0.144475241 AAS(ph)PAKPSSLDLVPNLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AASPAKPSSLDLVPNLPK 18 1 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 AAS(1)PAKPSSLDLVPNLPK;AAS(1)PAKPSSLDLVPNLPK 262.38 4.72E-31 1280460000 6270300 3789800 4638300 4602300 5325200 3335500 6384300 4451500 7074400 TRUE FALSE 5877853.116 4070400.735 4748322.666 4720402.81 4906980.273 4298404.703 5427033.484 5007279.574 5893636.938 0.997321888 0.690643278 0.805669354 0.800932066 0.832589507 0.729329741 0.920829284 0.849607743 1 22.49072676 0.997789133 0.879891567 0.996135832 0.796081775 0.279767949 0.086636531 0.675671208 1.142734063 0.074418151 0.026142266 9.949222272 -0.997789133 -0.200054057 AAS(ph)PERPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AASPERPPR 9 1 A0A1B0GV45 A0A1B0GV45 1 AAS(1)PERPPR;AAS(1)PERPPR 81.525 0.01274 543310000 588680 602020 642360 638070 710970 469720 643690 558950 755730 TRUE FALSE 551835.5696 646594.1872 657597.0825 654443.9564 655133.2841 605320.5387 547174.6602 628736.1379 629593.7808 0.876494633 1.027002183 1.044478365 1.039470173 1.04056505 0.961446185 0.86909159 0.998637784 1 19.26406176 2.066154648 6.080386142 0.935090289 1.014838539 0.092003936 0.061527939 0.259363677 17.74672414 0.022293357 0.016270809 116.4540638 -2.066154648 0.07974825 AAS(ph)PFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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;AAS(1)PFR;AAS(1)PFR 109.36 0.031078 5832210000 1937700 2658180 1925510 1777670 2758080 1505250 2126000 2281980 2830020 TRUE FALSE 1816422.816 2854994.413 1971184.006 1823288.022 2541471.522 1939791.239 1807226.037 2566890.226 2357671.379 0.770430872 1.210938233 0.836072416 0.77334273 1.077958338 0.822757258 0.766530082 1.088739613 1 21.16893121 3.741838218 23.79901967 0.888383216 1.022556219 0.022752792 0.157310869 464.1963314 750650.8732 0.0370622 0.066399922 5518.71819 -3.741838218 0.134173003 AAS(ph)PPASASDLIEQQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 AASPPASASDLIEQQQK 17 0 Q5VSL9;Q5VSL9-2;Q5VSL9-3 Q5VSL9 STRIP1 Striatin-interacting protein 1 1 AAS(1)PPASASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(0.997)PPAS(0.003)ASDLIEQQQK;AAS(0.979)PPAS(0.021)ASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(0.998)PPAS(0.002)ASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(1)PPASASDLIEQQQK 460.95 4.14E-206 4672210000 2068900 1843200 1979860 1901823 2008990 1564509 2392540 1768660 2392060 TRUE FALSE 1939411.242 1979672.446 2026823.214 1950626.998 1851212.029 2016157.351 2033800.838 1989481.094 1992809.733 0.973204421 0.993407656 1.017068103 0.978832533 0.928945699 1.011715929 1.020569503 0.998329676 1 20.92637254 AAS(ph)PS(ph)PQSVR ddPTM_SK-BR-3_Pertuzumab_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 166.24 8.20E-06 3303080000 3093050 3154990 3293210 3193490 3076030 2954250 3342140 2580360 2584280 TRUE FALSE 2899461.522 3388588.742 3371326.496 3275440.36 2834451.012 3807094.017 2841017.134 2902523.626 2152946.973 1.346740797 1.573930424 1.565912463 1.521375306 1.31654474 1.768317597 1.31959457 1.348163082 1 21.03788136 0.914964496 1.284276779 1.004634132 1.518287663 0.575621506 0.134606574 0.348467735 1.14863929 0.113422703 0.034568871 8.221754331 -0.914964496 0.513653531 AAS(ph)PSPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AASPSPAR 8 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 AAS(0.942)PS(0.058)PAR;AAS(0.954)PS(0.046)PAR 121.73 0.0014902 892940000 956280 1107550 1102260 1068810 1106520 916660 1207960 1016590 1048410 TRUE FALSE 896428.1418 1189554.154 1128406.128 1096237.474 1019618.383 1181284.861 1026837.612 1143513.499 873423.598 1.026338358 1.361944144 1.291934555 1.255104026 1.167381308 1.352476466 1.175646747 1.309231285 1 19.73632198 -1.545676756 2.997930857 0.988955207 1.254781213 0.358309064 0.100808227 29826853.2 33796703.51 2669609.258 0.021899629 0.02846579 1.545676756 0.265826006 AAS(ph)PSPQSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 AASPSPQSVR 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 AAS(0.981)PS(0.019)PQSVR;AAS(0.995)PS(0.005)PQSVR;AAS(0.985)PS(0.015)PQSVR;AAS(0.957)PS(0.043)PQSVR;AAS(0.982)PS(0.018)PQSVR;AAS(0.999)PS(0.001)PQSVR;AAS(0.966)PS(0.034)PQSVR 192.6 6.98E-07 7889021000 5579402 6179935 5687320 5808699 6447134 5121965 5861965 5522150 6077198 TRUE FALSE 5230197.188 6637503.818 5822225.916 5957760.05 5940802.102 6600593.147 4983017.768 6211602.583 5062874.394 1.033048972 1.31101491 1.14998427 1.176754465 1.173404995 1.303724453 0.984227018 1.226892492 1 22.27152526 0.790666236 0.557161403 0.999876966 1.197501212 0.177021833 0.104918967 1.670307394 1.142509109 0.111555475 0.045524238 6.175416248 -0.790666236 0.197624245 AAS(ph)QDHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AASQDHVR 8 0 Q9Y314;A0A075B6F9;M0R3B2;A0A075B797;M0R1K2 Q9Y314 NOSIP Nitric oxide synthase-interacting protein 1 AAS(1)QDHVR;AAS(1)QDHVR 101.12 0.0036221 134419000 153394 144815 130258 125677 92534 85830 149380 87289 161932 TRUE FALSE 143793.3434 155537.2533 133347.7813 128902.0846 85266.7529 110607.7277 126981.8558 98187.2238 134904.5031 1.065889871 1.152943376 0.988460565 0.955506167 0.632052681 0.819896483 0.941272181 0.727827623 1 17.04157898 3.314574777 1.960882265 0.831058648 1.100169371 0.526178922 0.107182214 0.236511868 1.853382111 0.031915772 0.047151844 2063.358909 -3.314574777 0.269110724 AAS(ph)QILENGEEAPGPDPSLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AASQILENGEEAPGPDPSLDR 21 0 A0A087X1N4;Q8IYJ3-2;Q8IYJ3 A0A087X1N4 SYTL1 Synaptotagmin-like protein 1 1 AAS(1)QILENGEEAPGPDPSLDR 59.339 0.068692 31296000 37515 37648 44759 44505 42387 30008 46676 41008 47084 TRUE FALSE 35167.00312 40435.49709 45820.70462 45647.07365 39058.096 38670.82246 39677.36712 46127.93907 39225.37623 0.896537051 1.030850459 1.168139328 1.163712832 0.995735408 0.985862372 1.011522921 1.175971871 1 15.25949966 AAS(ph)SDQLR ddPTM_SK-BR-3_Pertuzumab_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(0.931)S(0.069)DQLR 130.53 0.0010948 218390000 445920 426700 467300 402010 384550 412850 602650 420250 363200 TRUE FALSE 418010.6632 458293.312 478384.5767 412326.2572 354348.9942 532033.0929 512288.2272 472719.1376 302579.5736 1.381490026 1.514620787 1.581020724 1.362703544 1.171093574 1.758324551 1.693069433 1.562296925 1 18.20695507 2.211380475 24.99996028 1.582350431 1.440109366 0 0.233325091 576.052604 529842.6504 0.081306375 0.060063362 162.6973486 -2.211380475 -0.142241065 AASAIYSGYIFDYDYYRDDFYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AASAIYSGYIFDYDYYRDDFYDR 23 1 Q9UKM9;Q5QPM1 Q9UKM9 RALY RNA-binding protein Raly 0 66.045 0.026046 18153000 9051.5 11535 10341 11092 8548.7 6066.3 11835 10369 10516 FALSE TRUE 8484.982772 12389.0634 10586.2934 11376.6395 7877.319586 7817.542332 10060.45162 11663.59247 8760.811664 0.968515601 1.414145615 1.20836902 1.298582818 0.899154084 0.892330829 1.14834698 1.331336972 1 13.09684882 2.761288759 24.70100693 1.056826109 1.252021293 0.191973502 0.166537935 967.5487321 1051532.522 0.04950887 0.052474321 577.1500789 -2.761288759 0.195195184 AASAPAKES(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 AASAPAKESPR 11 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 AASAPAKES(1)PR;AASAPAKES(1)PR;AASAPAKES(1)PR;AASAPAKES(1)PR;AASAPAKES(1)PR;AASAPAKES(1)PR;AAS(0.001)APAKES(0.999)PR;AASAPAKES(1)PR;AASAPAKES(1)PR;AASAPAKES(1)PR;AASAPAKES(1)PR;AASAPAKES(1)PR 174.51 1.49E-05 66695940000 25610920 19852950 21994620 19929280 23702510 17703170 26314930 20500650 26000520 TRUE FALSE 24007978.23 21322883.07 22516342.77 20440699.06 21841010.48 22813787.79 22369250.54 23060201.28 21660865.24 1.108357305 0.984396645 1.039494153 0.943669555 1.008316622 1.053226062 1.032703463 1.064602038 1 24.36858754 2.250839981 24.77268287 1.039997599 1.01218385 0.044241911 0.044609245 507.0551185 1022942.129 0.014307564 0.0118786 178.1722158 -2.250839981 -0.027813749 AASAPAKES(ph)PRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AASAPAKESPRK 12 2 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 AASAPAKES(1)PRK;AASAPAKES(1)PRK;AASAPAKES(1)PRK;AASAPAKES(1)PRK;AASAPAKES(1)PRK 140.22 3.10E-05 5304580000 7779420 4204030 5393580 5024200 5891120 4082280 7021520 5103790 7384780 TRUE FALSE 7292519.989 4515300.755 5521518.265 5153129.478 5428455.199 5260767.966 5968708.261 5741009.416 6152212.51 1.185349169 0.733931207 0.897484971 0.837605897 0.882358207 0.855101796 0.970172641 0.933161754 1 22.55267391 1.704655187 6.76253204 0.963343345 0.876595748 0.051244977 0.115716103 0.286477574 30.04717266 0.052707028 0.027199218 50.65883373 -1.704655187 -0.086747597 AASDGQYENQS(ph)PEATSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AASDGQYENQSPEATSPR 18 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 AASDGQYENQS(1)PEATSPR 181.32 1.13E-14 0 36683 38484 36295 33539 35165 30359 39882 33731 51550 TRUE FALSE 34387.07651 41333.3954 37155.93454 34399.66752 32403.28275 39123.15046 33902.06435 37942.3896 42945.97197 0.800705513 0.96245104 0.865178568 0.800998695 0.754512734 0.91098533 0.78941197 0.88349123 1 15.3902352 0.976219654 23.00324664 1.000000004 0.850430319 0.391209888 0.061709468 856.5569199 828568.3607 0.060831217 0.015207804 9.467158627 -0.976219654 -0.149569685 AASDIAMTELPPTHPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AASDIAMTELPPTHPIR 17 0 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 104.26 0.0018473 0 249560 265850 249510 255920 284220 231380 274580 202370 204020 FALSE TRUE 233940.4851 285533.8106 255428.495 262487.3405 261898.5077 298175.6499 233409.2781 227636.34 169967.744 1.376381657 1.679929403 1.502805703 1.544336204 1.540871824 1.754307275 1.373256317 1.339291413 1 17.37490146 1.005688705 1.447995055 1.007624335 1.56721651 0.719870228 0.110327358 0.201324164 0.861856234 0.093423635 0.027851821 10.13184891 -1.005688705 0.559592175 AASDPLLS(ph)SVSPAVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AASDPLLSSVSPAVSK 16 0 P19532 P19532 TFE3 Transcription factor E3 1 AASDPLLS(0.743)S(0.059)VS(0.198)PAVSK 146.2 1.20E-06 84675000 235970 167140 196740 200310 206730 178740 232330 173310 211150 TRUE FALSE 221201.0589 179515.2195 201406.7657 205450.2937 190494.2597 230339.3364 197494.2733 194948.135 175907.7009 1.257483656 1.02050802 1.144957069 1.167943715 1.082921661 1.309432931 1.122715335 1.108241049 1 17.42445912 0.862061418 2.628939781 1.000360666 1.146886135 0.268056394 0.081426461 0.777571798 10.44378854 0.074289607 0.019791754 7.278827343 -0.862061418 0.146525469 AASDPLLSSVS(ph)PAVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AASDPLLSSVSPAVSK 16 0 P19532 P19532 TFE3 Transcription factor E3 1 AASDPLLS(0.391)S(0.184)VS(0.425)PAVSK;AASDPLLS(0.038)S(0.025)VS(0.937)PAVSK;AASDPLLS(0.083)S(0.047)VS(0.869)PAVSK 235.95 1.07E-19 365443000 678410 529180 636550 604370 596540 517200 639100 538180 604170 TRUE FALSE 635949.5291 568361.0378 651649.2666 619879.1574 549690.1547 666507.244 543272.8881 605372.9577 503330.1239 1.263483942 1.129201315 1.294675672 1.231555848 1.092106609 1.324195021 1.079356991 1.2027354 1 18.94114542 0.26830769 0.492124648 0.984398593 1.219110226 0.39766814 0.080538947 2.701343765 1.000593689 0.162705069 0.038024055 1.854845284 -0.26830769 0.234711633 AASEQQADTSGGDS(ph)PKDESKPPFSYAQLIVQAISSAQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AASEQQADTSGGDSPKDESKPPFSYAQLIVQAISSAQDR 39 2 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 AASEQQADT(0.124)S(0.124)GGDS(0.753)PKDESKPPFSYAQLIVQAISSAQDR 176.74 2.04E-21 45306000 90042 36594 49265 45869 57450 42030 71335 39275 72821 TRUE FALSE 84406.43195 39303.45784 50433.58906 47046.0762 52938.10874 54163.3787 60638.97899 44178.5702 60666.70466 1.391313941 0.647858789 0.831322376 0.775484287 0.872605642 0.892802386 0.999542984 0.728217734 1 15.88861733 2.224934309 3.772870209 0.916424822 0.852287303 0 0.207754984 1.206928982 37.32957172 0.075116661 0.056395478 167.8550103 -2.224934309 -0.06413752 AASGEDSTEEALAAAAAPWEGGPVPGVDRS(ph)PFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AASGEDSTEEALAAAAAPWEGGPVPGVDRSPFAK 34 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 1 AASGEDSTEEALAAAAAPWEGGPVPGVDRS(1)PFAK;AASGEDSTEEALAAAAAPWEGGPVPGVDRS(1)PFAK;AASGEDSTEEALAAAAAPWEGGPVPGVDRS(1)PFAK 225.51 1.11E-36 286716000 179200 133967 161723 187247 214281 133032 164711 139058 208075 TRUE FALSE 167984.1919 143886.0561 165559.1459 192052.075 197452.2346 171436.1788 140014.1147 156419.6974 173345.9383 0.969069097 0.8300515 0.955079465 1.107912172 1.139064674 0.988982958 0.807715001 0.902355711 1 17.40329451 -2.156615993 7.977145626 1.884934789 0.950161761 0.000246525 0.105124916 0.13065354 0.002565133 0.008037977 0.026156045 0.006972427 2.156615993 -0.934773028 AASIENVLQDS(ph)SPEHCGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AASIENVLQDSSPEHCGR 18 0 K7EPJ5;O60291-4;O60291;O60291-3;O60291-2 K7EPJ5 MGRN1 E3 ubiquitin-protein ligase MGRN1 1 AASIENVLQDS(0.621)S(0.379)PEHCGR 81.373 0.0045432 64642000 33421 37745 32064 37016 44711 24972 39522 34379 36436 TRUE FALSE 31329.23927 40539.67907 32824.57322 37965.89323 41199.57842 32181.01101 33596.043 38671.29383 30354.59621 1.032108582 1.33553676 1.081370775 1.250746113 1.357276444 1.0601693 1.106786029 1.273984788 1 14.88962736 -4.017875056 0.288441066 0.242016598 1.199116237 0.188724876 0.116869246 213.2366109 3.429875054 95.83337561 0.119561439 9.60E-05 4.017875056 0.957099639 AASIENVLQDSS(ph)PEHCGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AASIENVLQDSSPEHCGR 18 0 K7EPJ5;O60291-4;O60291;O60291-3;O60291-2 K7EPJ5 MGRN1 E3 ubiquitin-protein ligase MGRN1 1 AASIENVLQDS(0.119)S(0.881)PEHCGR 114.92 0.0001315 94456000 78995 86611 83227 78190 97278 75040 96363 79480 87216 TRUE FALSE 74050.84396 93023.76856 85201.18374 80196.48778 89638.17828 96702.82983 81914.26274 89403.25296 72659.08616 1.019154628 1.280277161 1.17261568 1.103736532 1.233681608 1.330911727 1.127378103 1.230448354 1 16.1488556 -0.199846979 8.174284975 0.999999999 1.194597803 0.29701005 0.089921585 0 0 0.078541027 0.018512298 0.631179698 0.199846979 0.194597803 AASIFGGAKPVDTAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AASIFGGAKPVDTAAR 16 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 185.63 1.49E-09 1780160000 2178200 2317300 2294300 2067240 2615700 1896100 2716300 2154100 2874100 FALSE TRUE 2041870.35 2488875.303 2348721.879 2120288.878 2410273.473 2443473.289 2309016.032 2423044.127 2394394.143 0.852771193 1.039459318 0.980925336 0.885522079 1.006631878 1.020497522 0.964342499 1.011965442 1 21.19122922 AASLT(ph)EDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.294)LT(0.706)EDR 169.77 0.0033431 1001400000 746600 571730 715970 558290 478560 607290 691520 576520 481990 TRUE FALSE 699871.6387 614061.4841 732953.1465 572616.6666 440975.828 782604.7645 587832.9958 648499.7911 401542.7552 1.742956708 1.529255543 1.825342724 1.426041584 1.09820392 1.948994856 1.463936251 1.615020524 1 18.61519408 -2.624073873 0.3537378 6.13E-16 1.613211874 0.375427477 0.235072684 70.94567528 2.704026174 54.5721455 0.168730712 0.002376436 2.624073873 1.613211874 AASLT(ph)EDRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.16)LT(0.84)EDRDR;AAS(0.484)LT(0.516)EDRDR 158.3 5.11E-05 2519850000 3181500 3146320 3391760 2763450 2839210 2426760 3154190 2960160 4296000 TRUE FALSE 2982375.594 3379276.807 3472214.149 2834364.806 2616229.899 3127326.217 2681248.492 3329742.492 3578969.847 0.833305594 0.944203766 0.970171389 0.791949898 0.731000822 0.873806249 0.749167667 0.930363382 1 21.77111296 3.236007418 24.99990355 0.824704242 0.929714027 0.083280722 0.088821775 88.39876548 865567.2067 0.022999495 0.028713803 1721.897987 -3.236007418 0.105009785 AASLTEDRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AASLTEDRDR 10 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;; 188.99 9.67E-07 4757860000 2137640 2864210 2529070 2812070 3020820 2319610 2866810 2644700 2930000 FALSE TRUE 2003848.928 3076279.089 2589060.735 2884232.477 2783576.983 2989243.751 2436958.455 2974896.617 2440964.071 0.820925204 1.260272171 1.060671382 1.181595629 1.14035967 1.224616038 0.998359002 1.218738388 1 21.21901963 -1.671836656 3.845894837 0.993415441 1.120394999 0.067176152 0.13012175 0.006687435 0.000570627 0.114688463 0.025716419 0.021289396 1.671836656 0.126979558 AASPPASAS(ph)DLIEQQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AASPPASASDLIEQQQK 17 0 Q5VSL9;Q5VSL9-2;Q5VSL9-3 Q5VSL9 STRIP1 Striatin-interacting protein 1 1 AAS(0.279)PPAS(0.33)AS(0.391)DLIEQQQK 55.755 0.074909 145540000 123570 176250 156550 176250 202510 176120 190960 167080 212170 TRUE FALSE 115835.9743 189299.7334 160263.4399 180772.8734 186605.6815 226962.9849 162327.3208 187940.3058 176757.4563 0.655338545 1.070957556 0.906685598 1.022717101 1.055716038 1.28403627 0.918361942 1.063266635 1 17.43141155 4.742068618 24.85039148 1.033164349 0.65533839 0.577184175 0.103368417 234.0240125 1657728.216 0.023789026 0.17477607 55216.46733 -4.742068618 -0.377825959 AASPYSQRPAS(ph)PTAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AASPYSQRPASPTAIR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 AASPY(0.001)S(0.025)QRPAS(0.959)PT(0.015)AIR;AASPYS(0.114)QRPAS(0.805)PT(0.08)AIR;AASPYSQRPAS(0.951)PT(0.048)AIR;AASPYS(0.003)QRPAS(0.932)PT(0.065)AIR 171.26 1.31E-08 314692000 263510 281562 260021 266305 288476 243894 298769 256611 322714 TRUE FALSE 247017.3795 302409.1434 266188.8209 273138.8372 265820.2586 314302.2385 253971.3621 288649.4482 268850.9486 0.918789317 1.124820816 0.990098128 1.015948943 0.988727248 1.169057577 0.944654886 1.073641175 1 18.03644704 -1.055157034 4.147946666 0.999996179 1.031718635 0.011277733 0.077064069 2.38E-06 5.42E-07 0.065233975 0.015373943 0.088073036 1.055157034 0.031722456 AASSDQLRDNS(ph)PPPAFKPEPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AASSDQLRDNSPPPAFKPEPPK 22 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 AASSDQLRDNS(1)PPPAFKPEPPK;AASSDQLRDNS(1)PPPAFKPEPPK;AASSDQLRDNS(1)PPPAFKPEPPK;AASSDQLRDNS(1)PPPAFKPEPPK;AASSDQLRDNS(1)PPPAFKPEPPK;AASSDQLRDNS(1)PPPAFKPEPPK 209.62 4.31E-23 6849790000 5314980 3596660 4196230 4137130 5856260 2854190 4565260 3652250 9462930 TRUE FALSE 4982324.889 3862960.449 4295766.557 4243295.76 5396332.963 3678148.319 3880741.645 4108241.452 7883505.85 0.631993555 0.490005401 0.544905609 0.53824984 0.684509286 0.466562515 0.492260895 0.52111859 1 22.91040592 -1.801533429 2.675561405 1.136007393 0.537966811 0.819732716 0.066779669 8689425.479 6149708.792 7663282.887 0.015404099 0.01579307 1.801533429 -0.598040582 AASSELPADISKPWIPSSPAPSSENGGPAS(ph)PGLPAEASGSGPGS(ph)PHLHPPDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AASSELPADISKPWIPSSPAPSSENGGPASPGLPAEASGSGPGSPHLHPPDK 52 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 AASSELPADISKPWIPSSPAPSSENGGPAS(1)PGLPAEAS(0.113)GS(0.264)GPGS(0.623)PHLHPPDK 88.983 2.16E-07 63160000 45055 41995 39975 48711 46125 29132 35303 25876 30801 TRUE FALSE 42235.08798 45104.3535 40923.22588 49961.00673 42502.52856 37541.93548 30009.64289 29106.67556 25660.11412 1.645943108 1.75776122 1.594818546 1.947029795 1.656365531 1.463046318 1.169505434 1.134315905 1 14.64723997 1.870998061 1.702783761 1.066303407 1.723291669 0.896704055 0.096622437 0.103703237 0.565794852 0.063671045 0.028308295 74.30158198 -1.870998061 0.656988263 AASSELPADISKPWIPSSPAPSSENGGPAS(ph)PGLPAEASGSGPGSPHLHPPDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AASSELPADISKPWIPSSPAPSSENGGPASPGLPAEASGSGPGSPHLHPPDK 52 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 AASSELPADISKPWIPSSPAPSS(0.001)ENGGPAS(0.999)PGLPAEASGSGPGSPHLHPPDK 112.18 2.55E-10 211780000 94646 100200 87352 76847 121790 92596 157870 106920 161220 TRUE FALSE 88722.27581 107618.9123 89424.03069 78819.02412 112225.1047 119326.962 134198.8591 120269.1974 134311.3405 0.660571739 0.801264524 0.665796577 0.586838191 0.835559412 0.888435493 0.999162532 0.895450801 1 17.0352216 2.372858998 2.550100956 0.955589107 0.697558226 0.785300178 0.065306957 0.129671166 1.725602569 0.025738535 0.020212526 235.9711983 -2.372858998 -0.258030882 AASVAAATT(ph)SPTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AASVAAATTSPTPR 14 0 Q9Y2D9 Q9Y2D9 ZNF652 Zinc finger protein 652 1 AASVAAAT(0.001)T(0.958)S(0.04)PTPR 162.37 4.97E-05 203440000 334680 289030 325380 287860 340750 275680 367230 282500 352900 TRUE FALSE 313732.9762 310430.0819 333098.1673 295246.9749 313988.8695 355264.3407 312167.2707 317770.7469 293998.7102 1.067123648 1.055889265 1.132991934 1.004245817 1.067994038 1.208387413 1.061798096 1.080857622 1 18.1654503 0.638009288 2.223414775 1.000053458 1.088330396 0.196893933 0.053827201 3.804896879 21.34497921 0.048824142 0.013245126 4.345195172 -0.638009288 0.088276938 AASVAAATTS(ph)PTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AASVAAATTSPTPR 14 0 Q9Y2D9 Q9Y2D9 ZNF652 Zinc finger protein 652 1 AASVAAAT(0.085)T(0.419)S(0.493)PT(0.002)PR;AASVAAATT(0.005)S(0.994)PTPR;AASVAAATT(0.001)S(0.997)PT(0.002)PR 227.91 1.94E-12 328070000 962440 882470 931590 857890 922300 804770 1003300 811230 985640 TRUE FALSE 902202.5984 947808.997 953687.7547 879904.9098 849866.2784 1037094.035 852864.4792 912513.8512 821130.3165 1.09873254 1.15427354 1.161432888 1.071577668 1.034995617 1.263007849 1.038646926 1.111289929 1 19.64725168 -0.88322067 0.296358744 0.934878068 1.139017829 0.234339265 0.066569142 17.64395634 1.397953188 1.053670167 0.072075455 0.130851688 0.88322067 0.204139761 AATAARPPAPPPAPQPPS(ph)PTPS(ph)PPRPTLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AATAARPPAPPPAPQPPSPTPSPPRPTLAR 30 2 Q96B36;Q96B36-3;H9KV91 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 2 AAT(0.006)AARPPAPPPAPQPPS(0.976)PT(0.02)PS(0.874)PPRPT(0.124)LAR;AATAARPPAPPPAPQPPS(0.97)PT(0.038)PS(0.992)PPRPTLAR;AATAARPPAPPPAPQPPS(0.993)PT(0.032)PS(0.964)PPRPT(0.011)LAR;AATAARPPAPPPAPQPPS(0.976)PT(0.059)PS(0.835)PPRPT(0.13)LAR 97.248 0.00035703 9854450000 258986 269161 261101 248460 257185 220854 293605 218820 259553 TRUE FALSE 242776.5286 289089.9605 267294.439 254835.9042 236986.7275 284610.9645 249581.6559 246140.1587 216231.9275 1.122759859 1.336943919 1.236146956 1.178530419 1.095983975 1.316230067 1.154231287 1.138315518 1 17.72222003 -0.269217664 0.284283916 0.916995911 1.25672166 0.405140066 0.077680463 6.902568485 0.731436077 0.658716153 0.101923847 0.538000075 0.269217664 0.339725748 AATAARPPAPPPAPQPPS(ph)PTPSPPRPT(ph)LAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AATAARPPAPPPAPQPPSPTPSPPRPTLAR 30 2 Q96B36;Q96B36-3;H9KV91 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 2 AATAARPPAPPPAPQPPS(0.884)PT(0.185)PS(0.319)PPRPT(0.612)LAR 70.151 0.0070258 483780000 242500 274490 266690 270540 266610 250820 311830 248410 280490 TRUE FALSE 227322.3579 294813.5252 273016.0127 277482.5144 245671.5261 323227.6623 265073.9864 279424.5353 233674.407 0.972816668 1.261642338 1.168360782 1.187474991 1.051341177 1.383239468 1.134373207 1.19578579 1 17.83414021 -1.382525128 5.626355617 0.999939355 1.180686695 0.181901885 0.110600675 7.33E-05 8.04E-06 0.093284067 0.021979902 0.04144526 1.382525128 0.180747339 AATAARPPAPPPAPQPPS(ph)PTPSPPRPTLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AATAARPPAPPPAPQPPSPTPSPPRPTLAR 30 2 Q96B36;Q96B36-3;H9KV91 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 AATAARPPAPPPAPQPPS(0.481)PT(0.481)PS(0.033)PPRPT(0.004)LAR;AATAARPPAPPPAPQPPS(0.989)PT(0.01)PSPPRPTLAR;AATAARPPAPPPAPQPPS(0.98)PT(0.02)PSPPRPTLAR 226.97 3.24E-35 1081400000 203775 230990 225075 227165 228817 174063 217090 203322 200326 TRUE FALSE 191021.0865 248092.7399 230413.8853 232994.4385 210846.6358 224312.1624 184539.3699 228707.1993 166890.2964 1.144590732 1.486561803 1.380630811 1.396093383 1.263384632 1.344069531 1.105752544 1.370404416 1 17.34854055 0.865637992 0.42281146 0.988923212 1.38825665 0.388616244 0.118247968 1.223664425 0.545283218 0.169665363 0.079593146 7.339018658 -0.865637992 0.399333438 AATAARPPAPPPAPQPPSPT(ph)PSPPRPTLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AATAARPPAPPPAPQPPSPTPSPPRPTLAR 30 2 Q96B36;Q96B36-3;H9KV91 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 AATAARPPAPPPAPQPPS(0.411)PT(0.573)PS(0.016)PPRPTLAR 166.27 1.35E-10 481840000 54357 46993 48345 50457 51836 40430 54007 42933 43132 TRUE FALSE 50954.8924 50472.41062 49491.76623 51751.81204 47765.00966 52101.48467 45909.15173 48293.27956 35932.99056 1.418053204 1.404625939 1.377335019 1.440231143 1.32928011 1.449962385 1.277632366 1.343981639 1 15.13302139 -0.333548147 0.432005966 0.922233615 1.409771275 0.883194838 0.044616583 1.888348533 0.364406679 0.263930047 0.023271151 0.463929355 0.333548147 0.48753766 AATEALGEKS(ph)PDSATVSGYDIMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AATEALGEKSPDSATVSGYDIMK 23 1 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;H7C3G6;J3QRL2;K7EL39;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 AATEALGEKS(0.983)PDS(0.017)ATVSGYDIMK;AATEALGEKS(0.997)PDS(0.001)AT(0.002)VSGYDIMK 202.14 1.29E-24 394790000 471040 271073 336630 319367 363023 232450 428490 293588 586450 TRUE FALSE 441558.4472 291143.527 344615.0226 327562.4979 334512.6379 299554.5415 364241.9024 330243.1081 488567.7064 0.903781485 0.595912344 0.705357759 0.670454665 0.684680206 0.613128002 0.745530041 0.675941336 1 18.89819898 -0.63030373 0.950340987 1.015555392 0.68828206 0.550276603 0.084838689 27.80197196 14.01810754 1.634053823 0.023204353 0.234258992 0.63030373 -0.327273332 AATESVPCS(ph)PSPLAGEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AATESVPCSPSPLAGEIR 18 0 J3QKZ5;J3QS16;Q8N9M1-2;Q8N9M1;J9JIE4 J3QKZ5 C19orf47 Uncharacterized protein C19orf47 1 AATES(0.014)VPCS(0.974)PS(0.011)PLAGEIR;AATES(0.001)VPCS(0.964)PS(0.035)PLAGEIR 194.27 8.52E-15 116019000 173859 166561 180833 177536 178575 193049 214830 146116 172050 TRUE FALSE 162977.4755 178893.3497 185122.4442 182091.8743 164550.4398 248779.1124 182618.2359 164358.9042 143333.7435 1.137048901 1.248089566 1.29154824 1.27040479 1.148023039 1.735663259 1.274077069 1.146686748 1 17.12901876 1.048356703 3.291172133 1.004778238 1.307776314 0.271447304 0.164658161 0.276037974 6.414041861 0.150160379 0.039303826 11.17780947 -1.048356703 0.302998076 AATFGLILDDVSLTHLTFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AATFGLILDDVSLTHLTFGK 20 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0 P35232 PHB Prohibitin 0 ;; 331.38 7.64E-80 364022000 1087190 1295390 1138360 1107890 1796660 1131960 1349460 1422930 1610000 FALSE TRUE 1019144.719 1391302.023 1165362.437 1136320.333 1655557.571 1458738.476 1147121.001 1600585.943 1341280.599 0.759829613 1.037293781 0.868843132 0.847190613 1.234311129 1.087571443 0.855243117 1.193326694 1 20.35517965 2.787567996 24.99923718 1.048935072 0.903215659 0.363191758 0.124487422 545.4754727 278252.3131 0.037524851 0.039801054 613.1517832 -2.787567996 -0.145719413 AATSDLEHYDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AATSDLEHYDK 11 0 P80303-2;P80303;E9PKG6;Q2L696;E9PLR0;E9PLE9;A0A2R8Y6G7 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 109.6 0.0019071 317170000 568790 700870 534850 621680 777910 443170 690570 666130 562700 FALSE TRUE 533190.4492 752763.1441 547536.8946 637633.3613 716816.0865 571105.9847 587025.4394 749297.7968 468781.7348 1.137395956 1.605785994 1.167999634 1.360192418 1.529104129 1.218276956 1.25223616 1.598393754 1 18.83855683 -1.637134196 3.067633019 0.972659416 1.354911507 0.30198671 0.171286914 50809108.52 64680675.21 11284817.55 0.037618756 0.023060345 1.637134196 0.382252092 AATTATPAATT(ph)SPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AATTATPAATTSPK 14 0 Q92766;Q92766-2;Q92766-5;Q92766-3;A0A087X055 Q92766 RREB1 Ras-responsive element-binding protein 1 1 AATTATPAAT(0.003)T(0.72)S(0.277)PK 216.54 6.81E-11 102170000 354840 193030 244790 219740 188110 161360 301350 165650 196240 TRUE FALSE 332631.1978 207322.142 250596.5344 225378.9004 173336.5994 207942.0125 256165.3651 186331.7671 163486.2762 2.034612357 1.268131777 1.532829178 1.378579937 1.060251682 1.271923352 1.566892164 1.139739502 1 17.31881001 4.741388542 24.71681436 1.325110019 2.034612657 0.605117218 0.188782339 160.911497 1406322.402 0.042719461 0.297410377 55130.06972 -4.741388542 0.709502638 AATTATPAATTS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AATTATPAATTSPK 14 0 Q92766;Q92766-2;Q92766-5;Q92766-3;A0A087X055 Q92766 RREB1 Ras-responsive element-binding protein 1 1 AATTATPAATTS(1)PK;AATTATPAATT(0.037)S(0.963)PK;AATTATPAATT(0.008)S(0.992)PK 228.73 1.62E-12 412600000 1356990 758560 939230 799690 699370 628790 1164030 635430 737880 TRUE FALSE 1272058.418 814724.5717 961508.9791 820211.3993 644444.3013 810311.4654 989494.5078 714764.8343 614723.0611 2.069319501 1.325352217 1.564133575 1.334277907 1.048348992 1.318173201 1.609659 1.162742834 1 19.22957708 6.696866765 1.432345099 1.336569432 200 0.574086655 0.203174357 310.1800494 3.036289567 0.05284473 200229.6565 4975844.101 -6.696866765 198.6634306 AAVAGEDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 168.23 0.00013814 2541050000 2118440 2382530 2261740 2184120 2713430 1941990 2599260 2259160 2901700 FALSE TRUE 1985850.622 2558935 2315389.541 2240168.217 2500328.153 2502610.987 2209525.093 2541221.099 2417387.524 0.821486254 1.058553904 0.957806524 0.92668974 1.034310026 1.035254365 0.914013608 1.051226199 1 21.20501734 4.753054124 24.78606273 0.991853111 0.821486121 0.539988559 0.050762208 1889.833628 3231836.157 0.011606919 0.255210183 56630.98606 -4.753054124 -0.170366991 AAVEWFDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAVEWFDGK 9 0 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;A0A0D9SFL3;C9JGE3;Q01844-2;H7BY36 B0QYK0 EWSR1 RNA-binding protein EWS 0 ; 172.21 0.0016369 119820000 572610 487600 514150 492090 533960 426320 585960 473270 529620 FALSE TRUE 536771.3622 523702.4113 526345.8808 504717.8625 492024.9355 549391.6633 498100.7378 532358.8013 441223.0005 1.216553447 1.186933616 1.192924848 1.14390651 1.115138909 1.245156446 1.128909275 1.206552697 1 18.75114847 -4.181698538 0.337960679 1.93E-11 1.184686769 0.654844828 0.040732785 121.9145837 1.773449904 86.27666961 0.030006474 6.58E-05 4.181698538 1.184686769 AAVEWFDGKDFQGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAVEWFDGKDFQGSK 15 1 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;A0A0D9SFL3;C9JGE3;Q01844-2;H7BY36 B0QYK0 EWSR1 RNA-binding protein EWS 0 ; 183.7 4.51E-07 3474300000 2518850 1978480 2291590 2203420 2476610 1659660 2845200 1947410 3792500 FALSE TRUE 2361199.675 2124968.718 2345947.597 2259963.488 2282107.041 2138776.9 2418588.674 2190548.425 3159507.25 0.747331621 0.67256333 0.742504261 0.715289857 0.722298403 0.67693369 0.765495529 0.693319639 1 21.59126815 -4.999988203 0.472717379 8.481243881 0.714238856 0.894762203 0.030451124 470.197235 2.478058799 3701.860345 0.013711497 1.00E-05 4.999988203 -7.767005025 AAVGQES(ph)PGGLEAGNAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 318.93 2.08E-58 1332060000 3056000 2499950 2825220 2681760 2940700 2486030 3890450 2984770 3789510 TRUE FALSE 2864730.415 2685048.899 2892235.553 2750578.502 2709749.284 3203706.504 3307113.14 3357425.105 3157016.3 0.907417049 0.85050207 0.916129433 0.871258885 0.858326035 1.014789345 1.047543891 1.063480447 1 21.59013028 2.172297044 5.189963718 1.03897752 0.881008456 0.895521312 0.025612237 0.054691952 2.80727065 0.009160039 0.006755885 148.6952324 -2.172297044 -0.157969064 AAVGRPLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAVGRPLDK 9 1 Q8WUM4;Q8WUM4-2;A0A3B3IT07;Q8WUM4-3;C9IZF9;F8WEQ7;F8WBR8 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 65.347 0.060937 525110000 367080 443890 471160 470420 621790 484410 717650 621860 682420 FALSE TRUE 344105.1181 476756.0775 482336.1377 482491.7736 572957.1216 624251.3033 610045.0448 699500.5899 568519.6934 0.605265081 0.838592019 0.848407088 0.848680845 1.007805232 1.098029339 1.073041184 1.230389374 1 19.1168508 2.936727515 0.725596807 1.129805308 0.72940283 0.771818987 0.083249123 0.321949212 0.374995307 0.0517034 0.064286946 864.4253905 -2.936727515 -0.400402478 AAVGRPLDKHEGALETLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAVGRPLDKHEGALETLLR 19 2 Q8WUM4;Q8WUM4-2;A0A3B3IT07;Q8WUM4-3;C9IZF9;F8WEQ7;F8WBR8 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 221.24 1.63E-19 2158880000 966660 1038180 1046620 1109150 1314340 864450 1276920 999440 1452690 FALSE TRUE 906158.4761 1115047.927 1071446.321 1137612.667 1211117.038 1114002.682 1085457.7 1124222.284 1210226.654 0.748751048 0.921354627 0.88532699 0.939999679 1.000735717 0.920490949 0.896904474 0.92893532 1 20.20684583 5.443838296 1.386687481 0.931643046 2.56E-15 0.688933687 0.03913228 4.767449806 1.967765618 0.010404513 10.01804117 277867.8472 -5.443838296 -0.931643046 AAVHLEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AAVHLEGK 8 0 P18206;P18206-2 P18206 VCL Vinculin 0 ;; 91.065 0.012752 591040000 3271500 3155410 3034680 2873350 3277600 2169970 3535800 3238500 3013910 FALSE TRUE 3066742.655 3389039.84 3106664.043 2947085.026 3020190.517 2796405.112 3005639.615 3642833.854 2510868.95 1.221386984 1.349747799 1.237286415 1.17373112 1.202846734 1.113720058 1.197051568 1.450825959 1 21.2597553 3.54611483 3.302000186 1.194792108 1.294145513 0.104350212 0.115024504 0.482979436 10.33211956 0.029416224 0.046788664 3516.534071 -3.54611483 0.099353404 AAVLS(ph)DS(ph)EDEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AAVLSDSEDEEK 12 0 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 AAVLS(1)DS(1)EDEEK;AAVLS(1)DS(1)EDEEK 209.84 7.38E-08 145393000 1059150 528460 718070 657360 611550 597950 945700 579860 668140 TRUE FALSE 992859.6921 567587.7283 735102.9595 674228.9705 563521.3299 770568.4581 803901.0644 652256.7974 556623.1177 1.783719829 1.019698446 1.320647555 1.211284528 1.012392968 1.384363016 1.444246635 1.171810471 1 19.0863413 4.752103027 24.4869674 1.223691445 1.783720323 0.574558367 0.157411031 1380.560624 2496228.558 0.037835615 0.731912344 56507.10103 -4.752103027 0.560028878 AAVPSGAS(ph)TGIYEALELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AAVPSGASTGIYEALELR 18 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798;P13929-3;P13929-2;P13929;E5RGZ4;P09104-2;F5H0C8;P09104;E5RI09;E5RG95;K7EPM1;K7EKN2;F5H1C3 P06733 ENO1;ENO3;ENO2 Alpha-enolase;Enolase;Beta-enolase;Gamma-enolase 1 AAVPSGAS(0.5)T(0.5)GIYEALELR;AAVPSGAS(0.985)T(0.015)GIYEALELR;AAVPS(0.002)GAS(0.973)T(0.025)GIYEALELR;AAVPSGAS(0.966)T(0.034)GIYEALELR 274.45 5.12E-39 450822000 63084 80963.2 68541.6 80071.3 85518.2 55081.4 82117.5 69889.4 90487.7 TRUE FALSE 59135.68505 86957.79957 70167.43912 82126.06512 78801.94554 70982.50601 69804.74322 78615.24544 75384.7183 0.784451894 1.153520256 0.930791289 1.089425907 1.045330504 0.941603386 0.925980023 1.042853873 1 16.20198448 2.23484208 24.99559313 0.965504543 1.016041822 0 0.102929983 305.1208982 2050963.471 0.034340218 0.026354555 171.7283829 -2.23484208 0.050537279 AAVPSGASTGIYEALELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AAVPSGASTGIYEALELR 18 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798;P13929-3;P13929-2;P13929;E5RGZ4;P09104-2;F5H0C8;P09104;E5RI09;E5RG95;K7EPM1;K7EKN2;F5H1C3 P06733 ENO1;ENO3;ENO2 Alpha-enolase;Enolase;Beta-enolase;Gamma-enolase 0 ;;; 236.3 1.89E-23 803020000 43487.5 55314 40331.1 37447.5 54527 34883.1 54522 41599.7 59176 FALSE TRUE 40765.695 59409.50611 41287.77274 38408.46625 50244.66937 44953.28469 46346.93226 46793.51412 49299.14331 0.826904734 1.205081917 0.83749473 0.779089933 1.019179361 0.911847178 0.940116382 0.949174995 1 15.58927496 3.869991321 7.821785705 0.91668775 1.039742429 0.101874063 0.113984474 0.384763211 24.99474379 0.026702175 0.048363857 7412.954264 -3.869991321 0.123054679 AAVPSGASTGIYEALELRDNDKTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AAVPSGASTGIYEALELRDNDKTR 24 2 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 ;;; 272.27 3.55E-52 1476710000 411469 444069 933610 837160 793510 1009130 697240 190893 328465 FALSE TRUE 385715.8898 476948.3308 955755.6701 858642.9429 731190.9255 1300449.449 592695.3349 214726.4113 273642.0695 1.40956356 1.7429642 3.492721977 3.137832368 2.672070587 4.752373973 2.165951076 0.784698097 1 18.06193052 4.264000575 3.530627322 2.764772291 1.494125781 0.09916588 1.156436611 0.420547862 10.77685419 0.273760713 0.814557858 18365.40774 -4.264000575 -1.270646511 AAVS(ph)PQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AAVSPQKR 8 1 E9PJF5;G5E9I4;Q9HCU9 E9PJF5 BRMS1 Breast cancer metastasis-suppressor 1 1 AAVS(1)PQKR;AAVS(1)PQKR;AAVS(1)PQKR;AAVS(1)PQKR 156.48 0.00024026 1812690000 2378990 2083710 2201290 2103900 2454760 1688400 2717830 1973590 2110690 TRUE FALSE 2230093.263 2237990.056 2253505.638 2157889.636 2261973.052 2175813.671 2310316.623 2219997.056 1758402.203 1.268249811 1.272740703 1.281564385 1.227187746 1.286379787 1.23738111 1.313872684 1.262508118 1 20.74583367 0.938643391 23.63420248 1 1.271819792 0.92418496 0.024191439 4749.11617 1829333.899 0.021293607 0.005323402 8.682472 -0.938643391 0.271819792 AAVT(ph)PGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AAVTPGKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AAVT(1)PGKK;AAVT(1)PGKK;AAVT(1)PGKK;AAVT(1)PGKK;AAVT(1)PGKK;AAVT(1)PGKK 93.096 0.0066285 6696400000 22341300 13510600 16516400 14079800 18308000 7676280 25373900 12436800 39532900 TRUE FALSE 20942997.91 14510938.88 16908176.81 14441111.51 16870163.53 9892297.422 21569319.25 13989561.86 32934603.6 0.635896462 0.440598559 0.513386377 0.438478376 0.512232172 0.300361818 0.654913583 0.424767883 1 24.97310085 -1.480697555 0.68953664 1.224513899 0.48788525 0.706258093 0.103144649 47.21003287 8.151330032 19.01725743 0.03293668 0.033059969 1.480697555 -0.736628649 AAVVT(ph)SPPPTTAPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 127.83 0.00027864 829100000 980190 870060 987280 1177670 1259640 677480 947840 749350 882630 TRUE FALSE 918841.6576 934480.1477 1010698.748 1207891.006 1160712.956 873057.478 805720.1913 842907.997 735313.351 1.249591968 1.270859759 1.374514343 1.6426888 1.578528329 1.187327113 1.095750798 1.146324891 1 19.48799965 2.059960087 6.752364165 1.103294847 1.405389381 0.614571636 0.125765433 0.166052944 14.75392602 0.052263346 0.038298214 114.8048107 -2.059960087 0.302094534 AAWEDPVEWVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AAWEDPVEWVR 11 0 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4 Q8NEY1-5 NAV1 Neuron navigator 1 0 ;; 130.66 0.00051094 88420000 188258 224486 244610 200993 233783 190747 231723 193613 264434 FALSE TRUE 176475.2678 241107.177 250412.2647 206150.8207 215422.6262 245812.5624 196978.2874 217786.0092 220298.2571 0.801074281 1.094457942 1.136696531 0.935780534 0.977868046 1.1158171 0.894143649 0.988596152 1 17.74909856 1.726792065 24.99999995 0.954721061 1.030469893 0.024058037 0.102135762 2.02508401 4282.558785 0.046310283 0.025681369 53.30796029 -1.726792065 0.075748832 AAWEVDSGRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AAWEVDSGRR 10 1 B7Z9I1;Q5T4U5;P11310;P11310-2 B7Z9I1 ACADM "Medium-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 ;;; 149.17 3.82E-05 1213610000 464851 587011 448611 447271 812640 434498 403316 572261 1050140 FALSE TRUE 435756.8057 630473.9052 459252.2648 458748.7311 748818.5324 559930.5191 342842.51 643709.0456 874864.8498 0.498084711 0.720652916 0.524940812 0.524365256 0.855924812 0.640019449 0.39188054 0.735781127 1 19.73870064 0.988729227 24.50281162 1.000000013 0.595887882 0.508979263 0.127569825 340.7959535 740897.0928 0.120629145 0.030157286 9.743819429 -0.988729227 -0.404112132 AAY(ph)GDLS(ph)SEEEEENEPESLGVVYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AAYGDLSSEEEEENEPESLGVVYK 24 0 O15541 O15541 RNF113A RING finger protein 113A 2 AAY(0.7)GDLS(0.65)S(0.65)EEEEENEPESLGVVYK 115.55 0.018807 61078000 66846 60519 56220 59299 61128 42156 60284 54966 73507 TRUE FALSE 62662.22818 64999.88973 57553.56495 60820.71273 56327.25346 54325.75285 51244.97385 61828.6261 61238.20683 1.023253806 1.061427058 0.939830997 0.993182457 0.919805729 0.887121875 0.836813756 1.009641355 1 15.90214442 3.601783594 0.968313593 0.912972972 1.04915261 0.314732336 0.056452391 0.5818599 1.071345421 0.021340819 0.056756391 3997.455093 -3.601783594 0.136179638 AAYEAELGDAR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 196.52 1.40E-07 3698360000 3698720 4437890 4184860 4108580 4222000 3661190 4523310 3863520 4471020 FALSE TRUE 3467223.718 4766475.993 4284126.855 4214013.119 3890421.151 4718116.119 3845081.658 4345888.977 3724777.878 0.93085382 1.279667177 1.150169754 1.131346152 1.044470644 1.266683886 1.032298243 1.166751178 1 21.82872296 -0.350914126 0.425491903 0.971111228 1.149334264 0.089484493 0.106984568 13.41849243 2.499234768 0.690120534 0.05996311 0.445744378 0.350914126 0.178223035 AAYEAELGDARK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AAYEAELGDARK 12 1 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;; 156.36 0.00010369 3366960000 2169710 2485110 2242290 2404670 2847980 1873090 2895130 2140560 3951500 FALSE TRUE 2033911.724 2669110.13 2295478.178 2466377.903 2624311.139 2413820.676 2461032.134 2407813.628 3291969.122 0.617840462 0.8107944 0.697296388 0.749210522 0.797185831 0.733245236 0.74758664 0.731420478 1 21.65051937 -4.999999999 0.453503868 6.994674216 0.738278616 0.711035101 0.052938807 702.0200763 4.005148196 4230.299615 0.02474648 1.00E-05 4.999999999 -6.256395601 ACANPAAGSVILLENLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ACANPAAGSVILLENLR 17 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 189.09 1.99E-17 0 101930 146030 97530 100780 159180 67620 124870 118050 134030 FALSE TRUE 95550.38325 156842.2131 99843.45766 103366.1854 146678.6449 87140.79628 106146.9027 132788.8024 111659.5271 0.855729786 1.40464694 0.894177687 0.925726519 1.313624092 0.780415237 0.950630058 1.189229489 1 16.76874683 3.835512091 8.001893571 0.998212605 1.165831593 0.053654171 0.198605166 0.516202564 34.36590956 0.04674109 0.08456925 6847.185461 -3.835512091 0.167618989 ACDEGHCTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ACDEGHCTAK 10 0 A0A0A0MT83;P26440;A0A0S2Z4K7;P26440-2;H0YLC3 A0A0A0MT83 IVD "Isovaleryl-CoA dehydrogenase, mitochondrial" 0 ;;;;; 135.86 0.00013302 948825000 2064620 1870419 1802345 1716548 2532240 1701559 1945827 2057720 2689470 FALSE TRUE 1935399.12 2008906.769 1845097.475 1760597.528 2333368.085 2192771.461 1654068.306 2314630.872 2240580.082 0.863793771 0.89660119 0.823490974 0.78577755 1.041412491 0.978662391 0.738232174 1.033049829 1 21.09544086 2.765984229 24.96711743 0.927091415 0.848292618 0.248621101 0.091309491 1458.335576 1327701.337 0.028408613 0.030126372 583.4239172 -2.765984229 -0.078798797 ACDLPAWVHFPDTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ACDLPAWVHFPDTER 15 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6 A0A499FIX8 ESYT2 Extended synaptotagmin-2 0 ; 127.88 7.55E-05 134171000 92481 96590 87337 98899 108722 85428 109453 91527 86793 FALSE TRUE 86692.77929 103741.6241 89408.67488 101436.9158 100183.4127 110089.6768 93041.53876 102954.3474 72306.6876 1.198959352 1.434744524 1.236520132 1.402870456 1.385534534 1.522537962 1.286762565 1.423856504 1 16.14184147 -1.164689983 4.848319447 0.999967859 1.360507511 0.577093156 0.097244287 3.04E-05 5.23E-06 0.084673585 0.019955979 0.068440003 1.164689983 0.360539652 ACESASHDNQSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ACESASHDNQSVR 13 0 Q8TBZ6 Q8TBZ6 TRMT10A tRNA methyltransferase 10 homolog A 0 ; 222.81 1.68E-11 565810000 264530 414720 390290 388930 408320 355560 384140 373950 383980 FALSE TRUE 247973.5395 445426.3003 399547.8631 398910.6023 376252.1943 458204.4 326541.7732 420638.4807 319891.2574 0.775180733 1.392430365 1.249011512 1.247019395 1.1761878 1.432375501 1.020789927 1.314942097 1 18.28722204 -1.087827052 4.855903744 0.999991865 1.218663413 0.093350732 0.189882257 1.48E-05 2.78E-06 0.1625705 0.03831681 0.081690762 1.087827052 0.218671548 ACGNFGIPCELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ACGNFGIPCELR 12 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 140.07 0.00013811 276530000 276150 426190 317010 327380 441760 257240 341860 365090 415010 FALSE TRUE 258866.2644 457745.5511 324529.6269 335781.1251 407065.9516 331501.0121 290601.2667 410672.2902 345742.1499 0.748726369 1.32395067 0.938646407 0.97118944 1.177368602 0.958809946 0.840514432 1.187799319 1 18.39933697 ACHQLHQEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ACHQLHQEGK 10 0 A0A499FJT0;Q8NHP1;Q8NHP1-3;O95154 A0A499FJT0;O95154 AKR7L;AKR7A3 Aflatoxin B1 aldehyde reductase member 4;Aflatoxin B1 aldehyde reductase member 3 0 ;;; 195.36 2.10E-07 713110000 857860 1093470 702040 761590 1305270 448678 808880 1035550 1330940 FALSE TRUE 804168.0739 1174431.657 718692.7203 781133.6888 1202759.359 578204.0549 687595.9533 1164840.697 1108797.516 0.725261432 1.059193983 0.648173098 0.704487228 1.084742112 0.521469472 0.62012761 1.050544108 1 20.0805645 3.969257146 24.69882758 0.768294281 0.908280474 0.006345814 0.208470323 666.1868242 2092305.035 0.05006782 0.092427125 9316.593487 -3.969257146 0.139986193 ACLISLGYDVENDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ACLISLGYDVENDR 14 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 158.4 1.18E-05 43913000 101920 107830 90005 101030 105280 79023 99165 97082 78163 FALSE TRUE 95541.00913 115813.8454 92139.9611 103622.6008 97011.73348 101835.6573 84296.12885 109202.9014 65117.09035 1.467218646 1.77854761 1.414988916 1.591327258 1.489804489 1.563885252 1.294531565 1.677023663 1 15.99074862 -3.039746643 0.21480841 1.46E-12 1.623241521 0.583907917 0.13875894 37.31874237 0.792608305 17.28842229 0.270593205 0.000912543 3.039746643 1.623241521 ACLISLGYDVENDRQGEAEFNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ACLISLGYDVENDRQGEAEFNR 22 1 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ;;; 327.06 1.09E-80 2153320000 837290 903140 810310 798150 852720 629733 931680 780420 1028540 FALSE TRUE 784885.5135 970009.4253 829530.9359 818631.8803 785750.8109 811526.6942 791983.2333 877857.1549 856870.0294 0.915991325 1.132037989 0.968094235 0.955374622 0.91700116 0.947082599 0.924274635 1.024492776 1 19.70871687 3.660831125 4.681573533 0.953305222 1.042698951 0.126472807 0.061015319 0.233727796 9.974507031 0.014813945 0.023863626 4579.637733 -3.660831125 0.089393729 ACNQLGQFLQHR ddPTM_SK-BR-3_Pertuzumab_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 ; 139.98 5.93E-05 954180000 965150 1451250 953730 933840 1524360 711180 1039080 1263330 1405820 FALSE TRUE 904742.9843 1558702.06 976352.926 957803.9154 1404642.915 916486.121 883279.6003 1421059.531 1171179.56 0.772505784 1.330882226 0.833649219 0.817811331 1.199340359 0.782532544 0.754179487 1.213357524 1 20.15953085 3.753074717 20.01996253 0.918423645 1.088785567 0.028149979 0.20921832 80.68390584 62233.2717 0.049773658 0.089614147 5663.367142 -3.753074717 0.170361923 ACPRPEGLNFQDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ACPRPEGLNFQDLK 14 1 Q5TEJ0;P15927;P15927-2;P15927-3 Q5TEJ0 RPA2 Replication protein A 32 kDa subunit 0 138.28 1.49E-05 457100000 351810 294600 307710 325100 343370 265560 414330 295610 404600 FALSE TRUE 329790.8401 316412.4905 315009.0265 333442.6164 316403.1053 342222.861 352205.063 332517.5592 337069.6462 0.978405632 0.938715468 0.934551746 0.989239524 0.938687624 1.015288279 1.044902936 0.986495115 1 18.36268719 2.229308076 24.23166754 1.018568636 0.952174598 0.579996771 0.023125861 78.63589606 205938.7885 0.008305151 0.006222085 169.5540143 -2.229308076 -0.066394038 ACQSIYPLHDVFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ACQSIYPLHDVFVR 14 0 P61247;D6RG13;D6RAT0;H0Y9Y4;D6RB09;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ;;; 161.84 4.53E-06 13259190000 5980540 7884530 6944400 6696260 7910810 6189760 7539040 6355790 7084620 FALSE TRUE 5606228.677 8468308.805 7109124.447 6868097.368 7289526.893 7976643.23 6408630.941 7149324.372 5902151.154 0.949861928 1.434783452 1.204497185 1.163660027 1.235062726 1.351480676 1.085812744 1.211308248 1 22.49280944 0.720607274 0.778513079 1.000808208 1.240350033 0.165911512 0.133880595 1.534365017 1.782107992 0.121986774 0.04308946 5.255418122 -0.720607274 0.239541824 ACRPPGS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 98.368 0.0032851 6342830000 3099640 3354080 3169970 3294410 3524930 2342800 2660060 2339350 2392700 TRUE FALSE 2905639.065 3602419.573 3245163.185 3378950.138 3248096.217 3019128.328 2261208.698 2631422.997 1993342.913 1.457671456 1.807225215 1.628000463 1.695117341 1.629471877 1.514605595 1.134380183 1.320105527 1 20.92675849 1.890330947 2.308451964 1.153625779 1.668198461 0.786745671 0.116494288 0.118387849 1.156767443 0.061530283 0.030346109 77.68388677 -1.890330947 0.514572682 ACRPPGS(ph)PGRAPPPTPAPSGCDPR ddPTM_SK-BR-3_Pertuzumab_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 120.64 6.93E-05 7752040000 1272490 1568600 1436830 1578740 1935150 1025136 1347690 1033038 2084670 TRUE FALSE 1192847.122 1684740.776 1470912.286 1619253.141 1783171.125 1321076.122 1145616.396 1162015.068 1736725.11 0.686837034 0.97006761 0.846945943 0.932360068 1.026743447 0.760670825 0.659641753 0.669084049 1 20.72793799 2.067170157 10.08129064 0.731374523 0.898581397 0.14701617 0.129686488 0.474498688 67.92507912 0.043793232 0.032329837 116.7266863 -2.067170157 0.167206874 ACRT(ph)PESFLGPSASSLVNLDSLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ACRTPESFLGPSASSLVNLDSLVK 24 1 Q9H201 Q9H201 EPN3 Epsin-3 1 ACRT(0.749)PES(0.251)FLGPSASSLVNLDSLVK;ACRT(0.842)PES(0.158)FLGPSASSLVNLDSLVK;ACRT(1)PESFLGPSASSLVNLDSLVK;ACRT(0.765)PES(0.234)FLGPSASSLVNLDSLVK 325.02 2.74E-74 1391491000 1234668 1010421 1076868 972561 1076675 996342 1580660 1119687 1659161 TRUE FALSE 1157392.334 1085233.622 1102411.817 997518.5618 992117.2886 1283969.761 1343654.707 1259482.387 1382236.311 0.837333186 0.785128863 0.797556691 0.72167006 0.717762427 0.928907562 0.972087549 0.911191796 1 20.39857285 2.149750034 6.020419699 0.955452628 0.775245201 0.829065042 0.040974792 0.083277682 4.544790473 0.01540722 0.011343732 141.1724767 -2.149750034 -0.180207428 ACS(ph)PCSSQSSSSGICTDFWDLLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ACSPCSSQSSSSGICTDFWDLLVK 24 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 ACS(0.988)PCS(0.012)SQSSSSGICTDFWDLLVK;ACS(0.822)PCS(0.088)S(0.088)QS(0.002)SSSGICTDFWDLLVK 207.88 4.52E-25 168536000 148760 144962 146972 142248 156039 128068 185879 134509 168084 TRUE FALSE 139449.3771 155695.1373 150458.2452 145898.3245 143784.3264 165039.1526 158008.1696 151302.7447 140029.6945 0.995855755 1.111872291 1.074473852 1.041909896 1.026813112 1.178601104 1.128390447 1.080504712 1 17.09537327 2.263794703 24.99769457 1.112340476 1.061532877 0.107644329 0.05465805 384.1661454 380566.2482 0.01785212 0.014930906 183.5670391 -2.263794703 -0.050807599 ACTGLSGPGSGSKS(ph)PPATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ACTGLSGPGSGSKSPPATR 19 1 I3L2J0;I3L2I4 I3L2J0 CIC 1 ACTGLSGPGS(0.001)GS(0.027)KS(0.972)PPATR;ACTGLSGPGSGS(0.015)KS(0.984)PPAT(0.001)R 153.93 2.48E-08 278530000 287670 297460 277720 302820 385430 181666 317890 261840 614550 TRUE FALSE 269665.2482 319484.2479 284307.6495 310590.8739 355159.8825 234110.0251 270225.3456 294531.3004 511977.6349 0.526712946 0.62401993 0.555312635 0.6066493 0.693701948 0.457266117 0.527806934 0.575281575 1 18.96572126 -1.499030174 2.52722857 1.023262753 0.570667195 0.819064228 0.063389986 2121627.663 2008960.295 341150.2704 0.01677875 0.031693473 1.499030174 -0.452595558 ACTLTVFPPEENPGS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ACTLTVFPPEENPGSPSR 18 0 Q9P2J3 Q9P2J3 KLHL9 Kelch-like protein 9 1 ACTLTVFPPEENPGS(0.996)PS(0.004)R;ACTLTVFPPEENPGS(0.966)PS(0.034)R 164.02 3.54E-11 43633000 106671 118891 130522 125208 122258 88731 103559 88715 81053 TRUE FALSE 99994.65252 127693.8133 133618.0435 128421.0493 112656.3498 114346.1993 88031.28934 99791.26304 67524.73068 1.480859702 1.891067348 1.978801576 1.901837267 1.668371702 1.693397339 1.303689603 1.477847628 1 16.04312836 1.508545954 0.793578616 1.054304963 1.857238393 0.700405697 0.164167903 0.286031449 0.374144771 0.145979262 0.060929066 32.25120558 -1.508545954 0.80293343 ACVQGECGVCHYCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ACVQGECGVCHYCR 14 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 0 128.96 7.07E-05 216010000 67751 80698 61441 67583 77259 66358 83967 65858 80937 FALSE TRUE 63510.58585 86672.96389 62898.40953 69317.2942 71191.38979 85514.47737 71376.92786 74080.51627 67428.09183 0.941900981 1.285413268 0.932822031 1.028018031 1.055812019 1.268232202 1.058563663 1.098659539 1 16.04106215 -1.304046224 5.214147716 0.999997284 1.091543293 0.044559828 0.116828592 2.71E-05 3.62E-06 0.10499536 0.024741829 0.049653947 1.304046224 0.091546008 ADAASSLTVDVT(ph)PPTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ADAASSLTVDVTPPTAK 17 0 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 1 ADAASSLTVDVT(1)PPTAK;ADAASSLTVDVT(1)PPTAK;ADAASSLTVDVT(1)PPTAK;ADAASSLTVDVT(0.994)PPT(0.006)AK;ADAASSLTVDVT(1)PPTAK 332.26 5.35E-71 804462000 1924610 1532010 1732060 1654040 1765100 1398120 2052660 1452490 2155780 TRUE FALSE 1804152.096 1645441.614 1773145.281 1696485.467 1626476.166 1801734.547 1744882.689 1633836.574 1795966.391 1.004557827 0.916187309 0.987293131 0.944608694 0.905627285 1.003211728 0.971556426 0.909725584 1 20.77632892 ADAEEEAATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADAEEEAATR 10 0 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 191.67 1.78E-06 153190000 147810 160280 148350 159780 141590 130450 172330 128160 128930 FALSE TRUE 138558.8359 172147.298 151868.9321 163880.2253 130470.0925 168108.7973 146490.7163 144161.0581 107410.7501 1.289990395 1.602700827 1.413908123 1.525733925 1.214683749 1.565102163 1.363836639 1.342147392 1 16.71277887 -0.649902616 0.379527185 0.855131187 1.470692516 0.549472717 0.119781896 6.712961966 0.866739262 1.268821626 0.077800391 0.22392232 0.649902616 0.615561329 ADAETLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ADAETLRK 8 1 P08758;D6RBE9;E9PHT9;D6RCN3 P08758 ANXA5 Annexin A5;Annexin 0 ;;; 135.83 0.00131 2234460000 2091550 2322210 1758103 1639453 1892430 1231682 2541680 1873284 4182280 FALSE TRUE 1960643.619 2494148.845 1799806.033 1681524.14 1743806.181 1587248.599 2160578.68 2107167.631 3484230.449 0.562719271 0.715839231 0.51655769 0.482609909 0.500485317 0.455552129 0.620102118 0.60477275 1 21.73240862 0.484236406 1.467970331 0.999891859 0.556177715 0.783287284 0.073828731 1.34570303 3.290855783 0.076158138 0.022111018 3.049554547 -0.484236406 -0.443714144 ADAGSHTEGS(ph)PSQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADAGSHTEGSPSQPR 15 0 Q86V15;Q86V15-2 Q86V15 CASZ1 Zinc finger protein castor homolog 1 1 ADAGSHTEGS(0.994)PS(0.006)QPR;ADAGSHT(0.01)EGS(0.974)PS(0.016)QPR 183.75 5.17E-07 418437000 181992 202434 228245 199350 203044 223554 275429 206932 285126 TRUE FALSE 170601.4456 217422.424 233659.0792 204465.6585 187097.7433 288090.4107 234130.9784 232767.9157 237536.6286 0.71821111 0.915321672 0.983675994 0.860775282 0.787658494 1.212825207 0.985662631 0.979924305 1 17.85779047 2.256446175 24.9999871 1.043271905 0.879758919 0.478395946 0.097157758 239.4500125 334696.6488 0.033248325 0.027763216 180.4871033 -2.256446175 -0.163512986 ADALQLSVEEFVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ADALQLSVEEFVER 14 0 B2WTI3;B2WTI4;K7EJU9;Q6NYC1-2;Q6NYC1;Q6NYC1-3 B2WTI3 JMJD6 Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 0 ;; 125.61 0.00020989 26669400 45245.9 48039.7 51032 48892.9 52411 41475 52708 44199 54905 FALSE TRUE 42414.03989 51596.60937 52242.50314 50147.57459 48294.85148 53448.15921 44804.92472 49717.34244 45741.0008 0.927265236 1.128016626 1.1421373 1.096337503 1.055832855 1.168495623 0.979535295 1.086931671 1 15.48120031 1.719008885 17.0115759 1.025109098 1.096802106 0.143481389 0.070805817 0.308231102 251.2901548 0.030522237 0.016879756 52.36111493 -1.719008885 0.071693008 ADAPDAGAQS(ph)DSELPSYHQNDVSLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ADAPDAGAQSDSELPSYHQNDVSLDR 26 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 ADAPDAGAQS(0.999)DS(0.001)ELPSYHQNDVSLDR;ADAPDAGAQS(0.998)DS(0.002)ELPSYHQNDVSLDR;ADAPDAGAQS(0.999)DS(0.001)ELPSYHQNDVSLDR;ADAPDAGAQS(1)DSELPSYHQNDVSLDR;ADAPDAGAQS(0.999)DS(0.001)ELPSYHQNDVSLDR 341.49 9.56E-96 6297780000 1097085 1891371 1639509 1787902 1757549 1492264 2216132 1598526 1467851 TRUE FALSE 1028420.408 2031410.077 1678398.928 1833782.592 1619518.191 1923056.392 1883843.58 1798105.49 1222857.185 0.840997968 1.661199771 1.37252244 1.499588516 1.324372306 1.572592789 1.540526239 1.470413317 1 20.22182449 -1.035878103 5.719441785 0.999999834 1.443943674 0.234114411 0.226032893 3.43E-06 5.78E-07 0.191814363 0.045210941 0.092070796 1.035878103 0.44394384 ADATNVNNWHWTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ADATNVNNWHWTER 14 0 O95433;O95433-2;G3V3W9 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ;;;;;;; 247.29 8.23E-18 5329130000 2329327 3045130 3120360 2554940 2872210 2201402 3112880 2571600 3445800 FALSE TRUE 2183538.581 3270594.594 3194376.413 2620504.086 2646638.213 2836911.021 2646132.543 2892669.921 2870673.719 0.760636281 1.139312549 1.112761925 0.912853338 0.921957168 0.988238754 0.921781018 1.007662383 1 21.45295793 3.229684719 24.99425766 0.953011174 1.048685273 0 0.108155946 348.2067476 980538.7558 0.029816234 0.03613988 1697.011242 -3.229684719 0.095674099 ADCILYYGFGDIFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADCILYYGFGDIFR 14 0 P46063 P46063 RECQL ATP-dependent DNA helicase Q1 0 ; 185.25 6.17E-07 135120000 403080 369040 512650 675990 823850 716300 507710 460080 293220 FALSE TRUE 377851.9423 396364.1056 524810.3001 693337.0478 759148.1443 923084.1818 431583.5988 517522.0008 244279.6877 1.546800497 1.622583152 2.148399259 2.838291854 3.10770065 3.778800401 1.766760073 2.118563379 1 17.89817438 3.688743945 2.250498848 2.541408153 1.619048705 0.159283398 0.756050712 0.472103454 4.720430691 0.206905993 0.395111132 4883.643401 -3.688743945 -0.922359449 ADDADEFGYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ADDADEFGYSR 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;; 325.13 2.57E-46 14064120000 4326080 4878740 4593080 4570820 4671560 3796250 5583690 4183570 5254990 FALSE TRUE 4055318.375 5239966.986 4702030.027 4688114.98 4304674.522 4892165.748 4746467.521 4705897.924 4377898.22 0.926316276 1.196913844 1.074038223 1.070859747 0.983274235 1.117469046 1.084188641 1.074921729 1 22.06180698 3.492055035 22.64863168 1.062791131 1.09854556 0 0.076930481 452.2046083 685807.6092 0.019076051 0.029063353 3104.953032 -3.492055035 0.035754429 ADDGRPFPQVIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ADDGRPFPQVIK 12 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;; 177.83 2.08E-05 69270390000 53786400 52971600 52489100 53019000 52976700 39527310 64841800 44666550 53432300 FALSE TRUE 50420005.24 56893672.38 53734166.24 54379557.3 48816123.68 50938202.72 55119374.05 50243267.09 44514103.94 1.132674833 1.278104406 1.207126764 1.221625339 1.09664397 1.14431603 1.238245167 1.128704447 1 25.40775918 -5 0.183644545 0.181120522 1.232559486 0.523871689 0.055234919 102.1653237 0.990519916 30.43351026 0.161379483 1.00E-05 5 1.051438964 ADDLGKGGNEESTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ADDLGKGGNEESTK 14 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;; 171.08 2.80E-06 2244650000 2032840 2027430 1860150 2227460 3003470 1196160 2385330 1615730 6051040 FALSE TRUE 1905608.173 2177543.027 1904273.636 2284620.395 2767589.582 1541471.974 2027671.911 1817457.447 5041082.333 0.378015681 0.431959425 0.377750949 0.453200373 0.549007019 0.305781948 0.402229477 0.360529213 1 22.26530209 -1.598046544 2.795622998 1.044557266 0.407527981 0.893941009 0.064157831 12841871.05 12647330.25 4205136.588 0.015326418 0.025232103 1.598046544 -0.637029285 ADDPYAHLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADDPYAHLSK 10 0 Q5STZ8;Q8NE71 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 80.979 0.022385 536850000 287400 324280 356470 328340 352780 290360 441330 321440 388050 FALSE TRUE 269412.147 348290.0286 364925.6367 336765.7603 325074.0818 374182.2184 375156.6636 361572.4916 323281.9481 0.833365886 1.077356873 1.128815385 1.04170914 1.005543563 1.157448539 1.160462766 1.118443185 1 18.30243342 2.23587276 24.99974892 1.127781765 1.041845383 0.165787479 0.089424055 123.3613966 1147363.515 0.031686661 0.024480615 172.1364173 -2.23587276 -0.085936382 ADDTDSQSWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ADDTDSQSWR 10 0 O75369-8 O75369-8 FLNB Filamin-B 0 ;;;;; 222.88 1.09E-08 1509874000 2402140 2719120 2632830 2643190 2849120 2191830 2946600 2368930 2716360 FALSE TRUE 2251794.345 2920446.474 2695281.971 2711018.73 2625361.608 2824575.74 2504784.685 2664696.125 2262981.968 0.995056248 1.290530157 1.19103113 1.197985123 1.160133684 1.248165376 1.106851367 1.177515404 1 21.10979366 0.330570164 0.68194317 0.995815319 1.193002177 0.287795426 0.080832352 2.558587643 1.703955517 0.0987191 0.02731866 2.14077076 -0.330570164 0.197186858 ADEASELACPT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 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 249.36 1.69E-16 33677571000 38877990 25583639 35268080 41349820 34081720 18154196 29919734 15349648 31176920 TRUE FALSE 36444686.01 27477878.25 36104655.51 42410926.39 31405079.19 23395017.68 25433547.65 17266085.34 25973290.64 1.403160135 1.057928263 1.39006859 1.632866893 1.20912978 0.900733681 0.979219306 0.664763105 1 24.63052547 2.314846808 3.978389293 0.892452499 1.329878324 0.653034198 0.165992469 0.153536796 4.720354863 0.062348649 0.05015295 206.4651747 -2.314846808 0.437425825 ADEASELACPT(ph)PKEDGLAQQQTQLNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 98.002 0.0063604 89072000 19404 36725 23315 47362 89268 11289 22775 17088 190080 TRUE FALSE 18189.53828 39444.15721 23868.04281 48577.3891 82257.25137 14547.95104 19360.10018 19221.47442 158354.42 0.114865997 0.24908782 0.15072546 0.306763708 0.519450302 0.091869561 0.122258035 0.12138262 1 17.27279761 -1.922967726 2.619019052 1.497473938 0.208286492 0.788764663 0.128552702 21107228.83 11312550.03 64323208.79 0.033611368 0.011940768 1.922967726 -1.289187446 ADEGISFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ADEGISFR 8 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;;;;;; 195.81 0.00036559 21463000000 11878370 12551350 12295000 12110120 12730530 10586740 14091340 10922930 13914850 FALSE TRUE 11134924.03 13480665.01 12586643.21 12420886.18 11730725.53 13642959.98 11978474.38 12286681.85 11592371.64 0.96053891 1.162891031 1.085769469 1.071470668 1.011934908 1.176891183 1.033306622 1.059893716 1 23.46667242 1.017533443 1.505687115 1.00242796 1.085222113 0.091584329 0.064723967 0.769231699 3.557358906 0.055624292 0.016458223 10.41198282 -1.017533443 0.082794153 ADEHVIDQGDDGDNFYVIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ADEHVIDQGDDGDNFYVIER 20 0 P13861-2;P13861;H7C1L0 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 0 ;;; 263.31 1.74E-36 2643820000 1470690 1486670 1534970 1533940 1540460 1254880 1758030 1321870 1640380 FALSE TRUE 1378642.138 1596744.594 1571380.213 1573303.497 1419478.486 1617143.485 1494429.722 1486908.379 1366589.981 1.008819147 1.168415264 1.14985492 1.15126228 1.038701078 1.18334212 1.093546523 1.088042793 1 20.38214902 0.809590632 1.389204525 1.000332766 1.125110281 0.27708618 0.055941131 0.787477598 2.780080158 0.048453162 0.014395734 6.450459196 -0.809590632 0.124777516 ADEIEMIMTDLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADEIEMIMTDLER 13 0 A0A2R8YDI1;A0A2R8Y852;P39880-6;P39880-4;P39880-5;P39880-2;P39880;P39880-3;P39880-9;Q13948-9;Q13948-10;Q13948-2;Q13948 A0A2R8YDI1 CUX1 Homeobox protein cut-like 1;Protein CASP 0 ; 137.17 0.00014855 10432000 13071.1 14985.3 11396.6 13078.5 14973 11532.1 17781.9 12178.5 14348.6 FALSE TRUE 12253.00318 16094.8272 11666.93273 13414.11645 13797.08098 14861.23006 15115.66917 13699.01253 11953.72596 1.025036313 1.346427654 0.976008047 1.122170317 1.154207568 1.243229944 1.264515283 1.146003562 1 13.54517275 2.463925257 22.01561804 1.196349262 1.132630584 0 0.120119328 175.7860534 293264.6556 0.039816039 0.033345727 291.0216221 -2.463925257 -0.063718678 ADELLCWEDSAGHWLYE ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADELLCWEDSAGHWLYE 17 0 Q13232;H3BPR2 Q13232 NME3 Nucleoside diphosphate kinase 3;Nucleoside diphosphate kinase 0 96.64 0.0052845 8081200 19394 21496 19426 22735 30709 18168 25003 24415 23119 FALSE TRUE 18180.16416 23087.58621 19886.79389 23318.41859 28297.23901 23412.80667 21254.03227 27463.26649 19260.28955 0.943919567 1.198714389 1.032528293 1.210699275 1.469201122 1.215599932 1.103515719 1.425901019 1 14.23334177 4.73869597 22.673079 1.197811242 0.943919696 0.23194808 0.149629229 4.729132532 788775.8166 0.034306485 0.198489471 54789.32753 -4.73869597 -0.253891546 ADEVAPAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ADEVAPAKK 9 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;; 108.67 0.0041275 2758520000 4206720 3100070 3593300 3379580 3636090 2449230 4333990 3068160 4799060 FALSE TRUE 3943428.904 3329602.408 3678534.773 3466305.744 3350526.159 3156282.941 3684148.434 3451226.53 3998065.883 0.986334148 0.832803287 0.920078578 0.866995654 0.838036755 0.789452459 0.921482672 0.863224027 1 21.93087082 -1.323398176 4.743688898 1.000077031 0.875188503 0.328766574 0.055024563 4.06E-05 5.79E-06 0.048247486 0.011365035 0.047489962 1.323398176 -0.124888528 ADEVVWVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ADEVVWVR 8 0 P14868;C9J7S3;H7C278;C9JLC1;C9JQM9 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ;;;;; 135.84 0.0018994 782921000 905451 959014 964128 968187 977721 763706 1077674 857941 890631 FALSE TRUE 848780.4382 1030020.394 986997.5715 993032.3176 900934.7366 984175.5245 916086.7883 965056.8224 741978.9324 1.143941426 1.388207063 1.330223175 1.338356487 1.214232234 1.326419769 1.234653369 1.300652593 1 19.5010187 -1.78168749 0.35316443 0.738195332 1.313426345 0.593297211 0.07269207 19.63719306 1.201483862 4.386069683 0.052348927 0.016531509 1.78168749 0.575231013 ADFCIIHYAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADFCIIHYAGK 11 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ; 149.31 3.44E-05 4576200000 8054200 8285200 8057600 7975900 9145500 6223500 9563300 8118500 8612100 FALSE TRUE 7550101.999 8898644.829 8248730.077 8180575.097 8427249.321 8020123.42 8129371.946 9132112.596 7174684.874 1.052325242 1.240283718 1.149699286 1.140199917 1.17458111 1.117836332 1.133063276 1.272824209 1 22.77448404 -1.501675762 5.645956659 0.99975092 1.162127278 0.40078905 0.061477632 0.00017403 1.54E-05 0.053743989 0.012648281 0.031500993 1.501675762 0.162376358 ADFDNTVAIHPTSSEELVTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ADFDNTVAIHPTSSEELVTLR 21 0 P00390-5;P00390-4;P00390-2;P00390-3;P00390 P00390-5 GSR "Glutathione reductase, mitochondrial" 0 ;; 212.39 9.79E-23 465330000 162477 626600 167352 166119 732620 173021 287905 690060 394648 FALSE TRUE 152307.8546 672994.116 171321.6685 170381.8948 675082.9804 222969.3539 244736.318 776215.51 328778.6993 0.463253413 2.046951696 0.521085061 0.518226683 2.053305101 0.678174573 0.744380091 2.360905715 1 18.32675731 1.26247012 24.99994518 1.680454966 1.046425132 0.146930922 0.671879575 388.3578729 406071.1459 0.417479834 0.152274143 18.3008019 -1.26247012 -0.634029834 ADFFEDENGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADFFEDENGQR 11 0 O95573 O95573 ACSL3 Long-chain-fatty-acid--CoA ligase 3 0 169.37 3.95E-05 94656000 109530 120850 104330 102100 120900 105240 141760 104260 111320 FALSE TRUE 102674.7128 129797.8597 106804.7569 104720.0589 111405.0017 135621.0796 120504.404 117277.0905 92739.97285 1.107124681 1.39958915 1.151658272 1.129179313 1.201261961 1.462379979 1.299379333 1.264579737 1 16.50090368 ADGTTPFYADSTAET(ph)Y(ph)GKIVHY(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADGTTPFYADSTAETYGKIVHYK 23 1 Q09013-5 Q09013-5 DMPK Myotonin-protein kinase 3 ADGT(0.001)T(0.001)PFY(0.003)ADS(0.003)T(0.003)AET(0.996)Y(0.996)GKIVHY(0.997)K 45.957 0.056663 1580600000 130800 997280 845210 887880 930370 833230 626400 726070 390660 TRUE FALSE 122613.4615 1071119.649 865258.7803 910664.504 857302.4931 1073769.975 532477.1352 816721.4378 325456.3222 0.376743216 3.291131792 2.65860185 2.798115881 2.634155291 3.299275206 1.636093997 2.509465578 1 18.31210441 -0.523955114 8.886902339 0.999827349 2.498093565 0.200477365 0.859482445 0 0 0.75376961 0.177665201 0.299257391 0.523955114 1.498266216 ADGYEPPVQES(ph)V ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADGYEPPVQESV 12 0 P61247;D6RAT0;H0Y9Y4;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 1 ADGYEPPVQES(1)V 78.763 0.026069 67202000 193000 118750 149760 123200 131460 100680 179740 121530 207660 TRUE FALSE 180920.4745 127542.3736 153312.3779 126361.5206 121135.6619 129744.6816 152789.6556 136703.288 173000.2045 1.045781854 0.737238282 0.886197669 0.73041255 0.700205311 0.749968371 0.883176156 0.790191482 1 17.40041422 -1.948450235 10.36486661 1.05516797 0.811203714 0.242194222 0.102383296 0.056293048 0.000279974 0.042755134 0.021288004 0.011260295 1.948450235 -0.243964256 ADGYVLEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADGYVLEGK 9 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 120.12 0.0016674 446190000 374230 281140 296250 291330 318710 234120 389650 268090 376190 FALSE TRUE 350807.6123 301955.8981 303277.1899 298806.021 293679.8022 301706.6434 331225.5998 301561.6266 313401.4587 1.119355391 0.963479555 0.967695527 0.953428941 0.937072225 0.962684235 1.056873191 0.962221516 1 18.25765237 ADHDFVVQEDFMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ADHDFVVQEDFMK 13 0 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ;;;;; 192.18 2.94E-06 1609020000 3030080 2627950 2829970 2773220 3041930 2109710 3342680 2443270 3603790 FALSE TRUE 2840432.702 2822526.152 2897098.225 2844385.52 2803029.088 2718749.029 2841476.166 2748317.638 3002294.168 0.946087406 0.940123117 0.96496148 0.947404006 0.933629062 0.905557176 0.946434962 0.915405848 1 21.51763391 2.810961213 5.046910649 0.934877968 0.950837898 0.009576971 0.025725653 0.549425475 26.30569376 0.007055838 0.007458317 647.0848219 -2.810961213 0.01595993 ADHGEPIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 ADHGEPIGR 9 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;; 146.79 9.40E-05 42592595000 9609812 10821558 10490505 10897524 11135084 9529755 11647230 9810339 10136319 FALSE TRUE 9008351.021 11622797.41 10739344.73 11177172.92 10260579.42 12280840.57 9900835.989 11035181.42 8444501.876 1.066771155 1.376374543 1.271755858 1.32360358 1.215060352 1.454300176 1.172459446 1.306788912 1 23.00958089 -1.109535553 4.388341203 0.99997432 1.28213878 0.387907361 0.107427999 3.18E-05 6.44E-06 0.090072068 0.021227567 0.07770777 1.109535553 0.28216446 ADHPPAEVTSHAASGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADHPPAEVTSHAASGAK 17 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 187.75 2.60E-10 400010000 634850 542580 596160 604880 658240 505330 716400 603000 945990 FALSE TRUE 595115.8717 582753.1878 610301.1967 620402.2449 606544.4856 651210.5677 608982.4707 678285.8774 788098.1577 0.755129124 0.739442393 0.774397441 0.787214434 0.769630635 0.82630642 0.77272414 0.860661671 1 19.5880158 -4.999999905 0.1666242 1.875836624 0.723290465 0.91931223 0.021534476 30.42509324 0.284874587 8.736483115 0.073344823 1.00E-05 4.999999905 -1.152546159 ADHQPLTEASYVNLPTIALCNTDSPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ADHQPLTEASYVNLPTIALCNTDSPLR 27 0 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;;;;; 289.14 1.89E-70 3048030000 1936820 2098950 2091490 2095870 2218160 1966380 2390820 1909650 2273170 FALSE TRUE 1815597.894 2254358.442 2141101.13 2149653.572 2043954.661 2534041.984 2032338.736 2148074.006 1893763.242 0.958724857 1.190411976 1.130606553 1.135122662 1.079308446 1.338098622 1.073174667 1.134288574 1 20.85282455 0.572794882 1.730769536 1.00020149 1.140674333 0.146323642 0.095993689 3.824411569 13.47745384 0.081630032 0.023025035 3.739339369 -0.572794882 0.140472843 ADHWMLYECESPWAGGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADHWMLYECESPWAGGSR 18 0 A0A494C0N6;O14734 A0A494C0N6 ACOT8 Acyl-coenzyme A thioesterase 8 0 145.62 8.97E-08 167480000 50159 57296 60166 58712 57732 55961 59014 49785 46895 FALSE TRUE 47019.63773 61538.25546 61593.16593 60218.64932 53197.9616 72116.03225 50165.39856 56000.76684 39067.92155 1.203535685 1.575160721 1.576566234 1.541383491 1.361678827 1.845914228 1.284055987 1.433420684 1 15.25369688 0.706584093 1.171442456 1.002916447 1.517685379 0.420151723 0.177651005 0.843128434 1.949365394 0.150531901 0.046430657 5.088433378 -0.706584093 0.514768932 ADIEER ddPTM_SK-BR-3_Pertuzumab_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 837730000 1009380 1262460 1211750 1303430 1297430 1034400 1451540 1131030 1272990 FALSE TRUE 946204.7076 1355933.852 1240493.282 1336878.221 1195535.081 1333014.488 1233895.052 1272241.585 1060519.745 0.892208478 1.27855597 1.169703146 1.26058777 1.127310535 1.256944526 1.163481451 1.199639696 1 20.01634005 -1.45720461 8.259557292 0.999994 1.182558077 0.178485768 0.11005741 1.05E-05 6.91E-07 0.092086316 0.02170424 0.034897586 1.45720461 0.182564077 ADIIYPGHGPVIHNAEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ADIIYPGHGPVIHNAEAK 18 0 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ;; 228.46 1.40E-19 690876000 1082120 871070 830660 782990 852540 571680 945850 790770 879740 FALSE TRUE 1014392.041 935564.9291 850363.6475 803082.849 785584.9474 736714.7356 804028.5733 889499.3752 732905.7107 1.384068955 1.276514722 1.160263367 1.095751933 1.071877236 1.005197155 1.097042309 1.213661406 1 19.48326808 4.238972321 0.852259834 1.076459203 1.43493551 0.754835591 0.059517555 0.607799943 0.552429154 0.021000754 0.177878379 17336.93501 -4.238972321 0.358476307 ADIKGPEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADIKGPEDK 9 1 P36542-2;P36542 P36542-2 ATP5C1 "ATP synthase subunit gamma, mitochondrial" 0 99.522 0.0048153 344380000 1118800 537060 738770 621050 866550 522530 827300 610300 1378600 FALSE TRUE 1048776.305 576824.4812 756293.9733 636987.1944 798494.6585 673375.9284 703254.0453 686497.2984 1148502.754 0.913168298 0.502240399 0.658504275 0.554624003 0.695248362 0.586307631 0.612322472 0.597732392 1 20.13132289 -1.482866834 3.003355148 1.010477883 0.625078263 0.504221472 0.111307194 43318772.21 51860258.68 3790263.193 0.0231759 0.032895248 1.482866834 -0.38539962 ADIKS(ph)PSLDVTVPEAELNLETPEISVGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ADIKSPSLDVTVPEAELNLETPEISVGGK 29 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ADIKS(0.761)PS(0.173)LDVT(0.066)VPEAELNLETPEISVGGK;ADIKS(0.415)PS(0.415)LDVT(0.17)VPEAELNLETPEISVGGK;ADIKS(0.71)PS(0.145)LDVT(0.145)VPEAELNLETPEISVGGK 290.18 7.37E-81 422038000 363978 212201 282773 327948 365936 182569 382901 223250 461798 TRUE FALSE 341197.2667 227912.5828 289480.5091 336363.7009 337196.8627 235273.7065 325488.5497 251123.2539 384720.9305 0.886869519 0.592410147 0.752442839 0.874305696 0.876471322 0.611543818 0.84603806 0.652741335 1 18.5534528 -1.494250106 3.03783767 1.007185026 0.75267264 0.307306702 0.111770772 46651454.02 54866383.96 2806071.957 0.026194687 0.032044234 1.494250106 -0.254512386 ADILEDKDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ADILEDKDGK 10 1 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;; 143.17 3.14E-05 5630480000 12235900 6189200 8315000 7638200 8617000 5631700 10447100 6816500 11372100 FALSE TRUE 11470076.86 6647454.808 8512235.727 7834209.143 7940255.579 7257480.367 8880654.341 7667555.03 9474023.043 1.210687034 0.70165069 0.898481636 0.826914723 0.838108113 0.766039974 0.937368877 0.809324085 1 23.17554575 -1.075720624 4.166958303 1.000017558 0.85898965 0.069012255 0.136918739 23505483.92 66359841.58 6717.482223 0.028788034 0.084000017 1.075720624 -0.141027909 ADKDES(ph)T(ph)MINEIT(ph)LAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 ADKDESTMINEITLAK 16 1 Q5THK1-4;Q5THK1-2;Q5THK1;H7BZH1 Q5THK1-4 PRR14L Protein PRR14L 3 ADKDES(1)T(1)MINEIT(1)LAK;ADKDES(1)T(1)MINEIT(1)LAK;ADKDES(1)T(1)MINEIT(1)LAK;ADKDES(1)T(1)MINEIT(1)LAK;ADKDES(1)T(1)MINEIT(1)LAK;ADKDES(1)T(1)MINEIT(1)LAK;ADKDES(1)T(1)MINEIT(1)LAK;ADKDES(1)T(1)MINEIT(1)LAK;ADKDES(1)T(1)MINEIT(1)LAK 56.648 0.050651 15200020000 10025650 7039350 7557660 8114200 9696760 8990810 9910570 6200460 10936270 TRUE FALSE 9398162.463 7560550.798 7736931.264 8322424.109 8935215.584 11586310.89 8424572.034 6974601.08 9110935.886 1.031525474 0.82983251 0.849191714 0.91345436 0.980713255 1.271692726 0.924665933 0.765519719 1 23.11916783 2.788764781 3.882410017 1.003125465 0.881220732 0.072224867 0.133989912 0.444674392 14.0422117 0.042353579 0.043995243 614.8437757 -2.788764781 -0.121904734 ADKDYHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ADKDYHFK 8 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;;; 123.88 0.0012116 26812600000 58775300 46125500 51447700 47254900 51737900 38858600 65124200 44878000 56799100 FALSE TRUE 55096658.89 49540680.01 52668063.74 48467540.74 47674614.03 50076447 55359430.79 50481117.09 47318963.27 1.164367414 1.046951932 1.113043484 1.02427309 1.00751603 1.05827439 1.169920619 1.066826355 1 25.49591513 4.748411507 24.1152446 1.071689832 1.164367496 0.266073132 0.051295506 1317.754372 3225787.429 0.012580413 0.161358949 56028.82404 -4.748411507 0.092677664 ADKDYHFKVDNDENEHQLSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ADKDYHFKVDNDENEHQLSLR 21 2 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;; 209.71 7.82E-23 4749710000 2290450 3108010 2420300 2849390 4834810 1363775 4078820 2396840 14056070 FALSE TRUE 2147094.823 3338130.294 2477710.659 2922510.171 4455103.525 1757474.703 3467238.807 2696090.75 11710021.11 0.183355333 0.285066121 0.211588915 0.249573433 0.38045222 0.150082966 0.296091593 0.230237907 1 23.48124034 -1.664199359 2.761757531 1.088475707 0.251241377 0.931881964 0.063865208 10876930.53 10071312.56 6810178.638 0.013821911 0.021667093 1.664199359 -0.83723433 ADKLAEEHSS ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADKLAEEHSS 10 1 P06576 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 ; 107.06 0.0021292 864710000 619520 1004900 819730 865940 1610400 685170 966020 1048460 3007310 FALSE TRUE 580745.3491 1079303.842 839174.3827 888161.4864 1483925.68 882967.4562 821174.2691 1179362.539 2505370.533 0.231800183 0.430796095 0.334950209 0.354503046 0.59229789 0.352429888 0.327765597 0.470733779 1 21.25659256 -5 0.356088051 8.401304454 0.366451351 0.813829417 0.09295901 185.861984 1.496839578 1052.637873 0.065574782 1.00E-05 5 -8.034853103 ADKNEVAAEVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADKNEVAAEVAK 12 1 P56192;H0YIP0 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 144.8 5.78E-05 256680000 732520 577470 627410 602040 683880 464470 837610 540090 890240 FALSE TRUE 686672.8808 620226.4797 642292.4615 617489.3657 630170.8234 598554.949 712018.1565 607521.4254 741653.1928 0.925867895 0.836275615 0.866028041 0.832585057 0.849683962 0.807055042 0.960041922 0.819144893 1 19.5003852 -0.490940691 0.510524037 1.023718234 0.857143634 0.430177365 0.048497649 8.277628292 1.860332061 0.396961762 0.021269368 0.322893505 0.490940691 -0.1665746 ADKVEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADKVEQR 7 1 Q99832-3;Q99832;Q99832-4 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 81.594 0.024421 303710000 577220 509760 562520 555330 590900 400970 576850 507910 571880 FALSE TRUE 541092.8306 547503.1608 575863.24 569580.708 544493.0976 516723.5298 490356.6977 571323.6815 476429.5335 1.135724787 1.149179726 1.208706009 1.195519312 1.142861765 1.084574934 1.02923237 1.19917772 1 18.86190332 2.32895196 3.298453164 1.074356702 1.17412123 0.398722494 0.054761655 0.224430697 4.875145406 0.019277041 0.015288401 213.2808977 -2.32895196 0.099764528 ADLAEEYSKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ADLAEEYSKDR 11 1 P68036-2;P68036;P68036-3 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ;; 169.89 1.49E-05 2040710000 2446910 2243490 2288680 2176730 2296870 1571530 2726940 1985070 3009890 FALSE TRUE 2293762.271 2409600.334 2342968.57 2232588.577 2116483.095 2025205.199 2318060.663 2232910.359 2507519.914 0.914753362 0.96094963 0.934376855 0.890357267 0.844054352 0.807652688 0.92444357 0.890485594 1 21.25782973 3.24715883 4.123219011 0.883021497 0.942608412 0.121024702 0.051401718 0.299854504 11.5716645 0.013833607 0.018084834 1766.683813 -3.24715883 0.059586915 ADLDVSGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADLDVSGPK 9 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 116.73 0.0029463 474720000 933310 702810 779660 784830 877870 627370 987600 683990 922580 FALSE TRUE 874895.7931 754846.7837 798153.9034 804970.0665 808925.6314 808481.5345 839518.5484 769387.6571 768595.4379 1.138304692 0.982111975 1.038457769 1.047326105 1.05247259 1.051894787 1.092276257 1.001030736 1 19.55186489 3.233578637 4.282410704 1.049977422 1.035517327 0 0.047275613 1.112293412 47.6935351 0.012858853 0.016591278 1712.29519 -3.233578637 -0.014460095 ADLELPWRPLYDMVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADLELPWRPLYDMVER 16 1 Q14997;F8WBH5 Q14997 PSME4 Proteasome activator complex subunit 4 0 ; 136.01 1.80E-05 207890000 175820 257030 233100 230190 257160 189357 262060 219100 200330 FALSE TRUE 164815.74 276060.7686 238629.2421 236097.0651 236963.6909 244021.2919 222766.5358 246455.1173 166893.6288 0.987549622 1.654112087 1.429828351 1.414655951 1.419848634 1.462136654 1.334781546 1.476719747 1 17.34856936 -2.671485697 0.555339761 1.18E-09 1.423956543 0.343637324 0.168768175 263.8092942 12.96272053 317.5493378 0.064948073 0.002130661 2.671485697 1.423956542 ADLES(ph)PQRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADLESPQRK 9 1 A0A087X1K6;Q9Y2Y9 A0A087X1K6 KLF13 Krueppel-like factor 13 1 ADLES(1)PQRK;ADLES(1)PQRK 114.72 0.00097529 464190000 1139870 826780 900970 858770 921970 731740 1245380 896810 1055980 TRUE FALSE 1068527.571 887995.6515 922341.4339 880807.4921 849562.1952 942981.4592 1058646.831 1008778.703 879730.1161 1.21460838 1.009395535 1.048436807 1.001224666 0.965707755 1.071898577 1.203376821 1.146691109 1 19.74670148 1.987462508 24.38276537 1.138874492 1.038768643 0.10113557 0.083087025 585.5424745 1138755.703 0.030274292 0.020652183 97.15440758 -1.987462508 -0.100105849 ADLHDEEDEQDILLAQDLEDMWEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADLHDEEDEQDILLAQDLEDMWEQK 25 0 A0A087WT90;Q9H2W6 A0A087WT90;Q9H2W6 MRPL46 "39S ribosomal protein L46, mitochondrial" 0 66.501 0.044971 11522000 13813 10169 10227 7925.9 13007 10830 11140 11553 13834 FALSE TRUE 12948.46899 10921.92334 10469.58927 8129.292013 11985.48269 13956.44519 9469.660419 12995.41748 11525.01603 1.123509846 0.947670989 0.908422968 0.705360582 1.039953668 1.210969699 0.821661366 1.127583463 1 13.49248114 ADLINNLGTIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADLINNLGTIAK 12 0 P08238;P07900;P07900-2;Q14568;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AA1;HSP90AA2P;HSP90AB2P Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2;Putative heat shock protein HSP 90-beta 2 0 ; 187.76 2.34E-05 402420000 2201420 1191000 1328270 1352290 1577710 1048410 1498520 1135440 1533550 FALSE TRUE 2063637.052 1279182.879 1359777.192 1386992.051 1453803.021 1351068.947 1273830.838 1277202.183 1277590.598 1.615256918 1.001246316 1.064329366 1.085631072 1.137925579 1.05751322 0.997057148 0.999695979 1 20.28499417 4.741228049 24.99990678 1.044945468 1.615257121 0.938419211 0.046073413 58.74222657 550518.0923 0.011502572 0.078809983 55109.70027 -4.741228049 0.570311653 ADLLLSTQPGREEGSPLELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADLLLSTQPGREEGSPLELER 21 1 F5GZS6;J3KPF3;P08195-2;P08195-3;P08195;P08195-4;F5GZI0 F5GZS6 SLC3A2 4F2 cell-surface antigen heavy chain 0 ; 137.09 3.53E-06 354600000 207711 251771 198483 190083 290314 168561 222456 229721 235273 FALSE TRUE 194710.7393 270412.3868 203191.1105 194960.8516 267513.9095 217221.8243 189100.788 258402.1725 196004.4164 0.993399755 1.379623948 1.036665981 0.99467581 1.364836132 1.108249642 0.9647782 1.318348726 1 17.58052664 -4.999999866 0.133898077 0.532101866 1.19941735 0.039252221 0.161152459 409.6977906 3.424943253 51.78103538 1.064349727 1.00E-05 4.999999866 0.667315484 ADLNQGIGEPQS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ADLNQGIGEPQSPSR 15 0 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 ADLNQGIGEPQS(0.562)PS(0.438)R;ADLNQGIGEPQS(0.916)PS(0.084)R;ADLNQGIGEPQS(1)PSR;ADLNQGIGEPQS(0.973)PS(0.027)R 325.5 2.39E-57 2242780000 2254670 2226410 2389240 2305860 2321350 1992270 2436090 2015840 1970320 TRUE FALSE 2113554.229 2391255.713 2445913.901 2365032.271 2139040.535 2567406.007 2070820.92 2267522.061 1641460.863 1.287605618 1.456785091 1.490083593 1.440809418 1.303132218 1.564098216 1.261571912 1.381404889 1 20.64654892 0.234575323 0.63747233 0.984726473 1.432050178 0.639767867 0.094341875 1.606954068 0.885445877 0.143348886 0.033560697 1.716229344 -0.234575323 0.447323705 ADLSIPDLHEIVTEELEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ADLSIPDLHEIVTEELEER 19 0 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 0 ;;;; 246.21 1.22E-24 177535000 191956 258201 237351 255076 276784 214611 304305 244175 258950 FALSE TRUE 179941.8166 277318.4707 242981.0778 261621.682 255046.5011 276565.7118 258677.2903 274660.7862 215729.5721 0.834108253 1.285491219 1.126322532 1.212729805 1.182250994 1.282001856 1.199081274 1.273171701 1 17.71886443 4.746357928 24.80576124 1.204376029 0.834108054 0.63645133 0.085496944 486.2150353 1546766.306 0.017505679 0.189189699 55764.51486 -4.746357928 -0.370267975 ADLVWQPWEDLESSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADLVWQPWEDLESSR 15 0 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 0 152.47 6.57E-06 15034000 23287 24614 23774 23995 25888 21259 25950 20248 17330 FALSE TRUE 21829.50824 26436.44617 24337.93051 24610.75232 23854.86091 27396.12819 22059.03841 22776.00737 14437.51104 1.511999414 1.831094438 1.685742815 1.70463955 1.652283474 1.897565869 1.527897595 1.577557745 1 13.81753443 0.581002269 1.034321998 0.999967689 1.717556031 0.782281669 0.113914154 0.55679883 0.911036391 0.097212575 0.030754908 3.81067814 -0.581002269 0.717588341 ADPSLLGFSVNAS(ph)SER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ADPSLLGFSVNASSER 16 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;Q6Y7W6-4;Q6Y7W6-5 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 ADPSLLGFSVNAS(0.714)S(0.286)ER;ADPSLLGFSVNAS(0.932)S(0.068)ER;ADPSLLGFSVNAS(0.965)S(0.035)ER 210.47 1.01E-11 336563000 173607 220852 217653 193594 232443 194802 245309 205564 205668 TRUE FALSE 162741.2478 237204.1119 222815.8319 198561.9498 214187.8644 251038.1751 208527.1928 231229.1179 171340.6821 0.949810902 1.384400417 1.300425732 1.15887218 1.250070104 1.465140514 1.217032582 1.349528408 1 17.38650821 -1.169207747 5.084950506 0.999983553 1.275820985 0.244942514 0.140534036 2.34E-05 3.83E-06 0.121659596 0.028673733 0.067731743 1.169207747 0.275837432 ADQCYEDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ADQCYEDVR 9 0 P31146;H3BRY3;H3BTU6;H3BRJ0;H3BNA2;H3BU76;H3BSL1 P31146 CORO1A Coronin-1A;Coronin 0 ;; 132.88 0.00068111 2253390000 1617700 1993380 1682780 1780050 2088600 1584340 2207450 1848910 1859590 FALSE TRUE 1516451.045 2140971.929 1722696.336 1825729.097 1924569.781 2041713.238 1876463.365 2079750.483 1549212.416 0.978852886 1.38197442 1.11198201 1.178488552 1.242289154 1.317903999 1.211236979 1.342456633 1 20.56310354 2.72939534 22.01751238 1.241478275 1.190875722 0.018599379 0.134624799 540.8566817 1299280.466 0.039197124 0.037542831 536.2846175 -2.72939534 -0.050602553 ADQDRLDLEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADQDRLDLEER 11 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 133.15 0.00015295 89795000 182060 237490 206440 214060 236810 175600 242050 200060 272540 FALSE TRUE 170665.1896 255074.0067 211336.8543 219553.142 218211.8978 226292.8694 205756.8496 225037.9314 227051.3133 0.751659117 1.123420089 0.930788953 0.966975873 0.961068644 0.996659592 0.90621299 0.991132481 1 17.79265886 ADQDSEAMKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADQDSEAMKR 10 1 Q9Y490 Q9Y490 TLN1 Talin-1 0 62.303 0.090216 115880000 164900 155010 162280 165220 181260 128550 166700 130690 201020 FALSE TRUE 154579.2034 166487.1017 166129.3582 169459.8249 167024.5708 165660.2982 141704.8826 147006.9342 167468.4634 0.923034703 0.994140021 0.992003837 1.011890965 0.997349396 0.989202951 0.846158612 0.877818613 1 17.35352992 1.757194375 25 0.893575741 0.988097661 0.37049909 0.045656555 5.981180621 8032.600823 0.018860659 0.010459243 57.17344677 -1.757194375 0.09452192 ADQEEQIHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ADQEEQIHPR 10 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;; 184.9 1.51E-06 2309630000 1200790 1226030 1236790 1181510 1372280 1100460 1265210 1227980 1894840 FALSE TRUE 1125634.697 1316806.537 1266127.243 1211829.547 1264506.664 1418144.938 1075503.506 1381296.006 1578578.963 0.713068351 0.834172105 0.802067728 0.767671162 0.801041122 0.898368071 0.681311186 0.875024968 1 20.590195 0.99306791 24.92420328 1.000000007 0.791070169 0.574571772 0.059879336 173.3957946 623443.8409 0.052705086 0.013176272 9.841649868 -0.99306791 -0.208929838 ADQELLMYSHDNIICGITSVAFSR ddPTM_SK-BR-3_Pertuzumab_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 ;; 319.63 8.11E-74 893150000 656447 656132 712365 571695 858842 667109 723311 656798 707332 FALSE TRUE 615361.1541 704712.696 729262.6342 586365.6616 791392.0137 859692.5387 614857.2304 738800.6761 589273.7197 1.044270487 1.195900432 1.237561781 0.995065013 1.342995602 1.458901882 1.043415326 1.253747879 1 19.1685784 -1.129687712 3.743449145 0.999901621 1.198636486 0.158126588 0.142400599 21894349.26 45530494.47 30314.06901 0.032038749 0.074184349 1.129687712 0.198734865 ADQEQQDPLEYLQS(ph)DEEDDEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADQEQQDPLEYLQSDEEDDEKR 22 1 Q7RTV3 Q7RTV3 ZNF367 Zinc finger protein 367 1 ADQEQQDPLEYLQS(1)DEEDDEKR 178.91 3.59E-17 54349000 35421 26821 25266 24850 33253 28455 37607 29150 37857 TRUE FALSE 33204.06284 28806.85475 25865.32145 25487.69307 30641.44352 36669.49657 31968.17948 32789.44167 31538.42213 1.052813064 0.913389219 0.820120973 0.808147375 0.971559179 1.162692807 1.013626469 1.039666523 1 14.94482286 2.476880119 24.99906129 1.056101391 0.888182445 0.463627992 0.078428962 6.878449995 712940.8853 0.026484256 0.022360711 299.8334756 -2.476880119 -0.167918946 ADRDESSPYAAMLAAQDVAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 ADRDESSPYAAMLAAQDVAQR 21 1 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ;;;;;;;;; 304.04 2.03E-55 14108140000 6016269 6236260 6389690 6129520 6113180 5518030 6815170 5265689 5916060 FALSE TRUE 5639721.463 6697999.179 6541256.464 6286813.86 5633075.502 7110995.683 5793298.527 5923121.863 4928631.367 1.144277395 1.358997799 1.327195316 1.275569908 1.142928956 1.442793172 1.17543758 1.201778226 1 22.23275565 0.863605759 1.184574215 1.001759282 1.28968387 0.441013227 0.094915134 0.531506293 1.453530946 0.081970449 0.025448674 7.304756762 -0.863605759 0.287924588 ADRDQS(ph)PFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ADRDQSPFSK 10 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 ADRDQS(1)PFSK;ADRDQS(1)PFSK;ADRDQS(1)PFSK;ADRDQS(0.999)PFS(0.001)K;ADRDQS(1)PFSK 144.09 1.99E-05 7330530000 24029500 19368600 20593500 20459200 21884400 16095400 25722600 18538400 23993500 TRUE FALSE 22525536.49 20802671.3 21081987.54 20984217.71 20165687.5 20741880.69 21865734.93 20852960.05 19988829.85 1.12690621 1.040714812 1.054688429 1.049797205 1.008847824 1.037673583 1.093897697 1.043230655 1 24.25269068 4.741096305 24.81617746 1.046527798 1.126906242 0.511333772 0.025881928 187.5027966 1834925.637 0.006087463 0.041315644 55092.98522 -4.741096305 0.080378444 ADRDQSPFS(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADRDQSPFSK 10 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 ADRDQS(0.336)PFS(0.664)K 142.97 0.006383 0 593020 441030 477060 500010 508000 373290 615240 441240 553010 TRUE FALSE 555903.9368 473684.3201 488376.0885 512841.1031 468103.7292 481052.7631 522990.4736 496329.7853 460709.0584 1.206626887 1.028163678 1.06005315 1.11315611 1.01605063 1.044157379 1.135186001 1.077317184 1 18.81349644 4.747790294 24.58285118 1.064474912 1.206626981 0.547294783 0.041882943 792.5306236 2110814.314 0.009897385 0.120733998 55948.73793 -4.747790294 0.142152069 ADRGEAERGS(ph)GGS(ph)S(ph)GDELREDDEPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADRGEAERGSGGSSGDELREDDEPVK 26 3 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WT54 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 3 ADRGEAERGS(1)GGS(1)S(1)GDELREDDEPVK 70.073 0.060709 101920000 116030 104350 100050 105230 113490 59464 113730 79734 170940 TRUE FALSE 108767.8894 112076.1826 102423.2332 107930.38 104576.9532 76630.29148 96677.24232 89688.96542 142409.0097 0.763771124 0.78700205 0.719218773 0.75789011 0.734342254 0.538100024 0.678870266 0.629798393 1 17.1196809 -1.218131853 3.733673876 1.000354711 0.703949987 0.622188472 0.07316362 4413416.497 2886946.978 11675.2981 0.018136156 0.060515712 1.218131853 -0.296404724 ADS(ph)LLAVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 118.23 0.0010727 33465000 65960 46445 57571 50647 63022 39139 65395 53331 78774 TRUE FALSE 61831.68134 49883.83613 58936.61131 51946.68777 58072.50634 50437.79393 55589.62685 59989.49275 65626.1105 0.942181106 0.760121783 0.898066499 0.791555181 0.884899408 0.768562902 0.847065694 0.914110135 1 16.00198231 1.010195378 2.684136276 0.998969505 0.835582543 0.446542225 0.057650876 0.202970173 3.324740393 0.047598595 0.01275495 10.2375345 -1.010195378 -0.163386962 ADS(ph)PHVS(ph)GSEADVASLAPVDSSFSLLSVSHALYDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADSPHVSGSEADVASLAPVDSSFSLLSVSHALYDSR 36 0 A0A499FJD3;A0A3B3ISA1;Q96S15 A0A499FJD3 WDR24 WD repeat-containing protein 24 2 ADS(0.95)PHVS(0.55)GS(0.498)EADVASLAPVDSSFSLLSVSHALYDSR 42.931 0.056501 8684000 4124.5 4955.5 3276.4 3570.8 3316.5 1950 3900.6 3684.9 4652.9 TRUE FALSE 3866.354907 5322.410376 3354.117755 3662.432773 3056.035468 2512.933344 3315.741241 4144.967876 3876.300931 0.997434146 1.373064288 0.865288277 0.94482674 0.788389633 0.648281284 0.855387985 1.069310136 1 11.92046486 3.788569847 3.832190406 0.858435045 1.197633501 0.419479256 0.146176327 0.17399023 5.110746884 0.036595876 0.067879858 6145.678642 -3.788569847 0.339198456 ADS(ph)PHVSGSEADVASLAPVDSSFSLLSVSHALYDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADSPHVSGSEADVASLAPVDSSFSLLSVSHALYDSR 36 0 A0A499FJD3;A0A3B3ISA1;Q96S15 A0A499FJD3 WDR24 WD repeat-containing protein 24 1 ADS(0.919)PHVS(0.04)GS(0.04)EADVASLAPVDSSFSLLSVSHALYDSR 56.728 0.066364 21665000 12813 19204 14421 17994 20670 15914 17646 15607 19630 TRUE FALSE 12011.0572 20625.88414 14763.07293 18455.7565 19046.66158 20508.11346 15000.14612 17555.56831 16353.62619 0.734458344 1.261242241 0.902740026 1.128542153 1.164675122 1.254040738 0.9172367 1.073496979 1 13.99732295 1.654269545 25 0.996415573 1.081954462 0.046946188 0.161886953 1.379566413 726.6438616 0.068799289 0.03815183 45.10965912 -1.654269545 0.085538889 ADS(ph)PVNGLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADSPVNGLPK 10 0 Q96S94;Q96S94-3;A0A0A0MSF3 Q96S94 CCNL2 Cyclin-L2 1 ADS(1)PVNGLPK;ADS(1)PVNGLPK 140.16 4.17E-05 963730000 3661200 2609000 2892200 2695600 3025800 2375200 3868100 2640600 4226300 TRUE FALSE 3432052.027 2802173.075 2960804.35 2764773.66 2788165.873 3060881.682 3288114.315 2970284.723 3520903.227 0.974764657 0.795867678 0.84092182 0.785245569 0.79188938 0.869345587 0.933883752 0.843614417 1 21.74751414 1.975726715 5.069147335 0.915568244 0.829893399 0.265791293 0.065303809 0.241677628 16.94416316 0.025777554 0.016306567 94.5641918 -1.975726715 -0.085674845 ADSGPTQPPLS(ph)LSPAPETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADSGPTQPPLSLSPAPETK 19 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 1 ADSGPTQPPLS(0.773)LS(0.227)PAPETK 273.01 2.40E-39 863470000 662630 546300 575510 591910 536760 414980 753630 438210 359880 TRUE FALSE 621157.1711 586748.6204 589161.369 607099.4127 494605.0348 534777.9894 640630.1779 492921.4831 299813.7031 2.071810477 1.957044039 1.965091532 2.024922165 1.649707901 1.783700958 2.136760833 1.644092575 1 18.1937068 -2.037972075 0.337917906 6.84E-16 1.98095889 0.78561769 0.152540057 17.03261056 0.86295332 13.36962901 0.125839222 0.009162794 2.037972075 1.98095889 ADSGPTQPPLSLS(ph)PAPETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 383.34 9.19E-127 3273390000 3534460 2770520 3082700 3126790 2766010 2351730 3930550 2337240 2193330 TRUE FALSE 3313244.458 2975652.184 3155823.1 3207028.725 2548778.732 3030636.274 3341200.517 2629049.559 1827249.054 1.813241852 1.628487467 1.727089744 1.755113086 1.394872104 1.658578653 1.828541386 1.438801981 1 20.80124186 0.949944601 5.013954687 1.000213058 1.681964402 0.766724647 0.121286365 0.119626593 9.324928359 0.112408823 0.028419686 8.911372576 -0.949944601 0.681751344 ADTLDPALLRPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ADTLDPALLRPGR 13 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;; 164.13 3.43E-05 2255330000 2876910 3111210 3050750 2903970 3090500 2731050 3462960 2756830 3009110 FALSE TRUE 2696849.339 3341567.226 3123115.231 2978490.787 2847784.596 3519459.8 2943721.297 3101026.294 2506870.101 1.075783439 1.332963852 1.245822521 1.188131282 1.135992086 1.403925875 1.1742616 1.237011161 1 21.25745581 0.179518943 1.429116549 0.999845828 1.237318429 0.352208696 0.094114355 9.609141738 15.52333363 0.084378985 0.023834598 1.511885645 -0.179518943 0.237472602 ADTLTLEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADTLTLEER 9 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40 Q9UHD8 9-Sep Septin-9 0 152.34 0.00018775 254100000 177140 216910 227040 209880 209170 185430 223600 198400 223110 FALSE TRUE 166053.1236 232970.2421 232425.496 215265.8761 192742.632 238960.6308 190073.2558 223170.6767 185871.4997 0.893375929 1.253394106 1.250463339 1.158143537 1.036967111 1.285622762 1.022605704 1.200671847 1 17.50394605 0.027922043 0.497600322 0.985554195 1.165146657 0.07062288 0.125406554 8.402812011 2.632324701 0.380100224 0.059293721 1.066404681 -0.027922043 0.179592462 ADTQTYQPYNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADTQTYQPYNK 11 0 P84090 P84090 ERH Enhancer of rudimentary homolog 0 162.36 0.0024318 0 49128 49143 51099 50036 55334 45948 61599 50643 68940 FALSE TRUE 46053.16618 52781.59885 52311.09241 51320.00847 50988.29085 59212.4417 52362.80181 56965.89003 57433.46863 0.801852426 0.919004199 0.910812 0.893555791 0.887780106 1.030974502 0.911712335 0.991858778 1 15.80960407 8 0.157877076 1.013274828 0.371871131 0.551112873 0.044229733 52.06299488 0.532395006 0.126122125 7.749402785 100000000 -8 -0.641403697 ADTQTYQPYNKDWIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADTQTYQPYNKDWIK 15 1 P84090 P84090 ERH Enhancer of rudimentary homolog 0 ; 245.76 3.67E-18 3338100000 4244700 4476700 4136600 4236400 5579900 3303300 5622900 4068100 8640700 FALSE TRUE 3979031.804 4808159.526 4234722.105 4345113.196 5141677.162 4256909.085 4779798.345 4576011.24 7198511.349 0.552757593 0.667938035 0.588277479 0.603612745 0.714269508 0.591359641 0.663998168 0.63568855 1 22.77926716 -5 0.326972421 4.678380076 0.614880848 0.872685097 0.044988683 104.4717419 0.910366272 266.6709931 0.034310742 1.00E-05 5 -4.063499228 ADTSS(ph)QGALVFLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADTSSQGALVFLSK 14 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 ADT(0.023)S(0.071)S(0.906)QGALVFLSK 89.468 0.0064376 33348000 131190 139350 134330 130190 143620 107300 192870 136970 183270 TRUE FALSE 122979.0521 149667.619 137516.371 133530.8958 132340.6645 138275.7681 163950.934 154071.006 152681.053 0.805463741 0.980263209 0.900677381 0.874574108 0.866778568 0.905651129 1.073813225 1.009103638 1 17.22016152 1.752071246 24.99997989 1.031236013 0.899399944 0.649880798 0.047565643 2.627756706 4869.483538 0.021414346 0.01187534 56.50296602 -1.752071246 -0.131836069 ADVFHAYLSLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADVFHAYLSLLK 12 0 Q86VP6;Q86VP6-2;A0A0C4DGH5;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 159.99 6.93E-05 173846000 592710 1382650 545580 580410 1585000 331880 628600 1395620 1250040 FALSE TRUE 555613.3391 1485022.845 558521.4152 595304.3032 1460520.494 427688.3684 534347.2656 1569866.229 1041400.248 0.533525261 1.425986643 0.536317728 0.571638334 1.402458369 0.410685871 0.513104607 1.507457129 1 19.99009323 3.954990907 24.24665877 0.793405079 1.035709371 0 0.430544832 840.9900301 921414.2674 0.102734567 0.185427871 9015.522602 -3.954990907 0.242304292 ADVIQATGDAICIFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADVIQATGDAICIFR 15 0 Q08945;E9PMD4 Q08945 SSRP1 FACT complex subunit SSRP1 0 92.856 0.011821 46260000 48643 85791 74307 83788 80645 79751 76927 63066 90281 FALSE TRUE 45598.52146 92143.05491 76069.59713 85938.14193 74311.46701 102773.8191 65392.51051 70939.92893 75212.51786 0.606262398 1.225102649 1.011395434 1.142604242 0.988019935 1.366445666 0.869436529 0.943193114 1 16.19868517 1.611970075 25 0.929732299 1.074841636 0.06923035 0.197791908 0.820434759 4966.802365 0.085046733 0.045005825 40.92324604 -1.611970075 0.145109336 ADVTPPPDGSTTHNLEVS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ADVTPPPDGSTTHNLEVSPK 20 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 ADVTPPPDGSTTHNLEVS(1)PK 193.39 4.84E-18 134410000 101330 79706 95913 86234 87148 68910 104590 76500 92148 TRUE FALSE 94987.93618 85607.51517 98188.10165 88446.91043 80303.74762 88803.19834 88907.70047 86051.1934 76767.9035 1.237339198 1.115147233 1.279025441 1.152133983 1.046058886 1.156775088 1.158136362 1.120926709 1 16.22821563 -5 0.120529681 0.451340243 1.243812229 0.471354884 0.058850829 140.9564101 1.100721144 18.70159362 0.556943469 1.00E-05 5 0.792471987 ADVVPQQADPEFPRAS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ADVVPQQADPEFPRASPR 18 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 ADVVPQQADPEFPRAS(1)PR;ADVVPQQADPEFPRAS(1)PR;ADVVPQQADPEFPRAS(1)PR;ADVVPQQADPEFPRAS(1)PR 170.55 9.37E-12 2052880000 1131050 1334550 1276020 1274990 1440750 1180520 1408790 1279370 1814690 TRUE FALSE 1060259.599 1433361.471 1306287.797 1307708.402 1327599.307 1521316.96 1197555.018 1439102.161 1511806.516 0.701319639 0.948111717 0.864057526 0.864997199 0.878154243 1.006290781 0.792135108 0.951908955 1 20.52784208 -3.301155899 0.017072609 2.006683123 1.65E-06 0.293232927 0.078987756 5241.841211 9.157379949 649.7602699 443.6771513 0.000499855 3.301155899 -2.006681475 VLSTS(ph)TDLEAAVADALKKPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLSTSTDLEAAVADALKKPVR 21 2 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 1 VLST(0.015)S(0.867)T(0.118)DLEAAVADALKKPVR 236.04 4.22E-30 401520000 558780 589210 544450 611740 692390 437720 945450 593780 1373600 TRUE FALSE 523806.9573 632835.7215 557364.6111 627438.2841 638012.4824 564082.6582 803688.5496 667914.7401 1144337.286 0.457738259 0.553015032 0.487063227 0.548298383 0.557538839 0.492933915 0.702317891 0.583669472 1 20.12608091 -0.634938451 0.32093406 1.185504739 0.488971089 0.886291609 0.05294155 2.87133405 0.292496304 0.587875973 0.048472521 0.23177231 0.634938451 -0.696533651 ADYDTLSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADYDTLSLR 9 0 Q9Y446;Q9Y446-2;E9PQ15;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 0 ; 186.91 9.57E-05 357620000 991280 1161790 989090 974420 1237030 829700 1127930 1131220 1073920 FALSE TRUE 929237.5543 1247810.14 1012551.682 999425.2669 1139878.654 1069220.921 958807.3677 1272455.307 894675.8142 1.038630462 1.394706463 1.131752603 1.117080904 1.274068926 1.195093132 1.071681331 1.42225294 1 19.77100549 -1.40790075 3.557666138 0.998397496 1.204949176 0.204086025 0.127629777 9578164.861 3892794.095 117327.0762 0.027325295 0.039093023 1.40790075 0.20655168 ADYQAVDDEIEANLEEFDISEDDIDDGFRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ADYQAVDDEIEANLEEFDISEDDIDDGFRR 30 1 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ; 178.91 1.26E-17 37725000 29988 35245 30586 29416 35785 28485 37640 29060 39950 FALSE TRUE 28111.10461 37854.57647 31311.51436 30170.86436 32974.59045 36708.15708 31996.23143 32688.20497 33282.08691 0.844631669 1.137385903 0.940791797 0.906519607 0.990760902 1.102940365 0.961364938 0.982156109 1 15.02245828 2.463838001 24.99318669 1.011747985 0.98099001 0.056096385 0.083055006 1073.027948 2018950.62 0.028435765 0.023802945 290.9631576 -2.463838001 -0.030757975 AEADKIYSFTDNAPS(ph)PSIGGSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEADKIYSFTDNAPSPSIGGSSR 23 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 AEADKIYSFTDNAPS(0.999)PS(0.001)IGGSSR 187.29 1.50E-17 149580000 197970 184540 197140 172890 226350 214010 338320 225660 333060 TRUE FALSE 185579.4111 198203.5336 201816.2539 177326.6501 208573.3841 275791.2128 287592.0568 253834.1477 277470.1344 0.668826616 0.714323846 0.727344059 0.639083736 0.751696699 0.993949181 1.036479322 0.914816106 1 18.08197297 2.287374704 4.238242588 0.99650808 0.698669353 0.928280625 0.039724073 0.047621507 1.792330888 0.013885051 0.011080999 193.8093404 -2.287374704 -0.297838727 AEADKNDK ddPTM_SK-BR-3_Pertuzumab_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 0 126.07 0.0011263 232550000 566420 496450 623040 616780 539840 475210 746840 453830 595360 FALSE TRUE 530968.7833 533207.6746 637818.803 632607.619 497443.144 612395.4126 634858.2753 510491.6745 495990.5698 1.070521932 1.075035912 1.285949455 1.275442836 1.002928633 1.234691645 1.279980536 1.029236654 1 18.91995317 -0.466674765 7.391128265 1.000005421 1.171518866 0.157003186 0.109455989 0 0 0.102048092 0.024052966 0.34144852 0.466674765 0.171513445 AEAEAGS(ph)PRPDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AEAEAGSPRPDPR 13 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 AEAEAGS(1)PRPDPR;AEAEAGS(1)PRPDPR;AEAEAGS(1)PRPDPR;AEAEAGS(1)PRPDPR;AEAEAGS(1)PRPDPR;AEAEAGS(1)PRPDPR 78.069 0.014675 15386070000 11383600 13372800 13687400 14725200 13153700 10178500 13299600 10193000 12919700 TRUE FALSE 10671120.8 14362936.03 14012071.59 15103073.56 12120661.46 13116867.72 11305448.45 11465618.49 10763318.61 0.991434072 1.334433789 1.301835624 1.403198597 1.126108211 1.21866389 1.05036828 1.065249382 1 23.35961963 1.877111996 1.28676701 1.019544769 1.27055533 0.368500141 0.1151583 0.404380243 1.243602008 0.083146728 0.035472237 75.35498638 -1.877111996 0.251010561 AEAGAGS(ph)ATEFQFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEAGAGSATEFQFR 14 0 P46783;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 1 AEAGAGS(0.952)AT(0.048)EFQFR;AEAGAGS(0.927)AT(0.073)EFQFR 213 1.73E-09 308100000 311270 322580 326030 334730 332990 294090 366690 285580 305070 TRUE FALSE 291788.1663 346464.1588 333763.5856 343319.7385 306838.3086 378989.0088 311708.2387 321235.2916 254151.8462 1.14808596 1.363217164 1.313244781 1.350844952 1.207303088 1.491191249 1.226464586 1.263950258 1 17.95533119 0.641536745 1.439380989 1.000580373 1.313736042 0.49454726 0.094546611 0.972941005 2.91683588 0.078649753 0.023027436 4.380631733 -0.641536745 0.31315567 AEAGAGSAT(ph)EFQFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEAGAGSATEFQFR 14 0 P46783;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 1 AEAGAGS(0.24)AT(0.76)EFQFR 172.19 3.24E-05 114560000 126360 117400 128490 122200 123290 104970 145870 118450 106920 TRUE FALSE 118451.3532 126092.4182 131537.8435 125335.8589 113607.3007 135273.135 123998.1477 133238.7432 89074.36127 1.329803004 1.415585993 1.476719469 1.407092424 1.275420886 1.518653999 1.392074509 1.495814748 1 16.44272261 -1.099321427 4.37086294 0.999956927 1.41808589 0.75809908 0.073442711 0.950701808 19473299.4 1953.240613 0.015647904 0.079557032 1.099321427 0.418128963 AEAGAGSATEFQFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEAGAGSATEFQFR 14 0 P46783;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 0 105.13 0.0051092 0 158140 141510 151850 144930 153340 127700 182310 131810 194970 FALSE TRUE 148242.2997 151987.5476 155451.9537 148649.1492 141297.2949 164564.917 154974.308 148266.7686 162428.2474 0.912663296 0.935721157 0.957049997 0.915168091 0.869905926 1.013154544 0.95410934 0.912813941 1 17.30944302 2.230609535 24.99954605 0.966577419 0.925682133 0.343500286 0.034654192 258.0865149 811460.3506 0.012667542 0.00952547 170.062882 -2.230609535 -0.040895286 AEAPAGPALGLPS(ph)PEAESGVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AEAPAGPALGLPSPEAESGVDR 22 0 Q53F19 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 AEAPAGPALGLPS(1)PEAESGVDR;AEAPAGPALGLPS(1)PEAESGVDR;AEAPAGPALGLPS(1)PEAESGVDR;AEAPAGPALGLPS(1)PEAESGVDR 288.37 9.79E-47 1138980000 534602 456297 566388 471504 426705 504249 620646 445756 393681 TRUE FALSE 501142.2151 490081.7047 579822.9908 483603.5909 393193.3105 649817.5005 527585.8941 501409.6178 327973.0978 1.527997932 1.494274097 1.767898022 1.47452213 1.198858422 1.981313421 1.608625517 1.528813251 1 18.32321796 0.785288574 4.221122907 1.0000131 1.592985112 0.444830476 0.201384747 2.506113251 48.49004518 0.183467417 0.046729356 6.099420485 -0.785288574 0.592972012 AEAPAGPALGLPS(ph)PEAESGVDRGEPEPMEVEEGELEIVPVRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AEAPAGPALGLPSPEAESGVDRGEPEPMEVEEGELEIVPVRR 42 2 Q53F19 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 AEAPAGPALGLPS(1)PEAESGVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(1)PEAESGVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(1)PEAESGVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(1)PEAESGVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(0.998)PEAES(0.002)GVDRGEPEPMEVEEGELEIVPVRR 318.7 1.94E-114 1406360000 117697.1 174791.2 154308.8 146068 184889.7 124308 153072.3 129725.9 240554.2 TRUE FALSE 110330.6486 187732.9223 157969.0776 149816.3522 170369.2088 160193.7016 130120.5297 145922.4642 200404.15 0.550540738 0.93677163 0.788252527 0.747571107 0.850128147 0.799353215 0.649290594 0.72814093 1 17.61255286 S(ph)CHDLDLLGQSPGWGQTQAVETNIVCK ddPTM_SK-BR-3_Pertuzumab_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 369.42 5.22E-127 2148690000 834780 797120 784140 677910 1170520 661700 1333600 916210 2192420 TRUE FALSE 782532.6099 856139.5942 802740.1711 695306.3183 1078592.081 852722.0482 1133639.061 1030600.835 1826490.938 0.428434981 0.468734652 0.439498579 0.380678767 0.590526927 0.466863553 0.620665034 0.56425182 1 20.80064317 -0.285610414 0.344197742 1.147136149 0.422030855 0.901337008 0.05525488 1.754136145 0.245416706 0.367565265 0.044709134 0.518071362 0.285610414 -0.725105294 AEAPPLEREDS(ph)GTFSLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEAPPLEREDSGTFSLGK 18 1 O75569;G5E9Q4 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 1 AEAPPLEREDS(0.986)GT(0.014)FS(0.001)LGK;AEAPPLEREDS(0.985)GT(0.015)FSLGK 153.6 1.94E-08 302060000 364790 341420 391570 355070 393940 242850 399630 324470 604920 TRUE FALSE 341958.4451 366699.092 400858.2253 364181.6973 363001.5415 312956.8527 339709.1915 364980.7937 503954.9441 0.678549638 0.727642612 0.79542473 0.722647335 0.720305547 0.621001652 0.674086435 0.724232986 1 18.94293523 0.938827783 21.5293066 1 0.710943538 0.807129393 0.044892354 2608.187768 917942.6479 0.049779642 0.012444911 8.68615917 -0.938827783 -0.289056462 AEAPSS(ph)PDVAPAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEAPSSPDVAPAGK 14 0 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 AEAPS(0.005)S(0.995)PDVAPAGK;AEAPS(0.022)S(0.978)PDVAPAGK 269.78 1.04E-25 217180000 816140 553470 675010 605859 562400 575294 813960 586925 486459 TRUE FALSE 765059.2543 594449.4947 691021.556 621406.3677 518231.3726 741372.0387 691914.2544 660203.8782 405265.8503 1.887796008 1.466813684 1.705106797 1.533330201 1.278744242 1.829347423 1.707309545 1.629063682 1 18.62850909 -1.815437513 2.487333545 0.783321366 1.623685162 0.559323946 0.175581533 6518585.874 4367387.174 8491911.551 0.040446292 0.015295458 1.815437513 0.840363796 AEAPSS(ph)PDVAPAGKEDSPSASGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEAPSSPDVAPAGKEDSPSASGR 23 1 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 AEAPS(0.155)S(0.845)PDVAPAGKEDSPSASGR;AEAPS(0.073)S(0.927)PDVAPAGKEDSPSASGR 251.51 1.49E-39 1291510000 987910 926070 931500 899040 1024960 794410 1163620 841590 1297260 TRUE FALSE 926078.4766 994637.1864 953595.6199 922110.8885 944463.7761 1023743.271 989145.9835 946664.3641 1080738.925 0.856893793 0.920330677 0.882355209 0.853222612 0.873905579 0.947262328 0.915249706 0.875941767 1 20.04358662 2.247776903 24.99230126 0.926936918 0.882791081 0.374721098 0.035779824 252.5347478 684811.6762 0.011799523 0.009745437 176.9199887 -2.247776903 -0.044145837 AEASS(ph)PVPYLSPETNPASSTSAVNHNVNLTNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AEASSPVPYLSPETNPASSTSAVNHNVNLTNVR 33 0 G3V1L9;Q07157 G3V1L9 TJP1 Tight junction protein ZO-1 1 AEAS(0.122)S(0.878)PVPYLSPETNPASSTSAVNHNVNLTNVR;AEAS(0.128)S(0.872)PVPYLSPETNPASSTSAVNHNVNLTNVR;AEAS(0.003)S(0.997)PVPYLSPETNPASSTSAVNHNVNLTNVR;AEAS(0.006)S(0.994)PVPYLSPETNPASSTSAVNHNVNLTNVR 362.74 5.12E-133 1351360000 282999 344666 320573 341209 387878 277700 340927 339130 440385 TRUE FALSE 265286.5978 370185.4293 328177.1429 349965.0006 357415.6265 357867.4819 289808.1614 381471.127 366881.8985 0.723084455 1.009004344 0.894503502 0.953890072 0.97419804 0.97542965 0.789922214 1.039765463 1 18.4849562 4.750138746 24.459225 0.940520504 0.723084279 0.503551589 0.071029254 1165.126595 2461309.967 0.016366507 0.257906318 56252.1007 -4.750138746 -0.217436225 AEASSGDHPTDTEMKEEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 AEASSGDHPTDTEMKEEQK 19 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;;;;; 292.13 8.60E-50 8334880000 10857120 7103680 8895900 8685840 9275620 6112480 11452140 7586310 11375520 FALSE TRUE 10177592.24 7629643.859 9106914.949 8908733.359 8547150.221 7877053.748 9734997.923 8533477.503 9476872.223 1.073940009 0.805080377 0.960962091 0.940049961 0.901895691 0.83118708 1.027237436 0.900452945 1 23.17597956 1.723219292 24.99999996 0.973965823 0.910745817 0.097472637 0.079236388 1.850681912 3003.634545 0.033284933 0.018458153 52.87121515 -1.723219292 -0.063220005 AECRPAASENYMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AECRPAASENYMR 13 1 P13984 P13984 GTF2F2 General transcription factor IIF subunit 2 0 98.676 0.0029276 159610000 78910 88361 83650 82192 102060 68768 104170 82330 125660 FALSE TRUE 73971.16396 94903.34038 85634.2175 84301.18587 94044.61929 88620.20524 88550.67557 92609.08173 104686.5342 0.706596742 0.906547734 0.818006042 0.805272488 0.89834495 0.846529173 0.845865003 0.884632225 1 16.67571636 -5 0.166812883 1.60830459 0.804190589 0.534635456 0.052066235 109.2204533 1.023125208 21.91333647 0.183028808 1.00E-05 5 -0.804114001 AEDEKQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEDEKQR 7 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 67.169 0.086145 0 79483 86078 95220 113460 116730 79775 100670 79025 128230 FALSE TRUE 74508.30091 92451.30468 97478.66337 116371.5757 107562.4967 102804.7475 85575.46807 88891.44521 106827.5846 0.697463124 0.865425396 0.912485888 1.089340137 1.006879422 0.962342712 0.801061527 0.832101985 1 16.7049247 4.906829695 1.366576928 0.933827864 0.523373311 0.458642341 0.084044964 2.037480041 2.548915176 0.025092904 1.283075399 80691.85422 -4.906829695 -0.410454553 RPS(ph)ANCDPFSVTEALIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPSANCDPFSVTEALIR 17 1 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 1 RPS(1)ANCDPFSVTEALIR;RPS(1)ANCDPFSVTEALIR 137.64 3.86E-06 84752000 62004 62761 64898 55388 66942 70975 72943 81210 209023 TRUE FALSE 58123.28032 67407.88974 66437.41121 56809.34985 61684.64535 91464.33032 62005.87432 91349.24727 174135.711 0.333781509 0.387099747 0.381526631 0.326236069 0.354233173 0.525247405 0.356077877 0.524586524 1 17.40985257 -0.253454022 0.535724338 1.074038396 0.363174063 0.924559905 0.055467769 1.477254882 0.422922235 0.268097933 0.023074725 0.557886661 0.253454022 -0.710864333 AEDGATPSPSNET(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AEDGATPSPSNETPK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 AEDGATPSPSNET(1)PK;AEDGATPSPSNET(1)PK;AEDGATPSPSNET(1)PK;AEDGATPSPSNET(1)PK;AEDGATPSPSNET(1)PK;AEDGATPSPSNET(1)PK 381.56 1.39E-97 6111640000 10118300 5921000 7123370 6809440 6746950 4763830 8806770 5858000 4695880 TRUE FALSE 9485013.665 6359397.001 7292339.7 6984181.759 6217071.763 6139070.387 7486276.597 6589384.195 3912107.291 2.424527999 1.625568147 1.864043892 1.785273572 1.589187438 1.569248983 1.913617403 1.684356717 1 21.89951451 -2.347821354 0.210658042 3.97E-23 1.945349321 0.582936826 0.228551197 30.85271364 0.83911721 15.69285575 0.508115181 0.0044893 2.347821354 1.945349321 AEDGATPSPSNET(ph)PKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AEDGATPSPSNETPKK 16 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 AEDGAT(0.001)PS(0.001)PS(0.008)NET(0.99)PKK;AEDGATPSPSNET(1)PKK;AEDGATPSPSNET(1)PKK;AEDGATPSPSNET(1)PKK;AEDGATPSPSNET(1)PKK 347.14 2.45E-87 5098260000 4463890 2165740 2850800 2822880 2935850 1921680 3862430 2209110 2381150 TRUE FALSE 4184503.093 2326093.643 2918422.322 2895319.88 2705280.184 2476437.82 3283294.479 2484922.246 1983720.682 2.109421518 1.172591315 1.471186114 1.459540099 1.363740474 1.2483803 1.655119346 1.252657327 1 20.91977747 -3.810742276 0.159256559 3.28E-14 1.574407229 0.303298118 0.253898224 130.6376827 1.700381815 44.56367394 1.079325902 0.000154617 3.810742276 1.574407229 AEDGENYDIKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AEDGENYDIKK 11 1 E5RJD8;O75347;E5RIW3;E5RHG6;O75347-2;E5RIX8;A0A494C144 E5RJD8 TBCA Tubulin-specific chaperone A 0 ;; 174.9 1.68E-05 2264400000 4710310 2980010 3652390 3379800 3416400 2608350 4500640 3008940 4279470 FALSE TRUE 4415500.105 3200653.041 3739026.416 3466531.39 3148089.725 3361338.302 3825810.814 3384612.782 3565198.811 1.238500387 0.897748824 1.048756777 0.972324848 0.883005378 0.942819315 1.07309887 0.949347557 1 21.7655511 4.74941228 24.75324031 0.976334679 1.238500559 0.665190009 0.059555839 900.1046706 2053142.379 0.014244941 0.211531614 56158.08372 -4.74941228 0.26216588 AEDGHAVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEDGHAVAK 9 0 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 101.65 0.003842 489540000 1083140 985310 984150 979660 1121550 791690 1295450 1033510 1244590 FALSE TRUE 1015348.201 1058263.378 1007494.503 1004799.734 1033467.987 1020238.051 1101209.299 1162545.999 1036859.889 0.979253043 1.020642605 0.97167854 0.969079569 0.996728679 0.983969061 1.062061819 1.121218027 1 19.98378952 1.689982205 4.850413221 1.070157467 0.988658604 0.533246948 0.032375874 0.106233601 5.823856026 0.015651722 0.0076293 48.97587511 -1.689982205 -0.081498864 AEDKEWMPVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AEDKEWMPVTK 11 1 P15880;E9PQD7;E9PPT0;E9PMM9 P15880 RPS2 40S ribosomal protein S2 0 ;;;; 166.6 1.84E-05 6314660000 10286320 7408685 8671740 7686205 7977670 6165391 10013506 7319576 9311660 FALSE TRUE 9642517.593 7957231.746 8877437.768 7883446.033 7351135.979 7945239.295 8512073.736 8233441.176 7757483.79 1.242995519 1.025749065 1.144370779 1.016237513 0.947618606 1.024203145 1.097272513 1.061354609 1 22.88715735 4.742893869 24.56664476 1.049363859 1.242995618 0.575680158 0.054306022 288.1586949 1633590.847 0.013472185 0.106356127 55321.48999 -4.742893869 0.193631759 AEDNADTLALVFEAPNQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEDNADTLALVFEAPNQEK 19 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 280.62 2.80E-39 27996000 107250 90191 97253 98609 113490 85380 131590 97301 135770 FALSE TRUE 100537.4139 96868.83548 99559.88709 101139.4739 104576.9532 110027.82 111859.3011 109449.244 113109.1099 0.888853374 0.856419395 0.880211039 0.894176198 0.924567025 0.972758252 0.988950415 0.96764305 1 16.7873556 2.498400404 1.311086981 0.987997697 0.870855523 0.947416249 0.011470145 0.078837813 0.274474362 0.00553875 0.004157694 315.065176 -2.498400404 -0.117142174 AEDNFEDIITKPPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEDNFEDIITKPPVR 15 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 101.53 0.0015835 141780000 44120 47334 45564 48274 49797 36579 48836 43063 56316 FALSE TRUE 41358.60796 50838.65861 46644.7996 49512.79257 45886.14449 47138.76349 41513.49517 48439.51034 46916.49578 0.881536595 1.083598802 0.994208941 1.055338677 0.978038614 1.004737517 0.884837933 1.03246224 1 15.51780764 2.195587877 2.630862174 0.959170665 1.013936929 0 0.065835613 0.566517647 7.979045994 0.026455746 0.018118112 156.8873319 -2.195587877 0.054766265 AEDQTES(ph)SCESHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEDQTESSCESHR 13 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 AEDQTES(0.947)S(0.053)CESHR;AEDQTES(0.797)S(0.203)CESHR 194.05 8.68E-07 441160000 567670 673550 598090 656510 681470 464880 954490 639020 735780 TRUE FALSE 532140.548 723420.3428 612276.9772 673357.1581 627950.0951 599083.3093 811373.0856 718803.0537 612973.5647 0.868129686 1.18018196 0.998863593 1.098509294 1.024432588 0.977339552 1.323667336 1.172649352 1 19.22546533 1.753500472 25 1.196310995 1.042401564 0.234056293 0.112680099 5.918167861 9916.151579 0.046890718 0.026003517 56.68921881 -1.753500472 -0.153909431 AEDQTESS(ph)CESHRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEDQTESSCESHRK 14 1 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 AEDQTES(0.122)S(0.867)CES(0.011)HRK 183.53 8.56E-07 380040000 135630 134550 111290 137040 143080 84924 201090 125290 175960 TRUE FALSE 127141.1604 144512.222 113929.8514 140556.6784 131843.074 109440.1802 170938.4213 140932.7323 146591.1393 0.867318182 0.985818261 0.777194665 0.95883475 0.899393201 0.746567499 1.166089725 0.961400075 1 17.16143838 1.735159697 24.99999998 1.050507267 0.878947277 0.450002959 0.088245297 0.340521936 2470.258887 0.037398594 0.020739371 54.34501295 -1.735159697 -0.171559991 AEDQTESSCESHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEDQTESSCESHR 13 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 0 89.992 0.0071952 56019000 33359 36472 40837 35082 31207 33307 34707 34259 33914 FALSE TRUE 31271.11974 39172.42483 41805.67292 35982.26351 28756.1281 42922.19021 29503.00755 38536.31156 28253.53431 1.106803821 1.38646105 1.479661711 1.273549112 1.017788705 1.519179503 1.044223609 1.363946583 1 14.78614373 0.193137886 0.326491756 0.940861939 1.34679222 0.160431845 0.177109058 6.257870608 1.113121789 0.746650306 0.17860486 1.560047729 -0.193137886 0.405930281 AEDREQLVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 AEDREQLVAK 10 1 Q13268;C9JZP6;Q13268-2;H0YJP4 Q13268;H0YJP4 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;;;;;;; 188.28 1.04E-06 30959190000 28806140 25353300 23688400 23071590 34995740 21473110 25865990 26499120 47189300 FALSE TRUE 27003215.12 27230484.71 24250300.03 23663646.06 32247315.75 27672048.27 21987624.93 29807593.46 39313100.98 0.686875735 0.692656749 0.616850348 0.601927741 0.820268942 0.703888719 0.559295105 0.758210182 1 25.22850683 0.981633605 22.52655731 1.000000004 0.664949648 0.68831069 0.070187809 186.6635295 228945.6543 0.066641349 0.016660337 9.585915694 -0.981633605 -0.335050357 AEDS(ph)DS(ph)EPEPEDNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEDSDSEPEPEDNVR 15 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 2 AEDS(1)DS(1)EPEPEDNVR;AEDS(1)DS(1)EPEPEDNVR 327.1 1.34E-68 458410000 718070 519500 651920 641640 514430 526230 713180 465670 638760 TRUE FALSE 673127.2805 557964.3205 667383.8503 658105.5687 474028.7429 678144.0584 606245.2798 523809.9246 532146.8295 1.264927729 1.048515728 1.254134786 1.23669922 0.890785619 1.274355161 1.139244371 0.98433345 1 19.02146484 1.260204484 6.685106601 0.991155505 1.156142229 0.257391255 0.117472841 0.193077403 32.590553 0.079218237 0.026498682 18.20557853 -1.260204484 0.164986725 INFDKYHPGYFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 INFDKYHPGYFGK 13 1 P46776;E9PLL6 P46776 RPL27A 60S ribosomal protein L27a 0 ; 141.46 2.39E-05 2260610000 4916500 6969200 5533700 5754900 8523800 3786300 7998000 5862000 15015800 FALSE TRUE 4608785.041 7485206.819 5664961.977 5902580.477 7854375.131 4879343.345 6798774.15 6593883.604 12509565.97 0.368420859 0.598358635 0.452850402 0.471845345 0.627869516 0.390048972 0.543486014 0.527107305 1 23.5765284 0.173537804 1.325772037 1.000636307 0.499413547 0.789972436 0.081620148 3.220124754 4.720920734 0.072210133 0.020296818 1.491206556 -0.173537804 -0.50122276 AEEAEAQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AEEAEAQKR 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 139.38 0.00017899 1565840000 1384550 1360750 1312230 1390650 1557770 1077300 1730530 1346170 1533520 FALSE TRUE 1297893.487 1461501.346 1343356.715 1426336.433 1435429.028 1388299.021 1471053.092 1514242.288 1277565.605 1.015911419 1.143973617 1.051497246 1.11644868 1.123565805 1.086675327 1.151450138 1.185255991 1 20.28496595 3.082616992 12.55945615 1.119474463 1.08351395 0.069511793 0.057703159 1.64070983 242.7616827 0.015167586 0.018131833 1209.530968 -3.082616992 -0.035960513 AEEDEILNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AEEDEILNR 9 0 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 ;;; 218.06 1.26E-06 1129370000 1989710 1783430 1616010 1500870 1868310 1556490 2255860 1719420 1619730 FALSE TRUE 1865177.603 1915477.013 1654342.52 1539384.865 1721580.469 2005823.395 1917614.735 1934093.372 1349386.599 1.382241089 1.419516849 1.225995961 1.140803433 1.27582449 1.486470517 1.421101067 1.433313013 1 20.36387231 AEEDEILNRS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 AEEDEILNRSPR 12 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR 256.04 9.77E-21 1.34236E+11 48089869 48976017 40891008 42099844 58528438 38742455 58750142 48510778 55023158 TRUE FALSE 45080009.94 52602252.26 41860962.02 43180197.27 53931850.57 49926772.83 49941103.62 54567455.42 45839437.47 0.983432879 1.147532674 0.913208458 0.94198794 1.176538229 1.089166351 1.089478981 1.190404124 1 25.450086 2.73853348 25 1.110789445 1.007817182 0.325579212 0.079761252 3.222606118 2968105.468 0.02474693 0.024698963 547.6883212 -2.73853348 -0.102972264 AEEDKLEQIKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEEDKLEQIKK 11 2 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 101.89 0.0016578 404360000 708390 414930 498260 568920 593810 312800 682050 407590 463730 FALSE TRUE 664053.1344 445651.8489 510078.9625 583519.4504 547174.5579 403100.2821 579782.9343 458478.5087 386330.4672 1.718873324 1.153550876 1.320317722 1.510415305 1.416338095 1.043407953 1.500743492 1.18675214 1 18.55947593 -3.961522205 0.207579386 1.76E-16 1.397454496 0.299136337 0.1895902 127.2114217 1.869270727 53.64011775 0.400639132 0.000109264 3.961522205 1.397454496 AEEFKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AEEFKK 6 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;;;; 100.07 0.061064 15695700000 19279000 15870030 18560040 19485230 20816400 15090800 27668400 18000680 26535200 FALSE TRUE 18072361.8 17045063.53 19000292.91 19985253.99 19181563.91 19447268.98 23519780.28 20248104.52 22106303.7 0.817520742 0.771049913 0.859496602 0.904052268 0.867696571 0.879715996 1.063939979 0.915942566 1 24.39795448 2.631308246 0.573537388 1.008229611 0.785818119 0.647951963 0.049888204 0.486438784 0.33402519 0.041389166 0.043434164 427.8664618 -2.631308246 -0.222411492 AEEGKS(ph)PFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEEGKSPFR 9 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 AEEGKS(1)PFR;AEEGKS(1)PFR 64.121 0.043355 531910000 804720 556640 644550 627340 630740 565990 825340 600270 615890 TRUE FALSE 754354.0117 597854.2048 659839.0304 643438.6065 581204.2247 729382.1249 701587.9291 675215.0309 513093.9802 1.470206318 1.165194346 1.286000335 1.254036553 1.132744189 1.421537093 1.367367298 1.315967555 1 18.96886357 4.757679823 23.44252637 1.263365782 1.470206759 0.239425306 0.122593257 2803.046656 3436752.344 0.027660707 0.900067471 57237.39008 -4.757679823 0.206840977 AEEIEHYAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEEIEHYAR 9 0 H0Y5G7;A2RRP1-2;A2RRP1;C9JCM7 H0Y5G7 NBAS Neuroblastoma-amplified sequence 0 65.404 0.082315 0 79544 93645 92250 91066 110020 101200 106890 91445 95716 FALSE TRUE 74565.48303 100578.5732 94438.21356 93402.90773 101379.473 130414.7972 90862.83682 102862.1095 79740.38125 0.935103167 1.261325462 1.184321069 1.171337612 1.271369304 1.635492521 1.139483351 1.2899626 1 16.28302288 4.739256278 23.45139022 1.255298359 0.935103006 0.261706552 0.162180066 31.78589719 1070975.437 0.035720218 0.213245594 54860.05997 -4.739256278 -0.320195352 AEEILEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AEEILEK 7 0 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ;;; 124.08 0.0097275 898100000 1847740 1584060 1670280 1601810 1688040 1226020 1875740 1434010 1817960 FALSE TRUE 1732093.252 1701345.451 1709899.83 1642915.156 1555468.148 1579952.071 1594490.201 1613049.305 1514530.732 1.143650119 1.123348252 1.128996457 1.084768452 1.027029769 1.043195782 1.052794881 1.06504891 1 20.53043942 3.034390783 2.904994337 1.042427659 1.130060496 0.84800192 0.018187843 0.091107877 1.570569678 0.005240483 0.006207089 1082.407476 -3.034390783 0.087632837 AEEKLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEEKLR 6 1 K7EM46 REV__Q08AD1-2 KIAA1328 0 74.743 0.072525 170960000 614370 542630 519880 473960 613960 456860 609530 496930 652810 FALSE TRUE 575917.6784 582806.8898 532211.7991 486122.616 565742.0582 588748.0655 518136.6351 558972.8044 543851.7937 1.058960704 1.071628147 0.97859712 0.893851269 1.040250423 1.082552402 0.952716606 1.02780355 1 19.05285403 4.026908333 3.768904619 0.995069102 1.064459893 0.239008521 0.050799173 0.321085048 9.353673554 0.01291425 0.029209118 10639.18431 -4.026908333 0.069390791 AEEKS(ph)PISINVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AEEKSPISINVK 12 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 1 AEEKS(0.991)PIS(0.009)INVK;AEEKS(0.962)PIS(0.038)INVK;AEEKS(0.995)PIS(0.005)INVK;AEEKS(0.999)PIS(0.001)INVK 193.77 1.44E-06 4753570000 6001270 3789780 4282430 4383150 4564820 3168920 5912240 3715690 5100710 TRUE FALSE 5625661.223 4070379.254 4384011.262 4495629.05 4206317.451 4083735.761 5025754.499 4179602.076 4249368.549 1.323881692 0.957878614 1.031685346 1.057952258 0.989868825 0.961021788 1.182706193 0.98358192 1 22.01881704 4.74702128 24.78847037 1.027971098 1.323881859 0.678966255 0.06536679 608.0780402 1781532.43 0.015855341 0.181845591 55849.75601 -4.74702128 0.295910762 AEELS(ph)PAALS(ph)PSLEPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEELSPAALSPSLEPIR 17 0 A0A2R8YF49;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 2 AEELS(1)PAALS(0.995)PS(0.005)LEPIR 133.52 2.93E-05 23792000 125130 126520 140300 158560 153480 119480 123830 99837 150360 TRUE FALSE 117298.3367 135887.6724 143627.9823 162628.918 141426.2999 153971.9364 105262.8411 112301.8692 125263.9446 0.936409411 1.08481074 1.146602741 1.298289931 1.129026396 1.229180007 0.840328327 0.896521897 1 16.93461169 1.724511883 9.397676325 0.904396599 1.138161441 0.525278305 0.100658494 0.078268515 21.44674063 0.047195497 0.025405148 53.02881023 -1.724511883 0.233764842 AEELS(ph)PAALSPLLEPIR ddPTM_SK-BR-3_Pertuzumab_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 177.58 1.07E-09 75865100 85433 93855 101864 132412 115425 73956 79177 61003.1 73637.8 TRUE FALSE 80085.90103 100804.1219 104280.2622 135809.9161 106359.9861 95305.89662 67305.14389 68619.47132 61347.17546 1.305453763 1.643174622 1.699838035 2.213792486 1.733738926 1.553549873 1.097118871 1.118543287 1 15.9047093 1.820361763 2.689892116 1.061541295 1.726544503 0.64698042 0.218852499 0.170316148 2.292816883 0.127464944 0.062116664 66.12440281 -1.820361763 0.665003209 AEELSPAALS(ph)PSLEPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AEELSPAALSPSLEPIR 17 0 A0A2R8YF49;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 AEELSPAALS(0.98)PS(0.02)LEPIR;AEELSPAALS(0.991)PS(0.009)LEPIR;AEELSPAALS(0.993)PS(0.007)LEPIR;AEELSPAALS(1)PSLEPIR 313.04 3.71E-58 267918000 292759 330229 378789 470015 502789 244661 245009 211272 323796 TRUE FALSE 274435.7368 354679.4988 387774.054 482076.3806 463301.9801 315290.659 208272.175 237649.7743 269752.3558 1.01736178 1.31483374 1.437518693 1.787107212 1.71750856 1.16881522 0.772086584 0.880992396 1 18.04127603 1.988307518 5.279093855 0.879996694 1.449709869 0.594617702 0.21555587 0.127219375 11.00753049 0.095003356 0.061888293 97.34362563 -1.988307518 0.569713175 AEENTDQAS(ph)PQEDYAGFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEENTDQASPQEDYAGFER 19 0 Q9NU22 Q9NU22 MDN1 Midasin 1 AEENTDQAS(1)PQEDYAGFER;AEENTDQAS(1)PQEDYAGFER 454.88 9.58E-192 343210000 367910 399940 393780 387270 369450 312370 490680 363380 411610 TRUE FALSE 344883.1698 429551.9737 403120.6476 397208.0038 340434.8873 402546.1481 417107.0892 408748.7929 342909.6319 1.005755271 1.252668149 1.175588581 1.15834601 0.9927831 1.173913214 1.216376125 1.192001492 1 18.3874689 2.989163869 24.59924006 1.133908062 1.171572029 0 0.096443291 1812.516364 4114628.252 0.028029155 0.031531517 975.3575914 -2.989163869 0.037663967 AEEQQLPPPLS(ph)PPS(ph)PSTPNHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEEQQLPPPLSPPSPSTPNHR 21 0 A0A494BZV2;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 2 AEEQQLPPPLS(0.995)PPS(0.912)PS(0.077)T(0.016)PNHR 99.536 0.00043436 781740000 109500 141370 145110 133700 143410 127230 139610 116440 140610 TRUE FALSE 102646.5905 151837.1819 148552.0777 137130.9684 132147.1571 163959.2356 118676.7766 130977.7903 117141.2826 0.87626316 1.296188487 1.268144538 1.170645952 1.12810065 1.399670824 1.013108051 1.118118117 1 16.83789007 1.616265077 25 1.049208006 1.20792373 0.188932148 0.139212586 0.943321412 2799.738977 0.060607061 0.032914163 41.32996872 -1.616265077 0.158715724 AEEQQLPPPLS(ph)PPSPSTPNHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEEQQLPPPLSPPSPSTPNHR 21 0 A0A494BZV2;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 AEEQQLPPPLS(0.992)PPS(0.007)PSTPNHR;AEEQQLPPPLS(0.999)PPS(0.001)PSTPNHR 136.53 3.09E-06 335080000 254479 304450 282710 264556 320290 301450 377850 310240 375320 TRUE FALSE 238551.6136 326991.7948 289416.0147 271344.9549 295135.7154 388473.7214 321194.9003 348974.1469 312676.6673 0.76293385 1.045782525 0.925607968 0.86781325 0.943900669 1.242413528 1.027242944 1.116086307 1 18.25431204 2.396610622 11.76294929 1.096094415 0.926620036 0.488665384 0.094420354 0.488259209 68.99039918 0.030354235 0.02538981 249.2359136 -2.396610622 -0.169474379 AEEQQLPPPLSPPS(ph)PSTPNHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AEEQQLPPPLSPPSPSTPNHR 21 0 A0A494BZV2;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 AEEQQLPPPLS(0.02)PPS(0.703)PS(0.212)T(0.065)PNHR;AEEQQLPPPLS(0.012)PPS(0.617)PS(0.285)T(0.086)PNHR;AEEQQLPPPLS(0.017)PPS(0.956)PS(0.023)T(0.005)PNHR 129.72 1.03E-05 819360000 839460 950990 881670 796730 901060 837330 1070010 873340 1042750 TRUE FALSE 786919.6971 1021402.289 902583.6288 817175.4407 830294.3823 1079053.578 909571.934 982378.4215 868708.2886 0.905850338 1.175771318 1.03899507 0.940678766 0.955780431 1.2421357 1.047039548 1.130849601 1 19.72851228 2.276026926 24.99998504 1.107053772 1.028918506 0.190027635 0.096508022 341.4663437 227847.6077 0.033048066 0.027649443 188.8108407 -2.276026926 -0.078135266 AEEYEFLTPVEEAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AEEYEFLTPVEEAPK 15 0 P52565;J3KTF8;J3QQX2;J3KRE2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;; 215.46 5.44E-12 147012000 483719 347897 384575 384806 412375 279228 501188 370186 465339 FALSE TRUE 453443.8913 373655.6559 393697.3006 394680.7734 379988.7309 359836.5907 426039.5122 416404.537 387670.9147 1.169661881 0.963847536 1.015545107 1.018081983 0.98018375 0.928201155 1.098972082 1.074118592 1 18.56447297 -0.713284487 4.646549731 0.999999976 1.022833663 0.007055514 0.070170522 1.61E-08 4.48E-09 0.063479928 0.014962347 0.193515392 0.713284487 0.022833686 AEFAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AEFAER 6 0 P06753-2;A0A087WWU8;P06753-6;P06753-5;P06753-7;A0A494C034;A0A2R8Y6A3;A0A494C0I0;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YE05;K7ENT6;A0A5F9UN72;K7EPB9;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2 TPM3;TPM1;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain 0 ;;;; 132.72 0.034376 8823610000 7868960 9754690 8580440 8525330 9757680 7584130 8998740 8105330 8832440 FALSE TRUE 7376455.84 10476937.4 8783972.089 8744104.401 8991351.173 9773545.213 7649462.477 9117298.293 7358248.704 1.002474384 1.423835728 1.193758521 1.188340426 1.221941733 1.328243391 1.039576506 1.239058186 1 22.81093101 0.746209047 0.515514611 0.994676963 1.248676822 0.183954327 0.124350558 1.803850179 1.046266273 0.148124672 0.059867166 5.57454014 -0.746209047 0.253999858 AEFEDQDDEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEFEDQDDEAR 11 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 0 ; 358.56 7.13E-71 882900000 959290 915990 951720 997990 1005170 833740 1051130 828780 978330 FALSE TRUE 899249.7513 983810.8527 974295.2478 1023600.113 926228.0029 1074427.203 893522.8147 932255.0074 815040.4027 1.103319232 1.207070041 1.195395031 1.2558888 1.13641974 1.318250236 1.096292664 1.143814471 1 19.63651205 0.952824865 1.269820913 1.003818049 1.199155812 0.461007893 0.065375344 0.407217436 1.334284337 0.054051813 0.016570197 8.970669666 -0.952824865 0.195337762 AEFEVHEVYAVDVLVSSGEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 18 AEFEVHEVYAVDVLVSSGEGK 21 0 Q9UQ80;Q9UQ80-2;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;;;;;;;;;;;;;;;;; 182.22 4.75E-17 609642300 1209109.4 1017188.2 1148621.9 1109478 1156316.9 930187.1 1397017.9 978838.5 1295544 FALSE TRUE 1133433.401 1092501.873 1175867.754 1137949.084 1065504.435 1198717.015 1187548.035 1101048.641 1079309.337 1.050146943 1.012223128 1.089463154 1.054330807 0.987209504 1.110633416 1.10028515 1.020141866 1 20.04167698 2.216255876 24.99967602 1.071372172 1.042704968 0 0.0427937 583.81273 654346.998 0.015329935 0.011331118 164.5340832 -2.216255876 -0.028667203 AEFFQHLIEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AEFFQHLIEDR 11 0 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 0 ;; 191.26 1.91E-06 165689000 286640 365231 350547 360989 393546 305335 377877 349696 339827 FALSE TRUE 268699.7141 392273.0833 358862.1404 370252.5889 362638.4846 393480.2578 321217.8519 393356.3154 283107.6783 0.949107829 1.385596765 1.2675818 1.307815426 1.280920697 1.389860777 1.134613705 1.389422985 1 18.11099135 -1.310320693 4.398909495 0.999748584 1.2717877 0.269619996 0.135429324 0.000292184 4.58E-05 0.114736367 0.027018807 0.048941729 1.310320693 0.272039116 AEFTS(ph)PPSLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AEFTSPPSLFK 11 0 Q6UN15;Q6UN15-5;Q6UN15-3;A0A0B4J203;Q6UN15-4 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 AEFT(0.009)S(0.92)PPS(0.07)LFK;AEFT(0.041)S(0.945)PPS(0.014)LFK;AEFT(0.001)S(0.998)PPS(0.001)LFK 207.47 2.40E-08 227637000 1586550 1256640 1516890 1350410 1437400 1223230 1862170 1255540 1725470 TRUE FALSE 1487250.668 1349682.933 1552871.347 1385063.807 1324512.402 1576356.644 1582954.896 1412296.933 1437477.91 1.034625059 0.938924295 1.080274929 0.963537455 0.921414091 1.096612777 1.101202937 0.982482529 1 20.45510836 2.218804747 24.9997962 1.060157739 0.992611911 0.168697193 0.0586068 354.2234716 448244.4573 0.021355519 0.015793485 165.502572 -2.218804747 -0.067545828 AEFTSPPS(ph)LFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEFTSPPSLFK 11 0 Q6UN15;Q6UN15-5;Q6UN15-3;A0A0B4J203;Q6UN15-4 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 AEFT(0.036)S(0.058)PPS(0.906)LFK 90.657 0.011878 25508000 246590 183980 218420 205070 209800 191290 273150 196980 234210 TRUE FALSE 231156.3721 197602.0706 223601.0255 210332.4434 193323.1543 246512.3177 232193.6933 221573.3866 195118.8379 1.184695309 1.012726771 1.145973541 1.077970972 0.990796974 1.263395786 1.190011665 1.135581725 1 17.57399355 2.239843536 24.99999502 1.169549601 1.08138922 0.098868535 0.086218827 52.27648924 1018725.822 0.028056697 0.022290726 173.7174862 -2.239843536 -0.08816038 AEGAGRPPPAT(ph)PPRPPPSTSAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEGAGRPPPATPPRPPPSTSAVR 23 2 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 AEGAGRPPPAT(1)PPRPPPSTSAVR;AEGAGRPPPAT(1)PPRPPPSTSAVR 135.3 0.00075136 469180000 22422.6 22171.1 30036 31662 31501 22599 32862 25739.8 28940 TRUE FALSE 21019.20949 23812.67131 30748.4681 32474.50052 29027.03853 29122.96444 27934.64818 28953.47069 24109.72704 0.871814494 0.987679009 1.275355298 1.346946005 1.203955502 1.207934225 1.158646389 1.200904126 1 14.5573277 4.289568145 2.222490154 1.208921287 0.883120734 0.622877365 0.088904877 0.20272206 1.857230186 0.021835938 0.089246843 19479.06673 -4.289568145 -0.325800553 AEGDVAALNRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AEGDVAALNRR 11 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;; 149.33 5.52E-05 799950000 623290 1052550 736730 817560 1092570 603310 945000 829790 1441620 FALSE TRUE 584279.3915 1130481.897 754205.5835 838539.9737 1006763.959 777475.8031 803306.0229 933391.1081 1201004.309 0.486492336 0.941280467 0.627979082 0.698198972 0.838268399 0.647354716 0.668861899 0.777175487 1 20.1958099 0.911345533 6.421043761 0.999996289 0.71721027 0.367487933 0.121856322 1.269123173 91.23179861 0.107125785 0.026902134 8.153527367 -0.911345533 -0.282786019 AEGEPQEES(ph)PLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AEGEPQEESPLK 12 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 AEGEPQEES(1)PLK;AEGEPQEES(1)PLK;AEGEPQEES(1)PLK 214.11 8.09E-10 873470000 2002320 1132080 1471310 1294730 1314080 1188290 1827290 1229020 1577830 TRUE FALSE 1876998.365 1215900.381 1506210.168 1327954.964 1210877.458 1531330.033 1553304.828 1382465.852 1314479.98 1.427939865 0.925004869 1.145860105 1.01025119 0.921183644 1.164970221 1.181687703 1.051720736 1 20.32606074 4.752393027 24.82790359 1.062433381 1.427940135 0.619288402 0.092657783 1606.436563 2883350.7 0.022731362 0.460402968 56544.84617 -4.752393027 0.365506754 AEGEPQEES(ph)PLKSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AEGEPQEESPLKSK 14 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 AEGEPQEES(1)PLKSK;AEGEPQEES(1)PLKSK;AEGEPQEES(1)PLKSK;AEGEPQEES(1)PLKSK;AEGEPQEES(0.998)PLKS(0.002)K 192.6 2.15E-07 1717710000 2862570 1504184 1961500 1950760 2181620 1435001 2544740 1610172 3198810 TRUE FALSE 2683406.854 1615555.348 2008027.706 2000819.804 2010284.365 1849262.493 2163179.861 1811205.519 2664907.946 1.006941669 0.606233079 0.753507343 0.750802596 0.754354149 0.693931097 0.811727799 0.679650313 1 21.34565427 -1.680742661 2.883813406 1.030584118 0.74516773 0.340403681 0.10507251 27842547.4 27373664.7 6267708.857 0.023153481 0.020857264 1.680742661 -0.285416388 AEGEWEDQEALDYFS(ph)DK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEGEWEDQEALDYFSDK 17 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 AEGEWEDQEALDYFS(1)DK 151.95 2.42E-07 26821000 52394 38150 41224 40763 41757 43469 54173 39604 41115 TRUE FALSE 49114.75307 40974.6657 42201.85275 41809.04759 38477.57366 56017.79464 46050.26157 44548.64658 34252.64089 1.433896826 1.196248366 1.232075882 1.220608003 1.123346191 1.635429946 1.344429521 1.300590128 1 15.0639276 AEGEWEDQEALDYFS(ph)DKESGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AEGEWEDQEALDYFSDKESGK 21 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDY(0.007)FS(0.991)DKES(0.002)GK;AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDYFS(1)DKESGK;AEGEWEDQEALDYFS(1)DKESGK 245.49 1.93E-30 12271320000 2251910 986090 1355604 1308976 1396703 1034975 1814996 1101671 1903522 TRUE FALSE 2110966.973 1059101.13 1387759.567 1342566.54 1287011.58 1333755.481 1542854.199 1239217.049 1585811.881 1.331158505 0.667860509 0.875109831 0.846611478 0.811578975 0.841055296 0.972911237 0.781440134 1 20.59679021 -0.182027152 6.756668554 0.999999996 0.871226123 0.02624862 0.175241351 21500971.95 140318379.9 0.150109305 0.037527325 0.657616721 0.182027152 -0.128773873 AEGFVDALHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AEGFVDALHR 10 0 Q96I24;A0A494C1K6 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ;;; 156.48 1.09E-05 1374290000 990830 1229750 1034400 1026080 1239920 907310 1093850 992300 1114300 FALSE TRUE 928815.719 1320801.97 1058936.456 1052410.95 1142541.685 1169235.668 929837.3473 1116190.839 928316.1313 1.000538165 1.422793297 1.140706728 1.133677327 1.230767888 1.259523161 1.001638683 1.202382251 1 19.82425666 1.286652387 0.483428451 1.000919406 1.232453148 0.13933544 0.124729701 1.323777249 0.83504149 0.130852417 0.074949089 19.34872654 -1.286652387 0.231533742 AEGGGGGGRPGAPAAGDGKTEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEGGGGGGRPGAPAAGDGKTEQK 23 2 Q00839 Q00839 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 56.766 0.048818 27505000 42691 28850 32064 32657 33390 24406 40987 26811 56999 FALSE TRUE 40019.04652 30986.08402 32824.57322 33495.03391 30767.68409 31451.616 34841.37985 30158.41237 47485.49867 0.842763531 0.652537825 0.691254681 0.705373953 0.647938528 0.662341491 0.733726734 0.635107837 1 15.53519938 -1.345809989 3.334268711 1.002025245 0.692379244 0.717328112 0.059851458 12962203.6 20646392.99 264454.2819 0.012756961 0.045101399 1.345809989 -0.309646 AEGIEGETLTAS(ph)PQAPGS(ph)PEDSEGVPLISLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEGIEGETLTASPQAPGSPEDSEGVPLISLPR 32 0 Q5T011-5;Q5T011 Q5T011-5 SZT2 Protein SZT2 2 AEGIEGETLTAS(1)PQAPGS(0.993)PEDS(0.007)EGVPLISLPR 119.03 3.89E-07 35963000 25653 25934 27502 30506 32421 22725 34928 25491 28168 TRUE FALSE 24047.42452 27854.18034 28154.36043 31288.83561 29874.78544 29285.33859 29690.87066 28673.60746 23466.57883 1.02475204 1.186972355 1.199764168 1.333336054 1.273078008 1.247959441 1.265240701 1.221891255 1 14.51831991 5.422608205 1.060042526 1.238948828 0.425383923 0.303452976 0.088321044 6.588389244 2.135167703 0.022631718 8.569541406 264611.1893 -5.422608205 -0.813564905 AEGKVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEGKVER 7 1 Q9ULH0-5;Q9ULH0-2;Q9ULH0-4;Q9ULH0 Q9ULH0-5 KIDINS220 Kinase D-interacting substrate of 220 kDa 0 60.961 0.086052 681400000 809050 524520 559050 545520 560020 392820 621760 487480 914920 FALSE TRUE 758413.0047 563356.0066 572310.93 559518.9668 516038.2882 506220.7571 528532.8601 548342.9511 762213.9414 0.995013294 0.739104831 0.750853401 0.734070759 0.677025518 0.664145235 0.693417991 0.719408189 1 19.53983647 -1.434890896 2.982980753 1.005421924 0.736940317 0.419580869 0.093034421 11814734.07 14416375.39 541715.9155 0.020865757 0.036737458 1.434890896 -0.268481607 AEGLEEADTGASGCHSHPEEQPTSIS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEGLEEADTGASGCHSHPEEQPTSISPSR 29 0 Q9BV36-2;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 AEGLEEADTGASGCHSHPEEQPTS(0.001)IS(0.997)PS(0.002)R 325.69 3.92E-93 701700000 175250 240640 269800 290620 319390 248180 288500 230460 219880 TRUE FALSE 164281.4153 258457.236 276199.7834 298077.8012 294306.3978 319825.5371 245242.1033 259233.4383 183180.6075 0.896827549 1.410942127 1.507800346 1.627234483 1.60664604 1.745957399 1.338799487 1.415179488 1 17.48290725 0.620796423 1.633790697 1.000738001 1.470821961 0.270412711 0.228244823 2.115001503 7.457374696 0.208769244 0.059569348 4.176345535 -0.620796423 0.470083961 AEGNDHIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEGNDHIER 9 0 A0A0G2JP90;A0A087WW46;J3KN36;A0A0G2JN29;A0A087X117;Q5JPE7-3;Q5JPE7-2;Q15155;P69849;Q5JPE7;A0A087WTD5 A0A0G2JP90 NOMO1;NOMO3;NOMO2 Nodal modulator 2;Nodal modulator 1;Nodal modulator 3 0 129.39 0.00039068 68109000 90171 87749 80961 77023 94748 69106 96658 87695 98752 FALSE TRUE 84527.35807 94246.02726 82881.43315 78999.54058 87306.87428 89055.78036 82165.03023 98643.91379 82269.65324 1.027442742 1.145574626 1.007436277 0.960251289 1.061228179 1.082486395 0.998728292 1.199031598 1 16.32807274 -0.336417667 7.502280393 0.999999979 1.056877797 0.065468197 0.070536429 0 0 0.063402447 0.0149441 0.460874133 0.336417667 0.056877818 AEGPLDS(ph)PSEGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEGPLDSPSEGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTK 42 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;F8W1U7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 AEGPLDS(0.908)PS(0.038)EGHS(0.043)YQNS(0.009)GLDHFQNS(0.002)NIDQSFWETFGSAEPTK;AEGPLDS(0.543)PS(0.198)EGHS(0.085)Y(0.051)QNS(0.085)GLDHFQNS(0.035)NIDQS(0.002)FWETFGSAEPTK 169.13 9.65E-20 229886000 46248 52320 62270 76361 78868 49544 59740 51231 63340 TRUE FALSE 43353.42024 56193.82724 63747.07381 78320.55254 72674.02542 63846.54852 50782.5416 57627.30312 52768.14481 0.82158318 1.064919516 1.208059788 1.484239266 1.377232906 1.209944916 0.962371176 1.09208507 1 15.68737964 1.754641635 14.81391656 1.020942187 1.199169525 0.179657601 0.177229901 0.590489024 543.9478741 0.086741764 0.04787756 56.83837259 -1.754641635 0.178227338 AEGPLDSPS(ph)EGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTK ddPTM_SK-BR-3_Pertuzumab_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(0.065)PS(0.267)EGHS(0.267)Y(0.238)QNS(0.082)GLDHFQNS(0.082)NIDQSFWETFGSAEPTK 80.184 0.0012156 432720000 11643 13439 14745 15996 20694 12556 16731 12741 19244 TRUE FALSE 10914.28541 14434.03754 15094.75836 16406.48444 19068.77672 16180.71337 14222.34187 14331.7419 16032.05208 0.680779064 0.900323768 0.941536261 1.023355236 1.189415842 1.009272755 0.887119241 0.893943073 1 13.96867148 5.350644884 0.988724948 0.990341384 6.64E-08 0.574914847 0.084385188 4.668950218 1.552701195 0.027666733 6.570096494 224204.7887 -5.350644884 -0.990341317 AEGPLDSPSEGHS(ph)YQNSGLDHFQNSNIDQSFWETFGSAEPTK ddPTM_SK-BR-3_Pertuzumab_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(0.026)PS(0.013)EGHS(0.946)YQNS(0.015)GLDHFQNSNIDQSFWETFGSAEPTK 151.48 1.69E-13 460800000 21137 22013 22551 29053 41846 19555 35006 28155 34164 TRUE FALSE 19814.0729 23642.86542 23085.92037 29798.54917 38559.58396 25200.21105 29757.17528 31670.21373 28461.80769 0.696163544 0.830687414 0.811119259 1.046966148 1.354783378 0.885404445 1.045512485 1.112726713 1 14.79673967 3.232430049 5.048658516 1.075968592 0.792429997 0.567410637 0.121560257 0.131223812 9.249737016 0.033664629 0.043022823 1707.772629 -3.232430049 -0.283538595 AEGS(ph)PNQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AEGSPNQGK 9 0 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 AEGS(1)PNQGK;AEGS(1)PNQGK;AEGS(1)PNQGK 137.01 0.0013084 309000000 1369130 836030 1390890 1159810 1157850 836810 1536570 971040 1003890 TRUE FALSE 1283438.597 897930.5311 1423882.568 1189572.688 1066917.132 1078383.463 1306175.593 1092276.482 836334.2736 1.534600025 1.073650285 1.702528059 1.422365106 1.275706575 1.2894168 1.561786518 1.306028601 1 19.67372016 0.97818775 22.58541181 0.999999986 1.404452575 0.354453972 0.173237505 544.5895076 563895.2448 0.159702922 0.03992573 9.510158395 -0.97818775 0.404452588 AEGS(ph)PNQGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEGSPNQGKK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 AEGS(1)PNQGKK 90.444 0.0066315 672520000 837960 423630 639920 551820 504740 383710 688400 463810 498330 TRUE FALSE 785513.5794 454996.006 655099.2046 565980.6354 465099.7564 494480.848 585180.8108 521717.6995 415155.5037 1.892094823 1.095965252 1.577961026 1.363297922 1.120302519 1.191073811 1.409546075 1.256680195 1 18.6632923 8 0.073653546 0.751633876 2.739327256 0.350232186 0.211014743 308.1549949 1.667182786 7.438759085 62.99123972 100000000 -8 1.98769338 AEGSEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AEGSEIR 7 0 P07237;H7BZ94;I3L3U6;I3L0S0;I3NI03;I3L514 P07237 P4HB Protein disulfide-isomerase 0 ;; 95.62 0.031016 3697240000 2118850 2597670 2461530 2370570 2395190 1993380 2452420 2294690 1865350 FALSE TRUE 1986234.961 2790004.19 2519918.654 2431402.84 2207081.439 2568836.446 2084702.388 2581187.098 1554011.034 1.2781344 1.795356743 1.621557761 1.564598182 1.420248242 1.653036169 1.341497803 1.660983764 1 20.56756532 -2.807621083 0.265413566 1.02E-10 1.617713055 0.501136941 0.163659477 40.27659777 1.115753183 22.97668662 0.200528507 0.001557324 2.807621083 1.617713055 AEGSEKEESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEGSEKEESR 10 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 88.155 0.011297 1296000000 1500400 1077300 1184200 1148900 1248800 1016400 1361400 984610 1519500 FALSE TRUE 1406492.642 1157064.413 1212289.783 1178382.719 1150724.285 1309818.18 1157270.709 1107540.726 1265885.634 1.111074022 0.914035504 0.95766138 0.93087613 0.909027052 1.034704989 0.914198469 0.874913733 1 20.27171564 4.744121266 24.67979247 0.940728345 1.11107411 0.566131121 0.046525276 356.7116715 1583134.163 0.010100866 0.087968406 55478.06006 -4.744121266 0.170345765 AEGTNFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEGTNFR 7 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 125.62 0.0093781 681050000 520700 698650 614700 691280 725610 569840 717890 586250 689000 FALSE TRUE 488110.3165 750378.7729 629280.9743 709019.4151 668623.5176 734343.5574 610249.0591 659444.603 574001.4489 0.850364259 1.307276792 1.09630555 1.235222344 1.164846393 1.279340947 1.063148987 1.148855293 1 19.13069485 0.755054926 1.161418808 1.002155918 1.164353439 0.093632412 0.129686527 1.672728693 4.011521756 0.108465746 0.033628573 5.689248787 -0.755054926 0.16219752 AEGTTYRDELLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEGTTYRDELLTK 13 1 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4;A0A2R8Y4J3 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 107.46 0.0011792 128570000 235760 210610 213070 220940 231450 178130 254360 167830 239310 FALSE TRUE 221004.2024 226203.7835 218124.121 226609.6945 213272.8506 229553.2393 216221.0794 188783.9449 199367.615 1.108526089 1.134606458 1.094080004 1.13664245 1.069746712 1.151406859 1.084534614 0.946913795 1 17.60507155 1.344496219 4.728884251 0.974667731 1.114412939 0.826672453 0.026525408 0.068588743 2.289391008 0.016690817 0.005740114 22.10529009 -1.344496219 0.139745208 AEGYEVAHGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AEGYEVAHGGR 11 0 H0YDU8;P53041;A8MU39 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 ;; 108.31 0.0020798 1463380000 1073450 1329210 1053660 1058130 1363390 905840 1328500 1202110 1671510 FALSE TRUE 1006264.681 1427626.091 1078653.313 1085283.407 1256314.849 1167341.303 1129303.758 1352196.08 1392524.183 0.722619178 1.025207396 0.774602931 0.779364137 0.902185301 0.838291584 0.810976048 0.971039567 1 20.40927095 1.152532161 5.659252064 0.995380063 0.847498831 0.35498742 0.082841275 0.243410562 11.81352223 0.07521101 0.019088911 14.20797423 -1.152532161 -0.147881232 AEHIPAGK ddPTM_SK-BR-3_Pertuzumab_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 ; 72.547 0.045871 571570000 1556330 1578730 1566970 1544050 1763210 1215860 1810430 1489840 1716120 FALSE TRUE 1458922.083 1695620.812 1604139.268 1583672.937 1624734.599 1566859.044 1538972.829 1675849.804 1429688.485 1.02044753 1.186007182 1.122020136 1.107704897 1.136425603 1.095944368 1.076439269 1.17217829 1 20.4472694 -4.314319709 0.397804766 1.02E-13 1.120730549 0.351117281 0.047538877 417.3019443 5.129316378 355.4747266 0.027877505 4.85E-05 4.314319709 1.120730549 AEIIDQDLYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AEIIDQDLYER 11 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 173.28 2.88E-05 518060000 580210 592960 627540 613660 643670 509060 653810 504580 616500 FALSE TRUE 543895.6918 636863.3754 642425.5451 629407.5545 593118.7546 656017.3581 555777.2602 567577.9237 513602.1673 1.05898247 1.239993551 1.250823275 1.225476827 1.154821363 1.277286974 1.082116267 1.10509254 1 18.97029176 1.347177261 1.431947821 1.015325939 1.210682969 0.474889573 0.067189643 0.289190243 1.112580764 0.05667549 0.017903038 22.24217538 -1.347177261 0.19535703 AEITFDDHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AEITFDDHK 9 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;;;;; 197.27 2.83E-05 6473410000 6738140 5742820 5744880 5591240 6425350 4305620 6809760 5256990 6163220 FALSE TRUE 6316411.845 6168024.368 5881151.267 5734720.684 5920728.93 5548582.598 5788699.707 5913336.774 5134538.766 1.230180963 1.201281098 1.145409848 1.116891107 1.153117972 1.080638953 1.127404032 1.15167828 1 22.29180325 8 0.01870637 1.53E-05 2.577819301 0.777594405 0.029712527 1592.537483 2.296706484 119.607964 208.210857 100000000 -8 2.577804024 AEKDEPGAWEETFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AEKDEPGAWEETFK 14 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;; 229.68 1.09E-12 1060840000 1785180 1108550 1413960 1387510 1351340 960620 1840040 1116220 1526050 FALSE TRUE 1673448.77 1190628.195 1447499.799 1423115.856 1245211.207 1237935.4 1564143.084 1255582.524 1271342.396 1.316284878 0.936512618 1.138560157 1.119380475 0.979445986 0.973723053 1.230308286 0.987603755 1 20.2779212 AEKDNAEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AEKDNAEIR 9 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;;; 93.258 0.0086833 5450500000 12892490 11570280 11979560 11923330 12951130 9493990 14374600 10801380 12699580 FALSE TRUE 12085572.06 12426955.57 12263720.82 12229302.83 11934000.49 12234750.79 12219262.18 12149956.07 10579938.06 1.142310286 1.174577347 1.159148641 1.155895504 1.127983966 1.156410437 1.154946476 1.148395766 1 23.33482784 -4.088887002 0.383194694 1.26E-07 1.158592577 0.940467262 0.012048841 61.95098567 0.923306325 50.30096928 0.0079975 8.15E-05 4.088887002 1.158592451 AEKDRES(ph)LRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AEKDRESLRR 10 3 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 AEKDRES(1)LRR;AEKDRES(1)LRR;AEKDRES(1)LRR 122.46 0.0026965 638350000 516030 294038 383257 307716 451090 299497 320813 283056 651230 TRUE FALSE 483732.6034 315808.8795 392348.037 315612.5135 415663.211 385956.922 272710.0689 318396.1647 542535.5059 0.891614647 0.582098086 0.723174857 0.581736145 0.766149324 0.711394771 0.502658473 0.586866963 1 19.04935803 -1.165023366 5.545997492 1.000008044 0.656236734 0.457976319 0.112769177 1.05E-05 1.58E-06 0.101900037 0.024017507 0.068387485 1.165023366 -0.34377131 AEKEEENR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 114.5 0.0024122 954710000 2894850 2164960 2496020 2448410 2446280 1797300 2707710 2177980 2775290 FALSE TRUE 2713666.506 2325255.891 2555226.773 2511240.346 2254159.037 2316151.333 2301714.023 2449905.597 2312076.17 1.17369252 1.005700384 1.105165481 1.086140837 0.974950162 1.001762556 0.99551825 1.05961284 1 21.1407575 2.750319525 24.34912835 1.004831716 1.080260854 0.45653219 0.045894736 513.7913834 1063904.114 0.013184143 0.013864981 562.7552114 -2.750319525 0.075429138 AEKEEENRR ddPTM_SK-BR-3_Pertuzumab_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 ;; 131.09 0.0001929 575190000 1602130 1288150 1380390 1408380 1494730 1074500 1707340 1247090 1846200 FALSE TRUE 1501855.543 1383525.966 1413133.503 1444521.415 1377339.935 1384690.707 1451340.217 1402791.932 1538057.293 0.976462678 0.899528238 0.918778194 0.9391857 0.895506261 0.900285518 0.943619086 0.912054407 1 20.55267781 -1.212419338 3.88074611 1.000069311 0.920981875 0.484340855 0.024819577 3318351.563 1036717.137 1927.219192 0.005275575 0.061316967 1.212419338 -0.079087436 AEKPPLSASS(ph)PQQRPPEPETGESAGTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AEKPPLSASSPQQRPPEPETGESAGTSR 28 2 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 AEKPPLSAS(0.127)S(0.873)PQQRPPEPETGESAGTSR;AEKPPLS(0.002)AS(0.174)S(0.821)PQQRPPEPET(0.002)GESAGTSR;AEKPPLS(0.008)AS(0.075)S(0.241)PQQRPPEPET(0.169)GES(0.169)AGT(0.169)S(0.169)R 185.47 5.16E-18 859010000 493450 371985 473008 436037 463590 360129 486868 374551 594119 TRUE FALSE 462565.8453 399527.1565 484227.9731 447226.4476 427181.5114 464092.3961 413866.6633 421314.5168 494956.7007 0.934558204 0.807196177 0.978323907 0.903566811 0.863068448 0.937642415 0.836167411 0.851214897 1 18.9169428 3.996798017 24.75327361 0.901591184 0.86565242 0.052065264 0.060866868 1168.94672 1470516.573 0.014120515 0.030431976 9926.542752 -3.996798017 -0.035938764 AELAESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AELAESR 7 0 P06753-2;A0A087WWU8;P06753-6;P06753-3;J3KN67;A0A2R2Y2Q3;A0A494C0P6 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;; 139.68 0.0062246 2011130000 1758140 2536790 2024430 2022190 2612270 2312040 2108560 2173010 2088220 FALSE TRUE 1648101.156 2724616.571 2072450.436 2074082.819 2407112.852 2979488.415 1792401.003 2444315.082 1739682.592 0.947357388 1.566157289 1.191280781 1.192219103 1.383650594 1.712662085 1.030303465 1.405035087 1 20.73039268 -0.403704284 6.644669657 1.000000004 1.313303693 0.144550818 0.231022437 0 0 0.201607768 0.047519407 0.394725984 0.403704284 0.313303689 AELELELGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 204251000 284515 338952 321331 320799 346214 240381 350341 303252 301986 FALSE TRUE 266707.714 364048.3588 328953.1231 329031.2455 319023.749 309775.0924 297810.6195 341113.6797 251582.5857 1.060119934 1.447033219 1.307535345 1.307845869 1.268067693 1.231305782 1.183748941 1.355871587 1 17.94067254 -3.52358162 0.241025079 0.268366794 1.316273884 0.356402905 0.106777715 75.39399416 1.429673605 27.38778008 0.160937829 0.000299515 3.52358162 1.04790709 AELESDPPY(ph)MEMKGKLSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AELESDPPYMEMKGKLSAK 19 2 Q1MSJ5-1;Q1MSJ5;E5RI67;F2Z2M5 Q1MSJ5-1 CSPP1 Centrosome and spindle pole-associated protein 1 1 AELES(0.335)DPPY(0.565)MEMKGKLS(0.1)AK 41.348 0.068186 1351800000 2202500 1012000 1510300 1322100 1541100 1006500 1631000 1078300 1807500 TRUE FALSE 2064649.457 1086929.533 1546125.029 1356027.324 1420068.222 1297060.211 1386446.691 1212928.129 1505816.573 1.371116173 0.721820674 1.026768503 0.900526232 0.943055248 0.861366672 0.920727475 0.805495271 1 20.52211461 4.752094445 24.90743265 0.897078745 1.371116501 0.738871487 0.088490743 1074.264224 1977021.887 0.019364181 0.384613283 56505.98437 -4.752094445 0.474037756 AELGFLESCLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AELGFLESCLR 11 0 Q92696;H0YLH3 Q92696 RABGGTA Geranylgeranyl transferase type-2 subunit alpha 0 75.294 0.089525 13811000 12419 13703 13117 12279 17224 11017 12980 16753 16462 FALSE TRUE 11641.71696 14717.58438 13428.14143 12594.09993 15871.29652 14197.42905 11033.7695 18844.64893 13714.38585 0.848868997 1.073149358 0.979128164 0.918313081 1.157273588 1.035221643 0.804539818 1.374078951 1 13.7434024 4.749948339 23.21203525 1.022016636 0.848868715 0.12734198 0.151072462 1383.309162 2819502.869 0.032799362 0.479143292 56227.44369 -4.749948339 -0.173147921 AELGMGDSTSQS(ph)PPIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 AELGMGDSTSQSPPIKR 17 1 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 1 AELGMGDS(0.005)T(0.005)S(0.026)QS(0.963)PPIKR;AELGMGDSTS(0.009)QS(0.991)PPIKR;AELGMGDSTS(0.002)QS(0.998)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTS(0.001)QS(0.999)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTS(0.006)QS(0.993)PPIKR;AELGMGDSTS(0.008)QS(0.991)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTSQS(1)PPIKR 204.17 5.53E-12 10019150000 4710150 4003980 4506990 4317050 4603420 3719540 5485680 4220970 6360820 TRUE FALSE 4415350.119 4300438.845 4613897.931 4427832.812 4241885.963 4793310.816 4663153.211 4747967.396 5299158.05 0.833217292 0.811532475 0.870685095 0.835572891 0.800483006 0.904541961 0.879980021 0.89598524 1 22.33733173 0.673707579 0.437873131 1.011176818 0.826958749 0.800775547 0.025622152 0.725999735 0.301560703 0.042090795 0.016373982 4.717452969 -0.673707579 -0.184218069 AELGSWS(ph)SQEHLEWEPACQTPQPSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AELGSWSSQEHLEWEPACQTPQPSAR 26 0 B7Z896;F5H3M2;Q9BVG8-5;Q9BVG8-2;Q9BVG8;Q9BVG8-6;H3BTL6 B7Z896 KIFC3 Kinesin-like protein;Kinesin-like protein KIFC3 1 AELGS(0.091)WS(0.455)S(0.455)QEHLEWEPACQTPQPSAR;AELGS(0.013)WS(0.539)S(0.448)QEHLEWEPACQTPQPSAR;AELGSWS(0.561)S(0.439)QEHLEWEPACQTPQPSAR;AELGS(0.004)WS(0.498)S(0.498)QEHLEWEPACQTPQPSAR 346.66 5.27E-110 965851000 399102 404635 445711 430453 385665 427346 534937 418645 453232 TRUE FALSE 374122.9182 434594.5964 456283.4754 441499.1527 355376.4266 550713.8528 454728.163 470913.7498 377584.6512 0.990831902 1.150985865 1.208426968 1.16927198 0.941183455 1.458517583 1.204307859 1.247173974 1 18.52644059 2.247501122 24.99948932 1.247859067 1.119527821 0.174141427 0.136400115 317.8432533 888755.3182 0.043793998 0.036147405 176.8076784 -2.247501122 -0.128331246 AELGSWSS(ph)QEHLEWEPACQTPQPSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AELGSWSSQEHLEWEPACQTPQPSAR 26 0 B7Z896;F5H3M2;Q9BVG8-5;Q9BVG8-2;Q9BVG8;Q9BVG8-6;H3BTL6 B7Z896 KIFC3 Kinesin-like protein;Kinesin-like protein KIFC3 1 AELGS(0.001)WS(0.111)S(0.887)QEHLEWEPACQTPQPSAR 260.21 5.83E-53 234580000 171670 178540 183330 184360 170710 167450 222270 183300 220920 TRUE FALSE 160925.4811 191759.2874 187678.6742 189090.9897 157303.1252 215790.0967 188942.677 206185.4085 184047.0248 0.874371543 1.041903761 1.019732182 1.027405849 0.854689856 1.172472616 1.026600007 1.120286561 1 17.4897149 2.224178436 24.99992988 1.079343805 0.984846483 0.336025245 0.078071187 312.8153255 543750.2422 0.027027465 0.020051901 167.5631193 -2.224178436 -0.094497322 AELNEFLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 AELNEFLTR 9 0 P23396;P23396-2;E9PPU1;E9PL09;F2Z2S8;H0YCJ7;H0YEU2;H0YF32;E9PQ96;E9PJH4;E9PK82;E9PQX2;H0YES8 P23396 RPS3 40S ribosomal protein S3 0 ;;;;;;; 222.22 9.10E-07 2873970000 2215197 2803350 2366270 2440700 2812140 1988999 2549390 2479030 2667150 FALSE TRUE 2076551.774 3010912.951 2422399.042 2503332.494 2591285.868 2563190.723 2167132.637 2788542.353 2221985.435 0.934547879 1.355055215 1.090195734 1.126619669 1.166202905 1.153558742 0.975313611 1.254977782 1 21.08341793 0.509024185 0.278122927 0.973502419 1.179566408 0.041396632 0.125268251 7.924509912 1.378518743 0.514807191 0.191203817 3.228673917 -0.509024185 0.206063988 AELNPWPEYIYTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AELNPWPEYIYTR 13 0 P26639;P26639-2;D6RCA5;D6R9F8;D6RDJ6 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ;;; 203.61 1.97E-07 250936000 281549 319971 311335 306575 331900 278806 334806 279185 313708 FALSE TRUE 263927.3507 343661.9858 318720.0132 314442.2335 305833.9128 359292.7662 284604.9485 314041.8618 261348.1082 1.009868992 1.314958766 1.21952294 1.20315481 1.17021667 1.374767044 1.08898798 1.201622862 1 17.99561319 0.641029145 0.986534626 1.001226504 1.219728127 0.256098529 0.102973644 1.404741471 2.266187927 0.088572327 0.028570138 4.375514681 -0.641029145 0.218501624 AELNSDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AELNSDKK 8 1 Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 Q10567-4 AP1B1 AP-1 complex subunit beta-1 0 ; 75.652 0.060666 381570000 1047450 647960 782550 762360 810060 535690 972190 703870 945780 FALSE TRUE 981891.9743 695935.6326 801112.4555 781923.4483 746441.1552 690335.0068 826419.1349 791749.7189 787923.208 1.246177247 0.883253121 1.016739255 0.99238535 0.94735267 0.876145035 1.04885746 1.004856452 1 19.5876955 4.749973171 24.99781509 0.970635038 1.246177409 0.706973628 0.055634586 972.144392 2129324.487 0.012980188 0.205720331 56230.65873 -4.749973171 0.275542372 AELRDDPIISTHLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AELRDDPIISTHLAK 15 1 O00231;O00231-2 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 123.03 6.32E-05 432350000 815510 1167100 1056900 1095200 1205400 876630 1345800 1106700 1468400 FALSE TRUE 764468.6848 1253513.298 1081970.167 1123304.686 1110732.746 1129698.85 1144009.784 1244873.931 1223314.554 0.624915875 1.024686001 0.884457856 0.91824681 0.907969862 0.923473727 0.935172217 1.01762374 1 20.22236398 4.747619367 24.8902567 0.943735118 0.6249157 0.81712858 0.048424935 462.2436577 1270054.201 0.01096218 0.134555736 55926.72224 -4.747619367 -0.318819418 AELSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AELSYR 6 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ;; 153.61 0.023518 889820000 675430 1079850 676490 696050 1066260 521490 749370 902230 950400 FALSE TRUE 633156.042 1159803.218 692536.6623 713911.8214 982520.2407 672035.6973 637008.9253 1014875.402 791772.1002 0.799669554 1.464819507 0.874666665 0.901663271 1.240912935 0.848774158 0.804535706 1.28177717 1 19.59472571 3.749983211 21.52461352 0.972464171 1.176752163 0.04866649 0.224040657 148.4143602 139727.9543 0.052966557 0.095320566 5623.195872 -3.749983211 0.204287993 AELYKEPTNEELNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AELYKEPTNEELNR 14 1 Q9H6R4-4;Q9H6R4;A0A0A0MRW6;Q9H6R4-3;Q9H6R4-2 Q9H6R4-4 NOL6 Nucleolar protein 6 0 69.261 0.043315 124850000 128340 114770 136280 124140 144760 87581 153390 117910 182760 FALSE TRUE 120307.4285 123267.6902 139512.626 127325.6426 133391.1335 112864.2129 130390.5935 132631.3231 152256.1753 0.790164525 0.809607163 0.916301921 0.8362593 0.876096705 0.741278393 0.856389524 0.871106362 1 17.21614122 0.782068227 2.283348115 0.99982228 0.836490223 0.551602638 0.047368963 0.699458018 5.841302844 0.044431483 0.012043915 6.054359801 -0.782068227 -0.163332056 AEMDMVAWGVDLASVEQHINSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AEMDMVAWGVDLASVEQHINSHR 23 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;;; 150.36 4.91E-08 378118600 311595.4 395613.5 371316 402364.1 469657.9 347783.3 454087.8 375483.9 349880.5 FALSE TRUE 292093.2001 424905.1352 380123.7909 412689.444 432772.863 448182.6929 386001.5499 422363.8915 291483.1842 1.0020928 1.457734642 1.304101957 1.415825908 1.484726689 1.537593649 1.324266959 1.449016322 1 18.15305313 -0.996314796 4.275494663 0.99998111 1.381366584 0.379623511 0.148983598 7317367.978 3422934.13 1250.624413 0.031324084 0.10085216 0.996314796 0.381385475 AEMDQILHGLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEMDQILHGLDK 12 0 A0A5F9ZHC6;A0A5F9ZHM8;P04424-3;P04424-2;P04424 A0A5F9ZHC6 ASL Argininosuccinate lyase 0 108.17 0.0017349 164180000 386840 451270 388590 425160 432780 287550 482580 350830 491660 FALSE TRUE 362628.3749 484682.5003 397807.5383 436070.3254 398791.2046 370561.017 410221.6091 394631.8978 409598.7698 0.88532584 1.18331044 0.971212727 1.064628015 0.973614264 0.9046927 1.001520608 0.963459675 1 18.64385186 2.683304037 6.941863798 0.96578873 1.043116383 0.098366109 0.079174482 0.414149341 44.05664202 0.0238199 0.022523411 482.2853138 -2.683304037 0.077327653 AENGERS(ph)DLEEDNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AENGERSDLEEDNER 15 1 Q8WU90 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 1 AENGERS(1)DLEEDNER;AENGERS(1)DLEEDNER 190.36 5.79E-07 592670000 912190 834530 934170 871680 857740 817780 1030620 767010 611210 TRUE FALSE 855097.6562 896319.4695 956328.9535 894048.7846 790376.5604 1053859.81 876088.0988 862772.8869 509195.1024 1.679312413 1.760267263 1.878118915 1.755807902 1.552207703 2.069658183 1.720535203 1.694385674 1 18.95785902 0.6117307 2.087731459 1.00014527 1.78585069 0.76588559 0.133374167 1.077620489 5.260458355 0.116553759 0.031903105 4.090069611 -0.6117307 0.78570542 AENGKLVINGNPITIFQERDPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AENGKLVINGNPITIFQERDPSK 23 2 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 195.24 3.69E-19 527680000 551040 370520 543480 597240 505740 404970 368270 403670 285300 FALSE TRUE 516551.39 397953.6863 556371.6022 612566.1895 466021.2205 521878.2649 313051.3324 454069.0881 237681.5869 2.173291574 1.674314328 2.340827531 2.577255552 1.960695511 2.195703385 1.317103847 1.910409191 1 17.85867062 1.258553725 0.864625332 1.083119159 2.141017126 0.547426258 0.318661513 0.42149892 0.690437649 0.295226416 0.109632471 18.13651022 -1.258553725 1.057897967 AENLQLLTENELHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AENLQLLTENELHR 14 0 O94992 O94992 HEXIM1 Protein HEXIM1 0 ;; 187.16 9.80E-07 635420000 854980 995220 1007230 990620 964530 920030 1162400 839730 949830 FALSE TRUE 801468.328 1068907.124 1031121.971 1016040.986 888779.7045 1185627.726 988108.9112 944572.139 791297.2369 1.012853692 1.350828835 1.303077937 1.284019379 1.123193237 1.498334217 1.248720285 1.193700793 1 19.59386019 0.890801362 2.630963834 1.000725694 1.279387008 0.2785392 0.129018288 0.491681923 7.157173983 0.110910596 0.029577639 7.776807742 -0.890801362 0.278661314 AENSHNAGQVDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AENSHNAGQVDTR 13 0 Q8IWZ3-6;Q8IWZ3;Q8IWZ3-4;E9PDP5;D6RHC4;Q8IWZ3-5;Q8IWZ3-3;Q8IWZ3-2 Q8IWZ3-6 ANKHD1 Ankyrin repeat and KH domain-containing protein 1 0 ; 182.02 1.16E-05 493020000 287034 331535 299976 299742 318084 268168 321071 269668 288024 FALSE TRUE 269069.0543 356082.1964 307091.5724 307433.8872 293102.9657 345583.7483 272929.3842 303336.6434 239950.9337 1.121350312 1.483979207 1.279809866 1.28123647 1.221512087 1.440226729 1.137438309 1.26416113 1 17.8723799 0.434494261 0.481167303 0.978911447 1.328900719 0.369839234 0.11396139 2.034947163 0.827480044 0.194523108 0.057326395 2.719532551 -0.434494261 0.349989272 AENYDIPSADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AENYDIPSADR 11 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;;; 237.84 3.16E-15 4503080000 5669960 5920410 5736870 5881130 6343030 5063930 6676770 5242350 5975650 FALSE TRUE 5315087.325 6358763.317 5872951.266 6032049.753 5844874.01 6525804.385 5675650.323 5896868.937 4978275.411 1.067656344 1.277302437 1.179716022 1.211674577 1.174076066 1.310856441 1.140083634 1.184520431 1 22.24721462 0.503818255 1.215595653 1.000167533 1.20575677 0.446593715 0.067297573 1.592878145 3.056063562 0.056655359 0.017129863 3.190202527 -0.503818255 0.205589237 AEPAKIEAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AEPAKIEAFR 10 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;; 138.99 4.56E-05 2071450000 2509210 3862730 2842030 3286190 4765400 2360120 3874320 2643550 7551600 FALSE TRUE 2352163.025 4148730.548 2909444.294 3370519.199 4391144.707 3041448.331 3293401.683 2973603.037 6291189.175 0.373882101 0.659450929 0.46246333 0.53575232 0.697983256 0.483445696 0.523494302 0.47266152 1 22.58490131 -1.180133976 4.24092106 1.000143916 0.53502175 0.713344884 0.094252667 12417417.97 3455445.286 17787.9229 0.019908815 0.066048966 1.180133976 -0.465122166 AEPDESNAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEPDESNAR 9 0 P61088;F8VSD4;F8VV71;Q5JXB2;F8VZ29 P61088 UBE2N;UBE2NL Ubiquitin-conjugating enzyme E2 N;Putative ubiquitin-conjugating enzyme E2 N-like 0 ; 186.16 9.77E-05 226130000 515320 549720 558840 524810 620450 477400 613630 517530 659880 FALSE TRUE 483067.0411 590421.8408 572095.9487 538277.5131 571722.3598 615217.6301 521621.8782 582144.7597 549741.765 0.878716284 1.073998518 1.040663062 0.979146114 1.039983491 1.119102948 0.948848917 1.05894221 1 19.06839456 4.748166899 24.6194946 1.03299848 0.878716182 0.501167561 0.048242126 885.8842456 2270334.24 0.010932945 0.139705091 55997.27566 -4.748166899 -0.154282298 AEPEDHYFLLTEPPLNTPENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AEPEDHYFLLTEPPLNTPENR 21 0 B4DXW1;P61158;F8WDR7 B4DXW1 ACTR3 Actin-related protein 3 0 ;;;; 238.64 6.74E-30 1725930000 1731959 1758338 1841238 1784782 1957792 1531456 1899332 1634849 1748570 FALSE TRUE 1623558.778 1888527.175 1884913.035 1830582.528 1804034.914 1973562.486 1614544.799 1838963.496 1456722.371 1.114528623 1.296422169 1.29394116 1.256644756 1.238420546 1.35479658 1.108340773 1.262398061 1 20.47429452 0.348012494 0.657855963 0.994245472 1.262263721 0.473476125 0.0782337 1.789336835 1.141855726 0.098760335 0.027614607 2.228499259 -0.348012494 0.268018249 AEPHFLSILQHLLLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEPHFLSILQHLLLVR 16 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 191.78 3.71E-10 15638000 21945 136420 51541 54067 114790 30015 26606 106210 69760 FALSE TRUE 20571.50162 146520.6787 52763.57686 55454.45076 105774.8564 38679.84325 22616.6773 119470.5523 58116.60533 0.353969429 2.521149986 0.907891584 0.954192875 1.820045335 0.665555791 0.38916033 2.055704245 1 15.82666282 3.730087772 24.94634016 1.043197036 1.629007115 0.011904669 0.718700712 282.7044241 2377311.941 0.174214295 0.297806225 5371.403422 -3.730087772 0.585810079 AEPPKPEVVDSTESIPVS(ph)DEDSDAMVDDPNDEDFVPFRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEPPKPEVVDSTESIPVSDEDSDAMVDDPNDEDFVPFRPR 40 2 A6NHN7;A6NHB5;Q14202-2;Q14202;A6NL54;Q14202-3 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 1 AEPPKPEVVDS(0.019)T(0.019)ES(0.06)IPVS(0.759)DEDS(0.143)DAMVDDPNDEDFVPFRPR 41.297 0.051521 17065000 15423 12900 13790 13073 15268 12419 14005 11461 14481 TRUE FALSE 14457.70196 13855.12942 14117.10531 13408.47531 14068.91287 16004.16369 11905.08027 12891.93108 12064.02755 1.198414203 1.148466328 1.170181787 1.111442697 1.166187064 1.326602051 0.986824692 1.068625799 1 13.55842401 1.641794642 11.20008469 1.021112258 1.17634421 0.634140025 0.059845586 0.070812196 16.99425623 0.026869962 0.014472223 43.83233853 -1.641794642 0.155231952 AEPSEVDMNS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AEPSEVDMNSPK 12 0 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 AEPSEVDMNS(1)PK;AEPSEVDMNS(1)PK;AEPSEVDMNS(1)PK;AEPSEVDMNS(1)PK 282.26 4.14E-28 1342170000 3430710 1749350 2443400 2259450 2163560 1787000 2886550 1760960 2319680 TRUE FALSE 3215987.985 1878873.694 2501358.602 2317431.312 1993642.725 2302877.89 2453738.625 1980819.732 1932510.422 1.664150396 0.972245051 1.294357108 1.199181793 1.031633621 1.191650955 1.269715597 1.024998214 1 20.88204476 4.75075734 24.88752259 1.146220275 1.664150734 0.678085908 0.116207262 1103.492141 2251641.972 0.026236864 0.452144325 56332.28133 -4.75075734 0.517930459 AEPYCSVLPGFTFIQHLPLSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEPYCSVLPGFTFIQHLPLSER 22 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ; 244.72 7.77E-31 538530000 591780 700140 618990 492040 872830 555480 681960 665300 1090660 FALSE TRUE 554741.5462 751979.0941 633672.7351 504666.5794 804281.4526 715838.0585 579706.429 748364.1695 908621.8001 0.610530747 0.827604064 0.697399881 0.555419845 0.885166361 0.7878284 0.638006296 0.823625594 1 19.79332039 0.965353163 7.139003685 0.999988595 0.723983304 0.455492056 0.100104296 0.287120745 55.85208973 0.08998798 0.02256282 9.233219569 -0.965353163 -0.276005292 AEQEEEFISNTLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEQEEEFISNTLFK 14 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 189.3 1.69E-07 0 24671 23549 21576 22757 24184 13861 28727 24235 28773 FALSE TRUE 23126.88615 25292.59246 22087.79291 23340.98315 22284.68619 17862.44569 24419.65304 27260.7931 23970.60042 0.964802122 1.05515056 0.921453469 0.973733771 0.929667418 0.745181404 1.018733474 1.137259502 1 14.54897843 1.490750465 12.13418087 1.07175053 0.941921377 0.322105461 0.083713687 0.108727885 58.97409934 0.045090801 0.0209071 30.95640109 -1.490750465 -0.129829152 AEQGS(ph)EEEGEGEEEEEEGGESKADDPYAHLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AEQGSEEEGEGEEEEEEGGESKADDPYAHLSK 32 1 Q5STZ8;Q8NE71 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 AEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK;AEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK;AEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK;AEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK;AEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK;AEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK 254.49 2.41E-59 1746010000 693496 646487 674135 756269 938722 425904 868117 590719 1647239 TRUE FALSE 650091.3233 694353.5701 690125.8005 775676.1429 864998.5607 548855.5708 737950.9151 664471.5675 1372304.169 0.473722472 0.505976434 0.502895652 0.565236309 0.630325681 0.399951835 0.537745881 0.484201376 1 20.38816886 -1.613219463 2.649309132 1.046008378 0.512962152 0.866984639 0.060008725 7966037.53 7254140.97 2533091.727 0.013595803 0.024365792 1.613219463 -0.533046226 AERPDVDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AERPDVDEK 9 1 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 104.39 0.0029797 1091430000 2833600 1558760 2088000 1910570 2146300 1390010 2591300 1871070 2433600 FALSE TRUE 2656250.034 1674172.212 2137528.346 1959598.461 1977738.256 1791283.322 2202758.621 2104677.208 2027416.438 1.310164988 0.82576632 1.054311441 0.966549557 0.975496804 0.883530038 1.086485529 1.038107992 1 20.95121102 -0.658128783 5.858355945 1.000000005 1.001250737 0 0.130548952 0 8.76E-19 0.111634094 0.026312408 0.219720823 0.658128783 0.001250732 AERPGLQNMELAPVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AERPGLQNMELAPVQR 16 1 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 0 139.49 2.35E-05 0 60580 79989 78663 64068 86397 61986 68207 61390 69925 FALSE TRUE 56788.40594 85911.46879 80528.92351 65712.09335 79611.72813 79880.35194 57979.99355 69054.67664 58254.06577 0.974840214 1.474772064 1.382374302 1.128025872 1.366629558 1.371240803 0.995295226 1.185405271 1 15.83007112 1.743373027 11.03808727 1.070322337 1.313828325 0.307214647 0.15276079 0.095341523 68.08096774 0.068265403 0.03724296 55.38256009 -1.743373027 0.243505988 AERS(ph)PNQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AERSPNQGK 9 1 Q9P2E9;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 AERS(1)PNQGK 96.89 0.0055023 0 228000 165570 201560 195550 179880 133750 198550 178440 208380 TRUE FALSE 213729.887 177828.9751 206341.0984 200568.1441 165752.9504 172361.4538 168779.2707 200718.6268 173600.0318 1.231162718 1.024360268 1.188600579 1.15534624 0.954797926 0.992865335 0.972230644 1.156213076 1 17.40540769 2.748065987 24.6476324 1.008233086 1.135405114 0.434242323 0.075337323 537.5282886 1393822.381 0.021968476 0.023007144 559.8426578 -2.748065987 0.127172029 AES(ph)GDSLGSEDRDLLYSIDAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AESGDSLGSEDRDLLYSIDAYR 22 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 AES(0.998)GDS(0.002)LGSEDRDLLYSIDAYR;AES(0.979)GDS(0.021)LGSEDRDLLYSIDAYR;AES(0.995)GDS(0.002)LGS(0.003)EDRDLLYSIDAYR 304.72 2.39E-56 433564000 441446 380101 397477 416855 344640 298934 488310 285154 574580 TRUE FALSE 413816.6829 408244.0735 406905.3421 427552.205 317573.3646 385231.393 415092.4487 320756.1046 478678.8861 0.864497464 0.852855819 0.850059098 0.893192112 0.663437168 0.804780416 0.867162645 0.670086177 1 18.86869865 AES(ph)GKEEDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AESGKEEDKK 10 2 Q99442 Q99442 SEC62 Translocation protein SEC62 1 AES(1)GKEEDKK 78.964 0.030135 0 436250 90233 158090 134210 137590 86805 214610 104240 108150 TRUE FALSE 408945.8912 96913.94521 161839.9695 137654.0558 126784.2364 111864.1943 182431.2228 117254.5935 90099.06632 4.538847159 1.075637619 1.79624469 1.527807795 1.40716482 1.241568852 2.024784832 1.301396321 1 16.45922454 4.743263613 24.97520368 1.485973862 4.538848413 0.905973972 0.314977223 132.3245315 702683.7136 0.070517756 0.574385787 55368.60901 -4.743263613 3.052874551 AES(ph)GPDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AESGPDLR 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 AES(1)GPDLR;AES(1)GPDLR;AES(1)GPDLR 119.21 0.0018234 5377600000 6255000 6874800 6279900 6515800 7307800 5110800 7874400 5976400 6750400 TRUE FALSE 5863510.715 7383817.345 6428862.194 6683006.459 6733874.866 6586204.993 6693706.822 6722566.696 5623714.631 1.042640159 1.312978668 1.14317006 1.18836159 1.197406929 1.171148507 1.190264311 1.195396128 1 22.42309196 -1.290410016 3.171321328 0.998938777 1.189186037 0.417500257 0.066123725 8509376.851 12138691.52 87079.56574 0.014523809 0.051237742 1.290410016 0.190247259 AES(ph)KPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AESKPR 6 1 E9PD25;O43897 E9PD25 TLL1 Metalloendopeptidase;Tolloid-like protein 1 1 AES(1)KPR 62.2 0.072251 98153000 341560 158030 385680 285580 198320 315640 461900 206650 273790 TRUE FALSE 320182.3693 169730.7056 394828.5117 292908.4663 182744.7472 406760.144 392642.3831 232450.7074 228092.6802 1.403738029 0.744130436 1.73100036 1.284164253 0.801186373 1.783310817 1.721415973 1.019106388 1 17.79926062 2.224087077 24.99961483 1.483335195 1.209191497 0.026605832 0.379223384 549.7170381 949499.9218 0.137200533 0.101775737 167.5278738 -2.224087077 -0.274143698 AES(ph)PAEKVPEESVLPLVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AESPAEKVPEESVLPLVQK 19 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 AES(1)PAEKVPEESVLPLVQK;AES(1)PAEKVPEESVLPLVQK;AES(1)PAEKVPEESVLPLVQK;AES(1)PAEKVPEESVLPLVQK 258.55 2.99E-31 1637950000 3544750 1700972 2291244 2003226 1951650 1910370 3387780 2050570 2260830 TRUE FALSE 3322890.425 1826913.737 2345593.39 2054632.171 1798375.282 2461862.807 2879813.84 2306588.178 1883482.867 1.76422652 0.969965678 1.245348938 1.090868521 0.954813719 1.307080011 1.528983294 1.224639851 1 20.84497148 2.0265151 24.95905072 1.33699579 1.169765642 0 0.261299084 520.0859218 489562.2368 0.08971563 0.06625742 106.2955541 -2.0265151 -0.167230148 AES(ph)PDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 107.57 0.0078114 1948330000 5265500 5553100 5930700 5669900 5674600 4901800 7154900 5319400 6341500 TRUE FALSE 4935941.754 5964257.302 6071379.005 5815399.233 5228939.806 6316870.086 6082089.168 5983538.799 5283062.682 0.934295512 1.128939341 1.149215781 1.100762869 0.989755398 1.19568335 1.151243045 1.132589023 1 22.3329431 2.210781728 24.99995595 1.136749623 1.083824184 0.061914142 0.081790496 550.2979956 495243.9508 0.029313482 0.021654119 162.4731978 -2.210781728 -0.052925439 AES(ph)PEEVACR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 224.42 4.17E-09 2860649000 3319544 1823020 2233240 2271000 2190680 1771760 2932640 1786811 2562880 TRUE FALSE 3111779.667 1957998.298 2286213.507 2329277.705 2018632.83 2283238.35 2492917.857 2009898.287 2135118.771 1.457426963 0.917044206 1.070766431 1.090935894 0.945442875 1.069372993 1.167578072 0.941351982 1 21.02588489 4.748682597 24.80849216 1.03568378 1.45742722 0.749432839 0.078319335 676.821878 1658821.282 0.018849271 0.256945907 56063.80859 -4.748682597 0.421743441 AES(ph)PESSAIESTQS(ph)TPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 AES(1)PESSAIEST(0.015)QS(0.667)T(0.317)PQK 385.32 2.67E-126 282930000 763090 518770 612320 610440 657300 503830 924750 597730 641920 TRUE FALSE 715329.5591 557180.2706 626844.5196 626104.9239 605678.3094 649277.542 786092.3225 672357.9063 534779.405 1.337616132 1.041888048 1.17215531 1.170772318 1.132575981 1.21410349 1.469937539 1.257262153 1 19.02858438 1.991599267 23.23538259 1.306466512 1.155191841 0 0.137527342 226.8813867 627526.0972 0.048270233 0.03390158 98.08424815 -1.991599267 -0.15127467 AES(ph)PESSAIESTQST(ph)PQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 AES(1)PESSAIESTQST(1)PQK 384.06 1.04E-125 317310000 979030 689290 854350 801440 858980 710810 1281500 817970 885680 TRUE FALSE 917754.2599 740325.7488 874615.5855 822006.3072 791519.1758 916009.308 1089350.972 920095.3551 737854.2863 1.243815042 1.003349527 1.18535001 1.114049647 1.072731013 1.241450141 1.47637683 1.246987884 1 19.49297641 2.07215154 5.58446688 1.309345721 1.116680027 0.089557322 0.134760917 0.225548512 12.62786626 0.04694529 0.034110609 118.0732562 -2.07215154 -0.192665694 AES(ph)PESSAIESTQSTPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 AES(1)PESSAIESTQSTPQK;AES(0.999)PESSAIESTQSTPQK 460.95 3.54E-214 1742690000 1930610 1451210 1592140 1625800 1617530 1132670 2092330 1405720 1942820 TRUE FALSE 1809776.566 1558659.098 1629906.313 1667520.78 1490495.719 1459653.442 1778604.541 1581227.236 1618550.791 1.118146293 0.962996717 1.007015858 1.030255454 0.920882883 0.901827394 1.098887073 0.97694014 1 20.62627121 -1.088030686 5.403047296 0.999999996 1.000333063 0 0.068710171 2.55E-09 5.13E-10 0.062056021 0.014626571 0.081652468 1.088030686 0.000333067 AES(ph)PGPGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AESPGPGSR 9 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 AES(1)PGPGSR 113.46 0.0018849 109960000 1523400 1487000 1500600 1428900 1764700 1331900 1852100 1608700 2180900 TRUE FALSE 1428053.113 1597099.027 1536194.941 1465567.993 1626107.58 1716397.908 1574394.799 1809549.736 1816893.701 0.785986056 0.879027225 0.845506229 0.806633868 0.89499324 0.944688128 0.866531046 0.995957956 1 20.79304259 1.546049852 0.584946023 1.005009419 0.836020188 0.676562838 0.040989986 0.458871306 0.363420587 0.038376823 0.020621161 35.16007978 -1.546049852 -0.168989231 AES(ph)PMSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AESPMSR 7 0 Q6ZUT6 Q6ZUT6 C15orf52 Uncharacterized protein C15orf52 1 AES(1)PMSR;AES(1)PMSR 113.18 0.024192 155417000 280980 311360 271640 292700 348010 248170 349580 289790 346950 TRUE FALSE 263393.9634 334413.4184 278083.4291 300211.1775 320678.6984 319812.6503 297163.7243 325970.9194 289041.8036 0.911265983 1.156972501 0.962087233 1.038642763 1.109454392 1.106458119 1.028099467 1.127763927 1 18.14091864 2.972665743 23.48162302 1.074668051 1.030424957 0.121953596 0.072775917 884.7569746 760054.6106 0.020661949 0.021980332 939.0003269 -2.972665743 -0.044243094 AES(ph)PSPAPPPGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AESPSPAPPPGLR 13 0 Q9BUA3 Q9BUA3 C11orf84 Uncharacterized protein C11orf84 1 AES(0.839)PS(0.161)PAPPPGLR;AES(0.998)PS(0.002)PAPPPGLR;AES(1)PSPAPPPGLR;AES(1)PSPAPPPGLR 282.2 1.77E-32 1609470000 1495540 1319430 1372510 1367400 1473770 1180740 1655510 1216580 1593380 TRUE FALSE 1401936.821 1417121.97 1405066.585 1402489.799 1358026.049 1521600.47 1407281.645 1368472.691 1327434.584 1.056124978 1.067564449 1.058482732 1.056541554 1.023045553 1.146271529 1.060151409 1.030915351 1 20.34020934 -1.892772729 2.725773092 0.96705798 1.064577976 0.260077126 0.032886427 13991782.82 7608058.349 2951629.459 0.007352402 0.01280051 1.892772729 0.097519996 AES(ph)PTPGMAQGMEPGAGQEGAMFVHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AESPTPGMAQGMEPGAGQEGAMFVHAR 27 0 A0A0A0MSQ9;Q86VX9-5;Q86VX9 A0A0A0MSQ9 MON1A Vacuolar fusion protein MON1 homolog A 1 AES(0.945)PT(0.055)PGMAQGMEPGAGQEGAMFVHAR 105.9 0.0012857 210660000 47559 39381 45524 40504 40156 36274 53912 34375 61562 TRUE FALSE 44582.36709 42296.81022 46603.85078 41543.40121 37002.30974 46745.71494 45828.39609 38666.79442 51286.90449 0.869273892 0.824709751 0.908689094 0.810019665 0.721476761 0.911455183 0.893569159 0.753931141 1 15.64630288 -1.391751352 5.585868292 1.000062135 0.844782572 0.388002685 0.063752054 4.74E-05 5.16E-06 0.059341217 0.013981271 0.040574077 1.391751352 -0.155279563 AES(ph)PTSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AESPTSAR 8 0 C9J6N8 C9J6N8 TFAP2A 1 AES(0.998)PT(0.002)SAR;AES(0.998)PT(0.002)SAR 118.71 0.0019237 103835000 207171 249996 258946 242444 249031 207330 257066 217409 230475 TRUE FALSE 194204.5369 268505.964 265088.3214 248665.5235 229473.1098 267182.8053 218521.3398 244552.9922 192007.2336 1.011443857 1.398415877 1.380616326 1.295084143 1.195127421 1.391524685 1.138089101 1.273665516 1 17.55080114 0.488115472 0.597848232 0.992749398 1.304375063 0.277359663 0.124675829 1.988934369 1.220419946 0.154640341 0.049570916 3.076914808 -0.488115472 0.311625665 AESGDS(ph)LGSEDRDLLYSIDAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AESGDSLGSEDRDLLYSIDAYR 22 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 AES(0.424)GDS(0.554)LGS(0.022)EDRDLLYSIDAYR 68.657 0.011774 579610000 19840 21029 21233 19668 23066 16651 26824 20465 27649 TRUE FALSE 18598.24982 22586.00904 21736.65679 20172.71418 21254.4894 21457.87339 22801.99022 23020.1003 23034.20328 0.807418845 0.98054223 0.943668705 0.875772169 0.922736035 0.931565687 0.989918772 0.999387737 1 14.49149008 1.743887029 2.859953625 0.999496452 0.920158689 0.433375407 0.045814545 0.263039971 4.469197733 0.026658955 0.012358392 55.44814599 -1.743887029 -0.079337763 AESGDSLGSEDRDLLYSIDAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AESGDSLGSEDRDLLYSIDAYR 22 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 0 ; 258.16 3.30E-37 686600000 511670 584790 522220 543020 573340 480530 607270 480620 656000 FALSE TRUE 479645.4881 628088.4601 534607.305 556954.8125 528312.1891 619251.2102 516215.5011 540626.465 546509.3621 0.87765283 1.149273011 0.978221678 1.019113031 0.966702907 1.133102657 0.94456845 0.989235505 1 19.05988668 1.622051398 25 0.975174356 1.029223222 0.053440618 0.079260592 1.956157106 3439.426678 0.03356077 0.018497709 41.88431318 -1.622051398 0.054048866 AESPES(ph)SAIESTQSTPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 AES(0.011)PES(0.494)S(0.494)AIESTQSTPQK;AES(0.001)PES(0.991)S(0.008)AIESTQSTPQK 478.32 1.58E-239 1263000000 1542390 1287690 1291480 1345610 1403090 935720 1707920 1094550 1632780 TRUE FALSE 1445854.563 1383031.907 1322114.515 1380140.631 1292896.971 1205847.174 1451833.252 1231206.977 1360258.47 1.062926345 1.016741993 0.971958304 1.014616458 0.950478898 0.886483856 1.067321604 0.905127227 1 20.37544938 5.189822752 0.798869662 0.972837808 1.190558958 0.262395149 0.051525042 6.830983214 2.021277506 0.016626208 1.558598885 154818.4633 -5.189822752 0.217721149 AESSQTCHSEQGDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AESSQTCHSEQGDKK 15 1 P46063 P46063 RECQL ATP-dependent DNA helicase Q1 0 ;;;; 260.18 4.44E-25 444481000 866837 586601 716483 712366 721773 520348 946706 614556 969908 FALSE TRUE 812583.2195 630033.5484 733478.3151 730646.5176 665087.8601 670564.0205 804756.2241 691284.6694 808024.089 1.00564232 0.779721245 0.907743129 0.904238534 0.823104 0.829881225 0.995955733 0.855524828 1 19.62403878 0.882672405 0.69163114 0.996390178 0.870359204 0.156615972 0.073545255 1.338877206 1.411085387 0.068361717 0.026467727 7.63259828 -0.882672405 -0.126030973 AESVVLEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AESVVLEHR 9 0 Q9BWS9-3;Q9BWS9;Q9BWS9-2;E9PKF1;E9PI70;E9PIP0;E9PRL3;E9PPH0;E9PPA0 Q9BWS9-3 CHID1 Chitinase domain-containing protein 1 0 ; 114.84 0.0015728 438410000 801540 1526810 1149490 1209510 1370560 1174490 1138010 1209310 880600 FALSE TRUE 751373.0422 1639856.601 1176756.446 1240548.074 1262921.746 1513546.197 967375.9653 1360295.016 733622.1711 1.024196203 2.23528768 1.604036099 1.690990435 1.721487976 2.063114034 1.318629675 1.854217428 1 19.48467771 -0.635172562 0.504960832 0.848129121 1.749092968 0.262939792 0.34756575 13.6674596 2.738844524 3.784852392 0.150337894 0.231647404 0.635172562 0.900963848 AET(ph)LELSDLYVSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AETLELSDLYVSDK 14 0 Q8NDI1-3;Q8NDI1-2;Q8NDI1 Q8NDI1-3 EHBP1 EH domain-binding protein 1 1 AET(1)LELSDLYVSDK;AET(1)LELSDLYVSDK 173.36 3.03E-05 46393000 144350 128882 108669 124381 120362 64492 158260 111047 156126 TRUE FALSE 135315.3912 138424.5574 111246.68 127572.827 110909.254 83109.79346 134530.3822 124911.4624 130067.562 1.040346948 1.064251188 0.855299187 0.980819699 0.852704951 0.638974024 1.034311554 0.960358298 1 16.98890168 4.048168497 3.566494688 0.897962344 1.051547242 0.234814035 0.111174617 0.32697973 8.129792331 0.027763445 0.064670191 11172.96652 -4.048168497 0.153584898 AET(ph)PPLPIPPPPPDIQPLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AETPPLPIPPPPPDIQPLER 20 0 U3KPW8;A0A669KB72;Q8IX15;Q8IX15-3 U3KPW8 HOMEZ Homeobox and leucine zipper protein Homez 1 AET(1)PPLPIPPPPPDIQPLER;AET(1)PPLPIPPPPPDIQPLER;AET(1)PPLPIPPPPPDIQPLER;AET(1)PPLPIPPPPPDIQPLER 184.21 4.57E-16 192000000 209438 179157 184611 193214 192303 144565 237848 157035 240513 TRUE FALSE 196329.6494 192421.9707 188990.0601 198172.1984 177200.2981 186298.5687 202184.9005 176641.1654 200369.8265 0.9798364 0.960334068 0.943206187 0.98903214 0.88436618 0.929773569 1.009058619 0.881575677 1 17.61230575 -1.156658809 4.479524313 1.000008188 0.950913181 0.132590132 0.041501977 3.09E-06 5.82E-07 0.036617653 0.008629424 0.069717401 1.156658809 -0.049095008 AET(ph)PTESVSEPEVATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AETPTESVSEPEVATK 16 0 P18858;P18858-3;P18858-2;M0R0Q7;B4E135 P18858 LIG1 DNA ligase 1;DNA ligase 1 AET(1)PTESVSEPEVATK;AET(0.983)PT(0.017)ESVSEPEVATK 446.64 4.55E-181 536870000 835910 526910 628390 643610 629300 458550 822240 538760 718450 TRUE FALSE 783591.8852 565922.9646 643295.7075 660126.1222 579877.3165 590925.9411 698952.7453 606025.372 598536.0536 1.309180759 0.945511906 1.074781884 1.102901184 0.968826043 0.987285457 1.167770498 1.012512727 1 19.19107863 4.751414695 24.84372564 1.040182949 1.309180945 0.624501917 0.067199639 1399.69481 2705208.202 0.016121255 0.29886716 56417.61135 -4.751414695 0.268997997 AETEKQS(ph)PPHGEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AETEKQSPPHGEAK 14 1 Q9Y6D6;E5RJN9 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 AET(0.009)EKQS(0.991)PPHGEAK 108.71 0.00048898 187240000 440480 220540 322940 291470 269350 263660 501020 288400 333760 TRUE FALSE 412911.1431 236869.0111 330600.2893 298949.6137 248196.3375 339774.3618 425896.7022 324407.3748 278053.2998 1.485007167 0.851883474 1.188981715 1.075152188 0.892621442 1.22197565 1.531708858 1.166709315 1 18.08500193 2.008389473 24.83079467 1.313124187 1.074720086 0.036195119 0.218954789 253.7959869 751170.2512 0.074652879 0.055045585 101.9505265 -2.008389473 -0.238404101 AETEQGEQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 204.48 4.33E-07 210570000 138381 149900 148651 148744 148940 131291 162407 137615 121968 FALSE TRUE 129719.9802 160998.752 152177.0719 152561.0229 137242.8532 169192.5804 138055.5781 154796.5357 101610.7529 1.276636346 1.584465693 1.497647322 1.501425967 1.350672536 1.665105076 1.358670949 1.523426717 1 16.63269356 -2.558418129 0.566293271 1.24E-06 1.48286214 0.61506385 0.116246955 144.9175764 7.99325352 178.8038145 0.042829199 0.002764279 2.558418129 1.482860897 AETPTES(ph)VSEPEVATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AETPTESVSEPEVATK 16 0 P18858;P18858-3;P18858-2;M0R0Q7;B4E135 P18858 LIG1 DNA ligase 1;DNA ligase 1 AET(0.371)PT(0.171)ES(0.454)VS(0.004)EPEVATK 343.16 2.24E-72 610830000 258420 189120 212760 191650 220930 170400 269510 194650 258720 TRUE FALSE 242245.9535 203122.6416 217806.7677 196568.0635 203579.049 219591.7138 229099.4775 218952.481 215537.9606 1.123913174 0.942398457 1.010526253 0.911988138 0.944515984 1.018807607 1.06291939 1.015841852 1 17.71758245 2.032131441 11.52219216 1.035150263 0.980568275 0.081621935 0.058958262 1.185633927 421.05998 0.020615618 0.015198554 107.6791059 -2.032131441 -0.054581989 AEVLGHKT(ph)PEPAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEVLGHKTPEPAPR 14 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EJ51;K7ER34 Q9UHD8 9-Sep Septin-9 1 AEVLGHKT(1)PEPAPR;AEVLGHKT(1)PEPAPR 110.74 0.0010149 285800000 636930 470820 563790 561620 581070 418460 712010 507340 848390 TRUE FALSE 597065.6883 505680.0027 577163.365 576032.12 535435.1061 539262.6089 605250.7105 570682.5158 706788.2282 0.84475896 0.715461835 0.816600139 0.814999595 0.757560872 0.762976217 0.856339546 0.807430703 1 19.43091849 -0.018290239 0.516388348 1.02064673 0.778843013 0.707415045 0.041354084 2.214591586 0.711393537 0.131921146 0.018724558 0.958759678 0.018290239 -0.241803717 AEVLISTVGPEDCVVPFLTRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEVLISTVGPEDCVVPFLTRPK 22 1 P56192;P56192-2;F5H2V6;F8VS26;F8W0M7;F8W0S4;F8VZZ9 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 111.38 0.0002982 52159000 123540 125730 115580 123170 153970 129780 158930 125500 141360 FALSE TRUE 115807.8519 135039.18 118321.6122 126330.7507 141877.8173 167245.3792 135099.9219 141168.9513 117766.1028 0.983371693 1.146672742 1.004717057 1.072725918 1.2047424 1.420148712 1.147188527 1.198723129 1 16.84556482 2.74062882 5.342669828 1.217949455 1.059000267 0.276864801 0.110671093 0.194720607 19.62020808 0.032394584 0.03248322 550.337137 -2.74062882 -0.158949189 AEVPEDKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEVPEDKPK 9 1 O95757;E9PDE8 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 81.771 0.018551 151440000 538140 320360 399710 370030 389400 277050 488670 337470 505270 FALSE TRUE 504458.778 344079.7877 409191.31 379525.5963 358818.0948 357029.8375 415398.4701 379603.8724 420937.1728 1.198418221 0.817413643 0.972095924 0.901620529 0.852426723 0.848178447 0.986841973 0.901806485 1 18.68324539 -0.55701888 7.572708609 0.999999998 0.924954288 0.027776604 0.107824443 0 0 0.091807062 0.021639132 0.277319954 0.55701888 -0.07504571 AEVPGATGGDS(ph)PHLQPAEPPGEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AEVPGATGGDSPHLQPAEPPGEPR 24 0 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WWC8;Q9P2K5-4 A0A0A0MQW0 MYEF2 Myelin expression factor 2 1 AEVPGAT(0.019)GGDS(0.981)PHLQPAEPPGEPR;AEVPGAT(0.002)GGDS(0.998)PHLQPAEPPGEPR;AEVPGAT(0.139)GGDS(0.861)PHLQPAEPPGEPR;AEVPGAT(0.239)GGDS(0.761)PHLQPAEPPGEPR 188.44 1.07E-17 2019380000 883860 903910 977760 933230 1066550 935640 1079860 949480 1017900 TRUE FALSE 828540.7803 970836.4369 1000952.929 957178.2618 982787.4653 1205744.079 917945.0179 1068024.668 848005.9141 0.977045993 1.144846304 1.180360788 1.128740078 1.1589394 1.421858102 1.082474783 1.259454268 1 19.6937148 5.599910793 1.11644086 1.186453084 1.78E-14 0.232965344 0.110911695 12.97883874 3.193180313 0.028398165 28.67461624 398025.4048 -5.599910793 -1.186453084 AEVSQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEVSQPR 7 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 113.5 0.014228 110990000 126400 144550 135440 127330 165470 125420 126830 146010 130840 FALSE TRUE 118488.8496 155252.6324 138652.7008 130597.5034 152474.6537 161626.718 107813.0189 164239.6699 109001.9587 1.087034132 1.424310482 1.272020268 1.198120702 1.398824897 1.482787281 0.989092491 1.506758886 1 16.73399453 -1.257749428 5.015883017 0.999945031 1.29054715 0.232596136 0.168159592 9.43E-05 1.40E-05 0.148528431 0.035001878 0.055239606 1.257749428 0.29060212 AEVWDLDMLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEVWDLDMLR 10 0 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 118.71 0.0061233 0 33085 46881 35696 32471 50166 27620 31841 44910 48750 FALSE TRUE 31014.26891 50352.11802 36542.72598 33304.26083 46226.16472 35593.44563 27066.73765 50517.11236 40613.31006 0.763647899 1.239793505 0.899772166 0.820033156 1.138202344 0.87639854 0.66644993 1.243856073 1 15.30966499 3.72564146 24.86621894 0.918195949 1.045946627 0 0.198190949 172.7318696 2902624.112 0.049012915 0.08068507 5316.691484 -3.72564146 0.127750678 AEVYGS(ph)ENESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEVYGSENESER 12 0 Q9BVS4-2;Q9BVS4 Q9BVS4-2 RIOK2 Serine/threonine-protein kinase RIO2 1 AEVYGS(1)ENESER;AEVYGS(1)ENESER 225.36 1.88E-11 853360000 562440 546620 599740 586500 521330 537340 679960 524660 381760 TRUE FALSE 527237.8844 587092.3136 613966.116 601550.5829 480386.8447 692461.335 578006.3104 590164.9559 318041.7897 1.657762915 1.845959658 1.930457367 1.89141994 1.51045196 2.177265244 1.817391076 1.855620786 1 18.27885682 -0.881582728 6.633621563 0.999999968 1.849985705 0.697457464 0.172770728 7.12E-08 1.28E-08 0.149377215 0.035208546 0.131346127 0.881582728 0.849985737 AEYEGDGIPTVFVAVAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AEYEGDGIPTVFVAVAGR 18 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 99.531 0.0023706 22693000 40665 46795 39996 41911 46686 43354 46888 38738 31171 FALSE TRUE 38119.85024 50259.75049 40944.72401 42986.50722 43019.46988 55869.59601 39857.57969 43574.52457 25968.35873 1.467934521 1.935422682 1.576715896 1.655341705 1.656611045 2.151448869 1.534851706 1.677985314 1 14.66446721 0.459952235 1.444232924 1.000318269 1.730725873 0.553998559 0.199591913 2.015451845 4.658581134 0.173072482 0.050375952 2.883714326 -0.459952235 0.730407604 AFAAVPTSHPPEDAPAQPPT(ph)PGPAASPEQLSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AFAAVPTSHPPEDAPAQPPTPGPAASPEQLSFR 33 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 AFAAVPTSHPPEDAPAQPPT(0.672)PGPAAS(0.312)PEQLS(0.015)FR 102.78 4.73E-05 342900000 43688 52988 48790 62579 87204 37483 36987 32467 42240 TRUE FALSE 40953.64607 56911.28665 49947.32184 64184.88309 80355.3496 48303.73361 31441.14272 36520.57642 35189.87112 1.163790738 1.617263288 1.419366433 1.823959027 2.283479508 1.372660146 0.89347138 1.037815009 1 15.10287261 1.994979315 24.9953961 1.007210571 1.646398531 0.543072165 0.286090088 174.9991043 871231.597 0.111377889 0.079976421 98.85060128 -1.994979315 0.63918796 AFAAVPTSHPPEDAPAQPPTPGPAAS(ph)PEQLSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AFAAVPTSHPPEDAPAQPPTPGPAASPEQLSFR 33 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 AFAAVPTSHPPEDAPAQPPT(0.118)PGPAAS(0.881)PEQLSFR 126.94 5.99E-08 325890000 225880 196770 208140 206730 246200 173860 221160 199470 210580 TRUE FALSE 211742.574 211339.0555 213077.1791 212035.0418 226864.4451 224050.5596 187999.1111 224374.2686 175432.8376 1.206972292 1.204672161 1.21457979 1.208639413 1.293169786 1.277130112 1.071630111 1.278975314 1 17.42055929 -1.480542798 3.206009011 0.995427871 1.21171229 0.546345106 0.062496083 9430033.181 9020073.123 362797.0494 0.014822465 0.033071752 1.480542798 0.216284419 AFAHITGGGLLENIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AFAHITGGGLLENIPR 16 0 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ; 210.34 9.94E-12 965990000 760260 1034350 942030 928670 1077130 852140 1087660 928600 1115010 FALSE TRUE 712676.6837 1110934.35 964375.3965 952501.2444 992536.5547 1098138.985 924575.4803 1044537.754 928907.6278 0.767220187 1.195957829 1.038182234 1.025399314 1.068498659 1.182183192 0.995336299 1.124479682 1 19.82517561 4.751997603 24.85484575 1.080943749 0.767219964 0.660506369 0.070176119 1249.567833 2311323.824 0.015666896 0.305933924 56493.38566 -4.751997603 -0.313723785 AFAMIIDKLEEDINSSMTNSTAASRPPVTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AFAMIIDKLEEDINSSMTNSTAASRPPVTLR 31 2 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 134.51 1.10E-05 423690000 155750 151530 134630 133260 149500 115380 166520 119820 186760 FALSE TRUE 146001.8855 162749.4389 137823.4872 136679.6772 137758.8731 148688.333 141551.8719 134779.7908 155588.5495 0.938384515 1.046024527 0.885820246 0.878468741 0.885404958 0.955650872 0.909783351 0.866257775 1 17.24737636 3.901314584 5.091976896 0.908691607 0.995466551 0.330959168 0.047346797 0.186934613 8.689844938 0.010992896 0.020578151 7967.362634 -3.901314584 0.086774944 AFAMIIDKLEEDISSSMTNSTAASRPPVTLR ddPTM_SK-BR-3_Pertuzumab_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 0 131.2 1.84E-05 340780000 183100 145790 156480 150430 177160 126980 189550 159200 166300 FALSE TRUE 171640.0978 156584.4433 160191.7795 154290.2885 163246.5682 163637.0647 161128.7372 179076.4704 138543.4557 1.238889972 1.130218981 1.15625656 1.113659882 1.178305878 1.181124463 1.163019476 1.292565351 1 17.07997904 -1.166669484 3.972701182 0.999925451 1.172020818 0.537570311 0.052289552 3.59E-05 7.53E-06 0.046624852 0.010984217 0.068128765 1.166669484 0.172095367 AFDIIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AFDIIER 7 0 H3BVG0;Q8N1F7;Q8N1F7-2;H3BV15;H3BRD9 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 ;;;;; 143.85 0.0055686 352781000 844303 1129010 1040075 1076345 1129950 910215 1204960 1035421 1026139 FALSE TRUE 791459.5824 1212603.075 1064746.07 1103965.835 1041208.285 1172979.294 1024287.434 1164695.591 854869.7718 0.925824738 1.418465262 1.245506749 1.291384807 1.217972982 1.372114599 1.198179498 1.362424582 1 19.70534514 -1.094773381 4.490145548 0.999976898 1.268069837 0.249255389 0.136595777 2.72E-05 5.49E-06 0.114076472 0.026885767 0.080394552 1.094773381 0.268092939 AFDQGADAIYDHINEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AFDQGADAIYDHINEGK 17 0 Q9UDW1 Q9UDW1 UQCR10 Cytochrome b-c1 complex subunit 9 0 ; 180.62 8.49E-10 475840000 788840 579530 654460 586580 926510 638230 632930 888450 962760 FALSE TRUE 739467.9125 622439.0042 669984.1003 601632.6359 853745.642 822476.6402 538028.0223 999374.9382 802069.1363 0.921950339 0.776041585 0.835319638 0.750100719 1.064428992 1.025443572 0.670800057 1.245996003 1 19.61336707 2.749008495 24.90176426 0.957509523 0.815795586 0.237869752 0.149378434 1178.656075 2809241.765 0.044294842 0.046504488 561.0589499 -2.749008495 -0.141713937 AFDTAGNGYCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 AFDTAGNGYCR 11 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;; 250.62 2.26E-16 9216230000 2628930 3746820 2845520 2953000 3798720 2669720 3541360 3515880 3449970 FALSE TRUE 2464389.964 4024238.451 2913017.078 3028778.979 3500383.854 3440424.825 3010365.944 3954845.357 2874147.719 0.8574333 1.400150182 1.013523786 1.053800735 1.217885856 1.197024357 1.047394302 1.376006296 1 21.45470278 2.72529339 24.41206815 1.162719694 1.123096988 0.03598538 0.167873254 3948.083237 7264565.326 0.05097496 0.048334825 531.2432068 -2.72529339 -0.039622706 AFEDDDITHVEGSVDPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AFEDDDITHVEGSVDPIR 18 0 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 ;; 206.74 8.19E-16 1060620000 1488630 1319380 1554450 1422720 1262390 1448230 1801280 1388670 934930 FALSE TRUE 1395459.306 1417068.268 1591322.288 1459229.404 1163246.982 1866310.491 1531194.786 1562048.506 778884.1431 1.791613448 1.819356936 2.04307958 1.873487112 1.493478834 2.396133632 1.965882602 2.005495323 1 19.57104922 -1.886529408 2.553425837 0.520636886 1.934132361 0.620712155 0.226753377 7492355.298 4336826.041 21656131.59 0.052290125 0.012985856 1.886529408 1.413495475 AFEDDDITHVEGSVDPIRDIEIIHEELQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AFEDDDITHVEGSVDPIRDIEIIHEELQLK 30 1 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 ;;;;; 128.27 7.30E-06 228298000 161546 121485 146779 134490 122254 126100 197738 124525 111612.1 FALSE TRUE 151435.1242 130479.8758 150260.6672 137941.2411 112652.664 162503.0229 168089.0226 140072.2204 92983.31947 1.628626781 1.403261107 1.615995945 1.483505234 1.211536269 1.747657794 1.807733081 1.5064231 1 16.50468431 AFEDDDITHVEGSVDPIRDIEIIHEELQLKDEEMIGPIIDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AFEDDDITHVEGSVDPIRDIEIIHEELQLKDEEMIGPIIDK 41 2 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 ;; 150.56 4.77E-14 113041000 201382 115784.4 141038 142223 147511 92245.4 178017 125789 147551 FALSE TRUE 188777.8601 124357.1974 144383.488 145872.683 135926.0811 118875.1495 151325.0035 141494.0335 122923.7849 1.535730943 1.011660986 1.174577305 1.186692088 1.105775267 0.967063857 1.231047381 1.15107124 1 16.90740457 4.747124515 24.88378188 1.113276466 1.53573117 0.705403809 0.087583455 583.82857 1696367.976 0.019794546 0.233358967 55863.03345 -4.747124515 0.422454704 AFEDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AFEDEK 6 0 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 111.28 0.065105 144610000 759670 601220 638930 677900 701810 527290 825450 577400 800840 FALSE TRUE 712123.6107 645734.9544 654085.7213 695296.0617 646692.6736 679510.0632 701681.4356 649489.661 667174.6304 1.067372137 0.967864971 0.980381585 1.042150031 0.969300456 1.018489062 1.051720799 0.973492743 1 19.34770491 2.054082376 24.99994883 1.019390076 0.998161923 0 0.036998278 255.5592221 118132.7542 0.013152423 0.009713708 113.2615174 -2.054082376 -0.021228153 AFEDEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AFEDEKK 7 1 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;;;; 112.17 0.010285 4623390000 10516250 5401870 7156630 6581470 7100770 4588470 8536770 5635610 9321970 FALSE TRUE 9858056.685 5801830.075 7326388.643 6750361.663 6543104.167 5913086.801 7256760.59 6339228.314 7766072.985 1.269374715 0.747073854 0.943383954 0.869211721 0.842524166 0.761399849 0.934418284 0.81627205 1 22.88875383 4.748538404 24.79933642 0.860500958 1.269374965 0.719449414 0.079467211 616.1676376 1531421.993 0.016982465 0.228488561 56045.19752 -4.748538404 0.408874007 AFEDWLNDDLGSYQGAQGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 234.85 3.69E-29 70054000 74675 77600 76813 73668 68808 74619 82555 62733 67270 FALSE TRUE 70001.22505 83345.58474 78635.04063 75558.4456 63404.09724 96160.29396 70176.64415 70565.35314 56042.20242 1.24908055 1.487193243 1.403139728 1.348241902 1.13136341 1.715855013 1.252210676 1.25914668 1 15.77422603 0.94450189 1.793024663 1.004482284 1.390878581 0.36330094 0.155898042 0.400040723 2.667723912 0.133325038 0.037915302 8.800389407 -0.94450189 0.386396298 AFELLHLHLDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AFELLHLHLDLR 12 0 Q9H4A4;A6NKB8;A0A087WU27 Q9H4A4 RNPEP Aminopeptidase B 0 ;; 186.17 7.00E-06 228110000 132872 435119 133614.4 138378.4 533502 62974.1 127487.5 455099 376523 FALSE TRUE 124555.7787 467335.6635 136783.7967 141929.424 491602.905 81153.70037 108371.9329 511919.1119 313678.8789 0.39708054 1.48985378 0.436063139 0.452467264 1.567217107 0.258715858 0.345486866 1.631984639 1 18.25892887 3.950262899 23.70464081 0.74093928 1.014202079 0 0.549341067 691.0043896 609866.5693 0.131755095 0.23763566 8917.906178 -3.950262899 0.273262799 AFELMHSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AFELMHSGK 9 0 P11766 P11766 ADH5 Alcohol dehydrogenase class-3 0 ; 138.11 0.00014568 1322980000 2482300 2209470 1940700 1832320 2558520 1408140 2218880 2068410 2607000 FALSE TRUE 2326937.274 2373061.458 1986734.32 1879340.433 2357584.16 1814647.159 1886179.543 2326655.542 2171874.858 1.071395649 1.092632685 0.91475543 0.865307882 1.085506447 0.835521049 0.868456825 1.071265931 1 21.05050955 4.003032565 3.289117275 0.934918055 1.081041001 0.284849858 0.085315882 0.264924654 5.887955055 0.021039644 0.047838841 10070.07175 -4.003032565 0.146122946 AFEVMDEFDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AFEVMDEFDGR 11 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IU26;B1AN86;U3KQJ2 Q9UDY2-7 TJP2 Tight junction protein ZO-2 0 ;;; 190.96 4.75E-06 322896000 510997 638649 557035 539370 673070 483220 585782 577166 724880 FALSE TRUE 479014.6099 685935.2365 570248.1333 553211.1474 620209.7972 622717.7696 497949.4272 649226.4456 603892.8451 0.793211269 1.135855876 0.944286951 0.916075015 1.027019615 1.031172624 0.824565867 1.075068948 1 19.20393305 AFFESHPAPSAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AFFESHPAPSAER 13 0 E9PLK3;P55786;P55786-2;H0YDG0 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ;;; 188.09 6.40E-06 1529900000 993530 1686920 1171000 1167360 1870520 820360 1217420 1673930 2082770 FALSE TRUE 931346.7308 1811821.312 1198776.673 1197316.434 1723616.905 1057184.615 1034879.173 1882923.845 1735142.232 0.536755266 1.044191813 0.690880927 0.690039359 0.993357705 0.609278361 0.596423252 1.08516974 1 20.7266225 1.223576261 24.99888926 1.042585121 0.755623363 0.366486762 0.16552074 315.4310094 526229.0086 0.153229303 0.038930439 16.73309438 -1.223576261 -0.286961758 AFFSEVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AFFSEVER 8 0 Q9UQ80;Q9UQ80-2;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;;;;; 222.91 1.12E-05 3440718000 1818913 2620547 2118314 2107080 2642219 1665261 2141742 2334464 2658850 FALSE TRUE 1705070.482 2814575.027 2168561.408 2161151.24 2434709.778 2145994.817 1820607.67 2625926.969 2215070.758 0.769758923 1.270647909 0.979003222 0.97565788 1.099156661 0.96881547 0.821918516 1.185482206 1 21.07892135 2.136508235 8.503313027 0.961171 1.045671543 0 0.152818027 0.762630078 57.30167035 0.054050711 0.03990042 136.9330354 -2.136508235 0.084500543 AFGFSHLEALLDDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AFGFSHLEALLDDSK 15 0 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 250.89 4.85E-19 867030000 2651790 2306100 2191160 2129890 2553290 1613800 2791650 2295510 2439660 FALSE TRUE 2485819.197 2476846.043 2243135.35 2184546.583 2352764.903 2079677.862 2373067.999 2582109.477 2032464.985 1.223056346 1.218641434 1.103652642 1.074826184 1.15759185 1.023229368 1.167581246 1.270432453 1 20.95479907 4.064466119 2.870202577 1.118629849 1.222438573 0.251181568 0.076272915 0.371201124 5.974170843 0.018562458 0.046885548 11600.21715 -4.064466119 0.103808724 AFGFSHLEALLDDSKELQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AFGFSHLEALLDDSKELQR 19 1 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 171.72 5.84E-12 210499000 291615 363430 328662 388240 471700 216303 400980 292517 764600 FALSE TRUE 273363.3377 390338.7353 336458.0178 398202.8957 434654.5847 278746.1647 340856.7715 329038.3914 636983.3205 0.429153055 0.61279271 0.528205382 0.625138654 0.682364154 0.437603554 0.535110984 0.516557311 1 19.28089607 -1.600459256 2.897425766 1.031227619 0.550707146 0.765144947 0.079030118 24399961.97 24965157.31 5804657.133 0.017700224 0.025092316 1.600459256 -0.480520473 AFGPGLQGGSAGS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AFGPGLQGGSAGSPAR 16 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 AFGPGLQGGS(0.017)AGS(0.983)PAR;AFGPGLQGGSAGS(1)PAR;AFGPGLQGGSAGS(1)PAR;AFGPGLQGGSAGS(1)PAR 184.37 1.92E-09 1858390000 781362 845801 822766 805110 997960 782770 952150 830045 1159860 TRUE FALSE 732457.9472 908424.9861 842282.3981 825770.4856 919584.2472 1008742.992 809383.9468 933677.9454 966271.873 0.758024701 0.940133943 0.87168262 0.854594352 0.951682723 1.043953591 0.837635835 0.966268368 1 19.88206964 2.731637794 23.92399529 0.947702313 0.872708696 0.342049417 0.068720282 457.6650787 1581600.311 0.021214949 0.020433293 539.0608526 -2.731637794 -0.074993616 AFGSGIDIKPGT(ph)PPIAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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;AFGS(0.001)GIDIKPGT(0.999)PPIAGR;AFGSGIDIKPGT(1)PPIAGR 125.23 4.88E-05 5674350000 7236600 5197580 6199500 5780690 6356580 5450590 8103600 5647190 6380340 TRUE FALSE 6783674.124 5582414.231 6346555.068 5929032.292 5857359.848 7024086.85 6888540.41 6352254.102 5315420.035 1.276225412 1.050230122 1.193989379 1.115440032 1.101956159 1.321454712 1.295954104 1.195061549 1 22.34175227 2.255909773 24.99586619 1.238430292 1.139164626 0.014849789 0.105714505 391.2980608 563763.3608 0.03312229 0.027649308 180.2643192 -2.255909773 -0.099265666 AFGSGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AFGSGYR 7 0 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;; 151.14 0.0044232 618828000 469123 702102 539382 549108 673309 514504 534832 597845 606150 FALSE TRUE 439761.4288 754086.3626 552176.3958 563199.0409 620430.0271 663032.9525 454638.9067 672487.2643 504979.6491 0.870849805 1.4933005 1.093462671 1.11529057 1.228623823 1.312989452 0.900311344 1.331711615 1 18.94586572 0.613934128 0.342338814 0.981341449 1.218665777 0.023584863 0.195083287 6.478655406 1.699920554 0.493811205 0.189400311 4.11087364 -0.613934128 0.237324328 AFHNEAQVNPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AFHNEAQVNPER 12 0 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;;;; 196.11 2.10E-07 13125030000 6676150 7517920 7315400 7184760 7499070 6851510 7774000 6814020 6368370 FALSE TRUE 6258301.689 8074554.619 7488924.743 7369133.105 6910123.292 8829429.712 6608360.87 7664765.397 5305447.906 1.179599121 1.521936463 1.411553723 1.388974736 1.302458042 1.664219472 1.245580201 1.444697136 1 22.33904312 -0.511775634 0.80677022 0.974280421 1.409280173 0.443320249 0.137859379 16.01771512 7.015208708 1.390566182 0.04050377 0.30776864 0.511775634 0.434999752 AFHNEAQVNPERK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AFHNEAQVNPERK 13 1 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;; 214.23 2.02E-11 3594290000 1482720 1493850 1417880 1454370 1776020 1136590 1866260 1298450 2651560 FALSE TRUE 1389919.202 1604456.208 1451512.783 1491691.596 1636538.553 1464705.082 1586431.639 1460564.341 2208997.506 0.629208135 0.726327759 0.657091182 0.675279892 0.740851245 0.663063257 0.718168144 0.661188768 1 21.07496036 -1.610265148 2.773056334 1.025888126 0.688053842 0.88884236 0.03510345 6444618.88 6359982.357 1213521.096 0.007460012 0.024532107 1.610265148 -0.337834284 AFHPTYEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AFHPTYEEK 9 0 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 82.749 0.017571 201500000 155050 197590 147240 171950 257090 90285 185970 191600 262900 FALSE TRUE 145345.6973 212219.7692 150732.6023 176362.5281 236899.1885 116348.8138 158085.525 215521.6818 219020.2916 0.663617495 0.968950263 0.688212956 0.805233738 1.081631235 0.531223902 0.721784835 0.984026093 1 17.74070501 1.225406225 23.67361838 0.99201359 0.784994729 0.24491373 0.154511538 200.1130134 360116.9448 0.137013566 0.035221711 16.80375053 -1.225406225 -0.207018861 AFHSLDVNPTSQQDDSSNGLDPQEAGSRVS(ph)PDLGNDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AFHSLDVNPTSQQDDSSNGLDPQEAGSRVSPDLGNDEK 38 1 Q68DA7-5;Q68DA7-3 Q68DA7-5 FMN1 Formin-1 1 AFHSLDVNPTSQQDDSSNGLDPQEAGS(0.136)RVS(0.864)PDLGNDEK 147.76 1.75E-13 118310000 62271 48869 52105 57940 58140 42956 60037 44087 55386 TRUE FALSE 58373.56927 52487.31161 53340.95521 59426.83849 53573.91893 55356.69987 51035.00921 49591.359 46141.71879 1.265093083 1.13752398 1.156024453 1.287919914 1.161073326 1.199710399 1.106049158 1.074761849 1 15.49378413 1.301148725 1.326997673 1.005482521 1.192162815 0.677263144 0.048273477 0.24883844 0.842427615 0.043845564 0.013934975 20.00546845 -1.301148725 0.186680294 AFITNIPFDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AFITNIPFDVK 11 0 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 129.89 0.0005481 46915000 134230 148270 135510 138460 149600 108740 140300 123840 143790 FALSE TRUE 125828.7839 159248.0651 138724.3612 142013.118 137851.0195 140131.4728 119263.3175 139301.6966 119790.5201 1.050406859 1.329387876 1.158057926 1.185512158 1.150767351 1.169804361 0.995598962 1.162877467 1 16.87015422 2.063175539 0.803391646 1.033806501 1.211420328 0.2707933 0.084392875 0.638519968 0.771483094 0.065435398 0.034983863 115.657963 -2.063175539 0.177613828 AFKES(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AFKESPK 7 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 AFKES(1)PK 58.676 0.065478 110870000 546920 246040 355830 297080 329910 247560 387520 203440 364220 TRUE FALSE 512689.2535 264257.0576 364270.4556 304703.5758 304000.1994 319026.5532 329414.9736 228839.9318 303429.329 1.68964963 0.870901499 1.200511687 1.004199484 1.001881395 1.051403153 1.085639858 0.754178683 1 18.21100102 4.746173282 24.9844355 1.016081486 1.689649954 0.764990499 0.120357001 428.6055925 1406631.205 0.026501009 0.280855247 55740.8109 -4.746173282 0.673568468 AFKPEETSSNSDPPS(ph)PPVLNNSHPVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AFKPEETSSNSDPPSPPVLNNSHPVPR 27 1 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 AFKPEETSSNSDPPS(1)PPVLNNSHPVPR;AFKPEETSSNSDPPS(1)PPVLNNSHPVPR;AFKPEETSSNSDPPS(1)PPVLNNSHPVPR 202.76 2.45E-25 1424960000 2015080 1740420 1795290 1833590 1729380 1261690 2196690 1443060 1762790 TRUE FALSE 1888959.74 1869282.508 1837875.127 1880643.024 1593561.471 1625919.421 1867316.728 1623229.218 1468568.961 1.286258793 1.272859877 1.251473493 1.28059565 1.085111774 1.107145435 1.271521309 1.105313581 1 20.48597958 -4.999999959 0.053170693 0.095238048 1.642339791 0.620411499 0.063507686 338.0537988 1.324776806 41.71203843 8.509153814 1.00E-05 4.999999959 1.547101743 AFLDFHALPYQVVEVNPVRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AFLDFHALPYQVVEVNPVRR 20 1 Q9H7Z7 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 ; 98.169 0.00054384 135762000 149352 188627 147118 141669 223001 128643 154579 179564 212089 FALSE TRUE 140004.3249 202593.1393 150607.7084 145304.4664 205487.401 165780.1458 131401.314 201982.9607 176689.9758 0.792372767 1.146602338 0.852384001 0.82236961 1.16298279 0.938254392 0.743682902 1.143148952 1 17.43086067 2.00170911 24.9996802 0.910590356 0.968779163 0 0.158245457 250.9547708 3670746.945 0.056402353 0.041362393 100.3943125 -2.00170911 0.058188807 AFLEENNLDYIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AFLEENNLDYIIR 13 0 H0YDU8;P53041;A8MU39 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 ; 174.1 1.35E-06 35353000 70389 97149 77385 74620 99970 56201 83380 72752 140269 FALSE TRUE 65983.47814 104342.013 79220.60874 76534.87553 92118.75946 72425.31635 70877.94306 81835.24735 116857.1977 0.564650526 0.892901893 0.677926651 0.654943615 0.788301972 0.619776255 0.60653468 0.700301299 1 16.83438707 -0.75338432 4.572921333 1.000000601 0.697715083 0.515270585 0.094649087 22481004.5 58639407.34 243.3761093 0.023171886 0.176447569 0.75338432 -0.302285519 AFLIEEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AFLIEEQK 8 0 P49207 P49207 RPL34 60S ribosomal protein L34 0 148.38 0.0012147 84377000 91451 79585 82119 83089 81511 67813 97120 66258 87954 FALSE TRUE 85727.24515 85477.55621 84066.90146 85221.20441 75109.45486 87389.51225 82557.75762 74530.45715 73273.9092 1.169955938 1.166548327 1.147296526 1.163049786 1.025050467 1.192641599 1.126700602 1.017148641 1 16.16101197 0.802108863 0.329737095 0.975322538 1.172895792 0.516706223 0.049704296 1.742337528 0.494128968 0.11803127 0.05569436 6.340286207 -0.802108863 0.197573254 AFLQAILEHEEQDEEEDEVPDDETVNQMIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AFLQAILEHEEQDEEEDEVPDDETVNQMIAR 31 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532-3;P51532-5;A0A2R8YF58;A0A2R8YF80;A0A2R8Y440;A0A2R8Y4C5 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 0 ;; 154.63 4.93E-09 96541000 50336 61760 61741 61916 52547 48125 62137 53032 62248 FALSE TRUE 47185.55961 66332.77466 63205.52568 63504.86938 48420.17058 62017.90626 52820.1337 59653.16194 51858.40666 0.909892198 1.279113242 1.218809635 1.224581962 0.933699543 1.195908441 1.018545249 1.150308422 1 15.66229026 2.779254139 24.99976283 1.068644919 1.188386667 0.113477187 0.123073353 815.9698012 501283.5262 0.034372361 0.036457004 601.525633 -2.779254139 0.119741748 AFLS(ph)PPTLLEGPLR ddPTM_SK-BR-3_Pertuzumab_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(0.949)PPT(0.051)LLEGPLR;AFLS(0.975)PPT(0.025)LLEGPLR;AFLS(0.992)PPT(0.008)LLEGPLR;AFLS(0.945)PPT(0.055)LLEGPLR 204.28 1.45E-08 535023000 495836 508548 406277 411825 620689 406989 513564 492711 455011 TRUE FALSE 464802.5099 546201.4231 415914.0823 422393.1267 571942.5897 524480.1174 436559.8459 554227.0529 379066.7246 1.226175973 1.440911026 1.097205466 1.114297561 1.508817716 1.383608962 1.151670188 1.462083103 1 18.53209229 -1.074626761 4.443063862 0.999977769 1.28739899 0.280086742 0.149321183 3.13E-05 6.52E-06 0.13765557 0.032443221 0.084211856 1.074626761 0.287421221 AFLSTHPNTETVFEAFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AFLSTHPNTETVFEAFLK 18 0 Q96S44 Q96S44 TP53RK TP53-regulating kinase 0 89.107 0.0029527 49505000 66434 93646 79001 90067 103170 83703 95167 81996 103950 FALSE TRUE 62276.01453 100579.6473 80874.94103 92378.2717 95067.44437 107866.6973 80897.59184 92233.3811 86600.07346 0.71912196 1.161426813 0.933889982 1.066722787 1.097775563 1.245572815 0.934151538 1.065049687 1 16.40208063 4.749490432 24.71144672 1.059015515 0.71912173 0.562701842 0.095230778 1030.393015 2329584.33 0.021587872 0.319057339 56168.19035 -4.749490432 -0.339893785 AFMGT(ph)PVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AFMGTPVQK 9 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 AFMGT(1)PVQK;AFMGT(1)PVQK 134.3 0.0026343 586900000 1089740 1067300 1022290 1061370 1186770 854420 1391350 949450 1976930 TRUE FALSE 1021535.119 1146324.003 1046539.202 1088606.551 1093565.871 1101077.184 1182729.984 1067990.922 1646967.612 0.620252099 0.696020975 0.63543399 0.660976296 0.663987478 0.668548171 0.718125831 0.648458971 1 20.65138075 -5 0.333247765 4.440412353 0.655219205 0.936601923 0.027495579 78.15997638 0.670393573 190.7128601 0.020969931 1.00E-05 5 -3.785193147 AFNADFH ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AFNADFH 7 0 A0A0A0MT83;P26440;A0A0S2Z4K7;P26440-2 A0A0A0MT83 IVD "Isovaleryl-CoA dehydrogenase, mitochondrial" 0 86.086 0.047307 94798000 227500 302480 228430 208590 325600 215360 212060 263190 342380 FALSE TRUE 213261.1811 324875.9339 233848.4675 213942.7725 300028.6894 277530.9359 180263.5717 296049.8509 285234.5661 0.747669485 1.138978134 0.819846173 0.750059067 1.051866516 0.972991947 0.631983613 1.03791716 1 18.1217893 3.744203287 23.80910237 0.870591001 0.973715796 0 0.163481752 668.4406493 931669.0854 0.039696353 0.071293497 5548.853866 -3.744203287 0.103124795 AFPMPGFDEH ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AFPMPGFDEH 10 0 P34897-3;P34897-2;P34897 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial" 0 129.4 0.0079458 0 26059 32404 24987 23825 38282 23724 26751 26228 44069 FALSE TRUE 24428.01371 34803.22588 25579.70344 24436.38984 35275.48614 30572.73367 22739.93589 29502.62353 36713.5992 0.6653669 0.947965512 0.696736468 0.665595048 0.960828873 0.832735944 0.619387268 0.80358843 1 15.16402693 3.933311314 24.79477291 0.774274975 0.826289606 0 0.138462189 956.4580152 541318.8138 0.033465314 0.060330906 8576.524143 -3.933311314 0.052014631 AFQGLLDTYSVWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AFQGLLDTYSVWR 13 0 Q6XQN6-3;Q6XQN6;Q6XQN6-2;C9J8U2;G5E977 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 0 168.83 6.87E-05 173120000 42974 73671 49486 43245 78077 34785 36150 65419 59000 FALSE TRUE 40284.33405 79125.67749 50659.83129 44354.73991 71945.14737 44826.86481 30729.6431 73586.70615 49152.51885 0.819578223 1.609799037 1.030666026 0.902389968 1.463712319 0.911995272 0.62518959 1.497109566 1 15.58497773 2.178141974 24.99913208 0.937274314 1.195558181 0.031391028 0.318570849 145.1314194 60048.87352 0.113357928 0.083720405 150.7099668 -2.178141974 0.258283867 AFQYVETHGEVCPANWTPDSPTIKPSPAASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AFQYVETHGEVCPANWTPDSPTIKPSPAASK 31 1 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 270.93 9.01E-72 451560000 592850 463660 463800 437470 689730 474030 544400 576000 979380 FALSE TRUE 555744.5768 497989.8688 474801.555 448696.2208 635561.388 610874.7658 462772.274 647914.8679 815915.151 0.681130355 0.610345167 0.58192516 0.549930002 0.778955247 0.748698887 0.567181861 0.79409589 1 19.63805961 -0.584706746 0.352360427 1.124258856 0.608826909 0.656040825 0.080589839 5.663146879 0.68148916 0.873327836 0.06671986 0.26019159 0.584706746 -0.515431947 AFS(ph)DPFVEAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AFSDPFVEAEK 11 0 P34932;A0A087WYC1;A0A087WTS8;P34932-2 P34932 HSPA4 Heat shock 70 kDa protein 4 1 AFS(1)DPFVEAEK;AFS(1)DPFVEAEK 162.32 2.65E-05 48828000 382720 268354 312800 310640 339720 245071 396720 273282 559370 TRUE FALSE 358766.2384 288223.2094 320219.7637 318611.5483 313039.7616 315819.0193 337235.519 307401.8593 466007.5333 0.769872186 0.618494743 0.687155766 0.683704716 0.671748286 0.677712262 0.723669672 0.659649978 1 18.82999375 -5 0.424464226 7.049839207 0.677467124 0.85450572 0.040476032 318.4942768 2.035735803 1799.012273 0.02111159 1.00E-05 5 -6.372372083 AFS(ph)FSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AFSFSK 6 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C103 Q9H8V3-2 ECT2 Protein ECT2 1 AFS(0.947)FS(0.053)K;AFS(1)FSK;AFS(0.913)FS(0.087)K;AFS(0.948)FS(0.052)K;AFS(0.993)FS(0.007)K 142.79 0.012044 1667010000 3798610 3457470 3262790 2974290 3065860 1860570 5250160 2436780 5035630 TRUE FALSE 3560861.781 3713464.676 3340184.92 3050615.317 2825079.723 2397686.355 4462947.248 2741017.347 4195150.822 0.848804234 0.885180256 0.796201391 0.727176554 0.673415532 0.571537582 1.063834755 0.653377546 1 22.00029125 -1.108612756 7.357577695 1.000000057 0.79500594 0.193992619 0.138515056 1.24E-07 1.49E-08 0.129295803 0.030475304 0.077873061 1.108612756 -0.204994117 AFS(ph)WLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 109.01 0.031386 256621000 302106 373833 266089 249411 387587 131766 382861 239351 548143 TRUE FALSE 283197.7247 401511.9843 272400.7567 255811.3085 357147.4805 169804.7052 325454.5474 269234.4992 456654.3922 0.620157672 0.879246956 0.596514041 0.560185806 0.782095796 0.371845115 0.712693347 0.589580444 1 18.80074318 -1.435014503 5.406880653 1.000307376 0.651278421 0.40698201 0.136222754 0.000477223 4.99E-05 0.124706828 0.02936823 0.036727004 1.435014503 -0.349028955 AFSFS(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AFSFSK 6 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C103 Q9H8V3-2 ECT2 Protein ECT2 1 AFS(0.346)FS(0.654)K 133.05 0.015348 394740000 1465900 1363800 1272900 1128600 1201800 727830 2016500 971440 1876900 TRUE FALSE 1374151.936 1464777.171 1303093.789 1157561.787 1107415.476 937942.7057 1714144.545 1092726.422 1563633.265 0.87881984 0.936777954 0.833375587 0.74030261 0.708232231 0.599848268 1.096257405 0.69883805 1 20.57647075 -0.749563376 6.227995885 1.000000002 0.829910201 0.139754491 0.140518548 4.94E-09 1.11E-09 0.13249547 0.031229481 0.178006813 0.749563376 -0.170089801 AFSS(ph)PQEEEEAGFTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AFSSPQEEEEAGFTGR 16 0 A0A024RAC6;Q14241 A0A024RAC6 TCEB3 Transcription elongation factor B polypeptide 3 1 AFS(0.027)S(0.973)PQEEEEAGFTGR 129.05 6.03E-05 61125000 130590 132600 124770 141680 139600 125390 144770 103960 158760 TRUE FALSE 122416.605 142417.842 127729.6033 145315.7487 128636.3791 161588.0575 123063.0825 116939.6348 132261.9304 0.925561911 1.076786355 0.965732187 1.098696717 0.972588097 1.221727651 0.930449768 0.884151883 1 17.01303834 1.596160217 25 0.930445393 1.040510003 0.244167444 0.086884738 1.068659243 2276.250187 0.04102937 0.019238443 39.4602849 -1.596160217 0.11006461 AFT(ph)FDDEDDELSQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AFTFDDEDDELSQLK 15 0 G3V4K3;Q9H9C1;Q9H9C1-2;G3V549 G3V4K3 VIPAS39 Spermatogenesis-defective protein 39 homolog 1 AFT(1)FDDEDDELSQLK;AFT(1)FDDEDDELSQLK 267.34 1.74E-20 0 70708 46591 49206 52996 42891 31337 81937 41721 60470 TRUE FALSE 66282.5125 50040.64612 50373.18956 54355.96708 39522.51387 40383.48319 69651.30752 46929.95869 50377.16635 1.315725304 0.993319985 0.99992106 1.078980241 0.784532294 0.801622761 1.382596771 0.931572021 1 15.62048235 -2.933779049 9.912514816 1.002725887 1.035972975 0 0.192559981 0 0 0 0.041067518 0.001164718 2.933779049 0.033247088 AFTHTAQYDEAISDYFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AFTHTAQYDEAISDYFR 17 0 P31939-2;P31939;C9JLK0 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ;;; 276.18 9.58E-36 1151860000 529573 668990 610440 625449 772950 554868 685870 634899 660320 FALSE TRUE 496427.9712 718522.7157 624919.9251 641499.0802 712245.6249 715049.3841 583030.1608 714167.5377 550108.3262 0.902418574 1.306147683 1.135994304 1.166132287 1.294737038 1.299833778 1.059846094 1.298230737 1 19.06935621 -1.043585508 4.329060264 0.999986375 1.188241185 0.163327897 0.129611523 1.51E-05 3.33E-06 0.111057693 0.026174655 0.090451233 1.043585508 0.18825481 AFVAIGDYNGHVGLGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AFVAIGDYNGHVGLGVK 17 0 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 ;;; 236.43 3.46E-20 938917000 1556002 1377584 1500036 1445316 1666083 1339402 1776064 1440358 1633977 FALSE TRUE 1458614.612 1479581.753 1535617.562 1482405.255 1535235.562 1726065.614 1509759.691 1620189.867 1361255.683 1.071521413 1.086924206 1.128089 1.088998396 1.127808377 1.267995158 1.109093398 1.190217156 1 20.37650664 2.47691844 24.99999968 1.156528225 1.099422265 0.080609324 0.068456042 13.37227208 1647922.612 0.020835681 0.017582037 299.859933 -2.47691844 -0.05710596 AFVDFLSDEIKEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AFVDFLSDEIKEER 14 1 Q07021 Q07021 C1QBP "Complement component 1 Q subcomponent-binding protein, mitochondrial" 0 ;;;;; 283.82 1.59E-33 3317917000 7602890 4916352 5630870 4949250 7367710 5175740 5905170 6148310 10142630 FALSE TRUE 7127038.686 5280363.818 5764436.895 5076256.134 6789079.777 6669892.117 5019744.579 6915940.038 8449759.529 0.843460534 0.62491291 0.682201295 0.600757467 0.803464259 0.789358809 0.594069519 0.818477735 1 23.01047885 0.975001488 6.578661532 0.999963769 0.694591743 0.545081408 0.086245632 0.128980682 26.78237866 0.07743392 0.019438529 9.44064111 -0.975001488 -0.305372026 AFVEDS(ph)EDEDGAGEGGSSLLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AFVEDSEDEDGAGEGGSSLLQK 22 0 A0A494C108;Q8N9T8;H0YFD2;F8WFC1 A0A494C108 KRI1 Protein KRI1 homolog 1 AFVEDS(1)EDEDGAGEGGSSLLQK;AFVEDS(1)EDEDGAGEGGSSLLQK;AFVEDS(1)EDEDGAGEGGSSLLQK;AFVEDS(1)EDEDGAGEGGSSLLQK 351.09 3.14E-96 790470000 596655 484069 535148 499990 566979 431065 641557 506253 769198 TRUE FALSE 559311.4286 519909.9724 547841.9633 512820.5899 522450.7564 555506.4677 545361.4838 569459.8015 640813.8846 0.872814154 0.811327571 0.854915876 0.80026448 0.815292504 0.866876454 0.851045049 0.888650847 1 19.28954588 0.675987049 0.895215605 1.000503938 0.8318482 0.832587635 0.023075035 0.388881985 0.551416245 0.020476153 0.006837564 4.742278433 -0.675987049 -0.168655737 AFVHWYVGEGMEEGEFSEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 33 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 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 338.41 3.74E-80 7540621100 4517481.9 5242238.2 5222295.7 5071232.2 5757174 4717519.5 5676322.2 5198141.7 4915088.8 FALSE TRUE 4234740.772 5630378.971 5346171.02 5201368.604 5305028.777 6079390.797 4825210.383 5847141.134 4094728.727 1.034193241 1.375031009 1.30562276 1.270259632 1.295575148 1.48468707 1.178395617 1.427967889 1 21.96533645 -1.520688343 9.777209481 0.999993768 1.302667023 0.35289193 0.125918393 1.49E-05 7.29E-07 0.106001152 0.024984197 0.03015169 1.520688343 0.302673255 AFVRPSGTEDVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AFVRPSGTEDVVR 13 1 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A087WT27;A0A494C1E2;A0A494C1Q4;J3KN95;H0Y8I3 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 133.71 9.49E-05 469650000 110290 212230 124390 126850 201460 94211 125280 156960 228970 FALSE TRUE 103387.1458 227943.73 127340.5895 130105.1858 185638.1443 121408.1863 106495.427 176556.8015 190753.4278 0.541993646 1.194965315 0.667566455 0.68205949 0.973183792 0.636466604 0.558288405 0.925576036 1 17.54134946 3.740927493 24.24967256 0.743657177 0.919964041 0 0.217411894 604.0277119 1060922.42 0.051404402 0.09200824 5507.157448 -3.740927493 0.176306864 AFWMAIGGDRDEIEGLS(ph)S(ph)DEEH ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AFWMAIGGDRDEIEGLSSDEEH 22 1 Q6PD74;Q6PD74-2 Q6PD74 AAGAB Alpha- and gamma-adaptin-binding protein p34 2 AFWMAIGGDRDEIEGLS(1)S(1)DEEH;AFWMAIGGDRDEIEGLS(1)S(1)DEEH 106.04 0.00032763 59998000 86943 103180 90920 103367 105390 93901 115729 92012 100428 TRUE FALSE 81501.39283 110819.5546 93076.66534 106019.5722 97113.09452 121008.6943 98376.51083 103499.9007 83665.91801 0.97412895 1.324548361 1.112480058 1.267177541 1.160724663 1.446331998 1.175825392 1.237061676 1 16.35235243 -1.11490994 4.591718885 0.999980963 1.22063569 0.217350589 0.125712693 2.14E-05 4.13E-06 0.106379092 0.025071631 0.076752063 1.11490994 0.220654727 AFYAELYHIISSNLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AFYAELYHIISSNLEK 16 0 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ; 272.97 3.43E-35 794710000 1116120 1708260 1256560 1305080 1993470 770410 1239660 1799620 1681240 FALSE TRUE 1046264.042 1834741.348 1286366.197 1338570.562 1836910.907 992814.8604 1053784.491 2024306.518 1400630.183 0.746995213 1.30993989 0.918419589 0.955691644 1.311488878 0.708834404 0.752364546 1.445282662 1 20.41764465 2.230073641 24.99996188 0.925341052 1.062198907 4.60E-05 0.259829031 576.2528948 1697445.266 0.090952522 0.068243767 169.853164 -2.230073641 0.136857855 AGAAAGDS(ph)DEESRADDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AGAAAGDSDEESRADDK 17 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 AGAAAGDS(1)DEESRADDK;AGAAAGDS(1)DEESRADDK;AGAAAGDS(1)DEESRADDK 213.15 5.65E-13 620160000 1193520 595790 790620 647220 766750 639080 862790 659560 850980 TRUE FALSE 1118819.714 639902.9115 809373.8798 663828.7609 706532.5479 823572.0214 733422.6492 741907.5179 708945.9405 1.578145314 0.902611716 1.141658106 0.936360198 0.996595802 1.161685221 1.034525494 1.046493781 1 19.4353161 4.747112435 24.9879858 1.033876066 1.578145588 0.82427931 0.079853256 428.4893599 1251996.754 0.017886771 0.209420417 55861.47961 -4.747112435 0.544269522 AGAAAGDS(ph)DEESRADDKGVMDYYLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AGAAAGDSDEESRADDKGVMDYYLK 25 2 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 AGAAAGDS(0.996)DEES(0.004)RADDKGVMDYYLK;AGAAAGDS(1)DEESRADDKGVMDYYLK;AGAAAGDS(0.997)DEES(0.003)RADDKGVMDYYLK;AGAAAGDS(1)DEESRADDKGVMDYYLK;AGAAAGDS(0.965)DEES(0.035)RADDKGVMDYYLK 210.68 8.83E-26 2639060000 2895610 1744770 2129640 1931200 2695260 1523550 2669390 1799150 4192700 TRUE FALSE 2714378.939 1873954.586 2180156.066 1980757.862 2483585.152 1963374.152 2269139.751 2023777.838 3492911.284 0.777110759 0.536502199 0.624165886 0.56707935 0.711035852 0.562102496 0.649641393 0.579395717 1 21.73599857 -1.757955837 2.687668197 1.085404708 0.618013267 0.717215848 0.073680282 16860079.14 13768771.89 9566620.299 0.015745305 0.017459997 1.757955837 -0.467391442 AGAAS(ph)MIHYMVLISAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGAASMIHYMVLISAR 16 0 C9IYN1;Q9NV64 C9IYN1 TMEM39A Transmembrane protein 39A 1 AGAAS(0.993)MIHY(0.007)MVLISAR;AGAAS(0.999)MIHY(0.001)MVLISAR 48.112 0.070972 322300000 718810 305420 390310 345790 399530 262024 379630 292490 458300 TRUE FALSE 673820.9652 328033.6146 399568.3375 354663.5568 368152.5254 337666.0752 322708.0058 329008.0203 381806.7693 1.764821945 0.859161338 1.046519784 0.928908509 0.964237816 0.884389965 0.845212898 0.861713429 1 18.54248316 4.741173203 24.99793952 0.922384601 1.764822244 0.942576479 0.065239056 55.12666365 527437.1878 0.016193912 0.111557283 55102.74105 -4.741173203 0.842437643 AGAASVTGRYPGMAQLERSAISGFS(ph)SK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGAASVTGRYPGMAQLERSAISGFSSK 27 2 H7C5E6 H7C5E6 SLC26A8 1 AGAASVTGRYPGMAQLERS(0.006)AIS(0.146)GFS(0.467)S(0.38)K 45.791 0.071012 313110000 697000 159480 300730 255100 276850 173720 421100 234550 522520 TRUE FALSE 653376.0142 171288.0651 307863.4576 261646.2979 255107.3178 223870.1439 357959.9643 263834.0838 435308.0364 1.500950958 0.393487027 0.707231275 0.601060114 0.586038613 0.514279832 0.822314165 0.606085948 1 18.73167713 -1.089039438 11.36340731 0.999990236 0.680855627 0.069254511 0.302680405 0 0 0.256868505 0.060544487 0.08146303 1.089039438 -0.319134608 AGAEDDEEKGEGT(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGAEDDEEKGEGTPR 15 1 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 AGAEDDEEKGEGT(1)PR 90.223 0.0098564 143360000 359610 149030 205420 175240 154940 176980 271660 161040 126550 TRUE FALSE 337102.652 160064.3363 210292.6594 179736.9551 142771.6374 228071.253 230927.105 181146.1985 105427.9875 3.19746834 1.518233821 1.994656869 1.70483151 1.354210024 2.16328945 2.190377627 1.718198392 1 16.68589838 4.74532796 24.67296653 1.786227968 3.19746912 0.609016085 0.370708524 460.1316097 1677535.487 0.083598008 0.814403684 55632.42096 -4.74532796 1.411241152 AGAES(ph)PTMSVDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AGAESPTMSVDGR 13 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 AGAES(0.99)PT(0.01)MSVDGR;AGAES(0.998)PT(0.002)MSVDGR;AGAES(0.5)PT(0.5)MSVDGR;AGAES(0.871)PT(0.129)MSVDGR;AGAES(0.849)PT(0.15)MSVDGR 328.35 2.47E-62 3723260000 2239010 2425420 2388260 2257750 2416800 1932510 2324240 1932100 1976250 TRUE FALSE 2098874.361 2605000.62 2444910.655 2315687.687 2226994.277 2490394.265 1975741.789 2173326.938 1646401.108 1.274825649 1.582239351 1.485003043 1.406514899 1.352643816 1.512629124 1.200036722 1.320047058 1 20.65088443 0.969850041 0.544286806 0.993179764 1.479717644 0.620302719 0.103378728 0.557966178 0.403581302 0.106447134 0.04832211 9.329321097 -0.969850041 0.48653788 AGAGMITQHSSNAS(ph)PINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AGAGMITQHSSNASPINR 18 0 Q9NWH9;Q9NWH9-3;H7C3F4;H0YKH2 Q9NWH9 SLTM SAFB-like transcription modulator 1 AGAGMITQHSSNAS(1)PINR;AGAGMITQHSSNAS(1)PINR;AGAGMITQHSSNAS(1)PINR;AGAGMITQHSSNAS(1)PINR;AGAGMITQHS(0.001)S(0.013)NAS(0.986)PINR 275.2 2.98E-39 2101410000 360081 972099 833216 835457 1088158 941233 1086137 1014262 1479830 TRUE FALSE 337544.173 1044074.221 852980.277 856896.241 1002698.46 1212951.687 923280.8401 1140894.843 1232836.813 0.27379469 0.84688761 0.691884172 0.695060556 0.813326184 0.983870432 0.748907585 0.925422433 1 20.23355042 4.740549633 24.95407665 0.815940183 0.273794501 0.718228034 0.110315044 94.24884652 1182351.866 0.024810749 0.163141226 55023.68008 -4.740549633 -0.542145682 AGAHLQGGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 AGAHLQGGAK 10 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;; 143.7 3.35E-05 91745248400 122786091.9 143782019 114341984 111799746.9 145419941 85740535.4 132181294 122620494 132620428 FALSE TRUE 115101129.6 154427789.3 117054229.9 114668717.7 133999245.4 110492436.1 112361936.1 137929932.6 110485221.8 1.041778509 1.397723485 1.059455988 1.037864755 1.212825057 1.000065296 1.016986111 1.248401645 1 26.71927817 3.74767952 8.417146629 1.077667769 1.240653398 0.179894603 0.119872331 0.269997616 93.76346311 0.028113754 0.049432674 5593.446906 -3.74767952 0.162985629 AGAHLQGGAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AGAHLQGGAKR 11 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 150.61 2.19E-05 964380000 1196860 1424720 1521220 1740110 1615460 1155330 1203660 1159120 1500730 FALSE TRUE 1121950.669 1530207.751 1557304.057 1784764.169 1488588.288 1488855.016 1023182.357 1303838.684 1250248.468 0.897382159 1.223922917 1.245595653 1.427527579 1.190633963 1.190847303 0.818383212 1.042863652 1 20.25378341 1.759145191 25 0.940670002 1.213632675 0.393973768 0.140181905 8.357754651 10159.38954 0.061573214 0.034146198 57.43084298 -1.759145191 0.272962673 AGAKPDQIGIITPYEGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGAKPDQIGIITPYEGQR 18 1 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 87.49 0.0029665 108600000 186700 142760 171060 128900 151930 119910 189270 142880 193670 FALSE TRUE 175014.7803 153330.0989 175117.624 132207.7922 139998.0307 154526.0704 160890.7206 160718.8825 161345.2258 1.084722398 0.950323123 1.085359812 0.819409385 0.867692427 0.957735623 0.997183026 0.996117993 1 17.29979136 7.999997348 0.736220094 0.95659307 19.49741271 0.188550666 0.074995944 657.7385165 2.979985976 0.027259916 20190.04232 99999389.36 -7.999997348 18.54081964 AGAPGALS(ph)PSYDGGLHGLQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGAPGALSPSYDGGLHGLQSK 21 0 K7ENH8;A0A0A0MRB7;P15923-2;X6REB3;P15923;P15923-3 K7ENH8 TCF3 Transcription factor E2-alpha 1 AGAPGALS(0.996)PS(0.004)YDGGLHGLQSK;AGAPGALS(0.977)PS(0.023)YDGGLHGLQSK 255.67 1.29E-36 620200000 375860 340970 389020 373650 426560 365230 484390 378590 539550 TRUE FALSE 352335.5935 366215.7736 398247.7381 383238.4916 393059.6983 470665.972 411760.2164 425857.7949 449495.6194 0.783846557 0.814726012 0.88598803 0.852596722 0.874446115 1.047098018 0.916049453 0.947412559 1 18.77794753 3.612586566 0.347147955 0.996766827 0.722480474 0.692958997 0.044462912 1.713069177 0.291735685 0.04585109 0.185755309 4098.137883 -3.612586566 -0.274286353 AGAPGESLECPAELRPQVPQPPS(ph)PAAVPRPPSNPPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGAPGESLECPAELRPQVPQPPSPAAVPRPPSNPPAR 37 2 O43734-5;O43734-2;O43734 O43734-5 TRAF3IP2 Adapter protein CIKS 1 AGAPGESLECPAELRPQVPQPPS(1)PAAVPRPPSNPPAR 117.28 2.50E-06 135500000 13635 21202 18641 20054 21537 16719 16754 14006 20496 TRUE FALSE 12781.60969 22771.81814 19083.17332 20568.61959 19845.5709 21545.50389 14241.89324 15754.67993 17075.08519 0.748553202 1.333628376 1.117603403 1.204598358 1.162253112 1.261809452 0.834074505 0.922670649 1 14.05960516 1.728784627 10.14076923 0.911924553 1.161702123 0.288146745 0.159230371 0.09909654 37.58886956 0.068140136 0.036914445 53.55310142 -1.728784627 0.24977757 AGAPVGGS(ph)PGLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGAPVGGSPGLAK 13 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 AGAPVGGS(1)PGLAK;AGAPVGGS(1)PGLAK 185.95 8.63E-06 411830000 713540 504080 623230 574200 634110 504670 792020 617140 810560 TRUE FALSE 668880.8051 541402.6077 638013.3099 588934.9441 584309.5585 650360.0364 673263.9538 694191.2875 675272.2996 0.990534938 0.801754504 0.944823755 0.872144385 0.865294725 0.963107826 0.997025873 1.028016828 1 19.36510985 2.019657608 2.859339886 1.006912162 0.888041848 0.512473864 0.050460932 0.196908869 3.124762711 0.022712006 0.013419516 104.630333 -2.019657608 -0.118870314 AGASCVCCSQPQQSSTS(ph)PPPSDALQWVVVEVSGTPNQLETHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AGASCVCCSQPQQSSTSPPPSDALQWVVVEVSGTPNQLETHR 42 0 Q13952-3;Q13952 Q13952-3 NFYC Nuclear transcription factor Y subunit gamma 1 AGASCVCCSQPQQS(0.009)S(0.137)T(0.137)S(0.568)PPPS(0.137)DALQWVVVEVS(0.009)GT(0.003)PNQLET(0.001)HR;AGASCVCCSQPQQS(0.004)S(0.042)T(0.148)S(0.551)PPPS(0.148)DALQWVVVEVS(0.047)GT(0.047)PNQLET(0.014)HR;AGASCVCCSQPQQSST(0.005)S(0.995)PPPSDALQWVVVEVSGTPNQLETHR;AGASCVCCSQPQQSS(0.008)T(0.171)S(0.819)PPPS(0.001)DALQWVVVEVSGTPNQLETHR;AGASCVCCSQPQQSS(0.001)T(0.003)S(0.996)PPPS(0.001)DALQWVVVEVSGTPNQLETHR 194.28 1.85E-28 393288000 211783.3 254207 248229.8 254620.1 277445 231709.3 280734.2 238875.4 253723.7 TRUE FALSE 198528.1613 273028.7508 254117.9281 261154.0828 255655.5889 298600.0134 238640.7129 268699.5195 211375.5754 0.939219969 1.291675967 1.202210462 1.235497916 1.209485005 1.412651452 1.128989064 1.27119474 1 17.68944916 -1.230042748 4.433089431 0.999914838 1.220579605 0.227228328 0.121446524 8.94E-05 1.55E-05 0.102816956 0.024224854 0.05887857 1.230042748 0.220664767 AGAVAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGAVAER 7 0 H3BS10;H3BP20;P06865;A0A087WUJ7 H3BS10 HEXA Beta-hexosaminidase;Beta-hexosaminidase subunit alpha 0 79.454 0.075798 458870000 230980 268430 228160 246200 285420 224350 284450 238040 292120 FALSE TRUE 216523.3741 288304.8365 233572.0629 252517.9088 263004.2645 289116.203 241799.3632 267759.818 243363.2848 0.889712572 1.184668578 0.959767054 1.037617112 1.080706421 1.18800255 0.993573716 1.100247386 1 17.89275201 AGAVTSTPNRNS(ph)SK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGAVTSTPNRNSSK 14 1 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 AGAVT(0.002)S(0.003)T(0.003)PNRNS(0.935)S(0.056)K 76.526 0.016481 79521000 47253 33426 40458 32209 33857 26250 41624 24618 48051 TRUE FALSE 44295.51908 35900.89582 41417.68287 33035.53747 31198.00779 33827.94887 35382.86762 27691.61149 40030.97768 1.106531033 0.896827854 1.034640802 0.825249329 0.779346636 0.845044284 0.883887171 0.691754564 1 15.28882923 3.230530659 24.85720014 0.833294382 0.990983163 0.435223947 0.092867643 150.1416737 464771.7684 0.024095773 0.029286084 1700.319982 -3.230530659 0.157688781 AGCECLNESDEHGFDNCLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGCECLNESDEHGFDNCLR 19 0 O43396;K7ER96;K7EML9 O43396 TXNL1 Thioredoxin-like protein 1 0 ; 261.97 3.50E-31 564070000 291880 277330 294490 303180 338330 327710 385960 277390 326370 FALSE TRUE 273611.7518 297863.8018 301475.4419 310960.1121 311758.9266 422314.5571 328088.8811 312022.7521 271896.7386 1.00630759 1.095503401 1.108786532 1.143669886 1.14660782 1.553216708 1.206667218 1.147578135 1 18.05269932 2.46177569 24.99817993 1.263467929 1.098297427 0.152960862 0.141682386 329.5613815 536857.8688 0.045278874 0.03789431 289.5847514 -2.46177569 -0.165170502 AGDEKPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGDEKPEK 8 1 Q8WW12;Q8WW12-2;G5E9V9;A0A0B4J1Z9 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 0 65.347 0.058831 406730000 909920 502380 673900 606690 646580 443770 721050 510710 739500 FALSE TRUE 852969.7315 539576.7379 689885.2262 622258.6925 595800.215 571879.195 612935.2464 574473.2677 616072.6726 1.384527783 0.875832936 1.119811439 1.010041055 0.967094048 0.928265804 0.994907376 0.932476465 1 19.23274102 4.748175647 24.99147588 0.983917348 1.384527997 0.797080885 0.064323506 583.1313628 1515649.74 0.01501325 0.195237971 55998.40362 -4.748175647 0.400610649 AGDGSS(ph)VKEVETYHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGDGSSVKEVETYHR 15 1 Q6PL18 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 AGDGS(0.038)S(0.962)VKEVETYHR;AGDGS(0.437)S(0.563)VKEVETYHR 149.36 2.04E-06 957140000 637920 528160 547210 506710 618720 358740 733500 539960 952490 TRUE FALSE 597993.7259 567265.516 560190.0796 519713.0365 570128.227 462302.4143 623518.4845 607375.1946 793513.2657 0.753602683 0.714878428 0.705961833 0.654951919 0.718486069 0.582601998 0.785769453 0.765425382 1 19.59789482 0.746304634 1.314745028 0.998743078 0.696206166 0.764799193 0.052316888 0.380590365 1.128573793 0.045531165 0.013661753 5.575767213 -0.746304634 -0.302536912 AGDKDDITEPAVCALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AGDKDDITEPAVCALR 16 1 P14923 P14923 JUP Junction plakoglobin 0 ;; 151.44 5.87E-07 830680000 981970 766050 812340 795820 947250 606840 1049620 774090 1234760 FALSE TRUE 920510.2506 822769.1391 831609.0884 816242.0885 872856.806 782024.8568 892239.2252 870736.8405 1028670.579 0.894854261 0.799837339 0.808430906 0.793492207 0.848528989 0.760228661 0.867371191 0.84646811 1 19.97234962 0.54162547 1.046631262 1.000015441 0.816109543 0.673586742 0.038192651 0.818536602 1.306969444 0.032551516 0.010225622 3.480370429 -0.54162547 -0.183905898 AGDLLEDS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 213.63 1.96E-08 58465040000 112717300 50631300 72025500 63724600 63154000 58105500 100056300 60241100 71248400 TRUE FALSE 105662525.4 54380094.13 73733978.87 65359881.12 58194139.59 74879614.59 85053786.69 67762333.94 59356581.76 1.780131575 0.916159464 1.242220773 1.101139574 0.980415952 1.261521677 1.432929326 1.141614492 1 25.82290468 2.051953771 24.99993791 1.26652269 1.161600792 0 0.258227383 378.2769744 182023.4753 0.08864134 0.065465956 112.7077476 -2.051953771 -0.104921899 AGDLLEDS(ph)PKRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 AGDLLEDSPKRPK 13 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK;AGDLLEDS(1)PKRPK 192.96 1.18E-06 56598073300 40128923 21930884.3 26376836 28316962 33377059 15947581.5 32339310 22432269 54569120 TRUE FALSE 37617325.34 23554669.79 27002507.01 29043623.19 30755759.42 20551389.39 27490330.69 25232987.16 45461181.34 0.827460357 0.518127094 0.593968441 0.638866442 0.676527941 0.45206457 0.604698995 0.555044687 1 25.43813184 -0.953823064 5.291992397 1.000001176 0.595605581 0.598724331 0.100285183 1.24E-06 2.46E-07 0.086704989 0.020436503 0.111218475 0.953823064 -0.404395595 AGDNIPEEQPVASTPTTVS(ph)DGENKKDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGDNIPEEQPVASTPTTVSDGENKKDK 27 2 Q9Y320-2;Q9Y320 Q9Y320-2 TMX2 Thioredoxin-related transmembrane protein 2 1 AGDNIPEEQPVAS(0.001)T(0.002)PT(0.159)T(0.159)VS(0.68)DGENKKDK;AGDNIPEEQPVASTPT(0.051)T(0.051)VS(0.899)DGENKKDK 95.042 0.0026167 556870000 1438920 450070 643090 609350 734100 438280 992660 553980 880120 TRUE FALSE 1348860.566 483393.6511 658344.3985 624986.9526 676446.7472 564804.3211 843819.8484 623145.6225 733222.2862 1.839633889 0.659272993 0.897878325 0.85238401 0.922567085 0.770304356 1.150837699 0.849872725 1 19.48389111 4.747010212 24.93772528 0.88614807 1.839634383 0.841339774 0.129886645 416.0020361 1227740.087 0.031800058 0.368370217 55848.33268 -4.747010212 0.953486313 AGDRNS(ph)EDDGVVMTFSSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 AGDRNSEDDGVVMTFSSVK 19 1 Q9NY61 Q9NY61 AATF Protein AATF 1 AGDRNS(1)EDDGVVMTFSSVK;AGDRNS(1)EDDGVVMTFSSVK;AGDRNS(1)EDDGVVMTFSSVK;AGDRNS(1)EDDGVVMTFSSVK;AGDRNS(0.996)EDDGVVMT(0.003)FS(0.001)SVK;AGDRNS(0.989)EDDGVVMT(0.011)FSSVK;AGDRNS(1)EDDGVVMTFSSVK;AGDRNS(1)EDDGVVMTFSSVK 344.4 4.05E-76 1368953000 3209221 1987492 2437499 2167949 1807889 1753537 2890744 2043226 1586274 TRUE FALSE 3008361.586 2134647.976 2495317.627 2223582.242 1665904.691 2259754.666 2457303.774 2298327.264 1321514.622 2.276449717 1.615304092 1.888225515 1.682601316 1.260602541 1.70997326 1.859460148 1.739161433 1 20.33376096 -2.438628463 0.288452926 1.20E-34 1.808043056 0.485112273 0.248262237 41.62626301 1.47137054 27.43676387 0.27105043 0.003642265 2.438628463 1.808043056 AGDSAVLVLPPS(ph)PGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 AGDSAVLVLPPSPGPR 16 0 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;Q96JY6-4;C9JS55;C9JSR2 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR;AGDSAVLVLPPS(1)PGPR 281.49 1.69E-35 9827491000 4579480 5549800 5247340 5984920 6206170 3572320 4116090 3322230 3276610 TRUE FALSE 4292858.521 5960712.967 5371809.383 6138503.18 5718762.443 4603590.792 3498920.516 3737017.729 2729722.623 1.572635434 2.183633207 1.967895689 2.248764445 2.094997636 1.686468344 1.2817861 1.369010059 1 21.38032293 1.89305674 2.147438994 1.209884115 2.042221714 0.76265222 0.202340382 0.136533568 1.163042763 0.112372936 0.054376331 78.17299296 -1.89305674 0.832337599 AGDTETLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGDTETLK 8 0 C9JNG9;P12111 C9JNG9 COL6A3 Collagen alpha-3(VI) chain 0 75.311 0.090077 790810000 515680 449260 404130 423540 538860 419490 442680 392830 599180 FALSE TRUE 483404.5093 482523.6779 413716.1544 434408.7535 496540.1093 540589.9531 376304.2436 441875.6902 499172.9871 0.968410795 0.966646213 0.828803171 0.870256934 0.99472552 1.082971168 0.753855383 0.88521555 1 18.92918034 1.719464771 24.99999997 0.858939906 0.93796133 0.097179134 0.090756415 1.843612752 2404.042237 0.041311681 0.022909377 52.41610805 -1.719464771 0.079021424 AGDWQCPNPGCGNQNFAWR ddPTM_SK-BR-3_Pertuzumab_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 ; 278.82 3.40E-39 392480000 211286 210622 204804 207524 227505 183874 248440 209683 226882 FALSE TRUE 198061.9864 226216.672 209662.0476 212849.4172 209637.675 236955.4389 211188.7284 235862.3841 189013.9285 1.047869795 1.196825408 1.109241257 1.126104403 1.109112311 1.253640093 1.117318338 1.247857161 1 17.52813303 AGEAGKLEEVMQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AGEAGKLEEVMQELR 15 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;;; 186.83 3.34E-07 1188361000 2027224 1882349 1930739 1919415 2173840 1284472 2201051 1654293 2802110 FALSE TRUE 1900343.669 2021720.079 1976537.041 1968670.438 2003115.375 1655278.215 1871023.836 1860835.123 2334419.739 0.814053975 0.866048228 0.846693081 0.843323249 0.858078495 0.709074802 0.801494181 0.797129621 1 21.15463256 AGELDQALGRPFTLSISNQYGDDEVTHTLQTESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGELDQALGRPFTLSISNQYGDDEVTHTLQTESR 34 1 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 0 293.99 5.44E-90 42218000 50752 56904 53718 58043 71604 53684 71033 52620 67706 FALSE TRUE 47575.52291 61117.23137 54992.21633 59532.48165 65980.51068 69181.69931 60382.26109 59189.72283 56405.4312 0.843456417 1.083534512 0.974945411 1.055438818 1.169754566 1.226507764 1.070504379 1.049362119 1 15.78354646 5.864471763 0.712026824 1.097390855 1.00E-17 0.42624857 0.078961819 12.60062311 1.428783391 0.02928868 16.06229202 731933.7322 -5.864471763 -1.097390855 AGELTEDEVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AGELTEDEVER 11 0 P62269 P62269 RPS18 40S ribosomal protein S18 0 ;;; 302.3 1.44E-35 5902280000 3261250 3065910 3271580 3091960 3175600 2593160 3596680 2790920 3220110 FALSE TRUE 3057134.184 3292913.166 3349183.423 3171304.928 2926201.186 3341763.196 3057391.224 3139372.506 2682652.838 1.139593667 1.227483899 1.248459501 1.182152563 1.090786383 1.245693497 1.139689482 1.170249263 1 21.35522894 -1.951791184 0.257025498 0.791767873 1.215144528 0.562406792 0.05005748 20.95459753 0.826045919 2.678474446 0.071553792 0.011174004 1.951791184 0.423376655 AGEPNS(ph)PDAEEANS(ph)PDVTAGCDPAGVHPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.999)PDVT(0.001)AGCDPAGVHPPR;AGEPNS(1)PDAEEANS(1)PDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANS(1)PDVTAGCDPAGVHPPR 263.51 9.87E-59 1897610000 497584 443231 445886 446545 494522 441235 594122 387968 613025 TRUE FALSE 466441.1057 476048.2844 456462.6265 458004.1007 455684.2369 568612.3816 505038.9217 436406.6588 510707.1672 0.913323986 0.932135507 0.893785433 0.896803746 0.892261292 1.11338242 0.988901183 0.854514459 1 18.96213678 AGEPNS(ph)PDAEEANSPDVTAGCDPAGVHPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGEPNSPDAEEANSPDVTAGCDPAGVHPPR 30 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 AGEPNS(1)PDAEEANSPDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANSPDVTAGCDPAGVHPPR 260.6 1.72E-58 1192770000 312840 292880 295010 319720 334390 296000 383380 244210 377730 TRUE FALSE 293259.9028 314565.1399 302007.7765 327924.5565 308128.3583 381450.3948 325895.7281 274700.1561 314684.4228 0.931917444 0.999620945 0.959716321 1.042074322 0.979166225 1.212168024 1.035627138 0.872938526 1 18.26354624 3.23538594 24.90690367 1.03692768 0.970861396 0.084375244 0.084851372 167.9545039 1317686.989 0.023546203 0.02930015 1719.435701 -3.23538594 -0.066066284 AGETRFT(ph)DTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AGETRFTDTR 10 1 P13639 P13639 EEF2 Elongation factor 2 1 AGET(0.197)RFT(0.803)DTR;AGET(0.026)RFT(0.974)DTR;AGETRFT(0.998)DT(0.002)R;AGETRFT(0.999)DT(0.001)R;AGETRFT(0.999)DT(0.001)R;AGETRFT(1)DTR 122.46 0.0007889 11791110000 8615700 16020200 9346600 12654000 10138420 4848410 17680900 9895280 19340600 TRUE FALSE 8076458.716 17206352.28 9568305.766 12978723.06 9342189.39 6248067.26 15029813.19 11130727.49 16112528.91 0.501253326 1.06788651 0.593842582 0.805505029 0.579809007 0.387776946 0.932802868 0.690811948 1 23.94167961 -1.783158801 7.538889814 1.006464712 0.721201071 0.173113891 0.202417975 0.02095363 0.000602689 0.186718297 0.043554064 0.016475598 1.783158801 -0.285263641 AGETRFT(ph)DTRKDEQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGETRFTDTRKDEQER 16 3 P13639 P13639 EEF2 Elongation factor 2 1 AGET(0.015)RFT(0.925)DT(0.059)RKDEQER 118.36 0.0002865 331010000 197020 411390 194570 406840 358160 82027 435000 206890 1753100 TRUE FALSE 184688.8699 441849.7437 199185.2923 417280.2032 330031.5583 105706.8633 369775.7883 232720.6719 1460496.285 0.126456241 0.302533973 0.136381923 0.285711239 0.2259722 0.072377359 0.253185025 0.159343556 1 20.47802726 -1.380405396 3.526007252 1.005214022 0.20155123 0.921671535 0.07370853 83162514.19 124233760.6 4448137.356 0.016055486 0.041648043 1.380405396 -0.803662792 AGETRFTDT(ph)RKDEQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGETRFTDTRKDEQER 16 3 P13639 P13639 EEF2 Elongation factor 2 1 AGET(0.003)RFT(0.039)DT(0.958)RKDEQER 112.58 0.00074861 398240000 198120 432690 183740 434940 392880 92078 496990 200040 1894000 TRUE FALSE 185720.0229 464726.8178 188098.3996 446101.2968 362024.7896 118659.4238 422470.9633 225015.4343 1577879.164 0.11770231 0.29452624 0.119209635 0.282722091 0.229437588 0.075201845 0.267746082 0.142606252 1 20.5895553 -1.550706239 3.190676431 1.029555027 0.197860872 0.916232185 0.076837761 94006542.07 112621212.9 23858753.9 0.016790961 0.028138035 1.550706239 -0.831694155 AGEVFIHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGEVFIHK 8 0 Q15233;Q15233-2;H7C367;C9JYS8;C9IZL7 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 111.04 0.0033105 2181400000 5284700 4730500 5170500 5095800 5684000 4164400 5800200 4669900 6306000 FALSE TRUE 4953940.06 5080751.142 5293146.702 5226566.855 5237601.568 5366594.677 4930513.856 5252947.295 5253487.862 0.942981157 0.967119612 1.00754905 0.994875594 0.996976048 1.021529852 0.938521985 0.999897103 1 22.32484413 4.495731567 2.241074514 0.990720804 0.94131365 0.380616572 0.021591517 0.468138321 3.860504233 0.005615239 0.037236571 31313.49672 -4.495731567 -0.049407153 AGFADPDDFTLGAGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGFADPDDFTLGAGPR 16 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 0 ; 146.5 2.60E-06 71185000 131713 139171 145795 139722 144724 121581 136443 107000 150913 FALSE TRUE 123469.3184 149475.3656 149253.3262 143307.5031 133357.9608 156679.461 115984.6388 120359.1855 125724.6454 0.982061378 1.188910617 1.18714454 1.139852116 1.060714552 1.246211199 0.922529059 0.957323723 1 16.93990796 1.687486473 8.200854822 0.956437281 1.143697716 0.5401642 0.075179853 0.08114122 10.0059029 0.034160391 0.018014676 48.69523573 -1.687486473 0.187260434 AGFAGDDAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 187 2.97E-06 67688340000 102223290 121139000 112923400 111208200 128925900 101030900 128196000 106783400 119643100 FALSE TRUE 95825316.75 130108257.6 115601996.4 114061990.7 118800579.9 130196880.7 108974199.9 120115542.5 99673893.69 0.961388316 1.30533937 1.159802152 1.14435171 1.191892636 1.306228501 1.093307343 1.205085285 1 26.57071235 -0.275482849 0.8976431 0.994867408 1.183305851 0.213435358 0.100125865 18.57517018 11.21526544 0.438741275 0.028499944 0.530294534 0.275482849 0.188438444 AGFDS(ph)DYDQALADIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGFDSDYDQALADIR 15 0 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;P52701-4 P52701 MSH6 DNA mismatch repair protein Msh6 1 AGFDS(1)DYDQALADIR 164.01 1.58E-06 66274000 64175 63087 61439 61715 60521 51252 79219 70002 59315 TRUE FALSE 60158.40131 67758.02712 62896.36209 63298.71138 55767.92479 66047.62039 67340.84638 78741.90379 49414.94331 1.21741314 1.371205198 1.272820687 1.280962946 1.128563974 1.33659205 1.362762797 1.593483641 1 15.59265977 2.020714661 24.94670261 1.356711279 1.27046227 0.023347849 0.155118238 639.1837306 769766.8765 0.052379658 0.038680832 104.8853087 -2.020714661 -0.086249008 AGFDSDYDQALADIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGFDSDYDQALADIR 15 0 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;P52701-4 P52701 MSH6 DNA mismatch repair protein Msh6 0 ; 212.59 1.87E-09 143526000 201947 213555 232578 214014 211392 212142 276960 227030 209391 FALSE TRUE 189307.4978 229366.8344 238094.86 219505.9616 194790.125 273383.9516 235432.4192 255375.1953 174442.2894 1.085215623 1.314857969 1.364891855 1.258329975 1.116645085 1.56718851 1.349629267 1.463952326 1 17.4123903 2.252562847 24.98646995 1.378569903 1.259881912 0.076841739 0.167364187 503.5062392 898487.2367 0.052792761 0.043968564 178.8804368 -2.252562847 -0.118687992 AGFESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AGFESER 7 0 Q13946-3;Q13946-2;Q13946;E5RG23 Q13946-3 PDE7A "High affinity cAMP-specific 3,5-cyclic phosphodiesterase 7A" 0 ;; 113.25 0.014357 976310000 1629730 1707860 1759510 1656470 1788590 1670740 1998530 1584730 2126390 FALSE TRUE 1527728.108 1834311.731 1801246.408 1698977.825 1648121.356 2153055.516 1698868.98 1782587.029 1771481.772 0.862401258 1.03546746 1.016802113 0.959071581 0.930363147 1.215398064 0.959010139 1.006268908 1 20.75652519 AGFIQDTSLILYEEVKPNLTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGFIQDTSLILYEEVKPNLTER 22 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 160.57 1.67E-11 108981100 133220 141028 143583 151006 146192 103938 163244 131666 160692 FALSE TRUE 124881.998 151469.8599 146988.8566 154881.0696 134710.67 133943.2133 138767.0777 148104.7899 133871.4671 0.932849999 1.131457383 1.097984953 1.156938614 1.006268721 1.000535934 1.036569485 1.10632081 1 17.03048898 2.709759717 24.96349567 1.030072913 1.091445567 0.112595947 0.066068153 1217.729871 1055479.822 0.020087522 0.018940359 512.577711 -2.709759717 0.061372654 AGFNYES(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AGFNYESPSK 10 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29;E7EVN4;F8W8T0 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 AGFNYES(0.993)PS(0.007)K;AGFNYES(0.993)PS(0.007)K;AGFNYES(1)PSK;AGFNYES(0.996)PS(0.004)K;AGFNYES(0.735)PS(0.265)K;AGFNYES(0.996)PS(0.004)K 211.52 6.01E-08 4561420000 5271060 2844070 3805680 3195810 3249500 3561920 5136210 3295490 3232170 TRUE FALSE 4941153.764 3054647.902 3895952.527 3277819.895 2994297.378 4590188.481 4366082.993 3706939.181 2692699.946 1.835018332 1.134418228 1.446857282 1.217298607 1.112005585 1.704678788 1.621451732 1.376662552 1 21.36062205 2.236255315 24.99999734 1.501024806 1.327178165 0 0.276932292 152.6260171 1655129.879 0.091880912 0.071128261 172.2881133 -2.236255315 -0.173846641 AGFNYES(ph)PSKGGNFPSFPHDEVTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AGFNYESPSKGGNFPSFPHDEVTDR 25 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 AGFNYES(0.975)PS(0.025)KGGNFPSFPHDEVTDR;AGFNYES(0.971)PS(0.029)KGGNFPSFPHDEVTDR;AGFNYES(0.949)PS(0.051)KGGNFPSFPHDEVTDR;AGFNYES(0.941)PS(0.059)KGGNFPSFPHDEVTDR;AGFNYES(0.999)PS(0.001)KGGNFPSFPHDEVTDR;AGFNYES(0.997)PS(0.003)KGGNFPSFPHDEVTDR 232.53 2.12E-35 4703180000 2890232 2137312 2597744 2242938 2753973 2129647 3349539 2260245 3829720 TRUE FALSE 2709337.538 2295560.804 2659363.714 2300495.586 2537687.07 2744441.517 2847306.723 2542441.564 3190514.991 0.849185021 0.719495383 0.833521774 0.721042087 0.795384782 0.860187626 0.892428567 0.796874978 1 21.60535788 0.549547494 0.360826333 1.023628286 0.766696436 0.57409099 0.053493048 1.652765005 0.450734463 0.132697813 0.046675826 3.544438901 -0.549547494 -0.25693185 AGGAAVVITEPEHTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGGAAVVITEPEHTK 15 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 134.21 3.66E-05 296950000 603680 501800 523690 547660 632790 455000 647620 491420 704400 FALSE TRUE 565896.7464 538953.7941 536112.1741 561713.8828 583093.226 586351.1137 550515.3932 552774.8687 586831.0894 0.964326459 0.91841384 0.913571526 0.957198575 0.993630427 0.999182089 0.938115589 0.941965889 1 19.16258578 3.080990795 5.345068326 0.970644365 0.926820458 0.358276897 0.025277927 0.212042228 10.38151663 0.007517559 0.009026182 1205.010401 -3.080990795 -0.043823907 AGGAS(ph)PAASSTAQPPTQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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;AGGAS(1)PAASSTAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR 210.22 1.20E-16 9393749000 1295893 1294523 1297990 1298864 1402399 1212935 1577926 1217951 1430755 TRUE FALSE 1214785.37 1390370.83 1328778.936 1332195.049 1292260.24 1563089.644 1341330.645 1370014.863 1191952.747 1.019155644 1.166464722 1.114791621 1.117657602 1.084153917 1.3113688 1.125321996 1.149386892 1 20.18489561 4.745459871 23.96004775 1.143144432 1.019155541 0.166719045 0.077905608 711.5632618 2471030.36 0.016705773 0.161290673 55649.3212 -4.745459871 -0.123988891 AGGDAEPRPAEPPAWAGGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGGDAEPRPAEPPAWAGGAR 20 1 Q96HS1;Q96HS1-2 Q96HS1 PGAM5 "Serine/threonine-protein phosphatase PGAM5, mitochondrial" 0 60.294 0.054419 268010000 110170 99137 89100 85722 135410 145510 143570 82173 142800 FALSE TRUE 103274.6564 106477.2066 91213.49408 87921.77165 124775.4448 187516.3748 122043.0113 92432.47994 118965.7575 0.868104054 0.895023987 0.766720576 0.739051081 1.048834954 1.576221417 1.025866719 0.776967103 1 16.86018685 2.606804417 5.565141144 1.129354412 0.823390643 0.29554543 0.20281948 0.263090652 10.84097742 0.065397535 0.061369532 404.3937333 -2.606804417 -0.305963769 AGGEEEDDDDEAAGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGGEEEDDDDEAAGGR 16 0 Q6DD87 Q6DD87 ZNF787 Zinc finger protein 787 0 243.85 1.18E-19 115950000 336690 244760 294770 275200 258110 262130 400350 252960 255320 FALSE TRUE 315617.1739 262882.2851 301762.0836 282262.0979 237839.0818 337802.6757 340321.2342 284542.6128 212705.4426 1.483822746 1.235898254 1.418685295 1.327009288 1.118161712 1.58812427 1.599964862 1.337730758 1 17.69849742 2.219005076 24.99997675 1.455102345 1.320067714 0 0.195509082 553.0079871 706965.9577 0.066766392 0.049378294 165.5789315 -2.219005076 -0.135034632 AGGGDLLLPPS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AGGGDLLLPPSPK 13 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 AGGGDLLLPPS(1)PK;AGGGDLLLPPS(1)PK;AGGGDLLLPPS(1)PK;AGGGDLLLPPS(1)PK;AGGGDLLLPPS(1)PK;AGGGDLLLPPS(1)PK 153.09 4.38E-05 1516478000 5207220 3810280 4204920 4562950 4988060 3179130 6071040 4099390 5121750 TRUE FALSE 4881309.395 4092397.096 4304662.688 4680043.022 4596317.888 4096893.222 5160743.913 4611207.865 4266896.837 1.143995175 0.959103829 1.008850894 1.096825914 1.077203894 0.960157552 1.209484107 1.080693544 1 22.0247558 2.762549819 1.068621188 1.092433183 1.02034076 0 0.081880131 1.131877118 2.712592531 0.040840172 0.039031011 578.8283838 -2.762549819 -0.072092423 AGGGGGLGAGS(ph)PALSGGQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AGGGGGLGAGSPALSGGQGR 20 0 A0A3B3ITT1;Q6IQ22 A0A3B3ITT1 RAB12 Ras-related protein Rab-12 1 AGGGGGLGAGS(0.999)PALS(0.001)GGQGR;AGGGGGLGAGS(0.998)PALS(0.002)GGQGR;AGGGGGLGAGS(0.514)PALS(0.486)GGQGR;AGGGGGLGAGS(1)PALSGGQGR;AGGGGGLGAGS(1)PALSGGQGR;AGGGGGLGAGS(0.999)PALS(0.001)GGQGR 293.84 1.60E-54 5760560000 3595960 4138430 3964390 3977130 4794930 3872080 5321070 4513750 4379290 TRUE FALSE 3370895.283 4444843.663 4058427.203 4079189.889 4418355.54 4989886.638 4523224.952 5077301.623 3648358.208 0.923948552 1.218313392 1.112398227 1.118089194 1.211053106 1.367707433 1.239797381 1.391667521 1 21.79881595 2.592123203 3.76396041 1.271855752 1.117458157 0.237090215 0.12766084 0.31604501 7.994042526 0.038534337 0.035716033 390.951787 -2.592123203 -0.154397595 AGGIETIANEFSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AGGIETIANEFSDR 14 0 Q92598-2;Q92598;Q92598-3;R4GN69 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;; 287.89 8.86E-34 510240000 349007 386320 379850 371410 440620 351910 408710 342453 382570 FALSE TRUE 327163.2749 414923.5348 388860.2214 380941.0094 406015.4826 453500.7042 347427.7298 385209.0109 318716.5955 1.026502164 1.301857326 1.220081498 1.195234308 1.273907566 1.422896425 1.090083587 1.20862552 1 18.28191462 0.798571637 1.244318565 1.003509185 1.237088811 0.280921422 0.108665918 0.873515697 2.479752346 0.094146239 0.028719256 6.288855802 -0.798571637 0.233579626 AGGIETIANEYSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGGIETIANEYSDR 14 0 P34932;A0A087WYC1;A0A087WTS8;P34932-2 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 128.57 0.00016981 352550000 156721 129831 156249 156437 154882 119370 175198 142249 194225 FALSE TRUE 146912.1124 139443.8223 159955.3001 160451.4383 142718.1925 153830.1812 148928.6864 160009.1008 161807.5928 0.907943254 0.86178788 0.988552498 0.991618722 0.882024076 0.950698163 0.920406044 0.988884996 1 17.30391978 AGGLDWPEATEVS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 AGGLDWPEATEVSPSR 16 0 Q9Y446;Q9Y446-2;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 1 AGGLDWPEATEVS(1)PSR;AGGLDWPEATEVS(0.975)PS(0.025)R;AGGLDWPEATEVS(1)PSR;AGGLDWPEATEVS(0.981)PS(0.019)R;AGGLDWPEATEVS(1)PSR;AGGLDWPEATEVS(0.997)PS(0.003)R;AGGLDWPEATEVS(1)PSR;AGGLDWPEAT(0.003)EVS(0.986)PS(0.012)R;AGGLDWPEAT(0.024)EVS(0.957)PS(0.019)R 328.34 1.88E-71 13132516000 6392000 6686030 6907400 6896400 7269180 6430020 7901370 6274370 7612990 TRUE FALSE 5991936.13 7181070.618 7071246.79 7073373.3 6698287.925 8286262.391 6716632.921 7057738.906 6342332.787 0.944752717 1.132244374 1.114928375 1.115263664 1.056123693 1.306500726 1.059016161 1.112798578 1 22.59658215 4.741062728 24.38299546 1.119958222 0.944752627 0.298952196 0.079740142 182.9890381 1783071.446 0.016754301 0.113271135 55088.72583 -4.741062728 -0.175205594 AGGPATPLS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AGGPATPLSPTR 12 0 Q03252 Q03252 LMNB2 Lamin-B2 1 AGGPAT(0.347)PLS(0.652)PT(0.002)R;AGGPATPLS(0.964)PT(0.036)R;AGGPAT(0.006)PLS(0.98)PT(0.014)R 196.75 2.13E-07 717920000 1158620 1244870 1083970 1129340 1334710 841140 1246060 1146190 1380210 TRUE FALSE 1086104.042 1337041.47 1109682.28 1158320.776 1229887.261 1083963.463 1059224.871 1289294.345 1149844.035 0.944566402 1.162802458 0.965071998 1.00737208 1.069612246 0.942704776 0.921190039 1.121277587 1 20.13300676 3.750081514 19.18287861 0.995219415 1.067672809 0.050778436 0.078136179 48.72503996 40704.20401 0.018786793 0.033774281 5624.468823 -3.750081514 0.072453393 AGGPS(ph)DDDNADKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGGPSDDDNADKPK 14 1 E7EVA0 E7EVA0 MAP4 Microtubule-associated protein 1 AGGPS(1)DDDNADKPK;AGGPS(1)DDDNADKPK 158.45 3.07E-06 1187360000 1393160 491300 742780 694240 771870 485850 1013010 529790 1022060 TRUE FALSE 1305964.602 527676.3632 760399.0924 712055.3737 711250.4438 626107.0079 861118.5548 595935.4477 851471.5832 1.533773561 0.619722811 0.893041068 0.836264401 0.835319061 0.735323433 1.011329763 0.699888827 1 19.69959886 4.749136543 24.79601896 0.826886176 1.533774007 0.76463031 0.122905629 626.423385 1468662.492 0.027366677 0.391802218 56122.43987 -4.749136543 0.706887831 AGGPTT(ph)PLSPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGGPTTPLSPTR 12 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 1 AGGPT(0.294)T(0.706)PLSPTR 125.38 0.0034244 356390000 418500 406050 407920 436640 402820 242590 375500 289410 338800 TRUE FALSE 392306.832 436114.3645 417596.055 447844.9216 371184.1421 312621.7949 319197.261 325543.4756 282252.0913 1.389916476 1.54512359 1.479514476 1.586684157 1.315080219 1.107597798 1.130894228 1.153378436 1 18.10662474 2.441481773 3.08204262 1.110363557 1.503546998 0.893120779 0.065377239 0.068976197 1.352403706 0.021820489 0.018330682 276.3641929 -2.441481773 0.393183441 AGGPTTPLS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AGGPTTPLSPTR 12 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 1 AGGPTTPLS(1)PTR;AGGPTTPLS(0.998)PT(0.002)R;AGGPTTPLS(0.966)PT(0.034)R;AGGPTT(0.005)PLS(0.994)PTR 200.05 1.73E-07 2073000000 2816010 3223550 2754620 2986870 3608480 1944263 2970630 2853180 3241110 TRUE FALSE 2639760.961 3462224.996 2819960.887 3063518.141 3325084.537 2505540.166 2525211.609 3209405.804 2700147.803 0.977635727 1.282235362 1.044372787 1.13457424 1.23144538 0.927927043 0.935212364 1.18860375 1 21.36460695 2.233650061 24.9995343 0.996944566 1.142054054 0.221913757 0.110347675 151.0783092 769127.9907 0.038036185 0.028981752 171.2576818 -2.233650061 0.145109488 AGGS(ph)PASYHGSTSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGGSPASYHGSTSPR 15 0 I3L2B2;O95208-3;O95208-2;F6PQP6 I3L2B2 EPN2 Epsin-2 1 AGGS(0.871)PAS(0.128)YHGSTSPR 57.708 0.050436 0 32246 88630 75971 94527 79686 86075 70322 72947 62311 TRUE FALSE 30227.78042 95192.25742 77773.068 96952.72285 73427.783 110923.4552 59777.86894 82054.59353 51910.89156 0.582301315 1.833762715 1.49820328 1.867675934 1.414496665 2.136805049 1.151547722 1.580681646 1 15.66374965 0.572297921 1.107717492 1.00369231 1.56380903 0.109455667 0.428837 2.797106189 5.054675386 0.362313684 0.112511637 3.735062909 -0.572297921 0.560116721 AGGSAALS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AGGSAALSPSK 11 0 Q92522 Q92522 H1FX Histone H1x 1 AGGSAALS(0.998)PS(0.002)K;AGGSAALS(0.996)PS(0.004)K;AGGSAALS(1)PSK;AGGSAALS(1)PSK;AGGSAALS(0.998)PS(0.002)K;AGGSAALS(0.985)PS(0.015)K 222.81 7.76E-12 3310560000 4278170 6549490 2394350 2755460 8209030 1361350 2932300 6038440 4387820 TRUE FALSE 4010406.976 7034421.054 2451145.113 2826169.769 7564325.897 1754349.645 2492628.837 6792352.526 3655464.496 1.097099146 1.924357647 0.670542722 0.773135609 2.069320029 0.479925232 0.681891136 1.858136643 1 21.80162331 3.975100777 24.95958874 1.029782778 1.535772317 0.092288333 0.550698612 174.5549722 2156380.342 0.131665441 0.253379984 9442.799693 -3.975100777 0.505989539 AGGSAALS(ph)PSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGGSAALSPSKK 12 1 Q92522 Q92522 H1FX Histone H1x 1 AGGSAALS(0.996)PS(0.004)KK 108.34 0.0010516 452470000 2396400 1351600 1641400 1502100 1817000 1145800 2157600 1409100 1169900 TRUE FALSE 2246413.602 1451673.87 1680334.783 1540646.429 1674300.149 1476573.859 1834087.91 1585029.237 974636.1322 2.304874124 1.489452138 1.724063707 1.580740112 1.717872029 1.515000122 1.881818096 1.626277935 1 19.89450418 0.960674074 22.05305694 0.999999995 1.711292483 0.495706021 0.232477549 1246.441197 698976.7446 0.197507455 0.049376864 9.134274813 -0.960674074 0.711292488 AGHCAVAINTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 118.4 0.00072507 404253000 281861 290521 306926 269855 319813 247506 305295 284658 340143 FALSE TRUE 264219.8231 312031.4771 314206.4297 276779.9362 294696.177 318956.9643 259518.849 320198.1779 283370.9359 0.932416807 1.101141428 1.108816713 0.976740735 1.039966135 1.125581081 0.915827335 1.129961253 1 18.11233227 1.756396168 25 1.00739501 1.057714432 0.022213572 0.078270387 18.41722147 25842.279 0.033817934 0.018753639 57.06846197 -1.756396168 0.050319422 AGHGAGKPTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGHGAGKPTAK 11 1 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ; 112.13 0.00094207 671000000 1261590 1078560 1211270 1149490 1299380 818700 1447330 1168100 1547030 FALSE TRUE 1182629.334 1158417.705 1240001.896 1178987.859 1197331.936 1055045.4 1230316.303 1313939.856 1288820.699 0.917605789 0.89881991 0.962121339 0.914780357 0.929013584 0.818613016 0.954606257 1.019490033 1 20.29762014 1.461445165 6.839553411 1.003518918 0.911590569 0.573038217 0.036501931 0.111330283 13.44336 0.021117455 0.009033398 28.93644434 -1.461445165 -0.091928348 AGHSENGVEEDTEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGHSENGVEEDTEGR 15 0 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 0 91.592 0.0055687 525380000 214820 94729 94498 84973 103490 60311 128710 84978 144090 FALSE TRUE 201374.7997 101742.8337 96739.53719 87153.55104 95362.31286 77721.80663 109411.1304 95587.69036 120040.4481 1.67755788 0.847571259 0.80589117 0.726034869 0.794418168 0.647463483 0.911452199 0.796295681 1 16.87316108 4.739834934 4.838810228 0.805031724 1.725745499 0.891210361 0.094642056 0.048377452 3.320042115 0.020315708 0.15029682 54933.2045 -4.739834934 0.920713776 AGHYAASIIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGHYAASIIIR 11 0 P55263-3;P55263-2;P55263;P55263-4;A0A5F9ZHJ1 P55263-3 ADK Adenosine kinase 0 133.23 0.00016607 190070000 91685 131020 85692 94630 122340 70219 89969 114010 103900 FALSE TRUE 85946.59951 140720.8571 87724.65471 97058.36601 112731.9099 90490.08539 76478.98368 128244.3995 86558.41878 0.992931719 1.625732761 1.013473397 1.121304749 1.302379497 1.045422117 0.883553382 1.481593602 1 16.40138652 3.802700428 7.06201737 1.105790048 1.347089714 0.099484132 0.225132036 0.379909683 29.93995827 0.053313814 0.096550992 6348.928377 -3.802700428 0.241299667 AGIIQDTWHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGIIQDTWHK 10 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 160.77 7.28E-06 890290000 1367940 1463190 1272680 1328350 1523810 1045420 1576880 1414170 1483330 FALSE TRUE 1282323.077 1571526.11 1302868.571 1362437.71 1404136.109 1347215.783 1340441.483 1590732.237 1235752.64 1.037685889 1.271715762 1.054311784 1.102516528 1.13625985 1.090198588 1.084716665 1.28725781 1 20.23695856 -2.05492803 2.758776701 0.812655059 1.132164922 0.198791572 0.083947037 4500515.657 8139643.341 5548860.644 0.018054876 0.008811949 2.05492803 0.319509863 AGIPVYAWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGIPVYAWK 9 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 140.53 0.00025332 81221000 225430 336600 213960 215220 366110 153450 227550 299670 333560 FALSE TRUE 211320.7387 361522.2142 219035.2322 220742.9096 337357.1974 197748.5239 193430.99 337084.4592 277886.6811 0.760456521 1.300969923 0.788217814 0.794363043 1.214009956 0.711615696 0.696078665 1.213028483 1 18.08413716 3.833862525 7.505697231 0.887498414 1.064856574 0.025019032 0.226035259 0.53791387 33.66377454 0.054420971 0.098584564 6821.227354 -3.833862525 0.177358161 AGKEPAKPS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AGKEPAKPSPSR 12 2 Q15311 Q15311 RALBP1 RalA-binding protein 1 1 AGKEPAKPS(0.892)PS(0.108)R;AGKEPAKPS(0.629)PS(0.371)R;AGKEPAKPS(0.98)PS(0.02)R;AGKEPAKPS(0.919)PS(0.081)R;AGKEPAKPS(0.617)PS(0.383)R 95.067 0.0032641 2325270000 2400956 1739149 1925770 1954928 2297845 1564777 2822628 1990812 3101900 TRUE FALSE 2250684.45 1867917.402 1971450.174 2005094.762 2117381.523 2016502.718 2399401.135 2239369.261 2584172.851 0.870949654 0.722829899 0.762894082 0.775913562 0.819365284 0.78032811 0.928498701 0.866571003 1 21.30127114 1.436692471 0.742279435 0.99111627 0.766433687 0.65899352 0.048758508 0.309960615 0.371839717 0.041930678 0.017891203 27.33332537 -1.436692471 -0.224682583 AGKEPAKPSPS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGKEPAKPSPSR 12 2 Q15311 Q15311 RALBP1 RalA-binding protein 1 1 AGKEPAKPS(0.395)PS(0.605)R;AGKEPAKPS(0.216)PS(0.784)R 109.83 0.00081187 1050090000 884090 626200 716170 713390 813500 552950 951610 674530 1121050 TRUE FALSE 828756.385 672564.4996 733157.8906 731696.7952 749610.9915 712577.6886 808924.9148 758746.5553 933939.5127 0.887376938 0.720137108 0.78501646 0.783452017 0.802633341 0.762980556 0.866142725 0.812415092 1 19.83296959 0.281975174 0.536884274 1.012324461 0.777792188 0.633169492 0.047360896 1.48676914 0.643629242 0.084008031 0.020220479 1.914146504 -0.281975174 -0.234532273 AGKES(ph)DEKEQEQDKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGKESDEKEQEQDKDR 16 3 F8VU11;Q6NWY9-2;Q6NWY9-3;Q6NWY9 F8VU11 PRPF40B Pre-mRNA-processing factor 40 homolog B 1 AGKES(1)DEKEQEQDKDR 104.18 0.0076326 55773000 178230 34826 70515 74172 75999 43631 99942 50328 73544 TRUE FALSE 167074.9024 37404.55328 72187.6491 76075.37909 70030.34511 56226.56141 84956.62492 56611.56159 61269.03129 2.726906219 0.610496894 1.178207776 1.241661203 1.142997427 0.917699533 1.386616095 0.923983298 1 15.90287042 4.748292655 24.99893254 1.064363293 2.726907111 0.860226604 0.212336134 495.0233788 1271553.296 0.051214953 0.68028228 56013.49291 -4.748292655 1.662543818 AGKFPSLLTHNENMVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGKFPSLLTHNENMVAK 17 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 112.91 0.0005886 266170000 317190 354850 360050 341510 399200 310970 493770 380710 479540 FALSE TRUE 297337.6441 381123.4632 368590.556 350273.7248 367848.4423 400741.9908 419733.7724 428242.4815 399501.6761 0.744271331 0.953997157 0.922625806 0.876776609 0.920768208 1.003104655 1.050643333 1.071941639 1 18.60784203 2.182909843 2.441821267 1.044999974 0.895429039 0.619960577 0.057983788 0.201699755 2.428629913 0.025361691 0.016788839 152.3736402 -2.182909843 -0.149570935 AGKPVICATQMLESMIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGKPVICATQMLESMIK 17 1 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 224.64 2.42E-15 816220000 1426190 1257240 1367760 1343040 1572550 1010650 1717570 1316820 1692300 FALSE TRUE 1336927.314 1350327.358 1400203.913 1377504.68 1449048.266 1302408.248 1460036.324 1481227.876 1409844.197 0.948280183 0.957784811 0.993162163 0.977061638 1.027807377 0.923795871 1.035601187 1.050632317 1 20.42710431 4.515091847 0.308908784 1.019861965 0.900222508 0.301801092 0.033679973 8.119562982 0.704579186 0.035589461 0.364738084 32740.99301 -4.515091847 -0.119639457 AGLESGAEPGDGDS(ph)DTTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AGLESGAEPGDGDSDTTK 18 0 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 AGLESGAEPGDGDS(0.912)DT(0.066)T(0.022)K;AGLESGAEPGDGDS(0.969)DT(0.031)TK;AGLESGAEPGDGDS(0.987)DT(0.013)TK;AGLESGAEPGDGDS(1)DTTK;AGLESGAEPGDGDS(1)DTTK;AGLESGAEPGDGDS(0.985)DT(0.015)TK 429.72 6.35E-169 5192090000 13762500 7832660 9747200 8956930 9248880 7068030 12134900 7861570 10870100 TRUE FALSE 12901129.69 8412598.296 9978408.187 9186779.988 8522510.273 9108455.521 10315384.4 8843104.32 9055810.086 1.424624586 0.928972474 1.101879135 1.014462527 0.941109651 1.005813443 1.139090186 0.97651168 1 23.11041227 4.746932359 24.91950403 1.023503454 1.424624795 0.795656985 0.065305448 478.4634948 1424171.297 0.015606136 0.180912849 55838.32201 -4.746932359 0.401121341 AGLESGAEPGDGDS(ph)DTTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AGLESGAEPGDGDSDTTKK 19 1 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 AGLESGAEPGDGDS(1)DTTKK;AGLESGAEPGDGDS(0.995)DT(0.002)T(0.003)KK;AGLESGAEPGDGDS(0.997)DT(0.002)T(0.002)KK;AGLESGAEPGDGDS(0.865)DT(0.067)T(0.067)KK 186.55 1.24E-14 3910130000 4885300 2185230 3056040 2757630 2919790 2019570 3801020 2267810 3785340 TRUE FALSE 4579537.794 2347026.703 3128530.712 2828395.454 2690481.471 2602587.074 3231092.338 2550951.071 3153542.3 1.452188478 0.744250903 0.992068732 0.896894725 0.853161688 0.825290047 1.024591406 0.808916079 1 21.58854185 4.74829643 24.88133998 0.895579375 1.452188798 0.789602955 0.090682848 544.2594615 1390906.986 0.020156998 0.267645898 56013.97969 -4.74829643 0.556609423 AGLESGAEPGDGDS(ph)DTTKKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGLESGAEPGDGDSDTTKKK 20 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 AGLESGAEPGDGDS(0.996)DT(0.002)T(0.002)KKK 183.25 2.32E-17 499380000 280300 141000 159180 203320 275690 105780 248610 118950 598950 TRUE FALSE 262756.5233 151439.7867 162955.8248 208537.5354 254038.4195 136316.9688 211333.2385 133801.1693 498981.3756 0.526585833 0.303497874 0.326576968 0.417926491 0.509114031 0.273190495 0.423529312 0.268148624 1 18.92862644 -1.718013955 2.66917834 1.110793329 0.373099524 0.820036508 0.091053016 15432836 12816515.12 11430838.65 0.021049916 0.019141944 1.718013955 -0.737693805 AGLGS(ph)PERPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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;AGLGS(1)PERPPK;AGLGS(1)PERPPK 166.71 5.29E-05 6458270000 16670530 13014740 15768080 13621110 14475930 11606360 17945470 12717630 17180580 TRUE FALSE 15627151.29 13978364.89 16142106.3 13970650.74 13339048.85 14956927.72 15254713.37 14305454.1 14313030.21 1.091812919 0.976618137 1.127790976 0.976079177 0.931951422 1.044986806 1.06579202 0.999470685 1 23.7708258 AGLGS(ph)PERPPKT(ph)SPGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGLGSPERPPKTSPGSPR 18 2 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 3 AGLGS(0.999)PERPPKT(0.501)S(0.501)PGS(1)PR;AGLGS(1)PERPPKT(0.514)S(0.514)PGS(0.973)PR 84.942 0.0059627 390300000 1073380 675580 884260 781550 823390 599330 990050 671400 983450 TRUE FALSE 1006199.062 725600.6461 905235.0648 801605.8962 758724.2708 772346.8417 841601.1937 755225.7679 819305.8417 1.228111666 0.885628552 1.10488052 0.978396412 0.926057441 0.942684407 1.02721249 0.921787359 1 19.64404258 3.029112114 24.62828791 0.966986825 1.037861669 0.209194962 0.089992175 357.2539242 302227.2409 0.024208569 0.028934341 1069.330893 -3.029112114 0.070874844 AGLGSGLSLSGLVHPELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGLGSGLSLSGLVHPELSR 19 0 P49748;P49748-3;P49748-2;G3V1M7 P49748 ACADVL "Very long-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 185.33 2.29E-14 335600000 184170 263430 162070 158620 267780 181990 191940 215760 291500 FALSE TRUE 172643.1285 282934.6313 165914.3769 162690.4577 246749.639 234527.5586 163160.3789 242698.1109 242846.7668 0.710913844 1.16507473 0.683206036 0.669930507 1.016071337 0.965742973 0.67186556 0.999387861 1 17.88968675 AGLGSPERPPKTS(ph)PGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGLGSPERPPKTSPGSPR 18 2 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 2 AGLGS(0.07)PERPPKT(0.411)S(0.519)PGS(1)PR 118.36 0.00051666 456160000 247720 158530 193330 175420 197900 147010 262170 174860 283120 TRUE FALSE 232215.6474 170267.7262 197915.8789 179921.5742 182357.7323 189449.4005 222860.0424 196691.6559 235865.443 0.984525942 0.721885004 0.839105027 0.762814476 0.773143068 0.803209653 0.944860932 0.833914682 1 17.84760454 1.199230377 0.864789631 0.986494356 0.802618159 0.298177715 0.079996184 0.579052393 0.959736458 0.068709724 0.025199287 15.82087055 -1.199230377 -0.183876197 AGLLAGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGLLAGDR 8 0 O14745;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 138.9 0.0031158 0 135370 254190 158830 138920 281230 118640 145350 210310 248660 FALSE TRUE 126897.4333 273010.4921 162597.5226 142484.9224 259143.3302 152889.442 123556.1169 236567.6664 207157.0396 0.612566358 1.317891454 0.784899818 0.687811154 1.250951118 0.73803643 0.596436969 1.141972616 1 17.66036532 AGLLALEFYTPEAFNWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGLLALEFYTPEAFNWR 17 0 G3V1D3;G3V180;Q9NY33-4;Q9NY33 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 153.38 2.42E-08 0 38509 46093 54902 57665 63404 53691 55563 43719 47335 FALSE TRUE 36098.79043 49505.77368 56204.30137 59144.78153 58424.5056 69190.7201 47231.84397 49177.41339 39434.4827 0.915411791 1.255393003 1.425257732 1.499823948 1.481558818 1.754574052 1.197729518 1.247066273 1 15.2671701 1.03488492 1.907623021 1.012125666 1.382379848 0.222929379 0.217465208 0.49472259 3.714529633 0.201812318 0.057204395 10.83639731 -1.03488492 0.370254182 AGLLVLAVLSDGAGDHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGLLVLAVLSDGAGDHIR 18 0 Q8TEX9;Q8TEX9-2;H0YN14 Q8TEX9 IPO4 Importin-4 0 137.17 4.73E-06 65322000 108770 126390 140590 140030 131520 122060 155170 129010 106180 FALSE TRUE 101962.2799 135748.0471 143924.8612 143623.4069 121190.9497 157296.7405 131903.699 145117.1825 88457.87205 1.15266485 1.534606745 1.627044127 1.623636241 1.370041432 1.778210767 1.491147096 1.6405231 1 16.43270292 -1.024764889 5.152763655 0.999995934 1.542428813 0.482251465 0.171040727 8.98E-06 1.70E-06 0.147816375 0.034840325 0.094457209 1.024764889 0.542432878 AGLNEMVEYITHSR ddPTM_SK-BR-3_Pertuzumab_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 0 147.1 8.13E-06 59374000 133940 239850 193800 193320 241030 192180 207940 207200 224910 FALSE TRUE 125556.9345 257608.7436 198397.0275 198280.9185 222100.4761 247659.2462 176761.3274 233069.3761 187371.068 0.670097768 1.374858703 1.058845582 1.058225907 1.185350964 1.321758203 0.94337578 1.243892019 1 17.51553868 -1.145966601 4.113215899 0.999966056 1.123749479 0.021198906 0.202026585 1.316052882 48951201.78 3657.300948 0.041798985 0.071455128 1.145966601 0.123783423 AGLQFPVGR ddPTM_SK-BR-3_Pertuzumab_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 ;;;; 186.11 9.79E-05 8912680000 5515520 11468210 5068040 4904720 10741770 3411480 5768770 8627700 9345570 FALSE TRUE 5170313.449 12317328.2 5188256.302 5030583.419 9898154.714 4396318.895 4903796.493 9704887.337 7785733.992 0.664075276 1.58203815 0.666379857 0.646128345 1.271319406 0.564663383 0.629843827 1.246496136 1 22.89240162 3.833566778 6.671332641 0.824298095 1.177043686 0.08394286 0.33308232 0.362498706 19.84644465 0.07868471 0.142993605 6816.583799 -3.833566778 0.35274559 AGLQS(ph)LEASGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGLQSLEASGR 11 0 O60784;O60784-4;O60784-2;O60784-3 O60784 TOM1 Target of Myb protein 1 1 AGLQS(1)LEASGR 102.9 0.0021889 0 134720 168220 169640 158690 169890 137300 211210 183170 172670 TRUE FALSE 126288.1157 180675.1838 173663.9409 162762.2541 156547.5247 176936.2811 179541.0213 206039.1777 143850.2615 0.877913702 1.255994824 1.207254954 1.131469991 1.088267224 1.230003194 1.248110496 1.432317019 1 17.13420832 2.093261717 6.644805187 1.25062071 1.145859239 0.106115381 0.144176819 0.4793172 28.71803784 0.050576142 0.037183524 123.9543343 -2.093261717 -0.104761471 AGLS(ph)PANCQSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGLSPANCQSDR 12 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 1 AGLS(1)PANCQSDR;AGLS(1)PANCQSDR 164.66 7.50E-05 408730000 308019 297487 315249 289361 332180 272011 334708 296396 288022 TRUE FALSE 288740.6406 319513.247 322726.8552 296786.4931 306091.9227 350536.16 284521.6427 333401.693 239949.2675 1.203340371 1.331586674 1.344979539 1.236871845 1.275652666 1.460876141 1.185757496 1.389467434 1 17.87236988 -1.311483705 4.833083007 0.999856523 1.305097989 0.562114078 0.084192784 0.000115421 1.64E-05 0.072287141 0.017030278 0.048810841 1.311483705 0.305241466 AGLTMNDIDAFEFHEAFSGQILANFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGLTMNDIDAFEFHEAFSGQILANFK 26 0 P55084-2;P55084;B5MD38;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 102.07 0.0038866 16276000 16818 15717 11662 14338 21297 14237 15428 16746 24930 FALSE TRUE 15765.3914 16880.70303 11938.62815 14705.93735 19624.41953 18346.99078 13114.71463 18836.77496 20769.02195 0.759082033 0.812782763 0.574828616 0.70807077 0.944888959 0.883382512 0.631455572 0.906964951 1 14.34214566 2.829642993 13.54419331 0.833536222 0.706993128 0.287662261 0.115564067 2.099414908 308.4226545 0.035913752 0.038095031 675.5274372 -2.829642993 -0.126543094 AGLVGPEFHEK ddPTM_SK-BR-3_Pertuzumab_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 ;;; 183.33 5.39E-06 1880550000 2951300 2990120 2985870 3125220 3223380 2415280 3839610 2820260 3290240 FALSE TRUE 2766583.401 3211511.596 3056696.246 3205418.436 2970228.737 3112532.127 3263896.126 3172375.669 2741077.688 1.009304995 1.171623705 1.115143967 1.169400798 1.083598889 1.135514014 1.19073463 1.157346135 1 21.38631179 4.748106192 24.34145945 1.137996265 1.009304894 0.296072909 0.055581009 939.0942266 2394642.777 0.011671677 0.144678251 55989.44876 -4.748106192 -0.12869137 AGLYGLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGLYGLPR 8 0 P49327;A0A0U1RQF0;A0A0U1RRG3 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 153.67 0.0010173 887330000 1135320 2276000 1219840 1073680 2404100 738730 1370560 2133000 2260100 FALSE TRUE 1064262.348 2444517.408 1248775.181 1101232.447 2215291.684 951989.3587 1165057.252 2399309.745 1882874.709 0.565232696 1.298290001 0.663227975 0.584867618 1.176547581 0.505604199 0.61876515 1.274280085 1 20.84450557 5.012844598 18.78554593 0.857813231 0.055403546 0.098442582 0.294925793 94169189.55 2425918261 0.067892269 2040310510 103001.7487 -5.012844598 -0.802409685 AGMSSNQS(ph)IS(ph)SPVLDAVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMSSNQS(0.949)IS(0.548)S(0.503)PVLDAVPR;AGMSS(0.001)NQS(0.974)IS(0.7)S(0.325)PVLDAVPR 132.08 3.20E-05 274670000 436390 402800 426780 421770 376410 384700 521680 370350 333790 TRUE FALSE 409077.1289 432623.7311 436903.4231 432593.3323 346848.277 495756.6449 443458.927 416589.0127 278078.2926 1.471086164 1.555762325 1.571152566 1.555653007 1.247304396 1.782795199 1.594726877 1.498099721 1 18.0851316 0.867140896 7.427627407 1.000000192 1.549418983 0.622635617 0.131012907 4.13937215 231.5593445 0.117644577 0.029482906 7.364459802 -0.867140896 0.549418791 AGMSSNQS(ph)ISS(ph)PVLDAVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMSSNQS(0.999)IS(0.002)S(0.998)PVLDAVPR;AGMSS(0.001)NQS(0.987)IS(0.274)S(0.738)PVLDAVPR;AGMSS(0.001)NQS(0.921)IS(0.106)S(0.972)PVLDAVPR 222.24 3.62E-19 775110000 847470 767040 791940 785070 747670 774060 1002720 713870 655950 TRUE FALSE 794428.3655 823832.4397 810725.1908 805216.2253 688951.0142 997518.5562 852371.4448 802998.2409 546467.7074 1.453751713 1.507559236 1.483573832 1.473492787 1.26073509 1.825393418 1.559783741 1.469434022 1 19.05977672 0.908011888 11.0162647 1.000000002 1.514932799 0.572638992 0.137239473 16.85328829 2019.011208 0.126435678 0.031618681 8.091180471 -0.908011888 0.514932798 AGMSSNQSIS(ph)SPVLDAVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AGMSSNQS(0.005)IS(0.497)S(0.497)PVLDAVPR;AGMSSNQS(0.007)IS(0.497)S(0.497)PVLDAVPR;AGMSSNQS(0.019)IS(0.756)S(0.226)PVLDAVPR;AGMSSNQS(0.002)IS(0.499)S(0.499)PVLDAVPR;AGMSSNQSIS(0.998)S(0.002)PVLDAVPR 459.15 1.69E-214 10290050000 1675590 1725390 1740990 1735340 1561520 1703260 2006310 1429760 1298250 TRUE FALSE 1570717.813 1853139.671 1782287.105 1779871.762 1438884.518 2194963.512 1705482.441 1608268.683 1081563.688 1.452265669 1.713389319 1.64787994 1.645646745 1.330374285 2.029435285 1.576867327 1.486984725 1 20.04468719 0.823022118 2.39902295 1.000869992 1.645120549 0.543137115 0.18021086 0.475460265 4.827028323 0.154582154 0.041654529 6.653070386 -0.823022118 0.644250557 AGMSSNQSISS(ph)PVLDAVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 15 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AGMSSNQS(0.004)IS(0.265)S(0.731)PVLDAVPR;AGMSSNQS(0.035)IS(0.135)S(0.83)PVLDAVPR;AGMSSNQS(0.001)IS(0.025)S(0.974)PVLDAVPR;AGMSSNQS(0.001)IS(0.031)S(0.969)PVLDAVPR;AGMSSNQSIS(0.007)S(0.993)PVLDAVPR;AGMS(0.003)S(0.003)NQS(0.146)IS(0.275)S(0.573)PVLDAVPR;AGMSSNQS(0.003)IS(0.024)S(0.973)PVLDAVPR;AGMSSNQSIS(0.022)S(0.977)PVLDAVPR;AGMSSNQSIS(0.016)S(0.984)PVLDAVPR;AGMSSNQS(0.003)IS(0.247)S(0.75)PVLDAVPR;AGMSSNQSIS(0.015)S(0.984)PVLDAVPR;AGMSSNQSIS(0.016)S(0.984)PVLDAVPR;AGMSSNQSIS(0.031)S(0.969)PVLDAVPR;AGMSSNQSIS(0.026)S(0.974)PVLDAVPR;AGMSSNQS(0.022)IS(0.135)S(0.843)PVLDAVPR 380.17 1.16E-108 9023814000 4651244 4558999 4901588 4643537 4426540 4754136 5468298 4207407 3685794 TRUE FALSE 4360130.941 4896552.03 5017855.982 4762698.021 4078897.404 6126577.886 4648377.48 4732711.026 3070611.17 1.419955409 1.594650628 1.634155451 1.551058651 1.328366627 1.995230769 1.513828102 1.541292845 1 21.55009441 0.596955349 2.309990597 1.000090071 1.590561034 0.518424586 0.173395459 2.543393852 13.67091673 0.150267379 0.040523535 3.953259731 -0.596955349 0.590470963 AGMSSNQSISS(ph)PVLDAVPRT(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 AGMSSNQSISSPVLDAVPRTPSR 23 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMSSNQS(0.001)IS(0.227)S(0.771)PVLDAVPRT(0.819)PS(0.181)R;AGMSSNQS(0.001)IS(0.375)S(0.623)PVLDAVPRT(0.825)PS(0.175)R;AGMSSNQSIS(0.013)S(0.987)PVLDAVPRT(0.884)PS(0.116)R;AGMSSNQS(0.002)IS(0.044)S(0.954)PVLDAVPRT(0.907)PS(0.093)R;AGMSSNQSIS(0.005)S(0.995)PVLDAVPRT(0.869)PS(0.131)R;AGMSSNQS(0.001)IS(0.023)S(0.977)PVLDAVPRT(0.908)PS(0.092)R;AGMSSNQSIS(0.011)S(0.988)PVLDAVPRT(0.973)PS(0.027)R 196.72 7.09E-24 4692160000 1260373 2046777 1633291 1895863 2235706 1282049 1784295 1605317 2329745 TRUE FALSE 1181488.504 2198322.499 1672033.434 1944514.054 2060122.669 1652155.734 1516756.529 1805744.361 1940895.509 0.6087337 1.132633101 0.861475245 1.001864369 1.061428943 0.851233735 0.781472533 0.930366603 1 20.88829102 AGMSSNQSISS(ph)PVLDAVPRTPS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGMSSNQSISSPVLDAVPRTPSR 23 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMS(0.001)S(0.001)NQS(0.001)IS(0.117)S(0.88)PVLDAVPRT(0.264)PS(0.736)R;AGMSS(0.001)NQS(0.015)IS(0.072)S(0.912)PVLDAVPRT(0.355)PS(0.645)R 91.151 0.0034721 397170000 187063 291880 237060 264410 335640 172058 254660 232130 379550 TRUE FALSE 175355.0607 313491.0989 242683.1751 271195.2082 309280.1883 221728.3515 216476.0971 261111.9415 316200.653 0.554568939 0.991430903 0.767497388 0.857668084 0.978113693 0.701226735 0.684616224 0.825779261 1 18.27048082 2.191377393 24.99999798 0.764073015 0.844650949 0 0.148832029 348.4099682 184602.5644 0.050728095 0.037465285 155.373659 -2.191377393 0.080577935 AGMSSNQSISSPVLDAVPRT(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGMSSNQSISSPVLDAVPRTPSR 23 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AGMSSNQSISSPVLDAVPRT(0.997)PS(0.003)R;AGMSSNQSISSPVLDAVPRT(1)PSR 268.77 2.52E-44 788460000 273050 393500 340620 397620 439920 223796 349260 313480 442860 TRUE FALSE 255960.2879 422635.1494 348699.6673 407823.6024 405370.4578 288402.2722 296891.7054 352618.6681 368943.805 0.69376497 1.145527161 0.945129482 1.105381353 1.098732252 0.781697018 0.804707116 0.955751698 1 18.49304157 2.237311382 24.99998583 0.859220272 1.015588951 0.116721193 0.140836184 47.73151948 955180.7022 0.046912953 0.036574313 172.7075734 -2.237311382 0.156368679 AGMSYYNS(ph)PGLHVQHMGTSHGITRPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AGMSYYNSPGLHVQHMGTSHGITRPSPR 28 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 AGMSYYNS(1)PGLHVQHMGT(0.09)S(0.077)HGIT(0.024)RPS(0.809)PR;AGMSYYNS(1)PGLHVQHMGT(0.193)S(0.173)HGIT(0.113)RPS(0.521)PR;AGMSYYNS(0.999)PGLHVQHMGT(0.051)S(0.045)HGIT(0.319)RPS(0.585)PR;AGMSYYNS(1)PGLHVQHMGT(0.003)S(0.002)HGIT(0.04)RPS(0.955)PR 159.41 1.38E-11 860306000 183719 265640 280355 299732 295814 288786 317819 242680 349189 TRUE FALSE 172220.3557 285308.262 287005.153 307423.6306 272581.9617 372153.8302 270164.9914 272979.1322 290907.1001 0.592011524 0.980753862 0.986586965 1.056775962 0.937006906 1.279287546 0.928698514 0.938372189 1 18.15019898 4.755307541 3.414362925 1.017349251 0.529118955 0.633037472 0.101173417 0.209708753 4.028216935 0.022730312 0.272241303 56925.59003 -4.755307541 -0.488230297 AGMSYYNSPGLHVQHMGT(ph)SHGITRPSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGMSYYNSPGLHVQHMGTSHGITRPSPR 28 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 AGMSYYNS(0.001)PGLHVQHMGT(0.302)S(0.302)HGIT(0.181)RPS(0.214)PR 94.73 0.0012818 73757000 23284 46880 37177 29661 48132 34402 36708 36376 43585 TRUE FALSE 21826.696 50351.04398 38058.856 30422.15148 44351.90688 44333.29893 31203.97618 40917.62367 36310.38193 0.60111447 1.386684505 1.048153558 0.837836174 1.221466273 1.220953804 0.859367887 1.126884971 1 15.14809448 1.736747088 25 0.985828938 1.088941956 0 0.226672536 0.882695352 11830.56018 0.098258107 0.054489275 54.54401311 -1.736747088 0.103113018 AGMTHIVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 AGMTHIVR 8 0 P39023;H7C422;H7C3M2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ;;;;;;;;;;;; 167.24 0.00031378 4722430000 4537016 6289929 4681370 4627925 6718825 3748282 5155526 5674634 6246940 FALSE TRUE 4253052.267 6755641.888 4792414.307 4746685.391 6191155.587 4830350.165 4382502.738 6383124.546 5204285.357 0.817221189 1.298092134 0.920859249 0.912072468 1.189626464 0.928148599 0.842095012 1.226513173 1 22.31126864 3.74618376 24.20853057 0.9868117 1.097245957 0 0.16727807 765.1918641 971750.7647 0.039699934 0.071406807 5574.215563 -3.74618376 0.110434256 AGNALT(ph)PELAPVQIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGNALTPELAPVQIK 15 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 AGNALT(1)PELAPVQIK;AGNALT(1)PELAPVQIK 161.48 1.84E-05 146285000 495150 397670 464080 388270 448100 345820 579350 440770 647150 TRUE FALSE 464159.4454 427113.9006 475088.1968 398233.6655 412908.0335 445652.6201 492481.8459 495801.1048 539136.4843 0.860931246 0.792218507 0.88120209 0.73865093 0.765869211 0.826604456 0.913464142 0.919620763 1 19.04029102 1.481681484 1.585240178 0.977384137 0.811201567 0.684325677 0.044148149 0.218430118 1.047788694 0.039060671 0.01281167 30.31666911 -1.481681484 -0.166182569 AGNEKEEGETADTVGCCSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGNEKEEGETADTVGCCSLR 20 1 P11387 P11387 TOP1 DNA topoisomerase 1 0 ; 264.66 1.28E-36 385190000 526150 345980 398740 324020 428380 257630 491160 330580 564340 FALSE TRUE 493219.2107 371596.7192 408198.3011 332334.9018 394736.7628 332003.5987 417515.1177 371853.6407 470148.0082 1.049072211 0.790382417 0.868233607 0.706872934 0.839601053 0.706168255 0.888050381 0.790928887 1 18.84275548 -0.627184539 5.845296453 1.000000002 0.825545268 0.22778324 0.098126764 1.87E-09 5.32E-10 0.083496908 0.01968041 0.235947544 0.627184539 -0.174454734 AGNLGGGVVTIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGNLGGGVVTIER 13 0 P35268;K7ERI7;K7EMH1;K7EP65;K7EKS7;K7ELC4;K7EJT5 P35268 RPL22 60S ribosomal protein L22 0 ; 149.23 0.00010155 509730000 295650 279090 308770 276920 307890 266030 323290 243610 314030 FALSE TRUE 277145.7943 299754.114 316094.1702 284026.236 283709.5614 342828.5424 274815.6658 274025.2448 261616.3643 1.059359551 1.145777386 1.208235467 1.085659289 1.084448835 1.310424687 1.050452889 1.047431591 1 17.99709326 1.567169737 10.49510338 1.033331053 1.152564197 0.366138308 0.072421544 0.119085792 22.44360518 0.036460562 0.017021509 36.91218355 -1.567169737 0.119233144 AGNS(ph)DS(ph)EEDDANGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 251.56 1.22E-19 103960000 359490 278730 309560 283880 256620 270950 358850 232430 248290 TRUE FALSE 336990.1626 299367.4592 316902.9094 291164.8414 236466.1004 349168.8665 305043.7739 261449.3971 206848.795 1.629161836 1.447276786 1.53205103 1.407621647 1.143183359 1.688039162 1.474718641 1.26396384 1 17.65821703 0.9833935 3.081417166 1.001879661 1.47454773 0.535339941 0.144643669 0.181478482 4.247547619 0.130098053 0.034152289 9.624839579 -0.9833935 0.472668068 AGPDLPSLPSHALEDEGWAAAAPS(ph)PGS(ph)AR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGPDLPSLPSHALEDEGWAAAAPSPGSAR 29 0 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 2 AGPDLPSLPSHALEDEGWAAAAPS(1)PGS(1)AR 103.94 0.00029149 58996000 38115 46312 45323 46513 51545 38056 60236 44042 47288 TRUE FALSE 35729.45019 49740.98867 46398.08296 47706.60233 47496.86362 49042.14941 51204.171 49540.74065 39395.32731 0.906946398 1.262611382 1.177755996 1.210971087 1.205647138 1.244872242 1.299752395 1.257528342 1 15.2657369 4.743059473 24.58857905 1.222623946 0.906946237 0.561308069 0.082502296 239.7557691 1310329.537 0.01741832 0.138745436 55342.58914 -4.743059473 -0.315677709 AGPDLPSLPSHALEDEGWAAAAPS(ph)PGSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 AGPDLPSLPSHALEDEGWAAAAPSPGSAR 29 0 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 AGPDLPSLPSHALEDEGWAAAAPS(0.993)PGS(0.007)AR;AGPDLPSLPSHALEDEGWAAAAPS(0.979)PGS(0.021)AR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(0.994)PGS(0.006)AR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(0.994)PGS(0.006)AR 340.73 7.76E-106 6790826000 1983976 2351953 2343707 2333559 2791401 2132900 2699352 2393575 3129546 TRUE FALSE 1859802.484 2526094.047 2399300.837 2393442.075 2572175.625 2748633.605 2294609.227 2692418.108 2607204.555 0.713332017 0.968889857 0.920257995 0.918010852 0.986564564 1.054245475 0.88010326 1.032683877 1 21.31407235 4.739702893 24.88380618 0.960794801 0.713331932 0.688891304 0.053905834 51.79520817 1128181.467 0.011909294 0.07350618 54916.50532 -4.739702893 -0.247462869 AGPGSS(ph)PLFSLLPGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AGPGSSPLFSLLPGYR 16 0 Q9H0W8-2;Q9H0W8 Q9H0W8-2 SMG9 Protein SMG9 1 AGPGS(0.015)S(0.985)PLFSLLPGYR;AGPGS(0.003)S(0.997)PLFSLLPGYR;AGPGS(0.289)S(0.709)PLFS(0.002)LLPGYR 307.07 6.61E-47 385502000 485086 571280 519509 527736 539155 435027 598905 468081 568933 TRUE FALSE 454725.3332 613578.1656 531831.9988 541278.5992 496811.9411 560612.2328 509104.7552 526521.9432 473974.4069 0.959387947 1.294538601 1.122069021 1.141999634 1.048183054 1.182790093 1.074118661 1.110865767 1 18.85444963 0.550126839 0.363873298 0.98338183 1.158863704 0.112830497 0.088840081 3.882755287 1.074305511 0.212629325 0.074676553 3.549170299 -0.550126839 0.175481874 AGPIWDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 AGPIWDLR 8 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5;O43390;O43390-3;B4DT28;O43390-2;O43390-4 O60506-2;O43390;O43390-2 SYNCRIP;HNRNPR Heterogeneous nuclear ribonucleoprotein Q;Heterogeneous nuclear ribonucleoprotein R 0 ;;;;;; 129.4 0.0025415 2207719000 4011372 6296320 3918307 4027885 6400320 3044865 4678310 5357580 6884350 FALSE TRUE 3760307.387 6762506.084 4011251.092 4131247.348 5897664.685 3923868.096 3976840.847 6026485.656 5735307.51 0.655641808 1.179100872 0.699395993 0.720318368 1.028308364 0.684160019 0.693396272 1.050769404 1 22.45143941 5.024882727 16.75872812 0.860162578 0.121413469 0.125758535 0.179527252 44297827.37 765914510.5 0.04192162 889763981.9 105896.7733 -5.024882727 -0.738749109 AGPLT(ph)PPKPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGPLTPPKPPR 11 1 Q8TDM6-4;Q8TDM6;Q8TDM6-3;A0A0J9YYG8 Q8TDM6-4 DLG5 Disks large homolog 5 1 AGPLT(1)PPKPPR;AGPLT(1)PPKPPR 116.24 0.0016422 1423170000 1604600 1300760 1577850 1471650 1620270 1138880 1852620 1345820 1762080 TRUE FALSE 1504170.95 1397069.624 1615277.347 1509415.03 1493020.53 1467656.168 1574836.83 1513848.59 1467977.465 1.024655342 0.951696915 1.10034206 1.028227658 1.017059571 0.99978113 1.072793601 1.03124784 1 20.48539839 3.996041976 23.85312111 1.039344999 0.988346605 0.23167954 0.035433981 308.3523424 388730.8838 0.008208201 0.017673259 9909.27717 -3.996041976 -0.050998394 AGPPPEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 107.01 0.0065514 105410000 109020 92656 101880 93477 103050 112250 103390 87596 122000 FALSE TRUE 102196.6328 99516.34665 104296.6417 95875.77808 94956.86868 144654.7528 87887.62933 98532.55342 101637.4118 1.005502117 0.979131059 1.026163888 0.94331188 0.934270826 1.423243175 0.86471731 0.969451619 1 16.63307202 AGPTLTDENGDDLGLPPS(ph)PGDTSYYQDQVDDFHEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AGPTLTDENGDDLGLPPSPGDTSYYQDQVDDFHEAR 36 0 Q9NQZ2 Q9NQZ2 UTP3 Something about silencing protein 10 1 AGPTLTDENGDDLGLPPS(0.902)PGDT(0.063)S(0.017)Y(0.015)Y(0.003)QDQVDDFHEAR;AGPTLTDENGDDLGLPPS(0.883)PGDT(0.082)S(0.026)Y(0.007)Y(0.002)QDQVDDFHEAR;AGPTLTDENGDDLGLPPS(0.516)PGDT(0.121)S(0.121)Y(0.111)Y(0.131)QDQVDDFHEAR;AGPTLTDENGDDLGLPPS(0.696)PGDT(0.191)S(0.053)Y(0.047)Y(0.013)QDQVDDFHEAR 109.56 3.09E-05 187809000 89663 91135 93231 87019 97629 79847 111335 74763 99608 TRUE FALSE 84051.15288 97882.73023 95442.48335 89252.05486 89961.61216 102897.5327 94641.35033 84097.32512 82982.78131 1.012874618 1.179554706 1.150148041 1.075549089 1.084099746 1.23998655 1.140493833 1.013431025 1 16.34052439 1.228943952 8.616903597 1.005914442 1.136535573 0.382372423 0.061999696 0.138902757 76.5571299 0.049345998 0.014264458 16.9411915 -1.228943952 0.130621131 AGQDMGLEHGFEKPLDSAMS(ph)AEEDTDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGQDMGLEHGFEKPLDSAMSAEEDTDVR 28 1 Q99549-2;Q99549;A0A0A0MT47 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 AGQDMGLEHGFEKPLDS(0.012)AMS(0.988)AEEDTDVR 219.07 1.73E-34 95103000 142200 123840 113370 112660 124400 90096 138450 94775 148850 TRUE FALSE 133299.9558 133009.2425 116059.1899 115551.0463 114630.1258 116105.2526 117690.7078 106607.8674 124005.9734 1.074947861 1.072603511 0.935916124 0.931818389 0.924391968 0.936287579 0.949072892 0.859699452 1 16.92005009 3.981320495 2.136915925 0.931570657 1.077806941 0.746039037 0.03386999 0.139139352 1.240689792 0.00821415 0.021629055 9579.007099 -3.981320495 0.146236284 AGQEHLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGQEHLLR 8 0 Q3KQV9;A0A087X226;Q16222;Q16222-3;Q16222-2 Q3KQV9;Q16222 UAP1L1;UAP1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1;UDP-N-acetylhexosamine pyrophosphorylase;UDP-N-acetylgalactosamine pyrophosphorylase;UDP-N-acetylglucosamine pyrophosphorylase 0 105.1 0.0044526 675480000 848370 846280 796250 833870 768270 699000 1080700 679940 793920 FALSE TRUE 795272.0361 908939.4518 815137.426 855268.5159 707933.1733 900789.9527 918659.0677 764832.0057 661409.6231 1.202389576 1.374245883 1.232424503 1.293099595 1.070339996 1.361924474 1.388941188 1.156366613 1 19.33518451 0.987175057 6.923839702 1.000040179 1.283407834 0.472239947 0.09441815 0.109118552 33.48054438 0.088512475 0.022202313 9.709012417 -0.987175057 0.283367654 AGQHS(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGQHSPLR 8 0 A0A087X0R7;Q9H4L4 A0A087X0R7 SENP3-EIF4A1;SENP3 Sentrin-specific protease 3 1 AGQHS(1)PLR 66.663 0.064091 44121000 87783 102630 95288 84968 95397 73204 114750 100730 87900 TRUE FALSE 82288.81873 110228.832 97548.27636 87148.42273 87904.90443 94336.80643 97544.30279 113306.3622 73228.92214 1.123720196 1.505263614 1.332100398 1.190082008 1.200412376 1.288245186 1.332046136 1.547289772 1 16.16012594 3.469006733 24.61922415 1.277471006 1.366586969 0.000997391 0.164882855 455.6029597 1382283.231 0.042329596 0.057656599 2944.46728 -3.469006733 0.089115963 AGQTQPNPGILPIQPALT(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AGQTQPNPGILPIQPALTPR 20 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 AGQTQPNPGILPIQPALT(1)PR;AGQTQPNPGILPIQPALT(1)PR;AGQTQPNPGILPIQPALT(1)PR 217.17 1.20E-23 227328000 258221 293475 282864 280906 322322 249283 309682 254457 499760 TRUE FALSE 242059.4085 315204.1944 289573.6677 288114.5235 297008.1303 321246.9553 263248.059 286226.5166 416346.8274 0.581388863 0.757071205 0.695510686 0.69200605 0.713367103 0.771584972 0.632280689 0.687471353 1 18.66742631 -1.414814396 3.215283936 1.003978861 0.697034466 0.756910485 0.054888736 13844229.6 16930870.48 498347.0375 0.012019352 0.038475618 1.414814396 -0.306944396 AGRPQYDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AGRPQYDTK 9 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;; 147.4 8.43E-05 1014460000 621070 766460 528340 548310 876090 360746 725470 762310 887340 FALSE TRUE 582198.3373 823209.4959 540872.4743 562380.5629 807285.4254 464887.514 616692.5084 857486.0816 739237.2216 0.787566319 1.113593136 0.731662934 0.760757909 1.092051918 0.628874603 0.834228162 1.159960641 1 19.49567787 1.24766321 24.98315564 1.079980331 0.85716989 0.274997159 0.155010099 225.2855614 618334.9468 0.102106769 0.036107128 17.68736794 -1.24766321 -0.222810441 AGS(ph)EECVFYTDETASPLAPDLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGSEECVFYTDETASPLAPDLAK 23 0 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 AGS(0.997)EECVFY(0.003)TDETASPLAPDLAK;AGS(0.981)EECVFY(0.019)TDETASPLAPDLAK 208.89 6.03E-25 101243000 593680 306850 372370 342460 434580 306560 594690 355710 567560 TRUE FALSE 556522.6285 329569.4933 381202.7922 351248.1034 400449.8398 395058.8954 505521.7553 400121.1765 472830.5694 1.177002217 0.69701393 0.806214354 0.74286251 0.846920368 0.835518938 1.069139324 0.846225271 1 18.85096379 1.847395518 8.378907374 0.975826281 0.82305717 0.123589507 0.139276762 0.451273647 31.36182401 0.054612575 0.03416842 70.37129086 -1.847395518 -0.152769112 AGS(ph)ISTLDSLDFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AGSISTLDSLDFAR 14 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 AGS(0.998)IS(0.002)TLDSLDFAR;AGS(1)ISTLDSLDFAR;AGS(0.868)IS(0.123)T(0.009)LDSLDFAR;AGS(0.985)IS(0.007)T(0.007)LDSLDFAR 248.67 5.87E-18 156899000 363798 295693 336468 332296 270833 269389 355027 253527 271291 TRUE FALSE 341028.5326 317586.4174 344449.1799 340823.2779 249562.8687 347157.2311 301793.9973 285180.404 226010.7795 1.508903838 1.405182612 1.524038723 1.507995675 1.104207814 1.53602068 1.335307979 1.261800011 1 17.78603206 -1.341432102 0.20571105 0.615740605 1.524318316 0.566247515 0.122020809 16.09287025 0.640840483 3.536956858 0.307639509 0.045558341 1.341432102 0.908577711 AGS(ph)PDVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGSPDVLR 8 0 Q8NDX6 Q8NDX6 ZNF740 Zinc finger protein 740 1 AGS(1)PDVLR;AGS(1)PDVLR 98.044 0.0081838 1057090000 2446200 1962110 1942150 1811400 2161740 1511630 2544700 1654910 2543300 TRUE FALSE 2293096.709 2107386.666 1988218.715 1857883.591 1991965.66 1948013.042 2163145.859 1861529.156 2118806.8 1.082258519 0.994610111 0.938367158 0.876853704 0.94013558 0.919391538 1.020926429 0.878574279 1 21.01482061 4.723421197 1.481771552 0.942120119 1.134497897 0.505990901 0.045368296 0.955310535 1.97526278 0.011824432 0.268701811 52895.80092 -4.723421197 0.192377778 VLGEKPELPDGGDDDDIIADISNRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VLGEKPELPDGGDDDDIIADISNRK 25 2 Q9Y6U3;Q9Y6U3-2;E5RHN8;E5RHX6 Q9Y6U3 SCIN Adseverin 0 ;;; 210.22 1.08E-25 774716000 1123582 681910 876018 767885 1117250 651405 1129674 975922 2620940 FALSE TRUE 1053259.008 732399.3259 896797.5606 787590.2291 1029505.692 839455.0488 960289.8711 1097768.01 2183488.182 0.482374495 0.335426283 0.410717845 0.360702767 0.471495885 0.384455962 0.43979623 0.502758851 1 21.05820329 0.183296814 0.837976803 1.009010653 0.395459524 0.942879518 0.045148003 0.6859409 0.549611525 0.053899894 0.013196506 1.525094706 -0.183296814 -0.613551129 AGS(ph)PFSPPPSSSSLTGEAAISR ddPTM_SK-BR-3_Pertuzumab_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(0.999)PFS(0.001)PPPSSSSLTGEAAISR;AGS(1)PFSPPPSSSSLTGEAAISR;AGS(0.999)PFS(0.001)PPPSSSSLTGEAAISR;AGS(1)PFSPPPSSSSLTGEAAISR;AGS(0.966)PFS(0.034)PPPSSSSLTGEAAISR;AGS(0.996)PFS(0.004)PPPSSSSLTGEAAISR 234.51 2.02E-30 4563620000 1731300 1418120 1454150 1370590 1488610 1116260 1915110 1453540 1318290 TRUE FALSE 1622941.023 1523119.08 1488643.125 1405761.66 1371700.575 1438506.141 1627957.035 1635017.669 1098258.883 1.477739948 1.386848861 1.355457396 1.279991159 1.248977447 1.309806061 1.482307187 1.488736121 1 20.06678674 4.849005368 1.172766691 1.335689297 1.568024456 0.117699248 0.137222226 4.864391934 4.772222938 0.037044234 1.467572974 70632.62849 -4.849005368 0.232335159 AGS(ph)PLCNSNLQDSEEDIEPSYSLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AGSPLCNSNLQDSEEDIEPSYSLFR 25 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 AGS(1)PLCNSNLQDSEEDIEPSYSLFR;AGS(1)PLCNSNLQDSEEDIEPSYSLFR;AGS(1)PLCNSNLQDSEEDIEPSYSLFR;AGS(0.999)PLCNS(0.001)NLQDSEEDIEPSYSLFR 239.34 1.01E-38 470520000 361397 321158 317734 322824 363345 270625 420891 319669 450275 TRUE FALSE 338777.8069 344936.8725 325270.8005 331108.2104 334809.3494 348750.0443 357782.3019 359580.3783 375121.1936 0.903115613 0.919534482 0.867108567 0.882669964 0.892536479 0.929699655 0.953777894 0.958571215 1 18.51699725 1.63729087 1.096185831 0.990007662 0.891801948 0.844006288 0.015728189 0.184958853 0.421497101 0.01460927 0.00551608 43.38013205 -1.63729087 -0.098205714 AGS(ph)PRGS(ph)PLAEGPQAFFPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGSPRGSPLAEGPQAFFPER 20 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 2 AGS(1)PRGS(1)PLAEGPQAFFPER 147.25 7.06E-08 43185000 29941 60035 51581 67173 74518 56166 47098 50054 58962 TRUE FALSE 28067.04626 64480.05387 52804.52568 68896.7729 68665.65687 72380.21242 40036.09214 56303.35208 49120.86129 0.571387503 1.312681663 1.074991853 1.402597004 1.397891956 1.473512689 0.815052731 1.146220783 1 15.58404824 1.725057877 24.99999667 0.98426367 1.217797022 0.129641372 0.265482275 1.701338468 3136.698593 0.115530504 0.064067453 53.0955198 -1.725057877 0.233533352 AGS(ph)SPAQGAQNEPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGSSPAQGAQNEPPR 15 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 AGS(0.6)S(0.4)PAQGAQNEPPR 144.15 4.50E-06 160230000 142370 172540 159590 157780 163100 145290 181830 135820 151210 TRUE FALSE 133459.3158 185315.0411 163375.5502 161828.9019 150290.7839 187232.8644 154566.2795 152777.426 125972.0741 1.059435726 1.471080336 1.296918791 1.284641084 1.193048419 1.48630453 1.226988446 1.212788049 1 16.94274442 0.891504218 1.669343172 1.001990411 1.313319404 0.34015581 0.124686538 0.492187695 2.722991829 0.106958035 0.030718538 7.789403795 -0.891504218 0.311328993 AGS(ph)STPGDAPPAVAEVQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGSSTPGDAPPAVAEVQGR 19 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 AGS(0.979)S(0.02)TPGDAPPAVAEVQGR 258.9 5.03E-31 145140000 194220 154950 165490 164200 172910 126480 210900 148000 208980 TRUE FALSE 182064.1169 166422.6592 169415.501 168413.65 159330.3461 162992.7228 179277.5029 166478.1258 174099.8879 1.04574517 0.95590331 0.973093682 0.967339221 0.915166276 0.936202342 1.029739335 0.956221901 1 17.40955575 1.744252391 25 0.99705955 0.963455434 0.119645297 0.037646777 2.125090667 9368.070126 0.016466729 0.009131736 55.49481288 -1.744252391 -0.033604115 AGSATVLSGS(ph)IAGLEGGSQLALR ddPTM_SK-BR-3_Pertuzumab_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;AGSATVLSGS(1)IAGLEGGSQLALR;AGSATVLSGS(1)IAGLEGGSQLALR 343.82 1.53E-87 442132000 330633 418585 405084 334137 457849 262382 449687 411734 469820 TRUE FALSE 309939.2707 449577.4689 414692.7838 342711.5211 421891.3864 338127.424 382260.609 463139.8962 391404.0068 0.79186535 1.148627661 1.059500609 0.875595331 1.077892354 0.863883399 0.976639488 1.183278373 1 18.578299 1.273780122 24.99612755 1.091639597 0.991270884 0.138370837 0.117047135 340.9391484 241972.6868 0.075498037 0.027566652 18.78365582 -1.273780122 -0.100368714 AGSIS(ph)TLDSLDFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGSISTLDSLDFAR 14 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 AGS(0.012)IS(0.98)T(0.008)LDSLDFAR;AGS(0.136)IS(0.864)TLDSLDFAR 340.39 7.09E-69 231750000 491780 372670 457030 404310 352040 371940 484420 351670 362700 TRUE FALSE 461000.3677 400262.8746 467870.9674 414685.2791 324392.1985 479313.0401 411785.7181 395576.7736 302163.0269 1.525667691 1.324658674 1.548405747 1.372389215 1.073566815 1.586272963 1.362793199 1.309150156 1 18.20496762 -3.470126827 0.247504306 1.57E-09 1.438655357 0.437043363 0.143169395 72.565951 1.429396546 37.15975506 0.204722267 0.000338745 3.470126827 1.438655355 AGSMKDPLLDDHGDFIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 199.76 7.81E-12 223610000 590510 592630 604140 582860 677190 471860 706060 574550 819580 FALSE TRUE 553551.0332 636508.9418 618470.4861 597817.1744 624006.2291 608078.322 600192.8577 646283.8322 682786.8033 0.810723099 0.932222091 0.905803222 0.87555467 0.913910793 0.890583003 0.879034063 0.946538259 1 19.38107565 1.006709957 3.787454182 0.999681812 0.893374813 0.571927902 0.032494058 0.137071353 5.077874336 0.02874799 0.007396111 10.15570219 -1.006709957 -0.106306999 AGSNEDPILAPSGT(ph)PPPTIPPDETFGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AGSNEDPILAPSGTPPPTIPPDETFGGR 28 0 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 AGSNEDPILAPS(0.345)GT(0.654)PPPTIPPDETFGGR;AGSNEDPILAPS(0.014)GT(0.986)PPPTIPPDETFGGR;AGSNEDPILAPS(0.034)GT(0.965)PPPTIPPDETFGGR;AGSNEDPILAPS(0.03)GT(0.97)PPPTIPPDETFGGR 110.89 0.0022944 629020000 721190 792830 773090 763200 827650 710560 915010 773750 936970 TRUE FALSE 676052.0053 851531.9581 791428.0599 782785.0041 762649.7076 915687.137 777812.745 870354.3907 780583.6539 0.866085271 1.090891353 1.013892689 1.002820134 0.977024953 1.173080082 0.996450209 1.115004633 1 19.57419373 AGSPFS(ph)PPPSSSSLTGEAAISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGSPFSPPPSSSSLTGEAAISR 22 0 Q96JY6;Q96JY6-5;Q96JY6-3;Q96JY6-4;C9JS55;C9JSR2;C9K0F0;C9J0X3;Q96JY6-2;C9J760;A0A087WXJ0 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 AGS(0.001)PFS(0.998)PPPS(0.001)S(0.001)SSLTGEAAISR;AGSPFS(1)PPPSSSSLTGEAAISR 209.73 5.60E-23 328170000 178849 187894 181331 269260 256420 122799 154775 116221 115357 TRUE FALSE 167655.1603 201805.8673 185632.257 276169.6675 236281.8075 158249.0778 131567.9256 130731.4477 96103.17147 1.744533066 2.099887696 1.931593454 2.873679019 2.458626536 1.646658226 1.369027927 1.360323969 1 16.55229642 2.001051153 3.253051748 1.301129879 2.193058904 0.658406101 0.32192423 0.172295975 3.63769301 0.157258513 0.094414098 100.24233 -2.001051153 0.891929024 AGSRLS(ph)AEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGSRLSAEER 10 1 Q86Y82;B1AJQ6 Q86Y82 STX12 Syntaxin-12 1 AGS(0.011)RLS(0.989)AEER 55.291 0.079673 189970000 191640 186710 167750 223360 214210 157870 215860 189170 204600 TRUE FALSE 179645.5945 200534.2027 171729.1092 229091.7957 197386.8107 203444.5062 183493.7969 212788.2909 170450.9382 1.053943125 1.17649222 1.007498762 1.344033645 1.158027129 1.193566362 1.076519724 1.248384392 1 17.37899702 4.751600745 22.64810512 1.146257559 1.053942898 0.076530239 0.104533193 1635.797277 2840856.273 0.022866886 0.384805097 56441.78563 -4.751600745 -0.092314661 AGSS(ph)PAQGAQNEPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGSSPAQGAQNEPPR 15 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 AGS(0.008)S(0.992)PAQGAQNEPPR 187.35 3.61E-07 128560000 128340 190050 190980 151080 152660 133720 155410 126770 137850 TRUE FALSE 120307.4285 204121.4997 195510.1358 154956.9686 140670.6994 172322.7932 132107.7133 142597.5136 114841.9445 1.047591358 1.777412432 1.702427948 1.349306382 1.22490698 1.500521382 1.150343752 1.241684946 1 16.80929014 1.883596499 0.612434991 1.036485717 1.575007461 0.263557915 0.223056253 0.78090706 0.59952826 0.204984362 0.121854608 76.48856251 -1.883596499 0.538521745 AGSSLSFSLSGS(ph)PGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGSSLSFSLSGSPGSR 16 0 A0A1B0GV45 A0A1B0GV45 1 AGSSLSFSLS(0.051)GS(0.919)PGS(0.029)R 89.911 0.0059053 50160000 66334 69708 64537 67668 77263 66205 82448 58201 73574 TRUE FALSE 62182.27335 74869.25285 66067.84812 69404.47544 71195.07564 85317.30875 70085.68781 65467.52297 61294.02409 1.014491613 1.221477199 1.077884004 1.132320425 1.161533717 1.391935185 1.143434272 1.068089817 1 15.9034588 1.110385165 3.337219781 1.005199856 1.169722618 0.245102131 0.098111605 0.303760917 6.225492875 0.089491189 0.023617815 12.89392574 -1.110385165 0.164522762 AGSSPCLGSSSAASS(ph)PPPPASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGSSPCLGSSSAASSPPPPASR 22 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 AGSSPCLGSSSAAS(0.051)S(0.949)PPPPASR;AGSSPCLGSSSAASS(1)PPPPASR 269.39 2.88E-38 206554000 327934 351276 350636 362992 419430 344520 415340 352087 426110 TRUE FALSE 307409.1963 377284.8405 358953.2515 372306.9893 386489.6597 443977.3312 353063.6228 396045.837 354989.4882 0.86596704 1.062805669 1.011165861 1.048783138 1.088735505 1.250677403 0.994574866 1.115655111 1 18.43741678 5.571695486 1.118604838 1.076994758 7.11E-30 0.412095654 0.075464571 9.166021056 2.387264652 0.020482025 18.17945325 372988.5381 -5.571695486 -1.076994758 AGSST(ph)PGDAPPAVAEVQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGSSTPGDAPPAVAEVQGR 19 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 AGS(0.003)S(0.024)T(0.973)PGDAPPAVAEVQGR;AGS(0.006)S(0.049)T(0.945)PGDAPPAVAEVQGR 187.78 1.97E-13 454790000 400290 474880 413610 441720 480920 333660 477090 384620 505140 TRUE FALSE 375236.5634 510040.6093 423421.0245 453055.283 443150.4831 429982.2255 405554.7836 432640.6537 420828.8707 0.891660695 1.211990538 1.006159639 1.076578426 1.053042018 1.021750777 0.963704755 1.028067901 1 18.68287416 2.163538131 2.875949406 0.993134896 1.066911823 0.049357615 0.080178784 0.492514573 8.222831703 0.032315079 0.022041134 145.7263645 -2.163538131 0.073776927 AGTEKLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGTEKLR 7 1 A0A0G2JR78;Q9NY99-2;Q9NY99 A0A0G2JR78 SNTG2 Gamma-2-syntrophin 0 ; 105.39 0.0072389 1169850000 1613220 1440630 1507990 1462090 1564270 1248290 1880040 1460140 2123110 FALSE TRUE 1512251.44 1547295.744 1543760.235 1499609.705 1441418.544 1608651.059 1598145.455 1642441.693 1768749.225 0.854983521 0.874796564 0.872797688 0.847836247 0.814936636 0.909485096 0.90354553 0.92858935 1 20.75429809 1.133388543 0.940805576 0.997502204 0.860089102 0.81113358 0.022120268 0.229804444 0.443870863 0.020973423 0.007295905 13.5952921 -1.133388543 -0.137413103 AGTFIAPPVYSNITPY(ph)QSHLRSPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGTFIAPPVYSNITPYQSHLRSPVR 25 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 AGTFIAPPVYSNIT(0.02)PY(0.528)QS(0.422)HLRS(0.03)PVR 155.76 6.07E-08 1017200000 310870 446360 329120 358760 532750 324760 415560 325560 565180 TRUE FALSE 291413.2016 479408.9588 336926.8818 367966.389 490909.964 418512.94 353250.6359 366206.8826 470847.8068 0.618911668 1.018182419 0.71557492 0.781497511 1.042608582 0.888849717 0.750243775 0.777760621 1 18.84490128 4.769039351 23.44459998 0.857065649 0.618910748 0.30557809 0.117971574 7143.274011 5494470.877 0.027300639 3.032150261 58754.25868 -4.769039351 -0.238154901 KIS(ph)ASEFDRPLRPIVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KISASEFDRPLRPIVVK 17 3 O76074-2;G5E9C5;O76074;C9JGT3 O76074-2 PDE5A "cGMP-specific 3,5-cyclic phosphodiesterase" 1 KIS(0.816)AS(0.184)EFDRPLRPIVVK 99.407 0.0087791 127190000 192930 155730 160250 166240 198760 144090 225190 196960 451060 TRUE FALSE 180854.8557 167260.4112 164051.2057 170505.9998 183150.1914 185686.4439 191424.8501 221550.8896 375775.172 0.481284739 0.44510767 0.436567442 0.453744719 0.487393008 0.494142396 0.509413246 0.589583629 1 18.51951022 0.184662365 0.637886374 1.02231902 0.449853767 0.992012158 0.014904744 0.243478324 0.128828775 0.027345683 0.00587273 1.529897607 -0.184662365 -0.572465253 AGTFQAFEQFGQQLLAHGHYAS(ph)PEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGTFQAFEQFGQQLLAHGHYASPEIK 26 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 AGTFQAFEQFGQQLLAHGHY(0.004)AS(0.996)PEIK;AGTFQAFEQFGQQLLAHGHYAS(1)PEIK 159.62 3.20E-11 81617000 156177 128379 129818 134426 172470 119279 148196 123684 181855 TRUE FALSE 146402.1604 137884.3147 132897.3443 137875.5987 158924.9019 153712.911 125975.3856 139126.2197 151502.2257 0.966336697 0.91011412 0.877197306 0.910056589 1.048993843 1.014591768 0.831508481 0.918311391 1 17.20897946 6.990742545 12.34613395 0.930341425 0.968125758 0 0.067397726 0 0 0.015115692 0 9789095.039 -6.990742545 0.037784333 AGTGYAS(ph)PDRTHVLAAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AGTGYASPDRTHVLAAGK 18 1 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 AGT(0.335)GYAS(0.665)PDRTHVLAAGK;AGTGYAS(0.808)PDRT(0.192)HVLAAGK;AGT(0.031)GYAS(0.969)PDRTHVLAAGK 220.86 3.97E-19 2575220000 3079140 2832050 2844140 2721190 3351140 2214750 3276450 2765790 4200990 TRUE FALSE 2886422.124 3041737.929 2911604.344 2791020.342 3087954.982 2854112.372 2785176.74 3111104.97 3499817.63 0.824735009 0.869113266 0.831930304 0.797475937 0.882318826 0.81550317 0.795806249 0.888933453 1 21.73884832 0.945527364 5.420305746 0.99997011 0.833112294 0.794194742 0.027441217 0.140035115 12.17172895 0.026477566 0.006676253 8.821193801 -0.945527364 -0.166857816 AGTLSITEFADMLSGNAGGFRS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGTLSITEFADMLSGNAGGFRSR 23 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 AGTLSITEFADMLS(0.016)GNAGGFRS(0.984)R 66.633 0.016864 59180000 77011 125890 98135 110720 139660 98530 111770 91311 181420 TRUE FALSE 72191.01898 135211.0266 100462.8085 113561.2626 128691.667 126974.0115 95011.12612 102711.3794 151139.83 0.477643908 0.894608831 0.664701082 0.751365558 0.851474208 0.84010953 0.628630627 0.679578503 1 17.20552438 -2.000866513 2.739036138 1.26596885 0.735467975 0.329405346 0.122929475 20891955.69 10546070.53 35040712.13 0.027220864 0.009980068 2.000866513 -0.530500875 AGTQIENIDEDFRDGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AGTQIENIDEDFRDGLK 17 1 O43707;F5GXS2;O43707-3;K7EP19 O43707 ACTN4 Alpha-actinin-4 0 ;;; 284.38 3.16E-36 1916760000 1582070 1303180 1249870 1263790 1606780 959260 1428590 1296840 1277510 FALSE TRUE 1483051.063 1399668.803 1279517.507 1296220.991 1480589.98 1236182.79 1214386.192 1458753.329 1064285.328 1.393471303 1.315125527 1.202231651 1.217926205 1.391158876 1.161514452 1.14103442 1.370641209 1 20.02145355 -5 0.11774269 0.191296333 1.38857998 0.464726423 0.092691463 143.939704 1.106030385 28.09507073 0.904284236 1.00E-05 5 1.197283646 AGTQIENIEEDFRDGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AGTQIENIEEDFRDGLK 17 1 P12814-3;P12814;P12814-2;P12814-4;G3V2N5;G3V5M4;G3V380 P12814-3 ACTN1 Alpha-actinin-1 0 ;; 258.38 3.34E-27 628120000 413680 347017 377527 315627 419580 280073 380680 332308 517670 FALSE TRUE 387788.5072 372710.4998 386482.1187 323726.5232 386627.8793 360925.5285 323600.5681 373797.3853 431267.5327 0.89918317 0.864221096 0.896153987 0.750639681 0.896491968 0.836894737 0.750347623 0.866741308 1 18.71822358 AGVHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGVHIK 6 0 P12532;P12532-2;P12277;H0YJG0;H0YJK0 P12532;P12277 CKMT1A;CKB "Creatine kinase U-type, mitochondrial;Creatine kinase B-type" 0 ; 87.758 0.052076 2310500000 9797100 9401200 8791200 9037500 11268500 7646900 11099600 9345100 10476900 FALSE TRUE 9183916.999 10097274.63 8999731.416 9269417.55 10383517.46 9854435.893 9435318.024 10511856.31 8728237.707 1.05220748 1.156851471 1.031105215 1.062003335 1.189646503 1.129029275 1.081010662 1.204350369 1 23.05725896 AGVLAGHDNR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 150.08 2.22E-05 7432130000 4669680 8475320 4202350 3608990 11222700 3232660 4170710 8133050 10123100 FALSE TRUE 4377413.064 9102841.511 4302031.726 3701602.793 10341314.41 4165876.464 3545350.754 9148479.196 8433489.212 0.519051244 1.079368371 0.51011291 0.43891712 1.226220151 0.493968316 0.420389552 1.084779854 1 23.00769821 1.213658972 24.98505312 1.04239054 0.683412498 0.240824975 0.274248616 396.1224217 397438.6712 0.254712931 0.063787702 16.35531722 -1.213658972 -0.358978042 AGVLAHLEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AGVLAHLEEER 11 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ;;;;; 185.08 4.62E-06 9261840000 5960450 7910000 6187770 6354970 7640210 4273090 6193090 6384800 6356500 FALSE TRUE 5587396.074 8495664.63 6334546.826 6518049.289 7040178.726 5506661.715 5264493.648 7181956.335 5295559.085 1.05510976 1.604299847 1.19619982 1.230851962 1.329449566 1.039864087 0.994133681 1.356222491 1 22.33635158 2.70363181 1.00168863 1.085998518 1.352095631 0.14491297 0.178298368 0.701465411 1.475648583 0.094785195 0.085011983 505.3960117 -2.70363181 0.266097113 AGVNFSEFTGVWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGVNFSEFTGVWK 13 0 O75340-2;O75340;A0A024QZ42 O75340-2 PDCD6 Programmed cell death protein 6 0 132.59 0.0002724 25747000 104140 122370 120740 136600 129780 91553 150740 115580 153180 FALSE TRUE 97622.0633 131430.4021 123604.0098 140105.3873 119587.6023 117982.8649 128137.9364 130010.4174 127613.2684 0.764983646 1.029911731 0.968582745 1.097890439 0.93710947 0.924534465 1.004111391 1.018784481 1 16.96141881 4.743827696 24.96605296 0.995306647 0.764983547 0.691106661 0.048855216 319.7626665 1515633.15 0.01107385 0.095384402 55440.57117 -4.743827696 -0.230323099 AGVVGPELHEQLLSAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AGVVGPELHEQLLSAEK 17 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 274.17 1.11E-35 528710000 1424470 1378710 1435500 1462550 1609120 1119630 1832740 1419550 1582290 FALSE TRUE 1335314.965 1480791.123 1469550.738 1500081.509 1482746.206 1442849.005 1557937.651 1596783.942 1318195.577 1.012986987 1.123347058 1.114819958 1.137980991 1.124830209 1.094563683 1.181871399 1.211340692 1 20.330133 4.745743093 4.096436787 1.130505178 1.002212511 0.274628267 0.055613285 0.286698772 10.38940065 0.012071539 0.109658004 55685.62434 -4.745743093 -0.128292667 AGWGS(ph)PCHLSGESVILLGPTVGTESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGWGSPCHLSGESVILLGPTVGTESK 26 0 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4;A8MXE8;Q7Z5J4-4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 AGWGS(0.341)PCHLS(0.329)GES(0.329)VILLGPTVGTESK 125.74 7.03E-05 89524000 55937 85672 95463 96124 89609 71180 123770 76552 101580 TRUE FALSE 52436.00302 92015.24402 97727.42744 98590.70458 82571.47061 91728.51049 105211.8375 86109.68571 84625.64177 0.619623106 1.087321078 1.154820518 1.165021647 0.975726374 1.08393282 1.243261916 1.017536575 1 16.36880725 4.738763362 5.059423624 1.110178769 0.596226892 0.758195447 0.083133216 0.074824245 6.164842246 0.019028232 0.134673623 54797.83013 -4.738763362 -0.513951877 AGWGSPCHLS(ph)GESVILLGPTVGTESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGWGSPCHLSGESVILLGPTVGTESK 26 0 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4;A8MXE8;Q7Z5J4-4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 AGWGS(0.368)PCHLS(0.627)GES(0.005)VILLGPTVGTESK 191.44 3.71E-18 81623000 101180 181160 171160 175450 179420 141740 227090 156100 204230 TRUE FALSE 94847.32441 194573.2749 175219.996 179952.344 165329.0769 182658.037 193039.9627 175589.4286 170142.6936 0.557457522 1.143588777 1.029841437 1.057655431 0.971708355 1.073557925 1.134576858 1.032012747 1 17.37638567 4.744052034 24.99824353 1.064166746 0.557457308 0.893204836 0.054030941 178.1849974 811116.4487 0.012748764 0.111163829 55469.21687 -4.744052034 -0.506709438 AGYTDKVVIGMDVAASEFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 AGYTDKVVIGMDVAASEFFR 20 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;;;;;;;; 196.55 1.59E-21 4528419000 7128846 8923878 8000669 8479883 11496640 7039029 10058625 7936512 13595409 FALSE TRUE 6682664.254 9584611.212 8190448.647 8697491.154 10593740.27 9071082.403 8550427.561 8927402.994 11326247.41 0.590015741 0.846230077 0.723138772 0.767905807 0.935326582 0.800890363 0.754921489 0.788204837 1 23.43316661 -5 0.157917713 1.773591107 0.721021328 0.446706899 0.083586968 134.7936002 1.232526031 32.9807318 0.350800446 1.00E-05 5 -1.052569779 AHALSDETWGLVECHPHLALER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AHALSDETWGLVECHPHLALER 22 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ;;; 231.06 5.19E-27 1365960000 345382 471156 396020 396637 442494 377727 472864 391969 370687 FALSE TRUE 323765.1571 506040.8805 405413.7814 406815.3769 407742.3062 486770.653 401962.4331 440907.1925 308816.945 1.048404767 1.638643503 1.312796425 1.317335022 1.320336571 1.576243341 1.301620392 1.427729921 1 18.23639239 -1.298097353 3.634656908 0.998913638 1.387214922 0.330543861 0.162481558 8300537.606 5929519.73 65176.57064 0.03391822 0.050338775 1.298097353 0.388301284 AHAS(ph)PFSGALTPSAPPGPEMNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AHASPFSGALTPSAPPGPEMNR 22 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 AHAS(0.992)PFS(0.008)GALTPSAPPGPEMNR;AHAS(0.984)PFS(0.016)GALTPSAPPGPEMNR;AHAS(0.95)PFS(0.05)GALTPSAPPGPEMNR;AHAS(0.998)PFS(0.002)GALTPSAPPGPEMNR 205.57 6.65E-23 1219390000 543966 653812 599782 555388 537163 567483 736441 537504 425975 TRUE FALSE 509920.1391 702220.9208 614009.1123 569640.1963 494976.3848 731306.1298 626018.5088 604612.5576 354877.0206 1.436892527 1.978772589 1.730202511 1.605176338 1.394782857 2.060731147 1.764043521 1.703724171 1 18.43695963 0.762384015 5.280987669 1.000000579 1.742615157 0.529423448 0.208414646 7.116615345 157.9073697 0.189758901 0.04787527 5.786074422 -0.762384015 0.742614579 AHATGAGPAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AHATGAGPAGR 11 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;; 175.43 9.83E-06 179032000 72708 109849 97465 93970 105723 88054 117738 92488 140244 FALSE TRUE 68157.33607 117982.3343 99776.91583 96381.42929 97419.94205 113473.7604 100084.2799 104035.3304 116836.3704 0.583357184 1.00980828 0.853988493 0.824926596 0.833815204 0.971219493 0.856619215 0.890436172 1 16.83412992 7.999914752 0.02650761 1.510060766 9.95E-07 0.234251676 0.106395387 3414.608619 6.952830099 133.0486173 291.5365443 99980372.91 -7.999914752 -1.510059771 AHCAICTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AHCAICTDR 9 0 P41743 P41743 PRKCI Protein kinase C iota type 0 ; 90.629 0.011301 135626000 95702 193924 130308 130709 175708 99767 129114 160230 154174 FALSE TRUE 89712.18265 208282.3347 133398.9673 134063.2142 161908.6025 128568.1133 109754.5543 180235.0682 128441.3634 0.698468003 1.621614169 1.038598188 1.043769785 1.26056434 1.000986831 0.854510972 1.403247859 1 16.97075036 3.718735154 24.59217696 1.067197132 1.257217925 0 0.268909005 607.7921176 1782350.775 0.065522852 0.103381116 5232.81226 -3.718735154 0.190020793 AHCGDPVSLAAAGDGS(ph)PDIGPTGELSGSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AHCGDPVSLAAAGDGSPDIGPTGELSGSLK 30 0 Q5JSP0-2;Q5JSP0-3;Q5JSP0 Q5JSP0-2 FGD3 "FYVE, RhoGEF and PH domain-containing protein 3" 1 AHCGDPVSLAAAGDGS(1)PDIGPTGELSGSLK 144.51 2.73E-08 170420000 94984 104250 94553 89700 101170 84510 92500 87640 117920 TRUE FALSE 89039.12099 111968.7785 96795.84181 92001.85386 93224.5163 108906.6651 78630.48373 98582.04692 98238.39021 0.906357696 1.139766014 0.985315838 0.936516301 0.948962174 1.108595783 0.800404847 1.003498192 1 16.5839993 3.561715947 4.266658672 0.955115684 1.045825712 0.036313858 0.094592615 0.394507179 13.06081564 0.024106402 0.037901978 3645.154557 -3.561715947 0.090710027 AHEEQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AHEEQLK 7 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 158.36 0.0014236 954890000 1835980 1755700 1593600 1734080 1986190 1298770 2097040 1622050 1836680 FALSE TRUE 1721069.289 1885693.855 1631400.945 1778579.429 1830202.649 1673703.815 1782608.32 1824566.513 1530126.243 1.12478908 1.232377958 1.066187154 1.162374306 1.196112189 1.093833808 1.165007351 1.192428744 1 20.54521926 -1.166147564 4.733190854 0.999982709 1.152966186 0.492167003 0.049193259 8.35E-06 1.47E-06 0.044300039 0.01044044 0.068210689 1.166147564 0.152983476 AHEILPNLVCCSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AHEILPNLVCCSAK 14 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 120.54 0.00012331 491980000 508210 505940 480000 425460 554680 394480 600650 513540 492370 FALSE TRUE 476402.0433 543400.324 491385.8267 436378.0239 511117.6703 508359.9722 510588.1087 577656.5994 410190.2662 1.161417231 1.324751875 1.197946093 1.063842953 1.246050217 1.239327244 1.244759203 1.40826501 1 18.64593373 AHFLDADPGFVHSDGTISHHDMYDYLHLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AHFLDADPGFVHSDGTISHHDMYDYLHLSR 30 0 M0R1K3;Q15102 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ;; 196.3 8.90E-26 592922200 174422 454201 356496 370187 506205 391996 369605 450395 422987 FALSE TRUE 163505.2384 487830.5146 364952.2535 379686.6251 466449.7012 505158.8817 314186.1615 506627.8072 352387.7371 0.463992418 1.384357239 1.035655373 1.077468326 1.323683126 1.433531387 0.891592211 1.43769988 1 18.42680419 4.74823107 24.90392372 1.188472713 0.463992007 0.585761952 0.193837187 882.3100031 2272127.907 0.042609255 0.558846511 56005.5504 -4.74823107 -0.724480706 AHFNAMFQPSS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 AHFNAMFQPSSPTR 14 0 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 AHFNAMFQPS(0.016)S(0.937)PT(0.047)R;AHFNAMFQPS(0.099)S(0.801)PT(0.099)R;AHFNAMFQPS(0.053)S(0.786)PT(0.161)R;AHFNAMFQPS(0.024)S(0.951)PT(0.024)R;AHFNAMFQPS(0.105)S(0.79)PT(0.105)R;AHFNAMFQPS(0.015)S(0.939)PT(0.046)R;AHFNAMFQPS(0.11)S(0.889)PT(0.001)R;AHFNAMFQPS(0.07)S(0.928)PT(0.001)R 159.54 3.59E-06 4211850000 1617410 1998730 1633810 1684730 1920950 1293085 1707280 1670130 1622870 TRUE FALSE 1516179.195 2146718.049 1672564.745 1727963.024 1770086.336 1666377.648 1451289.214 1878649.407 1352002.513 1.121432232 1.587806257 1.237101802 1.278076784 1.309233022 1.232525555 1.073436772 1.389531002 1 20.3666664 1.116294614 0.225323902 0.932002146 1.4355874 0.237866982 0.14506511 3.20906622 0.654589622 0.630958751 0.44110862 13.07057262 -1.116294614 0.503585254 AHFNLDESGVLSLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AHFNLDESGVLSLDR 15 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;;; 215.48 2.34E-12 669395000 462149 567003 532814 544150 520719 445788 585368 462078 432177 FALSE TRUE 433223.919 608984.4921 545452.5997 558113.8102 479823.8302 574479.7588 497597.5027 519769.4555 360043.8667 1.203253156 1.691417486 1.514961509 1.550127253 1.332681583 1.595582683 1.38204688 1.443628134 1 18.45781317 -0.378953947 0.465988441 0.909510832 1.518519907 0.51280537 0.140171682 5.261945683 1.108333426 0.91225061 0.068304338 0.417874676 0.378953947 0.609009076 AHGCFQDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AHGCFQDGR 9 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 0 ;; 138.26 0.00014162 163755000 149127 192779 165622 139425 209071 135401 152651 179113 225104 FALSE TRUE 139793.4073 207052.5577 169550.6321 143002.8815 192651.407 174489.0706 129762.3997 201475.6523 187532.6882 0.745434882 1.104087825 0.904112417 0.762549094 1.027295075 0.930446166 0.6919455 1.074349514 1 17.51678256 3.577263144 6.957251522 0.886877907 0.965674368 0 0.14556238 0.732166877 43.97056807 0.036466035 0.056685971 3778.010355 -3.577263144 0.078796461 AHGGYSVFAGVGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AHGGYSVFAGVGER 14 0 P06576;H0YH81;F8W079;F8W0P7;H0YI37 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ;;; 157.86 5.18E-06 1176570000 752560 898950 777310 707730 1170840 826410 780380 895250 1249320 FALSE TRUE 705458.613 965509.1934 795748.1603 725891.55 1078886.949 1064981.151 663369.2637 1007023.933 1040800.421 0.677803927 0.927660264 0.764554034 0.697435873 1.036593498 1.023232821 0.637364523 0.967547584 1 19.98926202 2.755064332 24.85006799 0.895693117 0.793278078 0.243394468 0.133458115 1717.627713 2586273 0.041615206 0.044024205 568.9372007 -2.755064332 -0.102415039 AHGLLAEENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AHGLLAEENR 10 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 97.456 0.0060461 223880000 55615 169130 62717 82980 167030 60876 82302 148380 150830 FALSE TRUE 52134.15643 181652.5612 64204.67686 85109.40728 153912.1376 78449.91296 69961.57915 166905.5696 125655.4986 0.414897533 1.445639572 0.510957957 0.677323382 1.224873876 0.624325349 0.556772922 1.328279076 1 16.93911428 1.229677888 24.99969217 1.164139517 0.809625274 0.184252993 0.331933027 388.0072177 1091973.057 0.288544946 0.076435802 16.96984548 -1.229677888 -0.354514243 AHGS(ph)FSHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AHGSFSHVR 9 0 Q8N3D4 Q8N3D4 EHBP1L1 EH domain-binding protein 1-like protein 1 1 AHGS(0.982)FS(0.018)HVR;AHGS(0.984)FS(0.016)HVR;AHGS(0.999)FS(0.001)HVR 138.76 8.21E-05 307550000 122571 147473 169056 140474 128396 128699 167062 111054 174981 TRUE FALSE 114899.4999 158392.0544 173066.0882 144078.8007 118312.2961 165852.312 142012.604 124919.3364 145775.5407 0.788194641 1.086547535 1.187209372 0.988360599 0.811605949 1.137723868 0.974186776 0.85692933 1 17.15338915 3.01940559 24.97715651 0.964167829 1.062217889 0.014774846 0.132323169 543.2468827 699214.3535 0.03736717 0.044657203 1045.696345 -3.01940559 0.09805006 AHGVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 AHGVDK 6 0 P30043;M0R192;A0A2R8Y7Y9;M0QZL1 P30043 BLVRB Flavin reductase (NADPH) 0 ;;;;;; 121.68 0.019546 3874076000 11874810 8492070 10965660 10014580 9229250 7415750 11554520 9527080 9872880 FALSE TRUE 11131586.84 9120831.699 11225770.63 10271571.08 8504421.934 9556556.64 9822026.993 10716556.91 8225032.547 1.353379063 1.10891132 1.364829935 1.24881829 1.03396818 1.161886787 1.19416269 1.302919697 1 22.97158996 2.961675912 24.72249404 1.154491749 1.259462728 0.257402949 0.107827645 791.913612 510855.703 0.031168524 0.033066476 915.5370242 -2.961675912 0.104970979 AHLDHIPDYTPPLLTTIS(ph)PEQESDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AHLDHIPDYTPPLLTTISPEQESDER 26 0 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;K7EM61 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 AHLDHIPDYTPPLLTT(0.001)IS(0.999)PEQESDER;AHLDHIPDYTPPLLTTIS(1)PEQESDER;AHLDHIPDYTPPLLTTIS(1)PEQESDER;AHLDHIPDYTPPLLTT(0.004)IS(0.996)PEQESDER 238.36 8.86E-45 730932000 297927 343047 328663 326876 369477 292760 357255 316793 357400 TRUE FALSE 279280.2809 368446.5568 336459.0416 335264.1916 340459.7668 377275.0594 303687.9293 356345.3034 297747.6311 0.9379765 1.237445804 1.130014168 1.126001205 1.143450799 1.267096763 1.019950783 1.196803152 1 18.1837305 -2.29833298 0.619499888 0.786558116 1.139518134 0.150477173 0.096916008 427.1062293 32.01829913 125.4184103 0.033708432 0.005031147 2.29833298 0.352960019 AHLLAEVIENLECDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AHLLAEVIENLECDPR 16 0 Q96C86;A0A3B3ITF0 Q96C86 DCPS m7GpppX diphosphatase 0 ;;;;; 225.67 6.66E-15 280622600 297974.5 345208 338433.5 326306 374874.7 340415 431306 312637.8 363238 FALSE TRUE 279324.8079 370767.5595 346461.3024 334679.5644 345433.5532 438687.2843 366635.6693 351671.3175 302611.2312 0.923048384 1.225227359 1.14490563 1.105972052 1.141509361 1.449672845 1.211573238 1.16212249 1 18.20710601 4.742417594 24.33579712 1.195854247 0.923048231 0.323586375 0.114822765 294.7130203 1859394.932 0.026126734 0.194552188 55260.85419 -4.742417594 -0.272806016 AHLMEIQVNGGTVAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AHLMEIQVNGGTVAEK 16 0 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ;; 174.52 3.84E-09 1102020000 580030 449980 519320 512060 554850 426580 625510 477820 570060 FALSE TRUE 543726.9577 483296.9874 531638.5156 525200.3265 511274.3192 549726.7211 531720.5825 537476.8788 474913.3033 1.144897298 1.017653083 1.1194433 1.105886744 1.076563481 1.157530685 1.119616104 1.131736835 1 18.85730464 3.733942352 24.33917189 1.109619922 1.071094872 0 0.052075839 441.4715079 1575251.609 0.011902944 0.020857634 5419.289502 -3.733942352 -0.038525049 AHLMEIQVNGGTVAEKLDWAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AHLMEIQVNGGTVAEKLDWAR 21 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 169.98 5.29E-12 193280000 155200 204950 177670 178730 243070 122780 221980 150200 450690 FALSE TRUE 145486.309 220124.7113 181884.4163 183316.5144 223980.2627 158224.5928 188696.1598 168952.8006 375466.9274 0.387481023 0.586269243 0.484421937 0.488236116 0.596537927 0.421407536 0.502563997 0.449980513 1 18.51832631 -1.497730862 3.091994694 1.014025199 0.498223993 0.85801589 0.065165511 20118999.96 24344513.8 2406695.262 0.014062038 0.031788434 1.497730862 -0.515801207 AHLS(ph)ENELEALEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AHLSENELEALEK 13 0 P98175-5;P98175-2;P98175;P98175-4;P98175-3 P98175-5 RBM10 RNA-binding protein 10 1 AHLS(1)ENELEALEK;AHLS(1)ENELEALEK 165.9 2.23E-05 96847000 313750 214475 252140 245010 223486 205903 287970 208890 183606 TRUE FALSE 294112.9476 230354.9522 258120.8799 251297.3714 205934.3111 265343.8535 244791.5719 234970.3763 152960.9725 1.922797318 1.505972069 1.687495024 1.64288555 1.346319311 1.734716047 1.600353135 1.536145937 1 17.22280407 -2.606077604 0.313920746 3.51E-15 1.655711246 0.656026448 0.144879761 33.17757628 1.161103159 22.69774055 0.125458085 0.002476979 2.606077604 1.655711246 AHPPELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AHPPELK 7 0 P62308;A8MWD9;C9JVQ0 P62308 SNRPG;SNRPGP15 Small nuclear ribonucleoprotein G;Putative small nuclear ribonucleoprotein G-like protein 15 0 ;; 78.616 0.034854 667838000 897390 1099140 795340 830800 1220290 648980 1002960 1047310 1226640 FALSE TRUE 841223.9618 1180521.469 814205.8404 852119.7345 1124453.346 836329.9907 852575.459 1178068.959 1021905.86 0.82319125 1.155215481 0.796752296 0.833853458 1.10034925 0.818402187 0.834299413 1.152815543 1 19.96283087 1.237107698 24.99952609 1.07640777 0.917354639 0.224822094 0.128588505 61.69435786 1061353.86 0.100125918 0.030202574 17.26265926 -1.237107698 -0.159053131 AHQLEEDIVSVTHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AHQLEEDIVSVTHK 14 0 B8ZZD4;Q86VP1-2;Q86VP1;Q86VP1-4;Q86VP1-3 B8ZZD4 TAX1BP1 Tax1-binding protein 1 0 ; 174.59 1.46E-06 53463000 86953 98653 99913 108518 114318 89917 119030 92214 144337 FALSE TRUE 81510.76695 105957.3708 102282.9835 111302.7556 105339.9254 115874.5782 101182.5565 103727.1209 120246.2222 0.677865511 0.881170059 0.850612864 0.92562372 0.876035217 0.96364423 0.841461417 0.8626227 1 16.87563204 5.328351316 1.504787522 0.894173436 1.37E-10 0.642319633 0.0515314 3.672137766 2.186119048 0.012292469 7.587042196 212986.1266 -5.328351316 -0.894173436 AHQLVMEGYNWCHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 252.36 7.01E-25 2571030000 591481 602966 608270 577249 657756 530010 694121 537026 618983 FALSE TRUE 554461.26 647610.23 622698.4516 592062.1866 606098.497 683015.283 590044 604074.8782 515670.7385 1.07522343 1.255859954 1.207550487 1.148139971 1.175359492 1.324518209 1.144226259 1.171435246 1 18.97609066 0.649205489 1.534468272 1.000384794 1.201386305 0.435619067 0.067020388 1.140301558 3.828531828 0.058426126 0.016887095 4.458671629 -0.649205489 0.201001511 AHQVVEDGYEFFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AHQVVEDGYEFFAK 14 0 F8W0W8;P36873;P36873-2;F8VYE8;P62140;P62136;P62136-2;P62136-3;E9PMD7 F8W0W8;P62140;P62136 PPP1CC;PPP1CB;PPP1CA Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit;Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 151.9 6.81E-06 670510000 1416400 1251900 1331900 1241200 1415400 1041200 1518800 1133400 1348700 FALSE TRUE 1327750.052 1344591.979 1363493.297 1273051.293 1304240.193 1341777.538 1291070.04 1274907.485 1123593.257 1.181699911 1.196689256 1.213511463 1.133017918 1.160776095 1.194184398 1.149054635 1.134669932 1 20.09968844 -3.410542189 0.206700104 0.593569488 1.207605678 0.866484725 0.021886799 22.92379321 0.411608795 3.993055322 0.050940169 0.00038856 3.410542189 0.61403619 AHS(ph)DDEKWGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AHSDDEKWGR 10 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 AHS(1)DDEKWGR 134.68 9.94E-05 239420000 368730 264210 280800 280170 296470 127250 322450 248570 363290 TRUE FALSE 345651.8475 283772.3833 287460.7086 287359.6365 273186.4421 163985.0093 274101.616 279604.5117 302654.5521 1.142067235 0.937611483 0.949798067 0.949464115 0.902634506 0.541822379 0.905658329 0.923840431 1 18.20731252 7.999996792 0.499123751 0.846681678 9.694603455 0.280577526 0.126831336 131.7558565 1.398305471 0.064516651 1221.904809 99999261.23 -7.999996792 8.847921777 AHS(ph)FTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AHSFTSK 7 0 P78314;P78314-3;P78314-4 P78314 SH3BP2 SH3 domain-binding protein 2 1 AHS(0.954)FT(0.045)SK 92.051 0.025823 0 130640 122110 110850 125400 137600 82742 189230 127050 124660 TRUE FALSE 122463.4756 131151.1515 113479.4143 128617.9763 126793.4511 106628.2722 160856.7182 142912.4722 103853.4407 1.17919517 1.262848401 1.092688058 1.238456574 1.220888304 1.026718725 1.548881936 1.376097617 1 16.66418949 1.745839373 25 1.361160903 1.176473592 0.124174811 0.152252945 2.054455987 7076.65492 0.062400383 0.03460439 55.69797075 -1.745839373 -0.184687311 AHS(ph)HEEASRPAATSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AHSHEEASRPAATSTR 16 1 Q96FS4;F6RY50;E9PIB3 Q96FS4 SIPA1 Signal-induced proliferation-associated protein 1 1 AHS(1)HEEASRPAATSTR;AHS(1)HEEASRPAATSTR 205.02 1.43E-11 1222500000 351109 339897 338391 404553 419043 307833 334430 283117 416598 TRUE FALSE 329133.7144 365063.3275 346417.7943 414934.5149 386133.0531 396699.3898 284285.3262 318464.7807 347065.1025 0.948334223 1.051858354 0.998134909 1.195552396 1.112566635 1.143011461 0.819112392 0.917593784 1 18.40484678 1.740288845 24.99999748 0.901013141 1.069479756 0.465990174 0.081660276 0.231693644 3371.169167 0.037314496 0.020692735 54.99064903 -1.740288845 0.168466615 AHS(ph)IQIMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AHSIQIMK 8 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 1 AHS(1)IQIMK;AHS(1)IQIMK 81.017 0.015427 478700000 1103910 871470 929780 937990 1027790 648590 1322750 755250 1431630 TRUE FALSE 1034818.244 935994.5456 951834.8207 962060.4114 947071.5193 835827.404 1124415.917 849544.625 1192681.704 0.867639908 0.784781507 0.798062733 0.806636346 0.794068959 0.700796701 0.942762778 0.712297859 1 20.18577765 -1.511462214 3.353827135 1.004462622 0.804957789 0.449894225 0.069065723 6910741.377 6236432.067 207819.1269 0.014560356 0.030799083 1.511462214 -0.199504834 AHS(ph)PAEGASVESSSPGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AHSPAEGASVESSSPGPK 18 0 C9J4C4;Q8NFG4-3;Q8NFG4-2;Q8NFG4 C9J4C4 FLCN Folliculin 1 AHS(0.997)PAEGAS(0.003)VESSSPGPK 82.707 0.0031195 251710000 142190 113900 119790 123370 128270 84140 168310 116990 131710 TRUE FALSE 133290.5817 122333.2745 122631.4754 126535.8831 118196.1916 108429.8521 143073.478 131596.459 109726.7501 1.214750109 1.114890165 1.117607832 1.153190839 1.077186661 0.988180658 1.303907004 1.199310641 1 16.74355576 1.731734195 25 1.195961273 1.112508522 0.048730705 0.093636087 1.204078337 4380.501649 0.039281849 0.021783834 53.91805224 -1.731734195 -0.083452751 AHS(ph)SPASLQLGAVSPGTLTPTGVVSGPAATPTAQHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AHSSPASLQLGAVSPGTLTPTGVVSGPAATPTAQHLR 37 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 1 AHS(0.844)S(0.156)PASLQLGAVSPGTLTPTGVVSGPAATPTAQHLR 239.26 1.43E-49 1016200000 181240 348410 331880 336180 370080 262190 414860 310100 303200 TRUE FALSE 169896.5119 374206.6389 339752.3503 344806.948 341015.4096 337879.9967 352655.5944 348816.6676 252593.9613 0.67260718 1.481455206 1.345053336 1.365064098 1.350053691 1.337640833 1.396136284 1.380938269 1 17.94646062 4.744888998 24.94489515 1.358206336 0.672606865 0.722763615 0.127439291 312.2418012 1230745.039 0.025766459 0.242946246 55576.21914 -4.744888998 -0.685599472 AHSAPSSGTSSRPGS(ph)IR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AHSAPSSGTSSRPGSIR 17 1 B7Z896;F5H3M2;Q9BVG8-5;Q9BVG8-2;Q9BVG8;Q9BVG8-6 B7Z896 KIFC3 Kinesin-like protein;Kinesin-like protein KIFC3 1 AHSAPS(0.002)S(0.011)GT(0.027)S(0.027)S(0.005)RPGS(0.929)IR;AHSAPS(0.002)S(0.002)GT(0.008)S(0.045)S(0.011)RPGS(0.933)IR 139.44 4.23E-07 603600000 207557 231610 246100 201559 267130 216590 243870 186692 279070 TRUE FALSE 194566.3779 248758.6454 251937.6082 206731.3452 246150.6874 279116.017 207303.9575 210000.9072 232491.4141 0.836875541 1.06996917 1.083642633 0.889199913 1.058751732 1.200543332 0.891662852 0.903263064 1 17.82681791 1.613637292 25 0.92309343 1.032788142 0.138842308 0.104924448 0.809405755 3492.030972 0.047360143 0.025364828 41.08064858 -1.613637292 0.109694712 AHSEKDQPPFGDSDDSVEADKS(ph)SPGIHLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AHSEKDQPPFGDSDDSVEADKSSPGIHLER 30 2 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AHSEKDQPPFGDS(0.001)DDS(0.115)VEADKS(0.442)S(0.442)PGIHLER 80.722 0.0011419 145870000 69677 54076 66699 74607 82943 37666 73841 47168 90781 TRUE FALSE 65316.04095 58079.84331 68281.13178 76521.54193 76428.99136 48539.56274 62769.22756 53057.02863 75629.06463 0.863636768 0.767956652 0.902842473 1.011800718 1.010576975 0.641810962 0.829961707 0.701542838 1 16.20665316 2.245421584 24.99999575 0.779696875 0.895210835 0.193723912 0.115629678 265.1933552 966312.9664 0.03945241 0.032321635 175.9630918 -2.245421584 0.11551396 AHSEVFTKPSGQQTLS(ph)PDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AHSEVFTKPSGQQTLSPDR 19 1 F5H212;P15822;A0A0D9SFF3;P15822-2;P15822-3 F5H212 HIVEP1 Zinc finger protein 40 1 AHSEVFTKPSGQQT(0.003)LS(0.997)PDR;AHSEVFTKPSGQQT(0.012)LS(0.988)PDR 294.21 7.49E-50 729860000 474820 420710 408410 449160 474430 361610 514930 385780 310370 TRUE FALSE 445101.8638 451859.8061 418097.6781 460686.206 437170.1816 466000.9368 437721.0269 433945.4822 258567.2419 1.721416296 1.747552408 1.616978527 1.781688208 1.690740785 1.802242748 1.69287116 1.67826937 1 17.98017999 0.3797303 1.892167299 0.999989696 1.717909734 0.951211019 0.051088643 1.508951486 4.357966849 0.046551985 0.012904089 2.397343687 -0.3797303 0.717920039 AHSIQIMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AHSIQIMK 8 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ;; 114.89 0.0019482 1795350000 3274870 4714670 3017370 2966660 5162620 2307890 3716180 4573230 4876900 FALSE TRUE 3069901.733 5063749.072 3088943.441 3042789.518 4757168.65 2974140.378 3158973.308 5144207.832 4062913.884 0.75559114 1.246334335 0.760277852 0.748918044 1.170876072 0.732021515 0.777514217 1.26613755 1 21.95408336 1.240234702 24.99991657 1.133068767 0.899329183 0.220142775 0.192934982 68.48912849 1022919.368 0.141325894 0.045485004 17.38740225 -1.240234702 -0.233739584 AHSLGGLDPAFT(ph)STEDLNCKENLEQDLGDDNSNDLLLSCPHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AHSLGGLDPAFTSTEDLNCKENLEQDLGDDNSNDLLLSCPHFR 43 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 AHSLGGLDPAFT(0.333)S(0.333)T(0.333)EDLNCKENLEQDLGDDNS(0.002)NDLLLSCPHFR 60.632 0.0049823 46113000 22485 20254 18735 18505 16891 13467 31299 18947 36128 TRUE FALSE 21077.70399 21753.62723 19179.40305 18979.86963 15564.449 17354.70428 26606.00552 21312.57466 30098.0034 0.700302399 0.72275981 0.637231739 0.630602282 0.517125631 0.576606496 0.883979085 0.708105929 1 14.87738017 1.076149155 1.033864479 0.981521414 0.645067791 0.584301955 0.091485143 0.378609746 0.864216788 0.08706998 0.028877918 11.916512 -1.076149155 -0.336453622 AHSLGGLDPAFTS(ph)TEDLNCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AHSLGGLDPAFTSTEDLNCK 20 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 AHSLGGLDPAFT(0.151)S(0.748)T(0.102)EDLNCK 65.881 0.015599 124730000 86596 68355 77975 84394 77107 82086 113670 73517 73304 TRUE FALSE 81176.11094 73416.07532 79824.60382 86559.69292 71051.32725 105782.8956 96626.23876 82695.75928 61069.08884 1.329250403 1.202180624 1.307119614 1.417406 1.163458119 1.732183952 1.582244645 1.354134487 1 15.8981547 2.263329576 24.99993009 1.487671188 1.281979614 0.05069319 0.201662036 341.0856985 344265.149 0.063485008 0.053094447 183.3705449 -2.263329576 -0.205691574 AHSNPMADHTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AHSNPMADHTLR 12 0 Q9UBP6;F8VSD9;H0YHX0;Q9UBP6-2 Q9UBP6 METTL1 tRNA (guanine-N(7)-)-methyltransferase 0 ;;; 95.273 0.0042976 109727000 44602.3 62769.9 50771.3 50766.8 62855.1 64248.1 61798.2 49893.2 52910.8 FALSE TRUE 41810.72166 67417.44871 51975.61921 52069.56204 57918.71399 82795.48349 52532.13362 56122.47585 44079.64566 0.948526719 1.529446249 1.179129696 1.181260903 1.313955979 1.878315541 1.191754898 1.273206148 1 15.42782501 2.473641037 24.9997826 1.383790315 1.256801734 0.023942817 0.262903561 355.7596625 2555520.851 0.085065669 0.071494512 297.6055576 -2.473641037 -0.126988581 AHSS(ph)PASLQLGAVS(ph)PGTLTPTGVVSGPAATPTAQHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AHSSPASLQLGAVSPGTLTPTGVVSGPAATPTAQHLR 37 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 2 AHS(0.424)S(0.51)PAS(0.066)LQLGAVS(1)PGTLTPTGVVSGPAATPTAQHLR 164.24 5.13E-18 65402000 13969 27504 21380 26428 30099 25330 24061 25488 25734 TRUE FALSE 13094.70523 29540.42478 21887.1437 27106.18722 27735.14595 32642.3598 20453.27642 28670.23291 21438.82915 0.610793861 1.377893567 1.020911335 1.264350167 1.293687531 1.522581274 0.954029545 1.337304043 1 14.3879385 4.748133706 24.79319125 1.216405206 0.610793496 0.527524745 0.181536704 909.868177 2356398.825 0.039762884 0.514037561 55992.99598 -4.748133706 -0.605611709 AHSSMVGVNLPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AHSSMVGVNLPQK 13 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 134.01 0.00010053 1554160000 782830 3604500 1329970 1625360 3832200 1307740 1846100 2800900 2572100 FALSE TRUE 733834.0677 3871380.93 1361517.516 1667069.489 3531234.47 1685263.309 1569294.443 3150598.531 2142799.894 0.342465048 1.806692702 0.635391816 0.777986547 1.647953447 0.786477222 0.732356973 1.470318596 1 21.0310657 AHSSPASLQLGAVS(ph)PGTLTPTGVVSGPAATPTAQHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AHSSPASLQLGAVSPGTLTPTGVVSGPAATPTAQHLR 37 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 1 AHSSPASLQLGAVS(0.999)PGT(0.001)LTPTGVVSGPAATPTAQHLR;AHSSPASLQLGAVS(1)PGTLTPTGVVSGPAATPTAQHLR;AHSSPASLQLGAVS(1)PGTLTPTGVVSGPAATPTAQHLR 188.4 3.85E-23 1326570000 47566.8 123990 108656 125453 137950 130692 122781 115267 144407 TRUE FALSE 44589.6789 133170.3486 111233.3716 128672.3364 127115.9635 168420.6588 104371.1289 129658.3387 120304.5388 0.370640039 1.106943678 0.924598296 1.069555128 1.056618185 1.399952657 0.867557699 1.077751014 1 16.87633155 4.741171007 24.97042569 1.05563556 0.370639791 0.705638242 0.140439777 127.7264469 1221733.93 0.031340712 0.213993887 55102.46238 -4.741171007 -0.684995769 AHT(ph)PLNTPDPSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AHTPLNTPDPSTK 13 0 Q9BYW2;H7C3H4;A0A1W2PPX9 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 AHT(1)PLNTPDPSTK 91.518 0.013346 0 703520 362760 452360 458510 470520 399740 610400 416730 510290 TRUE FALSE 659487.939 389619.1279 463090.1928 470276.1429 433567.2572 515138.4488 518876.1867 468759.6578 425119.3024 1.551300859 0.916493619 1.089318199 1.106221572 1.019871962 1.211750315 1.220542525 1.102654373 1 18.69750824 2.221377105 24.98876747 1.161576625 1.098785231 0 0.17636644 1085.883281 1579112.226 0.061105912 0.045236689 166.4857645 -2.221377105 -0.062791394 AHT(ph)PTPGIYMGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 AHTPTPGIYMGR 12 0 Q13595;Q13595-3;Q13595-4;Q13595-2 Q13595 TRA2A Transformer-2 protein homolog alpha 1 AHT(0.987)PT(0.013)PGIYMGR;AHT(1)PTPGIYMGR;AHT(0.996)PT(0.004)PGIYMGR;AHT(0.999)PT(0.001)PGIYMGR;AHT(1)PTPGIYMGR;AHT(0.978)PT(0.022)PGIYMGR;AHT(1)PTPGIYMGR;AHT(1)PTPGIYMGR;AHT(1)PTPGIYMGR;AHT(1)PTPGIYMGR;AHT(1)PTPGIYMGR 175.29 0.00010329 20960560000 6192340 4652740 5373520 5022150 5080860 4190220 5594670 4796100 4487420 TRUE FALSE 5804772.493 4997233.711 5500982.432 5151026.871 4681829.751 5399868.491 4755801.172 5394903.643 3738440.612 1.552725613 1.336716088 1.471464443 1.377854407 1.252348301 1.444417352 1.272135006 1.443089299 1 21.83400518 -3.709743764 0.214523801 6.03E-11 1.445987865 0.663831177 0.089087991 45.69932514 0.751728829 20.23643327 0.166133564 0.0001951 3.709743764 1.445987865 AHT(ph)PTPGIYMGRPTHSGGGGGGGGGGGGGGGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 20 AHTPTPGIYMGRPTHSGGGGGGGGGGGGGGGGR 33 1 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 AHT(0.973)PT(0.027)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.991)PT(0.009)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.884)PT(0.116)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.997)PT(0.003)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.71)PT(0.29)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.943)PT(0.057)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.992)PT(0.008)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.982)PT(0.018)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.992)PT(0.008)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.544)PT(0.451)PGIY(0.001)MGRPT(0.002)HS(0.002)GGGGGGGGGGGGGGGGR;AHT(0.965)PT(0.035)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.904)PT(0.096)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.997)PT(0.003)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.988)PT(0.012)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.799)PT(0.201)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.601)PT(0.302)PGIY(0.097)MGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.982)PT(0.018)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.958)PT(0.042)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.998)PT(0.002)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.474)PT(0.474)PGIY(0.031)MGRPT(0.021)HSGGGGGGGGGGGGGGGGR 324.02 8.62E-105 26323911000 2429247 2080320 2201363 2217795 2531663 1796133 2789869 2040358 3370662 TRUE FALSE 2277204.767 2234349.057 2253580.37 2274707.374 2332836.4 2314647.439 2371554.043 2295101.188 2808076.737 0.810948197 0.795686609 0.80253518 0.810058837 0.830759491 0.824282118 0.844547448 0.817321392 1 21.42115093 -5 0.230988487 2.005341058 0.795001055 0.96298019 0.011385011 26.12443752 0.261437815 12.26283223 0.018495587 1.00E-05 5 -1.210340003 AHTDFFEAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AHTDFFEAFK 10 0 P61201;P61201-2;B4DIH5;H0YKU5 P61201 COPS2 COP9 signalosome complex subunit 2 0 94.692 0.0079306 240680000 184300 281890 231260 234030 295700 189580 273170 254670 309220 FALSE TRUE 172764.992 302761.4289 236745.5964 240035.606 272476.9148 244308.6684 232210.6945 286466.1101 257609.1844 0.670647642 1.175274203 0.919010698 0.931782019 1.057714287 0.948369403 0.901406893 1.112018233 1 17.9748245 4.760186749 24.52751712 0.997349271 0.670647207 0.58463785 0.088504357 3414.286058 3872270.152 0.020795508 1.002423589 57568.74327 -4.760186749 -0.326702063 AHTMTDDVTFWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AHTMTDDVTFWK 12 0 A0A087WVQ6;Q00610-2;Q00610;J3KSQ2 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 167.84 4.81E-05 1884070000 3941190 4306470 4439730 4511750 4926280 3738480 5630690 4391050 4491040 FALSE TRUE 3694517.953 4625325.52 4545042.492 4627529.143 4539389.84 4817718.487 4786420.307 4939282.258 3741456.411 0.987454496 1.236236645 1.214778951 1.23682562 1.213268135 1.28765859 1.27929335 1.32014962 1 21.83516854 4.738585361 9.201512481 1.237153778 0.986472656 0.412185105 0.087259493 0.067479667 126.4546559 0.017976584 0.104901285 54775.37525 -4.738585361 -0.250681122 AHTPT(ph)PGIYMGRPTHSGGGGGGGGGGGGGGGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AHTPTPGIYMGRPTHSGGGGGGGGGGGGGGGGR 33 1 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 AHT(0.441)PT(0.559)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.285)PT(0.677)PGIY(0.024)MGRPT(0.014)HSGGGGGGGGGGGGGGGGR 200.59 8.36E-27 821080000 93466 87005 71416 93958 95852 54124 75710 67014 128627 TRUE FALSE 87616.1299 93446.94073 73110.02125 96369.12135 88324.17057 69748.72017 64357.98836 75380.84542 107158.3227 0.817632524 0.872045571 0.682261717 0.89931532 0.82423995 0.650894101 0.600587866 0.703453017 1 16.70938438 2.247037805 24.95932704 0.692265831 0.81130558 0.039031307 0.121671991 290.1795033 854374.0572 0.039123093 0.032244104 176.6191558 -2.247037805 0.119039749 AHVDEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AHVDEFK 7 0 A0A087WYS1;E7EUC7;Q16851;Q16851-2 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 ; 88.942 0.018237 1341940000 4187600 3003300 3478200 3193800 3950800 2424200 4010300 3155400 4821700 FALSE TRUE 3925505.591 3225667.457 3560704.547 3275758.315 3640520.105 3124027.186 3408992.745 3549358.636 4016927.121 0.977240929 0.803018666 0.886424981 0.81548861 0.906294786 0.777715675 0.848656857 0.883600456 1 21.93766086 0.840888001 3.498291182 0.999961399 0.852656218 0.370104307 0.05679098 0.793480815 15.83677442 0.047459074 0.012248939 6.932470037 -0.840888001 -0.147305182 AHVIVMAATNRPNSIDPALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AHVIVMAATNRPNSIDPALR 20 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 199.41 8.77E-22 2950100000 741710 727160 761690 686040 748430 692300 822230 651680 681570 FALSE TRUE 695287.6951 780999.683 779757.6465 703644.9479 689651.3268 892155.7714 698944.2447 733043.6825 567811.5639 1.224504289 1.375455754 1.373268345 1.239222645 1.214577812 1.571218038 1.230944012 1.290998157 1 19.11505271 0.607810185 1.513485033 1.000506624 1.332413384 0.460081025 0.107482067 1.327239832 4.084506497 0.094208912 0.027272228 4.053313406 -0.607810185 0.33190676 AHVIVMAATNRPNSIDPALRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AHVIVMAATNRPNSIDPALRR 21 2 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 143.39 8.26E-08 519040000 144920 167420 145490 144760 187390 146700 195610 156490 227340 FALSE TRUE 135849.7159 179815.951 148941.0915 148474.7867 172673.1453 189049.9085 166280.0965 176028.121 189395.4853 0.717280645 0.949420472 0.786402544 0.783940475 0.911706765 0.998175369 0.877951743 0.929420892 1 17.53104242 2.578897985 5.681905692 0.938579741 0.829349829 0.480926802 0.068337445 0.242385991 11.15321999 0.021592555 0.020220642 379.2258947 -2.578897985 -0.109229912 AHVLAASVEQATENFLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AHVLAASVEQATENFLEK 18 0 P35221-2;P35221;G3XAM7;E5RIB1;E5RJL0;E5RHV7;E5RG03;E5RIE0;E5RGY6;E5RFM3 P35221-2 CTNNA1 Catenin alpha-1 0 162.77 3.48E-11 88107000 121570 119520 132030 117130 142730 118550 153950 127510 127970 FALSE TRUE 113961.1507 128369.3852 135161.8139 120135.7541 131520.5615 152773.4605 130866.6267 143429.9042 106610.9803 1.068943841 1.204091594 1.267803875 1.126860984 1.233649303 1.432999304 1.227515462 1.345357709 1 16.70199651 5.800480749 0.960553709 1.252778397 1.17E-11 0.148076625 0.116413404 20.96503084 3.221027864 0.031904624 43.84429021 631656.179 -5.800480749 -1.252778397 AIAGDEHKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AIAGDEHKR 9 1 H0YDU8;P53041;A8MU39;M0R196;A0A087WY80;E7EU14 H0YDU8 PPP5C;PPP5D1 Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5;Protein PPP5D1 0 ;;;; 149.72 5.64E-05 1203510000 3215630 3006580 3243420 3107530 3468660 2529480 3643140 2952570 4226420 FALSE TRUE 3014369.458 3229190.312 3320355.454 3187274.481 3196245.436 3259699.813 3096884.978 3321204.864 3521003.198 0.856110969 0.917122232 0.943014041 0.905217718 0.907765559 0.925787234 0.879546199 0.943255282 1 21.74755511 0.970341127 7.633044633 0.999997406 0.90959465 0.615951588 0.024088662 0.218504251 53.60267504 0.022737029 0.005696624 9.339876352 -0.970341127 -0.090402755 AIAHYEQSADYYKGEESNSSANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 325.53 1.27E-74 1384040000 799460 572560 623780 673840 742890 460660 838190 561030 828920 FALSE TRUE 749423.2257 614952.9381 638576.3562 691131.8752 684546.4161 593645.0638 712511.1909 631075.8305 690567.897 1.085227432 0.890503223 0.924711906 1.000816688 0.991280393 0.859647641 1.031775723 0.913850518 1 19.39742374 -4.999990966 0.449208326 2.000903911 0.954986024 0.017971544 0.068483345 5210.391112 30.24544164 5187.152657 0.033615254 1.00E-05 4.999990966 -1.045917887 AICDHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AICDHVR 7 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 ;;; 160.03 0.0013616 1381170000 382902 3326000 228764 172422 3297580 199132 258167 2666120 2223360 FALSE TRUE 358936.8473 3572260.501 234190.3901 176846.6404 3038601.369 256618.1758 219457.2551 2998990.951 1852266.853 0.193782471 1.928588473 0.126434477 0.09547579 1.640477108 0.138542767 0.118480366 1.619092274 1 20.82086053 3.955767299 23.33221882 0.593193475 1.165401516 0.032438967 0.725634394 384.6406951 420274.9521 0.171760016 0.310155116 9031.654162 -3.955767299 0.572208041 AIEALHGHELRPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AIEALHGHELRPGR 14 1 Q96PK6;Q96PK6-2;A0A0A6YYI9;F8WDX3;A0A0A0MSL8;B8ZZ74;Q96PK6-3;Q96PK6-4 Q96PK6 RBM14;RBM14-RBM4 RNA-binding protein 14 0 ; 109.84 0.00044728 176181000 178866 199746 201897 195183 220266 167405 202476 182090 249280 FALSE TRUE 167671.0963 214535.4017 206686.0922 200191.7262 202967.1969 215732.1059 172116.6035 204824.3373 207673.5576 0.807378167 1.033041491 0.995245108 0.963973115 0.977337699 1.038803921 0.828784394 0.986280293 1 17.66395801 AIEALKEFNEDGALAVLQQFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AIEALKEFNEDGALAVLQQFK 21 1 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ; 326.67 5.14E-80 695280000 1950570 1797240 1889050 1953310 2439240 1405320 2473070 1704400 3525300 FALSE TRUE 1828487.306 1930309.52 1933859.158 2003435.242 2247671.93 1811013.071 2102256.112 1917198.092 2936904.656 0.622589944 0.657259852 0.658468485 0.682158761 0.76532002 0.616640063 0.715806728 0.652795483 1 21.485865 -5 0.334914464 4.418142427 0.660403755 0.849080083 0.043529331 126.350364 1.079067155 308.1418473 0.032499649 1.00E-05 5 -3.757738672 AIEDEGGNPDEIEITSEGNKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AIEDEGGNPDEIEITSEGNKK 21 1 Q15424;Q15424-3;Q15424-4;Q15424-2;K7ES42 Q15424 SAFB Scaffold attachment factor B1 0 58.848 0.041465 0 23768 24295 24892 22273 27652 20119 30410 22050 33426 FALSE TRUE 22280.40331 26093.82708 25482.44999 22844.56289 25480.32346 25927.0287 25850.30281 24802.99104 27846.98466 0.800101109 0.937043181 0.915088305 0.820360379 0.91501194 0.931053362 0.928298095 0.890688573 1 14.7652335 -5 0.13667733 1.343567042 0.861738489 0.406079571 0.044376744 160.211709 1.356023955 14.98726068 0.285316242 1.00E-05 5 -0.481828553 AIEEGTLEEIEEEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AIEEGTLEEIEEEVR 15 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3;K7EP28 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 0 ; 156.81 2.29E-08 9519200 50554 41124 66916 67045 35205 41708.8 58518 33352.5 57612 FALSE TRUE 47389.91538 44168.86375 68503.27912 68765.48821 32440.14131 53749.45347 49743.76915 37516.63304 47996.18501 0.987368379 0.920257803 1.427265086 1.432728209 0.675889996 1.119869287 1.036410897 0.781658647 1 15.55063212 2.74270632 24.99438489 0.950684319 1.185857047 0.296882956 0.203210408 543.6599641 3277721.663 0.064909963 0.066640435 552.9760481 -2.74270632 0.235172729 AIEEGVNHMWTVSAFQQHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AIEEGVNHMWTVSAFQQHPR 20 0 D6RAY7;D6R9P4;D6RFF8;P46926;V9GYW0;V9GYK3;Q8TDQ7-4;P46926-2;Q8TDQ7-3;Q8TDQ7;Q8TDQ7-5 D6RAY7;Q8TDQ7-3 GNPDA1;GNPDA2 Glucosamine-6-phosphate isomerase;Glucosamine-6-phosphate isomerase 1;Glucosamine-6-phosphate isomerase 2 0 ; 270 4.47E-38 884400000 301140 336950 315310 292530 335420 283189 366330 295510 305960 FALSE TRUE 282292.185 361898.1286 322789.3021 300036.8151 309077.4662 364941.0671 311402.2173 332405.074 254893.2994 1.107491588 1.419802441 1.266370292 1.177107502 1.212575878 1.431740528 1.221696365 1.304094987 1 17.95953392 -1.175078201 4.139725297 0.999897118 1.279797001 0.405496157 0.100878188 6764252.937 1920064.513 6546.401833 0.021846968 0.066822358 1.175078201 0.279899883 AIEIYTDMGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AIEIYTDMGR 10 0 P54920;M0R0Y2;M0R2M1;M0R058;M0R0I4;M0R027 P54920 NAPA Alpha-soluble NSF attachment protein 0 102.62 0.0097181 0 63303 76283 80844 84773 85569 77424 81851 69057 74986 FALSE TRUE 59340.97823 81931.07269 82761.65786 86948.4187 78848.75591 99775.05193 69578.20242 77678.91846 62470.35217 0.949906254 1.311519302 1.324814972 1.391834937 1.262178828 1.597158467 1.113779577 1.243452546 1 15.93088404 0.921751077 1.453191285 1.007216203 1.303369346 0.211598272 0.16768423 0.696517765 2.947475318 0.144458741 0.042762863 8.35124216 -0.921751077 0.296153143 AIELDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AIELDKK 7 1 H0YDU8;P53041 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 ; 94.302 0.022929 685750000 1464620 1053010 1113680 1099090 1318850 841420 1351790 1108030 1635040 FALSE TRUE 1372952.049 1130975.956 1140097.016 1127294.51 1215272.841 1084324.295 1149101.639 1246369.985 1362141.261 1.007936613 0.830292708 0.836988826 0.827590017 0.892178275 0.796043939 0.843599465 0.915007878 1 20.3774449 0.969684913 3.467394725 0.999638453 0.852974795 0.360697096 0.058077967 0.217593317 6.920868833 0.050425596 0.013059615 9.325774562 -0.969684913 -0.146663658 AIELLQEFSDQHPENAAEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AIELLQEFSDQHPENAAEIK 20 0 O76094-2;O76094;D6RDY6 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 ; 238.65 1.23E-29 111850000 144216 119809 130191 132071 147377 120715 182788 124845 165714 FALSE TRUE 135189.778 128679.783 133279.192 135460.1655 135802.6049 155563.4609 155380.6363 140432.1731 138055.2628 0.979243929 0.932088936 0.965404645 0.981202474 0.983682926 1.126820214 1.125495929 1.017217092 1 17.07488636 2.351862187 5.543495765 1.084237167 0.961524595 0.553245932 0.043211111 0.124313802 5.572496595 0.014639459 0.012139059 224.8341038 -2.351862187 -0.122712572 AIEMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AIEMER 6 0 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 100.67 0.087001 182550000 175900 224320 185650 191330 231740 159560 195380 182460 204850 FALSE TRUE 164890.733 240928.8862 190053.7057 196239.8517 213540.0752 205622.3818 166084.5828 205240.5326 170659.2116 0.966198844 1.411754361 1.113644578 1.149893111 1.251266036 1.204871274 0.973194363 1.202633779 1 17.38075876 1.761683644 25 1.058971665 1.202701653 0.165376095 0.126576254 18.03099538 19509.3892 0.053800151 0.029836187 57.7675094 -1.761683644 0.143729988 AIEQADLLQEEDES(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AIEQADLLQEEDESPR 16 0 A0A2R8YGH5;H7C1E4;P61966 A0A2R8YGH5 AP1S1 AP-1 complex subunit sigma-1A 1 AIEQADLLQEEDES(1)PR 257.93 1.35E-17 0 60920 70093 57001 71354 50131 57149 74217 60305 51154 TRUE FALSE 57107.12595 75282.75865 58353.09064 73185.06444 46193.91348 73646.98856 63088.84985 67834.212 42616.06693 1.340037457 1.766534645 1.369274427 1.717311561 1.083955344 1.728150762 1.480400572 1.591752052 1 15.37910983 -1.093566132 4.705431709 0.99997174 1.520393671 0.367952937 0.209512745 5.35E-05 1.03E-05 0.174813249 0.041201645 0.080618343 1.093566132 0.520421931 AIEVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AIEVGR 6 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;;;; 137.5 0.029562 2889860000 2210070 2628020 2404060 2436840 2518620 2154070 2585120 2159540 2293020 FALSE TRUE 2071745.664 2822601.335 2461085.438 2499373.44 2320817.745 2775915.041 2197505.255 2429163.323 1910300.149 1.084513167 1.477569552 1.288323953 1.308366877 1.214896909 1.453130307 1.15034554 1.271613429 1 20.8653679 0.48930041 0.62810903 0.992528279 1.321023912 0.341889204 0.120763543 1.711622074 1.14199474 0.136664556 0.044099799 3.085321389 -0.48930041 0.328495633 AIFTGHSAVVEDVAWHLLHESLFGSVADDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AIFTGHSAVVEDVAWHLLHESLFGSVADDQK 31 0 Q16576;E9PC52;Q16576-2;Q5JP01;Q5JP02 Q16576 RBBP7 Histone-binding protein RBBP7 0 71.882 0.0013055 72436000 36348 43548 37840 35977 51363 36335 31473 32323 38323 FALSE TRUE 34073.04356 46772.33923 38737.58267 36900.23073 47329.15717 46824.32465 26753.91583 36358.5977 31926.64372 1.06722911 1.464993929 1.213330878 1.155781705 1.48243447 1.466622206 0.837980843 1.138816783 1 14.96247328 1.739059309 18.78468478 0.99184122 1.316321285 0.480077607 0.154940212 0.040469719 451.3108823 0.067258986 0.037243555 54.83518453 -1.739059309 0.324480065 AIGDHFYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AIGDHFYK 8 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ;; 103.74 0.0047148 1132280000 4076930 4209440 4139900 3955290 4612770 3361660 4546210 4136520 4860910 FALSE TRUE 3821762.229 4521111.318 4238100.383 4056789.438 4250501.651 4332116.67 3864548.015 4652973.628 4049592.718 0.9437399 1.116436055 1.046549784 1.001777146 1.049612133 1.069766016 0.954305355 1.148997924 1 21.94934539 3.46877185 24.53665672 1.031738633 1.055790453 0 0.066373894 645.1062244 1895789.82 0.01683511 0.022924344 2942.875232 -3.46877185 0.02405182 AIGGIILTAS(ph)HNPGGPNGDFGIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 AIGGIILTASHNPGGPNGDFGIK 23 0 A0A3B3ITK7;P36871;P36871-2 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 1 AIGGIILT(0.003)AS(0.997)HNPGGPNGDFGIK;AIGGIILT(0.027)AS(0.973)HNPGGPNGDFGIK;AIGGIILT(0.003)AS(0.997)HNPGGPNGDFGIK;AIGGIILT(0.067)AS(0.933)HNPGGPNGDFGIK;AIGGIILT(0.11)AS(0.89)HNPGGPNGDFGIK;AIGGIILT(0.001)AS(0.999)HNPGGPNGDFGIK;AIGGIILT(0.005)AS(0.995)HNPGGPNGDFGIK 281.11 3.74E-52 22999610000 11105681 10410310 9798140 10417620 12086910 6932125 13223730 10567760 10522550 TRUE FALSE 10410596.25 11181100.18 10030556.51 10684953.77 11137652.84 8933316.954 11240954.45 11887168.1 8766268.427 1.187574432 1.275468608 1.144221922 1.218871388 1.270512412 1.019055831 1.282296401 1.356012333 1 23.06353142 -0.881498818 5.50086126 0.999999849 1.215133892 0.361252307 0.091477503 1.57E-07 3.18E-08 0.081546215 0.019220614 0.131371507 0.881498818 0.215134043 AIGPHDVLATLLNNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AIGPHDVLATLLNNLK 16 0 O75533;H7C341 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 218.31 1.35E-14 145555000 341190 408380 309400 307980 450430 227650 391540 392200 394720 FALSE TRUE 319835.5269 438616.8801 316739.1141 315883.2882 415055.0447 293368.8594 332832.2119 441167.0333 328838.682 0.972621363 1.333836024 0.963205156 0.960602586 1.26218437 0.8921361 1.012144343 1.341591052 1 18.32702049 3.952180651 22.09265977 1.053523781 1.175215989 0.046074835 0.163347527 216.7266951 191979.0188 0.038415311 0.069324245 8957.372838 -3.952180651 0.121692208 AIGSASEGAQSSLQEVYHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AIGSASEGAQSSLQEVYHK 19 0 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ;;; 366.82 7.23E-108 1843130000 1646630 1707660 1591240 1602400 1885380 1362760 1957140 1649870 2075270 FALSE TRUE 1543570.368 1834096.923 1628984.964 1643520.297 1737309.86 1756166.689 1663685.026 1855859.901 1728894.03 0.892807969 1.060849821 0.942212152 0.950619453 1.004867753 1.015774627 0.962282822 1.073437625 1 20.72141801 1.249785075 24.99993378 1.036718826 0.981875095 0.204811162 0.048851557 306.1686585 681930.4983 0.030338638 0.010859107 17.77399587 -1.249785075 -0.054843731 AIGSTSKPQES(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AIGSTSKPQESPK 13 1 F5H8D7;P18887;M0QYS5 F5H8D7 XRCC1 DNA repair protein XRCC1 1 AIGS(0.004)T(0.004)S(0.004)KPQES(0.988)PK;AIGSTSKPQES(1)PK;AIGSTSKPQES(1)PK;AIGS(0.003)T(0.003)S(0.003)KPQES(0.991)PK;AIGS(0.003)T(0.004)S(0.004)KPQES(0.988)PK 139 2.57E-05 3373340000 3703250 1724490 2514860 2179570 2378460 2010700 3322210 2224320 3074360 TRUE FALSE 3471470.193 1852173.034 2574513.667 2235501.456 2191665.346 2591156.449 2824075.452 2502031.248 2561229.455 1.355392109 0.723157791 1.005186654 0.872823578 0.855708317 1.01168462 1.102624932 0.976886801 1 21.28840508 2.034156077 12.05978179 1.042718664 0.931719572 0.01097541 0.165793666 1.983565544 695.8089922 0.056708373 0.0418344 108.1822668 -2.034156077 -0.110999092 AIGSTSKPQES(ph)PKGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AIGSTSKPQESPKGK 15 2 F5H8D7;P18887;M0QYS5 F5H8D7 XRCC1 DNA repair protein XRCC1 1 AIGS(0.099)T(0.099)S(0.133)KPQES(0.669)PKGK;AIGS(0.008)T(0.007)S(0.026)KPQES(0.959)PKGK 122.49 5.67E-05 902390000 2045550 826490 1299680 1201450 1442200 804810 1553770 997580 2387800 TRUE FALSE 1917522.677 887684.1796 1330509.023 1232281.241 1328935.43 1037145.582 1320796.613 1122130.059 1989260.754 0.963937318 0.446238221 0.668845962 0.619466924 0.668054918 0.521372364 0.66396354 0.564094002 1 20.92380097 -1.29686133 3.296841288 1.001806809 0.622851709 0.404016721 0.136276959 27314043.22 37362567.38 485417.5582 0.0281966 0.050482246 1.29686133 -0.3789551 AIGTEPDSDVLSEIMHSFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AIGTEPDSDVLSEIMHSFAK 20 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ;; 306.26 1.62E-55 877199800 916577 953316 1062347 1043183 1143834 928636 1189502 1005562 879578 FALSE TRUE 859210.0817 1023900.509 1087546.373 1069952.842 1054001.892 1196718.138 1011147.218 1131108.629 732770.7495 1.172549644 1.397299918 1.484156366 1.460146768 1.438378773 1.63314125 1.379895716 1.54360505 1 19.48300239 -1.09630142 5.026972294 0.99998729 1.443607389 0.572544518 0.11904415 1.55E-05 2.79E-06 0.105617928 0.024893672 0.080112185 1.09630142 0.443620099 AIGVKPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AIGVKPPR 8 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 108.09 0.0035368 2328500000 1556110 1612700 1635400 1556120 1783060 1440000 1918890 1460350 1886710 FALSE TRUE 1458715.853 1732105.986 1674192.46 1596052.674 1643025.66 1855704.624 1631170.259 1642677.912 1571805.912 0.928050875 1.101984649 1.065139434 1.015426053 1.045310777 1.180619445 1.037768242 1.045089536 1 20.58399165 4.747458021 24.52839285 1.067632018 0.928050781 0.401052502 0.050717383 846.6877741 2334086.174 0.011313914 0.1334124 55905.94857 -4.747458021 -0.139581237 AIHSWLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AIHSWLTR 8 0 P28070 P28070 PSMB4 Proteasome subunit beta type-4 0 ; 133.6 0.00091248 3046000000 987010 2779700 838430 773340 2708700 558580 988140 2310500 2495500 FALSE TRUE 925234.806 2985511.88 858317.9555 793185.2137 2495969.628 719832.9782 839977.5804 2598971.011 2078984.928 0.445041613 1.436043061 0.412854342 0.381525235 1.200571295 0.346242519 0.404032549 1.250115369 1 20.98744787 5.005678869 21.57955152 0.761039697 0.026027322 0.061984013 0.409591894 10755.99278 132152.4408 0.092413882 224667.6372 101316.1944 -5.005678869 -0.735012375 AIHVLDVEQGQLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AIHVLDVEQGQLER 14 0 Q9H6Y2 Q9H6Y2 WDR55 WD repeat-containing protein 55 0 ; 179.39 1.19E-07 409600000 485100 521570 467010 485870 546410 399680 564170 451420 571630 FALSE TRUE 454738.4569 560187.5855 478087.6977 498338.2468 503497.1627 515061.1277 479577.946 507780.7807 476221.2601 0.95488903 1.176317885 1.003919266 1.04644267 1.057275693 1.08155845 1.007048585 1.066270709 1 18.8612725 0.360247784 0.267200645 0.98475022 1.071700515 0.030119642 0.059130446 11.25534268 1.64947818 0.296193977 0.096499657 2.292175066 -0.360247784 0.086950294 AIIEEYLHLNDMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 227.91 8.31E-12 514840000 1598810 1431660 1392280 1314670 1401690 1060650 1874850 1343720 2104870 FALSE TRUE 1498743.336 1537661.596 1425305.539 1348406.658 1291606.922 1366842.437 1593733.648 1511486.4 1753553.599 0.854689208 0.876883146 0.812809794 0.768956625 0.736565408 0.779470007 0.908859386 0.861956202 1 20.7418501 0.996550585 1.179851686 0.994166677 0.813954065 0.594385325 0.048581897 0.399023446 1.14936649 0.049670485 0.015607764 9.920888871 -0.996550585 -0.180212612 AIIESDQEQGRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AIIESDQEQGRK 12 1 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 68.44 0.086536 0 48925 58322 63358 59057 56680 48171 54537 58899 94699 FALSE TRUE 45862.87158 62640.22156 64860.88168 60572.5026 52228.58144 62077.18571 46359.68315 66252.6698 78893.12512 0.581329127 0.793988341 0.822136043 0.767779227 0.662016891 0.78685165 0.587626401 0.83977748 1 16.26761197 -1.677942861 2.5320661 1.040558861 0.734778557 0.457743745 0.092169704 16091909.43 12976986.62 4195931.465 0.022903752 0.020992161 1.677942861 -0.305780304 AIIGLYNYAHEMTHGASDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AIIGLYNYAHEMTHGASDR 19 0 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 280.65 6.93E-40 145960000 72907 99859 93279 99061 101520 89986 102890 95907 86251 FALSE TRUE 68343.88101 107252.6643 95491.62193 101603.073 93547.02871 115963.4974 87462.59968 107881.2001 71855.1509 0.951134055 1.492623186 1.328946091 1.413998464 1.301883408 1.613850865 1.217207098 1.501370448 1 16.13280396 -1.283461418 4.918281025 0.999891088 1.364095127 0.269033278 0.181796877 0.000186132 2.71E-05 0.150908382 0.035558865 0.052064126 1.283461418 0.36420404 AIIVEFAQQGLNAALFYENKDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AIIVEFAQQGLNAALFYENKDPR 23 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 136.02 1.18E-05 579140000 529080 456010 504270 489560 569000 417430 632450 510690 607720 FALSE TRUE 495965.8272 489773.4549 516231.5225 502122.9384 524313.0352 537935.2646 537619.9939 574450.7707 506287.606 0.979612816 0.967381878 1.019640845 0.991774107 1.035603141 1.06250925 1.061886539 1.134633287 1 18.94959764 2.615045755 1.124742273 1.073460535 0.984091916 0.512914826 0.034466286 0.346942307 0.901597639 0.016899605 0.01390907 412.1409375 -2.615045755 -0.089368619 AIKVEQATKPSFESGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 92.996 0.002577 961400000 730690 792510 743330 735590 839210 543100 896990 676090 1233400 FALSE TRUE 684957.4172 851188.265 760962.1386 754466.4848 773301.8318 699884.1535 762494.6767 760501.3248 1027537.572 0.666600848 0.82837678 0.740568675 0.734247102 0.75257767 0.681127554 0.742060142 0.740120211 1 19.97075972 -0.668418153 6.504321191 1.000000001 0.74243166 0.783327528 0.043555774 6.11E-10 0 0.04102229 0.009669047 0.214576347 0.668418153 -0.25756834 AILDAEPGPRPALQPS(ph)PSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AILDAEPGPRPALQPSPSIR 20 1 B5MD46;Q9BXI6;Q9BXI6-2 B5MD46 TBC1D10A TBC1 domain family member 10A 1 AILDAEPGPRPALQPS(0.91)PS(0.09)IR;AILDAEPGPRPALQPS(0.999)PS(0.001)IR;AILDAEPGPRPALQPS(0.977)PS(0.023)IR 153.1 3.44E-08 439370000 585300 682170 628360 654220 727570 571010 763990 624270 697880 TRUE FALSE 548667.1178 732678.5766 643264.9959 671008.3928 670429.5871 735851.3174 649436.792 702211.4837 581399.3195 0.943700998 1.260198545 1.106408237 1.154126553 1.153131014 1.265655622 1.117023653 1.207795503 1 19.14916986 -1.055206385 4.125047715 0.999982062 1.158951134 0.208710086 0.091245152 5220347.281 1335389.208 939.8690693 0.018512847 0.088063028 1.055206385 0.158969072 AILELHYSQELSLLYLLQDDVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 AILELHYSQELSLLYLLQDDVDR 23 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;;;; 201.87 2.18E-24 119069300 135068.7 217901 165148 202746 225796 175065.9 205387.5 200484 136499.5 FALSE TRUE 126614.9912 234034.6168 169065.3885 207948.8056 208062.893 225604.5834 174591.5511 225514.8687 113716.8516 1.113423291 2.058046925 1.486722382 1.828654264 1.829657522 1.983915138 1.535318192 1.983126208 1 16.79508654 -1.068974956 4.416891841 0.999947441 1.737871657 0.390083144 0.28556088 0.000138276 2.91E-05 0.238600478 0.056234349 0.085314931 1.068974956 0.737924217 AILILDNDGDR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;; 249.24 1.89E-11 1272876000 1962003 2192887 2122654 2198873 2024465 2010348 2366568 2018244 1577350 FALSE TRUE 1839204.735 2355250.635 2173004.355 2255299.804 1865471.685 2590702.832 2011723.099 2270226.206 1314080.095 1.399613876 1.792318934 1.653631589 1.716257489 1.419602726 1.971495377 1.530898388 1.727616311 1 20.32562178 -1.129704294 3.716008848 0.999626584 1.663680691 0.586417526 0.171654441 22206386.12 36516866.16 101799.951 0.035515048 0.074181516 1.129704294 0.664054107 AILILDNDGDRLFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AILILDNDGDRLFAK 15 1 F8VYZ4;F8VVA7;P61923-5;P61923;P61923-4;F8VXB1;F8VUC5;F8W156;F8W651;F8VXR1 F8VYZ4 COPZ1 Coatomer subunit zeta-1 0 ; 238.47 8.24E-18 975700000 1181380 1617440 1363390 1583320 1959090 1117540 1804120 1316520 2710300 FALSE TRUE 1107439.535 1737196.941 1395730.255 1623950.672 1805230.974 1440155.656 1533608.955 1480890.42 2257933.421 0.490465983 0.769374741 0.618145 0.71921991 0.799505848 0.637820249 0.679209112 0.655860977 1 21.10657152 -1.906365679 2.273318332 1.196606818 0.679023424 0.592374888 0.08549819 6898898.979 3356331.466 7242305.66 0.01963328 0.012406073 1.906365679 -0.517583394 AILLPDLSEPNNEPLFS(ph)PASEVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AILLPDLSEPNNEPLFSPASEVPR 24 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2;H7C4S1 Q8WYP5 AHCTF1 Protein ELYS 1 AILLPDLSEPNNEPLFS(0.97)PAS(0.03)EVPR;AILLPDLSEPNNEPLFS(0.978)PAS(0.022)EVPR 95.48 0.0044847 31997000 27992 31971 30973 31747 33738 29689 35918 26877.6 40821 TRUE FALSE 26240.03069 34338.16611 31707.69419 32561.68177 31088.35357 38259.73234 30532.42935 30233.32752 34007.71139 0.771590607 1.009717053 0.932367775 0.957479361 0.914156005 1.125031082 0.897809 0.889013882 1 15.0535743 4.747022886 24.4331852 0.9646166 0.771590473 0.438718666 0.068988784 733.9464329 2119064.173 0.015180476 0.173263756 55849.96246 -4.747022886 -0.193026127 AILVDLEPGTMDS(ph)VR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.097)MDS(0.903)VR;AILVDLEPGT(0.105)MDS(0.895)VR 167.69 1.36E-06 22242000 65196 91806 76899 84658 104342 71581 99104 72969 133486 TRUE FALSE 61115.49874 98603.41176 78723.08059 86830.46761 96147.40022 92245.27268 84244.27524 82079.34027 111206.3242 0.549568553 0.886670901 0.707901112 0.780805122 0.864585723 0.829496643 0.757549319 0.738081587 1 16.76287931 -5 0.279188176 2.611702552 0.76049681 0.384349542 0.093918383 243.6000081 2.336576681 227.8013889 0.098422243 1.00E-05 5 -1.851205742 AILVDLEPGTMDSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 ;;;;;; 250.51 1.75E-18 640206000 996646 1220327 1191651 1150743 1339509 1031552 1271876 1161863 1487223 FALSE TRUE 934267.7059 1310681.281 1219917.524 1180273.014 1234309.366 1329344.317 1081170.001 1306924.153 1238995.873 0.754052314 1.057857664 0.984601765 0.952604475 0.996217496 1.072920697 0.872617919 1.054825267 1 20.24073995 4.748165058 24.84018799 0.993653067 0.754052174 0.634275757 0.058319914 798.0877601 2064066.731 0.013323268 0.173563775 55997.03834 -4.748165058 -0.239600893 AIMEMPSFYSHGLPR ddPTM_SK-BR-3_Pertuzumab_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 ; 194.85 3.46E-08 726040000 969830 892410 691290 697060 984960 613630 817310 835030 803100 FALSE TRUE 909130.0715 958484.965 707687.7253 714947.7397 907605.2147 790775.0195 694761.953 939285.3336 669057.4218 1.358822191 1.43258999 1.057738398 1.068589506 1.356543079 1.181923993 1.038419021 1.403893452 1 19.35177051 4.051408424 4.375815988 1.157622214 1.392196899 0.351808183 0.13371741 0.222496547 8.022458356 0.03148108 0.070890807 11256.63084 -4.051408424 0.234574685 AINEAYKEDYHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AINEAYKEDYHK 12 1 E5RK69;P08133;P08133-2;E7EMC6 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ; 171.73 2.26E-05 1101010000 2334200 1459350 1832180 1289150 2372500 875600 2390300 2042300 4892700 FALSE TRUE 2188106.589 1567401.792 1875640.175 1322231.772 2186173.42 1128371.506 2031896.705 2297285.651 4076076.762 0.536816826 0.384536868 0.460158207 0.324388339 0.536342554 0.276827835 0.498493239 0.563602156 1 21.95874979 0.744797317 1.622289054 0.99929038 0.421157327 0.820277713 0.083787081 0.308751835 1.329069333 0.068250025 0.019574642 5.5564488 -0.744797317 -0.578133053 AINVLLEGNPDTHSWEMVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AINVLLEGNPDTHSWEMVGK 20 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;Q5VU81;Q5VU80;Q5VU79;Q5VU78;Q5VU77 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 0 194.24 4.44E-18 256400000 470810 447480 477060 488300 540960 339690 478020 435470 456120 FALSE TRUE 441342.8425 480611.8848 488376.0885 500830.6047 498475.1837 437752.9886 406345.3387 489839.3881 379990.6254 1.161457186 1.264799321 1.28523194 1.318007791 1.311809162 1.152009969 1.06935622 1.289082823 1 18.5356043 2.139765803 5.577812537 1.123744094 1.272037337 0.417511517 0.082977968 0.189001081 8.865393971 0.028940742 0.021243068 137.9640081 -2.139765803 0.148293242 AIPELDAYEAEGLALDDEDVEELTAS(ph)QR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AIPELDAYEAEGLALDDEDVEELTASQR 28 0 P49736;F8WDM3;C9J013;C9JZ21;H7C4N9 P49736 MCM2 DNA replication licensing factor MCM2 1 AIPELDAYEAEGLALDDEDVEELT(0.009)AS(0.991)QR;AIPELDAYEAEGLALDDEDVEELT(0.002)AS(0.998)QR;AIPELDAYEAEGLALDDEDVEELT(0.001)AS(0.999)QR 159.36 6.71E-12 124307000 105513 133409 127283 125599 137006 106817 135765 123641 126255 TRUE FALSE 98909.12968 143286.7412 130302.2129 128822.083 126246.1014 137653.3339 115408.2986 139077.851 105182.2249 0.940359741 1.362271442 1.238823509 1.224751455 1.200260801 1.308712894 1.097222452 1.32225622 1 16.68253139 -1.560050989 3.068013686 0.990076219 1.222733281 0.226426574 0.12157484 35178163.49 48619697 2959212.66 0.026238112 0.027539054 1.560050989 0.232657062 AIPGDQHPES(ph)PVHTEPMGIQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 AIPGDQHPESPVHTEPMGIQGR 22 0 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(0.996)PVHT(0.004)EPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(0.985)PVHT(0.015)EPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(0.896)PVHT(0.104)EPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(1)PVHTEPMGIQGR 235.9 1.14E-30 7365740000 3499300 3601913 3853112 3455251 4120200 3838380 4362650 3601135 4054870 TRUE FALSE 3280285.059 3868602.386 3944509.636 3543918.59 3796616.112 4946457.995 3708511.133 4050744.632 3378086.002 0.971048416 1.145205416 1.167675907 1.049090695 1.123895635 1.46427829 1.097814304 1.199124187 1 21.68777463 4.774961589 2.804525885 1.16836364 0.924240884 0.176485341 0.123873666 0.839783182 8.448659005 0.028306287 0.489511942 59560.9463 -4.774961589 -0.244122756 AIPLFGNSLKPDSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AIPLFGNSLKPDSLR 15 1 O95154 O95154 AKR7A3 Aflatoxin B1 aldehyde reductase member 3 0 140.49 4.50E-06 197330000 432300 546030 382470 393580 572920 293390 496920 473070 705910 FALSE TRUE 405243.1147 586458.6293 391542.369 403679.9291 527925.1742 378086.9302 422411.4592 532133.8309 588089.0606 0.689084599 0.997227578 0.66578754 0.686426523 0.897695961 0.642907606 0.718278042 0.904852456 1 19.16567513 1.044832498 4.511241398 0.998623497 0.766556426 0.362775128 0.110996396 0.198881336 8.722779829 0.104649325 0.026624072 11.08747102 -1.044832498 -0.232067071 AIPTESITDS(ph)PISAQDLLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AIPTESITDSPISAQDLLSR 20 0 Q9UDV7-2;Q9UDV7 Q9UDV7-2 ZNF282 Zinc finger protein 282 1 AIPTESIT(0.02)DS(0.979)PIS(0.001)AQDLLSR;AIPTESIT(0.004)DS(0.995)PIS(0.001)AQDLLSR 117.65 3.30E-05 0 41151 45522 52586 50003 52571 39169 62219 47669 67395 TRUE FALSE 38575.43237 48892.49625 53833.36475 51286.16163 48442.28572 50476.45444 52889.83856 53620.57958 56146.33911 0.687051604 0.870804705 0.958804538 0.913437322 0.862786185 0.899015951 0.941999771 0.955014707 1 15.77690434 4.7867586 2.036824196 0.92616846 0.598624232 0.809016883 0.037424026 0.354859668 1.456342358 0.009113216 0.225056929 61201.01155 -4.7867586 -0.327544228 AIPTVNHSGTFS(ph)PQAPVPTTVPVVDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AIPTVNHSGTFSPQAPVPTTVPVVDVR 27 0 Q16513-3;Q16513-2;Q16513;Q16513-4;Q16513-5;B1AL79 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 AIPT(0.002)VNHS(0.339)GT(0.234)FS(0.425)PQAPVPTTVPVVDVR;AIPTVNHS(0.001)GT(0.26)FS(0.74)PQAPVPTTVPVVDVR 215.47 2.51E-34 386970000 113588 114736 129063 127448 124464 114958 142775 110159 152350 TRUE FALSE 106478.7298 123231.1728 132124.4353 130718.5314 114689.0995 148144.5084 121367.2142 123912.5936 126921.8008 0.838931761 0.970922033 1.040990866 1.029913936 0.903620172 1.167210893 0.956236151 0.976290857 1 16.95358037 4.761130531 2.156133199 1.01193224 0.786086325 0.385188909 0.067953955 0.703173519 3.541785979 0.015409055 0.313312063 57693.98414 -4.761130531 -0.225845915 AIPVS(ph)PSAVEEDEDEDGHTVVATAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AIPVSPSAVEEDEDEDGHTVVATAR 25 0 A0A087X0K9;G5E9E7;Q07157-2;H0Y3R8;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 AIPVS(0.85)PS(0.15)AVEEDEDEDGHTVVATAR 279.23 2.23E-53 253470000 123250 120990 140800 147070 160970 129550 124060 108720 144640 TRUE FALSE 115536.0025 129948.2255 144139.8425 150844.0652 148328.0655 166948.9819 105458.3547 122293.9313 120498.6496 0.958815745 1.078420596 1.196194671 1.251831997 1.230952098 1.385484256 0.875182876 1.014898771 1 16.87865745 1.679974001 10.67934003 0.960618388 1.177116986 0.442074241 0.116304907 0.113244893 18.16090304 0.055664763 0.030161959 47.86014399 -1.679974001 0.216498598 AIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAK 39 1 Q15417;E9PDU6;Q15417-2 Q15417 CNN3 Calponin-3;Calponin 0 102.53 1.06E-05 111060000 303320 268060 229210 207870 357100 198820 360040 296860 313610 FALSE TRUE 284335.7426 287907.4413 234646.9694 213204.2961 329054.8065 256216.1064 306055.3444 333923.6245 261266.465 1.08829789 1.101968602 0.898113615 0.816041569 1.259460553 0.980669702 1.171429883 1.278096002 1 17.99516243 2.727822344 24.92329123 1.137141529 0.984083977 0.293172513 0.12458087 943.1604324 2189050.585 0.039194039 0.037301172 534.3457308 -2.727822344 -0.153057552 AIQDHLLEVEQSKDQMEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AIQDHLLEVEQSKDQMEK 18 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 141.97 6.97E-08 87027000 102290 76512 97872 89507 92676 59737 106950 78995 122120 FALSE TRUE 95887.85149 82177.02809 100193.5701 91803.90115 85397.6008 76982.10215 90913.84038 88857.69964 101737.3831 0.942503617 0.807736798 0.984825509 0.902361535 0.839392544 0.756674684 0.893612924 0.873402647 1 16.63449036 -0.991052765 2.266835821 1.00064356 0.87472236 0.270002936 0.064558363 81562.72644 91519.90294 412.7892621 0.01652 0.102081545 0.991052765 -0.1259212 AIQEGANSIVSSLHQAAAAACLS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AIQEGANSIVSSLHQAAAAACLSR 24 0 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 AIQEGANSIVSSLHQAAAAACLS(1)R;AIQEGANSIVSSLHQAAAAACLS(1)R 250.21 1.22E-38 433520000 229594 412610 342080 340340 412930 316600 476650 375370 484540 TRUE FALSE 215224.1214 443160.0737 350194.2991 349073.7006 380500.1435 407997.2804 405180.7575 422235.7708 403667.1438 0.533172255 1.097835384 0.867532333 0.864756287 0.942608655 1.010726998 1.003749658 1.045999847 1 18.62280664 2.402086845 2.841121578 1.015225351 0.888354825 0.230775797 0.13844909 0.497052492 8.187177349 0.049805266 0.04051492 252.3985438 -2.402086845 -0.126870526 AIQWGEDGRPFHYLFYTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AIQWGEDGRPFHYLFYTGK 19 1 P82933 P82933 MRPS9 "28S ribosomal protein S9, mitochondrial" 0 108.49 0.00016459 94794000 215480 197590 172740 157530 285050 152780 169850 226420 254200 FALSE TRUE 201993.4914 212219.7692 176837.4744 161572.4865 262663.3228 196885.1058 144382.5693 254689.0354 211772.3778 0.953823598 1.002112605 0.835035599 0.762953546 1.240309645 0.92970154 0.681781877 1.202654652 1 17.6921549 4.212002052 22.55033947 0.921677941 0.977968085 0 0.175780534 659.7946037 984096.6335 0.04214516 0.091813054 16293.0373 -4.212002052 0.056290144 AIRPENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AIRPENR 7 1 P50402;Q5HY57 P50402 EMD Emerin 0 62.659 0.076725 33794000 211990 219130 227940 246820 276620 203420 285060 298340 262480 FALSE TRUE 198721.9243 235354.6132 233346.8444 253153.8191 254895.381 262144.0518 242317.8994 335588.4057 218670.3923 0.908773804 1.076298491 1.067116778 1.157695911 1.165660236 1.19880908 1.108142245 1.534676927 1 17.73839837 4.733904894 0.46660864 1.212641878 0.753337652 0.298516832 0.137749219 5.97195368 1.013248256 0.083517133 1.528602249 54188.22113 -4.733904894 -0.459304227 AIS(ph)SANLLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AISSANLLVR 10 0 G3V1D0;B7WPE2;H0Y3M3;Q32P44;Q32P44-2 G3V1D0 EML3 Echinoderm microtubule-associated protein-like 3 1 AIS(0.5)S(0.5)ANLLVR;AIS(0.5)S(0.5)ANLLVR;AIS(0.5)S(0.5)ANLLVR;AIS(0.903)S(0.097)ANLLVR 158.34 8.41E-06 258354000 258705 371234 258189 271517 385268 154630 454562 343061 649980 TRUE FALSE 242513.1159 398720.5516 264313.365 278484.5859 355010.6054 199269.1708 386404.648 385892.921 541494.139 0.44785917 0.736334012 0.488118607 0.514289197 0.655613016 0.367998758 0.713589715 0.712644687 1 19.0465862 0.943896437 1.430466522 0.995180519 0.559437271 0.625467882 0.111340847 0.303481558 1.255451306 0.096470525 0.028701713 8.788129276 -0.943896437 -0.435743247 AIS(ph)SDMFFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 17 AISSDMFFGR 10 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;Q8N6H7-3;H0YDN9;E9PMU9 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 AIS(0.944)S(0.056)DMFFGR;AIS(0.838)S(0.162)DMFFGR;AIS(0.5)S(0.5)DMFFGR;AIS(0.965)S(0.035)DMFFGR;AIS(0.5)S(0.5)DMFFGR;AIS(0.5)S(0.5)DMFFGR;AIS(0.762)S(0.238)DMFFGR;AIS(0.935)S(0.065)DMFFGR;AIS(0.885)S(0.115)DMFFGR;AIS(0.94)S(0.06)DMFFGR;AIS(0.921)S(0.079)DMFFGR;AIS(0.689)S(0.311)DMFFGR;AIS(0.962)S(0.038)DMFFGR;AIS(0.934)S(0.066)DMFFGR;AIS(0.964)S(0.036)DMFFGR;AIS(0.968)S(0.032)DMFFGR;AIS(0.971)S(0.029)DMFFGR 226.31 3.24E-09 4818706000 3932960 4658129 4046145 4694935 2962054 2831179 6101032 3846902 3547828 TRUE FALSE 3686803.054 5003021.718 4142121.47 4815414.981 2729426.227 3648494.417 5186238.891 4327196.183 2955672.587 1.247365175 1.692684684 1.401414178 1.629211233 0.923453511 1.234404119 1.754673002 1.464030963 1 21.49505503 AIS(ph)TGSLASSTLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AISTGSLASSTLNK 14 0 Q12923-3;Q12923;Q12923-4 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 AIS(0.5)T(0.5)GSLASSTLNK;AIS(0.5)T(0.5)GSLASSTLNK 225.21 3.00E-12 131419000 268610 290270 272930 257830 394470 239660 359100 363050 529530 TRUE FALSE 251798.1796 311761.8928 279404.0285 264446.3543 363489.9174 308845.9514 305256.2887 408377.5917 441148.0221 0.570779346 0.706705861 0.633356639 0.599450391 0.823963611 0.700095968 0.691958874 0.925715568 1 18.75090329 1.177337885 3.083642893 0.999500608 0.67523521 0.756178261 0.068638909 0.111835524 1.885259002 0.060630891 0.016593662 15.0431188 -1.177337885 -0.324265398 AISGVHTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 176.38 5.32E-05 758900000 453040 590380 546060 564120 632880 518380 651290 567490 576890 FALSE TRUE 424685.0351 634092.3495 559012.8011 578596.2743 583176.1577 668027.8908 553635.1108 638342.3757 480603.3321 0.883649793 1.31936736 1.163147993 1.203895678 1.213425124 1.389977651 1.151958536 1.328210466 1 18.87448713 4.747783799 24.85809646 1.230009139 0.883649597 0.483327373 0.109362692 871.9765435 2350076.602 0.022449169 0.278447697 55947.90112 -4.747783799 -0.346359542 AISHEHSPSDLEAHFVPLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AISHEHSPSDLEAHFVPLVK 20 0 P30153;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ;;; 118.24 3.96E-05 552279000 759347 796110 783640 751280 896300 685900 986220 785690 1025760 FALSE TRUE 711820.8267 855054.8128 802228.3109 770559.1167 825908.2135 883908.1953 838345.4666 883785.126 854554.0293 0.83297346 1.000586017 0.938768391 0.901709067 0.966478637 1.034350275 0.981032723 1.034206259 1 19.70481218 2.453164758 6.037094846 1.007967856 0.935319427 0.476100258 0.044795361 0.175368142 20.96490648 0.01479075 0.012570274 283.8995852 -2.453164758 -0.072648428 AIST(ph)PETPLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AISTPETPLTK 11 0 A0A3B3ITS5;Q14181;E9PIQ6 A0A3B3ITS5 POLA2 DNA polymerase alpha subunit B 1 AIS(0.02)T(0.98)PETPLTK;AIS(0.037)T(0.962)PETPLTK;AIS(0.013)T(0.987)PETPLTK;AIS(0.039)T(0.89)PET(0.065)PLT(0.006)K 134.99 0.0014461 382241000 1565360 1211280 1490470 1316990 1529470 1484320 1837570 1529060 1668770 TRUE FALSE 1467386.912 1300964.432 1525824.652 1350786.193 1409351.596 1912819.088 1562043.438 1719966.507 1390241.506 1.05549065 0.935783046 1.097524887 0.971619813 1.013745878 1.375889786 1.123577041 1.237171023 1 20.40690409 2.377303477 25 1.193534836 1.013313187 0.402286309 0.102267134 10.57662961 2635.356696 0.031167943 0.026076978 238.3984773 -2.377303477 -0.180221649 AIT(ph)PPQQPYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AITPPQQPYK 10 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 AIT(1)PPQQPYK;AIT(1)PPQQPYK;AIT(1)PPQQPYK;AIT(1)PPQQPYK;AIT(1)PPQQPYK;AIT(1)PPQQPYK 165.35 6.57E-05 3715380000 5060590 4842850 4448240 4215200 5369030 3673140 5307390 4717330 5784490 TRUE FALSE 4743856.705 5201419.653 4553754.353 4323369.168 4947368.041 4733515.89 4511596.141 5306299.035 4819021.25 0.984402529 1.079351882 0.944954197 0.897146733 1.026633373 0.982256696 0.936205903 1.101115509 1 22.20030873 -0.800748102 7.360606686 1 0.990744406 0 0.062596645 0 0 0.057787507 0.013620646 0.158216546 0.800748102 -0.009255594 AIT(ph)PPQQPYKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AITPPQQPYKK 11 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 AIT(1)PPQQPYKK;AIT(1)PPQQPYKK 85.958 0.0086892 481180000 1099680 876910 990210 945470 1024470 811550 1331730 920910 1419550 TRUE FALSE 1030852.992 941837.3288 1013698.249 969732.3609 944012.2587 1045831.311 1132049.45 1035887.641 1182617.934 0.871670353 0.796400343 0.857164617 0.81998787 0.798239424 0.884335744 0.957240218 0.875927559 1 20.17355263 2.002052561 4.332334728 0.93679001 0.828052759 0.659294596 0.037868176 0.115234369 5.24818138 0.014559727 0.009398996 100.4737383 -2.002052561 -0.108737251 AITHLNNNFMFGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AITHLNNNFMFGQK 14 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 178.67 1.96E-06 995400000 2455700 2913900 2361500 2262210 3218800 1857280 2922900 2823200 2945600 FALSE TRUE 2302002.121 3129648.188 2417515.895 2320262.139 2966008.432 2393446.586 2484638.28 3175682.735 2453960.331 0.938076338 1.275345876 0.985148727 0.945517378 1.208661931 0.975340374 1.012501404 1.294105163 1 21.2266805 3.815514525 15.13801207 1.054319871 1.130690138 0.011706845 0.136179505 4.862803441 825.1806584 0.031913629 0.057536272 6539.047994 -3.815514525 0.076370266 AITSLLGGGS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AITSLLGGGSPK 12 0 A0A590UJS4;Q6KC79-2;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 AITSLLGGGS(1)PK;AITSLLGGGS(1)PK 239.39 3.79E-16 2494600000 3216700 2214400 2375600 2452300 2507900 1821760 3326900 2118600 2757400 TRUE FALSE 3015372.489 2378356.48 2431950.354 2515230.17 2310939.65 2347672.538 2828062.23 2383111.874 2297172.127 1.312645428 1.035340997 1.058671366 1.094924556 1.005993249 1.02198373 1.231105931 1.037411105 1 21.13142753 4.743784433 24.73104103 1.071019031 1.312645546 0.578883626 0.067024614 384.0242832 1818013.601 0.016411598 0.138394974 55435.0486 -4.743784433 0.241626515 AITVFSPDGHLFQVEYAQEAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 197.31 2.02E-22 174460000 53016 60231 59232 52353 73624 46614 74419 56645 68522 FALSE TRUE 49697.8232 64690.56591 60637.01101 53696.46661 67841.86802 60070.70508 63260.56182 63717.25294 57085.23553 0.87058979 1.133227625 1.062218811 0.940636683 1.188431078 1.052298454 1.108177294 1.116177455 1 15.80083004 2.737727379 24.99957158 1.096896871 1.033686561 0.178247335 0.085788421 163.209912 4896715.489 0.025531869 0.025365505 546.6726902 -2.737727379 -0.06321031 AITVFSPDGHLFQVEYAQEAVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AITVFSPDGHLFQVEYAQEAVKK 23 1 O14818;O14818-4;Q8TAA3-2;Q8TAA3-5;Q8TAA3;F5GY34 O14818 PSMA7;PSMA8 Proteasome subunit alpha type-7;Proteasome subunit alpha type-7-like 0 222.57 1.04E-32 222680000 447730 444030 458160 439500 599820 354380 636980 523710 730880 FALSE TRUE 419707.3785 476906.4432 469027.7716 450778.3141 552712.5568 456683.7531 541470.7624 589096.3463 608891.4063 0.689297589 0.783237271 0.7702979 0.740326287 0.907735847 0.750024961 0.889273123 0.967489999 1 19.21582543 1.506438409 0.620082223 1.012915332 0.75165242 0.725544184 0.054460604 0.355279217 0.311703725 0.04823126 0.024232777 32.09507607 -1.506438409 -0.261262913 AIVAIENPADVSVISSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AIVAIENPADVSVISSR 17 0 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 247.32 2.27E-20 107177000 68737 68652 68892 71651 71084 61444 68667 59780 70006 FALSE TRUE 64434.87387 73735.06551 70526.15077 73489.68596 65501.34938 79181.88534 58371.02082 67243.66459 58321.54634 1.104821081 1.264285159 1.209264075 1.260077803 1.123107213 1.357678085 1.000848305 1.15298151 1 15.83174135 1.687987899 10.1160059 1.059254176 1.221424644 0.479978038 0.082451618 0.091645 14.7320927 0.033962331 0.018333789 48.75149057 -1.687987899 0.162170468 AIVDALPPPCESACTVPTDVDKWFHHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AIVDALPPPCESACTVPTDVDKWFHHQK 28 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ;; 192.57 1.72E-18 3697630000 5982250 4791190 5330930 5038270 5829660 4121120 6935200 4820250 6246450 FALSE TRUE 5607831.651 5145934.693 5457382.177 5167560.538 5371822.019 5310820.443 5895331.143 5422068.823 5203877.141 1.077625682 0.988865523 1.048714647 0.993021241 1.032273029 1.020550697 1.132872853 1.041928677 1 22.31115547 AIVDCGFEHPSEVQHECIPQAILGMDVLCQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AIVDCGFEHPSEVQHECIPQAILGMDVLCQAK 32 0 O00148;O00148-2;O00148-3;K7EPJ3;A0A0G2JJL7;F6QYI9;K7EIL8;K7ENP6;K7EN69;K7EL56;F6SXL5;Q13838-2;Q13838;Q5STU3;F6WLT2;F6S4E6;A0A0A0MT12;F6TRA5;F6R6M7;F6U6E2;F6S2B7;A0A0G2JHN7 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 162.49 3.82E-14 527820000 98832 111310 101950 115990 102040 114880 162000 104140 129390 FALSE TRUE 92646.28154 119551.5082 104368.3021 118966.4998 94026.19001 148043.9911 137709.6039 117142.1082 107793.9731 0.859475524 1.109074142 0.968220199 1.103647044 0.872276875 1.373397666 1.277526006 1.086722243 1 16.71791699 2.241983137 24.99970318 1.220960823 1.003345982 0.350902931 0.130652556 83.26589143 608217.4399 0.042470482 0.034208678 174.5754365 -2.241983137 -0.217614841 AIVHDNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AIVHDNK 7 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 ; 99.384 0.010568 485850000 1599090 1346440 1346900 1409580 1355740 1142160 1679710 1319370 1362990 FALSE TRUE 1499005.811 1446131.819 1378849.104 1445752.209 1249265.649 1471883.051 1427853.079 1484096.249 1135498.164 1.320130546 1.273565968 1.214312051 1.273231658 1.100191695 1.296244325 1.257468418 1.307000131 1 20.11489394 -1.169985443 3.813850383 0.999835853 1.25143137 0.622400435 0.062422029 3273731.236 2008588.562 4277.925517 0.013527061 0.067610564 1.169985443 0.251595517 AIVHDNKDGTYAVTYIPDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AIVHDNKDGTYAVTYIPDK 19 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 87.486 0.0016276 179030000 417920 279870 299890 298080 323390 185430 398490 297010 433430 FALSE TRUE 391763.1332 300591.866 307003.5324 305729.2374 297992.2539 238960.6308 338740.1239 334092.3523 361087.7329 1.084952762 0.832462138 0.850218671 0.846689626 0.825262746 0.661779975 0.938110307 0.925238721 1 18.46198988 1.558500451 12.14608471 0.951447686 0.843864244 0.185622424 0.102663503 0.196949377 40.03726497 0.051816593 0.024085078 36.18265668 -1.558500451 -0.107583442 AIVICPTDEDLKDR ddPTM_SK-BR-3_Pertuzumab_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 ; 188.13 7.92E-07 1285870000 729770 571040 564040 480650 681330 471060 704810 595000 1227190 FALSE TRUE 684094.9984 613320.3958 577419.2952 492984.2927 627821.0902 607047.375 599130.2836 669287.0598 1022364.061 0.669130523 0.599904104 0.564788334 0.482200335 0.614087598 0.593768304 0.586024398 0.654646505 1 19.9634776 0.5925651 1.655917465 1.000020747 0.582408957 0.885105344 0.046386406 0.570174023 1.953806971 0.042716821 0.012150162 3.913497853 -0.5925651 -0.41761179 AIVQQWLEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AIVQQWLEYR 10 0 O43324;H0YAL7;D6RBD7;C9J1V9;O43324-2;D6RCQ0 O43324 EEF1E1;EEF1E1-BLOC1S5 Eukaryotic translation elongation factor 1 epsilon-1 0 160.59 1.71E-05 114480000 39374 118090 46480 40891 118170 30092 51887 94464 94477 FALSE TRUE 36909.65162 126833.5065 47582.52755 41940.33229 108889.4049 38779.0719 44107.02605 106258.0383 78708.17836 0.46894303 1.611439994 0.604543626 0.532858633 1.383457312 0.492694313 0.560386823 1.350025379 1 16.26422593 3.77968741 12.92206815 0.801104507 1.117846165 0.019584579 0.422740751 3.217072678 786.8316544 0.099659247 0.179640221 6021.260401 -3.77968741 0.316741658 AIYHDLEQSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AIYHDLEQSIR 11 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 ;;;; 240.8 1.07E-15 1140654000 1036152 1379768 1158479 1209882 1460490 1040905 1248356 1238149 1538000 FALSE TRUE 971301.0959 1481927.458 1185958.669 1240929.62 1345789.007 1341397.376 1061176.607 1392734.628 1281297.864 0.758060341 1.156583102 0.925591701 0.968494255 1.05033267 1.046905184 0.828204461 1.086971786 1 20.28917447 AKADS(ph)PVNGLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AKADSPVNGLPK 12 1 Q96S94;Q96S94-3;A0A0A0MSF3 Q96S94 CCNL2 Cyclin-L2 1 AKADS(1)PVNGLPK;AKADS(1)PVNGLPK;AKADS(1)PVNGLPK 160.03 3.69E-05 2871320000 6067200 3207950 4274600 3901800 4322600 3016620 5642500 3681600 6490300 TRUE FALSE 5687464.782 3445469.956 4375995.531 4001926.794 3983120.433 3887469.223 4796459.507 4141255.864 5407027.001 1.05186543 0.637220779 0.809316382 0.74013442 0.736656287 0.71896612 0.887078889 0.765902568 1 22.36640413 0.283346743 0.741486784 1.003478204 0.771442293 0.228147558 0.113617908 3.394358207 2.474028198 0.13387604 0.035936636 1.920201228 -0.283346743 -0.23203591 AKAEKPPLSASS(ph)PQQRPPEPETGESAGTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKAEKPPLSASSPQQRPPEPETGESAGTSR 30 3 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 AKAEKPPLS(0.01)AS(0.485)S(0.504)PQQRPPEPETGESAGTSR;AKAEKPPLSAS(0.136)S(0.863)PQQRPPEPETGESAGTSR 152.3 1.28E-08 732730000 316461 222970 281082 253041 291950 207951 300880 235891 450930 TRUE FALSE 296654.2709 239478.9308 287749.3978 259534.4605 269021.4247 267983.0779 255765.8372 265342.5106 375666.8699 0.789673763 0.637476845 0.765969589 0.690863319 0.716116981 0.713352971 0.680831497 0.706323958 1 18.51909436 -1.976352072 2.657149087 1.252582681 0.708090404 0.819605534 0.042330946 5786297.099 3008813.33 8982133.85 0.009123873 0.010559611 1.976352072 -0.544492276 AKDDATLSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKDDATLSGK 10 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 106.01 0.002256 108400000 316350 265490 311360 326230 362680 251490 421350 308550 383230 FALSE TRUE 296550.2182 285147.1558 318745.6062 334601.6141 334196.5758 324091.0804 358172.4791 347073.1467 319266.4372 0.928848709 0.893132264 0.998368663 1.048032537 1.046763884 1.015111652 1.121860732 1.087095624 1 18.28440137 3.572304123 1.243951638 1.065672211 0.904875389 0.721208425 0.035850317 0.218895691 0.678364673 0.011784634 0.026196744 3735.116251 -3.572304123 -0.160796822 AKDDDDDDDDDAEM ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKDDDDDDDDDAEM 14 1 Q8IYL3 Q8IYL3 C1orf174 UPF0688 protein C1orf174 0 ; 138 3.90E-05 419320000 1718680 985100 1226710 1166350 1284040 842720 1530650 1096970 1523840 FALSE TRUE 1611110.887 1058037.829 1255808.14 1196280.516 1183196.678 1085999.584 1301143.242 1233929.119 1269501.26 1.269089632 0.833427947 0.989213781 0.942323221 0.932016939 0.855453727 1.024924735 0.971979437 1 20.2758304 -0.63315291 7.385724973 0.999999999 0.962306947 0 0.119349338 0 0 0.101487221 0.023920768 0.232727171 0.63315291 -0.037693053 AKDPFAHLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKDPFAHLPK 10 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 91.937 0.0058935 5772100000 32985000 30688000 23884000 20623000 28548000 12173300 35278000 27004000 49541000 FALSE TRUE 30920527.73 32960171.45 24450539.76 21152221.09 26305955.24 15687534.09 29988391.4 30375508.84 41272287.05 0.749183773 0.79860298 0.592420278 0.512504215 0.637375758 0.380098493 0.726598731 0.735978329 1 25.29867005 0.874442286 1.907720458 0.997773538 0.628235807 0.498047753 0.119027213 0.451029769 3.244690421 0.115250824 0.032280569 7.489318254 -0.874442286 -0.369537731 AKDQDILDLVGVLHDPETLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKDQDILDLVGVLHDPETLLR 21 1 F5H345;A0A3B3IRR1;A0A3F2YNY7;P08397-2;P08397 F5H345 HMBS Porphobilinogen deaminase 0 100.19 0.00043646 41435000 102550 95048 106210 96942 112330 84492 115890 92381 124110 FALSE TRUE 96131.57856 102085.4528 108729.3514 99429.69584 103508.0549 108883.4688 98513.37037 103914.9712 103395.2392 0.929748597 0.987332237 1.051589533 0.961646751 1.001091111 1.053080099 0.952784394 1.005026653 1 16.65781023 4.698854601 3.263736765 1.003661149 0.922577406 0.344813248 0.031846418 0.330928898 5.847414494 0.007499666 0.064046166 49986.71542 -4.698854601 -0.081083743 AKDYPAHTEEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKDYPAHTEEDK 12 1 E5RH53;Q96DB5-3;Q96DB5-2;Q96DB5;H0YC67;H0YB03;H0YC27;H0YBD9;H0YAP5 E5RH53 RMDN1 Regulator of microtubule dynamics protein 1 0 111.12 0.00085071 182290000 251780 143120 171870 184210 180090 148280 205350 155790 209000 FALSE TRUE 236021.5392 153716.7537 175946.8376 188937.1405 165946.4578 191086.0289 174559.6739 175240.7244 174116.5498 1.355537653 0.882838271 1.010511854 1.085118794 0.953076879 1.09746046 1.002544985 1.006456449 1 17.40969381 4.750964814 24.86200881 1.002999531 1.355537888 0.769941739 0.060254131 892.183572 1788188.492 0.014397153 0.250856548 56359.19927 -4.750964814 0.352538357 AKEAAEQDVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AKEAAEQDVEK 11 1 P26373;P26373-2;J3KS98 P26373 RPL13 60S ribosomal protein L13 0 ;; 188.09 3.01E-06 1626280000 1953160 1904730 1694170 1745050 2463470 1075664 2410500 1805550 3971320 FALSE TRUE 1830915.202 2045758.191 1734356.512 1789830.937 2269999.003 1386190.735 2049067.903 2030976.892 3308481.036 0.553400543 0.61833759 0.52421534 0.54098268 0.686115162 0.418981013 0.619337962 0.613869891 1 21.65773758 0.515467288 1.61496005 0.999910886 0.564594841 0.7914371 0.069605771 1.066807928 3.111932336 0.058882803 0.016798914 3.276930932 -0.515467288 -0.435316044 AKEEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKEEAER 7 1 A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P35241-2;B9A012;A0A087WT71;Q13402-3;Q13402-4;A0A590UJ94;H7C4D8;Q13402-5;Q13402-8;Q13402-2;Q13402-7;Q13402-6;Q13402 A0A2R8Y5S7;A0A590UJ94 RDX;MYO7A Radixin;Unconventional myosin-VIIa 0 ; 76.1 0.038008 370450000 1207060 939430 1137230 998120 1128500 860250 1052280 943960 1132440 FALSE TRUE 1131512.269 1008986.375 1164205.633 1023733.449 1039872.162 1108590.21 894500.3829 1061815.484 943428.4482 1.199362041 1.069489029 1.234015823 1.085120394 1.102226845 1.175065488 0.948138022 1.125485972 1 19.84755358 1.751361192 24.99998828 1.023058876 1.142065585 0.419672294 0.06629909 3.441207809 6731.258447 0.027835844 0.015436331 56.41066143 -1.751361192 0.119006709 AKEEDREK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKEEDREK 8 2 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 53.756 0.075687 114510000 197840 140640 150060 138410 161640 103650 160260 139470 251490 FALSE TRUE 185457.5476 151053.1319 153619.4941 141961.8349 148945.4464 133572.0724 136230.5008 156883.1365 209514.6943 0.885176804 0.720966768 0.733215847 0.677574599 0.710906922 0.637530808 0.650219314 0.748793 1 17.67669191 -1.899131488 5.794880759 1.07501043 0.711834057 0.618478755 0.068674901 0.040627174 0.000707176 0.040591465 0.015180547 0.012614456 1.899131488 -0.363176373 AKEEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AKEEELR 7 1 O75525-2;O75525;H0YAQ1;H0YAQ3;E5RJZ9;E5RG12;Q9H6N6;Q5STV6;A0A0A0MRT5;Q9UBC1-2;Q9UBC1-3;Q9UBC1;Q07666-2;Q07666;Q5VWX1 O75525-2;Q07666-2 KHDRBS3;MYH16;NFKBIL1;KHDRBS1;KHDRBS2 "KH domain-containing, RNA-binding, signal transduction-associated protein 3;Putative uncharacterized protein MYH16;NF-kappa-B inhibitor-like protein 1;KH domain-containing, RNA-binding, signal transduction-associated protein 1;KH domain-containing, RNA-binding, signal transduction-associated protein 2" 0 ;; 126.41 0.0036066 2211960000 6013800 5631800 5845700 5992300 6020500 4927400 6552800 5243600 6912800 FALSE TRUE 5637406.993 6048784.332 5984362.765 6146072.563 5547674.216 6349860.39 5570268.473 5898275.003 5759009.022 0.978884904 1.05031687 1.039130646 1.067210095 0.963303616 1.102596014 0.967226905 1.024182282 1 22.45738915 1.643680895 25 0.996780222 1.034761491 0.143627929 0.041871108 1.054673283 730.7776416 0.016948006 0.009397799 44.02312772 -1.643680895 0.037981269 AKEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKEEER 6 1 A0A087WY00;G3V394;F8WE88;F8W6H6;Q9Y4I1-2;Q9Y4I1;Q9Y4I1-3;H3BMZ1;H3BRL8;H3BS72;Q9P035;H3BPZ1 A0A087WY00;H3BS72 MYO5A;HACD3 Unconventional myosin-Va;Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3 0 67.757 0.089314 158680000 475410 298110 472740 423480 375750 280840 458540 380380 434210 FALSE TRUE 445654.9367 320182.3746 483953.616 434347.2137 346240.1107 361913.9489 389786.1839 427871.2803 361737.5459 1.231984188 0.885123422 1.337858405 1.200724721 0.957158345 1.000487655 1.077538642 1.182822422 1 18.46458382 2.751708973 24.86532304 1.0471444 1.146445425 0.173612587 0.127810851 1611.708668 3047956.165 0.039628456 0.041820223 564.5585289 -2.751708973 0.099301025 AKEELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AKEELER 7 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;; 110.87 0.006116 7635200000 10078000 9292600 9421600 9087200 11335800 7484800 11182500 9168300 12089700 FALSE TRUE 9447235.97 9980633.773 9645084.801 9320392.937 10445531.99 9645540.254 9505787.938 10312982.44 10071850.97 0.937984091 0.990943353 0.957627831 0.925390275 1.037101525 0.957673052 0.943797517 1.023941128 1 23.26382551 1.230696707 24.9989226 1.011970581 0.965998879 0.279737144 0.031676466 252.2289744 801789.1755 0.026303448 0.007060993 17.00970208 -1.230696707 -0.045971702 AKEGTSDPPS(ph)PLLLPSPGGWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKEGTSDPPSPLLLPSPGGWK 21 1 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 AKEGTSDPPS(0.999)PLLLPSPGGWK;AKEGT(0.007)S(0.007)DPPS(0.985)PLLLPSPGGWK 137.26 2.17E-06 721190000 2474400 1946090 2153300 2322000 2688300 1730100 3037100 1947750 2969600 TRUE FALSE 2319531.721 2090180.529 2204377.293 2381586.451 2477171.762 2229551.784 2581715.05 2190930.875 2473954.576 0.937580562 0.844874255 0.891033859 0.962663775 1.001300423 0.901209669 1.043557984 0.885598667 1 21.23838758 3.249308471 4.228095101 0.97093736 0.87972631 0.311529133 0.051376632 0.185538833 7.641129934 0.013301575 0.01740201 1775.450103 -3.249308471 -0.09121105 AKELATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKELATK 7 1 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 ; 77.677 0.034107 648140000 1159870 1470140 1385360 1649360 2067090 1241090 2033660 1628280 2584670 FALSE TRUE 1087275.807 1578990.695 1418221.393 1691685.37 1904749.09 1599372.536 1728731.563 1831574.342 2153271.879 0.504941256 0.73329834 0.658635543 0.785634822 0.884583646 0.742763861 0.802839427 0.850600595 1 21.03809906 5.920888935 0.116649 1.087479062 9.43E-16 0.745139824 0.066989504 31.08782464 0.415922687 0.59600269 5.345211855 833468.0083 -5.920888935 -1.087479062 AKEPAGENGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AKEPAGENGGR 11 1 E7EMD0;P16435;H0Y4R2 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 ;;; 179.35 6.51E-06 973040000 1155050 1061430 1003500 971410 1375540 948390 1409810 1209110 1416950 FALSE TRUE 1082757.482 1140019.382 1027303.494 996338.0252 1267510.637 1222174.797 1198422.079 1360070.045 1180451.891 0.917239822 0.965748278 0.870262907 0.84403103 1.073750355 1.035344859 1.015223143 1.152160503 1 20.17090782 2.729043577 24.99651244 1.051139546 0.90554887 0.694623517 0.051274201 400.1546246 1051004.556 0.016135692 0.015393825 535.8504217 -2.729043577 -0.145590676 AKESWEMNSEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKESWEMNSEEK 12 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 133.48 0.00014813 982810000 847640 393430 559090 540250 492670 409450 682290 424060 479060 FALSE TRUE 794587.7255 422559.9666 572351.8788 554113.7296 453977.6855 527651.5681 579986.9486 477004.8245 399101.7912 1.990940014 1.058777425 1.4341 1.388402012 1.137498492 1.32209772 1.453230633 1.1951959 1 18.60639723 7.999999999 0.030926595 8.35E-09 3.275334075 0.288053459 0.235990147 2235.195861 5.296209227 176.2196468 439.6924516 99999999.69 -7.999999999 3.275334067 AKEVELVS(ph)E ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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;AKEVELVS(1)E 118.77 0.0024626 4468010000 9526200 9114700 8949100 8801600 10005600 6873500 10730900 7568300 11539900 TRUE FALSE 8929972.147 9789561.872 9161376.878 9027463.957 9219800.537 8857767.868 9121901.166 8513218.915 9613816.139 0.928868622 1.018280538 0.95293864 0.939009424 0.959015692 0.921358152 0.948832496 0.885519214 1 23.19667778 3.574786189 3.594480661 0.939987866 0.981498933 0.102797404 0.035717737 0.334356798 8.09802922 0.008726559 0.013975987 3756.524183 -3.574786189 0.041511067 AKFAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKFAGR 6 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 85.061 0.05029 1572970000 2797500 3524300 3118700 3017400 3787100 2992800 3462800 2718400 4021100 FALSE TRUE 2622409.469 3785242.839 3192677.037 3094831.592 3489676.442 3856772.776 2943585.287 3057798.224 3349952.433 0.782819912 1.12993928 0.953051454 0.923843444 1.041709252 1.151291803 0.878694652 0.91278855 1 21.67570918 1.623029153 25 0.921805728 1.006880477 0.071239469 0.108147462 1.752126348 2882.041343 0.04663553 0.025734508 41.9787162 -1.623029153 0.085074748 AKFEELNMDLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKFEELNMDLFR 12 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 192.15 4.06E-06 3133700000 4417200 6296800 3777700 3965300 6247800 2394000 4036700 4945400 3951200 FALSE TRUE 4140735.337 6763021.624 3867308.828 4067056.311 5757122.99 3085108.937 3431434.31 5562844.076 3291719.194 1.257924839 2.054556062 1.174859883 1.235541695 1.74897148 0.937233328 1.042444421 1.689950979 1 21.65040984 3.80144362 5.400650192 1.249674426 1.694387347 0.196146171 0.328861807 0.269175458 14.01983955 0.079444502 0.144931186 6330.581729 -3.80144362 0.44471292 AKFENLCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKFENLCK 8 1 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 0 ; 121.64 0.0012993 5192700000 4444600 8797300 3340300 3332600 10566000 2462220 4480200 8586900 9398700 FALSE TRUE 4166420.42 9448661.246 3419533.493 3418120.158 9736188.981 3173022.943 3808435.602 9658993.367 7829996.252 0.532110142 1.206726152 0.436722239 0.436541736 1.243447464 0.405239395 0.486390476 1.233588505 1 22.90058019 1.231040377 24.99866852 1.116794391 0.693415995 0.253371933 0.312179611 272.9695725 907363.6951 0.269963777 0.072741432 17.02316767 -1.231040377 -0.423378397 AKGPSES(ph)SKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKGPSESSKER 11 2 Q8TEA8;A0A087WZV9 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1;D-tyrosyl-tRNA(Tyr) deacylase 1 AKGPS(0.007)ES(0.497)S(0.497)KER 90.412 0.0060038 258790000 701090 400010 476320 444530 488980 336990 634590 401300 706890 TRUE FALSE 657210.0284 429627.1566 487618.5353 455937.3924 450577.4833 434273.5424 539439.1207 451403.1884 588905.4923 1.115985565 0.72953498 0.82800813 0.774211479 0.765110003 0.737424847 0.916002869 0.766512105 1 19.1676766 -1.953326464 8.819330867 1.069911612 0.819624033 0.173902442 0.115430128 0.064914359 0.000343539 0.045723564 0.023371354 0.011134572 1.953326464 -0.250287579 AKGPSESS(ph)KER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKGPSESSKER 11 2 Q8TEA8;A0A087WZV9 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1;D-tyrosyl-tRNA(Tyr) deacylase 1 AKGPSES(0.354)S(0.646)KER;AKGPSES(0.018)S(0.982)KER 115.04 0.00092695 511860000 1134660 613920 760460 702270 806560 510960 1017470 617730 1027980 TRUE FALSE 1063643.656 659375.2756 778498.4703 720291.4371 743216.0311 658465.8573 864909.8192 694854.9503 856403.497 1.241988922 0.769935291 0.909032335 0.841065502 0.867833952 0.768873387 1.00993261 0.811363981 1 19.70793116 -0.288666891 8.059174216 0.999999997 0.891222829 0.040388826 0.140065988 0 0 0.118575139 0.027948428 0.514438081 0.288666891 -0.108777168 AKGS(ph)ETPGATPGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKGSETPGATPGSK 14 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 AKGS(0.702)ET(0.298)PGATPGSK 131.51 3.38E-05 716450000 361820 299440 315590 347310 389430 217550 426750 294200 477920 TRUE FALSE 339174.3321 321610.8492 323075.9438 356222.5626 358845.7387 280353.1534 362762.7993 330931.5176 398152.0645 0.851871338 0.807758838 0.811438575 0.894689729 0.901278106 0.704135878 0.911116208 0.831168659 1 18.60296001 -4.999993707 0.291628111 2.294630609 0.827120146 0.411203965 0.060159308 236.6058053 2.223535446 186.3518701 0.058584346 1.00E-05 4.999993707 -1.467510464 AKGSET(ph)PGATPGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKGSETPGATPGSK 14 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 AKGS(0.014)ET(0.986)PGATPGSK;AKGSET(0.999)PGATPGSK 201.57 5.24E-07 352190000 1115976 809875 907782 989979 1185185 692549 1284067 865082 1398284 TRUE FALSE 1046129.054 869838.9877 929315.0177 1015383.537 1092105.351 892476.6537 1091533.074 973089.392 1164901.367 0.898040885 0.746706127 0.797762835 0.871647648 0.937508858 0.766139245 0.937017592 0.835340587 1 20.15177638 -0.490631905 0.181439105 1.117885192 0.77005001 0.338835938 0.065818311 14.9832212 0.758595276 1.223107319 0.266159026 0.323123165 0.490631905 -0.347835183 AKHDELTYF ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKHDELTYF 9 1 P04080;A0A1W2PQG6 P04080 CSTB Cystatin-B 0 92.062 0.0080506 0 282870 379900 292710 292010 431240 223360 401330 338620 558300 FALSE TRUE 265165.6716 408028.1913 299653.2194 299503.471 397372.1499 287840.4061 341154.2923 380897.4524 465116.1232 0.570106385 0.877260905 0.644254638 0.643932678 0.854350409 0.61885708 0.733481974 0.818929797 1 18.82723143 0.91994522 2.435623839 0.999306529 0.715673405 0.481615349 0.09795477 0.315837994 4.109850923 0.085018157 0.022956795 8.316588621 -0.91994522 -0.283633124 AKIDDPTDSKPEDWDKPEHIPDPDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKIDDPTDSKPEDWDKPEHIPDPDAK 26 3 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 100.29 0.0029054 694960000 1093000 324580 527290 520130 537160 273870 714000 331220 622310 FALSE TRUE 1024591.081 348612.2409 539797.5678 533477.4164 494973.6204 352931.8231 606942.3285 372573.5461 518442.4407 1.976287049 0.672422266 1.041190932 1.029000279 0.954732062 0.680754111 1.170703401 0.718640136 1 18.9838243 4.746760877 24.998669 0.917716731 1.976287571 0.798427552 0.168564223 430.0990067 1311136.705 0.037134077 0.417800413 55816.27846 -4.746760877 1.058570841 AKKDDTDDEIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKKDDTDDEIAK 12 2 P27824;P27824-2;H0Y9Q7;D6RDP7;D6RAU8;D6RB85;D6RAQ8 P27824 CANX Calnexin 0 91.032 0.0047953 249500000 376420 150970 177700 196400 255040 117780 306650 195290 260980 FALSE TRUE 352860.5441 162147.9759 181915.1279 201439.9565 235010.1872 151781.174 260670.6793 219672.3864 217420.752 1.622938661 0.745779666 0.83669625 0.926498297 1.080900443 0.698098836 1.19892272 1.010356115 1 17.73013012 1.677753418 21.35969409 1.078380752 0.941838961 0.004570528 0.2619747 0.706932582 235.4449811 0.112376917 0.062283625 47.61605574 -1.677753418 -0.136541791 AKLEQLFQDEVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKLEQLFQDEVAK 13 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 129.93 0.00013495 256690000 842860 701370 749740 773610 886770 575370 1039300 773060 1015500 FALSE TRUE 790106.8971 753300.1646 767524.1869 793462.1423 817126.6613 741469.9786 883466.6134 869578.2427 846006.4896 0.933925338 0.890418896 0.907232032 0.937891319 0.965863349 0.876435332 1.044278766 1.027862379 1 19.6903092 1.707799146 7.881749034 1.025913802 0.916713624 0.767706305 0.027250395 0.052575518 7.413014852 0.013054177 0.006881095 51.02689543 -1.707799146 -0.109200178 AKLNWLSVDFNNWKDWEDDS(ph)DEDMSNFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AKLNWLSVDFNNWKDWEDDSDEDMSNFDR 29 2 A0A087WYT3;Q15185-4;Q15185;B4DDC6 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 1 AKLNWLSVDFNNWKDWEDDS(0.999)DEDMS(0.001)NFDR;AKLNWLSVDFNNWKDWEDDS(0.999)DEDMS(0.001)NFDR;AKLNWLSVDFNNWKDWEDDS(0.971)DEDMS(0.029)NFDR;AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR;AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR;AKLNWLSVDFNNWKDWEDDS(0.994)DEDMS(0.005)NFDR 200.03 1.84E-25 4905269000 740536 847179 606697 697690 1214233 382929.1 845834 653294 1711370 TRUE FALSE 694187.1737 909905.0146 621088.1393 715593.9066 1118872.038 493474.5148 719009.044 734859.194 1425731.291 0.486899024 0.638202318 0.435627767 0.501913587 0.784770626 0.346120281 0.504308946 0.515426153 1 20.44327067 -1.418263805 2.976599218 1.008766802 0.525775925 0.618634193 0.11679496 13358609.39 16079224.53 994851.0529 0.028218801 0.038171234 1.418263805 -0.482990877 AKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE 36 2 P62942;Q5W0X3;Q1JUQ5;Q5VVH2 P62942 FKBP1A;FKBP12-Exip2;FKBP1C Peptidyl-prolyl cis-trans isomerase FKBP1A;Peptidyl-prolyl cis-trans isomerase 0 127.77 1.04E-08 79436000 204070 260830 238030 229350 455930 249850 308250 238310 192600 FALSE TRUE 191297.623 280142.1246 243676.184 235235.5093 420123.0969 321977.639 262030.7742 268063.5281 160453.8158 1.192228568 1.745936195 1.518668676 1.466063666 2.618342823 2.006668632 1.63306041 1.670658481 1 17.29179857 AKLTPGCEAEAETEAICFFVQQFTDMEHNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 355.49 1.46E-120 1105500000 733148 946990 912283 993530 1356340 822700 1376780 826035 2115750 FALSE TRUE 687261.5754 1017106.125 933922.7836 1019025.662 1249818.528 1060200.135 1170344.62 929167.2881 1762617.657 0.389909617 0.577042968 0.529849897 0.578131995 0.709069561 0.601491838 0.663980992 0.527151923 1 20.74928813 -5 0.157262524 2.522970096 0.461075272 0.758913583 0.078132922 62.00450077 0.565847734 29.5610536 0.320090761 1.00E-05 5 -2.061894824 AKNS(ph)PPQAPSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AKNSPPQAPSTR 12 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 AKNS(1)PPQAPSTR;AKNS(1)PPQAPSTR;AKNS(1)PPQAPSTR;AKNS(1)PPQAPSTR;AKNS(1)PPQAPSTR 161.24 3.99E-05 2509990000 1507220 1278200 1413570 1456650 1388060 1251080 1946550 1303300 1980820 TRUE FALSE 1412885.791 1372839.258 1447100.548 1494030.105 1279047.367 1612246.486 1654682.898 1466019.874 1650208.345 0.856186308 0.831918746 0.876919906 0.905358471 0.775082353 0.976995717 1.002711508 0.888384717 1 20.65421675 2.213806873 24.99989936 0.971396673 0.853103262 0.623537343 0.045417208 139.8532633 141243.1078 0.015682375 0.011587206 163.6088807 -2.213806873 -0.118293411 AKNWEDEDFYDS(ph)DDDTFLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AKNWEDEDFYDSDDDTFLDR 20 1 A0A087X0M4;A0A087WWF4;Q9BWU0 A0A087X0M4 SLC4A1AP Kanadaptin 1 AKNWEDEDFYDS(1)DDDTFLDR;AKNWEDEDFYDS(1)DDDTFLDR;AKNWEDEDFYDS(1)DDDTFLDR;AKNWEDEDFYDS(1)DDDTFLDR 298.55 6.11E-55 2102060000 2489430 2251810 2303960 2257910 2785900 1762560 2827070 2075150 4021980 TRUE FALSE 2333621.02 2418536.355 2358611.019 2315851.793 2567106.652 2271382.459 2403177.099 2334237.045 3350685.555 0.696460764 0.721803439 0.703918939 0.691157602 0.766143707 0.67788589 0.717219524 0.696644614 1 21.67602487 -1.503935576 2.93324784 1.010168316 0.709945819 0.936255458 0.023869183 13447636.05 15432810.91 1103140.962 0.005289079 0.031337506 1.503935576 -0.300222497 AKPAMPQDSVPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 17 AKPAMPQDSVPSPR 14 1 P53396 P53396 ACLY ATP-citrate synthase 1 AKPAMPQDS(0.017)VPS(0.983)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDS(0.006)VPS(0.994)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDS(0.001)VPS(0.999)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDS(0.075)VPS(0.925)PR;AKPAMPQDS(0.001)VPS(0.999)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDS(0.044)VPS(0.956)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR 168.09 2.15E-06 60291830000 20152340 20372010 20641290 21432810 21833440 16344040 23017580 17546280 24524060 TRUE FALSE 18891041.01 21880374.82 21130911.15 21982812.19 20118729.69 21062299.02 19566307.56 19736971.68 20430835.95 0.924633777 1.070948583 1.034265617 1.075962444 0.984723765 1.030907354 0.957685119 0.966038381 1 24.2842449 1.980232326 1.822154715 0.971448451 1.031964054 0.130585245 0.045641301 0.48392027 2.989841569 0.025902376 0.012849253 95.55035959 -1.980232326 0.060515602 AKPAMPQDSVPSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKPAMPQDSVPSPR 14 1 P53396 P53396 ACLY ATP-citrate synthase 0 ; 126.48 7.76E-05 168780000 322960 283360 321000 309290 341300 279360 377360 307380 354800 FALSE TRUE 302746.5101 304340.2692 328614.2716 317226.905 314495.6747 360006.697 320778.3712 345757.0696 295581.5879 1.024240083 1.029632026 1.111754876 1.073229585 1.063989394 1.217960495 1.085244766 1.169751716 1 18.17319688 4.12742039 0.820684184 1.115914055 1.00061466 0.20635395 0.059485145 1.60447841 1.463247859 0.02068774 0.143588753 13409.74099 -4.12742039 -0.115299395 AKPDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKPDFK 6 1 P13489;E9PMJ3;E9PLZ3;E9PIM9 P13489 RNH1 Ribonuclease inhibitor 0 66.258 0.092919 1941600000 2477600 2176500 2380600 2364400 2566800 1715900 2832300 2344300 3435300 FALSE TRUE 2322531.439 2337650.325 2437068.956 2425074.507 2365213.882 2211252.475 2407622.909 2636991.015 2861926.237 0.811527358 0.816810124 0.851548487 0.847357446 0.826441245 0.772644817 0.841259596 0.921404256 1 21.44855506 1.066305194 2.578049565 0.998401424 0.823912226 0.883157456 0.021808861 0.082529077 1.131313727 0.0213145 0.005785024 11.64944389 -1.066305194 -0.174489199 AKPPADPAAAAS(ph)PCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AKPPADPAAAASPCR 15 1 Q9GZT9-2;Q9GZT9 Q9GZT9-2 EGLN1 Egl nine homolog 1 1 AKPPADPAAAAS(1)PCR;AKPPADPAAAAS(1)PCR;AKPPADPAAAAS(1)PCR;AKPPADPAAAAS(1)PCR;AKPPADPAAAAS(1)PCR 131.56 3.20E-05 5856260000 5627780 5288670 5383680 5416480 6660620 5260280 8033670 6483650 7865650 TRUE FALSE 5275547.296 5680248.63 5511383.432 5555476.047 6137521.773 6778837.442 6829095.764 7293147.975 6552822.201 0.805080183 0.866840036 0.841070193 0.84779899 0.936622662 1.034491282 1.042161004 1.112978157 1 22.64368496 2.418554485 1.907583085 1.056260028 0.842811781 0.907829129 0.031135869 0.0848063 0.629460555 0.012420766 0.00951084 262.1527906 -2.418554485 -0.213448247 AKPS(ph)PHPIKDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 56.599 0.061556 721010000 1112700 699640 806190 773110 956910 550220 1117100 774880 1447000 TRUE FALSE 1043058.093 751442.0736 825313.2075 792949.3115 881758.1486 709059.5819 949601.2256 871625.4737 1205486.352 0.865259147 0.623351789 0.684630901 0.657783732 0.731454277 0.588193786 0.787732872 0.723048811 1 20.20118389 0.414366619 0.916282975 1.001270375 0.686588042 0.572322797 0.079321328 1.349770933 1.537074738 0.071323401 0.022270464 2.596370219 -0.414366619 -0.314682334 AKPVATAPIPGTPWCVVWTGDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKPVATAPIPGTPWCVVWTGDER 23 1 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 ; 157.88 3.79E-14 363520000 277300 260503 278400 254860 328120 241589 321640 265320 352540 FALSE TRUE 259944.288 279790.9132 285003.7795 261400.1391 302350.7788 311331.8224 273413.068 298445.786 293698.7965 0.885071002 0.95264576 0.970394782 0.890027954 1.029458692 1.060037787 0.930930161 1.016162782 1 18.16397783 2.728103962 24.99412904 1.001508353 0.936863339 0.480030463 0.041706207 772.3781025 1846181.407 0.013490806 0.012843017 534.6923393 -2.728103962 -0.064645014 AKPVNSKPDSAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKPVNSKPDSAYR 13 2 O95573;C9JC11;F5H062 O95573 ACSL3 Long-chain-fatty-acid--CoA ligase 3 0 85.42 0.005227 251600000 323510 302260 255050 244150 368880 224850 390190 313930 369680 FALSE TRUE 303262.0866 324639.6449 261099.9064 250415.3023 339909.6528 289760.5449 331684.6318 353124.8515 307978.0198 0.984687436 1.054100046 0.847787471 0.813094722 1.103681532 0.940848133 1.076975013 1.146591084 1 18.23246786 2.031336706 1.442636518 1.079250347 0.944000176 0.250296784 0.092542915 0.573661259 2.233479097 0.061660879 0.030094441 107.4822394 -2.031336706 -0.135250172 AKS(ph)DVS(ph)KDVHHS(ph)T(ph)SLPNLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKSDVSKDVHHSTSLPNLEK 20 2 Q9UKL3;A0A087WTW5;A0A096LP21 Q9UKL3 CASP8AP2 CASP8-associated protein 2 4 AKS(0.8)DVS(0.8)KDVHHS(0.8)T(0.8)S(0.8)LPNLEK 54.974 0.070502 45895000 48978 33285 39264 40438 36422 25012 38904 33133 31169 TRUE FALSE 45912.55441 35749.45603 40195.36062 41475.70754 33561.56304 32232.55836 33070.70637 37269.72798 25966.69254 1.768132554 1.376742763 1.54795843 1.597265708 1.292485094 1.241303963 1.273581775 1.435289763 1 14.66437464 2.680712276 6.091329346 1.263263269 1.535621423 0.55319536 0.142727482 0.186873128 14.96816739 0.042561101 0.040296126 479.4157261 -2.680712276 0.272358154 AKS(ph)ESLELPQAAPPQIYHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKSESLELPQAAPPQIYHEK 20 1 H0YGT9;Q15040;B0QY58;B0QY55;B0QY57;B0QY56 H0YGT9 JOSD1 Josephin-1 1 AKS(0.5)ES(0.5)LELPQAAPPQIYHEK 49.618 0.088071 66062000 79157 76067 70743 67887 109780 51839 79376 73690 136600 TRUE FALSE 74202.70467 81699.07983 72421.05737 69629.09535 101158.3216 66804.07776 67474.30569 82890.35871 113800.5775 0.652041547 0.717914457 0.636385675 0.611851863 0.888908684 0.587027581 0.592917076 0.728382584 1 16.79614835 0.970249584 21.97154059 1.000000003 0.668118164 0.5852227 0.086852568 478.0877364 353082.8467 0.079529264 0.019882316 9.337907844 -0.970249584 -0.331881839 AKS(ph)LDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AKSLDRR 7 2 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 AKS(1)LDRR;AKS(1)LDRR;AKS(1)LDRR;AKS(1)LDRR;AKS(1)LDRR 96.143 0.010197 4587070000 7759020 7190440 7017990 7119100 8423970 4863180 9075200 6782750 11932000 TRUE FALSE 7273396.788 7722827.659 7184460.037 7301788.159 7762385.377 6267101.119 7714458.01 7629591.268 9940472.116 0.731695306 0.776907532 0.722748372 0.734551445 0.780886993 0.630463125 0.776065555 0.767528059 1 23.24488294 0.560405809 1.696408183 0.999896193 0.736577888 0.788606487 0.042672775 0.960114215 3.222211029 0.037147773 0.010512923 3.634174767 -0.560405809 -0.263318305 AKS(ph)PAPGLASGDRPPSVSSVHSEGDCNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKSPAPGLASGDRPPSVSSVHSEGDCNR 28 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 AKS(0.988)PAPGLAS(0.012)GDRPPSVSSVHSEGDCNR;AKS(1)PAPGLASGDRPPSVSSVHSEGDCNR 126.67 1.64E-05 706150000 91044 103224 102838 101279 107975 86512 119372 103791 91433 TRUE FALSE 85345.71856 110866.8124 105277.3659 103877.9906 99495.07905 111486.61 101473.2768 116749.5348 76172.24162 1.120430707 1.455475249 1.382096203 1.363725005 1.30618552 1.463612041 1.332155581 1.532704465 1 16.21697773 -1.617464179 2.975473753 0.972591477 1.377155173 0.521453792 0.111044685 64783150.97 68929943.57 13840625.5 0.023300458 0.024128805 1.617464179 0.404563695 AKS(ph)PAPGLASGDRPPSVSSVHSEGDCNRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKSPAPGLASGDRPPSVSSVHSEGDCNRR 29 3 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 AKS(0.594)PAPGLAS(0.402)GDRPPS(0.001)VS(0.001)S(0.001)VHSEGDCNRR 57.573 0.03449 139460000 16823 13303 14706 14133 11628 10428 16475 15086 14876 TRUE FALSE 15770.07846 14287.96796 15054.83326 14495.67671 10714.78379 13438.39432 14004.7267 16969.52031 12393.0995 1.272488651 1.152897059 1.21477547 1.169657091 0.864576597 1.084344906 1.130042303 1.369271691 1 13.59724943 2.983234577 24.86697377 1.091528172 1.199572418 0.166027627 0.127491753 1356.546502 2012074.185 0.037428118 0.040666618 962.131818 -2.983234577 0.108044246 AKS(ph)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 41 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(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(0.999)PQPPVEEEDEHFDDT(0.001)VVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(0.999)PQPPVEEEDEHFDDT(0.001)VVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK 318.56 4.75E-90 1.40852E+11 7608141.6 4626399.6 5664322.1 5679913.4 6139457.4 5292961.5 8711672.8 5242823 7197457 TRUE FALSE 7131961.598 4968943.04 5798682.495 5825669.594 5657289.181 6820953.561 7405438.339 5897400.992 5996154.929 1.189422502 0.828688234 0.967066823 0.971567557 0.943486159 1.13755459 1.235031187 0.983530456 1 22.51560623 2.238685497 24.99999952 1.123193161 0.957251193 0.139160545 0.114658412 3.745412823 749962.9159 0.038740749 0.030505916 173.2548883 -2.238685497 -0.165941968 AKS(ph)PT(ph)PDGSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AKSPTPDGSER 11 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 2 AKS(0.978)PT(0.621)PDGS(0.401)ER;AKS(0.966)PT(0.981)PDGS(0.053)ER;AKS(0.904)PT(0.966)PDGS(0.131)ER;AKS(0.997)PT(0.933)PDGS(0.07)ER;AKS(0.999)PT(0.977)PDGS(0.024)ER 154.48 0.00080206 3311410000 6494540 4133970 4648980 4871920 4993540 3680590 6072090 4071760 5676260 TRUE FALSE 6088058.334 4440053.44 4759256.001 4996941.715 4601367.511 4743116.584 5161636.475 4580128.199 4728855.536 1.287427431 0.938927698 1.006428715 1.056691556 0.973040406 1.00301575 1.091519171 0.968548979 1 22.17305964 4.747356505 24.96391318 1.008079761 1.287427577 0.806742984 0.043450289 523.5507495 1485875.215 0.010819962 0.13038753 55892.88219 -4.747356505 0.279347816 AKS(ph)PTPDGS(ph)ER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKSPTPDGSER 11 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 2 AKS(0.964)PT(0.043)PDGS(0.993)ER 95.264 0.094305 544200000 805480 500150 586990 593990 633300 473670 796470 544030 791160 TRUE FALSE 755066.4446 537181.6264 600913.68 609232.789 583563.1726 610410.8396 677046.7176 611953.3431 659110.2849 1.145584376 0.815010232 0.911704299 0.924326024 0.885380165 0.926113359 1.027213098 0.92845364 1 19.33016036 1.889863148 7.336833852 0.986368646 0.915154121 0.040514928 0.087765586 0.544806174 32.29366256 0.03479083 0.021592207 77.60025495 -1.889863148 -0.071214525 AKS(ph)PTPDGSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKSPTPDGSER 11 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 AKS(0.997)PT(0.003)PDGSER;AKS(0.852)PT(0.148)PDGSER 143.93 2.24E-05 680820000 524270 434200 439720 454970 474530 408545 532030 375641 542800 TRUE FALSE 491456.8765 466348.6198 450150.3661 466645.3005 437262.328 526485.3093 452257.0406 422540.6057 452203.1734 1.086805457 1.031281175 0.995460431 1.031937253 0.966959884 1.164267171 1.000119122 0.934404336 1 18.78661159 2.522900931 0.006191225 5.42E-07 2.048621831 0.085729377 0.061286979 18612.63029 53.19211107 8677.392971 8919.700943 333.3503617 -2.522900931 2.048621289 AKS(ph)PTPESSTIASYVTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKSPTPESSTIASYVTLR 18 1 Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;A0JP02;B4DJX4;Q9HAU0-5;Q9HAU0-8;H0YGJ6 Q9HAU0 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 AKS(0.648)PT(0.351)PES(0.001)STIASYVTLR 72.302 0.013377 317930000 76477 88756 101370 104240 126770 104370 122080 74259 135480 TRUE FALSE 71690.44109 95327.58659 103774.5443 106914.9749 116813.9956 134499.9247 103775.2373 83530.39961 112867.5128 0.635173393 0.844597212 0.919436796 0.947260839 1.034965622 1.191661988 0.919442936 0.740074779 1 16.78427076 5.36156365 0.776437113 0.979396956 9.23E-09 0.469794273 0.112044124 5.552552673 1.281674325 0.039269469 5.897620668 229913.0644 -5.36156365 -0.979396947 AKSEDS(ph)DVELS(ph)D ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKSEDSDVELSD 12 1 Q5VZL5-2;Q5VZL5-4;Q5VZL5;H7C1I7;Q5VZL5-3 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 2 AKS(0.004)EDS(0.996)DVELS(1)D;AKSEDS(1)DVELS(1)D 166.64 0.00061401 610580000 2074900 1489760 1644550 1694720 1853500 1174600 2117100 1510470 2070800 TRUE FALSE 1945035.713 1600063.38 1683559.503 1738209.384 1707933.587 1513687.952 1799660.509 1699055.504 1725170.102 1.127445758 0.927481515 0.975880292 1.007558259 0.990008802 0.87741374 1.043178587 0.984862596 1 20.71830719 AKT(ph)PTPEPFDSETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKTPTPEPFDSETR 14 1 Q9NSY0;H0YCB1;Q9NSY0-2;Q9NSY0-4 Q9NSY0 NRBP2 Nuclear receptor-binding protein 2 1 AKT(0.994)PT(0.006)PEPFDSETR;AKT(0.958)PT(0.042)PEPFDSETR 98.035 0.0044259 300050000 169976 170724 154383 167442 156171 115005 167843 129037 145777 TRUE FALSE 159337.5056 183364.5826 158045.0377 171738.8452 143905.9596 148205.0765 142676.5003 145147.5535 121445.8769 1.312004241 1.509846091 1.301361904 1.414118367 1.18493903 1.220338477 1.174815514 1.195162464 1 16.88995399 2.035727639 0.353962524 0.998853386 1.465802625 0.736153169 0.071988783 0.601570613 0.202792375 0.083865458 0.097871076 108.5744503 -2.035727639 0.466949239 AKT(ph)PVTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.985)PVT(0.015)LK;AKT(0.941)PVT(0.059)LK;AKT(1)PVTLK 105.46 0.0070869 6574880000 14614550 11128770 8811230 9263990 13295720 4772310 17560040 11115980 14772810 TRUE FALSE 13699851.4 11952755.71 9020236.537 9501719.667 12251527.78 6149998.425 14927075.02 12503834.57 12307132.57 1.113163551 0.97120557 0.732927551 0.772049834 0.995481905 0.499710098 1.212880005 1.015982764 1 23.55299133 1.630031562 24.99999993 1.085798332 0.85161372 0.27435473 0.175136717 1.022510524 1150.084014 0.075584378 0.041870957 42.6610521 -1.630031562 -0.234184612 AKT(ph)QTPPVS(ph)PAPQPTEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.663)QT(0.337)PPVS(1)PAPQPTEER 88.504 0.0070225 1542800000 824440 719990 791320 1090800 1016700 578380 565170 443300 508740 TRUE FALSE 772839.7721 773298.8087 810090.4841 1118791.775 936852.4832 745348.9168 480428.0053 498646.9808 423828.0074 1.823474991 1.824558064 1.911366096 2.639730634 2.210454398 1.758611757 1.133544732 1.176531452 1 18.6931194 1.83648106 2.935381228 1.099259649 2.04696471 0.774121126 0.240462472 0.135090287 2.092621687 0.144038335 0.072812078 68.624795 -1.83648106 0.947705061 AKT(ph)QTPPVS(ph)PAPQPTEERLPSSPVYEDAASFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.5)QT(0.5)PPVS(0.999)PAPQPT(0.001)EERLPSSPVYEDAASFK;AKT(0.454)QT(0.546)PPVS(0.874)PAPQPT(0.003)EERLPS(0.066)S(0.057)PVYEDAASFK 172.78 3.48E-14 2147110000 269610 228960 233020 365710 366050 175700 214230 157171 321980 TRUE FALSE 252735.5914 245912.4366 238547.3444 375094.7377 337301.9096 226421.7377 182108.2003 176794.1453 268239.4579 0.942201395 0.91676459 0.889307436 1.398357798 1.25746567 0.844103025 0.678901612 0.659090749 1 18.03316195 2.014646982 22.20723812 0.748115412 1.047101641 0.37156002 0.181563126 69.40003782 105220.3266 0.072173885 0.053264261 103.430109 -2.014646982 0.298986228 AKT(ph)QTPPVSPAPQPTEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKT(0.613)QT(0.386)PPVSPAPQPTEER 73.546 0.032376 4393000000 459140 336000 431070 402070 393410 269470 357830 302440 321080 TRUE FALSE 430403.247 360877.7896 441295.184 412387.7969 362513.1655 347261.6145 304176.7134 340200.2998 267489.6737 1.609046215 1.349127929 1.649765308 1.541696138 1.35524172 1.298224375 1.137153106 1.271825918 1 18.02912367 2.206747867 1.367943344 1.137431052 1.524867543 0.737534154 0.103863176 0.22265117 0.807098359 0.061332693 0.034687335 160.9710835 -2.206747867 0.387436491 AKT(ph)QTPPVSPAPQPTEERLPSSPVYEDAASFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKT(0.55)QT(0.45)PPVSPAPQPTEERLPSSPVYEDAASFK 100.28 0.0011871 1236900000 47270 45982 42301 48511 55816 30342 52451 34635 80922 TRUE FALSE 44311.45508 49386.55512 43304.3997 49755.87439 51432.43651 39101.24284 44586.45948 38959.25599 67415.59542 0.657287899 0.7325687 0.642349881 0.738046947 0.762916002 0.580002929 0.661367139 0.577896787 1 16.04079475 -1.579715219 3.480035199 1.011284063 0.672401383 0.736248691 0.062222004 7592609.701 3480304.167 648910.1352 0.014420331 0.026319933 1.579715219 -0.33888268 AKTQT(ph)PPVS(ph)PAPQPTEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.001)QT(0.999)PPVS(1)PAPQPTEER;AKT(0.004)QT(0.996)PPVS(1)PAPQPTEER;AKT(0.01)QT(0.99)PPVS(1)PAPQPTEER;AKT(0.011)QT(0.989)PPVS(1)PAPQPTEER;AKT(0.027)QT(0.973)PPVS(1)PAPQPTEER 161.68 8.59E-11 7397330000 7173550 5859970 6905160 9147140 8605880 5118380 5481840 4272970 4353720 TRUE FALSE 6724570.311 6293848.276 7068953.656 9381871.098 7930008.899 6595973.216 4659888.983 4806459.71 3627056.006 1.854002337 1.735249819 1.948950787 2.5866353 2.186348622 1.818547385 1.284757935 1.325168319 1 21.79036759 1.777455883 2.692215626 1.191638809 2.02601433 0.727638825 0.240109565 0.156809562 2.236398479 0.155836921 0.073264311 59.90400832 -1.777455883 0.834375521 AKTQT(ph)PPVS(ph)PAPQPTEERLPSSPVYEDAASFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.138)QT(0.862)PPVS(0.892)PAPQPT(0.108)EERLPSSPVYEDAASFK;AKT(0.176)QT(0.824)PPVS(0.752)PAPQPT(0.238)EERLPS(0.004)S(0.005)PVYEDAASFK 156.81 8.74E-11 5416000000 503750 457430 454970 733350 715720 312470 416800 333100 595270 TRUE FALSE 472221.1867 491298.5932 465762.1033 752169.0026 659510.2383 402675.0165 354304.7094 374688.2682 495915.5914 0.952220892 0.990689951 0.93919633 1.516727878 1.329884056 0.811982973 0.714445594 0.755548474 1 18.91973506 2.1330112 8.521433982 0.785111595 1.112909359 0.403236174 0.192444076 0.279578967 20.55130637 0.077221603 0.057003553 135.8348478 -2.1330112 0.327797764 AKTQT(ph)PPVSPAPQPTEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKT(0.027)QT(0.973)PPVSPAPQPTEER;AKT(0.005)QT(0.995)PPVSPAPQPTEER;AKT(0.213)QT(0.787)PPVSPAPQPTEER;AKT(0.044)QT(0.956)PPVSPAPQPTEER;AKTQT(1)PPVSPAPQPTEER;AKT(0.119)QT(0.881)PPVSPAPQPTEER;AKT(0.032)QT(0.968)PPVSPAPQPTEER 162.73 5.64E-11 14449180000 10311000 8902348 9697190 9418480 8940570 6644155 8772950 6669227 7200984 TRUE FALSE 9665652.916 9561487.109 9927211.926 9660174.142 8238413.697 8562214.69 7457527.592 7501894.672 5999093.25 1.611185643 1.593822051 1.6547854 1.610272376 1.373276486 1.427251475 1.24310913 1.250504761 1 22.51631303 1.720826823 0.572941388 1.013403949 1.646947276 0.930279341 0.055437287 0.170957434 0.123898447 0.051564652 0.030353368 52.58075565 -1.720826823 0.633543328 AKTQT(ph)PPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.002)QT(0.998)PPVSPAPQPT(0.001)EERLPS(0.551)S(0.447)PVYEDAASFK;AKT(0.036)QT(0.964)PPVS(0.001)PAPQPT(0.102)EERLPS(0.487)S(0.409)PVYEDAASFK 228.79 4.08E-36 1554570000 857020 721010 674830 1165550 1144370 510937 704490 552575 948180 TRUE FALSE 803380.648 774394.3306 690837.2863 1195459.986 1054495.796 658436.2175 598858.2647 621565.2051 789922.6325 1.017037131 0.980341996 0.874563227 1.5133887 1.33493554 0.833545199 0.758122682 0.78686846 1 19.59135183 2.11649996 10.2096214 0.815185127 1.101603495 0.357855654 0.193119781 0.398674157 33.79144155 0.078585236 0.058031171 130.7675418 -2.11649996 0.286418368 AKTQTPPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKTQTPPVSPAPQPTEERLPS(0.5)S(0.5)PVYEDAASFK;AKTQTPPVSPAPQPT(0.008)EERLPS(0.564)S(0.428)PVYEDAASFK;AKTQTPPVSPAPQPTEERLPS(0.734)S(0.266)PVYEDAASFK 269 1.73E-60 1270430000 534980 591020 507920 596040 911120 496100 783360 534520 1611800 TRUE FALSE 501496.5568 634779.7358 519968.1023 611335.3955 839564.3105 639316.0165 665902.4404 601255.9986 1342780.167 0.373476291 0.472735412 0.387232486 0.45527586 0.625243306 0.476113687 0.495913223 0.447769496 1 20.3567917 -5 0.27867839 4.867665206 0.430927574 0.864545783 0.066564466 76.48552257 0.734198832 170.9867807 0.074847329 1.00E-05 5 -4.436737632 AKVDEFPLCGHMVSDEYEQLSSEALEAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AKVDEFPLCGHMVSDEYEQLSSEALEAAR 29 1 P27635;X1WI28;A6QRI9;B8A6G2 P27635 RPL10 60S ribosomal protein L10 0 ;;;;; 246.44 5.83E-46 1156521000 346475 372520 356618 367034 439309 280236.4 449651 347361 552493 FALSE TRUE 324789.7482 400101.7684 365077.1474 376452.7138 404807.4432 361136.0994 382230.0069 390729.7855 460278.3491 0.705637684 0.869260458 0.793166023 0.81788056 0.879483999 0.784603708 0.830432298 0.848898903 1 18.81214706 -4.999999929 0.23892917 2.027972402 0.801083089 0.624194284 0.046546463 109.8258638 1.096362716 54.77539219 0.067101936 1.00E-05 4.999999929 -1.226889313 AKVEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKVEEAR 7 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 119.27 0.0043945 364698000 1010570 1315530 904230 913250 1537100 617180 1081370 1229590 1381290 FALSE TRUE 947320.2276 1412933.21 925678.7626 936685.5411 1416382.366 795349.8469 919228.6074 1383107.018 1150743.776 0.82322429 1.227843452 0.804417788 0.813982714 1.23084078 0.691161546 0.798812583 1.201924397 1 20.13413521 3.955908771 23.29396422 0.911520138 1.049647126 0.021942192 0.199832037 435.3059097 478021.1151 0.047785722 0.086294788 9034.596699 -3.955908771 0.138126988 AKVS(ph)PVNDVDVGVYQLMQSEQLLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKVSPVNDVDVGVYQLMQSEQLLSR 25 1 Q8WUX9 Q8WUX9 CHMP7 Charged multivesicular body protein 7 1 AKVS(1)PVNDVDVGVYQLMQSEQLLSR 96.242 0.0056382 16272000 24628 18430 19105 17708 21630 18570 26478 19980 29466 TRUE FALSE 23086.57744 19794.57638 19558.17962 18162.41726 19931.26705 23930.85754 22507.86971 22474.54698 24547.93424 0.940469256 0.806364242 0.796734236 0.739875587 0.811932558 0.974862378 0.916894655 0.9155372 1 14.583314 2.247474269 24.93866798 0.942967895 0.810695369 0.580892372 0.055551864 126.9783769 355261.0406 0.018640608 0.015380213 176.7967468 -2.247474269 -0.132272526 AKWDAWNELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AKWDAWNELK 10 1 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ; 145.09 2.83E-05 1125700000 2988900 2343900 2086770 1954550 2570600 1399710 2697900 2630800 3613000 FALSE TRUE 2801830.084 2517444.795 2136269.17 2004707.062 2368715.445 1803783.555 2293374.941 2959261.171 3009966.959 0.930850778 0.836369578 0.709731767 0.666022946 0.786957291 0.599270218 0.761926949 0.983154038 1 21.52131622 1.237821512 6.409516083 0.995373749 0.749704212 0.541875636 0.090073547 0.104647034 18.54729481 0.072392535 0.021960223 17.2910558 -1.237821512 -0.245669537 AKWDAWNELKGTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKWDAWNELKGTSK 14 2 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 104.45 0.00059438 148760000 476430 457210 452130 408260 447120 304780 629180 479620 993890 FALSE TRUE 446611.0968 491062.3041 462854.7371 418736.6428 412004.9988 392765.0383 534840.3 539501.6128 828003.3382 0.539383208 0.593068025 0.559001052 0.505718544 0.497588572 0.474351999 0.645939787 0.651569369 1 19.65927706 0.704096253 1.177692213 0.998859254 0.540261139 0.917870716 0.043235453 0.275183184 0.640329543 0.043439689 0.01337759 5.059367802 -0.704096253 -0.458598115 AKY(ph)ES(ph)KIQMYDEQVTSLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKYESKIQMYDEQVTSLEK 19 2 A8MVZ6;Q96G01-4;Q96G01-3;Q96G01 A8MVZ6 BICD1 Protein bicaudal D homolog 1 2 AKY(0.99)ES(0.412)KIQMY(0.017)DEQVT(0.291)S(0.291)LEK 41.136 0.092043 45977000 128770 85234 84362 93127 119760 70437 135750 78260 175500 TRUE FALSE 120710.5156 91544.81405 86363.10648 95516.79648 110354.5327 90771.01845 115395.5477 88030.93327 146207.9162 0.825608617 0.626127616 0.590686939 0.653294288 0.754778096 0.620835183 0.789256497 0.602094165 1 17.1576619 -5 0.331031064 4.305759109 0.6635419 0.575425602 0.08390837 245.7462836 2.119791921 571.7713119 0.066454001 1.00E-05 5 -3.64221721 AKYAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AKYAYR 6 1 J3KS46 J3KS46 HEXDC 0 81.455 0.056391 110640000 92077 368920 56178 51050 394350 38653 93278 323730 344600 FALSE TRUE 86314.06493 396235.2207 57510.56869 52360.02943 363379.3417 49811.49362 79291.82985 364148.4031 287084.0338 0.300657838 1.3802064 0.200326601 0.182385724 1.265759495 0.173508408 0.276197282 1.268438367 1 18.13111357 1.228559531 24.99467366 1.134219439 0.568794617 0.234063864 0.444599874 358.1228091 894988.1851 0.398249271 0.104284605 16.92620245 -1.228559531 -0.565424822 AKYPDYEVTWANDGY ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AKYPDYEVTWANDGY 15 1 Q9NRX4 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 ;;; 227.56 5.82E-12 452588000 1088070 1145450 1148580 1132240 1310100 987480 1377790 1018500 1505130 FALSE TRUE 1019969.641 1230260.31 1175824.86 1161295.195 1207210.031 1272549.446 1171203.18 1145661.967 1253914.079 0.813428653 0.981136052 0.937723628 0.92613618 0.96275339 1.014861757 0.934037826 0.913668636 1 20.25800706 4.744524153 24.91156185 0.9568433 0.813428588 0.662650844 0.032568459 388.2774491 1621908.266 0.007360706 0.067338378 55529.54986 -4.744524153 -0.143414712 ALAAFLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALAAFLKK 8 1 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 100.45 0.013841 0 75782 138100 82681 78014 168100 61315 99967 127340 183800 FALSE TRUE 71038.93989 148325.0677 84642.23236 80015.97132 154898.1041 79015.64513 84977.8764 143238.6793 153122.5926 0.463935065 0.968668732 0.55277429 0.522561498 1.011595359 0.516028653 0.554966285 0.93545098 1 17.22432764 1.126825614 5.980941456 0.993228267 0.671785306 0.319162078 0.189121681 0.251601714 11.49325955 0.17107899 0.043124873 13.39138864 -1.126825614 -0.321442961 ALAAGADS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALAAGADSPK 10 0 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 ALAAGADS(1)PK;ALAAGADS(1)PK 100.38 0.0042541 318040000 1261870 737530 967300 892960 846850 703770 1155310 838110 972500 TRUE FALSE 1182891.809 792137.4886 990244.8128 915874.8654 780341.817 906936.9742 982081.9909 942749.8784 810183.4674 1.460029557 0.977726059 1.222247618 1.130453659 0.963166799 1.119421724 1.212172342 1.163625174 1 19.62788912 4.752866022 24.56907477 1.111524091 1.460029863 0.595781216 0.093019969 1491.018004 2560720.253 0.021780055 0.463377796 56606.46336 -4.752866022 0.348505773 ALAAGADS(ph)PKTEEARPSPAPGPGTPTGTPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALAAGADSPKTEEARPSPAPGPGTPTGTPTR 31 2 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 ALAAGADS(0.986)PKT(0.014)EEARPSPAPGPGTPTGTPTR 244.85 2.15E-46 206590000 104750 64286 83466 82193 101290 50667 96587 68833 187310 TRUE FALSE 98193.88448 69045.80233 85445.85294 84302.21153 93335.09198 65293.74039 82104.67602 77426.95157 156046.7509 0.629259398 0.442468696 0.547565729 0.540236891 0.598122623 0.418424222 0.526154345 0.496177915 1 17.25161879 -1.337431214 3.584191708 1.002032071 0.51796429 0.846487663 0.063538096 2177465.06 1625522.491 31504.25771 0.013356052 0.045979981 1.337431214 -0.484067781 ALAAPAAEEKEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALAAPAAEEKEEAR 14 1 Q01650 Q01650 SLC7A5 Large neutral amino acids transporter small subunit 1 0 100.45 0.0016214 165540000 157330 146380 115440 126820 191510 85759 155510 152100 140310 FALSE TRUE 147482.9961 157218.1275 118178.2913 130074.4159 176469.5771 110516.2311 132192.7192 171090.0198 116891.3546 1.261710044 1.344993632 1.011009683 1.112780465 1.509688871 0.945461121 1.130902449 1.463667013 1 16.8348087 -2.328051824 2.116647375 4.25E-05 1.202126856 0.118584414 0.183308344 2985436.085 417746.9752 14280147.96 0.042973297 0.00469838 2.328051824 1.202084385 ALAEEAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 99.7 0.010626 1049890000 855930 1090980 975800 990680 1226280 728230 1084460 1013640 1245730 FALSE TRUE 802358.8692 1171757.294 998946.4368 1016102.526 1129972.915 938458.1792 921855.2906 1140195.185 1037809.615 0.773127226 1.12906768 0.96255269 0.979083746 1.088805595 0.904268148 0.888270138 1.098655446 1 19.98511038 2.203742625 24.99997612 0.95331368 1.002357333 0 0.109616165 646.2673028 464028.3197 0.03807576 0.028121813 159.8610366 -2.203742625 0.049043653 ALAEEAS(ph)EEELPS(ph)DVDLNDPYFAEEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALAEEASEEELPSDVDLNDPYFAEEVK 27 0 Q9H501 Q9H501 ESF1 ESF1 homolog 2 ALAEEAS(1)EEELPS(1)DVDLNDPYFAEEVK;ALAEEAS(1)EEELPS(1)DVDLNDPYFAEEVK 181.13 9.14E-18 382780000 378095 247257 321427 306844 300958 231218 373447 265372 369211 TRUE FALSE 354430.7089 265564.1656 329051.4002 314718.1365 277321.9727 297966.8831 317452.0893 298504.2784 307587.2989 1.152293057 0.863378191 1.069782144 1.023183134 0.901604109 0.968722974 1.032071514 0.970470105 1 18.23063641 -1.113310768 3.525085218 1.00000462 0.991723539 0 0.081696019 36319855062 9136563976 1942107.506 0.01739067 0.077035203 1.113310768 -0.008281081 ALAEEASEEELPS(ph)DVDLNDPYFAEEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALAEEASEEELPSDVDLNDPYFAEEVK 27 0 Q9H501 Q9H501 ESF1 ESF1 homolog 1 ALAEEASEEELPS(1)DVDLNDPYFAEEVK 151.35 5.45E-08 42112000 115450 85978 94397 85729 98416 72335 111840 76904 103100 TRUE FALSE 108224.1906 92343.90058 96636.14142 87928.95128 90686.80435 93216.94024 95070.63027 86505.63369 85891.94395 1.260003973 1.075117134 1.1250897 1.02371593 1.055824332 1.085281529 1.106863181 1.007144905 1 16.3902352 ALAEEVEQVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALAEEVEQVHR 11 0 E9PM95;J3KQL8;Q9BQE5 E9PM95 APOL2 Apolipoprotein L2 0 193.96 7.21E-07 72257000 122610 130080 139630 133530 153180 121350 130720 128680 208930 FALSE TRUE 114936.059 139711.2585 142942.0895 136956.6059 141149.8607 156381.775 111119.7495 144745.9813 174058.2333 0.660331067 0.802669635 0.821231417 0.786843594 0.810934697 0.898445147 0.638405593 0.831595142 1 17.40921053 0.979383181 24.69593122 1.000000006 0.779451228 0.467091585 0.075699385 1237.996422 1482940.594 0.069092502 0.017273126 9.536371932 -0.979383181 -0.220548777 ALAILSQPTPSLVVDHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALAILSQPTPSLVVDHER 18 0 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 ; 126.07 2.84E-05 772690000 563650 638580 606340 614790 664570 531870 673100 545050 580700 FALSE TRUE 528372.1526 685861.1276 620722.6711 630566.5522 612377.3529 685412.2348 572174.9038 613100.6923 483777.4185 1.092180272 1.417720425 1.283074917 1.303422872 1.265824591 1.416792534 1.182723463 1.267319781 1 18.8839839 0.483214829 0.873108182 0.998949813 1.30434398 0.445826492 0.096849684 1.405879081 1.590974264 0.087071059 0.02801555 3.042389607 -0.483214829 0.305394167 ALALLEDEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALALLEDEER 10 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6 A0A499FIX8 ESYT2 Extended synaptotagmin-2 0 ; 133.57 0.00045029 51917000 60441 64708 62483 63207 67990 55753.3 78461 60677 71637 FALSE TRUE 56658.1057 69499.04765 63965.12627 64828.99863 62650.33966 71848.37263 66696.50145 68252.65702 59680.32191 0.949359921 1.164521997 1.071795932 1.086270927 1.049765445 1.20388715 1.117562696 1.143637548 1 15.8649677 ALAMPGRPES(ph)PPVFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 122.87 6.43E-05 2209860000 1508780 1764170 1668500 1692170 1936040 1597510 1892860 1562800 2143600 TRUE FALSE 1414348.153 1894790.982 1708077.608 1735593.947 1783991.228 2058685.204 1609043.215 1757919.02 1785819.312 0.791988385 1.061020547 0.956467206 0.97187545 0.998976333 1.152795913 0.901011208 0.984376756 1 20.76815469 4.749148269 24.40895641 1.000693724 0.79198822 0.499211921 0.066472353 913.3855269 2105676.882 0.014992967 0.207806443 56123.95518 -4.749148269 -0.208705503 ALANECSQGDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ALANECSQGDKR 12 1 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 ;;;; 187.45 1.68E-05 2516870000 1448910 1145610 1333480 1184940 1333710 987900 1524270 1125240 1576740 FALSE TRUE 1358225.309 1230432.156 1365110.775 1215347.566 1228965.797 1273090.693 1295719.864 1265728.691 1313571.908 1.033993877 0.936707118 1.039235665 0.925223476 0.935590803 0.969182338 0.986409542 0.963577771 1 20.32506375 -1.449262919 2.982099298 1.000582117 0.974394493 0.043543394 0.038570062 439226272.8 589828301.6 2195831.165 0.008867421 0.035541609 1.449262919 -0.026187624 ALANSLACQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALANSLACQGK 11 0 P04075;J3KPS3;P04075-2;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ; 169.37 3.95E-05 199500000 318370 359060 283250 272790 346410 198772 343510 310410 323960 FALSE TRUE 298443.79 385645.176 289968.8238 279790.2532 319204.356 256154.2496 292003.8645 349165.3718 269888.9831 1.105802047 1.428902994 1.074400372 1.036686455 1.18272466 0.949109692 1.08194066 1.293737031 1 18.04200656 3.772202731 5.222768818 1.084547871 1.282581731 0.26803248 0.122069608 0.20406935 13.03137609 0.028862222 0.051987092 5918.378422 -3.772202731 0.19803386 ALAPTWEQLALGLEHSETVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALAPTWEQLALGLEHSETVK 20 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 267.7 6.50E-37 464920000 578460 551120 553750 564040 644360 456030 674550 507500 650490 FALSE TRUE 542255.2212 591925.4982 566885.2115 578514.2213 593754.5648 587678.458 573407.4897 570862.4921 541919.0167 1.000620396 1.092276669 1.046069974 1.067528918 1.095651835 1.08443963 1.058105496 1.053409226 1 19.04771775 0.720464703 1.848042885 1.000074454 1.066647635 0.343906326 0.027186575 1.121068521 5.755883163 0.02347773 0.006570647 5.253693147 -0.720464703 0.066573181 ALAS(ph)PEQLAQLPSSGVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALASPEQLAQLPSSGVPR 18 0 Q9Y3Q8;Q9Y3Q8-2;H7BZ77 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 ALAS(1)PEQLAQLPSSGVPR 107.72 0.00052909 0 21001 22715 28031 24309 27325 25073 25950 20052 45528 TRUE FALSE 19686.5849 24396.84223 28695.90856 24932.8101 25179.00472 32311.16807 22059.03841 22555.53634 37929.08268 0.519036673 0.643222575 0.756567429 0.657353364 0.663844284 0.851883721 0.581586394 0.594676558 1 15.21101686 -2.196034513 2.470185435 2.011863687 0.668246451 0.570470016 0.092780225 13600138.61 1346749.479 77755583.29 0.02214635 0.006367449 2.196034513 -1.343617236 ALASEKS(ph)PTADAKPAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ALASEKSPTADAKPAPK 17 2 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 ALAS(0.007)EKS(0.959)PT(0.034)ADAKPAPK;ALAS(0.001)EKS(0.735)PT(0.263)ADAKPAPK;ALAS(0.002)EKS(0.499)PT(0.499)ADAKPAPK;ALAS(0.002)EKS(0.82)PT(0.178)ADAKPAPK;ALAS(0.001)EKS(0.994)PT(0.006)ADAKPAPK 186.7 2.65E-10 4643820000 13691220 5715230 9068240 8526320 8734510 5479630 10717760 6022210 10639880 TRUE FALSE 12834310.98 6138391.576 9283342.935 8745119.806 8048536.818 7061510.227 9110731.387 6774096.175 8864015.292 1.447911647 0.69250688 1.047306737 0.986586724 0.908001233 0.796649148 1.027833446 0.764224333 1 23.07952894 2.72934497 7.334453093 0.902892047 0.98577045 0.083751881 0.199705295 0.564630078 211.1439696 0.058984066 0.057964891 536.2224218 -2.72934497 0.082878403 ALASNTSFFSGCS(ph)PIEEEAH ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ALASNTSFFSGCSPIEEEAH 20 0 O95239;Q2VIQ3 O95239 KIF4A;KIF4B Chromosome-associated kinesin KIF4A;Chromosome-associated kinesin KIF4B 1 ALASNTSFFSGCS(1)PIEEEAH;ALASNTSFFSGCS(1)PIEEEAH;ALASNTSFFSGCS(1)PIEEEAH;ALASNTSFFSGCS(1)PIEEEAH;ALASNTSFFSGCS(1)PIEEEAH 385.05 9.73E-131 764330000 683607 699253 704508 749597 799662 795726 936915 640523 800114 TRUE FALSE 640821.2581 751026.4197 721219.2625 768832.9281 736859.7722 1025439.179 796433.2936 720493.7065 666569.8045 0.961371568 1.126703332 1.081986099 1.153416976 1.105450273 1.538382285 1.19482354 1.080897607 1 19.34639644 2.436092835 24.99973841 1.240149518 1.092767469 0.114432083 0.147663776 235.7322414 143636.9665 0.047410963 0.039666882 272.9561194 -2.436092835 -0.147382049 ALAT(ph)PPKLHTCEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ALATPPKLHTCEK 13 1 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;B3KPU0;H0YBP7;E5RGS7 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 ALAT(1)PPKLHTCEK;ALAT(1)PPKLHTCEK;ALAT(1)PPKLHTCEK 191.37 5.30E-06 845780000 2764820 2040160 2126030 2241480 2649770 1537600 2900290 2167890 2589060 TRUE FALSE 2591774.852 2191215.569 2176460.436 2299000.172 2441667.753 1981480.159 2465418.439 2438555.839 2156929.16 1.201604067 1.015895937 1.009055131 1.065867259 1.132011101 0.918657968 1.143022444 1.130568349 1 21.04054736 1.623222747 25 1.102603764 1.048701824 0.02308118 0.08374423 2.115032637 3435.119318 0.035587022 0.019641741 41.99743306 -1.623222747 -0.053901941 ALCELESGIPAAESQIVYAERPLTDNHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALCELESGIPAAESQIVYAERPLTDNHR 28 1 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 0 ; 95.366 0.0013277 115255000 61870 81379 73148 68141 71546 63485 84065 60402 76643 FALSE TRUE 57997.66714 87404.38583 74883.1051 69889.61342 65927.06576 81812.08891 71460.23367 67943.32266 63850.78817 0.908331264 1.368884995 1.172782784 1.094577145 1.03251765 1.281301159 1.119175436 1.064095285 1 15.96241681 1.174848561 2.488137804 1.005780389 1.167929506 0.097397114 0.12715343 0.478398849 5.24585745 0.113193071 0.031644187 14.95714009 -1.174848561 0.162149117 ALDDISESIKELQFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALDDISESIKELQFYR 16 1 H0YG54;H0YGR4;F5GYG5;Q9Y3B8-2;Q9Y3B8-3;Q9Y3B8 H0YG54 REXO2 "Oligoribonuclease, mitochondrial" 0 ; 151.8 5.55E-07 400380000 680050 516370 696570 655020 726900 571500 703530 372320 624650 FALSE TRUE 637486.8844 554602.5721 713092.9693 671828.9221 669812.2062 736482.7725 598042.2078 418804.9716 520391.8796 1.225013128 1.06574025 1.370299955 1.291005776 1.287130396 1.415246474 1.149215103 0.804787676 1 18.98923892 1.407844879 4.9244197 0.909779251 1.26428045 0.683891424 0.103425632 0.121902618 4.811361963 0.072647969 0.026346439 25.57672175 -1.407844879 0.354501199 ALDDKNCWEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALDDKNCWEK 10 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 81.676 0.01851 383550000 493410 486300 422450 506410 583960 381900 673580 426260 759760 FALSE TRUE 462528.3489 522306.158 432470.7135 519405.338 538098.1372 492148.3304 572582.9322 479479.4993 632951.1478 0.73074889 0.825191896 0.683260809 0.820608889 0.850141656 0.777545522 0.90462421 0.757530026 1 19.27173463 -5 0.12773503 1.70619137 0.703091715 0.55771014 0.059798127 102.3198221 0.830413814 18.3807531 0.448066144 1.00E-05 5 -1.003099655 ALDDMISTLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALDDMISTLKK 11 1 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;E9PQ35;Q5SZW8;E9PM09 P49368 CCT3 T-complex protein 1 subunit gamma 0 90.614 0.018209 392600000 257410 271640 301610 295490 335510 191750 286180 292920 296840 FALSE TRUE 241299.1676 291752.5082 308764.3316 303072.7737 309160.398 247105.1122 243269.9658 329491.7068 247295.4863 0.975752413 1.17977288 1.248564364 1.225549152 1.250165956 0.999230175 0.983721819 1.332380593 1 17.91587638 2.239647035 24.99968453 1.064636958 1.188635235 0.120828967 0.125090073 48.12226345 1107381.86 0.042885597 0.034013845 173.6389035 -2.239647035 0.123998278 ALDEEVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ALDEEVHK 8 0 Q06210-2;Q06210;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ;;; 137 0.00076673 1434850000 4013070 3490260 3752790 3739510 3481320 2978490 4597500 3185530 3057240 FALSE TRUE 3761899.112 3748682.482 3841807.951 3835472.158 3207911.17 3838331.711 3908147.556 3583250.433 2546966.893 1.47701139 1.471822226 1.508385508 1.505897924 1.2595025 1.507020653 1.53443202 1.406869654 1 21.28034878 0.942727018 14.05037393 0.999999999 1.47064077 0.783026954 0.076508462 16.64023955 4082.729106 0.071391521 0.017848941 8.76449742 -0.942727018 0.470640771 ALDEYYDKHFTEFVPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALDEYYDKHFTEFVPLR 17 1 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 273.88 6.78E-36 1007160000 1229900 1671070 1429310 1424540 1928420 966660 1560580 1406880 2660500 FALSE TRUE 1152922.754 1794797.762 1463213.908 1461096.108 1776969.672 1245719.05 1326585.517 1582532.065 2216445.363 0.52016746 0.809764045 0.660162408 0.659206914 0.801720495 0.56203463 0.598519386 0.713995523 1 21.07981637 0.963578683 22.1529538 1.000000002 0.669375834 0.570461637 0.092025457 988.79381 601426.9177 0.085801854 0.021450464 9.195570609 -0.963578683 -0.330624167 ALDGAFTEENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALDGAFTEENR 11 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 80.688 0.055193 182350000 170740 147270 137750 136220 160860 116680 144000 123930 210920 FALSE TRUE 160053.6882 158174.024 141017.4951 139715.6358 148226.7045 150363.6219 122408.5368 139402.9333 175716.0894 0.910865298 0.900168132 0.802530352 0.795121473 0.843557952 0.855719145 0.696626799 0.793341883 1 17.42288677 4.062699728 2.327623353 0.808583708 0.909394378 0.121375753 0.076847991 0.458669364 4.840716504 0.019107715 0.053123599 11553.1318 -4.062699728 0.10081067 ALDKLDGTEINGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALDKLDGTEINGR 13 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ; 105.58 0.0013146 276920000 570840 512850 529680 511580 615590 467480 647700 501330 730430 FALSE TRUE 535112.1434 550821.9476 542244.2597 524708.0089 567244.0446 602433.8871 550583.398 563922.1541 608516.5142 0.879371604 0.905188166 0.891092102 0.862274066 0.932175268 0.990004171 0.904796148 0.92671627 1 19.21493689 2.567265185 6.273343653 0.946358833 0.88934941 0.549618274 0.029801973 0.205682266 11.81283414 0.009235143 0.008657368 369.2029691 -2.567265185 -0.057009423 ALDLDSSCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALDLDSSCK 9 0 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 161.92 0.00021457 147280000 783490 647310 642290 643650 733600 511870 815330 597820 712060 FALSE TRUE 734452.7595 695237.5059 657525.4221 660167.1487 675986.0152 659638.5595 693078.8357 672459.143 593212.5859 1.23809369 1.171987113 1.108414484 1.112867738 1.139534176 1.111976676 1.168348164 1.133588799 1 19.17818968 -5 0.182674072 0.417387277 1.17446193 0.647463674 0.035943097 96.41802996 0.933296826 20.53442581 0.111765922 1.00E-05 5 0.757074653 ALDLLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ALDLLDR 7 0 P27361;E9PBK7;E9PQW4;P27361-3;B3KR49;E9PRH7;H0YEX6 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 ;; 152.39 0.004227 116225000 186683 262730 232007 237885 259923 194394 259351 223714 276035 FALSE TRUE 174998.8443 282182.8026 237510.3156 243989.5318 239509.6961 250512.3921 220463.7252 251645.1854 229962.9752 0.760987042 1.227079282 1.032819807 1.060994847 1.041514165 1.089359675 0.958692263 1.094285657 1 17.81104208 1.760343788 25 1.014167683 1.058479719 0 0.119504069 47.98727245 55118.70539 0.050614259 0.028069038 57.58956368 -1.760343788 0.044312035 ALDSNSLENDDLSAPGREPGHFNPESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALDSNSLENDDLSAPGREPGHFNPESR 27 1 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ; 335.96 1.23E-95 526200000 185751 184404 189150 215497 190396 166050 217610 172490 232900 FALSE TRUE 174125.1765 198057.464 193636.7273 221027.0179 175443.0662 213985.9394 184981.4007 194025.7562 194027.4854 0.897425311 1.020770143 0.997986068 1.139153133 0.904217595 1.102864055 0.953377303 0.999991088 1 17.56590151 4.740701874 24.04222216 1.013873141 0.897425244 0.234350045 0.066653072 154.9993052 1740135.013 0.013752185 0.08999516 55042.97179 -4.740701874 -0.116447897 ALDVDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALDVDYR 7 0 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 81.784 0.061099 144110000 390320 600430 508280 540670 593840 471230 546270 537470 484070 FALSE TRUE 365890.5679 644886.4619 520336.6416 554544.5076 547202.2018 607266.4512 464361.8848 604574.3126 403275.5898 0.907296591 1.599120994 1.29027557 1.375100605 1.356893935 1.505834885 1.15147531 1.499159205 1 18.62140656 -1.580840054 4.83558109 0.996711877 1.349808226 0.220570219 0.196693058 0.006151584 0.000533234 0.168025197 0.039288007 0.026251852 1.580840054 0.353096349 ALDVMVSTFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ALDVMVSTFHK 11 0 P26447 P26447 S100A4 Protein S100-A4 0 ;;; 224.58 6.10E-12 12696040000 13441740 22296100 16366800 16061600 25240800 13900710 19421800 21293800 27146900 FALSE TRUE 12600445.49 23946926.44 16755028.22 16473767.85 23258489.38 17913619.32 16509681.39 23952377.8 22615907.01 0.557149686 1.058853241 0.740851482 0.728415086 1.02841285 0.792080517 0.730003063 1.059094282 1 24.43083452 1.227417091 24.9200984 1.029547296 0.823323912 0.279889229 0.1474316 316.0993247 706864.4312 0.126023255 0.032700858 16.8817355 -1.227417091 -0.206223384 ALDVS(ph)ASDDEIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALDVSASDDEIAR 13 0 C9JIF9;P13798;H7C393;H7C1U0;C9JLK2 C9JIF9 APEH Acylamino-acid-releasing enzyme 1 ALDVS(0.619)AS(0.381)DDEIAR 204.35 8.24E-08 166860000 184980 303900 199980 182660 297890 177580 240140 250310 239170 TRUE FALSE 173402.432 326401.0722 204723.62 187347.3648 274494.921 228844.4632 204133.2364 281561.7545 199250.9819 0.870271405 1.638140345 1.027466054 0.940258176 1.377633969 1.148523641 1.024503038 1.413100963 1 17.60422731 -4.999999999 0.116835155 0.443836641 1.283580647 0.010881685 0.242239161 532.8085865 4.072011807 72.3064886 2.387001756 1.00E-05 4.999999999 0.839744006 ALDVSAS(ph)DDEIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALDVSASDDEIAR 13 0 C9JIF9;P13798;H7C393;H7C1U0;C9JLK2 C9JIF9 APEH Acylamino-acid-releasing enzyme 1 ALDVS(0.44)AS(0.56)DDEIAR;ALDVS(0.044)AS(0.956)DDEIAR 206.45 6.48E-08 330960000 295090 493920 314720 320260 486620 296080 364080 387500 414250 TRUE FALSE 276620.8437 530490.3507 322185.307 328478.4138 448402.8281 381553.4895 309489.584 435880.228 345108.9988 0.801546307 1.53716754 0.933575503 0.951810631 1.299307841 1.105602841 0.896787928 1.263021913 1 18.39669257 3.757070746 24.167382 1.05776201 1.225942499 0.023459135 0.220008841 553.6003274 446716.7637 0.051589509 0.092985179 5715.717377 -3.757070746 0.168180489 ALEAASLSQHPPSLCIS(ph)DS(ph)EEEEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ALEAASLSQHPPSLCISDSEEEEEER 26 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 2 ALEAASLSQHPPSLCIS(1)DS(1)EEEEEER;ALEAASLSQHPPSLCIS(1)DS(1)EEEEEER;ALEAASLSQHPPSLCIS(1)DS(1)EEEEEER;ALEAASLSQHPPSLCIS(1)DS(1)EEEEEER 243.28 1.76E-45 1709440000 471496 767557 738932 698321 786193 788534 987760 670722 800121 TRUE FALSE 441985.907 824387.7189 756459.816 716241.0991 724448.5731 1016170.965 839654.5579 754463.1181 666575.6361 0.6630694 1.236750451 1.134844682 1.074508368 1.086821261 1.524464607 1.259653837 1.131849226 1 19.34640906 2.419884559 24.99964968 1.266910128 1.080178598 0.15577459 0.199272228 138.7334704 60594.44377 0.06439613 0.053877672 262.9568928 -2.419884559 -0.18673153 ALEAELDAQHLS(ph)ETFDNIDNLSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALEAELDAQHLSETFDNIDNLSPK 24 0 P25054-2;P25054-3;P25054;A0A2Q2SV78;E9PFT7 P25054-2 APC Adenomatous polyposis coli protein 1 ALEAELDAQHLS(0.333)ET(0.333)FDNIDNLS(0.333)PK 83.788 0.022156 64775000 79724 51220 59733 53931 58668 50563 55348 46127 67956 TRUE FALSE 74734.21715 55012.38209 61149.89497 55314.96076 54060.45194 65159.71728 47049.08123 51886.05749 56613.70459 1.320072899 0.971714932 1.080125306 0.977059551 0.954900449 1.150953073 0.831054628 0.916492886 1 15.78886371 4.740217481 24.49691987 0.987256889 1.320073047 0.600055157 0.085882699 78.15625111 1155413.157 0.020157004 0.128795156 54981.61356 -4.740217481 0.332816158 ALEAELDAQHLSETFDNIDNLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ALEAELDAQHLSETFDNIDNLSPK 24 0 P25054-2;P25054-3;P25054;A0A2Q2SV78;E9PFT7 P25054-2 APC Adenomatous polyposis coli protein 1 ALEAELDAQHLSETFDNIDNLS(1)PK;ALEAELDAQHLSETFDNIDNLS(1)PK;ALEAELDAQHLSETFDNIDNLS(1)PK;ALEAELDAQHLS(0.065)ET(0.215)FDNIDNLS(0.719)PK;ALEAELDAQHLSETFDNIDNLS(1)PK 279.93 2.21E-52 278057000 262930 235509 278042 280785 298294 230473 336227 249743 378603 TRUE FALSE 246473.6806 252946.3314 284637.2875 287990.4185 274867.1925 297006.8137 285812.8827 280923.9633 315411.7134 0.781434773 0.801956049 0.902430935 0.9130619 0.871455247 0.941648014 0.906158112 0.890657992 1 18.26687671 7.905426144 0.223206107 0.959955407 2.85E-18 0.776013957 0.029764446 22.1998932 0.297362982 0.043108967 7.65103108 80431495.59 -7.905426144 -0.959955407 ALEATTEHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ALEATTEHIR 10 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;; 199.67 2.74E-07 1129650000 863120 1063330 1060860 982620 1240740 889280 1008150 1058460 1306960 FALSE TRUE 809098.8599 1142060.06 1086024.1 1007835.693 1143297.285 1146000.7 856987.2667 1190611.061 1088819.933 0.743097032 1.048897091 0.997432236 0.925622008 1.05003339 1.052516275 0.787078966 1.093487569 1 20.05433395 4.748207892 24.54665088 0.984630021 0.743096864 0.449622845 0.086778691 1032.07946 2625966.075 0.020506843 0.264632251 56002.56154 -4.748207892 -0.241533157 ALEAVFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALEAVFGK 8 0 P38159;P38159-2;H3BT71;H0Y6E7;H3BR27;P38159-3;H3BNC1 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 0 ; 117.02 0.0050241 168252000 578310 546450 583440 516930 663830 437360 613310 538720 695500 FALSE TRUE 542114.6094 586909.7266 597279.4723 530195.299 611695.4696 563618.7321 521349.8592 605980.3779 579416.5569 0.935621537 1.012932267 1.030829142 0.915050308 1.055709338 0.972734944 0.899784193 1.045845809 1 19.14424138 2.01429265 24.97718179 0.962121059 0.996883606 0 0.05542822 591.3728056 1033452.557 0.019388401 0.014312847 103.3457568 -2.01429265 0.034762546 ALEEALSIQT(ph)PPS(ph)SPPTAFGSPEGAGALLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALEEALSIQTPPSSPPTAFGSPEGAGALLR 30 0 E7EMV7;A0A0A0MRZ4;Q15025-7;Q15025-8;Q15025-5;Q15025-6;Q15025-4;Q15025-3;Q15025-2;Q15025;H0YC17 E7EMV7 TNIP1 TNFAIP3-interacting protein 1 2 ALEEALS(0.116)IQT(0.87)PPS(0.513)S(0.485)PPT(0.013)AFGS(0.003)PEGAGALLR 59.954 0.057694 14965000 8533.7 12536 12331 15861 11799 9587.4 10883 7379.4 10750 TRUE FALSE 7999.59095 13464.17848 12623.49714 16268.02011 10872.35413 12355.12674 9251.195183 8300.734334 8955.755552 0.893234625 1.503410673 1.409540163 1.816487734 1.214007469 1.379573914 1.0329888 0.926860306 1 13.12859943 1.717753554 2.305073177 0.953100359 1.409992828 0.371582396 0.231774271 0.258868312 2.903364686 0.143738018 0.060935477 52.20998332 -1.717753554 0.456892469 ALEEGDGSVSGSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALEEGDGSVSGSSPR 15 0 Q8N3X1-2;Q8N3X1 Q8N3X1-2 FNBP4 Formin-binding protein 4 1 ALEEGDGSVSGS(0.002)S(0.998)PR;ALEEGDGSVSGS(0.014)S(0.985)PR 242.44 4.88E-14 399130000 700140 814840 802400 745780 801490 666360 818090 694860 848770 TRUE FALSE 656319.4872 875171.6014 821433.3069 764917.9774 738544.2085 858727.3145 695424.9993 781614.8006 707104.8037 0.928178516 1.237683009 1.161685372 1.081760403 1.044462157 1.214427211 0.983482216 1.105373343 1 19.43156453 1.506483348 0.694942325 1.00676774 1.134009221 0.04798454 0.097641644 1.193358657 1.253877077 0.08657906 0.03961853 32.09839727 -1.506483348 0.127241481 ALEEGLTPQEICDKYHIIHADIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ALEEGLTPQEICDKYHIIHADIYR 24 1 P56192;P56192-2;H0YHV5 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;;; 123.06 7.47E-05 1265880000 705304 822088 791837 829861 984460 633047 934023 747674 1011427 FALSE TRUE 661160.2816 882956.2509 810619.7476 851156.6382 907144.4827 815797.3922 793974.9222 841022.7447 842613.2996 0.784654458 1.04787837 0.962030564 1.010139098 1.076584577 0.96817531 0.942276751 0.998112355 1 19.68451116 4.747131497 24.87182341 0.996827001 0.784654342 0.744873516 0.039670715 570.6713105 1655991.21 0.009782706 0.115088902 55863.93153 -4.747131497 -0.212172658 ALEELQEALAEKEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ALEELQEALAEKEELR 16 1 Q9UJC3;Q9UJC3-2 Q9UJC3 HOOK1 Protein Hook homolog 1 0 ;;;; 211.13 7.19E-12 474644000 776871.3 696037.5 751033.9 732445.2 819198.8 586070.3 934606.7 689323.2 968372.9 FALSE TRUE 728248.3121 747572.8407 768848.7788 751240.9839 754862.2307 755259.2816 794471.1018 775386.7189 806745.2071 0.902699273 0.926652968 0.95302553 0.93119981 0.935688522 0.936180686 0.984785648 0.961129626 1 19.62175358 7.999997223 0.052783013 1.108575696 0.637940628 0.76592558 0.013813056 222.4383243 0.883441019 1.777511991 8.36686608 99999360.52 -7.999997223 -0.470635067 ALEENNNFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALEENNNFSK 10 0 E5RGX5;Q93045;Q93045-2 E5RGX5 STMN2 Stathmin;Stathmin-2 0 166.97 1.25E-05 81123000 50033 49593 46710 48762 58515 42294 57769 42285 66716 FALSE TRUE 46901.52384 53264.91732 47817.98326 50013.31547 53919.46794 54503.59121 49107.07475 47564.37533 55580.6686 0.843845981 0.958335311 0.860334797 0.899832923 0.970111899 0.980621367 0.88352796 0.855771917 1 15.76229557 2.960768187 24.61637934 0.930989819 0.896461956 0.158397309 0.052247826 1114.16723 699094.6254 0.015596099 0.016545412 913.6254461 -2.960768187 -0.034527863 ALEESESSQLIS(ph)PPLAQAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALEESESSQLISPPLAQAIR 20 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 ALEESESS(0.002)QLIS(0.998)PPLAQAIR;ALEESESSQLIS(1)PPLAQAIR 155.28 3.33E-08 30996000 61273 63992 70546 66894 69585 67370 73275 61586 128988 TRUE FALSE 57438.03231 68730.03426 72219.38443 68610.61329 64120.07479 86818.62534 62288.094 69275.14767 107459.0695 0.534510792 0.63959268 0.672064115 0.638481364 0.596693002 0.807922735 0.579644829 0.644665434 1 16.71342773 -5 0.369671899 5.683825681 0.634062583 0.719865347 0.070923627 272.6533192 2.107219887 1020.071803 0.045444027 1.00E-05 5 -5.049763098 ALEFAPACHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALEFAPACHR 10 0 Q99615;A0A6I8PUD4;A0A6I8PU73;A0A6I8PS32;A0A6I8PIK4;A0A6I8PR89;A0A6I8PLE7;A0A6I8PU89;A0A6I8PRZ0;K7EIH8;K7EK03;Q99615-2;K7ER44;K7EPP7;A0A6I8PUC2 Q99615 DNAJC7 DnaJ homolog subfamily C member 7 0 ; 98.048 0.0056425 405880000 219424 388490 253728 259163 420430 196857 249337 347190 256278 FALSE TRUE 205690.6435 417254.2038 259746.548 265813.5613 387411.1237 253686.4202 211951.2316 390537.4358 213503.5462 0.963406216 1.954319782 1.216591259 1.245007711 1.814541869 1.188207057 0.992729326 1.829184773 1 17.70390051 -3.923742965 0.146698536 7.69E-08 1.549399275 0.063041076 0.36288213 212.6007968 2.517719435 65.52603527 1.938008154 0.000119195 3.923742965 1.549399198 ALEHAFQLEHIMDLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ALEHAFQLEHIMDLTR 16 0 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 200.75 2.01E-11 627682000 252502.7 370454.1 296683.5 324126.8 423692.5 261238.1 364490.1 359727.4 347643.9 FALSE TRUE 236699.0067 397882.907 303720.9727 332444.4424 390417.4001 336653.2986 309838.1933 404640.1577 289619.8872 0.817274701 1.373810724 1.04868825 1.147864691 1.34803381 1.162397037 1.069809799 1.39714217 1 18.14380115 4.757934273 24.28313115 1.189733648 0.817274197 0.418363235 0.139338245 2917.628547 3656897.293 0.030419301 1.091459309 57270.93494 -4.757934273 -0.372459451 ALEHFTDLYDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALEHFTDLYDIK 12 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 161.99 6.39E-05 92957000 74072 78597 85328 77427 100060 62437 104090 80723 87419 FALSE TRUE 69435.96574 84416.40366 87352.02045 79413.9079 92201.69122 80461.54832 88482.67082 90801.44424 72828.20415 0.953421364 1.15911692 1.19942571 1.09042793 1.266016268 1.104813022 1.214950607 1.246789555 1 16.15220965 4.738684415 4.717407068 1.171751537 0.940644213 0.39114404 0.080098185 0.159521629 9.912841465 0.016349437 0.121739223 54787.86986 -4.738684415 -0.231107324 ALEHFTDLYDIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALEHFTDLYDIKR 13 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 93.623 0.0035892 1050400000 212590 278910 243900 265170 282290 228080 339110 229380 447680 FALSE TRUE 199284.3714 299560.7866 249685.4232 271974.7111 260120.0821 293922.9934 288263.6036 258018.5979 372959.3159 0.534332735 0.803199636 0.669470938 0.729234261 0.697448947 0.78808326 0.772908978 0.691814327 1 18.50865874 -5 0.192269306 2.209087638 0.67195331 0.621373891 0.072931329 89.46959622 0.878277142 41.44604114 0.174396385 1.00E-05 5 -1.537134328 ALEHSALAINHK ddPTM_SK-BR-3_Pertuzumab_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 0 199.19 1.01E-07 296300000 367660 531070 521670 522320 509440 414080 576300 486410 533920 FALSE TRUE 344648.8169 570390.9754 534044.2588 535723.6155 469430.6374 533618.174 489889.1651 547139.3592 444805.3027 0.774830729 1.282338524 1.200624758 1.204400245 1.055362053 1.199666845 1.101356396 1.23006483 1 18.76281446 -0.392836111 8.025326899 1.000002123 1.150207681 0.062863575 0.143003747 0 0 0.123602549 0.0291334 0.404728595 0.392836111 0.150205559 ALEIIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ALEIIPR 7 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;; 128.38 0.0087545 271566000 439957 599202 562049 572204 593078 486240 587632 502840 557377 FALSE TRUE 412420.8767 643567.5395 575381.0677 586887.7234 546500.0462 626609.5946 499522.0369 565620.6809 464347.1779 0.88817354 1.385961992 1.239118261 1.263898547 1.176921218 1.349442022 1.075751207 1.218098672 1 18.82484434 0.73473554 0.802017557 1.002267073 1.235419127 0.136627968 0.142440122 1.573310686 1.9446206 0.125920779 0.04413899 5.429196241 -0.73473554 0.233152054 ALELDHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ALELDHK 7 0 Q99615;A0A6I8PUD4;A0A6I8PU73;A0A6I8PS32;A0A6I8PR89;A0A6I8PLE7;A0A6I8PU89;A0A6I8PRZ0;K7EIH8;K7EK03;Q99615-2;K7ESP1;K7ER44;K7EPP7;A0A6I8PUC2;K7ELJ8;K7EJV7;K7EN19;K7EJL5;K7EJE9 Q99615 DNAJC7 DnaJ homolog subfamily C member 7 0 ;;;; 139.68 0.0026756 1256052000 2501369 2136577 2375704 2294793 2541310 1829988 2787840 2112652 2480200 FALSE TRUE 2344812.779 2294771.384 2432056.821 2353681.273 2341725.764 2358275.828 2369829.273 2376421.253 2066238.597 1.134821885 1.11060329 1.177045489 1.139113981 1.133327858 1.141337613 1.146929148 1.150119476 1 20.97857543 -1.711695927 2.611945951 0.974913484 1.142072603 0.879662866 0.016465776 2540686.424 2159900.252 419207.1527 0.004372534 0.019422453 1.711695927 0.167159119 ALELDSNLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ALELDSNLYR 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 240.46 6.54E-12 1602980000 1443320 2153420 1621270 1689050 2075110 1284580 1576630 1789140 1648330 FALSE TRUE 1352985.178 2312861.457 1659727.29 1732393.883 1912139.231 1655417.393 1340228.968 2012518.067 1373213.074 0.985269659 1.684269907 1.208645127 1.261562328 1.392456325 1.205506577 0.975980344 1.465554112 1 20.38912407 2.069896317 5.516513352 1.131792255 1.3412656 0.090025337 0.217129404 0.342569439 19.17123501 0.077937165 0.056532207 117.4617095 -2.069896317 0.209473344 ALELDSNNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALELDSNNEK 10 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 145.25 7.16E-05 171170000 334680 345810 320500 311370 386030 308700 386810 282320 369570 FALSE TRUE 313732.9762 371414.1322 328102.4114 319360.2813 355712.761 397816.6787 328811.4315 317568.2735 307886.3795 1.018989462 1.206335054 1.065660689 1.037266676 1.155337763 1.292089242 1.067963552 1.031446321 1 18.23203852 1.494298244 11.22798548 1.026982174 1.131825831 0.254623233 0.080683288 0.131837869 50.86797333 0.042436675 0.019677544 31.21032164 -1.494298244 0.104843657 ALELENDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALELENDR 8 0 Q03252 Q03252 LMNB2 Lamin-B2 0 110.38 0.0079978 245020000 431660 483630 442090 476450 559130 325170 536660 419450 851220 FALSE TRUE 404643.1711 519438.4684 452576.5836 488676.5136 515218.1852 419041.3003 456192.8151 471819.2558 709145.8829 0.570606388 0.732484642 0.63819955 0.689105761 0.726533422 0.590909868 0.643298969 0.665334548 1 19.43572292 0.901324026 18.75831559 1 0.66061925 0.812635237 0.051731295 2858.26278 543358.9478 0.046340413 0.011585103 7.967535846 -0.901324026 -0.33938075 ALELPLAASS(ph)IPRPRTPS(ph)PESHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALELPLAASSIPRPRTPSPESHR 23 2 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 2 ALELPLAAS(0.154)S(0.679)IPRPRT(0.185)PS(0.784)PES(0.198)HR 51.9 0.065633 50630000 14895 20194 17462 17460 25768 16685 21126 16574 40126 TRUE FALSE 13962.74854 21689.18477 17876.20689 17908.05316 23744.28522 21501.68864 17958.35242 18643.30038 33428.71138 0.41768731 0.64881905 0.534756087 0.535708749 0.710296157 0.643210215 0.537213422 0.557703232 1 15.02880012 -2.059208685 2.518974538 1.592885194 0.579465606 0.734789643 0.080508508 18615003.77 6792816.757 63464832.89 0.01848862 0.00872552 2.059208685 -1.013419587 ALEMAIEAGAEDVKETEDEEERNVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ALEMAIEAGAEDVKETEDEEERNVFK 26 2 Q9BSH4 Q9BSH4 TACO1 Translational activator of cytochrome c oxidase 1 0 ;; 217.93 2.02E-34 39724000 88002 47316 55617 53625 75619 41597.7 61966 52220 119835 FALSE TRUE 82494.11191 50819.32587 56936.2615 55001.10829 69680.18877 53606.28071 52674.77356 58739.78195 99833.76434 0.826314749 0.509039464 0.570310675 0.55092692 0.69796215 0.536955418 0.527624836 0.58837591 1 16.60724021 -1.46204454 2.707968737 1.01451799 0.584276801 0.624049575 0.096574791 6258605.107 6565721.82 684799.8564 0.022773305 0.034510834 1.46204454 -0.430241189 ALENDFFNS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ALENDFFNSPPR 12 0 F5H148;H3BMT1;Q9NYV6-3;Q9NYV6;Q9NYV6-2;A6NIE6 F5H148 RRN3;RRN3P2 RNA polymerase I-specific transcription initiation factor RRN3;Putative RRN3-like protein RRN3P2 1 ALENDFFNS(1)PPR;ALENDFFNS(1)PPR;ALENDFFNS(1)PPR;ALENDFFNS(1)PPR 235.71 4.92E-16 200951000 332445 409050 387028 465577 535240 436297 541870 412499 440867 TRUE FALSE 311637.8609 439336.4876 396208.4869 477524.494 493204.4095 562248.8612 460621.624 464000.4082 367283.4496 0.848494157 1.196178287 1.078753991 1.300152497 1.34284409 1.53083092 1.254131174 1.263330566 1 18.48653436 5.573534393 0.621629634 1.298835047 7.05E-15 0.394417242 0.147895721 8.324732995 1.126158879 0.05973765 9.742305242 374571.2093 -5.573534393 -1.298835047 ALENDFFNS(ph)PPRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALENDFFNSPPRK 13 1 F5H148;H3BMT1;Q9NYV6-3;Q9NYV6;Q9NYV6-2;A6NIE6 F5H148 RRN3;RRN3P2 RNA polymerase I-specific transcription initiation factor RRN3;Putative RRN3-like protein RRN3P2 1 ALENDFFNS(1)PPRK 86.8 0.0053046 227610000 199860 243480 226100 249610 368330 259590 293560 241280 277050 TRUE FALSE 187351.1194 261507.5125 231463.1988 256015.4152 339402.8476 334529.4189 249543.4033 271404.3391 230808.5652 0.811716494 1.133006101 1.002836262 1.109211068 1.470495028 1.449380436 1.081170463 1.175885041 1 17.81633724 5.642955545 0.59180098 1.220740001 9.80E-09 0.31752465 0.164487206 12.03084382 1.431567434 0.074850629 12.73638365 439496.6257 -5.642955545 -1.220739991 ALEQKPDDAQYYCQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALEQKPDDAQYYCQR 15 1 Q9Y2Z0;Q9Y2Z0-2 Q9Y2Z0 SUGT1 Suppressor of G2 allele of SKP1 homolog 0 ; 190.82 1.83E-07 884160000 723310 584510 589980 572170 655780 481360 848760 595200 965680 FALSE TRUE 678039.3182 627787.7286 603974.6042 586852.8509 604277.6841 620320.8178 721496.3175 669512.0302 804501.7695 0.842806497 0.780343503 0.750743662 0.729461231 0.751120392 0.771062092 0.896823779 0.832207032 1 19.61773607 1.101455548 0.870022116 0.99178192 0.76586577 0.727651042 0.042824793 0.290201423 0.489002919 0.039812893 0.014295731 12.63151808 -1.101455548 -0.225916151 ALEQSQSLPLPAPT(ph)STSPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALEQSQSLPLPAPTSTSPSR 20 0 O15068-4;O15068-10;O15068;H7BYP9;O15068-5;O15068-3;O15068-6;O15068-8;O15068-2;O15068-9;H3BLT1;H7C2S1;H0Y4M6;H0Y7A3 O15068-4 MCF2L Guanine nucleotide exchange factor DBS 1 ALEQSQSLPLPAPT(0.25)S(0.25)T(0.25)S(0.25)PS(0.001)R 88.264 0.0068364 0 54578 55818 54306 58896 62193 45966 64369 57274 63059 TRUE FALSE 51162.0604 59950.8228 55594.16397 60407.37107 57308.61265 59235.638 54717.46602 64424.78498 52534.04552 0.973883886 1.141180395 1.058250196 1.149870916 1.090885198 1.127566655 1.04156201 1.226343495 1 15.68096507 4.749542914 24.15581825 1.102944091 0.973883766 0.295970085 0.063250854 1205.01714 2650380.569 0.012931144 0.190618773 56174.97833 -4.749542914 -0.129060325 ALERPYTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ALERPYTSK 9 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;; 108.47 0.0023769 1931440000 1774200 2211530 1862220 2147920 2917980 1799600 2672890 2397910 3386170 FALSE TRUE 1663155.989 2375273.982 1906392.738 2203039.264 2688813.621 2319115.306 2272114.958 2697294.342 2820996.352 0.589563325 0.841998247 0.675787027 0.780943677 0.953143247 0.822090856 0.805429953 0.956149532 1 21.42777337 6.934019951 0.09041807 1.151241827 3.33E-12 0.580646731 0.082072206 94.9934865 0.770230922 1.576391668 13.6596112 8590529.842 -6.934019951 -1.151241827 ALES(ph)PERPFLAILGGAK ddPTM_SK-BR-3_Pertuzumab_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 236.38 2.10E-20 1210402000 1411366 1430782 1320166 1354289 1475453 844733 1705942 1296744 1578746 TRUE FALSE 1323031.121 1536718.588 1351480.961 1389042.349 1359576.873 1088593.704 1450151.834 1458645.343 1315243.094 1.00592136 1.1683913 1.02755222 1.056110734 1.03370767 0.827674906 1.102573236 1.109030985 1 20.32689804 3.707849287 4.985242091 1.020970816 1.099072841 0.085470076 0.086344202 0.356526011 24.51192789 0.022185506 0.036923088 5103.278708 -3.707849287 0.078102025 ALESLMTEFFHDCTTNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALESLMTEFFHDCTTNER 18 0 Q96QU8 Q96QU8 XPO6 Exportin-6 0 ; 183.74 6.18E-14 13209000 15457.4 19022.8 20003.6 20217.7 18207.3 16630.2 21391.7 17802.3 20243.7 FALSE TRUE 14489.94893 20431.26791 20478.09484 20736.52041 16777.3721 21431.06877 18184.21318 20024.95634 16864.89569 0.859178093 1.211467197 1.214243789 1.229567072 0.99481031 1.270750153 1.078228618 1.187375049 1 14.04173577 -1.474283769 4.6210039 0.999458376 1.145557443 0.085895763 0.125968451 0.000628378 7.15E-05 0.109036487 0.025605721 0.033551831 1.474283769 0.146099067 ALESPERPFLAILGGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALESPERPFLAILGGAK 17 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 227.4 1.61E-15 3133300000 4483800 5296300 4285600 4409100 5348600 2891200 6289900 4614500 5779700 FALSE TRUE 4203166.962 5688443.563 4387256.456 4522244.971 4928542.531 3725842.505 5346787.888 5190630.483 4815030.732 0.8729263 1.181392992 0.911158557 0.939193376 1.02357447 0.773794128 1.110436918 1.078005681 1 22.19911358 1.611157597 25 1.070668685 0.972526 0.171357281 0.109115503 0.599069551 4511.058101 0.051342205 0.026987485 40.84675843 -1.611157597 -0.098142685 ALEVIKPAHILQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALEVIKPAHILQEK 14 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 88.73 0.0038636 493530000 738110 569510 604360 581600 624220 546900 862490 586380 681580 FALSE TRUE 691913.0127 611677.113 618695.7046 596524.8406 575196.2792 704781.1518 733167.6315 659590.8338 567819.8948 1.218543096 1.077237903 1.089598498 1.050552906 1.012990711 1.241205457 1.291197505 1.161619802 1 19.11507387 2.226398865 24.99997015 1.209333215 1.086265062 0.117378388 0.093124267 272.1156452 559363.2823 0.032081482 0.023873356 168.4220174 -2.226398865 -0.123068153 ALFAGDIEEMEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALFAGDIEEMEER 13 0 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-4;Q9BQ52-3 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 0 187.42 1.62E-05 41583000 38187 42083 42763 40187 39987 40509 47678 38083 51163 FALSE TRUE 35796.94384 45198.86911 43777.35855 41218.26646 36846.58232 52203.29069 40529.12652 42837.74638 42623.56477 0.839839277 1.060419731 1.027069387 0.967030014 0.864465056 1.224751871 0.950861964 1.005024958 1 15.37936364 ALFARPDLLLLDEPTNMLDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALFARPDLLLLDEPTNMLDVR 21 1 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 ; 138.03 2.11E-06 246980000 253600 257120 266230 256780 257700 196322 235950 196681 185532 FALSE TRUE 237727.6287 276157.4323 272545.1013 263369.4095 237461.2815 252996.9744 200571.488 221237.0558 154565.5106 1.538037999 1.786669168 1.763298295 1.703933876 1.5363148 1.636826827 1.297647109 1.431348138 1 17.23785891 1.288168923 0.58343998 1.00803403 1.739471195 0.813307309 0.102457031 0.269394893 0.227677021 0.095553619 0.046874639 19.41640952 -1.288168923 0.731437165 ALFEEVPELLTEAEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALFEEVPELLTEAEKK 16 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 218.63 2.11E-14 46428000 135616 87057 104895 107233 127783 81378 146234 111331 185961 FALSE TRUE 127128.0366 93502.79086 107383.1589 109984.7803 117747.4386 104870.5075 124307.5693 125230.9204 154922.9077 0.820589017 0.603543996 0.69313932 0.709932327 0.760038914 0.676920599 0.802383399 0.808343467 1 17.24119096 0.78193485 0.599537975 1.006325875 0.685320836 0.69361873 0.059394511 0.557132645 0.430532389 0.060726363 0.02407007 6.052500723 -0.78193485 -0.321005039 ALGALVDSCAPGLCPDWDSWDASKPVTNAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALGALVDSCAPGLCPDWDSWDASKPVTNAR 30 1 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 135.72 3.40E-06 51984000 127210 97480 99862 92800 116890 86421 146610 100060 129820 FALSE TRUE 119248.1532 104697.5206 102230.7738 95181.40511 107709.9309 111369.3398 124627.1916 112552.7113 108152.2033 1.102595689 0.968057214 0.945249109 0.880069034 0.995910648 1.029746379 1.152331508 1.040688102 1 16.72270353 2.143147128 3.269892637 1.082457321 0.967078585 0.231009596 0.067439245 0.251380249 5.33005912 0.02701006 0.01870389 139.0423591 -2.143147128 -0.115378737 ALGALVDSCAPGLCPDWESWDPQKPVDNAR ddPTM_SK-BR-3_Pertuzumab_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 0 114.83 0.00012362 80249000 70291 88607 51978 46908 111860 47167 73307 84885 75888 FALSE TRUE 65891.61178 95167.55448 53210.94271 48111.7387 103074.9668 60783.34721 62315.2959 95483.0791 63221.80254 1.042229249 1.505296443 0.841654944 0.760999161 1.630370579 0.961430152 0.985661487 1.510287199 1 15.94813455 3.38620498 0.010835766 5.60E-07 2.286854733 0.000934282 0.303261409 26790.88822 76.6893189 7724.357789 8462.388692 2433.352239 -3.38620498 2.286854173 ALGEYLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALGEYLER 8 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 102.51 0.011517 166450000 404800 383440 368590 384780 415830 323430 468810 362070 414720 FALSE TRUE 379464.2906 411830.2966 377333.1289 394654.1062 383172.3892 416798.9906 398516.2927 407275.2365 345500.5528 1.098302991 1.191981585 1.09213466 1.142267655 1.109035531 1.206362731 1.15344618 1.178797641 1 18.39832849 -1.045861661 5.067370488 0.999997842 1.147605511 0.586478523 0.03866178 8.74E-07 1.64E-07 0.03469458 0.008177471 0.089978415 1.045861661 0.147607669 ALGHQLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALGHQLGR 8 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 155.51 0.00040783 128890000 99045 154620 118480 113640 182950 96509 129780 150750 145210 FALSE TRUE 92845.95025 166068.2257 121290.4016 116556.1948 168581.845 124369.5816 110320.6938 169571.4693 120973.5129 0.767489908 1.372765176 1.002619488 0.963485246 1.393543437 1.028072829 0.911940897 1.401723942 1 16.88433168 -2.078286282 2.352520928 0.837476007 1.106390744 0.02231146 0.218739415 33472739.98 10636755.45 29165677.97 0.047737966 0.008350524 2.078286282 0.268914738 ALGNICYDSHEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ALGNICYDSHEGR 13 0 P52306-4;P52306;P52306-5;D6RHH8 P52306-4 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 0 ;;; 213.18 7.96E-09 2790280000 1962060 2824220 2471220 2443670 2797100 2418650 2910130 2674440 2870460 FALSE TRUE 1839258.167 3033328.187 2529838.505 2506378.709 2577427.049 3116874.991 2473783.023 3008349.721 2391361.682 0.769125884 1.268452284 1.057907101 1.048096876 1.077807288 1.303389201 1.03446628 1.258006994 1 21.18940092 2.405817569 24.99999994 1.150415217 1.076771088 0.085630273 0.150411015 144.8130469 50770.09254 0.047810968 0.04000153 254.576065 -2.405817569 -0.073644129 ALGS(ph)PTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ALGSPTK 7 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 1 ALGS(0.948)PT(0.052)K;ALGS(0.966)PT(0.034)K;ALGS(0.889)PT(0.111)K;ALGS(0.979)PT(0.021)K;ALGS(0.995)PT(0.005)K;ALGS(0.948)PT(0.052)K 131.11 0.0036697 6400950000 10332230 7208500 8354870 8196380 8539500 7112540 9918890 6956280 9144030 TRUE FALSE 9685554.168 7742224.84 8553051.462 8406712.987 7868842.117 9165814.836 8431644.527 7824786.871 7617832.32 1.271431788 1.016329123 1.122767095 1.103557106 1.032950292 1.203205118 1.106829892 1.027167118 1 22.8609491 1.183598244 4.310433511 1.004724467 1.112463414 0.267882973 0.074040767 0.288380041 10.13098007 0.062481531 0.016616753 15.26153596 -1.183598244 0.107738947 ALHHGIDLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALHHGIDLEK 10 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ; 95.502 0.004267 319760000 492680 427580 425170 441110 488480 340850 549470 408070 471810 FALSE TRUE 461844.0383 459238.4681 435255.2332 452429.6294 450116.7512 439247.8618 467082.0745 459018.4378 393061.863 1.174990712 1.168361806 1.107345368 1.151039243 1.145154984 1.117503129 1.188316951 1.16780202 1 18.58439687 -1.417949745 3.310879186 0.998217996 1.150886263 0.786304869 0.024981621 193535644 446910739.5 3701977.871 0.006129322 0.038198847 1.417949745 0.152668267 ALHQGDSLECTAMTVQILLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALHQGDSLECTAMTVQILLK 20 0 O14579;O14579-3 O14579 COPE Coatomer subunit epsilon 0 169.39 1.08E-11 137990000 203690 242900 249850 260950 278680 218310 331780 245640 236160 FALSE TRUE 190941.4065 260884.5687 255776.56 267646.4188 256793.5969 281332.553 282032.6691 276308.6947 196743.3703 0.970509991 1.326014535 1.300051735 1.360383419 1.305221093 1.429946801 1.433505325 1.404411718 1 17.5859555 4.741284904 4.739921676 1.343217285 0.94826733 0.425914789 0.125092111 0.154709515 9.758459508 0.026548326 0.202852693 55116.91533 -4.741284904 -0.394949955 ALHSVLQAVPLNELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALHSVLQAVPLNELR 15 0 Q16401-2;Q16401;F2Z3J2 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ; 120.7 0.00011954 482330000 533940 790430 567470 587680 893330 463860 713760 751820 900620 FALSE TRUE 500521.6485 848954.2596 580930.6564 602760.8637 823171.4653 597768.8519 606738.3142 845686.382 750300.7038 0.667094734 1.131485357 0.774263776 0.803359054 1.097122075 0.796705706 0.808660196 1.127129933 1 19.51710939 1.236447253 24.99723726 1.063564993 0.883182813 0.229809713 0.146616045 87.24527435 1031827.547 0.111364818 0.033121571 17.23642736 -1.236447253 -0.180382179 ALHVNNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ALHVNNDR 8 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;;;; 141.2 0.00071989 724600000 1254790 1601800 1488840 1529960 1488760 1304340 1520880 1417760 1130200 FALSE TRUE 1176254.934 1720398.939 1524155.988 1569221.364 1371838.795 1680881.784 1292838.163 1594770.457 941562.3186 1.249258717 1.827174797 1.618752108 1.666614448 1.45698141 1.785205026 1.373077637 1.693749235 1 19.84469706 -2.564423427 0.361935849 3.68E-13 1.625686365 0.487383039 0.18414959 50.49007725 2.028733566 39.65366479 0.120886176 0.002726318 2.564423427 1.625686365 ALIEVLQPLIAEHQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALIEVLQPLIAEHQAR 16 0 P23381;P23381-2 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ; 174.87 2.80E-12 254230000 458030 601650 569860 589860 613570 493710 631000 499180 581520 FALSE TRUE 429362.7199 646196.792 583377.3483 604996.8062 565382.6872 636236.0623 536387.4079 561503.7218 484460.5552 0.886269718 1.333848102 1.204179251 1.248805088 1.167035543 1.313287646 1.107184893 1.159028771 1 18.88601968 0.867688515 1.172368492 1.002769158 1.208068375 0.151964505 0.125397406 0.959482021 2.580627357 0.105901484 0.032986423 7.373751794 -0.867688515 0.205299217 ALIFVSHGAGEHSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALIFVSHGAGEHSGR 15 0 A0A0C4DFN3;Q99685-2;Q99685;A0A3B3ITT3;C9JAM4 A0A0C4DFN3 MGLL Monoglyceride lipase 0 ; 183.96 2.80E-07 360960000 100246 138446 142044 126036 162887 123079 159771 148150 188067 FALSE TRUE 93971.7818 148696.6859 145413.3508 129270.2971 150094.5121 158609.9093 135814.8218 166646.8536 156677.4027 0.599778782 0.949062745 0.928106723 0.825073015 0.957984428 1.012334303 0.866843715 1.063630432 1 17.25743759 4.739488642 24.91741375 0.940006474 0.599778671 0.714936391 0.069300264 38.54647634 1034809.743 0.014956118 0.091040075 54889.42001 -4.739488642 -0.340227803 ALIQTCLNSPDS(ph)PPRSDPTTDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ALIQTCLNSPDSPPRSDPTTDQR 23 1 P11831 P11831 SRF Serum response factor 1 ALIQTCLNSPDS(1)PPRSDPTTDQR;ALIQTCLNSPDS(1)PPRSDPTTDQR;ALIQTCLNSPDS(1)PPRSDPTTDQR;ALIQTCLNSPDS(1)PPRSDPTTDQR 257.94 7.60E-44 1655000000 752610 978880 891170 886130 1061280 720340 979230 833730 1041860 TRUE FALSE 705505.4835 1051357.294 912308.9732 908869.596 977931.3498 928290.4643 832403.5522 937823.0258 867966.8353 0.812825392 1.211287403 1.051087364 1.047124797 1.126692069 1.069499924 0.95902691 1.080482557 1 19.72728039 1.879838956 10.00371537 1.00959644 1.074010775 0.005443155 0.104754559 1.043189482 81.8878332 0.04027267 0.025580792 75.82963328 -1.879838956 0.064414335 ALIRS(ph)PSLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALIRSPSLAK 10 1 Q5SW96 Q5SW96 LDLRAP1 Low density lipoprotein receptor adapter protein 1 1 ALIRS(0.997)PS(0.003)LAK 79.466 0.016303 152470000 568350 547070 521620 563120 790060 344550 563030 499350 1073000 TRUE FALSE 532777.988 587575.632 533993.0727 577570.6126 728011.8745 444015.9917 478608.8784 561694.9467 893909.3682 0.596008955 0.657310073 0.597368248 0.646117641 0.814413519 0.496712539 0.535410966 0.628357825 1 19.76976904 0.931614863 21.96477155 1 0.616663127 0.667530275 0.083940392 6792.002693 2181541.678 0.080972134 0.020243033 8.543087669 -0.931614863 -0.383336873 ALKDEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 88.948 0.016628 3624760000 7168300 4013430 4757500 4598850 4866200 3549820 6339800 4162000 5447800 FALSE TRUE 6719648.899 4310588.533 4870350.147 4716864.277 4484028.281 4574595.407 5389205.846 4681634.862 4538526.986 1.480579254 0.949776997 1.073112523 1.039294091 0.987991984 1.007947165 1.187435012 1.031531789 1 22.1137927 4.746068268 24.99126271 1.042881017 1.480579464 0.827670882 0.063850353 394.6805626 1313770.366 0.016070663 0.169140892 55727.33418 -4.746068268 0.437698447 ALKDEIDVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALKDEIDVLR 10 1 Q9UJC3;Q9UJC3-2 Q9UJC3 HOOK1 Protein Hook homolog 1 0 72.29 0.044167 178690000 424030 482630 434980 456500 489640 421350 538310 457460 570610 FALSE TRUE 397490.7192 518364.4274 445297.931 468214.5629 451185.6495 542986.905 457595.4129 514574.888 475371.5047 0.836168587 1.090440681 0.936736692 0.984944529 0.949122202 1.142236965 0.962605895 1.082468938 1 18.8586959 ALKEPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ALKEPPR 7 1 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;; 100.45 0.0089232 3632400000 7661700 7423800 7886900 7287700 8082000 6578300 8763500 7174100 7107700 FALSE TRUE 7182167.874 7973465.876 8073980.992 7474714.72 7447272.321 8477348.42 7449494.531 8069802.177 5921378.953 1.212921505 1.346555581 1.363530532 1.262326695 1.257692234 1.431651054 1.25806752 1.362824815 1 22.49750175 -1.303261712 3.472920404 0.998796603 1.317489791 0.687876848 0.065943474 10575187.22 13862851.02 128351.985 0.014426247 0.049743723 1.303261712 0.318693187 ALKEPPRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ALKEPPRDR 9 2 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;;;;; 103.7 0.0019009 8188120000 17946230 22002270 21568970 21308600 24670540 16647820 25079440 18820070 31276420 FALSE TRUE 16823007.5 23631340.96 22080596.15 21855414.75 22733015.3 21453775.38 21319010.8 21169797.17 26056183.45 0.645643578 0.906937926 0.847422501 0.838780353 0.872461439 0.823365994 0.818193917 0.812467306 1 24.63512245 -2.370154629 2.091021874 1.998655191 0.831963214 0.391176253 0.069045383 4113849.245 405849.114 19442235.15 0.015122766 0.004264277 2.370154629 -1.166691977 ALLDFERHDDDELGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALLDFERHDDDELGFR 16 1 Q96HU1;Q96HU1-2 Q96HU1 SGSM3 Small G protein signaling modulator 3 0 107.5 0.000675 15064000 11861 21551 16528 20482 19674 12972 17673 13109 20266 FALSE TRUE 11118.64118 23146.65846 16920.05197 21007.6028 18128.8834 16716.80582 15023.09772 14745.68751 16883.47368 0.658551753 1.370965413 1.002166514 1.244270178 1.073765017 0.990128343 0.88981083 0.873379957 1 14.04332414 2.123806582 2.720854157 0.912754964 1.111488726 0.09734658 0.186394614 0.434973554 6.41127005 0.077293024 0.050042984 132.9862017 -2.123806582 0.198733762 ALLDSLQLGPDSLTVHLIHEVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALLDSLQLGPDSLTVHLIHEVTK 23 0 Q14697;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 297.95 5.45E-62 838200000 1225100 1270500 1307270 1341090 1336270 1055380 1559070 1205060 1104830 FALSE TRUE 1148423.178 1364569.142 1338279.062 1375504.64 1231324.744 1360051.073 1325301.927 1355514.394 920426.7355 1.247707323 1.482539663 1.453976737 1.494420563 1.337775943 1.477630995 1.439877696 1.472702108 1 19.81194336 -1.559702519 5.967839664 0.998973506 1.435493876 0.748109071 0.077473341 0.000938418 6.92E-05 0.066528252 0.015647112 0.027561159 1.559702519 0.43652037 ALLDSQFSYQHAIEESVVLIYDPIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ALLDSQFSYQHAIEESVVLIYDPIK 25 0 A0A087WZK9;B3KS98;O15372;E5RJT0;E5RGU4 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ;;;;;; 220.49 1.23E-33 2270058000 1044729 1038420 1133777 1173888 1268888 994478 1390876 984779 1188383 FALSE TRUE 979341.2768 1115305.697 1160670.726 1204011.953 1169234.655 1281567.655 1182327.056 1107730.826 990034.2001 0.989199441 1.126532495 1.172354173 1.216131678 1.181004308 1.294468064 1.194228498 1.118881374 1 19.91711884 5.206487347 1.079133995 1.186348669 0.660300182 0.330257465 0.076271742 4.056500779 1.938548072 0.019986746 3.104937524 160874.5508 -5.206487347 -0.526048488 ALLELQLEPEELYQTFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ALLELQLEPEELYQTFQR 18 0 P13639 P13639 EEF2 Elongation factor 2 0 ;; 250.89 8.71E-25 289440000 1024711 1163987 1198675 1200392 1258364 1158318 1243992 1050849 944150 FALSE TRUE 960576.1677 1250169.809 1227108.137 1231196.091 1159537.167 1492705.603 1057466.948 1182049.811 786565.2656 1.221228816 1.589403783 1.560084319 1.565281541 1.474177946 1.897751742 1.34441094 1.502799402 1 19.58520695 0.511235267 1.295708798 1.000726191 1.545154823 0.465643544 0.174600129 1.641136665 3.491176446 0.149338029 0.044534528 3.245153666 -0.511235267 0.544428632 ALLEPELRPEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ALLEPELRPEDR 12 1 P0DPD7;P0DPD8 P0DPD7 0 ;;; 142.83 5.63E-05 408851000 621379 765045 786464 728551 823079 697459 822235 733936 814756 FALSE TRUE 582487.9976 821689.7278 805119.2975 747246.8521 758437.6955 898804.091 698948.495 825569.5252 678767.9601 0.858154821 1.210560569 1.186148058 1.100887042 1.117374037 1.324169884 1.029731125 1.216276509 1 19.37255894 -1.162583431 4.439821302 0.999972886 1.141635437 0.09111263 0.125057784 0.476275648 32865911.07 1718.238992 0.025999443 0.068772778 1.162583431 0.141662551 ALLETAS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALLETASPR 9 0 H3BMP6;H3BQS6;H3BN05;H3BTS2;H3BQJ0;I3L4F8;H3BUW2;H3BTR4;Q96BT3-3;Q96BT3-2;Q96BT3 H3BMP6 CENPT Centromere protein T 1 ALLETAS(1)PR;ALLETAS(1)PR 142.72 0.00010873 102690000 499010 569260 560260 511180 639100 453400 604070 598700 657260 TRUE FALSE 467777.8549 611408.6027 573549.6318 524297.7442 588907.664 584289.2197 513495.3114 673449.0129 547559.0599 0.854296621 1.116607591 1.047466244 0.957518161 1.075514419 1.067079814 0.937789818 1.229911186 1 19.06265506 1.250523612 24.99999503 1.114955674 1.021918031 0.169913993 0.094447188 357.2060332 746490.8866 0.058404343 0.020949766 17.80424705 -1.250523612 -0.093037644 ALLFIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALLFIPR 7 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 157.88 0.0033645 1824570000 1099860 1942450 1182990 1189560 1932190 897050 1260960 1716080 1426810 FALSE TRUE 1031021.726 2086271.019 1211051.081 1220086.124 1780443.591 1156013.773 1071890.754 1930336.366 1188666.193 0.867377008 1.755136161 1.018831938 1.02643293 1.497849944 0.972530201 0.901759266 1.623951599 1 20.1809122 3.742755839 24.12173435 1.129290159 1.378362884 0.031663743 0.316127877 599.053072 924237.2172 0.074534799 0.133706474 5530.391019 -3.742755839 0.249072725 ALLFVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALLFVPR 7 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 181.07 0.0015755 2346400000 1056130 1725110 1105840 1074840 1745880 994450 1265160 1432330 1335720 FALSE TRUE 990028.7085 1852838.939 1132071.047 1102422.214 1608765.627 1281531.571 1075461.003 1611159.553 1112779.703 0.889689762 1.665054579 1.017336175 0.990692238 1.445717983 1.151648946 0.966463533 1.447869286 1 20.08573658 -5 0.079204886 0.356525299 1.406121729 0.011116649 0.257355194 786.4592709 4.419388463 89.95974594 8.615380753 1.00E-05 5 1.049596429 ALLSLRS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALLSLRSPK 9 1 Q5H909;Q9UNF1-2;Q9UNF1 Q5H909 MAGED2 Melanoma-associated antigen D2 1 ALLS(0.001)LRS(0.999)PK 62.799 0.0486 349410000 491730 462600 472270 433810 636290 306160 559820 512900 690790 TRUE FALSE 460953.4971 496851.3853 483472.4674 444942.299 586318.3501 394543.4219 475880.1881 576936.694 575492.6863 0.800971946 0.863349608 0.840101845 0.773150223 1.018811123 0.685575041 0.826909185 1.002509168 1 19.13443807 1.23794476 24.98535864 1.00125468 0.83117652 0.425003132 0.082880122 14.3856241 583392.6464 0.059019917 0.018108015 17.29596348 -1.23794476 -0.17007816 ALLYEDALYTVLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALLYEDALYTVLHR 14 0 Q70J99;Q70J99-3;K7EQ37;Q70J99-2;K7EIH3 Q70J99 UNC13D Protein unc-13 homolog D 0 ; 237.3 2.73E-17 289380000 560050 904810 780310 699940 1013640 717880 855810 864350 705040 FALSE TRUE 524997.4702 971803.0739 798819.3217 717901.6454 934032.8032 925120.3022 727489.2355 972266.0002 587364.2693 0.893819215 1.654515136 1.360006666 1.222242623 1.590210457 1.575036737 1.238565697 1.655303278 1 19.16389598 -1.114146606 5.26465958 0.999991032 1.413446868 0.2135595 0.238973807 2.22E-05 3.73E-06 0.203909545 0.048060898 0.076887085 1.114146606 0.413455837 ALMTSHGS(ph)VEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ALMTSHGSVEGR 12 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C103 Q9H8V3-2 ECT2 Protein ECT2 1 ALMTSHGS(1)VEGR;ALMTSHGS(1)VEGR;ALMTSHGS(1)VEGR 181.72 4.76E-05 1098690000 578760 620526 586090 576440 401638 510287 759940 507929 562030 TRUE FALSE 542536.4447 666470.3907 599992.3316 591232.4263 370094.9716 657598.5731 645994.0519 571345.0537 468223.5621 1.158712394 1.423402077 1.281422765 1.262713956 0.790423638 1.404454253 1.379670107 1.22023986 1 18.83683801 3.179047208 4.166059669 1.203074669 1.317296409 0.05849954 0.189367402 0.635718586 22.22284123 0.055847879 0.06950346 1510.24431 -3.179047208 0.114221739 ALNHSVEDIEPDLLT(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALNHSVEDIEPDLLTPR 17 0 Q8IWR0;I3L2K5 Q8IWR0 ZC3H7A Zinc finger CCCH domain-containing protein 7A 1 ALNHSVEDIEPDLLT(1)PR;ALNHSVEDIEPDLLT(1)PR 190.85 1.01E-09 165042000 152905 181679 165574 182459 189085 145455 172699 150298 174674 TRUE FALSE 143334.949 195130.7022 169501.4935 187141.2068 174235.0268 187445.4972 146804.3882 169063.0361 145519.781 0.984986014 1.340922182 1.164800361 1.286019025 1.197328815 1.288110084 1.008827716 1.161787319 1 17.15085575 1.733352553 11.41030941 1.065638228 1.222558355 0.315791857 0.105181216 0.09053418 59.25284735 0.043719964 0.023868079 54.11934764 -1.733352553 0.156920127 ALNSIIDVYHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALNSIIDVYHK 11 0 P05109 P05109 S100A8 "Protein S100-A8;Protein S100-A8, N-terminally processed" 0 ; 117.98 0.00078252 1258970000 1354340 1449730 1356870 1152920 1275580 747280 1726980 1328990 2286860 FALSE TRUE 1269574.277 1557069.518 1389055.597 1182505.879 1175401.092 963007.6049 1468035.381 1494917.327 1905168.292 0.66638432 0.817287126 0.729098633 0.620683162 0.616953944 0.505471149 0.770554175 0.784664186 1 20.86148701 0.90754215 1.84504291 0.997459081 0.683733994 0.597782267 0.085600086 0.362767196 2.518995712 0.088653904 0.025023309 8.082433685 -0.90754215 -0.313725087 ALPAAHIPAPPHEGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ALPAAHIPAPPHEGSPR 17 0 P17029;E9PC66 P17029 ZKSCAN1 Zinc finger protein with KRAB and SCAN domains 1 1 ALPAAHIPAPPHEGS(1)PR;ALPAAHIPAPPHEGS(1)PR;ALPAAHIPAPPHEGS(1)PR;ALPAAHIPAPPHEGS(1)PR 127.37 6.77E-05 371424000 244846 247774 256773 229447 327175 293594 287987 228280 318970 TRUE FALSE 229521.5259 266119.4448 262863.7768 235334.9985 301479.9953 378349.8217 244806.0229 256781.2605 265731.8464 0.863733606 1.001458607 0.989206903 0.88561082 1.134527153 1.423803081 0.921252105 0.966317225 1 18.01961161 2.730200478 24.82565786 1.098696314 0.955112574 0.21784929 0.142291129 957.7100542 2843940.397 0.045560334 0.043595846 537.2797572 -2.730200478 -0.14358374 ALPAVQQNNLDEDLIRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ALPAVQQNNLDEDLIRK 17 1 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 349.94 1.95E-87 364210000 527540 491330 501480 517000 592080 411770 629860 493140 690340 FALSE TRUE 494522.2131 527708.5844 513375.3424 530267.0953 545580.4251 530641.3145 535418.3403 554709.6145 575117.7942 0.85986248 0.917566088 0.892643816 0.92201476 0.948641184 0.922665443 0.930971613 0.964514783 1 19.13349795 7.999996918 0.022721663 1.478841956 0.18901563 0.809808636 0.016582918 982.2202293 1.717624054 34.6817029 67.97274918 99999290.33 -7.999996918 -1.289826326 ALPESLGQHALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ALPESLGQHALR 12 0 O94760 O94760 DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1" 0 ;; 212.9 1.49E-08 1026480000 668580 1102090 949470 960160 1207320 1014990 995450 996880 1161860 FALSE TRUE 626734.7712 1183689.89 971991.8768 984799.3311 1112501.957 1308001.136 846191.5138 1121342.662 967938.0601 0.647494708 1.222898385 1.004188095 1.017419783 1.149352426 1.351327311 0.874220726 1.15848597 1 19.8845552 4.749055233 24.78133063 1.093275121 0.647494426 0.527142441 0.133818231 1066.378854 2518024.364 0.030013811 0.425817926 56111.93337 -4.749055233 -0.445780695 ALPFWNEEIVPQIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALPFWNEEIVPQIK 14 0 P18669;Q8N0Y7;P15259 P18669 PGAM1;PGAM4;PGAM2 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4;Phosphoglycerate mutase 2 0 174.84 5.77E-06 39913000 106670 99048 110830 100740 101950 85005 133110 89514 118050 FALSE TRUE 99993.71511 106381.617 113458.9399 103325.159 93943.25825 109544.5636 113151.3912 100690.0199 98346.69237 1.016747109 1.081699998 1.153662998 1.050621597 0.955225397 1.113861188 1.150535809 1.023827213 1 16.58558891 ALPLALVLHELGAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALPLALVLHELGAGR 15 0 C9JGI3;P19971;A0A494C0L6;P19971-2 C9JGI3 TYMP Thymidine phosphorylase 0 ; 198.14 8.07E-09 377120000 276630 395080 323670 339270 378110 257860 342880 306720 243270 FALSE TRUE 259316.2221 424332.1343 331347.6052 347976.2426 348414.7658 332299.996 291468.3271 345014.6672 202666.6654 1.279520841 2.093744097 1.634938852 1.71698805 1.719151816 1.639638148 1.438166097 1.702375013 1 17.62874929 -0.431251452 0.330569492 0.771198349 1.774454961 0.466318555 0.213738192 6.223256527 0.747631733 1.813889272 0.189281672 0.370466163 0.431251452 1.003256612 ALPLPHFDTINLPEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALPLPHFDTINLPEKK 16 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 0 139.65 1.15E-06 28081000 124550 96436 103480 104300 124400 80512 133780 97861 153380 FALSE TRUE 116754.6378 103576.2218 105934.5945 106976.5146 114630.1258 103754.5074 113720.931 110079.1613 127779.8871 0.913716865 0.810583137 0.829039662 0.837193685 0.897090523 0.811978393 0.889975203 0.861474867 1 16.96330124 -0.318769166 0.466845603 1.025884318 0.840907692 0.611643695 0.035749877 4.051472731 0.892007882 0.209570939 0.017593883 0.479988502 0.318769166 -0.184976626 ALPLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ALPLSPR 7 0 J3KTI7;J3QR52;J3QLN7;Q99741 J3KTI7 CDC6 Cell division control protein 6 homolog 1 ALPLS(1)PR;ALPLS(1)PR;ALPLS(1)PR;ALPLS(1)PR;ALPLS(1)PR 122.19 0.0045789 2065930000 2018580 2569460 2453140 2542790 3074830 2172890 2700950 2186000 2816080 TRUE FALSE 1892240.681 2759705.492 2511329.639 2608042.296 2833345.255 2800168.069 2295967.622 2458926.912 2346058.055 0.806561746 1.176315942 1.070446502 1.111669974 1.207704664 1.193562991 0.978649107 1.048110001 1 21.16180728 1.673454841 10.25118734 1.010776421 1.105946688 0.105382637 0.113781829 0.231350838 34.77455356 0.050410449 0.027193449 47.14708444 -1.673454841 0.095170267 ALPNNTSSS(ph)PQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ALPNNTSSSPQPK 13 0 P04637-7;P04637;P04637-4;A0A087WZU8;A0A0U1RQC9;A0A087X1Q1;A0A087WT22;J3KP33;A0A087WXZ1;E7ESS1;P04637-5;P04637-9;P04637-8;P04637-6;P04637-2;P04637-3 P04637-7 TP53 Cellular tumor antigen p53 1 ALPNNT(0.106)S(0.217)S(0.113)S(0.564)PQPK;ALPNNT(0.011)S(0.014)S(0.041)S(0.934)PQPK;ALPNNTS(0.001)S(0.009)S(0.99)PQPK;ALPNNT(0.001)S(0.009)S(0.071)S(0.919)PQPK;ALPNNTSS(0.006)S(0.994)PQPK;ALPNNTSS(0.004)S(0.996)PQPK;ALPNNTSS(0.068)S(0.932)PQPK;ALPNNTSSS(1)PQPK 330.25 2.19E-62 6352810000 7504550 5857640 6050650 5903880 6468680 4874170 7860320 5535550 5026670 TRUE FALSE 7034853.612 6291345.76 6194174.275 6055383.556 5960655.966 6281263.753 6681737.988 6226675.603 4187686.303 1.679890303 1.502344088 1.47913999 1.445997412 1.423376904 1.499936552 1.595567935 1.486901155 1 21.99772194 0.943557804 22.72354833 1 1.51230329 0.828770337 0.073541149 3210.658763 1292608.59 0.069774901 0.017443725 8.781279561 -0.943557804 0.51230329 ALPQT(ph)PRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 118.9 0.0014771 62036830000 4608520 5815850 4804680 4949890 5489010 4041440 5493280 4598110 5908930 TRUE FALSE 4320080.96 6246461.585 4918649.279 5076912.558 5057925.296 5208138.121 4669613.661 5172194.155 4922691.41 0.877585166 1.268911875 0.999178878 1.031328624 1.027471534 1.057985904 0.948589556 1.050684214 1 22.23101587 3.724172682 24.96692124 1.013960344 1.111053917 0.023486705 0.0988178 223.1127551 1889211.603 0.023383945 0.038076374 5298.740878 -3.724172682 0.097093573 ALPSLNTGSSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 ALPSLNTGSSSPR 13 0 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 ALPSLNTGSS(0.024)S(0.975)PR;ALPSLNT(0.002)GS(0.042)S(0.434)S(0.523)PR;ALPSLNTGSSS(1)PR;ALPSLNTGSSS(1)PR;ALPSLNTGSS(0.002)S(0.998)PR;ALPSLNTGSS(0.006)S(0.994)PR;ALPSLNTGSS(0.009)S(0.99)PR;ALPSLNTGSSS(1)PR;ALPSLNTGSS(0.081)S(0.918)PR;ALPSLNTGSS(0.005)S(0.995)PR 290.69 1.65E-40 21108570000 13323800 15899370 15514110 16046470 16376690 14708920 16716270 13333640 23669330 TRUE FALSE 12489887.14 17076575.9 15882112.02 16458249.59 15090530.83 18955146.42 14209820.5 14998374.3 19718765.91 0.633401055 0.86600632 0.805431338 0.834649068 0.765287792 0.961274479 0.72062423 0.760614248 1 24.23306593 -2.405213929 2.245633165 2.603270229 0.802766326 0.351296937 0.087407795 2336105.706 421015.1703 18879060.45 0.018933727 0.003933563 2.405213929 -1.800503903 ALPTSKPEGSLHS(ph)SPVGPSSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALPTSKPEGSLHSSPVGPSSSK 22 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 ALPTSKPEGSLHS(0.574)S(0.426)PVGPSSSK 123.79 1.43E-05 252670000 225340 194750 249190 240480 293820 221580 325120 245320 366980 TRUE FALSE 211236.3716 209169.4926 255100.9045 246651.1239 270744.5624 285546.5489 276371.2743 275948.742 305728.6672 0.690927591 0.68416709 0.834402959 0.80676479 0.885571395 0.933986831 0.903975662 0.902593612 1 18.22189231 5.174383745 0.242536578 0.997605501 0.300978065 0.925779082 0.027455985 2.955677069 0.126165523 0.039019607 0.640738885 149411.4033 -5.174383745 -0.696627437 ALPTSKPEGSLHSS(ph)PVGPSSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALPTSKPEGSLHSSPVGPSSSK 22 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 ALPTSKPEGSLHS(0.378)S(0.621)PVGPSSSK;ALPTSKPEGS(0.001)LHS(0.071)S(0.926)PVGPSSSK 95.823 0.00094093 565470000 608660 554330 628620 570770 686950 582070 824990 584560 935160 TRUE FALSE 570565.0571 595373.17 643531.1633 585416.9245 632999.718 750104.1599 701290.4083 657543.6028 779075.7546 0.73236146 0.764204465 0.826018727 0.751424904 0.812500857 0.962812866 0.90015689 0.844004705 1 19.57140409 2.376344221 5.232430047 0.917401878 0.777789251 0.715779262 0.047124944 0.116900661 5.047274267 0.015645992 0.01298873 237.8724912 -2.376344221 -0.139612627 ALQDEWDAVMLHSFTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ALQDEWDAVMLHSFTLR 17 0 Q9UMS4;F5GY56 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ;;;; 267.39 8.98E-28 843271000 1011946 1168746 1057031 1073309 1233564 1046220 1138583 1000235 1055819 FALSE TRUE 948610.1062 1255281.17 1082104.274 1100851.926 1136684.859 1348246.73 967863.0492 1125116.542 879595.988 1.078461156 1.427111068 1.230228752 1.251542687 1.292280632 1.532802273 1.10034955 1.279128778 1 19.7464815 0.686024994 1.073905452 1.002820237 1.295991529 0.28531888 0.134650369 1.214700573 2.366643118 0.116017818 0.036630807 4.853164301 -0.686024994 0.293171292 ALQEGEGDLSIS(ph)ADRLSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALQEGEGDLSISADRLSEK 19 1 P49589-3;P49589;B4DKY1;P49589-2 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 1 ALQEGEGDLS(0.001)IS(0.999)ADRLSEK 207.07 2.03E-16 92796000 67913 62596 53908 61058 70677 38137 81428 61673 94865 TRUE FALSE 63662.44656 67230.67297 55186.72322 62624.85165 65126.31352 49146.5328 69218.62734 69373.00981 79031.41865 0.80553339 0.850682857 0.698288404 0.792404498 0.824055985 0.621860693 0.875836832 0.877790264 1 16.27013868 1.14182716 1.816075163 0.990485517 0.772094046 0.52367368 0.070808269 0.245689478 1.529622754 0.061831276 0.01790512 13.8620404 -1.14182716 -0.21839147 ALQEVGSGGTLGLS(ph)SPKS ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALQEVGSGGTLGLSSPKS 18 1 A0A0M3HER3 A0A0M3HER3 1 ALQEVGSGGTLGLS(0.496)S(0.496)PKS(0.008) 75.239 0.0028328 0 51883 38416 47088 49088 61126 37950 47962 42076 62472 TRUE FALSE 48635.73564 41260.36061 48204.9496 50347.68119 56325.41053 48905.54893 40770.54336 47329.28122 52045.01962 0.93449356 0.792782113 0.926216379 0.967387111 1.082244006 0.939677788 0.783370698 0.909391169 1 15.66747249 5.267103187 0.010645257 1.763578581 3.74E-07 0.042705387 0.08642725 23669.9042 33.67052647 2544.414234 3051.727486 184970.8051 -5.267103187 -1.763578206 ALQEVGSGGTLGLSS(ph)PKS ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALQEVGSGGTLGLSSPKS 18 1 A0A0M3HER3 A0A0M3HER3 1 ALQEVGSGGTLGLS(0.027)S(0.971)PKS(0.002) 116.29 6.55E-05 0 74010 61353 65243 62348 78399 50635 80275 50814 90860 TRUE FALSE 69377.84621 65895.63996 66790.59477 63947.95523 72241.85879 65252.50251 68238.50899 57158.23976 75694.87902 0.916546101 0.870542906 0.882366094 0.844812173 0.95438238 0.86204646 0.901494393 0.755113695 1 16.20790808 7.978802119 5.173381305 0.883332627 0.89873217 0 0.065518326 0 0 0.012321777 0 95236213.23 -7.978802119 0.015399543 ALQHTES(ph)PSETNKPHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ALQHTESPSETNKPHSK 17 1 Q14669-3;Q14669;Q14669-2;G5E9G6;C9JLD7;C9JLJ5;C9JSX9 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 ALQHTES(0.991)PS(0.008)ET(0.001)NKPHSK;ALQHTES(0.891)PS(0.109)ETNKPHSK;ALQHTES(0.692)PS(0.308)ETNKPHSK;ALQHTES(0.992)PS(0.008)ETNKPHSK 246.67 6.78E-21 1353340000 1431260 924920 1170360 1070820 1097600 900690 1628080 984790 1284490 TRUE FALSE 1341679.991 993402.0392 1198121.492 1098299.054 1011398.924 1160704.582 1383964.518 1107743.199 1070100.321 1.253788982 0.928326083 1.119634738 1.026351486 0.945144024 1.084668941 1.293303526 1.035176962 1 20.02931462 1.991371374 24.87291299 1.153808644 1.042490949 0 0.120442675 669.7283836 1930563.366 0.04263756 0.029922402 98.03279244 -1.991371374 -0.111317694 ALQLEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ALQLEEER 8 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 241.3 2.04E-08 2646090000 2486520 3510990 2475980 2345900 3821840 1948250 2426120 2943370 3561380 FALSE TRUE 2330893.152 3770947.353 2534711.415 2406099.766 3521688.103 2510678.148 2062345.829 3310856.224 2966962.671 0.785615935 1.270979035 0.854311866 0.81096395 1.186967446 0.846211573 0.695103396 1.11590761 1 21.50055534 3.739474696 23.59324487 0.905130958 1.06287011 0.026091189 0.186211059 408.983083 781087.3183 0.045332461 0.080879484 5488.765743 -3.739474696 0.157739152 ALQLILDVLNPETSEDENDRVVVTDDSDERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALQLILDVLNPETSEDENDRVVVTDDSDERR 31 2 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 0 103.21 9.63E-05 45952000 33946 38552 40751 45627 45481 40565 43049 30611 37812 FALSE TRUE 31821.38046 41406.43019 41717.63296 46797.86607 41909.10572 52275.45698 36594.2021 34432.85073 31500.93293 1.010172636 1.314450918 1.324330078 1.485602543 1.330408398 1.659489168 1.161686296 1.093073999 1 14.94310694 1.52373799 7.641888969 1.072913406 1.354048114 0.390569144 0.162491078 0.122403746 13.72048474 0.084655933 0.03909322 33.39934811 -1.52373799 0.281134708 ALQLLHCFPLDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALQLLHCFPLDIR 13 0 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 89.629 0.0073617 47625000 70662 156920 59096 60090 146400 39860 77135 124400 118450 FALSE TRUE 66239.39156 168538.5201 60497.78503 61632.01113 134902.3345 51366.93493 65569.32284 139931.6138 98679.92978 0.671254952 1.70793109 0.613070816 0.624564805 1.367069624 0.520540854 0.664464628 1.418035199 1 16.59046907 3.900816527 7.7671004 0.849723636 1.249554658 0.081978941 0.39542379 0.422728703 37.84081477 0.093012875 0.168732238 7958.230735 -3.900816527 0.399831022 ALQLSNS(ph)PGASSAFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALQLSNSPGASSAFLK 16 0 Q12802-2;Q12802;Q12802-4;H0YMW2 Q12802-2 AKAP13 A-kinase anchor protein 13 1 ALQLS(0.001)NS(0.999)PGASSAFLK;ALQLSNS(1)PGASSAFLK 248.7 1.99E-20 228660000 835920 746120 817540 778790 872060 708490 953290 802850 985260 TRUE FALSE 783601.2594 801363.5011 836932.4349 798775.0699 803571.9253 913019.5616 810353.0144 903087.5898 820813.741 0.954663915 0.976303711 1.019637456 0.973150217 0.978994241 1.112334646 0.987255663 1.100234493 1 19.64669536 ALQS(ph)PALGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALQSPALGLR 10 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 1 ALQS(1)PALGLR 73.219 0.04788 74258000 52237 70609 59513 64742 70292 55205 65581 57965 73624 TRUE FALSE 48967.57942 75836.96383 60924.67646 66403.38933 64771.54986 71141.78732 55747.73787 65202.05785 61335.67877 0.798353917 1.236424954 0.993299132 1.082622556 1.056017495 1.159876091 0.908895752 1.063036379 1 15.90443891 1.733004759 24.99999973 0.985901194 1.069523999 0.049843125 0.119161576 1.326701295 5922.387564 0.049468266 0.027432573 54.0760248 -1.733004759 0.083622805 ALQS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ALQSPK 6 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 ALQS(1)PK;ALQS(1)PK;ALQS(1)PK 105.94 0.034145 8902990000 25731900 14999800 19232500 16877600 20258300 14212300 22006000 17808400 24768900 TRUE FALSE 24121386.31 16110400.8 19688703.98 17310707.79 18667294.84 18315160.29 18706404.59 20031817.94 20634810.58 1.168965725 0.780738972 0.954149974 0.838908006 0.904650652 0.887585579 0.906545981 0.970777893 1 24.29857686 1.133413606 3.403293758 0.998602387 0.904761793 0.054589349 0.101264732 0.496534844 10.28517393 0.083706656 0.022184719 13.5960767 -1.133413606 -0.093840593 ALQSGQCAGAALDVFTEEPPRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ALQSGQCAGAALDVFTEEPPRDR 23 1 A0A286YFA2;A0A286YF22;O43175;A0A2C9F2M7;A0A286YFL2;A0A286YF78 A0A286YFA2 PHGDH D-3-phosphoglycerate dehydrogenase 0 ;; 258.31 1.11E-43 521513000 128451 167416 148411 151467 185777 119685 169703 157722 165399 FALSE TRUE 120411.4812 179811.6548 151931.379 155353.8997 171186.8238 154236.1166 144257.6106 177413.9389 137792.8384 0.873858777 1.304941947 1.102607224 1.127445385 1.242349209 1.11933333 1.046916605 1.287541072 1 17.07214138 -1.270187758 5.280930311 0.999979773 1.144547618 0.105337354 0.125268657 2.65E-05 3.67E-06 0.107823799 0.025410759 0.053679967 1.270187758 0.144567845 ALQTS(ph)PQPPEGPGLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALQTSPQPPEGPGLPR 16 0 B7WPL9;Q6PFW1-7;Q6PFW1-4;Q6PFW1-3;Q6PFW1-2;A0A2R8YGT1;F8W9A8;Q6PFW1;H7C398;Q6PFW1-5 B7WPL9 PPIP5K1 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 1 1 ALQT(0.005)S(0.995)PQPPEGPGLPR;ALQT(0.004)S(0.996)PQPPEGPGLPR 213.36 2.23E-12 202713000 363350 436120 385230 441930 427750 348620 485510 350930 332730 TRUE FALSE 340608.5721 468410.7786 394367.8375 453270.672 394156.2405 449260.9346 412712.2828 394744.383 277195.2135 1.22876787 1.689822752 1.422707963 1.63520382 1.421944613 1.620738428 1.488886758 1.424066376 1 18.08054282 0.693400909 1.97518452 1.000175653 1.519113911 0.582062256 0.131889156 0.828911979 4.461141089 0.108204295 0.029925628 4.936292764 -0.693400909 0.518938258 ALRPGDLPPS(ph)PDDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALRPGDLPPSPDDVK 15 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 ALRPGDLPPS(1)PDDVK;ALRPGDLPPS(1)PDDVK 125.88 6.31E-05 242900000 840950 574310 707670 723050 673960 536090 790140 525120 764230 TRUE FALSE 788316.4406 616832.51 724456.2666 741604.6871 621029.9002 690850.4803 671665.8423 590682.3879 636675.0759 1.238177008 0.968834078 1.137874395 1.164808731 0.97542675 1.085091134 1.054958593 0.92776113 1 19.28019776 1.384475288 4.503153174 0.965322843 1.082431353 0.287289291 0.082517012 0.280606787 8.771678837 0.05499002 0.019244077 24.23680051 -1.384475288 0.117108511 ALRPGDLPPS(ph)PDDVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 155.87 1.13E-07 669930000 806380 701110 764120 763690 789550 569379 842260 619570 863710 TRUE FALSE 755910.1152 753020.9139 782245.2872 783287.5783 727541.9279 733749.4742 715970.9322 696924.6783 719551.2212 1.050529959 1.046514677 1.0871294 1.088577929 1.011105126 1.019732095 0.995024275 0.968554646 1 19.45673786 2.604522291 4.296261244 0.998080221 1.067564784 0.784094242 0.018161769 0.113325956 3.434333569 0.006383046 0.005959635 402.2743028 -2.604522291 0.069484563 ALRPPT(ph)SPGVFGALQNFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALRPPTSPGVFGALQNFK 18 1 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 ALRPPT(0.5)S(0.5)PGVFGALQNFK 135.86 1.21E-05 339150000 372120 299290 315530 368660 384160 257060 374110 267310 287460 TRUE FALSE 348829.6735 321449.743 323014.5206 378120.4397 353989.6232 331269.049 318015.6786 300684.2419 239481.0689 1.456606466 1.342276216 1.348810251 1.578915784 1.478152844 1.383278647 1.327936609 1.255565808 1 17.86955209 0.911765616 1.148903614 1.002358999 1.419349466 0.796724766 0.069394798 0.293432724 0.780204052 0.071423026 0.022456923 8.161417902 -0.911765616 0.416990468 ALRPPTS(ph)PGVFGALQNFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALRPPTSPGVFGALQNFK 18 1 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 ALRPPT(0.21)S(0.79)PGVFGALQNFK 162.11 2.21E-11 419450000 525350 487500 517510 585690 589010 433960 519350 430330 427000 TRUE FALSE 492469.2813 523595.0072 529785.5816 600719.797 542751.5306 559237.2072 441478.2889 484057.6478 355730.9415 1.384386973 1.471884917 1.489287323 1.688691443 1.525736075 1.572079181 1.241045513 1.360740918 1 18.44042694 1.070046603 0.995090311 1.016652116 1.517121706 0.707363793 0.103108102 0.288600836 0.615274862 0.095088683 0.031988108 11.75023637 -1.070046603 0.500469591 ALS(ph)DREEEEEDDEEEEEEVEAAAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALSDREEEEEDDEEEEEEVEAAAQR 25 1 Q8N3E9 Q8N3E9 PLCD3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-3" 1 ALS(1)DREEEEEDDEEEEEEVEAAAQR;ALS(1)DREEEEEDDEEEEEEVEAAAQR 339.74 1.71E-88 521780000 92960 76633 84234 81102 108846 65888 96384 85350 137507 TRUE FALSE 87141.79954 82306.98706 86232.07026 83183.21463 100297.6742 84908.796 81932.11399 96006.13538 114556.1934 0.760690426 0.718485702 0.75274909 0.726134591 0.875532534 0.741197778 0.715213308 0.83807023 1 16.80569593 0.936591719 4.2238651 0.999869956 0.752722775 0.744692386 0.04553899 0.140942953 6.773366484 0.042559869 0.010848485 8.641551422 -0.936591719 -0.247147181 ALS(ph)HDSIFIPESGQDATRPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ALSHDSIFIPESGQDATRPVR 21 1 Q6NV74;C9JFM2;C9JXD6;C9JK00 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 ALS(1)HDSIFIPESGQDATRPVR;ALS(0.977)HDS(0.023)IFIPESGQDATRPVR;ALS(0.5)HDS(0.5)IFIPESGQDATRPVR 235.76 4.99E-30 1799700000 241790 359830 346522 345470 368660 293935 449870 348670 420840 TRUE FALSE 226656.7955 386472.1876 354741.6655 354335.3451 339706.9307 378789.2629 382416.1699 392202.217 350599.0853 0.646484275 1.102319441 1.011815719 1.010656787 0.968932735 1.080405736 1.090750621 1.118662979 1 18.41946271 4.74304081 24.9914031 1.05052332 0.646484113 0.866130555 0.049592006 163.2137642 910406.5096 0.012036067 0.096537811 55340.21096 -4.74304081 -0.404039207 ALS(ph)IESLSPTDSSNGVNWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ALSIESLSPTDSSNGVNWR 19 0 H3BRG5;Q9Y3M8-5;Q9Y3M8-3;Q9Y3M8-4;Q9Y3M8-2;Q9Y3M8 H3BRG5;Q9Y3M8-3 STARD13 StAR-related lipid transfer protein 13 1 ALS(1)IESLSPTDSSNGVNWR;ALS(1)IESLSPTDSSNGVNWR;ALS(0.94)IES(0.06)LSPTDSSNGVNWR;ALS(0.994)IES(0.006)LSPTDSSNGVNWR;ALS(1)IESLSPTDSSNGVNWR;ALS(0.999)IES(0.001)LSPTDSSNGVNWR 370.05 6.03E-108 1849407000 984020 1118101 1093094 1075516 1239446 917192 1320039 1143110 1684107 TRUE FALSE 922431.9447 1200886.361 1119022.706 1103115.561 1142104.911 1181970.441 1122111.407 1285829.8 1403018.662 0.657462349 0.855930426 0.797582196 0.786244397 0.814034012 0.842448125 0.799783664 0.916473768 1 20.42010277 -4.999999997 0.125604126 1.659353483 0.721690142 0.654798294 0.052224409 97.0331053 0.778937125 15.97605204 0.413163968 1.00E-05 4.999999997 -0.937663341 ALS(ph)PAELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALSPAELR 8 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 ALS(1)PAELR;ALS(1)PAELR 113.62 0.0029509 95634000 274630 325410 302440 305310 348860 275530 304650 306100 385670 TRUE FALSE 257441.3985 349503.695 309614.0196 313144.7715 321461.9428 355071.0381 258970.5607 344317.2588 321299.1855 0.801251326 1.087782698 0.963631511 0.974620496 1.00050656 1.105110297 0.806010636 1.071640621 1 18.2935578 -3.14450375 10.49654986 0.999928023 0.979834846 0 0.10488385 0 0 0 0.021032452 0.000716962 3.14450375 -0.020093176 ALS(ph)PEGALRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALSPEGALRR 10 1 I3L100;I3L2W2;Q96JN8-2;Q96JN8;K7EPS7;I3L2Z9 I3L100 NEURL4 Neuralized-like protein 4 1 ALS(1)PEGALRR 71.888 0.030402 120570000 55790 64706 61438 54734 68974 55475 72251 57049 80925 TRUE FALSE 52298.20349 69496.89957 62895.33837 56138.5671 63557.06027 71489.73194 61417.6333 64171.69323 67418.0947 0.775729479 1.030834524 0.932914801 0.832692875 0.942729998 1.060393834 0.910996277 0.951846734 1 16.04084824 2.472327671 24.97361938 0.973782619 0.91915929 0.190031666 0.07697134 322.4207137 1679726.017 0.026182877 0.021979434 296.7069172 -2.472327671 -0.054623329 ALS(ph)PGLEESGLGLLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ALSPGLEESGLGLLAR 16 0 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 ALS(1)PGLEESGLGLLAR;ALS(1)PGLEESGLGLLAR;ALS(1)PGLEESGLGLLAR;ALS(1)PGLEESGLGLLAR;ALS(1)PGLEESGLGLLAR;ALS(1)PGLEESGLGLLAR 284.74 9.61E-36 1239588000 165170 177078 167461 173418 176840 142554 196732 155734 174635 TRUE FALSE 154832.3045 190189.0394 171433.254 177868.1995 162951.6997 183707.0256 167233.863 175177.7327 145487.2903 1.064232513 1.307255355 1.178338353 1.222568646 1.120040791 1.262701541 1.149474037 1.20407585 1 17.1505336 -4.104885886 0.32608894 2.18E-11 1.206025977 0.405472155 0.070096088 158.3330284 2.430752379 107.4204006 0.053906198 7.85E-05 4.104885886 1.206025977 ALS(ph)PVIPLIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 ALSPVIPLIPR 11 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 ALS(1)PVIPLIPR;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR;ALS(1)PVIPLIPR 198.81 5.50E-08 2031236300 1467071 1737845 1596331.7 1582506.7 1712716 1443120.5 1721986 1498217.1 1753008 TRUE FALSE 1375249.645 1866516.852 1634197.442 1623116.501 1578206.194 1859725.961 1463790.185 1685272.803 1460419.64 0.941681149 1.278068852 1.118991691 1.111404186 1.080652541 1.273418893 1.002307929 1.153964762 1 20.47795154 0.564729912 0.605262066 0.997703257 1.143116378 0.085506569 0.105607534 3.043150727 2.030535598 0.118161221 0.040640906 3.670539582 -0.564729912 0.145413121 ALS(ph)PVTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALSPVTSR 8 0 Q96L91-4;Q96L91-3;Q96L91-5;Q96L91-2;Q96L91;A0A0A0MR80;A0A0A0MR72 Q96L91-4 EP400 E1A-binding protein p400 1 ALS(1)PVTSR 87.806 0.0158 326690000 261410 310730 254870 275340 309770 269330 330120 270630 312510 TRUE FALSE 245048.8147 333736.7725 260915.6368 282405.6905 285441.9138 347081.1988 280621.5707 304418.7512 260350.0621 0.941228178 1.281877061 1.002172362 1.08471528 1.09637736 1.333132767 1.077862507 1.169267058 1 17.99009323 ALS(ph)SAGPIPIRPPIVPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALSSAGPIPIRPPIVPVK 18 1 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 ALS(0.5)S(0.5)AGPIPIRPPIVPVK;ALS(0.763)S(0.237)AGPIPIRPPIVPVK 195.39 1.45E-15 591180000 785190 777870 708680 710660 991280 480400 1140970 797650 1105000 TRUE FALSE 736046.3595 835464.3042 725490.2243 728896.7387 913428.8674 619083.6814 969892.1407 897238.3583 920568.3614 0.799556437 0.907552702 0.788089462 0.791789909 0.992244472 0.672501584 1.053579703 0.974656958 1 19.81216533 1.652217027 10.4880366 1.009904473 0.836061351 0.505799655 0.085202395 0.087361181 15.61744588 0.036045928 0.019382744 44.8969694 -1.652217027 -0.173843123 ALS(ph)SDSILS(ph)PAPDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 2 ALS(0.999)S(0.001)DSILS(1)PAPDAR 283.22 2.53E-27 0 331640 308570 347750 370250 381730 265160 355770 271350 334360 TRUE FALSE 310883.2444 331416.8439 355998.7942 379751.2418 351750.4656 341707.3875 302425.5913 305228.6448 278553.156 1.116064341 1.189779533 1.278028221 1.36329901 1.26277681 1.226722369 1.085701543 1.095764447 1 18.08759314 1.697292867 2.586961198 1.053283335 1.246236618 0.620886914 0.066446567 0.17541482 2.578990354 0.044394216 0.019075294 49.80728476 -1.697292867 0.192953282 ALS(ph)SDSILSPAPDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 ALS(0.95)S(0.05)DSILSPAPDAR;ALS(0.877)S(0.123)DSILSPAPDAR;ALS(0.705)S(0.295)DSILSPAPDAR;ALS(0.499)S(0.499)DS(0.003)ILSPAPDAR;ALS(0.5)S(0.5)DS(0.001)ILSPAPDAR;ALS(0.5)S(0.5)DSILSPAPDAR;ALS(0.5)S(0.5)DSILSPAPDAR;ALS(0.859)S(0.14)DSILSPAPDAR;ALS(0.996)S(0.004)DSILSPAPDAR 402.98 7.83E-133 14038339000 3849412 3877539 3596458 3819755 3727613 2882433 4523873 3008684 3957027 TRUE FALSE 3608484.174 4164636.022 3681767.682 3917776.38 3434861.311 3714544.615 3845560.241 3384324.82 3296573.63 1.094616586 1.263322616 1.116846792 1.188438912 1.041948913 1.126789519 1.166532489 1.026618908 1 21.65253587 0.830038023 0.230099086 0.95331708 1.208825152 0.385783781 0.062352741 3.454790297 0.582071384 0.309074856 0.168345294 6.761421703 -0.830038023 0.255508072 ALS(ph)VGNIDDALQCYSEAIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALSVGNIDDALQCYSEAIK 19 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 1 ALS(1)VGNIDDALQCYSEAIK 70.335 0.013942 8724900 12885 14373 10265 12088 13032 9950.3 15276 8640.3 12251 TRUE FALSE 12078.55085 15437.19188 10508.49065 12398.19854 12008.51929 12822.79008 12985.50562 9719.060475 10206.22896 1.183448941 1.512526511 1.029615414 1.214767825 1.176587292 1.256369041 1.272311808 0.952267534 1 13.31716229 6.716404347 0.028357398 1.70E-06 2.780262205 0.287324641 0.135827262 1570.529149 4.283135779 149.1162226 291.9274254 5204803.603 -6.716404347 2.78026051 ALSAIADLLTNEHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ALSAIADLLTNEHER 15 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30 O60716-13 CTNND1 Catenin delta-1 0 ;;;; 284.68 5.28E-34 971465000 1116821 1351535 1275566 1282537 1436556 1210821 1486671 1234326 1519990 FALSE TRUE 1046921.167 1451604.058 1305823.028 1315449.071 1323734.687 1560365.367 1263758.485 1388434.318 1266293.849 0.826760051 1.146340605 1.031216434 1.038818179 1.04536138 1.232230076 0.997997807 1.096455075 1 20.2721808 4.748720869 24.86864256 1.075856128 0.826759903 0.540683347 0.071457608 983.5467303 2407317.371 0.015494095 0.212595364 56068.74936 -4.748720869 -0.249096225 ALSAS(ph)HTDLAH ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ALSASHTDLAH 11 0 Q07866-6;Q07866-4;Q07866-7;H0YG16;H0YJK1 Q07866-6 KLC1 Kinesin light chain 1 1 ALSAS(0.993)HT(0.007)DLAH;ALSAS(0.998)HT(0.001)DLAH;ALSAS(0.987)HT(0.013)DLAH 197.3 3.71E-08 2722530000 2119150 3197640 2470610 2588780 2867960 2024420 3229420 2368370 2811020 TRUE FALSE 1986516.184 3434396.593 2529214.036 2655212.478 2642721.99 2608837.19 2745198.451 2664066.208 2341842.602 0.848270581 1.466536047 1.080010259 1.133813381 1.128479765 1.114010475 1.172238668 1.137594049 1 21.15921268 -4.168337319 0.191075495 0.504809824 1.192559469 0.033240924 0.151353611 225.47613 2.945651356 42.98327748 0.384923818 6.79E-05 4.168337319 0.687749646 ALSCHPDKNPDNPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALSCHPDKNPDNPR 14 1 H0YLQ7;Q9NVM6;S4R343;H0YK99 H0YLQ7 DNAJC17 DnaJ homolog subfamily C member 17 0 176.89 1.30E-06 128400000 220570 305310 317770 340970 366900 268320 400720 302890 401550 FALSE TRUE 206764.9174 327915.4701 325307.6545 349719.8675 338085.154 345779.6282 340635.7561 340706.4832 334528.7109 0.618078242 0.980231171 0.97243568 1.045410621 1.010631204 1.033632143 1.018255668 1.018467092 1 18.35177051 4.751771022 3.615431561 1.010533168 0.567808156 0.974819455 0.01984809 0.051354573 1.197535101 0.005729987 0.062552321 56463.91949 -4.751771022 -0.442725012 ALSDHHIYLEGTLLKPNMVTPGHACTQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ALSDHHIYLEGTLLKPNMVTPGHACTQK 28 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BU78 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;;;; 264.14 2.50E-54 11791644000 9388405 14873453 14017380 14578830 15057699 11307626 17850298 13387834 12659438 FALSE TRUE 8800801.49 15974698.94 14349878.87 14952947.46 13875128.06 14571954.06 15173811.53 15059334.55 10546496.01 0.834476349 1.514692549 1.36063 1.417811891 1.315614972 1.381686775 1.438753829 1.427899325 1 23.33026042 -0.830301266 5.098547993 0.999999604 1.363986287 0.229002317 0.188069067 7.45E-07 1.70E-07 0.16019571 0.03775845 0.14780827 0.830301266 0.363986682 ALSFLVNDCSLIHNNVCMAAVFVDR ddPTM_SK-BR-3_Pertuzumab_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 ;; 246.21 6.89E-39 83936000 46525.2 68954.3 48934.2 42735.7 73525.1 51012.8 59719.8 69342.8 34896.4 FALSE TRUE 43613.27078 74059.74812 50094.94233 43832.37041 67750.73523 65739.36724 50765.3704 78000.40122 29071.9654 1.500183086 2.547462722 1.72313573 1.507719544 2.330449087 2.261263259 1.746196712 2.68301094 1 14.82734099 -1.275671034 6.222103095 0.999967743 2.036267053 0.379271282 0.417093854 0.000168642 1.96E-05 0.364915611 0.086008776 0.05300648 1.275671034 1.03629931 ALSQTVPSSGTNGVSLPADCTGAVPAAS(ph)PDTAAWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALSQTVPSSGTNGVSLPADCTGAVPAASPDTAAWR 35 0 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EN31 Q9H6Z4 RANBP3 Ran-binding protein 3 1 ALSQTVPSSGTNGVSLPADCTGAVPAAS(0.968)PDT(0.032)AAWR;ALSQTVPSSGTNGVSLPADCTGAVPAAS(0.87)PDT(0.13)AAWR 266.75 1.28E-60 408220000 282720 293730 307350 301510 329580 305870 387080 314030 327080 TRUE FALSE 265025.0599 315478.0748 314640.4871 309247.2571 303696.1163 394169.7036 329040.9475 353237.3368 272488.235 0.972611019 1.157767692 1.154693843 1.134901318 1.11452928 1.446556779 1.20754185 1.296339773 1 18.05583442 ALSSDSILS(ph)PAPDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 ALSSDSILS(1)PAPDAR;ALSSDSILS(1)PAPDAR;ALSSDSILS(1)PAPDAR;ALSSDSILS(1)PAPDAR;ALSSDSILS(1)PAPDAR;ALSSDSILS(1)PAPDAR 298.78 3.67E-44 1317400000 1491280 1639740 1972990 2315460 2784740 1754330 1466430 1333190 1880330 TRUE FALSE 1397943.447 1761148.056 2019790.255 2374878.624 2566037.754 2260776.592 1246552.435 1499641.706 1566490.776 0.892404519 1.124263279 1.289372581 1.516050181 1.638080347 1.443210919 0.795761108 0.95732559 1 20.57910484 1.733306025 10.02591436 0.912483556 1.311663679 0.442808658 0.211026444 0.095753753 39.53683092 0.10773136 0.058347458 54.11354984 -1.733306025 0.399180122 ALSSGGSITS(ph)PPLS(ph)PALPK ddPTM_SK-BR-3_Pertuzumab_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(0.003)S(0.997)PPLS(1)PALPK;ALSSGGSIT(0.003)S(0.997)PPLS(1)PALPK;ALSSGGSIT(0.002)S(0.998)PPLS(1)PALPK;ALSSGGSIT(0.085)S(0.915)PPLS(1)PALPK 349.79 1.48E-90 929110000 1583100 1357340 1769610 2391870 2453900 1178740 1198980 815150 1199190 TRUE FALSE 1484016.597 1457838.866 1811585.985 2453249.434 2261180.593 1519023.103 1019204.08 916923.2719 999037.4419 1.485446425 1.459243472 1.813331422 2.455613104 2.263359207 1.520486659 1.020186068 0.917806714 1 19.93017922 1.850092876 3.208233167 0.971751831 1.851868567 0.646003353 0.306891004 0.18360465 3.281691335 0.181883683 0.095025227 70.80971984 -1.850092876 0.880116736 ALSSGGSITS(ph)PPLSPALPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ALSSGGSITSPPLSPALPK 19 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;C9JW88;C9JRZ2;C9J0V6;C9JXQ0;C9JPV7;F8WCD5;C9JHT0;Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 ALSSGGSITS(1)PPLSPALPK;ALSSGGSIT(0.001)S(0.999)PPLSPALPK;ALS(0.001)S(0.001)GGS(0.005)IT(0.161)S(0.833)PPLS(0.001)PALPK;ALSSGGSIT(0.001)S(0.999)PPLSPALPK;ALSSGGSIT(0.03)S(0.97)PPLSPALPK 319.45 7.56E-62 1445169000 3596150 3110954 3502140 3742395 4080720 2473620 2847798 2276680 3402230 TRUE FALSE 3371073.391 3341292.271 3585212.415 3838431.192 3760236.712 3187713.938 2420797.128 2560928.51 2834375.834 1.189352996 1.178845879 1.264903677 1.354242139 1.326654238 1.124661698 0.854084733 0.903524677 1 21.43459964 1.932075259 3.913764206 0.911106233 1.254919253 0.854126091 0.0645831 0.085402732 2.413575772 0.032508177 0.018791231 85.52149003 -1.932075259 0.34381302 ALSSLHGDDQDS(ph)EDEVLTIPEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 ALSSLHGDDQDSEDEVLTIPEVK 23 0 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 1 ALSSLHGDDQDS(1)EDEVLTIPEVK;ALSS(0.001)LHGDDQDS(0.999)EDEVLTIPEVK;ALS(0.001)S(0.006)LHGDDQDS(0.994)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK;ALS(0.005)S(0.005)LHGDDQDS(0.99)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK;ALS(0.037)S(0.16)LHGDDQDS(0.802)EDEVLTIPEVK 232.8 8.31E-35 6033540000 5560960 5783460 5731800 5724250 6252010 4508670 8682960 5834910 6212850 TRUE FALSE 5212909.44 6211673.396 5867761.003 5871143.946 5761002.354 5810249.837 7381030.757 6563411.358 5175885.198 1.007153219 1.200118078 1.133672942 1.13432654 1.11304678 1.122561574 1.426042208 1.268075142 1 22.30337419 1.801186348 25 1.278262448 1.13005311 0.131225599 0.115355893 218.5600925 87268.14796 0.043971485 0.027099558 63.26832663 -1.801186348 -0.148209338 ALSSQHQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ALSSQHQAR 9 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;;; 166.33 6.08E-05 360471000 72326.4 760390 89298 93551 600424 93922.9 80161.5 500599 331162 FALSE TRUE 67799.61973 816690.0668 91416.19073 95951.67704 553269.121 121036.9165 68142.02726 563099.8871 275888.9228 0.245749699 2.96021333 0.331351436 0.347790973 2.005405347 0.438716115 0.246990805 2.041038405 1 18.07372801 3.843816467 7.243276761 0.842624681 1.77100455 0.077651499 0.917725261 0.392722385 22.49864055 0.215967212 0.391664519 6979.373938 -3.843816467 0.928379869 ALSTGEK ddPTM_SK-BR-3_Pertuzumab_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 ;; 139.28 0.0062903 1856250000 2464580 2165380 2230940 2139310 2377680 1796770 2772510 2100610 3533110 FALSE TRUE 2310326.337 2325706.988 2283858.95 2194208.316 2190946.604 2315468.331 2356797.864 2362875.783 2943411.116 0.784914593 0.790140044 0.775922513 0.745464439 0.744356299 0.786661543 0.800702916 0.802767839 1 21.48905763 0.202809482 0.848257408 1.002930439 0.77244907 0.947529037 0.016563017 0.787809412 0.653957939 0.023189939 0.005894077 1.595179213 -0.202809482 -0.230481369 ALSTGEKGFGYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALSTGEKGFGYK 12 1 P62937;F8WE65;C9J5S7 P62937 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ; 145.17 5.40E-05 1116830000 901230 961500 1029160 1032910 1392270 858510 1111200 959030 669340 FALSE TRUE 844823.623 1032690.46 1053572.161 1059416.219 1282926.73 1106347.9 944585.8759 1078767.007 557622.8299 1.515044897 1.851951543 1.889399258 1.899879565 2.300706968 1.984043409 1.693951225 1.934581851 1 19.0889301 -1.421085512 8.577707205 0.999990429 1.88456273 0.658632496 0.199936658 3.57E-05 2.41E-06 0.188862465 0.04451483 0.037924031 1.421085512 0.884572301 ALSTGEKGFGYKGSCFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALSTGEKGFGYKGSCFHR 18 2 P62937;F8WE65;C9J5S7 P62937 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ; 160.97 2.36E-11 2857300000 740360 994740 1394420 1426940 1690180 1753330 1419180 581090 416600 FALSE TRUE 694022.1892 1068391.585 1427496.301 1463557.696 1557440.081 2259487.908 1206387.134 653640.3656 347066.7687 1.999679174 3.078345958 4.113030776 4.216934113 4.487436486 6.51023985 3.475951151 1.883327431 1 18.40485371 4.59921129 1.517674634 3.964188373 1.566224498 0.087253491 1.499104494 1.608156974 4.258564828 0.380389888 5.338176033 39738.48353 -4.59921129 -2.397963875 ALSYAS(ph)LDKEDLLSPINQNTLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALSYASLDKEDLLSPINQNTLQR 23 1 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 ALS(0.002)YAS(0.998)LDKEDLLSPINQNTLQR;ALSYAS(1)LDKEDLLSPINQNTLQR 313.19 1.86E-73 493610000 379610 256015 294245 323620 325920 220242 351050 230935 384680 TRUE FALSE 355850.8877 274970.617 301224.6304 331924.6371 300323.5579 283822.2901 298413.3115 259767.7431 320474.4229 1.110387795 0.858011115 0.939933451 1.035728949 0.937121768 0.885631644 0.931161086 0.810572466 1 18.28984969 2.466736963 14.72597788 0.904718846 0.959942752 0.145141568 0.0803971 3.880735349 5490.640899 0.026389325 0.022235463 292.9118644 -2.466736963 0.055223906 ALTAHLYSLLQTQHALGDAFADLSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALTAHLYSLLQTQHALGDAFADLSQK 26 0 A0A087X1E4;P53365;P53365-2;P53365-3;E9PRV8 A0A087X1E4 ARFIP2 Arfaptin-2 0 ; 153.94 4.25E-08 250840000 545890 563040 534720 531190 646660 398250 603870 542770 532330 FALSE TRUE 511723.7193 604728.0674 547403.8109 544821.2347 595873.9321 513218.31 513325.2996 610536.0293 443480.684 1.153880513 1.363595054 1.234335182 1.228511758 1.343629956 1.15725065 1.1574919 1.376691367 1 18.75851174 -4.049133744 0.282489026 2.33E-20 1.268933415 0.425960327 0.087926846 118.8745052 1.87572313 69.14058325 0.093878803 8.93E-05 4.049133744 1.268933415 ALTGGIAHLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALTGGIAHLFK 11 0 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 79.693 0.026447 355850000 598420 800020 524020 458870 1093600 417530 540470 855790 1081400 FALSE TRUE 560965.9604 859254.3132 536450.0019 470645.3811 1007713.067 538064.133 459431.541 962637.2653 900907.3539 0.622667756 0.953765456 0.595455237 0.522412631 1.118553493 0.59724691 0.509965358 1.068519711 1 19.78101923 1.218979684 24.94601704 1.034260286 0.709676466 0.335762028 0.193596699 321.3317965 409364.1752 0.17892273 0.044991627 16.5569251 -1.218979684 -0.32458382 ALTHIDHSLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ALTHIDHSLSR 11 0 P56192;P56192-2;F5H2V6 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;;;; 268.77 1.09E-21 2000440000 552829 960170 751186 751340 1008220 624396 776207 897660 853414 FALSE TRUE 518228.4197 1031261.986 769004.4867 770620.6564 929038.4682 804648.989 659821.9663 1009734.827 710973.6901 0.728899574 1.450492473 1.081621581 1.083894759 1.306712866 1.131756351 0.928053985 1.420214054 1 19.43943665 1.997751085 24.92807603 1.088547799 1.169732073 0 0.223769826 376.8042511 4176709.249 0.078015305 0.056684373 99.48350661 -1.997751085 0.081184274 ALTHNGT(ph)PR ddPTM_SK-BR-3_Pertuzumab_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 143 0.00037896 2376670000 1718920 2233110 2045820 2248910 3154210 2332210 2893550 2429330 2688570 TRUE FALSE 1611335.866 2398451.788 2094347.817 2306620.838 2906491.07 3005481.167 2459689.04 2732637.198 2239830.298 0.71940087 1.07081853 0.935047543 1.029819464 1.297638965 1.341834321 1.09815866 1.220019749 1 21.094958 2.934016232 4.674653368 1.200873644 0.949846532 0.496964017 0.128602609 0.184660482 7.897326956 0.037125317 0.040322669 859.0456286 -2.934016232 -0.251027112 ALTLDQWLEQHKGDFNLL ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALTLDQWLEQHKGDFNLL 18 1 I3L1Y8;Q9HBL8;I3L3Z0 I3L1Y8 NMRAL1 NmrA-like family domain-containing protein 1 0 ; 177.56 8.50E-14 185347000 348880 370120 354440 369150 416330 274850 450970 309100 386390 FALSE TRUE 327044.2236 397524.0699 362847.4842 378623.014 383633.1212 354194.7332 383351.2351 347691.8154 321899.0128 1.015983928 1.234934107 1.127209062 1.17621676 1.191780981 1.100328734 1.190905283 1.080127001 1 18.29624863 0.997945067 4.403880918 1.000241452 1.156014178 0.389321676 0.060330711 0.144422857 8.430101521 0.050499951 0.01285182 9.952795177 -0.997945067 0.155772726 ALTNLPHTDFTLCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALTNLPHTDFTLCK 14 0 Q9UBQ5;A0A087WVB9;K7ERF1;Q9UBQ5-2;K7ES31;K7EQM4 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 0 233.02 3.55E-17 246610000 561270 582220 523210 538460 683420 466450 677840 592690 585200 FALSE TRUE 526141.1126 625328.1746 535620.7883 552277.7952 629746.95 601106.5428 576204.1848 666688.6512 487526.3395 1.079205512 1.282655159 1.09864995 1.132816323 1.291718824 1.232972445 1.181893445 1.367492579 1 18.89512064 2.764821992 24.35851084 1.223690255 1.162438677 0.076982854 0.107239976 1473.544173 1366769.413 0.029550181 0.031334159 581.8646752 -2.764821992 -0.061251578 ALTSFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALTSFER 7 0 H0YFD6;P40939;A0A2R8Y4F5;A0A2R8YG21 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 102.71 0.019865 189030000 138260 158420 123100 128530 197310 132700 137620 151940 221340 FALSE TRUE 129606.5534 170149.5816 126019.9901 131828.2974 181814.0685 171008.3358 116985.1586 170910.0435 184396.9241 0.70286722 0.922735466 0.683416986 0.714915924 0.985992957 0.927392562 0.634420336 0.926859514 1 17.49245506 2.78587906 24.99975203 0.855619079 0.771681358 0.201411108 0.122730237 1023.607331 540800.4367 0.038097429 0.040408324 610.7719164 -2.78587906 -0.083937721 ALTT(ph)PTHYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALTTPTHYK 9 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3;H0YEN4;H0YCR0 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 ALT(0.287)T(0.709)PT(0.004)HYK 95.483 0.029488 320570000 945520 559210 646000 636380 681970 409760 749820 482220 841310 TRUE FALSE 886341.591 600614.4903 661323.4251 652710.5882 628410.8271 528051.0601 637391.452 542426.2285 700889.9259 1.264594565 0.856931264 0.943548196 0.931259766 0.896589898 0.753400842 0.909403072 0.773910722 1 19.41882836 4.740812137 24.77771285 0.881502848 1.264594716 0.721326192 0.074507979 90.48920023 995749.284 0.016271679 0.108636896 55056.94843 -4.740812137 0.383091869 ALTVPELTQQMFDAK ddPTM_SK-BR-3_Pertuzumab_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 0 130.07 0.00014424 75360000 107930 116730 112750 111960 126390 88429 124090 107670 121490 FALSE TRUE 101174.854 125372.8107 115424.4832 114833.0831 116463.8392 113957.0168 105483.8565 121112.8365 101212.5341 0.999627712 1.238708345 1.140416888 1.134573738 1.150685932 1.125918027 1.042201516 1.196618952 1 16.62702844 -0.926652292 0.290700513 0.927864824 1.153720032 0.200709006 0.070659413 18.07653657 1.362965678 1.188617597 0.07988133 0.118398911 0.926652292 0.225855208 ALTVPELTQQVFDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALTVPELTQQVFDAK 15 0 Q5JP53;P07437;Q5ST81 Q5JP53 TUBB Tubulin beta chain 0 ; 166.7 3.15E-06 161689000 393300 316800 349090 335050 381250 291880 438220 348200 425680 FALSE TRUE 368684.0551 340256.2016 357370.5797 343647.9502 351308.1629 376141.0177 372512.9792 391673.5365 354631.258 1.039626504 0.959464779 1.007724422 0.969028935 0.990629435 1.060653874 1.050423421 1.104452943 1 18.43596018 2.240849981 24.54879673 1.057355453 0.989546297 0.452359567 0.032884071 35.58574426 381591.7436 0.01041314 0.008328741 174.1205302 -2.240849981 -0.067809156 ALVADSHPESER ddPTM_SK-BR-3_Pertuzumab_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 7.45E-05 839420000 832350 996140 1015650 962950 1044500 859240 946490 892570 1020710 FALSE TRUE 780254.6993 1069895.242 1039741.698 987660.9273 962469.1833 1107288.639 804572.6113 1004009.329 850346.907 0.91757222 1.258186786 1.2227265 1.161480002 1.131854747 1.302161071 0.946169857 1.18070557 1 19.697692 1.732978196 24.99999917 1.045079945 1.181463042 0.18805448 0.117787769 0.817467282 3631.934421 0.049552236 0.027479235 54.07271747 -1.732978196 0.136383097 ALVAIGTHDLDTLSGPFTYTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALVAIGTHDLDTLSGPFTYTAK 22 0 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 180.08 5.45E-17 92712000 166900 160510 159870 163140 184670 139640 179200 160960 173800 FALSE TRUE 156454.0269 172394.3274 163662.1919 167326.4486 170166.7631 179951.8011 152330.6236 181056.2103 144791.6572 1.080545868 1.190637159 1.130328881 1.155635979 1.175252541 1.242832665 1.052067685 1.250460239 1 17.14361895 -1.427527877 3.470920156 0.998391494 1.156152442 0.390876551 0.062519815 0.000690989 0.000113968 0.053736406 0.012538711 0.037365614 1.427527877 0.157760948 ALVAT(ph)PGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ALVATPGKK 9 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 ALVAT(1)PGKK;ALVAT(1)PGKK;ALVAT(1)PGKK;ALVAT(1)PGKK;ALVAT(1)PGKK 101.71 0.0022255 9690130000 19479000 12512070 13923270 11751610 15475000 6270770 22384600 10068700 33520000 TRUE FALSE 18259844.16 13438476.68 14253536.54 12053176.21 14259655.92 8081039.502 19028237.04 11325799.36 27925295.45 0.653881861 0.481229526 0.510416678 0.431622155 0.510635812 0.289380627 0.681397877 0.405574916 1 24.73506921 -1.440183651 3.386294243 1.006374976 0.498532793 0.662862184 0.113050094 296172623.6 393132331.1 17954603.52 0.024197607 0.036292455 1.440183651 -0.507842183 ALVDHENVISCPHLGASTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALVDHENVISCPHLGASTK 19 0 A0A286YFA2;A0A286YF22;O43175;A0A2C9F2M7;A0A286YFL2;A0A286YF78 A0A286YFA2 PHGDH D-3-phosphoglycerate dehydrogenase 0 194.92 1.19E-15 250530000 214310 239110 244420 225990 279900 175380 292850 244930 244470 FALSE TRUE 200896.7197 256813.9532 250217.7578 231789.286 257917.7831 226009.3589 248939.8612 275510.0497 203666.3777 0.986401005 1.260954096 1.228566839 1.138083216 1.266373891 1.109703828 1.222292379 1.352751754 1 17.63584831 4.747177356 24.62360125 1.207897956 0.986400866 0.311148869 0.097518753 981.3443752 2804259.176 0.020321572 0.236420795 55869.83072 -4.747177356 -0.221497091 ALVEFESNPEETREPGS(ph)PPSVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ALVEFESNPEETREPGSPPSVQR 23 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 ALVEFESNPEETREPGS(0.997)PPS(0.003)VQR;ALVEFESNPEETREPGS(0.986)PPS(0.014)VQR;ALVEFESNPEETREPGS(1)PPSVQR;ALVEFESNPEETREPGS(1)PPSVQR;ALVEFESNPEETREPGS(0.998)PPS(0.002)VQR;ALVEFESNPEET(0.007)REPGS(0.984)PPS(0.008)VQR;ALVEFESNPEETREPGS(1)PPSVQR;ALVEFESNPEETREPGS(0.958)PPS(0.041)VQR 266 2.65E-44 20261060000 6937070 7147210 7989780 6915850 7408770 6573970 7960330 6594190 8789030 TRUE FALSE 6502891.172 7676396.865 8179301.355 7093322.42 6826915.09 8471768.42 6766752.417 7417489.137 7322084.114 0.88812025 1.048389604 1.117072848 0.968757298 0.932373213 1.157015993 0.924156608 1.013029763 1 22.80382292 1.642247724 25 0.976370662 1.029074824 0.038062091 0.082980724 1.722608678 1244.512168 0.036912831 0.020468045 43.87809098 -1.642247724 0.052704162 ALVFQPVAELKDQTDFEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALVFQPVAELKDQTDFEHR 19 1 A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 140.06 1.07E-07 156790000 174850 175460 180430 198910 238020 117340 181320 178040 301990 FALSE TRUE 163906.4506 188451.241 184709.8848 204014.3674 219326.8693 151214.1531 154132.7493 200268.6859 251585.9181 0.651492945 0.749053216 0.734182128 0.810913301 0.871777208 0.601043788 0.612644581 0.796025022 1 17.94069165 0.981879718 23.4223103 1.000000006 0.719262347 0.53031198 0.083470849 449.4158491 580917.4749 0.084650834 0.021162708 9.591349541 -0.981879718 -0.280737659 ALVHERDEAAYGELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ALVHERDEAAYGELR 15 1 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;; 199.37 4.48E-09 1182620000 539560 972840 736230 1046550 1220790 459170 743940 778080 1512450 FALSE TRUE 505789.9027 1044870.086 753693.7233 1073406.245 1124914.078 591724.925 632393.1034 875225.0008 1260012.324 0.401416631 0.829253862 0.598163771 0.851901386 0.892780218 0.469618363 0.501894379 0.694616222 1 20.26500641 -2.171841569 2.092116939 1.781692817 0.658473108 0.294989831 0.167559265 8292629.66 1655821.369 30713446.53 0.040267515 0.006732222 2.171841569 -1.123219709 ALVHQLS(ph)NESR ddPTM_SK-BR-3_Pertuzumab_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 191.06 1.29E-06 409660000 233640 203697 251710 205259 192374 253180 264180 216607 259200 TRUE FALSE 219016.8895 218778.9378 257680.6801 210526.2934 177265.722 326268.956 224568.6615 243650.8608 215937.8455 1.014258936 1.013156991 1.193309489 0.974939307 0.820910858 1.510939202 1.039968983 1.128337926 1 17.72025659 ALVLDCHYPEDEVGQEDEAESDIFSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ALVLDCHYPEDEVGQEDEAESDIFSIR 27 0 Q07021;I3L3Q7;I3L3B0 Q07021 C1QBP "Complement component 1 Q subcomponent-binding protein, mitochondrial" 0 ;;;;; 274.65 7.54E-61 3165490000 655352 621126 613135 550328 861847 769008 622085 675815 1157280 FALSE TRUE 614334.6882 667114.8153 627678.8517 564450.3482 794161.0131 991008.1258 528809.1294 760191.9904 964122.4917 0.637195682 0.691939895 0.651036416 0.585455015 0.823713812 1.027886119 0.548487494 0.788480714 1 19.87885693 2.727288839 24.26768061 0.804375139 0.651433887 0.331703804 0.133553231 728.1541825 1567683.087 0.042172582 0.040110187 533.6897216 -2.727288839 -0.152941253 ALVSEEGEGKNPVDYIQGLLDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALVSEEGEGKNPVDYIQGLLDLK 23 1 Q13618;Q13618-2;Q13618-3 Q13618 CUL3 Cullin-3 0 ; 122.3 6.03E-05 59369000 153402 115603 125547 135644 159463 105313 170171 105574 159659 FALSE TRUE 143800.8427 124162.3664 128525.0341 139124.8547 146939.4192 135715.1535 144655.4383 118755.1463 133010.8815 1.081120891 0.933475254 0.966274584 1.045965963 1.10471728 1.020331209 1.087545897 0.89282279 1 17.02118475 5.091261718 17.19687576 1.009272488 3.747226671 0.114313706 0.064932181 240.1221938 46693.50429 0.015596523 810.0974377 123384.816 -5.091261718 2.737954182 ALVTGYFMQVAHLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALVTGYFMQVAHLER 15 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 149 3.43E-06 204514000 195619 336330 188255 179691 327490 138965 214010 286630 241160 FALSE TRUE 183375.556 361232.2232 192720.4975 184302.1753 301770.2564 179081.9396 181921.1873 322416.3865 200908.838 0.91273016 1.797990704 0.959243503 0.917342298 1.502025791 0.891359192 0.905491212 1.604789464 1 17.6161815 3.798046545 7.587959269 1.091078125 1.409620096 0.079875536 0.326770217 0.451296385 42.16405923 0.076843153 0.138944602 6281.256742 -3.798046545 0.31854197 ALVVPEPEPDSDS(ph)NQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ALVVPEPEPDSDSNQER 17 0 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 1 ALVVPEPEPDSDS(1)NQER;ALVVPEPEPDS(0.002)DS(0.998)NQER;ALVVPEPEPDSDS(1)NQER;ALVVPEPEPDSDS(1)NQER 340.49 1.82E-72 1500370000 1210810 1282660 1209970 1083480 1426960 1317600 1498620 1425110 1878390 TRUE FALSE 1135027.563 1377629.481 1238671.06 1111283.931 1314892.318 1697969.731 1273915.844 1603038.121 1564874.574 0.725315359 0.880344983 0.791546543 0.710142493 0.840254126 1.085051645 0.814068977 1.024387607 1 20.5776156 2.461048787 24.69316032 0.954595602 0.794405959 0.561386356 0.083643775 177.5846851 272832.75 0.027269757 0.022821692 289.1004627 -2.461048787 -0.160189642 ALWEDEGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALWEDEGVR 9 0 P63092-4;P63092;P63092-3;A0A590UJ58;B0AZR9;A0A590UJF0;A0A590UJR6;A0A590UJI6;A0A590UJQ9;A0A590UKB4;A0A590UJQ2;A0A590UJG5;A0A590UJ22;S4R3E3;S4R3V9;Q5JWE9;A0A590UKA4;A0A590UJY8;A0A590UJB7;H0Y7F4;A0A590UJC9;P63092-2;A0A590UJB0;A0A590UJS2;A0A590UJJ0;A0A590UK28;A0A590UKA9;Q5JWF2 P63092-4;P63092-2;Q5JWF2 GNAS Guanine nucleotide-binding protein G(s) subunit alpha isoforms short;Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas 0 ; 133.68 0.00062852 507010000 1076310 1438180 1281010 1252680 1603790 1067730 1284970 1334310 1479960 FALSE TRUE 1008945.678 1544664.344 1311396.162 1284825.89 1477834.803 1375966.318 1092300.678 1500901.541 1232945.115 0.818321648 1.252824903 1.063628986 1.042078738 1.198621727 1.115999651 0.885928063 1.217330376 1 20.23367715 -1.391214582 5.052990562 0.999933272 1.079530112 0.026598773 0.138202711 9.64E-05 1.16E-05 0.124142658 0.02923619 0.040624256 1.391214582 0.07959684 ALWFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALWFER 6 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 111.69 0.064292 159500000 127710 353100 145920 153540 353110 136370 123580 308970 302930 FALSE TRUE 119716.8591 379243.8914 149381.2913 157480.0963 325378.165 175737.8052 105050.3263 347545.5846 252369.026 0.474372236 1.502735488 0.591916107 0.624007228 1.289295165 0.696352512 0.416256812 1.377132488 1 17.94517533 3.852212461 10.72682727 0.807156221 1.059835304 0 0.391352246 0.986383054 83.69542418 0.093407338 0.168519793 7115.615306 -3.852212461 0.252679083 ALWFQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ALWFQGR 7 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 148.53 0.0048334 389330000 486700 909570 475550 457080 963970 398210 542610 814820 800190 FALSE TRUE 456238.3158 976915.5092 486830.2706 468809.4466 888263.6847 513166.7626 461250.6678 916552.0706 666633.1196 0.684391913 1.465447006 0.730282154 0.703249558 1.332462577 0.76978888 0.691910819 1.374897292 1 19.34653347 3.939490545 21.49848692 0.91271719 1.126603268 0.017393527 0.308062777 142.6900073 81518.50455 0.072944983 0.131516257 8699.424932 -3.939490545 0.213886078 ALYDYEGQEHDELSFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ALYDYEGQEHDELSFK 16 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22;H0Y923 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 ;;; 259.98 9.11E-27 1077154000 1731700 1529420 1709780 1671290 1897460 1307990 1998070 1629450 2307720 FALSE TRUE 1623315.988 1642659.848 1750336.789 1714178.131 1748441.146 1685585.48 1698477.953 1832890.419 1922546.624 0.84435715 0.854418732 0.910426186 0.891618497 0.909440179 0.876746217 0.883452152 0.953365914 1 20.87458715 -5 0.115139228 1.375835371 0.826492376 0.776643006 0.021738345 82.02711112 0.62046341 7.163607013 0.247960696 1.00E-05 5 -0.549342995 ALYETELADAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ALYETELADAR 11 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 173.37 2.85E-05 133680000 136580 149610 142030 129640 136360 106740 157520 131880 128980 FALSE TRUE 128031.7016 160687.2801 145399.0187 132966.7819 125650.8356 137554.1052 133901.3383 148345.5083 107452.4048 1.191520114 1.495427491 1.353148112 1.237448172 1.169362714 1.280139849 1.246145572 1.380569459 1 16.71333824 -4.782928836 0.15207576 2.22E-10 1.401442018 0.417171881 0.101863847 112.8100426 1.076232289 34.53181236 0.500525381 1.65E-05 4.782928836 1.401442018 AMAATLGAGT(ph)PPRPQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 AMAATLGAGTPPRPQAR 17 1 P58107 P58107 EPPK1 Epiplakin 1 AMAATLGAGT(1)PPRPQAR;AMAATLGAGT(1)PPRPQAR;AMAATLGAGT(1)PPRPQAR;AMAATLGAGT(1)PPRPQAR;AMAATLGAGT(1)PPRPQAR;AMAATLGAGT(1)PPRPQAR;AMAAT(0.001)LGAGT(0.999)PPRPQAR;AMAAT(0.001)LGAGT(0.999)PPRPQAR 173.49 2.38E-09 7026710000 996801 1122713 1054301 1056198 1101039 846818 1119095 897969 1134798 TRUE FALSE 934413.0048 1205839.839 1079309.518 1083301.829 1014567.838 1091280.61 951297.0939 1010082.406 945392.8827 0.98838591 1.275490709 1.141651833 1.145874745 1.073170591 1.154314391 1.006245246 1.068426074 1 19.85055448 1.981763743 0.77967614 1.008445678 1.165557091 0.231428788 0.077487731 0.686778302 0.784407829 0.062176518 0.032207758 95.88788583 -1.981763743 0.157111414 AMASVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AMASVAR 7 0 H7C2G2;Q93070 H7C2G2 ART4 NAD(P)(+)--arginine ADP-ribosyltransferase;Ecto-ADP-ribosyltransferase 4 0 ; 100.67 0.053924 117350000 386300 809420 382370 388020 858270 334020 383100 648990 716920 FALSE TRUE 362122.1726 869350.299 391439.997 397977.2501 790864.9363 430446.1516 325657.7115 730017.8301 597261.4205 0.606304309 1.45556078 0.655391397 0.666336777 1.324152053 0.720699742 0.545251544 1.222275213 1 19.18800301 3.87937295 9.08283988 0.840264642 1.086513335 0.022816058 0.322863855 0.679621742 57.22336405 0.077434723 0.139910433 7574.831042 -3.87937295 0.246248693 AMDDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AMDDKR 6 1 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ; 80.377 0.067869 110813000 282430 256790 262100 263800 285500 195283 301750 253030 233060 FALSE TRUE 264753.2105 275802.9988 268317.1358 270569.5546 263077.9817 251658.0319 256505.3888 284621.3525 194160.7804 1.363577186 1.420487692 1.381932722 1.393533514 1.354949136 1.296132161 1.321097846 1.465905483 1 17.56689229 -3.054533718 0.400822958 1.22E-23 1.381604724 0.842045842 0.050478049 49.11030167 1.537512964 41.79632623 0.031149971 0.000881995 3.054533718 1.381604724 AMDSDWFAENYMGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AMDSDWFAENYMGR 14 0 P55084-2;P55084;B5MD38;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ;; 231.92 8.40E-13 526637000 420579 460916 464812 394267 591860 395044 379019 460801 682040 FALSE TRUE 394255.7111 495042.7002 475837.5601 404384.5587 545377.703 509086.7898 322188.6196 518333.0192 568203.1179 0.69386404 0.871242492 0.837442712 0.711690144 0.959828776 0.895959163 0.567030714 0.912231917 1 19.11604722 -2.490895716 1.448088721 2.012526488 0.80296993 0.207903175 0.118762791 406961.1122 30769.66273 1338763.302 0.032371401 0.003229269 2.490895716 -1.209556558 AMEGIFIKPSVEPSAGHDEL ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AMEGIFIKPSVEPSAGHDEL 20 1 Q9HCN8 Q9HCN8 SDF2L1 Stromal cell-derived factor 2-like protein 1 0 186.11 3.10E-17 130330000 177580 243600 227880 215300 247970 171030 272260 218410 190880 FALSE TRUE 166465.5848 261636.3975 233285.4212 220824.9625 228495.4365 220403.5846 231437.1405 245678.9693 159020.8949 1.046815797 1.645295718 1.467011121 1.388653753 1.436889389 1.386003926 1.455388241 1.544947722 1 17.27885682 -1.227328578 3.96584732 0.999621569 1.44424881 0.415998857 0.154809122 10465167.48 3261521.999 34388.87199 0.032715785 0.05924769 1.227328578 0.444627241 AMEVDERPTEQYSDIGGLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AMEVDERPTEQYSDIGGLDK 20 1 P17980;E9PM69;R4GNH3;E9PN50;E9PMD8 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ;;; 241.65 8.60E-30 1507270000 4436270 3607870 3997460 3821370 4130970 2989600 4858450 3479850 4935230 FALSE TRUE 4158611.78 3875000.449 4092281.639 3919432.824 3806540.28 3852648.988 4129970.526 3914316.933 4111508.23 1.011456513 0.942476637 0.995323713 0.953283468 0.925825772 0.93704032 1.004490395 0.952039182 1 21.97123629 0.399460412 0.907469676 0.999806031 0.964666464 0.10923667 0.029578449 5.048733649 5.582370743 0.029036498 0.00901061 2.508767483 -0.399460412 -0.035139567 AMEVDIEERPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AMEVDIEERPK 11 1 D6RIC3;A0A0C4DGU5;A0A087X2G6;Q9Y3C1;Q9Y3C1-3;Q9Y3C1-2 D6RIC3 NOP16 Nucleolar protein 16 0 97.214 0.0058673 130810000 232000 198910 227830 220480 247980 175930 274320 201320 305340 FALSE TRUE 217479.5341 213637.5034 233234.2352 226137.8901 228504.6511 226718.135 233188.2627 226455.2452 254376.7814 0.854950412 0.839846712 0.916884921 0.888987937 0.898292092 0.891268982 0.916704195 0.890235516 1 17.95660747 -5 0.101153506 1.353158301 0.812921534 0.799307347 0.019185672 81.02078658 0.556599291 6.049209848 0.310135289 1.00E-05 5 -0.540236767 AMGIMNSFVNDIFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 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 ;;;;;;;;;; 318.91 4.21E-56 18664563000 2602986 3840113 2933751 2848603 3775202 2248627 2917717 3134672 3083053 FALSE TRUE 2440069.753 4124438.962 3003340.959 2921702.976 3478712.863 2897769.111 2480232.423 3526042.699 2568471.537 0.950008485 1.605795082 1.169310586 1.137525931 1.354390272 1.128207601 0.965645282 1.37281751 1 21.29247866 2.641441336 0.782217177 1.092885816 1.316147997 0.027078464 0.203819113 1.266672987 1.626665282 0.13519055 0.118149334 437.9669472 -2.641441336 0.223262181 AMIEVINHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AMIEVINHK 9 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8;A0A494C0X4 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 124.23 0.00053548 201100000 563760 412690 460860 412340 530820 374610 510890 420880 527120 FALSE TRUE 528475.2679 443245.997 471791.8168 422921.3425 489131.5384 482753.8257 434286.7874 473427.7945 439140.2667 1.203431587 1.009349474 1.07435335 0.963066643 1.113838961 1.099315782 0.98894777 1.078078761 1 18.7443223 4.745713263 24.70686557 1.041789997 1.203431676 0.50885799 0.05018408 569.3341969 1966549.947 0.010925308 0.109121695 55681.79961 -4.745713263 0.161641679 AMKDEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AMKDEEK 7 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;; 107.47 0.0068139 1314500000 3630660 2029870 2544960 2331750 2562640 1674700 2970680 2136560 2956320 FALSE TRUE 3403423.472 2180163.687 2605327.653 2391586.653 2361380.592 2158158.704 2525254.112 2403314.219 2462891.093 1.381881432 0.885205072 1.057833073 0.97104848 0.958784007 0.876270457 1.025321062 0.975810187 1 21.2319214 4.745893099 24.97849873 0.970654917 1.381881628 0.844962538 0.055605074 317.7979586 1082569.231 0.012569675 0.130358899 55704.86157 -4.745893099 0.411226711 AMKPPGGESSNLFGS(ph)PEEATPSSRPNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AMKPPGGESSNLFGSPEEATPSSRPNR 27 2 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BMM8;B4E1P3 A6NGP5 HN1L Hematological and neurological expressed 1-like protein 1 AMKPPGGESSNLFGS(1)PEEATPSSRPNR;AMKPPGGESSNLFGS(1)PEEATPSSRPNR;AMKPPGGESSNLFGS(1)PEEATPSSRPNR;AMKPPGGES(0.001)S(0.003)NLFGS(0.993)PEEAT(0.002)PS(0.001)S(0.001)RPNR;AMKPPGGESSNLFGS(1)PEEATPSSRPNR;AMKPPGGESS(0.001)NLFGS(0.999)PEEATPSSRPNR 259.42 2.81E-53 2446669000 1340633 1130786 1307261 1292376 1452812 1145204 1648600 1178213 1570995 TRUE FALSE 1256725.174 1214510.572 1338269.848 1325540.556 1338714.006 1475805.804 1401407.735 1325315.487 1308785.785 0.960222206 0.927967423 1.022527799 1.012801767 1.022867165 1.127614481 1.070769373 1.012629799 1 20.31979755 3.562165566 1.044817368 1.058266763 0.938966158 0.506567864 0.038235749 0.39436893 0.861708501 0.013951821 0.033719336 3648.930283 -3.562165566 -0.119300606 AMLDQLMGTS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AMLDQLMGTSR 11 0 Q9Y383;V9GZ75;F8WEU3 Q9Y383 LUC7L2;C7orf55-LUC7L2 Putative RNA-binding protein Luc7-like 2 1 AMLDQLMGT(0.154)S(0.846)R;AMLDQLMGT(0.024)S(0.976)R;AMLDQLMGT(0.224)S(0.776)R;AMLDQLMGT(0.013)S(0.987)R 167.32 2.03E-05 390067000 829660 832930 905160 839640 881640 706170 985020 925870 1481540 TRUE FALSE 777733.0616 894601.0039 926630.8226 861186.5839 812399.5508 910029.8153 837325.3955 1041466.908 1234261.403 0.630120216 0.724806756 0.750757352 0.697734355 0.658207045 0.737307197 0.678401993 0.843797679 1 20.23521654 0.992533208 3.258693942 0.999349715 0.704409087 0.878444039 0.037235818 0.071767632 1.902600184 0.034870785 0.009099218 9.829540305 -0.992533208 -0.294940628 AMLDSGIYPPGS(ph)PGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AMLDSGIYPPGSPGK 15 0 O95295 O95295 SNAPIN SNARE-associated protein Snapin 1 AMLDSGIYPPGS(1)PGK 129.01 0.0002679 73104000 173290 125720 144730 139550 152420 123930 183420 128500 161530 TRUE FALSE 162444.0882 135028.4396 148163.0639 143131.0893 140449.548 159706.5792 155917.8738 144543.5079 134569.5995 1.207138082 1.003409686 1.101014379 1.063621277 1.043694479 1.186795382 1.158641137 1.074117099 1 17.037993 2.263671525 24.99770792 1.124904459 1.074251243 0 0.072716773 498.7221205 496472.146 0.023039621 0.019269401 183.514982 -2.263671525 -0.050653216 AMLPGS(ph)PLFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 AMLPGSPLFTR 11 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 AMLPGS(1)PLFTR;AMLPGS(1)PLFTR;AMLPGS(1)PLFTR;AMLPGS(1)PLFTR;AMLPGS(1)PLFTR;AMLPGS(1)PLFTR;AMLPGS(1)PLFTR 196.02 6.49E-08 546235000 1003671 1469457 1094553 1087411 1666966 770327 1351429 1131844 1606554 TRUE FALSE 940853.0237 1578257.125 1120516.314 1115315.807 1536049.215 992707.8997 1148794.768 1273157.215 1338409.759 0.702963362 1.179203241 0.837199749 0.833314163 1.147667375 0.74170701 0.858328147 0.951246213 1 20.35208844 2.201883655 24.99998976 0.869322952 0.953799329 0.016811753 0.156211177 507.2029505 345720.1297 0.054399878 0.040178135 159.178224 -2.201883655 0.084476377 AMNGESLDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AMNGESLDGR 10 0 P98179 P98179 RBM3 RNA-binding protein 3 0 87.149 0.030414 296400000 471070 570350 568540 506760 576860 472970 548030 536840 549650 FALSE TRUE 441586.5696 612579.3074 582026.0373 519764.3195 531555.7425 609508.761 465857.9892 603865.6557 457909.8641 0.964352603 1.337772683 1.271049355 1.13507998 1.160830513 1.331067113 1.017357401 1.318743497 1 18.80470412 -3.297245845 0.288877621 0.487392316 1.217366064 0.14497022 0.131571613 136.4957453 3.174079578 42.07293852 0.134383375 0.000504376 3.297245845 0.729973747 AMS(ph)LNTLNVDAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 AMSLNTLNVDAPR 13 0 Q6P597;Q6P597-3;Q6P597-2 Q6P597 KLC3 Kinesin light chain 3 1 AMS(0.999)LNT(0.001)LNVDAPR;AMS(1)LNTLNVDAPR;AMS(1)LNTLNVDAPR;AMS(1)LNTLNVDAPR;AMS(0.994)LNT(0.006)LNVDAPR;AMS(1)LNTLNVDAPR;AMS(1)LNTLNVDAPR;AMS(1)LNTLNVDAPR;AMS(1)LNTLNVDAPR;AMS(0.999)LNT(0.001)LNVDAPR;AMS(1)LNTLNVDAPR;AMS(1)LNTLNVDAPR;AMS(1)LNTLNVDAPR;AMS(0.948)LNT(0.052)LNVDAPR 271.33 4.59E-32 7759076000 6731833 7951370 6915655 6813301 7900890 4936168 8996100 6998835 9472400 TRUE FALSE 6310499.589 8540097.708 7079697.602 6988141.839 7280385.97 6361159.57 7647218.321 7872654.956 7891395.246 0.799668423 1.082203773 0.897141428 0.885539454 0.922572719 0.806088071 0.969057826 0.997625225 1 22.91184897 1.509748368 10.07799388 0.993651893 0.918070748 0.208797566 0.078224725 0.204159853 41.80717187 0.042414732 0.019678661 32.34062198 -1.509748368 -0.075581145 AMS(ph)QDGASQFQEVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AMSQDGASQFQEVIR 15 0 A0A087WYS1;E7EUC7;Q16851;C9J6Q0 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 1 AMS(1)QDGASQFQEVIR;AMS(1)QDGASQFQEVIR;AMS(1)QDGASQFQEVIR;AMS(1)QDGASQFQEVIR 223.65 1.30E-12 849519000 1090107 924634 975157 949519 804826 746665 1024699 700828 1123629 TRUE FALSE 1021879.149 993094.8634 998288.1845 973885.2651 741618.2125 962215.0644 871054.8978 788327.9185 936088.061 1.091648523 1.060898974 1.066446872 1.040377829 0.792252613 1.027910839 0.930526661 0.842151451 1 19.83628473 2.973395359 23.80258404 0.92396687 1.06746243 0.538071896 0.067741258 293.7918491 262849.2294 0.018691282 0.019892816 940.5791746 -2.973395359 0.14349556 AMS(ph)TTSISS(ph)PQPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AMSTTSISSPQPGK 14 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 2 AMS(0.969)T(0.03)T(0.001)S(0.001)IS(0.196)S(0.803)PQPGK;AMS(0.993)T(0.007)TSIS(0.357)S(0.643)PQPGK;AMS(0.972)T(0.028)TS(0.029)IS(0.328)S(0.643)PQPGK 278.89 4.96E-33 503220000 1742820 1353010 1435230 1639340 1161210 931930 2334890 1320350 1552960 TRUE FALSE 1633740.007 1453188.268 1469274.333 1681408.24 1070013.251 1200963.062 1984794.921 1485198.604 1293760.943 1.262783527 1.123227808 1.135661376 1.299628226 0.827056386 0.928272776 1.534128025 1.147969887 1 20.30313964 0.959660876 23.24789933 0.999999991 1.165038949 0.060852215 0.193447285 11259.70389 6489105.745 0.186155893 0.046538973 9.112989631 -0.959660876 0.165038958 AMS(ph)TTSISSPQPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 AMSTTSISSPQPGK 14 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 1 AMS(0.516)T(0.395)T(0.088)SISSPQPGK;AMS(0.485)T(0.485)T(0.029)SISSPQPGK;AMS(0.48)T(0.48)T(0.04)SISSPQPGK;AMS(0.898)T(0.102)T(0.001)SISSPQPGK;AMS(0.991)T(0.008)TSISSPQPGK;AMS(0.482)T(0.482)T(0.035)SISSPQPGK;AMS(0.725)T(0.138)T(0.138)SISSPQPGK;AMS(0.988)T(0.012)TSISSPQPGK;AMS(0.847)T(0.142)T(0.011)SISSPQPGK;AMS(0.988)T(0.011)T(0.001)SISSPQPGK 323.88 1.76E-56 13664470000 12507730 11830060 10056490 11642830 9492180 6102420 17137090 10564040 13451580 TRUE FALSE 11724893.51 12705969.95 10295034.69 11941604.73 8746702.472 7864089.589 14567542.45 11882983.65 11206424.4 1.046265347 1.133811241 0.918672569 1.06560347 0.780507873 0.701748329 1.299927785 1.060372446 1 23.4178227 -0.457460527 7.280122734 0.999987561 1.009075886 0 0.170694601 0 0 0.164162246 0.038693412 0.348770283 0.457460527 0.009088325 AMST(ph)TSISSPQPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AMSTTSISSPQPGK 14 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 1 AMS(0.029)T(0.905)T(0.066)SISSPQPGK;AMS(0.015)T(0.492)T(0.492)SISSPQPGK;AMS(0.006)T(0.497)T(0.497)SISSPQPGK;AMS(0.006)T(0.496)T(0.496)S(0.001)ISSPQPGK;AMS(0.056)T(0.74)T(0.204)SISSPQPGK 316.54 7.23E-55 6715090000 7457560 7159700 6011330 6829260 5480700 3631730 9844500 6291050 7902140 TRUE FALSE 6990804.632 7689811.638 6153921.586 7004510.374 5050267.93 4680151.495 8368408.617 7076501.441 6583221.784 1.061912368 1.168092446 0.934788738 1.063994288 0.767142304 0.710921134 1.271172215 1.074929825 1 22.65036237 -1.557924422 7.071349796 0.999988718 1.015082009 0 0.169179913 3.02E-05 1.89E-06 0.164175054 0.038667507 0.027674232 1.557924422 0.015093291 AMSTT(ph)SISSPQPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AMSTTSISSPQPGK 14 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 1 AMS(0.302)T(0.052)T(0.646)SISSPQPGK 264.08 1.21E-23 429550000 787010 783930 657530 714900 592160 428610 1086600 668870 867300 TRUE FALSE 737752.449 841972.9929 673126.9221 733245.5443 545654.1423 552342.7491 923674.4175 752379.8919 722542.027 1.021051263 1.16529276 0.931609369 1.014813695 0.755186718 0.764443767 1.278367739 1.041295681 1 19.46272198 -0.746476887 7.362468287 1.00000275 1.008874299 0 0.159304632 0 0 0.15673959 0.036943875 0.179276396 0.746476887 0.008871549 AMSTTSIS(ph)SPQPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AMSTTSISSPQPGK 14 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 1 AMSTT(0.004)S(0.329)IS(0.378)S(0.289)PQPGK 121.45 0.0004476 568720000 908750 754660 914690 883600 1010500 809970 1053800 902800 1191800 TRUE FALSE 851872.9597 810535.8116 936386.8787 906274.6719 931139.4062 1043795.19 895792.473 1015516.567 992880.8807 0.857981029 0.816347487 0.943100927 0.91277281 0.937815829 1.051279374 0.902215452 1.022797988 1 19.92126112 3.649099919 0.699154558 0.982114347 0.815322431 0.611444862 0.04505137 0.667103613 0.591944426 0.021832109 0.072267306 4457.587936 -3.649099919 -0.166791916 AMSTTSISS(ph)PQPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 AMSTTSISSPQPGK 14 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 1 AMSTTSIS(0.166)S(0.834)PQPGK;AMSTTS(0.014)IS(0.27)S(0.716)PQPGK;AMSTTSIS(0.018)S(0.982)PQPGK;AMSTTSISS(1)PQPGK;AMSTTSIS(0.003)S(0.997)PQPGK;AMSTTSIS(0.108)S(0.892)PQPGK;AMSTT(0.001)S(0.012)IS(0.027)S(0.96)PQPGK;AMSTT(0.01)S(0.445)IS(0.089)S(0.455)PQPGK;AMST(0.002)T(0.171)S(0.014)IS(0.103)S(0.71)PQPGK;AMSTTSIS(0.03)S(0.97)PQPGK 326.36 6.25E-58 7230850000 10919100 9042370 10468440 9876500 11619600 9505260 12489760 9961340 13375220 TRUE FALSE 10235693.02 9711876.483 10716756.34 10129947.71 10707043.49 12249274.26 10617036.44 11205035.23 11142809.37 0.918591773 0.871582395 0.961764307 0.909101769 0.960892637 1.099298556 0.952815047 1.005584395 1 23.40960968 2.474798502 24.99147973 1.01031076 0.917657756 0.558352516 0.041493827 54.96199327 591345.7218 0.013648821 0.011487453 298.3997822 -2.474798502 -0.092653004 AMT(ph)PEQEETASLLSSVTQGMESAYVSPSGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AMTPEQEETASLLSSVTQGMESAYVSPSGYR 31 0 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 AMT(0.934)PEQEET(0.053)AS(0.013)LLSSVTQGMESAYVSPSGYR 80.439 0.0059455 16200000 8409.1 8115.3 8918.8 7231.2 9143.3 6693.1 8726.9 7945.5 11410 TRUE FALSE 7882.789442 8716.165256 9130.358148 7416.764834 8425.2221 8625.289317 7418.382362 8937.513165 9505.597289 0.829278708 0.916950823 0.960524402 0.780252372 0.886343261 0.907390567 0.780422538 0.940236883 1 13.21456157 1.001640613 24.99510689 1.00000002 0.874555535 0.375458606 0.057935975 47.35371622 721429.4032 0.057768709 0.014442177 10.03784795 -1.001640613 -0.125444484 AMTGVEQWPYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AMTGVEQWPYR 11 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 110.38 0.0064037 123520000 45154 65816 55550 47326 71833 43028 57031 55080 59230 FALSE TRUE 42327.89174 70689.08512 56867.67223 48540.46528 66191.52594 55449.4851 48479.731 61956.85925 49344.13036 0.857810066 1.43257333 1.152470858 0.983713056 1.341426538 1.123730111 0.982482225 1.255607481 1 15.59059086 1.271580436 0.428694452 1.008082802 1.19745571 0.002149542 0.178240362 2.780449531 1.466054936 0.211593653 0.131719297 18.68875782 -1.271580436 0.189372909 AMTLS(ph)PQEEVAAGQMASSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AMTLSPQEEVAAGQMASSSR 20 0 Q9Y6A5;A0A494BZT8 Q9Y6A5 TACC3 Transforming acidic coiled-coil-containing protein 3 1 AMTLS(1)PQEEVAAGQMASSSR;AMTLS(1)PQEEVAAGQMASSSR;AMTLS(1)PQEEVAAGQMASSSR 439.78 1.60E-197 340343000 222923 206941 213363 200845 242065 185212 231265 191123 294422 TRUE FALSE 208970.6474 222263.127 218424.0711 205999.0227 223054.1913 238679.6977 196588.9602 214985.1273 245281.0662 0.851964037 0.906156885 0.890505225 0.839848856 0.90938202 0.973086514 0.801484449 0.876484804 1 17.90407635 -0.847601439 4.644312859 1.000000525 0.881924902 0.399285281 0.045817818 5586675.827 1202906.92 29.66799642 0.010265712 0.142036042 0.847601439 -0.118075623 ANAS(ph)PQKPLDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ANASPQKPLDLK 12 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 ANAS(1)PQKPLDLK;ANAS(1)PQKPLDLK;ANAS(1)PQKPLDLK;ANAS(1)PQKPLDLK 148.44 4.02E-05 3503110000 12808800 6681700 9134400 8231200 9381300 7352700 13468200 8132300 10347000 TRUE FALSE 12007120.07 7176420.02 9351072.282 8442426.527 8644530.54 9475305.129 11448768.44 9147635.556 8620018.856 1.392934316 0.832529504 1.084808797 0.979397687 1.002843577 1.099220928 1.328160487 1.0612083 1 23.03925959 1.996731707 16.60307606 1.178111808 1.029623965 0 0.165001928 3.155020194 16018.44523 0.057840336 0.041299041 99.25027238 -1.996731707 -0.148487843 ANASNS(ph)PEGNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ANASNSPEGNK 11 0 Q2TB10 Q2TB10 ZNF800 Zinc finger protein 800 1 ANASNS(1)PEGNK;ANASNS(1)PEGNK 170.74 1.61E-05 272028000 748840 405080 543830 446920 440850 347580 518060 424270 453890 TRUE FALSE 701971.4411 435072.5447 556729.9044 458388.7238 406227.4193 447920.7035 440381.7124 477241.0434 378132.8268 1.856414972 1.150581261 1.472313074 1.212242607 1.074298211 1.18455916 1.164621745 1.26209895 1 18.52853357 4.741991438 24.80690446 1.21338766 1.856415242 0.733998398 0.125366353 163.64767 1183212.677 0.029946945 0.218056996 55206.65549 -4.741991438 0.643027582 ANASNS(ph)PEGNKTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ANASNSPEGNKTK 13 1 Q2TB10 Q2TB10 ZNF800 Zinc finger protein 800 1 ANAS(0.073)NS(0.927)PEGNKT(0.001)K;ANAS(0.093)NS(0.906)PEGNKTK 82.449 0.0074598 221993000 279770 167106 200619 175461 230760 110764 216778 158460 373700 TRUE FALSE 262259.6951 179478.7021 205377.7774 179963.6263 212637.0404 142739.7687 184274.1514 178244.0798 311327.0558 0.84239288 0.576495678 0.659684963 0.578053282 0.683002124 0.458488159 0.591898931 0.572530002 1 18.24807143 -1.579781118 6.287365367 1.000885092 0.611797638 0.590762972 0.099086972 0.001110459 7.42E-05 0.086662192 0.020383367 0.02631594 1.579781118 -0.389087455 ANCDASLIVTEELHLITFETEVYHQGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 369.4 1.01E-127 359071000 234123 194024 235368 231726 227533 198664 281906 205207 237394 FALSE TRUE 219469.6594 208389.7388 240951.0401 237672.4815 209663.476 256015.0718 239636.8124 230827.5457 197771.4078 1.109713794 1.05368992 1.218331016 1.2017535 1.060130372 1.294499921 1.21168583 1.167143159 1 17.59347434 3.9952235 5.298830787 1.180508222 1.083378887 0.121816514 0.084790639 0.265094887 22.43640874 0.019510975 0.040937742 9890.619614 -3.9952235 -0.097129334 ANEHQGIGFLNDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ANEHQGIGFLNDPR 14 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 ;; 130.06 6.43E-05 924850000 1005630 1124740 1104660 1082510 1187600 1038080 1213460 1055820 1081850 FALSE TRUE 942689.4134 1208016.92 1130863.057 1110289.039 1094330.687 1337756.844 1031512.938 1187641.451 901282.246 1.045942509 1.340331428 1.254726876 1.231899379 1.214193103 1.484281811 1.144494905 1.317724227 1 19.78161945 -0.65559806 10.19520315 1 1.261658614 0.317801071 0.116591052 0 0 0.098678505 0.023258747 0.221004919 0.65559806 0.261658614 ANESS(ph)PKPVGPPPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ANESSPKPVGPPPER 15 1 Q9BQI0-3;Q9BQI0;Q9BQI0-2;A6PVM9 Q9BQI0-3 AIF1L Allograft inflammatory factor 1-like 1 ANES(0.002)S(0.998)PKPVGPPPER;ANES(0.082)S(0.918)PKPVGPPPER;ANES(0.157)S(0.843)PKPVGPPPER;ANES(0.427)S(0.573)PKPVGPPPER 168.99 7.40E-07 2588390000 1404420 800990 1060720 956990 1166030 812350 1206100 982020 1873500 TRUE FALSE 1316519.859 860296.133 1085880.779 981547.9836 1074454.707 1046862.258 1025256.502 1104627.359 1560800.747 0.843490024 0.551188955 0.69572031 0.628874625 0.688399663 0.670721269 0.656878531 0.707731183 1 20.57385494 0.687384248 2.612875388 0.999990548 0.664251396 0.654168354 0.072938638 1.205714618 9.401389417 0.061598914 0.016362138 4.868377511 -0.687384248 -0.335739153 ANFDKESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ANFDKESER 9 1 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;;; 123.96 0.00049537 3200800000 3427960 4370770 3321580 3199460 5378170 2270440 3921690 4014800 6301360 FALSE TRUE 3213410.103 4694386.359 3400369.446 3281563.56 4955790.223 2925879.17 3333668.992 4516056.618 5249622.308 0.612122152 0.894233163 0.647736017 0.625104697 0.944027957 0.557350415 0.635030255 0.860263149 1 22.3237822 1.008840928 4.968721148 0.99943444 0.711174096 0.393040888 0.12411879 0.153830218 12.02660692 0.113722235 0.028774391 10.20565605 -1.008840928 -0.288260344 ANGMELDGRR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 138.25 0.00011185 2003740000 1350623 1795890 1641800 1626501 2116950 1402940 1880044 1584529 2676810 FALSE TRUE 1266089.917 1928859.564 1680744.271 1668239.769 1950693.286 1807946.003 1598148.856 1782360.934 2230033.118 0.567744894 0.8649466 0.75368579 0.748078473 0.874737362 0.810726078 0.716648037 0.799253123 1 21.08863371 -5 0.424801092 5.291423466 0.771224538 0.421507861 0.086047764 963.6038345 6.151314045 3864.778119 0.044986993 1.00E-05 5 -4.520198928 ANGQENGHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ANGQENGHVK 10 0 P49006;P29966 P49006;P29966 MARCKSL1;MARCKS MARCKS-related protein;Myristoylated alanine-rich C-kinase substrate 0 ;;;;; 176.95 2.38E-06 1003827000 790668 745524 783593 754931 860343 611196 835903 714099 720040 FALSE TRUE 741181.5013 800723.3727 802180.196 774303.8076 792775.1312 787638.3633 710567.1053 803255.8321 599860.6724 1.235589422 1.334848923 1.337277526 1.290806088 1.321598777 1.313035509 1.184553577 1.339070669 1 19.19426792 -1.884519628 0.3242018 0.708921162 1.318516685 0.758498908 0.051603614 14.48492305 0.761169679 3.25297308 0.044656576 0.01304609 1.884519628 0.609595523 ANGTTVHVGIHPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ANGTTVHVGIHPSK 14 0 P61254;E5RIT6;J3QRI7;J3QQQ9;J3QQV1;J3QRC4;J3KS10;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 ; 139.66 5.88E-06 1072090000 861220 1474710 1459300 1466180 1561810 1304380 1813830 1437230 1616570 FALSE TRUE 807317.7775 1583899.063 1493915.285 1503804.661 1439151.743 1680933.331 1541863.03 1616671.329 1346754.024 0.599454513 1.176086379 1.109271076 1.116614196 1.068607717 1.248136855 1.144873528 1.200420642 1 20.36105494 4.740822976 24.96254093 1.140930247 0.599454321 0.854591793 0.069096819 64.50802217 711725.5232 0.01471096 0.098390295 55058.32254 -4.740822976 -0.541475926 ANGVTDLLVVHEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ANGVTDLLVVHEHR 14 0 B9A008;E7ENR5;B8ZZ47;H0Y714;Q96G21 B9A008 IMP4 U3 small nucleolar ribonucleoprotein protein IMP4 0 ; 127.71 4.51E-05 175670000 88812 105001 100888 99659 95658 87273 109063 89230 95482 FALSE TRUE 83253.41545 112775.3833 103281.111 102216.4187 88145.40655 112467.2983 92710.01564 100370.5619 79545.43736 1.046614592 1.417747982 1.29839139 1.285006684 1.108113922 1.413874913 1.165497591 1.261801622 1 16.27949156 -0.596654851 0.423564259 0.927935615 1.285005477 0.276927404 0.12116409 10.90081509 1.715916057 1.1941004 0.067321509 0.253130892 0.596654851 0.357069862 ANHEEVLAAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ANHEEVLAAGK 11 0 P00491 P00491 PNP Purine nucleoside phosphorylase 0 ;;; 128.28 0.00026905 4415700000 7729000 7320400 6964900 6476400 8145700 5782600 7906300 7377100 7583700 FALSE TRUE 7245255.687 7862410.033 7130110.717 6642595.389 7505969.58 7451942.747 6720823.713 8298147.174 6317931.477 1.146776554 1.244459529 1.128551448 1.051387691 1.188042258 1.17949091 1.063769643 1.313427853 1 22.59102086 -2.215613378 2.499941159 0.448848741 1.159301139 0.305773052 0.077541862 8702257.442 1720827.95 27873241.13 0.017645091 0.006086766 2.215613378 0.710452399 ANHPMDAEVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ANHPMDAEVTK 11 0 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 77.912 0.03132 319130000 348610 277590 276860 251420 320260 198960 366040 273930 393360 FALSE TRUE 326791.1224 298143.0524 283427.2499 257871.8629 295108.0715 256396.5222 311155.7001 308130.7635 327705.6748 0.997209226 0.909789105 0.864883558 0.786900816 0.900527803 0.782398786 0.949497443 0.940266792 1 18.32204113 1.582063083 9.729924488 0.960805597 0.873811433 0.3147035 0.062537107 0.137113846 28.69269049 0.032136816 0.015181863 38.19997539 -1.582063083 -0.086994163 ANHSFTPNCIYDMFVHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ANHSFTPNCIYDMFVHPR 18 0 Q8WTS6 Q8WTS6 SETD7 Histone-lysine N-methyltransferase SETD7 0 98.175 0.0007347 89881000 47080 142110 77827 113570 113710 56043 73386 82390 102200 FALSE TRUE 44133.34684 152631.9723 79673.09319 116484.3985 104779.6753 72221.70432 62382.45058 92676.57286 85142.15976 0.518348923 1.792672076 0.935765471 1.368116557 1.23064385 0.848248441 0.73268579 1.088492154 1 16.37758607 2.241396236 24.59916782 0.876008379 1.231366864 0.101798081 0.335223737 89.82575028 779252.7879 0.109551318 0.087884122 174.3396764 -2.241396236 0.355358485 ANILVTELFDTELIGEGALPSYEHAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ANILVTELFDTELIGEGALPSYEHAHR 27 0 H3BSS9;H3BPZ8;H3BNC0;Q9NVM4-4;Q9NVM4-3;Q9NVM4 H3BSS9 PRMT7 Protein arginine N-methyltransferase 7 0 192.57 2.02E-18 15385000 12810 14161 9974.2 13962 16192 13727 13047 10683 12776 FALSE TRUE 12008.24497 15209.49517 10210.79273 14320.28856 14920.34564 17689.76206 11090.72347 12016.79607 10643.60306 1.128212401 1.428979931 0.959336108 1.345436172 1.401813422 1.66200881 1.042008369 1.129015804 1 13.37769899 1.603364978 25 1.064099511 1.299773869 0.302614002 0.186950636 0.616266306 3405.100777 0.097201903 0.047370739 40.12037447 -1.603364978 0.235674358 ANIVAYHDSIMNPDYNVEFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ANIVAYHDSIMNPDYNVEFFR 21 0 Q9UBT2;K7EPL2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 ; 234.98 8.65E-30 424270000 89642 307640 234140 242920 295810 264770 295550 281170 248170 FALSE TRUE 84031.46724 330417.9857 239693.9114 249153.7385 272578.2758 341204.8008 251235.0213 316274.6934 206748.8238 0.406442299 1.598161381 1.159348368 1.205103535 1.318403031 1.650334907 1.215170257 1.52975329 1 17.6575196 2.68625356 4.22343392 1.37285419 1.186804821 0.088158242 0.340872676 0.662762193 25.14369033 0.103810803 0.0995276 485.5719152 -2.68625356 -0.186049369 ANIVHLMLSSPEQIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ANIVHLMLSSPEQIQK 16 0 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 ; 207.39 1.76E-11 447870000 461680 474370 490630 500190 537340 384540 628720 515590 557360 FALSE TRUE 432784.2729 509492.8484 502267.9753 513025.7222 495139.4839 495550.4555 534449.2728 579962.5465 464333.0153 0.932055785 1.097257424 1.081697744 1.104865916 1.066345635 1.067230714 1.151004247 1.249022851 1 18.82480034 4.741121646 4.835663754 1.104728593 0.922340841 0.407909894 0.064414442 0.177343246 12.11129888 0.014522423 0.109124183 55096.19993 -4.741121646 -0.182387752 ANKLDHVVTIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ANKLDHVVTIIK 12 1 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;Q99873-5;H0YDE4;E9PNR9 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ; 109 0.00098868 611330000 1597560 1609130 1554000 1580300 1879970 1346310 1950040 1641540 2361860 FALSE TRUE 1497571.571 1728271.659 1590861.614 1620853.173 1732324.74 1734967.841 1657649.605 1846489.882 1967650.308 0.761096403 0.878342891 0.808508304 0.823750626 0.880402749 0.881746027 0.842451323 0.938423802 1 20.90804242 0.505864722 0.339090217 1.027564026 0.815043879 0.713361365 0.035875254 1.562657022 0.372087334 0.103506935 0.035290093 3.205270758 -0.505864722 -0.212520147 ANLEAFTVDKDITLTNDKPATAIGVIGNFTDAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ANLEAFTVDKDITLTNDKPATAIGVIGNFTDAER 34 2 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 95.099 0.00015257 88778000 127470 86712 101570 96273 114110 76369 132580 94243 143440 FALSE TRUE 119491.8802 93132.2467 103979.2884 98743.52817 105148.2609 98415.49055 112700.8598 106009.446 119498.9373 0.999940944 0.779356275 0.870127306 0.826313023 0.879909589 0.823567914 0.943111816 0.887116223 1 16.86663826 0.993642123 0.799358041 0.996936293 0.852827187 0.281301413 0.062056116 0.723861531 1.031709063 0.053204111 0.019579071 9.854670836 -0.993642123 -0.144109106 ANLQQAIVT(ph)PLKPVDNTYYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ANLQQAIVTPLKPVDNTYYK 20 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 ANLQQAIVT(1)PLKPVDNTYYK 218.29 1.62E-24 258760000 595440 441300 491580 474060 590500 285750 800920 510820 1279700 TRUE FALSE 558172.4733 473974.3112 503240.5097 486225.1822 544124.512 368241.3862 680829.4814 574597.0015 1066109.803 0.523560023 0.444583016 0.472034408 0.456074206 0.510383181 0.345406623 0.638611032 0.538966061 1 20.0239246 0.370066575 0.766166697 1.007092819 0.462649807 0.850311467 0.06831122 0.709824737 0.588497737 0.070155564 0.020971926 2.3445882 -0.370066575 -0.544443012 ANNIDYTVHSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ANNIDYTVHSVR 12 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ;;; 230.14 6.52E-12 1414320000 1057450 1305090 1166620 1204470 1371740 1053070 1371910 1203120 1280020 FALSE TRUE 991266.0921 1401720.222 1194292.777 1235378.739 1264009.074 1357074.214 1166204.832 1353332.18 1066376.393 0.929564926 1.314470417 1.119954254 1.158482828 1.185331073 1.272603391 1.093614637 1.26909428 1 20.02428532 -0.803786895 19.70979013 0.999999373 1.17553825 0.18520671 0.109629295 0 0 0.091880954 0.021656548 0.157113356 0.803786895 0.175538878 ANPELCGSLHLNGS(ph)PSSCIASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ANPELCGSLHLNGSPSSCIASR 22 0 Q9NXR5 Q9NXR5 ANKRD10 Ankyrin repeat domain-containing protein 10 1 ANPELCGSLHLNGS(0.985)PS(0.015)SCIASR;ANPELCGSLHLNGS(0.968)PS(0.032)SCIASR 200.48 1.06E-22 272760000 174921 204031 236008 216109 259260 250700 265270 251758 301770 TRUE FALSE 163973.0069 219137.6675 241606.2212 221654.7228 238898.7654 323073.0202 225495.2261 283190.5405 251402.6375 0.652232644 0.871660177 0.961032961 0.881672225 0.95026356 1.285082064 0.89694853 1.126442202 1 17.93964026 5.631001452 0.47151196 1.048200189 1.19E-15 0.529773532 0.113758903 8.481025148 0.767702193 0.064217604 5.90416998 427564.3152 -5.631001452 -1.048200189 ANPFGGASHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ANPFGGASHAK 11 0 D6RD47;P62266;D6RDJ2;D6RIX0;D6R9I7 D6RD47 RPS23 40S ribosomal protein S23 0 ;;; 167.71 1.89E-05 2403590000 3151880 3506770 3171490 2986040 3893060 2426560 3611620 3607590 4290220 FALSE TRUE 2954609.457 3766414.9 3246719.24 3062666.842 3587314.771 3127068.48 3070091.11 4058005.553 3574154.566 0.826659676 1.053791835 0.908388034 0.856892668 1.003682047 0.874911373 0.858969877 1.135374947 1 21.7691706 1.239716236 24.99996349 1.067687481 0.921806959 0.41208574 0.076653187 30.51914627 660363.0926 0.05668371 0.018066869 17.36665738 -1.239716236 -0.145880522 ANQIS(ph)PSNSSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ANQISPSNSSLK 12 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 ANQIS(0.985)PS(0.015)NSSLK;ANQIS(0.861)PS(0.128)NS(0.008)S(0.003)LK 185.66 0.0001115 0 518490 409540 468630 432350 405470 420270 537540 415480 352580 TRUE FALSE 486038.6364 439862.7677 479746.1249 443444.833 373626.0218 541595.1265 456940.8673 467353.5926 293732.1202 1.65470033 1.497496315 1.633277711 1.509691322 1.271995795 1.84384032 1.555638065 1.591087799 1 18.16414151 -0.979451276 5.102511406 0.999996467 1.569501328 0.609923354 0.143185135 5.24E-06 1.05E-06 0.126316789 0.029772968 0.104845241 0.979451276 0.569504861 ANS(ph)FQSPTPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ANSFQSPTPSK 11 0 A0A2R8YFA9;E9PRG5;A0A2R8Y7K9 A0A2R8YFA9 MICALCL 1 ANS(1)FQSPTPSK 119.39 0.00062221 156450000 190720 150260 154600 159320 171310 103890 200620 136970 208930 TRUE FALSE 178783.1756 161385.4067 158267.185 163408.4209 157856.0036 133881.3565 170538.8935 154071.006 174058.2333 1.027145756 0.927192031 0.909277212 0.938814659 0.906914891 0.76917566 0.979780676 0.885169309 1 17.40921053 5.034327917 1.62168261 0.908581358 1.163870689 0.246285998 0.061836824 3.228451681 4.42557232 0.014744954 1.629594476 108225.0803 -5.034327917 0.255289331 ANS(ph)FVGTAQYVSPELLTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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(0.999)FVGT(0.001)AQYVSPELLTEK;ANS(0.998)FVGT(0.002)AQYVSPELLTEK;ANS(0.994)FVGT(0.006)AQYVSPELLTEK;ANS(1)FVGTAQYVSPELLTEK;ANS(0.978)FVGT(0.022)AQYVSPELLTEK;ANS(0.997)FVGT(0.003)AQYVSPELLTEK 430.99 2.33E-169 3369976000 6221918 4219060 4679222 4604923 4926162 3234115 6535000 4197244 6389720 TRUE FALSE 5832499.259 4531443.592 4790215.356 4723093.12 4539281.108 4167751.499 5555137.418 4721279.153 5323234.453 1.095668303 0.851257564 0.899869318 0.887260022 0.852729886 0.782935927 1.043564297 0.886919258 1 22.34387168 -1.233290233 3.200838463 1.000323113 0.907702747 0.079617571 0.092180659 18176131.52 24917153.19 57674.93026 0.021304283 0.058439941 1.233290233 -0.092620366 ANS(ph)GQAHKDEALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ANSGQAHKDEALK 13 1 Q8IY63-2;Q8IY63 Q8IY63-2 AMOTL1 Angiomotin-like protein 1 1 ANS(1)GQAHKDEALK;ANS(1)GQAHKDEALK;ANS(1)GQAHKDEALK 180.14 7.94E-06 1071700000 2029650 984660 1350730 1169020 1356890 962790 1771010 1150600 2088110 TRUE FALSE 1902617.83 1057565.251 1382769.953 1199019.032 1250325.333 1240731.843 1505463.492 1294254.943 1739590.951 1.093715639 0.607939039 0.794882241 0.689253431 0.718746744 0.713231948 0.865412349 0.743999583 1 20.73031668 0.131776181 0.744847466 1.005508565 0.755738557 0.19981421 0.132314955 5.17859339 3.331562007 0.198642197 0.041397716 1.354491177 -0.131776181 -0.249770008 ANS(ph)LGDLYAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 184.51 5.11E-06 375417000 1020700 825960 890690 877100 1010790 644550 1150360 812680 1169330 TRUE FALSE 956816.209 887114.9378 911817.5874 899607.8709 931406.6307 830621.1216 977874.1974 914144.8869 974161.2688 0.982194878 0.910644845 0.93600271 0.923469142 0.956111334 0.852652582 1.003811411 0.938391739 1 19.8938011 1.627911597 25 0.978321349 0.927108126 0.316598846 0.037263751 0.955179367 1188.220621 0.015153091 0.008389026 42.45331395 -1.627911597 -0.051213223 ANS(ph)LVTLGSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ANSLVTLGSHR 11 0 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 ANS(1)LVTLGSHR;ANS(1)LVTLGSHR 124.2 0.00022814 249420000 325340 359810 262100 261640 385210 191764 317570 342880 471860 TRUE FALSE 304977.5501 386450.7068 268317.1358 268354.1254 354957.1605 247123.1538 269953.3267 385689.3228 393103.5177 0.775819947 0.983076186 0.682561014 0.682655111 0.902961038 0.628646508 0.686723254 0.981139332 1 18.58454975 1.222738489 23.84153555 0.990570285 0.768216003 0.432378092 0.108184498 163.0055343 245612.2038 0.10526032 0.026733056 16.70084666 -1.222738489 -0.222354282 ANS(ph)RDGEAGR ddPTM_SK-BR-3_Pertuzumab_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 109.44 0.0012222 196467000 61666 56930 46413 63598 46263 32268 53710 42899 71131 TRUE FALSE 57806.43514 61145.15644 47513.93828 65230.03235 42629.6906 41583.24777 45656.68412 48255.03458 59258.77658 0.975491539 1.031832919 0.801804239 1.100765762 0.719381888 0.701723022 0.77046282 0.814310341 1 15.85474122 2.720619174 24.9942876 0.777576429 0.957255279 0.368756792 0.110888966 794.8151738 1107258.314 0.033062195 0.031228312 525.5562119 -2.720619174 0.17967885 ANSALT(ph)PPKPESGLTLQESNTPGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ANSALTPPKPESGLTLQESNTPGLR 25 1 Q9BW04;Q9BW04-2 Q9BW04 SARG Specifically androgen-regulated gene protein 1 ANSALT(1)PPKPESGLTLQESNTPGLR;ANS(0.001)ALT(0.997)PPKPES(0.003)GLTLQESNTPGLR;ANS(0.001)ALT(0.999)PPKPESGLTLQESNTPGLR;ANSALT(1)PPKPESGLTLQESNTPGLR 129.48 0.00016287 1664500000 2024450 1783270 1636210 1899610 1839130 1178110 2192740 1420980 1580000 TRUE FALSE 1897743.288 1915305.166 1675021.674 1948357.209 1694692.148 1518211.232 1863958.993 1598392.481 1316287.793 1.44173888 1.455080854 1.272534535 1.480190897 1.287478436 1.153403716 1.416072536 1.214318396 1 20.32804352 -4.449377855 0.114691789 5.22E-14 1.543201135 0.646202954 0.090810094 88.0554365 0.753686342 21.14881137 0.987200896 3.55E-05 4.449377855 1.543201135 ANSWQLVET(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ANSWQLVETPEK 12 0 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 ANSWQLVET(1)PEK;ANSWQLVET(1)PEK;ANSWQLVET(1)PEK;ANSWQLVET(1)PEK 230.86 5.38E-11 1030850000 2472210 1563650 1993220 1894440 2005600 1722470 2706550 1601210 2076420 TRUE FALSE 2317478.789 1679424.273 2040500.12 1943054.538 1848088.266 2219719.127 2300727.954 1801124.593 1729852.088 1.339697657 0.970848482 1.17958069 1.123248948 1.068350456 1.28318435 1.330014265 1.041201503 1 20.72221725 2.247696104 24.99861749 1.209273448 1.119077967 0 0.137024342 466.1157287 1275492.845 0.044560419 0.036798802 176.8870765 -2.247696104 -0.090195481 ANSWQLVET(ph)PEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ANSWQLVETPEKR 13 1 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR 225.69 7.04E-12 5180400000 2798880 1816550 2123870 2015840 2047970 1557410 2801360 1837530 2004910 TRUE FALSE 2623703.097 1951049.252 2174249.199 2067569.867 1887130.697 2007008.985 2381322.075 2066949.665 1670277.569 1.570818615 1.168098817 1.301729269 1.237860045 1.129830594 1.20160207 1.425704397 1.237488729 1 20.67165644 -1.711197666 2.165230307 0.934420316 1.276756611 0.32028257 0.129691257 2204773.01 1383731.851 781192.6686 0.032151613 0.019444749 1.711197666 0.342336295 ANT(ph)PELKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ANTPELKK 8 1 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C3G1 Q9H8V3-2 ECT2 Protein ECT2 1 ANT(1)PELKK;ANT(1)PELKK;ANT(1)PELKK;ANT(1)PELKK;ANT(1)PELKK 122.7 0.00080823 2344650000 8298330 3227640 4984140 4564090 4807880 3026580 6637650 3614840 6554680 TRUE FALSE 7778952.338 3466617.824 5102366.154 4681212.276 4430288.499 3900304.514 5642396.003 4066160.731 5460661.563 1.42454394 0.634834769 0.93438608 0.857261015 0.811309847 0.714254943 1.033280664 0.74462786 1 22.38064431 4.751497141 24.74693133 0.840760245 1.424544369 0.683602585 0.124711746 1050.811167 2010108.656 0.027833903 0.512676384 56428.32268 -4.751497141 0.583784124 ANTIPIIGS(ph)PSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ANTIPIIGSPSSK 13 0 E9PGM7;O94988-6;O94988-5;O94988-1;O94988 E9PGM7 FAM13A Protein FAM13A 1 ANTIPIIGS(0.974)PS(0.025)S(0.001)K;ANTIPIIGS(0.731)PS(0.209)S(0.06)K;ANTIPIIGS(0.992)PS(0.007)S(0.001)K;ANTIPIIGS(1)PSSK 181.86 1.23E-05 824020000 2858930 2290650 2492890 2430490 2833030 2133220 3284410 2633270 4178110 TRUE FALSE 2679994.675 2460252.109 2552022.528 2492860.488 2610535.252 2749045.984 2791943.211 2962039.556 3480756.449 0.769946049 0.706815356 0.733180435 0.716183544 0.749990782 0.789784067 0.802108177 0.850975815 1 21.73096944 0.897531559 0.622793461 1.003518617 0.724302 0.951100562 0.018872774 0.166312927 0.147041085 0.018152386 0.007443688 7.898262418 -0.897531559 -0.279216617 ANVSS(ph)PHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ANVSSPHR 8 0 Q5QPM7;Q5QPM9;H0Y555;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 ANVS(0.147)S(0.853)PHR;ANVS(0.031)S(0.969)PHR;ANVS(0.007)S(0.993)PHR;ANVS(0.013)S(0.987)PHR 104.82 0.0029024 2157070000 2842310 3809110 2605650 2598130 3816460 2249870 2779480 3382590 2620300 TRUE FALSE 2664414.891 4091140.468 2667457.248 2664802.414 3516730.626 2899370.945 2362722.777 3804913.807 2182955.002 1.220554197 1.874129546 1.221947885 1.22073172 1.610995473 1.328186308 1.082350655 1.743010645 1 21.05785096 -4.04079133 0.09737283 1.09E-12 1.70971979 0.141393972 0.265556295 248.3335048 2.032704509 56.038385 4.884141812 9.10E-05 4.04079133 1.70971979 ANVSS(ph)PHREFPPATAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ANVSSPHREFPPATAR 16 1 Q5QPM7;Q5QPM9;H0Y555;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 ANVS(0.205)S(0.795)PHREFPPATAR;ANVS(0.033)S(0.967)PHREFPPATAR 134.32 1.75E-05 790010000 79451 85309 58828 64648 90605 47055 76644 55605 85441 TRUE FALSE 74478.30373 91625.36712 60223.42794 66306.97713 83489.24878 60639.01463 65151.94373 62547.40665 71180.34513 1.046332433 1.287228475 0.846068221 0.93153492 1.172925597 0.851906724 0.915308062 0.878717384 1 16.11919131 3.964831583 7.505346558 0.941576297 1.169791809 0.420570492 0.109489279 0.117392683 40.61816494 0.026161559 0.050076462 9222.137284 -3.964831583 0.228215512 ANVSSPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ANVSSPHR 8 0 Q5QPM7;Q5QPM9;H0Y555;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 0 ; 117.04 0.0021563 37109000 27729 157647 24107 22254 136849 21008 33369 120825 101525 FALSE TRUE 25993.49139 169319.3479 24678.82942 22825.07532 126101.4316 27072.66856 28365.62823 135910.2672 84579.82162 0.307324973 2.001888212 0.291781526 0.269864311 1.490916263 0.320084248 0.335371105 1.606887608 1 16.3680259 3.921751592 11.06966402 0.694789132 1.259250143 0.050272617 0.635009701 1.256999382 248.215224 0.14909356 0.269155567 8351.252062 -3.921751592 0.56446101 ANVVTT(ph)PSTNRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ANVVTTPSTNRK 12 1 Q8IWZ3-6;Q8IWZ3;Q8IWZ3-4;E9PDP5;H0Y785;H0Y472;H0Y4P6 Q8IWZ3-6 ANKHD1 Ankyrin repeat and KH domain-containing protein 1 1 ANVVT(0.093)T(0.901)PS(0.005)T(0.002)NRK 50.352 0.095775 313530000 369980 348880 332860 374530 407020 228140 474430 326920 356300 TRUE FALSE 346823.6122 374711.4382 340755.5964 384141.0739 375054.291 294000.3145 403293.6259 367736.6816 296831.2282 1.168420231 1.262372024 1.147977585 1.294139691 1.263527067 0.990462884 1.358663064 1.238874642 1 18.17928335 ANWEAQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ANWEAQQR 8 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 100.98 0.0133 272460000 203350 309740 203540 193730 349120 171620 216600 292330 408880 FALSE TRUE 190622.6865 332673.4719 208368.0649 198701.4398 321701.5235 221163.908 184122.8408 328828.044 340635.2865 0.559609336 0.976626571 0.611704287 0.583326061 0.944416319 0.64926893 0.540527796 0.965337582 1 18.37786837 1.130863671 7.719707459 0.995927901 0.70890198 0.381725069 0.15158484 0.263482593 16.59258929 0.14254817 0.035729873 13.51648202 -1.130863671 -0.287025922 APAASEGNHTDGAEEAAGSCAQAPSHS(ph)PPNKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APAASEGNHTDGAEEAAGSCAQAPSHSPPNKPK 33 1 Q92560;F8W6N3 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 APAASEGNHTDGAEEAAGSCAQAPS(0.006)HS(0.994)PPNKPK;APAASEGNHTDGAEEAAGSCAQAPS(0.102)HS(0.898)PPNKPK 214.42 4.30E-36 282876000 137162 96444 119245 106149 114213 87489 153456 109816 139490 TRUE FALSE 128577.2753 103584.8141 122073.5477 108872.963 105243.1717 112745.654 130446.6974 123526.7693 116208.2179 1.10643875 0.891372538 1.050472591 0.936878347 0.905643109 0.970203795 1.122525582 1.062977917 1 16.82635257 1.756895904 25 1.072541698 0.971195481 0.239131235 0.070138926 8.493951169 11593.12599 0.029690386 0.016465079 57.1341675 -1.756895904 -0.101346217 APAKES(ph)PPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APAKESPPK 9 1 A0A0J9YWL0;Q9Y4K1;A0A494C1M5 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 APAKES(1)PPK 51.875 0.091955 251590000 1142200 446810 689980 626840 661670 578070 961070 626770 858270 TRUE FALSE 1070711.741 479892.2773 706346.6514 642925.7756 609705.1072 744949.4248 816966.4756 705023.6142 715019.1924 1.497458743 0.671159995 0.987870898 0.899172753 0.852711527 1.041859341 1.142579786 0.986020546 1 19.44762244 2.081287063 7.973052829 1.066979327 0.936725969 0 0.214166091 0.645356166 55.20009195 0.073982321 0.054544521 120.5832718 -2.081287063 -0.130253358 APAPLGTVADSLRAS(ph)DGQLQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APAPLGTVADSLRASDGQLQAK 22 1 Q9BRG2;Q9BRG2-2 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 APAPLGTVADS(0.019)LRAS(0.981)DGQLQAK 137.32 1.93E-06 143750000 115340 109950 115320 118380 134260 89051 139960 109110 200040 TRUE FALSE 108121.0753 118090.8124 118055.4449 121417.8312 123715.7612 114758.5781 118974.2973 122732.6237 166652.0317 0.648783421 0.708607097 0.708394873 0.728570963 0.742359754 0.688611935 0.713908472 0.736460411 1 17.34647938 -5 0.331470281 3.968895775 0.698710532 0.937780365 0.023714563 79.41695763 0.68428211 166.202637 0.01910578 1.00E-05 5 -3.270185243 APAPQPPSLPDRS(ph)PRPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 APAPQPPSLPDRSPRPQR 18 2 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 APAPQPPS(0.001)LPDRS(0.999)PRPQR;APAPQPPS(0.012)LPDRS(0.988)PRPQR;APAPQPPS(0.012)LPDRS(0.988)PRPQR;APAPQPPS(0.017)LPDRS(0.983)PRPQR 117.48 6.80E-05 960720000 577300 697820 659370 642540 779120 543517 693780 645220 739140 TRUE FALSE 541167.8235 749487.3189 675010.5678 659028.6642 717931.058 700421.5346 589754.1297 725777.1373 615772.759 0.878843397 1.217149197 1.096200762 1.070246539 1.165902596 1.137467555 0.957746378 1.178644438 1 19.23203852 0.358244511 0.519929788 0.997432058 1.103350828 0.028131447 0.104617541 6.668192207 2.909304349 0.178739219 0.047866861 2.281626283 -0.358244511 0.10591877 APASVLPAAT(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APASVLPAATPR 12 0 P13861-2;P13861;C9J830 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 1 APASVLPAAT(1)PR 94.673 0.072406 137440000 144550 116440 117470 121340 141610 99626 150320 119650 147800 TRUE FALSE 135502.8735 125061.3388 120256.4439 124453.7898 130488.5218 128386.4089 127780.9115 134588.5659 123131.2252 1.100475313 1.015675257 0.976652703 1.010741099 1.059751673 1.042679537 1.037762041 1.093049839 1 16.90983714 2.746431839 24.18051839 1.047675204 1.015978721 0.040366199 0.038462949 773.3985025 2375891.471 0.011465373 0.011940705 557.7400594 -2.746431839 -0.031696484 APDEPQQAQVPHVWGWEVAGAPALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APDEPQQAQVPHVWGWEVAGAPALR 25 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 ; 154.86 7.08E-08 250690000 53287 56728 58088 59361 64347 47910 60699 49158 53455 FALSE TRUE 49951.86179 60928.20015 59465.87479 60884.30376 59293.44618 61740.83925 51597.74845 55295.48451 44533.01517 1.121681557 1.368157982 1.3353211 1.367172277 1.331449172 1.386405996 1.158640354 1.241673942 1 15.44258767 0.950952123 0.957529402 1.006450766 1.326107869 0.54713917 0.086058535 0.424947042 0.822883442 0.074676478 0.025132779 8.932070101 -0.950952123 0.319657102 APDSGLPSGGGGRPGCAYPGS(ph)PGPGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APDSGLPSGGGGRPGCAYPGSPGPGAR 27 1 Q6PJ61 Q6PJ61 FBXO46 F-box only protein 46 1 APDSGLPSGGGGRPGCAYPGS(1)PGPGAR 169.26 3.88E-12 150170000 53759 56196 62054 62431 58573 54797 63971 55141 67421 TRUE FALSE 50394.32015 60356.81031 63525.95018 64033.08516 53972.91285 70616.00435 54379.14243 62025.47523 56167.99954 0.897206961 1.074576464 1.13099898 1.140027875 0.960919265 1.257228403 0.968151668 1.104284926 1 15.7774608 -1.575546605 7.826405562 0.999965272 1.07289108 0.036110021 0.10393667 5.54E-05 3.01E-06 0.088582238 0.020869098 0.026573784 1.575546605 0.072925807 APDWVDAEECHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 APDWVDAEECHR 12 0 O14964-2;O14964;I3L1P5 O14964-2 HGS Hepatocyte growth factor-regulated tyrosine kinase substrate 0 ;;; 188.29 9.40E-06 1539720000 1216781 1338770 1342940 1318470 1385210 1355520 1617300 1232211 1573920 FALSE TRUE 1140624.849 1437893.924 1374795.171 1352304.172 1276421.194 1746836.619 1374800.879 1386055.256 1311222.584 0.869894145 1.09660552 1.048483444 1.031330751 0.973458824 1.332219747 1.048487798 1.057070914 1 20.32248118 APEATVTLPVFIGNIAVNHAPVS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APEATVTLPVFIGNIAVNHAPVSPR 25 0 Q5T370;Q8N5I2 Q5T370 ARRDC1 Arrestin domain-containing protein 1 1 APEATVTLPVFIGNIAVNHAPVS(1)PR 200.66 4.22E-25 81832000 97928 83505 88883 104620 101850 97957 102090 95177 38023 TRUE FALSE 91798.86129 89687.79709 90991.34673 107304.7263 93851.11184 126235.5957 86782.55226 107060.058 31676.71566 2.89799177 2.831347733 2.8724994 3.387495328 2.962779123 3.985122607 2.739632264 3.37977141 1 14.95113514 3.432401131 24.98843997 3.058914246 2.858294316 0 0.776129256 730.4549205 408157.0054 0.185941155 0.251765903 2706.456999 -3.432401131 -0.20061993 APELPNTSSS(ph)PSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APELPNTSSSPSLK 14 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 APELPNTS(0.001)S(0.266)S(0.734)PSLK;APELPNT(0.001)SS(0.049)S(0.95)PSLK 283.98 1.77E-33 492910000 989410 669290 861030 766420 867930 785030 1097860 788890 1069970 TRUE FALSE 927484.5942 718844.928 881454.0382 786087.6347 799766.2789 1011655.417 933246.085 887384.6531 891385.0947 1.040498209 0.806435885 0.988858848 0.881872088 0.897217469 1.134925211 1.046961735 0.995512106 1 19.76568931 2.257051974 24.99295009 1.051218872 0.914200144 0.405143389 0.072436399 198.2754612 267988.9841 0.023147718 0.019334149 180.7390411 -2.257051974 -0.137018728 APEPHVEEDDDDELDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APEPHVEEDDDDELDSK 17 0 P52566;F5H3P3;F5H2R5;F5H6Q0 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ; 242.42 2.09E-20 443300000 824950 434420 626750 543430 488170 546940 717580 475420 496580 FALSE TRUE 773317.8521 466584.9088 641616.806 557375.3338 449831.0974 704832.6992 609985.5407 534777.2335 413697.59 1.869282952 1.127840529 1.55093194 1.34730138 1.087342804 1.703738954 1.474472067 1.292676695 1 18.65821703 0.92271608 4.175896427 1.000244179 1.427591692 0.268075519 0.235946878 0.482012652 20.68891751 0.205784936 0.052482966 8.369819258 -0.92271608 0.427347513 APEPHVEEDDDDELDSKLNYKPPPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APEPHVEEDDDDELDSKLNYKPPPQK 26 2 P52566;F5H3P3;F5H2R5;F5H6Q0 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 77.235 0.013308 85048000 197680 102290 144220 135410 131650 113690 197620 118340 216870 FALSE TRUE 185307.5617 109863.658 147640.9665 138884.8498 121310.7401 146510.4574 167988.7156 133115.0095 180672.996 1.025651679 0.608080125 0.817172294 0.768708401 0.671438138 0.810915082 0.929794266 0.736773134 1 17.46302137 1.99560747 24.64046646 0.878380054 0.758332111 0.12682519 0.125893765 258.6054027 1450684.54 0.043363865 0.031223788 98.9936802 -1.99560747 -0.120047943 APEPQLS(ph)PGSDASEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APEPQLSPGSDASEVR 16 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 APEPQLS(0.999)PGS(0.001)DASEVR;APEPQLS(0.91)PGS(0.09)DASEVR 272.63 3.68E-35 835180000 167402 185762 183273 183588 173659 145454 182539 142763 165197 TRUE FALSE 156924.6076 199516.0118 187620.3221 188299.1789 160020.5226 187444.2086 155168.9716 160587.2748 137624.5535 1.140236997 1.449712328 1.363276518 1.36820919 1.162732366 1.361996852 1.127480291 1.166850469 1 17.07037836 1.417656065 0.654388272 1.00426337 1.354225404 0.492096925 0.10134264 0.471364337 0.463541405 0.089438976 0.041686604 26.16110385 -1.417656065 0.349962034 APEVNLNAPDVDVHGPDWNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APEVNLNAPDVDVHGPDWNLK 21 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 272.38 1.10E-44 472890000 919330 700280 818910 785860 977540 663680 963080 782890 1047290 FALSE TRUE 861790.7764 752129.4598 838334.9319 806026.4981 900767.9516 855273.6421 818675.0948 880635.5399 872490.5332 0.987736535 0.862048849 0.960852754 0.923822629 1.03241 0.980266959 0.938319745 1.009335352 1 19.73477995 3.132270537 1.882753291 0.981991119 0.919509011 0.254875422 0.042187982 0.406281312 2.944725573 0.013194171 0.017179243 1356.033871 -3.132270537 -0.062482108 APEYLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APEYLHR 7 0 Q9UN86-2;Q9UN86;D6RB17;D6RAC7;D6RE13;D6RBW8;D6RGJ4;D6RBM9;D6REX8;D6RBR0;D6R9X5;D6R9A4 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 138.85 0.0027458 232980000 167760 190280 170720 161010 216570 139370 166490 177780 227090 FALSE TRUE 157260.2011 204368.5292 174769.559 165141.7892 199561.4658 179603.8565 141526.3701 199976.2243 189187.2119 0.831241179 1.080244944 0.92379161 0.872901437 1.054835915 0.949344592 0.748075775 1.057028233 1 17.52945505 1.978144772 24.6945794 0.89245987 0.965759882 0 0.110058101 1641.105534 1854310.36 0.041808488 0.027265077 95.092173 -1.978144772 0.073300012 APFDLFENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 APFDLFENR 9 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;; 140.14 0.00025547 187313000 95023 198697 82754 90315 164920 57185 83973 156180 133889 FALSE TRUE 89075.68005 213408.7326 84716.96396 92632.6358 151967.8485 73693.38118 71382.02822 175679.4168 111542.0609 0.798583775 1.91325793 0.759506891 0.830472694 1.362426399 0.660677959 0.639956153 1.575006014 1 16.76722831 3.828299277 6.182842567 0.934346507 1.41753986 0.125092677 0.398742247 0.30912098 15.94787129 0.094628179 0.172389175 6734.405716 -3.828299277 0.483193352 APGFGDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 APGFGDNR 8 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;; 107.67 0.0092075 2125410000 1931510 2086050 1845280 1878320 2449290 1913340 1725590 2144010 2269850 FALSE TRUE 1810620.237 2240503.313 1889050.913 1926520.871 2256932.643 2465690.198 1466853.799 2411694.368 1890997.371 0.957494846 1.184826244 0.998970671 1.018785589 1.193514427 1.303909902 0.775703775 1.275355749 1 20.85071593 -1.957686178 2.860477054 0.941466189 1.077347185 0.025226277 0.160038294 0.084266722 0.001246522 0.218572313 0.033512899 0.011023356 1.957686178 0.135880996 APGFGDNRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 APGFGDNRK 9 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;;;; 107.21 0.0045077 6503770000 3999670 3959670 3604610 3291550 5211560 2857450 3778420 4228970 7405010 FALSE TRUE 3749337.794 4252848.087 3690113.051 3376016.746 4802265.1 3682349.428 3211880.998 4756966.214 6169065.993 0.607764255 0.689382816 0.598163977 0.547249251 0.778442815 0.596905501 0.520642996 0.771099907 1 22.55662065 0.967256008 5.557947191 0.999885398 0.62195779 0.745544871 0.071792972 0.096856785 11.56241354 0.0677811 0.017079279 9.273763324 -0.967256008 -0.377927608 APGMEGTAALHGDS(ph)PARPQQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APGMEGTAALHGDSPARPQQAK 22 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 APGMEGTAALHGDS(1)PARPQQAK;APGMEGTAALHGDS(1)PARPQQAK 201.97 8.83E-23 393780000 284015 207749 261632 210660 243292 201123 275140 252920 175679 TRUE FALSE 266239.0081 223130.9521 267838.0346 216065.8922 224184.8277 259183.9451 233885.3113 284497.6187 146357.04 1.819106264 1.524565898 1.830031781 1.476293127 1.531766615 1.770901797 1.598046198 1.943860157 1 17.15913262 -1.214017224 4.397125054 0.999764726 1.67241768 0.659764829 0.154696374 10394678.05 2869927.547 23539.17097 0.032364913 0.06109178 1.214017224 0.672652955 APGPGLAQGLPQLHSLVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APGPGLAQGLPQLHSLVLR 19 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 144.17 1.38E-07 151120000 97757 111440 82402 80344 104820 80697 100630 92741 91604 FALSE TRUE 91638.56387 119691.1336 84356.61435 82405.76306 96587.86002 103992.9139 85541.4657 104319.918 76314.70062 1.200798315 1.568388955 1.105378304 1.07981506 1.265652086 1.362685211 1.120904164 1.366970153 1 16.21967337 -5 0.070017803 0.229359155 1.550098892 0.189406478 0.151810828 488.0537681 2.461460195 63.16416896 7.883948851 1.00E-05 5 1.320739737 APGPS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APGPSPAK 8 0 C9JPC9;Q9H9J4-2;Q9H9J4 C9JPC9 USP42 Ubiquitin carboxyl-terminal hydrolase 42 1 APGPS(1)PAK 61.353 0.090737 194660000 508340 356870 431260 375290 346660 319570 515100 357780 421780 TRUE FALSE 476523.9068 383293.0261 441489.6909 384920.5768 319434.722 411824.6712 437865.537 402449.6206 351382.1932 1.356141307 1.090815168 1.256437291 1.095447021 0.909080563 1.172013492 1.246123297 1.145332997 1 18.42268156 4.745856558 23.80535233 1.134545521 1.356141517 0.3248636 0.10604266 599.6727161 1956526.59 0.025431226 0.253173554 55700.17483 -4.745856558 0.221595996 APGT(ph)PHSHTKPYVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 APGTPHSHTKPYVR 14 1 J3QQ67;Q07020;F8VYV2;H0YHA7;Q07020-2;F8VUA6 J3QQ67 RPL18 60S ribosomal protein L18 1 APGT(1)PHSHTKPYVR;APGT(1)PHSHTKPYVR;APGT(1)PHSHTKPYVR 143.67 1.33E-05 249918000 401206 452243 394861 371190 447707 201582 565830 331688 667140 TRUE FALSE 376095.2326 485727.5423 404227.2894 380715.3638 412545.8982 259775.451 480989.0444 373099.9769 555790.0241 0.676685828 0.873940735 0.727302168 0.684998556 0.742269347 0.467398549 0.865415037 0.671296642 1 19.08418041 -1.190512865 4.313799825 1.000070233 0.728432017 0.379926237 0.11357667 8.96E-05 1.68E-05 0.103136395 0.024301672 0.064489222 1.190512865 -0.271638216 APGTPHSHTKPYVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APGTPHSHTKPYVR 14 1 J3QQ67;Q07020;F8VYV2;H0YHA7;Q07020-2;F8VUA6 J3QQ67 RPL18 60S ribosomal protein L18 0 ; 180.48 1.13E-06 4641400000 1925060 2563600 2271600 2400800 2625100 1971980 2430500 2232900 2867700 FALSE TRUE 1804573.931 2753411.611 2325483.425 2462408.593 2418935.235 2541258.614 2066069.089 2511682.48 2389062.344 0.755348196 1.152507225 0.973387501 1.030700852 1.012504023 1.063705441 0.864803338 1.051325633 1 21.18801307 APGYPSS(ph)PVTTASGTTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 APGYPSSPVTTASGTTLR 18 0 Q9HCK8-2;Q9HCK8;H0YJG4;H0YJA4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 APGYPS(0.198)S(0.782)PVT(0.01)T(0.008)AS(0.001)GTTLR;APGYPS(0.006)S(0.994)PVTTASGTTLR;APGYPS(0.002)S(0.998)PVTTASGTTLR;APGYPS(0.001)S(0.999)PVTTASGTTLR;APGYPS(0.001)S(0.998)PVTTASGTTLR 303.59 9.34E-50 1476570000 652862 693367 728666 655838 750423 715202 874419 734300 806102 TRUE FALSE 612000.5328 744704.6141 745950.3016 672667.9134 691487.8046 921669.2071 743307.9887 825978.9714 671558.3686 0.911313985 1.108920161 1.110775082 1.001652194 1.029676402 1.372433507 1.106840482 1.22994368 1 19.35715327 APIDTS(ph)DVEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APIDTSDVEEK 11 0 D6RIY6;Q06265-3;Q06265-4;Q06265;Q06265-2 D6RIY6 EXOSC9 Exosome complex component RRP45 1 APIDT(0.077)S(0.923)DVEEK;APIDT(0.104)S(0.896)DVEEK 180.61 6.91E-06 1328470000 4417700 2327300 3101100 2770300 2281400 2792300 4398900 2568700 1931290 TRUE FALSE 4141204.043 2499615.714 3174659.556 2841390.588 2102228.047 3598391.681 3739325.782 2889407.849 1608945.222 2.573862668 1.553574155 1.973130914 1.765995852 1.306587706 2.236491107 2.324085202 1.795839789 1 20.61768378 0.966125028 22.28834042 0.99999998 1.935725613 0.397940615 0.368263726 1248.402785 821399.9492 0.347123476 0.086780869 9.249644214 -0.966125028 0.935725633 APIQDIWYHEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APIQDIWYHEDR 12 0 J3QLR8;Q9Y3D9 J3QLR8 MRPS23 "28S ribosomal protein S23, mitochondrial" 0 ; 189.3 8.10E-06 234330000 271350 294020 282130 259010 380240 257280 250150 314620 424940 FALSE TRUE 254366.6879 315789.5467 288822.2568 265656.6351 350377.4842 331552.5594 212642.3298 353900.9996 354014.7688 0.718519989 0.892023651 0.815848044 0.750411165 0.989725613 0.936550078 0.600659488 0.999678631 1 18.43345002 1.0864817 24.99982218 1.000452863 0.820031591 0.323714557 0.11098004 23.66636127 6833.952431 0.103588619 0.025897155 12.20342396 -1.0864817 -0.180421272 APIQWEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APIQWEER 8 0 H0YL72;P50213;H0YLI6;H0YM64;H0YKD0 H0YL72 IDH3A "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial" 0 88.358 0.035695 0 163520 172850 144790 162700 187110 145420 170560 149940 173840 FALSE TRUE 153285.5751 185647.9939 148224.4872 166875.1575 172415.1354 187400.3933 144986.1114 168660.3391 144824.981 1.058419439 1.281878255 1.023473203 1.152253958 1.190506874 1.293978374 1.001112587 1.164580433 1 17.14395095 0.891834327 1.000207303 1.005918036 1.15591246 0.170072919 0.098535462 1.138291079 2.318369221 0.087593208 0.028802223 7.795326814 -0.891834327 0.149994423 APIRPDIVNFVHTNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APIRPDIVNFVHTNLR 16 1 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 ; 273.54 1.99E-35 10196800000 4705100 5599200 5326000 5108200 5874200 4622600 6025400 5516400 4922100 FALSE TRUE 4410616.19 6013770.594 5452335.235 5239285.06 5412864.027 5957069.578 5121947.207 6205134.683 4100569.712 1.075610586 1.46656953 1.329653101 1.277696864 1.320027315 1.452741935 1.249081851 1.513237213 1 21.96739293 -0.515209134 7.660493846 0.999999477 1.342835133 0.41319052 0.125415828 0 0 0.105499438 0.024866456 0.305345037 0.515209134 0.342835656 APKPDGPGGGPGGSHMGGNYGDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 APKPDGPGGGPGGSHMGGNYGDDR 24 1 P35637-2;P35637;H3BPE7 P35637-2 FUS RNA-binding protein FUS 0 ;;;;;;;;; 261.78 2.67E-44 13630440000 6650380 5339130 6775970 6139620 6712900 7304390 10080610 5255040 7090280 FALSE TRUE 6234144.587 5734444.741 6936699.208 6297173.044 6185695.913 9413048.816 8569116.114 5911143.312 5906866.463 1.055406386 0.970809951 1.174345019 1.066076757 1.047204292 1.593577386 1.450704222 1.000724047 1 22.49396157 2.305913311 24.99998308 1.325618489 1.065592977 0.181312126 0.188645961 62.04090002 23027.48536 0.062173979 0.052018465 202.2615407 -2.305913311 -0.260025511 APKPEDIDEEDDDVPDLVENFDEASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 APKPEDIDEEDDDVPDLVENFDEASK 26 1 Q96K17;Q96K17-2 Q96K17 BTF3L4 Transcription factor BTF3 homolog 4 0 ;;; 225.3 1.66E-34 432851000 1321730 526490 799730 686580 660000 608650 1055010 630860 659020 FALSE TRUE 1239005.279 565471.8674 818699.9733 704198.8052 608166.2623 784357.3744 896821.0447 709624.2597 549025.3046 2.256736198 1.029955929 1.49118805 1.282634515 1.107719912 1.428636108 1.633478525 1.29251649 1 19.06651312 7.999999989 0.028842254 2.45E-12 3.366129163 0.193382393 0.328584306 3765.367346 8.331140277 315.269143 739.9329214 99999997.47 -7.999999989 3.366129163 APLATGEDDDDEVPDLVENFDEASKNEAN ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 APLATGEDDDDEVPDLVENFDEASKNEAN 29 1 P20290-2;P20290 P20290-2;P20290 BTF3 Transcription factor BTF3 0 ;;; 188.22 4.87E-18 592352000 563714 456092 485140 496054 549222 374521 588017 442086 699262 FALSE TRUE 528432.147 489861.5262 496647.7499 508783.5855 506088.3196 482639.1329 499849.3097 497281.4103 582550.6548 0.907100769 0.840890869 0.852540025 0.873372266 0.868745602 0.828492988 0.858035787 0.85362776 1 19.15202398 -2.056359076 2.450954874 1.196313598 0.857184935 0.811389803 0.021110678 2059475.812 762322.2376 2263183.738 0.004862328 0.00878296 2.056359076 -0.339128663 APLDLDKYVEIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APLDLDKYVEIAR 13 1 O00743;O00743-2;O00743-3 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed" 0 ; 174.95 1.74E-05 855560000 960060 885310 969390 979710 1072910 756850 1141930 870380 1229070 FALSE TRUE 899971.5584 950859.2736 992384.3886 1004851.017 988647.9765 975340.3086 970708.1977 979048.8589 1023930.277 0.878938321 0.928636739 0.969191371 0.981366642 0.965542282 0.952545628 0.948021774 0.956167506 1 19.96568605 4.686389777 1.438726807 0.963782607 0.850364075 0.776329272 0.01540225 0.522346282 1.063269983 0.004135306 0.082927232 48572.42393 -4.686389777 -0.113418532 APLEHELAGEPQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 APLEHELAGEPQLR 14 0 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 ;;; 94.09 0.0043032 843225000 868260 1200310 1003190 1094230 1026080 798180 1208450 838440 674844 FALSE TRUE 813917.1565 1289182.201 1026986.141 1122309.794 945495.8158 1028601.609 1027254.141 943121.0796 562208.1767 1.447714904 2.293069106 1.826700825 1.996253062 1.681753939 1.829574259 1.827177518 1.677529994 1 19.10074491 -0.628011174 0.366850482 0.702086466 1.952118452 0.586851487 0.217899156 6.044057699 0.752033906 2.295180865 0.154013449 0.235498869 0.628011174 1.250031986 APLKPYPVS(ph)PSDKVLIQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APLKPYPVSPSDKVLIQEK 19 2 A0A0A0MSX9;P41252;J3KR24;Q5TCC6 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 1 APLKPYPVS(0.99)PS(0.01)DKVLIQEK;APLKPYPVS(0.5)PS(0.5)DKVLIQEK 198.39 3.88E-16 1847790000 3282760 2035850 2646680 2637320 2938440 1815170 3294470 2243830 4195700 TRUE FALSE 3077297.911 2186586.452 2709460.499 2704998.096 2707666.775 2339180.112 2800494.808 2523977.115 3495410.565 0.880382391 0.625559262 0.775147997 0.773871351 0.774634832 0.669214694 0.80119195 0.722083162 1 21.73703049 -4.999985006 0.481580392 8.163592309 0.742636925 0.542044789 0.070794078 1367.179877 6.939655995 10519.57729 0.031588828 1.00E-05 4.999985006 -7.420955384 APLS(ph)PSLNSRPSPISATPPALVPETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APLSPSLNSRPSPISATPPALVPETR 26 1 X6RKU3;Q6P3S6 X6RKU3 FBXO42 F-box only protein 42 1 APLS(0.615)PS(0.385)LNSRPSPISATPPALVPETR;APLS(0.956)PS(0.044)LNSRPSPISATPPALVPETR 196.85 4.08E-25 324130000 59926 86988 75758 93928 92330 62166 80484 54867 56538 TRUE FALSE 56175.33863 93428.68203 77555.01554 96338.3515 85078.77424 80112.31502 68416.17138 61717.26573 47101.44255 1.192645821 1.983563071 1.646552873 2.045337601 1.80628808 1.700846316 1.452528154 1.310305213 1 15.52348362 1.29060356 1.259225993 1.022955519 1.772071195 0.528236882 0.231717737 0.285780747 0.886086136 0.193796167 0.062329184 19.52556275 -1.29060356 0.749115676 APNTPDILEIEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APNTPDILEIEFK 13 0 P00966 P00966 ASS1 Argininosuccinate synthase 0 104.87 0.0034848 10768000 21829 25030 24300 24016 29223 23004 30332 25340 21572 FALSE TRUE 20462.76186 26883.24724 24876.40748 24632.29122 26927.94346 29644.88136 25783.99819 28503.75478 17971.49384 1.138623313 1.495882729 1.384214785 1.370631259 1.498369791 1.649550206 1.434716469 1.586053727 1 14.13342271 -1.164885578 5.05551036 0.999972931 1.451237136 0.50691019 0.137722725 3.86E-05 6.37E-06 0.122353013 0.028837155 0.068409186 1.164885578 0.451264205 APPARPVK ddPTM_SK-BR-3_Pertuzumab_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 67.981 0.052614 320970000 1507800 1072500 1044600 871270 1102600 553000 1010100 843570 1316000 FALSE TRUE 1413429.489 1151909.016 1069378.405 893628.2633 1016006.244 712642.1228 858644.8823 948891.5714 1096351.098 1.289212454 1.050675297 0.97539776 0.815093144 0.926716127 0.650012687 0.783184222 0.865499723 1 20.06427845 4.821859392 0.614560682 0.807184936 1.607982197 0.663309225 0.100102726 2.081837375 0.552856362 0.043200927 1.209075258 66352.82111 -4.821859392 0.800797261 APPCEYKDWLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APPCEYKDWLTK 12 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 116.51 0.00076042 478450000 1185800 1015200 1093500 1039800 1176000 662900 1469900 1090500 1428000 FALSE TRUE 1111582.895 1090366.464 1119438.336 1066483.028 1083641.704 854268.4687 1249502.141 1226651.325 1189657.575 0.934372141 0.916538076 0.940975252 0.896462185 0.91088539 0.718079292 1.050304026 1.031096133 1 20.18211494 1.609797937 24.99999997 1.030535842 0.896431142 0.512322027 0.064267139 0.155798964 1974.031059 0.030083908 0.015618061 40.71907812 -1.609797937 -0.1341047 APPHELTEEEKQQILHSEEFLSFFDHSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APPHELTEEEKQQILHSEEFLSFFDHSTR 29 1 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7;E7EQL5;E7EV09 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 304.8 6.85E-82 116720000 34615 34840 34753 38219 38660 25469 42213 33395 33396 FALSE TRUE 32448.50894 37419.58985 35577.35757 39199.76424 35623.79955 32821.48685 35883.55254 37564.43926 27821.99185 1.16628993 1.344964446 1.278749478 1.408948879 1.280418733 1.179695797 1.28975498 1.350170738 1 14.76393809 -1.457929815 3.083922987 0.993824924 1.290317208 0.601961008 0.07340467 27307783.63 33587941.13 1457853.871 0.016563999 0.034839361 1.457929815 0.296492284 APPKPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APPKPAR 7 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2;S4R349;S4R3C2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 70.268 0.052431 297380000 465580 524470 488430 506100 523140 429810 547630 485030 599010 FALSE TRUE 436440.1789 563302.3045 500015.7903 519087.3828 482054.6946 553889.1696 465517.9654 545587.0632 499031.3612 0.874574652 1.128791391 1.00197268 1.040189902 0.965980762 1.109928579 0.932843107 1.093292137 1 18.92877096 APPQTHLPSGASSGTGSASATHGGGS(ph)PPGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 APPQTHLPSGASSGTGSASATHGGGSPPGTR 31 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4;A0A0G2JJM1;X6REW1;F6S6P2;F6U341;F6TC96;F6WML8;F6VEM6;F6X9W3;A0A1B0GX79;A0A0G2JJR8;F6XTU0;F6U1F2;F6UR09 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 APPQTHLPSGAS(0.003)S(0.011)GT(0.011)GS(0.039)AS(0.027)AT(0.082)HGGGS(0.77)PPGT(0.058)R;APPQTHLPSGASSGTGSASAT(0.004)HGGGS(0.995)PPGT(0.001)R;APPQTHLPSGASS(0.001)GT(0.001)GS(0.007)AS(0.003)AT(0.013)HGGGS(0.614)PPGT(0.361)R;APPQTHLPSGASSGTGSASAT(0.009)HGGGS(0.584)PPGT(0.407)R;APPQTHLPSGASSGTGSAS(0.001)AT(0.018)HGGGS(0.971)PPGT(0.01)R;APPQTHLPSGAS(0.001)S(0.01)GT(0.001)GS(0.003)AS(0.002)AT(0.014)HGGGS(0.965)PPGT(0.003)R;APPQTHLPSGASSGTGSASAT(0.007)HGGGS(0.971)PPGT(0.021)R;APPQTHLPSGASSGTGSASAT(0.018)HGGGS(0.889)PPGT(0.093)R 197.26 8.38E-26 29608130000 728745 1306969 1239353 1238161 1317187 1272302 1331775 1133242 1156983 TRUE FALSE 683134.1513 1403738.345 1268751.038 1269934.307 1213740.446 1639594.933 1132087.702 1274729.758 963875.0629 0.708737239 1.456348855 1.316302379 1.317529996 1.259230053 1.70104508 1.174517057 1.322505175 1 19.87848663 0.269988827 1.669165383 1.000000797 1.311512696 0.102241321 0.24898415 19.57952066 42.17031253 0.213209048 0.060147058 1.862039233 -0.269988827 0.311511899 APPQTHLPSGASSGTGSASATHGGGS(ph)PPGTRGPGASVHDR ddPTM_SK-BR-3_Pertuzumab_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 APPQTHLPSGASSGTGSASATHGGGS(0.994)PPGT(0.005)RGPGAS(0.001)VHDR;APPQTHLPSGASSGTGSASATHGGGS(0.975)PPGT(0.011)RGPGAS(0.014)VHDR;APPQTHLPSGASSGTGSASATHGGGS(0.995)PPGT(0.002)RGPGAS(0.003)VHDR;APPQTHLPSGASSGTGSASATHGGGS(0.987)PPGT(0.006)RGPGAS(0.006)VHDR 275.95 1.70E-77 1050410000 10185.7 50417.1 28280.7 41505.9 67785.7 28157.8 52175.6 38005.9 166588 TRUE FALSE 9548.195219 54150.03454 28951.53156 42571.01166 62462.08456 36286.49976 44352.35315 42751.02028 138783.3866 0.068799267 0.390176633 0.20860949 0.306744292 0.450068889 0.261461409 0.319579701 0.308041339 1 17.08247535 -5 0.335223428 8.370020985 0.270085566 0.836886224 0.099168055 133.6467481 1.140462153 703.4457888 0.073621844 1.00E-05 5 -8.099935419 APQS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APQSPR 6 0 P12270 P12270 TPR Nucleoprotein TPR 1 APQS(1)PR;APQS(1)PR 79.059 0.071485 1948780000 1061570 1007820 1101040 1017580 1088960 845510 994370 1048640 943730 TRUE FALSE 995128.2287 1082440.041 1127157.189 1043692.826 1003437.474 1089595.011 845273.4498 1179565.012 786215.3663 1.265719638 1.37677294 1.433649401 1.327489732 1.276288301 1.385873462 1.075116929 1.500307757 1 19.58456504 -4.172452705 0.189550076 1.08E-15 1.393689449 0.402269733 0.119198979 88.17362544 1.14538293 33.73185761 0.311729035 6.72E-05 4.172452705 1.393689449 APQT(ph)SSSPPPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 APQT(0.378)S(0.361)S(0.076)S(0.184)PPPVR 111.12 0.015827 1672200000 198210 206780 204830 202520 216520 182690 228310 189700 200430 TRUE FALSE 185804.3899 222090.2064 209688.6643 207717.0061 199515.3926 235429.6373 194077.035 213384.4626 166976.9382 1.112754803 1.33006515 1.255794163 1.243986196 1.194867955 1.409953014 1.162298442 1.277927748 1 17.34928933 -0.534417226 0.839492979 0.984893206 1.257239567 0.460665051 0.083828529 18.05181324 8.224233004 0.949670054 0.024177995 0.29213445 0.534417226 0.272346361 APQTS(ph)SS(ph)PPPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 APQT(0.159)S(0.765)S(0.172)S(0.904)PPPVR 96.135 0.0082668 537780000 618130 598100 596950 536200 479190 442760 639600 485230 482180 TRUE FALSE 579442.3467 642383.9463 611109.9359 549959.7998 441556.3504 570577.6244 543697.9178 545812.0336 401701.043 1.442471601 1.599159269 1.521305325 1.369077351 1.09921634 1.420403642 1.353488937 1.358751846 1 18.61576268 -2.255023214 0.071104688 6.52E-12 2.02071883 0.582541084 0.116131738 110.324024 1.027521484 25.87376535 7.600467087 0.005558745 2.255023214 2.02071883 APQTS(ph)SSPPPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 APQT(0.028)S(0.407)S(0.407)S(0.158)PPPVR;APQT(0.058)S(0.401)S(0.401)S(0.14)PPPVR 145.83 6.74E-05 7886300000 553590 572610 537610 550650 550330 496950 613120 505470 516070 TRUE FALSE 518941.7901 615006.6402 550362.3631 564780.6112 507109.3017 640411.3977 521188.3479 568579.0422 429934.5831 1.207025 1.430465621 1.280107218 1.31364313 1.179503398 1.489555442 1.212250348 1.322478034 1 18.71375764 -3.348500431 0.365606809 5.16E-14 1.321688865 0.48509403 0.097776381 103.1216864 2.569417055 79.06940522 0.062124177 0.000448229 3.348500431 1.321688865 APQTSS(ph)S(ph)PPPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 APQT(0.25)S(0.368)S(0.429)S(0.953)PPPVR 118.58 0.00089246 466790000 424700 444530 441180 451950 436100 391340 435760 385810 373140 TRUE FALSE 398118.7851 477443.4637 451644.9979 463547.8021 401850.4651 504313.5051 370421.8334 433979.2278 310860.5234 1.280699076 1.535876793 1.452886307 1.491176162 1.292703431 1.622314405 1.191601395 1.396057701 1 18.24590789 0.53141104 0.594191671 0.988695378 1.457175119 0.514225624 0.126311322 1.172810204 0.738088325 0.143002756 0.047762837 3.399468647 -0.53141104 0.468479741 APQTSSS(ph)PPPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 APQT(0.046)S(0.102)S(0.102)S(0.749)PPPVR;APQT(0.003)S(0.201)S(0.201)S(0.595)PPPVR;APQT(0.007)S(0.211)S(0.062)S(0.72)PPPVR;APQT(0.02)S(0.271)S(0.271)S(0.438)PPPVR 148.69 6.81E-05 15972500000 1546970 1698830 1649060 1595640 1579090 1418030 1709060 1439590 1585780 TRUE FALSE 1450147.909 1824613.141 1688176.482 1636586.824 1455074.641 1827392.241 1452802.319 1619325.98 1321103.073 1.097679612 1.381128526 1.277853724 1.238803282 1.101408868 1.383232147 1.09968885 1.225737804 1 20.3333116 0.263856003 0.363124218 0.95967563 1.280936985 0.299703095 0.106167925 3.640674688 0.809828825 0.342297803 0.084747302 1.835929511 -0.263856003 0.321261355 APQTSSS(ph)PPPVRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 APQTSSSPPPVRR 13 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 APQT(0.008)S(0.025)S(0.148)S(0.819)PPPVRR;APQTS(0.002)S(0.008)S(0.99)PPPVRR;APQT(0.011)S(0.149)S(0.224)S(0.615)PPPVRR;APQT(0.052)S(0.052)S(0.309)S(0.587)PPPVRR 106.19 0.00085343 6195800000 384631 425490 383268 414834 436846 342066 452234 363721 499403 TRUE FALSE 360557.6323 456993.7223 392359.298 425479.3428 402537.8773 440814.9012 384425.71 409132.3675 416049.413 0.866622139 1.098412131 0.943059371 1.022665408 0.967524204 1.059525353 0.923990512 0.983374461 1 18.66639536 1.716525256 24.99999969 0.963775861 0.99954274 0.019873651 0.065887398 2.614290679 2953.805587 0.027196608 0.015081913 52.06252838 -1.716525256 0.035766879 APRPFGSVSS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 APRPFGSVSSPK 12 1 Q96HC4;A0A0D9SFR4 Q96HC4 PDLIM5 PDZ and LIM domain protein 5 1 APRPFGSVS(0.035)S(0.965)PK;APRPFGSVS(0.024)S(0.976)PK;APRPFGSVS(0.189)S(0.811)PK 118.47 0.00037676 1288940000 2060550 1466600 1790890 2079790 2185840 1389670 2066920 1425440 1947920 TRUE FALSE 1931583.854 1575188.59 1833370.757 2133160.932 2014172.944 1790845.17 1757004.534 1603409.322 1622799.568 1.190278758 0.970661209 1.129757977 1.314494393 1.241171728 1.1035529 1.082699656 0.988051361 1 20.63005339 1.480534916 2.191578158 0.992984112 1.143088283 0.355415094 0.089933184 0.424954731 3.968574273 0.083589589 0.027495488 30.23673654 -1.480534916 0.150104171 APRPTRPDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 APRPTRPDK 9 2 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;;;;; 125.97 0.00027372 12116600000 3425950 3478910 3681180 3869660 4030850 3141540 4821560 3576700 4347020 FALSE TRUE 3211525.905 3736492.116 3768499.328 3968962.027 3714283.301 4048451.599 4098611.839 4023258.868 3621474.279 0.886800694 1.031759949 1.04059812 1.095952013 1.025627414 1.117901519 1.131752298 1.110945035 1 21.7881457 6.053655423 0.646231723 1.090927247 2.24E-13 0.629531917 0.04410668 9.371141881 0.790465883 0.016790064 11.06947145 1131502.253 -6.053655423 -1.090927247 APS(ph)AS(ph)PLALHASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APSASPLALHASR 13 0 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 2 APS(1)AS(1)PLALHASR 65.949 0.030211 151550000 70099 132290 132970 114640 126590 120880 138000 128760 146400 TRUE FALSE 65711.62872 142084.8892 136124.1112 117581.8565 116648.132 155776.0937 117308.1811 144835.9694 121964.8942 0.538774941 1.164965461 1.116092561 0.96406312 0.956407438 1.27722075 0.961819234 1.187521789 1 16.89610642 4.74387643 24.9922873 1.082450869 0.538774714 0.705256154 0.109629876 299.2132234 1406707.193 0.024124629 0.206693238 55446.79275 -4.74387643 -0.543676155 APS(ph)ASPLALHASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APSASPLALHASR 13 0 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 APS(0.548)AS(0.452)PLALHASR 56.746 0.077179 305510000 864400 733510 807910 734780 806890 534230 962410 710720 969320 TRUE FALSE 810298.747 787819.8436 827074.0067 753635.6988 743520.1142 688453.5285 818105.5551 799454.9565 807534.23 1.003423405 0.975586934 1.02419684 0.933255422 0.920728914 0.85253789 1.013090869 0.989995132 1 19.62316389 3.231393793 24.9993268 0.948231252 0.998912574 0.194152905 0.04710815 263.5299744 919245.4288 0.013635804 0.016630159 1703.702628 -3.231393793 0.050681322 APS(ph)DS(ph)SLGTPSDGRPELR ddPTM_SK-BR-3_Pertuzumab_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(0.991)DS(0.514)S(0.49)LGT(0.002)PS(0.003)DGRPELR;APS(1)DS(0.592)S(0.408)LGTPSDGRPELR 195.38 2.97E-17 629530000 706210 775180 774430 796600 855570 592510 835140 702160 884780 TRUE FALSE 662009.5767 832575.1338 792799.8453 817042.1046 788376.9834 763558.0184 709918.5101 789826.2216 737104.5021 0.898121738 1.129521162 1.07555963 1.108448127 1.069559311 1.03588842 0.963117859 1.071525434 1 19.49150964 2.0631949 4.352616065 1.005652911 1.070854827 0.057787224 0.067468732 0.363627084 13.87579528 0.025217261 0.017610831 115.6631193 -2.0631949 0.065201916 APS(ph)DSS(ph)LGTPSDGRPELR ddPTM_SK-BR-3_Pertuzumab_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(1)DS(0.287)S(0.712)LGT(0.001)PSDGRPELR 137.86 1.85E-06 292790000 539980 532950 562980 553350 613270 463480 636190 532110 895340 TRUE FALSE 506183.6157 572410.1725 576334.1515 567549.8978 565106.248 597279.152 540799.2156 598545.1048 745901.9699 0.678619492 0.767406704 0.772667421 0.760890735 0.757614634 0.800747519 0.725027199 0.80244473 1 19.50862651 -5 0.311197083 3.157013881 0.747997955 0.84695053 0.032856829 105.9507245 0.957754353 149.8378094 0.028672487 1.00E-05 5 -2.409015926 APS(ph)DSSLGTPSDGRPELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 APSDSSLGTPSDGRPELR 18 1 Q15642;M0R0F9;W4VSQ9;Q15642-4;Q15642-2;Q15642-3;M0R2H7;Q15642-5 Q15642 TRIP10 Cdc42-interacting protein 4 1 APS(0.624)DS(0.188)S(0.188)LGTPSDGRPELR;APS(0.968)DS(0.031)S(0.001)LGTPSDGRPELR;APS(0.987)DS(0.011)S(0.002)LGTPSDGRPELR;APS(0.989)DS(0.005)S(0.007)LGTPSDGRPELR 230.29 8.56E-20 2543980000 1193166 1170320 1258716 1233920 1320640 1230236 1234750 1130592 1616490 TRUE FALSE 1118487.87 1256971.711 1288573.338 1265584.476 1216922.262 1585385.162 1049610.7 1271748.9 1346687.376 0.830547527 0.933380481 0.956846675 0.939776001 0.903641248 1.177248105 0.779401901 0.944353472 1 20.36098355 4.756519568 3.002849943 0.948289107 0.808473305 0.136341677 0.097628473 0.892325306 11.4996654 0.021951664 0.305624992 57084.67961 -4.756519568 -0.139815802 APS(ph)IDGKEELDLAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 APSIDGKEELDLAEK 15 1 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;B5MCW3;Q9H0E9-3;Q9H0E9;H0YAH7;H0YA84 H7C128 BRD8 Bromodomain-containing protein 8 1 APS(1)IDGKEELDLAEK;APS(1)IDGKEELDLAEK;APS(1)IDGKEELDLAEK;APS(1)IDGKEELDLAEK 183.09 3.15E-07 845570000 1695840 804060 1032670 1061630 1037960 771590 1430670 873000 1173850 TRUE FALSE 1589700.402 863593.439 1057165.42 1088873.223 956442.8085 994335.5073 1216154.315 981995.9717 977926.8516 1.625582117 0.883085926 1.081027091 1.113450583 0.978031033 1.016779021 1.243604584 1.004160966 1 19.89936703 4.748922546 24.99851868 1.049862717 1.625582435 0.789218647 0.094982067 722.7244829 1743564.023 0.023770493 0.333123351 56094.79256 -4.748922546 0.575719719 APS(ph)LDIKGPEVDVSGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APSLDIKGPEVDVSGPK 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 APS(1)LDIKGPEVDVSGPK 184.2 3.93E-10 246880000 758180 300410 416730 323400 448560 248080 508940 340480 551740 TRUE FALSE 710726.8672 322652.669 426615.0324 331698.9915 413331.907 319696.6688 432629.1718 382989.6775 459651.0296 1.546231426 0.701951368 0.92812809 0.721632217 0.899229808 0.695520402 0.941212233 0.833218361 1 18.81017945 4.745099422 24.99801489 0.834356987 1.546231747 0.81376082 0.106130008 276.4550912 1056866.982 0.021987675 0.211683235 55603.15336 -4.745099422 0.71187476 APS(ph)LTDLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 APSLTDLVK 9 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 APS(0.993)LT(0.007)DLVK;APS(0.997)LT(0.003)DLVK;APS(0.994)LT(0.006)DLVK;APS(0.998)LT(0.002)DLVK;APS(0.999)LT(0.001)DLVK 152.69 8.38E-05 484536000 1112253 983355 993339 1013554 1095502 701129 1084690 854009 1098351 TRUE FALSE 1042639.07 1056163.627 1016901.47 1039563.512 1009465.692 903533.5604 922050.8043 960633.9036 915029.1225 1.139459985 1.154240451 1.111332356 1.136098826 1.103206081 0.987436944 1.007673725 1.049839705 1 19.80345813 2.359660797 4.391496578 1.010820818 1.133245598 0.904258404 0.019218005 0.06010325 2.024869264 0.00685285 0.005637725 228.9079083 -2.359660797 0.122424781 APS(ph)LTNDEVEEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APSLTNDEVEEFR 13 0 A0A3B3ISR7;E9PIF2;Q13206 A0A3B3ISR7 DDX10 Probable ATP-dependent RNA helicase DDX10 1 APS(0.999)LT(0.001)NDEVEEFR;APS(1)LTNDEVEEFR 140.84 4.15E-05 115900000 49564 48805 56160 59593 57770 47220 51613 51576 67170 TRUE FALSE 46461.87771 52418.57298 57492.14172 61122.25727 53232.97723 60851.64745 43874.1098 58015.37713 55958.89307 0.830285861 0.936733558 1.027399553 1.092270664 0.951287174 1.087434796 0.784041774 1.036749906 1 15.7720798 -2.162942488 8.873425115 1.957045724 0.965717324 0.009064531 0.101147412 0.141149986 0.002591935 0.007218406 0.022001855 0.006871594 2.162942488 -0.991328401 APS(ph)PAPRPVPGSPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APSPAPRPVPGSPAR 15 1 Q5TZA2-2;Q5TZA2 Q5TZA2-2 CROCC Rootletin 1 APS(1)PAPRPVPGSPAR 68.567 0.043877 0 82270 93354 80162 88104 105110 77537 99909 90520 125870 TRUE FALSE 77120.86756 100266.0273 82063.4805 90364.8978 96855.08459 99920.67319 84928.57296 101821.6213 104861.4838 0.735454666 0.956175934 0.78258935 0.861754903 0.923647855 0.952882503 0.809911989 0.971010685 1 16.67812534 -5 0.086990404 1.436943875 0.755531546 0.341372615 0.071945504 285.7307122 1.738419764 23.14394975 1.773621347 1.00E-05 5 -0.681412329 APS(ph)PAPSSVPLGSEKPSNVSQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 APSPAPSSVPLGSEKPSNVSQDR 23 1 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 APS(0.999)PAPS(0.001)SVPLGSEKPSNVSQDR;APS(0.987)PAPS(0.006)S(0.007)VPLGSEKPSNVSQDR;APS(0.998)PAPS(0.001)S(0.001)VPLGSEKPSNVSQDR;APS(0.995)PAPS(0.004)SVPLGSEKPSNVSQDR 215.93 1.59E-32 6284500000 3190760 2823150 3181720 2791150 3223980 2631430 3438600 2790490 4010930 TRUE FALSE 2991056.027 3032178.963 3257191.901 2862775.634 2970781.616 3391081.123 2923013.852 3138888.819 3341479.871 0.895129147 0.907435951 0.974775257 0.856738854 0.889061652 1.014844097 0.874766261 0.93937086 1 21.67205575 0.97901672 23.59169324 1.000000003 0.91997766 0.238635951 0.046875932 1157.495531 1301385.738 0.041773289 0.010443322 9.528328456 -0.97901672 -0.080022344 APS(ph)PARPK ddPTM_SK-BR-3_Pertuzumab_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 83.883 0.010807 2410190000 4891140 4025620 4787080 4571790 4258400 3589700 5078300 3546560 3297590 TRUE FALSE 4585012.278 4323681.093 4900631.798 4689109.871 3923962.442 4625988.116 4316856.06 3989355.823 2747200.926 1.668975951 1.573849606 1.783863624 1.70686819 1.428349272 1.683891438 1.571365246 1.452152912 1 21.389531 0.316011226 0.620115486 0.975045288 1.66398952 0.82582996 0.092125203 0.93642347 0.528427697 0.137874377 0.036228705 2.070194859 -0.316011226 0.688944233 APS(ph)PEPAAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APSPEPAAPR 10 0 P20749 P20749 BCL3 B-cell lymphoma 3 protein 1 APS(1)PEPAAPR;APS(1)PEPAAPR 120.77 0.00055879 1050500000 718361 621840 594650 604775 703130 565210 769820 576270 832900 TRUE FALSE 673400.0673 667881.6806 608755.3788 620294.5504 647909.0061 728376.9516 654392.6377 648218.578 693883.6093 0.970479859 0.962526959 0.877316268 0.893946106 0.933743062 1.049710559 0.943087038 0.934189206 1 19.40433416 2.452550316 24.9996232 0.977936695 0.923001296 0.294174988 0.041518987 298.0371345 303235.1721 0.014463456 0.012101374 283.4982068 -2.452550316 -0.054935399 APS(ph)PGAYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 APSPGAYK 8 0 P54259 P54259 ATN1 Atrophin-1 1 APS(1)PGAYK;APS(1)PGAYK;APS(1)PGAYK;APS(1)PGAYK 116.52 0.0023665 829110000 2404060 1842360 2266580 2121710 2134470 1760420 2348360 1848380 2256570 TRUE FALSE 2253594.176 1978770.251 2320344.348 2176156.671 1966837.336 2268624.676 1996245.219 2079154.312 1879933.889 1.198762461 1.052574382 1.234269121 1.15757085 1.046226863 1.206757689 1.061869904 1.105972037 1 20.8422505 0.860630837 0.645885894 0.99915531 1.148458658 0.341234253 0.064100781 1.080910779 0.998491112 0.061534784 0.024460647 7.254890086 -0.860630837 0.149303348 APS(ph)PHVVQENLHSEVVEVCTSSTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APSPHVVQENLHSEVVEVCTSSTLK 25 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 APS(0.991)PHVVQENLHS(0.009)EVVEVCTSSTLK;APS(0.986)PHVVQENLHS(0.014)EVVEVCTSSTLK 107.88 0.0058659 366760000 133714 120540 133103 123046 115138 107023 167414 126644 127962 TRUE FALSE 125345.0794 129464.907 136260.266 126203.5687 106095.5259 137918.8027 142311.8249 142455.7822 106604.3155 1.175797422 1.214443396 1.278187148 1.183850467 0.995227308 1.293745024 1.334953695 1.336304084 1 16.70190632 APS(ph)PLGPTRDPVATFLETCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APSPLGPTRDPVATFLETCR 20 1 I3L2L9;E7EVV8;Q0VG06-3;Q0VG06 I3L2L9 C17orf70;FAAP100 Fanconi anemia-associated protein of 100 kDa 1 APS(0.977)PLGPT(0.023)RDPVATFLETCR 105.84 0.00015151 164750000 43132 41250 35875 41471 39657 37477 47509 40928 39966 TRUE FALSE 40432.44511 44304.19292 36725.97194 42535.21607 36542.49919 48296.00151 40385.4665 46037.95089 33295.41641 1.214354691 1.3306394 1.103033868 1.277509659 1.097523417 1.450530034 1.212943728 1.382711372 1 15.02303596 APS(ph)PLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APSPLPK 7 0 Q9BSL1 Q9BSL1 UBAC1 Ubiquitin-associated domain-containing protein 1 1 APS(1)PLPK 69.423 0.062705 176280000 243570 210110 238070 232960 254500 210620 288390 217330 301140 TRUE FALSE 228325.3885 225666.763 243717.1328 238938.148 234512.5966 271422.5749 245148.5968 244464.1289 250877.7886 0.910106031 0.899508738 0.971457594 0.952408539 0.934768271 1.081891611 0.977163416 0.974435124 1 17.93662522 3.548599808 0.673396526 1.002292997 0.892851497 0.470085968 0.037206456 0.846884824 0.731446039 0.020123288 0.058014645 3536.712912 -3.548599808 -0.1094415 APS(ph)PPLSQVFQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 APSPPLSQVFQTR 13 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 APS(0.997)PPLS(0.003)QVFQTR;APS(1)PPLSQVFQTR;APS(0.903)PPLS(0.097)QVFQTR;APS(0.997)PPLS(0.003)QVFQTR;APS(0.999)PPLS(0.001)QVFQTR 145.7 4.33E-05 1149422000 226735 242504 266478 245107 271733 196971 260577 214906 270563 TRUE FALSE 212544.0611 260459.2485 272798.984 251396.8606 250392.1863 253833.3301 221505.8979 241737.4872 225404.2874 0.942945955 1.155520383 1.210265284 1.115315345 1.110858135 1.126124676 0.982704901 1.072461797 1 17.78215543 1.751698924 25 1.020256926 1.127177706 0.244753627 0.071958469 4.703311267 8963.11013 0.032658999 0.018111305 56.45454669 -1.751698924 0.10692078 APS(ph)PPVEHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 APSPPVEHPR 10 0 Q86WR7;Q86WR7-2 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 APS(1)PPVEHPR;APS(1)PPVEHPR;APS(1)PPVEHPR;APS(1)PPVEHPR;APS(1)PPVEHPR;APS(1)PPVEHPR 108.72 0.0013619 2645280000 955798 963718 994674 953291 1042511 813339 989677 939612 885983 TRUE FALSE 895976.3093 1035072.683 1018268.137 977754.061 960636.3913 1048136.766 841284.1216 1056924.627 738106.7136 1.213884514 1.402334736 1.37956764 1.324678455 1.301487134 1.420034185 1.139786573 1.431940134 1 19.49346989 -3.646422171 0.274110384 2.60E-13 1.355158228 0.520738667 0.095561248 70.29109007 1.343448236 39.62896752 0.10635449 0.000225724 3.646422171 1.355158228 APS(ph)PRPGPGPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 APSPRPGPGPLR 12 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 APS(1)PRPGPGPLR;APS(1)PRPGPGPLR;APS(1)PRPGPGPLR;APS(1)PRPGPGPLR;APS(1)PRPGPGPLR;APS(1)PRPGPGPLR;APS(1)PRPGPGPLR 122.33 0.00021831 10454860000 2016268 3099690 2741930 2293160 2733740 1962953 2287060 2063292 2921910 TRUE FALSE 1890073.385 3329194.273 2806969.874 2352006.368 2519043.088 2529625.665 1944136.585 2320898.548 2434224.345 0.776458172 1.367661235 1.153127024 0.966224158 1.034844259 1.039191671 0.798667793 0.953444802 1 21.21503071 2.861373138 1.251515543 0.923240338 1.161642908 0.065663576 0.162479508 0.580745003 1.88461311 0.068317452 0.072606671 726.7300828 -2.861373138 0.23840257 APS(ph)PS(ph)GLMSPSRLPGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APSPSGLMSPSRLPGSR 17 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 APS(0.981)PS(0.725)GLMS(0.255)PS(0.038)RLPGS(0.001)R 84.508 0.0011908 0 51189 36110 40659 43275 49608 28912 45199 37107 62943 TRUE FALSE 47985.17186 38783.62197 41623.45068 44385.50976 45711.98779 37258.42505 38421.82956 41739.89063 52437.40667 0.915094298 0.739617468 0.793774012 0.846447461 0.871743869 0.710531421 0.732717958 0.795994563 1 15.67830872 2.250722613 24.99918512 0.778913728 0.815756945 0 0.092018065 878.2192163 1805192.584 0.029729977 0.024705564 178.1240713 -2.250722613 0.036843217 APS(ph)PSGLMS(ph)PSRLPGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 APSPSGLMSPSRLPGSR 17 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 APS(0.969)PS(0.072)GLMS(0.941)PS(0.017)RLPGSR;APS(0.997)PS(0.007)GLMS(0.922)PS(0.075)RLPGSR;APS(0.987)PS(0.015)GLMS(0.986)PS(0.011)RLPGS(0.001)R 136.43 0.0002997 293130000 385581 416063 431403 441695 521410 360596 385261 362364 542070 TRUE FALSE 361448.1735 446868.7374 441636.0829 453029.6415 480460.5619 464694.2114 327494.6896 407605.9431 451595.0151 0.80038123 0.989534256 0.977947205 1.003176799 1.0639191 1.029006512 0.725195537 0.902591768 1 18.78467004 -0.633764373 4.956579913 0.999999996 0.938924894 0.034808242 0.10442716 37.74104965 72390128.48 2.396261317 0.025647864 0.232399734 0.633764373 -0.061075102 APS(ph)PSGLMSPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 APSPSGLMSPSR 12 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 APS(0.831)PS(0.169)GLMSPSR;APS(0.847)PS(0.153)GLMSPSR;APS(0.938)PS(0.062)GLMSPSR;APS(0.992)PS(0.008)GLMSPSR;APS(0.923)PS(0.077)GLMSPSR;APS(0.963)PS(0.037)GLMSPSR;APS(0.983)PS(0.017)GLMSPSR;APS(0.989)PS(0.011)GLMSPSR;APS(0.99)PS(0.01)GLMSPSR;APS(0.996)PS(0.004)GLMSPSR;APS(0.987)PS(0.013)GLMSPSR 209.43 5.80E-08 4987450000 2034578 2819730 2246584 2126285 2751290 1879589 2368637 2469880 2495910 TRUE FALSE 1907237.395 3028505.743 2299874.033 2180849.073 2535214.782 2422195.832 2013481.871 2778249.955 2079326.497 0.917238057 1.456483985 1.106066814 1.04882474 1.219248052 1.164894419 0.968333676 1.336129732 1 20.98768488 3.718237792 24.22331047 1.114105407 1.242147632 0.001779152 0.167674034 475.0774921 1295439.427 0.040288296 0.063485604 5226.822978 -3.718237792 0.128042225 APS(ph)PSINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 APSPSINR 8 0 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 APS(0.559)PS(0.441)INR;APS(0.982)PS(0.018)INR;APS(0.5)PS(0.5)INR 129.83 0.0011267 1159490000 1206700 1427620 1399040 1370940 1412080 1244520 1566640 1260740 1376230 TRUE FALSE 1131174.801 1533322.47 1432225.889 1406120.641 1301180.933 1603792.721 1331736.876 1418146.164 1146528.322 0.986608686 1.33736118 1.249184919 1.226415967 1.134887737 1.39882521 1.161538577 1.236904607 1 20.12884056 0.078088368 1.284842655 0.99953292 1.232782481 0.257015885 0.112612277 12.92983602 16.57493346 0.112737669 0.028593112 1.196984063 -0.078088368 0.233249561 APS(ph)PSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 APSPSSR 7 0 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 APS(0.653)PS(0.341)S(0.006)R;APS(0.85)PS(0.139)S(0.011)R;APS(0.874)PS(0.124)S(0.002)R;APS(0.981)PS(0.017)S(0.002)R;APS(0.963)PS(0.037)SR;APS(0.991)PS(0.009)SR;APS(0.77)PS(0.228)S(0.002)R;APS(0.695)PS(0.302)S(0.003)R;APS(0.861)PS(0.138)SR;APS(0.998)PS(0.002)SR;APS(0.921)PS(0.079)SR 130.31 0.0037507 19861019000 2487803 2948204 2785258 2701432 2651453 2396520 2717204 2322228 2573905 TRUE FALSE 2332095.851 3166492.092 2851325.635 2770755.319 2443218.577 3088356.42 2309784.485 2612163.278 2144303.627 1.087577254 1.476699499 1.329721033 1.292146916 1.139399545 1.440260782 1.077172307 1.218187221 1 21.03207777 1.193197101 0.54890974 0.998768814 1.335534895 0.290399773 0.132823084 0.844583201 0.650916948 0.127954482 0.063616873 15.60260452 -1.193197101 0.336766082 APS(ph)PTAEQPPGGGDSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APSPTAEQPPGGGDSAR 17 0 Q15742;Q15742-2;Q15742-3 Q15742 NAB2 NGFI-A-binding protein 2 1 APS(0.991)PT(0.009)AEQPPGGGDSAR 180.78 8.82E-10 322410000 36208 42179 48571 49002 38369 24757 39847 33920 30260 TRUE FALSE 33941.80591 45301.97705 49723.12706 50259.47428 35355.65351 31903.944 33872.31227 38154.98667 25209.41051 1.346394272 1.797026433 1.972403402 1.993679077 1.402478392 1.265556923 1.343637617 1.513521574 1 14.62167476 2.61676427 5.351462119 1.314633874 1.811615905 0.542209801 0.215829486 0.167915012 6.680016775 0.06818121 0.064003897 413.7750213 -2.61676427 0.496982031 APS(ph)PTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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(0.894)PT(0.106)K;APS(0.55)PT(0.45)K;APS(0.994)PT(0.006)K;APS(0.81)PT(0.19)K;APS(0.992)PT(0.008)K;APS(0.948)PT(0.052)K;APS(0.874)PT(0.126)K 109.36 0.031078 43055240000 90729100 53708600 75150200 68948700 63554100 50541200 75592900 60484300 74160300 TRUE FALSE 85050527.59 57685240.63 76932798.23 70718040.37 58562817.35 65131623.97 64258446.42 68035898 61782466.84 1.376612685 0.933683027 1.245220565 1.144629601 0.947887327 1.054208861 1.040075764 1.101216923 1 25.88069414 2.813294173 12.28356433 1.033993809 1.146573251 0.266822363 0.116194042 1.898583005 309.2982335 0.033175772 0.035191878 650.57021 -2.813294173 0.112579442 APS(ph)PTKPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APSPTKPLR 9 1 Q96FF9;B5MBX0 Q96FF9 CDCA5 Sororin 1 APS(0.749)PT(0.251)KPLR;APS(0.986)PT(0.014)KPLR 117.94 0.0006476 1081190000 1156800 961290 1011130 984810 1069100 893020 1200670 964180 998970 TRUE FALSE 1084397.953 1032464.912 1035114.481 1010081.892 985137.1985 1150820.377 1020640.68 1084559.995 832235.4534 1.302994181 1.24059232 1.243775997 1.213697263 1.183724143 1.382806239 1.226384524 1.303188888 1 19.66663222 -1.106261942 4.328204044 0.999965081 1.257838547 0.680283432 0.056409761 1.73E-05 3.56E-06 0.049573019 0.011682892 0.078295726 1.106261942 0.257873466 APS(ph)PTKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.998)PT(0.002)KR;APS(0.945)PT(0.055)KR;APS(0.787)PT(0.213)KR;APS(0.991)PT(0.009)KR 102.07 0.005319 3790080000 4586670 3109620 3647330 3363370 3587910 2681660 4058460 3087840 4118550 TRUE FALSE 4299598.512 3339859.5 3733846.39 3449679.768 3306130.022 3455811.709 3449931.6 3473363.621 3431137.398 1.253111727 0.97339719 1.088224095 1.005404147 0.963566782 1.007191292 1.005477543 1.012306771 1 21.71025547 4.743991004 24.99022365 1.010930053 1.25311183 0.845468048 0.03303529 231.4573484 1065116.039 0.007996403 0.069996316 55461.4225 -4.743991004 0.242181778 APS(ph)PTSSAGEEGTKKPEPLSPASYHQPEGVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APSPTSSAGEEGTKKPEPLSPASYHQPEGVAR 32 2 O94964-2;H0YDM2;O94964;O94964-3 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 APS(0.853)PT(0.126)S(0.019)S(0.002)AGEEGTKKPEPLSPASYHQPEGVAR 254.49 2.09E-59 680320000 157800 141270 168010 163950 185130 135300 234690 163140 182470 TRUE FALSE 147923.5797 151729.7778 171995.2765 168157.2346 170590.6366 174358.9136 199500.4133 183508.3881 152014.5782 0.973088117 0.998126493 1.131439357 1.106191502 1.12219919 1.146988109 1.31237685 1.207176248 1 17.21385016 3.877682554 0.664277733 1.19371642 0.934182699 0.388413721 0.080661322 1.143488545 0.774910866 0.040276609 0.194348889 7545.404976 -3.877682554 -0.259533721 APS(ph)RQDVYGPQPQVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 204.71 2.89E-09 1148550000 186279 270970 249900 208030 326930 199922 269050 264250 488520 TRUE FALSE 174620.1299 291032.9007 255827.746 213368.402 301254.2366 257636.2359 228708.4502 297242.1942 406982.856 0.429060161 0.715098674 0.628595879 0.524268772 0.740213579 0.63303953 0.561960896 0.730355566 1 18.6346085 0.914998041 4.438908565 0.999913488 0.618963054 0.658966711 0.089848739 0.250695278 11.38398153 0.078722936 0.020007716 8.222389417 -0.914998041 -0.380950434 APS(ph)VATVGSICDLNLK ddPTM_SK-BR-3_Pertuzumab_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(0.5)VAT(0.5)VGSICDLNLK;APS(1)VATVGSICDLNLK 298.75 8.89E-46 181060000 188234 163104 154777 166937 183395 126662 251810 166052 331600 TRUE FALSE 176452.7699 175180.3899 158448.3835 171220.886 168991.8965 163227.2632 214053.4282 186783.9577 276253.8178 0.638734231 0.634128394 0.573560883 0.619795547 0.611726918 0.590859755 0.77484333 0.676131679 1 18.07563488 0.536598686 0.614729795 1.008345453 0.605349 0.867729318 0.04580804 0.518737846 0.347245689 0.053901132 0.018112346 3.440318776 -0.536598686 -0.402996453 APSDSS(ph)LGTPSDGRPELR ddPTM_SK-BR-3_Pertuzumab_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 APS(0.186)DS(0.145)S(0.669)LGTPSDGRPELR 187.43 2.60E-14 634600000 310260 297040 354840 328970 356800 338100 319750 315250 426220 TRUE FALSE 290841.3804 319033.1507 363256.9724 337411.9271 328778.3673 435703.9814 271806.4559 354609.6565 355081.1285 0.819084308 0.898479601 1.023025284 0.950238974 0.925924643 1.227054739 0.765477053 0.998672213 1 18.43778916 4.511259285 2.087578986 0.974169316 0.809504493 0.190216499 0.112638619 0.782183236 5.305564969 0.02706671 0.203197525 32453.33142 -4.511259285 -0.164664823 APSEEELHGDQTDFGQGS(ph)QSPQKQEEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APSEEELHGDQTDFGQGSQSPQKQEEQR 28 1 Q8TE77;Q8TE77-2;A0A087WWG1;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 APSEEELHGDQTDFGQGS(0.858)QS(0.142)PQKQEEQR 248.06 5.46E-46 227740000 135050 81385 99930 103230 106170 87217 121160 90420 108630 TRUE FALSE 126597.4616 87410.83008 102300.3868 105879.0566 97831.83647 112395.1321 102993.1828 101709.136 90498.95122 1.39888319 0.965876719 1.130404114 1.169947885 1.081027295 1.241949553 1.138059407 1.123870881 1 16.46561345 -2.625415503 1.272410114 0.132477382 1.138834825 0.145968874 0.111941021 176863.8263 9873.764866 437217.6555 0.029173187 0.002369106 2.625415503 1.006357442 APSEEELHGDQTDFGQGSQS(ph)PQKQEEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 APSEEELHGDQTDFGQGSQSPQKQEEQR 28 1 Q8TE77;Q8TE77-2;A0A087WWG1;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 APSEEELHGDQTDFGQGS(0.006)QS(0.994)PQKQEEQR;APSEEELHGDQTDFGQGS(0.006)QS(0.994)PQKQEEQR;APSEEELHGDQTDFGQGS(0.004)QS(0.996)PQKQEEQR;APSEEELHGDQTDFGQGS(0.035)QS(0.965)PQKQEEQR;APSEEELHGDQTDFGQGSQS(1)PQKQEEQR 302.41 7.07E-72 2795540000 1776300 1086640 1317963 1259186 1349659 1091616 1555160 1140108 1334992 TRUE FALSE 1665124.554 1167095.956 1349225.705 1291498.845 1243662.226 1406747.818 1321978.195 1282452.993 1112173.211 1.497180958 1.049383266 1.213143503 1.161238944 1.118227102 1.264863966 1.188644163 1.153105452 1 20.08495006 -4.98403332 0.229424377 2.89E-17 1.212914175 0.252856658 0.11641702 249.0595984 2.510073137 115.8708633 0.185164649 1.04E-05 4.98403332 1.212914175 APSPS(ph)SR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APSPSSR 7 0 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 APS(0.089)PS(0.899)S(0.011)R 118.32 0.0052783 762910000 171580 167270 171340 139480 146140 145040 174260 177100 166240 TRUE FALSE 160841.1141 179654.8448 175404.2657 143059.2929 134662.7539 186910.6935 148131.3308 199211.3248 138493.47 1.161362438 1.297208055 1.266516505 1.032967785 0.972340096 1.349599323 1.069590723 1.438416734 1 17.07945843 -2.348679955 2.011731833 6.65E-05 1.198857285 0.154743247 0.145795788 2429914.265 315161.4563 11011693.34 0.033984568 0.004480434 2.348679955 1.198790833 APSPT(ph)KR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.34)PT(0.66)KR;APS(0.391)PT(0.609)KR 78.264 0.020983 4267800000 4324600 3208400 3953900 3482400 3607600 2897900 4314500 3230800 4504100 TRUE FALSE 4053931.006 3445953.274 4047688.375 3571764.28 3324273.648 3734476.687 3667580.779 3634172.492 3752336.612 1.08037509 0.918348653 1.078711425 0.951877363 0.885920959 0.995240319 0.977412519 0.96850919 1 21.83935782 4.761240728 23.59693819 0.975737737 1.080375336 0.304791625 0.051161537 3803.177624 3956781.407 0.011992936 0.581926697 57708.62512 -4.761240728 0.104637599 APSQAAESS(ph)PAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APSQAAESSPAKK 13 1 Q8NFH8-3;Q8NFH8-2;Q8NFH8-4;Q8NFH8 Q8NFH8-3 REPS2 RalBP1-associated Eps domain-containing protein 2 1 APS(0.001)QAAES(0.212)S(0.787)PAKK 64.52 0.037415 90702000 123610 81909 99870 100940 107510 73194 137250 92897 119950 TRUE FALSE 115873.4708 87973.62759 102238.9636 103530.2913 99066.59827 94323.91959 116670.6367 104495.3949 99929.57009 1.159551378 0.88035631 1.023110211 1.03603259 0.9913642 0.943903987 1.167528656 1.045690428 1 16.60862403 1.750823919 25 1.086289714 0.993874836 0.102766778 0.082438216 5.163520125 10543.57683 0.034921448 0.019365787 56.34091801 -1.750823919 -0.092414878 APSRPYQDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 101.38 0.003074 321882000 402720 968730 319333 303667 958390 299746 408895 873050 929810 FALSE TRUE 377514.4741 1040455.777 326907.7296 311459.6093 883121.9154 386277.8042 347584.9907 982052.2143 774618.7042 0.487355227 1.343184423 0.422024059 0.402081189 1.140073059 0.498668315 0.448717529 1.267787892 1 19.56312681 1.228626096 24.99940223 1.133894071 0.70266155 0.249982962 0.326431461 347.3454695 874035.991 0.295235634 0.077354715 16.92879694 -1.228626096 -0.431232521 APSS(ph)PVAKPGPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APSSPVAKPGPVK 13 1 Q9GZR2;A0A0C4DG31;Q9GZR2-2 Q9GZR2 REXO4 RNA exonuclease 4 1 APS(0.212)S(0.788)PVAKPGPVK 75.911 0.018231 166990000 323940 233130 276700 268540 313860 201350 318770 245490 334360 TRUE FALSE 303665.1736 250391.1878 283263.4547 275431.191 289210.7017 259476.4764 270973.3978 276139.9669 278553.156 1.090151618 0.898899124 1.016909874 0.988792211 1.038260366 0.93151512 0.972788827 0.991336702 1 18.08759314 4.769003489 24.26233939 0.977068586 1.0901519 0.42765793 0.040003521 8186.231175 6524088.488 0.009164939 1.106848839 58749.40723 -4.769003489 0.113083313 APTISER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APTISER 7 0 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 0 139.27 0.0062933 175130000 67401 97970 92653 103680 114600 88276 89293 86549 99334 FALSE TRUE 63182.49172 105223.8007 94850.77291 106340.6043 105599.7783 113759.8482 75904.34361 97354.83317 82754.51368 0.763492998 1.27151736 1.146170386 1.28501274 1.276060647 1.374666385 0.917223004 1.176429283 1 16.33655038 1.725541039 24.99999996 1.034376685 1.198650488 0.14520109 0.175418187 1.551879267 2967.133532 0.074769263 0.041463339 53.15462256 -1.725541039 0.164273802 APTQTPTQTIILNS(ph)DDETLATLHTALQSSHGVLGPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APTQTPTQTIILNSDDETLATLHTALQSSHGVLGPER 37 0 Q9H4Z2-2;Q9H4Z2 Q9H4Z2-2 ZNF335 Zinc finger protein 335 1 APTQTPTQTIILNS(0.978)DDET(0.019)LAT(0.002)LHTALQSSHGVLGPER 108.24 2.96E-05 50091000 19549 32889 24242 27950 35264 25745 32172 24573 27314 TRUE FALSE 18325.46299 35324.13578 24817.03169 28667.24432 32494.50769 33177.16356 27348.10727 27640.99314 22755.11694 0.80533372 1.552360107 1.090613234 1.259815293 1.42800882 1.458008924 1.201844286 1.214715495 1 14.47390338 0.823142103 1.815027659 1.001455056 1.28268849 0.12032848 0.209560907 1.17796217 7.097248881 0.179320491 0.050537325 6.654908717 -0.823142103 0.281233434 APTQTPTQTIILNSDDET(ph)LATLHTALQSSHGVLGPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APTQTPTQTIILNSDDETLATLHTALQSSHGVLGPER 37 0 Q9H4Z2-2;Q9H4Z2 Q9H4Z2-2 ZNF335 Zinc finger protein 335 1 APTQTPTQTIILNS(0.405)DDET(0.547)LAT(0.039)LHT(0.004)ALQS(0.003)S(0.003)HGVLGPER 145.84 6.99E-13 55029000 10668 20431 18694 21399 16831 13322 19992 15931 16730 TRUE FALSE 10000.30892 21943.7325 19137.43051 21948.13457 15509.16115 17167.84514 16994.3852 17920.02042 13937.65492 0.717502979 1.574420706 1.373073922 1.574736546 1.112752557 1.231759951 1.219314533 1.285727084 1 13.76670022 2.703951807 24.99234573 1.191366034 1.36453826 0.049695577 0.249684104 1387.4304 1001915.477 0.074603092 0.070339439 505.7685344 -2.703951807 0.173172226 APVDEDRLS(ph)PLVAADSLLEHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 APVDEDRLSPLVAADSLLEHVR 22 1 Q01094 Q01094 E2F1 Transcription factor E2F1 1 APVDEDRLS(1)PLVAADSLLEHVR;APVDEDRLS(1)PLVAADSLLEHVR;APVDEDRLS(1)PLVAADSLLEHVR;APVDEDRLS(1)PLVAADSLLEHVR;APVDEDRLS(1)PLVAADSLLEHVR;APVDEDRLS(1)PLVAADSLLEHVR 360.26 8.32E-97 595660000 197838 220545 230413 210870 259224 215209 253693 237681 300633 TRUE FALSE 185455.6727 236874.3813 235878.5052 216281.2812 238865.5927 277336.3447 215654.0898 267355.9961 250455.4101 0.740473814 0.945774664 0.941798403 0.863552043 0.953725027 1.107328225 0.86104784 1.06747942 1 17.93419425 5.342348611 1.517985059 0.961756301 1.76E-07 0.451566677 0.078028325 5.808462114 3.367261707 0.018972457 13.18326671 219962.4817 -5.342348611 -0.961756125 APVIRPGGTLGLSEAADSDAHLFQDSTEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APVIRPGGTLGLSEAADSDAHLFQDSTEPR 30 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ; 178.63 4.81E-18 670980000 149425 194515 168179 175438 175016 157351 181393 151143 166261 FALSE TRUE 140072.756 208917.093 172168.2853 179940.0361 161270.9493 202775.6793 154194.8036 170013.5363 138510.965 1.011275576 1.508307252 1.242993905 1.299103187 1.164319008 1.463968425 1.113231747 1.227437382 1 17.07964066 0.860346111 0.797653616 1.001091439 1.2999263 0.219553982 0.148896617 1.022904599 1.367254175 0.129752727 0.046683488 7.250135293 -0.860346111 0.298834861 APVPEPGLDLSLS(ph)PRPDS(ph)PQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 APVPEPGLDLSLSPRPDSPQPR 22 1 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 2 APVPEPGLDLS(0.294)LS(0.706)PRPDS(1)PQPR;APVPEPGLDLS(0.388)LS(0.612)PRPDS(1)PQPR 96.44 0.00083311 83478000 68065 78137 73398 78149 86829 70899 83828 74260 87927 TRUE FALSE 63804.93315 83922.34478 75139.03522 80154.43565 80009.80059 91366.39035 71258.76962 83531.52447 73251.41567 0.871040274 1.145675398 1.025769052 1.094237359 1.092262857 1.247298629 0.972797167 1.14034007 1 16.16056902 4.748070616 24.51999995 1.088624724 0.871040121 0.4299991 0.079143055 908.7325816 2342955.798 0.016997126 0.214949101 55984.86252 -4.748070616 -0.217584603 APVPEPGLDLSLS(ph)PRPDSPQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APVPEPGLDLSLSPRPDSPQPR 22 1 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 1 APVPEPGLDLS(0.242)LS(0.758)PRPDSPQPR 121.3 1.67E-05 99858000 35927 56281 46237 54063 53999 47947 44373 37754 50876 TRUE FALSE 33678.3932 60448.1038 47333.76347 55450.34811 49758.13636 61788.52055 37719.68059 42467.67001 42384.46693 0.794592822 1.426185303 1.116771471 1.308270509 1.173971032 1.457810491 0.889941135 1.001963056 1 15.37124802 1.666104258 9.760068931 0.961145583 1.228091417 0.281963083 0.185755698 0.128286443 18.49542091 0.079177456 0.042431825 46.355819 -1.666104258 0.266945834 APVPEPGLDLSLSPRPDS(ph)PQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 APVPEPGLDLSLSPRPDSPQPR 22 1 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 1 APVPEPGLDLSLSPRPDS(1)PQPR;APVPEPGLDLSLSPRPDS(1)PQPR;APVPEPGLDLSLSPRPDS(1)PQPR;APVPEPGLDLSLSPRPDS(1)PQPR 185.96 2.04E-17 2322980000 1524230 1749870 1578650 1524310 1810070 1501830 1805880 1636380 1551310 TRUE FALSE 1428831.165 1879432.196 1616096.323 1563426.375 1667914.404 1935383.941 1535105.059 1840685.645 1292386.339 1.105575881 1.454234031 1.250474626 1.209720598 1.290569509 1.49752739 1.187806628 1.424253406 1 20.30160598 -1.077088447 5.156555745 0.999994634 1.308075276 0.367608221 0.124508065 6.81E-06 1.22E-06 0.10685043 0.025184449 0.083735873 1.077088447 0.308080641 APVPGT(ph)PDSLSSGSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APVPGTPDSLSSGSSR 16 0 A0A087WYB4;Q9UJZ1;Q9UJZ1-2 A0A087WYB4 STOML2 "Stomatin-like protein 2, mitochondrial" 1 APVPGT(0.872)PDS(0.119)LS(0.006)S(0.002)GSSR 112.24 0.0084364 134680000 99626 118240 115870 97893 126130 107690 100430 106950 162860 TRUE FALSE 93390.5865 126994.6126 118618.4911 100405.1001 116224.2586 138778.3548 85371.45385 120302.9429 135677.6139 0.688327159 0.936002698 0.874267226 0.740027019 0.856620744 1.02285374 0.629222842 0.886682331 1 17.04982318 APVPSTCSSTFPEELS(ph)PPSHQAK ddPTM_SK-BR-3_Pertuzumab_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(1)PPSHQAK;APVPSTCSSTFPEELS(0.999)PPS(0.001)HQAK;APVPSTCSSTFPEELS(0.999)PPS(0.001)HQAK 274.88 6.68E-52 10498500000 1405270 1138893 1260651 1207552 1274090 946514 1469860 1064031 1474501 TRUE FALSE 1317316.659 1223217.823 1290554.237 1238539.829 1174028.111 1219757.226 1249468.139 1196877.613 1228397.257 1.072386519 0.995783583 1.050600064 1.008256752 0.955739769 0.992966419 1.017153149 0.974340837 1 20.22834577 3.006747285 18.55611432 0.990846481 1.031482686 0.458844877 0.024940514 7.427511755 20420.45497 0.00693768 0.008240986 1015.657512 -3.006747285 0.040636205 APVPTGEVYFADSFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 APVPTGEVYFADSFDR 16 0 P27824;P27824-2;H0Y9Q7;D6RDP7;D6RAU8;D6RB85;D6RAQ8;D6RHJ3;D6RD16 P27824 CANX Calnexin 0 ;;; 178.32 6.53E-09 615140000 184464 210802 172271 191336 229490 157510 227802 217877 166353 FALSE TRUE 172918.7275 226409.9994 176357.3495 196246.0057 211466.7811 202980.58 193645.2049 245079.4231 138587.6096 1.247721409 1.633695826 1.272533309 1.416042937 1.525870759 1.464637283 1.397276462 1.768407895 1 17.08043875 -0.918431467 7.406158586 0.999999997 1.459147384 0.471448588 0.154848719 7.93E-09 1.61E-09 0.132995184 0.031347265 0.120661448 0.918431467 0.459147387 APVQPQQS(ph)PAAAPGGTDEKPSGK ddPTM_SK-BR-3_Pertuzumab_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 240.41 1.80E-37 1612750000 1154180 696390 891900 836770 859740 679110 1141930 756730 1213900 TRUE FALSE 1081941.934 747951.4402 913056.2892 858242.9348 792219.4884 875158.0326 970708.1977 851209.4063 1011292.248 1.069860801 0.739599697 0.902860959 0.84865966 0.783373441 0.865385881 0.959869118 0.841704668 1 19.94776854 0.634226659 0.66533954 0.999059333 0.85702602 0.119387459 0.092862837 2.295448612 1.903190927 0.092824708 0.033174373 4.307513614 -0.634226659 -0.142033313 APVS(ph)PLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 APVSPLK 7 0 Q9UBS0 Q9UBS0 RPS6KB2 Ribosomal protein S6 kinase beta-2 1 APVS(1)PLK;APVS(1)PLK;APVS(1)PLK 94.692 0.0147 1300120000 2996460 2071850 2498970 2619010 2316390 1843820 2810380 1756760 1846630 TRUE FALSE 2808916.917 2225251.93 2558246.748 2686218.231 2134470.073 2376100.902 2388989.609 1976095.353 1538415.523 1.825850607 1.446457018 1.662910124 1.746094075 1.387447046 1.544511782 1.552889693 1.284500399 1 20.55301379 0.919238411 1.086784758 0.994696012 1.60222531 0.709119619 0.128357272 0.324974142 0.781873781 0.112564858 0.036047256 8.303064484 -0.919238411 0.607529298 APVSGSRS(ph)PDREASGSGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APVSGSRSPDREASGSGGR 19 2 Q8N5F7 Q8N5F7 NKAP NF-kappa-B-activating protein 1 APVS(0.071)GS(0.071)RS(0.534)PDREAS(0.071)GS(0.253)GGR 68.309 0.019313 205880000 25068 51346 41159 44837 56704 23772 37778 35751 98330 TRUE FALSE 23499.03863 55147.71127 42135.31092 45987.59333 52250.69657 30634.59049 32113.53961 40214.59105 81918.08776 0.286860195 0.673205549 0.514359064 0.561385093 0.637840775 0.373966133 0.392020132 0.490912229 1 16.32189442 -1.340076379 4.507375456 1.000527423 0.502626854 0.644236748 0.118532688 0.000627973 9.19E-05 0.114720879 0.027012153 0.045700781 1.340076379 -0.497900569 APYS(ph)PTTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 APYSPTTSK 9 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 1 APYS(0.852)PT(0.124)T(0.024)SK 82.171 0.020149 388130000 835120 709640 728000 843610 844960 591180 863170 658560 848060 TRUE FALSE 782851.3299 762182.484 745268.5038 865258.4608 778600.25 761844.069 733745.6718 740782.6657 706513.3073 1.108048952 1.078794237 1.054854163 1.22468813 1.102031967 1.078315243 1.03854473 1.048504901 1 19.43035721 1.815209499 2.118781207 1.027493785 1.105456375 0.414006369 0.04559777 0.366229379 3.158672518 0.030223031 0.013656324 65.34456916 -1.815209499 0.077962589 AQAEAQQPTFDALRDELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AQAEAQQPTFDALRDELR 18 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;;; 251 2.90E-25 6683010000 2838040 3529630 3112790 3427460 3557540 2874400 3854810 3125460 3376730 FALSE TRUE 2660412.142 3790967.478 3186626.849 3515414.426 3278145.159 3704192.618 3276817.027 3515680.561 2813131.948 0.945711823 1.347596752 1.132768355 1.249644343 1.165300888 1.3167504 1.16482877 1.249738948 1 21.42374579 -0.69423221 7.209907144 0.999999991 1.207229398 0.228583346 0.111950205 0 0 0.092389187 0.02177634 0.202193779 0.69423221 0.207229407 AQAGEGVRPSPMQLELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AQAGEGVRPSPMQLELR 17 1 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;;;; 221.13 3.45E-15 1494200000 960213 1186620 1063081 992293 1098247 886616 1194471 1007690 1220435 FALSE TRUE 900114.9824 1274478.579 1088297.783 1017756.918 1011995.111 1142567.646 1015371.162 1133502.315 1016736.514 0.885298177 1.253499369 1.070383298 1.001003607 0.995336645 1.123759824 0.998657123 1.114843717 1 19.95551442 3.484498772 22.67342743 1.039575355 1.115670093 0 0.100833104 166.4123078 511430.424 0.024862827 0.036491168 3051.397398 -3.484498772 0.076094738 AQAVS(ph)EDAGGNEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AQAVSEDAGGNEGR 14 0 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 1 AQAVS(1)EDAGGNEGR;AQAVS(1)EDAGGNEGR 169.58 3.47E-06 289070000 239030 259330 267820 264820 260690 224990 237610 220496 256150 TRUE FALSE 224069.539 278531.063 274172.8169 271615.7295 240216.459 289940.9606 201982.5864 248025.411 213396.9102 1.050013043 1.305225379 1.284802187 1.272819411 1.12567918 1.35869334 0.946511297 1.162272737 1 17.70317976 1.732857241 14.48232488 1.041889993 1.244619876 0.441863072 0.103533195 0.069129395 105.445768 0.043493241 0.023972131 54.05765978 -1.732857241 0.202729883 AQAVS(ph)EEEEEEEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AQAVSEEEEEEEGK 14 0 G3V529;Q9GZR7;Q9GZR7-2 G3V529 DDX24 ATP-dependent RNA helicase DDX24 1 AQAVS(1)EEEEEEEGK;AQAVS(1)EEEEEEEGK 281.65 2.59E-33 969920000 1275170 654870 844140 788930 703520 742220 1163920 678650 638070 TRUE FALSE 1195359.386 703357.2562 864163.3994 809175.2795 648268.3771 956486.8651 989401.0013 763380.9464 531571.9949 2.248725285 1.323164619 1.625675182 1.522230831 1.219530719 1.79935526 1.861273752 1.436081949 1 19.01990557 4.748963187 24.53190577 1.528802076 2.24872581 0.45148663 0.262324709 1135.15139 2676906.804 0.060303263 0.841347958 56100.04209 -4.748963187 0.719923734 AQCPIVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQCPIVER 8 0 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 137.62 0.0017223 292920000 170780 215120 203720 178890 199830 160470 226440 164740 202640 FALSE TRUE 160091.1847 231047.7086 208552.3346 183480.6203 184136.1579 206795.084 192487.4242 185308.1516 168818.0749 0.948305949 1.368619496 1.235367331 1.08685412 1.090737221 1.224958193 1.14020625 1.097679569 1 17.36510985 0.712336237 0.382855802 0.981679883 1.213207664 0.107758254 0.11416329 3.028879995 1.029549864 0.229370131 0.095127595 5.156276962 -0.712336237 0.231527781 AQCYMDTEQYEEAVRDYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQCYMDTEQYEEAVRDYEK 19 1 Q99615;A0A6I8PUD4;A0A6I8PU73;A0A6I8PS32;A0A6I8PIK4;A0A6I8PR89;A0A6I8PLE7;A0A6I8PRZ0;Q99615-2 Q99615 DNAJC7 DnaJ homolog subfamily C member 7 0 169.39 1.30E-11 93663000 57671 64195 63125 67320 82553 43123 63140 53770 92986 FALSE TRUE 54061.47506 68948.06459 64622.35481 69047.54517 76069.62038 55571.91006 53672.74316 60483.30286 77466.03589 0.697873261 0.890042504 0.834202423 0.891326688 0.981973836 0.717371289 0.692855166 0.780771885 1 16.2412763 2.203528488 24.99995055 0.761701321 0.861378307 0.02831728 0.109335985 310.3644767 221483.4096 0.037408075 0.027628863 159.7822337 -2.203528488 0.099676986 AQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSR 33 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;; 279.78 8.49E-74 687957000 98471 121412 122068 112584 110897 110617 139427 105405 143160 FALSE TRUE 92307.87589 130401.4708 124963.5106 115473.096 102187.597 142550.3322 118521.2157 118565.0463 119265.6712 0.773968528 1.093369698 1.047774346 0.968200614 0.856806455 1.195233556 0.993758008 0.994125511 1 16.86381932 2.252942453 24.99633144 1.045097422 0.982363311 0.12661213 0.108424612 672.6729145 1169135.765 0.03692334 0.030762187 179.0368602 -2.252942453 -0.062734111 AQDGSHPLSLQDLIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQDGSHPLSLQDLIEK 16 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-7;H7BXG7;H0YAB3;H0Y9K1 D6REX3 SEC31A Protein transport protein Sec31A 0 199.76 3.73E-11 82495000 204240 179330 204680 196760 207180 154890 247030 183820 222370 FALSE TRUE 191456.983 192607.7798 209535.1063 201809.1947 190908.9185 199604.2286 209990.1448 206770.3316 185255.0104 1.033478029 1.039689989 1.131063099 1.089358902 1.030519596 1.077456572 1.133519381 1.116138944 1 17.49915304 4.22757089 4.936961213 1.089917735 1.035456469 0.154181121 0.042238532 0.260932217 18.4104772 0.010057108 0.02578692 16887.71496 -4.22757089 -0.054461266 AQDITLPHLCSVLLAFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQDITLPHLCSVLLAFAR 18 0 Q969Z0;Q969Z0-2;H7C4R5 Q969Z0 TBRG4 Protein TBRG4 0 83.213 0.0040461 50196000 56380 57392 45553 53359 72715 46325 64320 62841 62708 FALSE TRUE 52851.27644 61641.3634 46633.53867 54728.28228 67004.25722 59698.27548 54675.81312 70686.83718 52241.62969 1.01166975 1.179928034 0.892650917 1.047599062 1.282583595 1.14273379 1.046594707 1.353074887 1 15.67291228 2.964676808 24.2258247 1.156786587 1.032380113 0.225096074 0.121563566 649.713612 445595.1165 0.035226497 0.037380295 921.8851261 -2.964676808 -0.124406474 AQEEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AQEEAER 7 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 159.46 0.0032171 593130000 455100 432140 473100 426450 458000 381430 396200 436610 370480 FALSE TRUE 426616.1034 464136.0952 484322.1554 437393.429 422030.5275 491542.649 336793.4881 491121.7196 308644.4946 1.382224892 1.503788674 1.569190975 1.417143142 1.367367748 1.592585183 1.091201995 1.591221383 1 18.23558653 -1.048975531 0.253187569 0.707132315 1.52249799 0.43343566 0.152467918 13.5837715 0.801042874 3.022419075 0.231163517 0.089335581 1.048975531 0.815365675 AQEEAERLEADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AQEEAERLEADR 12 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;; 236.92 3.96E-16 5993940000 5933670 8355710 6870160 7323730 10650740 4887000 6537510 6417820 13213340 FALSE TRUE 5562292.187 8974375.463 7033123.44 7511669.311 9814273.843 6297797.566 5557271.067 7219098.954 11007948.19 0.505297817 0.815263236 0.638913203 0.682385961 0.891562503 0.572113663 0.504841681 0.655807861 1 23.39204225 -1.147850197 5.276384843 1.00001076 0.662647507 0.435133428 0.122270793 1.56E-05 2.52E-06 0.119230019 0.028101889 0.071145888 1.147850197 -0.337363253 AQELDALDNSHPIEVSVGHPSEVDEIFDAISYSK ddPTM_SK-BR-3_Pertuzumab_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 ;; 331.27 1.49E-117 341395000 144471 207489 206809 211030 224586 176787 274312 230599 293608 FALSE TRUE 135428.818 222851.7015 211714.6071 216445.3871 206947.9215 227822.537 233181.4622 259389.7928 244602.928 0.553668017 0.911075363 0.865544043 0.884884694 0.846056599 0.931397424 0.953306095 1.060452525 1 17.90008215 4.739496491 5.710060616 0.920951341 0.541685166 0.773925769 0.063986495 0.068634107 9.512433119 0.015222066 0.101361391 54890.412 -4.739496491 -0.379266176 AQELGHSQSALASAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AQELGHSQSALASAQR 16 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;; 230.33 2.36E-15 1228750000 662970 960260 721240 733590 991790 634489 798910 800710 989910 FALSE TRUE 621475.8911 1031358.65 738348.1534 752415.1614 913898.8141 817655.6742 679120.8622 900680.4061 824687.6259 0.753589446 1.25060522 0.895306453 0.91236383 1.108175733 0.991473194 0.823488604 1.092147351 1 19.65348824 3.746529221 24.71387399 0.962897545 1.048205683 0 0.14694133 1114.655517 1419379.59 0.034797262 0.062606351 5578.651356 -3.746529221 0.085308138 AQEPPAGGGGSIHDLPLFTETSPT(ph)SAPWDPLPGPPPVLPHSPHSHL ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQEPPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHSPHSHL 46 0 F8VZ44;Q9NRG9-2;Q9NRG9 F8VZ44 AAAS Aladin 1 AQEPPAGGGGSIHDLPLFTET(0.002)S(0.035)PT(0.807)S(0.156)APWDPLPGPPPVLPHSPHSHL 109.01 1.14E-07 160840000 8613.7 15007 17064 18045 20032 13315 16749 16542 15178 TRUE FALSE 8074.583893 16118.13389 17468.76614 18508.06525 18458.76753 17158.82435 14237.64294 18607.30511 12644.69375 0.638574888 1.274695474 1.381509627 1.463702136 1.459803448 1.356998018 1.125977681 1.471550477 1 13.62624447 4.74128614 4.031944231 1.32949663 0.575803989 0.663032409 0.152258911 0.136356944 4.707528897 0.034189791 0.301588784 55117.07217 -4.74128614 -0.753692641 AQEPPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHS(ph)PHSHL ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQEPPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHSPHSHL 46 0 F8VZ44;Q9NRG9-2;Q9NRG9 F8VZ44 AAAS Aladin 1 AQEPPAGGGGSIHDLPLFTET(0.002)S(0.001)PT(0.011)S(0.011)APWDPLPGPPPVLPHS(0.792)PHS(0.184)HL 124.39 3.43E-10 102710000 13557 26956 23355 31251 29141 22433 24818 24268 23842 TRUE FALSE 12708.49157 28951.85029 23908.99163 32052.95357 26852.38341 28909.04293 21096.7713 27297.91322 19862.61617 0.639819622 1.457605082 1.203718152 1.613732717 1.351905669 1.45544991 1.06213457 1.37433624 1 14.27776804 -1.58953688 2.764189025 0.979176648 1.285117369 0.087934728 0.269140663 29111372.13 28972002.62 4445293.585 0.059242989 0.025731382 1.58953688 0.305940721 AQEQQQQMAELHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AQEQQQQMAELHSK 14 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 137.19 2.27E-05 674680000 514378 413931 479612 411636 483298 355007 577308 451618 463930 FALSE TRUE 482183.9992 444578.8819 490988.6231 422199.2767 445341.7246 457491.7578 490746.0249 508003.5014 386497.0859 1.247574734 1.150277449 1.270355304 1.092373764 1.152251183 1.18368747 1.26972762 1.314378607 1 18.56009801 AQEQS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AQEQSPR 7 0 K7EMM8;Q49A26-4;Q49A26-2;Q49A26-3;Q49A26;K7EPU6 K7EMM8 GLYR1 Putative oxidoreductase GLYR1 1 AQEQS(1)PR;AQEQS(1)PR;AQEQS(1)PR 145.84 0.0023702 125714000 315250 278214 386403 310883 331662 294407 357259 310373 285483 TRUE FALSE 295519.0652 298813.254 395568.6616 318860.7841 305614.6044 379397.5216 303691.3296 349123.7523 237834.043 1.242543168 1.256393955 1.663212956 1.340686052 1.284990998 1.595219577 1.276904373 1.467930107 1 17.85959571 -1.200694765 4.02858375 0.99976217 1.398700879 0.417212588 0.144969522 10158013.96 3027557.536 21295.26621 0.03235344 0.062994877 1.200694765 0.398938709 AQFEGIVTDLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQFEGIVTDLIR 12 0 P38646;H0YBG6 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 146.16 0.00015007 64050000 297730 372890 303560 299920 478150 279970 315250 360580 426740 FALSE TRUE 279095.6108 400499.1636 310760.5866 307616.455 440598.0278 360792.7941 267981.1891 405599.2067 355514.3372 0.785047413 1.126534493 0.874115483 0.865271588 1.239325624 1.014847381 0.753784478 1.140880027 1 18.43954822 4.774018657 22.37481569 0.983265342 0.785045679 0.169841043 0.145568036 8120.606142 5123897.024 0.033908298 5.371117828 59431.76897 -4.774018657 -0.198219662 AQFSVAGVHTVPGS(ph)PQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AQFSVAGVHTVPGSPQAR 18 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 AQFSVAGVHTVPGS(1)PQAR;AQFSVAGVHTVPGS(1)PQAR;AQFSVAGVHTVPGS(1)PQAR;AQFSVAGVHTVPGS(1)PQAR;AQFSVAGVHTVPGS(1)PQAR;AQFSVAGVHT(0.003)VPGS(0.997)PQAR 161.46 2.45E-11 5010430000 1766060 1825550 2055570 1778860 2337460 2068820 2189240 2027710 3344700 TRUE FALSE 1655525.457 1960715.621 2104329.091 1824508.559 2153885.32 2666054.75 1860983.786 2280874.057 2786447.962 0.594134712 0.703661309 0.755201288 0.654779341 0.77298602 0.956793303 0.667869564 0.818559718 1 21.40999578 -4.999999991 0.065409313 1.911891495 0.383789545 0.573929047 0.084102491 267.8131977 1.270532075 37.95997601 5.415665123 1.00E-05 4.999999991 -1.52810195 AQGAGVTLPPT(ph)PSGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AQGAGVTLPPTPSGSR 16 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 AQGAGVTLPPT(0.994)PS(0.005)GS(0.001)R;AQGAGVTLPPT(0.94)PS(0.06)GSR;AQGAGVTLPPT(0.996)PS(0.003)GS(0.001)R 190.46 9.54E-09 380651000 556750 697080 547500 606510 683370 431071 727800 558180 751620 TRUE FALSE 521904.0113 748692.5285 560486.9585 622074.0734 629700.8768 555514.1998 618673.1466 627870.0017 626169.7663 0.833486443 1.195670198 0.895103834 0.993459133 1.005639222 0.887162284 0.988027816 1.002715295 1 19.25619433 3.776730342 24.7603946 0.966008956 1.041930266 0.022728332 0.096402383 371.8741286 185603.7286 0.021983671 0.039631533 5980.401503 -3.776730342 0.075921311 AQGEPVAGHES(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 142.4 3.46E-06 0 437130 222580 318980 260960 249670 257140 440020 258300 283100 TRUE FALSE 409770.8136 239060.0548 326546.3562 267656.6754 230061.9253 331372.1437 374043.0859 290549.3236 235848.7811 1.737430279 1.013615816 1.384558168 1.134865629 0.975463703 1.40501953 1.585944537 1.231930571 1 17.84750262 AQGEPVAGHES(ph)PKIPYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 AQGEPVAGHESPKIPYEK 18 1 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-7;H7BXG7;H0YAB3 D6REX3 SEC31A Protein transport protein Sec31A 1 AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK 241.29 3.31E-24 29047020000 12603370 7233250 8445420 9323460 9574800 6467800 11131650 7726500 12394930 TRUE FALSE 11814547.57 7768807.356 8645749.351 9562715.768 8822833.831 8334948.864 9462562.424 8691170.533 10326136.11 1.144140213 0.752344079 0.837268583 0.926069119 0.854417736 0.807170153 0.916370104 0.841667245 1 23.29979718 -1.964587936 6.045840299 1.079925052 0.869148529 0.088607772 0.105705778 0.07395843 0.000433194 0.066471024 0.021681411 0.010849558 1.964587936 -0.210776523 AQGGQT(ph)QSPTKSHTPSPTSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQGGQTQSPTKSHTPSPTSPK 21 1 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 1 AQGGQT(0.614)QS(0.375)PT(0.009)KS(0.002)HTPSPTSPK 86.551 0.0040094 56479000 39689 46583 44323 56912 87215 30916 69035 43026 229790 TRUE FALSE 37204.93634 50032.05379 45374.36249 58372.45827 80365.48571 39840.94732 58683.84264 48397.89081 191436.5645 0.19434603 0.261350562 0.237020355 0.30491802 0.419802173 0.208115662 0.306544587 0.252814247 1 17.54650689 -4.254806722 0.48307084 10 0.266485238 0.928300563 0.063464928 203.8503835 2.210350939 1938.392667 0.029450801 5.56E-05 4.254806722 -9.733514762 AQGGQTQS(ph)PTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 AQGGQTQSPTK 11 0 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 1 AQGGQT(0.006)QS(0.993)PT(0.001)K;AQGGQTQS(0.999)PTK;AQGGQT(0.03)QS(0.969)PTK;AQGGQT(0.017)QS(0.983)PTK;AQGGQT(0.081)QS(0.915)PT(0.003)K;AQGGQT(0.002)QS(0.998)PTK;AQGGQT(0.045)QS(0.953)PT(0.001)K 240.37 1.16E-15 5338614000 7060630 4853602 5667330 5072072 5676210 3878509 5833780 4853779 5543370 TRUE FALSE 6618717.772 5212967.742 5801761.744 5202229.955 5230423.363 4998171.586 4959058.847 5459783.993 4618145.735 1.433198117 1.128801047 1.256296807 1.126475918 1.132580837 1.082289705 1.073820345 1.182245928 1 22.13888227 8 0.368114792 1.08374408 4.713429441 0.607032912 0.074247225 46.00114001 0.637549847 0.053435022 117.842295 100000000 -8 3.629685361 AQGGQTQS(ph)PTKSHTPSPTSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQGGQTQSPTKSHTPSPTSPK 21 1 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 1 AQGGQT(0.209)QS(0.757)PT(0.033)KS(0.001)HTPSPTSPK 97.346 0.00069147 43596000 31049 38114 31267 35140 60811 21632 46180 28724 148690 TRUE FALSE 29105.69851 40936.00022 32008.66801 36041.75189 56035.14936 27876.80723 39255.73771 32310.25463 123872.6784 0.234964634 0.330468355 0.258399741 0.290958041 0.452360844 0.225044034 0.316903923 0.260834391 1 16.91849849 -1.418414863 3.133332358 1.010551128 0.298598635 0.921395536 0.06459585 11616216.34 14850722.05 1094905.361 0.014358774 0.038157959 1.418414863 -0.711952493 AQGPRPHQENNHQESYPLSVS(ph)PMENNHCPASSESHPKPS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AQGPRPHQENNHQESYPLSVSPMENNHCPASSESHPKPSSPR 42 2 P41212 P41212 ETV6 Transcription factor ETV6 2 AQGPRPHQENNHQESYPLS(0.034)VS(0.683)PMENNHCPAS(0.124)S(0.135)ES(0.046)HPKPS(0.51)S(0.468)PR;AQGPRPHQENNHQESYPLS(0.154)VS(0.828)PMENNHCPAS(0.086)S(0.079)ES(0.223)HPKPS(0.33)S(0.3)PR 110.07 2.57E-06 675240000 91735 114786 123286 127448 135923 103009 152803 112751 147088 TRUE FALSE 85993.4701 123284.8749 126210.4021 130718.5314 125248.1559 132746.0261 129891.6087 126828.2105 122538.0626 0.701769461 1.006094533 1.02996897 1.066758595 1.022116339 1.08330443 1.060010302 1.035010738 1 16.90287042 4.783847777 2.73524061 1.044379281 0.612566813 0.950399079 0.024236755 0.111301756 1.017363778 0.005996611 0.113889547 60792.18832 -4.783847777 -0.431812468 AQGPRPHQENNHQESYPLSVS(ph)PMENNHCPASSESHPKPSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQGPRPHQENNHQESYPLSVSPMENNHCPASSESHPKPSSPR 42 2 P41212 P41212 ETV6 Transcription factor ETV6 2 AQGPRPHQENNHQESYPLS(0.021)VS(0.962)PMENNHCPAS(0.014)S(0.004)ES(0.026)HPKPS(0.459)S(0.513)PR 166.32 4.27E-20 385200000 65569 84150 87348 89701 92497 67421 108550 79959 100850 TRUE FALSE 61465.15333 90380.55356 89419.93581 92002.87952 85232.65873 86884.34821 92273.93523 89942.05716 84017.48348 0.731575748 1.075735071 1.064301525 1.095044456 1.014463362 1.03412224 1.098270638 1.070515962 1 16.35840195 4.740005541 24.99682374 1.062003012 0.73157564 0.907407636 0.032583453 32.21308762 557224.8643 0.00721088 0.045409571 54954.78847 -4.740005541 -0.330427372 AQGS(ph)DEDKLQNS(ph)DDDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQGSDEDKLQNSDDDEK 17 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 2 AQGS(1)DEDKLQNS(1)DDDEK 55.469 0.067499 88407000 532340 143980 273420 215070 195330 181850 370150 170040 197110 TRUE FALSE 499021.7897 154640.429 279905.6515 220589.0603 179989.5697 234347.1429 314649.4438 191269.8683 164211.0676 3.038904727 0.941717457 1.704548028 1.343326388 1.096086715 1.427109307 1.916128117 1.164780615 1 17.32519184 4.748209084 24.86065612 1.386722537 3.038905684 0.748832559 0.310216615 644.7980962 1661377.797 0.073141656 0.955731913 56002.71522 -4.748209084 1.652183148 AQGVRS(ph)PLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 145.6 1.83E-05 929080000 549100 1236490 478390 574090 1669560 315371 517820 1042970 1719760 TRUE FALSE 514732.8112 1328041.006 489737.6367 588822.1213 1538439.492 406413.4881 440177.6982 1173187.1 1432720.946 0.359269412 0.926936268 0.341823464 0.410981722 1.073788651 0.283665489 0.307231984 0.81885248 1 20.45032621 1.025636621 7.361109861 0.999799777 0.540857587 0.27197501 0.267365699 0.200159593 39.76196073 0.248625884 0.062318247 10.60807597 -1.025636621 -0.45894219 AQHEDQVEQYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AQHEDQVEQYK 11 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;; 182.71 5.66E-06 2245900000 5425140 4035650 4912060 4919080 4703010 4408770 5905980 4282870 4538180 FALSE TRUE 5085590.172 4334453.725 5028576.383 5045311.921 4333654.566 5681510.329 5020433.127 4817595.747 3780728.44 1.345135006 1.146459946 1.330054899 1.334481437 1.146248569 1.502755466 1.327901013 1.27425067 1 21.8502328 0.941741123 18.00255838 0.999999999 1.298750656 0.464800648 0.101830581 426.2028127 131702.5916 0.095016234 0.023754059 8.744623638 -0.941741123 0.298750658 AQHEDQVEQYKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AQHEDQVEQYKK 12 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;; 255.23 6.29E-21 19093440000 22234030 16444780 18058910 18047560 20468680 13444920 23981800 17266230 28032670 FALSE TRUE 20842441.75 17662368.62 18487275.87 18510690.94 18861152.44 17326250.14 20385951.73 19421956.82 23353836.28 0.892463298 0.756294101 0.791616232 0.792618854 0.807625446 0.74190167 0.872916616 0.831638819 1 24.47715622 0.62011003 0.874357944 1.000028472 0.793436881 0.640178218 0.045234329 0.699049623 0.904887578 0.039763014 0.013248475 4.169750122 -0.62011003 -0.206591591 AQHQQALSSLELLNVLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQHQQALSSLELLNVLFR 18 0 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 0 222.7 5.55E-19 89986000 71817 84574 91544 85666 98888 80967 98987 86383 89051 FALSE TRUE 67322.10217 90835.94696 93715.46691 87864.33459 91121.73538 104340.8585 84144.8183 97168.1077 74187.81281 0.907455007 1.224405243 1.263219164 1.18434998 1.228257471 1.406442036 1.134213493 1.309758356 1 16.17889459 4.738475392 6.456482265 1.231231106 0.900823797 0.452181936 0.106966033 0.094270098 23.44696068 0.021881207 0.136468584 54761.50711 -4.738475392 -0.330407309 AQHTLPQDPAIVQS(ph)SLGSASASPFQPHVPYS(ph)PFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQHTLPQDPAIVQSSLGSASASPFQPHVPYSPFR 34 0 Q9BX40;Q9BX40-2;Q5TBQ1;A0A0C4DFV2 Q9BX40 LSM14B Protein LSM14 homolog B 2 AQHTLPQDPAIVQS(0.227)S(0.227)LGS(0.227)AS(0.227)AS(0.227)PFQPHVPY(0.421)S(0.443)PFR 40.986 0.070186 36406000 14517 15012 16211 14319 18026 9916.6 12891 13430 19690 TRUE FALSE 13608.40688 16123.5041 16595.53258 14686.44978 16610.31067 12779.36144 10958.11422 15106.76506 16403.6118 0.829598204 0.982924023 1.01169991 0.895318053 1.012600815 0.779057783 0.668030575 0.920941391 1 14.00172589 2.230575319 24.99993167 0.797406724 0.957982405 0.134667107 0.105556668 190.8738856 597572.4876 0.036662817 0.027558398 170.0494842 -2.230575319 0.160575681 AQIEDTLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQIEDTLRR 9 1 Q96CT7;M0R2F5 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 131.52 0.0019995 0 134490 202050 185980 168800 216360 141940 204600 154550 242700 FALSE TRUE 126072.511 217009.9922 190391.5334 173131.6938 199367.9584 182915.7738 173922.1294 173845.9077 202191.8021 0.623529291 1.073287789 0.941638244 0.856274547 0.986033837 0.90466464 0.860183883 0.859806906 1 17.62536498 2.005764502 24.49049891 0.888952407 0.92641842 0 0.122939414 626.5366569 2661823.811 0.043086028 0.031718433 101.3361737 -2.005764502 0.037466013 AQIHDLVLVGGSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 144.73 8.77E-06 2892760000 2187410 2612460 2005370 1858230 2788690 1548515 2428840 2506540 2969540 FALSE TRUE 2050503.913 2805889.257 2052938.323 1905915.328 2569677.536 1995546.142 2064657.99 2819487.037 2473904.59 0.828853271 1.134194612 0.829837307 0.770407774 1.038713274 0.80663828 0.834574623 1.139691097 1 21.23835843 1.238877685 24.99999012 1.069845563 0.902896672 0.280787287 0.117382907 11.68886429 922308.815 0.090323505 0.02829597 17.33315758 -1.238877685 -0.166948891 AQIWDTAGQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 119.45 0.0013604 437530000 372960 592410 522860 573660 623650 550310 613580 568900 521430 FALSE TRUE 349617.0994 636272.6528 535262.4861 588381.0868 574671.0447 709175.5635 521579.3752 639928.4173 434399.9644 0.804827643 1.464716171 1.232188144 1.354468543 1.32290767 1.632540565 1.200689268 1.473131836 1 18.72866446 4.746325047 24.69832115 1.346936284 0.804827332 0.482433391 0.172214812 625.8937964 1990885.665 0.035364509 0.380106503 55760.29293 -4.746325047 -0.542108952 AQLADSFHLQQFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQLADSFHLQQFFR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 197.06 2.40E-08 130950000 180140 312140 226520 197790 297200 197960 262640 282000 258960 FALSE TRUE 168865.359 335251.1704 231893.1614 202865.6263 273859.1108 255107.8384 223259.5702 317208.3208 215737.9031 0.782733848 1.553974363 1.074883727 0.940333726 1.269406567 1.182489654 1.034864839 1.47034117 1 17.71892014 3.725798732 24.99751515 1.134138305 1.250738612 0 0.238878801 211.4511557 3996826.119 0.056954632 0.093850499 5318.617179 -3.725798732 0.116600307 AQLEPVAS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 176.83 8.65E-06 837730000 2926400 2207800 2269500 2331800 2787100 1508890 2705100 2377300 1783700 TRUE FALSE 2743241.848 2371267.809 2323333.612 2391637.936 2568212.409 1944482.048 2299495.368 2674111.138 1485988.947 1.846071502 1.595750637 1.563493199 1.609458765 1.728285001 1.308544086 1.547451193 1.799549817 1 20.50299195 -2.574848991 0.378357006 6.10E-33 1.62261601 0.612991807 0.153517758 49.64564498 2.052340915 41.11330936 0.098987504 0.00266165 2.574848991 1.62261601 AQLEPVAS(ph)PAKKPK ddPTM_SK-BR-3_Pertuzumab_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 106.16 0.00049992 398570000 1285900 765150 1053200 1181900 1447500 726160 1666500 833710 1696700 TRUE FALSE 1205417.814 821802.5021 1078182.401 1212229.555 1333819.189 935790.6038 1416623.796 937800.5287 1413509.809 0.85278348 0.581391439 0.762769664 0.857602506 0.943622167 0.662033329 1.002203018 0.663455268 1 20.43085046 4.902982074 0.052886199 1.405892984 1.87E-08 0.169177956 0.13337907 292.07031 2.302077741 20.00898973 44.81697097 79980.12421 -4.902982074 -1.405892965 AQLGINEDHS(ph)EGDEKSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AQLGINEDHSEGDEKSEK 18 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1;C9J8U1;C9JLY8 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 AQLGINEDHS(1)EGDEKSEK;AQLGINEDHS(1)EGDEKSEK 253.13 1.02E-30 391020000 1088980 483560 641920 678030 726560 510980 881060 566840 806980 TRUE FALSE 1020822.686 519363.2855 657146.6455 695429.3977 669498.9084 658491.6309 748953.2324 637611.2218 672289.8247 1.5184265 0.772528851 0.977475222 1.034419044 0.995848641 0.979475825 1.114033271 0.948417183 1 19.35872379 AQLLHALS(ph)LDEGGPEPEPSLSDSSSGGSFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AQLLHALSLDEGGPEPEPSLSDSSSGGSFGR 31 0 O15049 O15049 N4BP3 NEDD4-binding protein 3 1 AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR 229.87 9.86E-36 1845430000 500153 586722 467954 572282 463175 361199 721104 505740 488768 TRUE FALSE 468849.3165 630163.5074 479054.0899 586967.725 426799.1039 465471.2877 612981.1496 568882.7523 407189.4632 1.15142792 1.547592863 1.176489406 1.441510103 1.048158517 1.143131956 1.505395412 1.397095956 1 18.6353407 3.942052418 23.09819125 1.272918846 1.375837075 0.029841751 0.191163983 412.2217544 271510.521 0.046625371 0.084062908 8750.893888 -3.942052418 0.102918228 AQLS(ph)PGIYDDTSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AQLSPGIYDDTSAR 14 0 O75376;O75376-2;A0A088AWL3;E7EVK1 O75376 NCOR1 Nuclear receptor corepressor 1 1 AQLS(1)PGIYDDTSAR;AQLS(1)PGIYDDTSAR;AQLS(1)PGIYDDTSAR 302.34 6.06E-44 2066260000 1490770 1626280 1620600 1578180 1857280 1558660 2017960 1662620 1839340 TRUE FALSE 1397465.367 1746691.463 1659041.397 1618678.771 1711416.721 2008619.839 1715385.632 1870201.767 1532342.271 0.91197991 1.139883364 1.082683307 1.056342829 1.116863218 1.3108167 1.119453313 1.220485659 1 20.54730715 2.472499088 24.99598875 1.177124285 1.070678704 0.217858794 0.097054992 186.2934448 1007433.65 0.030073332 0.02525298 296.8240509 -2.472499088 -0.106445581 AQLSVQT(ph)SPVPTPDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQLSVQTSPVPTPDPK 16 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 AQLSVQT(0.777)S(0.223)PVPTPDPK 176.33 3.58E-08 72588000 88816 60701 74614 71124 76847 59852 95021 69181 118620 TRUE FALSE 83257.1651 65195.3652 76383.87932 72949.16225 70811.74661 77130.30078 80773.48318 77818.40014 98821.55569 0.842500045 0.659728181 0.77294755 0.73819079 0.716561747 0.780500775 0.817367047 0.787463824 1 16.59253815 0.250384354 0.488466828 1.02013095 0.733131569 0.700640912 0.049288833 1.419681127 0.512086131 0.104759454 0.023816407 1.779853897 -0.250384354 -0.286999381 AQLSVQTS(ph)PVPTPDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AQLSVQTSPVPTPDPK 16 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 AQLSVQT(0.211)S(0.789)PVPTPDPK;AQLSVQT(0.339)S(0.661)PVPTPDPK 185.12 1.80E-09 130923000 203212 153994 167180 169549 197159 143301 225374 176055 274150 TRUE FALSE 190493.3237 165395.876 171145.5885 173899.9144 181674.9274 184669.6724 191581.261 198035.8543 228392.5939 0.834060862 0.724173552 0.749348241 0.761407852 0.795450169 0.808562437 0.838824314 0.867085271 1 17.80115634 0.964142562 0.579267312 1.003249361 0.754087815 0.855439765 0.029317044 0.295643118 0.23753462 0.029621344 0.012959643 9.207517691 -0.964142562 -0.249161547 AQLVVIAHDVDPIELVVFLPALCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQLVVIAHDVDPIELVVFLPALCR 24 0 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 118.54 0.00050649 260010000 200190 175360 171580 174350 180190 193320 208740 145300 189220 FALSE TRUE 187660.4652 188343.8369 175649.9586 178824.1162 166038.6043 249128.3457 177441.3748 163441.0248 157637.9596 1.19045226 1.19478733 1.114261813 1.134397557 1.053290747 1.580382963 1.12562593 1.036812613 1 17.26625546 1.323095243 4.820958789 1.018059375 1.201345851 0.230953769 0.14168791 0.303452944 11.21937438 0.100430637 0.034195669 21.04239858 -1.323095243 0.183286476 AQLYLPSTS(ph)PPHEGLDGFAQELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AQLYLPSTSPPHEGLDGFAQELSR 24 0 I3L1Z8;I3L1A6;Q8N137-4;Q8N137-5;Q8N137;Q8N137-3;Q8N137-2;I3L465 I3L1Z8 CNTROB Centrobin 1 AQLYLPS(0.005)T(0.152)S(0.842)PPHEGLDGFAQELSR;AQLYLPS(0.012)T(0.05)S(0.938)PPHEGLDGFAQELSR;AQLYLPS(0.33)T(0.241)S(0.43)PPHEGLDGFAQELSR 166.2 8.57E-12 530160000 249949 320327 264835 304321 309558 256629 328220 266317 266456 TRUE FALSE 234305.1383 344044.3444 271117.0113 312130.3921 285246.5634 330713.6263 279006.458 299567.2637 221982.7722 1.055510461 1.549869573 1.221342578 1.406101874 1.284994148 1.489816633 1.256883384 1.349506814 1 17.76008819 -0.153575292 1.056785869 0.996205685 1.342305134 0.344723007 0.140051894 14.06154878 11.56075551 0.339920206 0.036436856 0.702141606 0.153575292 0.34609945 AQNDLIWNIKDELKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AQNDLIWNIKDELKK 15 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 200.69 3.82E-09 914960000 2298580 1347190 1687740 1642090 1922330 1126450 2307590 1462960 2778300 FALSE TRUE 2154715.981 1446937.349 1727773.99 1684228.809 1771357.956 1451637.829 1961588.302 1645613.776 2314583.781 0.930930217 0.625139328 0.746472866 0.727659471 0.765303019 0.627170138 0.847490732 0.710976111 1 21.14232135 -0.510415991 0.599501676 1.034106288 0.731593842 0.411849125 0.092789361 9.779289214 2.772187023 0.795944285 0.033422443 0.30873368 0.510415991 -0.302512446 AQNEATS(ph)TPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQNEATSTPHR 11 0 Q13415 Q13415 ORC1 Origin recognition complex subunit 1 1 AQNEATS(0.947)T(0.053)PHR 119.87 0.00034048 99235000 76562 94525 81744 77816 103480 63131 127960 69111 126320 TRUE FALSE 71770.12109 101523.7294 83683.00628 79812.8903 95353.09822 81355.89485 108773.5859 77739.66048 105236.3759 0.681989668 0.964720881 0.795190879 0.75841542 0.906084967 0.773077694 1.033612047 0.738714725 1 16.68327395 1.759459105 25 0.925389396 0.830102695 0.175338795 0.109325666 18.35156857 21972.07391 0.045654069 0.025318157 57.47236978 -1.759459105 -0.095286701 AQNEATST(ph)PHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQNEATSTPHR 11 0 Q13415 Q13415 ORC1 Origin recognition complex subunit 1 1 AQNEATS(0.01)T(0.99)PHR 121.42 0.001516 83305000 63265 87288 79012 69269 95473 46350 107770 69789 117740 TRUE FALSE 59305.35658 93750.89434 80886.20195 71046.55981 87974.9357 59730.49257 91610.88899 78502.31027 98088.43337 0.60461111 0.955779302 0.824625281 0.724311291 0.896894085 0.608945321 0.9339622 0.800321787 1 16.5817954 0.4271993 1.053971242 0.999805547 0.807045191 0.213292309 0.121949706 3.649295933 5.190119445 0.108042186 0.033341196 2.674233346 -0.4271993 -0.192760357 AQNGRT(ph)PEDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AQNGRTPEDER 11 1 A0A0A0MRJ2;Q5VTZ4;P18847-5;P18847 A0A0A0MRJ2 ATF3 Cyclic AMP-dependent transcription factor ATF-3 1 AQNGRT(1)PEDER;AQNGRT(1)PEDER 100.11 0.0069071 234460000 442540 542120 506600 549050 498680 290450 370950 346630 412190 TRUE FALSE 414842.2114 582259.1289 518616.7912 563139.5525 459515.6844 374298.1999 315329.4912 389907.5185 343392.8262 1.208068951 1.695606561 1.510272643 1.639928122 1.33816332 1.090000057 0.918276292 1.135456215 1 18.38950037 2.347898006 2.606491082 1.00836205 1.542198581 0.723086234 0.139233916 0.122375613 1.701007313 0.051265214 0.03969138 222.7911862 -2.347898006 0.533836531 AQNTWGCGNSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AQNTWGCGNSLR 12 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 248.6 2.06E-16 648340000 299202 440860 285688 274656 422230 269996 354276 372720 449720 FALSE TRUE 280475.4809 473501.7331 292464.6543 281704.138 389069.759 347939.4622 301155.6027 419254.9125 374658.8267 0.748615703 1.263821107 0.780615946 0.751895105 1.038464147 0.928683478 0.803812913 1.119031189 1 18.51521792 3.941751749 23.15388143 0.902259166 1.040418724 0.031094511 0.169295645 264.544778 173178.1356 0.039491227 0.071199718 8744.837609 -3.941751749 0.138159558 AQPFGFIDS(ph)DTDAEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AQPFGFIDSDTDAEEER 17 0 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AQPFGFIDS(0.918)DT(0.082)DAEEER;AQPFGFIDS(0.983)DT(0.017)DAEEER;AQPFGFIDS(0.983)DT(0.017)DAEEER 259.49 3.49E-27 177458000 154770 128557 149925 137097 137207 150282 139950 109625 100126 TRUE FALSE 145083.222 138075.494 153481.2918 140615.1411 126431.3157 193665.9738 118965.7967 123311.9226 83414.32376 1.739308256 1.65529717 1.839987245 1.685743345 1.515702699 2.321735225 1.426203455 1.478306327 1 16.34800752 1.027371613 1.666153513 1.017604879 1.762479812 0.528138371 0.230433482 0.270721805 1.53516055 0.195123643 0.056618609 10.65053964 -1.027371613 0.744874933 AQPFGFIDS(ph)DTDAEEERIPATPVVIPMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AQPFGFIDSDTDAEEERIPATPVVIPMK 28 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AQPFGFIDS(0.998)DT(0.002)DAEEERIPATPVVIPMK;AQPFGFIDS(0.98)DT(0.02)DAEEERIPATPVVIPMK;AQPFGFIDS(0.977)DT(0.023)DAEEERIPATPVVIPMK;AQPFGFIDS(0.856)DT(0.144)DAEEERIPATPVVIPMK;AQPFGFIDS(0.996)DT(0.004)DAEEERIPATPVVIPMK;AQPFGFIDS(0.966)DT(0.034)DAEEERIPATPVVIPMK 327.26 5.22E-96 1523020000 1165410 973560 1108300 1019590 1144000 918861 1145720 928780 971561 TRUE FALSE 1092469.068 1045643.395 1134589.399 1045754.406 1054154.855 1184121.254 973929.9223 1044740.227 809401.1926 1.349725054 1.291872813 1.401763933 1.292009964 1.302388561 1.462959611 1.203272161 1.290756966 1 19.62649545 0.531598577 0.848413094 0.998801264 1.342245188 0.712446042 0.066336704 0.771854869 0.874567899 0.060454794 0.019847305 3.400936921 -0.531598577 0.343443924 AQPFGFIDS(ph)DTDAEEERIPATPVVIPMKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AQPFGFIDSDTDAEEERIPATPVVIPMKK 29 2 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AQPFGFIDS(0.5)DT(0.5)DAEEERIPATPVVIPMKK;AQPFGFIDS(0.957)DT(0.043)DAEEERIPATPVVIPMKK 304.69 1.10E-81 593600000 645620 571390 637890 581330 769020 492180 667420 552780 827220 TRUE FALSE 605211.7967 613696.3101 653021.052 596247.912 708624.2713 634264.3761 567346.567 621795.7998 689151.638 0.8781983 0.890509833 0.947572372 0.86519117 1.028255949 0.92035532 0.8232536 0.902262674 1 19.39446194 AQPNHDPNTHHCLCGADADLIMLGLATHEPNFTIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQPNHDPNTHHCLCGADADLIMLGLATHEPNFTIIR 36 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 68.543 0.0016631 36577000 15593 25063 16215 12799 29219 19466 23412 23523 21773 FALSE TRUE 14617.06196 26918.6906 16599.62746 13127.44401 26924.2576 25085.5182 19901.58795 26459.89833 18138.94564 0.805838567 1.484027304 0.915137395 0.723715935 1.484334213 1.382964517 1.097174463 1.458734088 1 14.14680298 2.716127698 24.88756847 1.282611347 1.054647239 0.241877458 0.251945704 1402.428355 1555882.836 0.080381921 0.075839847 520.1489166 -2.716127698 -0.227964108 AQPSMS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AQPSMSPK 8 0 Q969S3 Q969S3 ZNF622 Zinc finger protein 622 1 AQPS(0.164)MS(0.836)PK;AQPS(0.066)MS(0.934)PK;AQPS(0.077)MS(0.923)PK;AQPS(0.004)MS(0.996)PK;AQPS(0.001)MS(0.999)PK;AQPS(0.271)MS(0.729)PK 128.03 0.0012071 1768380000 3403000 3311890 2193070 2079630 4343990 1223340 2453900 3532490 4637200 TRUE FALSE 3190012.305 3557105.782 2245090.656 2132996.827 4002830.548 1576498.399 2085960.476 3973529.152 3863221.363 0.825738938 0.920761574 0.581144709 0.552129072 1.036138024 0.408078712 0.53995365 1.028553318 1 21.88137292 1.222779077 24.80761199 1.014277102 0.690870896 0.328177272 0.189939402 300.6967874 472662.4767 0.17873884 0.04530922 16.70240756 -1.222779077 -0.323406205 AQPYDPNFYDETYDYGGFTMMFDDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 AQPYDPNFYDETYDYGGFTMMFDDRR 26 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;;;;;; 238.63 8.33E-45 3409068000 1295423.8 1623768 1577610.5 1560298 1780876.4 1409725.4 1690570 1535238.2 1802344 FALSE TRUE 1214345.537 1743993.472 1615032.166 1600337.888 1641013.551 1816690.238 1437084.723 1726916.069 1501521.143 0.808743548 1.161484459 1.075597353 1.065811092 1.092900729 1.209899872 0.957085906 1.150111057 1 20.51799336 4.747643135 24.92193476 1.089844376 0.808743397 0.584509944 0.07428507 798.2160821 2190212.997 0.016267872 0.201409598 55929.7831 -4.747643135 -0.281100979 AQQELVPPQQQAS(ph)PPQLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AQQELVPPQQQASPPQLPK 19 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 AQQELVPPQQQAS(1)PPQLPK;AQQELVPPQQQAS(1)PPQLPK;AQQELVPPQQQAS(1)PPQLPK;AQQELVPPQQQAS(1)PPQLPK 151.91 3.93E-08 724401000 1429790 1229350 1304780 1297840 1283630 1019880 1591930 1051230 1326290 TRUE FALSE 1340301.996 1320372.353 1335729.998 1331144.772 1182818.878 1314302.8 1353234.875 1182478.38 1104923.631 1.213026818 1.194989695 1.208888977 1.204739164 1.070498308 1.189496507 1.22473159 1.070190144 1 20.07551523 -5 0.17082464 0.269397695 1.224424128 0.588243354 0.050033543 95.14633186 0.899785925 23.38810284 0.175234437 1.00E-05 5 0.955026433 AQQEQAAHQASLRK ddPTM_SK-BR-3_Pertuzumab_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 68.944 0.031406 89896000 57178 120520 100030 100770 119420 83605 88221 78460 115400 FALSE TRUE 53599.33105 129443.4262 102402.7588 103355.9288 110041.2349 107740.4063 74993.08005 88255.90371 96138.99449 0.557519156 1.346419597 1.065153213 1.075067712 1.144605636 1.120673322 0.780048517 0.918003191 1 16.55283409 1.751294053 25 0.882449271 1.091642776 0.086134329 0.205586348 6.055386432 11907.35967 0.08689205 0.048185985 56.40194135 -1.751294053 0.209193504 AQQMHTGPVLDVCWSDDGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQQMHTGPVLDVCWSDDGSK 20 0 P78406;E9PQ57;E9PPG9;B0QZ36 P78406 RAE1 mRNA export factor 0 207.67 6.44E-22 141690000 280520 213820 249260 233010 241510 193590 310990 213810 279720 FALSE TRUE 262962.7539 229651.4553 255172.5649 238989.4311 222542.7788 249476.2903 264359.9366 240504.6492 233032.9249 1.128436053 0.985489305 1.095006489 1.025560792 0.954984275 1.070562413 1.134431697 1.032062955 1 17.83017428 2.025734617 24.99077604 1.07845065 1.035876071 0 0.060270382 495.2125302 480896.3019 0.021110355 0.01559025 106.1046989 -2.025734617 -0.042574579 AQQNNVEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 AQQNNVEHK 9 0 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ;;;;;; 173.32 5.55E-05 7428120000 10179860 7957500 8595000 8069200 8438290 6957590 9981280 7912240 7691610 FALSE TRUE 9542720.734 8546681.58 8798877.459 8276269.333 7775580.742 8966133.286 8484679.726 8900100.581 6407830.601 1.489227997 1.333787066 1.373144517 1.291586786 1.213449797 1.399246304 1.324111116 1.388941302 1 22.61140458 -1.844948336 2.473466963 0.856707787 1.346540648 0.699932075 0.072297219 9501463.824 5667543.644 8044110.54 0.016150596 0.01429064 1.844948336 0.489832861 AQQNNVEHKVETFSGVYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQQNNVEHKVETFSGVYK 18 1 P62081;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 274.81 2.86E-39 875180000 865240 722750 815760 867090 1056700 622030 1103100 754970 1620900 FALSE TRUE 811086.1729 776263.162 835110.2124 889340.9974 973711.0445 801599.9632 937700.3957 849229.6664 1350361.319 0.600643814 0.574855893 0.618434637 0.658594841 0.72107445 0.593618872 0.694407032 0.628890694 1 20.36491405 -5 0.230291349 2.975786415 0.59237053 0.878108712 0.042897489 49.69578797 0.497386353 45.74360927 0.070267474 1.00E-05 5 -2.383415885 AQQQEEQGS(ph)VNDVKEEEKEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQQQEEQGSVNDVKEEEKEEK 21 2 Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2 Q9Y4W2-3 LAS1L Ribosomal biogenesis protein LAS1L 1 AQQQEEQGS(1)VNDVKEEEKEEK 197.08 4.85E-22 207890000 511300 118730 212400 193310 207960 139750 312730 162200 256190 TRUE FALSE 479298.6457 127520.8927 217438.2283 198270.6619 191627.6605 180093.5563 265839.0397 182451.027 213430.2339 2.24569236 0.597482795 1.018778944 0.928971768 0.897846837 0.843805271 1.245554741 0.854850898 1 17.70340503 4.747564367 24.91979542 0.929987927 2.24569307 0.867640835 0.162287426 413.6941435 1144961.263 0.039966458 0.490534917 55919.63999 -4.747564367 1.315705143 AQREEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQREEEAR 8 1 P50502;Q8NFI4 P50502 ST13;ST13P5 Hsc70-interacting protein;Putative protein FAM10A5 0 115.71 0.0045811 0 26474 47771 38394 38203 59880 28263 32132 36146 53248 FALSE TRUE 24817.0396 51308.01455 39304.72381 39183.35366 55177.26634 36422.06929 27314.1049 40658.90767 44360.5648 0.559439216 1.156613194 0.88602848 0.883292488 1.243835974 0.821046113 0.615729421 0.91655523 1 15.43699011 2.022587242 24.99913077 0.780645404 0.969322001 0.028277806 0.207247543 396.9360462 439319.4103 0.070967566 0.052409773 105.3385272 -2.022587242 0.188676597 AQRPGAHAEDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AQRPGAHAEDAR 12 1 E7EMB8;Q99952-2;Q99952 E7EMB8 PTPN18 Tyrosine-protein phosphatase non-receptor type 18 0 ; 113.77 0.00067906 121249000 105538 150955 121723 125277 142529 102574 145888 123288 115073 FALSE TRUE 98932.56497 162131.8653 124610.327 128491.8199 131335.3473 132185.4487 124013.4488 138680.7782 95866.5729 1.031981868 1.691224171 1.29983083 1.340319321 1.369980623 1.37884817 1.293604695 1.446602022 1 16.54874024 -3.156888341 0.355650551 1.29E-15 1.390916859 0.298839368 0.164320212 118.7942743 3.305918271 88.98860422 0.113084134 0.000696806 3.156888341 1.390916859 AQS(ph)LLSTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQSLLSTDR 9 0 O00231;O00231-2;J3QRY4 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 1 AQS(0.92)LLS(0.079)T(0.001)DR 189.41 0.0012414 0 275370 242680 228880 223230 229300 178440 272320 182160 303400 TRUE FALSE 258135.0832 260648.2797 234309.1417 228958.4597 211291.703 229952.7313 231488.1441 204903.077 252760.58 1.021263218 1.03120621 0.927000333 0.905831359 0.835936138 0.909765009 0.915839583 0.810660733 1 17.94741196 3.782528615 1.677430471 0.89195166 1.028764207 0.526008263 0.05014625 0.261566274 1.434737598 0.013264046 0.031648964 6060.781329 -3.782528615 0.136812547 AQS(ph)PGAVEEILDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AQSPGAVEEILDR 13 0 H7BXT7;A0A0C4DH16;B8ZZS0;Q9NYM9;E9PHY4 H7BXT7 BET1L BET1-like protein 1 AQS(1)PGAVEEILDR;AQS(1)PGAVEEILDR;AQS(1)PGAVEEILDR;AQS(1)PGAVEEILDR 232.01 1.54E-12 729760000 1155917 968995 1198189 1257871 1021530 1179021 1854118 1102976 1378512 TRUE FALSE 1083570.218 1040740.398 1226610.609 1290150.099 941303.1545 1519385.223 1576110.219 1240684.982 1148429.442 0.943523545 0.90622929 1.068076596 1.123403888 0.819643872 1.323011382 1.372404922 1.080331918 1 20.13123079 2.226862237 24.99996941 1.244268787 0.983134222 0.366611523 0.13754401 191.1088284 408405.4379 0.048553249 0.036153144 168.6018119 -2.226862237 -0.261134565 AQS(ph)PSYVISTGVSPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AQSPSYVISTGVSPSR 16 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 AQS(0.956)PS(0.044)YVISTGVSPSR;AQS(0.979)PS(0.021)YVISTGVSPSR 212.76 1.26E-12 191370000 218660 195882 207230 186946 212890 158134 243290 179094 340720 TRUE FALSE 204974.4609 210385.3071 212145.5935 191743.3509 196170.4782 203784.7187 206810.9231 201454.2801 283851.6309 0.722118313 0.741180547 0.747381978 0.675505546 0.69110217 0.71792689 0.728588109 0.709716832 1 18.11477751 -1.407760762 3.427778877 1.002601154 0.720311585 0.944092429 0.021650742 1142183.871 633775.5355 21271.16162 0.005535995 0.039105626 1.407760762 -0.282289569 AQS(ph)PVSGPNVAHLTDGATLNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQSPVSGPNVAHLTDGATLNDR 22 0 Q5THJ4-2;Q5THJ4 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 AQS(0.992)PVS(0.008)GPNVAHLTDGATLNDR 209.72 3.45E-23 851980000 266460 381310 323780 397960 350410 272080 409510 313420 279320 TRUE FALSE 249782.7442 409542.5892 331460.2145 408172.3273 322890.2121 350625.0792 348107.7772 352551.1769 232699.6875 1.073412461 1.759961921 1.424411945 1.75407338 1.387583351 1.506770735 1.495952921 1.515047917 1 17.82810975 -1.800020321 0.595280415 0.607273546 1.516610326 0.380825445 0.193637079 90.34542419 10.0354264 50.47635295 0.067957731 0.01584819 1.800020321 0.90933678 AQS(ph)TDS(ph)LGTSGSLQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AQSTDSLGTSGSLQSK 16 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 2 AQS(0.999)T(0.001)DS(0.999)LGT(0.001)SGSLQSK;AQS(0.987)T(0.013)DS(1)LGTSGSLQSK 294.39 1.84E-45 387910000 1977530 1380910 1526810 1509320 1279710 1116580 2291000 1369800 1389760 TRUE FALSE 1853759.927 1483154.013 1563026.654 1548051.706 1179206.739 1438918.52 1947485.819 1540822.545 1157800.078 1.601105375 1.281010463 1.349997019 1.337063053 1.018489082 1.242803958 1.68205708 1.330819176 1 20.14295473 4.74314627 23.78151707 1.316577417 1.601105591 0.196461217 0.191804356 450.4001254 2335636.135 0.046050092 0.361744432 55353.65087 -4.74314627 0.284528174 AQS(ph)TDSLGTSGSLQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQSTDSLGTSGSLQSK 16 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 AQS(0.749)T(0.008)DS(0.243)LGTSGSLQSK 289.7 1.78E-45 128770000 464530 317630 375410 341740 315460 297570 436660 304800 393950 TRUE FALSE 435455.8965 341147.6557 384314.9025 350509.627 290685.0441 383473.6284 371186.8868 342854.9509 328197.2 1.326811736 1.039459373 1.170987755 1.067984818 0.885702389 1.168424436 1.130987366 1.044661414 1 18.3242034 4.744168283 24.14980991 1.077949908 1.326811911 0.478353185 0.085230996 355.4251871 1530586.609 0.019732576 0.171698087 55484.06642 -4.744168283 0.248862003 AQS(ph)YDIQAWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AQSYDIQAWK 10 0 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 AQS(1)YDIQAWK;AQS(1)YDIQAWK;AQS(1)YDIQAWK 188.88 1.12E-06 748840000 1620000 1411630 1263570 1202780 1369420 650642 1156470 903560 1344720 TRUE FALSE 1518607.092 1516148.554 1293542.477 1233645.371 1261871.277 838471.7831 983068.0596 1016371.455 1120277.545 1.35556327 1.353368691 1.154662506 1.101196196 1.126391655 0.748450049 0.877521882 0.90724969 1 20.09542477 3.112196253 0.829641404 0.87026314 1.358303853 0.792230659 0.089242905 0.25054342 0.381783938 0.04656145 0.068682908 1294.780808 -3.112196253 0.488040712 AQS(ph)YPDNHQEFSDYDNPIFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AQSYPDNHQEFSDYDNPIFEK 21 0 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 1 AQS(1)YPDNHQEFSDYDNPIFEK;AQS(1)YPDNHQEFSDYDNPIFEK;AQS(1)YPDNHQEFSDYDNPIFEK 329.48 3.08E-80 763320000 760180 665260 691250 687850 812980 577270 917230 645560 1076660 TRUE FALSE 712601.6908 714516.5426 707646.7764 705501.3955 749131.8302 743918.4778 779699.8766 726159.5871 896958.4905 0.794464513 0.796599341 0.788940385 0.786548545 0.835191191 0.829378935 0.869270858 0.809579925 1 19.7746817 -5 0.167401357 1.737905832 0.766394663 0.894372659 0.020742956 37.19921698 0.348968723 9.058637679 0.074463935 1.00E-05 5 -0.971511169 AQSDGIWGEHEIDYILLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AQSDGIWGEHEIDYILLVR 19 0 Q13907;Q13907-2 Q13907 IDI1 Isopentenyl-diphosphate Delta-isomerase 1 0 ;; 206.74 3.50E-16 403310000 281346 338486 322822 313105 324693 329892 353571 297570 333619 FALSE TRUE 263737.0561 363547.8556 330479.4903 321139.8044 299192.9215 425126.4651 300556.3109 334722.2695 277935.8336 0.948913469 1.308028011 1.189049595 1.155445846 1.076481998 1.529584939 1.081387409 1.204314914 1 18.08439232 0.494607839 1.582999066 1.00026886 1.202937988 0.117862429 0.154752265 5.495483949 15.11144762 0.131957296 0.037770849 3.123257844 -0.494607839 0.202669128 AQSEGRPCEYNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AQSEGRPCEYNSR 13 1 O00622 O00622 CYR61 Protein CYR61 0 ; 142.95 3.70E-05 210192000 163153 220611 198277 205659 176120 121630 148973 127628 167242 FALSE TRUE 152941.545 236945.268 202980.2241 210936.5581 162288.2456 156742.6065 126635.8816 143562.6367 139328.2298 1.097706798 1.700626416 1.456849229 1.513954196 1.164790839 1.124988143 0.908903256 1.030391594 1 17.08812807 2.492523872 1.793930301 0.984573861 1.493504881 0.610774049 0.158600628 0.19304366 1.258575705 0.063558268 0.051198556 310.8306752 -2.492523872 0.508931019 AQSELAAHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AQSELAAHQK 10 0 P25786;P25786-2;F5GX11;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ;;;; 109.39 0.0020252 2314140000 2671630 3001350 2499240 2641420 3419460 1683390 2715410 2811490 2365220 FALSE TRUE 2504417.447 3223573.077 2558523.153 2709203.309 3150909.405 2169357.365 2308259.479 3162510.715 1970449.502 1.270987886 1.635958229 1.298446446 1.374916386 1.59908153 1.100945425 1.171438028 1.604969177 1 20.91009335 2.232783526 24.99981283 1.222223274 1.441650085 0.239744575 0.191424999 197.0381533 852655.5818 0.065523837 0.049698332 170.9163171 -2.232783526 0.21942681 AQSGSDS(ph)SPEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQSGSDSSPEPK 12 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AQSGS(0.001)DS(0.499)S(0.499)PEPK 119.32 0.00055676 212800000 537110 346790 449860 434730 506750 333910 484460 376050 529590 TRUE FALSE 503493.2439 372466.6924 460530.8916 445885.9078 466951.8991 430304.3964 411819.7205 423000.6703 441198.0077 1.141195642 0.844216624 1.043819064 1.010625388 1.058372638 0.97530902 0.933412466 0.958754715 1 18.75106675 -0.667201052 6.736635703 0.999989711 0.984075457 0 0.079809665 0 0 0.071467451 0.01684504 0.215178536 0.667201052 -0.015914254 AQSGSDSS(ph)PEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQSGSDSSPEPK 12 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AQSGSDS(0.134)S(0.866)PEPK 233.21 5.70E-16 187810000 839480 539270 701390 692060 781560 519430 823750 613200 828640 TRUE FALSE 786938.4453 579198.1119 718027.302 709819.4313 720179.4303 669381.0088 700236.3348 689759.3698 690334.6308 1.139937662 0.839010657 1.040114852 1.028225153 1.043232366 0.969647152 1.01434334 0.999166693 1 19.39693633 3.731616579 24.95100613 1.013306741 0.959454387 0 0.075426143 457.3673758 2538561.021 0.017611529 0.030404868 5390.3452 -3.731616579 -0.053852354 AQSLVISPPAPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQSLVISPPAPSPR 14 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 AQSLVIS(0.164)PPAPS(0.836)PR 112.28 0.00063199 382540000 168150 149250 152380 134530 162210 122840 159680 107590 145710 TRUE FALSE 157625.7917 160300.6253 155994.5256 137982.2676 149470.6809 158301.9139 135737.4664 121022.8483 121390.0597 1.298506583 1.320541614 1.285068365 1.136685062 1.231325541 1.304076415 1.1181926 0.996974947 1 16.88929076 1.507062386 2.808692286 0.999680603 1.266008473 0.814761548 0.052495625 0.10684219 1.740942315 0.042249776 0.015010397 32.14122209 -1.507062386 0.26632787 AQSNGSGNGS(ph)DSEMDTSSLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AQSNGSGNGSDSEMDTSSLER 21 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 AQSNGSGNGS(1)DSEMDTSSLER;AQSNGSGNGS(1)DSEMDTSSLER;AQSNGSGNGS(0.964)DS(0.036)EMDTSSLER 466.93 1.19E-223 251930000 274908 349506 342537 331967 341977 343846 395367 320088 373088 TRUE FALSE 257701.999 375383.7879 350662.1394 340485.8352 315119.5059 443108.7583 336085.3888 360051.6914 310817.2026 0.82911112 1.207731698 1.128194117 1.095453638 1.013841909 1.425624948 1.081295971 1.158403359 1 18.24570683 4.745123583 24.32987582 1.149489871 0.829110906 0.39629981 0.119486669 491.9496965 1823657.06 0.025630746 0.243734508 55606.24683 -4.745123583 -0.320378966 AQSTDS(ph)LGTSGSLQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AQSTDSLGTSGSLQSK 16 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 AQSTDS(0.997)LGT(0.002)SGSLQSK;AQSTDS(0.686)LGT(0.157)S(0.157)GSLQSK;AQSTDS(0.998)LGT(0.002)SGSLQSK;AQSTDS(1)LGTSGSLQSK 311.9 1.15E-57 781270000 1869690 1500780 1731170 1601030 1764710 1333120 2205940 1649220 2019920 TRUE FALSE 1752669.44 1611899.313 1772234.17 1642115.14 1626116.795 1717970.103 1875179.776 1855128.747 1682782.303 1.041530706 0.957877504 1.053157124 0.975833379 0.966326299 1.020910488 1.114332955 1.102417552 1 20.68241712 1.910441236 5.762053906 1.08232956 0.999213455 0.375270018 0.042516127 0.197480545 9.974410642 0.017341919 0.010494084 81.36567578 -1.910441236 -0.083116105 AQT(ph)PPGPSLSGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AQTPPGPSLSGSK 13 0 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AQT(0.999)PPGPS(0.001)LSGSK;AQT(0.938)PPGPS(0.06)LS(0.002)GSK;AQT(0.964)PPGPS(0.036)LSGSK;AQT(0.999)PPGPS(0.001)LSGSK;AQT(0.978)PPGPS(0.022)LSGSK;AQT(1)PPGPSLSGSK 152.11 0.0005037 6745710000 3939280 2514900 2947710 2755040 2640090 2415340 3863450 2521460 3078710 TRUE FALSE 3692727.497 2701105.813 3017631.073 2825738.991 2432747.981 3112609.448 3284161.539 2836269.831 2564853.412 1.439742123 1.05312288 1.176531594 1.10171559 0.948493965 1.213562317 1.280448046 1.105821416 1 21.29044494 4.747209634 24.53474388 1.127841209 1.43974233 0.516029509 0.099032417 786.8867919 2232104.678 0.024193685 0.280774741 55873.98335 -4.747209634 0.311901122 AQT(ph)PPGPSLSGSKS(ph)PCPQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AQTPPGPSLSGSKSPCPQEK 20 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AQT(0.985)PPGPS(0.016)LS(0.025)GS(0.055)KS(0.919)PCPQEK;AQT(0.997)PPGPS(0.002)LS(0.002)GS(0.032)KS(0.967)PCPQEK 108.02 0.00050007 8362600000 6070600 3121200 3981900 3822500 3983700 3041700 5200200 3285700 4639500 TRUE FALSE 5690651.982 3352296.896 4076352.548 3920591.821 3670836.271 3919789.412 4420478.286 3695926.878 3865137.478 1.472302606 0.867316341 1.054646199 1.014347315 0.949729807 1.014139713 1.143679445 0.956221324 1 21.8820883 4.749352519 24.967979 1.007155795 1.472302874 0.80973619 0.071874043 714.557048 1653156.217 0.017925201 0.265108534 56150.35666 -4.749352519 0.465147079 AQTAPNKDVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQTAPNKDVQR 11 1 P49588;P49588-2;H3BPK7 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 84.718 0.014367 111310000 106260 212670 131470 144630 264810 85083 176820 189220 348660 FALSE TRUE 99609.37628 228416.3081 134588.5305 148341.4507 244012.8908 109645.0809 150307.4825 212844.5335 290466.3936 0.342929091 0.786377747 0.463353192 0.510700907 0.840072711 0.377479403 0.517469442 0.73276819 1 18.14801173 0.954466715 3.815934691 0.999367045 0.562354073 0.459893829 0.15796547 0.211670413 8.539480325 0.139217437 0.035742077 9.004647464 -0.954466715 -0.437012972 AQTAPTKT(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQTAPTKTSPR 11 1 Q14669-3;Q14669;Q14669-2;Q14669-4 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 AQTAPT(0.021)KT(0.668)S(0.311)PR 85.42 0.024621 346630000 662390 608750 602320 639000 651640 495720 759910 551190 760720 TRUE FALSE 620932.1923 653822.4834 616607.3148 655397.8218 600462.823 638826.3167 645968.5502 620007.2848 633750.9176 0.979773244 1.031671064 0.97294899 1.034156801 0.947474483 1.008008508 1.019278288 0.978313826 1 19.27355641 -1.028764964 3.400099177 1.000000337 0.999182655 0 0.027758065 56051739988 16034471958 193327.0342 0.005812067 0.093591204 1.028764964 -0.000817681 AQTAPTKTS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AQTAPTKTSPR 11 1 Q14669-3;Q14669;Q14669-2;Q14669-4 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 AQTAPTKT(0.001)S(0.999)PR;AQTAPTKT(0.102)S(0.897)PR;AQTAPT(0.002)KT(0.011)S(0.987)PR;AQTAPT(0.004)KT(0.018)S(0.978)PR;AQT(0.013)APT(0.042)KT(0.129)S(0.816)PR 95.264 0.0047767 3370830000 4975270 4706650 4731970 4672660 4813437 3781275 5827370 4129960 5491890 TRUE FALSE 4663876.732 5055135.263 4844214.563 4792568.366 4435409.074 4872867.709 4953609.967 4645594.597 4575258.08 1.019369104 1.104885271 1.058784986 1.047496837 0.969433636 1.065047616 1.082695201 1.015373235 1 22.12542169 3.303346759 3.278768651 1.036712532 1.071737142 0.101830346 0.038275645 0.483374063 10.43032378 0.011161169 0.015287042 2010.6976 -3.303346759 0.03502461 AQTLPTSVVTITSESS(ph)PGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AQTLPTSVVTITSESSPGKR 20 1 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 AQTLPTSVVTITSES(0.036)S(0.964)PGKR;AQTLPTSVVTITSES(0.295)S(0.705)PGKR;AQTLPTSVVTITS(0.008)ES(0.256)S(0.736)PGKR;AQTLPTSVVTITSES(0.3)S(0.7)PGKR;AQTLPTSVVTITS(0.007)ES(0.178)S(0.815)PGKR;AQTLPTSVVTITSES(0.007)S(0.992)PGKR 283.44 4.12E-45 3404760000 2302960 1545060 1754800 1778960 1980650 1466300 2405840 1762600 2223990 TRUE FALSE 2158821.845 1659457.85 1796424.685 1824611.125 1825097.739 1889597.007 2045106.627 1982664.49 1852791.701 1.165172449 0.895652678 0.969577251 0.984790208 0.985052846 1.019864783 1.103797381 1.070095731 1 20.82126927 2.008970541 4.044116162 1.068612845 0.981554989 0.080769297 0.072491354 0.305382616 11.35606889 0.029620156 0.019028959 102.0870233 -2.008970541 -0.087057856 AQTPPGPSLSGSKS(ph)PCPQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AQTPPGPSLSGSKSPCPQEK 20 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AQTPPGPSLSGSKS(1)PCPQEK;AQTPPGPSLSGSKS(1)PCPQEK;AQTPPGPSLSGS(0.002)KS(0.998)PCPQEK 230.77 8.79E-26 5205090000 5116740 3037300 3757960 3785940 3925070 2765820 4889260 3296670 4914230 TRUE FALSE 4796492.377 3262184.852 3847100.586 3883093.63 3616810.835 3564267.335 4156160.853 3708266.506 4094013.266 1.171586916 0.796818339 0.939689331 0.948480959 0.883438963 0.870604735 1.015180114 0.905777843 1 21.96508435 1.73566479 24.99998522 0.972098973 0.918203469 0.013589759 0.100456208 1.079928253 9176.277106 0.042392293 0.023508845 54.40825405 -1.73566479 -0.053895504 AQVADVVVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AQVADVVVSR 10 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 159.83 1.76E-05 1673540000 1568010 1787520 1745450 1881660 1919070 1553370 2082960 1669560 1809870 FALSE TRUE 1469871.053 1919869.841 1786852.898 1929946.581 1768353.983 2001802.702 1770639.485 1878008.241 1507791.005 0.974850658 1.273299704 1.185079956 1.279982819 1.172811071 1.327639372 1.174326866 1.245536175 1 20.52400504 -0.926142348 4.60038938 0.999997559 1.212660805 0.305667325 0.095964144 2.07E-06 4.83E-07 0.079997829 0.018855453 0.118538015 0.926142348 0.212663245 AQVARPGGDTIFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AQVARPGGDTIFGK 14 1 P49773;D6REP8;D6RE99;D6RD60;D6RC06 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ; 162 4.11E-06 3066400000 3466900 3802400 3596500 3639900 4098300 2999000 4520700 3578900 5427200 FALSE TRUE 3249912.918 4083933.652 3681810.678 3733305.996 3776436.05 3864762.615 3842863.003 4025733.543 4521365.259 0.718790173 0.903252318 0.814313922 0.825703252 0.835242418 0.854777793 0.849934209 0.890380076 1 22.10832704 -4.999999995 0.181109948 1.674422504 0.807052557 0.61754976 0.044254357 91.72851256 0.885522853 22.1261783 0.12560461 1.00E-05 4.999999995 -0.867369947 AQVLATIHGHAGAFPAAGDAGEGAPGGGS(ph)SPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQVLATIHGHAGAFPAAGDAGEGAPGGGSSPER 33 0 Q86WR7;D3DRR9 Q86WR7 PROSER2;C10orf47 Proline and serine-rich protein 2 1 AQVLATIHGHAGAFPAAGDAGEGAPGGGS(0.557)S(0.443)PER 66.378 0.0081815 279130000 52533 44262 57503 59553 59801 46314 66357 49352 84203 TRUE FALSE 49245.0533 47539.20453 58866.99831 61081.2308 55104.47069 59684.09996 56407.38388 55513.70584 70148.97533 0.702006737 0.677689222 0.839171179 0.870735895 0.785534934 0.85081927 0.804108451 0.791368735 1 16.09813441 -5 0.030148779 2.162749158 1.28E-11 0.675941107 0.051038258 914.4648596 2.075549232 116.3257642 46.95497473 1.00E-05 5 -2.162749158 AQVLATIHGHAGAFPAAGDAGEGAPGGGSS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AQVLATIHGHAGAFPAAGDAGEGAPGGGSSPER 33 0 Q86WR7;D3DRR9 Q86WR7 PROSER2;C10orf47 Proline and serine-rich protein 2 1 AQVLATIHGHAGAFPAAGDAGEGAPGGGS(0.206)S(0.794)PER;AQVLATIHGHAGAFPAAGDAGEGAPGGGS(0.281)S(0.719)PER;AQVLATIHGHAGAFPAAGDAGEGAPGGGS(0.181)S(0.819)PER;AQVLATIHGHAGAFPAAGDAGEGAPGGGS(0.165)S(0.835)PER 146.58 5.28E-10 1912020000 529650 651300 607241 559130 728270 546674 670050 613600 650860 TRUE FALSE 496500.152 699522.9297 621645.0433 573478.2224 671074.6119 704489.9093 569582.2229 690209.3107 542227.2613 0.915668 1.290091774 1.14646586 1.057634434 1.237626102 1.299252103 1.050449256 1.272915178 1 19.04853812 -1.060887138 4.348245402 0.999988057 1.166395635 0.137251474 0.1237856 1.47E-05 3.17E-06 0.10661771 0.025127963 0.086918628 1.060887138 0.166407578 AQVLVEDISDILEEHAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AQVLVEDISDILEEHAEK 18 0 Q5VV41;Q5VV41-2;B0QZD3;B0QZD4 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 0 160.67 4.00E-11 269010000 61593 55171 60065 54110 71005 54370 74876 51550 66381 FALSE TRUE 57738.00408 59255.91825 61489.77016 55498.55421 65428.55372 70065.73638 63649.03891 57986.13098 55301.58226 1.044057 1.071504934 1.11189893 1.003561778 1.183122635 1.266975257 1.150944264 1.048543796 1 15.75503314 2.723338713 24.91907347 1.151476745 1.069071081 0.137838747 0.077916889 1191.583427 1950683.877 0.023905869 0.022629729 528.8575547 -2.723338713 -0.082405664 AQVWLEQVCAHLGLGVQEPHPGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AQVWLEQVCAHLGLGVQEPHPGER 24 0 Q6XQN6-3;Q6XQN6;Q6XQN6-2;C9J8U2;G5E977 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 0 ;; 295.99 3.36E-62 537867000 319952 396201 382216 330389 401948 335320 399395 332014 374072 FALSE TRUE 299926.7755 425536.1343 391282.344 338867.3411 370380.6255 432121.4405 339509.4276 373466.6788 311636.9666 0.962423613 1.365486704 1.25557102 1.087378512 1.188500291 1.386618042 1.089438879 1.19840301 1 18.24950685 0.655624025 0.986363884 1.001085292 1.221046775 0.157241004 0.12943474 1.764616096 2.888000395 0.116296665 0.037571678 4.525056696 -0.655624025 0.219961483 AQYDELAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 AQYDELAR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;; 255.1 1.21E-12 58594180000 31729050 38879540 34765470 33530920 39016680 31127300 38216860 34002430 48128280 FALSE TRUE 29743185.4 41758221.6 35590123.37 34391380.17 35952467.34 40113246.2 32486596.63 38247708.23 40095359.15 0.741811173 1.041472691 0.887636977 0.857739671 0.896674032 1.000446113 0.810233337 0.953918584 1 25.25693193 -1.148005673 7.110879947 1.000000082 0.90660536 0.111729907 0.087257475 1.03E-07 1.23E-08 0.07683006 0.018109003 0.071120422 1.148005673 -0.093394722 ARAEEAEAQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ARAEEAEAQKR 11 2 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 82.362 0.010769 128420000 139420 142630 108930 143510 148930 75480 162090 144360 166930 FALSE TRUE 130693.9511 153190.4736 111513.871 147192.7096 137233.6386 97269.85068 137786.1093 162383.6638 139068.3046 0.939782443 1.101548437 0.801864029 1.058420249 0.986807447 0.699439394 0.990780104 1.167654012 1 17.08543412 1.46856025 25 1.082291588 0.934836798 0.209427366 0.121538011 2.631279494 7688.527454 0.062695474 0.029023981 29.41441732 -1.46856025 -0.147454789 ARAPS(ph)PGDYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ARAPSPGDYK 10 1 P55198 P55198 MLLT6 Protein AF-17 1 ARAPS(0.984)PGDY(0.016)K 54.402 0.083174 193880000 404140 318160 307910 324220 365860 210650 361310 352570 449670 TRUE FALSE 378845.5988 341716.8974 315213.7706 332540.0341 337126.8314 271461.2354 307134.9197 396589.1406 374617.172 1.011287328 0.912176277 0.841429049 0.887679634 0.899923593 0.724636391 0.81986343 1.058651792 1 18.51505751 -1.248566858 7.52440958 1.000000268 0.879221524 0.091301426 0.094322701 4.05E-07 4.05E-08 0.087328928 0.02058358 0.056420008 1.248566858 -0.120778744 ARDDLITDLLNEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ARDDLITDLLNEAK 14 1 P36543;C9J8H1;P36543-2 P36543 ATP6V1E1 V-type proton ATPase subunit E 1 0 ;;;;; 294 1.34E-43 1321366000 3925280 3087190 3385050 3307110 3650210 2734030 4256170 3090370 4681360 FALSE TRUE 3679603.732 3315768.76 3465344.985 3391976.042 3363537.231 3523300.078 3617996.821 3476209.497 3900010.773 0.94348553 0.850194769 0.888547542 0.869735044 0.862443061 0.903407781 0.92768893 0.891333306 1 21.89504668 0.376837272 0.538996444 1.005245361 0.878839963 0.586796343 0.028370994 1.437098524 0.676187963 0.045144491 0.012468409 2.381426995 -0.376837272 -0.126405398 AREEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AREEAER 7 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 107.01 0.0069077 226460000 83246 109396 89677 98537 119706 69183 96853 91854 97945 FALSE TRUE 78035.78146 117495.7937 91804.18079 101065.6262 110304.7736 89155.00901 82330.79179 103322.1741 81597.34675 0.956351947 1.439946252 1.125087818 1.238589614 1.351818141 1.092621422 1.008988589 1.266244286 1 16.31623462 2.134822225 9.296556979 1.082522775 1.239367193 0.158081868 0.146071725 0.420950808 34.52046118 0.050068109 0.036969193 136.4024669 -2.134822225 0.156844419 AREEEEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AREEEEQK 8 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 109.29 0.0060195 0 139640 82989 117260 126930 102350 91920 118520 101690 96103 FALSE TRUE 130900.1817 89133.59191 120041.4626 130187.2387 94311.84386 118455.8118 100749.0263 114386.2203 80062.78845 1.634969056 1.113296122 1.499341516 1.626064258 1.177973509 1.479536425 1.258375186 1.428706426 1 16.28884424 -2.542272347 0.373202813 0.371956314 1.394450298 0.340728102 0.175129809 81.54747695 3.402145814 41.53317701 0.11316093 0.002868981 2.542272347 1.022493984 AREEEEQKEGGDGAAGDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AREEEEQKEGGDGAAGDPK 19 2 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ; 120.23 2.48E-05 1810640000 4695500 1990590 2972260 2693620 2836010 1867520 3490830 2220280 3807150 FALSE TRUE 4401617.037 2137975.355 3042763.411 2762742.849 2613281.215 2406642.707 2967412.449 2497486.845 3171712.07 1.387773209 0.674076117 0.959344147 0.871057268 0.823933938 0.758783475 0.935586959 0.787425463 1 21.59683038 4.750239353 24.83133511 0.847910019 1.387773563 0.747994176 0.097847387 769.6589836 1636416.121 0.021317182 0.344787712 56265.13342 -4.750239353 0.539863544 AREESWGPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AREESWGPPR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 160.98 6.58E-06 881070000 536890 582010 477470 520910 607510 443550 591940 521070 605560 FALSE TRUE 503287.0133 625102.626 488795.8139 534277.4325 559798.6152 571595.6846 503184.0923 586126.7365 504488.1239 0.99761915 1.239082936 0.96889459 1.059048582 1.109636855 1.133021091 0.997415139 1.161824647 1 18.94446078 1.001360789 0.008351173 6.22E-07 2.123439572 0.028775105 0.085766803 6832.233428 38.49494461 4943.888243 4839.2802 10.03138246 -1.001360789 2.123438949 AREETDKEEPASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AREETDKEEPASK 13 2 P05455 P05455 SSB Lupus La protein 0 ;;;; 219.84 1.23E-11 4745010000 7295720 4203190 5446250 5263230 5856770 3793260 7299590 4790520 8139370 FALSE TRUE 6839093.908 4514398.561 5575437.622 5398293.392 5396802.909 4888312.584 6205084.246 5388626.967 6780856.565 1.008588494 0.665756386 0.822232054 0.796107887 0.79588808 0.72089898 0.915088556 0.794682341 1 22.6930361 0.416082635 0.671217034 1.003455421 0.791244071 0.248973131 0.095922897 2.372189904 1.658664634 0.108517624 0.032961784 2.606649479 -0.416082635 -0.21221135 AREGSEEDLDALEHMFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AREGSEEDLDALEHMFR 17 1 P31944 P31944 CASP14 "Caspase-14;Caspase-14 subunit p17, mature form;Caspase-14 subunit p10, mature form;Caspase-14 subunit p20, intermediate form;Caspase-14 subunit p8, intermediate form" 0 ; 176.21 6.81E-10 48711000 50683 75950 57122 53444 99211 38513 57994 64493 54641 FALSE TRUE 47510.8415 81573.41703 58476.96081 54815.46352 91419.36826 49631.07789 49298.33809 72545.09302 45521.06411 1.043711135 1.791992754 1.284613222 1.204177991 2.008287154 1.090288175 1.082978596 1.593659868 1 15.47424666 0.795383832 0.418238949 0.989048812 1.47011737 0.088281038 0.328983784 3.185124832 1.332076598 0.51445782 0.22725353 6.242863399 -0.795383832 0.481068557 ARENIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 134.08 0.0029266 2429810000 2526760 2479120 1932780 2081120 2930290 1565590 2871960 2669280 3541890 FALSE TRUE 2368614.602 2662676.624 1978626.454 2134525.063 2700156.844 2017550.418 2441336.26 3002545.484 2950725.678 0.80272274 0.902380267 0.67055588 0.723389869 0.915082301 0.683747199 0.827368087 1.017561716 1 21.49263837 1.293860546 4.568763749 1.011537136 0.784833274 0.564436503 0.080799024 0.139573499 5.39970571 0.059989176 0.019579634 19.67254495 -1.293860546 -0.226703862 AREQAEAEVASLNR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 290.39 1.69E-43 1453030000 962470 1246150 1040540 1112810 1296760 888650 1242320 1046070 1264590 FALSE TRUE 902230.7208 1338416.243 1065222.1 1141366.589 1194917.7 1145188.829 1056045.649 1176674.142 1053521.759 0.856394956 1.270421072 1.011105932 1.083382074 1.134212644 1.087010134 1.002395669 1.116895908 1 20.00678868 0.715398098 0.520893629 1.000039245 1.091412335 0.007401942 0.107616447 4.458350382 2.576907954 0.128480508 0.050589641 5.192758175 -0.715398098 0.091373091 ARFEELCSDLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 203.97 1.08E-07 3510460000 2612930 4120580 1861070 1852120 4691470 1425045 2550240 4747090 5323520 FALSE TRUE 2449391.376 4425672.031 1905215.459 1899648.535 4323020.871 1836432.358 2167855.187 5339774.636 4434990.121 0.552287899 0.99789896 0.429587306 0.428332078 0.974753213 0.414078117 0.488807219 1.204010492 1 22.08049946 1.236316694 24.99997965 1.102005417 0.621784565 0.46597434 0.217786253 54.24633635 604299.6586 0.173997605 0.051588246 17.23124643 -1.236316694 -0.480220852 ARFEELNADLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 ARFEELNADLFR 12 1 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 ;;;;;;;;; 225.44 1.61E-11 19257905000 10620648 16262457 8337639 8280553 17009973 5669898 9987277 17808099 20077690 FALSE TRUE 9955920.6 17466546.24 8535411.734 8493046.009 15674078.34 7306705.509 8489777.531 20031479.36 16726593.83 0.595215063 1.044238081 0.51028989 0.507757054 0.937075324 0.436831646 0.507561648 1.197582697 1 23.99564035 1.234229605 24.99999323 1.098791513 0.660684753 0.461537712 0.201900216 108.5364365 626467.1915 0.172482301 0.04899201 17.14863691 -1.234229605 -0.43810676 ARGDS(ph)EALDEES ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 218.07 9.25E-11 4752220000 3908000 4299750 4002180 4104710 4543620 3365150 4302850 3720490 5127560 TRUE FALSE 3663405.256 4618107.964 4097113.6 4210043.808 4186782.413 4336614.176 3657677.588 4185001.366 4271737.111 0.857591458 1.081084309 0.959121194 0.985557795 0.980112377 1.015187514 0.856250629 0.97969544 1 22.02639143 1.777459215 25 0.929984431 0.989317349 0.027150627 0.066885367 94.38979047 60688.05117 0.027985424 0.015542399 59.90446793 -1.777459215 0.059332918 ARHDS(ph)PDLAPNVTYSLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ARHDSPDLAPNVTYSLPR 18 1 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 ARHDS(1)PDLAPNVTYSLPR;ARHDS(1)PDLAPNVTYSLPR;ARHDS(1)PDLAPNVTYSLPR;ARHDS(1)PDLAPNVTYSLPR;ARHDS(1)PDLAPNVTYSLPR;ARHDS(1)PDLAPNVTYSLPR;ARHDS(1)PDLAPNVTYSLPR 214.25 6.15E-19 3055620000 609898 718215 723279 731362 813195 635364 792664 662674 898209 TRUE FALSE 571725.5729 771392.3859 740435.5194 750129.9871 749329.945 818783.2725 673811.3919 745410.3076 748292.1152 0.764040622 1.030870659 0.98950063 1.002456089 1.001386931 1.094202726 0.900465711 0.99614882 1 19.51324205 4.743291068 24.91085872 0.999166158 0.764040521 0.716234397 0.047019953 256.9563104 1353100.499 0.010796466 0.088702243 55372.10934 -4.743291068 -0.235125636 ARIPS(ph)GK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ARIPSGK 7 1 Q9NTM9;A0A0B4J226 Q9NTM9 CUTC Copper homeostasis protein cutC homolog 1 ARIPS(1)GK;ARIPS(1)GK 68.657 0.037461 576610000 941610 805160 650850 820690 1020470 431900 959970 941350 1297430 TRUE FALSE 882676.3109 864774.8842 666288.4694 841750.2948 940326.4026 556582.5187 816031.4104 1058879.62 1080880.551 0.816627064 0.800065172 0.616431176 0.778763476 0.869963292 0.514934345 0.754969094 0.979645363 1 20.04377567 1.246431561 5.510509579 0.995686498 0.725728468 0.515977255 0.102238536 0.119254067 11.08643791 0.078150665 0.02410414 17.63727804 -1.246431561 -0.26995803 ARLEIEPEWAYGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ARLEIEPEWAYGK 13 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ;; 141.54 3.64E-05 551270000 1071490 974670 942810 990740 1171610 700560 1200910 1108630 1533370 FALSE TRUE 1004427.354 1046835.581 965173.8984 1016164.066 1079596.477 902800.2994 1020844.694 1247044.896 1277440.641 0.786281038 0.819478845 0.755552835 0.795468715 0.845124573 0.706725832 0.799132783 0.976205748 1 20.28482482 1.231139235 4.991727924 0.995579784 0.78496717 0.841225602 0.036469005 0.06060998 3.928331592 0.028892324 0.008388754 17.0270431 -1.231139235 -0.210612614 ARLS(ph)YSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 ARLSYSDK 8 1 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 ARLS(1)YSDK;ARLS(1)YSDK;ARLS(0.997)YS(0.003)DK;ARLS(1)YSDK;ARLS(0.995)YS(0.005)DK;ARLS(0.998)YS(0.002)DK;ARLS(0.991)Y(0.007)S(0.003)DK;ARLS(0.998)YS(0.002)DK;ARLS(1)YSDK 173.07 0.0001695 39062930000 15817210 12110940 12705220 12576250 12837990 10482530 16606910 12582860 11284390 TRUE FALSE 14827239.06 13007646.6 13006593.82 12898977.87 11829746.05 13508666.24 14116858.02 14153857.77 9400952.409 1.577206055 1.383652 1.383540013 1.372092667 1.258356126 1.436946562 1.50164126 1.505577005 1 23.16437549 4.738589643 7.650868414 1.381745888 1.579160803 0.164568149 0.146745252 0.182794024 111.4616083 0.031185739 0.186443027 54775.91528 -4.738589643 0.197414915 ARLS(ph)YSDKNLIDSMDQSAFAGFSFVNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.708)YS(0.292)DKNLIDSMDQSAFAGFSFVNPK;ARLS(0.317)Y(0.035)S(0.317)DKNLIDS(0.317)MDQS(0.013)AFAGFSFVNPK;ARLS(0.553)YS(0.447)DKNLIDSMDQSAFAGFSFVNPK;ARLS(0.498)Y(0.001)S(0.498)DKNLIDS(0.004)MDQS(0.001)AFAGFSFVNPK;ARLS(0.49)YS(0.49)DKNLIDS(0.02)MDQSAFAGFSFVNPK 309.46 6.49E-83 1392670000 1916724 1828200 1723800 1845311 2579169 1218669 2664656 1837291 3536178 TRUE FALSE 1796759.666 1963561.83 1764689.35 1892664.804 2376611.471 1570478.957 2265115.57 2066680.826 2945967.047 0.609904876 0.666525388 0.5990187 0.642459598 0.806733895 0.533094543 0.768886934 0.701528833 1 21.49030986 -4.999997514 0.198583372 2.548800608 0.607039863 0.678378668 0.074820974 74.43405684 0.735855577 45.51098566 0.161777458 1.00E-05 4.999997514 -1.941760745 ARLSYS(ph)DKNLIDSMDQSAFAGFSFVNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.391)YS(0.609)DKNLIDSMDQSAFAGFSFVNPK;ARLS(0.28)YS(0.72)DKNLIDSMDQSAFAGFSFVNPK 280.65 8.42E-62 3963720000 658590 712850 692230 733730 979290 486820 1033480 721990 1388130 TRUE FALSE 617370.0275 765630.1557 708650.0225 752558.754 902380.5137 627357.0311 878519.2684 812132.0408 1156442.135 0.533852934 0.662056606 0.612784679 0.650753489 0.780307536 0.542488908 0.759674212 0.702267771 1 20.14126165 -5 0.169152445 2.362926232 0.572044901 0.725945726 0.07057151 64.11558523 0.604000188 29.17546393 0.228716885 1.00E-05 5 -1.79088133 ARNDEYENLFNMIVEIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ARNDEYENLFNMIVEIPR 18 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;D6RGV9;D6RGI1;D6RAD3 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 119.31 7.06E-05 58829000 93146 90145 156100 126170 131460 78160 97990 59359 73973 FALSE TRUE 87316.15813 96819.4296 159802.7657 129407.7358 121135.6619 100723.5232 83297.30919 66770.10182 61626.42842 1.416862219 1.571069947 2.593088222 2.099874017 1.965644692 1.634420909 1.351649144 1.083465382 1 15.91126156 1.729042978 1.528294556 1.031965468 1.980036959 0.571734346 0.314813272 0.284612394 1.292215628 0.262973292 0.102198928 53.58496824 -1.729042978 0.948071491 ARNS(ph)GTQS(ph)DGEEKQPGLVMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ARNSGTQSDGEEKQPGLVMER 21 2 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 2 ARNS(0.908)GT(0.286)QS(0.806)DGEEKQPGLVMER 78.128 0.0063739 327020000 79963 61377 64503 67328 78125 50180 83474 58696 76678 TRUE FALSE 74958.25857 65921.41694 66033.04162 69055.75047 71989.37764 64666.1514 70957.84863 66024.32481 63879.94644 1.173423942 1.031957924 1.033705338 1.081023926 1.126947996 1.012307539 1.110800065 1.033568882 1 15.96307548 1.002702559 21.27151222 0.999999995 1.071896865 0.229878234 0.048921406 15.06489485 118562.0699 0.04368348 0.01092087 10.06242275 -1.002702559 0.07189687 ARNS(ph)GTQSDGEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ARNSGTQSDGEEK 13 1 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 1 ARNS(0.972)GT(0.028)QSDGEEK;ARNS(1)GTQSDGEEK 148.36 2.62E-05 600960000 1014630 619410 744640 672010 756310 613600 753850 712940 659110 TRUE FALSE 951126.1195 665271.7609 762303.2124 689254.9143 696912.4634 790736.359 640817.1909 801952.1284 549100.283 1.732153759 1.211566961 1.388276852 1.255244143 1.269189773 1.440058189 1.167031252 1.46048391 1 19.06671013 -4.999999999 0.117833056 2.54E-11 1.499090678 0.357482414 0.158702958 184.5434049 1.418786187 45.13940261 1.449224267 1.00E-05 4.999999999 1.499090678 ARNS(ph)GTQSDGEEKQPGLVMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 ARNSGTQSDGEEKQPGLVMER 21 2 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 1 ARNS(0.858)GT(0.141)QSDGEEKQPGLVMER;ARNS(0.99)GT(0.008)QS(0.002)DGEEKQPGLVMER;ARNS(0.958)GT(0.042)QSDGEEKQPGLVMER;ARNS(0.937)GT(0.063)QSDGEEKQPGLVMER;ARNS(0.665)GT(0.335)QSDGEEKQPGLVMER;ARNS(0.8)GT(0.197)QS(0.002)DGEEKQPGLVMER;ARNS(0.987)GT(0.013)QSDGEEKQPGLVMER;ARNS(0.839)GT(0.155)QS(0.006)DGEEKQPGLVMER;ARNS(0.988)GT(0.01)QS(0.002)DGEEKQPGLVMER;ARNS(0.993)GT(0.007)QSDGEEKQPGLVMER 281.03 2.76E-45 5854350000 2542880 2068316 2249477 2226848 2909290 1666400 2593880 2049503 3562140 TRUE FALSE 2383725.68 2221456.269 2302835.657 2283992.69 2680806.099 2147462.628 2204951.774 2305387.961 2967595.822 0.803251461 0.748571033 0.775993698 0.769644125 0.903359575 0.723637165 0.743009462 0.776853756 1 21.50086318 0.886477718 19.69182438 1 0.775556802 0.66343097 0.049011227 18818.12562 3264244.135 0.045334958 0.01133374 7.699769393 -0.886477718 -0.224443198 ARPAPSRDPS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ARPAPSRDPSPPR 13 2 Q5C9Z4 Q5C9Z4 NOM1 Nucleolar MIF4G domain-containing protein 1 1 ARPAPS(0.011)RDPS(0.989)PPR 61.127 0.04518 207110000 235350 245560 203770 194830 204270 132160 203770 141690 153610 TRUE FALSE 220619.8636 263741.5179 208603.5206 199829.6676 188227.4582 170312.4466 173216.5802 159380.3084 127971.4986 1.723976557 2.060939512 1.630077969 1.561516977 1.470854528 1.330862328 1.353555925 1.245435977 1 16.96546301 2.782951022 0.344366336 1.011348618 2.089298991 0.873289373 0.1027275 0.578726115 0.136436287 0.115271307 0.230646906 606.6679081 -2.782951022 1.077950373 ARPATDS(ph)FDDYPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 ARPATDSFDDYPPR 14 1 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 ARPAT(0.038)DS(0.962)FDDYPPR;ARPAT(0.016)DS(0.984)FDDYPPR;ARPAT(0.013)DS(0.987)FDDYPPR;ARPAT(0.016)DS(0.984)FDDYPPR;ARPATDS(1)FDDYPPR;ARPAT(0.016)DS(0.917)FDDY(0.067)PPR;ARPAT(0.113)DS(0.887)FDDYPPR;ARPAT(0.002)DS(0.998)FDDYPPR;ARPAT(0.019)DS(0.981)FDDYPPR 149.52 4.52E-06 1634030000 4372091 3616201 4176030 3650535 3330539 3077555 4081369 2979328 4551723 TRUE FALSE 4098449.629 3883948.285 4275087.404 3744213.908 3068971.902 3965995.169 3469405.608 3351303.659 3792011.026 1.080811633 1.024244987 1.127393189 0.987395312 0.80932568 1.045881761 0.914924979 0.883780041 1 21.85453173 3.023272008 8.191788014 0.930747856 1.071604705 0.49720074 0.067245518 0.154221797 44.5903436 0.017908636 0.02121248 1055.047489 -3.023272008 0.14085685 ARPATDSFDDYPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ARPATDSFDDYPPR 14 1 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;; 108.36 0.0007573 1119130000 794370 956060 880770 911500 1083660 862240 1005920 869030 1090920 FALSE TRUE 744651.7997 1026847.677 901662.2803 934890.6332 998553.7149 1111154.691 855091.6345 977530.3085 908838.4044 0.819344557 1.129846266 0.99210407 1.028665414 1.09871426 1.222609746 0.940862127 1.075582088 1 19.79366427 4.749365583 24.37418682 1.059253125 0.819344361 0.478956153 0.07920758 977.9060579 2205930.301 0.017905525 0.258395004 56152.04566 -4.749365583 -0.239908763 ARPDAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ARPDAEK 7 1 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ; 98.629 0.010143 205020000 427680 392430 338090 352340 445910 280230 392650 419080 384690 FALSE TRUE 400912.2722 421485.9255 346109.6545 361381.6409 410890.0273 361127.8518 333775.7777 471403.0605 320482.7538 1.25096364 1.31515946 1.079963431 1.127616499 1.282097156 1.126824603 1.041478125 1.470915533 1 18.2898872 ARPDAEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ARPDAEKK 8 2 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;; 86.624 0.0089434 700530000 1524670 1174030 1152180 1167130 1591470 827590 1507420 1267900 2118760 FALSE TRUE 1429243.626 1260956.403 1179510.254 1197080.532 1466482.366 1066501.798 1281396.365 1426200.106 1765125.268 0.809712292 0.71437219 0.668230337 0.678184463 0.83080923 0.604207428 0.725952083 0.80798804 1 20.75133914 0.901423121 2.522159357 0.999427971 0.710636595 0.648928316 0.065509548 0.229482917 3.126992719 0.057223061 0.015357949 7.969354036 -0.901423121 -0.288791376 ARPEDVISEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ARPEDVISEGR 11 1 P25325-2;P25325 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 0 ;;; 141.58 3.47E-05 772700000 583994 760420 653875 742250 890060 608817 697180 683850 868140 FALSE TRUE 547442.858 816722.288 669385.2238 761297.3916 820158.2779 784572.5846 592644.3313 769230.1778 723241.8256 0.756929202 1.129252014 0.925534448 1.052618038 1.134002831 1.084799796 0.819427625 1.063586411 1 19.46411859 -0.603852209 6.956756175 0.999996189 0.997922228 0 0.12727683 0 0 0.114326455 0.026947004 0.248970442 0.603852209 -0.002073961 ARPEYMLPVHFYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ARPEYMLPVHFYGR 14 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 127.07 4.91E-05 1848270000 946290 1652380 884620 800810 1647830 574830 1008310 1498130 1461450 FALSE TRUE 887063.3981 1774723.934 905603.6041 821360.1404 1518416.079 740774.0894 857123.2762 1685174.828 1217524.554 0.728579473 1.457649399 0.743807262 0.674614847 1.247133846 0.608426407 0.703988493 1.384099256 1 20.21551944 3.834193126 6.950602023 0.872822244 1.137182232 0.044919528 0.305853058 0.454893529 26.01490071 0.07241024 0.131428182 6826.421904 -3.834193126 0.264359988 ARPFPDGLAEDIDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ARPFPDGLAEDIDK 14 1 P13639;M0R0I6 P13639 EEF2 Elongation factor 2 0 ; 100.41 0.0016372 152935000 340208 238707 278922 238656 255915 231032 302123 262797 248850 FALSE TRUE 318914.9886 256381.1147 285538.1616 244780.317 235816.4682 297727.1879 256822.4609 295607.7839 207315.3274 1.538308781 1.236672261 1.377313319 1.180715001 1.137477249 1.436107941 1.238801126 1.425884847 1 17.66146726 -1.624599141 2.736406021 0.970993585 1.309032092 0.387681574 0.126094164 25346769.98 22906369.92 5209342.997 0.027538067 0.023735635 1.624599141 0.338038507 ARPFPDGLAEDIDKGEVSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ARPFPDGLAEDIDKGEVSAR 20 2 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;; 255.98 2.01E-36 8657308000 7570642 6171292 6893999 6790538 7760697 5591752 8913432 6341300 9089446 FALSE TRUE 7096809.031 6628220.881 7057527.912 6964794.701 7151203.163 7206000.028 7576945.62 7133025.264 7572358.743 0.937199263 0.875317864 0.932011828 0.91976555 0.944382511 0.951618944 1.00060574 0.941981951 1 22.85231133 2.471635581 0.802722573 0.986234855 0.903856509 0.59494291 0.023134454 0.370660848 0.480422638 0.015696883 0.011524459 296.2344625 -2.471635581 -0.082378346 ARPPS(ph)GSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ARPPSGSSK 9 1 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 ARPPS(0.988)GS(0.011)S(0.001)K;ARPPS(0.991)GS(0.007)S(0.002)K;ARPPS(1)GSSK;ARPPS(0.759)GS(0.085)S(0.155)K;ARPPS(0.999)GS(0.001)SK 98.156 0.0037576 1295588000 759963 683291 729408 717779 812117 541636 768776 623278 717455 TRUE FALSE 712398.2724 733882.5766 746709.9022 736198.4243 748336.6067 697997.5205 653505.1758 701095.6303 597707.1256 1.191885192 1.227829727 1.249290615 1.231704279 1.252012189 1.167791868 1.093353497 1.172975192 1 19.18907922 1.245068244 0.65028897 1.009030818 1.237338947 0.775530586 0.037061837 0.300084463 0.304492793 0.035678397 0.015856088 17.58199871 -1.245068244 0.228308129 ARPPSEGEFIDCFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ARPPSEGEFIDCFQK 15 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 ; 175.26 7.90E-07 1311440000 1141780 1004690 1054920 1068470 1096390 952010 1406070 967910 957900 FALSE TRUE 1070318.028 1079078.293 1079943.201 1095888.749 1010283.952 1226839.832 1195242.857 1088755.694 798020.3017 1.34121654 1.352194036 1.353277853 1.373259235 1.265987782 1.537354162 1.497759962 1.364320797 1 19.60606592 2.277316246 24.99998262 1.407956854 1.343067419 0 0.149140148 550.6271032 355189.4249 0.046180467 0.038636735 189.3722095 -2.277316246 -0.064889435 ARPS(ph)ETGSDDDWEYLLNSDYHQNVESHLLNR ddPTM_SK-BR-3_Pertuzumab_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(0.003)LLNSDYHQNVESHLLNR 52.931 0.039901 62497000 18319 38074 32153 29056 28005 31900 28149 28116 23898 TRUE FALSE 17172.44649 40893.03858 32915.68434 29801.62615 25805.60027 41109.01215 23928.31877 31626.34449 19909.26941 0.862535241 2.053969823 1.65328439 1.496871911 1.296160082 2.064817713 1.201868249 1.588523609 1 14.28115266 0.353870959 0.605258462 0.979424745 1.619843309 0.141204156 0.370067203 3.583618262 2.006349646 0.513137205 0.141028486 2.258764528 -0.353870959 0.640418564 ARPSQFPEQSSSAQQNGSVSDIS(ph)PVQAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ARPSQFPEQSSSAQQNGSVSDISPVQAAK 29 1 O00139-1;O00139-5;O00139;O00139-4 O00139-1 KIF2A Kinesin-like protein KIF2A 1 ARPSQFPEQSSSAQQNGSVS(0.014)DIS(0.986)PVQAAK;ARPSQFPEQSSSAQQNGSVS(0.009)DIS(0.991)PVQAAK 177.98 7.81E-18 293240000 135298 114509 125607 116474 124333 98258 146805 108271 160246 TRUE FALSE 126829.9397 122987.3655 128586.4574 119462.92 114568.3877 126623.4895 124792.9531 121788.8727 133499.9074 0.950037661 0.921254313 0.963195105 0.894853954 0.858190766 0.948491216 0.934779324 0.912276833 1 17.02647922 -1.35804706 5.848663609 1.000013123 0.925425434 0.386824852 0.030363054 5.16E-06 5.67E-07 0.029205756 0.006882652 0.043848318 1.35804706 -0.074587689 ARQEELYSELQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 238.88 7.86E-17 2069850000 747330 1132490 971140 1051300 1174070 1030070 1080830 983040 1089600 FALSE TRUE 700555.9493 1216340.738 994175.8994 1078278.138 1081863.278 1327434.487 918769.5754 1105774.708 907738.7209 0.771759465 1.339967889 1.095222531 1.187872802 1.191822331 1.46235305 1.012152015 1.218164085 1 19.79191757 -0.182687018 1.170836706 0.998737324 1.174421108 0.06314746 0.184917925 54.84049111 50.00984173 0.48963183 0.047741816 0.656618299 0.182687018 0.175683785 ARQPLSEASNQQPLS(ph)GGEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ARQPLSEASNQQPLSGGEEK 20 1 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 ARQPLSEASNQQPLS(1)GGEEK;ARQPLSEAS(0.004)NQQPLS(0.996)GGEEK;ARQPLSEASNQQPLS(1)GGEEK;ARQPLSEASNQQPLS(1)GGEEK 237.32 8.19E-30 1117780000 1718500 1133190 1173180 1255980 1364140 880240 1706330 1251240 1927130 TRUE FALSE 1610942.153 1217092.567 1201008.384 1288210.573 1257005.947 1134350.998 1450481.657 1407460.068 1605479.553 1.003402472 0.758086619 0.748068315 0.802383668 0.782947341 0.706549639 0.903456948 0.876660226 1 20.61457286 1.175966767 1.448452978 0.989355244 0.791019906 0.339228385 0.083629424 0.374070026 1.521227396 0.072314011 0.02197491 14.99570083 -1.175966767 -0.198335337 ARQPQS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ARQPQSPPR 9 1 O95613-2;O95613 O95613-2 PCNT Pericentrin 1 ARQPQS(1)PPR 81.676 0.01248 133360000 36796 60606 44806 46173 65008 43249 42867 54700 55625 TRUE FALSE 34493.00404 65093.3313 45868.81948 47357.87735 59902.53391 55734.28421 36439.49131 61529.41541 46340.82815 0.744332922 1.404664826 0.98981441 1.021947152 1.292651347 1.202703673 0.786336644 1.327758218 1 15.49999621 ARS(ph)DPTHQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ARSDPTHQHR 10 1 A0A2R8Y6L5;A0A2R8Y6I6;Q13627-2;Q13627;Q13627-5 A0A2R8Y6L5 DYRK1A Dual specificity tyrosine-phosphorylation-regulated kinase 1A 1 ARS(1)DPTHQHR;ARS(1)DPTHQHR;ARS(0.999)DPT(0.001)HQHR 159 4.72E-06 880740000 29097.4 42346.6 32731.6 34167.9 37726.4 28937.1 36544.1 34441.2 34182.4 TRUE FALSE 27276.24567 45481.98633 33508.00901 35044.70616 34763.52072 37290.77102 31064.65146 38741.25963 28477.13661 0.957829646 1.597140434 1.176663562 1.230626051 1.220751974 1.309498617 1.090862887 1.360433816 1 14.79751647 -5 0.15879178 0.021013702 1.332785411 0.120514748 0.172816616 215.4954773 1.975526158 66.17719499 0.687336596 1.00E-05 5 1.311771709 ARS(ph)MDSSDLSDGAVTLQEYLELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ARSMDSSDLSDGAVTLQEYLELK 23 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 ARS(0.92)MDS(0.033)S(0.033)DLS(0.013)DGAVTLQEYLELK 149.07 6.00E-08 36001000 44773 35274 32964 39260 40608 23473 46425 39008 51462 TRUE FALSE 41970.73785 37885.72366 33745.92165 40267.47807 37418.81148 30249.27405 39464.00224 43878.23467 42872.65974 0.978962773 0.883680273 0.787119853 0.939234428 0.872789599 0.705560939 0.920493444 1.023454923 1 15.3877703 1.435439751 5.682027618 1.003508872 0.855511315 0.398941007 0.075333295 0.18328247 11.48288128 0.047336828 0.018283308 27.25459614 -1.435439751 -0.147997558 ARS(ph)MDSSDLSDGAVTLQEYLELKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ARSMDSSDLSDGAVTLQEYLELKK 24 2 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 ARS(0.973)MDS(0.022)S(0.005)DLSDGAVTLQEYLELKK;ARS(0.998)MDS(0.002)S(0.001)DLSDGAVTLQEYLELKK 244.04 5.38E-38 190733000 294440 216460 201669 218408 337730 134775 261810 241750 528800 TRUE FALSE 276011.526 232486.9236 206452.6839 224012.719 311206.0481 173682.3546 222554.021 271933.0197 440539.8638 0.626530193 0.527731864 0.468635647 0.50849591 0.706419722 0.394248895 0.50518475 0.61727222 1 18.74891305 0.826996731 3.48004556 0.999923986 0.524733263 0.747026739 0.084540804 0.462495565 8.579186785 0.076073607 0.019640019 6.714237991 -0.826996731 -0.475190723 ARS(ph)PAAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ARSPAAPR 8 1 A0A5E8;Q99501 A0A5E8 GAS2L1 GAS2-like protein 1 1 ARS(1)PAAPR 84.687 0.010462 219220000 51564 44444 44339 38778 59242 32807 48513 37478 61695 TRUE FALSE 48336.70128 47734.68 45390.74202 39773.10913 54589.37229 42277.84832 41238.92602 42157.2108 51397.70594 0.940444722 0.928731723 0.883127782 0.773830435 1.062097448 0.822562944 0.802349546 0.820215806 1 15.64941635 ARS(ph)PDLGPQEQMNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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;ARS(1)PDLGPQEQMNPK 198.05 4.92E-09 1091460000 1202390 952150 1070470 975860 1053550 799960 1271920 916230 1228560 TRUE FALSE 1127134.556 1022648.177 1095862.054 1000902.22 970808.4328 1030895.466 1081207.404 1030623.332 1023505.399 1.101249253 0.999162464 1.070694942 0.977915916 0.94851325 1.007220349 1.056376844 1.006954466 1 19.96508728 4.744858168 24.42480358 1.014386066 1.101249307 0.39829054 0.035195499 628.4179919 2437202.982 0.008800724 0.082541152 55572.27397 -4.744858168 0.086863241 ARS(ph)PGREEVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ARSPGREEVAR 11 2 A0A494BZV2;A0A1W2PPU9 A0A494BZV2 1 ARS(1)PGREEVAR;ARS(1)PGREEVAR;ARS(1)PGREEVAR;ARS(1)PGREEVAR 79.744 0.020719 6750030000 3090810 3334390 3695480 3665340 3851130 3311900 3648810 3450280 4174870 TRUE FALSE 2897361.719 3581271.705 3783138.531 3759398.83 3548677.785 4267991.766 3101704.814 3881055.053 3478057.226 0.833040267 1.0296759 1.087716011 1.080890447 1.020304599 1.227119477 0.891792346 1.115868659 1 21.72985024 4.744208088 3.33368173 1.056545096 0.801546067 0.406902388 0.085530551 0.319385899 5.824115742 0.018831809 0.210615531 55489.15201 -4.744208088 -0.254999029 ARS(ph)PINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ARSPINR 7 1 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 1 ARS(1)PINR;ARS(1)PINR 80.231 0.018455 1082510000 193224 237190 223685 184303 211481 188920 224540 213850 221720 TRUE FALSE 181130.4548 254751.7944 228990.9138 189032.527 194872.1353 243458.1371 190872.3115 240549.6432 184713.4996 0.980602149 1.379172583 1.239708599 1.023382305 1.054996715 1.3180311 1.033342511 1.302285127 1 17.49492978 -4.999999993 0.168132646 0.322649662 1.224026837 0.06652225 0.144680454 282.0078818 2.650225642 64.07975201 0.516413447 1.00E-05 4.999999993 0.901377175 ARS(ph)PSVAAMASPQLCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 ARSPSVAAMASPQLCR 16 1 P25325-2 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 1 ARS(0.998)PS(0.002)VAAMASPQLCR;ARS(0.999)PS(0.001)VAAMASPQLCR;ARS(1)PSVAAMASPQLCR;ARS(1)PSVAAMASPQLCR;ARS(0.997)PS(0.003)VAAMASPQLCR;ARS(0.999)PS(0.001)VAAMASPQLCR;ARS(0.988)PS(0.012)VAAMASPQLCR;ARS(0.943)PS(0.057)VAAMASPQLCR;ARS(0.788)PS(0.212)VAAMASPQLCR 231.5 7.74E-16 6374820000 2174235 2624815 2096463 2194387 3111782 1695194 2462142 2366298 3289581 TRUE FALSE 2038153.512 2819159.034 2146192.092 2250698.686 2867395.194 2184568.989 2092966.665 2661735.514 2740528.68 0.743708149 1.028691674 0.783130681 0.821264416 1.046292715 0.797134146 0.76370909 0.971248918 1 21.3860228 1.064043011 9.074665049 0.999928931 0.862468016 0.214304768 0.104107093 0.423176378 53.59487998 0.096070037 0.024040447 11.58892124 -1.064043011 -0.137460915 ARS(ph)PTDDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ARSPTDDK 8 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 ARS(1)PTDDK;ARS(0.999)PT(0.001)DDK;ARS(0.997)PT(0.003)DDK;ARS(1)PTDDK 94.767 0.0061323 178170000 1763110 925200 1323580 1164050 1117970 991120 1371410 1123310 1083090 TRUE FALSE 1652760.092 993702.7707 1354975.943 1193921.494 1030169.146 1277240.255 1165779.802 1263557.726 902315.282 1.83168802 1.101281105 1.501665737 1.323175521 1.141695333 1.415514377 1.291987208 1.400350578 1 19.78327209 -4.544865721 0.151637661 1.62E-19 1.457476799 0.284906005 0.197601785 166.1493099 1.691766272 51.90187465 0.896603441 2.85E-05 4.544865721 1.457476799 ARS(ph)PTDDKVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ARSPTDDKVK 10 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 ARS(0.997)PT(0.003)DDKVK;ARS(0.98)PT(0.02)DDKVK;ARS(0.979)PT(0.021)DDKVK;ARS(0.985)PT(0.015)DDKVK;ARS(0.999)PT(0.001)DDKVK;ARS(0.993)PT(0.007)DDKVK;ARS(0.993)PT(0.007)DDKVK 153.39 8.53E-06 11290140000 15100010 8754400 9924550 9160900 11093800 6988030 12656690 9091360 14029440 TRUE FALSE 14154927.33 9402584.885 10159965.01 9395984.203 10222537.7 9005360.82 10758936.83 10226436.31 11687835.83 1.211081977 0.804476126 0.869276841 0.803911378 0.8746305 0.770490016 0.920524295 0.874964062 1 23.47850448 -0.491819286 12.97540865 1 0.876247559 0.060555576 0.122789653 0 0 0.105022613 0.024754067 0.322240938 0.491819286 -0.123752441 ARS(ph)PVRLPHEGSPSPGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ARSPVRLPHEGSPSPGEK 18 2 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 ARS(1)PVRLPHEGSPSPGEK;ARS(1)PVRLPHEGSPSPGEK;ARS(0.982)PVRLPHEGS(0.018)PSPGEK;ARS(1)PVRLPHEGSPSPGEK 168.75 1.04E-11 1009330000 423960 444463 448334 483650 578510 372068 537530 457192 791470 TRUE FALSE 397425.1004 477371.503 458968.6942 496061.2778 533076.1582 479477.9916 456932.3667 514273.4276 659368.5439 0.602735912 0.723982828 0.696073081 0.752327788 0.808464649 0.727177534 0.692984782 0.77994838 1 19.33072554 -5 0.208289873 2.320903184 0.68028859 0.779281655 0.048455072 69.72547641 0.694634083 38.45042584 0.105571235 1.00E-05 5 -1.640614594 ARS(ph)PYSPAEEDALFMDLPTGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ARSPYSPAEEDALFMDLPTGPR 22 1 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 ARS(0.971)PYS(0.028)PAEEDALFMDLPTGPR;ARS(0.902)PY(0.006)S(0.092)PAEEDALFMDLPTGPR;ARS(0.998)PY(0.001)S(0.001)PAEEDALFMDLPTGPR;ARS(0.999)PYS(0.001)PAEEDALFMDLPTGPR 218.04 7.34E-26 289164000 176993 189789 193757 186006 227455 160894 197404 185227 220134 TRUE FALSE 165915.3241 203841.175 198353.0075 190779.2289 209591.6018 207341.4859 167805.1028 208352.9987 183392.2133 0.90470212 1.11150398 1.081578132 1.040279876 1.142859874 1.130590455 0.915006694 1.136106026 1 17.48457286 -1.624522934 6.305665248 0.99974579 1.059268611 0.042701764 0.085808194 0.000288465 1.72E-05 0.07815444 0.018342747 0.023739801 1.624522934 0.05952282 ARS(ph)RT(ph)PPSAPSQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ARSRTPPSAPSQSR 14 2 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ARS(0.999)RT(0.978)PPS(0.021)APS(0.001)QSR 71.592 0.045234 3490000000 163450 190920 179310 189400 205460 153700 197370 183620 252840 TRUE FALSE 153219.9563 205055.9155 183563.3179 194260.3247 189324.0004 198070.6949 167776.2008 206545.3612 210639.3706 0.727404169 0.973492823 0.871457778 0.922241289 0.898806334 0.940330833 0.79650922 0.980563893 1 17.68441559 -5 0.296900785 1.889382252 0.885263138 0.192675673 0.076544105 467.1063858 4.347338367 258.0518934 0.070935761 1.00E-05 5 -1.004119114 ARS(ph)VDALDDLTPPSTAESGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ARSVDALDDLTPPSTAESGSR 21 1 S4R3V8;Q86X29-6;Q86X29-5;Q86X29-2;Q86X29-3;Q86X29-4;Q86X29 S4R3V8 LSR Lipolysis-stimulated lipoprotein receptor 1 ARS(1)VDALDDLTPPSTAESGSR 95.823 0.00082925 125670000 59245 84768 71252 73126 83955 38865 93905 63783 84343 TRUE FALSE 55536.96121 91044.31092 72942.13109 75002.53696 77361.51296 50084.69458 79824.81702 71746.44795 70265.60842 0.790386114 1.295716538 1.038091503 1.067414609 1.10098688 0.712791018 1.136043917 1.021074884 1 16.10053111 ARS(ph)VS(ph)PPPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ARSVSPPPKR 10 2 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 2 ARS(1)VS(1)PPPKR;ARS(1)VS(1)PPPKR;ARS(1)VS(1)PPPKR 84.753 0.0078872 13739300000 370722 357023 354632 343778 418410 299616 352198 348685 480300 TRUE FALSE 347519.1718 383457.3544 363044.0385 352599.9255 385549.7664 386110.2753 299389.1795 392219.0898 400134.8271 0.868505184 0.958320367 0.907304273 0.881202789 0.963549634 0.964950435 0.748220748 0.980217325 1 18.61012668 ARSDEGQLS(ph)PATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ARSDEGQLSPATR 13 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 ARSDEGQLS(1)PATR 111.7 0.00058081 479580000 127820 172000 185720 204630 232370 147770 221270 177820 279030 TRUE FALSE 119819.9744 184735.059 190125.3661 209881.1522 214120.5975 190428.8002 188092.6177 200021.2184 232458.0904 0.515447641 0.794702644 0.81789094 0.902877383 0.921114843 0.819196268 0.80914636 0.860461419 1 17.82661111 5.145843588 1.26757497 0.861943764 3.33E-14 0.777727149 0.059683653 1.648535444 1.146741659 0.01574533 2.370732424 139908.335 -5.145843588 -0.861943764 ARSMDSSDLS(ph)DGAVTLQEYLELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ARSMDSSDLSDGAVTLQEYLELK 23 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 ARS(0.225)MDS(0.233)S(0.233)DLS(0.31)DGAVTLQEYLELK 134.15 1.22E-05 50305000 36577 28391 28289 32065 37425 18075 34464 33084 41275 TRUE FALSE 34287.71086 30493.09918 28960.02844 32887.84219 34485.79147 23292.95908 29296.44315 37214.61023 34385.93585 0.997143454 0.886789858 0.84220562 0.956432953 1.002903967 0.677397852 0.851989118 1.082262539 1 15.06953099 1.241857144 24.99999444 1.041131304 0.877655999 0.304962384 0.095251696 91.08555246 690812.691 0.068221775 0.022606548 17.45247978 -1.241857144 -0.163475305 ARSPT(ph)DDKVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ARSPTDDKVK 10 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 ARS(0.213)PT(0.787)DDKVK 122.66 0.00077596 2973600000 4101400 2256600 2772100 2796600 3148900 2043800 3304500 2470300 4040800 TRUE FALSE 3844700.695 2423681.012 2837855.521 2868365.491 2901598.096 2633811.882 2809020.902 2778722.393 3366364.375 1.142092853 0.719969897 0.843003075 0.852066256 0.861938214 0.782390611 0.834437568 0.825437203 1 21.68275991 -0.818454312 7.716458726 0.99996387 0.840183645 0.124125972 0.110460367 0 9.07E-11 0.093958395 0.022146206 0.151895773 0.818454312 -0.159780224 ART(ph)PATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ARTPATK 7 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 ART(1)PATK;ART(1)PATK 83.862 0.035516 413010000 1007310 829150 998960 915680 1247810 672640 1262460 1218140 1413700 TRUE FALSE 944264.2652 890541.1287 1022655.803 939177.899 1149812.036 866820.2486 1073165.843 1370227.46 1177744.337 0.801756574 0.756141295 0.868317317 0.797437839 0.976283222 0.736000354 0.911204418 1.163433707 1 20.16759496 1.422997555 4.921392784 1.077153277 0.825339401 0.656927779 0.076423714 0.110511232 4.677589916 0.047214357 0.017451202 26.48485226 -1.422997555 -0.251813876 ART(ph)PLTAAQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ARTPLTAAQQK 11 1 I3L2J0 I3L2J0 CIC 1 ART(1)PLTAAQQK 159.22 4.68E-05 296550000 386170 312330 353490 344430 429900 266440 377210 369690 508970 TRUE FALSE 362000.309 335455.2382 361874.9497 353268.6569 396137.3881 343356.9027 320650.8623 415846.6103 424019.6189 0.853734811 0.791131408 0.853439165 0.833142244 0.934243064 0.809766547 0.756217043 0.980724928 1 18.69377149 1.172101375 8.280632959 0.993647999 0.829636211 0.662940073 0.046584359 0.180511076 19.72165348 0.045281115 0.011378876 14.86282538 -1.172101375 -0.164011787 ARTDEVPAGGS(ph)RS(ph)EAEDEDDEDYVPYVPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ARTDEVPAGGSRSEAEDEDDEDYVPYVPLR 30 2 Q9UJV9;D6RGI7;A0A499FJW5;D6RD33 Q9UJV9 DDX41 Probable ATP-dependent RNA helicase DDX41 2 ART(0.011)DEVPAGGS(0.992)RS(0.998)EAEDEDDEDYVPYVPLR 136.2 1.74E-06 43964000 29909 40364 30002 35737 36577 23209 43000 38727 52917 TRUE FALSE 28037.04908 43352.59256 30713.66161 36654.07192 33704.38996 29909.06153 36552.54919 43562.1512 44084.81084 0.635979798 0.98339069 0.696694871 0.831444464 0.764535207 0.678443685 0.829141568 0.988144224 1 15.42799405 1.283175218 3.991979953 1.000608259 0.783099661 0.479285097 0.096117827 0.187108249 5.441272472 0.074107307 0.023016202 19.19442993 -1.283175218 -0.217508598 AS(ph)ADFGAAGSPRPLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASADFGAAGSPRPLGR 16 1 Q86UD0 Q86UD0 SAPCD2 Suppressor APC domain-containing protein 2 1 AS(1)ADFGAAGSPRPLGR;AS(1)ADFGAAGSPRPLGR 90.718 0.0032434 303849000 99633 107195 103563 85657 106338 86518 125870 102284 130537 TRUE FALSE 93397.14838 115131.8293 106019.5633 87855.10364 97986.64243 111494.3421 106996.962 115054.3826 108749.5314 0.858828054 1.05868805 0.974896737 0.807866503 0.90103048 1.025239747 0.98388435 1.057975893 1 16.73064966 2.224259992 24.96203353 1.012402209 0.941479558 0.292757051 0.070224434 430.4119867 751288.0394 0.028425493 0.021092424 167.5945888 -2.224259992 -0.07092265 AS(ph)DKDITVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ASDKDITVSK 10 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 AS(1)DKDITVSK;AS(1)DKDITVSK;AS(0.999)DKDIT(0.001)VSK;AS(1)DKDITVSK;AS(1)DKDITVSK 194.55 2.73E-07 4510700000 10679530 4399220 6940800 6186100 5929890 5547800 8193140 5026390 6386080 TRUE FALSE 10011117.28 4724942.826 7105439.054 6344845.799 5464180.359 7149359.799 6964654.718 5653945.856 5320201.992 1.881717517 0.888113427 1.335558136 1.192594907 1.027062575 1.343813601 1.309095919 1.062731427 1 22.34304959 4.753122279 24.94221266 1.169644972 1.881718027 0.687009591 0.155504513 1533.33885 2626361.952 0.03606867 0.795829489 56639.87403 -4.753122279 0.712073055 AS(ph)DLEDEESAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASDLEDEESAAR 12 0 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 AS(1)DLEDEESAAR;AS(1)DLEDEESAAR;AS(1)DLEDEESAAR 359.14 6.06E-72 4610710000 2266280 1502120 1861480 1675490 1409040 1693980 2130050 1637010 1187810 TRUE FALSE 2124437.58 1613338.528 1905635.185 1718485.91 1298379.682 2183004.527 1810668.777 1841394.302 989556.8375 2.146857563 1.630364691 1.925746064 1.736621733 1.312081967 2.206042588 1.82977744 1.860827223 1 19.91642305 -1.984141425 2.719666199 0.256889852 1.820708369 0.518372135 0.251568974 66206280.18 60530812.82 309737243.8 0.057800374 0.010371906 1.984141425 1.563818517 AS(ph)DPGLPAEEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASDPGLPAEEPK 12 0 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 1 AS(1)DPGLPAEEPK;AS(1)DPGLPAEEPK;AS(1)DPGLPAEEPK;AS(1)DPGLPAEEPK 219.97 3.22E-11 1026850000 2800710 1458990 2035650 1854970 2021910 1663150 2699920 1977040 1824510 TRUE FALSE 2625418.561 1567015.138 2083936.579 1902571.671 1863117.345 2143274.406 2295092.061 2223877.796 1519987.494 1.727263264 1.030939494 1.371022188 1.251702187 1.22574518 1.410060553 1.50994141 1.463089535 1 20.53562802 2.221616703 24.34121176 1.402082789 1.285345647 0 0.223389986 531.1322291 763004.8726 0.075440733 0.055874963 166.5776394 -2.221616703 -0.116737142 AS(ph)GEMASAQYITAALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 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(0.999)GEMAS(0.001)AQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR 377.43 1.17E-104 2368382000 1871904 1565845 1776517.1 1751592.5 1576554 1551028.6 1744274.8 1622044.7 1013366.3 TRUE FALSE 1754744.87 1681781.793 1818656.925 1796541.329 1452737.808 1998785.378 1482736.987 1824560.551 844228.9179 2.078517844 1.992092142 2.154222493 2.128026286 1.720786599 2.367586961 1.756321011 2.161215415 1 19.68727472 -1.955201693 0.480418809 2.98E-17 2.055988723 0.742075938 0.192955476 29.1591117 2.262982848 32.6328603 0.08270683 0.011086598 1.955201693 2.055988723 AS(ph)GQAFELILS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASGQAFELILSPR 13 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 2 AS(1)GQAFELILS(1)PR;AS(1)GQAFELILS(1)PR;AS(1)GQAFELILS(1)PR;AS(1)GQAFELILS(1)PR 151.87 6.57E-05 223971000 264396 255323 292491 295044 309319 235471 305395 243279 345308 TRUE FALSE 247847.9263 274227.3806 299429.0246 302615.3285 285026.3335 303447.6551 259603.8549 273652.9187 287673.864 0.861558721 0.95325789 1.040862804 1.051938902 0.990796764 1.054832201 0.902424194 0.951260969 1 18.13407463 -0.186370184 6.974440091 1 0.980116774 0.010206514 0.063413249 0 0 0.060895734 0.014353262 0.651073196 0.186370184 -0.019883226 AS(ph)GQAFELILSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ASGQAFELILSPR 13 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 AS(1)GQAFELILSPR;AS(1)GQAFELILSPR;AS(1)GQAFELILSPR;AS(1)GQAFELILSPR;AS(1)GQAFELILSPR;AS(1)GQAFELILSPR;AS(1)GQAFELILSPR;AS(1)GQAFELILSPR 216.77 2.82E-11 1021118000 519075 613644 524580 580541 723410 474962 590457 556695 489778 TRUE FALSE 486587.0223 659078.8403 537023.2853 595438.6649 666596.2967 612075.819 501923.4544 626199.5962 408030.8877 1.19252497 1.61526703 1.316133904 1.459298016 1.633690774 1.500072268 1.230111419 1.534686748 1 18.63831884 -1.383047103 4.718231252 0.999466044 1.434942609 0.455045507 0.149680889 0.000786694 0.000102868 0.135614216 0.031926475 0.041395478 1.383047103 0.435476565 AS(ph)GVAVSDGVIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASGVAVSDGVIK 12 0 P23528;E9PP50;E9PS23 P23528 CFL1 Cofilin-1 1 AS(1)GVAVSDGVIK;AS(0.999)GVAVS(0.001)DGVIK;AS(1)GVAVSDGVIK 199.3 1.82E-07 840660000 1362350 1162750 1242270 1204920 1369020 963510 1582940 1389070 2037760 TRUE FALSE 1277082.945 1248841.22 1271737.231 1235840.287 1261502.692 1241659.696 1345592.842 1562498.447 1697644.692 0.75226751 0.735631682 0.74911861 0.727973464 0.74308994 0.731401395 0.792623362 0.920391914 1 20.69510311 1.188443354 1.988837244 0.99935818 0.739864322 0.991782596 0.008354275 0.021788147 0.154440949 0.007056701 0.002032705 15.43275119 -1.188443354 -0.259493858 AS(ph)HSSERPPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASHSSERPPPR 11 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 AS(0.999)HS(0.001)SERPPPR 131.79 0.00011865 992920000 127940 175080 186000 158690 145310 147510 205060 161130 156240 TRUE FALSE 119932.4638 188043.1054 190412.0078 162762.2541 133897.9388 190093.7424 174313.1567 181247.4352 130162.5347 0.921405411 1.444679192 1.462878764 1.250453938 1.028697998 1.460433625 1.339196084 1.392470081 1 16.98995472 AS(ph)LADALPLHIAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASLADALPLHIAPR 14 0 H3BRB6;Q8ND25;Q8ND25-2 H3BRB6 ZNRF1 E3 ubiquitin-protein ligase ZNRF1 1 AS(1)LADALPLHIAPR 76.82 0.017002 22419000 20527 24308 20823 23204 30034 16755 26143 25753 36926 TRUE FALSE 19242.25171 26107.78961 21316.93139 23799.45392 27675.25079 21591.89651 22223.09985 28968.31874 30762.81205 0.625503666 0.848680204 0.692944824 0.773643641 0.899633322 0.701883055 0.722401444 0.941666799 1 14.90889977 1.139925076 4.750828644 0.994000909 0.75732603 0.576935428 0.078356983 0.140985448 4.971394353 0.068987353 0.017661344 13.80146144 -1.139925076 -0.236674879 AS(ph)LEDAPVDDLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ASLEDAPVDDLTR 13 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 AS(1)LEDAPVDDLTR;AS(1)LEDAPVDDLTR;AS(1)LEDAPVDDLTR;AS(1)LEDAPVDDLTR;AS(1)LEDAPVDDLTR;AS(1)LEDAPVDDLTR 266.75 1.95E-24 2422490000 3952320 3242170 3576260 3367530 3175270 3225550 4111710 3302290 2817460 TRUE FALSE 3704951.346 3482223.64 3661090.576 3453946.521 2925897.103 4156713.923 3495197.257 3714588.176 2347207.725 1.57845056 1.483560063 1.559764199 1.471512932 1.246543743 1.770918645 1.489087319 1.582556216 1 21.16251409 -1.539979502 2.910606588 0.976115395 1.521508522 0.616322951 0.129629615 27853558.68 30388116.11 5229465.572 0.028965908 0.028841676 1.539979502 0.545393127 AS(ph)LENVHPPIAPPPTEIPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASLENVHPPIAPPPTEIPER 20 0 C9J2P9;Q75N03-2;Q75N03 C9J2P9 CBLL1 E3 ubiquitin-protein ligase Hakai 1 AS(1)LENVHPPIAPPPTEIPER;AS(1)LENVHPPIAPPPTEIPER 98.632 0.00049722 260080000 300120 292900 282670 301010 322090 238880 380430 281470 471990 TRUE FALSE 281336.0249 314586.6208 289375.0659 308734.4262 296794.3506 307840.7781 323388.0532 316612.1491 393211.8198 0.715482116 0.800043653 0.735926672 0.785160594 0.754795089 0.782887906 0.822427091 0.805194893 1 18.58494716 -0.421542558 0.377392837 1.062377692 0.753106005 0.896186933 0.025034765 2.109376707 0.311572127 0.192092881 0.017099523 0.378841408 0.421542558 -0.309271687 AS(ph)LGS(ph)LEGEAEAEASSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 AS(1)LGS(1)LEGEAEAEASSPK;AS(1)LGS(1)LEGEAEAEASSPK;AS(1)LGS(1)LEGEAEAEASSPK 233.79 1.17E-19 99465000 634230 326184 391380 333180 340251 393680 635310 393920 516870 TRUE FALSE 594534.6764 350335.0028 400663.7184 341729.9629 313529.059 507329.0251 540051.1634 443101.7791 430601.0579 1.380708815 0.813595314 0.930475462 0.793611527 0.728119574 1.17818806 1.254179834 1.029030865 1 18.71599234 2.213112825 24.99911162 1.150624402 0.907516148 0.175261998 0.190721791 286.9268261 281866.0882 0.066978471 0.049484841 163.3476253 -2.213112825 -0.243108254 AS(ph)LLTDEEDVDMALDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASLLTDEEDVDMALDQR 17 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;H7C3P6 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 AS(0.5)LLT(0.5)DEEDVDMALDQR 79.022 0.0058452 0 6310.8 7011.3 8841.6 9238.5 8131.2 6230.5 9542.2 5689.5 8579.9 TRUE FALSE 5915.818293 7530.423947 9051.326927 9475.575551 7492.608352 8029.144206 8111.435695 6399.846599 7147.859262 0.827634971 1.053521575 1.266298985 1.325652227 1.048231097 1.12329355 1.134806296 0.895351512 1 12.80329551 1.247439411 24.73332245 0.94767575 1.126837862 0.194515986 0.135648631 222.286213 619228.3868 0.092951321 0.032807559 17.67825569 -1.247439411 0.179162112 AS(ph)LSDLSSLDDVEGMSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASLSDLSSLDDVEGMSVR 18 0 A0A087WTM5;H7BYJ1;Q969K3;Q969K3-2 A0A087WTM5 RNF34 E3 ubiquitin-protein ligase RNF34 1 AS(0.999)LS(0.001)DLSSLDDVEGMSVR 145.91 9.19E-08 20622000 42292 39870 42090 42054 43318 40748 54727 39291 41799 TRUE FALSE 39645.01921 42822.01628 43088.39468 43133.17684 39915.97902 52511.28611 46521.19441 44196.56784 34822.47687 1.138489355 1.229723447 1.237373058 1.238659071 1.14627053 1.507971024 1.335953057 1.26919656 1 15.0877312 AS(ph)LSDLTDLEDIEGLTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASLSDLTDLEDIEGLTVR 18 0 J3KSI3;J3KSU7;K7EN88;Q8WZ73-3;Q8WZ73-2;Q8WZ73 J3KSI3 RFFL;hCG_2039718 E3 ubiquitin-protein ligase rififylin 1 AS(0.899)LS(0.1)DLT(0.001)DLEDIEGLTVR 73.166 0.021668 5207400 11191 11856 10803 10728 12376 11299 16193 12755 13258 TRUE FALSE 10490.57529 12733.83058 11059.25226 11003.29864 11404.03888 14560.83788 13765.00998 14347.48983 11045.15415 0.949789848 1.152888443 1.001276407 0.996210509 1.032492506 1.31830101 1.246248789 1.298985024 1 13.43112593 2.251480713 24.93522393 1.240384062 1.038939877 0.455260223 0.100852999 169.4189901 326970.8074 0.031669975 0.026341826 178.4352742 -2.251480713 -0.201444185 AS(ph)LSEIGFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASLSEIGFGK 10 0 Q00537;Q00537-2;F5H6Z0 Q00537 CDK17 Cyclin-dependent kinase 17 1 AS(0.995)LS(0.005)EIGFGK 68.548 0.062565 28586000 128360 146710 145680 140260 161560 123340 151170 127290 139320 TRUE FALSE 120326.1767 157572.5611 149135.5984 143859.3091 148871.7293 158946.2557 128503.4619 143182.4367 116066.592 1.03669949 1.357604789 1.284914081 1.239454925 1.282640653 1.36944019 1.107152883 1.233623167 1 16.82459325 0.801945928 0.883995386 1.003562992 1.270650986 0.34025361 0.102806975 0.83504572 1.286257465 0.090176891 0.03077958 6.337907959 -0.801945928 0.267087993 AS(ph)LSSAPVVLVGDHA ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASLSSAPVVLVGDHA 15 0 Q9HBH9 Q9HBH9 MKNK2 MAP kinase-interacting serine/threonine-protein kinase 2 1 AS(1)LSSAPVVLVGDHA;AS(0.999)LS(0.001)SAPVVLVGDHA;AS(0.992)LS(0.006)S(0.002)APVVLVGDHA 340.06 2.71E-69 189321000 178979 238198 221632 232698 244957 181473 222449 198244 237476 TRUE FALSE 167777.0239 255834.4278 226889.2157 238669.4246 225719.0653 233861.3091 189094.8376 222995.1998 197839.7214 0.848045189 1.29313985 1.146833477 1.206377682 1.140918839 1.182074598 0.955798139 1.127150797 1 17.59397259 1.751888405 25 1.027354688 1.158438038 0.133698347 0.121844469 6.151287198 11555.58395 0.051064021 0.028317619 56.47918293 -1.751888405 0.13108335 AS(ph)PAPGSGHPEGPGAHLDMNSLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 ASPAPGSGHPEGPGAHLDMNSLDR 24 0 O94826 O94826 TOMM70A Mitochondrial import receptor subunit TOM70 1 AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(0.994)PAPGS(0.006)GHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(0.999)PAPGS(0.001)GHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR 314.35 2.40E-73 11377610000 749142 801581 767803 760335 1053253 916802 854290 1051639 1241314 TRUE FALSE 702254.5395 860930.8913 786015.6497 779846.4833 970534.758 1181467.854 726197.1453 1182938.444 1034130.674 0.679077178 0.83251654 0.760073818 0.75410826 0.938503017 1.142474432 0.702229576 1.143896486 1 19.97998707 2.707577118 6.254471091 0.959258336 0.769579175 0.431671447 0.128305289 0.213739352 28.05662597 0.038983438 0.037417958 510.0081521 -2.707577118 -0.189679161 AS(ph)PDS(ph)SSCGERSPPPPPPPPSDEALLHCVLEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASPDSSSCGERSPPPPPPPPSDEALLHCVLEGK 33 1 Q9BRK4 Q9BRK4 LZTS2 Leucine zipper putative tumor suppressor 2 2 AS(0.979)PDS(0.311)S(0.286)S(0.264)CGERS(0.161)PPPPPPPPSDEALLHCVLEGK 79.29 0.0019829 33970000 9645.6 8146.7 7854.1 7403.8 11162 6952.2 9888.9 9499.6 12120 TRUE FALSE 9041.899114 8749.890145 8040.402961 7593.794043 10285.38155 8959.18728 8406.151249 10685.64597 10097.0937 0.895495217 0.866575116 0.796308641 0.752077208 1.018647727 0.887303569 0.832531766 1.058289275 1 13.30165247 1.239120082 24.99987442 1.029144695 0.858935834 0.481290407 0.07105906 12.03984795 538227.272 0.053733965 0.016917619 17.34283459 -1.239120082 -0.170208862 AS(ph)PEPELQLRPYQMEVAQPALEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ASPEPELQLRPYQMEVAQPALEGK 24 1 A0A3B3IRK8;Q9BYX4 A0A3B3IRK8 IFIH1 Interferon-induced helicase C domain-containing protein 1 1 AS(1)PEPELQLRPYQMEVAQPALEGK;AS(1)PEPELQLRPYQMEVAQPALEGK;AS(1)PEPELQLRPYQMEVAQPALEGK;AS(1)PEPELQLRPYQMEVAQPALEGK;AS(1)PEPELQLRPYQMEVAQPALEGK 228.47 2.17E-33 1728420000 1394804 1153068 1217127 1223878 1325792 1014509 1781050 1216043 1490434 TRUE FALSE 1307505.707 1238442.354 1245997.827 1255284.782 1221669.644 1307381.279 1513998.087 1367868.645 1241670.937 1.053021109 0.997399808 1.003484732 1.010964132 0.983891632 1.052920899 1.219323125 1.101635389 1 20.24385146 1.979525973 12.19592461 1.132568468 1.008186222 0.354101801 0.056572678 0.868014085 514.857221 0.020450987 0.013558502 95.39507924 -1.979525973 -0.124382246 AS(ph)PEPPGPESSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ASPEPPGPESSSR 13 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(0.999)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR 318.96 6.98E-51 19861507000 4760125 4611041 4632465 4464882 4198728 3766511 5223648 3582245 3583407 TRUE FALSE 4462197.273 4952447.273 4742349.257 4579458.431 3868976.84 4853841.582 4440410.476 4029496.174 2985313.222 1.494716615 1.658937239 1.588560029 1.533995963 1.296003653 1.625906972 1.487418621 1.349773332 1 21.50945088 -2.973742149 0.201877421 9.02E-18 1.636325533 0.738333638 0.099495574 26.88972035 0.5561181 11.64739018 0.242727205 0.001062326 2.973742149 1.636325533 AS(ph)PEPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASPEPQR 7 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 AS(1)PEPQR;AS(1)PEPQR;AS(1)PEPQR 87.308 0.022978 630960000 2145940 1650200 1917320 1770450 1554960 1784860 1996690 1560870 1297560 TRUE FALSE 2011629.446 1772382.525 1962799.736 1815882.744 1432839.714 2300120.107 1697304.871 1755748.055 1080988.853 1.860915993 1.63959371 1.815744658 1.679834846 1.325489814 2.127792622 1.570140955 1.624205513 1 20.04392022 0.584787176 1.575360595 1.000504804 1.72020481 0.54516147 0.204975823 1.315361635 4.140469879 0.174113565 0.049980411 3.844033605 -0.584787176 0.719700007 AS(ph)PEPQRENASPAPGTTAEEAMSR ddPTM_SK-BR-3_Pertuzumab_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 AS(1)PEPQRENASPAPGTTAEEAMSR 169.18 5.77E-12 400550000 25948 24126 27273 38388 38102 30499 34179 27069 41826 TRUE FALSE 24323.961 25912.31414 27919.92844 39373.10107 35109.62262 39303.56619 29054.17625 30448.62424 34844.97039 0.698062324 0.74364575 0.801261362 1.129950768 1.007595134 1.127955218 0.833812626 0.873831256 1 15.08866281 3.402417608 6.875754176 0.986201221 0.746215012 0.611141904 0.094104161 0.153290224 11.50888933 0.027080897 0.036859269 2525.908464 -3.402417608 -0.239986209 AS(ph)PGLLPVANGNSLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ASPGLLPVANGNSLNK 16 0 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK 306.2 1.52E-46 1351410000 2443980 2039180 2265560 2050660 2299580 1950150 2888200 2214520 2495120 TRUE FALSE 2291015.654 2190163.009 2319300.153 2103283.407 2118980.263 2513126.647 2455141.223 2491007.697 2078668.353 1.10215545 1.05363754 1.115762478 1.011841742 1.019393142 1.20900799 1.181112523 1.198367067 1 20.98722817 2.237721896 24.99971844 1.165910576 1.064927856 0.276346562 0.066380484 23.18153742 690937.1942 0.021790864 0.017053186 172.8709013 -2.237721896 -0.10098272 AS(ph)PIKMDLAPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ASPIKMDLAPSK 12 1 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 AS(1)PIKMDLAPSK;AS(1)PIKMDLAPSK;AS(1)PIKMDLAPSK;AS(1)PIKMDLAPSK;AS(1)PIKMDLAPSK 164.01 3.54E-05 2198470000 11273620 5998510 7872260 6875990 7253630 5950230 10918090 7133220 6856270 TRUE FALSE 10568024.25 6442645.922 8058993.725 7052439.544 6683959.16 7667964.807 9281023.763 8023818.219 5711914.244 1.850172078 1.127931136 1.41090944 1.234689325 1.170178486 1.342450968 1.624853485 1.40475117 1 22.44554289 4.752114806 24.52411061 1.321075315 1.850172536 0.49365987 0.175890235 1675.231543 3030990.967 0.042478257 0.821915125 56508.63363 -4.752114806 0.529097221 AS(ph)PITNDGEDEFVPSDGLDKDEYTFSPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASPITNDGEDEFVPSDGLDKDEYTFSPGK 29 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 AS(0.888)PIT(0.028)NDGEDEFVPS(0.084)DGLDKDEYTFSPGK 81.566 2.16E-06 0 101670 69106 76025 74606 75188 45314 103000 57636 80855 TRUE FALSE 95306.65619 74222.68014 77828.3489 76520.51627 69283.03777 58395.41619 87556.10621 64831.98147 67359.77816 1.414889698 1.101884272 1.155412785 1.135997154 1.028552048 0.866918179 1.29982771 0.962473204 1 16.03959977 7.390748862 1.162248305 1.080501962 199.965594 0.44549772 0.119381179 914.5102904 2.753177732 0.031976644 483071.6514 24589452.69 -7.390748862 198.885092 AS(ph)PNLIGATGANSLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASPNLIGATGANSLGK 16 0 Q02078-8;Q02078-7;Q02078-4;Q02078-6;Q02078-3;Q02078-5;Q02078-2;Q02078 Q02078-8 MEF2A Myocyte-specific enhancer factor 2A 1 AS(1)PNLIGATGANSLGK;AS(1)PNLIGATGANSLGK 105.59 0.0013336 75864000 140733 124068 130430 134902 142797 117145 179466 132404 152028 TRUE FALSE 131924.7727 133254.1238 133523.8612 138363.8137 131582.2996 150962.8598 152556.7394 148934.9309 126653.5447 1.04161927 1.052115234 1.054244961 1.092459071 1.038915255 1.191935529 1.204520093 1.175923905 1 16.95052793 2.24111704 24.99731376 1.166029049 1.056800038 0.318486717 0.05931707 55.49554492 542654.7254 0.018774406 0.015044166 174.2276345 -2.24111704 -0.10922901 AS(ph)PPAESMSVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASPPAESMSVYR 12 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 AS(1)PPAESMSVYR;AS(1)PPAESMSVYR 143.76 0.00029084 0 133054 118067 130968 119249 154621 104413 120428 101878 164710 TRUE FALSE 124726.3876 126808.8035 134074.6228 122309.1312 142477.6904 134555.3381 102370.9394 114597.6926 137218.8369 0.908959662 0.924135537 0.977086133 0.891343594 1.038324574 0.980589408 0.746041445 0.835145488 1 17.06611902 1.758915785 25 0.835293154 0.953640507 0.234568172 0.074750995 9.549968812 11739.57569 0.031259398 0.017335113 57.4005145 -1.758915785 0.118347353 AS(ph)PPGDLQNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ASPPGDLQNPK 11 0 O00273 O00273 DFFA DNA fragmentation factor subunit alpha 1 AS(1)PPGDLQNPK;AS(1)PPGDLQNPK;AS(1)PPGDLQNPK;AS(1)PPGDLQNPK;AS(1)PPGDLQNPK;AS(1)PPGDLQNPK 176.99 8.58E-06 2796130000 2150920 1388210 1739130 1626820 1616840 1317170 2051410 1495650 1409970 TRUE FALSE 2016297.757 1490994.513 1780382.985 1668566.955 1489859.908 1697415.597 1743820.115 1682385.195 1174636.898 1.716528537 1.26932375 1.515687944 1.420495949 1.268357831 1.445055573 1.484560989 1.432259788 1 20.16378343 -1.029969708 4.109232557 0.999956485 1.432769049 0.547301939 0.126545844 6200052.998 3108058.844 2311.253121 0.026455457 0.09333194 1.029969708 0.432812565 AS(ph)PPPQGPLPGPPGALHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASPPPQGPLPGPPGALHR 18 0 A0A087WXV6;Q96G74-2;Q96G74-3;Q96G74-5;Q96G74 A0A087WXV6 OTUD5 OTU domain-containing protein 5 1 AS(1)PPPQGPLPGPPGALHR;AS(1)PPPQGPLPGPPGALHR;AS(1)PPPQGPLPGPPGALHR;AS(1)PPPQGPLPGPPGALHR 160.57 2.59E-11 4339300000 913730 918310 1034340 925100 1017300 835120 1143160 901240 1347110 TRUE FALSE 856541.2704 986302.6279 1058875.033 948839.6322 937405.3616 1076205.587 971753.7706 1013761.798 1122268.638 0.76322303 0.87884718 0.943512985 0.845465693 0.835277161 0.958955414 0.865883388 0.903314735 1 20.09798663 -5 0.105831584 1.361558504 0.810022687 0.438875426 0.050943298 200.2040359 1.423726826 16.00720613 0.719308243 1.00E-05 5 -0.551535817 AS(ph)PS(ph)PPPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASPSPPPKR 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 AS(1)PS(1)PPPKR 55.426 0.048885 0 154160 118660 133310 134300 126740 106550 162970 117610 164740 TRUE FALSE 144511.4008 127445.7099 136472.1762 137746.3654 116786.3516 137309.2553 138534.1614 132293.8674 137243.8297 1.052953718 0.928607939 0.994377499 1.003661626 0.850940635 1.00047671 1.009401747 0.963933079 1 17.06638176 -1.024025056 4.961641062 1.000000375 0.973912135 0.018692677 0.054559515 2.08E-07 4.09E-08 0.048605696 0.011456308 0.094618257 1.024025056 -0.02608824 AS(ph)PTLDFTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASPTLDFTER 10 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 AS(0.975)PT(0.025)LDFTER;AS(0.992)PT(0.008)LDFTER 140.78 4.06E-05 616300000 494240 471580 498780 466230 503060 418750 566380 440570 453160 TRUE FALSE 463306.4006 506496.2739 510611.2971 478194.2511 463551.6968 539636.3272 481456.577 495576.1343 377524.6685 1.227221528 1.341624313 1.352524324 1.266656966 1.227871277 1.429406797 1.275298324 1.312698681 1 18.52621139 -0.028017466 1.633498525 0.999814107 1.312003461 0.706387831 0.061441826 19.35250671 29.58288958 0.067073029 0.015504194 0.937524302 0.028017466 0.312189354 AS(ph)PVAVGSSGAGADPSFQPVLSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASPVAVGSSGAGADPSFQPVLSAR 24 0 Q5TGY3 Q5TGY3 AHDC1 AT-hook DNA-binding motif-containing protein 1 1 AS(1)PVAVGSSGAGADPSFQPVLSAR;AS(1)PVAVGSSGAGADPSFQPVLSAR 226.29 5.60E-33 81344000 116639 104315 118083 112120 119681 119291 153994 114107 132155 TRUE FALSE 109338.7732 112038.5911 120883.9845 114997.189 110281.737 153728.3752 130904.0293 128353.5101 110097.4767 0.993108802 1.017630871 1.097972343 1.044503402 1.00167361 1.396293355 1.18898301 1.165817001 1 16.74842188 2.286944615 24.99987968 1.20885037 1.038908039 0.372638678 0.099138932 101.7455863 52571.20446 0.031135041 0.026049395 193.617503 -2.286944615 -0.169942331 AS(ph)PVSFQELNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASPVSFQELNR 11 0 F5H212;P15822 F5H212 HIVEP1 Zinc finger protein 40 1 AS(1)PVSFQELNR;AS(0.993)PVS(0.007)FQELNR;AS(1)PVSFQELNR;AS(0.995)PVS(0.005)FQELNR 202.92 4.03E-08 675170000 397261 403103 375265 423553 427751 316791 457454 369516 311222 TRUE FALSE 372397.1431 432949.1655 384166.463 434422.0871 394157.1619 408243.419 388863.0195 415650.886 259277.0376 1.436290489 1.669832275 1.481683324 1.675513154 1.520216235 1.574545215 1.499797371 1.603114914 1 17.98413492 -2.41947675 0.596124213 2.97E-10 1.562651295 0.834065398 0.078057441 84.38588116 5.478996798 110.6229497 0.027264829 0.003806477 2.41947675 1.562651295 AS(ph)S(ph)HSSQTQGGGSVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 AS(0.577)S(0.577)HS(0.498)S(0.342)QT(0.005)QGGGSVTK 100.39 0.001094 298580000 274680 244670 201990 215100 256190 171610 309080 211780 205870 TRUE FALSE 257488.2691 262785.6214 206781.2982 220619.8302 236069.8708 221151.0211 262736.3234 238221.1992 171508.967 1.501310827 1.532197563 1.205658816 1.286345746 1.376428737 1.289442908 1.531910126 1.38897227 1 17.38792448 -1.24822411 3.101640039 0.998201245 1.388252343 0.555215353 0.109427286 8512668.872 11619671.24 146313.9156 0.026960599 0.056464552 1.24822411 0.390051098 AS(ph)SHSSQTQGGGSVTK ddPTM_SK-BR-3_Pertuzumab_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 AS(0.406)S(0.406)HS(0.091)S(0.091)QT(0.006)QGGGSVTK;AS(0.496)S(0.496)HS(0.004)S(0.004)QTQGGGSVTK;AS(0.397)S(0.397)HS(0.088)S(0.088)QT(0.031)QGGGSVTK;AS(0.249)S(0.249)HS(0.249)S(0.249)QT(0.005)QGGGSVTK;AS(0.467)S(0.35)HS(0.066)S(0.117)QTQGGGSVTK 192.25 3.64E-10 676175000 468789.4 620482 595676 538754 620459 408011 607933 505037 580804 TRUE FALSE 439448.7083 666423.1329 609805.716 552579.3397 571730.653 525797.1522 516779.0904 568091.9812 483864.0603 0.908206962 1.377294136 1.260283138 1.142013605 1.181593551 1.08666296 1.068025367 1.174073522 1 18.88424226 2.570476294 1.419966056 1.082964477 1.22886116 0.050753616 0.127694653 0.671225652 2.744067705 0.057417462 0.047112524 371.9429182 -2.570476294 0.145896683 AS(ph)SHSSQTQGGGSVTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASSHSSQTQGGGSVTKK 17 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 AS(0.576)S(0.423)HS(0.001)SQTQGGGSVTKK;AS(0.488)S(0.488)HS(0.024)SQTQGGGSVTKK 202.95 4.76E-12 648670000 365740 768090 572910 743000 959700 570330 993020 676770 1004890 TRUE FALSE 342848.9863 824960.1828 586499.6957 762066.6379 884329.0332 734975.0125 844125.8697 761266.2243 837167.3672 0.40953458 0.985418466 0.700576395 0.910291858 1.056334812 0.877930795 1.008311961 0.90933576 1 19.67515655 4.743202537 24.83933069 0.918278505 0.409534354 0.733139776 0.098611283 246.2817362 1317825.808 0.024115315 0.194433097 55360.82292 -4.743202537 -0.50874415 AS(ph)SPCHSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASSPCHSPR 9 0 A0A494BYR6;Q86Y91-6;Q86Y91 A0A494BYR6 KIF18B Kinesin-like protein KIF18B 1 AS(0.5)S(0.5)PCHSPR 67.214 0.039634 176310000 100110 106460 110110 105510 106240 90698 118600 115620 143820 TRUE FALSE 93844.2938 114342.4092 112721.8612 108217.5652 97896.33895 116881.0402 100817.031 130055.4115 119815.5129 0.783239929 0.954320575 0.940795215 0.903201619 0.817058965 0.975508408 0.841435542 1.08546388 1 16.87045518 1.234880501 24.99999926 1.042731976 0.899303268 0.490310118 0.064812955 83.50159879 567206.5611 0.050086207 0.014423541 17.1743576 -1.234880501 -0.143428708 AS(ph)SPCPEFEQFQIVPAVETPYLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASSPCPEFEQFQIVPAVETPYLAR 24 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;A0A0U1RQL3 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 AS(0.5)S(0.5)PCPEFEQFQIVPAVETPYLAR;AS(0.534)S(0.466)PCPEFEQFQIVPAVETPYLAR 125.99 6.11E-05 194589000 212030 236168 241780 234330 257684 214696 296160 213779 244737 TRUE FALSE 198759.4208 253654.1245 247515.1358 240343.3045 237446.5381 276675.2499 251753.5574 240469.7787 203888.8136 0.974842206 1.244080634 1.213971141 1.178795934 1.164588355 1.356990827 1.234759048 1.179416244 1 17.6374231 4.742840711 24.59095858 1.215107337 0.974842085 0.360112991 0.089921921 322.5981981 1853374.779 0.019028392 0.148323499 55314.71907 -4.742840711 -0.240265252 AS(ph)SPNSTVSNTSTEGFGGIMSFASSLYR ddPTM_SK-BR-3_Pertuzumab_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(0.419)S(0.419)PNS(0.051)T(0.051)VS(0.051)NT(0.006)S(0.001)T(0.001)EGFGGIMSFASSLYR 203.04 2.32E-25 19026000 7574 5230.6 5419.7 6628.4 10328 8172.6 7276.2 7393.2 8091 TRUE FALSE 7099.95686 5617.879066 5548.257843 6798.495966 9516.880541 10531.89695 6185.201359 8316.257294 6740.55983 1.053318573 0.833443988 0.823115288 1.008595152 1.411882808 1.562466207 0.917609444 1.23376359 1 12.7186527 2.966164137 6.090621884 1.223063307 0.880497814 0.378412054 0.19136127 0.187311607 21.10509889 0.057913957 0.063316416 925.0477199 -2.966164137 -0.342565494 AS(ph)SPPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASSPPDR 7 0 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.729)S(0.271)PPDR;AS(0.691)S(0.309)PPDR;AS(0.5)S(0.5)PPDR 103.74 0.0087152 1908140000 1764460 1598260 1743010 1752550 1590320 1455350 1809690 1517300 1181900 TRUE FALSE 1654025.598 1716596.833 1784355.02 1797523.4 1465422.682 1875485.919 1538343.785 1706738.245 984633.2546 1.67983926 1.743387018 1.812202677 1.82557657 1.4882929 1.904755817 1.562352051 1.733374571 1 19.90922694 -2.339983854 0.358321237 3.15E-10 1.757051291 0.774508429 0.121974681 21.9936035 0.99833315 17.48338624 0.080550132 0.004571052 2.339983854 1.75705129 AS(ph)SPPDRIDIFGR ddPTM_SK-BR-3_Pertuzumab_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(0.679)S(0.321)PPDRIDIFGR;AS(0.5)S(0.5)PPDRIDIFGR;AS(0.5)S(0.5)PPDRIDIFGR;AS(0.5)S(0.5)PPDRIDIFGR 190.19 2.80E-06 24892110000 1638570 2181190 1942420 2046100 2393200 1608800 2319220 1787840 2840610 TRUE FALSE 1536014.829 2342687.577 1988495.12 2098606.39 2205247.726 2073234.443 1971474.492 2011055.76 2366493.84 0.649067749 0.989940281 0.840270567 0.886799853 0.931862863 0.876078529 0.833078227 0.849803927 1 21.17431974 4.753333936 24.99084568 0.892343266 0.649067576 0.64286292 0.058694815 1778.35455 3008249.596 0.013382953 0.306072429 56667.48469 -4.753333936 -0.24327569 AS(ph)SPSEHGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASSPSEHGPR 10 0 C9J052;Q9NSU2-2;Q9NSU2;Q9NSU2-1 C9J052 TREX1 Three-prime repair exonuclease 1 1 AS(0.5)S(0.5)PSEHGPR;AS(0.5)S(0.5)PSEHGPR;AS(0.5)S(0.5)PSEHGPR;AS(0.499)S(0.499)PS(0.002)EHGPR 122.33 0.0003166 762357000 383931 554163 479194 486494 592001 495493 546170 488357 588567 TRUE FALSE 359901.444 595193.8051 490560.708 498978.2597 545507.6295 638533.7854 464276.8789 549329.4465 490331.3654 0.733996374 1.213860355 1.00046773 1.017634797 1.112528522 1.30224952 0.946863512 1.120322878 1 18.90339753 4.751624093 24.46563497 1.088870652 0.733996063 0.519737493 0.107318615 1303.202458 2440614.68 0.024021722 0.447019159 56444.82004 -4.751624093 -0.354874588 AS(ph)SREDGRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASSREDGRPR 10 2 Q02040 Q02040 AKAP17A A-kinase anchor protein 17A 1 AS(0.5)S(0.5)REDGRPR 63.181 0.063208 238010000 96879 139710 111240 129920 142500 71314 130570 106330 177500 TRUE FALSE 90815.51632 150054.2738 113878.6653 133253.9672 131308.6248 91901.19411 110992.2407 119605.5346 147874.1033 0.614140774 1.014743423 0.770105534 0.901131193 0.887975798 0.621482681 0.750586061 0.808833541 1 17.17400989 AS(ph)SRSPVFTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASSRSPVFTPR 11 1 P52735-3 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 1 AS(0.563)S(0.089)RS(0.347)PVFTPR 89.624 0.0073243 249900000 99479 154430 108790 113920 148500 94466 130830 119920 130730 TRUE FALSE 93252.78697 165864.1579 111370.5502 116843.3801 136837.409 121736.8007 111213.2561 134892.276 108910.3185 0.856234637 1.522942548 1.022589519 1.072840312 1.256422816 1.117771047 1.021145266 1.238562864 1 16.73278112 0.968148942 0.235111716 0.967941061 1.22394484 0.007400119 0.182019517 8.297135724 1.605998267 0.784561979 0.478409979 9.292850328 -0.968148942 0.256003779 AS(ph)SWPHRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASSWPHRR 8 1 A0A2R8YF49;H0Y895;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 AS(0.5)S(0.5)WPHRR 83.783 0.0098096 0 101940 129490 127090 111930 123290 102000 141660 105720 116530 TRUE FALSE 95559.75737 139077.5743 130104.6348 114802.3133 113607.3007 131445.7442 120419.3981 118919.3747 97080.39019 0.984336354 1.432602136 1.340174206 1.182548948 1.170239433 1.353988626 1.240409086 1.224957733 1 16.56689229 0.608772171 1.550428913 1.000087868 1.272364367 0.250517487 0.124310593 1.991319813 6.364527824 0.113679593 0.032753085 4.062301667 -0.608772171 0.272276499 AS(ph)TASASAAVSAARPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASTASASAAVSAARPR 16 1 E9PC69;Q7KZI7-14;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7 E9PC69;Q7KZI7-12 MARK2 Serine/threonine-protein kinase MARK2 1 AS(0.539)T(0.024)AS(0.279)AS(0.017)AAVS(0.14)AARPR 88.768 0.0057905 0 75469 96502 86153 93397 112130 55260 127930 83441 110840 TRUE FALSE 70745.53001 103647.1085 88196.58984 95793.72514 103323.7621 71212.66493 108748.0841 93858.79253 92340.08795 0.766141029 1.122449748 0.955127852 1.037401277 1.118948058 0.771199882 1.177690931 1.016446861 1 16.49466949 4.751954745 24.3389622 1.028395686 0.766140779 0.346882227 0.111496401 1655.715861 3008584.957 0.023809909 0.447043027 56487.81096 -4.751954745 -0.262254907 AS(ph)TDNEELLQFPLELCSDSLPSHPFPPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASTDNEELLQFPLELCSDSLPSHPFPPAK 29 0 Q86YS7;Q86YS7-5;H0YFC4;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 AS(0.499)T(0.499)DNEELLQFPLELCS(0.001)DSLPSHPFPPAK;AS(0.807)T(0.193)DNEELLQFPLELCSDSLPSHPFPPAK 96.55 0.00069081 47187000 65939 64332 61821 60353 72249 45614 80218 63897 80595 TRUE FALSE 61811.99569 69095.20822 63287.42331 61901.76016 66574.85498 58782.02132 68190.05561 71874.6811 67143.17384 0.920599849 1.029072715 0.942574199 0.92193676 0.991535717 0.875472784 1.015591783 1.070468925 1 16.03495311 1.544174566 7.759082665 1.037444316 0.955892118 0.419526202 0.044937642 0.116975942 12.48594091 0.02316543 0.010755371 35.0085857 -1.544174566 -0.081552197 AS(ph)TFCGTPDYIAPEILQGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.445)T(0.445)FCGT(0.11)PDYIAPEILQGLK;AS(0.333)T(0.333)FCGT(0.333)PDYIAPEILQGLK;AS(0.587)T(0.41)FCGT(0.003)PDYIAPEILQGLK 241.13 6.38E-30 395348000 695090 541009 498154 499471 528433 300502 876170 512975 708120 TRUE FALSE 651585.5577 581065.8693 509970.4481 512288.2715 486932.0038 387252.0492 744796.4425 577021.0579 589930.1974 1.104512976 0.984973937 0.864458965 0.868387944 0.825406134 0.656437068 1.262516219 0.978117514 1 19.17018473 1.72691728 25 1.094423461 0.890559795 0.314863785 0.135654537 0.981921287 2098.803331 0.060643713 0.033629995 53.32333215 -1.72691728 -0.203863665 AS(ph)TPDWVSEGPQPGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASTPDWVSEGPQPGLR 16 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 AS(0.5)T(0.5)PDWVSEGPQPGLR 279.71 2.09E-35 214040000 200680 185440 196980 182710 203100 153340 245490 189900 174440 TRUE FALSE 188119.797 199170.1706 201652.4586 187398.6479 187149.3453 197606.7687 208681.0535 213609.433 145324.8371 1.294477949 1.370517074 1.387598037 1.289515624 1.287800138 1.359759094 1.435962756 1.469875606 1 17.14892177 -1.152175865 4.46808963 0.999940426 1.365770152 0.777566613 0.060806363 3.70E-05 7.02E-06 0.060364449 0.014225726 0.070440777 1.152175865 0.365829725 AS(ph)TPQPAPAGVPALASQHPPEEEVHYHLPVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASTPQPAPAGVPALASQHPPEEEVHYHLPVAR 32 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 AS(0.805)T(0.195)PQPAPAGVPALASQHPPEEEVHYHLPVAR 49.193 0.036895 340110000 59423 89038 82407 76975 90898 80874 101050 79977 100430 TRUE FALSE 55703.8205 95630.46616 84361.73296 78950.30882 83759.23774 104221.0109 85898.4906 89962.3045 83667.5842 0.665775414 1.142981085 1.008296508 0.943618841 1.001095449 1.245655793 1.026663928 1.075234876 1 16.35238116 2.447983145 24.99931302 1.092431451 0.984028033 0.176173354 0.13557082 419.7310798 360110.1774 0.044090387 0.036889011 280.5324764 -2.447983145 -0.108403418 AS(ph)TPVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASTPVLK 7 0 Q04724;A0A669KBK8;A0A669KAE5;F6T2C8 Q04724 TLE1 Transducin-like enhancer protein 1 1 AS(0.5)T(0.5)PVLK 95.099 0.014387 314930000 1350500 1021400 1182400 1068600 1295300 1002300 1760100 1255900 1237900 TRUE FALSE 1265974.616 1097025.519 1210447.086 1096022.085 1193572.363 1291647.739 1496189.345 1412701.88 1031286.493 1.227568309 1.063744678 1.173725337 1.062771686 1.157362548 1.252462578 1.450798934 1.369844257 1 19.97601374 2.153852193 3.551387411 1.328499264 1.127413739 0.162850494 0.127574524 0.241968792 6.008585517 0.046302501 0.032830792 142.5122488 -2.153852193 -0.201085525 AS(ph)TSKSESSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASTSKSESSQK 11 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 1 AS(0.451)T(0.451)S(0.095)KS(0.002)ESSQK 59.248 0.061282 200950000 162480 229860 238130 209240 255310 201710 267520 221440 315270 TRUE FALSE 152310.6668 246879.0736 243778.5561 214609.4526 235258.9825 259940.4025 227407.8595 249087.2714 262649.4003 0.579901065 0.939956738 0.928151961 0.817094775 0.895714904 0.989685879 0.865822878 0.948364136 1 18.00277876 4.740940995 24.79795977 0.917077618 0.579900932 0.795422042 0.05462296 81.94494664 853615.4975 0.012019822 0.081030105 55073.28665 -4.740940995 -0.337176686 AS(ph)WESLDEEWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASWESLDEEWR 11 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 AS(0.85)WES(0.15)LDEEWR 210.15 1.44E-08 96535000 163470 161240 158820 160240 129930 136840 189570 135050 136570 TRUE FALSE 153238.7045 173178.3774 162587.2854 164352.0297 119725.8219 176343.4866 161145.7384 151911.2898 113775.5847 1.346850512 1.522104921 1.429017357 1.444528104 1.052298015 1.5499238 1.416347266 1.335183556 1 16.79583148 -3.246064135 0.298497696 3.98E-12 1.430577498 0.443656684 0.136225922 74.07783961 1.799177582 46.26968002 0.133818545 0.000567461 3.246064135 1.430577498 AS(ph)YASTDQPSWMELAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASYASTDQPSWMELAR 16 0 Q6NV74 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 AS(0.999)YAS(0.001)TDQPSWMELAR 85.988 0.0073028 32446000 50187 63027 49028 50974 58072 42639 66770 55859 54649 TRUE FALSE 47045.88526 67693.58466 50190.96731 52282.07914 53511.25937 54948.18711 56758.45836 62833.11911 45527.72885 1.033345753 1.486864958 1.102426336 1.148356847 1.175355343 1.206916938 1.246678888 1.380106601 1 15.47445787 3.779362524 24.33728282 1.193473341 1.293143697 0.033063357 0.145660063 332.7731766 155024.1818 0.033936362 0.061179592 6016.757719 -3.779362524 0.099670355 ASAAFSS(ph)VGSVITK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASAAFSSVGSVITK 14 0 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 1 ASAAFS(0.008)S(0.98)VGS(0.012)VITK;ASAAFS(0.066)S(0.817)VGS(0.117)VITK 164.66 4.29E-06 231680000 823830 763140 764480 732510 1193350 585150 755710 821670 957430 TRUE FALSE 772267.9509 819643.6796 782613.8266 751307.4467 1099629.105 754073.3059 642398.3012 924257.3082 797628.7478 0.968204761 1.027600474 0.981175552 0.941926239 1.378622709 0.945393841 0.80538509 1.158756264 1 19.60535788 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEK 32 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;; 360.07 3.65E-132 1978840000 1045221 1119478 1173586 1191067 1248885 988889 1474794 1112984 1375111 FALSE TRUE 979802.4834 1202365.316 1201424.014 1221631.796 1150802.61 1274365.201 1253662.331 1251942.502 1145596.091 0.855277433 1.049554311 1.048732641 1.066372176 1.004544812 1.112403588 1.094331887 1.092830634 1 20.12766704 4.74505534 4.020358225 1.063691373 0.835446998 0.75435877 0.036452179 0.117318944 3.98420103 0.008572823 0.078724999 55597.50976 -4.74505534 -0.228244375 ASALLFS(ph)S(ph)DEEDQWNIPASQTHLASDSR ddPTM_SK-BR-3_Pertuzumab_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 2 ASALLFS(1)S(1)DEEDQWNIPASQTHLASDSR 129.59 1.41E-05 27442000 14303 13734 13455 13796 18708 10764 15856 13049 18064 TRUE FALSE 13407.80076 14750.87965 13774.15895 14150.02872 17238.74914 13871.39206 13478.54 14678.19637 15049.0017 0.89094287 0.980189912 0.915287221 0.940263613 1.145507821 0.921748322 0.895643463 0.975360138 1 13.87738017 4.747747959 23.30997911 0.962816045 0.890942771 0.104675068 0.070066994 1259.10672 3194400.162 0.016507495 0.193627497 55943.28426 -4.747747959 -0.071873274 ASALLFS(ph)SDEEDQWNIPASQTHLASDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASALLFSSDEEDQWNIPASQTHLASDSR 28 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;Q9Y4E1-5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 ASALLFS(0.564)S(0.436)DEEDQWNIPASQTHLASDSR;AS(0.001)ALLFS(0.538)S(0.461)DEEDQWNIPASQTHLASDSR 251.33 4.34E-47 549947000 48429 70425.3 73745 71138 71792.2 63967 86184 66951.6 83496 TRUE FALSE 45397.91534 75639.66249 75494.26622 72963.52152 66153.93021 82433.23448 73261.50929 75310.65464 69559.9782 0.652644186 1.087402044 1.085311816 1.04892962 0.951034372 1.185066997 1.053213517 1.0826722 1 16.08596986 4.740160477 24.96721883 1.068300874 0.652644046 0.815757532 0.061023137 51.72926478 807207.8204 0.013239188 0.084558769 54974.39737 -4.740160477 -0.415656828 ASALLFSS(ph)DEEDQWNIPASQTHLASDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ASALLFSSDEEDQWNIPASQTHLASDSR 28 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;Q9Y4E1-5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 ASALLFS(0.16)S(0.84)DEEDQWNIPASQTHLASDSR;ASALLFS(0.126)S(0.874)DEEDQWNIPASQTHLASDSR;ASALLFS(0.125)S(0.875)DEEDQWNIPASQTHLASDSR;ASALLFS(0.143)S(0.857)DEEDQWNIPASQTHLASDSR;ASALLFS(0.152)S(0.848)DEEDQWNIPASQTHLASDSR;ASALLFS(0.138)S(0.862)DEEDQWNIPASQTHLASDSR;ASALLFS(0.112)S(0.888)DEEDQWNIPASQTHLASDSR 325.66 3.73E-84 2855944000 452112 636654 596522 606458 667843 583435 719954 588954 763855 TRUE FALSE 423815.117 683792.5246 610671.7835 622020.739 615393.3047 751863.2132 612003.5814 662486.2033 636362.6658 0.6659962 1.074532749 0.959628552 0.977462652 0.967048097 1.181501137 0.96172138 1.041051336 1 19.27948967 4.744101646 24.99303087 1.018760436 0.66599605 0.728594763 0.067965383 305.3109449 1377076.268 0.015013606 0.13190116 55475.55371 -4.744101646 -0.352764387 ASAPERT(ph)PS(ph)PAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASAPERTPSPAPK 13 1 Q96P11-2;Q63ZY6;Q63ZY6-6;Q3KNT7-3 Q96P11-2 NSUN5;NSUN5P2 Probable 28S rRNA (cytosine-C(5))-methyltransferase;Putative methyltransferase NSUN5C 2 AS(0.003)APERT(0.997)PS(1)PAPK 96.153 0.01001 372080000 1233200 864650 1058300 1006200 1016000 825110 1349900 907550 1204600 TRUE FALSE 1156016.213 928669.5857 1083403.376 1032020.795 936207.4583 1063305.862 1147495.027 1020859.615 1003544.478 1.151933211 0.925389563 1.079576839 1.02837574 0.932900812 1.05955031 1.143442121 1.017253981 1 19.93667313 2.015292503 24.99790268 1.07750161 1.016260604 0.004440015 0.075831397 461.6735283 754672.3236 0.0261458 0.019303521 103.5839584 -2.015292503 -0.061241006 ASAPS(ph)PNAQVACDHCLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASAPSPNAQVACDHCLK 17 0 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 1 AS(0.001)APS(0.999)PNAQVACDHCLK;ASAPS(1)PNAQVACDHCLK 306.88 1.82E-47 2102400000 2855200 2259000 2404000 2114750 2262700 2373100 3418300 2099300 2465300 TRUE FALSE 2676498.129 2426258.71 2461024.015 2169018.065 2084996.669 3058175.446 2905757.649 2361402.226 2053825.504 1.303176986 1.181336343 1.198263441 1.05608683 1.015177125 1.489014252 1.414802593 1.149757962 1 20.96988218 2.245090123 24.99991132 1.317302717 1.157136768 0.068651061 0.156954292 244.9269857 937768.521 0.052442036 0.042914702 175.8288448 -2.245090123 -0.160165949 ASAS(ph)PSTSSTSSRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASASPSTSSTSSRPK 15 1 J3KP75;O75167-5;O75167-2;O75167;O75167-4;F6TH74;F5H858 J3KP75 PHACTR2 Phosphatase and actin regulator;Phosphatase and actin regulator 2 1 ASAS(0.994)PS(0.005)T(0.001)SSTSSRPK;ASAS(0.948)PS(0.052)TSSTSSRPK;ASAS(0.427)PS(0.427)T(0.089)S(0.015)S(0.015)T(0.023)S(0.004)S(0.001)RPK 180.11 4.47E-07 422601000 441705 399877 403550 403020 450673 295579 464629 365226 463485 TRUE FALSE 414059.4725 429484.3092 413122.3966 413362.1755 415278.9605 380907.859 394962.1949 410825.2701 386126.3593 1.072341897 1.112289536 1.069915033 1.070536019 1.075500158 0.986484993 1.022883275 1.063965876 1 18.55871352 2.345981714 6.979039423 1.019507263 1.083341244 0.639268247 0.023043986 0.134831266 7.886659052 0.00784755 0.006539283 221.8103024 -2.345981714 0.063833981 ASAVSELS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 ASAVSELSPR 10 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR 205.97 1.67E-07 51818061000 5891730 6707950 6390540 6382310 6589610 5688651 7106910 5755175 6789050 TRUE FALSE 5522977.136 7204613.598 6542126.627 6546090.88 6072088.612 7330872.196 6041294.823 6473721.267 5655913.696 0.976496006 1.273819578 1.156687845 1.157388749 1.073582261 1.296142867 1.068137731 1.144593361 1 22.43132868 0.639771117 0.954224918 1.000505391 1.163637315 0.169194092 0.094810416 1.744835792 2.660166553 0.081937709 0.02669045 4.362858393 -0.639771117 0.163131924 ASDADRPCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASDADRPCR 9 1 Q86U44;H0YFV6;Q86U44-2 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 0 ; 104.01 0.003036 417710000 717870 809340 793420 804360 827780 798530 965170 765860 850500 FALSE TRUE 672939.7981 869264.3757 812240.2971 825001.2394 762769.4979 1029052.648 820451.7187 861479.3069 708546.0556 0.949747434 1.226828332 1.14634792 1.164357959 1.07652776 1.45234405 1.157937035 1.215840947 1 19.43450211 4.743722237 24.37395806 1.191985203 0.949747288 0.270922467 0.117266988 474.1173501 2238750.997 0.025063657 0.210421673 55427.11029 -4.743722237 -0.242237915 ASDPQS(ph)PPQVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASDPQSPPQVSR 12 0 Q7L7X3-3;Q7L7X3;Q7L7X3-2 Q7L7X3-3 TAOK1 Serine/threonine-protein kinase TAO1 1 AS(0.001)DPQS(0.998)PPQVS(0.002)R 85.554 0.012177 275090000 294640 295300 330150 326470 387960 272740 309660 302650 377200 TRUE FALSE 276199.0083 317164.3193 337981.3139 334847.7729 357491.1866 351475.6104 263229.3577 340436.5187 314242.8832 0.878934808 1.009296745 1.075541665 1.065569949 1.137626994 1.118483916 0.837662114 1.083354745 1 18.26152055 -0.954230028 6.805679023 0.999999998 1.023583504 0.006402191 0.09760535 2.80E-09 4.11E-10 0.093920622 0.022137301 0.111114304 0.954230028 0.023583506 ASDSSS(ph)PSCSSGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASDSSSPSCSSGPR 14 0 Q92610;H0YM74 Q92610 ZNF592 Zinc finger protein 592 1 ASDS(0.002)S(0.086)S(0.912)PSCSSGPR;ASDSS(0.001)S(0.997)PS(0.002)CSSGPR 216.83 6.75E-12 233070000 444840 460290 458420 409730 517220 441140 504380 458490 634890 TRUE FALSE 416998.2585 494370.3505 469293.9389 420244.3655 476599.6276 568489.9567 428752.9014 515733.4858 528922.7575 0.788391599 0.934674002 0.887263655 0.794528803 0.901076047 1.074807141 0.810615341 0.975063898 1 19.01269752 2.471736909 24.99885616 0.945080258 0.868799591 0.294397691 0.07851895 253.7030862 1177899.143 0.02607622 0.021883477 296.3035867 -2.471736909 -0.076280667 ASDVHEVR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 167.04 0.00031497 24640920000 38717670 49644900 46549100 48175200 48884400 41606210 51124900 42555870 41192690 FALSE TRUE 36294400.15 53320660.05 47653266.63 49411457.19 45045216.41 53617247.41 43459195.87 47869064.05 34317363.92 1.057610376 1.553751628 1.388605102 1.439838366 1.312607125 1.562394114 1.266390856 1.394893388 1 25.0324354 0.005463807 0.835957692 0.991886913 1.39847719 0.379525227 0.146479342 5.236959804 3.584685478 0.257608766 0.042419844 1.012660353 -0.005463807 0.406590277 ASDVHEVRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ASDVHEVRK 9 1 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;; 78.098 0.019951 1261821000 2196718 2638330 2336970 2521320 3113490 1741169 2750100 2287730 4337070 FALSE TRUE 2059229.342 2833674.698 2392404.032 2586021.34 2868969.055 2243816.225 2337748.036 2573358.126 3613184.998 0.569920816 0.784259511 0.662131619 0.715717944 0.794027722 0.621007844 0.6470048 0.712213221 1 21.78483969 0.944912089 20.53895408 1.000000001 0.690951958 0.67253438 0.068513541 1085.500607 404719.0981 0.06202321 0.015505802 8.808705472 -0.944912089 -0.309048043 ASEAGEVPFNHEILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASEAGEVPFNHEILR 15 0 Q7L5N1;E7EM64 Q7L5N1 COPS6 COP9 signalosome complex subunit 6 0 ; 119.56 0.000203 1549410000 814480 837010 928290 846180 881180 790690 926140 794190 842920 FALSE TRUE 763503.1507 898983.0913 950309.4772 867894.4114 811975.6773 1018949.367 787273.9049 893346.3697 702231.2065 1.087253235 1.280181061 1.353271499 1.235909773 1.156279684 1.451016927 1.121103559 1.272154187 1 19.42158658 0.098917237 0.783046871 0.994488123 1.262214661 0.322362397 0.108907708 4.550466348 3.066736849 0.169433254 0.033853105 1.255790627 -0.098917237 0.267726537 ASEDTTS(ph)GSPPKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASEDTTSGSPPKK 13 1 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 ASEDTT(0.007)S(0.637)GS(0.355)PPKK;ASEDT(0.002)T(0.049)S(0.527)GS(0.422)PPKK 124.3 0.00022602 1160600000 1030160 508640 665950 654000 669520 479210 897310 575740 886840 TRUE FALSE 965684.1245 546300.2348 681746.6485 670782.7472 616938.5999 617550.1477 762766.6957 647622.4064 738820.6748 1.307061588 0.739421965 0.922749825 0.907910093 0.835031586 0.835859321 1.032411141 0.876562376 1 19.49486471 -0.591742642 5.071818609 1.000000005 0.914869377 0.007991237 0.153697832 15869231.54 6257806.957 1.07110421 0.032201787 0.256010253 0.591742642 -0.085130628 ASEDTTSGS(ph)PPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASEDTTSGSPPK 12 0 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 ASEDTTS(0.002)GS(0.998)PPK;ASEDTTS(0.001)GS(0.999)PPK;ASEDTT(0.001)S(0.002)GS(0.997)PPK;ASEDTT(0.001)S(0.002)GS(0.997)PPK 253.16 4.68E-21 915980000 2804470 1876890 2074430 2012810 2201960 1583170 2774920 1861030 2514430 TRUE FALSE 2628943.229 2015856.889 2123636.459 2064462.112 2029026.944 2040205.478 2358846.507 2093383.692 2094755.389 1.255012037 0.96233522 1.013787323 0.985538513 0.968622377 0.973958816 1.126072533 0.999345176 1 20.99835036 -3.097043203 8.946742034 1.000825637 1.026650599 0 0.091666874 0 0 0 0.018639422 0.000799755 3.097043203 0.025824962 ASEDTTSGS(ph)PPKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ASEDTTSGSPPKK 13 1 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 ASEDTT(0.005)S(0.283)GS(0.712)PPKK;ASEDT(0.001)T(0.004)S(0.031)GS(0.965)PPKK;ASEDT(0.001)T(0.037)S(0.161)GS(0.801)PPKK;ASEDTT(0.004)S(0.023)GS(0.972)PPKK;ASEDT(0.006)T(0.031)S(0.158)GS(0.805)PPKK;ASEDTT(0.008)S(0.046)GS(0.946)PPKK;ASEDTTS(0.017)GS(0.982)PPKK 229.9 5.29E-12 3359970000 5289420 2748344 3584470 3385400 3608510 2420086 4770070 2964520 4462090 TRUE FALSE 4958364.644 2951834.249 3669495.321 3472275.095 3325112.181 3118725.541 4054842.287 3334646.848 3717338.353 1.333848085 0.794071986 0.987129761 0.934075612 0.894487363 0.838967359 1.090791825 0.897052281 1 21.82583858 -0.043133739 8.913550535 1.000001375 0.95745954 0 0.15246981 17786119.39 1995401.542 0.130404199 0.031627664 0.905453727 0.043133739 -0.042541835 ASEEHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ASEEHLK 7 0 Q32Q12;P22392-2;J3KPD9;P22392;F6XY72 Q32Q12 NME1-NME2;NME2 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B 0 ;;;;;;; 114.72 0.0058414 33240080000 21751970 21620340 20735130 20257580 23755460 16059980 27151080 20208990 25951630 FALSE TRUE 20390553.03 23221132.47 21226977.08 20777423.8 21889802 20696235.51 23080027.61 22732126.89 21620135.3 0.94312791 1.07405121 0.981815182 0.961021914 1.012472942 0.957266697 1.067524661 1.051433147 1 24.36587222 1.710854486 12.21088725 1.044213031 0.997333429 0.242097495 0.040513736 0.174158361 58.78501916 0.018478728 0.010115926 51.38714459 -1.710854486 -0.046879602 ASEENLLSSSSVPSADRDS(ph)SPTTNSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASEENLLSSSSVPSADRDSSPTTNSK 26 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 ASEENLLSSSSVPSADRDS(0.888)S(0.112)PTTNSK 252.14 9.86E-53 353590000 377520 308980 364170 347440 377060 278390 427860 339760 413580 TRUE FALSE 353891.6971 331857.2007 372808.2844 356355.8986 347447.2286 358756.6737 363706.3651 382179.7839 344550.8262 1.027110284 0.963158917 1.082012452 1.034262209 1.008406314 1.041230049 1.055595684 1.109211631 1 18.39435729 3.97891856 24.83016237 1.047866286 0.994569017 0.275283496 0.035137611 89.00300659 1229558.878 0.008214185 0.016407117 9526.17511 -3.97891856 -0.053297269 ASEENLLSSSSVPSADRDSS(ph)PTTNSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASEENLLSSSSVPSADRDSSPTTNSK 26 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 ASEENLLSSSSVPSADRDS(0.219)S(0.625)PT(0.129)T(0.027)NSK;ASEENLLSSSSVPSADRDS(0.044)S(0.956)PT(0.001)TNSK;ASEENLLSSSSVPSADRDS(0.219)S(0.778)PT(0.002)TNSK 327.71 4.27E-95 1856850000 1153560 933570 1049030 1039620 1125480 855630 1366430 1045540 1238200 TRUE FALSE 1081360.739 1002692.494 1073913.487 1066298.409 1037089.341 1102636.491 1161546.507 1176077.971 1031536.421 1.048301075 0.972037898 1.041081503 1.033699235 1.005383154 1.068926379 1.126035381 1.140122585 1 19.97636333 2.065221518 4.187004243 1.101927208 1.017291948 0.344788397 0.042794291 0.178045901 6.2545315 0.015807879 0.010964765 116.2041179 -2.065221518 -0.08463526 ASEHKDQLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASEHKDQLSR 10 1 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 0 ;; 183.99 9.66E-07 356330000 285894 417370 385480 373682 384880 266514 464500 338362 493690 FALSE TRUE 268000.4049 448272.5091 394623.7676 383271.3128 354653.0773 343452.2653 394852.5372 380607.2405 411289.9496 0.651609418 1.089918461 0.959478266 0.931876194 0.862294539 0.835061167 0.96003449 0.925398836 1 18.64979629 0.582906459 1.664216467 0.999843829 0.922046353 0.04429211 0.113222971 7.805986466 26.50064851 0.103048127 0.029277457 3.827422967 -0.582906459 -0.077797476 ASEKPVS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 124.06 0.0014212 101590000 222840 100530 141620 149280 149080 77117 138080 91411 143400 TRUE FALSE 208892.8422 107973.3458 144979.2933 153110.7775 137371.8582 99379.42601 117376.1859 102823.8646 119465.6136 1.748560409 0.903802714 1.213565049 1.281630529 1.149886181 0.831866367 0.982510216 0.860698417 1 16.86623589 2.356979325 5.421230735 0.922423269 1.211034683 0.377689356 0.213606633 0.256280621 11.16880125 0.070908301 0.058789005 227.4989124 -2.356979325 0.288611413 ASEPLLS(ph)PPPFGESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASEPLLSPPPFGESR 15 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 ASEPLLS(1)PPPFGESR;ASEPLLS(1)PPPFGESR;ASEPLLS(1)PPPFGESR;ASEPLLS(1)PPPFGESR 234.63 1.23E-17 582570000 307253 321875 341962 404426 403970 247163 300202 222046 279513 TRUE FALSE 288022.5832 345706.9599 350073.5001 414804.2559 372243.8257 318514.9457 255189.497 249768.9319 232860.4746 1.236889102 1.484609874 1.503361619 1.781342482 1.598570244 1.367836024 1.095890136 1.072611968 1 17.82910625 1.823739932 2.567581173 1.046811009 1.524354974 0.714559096 0.134052859 0.150267553 1.851412751 0.079529062 0.038346089 66.6407585 -1.823739932 0.477543965 ASES(ph)PARGPSGSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASESPARGPSGSPR 14 1 O43237;O43237-2;J3KRZ2 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 AS(0.213)ES(0.787)PARGPSGSPR 78.95 0.012384 285930000 129660 147810 127650 148020 174070 120580 168500 149710 208560 TRUE FALSE 121544.812 158754.0062 130677.9183 151818.4438 160399.2444 155389.4885 143234.9893 168401.6231 173749.9887 0.699538532 0.913692182 0.752103176 0.873775273 0.923161179 0.89432805 0.824374093 0.969218038 1 17.40665336 4.778631573 0.032231478 1.598209679 2.01E-07 0.486248313 0.066331896 549.070333 2.724000356 52.78634625 85.00210745 60066.39575 -4.778631573 -1.598209478 ASES(ph)S(ph)SEEKDDYEIFVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASESSSEEKDDYEIFVK 17 1 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;H7C1M2 P18583-7 SON Protein SON 2 AS(0.498)ES(0.615)S(0.763)S(0.118)EEKDDY(0.007)EIFVK 87.772 0.002538 30544000 187160 84917 112830 113100 122120 77710 153940 91256 137770 TRUE FALSE 175445.9897 91204.34304 115506.3809 116002.3375 112529.1878 100143.6155 130858.1261 102649.5125 114775.297 1.528604101 0.79463391 1.006369697 1.010690807 0.980430378 0.872518897 1.140124483 0.894351966 1 16.80845264 4.74955043 24.93393943 0.966351415 1.528604436 0.783803541 0.093434685 736.547021 1671061.647 0.022080715 0.334012755 56175.95052 -4.74955043 0.562253021 ASES(ph)SSEEKDDYEIFVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASESSSEEKDDYEIFVK 17 1 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;H7C1M2 P18583-7 SON Protein SON 1 ASES(0.821)S(0.16)S(0.019)EEKDDYEIFVK 175.86 7.13E-10 155990000 380290 185930 266600 253890 237750 166250 322670 208730 283830 TRUE FALSE 356488.3277 199696.4507 272923.8779 260405.2472 219078.074 214243.6762 274288.629 234790.4 236456.9394 1.507624723 0.844536224 1.154222323 1.101279784 0.926503044 0.906057892 1.159993992 0.992952038 1 17.85121796 4.751728892 24.94193451 1.020447942 1.507625048 0.690747386 0.104313789 1278.529291 2421608.781 0.024387702 0.467291317 56458.4423 -4.751728892 0.487177106 ASESSKPWPDATYGT(ph)GSASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASESSKPWPDATYGTGSASR 20 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 ASESSKPWPDATYGT(0.584)GS(0.402)AS(0.014)R 135.58 1.12E-05 369990000 197420 179000 194480 199630 199060 159010 273710 201490 277740 TRUE FALSE 185063.8346 192253.3462 199093.1574 204752.8438 183426.6306 204913.6057 232669.7265 226646.47 231383.3997 0.799814657 0.830886513 0.860447023 0.884907232 0.792738938 0.885602018 1.005559287 0.979527789 1 17.81992584 1.861961105 3.642412369 0.994368914 0.839196851 0.873065992 0.027947267 0.076922464 1.688007021 0.013493333 0.007327414 72.77146289 -1.861961105 -0.155172063 ASESSKPWPDATYGTGS(ph)ASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASESSKPWPDATYGTGSASR 20 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 ASESSKPWPDATYGT(0.046)GS(0.766)AS(0.188)R 156.47 1.10E-08 317430000 241140 204180 224660 235190 252500 207460 329980 219990 315090 TRUE FALSE 226047.4778 219297.6996 229989.0413 241225.3736 232669.6685 267350.3342 280502.5624 247456.2358 262499.4434 0.861135075 0.835421579 0.876150586 0.918955752 0.886362521 1.018479623 1.068583456 0.942692421 1 18.00195484 2.264128825 4.690620478 1.020261424 0.870723458 0.752739959 0.037266277 0.086267981 4.568227127 0.013767544 0.010910463 183.7083197 -2.264128825 -0.149537966 ASESSKPWPDATYGTGSASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASESSKPWPDATYGTGSASR 20 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ; 247.55 3.50E-30 561420000 875430 819090 794960 841440 849370 627860 889410 701370 913760 FALSE TRUE 820638.399 879736.2759 813816.8266 863032.775 782663.9064 809112.9895 756051.2274 788937.5884 761247.5529 1.078017783 1.155650711 1.069056739 1.133708439 1.028133231 1.062877623 0.993173935 1.036374548 1 19.53800616 2.47988374 1.066301667 1.009101826 1.114589643 0.615490215 0.032421815 0.291278704 0.667344047 0.017654691 0.012584039 301.9143392 -2.47988374 0.105487817 ASET(ph)PPPVAQPKPEAPHPGLETTLQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASETPPPVAQPKPEAPHPGLETTLQER 27 1 Q6P1N0-2;Q6P1N0 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 AS(0.036)ET(0.964)PPPVAQPKPEAPHPGLETTLQER;ASET(1)PPPVAQPKPEAPHPGLETTLQER;AS(0.002)ET(0.998)PPPVAQPKPEAPHPGLETTLQER;AS(0.042)ET(0.958)PPPVAQPKPEAPHPGLETTLQER 209.2 2.60E-25 2785880000 1723480 1446130 1655250 1706990 1829090 1388780 1807290 1403920 2070990 TRUE FALSE 1615610.463 1553202.97 1694513.312 1750794.253 1685440.65 1789698.241 1536303.643 1579202.502 1725328.39 0.936407511 0.90023614 0.982139587 1.01476001 0.976881073 1.037308753 0.890441293 0.915305464 1 20.71843955 3.94758461 4.732122404 0.969931116 0.918409362 0.209621612 0.044248236 0.318683679 17.68860838 0.011812162 0.023238356 8863.078791 -3.94758461 -0.051521754 ASFDHS(ph)PDSLPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASFDHSPDSLPLR 13 0 H0Y6H0;Q8NB78;Q8NB78-2 H0Y6H0 KDM1B Lysine-specific histone demethylase 1B 1 AS(0.012)FDHS(0.986)PDS(0.001)LPLR 101.43 0.0020412 89287000 57365 66341 58236 60389 74517 59883 76160 68889 68817 TRUE FALSE 53774.62705 71252.95667 59617.38542 61938.68398 68664.73541 77170.24998 64740.51503 77489.94329 57330.99813 0.937967745 1.242834749 1.039880473 1.080369887 1.197689516 1.346047557 1.129241024 1.351623831 1 15.80702778 2.674385897 5.502432303 1.218820784 1.097366603 0.198345032 0.124771214 0.35215291 21.40363292 0.036637594 0.034687257 472.4826841 -2.674385897 -0.121454182 ASFNNPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ASFNNPDR 8 0 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ;;;;; 162.59 0.00079298 4551210000 2500940 3217000 2733670 2749970 3205700 2516680 3126100 2752500 3249610 FALSE TRUE 2344410.63 3455190.027 2798513.943 2820538.886 2953937.253 3243204.661 2657370.326 3096155.684 2707229.098 0.865981616 1.276282835 1.033718922 1.041854525 1.091129397 1.197979389 0.981583099 1.143662236 1 21.36838555 -2.241435669 0.366388091 0.885957517 1.093324949 0.028996135 0.114376106 164.3021077 8.060632059 15.40643919 0.075682406 0.005735408 2.241435669 0.207367432 ASGDGES(ph)LDEDSEFTLASDFEIGHFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASGDGESLDEDSEFTLASDFEIGHFFR 27 0 Q99733;Q99733-2;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 AS(0.032)GDGES(0.968)LDEDSEFTLASDFEIGHFFR 94.75 0.0032989 14013000 6732.1 6321.3 6996.3 6139.2 6993.7 5466.4 6450.2 6107.1 6090.6 TRUE FALSE 6310.749878 6789.335629 7162.25554 6296.742266 6444.443013 7044.46094 5483.052391 6869.584878 5074.039513 1.2437329 1.338053362 1.411549027 1.240972257 1.270081361 1.388333875 1.080608926 1.353869015 1 12.30891904 0.149816744 0.346795205 0.942748548 1.345581611 0.464998915 0.095936966 3.307269617 0.6284123 0.387374838 0.084638218 1.411941631 -0.149816744 0.402833063 ASGDGESLDEDSEFTLASDFEIGHFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ASGDGESLDEDSEFTLASDFEIGHFFR 27 0 Q99733;Q99733-2;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 ;;;; 182.39 1.58E-17 131621000 81916 89494 86856.5 89932 91854.2 70140.8 99602.7 79907.8 95449 FALSE TRUE 76789.02378 96120.22888 88916.7772 92239.80737 84640.34165 90389.31032 84668.1998 89884.46473 79517.94528 0.96568169 1.208786627 1.118197621 1.159987309 1.064418118 1.13671587 1.064768456 1.130367044 1 16.27899286 -0.30628221 0.418207758 0.976516878 1.124914418 0.167323144 0.066843649 9.442887341 1.764043957 0.401993127 0.038428307 0.493989582 0.30628221 0.14839754 ASGDPGASGMS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ASGDPGASGMSPR 13 0 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 ASGDPGASGMS(1)PR;ASGDPGASGMS(1)PR;ASGDPGAS(0.067)GMS(0.933)PR;ASGDPGAS(0.003)GMS(0.997)PR;ASGDPGAS(0.001)GMS(0.999)PR;ASGDPGASGMS(1)PR 187.77 3.14E-07 1036953000 1590680 1709870 1713170 1596310 1747170 1551140 1960330 1587360 1888730 TRUE FALSE 1491122.178 1836470.554 1753807.201 1637274.017 1609954.316 1998928.937 1666396.715 1785545.39 1573488.761 0.947653529 1.167132934 1.114597857 1.040537471 1.02317497 1.270380181 1.059045833 1.134768442 1 20.58553544 ASGGLPQFGDEYDFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASGGLPQFGDEYDFYR 16 0 Q01780;Q01780-2;K7EJ37 Q01780 EXOSC10 Exosome component 10 0 ; 158.81 2.68E-08 36941000 65490 83405 68636 78709 82923 60267 81404 73744 80407 FALSE TRUE 61391.0978 89580.39298 70264.07833 80728.80619 76410.56208 77665.10455 69198.22592 82951.10073 66986.55225 0.916468989 1.337289202 1.04892812 1.205149444 1.1406851 1.159413374 1.033016682 1.238324678 1 16.03158388 -4.707472194 0.30795126 7.60E-08 1.147833443 0.098245201 0.117966084 499.0756022 5.416073842 321.2820044 0.100891453 1.96E-05 4.707472194 1.147833367 ASGNYATVISHNPETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASGNYATVISHNPETK 16 0 P62917;E9PKZ0;G3V1A1 P62917 RPL8 60S ribosomal protein L8 0 162.59 8.03E-09 1000200000 1059100 928960 1024100 1026000 1090800 845720 1270300 962900 1271900 FALSE TRUE 992812.8215 997741.165 1048392.136 1052328.897 1005132.968 1089865.635 1079830.308 1083120.185 1059611.673 0.936959121 0.941610205 0.989411652 0.993126938 0.94858616 1.028551933 1.019081174 1.022185969 1 20.01510421 3.904930163 0.441209738 1.019581941 0.908252127 0.63119785 0.020489272 1.580138293 0.408628901 0.016511969 0.086578104 8033.969212 -3.904930163 -0.111329814 ASGQAFELILS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 18 ASGQAFELILSPR 13 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR 201.3 1.08E-07 7861160900 1577359 1739443.7 1857701 2271731 2431777 1429784 1514422 1188591 1624318 TRUE FALSE 1478634.916 1868233.921 1901766.545 2330027.463 2240795.044 1842539.43 1287348.48 1336989.203 1353208.832 1.092687899 1.380595424 1.405375504 1.721853573 1.655912222 1.3616076 0.951330238 0.988013949 1 20.36795307 1.798560972 4.261032673 0.97640418 1.451241918 0.623015454 0.168229598 0.145721652 4.784868812 0.087258938 0.046857974 62.88701367 -1.798560972 0.474837738 ASGQPAGPDNKENCPVPGKPGEAVAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASGQPAGPDNKENCPVPGKPGEAVAAR 27 2 P04183;K7ERV3 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 0 136.01 1.00E-05 119270000 92809 66786 75040 71591 94121 67111 105920 76272 166390 FALSE TRUE 87000.25036 71730.90493 76819.98424 73428.14626 86729.11633 86484.85624 90038.27931 85794.7271 138618.4341 0.627623959 0.517470172 0.554183033 0.529714152 0.625667985 0.623905881 0.649540445 0.618927256 1 17.0807596 -1.912733828 0.274434276 1.437228538 0.536440312 0.918912817 0.038588556 7.164115202 0.308834491 2.05534351 0.046984097 0.012225487 1.912733828 -0.900788225 ASGYQS(ph)SQKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASGYQSSQKK 10 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 ASGYQS(0.983)S(0.017)QKK 75.462 0.012534 0 131250 67947 98308 98202 131440 61763 118870 96441 195030 TRUE FALSE 123035.2968 72977.86658 100639.9122 100722.0296 121117.2326 79592.97546 101046.547 108481.8711 162478.2331 0.757241721 0.449154728 0.619405506 0.619910912 0.745436668 0.489868544 0.62190821 0.66767018 1 17.30988693 0.69938827 2.108479451 0.999873671 0.59809965 0.609078468 0.095601258 0.879982314 5.286935057 0.08512343 0.023303478 5.004817777 -0.69938827 -0.401774021 ASHEEVEGLVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASHEEVEGLVEK 12 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 127.56 0.00026759 431720000 448240 1718100 327690 305710 1878300 288410 462900 1674300 595060 FALSE TRUE 420185.4585 1845309.912 335462.9615 313555.0362 1730785.895 371669.2851 393492.4424 1883340.041 495740.6418 0.847591307 3.722329291 0.676690457 0.632498145 3.491313297 0.749725267 0.793746587 3.799043052 1 18.91922601 ASHGYGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASHGYGGK 8 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;; 130.22 0.0010572 2249280000 4343020 4310530 4353670 4300650 4698510 3538610 4667780 4357160 4788370 FALSE TRUE 4071198.131 4629686.126 4456941.108 4411011.96 4329507.977 4560149.262 3967889.723 4901161.017 3989160.113 1.020565236 1.160566634 1.117263028 1.10574954 1.085318176 1.14313518 0.994667953 1.228619779 1 21.9276536 ASHS(ph)SERPPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASHSSERPPPR 11 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 AS(0.22)HS(0.778)S(0.002)ERPPPR 193.62 5.29E-07 965560000 143400 174640 168540 172370 186910 123340 196020 150140 152130 TRUE FALSE 134424.85 187570.5273 172537.8484 176793.306 172230.8426 158946.2557 166628.6208 168885.3095 126738.5202 1.060647148 1.479980412 1.361368652 1.394945323 1.358946296 1.254127439 1.314743304 1.332549167 1 16.95149555 -0.868822299 0.468488297 0.896761132 1.351470356 0.435016215 0.111222474 12.43493861 1.910096109 1.920367564 0.053368171 0.135262591 0.868822299 0.454709224 ASHSSERPPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASHSSERPPPR 11 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 0 ; 118.28 0.00044572 31726000 7978.5 16569.1 11741.7 16759.3 18665.7 14995.5 13933.8 15382.4 14424.7 FALSE TRUE 7479.139927 17795.8934 12020.21867 17189.37201 17199.77122 19324.45742 11844.55605 17302.9265 12017.12438 0.622373514 1.480877857 1.00025749 1.430406432 1.431271797 1.608076675 0.985639798 1.439855822 1 13.55280409 4.748930792 24.79002594 1.289105249 0.622373095 0.467371268 0.226207572 1177.309486 2814309.46 0.050121355 0.703817091 56095.85763 -4.748930792 -0.666732154 ASHTAPQVLFSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASHTAPQVLFSHR 13 0 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;; 189.3 3.11E-06 1014397000 393524 752941 417893 381143 742631 327198 469467 633647 444847 FALSE TRUE 368894.0353 808689.5351 427805.6193 390923.7747 684307.7569 421654.751 399074.7817 712759.2228 370599.1619 0.995399 2.182113772 1.15436208 1.054842576 1.846490298 1.137764988 1.076836709 1.923261831 1 18.49950009 -2.370749741 0.063998459 5.81E-12 2.082757092 0.03099157 0.434742289 501.2005273 4.068293425 113.2848093 36.23410298 0.004258437 2.370749741 2.082757092 ASIANSDGPTAGSQT(ph)PPFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASIANSDGPTAGSQTPPFK 19 0 J3KP75;O75167-5;O75167-2;O75167;O75167-4;F6TH74;H9KVA6 J3KP75 PHACTR2 Phosphatase and actin regulator;Phosphatase and actin regulator 2 1 ASIANSDGPTAGS(0.006)QT(0.993)PPFK;ASIANSDGPTAGSQT(1)PPFK 251.44 1.01E-28 56346000 256840 217266 233330 238160 233662 189321 302930 210878 237732 TRUE FALSE 240764.8429 233352.6007 238864.6978 244271.5888 215311.1291 243974.8993 257508.4588 237206.5825 198052.9934 1.215658692 1.178233142 1.206064567 1.233364791 1.087138979 1.23186676 1.300199782 1.197692488 1 17.59552698 0.947913436 23.414004 1 1.209616734 0.599536283 0.053019049 6829.378019 3069951.6 0.052696638 0.013174159 8.869791999 -0.947913436 0.209616734 ASIANSDGPTAGSQT(ph)PPFKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASIANSDGPTAGSQTPPFKR 20 1 J3KP75;O75167-5;O75167-2;O75167;O75167-4;F6TH74;H9KVA6 J3KP75 PHACTR2 Phosphatase and actin regulator;Phosphatase and actin regulator 2 1 ASIANSDGPTAGS(0.048)QT(0.952)PPFKR 152.4 3.80E-08 399420000 242180 257750 241240 223540 267700 210160 346210 236850 305410 TRUE FALSE 227022.3861 276834.0782 246962.3267 229276.4149 246675.9218 270829.7803 294299.0246 266421.2439 254435.098 0.892260494 1.08803416 0.970629951 0.901119447 0.969504301 1.064435616 1.156676209 1.047108854 1 17.95693817 2.15495019 4.879427211 1.090679141 0.979244842 0.33853614 0.066930219 0.222822715 9.330200395 0.025663794 0.01879388 142.8730086 -2.15495019 -0.111434299 ASIDS(ph)SLENLSTASSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASIDSSLENLSTASSR 16 0 Q9UJF2;Q9UJF2-2;H0Y638 Q9UJF2 RASAL2 Ras GTPase-activating protein nGAP 1 ASIDS(0.593)S(0.407)LENLSTASSR 112.67 0.00075587 97235000 113360 152760 152180 143370 144360 113000 147800 137570 194660 TRUE FALSE 106265 164070.5093 155789.7815 147049.1169 133022.5479 145621.2656 125638.7621 154745.9173 162169.9884 0.655269208 1.011719313 0.960657289 0.906759126 0.820266124 0.897954467 0.774734976 0.954220438 1 17.30714733 2.978135833 22.79292156 0.867616107 0.919176648 0 0.113894235 880.1087391 917496.149 0.032412638 0.03473011 950.9021586 -2.978135833 0.051560541 ASIGQS(ph)PGLPSTTFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 289.59 7.44E-44 270810000 902630 750890 873140 867220 1101580 746430 1016440 906610 1288530 TRUE FALSE 846135.9995 806486.6769 893851.2931 889474.3334 1015066.35 961912.2237 864034.2582 1019802.254 1073466.019 0.788228025 0.751292228 0.832677772 0.828600364 0.945597096 0.896080739 0.80490136 0.950008884 1 20.03384509 8 0.06673965 1.181295732 0.103421183 0.661976543 0.046552696 173.4576035 0.857687017 2.536176261 17.72720118 100000000 -8 -1.077874549 ASIHEAWTDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASIHEAWTDGK 11 0 O43707;O43707-2;P12814-3;P12814;P12814-2;P12814-4;H9KV75 O43707;P12814-3 ACTN4;ACTN1 Alpha-actinin-4;Alpha-actinin-1 0 ;;; 141.71 3.80E-05 2136260000 4587510 4088280 4236070 3566940 3450850 3125730 5362630 4379610 4780520 FALSE TRUE 4300385.938 4390980.505 4336551.581 3658473.719 3179834.161 4028077.509 4558553.416 4926413.949 3982620.329 1.079788075 1.102535553 1.088868941 0.918609714 0.798427643 1.011413887 1.144611597 1.236978055 1 21.92528652 -0.883163732 7.909805493 1.000000004 1.050377806 0.014721721 0.120704655 0 0 0.122014363 0.028759061 0.130868844 0.883163732 0.050377803 ASKETS(ph)CKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASKETSCKR 9 2 A0A3B3ISA2;Q8WWF3 A0A3B3ISA2 SSMEM1 Serine-rich single-pass membrane protein 1 1 AS(0.012)KET(0.012)S(0.977)CKR;AS(0.014)KET(0.014)S(0.972)CKR 67.153 0.032197 190268000 705290 740180 615870 597890 812000 466230 579800 558830 792930 TRUE FALSE 661147.1579 794983.6974 630478.7272 613232.8696 748228.7955 600823.0324 492864.3726 628601.1556 660584.8605 1.000851211 1.20345431 0.954425033 0.92831808 1.132676269 0.909531944 0.74610304 0.951582746 1 19.33338438 2.07885219 6.474852581 0.860553171 1.047460013 0.292395043 0.104116802 0.19961388 13.12970348 0.038422111 0.028189961 119.9091128 -2.07885219 0.186906842 ASKS(ph)QDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASKSQDRK 8 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 AS(0.243)KS(0.757)QDRK 61.344 0.068172 39161000 74465 42776 65180 71454 80768 34931 87286 60435 129030 TRUE FALSE 69804.36857 45943.17955 66726.10038 73287.63061 74424.80708 45015.01264 74198.27462 67980.44278 107494.0594 0.649378849 0.427402033 0.620742213 0.681783077 0.692362047 0.418767445 0.690254652 0.63241116 1 16.71389741 -5 0.230605396 3.22970843 0.544133061 0.617379448 0.099089899 102.995732 1.030790803 107.0263059 0.163054958 1.00E-05 5 -2.685575369 ASLENSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ASLENSLR 8 0 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;; 283.17 4.29E-19 23383830000 5858860 8821130 6249030 5890440 9036210 5141760 6513280 7840710 9830180 FALSE TRUE 5492164.411 9474255.644 6397259.943 6041598.663 8326542.517 6626102.643 5536674.13 8819639.903 8189459.453 0.670638208 1.156884126 0.781157777 0.737728625 1.016738964 0.809101343 0.676073209 1.076950189 1 22.9653368 5.01848403 16.58450044 0.886305387 0.233796664 0.171810797 0.157334317 18397690.89 376854255.4 0.037118547 299901123.5 104347.9761 -5.01848403 -0.652508723 ASLGQAS(ph)IQNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASLGQASIQNGK 12 0 E9PC69;Q7KZI7-14;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 ASLGQAS(1)IQNGK 193.96 2.25E-06 45770000 85659 75759 70915 65545 96510 41926 87819 74936 138720 TRUE FALSE 80297.7561 81368.27519 72597.13729 67226.99567 88930.4939 54029.35559 74651.35622 84291.92455 115566.7358 0.694817203 0.704080414 0.628183679 0.581715795 0.76951636 0.467516498 0.645958854 0.729378778 1 16.81836667 0.84728312 2.97924034 0.999765296 0.641135579 0.665612324 0.079746777 0.372613095 5.954948321 0.071085167 0.018640206 7.035308078 -0.84728312 -0.358629717 ASLGS(ph)LEGEAEAEASS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 ASLGS(1)LEGEAEAEAS(0.051)S(0.949)PK;ASLGS(1)LEGEAEAEASS(1)PK;AS(0.003)LGS(0.997)LEGEAEAEAS(0.002)S(0.998)PK;ASLGS(1)LEGEAEAEAS(0.001)S(0.999)PK 371.21 1.79E-107 533350000 3454110 1831300 2424360 2624700 2797950 1672750 2673950 1779410 2409530 TRUE FALSE 3237923.421 1966891.357 2481866.964 2692054.246 2578210.293 2155645.77 2273016.021 2001573.255 2007363.877 1.61302266 0.979837976 1.236381203 1.341089315 1.284376153 1.073868966 1.132338809 0.997115311 1 20.93687073 1.757020994 1.374999153 1.008749616 1.240096287 0.322243175 0.161609346 0.597234383 2.145589035 0.12460114 0.049017354 57.15062626 -1.757020994 0.231346671 ASLGS(ph)LEGEAEAEASSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;AS(0.004)LGS(0.996)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;AS(0.004)LGS(0.996)LEGEAEAEASSPK;AS(0.141)LGS(0.859)LEGEAEAEASSPK 519.13 2.59E-295 6198645000 8740353 6051848 6944246 6001422 7784916 5991237 8823273 6888113 11218975 TRUE FALSE 8193309.908 6499933.123 7108966.794 6155428.649 7173520.1 7720809.862 7500305.125 7748109.071 9346455.595 0.87662214 0.695443642 0.760605635 0.658584271 0.76751235 0.826068212 0.802475874 0.828989021 1 23.15598793 0.725566684 0.630278389 1.002685373 0.742412028 0.60750627 0.059399601 0.719572831 0.583230584 0.060027103 0.022766833 5.315776151 -0.725566684 -0.260273345 ASLGSLEGEAEAEASS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ASLGSLEGEAEAEASS(1)PK;ASLGSLEGEAEAEAS(0.002)S(0.998)PK;ASLGSLEGEAEAEAS(0.003)S(0.997)PK;ASLGSLEGEAEAEASS(1)PK;ASLGSLEGEAEAEAS(0.002)S(0.998)PK;ASLGSLEGEAEAEASS(1)PK 478.18 1.59E-239 2063640000 4997350 3083780 3762010 4313620 4135070 2335830 3928860 2470610 3003680 TRUE FALSE 4684574.784 3312106.28 3851246.654 4424314.792 3810318.282 3010146.202 3339763.917 2779071.097 2502346.403 1.872072858 1.323600232 1.539054165 1.768066478 1.522698167 1.202929458 1.334652913 1.110586086 1 21.25485009 1.694485535 0.941968913 1.028407164 1.568428482 0.634707831 0.166719558 0.382165173 0.642565364 0.146318065 0.05971988 49.48636282 -1.694485535 0.540021318 ASLGSLEGEAEAEASS(ph)PKGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASLGSLEGEAEAEASSPKGK 20 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ASLGSLEGEAEAEAS(0.27)S(0.73)PKGK 131.64 8.47E-06 83620000 104180 104020 96196 142270 199350 58083 91000 80633 272090 TRUE FALSE 97659.55977 111721.749 98477.81455 145920.8891 183693.8551 74850.6192 77355.3948 90700.20755 226676.4212 0.430832458 0.492868859 0.43444225 0.643740925 0.810379192 0.33020911 0.341259115 0.400130755 1 17.7902748 -1.131555897 3.940988516 1.000191062 0.478780636 0.55445313 0.144838749 62317609.54 109548405.4 154238.9808 0.035618727 0.073865919 1.131555897 -0.521410426 ASLLHSMPTHS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASLLHSMPTHSSPR 14 0 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4X8;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 ASLLHSMPT(0.001)HS(0.64)S(0.359)PR 155.22 9.87E-06 124440000 40270 74311 60592 83881 71779 43648 65425 49092 66657 TRUE FALSE 37749.57258 79813.06376 62029.27085 86033.52847 66141.76688 56248.46903 55615.12863 55221.24426 55531.51608 0.679786457 1.437257064 1.117010217 1.5492739 1.191067191 1.01291074 1.001505677 0.99441269 1 15.76101916 2.270785136 4.768574654 1.001027597 1.235830271 0.140569026 0.226747903 0.30364277 16.28443235 0.075710016 0.060422061 186.5456542 -2.270785136 0.234802675 ASLLHSMPTHSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASLLHSMPTHSSPR 14 0 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4X8;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 ASLLHSMPTHS(0.106)S(0.894)PR;ASLLHSMPT(0.006)HS(0.341)S(0.653)PR;ASLLHSMPT(0.042)HS(0.212)S(0.747)PR 135.23 7.65E-05 382896000 250119 316967 332781 387959 399033 258395 327969 289257 365745 TRUE FALSE 234464.4983 340435.5665 340674.7225 397914.6848 367694.5578 332989.4418 278793.0932 325371.3732 304699.7967 0.769493452 1.117281896 1.118066786 1.305923696 1.206743693 1.092844319 0.914976302 1.067842436 1 18.21702901 1.913508736 7.483499805 0.988360017 1.119230525 0.109954195 0.140114786 0.534398703 40.80014601 0.058428411 0.03641293 81.94241052 -1.913508736 0.130870507 ASLLT(ph)DEEDVDMALDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASLLTDEEDVDMALDQR 17 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;H7C3P6 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 AS(0.131)LLT(0.869)DEEDVDMALDQR 89.541 0.04498 7318700 9803.7 11309 9294.1 10839 11077 7844.1 9668.8 8283.8 9028.3 TRUE FALSE 9190.103917 12146.33013 9514.560441 11117.14709 10207.0571 10108.56433 8219.053201 9318.050665 7521.418405 1.221857823 1.614898876 1.264995501 1.478065239 1.357065457 1.343970484 1.09275309 1.238868809 1 12.87678904 1.672601096 0.851630693 1.034879777 1.422172054 0.51675847 0.122444593 0.393202719 0.552218125 0.100366991 0.042609043 47.05449276 -1.672601096 0.387292277 ASLPQAATFGELSGPLKPGS(ph)PYRPPVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASLPQAATFGELSGPLKPGSPYRPPVPR 28 2 Q14687;Q14687-2;Q14687-3;H0Y613 Q14687 GSE1 Genetic suppressor element 1 1 ASLPQAATFGELSGPLKPGS(1)PYRPPVPR;ASLPQAATFGELSGPLKPGS(1)PYRPPVPR 273.01 9.48E-62 600490000 400022 301149 390380 312232 349425 297622 479703 344062 333621 TRUE FALSE 374985.3371 323446.3853 399639.998 320244.4017 321982.57 383540.6399 407775.9885 387018.8981 277937.4998 1.349171441 1.163737839 1.437877214 1.152217322 1.158471132 1.379952832 1.467149948 1.392467365 1 18.08440097 2.196362792 24.98906283 1.362611665 1.260976478 0 0.154370072 344.4365175 203969.2258 0.053337122 0.039392418 157.167517 -2.196362792 -0.101635187 ASLQVLGTVGEPINPEAWLWYHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASLQVLGTVGEPINPEAWLWYHR 23 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ; 229.1 5.87E-33 334020000 270070 413240 288380 248617 426320 268730 371510 352510 269170 FALSE TRUE 253166.8008 443836.7196 295220.5098 254996.9331 392838.5469 346307.9885 315805.5244 396521.6495 224243.7881 1.128980218 1.97925982 1.316515888 1.137141569 1.751836919 1.544337043 1.408313368 1.768261466 1 17.7747085 -1.123667587 4.63788474 0.999955166 1.519931485 0.247841244 0.274920914 0.000117684 2.22E-05 0.24579161 0.057928657 0.075219841 1.123667587 0.519976319 ASLRDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASLRDEK 7 1 Q86TX2;G3V4F2;A0A087X0W7;A0A087WT95;P49753;Q8N9L9 Q86TX2;Q8N9L9 ACOT1;ACOT2;ACOT4 "Acyl-coenzyme A thioesterase 1;Acyl-coenzyme A thioesterase 2, mitochondrial;Acyl-coenzyme A thioesterase 4" 0 68.787 0.078889 0 125170 126350 140130 139600 153780 83481 153740 125290 251130 FALSE TRUE 117335.8331 135705.0855 143453.9498 143182.3723 141702.7391 107580.6095 130688.1143 140932.7323 209214.7806 0.560839118 0.648640049 0.685677892 0.684379812 0.677307496 0.514211325 0.624660045 0.673627035 1 17.67462525 0.761293474 3.771872392 0.999990765 0.633618341 0.817008526 0.054845977 1.148646941 17.72012437 0.053752363 0.01378596 5.771563443 -0.761293474 -0.366372424 ASLSPDASDFEHITAETPSRPLS(ph)STSNPFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASLSPDASDFEHITAETPSRPLSSTSNPFK 30 1 Q5M775-4;Q5M775;Q5M775-5;Q5M775-3;Q5M775-2 Q5M775-4 SPECC1 Cytospin-B 1 ASLSPDASDFEHITAETPS(0.011)RPLS(0.895)S(0.042)T(0.042)S(0.011)NPFK 214.98 1.14E-34 232300000 140460 139570 150630 150200 199370 108120 181690 151520 174750 TRUE FALSE 131668.8593 149903.908 154203.0147 154054.3863 183712.2844 139332.4888 154447.2712 170437.6055 145583.0961 0.904424091 1.029679352 1.059209612 1.058188694 1.261906701 0.95706502 1.060887393 1.170723869 1 17.15148333 5.785142056 0.891906119 1.081691944 0.017649935 0.303673276 0.084455294 14.85429161 2.235355052 0.024826019 23.83938544 609736.3068 -5.785142056 -1.064042008 ASLVALPEQTAS(ph)EEETPPPLLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASLVALPEQTASEEETPPPLLTK 23 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 AS(0.001)LVALPEQT(0.212)AS(0.74)EEET(0.048)PPPLLTK;ASLVALPEQT(0.013)AS(0.987)EEETPPPLLTK 165.38 8.51E-12 106144000 173284 155272 166613 161360 174138 138275 204710 160434 223531 TRUE FALSE 162438.4638 166768.5004 170565.139 165500.7708 160461.9039 178192.7478 174015.6359 180464.5381 186222.232 0.872282874 0.89553486 0.915922536 0.888727243 0.86166889 0.956882247 0.934451456 0.969081597 1 17.50666579 1.516246473 0.94183567 0.996433257 0.892449218 0.755025682 0.021904376 0.255258438 0.449148319 0.019356702 0.007378311 32.82815486 -1.516246473 -0.103984039 ASMSEFLES(ph)EDGEVEQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASMSEFLESEDGEVEQQR 18 0 J3QQW9;Q15022 J3QQW9 SUZ12 Polycomb protein SUZ12 1 ASMSEFLES(1)EDGEVEQQR;ASMSEFLES(1)EDGEVEQQR;ASMSEFLES(1)EDGEVEQQR 208.82 6.19E-16 170853000 164518 176981 182716 183643 193335 162084 198551 166878 210143 TRUE FALSE 154221.1121 190084.8574 187050.1098 188355.5903 178151.249 208875.0196 168780.1208 187713.0856 175068.7757 0.880917293 1.085772472 1.06843787 1.075894828 1.017607213 1.193102646 0.964078946 1.072224815 1 17.41756227 4.743228283 24.79386899 1.061810834 0.880917211 0.458495765 0.060999536 362.3236637 1924529.863 0.012955678 0.103934324 55364.10487 -4.743228283 -0.180893623 ASNEDGDIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASNEDGDIKR 10 1 Q9UBT2;Q9UBT2-2;K7EPL2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 ;; 106 0.0039672 2660570000 2384420 1889360 2124990 2145800 2115590 1661480 2576850 1960670 2509520 FALSE TRUE 2235183.409 2029250.18 2175395.766 2200864.861 1949440.095 2141122.304 2190475.265 2205463.965 2090664.9 1.069125621 0.970624312 1.040528191 1.052710485 0.932449813 1.024134621 1.047740967 1.054910314 1 20.99553041 1.999614683 24.99999999 1.03862569 1.00996116 0.045045394 0.041710509 33.38476945 2166277.263 0.01472714 0.010770575 99.91131694 -1.999614683 -0.02866453 ASNGDAWVEAHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASNGDAWVEAHGK 13 0 P38646;D6RJI2;A0A3B3ITI4 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ; 153.2 3.99E-05 1311650000 2654800 2196300 2033100 1754950 3095500 1644560 2576000 2637000 4071500 FALSE TRUE 2488640.807 2358916.337 2081326.092 1799984.988 2852391.917 2119317.775 2189752.714 2966235.255 3391940.347 0.733692386 0.695447471 0.613609285 0.530665284 0.840932217 0.62480986 0.645575243 0.874495112 1 21.69367937 1.082432743 3.519545826 0.996856314 0.664123129 0.663754429 0.081721015 0.116765652 2.763022782 0.072771403 0.018974595 12.09017933 -1.082432743 -0.332733185 ASNIFGT(ph)PEENQASWAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASNIFGTPEENQASWAK 17 0 Q9UK76-3;J3KSH8 Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 ASNIFGT(1)PEENQASWAK;ASNIFGT(1)PEENQASWAK 205.55 8.70E-11 322900000 609650 415190 703220 660630 659850 999720 1225790 395310 312430 TRUE FALSE 571493.0948 445931.0996 719900.7105 677582.8842 608028.0427 1288322.935 1041994.169 444665.3237 260283.4146 2.195656975 1.713252073 2.765833972 2.603250327 2.336022999 4.949692768 4.003306053 1.708389005 1 17.98972386 3.346858038 1.174445735 3.215104677 1.974733575 0.006862706 1.145473128 0.886752753 2.560623304 0.41297958 0.728158029 2222.583257 -3.346858038 -1.240371102 ASNTST(ph)PTKGNTETSASASQTNHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASNTSTPTKGNTETSASASQTNHVK 25 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YD28;A0A2R8YCQ1;A0A2R8Y7Y0 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 ASNT(0.002)S(0.01)T(0.934)PT(0.054)KGNTETSASASQTNHVK;AS(0.012)NT(0.05)S(0.209)T(0.703)PT(0.025)KGNT(0.001)ETSASASQTNHVK;ASNT(0.003)S(0.047)T(0.946)PT(0.003)KGNTETSASASQTNHVK;AS(0.001)NT(0.031)S(0.234)T(0.729)PT(0.004)KGNTETSASASQTNHVK 282.62 3.31E-53 1734330000 577879 467310 572807 523757 600754 448199 786140 536327 780340 TRUE FALSE 541710.5849 501910.1186 586394.2525 537197.4913 553573.2042 577586.7754 668265.6052 603288.6066 650096.2128 0.833277558 0.772055134 0.902011488 0.826335365 0.851525041 0.888463529 1.027948774 0.927998956 1 19.31029372 1.956320363 3.650641049 0.985583674 0.837531767 0.740346907 0.039957059 0.115065051 2.997500524 0.018507275 0.010818309 90.43163087 -1.956320363 -0.148051906 ASPCKS(ph)PAPEAALGAQPALEGAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASPCKSPAPEAALGAQPALEGAAR 24 1 Q32MQ0 Q32MQ0 ZNF750 Zinc finger protein 750 1 AS(0.013)PCKS(0.987)PAPEAALGAQPALEGAAR 140.36 1.80E-07 204400000 118680 103880 106660 111550 98500 78753 121210 79873 100950 TRUE FALSE 111252.0306 111571.3833 109190.0256 114412.5619 90764.20733 101487.7127 103035.6858 89845.31987 84100.79284 1.322841639 1.3266389 1.298323379 1.360421917 1.079231292 1.206739071 1.225145237 1.068305266 1 16.35983178 1.666975192 0.331350226 0.978436692 1.36753219 0.708181064 0.066960657 0.730054429 0.262962806 0.09988593 0.096315911 46.44887415 -1.666975192 0.389095499 ASPDQNASTHT(ph)PQSSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASPDQNASTHTPQSSVK 17 0 Q14677-2;Q14677;Q14677-3;H0YD52 Q14677-2 CLINT1 Clathrin interactor 1 1 ASPDQNASTHT(0.999)PQSSVK;ASPDQNASTHT(1)PQSSVK;ASPDQNASTHT(1)PQSSVK;ASPDQNAST(0.002)HT(0.995)PQS(0.002)S(0.001)VK 260.06 1.16E-26 1959915000 1559310 1566086 1813726 1798100 2012747 1670648 2270261 1761356 2536542 TRUE FALSE 1461715.571 1682040.637 1856748.437 1844242.29 1854673.97 2152936.957 1929856.439 1981265.174 2113176.754 0.691714769 0.795977258 0.878652689 0.872734516 0.877671007 1.01881537 0.913248944 0.937576646 1 21.01098201 6.427360393 0.300421783 0.979082044 1.14E-16 0.846223552 0.037011286 7.688242441 0.253279237 0.036519166 3.352789799 2675225.485 -6.427360393 -0.979082044 ASPHAT(ph)PSTLHFPT(ph)SPIIQQPGPYFSHPAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASPHATPSTLHFPTSPIIQQPGPYFSHPAIR 31 0 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;B1AKN6 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 2 AS(0.201)PHAT(0.267)PS(0.267)T(0.267)LHFPT(0.552)S(0.445)PIIQQPGPY(0.001)FS(0.001)HPAIR 54.466 0.059688 66231000 53655 67608 64296 73142 77310 45294 80304 67084 102600 TRUE FALSE 50296.82933 72613.76667 65821.13148 75018.94755 71238.38445 58369.64251 68263.16071 75459.58507 85475.39718 0.588436334 0.849528274 0.770059381 0.877667142 0.833437302 0.682882378 0.798629348 0.882822281 1 16.3832216 -5 0.188472009 1.906929918 0.749267093 0.431396843 0.085261107 142.0986902 1.387865386 48.25819279 0.224798598 1.00E-05 5 -1.157662825 ASPITNDGEDEFVPS(ph)DGLDKDEYTFSPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASPITNDGEDEFVPSDGLDKDEYTFSPGK 29 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 ASPIT(0.001)NDGEDEFVPS(0.995)DGLDKDEY(0.002)T(0.002)FSPGK 58.432 0.0027671 0 157350 89289 110140 105920 102110 74509 146850 83535 120980 TRUE FALSE 147501.7444 95900.05047 112752.5728 108638.0865 94090.69249 96018.53875 124831.2058 93964.52863 100787.6564 1.463490169 0.951505907 1.118714104 1.077890789 0.933553729 0.95268153 1.238556488 0.93230195 1 16.62095944 4.746155948 24.77473653 1.0415184 1.463490399 0.658289294 0.098549915 526.8207526 1718357.018 0.022898144 0.242554112 55738.58608 -4.746155948 0.421971999 ASPS(ph)PQPSSQPLQIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ASPSPQPSSQPLQIHR 16 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 AS(0.143)PS(0.857)PQPSSQPLQIHR;AS(0.001)PS(0.999)PQPSSQPLQIHR;ASPS(1)PQPSSQPLQIHR;ASPS(1)PQPSSQPLQIHR;ASPS(1)PQPSSQPLQIHR 247.66 1.66E-20 4474150000 2434870 2616030 2767570 2412040 3026440 2606180 3508270 3035320 3746860 TRUE FALSE 2282475.833 2809723.583 2833218.067 2473937.03 2788755.61 3358541.858 2982237.483 3414286.384 3121484.86 0.73121477 0.900124046 0.907650748 0.792551347 0.893406739 1.075943664 0.955390661 1.093802 1 21.57380104 2.366737576 5.507078511 1.020784893 0.855388375 0.674198179 0.064456966 0.136794338 6.120124719 0.021675805 0.017996702 232.6684926 -2.366737576 -0.165396517 ASPSCS(ph)SPTRDSSGVPVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASPSCSSPTRDSSGVPVSK 19 1 Q8N5I9;J3KN91;A0A087WT30 Q8N5I9 C12orf45 Uncharacterized protein C12orf45 1 AS(0.001)PS(0.013)CS(0.485)S(0.485)PT(0.017)RDSSGVPVSK 133.15 7.42E-06 296060000 166640 215240 200370 192060 293910 135230 255750 149770 400660 TRUE FALSE 156210.2999 231176.5936 205122.871 196988.5848 270827.4942 174268.7057 217402.6618 168469.1142 333787.2576 0.467993599 0.692586635 0.61453176 0.590162088 0.811377571 0.522095142 0.651321034 0.504720028 1 18.34856936 -1.194012604 4.44477895 1.000097901 0.619408436 0.602923305 0.099807873 8.62E-05 1.56E-05 0.084630262 0.019942349 0.063971627 1.194012604 -0.380689465 ASPSCSS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ASPSCSSPTR 10 0 Q8N5I9;J3KN91;A0A087WT30 Q8N5I9 C12orf45 Uncharacterized protein C12orf45 1 ASPSCS(0.003)S(0.997)PTR;ASPSCS(0.002)S(0.998)PTR;ASPSCS(0.008)S(0.992)PTR;ASPSCS(0.002)S(0.998)PTR;ASPS(0.012)CS(0.061)S(0.815)PT(0.112)R 236.06 4.11E-12 3132199000 3896346 4037210 4145021 3822858 4091482 3634245 4179221 3492355 2908827 TRUE FALSE 3652480.659 4336129.229 4243342.856 3920959.008 3770153.508 4683392.534 3552585.609 3928383.209 2423324.982 1.507218671 1.78933047 1.751041601 1.618007918 1.555777098 1.932630815 1.465996363 1.62107156 1 21.20855646 0.17164936 0.699802106 0.979530044 1.700484073 0.691705159 0.137979826 1.69764317 1.027226063 0.210402269 0.045919269 1.484736413 -0.17164936 0.720954028 ASPSS(ph)PGRQDS(ph)DEDDGPQRVEEVDQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASPSSPGRQDSDEDDGPQRVEEVDQGR 27 2 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 AS(0.326)PS(0.093)S(0.581)PGRQDS(1)DEDDGPQRVEEVDQGR 127.31 3.44E-05 229960000 70007 76468 55424 79443 69661 44899 59802 61576 78734 TRUE FALSE 65625.38684 82129.77028 56738.68345 81481.64188 64190.10606 57860.61243 50835.24527 69263.89915 65592.78676 1.000497007 1.252115886 0.86501407 1.242234793 0.978615321 0.882118527 0.775012738 1.055968233 1 16.00124955 2.487828455 9.838359582 0.898522049 1.082618005 0.236982617 0.132880243 0.280077809 236.3420232 0.042060483 0.037474349 307.4882003 -2.487828455 0.184095956 ASPSSPGRQDS(ph)DEDDGPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASPSSPGRQDSDEDDGPQR 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 ASPSSPGRQDS(1)DEDDGPQR;ASPSSPGRQDS(1)DEDDGPQR;ASPSSPGRQDS(1)DEDDGPQR;ASPSSPGRQDS(0.999)DEDDGPQR 189.51 8.39E-15 1458080000 993770 920250 1019290 958210 1061720 914320 1139370 930930 990670 TRUE FALSE 931571.7096 988386.2675 1043468.04 982799.2908 978336.794 1178269.341 968532.0459 1047158.66 825320.777 1.128738953 1.197578317 1.264318153 1.190808857 1.185401872 1.427650162 1.173521948 1.268789892 1 19.65459543 -0.902794866 4.271243586 0.999995488 1.231877909 0.439085448 0.081518814 15442028.19 46350928.92 1280.494462 0.017965143 0.125084972 0.902794866 0.23188242 ASPSSPGRQDS(ph)DEDDGPQRVEEVDQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASPSSPGRQDSDEDDGPQRVEEVDQGR 27 2 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 ASPSSPGRQDS(1)DEDDGPQRVEEVDQGR 111.9 0.00063783 409480000 95201 123060 102570 116410 133900 78783 116550 106480 184890 TRUE FALSE 89242.53935 132171.4904 105003.0088 119397.2777 123384.0341 101526.3732 99074.4095 119774.2624 154030.6646 0.579381642 0.858085569 0.681701979 0.775152649 0.801035524 0.659130917 0.643212245 0.777600114 1 17.23285807 -2.207163058 1.394380336 1.533832796 0.725501923 0.521783646 0.083604674 52068.61968 7912.934628 87231.12328 0.022424063 0.00620636 2.207163058 -0.808330874 ASPVPSDPEKPGT(ph)PGEGMLSSDLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASPVPSDPEKPGTPGEGMLSSDLDR 25 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 ASPVPSDPEKPGT(0.98)PGEGMLS(0.009)S(0.011)DLDR 124.9 0.00023832 74329000 139930 100620 111240 104660 109150 92603 155450 103390 139090 TRUE FALSE 131172.0311 108070.0095 113878.6653 107345.7528 100577.7993 119335.9828 132141.7156 116298.4691 115874.9804 1.132013404 0.932643174 0.982771819 0.926392845 0.867985469 1.029868418 1.140381773 1.003654703 1 16.82220957 2.009518021 24.91512091 1.068988883 0.962329649 0.171759176 0.077752449 229.8379218 601639.6278 0.027177498 0.020046095 102.2157974 -2.009518021 -0.106659235 ASQEAS(ph)TEDPSGEQAQEEDQADSAFPLLSLGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASQEASTEDPSGEQAQEEDQADSAFPLLSLGPR 33 0 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 1 AS(0.001)QEAS(0.847)T(0.153)EDPSGEQAQEEDQADSAFPLLSLGPR 237.13 5.86E-47 16585000 15651 22184 19916 22943 21741 16156 24338 18562 17880 TRUE FALSE 14671.43185 23826.52644 20388.41693 23531.75622 20033.54956 20819.97493 20688.74284 20879.50656 14895.71249 0.984943275 1.59955601 1.368743988 1.57976708 1.344920531 1.39771595 1.388905892 1.401712511 1 13.86260951 -0.793173095 0.744891026 0.94837787 1.40923256 0.33285184 0.167148744 30.14941064 9.650489062 4.054565542 0.050980307 0.161000382 0.793173095 0.460854689 ASQEPS(ph)PKPGTEVIPAAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASQEPSPKPGTEVIPAAPR 19 1 I3L4I0;I3L1Y9;Q96CP2 I3L4I0 FLYWCH2 FLYWCH family member 2 1 ASQEPS(1)PKPGTEVIPAAPR;ASQEPS(0.999)PKPGTEVIPAAPR;ASQEPS(1)PKPGTEVIPAAPR;ASQEPS(1)PKPGTEVIPAAPR 196.2 5.13E-16 1345350000 1561590 1025660 1286680 1205130 1160220 943290 1630780 1022870 1221840 TRUE FALSE 1463852.869 1101600.934 1317200.657 1236055.676 1069101.001 1215602.51 1386259.678 1150577.571 1017907.011 1.438100783 1.08222158 1.294028476 1.214310996 1.050293386 1.194217642 1.361872611 1.130336621 1 19.95717434 0.994254192 24.76470705 0.999999985 1.224259878 0.300641672 0.115937526 227.6348771 981122.8204 0.104585372 0.026146343 9.868569233 -0.994254192 0.224259893 ASQPDLVDT(ph)PTSSKPQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASQPDLVDTPTSSKPQPK 18 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 ASQPDLVDT(0.766)PT(0.196)S(0.032)S(0.005)KPQPK;ASQPDLVDT(1)PTSSKPQPK 210.74 6.13E-16 453560000 778330 493610 651100 562130 576730 462470 798660 487440 935920 TRUE FALSE 729615.7147 530157.398 666544.3995 576555.2075 531435.9522 595977.5814 678908.3474 548297.957 779708.9057 0.935753984 0.679942725 0.854863135 0.739449304 0.681582509 0.764359079 0.870720268 0.703208535 1 19.57257609 -1.546157117 3.258084861 1.007338682 0.778845203 0.398947028 0.085351978 24944221.75 33846304.31 1622762.746 0.01877217 0.028434322 1.546157117 -0.22849348 ASQS(ph)RPNS(ph)SALETLGGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASQSRPNSSALETLGGEK 18 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 2 AS(0.005)QS(0.995)RPNS(0.917)S(0.083)ALETLGGEK;AS(0.029)QS(0.971)RPNS(0.917)S(0.083)ALETLGGEK;AS(0.019)QS(0.981)RPNS(0.921)S(0.079)ALETLGGEK 239.02 3.80E-24 1225750000 3431430 2727590 2767410 2752090 3400210 1991610 3915800 2950940 4678700 TRUE FALSE 3216662.922 2929543.602 2833054.272 2822713.289 3133171.222 2566555.476 3328662.143 3319371.355 3897794.744 0.825252003 0.751590013 0.726835161 0.724182127 0.803831763 0.658463476 0.853986 0.851602399 1 21.89422669 1.053350218 1.323385378 0.995413138 0.748550207 0.69862721 0.051662338 0.213873912 0.766111831 0.043313692 0.013253664 11.30707358 -1.053350218 -0.246862931 ASQSRPNS(ph)SALETLGGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASQSRPNSSALETLGGEK 18 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 ASQSRPNS(0.884)S(0.116)ALETLGGEK;ASQSRPNS(0.906)S(0.093)ALETLGGEK 238.7 4.15E-24 631590000 343830 239466 288000 292460 379520 235777 360500 282900 348420 TRUE FALSE 322310.2941 257196.3118 294831.496 299965.0187 349714.0301 303841.9924 306446.3717 318220.6877 290266.4511 1.11039458 0.886069716 1.015727084 1.033412637 1.204803479 1.04676924 1.055741614 1.096305434 1 18.14701831 3.244229618 2.786895243 1.080863594 0.975677422 0.148938906 0.075713701 0.324920471 5.152935582 0.021098686 0.028287975 1754.80805 -3.244229618 -0.105186171 ASQVSNSDHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASQVSNSDHK 10 0 E9PS17;Q96KG9-2;Q96KG9;E9PK59;Q96KG9-4;E9PPN3;H0YDH0 E9PS17 SCYL1 N-terminal kinase-like protein 0 ; 170.52 0.0026615 0 134404 169584 156562 162898 195047 130231 188077 156846 216929 FALSE TRUE 125991.8936 182140.1758 160275.7246 167078.2385 179728.7954 167826.5756 159876.5999 176428.5684 180722.1485 0.697158011 1.00784645 0.886862656 0.924503387 0.994503424 0.928644203 0.884654157 0.976242092 1 17.4634138 4.748319183 24.80993383 0.941460544 0.697157865 0.752729949 0.045359018 612.4918008 1557148.426 0.010386789 0.137108356 56016.9144 -4.748319183 -0.244302679 ASS(ph)ASVPAVGASAEGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASSASVPAVGASAEGTR 17 0 V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23;A0A2R8YFI4 V9GYZ0 PANK2 "Pantothenate kinase 2, mitochondrial" 1 ASS(1)ASVPAVGASAEGTR 308.98 4.83E-58 293590000 250260 281420 277510 329320 348580 275910 329530 257740 252330 TRUE FALSE 234596.6733 302256.6296 284092.6682 337770.9087 321203.9329 355560.738 280120.0357 289919.4064 210214.4929 1.115987152 1.437848673 1.351441874 1.60679173 1.527981865 1.691418765 1.332543879 1.379159935 1 17.68150261 0.668993056 1.669824511 1.000818379 1.446344343 0.431973297 0.157045405 1.235624759 4.898875359 0.143769118 0.040908774 4.666519193 -0.668993056 0.445525963 ASS(ph)DIVSLAGPSAGPGSSEGGCSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASSDIVSLAGPSAGPGSSEGGCSR 24 0 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 AS(0.127)S(0.873)DIVSLAGPSAGPGSSEGGCSR;AS(0.14)S(0.86)DIVSLAGPSAGPGSSEGGCSR;AS(0.129)S(0.871)DIVSLAGPSAGPGSSEGGCSR;AS(0.128)S(0.872)DIVSLAGPSAGPGSSEGGCSR 538.06 0 390681000 268125 277473 281975 286122 335055 222704 264763 233429 277972 TRUE FALSE 251343.5349 298017.3896 288663.5802 293464.3749 308741.1318 286995.0295 225064.2461 262573.1245 231576.6774 1.085357721 1.286905888 1.246514042 1.26724495 1.33321341 1.239308866 0.971877862 1.133849606 1 17.82113044 1.75247612 24.99999742 1.039455189 1.252936664 0.626432503 0.075385213 2.525549737 4543.693278 0.031611317 0.017530271 56.55566589 -1.75247612 0.213481475 ASS(ph)ESQGLGAGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASSESQGLGAGVR 13 0 Q9BV36-2;H7C2D8;Q9BV36-3 Q9BV36-2;Q9BV36-3 MLPH Melanophilin 1 AS(0.048)S(0.952)ESQGLGAGVR;AS(0.009)S(0.991)ESQGLGAGVR 141.75 4.20E-05 591860000 533140 759210 619460 1048810 1163770 480610 696960 585260 621180 TRUE FALSE 499771.7191 815422.6984 634153.8837 1075724.24 1072372.199 619354.3049 592457.3183 658330.9993 517501.045 0.965740502 1.575692854 1.225415658 2.078689986 2.072212624 1.196817496 1.144842748 1.272134628 1 18.98120225 2.039430028 24.99988095 1.159020855 1.562679406 0.283953513 0.339022555 222.8854752 141315.5116 0.12877777 0.095108537 109.5040112 -2.039430028 0.403658551 ASS(ph)ESQIFELNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASSESQIFELNK 12 0 Q9BV36;Q9BV36-4 Q9BV36 MLPH Melanophilin 1 ASS(1)ESQIFELNK;ASS(1)ESQIFELNK;AS(0.079)S(0.921)ESQIFELNK 334.24 2.97E-58 152467000 566830 538490 512670 675630 798560 335066 632060 519470 736240 TRUE FALSE 531353.1221 578360.3599 524830.7745 692967.8096 735844.3188 431794.1149 537288.4708 584326.973 613356.7877 0.866303484 0.942942789 0.855669628 1.129795616 1.199700294 0.703985223 0.875980313 0.95267059 1 19.226367 0.984951606 22.25279897 1.000000026 0.930796017 0.015476608 0.139963906 1078.760939 1595227.1 0.134064889 0.033516222 9.659432359 -0.984951606 -0.069204009 ASS(ph)FADMMGILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASSFADMMGILK 12 0 E9PPF9;E9PLD2;Q9H019-3;Q9H019 E9PPF9 MTFR1L Mitochondrial fission regulator 1-like 1 AS(0.001)S(0.999)FADMMGILK 164.11 6.10E-05 46213000 326490 361400 238930 283820 347150 143030 372520 367660 571000 TRUE FALSE 306055.5737 388158.432 244597.5324 291103.3017 319886.2393 184320.4391 316664.0843 413563.1603 475696.4112 0.643384239 0.815979316 0.514188307 0.611951856 0.672458803 0.387474942 0.66568525 0.869384655 1 18.85968162 1.143347196 3.13781167 0.990476011 0.616085928 0.608685271 0.109476008 0.160749745 2.856198573 0.102706806 0.027614049 13.91064271 -1.143347196 -0.374390083 ASS(ph)FSGISILTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASSFSGISILTR 12 0 A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5;H0YIX9;H7C0E9;Q9Y2K5-3;Q9Y2K5-2 A0A0U1RRA6 R3HDM2 R3H domain-containing protein 2 1 AS(0.003)S(0.997)FSGISILTR;AS(0.002)S(0.993)FS(0.004)GISILTR;AS(0.006)S(0.992)FS(0.002)GISILTR 196.7 2.14E-07 410970000 450690 570440 415742 527340 367516 323751 666940 430952 416865 TRUE FALSE 422482.1174 612675.9711 425603.5966 540872.4372 338652.7758 417212.658 566938.5386 484757.3058 347287.5384 1.216519658 1.764174937 1.225507827 1.557419652 0.975136561 1.201346469 1.632475905 1.395838469 1 18.40577112 3.835678756 6.8607789 1.322639568 1.523318161 0.087486163 0.248943481 0.500211225 27.95447415 0.060970494 0.110713556 6849.813642 -3.835678756 0.200678592 ASS(ph)FSGISVLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASSFSGISVLTR 12 0 Q15032-2;Q15032-4;Q15032;Q15032-3;H7C1X4;H7BZ47;H7C207 Q15032-2 R3HDM1 R3H domain-containing protein 1 1 AS(0.128)S(0.867)FS(0.005)GISVLTR;AS(0.005)S(0.995)FSGISVLTR;ASS(0.997)FS(0.002)GISVLTR;AS(0.003)S(0.99)FS(0.007)GISVLTR 202.72 1.40E-07 465934000 692173 731214 655704 671694 640772 536818 819965 638931 811477 TRUE FALSE 648851.1275 785353.8454 671257.6085 688930.8052 590448.3519 691788.6421 697018.8604 718702.9418 676036.2464 0.959787483 1.161703754 0.992931388 1.019073768 0.873397477 1.023301111 1.031037706 1.063113029 1 19.36674107 3.729991141 24.51163843 1.000522329 1.075813031 0.108571024 0.068936026 164.5963497 1405785.799 0.016953152 0.028901533 5370.208422 -3.729991141 0.075290702 ASS(ph)HS(ph)SQTQGGGSVTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASSHSSQTQGGGSVTKK 17 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 AS(0.015)S(0.985)HS(0.702)S(0.297)QT(0.001)QGGGSVTKK;AS(0.401)S(0.599)HS(0.925)S(0.075)QTQGGGSVTKK 138.04 1.74E-05 1847270000 1407850 1525870 1295650 1496300 1863960 941530 2135170 1209390 1806710 TRUE FALSE 1319735.182 1638847.002 1326383.43 1534697.591 1717572.1 1213334.427 1815021.08 1360385.004 1505158.429 0.876808153 1.088820267 0.881225128 1.019625284 1.141123796 0.806117418 1.205867133 0.903815158 1 20.52148392 3.03246655 24.98586219 1.027768255 0.966895111 0.040338104 0.124790482 605.1695766 465726.8896 0.032666806 0.039044088 1077.62225 -3.03246655 -0.060873144 ASS(ph)HSS(ph)QTQGGGSVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 AS(0.163)S(0.609)HS(0.433)S(0.749)QT(0.046)QGGGSVTK;AS(0.01)S(0.99)HS(0.006)S(0.741)QT(0.252)QGGGSVTK;AS(0.005)S(0.995)HS(0.032)S(0.968)QTQGGGSVTK;AS(0.027)S(0.973)HS(0.286)S(0.699)QT(0.015)QGGGSVTK 269.34 1.25E-27 7543473000 1786880 1790130 1448660 1862160 2000270 1210043 2280420 1649680 1581370 TRUE FALSE 1675042.37 1922673.088 1483022.899 1909946.178 1843176.863 1559362.771 1938492.191 1855646.179 1317429.131 1.2714478 1.459412915 1.125694631 1.449752502 1.399070978 1.183640724 1.47142047 1.408535864 1 20.32929393 -0.528263971 8.988181817 1 1.343474612 0.456742321 0.118599981 0 0 0.107658116 0.025375261 0.296302987 0.528263971 0.343474612 ASS(ph)HSS(ph)QTQGGGSVTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASSHSSQTQGGGSVTKK 17 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 AS(0.107)S(0.893)HSS(1)QTQGGGSVTKK;AS(0.03)S(0.97)HS(0.018)S(0.982)QTQGGGSVTKK;AS(0.062)S(0.938)HS(0.039)S(0.948)QT(0.013)QGGGSVTKK 232.02 9.81E-16 1559350000 2253210 2266980 1948330 2396990 2880850 1493400 3374390 2065640 3050740 TRUE FALSE 2112185.608 2434829.558 1994545.308 2458500.821 2654599.662 1924520.337 2868431.546 2323539.701 2541551.785 0.831061409 0.958009029 0.784774609 0.967322734 1.044479863 0.757222555 1.128614244 0.914220877 1 21.2772782 2.555282919 0.785697448 0.99938565 0.872124319 0.133292939 0.107760373 1.152738886 1.462287468 0.072512542 0.05807375 359.1558285 -2.555282919 -0.12726133 ASS(ph)HSSQT(ph)QGGGSVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 ASS(1)HSS(0.023)QT(0.977)QGGGSVTK;AS(0.009)S(0.991)HSS(0.159)QT(0.841)QGGGSVTK;ASS(1)HSS(0.016)QT(0.984)QGGGSVTK 395.88 5.04E-121 10896680000 10737100 11455300 9673150 11078400 12487600 7520480 15038000 9936000 9664000 TRUE FALSE 10065084.08 12303462.33 9902601.686 11362690.5 11506874.27 9691520.491 12783191.51 11176531.47 8051015.968 1.250163224 1.528187546 1.229981623 1.411336227 1.429244994 1.203763665 1.587773712 1.3882138 1 22.94073942 -1.259023548 4.000394969 0.999578414 1.388226746 0.475417437 0.124612397 85.13206073 30478160.62 21922.3582 0.026758989 0.055077783 1.259023548 0.388648333 ASS(ph)HSSQTQGGGSVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 ASS(0.496)HS(0.496)S(0.008)QTQGGGSVTK;AS(0.002)S(0.577)HS(0.209)S(0.209)QT(0.003)QGGGSVTK;AS(0.108)S(0.593)HS(0.149)S(0.149)QTQGGGSVTK;AS(0.376)S(0.413)HS(0.124)S(0.086)QTQGGGSVTK;AS(0.092)S(0.538)HS(0.225)S(0.144)QTQGGGSVTK;AS(0.149)S(0.815)HS(0.02)S(0.015)QTQGGGSVTK;AS(0.057)S(0.932)HS(0.005)S(0.006)QT(0.001)QGGGSVTK;AS(0.136)S(0.851)HS(0.005)S(0.008)QTQGGGSVTK 282.47 1.47E-35 46256260000 4685392.6 8299259 6578057 8055683 9386715 6061789 10200642 7498877 7657816 TRUE FALSE 4392142.241 8913744.772 6734091.618 8262405.464 8649520.268 7811729.079 8671150.43 8435128.301 6379677.038 0.688458399 1.397209407 1.055553687 1.295113438 1.355792811 1.224470931 1.359183291 1.322187354 1 22.60505196 4.747042917 24.82900328 1.26103481 0.688458082 0.646100379 0.130705489 586.44093 1716561.519 0.028558333 0.330716271 55852.53849 -4.747042917 -0.572576727 ASS(ph)LEDLVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 ASSLEDLVLK 10 0 Q15477 Q15477 SKIV2L Helicase SKI2W 1 AS(0.004)S(0.996)LEDLVLK;AS(0.001)S(0.999)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;AS(0.017)S(0.983)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK 287.83 6.92E-25 7287499000 5147230 4268495 4806225 4652684 5058616 3736571 6438553 4522005 6258978 TRUE FALSE 4825074.062 4584538.811 4920230.927 4772079.748 4661332.705 4815258.39 5473151.75 5086587.278 5214314.137 0.925351625 0.879221829 0.943600788 0.915188388 0.893949344 0.923469178 1.04963982 0.975504572 1 22.31404607 1.828341804 6.792784 1.011042544 0.911740852 0.765819421 0.024769052 0.101193934 6.323691187 0.010059769 0.00608591 67.35065198 -1.828341804 -0.099301693 ASS(ph)LGEIDESSELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ASSLGEIDESSELR 14 0 Q16513-3;Q16513-2;Q16513;Q16513-4;Q16513-5 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 ASS(1)LGEIDESSELR;ASS(1)LGEIDESSELR;ASS(1)LGEIDESSELR;ASS(1)LGEIDESSELR;ASS(1)LGEIDESSELR;ASS(1)LGEIDESSELR 376.24 2.25E-97 2194700000 2491600 2522830 2618450 2813680 2934810 2402260 2882130 2345320 2927210 TRUE FALSE 2335655.204 2709622.958 2680560.871 2885883.792 2704321.861 3095753.465 2449981.363 2638138.365 2438639.741 0.95776968 1.111120644 1.099203308 1.183398984 1.108946851 1.269459122 1.004650799 1.081807337 1 21.21764521 1.612452584 25 1.032418445 1.120971526 0.229981918 0.079971787 0.625517447 3391.370031 0.035867416 0.019051578 40.96873778 -1.612452584 0.088553081 ASS(ph)LNENVDHSALLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASSLNENVDHSALLK 15 0 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 1 AS(0.117)S(0.883)LNENVDHSALLK;AS(0.115)S(0.885)LNENVDHSALLK 208.17 1.95E-09 585620000 470570 470450 301940 315550 384150 111121 605960 288550 735460 TRUE FALSE 441117.8637 505282.6075 309102.1594 323647.5472 353980.4086 143199.8288 515101.9235 324576.1027 612706.9747 0.719949147 0.824672524 0.504486112 0.528225662 0.577731972 0.233716662 0.840698645 0.529741159 1 19.22483775 -0.831215813 9.459308676 1 0.606206131 0.342970296 0.175589726 0 0 0.162698895 0.038348497 0.14749734 0.831215813 -0.393793868 ASS(ph)LNFLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ASSLNFLNK 9 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 ASS(1)LNFLNK;ASS(1)LNFLNK;ASS(1)LNFLNK;ASS(1)LNFLNK;AS(0.001)S(0.999)LNFLNK;ASS(1)LNFLNK 220.5 4.76E-07 4418140000 11572060 11286840 10366370 9386800 12003450 7066920 14044350 10515450 20256900 TRUE FALSE 10847785.42 12122529.38 10612265.19 9627681.18 11060747.46 9107025.082 11938530.1 11828327.08 16875892.53 0.642797731 0.718334118 0.628841715 0.570499081 0.655417036 0.539647018 0.707431034 0.70090083 1 24.00846047 0.60885377 1.365791103 0.999610318 0.638214915 0.825664132 0.052287396 0.582988927 1.534376759 0.049316471 0.01458825 4.063064999 -0.60885377 -0.361395403 ASS(ph)LNVLNVGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ASSLNVLNVGGK 12 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;H0YG16;H0YJK1 Q07866-6 KLC1 Kinesin light chain 1 1 AS(0.002)S(0.998)LNVLNVGGK;AS(0.008)S(0.992)LNVLNVGGK;AS(0.006)S(0.994)LNVLNVGGK;AS(0.001)S(0.999)LNVLNVGGK;ASS(1)LNVLNVGGK;AS(0.001)S(0.999)LNVLNVGGK;ASS(1)LNVLNVGGK;AS(0.001)S(0.999)LNVLNVGGK 299.25 2.14E-36 4217898000 8302220 9115080 6999670 6639210 8923370 3971720 12492880 6734680 12433090 TRUE FALSE 7782598.87 9789970.007 7165705.478 6809583.369 8222564.515 5118291.089 10619688.62 7575519.623 10357926.96 0.751366456 0.945166928 0.691808844 0.657427244 0.793842682 0.49414242 1.025271627 0.731374111 1 23.30423195 -1.751161867 9.206986797 1.001145782 0.776049747 0.201111976 0.146921559 0.003258273 8.81E-05 0.134138041 0.031474255 0.017735283 1.751161867 -0.225096036 ASS(ph)LSESSPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.996)LS(0.003)ESSPPK;ASS(0.952)LS(0.048)ESSPPK;ASS(0.998)LS(0.002)ESSPPK;ASS(0.612)LS(0.388)ESSPPK 264.3 7.74E-21 2624650000 8061720 5720620 5937200 5941730 4944100 4043860 8139390 4895710 12182370 TRUE FALSE 7557151.336 6144180.657 6078033.188 6094204.851 4555810.33 5211256.735 6918964.032 5506950.17 10149053.75 0.744616348 0.605394435 0.598876835 0.600470251 0.448890157 0.513472178 0.681734889 0.542607253 1 23.27484189 -1.239809701 4.995345797 1.000064904 0.592914076 0.708968585 0.082148786 5.70E-05 8.68E-06 0.07638834 0.018002044 0.057569214 1.239809701 -0.407150828 ASS(ph)PAQCVTPVQTVV ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASSPAQCVTPVQTVV 15 0 Q13614;Q13614-2 Q13614 MTMR2 Myotubularin-related protein 2 1 AS(0.499)S(0.501)PAQCVTPVQTVV;AS(0.266)S(0.734)PAQCVTPVQTVV 143.31 4.65E-06 172614000 448450 438040 468210 459310 497090 465830 594740 426660 583570 TRUE FALSE 420382.315 470472.9374 479316.1623 471096.6722 458050.5566 600307.5589 505564.2583 479929.4402 486168.397 0.864684578 0.967716002 0.985905635 0.968998962 0.942164401 1.234772895 1.039895356 0.987167087 1 18.89109659 ASS(ph)PCPEFEQFQIVPAVETPYLAR ddPTM_SK-BR-3_Pertuzumab_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(0.164)S(0.836)PCPEFEQFQIVPAVETPYLAR 130.32 4.14E-05 147580000 122830 134370 140600 128000 131340 144590 161690 120170 153120 TRUE FALSE 115142.2896 144318.8946 143935.0984 131284.6967 121025.0862 186330.7858 137446.0856 135173.489 127563.2828 0.902628774 1.131351369 1.128342696 1.02917308 0.948745466 1.460692934 1.077473725 1.059658281 1 16.9608536 ASS(ph)PELPVSVENIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASSPELPVSVENIK 14 0 Q969R5 Q969R5 L3MBTL2 Lethal(3)malignant brain tumor-like protein 2 1 AS(0.19)S(0.81)PELPVSVENIK 69.456 0.049249 20544000 110110 79707 100440 95219 84656 85695 112200 87213 56546 TRUE FALSE 103218.4117 85608.58922 102822.4842 97662.48075 78007.45925 110433.7554 95376.65161 98101.73503 47108.1073 2.191096556 1.81727932 2.1826919 2.07315654 1.655924292 2.344262202 2.024633488 2.082480929 1 15.52368775 -1.382457209 2.821183931 0.981264575 2.039487434 0.743266031 0.193241457 6193984.336 7156684.527 948649.8048 0.04404695 0.041451742 1.382457209 1.058222859 ASS(ph)PFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASSPFR 6 0 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 AS(0.456)S(0.544)PFR;AS(0.056)S(0.944)PFR;AS(0.001)S(0.999)PFR;AS(0.002)S(0.998)PFR 138.55 0.012855 3836800000 5691970 6327470 5728420 5637880 6169710 4775830 6267960 5618080 5029440 TRUE FALSE 5335719.758 6795962.463 5864300.828 5782557.546 5685165.864 6154534.592 5328137.587 6319509.655 4189993.973 1.273443302 1.621950415 1.399596483 1.380087318 1.356843447 1.468864784 1.271633712 1.508238364 1 21.99851674 -3.370248853 0.250792904 5.20E-10 1.463993999 0.562308458 0.110074505 49.54356529 1.027138477 25.89915253 0.150226043 0.000426335 3.370248853 1.463993998 ASS(ph)PFRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASSPFRR 7 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 AS(0.069)S(0.931)PFRR;AS(0.001)S(0.999)PFRR;AS(0.11)S(0.89)PFRR 100.98 0.0083053 4911350000 2282230 2628210 2663710 2424510 2524100 2133310 2850620 2236890 2773570 TRUE FALSE 2139389.298 2822805.403 2726894.459 2486727.031 2325867.368 2749161.966 2423195.995 2516170.641 2310643.249 0.925884729 1.221653496 1.180145165 1.076205525 1.006588693 1.189782095 1.048710568 1.088948128 1 21.1398631 3.2144664 22.57498995 1.074715509 1.143450027 0 0.093773967 165.69147 155242.5962 0.025537299 0.030547446 1638.575285 -3.2144664 0.068734518 ASS(ph)PPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASSPPDR 7 0 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.324)S(0.676)PPDR;AS(0.168)S(0.832)PPDR 83.623 0.023228 286250000 847000 721100 786090 805410 725770 677790 799730 739620 580930 TRUE FALSE 793987.7819 774490.9943 804736.426 826078.1842 668770.9518 873456.97 679817.9108 831963.1851 483969.03 1.6405756 1.600290403 1.662784964 1.706882327 1.381846586 1.804778644 1.404672342 1.719042198 1 18.8845552 -2.525663802 0.391861067 8.61E-16 1.627122968 0.672741843 0.133937906 39.67941231 1.73830984 33.91480179 0.074605873 0.002980823 2.525663802 1.627122968 ASS(ph)PPDRIDIFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASSPPDRIDIFGR 13 1 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.096)S(0.904)PPDRIDIFGR;AS(0.089)S(0.911)PPDRIDIFGR;AS(0.196)S(0.804)PPDRIDIFGR 184.48 5.74E-06 6627170000 1101430 1449030 1269600 1305650 1597510 1082550 1540360 1134010 1912630 TRUE FALSE 1032493.462 1556317.689 1299715.512 1339155.189 1472048.009 1395064.611 1309397.318 1275593.645 1593399.697 0.64798146 0.976727743 0.815687058 0.840438963 0.923841025 0.875527097 0.821763253 0.800548442 1 20.60367677 -2.570731022 2.106490801 3.38238254 0.850465786 0.246441231 0.086653628 2191121.197 145938.8231 25219858.47 0.018966607 0.002687008 2.570731022 -2.531916754 ASS(ph)RS(ph)PVFTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASSRSPVFTPR 11 1 P52735-3 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 2 AS(0.443)S(0.562)RS(0.995)PVFTPR;AS(0.466)S(0.556)RS(0.978)PVFTPR 80.387 0.013969 418370000 460010 493450 460180 469960 540810 372680 561420 425380 416360 TRUE FALSE 431218.7952 529985.5514 471095.6869 482019.9692 498336.9641 480266.666 477240.283 478489.6294 346866.8262 1.243182578 1.527922278 1.358145695 1.389639864 1.436680958 1.384585177 1.375860264 1.379462068 1 18.40402234 -1.099167025 0.543208264 0.868577619 1.405628099 0.744214416 0.070949738 11.50090933 1.880771029 2.40867592 0.02793732 0.079585321 1.099167025 0.53705048 ASS(ph)SLGLQDFDLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASSSLGLQDFDLLR 14 0 P41743 P41743 PRKCI Protein kinase C iota type 1 AS(0.157)S(0.842)S(0.001)LGLQDFDLLR;AS(0.003)S(0.995)S(0.001)LGLQDFDLLR 195.2 5.93E-08 89838000 182917 224770 195865 189654 243030 155615 213582 210724 228090 TRUE FALSE 171468.5515 241412.2047 200511.0103 194520.8427 223943.4041 200538.5243 181557.3619 237033.3553 190020.3055 0.902369623 1.270454776 1.055208336 1.023684507 1.178523546 1.055353131 0.955462951 1.247410663 1 17.53579407 3.712096041 23.91703397 1.066185553 1.127742268 0 0.12261333 791.2597474 1259523.388 0.030053771 0.046782282 5153.425967 -3.712096041 0.061556715 ASS(ph)VTTFTGEPNTCPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 ASSVTTFTGEPNTCPR 16 0 P52943;H0YFA4;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 1 ASS(0.999)VT(0.001)TFTGEPNTCPR;AS(0.001)S(0.996)VT(0.004)TFTGEPNTCPR;ASS(0.989)VT(0.011)TFTGEPNTCPR;ASS(0.497)VT(0.497)T(0.005)FTGEPNTCPR;ASS(0.822)VT(0.173)T(0.002)FT(0.003)GEPNTCPR;ASS(0.966)VT(0.034)TFTGEPNTCPR;ASS(0.986)VT(0.014)TFTGEPNTCPR;AS(0.002)S(0.968)VT(0.029)TFTGEPNTCPR;AS(0.003)S(0.997)VT(0.001)TFTGEPNTCPR 420.34 6.31E-160 16930530000 8238700 8188070 6940680 6975350 7543810 5778919 10616350 7095870 10464650 TRUE FALSE 7723054.473 8794323.222 7105316.207 7154349.29 6951349.593 7447199.102 9024526.875 7981804.989 8718032.311 0.885871284 1.008750932 0.81501375 0.820638079 0.797353043 0.854229353 1.035156392 0.915551205 1 23.05557112 1.749941623 25 0.983202032 0.870571248 0.427764554 0.065058693 3.453956673 7600.618995 0.03227822 0.01790008 56.22657413 -1.749941623 -0.112630784 ASSEGGTAAGAGLDSLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASSEGGTAAGAGLDSLHK 18 0 A0A1W2PNV4;C9JEY1;C9K057;O15143 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 210.91 3.60E-16 484310000 257570 265450 290510 299250 273490 228390 350110 253790 360960 FALSE TRUE 241449.1535 285104.1942 297401.0344 306929.2616 252011.1986 294322.4854 297614.2558 285476.2402 300713.4441 0.802921047 0.94809261 0.98898483 1.020670235 0.838044336 0.978747346 0.989693882 0.949329821 1 18.19802984 4.742487407 3.502804845 0.966169732 0.782401977 0.515008547 0.049495819 0.239537689 5.131471145 0.011282238 0.117369752 55269.73821 -4.742487407 -0.183767756 ASSGDQGS(ph)PPCFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASSGDQGSPPCFLR 14 0 A6NN50;O75147-2;O75147-1;O75147-4;O75147 A6NN50 OBSL1 Obscurin-like protein 1 1 ASSGDQGS(1)PPCFLR;ASSGDQGS(1)PPCFLR;ASSGDQGS(1)PPCFLR 212 3.20E-09 352490000 622620 723380 672080 673250 736590 570240 765780 601980 697250 TRUE FALSE 583651.3256 776939.8079 688022.055 690526.7348 678741.1927 734859.0309 650958.3982 677138.5281 580874.4706 1.004780474 1.337534781 1.184459104 1.188771016 1.168481707 1.265090942 1.120652449 1.165722652 1 19.1478669 0.561346119 0.725338631 0.997873506 1.2072253 0.282645422 0.087169818 1.604475037 1.446456587 0.084620756 0.028757792 3.642051808 -0.561346119 0.209351794 ASSHS(ph)S(ph)QTQGGGSVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 AS(0.09)S(0.458)HS(0.66)S(0.788)QT(0.005)QGGGSVTK 126.9 3.65E-05 6877700000 1581700 1569500 1249500 1514000 1690700 1066500 1886200 1356600 1398800 TRUE FALSE 1482704.22 1685707.413 1279138.73 1552851.803 1557919.242 1374381.237 1603381.821 1525974.496 1165331.243 1.27234572 1.446547857 1.097661062 1.332541123 1.336889619 1.179391048 1.375902199 1.309477031 1 20.15230867 -1.57174006 3.091255966 0.986084421 1.293421293 0.472457648 0.097580527 12735296.97 13939004.09 1447045.97 0.023046629 0.026807724 1.57174006 0.307336872 ASSHS(ph)SQTQGGGSVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 AS(0.004)S(0.342)HS(0.523)S(0.106)QT(0.025)QGGGSVTK;ASS(0.185)HS(0.8)S(0.012)QT(0.003)QGGGSVTK;AS(0.185)S(0.185)HS(0.315)S(0.315)QTQGGGSVTK 311.09 1.22E-57 7822600000 1197750 2647940 2029060 2491990 2756630 1998620 3132370 2432420 2272120 TRUE FALSE 1122784.966 2843996.233 2077190.261 2555938.682 2540135.4 2575589.149 2662700.198 2736112.991 1892888.494 0.593159591 1.502463691 1.097365359 1.350284864 1.341936098 1.360666071 1.40668624 1.445469715 1 20.852158 4.747138949 24.98993183 1.325340449 0.59315922 0.68391437 0.153617655 598.6869618 1744024.087 0.033208779 0.391992779 55864.89015 -4.747138949 -0.732181229 ASSHSS(ph)QTQGGGSVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 ASS(0.004)HS(0.053)S(0.851)QT(0.091)QGGGSVTK;AS(0.007)S(0.286)HS(0.293)S(0.413)QTQGGGSVTK;AS(0.002)S(0.025)HS(0.238)S(0.734)QTQGGGSVTK 347.12 4.38E-87 11344964000 698930 1446640 1120897 1341420 1582140 1089380 1664910 1295500 1230778 TRUE FALSE 655185.2189 1553750.731 1147485.206 1375843.108 1457885.106 1403866.321 1415272.202 1457246.027 1025353.201 0.638984906 1.515332209 1.119112132 1.341823586 1.421836988 1.369153888 1.380277743 1.42121371 1 19.96768953 4.7478387 24.96928277 1.334186393 0.638984534 0.663115628 0.152538949 692.9689009 1864886.109 0.032572686 0.415574449 55954.97422 -4.7478387 -0.695201858 ASSHSSQT(ph)QGGGSVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 AS(0.177)S(0.177)HS(0.177)S(0.177)QT(0.291)QGGGSVTK 115.63 0.0018042 223150000 50862 302440 212890 266630 356730 347660 166160 248930 175650 TRUE FALSE 47678.63821 324832.9723 217939.8513 273472.1772 328713.8648 448023.7982 141245.8506 280009.4585 146332.8803 0.325823138 2.219822173 1.489343003 1.868836154 2.246343161 3.061675527 0.965236591 1.913510197 1 17.15889445 3.228720455 21.14406889 1.882671071 1.553079944 0.065207792 0.752699775 114.1270565 245229.9476 0.207182587 0.251532333 1693.247545 -3.228720455 -0.329591127 ASSHSSQTQGGGS(ph)VTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 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 ASSHSSQT(0.009)QGGGS(0.945)VT(0.045)K;ASSHSSQTQGGGS(0.999)VT(0.001)K;ASSHSSQT(0.001)QGGGS(0.994)VT(0.005)K;ASSHSSQT(0.007)QGGGS(0.968)VT(0.025)K;ASSHSSQTQGGGS(1)VTK;ASSHSSQTQGGGS(1)VTK;ASSHSSQTQGGGS(1)VTK;ASSHSSQTQGGGS(0.998)VT(0.002)K;ASSHSSQTQGGGS(0.997)VT(0.003)K;ASSHSSQTQGGGS(1)VTK 264.66 5.22E-27 5188986000 2284949 5292192 5006476 5391267 5693890 4217149 6727752 5594629 6977628 TRUE FALSE 2141938.121 5684031.402 5125231.975 5529616.039 5246714.847 5434571.457 5718988.045 6293130.746 5813016.81 0.368472721 0.977810935 0.881681946 0.951247213 0.902580367 0.934896911 0.983824446 1.082592903 1 22.47085565 4.739930208 24.99863124 0.954714889 0.368472531 0.917688236 0.056016788 31.22293541 569842.4402 0.01311238 0.08230324 54945.25682 -4.739930208 -0.586242358 ASSHSSQTQGGGS(ph)VTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASSHSSQTQGGGSVTKK 17 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 ASSHSSQTQGGGS(0.963)VT(0.037)KK;ASSHSSQTQGGGS(0.92)VT(0.08)KK;ASSHSSQTQGGGS(0.996)VT(0.004)KK 181.61 4.86E-10 361661000 215812 276890 273835 295597 331620 246878 427104 303919 380799 TRUE FALSE 202304.7122 297391.2237 280330.4955 303182.5195 305575.9029 318147.6709 363063.7202 341863.9562 317241.1868 0.637700023 0.937429426 0.883651011 0.955684609 0.963228974 1.002857397 1.144440682 1.077615298 1 18.27522056 5.926091957 0.345126879 1.079010656 1.22E-17 0.716959662 0.071240202 8.244271832 0.415801204 0.064064446 4.356271738 843513.344 -5.926091957 -1.079010656 ASSHSSQTQGGGSVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;; 216.29 1.53E-14 880250000 323081 924490 804510 845630 895510 790000 969660 894720 1046410 FALSE TRUE 302859.9369 992940.2015 823593.3571 867330.2974 825180.2569 1018060.175 824268.4849 1006427.762 871757.4109 0.347413091 1.139009762 0.944750623 0.994921622 0.946570969 1.167825088 0.945525068 1.154481452 1 19.7335672 4.744106473 24.99927818 1.03084024 0.3474128 0.858091613 0.088056392 197.7232377 891258.5177 0.018798795 0.165073525 55476.17034 -4.744106473 -0.68342744 ASSIIDELFQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASSIIDELFQDR 12 0 E7ERK6;H0YC35;H0YLK8;P10909-4;P10909-6;P10909;P10909-5;P10909-2;P10909-3 E7ERK6 CLU Clusterin;Clusterin;Clusterin beta chain;Clusterin alpha chain 0 ; 109.24 0.0037681 48876000 32755 41588 35944 37966 45157 36105 43322 41271 46765 FALSE TRUE 30704.92302 44667.21879 36796.60865 38940.27184 41610.55137 46527.92738 36826.26828 46423.7752 38959.61939 0.78812174 1.146500389 0.944480702 0.999503395 1.068043067 1.194260317 0.945241993 1.19158698 1 15.24969196 2.733485211 5.814200629 1.07541663 0.994667389 0.170844422 0.114754481 0.370739847 52.31296323 0.033782765 0.033531636 541.3588132 -2.733485211 -0.080749241 ASSLS(ph)ESSPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 ASS(0.166)LS(0.833)ESSPPK 185.84 4.50E-06 435590000 1057800 723920 805210 804420 603850 510870 1056600 659430 1555000 TRUE FALSE 991594.1862 777519.79 824309.9614 825062.7791 556426.0568 658349.8757 898172.639 741761.2871 1295460.454 0.765437635 0.600187978 0.636306542 0.636887661 0.429519909 0.508197586 0.693323085 0.572585049 1 20.30503355 -1.057512971 4.22365657 1.000040439 0.605523099 0.643318137 0.092361373 10036371.7 5028867.597 3574.926374 0.020842063 0.087596556 1.057512971 -0.39451734 ASSLSESS(ph)PPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASSLSESSPPK 11 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 ASSLS(0.001)ES(0.439)S(0.56)PPK;ASSLSES(0.02)S(0.98)PPK 162.31 2.65E-05 2207860000 2162650 1391070 1829570 1638220 1926110 1460780 2132340 1588570 2184620 TRUE FALSE 2027293.597 1494066.27 1872968.264 1680259.499 1774841.09 1882483.472 1812615.413 1786906.461 1819992.809 1.113901982 0.820918777 1.029107508 0.923223153 0.975191265 1.034335665 0.99594647 0.981820616 1 20.79550132 2.470473994 23.25272601 1.003304347 0.955497374 0.019595678 0.075390131 179.2151311 626894.2629 0.023931197 0.020081585 295.4431971 -2.470473994 -0.047806972 ASSNKDFT(ph)PNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASSNKDFTPNR 11 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;Q7Z6E9-4 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 ASSNKDFT(0.999)PNR;AS(0.001)S(0.001)NKDFT(0.999)PNR;ASS(0.001)NKDFT(0.999)PNR 95.631 0.012309 1317900000 3033360 2296090 2604260 2525120 3244380 2031440 3382530 2805430 5215700 TRUE FALSE 2843507.412 2466094.893 2666034.277 2589918.854 2989579.482 2617883.75 2875351.028 3155694.111 4345165.975 0.654407088 0.567549066 0.613563277 0.596046013 0.688024232 0.602481876 0.661735603 0.726253986 1 22.05097986 0.352914258 0.659736485 1.011436622 0.605737442 0.926956329 0.033186119 0.500622721 0.32230122 0.041876082 0.011791687 2.253794207 -0.352914258 -0.40569918 ASSPS(ph)PLTIGTPESQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASSPSPLTIGTPESQR 16 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 ASS(0.003)PS(0.997)PLTIGTPESQR;ASSPS(1)PLTIGTPESQR;ASSPS(1)PLTIGTPESQR;ASSPS(1)PLTIGTPESQR 440.55 6.67E-182 1396800000 1227030 1284360 1264610 1229390 1177030 1185810 1437210 1156630 927750 TRUE FALSE 1150232.383 1379455.351 1294607.146 1260938.229 1084590.812 1528134.097 1221713.703 1301037.802 772902.5315 1.488198493 1.784772717 1.674994056 1.631432396 1.40326984 1.977136877 1.580682755 1.683314194 1 19.55992697 -1.355959283 3.815208142 0.997673063 1.666744965 0.631189652 0.156548871 2501.606225 35474536.16 122369.9307 0.032657454 0.044059617 1.355959283 0.669071902 ASSQQEKEDKPAETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASSQQEKEDKPAETK 15 2 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 104.28 0.00079102 133410000 153770 63292 96937 87802 114330 59058 114910 80187 263610 FALSE TRUE 144145.8102 67978.20554 99236.39142 90055.14797 105350.983 76107.08587 97680.31227 90198.52346 219611.788 0.656366452 0.309538054 0.45187188 0.410065183 0.479714609 0.346552827 0.444786289 0.410718041 1 17.74459597 -1.411720891 3.462910558 1.005268439 0.425962349 0.782794001 0.092704188 138890896.5 207257035.8 7314928.16 0.019447916 0.03875066 1.411720891 -0.57930609 ASSRPGS(ph)PTADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASSRPGSPTADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHK 45 1 H0Y9C1;H0Y9Z5;Q96LI5-2;Q96LI5 H0Y9C1 CNOT6L CCR4-NOT transcription complex subunit 6-like 1 AS(0.123)S(0.123)RPGS(0.739)PT(0.016)ADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHK;AS(0.098)S(0.098)RPGS(0.586)PT(0.169)ADPNS(0.049)IPLVLCADLNSLPDSGVVEYLSNGGVADNHK 200.05 2.17E-36 134927000 69012 61023 64971 62124 57871 47926 82203 54774 50841 TRUE FALSE 64692.66211 65541.20641 66512.1428 63718.20702 53326.0451 61761.45819 69877.42329 61612.65447 42355.30865 1.527380254 1.547414208 1.570337814 1.504373573 1.259016798 1.458175141 1.649791384 1.454661917 1 15.37025518 0.961985106 23.51186938 0.999999998 1.512721091 0.707788761 0.100519354 1886.199205 1166598.7 0.100248286 0.025062072 9.161890691 -0.961985106 0.512721093 ASSRS(ph)PVFTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASSRSPVFTPR 11 1 P52735-3 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 1 AS(0.006)S(0.004)RS(0.99)PVFTPR;AS(0.207)S(0.159)RS(0.634)PVFTPR;AS(0.002)SRS(0.998)PVFTPR 125.97 0.00019205 1649890000 332000 517060 375336 428090 564390 282846 396600 448960 463900 TRUE FALSE 311220.7126 555343.6604 384239.1472 439075.5142 520065.086 364499.0486 337133.5119 505013.6443 386472.0931 0.80528638 1.436956692 0.994222232 1.136111823 1.345673065 0.943144551 0.872335979 1.306727325 1 18.56000472 2.203050474 24.99997146 1.001359654 1.162927557 0.057603431 0.205172883 359.7826058 253293.3005 0.071334905 0.052686222 159.6064631 -2.203050474 0.161567904 ASSSGPRS(ph)PLDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASSSGPRSPLDQR 13 1 O14646;O14646-2 O14646 CHD1 Chromodomain-helicase-DNA-binding protein 1 1 AS(0.003)S(0.002)S(0.002)GPRS(0.993)PLDQR;AS(0.242)S(0.195)S(0.157)GPRS(0.406)PLDQR;AS(0.093)S(0.077)S(0.064)GPRS(0.766)PLDQR;AS(0.039)S(0.032)S(0.027)GPRS(0.901)PLDQR 104.21 0.00093867 2228660000 3432320 4161950 3914570 4137110 4629710 3497400 4199270 3850890 4753490 TRUE FALSE 3217497.218 4470105.109 4007425.449 4243275.247 4266111.252 4507042.604 3569628.448 4331682.093 3960101.81 0.812478409 1.128785401 1.011950107 1.071506605 1.077273125 1.138112811 0.901398151 1.093830992 1 21.91710609 -0.341280832 6.096935791 0.99999903 1.034379287 0.006059903 0.102118141 0 0 0.08852519 0.020865587 0.45574212 0.341280832 0.034380257 ASSSKESPS(ph)PSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASSSKESPSPSVR 13 1 H0Y517;H7C1U3;Q5T0F9-3;Q5T0F9-2;Q5T0F9 H0Y517 CC2D1B Coiled-coil and C2 domain-containing protein 1B 1 ASS(0.003)S(0.061)KES(0.166)PS(0.77)PSVR 118.51 0.0011103 18723000 60817 62722 60581 59607 73588 59586 72835 64047 87217 TRUE FALSE 57010.57253 67366.00214 62018.00993 61136.61653 67808.69532 76787.5109 61914.06792 72043.40893 72659.91926 0.784622019 0.927141164 0.853538107 0.841407714 0.933233838 1.056806995 0.852107579 0.991515125 1 16.14887214 2.602848096 5.237679949 0.958696091 0.86503679 0.452963011 0.062278872 0.253522921 9.78482999 0.019456936 0.018234689 400.7265298 -2.602848096 -0.093659302 ASSTS(ph)TPEPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASSTSTPEPTR 11 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 ASST(0.001)S(0.499)T(0.499)PEPTR;AS(0.039)S(0.039)T(0.039)S(0.442)T(0.442)PEPTR 224.25 6.66E-12 1516217000 1029129 1144064 1064694 1105716 1161882 978842 1275135 1013075 1055670 TRUE FALSE 964717.6529 1228771.689 1089949.044 1134090.545 1070632.475 1261417.795 1083940.345 1139559.644 879471.8571 1.096928395 1.397169994 1.239322254 1.289513172 1.217358425 1.43429012 1.232490086 1.29573179 1 19.74627789 -1.089083206 1.555620499 0.989114422 1.284945358 0.455160113 0.094156229 2227.932175 1545.89927 122.3568542 0.022579303 0.081454821 1.089083206 0.295830935 ASSTST(ph)PEPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASSTSTPEPTR 11 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 ASSTST(1)PEPTR;ASSTS(0.157)T(0.843)PEPTR;ASSTS(0.123)T(0.876)PEPTR;ASSTS(0.006)T(0.994)PEPTR 281.54 2.31E-26 2982110000 2825200 3128060 2954170 3011380 3176190 2701470 3425700 2645790 3048980 TRUE FALSE 2648375.775 3359664.817 3024244.307 3088657.109 2926744.85 3481340.534 2912048.088 2976122.706 2540085.541 1.042632515 1.32265814 1.190607268 1.215965785 1.152222948 1.370560353 1.146437016 1.171662394 1 21.27644565 0.78804969 1.535951345 1.001132749 1.221251798 0.32847457 0.091130092 0.752105281 3.127574596 0.076712997 0.022280523 6.138322325 -0.78804969 0.220119049 ASSVSTKES(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ASSVSTKESPAR 12 1 Q13428-4;Q13428;Q13428-3;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 ASSVSTKES(1)PAR;ASSVSTKES(1)PAR;ASSVS(0.003)T(0.036)KES(0.961)PAR;ASS(0.002)VS(0.024)T(0.09)KES(0.884)PAR;ASS(0.001)VS(0.058)T(0.25)KES(0.691)PAR;ASSVS(0.001)T(0.001)KES(0.997)PAR 176.56 1.51E-05 4786890000 6972270 4921298 5809210 4878805 7268400 4902515 7680880 6521140 7607160 TRUE FALSE 6535888.067 5285676.025 5947007.205 5004003.396 6697569.183 6317791.495 6529203.35 7335318.684 6337475.852 1.031307767 0.834034898 0.938387355 0.789589343 1.056819677 0.996893975 1.030252975 1.157451145 1 22.59547691 2.713444526 24.74829524 1.044179281 0.894290265 0.486031357 0.076509473 535.1785104 527340.8535 0.022511226 0.021231544 516.945223 -2.713444526 -0.149889016 ASSVSTKES(ph)PARK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASSVSTKESPARK 13 2 Q13428-4;Q13428;Q13428-3;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 ASSVS(0.287)T(0.287)KES(0.427)PARK;ASS(0.001)VS(0.064)T(0.064)KES(0.87)PARK;AS(0.004)S(0.002)VS(0.062)T(0.044)KES(0.888)PARK;ASSVST(0.001)KES(0.999)PARK 142.4 3.18E-05 5548070000 6962600 3927860 5293110 4346670 6515220 4076400 7286110 5976260 8880880 TRUE FALSE 6526823.295 4218682.841 5418665.069 4458212.911 6003540.902 5253190.505 6193625.446 6722409.216 7398603.755 0.882169597 0.570199862 0.732390225 0.602574899 0.811442415 0.710024577 0.837134364 0.908605115 1 22.8188216 1.387667401 0.920993826 1.00160043 0.687443593 0.54597099 0.090445886 0.331418142 0.583282604 0.074632214 0.027674583 24.41559997 -1.387667401 -0.314156837 AST(ph)PDWVSEGPQPGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ASTPDWVSEGPQPGLR 16 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 AST(1)PDWVSEGPQPGLR;AS(0.003)T(0.996)PDWVSEGPQPGLR;AST(1)PDWVSEGPQPGLR;AST(1)PDWVSEGPQPGLR;AS(0.02)T(0.98)PDWVSEGPQPGLR 422.25 6.03E-159 3501940000 1889590 1686070 1841450 1880910 1974310 1729870 2416730 1600910 1693950 TRUE FALSE 1771323.935 1810908.377 1885130.064 1929177.335 1819255.657 2229255.387 2054363.772 1800787.138 1411218.802 1.25517314 1.283222967 1.335816998 1.367029218 1.28913791 1.579666728 1.455737246 1.276050982 1 20.42851026 0.949937003 9.578392004 1.0000003 1.367553288 0.599647126 0.094084146 1.518724445 290.7381767 0.097578254 0.024411592 8.911216672 -0.949937003 0.367552988 AST(ph)SKSESSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASTSKSESSQK 11 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 1 AS(0.012)T(0.448)S(0.448)KS(0.09)ES(0.001)SQK 145 0.00023215 37312000 109240 61143 90896 100170 142320 54732 139600 82978 233270 TRUE FALSE 102402.8634 65670.09134 93052.09604 102740.5318 131142.7613 70532.2399 118668.276 93337.98596 194335.73 0.52693791 0.337920831 0.478821347 0.528675462 0.674825784 0.362940155 0.610635399 0.480292461 1 17.56819165 -5 0.217373927 3.553200947 0.423499372 0.710895169 0.100167525 76.17595124 0.761913309 84.99068643 0.18346101 1.00E-05 5 -3.129701575 ASTAS(ph)ASAAVSAARPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASTASASAAVSAARPR 16 1 E9PC69;Q7KZI7-14;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7 E9PC69;Q7KZI7-12 MARK2 Serine/threonine-protein kinase MARK2 1 AS(0.198)T(0.198)AS(0.404)AS(0.147)AAVS(0.053)AARPR 177.3 7.82E-09 42951000 74596 93465 77187 74136 89582 44648 103640 69194 91202 TRUE FALSE 69927.16952 100385.2459 79017.91209 76038.45527 82546.59108 57537.1528 88100.14415 77833.02321 75979.79701 0.920338988 1.321209714 1.039985828 1.000772024 1.08642816 0.757269104 1.159520657 1.024391039 1 16.21332824 3.632152512 4.640488575 1.010376625 1.158319163 0.089069692 0.139721656 0.33979904 12.38979718 0.034482124 0.054975706 4286.990407 -3.632152512 0.147942539 ASTAS(ph)PCNNNINAATAVALQEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASTASPCNNNINAATAVALQEPR 23 0 Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4;Q71RC2-6 Q71RC2-5 LARP4 La-related protein 4 1 AS(0.001)T(0.006)AS(0.993)PCNNNINAATAVALQEPR;AS(0.004)T(0.023)AS(0.973)PCNNNINAATAVALQEPR 261.2 5.95E-44 320790000 176908 190596 193998 168461 200107 191908 225116 197944 237123 TRUE FALSE 165835.6441 204707.9262 198599.7242 172783.9945 184391.4034 247308.7242 191361.9457 222657.7441 197545.6394 0.839480155 1.036256365 1.005335905 0.874653548 0.933411661 1.251906774 0.968697392 1.127120521 1 17.59182648 ASTASASAAVS(ph)AARPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASTASASAAVSAARPR 16 1 E9PC69;Q7KZI7-14;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7 E9PC69;Q7KZI7-12 MARK2 Serine/threonine-protein kinase MARK2 1 AS(0.177)T(0.177)AS(0.006)AS(0.029)AAVS(0.611)AARPR 152.88 1.33E-06 50353000 84127 112730 85846 98290 117910 61250 143560 100980 130670 TRUE FALSE 78861.64124 121076.6465 87882.30766 100812.2878 108649.8242 78931.88069 122034.5107 113587.5753 108860.3328 0.724429544 1.112220065 0.80729413 0.926069994 0.998066251 0.725074769 1.121019085 1.043424839 1 16.73211883 1.649490811 12.86205894 1.06109182 0.906629921 0.292716919 0.122375803 0.154656244 39.2606583 0.052764227 0.028839313 44.61601843 -1.649490811 -0.154461898 ASTFCGT(ph)PDYIAPEILQGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASTFCGTPDYIAPEILQGLK 20 0 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 AS(0.302)T(0.302)FCGT(0.395)PDYIAPEILQGLK;AS(0.268)T(0.268)FCGT(0.462)PDY(0.001)IAPEILQGLK 150.28 3.28E-07 246204000 185044 137665 117327 128302 140966 86852 229460 132854 181742 TRUE FALSE 173462.4264 147857.8598 120110.0518 131594.4465 129895.099 111924.7625 195054.6032 149441.1143 151408.0861 1.145661575 0.976551938 0.793286904 0.869137507 0.857913882 0.739225793 1.288270714 0.987008806 1 17.20808273 1.742222618 25 1.112794247 0.891610527 0.309948865 0.135655885 0.669297524 4592.877712 0.05971868 0.033116942 55.23605056 -1.742222618 -0.221183719 ASTNIQDTEGNTPLHLACDEERVEEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASTNIQDTEGNTPLHLACDEERVEEAK 27 1 O75832;B1AJY5;B1AJY7 O75832 PSMD10 26S proteasome non-ATPase regulatory subunit 10 0 89.434 0.0042439 43404000 49148 49123 40689 40787 62018 32480 50293 44439 67730 FALSE TRUE 46071.91441 52760.11803 41654.16229 41833.66347 57147.35645 41856.44873 42752.03155 49987.30697 56425.42545 0.816509828 0.935041564 0.738216185 0.741397396 1.012794427 0.741801208 0.75767318 0.8859004 1 15.78405777 -1.42557179 6.21854934 1.000047105 0.824134789 0.251449586 0.092609904 5.74E-05 5.30E-06 0.085036539 0.020037947 0.03753429 1.42557179 -0.175912317 ASTRS(ph)PTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASTRSPTQR 9 1 A0A2R8Y575;Q5VVD7;Q8IWE5 A0A2R8Y575 PLEKHM2 Pleckstrin homology domain-containing family M member 2 1 AS(0.005)T(0.005)RS(0.495)PT(0.495)QR 96.229 0.0045476 187530000 66758 80898 63569 59536 63128 57308 63340 54326 60726 TRUE FALSE 62579.73595 86887.77209 65076.8867 61063.79455 58170.18153 73851.88928 53842.75502 61108.72069 50590.4383 1.236987424 1.717474191 1.286347557 1.207022446 1.149825609 1.459799357 1.064287182 1.207910482 1 15.62657712 2.941969485 0.292383859 1.005582078 1.621038209 0.350481186 0.164284489 2.668906558 0.427743303 0.220182588 0.566032169 874.9222979 -2.941969485 0.615456131 ASTVS(ph)PGGYMVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASTVSPGGYMVPK 13 0 Q5TGY3 Q5TGY3 AHDC1 AT-hook DNA-binding motif-containing protein 1 1 ASTVS(1)PGGYMVPK;AST(0.001)VS(0.999)PGGYMVPK 179.43 1.44E-05 238080000 424110 368890 423690 386560 463640 375080 562760 415230 503800 TRUE FALSE 397565.7122 396202.9994 433740.1269 396479.784 427227.5846 483359.5071 478379.3624 467072.3795 419712.5253 0.947233376 0.943986599 1.033421927 0.944646062 1.017905254 1.151644228 1.139778619 1.112838792 1 18.67904199 2.39128242 4.685180961 1.11631486 0.974904288 0.616532202 0.04895657 0.120246901 4.727157737 0.016163506 0.013423021 246.1968093 -2.39128242 -0.141410573 ASVALT(ph)PTAPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASVALTPTAPSR 12 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7;H7BZ26 E9PHV5 SSFA2 Sperm-specific antigen 2 1 ASVALT(1)PTAPSR 184.11 0.00016483 79536000 179380 183060 202650 186840 211270 173300 207910 167660 283390 TRUE FALSE 168152.926 196613.9529 207456.9537 191634.6307 194677.7064 223328.8967 176735.8256 188592.7201 236090.3782 0.71223964 0.832791045 0.878718376 0.8117003 0.824589752 0.945946626 0.748593937 0.798815782 1 17.84897972 -2.539552657 2.218190164 3.744431269 0.825594707 0.436814104 0.064159666 2990621.204 264846.5281 41347146.92 0.015531017 0.002887004 2.539552657 -2.918836562 ASVITQVFHVPLEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASVITQVFHVPLEER 15 0 Q00341;A0A024R4E5;Q00341-2;C9JIZ1;C9JZI8;C9J5E5;C9JHZ8;C9JES8;C9JK79;C9JHS7;C9JT62 Q00341 HDLBP Vigilin 0 ; 238.83 8.79E-18 801560000 841070 1042700 1005230 920080 1109560 900720 1143030 888550 1020570 FALSE TRUE 788428.9301 1119902.593 1029074.53 943690.8105 1022419.633 1160743.242 971643.2629 999487.4234 850230.2739 0.927312229 1.317175626 1.210348022 1.109923793 1.202520852 1.365210435 1.142800125 1.175549088 1 19.6974941 -0.424368499 7.014707433 0.999997368 1.198676446 0.174327605 0.118836601 0 0 0.104000859 0.024513238 0.376384301 0.424368499 0.198679078 ASVLDTSMSAGSGS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ASVLDTSMSAGSGSPSK 17 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 ASVLDTSMSAGSGS(1)PSK;ASVLDTSMSAGSGS(1)PSK;ASVLDTSMSAGSGS(1)PSK;ASVLDTSMSAGSGS(1)PSK 390.81 6.72E-122 779550000 1154810 774570 955370 870550 973070 768850 1161250 903230 1064400 TRUE FALSE 1082532.503 831919.9687 978031.8276 892889.7868 896649.0074 990804.5138 987131.343 1016000.254 886744.7637 1.220793793 0.93817297 1.102946268 1.006929867 1.011169216 1.117350284 1.113207975 1.14576403 1 19.75815938 2.226299836 24.97076155 1.105047293 1.044105631 0.032115554 0.082516162 467.7000031 952527.8301 0.027708779 0.020620221 168.3836176 -2.226299836 -0.060941661 ASVMLEHDPQYAVILAFDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASVMLEHDPQYAVILAFDVR 20 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 130.11 1.67E-05 50652000 63795 67608 69575 67659 82595 67905 84001 54349 79336 FALSE TRUE 59802.18483 72613.76667 71225.35186 69395.24449 76108.32187 87508.07115 71405.82988 61134.59229 66094.30907 0.904800817 1.098638713 1.077632142 1.049942808 1.151510969 1.323987986 1.080362756 0.924960003 1 16.01223844 4.738784965 6.92970033 1.101346096 0.901755376 0.227615246 0.103877096 0.158544347 56.3434664 0.024140994 0.148076039 54800.55597 -4.738784965 -0.199590721 ASVSGPNS(ph)PSETRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASVSGPNSPSETRR 14 1 A0A087X0X0;C9J453;A0A087X255;O15344-2;O15344 A0A087X0X0 MID1 E3 ubiquitin-protein ligase Midline-1 1 ASVSGPNS(0.998)PS(0.002)ETRR;ASVS(0.002)GPNS(0.859)PS(0.129)ET(0.011)RR 131.84 3.30E-05 391950000 310114 374130 356730 394850 359730 307350 418380 323100 353640 TRUE FALSE 290704.5183 401830.9745 365191.8041 404982.5195 331478.2569 396076.9556 355647.803 363439.7462 294615.1994 0.986726139 1.363918003 1.239555206 1.37461516 1.125122728 1.344387379 1.207160404 1.233608269 1 18.16847234 0.234435663 1.099889027 0.999185644 1.25362936 0.272021696 0.117751588 5.022296816 6.177405795 0.106370323 0.030478368 1.715677529 -0.234435663 0.254443716 ASVSQTS(ph)PQSASSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ASVSQTSPQSASSPR 15 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 ASVSQT(0.023)S(0.393)PQS(0.277)AS(0.277)S(0.031)PR 251.81 1.31E-24 122680000 264060 293230 251860 290740 277960 192760 325570 249670 307460 TRUE FALSE 247532.956 314941.0543 257834.2381 298200.8806 256130.1428 248406.6828 276753.8009 280841.8491 256142.9397 0.96638602 1.229551963 1.006602948 1.164197151 0.99995004 0.96979711 1.080466248 1.096426274 1 17.9665896 3.753123031 23.52146134 1.048935688 1.117159898 0.051012394 0.084819251 417.9937811 378116.2501 0.019875039 0.035809428 5663.997212 -3.753123031 0.06822421 ASWEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASWEER 6 0 P12270;G5E9W7;G5E9V5;P82650;H7C5L9;H7C5H3 P12270;G5E9W7 TPR;MRPS22 "Nucleoprotein TPR;28S ribosomal protein S22, mitochondrial" 0 ; 122.15 0.045 828070000 1472890 1929900 1733830 1722070 2022420 1554890 1741980 1753120 2003930 FALSE TRUE 1380704.444 2072791.804 1774957.266 1766261.232 1863587.291 2003761.501 1480786.271 1972000.891 1669461.137 0.82703599 1.241593325 1.063191725 1.057982838 1.116280727 1.200244472 0.886984571 1.181220004 1 20.67095108 1.749615607 25 1.013527032 1.10029309 0.036853947 0.130113059 7.187161628 16283.13617 0.054283591 0.030102512 56.18438185 -1.749615607 0.086766058 ASWES(ph)LDEEWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ASWESLDEEWR 11 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 AS(0.053)WES(0.947)LDEEWR;AS(0.11)WES(0.89)LDEEWR;AS(0.011)WES(0.989)LDEEWR 251.81 2.38E-20 213824000 483782 414615 473992 451843 358116 393380 579576 371302 341990 TRUE FALSE 453502.9482 445313.526 485235.3141 463438.0563 329991.0139 506942.42 492673.9593 417659.872 284909.6597 1.591742971 1.562999045 1.703119911 1.626614053 1.158230347 1.779309345 1.729228696 1.465937914 1 18.12014501 0.934714133 8.141868562 1.000001638 1.602913416 0.546228494 0.169030223 1.178222667 146.8585747 0.157333747 0.039396532 8.604272036 -0.934714133 0.602911778 ASYDDPYKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ASYDDPYKK 9 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ; 104.42 0.0052312 588270000 2583200 1703900 2179300 1998310 2269000 1456100 2674400 1851330 3209700 FALSE TRUE 2421522.123 1830058.529 2230994.025 2049590.018 2090801.893 1876452.432 2273398.548 2082472.626 2673980.335 0.90558711 0.684394909 0.834334492 0.766494051 0.781906234 0.701745038 0.850192695 0.778791302 1 21.35055742 -0.020864066 0.831385445 1.004869205 0.778225568 0.500908896 0.06601068 4.511494631 2.997835849 0.125993498 0.01922021 0.953094435 0.020864066 -0.226643637 ASYHFSPEELDENTS(ph)PLLGDAR ddPTM_SK-BR-3_Pertuzumab_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(0.037)S(0.963)PLLGDAR;ASYHFSPEELDENT(0.076)S(0.924)PLLGDAR;ASYHFSPEELDENT(0.069)S(0.931)PLLGDAR;ASYHFSPEELDENT(0.054)S(0.946)PLLGDAR 330.36 6.31E-81 1373270000 343473 985120 913820 1379080 1393470 547406 415370 355455 414150 TRUE FALSE 321975.638 1058059.31 935496.2419 1414469.528 1284032.487 705433.2258 353089.1246 399834.3392 345025.6895 0.933193231 3.066610232 2.711381414 4.099606408 3.721556181 2.044581744 1.023370535 1.158853823 1 18.39634426 1.958710113 3.808013866 1.110951943 2.957156235 0.507722584 0.825991651 0.186543189 5.413079195 0.379137207 0.224020449 90.93061177 -1.958710113 1.846204292 ASYNNPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ASYNNPHR 8 0 P54725-2;P54725;A0A494C0B4;K7ELU6;P54725-3 P54725-2;P54725-3 RAD23A UV excision repair protein RAD23 homolog A 0 ;;;;;; 131.06 0.0010211 618248000 617304.5 961063 694141 688893 992730 589908.3 783154 836181 971266 FALSE TRUE 578668.5133 1032221.105 710606.3523 706571.1607 914764.9903 760205.2498 665727.3281 940580.0385 809155.43 0.715151245 1.275677164 0.878207482 0.873220564 1.130518262 0.939504602 0.822743448 1.162421957 1 19.62605733 3.748863222 24.83933861 0.957296268 1.047898947 0 0.172644379 1276.950018 1458855.811 0.040597434 0.073104166 5608.713063 -3.748863222 0.090602678 AT(ph)NESEDEIPQLVPIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATNESEDEIPQLVPIGK 17 0 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 AT(0.621)NES(0.379)EDEIPQLVPIGK;AT(0.662)NES(0.338)EDEIPQLVPIGK 143.93 1.95E-06 2167060000 2321120 2004130 2219920 2094730 2031040 1683280 2676380 1822040 2078570 TRUE FALSE 2175845.243 2152517.87 2272577.551 2148484.318 1871530.311 2169215.61 2275081.665 2049525.705 1731643.239 1.256520508 1.243049274 1.312382077 1.240719953 1.080782848 1.252691987 1.313828169 1.183572724 1 20.7237103 0.975433507 18.47990161 0.999999996 1.248085558 0.587519924 0.063786375 45.83549609 34480.33609 0.062553799 0.015638871 9.450036954 -0.975433507 0.248085562 AT(ph)NESEDEIPQLVPIGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATNESEDEIPQLVPIGKK 18 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 AT(0.5)NES(0.5)EDEIPQLVPIGKK 50.202 0.088116 81125000 409210 260080 274330 283410 259760 195260 399540 228530 388630 TRUE FALSE 383598.2766 279336.5938 280837.2371 290682.7804 239359.4974 251628.3922 339632.6861 257062.4736 323765.1424 1.184804126 0.86277538 0.867410355 0.897819877 0.739299777 0.777194204 1.049009426 0.793978227 1 18.30458814 -0.909485264 7.496999287 1 0.892579607 0.056115108 0.132474497 1.76E-09 2.35E-10 0.118360876 0.027897926 0.123172778 0.909485264 -0.107420393 AT(ph)PAQTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATPAQTPR 8 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3ITP6;E5RFR3;E5RG53 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 1 AT(1)PAQTPR 84.054 0.056725 0 583430 331840 351290 301410 360680 254730 379030 322590 406240 TRUE FALSE 546914.1578 356409.7789 359622.7647 309144.6909 332353.6477 328266.4158 322197.9702 362866.0716 338435.9196 1.616005058 1.053108604 1.062602235 0.913451182 0.982028291 0.969951464 0.952020609 1.072185458 1 18.36852317 AT(ph)PPPSPLLSELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATPPPSPLLSELLK 14 0 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;Q9H0E9-3 H7C128 BRD8 Bromodomain-containing protein 8 1 AT(1)PPPSPLLSELLK;AT(0.998)PPPS(0.002)PLLSELLK 111.12 0.0074926 155341000 223270 149550 175463 182658 168686 131512 187101 127325 192433 TRUE FALSE 209295.9292 160622.8376 179625.0652 187345.3135 155438.082 169477.3795 159046.942 143221.8065 160314.6891 1.305531829 1.001922147 1.120452943 1.168609779 0.969581034 1.057154403 0.992092134 0.893379186 1 17.2905471 2.314253215 0.942718375 0.956726371 1.122293024 0.429294918 0.088372443 0.620794176 1.068623633 0.060369664 0.036898521 206.1831711 -2.314253215 0.165566653 AT(ph)PSENLVPSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATPSENLVPSSAR 13 0 Q8N684-2;Q8N684;Q8N684-3;F5H669;F5H6M0;F5H047 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 1 AT(0.901)PS(0.099)ENLVPSSAR;AT(0.993)PS(0.007)ENLVPSSAR 142.03 9.97E-06 0 149455 108289 131983 118979 117286 121282 146705 106853 123721 TRUE FALSE 140100.8783 116306.8302 135113.6991 122032.2026 108074.8307 156294.1446 124707.9472 120193.8323 103071.1658 1.359263546 1.128412872 1.310877761 1.183960631 1.048545729 1.516371172 1.209920798 1.166124699 1 16.65328127 0.914572743 2.711635118 1.000981132 1.2467089 0.281029878 0.128164775 0.47587206 7.8029924 0.112286484 0.029853889 8.214341296 -0.914572743 0.245727768 AT(ph)SFSSAGEVPKPRPPSTR ddPTM_SK-BR-3_Pertuzumab_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(0.499)S(0.499)FS(0.001)SAGEVPKPRPPSTR 114.37 0.0075704 366000000 122470 168320 100480 148080 188980 79621 238830 139390 186080 TRUE FALSE 114804.8213 180782.5879 102863.4331 151879.9835 174138.2731 102606.2902 203019.6587 156793.1483 155022.0459 0.740570934 1.16617341 0.663540676 0.979731513 1.123312959 0.661881925 1.309617981 1.011424842 1 17.24211387 1.728447203 24.99999955 1.125880874 0.907605575 0.218052735 0.19123664 1.161541481 2857.192324 0.080952795 0.044892351 53.51150964 -1.728447203 -0.218275298 AT(ph)SLPSIPNPFPELCSPPSQSPILGGPSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 AT(0.5)S(0.5)LPS(0.001)IPNPFPELCSPPSQSPILGGPSSAR;AT(0.5)S(0.5)LPS(0.001)IPNPFPELCSPPSQSPILGGPSSAR 139.96 9.61E-08 99730000 177748 197603 173976 173964 187785 163572 232758 180940 149509 TRUE FALSE 166623.07 212233.7317 178102.7929 178428.2108 173037.1236 210792.581 197858.0987 203530.7573 124554.982 1.337747132 1.703936111 1.429913039 1.432525683 1.389242893 1.692365713 1.58852015 1.63406356 1 16.9264232 3.769891532 24.46444611 1.493519522 1.552975995 0 0.210721285 1189.552759 680411.5968 0.049130582 0.088570697 5886.966066 -3.769891532 0.059456473 AT(ph)SNVFAMFDQSQIQEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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(0.581)S(0.419)NVFAMFDQSQIQEFK;AT(0.595)S(0.405)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.565)S(0.435)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.575)S(0.425)NVFAMFDQSQIQEFK 243.27 1.63E-23 2325308000 4040923 5607084 2560225 2078365 5588765 660940.2 6196003 3769434 13292550 TRUE FALSE 3788008.843 6022238.334 2620954.746 2131699.365 5149845.941 851742.9063 5266969.871 4240056.132 11073937.53 0.342065217 0.543820869 0.236677761 0.192496965 0.465041989 0.076914187 0.475618528 0.382886044 1 23.40066495 0.3598486 1.287957739 1.000298148 0.335145663 0.691580893 0.13938262 2.01108172 3.504926028 0.126200954 0.03732427 2.290069167 -0.3598486 -0.665152486 AT(ph)SPLVSLYPALECR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATSPLVSLYPALECR 15 0 A0A087WXV6;Q96G74-2;Q96G74-3;Q96G74-5;Q96G74;H7BZQ3;Q96G74-4 A0A087WXV6 OTUD5 OTU domain-containing protein 5 1 AT(0.5)S(0.5)PLVSLYPALECR 224.67 1.23E-11 98723000 82788 90386 88732 73443 101910 90324 113930 85926 136300 TRUE FALSE 77606.44686 97078.27349 90836.76494 75327.67172 93906.39969 116399.0725 96847.25417 96654.05025 113550.6495 0.68345225 0.85493367 0.799966934 0.663383891 0.827000111 1.025085044 0.852899166 0.851197688 1 16.79297643 2.468075894 24.95114341 0.917776359 0.773014799 0.538409462 0.077742564 178.2056442 491566.7922 0.026072476 0.021842378 293.8163057 -2.468075894 -0.14476156 AT(ph)SPSSSVSGDFDDGHHSVSTPGPSR ddPTM_SK-BR-3_Pertuzumab_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(0.451)S(0.451)PS(0.082)S(0.015)SVSGDFDDGHHSVSTPGPSR;AT(0.364)S(0.314)PS(0.314)S(0.007)SVSGDFDDGHHSVSTPGPSR 99.135 0.01029 545280000 77589 81948 72000 75248 78238 71887 96289 69957 76893 TRUE FALSE 72732.84299 88015.51519 73707.874 77178.99107 72093.50308 92639.60991 81851.35835 78691.28544 64059.06155 1.13540288 1.373974471 1.150623693 1.204809893 1.125422404 1.446159336 1.277748321 1.228417706 1 15.96711504 0.884584237 8.223677029 1.00000005 1.254091694 0.352537797 0.103063519 7.961757024 567.7228601 0.094074656 0.023554539 7.666272225 -0.884584237 0.254091644 ATAGDTHLGGEDFDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 206.43 2.09E-12 43365530000 22200500 26256900 20543960 18326910 27972400 16188050 25194500 26072400 29656300 FALSE TRUE 20811010.33 28200988.2 21031272.43 18797209.54 25775560.54 20861277.24 21416818.62 29327596.53 24706471.94 0.842330317 1.14144133 0.851245475 0.760821277 1.043271601 0.844364881 0.866850543 1.187041055 1 24.55838567 1.246997788 24.99721167 1.093520547 0.918748515 0.296119457 0.118393909 217.1469399 643365.0903 0.08039729 0.028299488 17.66028826 -1.246997788 -0.174772032 ATAPAS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATAPASPR 8 0 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 ATAPAS(1)PR;ATAPAS(1)PR 78.932 0.030784 1395320000 1238040 1473110 1346300 1399960 1773600 1016000 1301740 1247110 1921640 TRUE FALSE 1160553.286 1582180.597 1378234.872 1435885.344 1634308.61 1309302.707 1106556.172 1402814.429 1600905.87 0.724935368 0.988303327 0.860909375 0.896920532 1.0208649 0.81785115 0.691206268 0.876262905 1 20.61045705 2.033271327 24.99116052 0.804766549 0.906628178 0 0.111076225 312.2598537 234547.1547 0.037987839 0.028055728 107.9621008 -2.033271327 0.101861629 ATAPQTQHVS(ph)PMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 26 ATAPQTQHVSPMR 13 0 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;E9PPR1;E9PL12;E9PK06;P29692-3;E9PL71 P29692;P29692-3 EEF1D Elongation factor 1-delta 1 ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQT(0.001)QHVS(0.999)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQT(0.35)QHVS(0.65)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQT(0.07)QHVS(0.93)PMR;ATAPQTQHVS(1)PMR;ATAPQT(0.001)QHVS(0.999)PMR;ATAPQT(0.134)QHVS(0.866)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR 214.65 3.20E-11 2.50946E+11 37928408 39769024 40992838 38985342 40521105 39311664 44785636 35825683 40589572 TRUE FALSE 35554536.65 42713563.92 41965207.48 39985771.88 37338740.87 50660303.23 38070445.65 40298598.38 33814910.21 1.051445543 1.263157691 1.241026731 1.18248937 1.104209375 1.498164653 1.1258479 1.191740511 1 25.01115619 0.730280795 1.752509156 1.00088408 1.223374228 0.222806985 0.12096762 1.355143593 6.49609504 0.103715245 0.029307658 5.373791288 -0.730280795 0.222490147 ATAPQTQHVSPMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ATAPQTQHVSPMR 13 0 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;E9PPR1;E9PL12;E9PK06;P29692-3;E9PL71 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 ;;;;;;; 188.12 6.38E-06 3826210000 675509 1987580 1686960 1741970 1880340 1668260 1831090 1690830 1666600 FALSE TRUE 633230.0975 2134742.491 1726975.488 1786671.899 1732665.681 2149859.58 1556535.054 1901933.847 1388433.693 0.456075145 1.537518501 1.243830005 1.286825513 1.247928288 1.548406374 1.12107266 1.369841323 1 20.40502685 4.748105618 24.87589265 1.309789412 0.456074656 0.71138846 0.167561985 603.4754474 1572724.734 0.035716139 0.460757315 55989.37481 -4.748105618 -0.853714756 ATAVMPDGQFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATAVMPDGQFK 11 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ; 150.18 7.91E-05 290340000 778120 760700 762770 764600 814790 618880 906740 735890 1006600 FALSE TRUE 729418.8582 817023.0195 780863.2646 784220.9305 750799.6801 797540.6093 770782.7548 827767.4864 838591.9571 0.869813802 0.97427958 0.931159974 0.935163906 0.895309899 0.951047291 0.919139217 0.987092089 1 19.67760947 1.164711047 5.251150207 0.998034914 0.930627368 0.487455687 0.028809184 0.176916804 8.31036727 0.025035596 0.006422454 14.61204654 -1.164711047 -0.067407546 ATDAEADVASLNRR ddPTM_SK-BR-3_Pertuzumab_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 ; 157.09 8.65E-06 331190000 350310 517030 436940 447230 546190 361200 505140 402280 623770 FALSE TRUE 328384.7224 555311.4392 447304.4231 458706.679 503294.4406 465472.5764 429398.9465 452505.5435 519658.7573 0.631923773 1.068607873 0.860765679 0.882707493 0.968509495 0.895727379 0.826309459 0.870774402 1 18.98720504 4.062192771 0.007450641 1.771396341 5.58E-05 0.067800828 0.11247296 52905.94312 77.22299892 8789.637286 9578.447673 11539.65358 -4.062192771 -1.771340523 ATDCVGHDVVTLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ATDCVGHDVVTLLR 14 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;;;; 217.68 5.67E-12 3697812000 3938914 4395476 4178513 3850887 4261056 3432015 4221369 3732723 4526592 FALSE TRUE 3692384.404 4720921.617 4277629.302 3949707.28 3926409.85 4422782.016 3588413.908 4198761.683 3771074.552 0.979133229 1.251877032 1.134326368 1.047369185 1.041191256 1.172817444 0.951562707 1.113412537 1 21.84654424 3.30084659 4.662391507 1.052496317 1.153740959 0.080743421 0.08912954 0.299212846 12.85694648 0.023306193 0.031490875 1999.155564 -3.30084659 0.101244642 ATDDDMQSLASLMSVKPSDVGNLDDFAES(ph)DEDEAHGPGAPEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATDDDMQSLASLMSVKPSDVGNLDDFAESDEDEAHGPGAPEAR 43 1 Q8N3D4;A0A0U1RQH4;E9PIH6 Q8N3D4 EHBP1L1 EH domain-binding protein 1-like protein 1 1 ATDDDMQSLASLMSVKPS(0.001)DVGNLDDFAES(0.999)DEDEAHGPGAPEAR 68.545 0.0024751 27028000 20441 16575 18361 16450 20931 15021 24021 18266 20470 TRUE FALSE 19161.6343 17802.23025 18796.53159 16872.13485 19287.16369 19357.31885 20419.27405 20546.55031 17053.42476 1.123623822 1.043909391 1.102214473 0.989369296 1.130984771 1.135098617 1.197370871 1.204834255 1 14.05777388 2.500566239 20.29774141 1.152435851 1.066803734 0.190063399 0.066084712 83.5282918 72315.58713 0.019347379 0.018067241 316.6403371 -2.500566239 -0.085632117 ATDFVADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATDFVADR 8 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 149.91 0.0011576 268270000 445480 525990 385080 410250 625290 375570 443420 493460 628710 FALSE TRUE 417598.202 564934.8469 394214.2794 420777.7096 576182.2457 483990.9621 376933.2875 555069.5672 523774.2394 0.797286637 1.078584635 0.752641596 0.803357015 1.100058388 0.924044991 0.719648389 1.059749651 1 18.99858558 3.981636009 24.94196855 0.886977096 0.952726437 0 0.142377143 771.4639451 4261928.54 0.033983722 0.069693064 9585.968763 -3.981636009 0.065749341 ATDIPASAS(ph)PPPVAGVPFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ATDIPASASPPPVAGVPFFK 20 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 ATDIPASAS(1)PPPVAGVPFFK;ATDIPASAS(1)PPPVAGVPFFK;ATDIPASAS(1)PPPVAGVPFFK;ATDIPAS(0.002)AS(0.998)PPPVAGVPFFK;ATDIPAS(0.001)AS(0.999)PPPVAGVPFFK;ATDIPASAS(1)PPPVAGVPFFK 322.43 7.78E-67 1818703000 4760990 4424160 4736800 4603790 4826480 3896140 5623220 4342190 5031730 TRUE FALSE 4463008.135 4751729.41 4849159.133 4721931.046 4447427.73 5020892.369 4780070.364 4884321.98 4191901.757 1.064673839 1.133549803 1.156792171 1.126441248 1.060957052 1.197760029 1.140310685 1.165180451 1 21.99917347 -0.942132433 4.633189468 0.999998312 1.134523245 0.487773961 0.041932943 6.77E-07 1.55E-07 0.037559061 0.008852644 0.114252988 0.942132433 0.134524933 ATDS(ph)FSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATDSFSGR 8 0 Q9HBH9;Q9HBH9-2;K7EK27 Q9HBH9 MKNK2 MAP kinase-interacting serine/threonine-protein kinase 2 1 ATDS(1)FSGR 135.55 0.00086962 167210000 146720 176320 174010 167650 181760 165840 199170 179280 155550 TRUE FALSE 137537.0571 189374.9163 178137.5994 171952.1828 167485.3028 213715.3158 169306.3075 201663.5026 129587.7001 1.061343453 1.461364899 1.374648977 1.326917467 1.292447529 1.64919445 1.306499825 1.556193238 1 16.98356926 -0.725249085 8.383128442 1 1.387591038 0.357064107 0.159241245 0 0 0.13473543 0.031757445 0.188256905 0.725249085 0.387591038 ATDSDLSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ATDSDLSSPR 10 0 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 1 ATDSDLS(0.01)S(0.99)PR;ATDSDLS(0.016)S(0.984)PR;ATDSDLS(0.016)S(0.984)PR;ATDSDLS(0.018)S(0.982)PR 115.41 0.0012864 1131270000 2571640 2870060 2678880 2767290 2992940 2454010 3162030 2483280 3016950 TRUE FALSE 2410685.643 3082562.229 2742424.299 2838303.346 2757886.565 3162442.849 2687912.956 2793322.974 2513401.555 0.959132709 1.226450355 1.091120634 1.129267761 1.097272563 1.258232233 1.06943236 1.111371547 1 21.26120975 0.746368763 1.508225258 1.000826455 1.131314508 0.159893698 0.082366266 1.353984309 5.134499565 0.06926852 0.020158554 5.576590605 -0.746368763 0.130488054 ATEDGEEDEEMIESIENLEDLKGHSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ATEDGEEDEEMIESIENLEDLKGHSVR 27 1 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 ;; 297.98 5.95E-71 128224000 189476 189800 179295 189977 236038 134025 238923 178675 343295 FALSE TRUE 177617.0354 203852.9895 183547.9621 194852.1315 217500.5276 172715.8418 203098.7142 200982.9671 285996.8467 0.621045433 0.712780549 0.641783167 0.681308671 0.76049974 0.603908203 0.710143194 0.702745395 1 18.12563972 0.167681118 1.121264663 1.001182671 0.675629052 0.831065291 0.045674149 1.99904937 2.3585662 0.044012967 0.01195201 1.471231848 -0.167681118 -0.325553619 ATEETGQAQSGQANCQGLS(ph)PVSVASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ATEETGQAQSGQANCQGLSPVSVASK 26 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 ATEETGQAQSGQANCQGLS(0.999)PVS(0.001)VASK;ATEETGQAQSGQANCQGLS(0.992)PVS(0.008)VASK;ATEETGQAQSGQANCQGLS(0.998)PVS(0.002)VASK;ATEETGQAQSGQANCQGLS(0.997)PVS(0.003)VASK 363.58 9.12E-112 1675850000 1631110 1384180 1494740 1510270 1586860 1328530 1942600 1428810 1873630 TRUE FALSE 1529021.737 1486666.127 1530195.939 1549026.085 1462234.417 1712055.044 1651325.164 1607200.074 1560909.049 0.97957132 0.9524361 0.980323575 0.992387152 0.936783868 1.096832032 1.057925294 1.029656452 1 20.57395505 2.243290117 24.99997595 1.053319329 0.968871463 0.64101415 0.028705065 63.35558156 334896.9612 0.009302201 0.007549786 175.1016011 -2.243290117 -0.084447866 ATENDIANFFS(ph)PLNPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATENDIANFFSPLNPIR 17 0 P31942;P31942-3;P31942-2;P31942-4;P31942-5;P31942-6 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 1 ATENDIANFFS(1)PLNPIR;ATENDIANFFS(1)PLNPIR 235.7 3.80E-20 136916000 116424 123493 120721 129675 158721 123723 138339 135532 150232 TRUE FALSE 109137.2297 132636.5502 123584.5591 133002.68 146255.6929 159439.8216 117596.3512 152453.4685 125157.3087 0.872000451 1.059758728 0.987433818 1.062684085 1.168574928 1.27391539 0.939588367 1.218094813 1 16.93338302 3.062637632 3.940352426 1.114801994 0.994192677 0.275379897 0.106570869 0.331973702 10.47738272 0.030309695 0.036247429 1155.148003 -3.062637632 -0.120609317 ATENDIYNFFS(ph)PLNPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 277.98 8.63E-36 307647000 333783 347507 348531 327331 359886 275694 379862 343873 452723 TRUE FALSE 312892.1178 373236.7799 356798.3199 335730.8676 331622.0053 355282.3823 322905.2196 386806.301 377160.6066 0.829599148 0.989596404 0.946011629 0.890153589 0.879259391 0.941992287 0.856147789 1.025574501 1 18.52481947 1.220962775 24.9983953 1.012787356 0.914741495 0.463824696 0.04737171 278.7795845 396006.3603 0.045429843 0.011461778 16.63270081 -1.220962775 -0.098045861 ATENDIYNFFSPLNPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATENDIYNFFSPLNPVR 17 0 P52597;P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7;H0YBG7 P52597;P31943 HNRNPF;HNRNPH1 "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 ; 323.66 1.71E-58 152938000 272430 286230 258230 236472 273270 228904 262700 244118 295140 FALSE TRUE 255379.0926 307422.767 264355.3375 242540.2719 251808.4765 294984.8689 223310.5738 274596.6697 245879.2273 1.038636307 1.250299874 1.07514303 0.986420343 1.024114478 1.199714478 0.908212443 1.11679491 1 17.90759033 3.610838656 3.938327119 1.036068226 1.160403637 0.172419338 0.092273926 0.285404724 7.881019157 0.022976579 0.037003941 4081.677203 -3.610838656 0.124335411 ATEVSKT(ph)PEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATEVSKTPEAR 11 1 Q5H909;Q9UNF1-2;Q9UNF1 Q5H909 MAGED2 Melanoma-associated antigen D2 1 ATEVS(0.002)KT(0.998)PEAR 131.66 0.00032113 363640000 337880 233470 287150 316090 299740 233630 378290 235330 317110 TRUE FALSE 316732.6939 250756.3617 293961.3336 324201.4045 276199.6295 301075.1883 321568.9264 264711.4685 264182.2924 1.198917199 0.949179294 1.112721564 1.227188248 1.045488806 1.13964939 1.21722362 1.002003072 1 18.01117424 3.652424356 6.114902013 1.125865754 1.048877078 0 0.09941572 0.450904368 28.6725178 0.024272304 0.038092825 4491.840803 -3.652424356 -0.076988676 ATFIKVPQNQNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATFIKVPQNQNGK 13 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 178.15 1.35E-05 899250000 485840 574330 455820 515650 729110 380780 739970 524060 1010220 FALSE TRUE 455432.1416 616853.9908 466632.2657 528882.452 671848.6417 490705.0046 629018.368 589490.0446 841607.7557 0.541145372 0.732947132 0.554453381 0.628419176 0.798291885 0.583056657 0.747400869 0.700433237 1 19.68278847 -5 0.191030039 2.496163483 0.599297109 0.668014575 0.078766079 77.85747486 0.763077732 44.11998733 0.19190878 1.00E-05 5 -1.896866373 ATGAALT(ph)PTEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ATGAALTPTEER 12 0 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 ATGAALT(1)PTEER;ATGAALT(0.995)PT(0.005)EER;ATGAALT(0.975)PT(0.025)EER 267.08 9.39E-21 1107250000 1046180 1237780 1254580 1209030 1531340 1146750 1536550 1432760 1781520 TRUE FALSE 980701.4613 1329426.519 1284339.23 1240055.757 1411074.734 1477798.109 1306158.592 1611643.24 1484172.803 0.660773098 0.895735669 0.865356937 0.835519795 0.950748276 0.995704884 0.880058299 1.08588652 1 20.50122764 6.842060697 0.252670971 1.006976212 9.36E-13 0.628392958 0.070022702 20.49575013 0.467508353 0.086079907 7.815021248 6951214.602 -6.842060697 -1.006976212 ATGAALTPT(ph)EER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATGAALTPTEER 12 0 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 ATGAALT(0.22)PT(0.78)EER 132.06 0.0020981 292310000 268130 357410 346030 369790 467450 323390 458130 414720 539450 TRUE FALSE 251348.2219 383873.0083 354237.995 379279.4375 430738.3626 416747.4432 389437.6596 466498.7049 449412.31 0.559282014 0.854166652 0.788224949 0.843945368 0.958448073 0.927316484 0.866548715 1.038019419 1 18.77768012 6.044064169 0.314646485 0.975091074 2.13E-20 0.717820464 0.070917924 9.870826127 0.416542408 0.067664623 4.308857103 1106787.304 -6.044064169 -0.975091074 ATGDGS(ph)S(ph)PELPSLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATGDGSSPELPSLER 15 0 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2;H3BS99 H3BSS6 ZNF106 Zinc finger protein 106 2 ATGDGS(1)S(1)PELPSLER;ATGDGS(1)S(1)PELPSLER 245.39 6.25E-18 328910000 787960 682580 732860 702350 742410 590740 823950 669270 804780 TRUE FALSE 738642.9901 733118.9334 750243.7853 720373.4901 684104.1133 761277.0481 700406.3467 752829.8327 670457.0189 1.101700734 1.093461494 1.119003551 1.074451411 1.020354913 1.135459883 1.044670019 1.122860693 1 19.35478532 -5 0.215720219 0.568662043 1.100363726 0.361389727 0.036050168 155.3108514 1.552649325 29.12988714 0.06568972 1.00E-05 5 0.531701683 ATGDGSS(ph)PELPSLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATGDGSSPELPSLER 15 0 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2;H3BS99 H3BSS6 ZNF106 Zinc finger protein 106 1 ATGDGS(0.03)S(0.969)PELPSLER;ATGDGS(0.018)S(0.982)PELPSLER 220.46 1.75E-12 134486000 276220 259740 290490 252480 271340 253900 309250 251430 328910 TRUE FALSE 258931.8833 278971.4199 297380.56 258959.0642 250030.0509 327196.8083 262880.8334 282821.589 274012.7962 0.944962742 1.018096322 1.085279827 0.945061938 0.91247582 1.19409317 0.959374296 1.032147378 1 18.06388374 ATGDWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ATGDWK 6 0 P30050 P30050 RPL12 60S ribosomal protein L12 0 ;;; 122.98 0.044171 2990430000 4550440 3904080 4239940 4133240 4166470 3455480 4933990 3730110 4261410 FALSE TRUE 4265636.083 4193142.145 4340513.379 4239305.936 3839252.253 4453020.981 4194184.004 4195822.444 3550153.141 1.201535797 1.18111585 1.222627083 1.194119174 1.081432857 1.254317998 1.181409319 1.181870831 1 21.75944983 0.495501506 2.537195837 1.000002019 1.190084627 0.643425835 0.043827863 5.643557649 27.55458034 0.038641218 0.010286311 3.129691323 -0.495501506 0.190082608 ATGEADVEFVTHEDAVAAMSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ATGEADVEFVTHEDAVAAMSK 21 0 P31942;P31942-3;P31942-2;P31942-4;P31942-5;P31942-6 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;; 182.39 4.69E-17 251319900 326497 285659 301125 301514 332507 231268 366213 288454 413691 FALSE TRUE 306062.1356 306809.4896 308267.8272 309251.3597 306393.2415 298031.3173 311302.7604 324468.1169 344643.2996 0.888054797 0.890223283 0.894454723 0.897308493 0.889015518 0.864752971 0.903260736 0.941460685 1 18.39474444 1.010109957 2.091177588 0.999378943 0.88865702 0.940837978 0.009189717 0.067972602 0.634212817 0.008635669 0.002405038 10.23552108 -1.010109957 -0.110721923 ATGEGFVEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATGEGFVEFR 10 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 ; 83.456 0.036271 193410000 259370 294310 304950 277770 297150 256880 306370 257040 315570 FALSE TRUE 243136.4947 316101.0186 312183.558 284898.0485 273813.0376 331037.0859 260432.6627 289132.0098 262899.3283 0.924827371 1.202365258 1.187464266 1.083677354 1.041512884 1.259178135 0.990617452 1.099782231 1 18.00415093 1.631819685 20.45881128 1.033945157 1.130105763 0.13977945 0.097001952 0.552966839 466.1038079 0.042327544 0.023404512 42.83706281 -1.631819685 0.096160606 ATGEPGTFVCTSHLPAAASAS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ATGEPGTFVCTSHLPAAASASPK 23 0 Q8IY33;Q8IY33-4;Q8IY33-2 Q8IY33 MICALL2 MICAL-like protein 2 1 ATGEPGTFVCTSHLPAAASAS(1)PK;ATGEPGTFVCTSHLPAAASAS(1)PK;ATGEPGTFVCTSHLPAAAS(0.004)AS(0.996)PK;ATGEPGTFVCTSHLPAAASAS(1)PK 240.12 1.96E-37 1368430000 3476700 2145100 2571590 2432600 2757980 1966700 3313350 2316390 3163890 TRUE FALSE 3259099.553 2303925.436 2632589.329 2495024.634 2541379.376 2534454.363 2816543.927 2605596.391 2635816.319 1.236466869 0.874084214 0.998775715 0.946585168 0.964171652 0.961544378 1.068566086 0.988534888 1 21.32981841 1.759751163 25 1.025491088 0.979777656 0 0.096015124 34.83324578 41129.92424 0.040312084 0.022356091 57.51103235 -1.759751163 -0.045713432 ATGHSGGGCISQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ATGHSGGGCISQGR 14 0 Q9HA64;I3L3W5;I3L139;I3L407 Q9HA64 FN3KRP Ketosamine-3-kinase 0 ;;; 230.54 8.74E-13 543410000 260649 343789 288499 302053 339412 261057 324970 269941 316316 FALSE TRUE 244335.4444 369243.4953 295342.3325 309804.1914 312755.9506 336419.918 276243.7654 303643.7281 263520.8161 0.927195991 1.401192895 1.120755229 1.175634608 1.186835846 1.276635079 1.048280623 1.152257087 1 18.0075574 1.135449071 0.931327527 1.00789188 1.198392399 0.125110823 0.126294418 0.860304577 1.632378982 0.108105639 0.037792249 13.65994879 -1.135449071 0.190500519 ATGNDLRPPPPS(ph)PSSDLTHPMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATGNDLRPPPPSPSSDLTHPMK 22 1 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 AT(0.001)GNDLRPPPPS(0.948)PS(0.025)S(0.025)DLTHPMK;ATGNDLRPPPPS(0.988)PS(0.006)S(0.006)DLTHPMK 160.43 1.12E-11 503020000 324889 274488 324745 336423 365440 259147 365421 319345 406785 TRUE FALSE 304554.7774 294811.3771 332448.1048 345056.1837 336739.8165 333958.532 310629.5135 359215.9262 338889.9556 0.8986834 0.869932473 0.98099132 1.01819537 0.993655347 0.985448304 0.916608794 1.059978085 1 18.37045735 3.884172387 2.893632295 0.98670712 0.885134987 0.602638395 0.036505268 0.184034625 3.021115892 0.009707844 0.020347939 7659.005602 -3.884172387 -0.101572134 ATGSAGLLGDPECEGS(ph)PPEHSPEQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATGSAGLLGDPECEGSPPEHSPEQGR 26 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 ATGSAGLLGDPECEGS(0.962)PPEHS(0.038)PEQGR;ATGSAGLLGDPECEGS(0.995)PPEHS(0.005)PEQGR 138.61 3.92E-06 267610000 163615 169770 173225 162268 200388 183351 241150 167132 232751 TRUE FALSE 153374.6292 182339.9474 177333.9788 166432.0716 184650.3348 236281.4572 204991.7962 187998.7981 193903.3545 0.790984919 0.940365101 0.914548277 0.85832487 0.95228025 1.218552706 1.057185404 0.969548973 1 17.56497824 2.464299924 24.74058988 1.072433426 0.894400727 0.563525916 0.075960591 143.0948832 276119.9603 0.024847808 0.020801111 291.2727957 -2.464299924 -0.178032699 ATHGSNS(ph)LPSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ATHGSNSLPSSAR 13 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 ATHGS(0.01)NS(0.987)LPS(0.001)S(0.001)AR;ATHGS(0.149)NS(0.615)LPS(0.118)S(0.118)AR;ATHGS(0.016)NS(0.983)LPSSAR;ATHGS(0.002)NS(0.998)LPSSAR 114.52 0.00047447 1400660000 546551 1057286 864707 883375 1028266 761997 954111 890035 901863 TRUE FALSE 512343.3485 1135568.556 885218.2584 906043.8981 947510.1362 981973.1639 811050.9131 1001157.829 751336.239 0.681909539 1.511398621 1.178191883 1.205910019 1.261100007 1.306968988 1.079477963 1.332503048 1 19.51909916 -1.80129049 2.577791858 0.932820831 1.218536393 0.065241147 0.215376003 25677276.67 16945670.99 10758533.42 0.045731186 0.015801907 1.80129049 0.285715563 ATIAGGGVIPHIHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATIAGGGVIPHIHK 14 0 Q71UI9;P0C0S5;Q71UI9-4;Q71UI9-3 Q71UI9 H2AFV;H2AFZ Histone H2A.V;Histone H2A.Z 0 ; 150.21 4.21E-06 8258900000 7411000 7862100 7529500 6907300 9021700 6017000 8818100 6364100 9132000 FALSE TRUE 6947158.739 8444218.065 7708103.296 7084553.012 8313172.074 7754010.222 7495907.768 7158671.894 7607810.205 0.913161416 1.109940684 1.013182912 0.931221051 1.092715492 1.019217096 0.985291111 0.940963523 1 22.85904982 1.644631267 3.751875477 0.968915155 1.024342791 0.059964767 0.062330042 0.373912455 12.37832189 0.034662462 0.01555346 44.11956961 -1.644631267 0.055427636 ATIS(ph)DEEIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ATISDEEIER 10 0 C9J0A7;Q9UQN3;Q9UQN3-2 C9J0A7 CHMP2B Charged multivesicular body protein 2b 1 ATIS(1)DEEIER;AT(0.002)IS(0.998)DEEIER;ATIS(1)DEEIER;ATIS(1)DEEIER;ATIS(1)DEEIER 254.19 4.41E-17 7977230000 2467564 2662840 2563840 2436470 2746940 2325943 2660710 2142638 2656510 TRUE FALSE 2313123.574 2859999.444 2624655.496 2498993.945 2531206.413 2997404.986 2261761.236 2410151.071 2213121.319 1.04518607 1.292292212 1.185951928 1.129171692 1.143726912 1.354378976 1.021977971 1.089027994 1 21.07765111 1.615583329 21.49966897 1.041612688 1.19774868 0.408817883 0.087482718 0.245502779 676.6696718 0.038502634 0.02071335 41.26514061 -1.615583329 0.156135992 ATISNPITGDLETVHYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ATISNPITGDLETVHYR 17 0 P13674 P13674 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ;; 270.32 1.39E-35 825730000 599690 797290 656050 766860 775290 518340 706240 595330 383842 FALSE TRUE 562156.4734 856322.1812 671611.8158 786538.9259 714401.8508 667976.3435 600345.8684 669658.261 319776.2905 1.757967961 2.677878901 2.100255196 2.459653668 2.234067603 2.088886398 1.87739331 2.094146067 1 18.28670345 0.086994198 0.434374618 0.842618001 2.323364061 0.677394763 0.255182429 1.978289112 0.518640208 0.796797812 0.142797533 1.221783336 -0.086994198 1.480746061 ATLAENPNLFDDHEEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATLAENPNLFDDHEEGR 17 0 Q9BU68 Q9BU68 PRR15L Proline-rich protein 15-like protein 0 112.43 0.00046127 100680000 81046 122010 128400 133100 122150 121250 125200 119020 98329 FALSE TRUE 75973.47553 131043.7474 131445.7086 136515.5713 112556.8317 156252.9067 106427.4223 133879.909 81917.25467 0.927441671 1.599708729 1.604615647 1.666505694 1.374030809 1.907448038 1.299206409 1.634331003 1 16.32187975 -1.160897887 4.16090655 0.999831546 1.522293381 0.262145041 0.262480045 33.69823235 64149915.46 20879.30282 0.054149191 0.069040212 1.160897887 0.522461835 ATLECHPLTMTDPIEEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ATLECHPLTMTDPIEEHR 18 0 Q5JR89;Q5JR91;Q99661-2;Q99661 Q5JR89 KIF2C Kinesin-like protein;Kinesin-like protein KIF2C 0 ;; 206.95 4.60E-16 449564000 271784 316767 324504 313038 309132 288639 357397 273891 317563 FALSE TRUE 254773.5246 340220.7583 332201.3881 321071.0851 284854.0197 371964.3936 303808.6378 308086.8943 264559.6838 0.963009635 1.285988679 1.255676539 1.213605492 1.076709859 1.405975349 1.148355764 1.164526998 1 18.0132337 0.808522897 1.860846136 1.000887646 1.213074093 0.190033171 0.119733689 0.962733501 5.933794294 0.102731561 0.028807772 6.434619887 -0.808522897 0.212186447 ATLENITNLRPVGEDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ATLENITNLRPVGEDFR 17 1 Q9NWV4 Q9NWV4 C1orf123 UPF0587 protein C1orf123 0 ;;; 129.42 3.07E-05 2346140000 3019420 3652760 3417690 3465430 3689920 3128300 3864550 3234740 3845110 FALSE TRUE 2830439.892 3923214.151 3498759.221 3554358.801 3400128.568 4031389.426 3285096.604 3638604.41 3203336.301 0.883591239 1.224727529 1.092223511 1.109580284 1.061433533 1.258497094 1.025523484 1.135879617 1 21.61114384 -0.592614682 0.963581298 0.995157916 1.110146154 0.07273783 0.103849142 90.83701309 47.89685034 1.730248064 0.028243002 0.255496714 0.592614682 0.114988238 ATLLPEAGRS(ph)PEEAGFPGDPHEDKQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ATLLPEAGRSPEEAGFPGDPHEDKQ 25 2 Q8IV56 Q8IV56 PRR15 Proline-rich protein 15 1 AT(0.001)LLPEAGRS(0.999)PEEAGFPGDPHEDKQ;AT(0.081)LLPEAGRS(0.919)PEEAGFPGDPHEDKQ;ATLLPEAGRS(1)PEEAGFPGDPHEDKQ;ATLLPEAGRS(1)PEEAGFPGDPHEDKQ 177.1 1.64E-17 967890000 834789 676708 685750 740748 909367 528443 842607 679011 901171 TRUE FALSE 782541.0466 726812.1644 702016.3138 759756.8478 837948.984 680995.9155 716265.9027 763787.018 750759.7383 1.042332196 0.968102213 0.935074536 1.011984006 1.116134685 0.907075701 0.954054761 1.017352129 1 19.51799176 5.992807262 2.618715186 0.981098703 25.95190278 0.063930847 0.057191059 2146.873642 40.81136169 0.014121509 320153.8082 983574.5026 -5.992807262 24.97080408 ATLPS(ph)PDKLPGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATLPSPDKLPGFK 13 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 AT(0.001)LPS(0.999)PDKLPGFK 76.85 0.016683 332020000 315620 199720 227410 226600 272380 159480 284500 200380 291390 TRUE FALSE 295865.9076 214507.4766 232804.2726 232414.9396 250988.3735 205519.2871 241841.8662 225397.8841 242755.1265 1.218783355 0.883637267 0.959008676 0.957404867 1.033915852 0.846611522 0.996237936 0.928498966 1 17.88914224 4.746889749 24.97539315 0.947414078 1.218783492 0.699212451 0.055229099 542.0682064 1625386.279 0.011854917 0.135746048 55832.84386 -4.746889749 0.271369414 ATLPSPDKLPGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATLPSPDKLPGFK 13 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 135.02 8.09E-05 475210000 1241500 990920 1202700 1140100 1243100 916830 1496000 1109400 1498500 FALSE TRUE 1163796.731 1064288.748 1231228.612 1169356.896 1145471.94 1181503.938 1271688.688 1247911.032 1248390.669 0.932237608 0.852528599 0.986252655 0.936691474 0.917558877 0.946421634 1.018662442 0.999615796 1 20.25163805 2.579490317 0.450783039 1.015834262 0.892012834 0.497020062 0.034961794 0.940623349 0.39878647 0.034580128 0.044441627 379.743472 -2.579490317 -0.123821429 ATMAQNENVVVQPVVAENIPVIPLS(ph)DSPPPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATMAQNENVVVQPVVAENIPVIPLSDSPPPSR 32 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 ATMAQNENVVVQPVVAENIPVIPLS(0.526)DS(0.378)PPPS(0.096)R 112.6 1.35E-15 0 51552 53484 53378 49380 57210 51720 59723 50694 67837 TRUE FALSE 48325.45234 57444.01101 54644.15137 50647.1744 52716.95737 66650.7244 50768.09059 57023.25749 56514.56646 0.855097285 1.016446106 0.966903841 0.896179119 0.932803004 1.179354785 0.898318677 1.009001061 1 15.78633515 ATNES(ph)EDEIPQLVPIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 ATNESEDEIPQLVPIGK 17 0 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 ATNES(1)EDEIPQLVPIGK;ATNES(1)EDEIPQLVPIGK;ATNES(1)EDEIPQLVPIGK;ATNES(1)EDEIPQLVPIGK;AT(0.383)NES(0.617)EDEIPQLVPIGK;AT(0.057)NES(0.943)EDEIPQLVPIGK;ATNES(1)EDEIPQLVPIGK;AT(0.001)NES(0.999)EDEIPQLVPIGK;AT(0.182)NES(0.818)EDEIPQLVPIGK;AT(0.015)NES(0.985)EDEIPQLVPIGK 331.82 5.19E-72 21588790000 5750073 4988244 5267500 4970721 5114874 4152401 6404610 4224473 5096620 TRUE FALSE 5390186.195 5357578.776 5392447.587 5098278.116 4713172.428 5351131.76 5444298.188 4751907.753 4245961.197 1.269485505 1.261805873 1.270018104 1.200735918 1.110036623 1.260287486 1.28222985 1.119159487 1 22.01765976 -4.941992628 0.192848429 2.83E-11 1.27409623 0.631386577 0.05670199 91.88668719 0.921244352 35.24277563 0.153657483 1.14E-05 4.941992628 1.27409623 ATNVTYQAHHVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATNVTYQAHHVSR 13 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 71.879 0.02375 71978000 50759 115910 91250 82784 103450 67247 90476 117220 103780 FALSE TRUE 47582.0848 124492.097 93414.49309 84908.37759 95325.4543 86660.11724 76909.96374 131855.175 86458.44756 0.550346278 1.43990669 1.08045536 0.982071504 1.102558015 1.002332562 0.889559851 1.525069889 1 16.39971931 -1.355542679 4.032976912 0.999783939 1.085833738 0.004384973 0.271132191 20008849.14 6752366.175 37980.89709 0.057590417 0.044101902 1.355542679 0.086049799 ATQCLVKS(ph)PEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATQCLVKSPEVK 12 1 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 ATQCLVKS(1)PEVK 104.44 0.0012948 153110000 196100 140720 157490 162120 177360 98664 171110 138580 259830 TRUE FALSE 183826.451 151139.0552 161225.7372 166280.2737 163430.861 127146.6951 145453.644 155882.0181 216462.6944 0.849229247 0.698222184 0.744819968 0.768170581 0.755007053 0.58738387 0.671957098 0.720133409 1 17.72375888 -0.749362075 12.3836631 1 0.716612302 0.617353211 0.06795424 0 0 0.064886164 0.015293815 0.17808934 0.749362075 -0.283387698 ATQPETTEEVTDLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATQPETTEEVTDLKR 15 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 ; 148.24 5.72E-06 373290000 281780 255330 266050 280310 315610 235950 326310 257109 351180 FALSE TRUE 264143.8928 274234.8989 272360.8316 287503.2292 290823.2637 304064.9347 277382.8448 289209.6246 292565.7893 0.902852973 0.937344382 0.930938755 0.982695994 0.994043987 1.039304477 0.94810417 0.988528513 1 18.15840155 3.220901362 3.788349593 0.990907251 0.926706579 0.654683107 0.023474258 0.143701127 4.447918003 0.006816821 0.008780298 1663.034896 -3.220901362 -0.064200672 ATQQQHDFTLTQTADGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ATQQQHDFTLTQTADGR 17 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;;; 289.32 6.06E-46 3871880000 2281390 2361600 2232250 2496300 2263260 1908760 2826260 2127710 2231840 FALSE TRUE 2138601.872 2536455.321 2285200.024 2560359.284 2085512.689 2459788.026 2402488.551 2393359.277 1859331.486 1.150199353 1.364175964 1.229043902 1.377032177 1.121646519 1.322942167 1.292124922 1.287214946 1 20.82635257 -0.933833336 4.961088967 0.999998584 1.27572788 0.503978047 0.083262303 1.12E-06 2.42E-07 0.069480427 0.01637661 0.116457286 0.933833336 0.275729296 ATS(ph)FEESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATSFEESER 9 0 Q52LW3;F8VWZ8 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 AT(0.001)S(0.999)FEESER 163.66 0.0008737 0 1079800 1299500 1051100 1160000 966150 894000 1509300 1127200 1294700 TRUE FALSE 1012217.245 1395716.332 1076032.588 1189767.564 890272.4763 1152083.287 1282994.477 1267933.401 1078606.206 0.938449306 1.293999909 0.997613941 1.103060188 0.825391576 1.06812225 1.189492949 1.175529488 1 20.04073681 -1.25746956 5.361810022 0.999990853 1.08761633 0.020570102 0.133513767 1.41E-05 1.96E-06 0.125090624 0.029481066 0.055275215 1.25746956 0.087625477 ATS(ph)FSSAGEVPKPRPPSTR ddPTM_SK-BR-3_Pertuzumab_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(0.13)S(0.869)FS(0.001)SAGEVPKPRPPSTR 171.29 5.51E-12 314590000 195680 249060 178510 244270 319780 140050 367470 237470 306990 TRUE FALSE 183432.7381 267500.6615 182744.3415 250538.3817 294665.7687 180480.1615 312371.2849 267118.6522 255751.3858 0.717230671 1.045940223 0.714539008 0.979616908 1.152157076 0.705685957 1.22138648 1.044446549 1 17.96438253 2.638918504 0.906159005 1.059841243 0.858797432 0.177149518 0.167051326 0.964726987 1.652748983 0.098603957 0.083049204 435.4301565 -2.638918504 -0.20104381 ATS(ph)LPSIPNPFPELCSPPS(ph)QSPILGGPSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 AT(0.47)S(0.528)LPS(0.001)IPNPFPELCS(0.143)PPS(0.73)QS(0.127)PILGGPSSAR 139.7 1.40E-08 141590000 143010 174110 146000 169320 194850 183080 253590 172450 132610 TRUE FALSE 134059.2594 187001.2856 149463.1889 173665.0379 179547.267 235932.2239 215566.5337 193980.7621 110476.5343 1.213463657 1.692678782 1.352895345 1.571963123 1.625207272 2.13558676 1.951242724 1.755854882 1 16.75338044 2.570978457 3.417915178 1.823650004 1.479630809 0.067414575 0.324124867 0.37745723 8.327383876 0.100596584 0.092066644 372.3732348 -2.570978457 -0.344019195 ATS(ph)LPSIPNPFPELCSPPSQS(ph)PILGGPSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 AT(0.454)S(0.514)LPS(0.032)IPNPFPELCS(0.095)PPS(0.171)QS(0.734)PILGGPSSAR;AT(0.463)S(0.53)LPS(0.006)IPNPFPELCS(0.001)PPS(0.225)QS(0.772)PILGGPS(0.001)S(0.001)AR 131.99 1.83E-06 105009000 67620 83998 63131 82477 93865 89180 111407 85343 70314 TRUE FALSE 63387.78491 90217.29932 64628.49713 84593.49945 86493.22153 114924.8183 94702.5546 95998.26141 58578.13915 1.082106496 1.540118901 1.103286961 1.444113806 1.476544369 1.961906266 1.616687658 1.638806947 1 15.83807474 2.783443749 2.706570402 1.622244023 1.288749015 0.157245743 0.271731389 0.372159093 5.404740346 0.082355352 0.084578305 607.3565913 -2.783443749 -0.333495008 ATS(ph)PEAGGGGGALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATSPEAGGGGGALK 14 0 Q13233 Q13233 MAP3K1 Mitogen-activated protein kinase kinase kinase 1 1 ATS(1)PEAGGGGGALK;AT(0.001)S(0.999)PEAGGGGGALK 230.69 8.57E-13 441910000 1021040 921630 977690 968720 1097720 797570 1195250 914710 1348270 TRUE FALSE 957134.929 989868.4442 1000881.268 993578.9952 1011509.499 1027815.512 1016033.359 1028913.557 1123235.027 0.85212347 0.881265648 0.891070208 0.884569099 0.900532369 0.915049377 0.904559896 0.916026951 1 20.0992284 -5 0.123982257 1.363281105 0.842267901 0.947742652 0.0087674 30.72120233 0.244508149 2.768372217 0.074893122 1.00E-05 5 -0.521013203 ATS(ph)PESTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATSPESTSR 9 0 Q8N3X1-2;Q8N3X1 Q8N3X1-2 FNBP4 Formin-binding protein 4 1 AT(0.095)S(0.886)PES(0.018)T(0.001)SR;AT(0.228)S(0.771)PESTSR 112.89 0.0019811 139740000 282137 315746 307348 304603 315010 252986 304453 261474 302416 TRUE FALSE 264478.5488 339124.1624 314638.4397 312419.6287 290270.3853 326018.9513 258803.0991 294119.6045 251940.8159 1.049764596 1.346046932 1.248858541 1.240051667 1.152137196 1.29402991 1.027237679 1.167415464 1 17.94272534 1.517369318 0.80780281 1.016303558 1.24734192 0.312212911 0.096384348 0.54460039 0.731968348 0.081100123 0.033573233 32.9131401 -1.517369318 0.231038362 ATS(ph)PLVSLYPALECR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ATSPLVSLYPALECR 15 0 A0A087WXV6;Q96G74-2;Q96G74-3;Q96G74-5;Q96G74;H7BZQ3;Q96G74-4 A0A087WXV6 OTUD5 OTU domain-containing protein 5 1 AT(0.004)S(0.996)PLVSLYPALECR;ATS(1)PLVSLYPALECR;AT(0.002)S(0.998)PLVSLYPALECR;ATS(1)PLVSLYPALECR;AT(0.002)S(0.998)PLVSLYPALECR 343.98 6.31E-70 1435030000 1035380 1062880 1115470 1001230 1259620 1144930 1408860 1170640 1749650 TRUE FALSE 970577.414 1141576.741 1141929.475 1026923.257 1160694.526 1475452.705 1197614.522 1316796.981 1457622.112 0.665863536 0.783177431 0.783419424 0.704519538 0.796293166 1.012232658 0.821622087 0.903387078 1 20.47518532 2.426557284 8.021702471 0.911904828 0.75053841 0.676051631 0.064546866 0.163077692 22.74814442 0.020928239 0.017514038 267.028296 -2.426557284 -0.161366418 ATS(ph)PRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATSPRPR 7 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 AT(0.116)S(0.884)PRPR 69.423 0.036202 147860000 326730 369480 399250 375850 394240 293390 323990 312810 368590 TRUE FALSE 306280.5525 396836.6836 408720.3985 385494.9473 363277.9807 378086.9302 275410.7073 351865.0171 307069.9478 0.997429266 1.292333185 1.331033536 1.255397834 1.183046349 1.231272982 0.896898929 1.14587904 1 18.2282078 1.758490703 25 1.008929075 1.237695667 0.426670573 0.10757535 7.156955414 8985.754906 0.047393366 0.026282512 57.34435904 -1.758490703 0.228766592 ATS(ph)SSSGSLSATGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 ATS(0.776)S(0.223)S(0.001)SGSLSATGR;AT(0.201)S(0.76)S(0.037)S(0.001)SGSLSATGR 198.1 2.36E-08 500500000 739960 647600 638250 696290 747840 509520 826530 589160 627710 TRUE FALSE 693647.2245 695548.9778 653389.5914 714157.9802 689107.663 656610.1526 702599.4996 662717.9229 522941.1458 1.32643459 1.330071239 1.249451485 1.36565651 1.317753764 1.255610039 1.343553678 1.267289691 1 18.99628906 0.87600552 6.517350098 1.000000662 1.308823249 0.880151897 0.035958091 0.873214548 45.84037211 0.032395651 0.008133196 7.51632447 -0.87600552 0.308822587 ATSAGSS(ph)PSCSLAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATSAGSSPSCSLAGR 15 0 Q9BXB5;Q9BXB5-2 Q9BXB5 OSBPL10 Oxysterol-binding protein-related protein 10 1 ATSAGS(0.003)S(0.906)PS(0.09)CSLAGR;ATSAGS(0.252)S(0.735)PS(0.012)CS(0.001)LAGR 163.4 1.62E-06 386250000 505280 538890 532850 550440 619460 527400 710280 586390 788510 TRUE FALSE 473655.4268 578789.9763 545489.4536 564565.2223 570810.1104 679651.8184 603780.1079 659602.0823 656902.587 0.721043631 0.881089507 0.830396263 0.859435224 0.868941791 1.034631058 0.919131877 1.00410943 1 19.32531992 2.382591653 5.369717994 0.977257302 0.836624474 0.697403486 0.051579643 0.124004877 5.666438892 0.01677742 0.013946287 241.3190757 -2.382591653 -0.140632827 ATSILSYLS(ph)DSDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATSILSYLSDSDLR 14 0 A0A499FJE4;Q96MK2;Q96MK2-2 A0A499FJE4 FAM65C Protein FAM65C 1 ATSILSYLS(1)DSDLR;ATSILSYLS(1)DSDLR 223.7 3.59E-12 32869000 64614 63625 73650 62237 84873 59199 61816 56155 55040 TRUE FALSE 60569.92508 68335.8612 75397.01278 63834.10679 78207.41694 76288.79028 52547.26467 63166.07536 45853.46843 1.320945332 1.490309535 1.644303373 1.392132569 1.705594356 1.663751792 1.145982332 1.377563738 1 15.48474325 1.707951921 7.724694694 1.1997233 1.544025174 0.561439834 0.149707109 0.088058497 12.00199085 0.068409058 0.03597134 51.04484875 -1.707951921 0.344301873 ATSLPSIPNPFPELCS(ph)PPS(ph)QSPILGGPSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 ATSLPSIPNPFPELCS(0.882)PPS(0.616)QS(0.496)PILGGPS(0.003)S(0.003)AR 94.006 0.00022825 64141000 47643 53016 47278 53848 61052 61813 62842 42356 45587 TRUE FALSE 44661.10968 56941.3598 48399.45649 55229.83084 56257.22219 79657.40965 53419.4255 47644.23984 37978.2352 1.175965904 1.499315582 1.27439983 1.454249534 1.481301643 2.097448953 1.406579985 1.254514318 1 15.21288525 1.031541289 2.946621876 1.0071526 1.489835306 0.307753187 0.240631945 0.291069032 5.63912046 0.226890875 0.060135113 10.75328828 -1.031541289 0.482682706 ATSLPSIPNPFPELCS(ph)PPSQS(ph)PILGGPSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 ATSLPSIPNPFPELCS(0.965)PPS(0.255)QS(0.781)PILGGPSSAR;ATSLPSIPNPFPELCS(0.939)PPS(0.32)QS(0.74)PILGGPS(0.001)S(0.001)AR 113.47 4.52E-06 480495000 116855 117326 120070 130713 148034 157941 150782 115725 121767 TRUE FALSE 109541.2541 126012.9391 122918.1171 134067.3169 136408.0068 203536.0027 128173.6389 130173.521 101443.3011 1.079827381 1.242200695 1.211692796 1.321598523 1.344672397 2.006401612 1.263500276 1.283214561 1 16.63031407 2.996218389 2.355806292 1.434783338 1.194947667 0.094537904 0.256191364 0.551600901 6.150086125 0.078844111 0.092090253 991.3303184 -2.996218389 -0.239835671 ATSLPSIPNPFPELCS(ph)PPSQSPILGGPSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 ATSLPSIPNPFPELCS(0.829)PPS(0.164)QS(0.007)PILGGPSSAR 178.14 2.49E-18 71786000 167750 195310 203960 224740 233100 243490 233520 150740 164530 TRUE FALSE 157250.8269 209770.9556 208798.0275 230507.2089 214793.2663 313781.6103 198505.8439 169560.2208 137068.8801 1.147239452 1.53040541 1.523307314 1.681688861 1.56704619 2.289225753 1.448219638 1.237043891 1 17.06454154 1.16801924 3.007400927 1.03046441 1.617214461 0.354494865 0.281835969 0.261572496 4.210198048 0.253396795 0.069209497 14.72377731 -1.16801924 0.586750051 ATSLPSIPNPFPELCSPPSQS(ph)PILGGPSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 ATSLPSIPNPFPELCSPPS(0.002)QS(0.998)PILGGPSSAR 220.76 3.97E-35 134130000 133870 154220 134340 151310 147950 146950 172750 129080 105990 TRUE FALSE 125491.3157 165638.6093 137526.6082 155192.8708 136330.6038 189372.0795 146847.7412 145195.9221 88299.58428 1.421199394 1.875870771 1.557500065 1.75757193 1.543955217 2.144654259 1.663062657 1.644355671 1 16.43011903 0.668268707 2.551760515 1.000114793 1.723653921 0.552235024 0.198956838 1.724425386 12.40624428 0.170865418 0.04551068 4.658742504 -0.668268707 0.723539128 ATSS(ph)PMLYEVVYEAGALER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ATSSPMLYEVVYEAGALER 19 0 Q5T4L2;Q5T4K9;Q5T4L1;Q8TEY5-2;Q8TEY5 Q5T4L2 CREB3L4 Cyclic AMP-responsive element-binding protein 3-like protein 4;Processed cyclic AMP-responsive element-binding protein 3-like protein 4 1 AT(0.132)S(0.132)S(0.735)PMLYEVVYEAGALER;AT(0.011)S(0.099)S(0.889)PMLYEVVYEAGALER;AT(0.002)S(0.018)S(0.98)PMLYEVVYEAGALER 159.81 3.43E-11 65061000 67801 75904 74874 75643 75759 71628 106737 69492 70485 TRUE FALSE 63557.45644 81524.01114 76650.04664 77584.12744 69809.19374 92305.84082 90732.77775 78168.22917 58720.59815 1.082370726 1.388337546 1.305334909 1.321242118 1.188836557 1.571949941 1.545160993 1.331189253 1 15.84157904 2.25066716 24.99625132 1.428127028 1.284573883 0.011057676 0.179402086 429.9062039 887621.6803 0.057050832 0.047401259 178.1013288 -2.25066716 -0.143553145 ATSSHFS(ph)ASEESMDFLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.008)S(0.007)S(0.031)HFS(0.897)AS(0.058)EESMDFLDK;ATSSHFS(0.999)AS(0.001)EESMDFLDK;ATSSHFS(0.997)AS(0.003)EESMDFLDK 346.99 1.83E-90 426794000 791090 681368 757951 820230 779470 556602 871420 652259 818910 TRUE FALSE 741577.089 731817.1957 775929.9557 841278.4904 718253.5704 717283.9617 740758.6609 733694.9719 682228.6306 1.086992037 1.072686139 1.137345929 1.233132784 1.05280479 1.051383553 1.085792398 1.075438554 1 19.37989578 ATSSSNPS(ph)SPAPDWYKDFVTDADAEVLEHSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATSSSNPSSPAPDWYKDFVTDADAEVLEHSGK 32 1 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 AT(0.041)S(0.041)S(0.041)S(0.127)NPS(0.375)S(0.375)PAPDWYKDFVT(0.001)DADAEVLEHSGK 61.586 0.011699 40731000 11528 11268 11721 12612 13663 12170 16800 10216 12752 TRUE FALSE 10806.48306 12102.29444 11999.02766 12935.64527 12589.96309 15683.28144 14280.99596 11491.49009 10623.60882 1.017213947 1.139188636 1.129468136 1.217631926 1.185092873 1.476266842 1.344269749 1.08169364 1 13.37498631 3.173935739 1.542130986 1.268622299 1.097667188 0.098326328 0.13756448 0.572591337 2.81481235 0.04568938 0.063266853 1492.573543 -3.173935739 -0.170955111 ATSSSS(ph)GSLSATGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 ATSS(0.001)S(0.305)S(0.691)GS(0.003)LSATGR 132.51 5.24E-05 166520000 176740 168410 156360 159100 179260 140140 183560 147540 171840 TRUE FALSE 165678.1589 180879.2516 160068.933 163182.7754 165181.6427 180596.143 156036.8821 165960.6938 143158.7939 1.1573034 1.263486837 1.118121554 1.139872522 1.15383511 1.261509252 1.089956669 1.159276977 1 17.12725677 -4.999999999 0.176599219 0.303510873 1.207697833 0.497551491 0.054234471 108.1735082 1.035547955 26.3033918 0.168611785 1.00E-05 4.999999999 0.90418696 ATSTS(ph)PNSQSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ATSTSPNSQSSK 12 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;H7C5N8;A0A2R8YET2;A0A2R8Y7F4;A0A2R8Y424 E7EPN9 PRRC2C Protein PRRC2C 1 ATST(0.002)S(0.991)PNS(0.008)QSSK;ATST(0.018)S(0.982)PNSQSSK;ATST(0.024)S(0.976)PNSQSSK;ATST(0.002)S(0.997)PNS(0.002)QSSK;ATST(0.023)S(0.977)PNSQSSK;ATST(0.001)S(0.982)PNS(0.017)QSSK;ATS(0.002)T(0.017)S(0.98)PNSQSSK;ATST(0.003)S(0.979)PNS(0.017)QSSK 292.63 3.82E-36 6447170000 16564440 12109910 15484520 13903900 14175700 11387120 15676700 12312600 12406860 TRUE FALSE 15527701.27 13006540.34 15851820.13 14260697.61 13062397.7 14674396.69 13326124.37 13849855.21 10336074.91 1.502282191 1.25836359 1.533640212 1.379701456 1.263767708 1.419726232 1.289282874 1.33995306 1 23.3011851 -2.956142212 0.237196022 0.286855517 1.423659222 0.659686834 0.087356619 33.1203313 0.786943328 11.91085914 0.13859491 0.001106261 2.956142212 1.136803705 ATSVALPGWS(ph)PSETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ATSVALPGWSPSETR 15 0 Q16513-3;Q16513-2;Q16513;Q16513-4;Q16513-5;B1AL79 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 ATSVALPGWS(0.916)PS(0.084)ETR;ATSVALPGWS(0.989)PS(0.011)ETR;ATSVALPGWS(0.999)PS(0.001)ETR;ATSVALPGWS(0.985)PS(0.015)ETR 209.33 2.56E-09 396730000 773150 836100 849390 818120 896640 786250 993040 803620 983160 TRUE FALSE 724759.9216 898005.714 869537.9319 839114.3443 826221.5113 1013227.611 844142.8709 903953.726 819064.2445 0.884863338 1.09638007 1.0616236 1.024479276 1.008738346 1.237055113 1.030618632 1.103642031 1 19.64361709 ATVHDPETGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ATVHDPETGK 10 0 P13674-2;P13674-3 P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ;; 140.16 3.98E-05 632729000 1161770 1179450 986750 1146390 1212940 696108 1218420 947660 709697 FALSE TRUE 1089056.89 1266777.705 1010156.176 1175808.308 1117680.585 897063.0792 1035729.232 1065977.437 591243.9859 1.841975421 2.142563367 1.708526767 1.988702357 1.890388083 1.517246857 1.751779734 1.802940009 1 19.17339408 -2.025483604 0.205197411 5.90E-18 2.035369949 0.764493524 0.14994403 15.25332229 0.457740801 7.731953085 0.363621642 0.009430102 2.025483604 2.035369949 ATVT(ph)PS(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ATVTPSPVK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 ATVT(1)PS(1)PVK;ATVT(1)PS(1)PVK;AT(0.004)VT(0.996)PS(1)PVK 199.7 0.00012902 849990000 4750930 2666250 3578020 3139280 2865210 2734310 4110290 2991900 2733330 TRUE FALSE 4453577.772 2863661.924 3662892.324 3219839.24 2640187.964 3523660.909 3493990.173 3365445.301 2277119.565 1.955794435 1.257580835 1.608563898 1.413996563 1.159441957 1.547420242 1.5343903 1.477939654 1 21.11877861 -2.106949329 2.094003049 0.200022511 1.47762121 0.345344574 0.212810365 4172840.033 1059686.535 15886501.41 0.047953818 0.00781719 2.106949329 1.277598699 ATVT(ph)PS(ph)PVKGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ATVTPSPVKGK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 ATVT(1)PS(1)PVKGK;ATVT(1)PS(1)PVKGK;ATVT(1)PS(1)PVKGK;AT(0.236)VT(0.765)PS(1)PVKGK 142.38 8.63E-05 8296000000 25294000 13123300 17671100 16667400 17435000 12218200 22213100 14867600 21884600 TRUE FALSE 23710893.69 14094962.79 18090266.84 17095113.7 16065725.43 15745395.99 18882451.87 16723852.59 18231918.88 1.300515533 0.773092667 0.992230547 0.93764753 0.881186755 0.86361705 1.035680994 0.91728428 1 24.11996307 -0.392587426 6.718886182 1 0.947311057 0 0.140358492 0 0 0.119478421 0.028161334 0.404960416 0.392587426 -0.052688943 ATVT(ph)PSPVKGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ATVTPSPVKGK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 AT(0.024)VT(0.756)PS(0.22)PVKGK 107.09 0.01429 1409000000 835020 574500 648140 643250 646120 470580 862160 618080 898490 TRUE FALSE 782757.5888 617036.5778 663514.1869 659756.884 595376.3415 606428.8068 732887.1119 695248.6486 748526.2145 1.045731697 0.824335295 0.886427454 0.881407853 0.795398117 0.810163752 0.979106807 0.92882338 1 19.51369332 1.674823859 8.046723767 0.965022763 0.867087893 0.280658678 0.071129258 0.148217226 16.95759862 0.032539174 0.017051133 47.29593975 -1.674823859 -0.09793487 ATVTPS(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ATVTPSPVK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 ATVT(0.061)PS(0.939)PVK;ATVT(0.003)PS(0.997)PVK;ATVT(0.33)PS(0.67)PVK;ATVT(0.099)PS(0.901)PVK;ATVT(0.08)PS(0.92)PVK;ATVT(0.024)PS(0.976)PVK;ATVT(0.08)PS(0.92)PVK;ATVT(0.118)PS(0.882)PVK 190.26 3.91E-05 29660760000 22140960 24485410 13284850 11470800 25299010 9995530 16156000 25763610 19339940 TRUE FALSE 20755196.84 26298335.23 13599972.92 11765160.15 23312127.81 12881077.25 13733557.78 28980253.42 16111979.07 1.288184198 1.632222529 0.844090776 0.73021198 1.446881708 0.799472069 0.852381804 1.798677449 1 23.94163038 3.982163791 7.04467329 1.03542857 1.456075156 0.184123394 0.338518797 0.186015577 55.57478058 0.079480743 0.160117794 9597.62531 -3.982163791 0.420646586 ATVTPS(ph)PVKGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ATVTPSPVKGK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 ATVTPS(1)PVKGK;ATVT(0.005)PS(0.995)PVKGK;ATVT(0.004)PS(0.996)PVKGK;ATVT(0.002)PS(0.998)PVKGK;ATVT(0.001)PS(0.999)PVKGK;ATVT(0.003)PS(0.997)PVKGK;ATVT(0.005)PS(0.995)PVKGK;ATVT(0.002)PS(0.998)PVKGK 151.3 2.03E-05 87768900000 60197100 37446200 45171100 40171000 45503100 32729600 57602400 39277500 54175000 TRUE FALSE 56429470.97 40218755.61 46242579.82 41201855.87 41929470.08 42178104.2 48965454.87 44181382.34 45132842.52 1.250297296 0.89111949 1.024588243 0.91290186 0.929023472 0.934532412 1.084918479 0.978918674 1 25.42767431 1.747847614 25 1.028614381 0.977554999 0.007552358 0.104836627 7.529693432 20314.69982 0.044118114 0.024465847 55.95612276 -1.747847614 -0.051059382 AVAAPRPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AVAAPRPDR 9 1 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;;;;; 144.66 9.03E-05 1797040000 1352570 1872570 1443310 1433700 1990130 1227830 1596510 1627580 1890650 FALSE TRUE 1267915.058 2011217.031 1477545.995 1470491.169 1833833.218 1582284.589 1357128.147 1830786.946 1575088.301 0.804980303 1.276891607 0.938071849 0.933592846 1.164273277 1.004568816 0.861620359 1.162339245 1 20.58700128 3.74324815 24.75285071 0.998160359 1.084495263 0 0.147633327 1125.117608 1726910.279 0.035027899 0.062885323 5536.663767 -3.74324815 0.086334904 AVALYFEDKLTEIYSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVALYFEDKLTEIYSDR 17 1 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 0 167.71 2.00E-09 19706000 23123 23458 21503 30516 30398 21121 30453 21964 33004 FALSE TRUE 21675.77271 25194.85473 22013.06131 31299.09222 28010.6637 27218.28983 25886.85536 24706.25375 27495.41919 0.788341235 0.916329173 0.800608318 1.138338427 1.018739286 0.98992089 0.941497025 0.898558905 1 14.74690366 3.26808409 24.99979267 0.991751339 0.847574274 0.543363478 0.069872518 172.6460476 146191.5245 0.019222362 0.0260235 1853.890547 -3.26808409 -0.144177066 AVASS(ph)PAATNSEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVASSPAATNSEVK 14 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 AVASS(1)PAATNSEVK 264.85 1.07E-24 172200000 617980 535940 600210 680560 684880 428200 613030 440240 758670 TRUE FALSE 579301.7349 575621.5552 614447.2646 698024.3218 631092.2875 551814.3888 521111.8426 495204.9331 632043.0758 0.916554199 0.910731527 0.972160424 1.10439359 0.998495691 0.873064527 0.824487859 0.783498708 1 19.26966336 2.154510735 5.284301296 0.850138235 0.975281753 0.327549683 0.076414817 0.222345192 10.44565052 0.028967029 0.021275706 142.7285111 -2.154510735 0.125143518 AVCMLS(ph)NTTAIAEAWAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVCMLSNTTAIAEAWAR 17 0 P68363;P68363-2;P68366-2;P68366 P68363;P68366-2 TUBA1B;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain 1 AVCMLS(0.702)NT(0.116)T(0.182)AIAEAWAR 96.208 0.0024947 13902000 20326 21868 22859 25345 25244 17914 26711 19530 31696 TRUE FALSE 19053.83194 23487.12947 23401.22627 25995.39561 23261.43807 23085.48099 22705.93352 21968.36349 26405.73284 0.721579365 0.889470844 0.886217641 0.984460298 0.880923783 0.874260189 0.859886513 0.831954319 1 14.68856356 4.738963862 5.90411758 0.893992207 0.716614994 0.529714573 0.052762312 0.106870828 17.28438544 0.01170844 0.076190666 54823.13439 -4.738963862 -0.177377213 AVCMLSNTTAIAEAWAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVCMLSNTTAIAEAWAR 17 0 P68363;P68363-2;P68366-2;P68366 P68363;P68366-2 TUBA1B;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 183.6 1.59E-09 44996000 18713 19113 16991 14640 21753 15031 20086 18915 18554 FALSE TRUE 17541.78673 20528.14641 17394.03454 15015.68719 20044.60713 19370.20569 17074.29077 21276.57939 15457.21754 1.134860572 1.328062205 1.125301789 0.971435328 1.296779778 1.253149582 1.104616062 1.37648185 1 13.91599302 3.876617032 6.853717416 1.165356958 1.24248669 0.044072029 0.132796629 0.660808306 38.55779875 0.031578414 0.057446696 7526.915347 -3.876617032 0.077129732 AVCST(ph)YLQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVCSTYLQSR 10 0 Q5SQL3;J3KP92;Q86Z02;Q86Z02-2;H7BXX9;Q9H2X6-2;Q9H2X6-3;Q9H2X6 Q5SQL3 HIPK1;HIPK2 Homeodomain-interacting protein kinase 1;Homeodomain-interacting protein kinase 2 1 AVCS(0.215)T(0.516)Y(0.269)LQSR 97.741 0.065416 363870000 133280 151920 160890 163430 187880 128140 169030 147010 169020 TRUE FALSE 124938.2427 163168.3149 164706.3868 167623.8905 173124.6627 165131.9378 143685.5207 165364.5221 140809.4701 0.887285796 1.158787934 1.169711005 1.190430518 1.229495875 1.172733181 1.020425122 1.174384947 1 17.10338484 -1.614038656 6.996830062 0.999738407 1.131259692 0.13117632 0.100429768 0.000388353 2.14E-05 0.092147701 0.021676606 0.024319875 1.614038656 0.131521285 AVDFAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AVDFAER 7 0 P62917;E9PKZ0;G3V1A1;E9PKU4;E9PP36 P62917 RPL8 60S ribosomal protein L8 0 ;;; 132.53 0.0078173 3152110000 3811050 4603660 4012750 4053640 4884720 3263120 4479450 4174560 4689440 FALSE TRUE 3572523.183 4944519.777 4107934.325 4157663.265 4501093.795 4205129.772 3807798.058 4695763.005 3906742.169 0.914450718 1.265637598 1.051498703 1.064227708 1.152134848 1.076377603 0.974673499 1.201963888 1 21.89753462 2.002084479 24.63374889 1.048430192 1.107833247 0 0.105774813 159.0150435 1879161.667 0.036908723 0.027077563 100.4811228 -2.002084479 0.059403055 AVDHATNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AVDHATNR 8 0 P49748;P49748-3;P49748-2;J3KSR4 P49748 ACADVL "Very long-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 ;;; 138.1 0.00071989 348610000 323570 526441 383439 369499 599617 388468 350409 499625 630642 FALSE TRUE 303318.3313 565419.2394 392534.3542 378980.9699 552525.4996 500612.4053 297868.4235 562004.2811 525383.7761 0.577327175 1.076202321 0.747138324 0.721341212 1.051660757 0.952850903 0.566953981 1.06970239 1 19.00301213 AVDIPHMDIEALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AVDIPHMDIEALK 13 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;;; 208.28 4.72E-08 2564514000 8683150 7574930 8250760 7948390 7919960 6277710 9764100 7199110 8416600 FALSE TRUE 8139687.141 8135785.699 8446471.923 8152359.144 7297958.289 8089982.967 8300063.85 8097934.731 7011815.087 1.16085308 1.16029667 1.204605629 1.162660316 1.040808721 1.153764449 1.183725433 1.154898501 1 22.74135652 -1.523820126 2.676592796 0.991669666 1.157027074 0.554154041 0.042889347 7799689.498 7725462.399 471766.3343 0.010875 0.029935042 1.523820126 0.165357407 AVDIPHMDIEALKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AVDIPHMDIEALKK 14 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;; 167.55 2.36E-06 2213170000 10700400 7854710 9152100 8783400 9236420 6634790 11838500 7774120 11538800 FALSE TRUE 10030681.06 8436280.901 9369192.134 9008796.914 8511028.831 8550146.166 10063426.83 8744735.995 9612899.737 1.04346049 0.87760001 0.974647858 0.937157066 0.885375804 0.889445058 1.046866929 0.909687632 1 23.19654026 1.749150048 25 0.988467751 0.930858819 0.140574945 0.058695406 4.587661777 10851.67722 0.024670409 0.013680852 56.12418502 -1.749150048 -0.057608932 AVDLGPPKPSDQETGEQVS(ph)SPSSHPALHTTTEDSAGVQTEF ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVDLGPPKPSDQETGEQVSSPSSHPALHTTTEDSAGVQTEF 41 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 AVDLGPPKPS(0.001)DQET(0.063)GEQVS(0.353)S(0.353)PS(0.104)S(0.104)HPALHT(0.007)T(0.008)T(0.008)EDS(0.001)AGVQTEF;AVDLGPPKPSDQETGEQVS(0.498)S(0.498)PS(0.001)S(0.001)HPALHTTTEDSAGVQTEF 220.86 2.82E-44 540310000 120971 174156 179784 181667 204517 161819 226881 165909 234274 TRUE FALSE 113399.641 187050.6914 184048.5614 186328.8828 188455.0598 208533.5184 192862.3003 186623.1039 195172.1559 0.581023663 0.958388201 0.943006242 0.954689883 0.965583738 1.068459368 0.988165035 0.956197379 1 17.57438772 4.741876495 4.526622499 0.979316254 0.553853485 0.927104118 0.035150389 0.053366457 2.813824736 0.009114254 0.072710686 55192.04612 -4.741876495 -0.425462768 AVDTWSWGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AVDTWSWGER 10 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ;;; 264.62 3.45E-17 2594170000 376294 2005750 316206 320758 2031300 297660 392149 1707110 563990 FALSE TRUE 352742.4302 2154257.817 323706.5556 328989.1933 1871769.892 383589.6099 333349.898 1920246.441 469856.4255 0.750745145 4.584927863 0.688947811 0.7001909 3.983706065 0.816397497 0.70947183 4.086879177 1 18.84186045 AVDWIFSHIDDLDAEAAMDISEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVDWIFSHIDDLDAEAAMDISEGR 24 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 185.9 1.71E-17 17720000 13480 15562 16082 19068 18509 19277 19403 13630 20027 FALSE TRUE 12636.31086 16714.22667 16463.47263 19557.31716 17055.3778 24841.95696 16493.70028 15331.7355 16684.36432 0.757374427 1.001789841 0.986760557 1.172194324 1.022237196 1.488936377 0.988572292 0.918928358 1 14.0262091 5.500452068 0.745089205 1.105336521 6.56E-10 0.280162801 0.160568197 9.552473028 1.765161981 0.05500326 11.4893988 316557.107 -5.500452068 -1.10533652 AVEDIHGLFSLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVEDIHGLFSLSK 13 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 162.97 3.95E-05 259400000 1635630 1920310 1729430 1661540 2169400 1360290 1968570 1944590 2144100 FALSE TRUE 1533258.838 2062491.75 1770452.896 1704177.929 1999024.075 1752983.641 1673401.204 2187376.342 1786235.859 0.858374235 1.154658127 0.991164122 0.954060978 1.119126607 0.981384195 0.936831044 1.224573077 1 20.76849116 1.252133564 24.99838092 1.112286642 1.011711733 0.1710132 0.100539261 371.0470404 683394.2229 0.062876712 0.022694298 17.87037082 -1.252133564 -0.100574909 AVEELHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVEELHK 7 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ; 102.72 0.0085375 546390000 2241900 2002870 1945350 1850470 2098330 1487810 2095520 1754750 2402100 FALSE TRUE 2101583.481 2151164.579 1991494.621 1897956.193 1933535.626 1917316.594 1781316.23 1973834.4 2001173.992 1.050175292 1.074951297 0.995163154 0.948421377 0.966200657 0.958095899 0.890135609 0.986338224 1 20.93241518 3.613913533 1.608992931 0.947487794 1.063931875 0.647696652 0.030702799 0.199290833 1.024143631 0.009120157 0.018568711 4110.678707 -3.613913533 0.11644408 AVEES(ph)S(ph)DEERQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVEESSDEERQR 12 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 AVEES(1)S(1)DEERQR;AVEES(1)S(1)DEERQR 199.84 2.00E-06 468970000 1040050 1292300 1182670 1165090 1501810 984790 1273380 1148000 2070740 TRUE FALSE 974955.127 1387983.237 1210723.491 1194988.182 1383863.901 1269082.886 1082448.49 1291330.327 1725120.117 0.565152025 0.804571939 0.701819821 0.692698538 0.802184084 0.735648999 0.627462679 0.748545168 1 20.71826539 0.963557004 23.13202243 1.000000002 0.712451396 0.620793554 0.071879275 1532.389941 972678.9816 0.064865942 0.016216486 9.195111584 -0.963557004 -0.287548605 AVEHINK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AVEHINK 7 0 P06733;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8Y6I8 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;; 146.87 0.0021898 43786000000 42005100 46179400 36810100 34972100 49133000 25463900 43926900 42115500 49278300 FALSE TRUE 39376075.77 49598570.83 37683252.95 35869543.29 45274292.37 32814914.56 37340469.14 47373712.88 41053433.38 0.959142087 1.208146719 0.917907465 0.873728221 1.102813788 0.799322051 0.909557766 1.153952519 1 25.29099955 3.833676391 5.29776002 0.95113122 1.094918919 0.133359944 0.120090815 0.307134544 12.8101811 0.028665787 0.052678126 6818.304475 -3.833676391 0.143787699 AVEHINKTIAPALVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVEHINKTIAPALVSK 16 1 P06733;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8Y6I8 P06733 ENO1 Alpha-enolase;Enolase 0 ; 150.59 4.36E-07 587150000 354030 423820 1008270 1004400 949530 1161190 745660 177866 282740 FALSE TRUE 331871.8943 455200.0738 1032186.641 1030174.604 874957.744 1496406.703 633855.2054 200072.9616 235548.8674 1.408930121 1.932508013 4.382048837 4.373506932 3.71454872 6.35285034 2.690971144 0.849390463 1 17.84566687 4.23012644 2.988884182 3.602555303 1.52749193 0.140536351 1.633178839 0.411727955 7.360747576 0.395529006 1.20102686 16987.38151 -4.23012644 -2.075063373 AVEQHNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 AVEQHNGK 8 0 Q9BRA2;I3L0K2;I3L3M7 Q9BRA2 TXNDC17 Thioredoxin domain-containing protein 17 0 ;;;;;; 98.582 0.0074202 1714676000 3205791 2500592 3124297 2946286 2633681 2205846 3100759 2473159 2585003 FALSE TRUE 3005146.264 2685738.434 3198406.8 3021892.687 2426842.318 2842637.931 2635828.974 2781938.345 2153549.3 1.395438806 1.247121872 1.485179281 1.403215003 1.126903535 1.319978109 1.223946429 1.291792273 1 21.03828492 2.753964174 24.60785243 1.218205235 1.377209362 0.431697561 0.106115311 699.6871346 1117779.531 0.030087527 0.031807865 567.4977898 -2.753964174 0.159004127 AVET(ph)PPLSSVNLLEGLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVETPPLSSVNLLEGLSR 18 0 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 AVET(0.988)PPLS(0.006)S(0.006)VNLLEGLSR 84.035 0.043524 18784000 18318 19836 24491 22539 24895 22322 25926 22741 26758 TRUE FALSE 17171.50908 21304.67808 25071.93809 23117.3889 22939.84712 28765.99903 22038.63699 25580.26391 22291.91694 0.770302039 0.955713147 1.124709829 1.037030102 1.029065701 1.290422852 0.988638036 1.147512974 1 14.44423306 4.787561103 1.264599086 1.090960532 0.598765422 0.576290861 0.088302619 1.059424727 1.352742861 0.022360467 0.698132042 61314.2052 -4.787561103 -0.492195109 AVEVAWETLQEEFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVEVAWETLQEEFSR 15 0 O60313-10;O60313-9;O60313-2;E5KLJ9;O60313-13;O60313;O60313-11;A0A2R8YDM2;A0A2R8Y3X5;C9JMB8;A0A2R8YE78;A0A2R8YFD1 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 ; 222.94 3.11E-12 23677000 18094.3 13569.6 16719.5 15817.9 20867.3 16373.1 14711.6 16177.3 18980.8 FALSE TRUE 16961.81006 14574.3073 17116.09444 16223.81409 19228.46643 21099.74817 12505.73216 18197.07152 15812.78186 1.07266452 0.921678895 1.082421461 1.02599367 1.216007822 1.334347641 0.790862245 1.150782429 1 13.94880358 3.767874988 5.111331335 1.077917084 0.989446439 0.056847556 0.146391934 0.594448513 37.42611237 0.037960662 0.068180741 5859.694688 -3.767874988 -0.088470645 AVEVQGPSLESGDHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVEVQGPSLESGDHGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 212.9 3.30E-12 360030000 459100 470030 491350 477220 603720 404530 610050 472400 687620 FALSE TRUE 430365.7505 504831.5103 503005.054 489466.2731 556306.2665 521311.244 518578.6659 531380.1799 572851.7798 0.751268942 0.881260263 0.878071906 0.854437902 0.971117287 0.910028148 0.905258016 0.927605008 1 19.12780238 8 0.219610024 0.963948155 0.066663015 0.684961209 0.037850442 32.41272013 0.414493534 0.056328459 10.30875062 100000000 -8 -0.89728514 AVEYLLMGIPGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVEYLLMGIPGDR 13 0 P54727;P54727-2 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ; 190.56 1.00E-05 304550000 442940 497170 484040 486670 534030 443940 527410 478330 497380 FALSE TRUE 415217.1761 533980.9841 495521.6574 499158.7761 492089.438 572098.2712 448329.7667 538050.5534 414364.0648 1.002058845 1.2886759 1.195860596 1.204638188 1.187577495 1.380665747 1.081970675 1.298497141 1 18.66053937 -0.732486143 7.604227545 1.000007706 1.209488452 0.264399743 0.107223559 0 0 0.089947464 0.021200821 0.185145797 0.732486143 0.209480745 AVEYLLTGIPGS(ph)PEPEHGSVQESQVSEQPATEAAGENPLEFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVEYLLTGIPGSPEPEHGSVQESQVSEQPATEAAGENPLEFLR 43 0 P54725-2;P54725;A0A494C0B4 P54725-2 RAD23A UV excision repair protein RAD23 homolog A 1 AVEYLLTGIPGS(0.993)PEPEHGS(0.007)VQESQVSEQPATEAAGENPLEFLR;AVEYLLTGIPGS(0.757)PEPEHGS(0.243)VQESQVSEQPATEAAGENPLEFLR 211.77 4.81E-36 394920000 36900 71332 69635 67984 80216 57094 69165 61942 84303 TRUE FALSE 34590.49487 76613.4955 71286.77508 69728.58454 73916.15894 73576.11096 58794.35035 69675.59505 70232.28468 0.492515586 1.090858654 1.015014326 0.992828083 1.052452718 1.047610957 0.83714136 0.992073594 1 16.09984675 4.744799739 24.9979207 1.00059559 0.492515361 0.852623177 0.066754562 292.1234465 1170402.045 0.01768386 0.165280645 55564.79787 -4.744799739 -0.50808023 AVEYLLTGIPGS(ph)PEPEHGSVQESQVSEQPATEAGENPLEFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AVEYLLTGIPGSPEPEHGSVQESQVSEQPATEAGENPLEFLR 42 0 P54725-3 P54725-3 RAD23A UV excision repair protein RAD23 homolog A 1 AVEYLLT(0.001)GIPGS(0.839)PEPEHGS(0.156)VQES(0.004)QVSEQPATEAGENPLEFLR;AVEYLLTGIPGS(0.967)PEPEHGS(0.033)VQESQVSEQPATEAGENPLEFLR;AVEYLLTGIPGS(0.946)PEPEHGS(0.052)VQES(0.002)QVSEQPATEAGENPLEFLR 177.42 2.83E-27 163192800 33983.6 58090.5 52418.3 54450.9 50498.8 41254.5 54570 47962.2 52224.3 TRUE FALSE 31856.62714 62391.58106 53661.68683 55848.20228 46532.82795 53164.00444 46387.7351 53950.38625 43507.72695 0.732206194 1.434034491 1.233382909 1.283638705 1.069530201 1.221943966 1.066195326 1.240018499 1 15.40898403 2.73829356 24.99999523 1.127303792 1.225113283 0 0.192941771 76.86387699 7194926.175 0.056064616 0.055942272 547.3858412 -2.73829356 0.097809491 AVEYYFASDASAVIEHTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVEYYFASDASAVIEHTNR 19 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 111.77 0.00020972 30201000 20394 25758 21924 25254 23003 22966 26415 21295 20871 FALSE TRUE 19117.57594 27665.14912 22444.04763 25902.06039 21196.43717 29595.91138 22454.31597 23953.72763 17387.49527 1.099501432 1.591094559 1.290815456 1.489694749 1.219062139 1.70213771 1.291406015 1.377641072 1 14.0857625 0.470368166 1.567493248 1.000173114 1.403295623 0.311736113 0.177257638 3.373253031 8.828769149 0.14596067 0.041835374 2.953712127 -0.470368166 0.403122509 AVFHEEEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVFHEEEQR 9 0 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 118.18 0.0010317 209260000 553770 670690 558670 551040 726160 553140 557880 594470 672720 FALSE TRUE 519110.5242 720348.5855 571921.9162 565180.6193 669130.3228 712822.5385 474231.0731 668690.8881 560438.6861 0.926257479 1.285329873 1.020489717 1.00846111 1.193940282 1.271901024 0.846178333 1.193156191 1 19.09619702 1.741126024 25 1.002325417 1.1245784 0.107334582 0.140162071 0.798734985 7831.895574 0.059949633 0.033245205 55.0967553 -1.741126024 0.122252983 AVFPSIVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 178.99 0.00011707 1503829000 625520 711116 730166 651121 762120 556432 660641 741141 591895 FALSE TRUE 586369.8198 763767.7686 747485.8823 667829.8672 702266.1694 717064.8855 561584.0151 833674.0853 493103.9007 1.189140502 1.548898249 1.51587907 1.354339047 1.424174841 1.454186196 1.138875629 1.690666174 1 18.91153214 -3.097256356 0.337351196 2.21E-10 1.434752331 0.354360854 0.167133826 96.76613765 2.719528526 69.01043309 0.129497472 0.000799362 3.097256356 1.43475233 AVFPSIVGRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 AVFPSIVGRPR 11 1 C9JTX5;F8WCH0;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63267-2;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6;Q6S8J3;A5A3E0;P0CG38 C9JTX5;P60709;P63261;P68133;Q6S8J3 ACTB;ACTG2;ACTG1;ACTA1;ACTC1;ACTA2;POTEE;POTEF;POTEI "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I" 0 ;;;;;;; 241.03 9.51E-16 61674973700 8044946.4 14002519.7 9216668.6 8906777.5 14719129.3 7044272.42 9956032.5 10961147.5 13499043.5 FALSE TRUE 7541427.565 15039280.83 9435292.332 9135340.49 13563148.26 9077839.513 8463217.854 12329670.89 11245965.93 0.670589579 1.337304498 0.838993501 0.812321551 1.206045647 0.80720852 0.752555886 1.096363884 1 23.42290425 3.737771472 24.76640212 0.909655256 1.062543394 0 0.213342055 806.4580682 1875353.648 0.05084644 0.090461161 5467.281956 -3.737771472 0.152888138 AVFVDLEPTVIDEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 3013529000 1298284 1603336 1553404 1562478 1712404 1440395 1751590 1510504 1820892 FALSE TRUE 1217026.722 1722048.666 1590251.476 1602573.831 1577918.697 1856213.654 1488955.34 1699093.749 1516973.362 0.802272968 1.135187149 1.048305472 1.056428459 1.040175614 1.223629696 0.981530314 1.120055099 1 20.53276432 4.746077396 24.86451651 1.076973546 0.802272827 0.599445126 0.070226033 548.2404348 1813460.118 0.014858876 0.157144986 55728.50548 -4.746077396 -0.274700719 AVGHPFVIQLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVGHPFVIQLGR 12 0 O14980 O14980 XPO1 Exportin-1 0 130.94 0.00020756 694030000 943230 1690100 792130 825120 1706000 720890 1053100 1556100 818970 FALSE TRUE 884194.918 1815236.763 810919.6977 846293.9761 1572017.642 928999.2403 895197.4315 1750382.51 682278.6163 1.295944057 2.660550572 1.18854626 1.240393522 2.304069927 1.361612717 1.312070187 2.565495193 1 19.38000147 -2.021060135 3.078766727 0.154961063 1.727788772 0.142647406 0.570149095 3660420.217 104374538.9 26204246.74 0.125430947 0.009526642 2.021060135 1.572827709 AVGIWHCGSCMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVGIWHCGSCMK 12 0 Q6P4E4;E9PEL3;P61513;M0R0A1;C9J4Z3;M0R2L6 Q6P4E4 RPL37A 60S ribosomal protein L37a 0 ; 176.8 2.41E-05 849940000 2562780 3256800 2352800 2308300 4042200 1795420 3014200 3202900 3966100 FALSE TRUE 2402380.174 3497936.861 2408609.527 2367534.886 3724741.917 2313728.608 2562248.692 3602789.115 3304132.288 0.727083532 1.05865521 0.728968854 0.71653756 1.12729806 0.700253018 0.77546795 1.090388883 1 21.65584002 1.235022889 24.99833914 1.045194515 0.841346303 0.25868945 0.148543244 132.1298963 933586.4955 0.117297955 0.033839011 17.17998928 -1.235022889 -0.203848212 AVGKEELGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVGKEELGK 9 1 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 94.616 0.0078445 303090000 446960 361680 334740 387090 437760 265010 518540 362440 497430 FALSE TRUE 418985.5714 388459.1635 342680.1909 397023.3847 403380.0954 341514.0849 440789.7409 407691.4318 414405.7195 1.011051614 0.937388519 0.82691955 0.95805479 0.973394132 0.824105626 1.063667127 0.983797792 1 18.66068439 1.699129809 11.34454756 1.01686499 0.916096357 0.335531417 0.061942849 0.124297028 27.65372314 0.028279145 0.015410945 50.01840162 -1.699129809 -0.100768633 AVGMPSPVS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVGMPSPVSPK 11 0 Q9UHB7 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 AVGMPSPVS(1)PK;AVGMPSPVS(1)PK 170.95 1.59E-05 166126000 709660 503590 551440 566370 579350 391170 738280 500650 754480 TRUE FALSE 665243.6474 540876.3276 564520.4172 580904.0131 533850.188 504094.4289 627581.7679 563157.2546 628552.4139 1.058374183 0.860511098 0.898127833 0.924193433 0.84933281 0.80199267 0.998455744 0.895959099 1 19.26167353 0.962978318 1.189889983 0.994375256 0.898924527 0.104447663 0.074132902 1.025959192 2.977715118 0.064509147 0.020157351 9.182867507 -0.962978318 -0.095450729 AVGNIVTGTDEQTQVVLNCDALSHFPALLTHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVGNIVTGTDEQTQVVLNCDALSHFPALLTHPK 33 0 O00629;H7C4F6 O00629 KPNA4 Importin subunit alpha-3 0 ; 199.59 3.54E-27 255900000 164102 141688 148644 141832 178110 126703 198849 149261 169546 FALSE TRUE 153831.1488 152178.7269 152169.9059 145471.6492 164121.9591 163280.0992 169033.4385 167896.5644 141247.6773 1.089087989 1.077389235 1.077326784 1.029904718 1.161944481 1.155984313 1.196716588 1.18866779 1 17.10786762 2.721962413 24.10777966 1.157539314 1.071404125 0.256047558 0.057203459 518.2363342 752702.3773 0.016419793 0.015527473 527.1842332 -2.721962413 -0.086135189 AVGS(ph)PLCVPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AVGSPLCVPAR 11 0 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 1 AVGS(1)PLCVPAR;AVGS(1)PLCVPAR;AVGS(1)PLCVPAR;AVGS(1)PLCVPAR 146.16 3.77E-05 470740000 398050 563723 444582 435054 509784 351365 495208 442090 616096 TRUE FALSE 373136.761 605461.6375 455127.695 446218.2222 469747.621 452798.3716 420956.1577 497285.9097 513265.5975 0.726985722 1.179626378 0.886729399 0.869370993 0.915213533 0.882191158 0.820152685 0.96886663 1 18.96934604 3.717622378 24.45072457 0.891762535 0.999899635 0 0.12052678 470.0898862 1210044.638 0.028802661 0.045297496 5219.421592 -3.717622378 0.1081371 AVGWNELEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVGWNELEGR 10 0 P61457 P61457 PCBD1 Pterin-4-alpha-carbinolamine dehydratase 0 108.43 0.0050063 45093000 45382 51069 56802 52766 51860 51346 57075 50528 26971 FALSE TRUE 42541.62163 54850.2019 58149.37026 54120.06489 47787.12479 66168.75667 48517.13361 56836.53203 22469.36586 1.893316522 2.441110365 2.587939981 2.408615589 2.126767844 2.944843084 2.159256915 2.529512064 1 14.45567179 -0.968421313 5.536974911 0.999997265 2.408667458 0.696572171 0.287235579 8.58E-06 1.60E-06 0.246133311 0.058014065 0.107542143 0.968421313 1.408670193 AVIFCLSADKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVIFCLSADKK 11 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ; 158.05 4.86E-05 4076000000 3487300 3500700 3236300 3234200 5565000 2975120 4575800 4337900 6268900 FALSE TRUE 3269036.118 3759895.47 3313066.564 3317195.047 5127947.348 3833988.847 3889701.27 4879496.364 5222580.091 0.625942745 0.719930648 0.634373529 0.635164036 0.981880078 0.734117769 0.744785375 0.934307618 1 22.31633128 1.389015661 0.275376976 1.045950672 0.609890411 0.555602444 0.095790027 1.3797321 0.410305342 0.233708637 0.196649564 24.49151556 -1.389015661 -0.436060262 AVIFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AVIFDR 6 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 ;;; 109.7 0.068236 950490000 1022800 1570090 1139830 1065120 1830820 1069550 1081740 1474040 1437390 FALSE TRUE 958784.7738 1686341.097 1166867.306 1092452.782 1687034.782 1378311.722 919543.1294 1658077.139 1197480.323 0.8006685 1.408241175 0.974435474 0.912292888 1.408820462 1.151009913 0.767898321 1.384638317 1 20.19157052 -1.113241715 0.224513183 0.931690471 1.12204093 0 0.244034359 117.1034295 5.746727472 5.677147888 0.514148122 0.077047453 1.113241715 0.190350459 AVIGIGIEEEDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVIGIGIEEEDRK 13 1 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 196.57 2.26E-07 177920000 128950 110290 111260 106590 118900 84398 143630 91678 141580 FALSE TRUE 120879.2497 118455.9864 113899.1397 109325.2799 109562.0736 108762.3325 122094.0149 103124.2001 117949.3834 1.024840031 1.004295088 0.965661172 0.926883013 0.928890601 0.922110226 1.035139069 0.874308938 1 16.84780835 4.047431799 1.67495024 0.952861025 1.020519099 0.272329497 0.044133236 0.575676246 3.00985802 0.01193922 0.040575675 11154.02975 -4.047431799 0.067658074 AVIT(ph)PDFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVITPDFEK 9 0 Q5QJE6 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 AVIT(1)PDFEK 85.958 0.039786 0 94167 84671 81880 79256 93457 67310 99559 78261 133780 TRUE FALSE 88273.25556 90940.12894 83822.23227 81289.84314 86117.26421 86741.30431 84631.05221 88032.05812 111451.2537 0.792034657 0.815963265 0.752097706 0.729375762 0.772689955 0.778289175 0.759354869 0.789870505 1 16.76605332 0.807687213 5.60316439 0.999999789 0.772336268 0.906020318 0.022977467 1.736879112 50.51972119 0.023408124 0.005895778 6.422250076 -0.807687213 -0.227663522 AVITPHDFDECR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AVITPHDFDECR 12 0 Q9Y5P4-3;Q9Y5P4;Q9Y5P4-2;A0A2R8Y7C5;A0A2R8YE18;A0A2R8Y7Q9;A0A2R8Y5S9;A0A2R8YEA4;A0A2U3TZL3;A0A2R8YEK8;A0A2R8Y5H3;A0A2R8YFI2;A0A2R8YCI0 Q9Y5P4-3 COL4A3BP Collagen type IV alpha-3-binding protein 0 ;; 167.44 4.92E-05 587610000 488143 619470 547051 537667 605640 600460 714010 507721 541972 FALSE TRUE 457591.001 665336.2034 560027.3081 551464.4455 558075.4774 773803.0543 606950.829 571111.0845 451513.3719 1.013460574 1.473569211 1.240333826 1.221369022 1.236010963 1.713798754 1.344258812 1.264881884 1 18.78440919 AVIVSS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AVIVSSPK 8 0 Q14966;Q14966-3;Q14966-5 Q14966 ZNF638 Zinc finger protein 638 1 AVIVS(0.105)S(0.895)PK;AVIVS(0.097)S(0.903)PK;AVIVS(0.157)S(0.843)PK;AVIVS(0.005)S(0.995)PK;AVIVS(0.162)S(0.838)PK;AVIVS(0.019)S(0.981)PK 166.66 0.00033271 2575350000 9156720 6243630 6531330 6106940 8360650 4638740 8383600 7050150 10477800 TRUE FALSE 8583617.24 6705914.862 6686256.232 6263654.419 7704038.274 5977868.934 7126557.01 7930376.747 8728987.491 0.983346264 0.768235133 0.765983024 0.717569412 0.882580973 0.684829591 0.816424244 0.908510495 1 23.05738289 1.080774415 2.703959622 0.997161277 0.789772023 0.380248589 0.084131965 0.223148234 3.28103663 0.071640793 0.019352884 12.04410173 -1.080774415 -0.207389254 AVLDYHDDNFAIVFAAMGVNMETAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AVLDYHDDNFAIVFAAMGVNMETAR 25 0 P15313;C9JL73 P15313 ATP6V1B1 "V-type proton ATPase subunit B, kidney isoform" 0 ;; 138.62 7.56E-06 47773000 66765 83628 78240 77525 93292 73393 86315 78927 68571 FALSE TRUE 62586.29783 89819.90413 80095.88975 79514.42275 85965.22264 94580.36766 73372.86706 88781.20969 57126.05711 1.095582314 1.572310582 1.402090286 1.391911621 1.504833818 1.655643194 1.284402789 1.554128084 1 15.80186134 -1.529924401 9.339030053 0.999982013 1.441586885 0.420870459 0.159174293 5.25E-05 2.64E-06 0.13569813 0.031983058 0.02951723 1.529924401 0.441604873 AVLFCLSEDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVLFCLSEDKK 11 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 132.62 0.00028643 10971200000 3705600 2286700 2701700 2519100 3097800 2266220 3885400 2309600 3995500 FALSE TRUE 3473673.111 2456009.647 2765785.6 2583744.371 2854511.284 2920440.925 3302820.34 2597958.644 3328625.238 1.04357591 0.737845048 0.83090928 0.776219666 0.857564634 0.877371502 0.992247581 0.78048998 1 21.66649502 2.16904644 2.955457306 0.924727884 0.826712922 0.080581028 0.099798885 0.444723643 7.858030427 0.038988319 0.026904447 147.586434 -2.16904644 -0.098014962 AVLGDDEITREPR ddPTM_SK-BR-3_Pertuzumab_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 ; 102.62 0.0015276 227640000 474440 543880 544110 498780 660700 484870 543920 522650 897590 FALSE TRUE 444745.6473 584149.4411 557016.5461 511579.5392 608811.2871 624844.0978 462364.2455 587904.003 747776.4303 0.594757509 0.781181938 0.744897169 0.684134346 0.814162178 0.835602825 0.618318827 0.786202907 1 19.51224747 0.975195721 23.96147713 1.000000004 0.731797128 0.551810646 0.077530652 1030.756915 995735.3021 0.06965279 0.017413198 9.444864271 -0.975195721 -0.268202876 AVLPVTCHRDS(ph)FSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.934)FS(0.066)R;AVLPVTCHRDS(0.587)FS(0.413)R;AVLPVTCHRDS(0.922)FS(0.078)R 158.98 3.02E-06 1177850000 372400 589110 474040 516860 642180 483820 660990 542460 735720 TRUE FALSE 349092.1488 632728.3174 485284.4527 530123.5026 591745.7732 623490.9798 561880.6858 610187.3251 612923.5791 0.569552487 1.032311921 0.791753604 0.864909625 0.965447885 1.017240976 0.916722255 0.995535734 1 19.22534768 2.76395481 4.311391622 0.973134191 0.845565652 0.318945627 0.115657034 0.315343862 14.24804878 0.034403252 0.035229573 580.7039895 -2.76395481 -0.127568539 AVLPVTCHRDSFS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.299)FS(0.701)R;AVLPVT(0.024)CHRDS(0.416)FS(0.559)R 183.73 8.32E-07 895530000 178917 255596 227432 227394 293690 200418 330923 236567 354802 TRUE FALSE 167718.9043 274520.5938 232826.7944 233229.315 270624.7721 258275.4231 281304.1683 266102.9107 295583.2541 0.567416801 0.928742038 0.787686011 0.789047795 0.915561922 0.873782325 0.951691831 0.900263824 1 18.17320501 7.383920342 0.183033508 0.996108341 2.12E-14 0.526849841 0.083752498 40.34101998 0.55895494 0.177028835 10.74069513 24205850.24 -7.383920342 -0.996108341 AVLSDS(ph)PQLSEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVLSDSPQLSEGK 13 0 Q5VY60;Q7Z4H7-3;Q7Z4H7;Q5SYF9;Q7Z4H7-2 Q5VY60 HAUS6 HAUS augmin-like complex subunit 6 1 AVLSDS(1)PQLSEGK 251.05 3.94E-18 73080000 308780 267850 277960 289900 315900 240620 338210 267150 334100 TRUE FALSE 289454.011 287681.8927 284553.3425 297339.3248 291090.4883 310083.0879 287498.5503 300504.2656 278336.5516 1.039942506 1.033575687 1.022335517 1.068272647 1.045821997 1.114058093 1.03291698 1.07964356 1 18.08647085 3.238109284 24.9999996 1.060060975 1.030925657 0.12616498 0.029954746 18.6949274 1035556.598 0.007494273 0.009502777 1730.251697 -3.238109284 -0.029135317 AVLVDLEPGTMDSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 216.03 5.26E-12 211430000 218739 261020 266920 255450 294630 211690 268460 247780 313010 FALSE TRUE 205048.5165 280346.1924 273251.4684 262005.2795 271490.9483 272801.4665 228206.9153 278715.8784 260766.6089 0.786329651 1.075084704 1.047877524 1.004750112 1.041126199 1.046151835 0.875138563 1.068832699 1 17.99239962 -0.242521722 7.582362001 1.000010517 1.000214195 0 0.092964169 0 0 0.084138178 0.019831559 0.572108339 0.242521722 0.000203677 AVNTQALS(ph)GAGILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVNTQALSGAGILR 14 0 O60749;O60749-2 O60749 SNX2 Sorting nexin-2 1 AVNTQALS(1)GAGILR 78.191 0.023673 186210000 77086 89017 78260 92414 116180 71720 102420 94211 110330 TRUE FALSE 72261.32486 95607.9113 80116.36416 94785.4997 107055.6914 92424.39972 87063.07182 105973.4507 91915.21024 0.786173743 1.040175081 0.871633367 1.031227579 1.164722261 1.005539774 0.947210713 1.152947923 1 16.488016 6.04836956 0.615777451 1.030774795 1.80E-26 0.357937437 0.091802085 19.63615785 1.611551903 0.038185534 20.56649118 1117814.041 -6.04836956 -1.030774795 AVPAPS(ph)PGPTHNS(ph)PELGRPPAAGVLAPDMSDKDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVPAPSPGPTHNSPELGRPPAAGVLAPDMSDKDK 34 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 2 AVPAPS(0.984)PGPT(0.304)HNS(0.712)PELGRPPAAGVLAPDMSDKDK 135.01 1.26E-08 65464000 63057 33404 38898 44415 43037 31026 55806 32374 65993 TRUE FALSE 59110.37493 35877.26692 39820.67893 45554.76409 39657.04762 39982.70253 47438.40838 36415.96516 54978.34197 1.075157468 0.652570915 0.72429756 0.828594724 0.721321273 0.727244604 0.862856294 0.662369287 1 15.74657578 -1.692116317 2.887647816 1.029746124 0.769215706 0.230580327 0.123373888 53866034.38 53304066.95 11792552.64 0.026519495 0.020318128 1.692116317 -0.260530418 AVPAPSPGPTHNS(ph)PELGRPPAAGVLAPDMSDKDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AVPAPSPGPTHNSPELGRPPAAGVLAPDMSDKDK 34 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 AVPAPSPGPT(0.001)HNS(0.999)PELGRPPAAGVLAPDMSDKDK;AVPAPS(0.216)PGPT(0.216)HNS(0.568)PELGRPPAAGVLAPDMSDKDK;AVPAPS(0.001)PGPT(0.114)HNS(0.885)PELGRPPAAGVLAPDMSDKDK;AVPAPSPGPTHNS(1)PELGRPPAAGVLAPDMSDKDK 218.37 1.71E-36 1045130000 1031380 559989 751535 699401 799490 574124 1036664 634759 996502 TRUE FALSE 966827.7669 601451.1682 769361.7651 717348.8137 736701.2804 739864.2787 881225.8571 714010.0584 830179.3786 1.164601039 0.724483387 0.926741599 0.864088933 0.88740012 0.891210138 1.061488493 0.860067206 1 19.66306357 1.881770508 11.962146 0.97990538 0.887454686 0.038913496 0.118734193 1.220051731 117.5162994 0.044938811 0.028760896 76.16764157 -1.881770508 -0.092450694 AVPEHAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVPEHAAR 8 0 X6RA56;X6RLR1;O75935-2;O75935 X6RA56 DCTN3 Dynactin subunit 3 0 81.548 0.022576 29586000 50727 117070 86315 99196 108700 88413 74259 99756 74965 FALSE TRUE 47552.08762 125737.9846 88362.43256 101741.5373 100163.1405 113936.3978 63124.55234 112210.7562 62452.85721 0.76140772 2.013326375 1.414866133 1.629093397 1.603819984 1.824358451 1.010755235 1.796727343 1 15.93047996 -1.166671638 4.005612933 0.999779367 1.526221683 0.149763197 0.376973331 93.83128423 90805514.88 42102.26272 0.079620903 0.068128427 1.166671638 0.526442316 AVPIAVADEGES(ph)ESEDDDLKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVPIAVADEGESESEDDDLKPR 22 1 Q9Y2K6 Q9Y2K6 USP20 Ubiquitin carboxyl-terminal hydrolase 20 1 AVPIAVADEGES(1)ESEDDDLKPR 241.82 6.69E-31 99321000 112280 81803 89884 84736 94157 64591 114270 76502 152920 TRUE FALSE 105252.5952 87859.77924 92016.09093 86910.46922 86762.28903 83237.37315 97136.27433 86053.4431 127396.6641 0.826180151 0.689655258 0.722280223 0.68220365 0.68104051 0.653371686 0.762471098 0.675476424 1 16.95896798 -1.273559021 3.435062953 1.000920412 0.710092302 0.764090011 0.050358069 89680250.22 131183920.3 860547.9345 0.010939227 0.053264883 1.273559021 -0.29082811 AVPIGT(ph)PPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVPIGTPPK 9 0 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 AVPIGT(1)PPK 99.53 0.058959 240530000 939920 600120 723370 802930 890390 720620 1194800 823180 802880 TRUE FALSE 881092.085 644553.5092 740528.678 823534.5432 820462.3611 928651.2957 1015650.832 925955.835 668874.1412 1.317276347 0.96363945 1.107127085 1.231224968 1.226631904 1.388379724 1.518448344 1.384349877 1 19.35137525 2.751667302 1.55492175 1.377520361 1.092888317 0.138115381 0.163219156 0.394503698 1.91645824 0.061472678 0.06017031 564.5043623 -2.751667302 -0.284632044 AVPKEDIYSGGGGGGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVPKEDIYSGGGGGGSR 17 1 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 112.56 0.001034 0 164700 184270 164320 167840 201120 157260 208600 152880 320760 FALSE TRUE 154391.721 197913.5425 168217.748 172147.0586 185324.8465 202658.4091 177322.3665 171967.4045 267223.0838 0.577763413 0.740630412 0.629503056 0.64420729 0.693521098 0.758386612 0.663574284 0.64353499 1 18.02768511 -2.170419505 2.435647773 1.845422383 0.674944662 0.794100262 0.052906664 4598770.989 920429.5563 21516323.73 0.012337246 0.006754302 2.170419505 -1.170477721 AVPLIHQEGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVPLIHQEGNR 11 0 O00170;E9PMH2;V9GYQ3 O00170 AIP AH receptor-interacting protein 0 138.99 4.60E-05 326460000 253690 363100 267210 287120 415210 252480 265220 307490 393110 FALSE TRUE 237811.9957 389984.3018 273548.3474 294487.9853 382601.0815 325366.8773 225452.7232 345880.8034 327497.4014 0.72614926 1.19080121 0.835268757 0.89920709 1.168256847 0.993494531 0.688410724 1.05613297 1 18.32112393 AVPMAPAPAS(ph)PGSSNDSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVPMAPAPASPGSSNDSSAR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 AVPMAPAPAS(0.998)PGS(0.002)SNDSSAR;AVPMAPAPAS(0.999)PGSSNDSSAR 238.3 3.64E-27 293940000 259110 269070 277600 263090 260880 213890 276500 230450 265660 TRUE FALSE 242892.7676 288992.2228 284184.8031 269841.3348 240391.5371 275636.5708 235041.3919 259222.1898 221319.6298 1.097475031 1.305768598 1.284046984 1.219238145 1.086173592 1.245423061 1.061999752 1.171257109 1 17.75577189 1.539754875 0.487252136 1.008977825 1.255535133 0.371126969 0.080188019 0.755817391 0.46055079 0.080523048 0.051536211 34.65412003 -1.539754875 0.246557309 AVPPVS(ph)PELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AVPPVSPELR 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 AVPPVS(1)PELR;AVPPVS(1)PELR;AVPPVS(1)PELR;AVPPVS(1)PELR 132.25 0.00023982 2536490000 1857140 1917710 1867790 1945160 2104420 1750800 2138140 1859290 1991130 TRUE FALSE 1740904.922 2059699.244 1912094.861 1995076.099 1939147.342 2256227.538 1817545.757 2091426.449 1658797.54 1.049498134 1.241682119 1.152699359 1.202724293 1.169007848 1.360158479 1.095700779 1.260808748 1 20.66170638 -0.990780338 5.113473919 1.00000928 1.192533486 0.326483443 0.086445223 4807561.168 940204.8257 72.38535166 0.01753083 0.1021456 0.990780338 0.192524206 AVPS(ph)PTTGEEGSVHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AVPSPTTGEEGSVHSR 16 0 Q5SYE7-2;Q5SYE7 Q5SYE7-2 NHSL1 NHS-like protein 1 1 AVPS(0.997)PT(0.003)TGEEGSVHSR;AVPS(0.997)PT(0.003)TGEEGSVHSR;AVPS(0.995)PT(0.005)TGEEGSVHSR 169.43 3.62E-09 1071040000 534940 674620 736320 723040 820470 594480 660560 622900 954960 TRUE FALSE 501459.0603 724569.5667 753785.8581 741594.4305 756033.5958 766096.7254 561515.1603 700670.4362 795571.0067 0.630313393 0.910754113 0.947477789 0.932153666 0.950303102 0.962952042 0.705801438 0.88071389 1 19.60163117 -2.00485437 8.72327776 1.14002254 0.872985901 0.123361817 0.111279664 0.070369076 3.92E-05 0.025020069 0.024804379 0.009888846 2.00485437 -0.267036639 AVQALCAVYEHWVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVQALCAVYEHWVPR 15 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ; 158.17 1.84E-06 304930000 340320 441330 344670 338540 410300 322150 449290 356520 326930 FALSE TRUE 319019.9787 474006.5324 352845.7352 347227.5095 378076.6931 415149.4753 381923.1355 401032.3068 272363.271 1.171303229 1.740346746 1.29549676 1.274869069 1.388133913 1.524249117 1.402256384 1.472416987 1 18.05517264 -1.119864549 4.804507659 0.99997478 1.42693791 0.401093441 0.155502284 3.94E-05 7.22E-06 0.141324252 0.033308481 0.07588142 1.119864549 0.42696313 AVQGMLDFDYVCSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AVQGMLDFDYVCSR 14 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;; 215.53 1.50E-11 291949000 281017 318278 296486 301466 310673 256697 314748 278743 308237 FALSE TRUE 263428.6476 341843.6343 303518.7879 309202.1279 286273.9958 330801.2568 267554.4594 313544.6771 256790.2534 1.025851426 1.331217325 1.181971605 1.204103831 1.114816439 1.288215781 1.041918281 1.221014711 1 17.97023092 0.181219002 0.374221507 0.970213653 1.21372531 0.208716059 0.098957464 4.727164366 1.039763728 0.331207913 0.072491703 1.517815566 -0.181219002 0.243511656 AVQQHQHGYDS(ph)DEEVDSELGTWEHQLR ddPTM_SK-BR-3_Pertuzumab_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 455.86 1.54E-211 6931740000 1264308 1350723 1342825 1185831 1363976 1130653 1453218 1250439 1356050 TRUE FALSE 1185177.219 1450731.936 1374677.443 1216261.431 1256854.827 1457054.166 1235321.452 1406559.062 1129716.495 1.049092604 1.284155754 1.216834002 1.076607659 1.112540034 1.289752051 1.093479167 1.245054904 1 20.10752934 -1.967054462 2.647851551 0.853158468 1.179527541 0.271009381 0.087101178 17247613.01 9195839.886 15541266.97 0.019843277 0.010788114 1.967054462 0.326369074 AVQTLAGSQPTSDKPS(ph)QRPSESTNCSPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVQTLAGSQPTSDKPSQRPSESTNCSPTR 29 2 Q9NR48-2;Q9NR48 Q9NR48-2 ASH1L Histone-lysine N-methyltransferase ASH1L 1 AVQTLAGS(0.001)QPT(0.078)S(0.078)DKPS(0.162)QRPS(0.162)ES(0.162)T(0.162)NCS(0.162)PT(0.036)R 57.427 0.025638 389720000 10069 10506 10786 8355.8 11486 10500 13006 8937.3 9873.5 TRUE FALSE 9438.799264 11283.87517 11041.84901 8570.223974 10583.93589 13531.17955 11055.87104 10053.14158 8225.549065 1.147497777 1.371808141 1.342384433 1.041902967 1.286714821 1.645018398 1.344089125 1.222184866 1 13.00589627 2.46033851 24.99444604 1.359271341 1.259098693 0 0.185298306 736.3221739 1096593.806 0.060974704 0.051026421 288.6280334 -2.46033851 -0.100172648 AVQTLAGSQPTSDKPSQRPSESTNCS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVQTLAGSQPTSDKPSQRPSESTNCSPTR 29 2 Q9NR48-2;Q9NR48 Q9NR48-2 ASH1L Histone-lysine N-methyltransferase ASH1L 1 AVQTLAGSQPTSDKPS(0.001)QRPS(0.314)ES(0.155)T(0.155)NCS(0.319)PT(0.056)R 145.85 3.10E-08 354850000 182320 151880 165170 148580 189430 157940 216870 144180 183720 TRUE FALSE 170908.9167 163125.3532 169087.9104 152392.8143 174552.9319 203534.7141 184352.3568 162181.1904 153055.9451 1.116643437 1.065789069 1.104745786 0.995667396 1.140451825 1.329805999 1.204476943 1.059620325 1 17.22369956 2.484661064 24.96638681 1.18300393 1.074813036 0.092288552 0.09411406 499.9297205 1655413.312 0.029650181 0.02580895 305.2537891 -2.484661064 -0.108190894 AVRPEVNTVASSDEVCDGDREKEEPPS(ph)PIEATPPQSLLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVRPEVNTVASSDEVCDGDREKEEPPSPIEATPPQSLLEK 40 3 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 AVRPEVNTVASSDEVCDGDREKEEPPS(0.999)PIEAT(0.001)PPQSLLEK 102.21 9.86E-06 94065000 102230 61398 74466 83745 92231 49781 105960 60689 134410 TRUE FALSE 95831.60679 65943.9718 76232.36869 85894.03848 84987.5493 64151.96657 90072.28168 68266.15524 111976.1027 0.855821952 0.588911118 0.680791409 0.767074728 0.758979347 0.572907657 0.804388432 0.609649323 1 16.77283135 -1.471326401 3.910756695 1.002586843 0.697807392 0.489430167 0.094509154 0.001940334 0.000262303 0.083297108 0.019477394 0.033781085 1.471326401 -0.304779451 AVS(ph)EEQQPALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVSEEQQPALK 11 0 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 AVS(1)EEQQPALK;AVS(1)EEQQPALK 194.83 3.56E-07 611090000 1272390 755860 1045930 805360 699930 650500 1034680 590010 1221040 TRUE FALSE 1192753.381 811824.6609 1070739.954 826026.9011 644960.3212 838288.79 879539.3395 663674.0473 1017240.536 1.172538194 0.798065583 1.052592692 0.812027118 0.634029316 0.824081189 0.86463261 0.652425876 1 19.95622943 3.141452967 7.08424267 0.789000026 0.968660611 0.326494317 0.138253764 0.272070991 17.13441129 0.036844923 0.044222915 1385.010184 -3.141452967 0.179660585 AVS(ph)LDSPVSVGSSPPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AVSLDSPVSVGSSPPVK 17 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 AVS(0.999)LDS(0.001)PVSVGSSPPVK;AVS(1)LDSPVSVGSSPPVK;AVS(0.871)LDS(0.129)PVSVGSSPPVK;AVS(0.99)LDS(0.01)PVSVGSSPPVK;AVS(1)LDSPVSVGSSPPVK;AVS(1)LDSPVSVGSSPPVK 378.74 3.05E-105 861667000 1701330 1809960 1548970 1848960 1177698 1084725 2848540 1522100 1848470 TRUE FALSE 1594846.792 1943971.322 1585712.3 1896407.444 1085206.35 1397867.498 2421427.872 1712137.536 1539948.415 1.035649491 1.262361325 1.029717804 1.231474655 0.704703053 0.907736574 1.572408431 1.111814862 1 20.55445059 1.762995477 25 1.286502171 1.051051394 0.138422098 0.214148111 22.26253226 22793.51481 0.095482591 0.052952344 57.94226624 -1.762995477 -0.235450777 AVS(ph)PAPQSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 AVSPAPQSSSR 11 0 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 AVS(1)PAPQSSSR;AVS(1)PAPQSSSR;AVS(1)PAPQSSSR;AVS(1)PAPQSSSR;AVS(1)PAPQSSSR;AVS(1)PAPQSSSR;AVS(1)PAPQSSSR 121.86 0.00042244 11455201000 7274577 8351788 8030549 7967490 8806641 6312354 8799878 7776944 8286695 TRUE FALSE 6819274.211 8970163.074 8221037.415 8171949.282 8115002.94 8134628.127 7480417.988 8747912.578 6903592.07 0.987786379 1.299347207 1.190834761 1.183724241 1.175475442 1.178318192 1.083554461 1.26715375 1 22.71891579 -4.358464484 0.309922242 3.35E-11 1.187121939 0.24342492 0.088649119 245.1527242 3.261366773 157.8948751 0.077660654 4.38E-05 4.358464484 1.187121939 AVS(ph)PAVPFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AVSPAVPFSR 10 0 I3L2J0 I3L2J0 CIC 1 AVS(1)PAVPFSR;AVS(1)PAVPFSR;AVS(1)PAVPFSR;AVS(1)PAVPFSR 179.94 2.15E-06 814330000 1050210 1221470 1188830 1127220 1190860 1009480 1294090 975870 1169140 TRUE FALSE 984479.2308 1311908.91 1217029.609 1156146.374 1097334.659 1300900.488 1100053.218 1097709.518 974002.9811 1.01075587 1.346924943 1.249513228 1.187004964 1.126623512 1.335622697 1.129414632 1.127008376 1 19.89356666 1.07222587 1.410219502 1.003869977 1.225436334 0.28132421 0.099887171 0.446104407 1.794613625 0.087449634 0.026394475 11.80934663 -1.07222587 0.221566357 AVS(ph)PLDPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVSPLDPSK 9 0 Q14865;Q14865-2 Q14865 ARID5B AT-rich interactive domain-containing protein 5B 1 AVS(0.988)PLDPS(0.012)K 91.313 0.011368 84362000 452800 314570 384930 327530 333560 276340 431970 314670 333530 TRUE FALSE 424460.0563 337861.0901 394060.7214 335934.9743 307363.5431 356114.872 367200.1087 353957.2422 277861.6883 1.52759475 1.215932618 1.418190193 1.209000695 1.106174604 1.281626388 1.321521189 1.273861266 1 18.0840074 -5 0.129877003 0.084189707 1.409962387 0.454609188 0.109222159 145.6145495 1.194413111 35.25792464 0.809957604 1.00E-05 5 1.32577268 AVS(ph)PLLLTTTNSSEGLSMGNYIGLINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVSPLLLTTTNSSEGLSMGNYIGLINR 27 0 P19525-2;P19525;C9JZT2 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 1 AVS(0.996)PLLLT(0.004)TTNSSEGLSMGNYIGLINR 147.39 8.68E-08 24057000 30056 32640 33225 29883 32127 31509 31115 27866 26293 TRUE FALSE 28174.84861 35056.69956 34013.11269 30649.84837 29603.87501 40605.13679 26449.59461 31345.13144 21904.52844 1.286256798 1.600431603 1.552789086 1.399247122 1.351495655 1.853732524 1.207494363 1.430988644 1 14.41894154 0.734726469 0.982376808 1.003651442 1.504110633 0.39756958 0.179610161 0.85303062 1.495279387 0.155444125 0.050674268 5.42908285 -0.734726469 0.500459191 AVS(ph)PPHLDGPPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AVSPPHLDGPPSPR 14 0 P29590-2;P29590-5;P29590-9;P29590-3;P29590-8;P29590;P29590-4;H3BVD2;H3BRN3;P29590-12;P29590-13;P29590-11;H3BT57;H3BUJ5 P29590-2;P29590-12 PML Protein PML 2 AVS(1)PPHLDGPPS(1)PR;AVS(1)PPHLDGPPS(1)PR;AVS(1)PPHLDGPPS(1)PR;AVS(1)PPHLDGPPS(1)PR 127.37 4.22E-05 1629460000 1618910 1718570 1781560 1702030 1649180 1659090 1951330 1551340 1526380 TRUE FALSE 1517585.313 1845814.711 1823819.445 1745706.971 1519660.055 2138042.35 1658746.182 1745028.214 1271617.317 1.193429259 1.451548894 1.434251814 1.372824157 1.195060837 1.681356742 1.304438182 1.372290382 1 20.27823314 0.452705838 1.745561491 1.00007953 1.393373242 0.413763711 0.139554925 3.843440151 11.2421293 0.119405278 0.033565391 2.835997464 -0.452705838 0.393293713 AVS(ph)PSNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVSPSNPK 8 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 AVS(0.997)PS(0.003)NPK 144.55 0.00061218 3039200000 2033400 1649200 1885000 1496500 1808200 1599300 1885300 1668300 2491400 TRUE FALSE 1906133.124 1771308.484 1929713.09 1534902.724 1666191.266 2060991.948 1602616.767 1876590.927 2075569.245 0.918366433 0.853408523 0.929727156 0.739509283 0.802763517 0.992976723 0.772133607 0.904133135 1 20.98507563 0.985963562 24.04875541 1.000000009 0.860066698 0.261291225 0.075653316 623.1098208 1067582.684 0.067293111 0.016823278 9.68196619 -0.985963562 -0.139933311 AVS(ph)WTFSEENVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVSWTFSEENVIR 13 0 Q9Y320-2;Q9Y320 Q9Y320-2 TMX2 Thioredoxin-related transmembrane protein 2 1 AVS(0.999)WT(0.001)FSEENVIR 91.441 0.0068503 29342000 27500 34187 31499 25262 44640 21477 29760 27815 41801 TRUE FALSE 25778.82409 36718.24105 32246.17115 25910.26569 41134.15447 27677.06125 25297.76428 31287.76398 34824.14306 0.740257242 1.054390369 0.925971706 0.744031681 1.181196459 0.79476647 0.726443268 0.898450363 1 15.08780023 AVSDWIDEQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 188.28 0.001724 0 223324 154015 173726 168507 161847 144467 208555 144651 177900 FALSE TRUE 209346.5495 165418.4309 177846.8628 172831.1749 149136.1895 186172.2777 177284.1139 162710.9958 148207.3407 1.412524835 1.116128459 1.199986869 1.166144498 1.006267225 1.256160975 1.196189831 1.097860571 1 17.17725738 7.99998573 0.019238169 4.81E-08 2.645698793 0.358847152 0.096592152 4639.503478 6.879752442 354.7011433 627.2343418 99996714.24 -7.99998573 2.645698745 AVSEDVSNGSSGS(ph)PSPGDTLPWNLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVSEDVSNGSSGSPSPGDTLPWNLGK 26 0 Q15149-3;Q15149-2;H0YDN1;E9PMV1 Q15149-3 PLEC Plectin 1 AVSEDVSNGSS(0.002)GS(0.711)PS(0.287)PGDTLPWNLGK 207.69 1.62E-25 102990000 177450 153030 167560 186000 198270 151270 217080 156680 170090 TRUE FALSE 166343.7213 164360.5004 171534.6023 190773.0749 182698.674 194939.1933 184530.8693 176241.8429 141700.8802 1.173907467 1.159911641 1.210540133 1.346308327 1.289326317 1.375709121 1.302256338 1.243759691 1 17.11248919 3.428932627 6.000516526 1.285482914 1.175488878 0.088170377 0.103098661 0.276204517 22.8481503 0.025216216 0.034739833 2684.927898 -3.428932627 -0.109994035 AVSEDVSNGSSGSPS(ph)PGDTLPWNLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVSEDVSNGSSGSPSPGDTLPWNLGK 26 0 Q15149-3;Q15149-2;H0YDN1;E9PMV1 Q15149-3 PLEC Plectin 1 AVSEDVSNGSSGS(0.498)PS(0.502)PGDTLPWNLGK 213.41 1.92E-26 91883000 150620 152120 155990 168030 176100 129650 214100 142330 152640 TRUE FALSE 141192.9631 163383.1231 159690.1565 172341.9343 162269.8164 167077.8503 181997.6926 160100.2138 127163.3979 1.11032707 1.284828227 1.255787114 1.355279405 1.276073296 1.313883185 1.431211305 1.259011763 1 16.95632395 4.756846473 3.611523828 1.296667613 1.085293624 0.140017028 0.112253169 0.476267444 10.92076418 0.024219842 0.278072129 57127.6649 -4.756846473 -0.211373989 AVSELDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVSELDAK 8 0 F8W8M5;E7EQI0;P07101-6;P07101-5;P07101-3;P07101-4;P07101-2;P07101 F8W8M5 TH Tyrosine 3-monooxygenase 0 ; 75.38 0.038541 785810000 504474 1438740 1140330 1261180 1278160 1211920 1110520 1158330 931860 FALSE TRUE 472899.8729 1545265.807 1167379.166 1293544.014 1177778.469 1561781.63 944007.8356 1302950.05 776326.546 0.609150718 1.990484307 1.503721819 1.666236999 1.517117347 2.011758632 1.215993245 1.678353081 1 19.56630409 -0.185716834 8.411285673 0.999999868 1.563945617 0.138103229 0.400631209 0 0 0.339048757 0.079914558 0.652053404 0.185716834 0.563945749 AVSGAIVAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVSGAIVAQR 10 0 Q9HB21;Q5RGS4;Q9HB21-2 Q9HB21;Q5RGS4 PLEKHA1 Pleckstrin homology domain-containing family A member 1 0 64.654 0.071319 153860000 29026 108650 57545 52029 94111 55280 60050 79651 54613 FALSE TRUE 27209.31447 116694.5591 58909.99457 53364.15222 86719.90169 71238.4386 51046.05998 89595.60268 45497.73749 0.598036649 2.564843122 1.29478954 1.172896833 1.906026683 1.565757828 1.121947218 1.969232046 1 15.47350718 -2.902866928 0.229051877 1.59E-12 1.652617675 0.047662143 0.550925644 135.2402136 3.192545243 67.5194854 0.951499064 0.001250642 2.902866928 1.652617675 AVSHLVTWQDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVSHLVTWQDGR 12 0 A0A0B4J2A0;Q9UHJ6 A0A0B4J2A0 TRPV1;SHPK Sedoheptulokinase 0 178.1 2.24E-05 413500000 200850 276170 240690 232630 289790 218150 238830 258200 286960 FALSE TRUE 188279.157 296617.9142 246399.2805 238599.6796 267031.0624 281126.3636 203019.6587 290436.8384 239064.5222 0.787566283 1.240744178 1.030681082 0.998055577 1.116983231 1.175943469 0.849225376 1.214888917 1 17.86704052 -4.77283881 0.307625179 0.575221241 1.060088077 0.003701183 0.14824734 1651.030094 17.24140308 451.5942486 0.130330695 1.69E-05 4.77283881 0.484866836 AVSPPHLDGPPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AVSPPHLDGPPSPR 14 0 P29590-2;P29590-5;P29590-9;P29590-3;P29590-8;P29590;P29590-4;H3BVD2;H3BRN3;P29590-12;P29590-13;P29590-11;H3BT57;H3BUJ5 P29590-2;P29590-12 PML Protein PML 1 AVSPPHLDGPPS(1)PR;AVSPPHLDGPPS(1)PR;AVSPPHLDGPPS(1)PR;AVSPPHLDGPPS(1)PR 176.94 1.39E-06 1365770000 462047 567618 497246 521620 520063 463300 567446 457096 433705 TRUE FALSE 433128.303 609645.0273 509040.9099 535005.6523 479219.3498 597047.189 482362.7402 514165.4418 361316.8337 1.198749304 1.687286532 1.408849139 1.480710563 1.326313377 1.652420074 1.335013194 1.42303207 1 18.46290495 0.1159034 0.739415078 0.987303189 1.474428688 0.464133161 0.146948607 3.035516886 1.905626715 0.229076295 0.046018418 1.30588039 -0.1159034 0.487125499 AVSPPHLDGPPS(ph)PRS(ph)PVIGSEVFLPNSNHVASGAGEAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVSPPHLDGPPSPRSPVIGSEVFLPNSNHVASGAGEAEER 40 1 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 2 AVS(0.002)PPHLDGPPS(0.997)PRS(0.997)PVIGS(0.004)EVFLPNSNHVASGAGEAEER 54.781 0.012893 47556000 7218.8 9586.6 10525 7869.4 10056 6761.4 9887.3 7255.8 12610 TRUE FALSE 6766.988194 10296.40184 10774.65797 8071.342127 9266.242324 8713.306418 8404.791154 8161.702602 10505.30954 0.644149339 0.980114085 1.025639267 0.768310738 0.882053241 0.829419294 0.800051738 0.776912148 1 13.35883105 3.223474569 24.99988833 0.831661513 0.924380666 0 0.120545678 497.4184583 824296.8432 0.03317194 0.039794108 1672.917673 -3.223474569 0.092719153 AVSRLS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AVSRLSR 7 1 O43665 O43665 RGS10 Regulator of G-protein signaling 10 1 AVSRLS(1)R;AVSRLS(1)R;AVSRLS(1)R 83.647 0.0134 1563620000 961940 1157000 906280 895300 880210 606920 925030 636260 1283180 TRUE FALSE 901733.8925 1242665.484 927777.3896 918274.9137 811081.8572 782127.9515 786330.3391 715698.4616 1069008.968 0.843523225 1.162446266 0.867885506 0.858996455 0.758723155 0.731638344 0.73556945 0.669497154 1 20.02784253 3.370447425 1.57442832 0.75968707 1.022803855 0.339230083 0.117650465 0.299875491 1.521817031 0.034331701 0.056080599 2346.645165 -3.370447425 0.263116785 AVSTGLPHMIQELQNHIHDEGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVSTGLPHMIQELQNHIHDEGLR 23 0 A0A0A0MTN0;Q13617;Q13617-2;Q5T2B5 A0A0A0MTN0 CUL2 Cullin-2 0 ; 267.57 9.65E-45 234640000 94883 142638 125094 125951 138977 121370 135132 114759 132063 FALSE TRUE 88944.4424 153199.0659 128061.2888 129183.1159 128062.307 156407.5487 114870.2111 129086.9138 110020.8321 0.808432737 1.392455074 1.163973097 1.174169595 1.163982353 1.421617576 1.044076916 1.173295196 1 16.74741719 0.946429537 1.3297234 1.006733715 1.200617462 0.066999601 0.171723393 1.078351138 3.858132767 0.145234563 0.043974643 8.839537385 -0.946429537 0.193883747 AVSTVVVTTAPS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVSTVVVTTAPSPK 14 0 Q6P4R8-3;Q6P4R8;Q6P4R8-2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 AVSTVVVTT(0.007)APS(0.993)PK 243.9 1.54E-17 67096000 155160 101770 112340 129050 137720 96261 161120 102810 192720 TRUE FALSE 145448.8126 109305.1567 115004.7579 132361.6415 126904.0267 124049.988 136961.5518 115646.0548 160553.787 0.905919538 0.680800863 0.7163005 0.824406848 0.79041441 0.772638194 0.853057124 0.720294781 1 17.29269717 -4.999999996 0.239038051 2.289800911 0.750805144 0.456678372 0.070608418 141.440243 1.411893349 88.54452901 0.108162022 1.00E-05 4.999999996 -1.538995767 AVT(ph)PSSEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.498)PS(0.498)S(0.003)EAK;AVT(0.991)PS(0.009)SEAK;AVT(0.922)PS(0.078)SEAK;AVT(0.55)PS(0.17)S(0.28)EAK;AVT(0.99)PS(0.009)SEAK 168 0.00066573 2912650000 6582820 4938600 5733990 5233520 5883040 4541690 6840320 5088470 6303720 TRUE FALSE 6170813.047 5304259.083 5870002.951 5367820.984 5421009.769 5852802.175 5814677.518 5723776.681 5251588.408 1.175037449 1.010029475 1.117757618 1.022132842 1.032260975 1.114482271 1.107222628 1.08991342 1 22.32432242 2.221489879 24.99720708 1.09001089 1.067143133 0 0.057450207 954.6789339 1397954.979 0.01949638 0.014433026 166.5290017 -2.221489879 -0.022867757 AVT(ph)PVPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 AVTPVPTK 8 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 1 AVT(1)PVPTK;AVT(0.999)PVPT(0.001)K;AVT(1)PVPTK;AVT(1)PVPTK;AVT(1)PVPTK;AVT(1)PVPTK;AVT(1)PVPTK;AVT(1)PVPTK 144.77 0.0064847 25818810000 41098900 31594200 36914000 33284920 32984200 32901280 46543500 33313930 31682170 TRUE FALSE 38526593.21 33933467.44 37789617.51 34139067.4 30393753.98 42399345.43 39564734.26 37473247.49 26394211.15 1.459660718 1.285640523 1.43173885 1.293430109 1.151531061 1.606388052 1.498992868 1.419752509 1 24.65371821 AVT(ph)PVPTKTEEVSNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AVTPVPTKTEEVSNLK 16 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 1 AVT(1)PVPTKTEEVSNLK;AVT(1)PVPTKTEEVSNLK;AVT(0.994)PVPT(0.006)KT(0.001)EEVSNLK 210.92 1.36E-11 1567030000 4337750 3318730 3723370 3665280 4600440 2866420 5431420 3368810 7141470 TRUE FALSE 4066257.971 3564452.222 3811690.095 3759337.29 4239140 3693908.922 4617028.994 3789413.344 5949512.521 0.683460696 0.599116686 0.640672674 0.631873162 0.71251888 0.620875897 0.776034839 0.636928375 1 22.50434003 -5 0.210930952 2.658848766 0.611975709 0.815468463 0.050582604 52.82342707 0.52702098 36.97812409 0.094659959 1.00E-05 5 -2.046873057 AVT(ph)TPGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AVTTPGKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AVT(0.884)T(0.116)PGKK;AVT(0.5)T(0.5)PGKK;AVT(0.5)T(0.5)PGKK;AVT(0.752)T(0.248)PGKK 101.97 0.0084635 2675273000 10917930 6546320 8453180 7393140 8172250 4442710 10737150 6278670 13944360 TRUE FALSE 10234596.25 7031016.344 8653693.421 7582860.489 7530434.45 5725248.256 9127214.036 7062575.771 11616956.23 0.881004976 0.605237396 0.744919172 0.65274073 0.64822784 0.492835485 0.785680333 0.607954066 1 23.46972878 -1.140910932 4.973894299 1.000017317 0.675297009 0.472408416 0.107147171 1.82E-05 3.14E-06 0.091530004 0.021572679 0.072291805 1.140910932 -0.324720307 AVTEMNGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVTEMNGR 8 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YB86;Q4VXU2;A0A6I8PLA1;A0A6I8PS38;B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0YEU6 P11940-2;B1ANR0 PABPC1;PABPC3;PABPC1L;PABPC4 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3;Polyadenylate-binding protein 1-like;Polyadenylate-binding protein 4 0 94.806 0.035885 80018000 33737 47241 38856 42147 50644 40716 39529 39147 44105 FALSE TRUE 31625.46139 50738.77279 39777.68267 43228.56337 46666.62453 52470.04823 33601.99342 44034.58912 36743.59057 0.860706885 1.380887714 1.082574731 1.176492626 1.27006163 1.428005468 0.914499451 1.198429126 1 15.16520499 1.716848413 24.5785609 1.042384085 1.208966446 0.165586057 0.170646737 1.361748941 1534.316082 0.071769978 0.039798634 52.10128237 -1.716848413 0.166582361 AVTEQGAELSNEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AVTEQGAELSNEER 14 0 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;; 362.14 2.02E-82 2131300000 663803 769270 727700 771700 798790 725958 872900 660905 763550 FALSE TRUE 622256.7552 826227.5512 744961.3876 791503.1285 736056.2556 935530.2897 742016.7486 743420.4441 636108.5723 0.978224131 1.29887819 1.171123013 1.24428936 1.157123623 1.470708509 1.166493867 1.168700559 1 19.2789135 0.851072689 2.239731091 1.000925423 1.225748702 0.220446597 0.123700996 0.752294227 7.206104431 0.105465496 0.02874325 7.096965419 -0.851072689 0.224823279 AVTEQGHELSNEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 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 ;;;;;;;;;;; 327.62 5.78E-68 57622334000 21070612 22511747 21626969 22007613 23651819 19051412 24632322 21361451 24019490 FALSE TRUE 19751840.01 24178540.17 22139970.92 22572365.61 21794300.54 24551245.37 20938933.99 24028475.18 20010481.95 0.987074677 1.208293745 1.106418675 1.128027084 1.08914421 1.226919243 1.046398285 1.200794426 1 24.25425258 -1.276009568 3.478262041 0.99962395 1.127691505 0.213760699 0.074540908 12007443.68 20464079.67 49881.51905 0.015497978 0.052965177 1.276009568 0.128067555 AVTFS(ph)PDLGPVPHEGLGEYNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AVTFSPDLGPVPHEGLGEYNR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 AVT(0.001)FS(0.999)PDLGPVPHEGLGEYNR;AVT(0.003)FS(0.997)PDLGPVPHEGLGEYNR;AVT(0.157)FS(0.843)PDLGPVPHEGLGEYNR 238.07 4.53E-30 367810000 234793 264878 280478 285506 303015 242648 275383 220570 372102 TRUE FALSE 220097.7252 284489.8427 287131.0706 292832.5673 279217.4242 312696.5385 234091.8757 248108.65 309995.7723 0.710002345 0.917721686 0.926241892 0.944634067 0.900713652 1.008712268 0.755145381 0.800361399 1 18.24188901 -0.557808805 7.321954228 0.99998908 0.87968801 0.158614856 0.091601767 0 0 0.085613896 0.020179389 0.276816004 0.557808805 -0.12030107 AVTGYKDPYSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVTGYKDPYSGK 12 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 136.24 0.00010342 331570000 1763700 1618100 1778100 1787800 2026700 1406900 2452500 1671300 2166800 FALSE TRUE 1653313.165 1737905.808 1820277.372 1833677.975 1867531.157 1813049.191 2084770.393 1879965.484 1805147.082 0.915888341 0.962750252 1.008381749 1.015805301 1.034558999 1.004377543 1.154903339 1.041447261 1 20.78368496 3.918533354 0.551776868 1.070216352 0.893834824 0.485134464 0.043835532 1.409420041 0.606776281 0.027465255 0.145048635 8289.595775 -3.918533354 -0.176381528 AVTGYRDPYTGQSVSLFQALKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVTGYRDPYTGQSVSLFQALKK 22 2 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 153.36 1.94E-08 73157000 130260 166490 136890 139680 186610 105250 194300 144570 221170 FALSE TRUE 122107.2591 178817.0928 140137.0954 143264.4253 171954.4033 135633.9664 165166.5188 162619.8827 184255.2982 0.662706909 0.970485487 0.760559381 0.777532189 0.93323994 0.736119763 0.896400377 0.882579141 1 17.49134658 0.911546589 1.163943752 0.998674498 0.824234465 0.293518031 0.092226562 0.76476718 2.083639985 0.078523205 0.024592128 8.157302901 -0.911546589 -0.174440033 AVTIANS(ph)PSKPSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AVTIANSPSKPSEK 14 1 Q8NEF9 Q8NEF9 SRFBP1 Serum response factor-binding protein 1 1 AVTIANS(0.739)PS(0.261)KPSEK;AVTIANS(0.703)PS(0.295)KPS(0.002)EK;AVT(0.003)IANS(0.982)PS(0.015)KPSEK 209.7 3.80E-09 1402570000 3357720 1493540 2190070 1860640 1950670 1790210 2742870 1771400 1865530 TRUE FALSE 3147566.299 1604123.256 2242019.495 1908387.172 1797472.247 2307014.565 2331602.107 1992563.189 1554160.991 2.025251127 1.032147419 1.442591538 1.227921163 1.156554731 1.484411575 1.500232035 1.282082873 1 20.56770453 4.751966765 24.83156272 1.297987262 2.025251651 0.642075476 0.176760989 1418.02942 2626497.25 0.04143896 0.814472242 56489.37436 -4.751966765 0.727264389 AVTIANSPS(ph)KPSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVTIANSPSKPSEK 14 1 Q8NEF9 Q8NEF9 SRFBP1 Serum response factor-binding protein 1 1 AVTIANS(0.12)PS(0.879)KPSEK 142.58 5.67E-06 397880000 821700 394310 551270 477690 463130 412030 696130 458750 485190 TRUE FALSE 770271.2638 423505.1227 564346.3847 489948.3341 426757.638 530976.3723 591751.7691 516025.9473 404208.6546 1.905627836 1.047738879 1.396175907 1.212117377 1.055785504 1.313619504 1.463975999 1.276632604 1 18.62474069 4.749629386 24.92421073 1.24942397 1.905628231 0.657030239 0.15427499 1046.159152 2355652.694 0.03637287 0.55471547 56186.16444 -4.749629386 0.656204261 AVTLHDQGTAQWADLSSQFYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AVTLHDQGTAQWADLSSQFYLR 22 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 348.26 5.95E-96 3020189000 1587942 1669208 1626182 1547619 1779002 1224977 1660773 1514988 1407741 FALSE TRUE 1488555.545 1792797.897 1664755.805 1587333.524 1639286.359 1578607.974 1411755.507 1704137.587 1172779.933 1.269253935 1.52867375 1.419495473 1.353479437 1.397778316 1.34603938 1.203768471 1.453075329 1 20.16150089 -3.526190183 0.180130723 0.118517181 1.472915031 0.594087276 0.094153617 45.48945098 0.709591247 15.05079041 0.292762447 0.000297721 3.526190183 1.354397851 AVTNHSVYCSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AVTNHSVYCSTK 12 0 Q7Z4W1;J3KS22;J3QS36;J3QL34;J3QS45;J3KRZ4;J3KSZ5 Q7Z4W1 DCXR L-xylulose reductase 0 ;; 150.22 6.79E-05 1225410000 1271180 1637020 1345110 1338350 1786230 1206020 1563310 1594190 1774460 FALSE TRUE 1191619.113 1758226.664 1377016.644 1372694.327 1645946.701 1554178.396 1328906.179 1793228.131 1478291.163 0.806078764 1.189364253 0.931492171 0.92856831 1.113411717 1.051334429 0.898947523 1.21304123 1 20.49549902 2.747100594 24.57578153 1.036365287 0.996059997 0.082988187 0.12461685 2507.92364 7217155.238 0.036916744 0.038548384 558.5995665 -2.747100594 -0.04030529 AVTT(ph)PGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVTTPGK 7 0 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AVT(0.033)T(0.967)PGK;AVT(0.133)T(0.867)PGK 115.71 0.062803 1134870000 3905900 3317400 3374800 2933300 3931100 1767570 5267600 2644600 8558900 TRUE FALSE 3661436.691 3563023.748 3454851.85 3008573.444 3622367.263 2277838.765 4477772.282 2974784.131 7130364.297 0.513499246 0.499697294 0.484526695 0.421938251 0.508019943 0.319456155 0.627986467 0.41719946 1 22.76554436 -2.209528974 0.625889604 1.705580014 0.478301427 0.808885727 0.080202418 86.14556559 7.083129432 85.22308956 0.027656904 0.006172641 2.209528974 -1.227278587 AVTT(ph)PGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AVTTPGKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AVT(0.138)T(0.862)PGKK;AVT(0.124)T(0.876)PGKK;AVT(0.205)T(0.795)PGKK;AVT(0.021)T(0.979)PGKK 113.93 0.0029619 7782510000 18858400 11711800 14805300 13409600 15016300 8657430 18443400 10957000 24806700 TRUE FALSE 17678086.41 12578953.86 15156488.71 13753713.04 13836980.37 11156689.5 15677983.39 12325005.57 20666301.51 0.855406392 0.608669812 0.733391444 0.665514003 0.669543138 0.539849353 0.758625503 0.596381775 1 24.30077689 -1.262723737 3.952838654 1.000393711 0.676381193 0.561173691 0.089352519 98.21539154 40908804.73 27375.03821 0.018174458 0.054610514 1.262723737 -0.324012518 AVTTVTQSTPVPGPSVPPPEELQVS(ph)PGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AVTTVTQSTPVPGPSVPPPEELQVSPGPR 29 0 P51610-2;P51610;H7C1C4 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 1 AVTTVTQSTPVPGPSVPPPEELQVS(1)PGPR;AVTTVTQSTPVPGPSVPPPEELQVS(1)PGPR;AVTTVTQSTPVPGPSVPPPEELQVS(1)PGPR;AVTTVTQSTPVPGPSVPPPEELQVS(1)PGPR 152.75 1.66E-08 581410000 395866 413769 443310 467113 465990 413039 486310 381700 407970 TRUE FALSE 371089.4537 444404.8873 453825.5225 479099.9104 429393.0251 532276.6542 413392.3302 429356.0852 339877.1714 1.091834006 1.307545563 1.335263327 1.409626626 1.26337707 1.566085336 1.216299196 1.263268384 1 18.37465394 -0.372720814 7.670072788 0.999994377 1.315311247 0.376584818 0.123554984 0 0 0.108370342 0.025543135 0.423915392 0.372720814 0.31531687 AVVHTHLLNPEWLVNYFGSLSVEDSLECLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AVVHTHLLNPEWLVNYFGSLSVEDSLECLR 30 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 306.76 2.50E-82 1028718000 321050 547583 240204 217714 633799 298992 362204 580710 156272 FALSE TRUE 300956.0536 588126.6151 245901.7523 223300.9098 584022.9832 385306.1367 307894.8727 653212.9218 130189.1936 2.311682292 4.51747644 1.888803098 1.71520311 4.485955914 2.959586168 2.364980258 5.017412763 1 16.99025018 2.767077968 24.99155624 3.157536219 2.806574441 0.032705561 1.322944194 4353.713182 3815425.855 0.382327766 0.405454067 584.8950804 -2.767077968 -0.350961778 AVVIVDDR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 163.67 0.00077834 4549050000 5377570 6241880 6191980 6001620 6327760 5500660 6491830 5356750 6226320 FALSE TRUE 5040997.493 6704035.29 6338856.69 6155631.73 5830803.255 7088611.246 5518440.359 6025552.029 5187106.968 0.971832184 1.292442074 1.222040866 1.186717715 1.124095433 1.366582816 1.063876337 1.16164021 1 22.30649869 0.950317644 1.169087993 1.005060569 1.201405921 0.186100947 0.110913765 0.755555446 2.111841785 0.094310491 0.029592376 8.91903039 -0.950317644 0.196345352 AVVLPGGTATS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVVLPGGTATSPK 13 0 Q8N1G0;F8WCX2;Q8N1G0-2;H0Y5I5 Q8N1G0 ZNF687 Zinc finger protein 687 1 AVVLPGGTAT(0.38)S(0.62)PK 122.97 0.00024011 77400000 481920 297250 341970 324260 385260 299300 447640 339720 496160 TRUE FALSE 451757.4875 319258.6993 350081.6899 332581.0606 355003.2337 385703.0513 380520.5377 382134.7898 413347.6907 1.0929237 0.77237325 0.846942411 0.80460365 0.858848959 0.933120131 0.920582227 0.92448754 1 18.6569963 2.242111999 5.559309642 0.936433723 0.853703084 0.103663799 0.088652972 0.291165771 28.89344951 0.030185569 0.023628866 174.6272438 -2.242111999 -0.082730639 AVVMPLQLIQEQAAS(ph)PNAEIHILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVVMPLQLIQEQAASPNAEIHILK 24 0 H3BRB3;Q14807-2;Q14807;I3L306 H3BRB3 KIF22 Kinesin-like protein;Kinesin-like protein KIF22 1 AVVMPLQLIQEQAAS(1)PNAEIHILK;AVVMPLQLIQEQAAS(1)PNAEIHILK 260.58 3.27E-44 445130000 364150 311520 358450 367370 397530 319620 456590 320950 440610 TRUE FALSE 341358.5015 334585.2649 366952.6033 376797.3362 366309.5974 411889.1054 388128.5683 361021.314 367069.3446 0.929956442 0.911504243 0.999681964 1.026501782 0.997930235 1.122101618 1.057371241 0.983523466 1 18.48569311 3.64993822 1.213336293 1.0442614 0.915176893 0.553553636 0.039732886 0.324848816 0.938821061 0.012994997 0.03223139 4466.20054 -3.64993822 -0.129084507 AVVPSKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 81.32 0.044126 4006600000 1826900 5526600 2155900 2466100 9750600 2342100 3369200 6973000 8882100 FALSE TRUE 1712557.59 5935795.214 2207038.966 2529384.301 8984827.208 3018226.249 2864019.738 7843594.399 7399620.129 0.231438582 0.802175667 0.29826382 0.341826237 1.21422817 0.407889351 0.387049563 1.059999603 1 22.81901978 1.230179662 24.99421104 1.0300002 0.534324853 0.342279273 0.290212427 227.2781024 677776.9217 0.245345174 0.065386943 16.98946338 -1.230179662 -0.495675347 AVVS(ph)PPKFVFGSESVK ddPTM_SK-BR-3_Pertuzumab_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 170.38 3.21E-09 2795800000 3290900 1940410 2551010 2379660 2404080 1750020 3323200 2122850 2904300 TRUE FALSE 3084928.443 2084079.975 2611521.162 2440726.104 2215273.254 2255222.365 2824917.011 2387892.495 2419553.568 1.274999027 0.861348971 1.079340089 1.008750596 0.915571072 0.932082015 1.167536462 0.986914498 1 21.20630945 1.756542457 25 1.068065049 0.998563799 0.008893162 0.122153536 20.59041183 28656.27689 0.05135934 0.02848144 57.08768834 -1.756542457 -0.069501251 AVVSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AVVSQR 6 0 P14625 P14625 HSP90B1 Endoplasmin 0 99.384 0.090404 98648000 69446 81902 75013 77451 84309 76608 83548 69665 66210 FALSE TRUE 65099.49882 87966.1093 76792.34378 79438.52378 77687.71123 98723.48597 71020.75302 78362.8286 55159.12327 1.180212719 1.594769896 1.392196598 1.440170167 1.408429044 1.789794328 1.28756131 1.420668494 1 15.75131191 0.5618751 1.358452779 1.000885405 1.462903311 0.415035414 0.163674973 1.547100178 3.780292894 0.139201213 0.041161046 3.646490617 -0.5618751 0.462017906 AVVVS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AVVVSPK 7 0 O75909;G3V5E1;O75909-1 O75909 CCNK Cyclin-K 1 AVVVS(1)PK;AVVVS(1)PK;AVVVS(1)PK 98.044 0.012118 2236360000 8194700 5014000 6267900 5722000 5290600 5074200 8711400 5152900 5385300 TRUE FALSE 7681808.355 5385241.777 6416577.548 5868836.207 4875097.617 6539039.167 7405206.443 5796250.908 4486458.64 1.712220923 1.200332425 1.430209897 1.308122214 1.086624888 1.457505728 1.650568307 1.291943462 1 22.09714568 AVVVS(ph)PKEENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AVVVSPKEENK 11 1 O75909;G3V5E1;O75909-1 O75909 CCNK Cyclin-K 1 AVVVS(1)PKEENK;AVVVS(1)PKEENK;AVVVS(1)PKEENK 134.21 8.82E-05 1161920000 3241050 1605980 1979160 2202210 2424210 1021800 2247860 1571480 3414040 TRUE FALSE 3038198.466 1724888.43 2026106.61 2258722.437 2233822.325 1316777.072 1910814.261 1767682.737 2844214.668 1.068202938 0.606455079 0.71236065 0.794146258 0.785391606 0.462966838 0.671824909 0.621501168 1 21.43959893 -1.311277901 3.468390057 1.001234948 0.696626275 0.235494362 0.158005867 32579419.34 48918748.21 417210.6762 0.036043591 0.048833978 1.311277901 -0.304608673 AVYDEQGTVDEDSPVLTQDRDWEAYWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AVYDEQGTVDEDSPVLTQDRDWEAYWR 27 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 ;;;; 384.46 4.32E-145 2068683000 444471 533561 528260 483660 527961 441383 518297 463275 571619 FALSE TRUE 416652.3535 573066.4116 540790.5767 496071.5344 486497.0728 568803.1068 440583.1765 521115.9035 476212.0961 0.874930219 1.203384829 1.135608652 1.041702927 1.02159747 1.194432295 0.925182666 1.094293715 1 18.86124474 1.731160716 25 1.004332024 1.095972311 0.083214441 0.102478046 1.303877664 4377.85843 0.044554571 0.024707774 53.84690127 -1.731160716 0.091640287 AVYHNMPLIWKPGYLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVYHNMPLIWKPGYLDR 17 1 Q92552;Q92552-2;G5EA06;D6RH20 Q92552 MRPS27 "28S ribosomal protein S27, mitochondrial" 0 ; 90.754 0.0022378 328730000 402420 465420 407670 378800 596620 288580 370020 482290 586800 FALSE TRUE 377233.2505 499880.1811 417340.1249 388520.6493 549763.8718 371888.3613 314538.9361 542504.9682 488859.2891 0.771660187 1.022544098 0.853701943 0.794749446 1.124585099 0.760726797 0.643414052 1.109736442 1 18.89905974 AVYLGELPHDQDVVEYIMNQPNVVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AVYLGELPHDQDVVEYIMNQPNVVPR 26 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ; 290.78 3.12E-70 244938000 299110 369710 328510 388320 345480 288540 371070 288250 220192 FALSE TRUE 280389.239 397083.7131 336302.4123 398284.9486 318347.3944 371836.8139 315431.4983 324238.647 183440.5327 1.528502098 2.164645442 1.833304818 2.171193807 1.735425588 2.027015559 1.719529995 1.767540915 1 17.48495292 0.298967165 0.704755864 0.97870311 1.940782088 0.659489397 0.198525391 1.324585187 0.904164899 0.233933334 0.062856156 1.99052284 -0.298967165 0.962078977 AWDDFFPGSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 AWDDFFPGSDR 11 0 F8WF90;C9JQU6;F8WF33;O75915 F8WF90 ARL6IP5 PRA1 family protein 3 0 ;;;;;;; 195.36 2.54E-07 849649000 680883 813608 652497 657213 850302 634803 829509 768625 901846 FALSE TRUE 638267.7484 873848.3829 667974.537 674078.1982 783522.7109 818060.3209 705131.8262 864589.5232 751322.0765 0.849526147 1.163080935 0.889065499 0.897189394 1.042858629 1.088827743 0.938521372 1.150757512 1 19.51907197 AWEEYYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AWEEYYK 7 0 A0A087WTP3;Q92945;M0R3J3;M0R251;M0QYG1;M0R263;M0R0C6;Q96AE4;E9PEB5;Q96AE4-2 A0A087WTP3;Q96AE4 KHSRP;FUBP1 Far upstream element-binding protein 2;Far upstream element-binding protein 1 0 ;;; 148.07 0.0049062 2874640000 3311150 3611820 2978880 2887510 3944980 2051480 3274950 3556890 3901130 FALSE TRUE 3103911.032 3879242.911 3049540.44 2961608.395 3635157.184 2643708.973 2783901.651 4000975.546 3250006.201 0.955047726 1.193610926 0.938318345 0.911262383 1.118507769 0.813447363 0.856583489 1.23106705 1 21.63201104 3.796360324 5.716969159 0.961593497 1.086278899 0.059548446 0.134823739 0.397072517 23.90199167 0.032847878 0.059720214 6256.915998 -3.796360324 0.124685402 AWEVDTCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AWEVDTCR 8 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 134.08 0.0020747 768640000 498210 540930 470903 498200 614840 417997 608770 490769 535860 FALSE TRUE 467027.9254 580981.02 482073.0415 510984.6555 566552.9465 538665.9483 517490.59 552042.59 446421.5042 1.046159114 1.301418087 1.079860708 1.144623748 1.269098691 1.206630826 1.159197272 1.236594978 1 18.768047 -0.635062697 7.645179047 1.00000285 1.183229126 0.339143459 0.07907724 0 0 0.069096449 0.016286189 0.231706012 0.635062697 0.183226276 AWGGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AWGGKK 6 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 92.279 0.07526 6302900000 7271200 11403000 12827000 17366000 15103000 12849000 21701000 11068000 19284000 FALSE TRUE 6816108.571 12247289.98 13131262.5 17811640.96 13916871.3 16558297.71 18447136.51 12449864.16 16065375.82 0.42427321 0.762340708 0.817364165 1.108697435 0.866264908 1.030682251 1.148254278 0.774950073 1 23.93745139 4.929080041 0.678427837 1.00753826 8.46E-19 0.670212158 0.120768239 2.188099714 0.635641953 0.046380666 1.800604829 84933.69949 -4.929080041 -1.00753826 AWIHTEDNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AWIHTEDNK 9 0 Q13952-3;Q13952;E9PL11;Q5T6K7;E9PI99;A0A0A0MT00;Q5T6K5;Q13952-6;Q13952-7;Q13952-2;Q13952-5 Q13952-3 NFYC Nuclear transcription factor Y subunit gamma 0 124.23 0.00053548 115700000 498360 324610 409290 397960 407120 303150 495790 355680 365300 FALSE TRUE 467168.5372 348644.4622 418998.5521 408172.3273 375146.4374 390664.4838 421450.8922 400087.4309 304329.0701 1.535076939 1.145616691 1.376794376 1.341220302 1.232699976 1.283690985 1.384852561 1.314654005 1 18.21527262 -1.299317672 5.60175918 0.999962461 1.315906635 0.499718788 0.1022517 4.33E-05 5.41E-06 0.089366762 0.02106145 0.050197528 1.299317672 0.315944174 AWKPSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AWKPSSK 7 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 81.594 0.024421 1779990000 2478400 2436600 2302000 2146900 2953500 1930400 3028000 2615100 3245600 FALSE TRUE 2323281.368 2617008.399 2356604.527 2201993.089 2721544.024 2487675.143 2573979.511 2941600.992 2703888.393 0.859237154 0.967868499 0.871561316 0.81438017 1.006529719 0.920036178 0.951954791 1.087915093 1 21.36660417 1.437084562 3.596480402 1.042853268 0.910785051 0.478049301 0.058081126 0.191952283 4.49354298 0.040490531 0.014237657 27.35801366 -1.437084562 -0.132068217 AWLDEDSNLS(ph)PSPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AWLDEDSNLSPSPLR 15 0 Q9C086;B8ZZ93;B8ZZH7;F8WCL7;J3KQ70 Q9C086 INO80B;INO80B-WBP1 INO80 complex subunit B 1 AWLDEDSNLS(0.993)PS(0.007)PLR;AWLDEDSNLS(0.5)PS(0.5)PLR;AWLDEDS(0.004)NLS(0.987)PS(0.008)PLR;AWLDEDS(0.026)NLS(0.935)PS(0.039)PLR 278.89 1.29E-33 257042000 325132 351748 375824 340636 378334 329534 416174 307182 337441 TRUE FALSE 304782.5685 377791.7879 384738.7228 349377.2965 348621.1738 424665.1163 353772.5723 345534.3489 281119.9171 1.084172803 1.343881258 1.3685929 1.242805206 1.240115525 1.5106191 1.258440084 1.229135069 1 18.10082615 0.835169379 2.169660626 1.00077175 1.31033258 0.407882048 0.109235754 0.547984935 4.765613662 0.096372046 0.026377333 6.841784319 -0.835169379 0.30956083 AWLDEDSNLSPS(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AWLDEDSNLSPSPLR 15 0 Q9C086;B8ZZ93;B8ZZH7;F8WCL7;J3KQ70 Q9C086 INO80B;INO80B-WBP1 INO80 complex subunit B 1 AWLDEDSNLSPS(1)PLR;AWLDEDSNLSPS(1)PLR;AWLDEDSNLSPS(1)PLR;AWLDEDSNLSPS(1)PLR;AWLDEDSNLSPS(1)PLR 302.62 2.10E-44 714659000 885670 925830 953020 825180 915030 927230 1078370 884000 761820 TRUE FALSE 830237.4957 994379.4165 975626.0844 846355.5158 843167.2349 1194906.249 916678.4296 994369.3459 634667.3205 1.308145967 1.566772677 1.53722439 1.333541981 1.328518434 1.882728494 1.444344777 1.566756809 1 19.27564103 -1.019458539 6.458806679 0.999999764 1.508697414 0.460234575 0.168312772 5.27E-07 8.00E-08 0.150141998 0.035388792 0.095618397 1.019458539 0.50869765 AWLDEDSNLSPS(ph)PLRDLSGGLGGQEEEEEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AWLDEDSNLSPSPLRDLSGGLGGQEEEEEQR 31 1 Q9C086;B8ZZ93;B8ZZH7;F8WCL7;J3KQ70 Q9C086 INO80B;INO80B-WBP1 INO80 complex subunit B 1 AWLDEDS(0.003)NLS(0.041)PS(0.956)PLRDLSGGLGGQEEEEEQR;AWLDEDSNLS(0.034)PS(0.965)PLRDLSGGLGGQEEEEEQR;AWLDEDS(0.031)NLS(0.025)PS(0.943)PLRDLS(0.002)GGLGGQEEEEEQR 212.44 8.09E-27 195366000 56631 69176 61703 64483 76500 51899 80122 65676 110781 TRUE FALSE 53086.5668 74297.86302 63166.6243 66137.74295 70491.99859 66881.39879 68108.44992 73875.79317 92290.93543 0.575208893 0.805039657 0.684429343 0.716622306 0.763801973 0.72468004 0.737975508 0.800466404 1 16.49390134 -5 0.211094723 2.327375643 0.690609846 0.718038279 0.057256563 77.17677841 0.770058593 43.24784866 0.110230265 1.00E-05 5 -1.636765797 AWNDIKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AWNDIKK 7 1 P36578;H3BM89;H3BTP7 P36578 RPL4 60S ribosomal protein L4 0 ; 103.74 0.013322 2584700000 6341500 5559700 5593800 5223900 6563900 3528800 7054500 5484500 8628700 FALSE TRUE 5944596.835 5971345.973 5726487.578 5357954.118 6048397.771 4547507.275 5996743.216 6169251.898 7188514.226 0.82695765 0.830678745 0.796616296 0.74534931 0.841397482 0.632607397 0.834211775 0.858209597 1 22.77726218 0.918012711 2.125315334 0.998649593 0.786387815 0.554864258 0.061268128 0.292792228 2.801441396 0.054498398 0.015029503 8.279663961 -0.918012711 -0.212261777 AWNPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AWNPFR 6 0 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ; 130.84 0.036268 815030000 720960 2227560 833950 852380 2138020 675730 877120 1718040 1894620 FALSE TRUE 675836.4006 2392490.86 853731.6878 874253.5139 1970108.534 870802.2814 745603.9988 1932541.076 1578395.682 0.428179327 1.515773825 0.540885722 0.553887421 1.248171517 0.551700877 0.472380916 1.224370478 1 20.59002748 3.831871183 9.286056956 0.753453539 1.045851091 0.015720598 0.385057089 0.70307825 57.1372242 0.091006038 0.164337775 6790.022031 -3.831871183 0.292397552 AWRDPDEPVLLEEPVVLALAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AWRDPDEPVLLEEPVVLALAEK 22 1 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ;;;;; 221.92 8.17E-26 1044267000 730897 792037 725298 737794 915177 548140 890835 698574 1123730 FALSE TRUE 685151.4615 850680.2436 742502.4111 756727.0431 843302.6901 706379.1197 757262.5619 785792.5017 936172.2034 0.731864778 0.908679237 0.793125889 0.80832035 0.900798685 0.754539728 0.80889238 0.839367478 1 19.8364144 0.831606724 5.627466691 0.999999447 0.821310737 0.5183527 0.055306151 3.029853202 100.9728387 0.048747035 0.012276578 6.785888577 -0.831606724 -0.17868871 AWSS(ph)QDEVSTNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AWSSQDEVSTNVR 13 0 A1L390-3;A1L390;A0A0U1RR71 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 AWS(0.007)S(0.993)QDEVSTNVR;AWS(0.006)S(0.994)QDEVSTNVR 249.36 1.59E-17 406570000 355880 365640 337420 337180 273000 274890 458780 308250 402750 TRUE FALSE 333606.1061 392712.366 345423.7617 345832.6096 251559.6812 354246.2805 389990.1981 346735.691 335528.4231 0.994270777 1.170429505 1.029491804 1.030710324 0.749741792 1.055786205 1.162316428 1.033401844 1 18.35607546 0.977681759 23.13268817 0.999999979 1.043568474 0 0.115215709 5172.982298 5361776.224 0.113208073 0.028302018 9.499084665 -0.977681759 0.043568495 AWTVEQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AWTVEQLR 8 0 Q00688;G3V5F2 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ; 159.46 0.00083534 211830000 193382 497520 192837 208595 507900 144024 208593 417000 478850 FALSE TRUE 181278.5658 534356.8985 197411.1847 213947.9009 468011.5828 185601.3908 177316.4161 469063.3679 398926.8415 0.454415564 1.339485948 0.494855608 0.536308612 1.173176468 0.465251699 0.444483544 1.175813004 1 18.60576467 7.888867583 8.019602708 0.770341252 0.636090934 0 0.354822008 0 0 0.074488165 0 77422569.85 -7.888867583 -0.134250317 AWVESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 AWVESR 6 0 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;;;; 121.87 0.045283 7789440000 8952690 10888690 9987690 9973760 11365560 8951820 10756730 9861390 9878850 FALSE TRUE 8392357.114 11694899.94 10224602.72 10229703.57 10472954.76 11536065.11 9143858.197 11092606.25 8230006.115 1.019726717 1.421007442 1.242356637 1.242976424 1.272533048 1.401707964 1.111039053 1.347824788 1 22.97246207 -1.227755659 3.860066003 0.999724329 1.265646597 0.30195031 0.12242313 34.33318497 28194317.4 13916.0893 0.025653739 0.059189455 1.227755659 0.265922268 AWVWNTHADFADECPKPELLAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AWVWNTHADFADECPKPELLAIR 23 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;; 277.75 4.97E-52 1982921000 1493446 1237560 1242887 1003902 1438365 1070978 1682895 1201437 1250604 FALSE TRUE 1399973.881 1329190.23 1272368.867 1029663.825 1325401.615 1380151.963 1430560.518 1351439.054 1041870.113 1.343712487 1.275773451 1.221235594 0.988284251 1.272137091 1.324687161 1.373069925 1.297128152 1 19.990744 2.496328192 24.75816732 1.292281182 1.211923304 0 0.1352262 1845.620819 2379047.862 0.041840256 0.038870351 313.5654413 -2.496328192 -0.080357879 AWYPLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AWYPLGR 7 0 Q8TCJ2;P46977;A0A0C4DH80;E9PN73;E9PI32 Q8TCJ2;P46977 STT3B;STT3A Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B;Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A 0 136.19 0.019652 0 203330 256410 216660 174570 283790 171930 253470 257360 243080 FALSE TRUE 190603.9383 275394.8632 221799.2775 179049.7617 261502.2782 221563.3999 215464.5266 289491.9625 202508.3776 0.941215077 1.359918372 1.095259762 0.884159776 1.291315852 1.094094983 1.063978336 1.429530797 1 17.62762207 AYAQQLTEWAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AYAQQLTEWAR 11 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22;B0QYG7;B0QYG8 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 194.94 0.0019825 0 90439 84585 74487 69573 114610 63427 81980 89858 119910 FALSE TRUE 84778.58443 90847.76141 76253.86682 71358.36097 105608.9929 81737.34525 69687.86007 101076.9691 99896.24635 0.848666367 0.909421172 0.763330652 0.714324748 1.057186799 0.818222388 0.697602389 1.011819491 1 16.60814285 1.208504477 24.94309768 1.005910265 0.827805238 0.339310119 0.102122762 264.7807206 219730.8735 0.095739851 0.023947887 16.16234888 -1.208504477 -0.178105027 AYDATHLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AYDATHLVK 9 0 P10768;X6RA14;U3KQT1;H7BZT7 P10768 ESD S-formylglutathione hydrolase 0 ; 120.12 0.0007167 244470000 681860 907100 811460 798770 938200 672700 933550 824160 1001760 FALSE TRUE 639183.5998 974262.6278 830708.2144 819267.7905 864517.5565 866897.5696 793572.8442 927058.1902 834559.7844 0.765893123 1.167397047 0.995384908 0.981676575 1.035896496 1.038748315 0.950887952 1.110834967 1 19.67065588 4.75808145 24.6853364 1.032833615 0.765892833 0.641053921 0.063288131 2566.474454 3245408.321 0.015059376 0.560035824 57290.34663 -4.75808145 -0.266940782 AYEDGCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AYEDGCK 7 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 108.09 0.039207 0 474290 397150 414250 414870 466820 390440 548050 400690 477510 FALSE TRUE 444605.0355 426555.3992 424076.2056 425516.2666 430157.8403 503153.6897 465874.9903 450717.0285 397810.4962 1.117630228 1.072257779 1.066025682 1.06964565 1.081313451 1.264807476 1.171097784 1.13299431 1 18.60172182 2.425475006 24.99986874 1.163310665 1.077123968 0.138115887 0.066495807 119.7206396 57951.22789 0.020605093 0.017239461 266.3636795 -2.425475006 -0.086186697 AYEFAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 182.95 0.0015117 3521960000 3644040 5163690 4140650 4479350 5552020 3611730 4911690 4773020 5229230 FALSE TRUE 3415966.041 5546014.98 4238868.173 4594297.705 5115986.745 4654377.819 4175227.682 5368942.054 4356437.731 0.784119102 1.27306192 0.973012455 1.05459965 1.17435094 1.06839076 0.958404077 1.232415654 1 22.05471749 4.764687975 24.32858484 1.085159244 0.784118533 0.450843626 0.106488381 5816.728896 5416139.617 0.024150999 1.852691713 58168.51477 -4.764687975 -0.301040711 AYEKPPEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AYEKPPEKK 9 2 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 67.153 0.034706 552930000 1339000 965860 1152400 1264500 1372400 909470 1691200 1202500 2353600 FALSE TRUE 1255194.38 1037373.279 1179735.472 1296949.211 1264617.24 1172019.225 1437620.26 1352634.772 1960768.955 0.640154148 0.529064517 0.601669804 0.661449279 0.644959844 0.597734487 0.733192076 0.689849137 1 20.90298812 -1.225143389 0.2396112 1.292052789 0.55105863 0.890437822 0.041885841 5.237010376 0.264604875 1.034386685 0.07334042 0.059546551 1.225143389 -0.740994159 AYGELPEHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 131.28 0.0002542 10777200000 22771500 20018500 20530200 20176500 22057900 16157700 24832000 18939100 23422000 FALSE TRUE 21346272.46 21500690.57 21017186.04 20694263.15 20325561.51 20822165.69 21108672.13 21303688.33 19512716.89 1.09396721 1.101880927 1.077101982 1.060552627 1.041657173 1.067107457 1.081790519 1.091784832 1 24.21791133 3.622290378 2.198258791 1.062646348 1.097314913 0.294982016 0.025086021 0.405860201 3.871721237 0.006744589 0.012267708 4190.73673 -3.622290378 0.034668566 AYHEQLSVAEITNACFEPANQMVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AYHEQLSVAEITNACFEPANQMVK 24 0 P68363;P68363-2;C9JDS9;P68366-2;P68366 P68363;P68366-2 TUBA1B;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 ;; 278.52 3.96E-52 898480000 608710 551779 595246 540658 645570 481235 773410 578650 755770 FALSE TRUE 570611.9277 592633.2913 609365.5162 554532.1996 594869.5363 620159.7323 657444.3505 650895.7263 629627.1045 0.906269637 0.941244884 0.967819701 0.880731143 0.944796582 0.984963525 1.044180509 1.033779711 1 19.26413812 2.06952806 2.811883159 1.029314304 0.932792675 0.75208497 0.025773771 0.134092311 2.08594864 0.012073718 0.007487519 117.3621507 -2.06952806 -0.096521629 AYHLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AYHLQK 6 0 P61927;D6RG19;D6R9X9 P61927 RPL37 60S ribosomal protein L37;Ribosomal protein L37 0 ;; 142.27 0.011547 2830210000 5338970 9406040 5191750 5275030 9778680 3905870 6259920 8543430 9029010 FALSE TRUE 5004813.398 10102472.99 5314900.762 5410396.2 9010701.918 5033431.262 5321303.11 9610096.042 7522009.901 0.665355864 1.343054997 0.706579868 0.719275336 1.197911467 0.669160414 0.707431016 1.277596835 1 22.84268677 5.015137973 20.66354328 0.926855476 0.128141029 0.104797528 0.254127639 5001.072357 129264.1894 0.056952488 130262.5637 103547.1078 -5.015137973 -0.798714447 AYIDSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AYIDSFR 7 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ;; 164.89 0.0027471 517270000 1171060 1662580 1320790 1310080 1647730 1117950 1410420 1423040 1382810 FALSE TRUE 1097765.445 1785679.153 1352119.763 1343698.871 1518323.932 1440684.017 1198940.615 1600709.676 1152010.078 0.952913057 1.550055149 1.173704804 1.166395066 1.317977995 1.250582824 1.040737957 1.389492772 1 20.13572191 -4.999942418 0.164850782 0.064873191 1.304474614 0.103792132 0.173692084 235.5938456 2.196061021 71.75399451 0.632107516 1.00E-05 4.999942418 1.239601423 AYINKVEELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AYINKVEELK 10 1 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ; 122.7 0.00043924 946390000 2418130 1691530 1795340 1717430 1871370 1130590 2259000 1728360 3170400 FALSE TRUE 2266783.56 1816772.641 1837926.313 1761502.161 1724400.149 1456972.979 1920283.922 1944149.551 2641239.758 0.858227108 0.687848438 0.695857431 0.666922477 0.652875281 0.551624658 0.727038852 0.73607462 1 21.33278384 0.68755738 1.962927934 0.999767822 0.684419187 0.62129874 0.075109286 0.87982713 4.632642713 0.06785403 0.018782409 4.87031869 -0.68755738 -0.315348635 AYINKVEELKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AYINKVEELKK 11 2 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ; 110.08 0.0010365 1068990000 2565700 1320130 1474330 1325870 1447890 897090 1823360 1247760 2478700 FALSE TRUE 2405117.417 1417873.799 1509301.804 1359894.069 1334178.56 1156065.32 1549964.095 1403545.583 2064988.957 1.164711999 0.686625366 0.730900666 0.658547865 0.646094767 0.559840921 0.750591954 0.679686726 1 20.97770264 -0.861145145 7.706230952 1 0.719568411 0.20443082 0.162122807 0 2.75E-10 0.142079897 0.033488553 0.137674927 0.861145145 -0.28043159 AYLLIEEDIRDLAASDDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AYLLIEEDIRDLAASDDYR 19 1 H7C1J2 H7C1J2 DNTTIP1 0 ;; 214.24 3.96E-19 69237000 92293.8 105275 122458.7 118443.3 123784 107944.8 143451.6 90058.6 66336 FALSE TRUE 86517.29581 113069.6705 125363.4782 121482.7556 114062.504 139106.7114 121942.3643 101302.6145 55264.09305 1.565524575 2.045987988 2.2684436 2.198222189 2.063953241 2.517126469 2.206538777 1.833063909 1 15.7540548 0.882526869 3.402700966 1.000622577 2.150379835 0.684325765 0.239414569 0.278563795 6.513915163 0.221545258 0.057352256 7.630040954 -0.882526869 1.149757258 AYLPVNESFGFTADLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AYLPVNESFGFTADLR 16 0 P13639 P13639 EEF2 Elongation factor 2 0 ; 260.7 1.97E-26 654340000 216297 282260 211860 225041 273140 220502 256960 223994 233410 FALSE TRUE 202759.3569 303158.8241 216885.4192 230815.9331 251688.6862 284157.3478 218431.2335 251960.144 194452.3631 1.042719942 1.559039033 1.115365305 1.18700503 1.294346246 1.461321134 1.123314883 1.295742258 1 17.56905724 -0.204968261 0.640524123 0.980395357 1.280071501 0.199175341 0.159127758 10.16366316 3.978100889 0.643940616 0.057136058 0.623780421 0.204968261 0.299676144 AYNYVAQEVDDYHAFQTLTHIYNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AYNYVAQEVDDYHAFQTLTHIYNK 24 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ; 288.91 2.49E-54 398100000 665960 775670 720620 781160 784560 557890 890280 684610 570720 FALSE TRUE 624278.7524 833101.4139 737713.4467 801205.8881 722943.8224 718943.7864 756790.779 770085.0655 475463.145 1.312990836 1.752189255 1.551568096 1.685106189 1.520504439 1.512091513 1.591691779 1.619652487 1 18.85897399 -1.555222329 2.84610776 0.968377255 1.583378702 0.697990496 0.117088253 29624672.98 29961587.68 7110551.099 0.025656636 0.027846952 1.555222329 0.615001447 AYPLADAHLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AYPLADAHLTK 11 0 A0A3B3IUA2;B1AHD1;P55769 A0A3B3IUA2 NHP2L1 "NHP2-like protein 1;NHP2-like protein 1, N-terminally processed" 0 ;;; 189.58 2.65E-06 1104800000 2410430 2985530 2466960 2305490 3289470 1859640 2900190 2935740 3536240 FALSE TRUE 2259565.489 3206581.748 2525477.456 2364652.777 3031128.295 2396487.879 2465333.434 3302273.601 2946018.699 0.766989527 1.088445823 0.857250993 0.802660478 1.0288897 0.813466622 0.836835637 1.120927577 1 21.49033516 1.238466352 24.99999585 1.06046381 0.897740946 0.319866848 0.105128182 3.125952728 826866.6243 0.07920482 0.024594478 17.31674862 -1.238466352 -0.162722864 AYQQKPYPS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AYQQKPYPSPK 11 1 A0A2R8YDI1;A0A2R8Y852;P39880-6;P39880-4;P39880-5;P39880-2;P39880;P39880-3 A0A2R8YDI1 CUX1 Homeobox protein cut-like 1 1 AYQQKPYPS(1)PK;AYQQKPYPS(1)PK 103.85 0.0016221 313560000 1340260 633590 859330 785740 878780 595300 1087190 744800 1294090 TRUE FALSE 1256375.519 680501.6628 879713.7134 805903.4187 809764.1636 767153.4461 924175.9525 837789.9195 1078098.019 1.165362979 0.631205745 0.815986764 0.747523328 0.751104398 0.711580425 0.857228134 0.777099953 1 20.04005692 -0.042682955 1.005711774 1.002207949 0.786901857 0.139933816 0.142219515 14.84967549 12.555891 0.241514807 0.038338086 0.906394048 0.042682955 -0.215306092 AYRPPS(ph)GEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AYRPPSGEK 9 1 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 AYRPPS(1)GEK;AYRPPS(1)GEK;AYRPPS(1)GEK;AYRPPS(1)GEK 117.79 0.00066259 1517898000 2683370 1935290 2018870 1978920 2107260 1693110 2654670 1807560 2383180 TRUE FALSE 2515422.662 2078580.885 2066758.55 2029702.438 1941764.3 2181883.372 2256626.878 2033237.845 1985411.862 1.26695257 1.046926799 1.040972198 1.022308004 0.978015865 1.098957558 1.136603906 1.024088696 1 20.92100689 4.739305583 24.69101727 1.051489974 1.266952648 0.694715746 0.046285442 33.51824298 1110675.876 0.011834229 0.070640375 54866.28853 -4.739305583 0.215462674 AYS(ph)FCGTVEYMAPEVVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 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(0.998)FCGT(0.002)VEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR;AYS(1)FCGTVEYMAPEVVNR 333.07 6.00E-75 3459506000 2286595 2378350 2197351 2301407 2484117 1774720 2909348 2025257 2530458 TRUE FALSE 2143481.101 2554445.509 2249473.203 2360465 2289024.471 2287052.854 2473118.276 2278114.795 2108108.212 1.016779446 1.211724092 1.067057749 1.119707701 1.085819247 1.084883992 1.173145791 1.080644144 1 21.00751749 0.985000824 23.49063526 0.999999995 1.116472391 0.273517207 0.054378468 444.8586178 696708.38 0.047583708 0.011895927 9.660527117 -0.985000824 0.116472396 AYS(ph)GSDLPSSSSGGANGTAGGGGGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AYSGSDLPSSSSGGANGTAGGGGGAR 26 0 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 AYS(0.982)GS(0.018)DLPSSSSGGANGTAGGGGGAR;AYS(0.996)GS(0.004)DLPSSSSGGANGTAGGGGGAR 347.96 7.94E-110 433496000 222753 243112 217368 267543 336440 237190 313690 229868 306230 TRUE FALSE 208811.2874 261112.2654 222524.0716 274408.6063 310017.3595 305662.9025 266655.0967 258567.5258 255118.2347 0.818488289 1.023495109 0.872238991 1.075613457 1.215190909 1.198122521 1.045221628 1.013520363 1 17.96080649 3.148280982 5.995922311 1.1052168 0.926092453 0.498440122 0.08696386 0.172855418 9.281323365 0.024771243 0.029868668 1406.957508 -3.148280982 -0.179124347 AYS(ph)PEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 AYSPEYR 7 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR;AYS(1)PEYR 126.41 0.0041482 18248780000 12086180 12660300 12785170 12034950 13141220 11668720 14071290 11577130 14056590 TRUE FALSE 11329727.57 13597681.79 13088440.27 12343787.19 12109161.59 15037290.04 11961430.7 13022560.16 11710454.32 0.967488302 1.161157493 1.117671434 1.05408269 1.034047122 1.284091089 1.021431822 1.112045682 1 23.48129371 0.40776311 1.313534198 1.00014926 1.103471199 0.092603062 0.087445825 6.669301746 12.65665152 0.075729901 0.022404786 2.55719066 -0.40776311 0.103321938 AYS(ph)PEYRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.992)PEY(0.008)RR 53.47 0.074372 0 157110 291800 173100 249780 326270 169620 279380 215020 703860 TRUE FALSE 147276.7655 313405.1756 177206.0137 256189.7777 300646.0703 218586.5404 237489.5626 241865.7203 586381.2189 0.251162146 0.53447342 0.302202745 0.436899698 0.512714358 0.372772069 0.405008815 0.412471806 1 19.16147937 -1.603483222 1.61561597 1.135255767 0.408729888 0.829626187 0.084927383 11435.06214 5547.893515 6438.319472 0.020713577 0.024918206 1.603483222 -0.726525879 AYSDHDDRWETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AYSDHDDRWETK 12 1 A0A2R8Y4Z8;Q9Y3X0 A0A2R8Y4Z8;Q9Y3X0 CCDC9 Coiled-coil domain-containing protein 9 0 ;; 247.67 6.98E-17 682270000 580723 617730 624690 656650 688970 505840 834410 562000 619300 FALSE TRUE 544376.5841 663467.3719 639507.9418 673500.7507 634861.0754 651867.7964 709297.9668 632166.9371 515934.8292 1.055126643 1.285951896 1.239513027 1.305398885 1.230506334 1.263469259 1.374782098 1.225284477 1 18.97682932 0.966865899 23.50816638 0.999999997 1.262764352 0.47532866 0.081375986 1804.080421 1279971.091 0.07321052 0.01830263 9.265436814 -0.966865899 0.262764355 AYSGS(ph)DLPSSSSGGANGTAGGGGGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AYSGSDLPSSSSGGANGTAGGGGGAR 26 0 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 AYS(0.005)GS(0.995)DLPSSSSGGANGTAGGGGGAR 270.05 2.46E-54 251810000 110600 117750 109290 136930 173570 119840 139430 111970 145280 TRUE FALSE 103677.7434 126468.3325 111882.4104 140443.8556 159938.5123 154435.8626 118523.7659 125949.701 121031.8295 0.856615519 1.044917962 0.924404852 1.160387778 1.321458273 1.275993788 0.979277653 1.040632878 1 16.88502698 3.235810768 24.99313663 1.13713157 0.96152703 0.353324155 0.118402973 85.87396569 780503.9673 0.035037715 0.043680505 1721.118482 -3.235810768 -0.17560454 AYSPELIVHPVLDSPNAVHEVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AYSPELIVHPVLDSPNAVHEVEK 23 0 Q8IW45-2;Q8IW45 Q8IW45-2 CARKD ATP-dependent (S)-NAD(P)H-hydrate dehydratase 0 ; 210.66 3.60E-25 126553000 146532 149636 149797 141575 173751 109371 179799 151117 187776 FALSE TRUE 137360.8237 160715.2051 153350.2556 145208.0542 160105.2973 140944.6322 152839.8091 169984.2901 156434.9725 0.878069791 1.027361098 0.980281155 0.928232683 1.023462304 0.900979045 0.977018161 1.086613098 1 17.25520355 1.356055397 7.829283692 1.042364187 0.966246925 0.304858792 0.052131033 0.281796512 17.63865874 0.032222945 0.011741448 22.70154403 -1.356055397 -0.076117263 AYSSFGGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AYSSFGGGR 9 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;; 168.66 0.00013739 1153730000 608110 953520 671800 691820 953280 594781 765370 769200 819500 FALSE TRUE 570049.4806 1024119.613 687735.4132 709573.2724 878413.2341 766484.6192 650609.8738 865236.3132 682720.1558 0.834967996 1.50005768 1.007345993 1.039332538 1.286637324 1.122692237 0.952967139 1.267336706 1 19.38093482 1.405201652 0.300748535 0.997795308 1.193476265 0 0.193925943 5.035743624 1.670122901 0.376846878 0.312834312 25.42152806 -1.405201652 0.195680957 AYSSFGGGRGS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AYSSFGGGRGSR 12 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 1 AYSSFGGGRGS(1)R;AYSSFGGGRGS(1)R;AYSSFGGGRGS(1)R;AYS(0.001)S(0.001)FGGGRGS(0.999)R 96.707 0.0032296 2153720000 4044600 2580930 3170410 2819440 2506320 2304000 3130780 2090710 3543710 TRUE FALSE 3791455.706 2772024.743 3245613.622 2891791.604 2309483.737 2969127.398 2661348.604 2351739.746 2952241.908 1.284263222 0.938955827 1.099372519 0.979523933 0.782281334 1.005719548 0.901466982 0.796594527 1 21.49337951 8 0.523211081 0.912303767 12.56055385 0.501061225 0.102186548 103.2508594 1.022112588 0.048036729 1336.707446 100000000 -8 11.64825009 AYT(ph)PPPPLGPHPNLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AYTPPPPLGPHPNLGK 16 0 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 AY(0.006)T(0.994)PPPPLGPHPNLGK;AYT(1)PPPPLGPHPNLGK 131.67 0.00015933 468870000 1351850 975040 1106070 1089180 1146880 842970 1495730 1016910 1363660 TRUE FALSE 1267240.122 1047232.976 1132306.503 1117130.203 1056808.671 1086321.755 1271459.172 1143873.452 1136056.336 1.115472958 0.9218143 0.996699254 0.983340497 0.930243191 0.956221729 1.119186726 1.006880922 1 20.11560295 1.762203814 24.9999998 1.05350747 0.976173011 0.147061504 0.062084619 17.03945354 18030.55047 0.025961853 0.014397364 57.83674115 -1.762203814 -0.077334459 AYT(ph)PVVVTLWYR ddPTM_SK-BR-3_Pertuzumab_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 223.22 2.57E-10 2081690000 1385900 1284560 1034210 865140 1393380 815790 1156430 1225250 1105660 TRUE FALSE 1299158.993 1379670.159 1058741.95 887340.9571 1283949.555 1051295.33 983034.0573 1378225.16 921118.2032 1.410415068 1.497820968 1.149409431 0.963330172 1.39390314 1.141325105 1.067218142 1.496252224 1 19.81302678 3.941388386 3.453353621 1.168929827 1.450877754 0.332704508 0.164873151 0.24354754 5.992037539 0.039609609 0.08308692 8737.524093 -3.941388386 0.281947927 AYT(ph)PVVVTQWYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 118.58 0.006824 111190000 80247 88379 71126 79087 80009 54650 92431 68350 85836 TRUE FALSE 75224.48351 94922.67312 72813.14231 81116.50631 73725.41588 70426.56783 78571.82964 76883.64796 71509.41708 1.051952129 1.327415003 1.018231518 1.13434719 1.030988909 0.98485725 1.098761993 1.07515417 1 16.12584562 3.826696246 5.408276048 1.054735511 1.203006476 0.345799034 0.079522869 0.190615459 8.395847327 0.018362564 0.033665662 6709.594072 -3.826696246 0.148270965 AYTDELVELHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AYTDELVELHR 11 0 Q03111 Q03111 MLLT1 Protein ENL 0 102.4 0.002874 92671000 63947 80322 69354 77327 77924 71185 76998 72100 74668 FALSE TRUE 59944.67142 86269.12445 70999.10963 79311.34173 71804.16337 91734.95391 65452.86471 81101.84371 62205.42843 0.963656596 1.386842381 1.141365174 1.274990684 1.154307031 1.474709784 1.05220503 1.303774377 1 15.92475286 -1.344919787 3.663910916 0.999106249 1.225334744 0.169384753 0.151817248 326.5159396 31909848.42 43159.54566 0.030588888 0.045193941 1.344919787 0.226228496 AYVHEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AYVHEFK 7 0 Q9H4A4;A6NKB8;C9JMZ3;H7C2T3 Q9H4A4 RNPEP Aminopeptidase B 0 ;;;; 110.63 0.0067597 2255640000 4780290 4767160 4879250 4840210 5509320 3872490 5917410 4837820 5374290 FALSE TRUE 4481100.182 5120125.487 4994988.114 4964417.983 5076640.231 4990414.998 5030149.305 5441832.476 4477286.28 1.000851833 1.143577865 1.115628486 1.10880066 1.133865452 1.114607083 1.123481723 1.215430986 1 22.09419314 4.74412048 24.71697433 1.12422056 1.000851771 0.333368873 0.052305068 521.0434653 2316272.052 0.0106147 0.091744925 55477.95965 -4.74412048 -0.123368788 AYWQVHLDQVEVASGLTLCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AYWQVHLDQVEVASGLTLCK 20 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GU92;A0A1B0GU03;C9JH19;H7C469 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 146.64 1.31E-07 20223000 56027 53129 55100 44199 62219 45548 67442 64469 59768 FALSE TRUE 52520.37008 57062.72644 56406.99802 45333.22117 57332.57072 58696.96819 57329.6982 72518.09656 49792.33468 1.05478826 1.146014277 1.132845013 0.910445784 1.151433671 1.178835428 1.151375981 1.456410852 1 15.60363604 2.485076204 22.90462657 1.197374686 1.08153688 0.196626194 0.127057991 222.724943 641298.0177 0.040074898 0.035035401 305.5457194 -2.485076204 -0.115837806 AYYEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 AYYEFR 6 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;; 118.06 0.05163 2778510000 2138900 4333030 2209660 2162460 4356620 1561670 2360300 3884330 4698360 FALSE TRUE 2005030.067 4653852.05 2262074.179 2217952.385 4014468.639 2012498.777 2006394.927 4369297.151 3914173.363 0.512248662 1.188974432 0.57791875 0.566646436 1.025623616 0.514156781 0.512597359 1.116275838 1 21.90027623 1.221563499 24.97384402 1.058138216 0.722736829 0.284507512 0.234090226 392.4440682 576601.8308 0.221834445 0.056034986 16.65572337 -1.221563499 -0.335401387 CAAPRPPSS(ph)SPEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CAAPRPPSSSPEQR 14 1 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 CAAPRPPS(0.057)S(0.472)S(0.472)PEQR 115.8 0.00024128 470410000 233430 257030 267240 260320 250320 215970 289290 227400 222040 TRUE FALSE 218820.033 276060.7686 273579.059 267000.2519 230660.8769 278317.033 245913.6501 255791.3906 184980.0896 1.182938302 1.492380987 1.478964896 1.443399949 1.246949753 1.504578323 1.32940605 1.382804988 1 17.49701047 -0.704843062 0.524835859 0.91372536 1.413457256 0.546546567 0.107924493 9.125024762 1.849619137 1.439163765 0.045860486 0.197313563 0.704843062 0.499731897 CAAPRPPSSS(ph)PEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CAAPRPPSSSPEQR 14 1 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 CAAPRPPS(0.015)S(0.278)S(0.707)PEQR 142.21 5.73E-06 641370000 370160 345780 366600 368060 391350 319160 424960 325910 355900 TRUE FALSE 346992.3464 371381.911 375295.9251 377505.0427 360614.9496 411296.3109 361241.1931 366600.5809 296497.9908 1.170302522 1.252561307 1.265762119 1.273212819 1.216247532 1.387180769 1.218359666 1.236435296 1 18.1776628 -1.019265987 5.149778641 0.999997726 1.25642464 0.666004238 0.056135607 1.32E-06 2.52E-07 0.048850974 0.011514183 0.095660801 1.019265987 0.256426914 CAGNEDIITLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CAGNEDIITLR 11 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ; 179.31 1.67E-05 328920000 599660 528760 570240 582950 564240 466030 653130 494340 568550 FALSE TRUE 562128.351 567909.9406 583766.3621 597909.4839 519926.8664 600565.2956 555199.2199 556059.4372 473655.332 1.186787761 1.198994083 1.232470792 1.262330314 1.097690306 1.267937369 1.172158703 1.173974828 1 18.8534781 0.206960547 0.805092636 0.996503733 1.209133142 0.63758039 0.047850243 1.920358192 1.481656159 0.057276958 0.01427824 1.610499326 -0.206960547 0.212629409 CAHIEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CAHIEAK 7 0 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8;E9PS34;E9PNW0;E9PJJ2;C9J1B1 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 92.925 0.015312 248700000 393380 250840 326630 332320 370670 238780 388420 295870 412280 FALSE TRUE 368759.048 269412.4546 334377.8178 340847.8938 341559.0734 307711.9097 330180.0269 332810.0208 343467.8046 1.073634976 0.784389253 0.973534676 0.99237218 0.994442765 0.89589739 0.961312887 0.968970065 1 18.38981535 3.720522312 24.71174096 0.965135893 0.899534782 0.013070159 0.075483193 444.7241956 1665412.474 0.01820625 0.02896747 5254.390095 -3.720522312 -0.065601112 CALGWDHQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CALGWDHQEK 10 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ; 173.64 3.35E-06 1003950000 3038100 2370500 2694700 2696300 2792000 2028500 3307000 2224400 2930200 FALSE TRUE 2847950.744 2546014.287 2758619.557 2765491.623 2572727.582 2614095.02 2811146.051 2502121.237 2441130.69 1.166652304 1.042965171 1.130058119 1.132873235 1.053908172 1.070854187 1.1515754 1.024984548 1 21.2191181 1.084228246 6.274930309 1.000613312 1.102478948 0.480687244 0.04102854 0.161013162 8.789687046 0.036815861 0.009254624 12.14026721 -1.084228246 0.101865636 CALSS(ph)PSLAFT(ph)PPIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CALSSPSLAFTPPIK 15 0 Q8NFH5-2;Q8NFH5;Q8NFH5-3 Q8NFH5-2 NUP35 Nucleoporin NUP53 2 CALS(0.146)S(0.843)PS(0.039)LAFT(0.972)PPIK 97.417 0.017623 12677000 57646 42090 51144 53868 57513 39401 54265 41673 75011 TRUE FALSE 54038.03976 45206.38739 52357.15983 55250.34408 52996.16098 50775.42908 46128.46702 46875.96578 62491.17951 0.864730674 0.723404291 0.837832799 0.884130281 0.84805826 0.812521535 0.738159647 0.750121316 1 15.93136495 -2.102603221 2.594270085 1.36630982 0.801582157 0.546226262 0.054952654 5931016.941 3343559.152 12719651.68 0.013597689 0.007895812 2.102603221 -0.564727663 CAPSAGS(ph)PAAAVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 CAPSAGSPAAAVGR 14 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 CAPS(0.003)AGS(0.997)PAAAVGR;CAPSAGS(1)PAAAVGR;CAPSAGS(1)PAAAVGR;CAPS(0.035)AGS(0.965)PAAAVGR 241.22 2.08E-17 1924360000 1010110 864560 953450 897780 898460 806040 1209860 897150 1125490 TRUE FALSE 946889.0182 928572.922 976066.2843 920818.5547 827898.5758 1038730.663 1028452.725 1009161.152 937638.4481 1.009865818 0.990331533 1.04098364 0.98206143 0.88296142 1.107815774 1.096854259 1.07627962 1 19.8386722 2.188204896 24.99999996 1.081349566 0.990663626 0.429213135 0.049619786 97.49635824 48403.14387 0.017969157 0.01327112 154.2427982 -2.188204896 -0.09068594 CAPSAGSPAAAVGRES(ph)PGAAATSSSGPQAQQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 CAPSAGSPAAAVGRESPGAAATSSSGPQAQQHR 33 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR;CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR;CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR;CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR;CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR 336.81 1.45E-117 3770220000 857894 931910 931818 1030448 984747 733650 1130263 894700 1351790 TRUE FALSE 804199.9459 1000909.586 953921.163 1056891.04 907408.9429 945442.8452 960790.556 1006405.264 1126167.516 0.714103306 0.888775046 0.84705086 0.93848475 0.805749527 0.83952239 0.853150657 0.893655029 1 20.10299001 -5 0.205140371 1.69206944 0.829209706 0.449350209 0.056622264 139.7917531 1.389750192 39.70511911 0.118528623 1.00E-05 5 -0.862859735 CATITPDEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CATITPDEKR 10 1 O75874;C9J4N6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 125.74 0.00064307 662430000 343140 301230 340870 316650 379660 294320 503020 362000 579300 FALSE TRUE 321663.4799 323533.3826 348955.5974 324775.7751 349843.0351 379285.4061 427596.8208 407196.4969 482611.0876 0.66650661 0.670381164 0.723057564 0.672955478 0.72489639 0.785902802 0.886007039 0.843736307 1 18.88050154 1.603580793 0.631659775 0.991695653 0.672192063 0.931355208 0.028451031 0.160312794 0.139956798 0.026820896 0.013740561 40.14031657 -1.603580793 -0.31950359 CAVSDVEMQEHYDEFFEEVFTEMEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 CAVSDVEMQEHYDEFFEEVFTEMEEK 26 0 P0DN76;Q01081 P0DN76 U2AF1 Splicing factor U2AF 35 kDa subunit 0 ;; 104.33 0.0026033 31262400 34421.3 24166.5 28423.5 29737.4 29062.6 22598.8 37420.6 25233.5 38485.5 FALSE TRUE 32266.93228 25955.81281 29097.71884 30500.51203 26780.14063 29122.7067 31809.72843 28383.95802 32062.02142 1.006391077 0.809550105 0.907544738 0.951297226 0.835260518 0.908324098 0.992131095 0.88528286 1 14.96857777 1.246931916 0.58013138 0.994458362 0.888375389 0.119943838 0.063236566 1.19369915 1.004544676 0.060416063 0.02934694 17.65760981 -1.246931916 -0.106082973 CCHLFSTYVASHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CCHLFSTYVASHK 13 0 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 60.161 0.054306 167780000 277390 311380 291010 317570 307570 240350 328270 283200 287630 FALSE TRUE 260028.6551 334434.8992 297912.8946 325719.3838 283414.6929 309735.1432 279048.961 318558.1434 239622.6948 1.085158713 1.395672891 1.24325826 1.359301063 1.182753967 1.292595192 1.164534775 1.329415578 1 17.87040503 -3.86785975 0.297296848 3.88E-09 1.279630863 0.3957852 0.096429673 113.2170051 1.98134969 69.39109158 0.088202711 0.000135563 3.86785975 1.279630859 CCLTYCFNKPEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CCLTYCFNKPEDK 13 1 P62979;A0A2R8Y422 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ; 202.13 8.78E-08 3855000000 7708100 4055100 5190800 4861400 5319600 3667800 7949200 4232500 6542600 FALSE TRUE 7225663.78 4355343.823 5313928.227 4986151.754 4901820.074 4726634.318 6757291.257 4760936.942 5450597.793 1.32566446 0.79905801 0.974925766 0.91478989 0.899317884 0.867177234 1.239733973 0.873470603 1 22.37798304 CDENILWLDYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CDENILWLDYK 11 0 P14618;P14618-3;B4DNK4;H3BUW1;H3BTJ2;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 183.08 1.28E-05 123832000 309650 246380 270610 270630 287880 199635 305190 214930 271020 FALSE TRUE 290269.5592 264622.2316 277028.997 277574.824 265271.0661 257266.3837 259429.5927 241764.4836 225785.0111 1.285601545 1.172009737 1.226959202 1.229376665 1.17488342 1.139430746 1.149011582 1.070772955 1 17.78459019 1.291398578 0.581516822 0.996086174 1.224859105 0.853964073 0.031081316 0.267858394 0.22508036 0.029666137 0.014608971 19.56133895 -1.291398578 0.228772931 CDFITQVEEEISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CDFITQVEEEISR 13 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 ; 169.89 6.45E-05 28517000 28157 27269 32760 28028 32112 26542 32965 21627.5 34962 FALSE TRUE 26394.70363 29288.02513 33537.08267 28747.24593 29590.05305 34204.24453 28022.20428 24327.74098 29126.61634 0.906205627 1.005541625 1.151423917 0.98697513 1.015911107 1.174329491 0.962082377 0.835240891 1 14.83005049 1.514946813 7.5163573 0.911518456 1.047242379 0.264539167 0.086232327 0.133726469 15.57588287 0.044869497 0.020650505 32.73006086 -1.514946813 0.135723923 CDFTEDQTAGDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CDFTEDQTAGDGK 13 0 F8VPF3 F8VPF3 MYL6 0 62.088 0.079297 1137300000 1430400 2279200 2252900 2239500 1991300 2052100 2446700 2049100 1410400 FALSE TRUE 1340873.817 2447954.34 2306339.852 2296969.361 1834911.331 2644507.957 2079840.049 2304934.646 1174995.128 1.141173938 2.083374033 1.962850565 1.954875647 1.561633139 2.250654401 1.770083976 1.96165464 1 20.16422334 -0.851631956 5.66134295 0.999999724 1.875424309 0.415977731 0.308061563 9.45E-07 1.91E-07 0.262141443 0.061787312 0.140723959 0.851631956 0.875424585 CDGETDKHWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 CDGETDKHWR 10 1 Q9NXV6;J3KNE1;D6RGD2 Q9NXV6 CDKN2AIP CDKN2A-interacting protein 0 ;; 143.5 2.03E-05 311784000 359710 304361 375039 354757 398050 250560 439850 303892 470120 FALSE TRUE 337196.3932 326896.2051 383935.1022 363860.6652 366788.7587 322892.6045 373898.5759 341833.5851 391653.9349 0.860954948 0.834655741 0.980291701 0.929036154 0.93651238 0.824433449 0.954665695 0.872794972 1 18.57921993 -3.314281636 0.011723699 1.975144117 1.97E-06 0.252095033 0.052278214 11304.18458 13.52830093 1298.239609 998.1304484 0.000484974 3.314281636 -1.975142149 CDILVQEELLAS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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;CDILVQEELLAS(1)PK 261.17 1.79E-24 1169877000 1973075 858097 1245080 1108805 1099709 1011131 1724364 1055472 1100548 TRUE FALSE 1849583.758 921631.3947 1274613.886 1137258.814 1013342.291 1303028.105 1465811.626 1187250.003 916859.429 2.017303525 1.005204686 1.390195536 1.240385143 1.105231903 1.42118635 1.598731038 1.294909519 1 19.80634103 CDLEDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CDLEDER 7 0 F5H823;B7ZB78;F5GZG1;P61224-2;P61224-4;P61224-3;P62834;P61224;A6NIZ1;F5H004;A0A075B6Q0;F5GX62;E7ESV4;F5H7Y6;O95716 F5H823;O95716 RAP1B;RAP1A;RAB3D Ras-related protein Rap-1b;Ras-related protein Rap-1A;Ras-related protein Rap-1b-like protein;Ras-related protein Rab-3D 0 ; 114.78 0.013557 570640000 1492230 2090020 1367220 1437810 2404500 1332320 1932080 2050640 1552990 FALSE TRUE 1398833.988 2244767.255 1399651.104 1474706.639 2215660.269 1716939.156 1642382.541 2306666.918 1293785.936 1.081194306 1.735037607 1.081825876 1.139838205 1.712540079 1.327065867 1.269439166 1.782881428 1 20.3031675 -0.762500246 8.537498759 1.000001759 1.384906573 0.172932854 0.268567241 3.52E-09 0 0.23627426 0.055690377 0.1727825 0.762500246 0.384904814 CDLVNYSYGEATHWPNSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CDLVNYSYGEATHWPNSGR 19 0 A0A494C0U1;Q5VZU9;P29144;A0A494C0X4 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ; 232.54 8.04E-21 408211000 198403 206548 204804 217677 216412 173419 256469 177847 189696 FALSE TRUE 185985.3104 221841.0288 209662.0476 223262.9603 199415.8745 223482.2501 218013.8544 200051.5894 158034.5121 1.176865154 1.403750522 1.326685195 1.412748123 1.261850161 1.414135729 1.379533188 1.265872794 1 17.26988013 0.873937308 3.934141285 1.000067161 1.348827597 0.668528511 0.074560206 0.34871463 9.867791058 0.063131735 0.016155217 7.480615074 -0.873937308 0.348760436 CDNFTSSWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 160.36 0.00015204 1190410000 797300 929520 822490 847989 840660 685701 779430 736876 709820 FALSE TRUE 747398.4162 998342.628 841999.8512 869749.8334 774637.9547 883651.7473 662561.7074 828876.5907 591346.4564 1.26389261 1.688253336 1.423868939 1.470795714 1.309956196 1.494304629 1.120428981 1.40167677 1 19.17364409 1.21398887 0.386393599 0.983507586 1.533780297 0.456519766 0.143733906 0.893214862 0.401179616 0.190112928 0.121516662 16.36774575 -1.21398887 0.550272711 CDPAPFYLFDEIDQALDAQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CDPAPFYLFDEIDQALDAQHR 21 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 202.39 6.41E-22 80957000 142320 116270 108370 127290 131260 110410 130900 105840 120910 FALSE TRUE 133412.4452 124878.7518 110940.5876 130556.4769 120951.3691 142283.5746 111272.7602 119054.357 100729.3399 1.324464604 1.239745559 1.101373122 1.296111709 1.200756098 1.412533576 1.104670797 1.181923331 1 16.62012444 0.915146346 1.353567493 1.004587906 1.235506292 0.413652396 0.092100483 0.549297574 2.008106462 0.083316147 0.025060774 8.225197709 -0.915146346 0.230918386 CDPDAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CDPDAAR 7 0 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 94.407 0.033089 1202500000 964400 859470 946490 1006800 987030 762660 1015900 771040 977200 FALSE TRUE 904039.9255 923106.0531 968941.1898 1032636.193 909512.6453 982827.5612 863575.2262 867306.0413 814099.007 1.110479091 1.133899004 1.190200678 1.26844055 1.117201517 1.207258027 1.060774204 1.065356958 1 19.63484473 1.635413892 4.88334168 1.04213949 1.17061095 0.608762872 0.048967775 0.106615344 5.623055671 0.026237265 0.012334019 43.19305198 -1.635413892 0.12847146 CDRVDQLTAQLADLAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CDRVDQLTAQLADLAAR 17 1 P18206;P18206-2 P18206 VCL Vinculin 0 ; 188.84 3.54E-10 285387000 219778 176422 216750 222044 219249 165756 241761 169621 193091 FALSE TRUE 206022.4873 189484.4684 221891.4124 227742.025 202030.0679 213607.0664 205511.1824 190798.5552 160862.8647 1.280733671 1.177925488 1.37938245 1.415752638 1.255914896 1.327883019 1.277555158 1.186094476 1 17.29547179 0.907835918 1.84154403 1.00043333 1.302813981 0.694848111 0.064711206 0.26910317 1.861397722 0.063387735 0.017898032 8.087902698 -0.907835918 0.302380651 CDSWWAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CDSWWAK 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 120.52 0.010558 298980000 914740 807730 787850 857360 788720 543260 982820 714140 715700 FALSE TRUE 857488.0563 867535.1696 806538.174 879361.3091 726777.1127 700090.3429 835455.2651 803301.951 596245.0464 1.438147053 1.454997697 1.352695807 1.474832058 1.218923523 1.174165466 1.401194475 1.347268134 1 19.18554585 -4.430415006 0.129477699 2.50E-11 1.519404149 0.644870284 0.088481869 80.01284925 0.754595593 21.55686761 0.699732115 3.71E-05 4.430415006 1.519404149 CDVDIRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 93.262 0.024154 31407800000 27934200 25696100 26795700 26377600 30636700 18401900 34234300 21031400 40092300 FALSE TRUE 26185848.29 27598665.98 27431306.66 27054493.87 28230617.16 23714229.8 29101184.53 23657216.59 33400636.12 0.783992502 0.826291627 0.821280965 0.80999936 0.845211961 0.709993358 0.871276356 0.708286408 1 24.99337224 -1.140214241 4.637909782 1.000020093 0.804725212 0.58595013 0.053270446 9.46E-06 1.75E-06 0.044065947 0.010385375 0.072407868 1.140214241 -0.195294881 CEAFGWHAIIVDGHSVEELCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 CEAFGWHAIIVDGHSVEELCK 21 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ;;;; 323.3 1.85E-67 1075109000 1676261 1568411 1343835 1152934 2260976 1142905 1806092 1821591 1879497 FALSE TRUE 1571346.816 1684537.782 1375711.401 1182520.238 2083408.065 1472843.12 1535285.272 2049020.646 1565796.809 1.003544526 1.075834216 0.878601485 0.755219472 1.330573708 0.940634897 0.980513731 1.308612098 1 20.57846558 2.752988029 24.99868281 1.085735574 0.944605923 0.251363412 0.152757822 1442.902933 2500147.325 0.045501052 0.048065077 566.2236819 -2.752988029 -0.141129651 CEDKFTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CEDKFTK 7 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ; 75.378 0.039792 432190000 838920 635630 705010 707700 762840 488100 850600 606790 950340 FALSE TRUE 786413.4947 682692.7066 721733.1701 725860.7801 702929.6235 629006.5464 723060.4266 682549.0672 791722.1146 0.993294845 0.862288288 0.911599104 0.916812562 0.887848919 0.79447894 0.913275521 0.862106861 1 19.59463462 -1.242338722 3.407126419 1.000288649 0.889620722 0.305464707 0.050650755 10384557.52 14598156.48 30784.44326 0.0109424 0.057234946 1.242338722 -0.110667928 CEFQDAYVLLSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 CEFQDAYVLLSEK 13 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;; 194.7 1.86E-06 108812000 315159 254587 256869 241270 355708 210541 275629 265188 372406 FALSE TRUE 295433.7608 273436.8864 262962.054 247461.3967 327772.1285 271320.7689 234300.9903 298297.3056 310249.0328 0.952247161 0.881346459 0.847583799 0.797621815 1.056480743 0.874525753 0.755202968 0.961476988 1 18.24306719 4.737405953 5.910966565 0.878753474 0.954300976 0.00186168 0.091874067 0.434363761 70.97863268 0.020809787 0.132460471 54626.82419 -4.737405953 0.075547502 CEFQDAYVLLSEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CEFQDAYVLLSEKK 14 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 139.6 1.63E-05 347720000 361250 329230 292990 310160 470990 247110 340750 287690 745760 FALSE TRUE 338640.0073 353606.5318 299939.8612 318119.2307 434000.3453 318446.6455 289657.7009 323608.7298 621287.8382 0.545061381 0.569150899 0.482771177 0.512031962 0.698549559 0.512558956 0.466221424 0.52086764 1 19.24490229 -1.121337835 4.483508995 1.000053571 0.533954965 0.837305244 0.063919033 3.40E-05 6.67E-06 0.061518192 0.014498315 0.075624439 1.121337835 -0.466098606 CEGFELHFWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 CEGFELHFWR 10 0 Q9UGI8-2;Q9UGI8 Q9UGI8-2 TES Testin 0 ;;;; 147.95 2.60E-05 674125000 856881 2387949 1765445 1982024 2378209 2953608 1024697 1646748 1008277 FALSE TRUE 803250.3478 2564755.229 1807322.189 2032886.091 2191434.058 3806266.682 871053.1977 1852348.113 839989.055 0.956262874 3.053319818 2.15160207 2.420134024 2.608884063 4.531328901 1.036981604 2.205205058 1 19.680011 4.754672116 23.62556315 2.441243446 0.956260431 0.163970065 0.997796707 2492.526489 3654857.089 0.219048 5.298190915 56842.36193 -4.754672116 -1.484983015 CEGINISGNFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CEGINISGNFYR 12 0 P40429;M0QYS1 P40429 RPL13A 60S ribosomal protein L13a 0 ; 211.84 6.32E-08 147110000 254630 223470 190047 201037 256660 142631 232940 196502 230170 FALSE TRUE 238693.1628 240015.9513 194555.0046 206195.9498 236502.9589 183806.2543 198012.8095 221035.7073 191753.14 1.244794024 1.251692417 1.014611831 1.075319808 1.233372026 0.958556685 1.032644417 1.152709714 1 17.54889068 4.084659332 3.364338215 1.066586404 1.249335072 0.478347314 0.078580533 0.201244179 4.311047602 0.019382804 0.047193034 12152.32377 -4.084659332 0.182748668 CESAPGCGVWQRPVIDNPNYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CESAPGCGVWQRPVIDNPNYK 21 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 55.267 0.089037 100220000 104390 83354 73124 84878 91114 62937 124420 72882 75330 FALSE TRUE 97856.41624 89525.61689 74858.53581 87056.11318 83958.27398 81105.8902 105764.3761 81981.47813 62756.93635 1.559292437 1.426545368 1.192832859 1.387195077 1.337832579 1.292381288 1.685301772 1.306333338 1 15.9374873 4.615440282 3.044214723 1.353873313 1.567638302 0.149526546 0.172773877 0.653329591 9.834736117 0.041414489 0.284173314 41251.551 -4.615440282 0.213764989 CETS(ph)PPSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CETSPPSSPR 10 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2;O75335;H0YD72;B1APN9;M0QZB5;O75335-1;O75335-2 Q13136-2 PPFIA1;PPFIA4 Liprin-alpha-1;Liprin-alpha-4 2 CET(0.018)S(0.982)PPS(0.037)S(0.963)PR 99.498 0.0068044 99258000 181410 208240 219990 219590 243300 181050 252600 215630 281000 TRUE FALSE 170055.8719 223658.3063 225208.2667 225225.0512 224192.1994 233316.1959 214724.975 242551.8802 234099.2847 0.726426277 0.955399358 0.962020311 0.962092009 0.957679985 0.996654886 0.91723892 1.036106883 1 17.836761 4.740268021 4.745639974 0.967508317 0.712271133 0.853326652 0.0321392 0.060302024 3.828493928 0.006776256 0.051125614 54988.01225 -4.740268021 -0.255237184 CEYLMELMTPAACPEPPPEAPTEDDHDEL ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CEYLMELMTPAACPEPPPEAPTEDDHDEL 29 0 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 120 4.90E-05 12629000 12476 15177 15443 14072 15294 14384 16228 12897 13265 FALSE TRUE 11695.14943 16300.72087 15809.31525 14433.11134 14092.87093 18536.4273 13794.76205 14507.21884 11050.9858 1.05829015 1.475046766 1.430579636 1.306047406 1.275259165 1.677355091 1.248283393 1.312753368 1 13.43188745 0.73330057 1.586350962 1.001441439 1.380620885 0.31066945 0.161663152 1.007084827 4.091950518 0.139684055 0.040220099 5.411287018 -0.73330057 0.379179446 CEYSAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 CEYSAHK 7 0 Q9GZN8-2;Q9GZN8 Q9GZN8-2 C20orf27 UPF0687 protein C20orf27 0 ;; 100.45 0.0097841 483597000 410904 566780 468350 515080 597880 406202 568580 521460 534007 FALSE TRUE 385186.2521 608744.9809 479459.4832 528297.8248 550924.9165 523465.9233 483326.7074 586565.4289 444877.7819 0.86582488 1.368342061 1.077733037 1.18751227 1.238373636 1.176651082 1.086425817 1.318486678 1 18.76304952 -1.06549731 4.809457987 0.999994481 1.172311132 0.119649834 0.139309689 7.18E-06 1.40E-06 0.117487933 0.027691285 0.086000839 1.06549731 0.172316651 CFLAQPVTLLDIYTHWQQTSELGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CFLAQPVTLLDIYTHWQQTSELGR 24 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 0 ; 251.32 3.80E-39 315860000 231806 257814 241270 226971 286280 189872 270800 243460 226875 FALSE TRUE 217297.6762 276902.8168 246993.0383 232795.4601 263796.7236 244684.9641 230196.054 273856.5169 189008.0968 1.149673902 1.465031506 1.306785489 1.231669246 1.395690068 1.29457398 1.217916364 1.448914208 1 17.52808851 -1.862293428 2.532946812 0.857418494 1.318339625 0.488968811 0.100716513 14812256.35 8726619.862 12711918.78 0.023976114 0.013731139 1.862293428 0.460921131 CFSEENHEPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CFSEENHEPLR 11 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 228.28 3.39E-12 944150000 1188350 1278210 1277050 1248420 1297160 1030080 1570970 1217960 1284820 FALSE TRUE 1113973.295 1372849.998 1307342.229 1280456.571 1195286.286 1327447.374 1335417.633 1370024.987 1070375.242 1.04073156 1.282587587 1.221386835 1.196268861 1.116698368 1.240170103 1.247616332 1.279948315 1 20.02968522 4.753830889 23.8222932 1.213989059 1.040731315 0.231087443 0.085957455 1818.004777 2836074.939 0.018289145 0.411580149 56732.36503 -4.753830889 -0.173257744 CFSIDNPGYEPEVVAVHPGGDTVAIGGVDGNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CFSIDNPGYEPEVVAVHPGGDTVAIGGVDGNVR 33 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 103.78 1.21E-05 79570000 33242 31731 40971 35534 36131 32128 41294 27492 31127 FALSE TRUE 31161.44256 34080.39626 41942.85147 36445.8626 33293.41701 41402.83205 35102.34805 30924.43672 25931.70261 1.201673605 1.314236738 1.617435311 1.405455829 1.283888586 1.59661063 1.353646098 1.192533987 1 14.66242931 1.067822745 2.444990195 1.004851576 1.416787296 0.513920953 0.12868005 0.203889493 2.499678337 0.119040972 0.032574397 11.69022163 -1.067822745 0.41193572 CFVEHILCTKPLPCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CFVEHILCTKPLPCR 15 1 Q99567;J3KMX1 Q99567 NUP88 Nuclear pore complex protein Nup88 0 99.481 0.0015177 134700000 196670 191080 186230 196800 203480 159710 253190 176770 230820 FALSE TRUE 184360.7758 205227.762 190647.4635 201850.2212 187499.5016 205815.6843 215226.51 198840.1236 192294.6508 0.958741052 1.067256739 0.991434045 1.049692336 0.975063533 1.070314142 1.119253755 1.034038767 1 17.55295911 2.162082245 11.53553529 1.071831742 1.016028927 0.169392672 0.044921045 0.693038411 101.2890482 0.015368475 0.011350923 145.2386639 -2.162082245 -0.055802815 CGEDDETIPSEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CGEDDETIPSEYR 13 0 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;D6RAA8;P20810-5;E9PCH5;P20810-2;P20810-3;F8W7E0;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 124.67 0.00028206 0 43071 39105 36762 38610 48755 33282 50233 37519 49209 FALSE TRUE 40375.26299 42000.37489 37634.012 39600.79797 44925.97897 42889.97311 42701.02799 42203.32974 40995.7 0.984865803 1.024506836 0.91799901 0.965974431 1.095870517 1.046206629 1.041597728 1.029457473 1 15.32318497 2.763362774 24.69079975 1.045150075 0.972641978 0.497533389 0.034545917 535.0513183 532647.7793 0.01050796 0.011141805 579.9129056 -2.763362774 -0.072508097 CGESGHLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CGESGHLAK 9 0 P62633-2;P62633;P62633-7;P62633-3;P62633-5;P62633-6;D6RAT4;P62633-8;P62633-4 P62633-2;P62633-8 CNBP Cellular nucleic acid-binding protein 0 85.731 0.014617 158970000 234840 187140 237830 238910 201810 172220 304130 203010 228420 FALSE TRUE 220141.7836 200996.0403 243471.4399 245040.8351 185960.6567 221937.1182 258528.5299 228356.2454 190295.2264 1.156843437 1.056232698 1.279440607 1.287687767 0.977221869 1.166277907 1.358565503 1.200010372 1 17.53787985 1.969059413 24.90749363 1.235129859 1.154603591 0 0.127452645 1729.872755 1392563.438 0.050036351 0.032302449 93.12352632 -1.969059413 -0.080526268 CGESGHLAR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 207.29 1.19E-05 2063810000 2863420 2733690 3024480 2945510 2978570 2316280 3236040 2505190 3324080 FALSE TRUE 2684203.654 2936095.252 3096222.094 3021096.773 2744645.127 2984952.434 2750825.844 2817968.486 2769269.574 0.969282182 1.060241762 1.118064533 1.090936326 0.991107963 1.077884386 0.993339858 1.017585472 1 21.40107407 1.972378792 1.17519474 1.002101339 1.064476598 0.130537683 0.046114812 0.746874713 1.905011086 0.03483618 0.015888066 93.83801057 -1.972378792 0.06237526 CGETGHVAINCSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 CGETGHVAINCSK 13 0 P62633-2;P62633;P62633-7;P62633-3;P62633-5;P62633-6;P62633-8;P62633-4 P62633-2;P62633-8 CNBP Cellular nucleic acid-binding protein 0 ;;; 135.58 5.89E-06 896550000 1853990 1168390 1467570 1368640 1228500 1081490 1688510 1152160 1207310 FALSE TRUE 1737952.075 1254898.811 1502381.453 1403761.62 1132018.566 1393698.606 1435333.601 1296009.712 1005802.161 1.727926368 1.247659688 1.49371468 1.395663753 1.125488301 1.38565879 1.427053605 1.288533433 1 19.93991513 -4.247331138 0.143750081 1.77E-13 1.515923397 0.458944395 0.147022164 107.41906 1.146132953 32.20709486 0.824696212 5.66E-05 4.247331138 1.515923397 CGGVEQASSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_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(0.001)S(0.999)PR;CGGVEQASS(0.003)S(0.997)PR 143.56 6.26E-05 871230000 930570 864870 904970 984250 1003310 718550 1100520 776710 942780 TRUE FALSE 872327.2848 928905.8747 926436.3158 1009507.521 924514.0798 925983.7203 935507.2427 873683.9532 785423.9274 1.110645162 1.182680897 1.17953666 1.285302734 1.177089273 1.178960416 1.191085744 1.112372469 1 19.58311202 0.939293901 2.445050792 1.000178062 1.188748042 0.672073393 0.042021842 0.19273211 2.584574527 0.038058696 0.010282781 8.69548681 -0.939293901 0.18856998 CGHTNNLRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 CGHTNNLRPK 10 1 M0R2S1;P62987 M0R2S1 UBA52 Ubiquitin-60S ribosomal protein L40;Ubiquitin;60S ribosomal protein L40 0 ;;; 125.66 0.00024231 2135570000 3853500 3357134 3560538 3495626 3832860 2509728 4264400 3044755 4042590 FALSE TRUE 3612316.314 3605699.694 3644995.643 3585329.681 3531842.637 3234245.732 3624992.809 3424899.364 3367855.613 1.072586455 1.070621817 1.08228976 1.064573454 1.048691821 0.960327907 1.076350422 1.016937707 1 21.68339886 2.58494646 3.81340516 1.022037438 1.073692468 0.462847201 0.029062508 0.226040017 5.877365321 0.009284559 0.008588924 384.5443727 -2.58494646 0.05165503 CGLGQENS(ph)DNEHLVENEVSLLLEESDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 CGLGQENSDNEHLVENEVSLLLEESDLR 28 0 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 CGLGQENS(1)DNEHLVENEVSLLLEESDLR;CGLGQENS(0.999)DNEHLVENEVS(0.001)LLLEESDLR;CGLGQENS(1)DNEHLVENEVSLLLEESDLR 167.97 3.39E-12 48858000 52488.9 47295.3 48368.9 55133.7 60351 44517.9 61288.3 47151.3 58005.7 TRUE FALSE 49203.71344 50797.09322 49516.23315 56548.52408 55611.2759 57369.49504 52098.68839 53038.2436 48324.17394 1.018200818 1.051173545 1.024667969 1.170191221 1.150796203 1.187180046 1.078108204 1.097550962 1 15.56045745 3.255042905 24.99977605 1.121741669 1.034641657 0.34272597 0.053152712 237.2976955 359922.7469 0.013682281 0.018474015 1799.048641 -3.255042905 -0.087100012 CGQEEHDVLLSNEEDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CGQEEHDVLLSNEEDRK 17 1 Q9UGI8-2;Q9UGI8 Q9UGI8-2 TES Testin 0 209.73 2.61E-12 597450000 583630 399870 439350 442460 511730 320990 566530 386960 606960 FALSE TRUE 547101.6401 429476.7909 449771.5895 453814.2727 471540.79 413654.6022 481584.0859 435272.8078 505654.4549 1.081967408 0.849348378 0.889484084 0.897479036 0.932535619 0.818057862 0.952397593 0.860810784 1 18.94779231 -1.666508545 7.157222133 1.000398832 0.902800975 0.123941576 0.072611599 0.000405102 1.89E-05 0.061633249 0.014468351 0.021552192 1.666508545 -0.097597856 CGS(ph)GPVHISGQHLVAVEEDAESEDEEEEDVKLLSISGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CGSGPVHISGQHLVAVEEDAESEDEEEEDVKLLSISGK 38 1 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 1 CGS(0.333)GPVHIS(0.333)GQHLVAVEEDAES(0.333)EDEEEEDVKLLS(0.001)ISGK;CGS(0.333)GPVHIS(0.333)GQHLVAVEEDAES(0.333)EDEEEEDVKLLSISGK 45.751 0.032974 88306000 46476.1 66381 59319 66123 85200 36501.7 74362 50749 167618 TRUE FALSE 43567.24386 71295.91831 60726.07469 67819.82813 78508.73568 47039.14823 63212.10844 57085.12436 139641.4729 0.311993586 0.510564067 0.434871342 0.485671103 0.562216468 0.336856574 0.452674317 0.408797782 1 17.09136795 -1.707388617 2.790960607 1.084568018 0.445336115 0.847138844 0.074973378 20016361.75 17565192.3 11882334.85 0.018005203 0.019616042 1.707388617 -0.639231903 CGSGPVHISGQHLVAVEEDAES(ph)EDEEEEDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 33 CGSGPVHISGQHLVAVEEDAESEDEEEEDVK 31 0 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 1 CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGS(0.002)GPVHIS(0.002)GQHLVAVEEDAES(0.997)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGS(0.003)GPVHIS(0.003)GQHLVAVEEDAES(0.995)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGS(0.001)GPVHIS(0.001)GQHLVAVEEDAES(0.998)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(0.999)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGS(0.078)GPVHIS(0.07)GQHLVAVEEDAES(0.852)EDEEEEDVK 357.27 1.46E-120 48679595000 4779855.9 5633000.9 6001272 6247166 6173200 4820992 8005857 5550257.9 5872799.2 TRUE FALSE 4480693.252 6050074.148 6143625.006 6407478.856 5688381.773 6212734.128 6805453.066 6243219.816 4892591.074 0.915811925 1.236578749 1.255699672 1.309628939 1.1626522 1.269824932 1.390971157 1.276055923 1 22.22216728 4.742974289 4.104815878 1.260603148 0.885264342 0.476223217 0.10396182 0.179657491 6.592618118 0.022790672 0.200831816 55331.73507 -4.742974289 -0.375338806 CGSGPVHISGQHLVAVEEDAES(ph)EDEEEEDVKLLSISGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 CGSGPVHISGQHLVAVEEDAESEDEEEEDVKLLSISGK 38 1 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 1 CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGS(0.018)GPVHIS(0.018)GQHLVAVEEDAES(0.963)EDEEEEDVKLLS(0.001)ISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK 334.46 1.48E-129 5538492000 791496 1846664 1648023 2042448 2689908 1065810 2434687 1592870 4677236 TRUE FALSE 741957.6782 1983392.924 1687114.884 2094860.674 2478653.476 1373492.045 2069628.287 1791743.326 3896575.096 0.190412775 0.50900929 0.432973789 0.537615886 0.636110794 0.352486995 0.531140357 0.459825175 1 21.89377519 -5 0.255686615 4.33974463 0.420572064 0.68972913 0.11628199 105.870221 1.044933896 185.4070854 0.146826837 1.00E-05 5 -3.919172566 CGYAGSNFPEHIFPALVGRPIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CGYAGSNFPEHIFPALVGRPIIR 23 1 P61160;P61160-2;A0A1B0GWD0;A0A1B0GWH0 P61160 ACTR2 Actin-related protein 2 0 176.46 2.01E-13 184950000 90609 103420 88329 99229 109780 60233 96591 90090 93751 FALSE TRUE 84937.94443 111077.3244 90424.20559 101775.3841 101158.3216 77621.2893 82108.07626 101337.9348 78103.35245 1.087507025 1.422183823 1.157750631 1.303085987 1.295185398 0.993827882 1.051274672 1.297485084 1 16.25309685 2.250124522 24.9999343 1.082347391 1.265455839 0.3179847 0.12110432 227.8606546 492610.0191 0.039129972 0.032478215 177.8789356 -2.250124522 0.183108448 CGYFDEEMNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CGYFDEEMNR 10 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 93.649 0.03071 99053000 259780 181380 185270 187450 210030 142210 227080 162640 201820 FALSE TRUE 243520.8335 194809.5639 189664.6919 192260.2844 193535.091 183263.7184 193031.4621 182945.962 168134.9382 1.448365439 1.158650106 1.128050445 1.143488001 1.151070046 1.089979991 1.148074661 1.088090102 1 17.35926002 4.782607422 2.718071026 1.120376546 1.533790891 0.841231158 0.045925036 0.189676948 1.709197522 0.009773751 0.184816854 60618.81218 -4.782607422 0.413414345 CHEFLIFEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CHEFLIFEDR 10 0 P11172-2;P11172-3;P11172;P11172-4;E9PFD2 P11172-2 UMPS Uridine 5-monophosphate synthase;Orotate phosphoribosyltransferase;Orotidine 5-phosphate decarboxylase 0 ; 162.36 6.79E-06 170931000 232800 222610 218390 216170 233230 193601 253720 189271 217440 FALSE TRUE 218229.4636 239092.276 223570.3139 221717.2882 214913.0566 249490.4659 215677.0414 212901.901 181147.8593 1.204703519 1.319873594 1.234186895 1.22395754 1.186395784 1.377275265 1.19061325 1.175293497 1 17.46680823 0.879013659 1.603104705 1.001423312 1.257609579 0.647693434 0.058372327 0.302436323 1.521194762 0.050815876 0.014699026 7.568566978 -0.879013659 0.256186267 CHEHIEILTVNGELLFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CHEHIEILTVNGELLFFR 18 0 Q9ULC4-2;Q9ULC4;Q9ULC4-3 Q9ULC4-2 MCTS1 Malignant T-cell-amplified sequence 1 0 146.16 4.96E-08 16635000 15230 10897 12272 13380 16621 13005 15123 11022 9432.9 FALSE TRUE 14276.78149 11703.82522 12563.09764 13723.35345 15315.65371 16759.33238 12855.44655 12398.12096 7858.488051 1.81673388 1.489322773 1.598665997 1.746309642 1.948931347 2.132640817 1.635867671 1.57767256 1 12.94003605 0.787306377 2.167067948 1.00111011 1.741488287 0.638321862 0.180945513 0.619458621 4.803776656 0.192220677 0.052527643 6.127825329 -0.787306377 0.740378177 CHQPLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 CHQPLAR 7 0 Q15942;Q15942-2;H0Y2Y8;C9JJK5 Q15942 ZYX Zyxin 0 ;; 80.294 0.030303 263219000 302470 275701 299318 281270 345155 200863 283709 296257 338229 FALSE TRUE 283538.9426 296114.1889 306417.9643 288487.8644 318047.9186 258848.8874 241169.4693 333245.3386 281776.3949 1.006255129 1.050883588 1.087450794 1.023818424 1.128724494 0.918632263 0.855889541 1.18265882 1 18.10419123 2.229633636 24.99673645 0.962184419 1.060464497 0.098597406 0.090058911 288.474645 807761.2486 0.031658202 0.023722655 169.6811646 -2.229633636 0.098280078 CHTPPLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 CHTPPLYR 8 0 Q02543;M0R117 Q02543 RPL18A 60S ribosomal protein L18a 0 ;;; 139.68 0.00066172 1475000000 599212 621170 580084 594160 667850 423008 664960 584180 586100 FALSE TRUE 561708.3905 667162.0731 593843.8664 609407.1515 615399.755 545123.5426 565255.4212 657116.1589 488276.1236 1.150390862 1.366362271 1.216205007 1.24807895 1.26035193 1.116424736 1.157655257 1.345788023 1 18.89733771 -4.999999987 0.177146366 0.066945957 1.284846374 0.396533703 0.084293665 124.6243225 1.194310976 40.98531479 0.258878987 1.00E-05 4.999999987 1.217900417 CHWTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 CHWTQR 6 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;; 137.44 0.012735 721006000 635522 782120 874623 848481 803576 744599 883500 594120 641392 FALSE TRUE 595745.8125 840028.9786 895369.4706 870254.4589 740466.3824 959552.6437 751027.377 668297.1898 534339.5316 1.114919966 1.572088399 1.675656427 1.628654455 1.385760062 1.795773262 1.405524638 1.250697637 1 19.02739723 1.108819232 2.081377128 1.010205405 1.550208221 0.460882542 0.185183549 0.234439619 1.959772165 0.160634083 0.045315391 12.84751792 -1.108819232 0.540002816 CIACQAAKLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CIACQAAKLSPR 12 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 CIACQAAKLS(1)PR 143.93 3.79E-05 176170000 348990 339830 288410 260630 543500 214480 430440 451960 746060 TRUE FALSE 327147.3389 364991.3668 295251.2214 267318.207 500815.7024 276396.8942 365899.518 508388.2009 621537.7663 0.526351505 0.587239242 0.475033437 0.430091656 0.805768739 0.444698471 0.588700378 0.817952228 1 19.24548253 1.095162692 2.554075612 0.996368457 0.544282065 0.686801843 0.104816974 0.134630444 1.725779339 0.090456656 0.024704911 12.4498091 -1.095162692 -0.452086392 CIALAQLLVEQNFPAIAIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CIALAQLLVEQNFPAIAIHR 20 0 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6UJC5;A0A140T9X9;A0A140TA18;H0Y400;H0YCC6 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ; 217.88 1.03E-24 408220000 710600 677510 719910 663930 693360 598340 778160 648660 382810 FALSE TRUE 666124.8145 727673.5453 736986.6052 680967.5678 638906.3025 771071.0448 661482.1321 729646.6289 318916.538 2.088712046 2.28170527 2.310907455 2.13525323 2.003365227 2.417783191 2.074154374 2.287892104 1 18.28281939 -1.525190973 3.114777411 0.959868913 2.209106558 0.897640341 0.127313191 30215583.65 36872661.78 10315109.45 0.028406322 0.029840701 1.525190973 1.249237645 CIDHYTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CIDHYTK 7 0 A0A087WW66;Q99460-2;Q99460;C9J9M4;H7BZR6 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 105.12 0.0079989 210600000 390160 430830 423540 455310 441020 358140 494390 378290 482840 FALSE TRUE 365740.5821 462729.1015 433586.5688 466994.0254 406384.0682 461529.2041 420260.8092 425520.3392 402250.8847 0.909234997 1.150349493 1.077900846 1.16095214 1.010275138 1.147366536 1.044772865 1.057848113 1 18.61773607 0.964713766 1.387457342 1.001355816 1.085025159 0.066706788 0.075732414 1.011144891 3.957554589 0.062968479 0.018895971 9.219635798 -0.964713766 0.083669343 CIDLDTEEHIYHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CIDLDTEEHIYHLK 14 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 0 145.81 4.90E-06 51214000 61989 53175 59678 54864 65382 54002 79095 58719 77990 FALSE TRUE 58109.21914 57112.13233 61093.59034 56271.90312 60247.16146 69591.50075 67235.43903 66050.19641 64972.96517 0.894359969 0.87901379 0.940292477 0.866081808 0.927265076 1.071083959 1.034821773 1.016579684 1 15.98755193 2.346960944 5.313276031 1.034521368 0.899717056 0.857452482 0.026361295 0.067871195 2.919402832 0.008794301 0.007277745 222.310996 -2.346960944 -0.134804312 CIESLIAVFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CIESLIAVFQK 11 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ; 223.08 1.68E-11 210800000 956270 987220 894180 893350 1077940 690660 1029840 873230 955710 FALSE TRUE 896418.7677 1060314.796 915390.3719 916274.8734 993282.9406 890042.3301 875425.0526 982254.6877 796195.8269 1.12587725 1.331726141 1.149705061 1.150815971 1.247535979 1.11786862 1.099509722 1.233684798 1 19.60276378 -4.999999679 0.105036303 0.389135671 1.305226178 0.371026661 0.072368668 161.5677238 1.142439786 21.28451696 0.978098197 1.00E-05 4.999999679 0.916090507 CIIPNHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 CIIPNHEK 8 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4;P35749;P35749-2;P35749-4;P35749-3 P35579;P35580;P35749 MYH9;MYH10;MYH11 Myosin-9;Myosin-10;Myosin-11 0 ;;;;; 112.41 0.0030462 3665890000 6248150 5323060 5780430 5577170 5457690 4350530 7176210 5026040 5485210 FALSE TRUE 5857089.445 5717184.901 5917544.529 5720289.624 5029065.043 5606457.386 6100203.931 5653552.158 4569693.015 1.281724927 1.251109184 1.294954499 1.251788601 1.100525796 1.226878341 1.334926419 1.237184235 1 22.12366582 -1.313473116 2.529329657 0.995374492 1.25292822 0.617981268 0.060988825 1052727.386 1124453.111 36693.54511 0.016124935 0.048587761 1.313473116 0.257553729 CIIVEEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CIIVEEGK 8 0 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 111.01 0.007715 127980000 304820 203830 261210 261710 244250 241250 325510 223480 269170 FALSE TRUE 285741.8603 218921.7853 267406.0246 268425.9217 225067.5903 310894.9586 276702.7974 251381.9699 224243.7881 1.274246492 0.976266889 1.192479073 1.197027235 1.00367369 1.386415032 1.233937402 1.121020886 1 17.7747085 3.725166771 24.25491253 1.183416424 1.098092593 0 0.133225843 163.3204346 2026833.119 0.032572084 0.053415141 5310.883455 -3.725166771 -0.085323831 CIIVEEGKEILVGDVGVTITDPFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 CIIVEEGKEILVGDVGVTITDPFK 24 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;;;;;; 268.22 9.94E-45 1332790000 3140100 1981603 2544855 2472676 2810332 1950668 3389507 1991062 4592572 FALSE TRUE 2943566.746 2128322.948 2605220.162 2536129.052 2589619.861 2513794.185 2881281.892 2239650.474 3826042.064 0.769350336 0.556272752 0.680917805 0.662859689 0.676840405 0.657022098 0.753071149 0.58537006 1 21.8674213 -5 0.351060778 4.891878041 0.654286536 0.704944775 0.066614881 224.7365361 1.836463765 658.6139569 0.046471838 1.00E-05 5 -4.237591504 CILQDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CILQDGR 7 0 P14678-2;P14678;P14678-3;J3QLE5;P63162;P63162-2;J3KRY3;S4R3P3 P14678-2;S4R3P3 SNRPB;SNRPN Small nuclear ribonucleoprotein-associated proteins B and B;Small nuclear ribonucleoprotein-associated protein N 0 ; 111.82 0.035496 0 859020 966000 778000 800490 1050610 626800 995930 934350 1030550 FALSE TRUE 805255.4716 1037523.645 796454.5274 821031.9286 968099.3286 807746.9848 846599.5423 1051005.654 858544.5474 0.937930913 1.208468038 0.927679909 0.95630673 1.127605238 0.940832933 0.986086913 1.224171369 1 19.71153347 -0.562728318 5.973812175 1.000000006 1.036001906 0.011145731 0.111949899 0 0 0.099928596 0.023553396 0.273698037 0.562728318 0.0360019 CKDDEFTHLYTLIVRPDNTYEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CKDDEFTHLYTLIVRPDNTYEVK 23 2 P27797;K7EJB9 P27797 CALR Calreticulin 0 ; 312.01 2.00E-73 1505960000 3484500 1901880 2402700 2498200 2304100 1735900 3564600 2082500 2782200 FALSE TRUE 3266411.365 2042697.174 2459693.179 2562308.041 2123145.28 2237026.15 3030121.322 2342504.709 2317832.846 1.409252341 0.881296154 1.061203867 1.105475766 0.916004484 0.965136961 1.307307957 1.010644367 1 21.1443451 CKDGVVFGVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CKDGVVFGVEK 11 1 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 85.45 0.013869 255390000 901840 758730 619950 592000 899610 370060 776910 754810 835670 FALSE TRUE 845395.4442 814907.1587 634655.5068 607191.7223 828958.2595 476890.3146 660419.558 849049.69 696191.2784 1.214314902 1.17052193 0.911610827 0.872162208 1.190704746 0.684998979 0.948617971 1.219563813 1 19.40912422 4.146325912 2.652552612 0.959769219 1.204620001 0.256378699 0.152261438 0.344852372 4.723092452 0.037097158 0.10669311 14006.38022 -4.146325912 0.244850782 CKDISSALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CKDISSALR 9 1 P13489;E9PMJ3;E9PLZ3;E9PIM9;E9PMN0;E9PIK5;E9PMA9 P13489 RNH1 Ribonuclease inhibitor 0 98.04 0.0057304 242970000 275160 407220 306420 333590 578790 218140 320660 356190 795520 FALSE TRUE 257938.2268 437370.9925 313688.4271 342150.4842 533334.1681 281113.4768 272580.0099 400661.1056 662742.5727 0.389198216 0.659940994 0.473318661 0.516264532 0.804738054 0.424166921 0.411290931 0.604550126 1 19.33808907 0.967885172 22.59885159 1.000000003 0.530193055 0.583204227 0.125120824 859.5820021 604879.8697 0.115794361 0.02894859 9.287207987 -0.967885172 -0.469806949 CKELGITALHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CKELGITALHIK 12 1 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ; 117.92 0.00040977 526770000 1656590 1683730 1474520 1578950 2231400 848800 1848640 1440840 2740000 FALSE TRUE 1552906.989 1808395.121 1509496.311 1619468.53 2056154.845 1093834.781 1571453.594 1620732.046 2282676.299 0.680301009 0.792225828 0.661283561 0.709460439 0.900764969 0.479189617 0.688425948 0.710013963 1 21.12229486 0.906204586 16.4016763 1 0.701634402 0.441000394 0.105230164 961.75542 168182.0226 0.09458174 0.023645327 8.057579265 -0.906204586 -0.298365599 CKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIK 36 3 P63279;H3BQQ9;B0QYN7 P63279 UBE2I SUMO-conjugating enzyme UBC9 0 171.2 3.77E-18 479450000 700380 429580 414000 336280 589700 274720 611620 493290 373000 FALSE TRUE 656544.466 461386.5502 423820.2755 344909.5141 543387.3407 354027.2043 519913.259 554878.3424 310743.8903 2.112815365 1.484780762 1.363889327 1.109947854 1.748666209 1.139289348 1.673124638 1.78564522 1 18.2453665 4.740791586 4.026675129 1.429279787 2.174784542 0.396743018 0.271437666 0.236636086 8.137342337 0.058802555 0.516911411 55054.34321 -4.740791586 0.745504755 CLAFHDISPQAPTHFLVIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CLAFHDISPQAPTHFLVIPK 20 0 P49773;D6REP8;D6RE99;D6RD60 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ; 238.7 7.07E-30 977260000 2072000 1778120 1886990 1625030 1984590 1646730 2583000 1803300 2186570 FALSE TRUE 1942317.219 1909773.855 1931750.294 1666731.021 1828728.307 2122114.219 2195703.129 2028445.975 1821617.341 1.066259732 1.048394639 1.060458885 0.914973185 1.003903655 1.164961581 1.20535915 1.113541208 1 20.7967885 2.238226415 24.99996838 1.146247477 1.02379563 0.326623833 0.068550843 8.370768093 626105.8084 0.02399619 0.01883862 173.0718418 -2.238226415 -0.122451846 CLATHGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 129.2 0.0085695 199653000 130670 147586 144554 149251 144148 116314 150215 119067 120139 FALSE TRUE 122491.598 158513.421 147982.8891 153081.0333 132827.1975 149891.9636 127691.6553 133932.777 100087.0248 1.223850926 1.58375595 1.478542193 1.529479308 1.327117055 1.497616339 1.275806285 1.338163237 1 16.61089543 0.7198706 0.596327133 0.992077109 1.475965369 0.590106967 0.110590866 0.742513296 0.544527471 0.113780327 0.043664645 5.246511153 -0.7198706 0.48388826 CLDEFPNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CLDEFPNLK 9 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 81.594 0.048482 248210000 235590 215340 244960 240920 254850 189610 302160 221230 383260 FALSE TRUE 220844.8424 231283.9977 250770.5669 247102.4151 234835.109 244347.3289 256853.9131 248851.0525 319291.43 0.691671688 0.724366444 0.785397111 0.773908699 0.735488294 0.765279948 0.804449756 0.779385317 1 18.28451431 -5 0.187515185 2.034021973 0.713208214 0.913722671 0.024375866 38.10334452 0.371640363 14.66315885 0.070079796 1.00E-05 5 -1.320813759 CLEELVFGDVENDEDALLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CLEELVFGDVENDEDALLRR 20 1 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 0 ; 119.4 8.25E-05 37006000 18246.8 17669 18948.4 14253.9 21110.9 16497.3 15429.1 12914.2 23520 FALSE TRUE 17104.76536 18977.23114 19397.865 14619.67921 19452.93507 21259.8027 13115.64969 14526.5663 19594.36005 0.872943302 0.968504768 0.989971856 0.746116697 0.992782363 1.084996021 0.66935841 0.741364671 1 14.25815084 1.732039883 24.99999881 0.777846185 0.945395566 0.217487829 0.12095413 0.770534561 2933.872695 0.051901676 0.028782092 53.956017 -1.732039883 0.167549381 CLELFSELAEDKENYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CLELFSELAEDKENYK 16 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 248.2 2.02E-20 915740000 2937400 1242860 1941750 1622800 1557490 1375080 2447300 1456130 1317090 FALSE TRUE 2753553.377 1334882.648 1987809.227 1664443.795 1435171.018 1772043.273 2080350.085 1637931.036 1097259.17 2.50948313 1.21656094 1.811613228 1.516910353 1.307959921 1.614972398 1.895951422 1.492747639 1 20.0654729 CLELFSELAEDKENYKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CLELFSELAEDKENYKK 17 2 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 265.77 7.85E-28 2098200000 3838300 1649200 2560500 2404100 2508500 1678100 3492100 2100600 2913000 FALSE TRUE 3598067.655 1771308.484 2621236.269 2465793.276 2311492.529 2162540.228 2968492.024 2362864.534 2426801.481 1.482637819 0.729894265 1.080119775 1.016067155 0.952485214 0.891107182 1.223211724 0.973653821 1 21.21062467 1.751464462 25 1.087090367 0.994442921 0 0.20208599 13.64560639 26477.84199 0.084735933 0.046991127 56.42407679 -1.751464462 -0.092647446 CLELVEHFGPNELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CLELVEHFGPNELR 14 0 Q969Z0;C9J7P5;C9IZN7 Q969Z0 TBRG4 Protein TBRG4 0 114.7 0.00046202 39555000 27726 25434 29241 26318 34221 26985 21269 27270 30588 FALSE TRUE 25990.67915 27317.15982 29934.61033 26993.36444 31533.4207 34775.13144 18079.9109 30674.71953 25482.66519 1.019935668 1.071989904 1.174704847 1.059283408 1.237445945 1.364658334 0.709498428 1.203748481 1 14.63722855 1.742377739 24.99999996 0.94863578 1.146958464 0.237257749 0.153007106 0.856148099 5635.532936 0.065118841 0.036111705 55.25578325 -1.742377739 0.198322684 CLES(ph)PVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CLESPVGK 8 0 P48729-2;A0A5F9W493;E7ETM0 P48729-2 CSNK1A1 Casein kinase I isoform alpha 1 CLES(1)PVGK 67.414 0.062054 134870000 183370 201410 186670 186570 229300 156230 242640 177520 193230 TRUE FALSE 171893.199 216322.606 191097.9006 191357.7021 211291.703 201331.0648 206258.3846 199683.7628 160978.6647 1.067801124 1.343796747 1.187100793 1.188714681 1.312544761 1.250669244 1.28127777 1.240436198 1 17.29650997 -0.594901639 7.27229259 1 1.244171508 0.472354899 0.077080172 0 1.36E-10 0.066132198 0.015587509 0.254154826 0.594901639 0.244171508 CLIDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CLIDDR 6 0 O95373 O95373 IPO7 Importin-7 0 ; 106.29 0.075031 330350000 1587220 1844000 1860860 1832150 1792970 1553370 2191600 1628440 1668740 FALSE TRUE 1487878.733 1980531.679 1905000.478 1879166.071 1652157.369 2001802.702 1862989.926 1831754.319 1390216.514 1.070249647 1.424621028 1.370290498 1.351707488 1.18841731 1.439921539 1.340071786 1.317603626 1 20.40687816 0.735156599 4.985331585 1.000000219 1.332671062 0.430013134 0.111287925 9.475725122 177.9670718 0.096987199 0.024516726 5.434462533 -0.735156599 0.332670844 CLIKS(ph)PDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CLIKSPDR 8 1 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 CLIKS(1)PDR 72.006 0.028629 139090000 456110 314990 371290 349040 390190 292800 463850 321870 367980 TRUE FALSE 427562.8893 338312.1873 380097.1741 357996.9573 359546.0514 377326.6068 394299.9987 362056.178 306561.7608 1.394703919 1.103569429 1.239871448 1.167780862 1.172833984 1.230833897 1.286200855 1.181021981 1 18.22581823 0.969820081 22.981106 0.999999998 1.217679287 0.453731176 0.077617635 1167.506251 889023.2355 0.069025366 0.017256342 9.328677537 -0.969820081 0.21767929 CLIKS(ph)PDRLADINYEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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;CLIKS(1)PDRLADINYEGR 209.76 2.08E-12 232880000 280750 241717 270350 279680 357800 203272 326010 222128 499800 TRUE FALSE 263178.3587 259613.9782 276762.8297 286857.0623 329699.8313 261953.3266 277127.827 249861.1698 416380.1512 0.632062691 0.623502291 0.664687855 0.688930684 0.791824083 0.62912059 0.665564452 0.600079444 1 18.66754177 -1.911992819 2.528185957 1.202354944 0.662228707 0.803151443 0.052592286 10334127.6 5533067.108 12400117.64 0.012382168 0.012246364 1.911992819 -0.540126237 CLKDEDPYVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 88.338 0.011184 626700000 1071100 918180 1028200 992700 1114400 817750 1308200 946700 1359200 FALSE TRUE 1004061.763 986163.0026 1052589.39 1018174.363 1026879.519 1053821.15 1112047.555 1064897.579 1132340.739 0.88671345 0.870906582 0.929569478 0.899176659 0.906864413 0.930657278 0.982078553 0.940439165 1 20.11087672 2.000204601 0.385305048 1.003345463 0.874621907 0.787064233 0.018528992 0.531288009 0.203493907 0.022062485 0.023126455 100.0471222 -2.000204601 -0.128723556 CLLADLPLPPELPGGDDLS(ph)KSPEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CLLADLPLPPELPGGDDLSKSPEEK 25 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61;A0A2R8YD28;A0A2R8YCQ1;A0A2R8Y7Y0;Q9BVE2;A0A087X209 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 CLLADLPLPPELPGGDDLS(0.579)KS(0.421)PEEK 126.88 7.70E-05 66640000 471590 162670 257490 234540 282520 192290 384080 203290 356710 TRUE FALSE 442074.0237 174714.2561 263597.7844 240558.6935 260332.0188 247801.0014 326490.7696 228671.204 297172.7966 1.487599231 0.587921432 0.887018554 0.809490964 0.876029104 0.83386166 1.098656315 0.76948902 1 18.18094253 CLPAAEGDPQGQGLHDGSFGPASGTLGQEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CLPAAEGDPQGQGLHDGSFGPASGTLGQEDR 31 0 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 0 206.93 5.57E-26 188480000 78423 92686 92289 78294 91747 83591 123870 77459 71182 FALSE TRUE 73514.64442 99548.56788 94478.13866 80303.15659 84541.56071 107722.3647 105296.8435 87129.92666 59301.26435 1.239680894 1.678692166 1.59318928 1.354155893 1.425628301 1.816527285 1.775625606 1.469276037 1 15.85577524 4.750772786 23.93234485 1.571172792 1.239680519 0.073108246 0.240126305 1976.622601 3873482.089 0.053095888 0.86631724 56334.28492 -4.750772786 -0.331492273 CLQDNNWDYTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CLQDNNWDYTR 11 0 Q9UBU9;H0YDU0 Q9UBU9 NXF1 Nuclear RNA export factor 1 0 172.27 3.15E-05 76724000 73326 83540 76939 72543 88339 65021 88445 75126 88076 FALSE TRUE 68736.65655 89725.38852 78764.02941 74404.5762 81401.21128 83791.50717 75183.49333 84505.64647 73375.54661 0.936778801 1.222824124 1.073437038 1.014024149 1.10937792 1.141954112 1.024639636 1.151686773 1 16.16301173 -1.853511558 2.72364272 0.963308539 1.091968985 0.090974863 0.080641133 18301224.36 13484672.57 4370467.276 0.017893114 0.014011623 1.853511558 0.128660446 CLRPEELTNQMNQIEISMQHEQLEESFQELVEDYRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CLRPEELTNQMNQIEISMQHEQLEESFQELVEDYRR 36 2 O14929;O14929-2 O14929 HAT1 Histone acetyltransferase type B catalytic subunit 0 47.749 0.046905 23611000 3494.1 3568.1 4288.1 4430.8 5171.4 3019.4 4462.2 4418.7 5894.7 FALSE TRUE 3275.410518 3832.285837 4389.815757 4544.501829 4765.259104 3891.051764 3793.134535 4970.384422 4910.836489 0.66697609 0.780373333 0.893903873 0.925402798 0.970355889 0.792339915 0.772400902 1.012125823 1 12.26175307 4.561149467 1.383231342 0.888612745 0.618965184 0.490097843 0.080925401 0.893845578 1.960964615 0.022880992 0.306897278 36404.03027 -4.561149467 -0.269647561 CLS(ph)PGGHPTYRPAYLLENEEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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;CLS(1)PGGHPTYRPAYLLENEEEER;CLS(0.999)PGGHPT(0.001)YRPAYLLENEEEER 216.71 1.51E-32 591962000 270642 394712 353314 390173 436031 324900 435287 345734 400091 TRUE FALSE 253703.0003 423936.8872 361694.7749 400185.4997 401786.8841 418693.3557 370019.7554 388899.651 333313.2274 0.761154912 1.271887379 1.085149779 1.200628918 1.205433361 1.256155836 1.110126226 1.16676933 1 18.34651905 4.747527637 24.90732158 1.169214359 0.761154691 0.704994544 0.081374999 567.901261 1577400.442 0.017259625 0.211417518 55914.91086 -4.747527637 -0.408059667 CLTTDEYDGHSTYPSHQYQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 CLTTDEYDGHSTYPSHQYQ 19 0 P30043;M0R192;A0A2R8YEP4 P30043 BLVRB Flavin reductase (NADPH) 0 ;;; 202.96 5.28E-16 3612130000 2620450 2725170 2604800 2677540 2781820 2387190 3504890 2512560 2956260 FALSE TRUE 2456440.712 2926944.422 2666587.086 2746250.209 2563347.079 3076333 2979364.282 2826258.647 2462841.108 0.997401215 1.188442248 1.082728024 1.11507405 1.040808954 1.249099258 1.209726552 1.147560286 1 21.23189212 2.244797054 24.99860296 1.17628745 1.10008857 0.093938824 0.082133605 248.6590614 996745.7761 0.026423025 0.021594628 175.7102328 -2.244797054 -0.07619888 CLVAGLLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CLVAGLLSPR 10 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 CLVAGLLS(1)PR 121.68 0.00053353 20350000 35910 55693 37092 41659 48817 19786 40144 37417 43365 TRUE FALSE 33662.4572 59816.56767 37971.83976 42728.04047 44983.10974 25497.897 34124.77988 42088.59481 36127.10135 0.931778525 1.655725631 1.051062453 1.18271433 1.245134762 0.705783084 0.94457564 1.165014442 1 15.14079388 2.947432346 1.089575106 0.956886239 1.316650138 0.16355248 0.228376107 0.608236132 1.537451909 0.1001233 0.116308162 885.9971938 -2.947432346 0.359763899 CLWEESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CLWEESR 7 0 P40763;P40763-2;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 ; 138.85 0.0063879 794200000 550730 534010 561350 588490 658140 580880 716930 519920 683650 FALSE TRUE 516260.7924 573548.656 574665.4871 603591.6497 606452.3392 748570.6262 609433.0022 584833.1565 569544.3985 0.906445211 1.007030633 1.008991553 1.059779802 1.06480257 1.314332347 1.070035986 1.026843839 1 19.11944879 3.204759838 1.481746376 1.114056249 0.973823696 0.27722759 0.088601966 0.471217702 2.144986596 0.029909974 0.042859708 1602.35905 -3.204759838 -0.140232552 CMIDQAHQEERPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 CMIDQAHQEERPIR 14 1 Q9UBQ5;A0A087WVB9;K7ERF1;Q9UBQ5-2;K7ES31;K7EQM4 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 0 ;;;; 213.34 7.08E-10 1511110000 677704 779002 804068 791283 797974 678873 868044 675593 684922 FALSE TRUE 635287.7164 836680.1186 823140.8727 811588.6614 735304.3409 874852.6145 737888.8607 759942.2732 570604.0934 1.1133599 1.466305847 1.442577931 1.42233235 1.288641896 1.533204238 1.293171341 1.331820577 1 19.12213057 0.523295947 1.144333562 1.000043322 1.391252397 0.479752486 0.117609792 1.339948129 2.404391912 0.101737213 0.031229955 3.336537017 -0.523295947 0.391209075 CNAEEHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CNAEEHVR 8 0 P11279-2;P11279 P11279-2 LAMP1 Lysosome-associated membrane glycoprotein 1 0 111.06 0.003306 389590000 194690 159800 180670 164570 218660 133690 228410 156320 235610 FALSE TRUE 182504.7004 171631.7583 184955.5777 168793.1448 201487.3256 172284.1327 194162.041 175836.8961 196285.1689 0.929793634 0.874400034 0.942279943 0.859938353 1.026503056 0.877723639 0.989183452 0.895823648 1 17.58259164 -5 0.057914836 1.292402211 0.797020755 0.180952217 0.051983863 600.7221374 2.549271826 25.18748394 4.471098612 1.00E-05 5 -0.495381456 CNEIINWLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CNEIINWLDK 10 0 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 185.18 3.44E-06 853852000 1087593 703098 886325 761823 652742 705918 1278046 800220 1021800 FALSE TRUE 1019522.496 755156.1075 907349.0476 781372.6679 601478.2764 909705.067 1086414.867 900129.2285 851254.9789 1.197669935 0.887109181 1.06589573 0.917906723 0.706578277 1.068663432 1.276250823 1.057414348 1 19.69923181 2.00617777 24.9966443 1.149551505 0.953235111 0.191506482 0.143685131 189.8346563 768109.2141 0.050806324 0.037426676 101.4326496 -2.00617777 -0.196316394 CNEIINWLDKNQTAEKEEFEHQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CNEIINWLDKNQTAEKEEFEHQQK 24 2 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 202.46 7.84E-25 3364600000 1777480 789610 1170650 1080660 1093730 824080 1611090 917750 1684710 FALSE TRUE 1666230.7 848073.546 1198418.371 1108391.565 1007832.858 1061978.518 1369522.011 1032333.108 1403521.017 1.187179016 0.60424713 0.853865639 0.7897221 0.718074646 0.756653093 0.975775919 0.735530922 1 20.42061924 -1.279326985 4.643170659 1.000083615 0.814436108 0.098036528 0.15991773 0.000124745 1.94E-05 0.139542873 0.032875784 0.052562137 1.279326985 -0.185647507 CNFYDNKDLECVTNLQEVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 241.65 8.60E-30 368130000 525230 388630 401010 432910 549430 335970 651480 371140 925860 FALSE TRUE 492356.7919 417404.5696 410522.1466 444019.2035 506279.9841 432959.085 553796.622 417477.646 771327.9847 0.638323517 0.541150558 0.532227735 0.575655509 0.656374453 0.561316448 0.717978127 0.541245299 1 19.55698493 -5 0.239976445 3.343384286 0.551196644 0.806650484 0.061737752 66.14163776 0.659964025 75.53407365 0.090033888 1.00E-05 5 -2.792187642 CNREPS(ph)KGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CNREPSKGR 9 2 Q02040 Q02040 AKAP17A A-kinase anchor protein 17A 1 CNREPS(1)KGR;CNREPS(1)KGR 108.56 0.0013519 165354000 182515 140133 136346 153594 156174 87019 209220 116254 186394 TRUE FALSE 171091.7119 150508.5931 139580.1915 157535.4821 143908.724 112139.9727 177849.4033 130768.5678 155283.6372 1.101801291 0.969249535 0.898872502 1.014501495 0.926747509 0.722162197 1.145319664 0.842127156 1 17.24454629 4.734963231 2.955150563 0.941477585 1.128068798 0.179023661 0.110711738 0.68308315 8.763116059 0.024860284 0.301724735 54320.43393 -4.734963231 0.186591213 CNTDQAGRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CNTDQAGRPK 10 1 P33992;B1AHB1;B1AHB2 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ; 83.081 0.014669 43426000 171824 123178 143246 137014 137397 109942 174879 130450 148066 FALSE TRUE 161069.8426 132298.2273 146643.8628 140530.0112 126606.3939 141680.4706 148657.5174 146736.9697 123352.8281 1.3057653 1.072518801 1.188816382 1.139252447 1.026376094 1.148579022 1.205140732 1.189571183 1 16.91243127 4.751684007 24.21995445 1.133047049 1.305765474 0.395610177 0.070337542 1522.078745 2809004.926 0.015969745 0.289208163 56452.6076 -4.751684007 0.172718424 CNVWILDGDLYHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CNVWILDGDLYHK 13 0 O43237;B4E2E0;Q9Y6G9;C9JGM7;C9JLW1 O43237;Q9Y6G9 DYNC1LI2;DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 2;Cytoplasmic dynein 1 light intermediate chain 1 0 129.17 0.0001568 297790000 415280 329640 358810 385440 371310 313230 486060 328780 425250 FALSE TRUE 389288.3661 354046.8886 367321.1426 395331.0429 342148.8104 403654.4161 413179.8154 369828.9067 354273.0278 1.098837155 0.999361681 1.036830675 1.115893709 0.965777193 1.139387942 1.166275113 1.043909295 1 18.43450211 2.212655399 24.99895475 1.109578488 1.039753224 0.058293754 0.063965075 327.6930076 316227.0807 0.022162868 0.016373459 163.175668 -2.212655399 -0.069825264 CPEALFQPSFLGMESCGIHETTFNSIMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 340.09 2.44E-96 3418225000 2817885 3576153 3544130 3316273 4027042 2935351 4408877 3529373 3159042 FALSE TRUE 2641518.608 3840935.089 3628198.437 3401374.18 3710774.366 3782739.182 3747806.824 3970022.988 2631777.482 1.003701349 1.459445229 1.378611399 1.292424684 1.409987885 1.437332452 1.424059158 1.50849493 1 21.32760608 2.727539154 23.41078871 1.391987213 1.328706548 0 0.181709384 1373.375195 2917189.415 0.053074741 0.050536798 533.9974143 -2.727539154 -0.063280665 CPFPAGAALACCS(ph)EDEEDDEEHEGGGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CPFPAGAALACCSEDEEDDEEHEGGGSR 28 0 Q147X3 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 CPFPAGAALACCS(1)EDEEDDEEHEGGGSR;CPFPAGAALACCS(1)EDEEDDEEHEGGGSR 200.06 2.94E-25 332020000 118946 120000 121381 117973 130870 140692 196218 111160 144038 TRUE FALSE 111501.3822 128884.9249 124260.2146 121000.3869 120591.9981 181307.4965 166796.9325 125038.5707 119997.1273 0.929200429 1.074066753 1.035526578 1.008360697 1.004957376 1.510931975 1.390007713 1.042013034 1 16.87264034 2.273231369 24.99902348 1.289953213 1.022430569 0.316762481 0.155070858 165.6159366 119415.2139 0.050582782 0.042318796 187.5993674 -2.273231369 -0.267522644 CPGESSHICDFIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CPGESSHICDFIR 13 0 A0A2C9F2P4;A0A286YFF7;P50897;Q5T0S4;A0A286YFE3;A0A286YFL8;P50897-2;A0A286YFL6 A0A2C9F2P4 PPT1 Palmitoyl-protein thioesterase 1 0 ; 166.6 3.33E-05 1316590000 484900 1024810 536830 501250 1088200 297230 563320 954540 1200380 FALSE TRUE 454550.9746 1100687.999 549563.8611 514112.9236 1002737.162 383035.4759 478855.3956 1073716.42 1000028.823 0.454537873 1.100656274 0.549548021 0.514098106 1.00270826 0.383024436 0.478841594 1.073685473 1 19.93161015 1.22410945 24.99360774 1.036843111 0.662826936 0.324949101 0.23579782 344.9636925 596605.2119 0.220749968 0.056197162 16.75365046 -1.22410945 -0.374016174 CPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTGSQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTGSQDR 37 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 340.01 9.77E-130 720700000 581590 702120 498200 336160 805880 467320 594270 626870 261772 FALSE TRUE 545189.3201 754105.6954 510017.5393 344786.4347 742589.4356 602227.6977 505164.7304 705136.0994 218080.5621 2.499944584 3.457922559 2.338665741 1.581004888 3.405115194 2.761491863 2.316413373 3.233374367 1 17.73450166 3.8277595 5.313342598 2.456137017 3.021303899 0.093595913 0.744008051 0.473046738 20.26961026 0.173749833 0.318943088 6726.040841 -3.8277595 0.565166882 CPLLKPWALTFS(ph)YGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CPLLKPWALTFSYGR 15 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 1 CPLLKPWALT(0.076)FS(0.924)YGR 65.808 0.036606 55250000 76028 120580 78167 71016 153980 47222 78008 90658 140000 TRUE FALSE 71269.54319 129507.8687 80021.15815 72838.39079 141887.0319 60854.22481 66311.42459 101976.8509 116633.0956 0.611057632 1.110386962 0.686093066 0.624508768 1.216524617 0.521757778 0.56854724 0.874338886 1 16.8316177 CPPGVVPACHNSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 196.38 1.42E-07 3717900000 2046170 4698740 4358720 4818630 4994580 4066430 6127340 5021890 4909040 FALSE TRUE 1918103.872 5046639.599 4462110.897 4942284.204 4602325.834 5240342.328 5208602.25 5648884.021 4089689.51 0.469009656 1.23399089 1.091063487 1.208474186 1.12534847 1.281354566 1.273593567 1.381250094 1 21.96355989 4.739943117 24.85925552 1.204889318 0.469009396 0.820342432 0.107389631 43.03331089 773713.0894 0.024280165 0.152437933 54946.89005 -4.739943117 -0.735879922 CPQDQS(ph)PDRVGTEMEQVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CPQDQSPDRVGTEMEQVSK 19 1 Q9H116 Q9H116 GZF1 GDNF-inducible zinc finger protein 1 1 CPQDQS(1)PDRVGTEMEQVSK 107.75 0.00054496 0 167870 143600 152180 152520 157160 125440 168810 120850 178160 TRUE FALSE 157363.3164 154232.2934 155789.7815 156433.9214 144817.2876 161652.4917 143498.5077 135938.3885 148423.945 1.060228633 1.039133499 1.049627009 1.053966874 0.975700299 1.089126769 0.966815076 0.915879095 1 17.17936433 1.607574621 6.400710661 0.952920009 1.042112656 0.564231568 0.034603303 0.081832778 7.155294668 0.016328158 0.007823036 40.51115461 -1.607574621 0.089192647 CPQIVIAFYEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CPQIVIAFYEER 12 0 Q13185;P45973 Q13185;P45973 CBX3;CBX5 Chromobox protein homolog 3;Chromobox protein homolog 5 0 ; 139.86 0.00013769 787890000 463700 444120 411970 444290 533590 365300 515410 462720 521810 FALSE TRUE 434677.8447 477003.1069 421742.1229 455691.2336 491683.9938 470756.1798 438129.0553 520491.6106 434716.54 0.999910987 1.097273885 0.970154306 1.048249127 1.131045057 1.08290377 1.007849978 1.197312646 1 18.72971546 2.992375465 24.65696424 1.079030459 1.028284454 0.158945576 0.064089677 615.9508447 1991933.748 0.017675243 0.020304584 982.5970695 -2.992375465 -0.050746005 CPS(ph)LDNLAVPESPGVGGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CPSLDNLAVPESPGVGGGK 19 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 CPS(0.969)LDNLAVPES(0.031)PGVGGGK 72.09 0.011744 0 158800 122860 138670 145800 142510 110600 165700 111600 117760 TRUE FALSE 148860.9915 131956.6822 141959.3179 149541.4748 131317.8395 142528.4246 140854.8233 125533.5057 98105.09524 1.517362489 1.345054321 1.447012691 1.524298758 1.3385425 1.452813681 1.435754412 1.279581915 1 16.58204045 0.905674967 2.587988084 1.000423727 1.430343863 0.840884378 0.060831979 0.139997553 2.034651793 0.053763415 0.014379866 8.047759083 -0.905674967 0.429920136 CPS(ph)QSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CPSQSSSR 8 0 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 CPS(0.706)QS(0.277)S(0.017)SR 65.627 0.077327 0 17463 23898 25125 24014 25011 20119 21034 22832 18937 TRUE FALSE 16370.022 25667.43279 25720.97686 24630.2399 23046.73695 25927.0287 17880.14697 25682.62546 15776.29236 1.037634295 1.626962292 1.630356251 1.561218525 1.460846213 1.643417103 1.133355453 1.627925299 1 13.94547057 0.026267162 0.516230432 0.958745258 1.515611009 0.274100206 0.2211246 4.733445629 1.571994511 0.645767186 0.099771237 1.062348873 -0.026267162 0.556865751 CPS(ph)QSSSRPAAMISQPPTPPTGQPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CPSQSSSRPAAMISQPPTPPTGQPVR 26 1 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 CPS(0.986)QS(0.012)S(0.002)SRPAAMISQPPTPPTGQPVR 185.47 8.67E-18 924320000 152550 135410 158540 169900 184720 103350 176690 122910 120430 TRUE FALSE 143002.1678 145435.8973 162300.6437 174259.9216 170212.8363 133185.4673 150196.9748 138255.5841 100329.455 1.425325871 1.449583249 1.617676919 1.736876988 1.696539031 1.327481219 1.497037683 1.378015898 1 16.61438569 0.698655337 0.833502292 0.999702147 1.560746535 0.673268403 0.119904416 0.661686075 0.848051046 0.120090769 0.041226811 4.996378567 -0.698655337 0.561044388 CPS(ph)QSSSRPAAMISQPPTPPTGQPVREDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CPSQSSSRPAAMISQPPTPPTGQPVREDAK 30 2 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 CPS(0.512)QS(0.019)S(0.068)S(0.401)RPAAMISQPPTPPTGQPVREDAK;CPS(0.877)QS(0.041)S(0.041)S(0.041)RPAAMISQPPTPPTGQPVREDAK 162.19 2.05E-12 1999710000 172611 157624 169283 190162 246544 118548 226605 146273 241885 TRUE FALSE 161807.5856 169294.645 173298.4727 195041.8789 227181.4288 152770.8831 192627.6839 164535.506 201512.8309 0.802964183 0.840118439 0.859987287 0.967888139 1.127379471 0.75811988 0.955907786 0.816501388 1 17.62051218 3.389407253 5.0434635 0.932969307 0.835220885 0.195733117 0.099617205 0.354547561 15.27224265 0.02641862 0.0363454 2451.360892 -3.389407253 -0.097748422 CPSPPMINLISVGGQHQGVFGLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CPSPPMINLISVGGQHQGVFGLPR 24 0 A0A2C9F2P4;A0A286YFF7;P50897;Q5T0S4;A0A286YFE3;A0A286YFL8 A0A2C9F2P4 PPT1 Palmitoyl-protein thioesterase 1 0 284.95 1.54E-52 125350000 38190 44274 46384 41917 64826 33713 62793 58417 65025 FALSE TRUE 35799.75607 47552.09303 47484.25038 42992.66119 59734.82746 43445.39582 53377.77259 65710.49104 54171.90742 0.660854634 0.877799865 0.876547507 0.793633882 1.102690127 0.801991251 0.985340468 1.212999397 1 15.72525727 6.588749668 0.219068062 1.068737167 1.50E-21 0.453664286 0.118289081 26.70678617 0.579925115 0.17977871 8.889015446 3879266.969 -6.588749668 -1.068737167 CPSQSSS(ph)RPAAMISQPPTPPTGQPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CPSQSSSRPAAMISQPPTPPTGQPVR 26 1 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 CPS(0.379)QS(0.075)S(0.104)S(0.443)RPAAMISQPPTPPTGQPVR 93.807 0.0051982 1065500000 84203 81108 79582 87942 88680 66572 77517 61915 52326 TRUE FALSE 78932.88454 87113.32071 81469.72262 90198.74061 81715.43052 85790.25569 65894.04548 69645.22404 43592.45256 1.810700704 1.998357871 1.868895137 2.069136635 1.874531615 1.96800709 1.511592985 1.597644086 1 15.41179075 1.029010474 0.831206569 1.011387166 1.949534623 0.875541285 0.110730275 0.185610963 0.286043754 0.095147848 0.03453127 10.69080663 -1.029010474 0.938147457 CPSQSSSRPAAMISQPPT(ph)PPTGQPVREDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CPSQSSSRPAAMISQPPTPPTGQPVREDAK 30 2 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 CPSQSSSRPAAMIS(0.001)QPPT(0.997)PPT(0.001)GQPVREDAK 95.784 0.0010076 71101000 84149 58594 75230 70804 78527 48646 86670 63845 116880 TRUE FALSE 78882.2643 62932.36073 77014.49113 72620.95051 72359.80618 62689.3105 73674.6381 71816.18879 97371.97293 0.810112622 0.646308777 0.790930786 0.745809583 0.743127658 0.643812676 0.756630844 0.737544764 1 16.57121895 0.286884931 1.747550448 1.000018217 0.728625988 0.708727512 0.05347697 5.209202411 12.08730703 0.04678878 0.013114908 1.935908965 -0.286884931 -0.271392229 CPSSSGKPNHADILLINLQYVSEVEIINDRTET(ph)PPPLASLNVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CPSSSGKPNHADILLINLQYVSEVEIINDRTETPPPLASLNVSK 44 2 K7ELG9;Q3MHD2 K7ELG9 LSM12 Protein LSM12 homolog 1 CPSSSGKPNHADILLINLQYVSEVEIINDRT(0.006)ET(0.994)PPPLASLNVSK 111.23 1.89E-06 27401000 23717 19639 23212 25826 29455 16695 29859 24315 32302 TRUE FALSE 22232.59531 21093.09199 23762.5996 26488.73888 27141.72312 21514.57548 25381.92015 27350.78127 26910.58752 0.826165363 0.783821311 0.883020469 0.984324064 1.008589021 0.799483678 0.943194575 1.016357642 1 14.71588627 3.595841825 2.653785804 0.946038434 0.808183123 0.491082035 0.063502017 0.238209341 3.289368872 0.01769112 0.030059218 3943.136621 -3.595841825 -0.137855311 CPT(ph)PEIQKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CPTPEIQKK 9 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 CPT(1)PEIQKK;CPT(1)PEIQKK 96.745 0.004196 1011700000 2084710 1495660 1643860 1635810 1824340 1288340 2410330 1513000 2485400 TRUE FALSE 1954231.722 1606400.223 1682853.135 1677787.654 1681063.695 1660262.844 2048923.393 1701901.381 2070570.684 0.943813094 0.775824866 0.81274846 0.810302042 0.811884235 0.801838284 0.989545254 0.821947975 1 20.98159702 1.751889126 25 0.931975181 0.817582178 0.388275555 0.065048955 3.682192782 6916.858673 0.026671828 0.014790916 56.47927669 -1.751889126 -0.114393003 CPTQFPLILWHPYAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CPTQFPLILWHPYAR 15 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 139.65 5.08E-06 203662000 576730 767730 592930 569110 811090 418680 598790 662390 631530 FALSE TRUE 540633.4988 824573.528 606994.5796 583714.3261 747390.2632 539546.1193 509006.9984 745090.8496 526123.5632 1.02757895 1.567262114 1.153711071 1.109462429 1.420560331 1.025512174 0.967466645 1.416189849 1 19.00504214 2.93244476 0.796572654 1.099030504 1.323777521 0.039450839 0.204920218 1.25565067 1.760233845 0.118691128 0.14222029 855.9428328 -2.93244476 0.224747017 CPVTVCGDVHGQFHDLMELFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 CPVTVCGDVHGQFHDLMELFR 21 0 P67775;P62714;P67775-2;E7ESG8 P67775 PPP2CA;PPP2CB Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform;Serine/threonine-protein phosphatase 0 ;; 178.22 3.58E-17 188398000 117043 126602 122861.2 128216 127752 109032 139289 111136 122996 FALSE TRUE 109717.4876 135975.7438 125775.5257 131506.2396 117718.8732 140507.7684 118403.9075 125011.5742 102467.173 1.070757437 1.327017618 1.227471413 1.283398729 1.148844745 1.371246657 1.155530147 1.220015841 1 16.64480227 0.410811457 1.00095615 0.999469258 1.242594261 0.386222508 0.088507319 2.037981781 2.639365351 0.076266489 0.023612183 2.575202927 -0.410811457 0.243125003 CQEHSKES(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 CQEHSKESPAR 11 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 CQEHS(0.094)KES(0.906)PAR;CQEHS(0.026)KES(0.974)PAR;CQEHSKES(1)PAR;CQEHS(0.005)KES(0.995)PAR 150.12 2.06E-05 839433000 576680 369787 497917 458787 451263 372081 584658 400177 577294 TRUE FALSE 540586.6282 397166.4142 509727.8264 470560.2511 415822.6243 479494.7445 496993.9606 450139.9793 480939.9019 1.124021164 0.825812981 1.059857634 0.978417988 0.864604127 0.996995139 1.033380592 0.935958895 1 18.8754971 2.050970536 24.99998742 0.998915467 0.960632155 0.004037657 0.087818084 371.8765045 182395.8522 0.030616666 0.022611903 112.4528679 -2.050970536 -0.038283312 CQEVISWLDANTLAEKDEFEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 CQEVISWLDANTLAEKDEFEHK 22 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ;;; 368.62 3.31E-113 1976720000 3505730 1653593 2181290 2046540 2260130 1566264 3307590 1961720 2947680 FALSE TRUE 3286312.617 1776026.746 2233031.229 2099057.681 2082628.507 2018418.991 2811647.586 2206645.06 2455693.165 1.33824236 0.723228281 0.909328275 0.854771969 0.84808173 0.821934523 1.144950691 0.898583378 1 21.22769888 1.75266333 25 1.025898361 0.887972179 0.050765999 0.172706446 9.170113557 16278.49915 0.072387681 0.040143419 56.58005035 -1.75266333 -0.137926183 CQHAAEIITDLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CQHAAEIITDLLR 13 0 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 184.21 9.70E-06 673070000 952170 993410 922810 902640 1119800 751160 992980 876840 1005900 FALSE TRUE 892575.3794 1066963.11 944699.489 925803.2706 1031855.425 968007.6979 844091.8674 986315.4042 838008.7916 1.065114577 1.273212311 1.127314532 1.104765582 1.231318138 1.155128332 1.007258964 1.176975008 1 19.67660585 1.244385343 0.480542369 1.002418063 1.181053371 0.236364737 0.077254236 1.10707475 0.69216653 0.083389404 0.047001998 17.55437385 -1.244385343 0.178635308 CQHGEEECK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CQHGEEECK 9 0 P13284 P13284 IFI30 Gamma-interferon-inducible lysosomal thiol reductase 0 160.53 6.52E-05 654980000 1281800 749180 827170 835790 774740 737510 1199500 685270 1038200 FALSE TRUE 1201574.426 804650.0667 846790.863 857237.7864 713895.0456 950417.1645 1019646.111 770827.468 864917.713 1.38923554 0.930319792 0.97904211 0.991120627 0.82539071 1.0988527 1.178893778 0.891214802 1 19.72220336 4.744565688 24.78121946 0.996891007 1.389235735 0.616849769 0.09938382 449.6633551 1855573.247 0.025132785 0.228815057 55534.86086 -4.744565688 0.392344728 CQHLQAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CQHLQAEK 8 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 90.629 0.013061 692370000 2130100 3239400 1430010 1425270 3649900 875950 1717110 2939900 3634400 FALSE TRUE 1996780.843 3479248.547 1463930.512 1461844.841 3363251.577 1128822.545 1459645.296 3306952.987 3027795.161 0.659483465 1.149103014 0.48349721 0.482808368 1.110792309 0.372819985 0.482081917 1.092198386 1 21.52983618 1.221953759 24.94055683 1.046099569 0.687359776 0.253246765 0.262890968 405.4976122 608968.5212 0.24949219 0.063085193 16.67069704 -1.221953759 -0.358739794 CQVFEETQIGGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 CQVFEETQIGGER 13 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;; 237.67 2.20E-16 655000000 541460 531000 569410 561930 559080 462490 673340 493310 558970 FALSE TRUE 507570.9851 570315.7925 582916.6741 576350.0751 515172.112 596003.3551 572378.918 554900.8394 465674.2959 1.089969942 1.224709625 1.251769057 1.237667787 1.106292781 1.279871705 1.22914003 1.19160719 1 18.82896173 0.852747976 6.564595763 1.000000204 1.212272048 0.515382778 0.060922424 3.698007296 164.8338818 0.054307181 0.013632559 7.124394767 -0.852747976 0.212271844 CQYVTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 157.58 0.0034116 2719960000 2334590 1929120 1914710 1922850 1892790 1414330 2325760 1636820 1610400 FALSE TRUE 2188472.179 2071954.052 1960127.825 1972193.586 1744137.909 1822624.111 1977033.879 1841180.58 1341613.836 1.63122362 1.544374391 1.461022369 1.470015837 1.300029756 1.358531093 1.473623651 1.372362546 1 20.35553804 -3.59253325 0.123133334 5.66E-15 1.691987141 0.841700064 0.067731111 41.35394335 0.463395816 11.46909823 0.696417033 0.000255545 3.59253325 1.691987141 CRDDSFFGETSHNYHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 CRDDSFFGETSHNYHK 16 1 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 270.17 8.10E-29 2253351000 2210116 1948220 2071030 2153130 2217580 1794800 2438260 1942750 2029590 FALSE TRUE 2071788.785 2092468.236 2120155.81 2208382.961 2043420.212 2312929.624 2072665.549 2185306.614 1690838.317 1.225302717 1.237533012 1.253908069 1.306087601 1.208524902 1.36791886 1.225821255 1.292439727 1 20.68930728 -1.097901851 4.036621051 0.999941781 1.262721545 0.754611971 0.04742418 0.779156626 11214946.74 1397.441192 0.009758051 0.079817505 1.097901851 0.262779763 CRDDSFFGETSHNYHKFDSEYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 CRDDSFFGETSHNYHKFDSEYER 23 2 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;; 279.44 2.26E-52 3943080000 923373 1022530 1038330 1062460 1399020 765059 1392090 969050 2222440 FALSE TRUE 865580.7322 1098239.185 1062959.678 1089724.522 1289146.613 985919.1136 1183359.028 1090038.026 1851500.406 0.467502318 0.593161731 0.57410718 0.58856294 0.69627131 0.532497379 0.639135171 0.588732264 1 20.82026344 -5 0.270698153 3.837727816 0.559095273 0.843756504 0.056698821 73.22436789 0.710774622 116.1682311 0.062422595 1.00E-05 5 -3.278632543 CREEWAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CREEWAK 7 1 Q96PZ0;Q96PZ0-2;E7EUH7 Q96PZ0 PUS7 Pseudouridylate synthase 7 homolog 0 62.464 0.077793 160340000 134130 249140 213730 211790 246430 166750 224830 212120 231520 FALSE TRUE 125735.0427 267586.5848 218799.7765 217224.89 227076.3819 214888.018 191118.8287 238603.6489 192877.8163 0.651889601 1.387337279 1.134395757 1.126230554 1.177306889 1.114114739 0.990880301 1.237071497 1 17.5573277 1.991249657 22.99590859 1.069352355 1.142263827 0 0.194699823 628.0469957 1650506.091 0.07011419 0.049125182 98.00532144 -1.991249657 0.072911472 CRHENLLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CRHENLLLR 9 1 Q6ZMV8 Q6ZMV8 ZNF730 Putative zinc finger protein 730 0 68.735 0.052194 553220000 14858 14893 9998.1 14589 18583 7212.8 11774 15713 11947 FALSE TRUE 13928.0643 15995.69322 10235.25965 14963.37844 17123.56614 9295.01827 10008.598 17674.80264 9952.968519 1.399387959 1.607127882 1.028362506 1.503408597 1.720448136 0.933894069 1.005589236 1.775832266 1 13.28091117 2.227050742 24.98624079 1.151919136 1.417549353 0.169501397 0.292147311 404.5078665 878120.6767 0.106196909 0.079100328 168.6750091 -2.227050742 0.265630217 CRS(ph)PGMLEPLGSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 CRSPGMLEPLGSSR 14 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(0.574)PGMLEPLGS(0.056)S(0.369)R;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR 176.91 1.31E-06 14714380000 2698980 3023138 2946710 3094579 3431866 2360286 3093589 2669283 3185920 TRUE FALSE 2530055.66 3246974.283 3016607.353 3173991.136 3162341.088 3041662.252 2629734.049 3002548.858 2654169.37 0.95323821 1.223348562 1.136554203 1.195851015 1.191461677 1.14599403 0.990793609 1.131257444 1 21.33982901 1.759384022 24.99973779 1.042532679 1.154090985 0.238705824 0.082334049 11.69646185 14054.41781 0.034340652 0.019044419 57.46243458 -1.759384022 0.111558305 CS(ph)PTVAFVEFPSSPQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.988)PT(0.012)VAFVEFPSSPQLK;CS(0.976)PT(0.024)VAFVEFPSSPQLK;CS(0.945)PT(0.055)VAFVEFPSSPQLK;CS(0.877)PT(0.123)VAFVEFPSSPQLK;CS(0.938)PT(0.062)VAFVEFPSSPQLK;CS(0.893)PT(0.107)VAFVEFPSSPQLK 290.63 5.90E-46 253546000 952769 691059 755147 713303 878130 584594 987459 723708 1128296 TRUE FALSE 893136.889 742225.7274 773059.4434 731607.5626 809165.212 753356.7977 839398.6901 814064.5369 939976.1085 0.950169777 0.789621907 0.822424566 0.7783257 0.860835935 0.801463772 0.893000027 0.866048115 1 19.84226456 0.710398538 0.821310934 0.999719047 0.826019002 0.485688434 0.050860074 0.780867694 0.985645148 0.044754109 0.015477765 5.133322365 -0.710398538 -0.173700045 CSATPSAQVKPIVSAS(ph)PPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CSATPSAQVKPIVSASPPSR 20 1 Q96EV2;H0Y3K4 Q96EV2 RBM33 RNA-binding protein 33 1 CSATPSAQVKPIVS(0.001)AS(0.995)PPS(0.004)R 198.18 9.57E-22 293910000 501890 385610 408760 407890 458420 311740 534240 365420 501180 TRUE FALSE 470477.6008 414160.9656 418455.9802 418357.148 422417.5424 401734.2773 454135.6716 411043.4914 417529.8203 1.126811974 0.991931463 1.002218189 1.001981482 1.011706283 0.962169066 1.087672424 0.984464993 1 18.67151971 CSCSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 CSCSFR 6 0 Q9H3K6;A0A087WZT3;H3BV85;Q9H3K6-2;H3BTW0;A0A0B4J295;H3BVE0 Q9H3K6 BOLA2;BOLA2B BolA-like protein 2 0 ;;; 122.15 0.045 942920000 1131790 994850 907790 887590 1062850 669460 1059050 910910 1074930 FALSE TRUE 1060953.284 1068509.729 929323.2075 910367.0621 979378.0483 862722.2342 900255.2842 1024639.119 895517.2387 1.18473798 1.193176058 1.037750216 1.016582398 1.093645109 0.963378701 1.005290848 1.144186928 1 19.77236168 3.951806699 2.329175931 1.031904467 1.19095117 0.6035168 0.050869704 0.187602487 2.003775667 0.013069416 0.03183296 8949.663349 -3.951806699 0.159046703 CSDAAGYPHATHDLEGPPLDAYSIQGQHT(ph)ISPLDLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAK 37 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 CSDAAGYPHATHDLEGPPLDAYSIQGQHT(0.626)IS(0.374)PLDLAK 308.86 2.45E-109 994340000 354200 272710 371930 352550 391760 263150 488390 312010 495430 TRUE FALSE 332031.2543 292901.7322 380752.3552 361597.0299 360992.7499 339117.1331 415160.4535 350965.1353 412739.5324 0.804457117 0.709652721 0.922500331 0.876090128 0.874626057 0.821625036 1.005865494 0.850330796 1 18.6548721 7.999999996 0.14969643 1.013941104 0.034289429 0.485877191 0.063582865 51.31543547 0.503974138 0.208746777 10.92381397 99999998.98 -7.999999996 -0.979651676 CSDAAGYPHATHDLEGPPLDAYSIQGQHTIS(ph)PLDLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 CSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAK 37 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 CSDAAGYPHATHDLEGPPLDAYSIQGQHT(0.001)IS(0.999)PLDLAK;CSDAAGYPHATHDLEGPPLDAYS(0.013)IQGQHT(0.088)IS(0.899)PLDLAK;CSDAAGYPHATHDLEGPPLDAYSIQGQHT(0.001)IS(0.999)PLDLAK 374.87 9.13E-162 3392350000 1211100 939320 1252450 1209790 1390960 950640 1811300 1118650 1928150 TRUE FALSE 1135299.413 1008868.23 1282158.705 1240835.26 1281719.612 1225074.336 1539712.38 1258315.915 1606329.309 0.706766294 0.62805816 0.79819169 0.772466301 0.797918338 0.762654537 0.958528474 0.783348662 1 20.61533626 4.618294478 0.115714525 1.125227323 0.237838139 0.688942569 0.060475541 20.21478305 0.39842406 0.650417673 3.010916156 41523.55022 -4.618294478 -0.887389184 CSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAK 37 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ; 215.84 1.76E-39 694020000 473472 436326 522845 484348 534430 384693 609850 438334 498254 FALSE TRUE 443838.2327 468632.031 535247.1303 496777.1897 492458.0236 495747.6241 518408.6541 493060.9648 415092.1886 1.069252192 1.128983016 1.289465678 1.196787613 1.186382296 1.194307284 1.248900048 1.187834843 1 18.66307226 0.939124082 21.91399626 1 1.196538119 0.488381781 0.059861768 5551.061801 1998263.843 0.057896882 0.01447422 8.692087352 -0.939124082 0.19653812 CSDIVFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CSDIVFAR 8 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 109.36 0.013182 0 137880 155140 192540 182000 198010 182220 198500 141960 159690 FALSE TRUE 129250.3369 166626.727 197107.1397 186670.4281 182459.0933 234823.9559 168736.7678 159684.0185 133036.7074 0.971538904 1.252486854 1.481599655 1.403149791 1.371494356 1.765106492 1.268347444 1.200300441 1 17.02146484 1.059525471 2.450795038 1.008795364 1.379651717 0.261861265 0.197608243 0.346018501 4.318311001 0.181138767 0.0494901 11.46899785 -1.059525471 0.370856353 CSDVSELSS(ph)SPPGPYHQEPYVCKPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CSDVSELSSSPPGPYHQEPYVCKPEER 27 1 Q9Y478;F5H610;F5H2X8 Q9Y478 PRKAB1 5-AMP-activated protein kinase subunit beta-1 1 CSDVSELS(0.007)S(0.496)S(0.496)PPGPYHQEPYVCKPEER 70.632 0.01257 52830000 52348 42135 43607 52707 51864 39672 60227 42690 42202 TRUE FALSE 49071.63212 45254.71924 44641.37863 54059.55085 47790.81065 51124.66238 51196.52047 48019.94047 35158.21356 1.395737358 1.287173455 1.269728297 1.537608012 1.359307138 1.454131402 1.456175251 1.365824244 1 15.10157415 0.939594793 21.83580655 0.999999999 1.383372425 0.704015323 0.07958012 3907.36098 1412470.193 0.084912734 0.021228184 8.701513397 -0.939594793 0.383372425 CSDVSELSSS(ph)PPGPYHQEPYVCKPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 CSDVSELSSSPPGPYHQEPYVCKPEER 27 1 Q9Y478;F5H610;F5H2X8 Q9Y478 PRKAB1 5-AMP-activated protein kinase subunit beta-1 1 CSDVSELS(0.003)S(0.124)S(0.873)PPGPYHQEPYVCKPEER;CSDVSELS(0.005)S(0.146)S(0.849)PPGPYHQEPYVCKPEER;CSDVSELSS(0.18)S(0.82)PPGPYHQEPYVCKPEER;CSDVSELS(0.002)S(0.249)S(0.749)PPGPYHQEPYVCKPEER 196.01 3.90E-25 1737100000 1071890 846020 954900 1089730 1087120 892290 1332120 865387 888394 TRUE FALSE 1004802.318 908660.2011 977550.6789 1117694.317 1001741.98 1149879.638 1132380.973 973432.4719 740115.3022 1.357629433 1.227727894 1.320808631 1.510162421 1.353494486 1.553649323 1.530006162 1.315244353 1 19.49739052 3.420536329 7.550210853 1.422459151 1.283305571 0 0.163238514 0.418489158 47.4014453 0.040507765 0.055131076 2633.518232 -3.420536329 -0.13915358 CSGPGLS(ph)PGMVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 225.72 1.78E-11 2108640000 2024770 1896670 1860420 1936200 2133590 1416280 2140570 1714770 2247650 TRUE FALSE 1898043.26 2037101.42 1904550.041 1985886.17 1966026.448 1825137.045 1819611.401 1928862.809 1872502.695 1.013639802 1.087903065 1.017114713 1.060551836 1.049945858 0.974704629 0.971753689 1.030098816 1 20.83653636 2.246123793 24.98609231 0.989029137 1.048321418 0.483182426 0.026260055 120.2447179 397247.386 0.008660151 0.007115878 176.2478359 -2.246123793 0.059292281 CSKQSPSGAHGT(ph)HFGDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 CSKQSPSGAHGTHFGDDR 18 1 A0A0A0MRP9;Q96C92-3;Q96C92 A0A0A0MRP9 SDCCAG3 Serologically defined colon cancer antigen 3 1 CS(0.002)KQS(0.002)PS(0.002)GAHGT(0.993)HFGDDR;CS(0.004)KQS(0.004)PS(0.004)GAHGT(0.989)HFGDDR;CS(0.004)KQS(0.004)PS(0.004)GAHGT(0.987)HFGDDR 73.464 0.029557 958580000 82797 305022 315196 331490 303270 501293 266008 231138 163728 TRUE FALSE 77614.88357 327606.1463 322672.598 339996.5946 279452.3975 646008.1513 226122.5699 259996.0881 136400.7391 0.56902099 2.401791577 2.365622064 2.492630149 2.048760142 4.736104479 1.657781119 1.90611935 1 17.05749194 4.738662571 6.954282184 2.42865672 0.540695919 0.240891636 0.965232206 0.143442651 52.00031133 0.2081867 1.273196593 54785.11417 -4.738662571 -1.887960801 CSNNVVHVHSCADSCALLVNLLQYVMSTGDLHPPPRPPS(ph)PTEIAGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CSNNVVHVHSCADSCALLVNLLQYVMSTGDLHPPPRPPSPTEIAGQK 47 1 H7C3T2;Q2TAZ0-3;Q2TAZ0 H7C3T2;Q2TAZ0 ATG2A Autophagy-related protein 2 homolog A 1 CSNNVVHVHSCADSCALLVNLLQYVMSTGDLHPPPRPPS(0.818)PT(0.182)EIAGQK 105.3 7.52E-08 92470000 57969 53110 56401 53106 56971 44553 76643 51035 50825 TRUE FALSE 54340.82377 57042.31966 57738.85835 54468.78987 52496.72747 57414.72784 65151.09367 57406.83209 42341.97916 1.283379399 1.347181232 1.363631543 1.286401603 1.239826964 1.35597648 1.538687963 1.355790004 1 15.36980109 6.741957861 5.472370665 1.338209903 1.30045066 0 0.137960757 0 0 0.028280647 0 5520238.748 -6.741957861 -0.037759243 CSS(ph)PTVGPPPLPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CSSPTVGPPPLPQK 14 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 CS(0.034)S(0.966)PTVGPPPLPQK;CS(0.006)S(0.993)PT(0.001)VGPPPLPQK 223.03 3.85E-12 253450000 635270 579060 587900 672510 676740 354380 722990 457060 403300 TRUE FALSE 595509.5847 621934.2049 601845.2656 689767.7452 623591.5702 456683.7531 614584.3614 514124.9471 335986.6246 1.772420511 1.851068344 1.791277454 2.052961918 1.856001176 1.359231945 1.829192939 1.530194685 1 18.35804428 0.293164813 0.456811027 0.925621555 1.861350262 0.708359967 0.163958348 1.485141933 0.495094823 0.375163073 0.091144884 1.964105505 -0.293164813 0.935728706 CSWQDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 98.629 0.025875 478940000 1606540 1072590 1207250 1181000 1296860 936360 1495170 1024440 1446730 FALSE TRUE 1505989.529 1152005.68 1235886.54 1211306.459 1195009.847 1206671.931 1270983.139 1152343.589 1205261.417 1.249512768 0.955813953 1.025409528 1.005015545 0.991494318 1.001170298 1.054529019 0.956094315 1 20.20091466 4.745238383 24.9983633 1.002677213 1.24951288 0.878570622 0.029271653 252.591659 945558.1278 0.006799008 0.066015712 55620.94757 -4.745238383 0.246835667 CT(ph)CPDQFPMIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CTCPDQFPMIK 11 0 A0A5E8;Q99501;Q99501-4;Q99501-2;Q99501-3 A0A5E8 GAS2L1 GAS2-like protein 1 1 CT(1)CPDQFPMIK 98.898 0.057875 483940000 80154 470800 376460 373750 372380 666590 319940 425240 181910 TRUE FALSE 75137.30422 505658.5219 385389.809 383341.0578 343134.7769 859023.7118 271967.9672 478332.1501 151548.0458 0.495798569 3.336621856 2.543020643 2.52950182 2.264197965 5.668325891 1.794598972 3.156306949 1 17.20941572 4.745420014 24.47010647 2.881256302 0.495797087 0.255407112 1.219727343 759.8471793 2710572.052 0.2574801 2.514865806 55644.2142 -4.745420014 -2.385459215 CTGDFSPS(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CTGDFSPSPEK 11 0 A0A2R8YH03;Q5VWN6;Q5VWN6-2 A0A2R8YH03 FAM208B Protein FAM208B 1 CTGDFSPS(1)PEK;CTGDFS(0.002)PS(0.998)PEK 168.61 1.87E-05 189102000 804630 439720 585220 513780 588640 413090 770050 452750 645620 TRUE FALSE 754269.6446 472277.3263 599101.6948 526964.4646 542410.5889 532342.377 654588.1513 509276.8341 537861.8511 1.402348285 0.878064368 1.113857942 0.979739432 1.008457074 0.989738119 1.21701911 0.946854351 1 19.03687614 4.753685329 24.83781708 1.029830744 1.402348577 0.628018803 0.092784966 1833.407749 3010768.469 0.021937614 0.523071612 56713.35358 -4.753685329 0.372517834 CTHWAEGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 CTHWAEGGK 9 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ;;;; 114.97 0.0015521 2242820000 8992760 6773030 7542910 7487580 8108840 5541440 9689780 6789000 9569080 FALSE TRUE 8429919.204 7274512.189 7721831.387 7679723.979 7472004.416 7141163.77 8236887.445 7636621.594 7971938.729 1.057449071 0.912514814 0.968626535 0.963344582 0.937288239 0.895787589 1.033235167 0.957937818 1 22.92649919 1.722089288 24.99999608 0.997137936 0.951887553 0.14612453 0.046323864 1.518690398 2295.85104 0.019431477 0.010775706 52.73382669 -1.722089288 -0.045250383 CTKEEHLCTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 CTKEEHLCTQR 11 1 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;;; 177.16 4.87E-06 5510400000 6018620 6700800 6005910 6587840 7694300 4042530 7124450 5232410 9019900 FALSE TRUE 5641925.318 7196934.204 6148373.021 6756895.128 7090020.715 5209542.786 6056204.863 5885687.906 7514420.419 0.750813104 0.95774974 0.818209879 0.899190457 0.943521964 0.693272734 0.805944374 0.78325241 1 22.8412304 2.259847585 24.999926 0.800636039 0.878887466 0.052669777 0.095741074 436.2500754 512341.398 0.029481844 0.024644285 181.9062348 -2.259847585 0.078251427 CTLAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 CTLAEK 6 0 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;; 122.79 0.04436 1376720000 1569160 1349640 1320800 1270260 1486940 1002430 1657500 1239390 1698450 FALSE TRUE 1470949.077 1449568.75 1352130 1302857.022 1370161.73 1291815.268 1408973.262 1394130.57 1414967.723 1.039563697 1.024453581 0.955590702 0.920768016 0.968334266 0.912964478 0.995763536 0.985273761 1 20.43233771 4.109262864 2.331491033 0.960343396 1.036143138 0.50248673 0.028700591 0.240193837 2.52884567 0.007333015 0.021634241 12860.64837 -4.109262864 0.075799742 CTLPEHES(ph)PSQDISDACEAESTER ddPTM_SK-BR-3_Pertuzumab_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(1)PSQDISDACEAESTER;CTLPEHES(1)PSQDISDACEAESTER;CTLPEHES(0.975)PS(0.025)QDISDACEAESTER;CTLPEHES(0.998)PS(0.002)QDISDACEAESTER 338.44 2.42E-87 2754100000 804160 786930 819400 837830 901370 922450 1141880 731140 881850 TRUE FALSE 753829.0611 845195.116 838836.5549 859330.1362 830580.0362 1188746.34 970665.6947 822424.4384 734663.538 1.026087484 1.150451972 1.141796906 1.1696921 1.130558403 1.618082672 1.321238423 1.11945727 1 19.48672415 2.38680008 23.34194176 1.314822383 1.13179324 0.122341316 0.164098177 16.52598144 4263.30809 0.05243896 0.043873464 243.6688874 -2.38680008 -0.183029142 CTMHCNDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 CTMHCNDK 8 0 E7EQY1;Q96C01;C9JF51 E7EQY1 FAM136A Protein FAM136A 0 ;; 77.677 0.024723 141357000 150474 134669 107845 113503 172956 69158 127181 143266 186755 FALSE TRUE 141056.1009 144640.0329 110403.1343 116415.6791 159372.7334 89122.79191 108111.3897 161153.0755 155584.384 0.9066212 0.929656493 0.709602927 0.748247839 1.024349162 0.572826074 0.694873013 1.035792098 1 17.24733774 1.225785083 24.99705068 1.017896267 0.792201689 0.329023772 0.130329371 304.2292633 595247.6033 0.121380069 0.031140869 16.81841571 -1.225785083 -0.225694578 CTVDVPEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CTVDVPEDLR 10 0 B4DXZ6;P51114;P51114-3;C9JZE0;C9JY20;C9J5B4;C9IZ22;C9JAJ4;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 96.331 0.01585 104820000 64915 72736 70240 76130 70121 69138 80397 64901 63959 FALSE TRUE 60852.08603 78121.44912 71906.12597 78083.62469 64613.97951 89097.01824 68342.21622 73004.03271 53283.82971 1.142036643 1.46613803 1.349492451 1.465428163 1.212637678 1.672121143 1.282607061 1.370097328 1 15.70141016 0.398531392 1.598334024 1.000061316 1.385074999 0.381125474 0.14744368 4.325183479 10.46930252 0.121833559 0.034746088 2.503406593 -0.398531392 0.385013683 CTVFHGAQVEDAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 CTVFHGAQVEDAFR 14 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;; 229.48 1.27E-12 52843080000 26328890 33297160 28092600 29554560 35295770 21193180 34464690 31689440 33658500 FALSE TRUE 24681011.77 35762516.37 28758969.74 30312980.05 32523782.6 27311307.02 29297029.69 35645936.34 28040678.91 0.880185956 1.275379833 1.025616029 1.081035882 1.159878572 0.973988794 1.044804578 1.2712223 1 24.74101794 3.744160855 24.93488163 1.076290284 1.11935709 0 0.127540396 2112.84967 3091817.414 0.029900668 0.053721844 5548.311743 -3.744160855 0.043066806 CVELVHEEMQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CVELVHEEMQR 11 0 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;O00429-7;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 0 81.525 0.021436 135130000 222890 274230 226540 242970 274630 202730 285010 222040 304230 FALSE TRUE 208939.7128 294534.2745 231913.6358 249205.0215 253061.6676 261254.86 242275.3964 249762.1828 253452.0476 0.824375714 1.162090728 0.915019776 0.983243276 0.998459748 1.030786148 0.955902305 0.985441566 1 17.95135329 CVFELPAENDKPHDVEINK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CVFELPAENDKPHDVEINK 19 1 O95292 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 0 ; 254.72 3.93E-31 456290000 754490 428890 490250 418530 635690 395850 793200 504990 840890 FALSE TRUE 707267.8177 460645.4619 501878.9615 429270.1884 585765.4717 510125.4689 674267.0237 568039.1131 700540.0266 1.009603721 0.657557662 0.716417253 0.612770394 0.836162745 0.728188896 0.962496072 0.810858897 1 19.41810796 1.75490991 11.06759582 0.913687689 0.740481867 0.289574135 0.118287177 0.168297966 94.70788233 0.051118472 0.027985858 56.87349402 -1.75490991 -0.173205822 CVFSYNS(ph)NCQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CVFSYNSNCQEK 12 0 Q6NT55 Q6NT55 CYP4F22 Cytochrome P450 4F22 1 CVFS(0.1)Y(0.084)NS(0.815)NCQEK;CVFS(0.053)Y(0.047)NS(0.901)NCQEK 64.55 0.040671 2629500000 1246280 1430430 1270830 1453450 1821410 219676 316310 879140 2190300 TRUE FALSE 1168277.559 1536340.526 1300974.688 1490747.988 1678363.806 283092.8951 268882.252 988902.5642 1824724.78 0.64024864 0.841957397 0.712970362 0.816971416 0.91979011 0.155142791 0.147354963 0.541946147 1 20.79924745 2.243946064 24.99999696 0.355663597 0.78534404 0.246724095 0.254305964 121.7462394 565164.8532 0.081783324 0.066576064 175.3662697 -2.243946064 0.429680444 CVGAELEYDS(ph)EHSDWHGFD ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CVGAELEYDSEHSDWHGFD 19 0 Q9GZN8-2;Q9GZN8;H7BYU9 Q9GZN8-2 C20orf27 UPF0687 protein C20orf27 1 CVGAELEYDS(1)EHSDWHGFD;CVGAELEYDS(1)EHSDWHGFD 356.71 3.32E-91 318160000 382530 400980 424910 391330 415760 381680 531310 352780 444460 TRUE FALSE 358588.1301 430668.9764 434989.0659 401372.1903 383107.8867 491864.8199 451644.9979 396825.3596 370276.7547 0.968432735 1.163100224 1.174767415 1.083978903 1.034652815 1.328370776 1.219749801 1.071699356 1 18.49824446 CVGAELEYDSEHSDWHGFD ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 CVGAELEYDSEHSDWHGFD 19 0 Q9GZN8-2;Q9GZN8;H7BYU9 Q9GZN8-2 C20orf27 UPF0687 protein C20orf27 0 ;;; 278.2 1.55E-39 512616000 485323 616395 624662 631887 621703 595901 772623 574255 658838 FALSE TRUE 454947.4998 662033.5272 639479.2776 648102.2902 572876.9542 767927.9451 656775.3538 645952.0008 548873.6815 0.828874685 1.206167374 1.165075498 1.180785875 1.04373187 1.399097772 1.196587441 1.176868235 1 19.06611464 4.740534055 24.75782243 1.186092253 0.828874546 0.502257153 0.106111191 116.1039967 1456463.425 0.022789326 0.149045323 55021.70644 -4.740534055 -0.357217707 CVLFTYFQGDISSVVDEHFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CVLFTYFQGDISSVVDEHFSR 21 0 Q99990;Q8N8G2-2;Q8N8G2 Q99990 VGLL1;VGLL2 Transcription cofactor vestigial-like protein 1;Transcription cofactor vestigial-like protein 2 0 153.19 4.55E-08 22051000 18035 34611 30554 29669 33598 24064 33330 26554 28710 FALSE TRUE 16906.22154 37173.63445 31278.75531 30430.35677 30959.34861 31010.88615 28332.47592 29869.32535 23918.11553 0.706837523 1.554204152 1.307743299 1.272272338 1.294389124 1.296543874 1.184561379 1.248816 1 14.54581611 0.460829063 0.734762487 0.997218536 1.285501104 0.070613809 0.214577922 3.547585422 2.987712583 0.219092507 0.070055359 2.889542343 -0.460829063 0.288282568 CVLLSNLSSTSHVPEVDPGSAELQK ddPTM_SK-BR-3_Pertuzumab_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 0 231.29 1.58E-34 366350000 464160 505340 570330 544670 651450 431120 779280 577590 620080 FALSE TRUE 435109.0541 542755.8994 583858.4969 558647.1543 600287.7448 555577.3454 662434.1985 649703.3829 516584.6421 0.842280274 1.050662089 1.130228136 1.081424241 1.162031729 1.075481731 1.282334286 1.257690086 1 18.97864523 5.693691445 0.659115586 1.167761682 1.43E-11 0.547491037 0.084685691 7.209322288 0.923397895 0.032210053 8.43053481 493959.6171 -5.693691445 -1.167761682 CVNMDGWQANMILDDGGDLTHWVYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CVNMDGWQANMILDDGGDLTHWVYK 25 0 O43865-2;O43865 O43865-2 AHCYL1 Putative adenosylhomocysteinase 2 0 128.36 0.00011209 47544000 79199 82706 77515 69139 92469 61827 94990 76381 92474 FALSE TRUE 74242.07596 88829.6383 79353.69241 70913.22379 85206.85774 79675.45122 80747.13134 85917.33599 77039.492 0.963688545 1.153040291 1.030039144 0.92047886 1.106015312 1.034215688 1.048126477 1.115237572 1 16.23331057 1.443069255 24.99739592 1.06563983 1.045660077 0 0.070479662 192.5724712 141384.7713 0.036720384 0.016884936 27.73762391 -1.443069255 -0.019979753 CVPASGELS(ph)PELQEWAPYSPGHSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CVPASGELSPELQEWAPYSPGHSSR 25 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1 Q8TDM6-4 DLG5 Disks large homolog 5 1 CVPAS(0.001)GELS(0.999)PELQEWAPYSPGHSSR 185.72 1.07E-17 107280000 26802 51501 41497 59594 60836 51720 55795 56162 80042 TRUE FALSE 25124.51066 55314.18763 42481.32844 61123.28293 56058.18596 66650.7244 47429.05773 63173.94933 66682.47311 0.376778327 0.829516139 0.63706888 0.916631914 0.840673469 0.999523882 0.711267227 0.947384618 1 16.02501999 5.182706169 0.662312323 0.872270159 7.39E-37 0.552751938 0.128216494 4.523979657 0.986525906 0.048639689 3.392397594 152302.1971 -5.182706169 -0.872270159 CVPDPDTGLYMLQLAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 CVPDPDTGLYMLQLAGR 17 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 102.4 0.0022091 34503000 38631 40635 38686 40779 43947 35698 45768 35088 38599 FALSE TRUE 36213.15467 43643.65768 39603.65019 41825.45818 40495.57989 46003.43309 38905.51329 39468.81404 32156.57754 1.126150773 1.357223343 1.23158785 1.300681272 1.259324934 1.430607254 1.209877302 1.227394737 1 14.97282625 -0.971351449 4.942844196 0.99999773 1.275710731 0.503055013 0.08334183 1.85E-06 3.85E-07 0.071625698 0.0168822 0.106819011 0.971351449 0.275713001 CYEMASHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 CYEMASHLR 9 0 P07737;K7EJ44;CON__P02584 P07737 PFN1 Profilin-1 0 ;;;;;;;;;;;; 185.81 4.24E-05 16383660000 11856150 18645890 11154840 11597970 18307880 8017892 12465023 15587170 15031510 FALSE TRUE 11114094.74 20026451.1 11419438.07 11895593.55 16870052.96 10332527.26 10596008.52 17533262.49 12522653.87 0.887519119 1.599217809 0.911902396 0.949925923 1.34716276 0.825106832 0.846147201 1.400123541 1 23.578037 3.806200238 7.088701524 1.019199599 1.286098785 0.088011033 0.256935131 0.394497806 29.93838294 0.061059545 0.110606433 6400.298626 -3.806200238 0.266899186 CYPDRVDYVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 CYPDRVDYVDK 11 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 168.98 1.59E-05 776950000 1951930 1564960 1731650 1726250 1851780 1353740 2231500 1642510 1629890 FALSE TRUE 1829762.186 1680831.267 1772725.556 1770548.498 1706348.669 1744542.762 1896907.291 1847580.989 1357850.83 1.347542857 1.237861502 1.305537779 1.303934467 1.256653994 1.284782337 1.396992402 1.360665656 1 20.37289357 -0.983524577 4.440416915 0.999991026 1.308120938 0.809025907 0.047571346 0.032552003 15252426.54 337.1601831 0.012064215 0.103866482 0.983524577 0.308129912 CYQSEFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 CYQSEFGR 8 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;;;;; 176.09 0.00061035 2034480000 2103730 2323350 2117430 1867810 2165760 710610 2789860 2071520 2990240 FALSE TRUE 1972061.295 2495373.251 2167656.44 1915741.167 1995669.946 915751.5712 2371546.393 2330153.832 2491149.626 0.791626996 1.001695452 0.870143012 0.769018909 0.801104006 0.367601994 0.95198874 0.935372893 1 21.24838025 -0.878351298 5.846070255 1.000000049 0.82174081 0.100785504 0.174787999 1.12E-07 2.13E-08 0.167510037 0.039482483 0.132327072 0.878351298 -0.17825924 CYYSNTDAVIYVVDSCDRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 CYYSNTDAVIYVVDSCDRDR 20 1 B4DZG7;F8VYN9;P40616-2;P40616 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ;; 225.69 4.50E-25 576070000 279793 296242 285281 296458 312728 265571 356786 268819 304817 FALSE TRUE 262281.2556 318176.0659 292048 304065.6142 288167.6044 342237.0365 303289.2515 302381.6439 253941.0735 1.032842982 1.252952354 1.150062083 1.197386504 1.13478139 1.347702567 1.194329249 1.190755161 1 17.95413424 0.661732153 4.521170583 1.00000013 1.196204502 0.343306113 0.080805487 20.4067949 271.947894 0.069949472 0.017752458 4.589148939 -0.661732153 0.196204372 DAAAVGNHVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DAAAVGNHVAK 11 0 Q13564-2;Q13564;Q13564-4;Q13564-3 Q13564-2 NAE1 NEDD8-activating enzyme E1 regulatory subunit 0 90.653 0.011326 140560000 330910 280890 312160 306490 332540 246460 396980 284280 403630 FALSE TRUE 310198.9338 301687.3879 319564.5826 314355.0523 306423.6498 317609.0011 337456.5344 319772.9838 336261.5455 0.922493036 0.897180757 0.95034531 0.934852815 0.911265811 0.944529654 1.003553748 0.950965069 1 18.35922428 1.941581561 5.069463515 0.983588073 0.924083503 0.673443653 0.019556463 0.123328271 6.484696598 0.008384102 0.005074791 87.41411409 -1.941581561 -0.05950457 DAADKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DAADKPR 7 1 Q13185 Q13185 CBX3 Chromobox protein homolog 3 0 ;;;; 124.08 0.0038134 8124660000 21426700 14772700 18747200 17540400 17446000 12983700 19115800 15715200 19775600 FALSE TRUE 20085641.09 15866486.08 19191892.44 17990516.36 16075861.53 16731883.42 16249563.25 17677277.31 16474924.6 1.219164371 0.963068813 1.164915342 1.091993851 0.975777548 1.015596964 0.986320948 1.072980772 1 23.97376853 2.754928672 22.42237077 1.007845926 1.094521123 0.326045264 0.069628598 272.04282 372665.8727 0.01995829 0.021088026 568.7595103 -2.754928672 0.086675197 DAAEFELFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DAAEFELFFR 10 0 Q6XQN6-3;Q6XQN6;Q6XQN6-2;C9J8U2;G5E977;H0YF31 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 0 ;;; 172.23 8.79E-06 772950000 859590 1042360 970700 973240 1004720 767220 1084960 881550 859010 FALSE TRUE 805789.7963 1119537.419 993725.4624 998214.9861 925813.344 988703.9592 922280.3203 991613.458 715635.6816 1.125977669 1.56439575 1.388591273 1.39486475 1.29369366 1.38157443 1.288756757 1.385640045 1 19.4488658 -2.777760097 0.277675564 0.335753334 1.405296535 0.469721794 0.11372208 42.7836356 1.245672248 16.92082717 0.12669451 0.001668168 2.777760097 1.069543201 DAAGLECKPRPLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DAAGLECKPRPLHK 14 2 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 154.47 3.67E-06 883740000 1721600 1554770 1727330 1646060 2031320 1333010 2411460 1702730 3389100 FALSE TRUE 1613848.129 1669886.789 1768303.083 1688300.686 1871788.321 1717828.347 2049883.96 1915319.589 2823437.316 0.571589856 0.591437529 0.626294437 0.59795933 0.662946654 0.608417385 0.72602425 0.678364481 1 21.42902117 -5 0.176652661 2.523806991 0.549714382 0.950831189 0.027535744 23.32630585 0.223327006 12.38854077 0.079299582 1.00E-05 5 -1.974092609 DAALATALGDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DAALATALGDKK 12 1 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 94.728 0.010337 546360000 1080700 947080 1030700 1019100 1157900 744310 1512600 1066900 1374100 FALSE TRUE 1013060.916 1017202.789 1055148.691 1045251.831 1066963.205 959180.2141 1285799.672 1200104.814 1144753.833 0.884959619 0.888577753 0.921725405 0.913080001 0.932045977 0.837892118 1.123210629 1.048351863 1 20.12660596 1.737004397 12.07045139 1.062825692 0.900429736 0.78944561 0.039065012 0.030102351 28.30537275 0.016399781 0.008980172 54.57633867 -1.737004397 -0.162395955 DADAGDEDEESEEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DADAGDEDEESEEPR 15 0 Q9NZT2-2;Q9NZT2;A0A087X028 Q9NZT2-2 OGFR Opioid growth factor receptor 0 ; 351.63 5.12E-82 928280000 745610 648100 716790 706330 713670 539930 859830 572810 722830 FALSE TRUE 698943.6011 696085.9983 733792.5973 724455.6236 657621.237 695799.026 730906.4738 644326.5894 602185.0033 1.160679189 1.155933799 1.218550102 1.203044944 1.092058476 1.155457247 1.21375735 1.069981128 1 19.19984725 1.045271229 4.484102969 1.000819973 1.173668028 0.719861907 0.036710559 0.09092216 3.925820617 0.035476623 0.009029049 11.09867742 -1.045271229 0.172848055 DADDAVYELDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DADDAVYELDGK 12 0 Q13243;Q13243-3;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ; 207.29 1.87E-07 259040000 1051370 653230 849230 705870 735110 628890 983370 658750 726010 FALSE TRUE 985566.6284 701595.8289 869374.1366 723983.8192 677377.4259 810440.3338 835922.7977 740996.3876 604834.2408 1.629482199 1.159980341 1.437375859 1.196995425 1.119938952 1.339937919 1.382069237 1.225123079 1 19.20618029 -4.302351312 0.205337147 1.47E-18 1.356160142 0.340988898 0.145507209 131.8733116 1.699850762 55.08538281 0.314289564 4.98E-05 4.302351312 1.356160142 DADDAVYELNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DADDAVYELNGK 12 0 Q08170;A0A0D9SEM4;Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q08170;Q13247 SRSF4;SRSF6 Serine/arginine-rich splicing factor 4;Serine/arginine-rich splicing factor 6 0 ; 283.82 7.08E-28 463250000 1543570 930160 1254570 1110540 1056100 989840 1524040 1062240 1058510 FALSE TRUE 1446960.709 999030.0142 1284328.993 1139038.337 973158.1661 1275590.739 1295524.35 1194863.002 881837.8428 1.640846694 1.132895376 1.456423087 1.29166416 1.103556821 1.446513948 1.46911857 1.354969071 1 19.75015386 -1.993167214 2.461500563 0.660797089 1.352602971 0.334566263 0.159955816 13897440.59 5689902.329 26748740.92 0.035796065 0.010158575 1.993167214 0.691805882 DADLWSSHDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DADLWSSHDK 10 0 P34896-2;P34896;P34896-3;J3KRZ5;J3KRK5 P34896-2 SHMT1 "Serine hydroxymethyltransferase, cytosolic" 0 ; 135.86 0.00013302 555600000 1215080 1206400 1387980 1276860 1392590 1042513 1490460 1211880 1597680 FALSE TRUE 1139030.312 1295723.111 1420903.541 1309626.389 1283221.599 1343469.579 1266979.36 1363185.886 1331016.887 0.855759475 0.973483601 1.067532317 0.983929207 0.964091148 1.009355774 0.951888269 1.024168739 1 20.34409744 4.718643131 3.314560394 0.999084951 0.839483209 0.667205139 0.031830381 0.189464786 3.491917445 0.008029596 0.075229096 52317.03591 -4.718643131 -0.159601743 DADPILISLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DADPILISLR 10 0 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;;;; 190.02 2.20E-06 453581000 1010181 1262250 979202 979486 1275261 754685 1074805 1055824 1156842 FALSE TRUE 946955.5744 1355708.303 1002429.134 1004621.269 1175107.145 972550.3082 913647.9683 1187645.951 963757.5967 0.982566132 1.406690135 1.040125792 1.042400363 1.219297414 1.009123364 0.948005983 1.232307745 1 19.8783108 3.73227984 24.258242 1.062276142 1.224468323 0.116465729 0.135783643 219.4738372 1032061.175 0.032416185 0.056239502 5398.583714 -3.73227984 0.162192181 DADSQNPDAPEGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DADSQNPDAPEGKR 14 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 92.773 0.007738 137680000 81514 89617 81042 92144 108560 65353 135220 81239 169290 FALSE TRUE 76412.18425 96252.33593 82964.35451 94508.57104 100034.1355 84219.35018 114945.0163 91381.86798 141034.4053 0.541798181 0.68247415 0.588256137 0.67011004 0.709288881 0.597154644 0.815014011 0.647940251 1 17.10568763 -5 0.155306051 2.272508459 0.560286254 0.740795536 0.066826969 61.37810927 0.556781337 23.91489246 0.273143036 1.00E-05 5 -1.712222205 DADVQFLASVLPPDTDPAFFEHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DADVQFLASVLPPDTDPAFFEHLR 24 0 Q6XQN6-3;Q6XQN6;Q6XQN6-2;C9J8U2;G5E977;H0YF31;H0YDA6 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 0 ;;;;; 197.33 1.88E-24 1666164000 1573201 1677614 1630674 1603151 1594045 1298965 1957835 1492602 1475454 FALSE TRUE 1474737.158 1801826.286 1669354.357 1644290.569 1468855.136 1673955.109 1664275.817 1678956.645 1229191.196 1.19976222 1.465863319 1.358091697 1.337701226 1.194976942 1.361834607 1.353960086 1.365903572 1 20.22927791 -1.530698004 2.833049491 0.983962045 1.342957678 0.618470308 0.080808147 9257836.513 10122491.59 1145133.236 0.019053839 0.029464698 1.530698004 0.358995633 DADVQNFVSFISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DADVQNFVSFISK 13 0 H3BS70;Q96DC0;P42126-2;P42126 H3BS70 ECI1;DCI "Enoyl-CoA delta isomerase 1, mitochondrial" 0 144.27 6.74E-06 0 104540 100580 94983 95353 136820 71076 99600 106060 111200 FALSE TRUE 97997.02801 108027.0479 97236.04161 97799.91941 126074.7091 91594.48738 84665.90464 119301.8245 92640.00162 1.057826277 1.166095056 1.04961183 1.055698593 1.360910049 0.988714225 0.913923825 1.287800328 1 16.49934766 -1.261450178 4.835477551 0.999974106 1.096481965 0.054352976 0.134025962 3.59E-05 5.48E-06 0.124530411 0.029344226 0.054770893 1.261450178 0.096507859 DAEDALHNLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 178.1 7.69E-06 2090540000 3974830 3269370 3599940 3371760 3508020 3041020 3936650 3251870 2748880 FALSE TRUE 3726052.486 3511437.557 3685332.277 3458285.07 3232514.26 3918913.107 3346385.879 3657873.128 2290074.17 1.627044458 1.533329184 1.609263283 1.510119242 1.411532562 1.711260342 1.461256549 1.597272777 1 21.12696289 -1.716294956 2.704951851 0.905348955 1.554241565 0.806651443 0.085784235 7452343.905 6246698.774 4780389.099 0.018366159 0.019217861 1.716294956 0.64889261 DAEDALHNLDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DAEDALHNLDRK 12 1 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 0 ;;;;; 260.81 1.61E-21 2017988000 3491190 2668337 2869654 2741388 3223396 1960287 3630140 2612462 4245850 FALSE TRUE 3272682.65 2865903.448 2937723.548 2811736.657 2970243.481 2526190.034 3085834.208 2938633.631 3537190.206 0.925220997 0.810220339 0.830524619 0.794906831 0.839718338 0.714179868 0.872397024 0.830781909 1 21.75417237 0.42060062 1.43176964 0.999945568 0.821356279 0.504453317 0.053747109 2.563316972 5.55098214 0.04604335 0.013407567 2.633908115 -0.42060062 -0.178589289 DAEDAMDAMDGAVLDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DAEDAMDAMDGAVLDGR 17 0 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;; 265.41 3.50E-27 705920000 707402 677209 715551 663618 803101 604059 753936 603576 796557 FALSE TRUE 663126.9716 727350.259 732524.2076 680647.5614 740028.687 778441.0272 640890.296 678933.7922 663606.4907 0.999277404 1.096056577 1.103853289 1.025679482 1.115161918 1.173046132 0.965768577 1.023096973 1 19.33996847 1.671090362 10.34629844 0.996500848 1.087536905 0.421260578 0.049165719 0.106148203 16.12279978 0.022157694 0.011958343 46.89109367 -1.671090362 0.091036057 DAEDAVYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DAEDAVYGR 9 0 J3KTL2;Q07955;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;; 225.99 5.88E-07 2468330000 5292800 4152710 4729090 4358570 4247350 4265900 5443870 4150500 3719390 FALSE TRUE 4961533.096 4460180.969 4841266.248 4470418.285 3913780.264 5497396.079 4627612.232 4668699.061 3098599.781 1.601217791 1.439418216 1.562404502 1.442722068 1.263080275 1.774154931 1.493452707 1.506712513 1 21.563185 0.431663186 3.623344724 1.000000061 1.510164037 0.604365971 0.129783063 54.96920486 348.7331852 0.11458463 0.029458457 2.70186214 -0.431663186 0.510163976 DAEDDGEEEDD ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DAEDDGEEEDD 11 0 Q9BTT0;Q5TB19;Q9BTT0-3;Q9BTT0-2;Q5TB25;H0YCE2 Q9BTT0 ANP32E Acidic leucine-rich nuclear phosphoprotein 32 family member E 0 ; 226.46 1.10E-11 226510000 721200 572720 636090 622990 705390 503000 651450 590410 886320 FALSE TRUE 676061.3794 615124.7847 651178.3552 638976.9781 649991.5148 648207.9345 553771.1203 664123.9882 738387.4662 0.915591624 0.833065041 0.881892482 0.865368126 0.880285141 0.877869634 0.749973619 0.899424785 1 19.49401854 DAEDVDLNHYR ddPTM_SK-BR-3_Pertuzumab_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 0 201.6 4.29E-08 410360000 731220 611930 652240 651270 657670 530080 822820 563310 487390 FALSE TRUE 685454.2455 657237.9339 667711.4408 667982.6908 606019.2511 683105.4909 699445.7797 633640.4935 406041.4603 1.688138558 1.61864735 1.644441531 1.645109566 1.492505841 1.682354039 1.722596946 1.560531511 1 18.63126752 0.950748832 17.09772228 0.999999999 1.641142166 0.915770615 0.060706362 40.84082257 14178.42701 0.058118563 0.014530006 8.927890034 -0.950748832 0.641142167 DAEFCLFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DAEFCLFDR 9 0 Q8IZH2-2;Q8IZH2;H7C5E4 Q8IZH2-2 XRN1 5-3 exoribonuclease 1 0 80.165 0.046331 0 34508 37672 36639 33915 39088 29254 43198 34047 44842 FALSE TRUE 32348.20588 40461.27408 37508.09438 34785.31632 36018.18615 37699.1549 36720.86093 38297.8429 37357.58051 0.865907413 1.08308069 1.004029005 0.931144786 0.964146651 1.009143376 0.982956081 1.025169253 1 15.1891134 1.24790488 24.69055349 1.012584627 0.989562303 0.029337612 0.056811457 716.084915 1892163.781 0.038173285 0.013487146 17.69721307 -1.24790488 -0.023022324 DAEGILEDLQSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DAEGILEDLQSYR 13 0 E5RI16;Q9NUQ9;E5RGI7;E5RJE1;E5RIR8;E5RJL8;E5RK61;E5RFS4;E5RHU5 E5RI16 FAM49B Protein FAM49B 0 ;; 261.22 1.10E-23 98311000 146192 150635 154774 160523 160954 123252 189482 150392 186783 FALSE TRUE 137042.1037 161788.1721 158445.3124 164642.2919 148313.3221 158832.8516 161070.9332 169168.7723 155607.7106 0.880689672 1.039718221 1.018235611 1.058059985 0.953123219 1.0207261 1.035108945 1.087149034 1 17.24755402 4.741772248 24.61145035 1.026486806 0.880689604 0.629792539 0.035136589 155.6718177 1192876.319 0.007786916 0.055909471 55178.79959 -4.741772248 -0.145797201 DAEILRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DAEILRK 7 1 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;;; 127.84 0.0061177 801880000 1208470 1342270 1167020 884230 1350490 349174 1698910 1148460 2762010 FALSE TRUE 1132834.02 1441653.067 1194702.266 906920.8388 1244427.963 449974.8654 1444174.217 1291847.759 2301012.688 0.492319762 0.626529821 0.519207161 0.394139869 0.540817515 0.195555143 0.627625491 0.561425744 1 21.13383751 0.631876014 1.570987578 0.999184838 0.491394172 0.63472927 0.122341997 0.958554684 3.245343837 0.112240415 0.032275566 4.284261919 -0.631876014 -0.507790666 DAELAGSPELLEFLGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DAELAGSPELLEFLGTR 17 0 Q53T59;F6TR53 Q53T59 HS1BP3 HCLS1-binding protein 3 0 144.27 1.21E-06 9727600 20729 14344 14928 15578 15183 11768 19497 12263 18901 FALSE TRUE 19431.60889 15406.04468 15282.09921 15977.75785 13990.58843 15165.23056 16573.60585 13794.06254 15746.30099 1.23404277 0.97839135 0.970519947 1.014699126 0.888499999 0.963097972 1.052539632 0.876019235 1 13.94272534 4.738695709 6.249113785 0.972540365 1.24013438 0.711973321 0.053128434 0.065722439 13.91603504 0.011782789 0.074607209 54789.29456 -4.738695709 0.267594015 DAELAWIDGVLDMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DAELAWIDGVLDMR 14 0 Q9P2I0;H0YJF4 Q9P2I0 CPSF2 Cleavage and polyadenylation specificity factor subunit 2 0 ;; 153.95 1.45E-05 21994900 57251 56029 64757 54035 58896 47167 66776 52560 58454 FALSE TRUE 53667.76211 60177.44546 66293.06662 55421.62958 54270.54574 60783.34721 56763.55872 59122.2317 48697.64977 1.10206062 1.235736134 1.361319631 1.138076064 1.114438705 1.248178249 1.165632407 1.214067454 1 15.57156453 -2.781450798 0.267607387 0.625064293 1.232662644 0.36314006 0.078167115 56.13164245 1.584001217 12.09310741 0.105265342 0.001654052 2.781450798 0.607598351 DAELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DAELLR 6 0 A0A087WYM3 A0A087WYM3 SIRT2 0 ;;; 136.08 0.030994 1861930000 2342180 2575560 2210480 1754550 2457080 862010 2822350 2374450 3284910 FALSE TRUE 2195587.135 2766257.142 2262913.629 1799574.723 2264110.848 1110858.293 2399164.819 2670905.309 2736637.3 0.802293799 1.010823445 0.826895705 0.657586127 0.827333183 0.405920906 0.876683519 0.975980745 1 21.38397281 1.478255306 25 0.967442006 0.779702695 0.273000416 0.154265723 0.22795021 4816.795258 0.087338534 0.04043284 30.07843983 -1.478255306 -0.187739311 DAELQDQEFGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DAELQDQEFGKR 12 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ;; 117.93 0.0010906 1104630000 1567450 1128850 1318150 1310600 1348420 978770 1569940 1097930 1335210 FALSE TRUE 1469346.102 1212431.229 1349417.14 1344232.215 1242520.532 1261325.01 1334542.072 1235008.977 1112354.825 1.320932916 1.089968058 1.213117532 1.208456317 1.117018153 1.13392326 1.199744939 1.110265312 1 20.08518563 -4.999999997 0.178164396 0.299604379 1.207668091 0.484817427 0.062349898 122.2159061 1.173521045 30.19681198 0.185571541 1.00E-05 4.999999997 0.908063712 DAELQDQEFGKRDS(ph)LGTYSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DAELQDQEFGKRDSLGTYSSR 21 2 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DAELQDQEFGKRDS(0.999)LGT(0.001)YSSR;DAELQDQEFGKRDS(0.995)LGT(0.003)YS(0.001)S(0.001)R;DAELQDQEFGKRDS(1)LGTYSSR;DAELQDQEFGKRDS(0.978)LGT(0.022)YSSR;DAELQDQEFGKRDS(1)LGTYSSR 258.85 8.18E-37 4665290000 1437560 1268310 1244560 1428490 1615180 931959 1768520 1174300 2487860 TRUE FALSE 1347585.686 1362216.992 1274081.551 1465147.472 1488330.278 1201000.434 1503346.844 1320913.94 2072620.094 0.650184609 0.657243938 0.614720254 0.706905948 0.718091213 0.579459997 0.725336423 0.637315996 1 20.98302427 -5 0.384097273 5.922827472 0.652849058 0.839481869 0.046463854 218.3043355 1.610534814 896.4341999 0.028029866 1.00E-05 5 -5.269978414 DAENHEAQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DAENHEAQLK 10 0 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 ;;; 152.7 1.76E-05 2462410000 3515960 2860120 3256190 3054910 3446100 2455750 3917170 2757680 3739970 FALSE TRUE 3295902.34 3071886.261 3333428.364 3133304.163 3175457.207 3164685.159 3329826.724 3101982.418 3115744.846 1.057821645 0.985923563 1.069865643 1.005635672 1.019164715 1.01570742 1.068709695 0.995582941 1 21.57114566 DAEQSGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DAEQSGSPR 9 0 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5 P08651-3 NFIC Nuclear factor 1 C-type 1 DAEQS(0.005)GS(0.995)PR 65.842 0.068619 33348000 32013 45467 44313 45477 46835 47856 40246 41194 35612 TRUE FALSE 30009.36347 48833.42399 45364.12529 46644.01681 43156.76802 61671.25032 34211.48593 46337.16158 29668.12714 1.011501782 1.645989441 1.529052544 1.572192832 1.454650906 2.078703857 1.153139386 1.561849906 1 14.85662624 -1.222766004 9.841036523 0.999999988 1.515947664 0.232813132 0.284585558 6.56E-08 5.19E-09 0.244604357 0.057653798 0.05987341 1.222766004 0.515947676 DAESIHQYLLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DAESIHQYLLQR 12 0 E9PLK3;P55786;P55786-2;H0YDG0 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ; 234.3 5.11E-16 982590000 1026410 1705670 1417550 1489120 1821440 1249930 1702670 1673920 2091400 FALSE TRUE 962168.8303 1831959.582 1451174.955 1527333.34 1678391.45 1610764.5 1447370.44 1882912.597 1742331.829 0.552230531 1.051441265 0.83289241 0.876603018 0.963301836 0.924487789 0.830708833 1.080685416 1 20.73258798 4.750409583 24.7243229 0.928980295 0.552230265 0.672152304 0.085561309 946.3994995 1974736.224 0.019055413 0.311192144 56287.19188 -4.750409583 -0.37675003 DAEVERDEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DAEVERDEER 10 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;A1L2Z2 Q7Z406 MYH14 Myosin-14 0 ;;; 170.52 3.92E-06 1556490000 1218049 1231604 1145075 1223988 1466105 876905 1380997 1193260 1419156 FALSE TRUE 1141813.487 1322793.242 1172236.72 1255397.604 1350963.027 1130053.238 1173929.32 1342241.138 1182289.696 0.96576456 1.118840202 0.991497028 1.061835867 1.142666668 0.955817548 0.992928658 1.135289551 1 20.17315215 -1.581014893 8.708665753 0.999990363 1.042930068 0.039721796 0.069350997 1.20E-05 5.80E-07 0.062329745 0.014687965 0.026241286 1.581014893 0.042939705 DAEYIYPSLES(ph)DDDDPALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DAEYIYPSLESDDDDPALK 19 0 Q9UPP1-4;Q9UPP1-3;Q9UPP1-2;Q9UPP1;H0Y3N9;Q9UPP1-5;H0Y589 Q9UPP1-4 PHF8 Histone lysine demethylase PHF8 1 DAEYIYPSLES(1)DDDDPALK;DAEYIYPSLES(1)DDDDPALK 171.42 6.64E-12 119182000 366510 250100 298920 291240 315410 254850 362640 257370 355470 TRUE FALSE 343570.7933 268617.6642 306010.5236 298713.7115 290638.9709 328421.0579 308265.4986 289503.211 296139.7606 1.160164352 0.907063826 1.033331434 1.008691676 0.981425022 1.109006968 1.040945998 0.977589806 1 18.17591868 DAFDRNPELQNLLLDDFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DAFDRNPELQNLLLDDFFK 19 1 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;; 178.77 3.40E-14 1037852000 1585953 1306158 1441999 1520241 1491902 1104298 1874716 1366345 1525952 FALSE TRUE 1486691.033 1402867.297 1476203.897 1559252.958 1374734.035 1423090.906 1593619.74 1536936.181 1271260.753 1.169461913 1.103524429 1.161212516 1.226540624 1.081394223 1.119432738 1.253574246 1.208985786 1 20.27782855 DAFEHIVTQFSSVPVSVVSDSYDIYNACEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DAFEHIVTQFSSVPVSVVSDSYDIYNACEK 30 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ; 269.3 2.77E-59 151544000 176362 130966 152274 140810 168004 120847 201098 137451 145990 FALSE TRUE 165323.8172 140662.8589 155886.0112 144423.423 154809.6435 155733.5671 170945.2218 154612.0599 121623.3259 1.359310116 1.156545078 1.281711465 1.187464838 1.272861455 1.280458054 1.405529906 1.271236901 1 16.89206042 -1.16581221 5.769731297 0.99999579 1.273748923 0.596823035 0.071479711 4.08E-06 5.89E-07 0.072875511 0.017176659 0.06826338 1.16581221 0.273753133 DAFELFDTDKDEAIDYHELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DAFELFDTDKDEAIDYHELK 20 1 H0YBL5;E5RH67;E5RFM2;E5RK82;E5RJF8;O15182 H0YBL5 CETN3 Centrin-3 0 108.92 0.00012322 18208000 34883 18963 22788 23722 29499 17436 29418 20197 24434 FALSE TRUE 32699.7353 20367.04025 23328.54212 24330.74668 27182.26753 22469.49015 25007.044 22718.63991 20355.80755 1.606408157 1.000551818 1.146038646 1.195272977 1.335356874 1.103836834 1.228496779 1.116076572 1 14.31315284 -5 0.180701666 0.216551572 1.231895192 0.176533208 0.160855345 289.8876202 2.796485466 81.60807045 0.468386854 1.00E-05 5 1.01534362 DAFPEAIIVKPSDIFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DAFPEAIIVKPSDIFGR 17 1 Q16795;A0A3B3ISG8 Q16795 NDUFA9 "NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial" 0 69.188 0.032182 185370000 291840 326780 283170 289140 356090 361960 537930 320090 313050 FALSE TRUE 273574.2553 350975.1312 289886.9261 296559.8219 328124.1278 466451.9761 457272.3904 360053.9411 260799.9326 1.048981311 1.345763888 1.111529912 1.137116175 1.258144987 1.788543315 1.753345508 1.380575284 1 17.99258397 2.380676651 6.824867758 1.57321293 1.184925853 0.255932602 0.234983372 0.212307921 12.87703116 0.075433331 0.062909919 240.2573326 -2.380676651 -0.388287077 DAGDKDKEQELSEEDKQLQDELEMLVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DAGDKDKEQELSEEDKQLQDELEMLVER 28 3 Q13200;C9JPC0 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 194.27 5.16E-19 87256000 265935 67298 121508 121796 120844 75067 172551 84688 179766 FALSE TRUE 249290.6031 72280.81394 124390.2271 124921.4916 111353.3997 96737.62429 146678.5794 95261.48322 149761.8933 1.664579671 0.482638222 0.830586636 0.83413403 0.743536271 0.645942851 0.979411893 0.636086264 1 17.19231105 4.749721825 24.90810733 0.762034095 1.664580222 0.762825308 0.156887457 745.172618 1662944.443 0.035520172 0.54571748 56198.12493 -4.749721825 0.902546126 DAGGPRPES(ph)PVPAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DAGGPRPESPVPAGR 15 1 Q9BVG9;E9PS47;E9PLE4 Q9BVG9 PTDSS2 Phosphatidylserine synthase 2 1 DAGGPRPES(1)PVPAGR;DAGGPRPES(1)PVPAGR;DAGGPRPES(1)PVPAGR;DAGGPRPES(1)PVPAGR 112.58 0.00045564 2856790000 2400850 2547460 2251420 2241500 2704500 2143750 3009190 2537550 2166350 TRUE FALSE 2250585.084 2736076.589 2304824.746 2299020.685 2492099.479 2762615.824 2557989.895 2854368.703 1804772.19 1.247018929 1.516023244 1.277072396 1.273856444 1.380838808 1.530728277 1.417347801 1.581567313 1 20.78338531 2.471293674 24.86180357 1.425576926 1.348794753 0 0.171806344 505.8349667 2157983.794 0.052994931 0.044449188 296.001338 -2.471293674 -0.076782174 DAGHPLYPFNDPY ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DAGHPLYPFNDPY 13 0 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ;;;;;;; 169.65 6.55E-05 3310396000 4276210 4606060 4238030 4261990 5000200 3233326 5002340 4225190 5600110 FALSE TRUE 4008569.649 4947097.475 4338558.073 4371359.879 4607504.462 4166734.728 4252285.556 4752714.272 4665415.463 0.859209578 1.060376619 0.929940347 0.93697119 0.987587172 0.893111184 0.911448421 1.018711905 1 22.15357413 3.727712134 24.9967008 0.945236802 0.980461066 0 0.062752254 82.57782978 3493171.058 0.015069794 0.025222812 5342.101482 -3.727712134 0.035224264 DAGLHCLELGHTGEAGPHAMVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DAGLHCLELGHTGEAGPHAMVR 22 0 O15067;H0YGH1 O15067 PFAS Phosphoribosylformylglycinamidine synthase 0 208.47 2.38E-23 319920000 55857 104880 86893 99023 113420 78963 75360 94030 92095 FALSE TRUE 52361.01008 112645.4243 88954.14299 101564.0978 104512.4507 101758.3362 64060.46761 105769.8525 76723.74954 0.682461564 1.468194985 1.159408182 1.323763482 1.362191646 1.326295141 0.834949647 1.378580337 1 16.22738561 -1.372922281 4.532324104 0.999710197 1.201475456 0.053722994 0.250412038 0.000679501 9.40E-05 0.224673535 0.052880487 0.042371879 1.372922281 0.201765259 DAGNFDQNKLEEEMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DAGNFDQNKLEEEMR 15 1 A0A0C4DG89;Q7L014;D6RJA6 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 66.335 0.053697 126890000 128440 119850 127620 122530 144060 133730 117980 121060 154540 FALSE TRUE 120401.1697 128723.8187 130647.2067 125674.3272 132746.1087 172335.6801 100289.9943 136174.6075 128746.2756 0.935181768 0.999825572 1.01476494 0.976139516 1.031067563 1.338568275 0.778973945 1.05769745 1 16.97417117 6.154718043 0.895899845 1.022024692 1.61E-08 0.044189167 0.134690201 96.41871345 7.843353409 0.040070444 168.0477389 1427966.579 -6.154718043 -1.022024676 DAGPQGLHPSVQHQGRLS(ph)LDLSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DAGPQGLHPSVQHQGRLSLDLSHR 24 1 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1 Q8TDM6-4 DLG5 Disks large homolog 5 1 DAGPQGLHPSVQHQGRLS(1)LDLSHR 192.89 3.04E-18 892720000 74279 188870 149200 155400 168250 107010 174420 144770 168880 TRUE FALSE 69630.00998 202854.1313 152739.0945 159387.8271 155036.3237 137902.0498 148267.3402 162844.8532 140692.837 0.494907996 1.441822737 1.085620972 1.132878052 1.101948948 0.980163971 1.053837163 1.157449495 1 17.10218935 2.449235535 22.91458739 1.048821153 1.114142432 0 0.238260538 495.2460252 406952.0794 0.07682014 0.064274463 281.3426251 -2.449235535 0.06532128 DAGQISGLNVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DAGQISGLNVLR 12 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 113.61 0.002669 61308000 36798 39172 34390 33416 41399 28271 39267 40840 50813 FALSE TRUE 34494.87887 42072.33564 35205.74704 34273.51113 38147.68954 36432.37876 33379.27789 45938.9639 42331.98204 0.814865669 0.993866425 0.831658367 0.809636343 0.90115529 0.860634844 0.788512049 1.085207016 1 15.36946042 1.231984688 24.99999896 1.042603578 0.864439789 0.609373752 0.061503908 119.7863247 455375.8872 0.055026025 0.015024254 17.06022239 -1.231984688 -0.178163789 DAGRPGERGS(ph)GGLFSPSTAHVPDGALGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DAGRPGERGSGGLFSPSTAHVPDGALGQR 29 2 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DAGRPGERGS(0.968)GGLFS(0.03)PS(0.001)TAHVPDGALGQR;DAGRPGERGS(1)GGLFSPSTAHVPDGALGQR;DAGRPGERGS(0.998)GGLFS(0.002)PSTAHVPDGALGQR 113.17 0.00012483 3247660000 478228 707623 694338 766784 861094 557481 823768 676749 1172960 TRUE FALSE 448296.5631 760016.1432 710808.0253 786460.9756 793467.1507 718416.7148 700251.6359 761242.6024 977185.3984 0.45876306 0.777760438 0.727403445 0.804822685 0.811992435 0.735189777 0.716600593 0.779015531 1 19.89827278 -5 0.081159397 1.760419894 0.500194366 0.544964266 0.089152636 225.5447185 1.294200792 31.66791885 2.867386655 1.00E-05 5 -1.260225528 DAGTIAGLNVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DAGTIAGLNVLR 12 0 P11142;E9PKE3;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;; 244.28 5.03E-16 1186910000 781240 983890 675370 654220 1061700 555840 828560 922060 1135120 FALSE TRUE 732343.583 1056738.239 691390.0953 671008.3928 978318.3647 716301.9847 704325.12 1037181.221 945661.1388 0.774424953 1.117459728 0.731118227 0.709565367 1.034533751 0.757461585 0.744796514 1.096778939 1 19.85096379 1.228693959 24.99928694 1.04838956 0.848478138 0.286152756 0.137128814 315.013215 798125.6435 0.124593023 0.03267406 16.93144246 -1.228693959 -0.199911422 DAHNALLDIQSSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DAHNALLDIQSSGR 14 0 Q99613-2;Q99613;B5ME19 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 ;;;; 179.25 1.89E-06 2215280000 1260710 1642434 1662542 1611048 1782220 1491250 1795397 1544607 1717407 FALSE TRUE 1181804.412 1764041.522 1701978.281 1652390.219 1642251.63 1921749.667 1526193.887 1737454.584 1430760.677 0.825997269 1.232939618 1.189561825 1.154903294 1.147817142 1.343166399 1.06670103 1.214357238 1 20.44835094 4.74400591 24.86292191 1.178444913 0.825997107 0.572623149 0.092698844 358.9738414 1639001.479 0.019367646 0.168808728 55463.3261 -4.74400591 -0.352447805 DAIAQAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DAIAQAVR 8 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 84.097 0.041162 344840000 174570 369570 162130 144200 381710 169200 174630 330220 355250 FALSE TRUE 163643.9753 396933.3473 165975.8002 147900.4161 351732.0363 218045.2933 148445.8527 371448.6939 295956.48 0.552932564 1.341188229 0.560811509 0.499737043 1.188458642 0.736747826 0.501580005 1.255078767 1 18.17502552 5.008022463 20.51561907 0.848805766 0.12072882 0.090138414 0.313339431 5063.656583 66724.19187 0.070069394 103916.882 101864.4075 -5.008022463 -0.728076946 DAIFIMTSNVASDEIAQHALQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DAIFIMTSNVASDEIAQHALQLR 23 0 Q9H078-5;Q9H078-3;Q9H078-2;H0YGM0;Q9H078-4;Q9H078;A0A2R8Y602;A0A2U3TZY2 Q9H078-5 CLPB Caseinolytic peptidase B protein homolog 0 139.28 3.79E-07 59073000 121630 118550 113870 102450 165960 98359 128120 132840 191120 FALSE TRUE 114017.3954 127327.5654 116571.0502 105079.0404 152926.1711 126753.6466 108909.5954 149425.3664 159220.8373 0.716095942 0.799691595 0.732134387 0.659957844 0.960465814 0.796087049 0.68401597 0.938478713 1 17.28066963 1.09401524 5.447714051 0.997590483 0.765584843 0.520321209 0.0828573 0.147201602 6.238915054 0.075556923 0.019078762 12.41695878 -1.09401524 -0.23200564 DAIHFYNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DAIHFYNK 8 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 106.04 0.0042717 1047380000 1127090 1506430 1045480 1054100 1614450 805530 1121610 1540250 1261280 FALSE TRUE 1056547.449 1617967.645 1070279.279 1081149.991 1487657.609 1038073.434 953434.993 1732553.603 1050764.22 1.005503831 1.539800856 1.018572254 1.028917782 1.415786321 0.987922328 0.907372915 1.64885097 1 20.00300755 3.855687692 7.340205275 1.124124057 1.305713831 0.033132777 0.259601895 0.573470538 32.8937088 0.061670206 0.111837015 7172.782993 -3.855687692 0.181589774 DAINQGMDEELERDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DAINQGMDEELERDEK 16 1 F8WF02;C9J634;P11177-3;P11177-2;P11177 F8WF02 PDHB "Pyruvate dehydrogenase E1 component subunit beta, mitochondrial" 0 86.122 0.0063079 470450000 250360 227900 330410 355400 431920 734210 380460 202020 329430 FALSE TRUE 234690.4145 244773.9531 338247.4812 364520.1657 397998.7455 946164.5081 323413.555 227242.6417 274446.0048 0.855142397 0.891883827 1.232473694 1.328203579 1.450189613 3.447543384 1.178423258 0.828004918 1 18.06616281 3.224979327 1.645288976 1.691553802 0.938 0.119195343 0.720393106 0.665008361 3.708463005 0.236704643 0.33790307 1678.724106 -3.224979327 -0.753553803 DAKLDK ddPTM_SK-BR-3_Pertuzumab_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 73.637 0.075182 248940000 430700 395780 483480 486150 591060 229880 460610 334330 1100500 FALSE TRUE 403743.2558 425083.963 494948.3739 498625.432 544640.5318 296242.6242 391545.8066 376071.8365 916819.4405 0.440373794 0.463650687 0.539853707 0.543864375 0.594054301 0.32311992 0.427069703 0.410191822 1 19.80627811 -1.394853625 3.014802732 1.007934478 0.470203357 0.824341128 0.077204168 21790368.22 27075787.15 1500186.55 0.019914483 0.040285279 1.394853625 -0.537731121 DALDGPAAEAEPEHSFDGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DALDGPAAEAEPEHSFDGLR 20 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 283.83 6.25E-45 2359970000 1745490 1652880 1809840 1756050 1759170 1445700 2055930 1588190 1297410 FALSE TRUE 1636242.897 1775260.955 1852770.259 1801113.216 1621011.884 1863050.121 1747662.383 1786479.018 1080863.889 1.513828811 1.642446355 1.714156868 1.666364501 1.499737294 1.723667651 1.616912546 1.652825148 1 20.04375343 -1.246766091 5.024950782 0.999895388 1.637597551 0.877199215 0.073864997 8.02E-05 1.20E-05 0.066234972 0.015609195 0.056654434 1.246766091 0.637702163 DALDGPAAEAEPEHSFDGLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DALDGPAAEAEPEHSFDGLRR 21 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 212.83 4.77E-23 1098700000 477163 631620 528565 589690 685530 408268 696380 482954 788830 FALSE TRUE 447298.2196 678385.802 541102.8114 604822.4437 631691.2391 526128.3439 591964.2839 543251.87 657169.177 0.680643943 1.032284875 0.823384344 0.920345118 0.961230778 0.800598023 0.900779137 0.826654519 1 19.32590529 DALEPGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DALEPGQR 8 0 H3BQB1;P07741-2;P07741;H3BQZ9 H3BQB1 APRT Adenine phosphoribosyltransferase 0 94.302 0.024324 188480000 392640 381430 427960 368310 385560 332370 434290 347740 302930 FALSE TRUE 368065.3633 409671.4741 438111.4133 377761.4581 355279.6729 428319.8234 369172.2463 391156.1045 252369.026 1.458441113 1.623303305 1.735995182 1.496861418 1.407778437 1.697196483 1.462827083 1.549937053 1 17.94517533 -2.696734382 0.311436743 1.18E-11 1.608281818 0.722967552 0.107207928 29.92695802 0.992821521 20.05446049 0.101025881 0.002010322 2.696734382 1.608281818 DALGDSLQVPVS(ph)PSSTTSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DALGDSLQVPVSPSSTTSSR 20 0 Q9Y2D5;Q9Y2D5-5;Q9Y2D5-7;Q9Y2D5-6;Q9Y2D5-4;C9JVY5 Q9Y2D5 AKAP2 A-kinase anchor protein 2 1 DALGDSLQVPVS(0.978)PS(0.02)S(0.002)TTSSR;DALGDSLQVPVS(0.918)PS(0.075)S(0.006)T(0.001)TSSR;DALGDSLQVPVS(0.913)PS(0.037)S(0.01)T(0.01)T(0.01)S(0.01)S(0.01)R 286.6 3.07E-45 302210000 548461 577032 579769 687094 702326 349177 407684 368103 511777 TRUE FALSE 514133.805 619756.0497 593521.3945 704725.9953 647168.149 449978.7315 346555.569 414061.4698 426358.1125 1.205873161 1.45360445 1.392072479 1.652896883 1.517898053 1.05540089 0.81282743 0.971158887 1 18.70170618 2.122422185 4.360338799 0.913302946 1.447324795 0.800089034 0.121352507 0.086667609 2.891410487 0.046679804 0.033570137 132.5629577 -2.122422185 0.534021849 DALGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DALGQR 6 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 124.86 0.042275 416660000 531560 671350 593990 578650 696610 435770 617010 561240 591190 FALSE TRUE 498290.6085 721057.4525 608079.7233 593499.1387 641901.0606 561569.7249 524495.0785 631312.0494 492516.5698 1.011723542 1.46402679 1.234638103 1.205033851 1.303308559 1.140204735 1.064928798 1.281808752 1 18.90981274 2.171685098 5.932031028 1.118739 1.270659393 0.160693065 0.131199188 0.28907985 18.68282693 0.046300521 0.034202317 148.4858599 -2.171685098 0.151920393 DALHSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DALHSEK 7 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ;; 98.299 0.011364 893860000 1905920 1589620 1807020 1688650 1775560 1374100 2210770 1752500 1892140 FALSE TRUE 1786631.869 1707317.119 1849883.368 1731983.618 1636114.68 1770780.363 1879285.562 1971303.483 1576329.61 1.133412617 1.083096522 1.173538425 1.098744581 1.037926757 1.123356658 1.192190739 1.250565535 1 20.5881378 1.916488734 6.945241039 1.166851056 1.108878533 0.044861061 0.071556757 0.533794906 37.94563257 0.028255131 0.017493627 82.50660818 -1.916488734 -0.057972523 DALKTEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DALKTEFK 8 1 Q5VTU8;P56381 Q5VTU8 ATP5EP2;ATP5E "ATP synthase subunit epsilon-like protein, mitochondrial;ATP synthase subunit epsilon, mitochondrial" 0 60.102 0.086109 483910000 779000 996970 621970 713780 1346900 437540 691750 894270 1417000 FALSE TRUE 730243.7806 1070786.696 636723.4221 732096.8032 1241119.907 563850.6951 588028.5094 1005921.578 1180493.546 0.61859193 0.907066964 0.539370524 0.620161631 1.051356792 0.477639795 0.498120902 0.852119507 1 20.17095872 -1.032640533 8.294014179 1.000000003 0.685163249 0.203456364 0.188319072 1.01E-08 1.26E-09 0.175591019 0.041387199 0.092759728 1.032640533 -0.314836754 DALSDLALHFLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DALSDLALHFLNK 13 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 196.38 1.42E-07 1412600000 4284500 4546900 4224800 4115000 5457400 3104000 4780000 4684400 4794400 FALSE TRUE 4016340.793 4883557.207 4325014.251 4220597.867 5028797.818 4000074.411 4063283.375 5269257.652 3994183.667 1.005547348 1.222667162 1.082828085 1.056685976 1.259030189 1.00147483 1.017300083 1.319232687 1 21.92946924 0.017790576 10.33117286 1 1.115887873 0.101534978 0.11196398 0 0 0.099345826 0.023416036 1.041814928 -0.017790576 0.115887873 DALSEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DALSEER 7 0 H7BZ55 H7BZ55 Putative ciliary rootlet coiled-coil protein-like 3 protein 0 102.98 0.044286 0 927010 430810 657350 513260 691750 514650 932740 688100 1025700 FALSE TRUE 868990.0989 462707.6207 672942.6524 526431.1205 637422.7454 663221.1004 792884.2961 774010.7997 854504.0437 1.016952588 0.541492605 0.787524246 0.616066272 0.745956383 0.77614741 0.92788829 0.905801213 1 19.70472779 1.805067224 1.785228354 0.958161229 0.713278374 0.348717978 0.125421267 0.322637505 1.985594336 0.079151773 0.03374344 63.836229 -1.805067224 -0.244882855 DAMEQCHNYNAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DAMEQCHNYNAR 12 0 Q92785;J3KMZ8;Q92785-2;E9PN04 Q92785 DPF2 Zinc finger protein ubi-d4 0 ; 142.47 4.66E-05 222210000 107961 92215 93054 105333 116318 81589 104125 85253 136386 FALSE TRUE 101203.9137 99042.69455 95261.28482 108036.0231 107182.8535 105142.4198 88512.4229 95897.02472 113622.2955 0.89070471 0.871683626 0.8384031 0.950834716 0.943325894 0.925367854 0.779005762 0.843998304 1 16.79388643 DANDPVDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DANDPVDDR 9 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 138.08 0.00034118 176490000 479910 577690 589100 585530 589610 482960 711870 529420 636800 FALSE TRUE 449873.2898 620462.7687 603073.7302 600555.6911 543304.409 622382.7118 605131.7022 595519.2524 530513.9661 0.847995187 1.169550301 1.13677258 1.132026166 1.024109531 1.173169326 1.140651785 1.122532658 1 19.01703121 4.744394901 24.84657065 1.123922782 0.847995056 0.668015436 0.058060518 318.0168768 1354301.697 0.012525781 0.111947397 55513.02597 -4.744394901 -0.275927726 DANEVEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DANEVEKK 8 1 Q9Y6U3;Q9Y6U3-3 Q9Y6U3 SCIN Adseverin 0 ; 105.4 0.0070485 1404290000 1289110 858100 1028300 1010230 1418100 695820 1157740 1114850 2869800 FALSE TRUE 1208426.906 921634.6169 1052691.762 1036154.212 1306728.146 896691.9383 984147.6349 1254041.477 2390811.84 0.505446261 0.385490234 0.440307239 0.433390112 0.546562521 0.375057511 0.411637427 0.524525375 1 21.18906916 0.792120524 3.460702774 0.999964103 0.436033324 0.918630226 0.051702372 0.359258127 5.671262661 0.046870202 0.012102517 6.196130037 -0.792120524 -0.56393078 DANQVHSTTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DANQVHSTTR 10 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 ;;; 136.96 0.00012963 454200000 314630 465219 390443 411774 453476 324552 417430 379888 370140 FALSE TRUE 294937.8699 499664.2988 399704.4923 422340.818 417861.8242 418244.8937 354840.2467 427317.853 308361.2428 0.956468677 1.620386188 1.296221564 1.369630029 1.355104878 1.356347153 1.150729072 1.385770304 1 18.23426192 0.091418976 0.434668535 0.958982373 1.36698954 0.204563658 0.174999072 4.932719317 1.29888224 0.547280482 0.09874623 1.234295019 -0.091418976 0.408007168 DANSSFFDNSSS(ph)PHLLDQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DANSSFFDNSSSPHLLDQLK 20 0 P49454 P49454 CENPF Centromere protein F 1 DANSSFFDNS(0.001)S(0.03)S(0.969)PHLLDQLK 161.39 1.46E-11 122540000 168960 130400 160510 153240 144060 123560 212390 137580 211590 TRUE FALSE 158385.0952 140054.9517 164317.373 157172.3978 132746.1087 159229.7662 180544.0912 154757.1659 176274.2621 0.898515151 0.794528651 0.932168832 0.891635546 0.753065746 0.903306951 1.024222647 0.877933988 1 17.42746232 1.994516309 24.96834021 0.968498924 0.855743436 0.404384149 0.062847188 221.0376388 1006429.584 0.022628617 0.016215327 98.74527158 -1.994516309 -0.112755488 DAPAPRPLPASEGHLQPPAQTSGPTGS(ph)PPCIQTSPDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DAPAPRPLPASEGHLQPPAQTSGPTGSPPCIQTSPDPR 38 1 B4DF95;Q15735 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 DAPAPRPLPASEGHLQPPAQT(0.052)S(0.04)GPT(0.355)GS(0.547)PPCIQT(0.004)S(0.001)PDPR 76.371 0.0014695 608580000 33767 46330 45204 51114 55723 41180 49789 38129 108160 TRUE FALSE 31653.58375 49760.32141 46276.26023 52425.67178 51346.74036 53067.9975 42323.60167 42889.48958 90107.39726 0.351287294 0.552233478 0.513567827 0.581813185 0.569839346 0.588941631 0.469701744 0.475981894 1 16.45935793 -2.092376307 2.572056775 1.829724264 0.519911734 0.823678483 0.070757568 4674960.004 1446241.774 22742656.99 0.01602416 0.008083951 2.092376307 -1.30981253 DAPSLEEVEGHVADGS(ph)ATEMGTTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DAPSLEEVEGHVADGSATEMGTTK 24 0 C9J470;E9PHA2;Q15003;Q15003-2 C9J470 NCAPH Condensin complex subunit 2 1 DAPSLEEVEGHVADGS(0.987)AT(0.012)EMGT(0.001)TK 122.47 0.00040169 96132000 73917 50515 71254 60967 74083 57382 84678 62732 109640 TRUE FALSE 69290.66692 54255.18316 72944.17853 62531.51644 68264.82002 73947.25188 71981.32001 70564.22829 91340.3757 0.758598444 0.593989052 0.798597312 0.684598853 0.74736741 0.80957902 0.788055878 0.772541472 1 16.4789651 -4.999999991 0.118458071 1.889258266 0.601926559 0.706254206 0.055528452 76.38229255 0.589395513 16.14044147 0.509240603 1.00E-05 4.999999991 -1.287331707 DAPTS(ph)PASVASSSSTPSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DAPTSPASVASSSSTPSSK 19 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 DAPTS(1)PASVASSSSTPSSK;DAPT(0.001)S(0.94)PAS(0.05)VAS(0.008)SSSTPSSK;DAPTS(0.994)PAS(0.006)VASSSSTPSSK;DAPT(0.014)S(0.985)PAS(0.001)VASSSSTPSSK;DAPTS(0.974)PAS(0.026)VASSSSTPSSK;DAPT(0.141)S(0.859)PASVASSSSTPSSK 440.14 6.46E-191 3770420000 2115646 1574342 1798332 1715465 1901007 1367291 2023957 1662724 2647784 TRUE FALSE 1983231.493 1690907.92 1840989.284 1759486.736 1751709.579 1762005.716 1720483.437 1870318.752 2205851.745 0.899077419 0.76655556 0.834593389 0.797645055 0.794119361 0.798787008 0.779963314 0.847889599 1 21.0729044 0.887538463 4.925883446 0.999989284 0.805740724 0.724560061 0.03652354 0.394155821 16.66573588 0.0310104 0.007843798 7.718598718 -0.887538463 -0.19424856 DAQHYGGWEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DAQHYGGWEHR 11 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;; 166.7 1.16E-05 15026990000 2912890 3078810 3093570 3158120 3302830 2444610 3407280 2837710 2577680 FALSE TRUE 2730577.415 3306768.296 3166950.941 3239162.706 3043439.055 3150329.222 2896389.996 3192004.34 2147448.556 1.271544973 1.539859145 1.474750551 1.508377324 1.417234907 1.467010334 1.348758734 1.48641714 1 21.03419214 -2.439569187 0.380714041 0.318880299 1.46372455 0.738452722 0.081301694 30.1629951 1.3615796 17.14885641 0.050574771 0.003634384 2.439569187 1.144844251 DAQIGWIQTVEDLHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DAQIGWIQTVEDLHER 16 0 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 ;; 175.51 3.49E-09 242613000 300999 335418 341205 356666 374188 291850 408102 323256 348628 FALSE TRUE 282160.0099 360252.6977 349298.5437 365818.6534 344800.7839 376102.3572 346910.8937 363615.2232 290439.7346 0.971492452 1.240369877 1.202654121 1.259533768 1.187168086 1.294941127 1.194433311 1.251947237 1 18.14787931 4.741995395 24.84556063 1.216383576 0.971492352 0.445387254 0.080428751 234.6540075 1697293.339 0.015838624 0.116254755 55207.15849 -4.741995395 -0.244891224 DAQNSSDS(ph)SFEKNVEITEQLANGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DAQNSSDSSFEKNVEITEQLANGR 24 1 Q6PL18 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 DAQNSSDS(0.5)S(0.5)FEKNVEITEQLANGR;DAQNSSDS(0.5)S(0.5)FEKNVEITEQLANGR 202.14 8.13E-25 308930000 207852 138504 152534 148669 175597 109788 208765 143877 202901 TRUE FALSE 194842.9143 148758.9803 156152.1785 152484.0982 161806.3199 141482.0133 177462.6263 161840.3602 169035.5123 1.152674439 0.880045727 0.923783271 0.902083214 0.957232701 0.836995797 1.049854104 0.95743408 1 17.36696685 1.688804752 14.58012706 1.002419072 0.931912881 0.090983093 0.085840658 0.26983536 69.23390178 0.036287829 0.019996633 48.84327231 -1.688804752 -0.070506191 DAQNSSDSS(ph)FEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DAQNSSDSSFEK 12 0 Q6PL18 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 DAQNSSDS(0.038)S(0.962)FEK 204.52 1.18E-07 110330000 666090 361800 464770 438170 414740 405370 691650 419440 313340 TRUE FALSE 624400.6159 388588.0485 475794.5639 449414.184 382167.9934 522393.7384 587943.5035 471808.0073 261041.5297 2.391958921 1.488606234 1.822677657 1.721619485 1.464012235 2.001190151 2.252298721 1.807405924 1 17.99391982 0.944096169 22.40424576 0.999999998 1.852544412 0.464174492 0.293316038 6222.363992 2493703.745 0.285278239 0.07131956 8.792171861 -0.944096169 0.852544414 DAS(ph)PSKEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DASPSKEER 9 1 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 DAS(1)PSKEER;DAS(0.976)PS(0.024)KEER;DAS(0.685)PS(0.315)KEER;DAS(0.758)PS(0.242)KEER;DAS(0.989)PS(0.011)KEER 174.42 3.31E-05 12554310000 15845070 8408200 10403880 10043190 10725710 7618120 12539820 8123820 12269160 TRUE FALSE 14853355.35 9030751.877 10650664.95 10300915.26 9883356.002 9817347.574 10659590.4 9138096.81 10221357.93 1.453168498 0.88351782 1.042000976 1.00778344 0.966931798 0.960473905 1.042874193 0.894019842 1 23.28508354 4.745715521 24.99648268 0.979660471 1.453168718 0.885857934 0.053949358 258.4653 902955.7405 0.01207225 0.123298542 55682.08917 -4.745715521 0.473508247 DASDDLDDLNFFNQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DASDDLDDLNFFNQK 15 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;;; 253.79 2.59E-24 385727000 1285394 807140 1028767 933558 1026864 772010 1244643 858952 1079168 FALSE TRUE 1204943.484 866901.4854 1053169.839 957514.6788 946218.2436 994876.7545 1058020.337 966194.048 899047.8891 1.340243939 0.964243947 1.171427965 1.065031897 1.05246701 1.106589278 1.176823114 1.074685853 1 19.77803844 4.757394882 24.80198002 1.088118226 1.340244185 0.60162858 0.066869966 2897.956743 3816116.835 0.015550602 0.561726429 57199.8489 -4.757394882 0.252125959 DASIVGFFDDSFSEAHSEFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DASIVGFFDDSFSEAHSEFLK 21 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;;; 406.23 1.44E-151 1201875000 3176557 2696196 2913189 2888010 2626121 2194531 3581176 2542486 1728774 FALSE TRUE 2977741.968 2895825.157 2982291.219 2962121.226 2419876.05 2828056.474 3044211.905 2859920.974 1440230.451 2.067545486 2.010667914 2.070704182 2.056699484 1.680200587 1.963613859 2.113697778 1.985738443 1 20.45786824 -1.295034465 2.974598673 0.991991555 2.001591255 0.871084043 0.120092226 7295300.266 9230881.168 520329.5025 0.03091025 0.050695048 1.295034465 1.0095997 DASNWSTDKLK ddPTM_SK-BR-3_Pertuzumab_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 339090000 455630 468910 385140 381800 653430 246380 479290 470220 796410 FALSE TRUE 427112.9316 503628.5843 394275.7027 391597.6344 602112.2436 317505.9064 407424.914 528928.0021 663484.026 0.6437426 0.759066631 0.594250483 0.590214111 0.907500739 0.478543407 0.614068912 0.797197794 1 19.33970221 0.966040915 3.997483247 0.99943765 0.655971174 0.49256967 0.113385887 0.172839439 8.055471944 0.101669262 0.026018891 9.247852939 -0.966040915 -0.343466477 DASPS(ph)KEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DASPSKEER 9 1 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 DAS(0.206)PS(0.794)KEER;DAS(0.446)PS(0.554)KEER 138.42 8.30E-05 1307530000 3116820 1613150 1938900 2113410 2313440 1522640 2501550 1669980 2390210 TRUE FALSE 2921743.8 1732589.304 1984891.624 2167643.679 2131751.754 1962201.45 2126465.801 1878480.679 1991268.51 1.46727766 0.870093258 0.996797576 1.088574277 1.070549624 0.985402742 1.067895058 0.943358804 1 20.92525634 4.748807676 24.98956299 1.003104674 1.467277918 0.835773933 0.064701083 612.818663 1494454.724 0.016429455 0.230311318 56079.95756 -4.748807676 0.464173243 DASRPHVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DASRPHVVK 9 1 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ; 87.258 0.0081612 550140000 1713030 1630920 1663280 1679310 1786590 1165370 1937630 1501800 1615290 FALSE TRUE 1605814.51 1751675.014 1702733.787 1722403.938 1646278.428 1501793.401 1647100.37 1689303.036 1345687.664 1.193304028 1.301695082 1.265326147 1.279943321 1.223373352 1.116004435 1.223984149 1.255345561 1 20.35991217 2.469093627 6.428382626 1.171161986 1.266530112 0.318348008 0.073793896 0.182337836 33.98184604 0.022909946 0.019775237 294.5056474 -2.469093627 0.095368126 DASSGKENRS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DASSGKENRSPSR 13 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 DASSGKENRS(0.985)PS(0.015)R 73.498 0.019132 27115000 21754 23686 23236 24742 37074 15023 22839 20736 52325 TRUE FALSE 20392.45597 25439.73609 23787.16889 25376.92161 34162.35759 19359.89622 19414.50398 23324.93525 43591.61947 0.467806799 0.58359236 0.545682156 0.582151384 0.783690948 0.444119683 0.445372395 0.535078429 1 15.41176318 -1.818342899 2.607936563 1.15209196 0.547104411 0.678385944 0.097708676 15641377.36 10378442.27 14948481.89 0.024034453 0.015193475 1.818342899 -0.604987549 DASVPLIDVTNLPT(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DASVPLIDVTNLPTPR 16 0 Q96A65;Q96A65-2 Q96A65 EXOC4 Exocyst complex component 4 1 DASVPLIDVTNLPT(1)PR;DASVPLIDVTNLPT(1)PR;DASVPLIDVTNLPT(1)PR;DASVPLIDVTNLPT(1)PR;DASVPLIDVTNLPT(1)PR;DASVPLIDVTNLPT(1)PR 238.8 9.36E-19 251850000 181670 192054 201939 197294 209649 155410 227982 163567 235206 TRUE FALSE 170299.599 206273.878 206729.0884 202356.8981 193184.0132 200274.3441 193798.2156 183988.7 195948.5991 0.869103427 1.052693813 1.055016925 1.032703979 0.98589127 1.022075917 0.989025777 0.9389641 1 17.58011573 1.540337565 4.34289899 0.967729005 1.014957891 0.027803346 0.055201199 0.369084139 15.37075317 0.032126994 0.013668415 34.70064637 -1.540337565 0.047228886 DATLLIHEATLEDGLEEEAVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DATLLIHEATLEDGLEEEAVEK 22 0 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-4;Q9BQ52-3 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 0 ;; 310.92 3.42E-67 126090000 171366 121480 152538 146609 156761 116615 184140 133008 213380 FALSE TRUE 160640.508 130474.5056 156156.2734 150371.2351 144449.6234 150279.8574 156529.9165 149614.3416 177765.4995 0.903665269 0.733969786 0.878439707 0.84589662 0.812585253 0.845382585 0.880541595 0.841638799 1 17.43961583 -5 0.192779618 1.722700653 0.808527994 0.527243314 0.046492242 98.08024604 0.963412959 27.11837678 0.112561289 1.00E-05 5 -0.914172659 DATLTALDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DATLTALDR 9 0 H0YFD6;P40939;A0A2R8Y4F5;A0A2R8YG21 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 140.35 0.00025428 62037000 74692 107670 82625 80775 128580 74653 73253 93937 137890 FALSE TRUE 70017.16105 115641.9988 84584.90402 82847.82325 118481.8455 96204.10921 62269.3927 105665.2412 114875.2682 0.609505964 1.006674462 0.736319535 0.721198083 1.031395594 0.837465807 0.542060912 0.91982585 1 16.8097087 1.007949491 24.99571761 1.000000172 0.79313569 0.195684091 0.152568114 242.7213978 763189.2759 0.14474374 0.036185935 10.18472932 -1.007949491 -0.206864482 DATMEVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DATMEVQR 8 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 114.65 0.006085 388940000 427210 675410 487820 456000 691900 406950 476340 583110 625430 FALSE TRUE 400471.6887 725418.0592 499391.3208 467701.732 637560.965 524429.8587 404917.2391 655912.5671 521041.6926 0.768598165 1.392245706 0.958447909 0.89762823 1.223627541 1.006502678 0.777130208 1.258848527 1 18.99103929 3.728096816 24.98397512 0.997707328 1.140081781 0 0.205781817 113.1291363 2897102.864 0.049930519 0.083914939 5346.835413 -3.728096816 0.142374453 DATNRS(ph)PTQIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DATNRSPTQIVK 12 1 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 DATNRS(0.952)PT(0.048)QIVK;DATNRS(0.993)PT(0.007)QIVK;DATNRS(0.997)PT(0.003)QIVK;DATNRS(0.999)PT(0.001)QIVK 223.68 1.32E-11 2722350000 2534180 2054590 2175650 2309670 2430820 1677960 2748740 1980620 2756460 TRUE FALSE 2375570.197 2206713.981 2227257.445 2368940.042 2239913.203 2162359.813 2336591.955 2227904.767 2296389.019 1.034480734 0.960949544 0.96989553 1.031593525 0.975406686 0.941634799 1.017507023 0.970177417 1 21.13093563 DATNVGDEGGFAPNILENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DATNVGDEGGFAPNILENK 19 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;; 388.06 1.50E-126 622280000 1373510 1101290 1113880 1028120 1391000 691100 1374140 1152350 1463380 FALSE TRUE 1287544.461 1182830.657 1140301.76 1054503.3 1281756.471 890609.3509 1168100.464 1296223.434 1219132.424 1.056115345 0.970223278 0.935338719 0.864962066 1.051367715 0.730527163 0.958140757 1.06323432 1 20.21742341 1.368773996 7.140396572 1.028641182 0.932213005 0.150218018 0.093322921 0.388741356 22.40283519 0.058532144 0.021303177 23.37620441 -1.368773996 -0.096428178 DATNVGDEGGFAPNILENKEGLELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DATNVGDEGGFAPNILENKEGLELLK 26 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 229.6 7.21E-35 193617000 198695 178754 171498 192492 303360 137351 275310 180757 632210 FALSE TRUE 186259.0346 191989.1322 175566.0135 197431.6706 279535.3293 177002.004 234029.8214 203324.9093 526690.0668 0.353640682 0.364520131 0.33333838 0.374853606 0.530739702 0.336064823 0.444340678 0.386042802 1 19.00659473 -4.999999999 0.314733333 6.611814249 0.35982576 0.917420767 0.057582508 75.27793898 0.675179581 280.6101673 0.049112879 1.00E-05 4.999999999 -6.251988489 DATSLLAAGEGGLLDEVEPLRPDELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DATSLLAAGEGGLLDEVEPLRPDELER 27 1 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 0 168.25 6.62E-12 18179000 10467 11057 10791 13813 12931 7270.7 13884 9180.2 12790 FALSE TRUE 9811.889154 11875.67178 11046.96762 14167.46497 11915.45142 9369.63306 11802.22309 10326.36818 10655.26637 0.920848791 1.11453542 1.036761281 1.329620909 1.118268751 0.879342921 1.107642238 0.969132804 1 13.37927904 DAVAHCHEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DAVAHCHEAER 11 0 P49792;O14715;Q99666;J3KQ37;F8W705;Q99666-2;H0YBN8 P49792 RANBP2;RGPD8;RGPD5 E3 SUMO-protein ligase RanBP2;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6 0 137.16 4.87E-05 246230000 170020 104080 140110 100480 124990 102270 134330 98938 125980 FALSE TRUE 159378.7517 111786.1915 143433.4754 103058.4869 115173.7896 131793.6888 114188.4636 111290.6271 104953.1241 1.518570819 1.065105898 1.366643219 0.981947777 1.097383146 1.255738596 1.087994898 1.060384129 1 16.67938559 DAVDFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DAVDFLR 7 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 ;;;;;;; 148.33 0.0048655 1441250000 4140780 4694820 4359910 4278180 4909160 3631730 4840150 3899010 4709500 FALSE TRUE 3881615.971 5042429.358 4463329.124 4387965.342 4523614.376 4680151.495 4114414.441 4385809.981 3923454.025 0.989336423 1.285201592 1.137601994 1.118393465 1.152967346 1.19286513 1.048671506 1.117844112 1 21.90369286 1.112368092 0.688507219 1.002259628 1.164297964 0.204472181 0.078891664 0.866813824 0.973349829 0.071358772 0.029392115 12.9529322 -1.112368092 0.162038337 DAVLLVFANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DAVLLVFANK 10 0 P61204;F5H423;P61204-2;P84077;P84085;C9J1Z8 P61204;P84077;P84085 ARF3;ARF1;ARF5 ADP-ribosylation factor 3;ADP-ribosylation factor 1;ADP-ribosylation factor 5 0 ; 164.96 1.40E-05 261590000 1921860 1739270 1849880 1708990 1853440 1423790 2180340 1679440 1745850 FALSE TRUE 1801574.213 1868047.361 1893760.027 1752845.577 1707878.299 1834815.06 1853418.258 1889121.781 1454456.356 1.238658146 1.284361234 1.302039775 1.205155156 1.174238258 1.261512627 1.27430311 1.298850785 1 20.47204858 -1.081024407 4.471371684 0.999980648 1.259277234 0.795122587 0.04060741 8.63E-06 1.77E-06 0.041544019 0.009791258 0.082980413 1.081024407 0.259296586 DAVSGMGVIVHIIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DAVSGMGVIVHIIEK 15 0 P49720 P49720 PSMB3 Proteasome subunit beta type-3 0 ; 157.38 1.96E-06 371670000 2425000 1730990 1999060 1788300 1986230 1633730 2395500 2033610 1264020 FALSE TRUE 2273223.579 1859154.301 2046478.647 1834190.806 1830239.508 2105361.33 2036317.014 2287510.685 1053046.896 2.158710678 1.765500005 1.943387949 1.741794038 1.738041786 1.999304435 1.933738204 2.172278076 1 20.00613826 -1.849612691 2.837969536 0.659043799 1.911057427 0.778376715 0.155879958 16116505.73 7802506.716 36801404.4 0.035082605 0.014137978 1.849612691 1.252013628 DAVTYTEHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DAVTYTEHAK 10 0 P62805 P62805 HIST1H4A Histone H4 0 ;;; 201.48 2.41E-07 10384800000 11301800 9076500 7812600 8086700 12360400 7704000 10751500 9452000 11924200 FALSE TRUE 10594440.51 9748533.504 7997918.561 8294218.413 11389664.04 9928019.736 9139412.387 10632103.01 9933973.987 1.066485631 0.981332699 0.805107661 0.834934581 1.146536528 0.999400617 0.920015736 1.070276912 1 23.24393954 2.761597753 24.99222183 1.011546123 0.912383499 0.231776085 0.092097938 1295.092493 1405000.164 0.029087447 0.030835921 577.5608584 -2.761597753 -0.099162624 DAVVYPILVEFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DAVVYPILVEFTR 13 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 112.13 0.0021529 99360000 255170 195364 206190 201466 222520 170309 238280 161448 176757 FALSE TRUE 239199.3652 209828.9538 211080.9242 206635.9586 205044.1768 219474.4436 202552.1261 181605.1382 147255.1148 1.624387482 1.42493491 1.43343696 1.403251486 1.392441798 1.49043681 1.375518442 1.233268796 1 17.16795822 -3.550908044 0.164350126 7.72E-22 1.55612129 0.833609222 0.067059961 30.60415646 0.441459052 10.51385152 0.276484341 0.00028125 3.550908044 1.55612129 DAYSGGAVNLYHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DAYSGGAVNLYHVR 14 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;; 223.03 3.67E-12 1613180000 1469190 2744100 1305320 1281230 2770950 827350 1488750 2471310 2423040 FALSE TRUE 1377236.02 2947276.019 1336282.807 1314108.531 2553330.764 1066192.514 1265525.758 2779858.494 2018618.971 0.682266461 1.460045735 0.661978722 0.650993848 1.264889908 0.528179181 0.626926516 1.37710907 1 20.94493719 3.886958714 7.516706993 0.83184542 1.11734852 0.042448132 0.335941197 0.484147119 34.88084103 0.079784487 0.144750196 7708.301873 -3.886958714 0.2855031 DCDHADEQK ddPTM_SK-BR-3_Pertuzumab_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 ;;; 206.43 1.33E-05 1865001000 6287040 3318230 4606490 4122890 3546170 3429940 4858370 3604600 3490760 FALSE TRUE 5893545.389 3563915.202 4715758.118 4228690.337 3267668.113 4420107.998 4129902.521 4054642.245 2908129.605 2.026575906 1.225500815 1.621577701 1.454092806 1.123632216 1.519914377 1.420123269 1.394243997 1 21.47166014 0.658073296 0.049964692 4.21E-23 2.567108972 0.390787745 0.221137792 95.84169328 2.37460355 66.24301946 54.00294695 4.550648548 -0.658073296 2.567108972 DCDLQEDACYNCGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DCDLQEDACYNCGR 14 0 P62633-2;P62633;P62633-7;P62633-3 P62633-2 CNBP Cellular nucleic acid-binding protein 0 354.26 1.12E-81 258380000 343460 265020 301070 296760 241230 243920 307240 249300 179030 FALSE TRUE 321963.4517 284642.3566 308211.5226 304375.364 222284.7689 314335.7443 261172.2143 280425.6538 149148.7364 2.15867368 1.908446316 2.066470893 2.040750537 1.490356366 2.107532064 1.751085665 1.880174519 1 17.18639223 -1.991934931 0.265173847 4.36E-17 2.042964547 0.726546241 0.183153415 15.38600271 0.616025493 9.815806001 0.227210004 0.01018744 1.991934931 2.042964547 DCDPGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 118.81 0.0019032 3433650000 12427250 10810000 11855740 11505520 11443020 10571790 13910050 9342250 10107500 TRUE FALSE 11649450.61 11610383.65 12136963.75 11800771.12 10544331.37 13623694.15 11824367.14 10508650.48 8420492.953 1.383464207 1.378824697 1.441360241 1.401434713 1.252222575 1.617921211 1.404236926 1.247985188 1 23.00547326 0.957598064 2.919195095 1.001371008 1.414859251 0.690905787 0.088891671 0.148067192 3.054861168 0.079227667 0.020907644 9.069807384 -0.957598064 0.413488243 DCEECIQLEPTFIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DCEECIQLEPTFIK 14 0 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 140.39 2.32E-05 37444000 68413 50187 59186 50364 53506 46565 80780 49362 50261 FALSE TRUE 64131.15245 53902.8977 60589.91987 51656.42551 49303.85459 60007.55958 68667.78892 55524.95436 41872.1144 1.53159575 1.287322087 1.447023174 1.233671293 1.177486623 1.433115104 1.639940803 1.326060438 1 15.35370215 DCEQAENWMAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DCEQAENWMAAR 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 93.345 0.016807 109930000 111230 120760 105040 150650 156800 89135 114500 113750 154430 FALSE TRUE 104268.3129 129701.1961 107531.5984 154515.934 144485.5605 114866.8275 97331.78797 127951.9379 128654.6353 0.810451272 1.008134652 0.835815967 1.201013346 1.123049785 0.892830851 0.756535415 0.99453811 1 16.97314391 1.03988052 24.99973662 1.00000697 0.940133336 0.021088784 0.137350427 628.0407158 393695.3162 0.13546508 0.03386627 10.96176583 -1.03988052 -0.059873633 DCEVIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DCEVIER 7 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 97.093 0.028499 303400000 383640 372630 354010 367680 412430 353910 443770 349460 381720 FALSE TRUE 359628.6572 400219.9129 362407.2844 377115.2913 380039.4115 456078.0718 377230.8083 393090.8503 318008.466 1.13087762 1.25851968 1.139615209 1.185865572 1.195060673 1.434169591 1.186228823 1.236101841 1 18.27870565 -1.52321159 6.510391094 0.999825319 1.2219854 0.400147464 0.084950803 0.000203791 1.49E-05 0.077824352 0.018329078 0.029977017 1.52321159 0.22216008 DCFGCLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DCFGCLR 7 0 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 ;;;;; 141.55 0.0059305 3352740000 2789000 3875170 2721770 2522060 3971890 2341350 3190640 3426260 3910600 FALSE TRUE 2614441.469 4162091.619 2786331.67 2586780.329 3659953.781 3017259.736 2712233.152 3854036.103 3257895.597 0.802493939 1.277539901 0.855255053 0.794003446 1.123410396 0.926137639 0.832510764 1.182983306 1 21.63550894 3.813211584 9.73898634 0.943550472 1.072348814 0.024711188 0.166864822 0.840561723 89.27915558 0.039149507 0.070660331 6504.465049 -3.813211584 0.128798342 DCGATWVVLGHSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DCGATWVVLGHSER 14 0 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3;U3KPS5 P60174 TPI1 Triosephosphate isomerase 0 ;;;;; 225.32 2.82E-12 26361500000 13504950 18021200 13064040 13225370 17251600 9661810 17863500 15380850 23658300 FALSE TRUE 12659699.29 19355508.4 13373925.2 13564755.38 15896728.93 12451017.7 15185034.01 17301182.98 19709576.89 0.642312078 0.982035713 0.678549584 0.688231689 0.806548462 0.631724251 0.77043937 0.877805905 1 24.23239347 1.025960584 2.875707281 0.998077975 0.755256408 0.416826957 0.101460409 0.248845539 4.628556669 0.094826926 0.025202631 10.61599205 -1.025960584 -0.242821567 DCGEYAHTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DCGEYAHTR 9 0 Q5T8A0;Q9Y399 Q5T8A0 MRPS2 "28S ribosomal protein S2, mitochondrial" 0 91.584 0.010654 126260000 130860 204070 198210 174600 249980 218610 178860 204040 258950 FALSE TRUE 122669.7062 219179.5551 202911.6348 179080.5316 230347.5792 281719.1582 152041.6035 229514.8431 215729.5721 0.568627217 1.015992165 0.940583309 0.830115824 1.067760794 1.305890312 0.704778682 1.063900702 1 17.71886443 4.741947951 23.71292073 0.978219373 0.56862689 0.413954662 0.157321095 160.9335285 1126497.767 0.035424602 0.254337973 55201.12782 -4.741947951 -0.409592483 DCHEEVYAGSHQYPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DCHEEVYAGSHQYPGR 16 0 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 ;;; 216.01 9.01E-15 1005360000 198204 259796 253533 232624 246256 231432 255844 222230 299209 FALSE TRUE 185798.7654 279031.5662 259546.9225 238593.5257 226916.0471 298242.6614 217482.5673 249975.9047 249269.0849 0.745374283 1.119399007 1.041231898 0.95717255 0.910325671 1.196468714 0.872481108 1.002835569 1 17.92734444 4.752975326 24.66198608 1.014871802 0.745374056 0.443582799 0.09398492 2015.078162 3447506.559 0.021557761 0.461143489 56620.712 -4.752975326 -0.269497745 DCLFRPLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DCLFRPLNK 9 1 A0A590UJ56;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;Q13616;A0A590UJC4;A0A590UK34;A0A590UJM8 A0A590UJ56 CUL1 Cullin-1 0 ; 97.431 0.0061068 470540000 792140 757490 749280 758550 872760 604150 888220 747620 884370 FALSE TRUE 742561.3714 813575.3478 767053.2754 778015.6772 804216.9501 778558.2974 755039.6568 840962.0027 736762.9338 1.007870154 1.104256621 1.041112738 1.055991882 1.091554574 1.056728375 1.02480679 1.141428218 1 19.49084096 -1.54858206 6.838064519 0.999947642 1.063944781 0.216707724 0.039021079 2.76E-05 1.82E-06 0.033500299 0.007889642 0.028275998 1.54858206 0.063997139 DCLHGIEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DCLHGIEAK 9 0 Q8N684-2;Q8N684;Q8N684-3;F5H669 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 0 ;;; 137.95 0.0001502 1195740000 3489280 2760780 3092970 2897150 3371480 2363900 3659680 2807370 4434360 FALSE TRUE 3270892.193 2965191.024 3166336.709 2971495.774 3106697.561 3046319.555 3110944.959 3157876.324 3694236.669 0.885404073 0.802653238 0.857101749 0.804359883 0.840957913 0.824614075 0.84210765 0.854811591 1 21.81684486 0.432370077 1.395606513 1.00005088 0.833492916 0.81700247 0.024078139 1.08044995 2.297047458 0.019861993 0.005814776 2.706263481 -0.432370077 -0.166557964 DCLIPMGITSENVAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DCLIPMGITSENVAER 16 0 P09110;C9JDE9;H0Y4D4 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 107.37 0.005057 0 34405 38205 40123 42922 41811 34199 48076 34823 39447 FALSE TRUE 32251.65246 41033.73795 41074.73651 44023.45119 38527.33272 44071.69613 40867.45012 39170.7282 32863.04086 0.981395867 1.24862876 1.249876318 1.339603702 1.172360552 1.341071762 1.243568734 1.191938639 1 15.00417836 0.824705298 3.46509072 1.000045264 1.237444794 0.321834348 0.100726834 1.085982532 19.81500586 0.087496023 0.022596683 6.678905487 -0.824705298 0.237399531 DCMEHAVLPVDGATLAEVMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DCMEHAVLPVDGATLAEVMR 20 0 K7EIG1;A0A494C0R8;O75153 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ; 112.55 0.00015184 322600000 121346 139265 139680 143291 142911 117845 165418 137767 145705 FALSE TRUE 113751.1705 149576.3255 142993.2756 146968.0897 131687.3465 151864.9384 140615.1066 154967.5132 121385.8942 0.937103699 1.232238115 1.178005702 1.210750974 1.084865316 1.251092142 1.158413895 1.276651741 1 16.88924126 4.745539653 24.87560663 1.183612831 0.937103576 0.4484642 0.081949692 606.1407961 2160429.511 0.016512776 0.16412217 55659.54519 -4.745539653 -0.246509256 DCQLNAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DCQLNAHK 8 0 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;;; 156.01 0.00039986 3338190000 4498480 4334580 3645720 3248210 4763710 3031930 4965600 4498840 4705620 FALSE TRUE 4216928.167 4655516.813 3732198.2 3331564.568 4389587.432 3907198.972 4221054.378 5060530.077 3920221.623 1.075686166 1.1875647 0.952037553 0.849840873 1.119729407 0.996678083 1.076738711 1.290878569 1 21.90250379 1.449942704 9.657635315 1.158307592 1.036932716 0.142742036 0.114273282 0.331100136 93.3147419 0.062929272 0.027589322 28.18011127 -1.449942704 -0.121374875 DCQLNAHKDHQYQFLEDAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DCQLNAHKDHQYQFLEDAVR 20 1 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;; 260.08 1.64E-36 1935120000 2210480 1965390 1975800 2090080 2641670 1222570 2472470 1861430 4563180 FALSE TRUE 2072130.003 2110909.521 2022666.909 2143714.991 2434203.894 1575506.112 2101746.077 2093833.633 3801555.779 0.545074207 0.555275167 0.532062931 0.563904653 0.640317816 0.414437195 0.552864721 0.550783352 1 21.85815853 0.46564324 3.090675886 0.999999611 0.541928183 0.873145537 0.054587746 8.211076202 46.92905499 0.048212688 0.012560712 2.92175126 -0.46564324 -0.458071428 DCSCTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DCSCTSR 7 0 B1AH88 B1AH88 TSPO Putative peripheral benzodiazepine receptor-related protein 0 ; 84.064 0.050763 530910000 117246 128820 121270 124839 154026 93692 137650 132747 182597 FALSE TRUE 109907.7822 138357.9668 124146.5817 128042.5801 141929.4193 120739.3594 117010.6604 149320.7552 152120.3811 0.722505304 0.909529452 0.816107485 0.84171877 0.933007256 0.793709289 0.769197786 0.981595984 1 17.21485393 1.19838434 11.05972764 0.991377167 0.832933897 0.54928247 0.061648853 0.533911776 142.5138385 0.05622402 0.014183859 15.79008036 -1.19838434 -0.15844327 DCSPS(ph)SPLKLDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DCSPSSPLKLDAR 13 1 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 DCS(0.102)PS(0.449)S(0.449)PLKLDAR 58.814 0.063062 191470000 528390 504000 455400 580390 603430 332130 566810 395180 662680 TRUE FALSE 495319.0131 541316.6844 466202.3031 595283.79 556039.0419 428010.5393 481822.1025 444519.0929 552074.4269 0.897196083 0.980513963 0.84445553 1.078267279 1.007181305 0.77527688 0.872748454 0.805179648 1 19.07450325 2.246610761 24.99990743 0.852080319 0.953455371 0.24173299 0.084753632 241.7342899 750712.4768 0.028109552 0.023131881 176.4455706 -2.246610761 0.101375052 DCTSALALVPFSIKPLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DCTSALALVPFSIKPLLR 18 1 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 ; 155.22 1.86E-08 147274000 316040 355000 330970 311720 431670 328590 482830 380210 395730 FALSE TRUE 296259.6205 381284.5694 338820.7647 319719.2629 397768.3795 423448.5988 410434.1239 427680.0554 329680.1065 0.898627532 1.156528895 1.027725841 0.969786337 1.206528303 1.284422658 1.244946589 1.297257696 1 18.33070731 2.644694879 5.975666179 1.232111588 1.039900736 0.436663105 0.105366271 0.2036221 10.61436691 0.031321626 0.029488101 441.2603236 -2.644694879 -0.192210852 DCVGPEVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DCVGPEVEK 9 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;;;; 117.89 0.0025103 2328500000 5396940 4448550 4074020 4065440 4557790 2444310 5912540 3810590 5380720 FALSE TRUE 5059155.159 4777925.271 4170657.678 4169766.073 4199839.559 3149942.617 5026009.516 4286350.55 4482643.071 1.128609858 1.065872342 0.930401464 0.930202563 0.936911436 0.70269762 1.121215639 0.95621054 1 22.0959182 4.263592932 1.691390313 0.940427606 1.130439302 0.300331206 0.101990867 0.588373773 2.879228347 0.027021916 0.134677942 18348.17747 -4.263592932 0.190011696 DDAT(ph)PVRDEPMDAESITFK ddPTM_SK-BR-3_Pertuzumab_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 260.32 6.78E-31 152072000 569090 313350 399740 367870 380090 343230 524690 358540 386910 TRUE FALSE 533471.6728 336550.76 409222.0216 377310.167 350239.2646 442314.9291 446017.6055 403304.5082 322332.2215 1.655036752 1.04411144 1.269565977 1.170562984 1.086578509 1.372233055 1.383720199 1.251207547 1 18.29818889 2.207955263 24.9956275 1.297635596 1.217688951 0 0.196418548 779.1887951 636365.4418 0.066977686 0.049472231 161.4192271 -2.207955263 -0.079946645 DDAYWPEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDAYWPEAK 9 0 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 113.62 0.004119 67843000 152380 118950 126070 126330 135840 101720 165510 117030 171680 FALSE TRUE 142842.8078 127757.1818 129060.4399 129571.8417 125171.6744 131084.9127 140693.312 131641.4531 143025.4989 0.998722668 0.893247587 0.902359656 0.905935254 0.875170339 0.916514284 0.983693908 0.920405481 1 17.12591285 1.826339571 6.493577274 0.964639806 0.909028272 0.288791744 0.038136349 0.26824379 15.92261192 0.015556668 0.009330404 67.04085903 -1.826339571 -0.055611533 DDDDIDLFGS(ph)DDEEESEEAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DDDDIDLFGSDDEEESEEAKR 21 1 P24534;C9JZW3 P24534 EEF1B2 Elongation factor 1-beta 1 DDDDIDLFGS(1)DDEEESEEAKR;DDDDIDLFGS(1)DDEEESEEAKR;DDDDIDLFGS(1)DDEEESEEAKR;DDDDIDLFGS(1)DDEEESEEAKR 250.71 2.84E-31 1532160000 2595710 918170 1401270 1175880 1026170 1036180 1737420 1007280 1005950 TRUE FALSE 2433249.145 986152.2622 1434508.786 1206055.072 945578.7476 1335308.345 1476910 1133041.125 838050.4463 2.903463813 1.176721839 1.711721284 1.439119896 1.128307671 1.593350795 1.762316346 1.351996327 1 19.67667756 4.745209112 24.99783121 1.45124866 2.903464471 0.77546876 0.253438928 364.370105 1369968.139 0.057752879 0.560941691 55617.19881 -4.745209112 1.452215811 DDDRTPGLHGDCDDDKYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDDRTPGLHGDCDDDKYR 18 2 O95159 O95159 ZFPL1 Zinc finger protein-like 1 0 119.31 4.65E-05 182830000 292420 227380 248090 227150 330140 199220 328600 250850 354680 FALSE TRUE 274117.9542 244215.4518 253974.812 232979.0536 304212.1361 256731.5799 279329.4806 282169.1747 295481.6167 0.927698844 0.826499647 0.859528301 0.788472245 1.029546743 0.868858045 0.94533624 0.954946632 1 18.17270885 2.746359824 24.99990745 0.947927259 0.848037832 0.496144727 0.053924953 501.7388617 1608295.137 0.015023774 0.015675771 557.6475823 -2.746359824 -0.099889427 DDDSNFHMDFIVAASNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDDSNFHMDFIVAASNLR 18 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 181.14 7.50E-14 142860000 83617 76566 79466 81965 73814 92437 101820 72724 52137 FALSE TRUE 78383.56123 82235.02631 81350.97105 84068.36067 68016.94619 119122.0613 86553.03625 81803.75149 43434.99788 1.804617591 1.89328952 1.872935997 1.93549821 1.565947957 2.742536367 1.99270267 1.883360319 1 15.40657035 DDDVPLMWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DDDVPLMWR 9 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ;;; 193.28 7.86E-05 302118000 532778 494002 521277 477396 514036 363681 538654 440288 590704 FALSE TRUE 499432.376 530578.4221 533641.9366 489646.7896 473665.6861 468669.8008 457887.8333 495258.926 492111.6863 1.014876074 1.078166678 1.08439192 0.994991184 0.962516639 0.952364705 0.93045511 1.006395377 1 18.90862625 3.084584444 3.827321464 0.962670477 1.066617298 0.649422657 0.029250756 0.111351755 3.174070027 0.008540162 0.010312676 1215.022846 -3.084584444 0.103946821 DDDYRGGGDRYEDRYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDDYRGGGDRYEDRYDR 17 3 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 95.767 0.0010896 978750000 275410 454520 339680 383600 607490 250430 447550 287760 1608200 FALSE TRUE 258172.5797 488173.1337 347737.37 393443.8254 559780.1859 322725.0756 380444.0324 323687.4694 1339781.031 0.192697593 0.36436785 0.259547913 0.293662783 0.417814682 0.240878971 0.283959859 0.241597292 1 20.3535658 -1.708793273 2.696290284 1.115979713 0.292722877 0.923807794 0.064347919 22067125.38 18512695.07 17330109.71 0.015056578 0.0195527 1.708793273 -0.823256835 DDEENYLDLFSHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DDEENYLDLFSHK 13 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ;; 198.23 1.28E-07 233576000 631994 397497 463247 467759 472416 349533 599694 373128 567281 FALSE TRUE 592438.6237 426928.0915 474235.4376 479762.4879 435314.353 450437.5029 509775.452 419713.8522 472598.1363 1.253577994 0.903363891 1.003464468 1.0151595 0.921108907 0.953108928 1.078665811 0.88809883 1 18.85025441 4.747812047 24.9466042 0.975547898 1.253578144 0.703869234 0.057643166 681.8036369 1838452.328 0.013249689 0.165812798 55951.54032 -4.747812047 0.278030246 DDEKEAEEGEDDRDS(ph)ANGEDDS ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDEKEAEEGEDDRDSANGEDDS 22 2 P07910;G3V2Q1;P07910-3;P07910-2;G3V4C1;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 DDEKEAEEGEDDRDS(1)ANGEDDS;DDEKEAEEGEDDRDS(1)ANGEDDS 236.65 1.33E-30 3639100000 7698400 2544900 4053600 3387300 3028500 3017900 5446400 3209900 2897700 TRUE FALSE 7216570.886 2733327.044 4149753.306 3474223.853 2790653.826 3889118.738 4629762.882 3610663.081 2414055.15 2.989397689 1.132255427 1.718996895 1.439165071 1.156002516 1.611031437 1.917836418 1.495683759 1 21.2030272 4.747006717 24.96776518 1.489432995 2.989398452 0.743918846 0.285166179 570.4243419 1686210.503 0.067383757 0.782125126 55847.88322 -4.747006717 1.499965457 DDEKEAEEGEDDRDSANGEDDS(ph) ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDEKEAEEGEDDRDSANGEDDS 22 2 P07910;G3V2Q1;P07910-3;P07910-2;G3V4C1;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 DDEKEAEEGEDDRDS(0.453)ANGEDDS(0.547) 59.691 0.024989 0 64981 22393 31378 27029 26650 25572 39769 23864 23099 TRUE FALSE 60913.9552 24051.00102 32122.30098 27722.6099 24557.0165 32954.22127 33806.00765 26843.47293 19243.62767 3.165409154 1.249816377 1.669243529 1.440612465 1.2761116 1.712474479 1.756737774 1.394927889 1 14.23209317 4.743593859 24.99753593 1.490718104 3.165409847 0.838074902 0.237672522 202.4952383 1005657.725 0.05349 0.449106645 55410.72832 -4.743593859 1.674691743 DDEVQVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DDEVQVVR 8 0 P61254;E5RIT6;J3QRI7;J3QQQ9;J3QQV1;J3QRC4;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 ;; 183.9 0.00051381 1248750000 1306280 1097540 1135190 1159510 1287330 1014520 1447000 1061300 1505680 FALSE TRUE 1224522.267 1178803.004 1162117.243 1189264.99 1186228.295 1307395.455 1230035.783 1193805.641 1254372.281 0.976203225 0.939755304 0.926453223 0.948095719 0.945674831 1.042270684 0.980598664 0.951715579 1 20.25853415 2.425975181 24.99931788 0.99277089 0.943195879 0.450523782 0.025258307 86.48714345 42272.91335 0.008398023 0.007026291 266.6706266 -2.425975181 -0.049575011 DDEYDYLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDEYDYLFK 9 0 H3BMH2;H3BSC1;P62491-2;Q15907-2;P62491;Q15907;B4DQU5 H3BMH2 RAB11A;RAB11B Ras-related protein Rab-11A;Ras-related protein Rab-11B 0 149.94 0.00020109 62223000 274050 153230 210010 184650 186760 149780 276480 179240 168640 FALSE TRUE 256897.6997 164575.3086 214991.5364 189388.4316 172092.623 193019.0545 235024.3907 201618.5086 140492.8945 1.828545853 1.171413751 1.530266261 1.348028541 1.224920474 1.37387058 1.672856065 1.435079754 1 17.10013764 4.757003007 24.30087021 1.3829067 1.82854642 0.375939713 0.190354093 3232.205544 4258858.471 0.043781296 1.432466604 57148.2594 -4.757003007 0.44563972 DDFLGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDFLGGR 7 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ; 139.27 0.0062933 282820000 212590 169910 183892 172275 182089 201540 246350 143233 108524 FALSE TRUE 199284.3714 182490.3132 188254.0051 176695.8682 167788.4645 259721.3263 209412.1045 161115.9553 90410.64331 2.20421362 2.01846051 2.082210658 1.954370212 1.855848585 2.872685303 2.316232877 1.782046333 1 16.464205 DDFNSGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DDFNSGFR 8 0 Q15056 Q15056 EIF4H Eukaryotic translation initiation factor 4H 0 ;;; 230.54 2.65E-06 1299280000 1781930 1641560 1894330 1818150 1530640 1665550 2069530 1318810 1363560 FALSE TRUE 1670402.182 1763102.81 1939264.402 1864806.807 1410429.709 2146367.247 1759223.189 1483466.332 1135973.027 1.47045937 1.552063974 1.70713948 1.641594266 1.241604928 1.889452651 1.548648733 1.305899257 1 20.11549715 1.016890282 2.745194475 1.004269428 1.594076175 0.572283821 0.164982358 0.164647 2.809320017 0.144065258 0.038505188 10.39657479 -1.016890282 0.589806747 DDFNSGFRDDFLGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDFNSGFRDDFLGGR 15 1 Q15056 Q15056 EIF4H Eukaryotic translation initiation factor 4H 0 228.49 5.38E-13 149720000 83587 113210 103210 103550 111690 84615 127210 85837 110160 FALSE TRUE 78355.43888 121592.1862 105658.1899 106207.2683 102918.3179 109041.9769 108136.0415 96553.9384 91773.58434 0.853790766 1.324914866 1.151291962 1.157274929 1.121437271 1.188162996 1.178291577 1.052088562 1 16.48579133 1.102634275 4.012634671 1.002217779 1.161867742 0.123487037 0.117588254 0.316729559 8.742622012 0.100657179 0.025956644 12.66584808 -1.102634275 0.159649963 DDFTEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDFTEER 7 0 P21912 P21912 SDHB "Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial" 0 ; 137.18 0.0067653 1161240000 2530600 2133590 2167950 1914340 2702800 1738210 2018280 2214650 3354600 FALSE TRUE 2372214.263 2291563.224 2219374.798 1963465.205 2490532.991 2240003.01 1715657.651 2491153.928 2794695.588 0.848827426 0.819968813 0.794138298 0.702568542 0.891164319 0.8015195 0.613897863 0.891386503 1 21.41425972 1.97476807 24.98565222 0.771073106 0.80864902 0 0.111356155 3613.804179 3578529.463 0.042145003 0.02733868 94.35568465 -1.97476807 0.037575914 DDFTEFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DDFTEFGK 8 0 O75822;O75822-3;H0YGJ7;H0YLP3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 ;;; 123.69 0.00311 563896000 1787180 1245180 1399020 1354900 1358550 1021940 1744830 1212670 1588130 FALSE TRUE 1675323.594 1337374.423 1432205.415 1389669.028 1251854.963 1316957.488 1483208.94 1364074.519 1323060.843 1.266248338 1.010818535 1.082493993 1.050344007 0.946180948 0.995386943 1.121043637 1.030999085 1 20.33544798 4.74263667 24.91165133 1.037445144 1.266248432 0.696838301 0.048802553 238.4474727 1457264.975 0.011866114 0.090496711 55288.73706 -4.74263667 0.228803288 DDGGFEYKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDGGFEYKR 9 1 Q9UBF2;Q9UBF2-2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 72.643 0.07403 179430000 388170 377500 358780 392610 432670 393450 528600 331810 521530 FALSE TRUE 363875.1326 405450.4928 367290.431 402685.0373 398689.8435 507032.6279 449341.3373 373237.2089 434483.2738 0.837489392 0.933178599 0.84534999 0.926813669 0.917618393 1.166978474 1.03419709 0.859037002 1 18.72894111 2.452919518 24.99952632 1.027138589 0.89042561 0.373545818 0.079292445 218.4205356 225619.2541 0.026246985 0.021960693 283.7393163 -2.452919518 -0.136712979 DDGLFSGDPNWFPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDGLFSGDPNWFPK 14 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ; 168.94 7.94E-06 116717000 320760 266200 263060 257720 273280 167314 355020 260790 440390 FALSE TRUE 300684.2042 285909.725 269299.9074 264333.5315 251817.6912 215614.8357 301788.0468 293350.2056 366886.064 0.819557442 0.779287504 0.73401509 0.720478529 0.686364831 0.587688814 0.822566122 0.799567589 1 18.48497258 0.842275819 1.556828944 0.99790164 0.731210849 0.617999218 0.066124872 0.410832155 1.876213381 0.062504902 0.01815076 6.954658651 -0.842275819 -0.266690792 DDGLFSGDPNWFPKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDGLFSGDPNWFPKK 15 1 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ; 214.18 4.02E-12 3281000000 10654100 9684500 9611900 9311500 10694400 6425200 13441100 8891300 20267400 FALSE TRUE 9987278.899 10401550.46 9839898.807 9550448.854 9854504.963 8280050.936 11425731.84 10001398.38 16884640.01 0.591500849 0.616036259 0.5827722 0.565629403 0.583637256 0.490389545 0.676693837 0.592337081 1 24.00920808 -0.086689998 0.87054553 1.008856009 0.583624258 0.892609871 0.045051524 2.187592358 1.468939317 0.1059971 0.013505614 0.819049221 0.086689998 -0.425231751 DDGSWEVIEGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DDGSWEVIEGYR 12 0 P00367;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ;;; 260.28 6.07E-21 883780000 1189350 1149870 1064290 903310 1413410 1000590 1064640 1113990 1770670 FALSE TRUE 1114910.707 1235007.571 1089535.461 926490.4639 1302406.48 1289444.09 905007.1156 1253074.104 1475133.738 0.755803137 0.837217358 0.738601141 0.628072181 0.882907391 0.874120127 0.613508519 0.849464744 1 20.49241433 0.99042548 24.86590238 1.000000013 0.76245708 0.418259291 0.090323104 378.2402845 982327.2425 0.084003671 0.021000918 9.781950925 -0.99042548 -0.237542933 DDGVFVQEVTQNS(ph)PAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DDGVFVQEVTQNSPAAR 17 0 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2;E9PQE3 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 DDGVFVQEVTQNS(1)PAAR;DDGVFVQEVTQNS(1)PAAR;DDGVFVQEVTQNS(1)PAAR;DDGVFVQEVTQNS(1)PAAR 439.19 2.51E-182 1594010000 746200 635898 733790 768010 797640 615284 831490 585593 919920 TRUE FALSE 699496.674 682980.5496 751195.8453 787718.4368 734996.5719 792906.5025 706815.7937 658705.5751 766379.4091 0.912728951 0.891178105 0.980187928 1.027843947 0.959050521 1.034613526 0.922279207 0.859503227 1 19.54769927 3.977005834 3.85750773 0.968797812 0.902859546 0.229443657 0.050987375 0.320224865 10.66399833 0.013045118 0.027771507 9484.31204 -3.977005834 -0.065938267 DDGYSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DDGYSTK 7 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;; 116.9 0.012449 1267040000 1960910 1383380 1625790 1585060 1645480 1268230 1832310 1434470 1899590 FALSE TRUE 1838180.143 1485806.895 1664354.507 1625735.323 1516250.638 1634347.413 1557572.126 1613566.737 1582536.157 1.161540692 0.93887706 1.051700777 1.027297427 0.958114373 1.032739382 0.984225301 1.019608133 1 20.59380703 4.75311396 24.93347611 1.001930234 1.161540808 0.682223187 0.034310735 1473.317286 2524112.813 0.007618874 0.172053721 56638.7891 -4.75311396 0.159610573 DDHDDFFSTT(ph)PLQHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDHDDFFSTTPLQHQR 16 0 Q6P0N0 Q6P0N0 MIS18BP1 Mis18-binding protein 1 1 DDHDDFFS(0.05)T(0.299)T(0.652)PLQHQR 104.92 0.0024707 51212000 44320 52021 54795 48745 55287 47270 56486 49240 50569 TRUE FALSE 41546.09031 55872.68897 56094.76328 49995.87923 50944.98204 60916.08164 48016.44869 55387.72239 42128.70721 0.986170549 1.326237919 1.331509248 1.186741358 1.209270006 1.445951838 1.139756044 1.314726372 1 15.36251602 -1.257344183 4.336162777 0.999845966 1.255796132 0.261886244 0.126237425 0.000169331 2.90E-05 0.110103065 0.025935986 0.055291175 1.257344183 0.255950166 DDIIENAPTTHTEEYSGEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDIIENAPTTHTEEYSGEEK 20 0 O14744-2;O14744;G3V580;O14744-3;O14744-5;G3V5L5;G3V2X6;H0YJX6 O14744-2 PRMT5 "Protein arginine N-methyltransferase 5;Protein arginine N-methyltransferase 5, N-terminally processed" 0 ; 280.39 1.04E-44 632160000 1024630 597400 809760 763750 763460 606560 1029710 674440 779300 FALSE TRUE 960500.2373 641632.1176 828967.8896 783349.118 703500.9312 781664.0253 875314.5449 758645.3186 649229.7955 1.479445712 0.988297398 1.27684819 1.206582205 1.083593107 1.203986679 1.348235326 1.168531272 1 19.30836969 1.998153279 24.99925354 1.227239011 1.183079113 0 0.154466772 400.6386114 5423559.223 0.05349703 0.038941481 99.57567963 -1.998153279 -0.044159898 DDILNGSHPVSFDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DDILNGSHPVSFDK 14 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;; 199.68 2.03E-08 1203560000 2708610 2088120 2453700 2393090 2708400 1901820 2969250 2187320 3389000 FALSE TRUE 2539082.935 2242726.577 2511902.923 2454500.741 2495693.189 2450844.561 2524038.528 2460411.717 2823354.006 0.899314407 0.794348343 0.889687555 0.869356353 0.883946251 0.868061375 0.893985849 0.871449953 1 21.4289786 -5 0.177651268 1.541933052 0.838621265 0.660743307 0.029099404 73.23288134 0.702496422 13.96071917 0.086988915 1.00E-05 5 -0.703311787 DDIPVFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DDIPVFLR 8 0 A0A1W2PQD2;Q9UBB4-2;Q9UBB4;B1AHE4 A0A1W2PQD2 ATXN10 Ataxin-10 0 ;;; 116.88 0.0050846 125613000 444827 438437 469224 425907 436935 414765 526340 410396 396428 FALSE TRUE 416986.0721 470899.3317 480354.2149 436836.4947 402619.8876 534500.9224 447420.2033 461634.844 330261.6058 1.262593244 1.425837347 1.454465813 1.322698391 1.219093835 1.618416773 1.354744831 1.39778538 1 18.33324973 -0.935697554 3.492220179 0.999931587 1.393447089 0.540317162 0.110266154 8790003.991 15985526.65 8296.71845 0.024186842 0.115958462 0.935697554 0.393515503 DDIVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DDIVDR 6 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;;; 144.9 0.026088 4738800000 6124500 5686380 5661990 5592590 6174000 4592680 6387300 5039800 6441200 FALSE TRUE 5741178.478 6107405.492 5796295.077 5736105.328 5689118.945 5918512.16 5429583.662 5669030.124 5366122.108 1.069893372 1.138141356 1.080164588 1.068947969 1.060191854 1.102940269 1.011826334 1.056448215 1 22.35544845 1.88279959 0.371358573 0.997175731 1.115072035 0.537127635 0.027029862 0.804653592 0.307533343 0.031497943 0.031904052 76.34833843 -1.88279959 0.117896305 DDIVPWHTSMQVADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDIVPWHTSMQVADR 15 0 Q9NUJ1-2;Q9NUJ1 Q9NUJ1-2 ABHD10 "Mycophenolic acid acyl-glucuronide esterase, mitochondrial" 0 58.21 0.081041 390190000 55491 75185 85395 69010 87878 68110 72152 75435 64387 FALSE TRUE 52017.91736 80751.77563 87420.60973 70780.91343 80976.41636 87772.25133 61333.47743 84853.2258 53640.39374 0.969752713 1.505428465 1.629753319 1.319545001 1.509616368 1.636308856 1.143419598 1.581890435 1 15.71103221 -1.417641803 0.564533883 0.796276533 1.43484885 0.24984598 0.21834462 61.63145655 8.528505189 18.68417341 0.086474633 0.038225942 1.417641803 0.638572317 DDKEEEEDGTGS(ph)PQLNNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDKEEEEDGTGSPQLNNR 18 1 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 DDKEEEEDGT(0.002)GS(0.998)PQLNNR;DDKEEEEDGT(0.014)GS(0.986)PQLNNR 220.49 4.09E-19 1232330000 2267610 973390 1299290 1344670 1483650 1172370 1685190 1276180 1928930 TRUE FALSE 2125684.338 1045460.808 1330109.772 1379176.509 1367130.114 1510814.187 1432511.404 1435513.882 1606979.122 1.322782797 0.650575228 0.827708185 0.85824171 0.850745411 0.940157944 0.891431248 0.893299647 1 20.61591975 2.247644803 24.08050807 0.919523112 0.855602348 0 0.173038687 531.0854351 1407810.162 0.056788707 0.046837857 176.8661828 -2.247644803 -0.063920764 DDKGNLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDKGNLNR 8 1 E9PM90;Q9UK41;Q9UK41-2;E9PQR7 E9PM90 VPS28 Vacuolar protein sorting-associated protein 28 homolog 0 ; 76.064 0.033534 236830000 499710 710560 534800 584530 630880 436900 621040 570120 544510 FALSE TRUE 468434.0431 763170.6017 547485.7086 599530.0294 581333.2296 563025.9375 527920.8175 641300.737 453627.7633 1.032639712 1.682371899 1.206905205 1.32163434 1.281520393 1.241162872 1.163775369 1.413715801 1 18.79114941 -4.859278604 0.122777801 3.10E-10 1.459405293 0.171518927 0.176395119 196.0738782 1.603043653 48.65077522 1.472046478 1.38E-05 4.859278604 1.459405292 DDKHGSYEDAVHSGALND ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDKHGSYEDAVHSGALND 18 1 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 263.52 4.01E-31 2775200000 2126560 3591900 3239000 3519100 4416000 2268810 4063900 3049800 6127600 FALSE TRUE 1993462.406 3857848.013 3315830.61 3609406.064 4069185.173 2923778.616 3454555.922 3430574.243 5104863.974 0.390502551 0.755720041 0.649543382 0.707052349 0.797119217 0.572743687 0.676718506 0.672020696 1 22.28344109 -5 0.367657737 5.345485753 0.655662385 0.496041804 0.110422905 436.6779687 3.396120619 1506.337544 0.070519042 1.00E-05 5 -4.689823368 DDKLTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DDKLTPK 7 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;; 103.56 0.0076133 1798340000 6550570 3449990 4702330 4086450 4856590 3444570 5605950 3876900 5469170 FALSE TRUE 6140581.517 3705430.849 4813871.488 4191315.225 4475173.012 4438961.441 4765389.841 4360939.499 4556330.195 1.347703361 0.813248973 1.056523843 0.919888385 0.982188037 0.974240507 1.04588334 0.957116651 1 22.11944087 4.754214808 24.81355265 0.971220127 1.347703669 0.754252629 0.067985109 1362.543315 2159735.624 0.015725136 0.39542254 56782.53902 -4.754214808 0.376483542 DDLITDLLNEAKQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDLITDLLNEAKQR 14 1 P36543;C9J8H1;P36543-2 P36543 ATP6V1E1 V-type proton ATPase subunit E 1 0 60.157 0.086801 78169000 36719 194010 128000 159340 182930 160060 104620 138700 89915 FALSE TRUE 34420.82334 208374.7023 131036.2204 163428.9342 168563.4157 206266.7236 88933.20224 156017.0003 74907.60563 0.459510393 2.781756279 1.749304618 2.181740196 2.250284391 2.753615229 1.187238619 2.082792515 1 16.19282459 -1.25887901 8.62478119 0.999999601 1.98506815 0.146091487 0.696290892 4.79E-06 4.12E-07 0.604102105 0.142388174 0.055096117 1.25887901 0.985068549 DDLLGFALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDLLGFALR 9 0 Q9Y617;Q9Y617-2 Q9Y617 PSAT1 Phosphoserine aminotransferase 0 ; 150.88 0.00019585 43447000 69613 91769 62653 56846 82594 42514 77503 77186 73746 FALSE TRUE 65256.04659 98563.67225 64139.15875 58304.7646 76107.40041 54787.10164 65882.14465 86822.84201 61437.31618 1.06215653 1.604296515 1.043977223 0.949012233 1.238781333 0.891756103 1.072347374 1.413193925 1 15.90682757 3.771774992 6.059152488 1.078175346 1.36131513 0.209912325 0.195976105 0.229967437 21.06627907 0.046030987 0.082712748 5912.552251 -3.771774992 0.283139783 DDNGKPYVLPSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DDNGKPYVLPSVR 13 1 P00505;P00505-2 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 ;;; 145.69 3.82E-05 2270740000 2864460 2646760 2210030 2566280 3833040 2104250 2611170 2972130 4020700 FALSE TRUE 2685178.562 2842728.864 2262452.955 2632135.09 3532008.5 2711712.815 2219649.299 3343206.973 3349619.195 0.801636964 0.848672252 0.67543587 0.785801291 1.054450758 0.809558537 0.662657207 0.998085686 1 21.67556566 1.209201825 24.41108901 0.99904364 0.797985601 0.362173862 0.106444191 203.9996849 169614.2765 0.103632904 0.025927222 16.18832165 -1.209201825 -0.20105804 DDNGVPFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDNGVPFVR 9 0 P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5;J3QKK1 P09972 ALDOC Fructose-bisphosphate aldolase C;Fructose-bisphosphate aldolase 0 138.26 0.00032946 122920000 290610 289660 291040 291050 281960 221060 310940 233910 223950 FALSE TRUE 272421.2389 311106.7278 297943.6062 298518.8357 259815.999 284876.4334 264317.4336 263114.1784 186571.2982 1.460145486 1.667495112 1.596942344 1.600025505 1.392582897 1.526903849 1.416710052 1.410260747 1 17.50936754 0.003412006 0.32910959 0.866462026 1.62072922 0.841787767 0.073325856 1.729262737 0.272999919 0.376338963 0.070517189 1.007887377 -0.003412006 0.754267194 DDNMFQIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DDNMFQIGK 9 0 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 ;;; 112.11 0.0046906 412037000 824080 663630 724990 719810 734500 554100 836860 612060 846440 FALSE TRUE 772502.3038 712765.8557 742187.1052 738281.5432 676815.3328 714059.6749 711380.612 688477.0383 705163.6958 1.095493583 1.010780702 1.052503283 1.046964765 0.95979889 1.012615481 1.008816274 0.976336477 1 19.42759868 2.767258174 24.56398379 0.995203626 1.04483773 0.566933716 0.025625788 476.6230969 407970.0824 0.007345856 0.007790123 585.1378264 -2.767258174 0.049634104 DDPDGKQEAKPQQAAGMLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_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 137.9 1.32E-06 2649200000 2649600 684100 1263780 1105660 1292370 778640 1758850 907050 1607680 TRUE FALSE 2483766.266 734751.4758 1293757.458 1134033.107 1190872.473 1003420.728 1495126.771 1020297.189 1339347.822 1.85445948 0.548588995 0.965960774 0.846705455 0.889143547 0.749186068 1.116309555 0.761786574 1 20.35309924 4.74987713 24.99817521 0.861132508 1.854460061 0.802499401 0.155086496 741.2128833 1637308.515 0.036075668 0.566479057 56218.22504 -4.74987713 0.993327553 DDPSKPVHLTAFLGYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDPSKPVHLTAFLGYK 16 1 P39023;H7C422;H7C3M2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ; 174.95 2.22E-09 2953800000 4864600 5744700 6142700 6365800 6562900 4917100 8299400 6445200 6097400 FALSE TRUE 4560133.37 6170043.565 6288407.745 6529157.205 6047476.307 6336586.948 7054982.018 7249897.408 5079704.549 0.89771626 1.214646148 1.237947539 1.285341921 1.190517332 1.247432185 1.388856763 1.427228166 1 22.27631316 5.292520512 1.300537872 1.273702048 4.25E-13 0.466371799 0.116539075 4.14422444 2.239624324 0.029695489 9.981035952 196119.3804 -5.292520512 -1.273702048 DDREDLVYQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DDREDLVYQAK 11 1 P62258;B4DJF2;I3L3T1;I3L0W5 P62258 YWHAE 14-3-3 protein epsilon 0 ;;; 198.57 4.85E-08 3471360000 4412510 2733540 3946730 4042710 3246460 3019120 4728800 2527470 4659050 FALSE TRUE 4136338.876 2935934.146 4040348.299 4146452.783 2991496.127 3890690.933 4019760.34 2843030.193 3881424.456 1.065675481 0.75640636 1.040944721 1.068281202 0.770721203 1.002387391 1.035640494 0.73247083 1 21.88815478 3.942655996 24.45586537 0.957951533 0.89016582 0.006454388 0.134755201 802.8489557 569685.4719 0.03185269 0.057427209 8763.064243 -3.942655996 -0.067785713 DDREQFYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDREQFYK 8 1 P60604-2;P60604 P60604-2 UBE2G2 Ubiquitin-conjugating enzyme E2 G2 0 120.33 0.0013881 494010000 382240 356090 363330 309800 418900 317610 417830 344930 529430 FALSE TRUE 358316.2807 382455.2741 371948.3592 317749.9925 386001.2838 409298.851 355180.2704 387995.2698 441064.7128 0.812389362 0.867118278 0.843296569 0.72041581 0.875157936 0.927979136 0.805279271 0.879678783 1 18.75063082 -0.788142623 0.413449566 1.052924467 0.831725686 0.482804374 0.05355196 10.96107364 1.47457647 0.783277375 0.032614859 0.162876106 0.788142623 -0.221198781 DDRGPPQRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DDRGPPQRPK 10 2 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;; 118.28 0.00047591 2083670000 918430 934050 900120 897710 1064310 688620 1040420 856720 1276000 FALSE TRUE 860947.1057 1003208.034 921471.2715 920746.7584 980723.3858 887413.4152 884418.6798 963683.3779 1063027.357 0.809901175 0.943727391 0.866836837 0.866155281 0.922575868 0.834798286 0.83198111 0.906546169 1 20.01974729 0.980085445 22.43942805 1.000000002 0.873148462 0.513493383 0.040385505 318.6910303 359097.9271 0.03854632 0.00963658 9.551804937 -0.980085445 -0.12685154 DDRNEEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DDRNEEKR 8 2 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 140.75 0.00036249 2140464000 993243 603117 705610 641166 696020 433272 710548 649640 623756 FALSE TRUE 931077.6936 647772.4102 722347.4024 657619.4051 641357.3968 558350.5928 604007.9238 730748.984 519647.094 1.791750025 1.246562172 1.390073015 1.265511561 1.23421723 1.074480353 1.162342541 1.406240875 1 18.98717266 7.434736709 1.048666943 1.216989361 200 0.648015619 0.129311373 376.9590695 1.538922006 0.036018047 178809.0082 27210511.73 -7.434736709 198.7830106 DDS(ph)HS(ph)AEDS(ph)EDEKEDHK ddPTM_SK-BR-3_Pertuzumab_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 169.08 9.09E-09 286600000 681290 149480 243650 238800 224210 168760 327180 154810 182800 TRUE FALSE 638649.275 160547.6547 249429.4931 244928.0123 206601.451 217478.2724 278122.3964 174138.3693 152289.4991 4.19365274 1.054226691 1.637864033 1.608305325 1.356636224 1.42805823 1.826274287 1.143469316 1 17.21645694 4.74341687 24.99992445 1.437037111 4.193653865 0.914897776 0.269039965 133.2470767 685931.4011 0.06054918 0.500721238 55388.15138 -4.74341687 2.756616754 DDS(ph)HS(ph)AEDS(ph)EDEKEDHKNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDSHSAEDSEDEKEDHKNVR 20 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 DDS(1)HS(1)AEDS(1)EDEKEDHKNVR;DDS(1)HS(1)AEDS(1)EDEKEDHKNVR 101.45 0.00027479 546320000 1167510 340330 491060 512260 598400 342220 729400 328200 664070 TRUE FALSE 1094437.633 365528.3873 502708.1751 525405.4589 551404.0778 441013.3585 620033.2414 369176.4925 553232.4269 1.978260094 0.660713959 0.908674457 0.949701126 0.996695152 0.797157464 1.120746383 0.667308123 1 19.07752619 4.746040921 24.97384572 0.89101293 1.978260618 0.846663698 0.145858001 327.9160557 1094758.458 0.033422253 0.352465742 55723.82515 -4.746040921 1.087247688 DDS(ph)HSAEDS(ph)EDEKEDHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDSHSAEDSEDEKEDHK 17 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 DDS(0.872)HS(0.128)AEDS(1)EDEKEDHK;DDS(0.974)HS(0.026)AEDS(1)EDEKEDHK 159.78 4.21E-09 302037000 366950 115725 179210 168236 156781 148946 215928 138802 132879 TRUE FALSE 343983.2545 124293.3994 183460.9458 172553.2206 144468.0527 191944.2923 183551.601 156131.7352 110700.6365 3.107328607 1.122788481 1.657270922 1.558737385 1.305033623 1.733904144 1.658089843 1.410396003 1 16.75630399 4.746207075 24.94337687 1.475467724 3.107329414 0.82575098 0.241260809 357.4469173 1165993.041 0.053835814 0.576981764 55745.14828 -4.746207075 1.63186169 DDS(ph)PVSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDSPVSHR 8 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8YFE7 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 DDS(1)PVSHR;DDS(1)PVSHR 96.229 0.0058543 161455000 242305 159332 193826 167014 143577 156144 212550 141926 123948 TRUE FALSE 227139.5626 171129.1071 198423.6443 171299.862 132301.0416 201220.238 180680.1007 159645.7735 103260.2781 2.199679943 1.657259793 1.921587352 1.658913429 1.281238479 1.948670309 1.749754156 1.546052136 1 16.65592586 -2.361347643 0.200302667 3.74E-12 1.918348907 0.555566618 0.226953663 32.82221976 0.844759387 15.70686977 0.583192561 0.004351634 2.361347643 1.918348907 DDSFFGETSHNYHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDSFFGETSHNYHK 14 0 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 198.33 1.28E-08 359620000 824440 600600 777300 680230 650150 649830 912960 676510 532490 FALSE TRUE 772839.7721 645069.0489 795737.9231 697685.8534 599089.8416 837425.3719 776070.1235 760973.7627 443613.979 1.742144767 1.454122457 1.793762056 1.572731894 1.350475571 1.887734408 1.749426664 1.715396265 1 18.7589453 4.001848672 24.32812453 1.634095067 1.583358359 0 0.266236064 2701.50502 2657855.851 0.059544281 0.128525548 10042.65798 -4.001848672 -0.050736708 DDSHS(ph)AEDS(ph)EDEKEDHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DDSHSAEDSEDEKEDHK 17 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 DDS(0.002)HS(0.998)AEDS(1)EDEKEDHK;DDS(0.003)HS(0.997)AEDS(1)EDEKEDHK;DDS(0.016)HS(0.984)AEDS(1)EDEKEDHK;DDS(0.01)HS(0.99)AEDS(1)EDEKEDHK;DDS(0.311)HS(0.689)AEDS(1)EDEKEDHK 193.77 1.48E-10 10948940000 10221100 2538850 4239590 4029410 4080910 3102810 5248850 3087520 2885990 TRUE FALSE 9581379.596 2726829.096 4340155.077 4132811.482 3760411.79 3998540.877 4461833.67 3473003.668 2404299.625 3.985102147 1.134146954 1.805163979 1.718925312 1.564036259 1.663079275 1.855772727 1.444497031 1 21.19718527 4.745044546 24.9986576 1.578166541 3.985103226 0.883806707 0.279903517 227.5372609 877242.0667 0.062131146 0.59293248 55596.12804 -4.745044546 2.406936685 DDSHS(ph)AEDS(ph)EDEKEDHKNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 DDSHSAEDSEDEKEDHKNVR 20 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 DDS(0.003)HS(0.997)AEDS(1)EDEKEDHKNVR;DDS(0.002)HS(0.998)AEDS(1)EDEKEDHKNVR;DDSHS(1)AEDS(1)EDEKEDHKNVR;DDS(0.104)HS(0.896)AEDS(1)EDEKEDHKNVR;DDSHS(1)AEDS(1)EDEKEDHKNVR;DDS(0.023)HS(0.977)AEDS(1)EDEKEDHKNVR;DDS(0.1)HS(0.9)AEDS(1)EDEKEDHKNVR;DDS(0.003)HS(0.997)AEDS(1)EDEKEDHKNVR;DDS(0.035)HS(0.965)AEDS(1)EDEKEDHKNVR;DDS(0.084)HS(0.916)AEDS(1)EDEKEDHKNVR 214.44 6.78E-25 16105086000 12170550 4221637 5501527 6593574 6997170 4088264 7859727 4324462 7427848 TRUE FALSE 11408817 4534211.396 5632025.818 6762776.272 6447640.493 5268479.449 6681233.902 4864380.6 6188092.183 1.843672761 0.732731715 0.910139289 1.092869348 1.041943187 0.851389943 1.079692045 0.786087288 1 22.56106326 4.746439299 24.96546335 0.935046095 1.84367321 0.846819946 0.121204709 367.1249623 1163294.61 0.029264998 0.319342257 55774.96409 -4.746439299 0.908627115 DDSHSAEDS(ph)EDEKEDHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDSHSAEDSEDEKEDHK 17 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 DDSHSAEDS(1)EDEKEDHK;DDSHSAEDS(1)EDEKEDHK 317.72 1.39E-58 949520000 1550500 409950 675160 656570 656290 514500 902850 515130 607200 TRUE FALSE 1453456.973 440303.1246 691175.114 673418.6978 604747.6307 663027.7978 767476.0241 579445.1144 505854.3973 2.873271401 0.870414742 1.366351894 1.331250062 1.195497428 1.310708776 1.51718761 1.145478061 1 18.94836266 4.746705345 24.99665747 1.24518619 2.873272203 0.88585415 0.186591328 337.986107 1037276.135 0.045089146 0.506758247 55809.14194 -4.746705345 1.628086013 DDSHSAEDS(ph)EDEKEDHKNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 347.39 2.50E-95 3135980000 3364470 1136266 1659990 1876400 2003190 1315300 2345650 1435170 2884300 TRUE FALSE 3153893.828 1220396.317 1699365.747 1924551.601 1845867.538 1695005.758 1993941.558 1614354.134 2402891.697 1.312540983 0.507886526 0.707216954 0.800931479 0.768185907 0.705402478 0.829809168 0.671838076 1 21.19634019 -1.83263677 3.131450328 1.072641645 0.757180255 0.076580706 0.208258309 46806156.2 99496095.83 26844964.73 0.046616358 0.014701554 1.83263677 -0.31546139 DDSPLYIFDSSYGEHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDSPLYIFDSSYGEHPK 17 0 B2WTI3;B2WTI4;K7EJU9;Q6NYC1-2;Q6NYC1;Q6NYC1-3 B2WTI3 JMJD6 Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 0 124.5 0.00041766 0 70471 55554 74017 62225 64288 50181 85515 59668 61931 FALSE TRUE 66060.3459 59667.27596 75772.71819 63821.79885 59239.07981 64667.44008 72692.81963 67117.68115 51594.31601 1.280380302 1.156469948 1.468625307 1.236992828 1.148170659 1.253383029 1.408930775 1.300873552 1 15.65492452 DDSQNAIDHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DDSQNAIDHK 10 0 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 ;; 165.63 5.79E-06 1320450000 2439530 1557770 1911290 1854550 1698480 1482370 2482830 1688690 1786500 FALSE TRUE 2286844.172 1673108.912 1956626.701 1902140.893 1565088.232 1910306.155 2110552.691 1899526.664 1488321.609 1.536525546 1.12415818 1.314653157 1.278044262 1.051579325 1.283530484 1.418075689 1.276287768 1 20.50525488 4.753832529 24.13400558 1.242099149 1.536525892 0.364211597 0.128767311 2115.96177 3343734.726 0.029784157 0.690026035 56732.57938 -4.753832529 0.294426743 DDTHKVDVINFAQNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDTHKVDVINFAQNK 15 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 145.29 2.46E-06 229170000 582310 382280 455190 501030 545590 318670 605380 424520 597410 FALSE TRUE 545864.2566 410584.409 465987.3218 513887.278 502741.5622 410664.8558 514608.8891 477522.2565 497698.4116 1.096777172 0.824966284 0.936284527 1.032527463 1.010132945 0.825127921 1.033977359 0.959461082 1 18.92491226 1.465586915 0.446978158 1.002215013 0.936740434 0 0.089116336 3.638909209 2.005034423 0.098233889 0.065831642 29.21372354 -1.465586915 -0.065474579 DDTIYEDEDVKEAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDTIYEDEDVKEAIR 15 1 B7Z2R2;P14927;P14927-2;E5RHG9 B7Z2R2 UQCRB Cytochrome b-c1 complex subunit 7 0 ; 161.14 1.52E-06 271530000 250035 222963 135029 146143 315754 129035 154680 263474 404470 FALSE TRUE 234385.7557 239471.4125 138231.9516 149893.2768 290955.9545 166285.3098 131487.17 296369.3089 336961.344 0.695586481 0.710679183 0.410230889 0.444838197 0.86346983 0.493484825 0.390214404 0.879535039 1 18.36222357 1.080311955 5.741539212 0.996868869 0.564271403 0.515840488 0.149940918 0.146131589 7.249082327 0.143838732 0.036241229 12.03128336 -1.080311955 -0.432597466 DDVFLDGTGWEGGDEWIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDVFLDGTGWEGGDEWIR 18 0 H7C0I1;B8ZZW5;Q8NBF6-2;Q8NBF6 H7C0I1 AVL9 Late secretory pathway protein AVL9 homolog 0 72.265 0.031036 0 13861 11884 12527 13987 14707 11415 15464 11190 10637 FALSE TRUE 12993.46475 12763.90373 12824.14636 14345.9301 13551.97155 14710.32519 13145.31676 12587.09613 8861.615982 1.466263577 1.44035848 1.447156634 1.6188842 1.529288966 1.660004814 1.483399505 1.420406409 1 13.11335409 0.731773646 2.245111691 1.00021711 1.514487758 0.840150566 0.070989561 0.509988443 3.637255029 0.072655563 0.019717451 5.392295027 -0.731773646 0.514270648 DDVVLPALHFHQGDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDVVLPALHFHQGDSK 16 0 Q8TC07-2;Q8TC07-3;Q8TC07;C9JA93;F8VV61 Q8TC07-2 TBC1D15 TBC1 domain family member 15 0 131.82 2.45E-05 49172000 137130 106720 124360 105920 124260 94463 154180 119560 102120 FALSE TRUE 128547.2781 114621.6598 127309.8779 108638.0865 114501.1208 121732.9346 131062.1403 134487.3292 85075.51228 1.510978596 1.347293208 1.496433868 1.27696071 1.345876361 1.430881006 1.54053895 1.580799522 1 16.37645631 -1.856395333 2.822366679 0.828043683 1.437249274 0.677296879 0.095677899 16726903.49 16631407.21 19624168.45 0.02400447 0.013918892 1.856395333 0.609205591 DDWEEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DDWEEKR 7 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;; 157.58 0.0023513 4678510000 5341430 3483980 4074730 4000120 4181220 3041190 5020650 3280930 5659530 FALSE TRUE 5007119.431 3741937.504 4171384.52 4102769.851 3852843.847 3919132.183 4267850.142 3690561.333 4714917.881 1.061973837 0.793637895 0.884720503 0.870167828 0.817160329 0.831219606 0.905180164 0.782741381 1 22.16880121 -1.072125838 4.074253076 1.000021231 0.863127439 0.21261283 0.079054095 59251267907 37455925.66 12613403.29 0.016612656 0.084698196 1.072125838 -0.136893792 DDWLEWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDWLEWLR 8 0 P42345 P42345 MTOR Serine/threonine-protein kinase mTOR 0 ; 78.496 0.059693 5103800 22155 21183.7 20168.5 22403 26056 15097 23573 20392.9 22755 FALSE TRUE 20768.3581 22752.16319 20646.90634 22977.89891 24009.66686 19455.25882 20038.44749 22938.99846 18957.0435 1.09554837 1.200195758 1.089141687 1.212103507 1.266530135 1.026281278 1.057044971 1.210051476 1 14.21044636 -1.174793453 4.214487608 0.999956989 1.138871441 0.252644233 0.077609421 3.35E-05 6.56E-06 0.074727702 0.017607632 0.066866185 1.174793453 0.138914452 DDYPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 129.67 0.037443 2463920000 1460566 1343918 1425849 1437189 1414723 1232044 1585144 1283193 1610835 FALSE TRUE 1369151.781 1443423.087 1459670.812 1474069.703 1303616.362 1587715.102 1347466.373 1443402.471 1341976.232 1.020250395 1.07559512 1.087702432 1.098432049 0.971415388 1.183117155 1.004091087 1.075579758 1 20.35592769 0.460583503 0.908171045 1.000011747 1.069386409 0.102504521 0.058209714 3.890891081 4.577984089 0.050822863 0.016152228 2.887908992 -0.460583503 0.069374661 DDYSRDDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDYSRDDYR 9 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 73.499 0.034993 0 43860 64730 54111 56317 67592 51346 67306 58656 79404 FALSE TRUE 41114.88089 69522.67655 55394.53847 57762.18956 62283.59697 66168.75667 57214.09014 65979.33072 66150.95943 0.621531135 1.050970041 0.837395844 0.87318748 0.941537319 1.00026904 0.864901895 0.997405499 1 16.01347446 4.752138685 24.85849533 0.934956236 0.621530911 0.676936384 0.070031666 1286.286194 2354866.541 0.015788778 0.312445048 56511.74074 -4.752138685 -0.313425324 DDYVFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DDYVFR 6 0 E7ESC6;Q9UIA9;H0YBE1 E7ESC6 XPO7 Exportin-7 0 97.596 0.095131 54117000 167670 181470 173320 177370 169320 134280 187940 172810 129030 FALSE TRUE 157175.834 194906.2276 177431.2322 181921.6145 156022.2902 173044.4561 159760.1417 194385.7089 107494.0594 1.462181583 1.813181386 1.650614305 1.692387611 1.45145035 1.609804831 1.486222984 1.808339083 1 16.71389741 -2.515196 0.379895293 2.06E-16 1.650172296 0.668165206 0.134946333 39.74298176 1.709797409 33.12793548 0.086634523 0.003053543 2.515196 1.650172296 DDYVHEFCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DDYVHEFCR 9 0 Q13564-2;Q13564;Q13564-4;Q13564-3 Q13564-2 NAE1 NEDD8-activating enzyme E1 regulatory subunit 0 ; 121.83 0.00060287 399850000 386870 422940 384720 377830 445610 305029 444560 405370 400020 FALSE TRUE 362656.4973 454254.9177 393845.7401 387525.7575 410613.5881 393085.9206 377902.3551 455981.3368 333254.0778 1.088228236 1.36308885 1.181818217 1.16285376 1.232133725 1.179538217 1.133976687 1.368269339 1 18.346263 -1.498688482 3.481879823 0.996125117 1.215657745 0.355876664 0.090336259 2715.739374 19563094.62 87417.90938 0.01973366 0.031718418 1.498688482 0.219532628 DEAAYGELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DEAAYGELR 9 0 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;; 123.98 0.0012619 3061430000 2650840 2901920 2752210 2801120 2942250 2331480 3244200 2590100 2441810 FALSE TRUE 2484928.656 3116781.176 2817493.721 2873001.481 2711177.553 3004540.428 2757762.328 2913479.687 2034256.136 1.221541679 1.532147855 1.385024074 1.412310589 1.332761153 1.476972528 1.355661305 1.432208872 1 20.95606991 -1.335507437 2.987740819 0.995822321 1.404085662 0.682347277 0.084122095 7024956.753 9094325.249 260126.5235 0.01792445 0.046184108 1.335507437 0.408263341 DEADVLEVDQGFDDHNLPCDVIWLDIEHADGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DEADVLEVDQGFDDHNLPCDVIWLDIEHADGK 32 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 62.848 0.0075511 13559000 9804.7 7129 8970.6 7592.1 6688.6 8841.2 11684 4920.2 4980.9 FALSE TRUE 9191.041329 7656.838578 9183.386868 7786.926139 6163.304337 11393.51092 9932.092669 5534.497801 4149.555612 2.214945933 1.845218933 2.213101288 1.87656869 1.485292622 2.745718332 2.393531645 1.333756748 1 12.01874113 3.202808743 24.98587417 1.958741131 2.055833513 0.007599856 0.521054518 1522.444788 1063986.415 0.146525556 0.175136927 1595.176501 -3.202808743 0.097092382 DEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR 33 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 264.32 4.51E-60 295753000 143853.6 108777 116252.1 112879.1 110840.2 104404.7 174075 106362.9 104979 FALSE TRUE 134850.06 116830.9623 119009.6547 115775.7688 102135.2578 134544.642 147974.0698 119642.5422 87457.32671 1.541895517 1.33586249 1.360773982 1.323797253 1.167829634 1.538403323 1.691957385 1.368010511 1 16.41629163 2.188702575 24.99968533 1.485300708 1.34564307 0 0.201586874 248.570448 124635.8083 0.069256651 0.051149495 154.419654 -2.188702575 -0.139657638 DEALQNIS(ph)ADDLPDSASQAAHPQDSAFSYR ddPTM_SK-BR-3_Pertuzumab_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 312.05 1.84E-92 937220000 172582 199617 210878 220218 198576 184567 257352 205297 190342 TRUE FALSE 161780.4007 214396.8504 215880.1257 225869.1667 182980.642 237848.4967 218764.4567 230928.7824 158572.6905 1.020228642 1.35204145 1.361395364 1.424388815 1.153922793 1.499933538 1.379584694 1.456296047 1 17.27478481 4.738627345 24.61108032 1.351415617 1.02022852 0.284478746 0.149730276 4.671464674 1718604.193 0.030529209 0.17542338 54780.67065 -4.738627345 -0.331187097 DEALQNISADDLPDSASQAAHPQDSAFSYR ddPTM_SK-BR-3_Pertuzumab_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 0 244.04 9.33E-46 132220000 79588 88334 99075 108410 99268 96302 121260 97916 117720 FALSE TRUE 74606.72915 94874.34127 101425.1058 111191.9841 91471.89171 124102.8241 103078.1887 110141.0281 98071.7715 0.76073602 0.967397038 1.034192655 1.133781744 0.932703573 1.265428596 1.051048504 1.123065551 1 16.58155032 5.534899412 0.720905858 1.092453136 2.06E-18 0.563083302 0.088711467 5.325781432 0.906050221 0.028900564 6.163456891 342688.4064 -5.534899412 -1.092453136 DEATAAVIDLNDRPIGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DEATAAVIDLNDRPIGSR 18 1 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 ; 242.45 4.43E-24 713330000 416620 394290 426490 383280 444390 361150 447190 353560 457400 FALSE TRUE 390544.4979 423483.6419 436606.5442 393115.6137 409489.402 465408.1422 380138.011 397702.7443 381056.9851 1.024897885 1.111339402 1.145777564 1.031645211 1.074614606 1.221361005 0.997588355 1.043683123 1 18.53964724 1.612921348 25 1.015472647 1.104485228 0.344148493 0.057057881 0.486331299 2393.728586 0.025777115 0.013738895 41.01298207 -1.612921348 0.089012582 DECSFHIFYQLLGGAGEQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DECSFHIFYQLLGGAGEQLK 20 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43;A0A2R8Y4C3 Q7Z406 MYH14 Myosin-14 0 130.85 1.54E-05 65791000 119430 132350 124400 121510 140560 96165 171100 132130 120960 FALSE TRUE 111955.0895 142149.3317 127350.8267 124628.1523 129520.9846 123926.2744 145445.1434 148626.7214 100770.9946 1.110985259 1.410617533 1.26376471 1.236746277 1.285300251 1.229781198 1.443323488 1.474895847 1 16.62072091 1.760985709 25 1.353449629 1.275260616 0 0.147890993 35.14441059 39210.59152 0.061235729 0.033960722 57.67474845 -1.760985709 -0.078189013 DEDDADYKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DEDDADYKPK 10 1 P11387 P11387 TOP1 DNA topoisomerase 1 0 67.022 0.058568 485280000 404100 176350 221580 208710 233940 154200 279100 166960 347070 FALSE TRUE 378808.1023 189407.1375 226835.9822 214065.8519 215567.2961 198715.0368 237251.546 187805.3235 289141.7748 1.310111977 0.655066663 0.784514733 0.740349097 0.745541858 0.687258134 0.820537074 0.649526772 1 18.14141754 4.744466676 24.9854128 0.749417096 1.310112223 0.744391672 0.101062562 282.5592922 1195324.819 0.020372347 0.185830221 55522.20126 -4.744466676 0.560695127 DEDGES(ph)GGQRS(ph)EAEEGEVR ddPTM_SK-BR-3_Pertuzumab_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 150.65 8.78E-07 686630000 946460 564190 728510 562490 611360 667210 911520 652350 684820 TRUE FALSE 887222.7581 605963.2146 745790.6012 576924.4457 563346.2517 859822.6958 774846.0381 733797.3335 570519.1179 1.55511486 1.062126046 1.30721404 1.011227192 0.987427474 1.507088314 1.358142109 1.286192365 1 19.12191571 2.236034571 24.99983382 1.328797657 1.176753482 0.042112268 0.20524563 143.0390986 1415609.396 0.068899146 0.053261806 172.2005646 -2.236034571 -0.152044174 DEDGESGGQRS(ph)EAEEGEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DEDGESGGQRSEAEEGEVR 19 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 DEDGES(0.002)GGQRS(0.998)EAEEGEVR;DEDGESGGQRS(1)EAEEGEVR 253.18 4.36E-31 692440000 410790 269620 337130 262034 295670 309090 361210 319210 461360 TRUE FALSE 385079.3872 289582.9453 345126.8828 268758.2361 272449.2709 398319.2653 307049.9138 359064.0712 384356.0355 1.001881983 0.753423697 0.89793538 0.699242919 0.708846085 1.036328894 0.798868459 0.934196521 1 18.5520838 1.044374849 3.993552792 0.999793177 0.837687887 0.184763403 0.112868273 0.291987301 10.06014318 0.098856415 0.025364455 11.07579347 -1.044374849 -0.162105289 DEDGSTLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DEDGSTLFR 9 0 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 106.94 0.0066403 255850000 328710 264260 288500 291030 328440 231210 307490 282930 348170 FALSE TRUE 308136.6279 283826.0854 295343.3562 298498.3225 302645.6473 297956.5736 261384.7291 318254.4333 290058.1777 1.06232698 0.978514337 1.018221098 1.02909811 1.043396361 1.027230385 0.901145871 1.097208966 1 18.14598277 DEDHIAHIIELLGSIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DEDHIAHIIELLGSIPR 17 0 P78362;P78362-2;H7C521;F8WBW4 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 0 139.65 4.00E-07 37483000 86771 74272 82225 72814 77034 65761 87340 73454 54183 FALSE TRUE 81340.158 79771.17616 84175.41583 74682.53051 70984.06038 84745.13316 74244.17782 82624.89359 45139.50726 1.801972661 1.767214154 1.864783666 1.654482626 1.57254841 1.877404923 1.644771561 1.830434105 1 15.46210305 -1.959896932 2.555167027 0.405643982 1.7525527 0.847264704 0.100301066 3889713.507 1891320.136 13704026.04 0.023847 0.010967384 1.959896932 1.346908717 DEDHIALIIELLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DEDHIALIIELLGK 14 0 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3 H3BLV9 SRPK1 SRSF protein kinase 1 0 89.959 0.0059424 25807000 93652 67536 82864 62095 76101 62560 91200 77032 50978 FALSE TRUE 87790.48849 72536.43571 84829.57321 63688.46283 70124.33444 80620.05642 77525.40666 86649.61477 42469.44247 2.067144831 1.707967694 1.997426109 1.499630302 1.651171533 1.898307388 1.825439708 2.040281429 1 15.37413755 -1.785015672 2.826747213 0.796141673 1.826115294 0.681683457 0.17940598 39742857.54 31454988.01 55903867.08 0.040914079 0.016405306 1.785015672 1.029973621 DEDLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 129.96 0.037149 1422720000 2363730 2658900 2676640 2336480 2570520 1896280 2760620 2126320 2952800 FALSE TRUE 2215788.359 2855767.723 2740131.165 2396438.032 2368641.728 2443705.252 2346690.659 2391795.733 2459958.604 0.900742132 1.160900723 1.113893201 0.974178195 0.962878694 0.993392835 0.953955345 0.972291049 1 21.23020261 3.230328135 24.8097251 0.973088372 1.088364054 0.202520364 0.068899231 159.4195253 480432.166 0.018822778 0.022861233 1699.527261 -3.230328135 0.115275682 DEDMLYS(ph)PELAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DEDMLYSPELAQR 13 0 Q9Y2W2 Q9Y2W2 WBP11 WW domain-binding protein 11 1 DEDMLYS(1)PELAQR;DEDMLYS(1)PELAQR 245.4 4.41E-17 269280000 583940 398090 471250 427300 453950 402730 595750 393730 518640 TRUE FALSE 547392.2378 427564.9978 482428.2725 438265.2414 418298.5981 518991.6132 506422.8182 442888.0572 432075.6335 1.266889858 0.989560541 1.116536632 1.014325288 0.968114297 1.201159179 1.172069839 1.025024377 1 18.72092435 2.228021787 24.99996829 1.123250992 1.063586202 0 0.102442239 579.8689901 1375542.163 0.035371064 0.026395574 169.0525736 -2.228021787 -0.059664789 DEDSLHQTDLFDSHMLWFLMHHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DEDSLHQTDLFDSHMLWFLMHHLR 24 0 Q5TAQ9;V9GY98 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 0 89.365 0.0031548 18158000 20779 38249 27532 25221 34239 16928 25638 32304 15775 FALSE TRUE 19478.47948 41080.99576 28185.07204 25868.21356 31550.00705 21814.8388 21793.81991 36337.22551 13142.05059 1.482149178 3.12591977 2.144647964 1.968354435 2.400691341 1.659926558 1.658327197 2.764958578 1 13.68190278 -1.369704782 0.196825918 1.05E-12 2.523125449 0.25811012 0.539524598 28.29534263 1.056491015 16.76463889 1.555101379 0.042686959 1.369704782 2.523125449 DEDYKQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 130.04 0.0032851 1602120000 1560880 1442970 1494380 1529740 1915360 993200 2040080 1337010 3493000 FALSE TRUE 1463187.307 1549809 1529827.399 1568995.718 1764935.352 1279920.717 1734188.943 1503938.642 2909995.734 0.502814245 0.532581193 0.525714654 0.539174577 0.606507883 0.439835943 0.595942091 0.51681816 1 21.47258561 -4.679711961 0.478511206 10 0.529981437 0.909012028 0.046474443 320.5140359 2.292564532 3052.051509 0.019951616 2.09E-05 4.679711961 -9.470018563 DEEPSGWEEPS(ph)PQSISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DEEPSGWEEPSPQSISR 17 0 Q9UPQ9-1;Q9UPQ9;H0Y720 Q9UPQ9-1 TNRC6B Trinucleotide repeat-containing gene 6B protein 1 DEEPSGWEEPS(1)PQSISR 291.67 3.11E-33 0 94562 73064 88958 78092 74490 74693 97380 70751 73714 TRUE FALSE 88643.53322 78473.73458 91068.12577 80095.97293 68639.85588 96255.65656 82778.77303 79584.41809 61410.65719 1.443455212 1.277852057 1.482936838 1.304268291 1.11771896 1.567409648 1.347954522 1.295938225 1 15.90620142 0.786943116 2.781621199 1.000149431 1.364970564 0.464086425 0.121888795 0.913208237 10.51077506 0.108205537 0.028566111 6.122701918 -0.786943116 0.364821133 DEESGGGSNPFQHLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DEESGGGSNPFQHLEK 16 0 Q9Y678;D6RG17 Q9Y678 COPG1 Coatomer subunit gamma-1 0 245.96 3.68E-20 196720000 314370 266380 268680 277060 292940 209300 374530 263680 311440 FALSE TRUE 294694.1429 286103.0524 275053.2165 284169.8287 269933.6741 269721.5123 318372.7035 296601.0284 259458.652 1.135803877 1.102692279 1.060104238 1.09524129 1.040372606 1.039554897 1.22706528 1.143153355 1 17.98514512 1.762524201 25 1.147099648 1.078665723 0.059991719 0.062809881 20.15565533 21042.59524 0.026325043 0.014598885 57.87942405 -1.762524201 -0.068433925 DEEVEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DEEVEEAR 8 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 157.34 0.00088039 250570000 813650 678880 733150 684190 752820 602290 823350 658800 751770 FALSE TRUE 762725.0989 729144.9816 750540.6642 701747.4737 693696.5539 776161.3456 699896.3111 741052.6302 626294.7304 1.217837325 1.164220208 1.198382531 1.120474818 1.107619976 1.239290877 1.11751908 1.18323306 1 19.25648221 -4.905143278 0.257405916 1.07E-11 1.181390057 0.597123791 0.043589026 120.9072289 1.247676215 63.79254784 0.05403202 1.24E-05 4.905143278 1.181390057 DEEVHAGLGELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DEEVHAGLGELLR 13 0 P50454;E9PR70;E9PPV6;E9PK86;E9PMI5;E9PQ34;E9PIG2;E9PRS3;E9PNX1;E9PJH8 P50454 SERPINH1 Serpin H1 0 ; 130.24 0.00014441 87845000 210497 208390 209380 204842 176297 166382 239440 169693 143711 FALSE TRUE 197322.3685 223819.4124 214346.5925 210098.5925 162451.3448 214413.7824 203538.1949 190879.5446 119724.7057 1.648134087 1.869450513 1.790328832 1.754847434 1.356874037 1.790890035 1.700051745 1.594320433 1 16.86936136 -2.414377327 0.2700488 7.94E-18 1.788928277 0.720992545 0.136325949 21.91126623 0.736896593 13.26716054 0.173854168 0.003851436 2.414377327 1.788928277 DEEVLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DEEVLKK 7 1 O00148;O00148-2;O00148-3;K7EQN7;K7EPJ3;A0A0G2JJL7;F6QYI9;A0A0D9SEM9;A0A140T9N3;A0A140T9K2;Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;F6S4E6;A0A0A0MT12;F6TRA5;A0A140T9K1;A0A140T973;A0A140T9L4;F6R6M7 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 98.299 0.036712 0 150890 105190 146020 135610 150610 88575 177980 120960 165860 FALSE TRUE 141446.0642 112978.3771 149483.6634 139089.9822 138781.6981 114145.1646 151293.5513 136062.1223 138176.8945 1.023659308 0.81763581 1.081828217 1.006608107 1.004377024 0.826079968 1.094926556 0.984695182 1 17.07615687 3.972226756 24.97930481 1.00051882 0.911406644 0.123912569 0.086698202 348.3600048 1777887.555 0.020331494 0.038195724 9380.516601 -3.972226756 -0.089112175 DEEWFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DEEWFR 6 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 149.06 0.024861 142368000 395690 312070 383670 333000 303890 342800 457770 324240 289060 FALSE TRUE 370924.4692 335175.9875 392770.8336 341545.3438 280023.7052 441760.7951 389131.6382 364722.0777 240814.0186 1.540294337 1.39184583 1.631013161 1.418295105 1.162821446 1.834448001 1.615901103 1.514538397 1 17.87755985 2.233965607 24.99951677 1.56083127 1.450894641 0 0.240957425 400.2266921 2177441.79 0.080813293 0.061667808 171.382158 -2.233965607 -0.109936628 DEFEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DEFEER 6 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 128.38 0.038736 394280000 1177400 989540 1071550 1007910 988430 899730 1264530 892500 1007660 FALSE TRUE 1103708.636 1062806.571 1096967.672 1033774.677 910802.6949 1159467.445 1074925.466 1003930.59 839475.0363 1.314760521 1.266037137 1.306730545 1.231453745 1.08496698 1.381181566 1.280473414 1.195902851 1 19.6791279 0.88105477 3.434030646 1.000147591 1.268890608 0.550843693 0.075713262 0.382719923 9.031944342 0.069400779 0.017950661 7.604221691 -0.88105477 0.268743017 DEFEFLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DEFEFLEK 8 0 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 112.84 0.011179 0 23390 19283 22661 20090 20004 16805 25150 18301 21860 FALSE TRUE 21926.06165 20710.73338 23198.52962 20605.54341 18432.96653 21656.33069 21378.99098 20585.92014 18211.42478 1.203972886 1.137238499 1.273844848 1.131462456 1.012164987 1.189161801 1.173932915 1.130384931 1 14.15255618 -4.999999985 0.169325762 0.366151332 1.202595968 0.382292992 0.065065919 145.7991458 1.37405884 31.02856293 0.242105829 1.00E-05 4.999999985 0.836444636 DEFEGLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DEFEGLFK 8 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;; 130.27 0.0024544 1678950000 3707070 2900050 3258620 3240110 3430750 2376620 3953710 2824590 3664050 FALSE TRUE 3475051.106 3114772.719 3335916.005 3323256.708 3161312.734 3062711.613 3360887.89 3177246.279 3052496.384 1.138429229 1.020401772 1.092848471 1.088701276 1.035648314 1.003346516 1.101029278 1.040868155 1 21.54155816 2.733679257 24.63561865 1.04445943 1.075605165 0.242412081 0.040028755 716.7256028 3617235.005 0.012377465 0.011960044 541.6007496 -2.733679257 0.031145735 DEFSHQVQEWNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DEFSHQVQEWNR 12 0 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ; 200.93 1.54E-07 470940000 537780 536000 542760 507400 611860 408960 555110 506100 603290 FALSE TRUE 504121.3098 575685.9977 555634.5235 520420.743 563806.9837 527020.1131 471876.4089 569287.6991 502597.0016 1.003032864 1.145422666 1.105526937 1.035463286 1.1217874 1.048593826 0.938876291 1.132692191 1 18.93904254 2.00344465 17.03170697 1.011232346 1.091350573 0.138119436 0.062439861 2.461148331 12161.25847 0.021976783 0.016011224 100.7963137 -2.00344465 0.080118227 DEFSYQEMIANLPLCSHPNPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DEFSYQEMIANLPLCSHPNPR 21 0 P19623;K7ESL0 P19623 SRM Spermidine synthase 0 ; 256.92 1.83E-36 259730000 407860 387560 412260 384610 328500 339860 475340 337870 271110 FALSE TRUE 382332.7707 416255.3457 422039.0019 394479.7437 302700.9351 437972.0648 404067.1798 380053.8132 225859.9896 1.69278663 1.842979567 1.86858683 1.746567617 1.340214952 1.939130811 1.789016198 1.682696497 1 17.7850692 0.763104447 3.86693075 1.000013772 1.763875496 0.674964398 0.161067438 1.624123585 25.95531216 0.150379508 0.038503093 5.795680643 -0.763104447 0.763861724 DEGGNQQDEAITWFNVIYPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DEGGNQQDEAITWFNVIYPR 20 0 B2WTI3;B2WTI4;K7EJU9;Q6NYC1-2;Q6NYC1;Q6NYC1-3 B2WTI3 JMJD6 Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 0 84.468 0.0064799 5012200 8925.9 7777.4 9886.7 6808.1 7615.5 7707.5 9536.1 6578.2 9620.4 FALSE TRUE 8367.243852 8353.246788 10121.21719 6982.807372 7017.409349 9932.530129 8106.250334 7399.50275 8014.69309 1.043988055 1.04224163 1.262832785 0.871250751 0.875568069 1.239290141 1.011423674 0.923242184 1 12.96843156 3.235218636 24.99999946 1.001153971 1.121398406 0.201543361 0.119161169 148.5203173 1111022.128 0.034487202 0.042852422 1718.773448 -3.235218636 0.120244435 DEGGWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DEGGWR 6 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 106.84 0.073922 122620000 239070 188340 238560 230220 234680 186490 278130 198320 264060 FALSE TRUE 224107.0355 202284.8896 244218.7559 236127.835 216249.1795 240326.6356 236426.9885 223080.6886 219986.6801 1.018730022 0.919532444 1.110152468 1.073373328 0.983010332 1.092459941 1.074733199 1.014064526 1 17.74705665 3.979398851 24.98023864 1.055367248 0.968645273 0.330326654 0.047145248 98.54453811 1080791.164 0.010842217 0.021811157 9536.716031 -3.979398851 -0.086721975 DEHLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DEHLLK 6 0 O00505;O00629 O00505;O00629 KPNA3;KPNA4 Importin subunit alpha-4;Importin subunit alpha-3 0 ;;;; 111.69 0.027635 1991492000 6747340 5625870 6099560 5637190 6349710 4499510 7545180 5586890 7081900 FALSE TRUE 6325036.034 6042415.269 6244244.444 5781849.839 5851029.39 5798445.494 6413850.305 6284425.515 5899885.139 1.072060877 1.024158119 1.05836712 0.979993627 0.991719203 0.982806505 1.087114436 1.065177604 1 22.49225544 -0.19064749 6.617321369 1.000000001 1.033207691 0.066706698 0.038363444 2524882.737 381556.5667 0.037398646 0.009070504 0.64469234 0.19064749 0.03320769 DEILEWESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DEILEWESR 9 0 Q13596-2;Q13596;H0YK42;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 0 ;;; 204.27 3.92E-05 512210000 893310 815980 901670 832460 968230 749060 1000950 829490 1062320 FALSE TRUE 837399.3217 876396.0082 923058.0382 853822.333 892189.1215 965301.462 850866.8399 933053.6524 885011.9292 0.946201169 0.990264627 1.042989374 0.964757993 1.008109712 1.090721413 0.961418498 1.054283701 1 19.75533738 4.633402631 2.289560544 1.015681574 0.9372897 0.255486012 0.039043056 0.644128632 4.751908999 0.008971384 0.09248263 42993.48309 -4.633402631 -0.078391874 DEILPTT(ph)PISEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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(0.003)T(0.997)PISEQK;DEILPT(0.018)T(0.982)PISEQK;DEILPT(0.023)T(0.977)PISEQK;DEILPT(0.013)T(0.987)PISEQK;DEILPT(0.02)T(0.98)PISEQK;DEILPT(0.229)T(0.771)PISEQK 350.18 6.97E-75 21456550000 24765000 15727580 19192500 17822100 18492200 13124420 23002300 14888200 19805200 TRUE FALSE 23215002.86 16892066.39 19647755.16 18279445.26 17039897.21 16913227 19553318.66 16747024.54 16499584.17 1.407005329 1.0237874 1.19080305 1.107873087 1.03274707 1.025069894 1.185079482 1.014996764 1 23.97592633 4.745716744 24.91029824 1.088293466 1.407005486 0.685684681 0.07045165 481.9609474 1677650.065 0.015872046 0.162510614 55682.24587 -4.745716744 0.318712019 DEKDEHGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DEKDEHGR 8 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;; 126.07 0.00074205 529613000 3905290 1794120 2905070 2577460 2334950 1885190 2955980 2279220 2679270 FALSE TRUE 3660864.87 1926958.512 2973979.632 2643601.987 2151572.446 2429413.749 2512758.241 2563785.634 2232082.528 1.64011179 0.863300746 1.332378886 1.184365701 0.963930508 1.088406777 1.125746118 1.148607008 1 21.08995894 4.755245329 24.6691278 1.101153447 1.640112298 0.643735246 0.128687692 1860.092847 2750180.285 0.029525219 0.826496634 56917.43611 -4.755245329 0.53895885 DEKKEES(ph)EES(ph)DDDMGFGLFD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DEKKEESEESDDDMGFGLFD 20 2 P05387;H0YDD8 P05387 RPLP2 60S acidic ribosomal protein P2 2 DEKKEES(1)EES(1)DDDMGFGLFD 71.656 0.084238 30175000 86249 34249 43464 52638 56508 30260 64654 31871 100120 TRUE FALSE 80850.82905 36784.8316 44494.98661 53988.7802 52070.08962 38995.57077 54959.73292 35850.16451 83409.3252 0.969326018 0.441015816 0.533453382 0.647275111 0.624271801 0.467520516 0.658915928 0.429810029 1 16.34792107 -1.581625747 2.934128047 1.02486279 0.579396969 0.391756705 0.156752415 98760896.64 105626440.3 19150468.91 0.033155448 0.026204402 1.581625747 -0.445465821 DEKRS(ph)AEGSPGAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DEKRSAEGSPGAER 14 2 P24588 P24588 AKAP5 A-kinase anchor protein 5 1 DEKRS(0.843)AEGS(0.157)PGAER 73.983 0.017904 197490000 48132 150070 104330 107250 125900 107140 93924 100640 141170 TRUE FALSE 45119.50404 161181.3389 106804.7569 110002.2166 116012.3219 138069.5787 79840.96815 113205.1255 117607.815 0.383643757 1.370498542 0.908143365 0.935330841 0.986433783 1.173983028 0.678874683 0.962564652 1 16.8436244 1.738922065 25 0.852962577 1.001224701 0 0.263476539 0.177536612 10554.98473 0.111227042 0.061681128 54.8178584 -1.738922065 0.148262124 DELDVS(ph)NFAEEFTEMDPTYSPAALPQSSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DELDVSNFAEEFTEMDPTYSPAALPQSSEK 30 0 O75582-3;O75582;O75582-2 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 1 DELDVS(0.944)NFAEEFT(0.05)EMDPT(0.003)Y(0.003)S(0.001)PAALPQSSEK 50.144 0.05454 11251000 11615 7113.4 10210 6389.3 7020.4 5057.7 16601 9285.8 11300 TRUE FALSE 10888.03788 7640.083537 10452.18602 6553.260255 6469.046103 6517.775885 14111.83417 10445.15257 9413.956999 1.156584621 0.811569836 1.110286145 0.696121754 0.687176084 0.692352417 1.499033209 1.109539014 1 13.20058555 1.746126114 25 1.242056547 0.869658207 0.377838959 0.205654556 1.578835259 5231.66754 0.091494191 0.05073819 55.73475724 -1.746126114 -0.37239834 DELDVSNFAEEFTEMDPTYSPAALPQS(ph)SEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DELDVSNFAEEFTEMDPTYSPAALPQSSEK 30 0 O75582-3;O75582;O75582-2 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 1 DELDVSNFAEEFTEMDPTYSPAALPQS(0.815)S(0.185)EK 117.66 5.06E-05 22675000 88675 46648 69719 62233 55164 46597 73742 48620 56619 TRUE FALSE 83124.99004 50101.86646 71372.7676 63830.00414 50831.64196 60048.79746 62685.07169 54690.31403 47168.92313 1.762282972 1.062179569 1.513131165 1.353221569 1.077651101 1.273058477 1.328948543 1.15945649 1 15.52554904 7.999930302 0.032089614 5.68E-06 3.199637125 0.343336039 0.186372838 1606.196773 3.946042859 121.4540597 313.5585864 99983952.76 -7.999930302 3.199631444 DELEVIHLIEEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DELEVIHLIEEHR 13 0 P10155-3;P10155-5;P10155-4;P10155 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 ;;;;; 248.77 1.11E-17 333924000 474434 437943 467969 456502 463759 401018 542797 405404 486307 FALSE TRUE 444740.0228 470368.7554 479069.4457 468216.6142 427337.2389 516785.3866 461409.6289 456019.5818 405139.22 1.097746159 1.161005235 1.182481039 1.155693132 1.054791088 1.275574817 1.138891537 1.125587352 1 18.62805823 0.789087807 2.466163342 1.000152494 1.157876633 0.410252787 0.056785799 0.817871042 7.888679908 0.04926526 0.013210294 6.153012632 -0.789087807 0.157724139 DELHHSGWNTCSSCFGDSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DELHHSGWNTCSSCFGDSTK 20 0 Q13228;Q13228-4;Q13228-2;A6PVX1;F2Z2W8;F8WCR4;C9JVL0 Q13228 SELENBP1 Selenium-binding protein 1 0 ;; 191.95 7.37E-18 1345180000 260824 481651 463420 495031 485867 434645 708790 570320 487090 FALSE TRUE 244499.4914 517312.9412 474412.5412 507734.3335 447708.9657 560119.9556 602513.5196 641525.7074 405791.5323 0.602524873 1.274824387 1.169104093 1.251219637 1.10329795 1.380314548 1.484785836 1.580924333 1 18.63037923 4.739659023 5.670819515 1.293343029 0.579391984 0.60486928 0.172017349 0.100725896 13.52710004 0.041546549 0.278209023 54910.95827 -4.739659023 -0.713951045 DELHIVEAEAMNYEGS(ph)PIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 DELHIVEAEAMNYEGSPIK 19 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK 299.94 4.61E-50 3569901700 5035329 2281707 3304691 2818425 2306278 2749755 4105245 2790516 1740505 TRUE FALSE 4720176.746 2450646.96 3383079.831 2890750.557 2125152.229 3543564.63 3489701.623 3138918.065 1450003.471 3.255286514 1.690097306 2.333152918 1.993616301 1.465618718 2.443831825 2.406685013 2.164765897 1 20.46762492 -1.693484356 2.479116648 0.794940555 2.179739172 0.385498013 0.481452699 7525551.062 5765143.127 9643168.362 0.114695101 0.020254226 1.693484356 1.384798617 DELHIVEAEAMNYEGS(ph)PIKVTLATLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 21 DELHIVEAEAMNYEGSPIKVTLATLK 26 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.094)EGS(0.905)PIKVT(0.001)LATLK;DELHIVEAEAMNY(0.134)EGS(0.866)PIKVTLATLK;DELHIVEAEAMNY(0.024)EGS(0.976)PIKVTLATLK;DELHIVEAEAMNY(0.156)EGS(0.843)PIKVT(0.002)LATLK;DELHIVEAEAMNY(0.023)EGS(0.977)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.002)EGS(0.998)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.004)EGS(0.991)PIKVT(0.004)LATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.007)EGS(0.992)PIKVT(0.001)LATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.002)EGS(0.985)PIKVT(0.01)LAT(0.002)LK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.129)EGS(0.84)PIKVT(0.032)LATLK;DELHIVEAEAMNY(0.004)EGS(0.996)PIKVTLATLK;DELHIVEAEAMNY(0.456)EGS(0.534)PIKVT(0.011)LATLK 348.19 9.40E-110 10138691600 6969514 3573588 4839917 4497759 4434006 3625031 6678079 4059062 4480878 TRUE FALSE 6533304.56 3838180.174 4954722.117 4613179.111 4085777.055 4671518.602 5676763.05 4565844.826 3732990.514 1.750153003 1.028178389 1.327279589 1.235786454 1.094505073 1.251414539 1.520701172 1.223106463 1 21.83190041 4.753889469 24.65247337 1.237949323 1.750153455 0.547020257 0.152583243 2027.169828 3260109.132 0.037042241 0.874996049 56740.01801 -4.753889469 0.512204132 DELHIVEAEAMNYEGSPIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DELHIVEAEAMNYEGSPIK 19 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;;;; 282.49 9.35E-40 5864019000 8419449 5534573 6861218 6207959 5838968 5708613 8797065 5921339 5746055 FALSE TRUE 7892490.716 5944358.544 7023969.331 6367265.738 5380399.007 7356596.902 7478026.771 6660631.209 4787001.3 1.648733773 1.241770823 1.467300486 1.330115732 1.123960214 1.536786067 1.562152651 1.391399499 1 22.19069077 -2.088534634 2.379306413 0.336823518 1.408291902 0.411410172 0.155080206 3715440.526 1285279.345 13335625.44 0.037391378 0.008155777 2.088534634 1.071468383 DELLAQHAAGALGLPDLVAVLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DELLAQHAAGALGLPDLVAVLTR 23 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 190.87 1.39E-17 834390000 853030 854190 851820 792720 769300 763210 1154350 780640 548240 FALSE TRUE 799640.375 917435.1164 872025.5727 813062.5373 708882.2812 983536.3373 981265.934 878104.6224 456735.2022 1.750774565 2.008680548 1.909258512 1.780161751 1.552064036 2.153406027 2.148435087 1.922568302 1 18.80099846 3.445535887 23.18538942 1.854691074 1.919348744 0 0.340613089 740.5594939 543606.8157 0.088592753 0.119948381 2789.561155 -3.445535887 0.06465767 DELTDLDQS(ph)NVTEETPEGEEHHPVADTENKENEVEEVKEEGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DELTDLDQSNVTEETPEGEEHHPVADTENKENEVEEVKEEGPK 43 2 Q8NC51-3;Q8NC51-4 Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 DELTDLDQS(0.994)NVT(0.005)EETPEGEEHHPVADTENKENEVEEVKEEGPK;DELT(0.002)DLDQS(0.979)NVT(0.016)EET(0.004)PEGEEHHPVADTENKENEVEEVKEEGPK 105.15 2.38E-06 161105000 257856 59039 109919 95487 98101 59590 166668 74730 141162 TRUE FALSE 241717.2532 63410.30899 112526.3306 97937.35808 90396.54318 76792.66564 141677.6807 84060.205 117601.1503 2.055398716 0.539198034 0.956847194 0.832792518 0.76867057 0.65299247 1.204730399 0.71479067 1 16.84354265 4.747348718 24.95402368 0.839758264 2.05539935 0.806346006 0.188127858 480.8320689 1365304.186 0.043810289 0.526082346 55891.87998 -4.747348718 1.215641086 DELTES(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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;DELTES(1)PK;DELTES(1)PK;DELTES(1)PK 203.52 9.96E-05 2403680000 9113000 3474580 6184280 6437920 4359040 3042720 4568680 2402140 2309590 TRUE FALSE 8542633.597 3731841.518 6330974.042 6603127.927 4016698.582 3921103.87 3883648.848 2702052.467 1924104.508 4.43979709 1.939521217 3.290348323 3.431792763 2.087567782 2.03788508 2.01841887 1.404316894 1 20.87575573 1.820063943 0.630954561 1.013779744 3.117024316 0.592436807 0.657816671 0.552083729 0.450623263 0.587126299 0.329508001 66.0790732 -1.820063943 2.103244572 DELTES(ph)PKYIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DELTESPKYIQK 12 1 Q8NC51;Q8NC51-2 Q8NC51 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 DELTES(1)PKYIQK;DELT(0.023)ES(0.977)PKYIQK;DELT(0.004)ES(0.996)PKYIQK;DELTES(1)PKYIQK 184 9.01E-06 2128490000 7875200 4363030 6132200 7715300 7232000 2086670 4147540 2487890 5732430 TRUE FALSE 7382305.29 4686073.281 6277658.68 7913287.66 6664027.892 2689057.755 3525654.881 2798508.543 4775650.4 1.545821966 0.981242949 1.314513868 1.657007318 1.395417867 0.56307676 0.738256486 0.585995269 1 22.1872658 2.242397494 24.99668443 0.699226042 1.328467775 0.700509106 0.211809566 57.56611685 375036.9626 0.076514381 0.061771562 174.7420773 -2.242397494 0.629241733 DENGELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DENGELR 7 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ; 169.37 0.0023599 736920000 1577290 1687190 1684660 1662160 1793600 1449670 1867980 1468860 1801020 FALSE TRUE 1478570.234 1812111.303 1724620.931 1704813.84 1652737.891 1868166.196 1587893.74 1652250.404 1500418.127 0.985438797 1.207737544 1.149426883 1.136225835 1.101518211 1.245097058 1.058300824 1.10119331 1 20.51693317 1.034016956 1.338566876 1.004454393 1.143408956 0.226820611 0.072082294 0.542612582 1.989736948 0.060970858 0.018567101 10.81476173 -1.034016956 0.138954563 DENQSINHQMAQEDAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DENQSINHQMAQEDAQR 17 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;;;;;; 275.37 1.02E-35 4517150000 1452083 1855508 1705576 1266724 1447243 629433 2172169 1684107 2010083 FALSE TRUE 1361199.717 1992891.743 1746033.068 1299230.282 1333582.373 811140.0891 1846472.424 1894371.466 1674587.162 0.812856893 1.190079435 1.042664788 0.775851095 0.796364861 0.484382126 1.102643366 1.131246859 1 20.67537404 3.31780528 8.055032183 0.870711243 1.058034242 0.072032463 0.205438783 0.483573653 43.13015435 0.056773501 0.076904675 2078.764445 -3.31780528 0.187322999 DEPDWESLIFLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DEPDWESLIFLAR 13 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;;;;; 223.78 3.54E-11 717487000 549144 548380 486791 450270 578184 424920 608287 490631 426855 FALSE TRUE 514774.0573 588982.6258 498337.9124 461824.6905 532775.7609 547587.506 517080.0114 551887.3604 355610.1429 1.447579794 1.656259355 1.401360232 1.298682559 1.498201813 1.539853452 1.454064294 1.551944936 1 18.43993695 -1.273208023 4.996247996 0.999886637 1.484958982 0.717152063 0.094902905 0.000119957 1.74E-05 0.091980033 0.021674873 0.053307949 1.273208023 0.485072345 DEPLLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DEPLLFR 7 0 Q70Z35-3;Q70Z35-4;Q70Z35 Q70Z35-3 PREX2 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 2 protein" 0 92.692 0.036019 54999000 88298 120290 102080 102390 114590 92289 114900 107660 102100 FALSE TRUE 82771.5858 129196.3968 104501.3858 105017.5007 105590.5636 118931.3361 97671.81168 121101.588 85058.85041 0.973109622 1.518905983 1.228577453 1.234645193 1.241382444 1.398224118 1.148285113 1.423738828 1 16.37617374 -1.678006988 2.569808402 0.957910002 1.282975923 0.233731772 0.152731848 17611897.7 14554250.3 4841350.618 0.035018999 0.020989061 1.678006988 0.325065921 DEPNSTPEKTEQFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DEPNSTPEKTEQFYR 15 1 O76021;J3QSV6;I3L3U9;I3L3C4;I3L234 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 124.09 9.00E-05 270900000 129650 94274 121630 115180 123340 69669 123140 84601 155270 FALSE TRUE 121535.4379 101254.1451 124515.121 118135.7138 113653.3739 89781.30932 104676.3002 95163.62108 129354.4339 0.939553707 0.782765167 0.962588736 0.913271468 0.878619855 0.694072144 0.809220813 0.735681168 1 16.98096998 2.443101676 24.81994423 0.791231312 0.891124543 0.164484037 0.09196525 241.8337184 176435.3363 0.028677707 0.023993588 277.3969465 -2.443101676 0.099893231 DEPPPLS(ph)PAPLTPATPSSLDPFFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DEPPPLSPAPLTPATPSSLDPFFSR 25 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 DEPPPLS(1)PAPLTPATPSSLDPFFSR;DEPPPLS(1)PAPLTPATPSSLDPFFSR 158.1 1.63E-11 44547000 27923 29697 30246 35061 32497 20268 27107 17095.5 17769.6 TRUE FALSE 26175.34927 31895.79678 30963.4494 35960.72462 29944.81671 26119.04258 23042.557 19229.91081 14803.73896 1.768157986 2.154577087 2.091596554 2.429165004 2.022787404 1.76435444 1.556536295 1.29899013 1 13.85367398 1.549342395 1.090874073 1.039940744 2.122372179 0.843523646 0.167170851 0.163846091 0.375523935 0.144458305 0.052612669 35.427654 -1.549342395 1.082431435 DEPQEPSNKVPEQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DEPQEPSNKVPEQQR 15 1 P12270 P12270 TPR Nucleoprotein TPR 0 ; 166.04 1.27E-06 1043200000 415150 304140 309590 337700 367630 267740 429840 274640 443380 FALSE TRUE 389166.5026 326658.8421 316933.621 346365.9537 338757.8227 345032.1916 365389.4824 308929.4086 369377.0137 1.053575312 0.884350758 0.858022046 0.937703054 0.917105857 0.934092212 0.989204712 0.836352553 1 18.49473456 2.163059243 4.279329599 0.945201475 0.914302105 0 0.06736026 0.807942051 28.26518945 0.025170155 0.018339862 145.5657637 -2.163059243 -0.03089937 DEPSVAAMVYPFTGDHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DEPSVAAMVYPFTGDHK 17 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;;;;;; 255.21 4.64E-27 2822356000 5152722 3778679 4475441 4239546 4665075 3282638 5577138 3869209 5827412 FALSE TRUE 4830222.328 4058456.325 4581600.574 4348339.928 4298698.828 4230282.301 4740897.933 4352288.261 4854779.291 0.994941693 0.835971335 0.943729941 0.89568231 0.885457107 0.871364494 0.976542423 0.896495597 1 22.21097428 0.559485546 0.669726702 1.000446535 0.902626901 0.223720351 0.048697862 1.991109376 1.569125129 0.050028295 0.017093962 3.626482165 -0.559485546 -0.097819634 DEQGACAVLAVHLNTLLGERPVQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DEQGACAVLAVHLNTLLGERPVQHR 25 1 P40121-2;P40121;E7ENU9;B8ZZL6 P40121-2 CAPG Macrophage-capping protein 0 ; 110.68 0.0017925 125578000 78800 65398 78117 73687 80909 70222 82244 66434 92802 FALSE TRUE 73868.04866 70240.13597 79969.97213 75577.93317 74554.73351 90493.95144 69912.27572 74728.43114 77312.74668 0.95544463 0.908519474 1.034369823 0.977561093 0.96432654 1.170491999 0.904278773 0.966573228 1 16.23841867 3.999030231 6.30781747 1.000666965 0.933273644 0.150799013 0.069437662 0.310676071 45.5441472 0.016492311 0.034607659 9977.695149 -3.999030231 -0.067393322 DEQLESLFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DEQLESLFQR 10 0 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ;; 188.91 2.49E-06 140704000 198599 177094 185778 173701 202960 139436 228880 151897 254612 FALSE TRUE 186169.0431 190206.224 190184.7419 178158.4617 187020.3403 179688.9096 194561.5688 170861.6748 212115.6123 0.87767723 0.896710157 0.896608881 0.839912064 0.881690594 0.847127223 0.917243039 0.805512017 1 17.69449129 -1.121421512 4.801036735 1.000007476 0.876466717 0.60064833 0.032894755 2.37E-06 4.34E-07 0.028679094 0.006759318 0.075609869 1.121421512 -0.123540759 DESETEKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DESETEKEK 9 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;; 125.75 0.00044953 1189390000 1909420 856970 1270560 1361940 1295580 903740 1568190 1068760 1734170 FALSE TRUE 1789912.811 920420.9505 1300698.283 1396889.686 1193830.373 1164635.067 1333054.468 1202197.039 1444725.824 1.238929063 0.637090398 0.900308046 0.966889124 0.826336979 0.806128781 0.922704119 0.832128158 1 20.4623643 -1.393603953 3.484704282 1.001000304 0.869803303 0.031224076 0.153089298 15555871.66 12614802.16 107569.4976 0.032128139 0.040401366 1.393603953 -0.131197001 DETAVQDYHGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DETAVQDYHGHK 12 0 P48147 P48147 PREP Prolyl endopeptidase 0 97.911 0.002692 274210000 363070 263600 296050 296890 316020 248500 402490 264870 256460 FALSE TRUE 340346.0968 283117.2183 303072.4458 304508.7 291201.064 320237.9159 342140.361 297939.6026 213655.1692 1.592969166 1.325112888 1.418512114 1.425234415 1.362948835 1.498854051 1.601367111 1.394488154 1 17.7049247 0.964298197 23.59779781 0.999999997 1.451183559 0.72466178 0.088412352 1687.821557 1115599.745 0.09033925 0.022584812 9.210817922 -0.964298197 0.451183562 DETEFYLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DETEFYLGK 9 0 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ;;;;;; 233.21 8.90E-10 2136620000 3672740 2818155 3246186 3200520 3068570 2313090 3746250 2756315 2894713 FALSE TRUE 3442869.759 3026814.128 3323187.065 3282650.762 2827576.89 2980841.533 3184534.591 3100446.995 2411566.7 1.427648574 1.255123538 1.378019967 1.361210852 1.172506193 1.236060165 1.320525197 1.285656746 1 21.20153928 -4.256183353 0.20638973 5.81E-20 1.352567665 0.673492317 0.069046688 62.84918617 0.825844955 26.2369759 0.152533059 5.54E-05 4.256183353 1.352567665 DETEFYLGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DETEFYLGKR 10 1 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ;; 178.08 3.62E-06 1001300000 875800 1154500 1004350 1115270 1444730 702640 1269800 854600 2129610 FALSE TRUE 820985.2413 1239980.381 1028173.656 1143889.716 1331266.734 905480.7616 1079405.278 961298.6912 1774164.333 0.462744756 0.698909542 0.579525604 0.644748457 0.750362697 0.510370288 0.608402084 0.541831821 1 20.75870822 -2.150799145 2.506213746 1.934693077 0.608546194 0.683209048 0.085490515 3383768.198 1187265.171 17928263.44 0.019004362 0.007066443 2.150799145 -1.326146883 DETNYGIPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 244.68 4.06E-12 3304610000 2598440 2427710 2572070 2440170 2448360 2142140 2807930 2161720 1984130 FALSE TRUE 2435808.279 2607460.174 2633080.715 2502788.893 2256075.682 2760541.043 2386906.964 2431615.501 1652965.885 1.473598639 1.577443429 1.592943169 1.514120113 1.364865241 1.670053247 1.444014656 1.471062121 1 20.65662552 -1.908618386 0.360765314 0.487994871 1.552316695 0.790885531 0.083436323 14.76727446 0.862241826 6.423551655 0.057954033 0.012341888 1.908618386 1.064321825 DETVSDCSPHIANIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DETVSDCSPHIANIGR 16 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;; 224.59 7.66E-15 1661200000 1337250 1195150 1286580 1231620 1198510 1237570 1760610 1185490 1157460 FALSE TRUE 1253553.91 1283640.15 1317098.285 1263225.454 1104383.859 1594836.369 1496622.875 1333501.036 964272.4485 1.299999716 1.331200691 1.365898494 1.310029604 1.145302721 1.653927136 1.552074704 1.382908988 1 19.8790813 2.24526835 24.99999636 1.462420202 1.30721007 0.022909751 0.181095814 283.4462707 1056417.847 0.057751154 0.047308247 175.9010166 -2.24526835 -0.155210132 DETYKPHLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DETYKPHLER 10 1 A0A0A6YYC7;Q96JP5-2;Q96JP5;H3BTR0 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 0 ;; 136.7 6.66E-05 696060000 931640 786290 982230 946390 815530 859370 1120330 671850 887840 FALSE TRUE 873330.3154 844507.7297 1005528.959 970675.9696 751481.5635 1107456.168 952346.9171 755731.9514 739653.7683 1.180728542 1.14176087 1.359458983 1.312338301 1.015990989 1.49726293 1.287557717 1.021737445 1 19.49649058 -0.594330712 6.997463002 0.999982956 1.242980135 0.180036697 0.148928685 0 0 0.13340937 0.03144489 0.25448916 0.594330712 0.242997179 DEVFEYIIFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DEVFEYIIFR 10 0 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9;I3L4Q1 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 107.47 0.0053049 4163500 17067 10960 14189 14058 12763 10183 17749 14223 10640 FALSE TRUE 15998.80694 11771.4898 14525.56978 14418.75208 11760.64546 13122.66679 15087.70222 15998.77286 8864.115263 1.804896085 1.327993765 1.638693694 1.626643117 1.326770367 1.48042601 1.702110338 1.804892241 1 13.11376093 DEVFHIHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DEVFHIHK 8 0 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 ; 107.47 0.0023119 132913000 281250 284630 268320 278870 339010 196107 320260 296180 266370 FALSE TRUE 263647.0645 305704.3014 274684.6771 286026.2763 312385.5221 252719.9074 272239.9861 333158.725 221911.1262 1.188075015 1.3775979 1.237813902 1.288922648 1.407705542 1.138833873 1.226797371 1.501316003 1 17.75962248 -1.862736632 2.791316142 0.880261385 1.28942485 0.421842137 0.108626908 21414399.8 14130236.2 17007407.11 0.023995683 0.013717134 1.862736632 0.409163465 DEVLDNLLAFVCDIRPEIHENYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DEVLDNLLAFVCDIRPEIHENYR 23 1 O75348 O75348 ATP6V1G1 V-type proton ATPase subunit G 1 0 181.81 2.49E-17 274550000 281480 226540 251750 242760 238060 240380 323570 219410 269730 FALSE TRUE 263862.6693 243313.2573 257721.6289 248989.6326 219363.7279 309773.8038 275053.6824 246803.8215 224710.3205 1.17423476 1.082786304 1.146906063 1.108047161 0.976206733 1.378547292 1.224036714 1.098319921 1 17.77770686 2.256636323 24.99959768 1.203719919 1.102803114 0.085380125 0.109082439 406.5721565 562308.4089 0.034930244 0.029168783 180.5661437 -2.256636323 -0.100916805 DEVQEVVFVPAGTHT(ph)PGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DEVQEVVFVPAGTHTPGSR 19 0 J3KS57;J3KT79;J3QR84;J3QRJ1;J3QL71;Q96FV2-2;Q96FV2 J3KS57 SCRN2 Secernin-2 1 DEVQEVVFVPAGT(0.07)HT(0.93)PGSR;DEVQEVVFVPAGT(0.004)HT(0.996)PGSR 165.96 7.66E-11 287560000 336910 303570 321610 323650 331940 295200 377610 286760 360100 TRUE FALSE 315823.4045 326046.6387 329238.7411 331955.4069 305870.7714 380419.4478 320990.8861 322562.6172 299996.9837 1.052755267 1.086833056 1.097473505 1.106529149 1.019579489 1.268077576 1.069980378 1.075219535 1 18.19458847 0.882086002 2.43945814 1.000579657 1.102511469 0.191065614 0.064989502 0.730727198 8.907034731 0.056499613 0.01522312 7.62229937 -0.882086002 0.101931812 DEVQEVVYFSAADHEPESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DEVQEVVYFSAADHEPESK 19 0 Q12765;Q12765-2;C9K052;B8ZZP4;C9J7U9 Q12765 SCRN1 Secernin-1 0 ;;; 284.07 7.08E-40 507699000 988235 745929 857409 802916 904473 646607 1055360 742865 1389298 FALSE TRUE 926383.1354 801158.3593 877747.1464 823520.1839 833439.339 833271.9441 897118.5655 835613.3305 1157415.189 0.800389648 0.692196169 0.758368436 0.711516655 0.720086748 0.71994212 0.77510523 0.721965064 1 20.14247505 -2.075030213 0.526225975 1.292482446 0.732905185 0.863575116 0.032727515 30.34050095 2.372072326 10.64455372 0.013176671 0.008413366 2.075030213 -0.55957726 DEWLRPEDLPIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DEWLRPEDLPIK 12 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ;;; 170.18 3.82E-05 1077200000 2055280 1606570 1838270 1783090 1937130 1377660 2249740 1615530 1833030 FALSE TRUE 1926643.694 1725522.114 1881874.632 1828847.108 1784995.624 1775368.078 1912412.373 1817232.477 1527085.451 1.261647599 1.129944702 1.232330929 1.197606268 1.168890465 1.162585942 1.25232833 1.190000517 1 20.54234936 -1.253125997 2.946293431 0.998759574 1.197611881 0.702084272 0.040809028 3671002.302 4895916.289 41496.18179 0.009108396 0.05583082 1.253125997 0.198852307 DFAAEVVHPGDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFAAEVVHPGDLK 13 0 P54577;A0A0C4DGZ5 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed;Tyrosine--tRNA ligase" 0 ; 134.21 9.83E-05 511910000 2425900 1601200 2007710 1857960 1763440 1676760 2580100 1703630 1617540 FALSE TRUE 2274067.249 1719754.514 2055333.829 1905638.399 1624946.536 2160813.392 2193237.957 1916331.956 1347562.124 1.687541679 1.276196832 1.525223804 1.414137697 1.20584165 1.603498164 1.627559812 1.42207318 1 20.36192035 DFAKS(ph)SGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DFAKSSGLK 9 1 Q8NC26-2;Q8NC26 Q8NC26-2 ZNF114 Zinc finger protein 114 1 DFAKS(0.982)S(0.018)GLK;DFAKS(0.973)S(0.027)GLK;DFAKS(0.771)S(0.229)GLK 67.563 0.036667 1910900000 1397070 1345640 1372000 1370900 1501000 1053510 1640890 1225770 1652510 TRUE FALSE 1309629.883 1445272.586 1404544.488 1406079.615 1383117.515 1357641.235 1394853.778 1378810.083 1376695.405 0.951285141 1.049812893 1.020228935 1.021344017 1.004664873 0.986159487 1.013189826 1.001536053 1 20.39277797 2.663598677 5.197598023 1.00137351 1.018770745 0 0.025612723 0.535786738 26.45650642 0.007886403 0.007452298 460.8914768 -2.663598677 0.017397235 DFATPSLHTSDQS(ph)PGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFATPSLHTSDQSPGK 16 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 1 DFATPSLHTSDQS(1)PGK;DFATPSLHTSDQS(1)PGK 225.29 4.52E-15 450130000 244528 421830 419000 485660 481820 354660 638040 449560 377350 TRUE FALSE 229223.429 453062.7321 428938.8779 498122.8578 443979.8008 457044.5846 542371.8253 505688.5556 314367.8472 0.729156722 1.44118661 1.364448946 1.584522279 1.412293925 1.453852831 1.725277665 1.608588665 1 18.26209414 4.743725978 4.373188917 1.480809522 0.671805649 0.573602454 0.19354364 0.143108675 6.604340275 0.043130068 0.361542815 55427.58774 -4.743725978 -0.809003873 DFAVLEDHTLAHSLQEQEIEHHLASNVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFAVLEDHTLAHSLQEQEIEHHLASNVQR 29 0 Q8IVM0-2;Q8IVM0 Q8IVM0-2 CCDC50 Coiled-coil domain-containing protein 50 0 180.88 3.31E-18 287800000 26301 27600 31440 29490 26138 33168 43760 27859 36189 FALSE TRUE 24654.86736 29643.53272 32185.77165 30246.76333 24085.22692 42743.06316 37198.59425 31337.25748 30148.82211 0.817772159 0.983240161 1.067563155 1.003248592 0.798877874 1.417735758 1.233832423 1.039418965 1 14.87981402 2.245781025 24.99999966 1.204743605 0.962171127 0.402065765 0.139928034 156.412569 541564.9891 0.047071804 0.038626745 176.1087865 -2.245781025 -0.242572478 DFAYGETDPLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DFAYGETDPLIR 12 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ;;; 162.36 0.00014632 408862000 1077550 1197940 1177850 1196110 1329950 1021090 1372500 1173800 1277200 FALSE TRUE 1010108.069 1286636.724 1205789.158 1226804.208 1225501.092 1315862.107 1166706.367 1320351.514 1064027.069 0.949325537 1.209214278 1.133231657 1.152982141 1.151757439 1.236681044 1.096500644 1.240900304 1 20.02110342 4.7472569 24.82045575 1.15832173 0.949325419 0.447053189 0.070819166 824.4050412 2352915.895 0.014260637 0.167802311 55880.06471 -4.7472569 -0.208996311 DFAYVCEAEFPSKPVAEYLTRPHLGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFAYVCEAEFPSKPVAEYLTRPHLGGR 27 2 Q92754;Q92754-2 Q92754 TFAP2C Transcription factor AP-2 gamma 0 93.111 0.0034354 508560000 180170 134040 158730 142110 171620 113430 176740 148560 164000 FALSE TRUE 168893.4813 143964.4611 162495.1506 145756.7832 158141.6575 146175.3996 150239.4778 167108.043 136627.3405 1.236161669 1.053701701 1.189331139 1.066820028 1.157467143 1.069883956 1.099629673 1.223093726 1 17.05988668 -1.652977215 2.770187276 0.986057802 1.127654248 0.29142645 0.065716536 12664631.42 10653875.29 1244951.845 0.014117612 0.022234265 1.652977215 0.141596446 DFDDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFDDEK 6 0 J3QRS9;O43670-2;O43670;O43670-4;X6R4W8;O43670-3 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 110.35 0.066956 162810000 773220 469850 587200 552140 549670 409650 644580 491190 712660 FALSE TRUE 724825.5404 504638.1829 601128.6613 566308.8472 506501.1355 527909.3049 547931.213 552516.1527 593712.442 1.22083603 0.849970705 1.012491265 0.953843657 0.853108508 0.889166653 0.922889894 0.930612387 1 19.17940482 4.747455393 24.95065105 0.924164449 1.220836186 0.745622151 0.054011547 568.2927069 1594077.651 0.012392482 0.151238827 55905.61033 -4.747455393 0.296671737 DFDFESANAQFNKEEIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DFDFESANAQFNKEEIDR 18 1 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;; 243.41 3.97E-24 927200000 507890 426490 484960 502940 526690 333201 597120 393500 582560 FALSE TRUE 476102.0715 458067.7634 496463.4802 515846.2919 485325.892 429390.7196 507587.3994 442629.3412 485326.9725 0.9809924 0.943833311 1.022946402 1.062884037 0.999997774 0.884745221 1.045866865 0.912022958 1 18.88859752 DFDPAVTEYIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DFDPAVTEYIQR 12 0 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;;; 287.65 3.85E-21 661860000 814720 1203100 635259 432412 1522800 734840 798100 1354420 2335960 FALSE TRUE 763728.1295 1292178.776 650327.6435 443508.424 1403205.431 946976.3789 678432.3142 1523522.318 1946073.185 0.392445739 0.663992899 0.3341743 0.22789915 0.721044533 0.486608821 0.348616033 0.782870002 1 20.89213454 1.047407858 4.353699284 0.997194385 0.461271993 0.616340895 0.148699472 0.116205869 4.657421157 0.137576007 0.035081494 11.15341491 -1.047407858 -0.535922392 DFDS(ph)S(ph)EDEKHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFDSSEDEKHSK 12 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 2 DFDS(1)S(1)EDEKHSK;DFDS(1)S(1)EDEKHSK 135.09 7.62E-05 382400000 5847920 1925550 3037740 2992190 3046160 1828800 4033260 2210900 4113720 TRUE FALSE 5481909.126 2068119.726 3109796.627 3068974.661 2806926.881 2356744.872 3428510.106 2486935.732 3427113.556 1.599570319 0.603458185 0.907409859 0.895498387 0.819035271 0.68767633 1.0004075 0.725664817 1 21.70856257 4.748873825 24.97607518 0.826284233 1.599570753 0.777218575 0.129489817 646.7366842 1566207.513 0.028890289 0.405937533 56088.49987 -4.748873825 0.77328652 DFDTALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFDTALK 7 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 124.59 0.0096111 583730000 1068950 880110 912160 955210 1000160 788400 1183950 895540 1055070 FALSE TRUE 1002046.328 945274.2602 933796.866 979722.3058 921611.4681 1015998.281 1006427.689 1007350.14 878972.001 1.140020759 1.075431594 1.062373847 1.114622883 1.048510609 1.155893794 1.145005401 1.146054868 1 19.74545768 2.232896411 24.99893476 1.127237323 1.084132649 0.007954559 0.051155058 253.6345578 1119402.156 0.016765275 0.012729743 170.9607485 -2.232896411 -0.043104674 DFDWNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 139.31 0.0062827 759257000 1651350 1406410 1527810 1404320 1591980 1161470 1747660 1362910 1978780 FALSE TRUE 1547994.951 1510542.06 1564050.375 1440357.229 1466952.313 1496767.534 1485614.607 1533072.314 1648508.835 0.939027392 0.916308137 0.948766753 0.8737334 0.889866212 0.907952389 0.901186925 0.929975188 1 20.65273019 -0.990066263 5.307906834 1.000000376 0.913726927 0.597334368 0.022355672 1.02E-07 1.93E-08 0.022114281 0.005212363 0.102313687 0.990066263 -0.086273449 DFEEYPEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFEEYPEHR 9 0 O14980 O14980 XPO1 Exportin-1 0 127.3 0.00044929 414110000 595670 536880 568490 571870 455500 462240 635520 518970 335030 FALSE TRUE 558388.078 576631.1538 581974.8513 586545.1524 419726.8674 595681.1842 540229.6759 583764.5469 279111.3286 2.000592669 2.065953957 2.085099355 2.101473829 1.503797318 2.134206401 1.935534751 2.091511476 1 18.09048116 -1.651560193 2.691935284 0.885158528 1.995919084 0.744899026 0.181999101 8849586.67 7831143.389 7022552.913 0.043600403 0.02230693 1.651560193 1.110760556 DFEPQPGNMSHPRPWLGLDHFNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFEPQPGNMSHPRPWLGLDHFNK 23 1 Q93009;A0A669KBL1;Q93009-3 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7 0 89.462 0.0037604 185390000 638960 622230 461670 389540 671210 308920 574360 574500 610050 FALSE TRUE 598968.6342 668300.5566 472621.0304 399536.2559 618495.8741 398100.1891 488240.0501 646227.5896 508228.7139 1.178541507 1.31496025 0.929937679 0.786134756 1.216963657 0.783309125 0.960669944 1.271529081 1 18.95511836 3.952836466 4.197029332 0.978962322 1.244284598 0.299415266 0.160108794 0.218133083 8.856180388 0.038345343 0.077766223 8970.90931 -3.952836466 0.265322276 DFEQDILEDMYHAIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 179.17 6.82E-07 49371000 140531 117288 133501 132339 112624 112719 197893 122378 100304 FALSE TRUE 131735.4156 125972.1256 136667.7068 135735.0428 103778.9653 145259.1455 168220.7818 137657.1627 83562.61441 1.576487482 1.507517763 1.635512576 1.624351317 1.24193057 1.73832696 2.013110564 1.647353468 1 16.35057001 DFESHITSYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DFESHITSYK 10 0 Q99613-2;Q99613;B5ME19;H3BPE3 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 ;;; 166.97 5.38E-06 1872630000 5050400 5435000 5856300 5577300 6316200 4638050 7387800 5626500 7438000 FALSE TRUE 4734304.479 5837413.055 5995214.202 5720422.96 5820151.13 5976979.743 6280067.975 6328980.91 6196549.749 0.764022669 0.942042474 0.967508443 0.923162597 0.939256742 0.964565764 1.013478182 1.021371758 1 22.56303371 5.441736309 1.264349931 0.974786218 6.65E-13 0.815710534 0.031221613 3.287861022 1.251358627 0.009258463 6.426053971 276526.2152 -5.441736309 -0.974786218 DFFELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFFELR 6 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 ; 159.42 0.02122 122432000 462160 469820 462800 467230 472110 361980 508980 479280 271820 FALSE TRUE 433234.2306 504605.9616 473777.8345 479219.9128 435032.385 466477.7497 432663.1741 539119.163 226451.486 1.913143686 2.228318174 2.092182493 2.116214476 1.921084258 2.059945634 1.910621925 2.380726983 1 17.78884248 -1.151489516 4.304191664 0.999760334 2.075888525 0.840409324 0.147599468 0.000313142 6.17E-05 0.131830875 0.031066097 0.070552188 1.151489516 1.07612819 DFFHGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFFHGLR 7 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 ; 107.32 0.0075045 706410000 1076440 1480590 1316870 1221050 1609060 988880 1352230 1296530 1475260 FALSE TRUE 1009067.542 1590214.424 1348106.778 1252384.21 1482690.918 1274353.603 1149475.665 1458404.625 1229029.575 0.821027876 1.293878077 1.096887174 1.0190025 1.206391569 1.036877898 0.935270955 1.186631025 1 20.2290882 2.028571124 24.69130272 1.021599974 1.114422096 0.002027571 0.137965326 427.9765292 369857.3381 0.048171251 0.035576226 106.7999682 -2.028571124 0.092822122 DFFQSYGNVVELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DFFQSYGNVVELR 13 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ;;; 247.13 7.04E-17 303501000 191282 166350 176846 175063 175779 173915 199972 169334 137008 FALSE TRUE 179310.0011 178666.7271 181040.8706 179555.413 161974.0264 224121.4372 169988.055 190475.7227 114140.4797 1.570958888 1.565323079 1.586123268 1.573108974 1.419076097 1.96355787 1.489288073 1.668783267 1 16.80045101 -1.556329719 6.417053481 0.999145776 1.600659435 0.637294579 0.143299736 0.001543405 0.00010671 0.122280278 0.028785413 0.027776037 1.556329719 0.601513659 DFGEEHPFYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFGEEHPFYDR 11 0 Q68CQ4 Q68CQ4 DIEXF Digestive organ expansion factor homolog 0 ; 126.76 0.00030066 546450000 680630 745390 713780 728670 801720 593720 917190 693140 901070 FALSE TRUE 638030.5833 800579.4512 730711.1987 747368.9058 738756.1452 765117.3258 779665.8743 779680.0548 750675.5959 0.849941821 1.06647859 0.973404761 0.995595048 0.984121702 1.01923831 1.038618917 1.038637807 1 19.51783006 2.14235204 4.116087373 1.029794749 0.987404106 0.149542483 0.054247269 0.471715476 14.76479417 0.019863018 0.014295398 138.7880393 -2.14235204 -0.042390644 DFIDNLDRPPGSSYFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFIDNLDRPPGSSYFR 16 1 Q3YEC7;G3V154;F2Z2T0;Q3YEC7-4;Q3YEC7-6;Q3YEC7-3 Q3YEC7 RABL6 Rab-like protein 6 0 ; 149.59 7.49E-07 138819000 139802 175962 114870 133043 172713 102333 149401 152781 140008 FALSE TRUE 131052.0424 188990.4096 117594.7706 136457.1086 159148.8177 131874.8759 126999.707 171856.0442 116639.7603 1.123562343 1.620291477 1.008187691 1.169902169 1.3644474 1.130616828 1.088820027 1.473391609 1 16.83170013 7.999145278 0.023891168 1.09E-07 2.881822651 0.087427329 0.195147187 4440.885078 8.16205226 344.0773289 697.9568251 99803386.61 -7.999145278 2.881822542 DFIEDYVDILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DFIEDYVDILR 11 0 Q9NRL2;Q9NRL2-2;A0A087WWN7 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 0 ;; 177.78 1.82E-05 56930900 120636 128565 144107 136383 139191 104588 159631 124419 149412 FALSE TRUE 113085.6081 138084.0864 147525.2861 139882.8187 128259.5003 134780.8578 135695.8135 139952.986 124474.172 0.908506611 1.109339264 1.185187929 1.123789911 1.030410553 1.082801802 1.090152369 1.124353622 1 16.92548689 -0.89310311 7.741318046 1.000000001 1.093083107 0.091877057 0.07361985 0 0 0.068804764 0.016217438 0.127907759 0.89310311 0.093083106 DFIGVDSTGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFIGVDSTGKR 11 1 Q9NR50-3;Q9NR50-2;Q9NR50 Q9NR50-3 EIF2B3 Translation initiation factor eIF-2B subunit gamma 0 ; 93.345 0.014942 285420000 332850 302600 323260 334210 365150 262100 410890 283240 460190 FALSE TRUE 312017.5127 325004.8189 330927.8799 342786.3944 336472.5919 337764.0152 349280.859 318603.1375 383381.3161 0.813856856 0.847732545 0.863182075 0.894113458 0.877644731 0.881013239 0.91105342 0.831034597 1 18.5484205 -5 0.133060312 1.427827513 0.816455553 0.699665327 0.028102801 76.1499529 0.634143104 8.751508023 0.184097601 1.00E-05 5 -0.61137196 DFIHTASISFLTPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFIHTASISFLTPLR 15 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39 B7ZC38 SH3GLB2 Endophilin-B2 0 ; 218.16 1.98E-12 153029000 208472 324200 227970 206105 377950 167038 231210 322290 239610 FALSE TRUE 195424.1097 348204.1053 233377.5561 211394.0032 348267.3316 215259.159 196542.2069 362528.6159 199617.5431 0.978992661 1.744356232 1.169123477 1.058995116 1.744672969 1.078357922 0.984593859 1.816116011 1 17.60687899 -4.04986329 0.240870242 3.40E-19 1.348171199 0.055549217 0.336135931 303.5939671 4.59964278 151.3489237 0.50117535 8.92E-05 4.04986329 1.348171199 DFKPGDLIFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFKPGDLIFAK 11 1 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 0 ; 126.95 0.00027072 715060000 2623100 2027900 2284100 2125800 2790500 1615870 3061600 2197200 3276400 FALSE TRUE 2458924.853 2178047.826 2338279.931 2180351.627 2571345.386 2082345.438 2602541.503 2471525.257 2729547.674 0.900854335 0.797951927 0.856654732 0.79879595 0.942040841 0.762890298 0.953469884 0.905470632 1 21.38023046 1.233488563 0.947537317 0.996442252 0.839557581 0.412380356 0.058444472 0.426288818 0.821853364 0.047315337 0.016705213 17.11940093 -1.233488563 -0.156884671 DFKPGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFKPGDR 7 1 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 0 ; 62.2 0.079245 701080000 1343190 1133420 1237170 1217330 1297680 920040 1523380 1122340 1422910 FALSE TRUE 1259122.136 1217339.596 1266516.257 1248568.749 1195765.447 1185640.612 1294963.311 1262466.62 1185417.129 1.062176432 1.026929312 1.068414 1.053273754 1.008729686 1.000188528 1.092411507 1.064997788 1 20.17696338 1.727041015 25 1.061094256 1.038735958 0.027597864 0.031439155 2.036120918 4398.722976 0.013840235 0.007674979 53.33852658 -1.727041015 -0.022358298 DFLDEHYDIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFLDEHYDIPK 11 0 Q8NEM2 Q8NEM2 SHCBP1 SHC SH2 domain-binding protein 1 0 61.435 0.087328 29588000 27768 19764 24208 22739 22068 18167 28885 17587 28784 FALSE TRUE 26030.05045 21227.34712 24782.22519 23322.52124 20334.8683 23411.51798 24553.96241 19782.77566 23979.76445 1.085500673 0.885219168 1.033464079 0.972591757 0.84800117 0.976303084 1.023945104 0.824977898 1 14.54952987 4.759179 23.93370485 0.953213169 1.085500905 0.266260241 0.072016922 4039.169437 4688510.373 0.016077196 0.646505751 57435.31405 -4.759179 0.132287736 DFLDEYIFLAVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFLDEYIFLAVGR 13 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ; 177.76 3.53E-05 233380000 510910 479820 550340 568880 637490 508860 550730 502080 503110 FALSE TRUE 478933.0551 515346.3721 563394.3247 583478.4239 587424.1069 655759.6213 468153.1492 564765.7932 419137.6908 1.142662819 1.22953956 1.344174807 1.392092472 1.401506283 1.564544625 1.116943571 1.347446926 1 18.67706474 0.342183725 1.065284772 0.999972164 1.320794003 0.36169053 0.131365301 3.361743687 4.428821007 0.127678565 0.038507553 2.198789856 -0.342183725 0.320821839 DFLFPHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFLFPHLR 8 0 Q9H2M9;F8WDJ2;Q9H2M9-2 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 75.38 0.038541 191160000 55962 75368 68068 68646 78868 48925 70968 68020 85327 FALSE TRUE 52459.43832 80948.32514 69682.6051 70407.57258 72674.02542 63048.85327 60327.00723 76512.44673 71085.37247 0.737977962 1.138747992 0.980266441 0.990464988 1.022348521 0.886945529 0.84865571 1.076345865 1 16.1172651 2.247491896 24.89294162 0.928639523 0.998042092 0 0.117113896 486.2519548 1355265.453 0.038332748 0.03162268 176.8039226 -2.247491896 0.06940257 DFLLKPELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFLLKPELLR 10 1 O00148;O00148-2;O00148-3;K7EQN7;K7EPJ3;A0A0G2JJL7;F6QYI9;K7EIL8;K7ENP6;K7EN69;K7EL56;F6SXL5;Q13838-2;Q13838;Q5STU3;F6WLT2;F6S4E6;A0A0A0MT12;F6TRA5;F6R6M7;F6U6E2;F6S2B7;A0A0G2JHN7 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ; 155.97 1.07E-05 5698600000 7903300 9457700 7222700 7200600 10417900 5096100 8167400 8853900 10093500 FALSE TRUE 7408646.561 10157957.95 7394025.855 7385379.587 9599720.158 6567261.342 6942774.192 9959328.905 8408829.643 0.881055614 1.20801091 0.879316881 0.878288644 1.141623813 0.780995884 0.825652854 1.184389425 1 23.00347359 3.83612484 6.5925639 0.935894967 1.063592287 0.040738025 0.15095646 0.45975891 24.50394244 0.036385788 0.066158798 6856.853014 -3.83612484 0.12769732 DFLLPFLEEPMDTEADLQFRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFLLPFLEEPMDTEADLQFRPR 22 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 231.77 8.35E-27 361920000 392510 468910 448890 440470 503150 404400 494160 400350 406380 FALSE TRUE 367943.4998 503628.5843 459537.8828 451773.2059 463634.6286 521143.7151 420065.2956 450334.5788 338552.5527 1.086813544 1.487593522 1.357360561 1.334425637 1.369461329 1.53932886 1.24076836 1.330176291 1 18.36902027 0.522173373 1.15041415 1.000442208 1.369356694 0.42596975 0.124084468 1.502201278 2.713698201 0.106761281 0.032728775 3.327923796 -0.522173373 0.368914486 DFLPIEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFLPIEIR 8 0 Q5VT06 Q5VT06 CEP350 Centrosome-associated protein 350 0 61.999 0.082414 248360000 58759 162040 99255 130220 149640 117110 97735 125100 96162 FALSE TRUE 55081.37908 174037.6102 101609.3755 133561.6657 137887.878 150917.7559 83080.54408 140719.0104 80111.94097 0.687555169 2.172430328 1.26834245 1.667187988 1.721190079 1.883835968 1.037055688 1.756529784 1 16.28972968 -1.21996196 5.045508019 0.999936507 1.547540887 0.125655919 0.430742172 0.000275238 4.26E-05 0.373132162 0.087937946 0.060261237 1.21996196 0.54760438 DFLTHVSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFLTHVSAR 9 0 O15067 O15067 PFAS Phosphoribosylformylglycinamidine synthase 0 ; 140.45 0.00010908 134727000 96045 239140 185822 199171 230850 183970 234060 217249 203972 FALSE TRUE 90033.7149 256846.1744 190229.7856 204282.0651 212719.9722 237079.1525 198964.8759 244373.0159 169927.7555 0.52983525 1.511502189 1.119474479 1.20217009 1.25182594 1.395176155 1.170879209 1.438099475 1 17.37456199 4.750588655 24.70058907 1.268316724 0.529834721 0.691049697 0.153604109 845.2820719 1735820.209 0.032773057 0.548816439 56310.40552 -4.750588655 -0.738482003 DFMHVLEHECQHHHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DFMHVLEHECQHHHSK 16 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;;;; 234.77 3.39E-20 2296570000 664800 1183790 1154740 1170580 1184800 924580 1287250 1171450 1105720 FALSE TRUE 623191.3547 1271439.043 1182130.978 1200619.065 1091750.587 1191491.237 1094238.813 1317708.111 921168.1888 0.676522879 1.380246364 1.283295486 1.303365747 1.185180514 1.293456777 1.187881677 1.43047505 1 19.81310507 4.745050685 24.98662441 1.270603522 0.676522609 0.702549372 0.118651434 367.1396637 1413442.394 0.024735959 0.237274246 55596.91386 -4.745050685 -0.594080912 DFMIQGGDFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFMIQGGDFTR 11 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ; 179.57 1.64E-05 474290000 410790 530030 366240 327980 357980 246680 471200 360500 531540 FALSE TRUE 385079.3872 569273.9727 374927.3858 336396.5221 329865.6948 317892.5115 400547.9344 405509.2186 442822.5401 0.869602047 1.285557805 0.846676381 0.759664406 0.744916225 0.717877892 0.904533754 0.915737529 1 18.75636913 3.737344135 4.723065419 0.82607203 1.099241662 0.353552003 0.131094033 0.154297433 9.216760736 0.03188353 0.055525051 5461.904913 -3.737344135 0.273169632 DFNDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFNDIR 6 0 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2;E9PCS8;O94776;O94776-2 Q9BTC8;O94776 MTA3;MTA2 Metastasis-associated protein MTA3;Metastasis-associated protein MTA2 0 107.66 0.072303 271970000 1243700 1172000 1355400 1210900 1259400 1075300 1372500 1146900 1095800 FALSE TRUE 1165859.037 1258776.099 1387550.728 1241973.744 1160491.804 1385721.654 1166706.367 1290092.99 912903.9009 1.27708846 1.378870326 1.519930769 1.360464933 1.271209164 1.517927191 1.27801663 1.413175021 1 19.80010347 -1.943749616 0.441820938 0.627105748 1.395057565 0.623382046 0.091310046 32.99618171 2.356085096 12.67173624 0.047676207 0.011382834 1.943749616 0.767951816 DFNGDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DFNGDFR 7 0 A0A2R8YFH5;Q15437 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;; 108.09 0.017056 2558240000 6205000 7195000 7170600 7273200 6899600 6210300 8369300 6161700 6248600 FALSE TRUE 5816640.126 7727725.286 7340690.018 7459842.625 6357733.248 8003112.794 7114401.162 6931001.809 5205668.293 1.117366647 1.484482847 1.410134032 1.433023045 1.221309713 1.537384317 1.366664329 1.331433626 1 22.31165195 0.704650681 2.468765252 1.000081581 1.387229127 0.460129571 0.122622419 1.3821739 10.49210999 0.104719869 0.028027013 5.065830809 -0.704650681 0.387147546 DFNHINVELSLLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DFNHINVELSLLGK 14 0 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ;; 207.72 9.04E-09 1562008000 5466100 5148180 5394080 5086090 5613850 3994205 6044500 4867220 5576610 FALSE TRUE 5123986.558 5529356.604 5522030.125 5216607.68 5172960.866 5147267.143 5138183.339 5474903.131 4645837.765 1.102919822 1.190174277 1.188597279 1.122856187 1.113461367 1.107930884 1.105975628 1.178453362 1 22.14750734 -4.999999999 0.167769906 0.446557849 1.178459769 0.55779257 0.037110611 93.60090222 0.878863538 17.22110042 0.140153957 1.00E-05 4.999999999 0.731901921 DFNLDGAPYGYTPFCDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFNLDGAPYGYTPFCDSR 18 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ; 80.632 0.011227 40944000 86412 82973 74278 82386 88933 67863 91281 70710 75978 FALSE TRUE 81003.62717 89116.40725 76039.90924 84500.16424 81948.56092 87453.94644 77594.26146 79538.29915 63296.78096 1.279743234 1.407913734 1.201323481 1.334983596 1.294671856 1.381649195 1.225880057 1.256593115 1 15.94984451 0.492764705 0.911739122 0.998867446 1.312313168 0.714299749 0.060658123 0.887817281 1.085451123 0.056422274 0.018095122 3.110030909 -0.492764705 0.313445722 DFNVGDYIQAVLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFNVGDYIQAVLDR 14 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ; 125.61 0.00020989 14559000 13283 16726.1 15940.2 14445.4 16707.2 10643 13225.1 13583.9 11157.6 FALSE TRUE 12451.64074 17964.51785 16318.30907 14816.09342 15395.08391 13715.46133 11242.11903 15279.87982 9295.324479 1.339559557 1.932640209 1.755539477 1.593929664 1.65621802 1.475522598 1.209438041 1.643824253 1 13.18228951 1.387164629 0.453641024 1.021990282 1.764922424 0.449295935 0.201855196 0.712784257 0.406135454 0.22050553 0.140052556 24.38735098 -1.387164629 0.742932142 DFPLNDLLSATELDKIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFPLNDLLSATELDKIR 17 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 228.3 1.35E-15 211100000 342080 385120 389360 433950 521350 276830 448340 382740 485720 FALSE TRUE 320669.8234 413634.6855 398595.8031 445085.8917 480405.274 356746.327 381115.5792 430525.9315 404650.1941 0.792461805 1.022203107 0.985037963 1.099927538 1.187211278 0.881616597 0.941839605 1.063945941 1 18.62631576 4.739723027 24.27811811 1.014971443 0.792461705 0.423170974 0.084054768 71.83776316 1500123.459 0.020453247 0.126272977 54919.05132 -4.739723027 -0.222509738 DFPLSGYVELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DFPLSGYVELR 11 0 O75489 O75489 NDUFS3 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial" 0 ;;; 146.11 8.36E-05 142302000 179239 211590 195166 184863 236739 178787 179493 197760 242825 FALSE TRUE 168020.7509 227256.3438 199795.4297 189606.8976 218146.4739 230399.9045 152579.691 222450.7713 202295.9388 0.830569076 1.123385596 0.987639351 0.937274859 1.078353205 1.138925012 0.75424001 1.099630436 1 17.62610783 1.76197155 25 0.926252989 1.024505745 0.042290672 0.123574173 26.21674776 28017.12142 0.051949489 0.028809489 57.80581782 -1.76197155 0.098252756 DFPWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFPWLR 6 0 Q96DT7-3;Q96DT7-2;Q96DT7 Q96DT7-3 ZBTB10 Zinc finger and BTB domain-containing protein 10 0 ; 110.54 0.066582 193601000 304980 568100 479120 515480 549810 571400 483640 413560 412810 FALSE TRUE 285891.8462 610162.7151 490484.9527 528708.0895 506630.1404 736353.9041 411122.6719 465193.8764 343909.3441 0.831300024 1.774196385 1.426204205 1.537347265 1.473150262 2.141127936 1.195439086 1.352664254 1 18.39166879 -0.561150007 6.758389381 1.000010743 1.500174366 0.148633174 0.342459887 0 0 0.29645566 0.069875269 0.274694518 0.561150007 0.500163623 DFPYEEDSRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFPYEEDSRPR 11 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 0 ; 184.03 4.64E-06 290170000 282540 317540 326110 275980 327510 273690 351230 293640 333070 FALSE TRUE 264856.3257 341050.992 333845.4832 283062.114 301788.6857 352699.86 298566.3222 330301.6004 277478.4653 0.954511282 1.229107966 1.203140153 1.020122818 1.087611197 1.271089126 1.075998175 1.190368413 1 18.08201628 -1.099363329 4.249802327 0.999985507 1.14158208 0.133773673 0.098637551 1.83E-05 3.88E-06 0.088777873 0.020922034 0.079549357 1.099363329 0.141596573 DFQDYMEPEEGCQGS(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFQDYMEPEEGCQGSPQR 18 0 O43237;O43237-2;B4E2E0;H3BUM4 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 DFQDYMEPEEGCQGS(1)PQR 194.15 1.56E-18 0 141930 152360 133540 143930 137900 127520 164970 125980 116350 TRUE FALSE 133046.8547 163640.8929 136707.6319 147623.4875 127069.8903 164332.9539 140234.28 141708.8803 96930.43335 1.372601463 1.688230283 1.41036852 1.52298388 1.310939051 1.695370053 1.446751811 1.461964787 1 16.56466208 0.471539955 1.703736143 1.000049715 1.506102506 0.607067245 0.123551116 2.278241405 6.654724787 0.105939758 0.029912913 2.961692431 -0.471539955 0.506052791 DFQDYMEPEEGCQGS(ph)PQRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 207.6 1.90E-16 2845950000 2220120 2376060 2299730 2328100 2579860 2028970 2730680 2188550 2308500 TRUE FALSE 2081166.652 2551985.955 2354280.682 2387842.987 2377248.202 2614700.701 2321239.884 2461795.285 1923196.437 1.082139407 1.32695023 1.224149877 1.241601192 1.236092246 1.359559872 1.20696973 1.280053997 1 20.8750747 -1.149687639 3.310716892 0.999617233 1.251675211 0.513992115 0.074501091 10123012.84 15220555.04 41197.44323 0.015710358 0.070845515 1.149687639 0.252057978 DFQEYVEPGEDFPAS(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFQEYVEPGEDFPASPQR 18 0 Q9Y6G9;E9PHI6;C9JGM7 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 DFQEYVEPGEDFPAS(1)PQR 220.36 7.16E-19 284460000 255590 234700 270160 256080 235960 241440 284220 223320 204110 TRUE FALSE 239593.0781 252077.4322 276568.3228 262651.4463 217428.6534 311139.8085 241603.8496 251201.9936 170042.7224 1.40901695 1.482435876 1.626463743 1.544620332 1.278670738 1.829774331 1.420842046 1.477287531 1 17.37553774 0.512148533 1.644384545 1.000188398 1.525526811 0.5495792 0.145060988 1.954979438 5.811965581 0.124215423 0.035318971 3.251984998 -0.512148533 0.525338413 DFQEYVEPGEDFPAS(ph)PQRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 211.68 7.22E-17 8523860000 1857830 2027350 2130680 2265320 2222080 1769920 2306170 1750880 2148940 TRUE FALSE 1741551.737 2177457.103 2181220.736 2323451.946 2047566.8 2280867.172 1960381.218 1969481.222 1790268.031 0.972788268 1.21627436 1.218376633 1.297823513 1.143720809 1.274036698 1.095021072 1.100104112 1 20.77174417 1.234361247 1.56577864 1.010798172 1.195675658 0.290179735 0.09128146 0.398353512 1.812957374 0.077672215 0.023451233 17.15383575 -1.234361247 0.184877486 DFQYIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 104.06 0.019163 170570000 200670 211940 220190 231680 231260 195530 247480 190640 208610 FALSE TRUE 188110.4229 227632.2581 225413.0108 237625.301 213097.7725 251976.3368 210372.6715 214441.8237 173791.6433 1.082390495 1.309799791 1.297030205 1.367299926 1.226168119 1.449876024 1.210487843 1.233901812 1 17.40699919 0.722492596 1.536544539 1.000851922 1.290857236 0.444359509 0.09683548 0.802543514 3.033525389 0.082104063 0.023781786 5.278282085 -0.722492596 0.290005314 DFS(ph)PEALKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DFSPEALKK 9 1 A0A087WZK9;B3KS98;O15372;E5RJT0;E5RGU4 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 1 DFS(1)PEALKK;DFS(1)PEALKK;DFS(1)PEALKK 122.7 0.00035432 571173000 836680 397372 552900 512490 565260 409580 724590 432470 826210 TRUE FALSE 784313.6923 426793.8363 566015.0491 525641.361 520866.7597 527819.097 615944.4563 486464.8315 688310.2135 1.139477051 0.620060298 0.822325513 0.763669274 0.756732574 0.766833161 0.894864618 0.706752307 1 19.39269939 -1.45037515 4.688946484 1.000540747 0.795753193 0.154047298 0.13778113 0.000689109 8.08E-05 0.118032915 0.027748117 0.035450703 1.45037515 -0.204787553 DFS(ph)PLQTQTFNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFSPLQTQTFNR 12 0 Q6P4F7-3;Q6P4F7 Q6P4F7-3 ARHGAP11A Rho GTPase-activating protein 11A 1 DFS(0.997)PLQT(0.003)QTFNR;DFS(1)PLQTQTFNR 124.62 0.00033534 132987000 191027 248560 228650 220640 228490 201365 243740 197552 224610 TRUE FALSE 179070.9611 266963.641 234073.686 226301.9959 210545.3171 259495.8066 207193.4498 222216.8021 187121.14 0.956978784 1.426688834 1.250920586 1.209387651 1.125181886 1.386779744 1.107269065 1.187555837 1 17.51361303 0.770151945 0.757408221 0.999207136 1.248892259 0.168394041 0.135904883 1.385286627 1.593452649 0.123930016 0.044758042 5.890497085 -0.770151945 0.249685123 DFSAFINLVEFCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFSAFINLVEFCR 13 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 136.01 0.00017976 140241000 176841 200513 198127 201767 258650 202330 215804 192829 190405 FALSE TRUE 165772.8375 215359.1912 202826.666 206944.6828 238336.6723 260739.3864 183446.1936 216904.1251 158625.1754 1.045060073 1.357660854 1.278653691 1.304614367 1.502514791 1.643745299 1.156475907 1.36740038 1 17.27526223 0.149137798 1.289621355 0.999579339 1.337487353 0.282760274 0.165307638 10.77760859 14.89339043 0.162693765 0.044831284 1.409736023 -0.149137798 0.337908014 DFSALESQLQDTQELLQEENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFSALESQLQDTQELLQEENR 21 0 P35579 P35579 MYH9 Myosin-9 0 ; 255.6 2.01E-36 58736000 40899 53039 51053 51585 52977 37578 55933 40937 51784 FALSE TRUE 38339.2046 56966.06275 52264.00127 52908.75843 48816.40012 48426.15857 47546.36591 46048.07456 43140.91586 0.888697049 1.320464844 1.21147176 1.226417135 1.131556879 1.122511138 1.102117675 1.067387505 1 15.39676918 1.563817421 0.839793811 1.009809615 1.193358631 0.135932792 0.112145779 0.788875394 1.116165354 0.095915554 0.039409748 36.62835549 -1.563817421 0.183549015 DFSAPTLEDHFNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFSAPTLEDHFNK 13 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 0 ; 225.63 1.21E-11 664350000 623610 501530 512500 542860 586500 439980 692980 496950 707830 FALSE TRUE 584579.3633 538663.803 524656.742 556790.7067 540438.6558 566995.0835 589074.0823 558995.3014 589688.6002 0.991335703 0.913471624 0.889718305 0.944211413 0.916481437 0.961516101 0.998957894 0.947949988 1 19.16959378 2.087927734 4.100603338 0.98193422 0.923714342 0.36849068 0.030023908 0.199021814 6.31620219 0.01178122 0.008263257 122.4412442 -2.087927734 -0.058219878 DFSASYFSGEQEVT(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DFSASYFSGEQEVTPSR 17 0 P49454 P49454 CENPF Centromere protein F 1 DFSASYFSGEQEVT(0.994)PS(0.006)R;DFSASYFSGEQEVT(0.934)PS(0.066)R;DFSASYFSGEQEVT(0.998)PS(0.002)R 388.46 8.77E-121 304067000 166006 172372 173016 171729 170455 135508 203433 156978 202346 TRUE FALSE 155615.9808 185134.6022 177120.0212 176135.8569 157068.1519 174626.9598 172930.1102 176577.0489 168573.1454 0.923136247 1.09824493 1.050701289 1.044863086 0.931750734 1.035912093 1.025846138 1.0474803 1 17.3630152 DFSDITKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFSDITKK 8 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 105.4 0.0070485 527720000 1326400 905130 1133200 1167600 1209500 946010 1464700 881590 1985700 FALSE TRUE 1243382.992 972146.767 1160080.039 1197562.593 1114510.749 1219107.73 1245081.833 991658.4521 1654273.842 0.751618602 0.587657704 0.701262397 0.723920407 0.673715996 0.736944331 0.752645542 0.599452417 1 20.65776664 -5 0.333443345 4.198035357 0.67793489 0.712753471 0.060599331 193.2096474 1.656365359 438.7703281 0.048010188 1.00E-05 5 -3.520100467 DFSDKINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFSDKINR 8 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 153.08 0.00040744 594880000 656080 847930 768000 818510 1011940 653990 1091570 675190 1596700 FALSE TRUE 615017.1239 910711.6195 786217.3227 839514.3523 932466.3144 842786.2964 927899.2121 759488.9578 1330200.455 0.462349206 0.684642391 0.591051762 0.631118678 0.700996839 0.633578415 0.697563445 0.570958275 1 20.34321224 -5 0.265111271 3.439077423 0.603801931 0.738884979 0.070736499 97.44960996 0.952453963 129.8612747 0.080588788 1.00E-05 5 -2.835275491 DFSELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFSELR 6 0 Q14320;B0S8I6 Q14320 FAM50A Protein FAM50A 0 ; 119.7 0.04836 405670000 1058710 1613920 1397800 1387420 1604710 1238140 1348270 1425760 1370490 FALSE TRUE 992447.231 1733416.316 1430956.476 1423023.546 1478682.55 1595570.918 1146109.43 1603769.274 1141746.365 0.869236164 1.518214876 1.253305042 1.246356975 1.295105984 1.39748281 1.003821396 1.40466335 1 20.12281077 -0.452565173 0.423898553 0.940372792 1.282618596 0.10766177 0.194139769 14.81965375 2.564944398 1.498700454 0.109279182 0.35272385 0.452565173 0.342245804 DFSESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DFSESR 6 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;;; 132.96 0.034132 5953090000 9560890 9977140 10199280 9776200 10219560 8567290 11082110 9561140 9672180 FALSE TRUE 8962490.962 10715857.83 10441211.74 10027073.84 9416956.981 11040527.54 9420450.487 10754869.38 8057830.673 1.112270948 1.329868827 1.295784456 1.24438875 1.16867149 1.370161274 1.169105044 1.334710273 1 22.94196006 -1.297051743 3.582965985 0.999216592 1.259525217 0.475334137 0.083332817 14071752.91 17808016 111906.7034 0.01796257 0.050460117 1.297051743 0.260308624 DFSETYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFSETYER 8 0 O94992;Q96MH2 O94992;Q96MH2 HEXIM1;HEXIM2 Protein HEXIM1;Protein HEXIM2 0 ; 119.41 0.0039554 554360000 720390 712110 737090 701140 793590 597640 791170 670870 772220 FALSE TRUE 675302.0758 764835.3653 754574.1229 719132.4394 731264.6426 770168.9661 672541.4034 754629.5963 643331.4933 1.049695348 1.188866663 1.172916499 1.117825642 1.136684043 1.197157257 1.045404135 1.173002727 1 19.29520279 -0.321952804 0.42846909 0.972195423 1.150612236 0.351787072 0.054668557 6.683565411 1.283288525 0.341578925 0.031002797 0.476482764 0.321952804 0.178416813 DFSGGWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DFSGGWR 7 0 Q9UG63;Q9UG63-2;C9JHK9;C9JZV3 Q9UG63 ABCF2 ATP-binding cassette sub-family F member 2 0 ;; 118.69 0.011517 953820000 758180 876690 870460 808810 955730 765300 977200 821470 924420 FALSE TRUE 710726.8672 941601.0398 891107.7223 829565.4339 880670.821 986229.6864 830677.9319 924032.3378 770128.33 0.922868098 1.222654723 1.157089913 1.077178181 1.143537754 1.280604346 1.078622743 1.199842029 1 19.55473934 -0.95057153 4.13318008 0.999993553 1.14512796 0.152788891 0.097720156 4696584.682 2272845.304 261.5718842 0.020357377 0.112054285 0.95057153 0.145134408 DFSHDDTLDVPTQVELLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFSHDDTLDVPTQVELLIK 19 0 P42345;B1AKP8 P42345 MTOR Serine/threonine-protein kinase mTOR 0 113.54 0.00017503 50437000 71571 65853 71062 70287 85360 58809 91142 73977 99469 FALSE TRUE 67091.49887 70728.82464 72747.6242 72090.68342 78656.16993 75786.20362 77476.10322 83213.19129 82866.98131 0.809628851 0.853522398 0.877884328 0.869956674 0.949185896 0.914552484 0.934945403 1.0041779 1 16.33850975 2.998635299 0.288612288 1.014858814 0.775886501 0.874399238 0.022095717 0.982470178 0.149463453 0.0296853 0.080244584 996.8625915 -2.998635299 -0.238972314 DFSHPCTWQVLDGAEDTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFSHPCTWQVLDGAEDTLR 19 0 Q9BSH5 Q9BSH5 HDHD3 Haloacid dehalogenase-like hydrolase domain-containing protein 3 0 151.95 6.06E-08 102730000 68062 73306 68417 63858 82036 56945 62062 69558 75556 FALSE TRUE 63802.12091 78733.65251 70039.88355 65496.70439 75593.22348 73384.09708 52756.37926 78242.46942 62945.21549 1.013613512 1.250828231 1.112711792 1.040535073 1.200936765 1.165840747 0.838131681 1.243024888 1 15.9418091 DFSNSPLHR ddPTM_SK-BR-3_Pertuzumab_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 ; 174.41 5.47E-05 678630000 503020 835930 687750 735160 880210 667530 833100 738170 815070 FALSE TRUE 471536.8761 897823.127 704063.7548 754025.4502 811081.8572 860235.0746 708184.3891 830332.1494 679029.5514 0.694427621 1.322215101 1.03686762 1.110445707 1.194472104 1.266859554 1.042936037 1.222821816 1 19.37311484 4.752181332 24.98635019 1.151689236 0.694427314 0.650411994 0.104857271 1403.082955 2573822.626 0.022997877 0.464246463 56517.29037 -4.752181332 -0.457261922 DFSSMKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFSSMKK 7 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ; 94.302 0.022929 1435640000 1246160 1374280 1244080 1332090 1758090 928430 1739710 1344530 2595000 FALSE TRUE 1168165.07 1476033.121 1273590.165 1366273.685 1620016.703 1196452.669 1478856.636 1512397.53 2161877.736 0.540347426 0.682755133 0.589112948 0.631984715 0.749356301 0.553432162 0.684061181 0.699575885 1 21.0438535 -4.999999996 0.253188277 3.240974987 0.609891637 0.784436493 0.060672758 78.42896753 0.775792725 90.952534 0.076849878 1.00E-05 4.999999996 -2.63108335 DFSSVFQFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFSSVFQFLR 10 0 P31937 P31937 HIBADH "3-hydroxyisobutyrate dehydrogenase, mitochondrial" 0 ; 166.07 1.32E-05 89838000 123258 244840 110318 108333 292950 90952 137169 215436 182167 FALSE TRUE 115543.5018 262968.2084 112934.7951 111113.0082 269942.8887 117208.3659 116601.7819 242333.6588 151762.1509 0.761345969 1.732765428 0.744156527 0.732152303 1.778723398 0.772316189 0.76831925 1.596799053 1 17.21145251 3.95649023 23.82956412 1.026791587 1.306695114 0.025486196 0.43053325 601.7593119 695054.3485 0.102721416 0.185507169 9046.700853 -3.95649023 0.279903526 DFSWSPGGNIIAFWVPEDKDIPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFSWSPGGNIIAFWVPEDKDIPAR 24 1 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ; 180.66 3.18E-17 561650000 659890 706850 533020 505470 862190 529040 944930 677970 776670 FALSE TRUE 618588.6628 759185.9095 545663.4861 518441.216 794477.0753 681765.2598 803246.5188 762616.0469 647038.7595 0.956030305 1.173323697 0.843324265 0.801252179 1.227866281 1.053669892 1.241419478 1.178624983 1 19.30349261 2.720439614 24.99884589 1.154933082 0.965096389 0.38518936 0.121441874 899.3050815 1240635.762 0.039455005 0.037264586 525.3389654 -2.720439614 -0.189836693 DFSYNYFGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFSYNYFGFK 10 0 P23921 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 135.43 0.00033597 119820000 197800 214250 185470 192690 249310 147860 200670 202860 195370 FALSE TRUE 185420.0511 230113.2929 189869.436 197634.7516 229730.1983 190544.7817 170581.3964 228187.5175 162761.4849 1.139213317 1.413806793 1.166550159 1.214259945 1.411453075 1.170699455 1.048045221 1.401974907 1 17.31239982 -5 0.164980184 0.073516085 1.303254212 0.225991588 0.130203025 182.2944778 1.699774432 55.13541485 0.483984907 1.00E-05 5 1.229738128 DFT(ph)PVCTTELGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFTPVCTTELGR 12 0 P30041 P30041 PRDX6 Peroxiredoxin-6 1 DFT(1)PVCTTELGR 124.45 0.0036079 68894000 70786 56375 58529 59756 57086 43871 70894 49052 82932 TRUE FALSE 66355.63062 60549.06366 59917.33552 61289.44013 52602.69583 56535.84551 60264.10285 55176.25018 69090.11344 0.960421503 0.876378119 0.86723458 0.887094218 0.761363576 0.818291398 0.872253639 0.798612818 1 16.07619166 7.999998706 0.796359223 0.847888942 28.14499825 0.19028347 0.063613179 697.070806 2.43733152 0.018852807 34319.01546 99999702.13 -7.999998706 27.29710931 DFTNEAPPAPLPDAS(ph)ASPLSPHRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFTNEAPPAPLPDASASPLSPHRR 24 1 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 DFTNEAPPAPLPDAS(0.333)AS(0.333)PLS(0.333)PHRR;DFTNEAPPAPLPDAS(0.333)AS(0.333)PLS(0.333)PHRR 66.383 0.017318 618960000 434500 476710 497560 511770 527600 398620 490940 394750 493490 TRUE FALSE 407305.4206 512006.1044 509362.3582 524902.8846 486164.4242 513695.1229 417328.1047 444035.4065 411123.3309 0.990713467 1.245383236 1.238952693 1.27675285 1.182526964 1.249491538 1.015092244 1.08005402 1 18.64921172 1.718291048 7.316934873 1.037340002 1.210066255 0.467580541 0.08227917 0.098506883 13.52187552 0.037748372 0.019779151 52.27463968 -1.718291048 0.172726253 DFTNEAPPAPLPDASAS(ph)PLSPHRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFTNEAPPAPLPDASASPLSPHRR 24 1 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 DFTNEAPPAPLPDAS(0.084)AS(0.458)PLS(0.458)PHRR 109.05 0.0010433 603310000 359260 372340 423590 391100 426200 295630 374660 335020 394490 TRUE FALSE 336774.5579 399908.441 433637.7548 401136.2881 392727.9712 380973.5818 318483.2112 376847.9845 328647.0705 1.024730138 1.216832514 1.31946332 1.22056858 1.19498394 1.159217945 0.969073635 1.146664669 1 18.3261796 1.944072463 4.68296573 1.038821557 1.21415092 0.404581244 0.085359117 0.18960195 8.473743417 0.038123872 0.022899528 87.9169195 -1.944072463 0.175329363 DFTNEAPPAPLPDASASPLS(ph)PHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DFTNEAPPAPLPDASASPLSPHR 23 0 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 DFTNEAPPAPLPDASAS(0.017)PLS(0.983)PHR;DFTNEAPPAPLPDAS(0.001)AS(0.013)PLS(0.987)PHR;DFTNEAPPAPLPDASAS(0.003)PLS(0.997)PHR;DFTNEAPPAPLPDASAS(0.003)PLS(0.997)PHR 199.8 1.64E-24 976270000 1457980 1455810 1570050 1583130 1617640 1199130 1485080 1215800 1472140 TRUE FALSE 1366727.634 1563599.687 1607292.327 1623755.796 1490597.08 1545299.365 1262406.041 1367595.306 1226430.324 1.114394848 1.274919298 1.310545162 1.323969055 1.215394834 1.259997682 1.029333682 1.115102326 1 20.22603384 1.753597356 6.503807107 1.055515682 1.261645373 0.679775271 0.064791764 0.083952746 9.925784308 0.030369689 0.016207443 56.70186658 -1.753597356 0.206129691 DFTNEAPPAPLPDASASPLS(ph)PHRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFTNEAPPAPLPDASASPLSPHRR 24 1 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 DFTNEAPPAPLPDASASPLS(0.999)PHRR 238.89 1.06E-37 934810000 226590 230110 315330 314610 318280 230650 280830 242220 298320 TRUE FALSE 212408.1364 247147.5838 322809.7765 322683.4252 293283.5727 297234.9107 238722.1486 272461.7002 248528.4648 0.854663214 0.994443771 1.298884523 1.298376126 1.18008041 1.195979346 0.960542483 1.096299776 1 17.92305157 -0.915630323 6.711488661 0.999999994 1.116432655 0.053242695 0.143326523 1.28E-08 2.23E-09 0.143305375 0.033777399 0.121442214 0.915630323 0.116432661 DFTPAELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DFTPAELR 8 0 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 0 ;;; 132.29 0.0022538 866190000 1287850 1931380 1403460 1383190 2092080 1301040 1541270 1872090 1577960 FALSE TRUE 1207245.767 2074381.385 1436750.734 1418684.997 1927776.476 1676629.127 1310170.872 2105824.557 1314588.282 0.918345146 1.577970391 1.092928298 1.079185793 1.466448851 1.275402459 0.996639701 1.601889037 1 20.3261796 -1.675047267 2.838842894 0.970221138 1.249707296 0.09952882 0.23732938 142044706.9 140383265.8 30841730.2 0.052018005 0.02113259 1.675047267 0.279486158 DFTPVCTTELGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DFTPVCTTELGR 12 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;; 173.64 7.57E-05 2642980000 803288 885830 832048 816834 899979 712059 963900 826082 1095150 FALSE TRUE 753011.638 951417.7749 851784.5715 837795.3433 829298.2797 917618.874 819372.1434 929220.1561 912362.3901 0.8253427 1.042806877 0.933603337 0.918270363 0.908957108 1.005761399 0.89807751 1.018477051 1 19.79924745 1.21635172 24.99626469 1.009238613 0.944083569 0.203450458 0.059579201 467.9554708 526673.2464 0.05228468 0.013113084 16.45703984 -1.21635172 -0.065155044 DFTSEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFTSEPR 7 0 P41091;Q2VIR3;Q2VIR3-2 P41091 EIF2S3;EIF2S3L Eukaryotic translation initiation factor 2 subunit 3;Putative eukaryotic translation initiation factor 2 subunit 3-like protein 0 ; 104.45 0.042826 0 2038310 2122800 2107300 2022570 2341800 1842640 2414400 1863100 2239100 FALSE TRUE 1910735.816 2279974.321 2157286.151 2074472.57 2157884.474 2374580.255 2052383.134 2095712.136 1865379.745 1.024314658 1.222257466 1.156486317 1.112091292 1.156807069 1.272974182 1.100249501 1.123477481 1 20.83103793 0.828158528 1.553106624 1.001237778 1.161345633 0.321954672 0.067059703 0.67049812 2.998469128 0.058126115 0.016875469 6.732223545 -0.828158528 0.160107855 DFTVSALHGDMDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DFTVSALHGDMDQK 14 0 Q14240;Q14240-2;E7EQG2 Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ;;; 250.89 1.34E-18 1853060000 2707810 2355410 2502880 2552020 3022110 1833800 3104520 2566110 3796240 FALSE TRUE 2538333.006 2529807.007 2562249.496 2617509.154 2784765.671 2363188.291 2639026.047 2886494.482 3162623.019 0.802603722 0.799907859 0.810165954 0.827638684 0.880524063 0.747224148 0.83444218 0.912690025 1 21.59269017 1.058567303 2.453286763 0.998321647 0.811649502 0.786347697 0.032638663 0.109397534 1.370213863 0.028829361 0.007874395 11.44372211 -1.058567303 -0.186672145 DFTVSAMHGDMDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 18 DFTVSAMHGDMDQK 14 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QL52 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;;;;;;;;;;;;;;;;; 293.6 1.51E-43 17882220000 19245533 16922741 20449789 19368006 20251458 15767299 25284230 17525462 23060345 FALSE TRUE 18040989.44 18175718.35 20934867.65 19865021.82 18660990.18 20319062.26 21493094.44 19713554.51 19211424.44 0.939076095 0.946089053 1.089709288 1.034021287 0.971348597 1.057655163 1.11876631 1.026137055 1 24.19546116 4.143919004 3.385130811 1.049555137 0.940216199 0.488384804 0.04200866 0.193558567 4.264962878 0.011130063 0.028465872 13928.97004 -4.143919004 -0.109338939 DFVAEPMGEKPVGSLAGIGEVLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DFVAEPMGEKPVGSLAGIGEVLGK 24 1 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 ;; 235.57 1.99E-37 347300000 1359487 972166 1076545 1034256 1156655 821720 1421315 971690 1494760 FALSE TRUE 1274399.135 1044146.182 1102081.156 1060796.76 1065815.982 1058937.224 1208202.011 1093007.635 1245274.899 1.023387797 0.838486492 0.885010335 0.851857498 0.855888112 0.850364225 0.970229153 0.877723976 1 20.24803283 0.798253198 0.817398149 0.997084294 0.880301011 0.212455224 0.059953869 1.181242371 1.582587831 0.053473451 0.018828548 6.284246293 -0.798253198 -0.116783282 DFVDDDDDDDLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFVDDDDDDDLER 13 0 G3V4K3;Q9H9C1;Q9H9C1-2 G3V4K3 VIPAS39 Spermatogenesis-defective protein 39 homolog 0 ; 345.97 1.90E-75 1020050000 1051270 1067620 1046700 1123280 1116740 913170 1294780 953780 1123960 FALSE TRUE 985472.8873 1146667.696 1071528.218 1152105.267 1029035.745 1176787.355 1100639.759 1072861.533 936363.8149 1.052446572 1.224596335 1.144350306 1.230403448 1.098970004 1.256762955 1.175440295 1.145774234 1 19.83670966 -1.209324947 6.090973584 0.999997349 1.173505305 0.410291752 0.062015255 1.91E-06 2.48E-07 0.051490908 0.012136338 0.061755416 1.209324947 0.173507956 DFVDHIDLVDPVDGVVLVDPEYLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DFVDHIDLVDPVDGVVLVDPEYLK 24 0 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 ;;; 188.69 1.59E-17 349415000 668600 456099 567001 514050 624702 438811 667066 552803 872800 FALSE TRUE 626753.5195 489869.0445 580450.5315 527241.3933 575640.4248 565488.6122 567045.646 621821.6714 727124.0415 0.861962311 0.673707671 0.798282684 0.725105158 0.791667435 0.777705838 0.779847198 0.855179634 1 19.47184197 0.80277923 1.143176488 1.000605178 0.759452816 0.684521274 0.049169721 0.381363544 0.929973373 0.041654131 0.013012314 6.350080484 -0.80277923 -0.241152362 DFVEHSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFVEHSAR 8 0 Q16822;H0YM31;Q16822-2 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 104.2 0.0079289 0 135410 163600 116980 115470 185480 94170 121140 145690 181650 FALSE TRUE 126934.9298 175713.1142 119754.8208 118433.1557 170913.149 121355.3503 102976.1816 163879.7172 151331.4415 0.838787555 1.161114389 0.791341308 0.782607729 1.129396161 0.801917626 0.680467856 1.082919158 1 17.20735224 3.921530908 8.017672872 0.870730564 1.016883393 0.048662914 0.161992599 0.515660815 67.30513489 0.039596482 0.071965552 8347.009497 -3.921530908 0.146152829 DFVNYLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFVNYLVR 8 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 128.61 0.0026201 485550000 466740 1229540 412270 408080 1221650 271940 406080 1054720 740970 FALSE TRUE 437527.5766 1320576.421 422049.2391 418552.0237 1125706.537 350444.6634 345192.0739 1186404.114 617297.3202 0.708779323 2.139287468 0.683704959 0.678039593 1.823605093 0.567708059 0.559199048 1.921933038 1 19.235606 3.873088271 7.140962544 0.980467927 1.50893269 0.060232948 0.592834924 0.442370902 26.43268977 0.141258878 0.256535807 7466.004899 -3.873088271 0.528464764 DFVSEQLTSLLVNGVQLPALGENKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFVSEQLTSLLVNGVQLPALGENKK 25 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 186.28 2.52E-17 79770000 317160 225855 270900 272100 274660 191607 341790 239374 355800 FALSE TRUE 297309.5217 242577.5392 277325.8759 279082.5467 253089.3115 246920.8304 290541.7625 269260.3708 296414.6814 1.00301888 0.818372214 0.935601012 0.941527408 0.853835277 0.833024968 0.980186815 0.908390804 1 18.17725738 1.04158308 1.141301575 0.994460478 0.896428136 0.170793635 0.060724447 0.758405427 2.065582412 0.053101599 0.016938468 11.00482345 -1.04158308 -0.098032342 DFVTTAEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFVTTAEDR 9 0 Q9Y263;E5RIM3;H0YAU9 Q9Y263 PLAA Phospholipase A-2-activating protein 0 ; 106.04 0.0069793 241290000 386030 385080 400670 415440 434770 344150 443040 338660 438530 FALSE TRUE 361869.0714 413591.7239 410174.0816 426100.8937 400624.918 443500.5182 376610.265 380942.4465 365336.51 0.990508918 1.132084291 1.122729512 1.166324422 1.096591518 1.213950717 1.03085855 1.042716608 1 18.47886641 1.604945604 12.33904791 1.026936127 1.122952183 0.383514896 0.057211436 0.076239894 55.23915984 0.026503371 0.013187844 40.2666597 -1.604945604 0.096016056 DFWEQEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DFWEQEVR 8 0 Q16822;Q16822-3;H0YML5 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 ;; 115.49 0.0057067 177100000 231662 287236 210001 208353 346018 182144 210576 254766 340152 FALSE TRUE 217162.6889 308503.2523 214982.3229 213699.6907 318843.142 234726.0159 179002.0837 286574.0959 283378.4337 0.766334566 1.088661717 0.758640381 0.754114164 1.125149638 0.828312913 0.631671512 1.011277013 1 18.11237044 2.0275506 24.99634586 0.812540829 0.905340986 0 0.167659198 621.3354102 563728.0741 0.059703881 0.044093429 106.5492998 -2.0275506 0.092800157 DFYELEPEKFQNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFYELEPEKFQNK 13 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 172.99 2.05E-05 183706000 174174 132680 153013 146715 162131 111596 187484 139310 209768 FALSE TRUE 163272.7602 142503.7653 156642.5406 150479.9553 149397.8853 143811.9536 159372.5147 156703.1602 174756.3656 0.934287914 0.815442486 0.896348125 0.861084257 0.85489238 0.82292827 0.911969725 0.896695005 1 17.41498548 0.786880194 1.152533137 0.999104626 0.863328457 0.560561545 0.036123644 0.520941674 1.270908256 0.03081336 0.009593052 6.121814901 -0.786880194 -0.13577617 DFYFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DFYFGK 6 0 Q15691;Q15555-4;Q15555-5;Q15555-3;Q15555 Q15691;Q15555-4 MAPRE1;MAPRE2 Microtubule-associated protein RP/EB family member 1;Microtubule-associated protein RP/EB family member 2 0 ; 103.71 0.080148 1625510000 2186500 2144400 2204940 2153460 2333700 1754310 2590900 1939740 2541500 FALSE TRUE 2049650.868 2303173.607 2257242.218 2208721.429 2150420.616 2260750.818 2202418.598 2181920.809 2117307.231 0.968046034 1.08778432 1.066091016 1.043174744 1.015639386 1.067748121 1.040197929 1.030516864 1 21.0137992 0.91524365 1.740097034 1.000156634 1.048941763 0.103367775 0.033134107 0.787896028 4.848795956 0.029715555 0.008480398 8.227040778 -0.91524365 0.048785129 DFYLATS(ph)PPDSFLDDHHLTRPHPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DFYLATSPPDSFLDDHHLTRPHPER 25 1 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 1 DFYLAT(0.037)S(0.962)PPDS(0.001)FLDDHHLTRPHPER;DFYLAT(0.042)S(0.958)PPDSFLDDHHLTRPHPER;DFYLAT(0.016)S(0.981)PPDS(0.003)FLDDHHLTRPHPER;DFYLAT(0.029)S(0.97)PPDSFLDDHHLTRPHPER;DFYLAT(0.023)S(0.977)PPDSFLDDHHLTRPHPER;DFYLAT(0.009)S(0.991)PPDSFLDDHHLTRPHPER 154.88 3.53E-08 2101212000 519569 728649 752493 848646 892104 677527 795912 723747 834213 TRUE FALSE 487050.1037 782598.9301 770342.4893 870423.6931 822041.7504 873118.0462 676572.3845 814108.4061 694977.4611 0.700814244 1.126078145 1.108442406 1.252448809 1.182832245 1.256325701 0.973517017 1.171416991 1 19.40660666 4.738788978 6.479392719 1.134179651 0.692010181 0.683739925 0.092580547 0.068230653 17.23364453 0.021151281 0.132392065 54801.06244 -4.738788978 -0.442169471 DFYLATSPPDSFLDDHHLTRPHPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DFYLATSPPDSFLDDHHLTRPHPER 25 1 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 0 67.413 0.014645 67651000 8316.9 11889 13446 12077 13079 9175.9 14040 11832 12860 FALSE TRUE 7796.360075 12769.27393 13764.94547 12386.91627 12051.8281 11824.83337 11934.83234 13309.25125 10713.58292 0.727708007 1.19187708 1.28481252 1.156188024 1.124911077 1.103723512 1.113990756 1.242278269 1 13.38715342 4.740701098 24.87959211 1.165094026 0.727707846 0.738218054 0.079116771 92.64659178 1076787.107 0.018926998 0.125537203 55042.87355 -4.740701098 -0.43738618 DGADFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 ;;;;;; 145.04 0.0053813 12046650000 21584580 20388440 20509130 19484770 20786000 14406130 26303200 17619880 23759650 FALSE TRUE 20233639.67 21898021.31 20995616.25 19984782.19 19153551.41 18564945.87 22359279.35 19819760.8 19794010.92 1.02221019 1.106295303 1.0607055 1.009637828 0.967643773 0.937907226 1.129598212 1.001300893 1 24.23856064 3.329133623 4.513324186 1.015335442 1.073776523 0.179269407 0.053270376 0.359545529 13.01108735 0.015564858 0.021242631 2133.701307 -3.329133623 0.058441081 DGAGFLINLIDSPGHVDFSSEVTAALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DGAGFLINLIDSPGHVDFSSEVTAALR 27 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;; 312.62 4.68E-82 2863016000 938010 1248732 1194798 1171211 1314700 1038756 1305323 1099408 1117114 FALSE TRUE 879301.6285 1341189.417 1223139.173 1201266.257 1211448.765 1338627.994 1109601.934 1236671.509 930660.4566 0.944814645 1.441115723 1.314270059 1.290767485 1.301708649 1.43836346 1.192273644 1.328810631 1 19.82789538 -0.752692876 11.89778322 1 1.29870099 0.277148993 0.140463859 0 0 0.120648065 0.028437022 0.176728717 0.752692876 0.29870099 DGAHVVISSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 15 DGAHVVISSR 10 0 Q13268;C9JZP6;Q13268-2 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;;;;;;;;;;;;;; 188.99 1.06E-06 84036025400 11500337.7 11137594.2 10677791.8 10059868.6 13280521.2 10660458.4 10761083.6 10889368.4 14000406.4 FALSE TRUE 10780552.09 11962233.26 10931074.06 10318021.86 12237522.64 13737959.68 9147559.015 12248930.02 11663648.13 0.924286465 1.025599635 0.937191687 0.884630756 1.049201974 1.177844147 0.784279405 1.050180002 1 23.47551577 2.722062337 24.37728209 0.995110061 0.955749965 0.082578248 0.102791667 2659.294944 3929273.262 0.033289119 0.031478248 527.3055429 -2.722062337 -0.039360096 DGASS(ph)SPESASR ddPTM_SK-BR-3_Pertuzumab_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(0.059)S(0.471)S(0.471)PESASR 70.488 0.049453 18106000 50262 65798 57820 61700 67400 57226 64555 62827 70015 TRUE FALSE 47116.19114 70669.75238 59191.5177 63283.32646 62106.67588 73746.21721 54875.57705 70671.08925 58329.04419 0.807765527 1.211570554 1.014786348 1.084936798 1.064764162 1.264313829 0.940793353 1.211593473 1 15.83192681 4.753915105 24.2239102 1.095409726 0.807765203 0.439488069 0.103321941 1668.473109 2632187.352 0.021889876 0.506460419 56743.36744 -4.753915105 -0.287644523 DGATILTHAYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGATILTHAYSR 12 0 F5H0D0;Q14232-2;Q14232 F5H0D0 EIF2B1 Translation initiation factor eIF-2B subunit alpha 0 150.69 0.00035767 0 188490 247200 228180 220200 270460 197870 271150 219490 197160 FALSE TRUE 176692.7474 265502.9452 233592.5374 225850.7048 249219.1626 254991.8568 230493.5747 246893.8097 164252.7223 1.075737101 1.616429497 1.422153217 1.375019553 1.517290911 1.552436107 1.403286177 1.503133745 1 17.32555776 -1.548988851 4.679135738 0.996500724 1.451149643 0.45777213 0.147013024 0.004747033 0.000457556 0.1259107 0.029491219 0.028249525 1.548988851 0.454648919 DGAWGAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DGAWGAFR 8 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;; 199.65 0.0002936 8874170000 2403805 9422850 2060940 2027534 10422350 1273084 2028425 8638570 6143870 FALSE TRUE 2253355.136 10120527.62 2109826.47 2079563.955 9603820.673 1640602.684 1724281.502 9717114.48 5118418.406 0.440244419 1.977276341 0.412202814 0.40629034 1.876325832 0.320529225 0.336877794 1.898460366 1 22.28726665 3.954438856 23.75301584 0.820164372 1.303072239 0.022628474 0.693660876 531.9598972 557069.0932 0.16539882 0.298515571 9004.069857 -3.954438856 0.482907867 DGCLYEVAYQAEAGWFSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGCLYEVAYQAEAGWFSQR 19 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 61.212 0.07696 0 12761 13782 12626 14230 13065 10572 15080 10361 15491 FALSE TRUE 11962.31179 14802.43362 12925.49468 14595.16589 12038.9276 13623.96478 12818.894 11654.59366 12905.45202 0.926919241 1.146990713 1.001553038 1.130930235 0.932855942 1.055675133 0.99329291 0.903075199 1 13.65569305 2.072000066 0.968529449 0.962201921 1.055040131 0.127341945 0.076409641 0.906064236 1.575888626 0.054491117 0.027307988 118.0320814 -2.072000066 0.09283821 DGDDVIIIGVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGDDVIIIGVFK 12 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 199.67 3.93E-07 37655000 267770 171064 201988 203519 173353 171957 287220 169040 138561 FALSE TRUE 251010.7537 183729.7566 206779.2507 208741.6421 159738.5547 221598.1944 244154.0274 190145.0161 115434.274 2.174490687 1.591639556 1.791315903 1.808315979 1.383805253 1.919691499 2.11509129 1.647214554 1 16.81671212 0.974733748 23.82164157 0.99999999 1.809074073 0.562077765 0.228000809 1026.834006 968125.9073 0.216755296 0.054188824 9.434822792 -0.974733748 0.809074083 DGDILGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DGDILGK 7 0 P61604;B8ZZ54 P61604 HSPE1 "10 kDa heat shock protein, mitochondrial" 0 ;; 94.662 0.032653 1343940000 4941040 3419680 3845960 3641980 4926050 3524870 4213800 3617000 5931780 FALSE TRUE 4631789.126 3672876.665 3937187.987 3735439.373 4539177.904 4542442.748 3581979.809 4068590.412 4941727.597 0.937281353 0.743237379 0.79672299 0.755897467 0.918540695 0.919201364 0.724843638 0.823313372 1 22.23658406 2.75583764 24.9086394 0.85270047 0.795516596 0.087372876 0.089484278 2029.675591 2926222.756 0.026493376 0.0280387 569.9511574 -2.75583764 -0.057183875 DGDKPEETQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DGDKPEETQGK 11 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;; 170.66 1.41E-05 3861410000 8325250 3759960 5148440 5159390 5046800 3433040 7122070 4056530 5416740 FALSE TRUE 7804187.463 4038351.351 5270563.428 5291788.682 4650444.686 4424102.917 6054181.722 4562996.7 4512651.101 1.729401917 0.894895542 1.167952787 1.172656287 1.030534952 0.980377791 1.341601996 1.011156546 1 22.10554381 4.749678274 24.92963382 1.091733532 1.7294023 0.72359036 0.126750152 899.230743 2016346.688 0.029997085 0.460282165 56192.48956 -4.749678274 0.637668768 DGDKS(ph)PMSSLQISNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DGDKSPMSSLQISNEK 16 1 Q9UER7-3;Q9UER7;Q9UER7-2;Q9UER7-5;Q9UER7-4 Q9UER7-3 DAXX Death domain-associated protein 6 1 DGDKS(1)PMSSLQISNEK;DGDKS(0.999)PMS(0.001)SLQISNEK;DGDKS(0.97)PMS(0.015)S(0.015)LQISNEK;DGDKS(0.903)PMS(0.085)S(0.012)LQISNEK 215.59 9.67E-15 1498996000 2656320 1054750 1567140 1448850 1484310 1062834 2056350 1267580 1662830 TRUE FALSE 2490065.673 1132844.787 1604313.301 1486029.944 1367738.28 1369656.922 1748019.408 1425840.153 1385292.931 1.797501177 0.817765515 1.158104012 1.072718925 0.987327842 0.98871285 1.261840993 1.029269782 1 20.40175965 4.749853763 24.95340694 1.051611218 1.797501623 0.806941099 0.116389237 748.6356986 1654158.453 0.028250557 0.440104877 56215.20042 -4.749853763 0.745890405 DGDSVMVLPTIPEEEAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGDSVMVLPTIPEEEAKK 18 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 111.18 0.00050056 166130000 383240 242060 291280 298720 301990 222500 379950 275240 329270 FALSE TRUE 359253.6925 259982.3743 298189.2992 306385.6609 278272.9236 286732.138 322980.0248 309604.3199 274312.7098 1.30965019 0.947759127 1.087041498 1.116921127 1.014436858 1.045274709 1.177415458 1.128654666 1 18.06546194 1.764764733 25 1.120694658 1.069192659 0 0.103591396 55.38105371 52870.40532 0.043759095 0.024267958 58.17879644 -1.764764733 -0.051501999 DGDSYDPYDFS(ph)DT(ph)EEEMPQVHTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGDSYDPYDFSDTEEEMPQVHTPK 24 0 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 2 DGDSYDPY(0.003)DFS(0.998)DT(1)EEEMPQVHTPK;DGDSYDPYDFS(1)DT(1)EEEMPQVHTPK 182.54 1.28E-17 703760000 398420 273395 297062 327010 316100 213567 376300 262502 374260 TRUE FALSE 373483.6034 293637.4503 304108.4509 335401.6302 291274.7811 275220.3259 319877.3084 295275.9525 311793.5882 1.197855304 0.941768726 0.975351843 1.075716894 0.934191055 0.882700403 1.025926512 0.947023812 1 18.25023173 4.743292891 24.94810019 0.97224722 1.197855398 0.639237982 0.053123924 303.4361968 1599631.044 0.012063324 0.098288538 55372.34183 -4.743292891 0.225608178 DGDSYDPYDFS(ph)DTEEEMPQVHT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DGDSYDPYDFSDTEEEMPQVHTPK 24 0 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 2 DGDSYDPYDFS(1)DTEEEMPQVHT(1)PK;DGDSYDPYDFS(0.996)DT(0.004)EEEMPQVHT(1)PK;DGDSYDPYDFS(0.998)DT(0.002)EEEMPQVHT(1)PK;DGDSYDPYDFS(1)DTEEEMPQVHT(1)PK;DGDSYDPY(0.019)DFS(0.98)DT(0.001)EEEMPQVHT(1)PK;DGDS(0.001)Y(0.001)DPY(0.006)DFS(0.99)DT(0.004)EEEMPQVHT(0.999)PK;DGDSYDPYDFS(1)DTEEEMPQVHT(1)PK 276.1 8.65E-52 2710170000 3154392 1842270 2199751 2190541 2434748 1869996 2745205 2136617 3117921 TRUE FALSE 2956964.235 1978673.588 2251930.133 2246753.991 2243532.713 2409833.488 2333586.995 2403378.336 2597519.843 1.138379845 0.761754946 0.866953967 0.864961243 0.863721107 0.927744015 0.89839044 0.925258894 1 21.30870334 0.859667721 0.778186337 0.999463736 0.876954286 0.053915472 0.0964946 1.680405487 2.149859369 0.08611038 0.031330951 7.238819064 -0.859667721 -0.12250945 DGDSYDPYDFS(ph)DTEEEMPQVHTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 DGDSYDPYDFSDTEEEMPQVHTPK 24 0 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 1 DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(0.999)DT(0.001)EEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(0.999)DT(0.001)EEEMPQVHTPK;DGDSYDPYDFS(0.999)DT(0.001)EEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(0.999)DT(0.001)EEEMPQVHTPK;DGDSYDPYDFS(0.996)DT(0.004)EEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(0.962)DT(0.038)EEEMPQVHTPK 296.35 3.63E-62 9956780000 9470030 6713820 7779750 7926540 7615350 5511380 9173450 6244100 8200870 TRUE FALSE 8877317.727 7210918.219 7964289.344 8129948.436 7017271.13 7102425.936 7797976.335 7023689.63 6832091.817 1.299355741 1.055448084 1.165717551 1.189964751 1.027104336 1.03956828 1.141374639 1.028043799 1 22.70389593 8 0.123755172 0.974838711 1.686135616 0.434363513 0.07079858 102.3251944 0.864899159 0.418850391 12.61249533 99999999.97 -8 0.711296906 DGDSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGDSYR 6 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ; 103.71 0.080148 241095000 755790 701400 713090 690570 768130 629380 779230 680470 752490 FALSE TRUE 708486.453 753332.3858 730004.8315 708291.1953 707804.1683 811071.7889 662391.6955 765428.1774 626894.5577 1.130152502 1.201689146 1.164477858 1.129841034 1.129064146 1.293792997 1.056623777 1.220983925 1 19.25786328 -3.661863241 0.468984514 2.48E-07 1.166417083 0.394178201 0.064075668 396.757899 7.737551423 399.2128923 0.028969994 0.00021784 3.661863241 1.166416835 DGDVTVTNDGATILSMMDVDHQIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGDVTVTNDGATILSMMDVDHQIAK 25 0 P48643;B7ZAR1;E9PCA1 P48643 CCT5 T-complex protein 1 subunit epsilon 0 226.14 6.68E-34 95422000 134700 70773 91045 88322 91451 86480 131060 83352 73223 FALSE TRUE 126269.3674 76013.10656 93204.63039 90588.49205 84268.80736 111445.3721 111408.7697 93758.68068 61001.60826 2.069935057 1.246083648 1.527904477 1.485018094 1.381419437 1.826925147 1.826325123 1.53698703 1 15.89655966 2.254700008 24.99662927 1.646427739 1.497184787 0 0.316293919 782.1774254 1211431.16 0.099847204 0.083297842 179.7628761 -2.254700008 -0.149242952 DGEDLKDHSTESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGEDLKDHSTESK 13 1 Q9UHB6;Q9UHB6-4;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 170.74 1.58E-05 1241080000 2281500 964170 1459000 1323230 1505020 882930 1656440 1128180 2197300 FALSE TRUE 2138704.988 1035558.15 1493608.169 1357186.322 1386821.8 1137817.558 1408072.2 1269035.756 1830556.435 1.168336003 0.56570676 0.815931233 0.741406436 0.757595764 0.621569232 0.769204474 0.69325137 1 20.80385082 -1.090081106 3.834060254 1.000079225 0.747174585 0.162246855 0.161364527 61307740.86 145478018.6 69372.74876 0.033759941 0.081267873 1.090081106 -0.25290464 DGEEAGAYDGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DGEEAGAYDGPR 12 0 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;; 242.12 6.52E-16 3610270000 3520000 3026260 2996080 3236610 2993750 2096390 3526990 2374720 2363410 FALSE TRUE 3299689.483 3250327.439 3067148.432 3319666.892 2758632.951 2701583.761 2998150.592 2671209.019 1968941.603 1.675869654 1.65079931 1.557765059 1.686015922 1.401074033 1.372099486 1.522721948 1.356672547 1 20.90898889 -2.615159889 0.127834735 1.17E-13 1.849060331 0.86541176 0.075411768 22.91536858 0.347903906 7.133632203 0.68735647 0.002425717 2.615159889 1.849060331 DGELLFVHSAEGSEFWSALLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DGELLFVHSAEGSEFWSALLEK 22 0 P17655;P17655-2;C9JWY7 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;; 303.86 5.07E-56 1108386000 1592849 1258020 1477350 1377363 1517906 1062307 1802802 1354763 1829208 FALSE TRUE 1493155.424 1351165.11 1512393.44 1412708.466 1398695.786 1368977.786 1532488.576 1523908.143 1523901.368 0.979824191 0.886648663 0.992448377 0.927034056 0.917838789 0.898337527 1.005635016 1.000004446 1 20.5393381 1.659480148 7.392321969 1.002320779 0.934328714 0.495932434 0.03232835 0.102806225 10.61159474 0.015569923 0.007991483 45.65413809 -1.659480148 -0.067992065 DGELPVEDDIDLSDVELDDLGKDEL ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DGELPVEDDIDLSDVELDDLGKDEL 25 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;;; 275.02 4.51E-53 283950000 712358 398932 400418 376798 387666 235997 583959 368045 541549 FALSE TRUE 667772.7844 428469.3404 409916.1041 386467.2746 357220.2761 304125.5028 496399.7692 413996.2284 451160.9734 1.480120897 0.94970391 0.908580592 0.856606173 0.79178009 0.674095325 1.100271962 0.917624203 1 18.78328275 4.751391961 3.464781133 0.896435282 1.561258378 0.72407742 0.113056006 0.175372872 3.563799295 0.02739362 0.311749688 56414.65822 -4.751391961 0.664823096 DGFIDKEDLHDMLASLGK ddPTM_SK-BR-3_Pertuzumab_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 ; 237.86 4.39E-24 3216000000 19256200 12986900 15192800 13571100 15138400 10881600 19423200 13960800 12790800 FALSE TRUE 18050988.82 13948463.59 15553180.39 13919357.4 13949491.13 14022941.27 16510871.48 15703836.61 10655932.85 1.693984851 1.308985688 1.45957943 1.306254234 1.309082117 1.315975004 1.549453409 1.473717678 1 23.34515356 4.745539943 24.40151538 1.371434844 1.693985061 0.33753056 0.150184248 697.9666179 2440182.883 0.032384989 0.3198367 55659.58231 -4.745539943 0.322550218 DGFNPADVEAGLYGSHLYVWDWQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DGFNPADVEAGLYGSHLYVWDWQR 24 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ;;;;; 323.36 3.67E-74 2452530000 2015999 2457006.8 1949478.5 1870249.8 2673914.8 1623460.9 2316680.6 2252295.6 1923173.9 FALSE TRUE 1889821.221 2638926.14 1995721.051 1918243.576 2463916.318 2092127.707 1969315.851 2533499.664 1602183.752 1.17952839 1.647080828 1.245625571 1.19726815 1.537848773 1.305797606 1.229144815 1.581279089 1 20.61160819 -1.903404746 2.817869295 0.803852742 1.367097617 0.317626623 0.168321336 81279070.8 91925752.01 107441541.1 0.037958977 0.012490944 1.903404746 0.563244876 DGFQHPAR ddPTM_SK-BR-3_Pertuzumab_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 ;; 125.31 0.0012673 895200000 1135840 1308170 1061690 1073330 1464320 797360 1166750 1213860 1581000 FALSE TRUE 1064749.802 1405028.268 1086873.788 1100873.465 1349318.214 1027544.888 991806.6691 1365413.093 1317120.886 0.808391859 1.066742075 0.825189092 0.835818091 1.024445234 0.780144707 0.753011116 1.036664977 1 20.32895633 3.828694363 7.791414368 0.872367782 0.954145675 0 0.118631208 0.642216733 43.66282824 0.028707617 0.051959293 6740.534924 -3.828694363 0.081777892 DGFVMGEGAAVLVLEEYEHAVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGFVMGEGAAVLVLEEYEHAVQR 23 0 Q9NWU1 Q9NWU1 OXSM "3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial" 0 137.09 8.87E-06 9755700 11109 9710.7 9270 10148 11860 8750.5 9331.4 10984 12571 FALSE TRUE 10413.70752 10429.69033 9489.888778 10408.41486 10928.56344 11276.6273 7932.243198 12355.37658 10472.81889 0.994355735 0.995881858 0.906144647 0.993850364 1.043516894 1.076751868 0.75741243 1.17975654 1 13.35436219 1.186844321 24.99999897 1.089877663 0.962448745 0.217702267 0.096681539 173.2666841 83753.94321 0.088387319 0.022096914 15.37603366 -1.186844321 -0.127428918 DGFYEAELCPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DGFYEAELCPDR 12 0 Q04206;Q04206-4;Q04206-2;A0A087X0W8;E9PKH5;Q2TAM5;Q04206-3;A0A087WVP0;E9PKV4;E9PQS6;E9PI38;E9PMD5;E9PNV4;E9PRX2;E9PJR1 Q04206 RELA Transcription factor p65 0 ;;; 162.36 0.00014629 401139000 431797 434175 432219 449769 457965 373620 519750 417209 525050 FALSE TRUE 404771.5965 466321.7688 442471.4388 461310.834 421998.2762 481478.0288 441818.3126 469298.462 437415.763 0.925370393 1.066083594 1.011558056 1.054627823 0.964753244 1.100733146 1.010064908 1.072888775 1 18.73864569 2.244198332 24.99918138 1.044756378 1.016124199 0.1246338 0.049448084 369.9392034 1640412.601 0.015674942 0.01277157 175.4681639 -2.244198332 -0.028632179 DGGFCEVCKK ddPTM_SK-BR-3_Pertuzumab_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 ; 110.66 0.0029765 332590000 679070 607120 643300 760950 1086990 572270 1104210 828780 2226300 FALSE TRUE 636568.2209 652071.7965 658559.3798 780477.2653 1001622.19 737475.059 938643.9615 932255.0074 1854716.148 0.34321598 0.351574982 0.355072867 0.420806853 0.540040691 0.397621523 0.506084968 0.50264026 1 20.82276698 -5 0.180216641 3.425585329 0.295808125 0.945857263 0.044909044 26.49824819 0.2554019 22.91211405 0.133231326 1.00E-05 5 -3.129777204 DGGNPFAEPSELDNPFQDPAVIQHRPS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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;DGGNPFAEPSELDNPFQDPAVIQHRPS(1)R;DGGNPFAEPS(0.001)ELDNPFQDPAVIQHRPS(0.999)R 204.15 1.96E-25 513039000 268941 307717 262609.5 227885.1 333552 208578.8 370023 367242 609672 TRUE FALSE 252108.4629 330500.6869 268838.7214 233733.0175 307356.1714 268792.1136 314541.4863 413092.9721 507913.8046 0.496360722 0.650702312 0.529299891 0.460182447 0.60513451 0.529208128 0.619281231 0.813313142 1 18.95422416 1.090296303 1.921510785 0.998741769 0.553713169 0.892247759 0.053440509 0.093567053 0.680281283 0.048903911 0.013932736 12.31108424 -1.090296303 -0.445028601 DGGQTES(ph)NEEGKENR ddPTM_SK-BR-3_Pertuzumab_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 DGGQTES(1)NEEGKENR;DGGQTES(1)NEEGKENR;DGGQT(0.007)ES(0.993)NEEGKENR 197.72 2.83E-11 1045730000 886170 449490 584740 559590 558830 426940 742840 464290 637540 TRUE FALSE 830706.2016 482770.7073 598610.3089 573950.0268 514941.746 550190.6472 631458.0382 522257.6285 531130.4553 1.564034209 0.908949397 1.12704949 1.080619688 0.969520277 1.035886084 1.188894427 0.983294449 1 19.01870673 4.748232256 24.99414498 1.048761584 1.564034484 0.80537886 0.081265834 589.6237026 1523717.196 0.019339063 0.25269027 56005.70333 -4.748232256 0.5152729 DGGQTESNEEGKENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DGGQTESNEEGKENR 15 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;Q5VU81;Q5VU80;Q5VU79;Q5VU78;Q5VU77 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 0 ;;; 263.99 3.89E-25 3221140000 2346340 1536670 1895170 1799290 1983270 1435840 2442480 1629400 2664380 FALSE TRUE 2199486.768 1650446.646 1940124.327 1845462.828 1827511.974 1850343.699 2076252.799 1832834.177 2219677.765 0.990903636 0.743552362 0.874056747 0.831410242 0.823323098 0.833609152 0.93538478 0.825720834 1 21.08191882 0.085800869 0.481584047 1.014555128 0.838217645 0.272884146 0.068844219 4.230251384 1.312578092 0.191552538 0.03331379 1.218430799 -0.085800869 -0.176337483 DGGS(ph)GNS(ph)TIIVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGGSGNSTIIVSR 13 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 2 DGGS(1)GNS(0.975)T(0.025)IIVSR;DGGS(0.999)GNS(0.873)T(0.128)IIVSR 211.9 2.66E-08 238490000 705210 609840 612320 573320 666010 451280 822750 590680 697260 TRUE FALSE 661072.1649 654993.1881 626844.5196 588032.3618 613704.2612 581557.2101 699386.2755 664427.6982 580882.8015 1.138047405 1.127582339 1.079123909 1.012308094 1.056502722 1.001161006 1.204005823 1.143824015 1 19.14788759 -0.174777395 8.405774904 0.999998984 1.096898655 0.188964434 0.061983579 0 0 0.061421301 0.014477139 0.668686576 0.174777395 0.096899671 DGGS(ph)GNST(ph)IIVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGGSGNSTIIVSR 13 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 2 DGGS(0.973)GNS(0.446)T(0.58)IIVSR 91.657 0.03412 157880000 272960 226600 242430 239220 258820 168250 315320 228710 286800 TRUE FALSE 255875.9208 243377.6998 248180.5541 245358.7902 238493.3212 216821.0437 268040.6933 257264.947 238931.2272 1.070918707 1.018609843 1.038711252 1.02690131 0.99816723 0.907462144 1.121831987 1.076732204 1 17.86623589 -0.819348965 4.689794614 1.000000185 1.03168914 0.031603176 0.056266169 5.25E-08 1.30E-08 0.05261601 0.012401677 0.151583187 0.819348965 0.031688954 DGGS(ph)GNSTIIVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DGGSGNSTIIVSR 13 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 DGGS(1)GNSTIIVSR;DGGS(1)GNSTIIVSR;DGGS(0.997)GNS(0.002)T(0.001)IIVSR 196.41 1.49E-07 935070000 798100 681440 779720 790500 817510 734710 857280 689710 803870 TRUE FALSE 748148.3456 731894.5266 798215.3266 810785.5683 753306.0623 946808.85 728738.8226 775821.8117 669698.9038 1.117141362 1.092871024 1.191901797 1.210671787 1.124842908 1.413782888 1.0881589 1.158463613 1 19.35315308 0.701172051 1.717089671 1.000716787 1.177161068 0.261769068 0.093305389 1.576840628 6.926218094 0.083578738 0.023682871 5.025416384 -0.701172051 0.176444281 DGHADAAQDTEQFVATVLQAASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DGHADAAQDTEQFVATVLQAASR 23 0 Q6PJG6;Q6PJG6-3 Q6PJG6 BRAT1 BRCA1-associated ATM activator 1 0 ;;;; 248.7 7.70E-38 158494100 162801 175119 181296 188604 182896 170093 221325 173349 185475 FALSE TRUE 152611.576 188084.993 185596.4267 193443.8979 168532.0859 219196.0879 188139.3709 194992.0042 154518.0243 0.987661968 1.21723659 1.201131244 1.251918013 1.09069532 1.418579411 1.21758851 1.26193695 1 17.23741561 4.738878132 6.385256523 1.221758641 0.982621255 0.276425408 0.109574879 0.138847699 32.61057145 0.022799783 0.143626354 54812.31337 -4.738878132 -0.239137385 DGHFALEELAQAGYEVVGLDWTVAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGHFALEELAQAGYEVVGLDWTVAPK 26 0 A0A1B0GVZ4;A0A494C085;P06132;A0A1B0GVN9;A0A494BZY8;A0A494C0Q8 A0A1B0GVZ4 UROD Uroporphyrinogen decarboxylase 0 204.61 3.72E-25 130420000 157980 142880 135910 148780 157860 122790 188430 118780 186960 FALSE TRUE 148092.3138 153458.9839 139133.8494 152597.9467 145462.3124 158237.4797 160176.6708 133609.9445 155755.1682 0.950801925 0.985257733 0.893285603 0.979729587 0.933916441 1.015937266 1.028387518 0.857820296 1 17.24892051 2.256580813 24.97023054 0.984669487 0.947469701 0.048781238 0.052508235 541.3029635 750070.6819 0.017338016 0.014478263 180.5430657 -2.256580813 -0.037199786 DGHGEAIMFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGHGEAIMFK 10 0 Q9Y2J8 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 96.143 0.0069415 142680000 267680 343420 276450 306700 336810 205460 302770 300730 213860 FALSE TRUE 250926.3866 368847.1741 283007.5245 314570.4412 310358.3012 264772.9666 257372.4493 338276.8025 178165.3844 1.408390229 2.070251611 1.588454039 1.765609197 1.741967455 1.486107795 1.444570449 1.898667374 1 17.44285754 -2.517510942 0.228972415 1.78E-17 1.794926209 0.466715138 0.216616893 34.98122897 0.964188545 18.13922395 0.380669978 0.00303731 2.517510942 1.794926209 DGHNLISLLEVLSGDSLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGHNLISLLEVLSGDSLPR 19 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;E9PIA2;Q15149-4;Q15149-5;Q15149-8;E9PKG0 Q15149-3;Q15149-4;Q15149-5;Q15149-8;E9PKG0 PLEC Plectin 0 157.97 6.35E-10 245650000 434820 446850 447440 544410 565500 405400 526420 387550 435170 FALSE TRUE 407605.3924 479935.2389 458053.4881 558380.4823 521087.9111 522432.3989 447488.208 435936.4706 362537.3157 1.124312932 1.323823006 1.263465768 1.540201403 1.437335934 1.441044484 1.234323168 1.202459586 1 18.46776997 1.034176221 1.594365237 1.006426197 1.347880887 0.48821269 0.114631882 0.337095415 1.742865162 0.108228828 0.031694101 10.81872847 -1.034176221 0.34145469 DGHQSSHGDIFSHFFGDFGFMFGGTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGHQSSHGDIFSHFFGDFGFMFGGTPR 27 0 Q9UBS4 Q9UBS4 DNAJB11 DnaJ homolog subfamily B member 11 0 ; 47.38 0.044067 14820800 7458.8 28582 20020.9 24053.6 29184 16146.2 20267 28559.6 13637.9 FALSE TRUE 6991.967022 30698.24102 20495.8052 24670.8561 26892.00636 20807.34583 17228.1515 32125.32893 11361.64639 0.615400866 2.701918364 1.803946761 2.171415591 2.366911049 1.831367138 1.516342871 2.827524096 1 13.47188429 -1.024802089 5.05753543 0.999988276 2.002730836 0.192396384 0.628964512 7.35E-05 1.42E-05 0.538572835 0.126941354 0.094449119 1.024802089 1.002742561 DGHRYS(ph)RS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGHRYSRSPAR 11 2 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 2 DGHRY(0.052)S(0.965)RS(0.984)PAR 56.793 0.062611 621870000 49658 51300 65435 40813 45628 46214 56992 38733 71231 TRUE FALSE 46549.99442 55098.30538 66987.1491 41860.33068 42044.56093 59555.23158 48446.57869 43568.90031 59342.08593 0.784434751 0.928486158 1.128830375 0.705407133 0.708511679 1.003591813 0.81639494 0.734199003 1 15.85676802 3.2287231 24.99990477 0.825418226 0.969169523 0.144183701 0.13332106 311.699486 792115.2589 0.03765056 0.045518603 1693.25786 -3.2287231 0.143751297 DGIDDESYEAIFKPVMSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGIDDESYEAIFKPVMSK 18 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 0 ; 238.94 6.13E-24 203180000 794140 513930 608480 572290 591520 423190 817950 527910 665910 FALSE TRUE 744436.195 551981.9119 622913.4329 586975.9303 545064.4053 545358.0831 695305.991 593820.7256 554765.3191 1.341893895 0.994982731 1.122841338 1.058061689 0.982513482 0.983042855 1.253333558 1.07039987 1 19.08151808 4.74874665 24.43995651 1.070661453 1.341894102 0.529742496 0.083278691 930.9215445 2233554.641 0.020346315 0.27585508 56072.0778 -4.74874665 0.271232649 DGIDDESYGQIFKPIISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGIDDESYGQIFKPIISK 18 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 0 ; 233.42 8.81E-24 741350000 2772650 1732910 2162510 2041960 2184920 1632420 2840790 1938700 2634660 FALSE TRUE 2599114.786 1861216.459 2213805.758 2094360.151 2013325.197 2103673.154 2414839.912 2180750.963 2194918.225 1.184151079 0.847966197 1.008605119 0.954185958 0.917266609 0.958428943 1.100195845 0.993545426 1 21.06573576 1.768489134 24.99999972 1.041071235 0.963576046 0.051013781 0.090521391 45.00398474 37613.4702 0.03782467 0.020978966 58.67986872 -1.768489134 -0.077495189 DGIEPMWEDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DGIEPMWEDEK 11 0 D6RBW1;P06730;P06730-3;P06730-2;H0Y8J7 D6RBW1 EIF4E Eukaryotic translation initiation factor 4E 0 ;;; 152.04 7.71E-05 306059000 728660 548700 601460 567420 608930 485940 752650 526620 595230 FALSE TRUE 683054.4713 589326.3189 615726.9152 581980.9578 561107.0941 626222.9894 639797.1198 592369.6662 495882.2677 1.377452907 1.188439993 1.241679639 1.173627282 1.131532887 1.262846103 1.290219799 1.194577231 1 18.91963811 0.96788484 22.08894977 0.999999998 1.232567974 0.547360363 0.067449188 691.1420055 475372.0537 0.061988134 0.015497034 9.287200886 -0.96788484 0.232567976 DGISCEASNPHGNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DGISCEASNPHGNKR 15 1 P50895;A0A087WXM8 P50895 BCAM Basal cell adhesion molecule 0 ;;; 206.49 2.51E-09 322744000 554968 479312 435935 420120 630187 353071 556352 539805 693690 FALSE TRUE 520233.5435 514800.7592 446275.5841 430900.9905 580694.6551 454996.8661 472932.1825 607200.8425 577908.6576 0.900200294 0.890799528 0.772225123 0.745621276 1.004820827 0.787316231 0.818351095 1.050686531 1 19.14048196 1.239103144 24.99999791 1.025343335 0.84081312 0.493803497 0.075528396 11.05661712 509712.5169 0.055370128 0.017416692 17.3421582 -1.239103144 -0.184530215 DGIVLGADTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DGIVLGADTR 10 0 Q99436;Q5TBG5;Q99436-2 Q99436 PSMB7 Proteasome subunit beta type-7;Proteasome subunit beta type 0 ;;; 150.81 4.87E-05 463100000 1064540 1764510 976520 917360 1850710 630580 1050380 1587700 1663150 FALSE TRUE 997912.3417 1895156.156 999683.5155 940901.0107 1705362.702 812618.2094 892885.2702 1785927.84 1385559.521 0.720223366 1.367791227 0.721501675 0.679076573 1.230811579 0.586491015 0.644422168 1.288957864 1 20.40203726 3.845884701 6.811969319 0.841095558 1.082521149 0.038487544 0.285694079 0.459940522 24.54344652 0.068199962 0.123919287 7012.690971 -3.845884701 0.241425591 DGKPSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGKPSAR 7 1 J3QQZ9;Q9NVS9-3;Q9NVS9;Q9NVS9-4;J3QQV6;A0A286YFL3 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 69.198 0.055076 99875000 135430 107960 125170 114690 133380 74644 107810 112600 151390 FALSE TRUE 126953.678 115953.4707 128139.0915 117633.1396 122904.8728 96192.51106 91644.89136 126658.3579 126122.031 1.006593987 0.919375226 1.015992928 0.932693033 0.974491704 0.762693958 0.72663666 1.004252444 1 16.94446078 2.256960441 24.9406359 0.83419199 0.967556314 0.152481684 0.094603263 266.4120163 361115.9878 0.031000315 0.025891385 180.700952 -2.256960441 0.133364323 DGKQPVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGKQPVGR 8 1 A0A499FJT0;Q8NHP1;O43488;H3BLU7 A0A499FJT0;O43488 AKR7L;AKR7A2 Aflatoxin B1 aldehyde reductase member 4;Aflatoxin B1 aldehyde reductase member 2 0 60.019 0.086589 88831000 63350 62222 63732 63461 74040 51738 76151 57962 82089 FALSE TRUE 59385.03658 66828.98162 65243.75314 65089.5167 68225.19706 66673.9207 64732.8645 65198.68329 68387.81558 0.868356974 0.977205969 0.954025985 0.951770665 0.997622113 0.974938593 0.946555522 0.953366952 1 16.06145169 4.742373788 24.93712161 0.966504023 0.868356935 0.736819154 0.018912925 187.1631579 1223945.716 0.004283763 0.032055921 55255.28054 -4.742373788 -0.098147089 DGLAFNALIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DGLAFNALIHR 11 0 O43707 O43707 ACTN4 Alpha-actinin-4 0 ;;; 207.29 2.35E-08 796229000 1155382 1503230 965503 924947 1541970 785165 1060870 1511810 968645 FALSE TRUE 1083068.703 1614530.713 988405.1871 948682.706 1420869.896 1011829.389 901802.3921 1700562.806 806971.8918 1.342139316 2.000727324 1.224832237 1.175608117 1.760742735 1.253859521 1.117514007 2.107338339 1 19.6221589 -4.177542008 0.093925225 6.10E-21 1.798181785 0.089476128 0.365518584 364.054011 2.800988055 83.5944553 7.467369425 6.64E-05 4.177542008 1.798181785 DGLAPEKT(ph)SPDRDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DGLAPEKTSPDRDK 14 2 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 DGLAPEKT(0.5)S(0.5)PDRDK;DGLAPEKT(0.698)S(0.302)PDRDK;DGLAPEKT(0.599)S(0.401)PDRDK 230.29 1.56E-12 2368240000 4006590 1325680 2060650 1851730 1880390 1504770 2737900 1663780 2050240 TRUE FALSE 3755824.684 1423834.727 2109529.591 1899248.527 1732711.755 1939172.671 2327377.312 1871506.595 1708041.699 2.198906904 0.833606538 1.23505743 1.111945058 1.014443474 1.13531928 1.362599821 1.095703106 1 20.70391177 4.747902028 24.92424867 1.116890485 2.198907499 0.856704664 0.141247681 465.9629699 1243230.279 0.034983803 0.443549709 55963.13405 -4.747902028 1.082017014 DGLAPEKTS(ph)PDRDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGLAPEKTSPDRDK 14 2 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 DGLAPEKT(0.18)S(0.82)PDRDK;DGLAPEKT(0.099)S(0.901)PDRDK 208.59 6.17E-09 1618540000 1782750 710080 1068930 986960 953320 831380 1462390 890290 1243140 TRUE FALSE 1671170.86 762655.062 1094285.524 1012287.065 878450.0927 1071385.91 1243118.196 1001444.666 1035651.903 1.613641471 0.736400966 1.056615182 0.977439487 0.848209799 1.034503878 1.200324348 0.966970334 1 19.98210774 -0.355812705 7.808585445 0.999962802 1.0294328 0 0.234895387 0 0 0.205352561 0.048402063 0.440744899 0.355812705 0.029469999 DGLILTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DGLILTSR 8 0 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ;;;;; 161.02 0.00081417 1328812000 1184857 1447110 1309354 1262900 1523860 1056021 1343440 1251437 1535670 FALSE TRUE 1110698.915 1554255.53 1340412.495 1295308.152 1404182.183 1360877.12 1142003.644 1407681.664 1279356.756 0.868169813 1.214872648 1.047723779 1.012468294 1.097568896 1.063719805 0.892638928 1.100304241 1 20.28698719 1.955595615 24.61862255 0.983833823 1.070164885 0.031197268 0.099145817 712.3482555 394937.8702 0.038039303 0.024549438 90.28084485 -1.955595615 0.086331063 DGLIPLEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DGLIPLEIR 9 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ;;;; 141.23 0.00024941 958700000 841778 1066110 834792 860536 1091180 657280 964470 927240 977040 FALSE TRUE 789092.6176 1145045.894 854593.6605 882618.8106 1005483.124 847026.066 819856.6772 1043007.955 813965.7121 0.969442086 1.406749543 1.049913587 1.084343969 1.235289287 1.040616396 1.007237363 1.28139053 1 19.6346085 3.738720548 24.43902664 1.095962488 1.222031946 0.052831404 0.139091248 547.7833851 1154137.887 0.032537904 0.057998463 5479.242829 -3.738720548 0.126069458 DGLKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGLKPR 6 1 P56192;P56192-2 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 67.741 0.089354 303600000 573830 662310 686570 691290 692230 601760 751960 620920 709220 FALSE TRUE 537915.0046 711348.1215 702855.7646 709029.6718 637865.0481 775478.3432 639210.5789 698443.2288 590846.6003 0.910413979 1.203947219 1.189574019 1.200023274 1.079578097 1.312486765 1.081855389 1.18210586 1 19.17242409 -1.802164081 6.598182414 0.992280791 1.155930209 0.147887356 0.106547747 0.010989288 0.000329496 0.093703687 0.021332768 0.015770153 1.802164081 0.163649417 DGLLENQTPEFFQDVCKPK ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 292.6 1.27E-49 9297014000 10197311 6377921 8352357 8130202 8783229 6537577 12434033 7616079 11131916 FALSE TRUE 9559079.507 6850148.907 8550478.852 8338836.748 8093429.624 8424869.351 10569665.18 8566963.228 9273927.305 1.030747729 0.738645957 0.921991145 0.89916995 0.8727079 0.908446775 1.139718356 0.923768642 1 23.14474899 1.928005869 8.397488597 1.034261767 0.877131332 0.301804859 0.088067533 0.333651049 36.18080452 0.034457235 0.021700358 84.7238864 -1.928005869 -0.157130435 DGLLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DGLLLR 6 0 O14746-3;O14746 REV__O43296 TERT Telomerase reverse transcriptase 0 ;; 122.51 0.044642 3244440000 2802520 3235680 3123190 3085150 3198910 2681220 3483670 2772550 3258310 FALSE TRUE 2627115.276 3475253.114 3197273.542 3164320.172 2947680.512 3455244.688 2961326.024 3118708.971 2714477.012 0.967816366 1.28026618 1.177859871 1.165720011 1.085911024 1.272895174 1.090937964 1.148917069 1 21.37224284 0.479913755 0.819905938 0.998900173 1.170971474 0.186086301 0.091979543 2.412375031 2.464174795 0.086385198 0.027925149 3.019352055 -0.479913755 0.172071301 DGLLMPSMS(ph)ESDLTTSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGLLMPSMSESDLTTSGR 18 0 Q16825 Q16825 PTPN21 Tyrosine-protein phosphatase non-receptor type 21 1 DGLLMPS(0.177)MS(0.762)ES(0.055)DLT(0.002)T(0.002)S(0.002)GR 90.385 0.0028485 14579000 31384 38254 32065 29944 40527 24788 41978 35016 41125 TRUE FALSE 29419.73146 41086.36596 32825.59694 30712.41374 37344.1729 31943.8932 35683.7886 39387.82468 34260.97182 0.858695183 1.199217762 0.958104665 0.896425644 1.089991641 0.932369734 1.041528792 1.149641198 1 15.06427845 1.470341194 11.51356371 1.08174627 1.00869305 0.088411708 0.104184284 0.233031182 174.0128249 0.053649968 0.024749777 29.53528688 -1.470341194 -0.07305322 DGLLPENTFIVGYAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DGLLPENTFIVGYAR 15 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;; 260.28 1.58E-24 543870000 395025 471059 457311 436704 522822 373457 528109 431692 471845 FALSE TRUE 370301.0904 505936.6985 468158.6329 447910.564 481761.6691 481267.9733 448923.9582 485589.6965 393091.0213 0.942023782 1.28707264 1.190967505 1.139457631 1.225572814 1.224316882 1.142035645 1.235311086 1 18.58450389 -1.297389216 6.385548659 0.999993974 1.184749702 0.245032358 0.093742509 7.11E-06 7.82E-07 0.080218189 0.018906992 0.050420922 1.297389216 0.184755728 DGLNDDDFEPYLS(ph)PQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DGLNDDDFEPYLSPQAR 17 0 Q9Y5A9;S4R3J8 Q9Y5A9 YTHDF2 YTH domain-containing family protein 2 1 DGLNDDDFEPYLS(1)PQAR;DGLNDDDFEPYLS(1)PQAR;DGLNDDDFEPYLS(1)PQAR;DGLNDDDFEPYLS(1)PQAR 366.82 1.25E-104 539743000 1045260 1056410 915840 915060 1410230 732452 869150 914950 581230 TRUE FALSE 979839.0424 1134627.696 937564.1573 938541.9888 1299476.224 943899.002 738829.0263 1029183.522 484218.9581 2.023545394 2.343212046 1.936240086 1.938259486 2.683654166 1.94932269 1.525815985 2.125450696 1 18.88530004 0.293441479 0.454215182 0.902660523 2.180308404 0.572445478 0.29337528 2.019474115 0.666952862 0.698750434 0.16990668 1.96535713 -0.293441479 1.277647881 DGLNQTTIPVS(ph)PPSTTKPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DGLNQTTIPVSPPSTTKPSR 20 1 Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4;X6RLN4;Q71RC2-2;Q71RC2-6 Q71RC2-5 LARP4 La-related protein 4 1 DGLNQTTIPVS(0.998)PPST(0.001)T(0.001)KPSR;DGLNQTTIPVS(0.747)PPS(0.063)T(0.094)T(0.094)KPS(0.001)R;DGLNQT(0.002)TIPVS(0.99)PPS(0.002)T(0.003)T(0.003)KPSR;DGLNQTTIPVS(0.663)PPS(0.087)T(0.123)T(0.123)KPS(0.003)R 198.09 9.63E-22 3058920000 3010310 2166000 2820450 2812440 2650740 1979260 2801110 1883520 3028030 TRUE FALSE 2821900.071 2326372.894 2887352.406 2884611.972 2442561.573 2550640.231 2381109.56 2118681.618 2522632.231 1.118633163 0.922200575 1.14457921 1.143492871 0.968259084 1.011102689 0.943898809 0.8398694 1 21.26649846 2.056626421 1.556696613 0.920854213 1.061069967 0.38236393 0.078850774 0.438617427 2.001606411 0.049449717 0.025106752 113.9269369 -2.056626421 0.140215754 DGLPRT(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DGLPRTPSR 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DGLPRT(0.997)PS(0.003)R;DGLPRT(0.997)PS(0.003)R;DGLPRT(0.962)PS(0.038)R 102.4 0.0058049 1869960000 1651410 1910340 1941840 1809350 2184630 1495810 1860950 1789040 2046720 TRUE FALSE 1548051.196 2051783.561 1987901.362 1855780.984 2013057.972 1927626.065 1581917.824 2012405.582 1705109.21 0.907889763 1.203315043 1.165849877 1.088364882 1.180603542 1.13050006 0.927751615 1.180220933 1 20.70143271 1.859980213 18.12284614 1.028145834 1.131024207 0.092197143 0.102471556 3.883526318 562.0556784 0.038821928 0.025026932 72.44029549 -1.859980213 0.102878373 DGLPRTPS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGLPRTPSR 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DGLPRT(0.215)PS(0.785)R 90.434 0.0069238 571790000 302480 286220 312090 321670 306480 247760 342890 288970 297710 TRUE FALSE 283548.3167 307412.0266 319492.9222 329924.5968 282410.2971 319284.29 291476.8277 325048.5406 248020.2777 1.143246509 1.239463279 1.288172585 1.33023235 1.138658096 1.287331394 1.175213698 1.31057244 1 17.92009855 -1.638292736 2.865516366 0.977889161 1.240541679 0.55027178 0.067923346 17805442.28 17155731.37 2913237.37 0.01484032 0.022998911 1.638292736 0.262652518 DGMDNQGGYGSVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGMDNQGGYGSVGR 14 0 P31942;P31942-3;P31942-2;P31942-4 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 74.29 0.040675 0 634780 529430 589440 590480 628210 507700 707660 539210 728890 FALSE TRUE 595050.2529 568629.5481 603421.7952 605632.7165 578872.9207 654264.7482 601552.9526 606531.5554 607233.5502 0.97993639 0.936426434 0.993722753 0.997363727 0.953295352 1.07745158 0.990645119 0.998843946 1 19.21189198 3.37470667 0.96305532 1.009934526 0.955523407 0.240018198 0.032068233 0.700490063 1.371258783 0.012622872 0.024824566 2369.772582 -3.37470667 -0.054411119 DGMEYPFIGEGEPHVDGEPGDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DGMEYPFIGEGEPHVDGEPGDLR 23 0 Q9UBS4;H7C2Y5 Q9UBS4 DNAJB11 DnaJ homolog subfamily B member 11 0 ;;;;; 217.86 2.33E-32 864198000 570680 629820 611993 631396 671396 496718 700912 559234 587138 FALSE TRUE 534962.1575 676452.5281 626509.763 647598.6903 618667.2664 640112.4231 595816.7525 629055.5959 489140.8747 1.093677068 1.382940096 1.280837066 1.323951286 1.26480386 1.308646355 1.218088251 1.286041769 1 18.8998905 -0.590274006 0.548601785 0.951489792 1.289380941 0.538959145 0.077114636 7.862275166 1.842401622 0.781685309 0.030321501 0.256877457 0.590274006 0.337891149 DGMVSFHDNPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGMVSFHDNPEK 12 0 Q9UNS2-2;Q9UNS2;H7C3P9;K7ELN6 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 0 ; 172.09 3.67E-05 419150000 689660 814250 816070 818130 844190 668930 1020390 766480 810270 FALSE TRUE 646495.4117 874537.9172 835427.5658 839124.6009 777890.7227 862039.2318 867391.9923 862176.7152 675030.7025 0.957727418 1.295552801 1.237614175 1.243091015 1.152378284 1.277037072 1.284966727 1.277240742 1 19.3645936 4.745668991 24.8269926 1.23914801 0.957727273 0.447140829 0.090003799 597.4285769 2086545.481 0.018633682 0.18674297 55676.12365 -4.745668991 -0.281420737 DGNASGTTLLEALDCILPPTRPTDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGNASGTTLLEALDCILPPTRPTDK 25 1 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 95.834 0.0087699 88728000 40613 31651 33201 35648 33609 29309 40807 32037 41520 FALSE TRUE 38071.10483 33994.47297 33988.5434 36562.78803 30969.48471 37770.03251 34688.36918 36036.88997 34590.04377 1.10063766 0.982782017 0.982610592 1.057032141 0.895329446 1.091933643 1.002842593 1.0418284 1 15.07806922 DGNASGTTLLEALDCILPPTRPTDKPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 266.17 2.49E-54 9134565000 8107210 5671234 6964505 5851977 5960530 6007724 8211980 5940674 5905189 FALSE TRUE 7599794.198 6091138.066 7129706.347 6002148.637 5492414.017 7742056.392 6980669.835 6682380.226 4919574.807 1.544807122 1.238143194 1.449252553 1.220054349 1.116440797 1.573724701 1.418957961 1.358324751 1 22.2301022 -2.221372906 1.987563694 0.000135641 1.362938393 0.390345122 0.143320728 3480544.184 572529.8844 15634305.58 0.03347457 0.006006578 2.221372906 1.362802751 DGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYK ddPTM_SK-BR-3_Pertuzumab_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 ;; 238.77 5.09E-50 4755360000 778961 663407 653046 674556 911655 531427 1057399 652269 1301694 FALSE TRUE 730207.2215 712526.3446 668536.5595 691866.249 840057.2937 684841.3479 898851.8364 733706.2205 1084432.862 0.673354015 0.657049753 0.616484969 0.637998232 0.77465127 0.631520283 0.828868128 0.676580585 1 20.04850931 -0.653999555 0.27029267 1.159849913 0.623908082 0.72916837 0.061698589 5.209887685 0.411529209 0.77274419 0.081974468 0.221819869 0.653999555 -0.535941831 DGNDLHMTYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DGNDLHMTYK 10 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ;;;;; 135.99 0.00012963 3223350000 8598170 9624980 9990960 9493930 10779820 8018890 12385720 9318500 12937320 FALSE TRUE 8060025.888 10337623.53 10227950.29 9737560.317 9933216.421 10333813.37 10528596.27 10481935.24 10777997.71 0.747822193 0.959141374 0.948965713 0.903466541 0.92161983 0.95878786 0.976860132 0.972530846 1 23.36158585 4.739647509 24.78878527 0.952785747 0.747822119 0.850809746 0.027270949 30.89156998 704443.6103 0.006545818 0.040285389 54909.50247 -4.739647509 -0.204963627 DGNEVEPDDDHFSIGVGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGNEVEPDDDHFSIGVGSR 19 0 H3BV98;F8VSA1;Q15633-2;Q15633 H3BV98 TARBP2 RISC-loading complex subunit TARBP2 0 107.41 0.00047383 0 63051 65927 72722 64068 75653 58096 76440 68483 90020 FALSE TRUE 59104.75046 70808.30368 74447.00018 65712.09335 69711.51855 74867.37209 64978.53163 77033.2533 74995.08045 0.788115035 0.944172648 0.992691784 0.876218719 0.929547887 0.99829711 0.866437255 1.027177421 1 16.19450834 4.738041591 6.24189102 0.948445468 0.784406653 0.486945634 0.053332225 0.104770849 22.13262461 0.011637627 0.073015816 54706.83519 -4.738041591 -0.164038816 DGNGYISAAELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGNGYISAAELR 12 0 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2 P0DP25 CALM2;CALM1 0 ; 215.71 9.49E-11 598030000 560240 412670 389780 347970 357980 211425 488580 504140 372880 FALSE TRUE 525175.5785 443224.5162 399025.7657 356899.4993 329865.6948 272459.9653 415321.9648 567082.9887 310643.9191 1.690603119 1.426792829 1.284511755 1.148902255 1.061877199 0.877081277 1.336971173 1.825508094 1 18.24490229 4.674105844 1.058120805 1.209439338 1.883962121 0.267460462 0.254305415 2.288520764 2.244371502 0.076020634 1.697221615 47217.8104 -4.674105844 0.674522782 DGNLELLTRPDTPPWAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGNLELLTRPDTPPWAR 17 1 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 62.94 0.052681 60692000 207540 133750 163150 158710 159970 126540 190870 142410 157230 FALSE TRUE 194550.4419 143652.9892 167019.995 162782.7673 147406.6015 163070.0438 162250.8155 160190.202 130987.2973 1.485261899 1.096694047 1.275085436 1.242737049 1.125350355 1.244930212 1.238675954 1.222944555 1 16.99906738 -4.000805373 0.312208818 1.01E-17 1.240889175 0.359685424 0.102335419 171.0089181 2.795885172 110.7812292 0.086341723 9.98E-05 4.000805373 1.240889175 DGNLHEGDIILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 147.18 6.54E-05 843284000 2669400 2086210 2365140 2299460 2642240 1936070 2760430 2162920 3366230 FALSE TRUE 2502327.019 2240675.159 2421242.238 2358468.037 2434729.129 2494981.98 2346529.148 2432965.323 2804384.466 0.892291 0.798990005 0.863377424 0.840993118 0.868186641 0.889671873 0.836735896 0.867557695 1 21.41925272 -4.999999988 0.277653482 2.067183749 0.842485219 0.728178717 0.027335856 107.7896832 1.036264281 66.17564194 0.029739167 1.00E-05 4.999999988 -1.22469853 DGNVLLHEMQIQHPTASLIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGNVLLHEMQIQHPTASLIAK 21 0 P40227 P40227 CCT6A T-complex protein 1 subunit zeta 0 ; 271.94 6.53E-45 4848300000 3438600 3802000 3872100 3808600 4424800 3233600 4815400 3935900 4929600 FALSE TRUE 3223384.164 4083504.036 3963948.041 3906335.124 4077294.057 4167087.827 4093375.474 4427305.779 4106817.914 0.784886068 0.994323128 0.965211539 0.951182937 0.992811014 1.014675575 0.996726799 1.078038002 1 21.96958955 4.738580434 10.06973548 0.994764479 0.784396835 0.800356125 0.033563767 0.03197054 110.6681929 0.007864511 0.045605194 54774.75379 -4.738580434 -0.210367644 DGPEETDWWWAALHGQEGYVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGPEETDWWWAALHGQEGYVPR 22 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 0 ; 190.37 1.80E-17 152463000 250540 223320 234320 211900 251480 184073 283940 202546 251170 FALSE TRUE 234859.1486 239854.8452 239878.1811 217337.7127 231729.7752 237211.8869 241365.833 227834.314 209248.1044 1.122395585 1.146270098 1.146381621 1.038660366 1.10744026 1.133639359 1.153491133 1.08882379 1 17.67485503 -4.060237942 0.439070876 2.12E-06 1.124631844 0.533555896 0.034206367 371.0571037 5.261495424 350.460798 0.019313063 8.70E-05 4.060237942 1.124629725 DGPEPPS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGPEPPSPAK 10 0 Q9H4Z2-2;Q9H4Z2 Q9H4Z2-2 ZNF335 Zinc finger protein 335 1 DGPEPPS(1)PAK 100.55 0.0046879 0 261140 147440 204830 181170 195710 135850 260100 164620 239070 TRUE FALSE 244795.7135 158356.611 209688.6643 185819.1289 180339.7261 175067.6897 221100.4197 185173.1694 199167.6725 1.229093609 0.795091939 1.052824797 0.932978362 0.905466855 0.878996513 1.110122023 0.929735067 1 17.60362397 -0.961161285 5.064505108 1.000000155 0.971636743 0 0.124468946 1.96E-07 4.01E-08 0.10803379 0.025463669 0.109355018 0.961161285 -0.028363412 DGPIS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGPISPK 7 0 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 DGPIS(1)PK 81.263 0.029029 236050000 1266700 564880 792790 654090 749330 566990 1107200 696270 859410 TRUE FALSE 1187419.508 606704.303 811595.3532 670875.0568 690480.6445 730670.8087 941185.6387 783200.8422 715968.919 1.658479128 0.847389163 1.13356227 0.937017011 0.964400306 1.020534257 1.314562146 1.09390341 1 19.44953743 -0.7093165 8.292599785 1 1.09919504 0.018979798 0.229602517 0 0 0.202836618 0.047809049 0.195291572 0.7093165 0.09919504 DGPLNMILDDGGDLTNLIHTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGPLNMILDDGGDLTNLIHTK 21 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 234.23 9.04E-30 846100000 683280 522230 638870 628210 694110 499930 754430 555670 668640 FALSE TRUE 640514.7245 560896.4526 654024.2981 644330.9322 639597.4005 644251.6753 641310.2253 625046.6227 557039.6644 1.149854787 1.006923723 1.174107231 1.156705659 1.148208003 1.156563377 1.151282873 1.122086384 1 19.08742053 3.913478451 7.170108896 1.139874981 1.071152461 0.093299658 0.059757225 0.315860725 30.11983269 0.013247834 0.024154156 8193.669669 -3.913478451 -0.06872252 DGQAMLWDLNEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 324.67 3.67E-51 375741000 1124480 876590 976670 966950 985560 731260 1200490 828660 1117200 FALSE TRUE 1054100.804 941493.6357 999837.0736 991763.574 908158.0932 942362.891 1020487.669 932120.0251 930732.1026 1.132550173 1.011562439 1.074247972 1.065573618 0.975745965 1.012496387 1.096435447 1.001491216 1 19.82800644 DGQDAIAQS(ph)PEK ddPTM_SK-BR-3_Pertuzumab_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 271.45 1.08E-27 1451640000 5634300 2550120 3510000 3043650 2950980 2760250 4615780 2802700 3562310 TRUE FALSE 5281659.221 2738933.538 3593258.858 3121755.212 2719221.934 3557089.366 3923686.64 3152623.265 2967737.448 1.779692211 0.922902914 1.210773837 1.051897369 0.91626095 1.198586273 1.322113802 1.062298576 1 21.50093203 4.74829107 24.88570375 1.105998551 1.779692596 0.736711576 0.12989435 715.5765759 1830052.517 0.032290705 0.424197434 56013.28846 -4.74829107 0.673694045 DGQDAIAQS(ph)PEKESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DGQDAIAQSPEKESK 15 1 Q9NWH9;H7BXE3;H0YL55 Q9NWH9 SLTM SAFB-like transcription modulator 1 DGQDAIAQS(1)PEKESK;DGQDAIAQS(1)PEKESK;DGQDAIAQS(1)PEKESK;DGQDAIAQS(1)PEKESK;DGQDAIAQS(0.994)PEKES(0.006)K;DGQDAIAQS(1)PEKESK 225.3 6.17E-13 8796130000 11810144 4479366 6628673 5947813 7051769 4373745 8571190 5022439 11254081 TRUE FALSE 11070968.17 4811022.919 6785908.254 6100443.951 6497951.508 5636374.18 7286019.631 5649501.565 9375702.177 1.18081483 0.513137345 0.723776004 0.650665287 0.693062918 0.601168219 0.777117222 0.602568369 1 23.16049531 -1.138233535 4.367516808 1.000052037 0.697942895 0.186540826 0.181038653 7.95E-05 1.57E-05 0.152001086 0.035820839 0.072738856 1.138233535 -0.302109142 DGQPCMDHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DGQPCMDHDR 10 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRU9 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ;;;;; 147.58 2.02E-05 2118719000 1922377 2243410 1995434 2013485 2453410 1481532 2089207 2003235 2450600 FALSE TRUE 1802058.855 2409514.411 2042766.637 2065154.434 2260729.075 1909226.238 1775949.806 2253343.299 2041579.029 0.882678961 1.180220984 1.000581711 1.011547633 1.107343406 0.935171361 0.869890306 1.103725728 1 20.96125398 2.224053575 24.99389202 0.954905241 1.050048813 0.055133589 0.0965905 389.5382119 671123.0914 0.033862211 0.025119174 167.5149513 -2.224053575 0.095143572 DGQS(ph)SPQPSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGQSSPQPSPR 11 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 DGQS(0.629)S(0.371)PQPSPR 80.979 0.024051 22249000 54727 45873 55431 52464 59610 44126 53774 44991 54489 TRUE FALSE 51301.73476 49269.48465 56745.8495 53810.31506 54928.47106 56864.45987 45711.08791 50608.22539 45394.43389 1.130132714 1.085364007 1.250061839 1.185394562 1.210026568 1.252674723 1.006975613 1.114855304 1 15.47022779 1.713980869 9.494706233 1.047374508 1.18233081 0.574133898 0.058658816 0.085410521 18.96513858 0.028175164 0.0151621 51.75840317 -1.713980869 0.134956301 DGQSS(ph)PQPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGQSSPQPSPR 11 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 2 DGQS(0.163)S(0.837)PQPS(1)PR 68.277 0.075151 0 105960 112840 130690 167820 182500 84132 69917 58506 78527 TRUE FALSE 99328.15274 121194.791 133790.0285 172126.5453 168167.1862 108419.5426 59433.59493 65810.60289 65420.3364 1.51830697 1.852555301 2.045083164 2.631086216 2.570564375 1.657275835 0.908488067 1.005965523 1 15.99745156 1.904981161 3.697224513 0.979533998 2.101159468 0.724990389 0.322267267 0.136960893 3.213020121 0.169206422 0.094790007 80.34912668 -1.904981161 1.12162547 DGQSS(ph)PQPSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DGQSSPQPSPR 11 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 DGQS(0.027)S(0.973)PQPSPR;DGQS(0.019)S(0.981)PQPSPR;DGQS(0.007)S(0.993)PQPSPR;DGQS(0.012)S(0.988)PQPSPR;DGQS(0.088)S(0.912)PQPSPR;DGQS(0.1)S(0.9)PQPSPR;DGQS(0.248)S(0.752)PQPSPR 175.74 9.93E-06 2016115000 1694967 1663098 1640952 1594785 1827796 1355415 1764468 1394073 1754297 TRUE FALSE 1588882.041 1786235.506 1679876.156 1635709.883 1684248.275 1746701.307 1499902.404 1568126.083 1461493.498 1.087163264 1.222198737 1.149424311 1.119204352 1.152415853 1.195148189 1.026280587 1.072961382 1 20.47901198 1.702881351 7.012824866 1.037939227 1.160005676 0.655715671 0.041093812 0.073793385 8.129188777 0.019424534 0.010068371 50.45234432 -1.702881351 0.122066449 DGQWFTDWDAVPHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DGQWFTDWDAVPHSR 15 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ;;;;; 203.99 5.13E-09 1634350000 1655660 1884930 1840790 1841640 2007290 1548480 2041670 1651400 2416150 FALSE TRUE 1552035.196 2024492.178 1884454.408 1888899.6 1849645.54 1995501.039 1735540.537 1857580.925 2012878.956 0.771052423 1.005769459 0.936198574 0.938406949 0.918905498 0.991366636 0.862218035 0.922847804 1 20.94082899 -1.397612381 0.00594137 1.914374414 3.32E-06 0.109551768 0.066345154 67992.45414 67.44725712 11311.16863 10432.67168 0.040030187 1.397612381 -1.914371091 DGQYFEPVVPLPDLVEVSSGEENEQVVFSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGQYFEPVVPLPDLVEVSSGEENEQVVFSHR 31 0 P49792;J3KNE0;A6NKT7;O14715;Q99666;J3KQ37;F8VYC4;A0A286YES2;P0DJD0 P49792;F8VYC4 RANBP2;RGPD3;RGPD8;RGPD5;RGPD1 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6;RANBP2-like and GRIP domain-containing protein 1 0 ; 96.242 0.00036167 38352000 61471 61512 68013 65382 65566 70122 81242 54712 44513 FALSE TRUE 57623.63984 66066.41248 69626.30048 67059.81281 60416.71084 90365.08306 69060.51631 61542.91364 37083.49274 1.553889226 1.781558521 1.877555088 1.80834673 1.629207671 2.436800754 1.862298053 1.659577054 1 15.17848951 4.753554786 2.624794836 1.830921025 1.491166576 0 0.354537133 1.621482397 14.225788 0.077723719 1.232635138 56696.30888 -4.753554786 -0.339754449 DGRHPQGEQMYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DGRHPQGEQMYR 12 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 161.48 4.29E-05 360959000 64871.2 103674.3 90896.4 97154.9 139655.8 75398.4 90035 80991.2 114228.5 FALSE TRUE 60811.02739 111350.453 93052.50553 99648.05922 128687.7968 97164.69409 76535.08759 91103.1296 95163.02541 0.639019484 1.17010207 0.97782206 1.047130004 1.352287785 1.021034101 0.804252358 0.957337466 1 16.53811352 1.979676122 24.19831751 0.902245911 1.059304486 0.069818509 0.183707522 987.5272637 1175782.943 0.069935997 0.045789163 95.42806591 -1.979676122 0.157058576 DGSAFEDGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGSAFEDGLR 10 0 A0A3B3IRQ9;P55265-3;P55265-2;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 129.29 0.00071433 812830000 1406440 1439370 1437180 1461160 1510350 1299200 1652380 1312080 1340030 FALSE TRUE 1318413.431 1545942.452 1471270.588 1498655.839 1391733.203 1674257.949 1404620.959 1475896.076 1116370.336 1.180982142 1.38479356 1.317905484 1.342436099 1.246659069 1.499733462 1.258203406 1.322048812 1 20.09038426 0.227479794 1.42046119 0.999820488 1.32913406 0.576057224 0.085733365 4.875018853 8.242976703 0.07296469 0.020901877 1.688417301 -0.227479794 0.329313571 DGSCSAEYIPFAPGDYDVNITYGGAHIPGSPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGSCSAEYIPFAPGDYDVNITYGGAHIPGSPFR 33 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ; 139.74 5.05E-10 307410000 208588 205910 175901 163713 189963 168806 261400 198654 227230 FALSE TRUE 195532.8494 221155.7906 180073.4548 167914.1527 175044.0723 217537.5519 222205.4967 223456.3892 189303.845 1.032904796 1.168258313 0.951240345 0.887008675 0.924672567 1.14914492 1.173803399 1.180411254 1 17.53034419 2.21674786 24.95206564 1.144225763 1.006261764 0.334130334 0.090595372 280.7403196 321142.6138 0.036012589 0.026619596 164.720579 -2.21674786 -0.137963999 DGSDEPGTAACPNGSFHCTNTGYKPLYIPSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGSDEPGTAACPNGSFHCTNTGYKPLYIPSNR 32 1 K7ELL7;P14314-2;P14314;K7EPW7;K7EKX1;K7EJ70 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 301.78 4.98E-90 650110000 228065 306300 344720 368610 322080 248338 378640 331870 249866 FALSE TRUE 213790.8188 328978.7707 352896.9212 378069.1567 296785.136 320029.1492 321866.4471 373304.7 208161.7504 1.0270418 1.580399714 1.695301469 1.816227794 1.425742892 1.537406121 1.54623242 1.793339551 1 17.66734547 -1.064661045 6.970353135 0.999999828 1.56960666 0.377799718 0.221973649 5.48E-07 7.35E-08 0.197699268 0.04659815 0.0861666 1.064661045 0.569606832 DGSDVIYPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGSDVIYPAR 10 0 P25685;P25685-2;M0R080 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 138.98 0.0001174 187460000 426660 446050 430310 447190 470590 370630 500230 403860 485410 FALSE TRUE 399956.1122 479076.0061 440517.1564 458665.6525 433631.7597 477624.8643 425225.1554 454282.81 404391.9351 0.989030882 1.184682395 1.0893322 1.134210682 1.072305657 1.181093941 1.051517398 1.123372576 1 18.6253947 -0.323960969 0.65179685 0.991101519 1.111582172 0.217960013 0.05924465 11.4773843 4.222156071 0.307316004 0.019663992 0.474284609 0.323960969 0.120480652 DGSGDSHPDFPEDADIDLKDVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DGSGDSHPDFPEDADIDLKDVDK 23 1 Q08752 Q08752 PPID Peptidyl-prolyl cis-trans isomerase D 0 ;; 169.84 4.82E-12 177352000 648000 313542 392802 383461 430590 251045 533800 325049 567770 FALSE TRUE 607442.8367 336756.9759 402119.4489 393301.2585 396773.1983 323517.6161 453761.6456 365632.0832 473005.5191 1.284219343 0.711951473 0.850136907 0.831494016 0.838834183 0.68396161 0.959315753 0.772997499 1 18.85149749 -0.781191444 5.743122559 1.000000015 0.849432152 0.050363168 0.1678864 2.75E-08 6.08E-09 0.142115639 0.033496974 0.165504023 0.781191444 -0.150567863 DGSGT(ph)PSRHS(ph)LSGS(ph)SPGMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGSGTPSRHSLSGSSPGMK 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 DGS(0.005)GT(0.993)PS(0.003)RHS(0.999)LS(0.019)GS(0.669)S(0.314)PGMK 163.72 1.09E-08 306450000 338280 311900 336990 352180 335000 256210 422210 314390 343810 TRUE FALSE 317107.6586 334993.4005 344983.5619 361217.535 308690.4513 330173.6678 358903.5301 353642.2836 286425.8899 1.107119397 1.169563969 1.204442664 1.261120408 1.077732364 1.152736814 1.253041512 1.234672898 1 18.12780238 DGSGT(ph)PSRHS(ph)LSGSS(ph)PGMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGSGTPSRHSLSGSSPGMK 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 DGS(0.007)GT(0.988)PS(0.005)RHS(0.897)LS(0.164)GS(0.337)S(0.602)PGMK 168.43 6.97E-09 272930000 471690 407240 468980 479530 477030 352000 626230 419930 482790 TRUE FALSE 442167.7649 437392.4733 480104.4271 491835.5516 439565.988 453616.6858 532332.6251 472359.1849 402209.2301 1.099347633 1.087474977 1.193668348 1.222835069 1.092878918 1.12781272 1.323521653 1.174411599 1 18.61758666 4.006469064 3.275226614 1.181368333 1.093938843 0.066431409 0.085552363 0.454750689 9.98598516 0.021502015 0.049123007 10150.07063 -4.006469064 -0.08742949 DGSTEDTASSLCGEEDT(ph)EDEELEAAASHLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGSTEDTASSLCGEEDTEDEELEAAASHLNK 31 0 Q92994-9;Q92994-3;Q92994-7;Q92994-8;Q92994-5;Q92994;F8VS45 Q92994-9 BRF1 Transcription factor IIIB 90 kDa subunit 1 DGSTEDT(0.001)AS(0.002)S(0.005)LCGEEDT(0.991)EDEELEAAAS(0.001)HLNK 69.578 0.018215 103610000 67122 54864 65152 95691 74767 47440 62840 43750 64357 TRUE FALSE 62920.95384 58926.18765 66697.43621 98146.59306 68895.10142 61135.15788 53417.72538 49212.28381 53615.40094 1.173561192 1.09905338 1.243997714 1.830567176 1.284987153 1.140253674 0.996313083 0.917875889 1 15.71035985 1.949267153 2.515045763 0.967822977 1.305196598 0.40681115 0.195668432 0.342231868 3.971947476 0.113638563 0.060337803 88.97482709 -1.949267153 0.337373621 DGTAPPPQSPGSPGTGQDEEWS(ph)DEESPRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGTAPPPQSPGSPGTGQDEEWSDEESPRK 29 1 A0A0C4DGG1;Q9UKS6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 DGTAPPPQSPGSPGTGQDEEWS(0.995)DEES(0.005)PRK 173.81 7.53E-13 103970000 57758 45994 48610 53009 52624 39430 63131 45463 45145 TRUE FALSE 54143.02988 49399.44362 49763.05216 54369.30068 48491.12332 50812.80091 53665.09263 51139.15563 37610.00785 1.439591028 1.31346539 1.323133256 1.445607268 1.289314363 1.351044677 1.426883314 1.359722014 1 15.19882899 0.910490418 21.87161162 1 1.363686248 0.820819048 0.05408237 15953.104 3898136.902 0.050654779 0.012663695 8.137489071 -0.910490418 0.363686247 DGTGVVEFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DGTGVVEFVR 10 0 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;; 211.85 1.19E-07 1028930000 1508720 1596560 1517350 1459260 1757310 1338700 1725290 1425980 1945140 FALSE TRUE 1414291.908 1714770.964 1553342.259 1496707.082 1619297.961 1725160.958 1466598.781 1604016.742 1620483.568 0.872759179 1.058184728 0.958567115 0.923617562 0.999268362 1.064596391 0.905037737 0.989838326 1 20.62799296 3.711134273 24.45398847 0.973275056 0.987614433 0 0.062817391 2350.922579 3596023.166 0.015751973 0.024494707 5142.026056 -3.711134273 0.014339377 DGTS(ph)PEEEIEIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGTSPEEEIEIER 13 0 Q9H501 Q9H501 ESF1 ESF1 homolog 1 DGT(0.001)S(0.999)PEEEIEIER;DGT(0.014)S(0.986)PEEEIEIER 298.62 8.84E-41 487270000 937740 779270 800310 769690 829650 658150 875150 673420 880890 TRUE FALSE 879048.5273 836967.9616 819293.7311 789441.5485 764492.6356 848147.2208 743929.382 757497.9694 733863.7682 1.197836118 1.140495004 1.116411201 1.075733103 1.041736449 1.15572843 1.013715916 1.032205161 1 19.48515275 8 0.156329603 0.981200328 1.768917742 0.690557308 0.036544987 35.12989696 0.356582072 0.106380133 6.343645354 100000000 -8 0.787717414 DGTSLWDLLSSCHFTEEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DGTSLWDLLSSCHFTEEQR 19 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 273.32 2.25E-39 400623000 514870 777820 835370 842980 875470 693140 966370 764650 654960 FALSE TRUE 482645.2058 835410.6021 855185.3709 864612.294 806714.1177 893238.2658 821471.7898 860118.2357 545642.9448 0.884544023 1.531057279 1.567298504 1.584575229 1.478465222 1.637038056 1.505511613 1.576338967 1 19.05759767 -1.123482665 5.116259363 0.999983731 1.496442516 0.315787413 0.214725115 3.59E-05 6.16E-06 0.187521523 0.0441978 0.075251877 1.123482665 0.496458786 DGTSLWDLLSSCHFTEEQRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGTSLWDLLSSCHFTEEQRR 20 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 131.48 9.26E-06 255360000 122390 295580 232730 234170 245560 180120 230040 197900 283720 FALSE TRUE 114729.8284 317465.0508 238250.4655 240179.1986 226274.7081 232117.72 195547.6376 222608.2506 236365.2991 0.485392013 1.34311192 1.007975648 1.016135615 0.957309339 0.982029599 0.827311108 0.941797512 1 17.85065872 2.494293727 1.60680985 0.9107319 1.036515487 0 0.215480031 1.175368485 6.151357294 0.092999987 0.073085861 312.0999698 -2.494293727 0.125783587 DGTTHQTSLELFMYLNEVAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DGTTHQTSLELFMYLNEVAGK 21 0 P00966 P00966 ASS1 Argininosuccinate synthase 0 ;; 218.07 5.57E-25 1285534000 693130 765940 836770 810850 894250 677040 1035550 804060 779000 FALSE TRUE 649748.2306 822650.9946 856618.5796 831657.7838 824019.2122 872490.4572 880278.8911 904448.661 648979.8675 1.001183955 1.26760634 1.319946307 1.28148472 1.269714599 1.344402964 1.356404005 1.393646716 1 19.3078142 4.751108393 3.244574852 1.301377522 0.954031835 0.3831178 0.108525801 0.312273535 5.159113536 0.022742688 0.277752616 56377.83477 -4.751108393 -0.347345687 DGTVLCELINALYPEGQAPVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DGTVLCELINALYPEGQAPVKK 22 1 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ;; 218.57 1.87E-25 389220000 1755660 1421690 1399930 1409930 1581740 990000 2063430 1395890 2526520 FALSE TRUE 1645776.375 1526953.407 1433137.001 1446111.191 1457516.521 1275796.929 1754037.827 1570169.939 2104827.49 0.781905587 0.725452995 0.680880978 0.687044994 0.692463647 0.606128975 0.833340421 0.745985097 1 21.00527057 0.659154801 0.96575554 0.998618714 0.701991003 0.704417386 0.05839587 0.588355616 0.932746025 0.052726443 0.017151121 4.561994955 -0.659154801 -0.296627711 DGVADVSIEDSVISLSGDHCIIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGVADVSIEDSVISLSGDHCIIGR 24 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ; 341.24 2.19E-87 299330000 267427 261850 267430 230964 224816 291930 322530 254850 211440 FALSE TRUE 250689.2214 281237.6465 273773.5659 236890.9273 207159.8582 376205.4519 274169.6207 286668.5835 176149.298 1.423163329 1.596586813 1.55421321 1.344830379 1.176047027 2.13571928 1.556461614 1.627418256 1 17.4264392 DGVLALDNFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGVLALDNFHR 11 0 Q70J99;Q70J99-3;K7EMK8 Q70J99 UNC13D Protein unc-13 homolog D 0 ; 197.3 5.75E-08 445180000 780250 862100 796960 831770 990710 701080 1025560 904360 839740 FALSE TRUE 731415.5453 925930.781 815864.2676 853114.6264 912903.6329 903470.4149 871786.7988 1017271.337 699581.9691 1.045503712 1.323548665 1.166216832 1.219463428 1.304927333 1.291443254 1.2461539 1.454113144 1 19.41613358 2.877655116 5.956372152 1.274313555 1.206101292 0.055769183 0.129443778 0.689286206 30.8175239 0.035295437 0.037594788 754.4928286 -2.877655116 -0.068212263 DGVLEEQIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DGVLEEQIER 10 0 Q09161;X6R941 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 ;; 194.94 9.51E-07 763840000 486110 486690 500957 500922 467674 340817 552366 439057 485307 FALSE TRUE 455685.2428 522725.034 512839.9366 513776.5066 430944.7705 439205.3352 469543.8462 493874.2329 404306.1265 1.127079737 1.29289417 1.268444634 1.270761121 1.065887312 1.086318773 1.161357238 1.221535368 1 18.62508854 2.747986261 24.92913634 1.118787073 1.25341975 0.438239302 0.073317331 573.978123 1518069.027 0.021301684 0.022336507 559.7398933 -2.747986261 0.134632677 DGVPEGAQLQGPVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGVPEGAQLQGPVHR 15 0 P16989;P16989-3;P16989-2 P16989;P16989-2 YBX3 Y-box-binding protein 3 0 ; 161.49 1.65E-06 719120000 596890 538820 582290 576320 572320 542210 689680 529570 437030 FALSE TRUE 559531.7204 578714.7934 596102.1938 591109.3469 527372.2958 698737.225 586268.8867 595687.9802 364086.8697 1.536808292 1.589496468 1.637252654 1.623539315 1.448479305 1.91914975 1.61024452 1.636114976 1 18.47392319 -0.993022576 4.517729016 0.999983495 1.629440493 0.731633601 0.118960097 0.250147658 32838874.27 1353.107848 0.025530066 0.101619587 0.993022576 0.629456998 DGVTVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGVTVAK 7 0 P10809;E7EXB4;E7ESH4;P10809-2;C9JCQ4;C9JL25;C9JL19 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 89.142 0.042085 88426000 259190 269960 260060 261000 353110 234020 287450 275130 356780 FALSE TRUE 242967.7606 289948.1193 266228.746 267697.7019 325378.165 301577.775 244349.5411 309480.5861 297231.1131 0.817437172 0.975497202 0.895696091 0.900638224 1.094697529 1.014623846 0.822086014 1.041211947 1 18.18122561 4.74430344 23.6991519 0.954232995 0.817437047 0.245582487 0.079757451 483.3719705 1994623.412 0.018603348 0.161743157 55501.33635 -4.74430344 -0.136795949 DGVVEITGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGVVEITGK 9 0 P04792 P04792 HSPB1 Heat shock protein beta-1 0 145.17 0.00022753 118390000 739720 602040 666950 600670 764160 465050 766010 653160 1030900 FALSE TRUE 693422.2456 646615.668 682770.369 616084.2091 704145.9561 599302.3855 651153.9118 734708.4638 858836.1301 0.807397618 0.752897608 0.79499493 0.717347801 0.819883947 0.697807608 0.758181787 0.855469906 1 19.71202336 0.947024769 3.025636066 0.999504669 0.763038505 0.802200596 0.037735764 0.109999534 2.453693286 0.032497497 0.008533624 8.851660915 -0.947024769 -0.236466164 DGVVEITGKHEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGVVEITGKHEER 13 1 P04792 P04792 HSPB1 Heat shock protein beta-1 0 154.07 2.77E-05 151320000 87769 121160 73355 103690 231260 47202 123530 103360 605530 FALSE TRUE 82275.69496 130130.8125 75095.01524 106350.8609 213097.7725 60828.45114 105007.8233 116264.7235 504463.1311 0.163095556 0.257959015 0.148861256 0.210819888 0.42242487 0.120580569 0.208157577 0.230472192 1 18.94438931 0.691054635 5.687304473 0.999999988 0.217052495 0.8988266 0.082217752 12.46088309 229.4038879 0.073446994 0.018491477 4.909696376 -0.691054635 -0.782947493 DGVVRPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DGVVRPLK 8 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;; 122.52 0.001265 31450920000 30528730 27821420 32152320 30476830 29987010 25020640 40206140 28976430 27820790 FALSE TRUE 28617991.28 29881346.88 32914988.21 31258917.05 27631951.2 32243692.59 34177602.56 32594201.07 23177320.42 1.234741151 1.289249419 1.420137773 1.348685546 1.192197834 1.391174303 1.47461406 1.406297211 1 24.46621045 4.460315195 2.904347845 1.349782043 1.238093472 0 0.138518192 0.769343948 12.26649237 0.031666698 0.147639142 28861.25389 -4.460315195 -0.111688571 DGVYFLYEALHGPPKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGVYFLYEALHGPPKK 16 1 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 180.49 1.60E-09 150130000 663180 522710 657940 590350 699310 472090 818930 575610 995000 FALSE TRUE 621672.7476 561411.9923 673546.6475 605499.3805 644389.0135 608374.7193 696139.0491 647476.1756 828928.0721 0.749971884 0.677274677 0.812551378 0.730460701 0.777376271 0.733929444 0.839806339 0.781100553 1 19.6608874 -5 0.163799203 1.926628629 0.698944118 0.798654868 0.039095062 52.86126087 0.491382768 15.8132446 0.143332901 1.00E-05 5 -1.227684512 DGWGGYGSDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGWGGYGSDKR 11 1 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 77.74 0.050972 341090000 427660 397940 379850 396700 449410 272780 397230 391340 559420 FALSE TRUE 400893.524 427403.8917 388860.2214 406879.9936 414115.1514 351527.1578 337669.0492 440199.6604 466049.188 0.860195735 0.917078932 0.834375923 0.873040881 0.888565332 0.754270508 0.724535216 0.944534765 1 18.8301227 2.288826252 24.99996661 0.818463228 0.87487168 0 0.085388296 255.263417 126955.9139 0.027798674 0.023258001 194.4581959 -2.288826252 0.056408452 DGWLYGEHDVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGWLYGEHDVSK 12 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 0 ; 102.66 0.00233 126480000 382220 323440 350930 339250 390340 284970 419930 320890 397250 FALSE TRUE 358297.5325 347387.8341 359254.2253 347955.7293 359684.271 367236.2129 356965.3949 360953.8229 330946.4087 1.082645175 1.049680024 1.085535954 1.051395997 1.086835396 1.109654625 1.078619938 1.090671521 1 18.33623809 3.951986682 18.2293042 1.077162489 1.064283055 0 0.030862445 61.07213486 44294.02987 0.007021518 0.012688992 8953.373095 -3.951986682 -0.012879434 DGWPAMCIHGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DGWPAMCIHGDK 12 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;; 146.5 6.26E-05 2161620000 3492400 2986560 3223220 3023350 3747160 2420150 3857140 3091340 4206880 FALSE TRUE 3273816.918 3207688.01 3299676.301 3100934.28 3452873.169 3118808.017 3278797.665 3477300.604 3504724.551 0.934115327 0.915246823 0.941493762 0.884786874 0.985205291 0.889886772 0.935536479 0.992175149 1 21.74086963 1.247163516 4.405844405 0.998951282 0.925593616 0.523035776 0.027775497 0.13445393 5.704668945 0.0200756 0.005983858 17.66702874 -1.247163516 -0.073357667 DGWPAMGIHGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DGWPAMGIHGDK 12 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;; 122.45 0.00035835 1877270000 2017080 1681440 1754380 1728910 2019020 1410630 2031680 1620490 2508980 FALSE TRUE 1890834.563 1805935.567 1795994.722 1773276.758 1860454.314 1817855.981 1727048.445 1822811.744 2090215.029 0.904612462 0.863995111 0.859239216 0.848370494 0.890077952 0.869698072 0.82625396 0.872069006 1 20.99521994 0.951245097 23.43615974 1 0.862857185 0.793476946 0.021331552 3072.510264 1476937.276 0.020078062 0.005019516 8.938097681 -0.951245097 -0.137142816 DGWPVSLSNSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGWPVSLSNSVR 12 0 Q96RW7-2;Q96RW7 Q96RW7-2 HMCN1 Hemicentin-1 0 57.164 0.066589 259940000 210500 160950 152520 130440 172310 101640 152550 131390 186120 FALSE TRUE 197325.1808 172866.9055 156137.8464 133787.3112 158777.4677 130981.818 129676.5437 147794.3307 155055.3696 1.272611076 1.1148721 1.006981227 0.862835718 1.024004961 0.844742226 0.836324108 0.953171316 1 17.24242396 4.687031743 0.663430556 0.897037354 1.482722667 0.743944111 0.067310242 1.381076412 0.4798547 0.027469511 0.607776379 48644.27593 -4.687031743 0.585685313 DGWQVEEADDWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DGWQVEEADDWLR 13 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ;; 189.33 1.25E-05 336911000 523750 659430 565290 618490 637190 409070 636270 531720 324852 FALSE TRUE 490969.4224 708254.8833 578698.9457 634361.5005 587147.6677 527161.8683 540867.2203 598106.4125 270632.1026 1.814158105 2.61703943 2.138323356 2.343999453 2.169541832 1.947891116 1.99853312 2.210034977 1 18.04597346 -1.644929538 0.298039007 7.35E-11 2.305563227 0.719765788 0.224728168 11.97017727 0.645240986 9.036263199 0.226070796 0.022650118 1.644929538 2.305563227 DGWSLWYSEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DGWSLWYSEYR 11 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;; 210.27 3.10E-08 431018000 803320 898580 528569 447452 680940 350905 665109 828230 384900 FALSE TRUE 753041.6352 965111.7982 541106.9063 458934.3759 627461.7192 452205.577 565382.08 931636.3387 320657.7035 2.34842833 3.009788281 1.687490743 1.431228288 1.956796024 1.410243921 1.763195064 2.905392038 1 18.29067454 3.876981846 3.817327207 1.746443626 2.682491148 0.365450148 0.514970392 0.217970674 5.839811293 0.123170895 0.239323503 7533.240737 -3.876981846 0.936047521 DGYAQILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DGYAQILR 8 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ; 81.215 0.053078 112610000 283877 400890 320420 315606 455180 269744 305789 405110 422640 FALSE TRUE 266109.6453 430572.3127 328020.5137 323704.9843 419431.9989 347614.7139 259938.7783 455688.8753 352098.6536 0.755781491 1.222874067 0.931615359 0.919358768 1.191234316 0.987265104 0.73825553 1.294207946 1 18.42562019 2.001625616 24.9986512 0.951993904 1.025996593 0 0.189871014 220.6420038 3392974.654 0.066526993 0.048779156 100.3750133 -2.001625616 0.074002689 DGYDYDGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DGYDYDGYR 9 0 J3KTL2;Q07955;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;;; 159.46 0.00015364 13543310000 7762120 8469390 8214580 7989250 9151000 6745920 9183700 7733900 10079840 FALSE TRUE 7276302.765 9096472.448 8409433.717 8194267.681 8432317.373 8693357.593 7806689.442 8699494.439 8397449.586 0.866489604 1.083242281 1.001427116 0.975804332 1.004152188 1.035237843 0.929650052 1.035968642 1 23.0015198 DGYGGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DGYGGSR 7 0 P38159;P38159-2;H3BUY5;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 101.41 0.02112 82331000 239610 231300 245560 234940 246220 202240 246050 211710 248620 FALSE TRUE 224613.2378 248425.6927 251384.7992 240968.9582 226882.8744 260623.4049 209157.0867 238142.4595 207123.7159 1.084439978 1.19940728 1.213693942 1.163405925 1.095397857 1.258298229 1.00981718 1.149759498 1 17.66013323 1.249409228 0.70611277 1.007177156 1.178490647 0.31389507 0.070069637 0.640710741 0.745375253 0.061210098 0.025671024 17.75862056 -1.249409228 0.17131349 DGYGGSRDS(ph)YSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.999)YSSSR;DGYGGSRDS(1)YSSSR 145.18 5.24E-06 611640000 308290 346250 311910 317100 429650 273210 411970 349110 514120 TRUE FALSE 288994.6792 371886.7103 319308.6525 325237.3228 395907.0221 352081.2918 350198.923 392697.152 428310.0507 0.674732425 0.868265196 0.745508194 0.759350201 0.924346794 0.822024352 0.817629478 0.916852526 1 18.70829601 -5 0.089313524 1.646737647 0.649675757 0.571692496 0.062803476 164.0290867 1.020001408 19.94002131 1.430153136 1.00E-05 5 -0.99706189 DGYNYTLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DGYNYTLSK 9 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;;;;; 183.43 0.0001051 5149750000 3170780 3511430 2760870 2712420 3967600 2084878 3077040 3428830 4041620 FALSE TRUE 2972326.54 3771419.931 2826359.14 2782025.289 3656000.701 2686748.433 2615666.418 3856926.973 3367047.512 0.882769408 1.120097034 0.839417659 0.826250678 1.085817972 0.797953823 0.776842741 1.145492292 1 21.68305265 DGYSYGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DGYSYGSR 8 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;; 113.14 0.0067622 2360510000 1593400 1774930 1572690 1587650 1945610 1255510 1912660 1625350 2003950 FALSE TRUE 1493671.938 1906347.664 1609994.949 1628391.787 1792809.639 1617955.355 1625874.389 1828278.525 1669477.799 0.894694101 1.141882609 0.964370386 0.975389902 1.073874501 0.969138587 0.973882007 1.095119999 1 20.67096548 3.759006258 24.97218976 1.003577036 1.04109923 0 0.074031429 1148.362274 899385.0525 0.017248583 0.031091449 5741.247355 -3.759006258 0.037522194 DHAGVMGESNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DHAGVMGESNR 11 0 P52306-4;P52306;P52306-5;P52306-6;P52306-2;P52306-3 P52306-4 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 0 ;;; 103.46 0.002731 935730000 457171 430827 441496 445156 514278 394458 543700 461150 556126 FALSE TRUE 428557.4832 462725.8794 451968.4936 456579.4566 473888.6804 508331.6211 462177.2325 518725.5926 463304.9779 0.925000817 0.998750071 0.97553127 0.985483598 1.022843921 1.097185753 0.997565868 1.119620158 1 18.82160266 2.655580944 3.121386619 1.049840425 0.975684677 0.462400841 0.041666685 0.235741327 4.47047942 0.012803803 0.012149802 452.4607843 -2.655580944 -0.074155748 DHAISLSEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DHAISLSEPR 10 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 ; 173.64 1.35E-05 505070000 276510 399830 355640 352040 400900 350310 392160 326670 374430 FALSE TRUE 259203.7327 429433.8292 364075.9487 361073.9424 369414.9312 451438.8102 333359.2486 367455.4686 311935.2141 0.83095374 1.376676341 1.167152448 1.157528634 1.184268125 1.447219774 1.068681039 1.177986492 1 18.2508869 0.830337074 1.448868875 1.003236466 1.204770391 0.084643 0.166486474 1.313610852 5.141082199 0.141598648 0.041720029 6.766079159 -0.830337074 0.201533925 DHALLEEQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DHALLEEQSK 10 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 99.985 0.0043221 330550000 569400 515400 520880 489730 603860 445730 688710 595700 1728100 FALSE TRUE 533762.2704 553560.7523 533235.5196 502297.3009 556435.2715 574405.0152 585444.3292 670074.4563 1439668.946 0.370753479 0.384505586 0.370387596 0.348897781 0.386502239 0.398984098 0.406652051 0.465436487 1 20.45730567 0.013218827 0.785467008 1.016464324 0.372069919 0.996897593 0.010788222 0.251264248 0.158283799 0.022339157 0.003636443 1.030905429 -0.013218827 -0.644394404 DHASIQMNVAEVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DHASIQMNVAEVDK 14 0 Q8WVC2;P63220;Q9BYK1 Q8WVC2 RPS21 40S ribosomal protein S21 0 ;; 126.88 8.28E-05 1495640000 903100 1351910 1444670 1318190 1445180 1250610 1838820 1324840 1140270 FALSE TRUE 846576.5831 1452006.823 1478938.255 1352016.987 1331681.392 1611640.805 1563106.012 1490249.19 949951.5706 0.891178676 1.528506156 1.556856476 1.423248331 1.40184135 1.696550493 1.645458632 1.568763331 1 19.85749444 4.739050078 24.42963725 1.519847602 0.891178429 0.458443672 0.195601024 22.59164111 1127130.952 0.04127544 0.244086637 54834.01892 -4.739050078 -0.628669174 DHASIQMNVAEVDKVTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DHASIQMNVAEVDKVTGR 18 1 Q8WVC2;P63220;Q9BYK1 Q8WVC2 RPS21 40S ribosomal protein S21 0 ;;; 278.22 2.17E-39 2856200000 1025590 2301720 2107370 2126930 2541610 1720950 2706420 2152770 2601020 FALSE TRUE 961400.1526 2472141.744 2157357.812 2181510.625 2342002.203 2217760.328 2300617.446 2421548.073 2166892.959 0.443676809 1.140869342 0.995599622 1.00674591 1.080811211 1.023474795 1.061712549 1.117520856 1 21.04719646 4.743559565 24.99999059 1.053699742 0.443676558 0.93797284 0.049270714 113.0377827 565289.5339 0.011067185 0.091915748 55406.35299 -4.743559565 -0.610023184 DHAVVVGVYRPPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DHAVVVGVYRPPPK 14 1 P22087 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ; 96.306 0.0020572 643910000 897490 831200 881610 828990 931970 642600 1054940 857230 1143360 FALSE TRUE 841317.703 892742.9129 902522.2055 850263.2869 858776.8356 828108.1883 896761.5406 964257.0525 952525.8296 0.883249227 0.937237485 0.94750418 0.892640662 0.901578528 0.869381346 0.941456402 1.012315911 1 19.86139869 1.358534634 4.032951979 1.005907602 0.912819176 0.739059293 0.024202631 0.128727414 3.27632065 0.020001899 0.006705815 22.83150993 -1.358534634 -0.093088426 DHENIVIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DHENIVIAK 9 0 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ;;;;; 140.16 0.00010975 8063910000 27980800 19690300 23456600 22163700 18569600 18598700 31082900 18696500 14485010 FALSE TRUE 26229531.68 21148190.3 24013001.63 22732458.07 17111218.52 23967842.77 26422307.7 21030799.18 12067368.25 2.173591716 1.75251056 1.989912061 1.883795836 1.417974339 1.986169831 2.189566702 1.74278258 1 23.52460774 0.97242074 23.57579556 0.999999993 1.908986935 0.631532884 0.217934646 937.1990552 801154.6519 0.206552735 0.051638184 9.384707485 -0.97242074 0.908986943 DHFEEAMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DHFEEAMR 8 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;; 190.26 0.00017299 5283100000 4419570 6978270 4050140 4009940 7269370 2494830 3779430 5829550 7500720 FALSE TRUE 4142957.003 7494948.372 4146211.233 4112841.849 6698463.003 3215046.921 3212739.558 6557382.15 6248801.375 0.663000271 1.199421764 0.663521047 0.658180922 1.071959661 0.514506179 0.51413693 1.049382394 1 22.57514805 3.807128879 6.550203782 0.738840252 0.961774321 0.035786414 0.243717645 0.429783119 28.72039646 0.059114644 0.107282656 6413.998868 -3.807128879 0.222934069 DHFNKK ddPTM_SK-BR-3_Pertuzumab_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 0 106.84 0.02063 186200000 867970 672910 777560 856700 867080 618520 933950 750760 867350 FALSE TRUE 813645.3071 722732.9566 796004.0904 878684.3724 798983.0344 797076.6832 793912.8679 844494.0386 722583.6817 1.126022256 1.000206585 1.101608174 1.216031298 1.105730803 1.10309256 1.098714084 1.168714517 1 19.46280515 3.64540122 4.909436008 1.12028288 1.053258343 0.094039903 0.062513671 0.322614427 13.62662959 0.015192055 0.024190151 4419.785776 -3.64540122 -0.067024537 DHGDMTNRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DHGDMTNRK 9 1 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 46.606 0.088946 15319000 16622 16647 15381 14781 18676 12252 16737 16497 17380 FALSE TRUE 15581.65869 17879.5612 15745.84458 15160.30548 17209.2623 15788.95351 14227.44223 18556.68676 14479.16572 1.076143404 1.234847473 1.087482862 1.047042749 1.188553445 1.090460169 0.982614779 1.281612983 1 13.82169086 1.368582374 0.014443902 1.09E-06 2.17783453 0.069982348 0.094014307 996.3897712 13.69962852 1037.556448 1024.668386 23.36589251 -1.368582374 2.177833445 DHGGALGPEEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DHGGALGPEEFK 12 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 66.498 0.057896 153510000 151050 439420 319430 365630 493730 376150 352790 319070 720870 FALSE TRUE 141596.0501 471955.114 327007.0304 375012.6848 454954.4374 484738.3987 299892.4146 358906.5919 600552.14 0.235776448 0.785868674 0.544510641 0.624446505 0.757560263 0.807154561 0.499361162 0.597627696 1 19.19592998 -2.693416099 1.985238817 9.99997233 0.621922125 0.351578204 0.166768658 4106729.204 131068.4784 167197524.8 0.037852833 0.002025741 2.693416099 -9.378050205 DHGGIFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DHGGIFSR 8 0 Q5VT52-2;Q5VT52-3;Q5VT52 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 0 90.15 0.0134 129420000 25303 39894 33649 30342 45003 34624 29749 30296 34907 FALSE TRUE 23719.3304 42847.79327 34447.17017 31120.62709 41468.64591 44619.38673 25288.41363 34078.52229 29080.79619 0.815635523 1.473405095 1.184533255 1.070143571 1.425980418 1.534324797 0.869591515 1.171856577 1 14.82777915 1.704913415 13.4796106 1.017100543 1.268491627 0.202103087 0.219850205 0.188152585 63.20803681 0.095466094 0.052480775 50.68896402 -1.704913415 0.251391084 DHIIDDALVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DHIIDDALVR 10 0 A0A1B0GVL3;Q05086-2;Q05086-3;Q05086;A0A0D9SG77 A0A1B0GVL3 UBE3A Ubiquitin-protein ligase E3A 0 146.11 2.92E-05 84010000 109540 132210 120400 118280 135130 99493 116060 106370 122440 FALSE TRUE 102684.0869 141998.966 123255.9449 121315.265 124517.4349 128215.014 98657.88045 119650.5286 102003.973 1.006667524 1.392092502 1.20834455 1.189319018 1.220711618 1.256960981 0.967196449 1.172998709 1 16.63826582 1.750007238 25 1.04997818 1.232062827 0.335366001 0.107515162 3.058842355 6692.488742 0.04577515 0.025384684 56.23506977 -1.750007238 0.182084647 DHIMEIFSTYGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DHIMEIFSTYGK 12 0 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BV80 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 0 ; 160.86 6.69E-05 701548000 2015740 1778100 1860560 1815220 2210730 1568720 2270870 1875180 2586750 FALSE TRUE 1889578.432 1909752.374 1904693.362 1861801.618 2037108.183 2021583.998 1930374.125 2109300.351 2155004.714 0.876832621 0.886194059 0.883846494 0.863943177 0.945291753 0.93808797 0.895763296 0.978791525 1 21.03925959 1.285838927 0.396028774 1.007053134 0.873015452 0.716943795 0.02434994 0.619651291 0.291737163 0.03257729 0.021574618 19.31251913 -1.285838927 -0.134037682 DHINLPGFSGQNPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DHINLPGFSGQNPLR 15 0 P00491;G3V5M2 P00491 PNP Purine nucleoside phosphorylase 0 ;;; 184.99 4.41E-07 1925980000 1299050 2431110 1004300 1029300 2589080 975134 1181810 2504650 1248740 FALSE TRUE 1217744.779 2611111.914 1028122.47 1055713.581 2385744.101 1256639.356 1004608.562 2817361.066 1040317.227 1.170551393 2.509918943 0.988277848 1.014799672 2.293285201 1.20793862 0.965675215 2.708174962 1 19.98859209 3.964764187 24.41687342 1.421643232 1.91255354 0.049575815 0.675526377 660.2075766 1304537.322 0.15892085 0.289266632 9220.706257 -3.964764187 0.490910308 DHINLPGFSGQNPLRGPNDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DHINLPGFSGQNPLRGPNDER 21 1 P00491;G3V5M2 P00491 PNP Purine nucleoside phosphorylase 0 60.747 0.032669 495500000 121820 140690 122980 99974 130610 106470 140170 97902 125450 FALSE TRUE 114195.5037 151106.834 125897.1437 102539.5021 120352.4175 137206.1606 119152.8098 110125.2802 104511.5846 1.09265881 1.44583813 1.204623815 0.981130489 1.151570115 1.312832077 1.140091888 1.053713621 1 16.67330334 1.946500045 0.127728319 0.862481084 1.449079277 0.189630104 0.127512448 10.43309532 1.111886465 2.034115295 2.533092106 88.40972617 -1.946500045 0.586598193 DHNEEEGEETGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DHNEEEGEETGLR 13 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ; 203.11 8.85E-08 278240000 285190 220390 263790 231010 207832 239080 323120 224520 192492 FALSE TRUE 267340.467 236707.9049 270047.2234 236938.1077 191509.7131 308098.5149 274671.1557 252551.8162 160363.8417 1.667086946 1.476067812 1.68396579 1.477503315 1.194220038 1.921246783 1.712799799 1.574867586 1 17.29098936 -1.861714812 2.346528864 0.717899204 1.595526903 0.488059803 0.189285996 5879050.251 3216304.659 9249591.968 0.046482731 0.013749446 1.861714812 0.877627699 DHNS(ph)EDEDEDKYADDIDMPGQNFDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DHNSEDEDEDKYADDIDMPGQNFDSK 26 1 O95391 O95391 SLU7 Pre-mRNA-splicing factor SLU7 1 DHNS(0.818)EDEDEDKY(0.182)ADDIDMPGQNFDSK;DHNS(1)EDEDEDKYADDIDMPGQNFDSK;DHNS(0.948)EDEDEDKY(0.052)ADDIDMPGQNFDSK 179.64 1.37E-17 496890000 915940 312721 489380 446845 428182 313579 619410 356478 532630 TRUE FALSE 858612.9504 335875.1882 500988.3247 458311.7992 394554.3129 404104.1668 526535.2208 400985.063 443730.6121 1.934986965 0.756934904 1.129037103 1.032860449 0.889175329 0.910697067 1.186610088 0.903667793 1 18.75932456 4.74722735 24.91849667 0.987721643 1.934987467 0.855655046 0.123687219 390.5853546 1122981.048 0.029011124 0.342521786 55876.26259 -4.74722735 0.947265824 DHNVGSPPKS(ph)PTHASPQHTQTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DHNVGSPPKSPTHASPQHTQTEK 23 1 A0A0C4DGH6;A0JNW5;F8W665;A0JNW5-2 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 DHNVGSPPKS(0.994)PT(0.006)HASPQHTQTEK;DHNVGSPPKS(0.997)PT(0.003)HASPQHTQTEK;DHNVGS(0.001)PPKS(0.966)PT(0.022)HAS(0.001)PQHT(0.001)QT(0.01)EK;DHNVGSPPKS(0.993)PT(0.006)HASPQHTQTEK;DHNVGSPPKS(0.993)PT(0.007)HASPQHTQTEK 261.94 4.26E-44 982787000 239696 346782 405484 476119 497658 297685 388913 260697 366517 TRUE FALSE 224693.8552 372458.1001 415102.272 488337.0196 458573.9481 383621.827 330599.1061 293245.5943 305342.9449 0.735873741 1.219802541 1.359462463 1.599306707 1.501832467 1.256363814 1.082714082 0.960381103 1 18.22007099 1.651065115 2.935309946 0.989338615 1.304127912 0.237179575 0.226511797 0.315469667 6.340119865 0.146083627 0.061909316 44.77804362 -1.651065115 0.314789297 DHPESYHSFMWNNFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DHPESYHSFMWNNFFK 16 0 D6RAY7;D6R9P4;D6RFF8;P46926;D6R917;D6RB13 D6RAY7 GNPDA1 Glucosamine-6-phosphate isomerase;Glucosamine-6-phosphate isomerase 1 0 81.311 0.0075951 268040000 450320 620170 484280 504700 704670 355260 637000 617390 679080 FALSE TRUE 422135.275 666088.0321 495767.3503 517651.4565 649328.0607 457817.7948 541487.7636 694472.5005 565737.161 0.746168546 1.177380731 0.876320992 0.915003454 1.147755717 0.809241157 0.957136637 1.227553268 1 19.10977241 1.27028701 24.78942731 1.113776652 0.961264081 0.183545046 0.143807458 260.515412 203553.9833 0.087129451 0.031811111 18.63318132 -1.27028701 -0.152512571 DHPLPEVAHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DHPLPEVAHVK 11 0 H3BN72;H3BNV9;P13073;Q86WV2;H3BPG0 H3BN72 COX4I1 "Cytochrome c oxidase subunit 4 isoform 1, mitochondrial" 0 ;;; 165.66 1.23E-05 806080000 1596160 1380260 1198880 1277060 1977310 1296890 1390110 1882010 2415990 FALSE TRUE 1496259.195 1482455.887 1227318 1309831.522 1822020.049 1671281.09 1181675.911 2116983.091 2012745.661 0.743392086 0.736534136 0.60977302 0.650768523 0.905241076 0.830348872 0.587096489 1.051788675 1 20.94073345 1.226562298 24.99775378 1.02589462 0.715955054 0.629617117 0.096356389 162.0110985 337529.5791 0.090801618 0.023406847 16.84854095 -1.226562298 -0.309939566 DHPSSHSAQPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DHPSSHSAQPPR 12 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 ; 131.17 0.00011764 82440700 15295.4 23838.7 23017.6 23342.3 27184.5 18460.7 25845.3 24400 26241.7 FALSE TRUE 14338.08822 25603.74215 23563.58834 23941.30294 25049.53903 23790.00441 21970.0372 27446.39371 21861.79074 0.655851498 1.171163994 1.077843468 1.095120853 1.145813686 1.08820017 1.004951399 1.25545039 1 14.41612396 4.743968431 24.9881853 1.102267755 0.655851308 0.778775962 0.075190543 251.8924968 1163898.033 0.016328255 0.141116144 55458.53988 -4.743968431 -0.446416446 DHQPCIIFMDEIDAIGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DHQPCIIFMDEIDAIGGR 18 0 A0A087X2I1;P62333;H0YJX2 A0A087X2I1;H0YJX2 PSMC6 26S protease regulatory subunit 10B 0 ;;;;;; 189.44 3.27E-14 605147900 310335 323861.1 332403.5 332491.2 338245 279036.4 375138 298483.7 337217.9 FALSE TRUE 290911.6863 347840.1128 340288.268 341023.4871 311680.6021 359589.6789 318889.5395 335750.047 280934.054 1.035515923 1.238155745 1.211274544 1.213891596 1.109444005 1.279978962 1.135104609 1.1951205 1 18.09987199 -1.26639307 2.550448025 0.99750379 1.185689303 0.383046686 0.070005074 1150057.62 1266734.38 22222.78801 0.015771073 0.054151056 1.26639307 0.188185513 DHQYQFLEDAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DHQYQFLEDAVR 12 0 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;; 230.96 4.58E-12 1876680000 2292320 2739580 2036320 2037870 2826740 1649050 2476040 2507010 2552970 FALSE TRUE 2148847.783 2942421.354 2084622.472 2090165.194 2604739.243 2125103.965 2104780.788 2820015.717 2126862.814 1.010336806 1.383456109 0.980139602 0.982745657 1.224686061 0.999173031 0.98961756 1.325903908 1 21.02029555 3.901696759 7.468497397 1.065454945 1.217839083 0.107630417 0.146151739 0.388452423 33.24959495 0.034165839 0.0620677 7974.376919 -3.901696759 0.152384138 DHRDNLEFFLAGIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 166.9 8.06E-07 2651602000 2127263 3133256 2951530 3279428 3935838 2319691 3574557 2941860 4951401 FALSE TRUE 1994121.406 3365245.534 3021541.685 3363583.675 3626733.16 2989348.135 3038585.362 3309157.697 4124980.186 0.483425693 0.815821018 0.732498473 0.815418141 0.879212262 0.724693938 0.736630293 0.802223901 1 21.97595576 -4.999999957 0.032064142 2.120551638 1.66E-06 0.475065754 0.095487703 1385.213074 3.339323946 177.379341 67.61736854 1.00E-05 4.999999957 -2.120549981 DHRPPCAQEAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DHRPPCAQEAPR 12 1 Q13501;Q13501-2;E7EMC7;C9JRJ8;E9PFW8;E3W990 Q13501 SQSTM1 Sequestosome-1 0 ;;; 130.15 0.00013309 459579000 263741 305905 259218 270668 305959 214487 264435 273632 332112 FALSE TRUE 247233.9216 328554.5245 265366.7734 277613.7991 281930.2143 276405.915 224785.4266 307795.5575 276680.3617 0.893572352 1.187487693 0.959109536 1.003373703 1.018974432 0.999008073 0.81243723 1.112458997 1 18.07786072 3.728802787 24.93082879 0.97184766 1.065056377 0.019126901 0.102462328 146.4758312 2171640.134 0.025220695 0.042624502 5355.534081 -3.728802787 0.093208717 DHS(ph)PTPSVFNS(ph)DEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DHSPTPSVFNSDEER 15 0 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 2 DHS(0.961)PT(0.04)PS(0.001)VFNS(0.998)DEER;DHS(0.929)PT(0.071)PSVFNS(1)DEER 137.09 9.97E-06 1103840000 346930 284950 306280 314790 288960 279220 406860 253760 285390 TRUE FALSE 325216.2706 306047.9945 313545.1062 322868.0443 266266.2472 359826.2812 345855.1201 285442.4946 237756.5653 1.367854007 1.28723257 1.318765292 1.357977408 1.119911229 1.513423113 1.454660651 1.200566194 1 17.85912565 0.977319459 6.395741318 1.000063125 1.343476727 0.542611769 0.103200191 0.132405581 26.62967518 0.099500629 0.024990537 9.491163598 -0.977319459 0.343413602 DHS(ph)PTPSVFNSDEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DHSPTPSVFNSDEER 15 0 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 DHS(0.989)PT(0.011)PSVFNSDEER;DHS(0.991)PT(0.009)PSVFNSDEER;DHS(0.993)PT(0.007)PSVFNSDEER;DHS(0.801)PT(0.199)PSVFNSDEER;DHS(0.5)PT(0.5)PSVFNSDEER;DHS(0.99)PT(0.01)PSVFNSDEER;DHS(0.82)PT(0.18)PSVFNSDEER 256.79 5.88E-25 5920471000 2471899 2170530 2329860 2354229 2376642 1913902 2819277 1931114 2278832 TRUE FALSE 2317187.254 2331238.3 2385125.379 2414642.502 2189990.124 2466414.438 2396552.587 2172217.834 1898480.217 1.220548538 1.227949745 1.256334071 1.271881835 1.153549088 1.299152035 1.262353205 1.144187763 1 20.85641354 0.96037612 3.47160131 1.000444337 1.243149031 0.803274714 0.038664432 0.09608128 3.05706035 0.034794476 0.009007426 9.128010275 -0.96037612 0.242704694 DHSDSKDQSDKHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DHSDSKDQSDKHDR 14 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 0 ; 137.46 6.80E-06 104487000 84381 71440 81659 75392 108141 48603 86961 71617 170727 FALSE TRUE 79099.74383 76729.49193 83595.99004 77326.68636 99648.04208 62633.8971 73922.00536 80558.5401 142231.5608 0.556133557 0.539468818 0.587745713 0.543667565 0.700604293 0.440365674 0.519729974 0.566390045 1 17.1178821 -1.519646423 2.240293037 1.037407017 0.554113962 0.82438067 0.064282201 378523.7957 304344.7191 85653.31702 0.015859551 0.030224114 1.519646423 -0.483293056 DHSFFIPDIEYLSDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DHSFFIPDIEYLSDIK 16 0 Q969S3 Q969S3 ZNF622 Zinc finger protein 622 0 98.312 0.0027766 68371000 123240 94866 94594 114400 118860 92794 125220 104160 129960 FALSE TRUE 115526.6284 101889.9773 96837.81435 117335.6977 109525.2151 119582.1214 106444.4235 117164.6053 108268.8364 1.067034912 0.941083147 0.894420015 1.083743961 1.01160425 1.104492533 0.983149233 1.082163706 1 16.72425852 3.232693182 24.99999466 1.041894417 0.951407406 0.266488598 0.057868673 147.2079033 627223.7446 0.015725633 0.019276096 1708.80766 -3.232693182 -0.090487011 DHSGGIGDICK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DHSGGIGDICK 11 0 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ; 156.01 3.13E-05 1147250000 2367600 2150400 1782760 1804900 2445700 1277800 2121880 1936170 2589800 FALSE TRUE 2219416.142 2309617.853 1825047.909 1851216.79 2253624.587 1646680.117 1803723.793 2177905.087 2157545.649 1.028676331 1.070483887 0.845890751 0.858019755 1.04453159 0.763219132 0.836007244 1.009436388 1 21.04095965 4.027181148 4.021300203 0.892773402 1.047451484 0.287023676 0.089837937 0.23437539 7.86951913 0.021748845 0.048683323 10645.86973 -4.027181148 0.154678082 DHSVAESLNYVASWNMSMLQTQDLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DHSVAESLNYVASWNMSMLQTQDLVK 26 0 Q13011 Q13011 ECH1 "Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial" 0 ;;; 338.88 2.54E-95 213651800 255072.8 213815.8 213223.7 221323.6 287268.5 186524.5 242454.9 201930.6 275564 FALSE TRUE 239108.2488 229646.9443 218281.4669 227003.1383 264707.5908 240371.0952 206101.0386 227142.0799 229570.5882 1.041545656 1.000332604 0.950825054 0.988816294 1.153055332 1.047046562 0.897767611 0.989421518 1 17.8085783 1.754606533 25 0.953174811 1.020777392 0.210732686 0.05918714 9.477336633 14783.5156 0.028811501 0.015977491 56.83377888 -1.754606533 0.067602582 DHSVDSFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DHSVDSFK 8 0 Q641Q2;Q641Q2-2;F8W7U3;A0A087WYF6;B1AP61 Q641Q2 FAM21A WASH complex subunit FAM21A 0 75.043 0.039411 77917000 92806 113540 104970 111060 114860 99376 121700 104600 118640 FALSE TRUE 86997.43812 121946.6197 107459.938 113909.9876 105839.3589 128064.238 103452.2148 117659.5403 98838.21756 0.880200395 1.233800272 1.087230634 1.152489295 1.070834355 1.295695543 1.04668232 1.190425558 1 16.59278137 4.752094145 24.44448971 1.139539385 0.88020016 0.444853459 0.08917974 1390.632558 2511724.003 0.018375435 0.349338058 56505.94533 -4.752094145 -0.259339225 DHTLEDEDVIQIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DHTLEDEDVIQIVK 14 0 Q9Y295 Q9Y295 DRG1 Developmentally-regulated GTP-binding protein 1 0 ;;; 132.86 4.80E-05 396226000 1000143 786227 858566 820592 893248 681566 1075900 761477 864118 FALSE TRUE 937545.8349 844440.0651 878931.591 841649.78 823095.9053 878323.0399 914578.7832 856549.0797 719891.1234 1.30234393 1.173010804 1.220922946 1.169134821 1.143361654 1.220077608 1.270440423 1.189831423 1 19.4574192 0.959105865 23.0876054 0.999999999 1.211418328 0.669282132 0.046917347 1948.44206 1100033.846 0.044166305 0.011041576 9.10135104 -0.959105865 0.211418329 DHTPSQELALTQSVGGDSSADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DHTPSQELALTQSVGGDSSADR 22 0 Q86U44;H0YFV6;Q86U44-2 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 0 88.79 0.001022 0 218940 430600 366960 362440 432120 293970 403830 372260 423680 FALSE TRUE 205236.9362 462482.072 375664.4645 371740.824 398183.0383 378834.3668 343279.4405 418737.4804 352965.0709 0.581465287 1.310277164 1.064310595 1.053194366 1.128108901 1.073291376 0.972559238 1.186342545 1 18.4291659 -1.05079898 7.861811661 0.999999998 1.068195837 0 0.18928834 6.92E-09 6.16E-10 0.162550352 0.038313485 0.088961279 1.05079898 0.068195839 DHTTLLSEVMTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DHTTLLSEVMTPR 13 0 P20839-3;P20839-7;P20839-5;P20839-6;P20839;A0A3B3IRL5;C9J381;P20839-2;P20839-4;C9K0R9;C9J029 P20839-3 IMPDH1 Inosine-5-monophosphate dehydrogenase 1;Inosine-5-monophosphate dehydrogenase 0 ; 226.42 1.08E-11 277800000 136938 175960 188324 171961 186051 170751 204314 164728 180389 FALSE TRUE 128367.295 188988.2615 192791.1342 176373.8104 171439.305 220044.0418 173679.0125 185294.6534 150280.9105 0.854182308 1.257566652 1.282871747 1.173627507 1.140792296 1.464218183 1.155695769 1.232988626 1 17.19730224 4.740937285 24.79853798 1.231971104 0.854182159 0.465648918 0.119504451 152.7633351 1593847.162 0.025089609 0.169631024 55072.81616 -4.740937285 -0.377788945 DHTYAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DHTYAK 6 0 Q06210-2;Q06210;A0A6I8PRN4 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ;; 88.591 0.05113 907820000 1039400 909780 958280 988960 928570 702920 1045530 866330 820730 FALSE TRUE 974345.8094 977141.0578 981010.8541 1014338.388 855643.8579 905841.593 888762.4827 974493.2075 683744.8609 1.425013722 1.429101868 1.434761576 1.483504222 1.251408101 1.324823988 1.299845211 1.425229297 1 19.38309856 -3.875529597 0.178684801 4.66E-13 1.476752252 0.765386372 0.067979517 38.73985392 0.536033733 14.23682038 0.214976344 0.00013319 3.875529597 1.476752252 DHVFLCEGEEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DHVFLCEGEEPK 12 0 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BTV5;Q9H910-2;H3BU16;H3BMT0 A6NGP5;Q9H910-2 HN1L Hematological and neurological expressed 1-like protein 0 ;; 213.63 6.36E-09 1451210000 5065100 3068370 3712600 3684000 3888200 3002890 5218600 3271100 4051100 FALSE TRUE 4748084.432 3295555.307 3800664.625 3778537.677 3582836.456 3869775.595 4436119.377 3679504.036 3374945.239 1.406862659 0.976476676 1.126141124 1.119584885 1.061598397 1.146618781 1.314427069 1.090241108 1 21.68643266 1.997779684 24.84354291 1.185000025 1.112818607 0 0.136566398 243.0763232 2719846.135 0.047550257 0.034554317 99.49005788 -1.997779684 -0.072181418 DHYEATAMHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DHYEATAMHR 10 0 O75832;B1AJY5;B1AJY7;O75832-2;B1AJY6 O75832 PSMD10 26S proteasome non-ATPase regulatory subunit 10 0 ;;; 189.72 6.86E-07 309272000 339380 400850 341903 296926 433909 299797 351703 366704 389019 FALSE TRUE 318138.8116 430529.3511 350013.1006 304545.6239 399831.5374 386343.5271 298968.4002 412487.8016 324089.2157 0.981639611 1.328428501 1.079989965 0.939696877 1.233708245 1.192090043 0.922487962 1.272760035 1 18.30603149 -4.99999939 0.081591156 0.611736462 1.237096009 0.018155417 0.143863431 701.8666261 4.045675321 49.13945217 4.394623824 1.00E-05 4.99999939 0.625359546 DHYPCVSS(ph)LEQLTELGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DHYPCVSSLEQLTELGR 17 0 Q8WWK9-6;Q8WWK9-5;Q8WWK9 Q8WWK9-6 CKAP2 Cytoskeleton-associated protein 2 1 DHYPCVS(0.203)S(0.797)LEQLTELGR 180.13 5.65E-10 20590000 22075 19656 22282 21850 23139 20956 24619 19216 23329 TRUE FALSE 20693.36516 21111.35069 22810.53956 22410.70799 21321.75628 27005.65701 20927.6095 21615.1599 19435.23919 1.064734267 1.086240848 1.173669094 1.153096588 1.097066832 1.389520178 1.076786825 1.112163308 1 14.24638724 0.919688811 2.049935622 1.002211453 1.152169508 0.207195021 0.092470267 0.636964407 5.632478591 0.082668638 0.022935861 8.311679927 -0.919688811 0.149958055 DIAAHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DIAAHIK 7 0 P63167;F8VXL2;F8VRV5 P63167 DYNLL1 "Dynein light chain 1, cytoplasmic" 0 ;;;;; 104.45 0.0081492 6902410000 11620800 11044100 10901000 10644100 12803700 8323700 12623600 10943900 13399700 FALSE TRUE 10893474.87 11861816.66 11159576.87 10917245.63 11798149.05 10726617.07 10730808.37 12310270.01 11163203.5 0.975837704 1.06258178 0.999675126 0.977967088 1.056878435 0.960890578 0.961266035 1.102754241 1 23.41224776 3.725011849 24.19185656 1.00221696 1.02712256 0 0.048267075 205.8497922 2360841.251 0.01189354 0.019462065 5308.989281 -3.725011849 0.024905599 DIAAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DIAAYR 6 0 P26583;P09429;P23497 P26583;P09429;P23497 HMGB2;HMGB1;SP100 High mobility group protein B2;High mobility group protein B1;Nuclear autoantigen Sp-100 0 ;;;; 138.38 0.028678 10197920000 7423230 8912190 8207380 8545080 8866130 6963950 8631020 7343620 8373090 FALSE TRUE 6958623.285 9572057.821 8402062.929 8764361.22 8169819.914 8974329.315 7336878.677 8260487.122 6975567.187 0.997570964 1.372226453 1.204498889 1.256437073 1.171205107 1.286537578 1.051796719 1.184202933 1 22.7338791 1.204492332 0.73334261 1.008917733 1.236745405 0.231756917 0.107721988 0.722018936 0.901324862 0.092841678 0.037539053 16.01372375 -1.204492332 0.227827672 DIAWTEDSKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DIAWTEDSKR 10 1 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ;;; 202.56 3.55E-07 1894890000 2035700 1560950 1734460 1658750 1803820 1261820 2134020 1565970 1591460 FALSE TRUE 1908289.171 1676524.362 1775602.21 1701316.333 1662155.253 1626086.95 1814043.512 1761484.802 1325835.045 1.439311156 1.264504486 1.339233125 1.283203623 1.253666706 1.22646249 1.368227156 1.328585188 1 20.33846986 -1.235848445 3.572583847 0.999439496 1.308831294 0.716886231 0.061749265 9623837.157 13633937.07 58995.7827 0.01379223 0.058096712 1.235848445 0.309391798 DICNDVLSLLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DICNDVLSLLEK 12 0 P63104;E7EX29;B0AZS6;E7ESK7 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;; 248.05 2.44E-16 498428800 1194781 1033818 1091624 1094485 1153626 868468 1416808 971504 1041704 FALSE TRUE 1120001.79 1110362.96 1117517.837 1122571.338 1063024.867 1119180.613 1204370.793 1092798.413 867836.8727 1.290567185 1.279460455 1.28770495 1.29352805 1.224913231 1.289620951 1.387784768 1.259220998 1 19.72706436 0.964401004 24.02161067 0.999999999 1.295405607 0.844359148 0.039266936 1465.677933 989016.2938 0.040386325 0.010096581 9.21299858 -0.964401004 0.295405608 DIDAFWLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DIDAFWLQR 9 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;;; 161.02 0.00015087 490611000 651326 870897 759399 716866 772919 591140 876377 738931 931596 FALSE TRUE 610560.6683 935379.12 777412.3029 735261.9952 712217.0595 761792.5216 744972.4047 831188.1619 776106.6093 0.786696906 1.205219887 1.001682364 0.947372418 0.917679415 0.981556545 0.959884114 1.070971632 1 19.56589532 3.487881468 21.9361786 0.973798795 1.049704822 0 0.109335723 172.5835425 351828.9185 0.027030586 0.04045683 3075.257372 -3.487881468 0.075906027 DIDEVSSLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DIDEVSSLLR 10 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;;;;; 309.22 1.76E-41 2735386000 2519705 2810804 2645425 2662512 3094076 2023182 2773693 2579989 2915037 FALSE TRUE 2362001.162 3018918.853 2708175.73 2730836.566 2851079.752 2607241.8 2357803.484 2902106.306 2428498.493 0.972617924 1.243121567 1.115164674 1.124495886 1.174009274 1.073602396 0.970889416 1.195020839 1 21.21163316 2.074492595 6.110672973 1.044905695 1.139819217 0.108372466 0.088638382 0.307997662 19.43129338 0.030935504 0.02262425 118.711446 -2.074492595 0.094913522 DIDFLAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DIDFLAEK 8 0 P20839-3;P20839-7;P20839-5;P20839-6;P20839;A0A3B3IRL5;C9J381;P20839-2;P20839-4;C9K0R9;C9J029;H7C5T1;H7C511 P20839-3 IMPDH1 Inosine-5-monophosphate dehydrogenase 1;Inosine-5-monophosphate dehydrogenase 0 ;;; 114.89 0.0059752 278088000 1250040 901580 1037800 954370 1072940 844250 1387440 959190 1217010 FALSE TRUE 1171802.228 968333.9213 1062417.106 978860.7499 988675.6204 1087971.27 1179406.252 1078946.983 1013883.169 1.155756663 0.955074461 1.047869359 0.965457145 0.97513762 1.073073608 1.163256565 1.064172891 1 19.95145999 2.060244305 6.727183028 1.099871411 1.012843819 0.098367427 0.069871615 0.266173333 23.3994095 0.024176018 0.017714206 114.8799676 -2.060244305 -0.087027592 DIDFLKEEEHDCFLEEIMTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DIDFLKEEEHDCFLEEIMTK 20 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ;;; 206.28 4.69E-22 555923000 3009480 1725110 2314250 2174190 2349600 1882380 3321740 1913080 3113620 FALSE TRUE 2821122.019 1852838.939 2369145.103 2229983.396 2165071.894 2425792.548 2823675.925 2151932.249 2593936.707 1.087583213 0.714296125 0.913339595 0.859690751 0.834666431 0.935178002 1.088567781 0.829600909 1 21.30671185 2.026778453 6.578467482 0.989809619 0.863641335 0.106083923 0.111222632 0.241493458 36.02881729 0.03930918 0.028255988 106.3600304 -2.026778453 -0.126168283 DIDHETVVEEQIIGENS(ph)PPDYSEYMTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 DIDHETVVEEQIIGENSPPDYSEYMTGK 28 0 P25490;A0A494C032;H0YJV7;H0YJU4 P25490 YY1 Transcriptional repressor protein YY1 1 DIDHETVVEEQIIGENS(0.998)PPDY(0.002)SEYMTGK;DIDHETVVEEQIIGENS(1)PPDYSEYMTGK;DIDHETVVEEQIIGENS(1)PPDYSEYMTGK;DIDHETVVEEQIIGENS(1)PPDYSEYMTGK;DIDHETVVEEQIIGENS(0.999)PPDYS(0.001)EYMTGK;DIDHETVVEEQIIGENS(1)PPDYSEYMTGK;DIDHETVVEEQIIGENS(1)PPDYSEYMTGK;DIDHETVVEEQIIGENS(1)PPDYSEYMTGK;DIDHETVVEEQIIGENS(1)PPDYSEYMTGK 301.49 4.59E-71 3017595000 1811400 1601302 1684740 1691620 1898120 1343743 2118840 1560813 2125400 TRUE FALSE 1698027.707 1719864.066 1724702.828 1735029.833 1749049.312 1731659.79 1801139.612 1755683.939 1770657.009 0.958981722 0.97131407 0.974046819 0.979879121 0.987796791 0.977975848 1.017215419 0.991543777 1 20.75585335 2.586077417 0.687323982 1.004557134 0.966039852 0.670809921 0.009308469 0.395168357 0.387358147 0.006869726 0.006047172 385.5470791 -2.586077417 -0.038517282 DIDIEDLEELDPDFIMAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DIDIEDLEELDPDFIMAK 18 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;;;; 239.39 1.51E-23 53262600 195636.8 171506.5 191748.6 190734.7 193120.3 144204 229856.9 170012 229893.5 FALSE TRUE 183392.2419 184205.0197 196296.9673 195629.2753 177953.4106 185833.3538 195391.9917 191238.3724 191522.7897 0.957547884 0.961791649 1.024927465 1.021441238 0.929150055 0.970293688 1.020202306 0.998514969 1 17.54715655 4.233360199 5.313977326 0.995270592 0.959007961 0.211756165 0.028319814 0.266018512 24.24103888 0.007194619 0.018480751 17114.3417 -4.233360199 -0.036262631 DIDIHEVR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;; 204.62 8.60E-05 19239540000 36090490 37652530 40425410 38271880 40011880 34005930 44357670 34745940 38274490 FALSE TRUE 33831650.65 40440362.5 41384319.82 39254001.23 36869508.34 43822889.95 37706649.18 39084047.09 31886230.36 1.061011298 1.268270412 1.297874329 1.231064343 1.156283071 1.374351545 1.182537063 1.225734327 1 24.92643021 0.375557902 1.425217742 0.999989268 1.239066413 0.404183371 0.08447777 3.697251567 7.502463332 0.073915914 0.021502812 2.374421972 -0.375557902 0.239077145 DIDISS(ph)PEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DIDISSPEFK 10 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 DIDIS(0.001)S(0.999)PEFK;DIDIS(0.065)S(0.935)PEFK;DIDIS(0.002)S(0.998)PEFK;DIDISS(1)PEFK;DIDIS(0.001)S(0.999)PEFK;DIDISS(1)PEFK;DIDIS(0.004)S(0.996)PEFK;DIDIS(0.005)S(0.995)PEFK 308.91 8.08E-42 7987921000 40730640 25594910 32127500 32842690 35359300 21540530 36965960 24102020 36922200 TRUE FALSE 38181381.95 27489983.77 32889579.47 33685489.03 32582323.21 27758931.33 31423257.47 27111210.25 30759646.29 1.241281567 0.893702857 1.069244398 1.095119518 1.059255458 0.902446376 1.021574084 0.881388882 1 24.87453558 2.257884519 24.95127794 0.958670453 1.048171505 0.270632292 0.093524621 393.9829993 508714.7662 0.0308035 0.025736326 181.0858513 -2.257884519 0.089501052 DIDLICSNALEYNPDRDPGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DIDLICSNALEYNPDRDPGDR 21 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 ;;;; 174.91 2.18E-12 3119890000 3330850 3357610 3593250 3337220 3560130 3035680 4059480 3087460 3796290 FALSE TRUE 3122378.044 3606210.938 3678483.587 3422858.715 3280531.751 3912031.536 3450798.66 3472936.177 3162664.674 0.987261808 1.14024448 1.163096302 1.082270512 1.037268281 1.236941611 1.091104817 1.098104458 1 21.59270917 0.733200729 2.252642841 1.000127806 1.116465031 0.176014463 0.06829508 1.865898705 13.42315152 0.060492368 0.016409026 5.410043149 -0.733200729 0.116337225 DIDNNLITST(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DIDNNLITSTPR 12 0 Q05D32-2;Q05D32;H0YMH7;H0YNU2;H0YNW9 Q05D32-2 CTDSPL2 CTD small phosphatase-like protein 2 1 DIDNNLIT(0.012)S(0.32)T(0.668)PR;DIDNNLITS(0.019)T(0.981)PR 153.7 0.00079223 284965000 471090 477840 493980 424960 489170 361070 565890 390450 618450 TRUE FALSE 441605.3178 513219.7708 505697.4389 435865.1931 450752.5614 465305.0475 481040.048 439198.542 515226.6997 0.85710876 0.996104765 0.981504722 0.845967791 0.874862583 0.903107405 0.93364736 0.852437465 1 18.97484783 3.259707556 24.99977556 0.89971407 0.961105614 0.090532257 0.057172262 358.9590346 424356.3502 0.014711367 0.01989929 1818.475924 -3.259707556 0.061391544 DIDPQNDLTFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DIDPQNDLTFLR 12 0 Q9NP97;B1AKR6;Q8TF09;H3BQI1 Q9NP97 DYNLRB1;DYNLRB2 Dynein light chain roadblock-type 1;Dynein light chain roadblock-type 2 0 ;;; 174.42 7.08E-05 617986000 652396 737819 691855 691259 790822 542301 774108 652912 749175 FALSE TRUE 611563.6989 792447.8865 708266.1273 708997.8762 728714.0301 698854.4952 658037.6919 734429.5004 624132.8526 0.979861413 1.269678215 1.134800266 1.135972691 1.167562366 1.119720733 1.054323113 1.176719824 1 19.25149363 0.246759335 0.371335199 0.980121137 1.160686447 0.165558091 0.078532737 4.824327669 1.099351906 0.253063919 0.060693735 1.765059438 -0.246759335 0.180565309 DIDTHTHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DIDTHTHR 8 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 146.81 0.00054736 77226000 242960 246830 233840 257210 281810 218220 266460 226880 272610 FALSE TRUE 227753.5673 265105.55 239386.7952 263810.4441 259677.7794 281216.5715 226506.7967 255206.4674 227109.6299 1.002835359 1.167302109 1.054058321 1.161599551 1.143402768 1.238241512 0.997345629 1.123714867 1 17.79302935 1.021235571 1.191550307 1.00848128 1.119585655 0.16377408 0.075872014 0.816667145 2.404440459 0.065436585 0.02055054 10.50111878 -1.021235571 0.111104374 DIEDVFYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DIEDVFYK 8 0 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;; 148.38 0.0012147 435320000 1104590 917090 939250 885510 1002450 767370 1183930 883260 1110930 FALSE TRUE 1035455.684 984992.2978 961529.4535 908233.6858 923721.6207 988897.2618 1006410.688 993536.9553 925508.6061 1.118796386 1.064271354 1.038920057 0.981334673 0.998069186 1.068490617 1.087413646 1.073503746 1 19.81988688 -0.286742026 7.580865378 1.000000008 1.052851303 0.149187066 0.040352099 0 0 0.040590964 0.009567382 0.516723216 0.286742026 0.052851295 DIEEHLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DIEEHLQR 8 0 Q9UNE7;Q9UNE7-2;H3BTA3 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ;;;; 180.03 0.00024123 1911630000 2646454 3020670 2724480 2687200 3099270 2213292 2893768 2616563 2993131 FALSE TRUE 2480817.168 3244323.55 2789105.952 2756158.101 2855865.836 2852233.471 2459874.353 2943246.65 2493558.1 0.994890461 1.301081996 1.11852455 1.105311363 1.145297491 1.143840792 0.986491694 1.180340113 1 21.24977439 1.834755437 0.466627479 1.016123153 1.175670707 0.094050173 0.092242434 1.429430587 0.74836063 0.090117053 0.069684896 68.35266273 -1.834755437 0.159547554 DIEEIIDELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DIEEIIDELK 10 0 E7EPT4;P19404 E7EPT4 NDUFV2 "NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial" 0 ;; 205.14 4.05E-07 48427600 206328 131199 148713 124225 176889 115450 158999 130361 246114 FALSE TRUE 193414.2988 140913.1105 152240.5426 127412.8238 162996.8515 148778.5408 135158.576 146636.8578 205035.9834 0.943318805 0.687260393 0.742506462 0.621416893 0.794967053 0.725621612 0.659194419 0.715176211 1 17.6455176 -1.888563647 6.974720463 1.045881217 0.725291348 0.467473283 0.087809466 0.042361557 0.000676818 0.05749028 0.017907004 0.012925173 1.888563647 -0.320589869 DIEIS(ph)T(ph)EEEKDTGDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DIEISTEEEKDTGDLK 16 1 Q4G0J3;Q4G0J3-3 Q4G0J3 LARP7 La-related protein 7 2 DIEIS(1)T(1)EEEKDTGDLK 169.85 1.26E-08 148600000 1591800 553280 895400 899510 794640 714990 1276300 678760 877210 TRUE FALSE 1492172.079 594245.4269 916639.3108 922592.9495 732232.1798 921396.0061 1084930.664 763504.6801 730797.984 2.041839348 0.813145958 1.254299178 1.262445942 1.001962507 1.260808084 1.484583547 1.044754771 1 19.47911313 4.753489051 24.77784839 1.165360854 2.041840053 0.690904981 0.188854242 1542.568754 2560269.216 0.047009609 1.068413955 56687.72793 -4.753489051 0.876479199 DIEIS(ph)TEEEKDTGDLKDSSLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DIEISTEEEKDTGDLKDSSLLK 22 2 Q4G0J3;Q4G0J3-3 Q4G0J3 LARP7 La-related protein 7 1 DIEIS(0.882)T(0.118)EEEKDTGDLKDSSLLK 188.22 1.34E-17 193410000 493380 170230 277520 281050 281840 171520 359600 191600 500850 TRUE FALSE 462500.2265 182834.0063 284102.9055 288262.2188 259705.4233 221035.0396 305681.3184 215521.6818 417254.8994 1.1084357 0.438183007 0.680885727 0.690854006 0.622414317 0.529736235 0.732600908 0.516522831 1 18.67056946 -1.326110284 4.410870564 1.000377208 0.645985537 0.245011369 0.182149379 0.00058846 8.99E-05 0.153601793 0.036166297 0.047194318 1.326110284 -0.354391671 DIEIST(ph)EEEKDTGDLKDSSLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DIEISTEEEKDTGDLKDSSLLK 22 2 Q4G0J3;Q4G0J3-3 Q4G0J3 LARP7 La-related protein 7 1 DIEIS(0.461)T(0.536)EEEKDT(0.003)GDLKDSSLLK 118.01 0.0053619 253010000 431440 147060 256800 245990 247820 154370 305410 158650 383760 TRUE FALSE 404436.9405 157948.4754 262891.4173 252302.5199 228357.2169 198934.113 259616.6058 178457.8017 319707.9768 1.265019861 0.494039833 0.822286075 0.789165545 0.714268124 0.622236939 0.812042941 0.558190019 1 18.28639521 -1.194178322 3.395470621 1.000471194 0.740211727 0.108257746 0.210301266 58065170.72 89703460.39 295852.4083 0.043734915 0.063947221 1.194178322 -0.260259467 DIELVMSQANVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DIELVMSQANVSR 13 0 F8VZJ2;H0YHX9;Q13765;E9PAV3-2;E9PAV3;F8W0W4 F8VZJ2 NACA "Nascent polypeptide-associated complex subunit alpha;Nascent polypeptide-associated complex subunit alpha, muscle-specific form" 0 ; 104.59 0.0035349 126707000 138627 153933 138097 147394 167416 108771 150991 141105 190859 FALSE TRUE 129950.5835 165330.3595 141372.7261 151176.3796 154267.8227 140171.422 128351.3013 158722.2699 159003.3999 0.817281791 1.039791348 0.88911763 0.95077451 0.970217132 0.88156242 0.807223628 0.998231924 1 17.27869809 2.227500871 24.83389824 0.894278152 0.942684032 0 0.080672259 534.5111639 1200197.956 0.0279505 0.020842379 168.8499248 -2.227500871 0.04840588 DIEREDIEFICK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DIEREDIEFICK 12 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;; 245.15 1.74E-16 7260610000 7636000 6366070 7018800 6601000 7600800 5940620 9554900 6453420 8296000 FALSE TRUE 7158076.391 6837420.447 7185289.251 6770392.835 7003863.828 7655580.556 8122231.448 7259143.693 6911344.006 1.035699624 0.989304026 1.039637044 0.979605823 1.013386661 1.107683332 1.17520289 1.050323018 1 22.72053486 2.242408734 9.072944161 1.106613129 1.010809588 0.295281815 0.049589975 0.094002181 88.39352173 0.016501836 0.013093955 174.7466 -2.242408734 -0.09580354 DIEVLS(ph)EDT(ph)DYEEDEVTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DIEVLSEDTDYEEDEVTKK 19 1 Q4LE39-2;Q4LE39;H0Y7Y8;Q4LE39-4;Q4LE39-3;H7C5R6 Q4LE39-2 ARID4B AT-rich interactive domain-containing protein 4B 2 DIEVLS(1)EDT(1)DYEEDEVTKK 106.93 0.00026348 44268000 140190 67665 86281 92670 91554 69702 112330 69600 111770 TRUE FALSE 131415.7581 72674.98701 88327.62606 95048.06909 84363.71815 89823.83588 95487.15932 78289.71321 93114.86494 1.411329525 0.780487488 0.948587813 1.020761499 0.906017726 0.964656244 1.025477075 0.840786412 1 16.50672388 4.750307773 24.98193355 0.935426985 1.411329812 0.786919021 0.07775763 854.3325998 1816821.494 0.01886305 0.310026233 56273.9983 -4.750307773 0.475902827 DIFDCLEGAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DIFDCLEGAAR 11 0 Q9Y5U2-2;Q9Y5U2;A6NCC9;E9PME3;C9JHT9;C9JJV1;E9PL88;C9JDU0 Q9Y5U2-2 TSSC4 Protein TSSC4 0 ; 119.68 0.0012879 50102000 47444 39180 41545 46803 48505 39905 49178 41668 51617 FALSE TRUE 44474.56473 42080.92797 42530.46702 48004.04422 44695.61296 51424.9257 41804.21545 46870.34152 43001.78924 1.034249168 0.978585513 0.989039474 1.116326671 1.03938961 1.195878744 0.972150605 1.089962589 1 15.39210907 3.261391146 24.98516202 1.068395861 0.99424696 0.205272666 0.062954532 313.7497367 343357.4714 0.015946541 0.021577308 1825.539127 -3.261391146 -0.074148901 DIFQEIFDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DIFQEIFDK 9 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 159.83 0.0024789 32592000 234758 228064 201435 192160 286290 168268 205889 216051 252184 FALSE TRUE 220064.9158 244950.0959 206213.1333 197091.1509 263805.9382 216844.24 175017.8558 243025.4429 210092.8612 1.047464985 1.165913465 0.981533271 0.938114459 1.255663504 1.032135213 0.833049989 1.156752502 1 17.68066762 3.947867102 0.391511627 0.993305404 1.143699913 0.014115133 0.121181219 9.268705501 1.772552816 0.111244631 0.622827187 8868.845766 -3.947867102 0.150394509 DIFQEIYDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DIFQEIYDK 9 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 136.63 0.00043555 48972000 112902 96906 99237 98705 118282 78990 123794 105983 116860 FALSE TRUE 105835.6654 104081.0211 101590.9485 101237.9374 108992.6088 101793.1307 105232.2389 119215.2108 97355.31106 1.087107259 1.069084161 1.043506999 1.039880992 1.119534288 1.045583745 1.080909072 1.224537311 1 16.57097206 1.449723482 17.39047721 1.125752187 1.066052619 0.079733266 0.058211427 2.355157171 1494.922615 0.02723942 0.012499591 28.16589019 -1.449723482 -0.059699567 DIFTPNDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DIFTPNDER 9 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 0 89.698 0.027757 83909000 98279 109870 98661 100740 129160 97559 113920 107070 151250 FALSE TRUE 92127.89282 118004.8891 101001.2855 103325.159 119016.2946 125722.6996 96838.75358 120437.9252 126005.3979 0.73114243 0.936506619 0.801563165 0.820005815 0.944533303 0.997756459 0.768528612 0.955815602 1 16.94312601 2.745565021 24.63167132 0.91210323 0.8378813 0.282453527 0.082594829 836.9960979 2943377.149 0.024841851 0.025831323 556.6279643 -2.745565021 -0.07422193 DIGKPIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DIGKPIEK 8 1 O60869 O60869 EDF1 Endothelial differentiation-related factor 1 0 ; 110.14 0.0031775 1339480000 2467700 1770060 2015360 2067100 2101200 1472660 2712700 1923690 2117280 FALSE TRUE 2313251.062 1901117.084 2063165.291 2120145.286 1936180.228 1897793.035 2305955.818 2163866.931 1763892.29 1.311446892 1.077796584 1.169666256 1.201969813 1.097674863 1.075912087 1.307311014 1.22675684 1 20.75033104 1.753558083 25 1.210107627 1.147900972 0 0.10362059 13.56633112 22643.53048 0.043137269 0.02392207 56.69673933 -1.753558083 -0.062206655 DIGTAIQFLHSHNIAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DIGTAIQFLHSHNIAHR 17 0 C9J8E1;Q16644 C9J8E1 MAPKAPK3 MAP kinase-activated protein kinase 3 0 51.606 0.052172 29316000 10874 17867 15846 12745 18142 14534 16764 15002 20834 FALSE TRUE 10193.41575 19189.89127 16221.8746 13072.05828 16717.2005 18729.72986 14250.39383 16875.03272 17356.67081 0.587290954 1.105620512 0.934619017 0.753143182 0.963157087 1.079108434 0.821032673 0.972250549 1 14.08320263 DIHEELPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DIHEELPK 8 0 Q9BVP2-2;Q9BVP2 Q9BVP2-2 GNL3 Guanine nucleotide-binding protein-like 3 0 105.78 0.0043212 346140000 307080 225780 273210 244230 258150 177560 304220 199730 305060 FALSE TRUE 287860.411 242496.9861 279690.6702 250497.3553 237875.9403 228818.6896 258605.0352 224666.7302 254143.5152 1.132668723 0.954173416 1.100522553 0.985653146 0.935990596 0.900352265 1.01755512 0.884015199 1 17.95528389 3.029787168 7.724967272 0.951413625 1.044757467 0.417219618 0.060709271 0.213060488 44.45716968 0.016308115 0.019369072 1070.994321 -3.029787168 0.093343842 DIHFMPCSGLTGANLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DIHFMPCSGLTGANLK 16 0 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 153.24 4.71E-07 260860000 259530 242930 233440 229690 272570 191590 255080 228360 274220 FALSE TRUE 243286.4806 260916.79 238977.307 235584.2343 251163.4517 246898.9228 216833.122 256871.2487 228450.9105 1.06493986 1.142113154 1.04607728 1.031224755 1.099419789 1.080752632 0.949145362 1.124404574 1 17.80152467 3.440309607 0.274395191 1.005188826 1.141780174 0.135711593 0.053504088 6.392671151 0.714784438 0.073733358 0.286606134 2756.192883 -3.440309607 0.136591347 DIHYSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DIHYSVK 7 0 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ;;; 139.31 0.0027006 956020000 1127390 3295120 2440410 2567970 3577170 1925790 2852900 3339820 3504480 FALSE TRUE 1056828.672 3539094.113 2498297.678 2633868.458 3296233.498 2481734.31 2425134.13 3756803.879 2919559.648 0.361982216 1.212201338 0.855710442 0.902145794 1.12901735 0.850037201 0.830650654 1.286770723 1 21.47731936 4.751628122 24.99723403 0.98747 0.361981816 0.61694383 0.159303579 1507.121562 2882968.468 0.03612248 0.686951331 56445.34367 -4.751628122 -0.625488184 DIIFELR ddPTM_SK-BR-3_Pertuzumab_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 93.262 0.035045 29368000 29351 42031 33285 39310 43153 27845 39365 39252 41702 FALSE TRUE 27513.9733 45143.01897 34074.53592 40318.76115 39763.93745 35883.39947 33462.5837 44152.6986 34741.66679 0.791958931 1.299391283 0.980797384 1.16053042 1.144560441 1.032863497 0.963183024 1.270886019 1 15.08437935 1.254627423 24.99978235 1.135443264 1.070611956 0.040053889 0.149541313 869.670531 1353209.633 0.091802854 0.033283803 17.97328342 -1.254627423 -0.064831308 DIIHDPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DIIHDPGR 8 0 P62917;E9PKZ0;G3V1A1;E9PKU4 P62917 RPL8 60S ribosomal protein L8 0 ;;;;;;; 157.91 0.00036932 28722540000 20060840 22396960 22385570 22763170 23483310 20019360 25465600 19843730 24919850 FALSE TRUE 18805267.83 24055254.22 22916566.29 23347311.48 21639025.56 25798624.24 21647269.69 22321263.37 20760566.05 0.90581672 1.158699342 1.103850745 1.124598984 1.042313852 1.242674414 1.042710957 1.075176049 1 24.30734244 -0.806808669 7.70274466 1.000000027 1.097579869 0.077968745 0.087494343 0 0 0.074382781 0.01753219 0.156023973 0.806808669 0.097579842 DIIHFFR ddPTM_SK-BR-3_Pertuzumab_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 390010000 557890 784700 617410 554970 798180 462390 633220 671530 766360 FALSE TRUE 522972.6608 842800.0045 632055.2568 569211.4698 735494.1625 595874.4867 538274.5395 755371.9987 638449.5651 0.819129167 1.320072956 0.98998463 0.891552757 1.152000413 0.933314892 0.843096415 1.183134957 1 19.28421313 3.713420402 20.27484873 0.981942822 1.120276497 0.002494004 0.159934104 71.91551848 106423.5532 0.039203435 0.061358841 5169.165079 -3.713420402 0.138333676 DIILPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DIILPFR 7 0 A0A087WY71;Q96CW1-2;Q96CW1;E9PFW3;C9JJ47 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 ;;; 155.73 0.0087545 37561000 450107 568613 548793 556916 590004 455499 598610 509576 603414 FALSE TRUE 421935.6063 610713.6982 561810.6291 571207.4074 543667.4658 586994.1669 508853.9877 573197.6853 502700.3052 0.839338274 1.214866376 1.117585614 1.136278219 1.081494203 1.167682137 1.012241255 1.140237393 1 18.93933904 -1.52276659 5.847763833 0.99983691 1.100734032 0.056710605 0.103893646 0.000197649 1.61E-05 0.090003607 0.021179865 0.030007748 1.52276659 0.100897122 DIILREDLEELQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DIILREDLEELQAR 14 1 Q9UHQ9;H7C0R7 Q9UHQ9 CYB5R1 NADH-cytochrome b5 reductase 1 0 ; 162.64 4.02E-06 118112000 72429 102798 83252 88259 111799 80916 90124 96978 155441 FALSE TRUE 67895.79818 110409.2709 85226.77675 90523.87536 103018.7575 104275.1356 76610.74287 109085.9168 129496.8929 0.524304457 0.852601699 0.658137619 0.699042837 0.795530728 0.805232723 0.591602942 0.842382503 1 16.98255796 0.991177524 10.7555008 0.999999446 0.715710159 0.489051884 0.099306745 0.222598001 264.3624807 0.087096596 0.021781949 9.798904479 -0.991177524 -0.284289286 DIINMLFYHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DIINMLFYHDR 11 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ; 155.42 3.15E-05 166899000 324630 669860 357630 400480 713510 223390 370740 581440 270690 FALSE TRUE 304311.9878 719457.1314 366113.1525 410756.9948 657473.8028 287879.0666 315150.9788 654034.0639 225510.0903 1.349438455 3.1903545 1.623489007 1.821457276 2.915496162 1.276568451 1.397502783 2.900243014 1 17.78283246 -1.565390058 0.180752561 7.06E-09 2.39983343 0.125394852 0.732281438 52.32929469 1.634804211 27.81139663 2.606939928 0.02720257 1.565390058 2.399833423 DIIRQPS(ph)EEEIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DIIRQPSEEEIIK 13 1 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 1 DIIRQPS(1)EEEIIK;DIIRQPS(1)EEEIIK;DIIRQPS(1)EEEIIK 246.21 2.21E-17 1451030000 616300 861990 617340 906020 1018060 445302 1003270 665710 2669530 TRUE FALSE 577726.8831 925812.6365 631983.5963 929270.0071 938105.6743 573853.4585 852838.9774 748825.3589 2223968.197 0.259772997 0.416288613 0.28416935 0.417843208 0.421816137 0.258031324 0.383476247 0.336706865 1 21.08470473 -1.756371287 2.563827425 1.154132166 0.350585691 0.912268254 0.063607322 9537401.7 7077728.117 9290161.017 0.014085307 0.017523817 1.756371287 -0.803546475 DIISDTSGDFRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DIISDTSGDFRK 12 1 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;A6NMY6;H0YL33;H0YNP5;H0YN28;H0YKS4;H0YNA0;H0YN52 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 ; 162.68 9.94E-05 635230000 792780 530820 681250 510510 654980 403790 943510 665700 1453440 FALSE TRUE 743161.315 570122.4651 697409.5717 523610.5509 603540.5129 520357.618 802039.4346 748814.1104 1210851.474 0.61375101 0.470844259 0.575966241 0.432431691 0.498443059 0.429745207 0.662376395 0.618419456 1 20.20759048 0.682687961 0.989793292 0.998727714 0.508647654 0.824253029 0.069588872 0.389121647 0.657930624 0.061218754 0.019809696 4.816016444 -0.682687961 -0.490080059 DIISIAEDEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DIISIAEDEDLR 12 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;;; 294.93 7.18E-36 3111183000 3102255 2618687 2810162 2772046 2916686 2432209 3377090 2492801 2735153 FALSE TRUE 2908090.397 2812577.31 2876820.37 2843181.393 2687621.247 3134348.255 2870726.706 2804032.692 2278638.295 1.276240465 1.234323726 1.262517345 1.247754591 1.179485684 1.375535671 1.259843088 1.230573847 1 21.1197405 0.73959814 3.274553095 1.000015852 1.261354237 0.742323775 0.048172108 1.128448733 13.62988217 0.043333725 0.011239275 5.490326101 -0.73959814 0.261338385 DIKEES(ph)DEEEEDDEESGR ddPTM_SK-BR-3_Pertuzumab_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 258.9 6.79E-31 1984700000 1818510 934750 1148000 1214600 1218630 900230 1430410 1048540 1334180 TRUE FALSE 1704692.705 1003959.863 1175231.102 1245768.692 1122923.716 1160111.787 1215933.3 1179452.527 1111496.739 1.533691144 0.90325039 1.057341026 1.120802832 1.010280711 1.043738363 1.093960294 1.06113899 1 20.08407228 4.748230821 24.97119191 1.037695691 1.533691415 0.875414546 0.058965764 464.7968436 1200211.493 0.014739884 0.194340638 56005.51836 -4.748230821 0.495995723 DIKPDNFLMGIGR ddPTM_SK-BR-3_Pertuzumab_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 86.498 0.0080247 265470000 525330 536170 520660 529190 569630 424880 618020 479930 577190 FALSE TRUE 492450.533 575868.5847 533010.3011 542769.9113 524893.5576 547535.9586 525353.6384 539850.317 480853.2602 1.024118112 1.197597339 1.108467687 1.128764129 1.091587811 1.138675775 1.092544612 1.122692434 1 18.87523717 -2.739078622 0.317290171 0.782573236 1.126890614 0.372834569 0.044421748 57.69115616 1.898965036 8.530145841 0.037140412 0.001823566 2.739078622 0.344317378 DILDEEKFNVELIVQCIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DILDEEKFNVELIVQCIR 18 1 Q5T3Q7;Q9H583 Q5T3Q7 HEATR1 "HEAT repeat-containing protein 1;HEAT repeat-containing protein 1, N-terminally processed" 0 75.018 0.01604 9622600 27223 27838 24484 29984 29313 20718 35091 23136 24915 FALSE TRUE 25519.16102 29899.15449 25064.77204 30753.4402 27010.87522 26698.95027 29829.43032 26024.58053 20756.52554 1.229452442 1.440470103 1.207561063 1.481627556 1.301319682 1.28629188 1.437110959 1.253802351 1 14.34127735 0.978213139 20.89289242 0.999999996 1.342781228 0.583134137 0.090527792 121.6867145 116694.6579 0.077459801 0.01936495 9.510714365 -0.978213139 0.342781231 DILETHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DILETHLR 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;;;; 195.06 0.00016209 2422100000 2834600 3709519 2831602 2998941 3213549 1985305 3122428 3324414 2430414 FALSE TRUE 2657187.446 3984175.647 2898768.937 3075898.903 2961169.824 2558430.325 2654248.909 3739474.406 2024762.202 1.312345441 1.967725218 1.431658954 1.519140816 1.462477826 1.263570765 1.310894141 1.846870907 1 20.94932105 3.70534595 5.717620283 1.408691299 1.691767884 0.114683524 0.263513136 0.257823912 27.429453 0.063116983 0.10319741 5073.947277 -3.70534595 0.283076585 DILFSREDMKIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DILFSREDMKIR 12 2 Q8WZ42-6 Q8WZ42-6 TTN Titin 0 56.225 0.068509 178620000 2125900 420630 714090 495410 578890 435850 762430 383250 712250 FALSE TRUE 1992843.714 451773.8829 731028.552 508123.0593 533426.3145 561672.8196 648110.6996 431099.6061 593370.8737 3.358512866 0.761368485 1.231992645 0.856332998 0.898976236 0.946579693 1.092252297 0.726526402 1 19.17857459 4.741456883 25 0.960782642 3.358513732 0.962606855 0.149796472 44.48780877 383990.3331 0.033161443 0.232300687 55138.74577 -4.741456883 2.397731091 DILIQYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DILIQYDR 8 0 P62249;M0R210 P62249 RPS16 40S ribosomal protein S16 0 ;;;;;;; 153.08 0.0010396 6910370000 7656500 8720860 7673900 7507590 8489590 6460850 8314720 7340190 7036060 FALSE TRUE 7177293.332 9366561.548 7855928.532 7700247.47 7822851.847 8325992.512 7068004.926 8256628.879 5861696.131 1.224439679 1.597926835 1.340214224 1.313655177 1.334571372 1.420406709 1.205795177 1.408573337 1 22.48288675 -3.992213538 0.172084028 1.61E-10 1.462639916 0.483760714 0.112405109 67.7191213 0.880532423 23.7824591 0.378691035 0.000101809 3.992213538 1.462639916 DILKPEIMEEIVMETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DILKPEIMEEIVMETR 16 1 A3KFL2;Q13868-3;Q13868-2;Q13868 A3KFL2 EXOSC2 Exosome complex component RRP4 0 ; 189.64 8.98E-10 97928000 162158 133628 150042 139980 147481 117839 173818 129006 146917 FALSE TRUE 152008.8202 143521.9562 153601.0671 143572.1238 135898.4372 151857.2063 147755.6045 145112.6831 122395.6036 1.241946735 1.17260712 1.254955755 1.173017 1.11032123 1.240708015 1.207196993 1.185603721 1 16.90119221 0.744281699 4.193877527 1.000001021 1.201093565 0.686806949 0.042187789 2.663740953 43.23123894 0.038714503 0.009863358 5.549855798 -0.744281699 0.201092543 DILLRPELEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DILLRPELEELR 12 1 P00387-2;P00387;P00387-3 P00387-2 CYB5R3 NADH-cytochrome b5 reductase 3;NADH-cytochrome b5 reductase 3 membrane-bound form;NADH-cytochrome b5 reductase 3 soluble form 0 ;;; 156.6 6.19E-05 839160000 1208830 1309010 1046330 961420 1482380 1095860 1320540 1540190 1402930 FALSE TRUE 1133171.488 1405930.462 1071149.442 986091.6649 1365959.854 1412216.992 1122537.286 1732486.112 1168771.92 0.969540309 1.202912595 0.916474313 0.84369897 1.168713785 1.208291343 0.960441697 1.482313258 1 20.15656199 DILQDVHDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DILQDVHDK 9 0 Q92621 Q92621 NUP205 Nuclear pore complex protein Nup205 0 ; 103.08 0.0034799 742520000 838150 759010 716370 819370 859320 557340 1060440 788700 822990 FALSE TRUE 785691.6876 815207.8901 733362.6347 840396.4214 791832.4735 718235.0103 901436.8666 887170.9311 685627.6523 1.145945157 1.188995058 1.069622312 1.225732974 1.154901601 1.047558406 1.314761538 1.29395442 1 19.38706577 1.734611242 25 1.232213355 1.1405664 0.060039015 0.098919649 0.78352413 4904.333545 0.040933429 0.022699713 54.27642596 -1.734611242 -0.091646955 DILQDYTHEFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DILQDYTHEFHK 12 0 B4DQA8;E9PCW1;K7EJC8;G5E9T8;O95249;O95249-2 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 0 ;;; 166.86 2.94E-05 356274000 804354 877101 763933 785896 927530 672570 1058060 947020 896225 FALSE TRUE 754010.919 942042.4707 782053.8515 806063.4219 854685.5353 866730.0407 899413.7255 1065257.532 746639.2577 1.009873123 1.261710339 1.047432001 1.079588856 1.144710148 1.160841774 1.204616173 1.426736568 1 19.51005184 1.835123182 2.509997463 1.236257286 1.121218954 0.114610139 0.121387581 0.51496946 6.026447503 0.064457208 0.031159312 68.41056567 -1.835123182 -0.115038332 DILVDLGHLEGADAGEEDLEQQFHYHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DILVDLGHLEGADAGEEDLEQQFHYHLR 28 0 Q9NPA3 Q9NPA3 MID1IP1 Mid1-interacting protein 1 0 42.791 0.052592 10831000 12366 9135.5 14187 12120 8596 11434 11779 10045 10472 FALSE TRUE 11592.03413 9811.901925 14523.52234 12431.01972 7920.904835 14734.81018 10012.8483 11299.14036 8724.155548 1.328728502 1.124682139 1.664748211 1.424896616 0.90792797 1.688966927 1.147715472 1.295155766 1 13.09079978 0.595845192 0.832780632 0.998742139 1.350597451 0.162422152 0.23569176 2.366693934 2.763926524 0.218329824 0.073286006 3.943167193 -0.595845192 0.351855312 DILYIGDHIFGDILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DILYIGDHIFGDILK 15 0 P49902-2;P49902;Q5JUV6 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ; 153.09 2.72E-06 65993000 272490 213724 220341 242720 237952 155660 275850 200908 156132 FALSE TRUE 255435.3373 229548.3473 225567.5926 248948.6061 219264.2098 200596.5151 234488.8534 225991.8061 130072.5605 1.963791104 1.764771497 1.734167388 1.913921007 1.685706877 1.542189331 1.802754189 1.737428748 1 16.98895712 -2.314976696 0.320065179 1.46E-12 1.812308981 0.833958243 0.109093997 17.37914479 0.720012774 12.53961141 0.096863946 0.004841983 2.314976696 1.812308981 DIMEDTIEDKLDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DIMEDTIEDKLDTK 14 1 A0A1B0GWF2;A0A1B0GVQ5;A0A2R8Y5D4;A0A0D9SG72;A0A1B0GTP9;P61764;P61764-2 A0A1B0GWF2 STXBP1 Syntaxin-binding protein 1 0 167.61 3.30E-06 58490000 200530 117590 142460 140700 152180 97852 196920 117300 201670 FALSE TRUE 187979.1853 126296.486 145839.2185 144310.6002 140228.3967 126100.2839 167393.6741 131945.1632 168009.9742 1.118857295 0.751720168 0.868039051 0.858940673 0.834643285 0.750552368 0.996331765 0.785341251 1 17.35818736 -1.685744218 2.643235708 1.020214718 0.862855476 0.111284523 0.113118658 18789491.61 16082140.92 2550671.663 0.02408518 0.020618439 1.685744218 -0.157359242 DINAVLIDMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 163.12 5.66E-05 216148000 238494 287176 288057 297545 324216 243951 311118 282713 352294 FALSE TRUE 223567.0863 308438.8098 294889.8481 305180.5084 298753.3832 314375.6935 264468.7442 318010.3404 293493.8555 0.761743669 1.050920842 1.004756463 1.039819072 1.017920401 1.071149149 0.901104876 1.083533213 1 18.16297077 4.743426553 24.74548839 1.015910252 0.761743548 0.721678651 0.050534297 234.0179224 1190041.135 0.011433636 0.093385601 55389.38628 -4.743426553 -0.254166704 DINAYNCEEPTEKLPFPIIDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DINAYNCEEPTEKLPFPIIDDR 22 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;; 240.41 1.15E-30 6754110000 2390480 2403970 2317270 2278940 2967000 1966420 3314930 2207140 4477560 FALSE TRUE 2240864.124 2581962.44 2372236.739 2337421.459 2733983.788 2534093.532 2817887.021 2482706.288 3730226.31 0.600731414 0.692173135 0.635949817 0.626616528 0.732927056 0.679340426 0.755419856 0.665564521 1 21.83083173 -5 0.205298377 2.526777772 0.627249975 0.864292527 0.041514259 45.7867795 0.45524452 28.65950755 0.085196332 1.00E-05 5 -1.899527798 DINLDVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DINLDVNR 8 0 P26640;A0A140T936;H0Y426 P26640 VARS Valine--tRNA ligase 0 ; 98.033 0.018168 281020000 549020 1133840 518300 502440 1208760 353970 501370 975110 1000890 FALSE TRUE 514657.8182 1217790.693 530594.3208 515333.461 1113828.866 456155.3928 426194.223 1096854.63 833834.993 0.617217822 1.460469642 0.63633012 0.618028106 1.335790504 0.547057148 0.511125374 1.315433676 1 19.66940239 3.860547286 7.426166492 0.806138449 1.091089095 0.028564486 0.358548074 0.513015694 30.08252082 0.0860307 0.155985511 7253.494504 -3.860547286 0.284950645 DINTFVGT(ph)PVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DINTFVGTPVEK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 DINTFVGT(1)PVEK;DINTFVGT(1)PVEK;DINTFVGT(1)PVEK;DINTFVGT(1)PVEK 251.74 5.40E-20 605130000 2510110 1608930 2161700 1948640 1754030 1707500 2654950 1686510 2041330 TRUE FALSE 2353006.696 1728056.851 2212976.545 1998645.401 1616275.559 2200427.531 2256864.895 1897074.486 1700618.836 1.38361792 1.016134136 1.301277217 1.175245951 0.950404362 1.29389813 1.327084499 1.115520096 1 20.69762839 3.037959969 24.97693295 1.172246161 1.201910423 0.040104568 0.148428316 1378.551895 907053.3425 0.042649193 0.050975468 1091.339738 -3.037959969 0.029664262 DINVSVGSQQPDTKDS(ph)PVCPHFTTNGNENSSIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DINVSVGSQQPDTKDSPVCPHFTTNGNENSSIEK 34 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 DINVSVGSQQPDT(0.024)KDS(0.976)PVCPHFTTNGNENSSIEK;DINVSVGSQQPDT(0.009)KDS(0.987)PVCPHFT(0.002)T(0.002)NGNENSSIEK;DINVSVGSQQPDT(0.007)KDS(0.993)PVCPHFTTNGNENSSIEK 339.21 6.67E-118 1038350000 613163 432185 506302 568120 604646 434662 802537 526402 682048 TRUE FALSE 574786.2224 464184.4271 518311.7225 582698.921 557159.5422 560141.8633 682204.0272 592124.4485 568209.7826 1.011573964 0.816924385 0.912183736 1.025499629 0.980552534 0.985801161 1.200619997 1.04208774 1 19.11606414 2.745362963 1.020068546 1.089223579 0.890075284 0.335270503 0.079021034 0.417853699 0.915369639 0.041576979 0.038985959 556.3690499 -2.745362963 -0.199148295 DINWDSSQWQPLIQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DINWDSSQWQPLIQDR 16 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 ; 251.68 3.82E-26 225448000 310010 356060 327040 303890 350260 274611 354220 309670 403270 FALSE TRUE 290607.0275 382423.0529 334797.5432 311688.3319 322751.9925 353886.7378 301107.9994 348332.9812 335961.6318 0.865000643 1.138293831 0.996535055 0.927749786 0.960681107 1.053354622 0.896257105 1.036823697 1 18.35793696 3.485398397 23.14131927 0.972093315 1.034530872 0 0.0809164 231.6583404 647666.1937 0.019938867 0.02943301 3057.724807 -3.485398397 0.062437557 DIPGLTDTTVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DIPGLTDTTVPR 12 0 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ;; 148.9 0.00014926 241393000 381695 450610 447550 479830 503570 412449 491010 428490 471990 FALSE TRUE 357805.3913 483973.6333 458166.0973 492143.2502 464021.6435 531516.3307 417387.6088 481987.9197 393211.8198 0.909955839 1.230821681 1.165189026 1.251598312 1.180080608 1.351730299 1.061482864 1.225771697 1 18.58494716 -1.319270842 2.914592165 0.998149944 1.178636242 0.170560016 0.118475069 8539461.435 10691606.03 137220.3673 0.025873571 0.047943436 1.319270842 0.180486298 DIPRT(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DIPRTPSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DIPRT(0.703)PS(0.297)R;DIPRT(0.978)PS(0.022)R;DIPRT(0.995)PS(0.005)R 113.22 0.0046717 5237040000 1362214 1397750 1398260 1434339 1520780 1189952 1500100 1361590 1472660 TRUE FALSE 1276955.457 1501240.864 1431427.388 1471146.567 1401344.073 1533471.825 1275173.931 1531587.509 1226863.532 1.040829256 1.223641281 1.166737253 1.199111823 1.142216747 1.249912305 1.039377158 1.248376424 1 20.22654335 -3.849116564 0.420200824 2.05E-11 1.167395366 0.308555714 0.075561035 365.6554611 6.330770361 327.2590236 0.039311949 0.000141541 3.849116564 1.167395366 DIPSFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DIPSFER 7 0 K7EJR3;R4GMR5;P48556 K7EJR3 PSMD8 26S proteasome non-ATPase regulatory subunit 8 0 ;;; 204.1 9.81E-05 551150000 818160 904940 906390 957350 982000 855220 1077000 806730 798780 FALSE TRUE 766952.8261 971942.6992 927889.9988 981917.2218 904877.6812 1102108.131 915513.8484 907452.0163 665458.4577 1.152517963 1.460561043 1.394362019 1.475549992 1.359780871 1.656163684 1.375764088 1.363649385 1 19.34398908 0.689393432 2.267703676 1.000172201 1.423584404 0.514324465 0.124073395 1.248305714 8.117743847 0.106658738 0.028877199 4.89095235 -0.689393432 0.423412204 DIPVTIHNLEEYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DIPVTIHNLEEYLR 14 0 Q14669-3;Q14669;Q14669-2;Q14669-4;H7C2Y1 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 0 ; 205.3 1.24E-08 45692000 54534 59915 52816 52881 56948 44250 65658 49244 52693 FALSE TRUE 51120.81429 64351.16894 54068.82046 54238.01599 52475.5338 57024.25666 55813.19244 55392.2218 43898.19789 1.164531046 1.465918239 1.231686563 1.235540833 1.195391527 1.299011335 1.271423319 1.261833616 1 15.42187409 -4.145541146 0.241800043 3.09E-18 1.309258833 0.495359431 0.08244581 87.56092286 1.274493612 43.10177712 0.125878557 7.15E-05 4.145541146 1.309258833 DIPVVHQLLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DIPVVHQLLTR 11 0 P30419;P30419-2 P30419 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 0 ; 172.09 3.57E-05 269310000 944270 1237140 984360 939810 1360390 754270 1025570 1084010 1337020 FALSE TRUE 885169.8263 1328739.133 1007709.484 963927.1157 1253550.457 972015.5044 871795.2994 1219351.035 1113862.725 0.794684845 1.192911033 0.904698094 0.865391304 1.125408391 0.872652871 0.782677506 1.094704947 1 20.08714001 DIQDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DIQDLK 6 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 97.068 0.09653 310350000 1778900 1280500 1473400 1418100 1429100 1151200 1820600 1262900 1485000 FALSE TRUE 1667561.824 1375309.552 1508349.744 1454490.847 1316864.251 1483532.752 1547617.932 1420575.845 1237143.907 1.347912572 1.111681143 1.219219313 1.175684445 1.064439023 1.199159406 1.250960315 1.148270494 1 20.2385819 0.975165355 22.74192619 0.999999997 1.188658945 0.393382432 0.075874079 715.7006971 655393.2478 0.067558485 0.016889621 9.444203901 -0.975165355 0.188658948 DIQHWESLKPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DIQHWESLKPEER 13 1 P31350;P31350-2;A0A286YFD6;C9JXC1 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 0 165.64 2.10E-05 119110000 709000 537440 582730 531790 593370 454450 678020 599750 693000 FALSE TRUE 664624.9556 577232.6168 596552.6308 545436.6317 546769.1137 585642.3376 576357.1954 674630.1077 577333.823 1.151196984 0.999824701 1.0332889 0.94475087 0.947058862 1.014391179 0.998308383 1.168526909 1 19.13904622 -0.197121531 6.830454855 1 1.021681906 0.000785109 0.075304219 0 3.50E-18 0.066863148 0.015759795 0.635153168 0.197121531 0.021681906 DIQLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DIQLAR 6 0 K7EK07;Q71DI3;Q16695;P84243;P68431;Q6NXT2 K7EK07 H3F3B;HIST2H3A;HIST3H3;H3F3A;HIST1H3A;H3F3C Histone H3;Histone H3.2;Histone H3.1t;Histone H3.3;Histone H3.1;Histone H3.3C 0 ;;;;; 161.58 0.019678 1728022000 1373378 1710250 1325304 1450248 2098630 1385298 1592600 1569944 1923290 FALSE TRUE 1287420.723 1836878.69 1356740.837 1487463.819 1933812.065 1785211.044 1353804.415 1765954.964 1602280.474 0.803492736 1.1464152 0.846756145 0.928341725 1.206912333 1.114168882 0.844923493 1.102150961 1 20.61169528 DIQNTQCLLNVEHLSAGCPHVTLQFADSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DIQNTQCLLNVEHLSAGCPHVTLQFADSK 29 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 293.21 5.82E-81 2870780000 945145 1885260 1749970 1785830 2145160 1673950 2314780 1972360 1859270 FALSE TRUE 885990.0616 2024846.612 1791480.115 1831657.421 1976687.787 2157192.191 1967700.228 2218613.488 1548945.826 0.571995513 1.307241724 1.156580227 1.182518711 1.276150369 1.392684079 1.270347998 1.432337691 1 20.56285526 4.74092809 24.87247394 1.260628589 0.571995253 0.753618565 0.12214988 91.41396958 960323.8709 0.026551425 0.178450646 55071.65016 -4.74092809 -0.688633335 DIREEAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DIREEAEK 8 1 P25788-2;P25788;G3V4X5;H0YJ03 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;;;; 140.45 0.00059228 4059670000 6819440 6584030 5746550 5592190 7881600 3616350 6494420 6078280 9852850 FALSE TRUE 6392623.423 7071518.432 5882860.88 5735695.063 7262610.929 4660331.538 5520642.012 6837166.638 8208345.683 0.778795591 0.861503487 0.716692633 0.698763829 0.884783757 0.567755272 0.672564512 0.832953058 1 22.96866006 0.957917174 6.187512992 0.99996876 0.741663619 0.457962554 0.090509968 0.275171721 36.3345133 0.088337276 0.022200444 9.076474128 -0.957917174 -0.258305141 DIRPVCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DIRPVCR 7 1 O00148;O00148-2;O00148-3;K7EQN7 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ;;; 113.89 0.0054978 2826740000 163621 199835 176851 182844 199055 136389 200406 158233 200681 FALSE TRUE 153380.2537 214630.9913 181045.9892 187536.0866 183422.0232 175762.2902 170356.9808 177988.7384 167186.0447 0.917422588 1.283785329 1.082901325 1.121720937 1.097113241 1.051297616 1.018966512 1.064614805 1 17.3510949 2.352003493 1.24622105 1.02502881 1.133080335 0.083676028 0.090496412 0.724105509 2.230241198 0.050131281 0.032083547 224.9072693 -2.352003493 0.108051525 DIS(ph)ENKR ddPTM_SK-BR-3_Pertuzumab_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 115.78 0.003432 3062570000 8551500 5084200 6310600 5891100 6474000 4122670 7409900 5363300 8334200 TRUE FALSE 8016276.88 5460639.458 6460290.412 6042275.6 5965558.155 5312817.903 6298854.285 6032919.811 6943168.179 1.154556058 0.786476622 0.93045282 0.870247622 0.85919828 0.765186406 0.907201745 0.868900141 1 22.72716269 4.748583379 24.86630917 0.866839191 1.154556227 0.634408757 0.066894044 773.3705693 1918678.402 0.014230436 0.194992406 56051.00183 -4.748583379 0.287717036 DIS(ph)LDSELHDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DISLDSELHDLR 12 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 1 DIS(1)LDSELHDLR;DIS(1)LDSELHDLR 205.27 6.68E-08 56780000 121652 127306 141206 139456 137305 115509 170730 116057 134547 TRUE FALSE 114038.0185 136731.8687 144555.473 143034.6771 126521.6192 148854.5732 145130.6215 130546.9719 112090.2365 1.01737691 1.219837454 1.289634829 1.276067225 1.128747901 1.327988751 1.294765949 1.164659617 1 16.77430109 0.947119028 6.956469362 1.000006413 1.235137248 0.360470972 0.091772877 0.562505862 72.50920394 0.083655487 0.020982037 8.853582286 -0.947119028 0.235130836 DISDIEGEKDGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DISDIEGEKDGIR 13 1 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 ;; 153 4.15E-05 1347270000 3123600 2607830 2774390 3032900 3115250 1878150 3621000 2619600 2896770 FALSE TRUE 2928099.452 2800916.447 2840199.841 3110729.349 2870590.831 2420341.416 3078064.666 2946662.826 2413280.373 1.213327504 1.160626207 1.176904214 1.289004536 1.189497442 1.002925911 1.27546915 1.221019679 1 21.20256411 2.454450836 24.99555373 1.148800248 1.20053411 0.140905068 0.091179428 683.157027 753218.8632 0.030360329 0.025403091 284.7415442 -2.454450836 0.051733862 DISDIEGEKDGIRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DISDIEGEKDGIRK 14 2 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 ; 116.96 0.00018622 332360000 640410 480110 553150 626620 644680 327180 778820 446750 791640 FALSE TRUE 600327.8813 515657.844 566270.9792 642700.1301 594049.4333 421631.5547 662043.1712 502527.7209 659510.1698 0.910263266 0.781880049 0.858623574 0.974511326 0.900743401 0.639310164 1.003840731 0.761971148 1 19.33103538 -1.186774991 3.543220361 1.000188738 0.854410102 0.156693719 0.106516287 26671835.14 45364011.22 57753.85264 0.0232393 0.065046661 1.186774991 -0.145778636 DISEASVFDAYVLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DISEASVFDAYVLPK 15 0 P62854 P62854 RPS26 40S ribosomal protein S26 0 ; 218.54 4.48E-12 81467000 242068 207016 222719 217833 226007 178826 255851 202313 232487 FALSE TRUE 226917.396 222343.68 228001.9999 223422.9636 208257.3219 230450.1632 217488.5178 227572.2234 193683.4178 1.171589177 1.147974786 1.177189057 1.153547196 1.075246009 1.189829082 1.122907269 1.174970093 1 17.56334092 -2.251244893 2.386977975 0.399198073 1.151001515 0.677378011 0.032889609 2075885.215 582076.549 6687382.742 0.007318721 0.005607317 2.251244893 0.751803443 DISENKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 DISENKR 7 1 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;;;;; 172.15 0.0014613 74093000000 22043480 22351080 17838240 15684490 23751020 12390030 22253870 20781070 26409330 FALSE TRUE 20663817.94 24005977.22 18261371.48 16086980.57 21885710.7 15966830.53 18917108.79 23375632.33 22001442.21 0.939202882 1.091109255 0.830007929 0.731178457 0.994739821 0.725717449 0.859812216 1.062459093 1 24.39109476 3.924231284 5.096549923 0.869037585 1.018152496 0.161059267 0.116985001 0.261840256 14.70431143 0.02771885 0.052556502 8399.071611 -3.924231284 0.149114911 DISGPS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DISGPSPSK 9 0 Q96GX9;S4R3D6;Q96GX9-3 Q96GX9 APIP Methylthioribulose-1-phosphate dehydratase 1 DISGPS(1)PSK;DISGPS(0.992)PS(0.008)K 235.47 3.52E-10 1686070000 4860000 3115900 3652000 3362000 3549400 2552400 4545600 3103500 3751300 TRUE FALSE 4555821.275 3346604.478 3738627.165 3448274.612 3270644.442 3289236.445 3864029.479 3490978.807 3125183.796 1.45777707 1.070850451 1.196290333 1.103382981 1.046544669 1.05249376 1.236416714 1.117047519 1 21.57550961 4.743449844 24.94409123 1.118216505 1.457777213 0.705438432 0.071463461 284.6701641 1452294.595 0.016527187 0.135665586 55392.35685 -4.743449844 0.339560708 DISGPS(ph)PSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DISGPSPSKK 10 1 Q96GX9;S4R3D6;Q96GX9-3 Q96GX9 APIP Methylthioribulose-1-phosphate dehydratase 1 DISGPS(0.999)PS(0.001)KK;DIS(0.002)GPS(0.986)PS(0.011)KK;DIS(0.009)GPS(0.854)PS(0.137)KK;DISGPS(0.997)PS(0.003)KK;DIS(0.081)GPS(0.875)PS(0.044)KK;DISGPS(0.999)PS(0.001)KK 150.49 1.32E-05 8548710000 27632800 13170000 17842200 16868400 17791300 11987500 23044300 14507700 20375500 TRUE FALSE 25903312.37 14145120.5 18265425.41 17301271.7 16394043.06 15448096.65 19589021.15 16319018.28 16974697.42 1.525995529 0.833306194 1.07603835 1.019238887 0.965792948 0.910066098 1.15401298 0.961373147 1 24.01688252 4.749652696 24.99848569 0.996746374 1.525995834 0.789557544 0.086904846 767.5207017 1729747.122 0.020508625 0.315543174 56189.18028 -4.749652696 0.52924946 DISILQCHGDCDPLVPLMFGSLTVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DISILQCHGDCDPLVPLMFGSLTVEK 26 0 B4DP64;E5RGR0;O75608-2;O75608;A0A087X1K9 B4DP64 LYPLA1 Acyl-protein thioesterase 1 0 71.528 0.029311 51565000 105590 93938 89324 87292 115940 77750 139210 86546 224000 FALSE TRUE 98981.31038 100893.2673 91442.80746 89532.06051 106834.5401 100195.1628 118336.7529 97351.45861 186612.9529 0.530409647 0.540655221 0.490013185 0.479774095 0.572492629 0.536914299 0.634129363 0.521675785 1 17.5096896 -5 0.26930983 4.175229353 0.505356059 0.927011724 0.040870398 49.19143064 0.47834329 86.72920034 0.048299778 1.00E-05 5 -3.669873294 DISLDSELHDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DISLDSELHDLR 12 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 ;;; 211.26 3.39E-08 296449000 383790 485520 456060 465800 502050 377057 512880 424804 491360 FALSE TRUE 359769.269 521468.406 466877.9586 477753.2166 462621.0182 485907.2349 435978.4053 477841.7145 409348.8417 0.878881854 1.273897353 1.140538121 1.167105334 1.130138823 1.187024819 1.065053473 1.167321526 1 18.64297129 -0.258789222 0.586484348 0.986646087 1.145028103 0.102134086 0.103882197 12.79386797 4.201657398 0.482685067 0.038876742 0.551075087 0.258789222 0.158382015 DISLSDYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DISLSDYK 8 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;;;;; 180.93 0.00055023 6149460000 11287600 13041170 9185040 8998350 14940260 5975180 10645260 12194210 15969450 FALSE TRUE 10581129.26 14006751.8 9402913.486 9229262.895 13766912.25 7700117.467 9049102.089 13716683.96 13304045.63 0.795331703 1.052818984 0.706770989 0.693718524 1.034791418 0.578780146 0.680176718 1.031016004 1 23.66536169 3.9672144 22.6605562 0.787837432 0.93463325 0.039224857 0.172959131 209.7331539 479741.2243 0.041101567 0.075478993 9272.874894 -3.9672144 0.146795817 DISMEIDS(ph)PENMMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 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;DISMEIDS(1)PENMMR 328.41 2.49E-68 1153197000 2272220 2419090 2470357 2328558 2665218 2129489 2667027 2289526 2748041 TRUE FALSE 2130005.806 2598201.941 2528955.035 2388312.741 2455902.529 2744237.905 2267131.061 2575378.361 2289375.204 0.930387384 1.134895641 1.104648565 1.043215955 1.072739202 1.198684209 0.990283749 1.124926293 1 21.12652249 -1.56516084 3.105619122 0.996411344 1.080768513 0.08388496 0.075741274 3487244.374 3685583.623 76562.05507 0.015892775 0.027216931 1.56516084 0.084357168 DISPVLKDPASFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DISPVLKDPASFR 13 1 H3BQB1;P07741-2;P07741;H3BQZ9;H3BQF1;H3BSW3 H3BQB1 APRT Adenine phosphoribosyltransferase 0 ;; 127.36 0.00016223 3563000000 8660100 8739350 8843760 8459010 9631790 6489930 10303160 8120130 10053610 FALSE TRUE 8118079.8 9386420.567 9053538.164 8676082.518 8875348.066 8363467.436 8758296.808 9133946.105 8375597.542 0.969253807 1.120686676 1.080942359 1.035876243 1.059667447 0.998551732 1.045692175 1.090542622 1 22.99776069 3.234962038 24.76357635 1.039214366 1.074042378 0 0.046548882 176.1628103 1212265.886 0.012491956 0.015478928 1717.758229 -3.234962038 0.034828012 DISQNKR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;; 147.34 0.0034608 9518520000 5572260 6423490 4368500 4027550 7239590 2837640 5202270 6460770 7415210 FALSE TRUE 5223502.193 6899091.883 4472122.883 4130903.752 6671021.805 3656820.603 4422237.909 7267411.356 6177563.547 0.845560253 1.116798205 0.723929887 0.668694659 1.079879107 0.59195192 0.715854702 1.176420332 1 22.55860652 1.235518217 24.99999942 1.088210215 0.826889815 0.294099356 0.172276356 109.603973 900559.0166 0.143319696 0.041779713 17.19959484 -1.235518217 -0.2613204 DISSALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DISSALR 7 0 P13489;E9PMJ3;E9PLZ3;E9PIM9;E9PMN0;E9PIK5;E9PMA9 P13489 RNH1 Ribonuclease inhibitor 0 ;;; 133.47 0.0076042 578407000 482299 690747 561975 543986 728884 472400 629899 644199 646728 FALSE TRUE 452112.7665 741890.6266 575305.3124 557945.6017 671640.3908 608774.2112 535451.4926 724628.6632 538784.9188 0.839134042 1.37696992 1.06778288 1.035562768 1.246583502 1.1299021 0.993813067 1.344931229 1 19.03934994 -1.233358475 3.896167156 0.999859746 1.136106361 0.057642713 0.162304181 10966240.93 3480196.724 12936.73819 0.034320406 0.058430759 1.233358475 0.136246615 DISTNKVEQIPYGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DISTNKVEQIPYGER 15 1 P49750;P49750-1;H0YIQ2;P49750-3;F8VU51;H0YI23 P49750 YLPM1 YLP motif-containing protein 1 0 111.78 0.00074407 143220000 195090 158990 170650 161410 188590 133240 195820 140550 249120 FALSE TRUE 182879.6651 170761.785 174697.8986 165552.0539 173778.9021 171704.225 166458.6089 158097.9769 207540.2626 0.881176803 0.82278871 0.841754252 0.797686443 0.837326213 0.827329709 0.802054535 0.76177015 1 17.66303172 -1.123889001 4.675009529 1.000014279 0.821956469 0.763530697 0.0312202 4.35E-06 8.15E-07 0.028299762 0.006669783 0.075181502 1.123889001 -0.17805781 DISTNYYASQKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DISTNYYASQKK 12 1 P14625;H0YIV0 P14625 HSP90B1 Endoplasmin 0 ; 127.36 0.00043485 474900000 396290 416750 379290 377450 456120 261530 473380 331850 492390 FALSE TRUE 371486.9163 447606.6036 388286.9379 387136.006 420298.1751 337029.4654 402401.0636 373282.203 410206.928 0.905608587 1.091172706 0.946563579 0.943757844 1.024600382 0.821608419 0.98097091 0.909985126 1 18.64599233 3.721976582 19.19219273 0.943678987 1.013812203 0.074300907 0.070591552 17.3077365 64575.05999 0.016612159 0.026823512 5272.01433 -3.721976582 0.070133216 DITDPLSLNTCTDEGHVVLAS(ph)PLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DITDPLSLNTCTDEGHVVLASPLK 24 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 DITDPLSLNTCTDEGHVVLAS(1)PLK;DITDPLSLNTCTDEGHVVLAS(1)PLK;DITDPLSLNTCTDEGHVVLAS(1)PLK;DITDPLSLNTCTDEGHVVLAS(1)PLK;DITDPLSLNTCTDEGHVVLAS(1)PLK;DITDPLSLNTCTDEGHVVLAS(1)PLK;DITDPLSLNTCTDEGHVVLAS(1)PLK;DITDPLSLNTCTDEGHVVLAS(1)PLK 251.91 6.18E-44 5713102000 4330228 2557290 3297382 2988935 3085657 2801299 4682899 2938940 4488417 TRUE FALSE 4059206.759 2746634.412 3375597.458 3065636.132 2843321.946 3609988.546 3980741.769 3305873.128 3739271.206 1.085560938 0.734537363 0.902742078 0.819848565 0.760394684 0.965425706 1.064576905 0.884095575 1 21.83432568 2.083955729 7.327932758 0.996170452 0.847708336 0.232524599 0.104404607 0.253378301 18.74734299 0.035870841 0.026415993 121.3265166 -2.083955729 -0.148462116 DITDTLVAVTISEGAHHLDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DITDTLVAVTISEGAHHLDLR 21 0 P42785;P42785-2 P42785 PRCP Lysosomal Pro-X carboxypeptidase 0 ;;;;; 163.96 9.62E-12 273395100 216225.3 307625 257334 253455.4 315415 228835.9 293992 267044.9 303121 FALSE TRUE 202692.1444 330401.8751 263438.084 259959.4947 290643.5782 294897.1095 249910.6289 300386.0436 252528.1469 0.802651692 1.308376429 1.043202856 1.0294278 1.150935378 1.167779169 0.989634748 1.189515099 1 17.94608467 -1.910276134 2.584242194 0.942924816 1.097372949 0.030581367 0.136160729 15636574.03 8174470.516 5399159.619 0.030061298 0.012294868 1.910276134 0.154448133 DITEEIMSGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DITEEIMSGAR 11 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JHW9;F8WCF2 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 251.43 3.98E-17 275300000 197617 212380 207300 216120 213260 177818 228600 184970 231320 FALSE TRUE 185248.5047 228104.8362 212217.2539 221666.0051 196511.4198 229151.17 194323.5522 208063.9117 192711.1976 0.96127525 1.183661557 1.101219112 1.150249741 1.019719779 1.1890911 1.008366689 1.079666954 1 17.55608088 1.65371686 11.45869728 1.033363607 1.109060488 0.17029811 0.072625212 0.174806709 34.66614694 0.030675289 0.016643478 45.05228889 -1.65371686 0.07569688 DITLFHAMDTLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DITLFHAMDTLQR 13 0 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 0 111.95 0.00093925 243670000 680440 811890 677350 694460 880780 527250 653670 691250 882880 FALSE TRUE 637852.475 872003.1804 693417.0619 712281.0193 811607.0917 679458.5158 555658.2519 777554.0841 735521.6244 0.867211043 1.185557503 0.942755507 0.968402554 1.103444229 0.923777756 0.755461476 1.057146464 1 19.48840823 2.067183348 8.166638868 0.892858307 1.024743999 0.057029755 0.117439791 0.37306251 40.20762453 0.041431516 0.030537002 116.7302318 -2.067183348 0.131885692 DITLFHAMDTLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DITLFHAMDTLYR 13 0 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2;E9PCS8 Q9BTC8 MTA3 Metastasis-associated protein MTA3 0 ; 138.02 5.39E-05 348930000 223562 313405 244391 248538 331860 176064 255595 281270 332660 FALSE TRUE 209569.6535 336609.8323 250188.0699 254915.9059 305797.0543 226890.8186 217270.9026 316387.1787 277136.8969 0.756195425 1.214597681 0.902759873 0.919819442 1.103415163 0.818695818 0.783984035 1.141627774 1 18.08023927 2.230012314 24.99941137 0.900159373 0.998284316 0 0.156397235 488.0153908 1427183.563 0.054900128 0.041193569 169.8291805 -2.230012314 0.098124943 DIVEAHYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DIVEAHYR 8 0 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ;;; 144.12 0.00059047 1353930000 1959510 2126660 2113450 1935670 2477820 1693450 2004580 2195040 2530750 FALSE TRUE 1836867.767 2284120.119 2163582.032 1985342.569 2283222.012 2182321.524 1704011.839 2469095.576 2108351.476 0.871234132 1.083367809 1.026196086 0.941656357 1.082941833 1.035084306 0.808220004 1.171102449 1 21.00768396 DIVENYFMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 DIVENYFMR 9 0 Q13263;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;;;;;;; 283.57 3.19E-21 2165412000 1010200 1311733 983220 980301 1429074 754828 953756 1165478 1365375 FALSE TRUE 946973.3853 1408855.076 1006542.443 1005457.183 1316840.293 972734.59 810749.142 1310990.494 1137485.092 0.832514986 1.238570146 0.884884074 0.883929988 1.157676968 0.855162496 0.71275584 1.152534221 1 20.11741621 2.182361242 24.99987932 0.883630335 1.01123004 0.005402069 0.167696093 184.403364 82028.93822 0.059980242 0.044298366 152.1812833 -2.182361242 0.127599705 DIVNGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DIVNGLR 7 0 P47756-2;B1AK88;B1AK87;P47756 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;; 118.69 0.017705 606490000 619947 765930 631529 609829 760600 527068 652610 649146 704428 FALSE TRUE 581145.6239 822640.2541 646509.1661 625478.2446 700865.5441 679223.9754 554757.189 730193.307 586854.416 0.990272218 1.401779098 1.101651702 1.065815009 1.194274977 1.157397741 0.945306321 1.244249489 1 19.16264313 3.720084421 22.1578186 1.095597568 1.233307941 0.065809092 0.131551756 102.0565986 321364.6053 0.031882572 0.050766019 5249.094863 -3.720084421 0.137710373 DIVNMLMHHDR ddPTM_SK-BR-3_Pertuzumab_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 ; 127.37 0.00016654 379440000 932010 1217870 967070 920310 1253820 745100 976840 1181730 911350 FALSE TRUE 873677.1578 1308042.362 990009.3571 943926.7127 1155350.035 960198.2743 830371.9105 1329271.592 759239.7975 1.150726241 1.722831662 1.303948187 1.243252416 1.521719539 1.264683803 1.093688599 1.750792828 1 19.53419609 -4.083673416 0.178732172 1.31E-12 1.463512763 0.157148788 0.232406616 151.1680943 1.955493979 56.01826623 0.713889495 8.25E-05 4.083673416 1.463512763 DIVPGDIVEVAVGDKVPADLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DIVPGDIVEVAVGDKVPADLR 21 1 Q93084-4;Q93084-2;Q93084-3;Q93084-7;Q93084;Q93084-6;Q93084-5 Q93084-4 ATP2A3 Sarcoplasmic/endoplasmic reticulum calcium ATPase 3 0 ; 116.73 2.61E-05 47190000 138493 126875 118662 124282 154022 106766 155531 127728 131355 FALSE TRUE 129824.9703 136268.957 121476.7187 127471.2865 141925.7334 137587.611 132210.5704 143675.122 109431.0019 1.186363718 1.245250017 1.110075907 1.164855336 1.296942648 1.257300112 1.208163757 1.312928873 1 16.73966199 -1.004968863 4.550578852 0.999994295 1.216104901 0.567999444 0.060802386 0.018303857 18570392.12 272.6190312 0.01433304 0.098862397 1.004968863 0.216110605 DIWAELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DIWAELR 7 0 A0A1B0GV75;A0A1B0GTB8;A0A1B0GWC0;A0A1B0GVF3;P23786 A0A1B0GV75 CPT2 "Carnitine O-palmitoyltransferase 2, mitochondrial" 0 88.942 0.042427 25363000 44837 56882 52846 50250 68030 50359 50304 52753 66957 FALSE TRUE 42030.73221 61093.60247 54099.53208 51539.50007 62687.19822 64896.82579 42761.3822 59339.32817 55781.44414 0.753489496 1.095231639 0.96984818 0.923954209 1.123800202 1.163412436 0.766587937 1.063782573 1 15.76749766 -3.381975147 1.556320831 3.028340055 0.985691736 0.001091936 0.139340763 5931285.991 57289.65053 43051702.25 0.032330378 0.000414978 3.381975147 -2.04264832 DIWDFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DIWDFLR 7 0 Q8NFF5-2;Q8NFF5;Q8NFF5-3;Q5T190 Q8NFF5-2 FLAD1 FAD synthase;Molybdenum cofactor biosynthesis protein-like region;FAD synthase region 0 ; 114.78 0.013557 48646000 250920 409080 271640 275660 471380 196986 226972 361440 250390 FALSE TRUE 235215.3651 439368.7088 278083.4291 282733.9023 434359.7163 253852.6604 192939.6557 406566.5796 208598.2914 1.127599673 2.106291024 1.333105018 1.355398936 2.082278399 1.216945061 0.924934017 1.949040794 1 17.67036782 1.266934367 0.30640403 0.977400333 1.697515543 0.077269513 0.422169837 3.103287221 1.024083318 0.860167113 0.633471876 18.48989168 -1.266934367 0.72011521 DIYDKDNYELDEDT(ph)D ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DIYDKDNYELDEDTD 15 1 Q9UBW7 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1 DIYDKDNYELDEDT(1)D 101.47 0.011207 40836000 169800 129730 146740 146430 144940 117080 189750 127460 142970 TRUE FALSE 159172.5211 139335.3442 150220.7421 150187.6417 133556.9971 150879.0954 161298.7491 143373.6616 119107.3834 1.336378288 1.169829613 1.261221075 1.260943171 1.121315852 1.266748468 1.354229641 1.203734458 1 16.86190332 0.972938701 24.02871537 0.999999997 1.249318845 0.572930775 0.068206798 1339.461679 1189358.67 0.065550137 0.016387534 9.395906812 -0.972938701 0.249318848 DIYLS(ph)PDRTGSSFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DIYLSPDRTGSSFGK 15 1 Q15696 Q15696 ZRSR2 U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 1 DIYLS(1)PDRTGSSFGK 155.79 1.36E-06 224480000 340870 331780 307210 331820 359820 212950 391450 270710 508350 TRUE FALSE 319535.5552 356345.3364 314497.1663 340335.063 331561.1886 274425.208 332755.7065 304508.7394 423503.1009 0.754505822 0.841423205 0.742608887 0.803618822 0.782901443 0.647988663 0.785722007 0.719023636 1 18.69201301 -1.856536823 8.22151815 1.015602994 0.764118944 0.676817873 0.052100957 0.013985718 0.000244047 0.047348805 0.011380147 0.013914358 1.856536823 -0.25148405 DIYLSPDRT(ph)GSSFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DIYLSPDRTGSSFGK 15 1 Q15696 Q15696 ZRSR2 U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 1 DIYLS(0.179)PDRT(0.811)GS(0.01)SFGK 223.32 8.17E-12 84139000 112890 124000 116820 106660 125810 72359 127960 96681 150980 TRUE FALSE 105824.4164 133181.089 119591.0256 109397.0762 115929.3901 93247.86865 108773.5859 108751.8357 125780.4626 0.841342242 1.058837646 0.950791745 0.869746174 0.921680424 0.741354155 0.864789202 0.86461628 1 16.94054832 3.275954986 2.816917285 0.860815544 0.978136031 0.109151298 0.083403696 0.315833549 5.094326007 0.022797284 0.031130999 1887.795672 -3.275954986 0.117320487 DIYQFLCNASER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DIYQFLCNASER 12 0 O75509 O75509 TNFRSF21 Tumor necrosis factor receptor superfamily member 21 0 83.948 0.029109 255600000 41686 46343 51432 44519 36871 41731 51674 34797 44643 FALSE TRUE 39076.94767 49774.28394 52651.99133 45661.43291 33975.30039 53778.06225 43925.96342 39141.48205 37191.7949 1.05068733 1.338313574 1.415688366 1.227728671 0.913516018 1.445965768 1.181065973 1.052422508 1 15.18269675 3.000701915 24.9954048 1.152088456 1.306487661 0.11888585 0.168508513 44.5161934 1585115.99 0.046920487 0.055634476 1001.617526 -3.000701915 0.154399205 DKADFCIIHYAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKADFCIIHYAGK 13 1 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ; 127.26 0.00010754 4440200000 10961400 9090300 9782100 9893100 11124200 7445900 13612500 9498700 11750100 FALSE TRUE 10275345.54 9763355.27 10014136.03 10146973.69 10250550.2 9595410.456 11571432 10684633.6 9788932.401 1.049690111 0.997387138 1.023005944 1.036576133 1.047157114 0.980230536 1.18209336 1.091501419 1 23.22272009 1.75233705 25 1.108403459 1.021040319 0.285911533 0.048808277 3.819060438 6940.311092 0.019918867 0.011045871 56.53755843 -1.75233705 -0.08736314 DKADKDEQIR ddPTM_SK-BR-3_Pertuzumab_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 ; 117.79 0.00051217 322390000 579130 350410 453710 430390 424220 308500 588690 411920 635170 FALSE TRUE 542883.2871 376354.721 464472.2155 441434.536 390903.4724 397558.9419 500421.3996 463349.1187 529156.0236 1.025941807 0.711235825 0.877760424 0.834223776 0.738730081 0.7513076 0.945697256 0.875637993 1 19.01333364 1.673879902 7.666610916 0.932679846 0.813978844 0.255481661 0.092891993 0.160037813 17.22607913 0.042125688 0.021905538 47.19325165 -1.673879902 -0.118701002 DKAIT(ph)PPLPESTVPFSNGVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKAITPPLPESTVPFSNGVLK 21 1 Q92667-2;Q92667;I3NI36 Q92667-2 AKAP1 "A-kinase anchor protein 1, mitochondrial" 1 DKAIT(1)PPLPESTVPFSNGVLK 131.95 2.00E-05 184740000 708780 388710 443520 439950 614800 414730 679580 533810 756180 TRUE FALSE 664418.725 417490.4929 454040.5038 451239.8618 566516.088 534455.8184 577683.2879 600457.3536 629968.6729 1.054685342 0.662716276 0.720735051 0.716289367 0.899276603 0.848384755 0.917003198 0.953154307 1 19.26492056 1.977451029 0.983089494 0.978298643 0.760896748 0.263218883 0.11079891 0.585769228 1.042163804 0.085876544 0.040221789 94.94039377 -1.977451029 -0.217401895 DKANMQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 DKANMQHR 8 1 P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7;H0YBG7;H0YBK1;P55795 P31943;P55795 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 ;;;;;;;;;; 155.07 0.0002493 1545075000 2278891 3506476 1902092 1847290 3864510 1287701 2168330 3222922 4055640 FALSE TRUE 2136259.28 3766099.132 1947210.52 1894694.589 3561006.973 1659439.375 1843209.046 3625310.906 3378727.484 0.632267412 1.11465016 0.57631476 0.560771651 1.053949154 0.491143303 0.545533505 1.072981152 1 21.68804856 1.22153776 24.99598184 1.036490915 0.723953765 0.287065229 0.212673572 386.7845144 567930.3667 0.201895543 0.050992674 16.65473627 -1.22153776 -0.31253715 DKAPVQPQQS(ph)PAAAPGGTDEKPSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 224.07 4.56E-34 4934210000 5070560 2441990 3418920 3053760 3226710 2425840 4613540 2718040 4623040 TRUE FALSE 4753202.701 2622797.48 3500018.397 3132124.652 2973297.213 3126140.628 3921782.507 3057393.277 3851424.758 1.234141389 0.680994085 0.908759386 0.813237918 0.771999299 0.811684201 1.01826798 0.793834352 1 21.87696081 -0.87663879 5.507208263 1.000000086 0.867123603 0.052348681 0.154316254 1.48E-07 2.99E-08 0.134066284 0.031599706 0.132849893 0.87663879 -0.132876483 DKAPVQPQQSPAAAPGGTDEKPSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKAPVQPQQSPAAAPGGTDEKPSGK 25 2 Q13200;C9JPC0;F8WBS8 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 143.32 1.84E-07 146650000 428610 239600 292720 299860 295790 206260 402120 217180 384670 FALSE TRUE 401784.0652 257340.2333 299663.4566 307554.9153 272559.8466 265803.9136 341825.8391 244295.4011 320466.0919 1.253749071 0.803018603 0.935086314 0.959711255 0.85051072 0.829429136 1.066652129 0.762312791 1 18.28981219 4.749046879 24.77688483 0.904483971 1.253749293 0.584991853 0.093370587 932.8670626 2204124.087 0.02071543 0.293610369 56110.85403 -4.749046879 0.349265322 DKAS(ph)PEPEKDFSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.996)PEPEKDFS(0.004)EK;DKAS(1)PEPEKDFSEK 120.92 6.14E-05 2918150000 8807700 2761430 4505700 4466200 4735400 3103570 6077300 3539760 6452800 TRUE FALSE 8256441.779 2965889.15 4612577.332 4580810.253 4363500.786 3999520.277 5166065.284 3981706.828 5375785.993 1.535857601 0.551712653 0.858028452 0.852119162 0.811695404 0.743988001 0.960987898 0.740674356 1 22.35804428 -1.061024199 7.092678217 1.000000033 0.849352228 0.006551593 0.257499717 1.20E-07 1.56E-08 0.21873407 0.051556103 0.086891201 1.061024199 -0.150647805 DKASGDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKASGDVK 8 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 0 ; 74.841 0.03642 319610000 600540 485080 554930 547100 631800 370270 554090 539020 701590 FALSE TRUE 562953.2734 520995.8279 568093.2017 561139.5122 582180.9766 477160.9382 471009.3484 606317.8335 584490.0966 0.963152801 0.891368102 0.971946668 0.960049649 0.996049343 0.816371297 0.805846585 1.037344922 1 19.15681905 2.25179822 24.99772019 0.885820735 0.949895156 0.004659132 0.077126422 451.7276343 853035.9381 0.025865415 0.021522815 178.5657737 -2.25179822 0.064074421 DKAVESLR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 125.48 0.0011493 2454470000 1784620 1849290 1830420 1716930 2200690 1369870 2143890 1944290 2824930 FALSE TRUE 1672923.82 1986213.356 1873838.427 1760989.331 2027856.685 1765329.231 1822433.597 2187038.886 2353430.933 0.710844664 0.843965008 0.796215602 0.748264717 0.861659739 0.750108791 0.774373096 0.929298096 1 21.16633408 1.099654155 3.813569448 0.997277096 0.789798455 0.74337161 0.045031025 0.098618867 2.541364651 0.039776589 0.010306069 12.57923282 -1.099654155 -0.207478641 DKDAVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DKDAVDK 7 1 P25815 P25815 S100P Protein S100-P 0 ;;;;; 116.05 0.005055 7462900000 20620800 8879420 12673450 11350260 9464500 8697710 14409100 8461540 6730690 FALSE TRUE 19330180.94 9536861.496 12974070.22 11641526.89 8721196.348 11208597.68 12248589.22 9517981.895 5607294.357 3.44732766 1.700795587 2.313784402 2.076139783 1.555330573 1.998931564 2.184402752 1.697428615 1 22.41887338 8 0.061189508 9.87E-15 6.295665086 0.502802036 0.44668592 332.9229306 1.519096835 31.08436225 185.8788548 100000000 -8 6.295665086 DKDAVDKLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKDAVDKLLK 10 2 P25815 P25815 S100P Protein S100-P 0 126.1 0.0002202 579170000 2687000 1761700 2063400 2317200 2460800 1541000 3538100 1673400 2926000 FALSE TRUE 2518825.466 1892138.101 2112344.822 2376663.275 2267538.694 1985861.684 3007594.751 1882327.674 2437631.697 1.033308465 0.776219846 0.866556184 0.974988665 0.930222025 0.814668469 1.233818363 0.772195273 1 21.21704873 DKDAYSSFGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DKDAYSSFGSR 11 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y650;A0A2R8YCU0;A0A2R8YF89;A0A087WX09;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;O15523-2;O15523;O15523-3;C9J8G5;C9J081 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;;; 178.15 6.99E-06 4778060000 4763690 4334960 4580020 4259430 5056660 3469090 5325800 4342420 6304200 FALSE TRUE 4465539.146 4655924.949 4688660.237 4368734.185 4659530.321 4470559.967 4527245.732 4884580.696 5251988.293 0.850256874 0.886507107 0.89274004 0.831824814 0.887193585 0.851212858 0.862006059 0.930044094 1 22.32443227 0.991798767 3.219217763 0.999600207 0.86920556 0.838668584 0.019377202 0.087464488 2.25336428 0.018531239 0.00484204 9.812931505 -0.991798767 -0.130394647 DKDDDEVFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 104.87 0.002394 323170000 314170 128850 189400 179100 183650 128630 253170 162570 203030 FALSE TRUE 294506.6605 138390.1881 193892.6574 183696.0092 169226.8698 165763.3929 215209.5088 182867.2224 169142.9814 1.741169856 0.818184633 1.146323991 1.086039797 1.000495962 0.980019339 1.27235258 1.081139879 1 17.36788379 4.751295058 24.98149879 1.057836944 1.741170292 0.77281114 0.117995904 1042.813054 2045677.641 0.029076221 0.527394499 56402.07194 -4.751295058 0.683333348 DKDDDEVFEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKDDDEVFEKK 11 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 122.97 0.00021361 817520000 2522330 801030 1385310 1269250 1333440 957170 1931700 1056020 1702600 FALSE TRUE 2364461.868 860339.0947 1418170.207 1301821.104 1228717.001 1233489.441 1642059.518 1187866.422 1418425.061 1.66696284 0.606545329 0.999820327 0.917793361 0.866254436 0.869619041 1.157663921 0.83745448 1 20.4358585 -0.521578855 8.443085517 1 0.960224287 0 0.278693559 0 0 0.238978765 0.056327835 0.300899277 0.521578855 -0.039775713 DKDDDGGEDDDANCNLICGDEYGPETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DKDDDGGEDDDANCNLICGDEYGPETR 27 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;; 333.78 2.31E-95 1515980000 1333390 668817 846901 793498 876887 826292 1424360 714045 1256400 FALSE TRUE 1249935.5 718336.9066 866989.8917 813860.5021 808019.8322 1064829.087 1210790.441 803195.0901 1046698.723 1.194169317 0.686288127 0.828308922 0.777549914 0.771969827 1.017321473 1.156770725 0.767360342 1 19.99741481 2.229426643 24.78580834 1.016067571 0.822554519 0.115385166 0.164382969 239.5214111 649956.1035 0.056694635 0.042467915 169.6003106 -2.229426643 -0.193513052 DKDDELSFMEGAIIYVIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKDDELSFMEGAIIYVIK 18 1 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 0 ; 155.28 1.82E-08 201173000 1357000 721720 975360 903650 973290 685730 1188170 805220 1151470 FALSE TRUE 1272067.792 775156.8997 998495.9998 926839.1889 896851.7295 883689.1191 1010014.939 905753.4895 959282.2182 1.3260621 0.808059281 1.040878253 0.966179891 0.934919581 0.921198269 1.052886126 0.944199186 1 19.87159579 4.754170935 24.72241258 0.960553746 1.326062414 0.739454837 0.068550848 1346.444237 2132352.425 0.016027606 0.397510595 56776.80302 -4.754170935 0.365508668 DKDDQEWESPS(ph)PPKPTVFISGVIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DKDDQEWESPSPPKPTVFISGVIAR 25 2 P51397 P51397 DAP Death-associated protein 1 1 DKDDQEWES(0.1)PS(0.897)PPKPT(0.002)VFISGVIAR;DKDDQEWES(0.32)PS(0.679)PPKPTVFISGVIAR;DKDDQEWESPS(0.999)PPKPTVFISGVIAR 201.53 4.83E-25 935870000 1847060 719805 1077870 1047130 1070350 775273 1455560 738793 1426520 TRUE FALSE 1731455.812 773100.1112 1103437.585 1074001.129 986289.0286 999081.7296 1237312.291 831032.9323 1188424.596 1.456933673 0.650525169 0.928487671 0.903718361 0.829913006 0.840677425 1.041136556 0.699272747 1 20.18061894 4.751757637 24.75290924 0.86368221 1.456934113 0.707773632 0.120190239 1061.397647 1990763.554 0.027534859 0.521646041 56462.17936 -4.751757637 0.593251904 DKDDQEWESPSPPKPTVFISGVIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKDDQEWESPSPPKPTVFISGVIAR 25 2 P51397 P51397 DAP Death-associated protein 1 0 119.33 0.00029535 186280000 130640 82891 88889 99227 101270 72176 118050 82066 120300 FALSE TRUE 122463.4756 89028.33589 90997.48906 101773.3328 93316.6627 93012.03952 100349.4984 92312.12075 100221.1528 1.221932418 0.888318817 0.907966896 1.015487549 0.931107457 0.928067947 1.001280624 0.921084204 1 16.61282751 4.745777915 24.86279707 0.944775802 1.221932558 0.796938452 0.043220647 361.6779593 1245907.593 0.010575203 0.107722062 55690.08944 -4.745777915 0.277156757 DKDFAIDIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DKDFAIDIIK 10 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;; 124.86 0.00038711 5734650000 31521850 24148900 25087960 24819030 30071660 17171090 30694980 24538430 33418730 FALSE TRUE 29548953.68 25936909.68 25683058.26 25455928.33 27709953.13 22128104.93 26092552.71 27602107 27840928.07 1.061349449 0.931610815 0.922492892 0.914334762 0.995295597 0.79480486 0.937201254 0.991421943 1 24.73070397 1.242689333 6.556359022 0.996681237 0.92927657 0.111803448 0.066849235 0.253111269 49.46852777 0.048881 0.015204268 17.48595406 -1.242689333 -0.067404668 DKDGQVDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKDGQVDAR 9 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 0 67.334 0.066781 0 778980 614150 686850 686950 739030 517250 772730 615480 874770 FALSE TRUE 730225.0323 659622.305 703142.4064 704578.3 680989.5649 666571.6781 656866.3102 692324.0328 728765.2358 1.002003109 0.905123176 0.964840763 0.966811074 0.934442989 0.914658995 0.901341444 0.949995964 1 19.47509461 2.498900586 21.22064212 0.928610902 0.951374031 0 0.035922917 280.8386011 273635.3204 0.010915896 0.010171278 315.4282493 -2.498900586 0.02276313 DKDNFWMTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DKDNFWMTR 9 1 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ;;; 162.26 5.83E-05 2660800000 4306510 4620050 4308490 4190930 4855190 2865340 4552490 3960670 4718960 FALSE TRUE 4036973.226 4962123.309 4410689.417 4298476.359 4473882.962 3692517.143 3869886.388 4455168.368 3931335.09 1.026870804 1.262198005 1.121931689 1.093388444 1.138006011 0.939252711 0.984369508 1.133245644 1 21.90658791 2.278679657 13.21032091 1.007239623 1.144258721 0.346993684 0.075931305 1.207587546 396.4185656 0.025703231 0.021481115 189.9676529 -2.278679657 0.137019098 DKDNPNQYHYVA ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKDNPNQYHYVA 12 1 Q13619;A0A0A0MR50;Q13619-2 Q13619 CUL4A Cullin-4A 0 ; 86.313 0.010198 601370000 1560600 1540880 1330110 1359320 1902730 883300 1514800 1488750 2069400 FALSE TRUE 1462924.832 1654968.358 1361660.837 1394202.453 1753297.261 1138294.371 1287669.803 1674623.715 1724003.771 0.848562431 0.959956345 0.789824744 0.80870035 1.016991546 0.660262112 0.746906604 0.971357338 1 20.7173315 3.972619236 23.50133624 0.833221239 0.907550413 0 0.118670333 250.2554245 1306406.351 0.028715382 0.054191422 9388.997776 -3.972619236 0.074329174 DKDPILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DKDPILR 7 1 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;; 107.66 0.006773 1515530000 1458830 1707330 1801540 2081210 1997650 1658150 2476630 1800350 2067160 FALSE TRUE 1367524.434 1833742.49 1844273.38 2134617.372 1840762.627 2136830.987 2105282.323 2025127.661 1722137.642 0.794085444 1.064805998 1.070921008 1.239516123 1.068882407 1.240801511 1.222482032 1.175938329 1 20.71576902 5.475976049 0.774347015 1.170112332 5.50E-15 0.62546848 0.083274084 4.259522418 0.8526916 0.026457778 5.623484202 299209.962 -5.475976049 -1.170112332 DKDPPIPVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DKDPPIPVAK 10 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;; 85.813 0.012754 1296250000 3300230 2486630 2653120 2731890 2784300 1805490 3697240 2424570 3145110 FALSE TRUE 3093674.495 2670742.673 2716053.259 2801994.922 2565632.309 2326705.653 3142873.185 2727282.902 2620170.823 1.18071481 1.019300974 1.036593964 1.069393987 0.979185131 0.887997696 1.199491712 1.040879807 1 21.32122944 -0.493049783 6.155896385 0.999981469 1.049657012 0.031385216 0.089619767 0 0 0.081888285 0.019301254 0.321329218 0.493049783 0.049675543 DKDPVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DKDPVNK 7 1 P62851;E9PQK3;E9PK60 P62851 RPS25 40S ribosomal protein S25 0 ;; 90.709 0.015449 3381080000 15804300 9895700 12498400 11938900 13109600 8892400 15125600 9624100 15291500 FALSE TRUE 14815137.07 10628387.92 12794867.95 12245272.39 12080024.9 11459491.52 12857656.7 10825690.07 12739249.86 1.162952076 0.834302493 1.004365884 0.961223975 0.94825245 0.899542096 1.009294647 0.84979023 1 23.60277699 4.75687494 24.72792917 0.940707183 1.162952297 0.56828072 0.061493088 2556.16656 3451261.162 0.013428041 0.452695849 57131.40971 -4.75687494 0.222245114 DKDQSDGFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DKDQSDGFGK 10 1 Q9Y6U3;Q9Y6U3-3;Q9Y6U3-2 Q9Y6U3 SCIN Adseverin 0 ;;; 158.06 7.39E-06 3770890000 7182830 3787730 4944190 4320120 5947830 3606230 6476650 5593560 13139600 FALSE TRUE 6733269.492 4068177.47 5061468.522 4430981.593 5480711.424 4647290.059 5505536.459 6291928.279 10946515.87 0.615106173 0.371641307 0.462381691 0.40478465 0.5006809 0.424545135 0.502948748 0.574788211 1 23.38396842 0.572408364 1.178389274 1.000372633 0.450399192 0.863067281 0.066120909 0.451446997 0.899249858 0.055730912 0.017039944 3.736012876 -0.572408364 -0.549973441 DKDTDKFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DKDTDKFK 8 2 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;; 111.06 0.0018598 5187960000 8369740 4077500 5366970 5019100 6142500 3560350 6517640 4666680 7300800 FALSE TRUE 7845892.914 4379402.343 5494277.063 5147898.603 5660092.828 4588165.248 5540380.389 5249325.271 6082249.315 1.289965687 0.720030061 0.903329801 0.846380728 0.930592045 0.754353367 0.910909781 0.863056576 1 22.53617352 4.749894878 24.98124778 0.856523056 1.289965942 0.724565718 0.081945233 826.7161341 1822087.165 0.017553965 0.277188411 56220.52254 -4.749894878 0.433442886 DKDVTLS(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKDVTLSPVK 10 1 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 DKDVT(0.001)LS(0.999)PVK 86.641 0.0081267 407150000 1044200 675630 667970 614720 864310 427200 842230 775490 860000 TRUE FALSE 978845.386 725654.3482 683814.5638 630494.7559 796430.5791 550525.705 715945.4304 872311.6336 716460.4442 1.366223905 1.012832396 0.954434497 0.88001335 1.111618353 0.76839651 0.999281169 1.21752937 1 19.45052753 4.743248134 3.793606346 0.978761802 1.407562128 0.486549839 0.120252994 0.210568363 5.86931394 0.02656012 0.254367192 55366.63558 -4.743248134 0.428800326 DKEDPQEMPHS(ph)PLGSMPEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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;DKEDPQEMPHS(0.999)PLGS(0.001)MPEIR 214.08 6.25E-24 674330000 1437330 1065130 1222750 1246640 1212350 912400 1561100 1005710 1339070 TRUE FALSE 1347370.081 1143993.333 1251754.207 1278630.893 1117136.921 1175795.068 1327027.548 1131275.107 1115570.566 1.207785614 1.025478233 1.122075327 1.146167649 1.001404084 1.053985381 1.18955052 1.014077586 1 20.08935034 0.844046422 0.009514588 8.10E-05 2.137963407 0.191641576 0.070201133 4603.199899 25.3325261 2888.703074 2799.982557 6.983070424 -0.844046422 2.137882427 DKEEIVICDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKEEIVICDR 10 1 Q9NRR5;Q9NRR5-2 Q9NRR5 UBQLN4 Ubiquilin-4 0 ; 109.72 0.0018067 437220000 889220 689120 747890 704900 766970 533860 936570 663180 1037880 FALSE TRUE 833565.3075 740143.1618 765630.304 722988.9274 706735.27 687976.7155 796140.0232 745979.4828 864651.123 0.964048141 0.856002082 0.885478875 0.836162596 0.817364659 0.795669718 0.920764459 0.862751997 1 19.72175861 0.330914886 1.152795884 1.000070804 0.863668952 0.420292015 0.048784669 3.27226664 4.751067383 0.045533483 0.013605151 2.142470673 -0.330914886 -0.136401852 DKEEKESS(ph)REK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKEEKESSREK 11 3 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 DKEEKES(0.349)S(0.651)REK 95.822 0.041287 159280000 213700 69344 115240 133590 155500 65441 130300 82444 227440 TRUE FALSE 200324.8985 74478.30191 117973.5472 137018.1456 143287.6573 84332.75435 110762.7246 92737.31488 189478.7947 1.057241782 0.393069325 0.622621373 0.72313182 0.756220017 0.445077532 0.58456528 0.489433739 1 17.53167687 -2.142581731 2.429944502 1.871728452 0.607487111 0.259002873 0.189975835 6905804.569 2462846.504 33016925.99 0.042965412 0.007201422 2.142581731 -1.264241341 DKEIS(ph)PSVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DKEISPSVTK 10 1 Q8N488 Q8N488 RYBP RING1 and YY1-binding protein 1 DKEIS(0.999)PS(0.001)VTK;DKEIS(0.988)PS(0.012)VTK;DKEIS(0.902)PS(0.093)VT(0.005)K;DKEIS(0.979)PS(0.02)VT(0.001)K 104.41 0.001626 864770000 4749410 2257360 3116060 2957060 3072610 2254260 4273430 2810530 3004570 TRUE FALSE 4452152.906 2424497.283 3189974.415 3032943.166 2831299.605 2905028.267 3632668.844 3161430.857 2503087.857 1.778664258 0.968602551 1.274415681 1.211680668 1.131122744 1.160577828 1.451275006 1.263012342 1 21.2552775 DKEIS(ph)PSVTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKEISPSVTKK 11 2 Q8N488 Q8N488 RYBP RING1 and YY1-binding protein 1 DKEIS(0.699)PS(0.293)VT(0.007)KK 79.346 0.014295 524500000 472800 204960 316370 308910 358730 237760 466620 296800 437530 TRUE FALSE 443208.292 220135.4517 323874.4458 316837.1536 330556.7928 306397.4523 396654.6629 333856.1333 364503.4164 1.215923561 0.603932478 0.888536105 0.869229585 0.906868847 0.840588698 1.088205611 0.91592045 1 18.47557281 1.755167577 25 1.006500596 0.854951487 0.084019109 0.153647363 10.39741127 15670.03415 0.066287779 0.036760377 56.90724708 -1.755167577 -0.151549109 DKENALMPNWLHLPVGYHGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKENALMPNWLHLPVGYHGR 20 1 P16930;P16930-2 P16930 FAH Fumarylacetoacetase 0 ; 178.77 3.91E-17 582090000 901550 787640 854010 837180 874060 568220 1050890 784290 899500 FALSE TRUE 845123.5948 845957.6851 874267.5205 858663.4561 805414.8534 732255.8897 893318.8005 882210.3329 749367.639 1.127782347 1.128895406 1.166673706 1.14585073 1.07479268 0.977165081 1.192096848 1.177273059 1 19.51531415 2.753448779 23.07177376 1.094998488 1.14412856 0.145405805 0.067103067 678.0256998 1050715.663 0.020410552 0.021537903 566.8247156 -2.753448779 0.049130072 DKEPEVVFIGDSLVQLMHQCEIWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKEPEVVFIGDSLVQLMHQCEIWR 24 1 M0R1K3;Q15102;M0R389;M0QZT2;M0QXS6;M0R323 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ; 237.97 1.12E-37 1277040000 952620 690580 844830 796640 916800 685450 1036490 746420 982860 FALSE TRUE 892997.2147 741711.2617 864869.7666 817083.1311 844798.2262 883328.2876 881077.9468 839612.1801 818814.3165 1.09059795 0.905835727 1.056246513 0.997885741 1.03173358 1.078789501 1.076041209 1.025399976 1 19.6431768 3.732887043 24.77963687 1.043699853 0.983826002 0.069514408 0.05207269 329.4523747 1415874.659 0.012476578 0.021746105 5406.136944 -3.732887043 -0.059873851 DKEQWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DKEQWK 6 1 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;;; 89.55 0.045636 6495640000 11932620 8124380 10287320 9967000 9308950 7504670 13284140 8613870 7531630 FALSE TRUE 11185778.61 8725917.549 10531340.09 10222770.09 8577862.617 9671146.401 11292306.53 9689330.631 6274552.297 1.782721394 1.390683691 1.67842096 1.62924295 1.367087596 1.541328519 1.799699165 1.544226611 1 22.58108109 0.954530519 23.24506088 0.999999997 1.591960717 0.632596062 0.14222604 3307.869834 1691062.541 0.133411953 0.033352988 9.005970476 -0.954530519 0.591960719 DKETGGILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKETGGILR 9 1 O95347-2;O95347 O95347-2 SMC2 Structural maintenance of chromosomes protein 2 0 ; 84.658 0.013993 407290000 466190 495810 521180 500120 589610 381620 551700 488260 646460 FALSE TRUE 437012.0001 532520.2883 533542.6357 512953.9259 543304.409 491787.4989 468977.7067 549220.3358 538561.6497 0.81144285 0.988782414 0.990680707 0.952451639 1.008806344 0.913149867 0.870796699 1.019791023 1 19.03875198 3.675800667 0.004876545 1.889822992 5.16E-05 0.094850135 0.064072505 92595.72256 103.7130904 19618.88968 20576.06569 4740.243676 -3.675800667 -1.889771438 DKEVS(ph)DDEAEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 254.56 1.08E-20 904450000 4337010 1086877 1987642 1781900 1505294 1570956 2690879 1367715 1095908 TRUE FALSE 4065564.286 1167350.504 2034789.807 1827626.571 1387074.281 2024465.495 2287406.675 1538477.228 912993.875 4.453002805 1.278596205 2.228700392 2.001794997 1.519259131 2.217392198 2.505391041 1.685090416 1 19.80024566 4.747224559 24.99728939 1.901840784 4.453004099 0.757128323 0.468540792 561.9041861 1621176.011 0.107087704 1.269851246 55875.90359 -4.747224559 2.551163314 DKEVS(ph)DDEAEEKEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKEVSDDEAEEKEDK 15 2 P07900;P07900-2;G3V2J8 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 DKEVS(1)DDEAEEKEDK 122.73 8.43E-05 333030000 596730 240610 348590 326170 298060 283450 487950 298120 306450 TRUE FALSE 559381.7345 258425.0148 356858.7194 334540.0744 274651.5699 365277.4136 414786.4274 335340.9382 255301.5153 2.19106312 1.012234551 1.39779319 1.310372459 1.075792949 1.430768686 1.624692384 1.313509393 1 17.96184257 4.750558466 24.62866729 1.3031585 2.191063785 0.675908151 0.19917059 999.1589868 2050983.966 0.048914232 0.812077725 56306.49131 -4.750558466 0.887905285 DKEVS(ph)DDEAEEKEDKEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKEVSDDEAEEKEDKEEEK 19 3 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 DKEVS(1)DDEAEEKEDKEEEK 216.14 2.78E-19 2267000000 7713600 721500 1938400 1717100 1720400 1354200 2857300 1053600 1159500 TRUE FALSE 7230819.545 774920.6107 1984379.763 1761163.693 1585286.724 1745135.556 2428874.391 1185144.279 965971.9593 7.485537727 0.802218536 2.054282988 1.823203744 1.641131203 1.806610989 2.514435711 1.226893046 1 19.88162178 4.744003136 24.99963465 1.700998654 7.48554017 0.929027731 0.509917747 145.6245131 668890.7003 0.120110224 1.043876633 55462.97176 -4.744003136 5.784541516 DKFNECGHVLYADIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKFNECGHVLYADIK 15 1 A0A087X0X3;P52272-2;P52272 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 155.1 1.42E-06 2382500000 7013300 5042300 5431700 5310100 6610400 3576500 6911500 5472100 8532700 FALSE TRUE 6574350.072 5415637.139 5560542.489 5446366.156 6091245.849 4608977.49 5875184.738 6155303.731 7108537.247 0.924852729 0.761849724 0.782234417 0.766172557 0.856891599 0.648372138 0.826497004 0.865903 1 22.76112129 0.94668298 2.204360669 0.99858757 0.785561341 0.457708056 0.071040117 0.281031793 2.983135593 0.060274247 0.016556586 8.844697415 -0.94668298 -0.213026229 DKFPGEFMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKFPGEFMK 9 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 101.93 0.0033445 380070000 496860 734790 659950 816010 978640 667080 1031500 818030 1077400 FALSE TRUE 465762.4195 789194.6161 675604.3257 836950.1981 901781.562 859655.1669 876836.151 920162.8462 897574.9797 0.518911991 0.879252022 0.752699597 0.93245714 1.004686608 0.957753042 0.9768946 1.025165437 1 19.77567294 5.536833831 0.394660175 1.010374474 6.49E-15 0.753090171 0.076618793 5.395928202 0.409714615 0.056361952 2.920139785 344218.2014 -5.536833831 -1.010374474 DKFQETSDEFEAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DKFQETSDEFEAAR 14 1 G8JLG1;Q14683;V9GY57 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 ;;; 216.01 5.73E-12 908900000 1070231 863722 984843 969107 1063234 704949 1181601 884301 1288949 FALSE TRUE 1003247.152 927672.8756 1008203.941 993975.9263 979731.8905 908456.3324 1004430.899 994707.9264 1073815.085 0.934282975 0.863903747 0.938899029 0.925649062 0.912384175 0.846008168 0.93538535 0.926330744 1 20.03431415 0.787708751 1.568187939 0.999532171 0.904961079 0.473139461 0.030555353 0.624950423 2.700609913 0.027358755 0.007912701 6.133505389 -0.787708751 -0.094571092 DKFS(ph)PFPVQDRPESSLVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKFSPFPVQDRPESSLVFK 19 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DKFS(1)PFPVQDRPESSLVFK 125.05 1.47E-05 1414900000 1937900 1094100 1480400 1446700 1502800 1101700 1856100 1268700 1761200 TRUE FALSE 1816610.298 1175108.302 1515515.787 1483824.771 1384776.15 1419742.905 1577795.036 1427099.988 1467244.342 1.238110277 0.800894758 1.032899391 1.011300387 0.943793825 0.967625408 1.075345797 0.972639626 1 20.48467771 1.787465244 25 1.024076294 0.978474941 0 0.11063414 441.4172601 225720.0439 0.04664088 0.026214877 61.30067324 -1.787465244 -0.045601352 DKFSFDLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKFSFDLGK 9 1 Q02790;F5H1U3 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ; 137.89 0.00013848 5393500000 12042100 7906500 9570300 8651900 10234400 8007500 13992600 9921900 9175500 FALSE TRUE 11288406.46 8491905.487 9797312.035 8873922.402 9430631.508 10319135.26 11894539.53 11160671.06 7644049.774 1.47675732 1.110917084 1.281691293 1.160892807 1.233721886 1.349956576 1.556052077 1.460046884 1 22.86590574 2.128798464 4.404816245 1.411565929 1.233400551 0 0.1748275 0.341298592 11.58318449 0.061373011 0.044280044 134.5235949 -2.128798464 -0.178165378 DKFSPFPVQDRPESSLVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKFSPFPVQDRPESSLVFK 19 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ; 193.06 3.43E-15 658990000 1083160 874960 967560 935870 1053180 739440 1226850 881790 1149060 FALSE TRUE 1015366.949 939742.9488 990510.9801 959886.0086 970467.4911 952904.3242 1042895.232 991883.4226 957274.4628 1.060685298 0.981686011 1.034719946 1.002728106 1.013781866 0.995434811 1.089442237 1.036153644 1 19.8685731 1.760442597 25 1.050865465 1.012801333 0.123867061 0.030618427 13.96693338 15970.04424 0.012529538 0.006948732 57.60266774 -1.760442597 -0.038064132 DKGETIQGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKGETIQGLR 10 1 F5H0D0;Q14232-2;Q14232;H0YGG4 F5H0D0;H0YGG4 EIF2B1 Translation initiation factor eIF-2B subunit alpha 0 113.22 0.001383 281780000 362010 349760 356940 353260 397570 270190 409160 338270 441520 FALSE TRUE 339352.4403 375656.5943 365406.7854 362325.2497 366346.4559 348189.4668 347810.2565 380503.7541 367827.4597 0.922585934 1.021284802 0.993418995 0.985041329 0.995973645 0.946610857 0.945579911 1.03446261 1 18.48866966 DKGFGFIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKGFGFIR 8 1 Q15233;Q15233-2;H7C367;C9JYS8;C9IZL7 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 85.731 0.01508 806460000 1338590 2382030 1364830 1495670 3363700 1070870 1729060 2679500 2728660 FALSE TRUE 1254810.041 2558397.98 1397204.412 1534051.424 3099528.571 1380012.785 1469803.505 3014041.473 2273229.018 0.551994555 1.125446648 0.61463425 0.674833645 1.363491556 0.607071603 0.6465708 1.325885535 1 21.11631161 1.238601354 25 1.162942784 0.809098769 0.241255882 0.268680883 1.530839058 944465.9515 0.196403051 0.06113617 17.32213241 -1.238601354 -0.353844015 DKGLQTSQDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DKGLQTSQDAR 11 1 P27797 P27797 CALR Calreticulin 0 ;;;;; 153.39 2.96E-05 2186800000 6647660 6732200 6449050 6871930 7175640 5225490 8629550 6130490 6606320 FALSE TRUE 6231594.827 7230659.093 6602024.511 7048275.358 6612094.18 6734004.134 7335629.09 6895895.171 5503682.514 1.13225914 1.313785647 1.199564927 1.280647156 1.201394551 1.223545166 1.332858331 1.252960205 1 22.39196582 -1.670353473 2.679705631 0.967298929 1.250016734 0.622099061 0.059022772 11184595.25 9411249.191 2490396.483 0.013167258 0.021362227 1.670353473 0.282717805 DKGLVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKGLVEK 7 1 H0YFD6;P40939;A0A2R8YG21;A0A2R8Y688 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 61.78 0.081555 177900000 485550 238480 604530 843700 327960 697710 627400 230240 850560 FALSE TRUE 455160.2922 256137.3073 618869.7371 865350.7704 302203.3445 899127.5506 533327.1945 258985.9708 708596.0412 0.642341004 0.361471547 0.873374534 1.221218748 0.426481842 1.268885936 0.752653365 0.365491699 1 19.43460388 3.867152622 4.057559087 0.851398242 0.49920259 0.184259091 0.298211836 0.328538507 9.546471475 0.071459642 0.136591713 7364.658644 -3.867152622 -0.352195652 DKGQS(ph)FNDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DKGQSFNDKR 10 2 A0A590UJ08;Q12959-4;Q12959-2;A0A590UJC5;A0A590UJL2;A0A590UJ25 A0A590UJ08 DLG1 Disks large homolog 1 1 DKGQS(1)FNDKR;DKGQS(1)FNDKR;DKGQS(1)FNDKR;DKGQS(1)FNDKR 134.21 9.22E-05 704150000 2021860 1008320 1240540 1028470 1302440 724672 1351680 817200 2165560 TRUE FALSE 1895315.392 1082977.062 1269966.195 1054862.281 1200151.616 933873.0423 1149008.132 919229.2189 1804114.046 1.050551874 0.60028193 0.703927891 0.584698226 0.66523046 0.517635259 0.636882205 0.509518354 1 20.78285911 -1.17837039 3.841355547 1.000228583 0.648260976 0.330653859 0.152026685 43298034.72 75669833.17 128496.8757 0.032719783 0.066317724 1.17837039 -0.351967606 DKGS(ph)FNDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKGSFNDKR 9 2 A0A590UJD9;A0A0C4DFT3;A0A590UK02;A0A590UK70 A0A590UJD9 DLG1 1 DKGS(1)FNDKR;DKGS(1)FNDKR 115.14 0.00079566 473640000 1573770 804410 1054630 878200 1117030 680270 993570 667400 1465110 TRUE FALSE 1475270.545 863969.3534 1079646.322 900736.0988 1029302.97 876652.9057 844593.4024 750726.3591 1220573.676 1.208669803 0.707838757 0.884540067 0.737961269 0.84329442 0.718230225 0.691964294 0.615060257 1 20.21912795 4.74319035 24.94304959 0.766308154 1.208669988 0.603640645 0.110279544 299.7943788 1615108.638 0.024145345 0.194609428 55359.26943 -4.74319035 0.442361834 DKHIEEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DKHIEEVR 8 1 P16949 P16949 STMN1 Stathmin 0 ;;;;;;; 160.36 0.00021258 5251210000 11396350 10421330 11057400 10700400 11990450 9083180 13437070 10699330 12989880 FALSE TRUE 10683072.8 11192936.12 11319686.75 10974990.38 11048768.42 11705346.61 11422306.1 12035164.9 10821785.11 0.987182123 1.034296653 1.046009197 1.014157116 1.020974665 1.081646558 1.05549186 1.112123811 1 23.36743516 2.248014101 24.99792726 1.066238545 1.0255879 0.291647059 0.031562499 236.4215623 625171.9688 0.009965876 0.008230903 177.0166434 -2.248014101 -0.040650644 DKHIEEVRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DKHIEEVRK 9 2 P16949 P16949 STMN1 Stathmin 0 ;;;; 125.74 0.00027733 2253976000 5845280 4708170 5133580 5269090 6387930 3765840 6388350 5234750 8965000 FALSE TRUE 5479434.359 5056767.806 5255350.942 5404303.77 5886247.745 4852976.875 5430476.224 5888320.061 7468683.584 0.733654639 0.677062798 0.703651572 0.723595224 0.788123861 0.64977674 0.727099517 0.788401329 1 22.83242255 0.812389859 2.067513646 0.999749301 0.709398983 0.860043489 0.036193716 0.225107601 1.701619132 0.032778665 0.009032443 6.492169636 -0.812389859 -0.290350318 DKHKEEDKNSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKHKEEDKNSER 12 3 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 108.17 0.00075999 107790000 359890 172710 248640 223270 256480 157220 319020 181810 489150 FALSE TRUE 337365.1273 185497.6281 254537.8582 228999.4862 236337.0954 202606.8617 271185.9126 204509.3787 407507.705 0.82787423 0.455200296 0.624620971 0.561951304 0.579957366 0.497185352 0.665474319 0.501854017 1 18.63646781 -1.415290839 3.351109304 1.004586438 0.581477496 0.600593661 0.105094008 21605907.32 28129545.28 938244.2495 0.0226666 0.038433431 1.415290839 -0.423108942 DKIIVNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DKIIVNDR 8 1 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;;;; 132.78 0.00086424 4097650000 5856080 5719280 5890840 5745980 6500730 4977190 7109270 5388910 8610100 FALSE TRUE 5489558.406 6142741.442 6030573.507 5893431.575 5990188.888 6414023.955 6043300.963 6061727.276 7173018.687 0.765306581 0.85636769 0.84073021 0.821611072 0.835100137 0.894187543 0.842504561 0.845073398 1 22.77414896 -5 0.210111198 1.76307507 0.81821887 0.767080245 0.029034139 69.22880741 0.690403084 22.25118245 0.058212097 1.00E-05 5 -0.944856201 DKKS(ph)PLIESTANMDNNQSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DKKSPLIESTANMDNNQSQK 20 2 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 DKKS(1)PLIESTANMDNNQSQK;DKKS(0.97)PLIES(0.015)T(0.015)ANMDNNQSQK;DKKS(0.992)PLIES(0.004)T(0.004)ANMDNNQSQK 186.82 1.64E-17 1335810000 1580910 768270 957870 921350 1092790 461620 1079410 734250 1716100 TRUE FALSE 1481963.665 825153.5102 980591.1287 944993.4008 1006966.682 594882.2002 917562.4913 825922.7288 1429671.824 1.036576115 0.577162882 0.685885469 0.660986238 0.704334145 0.41609703 0.641799381 0.577700921 1 20.44725259 -1.165231583 4.23665434 1.000102658 0.646798222 0.310977897 0.156289563 20300339.81 5583329.17 19228.30569 0.032908933 0.068354706 1.165231583 -0.353304437 DKLDETGNSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DKLDETGNSLK 11 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 ;;; 134.68 0.00012377 1800500000 2474340 1456730 1806120 1794010 1811070 1176380 2583780 1558700 2497260 FALSE TRUE 2319475.476 1564587.805 1848962.019 1840047.334 1668835.868 1515981.809 2196366.176 1753307.126 2080451.173 1.114890609 0.75204255 0.888731273 0.884446296 0.802150942 0.72867935 1.055716281 0.842753317 1 20.988465 1.728921382 24.99999654 0.964348897 0.850834999 0.145295218 0.117259352 1.327412834 3425.291899 0.049112993 0.027235632 53.56996739 -1.728921382 -0.113513898 DKLESEMEDAYHEHQANLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 DKLESEMEDAYHEHQANLLR 20 1 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;;;;;; 370.16 2.65E-112 5686683000 4495346 3400000 3930401 3779737 4123759 2962714 4819864 3497076 5261326 FALSE TRUE 4213990.318 3651739.538 4023631.968 3876731.45 3799895.603 3818001.436 4097170.139 3933693.637 4383176.701 0.961400967 0.833126243 0.917971654 0.884457031 0.866927314 0.87105807 0.934749023 0.897452671 1 22.06354541 0.446571577 0.738747283 1.001177853 0.886340199 0.443947196 0.036405174 1.547851253 1.298229308 0.037151155 0.011761842 2.796221542 -0.446571577 -0.114837654 DKLFDQR ddPTM_SK-BR-3_Pertuzumab_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 ;;;; 76.827 0.036211 2578890000 11812200 12795500 11055300 10961500 15124800 8214400 12885800 12681900 14967700 FALSE TRUE 11072895.49 13742892.13 11317536.94 11242790.65 13936959.22 10585763.93 10953693.92 14265263.13 12469494.17 0.88799877 1.10212106 0.907617966 0.901623634 1.117684408 0.848932906 0.878439315 1.144012975 1 23.57189961 DKLNNLVLFDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKLNNLVLFDK 11 1 P62851 P62851 RPS25 40S ribosomal protein S25 0 ; 184.34 4.51E-06 6205400000 16346000 13367800 14355100 13748500 16247200 11039500 18266700 13498200 18837900 FALSE TRUE 15322933.04 14357565.82 14695609.75 14101309.79 14971210.45 14226424.44 15527777.91 15183479.98 15693732.79 0.97637275 0.914859837 0.936399896 0.898531278 0.953961091 0.906503547 0.989425404 0.967486842 1 23.90368521 1.68687323 7.373998351 0.983596349 0.929550113 0.534009066 0.023894936 0.088428942 9.456998414 0.010450656 0.005427535 48.62652447 -1.68687323 -0.054046236 DKLPLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKLPLEK 7 1 Q92831 Q92831 KAT2B Histone acetyltransferase KAT2B 0 ; 109.21 0.0064555 1067590000 2545000 1793240 1993650 2159400 2402300 1808560 2179500 1635210 2619200 FALSE TRUE 2385712.993 1926013.355 2040940.319 2214813.86 2213633.048 2330661.912 1852704.208 1839369.568 2182038.599 1.093341334 0.88266695 0.935336488 1.015020477 1.014479326 1.068112138 0.849070318 0.842959226 1 21.05724519 1.683398523 10.42778281 0.885378705 0.981059259 0.27009552 0.074937458 0.164207566 26.24185512 0.035756146 0.019343387 48.2390252 -1.683398523 0.095680554 DKLSGEYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DKLSGEYEK 9 1 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;; 88.187 0.011814 1224660000 2274390 1548690 1879710 1739120 2009390 1345160 2439090 1705600 2634580 FALSE TRUE 2132039.99 1663356.619 1924297.609 1783748.764 1851580.615 1733485.855 2073371.098 1918547.914 2194851.578 0.971382307 0.757844692 0.876732453 0.812696759 0.843601742 0.789796391 0.944652075 0.874112826 1 21.06569195 1.060570768 0.93553967 0.994443748 0.836516714 0.335563888 0.064079971 0.550353131 1.050748732 0.053899449 0.018585507 11.49663564 -1.060570768 -0.157927034 DKMMNGGHYTYSENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DKMMNGGHYTYSENR 15 1 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ;; 167.69 7.79E-07 408870000 345547 531662 438274 468403 634870 386474 627070 482455 798440 FALSE TRUE 323919.8301 571026.8077 448670.0662 480423.014 585009.8711 498042.7699 533046.6749 542690.5688 665175.2059 0.486969188 0.858460752 0.674514116 0.722250333 0.879482377 0.748739228 0.801362814 0.81586109 1 19.34337487 -4.999999997 0.046117068 2.033477231 0.207444163 0.514029974 0.095069749 566.2483703 1.93962291 75.33105375 18.91658601 1.00E-05 4.999999997 -1.826033068 DKNEQAFEEVFQNANFR ddPTM_SK-BR-3_Pertuzumab_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 ; 243.01 1.79E-20 528490000 1056920 797750 959260 938580 880300 735090 1074830 798680 756570 FALSE TRUE 990769.2639 856816.2401 982014.1002 962665.5518 811164.789 947298.5498 913669.2197 898396.9561 630293.5794 1.571917113 1.359392302 1.558026501 1.527328825 1.286963433 1.502948119 1.449593094 1.425362697 1 19.26566444 -2.860492976 0.378399479 1.09E-19 1.473615868 0.740536359 0.086265186 45.95020672 1.589062467 37.03498074 0.054476211 0.001378818 2.860492976 1.473615868 DKNNMQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 DKNNMQHR 8 1 P31942;P31942-3;P31942-2;P31942-4 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;;;;;;;;;;;;; 183.65 0.0001335 3636877000 3976346 4957464 3522238 3378125 5672058 2438761 3790457 4940222 6005209 FALSE TRUE 3727473.602 5324519.793 3605787.149 3464813.407 5226597.445 3142791.711 3222113.162 5557019.591 5002900.823 0.745062462 1.064286497 0.720739282 0.692560882 1.044713383 0.628193886 0.644048978 1.110759495 1 22.25433342 1.223959063 24.99935841 1.055379909 0.800610368 0.338593718 0.152979261 336.4247106 575977.2483 0.14584033 0.03710717 16.74785 -1.223959063 -0.254769542 DKNSVNFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKNSVNFK 8 1 P12956;B1AHC9 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 140.45 0.00059228 3466400000 3111180 2400930 2693890 2519930 2869620 1800090 3066020 2507880 3358320 FALSE TRUE 2916456.797 2578697.355 2757790.343 2584595.67 2644251.621 2319746.761 2606298.765 2820994.339 2797794.696 1.042412726 0.921689271 0.985701469 0.923797473 0.945119963 0.829134019 0.931554688 1.008292117 1 21.41585867 4.744063487 24.11780233 0.937583974 1.042412801 0.265731143 0.051107666 473.216521 2073891.656 0.01172109 0.099448037 55470.67966 -4.744063487 0.104828828 DKPAQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DKPAQIR 7 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;;;; 132.57 0.003061 8499130000 7802060 7406170 7157110 7010030 8135040 5855630 8553810 6845780 8749010 FALSE TRUE 7313742.992 7954530.533 7326880.029 7189919.238 7496146.774 7546055.323 7271245.6 7700490.702 7288743.71 1.003429848 1.091344524 1.005232221 0.986441494 1.028455255 1.035302601 0.997599297 1.056490804 1 22.79723874 3.780793841 7.112599027 1.015035831 1.052395314 0.164372989 0.029198534 0.305990289 33.66452494 0.006803139 0.012268383 6036.620042 -3.780793841 0.037359483 DKPHNIFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKPHNIFK 8 1 P25685;P25685-2;M0R080 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 125.82 0.00074849 1446950000 4126900 3856300 3614600 3390100 4731800 2713500 4230300 4095700 4697000 FALSE TRUE 3868604.696 4141824.464 3700340.019 3477095.705 4360183.515 3496843.4 3596005.787 4607057.161 3913040.356 0.988644211 1.058467097 0.945643204 0.888591834 1.11427001 0.893638471 0.91897999 1.177359992 1 21.89985856 1.249134104 24.9999764 1.08868003 0.973713279 0.257744816 0.081875213 247.3235173 584781.4665 0.052794636 0.018826491 17.74737412 -1.249134104 -0.114966751 DKPHVNVGTIGHVDHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DKPHVNVGTIGHVDHGK 17 1 P49411;H3BNU3 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ;;; 229.96 3.17E-16 4700540000 4496190 3027050 3317960 3256860 4794510 2916440 3652480 3748270 6933000 FALSE TRUE 4214781.494 3251175.932 3396663.578 3340436.541 4417968.525 3758368.884 3104824.532 4216249.76 5775837.511 0.729726466 0.562892555 0.588081568 0.578346696 0.764905265 0.650705439 0.537553996 0.729980674 1 22.46159873 0.933823771 5.848592709 0.999975372 0.619682139 0.721230097 0.072173316 0.248720972 20.96776588 0.067794749 0.017058582 8.586650204 -0.933823771 -0.380293233 DKPLCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKPLCK 6 1 Q96HC4;Q96HC4-4;A0A0A0MSP3;Q96HC4-6 Q96HC4;Q96HC4-6 PDLIM5 PDZ and LIM domain protein 5 0 ; 84.244 0.051138 982420000 1288670 1496520 1524010 1833980 2278200 1506190 2514200 2031720 2841200 FALSE TRUE 1208014.445 1607323.898 1560160.237 1881043.032 2099279.362 1941002.602 2137219.051 2285384.714 2366985.365 0.510359913 0.6790595 0.659133875 0.794699899 0.886900018 0.820031518 0.902928714 0.965525494 1 21.17461936 3.993736069 0.279551836 1.022561138 0.313071498 0.910638269 0.045038625 1.477147667 0.133373537 0.057331484 0.351089582 9856.80282 -3.993736069 -0.70948964 DKPLIIYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKPLIIYK 8 1 Q9Y6U3;Q9Y6U3-3;Q9Y6U3-2 Q9Y6U3 SCIN Adseverin 0 105.4 0.0070687 0 1475900 1178700 1148100 883590 1666200 712850 1210000 1432100 3050100 FALSE TRUE 1383526.054 1265972.174 1175333.474 906264.4153 1535343.373 918638.2228 1028571.733 1610900.837 2541018.606 0.544476947 0.498214445 0.462544222 0.356653986 0.604223586 0.361523611 0.404787171 0.633958694 1 21.27697551 0.918473633 3.792683576 0.999673627 0.460229519 0.831313747 0.076967511 0.12954506 4.463852669 0.069890768 0.017940391 8.288455933 -0.918473633 -0.539444108 DKPLKDVIIADCGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKPLKDVIIADCGK 14 2 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ; 170.45 1.78E-06 2630500000 3784130 2661450 2442030 2198010 2603030 1492150 4435930 2418000 6642800 FALSE TRUE 3547288.058 2858506.527 2499956.105 2254414.658 2398598.524 1922909.482 3770803.478 2719892.623 5534073.766 0.640990382 0.516528447 0.451738847 0.407369824 0.433423663 0.347467266 0.681379331 0.491481093 1 22.39991044 0.259748643 0.83545879 1.005411566 0.47833662 0.71158411 0.100813426 1.583509562 1.353991393 0.116988743 0.031940279 1.818647975 -0.259748643 -0.527074946 DKPSGDTAAVFEEGGDVDDLLDMI ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DKPSGDTAAVFEEGGDVDDLLDMI 24 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;; 162.86 1.60E-11 57864000 179550 155411 177946 176872 185192 127448 216044 158327 204760 FALSE TRUE 168312.286 166917.7921 182166.9632 181410.835 170647.7673 164240.1687 183650.2079 178094.4745 170584.2332 0.986681376 0.978506565 1.067900355 1.063467775 1.00037245 0.962809784 1.076595441 1.044026585 1 17.38012478 4.15953271 4.800705831 1.033237307 0.982474989 0.238773689 0.035442801 0.273429093 12.05627444 0.008911424 0.020684153 14438.85351 -4.15953271 -0.050762318 DKPSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DKPSLR 6 1 P13489 P13489 RNH1 Ribonuclease inhibitor 0 ;;;;;;; 124.37 0.016766 6136480000 11273660 10832960 11055570 11204380 12749540 9113290 13635950 11087020 15777100 FALSE TRUE 10568061.74 11635043.63 11317813.34 11491903.36 11748242.56 11744148.88 11591365.89 12471258.85 13143800.09 0.804033969 0.885211549 0.861076193 0.874321223 0.893823893 0.89351244 0.881888481 0.948832055 1 23.64787911 -4.999999668 0.092945466 1.419648393 0.778388055 0.812297617 0.022387029 84.61698166 0.543595814 6.87971455 0.444999828 1.00E-05 4.999999668 -0.641260338 DKPSVEPVEEYDYEDLKESSNS(ph)VSNHQLSGFDQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DKPSVEPVEEYDYEDLKESSNSVSNHQLSGFDQAR 35 2 Q9Y450;E9PN23;G5E991;E9PLR4;E9PMN1;Q9Y450-2 Q9Y450;Q9Y450-2 HBS1L HBS1-like protein 1 DKPSVEPVEEYDYEDLKES(0.007)S(0.034)NS(0.954)VS(0.005)NHQLSGFDQAR;DKPSVEPVEEYDYEDLKES(0.078)S(0.159)NS(0.762)VS(0.001)NHQLSGFDQAR;DKPSVEPVEEYDYEDLKES(0.141)S(0.141)NS(0.716)VS(0.002)NHQLSGFDQAR 231.13 1.06E-37 355087000 108550 99320 105217 152942 217709 109046 220720 161427 225231 TRUE FALSE 101756.0493 106673.7561 107712.7969 156866.7507 200611.0133 140525.81 187625.0851 181581.5163 187638.4911 0.542298378 0.56850679 0.57404425 0.836005181 1.069135721 0.748917822 0.999928554 0.967719977 1 17.51759628 3.153163085 3.481347659 0.944421085 0.561490794 0.825030509 0.082986139 0.083693973 2.000608349 0.022483439 0.02804918 1422.862998 -3.153163085 -0.382930291 DKPTYDEIFYTLS(ph)PVNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DKPTYDEIFYTLSPVNGK 18 1 A0A024R571;Q9H4M9 A0A024R571 EHD1 EH domain-containing protein 1 1 DKPTYDEIFYTLS(1)PVNGK;DKPTYDEIFYT(0.01)LS(0.99)PVNGK;DKPTYDEIFYT(0.027)LS(0.973)PVNGK;DKPTYDEIFYTLS(1)PVNGK;DKPTYDEIFYTLS(1)PVNGK 329.5 4.49E-75 3885892000 5512170 3167930 4375280 3935500 4311650 3306070 6030560 3791260 6885640 TRUE FALSE 5167173.119 3402486.833 4479063.708 4036491.593 3973030.401 4260478.739 5126333.513 4264607.157 5736382.201 0.900772114 0.593141585 0.78081682 0.703665037 0.692602107 0.742711798 0.893652712 0.743431488 1 22.45170972 0.788961338 0.547102757 1.002549335 0.713962473 0.409066775 0.091283283 1.026837522 0.679678377 0.099719049 0.040883282 6.151221109 -0.788961338 -0.288586862 DKPTYDEIFYTLSPVNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKPTYDEIFYTLSPVNGK 18 1 A0A024R571;Q9H4M9 A0A024R571 EHD1 EH domain-containing protein 1 0 ; 190.81 2.35E-14 437160000 2070770 1551260 1807780 1686100 1902310 1427850 2439080 1717880 2648000 FALSE TRUE 1941164.202 1666116.904 1850661.395 1729368.181 1752910.246 1840047.116 2073362.597 1932361.1 2206031.693 0.879934866 0.755255199 0.838909704 0.783927169 0.79459885 0.834098223 0.939860748 0.875944396 1 21.07302209 1.523342661 0.971207334 0.979208328 0.802498102 0.648230106 0.043595083 0.275106883 0.510689742 0.036299923 0.013680987 33.36895922 -1.523342661 -0.176710226 DKPVYDELFYTLS(ph)PINGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DKPVYDELFYTLSPINGK 18 1 Q9H223 Q9H223 EHD4 EH domain-containing protein 4 1 DKPVYDELFYTLS(1)PINGK;DKPVYDELFYT(0.001)LS(0.999)PINGK;DKPVYDELFYT(0.005)LS(0.995)PINGK 282.37 1.35E-39 457279000 1472070 874210 1260070 1137600 1320730 964820 1677170 1106290 2281770 TRUE FALSE 1379935.766 938937.418 1289959.455 1166792.742 1217005.193 1243347.871 1425693.929 1244412.742 1900927.846 0.725927483 0.493936379 0.678594644 0.613801699 0.640216406 0.654074206 0.749998971 0.65463439 1 20.85827234 -1.967843722 0.235075432 1.409436923 0.581205347 0.735501718 0.066480772 14.00973621 0.497910658 3.240793043 0.110742697 0.010768526 1.967843722 -0.828231576 DKQDEEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DKQDEEQR 8 1 P27797;K7EL50 P27797 CALR Calreticulin 0 ;;; 138.08 0.00065725 7543560000 9350200 5969000 7234400 7404600 6974300 4666700 8468600 6116600 6609900 FALSE TRUE 8764987.673 6410950.971 7406003.384 7594614.572 6426566.611 6013900.532 7198812.049 6880270.974 5506664.988 1.591705268 1.164216633 1.344916279 1.379167715 1.167052404 1.09211302 1.307290722 1.249444262 1 22.39274741 4.364365738 0.030886774 6.77E-12 2.681822187 0.444117742 0.123557607 613.4112941 3.336966592 117.838711 175.4407667 23140.12702 -4.364365738 2.681822187 DKQFVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DKQFVAK 7 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;; 111.04 0.006082 3742490000 5720909 5092779 5219822 5492595 5895402 3990729 6585736 4981042 7128295 FALSE TRUE 5362847.518 5469853.656 5343638.643 5633544.287 5432400.908 5142787.678 5598266.026 5602936.058 5938536.514 0.903058776 0.921077717 0.899824162 0.948641854 0.914770987 0.866002535 0.942701289 0.943487683 1 22.50167601 0.969586016 1.593908171 0.998823035 0.911612735 0.618301092 0.02211471 0.267059569 1.390254342 0.019539145 0.005691748 9.323651152 -0.969586016 -0.0872103 DKQLNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKQLNEK 7 1 Q9BQ69 Q9BQ69 MACROD1 O-acetyl-ADP-ribose deacetylase MACROD1 0 ; 89.247 0.016428 334560000 398730 265800 331020 328540 337900 234250 363230 279030 452490 FALSE TRUE 373774.2011 285480.1086 338871.9507 336970.8926 311362.697 301874.1723 308767.0336 313867.5097 376966.4958 0.991531622 0.75730897 0.89894448 0.893901438 0.825969152 0.800798415 0.819083492 0.832613808 1 18.52407678 -0.939304179 4.60530063 1.000001782 0.844388651 0.332920657 0.064704597 1.22E-06 2.81E-07 0.056696734 0.013363374 0.114999465 0.939304179 -0.155613131 DKQS(ph)PSQANGCSDHRPIDILEMLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKQSPSQANGCSDHRPIDILEMLSR 25 2 Q9NPI6-2;Q9NPI6;A0A087WVE6;A0A087WT55 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 DKQS(0.932)PS(0.068)QANGCSDHRPIDILEMLSR;DKQS(0.573)PS(0.427)QANGCSDHRPIDILEMLSR 111.04 0.0014009 187416000 188244 204220 229300 221220 245650 185991 308790 223350 302730 TRUE FALSE 176462.1441 219340.6613 234739.1043 226896.8797 226357.6399 239683.5824 262489.8062 251235.7392 252202.4073 0.699684614 0.869700903 0.930756795 0.899661832 0.897523709 0.950361993 1.040790249 0.996167094 1 17.94422252 6.393094202 0.3391993 1.005633429 2.61E-18 0.815328353 0.040468763 9.571089895 0.363549125 0.039322329 4.943287286 2472260.341 -6.393094202 -1.005633429 DKQVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKQVYR 6 1 P63092-4;P63092;P63092-3;Q5JWD1;A2A2R6;P63092-2 P63092-4;P63092-2 GNAS Guanine nucleotide-binding protein G(s) subunit alpha isoforms short 0 114.02 0.023383 190760000 299560 314180 275730 244290 405770 178770 320520 329170 383270 FALSE TRUE 280811.0743 337442.2141 282270.4458 250558.895 373902.461 230377.9969 272461.0016 370267.5991 319299.761 0.879459081 1.056819501 0.884029618 0.784713694 1.171007645 0.721510083 0.853307878 1.15962379 1 18.28455195 1.242904628 24.99923589 1.079811907 0.912282438 0.225357058 0.13274499 151.6164566 872573.3475 0.09051138 0.030476947 17.49462461 -1.242904628 -0.167529469 DKQWLEHVQQEDEHQRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKQWLEHVQQEDEHQRPR 18 2 F8W7U0;Q15811-6;Q15811-12;Q15811-11;Q15811-3;Q15811-10;Q15811-7;Q15811-2;Q15811-4;Q15811-9;Q15811-8;Q15811;A8CTZ0;Q15811-13;Q15811-5 F8W7U0 ITSN1 Intersectin-1 0 ; 221.79 1.95E-19 351690000 233820 235290 269040 269300 303890 216910 298040 249050 358020 FALSE TRUE 219185.6236 252711.1164 275421.7558 276210.6939 280023.7052 279528.3958 253351.6689 280144.4407 298264.1491 0.734870833 0.847272853 0.923415559 0.926060657 0.938844665 0.937184025 0.849420454 0.939249459 1 18.18623105 4.889601555 1.150445404 0.920970222 0.597354151 0.740792926 0.037283296 1.14244916 1.011804504 0.010476928 0.482265222 77553.52727 -4.889601555 -0.323616071 DKRPLS(ph)GPDVGTPQPAGLASGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DKRPLSGPDVGTPQPAGLASGAK 23 2 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 DKRPLS(1)GPDVGTPQPAGLASGAK;DKRPLS(1)GPDVGTPQPAGLASGAK;DKRPLS(0.998)GPDVGT(0.002)PQPAGLASGAK;DKRPLS(1)GPDVGTPQPAGLASGAK 273.43 9.01E-52 5286410000 4599940 3199400 3669530 3776130 4175390 2543910 4907950 3149850 4521490 TRUE FALSE 4312037.967 3436286.905 3756572.984 3873031.889 3847471.712 3278295.52 4172048.461 3543115.706 3766824.109 1.144740992 0.912250428 0.997278576 1.028195577 1.021409973 0.870307566 1.10757719 0.940610871 1 21.84491724 DKS(ph)FDDEESVDGNRPSSAASAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKSFDDEESVDGNRPSSAASAFK 23 2 E7ERI8;E7EW49;O75122-3 E7ERI8 CLASP2 CLIP-associating protein 2 1 DKS(1)FDDEESVDGNRPSSAASAFK;DKS(0.994)FDDEES(0.004)VDGNRPS(0.001)S(0.001)AAS(0.001)AFK 147.8 5.91E-08 850440000 1170070 471710 602230 667990 551850 425310 955750 474230 844900 TRUE FALSE 1096837.407 506635.8992 616515.18 685131.7543 508509.9271 548090.0927 812444.1602 533438.6594 703880.7317 1.558271676 0.719775207 0.875880177 0.973363417 0.722437629 0.778668982 1.154235545 0.75785376 1 19.42497147 4.746636046 24.94850046 0.875389072 1.558272021 0.706304727 0.138909098 566.3650378 1749705.88 0.033073441 0.368544333 55800.23728 -4.746636046 0.682882949 DKS(ph)HSHTPS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKSHSHTPSR 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 DKS(0.999)HS(0.018)HT(0.076)PS(0.907)R 110.57 0.001063 102130000 359920 229490 288940 277860 284010 239280 337520 237480 305820 TRUE FALSE 337393.2497 246481.6784 295793.7932 284990.358 261705.0002 308356.2516 286912.0094 267129.9008 254776.6663 1.324270604 0.967442121 1.160992478 1.118588928 1.027193754 1.210300206 1.126131421 1.048486522 1 17.95887363 1.065205954 3.791962043 1.001402366 1.119786275 0.180062049 0.096381724 0.354277932 10.04757747 0.083268821 0.021495068 11.61999535 -1.065205954 0.11838391 DKS(ph)PAPEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKSPAPEEK 9 1 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 DKS(1)PAPEEK;DKS(1)PAPEEK 127.71 0.00026505 1608180000 5812600 2220100 3423400 3489800 3871900 2560800 4899600 3344700 5747100 TRUE FALSE 5448799.742 2384478.514 3504604.665 3579354.176 3567816.592 3300061.389 4164950.466 3762293.158 4787871.882 1.138042094 0.498024712 0.731975448 0.74758771 0.745177958 0.689254322 0.869895972 0.78579654 1 22.19095312 0.868038474 0.721540867 0.997974437 0.72134832 0.129593165 0.162544352 1.311696616 1.476976542 0.147471312 0.055711674 7.379696039 -0.868038474 -0.276626117 DKS(ph)PVREPIDNLTPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 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(0.998)PVREPIDNLT(0.002)PEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER;DKS(1)PVREPIDNLTPEER 277.91 4.32E-36 74227700000 21515857 13482409 15652035 15753999 16939484 12572468 20939021 14120631 21083773 TRUE FALSE 20169217.92 14480660.59 16023308.66 16158273.29 15609125.26 16201935.41 17799409.19 15883622.86 17564755.08 1.148277777 0.824415742 0.912242077 0.919925909 0.888661708 0.92241169 1.013359373 0.904289459 1 24.06618012 1.879168971 9.132439422 0.973002035 0.917616148 0.009484613 0.088093528 0.880305058 62.4545647 0.034167373 0.021584727 75.71274129 -1.879168971 -0.055385887 DKSDS(ph)DTEGLLFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKSDSDTEGLLFSR 14 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 DKS(0.015)DS(0.983)DT(0.001)EGLLFSR;DKS(0.062)DS(0.882)DT(0.056)EGLLFSR 104.03 0.00065505 547590000 546490 843630 562812 512534 866393 521845 561629 671527 679654 TRUE FALSE 512286.1664 906093.243 576162.1664 525686.4902 798349.9886 672493.1801 477417.9454 755368.6242 566215.3567 0.904754985 1.600262572 1.017567185 0.928421464 1.409975867 1.187698589 0.843173785 1.334065944 1 19.11099135 3.739759943 23.42333325 1.091945703 1.304206103 0.052214778 0.240082968 357.0348411 661685.0721 0.057425167 0.10249741 5492.371981 -3.739759943 0.2122604 DKSDS(ph)PAIQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKSDSPAIQLR 11 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 DKS(0.008)DS(0.992)PAIQLR;DKS(0.052)DS(0.948)PAIQLR 102.65 0.00172 311940000 753220 686060 728750 795360 800700 647440 865450 679290 851520 TRUE FALSE 706077.3047 736856.5962 746036.2941 815770.2841 737816.2519 834345.4177 735683.8069 764100.8518 709395.811 0.995322067 1.038710104 1.051650267 1.149950805 1.040062882 1.176135247 1.037056881 1.077114976 1 19.43623129 4.207534019 1.26445469 1.082661721 0.997937758 0.190152758 0.052837974 0.954395471 2.360050604 0.014056331 0.082534647 16126.2734 -4.207534019 -0.084723963 DKSDSDT(ph)EGLLFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKSDSDTEGLLFSR 14 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 DKSDS(0.176)DT(0.824)EGLLFSR 165.16 2.55E-05 89835000 119080 63815 84278 64641 76868 75112 102940 74261 134240 TRUE FALSE 111626.9954 68539.929 86277.11396 66299.7975 70831.09735 96795.61506 87505.10265 83532.64932 111834.4768 0.998144746 0.612869403 0.771471522 0.592838626 0.633356541 0.865525711 0.782451934 0.746931105 1 16.77100549 0.308033554 0.618278368 1.008152743 0.721469258 0.278660909 0.12304855 2.907861309 1.6221095 0.177909424 0.046171878 2.032514038 -0.308033554 -0.286683485 DKSEEVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKSEEVQK 8 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 74.162 0.038023 248920000 108330 99154 107610 94852 134380 68210 106380 96460 122550 FALSE TRUE 101549.8187 106495.4653 110162.56 97286.0629 123826.3369 87901.1197 90429.30658 108503.2433 102095.6133 0.994654084 1.043095407 1.079013647 0.952891704 1.21284679 0.860968624 0.885731558 1.062761071 1 16.63956135 2.206334528 24.99998333 0.933799821 1.053033174 0.248896268 0.087164662 224.0482673 173808.3179 0.029887259 0.022074874 160.8179522 -2.206334528 0.119233353 DKSHS(ph)HTPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKSHSHTPSR 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DKS(0.344)HS(0.656)HTPSR;DKS(0.437)HS(0.563)HTPSR 123.84 0.00027266 122526000 169502 153656 153298 160479 159906 110405 146271 127618 158026 TRUE FALSE 158893.1724 165032.8501 156934.301 164597.1628 147347.6278 142277.1312 124339.0215 143551.3882 131650.4397 1.206932333 1.253568545 1.192052995 1.250259119 1.119233845 1.080718997 0.944463397 1.090398092 1 17.00635281 2.35877905 1.901431776 1.007783855 1.225224965 0.822799165 0.043207933 0.115499118 0.852857501 0.017836938 0.012917576 228.4436285 -2.35877905 0.21744111 DKSHS(ph)HTPSRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKSHSHTPSRR 11 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DKS(0.002)HS(0.499)HT(0.499)PS(0.001)RR 57.136 0.054408 244220000 20239 23400 20544 21428 22747 17828 25340 16243 21888 TRUE FALSE 18972.27712 25132.56035 21031.31338 21977.87876 20960.54238 22974.65419 21540.50225 18270.97431 18234.7514 1.040446163 1.378278201 1.153364415 1.205274384 1.149483309 1.259937889 1.181288506 1.001986477 1 14.15440291 1.269114514 4.260199027 0.994894478 1.21217179 0.462882021 0.086235741 0.155197384 5.608329081 0.064994108 0.020072459 18.58294382 -1.269114514 0.217277312 DKSHSHT(ph)PSRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKSHSHTPSRR 11 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DKSHS(0.018)HT(0.982)PSRR;DKSHS(0.14)HT(0.859)PS(0.001)RR 92.939 0.0096686 122903000 54935 68503 73129 73994 78696 61864 74132 64707 79531 TRUE FALSE 51496.71641 73575.0334 74863.65441 75892.81131 72515.5336 79723.13252 63016.59481 72785.81139 66256.76231 0.777229593 1.110453195 1.129902093 1.145434951 1.094462378 1.20324522 0.951096803 1.098541626 1 16.01578009 1.712181679 24.99999982 1.017686796 1.090124217 0.046433962 0.118817141 2.273743005 2144.845534 0.051309869 0.028453933 51.54442259 -1.712181679 0.072437421 DKSTT(ph)PGGTGIKPFLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKSTTPGGTGIKPFLER 17 2 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 DKS(0.043)T(0.127)T(0.83)PGGTGIKPFLER 108.08 0.032076 474560000 1581700 1023500 1381600 1300300 1432000 995290 1784600 1240900 2506100 TRUE FALSE 1482704.22 1099281.005 1414372.204 1333667.899 1319536.496 1282614.066 1517015.797 1395829.097 2087815.72 0.710170063 0.526522046 0.677441113 0.638786214 0.632017703 0.614332986 0.726604261 0.66855953 1 20.99356295 -1.273776223 0.331298882 1.223388913 0.610640121 0.813847815 0.05320727 6.921504767 0.516056469 1.399482324 0.043803421 0.053238251 1.273776223 -0.612748792 DKTEFAQDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKTEFAQDK 9 1 Q9UJA5;Q9UJA5-2;Q9UJA5-3 Q9UJA5 TRMT6 tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 0 111.63 0.0019094 178530000 453520 307110 334830 336900 413800 253750 406840 336360 522680 FALSE TRUE 425134.9928 329848.7439 342772.3257 345545.4244 381301.8172 327003.5057 345838.1189 378355.2864 435441.3314 0.976331281 0.757504445 0.787183717 0.793552195 0.875667489 0.750970296 0.794224374 0.86890072 1 18.73211883 0.911833883 3.517390244 0.999848671 0.807524465 0.415059673 0.06640604 0.315936266 9.024096289 0.057780287 0.014921478 8.162700886 -0.911833883 -0.192324206 DKVQAGDVITIDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKVQAGDVITIDK 13 1 Q9Y230;Q9Y230-2;M0R0Y3 Q9Y230 RUVBL2 RuvB-like 2 0 ; 154.6 4.22E-05 266715000 1101980 750260 947460 915120 976660 701510 1211180 836380 1249280 FALSE TRUE 1033009.039 805810.031 969934.1986 938603.5285 899957.0633 904024.5489 1029574.803 940803.8841 1040767.097 0.992545827 0.774246258 0.931941643 0.901838203 0.864705529 0.86861369 0.989246111 0.90395237 1 19.98921583 1.749493455 18.04344019 0.959822317 0.880260739 0.247753716 0.060518777 0.524572045 871.9739691 0.025877144 0.014323827 56.16858135 -1.749493455 -0.079561578 DKVTLVVGASQDIIPQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKVTLVVGASQDIIPQLK 18 1 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ; 173.27 7.96E-12 188773000 856890 571140 716610 656940 765250 580790 909940 661420 1084270 FALSE TRUE 803258.7845 613427.7999 733608.3276 673798.1926 705150.3519 748454.6447 773502.9445 743999.743 903298.3323 0.889250822 0.679097678 0.812144008 0.74593096 0.780639493 0.828579682 0.856309501 0.823647865 1 19.78484302 0.591701167 0.450949395 1.013627495 0.762098384 0.566951049 0.056101181 1.180259978 0.485159584 0.089168599 0.031703301 3.905720555 -0.591701167 -0.251529111 DKVVEDDEDDFPTTR ddPTM_SK-BR-3_Pertuzumab_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 ; 136.35 2.14E-05 676740000 1036730 717430 859710 816040 898350 675120 1103300 760980 1162390 FALSE TRUE 971842.9199 770549.2637 880102.7272 836980.968 827797.2148 870016.1843 937870.4075 855990.0281 968379.5997 1.003576408 0.79570993 0.908840632 0.864310822 0.854827193 0.898424734 0.968494594 0.883940583 1 19.88521316 1.184589847 0.656235315 0.993284181 0.873948916 0.208476568 0.05876853 0.866963896 0.898099573 0.052869927 0.022939854 15.29642168 -1.184589847 -0.119335265 TPSKQPGSIGS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPSKQPGSIGSR 12 1 Q66K14-2;Q66K14 Q66K14-2 TBC1D9B TBC1 domain family member 9B 1 TPSKQPGS(0.111)IGS(0.889)R 52.453 0.089959 139790000 135800 142340 148430 132700 166250 100470 202810 152180 401650 TRUE FALSE 127300.5204 152879.0017 151950.8297 136105.3067 153193.3956 129474.058 172400.5233 171180.008 334612.0202 0.380442162 0.456884369 0.454110494 0.406755581 0.457823946 0.386937857 0.515225135 0.511577581 1 18.35212975 0.186209893 0.833541292 1.008368024 0.431438238 0.96372726 0.034266466 0.564309964 0.449836946 0.042209265 0.010355658 1.535358835 -0.186209893 -0.576929785 DKWLAPDGLIFPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKWLAPDGLIFPDR 14 1 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;H0YDE4;E9PNR9 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ; 165.45 3.61E-06 1124690000 1371410 1342860 1458580 1380190 1512360 1203080 1782440 1341620 1840610 FALSE TRUE 1285575.896 1442286.752 1493178.206 1415608.012 1393585.346 1550389.666 1515179.669 1509124.21 1533400.3 0.838382447 0.940580716 0.973769345 0.923182297 0.908820317 1.011079537 0.988117499 0.984168459 1 20.54830294 5.827382845 0.978893273 0.970775376 9.68E-23 0.625243809 0.031836853 9.857297923 1.457761932 0.009903353 16.53612358 672021.001 -5.827382845 -0.970775376 DKYEESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKYEESR 7 1 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 0 116.05 0.005055 348060000 929940 729440 761530 752210 817180 629950 935370 808620 798390 FALSE TRUE 871736.7154 783448.4966 779593.8512 771512.9821 753001.9791 811806.3386 795119.952 909577.987 665133.5512 1.310619069 1.177881487 1.172086192 1.159936949 1.132106444 1.220516297 1.195429024 1.367511811 1 19.34328452 DKYEESRR ddPTM_SK-BR-3_Pertuzumab_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 86.624 0.0089434 84772000 136490 138380 144320 122350 203020 104280 154590 156330 220260 FALSE TRUE 127947.3345 148625.7992 147743.3386 125489.7081 187075.6281 134383.9432 131410.6646 175848.1446 183497.1831 0.697271383 0.809962293 0.80515317 0.683878118 1.019501362 0.732348807 0.716145406 0.958315227 1 17.48539839 1.134687318 5.873355907 0.994925293 0.785191877 0.429791187 0.095354084 0.191055845 8.78249826 0.084239133 0.021265641 13.6360102 -1.134687318 -0.209733416 DKYEPAAVSEQGDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKYEPAAVSEQGDKK 15 2 P05023-4;P05023;P05023-2 P05023-4 ATP1A1 Sodium/potassium-transporting ATPase subunit alpha-1 0 ; 125.45 5.08E-05 193872000 672520 274930 379070 352740 536040 262040 542700 445750 771000 FALSE TRUE 630428.1737 295286.1033 388061.7194 361791.9056 493941.5807 337686.6941 461327.1732 501402.8687 642315.1191 0.981493592 0.459721552 0.604160961 0.563262322 0.769001952 0.525733684 0.718225618 0.780618195 1 19.29292173 0.955975961 1.379770165 0.998434211 0.623347874 0.34645909 0.146523714 0.458368833 1.770165484 0.125220083 0.037601506 9.035994563 -0.955975961 -0.375086337 DKYGPPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKYGPPTR 8 1 Q08170;A0A0D9SEM4 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 0 81.338 0.021086 267230000 145860 149860 151860 170140 183160 142000 175830 154490 211970 FALSE TRUE 136730.883 160955.7903 155462.1909 174506.0804 168775.3524 182993.0948 149465.9238 173778.4166 176590.8376 0.774280732 0.91146173 0.880352531 0.98819442 0.955742408 1.036254753 0.846396822 0.9840738 1 17.43005097 6.046871643 0.65340805 0.953326194 2.16E-17 0.504203409 0.056136662 13.88566613 1.189019465 0.021475437 14.51288651 1113965.249 -6.046871643 -0.953326194 DKYGPPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DKYGPPVR 8 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;; 107.15 0.0037006 1772410000 2048280 2468630 2413700 2359000 2761130 2116050 2606850 2248730 2867640 FALSE TRUE 1920081.811 2651409.934 2470954.104 2419535.934 2544281.988 2726919.284 2215977.043 2529488.891 2389012.358 0.803713637 1.109835169 1.034299423 1.01277665 1.06499323 1.1414421 0.927570356 1.058801091 1 21.18798289 4.748453166 24.91617734 1.043546517 0.803713501 0.622497591 0.058736192 902.1308063 2272132.119 0.013649008 0.185458078 56034.19867 -4.748453166 -0.239833016 DKYGVFPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DKYGVFPLR 9 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 ; 132.78 0.00026947 1310120000 1645770 2057030 1986630 2123570 2456890 1952090 2636400 2066560 2884130 FALSE TRUE 1542764.193 2209334.642 2033753.802 2178064.401 2263935.77 2515626.693 2241096.295 2324574.565 2402750.071 0.642082675 0.919502477 0.846427528 0.906488123 0.942226908 1.046978096 0.932721352 0.967464154 1 21.19625516 5.829986419 0.530437337 0.970056951 7.88E-33 0.705003128 0.059393455 7.182443155 0.636180225 0.029082056 5.559945924 676061.8335 -5.829986419 -0.970056951 DLADELALVDVIEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 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 ;;;;;;;;;; 359.9 1.66E-82 2631472000 1818626 1098465 1408460 1362123 1263634 977913 1670912 1095675 905987 FALSE TRUE 1704801.445 1179796.492 1441869.336 1397077.382 1164393.283 1260220.608 1420374.258 1232472.436 754771.9168 2.258697505 1.563116572 1.910337818 1.850992798 1.542708806 1.669670771 1.881858911 1.632907118 1 19.52568122 -2.2902266 0.295328416 6.14E-14 1.845439089 0.626501568 0.198676347 27.06163245 1.051113513 18.18171485 0.199295195 0.005125939 2.2902266 1.845439089 DLADELALVDVIEDKLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLADELALVDVIEDKLK 17 1 F5GZQ4;P00338;P00338-3;P00338-4;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2;F5H5J4;F5H6W8 F5GZQ4;P00338 LDHA L-lactate dehydrogenase A chain 0 261.98 2.33E-27 410500000 604710 412230 463660 488570 588730 257110 638410 398040 639810 FALSE TRUE 566862.2805 442751.9381 474658.2342 501107.5333 542493.5206 331333.4832 542686.3472 447736.1702 533021.5777 1.06348843 0.830645431 0.890504726 0.940126168 1.017770281 0.62161364 1.018132042 0.839996332 1 19.02383441 -1.469861926 3.237329656 1.001970903 0.896275796 0.053566199 0.125804126 802168671.6 1162953242 14747911.72 0.026597579 0.03389519 1.469861926 -0.105695107 DLAEDAPWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLAEDAPWK 9 0 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98;O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;O75369-5;O75369-4;Q14315-2;Q14315 Q60FE5;O75369-8;Q14315-2 FLNA;FLNB;FLNC Filamin-A;Filamin-B;Filamin-C 0 ; 122.13 0.0013826 137063000 665650 670400 573530 535800 741430 420200 658450 671590 529240 FALSE TRUE 623988.1547 720037.1136 587134.4024 549549.5351 683201.0786 541504.9186 559721.5353 755439.4899 440906.425 1.415239424 1.63308374 1.331653088 1.246408544 1.549537589 1.228162912 1.269479199 1.713378275 1 18.75011297 -3.532384664 0.245303832 2.84E-26 1.457451126 0.33889264 0.172462078 91.53845315 1.746558553 47.34031598 0.253699539 0.000293505 3.532384664 1.457451126 DLAEDAPWKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 2213420000 5796010 4728890 4831200 4473030 6440910 3499410 6461150 5297870 6418850 FALSE TRUE 5433248.08 5079021.936 4945798.345 4587815.523 5935066.91 4509632.859 5492360.54 5959320.732 5347502.468 1.016034703 0.949793285 0.924880049 0.857936121 1.109876423 0.843315713 1.027088921 1.114411965 1 22.35043381 1.535186768 7.476610223 1.061307114 0.948974642 0.252865488 0.079598498 0.142443926 14.70062684 0.038562857 0.01784068 34.29152253 -1.535186768 -0.112332472 DLAEITTLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLAEITTLDR 10 0 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 ;; 166.33 1.30E-05 114910000 130601 156328 142448 133425 162816 111206 157433 139059 132209 FALSE TRUE 122426.9165 167902.6878 145826.9338 136848.9114 150029.0881 143309.3669 133827.3832 156420.8223 110142.4638 1.111532395 1.524413764 1.323984672 1.242471856 1.362136663 1.301127304 1.215038947 1.420168179 1 16.74901126 -3.67248632 0.277255115 2.38E-13 1.34917365 0.389075428 0.116773061 92.79721932 1.759126197 53.07557795 0.129673821 0.000212576 3.67248632 1.34917365 DLAEVGEGGGHSQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLAEVGEGGGHSQAR 15 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ; 147.51 3.70E-06 3019630000 845640 2913090 1834770 2045040 2186770 1941080 1571000 1773190 1608720 FALSE TRUE 792712.9019 3128778.215 1878291.611 2097519.189 2015029.905 2501438.285 1335443.134 1994576.675 1340214.239 0.591482226 2.33453587 1.401486088 1.565062605 1.503513279 1.866446581 0.996440043 1.488252114 1 20.35403221 1.728399483 12.56772212 1.185378807 1.617810432 0.121911612 0.453810931 0.158358522 114.5761556 0.194046851 0.106412539 53.50563017 -1.728399483 0.432431626 DLAFTLEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLAFTLEER 9 0 P48163 P48163 ME1 NADP-dependent malic enzyme 0 ;;; 159.28 0.00015395 590577000 926020 1091320 1010380 1025930 1155160 862680 1139530 1002000 1052430 FALSE TRUE 868062.0612 1172122.468 1034346.691 1052257.101 1064438.393 1111721.712 968668.0554 1127101.906 876772.634 0.990065186 1.336860234 1.179720546 1.200148202 1.214041534 1.267970359 1.104811005 1.285512186 1 19.74184324 -1.561825904 2.927950859 0.989337364 1.204591747 0.28759373 0.097048316 12315388.91 13638572.98 1030745.563 0.021109039 0.027426734 1.561825904 0.215254383 DLAGAPPGEVVGCFT(ph)PQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DLAGAPPGEVVGCFTPQSR 19 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 1 DLAGAPPGEVVGCFT(0.998)PQS(0.002)R;DLAGAPPGEVVGCFT(0.996)PQS(0.004)R;DLAGAPPGEVVGCFT(1)PQSR;DLAGAPPGEVVGCFT(0.998)PQS(0.002)R;DLAGAPPGEVVGCFT(0.997)PQS(0.003)R 380.95 8.40E-108 732870000 231300 238824 216226 213659 260602 204976 318194 201040 277239 TRUE FALSE 216823.3459 256506.7775 221354.9828 219141.8517 240135.3701 264149.2437 270483.7637 226140.2865 230966.0199 0.938767296 1.110582317 0.958387658 0.948805594 1.039699997 1.143671454 1.171097652 0.979106306 1 17.81732109 2.449448755 7.78692808 1.098084312 1.003231879 0.175891209 0.075896167 0.273442966 61.5638731 0.025652008 0.021619548 281.480786 -2.449448755 -0.094852432 DLAHCHAYLVEMSQLLQSMDVLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLAHCHAYLVEMSQLLQSMDVLHR 24 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 0 186.62 1.20E-17 37135000 191420 247150 215260 232270 310810 212610 256800 227390 233480 FALSE TRUE 179439.3639 265449.2432 220366.0689 238230.4414 286400.2363 273987.0556 218295.224 255780.142 194510.6797 0.92251677 1.364702666 1.132925294 1.224767925 1.472413941 1.408596464 1.122278861 1.314992794 1 17.56948984 -1.095528859 4.215602908 0.999964832 1.249951159 0.18838989 0.159825978 5.31E-05 1.14E-05 0.142239995 0.033521136 0.080254823 1.095528859 0.249986327 DLAILQCHGELDPMVPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DLAILQCHGELDPMVPVR 18 0 O95372;Q5QPQ1;Q5QPQ0 O95372 LYPLA2 Acyl-protein thioesterase 2 0 ;;;;;; 202.6 1.27E-15 1090204000 929017 1102237 1037373 1049912 1139506 945611 1193082 985987 1252553 FALSE TRUE 870871.4843 1183847.774 1061979.977 1076854.519 1050013.795 1218593.545 1014190.43 1109089.647 1043493.812 0.834572734 1.134503876 1.017715644 1.031970201 1.006248224 1.167801409 0.97191801 1.062861738 1 19.99299062 4.75291487 24.79690726 1.050615515 0.834572568 0.552907488 0.060620403 1681.207094 2904221.674 0.013239583 0.287421736 56612.83065 -4.75291487 -0.216042947 DLAMMIHDQGDLIDSIEANVESSEVHVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLAMMIHDQGDLIDSIEANVESSEVHVER 29 0 Q86Y82 Q86Y82 STX12 Syntaxin-12 0 ; 72.881 0.0039309 15777000 10859.5 14010.5 13748.8 11785.9 18955.6 13499.3 15119.1 12802.6 17875 FALSE TRUE 10179.82328 15047.852 14074.92803 12088.34615 17466.90364 17396.32877 12852.13131 14401.03279 14891.54702 0.68359743 1.010496221 0.945162246 0.811758921 1.172940838 1.16820158 0.863048768 0.967060895 1 13.86220602 4.741320712 24.11384614 0.987267995 0.683597249 0.420820957 0.113689685 162.18629 1416825.244 0.026685681 0.184090124 55121.45993 -4.741320712 -0.303670746 DLANDIMTLMSHTKPYIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLANDIMTLMSHTKPYIR 18 1 O14617-5;O14617-2;O14617;O14617-4;A0A2R8Y4J3 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 ; 149.36 3.77E-08 80612000 258020 300630 281560 291910 332250 233360 353420 272310 314040 FALSE TRUE 241870.9888 322888.958 288238.7362 299400.9048 306156.4252 300727.2437 300427.952 306308.5029 261624.6952 0.924496017 1.234168501 1.101726027 1.14439084 1.170212258 1.149460465 1.148316491 1.170793539 1 17.9971392 -1.086953048 4.373750762 0.999988024 1.140221139 0.196163586 0.08086184 9.69E-06 2.02E-06 0.067605804 0.015933223 0.081855328 1.086953048 0.140233116 DLAQGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLAQGTK 7 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 126.52 0.0091752 147700000 552510 497710 544150 541920 564820 414880 656780 492800 557420 FALSE TRUE 517929.3854 534560.9663 557057.495 555826.5847 520461.3156 534649.121 558301.9362 554327.1648 464383.0009 1.115306513 1.151120875 1.199564786 1.19691415 1.120758758 1.151310707 1.202244559 1.193685306 1 18.82495564 -1.81945754 2.543994421 0.941209373 1.169306232 0.725448212 0.032118571 8241779.408 5264028.275 2967094.234 0.007936943 0.01515453 1.81945754 0.228096859 DLAVPAALT(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLAVPAALTPR 11 0 Q8TEM1 Q8TEM1 NUP210 Nuclear pore membrane glycoprotein 210 1 DLAVPAALT(1)PR;DLAVPAALT(1)PR;DLAVPAALT(1)PR 135.04 0.0014339 533840000 1077630 1151340 933780 1004140 1027670 776050 1203170 1045740 841100 TRUE FALSE 1010183.062 1236586.412 955929.7026 1029907.932 946960.9436 1000083.037 1022765.828 1176302.941 700714.9763 1.44164617 1.764749511 1.364220453 1.469795805 1.351421014 1.427232285 1.459603209 1.678718139 1 19.41846821 -1.664002592 2.943039803 0.949118085 1.496392859 0.586106055 0.130633266 18744945.14 17765916.31 7162794.66 0.03134685 0.021676912 1.664002592 0.547274774 DLCNTHLMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLCNTHLMR 9 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 109.42 0.0018601 373740000 149564 228130 167054 168607 203100 150307 193011 195137 202787 FALSE TRUE 140203.0562 245020.9826 171016.5998 172933.7411 187149.3453 193698.1909 164070.7924 219500.284 168940.5396 0.829895871 1.450338581 1.012288703 1.023636727 1.107782334 1.146546538 0.971174786 1.299275381 1 17.36615604 3.735874301 24.97069698 1.0754342 1.198498296 0 0.175983017 788.7928665 2250251.923 0.040539281 0.07174372 5443.450793 -3.735874301 0.123064096 DLDANGDAQVDFSEFIVFVAAITSACHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 DLDANGDAQVDFSEFIVFVAAITSACHK 28 0 P25815 P25815 S100P Protein S100-P 0 ;;;;;;;;;;;; 365.19 2.31E-127 15112500000 20940394 21370567 20381261 22128715 21886926 21959329 32223801 18003988 15995238 FALSE TRUE 19629772.12 22952866.02 20864714.14 22696575.29 20168015.12 28298630.8 27392141.19 20251825.53 13325529.44 1.473095099 1.7224731 1.565769992 1.703240039 1.513486965 2.123640259 2.055613723 1.519776427 1 23.66768952 DLDDFQSWLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLDDFQSWLSR 11 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;; 235.01 3.81E-15 355419000 665100 823520 715390 749470 914890 538959 826190 680500 1322640 FALSE TRUE 623472.5782 884494.2777 732359.3886 768702.669 843038.2299 694547.714 702310.4795 765461.923 1101882.839 0.565824746 0.802711728 0.66464361 0.6976265 0.76508881 0.630328098 0.637373098 0.694685402 1 20.0715394 -2.054958386 2.344125549 1.419393771 0.688293113 0.687636897 0.067187766 7665154.602 2527965.708 17216982.76 0.01545301 0.008811333 2.054958386 -0.731100657 DLDDIEDENEQLKQENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLDDIEDENEQLKQENK 17 1 Q96IZ0;H0YHP5 Q96IZ0 PAWR PRKC apoptosis WT1 regulator protein 0 ; 274.23 1.01E-35 479650000 1239060 522640 709520 683940 761100 449280 922650 577900 845230 FALSE TRUE 1161509.446 561336.8094 726350.1495 701491.0583 701326.2761 578979.8425 784307.198 650052.0871 704155.6526 1.649506671 0.797177169 1.031519305 0.996215902 0.995981888 0.822232756 1.11382646 0.923165332 1 19.42553484 4.747140382 24.93141306 0.962922992 1.649507031 0.840967183 0.094221641 395.5051587 1149248.074 0.021373059 0.250806339 55865.07449 -4.747140382 0.686584039 DLDEDELLGNLS(ph)ETELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLDEDELLGNLSETELK 17 0 Q9NYL9;H0YNU8 Q9NYL9 TMOD3 Tropomodulin-3 1 DLDEDELLGNLS(0.996)ET(0.004)ELK 128.26 3.94E-05 16191000 74487 45349 54643 45759 49147 42600 71944 46093 49877 TRUE FALSE 69824.99163 48706.68715 55939.15776 46933.25341 45287.19287 54897.92845 61156.6651 51847.81251 41552.20648 1.680415977 1.172180523 1.346237962 1.129500871 1.089886596 1.321179622 1.471803071 1.247775194 1 15.34263747 4.745274672 24.73142417 1.25292444 1.680416204 0.507707669 0.138886699 621.2515761 2288329.426 0.033252316 0.324280003 55625.59535 -4.745274672 0.427491764 DLDEEGS(ph)EK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLDEEGSEK 9 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 DLDEEGS(1)EK;DLDEEGS(1)EK;DLDEEGS(1)EK 205.52 1.55E-05 1178250000 5801690 2031170 3304150 2786840 2160900 2712790 4432860 2424870 1639180 TRUE FALSE 5438572.579 2181559.94 3382525.998 2858355.033 1991191.631 3495928.435 3768193.796 2727620.357 1365590.268 3.982580064 1.597521592 2.476969906 2.093127857 1.458117912 2.560012703 2.75938829 1.997392937 1 20.38109325 4.748432469 24.71563361 2.110096532 3.982581259 0.558802602 0.546881496 915.2286629 2291354.824 0.124002469 1.638984922 56031.52836 -4.748432469 1.872484727 DLDEEGS(ph)EKELHENVLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLDEEGSEKELHENVLDK 18 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 DLDEEGS(1)EKELHENVLDK;DLDEEGS(1)EKELHENVLDK;DLDEEGS(1)EKELHENVLDK;DLDEEGS(1)EKELHENVLDK 241.52 3.23E-24 1174330000 6981030 1893256 3400490 2835650 2399010 2679590 4521900 2548280 2086180 TRUE FALSE 6544099.794 2033434.644 3481151.229 2908417.58 2210601.432 3453144.133 3843883.074 2866438.367 1737983.081 3.765341485 1.169996801 2.002983382 1.673444127 1.271934955 1.986868671 2.211691884 1.649290145 1 20.72898261 4.747655798 24.88925137 1.697131923 3.765342626 0.744116733 0.392961918 599.4309271 1640324.561 0.091614316 1.131351024 55931.4139 -4.747655798 2.068210703 DLDEEIFDDDDFYHQLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DLDEEIFDDDDFYHQLLR 18 0 Q9NY61;A0A087WTH8;A0A087WWS8 Q9NY61 AATF Protein AATF 0 ;;;;; 297.45 2.21E-49 529716000 563146 558872 592388 558217 586193 461320 672663 512161 602279 FALSE TRUE 527899.6971 600251.4644 606439.7231 572541.7933 540155.7664 594495.5951 571803.4278 576105.4283 501754.744 1.052107037 1.196304512 1.208637746 1.141078983 1.076533451 1.184833033 1.139607417 1.148181328 1 18.93662283 -4.37020355 0.337244531 1.93E-11 1.158830934 0.428643581 0.050329745 216.1016053 2.786409061 152.9314311 0.040345736 4.26E-05 4.37020355 1.158830934 DLDELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLDELSR 7 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;; 172.03 0.0021301 888380000 2888710 3356930 3599750 3344360 4152320 3930410 3876990 2782920 2801590 FALSE TRUE 2707910.798 3605480.59 3685137.77 3430181.94 3826213.537 5065055.562 3295671.342 3130373.688 2333986.53 1.160208409 1.544773521 1.578902758 1.469666554 1.63934688 2.170130589 1.412035288 1.341213262 1 21.1543648 1.019845123 2.308274803 1.010541333 1.590446619 0.352790277 0.250457861 0.308395144 3.559278568 0.228002349 0.062569538 10.4675519 -1.019845123 0.579905285 DLDELSRYPEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DLDELSRYPEDK 12 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;; 206.32 8.35E-08 2853850000 6662830 4971220 5754000 5658890 6223810 4075990 7316940 4928350 8784700 FALSE TRUE 6245815.364 5339294.301 5890487.597 5804106.698 5735017.068 5252662.145 6219832.774 5543665.346 7318476.819 0.853431051 0.729563601 0.804878904 0.793075778 0.78363534 0.717726144 0.849880778 0.757488953 1 22.80311198 -3.696561235 0.481100729 2.425028508 0.782404419 0.691270329 0.044730151 246.4094498 4.604178588 363.5947281 0.019766327 0.000201112 3.696561235 -1.642624089 DLDEMDDDDDDDDVGDHDDDHPGMEVVLHEDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLDEMDDDDDDDDVGDHDDDHPGMEVVLHEDKK 33 1 Q15029;Q15029-3;K7EIV5;K7EIT3 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ; 232.73 1.84E-38 467040000 464780 297136 334027 342150 345400 227206 399460 274016 448500 FALSE TRUE 435690.2495 319136.2586 341950.2782 350930.1483 318273.6773 292796.6838 339564.6814 308227.5008 373642.4526 1.166061957 0.854122053 0.915180478 0.939213801 0.851813479 0.783627989 0.908795773 0.82492634 1 18.51129886 4.741738316 24.95819007 0.880155408 1.166062065 0.675340089 0.061234016 162.3085237 1274737.782 0.013221813 0.094724269 55174.48859 -4.741738316 0.285906657 DLDEVLQTHSVFVNVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLDEVLQTHSVFVNVSK 17 0 Q9Y3A5;A0A087X020;F8WE72 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ; 209.25 4.44E-12 910200000 2681300 2546400 2563960 2721690 2898160 2022850 3582510 2365570 3000800 FALSE TRUE 2513482.219 2734938.106 2624778.342 2791533.173 2670550.204 2606813.957 3045345.884 2660916.622 2499947.094 1.005414165 1.093998394 1.049933556 1.1166369 1.068242688 1.04274765 1.218164133 1.064389174 1 21.25346613 3.244467516 24.97336105 1.100378006 1.059278612 0.022977343 0.061515106 356.5899681 1507585.465 0.016686058 0.022021466 1755.769563 -3.244467516 -0.041099394 DLDGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLDGFR 6 0 A0A087WYS1;E7EUC7;Q16851;Q16851-2;C9JVG3;C9JQU9;C9JNZ1;C9JWG0;C9JTZ5;C9JUW1;F2Z3H1 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 ; 143.18 0.026596 812800000 2168050 2354600 2513500 2448500 2573300 2164170 2620800 2146810 2238700 FALSE TRUE 2032355.621 2528937.034 2573121.407 2511332.655 2371203.398 2788930.747 2227835.37 2414843.954 1865046.507 1.089707743 1.355964596 1.379655358 1.346525486 1.271391029 1.495367936 1.194520009 1.294790207 1 20.83078018 0.523018727 1.07122448 1.000412251 1.32642975 0.429410128 0.109110107 1.443391533 2.340220759 0.095132184 0.029659957 3.334407905 -0.523018727 0.326017499 DLDGFRK ddPTM_SK-BR-3_Pertuzumab_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 ;; 86.953 0.031584 1263610000 2237020 2278930 2271840 2255330 2701540 1641300 2876150 2166310 3497780 FALSE TRUE 2097008.911 2447664.348 2325729.118 2313205.586 2489371.946 2115116.666 2444898.008 2436778.572 2913977.921 0.719637886 0.839973539 0.7981286 0.793830855 0.854286482 0.725851987 0.839024205 0.836237829 1 21.47455852 0.627610775 1.376101584 0.99979942 0.79892251 0.678352456 0.044181467 0.738990078 2.021156731 0.037261334 0.011010979 4.2423918 -0.627610775 -0.20087691 DLDIFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DLDIFDR 7 0 Q14165;F5H1S8;H0YG07 Q14165 MLEC Malectin 0 ;;;;; 153.73 0.004017 358887000 1111950 1285500 1033790 1094210 1447080 905136 1306440 1316520 1208370 FALSE TRUE 1042355.034 1380679.758 1058311.987 1122289.281 1333432.174 1166434.07 1110551.45 1480890.42 1006685.241 1.035432916 1.371510877 1.051283901 1.114836332 1.324577058 1.158687962 1.10317645 1.471056056 1 19.94118124 -1.471956031 5.631493662 0.999790588 1.197095985 0.164153071 0.143830501 0.000339548 3.18E-05 0.12504355 0.029441984 0.033732146 1.471956031 0.197305397 DLDIIDNYDYSHTVK ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;; 307.32 1.63E-45 3521098000 4854092 4274955 4055814 3990678 4160359 2943101 5753328 3918286 5436508 FALSE TRUE 4550283.047 4591477.116 4152019.823 4093085.554 3833621.186 3792726.481 4890669.878 4407492.632 4529119.694 1.00467273 1.013768111 0.916738816 0.903726514 0.846438479 0.837409196 1.079827915 0.973145541 1 22.11079924 -1.06789785 6.773458327 1.000000024 0.95068198 0.044647461 0.075375011 2.85E-08 3.83E-09 0.075745275 0.017853324 0.085526786 1.06789785 -0.049318044 DLDKADSMIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 214.26 7.97E-09 971210000 1868200 2080280 1807710 2159040 2725120 1364780 2556140 2043780 2943190 FALSE TRUE 1751272.697 2234306.096 1850589.735 2214444.622 2511100.068 1758769.831 2172870.537 2298950.432 2451952.575 0.714235958 0.911235445 0.754741243 0.903135176 1.024122609 0.717293576 0.886179675 0.937599877 1 21.22549964 -4.999999662 0.062497424 1.534575195 0.635648856 0.271114855 0.094003472 551.8067016 2.511610388 44.4167963 6.89722166 1.00E-05 4.999999662 -0.89892634 DLDKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLDKPR 6 1 Q8NAV1;Q8NAV1-2 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 0 67.035 0.091051 261790000 279530 306060 301780 316670 312070 261120 314710 256060 309530 FALSE TRUE 262034.7163 328721.0009 308938.3641 324796.2883 287561.281 336501.1051 267522.1571 288029.6547 257867.4434 1.016160524 1.274767363 1.198051061 1.259547479 1.115151557 1.304938307 1.037440608 1.116967892 1 17.97627011 1.659854755 8.565296827 1.058247955 1.203480615 0.368768518 0.087511227 0.113411885 14.31893216 0.038012877 0.019982737 45.69353472 -1.659854755 0.14523266 DLDLDAFAEELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLDLDAFAEELER 13 0 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;;; 166.14 7.94E-05 131941000 219144 201925 225948 207812 213874 196423 260030 192896 200651 FALSE TRUE 205428.1682 216875.7371 231307.5933 213144.8077 197077.1988 253127.1314 221040.9155 216979.4902 167161.0518 1.22892364 1.297405913 1.383740953 1.275086543 1.178966013 1.51427099 1.322323071 1.298026591 1 17.35087922 0.722658936 3.818752625 1.000004604 1.323079358 0.542664062 0.089958611 3.289954707 44.60744035 0.081445632 0.02086838 5.280304117 -0.722658936 0.323074754 DLDLEPLS(ph)DLEEGLEETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLDLEPLSDLEEGLEETR 18 0 P29375;P29375-2 P29375 KDM5A Lysine-specific demethylase 5A 1 DLDLEPLS(1)DLEEGLEETR 278.34 3.75E-39 74880000 199750 171600 196320 196980 187780 168740 235840 172210 150480 TRUE FALSE 187248.0041 184305.4425 200976.8031 202034.8403 173032.5163 217452.4987 200477.9814 193710.7976 125363.9159 1.493635571 1.470163414 1.603147139 1.611586866 1.380241795 1.734570089 1.59916815 1.545187834 1 16.93576262 0.921592626 20.03155969 1 1.559831257 0.770847735 0.095050002 2558.456551 653638.156 0.087377608 0.021844402 8.34819578 -0.921592626 0.559831257 DLDLKKPIYQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLDLKKPIYQR 11 2 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 62.924 0.043811 405050000 612300 557650 612960 611120 782530 364640 673640 528260 1216800 FALSE TRUE 573977.236 598938.9862 627499.7007 626802.3738 721073.2504 469905.6486 572633.9358 594214.4238 1013708.219 0.566215431 0.590839627 0.619014119 0.618326222 0.711322289 0.463551187 0.564890296 0.586178954 1 19.95121102 -1.765682052 2.644993217 1.098483092 0.589660461 0.816538701 0.061069409 15716919.29 12155391.25 10072748.34 0.014728815 0.017152126 1.765682052 -0.508822632 DLDLLASVPS(ph)PSSSGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DLDLLASVPSPSSSGSR 17 0 A0A087WV97;Q8WU79-3;Q8WU79-2;Q8WU79 A0A087WV97 SMAP2 Stromal membrane-associated protein 2 1 DLDLLASVPS(1)PSSSGSR;DLDLLAS(0.001)VPS(0.825)PS(0.132)S(0.029)S(0.007)GS(0.007)R;DLDLLASVPS(0.998)PS(0.002)SSGSR;DLDLLASVPS(0.999)PS(0.001)SSGSR;DLDLLASVPS(0.984)PS(0.016)SSGSR;DLDLLASVPS(0.986)PS(0.012)S(0.001)SGSR;DLDLLASVPS(0.999)PS(0.001)SSGSR;DLDLLAS(0.015)VPS(0.845)PS(0.112)S(0.023)S(0.002)GS(0.002)R 300.18 2.61E-46 2231071000 2621510 2672790 2823760 2892700 2953180 2494565 3212100 2430772 2844280 TRUE FALSE 2457434.369 2870686.153 2890740.921 2966931.579 2721249.155 3214705.42 2730475.425 2734259.235 2369551.293 1.037088488 1.211489349 1.219952878 1.252106923 1.148423823 1.356672645 1.152317501 1.153914348 1 21.17618246 0.83364401 1.880756439 1.000916836 1.20695414 0.364824479 0.081192335 0.592671829 3.894685004 0.069582636 0.019497795 6.817796117 -0.83364401 0.206037304 DLDRPESQS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLDRPESQSPK 11 1 Q8WUA4;A0A087WZD8;Q8WUA4-2 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 DLDRPES(0.097)QS(0.903)PK;DLDRPES(0.007)QS(0.993)PK 135.14 7.65E-05 824550000 1557080 889100 1148140 1040470 1319900 987600 1784020 1187570 1781690 TRUE FALSE 1459625.142 954929.8891 1175374.423 1067170.222 1216240.378 1272704.088 1516522.763 1335840.729 1484314.429 0.983366539 0.643347441 0.791863503 0.718965066 0.819395375 0.857435637 1.021699132 0.899971531 1 20.50136531 2.080218627 2.196862103 0.974647504 0.764201206 0.433112683 0.092448399 0.240768796 2.24098693 0.044098349 0.025458559 120.2869815 -2.080218627 -0.210446298 DLDSLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DLDSLHR 7 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;;;;;; 153.73 0.0017267 7637660000 8397340 10904610 10840960 10946850 11516480 8846780 12354000 9631800 11018870 FALSE TRUE 7871765.479 11711998.67 11098112.69 11227764.7 10612022.12 11400701.77 10501632.39 10834351.43 9179749.412 0.857514201 1.275851676 1.208977739 1.223101438 1.156025251 1.241940412 1.143999898 1.180244792 1 23.13002334 -0.027162804 1.195165063 0.999227917 1.179598761 0.142862711 0.116175598 20.99486363 22.36993982 0.160646613 0.03018804 0.939371103 0.027162804 0.180370844 DLDTGEEVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLDTGEEVTR 10 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 207.68 2.97E-07 156450000 210100 218310 223080 242360 248960 182360 263950 224200 234740 FALSE TRUE 196950.216 234473.8996 228371.5629 248579.3679 229407.6859 235004.3716 224373.1479 252191.8635 195560.3775 1.007106954 1.198984695 1.167780334 1.271113152 1.173078559 1.201697269 1.147334397 1.289585686 1 17.57725457 4.74089765 24.33519428 1.187209011 1.00710686 0.326063485 0.078233133 150.8748763 1570889.855 0.015723447 0.10528819 55067.79032 -4.74089765 -0.180102151 DLDWDCLIFHDVDHIPESDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLDWDCLIFHDVDHIPESDR 20 0 O43286 O43286 B4GALT5 "Beta-1,4-galactosyltransferase 5" 0 58.997 0.040557 13666000 10777 19055 15499 13820 20465 16169 15348 18107 13839 FALSE TRUE 10102.48681 20465.85203 15866.6436 14174.6446 18857.76145 20836.72782 13046.70988 20367.69881 11529.1815 0.876253601 1.775134864 1.376215962 1.229458015 1.635654834 1.807303305 1.131624989 1.766621405 1 13.49300247 -1.119187753 5.096012225 0.999984992 1.462610658 0.172882753 0.308047891 4.66E-05 8.06E-06 0.264705721 0.062389714 0.075999765 1.119187753 0.462625666 DLDWEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLDWEVR 7 0 Q6PJG6;Q6PJG6-3 Q6PJG6 BRAT1 BRCA1-associated ATM activator 1 0 ; 127.12 0.0090405 124143000 310970 326270 349890 331570 370910 306610 408920 315360 345890 FALSE TRUE 291506.9428 350427.3703 358189.556 340078.6475 341780.2248 395123.3296 347606.2422 354733.3902 288158.7245 1.011619354 1.216091482 1.24302867 1.18017821 1.18608321 1.371200301 1.206301294 1.231034704 1 18.13650417 4.738458539 6.307085096 1.220926958 1.006930418 0.290760614 0.091329638 0.12993168 28.80888641 0.018944848 0.11912067 54759.38209 -4.738458539 -0.21399654 DLEADIIGDTSGHFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DLEADIIGDTSGHFQK 16 0 P08133;P08133-2;E5RJF5;E5RK63 P08133 ANXA6 Annexin A6;Annexin 0 ;;;; 268.56 1.54E-27 1809246000 2639996 2225163 2506468 2051512 3299941 1589230 3138333 2877372 4914386 FALSE TRUE 2474763.363 2389916.384 2565922.605 2104157.271 3040776.945 2048014.902 2667769.102 3236618.228 4094143.228 0.604464286 0.583740297 0.626730053 0.513943249 0.742713866 0.500230399 0.651606198 0.790548363 1 21.96513014 1.011560734 2.075116859 0.997977891 0.598471377 0.797579504 0.066363011 0.118372757 1.08467566 0.054042773 0.015071927 10.26977038 -1.011560734 -0.399506513 DLEAEHVEVEDTTLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DLEAEHVEVEDTTLNR 16 0 Q9H3K6;A0A087WZT3;H3BV85;Q9H3K6-2;H3BTW0;A0A0B4J295;H3BVE0 Q9H3K6 BOLA2;BOLA2B BolA-like protein 2 0 ;;;;;; 273.99 3.21E-35 9346620000 6146000 6414200 6402840 6256870 6625020 5382410 7173660 5625170 6986740 FALSE TRUE 5761332.831 6889114.042 6554718.388 6417431.877 6104717.653 6936224.391 6098036.28 6327484.857 5820607.958 0.989816334 1.183572935 1.126122638 1.102536354 1.048811 1.191666651 1.047663118 1.087083154 1 22.47273842 0.846469719 0.904794722 1.000644018 1.11531762 0.185429614 0.061705696 1.05918628 1.753071937 0.054014878 0.018370313 7.022143799 -0.846469719 0.114673602 DLEAHIDSANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLEAHIDSANK 11 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 206.97 2.46E-08 8162430000 18497380 16228870 17180710 17010210 18134990 12262710 21016900 15186940 18738450 FALSE TRUE 17339662 17430472.42 17588244.55 17446720.79 16710741.04 15802755.31 17865610.96 17083062.89 15610881.64 1.110742007 1.11655913 1.126665678 1.117599966 1.070454663 1.012291021 1.144433182 1.094304811 1 23.89604868 2.743725233 21.80640593 1.074665028 1.119131945 0.281937247 0.04065101 112.667892 475711.9808 0.012184592 0.012534131 554.274926 -2.743725233 0.044466917 DLEALMFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DLEALMFDR 9 0 A0A3B3ITK7;P36871;P36871-2;P36871-3 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 0 ;;;;; 161.79 0.00014952 379957000 448174 632226 486443 505293 692797 352803 493701 584915 540127 FALSE TRUE 420123.5894 679036.6709 497981.6577 518259.6738 638387.5182 454651.4988 419675.1183 657942.9253 449976.3143 0.933657119 1.509049808 1.106684156 1.151748786 1.418713603 1.010389846 0.932660464 1.462172351 1 18.77948954 2.211270938 24.97207568 1.075179559 1.243568818 0.066468631 0.211947152 436.4217999 399355.5024 0.074007039 0.05467129 162.6563182 -2.211270938 0.168389259 DLEDKEGEIQAGAK ddPTM_SK-BR-3_Pertuzumab_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 ; 208.39 7.40E-09 499500000 1120340 557520 760340 745180 798790 511550 1007330 639420 958250 FALSE TRUE 1050219.919 598799.3609 778375.6239 764302.5804 736056.2556 659226.1807 856290.2181 719252.9945 798311.8845 1.315550901 0.750081982 0.975026978 0.957398475 0.922015906 0.825775231 1.072626169 0.900967415 1 19.60659296 -1.56909183 5.669448611 1.000186962 0.948147186 0 0.152170267 0.000319514 2.43E-05 0.13090981 0.030745055 0.026971691 1.56909183 -0.052039776 DLEDSLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 201.49 0.00025906 4564160000 6937160 6402910 6835980 6582540 6638220 5748610 7774500 6275830 6728760 FALSE TRUE 6502975.539 6876988.119 6998132.674 6751459.121 6116880.978 7408140.386 6608785.9 7059381.19 5605686.487 1.160067648 1.226787858 1.24839887 1.204394705 1.09119213 1.321540262 1.178943188 1.25932501 1 22.41845963 -1.066725106 4.72745195 0.999991693 1.214521233 0.535950862 0.061736195 4.81E-06 9.49E-07 0.0531433 0.012525511 0.085758049 1.066725106 0.21452954 DLEEAEEYKEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLEEAEEYKEAR 12 1 E5RJD8;O75347;E5RIW3;E5RHG6;E5RIX8 E5RJD8 TBCA Tubulin-specific chaperone A 0 158.42 0.00025853 0 309440 177820 228410 229830 203520 195420 304510 164460 209860 FALSE TRUE 290072.7028 190985.9778 233827.9931 235727.8269 187536.3602 251834.5816 258851.5524 184993.193 174833.0103 1.659141499 1.092390834 1.337436178 1.348302741 1.072659905 1.440429249 1.480564523 1.058113641 1 17.41561808 1.113742171 6.617425189 1.004098706 1.32391587 0.365954564 0.172706777 0.233285936 11.78826448 0.157538202 0.03957507 12.99397933 -1.113742171 0.319817164 DLEEALEMGVDWSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLEEALEMGVDWSLR 15 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ; 149.26 7.88E-06 16706000 32951 35390 39194 35107 44382 34931 40373 30766 42521 FALSE TRUE 30888.65573 38010.31242 40123.70019 36007.90506 40896.41675 45015.01264 34319.44345 34607.20282 35423.9704 0.871970459 1.073011071 1.132670893 1.016484167 1.154484274 1.270750064 0.968819787 0.976943082 1 15.1124383 1.602674028 25 0.979644007 1.092347675 0.189800894 0.101406896 0.756055194 3624.5404 0.050533467 0.024489096 40.05659489 -1.602674028 0.112703668 DLEEDHACIPIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLEEDHACIPIK 12 0 P13639 P13639 EEF2 Elongation factor 2 0 ;; 132.32 0.00018301 2382600000 5599060 4532010 4937910 4438510 5062330 3869930 6126580 4341160 4991820 FALSE TRUE 5248624.829 4867564.736 5055039.557 4552409.681 4664755.022 4987115.968 5207956.205 4883163.382 4158652.994 1.262097327 1.170466674 1.215547333 1.094683708 1.121698547 1.199214259 1.252318049 1.174217563 1 21.98768488 -2.325077648 2.069173456 0.114399548 1.188188099 0.560956643 0.051767088 1404238.145 156410.9584 5827066.221 0.012776249 0.004730667 2.325077648 1.073788552 DLEEDHACIPIKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DLEEDHACIPIKK 13 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;; 188.29 4.05E-06 27853400000 39648000 25514700 32743000 30069100 32258800 24980800 44484200 27861000 42060500 FALSE TRUE 37166502.45 27403834.94 33519679.42 30840724.01 29725323.97 32192351.43 37814207.18 31339507.18 35040330.83 1.060677841 0.782065531 0.956602824 0.880149339 0.848317447 0.918722817 1.07916239 0.894383884 1 25.06251306 1.97648933 21.62846782 0.999719214 0.893609728 0.17032981 0.084301967 175.6940341 161626.9446 0.031140442 0.020291319 94.730391 -1.97648933 -0.106109486 DLEEHWQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLEEHWQR 8 0 O60447-2;O60447;A0A1B0GUF4 O60447-2 EVI5 Ecotropic viral integration site 5 protein homolog 0 88.948 0.014253 115860000 100860 137670 102410 101250 184580 99560 117380 115780 339830 FALSE TRUE 94547.35264 147863.23 104839.2136 103848.2464 170083.8314 128301.3558 99779.9587 130235.3879 283110.1776 0.333959568 0.522281577 0.370312415 0.366812127 0.600769046 0.453185247 0.352442147 0.460016623 1 18.11100409 -1.767029769 1.88413109 1.206386718 0.432932425 0.822314232 0.082907873 142488.5804 69026.68157 135220.9638 0.020910883 0.017098981 1.767029769 -0.773454293 DLEELEVILRD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLEELEVILRD 11 1 Q96TC7;H0YMB1;Q96TC7-2 Q96TC7 RMDN3 Regulator of microtubule dynamics protein 3 0 111.65 0.033449 3972600 17703 14767 14793 13447 18922 13212 18738 14030 19668 FALSE TRUE 16595.00083 15860.36405 15143.89695 13792.07279 17435.94245 17026.08992 15928.41086 15781.67638 16385.28374 1.012799113 0.967963955 0.924237699 0.841735365 1.064122094 1.039108641 0.972116877 0.963161617 1 14.00011304 2.714329233 24.99972649 1.005804594 0.939822938 0.321996601 0.05107575 1039.368467 1072324.054 0.016696316 0.015747712 517.9993719 -2.714329233 -0.065981656 DLEEWNQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLEEWNQR 8 0 P09497-2;P09497 P09497-2 CLTB Clathrin light chain B 0 ;;; 189.78 0.00044184 3693590000 2244390 2249810 2302110 2291670 2396840 1949080 2705910 1924070 2894380 FALSE TRUE 2103917.636 2416388.273 2356717.136 2350478.132 2208601.855 2511747.755 2300183.916 2164294.375 2411289.28 0.872528093 1.002114634 0.977368065 0.97478065 0.915942303 1.041661727 0.953922839 0.897567286 1 21.20137331 4.749454242 24.3683277 0.972483194 0.872528011 0.352210645 0.041638337 1226.155231 2742753.513 0.009173931 0.134605771 56163.5101 -4.749454242 -0.099955184 DLEFTIYDDDDVSPFLEGLEERPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DLEFTIYDDDDVSPFLEGLEERPQR 25 1 P25786;P25786-2;F5GX11 P25786 PSMA1 Proteasome subunit alpha type-1 0 ;;;;;;; 347.32 7.01E-103 1431382000 264745 271364 259543 243707 289647 221086 301389 253447 284027 FALSE TRUE 248175.083 291456.0729 265699.4825 249960.9342 266899.293 284909.9392 256198.5174 285090.4159 236621.0588 1.04882923 1.231741901 1.122890261 1.056376535 1.12796086 1.20407685 1.0827376 1.204839575 1 17.85221895 -0.996888765 4.47140879 0.999997191 1.138876433 0.310462687 0.062952569 2.64E-06 5.91E-07 0.056355979 0.013282797 0.100718961 0.996888765 0.138879242 DLEFTIYDDDDVSPFLEGLEERPQRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLEFTIYDDDDVSPFLEGLEERPQRK 26 2 P25786;P25786-2;F5GX11 P25786 PSMA1 Proteasome subunit alpha type-1 0 ;; 242.16 2.13E-45 271907000 158935 207394 169628 170713 272924 112070 241997 156476 543370 FALSE TRUE 148987.5421 222749.6676 173651.6563 175093.7846 251489.65 144422.7897 205711.7964 176012.373 452678.0367 0.329124742 0.492070853 0.383609635 0.386795405 0.555559646 0.319040859 0.454432908 0.388824636 1 18.78812579 -1.428902478 3.025697013 1.010843148 0.419789335 0.867602847 0.071945257 22812537.67 27939191.06 2123896.853 0.016130587 0.037247534 1.428902478 -0.591053813 DLEGENIEIVFAKPPDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLEGENIEIVFAKPPDQK 18 1 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ; 144.72 8.78E-08 356279000 1840210 1223000 1382600 1430840 1513620 1087460 1897330 1260320 1640450 FALSE TRUE 1725034.541 1313552.193 1415395.925 1467557.777 1394746.391 1401392.049 1612842.98 1417673.726 1366648.297 1.262237362 0.961148669 1.035669475 1.073837197 1.020559857 1.025422599 1.180144872 1.037336182 1 20.38221059 DLEGSDIDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLEGSDIDTR 10 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;;; 220.39 1.36E-08 5233290000 6761500 7351600 7191800 7278000 7690200 6102600 9029700 7083600 7504100 FALSE TRUE 6338309.785 7895920.113 7362392.892 7464765.802 7086242.713 7864321.553 7675780.313 7968003.053 6251617.232 1.01386722 1.263020403 1.17767813 1.194053558 1.133505531 1.257965941 1.227807146 1.274550689 1 22.57579802 4.749973916 24.55200509 1.203789566 1.013867076 0.309908312 0.081154165 1383.595798 2976284.421 0.016803296 0.256400738 56230.75522 -4.749973916 -0.18992249 DLEGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLEGYR 6 0 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4;Q6N069;Q6N069-5;Q6N069-4;Q6N069-3;Q6N069-2 A0A0B4J1W3;Q6N069 NAA15;NAA16 "N-alpha-acetyltransferase 15, NatA auxiliary subunit;N-alpha-acetyltransferase 16, NatA auxiliary subunit" 0 ; 122.15 0.045 494920000 882010 1055220 986870 1018120 1078860 844270 1082600 884520 933370 FALSE TRUE 826806.5685 1133349.587 1010279.022 1044246.683 994130.6875 1087997.043 920274.1804 994954.2691 777584.5172 1.063301224 1.457525917 1.299253007 1.342936568 1.278485702 1.399201012 1.183503735 1.279544856 1 19.56863997 0.476376827 0.71850604 0.996206346 1.322433539 0.397557773 0.109624592 1.52282005 1.254118897 0.110317051 0.035620094 2.994862079 -0.476376827 0.326227193 DLEHLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLEHLSK 7 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;; 113.89 0.0060283 783670000 1585890 2232820 2315080 2337680 2088810 2040110 3235160 2277930 1630705 FALSE TRUE 1486631.976 2398140.316 2369994.791 2397668.826 1924763.288 2629056.639 2750077.792 2562334.575 1358529.801 1.094294711 1.76524675 1.744529115 1.764899692 1.416798724 1.935221912 2.024304355 1.886108478 1 20.37361478 4.739387131 23.41412505 1.750608846 1.094294265 0.265647891 0.298635727 32.70948198 926200.0747 0.064273165 0.387362413 54876.59183 -4.739387131 -0.656314581 DLEIERPILGQNDNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DLEIERPILGQNDNK 15 1 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 0 ;;;;; 268.2 1.30E-25 5903590000 6363700 4500950 5442390 4980540 5907730 4093968 6898320 5184830 8221700 FALSE TRUE 5965407.377 4834205.021 5571486.061 5108349.088 5443760.716 5275830.102 5863980.957 5832167.439 6849445.156 0.870932936 0.705780528 0.813421516 0.745804802 0.79477397 0.770256566 0.85612496 0.851480274 1 22.7075557 0.852773137 0.780049573 0.99991495 0.773440552 0.683276823 0.045529506 0.417386494 0.534038212 0.039175453 0.014219163 7.124807526 -0.852773137 -0.226474399 DLEIERPMPGTHTVTLQCPALLVVGDSSPAVDAVVECNSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLEIERPMPGTHTVTLQCPALLVVGDSSPAVDAVVECNSK 40 1 Q92597;Q92597-3;Q92597-2 Q92597 NDRG1 Protein NDRG1 0 ; 273.81 5.30E-77 259560000 47831 46190 43803 46804 46175 24173.2 52169 39652 31827 FALSE TRUE 44837.34309 49609.95566 44842.02785 48005.06988 42548.60176 31151.61042 44346.74276 44602.63948 26514.86809 1.691026444 1.871024042 1.691203128 1.810496274 1.604707277 1.174873294 1.672523605 1.68217467 1 14.69451395 2.477263889 24.99945057 1.446065042 1.764656757 0.408465295 0.2118129 5.530410207 969625.2635 0.067254837 0.056824623 300.0985444 -2.477263889 0.318591715 DLEKPFLLPVEAVYSVPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLEKPFLLPVEAVYSVPGR 19 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ; 218.07 3.15E-19 2165300000 3612300 3060200 2994100 2676200 4231700 2927300 3332400 3310900 5784700 FALSE TRUE 3386212.591 3286780.392 3065121.466 2744875.823 3899359.352 3772363.989 2832737.556 3724273.153 4819196.199 0.702650909 0.682018382 0.636023382 0.569571296 0.80913065 0.78277867 0.587802911 0.772799654 1 22.20036111 -4.999999837 0.291200424 3.508058939 0.664396614 0.610482061 0.078266477 166.8977277 1.569631725 254.1979903 0.080788636 1.00E-05 4.999999837 -2.843662325 DLELALS(ph)PIHNSSALPTTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLELALSPIHNSSALPTTGR 20 0 A0A087WUU7;Q96GX5-2;Q96GX5-3;Q96GX5 A0A087WUU7 MASTL Serine/threonine-protein kinase greatwall 1 DLELALS(1)PIHNSSALPTTGR 191.42 9.47E-18 174110000 67202 132590 112460 106800 110230 107610 148460 125420 135600 TRUE FALSE 62995.94678 142407.1016 115127.6043 109540.6688 101572.9804 138675.2601 126199.8012 141078.9631 112967.484 0.557646719 1.260602578 1.019121611 0.969665473 0.899134661 1.227567927 1.117133858 1.248845757 1 16.78554805 2.232796058 24.99836806 1.156232945 0.996697779 0.203141728 0.186418602 268.0562231 1162430.607 0.065140595 0.049410163 170.921249 -2.232796058 -0.159535166 DLELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLELER 6 0 A0A494BX66;A0A590UJT6;Q2TAC2-2;Q2TAC2 A0A494BX66 CCDC57 Coiled-coil domain-containing protein 57 0 ; 128.38 0.038736 1054920000 2554200 2409400 2450500 2569100 2492100 1750980 2801900 2292900 1465110 FALSE TRUE 2394337.181 2587794.483 2508627.017 2635027.455 2296380.519 2256459.501 2381781.107 2579173.612 1220573.676 1.961649041 2.12014607 2.055285204 2.158843425 1.881394433 1.848687667 1.951362014 2.113083104 1 20.21912795 -1.969798528 0.413928734 9.65E-17 2.047227001 0.895461972 0.108010764 14.15763746 0.926327628 13.73329167 0.064763323 0.010720165 1.969798528 2.047227001 DLELPLS(ph)PSLLGGPGPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLELPLSPSLLGGPGPER 18 0 P19419 P19419 ELK1 ETS domain-containing protein Elk-1 1 DLELPLS(0.916)PS(0.084)LLGGPGPER;DLELPLS(0.992)PS(0.008)LLGGPGPER 139.04 7.64E-07 31947000 50670 51472 58390 65701 71845 45856 53585 44176 51781 TRUE FALSE 47498.65515 55283.04044 59775.03837 67386.99889 66202.58351 59093.88279 45550.42671 49691.47084 43138.41658 1.101075536 1.281526881 1.385656756 1.562111089 1.534654926 1.369866756 1.055913274 1.151907622 1 15.3966856 1.748660565 5.888547603 1.079167975 1.377711545 0.538371845 0.132067655 0.133989944 12.0714228 0.068629121 0.036122828 56.06096445 -1.748660565 0.29854357 DLEPHSFGGLLEGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLEPHSFGGLLEGIR 15 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 0 117 0.0013728 0 29294 38187 31344 28831 35428 21946 33856 32455 50308 FALSE TRUE 27460.54083 41014.40521 32087.49448 29570.85227 32645.62779 28281.45394 28779.6071 36507.07819 41911.2698 0.655206606 0.978600873 0.7656054 0.705558491 0.778922422 0.674793536 0.686679436 0.871056362 1 15.35505061 0.986260264 6.218742232 0.999929224 0.765875296 0.442668736 0.091838653 0.146507228 29.83479437 0.094899416 0.023848273 9.68858299 -0.986260264 -0.234053928 DLES(ph)PCQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 70.488 0.033667 190300000 70930 75057 67971 71525 77746 66364 74835 67699 87571 TRUE FALSE 66490.61791 80614.29838 69583.30422 73360.45259 71640.14277 85522.20947 63614.18648 76151.36917 72954.83437 0.911394269 1.104989122 0.953786063 1.005559854 0.981979377 1.172262403 0.871966704 1.043815257 1 16.15471596 DLESAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLESAEER 8 0 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 98.629 0.017184 946030000 1138080 1609480 1474960 1547090 1564520 1259000 1541680 1222670 1404530 FALSE TRUE 1066849.604 1728647.574 1509946.748 1586790.949 1441648.91 1622452.862 1310519.396 1375323.041 1170104.869 0.911755546 1.477344142 1.290437111 1.356110029 1.232068123 1.386587565 1.12000166 1.175384427 1 20.1582064 1.244946047 1.165685106 1.014204182 1.30246577 0.212742105 0.154507477 0.533240424 1.463850039 0.129358534 0.042208805 17.57705239 -1.244946047 0.288261588 DLESAEERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLESAEERR 9 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 97.277 0.010903 336530000 234348 248132 235444 285455 327589 237882 466390 283751 438540 FALSE TRUE 219680.577 266503.9515 241028.8429 292780.2586 301861.4814 306554.6717 396459.1493 319177.937 365344.8409 0.601296508 0.729458642 0.659729702 0.801380575 0.826237153 0.839083073 1.08516422 0.873634718 1 18.47889931 2.49555389 0.928807159 0.999225519 0.669559145 0.75993515 0.070797536 0.244804274 0.426636593 0.043953815 0.03190185 313.0068845 -2.49555389 -0.329666374 DLESCS(ph)DDDNQGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLESCSDDDNQGSK 14 0 A0A0A0MRK1;E9PAV9;Q5T3I0;Q5T3I0-3;F8W895 A0A0A0MRK1 GPATCH4 G patch domain-containing protein 4 1 DLESCS(1)DDDNQGSK;DLESCS(1)DDDNQGSK 423.17 1.03E-152 477590000 1646120 839450 1136030 1020950 978360 987230 1599000 854050 1015370 TRUE FALSE 1543092.288 901603.7514 1162977.168 1047149.305 901523.5521 1272227.275 1359244.794 960680.0225 845898.1875 1.824205691 1.065853746 1.37484296 1.237914114 1.065758936 1.503995745 1.606865713 1.135692258 1 19.69012451 DLESLFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLESLFHR 8 0 Q03252 Q03252 LMNB2 Lamin-B2 0 152.63 0.00045401 122400000 63748 89277 78458 74559 90554 56210 91346 88849 78112 FALSE TRUE 59758.12647 95887.16197 80319.06081 76472.31017 83442.25412 72436.91451 77649.51531 99941.99323 65074.60258 0.918301828 1.473495929 1.234261258 1.175148324 1.282255301 1.113136487 1.19323841 1.535806433 1 15.98980698 3.494369023 23.77223518 1.218467506 1.27488873 0 0.192269385 1303.610065 1796725.793 0.046895697 0.071952862 3121.540851 -3.494369023 0.056421223 DLESLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLESLR 6 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;; 160.17 0.020687 1347960000 1883950 2329990 2053920 2074510 2341060 1558160 2188990 1962220 2096580 FALSE TRUE 1766036.932 2502504.884 2102639.952 2127745.439 2157202.591 2007975.497 1860771.271 2207207.486 1746647.254 1.011101085 1.432747728 1.203814879 1.218188409 1.235053378 1.14961707 1.065338904 1.263682453 1 20.73615685 1.322016529 0.39149198 1.004085687 1.272373673 0.169202594 0.117967767 1.440032146 0.668949619 0.151372256 0.10344892 20.99019771 -1.322016529 0.268287986 DLEWVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLEWVER 7 0 H7C2Q8;Q99848 H7C2Q8 EBNA1BP2 Probable rRNA-processing protein EBP2 0 122.13 0.010169 337670000 334940 323330 293720 308080 293260 246480 349850 278780 346550 FALSE TRUE 313976.7033 347269.6896 300687.1771 315985.8544 270228.5426 317634.7747 297393.2403 313586.2967 288708.5662 1.087521259 1.202838191 1.04149032 1.094480356 0.935990733 1.100191722 1.03008111 1.086169007 1 18.13925439 3.803935843 3.795453119 1.042727069 1.148793937 0.37375422 0.05576952 0.201794258 5.601882017 0.01305707 0.024475479 6367.014555 -3.803935843 0.106066868 DLFAFQES(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLFAFQESPPR 11 0 E7EX48;P51957-3;P51957-2;P51957 E7EX48 NEK4 Serine/threonine-protein kinase Nek4 1 DLFAFQES(1)PPR;DLFAFQES(1)PPR 162.48 2.63E-05 109082000 162042 174111 184773 170644 181695 171363 220190 187146 226510 TRUE FALSE 151900.0805 187002.3596 189155.9028 175023.0139 167425.4076 220832.7163 187174.5536 210511.5901 188704.0177 0.80496474 0.990982396 1.002394677 0.927500199 0.887238172 1.170259748 0.991894905 1.115564961 1 17.52576561 2.253923407 24.99991163 1.064144741 0.943039636 0.470264557 0.075631087 239.1127392 389108.1773 0.024949578 0.020803707 179.4417132 -2.253923407 -0.121105105 DLFDFSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DLFDFSTR 8 0 U3KQC1;A0A0A0MQU0;Q9BV38;K7EIR0 U3KQC1 WDR18 WD repeat-containing protein 18 0 ;;;;;; 174.52 0.00063155 474362400 1503468 1691425 1693007 1677535 1739649 1457932 1953341 1494366 1836459 FALSE TRUE 1409368.622 1816659.867 1733165.926 1720583.388 1603023.985 1878813.301 1660455.651 1680940.885 1529942.129 0.921190805 1.187404303 1.132831035 1.124606843 1.047767726 1.228028999 1.085306182 1.09869573 1 20.54504565 0.72465418 1.905685951 1.000234939 1.118316794 0.11639102 0.082913443 1.90581854 10.37074343 0.0706857 0.019682062 5.304618796 -0.72465418 0.118081855 DLFDLILTCEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLFDLILTCEER 12 0 Q9NP77 Q9NP77 SSU72 RNA polymerase II subunit A C-terminal domain phosphatase SSU72 0 ; 149.23 0.00014176 30501000 58741 58679 61831 58456 75922 56633 76255 64877 74037 FALSE TRUE 55064.50567 63023.65422 63297.66052 59956.07993 69959.39237 72982.02774 64821.27067 72977.03626 61679.7464 0.892748574 1.021788478 1.026230881 0.972054579 1.134236057 1.183241372 1.050932834 1.183160446 1 15.91250921 2.738141958 24.99981698 1.114272573 0.993473643 0.489141081 0.06620675 33.04441796 1973181.131 0.019148339 0.019113044 547.1947951 -2.738141958 -0.12079893 DLFDLNS(ph)S(ph)EEDDTEGFSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLFDLNSSEEDDTEGFSER 19 0 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 2 DLFDLNS(1)S(1)EEDDTEGFSER;DLFDLNS(1)S(1)EEDDTEGFSER;DLFDLNS(1)S(1)EEDDTEGFSER;DLFDLNS(1)S(1)EEDDTEGFSER 223.82 3.09E-19 125760000 527046 483225 489739 480348 473409 389407 578438 403972 472068 TRUE FALSE 494059.1317 519003.4818 501355.8404 492674.5429 436229.3668 501822.4794 491706.5919 454408.7935 393276.8011 1.256263096 1.319690051 1.274816717 1.252742449 1.109217135 1.276003258 1.250281203 1.155442661 1 18.58518556 -4.999999999 0.145352792 0.103550988 1.333045869 0.697503891 0.052948025 75.71526066 0.663766839 19.4908793 0.29228798 1.00E-05 4.999999999 1.229494881 DLFDMKPFEDALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLFDMKPFEDALR 13 1 P29353-2;P29353-7;P29353;P29353-6;H0Y539;X6R6D0;P29353-5;P29353-3 P29353-2 SHC1 SHC-transforming protein 1 0 79.004 0.019781 49595000 144240 134400 135160 133040 159460 93932 144670 133550 134580 FALSE TRUE 135212.2759 144351.1158 138366.059 136454.0316 146936.6548 121048.6435 122978.0766 150224.0115 112117.7286 1.205984795 1.2874959 1.234114005 1.217060258 1.310556829 1.079656581 1.096865573 1.339877407 1 16.7746549 2.236481518 24.99999577 1.130799348 1.252160243 0.311675866 0.090023352 64.34523745 773698.5767 0.029905794 0.023187805 172.3778733 -2.236481518 0.121360895 DLFDPIIEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DLFDPIIEDR 10 0 P12277;G3V4N7;G3V461 P12277 CKB Creatine kinase B-type 0 ;;;;;; 172.59 8.54E-06 844300000 539696 576045 569861 612520 463577 445715 660380 396408 272839 FALSE TRUE 505917.3907 618695.9712 583378.372 628238.3002 427169.5324 574385.6849 561362.1497 445900.4114 227300.4083 2.225765429 2.721930752 2.56655224 2.763911886 1.879317048 2.526989235 2.469692659 1.961722879 1 17.79424075 0.23096324 0.586885411 0.920614427 2.545784404 0.75048748 0.26292971 1.310861268 0.630261575 0.465730939 0.105423096 1.702014438 -0.23096324 1.625169977 DLFDYS(ph)PPLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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;DLFDYS(1)PPLHK;DLFDYS(1)PPLHK;DLFDY(0.001)S(0.999)PPLHK 138.31 3.88E-05 3631715000 4457390 3254400 3801890 3492890 3555690 3083510 4637570 3267830 4487330 TRUE FALSE 4178409.917 3495359.162 3892072.626 3582523.471 3276440.45 3973669.28 3942209.432 3675825.769 3738365.634 1.117710338 0.934996601 1.041116094 0.958312755 0.876436596 1.062942919 1.054527518 0.9832708 1 21.83397625 DLFEDELVPLFEK ddPTM_SK-BR-3_Pertuzumab_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 ;;; 248.42 5.01E-17 126249000 612876 512195 547724 509731 534929 393491 703926 498558 783409 FALSE TRUE 574517.1852 550118.4507 560716.2719 522811.5604 492917.8341 507085.4639 598378.8312 560804.0638 652652.9769 0.880279728 0.842895796 0.859133861 0.801055965 0.755252564 0.776960317 0.916840729 0.859268376 1 19.31595657 0.862849753 1.138011815 0.996726645 0.8279686 0.574728971 0.04591661 0.508508931 1.289344123 0.044865693 0.014093933 7.292051939 -0.862849753 -0.168758045 DLFEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLFEQR 6 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;E9PN68;E9PLN2;E9PNT0;E9PLH1 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 ; 102.8 0.08196 1381420000 1987910 2370500 2429400 2237400 2452100 2194000 2645200 1808240 2189450 FALSE TRUE 1863490.262 2546014.287 2487026.515 2294815.472 2259521.957 2827372.183 2248576.817 2034002.744 1824016.651 1.021641037 1.395828424 1.363488932 1.258111033 1.238761695 1.550080249 1.232761124 1.115122904 1 20.79868747 1.187250895 2.725206609 1.013182912 1.321194802 0.360897733 0.135068852 0.241679233 3.139861941 0.114941368 0.031984879 15.390435 -1.187250895 0.30801189 DLFNGLDS(ph)EEEKDGEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLFNGLDSEEEKDGEEK 17 1 Q96S90;Q96S90-2 Q96S90 LYSMD1 LysM and putative peptidoglycan-binding domain-containing protein 1 1 DLFNGLDS(1)EEEKDGEEK 83.063 0.0035424 38628000 105950 35122 52667 49193 51635 36922 67932 42985 58036 TRUE FALSE 99318.77863 37722.46942 53916.28611 50455.37566 47579.79539 47580.78202 57746.22725 48351.77187 48349.41667 2.054187733 0.780205265 1.115138296 1.043557071 0.984082098 0.984102504 1.194352098 1.000048712 1 15.56121086 4.746793758 24.99304248 1.020586961 2.054188246 0.905176246 0.10591124 308.9242717 937768.89 0.025902767 0.292603729 55820.50455 -4.746793758 1.033601285 DLFPYEESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DLFPYEESK 9 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;;;;; 169.44 0.00013602 1066955000 3218770 2312040 2644140 2542270 2722610 2033310 3315040 2367930 3109210 FALSE TRUE 3017312.931 2483225.847 2706860.249 2607508.952 2508787.193 2620293.589 2817980.527 2663571.273 2590262.765 1.164867508 0.958677197 1.045013767 1.006658084 0.968545442 1.011593737 1.087912997 1.028301572 1 21.30466703 DLFPYEESKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLFPYEESKEK 11 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 74.46 0.037176 125870000 163230 161610 150020 163160 237770 95111 159910 132120 460290 FALSE TRUE 153013.7257 173575.7726 153578.5452 167346.9618 219096.5033 122568.0017 135932.98 148615.4728 383464.6254 0.399029573 0.45265133 0.400502511 0.436407822 0.571360404 0.319633138 0.354486362 0.387559798 1 18.54873397 -1.355438172 3.218471261 1.004913945 0.413827448 0.882905132 0.066928032 29194720.02 39085706.11 1354625.416 0.017571703 0.044112516 1.355438172 -0.591086497 DLFQFNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLFQFNK 7 0 J3QRV5;Q6P1M3;Q6P1M3-2;J3KRE1;J3QLV4;J3QRZ8;J3QL58;J3QSA6;Q6P1M3-3 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 0 83.753 0.051295 28933000 135160 118130 112650 106310 142500 97800 119830 96596 137890 FALSE TRUE 126700.5769 126876.4681 115322.1112 109038.0946 131308.6248 126033.2723 101862.6039 108656.2232 114875.2682 1.102940423 1.104471573 1.00388981 0.949186855 1.143053913 1.097131474 0.886723535 0.945862629 1 16.8097087 1.745045105 17.1760299 0.937527945 1.062282431 0.467612968 0.061396511 0.149593905 388.2202158 0.028514526 0.015773074 55.5961995 -1.745045105 0.124754486 DLFSLDSEDPSPAS(ph)PPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DLFSLDSEDPSPASPPLR 18 0 Q9BTK6;H3BTX0 Q9BTK6 PAGR1 PAXIP1-associated glutamate-rich protein 1 1 DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPS(0.002)PAS(0.998)PPLR;DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPS(0.091)PAS(0.909)PPLR 319.55 1.75E-61 2472928000 891871 901231 959026 946525 1017038 816674 1089757 864372 1082146 TRUE FALSE 836050.3861 967959.081 981774.5496 970814.434 937163.938 1052434.526 926358.0547 972290.7469 901528.8417 0.927369539 1.073686205 1.089010694 1.07685344 1.039527406 1.167388638 1.02754123 1.078491005 1 19.78201412 4.73855774 12.40044234 1.073776029 0.927285739 0.498415995 0.044448027 0.043125537 752.0311183 0.009199849 0.052959598 54771.89162 -4.73855774 -0.14649029 DLGDLIEATEFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLGDLIEATEFDR 13 0 E5RHM7;E5RIH5;Q6NXR4 E5RHM7 TTI2 TELO2-interacting protein 2 0 ;;; 141.95 9.09E-05 68397000 99806 112843 106157 99638 113093 92291 123126 104522 123032 FALSE TRUE 93559.32062 121198.0131 108675.0942 102194.8798 104211.132 118933.9135 104664.3993 117571.8018 102497.1644 0.912799112 1.182452352 1.060274153 0.9970508 1.016722098 1.160362964 1.021144341 1.147073702 1 16.64522447 DLGEELEALKTELEDTLDSTAAQQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLGEELEALKTELEDTLDSTAAQQELR 27 1 P35579 P35579 MYH9 Myosin-9 0 165.87 8.48E-12 747590000 100400 69992 83380 88300 84751 56097 104710 73114 103910 FALSE TRUE 94116.14322 75174.28051 85357.81297 90565.92749 78094.99833 72291.29324 89009.70758 82242.44384 86566.74972 1.087208929 0.868396708 0.986034629 1.04619762 0.902136196 0.835093075 1.02822051 0.950046572 1 16.40152537 1.624680293 24.99999997 0.991859294 0.94821877 0.047974398 0.078015745 2.555000874 3789.852953 0.034412034 0.019017908 42.13861849 -1.624680293 -0.043640524 DLGEELEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLGEELEALR 10 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ; 153.05 3.94E-05 78001000 132274 116530 127841 125370 116615 112010 156183 127601 92173 FALSE TRUE 123995.2065 125158.0024 130873.4489 128587.2065 107456.5283 144345.4687 132764.8091 143532.2657 76788.73084 1.614757857 1.629900652 1.704331449 1.674558298 1.399378882 1.879774116 1.728962149 1.869183983 1 16.22860698 4.400390392 4.522157573 1.656240248 1.617873369 0 0.258174936 2.510298346 93.42459129 0.055281343 0.170219774 25141.45408 -4.400390392 -0.038366879 DLGEELEALRGELEDTLDSTNAQQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLGEELEALRGELEDTLDSTNAQQELR 27 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ;; 226.4 1.32E-34 416812000 178332 198646 174512 197439 227309 131532 208379 176764 223764 FALSE TRUE 167170.5185 213353.9565 178651.5071 202505.619 209457.0681 169503.1532 177134.5034 198833.3745 186416.3428 0.896758921 1.144502426 0.958346808 1.086308292 1.123598204 0.909271959 0.95020909 1.066609137 1 17.50816882 2.231796394 24.99897928 0.972030678 1.04651818 0.110482497 0.082643647 284.0122691 1049633.626 0.028427947 0.02146852 170.528273 -2.231796394 0.074487502 DLGHAQMVVDELFSSHSDLDSDSELDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLGHAQMVVDELFSSHSDLDSDSELDR 27 0 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 0 150.95 5.19E-08 29306000 10792 21283 13750 14415 19084 13447 20561 15199 20429 FALSE TRUE 10116.54798 22858.81546 14076.15649 14784.9133 17585.21962 17328.93061 17478.06893 17096.62861 17019.26792 0.594417341 1.343113909 0.827071796 0.868716173 1.033253586 1.01819483 1.02695774 1.004545477 1 14.05488136 DLGHPVEEEDELES(ph)GDQEDEDDESEDPGKDLDHI ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DLGHPVEEEDELESGDQEDEDDESEDPGKDLDHI 34 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 1 DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI 451.17 7.04E-232 3399600000 1526965 1064189 1279708 1349890 1217013 887280 1547392 1016205 1176210 TRUE FALSE 1431394.986 1142982.661 1310063.278 1384530.463 1121433.708 1143423.332 1315374.935 1143080.431 979892.9524 1.460766692 1.16643625 1.336945301 1.412940525 1.144445121 1.166885964 1.342365951 1.166536027 1 19.90226463 -4.756589243 0.172965571 3.25E-11 1.337686158 0.459300173 0.104351899 118.1255123 1.211749514 40.54825761 0.34729136 1.75E-05 4.756589243 1.337686158 DLGLSESGEDVNAAILDESGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLGLSESGEDVNAAILDESGKK 22 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 241.76 1.78E-30 295480000 350400 231320 284070 266870 279410 181648 358770 228870 284260 FALSE TRUE 328469.0895 248447.1735 290808.2745 273718.336 257466.2657 234086.8288 304975.7692 257444.9233 236815.1696 1.387027233 1.049118491 1.227996817 1.155831092 1.087203434 0.988479029 1.287821932 1.087113312 1 17.85340197 6.909739026 0.017205046 2.49E-06 2.504642896 0.246738366 0.111017383 6405.618969 10.23674848 601.4575993 918.7510483 8123422.203 -6.909739026 2.504640406 DLGMMIHEQGDVIDSIEANVENAEVHVQQANQQLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLGMMIHEQGDVIDSIEANVENAEVHVQQANQQLSR 36 0 O15400-2;O15400 O15400-2 STX7 Syntaxin-7 0 268.65 3.67E-63 20567000 30782 32524 31856 34458 40120 29526 42681 33422 34600 FALSE TRUE 28855.40957 34932.1108 32611.63936 35342.25062 36969.13704 38049.67689 36281.38028 37594.81027 28825.03648 1.001053705 1.211867011 1.131365068 1.226095608 1.282535655 1.320021812 1.258675954 1.304241551 1 14.81503481 6.069840371 0.641813252 1.245594952 1.06E-12 0.282758185 0.097865695 17.86451004 1.472802818 0.035742887 23.98355846 1174465.789 -6.069840371 -1.245594952 DLGNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLGNLR 6 0 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 104.94 0.077699 187550000 208990 241900 224790 214090 266990 197370 246830 245250 279620 FALSE TRUE 195909.689 259810.5277 230122.125 219583.9119 246021.6824 254347.515 209820.133 275870.0024 232949.6156 0.840995974 1.115307819 0.987862222 0.942624058 1.056115426 1.091856341 0.900710364 1.184247511 1 17.82965842 2.678520764 24.99656619 1.032686059 0.998325899 0.090385792 0.098407637 1138.346742 473929.3288 0.030195541 0.02846863 477.0026197 -2.678520764 -0.03436016 DLGQSNS(ph)DLDMPFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLGQSNSDLDMPFAK 15 0 F5GZP6;Q86W92-3;Q86W92-4;Q86W92;Q86W92-2 F5GZP6;Q86W92-2 PPFIBP1 Liprin-beta-1 1 DLGQS(0.443)NS(0.557)DLDMPFAK 100.56 0.0022133 14185000 18824 11161 12376 12403 15489 11648 17117 13503 20184 TRUE FALSE 17645.83944 11987.37205 12669.56456 12721.28198 14272.55642 15010.58851 14550.46476 15188.87927 16815.16001 1.049400626 0.712890751 0.753460839 0.756536481 0.848790997 0.892681872 0.865318246 0.903284849 1 14.03747489 1.355105494 0.709173674 0.99132831 0.794050643 0.214971627 0.094353995 0.753559616 0.860915111 0.085516682 0.036798014 22.65194477 -1.355105494 -0.197277667 DLGSTEDGDGTDDFLT(ph)DKEDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLGSTEDGDGTDDFLTDKEDEK 22 1 Q15527 Q15527 SURF2 Surfeit locus protein 2 1 DLGSTEDGDGTDDFLT(1)DKEDEK 308.65 6.34E-67 69282000 835990 263290 449320 448200 414570 353050 596900 295460 446100 TRUE FALSE 783666.8782 282784.2656 459978.0826 459701.5708 382011.3445 454969.8037 507400.3863 332348.8314 371643.0281 2.108654862 0.760902921 1.23768791 1.236943884 1.02789859 1.224211863 1.365289668 0.894268979 1 18.50355802 4.751672317 24.93753971 1.1173784 2.108655523 0.752222341 0.182659573 1114.232809 2119154.45 0.043876949 0.829380886 56451.08802 -4.751672317 0.991277123 DLGTESQIFISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DLGTESQIFISR 12 0 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;;; 210.98 8.66E-08 1041540000 1187019 1405112 1355122 1288823 1470656 1058080 1415195 1265991 1526623 FALSE TRUE 1112725.6 1509147.954 1387266.134 1321896.38 1355156.61 1363530.52 1202999.648 1424052.763 1271819.759 0.87490825 1.186605212 1.090772591 1.039373992 1.065525677 1.072109872 0.945888471 1.119696996 1 20.2784628 1.942208785 24.97909483 1.014136799 1.074195944 0 0.088137893 654.1843718 282756.2171 0.034202775 0.022077349 87.54045216 -1.942208785 0.060059145 DLHILPPPLIPT(ph)PPPDDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLHILPPPLIPTPPPDDPR 19 0 Q9NRS6;E9PK26;E9PMW6;Q9NRS6-2 Q9NRS6 SNX15 Sorting nexin-15 1 DLHILPPPLIPT(1)PPPDDPR;DLHILPPPLIPT(1)PPPDDPR;DLHILPPPLIPT(1)PPPDDPR;DLHILPPPLIPT(1)PPPDDPR 93.583 0.006377 167279000 209287 217700 217751 221206 268247 225966 276568 225675 329912 TRUE FALSE 196188.1003 233818.7345 222916.1565 226882.5205 247179.9627 291198.7159 235099.1959 253851.0205 274847.5559 0.713806967 0.850721535 0.811053807 0.825484948 0.899334767 1.059491743 0.85538034 0.923606614 1 18.06827212 2.668549597 3.469655536 0.944857583 0.809273095 0.578226072 0.06335964 0.194724064 4.613854976 0.020226724 0.019306921 466.1756632 -2.668549597 -0.135584488 DLHSGVYGGSVHEAMTDLILLMGSLVDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLHSGVYGGSVHEAMTDLILLMGSLVDKR 29 1 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ;; 262.79 1.18E-58 214429000 186678 337927 315848 321810 354361 301144 309772 308795 192058 FALSE TRUE 174994.1572 362947.4667 323340.0637 330068.1894 326530.9165 388079.3841 263324.5644 347348.7355 160002.2791 1.093697904 2.268389356 2.020846613 2.0628968 2.040789159 2.425461602 1.645755085 2.170898674 1 17.28773293 -0.780232204 5.877068251 0.999999947 1.997504988 0.39975153 0.370267209 2.92E-07 6.02E-08 0.316338504 0.074561696 0.165869981 0.780232204 0.997505041 DLIADLKYELTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLIADLKYELTGK 13 1 P08133;P08133-2;E5RFF0;E5RJF5;E5RK63;E5RIU8;E5RJR0;E5RI05 P08133 ANXA6 Annexin A6;Annexin 0 ; 133.16 0.00010073 210710000 1098410 595790 737700 649440 995920 476560 959030 687160 1722510 FALSE TRUE 1029662.479 639902.9115 755198.5924 666105.7299 917704.4605 614135.1357 815232.3547 772953.4386 1435011.953 0.717528852 0.445921659 0.526266412 0.464181311 0.639509977 0.427965171 0.568101438 0.538639025 1 20.45263132 -0.074373418 1.236979475 1.00195515 0.527014964 0.724198014 0.088710839 7.750852977 8.261765068 0.137187659 0.022278644 0.842609947 0.074373418 -0.474940186 DLIADLKYELTGKFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLIADLKYELTGKFER 16 2 P08133;P08133-2;E5RFF0;E5RJF5;E5RK63;E5RIU8;E5RJR0;E5RI05 P08133 ANXA6 Annexin A6;Annexin 0 75.911 0.015849 19778000 98453 98038 118400 111080 153620 59765 121150 105230 352750 FALSE TRUE 92291.00247 105296.8355 121208.5039 113930.5009 141555.3049 77018.1853 102984.6822 118368.1971 293873.7461 0.314049838 0.358306371 0.412450944 0.387685196 0.481687482 0.262079163 0.350438525 0.402785886 1 18.16483695 0.744208816 4.867808959 0.99999944 0.369056743 0.921933372 0.057594817 2.155931074 40.89736763 0.053546905 0.013547891 5.548924504 -0.744208816 -0.630942696 DLIDDATNLVQLYHVLHPDGQSAQGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLIDDATNLVQLYHVLHPDGQSAQGAK 27 0 G5E9W7;G5E9V5;P82650 G5E9W7 MRPS22 "28S ribosomal protein S22, mitochondrial" 0 262.78 2.15E-53 96392000 161190 141970 141850 134130 179140 134800 151190 160730 238900 FALSE TRUE 151101.4056 152481.6065 145214.749 137572.0029 165071.067 173714.5717 128520.4631 180797.4943 199026.0466 0.759204175 0.766138951 0.729626858 0.691226124 0.829394292 0.872823304 0.645746952 0.908411222 1 17.60259772 1.036920448 6.248114324 0.999653888 0.755729581 0.641764064 0.063501841 0.091124976 9.236203019 0.058188191 0.014623499 10.88730647 -1.036920448 -0.243924306 DLIDFDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DLIDFDDR 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;;;; 205.7 0.00017999 2173116000 4971760 5407770 5226610 5279140 5636850 4308870 6326960 5008890 4382440 FALSE TRUE 4660586.416 5808166.918 5350587.657 5414611.67 5194154.539 5552770.82 5378291.085 5634260.942 3650982.452 1.276529394 1.590850406 1.46551996 1.483056065 1.422673104 1.520897702 1.473107898 1.543217755 1 21.7998533 -1.257720577 4.708900088 0.999845798 1.48240315 0.757058117 0.083841521 0.00011891 1.87E-05 0.071120531 0.016757961 0.055243276 1.257720577 0.482557353 DLIDYVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLIDYVR 7 0 D6RIC3;A0A0C4DGU5;A0A087X2G6;Q9Y3C1;Q9Y3C1-3;Q9Y3C1-2 D6RIC3 NOP16 Nucleolar protein 16 0 ; 96.285 0.029881 170686000 567800 608700 615770 587450 636030 526860 701980 533330 673780 FALSE TRUE 532262.4116 653768.7814 630376.3552 602524.9616 586078.7694 678955.9291 596724.6159 599917.4245 561321.7652 0.948230488 1.164695228 1.123021401 1.073403881 1.044104836 1.209566369 1.063070511 1.06875853 1 19.09846848 0.957340837 1.938989663 1.001476865 1.103024193 0.119073591 0.070826071 0.637577152 5.076015496 0.061419188 0.017244997 9.064437044 -0.957340837 0.101547329 DLIEAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DLIEAIR 7 0 Q9BRT3 Q9BRT3 MIEN1 Migration and invasion enhancer 1 0 ;;;;;; 164 0.0028245 1057342000 2053539 2226640 2119926 1979605 1974488 1876946 2545150 1968887 1955732 FALSE TRUE 1925011.66 2391502.742 2170211.646 2030405.016 1819419.677 2418789.841 2163528.386 2214706.876 1629307.695 1.181490559 1.467803012 1.331983917 1.246176534 1.116682676 1.484550677 1.327882016 1.359293204 1 20.63582765 -2.10323488 2.332907158 0.42648346 1.329342749 0.421629707 0.114585283 3116099.394 853182.7917 9490421.295 0.026844017 0.007884336 2.10323488 0.902859289 DLIEAIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DLIEAIRR 8 1 Q9BRT3 Q9BRT3 MIEN1 Migration and invasion enhancer 1 0 ;;;; 172.21 0.00045678 2557893000 2009489 2722910 2209754 2217428 2944510 1808358 2505540 2254039 3152920 FALSE TRUE 1883718.671 2924517.09 2262170.408 2274330.957 2713260.062 2330401.598 2129857.537 2535460.731 2626677.283 0.717148879 1.113390331 0.861228908 0.86585854 1.032962854 0.887205144 0.810856191 0.965273026 1 21.32480753 DLIHDQDEDEEEEEGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DLIHDQDEDEEEEEGQR 17 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;R4GNE6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ;;;;; 336.88 3.07E-72 9911680000 6409590 6212860 6410370 6085490 6371770 5406500 7531260 5568680 7602250 FALSE TRUE 6008425.203 6672866.619 6562427.004 6241653.976 5871356.887 6967268.783 6402017.48 6263941.956 6333385.363 0.948690923 1.053601863 1.036164173 0.985516216 0.927048735 1.100086034 1.010836561 0.989035342 1 22.59454543 1.323263539 7.457219908 0.99480502 1.016811928 0 0.049912777 0.923138049 67.32362274 0.03260791 0.011810922 21.05055443 -1.323263539 0.022006909 DLIHDVSFDFHGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DLIHDVSFDFHGR 13 0 K7ELV2;Q96EE3;Q96EE3-1;K7EP88;K7ENI5 K7ELV2 SEH1L Nucleoporin SEH1 0 ;;;; 235.73 6.22E-17 595500000 482193 585148 560237 585090 569727 482695 658509 544284 544923 FALSE TRUE 452013.4009 628472.9668 573526.0862 600104.4 524982.9396 622041.2106 559771.6887 612239.0555 453971.831 0.99568601 1.384387585 1.263351704 1.321897878 1.156421839 1.370219842 1.233053794 1.348627853 1 18.79224326 -1.069549344 6.293715861 0.999999622 1.271678926 0.324242396 0.116368268 5.33E-07 7.88E-08 0.097088388 0.022883921 0.08520217 1.069549344 0.271679305 DLIHTGVANDHEEDFELRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLIHTGVANDHEEDFELRK 19 1 E9PFH4;C9J7E5;Q9Y5L0-5;Q9Y5L0-3;Q9Y5L0;Q9Y5L0-1 E9PFH4 TNPO3 Transportin-3 0 ; 251.13 4.34E-26 154009000 170198 154531 166748 166613 175842 122544 214438 161801 181022 FALSE TRUE 159545.611 165972.636 170703.3413 170888.5717 162032.0786 157920.4635 182285.0126 182002.211 150808.2588 1.057936829 1.100554024 1.131923031 1.133151281 1.074424438 1.047160578 1.208720359 1.206845119 1 17.20235591 1.738489462 25 1.158339038 1.097709483 0.07678781 0.064184111 0.068413115 6112.47407 0.027003698 0.014974895 54.76328132 -1.738489462 -0.060629555 DLIQGLLTVDPNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLIQGLLTVDPNKR 14 1 O75582-3;O75582 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 0 87.427 0.011139 123400000 69114 48167 101930 144480 68356 89247 114500 51116 193240 FALSE TRUE 64788.27811 51733.3348 104347.8277 148187.6014 62987.59549 115011.1601 97331.78797 57497.94512 160986.9956 0.402444172 0.321351017 0.648175508 0.920494235 0.391258904 0.714412737 0.604594101 0.357158943 1 17.29658463 -5 0.141479394 2.380227068 0.407009472 0.337283868 0.191338753 166.4656118 1.437556037 66.51668308 1.109458582 1.00E-05 5 -1.973217596 DLISHDEMFSDIYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 DLISHDEMFSDIYK 14 0 Q5W0H4;A0A0B4J2C3;P13693 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 ;;;;;;;; 302.35 5.76E-44 9075821000 14330890 12548538 13557703 13105396 14321280 9883700 15184820 11906843 15925910 FALSE TRUE 13433945.18 13477644.81 13879298.12 13441702.65 13196544.44 12736963.74 12907997.21 13393438.56 13267772.74 1.012524517 1.015818184 1.046091035 1.013109202 0.99463148 0.959992607 0.972883503 1.009471509 1 23.66142287 2.734867735 2.921369018 0.981297579 1.025960675 0.515208146 0.016559787 0.176764823 3.053172253 0.005523154 0.005503093 543.0849091 -2.734867735 0.044663096 DLISLDS(ph)SPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLISLDSSPAK 11 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLIS(0.003)LDS(0.499)S(0.499)PAK 69.864 0.055949 61971000 194930 101630 115250 109510 118320 106080 158510 106760 132330 TRUE FALSE 182729.6793 109154.7909 117983.7844 112320.212 109027.6245 136703.5739 134742.897 120089.221 110243.2681 1.657513265 0.990126588 1.070213052 1.018839644 0.988973081 1.240017429 1.222232426 1.089311149 1 16.75033104 4.744555756 24.98096504 1.087454479 1.657513516 0.802798536 0.090227411 328.2685463 1367813.961 0.023993171 0.216960935 55533.59084 -4.744555756 0.570059037 DLISLDS(ph)SPAKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DLISLDSSPAKER 13 1 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLIS(0.005)LDS(0.603)S(0.393)PAKER;DLISLDS(0.543)S(0.457)PAKER;DLISLDS(0.55)S(0.45)PAKER;DLIS(0.001)LDS(0.643)S(0.356)PAKER;DLISLDS(0.597)S(0.403)PAKER 92.8 0.0035771 1150730000 1806380 1128330 1499740 1342270 1608390 1188950 1820690 1339060 2281200 TRUE FALSE 1693321.9 1211872.727 1535314.541 1376714.921 1482073.537 1532180.564 1547694.437 1506244.589 1900452.983 0.891009625 0.637675722 0.807867679 0.724414091 0.779852778 0.806218611 0.814381861 0.792571351 1 20.8579119 -0.61612091 0.326726185 1.089580911 0.742863028 0.520774807 0.065588352 6.832168798 0.722170103 0.698539571 0.057434509 0.242035511 0.61612091 -0.346717883 DLISLDSS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLISLDSSPAK 11 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLISLDS(0.056)S(0.944)PAK;DLISLDSS(1)PAK;DLISLDS(0.003)S(0.997)PAK;DLISLDSS(1)PAK 259.47 1.40E-20 349314000 2437710 1172430 1771660 1430720 1493300 1643480 2466930 1577500 1709170 TRUE FALSE 2285138.083 1259237.937 1813684.612 1467434.697 1376022.242 2117925.996 2097036.748 1774454.348 1423898.485 1.604846206 0.884359349 1.273745727 1.030575362 0.966376645 1.487413617 1.472743155 1.24619442 1 20.44141486 2.233605838 24.99993305 1.360329867 1.126572749 0.059652238 0.2393516 199.5384981 1006783.539 0.080178378 0.061063204 171.2402441 -2.233605838 -0.233757118 DLISLDSS(ph)PAKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLISLDSSPAKER 13 1 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLISLDS(0.202)S(0.798)PAKER 124.29 0.00012933 408300000 696740 416760 561710 484430 606650 449610 700870 481230 863340 TRUE FALSE 653132.2871 447617.344 575034.0265 496861.2939 559006.1561 579405.1082 595781.0501 541312.6248 719242.9766 0.908082954 0.622345103 0.79949898 0.690811464 0.777214619 0.805576317 0.82834462 0.752614405 1 19.4561197 -0.8846865 0.311169281 1.117360919 0.734534982 0.441041503 0.078308791 10.46003472 0.885677374 1.198092121 0.074446333 0.130410782 0.8846865 -0.382825938 DLKDEIVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLKDEIVR 8 1 P15924;P15924-3 P15924 DSP Desmoplakin 0 ;; 72.643 0.041609 1456210000 794800 677999 724981 729730 798700 505969 877670 697660 804330 FALSE TRUE 745054.8868 728198.7514 742177.8917 748456.1072 735973.3238 652034.0366 746071.5314 784764.3867 670082.1268 1.111885927 1.0867306 1.107592431 1.116961753 1.098333017 0.973065853 1.113403121 1.171146573 1 19.3539784 2.446970526 24.99996922 1.069642921 1.103388919 0.113465471 0.054718271 539.1136285 447012.2481 0.018108454 0.015150782 279.879137 -2.446970526 0.033745997 DLKDYFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLKDYFSK 8 1 Q14103-3;Q14103;H0Y8G5;H0YA96;D6RAF8;D6RD83;D6RF44;Q14103-2;Q14103-4;D6RBQ9 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ; 89.827 0.012431 3885900000 10895400 9294700 9768900 10496400 12089800 7522400 12991900 8684300 16694300 FALSE TRUE 10213476.36 9982889.259 10000622.92 10765755.39 11140315.88 9693994.764 11043885.21 9768553.972 13907913.48 0.734364387 0.717784826 0.719059903 0.774074084 0.801005549 0.697012875 0.794072038 0.702373795 1 23.72940266 -5 0.368772301 4.363588559 0.735653435 0.821084464 0.037552922 201.4686797 1.561441908 539.7768792 0.024585344 1.00E-05 5 -3.627935124 DLKDYFTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLKDYFTK 8 1 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ; 105.86 0.0039271 2876200000 6188300 5163600 5810500 5669700 6523200 4544400 7452700 5229900 8388200 FALSE TRUE 5800985.349 5545918.317 5948327.804 5815194.101 6010894.185 5856294.508 6335236.822 5882864.527 6988155.23 0.830116842 0.793616932 0.851201441 0.832150104 0.860154646 0.838031543 0.906567844 0.841833693 1 22.73648022 -5 0.131625793 1.543152361 0.777718273 0.827455953 0.023462239 49.30314996 0.407826071 7.002723297 0.153269427 1.00E-05 5 -0.765434088 DLKEEFTEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLKEEFTEALR 11 1 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ; 158.25 2.74E-05 283960000 957490 873070 942850 1003250 1135210 737350 1229520 985680 1251210 FALSE TRUE 897562.4101 937713.0112 965214.8472 1028995.093 1046055.186 950210.9751 1045164.89 1108744.318 1042374.968 0.86107441 0.899592795 0.925976618 0.987164049 1.003530609 0.911582688 1.002676506 1.063671281 1 19.99144291 4.747060894 0.328235268 1.018466894 0.737507278 0.656834708 0.035853322 4.355687654 0.37914754 0.03608863 0.494752817 55854.85055 -4.747060894 -0.280959615 DLKIES(ph)DVQEPTEPEDDLDIMLGNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLKIESDVQEPTEPEDDLDIMLGNK 25 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 DLKIES(0.999)DVQEPT(0.001)EPEDDLDIMLGNK 62.284 0.037543 15633000 28798 18555 21612 19915 27083 12873 22785 16926 42789 TRUE FALSE 26995.58459 19928.83151 22124.64685 20426.05262 24956.01043 16589.22612 19368.60078 19039.24836 35647.23947 0.75729804 0.559056797 0.620655265 0.573005173 0.700082553 0.465371972 0.543340833 0.53410162 1 15.12150274 -1.7051654 6.633124885 1.004575205 0.586871408 0.697221127 0.083938436 0.005282656 0.000234808 0.075597569 0.017709514 0.019716717 1.7051654 -0.417703796 DLKPENILLDEEGHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLKPENILLDEEGHIK 16 1 E9PGT3;Q15418-4;Q15418;Q15418-2;Q15418-3;B7Z3B5;F2Z2J1;Q15349;Q15349-3;Q15349-2;E9PMM7;D6R910;A0A2R8Y7S9;B4DG22;B1AXG1;B7ZB17;P51812 E9PGT3;B4DG22 RPS6KA1;RPS6KA2;RPS6KA3 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1;Ribosomal protein S6 kinase alpha-2;Ribosomal protein S6 kinase alpha-3 0 209.7 6.96E-12 154910000 491800 288380 391700 368440 403190 255640 495900 328350 464090 FALSE TRUE 461019.1159 309731.9553 400991.309 377894.7942 371525.0838 329439.118 421544.3987 369345.2203 386630.3809 1.192402715 0.801106097 1.037143817 0.977405845 0.96093091 0.85207768 1.090303348 0.955292803 1 18.56059548 1.715696454 24.99999934 1.019842887 0.958312404 0.028570832 0.108989735 2.527175006 2751.673192 0.045708248 0.025347581 51.96326776 -1.715696454 -0.061530483 DLKPQNLLIDDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLKPQNLLIDDK 12 1 P06493;A0A024QZP7;A0A087WZZ9;E5RIU6 P06493 CDK1;CDC2 Cyclin-dependent kinase 1 0 144.68 5.77E-05 312330000 1485400 771450 1139600 905630 1014100 805540 1265700 818820 1043800 FALSE TRUE 1392431.466 828568.9607 1166631.85 928869.999 934456.6767 1038086.321 1075920.035 921051.4794 869583.0368 1.601263372 0.952834779 1.341599135 1.068178609 1.074603157 1.193774806 1.237282686 1.059187496 1 19.72996427 DLKPSNILYVDESGNPECLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLKPSNILYVDESGNPECLR 20 1 E9PGT3;Q15418-4;Q15418;Q15418-2;Q15418-3 E9PGT3 RPS6KA1 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1 0 ; 212.65 1.39E-22 260530000 584550 503250 500670 509900 551560 441860 680460 492500 593920 FALSE TRUE 547964.059 540511.1536 512546.1288 522984.8973 508242.7025 569417.809 578431.3401 553989.7091 494790.9151 1.107465885 1.092403149 1.035884276 1.056981608 1.027186812 1.150825109 1.169041958 1.11964406 1 18.91645949 2.230278932 24.99991046 1.129753636 1.063709502 0.11516413 0.051442695 228.1013964 688564.3754 0.017656725 0.013262515 169.9334726 -2.230278932 -0.066044134 DLKPSNLLLNTTCDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLKPSNLLLNTTCDLK 16 1 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 157.74 3.46E-08 251790000 572660 401380 446060 459380 530830 350400 626240 437970 644090 FALSE TRUE 536818.2328 431098.5928 456640.7538 471168.4685 489140.7531 451554.7917 532341.1257 492651.5186 536587.218 1.000430526 0.803408241 0.851009377 0.87808366 0.911577348 0.841531025 0.992086855 0.918120116 1 19.03345316 1.73547388 9.925140677 0.96512054 0.86966945 0.343645831 0.056406917 0.093725535 39.32062721 0.025204398 0.013645731 54.38434222 -1.73547388 -0.09545109 DLLDDLKSELTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLLDDLKSELTGK 13 1 P08758;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 ; 214.18 2.85E-11 888030000 2649670 1650380 1432480 1364690 1788720 1005840 3236050 1728620 5417510 FALSE TRUE 2483831.884 1772575.852 1466459.102 1399710.256 1648241.147 1296209.68 2750834.345 1944442.012 4513292.583 0.550336997 0.392745611 0.324920017 0.310130626 0.365197052 0.287198239 0.609496126 0.430825606 1 22.10574888 0.365152103 0.733438841 1.009022172 0.371888147 0.779716461 0.099579706 0.955413801 0.736324884 0.114569531 0.033733682 2.318206412 -0.365152103 -0.637134025 DLLDDLKSELTGKFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLLDDLKSELTGKFEK 16 2 P08758;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 68.944 0.026766 403030000 168120 123520 150400 144910 167870 108200 193140 136690 231620 FALSE TRUE 157597.6693 132665.5493 153967.559 148628.6359 154686.1674 139435.5835 164180.45 153756.0474 192961.1257 0.816732742 0.687524748 0.797920091 0.770251704 0.801644201 0.722609712 0.850847286 0.796823955 1 17.5579507 -1.323781062 0.27797818 1.165806802 0.744003164 0.715249155 0.044357549 9.144917797 0.530751275 1.144216401 0.051859905 0.047448112 1.323781062 -0.421803639 DLLDQILMLDPAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLLDQILMLDPAKR 14 1 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 0 112.72 0.0009252 37242000 60271 50738 53058 66275 60437 46929 60204 47522 67405 FALSE TRUE 56498.7457 54494.69431 54316.56082 67975.7287 55690.52181 60476.64047 51176.96911 53455.22631 56154.67005 1.006127285 0.970439222 0.967267028 1.210508915 0.991734468 1.076965467 0.911357311 0.95192842 1 15.77711839 -0.775691292 5.669004678 1 1.004671888 0 0.08288226 1.16E-09 3.11E-18 0.078042023 0.018394679 0.167613389 0.775691292 0.004671888 DLLDTVLPHLYNETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLLDTVLPHLYNETK 15 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 258.36 8.07E-25 645400000 3377860 2939180 3319080 3346100 3543700 2482760 4268700 3137350 4292700 FALSE TRUE 3166445.772 3156799.945 3397810.145 3431966.591 3265392.097 3199492.508 3628648.064 3529055.054 3576220.638 0.885416783 0.88271957 0.950112001 0.95966299 0.91308463 0.89465747 1.014660009 0.986811333 1 21.77000432 5.737608152 0.158523314 1.026164949 0.694101721 0.564496068 0.031735501 23.79934201 0.469926736 0.117304889 1.65337473 546522.6328 -5.737608152 -0.332063228 DLLEEEEAWEASHKNDLQDTEIS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLLEEEEAWEASHKNDLQDTEISPR 25 1 Q9NS91 Q9NS91 RAD18 E3 ubiquitin-protein ligase RAD18 1 DLLEEEEAWEASHKNDLQDT(0.001)EIS(0.999)PR 252.89 5.14E-45 194050000 345520 182280 260970 217160 204710 234320 356200 211980 198290 TRUE FALSE 323894.52 195776.2009 267160.3316 222732.6933 188632.9024 301964.3801 302791.1168 238446.1696 165194.118 1.960690392 1.185128159 1.617250874 1.348308862 1.141886313 1.827936635 1.832941272 1.443430145 1 17.33380279 2.220961952 24.99973501 1.62923172 1.432510791 0 0.329526528 642.4145873 912574.4578 0.112522822 0.083287265 166.3266929 -2.220961952 -0.196720929 DLLFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLLFGR 6 0 O43633;M0R1L7;M0QXX8 O43633 CHMP2A Charged multivesicular body protein 2a 0 ;; 138.53 0.028531 505311000 539400 625140 614800 615810 619540 530530 676500 507960 646120 FALSE TRUE 505639.9169 671426.0161 629383.3463 631612.7272 570883.8275 683685.3986 575065.1053 571379.9242 538278.3979 0.939365055 1.247358279 1.16925247 1.173394157 1.060573543 1.27013345 1.068341415 1.061495179 1 19.037993 1.555639853 7.705075038 1.04244916 1.157244246 0.195590894 0.094439668 0.168217804 18.08198238 0.046710953 0.021757388 35.94511298 -1.555639853 0.114795086 DLLHNEDRHDDYFQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DLLHNEDRHDDYFQER 16 1 Q8N684-2;Q8N684;Q8N684-3 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 0 ;;;; 196.66 2.92E-11 1700630000 833848 1152979 1121429 1145790 1326392 887242 1042174 1034477 1857560 FALSE TRUE 781658.9421 1238346.765 1148029.825 1175192.911 1222222.523 1143374.362 885909.6838 1163633.731 1547521.236 0.505103855 0.8002131 0.741850773 0.759403415 0.7897937 0.738842438 0.572470131 0.751933934 1 20.56152778 0.967058112 23.90389104 1.000000003 0.711464528 0.492688337 0.094214265 2458.1693 1783743.654 0.08860293 0.022150732 9.269538481 -0.967058112 -0.288535474 DLLHPS(ph)PEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLLHPSPEEEK 11 0 P42677 P42677 RPS27 40S ribosomal protein S27 1 DLLHPS(1)PEEEK 166.48 0.0008446 0 283130 153580 211150 191400 180910 160850 258080 176800 202120 TRUE FALSE 265409.3987 164951.223 216158.5777 196311.648 166702.0584 207284.7838 219383.2999 198873.8692 168384.8663 1.576206963 0.979608362 1.28371737 1.165850901 0.990006181 1.231017896 1.302868273 1.181067358 1 17.36140296 4.755242427 24.37548766 1.160950959 1.576207425 0.561796288 0.119518786 1888.43326 2759317.156 0.028089933 0.754348441 56917.05582 -4.755242427 0.415256465 DLLHPS(ph)PEEEKRK ddPTM_SK-BR-3_Pertuzumab_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 142.32 2.10E-05 2672320000 4498380 2145180 3019830 2996240 3453820 1893600 3838300 2495260 5059590 TRUE FALSE 4216834.426 2304011.359 3091461.794 3073128.591 3182570.909 2440251.58 3262782.548 2806798.704 4215111.743 1.000408692 0.546607421 0.733423449 0.72907405 0.755038325 0.578929274 0.774067865 0.665889513 1 22.00713945 -1.251100351 4.692281062 1.000089481 0.707724565 0.325265051 0.123700979 0.000101427 1.62E-05 0.104908557 0.024719639 0.056091835 1.251100351 -0.292364916 DLLHPSLEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLLHPSLEEEK 11 0 H0YMV8;Q71UM5;C9JLI6 H0YMV8 RPS27L 40S ribosomal protein S27;40S ribosomal protein S27-like 0 ;;; 210.35 1.30E-08 609480000 2755130 2611010 2660930 2675110 3142710 1796460 3367160 2612510 3099040 FALSE TRUE 2582691.331 2804331.897 2724048.516 2743757.852 2895894.234 2315068.839 2862285.617 2938687.624 2581790.203 1.000349032 1.086196661 1.055100648 1.062734628 1.12166133 0.89669131 1.108643767 1.138236415 1 21.29994034 -1.090579383 4.350674663 0.99999345 1.059271545 0.06612185 0.069301354 5189.139502 18177453.51 249.6498904 0.014675275 0.081174686 1.090579383 0.059278096 DLLHPSPEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 DLLHPSPEEEK 11 0 P42677 P42677 RPS27 40S ribosomal protein S27 0 ;;;;;;;; 190.53 2.23E-06 10432770000 20896680 16295810 20233580 19018670 19471980 15884370 26215330 17026600 21724990 FALSE TRUE 19588794.1 17502368.73 20713530.07 19506721.27 17942729.24 20469929.76 22284584.64 19152408.49 18098948.82 1.082316675 0.96703786 1.144460393 1.077782001 0.991368583 1.13100103 1.231264029 1.058205572 1 24.10940257 2.121786022 9.700026362 1.136814743 1.05466931 0.037197673 0.078081067 0.460985803 37.07947581 0.027949143 0.020637591 132.3689189 -2.121786022 -0.082145433 DLLHPSPEEEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DLLHPSPEEEKR 12 1 P42677 P42677 RPS27 40S ribosomal protein S27 0 ;;;; 176.51 1.61E-05 2473890000 2371010 2114550 2444650 2375650 2484780 1876790 3055650 2190590 2690340 FALSE TRUE 2222612.716 2271113.482 2502638.252 2436613.201 2289635.402 2418588.806 2597483.65 2464089.984 2241304.874 0.991660145 1.013299667 1.116598764 1.087140455 1.021563567 1.079098535 1.158915808 1.099399735 1 21.09590747 4.205450086 2.732624462 1.089106531 0.996038239 0.329544638 0.045249234 0.287117589 4.214416303 0.011653103 0.035780608 16049.07794 -4.205450086 -0.093068292 DLLHPSPEEEKRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLLHPSPEEEKRK 13 2 P42677 P42677 RPS27 40S ribosomal protein S27 0 ;;; 205.8 4.02E-08 1499670000 1377220 1676180 1578350 1916200 2688890 877440 2015070 1497640 5417250 FALSE TRUE 1291022.259 1800286.111 1615789.207 1965372.936 2477715.426 1130742.684 1712928.96 1684623.651 4513075.978 0.286062602 0.398904455 0.358023932 0.435484123 0.549008135 0.250548116 0.379548 0.373276156 1 22.10567964 -1.874957716 2.299180747 1.319913892 0.379792653 0.855113753 0.080351006 3435071.332 1775645.055 5981365.262 0.019565324 0.013336513 1.874957716 -0.940121239 DLLIAYYDVDYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DLLIAYYDVDYEK 13 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;; 204.64 1.77E-07 457849000 1330010 1164110 1254610 1268020 1359400 924440 1589650 1092530 1158430 FALSE TRUE 1246767.048 1250301.916 1284369.942 1300559.54 1252638.208 1191310.821 1351296.74 1228934.775 965080.5493 1.291878744 1.295541514 1.330842221 1.347617607 1.29796234 1.234415948 1.400190628 1.273401248 1 19.88028983 0.966562651 24.13247246 0.999999999 1.31604647 0.841174972 0.042545401 1154.076991 832923.9246 0.038552372 0.009638093 9.258969445 -0.966562651 0.31604647 DLLIFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLLIFR 6 0 H3BPB8;P34949-2;P34949;F5GX71 H3BPB8 MPI Mannose-6-phosphate isomerase 0 131.65 0.035445 29371000 39941 43129 39375 39331 46238 33507 41399 45549 49217 FALSE TRUE 37441.16411 46322.31604 40308.99359 40340.30005 42606.654 43179.92696 35191.60428 51235.89292 41002.36475 0.913146457 1.129747426 0.983089484 0.983853012 1.039126749 1.05310821 0.858282309 1.249583853 1 15.3234195 1.232679085 24.99983228 1.124791799 1.003426164 0.242565407 0.094786236 226.1600775 961260.7486 0.076917323 0.02126069 17.08752191 -1.232679085 -0.121365634 DLLLTGHEDGTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLLLTGHEDGTVR 13 0 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 0 ; 167.98 8.18E-07 174660000 225230 257080 254060 257570 286860 195857 262450 240490 278100 FALSE TRUE 211133.2563 276114.4707 260086.4232 264179.6823 264331.1727 252397.7364 223098.059 270515.7059 231683.3134 0.911301091 1.191775388 1.122594542 1.140262017 1.140915886 1.089408351 0.96294401 1.167609794 1 17.82179461 1.98824437 22.89084021 1.036094483 1.118093469 0.06150775 0.090169445 327.8287567 638354.9447 0.03258444 0.022333696 97.32947269 -1.98824437 0.081998986 DLLPHQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLLPHQELR 9 0 Q15650;H0YL91 Q15650 TRIP4 Activating signal cointegrator 1 0 152.97 7.92E-05 28745000 31584 43384 30693 37053 40151 30463 38385 34314 45550 FALSE TRUE 29607.21382 46596.1965 31421.05245 38003.84271 36997.70242 39257.17357 32629.5256 38598.17843 37947.41074 0.78021697 1.227915043 0.828015716 1.00148711 0.97497304 1.03451521 0.859861713 1.017149199 1 15.21171383 3.936077109 24.99164056 0.952924071 1.035034962 0.006183866 0.125715854 621.796803 378609.6466 0.028691259 0.051724614 8631.317835 -3.936077109 0.082110891 DLLPSDMAVALLEAQAGTGHIIDPATSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLLPSDMAVALLEAQAGTGHIIDPATSAR 29 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 218.98 2.24E-34 260190000 119054 150546 134364 146388 163929 127021 165749 141675 133433 FALSE TRUE 111602.6227 161692.5825 137551.1775 150144.5639 151054.6776 163689.9007 140896.4762 159363.4356 111162.1703 1.003962251 1.454564822 1.237391976 1.350680394 1.358867654 1.47253243 1.267485835 1.433612129 1 16.76230638 -0.97363052 4.895763914 0.99999998 1.330561782 0.355273968 0.136089928 4.01E-06 8.41E-07 0.113965428 0.026861656 0.106259919 0.97363052 0.330561802 DLLPYGFAIHHAGMTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLLPYGFAIHHAGMTR 16 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 116.35 0.00025144 241710000 271520 379650 329780 312730 364610 250460 393190 361200 298610 FALSE TRUE 254526.0479 407759.681 337602.5373 320755.1813 335975.0014 322763.7361 334234.8097 406296.6151 248770.0619 1.023137776 1.639102704 1.35708668 1.289364077 1.350544349 1.297438018 1.343549168 1.633221506 1 17.92445335 3.494909293 23.55797282 1.335182337 1.414607485 0 0.213086087 911.1535067 1206696.418 0.051293729 0.078767272 3125.426522 -3.494909293 0.079425147 DLLQFFKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLLQFFKPR 9 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 180.8 4.40E-05 939870000 845600 947850 941840 874630 1048420 716980 1055630 899780 1123580 FALSE TRUE 792675.4054 1018029.8 964180.8896 897074.4865 966081.3223 923960.4868 897348.0815 1012119.514 936047.2394 0.846832694 1.087583786 1.030055802 0.958364545 1.032086076 0.987087454 0.958656832 1.081269696 1 19.83622181 DLLSDLQDIS(ph)DSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.817)DS(0.183)ER;DLLSDLQDIS(0.959)DS(0.041)ER;DLLSDLQDIS(0.792)DS(0.208)ER;DLLSDLQDIS(0.979)DS(0.021)ER;DLLSDLQDIS(1)DSER;DLLSDLQDIS(0.937)DS(0.063)ER 389.23 5.54E-114 4251720000 3809120 3350490 3889730 3708530 3136040 3547670 4280750 3037350 2749070 TRUE FALSE 3570713.979 3598563.766 3981996.232 3803697.158 2889748.069 4571824.737 3638891.278 3416569.834 2290232.457 1.559105482 1.571265726 1.73868649 1.660834535 1.261770638 1.99622738 1.588874206 1.49180046 1 21.12706261 0.811751853 2.572673406 1.000536725 1.635362822 0.540582395 0.180362909 0.560813361 6.205907196 0.156717099 0.041807659 6.482639234 -0.811751853 0.634826097 DLLSDLQDIS(ph)DSERK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLLSDLQDISDSERK 15 1 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;Q9UQ88-9;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;J3KS35;E7ESP2 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 DLLSDLQDIS(0.999)DS(0.001)ERK 98.443 0.0017923 25429000 47295 30091 43324 35771 37400 31765 43978 32826 49932 TRUE FALSE 44334.89037 32318.96895 44351.66574 36688.94442 34462.75486 40935.03984 37383.90717 36924.39836 41598.02663 1.065793115 0.776935147 1.066196388 0.881987618 0.828470907 0.984062062 0.898694246 0.887647837 1 15.34422747 -1.061490956 4.378695702 1.000006192 0.92033455 0.06077433 0.093395571 1.705E+11 36536945924 11133420.66 0.019551942 0.086797865 1.061490956 -0.079671642 DLLTPPADKPGQDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLLTPPADKPGQDNR 15 1 I3VM54;Q9Y2K7;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 0 150.59 2.88E-06 212220000 171400 143580 163530 156570 184650 137650 206280 141040 211430 FALSE TRUE 160672.38 154210.8126 167409.0088 160587.8513 170148.3338 177387.3204 175350.229 158649.1545 176140.9671 0.912180639 0.87549657 0.950426307 0.911700747 0.965978197 1.007075886 0.995510766 0.90069424 1 17.42637097 3.177550955 0.979400584 0.979208876 0.895714946 0.436342704 0.034365482 0.46406786 0.96584423 0.015003599 0.022978058 1505.050092 -3.177550955 -0.083493931 DLLVEGLAEILHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLLVEGLAEILHQK 14 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 0 ; 164.33 4.14E-06 94738000 201046 198380 216627 232750 235879 176489 272120 213291 284850 FALSE TRUE 188462.8897 213068.2616 221765.4947 238722.759 217354.0148 227438.5092 231318.1322 239920.8509 237306.6948 0.794174349 0.897860306 0.934510065 1.005967233 0.915920282 0.958415899 0.97476446 1.011015939 1 17.85639328 6.272119755 0.522500199 0.979063803 3.69E-15 0.806862706 0.028584655 7.836692169 0.461000174 0.013706558 6.649522216 1871198.045 -6.272119755 -0.979063803 DLLVGPGVELLLT(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLLVGPGVELLLTPR 15 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;Q5VY93 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 DLLVGPGVELLLT(1)PR;DLLVGPGVELLLT(1)PR;DLLVGPGVELLLT(1)PR;DLLVGPGVELLLT(1)PR 139.08 7.38E-05 115373000 138299 144773 193422 237116 216480 100366 87172 76974 118196 TRUE FALSE 129643.1125 155492.1436 198010.0612 243200.798 199478.534 129340.0349 74101.36787 86584.37334 98468.32402 1.316597126 1.579108257 2.010901101 2.469837894 2.025814251 1.313519207 0.752540155 0.879311943 1 16.58737208 2.028383511 3.652659055 0.873587869 1.881074936 0.695796832 0.304552837 0.136646719 3.838798742 0.143952092 0.092482781 106.7538412 -2.028383511 1.007487067 DLLYFDGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DLLYFDGLR 9 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ;;;; 163.99 0.00014564 349013000 676227 895311 748097 723955 916555 611950 778788 834387 714225 FALSE TRUE 633903.1592 961600.758 765842.2141 742532.911 844572.4675 788610.0308 662015.9693 938562.0537 595016.2334 1.065354395 1.616091636 1.287094656 1.247920425 1.419410799 1.32535885 1.112601526 1.577372181 1 19.1825695 -3.623560083 0.279956398 2.08E-09 1.36182854 0.219525717 0.180222276 136.1827892 2.654330397 79.06523532 0.195074794 0.000237925 3.623560083 1.361828538 DLLYFDGLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLLYFDGLRK 10 1 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ; 125.22 0.00066531 414940000 540130 699560 610460 587590 808440 454520 651530 597080 810700 FALSE TRUE 506324.2275 751356.1503 624940.3995 602668.5542 744948.3835 585732.5455 553839.125 671626.7523 675388.9327 0.749678005 1.112479216 0.925304472 0.892328146 1.102991695 0.867252211 0.820029909 0.994429609 1 19.36535901 DLMLMSHLQDNIQHADPPVQILYNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 198.39 4.43E-25 320050000 165106 206898 188133 184332 210099 167936 213670 172884 171013 FALSE TRUE 154772.3102 222216.9432 192595.6036 189062.2712 193598.672 216416.397 181632.1671 194468.948 142469.8255 1.086351511 1.559747423 1.351834347 1.327033781 1.358874915 1.519033214 1.274881656 1.364983408 1 17.12029687 0.129777463 0.940941383 0.996443707 1.380655435 0.415408634 0.130095398 4.181502424 3.763176391 0.154330167 0.036639382 1.348271837 -0.129777463 0.384211728 DLMPHDLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 DLMPHDLAR 9 0 P55084-2;P55084;B5MD38;C9JEY0;C9JE81;C9K0M0 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ;;;;;;;; 127.94 0.00043119 2672164000 1642262 2031707 1414749 1379845 2526048 1270568 1370603 1935871 2874770 FALSE TRUE 1539475.753 2182136.7 1448307.514 1415254.159 2327662.38 1637360.356 1165093.804 2177568.756 2394952.315 0.642800169 0.911139936 0.604733341 0.590932082 0.971903434 0.683671381 0.486478915 0.909232615 1 21.1915655 1.014913433 23.75603831 1.000000072 0.704010805 0.358970266 0.144834123 113.7000741 181114.8799 0.138959811 0.034739953 10.34935854 -1.014913433 -0.295989267 DLMSWINGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLMSWINGIR 10 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 128.36 0.00077152 55671000 72820 79406 82658 79356 93015 80430 91537 74645 75040 FALSE TRUE 68262.32619 85285.30286 84618.68679 81392.40931 85709.9771 103648.8353 77811.87664 83964.59256 62515.33922 1.091929229 1.364230026 1.353566786 1.301959012 1.371023147 1.657974453 1.244684546 1.343103846 1 15.9319226 0.435055768 1.715525832 1.000102695 1.353660225 0.368051364 0.139792517 4.684634717 13.05504282 0.12405544 0.034967465 2.723050954 -0.435055768 0.35355753 QVKPYVEEGLHPQIIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QVKPYVEEGLHPQIIIR 17 1 Q99832-3;Q99832;Q99832-4;F8WAM2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 168.32 1.27E-09 1294260000 4051130 4100720 3783270 3842650 5274800 4349800 7179800 3955810 9523500 FALSE TRUE 3797577.005 4404341.576 3873010.951 3941258.905 4860538.486 5605516.647 6103255.644 4449701.586 7933966.326 0.478647986 0.555124813 0.488155708 0.496757705 0.612624038 0.706521356 0.76925656 0.560842006 1 22.91961084 0.195411202 0.219316981 1.180189357 0.423514293 0.782713305 0.075101671 3.141254424 0.30703325 0.671231988 0.214155637 1.568235216 -0.195411202 -0.756675064 DLMVGDEASELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DLMVGDEASELR 12 0 P61160 P61160 ACTR2 Actin-related protein 2 0 ;;;; 223.78 5.03E-11 1130996000 818530 932127 891400 859149 931018 714087 1006919 775409 976923 FALSE TRUE 767299.6684 1001142.653 912544.4289 881196.2179 857899.6018 920232.3247 855940.8437 872220.5205 813868.2401 0.942781191 1.230104093 1.121243445 1.082725894 1.054101339 1.130689563 1.051694613 1.071697454 1 19.63443573 1.160317415 0.483446788 0.99898699 1.122915331 0.077805122 0.074000766 1.585194981 0.992959275 0.080980414 0.043535553 14.46496592 -1.160317415 0.123928341 DLNES(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLNESPVK 8 0 Q96RL1-2;Q96RL1-3;Q96RL1;Q96RL1-4 Q96RL1-2 UIMC1 BRCA1-A complex subunit RAP80 1 DLNES(1)PVK;DLNES(1)PVK;DLNES(1)PVK;DLNES(1)PVK 137.78 0.00076945 1873290000 5354480 3244900 3877060 3396190 3868180 3041590 4958860 3634680 4321910 TRUE FALSE 5019352.655 3485155.772 3969025.694 3483341.985 3564388.746 3919647.657 4215324.979 4088477.799 3600555.3 1.394049594 0.967949519 1.102337102 0.967445767 0.989955284 1.088623096 1.170743018 1.135513124 1 21.77978799 -0.854129244 7.895264868 1.000000005 1.088275071 0.051859552 0.125376347 0 0 0.111895843 0.026374103 0.139917087 0.854129244 0.088275066 DLNHVCVISETGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLNHVCVISETGK 13 0 P00492 P00492 HPRT1 Hypoxanthine-guanine phosphoribosyltransferase 0 ; 162.37 4.06E-05 740260000 693230 584710 647790 665260 659690 521300 813710 554450 654880 FALSE TRUE 649841.9718 628002.5368 663155.8847 682331.6979 607880.6085 671790.8474 691701.7396 623674.303 545576.2973 1.191111078 1.151081049 1.215514472 1.250662284 1.11419908 1.231341704 1.26783686 1.143147725 1 19.05742144 0.982851797 22.23795652 0.999999997 1.202636492 0.671715338 0.044918903 150.6791413 195403.2611 0.043497102 0.010874276 9.612841836 -0.982851797 0.202636494 DLNYCFSGMSDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 DLNYCFSGMSDHR 13 0 P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7;H0YBG7;P55795 P31943;P55795 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 ;;;;;;;;;;; 218.6 2.39E-11 14810520000 4485640 8949620 7253660 7264840 8923550 6394840 8104130 7870310 8741400 FALSE TRUE 4204891.799 9612259.177 7425720.241 7451268.094 8222730.379 8240926.496 6888990.942 8852935.528 7282403.868 0.577404367 1.319929429 1.019679817 1.023187979 1.129123093 1.131621734 0.945977601 1.215661159 1 22.79598332 4.754656835 24.90881358 1.096150832 0.577403958 0.687259271 0.110389884 1787.271504 2765744.959 0.025711627 0.676106284 56840.36197 -4.754656835 -0.518746875 DLPAIQES(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLPAIQESPTR 11 0 P49796-1;P49796-4;P49796-6;P49796 P49796-1 RGS3 Regulator of G-protein signaling 3 1 DLPAIQES(0.997)PT(0.003)R;DLPAIQES(0.842)PT(0.158)R;DLPAIQES(0.5)PT(0.5)R 231.69 9.21E-13 1775808000 765965 719310 749327 698468 670647 720776 857998 645415 655510 TRUE FALSE 718024.6179 772568.4608 767101.3903 716391.8714 617977.0899 928852.3304 729349.1652 725996.4835 546101.1462 1.314819833 1.414698479 1.404687384 1.311830009 1.131616541 1.700879657 1.335556921 1.329417615 1 19.05880866 0.719388835 2.529884029 1.000155688 1.383296233 0.406459123 0.14044073 1.5306867 12.50651757 0.123677611 0.033002063 5.240694396 -0.719388835 0.383140544 DLPAIQES(ph)PTRDLPPCQDLPPSQVSLPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLPAIQESPTRDLPPCQDLPPSQVSLPAK 29 1 P49796-1;P49796-4;P49796-6;P49796 P49796-1 RGS3 Regulator of G-protein signaling 3 1 DLPAIQES(0.976)PT(0.024)RDLPPCQDLPPSQVSLPAK;DLPAIQES(0.971)PT(0.029)RDLPPCQDLPPSQVSLPAK;DLPAIQES(0.981)PT(0.019)RDLPPCQDLPPSQVSLPAK 218.79 1.37E-34 192922000 105307.9 100441.7 103946.2 112335 120550.9 77684.1 126188 89460.5 190386 TRUE FALSE 98716.86652 107878.508 106411.853 115217.7063 111083.3186 100110.2386 107267.2809 100629.8404 158609.3467 0.62238997 0.680152275 0.67090531 0.726424443 0.700357961 0.6311749 0.676298611 0.634450885 1 17.27511826 -1.226912246 5.010435289 1.000044069 0.670664642 0.913245331 0.03216966 1.49E-05 2.31E-06 0.02939502 0.006927547 0.059304514 1.226912246 -0.329379427 DLPDEVR ddPTM_SK-BR-3_Pertuzumab_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 ; 89.703 0.041126 412550000 826310 1049290 854530 926620 952820 719770 1050400 795800 917300 FALSE TRUE 774592.7321 1126980.523 874799.8551 950398.638 877989.3607 927555.9145 892902.2714 895157.3818 764196.704 1.013603864 1.474725705 1.144731259 1.243657075 1.14890493 1.213765919 1.168419422 1.171370378 1 19.54358451 -0.150965868 0.245929272 0.905703767 1.278226429 0.205298413 0.11675427 10.10861611 0.932236635 1.029278907 0.212799767 0.706373067 0.150965868 0.372522661 DLPDGHAAS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLPDGHAASPR 11 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 DLPDGHAAS(1)PR;DLPDGHAAS(1)PR;DLPDGHAAS(1)PR 141.37 4.00E-05 2023320000 1007180 1060930 1074320 1156800 1210570 756723 795661 667976 969530 TRUE FALSE 944142.4017 1139482.361 1099803.378 1186485.446 1115496.715 975176.6457 676359.0196 751374.274 807709.1796 1.168913794 1.410758216 1.361632882 1.468951296 1.381062322 1.207336341 0.837379389 0.930253479 1 19.62347641 1.93194738 3.469681654 0.91258879 1.368792956 0.839166428 0.086718521 0.08151663 1.791456237 0.040092997 0.022651594 85.4963117 -1.93194738 0.456204166 DLPEFGTQGGVHVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLPEFGTQGGVHVHK 15 0 A0A3B3IS07;A0A3B3IRM4;O75191 A0A3B3IS07 XYLB Xylulose kinase 0 129.71 3.71E-05 21939000 49813 51131 50331 44520 53111 44627 54202 47398 57050 FALSE TRUE 46695.29325 54916.79244 51524.87509 45662.45857 48939.8763 57510.09044 46074.91329 53315.74464 47527.98644 0.98247994 1.155462214 1.084095476 0.960748855 1.029706494 1.210025813 0.969426999 1.121775792 1 15.53648966 -5 0.273709526 0.517535692 1.074026731 0.041028214 0.082915603 686.7918789 6.639796992 187.810445 0.09339849 1.00E-05 5 0.556491039 DLPEHAVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 ;;;;;; 109.44 0.002449 8837910000 17338680 16978210 15106150 14421930 19190480 11288530 16498230 15854930 19948910 FALSE TRUE 16253482.97 18235294.33 15464475.01 14792021.14 17683337.11 14547345.36 14024473.57 17834452.91 16619308.05 0.977987948 1.097235474 0.930512568 0.890050362 1.064023668 0.875327981 0.843866275 1.073116454 1 23.98635698 3.829842314 4.396418732 0.938826694 1.041111228 0.133151169 0.081755312 0.31504269 10.41241651 0.020404346 0.038060091 6758.375435 -3.829842314 0.102284534 DLPERDQFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLPERDQFR 9 1 Q9NV31 Q9NV31 IMP3 U3 small nucleolar ribonucleoprotein protein IMP3 0 108.43 0.0023825 164200000 344670 414370 338580 324470 346590 287810 364700 311940 342450 FALSE TRUE 323097.72 445050.386 346611.2775 332796.4495 319370.2195 370896.0748 310016.6207 350886.3957 285292.8827 1.132512374 1.559977178 1.214931386 1.166508068 1.119446852 1.300053725 1.0866609 1.229916402 1 18.12208423 2.875840425 0.220093921 0.985244952 1.492251402 0.262791481 0.129808672 5.209232362 0.536862015 0.303648359 0.805320331 751.3467715 -2.875840425 0.50700645 DLPLLLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLPLLLFR 8 0 A0A286YFA2;A0A286YF22;O43175;A0A2C9F2M7 A0A286YFA2 PHGDH D-3-phosphoglycerate dehydrogenase 0 ; 94.662 0.02373 49928000 109328 238820 115222 122686 285630 93788 116782 218440 175940 FALSE TRUE 102485.3556 256502.4813 117955.1203 125834.3305 263197.772 120863.0731 99271.62325 245712.7148 146574.4774 0.699203282 1.749980528 0.80474529 0.858500966 1.795658949 0.824584711 0.677277689 1.676367668 1 17.16127439 DLPS(ph)PDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLPSPDSR 8 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 DLPS(0.999)PDS(0.001)R;DLPS(1)PDSR 116.52 0.0023665 368080000 805400 855310 835540 905960 940220 675430 862040 718630 889550 TRUE FALSE 754991.4517 918638.0423 855359.4034 929208.4674 866378.9139 870415.6763 732785.1048 808352.5374 741078.3583 1.018774119 1.239596369 1.154209125 1.253859942 1.169078687 1.174525833 0.988809208 1.090778766 1 19.49926657 1.763261183 11.11627638 1.030354639 1.178277202 0.48577998 0.068228478 0.178928684 76.28994578 0.028639126 0.015771828 57.97772668 -1.763261183 0.147922563 DLPSHTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLPSHTK 7 0 Q9P013 Q9P013 CWC15 Spliceosome-associated protein CWC15 homolog 0 ; 82.452 0.02445 585600000 700330 681140 746500 670350 751960 534850 815740 695280 777580 FALSE TRUE 656497.5954 731572.3143 764207.3325 687552.3159 692904.0949 689252.5124 693427.36 782087.2385 647796.8746 1.013431248 1.129323624 1.179702099 1.061370227 1.069631735 1.06399481 1.070439496 1.207303198 1 19.30518198 3.185908243 24.99955548 1.079997314 1.1224831 0.02433615 0.06550772 239.7060135 113812.2687 0.018030768 0.021550904 1534.292787 -3.185908243 0.042485786 DLPTIPGVT(ph)SPSSDEPPMEASQSHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLPTIPGVTSPSSDEPPMEASQSHLR 26 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVT(0.651)S(0.295)PS(0.053)S(0.001)DEPPMEASQSHLR;DLPTIPGVT(0.628)S(0.363)PS(0.008)S(0.002)DEPPMEASQSHLR 176.26 2.00E-12 463030000 412550 343800 407450 360550 399410 371690 448370 384430 501020 TRUE FALSE 386729.2319 369255.3097 417114.9064 369802.3234 368041.9497 478990.8691 381141.081 432426.9317 417396.5253 0.926527195 0.884663114 0.999325297 0.885973651 0.881756142 1.147567936 0.913139084 1.036009898 1 18.67105906 DLPTIPGVTS(ph)PSSDEPPMEASQSHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLPTIPGVTSPSSDEPPMEASQSHLR 26 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVT(0.002)S(0.992)PS(0.006)S(0.001)DEPPMEASQSHLR;DLPTIPGVT(0.394)S(0.534)PS(0.054)S(0.018)DEPPMEASQSHLR;DLPTIPGVT(0.042)S(0.957)PS(0.001)SDEPPMEASQSHLR;DLPTIPGVT(0.154)S(0.8)PS(0.036)S(0.009)DEPPMEASQSHLR 219.09 2.14E-34 812750000 644487 552650 694076 573822 657430 598341 675840 626313 781040 TRUE FALSE 604149.7091 593568.781 710539.8105 588547.244 605798.0997 771072.3334 574504.0662 704509.5567 650679.3783 0.928490635 0.91222928 1.091996818 0.904511905 0.931023973 1.185026542 0.882929574 1.082729191 1 19.31158731 DLPTIPGVTSPSSDEPPMEAS(ph)QSHLRNSPEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDK 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEAS(0.333)QS(0.333)HLRNS(0.333)PEDK;DLPTIPGVTSPSSDEPPMEAS(0.366)QS(0.366)HLRNS(0.268)PEDK;DLPTIPGVTSPSSDEPPMEAS(0.36)QS(0.36)HLRNS(0.28)PEDK 150.8 3.44E-10 308270000 556850 409703 517300 453548 515700 326566 526130 413527 782210 TRUE FALSE 521997.7525 440037.8364 529570.6003 465186.8095 475199.0022 420840.3028 447241.6909 465156.7562 651654.0977 0.801035019 0.675262901 0.812655981 0.71385542 0.729219695 0.645803202 0.686317622 0.713809301 1 19.31374685 -0.577817822 5.709104885 1.000000002 0.720144668 0.741063362 0.051584812 6.23E-09 38905371.76 0.208999548 0.011967278 0.264351743 0.577817822 -0.279855334 DLPTIPGVTSPSSDEPPMEAS(ph)QSHLRNSPEDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 33 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTS(0.002)PS(0.024)S(0.083)DEPPMEAS(0.297)QS(0.297)HLRNS(0.297)PEDKR;DLPTIPGVT(0.001)S(0.001)PS(0.003)S(0.012)DEPPMEAS(0.327)QS(0.327)HLRNS(0.327)PEDKR;DLPTIPGVTSPSSDEPPMEAS(0.333)QS(0.333)HLRNS(0.333)PEDKR;DLPTIPGVTSPSSDEPPMEAS(0.333)QS(0.333)HLRNS(0.333)PEDKR;DLPTIPGVT(0.001)S(0.001)PS(0.014)S(0.014)DEPPMEAS(0.323)QS(0.323)HLRNS(0.323)PEDKR;DLPTIPGVTSPSSDEPPMEAS(0.333)QS(0.333)HLRNS(0.333)PEDKR;DLPTIPGVTSPSSDEPPMEAS(0.726)QS(0.137)HLRNS(0.137)PEDKR 157.78 3.34E-12 3459600000 2093060 1759000 2016830 1838660 2098430 1330738 2241720 1688040 3502850 TRUE FALSE 1962059.111 1889238.19 2064670.16 1885843.128 1933627.772 1714900.458 1905594.897 1898795.51 2918201.706 0.672352123 0.647398083 0.707514548 0.646234674 0.662609363 0.587656588 0.653003147 0.650673155 1 21.47664817 -1.444971824 2.885752827 1.008635936 0.654719434 0.931885502 0.029444531 4515953.738 5252212.794 317216.7463 0.007206651 0.035894522 1.444971824 -0.353916501 DLPTIPGVTSPSSDEPPMEASQS(ph)HLRNSPEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDK 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEAS(0.107)QS(0.634)HLRNS(0.259)PEDK;DLPTIPGVTSPSSDEPPMEAS(0.084)QS(0.516)HLRNS(0.399)PEDK 277.43 1.88E-60 465670000 509720 351860 453760 426520 464940 323390 496360 373760 664580 TRUE FALSE 477817.5351 377912.0805 464523.4015 437465.2253 428425.4879 416747.4432 421935.426 420424.7587 553657.3046 0.863020376 0.682573999 0.839008892 0.790137187 0.773809872 0.752717321 0.762087707 0.759359183 1 19.07863375 -2.043230529 2.596859532 1.293849259 0.773087072 0.66874307 0.049037286 4513370.018 1321096.309 7905905.986 0.011178428 0.00905252 2.043230529 -0.520762188 DLPTIPGVTSPSSDEPPMEASQS(ph)HLRNSPEDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 33 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEAS(0.147)QS(0.54)HLRNS(0.313)PEDKR;DLPTIPGVTSPSSDEPPMEAS(0.118)QS(0.679)HLRNS(0.202)PEDKR;DLPTIPGVTSPSSDEPPMEAS(0.139)QS(0.783)HLRNS(0.078)PEDKR 245.8 3.23E-47 1614630000 562340 463210 549570 480460 557730 372975 594040 441070 924990 TRUE FALSE 527144.1432 497506.5504 562606.0599 492789.417 513928.1356 480646.8278 504969.2168 496138.5604 770603.1933 0.684066907 0.645606656 0.730085295 0.639485304 0.666916696 0.623728051 0.655290844 0.643831436 1 19.55562864 -1.652767895 2.926543798 1.03244692 0.66317585 0.929075917 0.029419818 7050210.479 7223437.432 1728214.499 0.007295843 0.022244984 1.652767895 -0.36927107 DLPTIPGVTSPSSDEPPMEASQSHLRNS(ph)PEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDK 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEASQS(0.001)HLRNS(0.999)PEDK;DLPTIPGVTSPSSDEPPMEAS(0.004)QS(0.017)HLRNS(0.979)PEDK 208.34 2.02E-27 597810000 459880 349790 389420 354890 386460 259242 425970 309100 640870 TRUE FALSE 431096.9317 375688.8156 398657.2263 363997.0782 356108.9905 334080.957 362099.753 347691.8154 533904.6568 0.80744179 0.703662743 0.74668243 0.681764194 0.666989857 0.625731491 0.678210516 0.651224542 1 19.02622261 -1.774087504 6.205283328 1.012091688 0.694973216 0.779589937 0.050930703 0.008638578 0.0003145 0.050000916 0.011674299 0.016823351 1.774087504 -0.317118472 DLPTIPGVTSPSSDEPPMEASQSHLRNS(ph)PEDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 33 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEAS(0.116)QS(0.116)HLRNS(0.767)PEDKR;DLPTIPGVTSPSSDEPPMEAS(0.145)QS(0.145)HLRNS(0.709)PEDKR 192.52 2.21E-20 560900000 376097 300172 360916 324804 376054 249305 402486 311588 602329 TRUE FALSE 352557.7601 322397.0472 369477.098 333139.0205 346520.2358 321275.3064 342136.9608 350490.4477 501796.3987 0.702591252 0.642485773 0.736308788 0.663892809 0.690559431 0.640250323 0.681824265 0.698471429 1 18.93674259 0.569325176 2.751658247 0.999997559 0.679810635 0.927550474 0.027974002 1.598364738 9.919203138 0.025257511 0.006661791 3.709583715 -0.569325176 -0.320186924 DLPVSEQQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLPVSEQQER 10 0 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2;H0YD73;E9PL38 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 121.93 0.0011679 186950000 103300 92258 99760 109140 102110 73280 106570 83388 113980 FALSE TRUE 96834.6374 99088.87831 102126.3543 111940.7172 94090.69249 94434.7464 90590.81785 93799.17536 94956.00166 1.019784276 1.043524123 1.075512369 1.178869321 0.990887262 0.99451056 0.954029406 0.987817239 1 16.53497157 2.512128356 24.98941668 0.979799862 1.073996832 0.545518202 0.042453855 455.4902429 325145.983 0.013616977 0.012832675 325.1833915 -2.512128356 0.094196969 DLPVTEAVFSALVTGHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLPVTEAVFSALVTGHAR 18 0 P42704;B8ZZ38;A0A0C4DG06;C9JCA9 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ; 211.78 2.65E-16 113962000 138683 155457 148062 132446 184098 136001 130917 146071 213100 FALSE TRUE 130003.0786 166967.198 151574.1006 135844.7886 169639.6857 175262.2809 111287.2112 164308.2859 177532.2333 0.732278731 0.940489481 0.853783551 0.765183798 0.955543016 0.987213858 0.626856369 0.925512414 1 17.43772146 -0.623607776 8.072568729 0.999999998 0.847558086 0.151220161 0.11289152 0 0 0.104524362 0.024636628 0.237898785 0.623607776 -0.152441912 DLQANVEHLVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLQANVEHLVQK 12 0 A0A2R8Y891;P08237;P08237-3;P08237-2 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 138.02 8.19E-05 214650000 409790 401970 388000 379710 427710 305900 452910 364070 468900 FALSE TRUE 384141.9754 431732.277 397203.5432 389454.0014 394119.3819 394208.3641 385000.3501 409524.9409 390637.5608 0.983371836 1.105199091 1.016808375 0.996970186 1.008913175 1.009140963 0.985569205 1.048350138 1 18.57547115 3.633545221 4.542799602 1.006197905 1.055277007 0.144009061 0.033355424 0.241513115 8.578871972 0.008096812 0.012942164 4300.760127 -3.633545221 0.049079101 DLQEQDADAGS(ph)ER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLQEQDADAGSER 13 0 Q6P158-2;Q6P158;A0A087WW12;A0A087WZ11;Q6P158-3 Q6P158-2 DHX57 Putative ATP-dependent RNA helicase DHX57 1 DLQEQDADAGS(1)ER;DLQEQDADAGS(1)ER 307.07 6.48E-42 2260900000 2660300 2809600 2745700 2720700 2780000 2392500 3291100 2418400 2410100 TRUE FALSE 2493796.572 3017625.707 2810829.301 2790517.768 2561670.014 3083175.911 2797630.108 2720342.564 2007838.74 1.242030309 1.502922345 1.399927815 1.389811698 1.275834539 1.53556949 1.393353984 1.35486108 1 20.93721197 0.693958953 2.657453139 1.000042467 1.405308531 0.653845089 0.088386443 1.225204956 9.937922325 0.077012325 0.020415347 4.942639702 -0.693958953 0.405266064 DLQGAT(ph)EER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLQGATEER 9 0 A0A087WWW8;Q9Y6J0;Q9Y6J0-2 A0A087WWW8 CABIN1 Calcineurin-binding protein cabin-1 1 DLQGAT(1)EER 95.483 0.089589 181450000 121280 247290 221350 211480 233200 207170 178130 203820 200070 TRUE FALSE 113689.3013 265599.6089 226600.5265 216906.9348 214885.4127 266976.6159 151421.0602 229267.3757 166677.0245 0.682093418 1.593498622 1.359518669 1.301360733 1.289232354 1.601760151 0.908469902 1.37551877 1 17.34669572 1.7289939 24.99999422 1.101519476 1.343542368 0.102016743 0.277749567 1.469649965 3820.971835 0.116324786 0.064507953 53.5789132 -1.7289939 0.242022891 DLQGLTVEHAIDSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLQGLTVEHAIDSFR 15 0 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 ; 172.24 1.04E-06 289420000 350900 762350 639290 668440 705420 613350 551760 554980 484200 FALSE TRUE 328937.7954 818795.1872 654454.2607 685593.3021 650019.1587 790414.1881 469028.7103 624270.4747 403383.8919 0.815446035 2.029816271 1.622410497 1.699605056 1.611415755 1.959458977 1.162735349 1.547584044 1 18.62179395 1.074291247 0.993791518 1.030097718 1.661076631 0.178903714 0.356541723 0.725082411 1.542614958 0.302155621 0.101759389 11.86564217 -1.074291247 0.630978913 DLQHPNEFIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLQHPNEFIR 10 0 P53618;E9PP73;E9PP63;E9PKQ1 P53618 COPB1 Coatomer subunit beta 0 ;;; 132.17 0.0002307 2376250000 2399920 3864610 2444640 2665380 3728140 1823180 2852270 3192970 3595010 FALSE TRUE 2249713.291 4150749.746 2502628.015 2733778.163 3435346.923 2349502.469 2424598.593 3591619.333 2994979.606 0.751161472 1.385902507 0.835607698 0.912786904 1.147035164 0.78448029 0.809554291 1.199213285 1 21.51411475 3.752024306 22.91930843 0.935633142 1.112936231 0.034061307 0.203570922 295.8919054 272316.9797 0.047959861 0.086387445 5649.68594 -3.752024306 0.177303089 DLQNVNITLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLQNVNITLR 10 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 115.91 0.0026978 62694000 49398 53647 47678 49173 58403 44963 54700 46099 60868 FALSE TRUE 46306.26736 57619.0797 48808.94468 50434.86243 53816.26397 57943.08819 46498.24281 51854.56163 50708.73758 0.91318123 1.136275176 0.962535196 0.994599054 1.061281872 1.142664774 0.916967076 1.022596186 1 15.62994674 1.705938538 24.99999981 0.976509208 1.037849154 0.106496717 0.074928892 1.465778469 1116.143967 0.032323814 0.017925183 50.80875324 -1.705938538 0.061339946 DLQS(ph)PDFTTGFHSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLQSPDFTTGFHSDK 15 0 E9PDR5;Q9P2D0-2;Q9P2D0;E7EPI0 E9PDR5 IBTK Inhibitor of Bruton tyrosine kinase 1 DLQS(0.911)PDFT(0.088)T(0.001)GFHSDK 129.77 4.11E-05 169830000 271070 197510 247240 223750 214810 181700 302360 187240 175850 TRUE FALSE 254104.2126 212133.8459 253104.6496 229491.8038 197939.6891 234153.8403 257023.925 210617.3262 146499.499 1.734505677 1.448017552 1.727682697 1.566502312 1.351128779 1.598325196 1.754435522 1.437665846 1 17.16053621 0.9772224 19.5816525 0.999999994 1.594346361 0.688003106 0.126670959 57.11003552 49097.74597 0.11865087 0.029662718 9.48904267 -0.9772224 0.594346367 DLQS(ph)PDFTTGFHSDKIEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLQSPDFTTGFHSDKIEAK 19 1 E9PDR5;Q9P2D0-2;Q9P2D0;E7EPI0 E9PDR5 IBTK Inhibitor of Bruton tyrosine kinase 1 DLQS(0.997)PDFT(0.003)TGFHSDKIEAK 274.34 1.27E-39 574130000 1324200 712880 1031600 967930 889950 696960 1243500 722930 1202200 TRUE FALSE 1241320.686 765662.377 1056070.039 992768.7225 820056.9169 898161.0378 1057048.719 813189.4019 1001545.053 1.239405738 0.764481213 1.054440872 0.991237208 0.81879184 0.896775472 1.055418042 0.811934919 1 19.93379589 4.760006023 24.56079416 0.931331213 1.239406136 0.481193102 0.102638134 4047.123029 4634957.199 0.023306696 1.100574538 57544.79177 -4.760006023 0.308074923 DLQS(ph)SPPSLPLGFLGEGDAVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLQSSPPSLPLGFLGEGDAVTK 22 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLQS(0.544)S(0.399)PPS(0.058)LPLGFLGEGDAVTK 138.02 1.36E-06 33343000 25562 19071 22666 23388 21269 17537 26955 18714 29325 TRUE FALSE 23962.12005 20483.03668 23203.64822 23988.17568 19598.61854 22599.64721 22913.34799 21050.48409 24430.46805 0.980829348 0.838421787 0.949783204 0.98189587 0.802220346 0.925059936 0.937900491 0.861648825 1 14.57639388 -1.810561826 2.605312835 1.029269483 0.908731993 0.185111353 0.059496655 16767458.66 10690254.64 3081435.814 0.013648308 0.015468143 1.810561826 -0.120537491 DLQSNVEHLTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLQSNVEHLTEK 12 0 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ;;; 176.89 2.40E-05 2323310000 3853340 4276290 4076950 4271950 4412240 2923870 4993350 3617990 3054310 FALSE TRUE 3612166.328 4592910.961 4173657.179 4381575.469 4065720.469 3767943.804 4244643.523 4069704.016 2544525.929 1.419583226 1.805016372 1.64024942 1.721961415 1.597830237 1.480803854 1.66814709 1.599395773 1 21.27896546 -2.497126352 0.363862914 5.00E-15 1.66223243 0.749170171 0.11145245 28.59078577 1.200447423 22.73066869 0.075476245 0.003183271 2.497126352 1.66223243 DLQSS(ph)PPSLPLGFLGEGDAVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLQSSPPSLPLGFLGEGDAVTK 22 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLQS(0.313)S(0.555)PPS(0.132)LPLGFLGEGDAVTK;DLQS(0.191)S(0.802)PPS(0.007)LPLGFLGEGDAVTK;DLQS(0.047)S(0.857)PPS(0.097)LPLGFLGEGDAVTK 189.12 1.45E-17 209766000 167724 113889 145709 133155 149770 111017 172216 122675 188055 TRUE FALSE 157226.4542 122321.4601 149165.2863 136571.9827 138007.6683 143065.8057 146393.8096 137991.2438 156667.4056 1.003568379 0.780771594 0.952114358 0.871731948 0.880895856 0.913181687 0.934424164 0.880791019 1 17.25734554 -1.986714054 0.260683887 1.114844508 0.883141768 0.189230515 0.059285594 44.0796386 1.736874123 3.137663766 0.077087996 0.010310648 1.986714054 -0.23170274 DLQSSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DLQSSDR 7 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;; 231.29 8.62E-06 8810280000 7123280 7934680 7672180 7407370 8156450 6625710 8421880 7267410 9087980 FALSE TRUE 6677446.62 8522171.963 7854167.733 7597455.655 7515875.319 8538444.918 7159097.279 8174762.136 7571137.427 0.881960826 1.125613165 1.037382799 1.003476126 0.99270095 1.127762506 0.94557751 1.079727084 1 22.85207862 DLRPVDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLRPVDNR 8 1 P42285 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 ;; 78.334 0.028174 1175780000 996650 1008670 1088500 1119010 1055890 948670 1317920 1000720 1073820 FALSE TRUE 934271.4556 1083352.976 1114319.734 1147725.691 972964.6587 1222535.629 1120310.131 1125662.095 894592.5049 1.044354218 1.211001624 1.245617114 1.282959208 1.08760654 1.366583804 1.252313344 1.258295915 1 19.77087115 4.748594584 3.325379231 1.231736735 1.016821633 0.19174706 0.103609716 0.455938153 8.179133276 0.021865358 0.254266291 56052.448 -4.748594584 -0.214915102 DLS(ph)LEEIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DLSLEEIQK 9 0 P16949;P16949-2;A2A2D0;E5RGX5;Q93045;Q93045-2 P16949;E5RGX5 STMN1;STMN2 Stathmin;Stathmin-2 1 DLS(1)LEEIQK;DLS(1)LEEIQK;DLS(1)LEEIQK;DLS(1)LEEIQK;DLS(1)LEEIQK;DLS(1)LEEIQK 181.31 5.00E-05 286578000 731290 440071 521755 532286 596374 359381 639123 428833 695779 TRUE FALSE 685519.8643 472654.3147 534131.275 545945.3599 549537.1917 463128.4606 543292.4395 482373.744 579648.99 1.182646526 0.815414713 0.921473658 0.941855104 0.948051668 0.798980881 0.937278334 0.832182497 1 19.14482001 DLS(ph)PEPAPDEGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLSPEPAPDEGPR 13 0 Q8TBE0-3;Q8TBE0-2;Q8TBE0 Q8TBE0-3 BAHD1 Bromo adjacent homology domain-containing 1 protein 1 DLS(1)PEPAPDEGPR;DLS(1)PEPAPDEGPR 213.06 9.40E-09 468110000 579780 468970 537760 498190 492630 434220 638110 438360 487860 TRUE FALSE 543492.6047 503693.0268 550515.9211 510974.3988 453940.827 559572.265 542431.3294 493090.2109 406433.0143 1.337225534 1.239301457 1.354505913 1.257216764 1.11688965 1.376788414 1.334614341 1.21321397 1 18.63265807 0.91163683 5.018555303 1.000033514 1.289267707 0.598655109 0.074198635 0.384346544 20.51845104 0.069058622 0.01745656 8.15899806 -0.91163683 0.289234192 DLS(ph)PEPAPDEGPRR ddPTM_SK-BR-3_Pertuzumab_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 114.96 0.0002738 941470000 1002510 904520 983220 960660 1040744 846795 1149320 820601 1198820 TRUE FALSE 939764.6886 971491.602 1006542.443 985312.162 959008.1644 1091250.97 976990.1358 923054.8412 998729.1973 0.940960464 0.972727747 1.007823187 0.986565893 0.960228425 1.092639499 0.978233277 0.924229354 1 19.92973402 4.626534493 1.770867326 0.99561081 0.929921123 0.130443737 0.042593139 1.385449959 5.267751904 0.0106157 0.141961454 42318.9119 -4.626534493 -0.065689687 DLS(ph)PQHMVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLSPQHMVVR 10 0 A0A2R8Y3N3;A0A2R8Y5P7;P49590-2;P49590;A0A2R8Y5E8;D6RB22 A0A2R8Y3N3 HARS2 "Probable histidine--tRNA ligase, mitochondrial" 1 DLS(1)PQHMVVR 173.19 2.25E-06 64959000 74669 65372 62085 54056 81443 63958 59760 61746 108470 TRUE FALSE 69995.60058 70212.2109 63557.68552 55443.16848 75046.79531 82421.63633 50799.54278 69455.12402 90365.65626 0.774581887 0.77697893 0.703338947 0.613542476 0.830479171 0.912090276 0.562155413 0.768600892 1 16.46348696 DLS(ph)PTLIDNSAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLSPTLIDNSAAK 13 0 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 1 DLS(0.995)PT(0.005)LIDNSAAK 178.22 1.55E-05 80968000 274810 199110 230420 209390 230780 167220 249750 179860 199640 TRUE FALSE 257610.1326 213852.3116 235885.6712 214763.3019 212655.4697 215493.6994 212302.3061 202315.9169 166318.7943 1.5488937 1.28579763 1.418274298 1.291275005 1.278601559 1.295666556 1.276478145 1.216434485 1 17.34359168 -4.438178451 0.087147387 3.84E-10 1.631596001 0.785488807 0.064279611 85.86278783 0.585395992 16.7017128 1.591651421 3.65E-05 4.438178451 1.631596 DLSDFHQSMAQWLAYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLSDFHQSMAQWLAYSR 17 0 Q70J99;Q70J99-3;K7EM66 Q70J99 UNC13D Protein unc-13 homolog D 0 139.17 1.20E-06 68042000 79611 223480 249750 165560 187460 159300 205480 185120 155270 FALSE TRUE 74628.28962 240026.6917 255674.1879 169808.5499 172737.6478 205287.324 174670.1816 208232.6395 129354.4339 0.576928733 1.855573748 1.976539808 1.312738534 1.335382503 1.587014204 1.350322338 1.609783547 1 16.98096998 DLSGFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLSGFYR 7 0 Q9H0G5;A0A024QZ33;K7ERM9 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 0 ; 88.029 0.043988 297620000 245240 290300 258480 266180 302930 227520 292020 220410 319200 FALSE TRUE 229890.8662 311794.1141 264611.2677 273010.6294 279139.0998 293201.3305 248234.312 247928.6737 265923.4579 0.864500138 1.172495712 0.995065534 1.026651171 1.049697165 1.10257791 0.93348031 0.932330963 1 18.02065152 1.681603613 8.257655688 0.950350323 1.046454282 0.168608079 0.080523034 0.16645114 20.04713327 0.035973143 0.018959439 48.040068 -1.681603613 0.096103958 DLSHIGDAVVISCAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLSHIGDAVVISCAK 15 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ;;; 240.59 1.76E-17 3088138000 9725760 8517290 9120040 8873090 10089560 7455850 11428090 9069450 11417090 FALSE TRUE 9117042.043 9147919.014 9336371.656 9100788.512 9297166.657 9608232.859 9714553.998 10201790.8 9511503.922 0.958527917 0.961774194 0.981587321 0.956819088 0.977465471 1.010169679 1.021347841 1.072573894 1 23.18124204 2.071314938 1.761570095 1.035417954 0.966618602 0.715184103 0.018928957 0.177997458 1.048309229 0.010123957 0.005394509 117.8460249 -2.071314938 -0.068799352 DLSIEEQSECAQDFYHNVAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLSIEEQSECAQDFYHNVAER 21 0 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 0 ; 195.39 2.47E-19 156205000 86994 95275 98867 99098 104673 92368 114624 84906 109832 FALSE TRUE 81549.20083 102329.2601 101212.1719 101641.0225 96452.40481 119033.1421 97437.19532 95506.701 91500.32966 0.891244885 1.118348541 1.10613997 1.110826844 1.054120845 1.30090397 1.064883544 1.043785321 1 16.48148932 4.739965389 24.41641796 1.109725198 0.891244785 0.39476851 0.080365871 81.63223822 1418651.8 0.017335824 0.108589115 54949.70798 -4.739965389 -0.218480413 DLSLDDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DLSLDDFK 8 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 ;;;; 141.39 0.0014757 739090000 2797730 1857220 2029460 1829780 2848660 1674100 2170100 2165810 3552980 FALSE TRUE 2622625.073 1994730.501 2077599.75 1876735.253 2624937.735 2157385.493 1844713.651 2436216.146 2959964.685 0.886032555 0.67390348 0.701900182 0.634039745 0.886813869 0.728855146 0.623221507 0.823055815 1 21.49714853 0.975188915 9.688404915 0.999999169 0.721334618 0.461874026 0.090945704 0.50750643 197.3166833 0.081805382 0.020464776 9.444716246 -0.975188915 -0.278664551 DLSLEVDRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLSLEVDRDR 10 1 E7EMW7;O95071-2;O95071;E5RFK7 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 0 104.43 0.0024463 70896000 80772 99846 86414 90782 96023 73721 100910 84494 100630 FALSE TRUE 75716.6247 107238.7017 88463.78089 93111.61981 88481.74092 95003.05594 85779.4823 95043.26189 83834.20291 0.903171046 1.279176017 1.055223021 1.110663865 1.055437254 1.133225493 1.023203887 1.133705082 1 16.35525134 -0.080155032 0.295172434 0.971157762 1.1182361 0.02863341 0.097657938 14.75507993 1.862456116 0.619193542 0.115065925 0.831466905 0.080155032 0.147078338 DLSLLSHGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLSLLSHGGR 10 0 A6NP24;Q08257;Q08257-2 A6NP24 CRYZ Quinone oxidoreductase 0 ;; 145.99 2.95E-05 801460000 675083 881400 791230 793040 974850 764150 756160 804890 932660 FALSE TRUE 632830.7601 946659.7731 809998.3492 813390.749 898289.2134 984747.7001 642780.8278 905382.2883 776993.0208 0.814461318 1.21836329 1.042478282 1.046844344 1.156109758 1.267382941 0.827267183 1.165238637 1 19.56754211 1.736053207 25 0.985213704 1.100864135 0.079336939 0.145493413 0.641453697 6276.360588 0.060845963 0.033742143 54.45693665 -1.736053207 0.115650432 DLSSAEAILALFPENFHQNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLSSAEAILALFPENFHQNLK 21 0 Q9P000;E9PJ95;Q9P000-2 Q9P000 COMMD9 COMM domain-containing protein 9 0 131.09 1.38E-05 95495000 246520 182730 218700 247200 270920 206060 272620 218050 190900 FALSE TRUE 231090.7533 196259.5193 223887.6673 253543.5705 249643.036 265546.1769 231743.1619 245274.0225 159037.5567 1.453057743 1.234045111 1.407766014 1.594237083 1.569711213 1.669707347 1.457159973 1.542239629 1 17.27900797 3.468274635 4.869807716 1.509983187 1.329800807 0.048552064 0.189933232 0.305953154 19.58373989 0.046059386 0.0668165 2939.507921 -3.468274635 -0.18018238 DLSSHQLNEFLAQTLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLSSHQLNEFLAQTLQR 17 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 293.2 4.78E-46 2180900000 1196360 1395840 1369340 1518240 1509990 1289280 1647290 1453910 1560600 FALSE TRUE 1121481.963 1499189.446 1401821.391 1557200.609 1391401.476 1661474.206 1400294.157 1635433.864 1300125.778 0.862594975 1.153111084 1.078219827 1.197730739 1.070205283 1.277933439 1.077045145 1.257904344 1 20.31021977 4.740250268 24.60595291 1.139846483 0.862594862 0.497194661 0.087356863 89.26322163 1299776.882 0.017640395 0.112750357 54985.76453 -4.740250268 -0.277251621 DLSSS(ph)PPGPYGQEMYAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DLSSSPPGPYGQEMYAFR 18 0 O43741;O43741-2 O43741 PRKAB2 5-AMP-activated protein kinase subunit beta-2 1 DLSS(0.01)S(0.99)PPGPYGQEMYAFR;DLSS(0.026)S(0.974)PPGPYGQEMYAFR;DLSSS(1)PPGPYGQEMYAFR;DLS(0.006)S(0.395)S(0.599)PPGPYGQEMYAFR;DLSSS(1)PPGPYGQEMYAFR;DLSS(0.214)S(0.785)PPGPYGQEMYAFR;DLSSS(1)PPGPYGQEMYAFR;DLSSS(1)PPGPYGQEMYAFR 291.68 3.95E-49 2948770000 2157920 2303850 2187920 2276290 2478140 1756120 2608690 2151420 2720290 TRUE FALSE 2022859.639 2474429.451 2239818.496 2334703.455 2283516.881 2263083.336 2217541.152 2420029.523 2266256.025 0.892599784 1.091857859 0.988334271 1.030202867 1.007616463 0.99860003 0.97850425 1.067853542 1 21.11187942 -1.546894054 3.065298483 0.999558394 1.010812877 0 0.053624973 996046438.5 147235062.8 3172422.754 0.011142307 0.028386114 1.546894054 0.011254484 DLSYCLSGMYDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DLSYCLSGMYDHR 13 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ;;;;;;; 210.91 2.62E-08 5558540000 4656540 7263920 5129480 4811490 8074720 3873030 5089230 6651160 7162040 FALSE TRUE 4365095.474 7801748.195 5251153.688 4934960.979 7440564.063 4991110.888 4326147.208 7481571.967 5966649.255 0.731582382 1.307559379 0.880084192 0.827090846 1.247025549 0.836501472 0.72505472 1.253898402 1 22.50848954 DLTDYLMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 DLTDYLMK 8 0 P60709;A0A2R8Y793;P63267-2;A0A2R8YEA7;Q562R1;P63261;I3L3I0;I3L1U9;I3L4N8;P68133;P68032;P63267;P62736 P60709;P63261;P68133 ACTB;ACTG2;ACTBL2;ACTG1;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Beta-actin-like protein 2;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 ;;;;;;;;; 203.57 0.00021994 12309223000 10939710 11760270 10055280 10000720 13616650 7228408 10492920 11024050 12124800 FALSE TRUE 10255013.08 12631012.63 10293795.99 10257355.41 12547253.24 9315132.046 8919604.057 12400426.91 10101092.55 1.015238008 1.250460043 1.019077485 1.015469896 1.242167931 0.922190545 0.883033594 1.227632243 1 23.26800801 2.217411642 24.99932331 0.983374892 1.111423806 0.126315018 0.123451215 380.4624843 449726.2026 0.044071423 0.032581978 164.9725329 -2.217411642 0.128048914 DLTEYLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DLTEYLSR 8 0 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 ;;;;; 233.83 3.52E-08 2449890000 2084510 2644810 2267340 2113280 2824960 1868580 2210720 2359120 3075240 FALSE TRUE 1954044.24 2840634.484 2321122.376 2167510.343 2603099.037 2408008.712 1879243.059 2653661.325 2561962.577 0.762713811 1.108772825 0.905993864 0.84603513 1.01605662 0.93990784 0.733516983 1.035792384 1 21.28881797 1.965980845 24.87548626 0.879298536 0.948542405 0 0.123555553 1733.058694 1267244.895 0.047652836 0.030759805 92.46573896 -1.965980845 0.069243869 DLTPEHLPLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLTPEHLPLLR 11 0 Q96C86;A0A3B3ITF0 Q96C86 DCPS m7GpppX diphosphatase 0 ;;; 163.12 2.43E-05 371050000 653530 715990 684280 658830 714330 555467 765620 607456 697370 FALSE TRUE 612626.7239 769002.6446 700511.4447 675736.6932 658229.4033 715821.3056 650822.3887 683298.2188 580974.4418 1.054481367 1.323642813 1.205752602 1.163109157 1.132974802 1.23210464 1.120225507 1.176124403 1 19.14811517 -0.541119031 0.286028551 0.916352793 1.223071794 0.342389596 0.073172198 9.377062266 0.854282401 0.809864223 0.089968729 0.287660989 0.541119031 0.306719001 DLTQMADELRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLTQMADELRR 11 1 P41227-2;P41227;C9JN83 P41227-2 NAA10 N-alpha-acetyltransferase 10 0 ;; 204.09 5.52E-08 797140000 618459 781396 749086 782068 823217 627768 777743 663772 857990 FALSE TRUE 579750.7552 839251.3729 766854.6737 802137.1889 758564.8575 808994.4306 661127.6574 746645.3953 714785.9262 0.811083058 1.174129683 1.072845233 1.122206187 1.061247612 1.131799607 0.924930994 1.044572043 1 19.4471517 1.74161503 24.99999917 0.986174942 1.07862769 0.086554708 0.101715717 0.919232954 7567.199361 0.042590109 0.023618397 55.15882798 -1.74161503 0.092452748 DLTTAGAVTQCYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLTTAGAVTQCYR 13 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 290.07 3.80E-40 327410000 173260 227345 155639 153878 228930 123772 167814 191968 183248 FALSE TRUE 162415.9659 244177.8604 159330.8306 157826.77 210950.7613 159502.9671 142651.8486 215935.6274 152662.725 1.063887507 1.599459596 1.043678675 1.033826496 1.381809222 1.044806236 0.934424881 1.414462027 1 17.21998832 3.806292556 6.059975963 1.11100722 1.360344771 0.150982745 0.20254252 0.301027846 18.040929 0.048211086 0.087678912 6401.659279 -3.806292556 0.249337551 DLTTGYDDSQPDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DLTTGYDDSQPDKK 14 1 Q96G03 Q96G03 PGM2 Phosphoglucomutase-2 0 ;;; 230.26 1.57E-12 1489050000 2132330 1100720 1433350 1386620 1517940 982980 1872250 1210040 2132380 FALSE TRUE 1998871.272 1182218.454 1467349.739 1422203.017 1398727.115 1266750.369 1591523.494 1361116.158 1776472.002 1.125191542 0.66548668 0.825990917 0.80057722 0.787362319 0.713070832 0.895889995 0.766190605 1 20.76058352 -1.89845839 8.411960047 1.026772611 0.808638442 0.159019006 0.124750808 0.049402599 0.000596344 0.095267788 0.02498639 0.012634021 1.89845839 -0.21813417 DLTVLCHLEQLLLVTHLDLSHNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLTVLCHLEQLLLVTHLDLSHNR 23 0 Q92696;H0YKZ8;H0YMG5;H0YLG7 Q92696 RABGGTA Geranylgeranyl transferase type-2 subunit alpha 0 ;; 315.39 8.89E-74 375414000 132902.3 183800 161426 161794 202566 118743.4 174995 182739.1 136631.7 FALSE TRUE 124584.1823 197408.7432 165255.101 165945.908 186657.2835 153022.6919 148756.1243 205554.4789 113826.9866 1.094504792 1.734287704 1.451809504 1.457878425 1.639833304 1.344344575 1.306861657 1.805850133 1 16.79648311 -1.515833939 2.928104244 0.981487971 1.484605129 0.340742524 0.209462128 26054478.48 30094168.75 3874419.765 0.04554745 0.030490606 1.515833939 0.503117159 DLVDDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLVDDFR 7 0 Q6NUQ1 Q6NUQ1 RINT1 RAD50-interacting protein 1 0 107.32 0.017459 52043000 265200 295760 295980 301880 306990 257650 368970 261580 311070 FALSE TRUE 248601.6054 317658.3781 303000.7854 309626.7519 282880.2437 332029.3724 313646.3738 294238.8388 259150.4074 0.959294673 1.225768392 1.169208215 1.19477625 1.091567814 1.281222653 1.210287018 1.13539794 1 17.98343014 0.929037476 7.509140123 1.00000096 1.175068136 0.238951382 0.08758098 1.645487197 173.7258126 0.076048388 0.019056425 8.492537562 -0.929037476 0.175067176 DLVEAVAHILGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLVEAVAHILGIR 13 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 221.52 4.42E-11 2652592000 1859033 2443120 2253807 2529734 2721379 1822705 2838733 2151629 2582083 FALSE TRUE 1742679.443 2624011.147 2307268.366 2594651.257 2507652.871 2348890.344 2413091.34 2420264.617 2151116.666 0.810127814 1.219836742 1.072590995 1.206188069 1.165744708 1.091940005 1.121785433 1.125120108 1 21.03665434 4.748388284 24.81960387 1.13180503 0.810127622 0.703791297 0.06415909 618.8090263 1562756.587 0.013598058 0.180465886 56025.82807 -4.748388284 -0.321677408 DLVHSNKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLVHSNKK 8 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 135.83 0.00053034 659840000 1969000 1584500 1699700 1628700 1972700 1228800 2113000 1732400 2515000 FALSE TRUE 1845763.805 1701818.029 1740017.687 1670495.199 1817772.099 1583534.612 1796175.266 1948693.953 2095230.252 0.880936022 0.812234372 0.830466095 0.797284784 0.867576295 0.755780712 0.857268677 0.930061959 1 20.99867736 1.127223673 2.403470113 0.997083548 0.823166801 0.741140532 0.035148435 0.116303816 1.261481719 0.028857303 0.008001555 13.40366832 -1.127223673 -0.173916748 DLVHTEGQLQNEEIVAHDGSATYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLVHTEGQLQNEEIVAHDGSATYLR 25 0 Q9Y547 Q9Y547 HSPB11 Intraflagellar transport protein 25 homolog 0 ;; 400.47 9.78E-140 481909000 153012 170557 164524 170314 167002 136980 204741 155444 164716 FALSE TRUE 143435.2521 183185.2177 168426.587 174684.5456 153886.3366 176523.9023 174041.9878 174851.5256 137223.8355 1.045264852 1.334937309 1.227385799 1.27298982 1.121425706 1.286393881 1.268307267 1.274206663 1 17.06617157 -1.297777963 4.41620053 0.999809108 1.240957715 0.405500385 0.085987047 0.000143682 2.28E-05 0.074020178 0.01743298 0.050375809 1.297777963 0.241148607 DLVIERPRPDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLVIERPRPDSR 12 2 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 ;; 158.58 4.11E-05 611900000 225393 215043 217732 209168 231057 188546 225284 203015 180850 FALSE TRUE 211286.0545 230965.0075 222896.7059 214535.605 212910.7153 242976.1694 191504.7556 228361.8696 150664.9667 1.402356893 1.532970886 1.479419608 1.423924949 1.413140161 1.612691887 1.271063605 1.515693228 1 17.20098447 -3.013515992 0.311138439 6.86E-15 1.485488453 0.701804554 0.092760018 37.45859298 1.052156856 24.57719047 0.079508064 0.000969358 3.013515992 1.485488453 DLVILLYETALLSSGFSLEDPQTHANR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DLVILLYETALLSSGFSLEDPQTHANR 27 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;; 278.26 5.65E-61 36715010000 14458096 14324997 14887844 14026513 16078978 13242896 18255750 14727291 14401621 FALSE TRUE 13553189.58 15385634.68 15240990.69 14386457.07 14816199.93 17065905.09 15518469.77 16566025.7 11997897.42 1.129630393 1.282360913 1.270305134 1.19908152 1.234899701 1.422407985 1.293432443 1.380744069 1 23.51627827 DLVLPTQALPAS(ph)PALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLVLPTQALPASPALK 16 0 Q15554;J3KSZ6;U3KQ35;H3BR06 Q15554 TERF2 Telomeric repeat-binding factor 2 1 DLVLPTQALPAS(1)PALK;DLVLPTQALPAS(1)PALK 208.37 1.58E-11 202813000 760060 529790 647100 582490 668480 552740 869170 605580 764040 TRUE FALSE 712489.2013 569016.2028 662449.5176 597437.6796 615980.2773 712307.065 738846.0275 681187.996 636516.7881 1.119356496 0.893953174 1.040741627 0.938604748 0.967736105 1.11907035 1.1607644 1.070180722 1 19.27983904 2.237432206 24.99963521 1.107963774 0.982902973 0.274002519 0.073078582 27.69198999 613483.9131 0.024096554 0.018807784 172.7556284 -2.237432206 -0.125060801 DLVMGS(ph)SPQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLVMGSSPQLK 11 0 Q53LP3 Q53LP3 SOWAHC Ankyrin repeat domain-containing protein SOWAHC 1 DLVMGS(0.747)S(0.253)PQLK 174.72 1.12E-05 64835000 449040 316110 369550 377610 313030 262950 457730 264210 271660 TRUE FALSE 420935.388 339515.1133 378315.9005 387300.1119 288445.8865 338859.3964 389097.6359 297197.2001 226318.191 1.859927327 1.50016714 1.671610659 1.711307916 1.274514811 1.497269817 1.71925038 1.313182996 1 17.78799302 -2.828742686 0.202617055 4.12E-19 1.697887793 0.598154883 0.161923464 37.69936408 0.824758714 16.78802378 0.394226905 0.001483397 2.828742686 1.697887793 DLVMGSS(ph)PQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLVMGSSPQLK 11 0 Q53LP3 Q53LP3 SOWAHC Ankyrin repeat domain-containing protein SOWAHC 1 DLVMGS(0.42)S(0.58)PQLK 197.79 5.86E-08 67679000 486850 368360 396590 403870 365000 305230 498440 302390 297280 TRUE FALSE 456378.9276 395633.7577 405997.3021 414233.988 336334.3723 393344.946 423703.5493 340144.0571 247662.0475 1.842748746 1.597474307 1.639319816 1.67257758 1.358037599 1.588232634 1.710813399 1.373420193 1 17.91801328 -2.716241888 0.231892187 2.52E-14 1.698909761 0.723638814 0.124612974 26.55319987 0.683006659 13.51367662 0.220804374 0.001922021 2.716241888 1.698909761 DLVPNHLSYYLYNHVAMWPEQSDKWPTAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLVPNHLSYYLYNHVAMWPEQSDKWPTAVR 30 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PRP1 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 106.37 0.00019731 115380000 105240 207120 106430 96336 202000 94639 162550 231820 103740 FALSE TRUE 98653.21626 222455.3803 108954.5699 98808.14486 186135.7348 121959.743 138177.1365 260763.2373 86425.12381 1.141487705 2.573966579 1.260681675 1.143280339 2.153722513 1.411160755 1.598807505 3.017215664 1 16.39916314 DLVQPDKPAS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DLVQPDKPASPK 12 1 Q6PJT7-5;Q6PJT7;G3V411;G3V4R5;Q6PJT7-9;Q6PJT7-2;H0YJA2 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 1 DLVQPDKPAS(1)PK;DLVQPDKPAS(1)PK;DLVQPDKPAS(1)PK;DLVQPDKPAS(1)PK;DLVQPDKPAS(1)PK;DLVQPDKPAS(1)PK 188.47 5.55E-06 5275100000 19715600 7151630 10831390 10435890 11132260 7411290 15475800 8700220 15137100 TRUE FALSE 18481635.79 7681144.126 11088315.69 10703692.61 10257977.2 9550809.111 13155347.46 9786461.619 12610620.22 1.465561207 0.609101217 0.879283928 0.848783995 0.813439547 0.757362362 1.043195912 0.776049191 1 23.5881359 -0.377141351 6.784720909 0.999999996 0.873604011 0.008017972 0.230080562 26669835.33 3930865.623 0.197302311 0.047852839 0.419622386 0.377141351 -0.126395984 DLVSSLTSGLLTIGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLVSSLTSGLLTIGDR 16 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 281.12 3.93E-35 502740000 279230 339330 292920 281130 336390 282530 333170 256070 307960 FALSE TRUE 261753.4927 364454.3463 299868.2007 288344.2718 309971.2863 364091.8245 283214.2515 288040.9032 256559.4865 1.020244842 1.420545197 1.168805741 1.12388856 1.208184856 1.419132184 1.103893118 1.12270611 1 17.96893385 1.573270793 9.573946271 1.080182682 1.239482131 0.243273858 0.125053616 0.152197541 26.81999425 0.063170814 0.029635578 37.43439275 -1.573270793 0.159299449 DLVVLLFETALLSSGFSLEDPQTHSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 DLVVLLFETALLSSGFSLEDPQTHSNR 27 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;;; 256.76 6.70E-53 34024540000 17396262.1 17758280.6 18201395.1 17962267.3 20534985.8 18132444.7 20874857.4 18096523.1 18687420.8 FALSE TRUE 16307461.11 19073122.17 18633140.79 18423209.49 18922250.85 23366987.13 17744866.33 20355913.84 15568369.54 1.047473922 1.225120082 1.196858845 1.183374369 1.215429194 1.50092706 1.139802487 1.307517386 1 23.89211452 4.740433309 5.236038517 1.231283533 1.039400864 0.152918061 0.126541234 0.275564241 26.11388419 0.026971904 0.190625565 55008.94419 -4.740433309 -0.191882669 DLVWLEEIQEEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLVWLEEIQEEAER 14 0 Q9NQS7-2;Q9NQS7;E9PM67 Q9NQS7-2 INCENP Inner centromere protein 0 129.84 0.00015255 9790300 12684 13083 11807 12153 10758 9937 13738 11157 10065 FALSE TRUE 11890.13108 14051.67893 12087.06762 12464.86655 9913.110076 12805.65059 11678.11444 12549.97601 8385.086478 1.418009357 1.675794158 1.441495881 1.486551938 1.182231108 1.527193622 1.392724389 1.496702037 1 13.03360995 -3.43586974 0.195721591 8.04E-15 1.556754374 0.561847665 0.124533322 49.30428885 0.843394566 20.474602 0.315697097 0.000366547 3.43586974 1.556754374 DLYANTVLSGGTTMYPGIADR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;; 283.49 8.51E-45 1159950000 931285 909005 951343 913721 1042211 805890 1055751 826590 1062299 FALSE TRUE 872997.5342 976308.676 973909.3052 937168.6278 960359.9521 1038537.36 897450.9387 929791.581 884994.4342 0.986444096 1.103180583 1.100469413 1.058954262 1.085159313 1.173495923 1.014075235 1.050618563 1 19.75530886 1.610278312 25 1.024255439 1.088064731 0.279544699 0.047435401 0.287016287 2932.251887 0.021388183 0.011154112 40.76414257 -1.610278312 0.063809292 DLYCHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLYCHK 6 0 P16220-1;P16220;P16220-3;Q03060-6;G5E998;Q03060-26;Q03060-32;Q03060-21;Q03060-31;E9PAR2;Q03060-23;Q03060-9;Q03060-24;Q03060-8 P16220-1;Q03060-6 CREB1;CREM Cyclic AMP-responsive element-binding protein 1;cAMP-responsive element modulator 0 76.592 0.07465 90704000 73167 93285 67265 74902 117270 50778 75068 102680 90583 FALSE TRUE 68587.60808 100191.9185 68860.55756 76824.11213 108060.0872 65436.78429 63812.2503 115499.824 75464.11211 0.908877162 1.32767637 0.912494107 1.018021812 1.431940087 0.86712455 0.845597311 1.530526508 1 16.2035031 DLYDAGVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DLYDAGVKR 9 1 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;H0YL33;H0YNP5;H0YN28 P07355-2 ANXA2 Annexin A2;Annexin 0 81.95 0.031799 694220000 553710 497570 559960 502590 650070 331770 637650 538500 1227100 FALSE TRUE 519054.2795 534410.6005 573242.5156 515487.3103 599016.1245 427546.6132 542040.3022 605732.9104 1022289.083 0.507737281 0.522758787 0.560744045 0.504248083 0.585955709 0.418224767 0.530222137 0.592526048 1 19.96337179 0.713330925 2.526367073 0.999930602 0.520727404 0.923156149 0.043325636 0.402477028 3.226981914 0.038817236 0.01035884 5.168100193 -0.713330925 -0.479203197 DLYDDKDGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DLYDDKDGLR 10 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ;;;; 153.11 1.54E-05 1198023000 5757220 3886970 4775070 4396360 4575710 3442600 5838100 3919130 5080570 FALSE TRUE 5396885.877 4174765.303 4888336.915 4509178.041 4216352.194 4436422.734 4962731.103 4408442.008 4232590.045 1.27507881 0.986338213 1.154928038 1.065347221 0.996163614 1.04815791 1.172504554 1.041547128 1 22.01310933 7.99999922 0.009981922 2.86E-13 2.310689891 0.164888824 0.084576883 32581.29558 25.13892432 2507.314944 3371.248994 99999820.31 -7.99999922 2.310689891 DLYDDKDGLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DLYDDKDGLRK 11 2 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ; 61.375 0.04933 257720000 937800 639320 724560 680990 753330 491490 897220 625920 951180 FALSE TRUE 879104.772 686655.918 741746.9054 698465.3563 694166.5006 633375.1843 762690.1904 704067.4898 792421.9131 1.10938978 0.86652818 0.936050471 0.881431148 0.876006189 0.799290345 0.962479934 0.888500782 1 19.59590925 4.743797885 24.94777454 0.898077693 1.109389871 0.582005929 0.055365481 366.4164799 1745371.953 0.011896701 0.102175354 55436.76577 -4.743797885 0.211312178 DLYEDELVPLFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DLYEDELVPLFEK 13 0 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;;;;; 250.94 1.05E-17 463926200 1500021 1272283 1366439 1247503 1439627 1044415 1665989 1183678 1799411 FALSE TRUE 1406137.363 1366484.157 1398851.578 1279516.039 1326564.503 1345920.656 1416189.416 1331462.804 1499077.679 0.938001668 0.911549932 0.933141489 0.853535515 0.884920455 0.897832497 0.944707159 0.888187999 1 20.51564371 -1.128111592 4.100936403 1.000023446 0.909352139 0.526399862 0.027758006 15500113842 3295553258 3684909.648 0.006471218 0.074454064 1.128111592 -0.090671307 DMAAFNERPIIFALSNPTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DMAAFNERPIIFALSNPTSK 20 1 P48163;P48163-2 P48163 ME1 NADP-dependent malic enzyme 0 196.89 1.56E-21 133340000 110660 114220 115480 106800 133670 100630 135370 103520 164070 FALSE TRUE 103733.9881 122676.9676 118219.2401 109540.6688 123172.0974 129680.2474 115072.5252 116444.6999 136685.6571 0.758923726 0.897511636 0.864898649 0.80140573 0.901134033 0.948748027 0.841877105 0.851916012 1 17.06050234 -5 0.19261473 1.57896346 0.84022038 0.445403521 0.051396061 139.4916444 1.369906124 31.13095469 0.129787599 1.00E-05 5 -0.738743079 DMAEAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DMAEAHK 7 0 F5H169;F5H5V4;F5GX23;J3KN29;O00233-2;O00233 F5H169 PSMD9 26S proteasome non-ATPase regulatory subunit 9 0 65.038 0.054364 32809000 52952 49091 53227 52049 50933 41798 53107 47292 61850 FALSE TRUE 49637.82884 52725.74872 54489.56958 53384.66546 46932.92763 53864.40407 45144.09837 53196.5103 51526.83543 0.963339363 1.023267745 1.057498857 1.036055582 0.910844364 1.045366043 0.876127905 1.032403986 1 15.65303637 2.768850267 24.87225405 0.964033087 1.026821366 0.133519137 0.055984705 891.7699819 732272.7272 0.015591035 0.016534815 587.2868367 -2.768850267 0.06278828 DMDEPS(ph)PVPNVEEVTLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DMDEPSPVPNVEEVTLPK 18 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK 297.23 2.37E-49 1439883000 2376520 1501538 1797510 1704005 1747344 1409228 2378440 1573722 2085470 TRUE FALSE 2227777.855 1612713.436 1840147.786 1747732.653 1610114.651 1816049.247 2021815.002 1770204.656 1737391.584 1.282254315 0.928238314 1.05914395 1.005952066 0.926742517 1.045273422 1.163707146 1.018886399 1 20.72849152 1.989893173 24.91715495 1.085413223 1.022796181 0 0.10798255 1294.046348 3190312.927 0.038665622 0.026895794 97.69968709 -1.989893173 -0.062617042 DMEESIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DMEESIR 7 0 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;; 147.69 0.0049651 1133180000 2066980 2067940 1985010 2145560 2198530 1557968 2347090 1908920 1771600 FALSE TRUE 1937611.411 2221052.429 2032095.375 2200618.702 2025866.322 2007728.07 1995165.644 2147252.864 1475908.515 1.31282623 1.504871343 1.376843723 1.491026496 1.372623236 1.360333686 1.351822029 1.454868538 1 20.49317187 -3.055026759 0.358220181 1.43E-10 1.421575679 0.791999518 0.064402539 40.11745163 1.192439607 30.36087954 0.043715498 0.000880995 3.055026759 1.421575679 DMES(ph)PTKLDVTLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 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(0.71)PT(0.29)KLDVTLAK;DMES(0.997)PT(0.003)KLDVTLAK;DMES(0.807)PT(0.193)KLDVTLAK;DMES(0.985)PT(0.015)KLDVTLAK;DMES(0.91)PT(0.09)KLDVTLAK;DMES(0.726)PT(0.274)KLDVTLAK;DMES(0.963)PT(0.037)KLDVTLAK;DMES(0.976)PT(0.024)KLDVTLAK;DMES(0.984)PT(0.016)KLDVTLAK;DMES(0.957)PT(0.043)KLDVTLAK;DMES(0.983)PT(0.017)KLDVTLAK;DMES(0.905)PT(0.095)KLDVTLAK;DMES(0.884)PT(0.116)KLDVTLAK 260.56 4.79E-24 9032460000 22448650 11052370 15024200 14317590 14396980 9188320 18210620 11168570 16534840 TRUE FALSE 21043629.07 11870698.97 15380581.12 14685003.6 13266299.27 11840838.82 15480106.59 12562990.55 13775068.38 1.527660588 0.861752453 1.11655207 1.066056675 0.963065946 0.859584758 1.123777114 0.912009305 1 23.71555615 4.747650339 24.98512412 0.997338194 1.527660865 0.761848513 0.094717825 579.6619099 1593295.83 0.021378107 0.266138446 55930.71087 -4.747650339 0.53032267 DMFCAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DMFCAGR 7 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;; 144.29 0.0054992 1842490000 1434060 2078710 1805220 1896410 2033430 1645200 1841000 1803470 1609340 FALSE TRUE 1344304.744 2232619.851 1848040.671 1945075.091 1873732.61 2120142.532 1564959.141 2028637.199 1340730.757 1.002665701 1.665226101 1.37838314 1.450757418 1.397545779 1.581333553 1.16724341 1.513083211 1 20.35458812 -0.760446428 0.483808954 0.893633248 1.427254847 0.269617689 0.195141007 15.52808915 2.684525765 2.6980519 0.088155671 0.17360154 0.760446428 0.533621599 DMFQETMEAMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DMFQETMEAMR 11 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 132.17 0.00043751 61761000 62289 127390 93377 101787 117217 56511 74491 111096 79968 FALSE TRUE 58390.44268 136822.0881 95591.94654 104399.0267 108011.2497 72824.80832 63321.76609 124966.5802 66620.82419 0.876459326 2.053743553 1.434865865 1.567062972 1.6212836 1.093123797 0.950480077 1.875788564 1 16.02368558 2.243471238 24.96569401 1.191495655 1.57696082 0.100942742 0.381949762 188.6751302 959231.7461 0.125183818 0.101645112 175.1746416 -2.243471238 0.385465166 DMGEDLECLCQIMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DMGEDLECLCQIMR 14 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 89.548 0.014204 17114000 23430 23198 24283 25787 24672 20300 31028 22341 26728 FALSE TRUE 21963.55812 24915.60406 24859.00423 26448.73808 22734.36064 26160.28046 26375.63945 25130.32303 22266.92413 0.986375936 1.118951316 1.116409437 1.187803844 1.020992415 1.17484931 1.18452101 1.128594272 1 14.44261466 4.743467361 4.225363266 1.127615673 0.974656302 0.27716099 0.064010974 0.25888216 10.53455728 0.013983083 0.120513833 55394.59104 -4.743467361 -0.152959372 DMGITLHLLLHSDRDPIPDVPAVYFVMPTEENIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DMGITLHLLLHSDRDPIPDVPAVYFVMPTEENIDR 35 1 Q8WVM8;G3V363;H0YJS6;J3KNG4;G3V2M8 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 87.893 0.00046215 75630000 59078 68874 61355 64289 76903 51129 72982 57897 69671 FALSE TRUE 55380.41344 73973.50262 62810.36957 65938.76458 70863.34859 65889.11229 62039.02663 65125.5679 58042.46001 0.954136221 1.274472216 1.082145201 1.136043589 1.220888098 1.135188141 1.068855914 1.122033213 1 15.82482105 0.869795499 0.828207339 1.002765894 1.14582629 0.15519761 0.086475154 1.203796405 1.728668059 0.075803025 0.02685638 7.409612545 -0.869795499 0.143060395 DMGSCEIYPQTIQHNPNGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DMGSCEIYPQTIQHNPNGR 19 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ;;;;; 287.54 2.12E-40 4237910000 2564657 2977557 2841755 3178128 3182555 2523781 3553113 2679717 3085725 FALSE TRUE 2404139.696 3198018.418 2909162.771 3259684.145 2932609.968 3252355.605 3020356.691 3014285.566 2570697.563 0.935209078 1.244027483 1.131662788 1.268015418 1.140783735 1.26516462 1.174917164 1.1725555 1 21.29372846 0.613118499 4.004446864 1.000000144 1.177192355 0.223845846 0.095693003 26.2768455 270.5165124 0.080073823 0.020452037 4.10316044 -0.613118499 0.17719221 DMGYGNWISKPQEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DMGYGNWISKPQEEK 15 1 A0A3B3IRQ9;P55265-3;P55265-2;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 206.95 3.32E-09 441610000 452540 305650 393460 401260 419590 248480 487120 354900 493580 FALSE TRUE 424216.3292 328280.644 402793.057 411557.0109 386637.0939 320212.1423 414080.8782 399210.0462 411198.3094 1.031658739 0.798351152 0.979559127 1.000872332 0.940269172 0.778729229 1.007010167 0.970845544 1 18.64947481 1.604221133 25 0.991703348 0.916032331 0.144542307 0.080712862 0.64835329 4416.030402 0.039562294 0.019425758 40.19954454 -1.604221133 -0.075671017 DMHGQFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DMHGQFK 7 0 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ; 64.836 0.054779 182257000 155344 199858 196957 188057 244570 136532 204422 180647 276690 FALSE TRUE 145621.2963 214655.6943 201628.913 192882.861 225362.4587 175946.572 173770.8189 203201.1756 230508.6515 0.631738962 0.931226194 0.874712995 0.836770593 0.977674622 0.763297043 0.753858121 0.881533835 1 17.81446137 -2.433588889 1.63360692 1.821062813 0.839285614 0.222075837 0.098205299 1367860.864 118131.4813 4127806.982 0.02587963 0.003684776 2.433588889 -0.981777199 DMHSAYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DMHSAYK 7 0 P08621;P08621-2 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;;;;; 151.29 0.0018911 3054210000 5054950 5105980 4983640 4767820 5783750 3891410 5582020 4847680 6423270 FALSE TRUE 4738569.703 5484032.072 5101854.294 4890170.333 5329517.606 5014796.895 4745047.922 5452923.519 5351184.741 0.885517868 1.024825779 0.953406496 0.913848161 0.995950965 0.937137688 0.886728482 1.019012384 1 22.35142691 3.50000771 22.40977779 0.947656944 0.972144017 0 0.053134139 440.8318597 431644.1203 0.013233681 0.020427981 3162.333798 -3.50000771 0.024487073 DMIHIADTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DMIHIADTK 9 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90;H0Y7E6 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 111.06 0.0026203 0 427190 364200 452900 441940 365790 409940 552430 394870 406430 FALSE TRUE 400452.9405 391165.7469 463643.0019 453280.9286 337062.3289 528283.0232 469598.25 444170.3887 338594.2074 1.182692827 1.155264143 1.369317584 1.338714363 0.995475769 1.560224634 1.386905741 1.311807406 1 18.36919777 2.229790525 24.99996786 1.358870626 1.22894788 0.054197687 0.171969957 401.8389813 1145470.062 0.058778725 0.044080282 169.742473 -2.229790525 -0.129922747 DMLEAGILDTYLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DMLEAGILDTYLGK 14 0 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 234.17 7.74E-17 92348000 363830 332480 355500 362220 390020 281600 411190 321030 342300 FALSE TRUE 341058.5298 357097.1651 363932.6279 371515.1784 359389.4025 362893.3486 349535.8768 361111.3022 285167.9187 1.195991931 1.252234707 1.276204664 1.302794438 1.260272909 1.272560218 1.225719493 1.266311105 1 18.12145216 -0.99144904 0.700014746 0.948841485 1.260055856 0.883635481 0.029215041 11.68571649 2.970410028 1.316555101 0.010142263 0.101988443 0.99144904 0.311214371 DMLLANKVPAAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DMLLANKVPAAAR 13 1 F8VWS0;P05388;P05388-2;F8VU65;F8VW21;F8VQY6;F8VRK7;G3V210;Q8NHW5;F8VWV4;F8VPE8 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 0 ; 150.11 4.02E-05 2329300000 2292370 3194900 2221780 2154520 3609600 1632800 3012700 2867400 3904700 FALSE TRUE 2148894.654 3431453.72 2274481.671 2209808.631 3326116.576 2104162.854 2560973.604 3225401.202 3252980.345 0.660592572 1.054864572 0.699199328 0.679318163 1.022482839 0.646841552 0.787269929 0.991521885 1 21.63333067 1.234335014 24.02911731 0.995761187 0.805214579 0.255929471 0.142585356 98.35718306 559252.6172 0.11324747 0.032334109 17.15279962 -1.234335014 -0.190546608 DMLLELEEQLAESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 159.5 1.14E-05 72229000 100919 109109 109757 104974 103811 93330 123804 89164 96182 FALSE TRUE 94602.65994 117187.5439 112360.4879 107667.8106 95658.10281 120272.8559 105240.7395 100296.3217 80128.60284 1.180635336 1.462493289 1.402251929 1.343687606 1.193807198 1.500997792 1.31339791 1.251691882 1 16.2900297 0.85146657 1.923703593 1.0008087 1.362701636 0.521877371 0.102279788 0.402372651 2.847525799 0.090678552 0.025332054 7.103404887 -0.85146657 0.361892937 DMPGGFLFEGLS(ph)DDEDDFHPNTR ddPTM_SK-BR-3_Pertuzumab_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 303.44 1.39E-61 2186025000 1093167 1156289 1170618 1120754 1204779 1038974.4 1300958 1036145 1390476 TRUE FALSE 1024747.629 1241901.841 1198385.612 1149514.445 1110160.517 1338909.443 1105891.425 1165509.984 1158396.573 0.884625916 1.072086943 1.034521027 0.992332395 0.958359635 1.155829941 0.95467429 1.006140739 1 20.14369781 4.750922901 24.72408032 1.02472631 0.884625815 0.350438017 0.058542607 1939.404987 3878650.948 0.01296983 0.23397184 56353.76041 -4.750922901 -0.140100495 DMQGLS(ph)LDAASQPSK ddPTM_SK-BR-3_Pertuzumab_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 318.94 1.89E-56 928130000 2296390 2409450 1648390 2119260 1713650 988540 3662630 2006690 2571420 TRUE FALSE 2152663.049 2587848.185 1687490.589 2173643.799 1579066.842 1273915.45 3113452.634 2257229.664 2142233.39 1.004868591 1.208014121 0.787724903 1.014662459 0.737112422 0.594666975 1.453367615 1.053680553 1 21.03068424 1.730350827 25 1.199884539 0.914616619 0.280731999 0.20542555 0.933184094 2825.523537 0.093781577 0.052006654 53.74657906 -1.730350827 -0.28526792 DMQPLS(ph)PISVHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DMQPLSPISVHER 13 0 P28749;P28749-2 P28749 RBL1 Retinoblastoma-like protein 1 1 DMQPLS(1)PISVHER;DMQPLS(1)PISVHER 155.94 0.00015721 780670000 621960 973870 949480 936180 990000 873130 1180630 957940 818220 TRUE FALSE 583032.6338 1045976.348 972002.114 960203.9637 912249.3935 1125188.457 1003605.492 1077540.918 681653.7961 0.855320747 1.534468603 1.425946895 1.408638768 1.338288437 1.65067438 1.472309694 1.580774469 1 19.37867967 4.743181477 24.91059261 1.455405729 0.855320492 0.498763469 0.177810661 324.1989241 1747661.151 0.036380946 0.29165614 55358.13843 -4.743181477 -0.600085237 DMS(ph)PLS(ph)ETEMALGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DMSPLSETEMALGK 14 0 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 2 DMS(1)PLS(0.836)ET(0.164)EMALGK;DMS(1)PLS(0.849)ET(0.151)EMALGK;DMS(1)PLS(0.898)ET(0.102)EMALGK;DMS(1)PLS(0.965)ET(0.035)EMALGK 114.69 0.00018211 96059000 818860 497576 600180 590010 565389 411435 687890 481863 524720 TRUE FALSE 767609.0143 534417.0448 614416.553 605150.6555 520985.6286 530209.6054 584747.2806 542024.6563 437140.8422 1.755976427 1.222528287 1.405534541 1.384337946 1.191802683 1.212903381 1.337663344 1.2399314 1 18.73773865 8 0.06037613 0.614134471 2.767873084 0.542200863 0.132702831 296.7766134 1.337385376 9.604229179 56.12536579 100000000 -8 2.153738614 DMS(ph)PLSET(ph)EMALGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DMSPLSETEMALGK 14 0 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 2 DMS(0.999)PLS(0.457)ET(0.544)EMALGK 73.91 0.0097959 0 70477 48571 55548 54388 56444 37134 65980 49402 63585 TRUE FALSE 66065.97038 52167.24738 56865.62479 55783.68816 52011.11592 47853.98298 56086.91153 55569.94845 52972.25273 1.247180684 0.984803264 1.073498329 1.053073737 0.981855844 0.903378288 1.05879793 1.0490388 1 15.69294924 4.743310492 24.73239699 1.015895055 1.247180794 0.68210639 0.050196949 262.9791086 1369267.031 0.011986071 0.098199613 55374.58602 -4.743310492 0.231285739 DMS(ph)PLSETEMALGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 DMSPLSETEMALGK 14 0 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 DMS(0.999)PLS(0.001)ETEMALGK;DMS(1)PLSETEMALGK;DMS(0.997)PLS(0.003)ETEMALGK;DMS(0.998)PLS(0.002)ETEMALGK;DMS(1)PLSETEMALGK;DMS(0.999)PLS(0.001)ETEMALGK;DMS(1)PLSETEMALGK;DMS(1)PLSETEMALGK;DMS(1)PLSETEMALGK;DMS(1)PLSETEMALGK;DMS(1)PLSETEMALGK 402.38 2.27E-132 1129141000 1972702 1255216 1545199 1477015 1410958 1029877 1564904 1114979 1374684 TRUE FALSE 1849234.103 1348153.499 1581851.85 1514917.705 1300147.05 1327185.771 1330261.173 1254186.583 1145240.36 1.614712656 1.177179522 1.381240049 1.322794549 1.135261292 1.158870939 1.161556316 1.09512957 1 20.12721899 8 0.133376369 0.927167049 2.708031836 0.65189315 0.102574971 52.51862271 0.471362358 0.474456807 17.68437985 99999999.97 -8 1.780864787 DMSGHYQNALYLGDVSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DMSGHYQNALYLGDVSER 18 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;;;; 160.27 3.43E-11 1129120000 766840 995640 933340 998370 969630 828380 1087870 881960 1038110 FALSE TRUE 718844.8532 1069358.222 955479.2656 1023989.864 893479.1711 1067519.858 924753.9928 992074.6474 864842.7346 0.83118563 1.236477083 1.104801171 1.184018578 1.033111727 1.234351421 1.069274165 1.147115664 1 19.72207829 -1.068355342 4.315804327 0.999990541 1.119074553 0.061776846 0.117865077 1.11E-05 2.39E-06 0.098216663 0.023147683 0.085436738 1.068355342 0.119084012 DMSPLSETEMALGKDVT(ph)PPPETEVVLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DMSPLSETEMALGKDVTPPPETEVVLIK 28 1 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 DMSPLSETEMALGKDVT(0.998)PPPET(0.002)EVVLIK;DMSPLSETEMALGKDVT(0.999)PPPET(0.001)EVVLIK;DMSPLSETEMALGKDVT(0.999)PPPET(0.001)EVVLIK;DMS(0.008)PLS(0.008)ET(0.007)EMALGKDVT(0.948)PPPET(0.03)EVVLIK 194.26 1.92E-18 414440000 1418277 1018716 1137642 1179365 1413490 770027 1473378 1011648 1931330 TRUE FALSE 1329509.574 1094142.793 1164627.405 1209629.503 1302480.197 992321.2946 1252458.647 1137954.48 1608978.546 0.826306589 0.680023233 0.723830289 0.751799647 0.809507498 0.616739917 0.778418488 0.707252736 1 20.61771366 -1.960351218 2.730109439 1.2094409 0.731268305 0.642321801 0.061619985 15827690.36 11113383.98 21048501.97 0.013241935 0.010955918 1.960351218 -0.478172594 DMVTELFDPLVQGEVQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DMVTELFDPLVQGEVQHR 18 0 Q9BXV9 Q9BXV9 C14orf142 Uncharacterized protein C14orf142 0 ;;;;; 230.93 1.06E-19 474716000 649414 678911 732463 687156 765696 615819 798230 672005 867713 FALSE TRUE 608768.337 729178.2768 749837.3683 704789.5863 705561.3248 793595.9483 678542.8219 755906.3035 722886.0947 0.842135907 1.008704251 1.037282877 0.974966307 0.976033887 1.097816038 0.938658008 1.045678301 1 19.46340881 4.73853723 9.922745268 1.009173514 0.841710968 0.591054456 0.043849734 0.04848948 152.1074582 0.009404415 0.054524473 54769.30495 -4.73853723 -0.167462546 DNAGQVTLVPEEPEDMWHTYNLVQVGDSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DNAGQVTLVPEEPEDMWHTYNLVQVGDSLR 30 0 Q9BRX2 Q9BRX2 PELO Protein pelota homolog 0 ; 127.59 1.20E-05 130631000 92959 96665 102305 100135 102211 90440 112297 94299 113247 FALSE TRUE 87140.86213 103822.1772 104731.7229 102704.6336 94183.76036 116548.5598 95459.10736 106072.4377 94345.3441 0.923637122 1.100448339 1.110088939 1.088603095 0.998287316 1.235339814 1.011805175 1.124299654 1 16.5256637 4.741177001 24.21001108 1.088446872 0.923637031 0.332447789 0.070946727 161.8127332 1497153.703 0.014604612 0.09947532 55103.22295 -4.741177001 -0.164809841 DNALLSAIEESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DNALLSAIEESR 12 0 H3BVG0;Q8N1F7;H3BM93;H3BNN5;H3BV11;H3BRI8 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 ; 168.82 0.00010584 37257000 45179 49831 54289 56379 57158 45751 62288 51931 54518 FALSE TRUE 42351.32704 53520.53909 55576.76072 57825.78059 52669.04124 58958.57099 52948.49265 58414.69966 45418.5936 0.932466721 1.178383892 1.223656576 1.273174178 1.159636111 1.298115294 1.165788908 1.286140654 1 15.47099541 4.755956304 3.100362522 1.210900538 0.883212998 0.484209168 0.085957857 0.286252449 4.067358581 0.017528243 0.234443125 57010.69083 -4.755956304 -0.32768754 DNDFIYHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DNDFIYHDR 9 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;; 133.91 0.00026367 2998020000 5649800 5657100 5685800 5524800 5648100 4648300 6703100 5068280 5316570 FALSE TRUE 5296189.103 6075957.57 5820669.861 5666575.721 5204521.009 5990188.751 5698032.384 5701065.915 4429200.121 1.195743917 1.371795675 1.314158246 1.279367734 1.175047609 1.352431272 1.286469843 1.287154737 1 22.07861475 0.399189255 2.666605809 1.000000254 1.293406047 0.674722998 0.061326602 13.50260232 58.85525365 0.056452442 0.014934936 2.507201592 -0.399189255 0.293405793 DNDKTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DNDKTR 6 1 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 102.71 0.032198 75795000 83711 98759 186930 158990 192430 195710 170750 70973 145580 FALSE TRUE 78471.67794 106071.2191 191364.0679 163069.9526 177317.324 252208.2999 145147.6227 79834.13528 121281.7575 0.647019631 0.874585109 1.577847088 1.344554663 1.462027989 2.079523789 1.196780337 0.65825345 1 16.88800304 4.274005154 2.408714991 1.381313585 0.675827691 0.290664202 0.371478232 0.360977317 3.976537499 0.093369956 0.347873597 18793.39118 -4.274005154 -0.705485893 DNEEKDSAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DNEEKDSAFR 10 1 O14787-2;O14787;Q92973-2;Q92973;Q92973-3;S4R398 O14787-2;Q92973-2 TNPO2;TNPO1 Transportin-2;Transportin-1 0 ; 151.79 1.75E-05 1046010000 2338500 1698210 1959010 1932880 1963530 1297280 2476900 1673110 2328400 FALSE TRUE 2192137.459 1823947.235 2005478.642 1982480.973 1809322.274 1671783.676 2105511.839 1882001.466 1939774.998 1.130098832 0.940288042 1.033871786 1.022015943 0.932748528 0.86184412 1.085441271 0.970216375 1 20.88745789 4.749945758 24.13350412 0.984782456 1.130098973 0.365507921 0.061619943 1218.084039 2581936.586 0.014264718 0.216031069 56227.10954 -4.749945758 0.145316517 DNFFEVFTPVFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 147.33 9.94E-05 125481000 144590 169186 182639 170132 193477 158935 185051 172572 171810 FALSE TRUE 135540.37 181712.7075 186971.2833 174497.8752 178282.0969 204816.9544 157304.3205 194117.9941 143133.8011 0.946948722 1.26953037 1.306269253 1.219124161 1.245562512 1.430947497 1.099001908 1.356199532 1 17.12700488 -1.010813433 4.408177475 0.999989962 1.24185454 0.229998159 0.134020258 0.090385104 35164921.32 844.4862277 0.028017825 0.097540857 1.010813433 0.241864578 DNFGFIETANHDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DNFGFIETANHDK 13 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ; 231.58 2.19E-12 864210000 868450 571850 732790 667590 643240 636930 921880 609080 482670 FALSE TRUE 814095.2647 614190.369 750172.1248 684721.4896 592722.5251 820801.3513 783652.6523 685124.9788 402109.2588 2.024562347 1.527421604 1.865592767 1.70282448 1.474033517 2.041239622 1.948855032 1.703827912 1 18.61722803 -1.808557811 1.817300636 0.648973695 1.782083329 0.622560177 0.192324063 187984.6152 81514.09877 288731.5393 0.0503108 0.015539684 1.808557811 1.133109634 DNFHGLAIFLDTYPNDETTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DNFHGLAIFLDTYPNDETTER 21 0 Q12907;D6RBV2;D6RIU4 Q12907 LMAN2 Vesicular integral-membrane protein VIP36 0 ;;;;; 164.27 1.62E-11 466266000 486105 633112 427766 465531 658506 337687 623039 592225 445099 FALSE TRUE 455680.5558 679988.2712 437912.8115 477477.3136 606789.595 435171.755 529620.086 666165.5949 370809.1015 1.228881799 1.833796065 1.18096565 1.287663414 1.636393478 1.173573554 1.428282326 1.796518997 1 18.50031713 -2.15404572 2.286599315 2.96E-05 1.444378723 0.251182838 0.241867264 9655652.242 2454532.361 49975021.07 0.059372891 0.007013815 2.15404572 1.444349161 DNFWEMGDTGPCGPCSEIHYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DNFWEMGDTGPCGPCSEIHYDR 22 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;; 316.48 2.19E-67 1261360000 683950 759040 739500 722210 836000 595200 879940 663280 782700 FALSE TRUE 641142.7904 815240.1114 757041.2892 740743.1313 770343.9323 767024.5777 748001.166 746091.9681 652062.3136 0.983253866 1.250248779 1.160995312 1.136000526 1.181396189 1.176305641 1.147131417 1.14420348 1 19.31465031 0.370838885 1.309122042 0.999904419 1.161516201 0.306088183 0.067538534 3.777887763 6.818355667 0.058436887 0.0172529 2.348761313 -0.370838885 0.161611782 DNGIRPSSLEQMAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DNGIRPSSLEQMAK 14 1 P55084-2;P55084;B5MD38;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 66.059 0.059221 91676000 72115 59838 59965 43389 76232 55157 65630 53190 76597 FALSE TRUE 67601.45088 64268.46778 61387.39812 44502.4352 70245.04623 71079.9305 55789.39078 59830.88859 63812.46586 1.059376878 1.007145969 0.961996959 0.697394069 1.100804447 1.113887852 0.874271038 0.937605024 1 15.96155066 4.367465887 1.868515318 0.952368654 1.057678099 0.079440238 0.116467352 1.220400134 7.117601934 0.030369639 0.173193995 23305.90044 -4.367465887 0.105309445 DNHLLGTFDLTGIPPAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DNHLLGTFDLTGIPPAPR 18 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 133.21 1.32E-05 182000000 233170 235800 207070 215570 253690 214510 258440 219460 216930 FALSE TRUE 218576.3059 253258.8773 211981.7982 221101.8912 233766.2107 276435.5547 219689.3212 246860.0641 180722.9816 1.209454957 1.40136509 1.172965366 1.223429855 1.293505722 1.529609308 1.215613639 1.365958341 1 17.46342045 -1.17167836 5.069544732 0.999981021 1.300252273 0.435522069 0.107859346 2.15E-05 3.52E-06 0.09719224 0.022906984 0.067347525 1.17167836 0.300271252 DNHVVAAGGVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DNHVVAAGGVEK 12 0 Q15274 Q15274 QPRT Nicotinate-nucleotide pyrophosphorylase [carboxylating] 0 ;;;;; 152.95 6.23E-05 4224540000 7669110 6946660 7211990 6984690 8187870 5599180 8219210 7060630 11427250 FALSE TRUE 7189114.095 7460997.934 7383061.809 7163928.97 7544827.718 7215572.371 6986815.764 7942165.198 9519968.152 0.75516157 0.783720892 0.775534297 0.752516065 0.792526571 0.75794081 0.733911674 0.834263841 1 23.18252532 0.912146995 4.337358685 0.999941347 0.766520443 0.951008364 0.016900683 0.091035966 3.887380645 0.017218698 0.004381483 8.168588062 -0.912146995 -0.233420904 DNIACVILTFKEPFGTEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DNIACVILTFKEPFGTEGR 19 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 229.75 6.65E-20 2105610000 2068670 2218310 2240570 2246580 2876490 1685850 2887930 2123590 3764650 FALSE TRUE 1939195.637 2382555.981 2293717.378 2304231.046 2650582.079 2172527.528 2454911.707 2388724.886 3136305.594 0.618305704 0.759669589 0.731343713 0.734695959 0.845128767 0.692702756 0.782739957 0.761636522 1 21.58063471 -5 0.198640152 2.15096999 0.702013435 0.713857602 0.053672787 73.24470503 0.724137804 33.43102149 0.118656972 1.00E-05 5 -1.448956555 DNIPALVEEYLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DNIPALVEEYLER 13 0 Q9H1I8;B1AH59 Q9H1I8 ASCC2 Activating signal cointegrator 1 complex subunit 2 0 ; 96.734 0.0095419 10975900 17130 17478.8 18930.3 18961 18190.9 12480.7 22024 16883.8 16386.2 FALSE TRUE 16057.86388 18772.94854 19379.33566 19447.57136 16762.26009 16083.67548 18721.70566 18991.7796 13651.23736 1.176293654 1.375182926 1.419602864 1.424601364 1.227893095 1.178184443 1.371429209 1.391213052 1 13.7367441 2.72934518 24.2957948 1.261222725 1.365077767 0.143198927 0.12803823 893.4823146 2355592.063 0.038914408 0.037170862 536.222682 -2.72934518 0.103855042 DNIQGITKPAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DNIQGITKPAIR 12 1 P62805 P62805 HIST1H4A Histone H4 0 ;;; 174.39 2.78E-05 3927860000 3969110 3857040 3560800 3980240 5575590 3568460 4914000 4252550 5567040 FALSE TRUE 3720690.49 4142619.255 3645263.858 4082379.697 5137705.652 4598616.473 4177191.319 4783490.229 4637865.06 0.802242075 0.893216858 0.785978852 0.880228218 1.107773854 0.991537359 0.900671164 1.031399182 1 22.14502941 2.983021993 23.00081666 0.99105657 0.835133018 0.67082901 0.058091754 165.8528649 224688.5947 0.017605443 0.01913211 961.6609754 -2.983021993 -0.155923553 DNKPLVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DNKPLVER 8 1 Q9UHB9;Q9UHB9-4;Q9UHB9-2;Q9UHB9-3 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;;; 103.01 0.0044286 1285430000 2315300 2186100 2163610 2276280 2335230 1751320 2750530 2151580 2487400 FALSE TRUE 2170389.506 2347961.119 2214931.851 2334693.199 2151830.456 2256897.654 2338113.561 2420209.499 2072236.871 1.047365548 1.133056337 1.068860362 1.126653633 1.038409501 1.089111812 1.128304198 1.167921261 1 20.98275749 1.767983204 24.99999928 1.112568469 1.087737866 0 0.051610577 75.22504722 63953.60711 0.021222042 0.011771798 58.61154964 -1.767983204 -0.024830604 DNLEFFLAGIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 234.39 1.18E-15 5456074100 5316675 6631147 5643909 5919656 7195254 4914667 7076591 6714252 6545650 FALSE TRUE 4983913.802 7122124.024 5777785.187 6071564.395 6630167.775 6333451.58 6015521.875 7552541.142 5453138.728 0.913953239 1.30605957 1.059533871 1.113407287 1.215844325 1.161432323 1.103130174 1.384989731 1 22.37865543 DNLEWLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DNLEWLAR 8 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;;;; 166.82 0.0007357 1552729000 2318530 2666060 2546790 2617870 2608630 2002750 2909990 2343950 2497780 FALSE TRUE 2173417.346 2863457.856 2607201.061 2685048.976 2403758.723 2580911.413 2473664.015 2636597.317 2080884.382 1.044468095 1.376077346 1.252929324 1.290340299 1.155162076 1.240295442 1.188756106 1.267056133 1 20.98876538 -4.161161179 0.272742087 7.94E-13 1.258201614 0.363771278 0.089924045 124.126167 1.841885601 69.25474477 0.100597768 6.90E-05 4.161161179 1.258201614 DNLGEVPLT(ph)PTEEASLPLAVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DNLGEVPLTPTEEASLPLAVTK 22 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 DNLGEVPLT(0.471)PT(0.471)EEAS(0.059)LPLAVTK 78.975 0.029825 41887000 105410 101870 113120 150960 115560 66563 89726 57603 91385 TRUE FALSE 98812.57626 109412.5608 115803.2598 154833.8892 106484.3837 85778.65754 76272.41928 64794.86135 76132.25313 1.297906895 1.437138089 1.521080161 2.033748941 1.398676374 1.126705884 1.001841088 0.851082934 1 16.21622015 2.196706616 2.732125826 0.970287024 1.553266654 0.673144894 0.193046993 0.168554833 2.565781358 0.084702217 0.05866574 157.2919933 -2.196706616 0.58297963 DNLHQIDAVEGPAAFLDILAPPYDPDDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DNLHQIDAVEGPAAFLDILAPPYDPDDGR 29 0 Q96SZ5 Q96SZ5 ADO 2-aminoethanethiol dioxygenase 0 ; 102.57 0.00059479 44359000 61067 66724 58422 52437 67657 48411 63493 67481 59335 FALSE TRUE 57244.92548 71664.31439 59807.79743 53782.6222 62343.49214 62386.46981 53972.81409 75906.15139 49431.60518 1.158063253 1.44976709 1.209910081 1.088020953 1.261207114 1.262076552 1.09186853 1.535579335 1 15.59314614 -2.269780758 2.210235079 2.40E-05 1.253347901 0.242891099 0.142496656 1728782.727 321991.8935 8672976.837 0.03305388 0.00537303 2.269780758 1.253323874 DNLLFGDEIITNGFHSCES(ph)DEEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DNLLFGDEIITNGFHSCESDEEDR 24 0 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 DNLLFGDEIITNGFHS(0.003)CES(0.997)DEEDR;DNLLFGDEIITNGFHS(0.084)CES(0.916)DEEDR;DNLLFGDEIIT(0.002)NGFHS(0.259)CES(0.739)DEEDR 159.92 1.37E-11 58568000 62144 58356 64371 69942 65682 72892 76284 56847 37965 TRUE FALSE 58254.51797 62676.73896 65897.91052 71736.83013 60523.60067 93934.7371 64845.92239 63944.47309 31628.39624 1.841842297 1.981660356 2.083504646 2.26811469 1.913584243 2.969949421 2.050243771 2.021742507 1 14.94893278 4.344617947 1.245037971 2.142396694 1.819806817 0 0.481354914 2.947060807 6.253382122 0.126227678 1.022822919 22111.48683 -4.344617947 -0.322589876 DNLSYIEHIFEISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DNLSYIEHIFEISR 14 0 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ;;;;; 236.43 2.90E-17 815797000 888249.6 967212.7 959054.7 857254.4 1001104.8 849889.7 1113033 977769.9 959213.6 FALSE TRUE 832655.6431 1038826.135 981803.9304 879252.9992 922482.0673 1095239.06 946144.0345 1099846.624 799114.6534 1.041972688 1.299971325 1.2286146 1.100283915 1.154380117 1.370565606 1.183990345 1.376331443 1 19.60804298 DNLTLWTSDQQDDDGGEGNN ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DNLTLWTSDQQDDDGGEGNN 20 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;;;; 477.34 1.02E-248 4910870000 6900620 6892430 7059270 6775840 7370080 6108840 8038680 6344700 8167520 FALSE TRUE 6468722.512 7402752.689 7226719.218 6949719.526 6791263.646 7872362.939 6833354.561 7136849.761 6804308.148 0.950680418 1.087950829 1.062079944 1.021370487 0.998082906 1.156967434 1.004268827 1.048872215 1 22.69801705 0.70702645 1.522256187 1.00046436 1.048845931 0.03589149 0.056126881 3.021926226 10.97524047 0.048413001 0.014041787 5.093618921 -0.70702645 0.048381571 DNLTLWTSENQGDEGDAGEGEN ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 ;;;;;; 373.51 8.32E-113 3072730000 3962160 4038010 4073970 4101330 4395040 3532980 4566470 3809720 4384100 FALSE TRUE 3714175.478 4336988.462 4170606.492 4206577.071 4049871.287 4552893.973 3881770.217 4285371.928 3652365.388 1.016923304 1.187446491 1.141891911 1.151740482 1.108835195 1.246560377 1.062809934 1.173314133 1 21.80039967 -3.06101393 0.739725387 0.145183548 1.140291152 0.306157578 0.064105638 2398.720019 76.49753117 3333.433553 0.019515146 0.000868933 3.06101393 0.995107604 DNNLLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DNNLLGK 7 0 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PS65;E9PM13;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 ;;; 114.93 0.013479 827840000 1553320 1072130 1181560 1054850 1052340 923730 1480260 1122970 1520330 FALSE TRUE 1456100.474 1151511.621 1209587.161 1081919.237 969693.4613 1190395.855 1258308.755 1263175.276 1266577.101 1.149634296 0.909152407 0.95500476 0.854207167 0.765601605 0.939852658 0.993471897 0.997314159 1 20.27250347 -0.722774432 8.360081196 0.999999998 0.938845996 0.024934953 0.099529672 0 0 0.092606585 0.021827581 0.189332674 0.722774432 -0.061154002 DNNLLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DNNLLGR 7 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931;P17066 A0A0G2JIW1;Q53FA3;P17066 HSPA1B;HSPA1A;HSPA1L;HSPA6 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like;Heat shock 70 kDa protein 6 0 ;;; 154.35 0.0039189 2981150000 2393070 2563150 2527160 2439810 2898230 2081480 2888360 2442000 2850260 FALSE TRUE 2243292.02 2752928.293 2587105.429 2502419.655 2670614.707 2682369.486 2455277.232 2746889.076 2374533.193 0.944729696 1.159355574 1.089521695 1.053857517 1.124690409 1.129640762 1.034004174 1.156812246 1 21.17921249 -1.027480036 4.454708565 0.999995758 1.091180209 0.147025001 0.064696023 2.41E-06 5.26E-07 0.055392399 0.013055506 0.093868519 1.027480036 0.091184451 DNPAQDFSTLYGSS(ph)PLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DNPAQDFSTLYGSSPLER 18 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 DNPAQDFSTLYGS(0.356)S(0.643)PLER;DNPAQDFSTLYGS(0.009)S(0.991)PLER;DNPAQDFSTLYGS(0.039)S(0.961)PLER;DNPAQDFSTLYGS(0.051)S(0.949)PLER 310.99 3.91E-61 395952000 606267 545575 622674 567018 602626 551343 713364 580674 799989 TRUE FALSE 568321.8307 585969.9407 637444.1213 581568.6418 555298.1848 710506.7738 606401.6907 653172.4271 666465.6678 0.852739846 0.879219994 0.956454551 0.872616055 0.833198485 1.066081583 0.909876862 0.980054125 1 19.34617103 2.252430943 24.99999754 0.976840784 0.889196668 0.536109515 0.049841708 219.752415 396083.2167 0.016950842 0.014113534 178.8261155 -2.252430943 -0.087644116 DNPGVVTCLDEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DNPGVVTCLDEAR 13 0 P22314;P22314-2;Q5JRR9;Q5JRS0 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 271.01 1.04E-31 940590000 224890 214540 220220 217260 241110 176403 256230 197682 253220 FALSE TRUE 210814.5363 230424.7648 225443.7224 222835.2594 222174.1932 227327.6824 217810.6902 222363.0329 210955.9461 0.999329671 1.092288551 1.068676785 1.05631182 1.053178151 1.077607371 1.032493723 1.054073312 1 17.68658223 0.536874001 0.663248203 0.999122354 1.063049775 0.285295162 0.025690592 1.706616664 1.298155659 0.027299857 0.009186829 3.442500415 -0.536874001 0.063927421 DNPIEDELVFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DNPIEDELVFR 11 0 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 0 ;; 146.16 8.35E-05 77332000 150650 135418 149826 136678 142216 122644 168946 133032 148531 FALSE TRUE 141221.0854 145444.4896 153379.9435 140185.3889 131046.929 158049.3318 143614.1157 149641.338 123740.2166 1.141270715 1.175401932 1.239531882 1.132900788 1.05904881 1.277267296 1.160609862 1.20931854 1 16.91695494 -1.091355817 4.490005738 0.999985114 1.17889517 0.45253597 0.060111245 8.40E-06 1.70E-06 0.054599639 0.012868188 0.081029691 1.091355817 0.178910056 DNQESS(ph)DAELSSSEYIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DNQESSDAELSSSEYIK 17 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 DNQES(0.001)S(0.999)DAELSSSEYIK;DNQES(0.009)S(0.991)DAELSSSEYIK;DNQES(0.008)S(0.992)DAELSSSEYIK 296.79 3.78E-46 351567000 804170 562500 655590 612660 616130 491010 794620 539130 660710 TRUE FALSE 753838.4352 604148.0853 671140.9044 628381.8928 567741.6351 632756.6161 675474.1079 606441.5673 550433.2327 1.369536559 1.0975865 1.219295756 1.141613289 1.031445054 1.14956107 1.227168107 1.101753185 1 19.07020805 6.367108941 0.018104095 3.42E-06 2.505497112 0.373513341 0.083698006 3837.406066 7.17840011 405.5125845 605.292474 2328675.325 -6.367108941 2.505493694 DNQHQGSYSEGAQMNGIQPEEIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DNQHQGSYSEGAQMNGIQPEEIGR 24 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 119.83 5.44E-07 0 15441 19555 18936 19681 20229 17401 20969 16828 22560 FALSE TRUE 14474.57537 21002.87255 19385.17086 20186.04778 18640.29594 22424.38622 17824.89312 18929.01284 18794.59026 0.770145833 1.117495634 1.031422904 1.074035002 0.991790493 1.193129827 0.948405518 1.007152196 1 14.19802984 4.747461794 24.74196245 1.048414375 0.770145667 0.605099417 0.0698526 659.7584999 1833837.533 0.015284951 0.183702366 55906.43429 -4.747461794 -0.278268707 DNS(ph)PPPAFKPEPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DNSPPPAFKPEPPK 14 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 DNS(1)PPPAFKPEPPK;DNS(1)PPPAFKPEPPK;DNS(1)PPPAFKPEPPK;DNS(1)PPPAFKPEPPK;DNS(1)PPPAFKPEPPK 212.69 1.26E-09 10970280000 18470070 6089110 9771620 8705630 9523380 7145840 12216920 7675920 11612680 TRUE FALSE 17314061.29 6539954.04 10003407.44 8929031.204 8775452.15 9208728.005 10385106.26 8634275.509 9674448.687 1.789669039 0.676002763 1.034002842 0.922949875 0.907075166 0.951860752 1.073457165 0.892482434 1 23.20574802 4.749395888 24.99687464 0.934381358 1.789669526 0.863535205 0.107118444 573.2007372 1322343.791 0.025887186 0.384293245 56155.96416 -4.749395888 0.855288168 DNSEEFLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DNSEEFLKR 9 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;A0A5F9ZH85;F8WB06;F8VRK6 Q99700;F8WB06 ATXN2 Ataxin-2 0 70.808 0.082357 562530000 499370 424530 402940 457950 423090 315620 570080 390490 542750 FALSE TRUE 468115.3231 455962.6429 412497.9271 469701.7723 389862.2181 406734.3703 484601.7964 439243.5361 452161.5187 1.035283419 1.008406563 0.912280037 1.038792009 0.862218924 0.89953336 1.071744888 0.971430601 1 18.78647869 -1.101840091 3.242841769 1.000030147 0.974744511 0.013550756 0.067115792 11914888043 17502793270 3865791.321 0.01546355 0.079096981 1.101840091 -0.025285636 DNSEEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DNSEEFR 7 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7;H3BSK9 Q8WWM7 ATXN2L Ataxin-2-like protein 0 ; 159.46 0.0032171 367970000 628150 653140 676080 641250 706860 613010 759710 602800 733840 FALSE TRUE 588835.2128 701499.1652 692116.9369 657705.5606 651346.0669 789976.0356 645798.5383 678060.9069 611357.3632 0.963160417 1.147445353 1.132098799 1.075811956 1.065409703 1.292167369 1.056335586 1.109107288 1 19.22165641 0.609921894 1.766399036 1.000217364 1.115358002 0.125988146 0.083807872 3.504157244 13.57571727 0.072584617 0.020416074 4.073070184 -0.609921894 0.115140638 DNSTMGYMAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DNSTMGYMAAK 11 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 139.86 0.0031746 84997000 121293 103454 103597 98661 124005 69942 129899 105217 132509 FALSE TRUE 113701.4876 111113.8418 106054.3698 101192.8083 114266.1475 90133.11999 110421.8509 118353.5741 110392.3919 1.029975759 1.006535323 0.960703614 0.916664696 1.035090785 0.816479455 1.000266857 1.072117128 1 16.75228122 1.478011977 25 1.036104708 0.962505052 0.189449354 0.06479725 0.176043344 4639.355945 0.03251981 0.015054864 30.06159203 -1.478011977 -0.073599656 DNTFFRES(ph)PVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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;DNTFFRES(1)PVGR;DNTFFRES(1)PVGR 207.06 3.73E-05 11821240000 5098850 5588470 5201260 5168630 6404950 4546800 6313930 5280240 7484600 TRUE FALSE 4779722.08 6002246.134 5324636.343 5301265.796 5901931.063 5859387.349 5367214.812 5939489.587 6235371.908 0.766549638 0.962612371 0.853940458 0.850192398 0.946524305 0.939701342 0.860768995 0.952547767 1 22.57204418 -4.999999929 0.104407496 1.345615091 0.825393184 0.364190668 0.055912986 223.5566944 1.573575816 16.61776835 0.777284715 1.00E-05 4.999999929 -0.520221906 DNTIEHLLPLFLAQLKDECPEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DNTIEHLLPLFLAQLKDECPEVR 23 1 P30153;B3KQV6 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ; 217.94 1.39E-32 449000000 1046530 986920 1024360 1068670 1304160 756570 1318340 980230 1610950 FALSE TRUE 981029.5554 1059992.584 1048658.303 1096093.881 1201736.534 974979.4771 1120667.156 1102613.873 1342072.038 0.730981294 0.789817949 0.781372589 0.816717621 0.895433703 0.726473281 0.835027572 0.821575774 1 20.35603068 -5 0.19715781 1.899639571 0.765200791 0.669957122 0.045867755 80.86810213 0.798305547 28.60540903 0.105625283 1.00E-05 5 -1.13443878 DNTINLIHTFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DNTINLIHTFR 11 0 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;;;; 150.21 3.40E-05 3876360000 4919990 5059410 5025170 5068900 5537570 4199920 5396080 4655310 4656370 FALSE TRUE 4612056.608 5434013.981 5144369.405 5198976.556 5102671.59 5412368.724 4586987.899 5236535.701 3879191.766 1.188922045 1.400810867 1.32614465 1.34022159 1.315395551 1.39523103 1.182459692 1.349903799 1 21.88732467 -0.501021593 0.475274169 0.935977024 1.334318072 0.619606437 0.075797038 5.290021865 1.057537559 0.621130271 0.035684238 0.315484776 0.501021593 0.398341048 DNTRPGANS(ph)PEMWSEAIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DNTRPGANSPEMWSEAIK 18 1 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 1 DNT(0.002)RPGANS(0.998)PEMWSEAIK;DNTRPGANS(1)PEMWSEAIK 215.84 5.63E-19 315860000 386060 285480 337630 294040 315650 231310 369680 263410 360330 TRUE FALSE 361897.1937 306617.2362 345638.743 301585.5642 290860.1223 298085.442 314249.9159 296297.3183 300188.5952 1.205566099 1.021415341 1.151405312 1.004653638 0.968924626 0.992993894 1.046841622 0.987037226 1 18.19550964 7.999999999 0.3417002 0.997719296 2.871671629 0.512682312 0.053616486 53.66619195 0.761196281 0.045361967 64.253881 99999999.78 -7.999999999 1.873952333 DNTSVYHISGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DNTSVYHISGK 11 0 Q9NTJ3;E9PD53;Q9NTJ3-2;C9JR83;C9J578;C9JVD8;C9J9E4 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 0 ; 74.392 0.040948 405680000 318470 644000 629710 622770 705410 567860 742610 647440 687680 FALSE TRUE 298537.5312 691682.4301 644647.0186 638751.3325 650009.9441 731791.9636 631262.5246 728274.3092 572901.7654 0.521097244 1.207331644 1.125231335 1.114940416 1.134592322 1.277342832 1.101868702 1.271202767 1 19.12792826 4.741194649 24.99806433 1.159061951 0.521097017 0.853369917 0.082433585 77.01434389 730857.663 0.016945664 0.116929984 55105.4621 -4.741194649 -0.637964934 DNVSSPGGATIHALHVLESGGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DNVSSPGGATIHALHVLESGGFR 23 0 J3QKT4;J3KQ22;E2QRB3;P32322-2;P32322;P32322-3 J3QKT4 PYCR1 "Pyrroline-5-carboxylate reductase;Pyrroline-5-carboxylate reductase 1, mitochondrial" 0 142.21 1.01E-07 120620000 111060 122560 118850 111980 153850 109560 101070 101430 131110 FALSE TRUE 104108.9528 131634.4699 121669.1781 114853.5964 141767.2416 141188.1934 85915.49179 114093.7588 109226.894 0.953143947 1.205147058 1.113912276 1.051513892 1.29791516 1.292613827 0.786578183 1.044557385 1 16.7369686 1.739891718 25 0.931941568 1.155744732 0.393461372 0.121788566 0.185714104 3499.66635 0.052649686 0.029196953 54.94038742 -1.739891718 0.223803163 DNYNHPNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DNYNHPNKR 9 1 O14647;O14647-2 O14647 CHD2 Chromodomain-helicase-DNA-binding protein 2 0 122.13 0.0003858 30636000 24061 24573 19365 25647 27445 16067 26045 24823 29001 FALSE TRUE 22555.06496 26392.41049 19824.34694 26305.14544 25289.58041 20705.28207 22139.79404 27922.20619 24160.54575 0.933549482 1.092376421 0.820525627 1.088764539 1.046730512 0.85698735 0.916361504 1.155694349 1 14.56036542 1.24836549 24.99292331 1.077847197 0.962503461 0.186258298 0.097912777 289.0093776 736706.3213 0.06456658 0.022953908 17.71599258 -1.24836549 -0.115343737 DNYSPGWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DNYSPGWK 8 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;;; 131.06 0.0023757 1242160000 1203410 1095090 1206670 1155180 1264400 914430 1467860 1070510 1437410 FALSE TRUE 1128090.716 1176171.603 1235292.782 1184823.875 1165099.124 1178411.096 1247768.02 1204165.53 1197496.985 0.942040548 0.982191703 1.031562332 0.989417 0.972945351 0.984061848 1.041980093 1.005568736 1 20.19159059 1.760754654 25 1.019764386 0.988856927 0.255567898 0.024545016 16.50181884 18602.93248 0.011639627 0.006455482 57.64407234 -1.760754654 -0.030907459 DNYVPEVSALDQEIIEVDPDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DNYVPEVSALDQEIIEVDPDTK 22 0 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 98.74 0.0011139 12584000 126910 81415 102320 90165 94535 81736 117030 80557 102030 FALSE TRUE 118966.9296 87443.05131 104747.0787 92478.78655 87110.60244 105331.8563 99482.43795 90614.71878 85000.53386 1.399602146 1.028735319 1.232310833 1.087978891 1.02482418 1.239190527 1.170374272 1.066048819 1 16.37518428 -4.9998662 0.022006743 9.99E-06 1.918843131 0.24840619 0.108159063 4905.27163 8.165070957 494.029201 254.5124366 1.00E-05 4.9998662 1.918833145 DPALNT(ph)S(ph)LPQKVLGT(ph)T(ph)EEISGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DPALNTSLPQKVLGTTEEISGK 22 1 E9PCH4;Q8TEU7-2;Q8TEU7-5;Q8TEU7-3;Q8TEU7;Q8TEU7-4;D6RE77;A0A5F9ZHG7 E9PCH4 RAPGEF6 Rap guanine nucleotide exchange factor 6 4 DPALNT(1)S(1)LPQKVLGT(1)T(1)EEISGK 51.119 0.054693 2827500000 619170 1178200 1214000 1124700 990090 1301200 1464900 1276800 627470 TRUE FALSE 580417.255 1265435.154 1242796.653 1153561.706 912332.3252 1676835.317 1245251.844 1436211.291 522741.2034 1.110333854 2.420767955 2.377460673 2.206754889 1.745284893 3.20777338 2.382157435 2.747461423 1 18.99573735 4.740533632 24.53939053 2.351646883 1.1103333 0.26311317 0.58799231 158.3948149 1969846.261 0.122081645 0.798328608 55021.6528 -4.740533632 -1.241313583 DPDQTDGLGLSYLSSHIANVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DPDQTDGLGLSYLSSHIANVER 22 0 P06396-2;A0A0A0MS51;A0A0A0MT01;P06396-4;P06396-3;P06396 P06396-2 GSN Gelsolin 0 ;; 279.73 1.33E-45 508764000 225460 269189 263882 270583 273741 232742 305789 247240 272049 FALSE TRUE 211348.8611 289120.0337 270141.4057 277526.6179 252242.4861 299930.8371 259938.7783 278108.4582 226642.2644 0.932521838 1.275666895 1.191928639 1.224513965 1.112954315 1.323366751 1.146912201 1.227081184 1 17.7900574 -0.698634149 7.502338433 1.000008014 1.191595026 0.211637869 0.106497123 0 0 0.089208816 0.02102672 0.200154727 0.698634149 0.191587012 DPEEIEKEEQAAAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DPEEIEKEEQAAAEK 15 1 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;; 186.68 3.39E-07 1081940000 1554310 676900 979780 907230 775620 713260 1150090 688270 724090 FALSE TRUE 1457028.512 727018.3803 1003020.844 930511.0577 714705.9339 919166.5832 977644.6814 774202.0246 603234.7012 2.415359244 1.205199865 1.66273731 1.542535693 1.184789158 1.523729622 1.620670494 1.283417587 1 19.2023599 8 0.053969219 0.311009136 3.794270565 0.36944498 0.309140308 575.9185642 2.335915293 33.41773468 162.7338497 100000000 -8 3.48326143 DPEGFVGHPVNAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DPEGFVGHPVNAFK 14 0 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 134.21 4.01E-05 401800000 1045400 1001210 1033820 1081030 1111160 621260 1234720 1008210 635020 FALSE TRUE 979970.2801 1075340.63 1058342.699 1108771.06 1023893.976 800607.6767 1049585.199 1134087.238 529031.0596 1.852387043 2.032660674 2.000530365 2.095852483 1.935413729 1.513347207 1.983976516 2.143706342 1 19.0129929 -1.864442634 2.711920728 0.59450054 1.945400682 0.746419604 0.173052353 10142058.57 4673499.668 26257283.13 0.042549302 0.013663355 1.864442634 1.350900142 DPEKRPTAAELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DPEKRPTAAELLR 13 2 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 0 ;;; 92.495 0.0034009 996710000 921790 1073750 957840 962890 1316220 717430 1253200 953000 1757230 FALSE TRUE 864096.8093 1153251.567 980560.4171 987599.3876 1212849.391 924540.3945 1065294.294 1071984.148 1463936.961 0.590255477 0.787774063 0.669810547 0.674618794 0.828484711 0.631543857 0.727691371 0.73226114 1 20.481422 0.467954151 1.808875338 0.999989885 0.707539625 0.641889662 0.0694665 2.535707717 7.940525684 0.058645823 0.016390475 2.937339535 -0.467954151 -0.29245026 DPETLVGYSMVGCQR ddPTM_SK-BR-3_Pertuzumab_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 ; 232.17 2.24E-13 213296000 83969 79873 89439 85759 98021 75036 109355 71102 70238 FALSE TRUE 78713.53018 85786.88003 91560.53532 87959.72113 90322.82606 96697.67509 92958.23295 79979.24121 58514.82405 1.345189556 1.466070888 1.564740847 1.503204061 1.543588783 1.652532955 1.588627061 1.366820161 1 15.83651454 -0.260825186 7.771787294 1.000000011 1.518942169 0.732401785 0.095324937 0 0 0.09009191 0.021234867 0.548497704 0.260825186 0.518942157 DPGMS(ph)QSHNDLVFLEQPEGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DPGMSQSHNDLVFLEQPEGSR 21 0 Q9Y426-2;Q9Y426-3;Q9Y426;H7BZB0 Q9Y426-2 C2CD2 C2 domain-containing protein 2 1 DPGMS(0.648)QS(0.352)HNDLVFLEQPEGSR 232.2 8.61E-26 200790000 1500700 640780 876510 834280 859420 621490 1203200 741210 943030 TRUE FALSE 1406773.866 688224.0179 897301.2311 855689.0372 791924.6199 800904.074 1022791.33 833751.7001 785632.2008 1.790626535 0.876012996 1.14213907 1.089172562 1.00800937 1.01943896 1.301870429 1.061249398 1 19.58349454 4.748528571 24.90037963 1.075092295 1.790626948 0.811579735 0.110142511 603.7112447 1508064.529 0.027406574 0.37210918 56043.92855 -4.748528571 0.715534653 DPGMSQS(ph)HNDLVFLEQPEGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DPGMSQSHNDLVFLEQPEGSR 21 0 Q9Y426-2;Q9Y426-3;Q9Y426;H7BZB0 Q9Y426-2 C2CD2 C2 domain-containing protein 2 1 DPGMS(0.288)QS(0.712)HNDLVFLEQPEGSR 208.82 9.77E-22 275040000 217450 202960 200250 178140 221540 182580 317680 210920 274150 TRUE FALSE 203840.1927 217987.3696 205000.0246 182711.374 204141.142 235287.8821 270046.8332 237253.8263 228392.5939 0.892499136 0.954441498 0.897577373 0.799988173 0.89381682 1.030190507 1.182379991 1.038798247 1 17.80115634 2.127632535 4.008887521 1.096354363 0.894074027 0.671121426 0.060565446 0.119239166 3.534239399 0.023846437 0.016994755 134.1629303 -2.127632535 -0.202280336 DPGVLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DPGVLDR 7 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;;; 120.49 0.010575 15974300000 5539310 6423140 5798140 5871160 6020230 5250110 6721990 5524230 6049010 FALSE TRUE 5192614.475 6898715.969 5935674.619 6021823.905 5547425.42 6765731.529 5714090.003 6213942.276 5039391.153 1.030405126 1.368958225 1.177855507 1.194950684 1.100812628 1.342569236 1.133884993 1.233074014 1 22.26481801 -3.743195357 0.383641477 2.10E-10 1.214845674 0.254161399 0.103072516 263.934835 5.054576056 213.3020526 0.061755684 0.000180636 3.743195357 1.214845674 DPHLACVAYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 0.0008517 954790000 259363 530340 354356 352224 437075 243414 329473 432006 388693 FALSE TRUE 243129.9328 569606.9254 362761.4917 361262.6642 402748.8926 313683.6703 280071.5823 485942.9001 323817.6272 0.75082365 1.75903619 1.120264807 1.115636191 1.243752219 0.96870474 0.864905301 1.50066846 1 18.304822 3.66059252 6.508089463 1.091497806 1.360109273 0.005183577 0.297491381 0.396807156 30.88763634 0.073329504 0.114910855 4577.122329 -3.66059252 0.268611467 DPILVSLRPGSELLRPHPLPAERPIFNSMAPAS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DPILVSLRPGSELLRPHPLPAERPIFNSMAPASPR 35 3 Q92828 Q92828 CORO2A Coronin-2A 1 DPILVSLRPGSELLRPHPLPAERPIFNS(0.008)MAPAS(0.992)PR;DPILVSLRPGSELLRPHPLPAERPIFNS(0.059)MAPAS(0.941)PR 89.119 0.00046811 427680000 238930 282500 205505 178754 352000 126020 126627 144811 106017 TRUE FALSE 223975.7978 303416.5939 210379.6756 183341.1303 324355.3399 162399.9282 107640.4569 162890.9721 88322.0778 2.535898196 3.435342572 2.381960217 2.075824469 3.672415187 1.838724046 1.218726502 1.844283742 1 16.43048649 2.045843095 7.778892937 1.41480009 2.809563001 0.642398555 0.508622478 0.137552222 20.07049286 0.180780558 0.132737875 111.1330144 -2.045843095 1.39476291 DPLELFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DPLELFR 7 0 Q16401-2;Q16401;Q4VXH0 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ;;; 114.72 0.01359 176635000 341497 402973 357491 352796 431624 288477 398335 378214 348754 FALSE TRUE 320123.3124 432809.5402 365970.8553 361849.3426 397725.9921 371755.6269 338608.3647 425434.8505 290544.7044 1.101803982 1.489648697 1.259602567 1.245417098 1.36889775 1.279512658 1.165426042 1.464266407 1 18.14840063 -2.061624668 2.567408031 0.567457845 1.300517454 0.37534735 0.120253541 3253687.37 1933328.305 8244018.58 0.027236482 0.008677115 2.061624668 0.733059609 DPLGGLADMFGQMPGSGIGTGPGVIQDRFS(ph)PTMGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DPLGGLADMFGQMPGSGIGTGPGVIQDRFSPTMGR 35 1 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 DPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.966)PT(0.034)MGR;DPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.992)PT(0.007)MGR;DPLGGLADMFGQMPGSGIGT(0.081)GPGVIQDRFS(0.914)PT(0.004)MGR;DPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.995)PT(0.005)MGR 319.06 3.25E-105 1064550000 620220 691960 670360 716390 783570 575490 811820 631630 708160 TRUE FALSE 581401.5373 743193.4384 686261.2558 734773.7802 722031.573 741624.6207 690095.1276 710490.3959 589963.5211 0.985487266 1.259727783 1.163226591 1.245456293 1.223857997 1.257068605 1.169725081 1.20429547 1 19.17026623 -0.684271767 8.081510334 1.000000754 1.196517451 0.352247569 0.079739056 0 0 0.067512926 0.015912949 0.206884633 0.684271767 0.196516697 DPLNPIKQDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DPLNPIKQDVK 11 1 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 136.3 0.0013201 0 915520 600430 652710 635950 757310 506990 858900 580950 747490 FALSE TRUE 858219.2374 644886.4619 668192.5894 652269.5537 697833.9274 653349.7827 730115.9186 653482.8863 622729.09 1.378158257 1.035581077 1.073006866 1.047437102 1.120605956 1.049171772 1.172445499 1.049385514 1 19.24824515 4.743344206 24.88548144 1.076647015 1.378158388 0.801097483 0.048345364 205.2888988 1067927.826 0.011117812 0.091066489 55378.88485 -4.743344206 0.301511374 DPNDVRPIQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DPNDVRPIQAR 11 1 Q9H307;G3V5F0;G3V579 Q9H307 PNN Pinin 0 ;;; 122.55 0.00035432 1935360000 1775090 1903920 1846340 1786500 1961660 1568450 2013090 1677860 1640710 FALSE TRUE 1663990.286 2044888.218 1890136.057 1832344.615 1807599.137 2021236.053 1711245.843 1887344.514 1366864.902 1.217377287 1.496042671 1.382825804 1.340545516 1.322441694 1.478738719 1.251949509 1.380783508 1 20.38243923 -1.525233653 0.375933572 0.741970627 1.389788206 0.61261551 0.088462767 15.69154 1.195804206 3.880738565 0.057190776 0.029837769 1.525233653 0.647817579 DPNNYRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DPNNYRPR 8 1 P61221 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 ;; 103.56 0.0043308 274082000 92985 104917 100072 103332 118547 87758 94353 90931 111630 FALSE TRUE 87165.23483 112685.1638 102445.7551 105983.6741 109236.7968 113092.31 80205.64358 102283.9355 92998.23184 0.93727841 1.211691466 1.101588203 1.139631066 1.174611545 1.216069464 0.862442672 1.099848174 1 16.50491567 1.747175678 25 0.978853359 1.138334741 0.325409491 0.096121412 1.935103801 5629.052585 0.039688643 0.022009391 55.86961486 -1.747175678 0.159481382 DPPHNNFFFFDGMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DPPHNNFFFFDGMK 14 0 Q9UBE0;M0QZS6 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 105.39 0.0010024 360560000 892410 867870 814570 887560 972060 672200 1014300 813870 1053000 FALSE TRUE 836555.6511 932127.9978 833891.9851 910336.2922 895718.3287 866253.2277 862215.1313 915483.461 877247.4974 0.953614178 1.062559883 0.950577787 1.037718882 1.021055439 0.987467312 0.982864168 1.04358629 1 19.7426244 DPQALSEHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DPQALSEHLK 10 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;; 155.97 1.18E-05 2245550000 2635470 2657910 2704470 2587970 2856190 2103360 3021320 2918160 2108110 FALSE TRUE 2470520.637 2854704.422 2768621.306 2654381.692 2631876.359 2710565.887 2568301.115 3282498.7 1756252.822 1.406699882 1.625451863 1.576436644 1.511389282 1.498574878 1.543380231 1.462375509 1.869035402 1 20.74406911 -0.621097572 7.505282453 1 1.557407497 0.66748116 0.124554172 0 0 0.107042174 0.025230082 0.239277812 0.621097572 0.557407497 DPQALSEHLKNPVIAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DPQALSEHLKNPVIAQK 17 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 249.16 3.34E-21 2808300000 3215000 3334700 3482600 3402400 3977100 2662600 4788000 3171500 4646400 FALSE TRUE 3013778.889 3581604.658 3565208.917 3489711.344 3664754.609 3431249.396 4070083.85 3567468.756 3870885.823 0.778576023 0.925267451 0.921031795 0.901527842 0.946748309 0.886424853 1.051460579 0.921615599 1 21.88423232 7.728961495 0.269572027 0.986787263 5.26E-22 0.506692541 0.049988761 38.11004155 0.609085648 0.055487532 17.00569456 53574915.59 -7.728961495 -0.986787263 DPS(ph)KIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DPSKIK 6 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 DPS(1)KIK;DPS(1)KIK;DPS(1)KIK 68.224 0.058564 4117200000 11039300 4676780 6662800 6523400 5935200 4285210 7815800 4475570 7063600 TRUE FALSE 10348369.92 5023053.657 6820844.762 6690801.488 5469073.333 5522280.562 6643893.348 5034354.766 5884639.527 1.758539307 0.853587316 1.159093047 1.136994281 0.929381198 0.938422912 1.129022996 0.855507758 1 22.48852261 4.746219888 24.88525866 1.014324987 1.758539689 0.817952969 0.112250967 358.0269396 1163213.766 0.025439731 0.271646649 55746.7929 -4.746219888 0.744214701 DPS(ph)PESNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DPSPESNK 8 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 DPS(0.999)PES(0.001)NK;DPS(0.999)PES(0.001)NK 106.37 0.0044156 920600000 2564630 1244250 1658050 1536700 1476320 1222090 1975760 1374580 1311970 TRUE FALSE 2404114.386 1336375.565 1697379.729 1576134.324 1360375.782 1574887.544 1679513.13 1546199.339 1092993.731 2.199568321 1.222674501 1.552963828 1.442034184 1.24463274 1.440893483 1.536617349 1.414646118 1 20.0598537 8 0.036726396 4.95E-11 3.729594056 0.370441358 0.247782621 1260.601402 3.533037396 103.2330618 305.255737 99999999.94 -8 3.729594056 DPS(ph)PESNKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DPSPESNKK 9 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 DPS(0.999)PES(0.001)NKK 59.198 0.050023 0 501030 211020 279690 288850 246720 223610 411510 235260 260710 TRUE FALSE 469671.4267 226644.1404 286324.3789 296262.38 227343.6064 288162.577 349807.8958 264632.7289 217195.8167 2.162433115 1.043501407 1.318277595 1.364033546 1.046721847 1.326740917 1.610564609 1.218406196 1 17.72863679 4.747755207 24.82061359 1.272172124 2.16243363 0.70793446 0.185033962 671.9905005 1813982.778 0.045160536 0.562564783 55944.21798 -4.747755207 0.890261506 DPSEEIEILLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DPSEEIEILLR 11 0 E9PGT3;Q15418-4;Q15418;Q15418-2;Q15418-3;Q5SVM6;B7Z3B5;F2Z2J1;Q15349;Q15349-3;Q15349-2 E9PGT3 RPS6KA1;RPS6KA2 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1;Ribosomal protein S6 kinase alpha-2 0 ;;; 112.75 0.0034531 60984000 69996 86997 83966 79399 83935 70116 90030 74778 73330 FALSE TRUE 65615.07531 93438.3484 85957.71317 81436.51276 77343.08368 90357.35096 76530.8373 84114.19791 61090.74927 1.074059102 1.529500776 1.407049581 1.333041643 1.266035932 1.47906765 1.252740197 1.376872913 1 15.89866631 -1.307210189 0.434999212 0.813748155 1.373440889 0.386505714 0.129913825 22.29702321 2.338865886 4.888355942 0.068291106 0.049293518 1.307210189 0.559692734 DPSQQELPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 143.21 0.00023841 2414700000 1964850 1703080 1736890 1746430 2193780 1360670 2272640 1626000 2377120 FALSE TRUE 1841873.546 1829177.815 1778089.851 1791246.35 2021489.368 1753473.34 1931878.73 1829009.679 1980363.315 0.930068504 0.923657695 0.897860427 0.904503904 1.020766923 0.885430126 0.975517328 0.923572794 1 20.9173337 DPSSNDINGGMEPTPSTVSTPS(ph)PSADLLGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DPSSNDINGGMEPTPSTVSTPSPSADLLGLR 31 0 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 1 DPSSNDINGGMEPTPSTVS(0.003)T(0.04)PS(0.75)PS(0.207)ADLLGLR;DPSSNDINGGMEPTPSTVS(0.011)T(0.164)PS(0.661)PS(0.164)ADLLGLR 124.57 4.48E-06 77686000 57169 55207 60030 56210 63189 54677 70630 49282 69560 TRUE FALSE 53590.89434 59294.58372 61453.93995 57652.44376 58226.39083 70461.36229 60039.6872 55434.96618 57949.98663 0.924778373 1.023202716 1.060465127 0.994865523 1.004769703 1.215899544 1.036060415 0.956600155 1 15.82252071 DPSVDIT(ph)QDLVDESEEERFDDMSSPGLELPSCELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DPSVDITQDLVDESEEERFDDMSSPGLELPSCELSR 36 1 Q6IN85-2;Q6IN85;G3V5Z3;G3V231;H0YIY8;Q6IN85-5 Q6IN85-2 SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3A 1 DPS(0.102)VDIT(0.475)QDLVDES(0.423)EEERFDDMSSPGLELPSCELSR 88.744 0.0011837 15738000 28466 33274 30803 29550 34742 24055 33330 28451 34370 TRUE FALSE 26684.36387 35737.64158 31533.66171 30308.30303 32013.50346 30999.288 28332.47592 32003.16998 28633.42496 0.931930564 1.248109216 1.101288503 1.058493808 1.118046601 1.082625919 0.98948959 1.117685712 1 14.80541263 2.282264775 0.934162527 1.030253114 1.122789506 0.017593912 0.086146083 1.094265887 1.836028163 0.059893361 0.035660256 191.5423338 -2.282264775 0.092536392 DPSVDITQDLVDESEEERFDDMSS(ph)PGLELPSCELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DPSVDITQDLVDESEEERFDDMSSPGLELPSCELSR 36 1 Q6IN85-2;Q6IN85;G3V5Z3;G3V231;H0YIY8;Q6IN85-5 Q6IN85-2 SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3A 1 DPSVDITQDLVDESEEERFDDMS(0.019)S(0.981)PGLELPSCELSR;DPSVDITQDLVDESEEERFDDMS(0.038)S(0.962)PGLELPSCELSR;DPSVDITQDLVDESEEERFDDMS(0.036)S(0.964)PGLELPSCELSR 215.22 8.63E-39 100635000 79889 84414 78881 82401 81618 69419 90961 79294 102880 TRUE FALSE 74888.8901 90664.10039 80752.09457 84515.54916 75208.05151 89459.13838 77322.24249 89194.03045 85708.66337 0.873761031 1.057817224 0.942169571 0.986079421 0.877484825 1.043758412 0.902152005 1.040665283 1 16.38715342 1.206902535 24.99991541 1.020332686 0.963501756 0.144820356 0.063547273 461.3225713 364289.1718 0.05401555 0.013508881 16.10284212 -1.206902535 -0.05683093 DPSVEVTQDLIDES(ph)EEERFEEMPETSHLIDLPTCELNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DPSVEVTQDLIDESEEERFEEMPETSHLIDLPTCELNK 38 1 Q5MIZ7-3;Q5MIZ7-2;Q5MIZ7 Q5MIZ7-3 SMEK2 Serine/threonine-protein phosphatase 4 regulatory subunit 3B 1 DPSVEVTQDLIDES(1)EEERFEEMPETSHLIDLPTCELNK;DPSVEVT(0.003)QDLIDES(0.997)EEERFEEMPETSHLIDLPTCELNK 260.96 1.16E-62 107597000 193158 153042 177883 173198 159507 143643 200201 144979 137873 TRUE FALSE 181068.5856 164373.3889 182102.4688 177642.5539 146979.9636 185110.4023 170182.7186 163079.9473 114861.1056 1.576413396 1.431062221 1.585414556 1.546585791 1.279632151 1.611602128 1.481639217 1.419801302 1 16.80953083 0.688279613 2.158345383 1.000101182 1.501881155 0.730952139 0.095018444 0.761564305 4.610073855 0.082649977 0.022540341 4.878424781 -0.688279613 0.501779974 DPTLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DPTLYR 6 0 P07814;V9GYZ6;H0Y547;E9PEJ6;P98196 P07814 EPRS;ATP11A Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase;Phospholipid-transporting ATPase;Probable phospholipid-transporting ATPase IH 0 ; 114.6 0.058509 343390000 328440 384940 380880 389110 395560 330730 400720 374340 382650 FALSE TRUE 307883.5267 413441.3581 389914.6535 399095.2214 364494.3132 426206.382 340635.7561 421077.173 318783.243 0.965808377 1.296935668 1.223134095 1.251932873 1.143392325 1.336978626 1.068549755 1.320888667 1 18.28221627 -1.145798421 4.099626359 0.999940305 1.207089943 0.226389869 0.116251328 2.187997209 27722193.28 3555.047686 0.023750193 0.071482804 1.145798421 0.207149638 DPTSLLGVLQAEADS(ph)TSEGLEDAVHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DPTSLLGVLQAEADSTSEGLEDAVHSR 27 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 DPTSLLGVLQAEADS(0.445)T(0.445)S(0.11)EGLEDAVHSR;DPTSLLGVLQAEADS(0.936)T(0.062)S(0.002)EGLEDAVHSR;DPTSLLGVLQAEADS(0.333)T(0.333)S(0.333)EGLEDAVHS(0.001)R;DPTSLLGVLQAEADS(0.431)T(0.431)S(0.135)EGLEDAVHS(0.002)R;DPTSLLGVLQAEADS(0.928)T(0.06)S(0.013)EGLEDAVHSR;DPTSLLGVLQAEADS(0.941)T(0.053)S(0.006)EGLEDAVHSR;DPT(0.001)S(0.001)LLGVLQAEADS(0.332)T(0.332)S(0.332)EGLEDAVHSR 169.94 3.75E-12 189795400 153215.5 158350.6 148324.1 169404.7 158650.3 141509.4 212572.8 144539.2 118005.6 TRUE FALSE 143626.0154 170075.0432 151842.4177 173751.9114 146190.5454 182360.8666 180699.4821 162585.2373 98309.70301 1.460954626 1.729992442 1.544531344 1.76739331 1.487040861 1.85496305 1.838063554 1.653806616 1 16.58504619 DPTSLLGVLQAEADST(ph)SEGLEDAVHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DPTSLLGVLQAEADSTSEGLEDAVHSR 27 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 DPTSLLGVLQAEADS(0.08)T(0.46)S(0.46)EGLEDAVHSR;DPTSLLGVLQAEADS(0.022)T(0.58)S(0.398)EGLEDAVHSR;DPTSLLGVLQAEADS(0.276)T(0.696)S(0.028)EGLEDAVHSR 181.88 6.04E-17 122622000 102781.4 121990.3 108763.5 116792 108048 95545.9 151628 103486.2 67296.7 TRUE FALSE 96348.49564 131022.5887 111343.4216 119789.0804 99562.34592 123128.4503 128892.789 116406.6799 56064.44602 1.718531128 2.336999615 1.985989865 2.13663184 1.775855341 2.196194897 2.299011195 2.076301259 1 15.77479854 0.920316331 21.16575009 1 2.098447572 0.730634131 0.2025379 6371.093636 1692307.177 0.181940934 0.045485234 8.323698308 -0.920316331 1.098447572 DPTSLLGVLQAEADSTSEGLEDAVHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DPTSLLGVLQAEADSTSEGLEDAVHSR 27 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 ;;; 260.08 5.06E-53 162648000 160988 177196 169827 188982 168004 170582 225488 167064 141491 FALSE TRUE 150912.0485 190315.7762 173855.3766 193831.5981 154809.6435 219826.2542 191678.1677 187922.3082 117875.238 1.2802693 1.614552635 1.474910079 1.644379272 1.313334727 1.864906132 1.626110546 1.594247539 1 16.84690116 DPTVHDDVLELEMDELNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DPTVHDDVLELEMDELNR 18 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;;;;; 361.93 3.27E-91 1880892000 2028146 2136238 2196576 2217165 1820166 1878369 2690302 2045183 1438526 FALSE TRUE 1901207.962 2294407.284 2248679.82 2274061.208 1677217.505 2420623.638 2286916.191 2300528.6 1198426.717 1.586419874 1.914516133 1.876359887 1.89753881 1.399516116 2.019834507 1.908265359 1.919623925 1 20.19271026 DPVQEAWAEDVDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DPVQEAWAEDVDLR 14 0 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;; 203.74 3.40E-08 6736849000 3001503 2829168 3048583 2920587 2650189 2303185 2919088 2655927 1626143 FALSE TRUE 2813644.285 3038642.542 3120896.828 2995534.207 2442053.846 2968077.12 2481397.854 2987525.332 1354729.228 2.076905279 2.242988842 2.303705245 2.211168214 1.802613981 2.190900631 1.831655952 2.205256424 1 20.3695731 -1.736463271 0.291506249 1.34E-14 2.236982061 0.807600766 0.169607546 10.36043882 0.520123826 7.566682639 0.179378837 0.018345803 1.736463271 2.236982061 DPWDAVLLEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DPWDAVLLEER 11 0 O00443;A0A0C4DGF9;O00443-2 O00443 PIK3C2A Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha 0 101.11 0.008216 8417800 10943 10616 11769 10958 11332 8483.8 14250 10555 10743 FALSE TRUE 10258.09716 11402.01969 12048.16624 11239.20083 10442.03043 10932.93534 12113.34479 11872.81498 8949.923898 1.146165854 1.273979513 1.346175272 1.255787307 1.166717231 1.221567408 1.353457854 1.326582787 1 13.1276597 -1.204682554 4.025829972 0.999829474 1.271396231 0.572322508 0.070510153 5270874.089 1577253.613 7839.366555 0.016743206 0.062419092 1.204682554 0.271566757 DQADFSVLHYAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQADFSVLHYAGK 13 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 ; 147.35 4.25E-05 473700000 1473430 1594180 1513050 1588710 1827690 1199850 1888070 1585580 1729540 FALSE TRUE 1381210.646 1712214.746 1548940.261 1629478.988 1684150.6 1546227.217 1604971.431 1783543.153 1440868.601 0.95859584 1.188321229 1.075004521 1.130900477 1.168843987 1.073121599 1.1138916 1.237824984 1 20.45850735 4.752631099 24.5666301 1.125280501 0.958595695 0.378499106 0.066368412 1903.283752 3323003.141 0.013923212 0.28457635 56575.85144 -4.752631099 -0.166684806 DQDELNPYAAWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQDELNPYAAWR 12 0 O43615;M0QXM9 O43615 TIMM44 Mitochondrial import inner membrane translocase subunit TIM44 0 ; 205.52 2.34E-07 203407000 277690 257630 247460 234840 336490 224400 230100 258500 400620 FALSE TRUE 260309.8786 276705.1933 253329.8681 240866.392 310063.4327 289180.6372 195598.6411 290774.294 333753.9339 0.779945499 0.829069459 0.759031856 0.721688548 0.929018062 0.866448625 0.586056436 0.871223571 1 18.34842532 0.994316943 24.99933616 1.000000028 0.778377163 0.380022179 0.090428937 213.6237662 939719.065 0.087046565 0.021761641 9.869995231 -0.994316943 -0.221622866 DQDGYYWITGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DQDGYYWITGR 11 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ;;;;; 218.07 2.53E-11 1331925000 994097 1081076 1091628 1135289 1115724 940420 1291290 995307 1335790 FALSE TRUE 931878.2433 1161119.992 1117521.932 1164422.438 1028099.538 1211903.988 1097673.052 1119573.27 1112838.019 0.837388934 1.043386343 1.004208979 1.046353932 0.923853714 1.089021013 0.986372709 1.006052319 1 20.08581218 4.744502875 24.81831244 1.01372993 0.837388849 0.618624948 0.043175141 357.7370216 1494069.615 0.008935648 0.080841776 55526.82933 -4.744502875 -0.176341081 DQDMDS(ph)DRAYQYQEFTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQDMDSDRAYQYQEFTK 17 1 Q9NW75-2;Q9NW75 Q9NW75-2 GPATCH2 G patch domain-containing protein 2 1 DQDMDS(1)DRAYQYQEFTK;DQDMDS(1)DRAYQYQEFTK 133.95 2.82E-05 305530000 792490 591960 662110 672940 728460 511380 874960 605200 796450 TRUE FALSE 742889.4655 635789.3343 677815.5619 690208.7797 671249.6901 659007.1044 743767.8707 680760.5522 663517.3497 1.119623271 0.958210565 1.021549116 1.040227177 1.011653562 0.993202521 1.120947133 1.025987568 1 19.33977466 DQDMS(ph)SPTTMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DQDMSSPTTMK 11 0 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A1B0GWJ4;Q5VW27;O00712-5;Q5VW26;A0A2R8Y7V8;Q5VW30;A0A1B0GWI9;Q5VW31;A0A1B0GVN4;A0A1B0GWB8;O00712-6 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 DQDMS(0.499)S(0.499)PT(0.002)TMK 98.902 0.0034459 195720000 1070700 692240 884170 733920 887360 734020 1220900 844290 1010300 TRUE FALSE 1003686.798 743494.1699 905142.9299 752753.6297 817670.325 945919.6582 1037837.379 949701.465 841674.4032 1.192488205 0.88335129 1.075407457 0.894352527 0.971480565 1.12385461 1.23306278 1.128347805 1 19.68290272 2.169941392 5.329726341 1.153088519 0.991973428 0.211633003 0.105229435 0.213147529 11.2645692 0.036364393 0.026814664 147.8908798 -2.169941392 -0.161115091 DQDMSS(ph)PTTMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DQDMSSPTTMK 11 0 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A1B0GWJ4;Q5VW27;O00712-5;Q5VW26;A0A2R8Y7V8;Q5VW30;A0A1B0GWI9;Q5VW31;A0A1B0GVN4;A0A1B0GWB8;O00712-6 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 DQDMS(0.019)S(0.915)PT(0.06)T(0.005)MK;DQDMS(0.188)S(0.808)PT(0.003)TMK;DQDMS(0.024)S(0.75)PT(0.219)T(0.007)MK 197.38 2.60E-05 204950000 2303560 1515170 1939450 1747310 2022430 1494810 2611760 1863860 2105540 TRUE FALSE 2159384.292 1627354.763 1985454.67 1792148.933 1863596.506 1926337.381 2220150.834 2096567.024 1754111.772 1.231041446 0.927737211 1.131886064 1.021684571 1.062416054 1.098183942 1.265683789 1.195230006 1 20.74230925 1.959720476 8.9629794 1.183057955 1.061834927 0.080404426 0.101990807 0.567668123 120.8015605 0.038342677 0.024521034 91.14240319 -1.959720476 -0.121223028 DQDS(ph)SDDERALEDWVSSETSALPRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 211.87 4.67E-26 125831000 102314 120081 105108 114050 131083 75376 114875 86943 166151 TRUE FALSE 95910.34938 128971.9222 107601.2114 116976.7161 120788.2699 97135.82757 97650.5602 97798.02494 138419.3247 0.692897105 0.931747951 0.777356858 0.845089487 0.872625771 0.70175048 0.705469127 0.706534475 1 17.07868585 2.240863836 24.99999017 0.746843593 0.83325252 0.001687834 0.107328119 115.0727442 1249057.428 0.034050248 0.027227585 174.1260852 -2.240863836 0.086408927 DQDSS(ph)DDERALEDWVSSETSALPRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DQDSSDDERALEDWVSSETSALPRPR 26 2 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 DQDS(0.058)S(0.302)DDERALEDWVS(0.302)S(0.302)ET(0.017)S(0.017)ALPRPR 118.97 0.00037838 69025000 52628 57877 53368 67405 66804 36205 65323 42545 79090 TRUE FALSE 49334.10742 62162.2733 54633.91416 69134.72642 61557.48331 46656.79576 55528.42258 47856.8369 65889.36806 0.748741548 0.943434049 0.829176478 1.049254659 0.934255178 0.708108108 0.842752393 0.726321079 1 16.00775807 2.268677795 24.99997873 0.806605564 0.90371238 0.115676901 0.109605442 350.5963135 291025.4038 0.034431184 0.028803722 185.6426653 -2.268677795 0.097106816 DQDSSDDERALEDWVS(ph)SETSALPRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DQDSSDDERALEDWVSSETSALPRPR 26 2 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 DQDSSDDERALEDWVS(0.25)S(0.25)ET(0.25)S(0.25)ALPRPR 124.8 9.19E-05 24677000 17895 18061 16044 17313 20151 10586 17945 15016 25844 TRUE FALSE 16774.98389 19398.25523 16424.57126 17757.28089 18568.42175 13642.00635 15254.31384 16890.78065 21530.46944 0.779127642 0.900967593 0.762852445 0.824751218 0.862425308 0.633613976 0.708498897 0.784505916 1 14.39409216 DQDWPALAVDLAHHLQVSEDVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DQDWPALAVDLAHHLQVSEDVVR 23 0 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 114.2 0.00040038 8875200 10288 14248 15207 13839 15848 11910 13552 11857 14783 FALSE TRUE 9644.092445 15302.93675 15567.71722 14194.13217 14603.36201 15348.22366 11520.00341 13337.37255 12315.6218 0.783077997 1.242563063 1.264062625 1.152530697 1.185759213 1.246240256 0.935397627 1.082963797 1 13.58820185 1.737880032 14.76766972 1.007714695 1.172338171 0.160224569 0.142150432 0.093423163 238.1685659 0.06231416 0.034365631 54.68648778 -1.737880032 0.164623475 DQECDKFNQCGTCNEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DQECDKFNQCGTCNEFK 17 1 Q9UBR2 Q9UBR2 CTSZ Cathepsin Z 0 285.47 2.42E-36 909680000 1080100 664750 724800 747060 846690 510660 1036000 681590 739320 FALSE TRUE 1012498.469 713968.7817 741992.5983 766230.8244 780194.3828 658079.2521 880661.4178 766688.0119 615922.7158 1.643872588 1.159185663 1.20468458 1.244037287 1.266708246 1.068444523 1.429824546 1.244779568 1 19.23238981 4.74365123 24.55900865 1.219805643 1.643872816 0.582212662 0.116736558 304.1252822 1467152.213 0.025836764 0.216062592 55418.04872 -4.74365123 0.424067173 DQEDDEQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DQEDDEQQR 9 0 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 99.653 0.012078 13071000 28141 26820 26081 25205 27711 20806 31040 26398 29544 FALSE TRUE 26379.70504 28805.78071 26699.65364 25851.80297 25534.68984 26812.35444 26385.84016 29693.84841 24612.91554 1.071783024 1.170352235 1.084782239 1.050334851 1.037450838 1.089361169 1.072032288 1.206433604 1 14.58712794 -2.403463157 2.289747209 0.180687283 1.097636174 0.257354046 0.052219455 2538174.59 682926.1981 10591404.69 0.012688685 0.003949452 2.403463157 0.916948891 DQEFTVDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DQEFTVDTR 9 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 125.18 0.0033062 0 650300 557370 564630 572570 552780 481830 683880 559510 612850 FALSE TRUE 609598.8838 598638.2547 578023.2902 587263.1156 509366.8886 620926.4991 581338.5428 629366.0551 510561.3758 1.193977674 1.172509875 1.13213282 1.150230204 0.997660443 1.216164263 1.138626168 1.232694216 1 18.96172488 4.245480999 1.53936818 1.131327361 1.194954513 0.090746585 0.076757501 1.418851749 5.5768333 0.019642424 0.103315317 17598.71666 -4.245480999 0.063627152 DQEGQDVLLFIDNIFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQEGQDVLLFIDNIFR 16 0 P06576;H0YH81;F8W0P7 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ; 180.97 5.54E-09 228655000 44897 38067 45157 39360.4 52196 34019.7 41148 41122 57469 FALSE TRUE 42086.97691 40885.52029 46228.14536 40370.4545 48096.73671 43840.63513 34978.2394 46256.17222 47877.05264 0.879063656 0.853969032 0.965559549 0.843210939 1.004588505 0.915692022 0.730584643 0.966144942 1 15.54704672 DQETLHSHGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQETLHSHGVR 11 0 B4DML5;G3XAG9;Q9BYM8-4;Q9BYM8-3;Q9BYM8;H0Y4S7 B4DML5 RBCK1 RanBP-type and C3HC4-type zinc finger-containing protein 1 0 ; 138.24 3.57E-05 145917000 90303 108671 119304 118568 110358 98374 125328 105352 108806 FALSE TRUE 84651.09643 116717.1139 122133.9472 121610.6556 101690.9278 126772.9768 106536.2299 118505.4291 90645.57569 0.933869036 1.287620637 1.347379023 1.341606082 1.121852082 1.398556696 1.175305348 1.307349291 1 16.46794898 -1.166559632 3.700430504 0.999809454 1.254032504 0.226752954 0.136387953 29910184.19 66557566.48 79881.51957 0.029648245 0.068146 1.166559632 0.25422305 DQFLDTLQAHGHDVNSFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQFLDTLQAHGHDVNSFVR 19 0 Q15021;E7EN77 Q15021 NCAPD2 Condensin complex subunit 1 0 ; 243.18 1.10E-24 251900000 228090 267330 271070 270870 287440 217290 328560 264260 272890 FALSE TRUE 213814.2541 287123.3914 277499.9084 277820.9828 264865.6219 280018.0956 279295.4782 297253.4427 227342.8961 0.940492348 1.262952994 1.220622739 1.22203503 1.165049036 1.231699342 1.228520807 1.307511463 1 17.7945104 4.744272675 24.91087015 1.217908341 0.940492222 0.500238914 0.082099608 426.3541695 1859316.167 0.016630116 0.14822823 55497.40487 -4.744272675 -0.277416119 DQGADSSQIHVPVEPQEDNNLPTHGGQEQALGSELQSQLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DQGADSSQIHVPVEPQEDNNLPTHGGQEQALGSELQSQLPK 41 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 200.47 1.73E-35 202340000 115140 83319 100630 99627 116240 76739 123030 89151 107970 FALSE TRUE 107933.5929 89488.02545 103016.9911 102183.5975 107110.9793 98892.30355 104582.7937 100281.6986 89949.10949 1.19994065 0.994873946 1.145280834 1.136015666 1.190795327 1.099425043 1.162688483 1.1148715 1 16.45682138 5.078905251 20.16739423 1.112081288 4.62850218 0.170450083 0.064031064 795.9476954 209403.015 0.014288399 3716.882869 119923.7639 -5.078905251 3.516420892 DQGELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DQGELER 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 147.19 0.005045 3231160000 3395680 3292110 3411070 3441670 3491960 2818920 3938380 2930510 3460630 FALSE TRUE 3183150.45 3535861.25 3491982.191 3529989.079 3217715.547 3632696.443 3347856.481 3296390.624 2883028.496 1.104099545 1.226439924 1.211220144 1.224403118 1.116088707 1.260027935 1.161229064 1.143377746 1 21.45915367 0.766909209 1.516390063 1.000330432 1.195591008 0.586137903 0.04895478 0.499770367 1.970937619 0.041564916 0.012092904 5.846678438 -0.766909209 0.195260576 DQGGELLSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 179.57 4.87E-06 638060000 884570 999690 926740 927330 1061290 761100 973260 901060 1092130 FALSE TRUE 829206.3427 1073708.088 948722.7104 951126.8578 977940.5644 980817.2146 827328.6983 1013559.324 909846.4476 0.911369545 1.180098126 1.042728378 1.045370744 1.074841329 1.078003016 0.909305851 1.113989429 1 19.79526356 DQGGFGDRNEYGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DQGGFGDRNEYGSR 14 1 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;;;; 253.79 2.81E-24 4602040000 1696810 1916750 1791440 1815840 1905340 1534945 2020410 1621118 2238940 FALSE TRUE 1590609.691 2058668.164 1833933.803 1862437.529 1755702.282 1978058.704 1717468.277 1823518.151 1865246.45 0.852761141 1.103697672 0.983212595 0.998494075 0.941270942 1.060481152 0.920772843 0.977628533 1 20.83093483 3.514293236 23.92732325 0.979648903 1.010842304 0 0.071381817 705.8407677 454339.4163 0.017356515 0.026885226 3268.084188 -3.514293236 0.031193401 DQGTYEDYVEGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 199.12 2.80E-07 2032290000 2305930 2165570 2251990 2146890 2070900 1915130 2422860 1991390 1834960 FALSE TRUE 2161605.958 2325911.056 2305408.266 2201982.832 1908259.868 2467996.941 2059574.636 2240019.425 1528693.322 1.41402198 1.521502726 1.508090755 1.440434651 1.248294763 1.614448697 1.34727784 1.46531642 1 20.54386758 -3.029127645 0.314494531 4.19E-18 1.478903143 0.660773477 0.099780011 42.76685976 1.199296954 28.39366493 0.085130705 0.000935131 3.029127645 1.478903143 DQHDTFFLRDPAEALQLPMDYVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DQHDTFFLRDPAEALQLPMDYVQR 24 1 K7ER00;Q9Y285;Q9Y285-2;K7EPH2;K7ERS0 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ;;;; 153.17 4.91E-08 447292000 307771 472312 432399 435840 491670 373969 483680 416085 488797 FALSE TRUE 288508.1625 507282.4719 442655.7085 447024.3923 453056.2215 481927.7794 411156.6743 468034.1282 407213.623 0.708493396 1.245740425 1.087035609 1.097763845 1.112576289 1.183476564 1.009683004 1.149357737 1 18.6354263 4.750131719 24.95681966 1.115272075 0.70849315 0.748022614 0.073320831 857.0661 1848504.919 0.016653017 0.271576362 56251.19061 -4.750131719 -0.406778925 DQHFDQNLNFMYIEVDKVTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DQHFDQNLNFMYIEVDKVTER 21 1 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 0 ;; 213.15 3.40E-23 131433000 119116 99334 102566 110645 116748 87941.6 121258 97846 124038 FALSE TRUE 111660.7422 106688.7927 104998.914 113484.338 107579.083 113328.9123 103076.4886 110062.2885 103335.2565 1.080567717 1.032452972 1.016099611 1.09821509 1.041068525 1.096710998 0.997495841 1.065099098 1 16.65697304 0.244032922 0.746559037 0.999366185 1.049539499 0.182115383 0.033578754 5.386107356 3.831906314 0.043961635 0.01119247 1.754013461 -0.244032922 0.050173314 DQHFVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQHFVK 6 0 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ; 83.614 0.056787 728460000 1373230 1362320 1257270 1111160 1710970 959650 1498760 1580490 1842890 FALSE TRUE 1287281.986 1463187.59 1287093.038 1139674.247 1576597.318 1236685.376 1274034.852 1777817.656 1535299.753 0.838456453 0.953030564 0.838333384 0.742313834 1.026898698 0.805500928 0.829828083 1.157961272 1 20.55008893 1.245693993 24.99956773 1.078980657 0.865605727 0.519188341 0.086736406 110.2444481 386371.6415 0.055859479 0.019451427 17.60734985 -1.245693993 -0.213374929 DQHHLGS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQHHLGSPSR 10 0 Q9H8M2;Q9H8M2-3;Q9H8M2-1;Q9H8M2-6;Q9H8M2-2 Q9H8M2 BRD9 Bromodomain-containing protein 9 1 DQHHLGS(0.985)PS(0.015)R;DQHHLGS(0.651)PS(0.349)R 110.44 0.0012148 1578940000 585330 677010 676640 657240 593450 538450 666930 603040 534130 TRUE FALSE 548695.2401 727136.5248 692690.2203 674105.8911 546842.8309 693891.774 566930.038 678330.8715 444980.2524 1.233077731 1.634087178 1.556676317 1.514911926 1.228914829 1.559376557 1.274056624 1.524406685 1 18.76338179 -3.252754695 0.224437638 1.88E-13 1.527523454 0.436829082 0.151294745 53.63800982 1.084597618 25.18616543 0.268796157 0.000558786 3.252754695 1.527523454 DQHLNNSS(ph)SSPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DQHLNNSSSSPQR 13 0 A0A4W8VX11;A0A5H1ZRS1;E7EV93;E9PGW9 A0A4W8VX11 PCM1 1 DQHLNNS(0.032)S(0.475)S(0.3)S(0.193)PQR 104.88 0.00096407 112170000 63276 76105 83364 79358 78158 68509 91799 63523 71462 TRUE FALSE 59315.66811 81739.89339 85341.43345 81394.46063 72019.78595 88286.43615 78034.59217 71453.98638 59534.53054 0.996323773 1.372982917 1.433477894 1.367180692 1.209714519 1.48294503 1.310745066 1.200210798 1 15.86143907 0.956249377 2.578210708 1.001313972 1.33506505 0.339766308 0.135351515 0.305385443 4.683357031 0.119438601 0.032054819 9.041685096 -0.956249377 0.333751078 DQHLNNSSSS(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DQHLNNSSSSPQR 13 0 A0A4W8VX11;A0A5H1ZRS1;E7EV93;E9PGW9 A0A4W8VX11 PCM1 1 DQHLNNS(0.094)S(0.038)S(0.163)S(0.705)PQR;DQHLNNSS(0.002)S(0.169)S(0.829)PQR;DQHLNNSS(0.025)S(0.031)S(0.944)PQR 209.89 3.59E-08 271370000 294191 338734 357594 339146 345011 314467 403908 299108 307793 TRUE FALSE 275778.1105 363814.2178 366076.2985 347849.0605 317915.2278 405248.518 343345.7451 336452.2922 256420.3599 1.075492253 1.418819543 1.42764131 1.356557883 1.239820535 1.580406946 1.338995645 1.312112238 1 17.96815129 0.730259861 2.534057085 1.000127861 1.368951551 0.400885961 0.130963958 1.34691397 11.37662543 0.11413844 0.030455652 5.37353227 -0.730259861 0.36882369 DQHSFELDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQHSFELDEK 10 0 Q6DD88;F5H6I7;F5GWF8 Q6DD88 ATL3 Atlastin-3 0 ; 169.65 4.57E-06 232572000 556750 555190 525120 518180 601970 499640 645060 554820 601610 FALSE TRUE 521904.0113 596296.8453 537576.0944 531477.3761 554693.7044 643877.957 548339.2414 624090.4983 501197.4045 1.041314274 1.18974448 1.072583556 1.06041526 1.106736985 1.284679352 1.094058422 1.245198983 1 18.93501942 2.432345474 24.99981556 1.165044519 1.102314873 0.104880509 0.086294386 274.8567051 153460.3657 0.026750875 0.022381392 270.6110172 -2.432345474 -0.062729646 DQITAGNAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DQITAGNAAR 10 0 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;; 175.43 6.52E-06 344710000 311989 363834 350750 383192 407998 310926 380659 336686 384189 FALSE TRUE 292462.1654 390772.6479 359069.9556 393025.3555 375955.4829 400685.2887 323582.7168 378721.9882 320065.3739 0.913757592 1.2209151 1.121864422 1.227953373 1.174620916 1.251885775 1.010989451 1.18326448 1 18.28800708 -1.185913888 5.499553757 0.99999523 1.143110235 0.145865529 0.104455881 5.50E-06 8.14E-07 0.091034951 0.021456429 0.065175761 1.185913888 0.143115006 DQIYDIFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQIYDIFQK 9 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;J3QR64;J3KTN0 P60842;J3KTN0 EIF4A1 Eukaryotic initiation factor 4A-I 0 ; 129.85 0.00087862 484430000 513870 466370 477470 482400 488130 340790 513730 468840 470670 FALSE TRUE 481707.794 500900.5201 488795.8139 494779.2007 449794.2388 439170.5407 436700.9557 527375.706 392112.1364 1.228494987 1.277442021 1.2465715 1.261830876 1.147106139 1.120012619 1.113714459 1.344961446 1 18.58090677 2.736581074 23.14983203 1.146760492 1.256392157 0.289597464 0.084312411 75.56774665 883719.7431 0.024123258 0.023842854 545.2316697 -2.736581074 0.109631665 DQKLPHLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DQKLPHLER 9 1 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ;;; 89.548 0.0072297 442110000 945220 1090440 981070 987810 1371880 752460 1182810 1017260 1786090 FALSE TRUE 886060.3675 1171177.312 1004341.444 1013158.877 1264138.079 969682.9868 1005458.621 1144267.15 1487980.04 0.595478665 0.787092085 0.674969701 0.680895475 0.849566556 0.651677415 0.675720503 0.769007056 1 20.50492374 0.876041444 4.647417692 0.99998006 0.708371263 0.634072945 0.07075776 0.559282282 20.15584269 0.062169447 0.015762892 7.516946236 -0.876041444 -0.291608797 DQLIYNLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQLIYNLLK 9 0 F5GZQ4;P00338;P00338-3;P00338-4;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2;F5H5J4;F5H6W8;F5GXC7;F5H8H6;F5GXU1;F5GWW2 F5GZQ4;P00338 LDHA L-lactate dehydrogenase A chain 0 ; 156.92 0.00016235 884590000 2816800 3453700 2406500 2462900 3603300 1725530 2707400 3030600 2417100 FALSE TRUE 2640501.516 3709415.542 2463583.316 2526102.184 3320311.353 2223662.499 2301450.504 3408977.081 2013670.395 1.311287847 1.84211654 1.223429278 1.254476497 1.64888522 1.104283256 1.142913215 1.692917118 1 20.94139613 8 0.038243573 0.007451036 3.561397833 0.170382008 0.254193343 1196.237258 3.487163218 91.12186797 281.6428563 99999999.99 -8 3.553946797 DQLIYNLLKEEQTPQNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQLIYNLLKEEQTPQNK 17 1 F5GZQ4;P00338;P00338-3;P00338-4;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2;F5H5J4;F5H6W8;F5GXC7;F5H8H6;F5GXU1;F5GWW2 F5GZQ4;P00338 LDHA L-lactate dehydrogenase A chain 0 ; 182.31 6.88E-10 1606130000 1281660 1368590 1255870 1455490 2058410 703670 1598580 1087580 2944600 FALSE TRUE 1201443.188 1469921.828 1285659.829 1492840.338 1896750.782 906808.1059 1358887.769 1223366.757 2453127.237 0.489759834 0.599203256 0.524090153 0.608545825 0.773197066 0.369653923 0.553941006 0.498696822 1 21.22619063 -1.928458075 2.707153375 1.285560983 0.55395056 0.652052159 0.102809317 8092557.3 4853595.694 14621989.49 0.022799879 0.011790763 1.928458075 -0.731610423 DQMEYMLQNHVFPLFSSELGYMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQMEYMLQNHVFPLFSSELGYMR 23 0 O95373 O95373 IPO7 Importin-7 0 ; 146.5 1.28E-07 116262000 117032 136682 106020 104656 151849 80505 117452 153097 75938 FALSE TRUE 109707.176 146802.0775 108534.8445 107341.6501 139923.3921 103745.4866 99841.16297 172211.4975 63263.45722 1.734131849 2.32048775 1.715600905 1.696740186 2.211756964 1.639895939 1.578180633 2.722132255 1 15.94908478 -1.161509674 4.755812643 0.999904912 1.924412168 0.398344429 0.366404341 0.000340063 6.00E-05 0.326557075 0.076962409 0.068943024 1.161509674 0.924507256 DQNGNHVVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DQNGNHVVQK 10 0 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;A0A0C4DG68;H0YC97;Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38;H0YDK8 Q8TB72-3;Q5T1Z4 PUM2;PUM1 Pumilio homolog 2;Pumilio homolog 1 0 84.896 0.014609 145200000 188930 175150 187180 183710 203330 156420 238210 181770 233910 FALSE TRUE 177105.2085 188118.2882 191619.998 188424.3096 187361.282 201575.9147 202492.6219 204464.3846 194868.9099 0.908842815 0.965358139 0.983327705 0.966928535 0.961473444 1.034418034 1.039122259 1.049240665 1 17.57214441 2.238104958 24.86189774 1.034525551 0.962308083 0.71281447 0.023000959 5.994880001 327064.5756 0.007975331 0.006250899 173.0234462 -2.238104958 -0.072217468 DQPAFTPSGILT(ph)PHALGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DQPAFTPSGILTPHALGSR 19 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 1 DQPAFTPSGILT(1)PHALGSR 122.84 0.00011922 95201000 54228 55709 58187 60341 64774 47479 70451 44831 85854 TRUE FALSE 50833.96628 59833.75233 59567.22312 61889.45222 59686.91133 61185.41654 59887.52659 50428.24904 71524.41276 0.710721896 0.836550068 0.832823659 0.865291302 0.834497048 0.85544801 0.837301898 0.705049466 1 16.12614813 -2.532145851 2.396578307 4.394899396 0.819927399 0.516069938 0.057153941 3250429.651 605813.9845 60744213.33 0.012577963 0.002936663 2.532145851 -3.574971997 DQPGRQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DQPGRQEK 8 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 100.02 0.0058391 1694050000 2302280 1873170 1985500 1947450 2163800 1059050 1800010 1334510 2688010 FALSE TRUE 2158184.404 2011861.456 2032596.998 1997424.864 1993863.876 1364780.543 1530115.211 1501126.511 2239363.766 0.963748917 0.898407613 0.907667181 0.891960875 0.890370697 0.609450132 0.683281222 0.670336162 1 21.09465747 2.323157397 7.553934758 0.707726765 0.9088433 0.372506916 0.105757252 0.186295099 14.26521747 0.032297505 0.026923964 210.4541031 -2.323157397 0.201116535 DQPPFGDS(ph)DDS(ph)VEADKSSPGIHLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQPPFGDSDDSVEADKSSPGIHLER 25 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 2 DQPPFGDS(1)DDS(1)VEADKSSPGIHLER;DQPPFGDS(1)DDS(1)VEADKSSPGIHLER 164.84 9.18E-12 364990000 1038730 695290 793530 749610 836310 646560 1076900 718280 791250 TRUE FALSE 973717.7435 746769.995 812352.9063 768846.2617 770629.5861 833211.376 915428.8424 807958.8391 659185.2633 1.477153386 1.132868158 1.232359022 1.166358389 1.169063735 1.264001825 1.388727712 1.225693116 1 19.33032446 2.046203592 23.9889631 1.267590463 1.217854646 0 0.136518461 346.5519771 179927.9074 0.046698738 0.034489287 111.2253017 -2.046203592 -0.049735817 DQQEAALVDMVNDGVEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQQEAALVDMVNDGVEDLR 19 0 A8MX94;P09211 A8MX94 GSTP1 Glutathione S-transferase P 0 ; 209.57 5.05E-16 30520000 61707 61009 56444 63366 61212 45730 72742 54714 51161 FALSE TRUE 57844.86902 65526.16984 57782.87833 64992.07884 56404.65644 58931.50864 61835.0124 61545.16334 42621.89859 1.357163124 1.537382707 1.355708691 1.524851801 1.323372687 1.38265799 1.450780337 1.443979864 1 15.37930724 -1.679379786 2.63134503 0.938882673 1.426559117 0.777522842 0.070901972 10939642.44 9410345.914 4476842.034 0.015579227 0.02092282 1.679379786 0.487676445 DQQNLPYGVTPAS(ph)PSGHSQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.987)PS(0.012)GHSQGR;DQQNLPYGVTPAS(0.999)PS(0.001)GHSQGR 219.94 3.14E-25 1048110000 358640 426260 448740 526770 491990 340310 500120 357850 427370 TRUE FALSE 336193.3626 457820.7339 459384.3247 540287.81 453351.09 438551.9725 425131.6489 402528.3602 356039.1861 0.94425944 1.285871757 1.290263383 1.517495352 1.27331796 1.23175198 1.194058591 1.130573195 1 18.44167651 1.149518945 1.214925548 1.005368575 1.276831362 0.267030017 0.137592712 0.54627355 1.647001274 0.123257798 0.039077206 14.10973786 -1.149518945 0.271462787 DQRPS(ph)SPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DQRPSSPIR 9 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 DQRPS(0.651)S(0.349)PIR 115.14 0.00092349 1124200000 129650 183170 133780 155880 182830 119990 139860 162880 186270 TRUE FALSE 121535.4379 196732.0974 136953.3248 159880.1447 168471.2693 154629.1651 118889.2914 183215.9265 155180.3336 0.783188405 1.267764367 0.882543049 1.030286125 1.085648325 0.996448206 0.766136331 1.1806646 1 17.24358621 1.989904327 24.66392172 0.937534669 1.02964983 0 0.161455147 1164.735325 2845471.106 0.058555434 0.040652299 97.70219642 -1.989904327 0.092115161 DQRPSS(ph)PIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DQRPSSPIR 9 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 DQRPS(0.123)S(0.877)PIR 105.17 0.0019024 1184700000 100710 161370 65956 131150 106190 64444 119860 87557 143000 TRUE FALSE 94406.74087 173318.0027 67520.50747 134515.531 97850.26575 83047.93664 101888.1057 98488.68419 119132.3762 0.792452429 1.454835438 0.566768746 1.129126568 0.821357459 0.697106356 0.855251184 0.826716358 1 16.86220602 3.973255802 24.99960539 0.835743645 1.150937657 0.221580219 0.217602084 191.5116384 1238605.049 0.048406572 0.091661361 9402.769768 -3.973255802 0.315194012 DQS(ph)LS(ph)PSKGENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQSLSPSKGENK 12 1 Q5TCQ9;Q5TCQ9-1 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 2 DQS(1)LS(0.752)PS(0.248)KGENK;DQS(1)LS(0.996)PS(0.004)KGENK 103.88 0.0012512 670050000 3603300 1093330 1711610 1661580 1892380 1083950 2174280 1295000 2542900 TRUE FALSE 3377775.885 1174281.291 1752210.197 1704218.956 1743760.108 1396868.769 1848266.899 1456683.601 2118473.562 1.594438536 0.554305379 0.827109778 0.804456089 0.823121015 0.659375124 0.87245219 0.687609997 1 21.01459369 4.747729073 24.88833968 0.766852914 1.594438995 0.812016674 0.123255468 444.4418184 1206437.657 0.026738704 0.333530793 55940.85158 -4.747729073 0.827586082 DQS(ph)PFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DQSPFSK 7 0 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 DQS(1)PFSK;DQS(1)PFSK;DQS(0.987)PFS(0.013)K;DQS(1)PFSK;DQS(0.984)PFS(0.016)K;DQS(1)PFSK;DQS(1)PFSK 173.24 0.00091349 10887310000 16229200 10391390 12281600 11547870 11444470 8579110 15226600 9763930 12613630 TRUE FALSE 15213443.34 11160779.33 12572925.35 11844207.89 10545667.49 11055759.79 12943512.69 10982978.15 10508333.67 1.447750312 1.062088404 1.196471843 1.12712522 1.003552783 1.052094475 1.231737885 1.045168388 1 23.32503058 4.743281802 24.72842079 1.107543343 1.447750474 0.668921669 0.078263793 266.9596937 1398213.796 0.018062933 0.146862403 55370.92797 -4.743281802 0.340207131 DQS(ph)PPPS(ph)PPPSYHPPPPPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQSPPPSPPPSYHPPPPPTK 20 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 2 DQS(1)PPPS(0.996)PPPS(0.004)YHPPPPPTK;DQS(1)PPPS(0.984)PPPS(0.005)Y(0.011)HPPPPPTK 103.63 0.0001492 442780000 827860 1018370 1071610 1021650 1188960 822710 1228940 906920 1322990 TRUE FALSE 776045.7204 1093771.174 1097029.095 1047867.269 1095583.878 1060213.021 1044671.856 1020150.958 1102174.422 0.704104273 0.992375755 0.995331658 0.95072726 0.994020416 0.96192853 0.947828071 0.925580324 1 20.07192112 4.741277788 24.99491878 0.971509802 0.704104177 0.919857469 0.024755127 68.23749396 627674.251 0.006107838 0.042354375 55116.01219 -4.741277788 -0.267405625 DQS(ph)TPIIEVEGPLLSDTHVTFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQSTPIIEVEGPLLSDTHVTFK 22 0 P49116;P49116-2 P49116 NR2C2 Nuclear receptor subfamily 2 group C member 2 1 DQS(0.5)T(0.5)PIIEVEGPLLSDTHVTFK;DQS(0.5)T(0.5)PIIEVEGPLLSDTHVTFK 178.91 3.78E-17 266433000 246634 269270 269973 279937 301830 201263 348930 262656 300640 TRUE FALSE 231197.6182 289207.031 276376.8871 287120.6574 278125.4893 259364.3609 296611.1858 295449.1798 250461.2418 0.923087407 1.154697744 1.103471679 1.146367619 1.110453208 1.035546893 1.184259823 1.179620358 1 17.93422784 4.744463475 24.7792787 1.12158392 0.923087309 0.503390599 0.059296077 443.5546395 1861912.857 0.012745682 0.115526792 55521.79202 -4.744463475 -0.198496611 DQSPFS(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DQSPFSK 7 0 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 DQS(0.254)PFS(0.746)K 153.24 0.0018453 2892600000 2838700 1774000 2168600 2041200 1986000 1516500 2551500 1689100 2164100 TRUE FALSE 2661030.834 1905348.806 2220040.216 2093580.648 1830027.571 1954288.932 2168926.262 1899987.853 1802897.729 1.475974367 1.056825784 1.23137335 1.161230953 1.015047909 1.083971043 1.203022349 1.053852264 1 20.78188613 4.74465167 24.91551455 1.118633347 1.475974531 0.687767657 0.078647194 385.750732 1577871.062 0.017895661 0.164237236 55545.85673 -4.74465167 0.357341184 DQSSWQNSDASQEVGGHQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DQSSWQNSDASQEVGGHQER 20 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ;; 338.53 3.68E-80 1333130000 520930 607330 539940 587900 609510 504700 646210 509020 538110 FALSE TRUE 488325.9212 652297.3451 552747.6318 602986.5093 561641.5432 650398.6969 549316.8096 572572.2675 448295.9647 1.089293591 1.455059596 1.232997116 1.345063433 1.252836491 1.45082434 1.225344087 1.277219321 1 18.77409199 0.476090712 1.233705372 1.000096725 1.309878126 0.412316186 0.108625667 1.898185561 3.594935954 0.090737616 0.027300897 2.992889705 -0.476090712 0.309781402 DQST(ph)PIIEVEGPLLSDTHVTFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DQSTPIIEVEGPLLSDTHVTFK 22 0 P49116;P49116-2 P49116 NR2C2 Nuclear receptor subfamily 2 group C member 2 1 DQS(0.18)T(0.82)PIIEVEGPLLSDTHVTFK 178.91 2.16E-16 188050000 88833 91115 101950 104630 112600 77249 141630 100690 120690 TRUE FALSE 83273.1011 97861.24941 104368.3021 107314.9829 103756.8502 99549.53227 120393.8963 113261.3681 100546.0593 0.828208501 0.973297711 1.038014845 1.06732162 1.031933533 0.99008885 1.197400447 1.126462528 1 16.61749701 6.04845165 0.513704984 1.091189149 2.53E-17 0.604572103 0.061177283 10.14435161 0.719709884 0.032198831 8.934519978 1118025.348 -6.04845165 -1.091189149 DQTDFEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DQTDFEHR 8 0 A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 ;;; 166.07 0.00032059 1863530000 1941660 1968080 1973060 1963320 1970670 1675800 2231210 1913540 1819910 FALSE TRUE 1820134.967 2113798.691 2019861.915 2013702.115 1815901.528 2159576.256 1896660.774 2152449.681 1516155.264 1.200493782 1.394183525 1.332226298 1.328163522 1.197701562 1.424376716 1.250967377 1.419676291 1 20.53198607 -1.21377105 4.668537232 0.999931128 1.322567925 0.597395084 0.082103456 5.12E-05 8.62E-06 0.069140436 0.016293087 0.061126418 1.21377105 0.322636797 DQVANSAFVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DQVANSAFVER 11 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;; 288.49 3.44E-28 11830210000 3153530 3203870 3235770 3269980 3636760 2860400 3709400 2949130 3206920 FALSE TRUE 2956156.187 3441087.868 3312523.992 3353893.223 3351143.54 3686151.045 3153209.906 3317335.372 2671664.335 1.106484878 1.287994088 1.23987282 1.255357262 1.254328059 1.379720872 1.180241794 1.241673712 1 21.34930733 -0.898205199 6.434410398 0.99999998 1.248624786 0.544325401 0.069776533 1.80E-08 3.08E-09 0.060506108 0.014261425 0.126413892 0.898205199 0.248624806 DQVLHEHIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DQVLHEHIQR 10 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 0 ; 151.26 1.16E-05 694720000 504020 539000 553470 531460 541060 474350 627160 524890 636090 FALSE TRUE 472474.2879 578908.1208 566598.5698 545098.1634 498567.3301 611287.1446 533123.1803 590423.6719 529922.4697 0.891591346 1.092439279 1.069210313 1.028637573 0.940830704 1.153540715 1.00603996 1.114169913 1 19.01542178 2.240989466 24.99975502 1.065222987 1.026441562 0.117842527 0.074278749 200.4159218 2062872.038 0.025153259 0.020126356 174.1764626 -2.240989466 -0.038781425 DQVNLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DQVNLSPK 8 0 Q5FBB7-6;Q5FBB7 Q5FBB7-6 SGOL1 Shugoshin-like 1 1 DQVNLS(1)PK;DQVNLS(1)PK;DQVNLS(1)PK;DQVNLS(1)PK 123.62 0.0014055 760260000 3426020 1989210 2381100 2214130 2364630 1574790 3044550 1880880 3086480 TRUE FALSE 3211591.524 2136493.178 2437580.816 2270948.324 2178921.498 2029406.308 2588047.992 2115712.008 2571326.549 1.249001814 0.830891424 0.947985707 0.883181611 0.847391981 0.789244878 1.006503041 0.822809538 1 21.29408141 4.744551373 24.95613146 0.891778323 1.249001974 0.699005595 0.073827154 348.4506841 1451524.828 0.016028509 0.146106061 55533.03031 -4.744551373 0.357223651 DQVTAQEIFQDNHEDGPTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DQVTAQEIFQDNHEDGPTAK 20 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;; 344.69 2.60E-81 1297990000 2249840 1644940 1878460 1735170 1778750 1431750 2421700 1720540 2070890 FALSE TRUE 2109026.53 1766733.069 1923017.958 1779697.4 1639054.15 1845072.982 2058588.567 1935353.206 1725245.081 1.222450395 1.024047591 1.114634657 1.031562078 0.950041341 1.069455582 1.19321515 1.121784509 1 20.71836989 -0.913065786 7.770878437 0.999999998 1.087956815 0.112053685 0.080035818 5.74E-10 7.38E-11 0.077019524 0.018153676 0.12216146 0.913065786 0.087956817 DQWEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DQWEDR 6 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;; 224.39 1.02E-05 13406200000 12281130 12448210 12799800 11595100 14632900 10400440 13644400 10760210 13864500 FALSE TRUE 11512476 13369888.42 13103417.3 11892649.9 13483691.06 13402878.19 11598548.89 12103645.9 11550425.38 0.99671446 1.157523466 1.134453223 1.029628737 1.167376145 1.160379618 1.004166384 1.047896117 1 23.46144265 1.695138185 7.978637778 1.020353575 1.115690405 0.346281767 0.057597242 0.124208911 15.65609714 0.026588856 0.013996525 49.56078599 -1.695138185 0.09533683 DQYSHLLSDHFLPYQGHNS(ph)FR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DQYSHLLSDHFLPYQGHNSFR 21 0 Q7Z4G4-2;Q7Z4G4 Q7Z4G4-2 TRMT11 tRNA (guanine(10)-N2)-methyltransferase homolog 1 DQYSHLLSDHFLPYQGHNS(1)FR 87.196 0.0044127 64301000 17878 20930 21311 17108 21795 20109 22075 13154 29235 TRUE FALSE 16759.04789 22479.67898 21816.50698 17547.02024 20083.30862 25914.14186 18765.05868 14796.30586 24355.48963 0.688101457 0.922982018 0.895753167 0.720454423 0.824590633 1.063995931 0.770465261 0.607514202 1 14.57195937 -1.144901013 4.233716054 1.000033047 0.833471637 0.152532235 0.130827862 17715616.27 4790739.799 6518.169614 0.029160456 0.071630666 1.144901013 -0.166561409 DQYSVIFESGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DQYSVIFESGDR 12 0 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;;; 246.08 3.79E-16 1986120000 2020230 2149990 2419260 2297770 2195690 2062320 2503960 1977030 2059180 FALSE TRUE 1893787.411 2309177.497 2476645.99 2356734.668 2023249.364 2657678.305 2128514.444 2223866.547 1715489.555 1.103934096 1.346074938 1.443696339 1.373797154 1.179400573 1.549224416 1.240762112 1.29634514 1 20.71018891 0.575065038 1.367679762 1.00043105 1.340476792 0.375967479 0.127308409 1.597279348 4.016547515 0.110878072 0.032751978 3.758936927 -0.575065038 0.340045742 DRAEAEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 179.8 0.00022108 1336560000 1238930 1568720 1292140 1358830 1573580 1008975 1379240 1331270 1442790 FALSE TRUE 1161387.583 1684869.661 1322790.171 1393699.878 1449997.374 1300249.703 1172435.766 1497481.99 1201979.028 0.96622949 1.401746305 1.100510192 1.159504322 1.206341658 1.081757396 0.97542115 1.24584702 1 20.19698029 2.180988416 5.65531201 1.061576896 1.189511408 0.092946241 0.128821452 0.329997293 21.48725966 0.045646404 0.033801953 151.7009904 -2.180988416 0.127934512 DRAS(ph)PAAAEEVVPEWASCLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DRASPAAAEEVVPEWASCLK 20 1 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 DRAS(1)PAAAEEVVPEWASCLK;DRAS(1)PAAAEEVVPEWASCLK;DRAS(1)PAAAEEVVPEWASCLK;DRAS(1)PAAAEEVVPEWASCLK;DRAS(1)PAAAEEVVPEWASCLK;DRAS(1)PAAAEEVVPEWASCLK 228.3 1.90E-25 1186312000 2180980 1825750 1918390 1881840 2170780 1507581 2594400 1816750 2446950 TRUE FALSE 2044476.355 1960930.43 1963895.117 1930131.2 2000295.695 1942795.161 2205393.805 2043575.237 2038538.237 1.002912929 0.961929678 0.963383998 0.94682119 0.981240214 0.953033466 1.081850595 1.002470888 1 20.95910359 1.756822591 25 1.035225653 0.966614034 0.513851451 0.027136913 4.630670027 6345.658147 0.011048968 0.006127184 57.12452353 -1.756822591 -0.068611618 DRCPLPCIPTLIGT(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRCPLPCIPTLIGTPVK 17 1 Q9H0H5 Q9H0H5 RACGAP1 Rac GTPase-activating protein 1 1 DRCPLPCIPTLIGT(1)PVK;DRCPLPCIPTLIGT(1)PVK 174.47 2.18E-09 660150000 1107300 739110 828770 711760 762670 869620 1481470 828170 1174950 TRUE FALSE 1037996.07 793834.4734 848428.8158 730024.9666 702772.9747 1120665.177 1259337.327 931568.8475 978843.2545 1.060431346 0.810992434 0.86676678 0.745803747 0.717962729 1.144887265 1.286556679 0.951703803 1 19.90071833 2.225143649 24.96112564 1.138448572 0.835679665 0.47829323 0.129118066 160.1343898 297914.3907 0.045933695 0.034114971 167.9359397 -2.225143649 -0.302768907 DRDAS(ph)PSKEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DRDASPSKEER 11 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 DRDAS(0.981)PS(0.019)KEER;DRDAS(0.998)PS(0.002)KEER;DRDAS(0.643)PS(0.357)KEER;DRDAS(0.979)PS(0.021)KEER;DRDAS(0.984)PS(0.016)KEER;DRDAS(0.994)PS(0.006)KEER 158.93 1.53E-05 5132561000 5378042 3218048 3722885 3648506 3922171 2936510 4544537 3094925 4594079 TRUE FALSE 5041439.951 3456315.622 3811193.59 3742132.841 3614139.511 3784232.767 3863125.866 3481333.199 3827297.536 1.317232304 0.903069487 0.995792345 0.977748086 0.944305865 0.988747995 1.009361261 0.909606104 1 21.86789463 4.745082733 24.99680602 0.967882014 1.317232461 0.899699628 0.036842604 215.2271865 824862.6844 0.008435996 0.080992332 55601.01666 -4.745082733 0.349350447 DRDGYSYGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DRDGYSYGSR 10 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;; 157.47 8.31E-06 993090000 381766 478663 417833 445773 544640 350833 494928 428423 614740 FALSE TRUE 357871.9475 514103.7066 427744.1961 457212.2899 501866.1714 452112.7918 420718.1411 481912.5546 512135.9226 0.698783139 1.003842308 0.835216155 0.89275575 0.979947216 0.882798437 0.821497033 0.940985651 1 18.96616723 DRDGYTAADLSDFNGHSHCTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRDGYTAADLSDFNGHSHCTR 21 1 B1AK53;A0A1B0GUN9;Q5JYL1 B1AK53 ESPN Espin 0 96.391 0.00082937 186320000 79520 98104 103610 90908 118310 97548 118480 92884 124670 FALSE TRUE 74542.98515 105367.7222 106067.6781 93240.85319 109018.4098 125708.524 100715.0239 104480.7719 103861.7716 0.717713399 1.014499566 1.021238869 0.897739869 1.049649049 1.2103445 0.969702542 1.005959847 1 16.66430521 4.738935807 5.699578832 1.023756752 0.707753623 0.597392287 0.078298093 0.098020405 13.49938595 0.018225669 0.120544642 54819.59295 -4.738935807 -0.316003129 DRDLEVDTTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRDLEVDTTLK 11 1 P02452 P02452 COL1A1 Collagen alpha-1(I) chain 0 114.72 0.0011122 82670000 258670 195240 225310 234350 264860 223750 284350 186190 321400 FALSE TRUE 242480.3064 209695.7727 230654.4596 240363.8178 244058.964 288342.9927 241714.3573 209436.2314 267756.2637 0.905600874 0.783159168 0.861434412 0.897696339 0.911496749 1.076886078 0.902740253 0.782189849 1 18.0305608 3.141805118 1.9846965 0.937491864 0.833127535 0.188639843 0.079684698 0.453050501 3.645800801 0.025144357 0.032759447 1386.133688 -3.141805118 -0.104364329 DRDNQDREENDKDPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRDNQDREENDKDPER 16 3 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 172.93 1.93E-09 1708770000 2000000 1049680 1510840 1244120 1273340 1147400 1808580 1220830 1456240 FALSE TRUE 1874823.57 1127399.399 1546677.838 1276046.225 1173337.013 1478635.754 1537400.219 1373253.313 1213184.136 1.545374287 0.929289599 1.274891249 1.051815786 0.967154925 1.218805711 1.267243919 1.13194137 1 20.21036711 4.756135893 24.74686032 1.124175583 1.545374685 0.555568506 0.12269678 2705.298752 3809123.266 0.029191095 0.900112836 57034.2708 -4.756135893 0.421199102 DRDPEAQFEMPYVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRDPEAQFEMPYVVR 15 1 O14744-2;O14744;O14744-4;O14744-3;O14744-5;H0YJD3;H7BZ44 O14744-2 PRMT5 "Protein arginine N-methyltransferase 5;Protein arginine N-methyltransferase 5, N-terminally processed" 0 ; 193.32 8.91E-08 211440000 109925 99917 106968 114248 105058 92600 130568 98332 113638 FALSE TRUE 103044.9905 107314.9586 109505.3315 117179.7971 96807.16846 119332.1168 110990.5405 110608.9667 94671.08367 1.088452635 1.133555828 1.15669249 1.237757006 1.022563223 1.260491717 1.172380586 1.168350064 1 16.53063622 4.744017759 1.482180251 1.158345862 1.060465932 0.026710146 0.082049764 3.321792246 6.646236625 0.019485292 0.481426943 55464.83928 -4.744017759 -0.09787993 DRDS(ph)QRDLVEAVAHILGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 308.19 9.82E-62 578130000 259240 364010 291910 358460 474610 200980 346820 288480 834340 TRUE FALSE 243014.6312 390961.6792 298834.243 367658.6905 437336.0451 258999.6634 294817.5607 324497.363 695083.264 0.349619454 0.562467404 0.429925821 0.528941941 0.629185117 0.372616745 0.424147114 0.46684675 1 19.40682628 -1.581066337 2.591838203 1.043198343 0.473495844 0.792782384 0.085068056 5059072.47 4620056.685 1497124.503 0.020705541 0.026238177 1.581066337 -0.569702499 DRDVSEEHKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRDVSEEHKK 10 2 Q14CX7;Q14CX7-2 Q14CX7 NAA25 "N-alpha-acetyltransferase 25, NatB auxiliary subunit" 0 80.979 0.013444 75153000 78857 71007 73822 71969 106230 48737 92695 76178 129030 FALSE TRUE 73921.48113 76264.43216 75573.0927 73815.84638 97887.12431 62806.58072 78796.24529 85688.99099 107494.0594 0.687679687 0.709475785 0.703044364 0.686696984 0.910628223 0.58427955 0.733028836 0.797150944 1 16.71389741 0.863345053 2.487932951 0.999581283 0.714244456 0.557635161 0.079808664 0.360473163 4.368515667 0.068607903 0.018418573 7.300373047 -0.863345053 -0.285336827 DRDVTFSPATIENELIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRDVTFSPATIENELIK 17 1 P55145;H7C2D6 P55145 MANF Mesencephalic astrocyte-derived neurotrophic factor 0 ; 223.86 2.65E-15 121933000 213338 182200 186803 192999 203743 134525 223481 155090 219076 FALSE TRUE 199985.5554 195690.2776 191234.0554 197951.6811 187741.8466 173360.1837 189972.0987 174453.3279 182510.8003 1.095746416 1.07221204 1.047795829 1.084602559 1.028661571 0.949862602 1.040881408 0.955852079 1 17.47762231 2.49945115 5.512768836 0.993300653 1.069205911 0.685297241 0.027948771 0.107806596 10.21637946 0.008707772 0.007828986 315.8283783 -2.49945115 0.075905258 DRDWER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRDWER 6 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6;X6RC15 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 0 ; 98.997 0.035841 434560000 252460 280070 274270 271970 320450 248550 275860 279560 501560 FALSE TRUE 236658.9793 300806.6742 280775.8139 278949.2106 295283.1496 320302.3501 234497.354 314463.6814 417846.3958 0.566377936 0.719897736 0.671959401 0.667587931 0.706678704 0.766555254 0.561204683 0.752582012 1 18.67261317 0.979698562 23.90477047 1.000000003 0.671648507 0.734725675 0.06312132 417.8972063 492071.4494 0.055954268 0.013988567 9.543299691 -0.979698562 -0.328351496 DRDYSDHPSGGSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 181.75 9.62E-07 4291490000 2108774 5533640 4734104 5218170 5787120 4365365 5672620 5014711 6158770 FALSE TRUE 1976789.6 5943356.463 4846399.182 5352077.077 5332622.939 5625575.01 4822063.293 5640808.707 5130831.5 0.385276655 1.158361264 0.944564089 1.043120803 1.039329189 1.096425601 0.93982102 1.099394651 1 22.29076122 4.745245728 24.97162987 1.035003108 0.385276356 0.901373907 0.068056297 212.1441284 792424.3815 0.01509503 0.147689738 55621.88828 -4.745245728 -0.649726752 DREDYVPYTGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DREDYVPYTGEK 12 1 Q9NYL9 Q9NYL9 TMOD3 Tropomodulin-3 0 ;;;;; 206.49 8.16E-08 3381630000 5057010 3843820 4428310 4228250 4690420 3186070 5396010 3691967 5228650 FALSE TRUE 4740500.771 4128420.432 4533351.604 4336754.053 4322053.333 4105836.687 4586928.395 4152917.207 4355954.537 1.08828059 0.947764812 1.040725188 0.99559213 0.992217273 0.942580243 1.053024855 0.953388556 1 22.05455747 4.75867388 24.03038033 0.994936068 1.08828074 0.405649191 0.036813152 2837.600222 3390138.628 0.008057779 0.304576468 57368.55092 -4.75867388 0.093344672 DREEALHQFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DREEALHQFR 10 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A087WVZ1;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;;; 189.57 5.99E-07 5470920000 3770500 4135810 3791580 3733570 4619580 2930360 4081580 3963210 5456400 FALSE TRUE 3534511.136 4442029.676 3881518.068 3829379.727 4256776.821 3776307.362 3469584.971 4458025.493 4545691.59 0.777551901 0.977195568 0.853889445 0.842419608 0.936442065 0.830744296 0.763268889 0.980714464 1 22.11606837 1.092883214 8.668516131 0.999678731 0.862856415 0.432716369 0.064312691 0.252699699 19.75931885 0.063350539 0.015857358 12.38463508 -1.092883214 -0.136822316 DREEDEEDAYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DREEDEEDAYER 12 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 261.67 2.05E-21 667280000 650590 554020 586680 599890 606680 493460 682550 522210 679600 FALSE TRUE 609870.7332 595040.2173 600596.3267 615284.193 559033.8 635913.8913 580207.964 587409.068 566170.3696 1.07718589 1.050991449 1.060804943 1.086747428 0.987395014 1.12318469 1.02479394 1.037512911 1 19.11087672 1.101772222 1.634101104 1.002353272 1.060081202 0.237164969 0.035386492 0.483272719 2.537984791 0.028783255 0.00844759 12.64073194 -1.101772222 0.05772793 DREGPTDHLESACPLNLPLQNNHTAADMY(ph)LSPVRS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DREGPTDHLESACPLNLPLQNNHTAADMYLSPVRSPK 37 2 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 2 DREGPTDHLESACPLNLPLQNNHT(0.336)AADMY(0.451)LS(0.41)PVRS(0.803)PK 59.443 0.010988 149220000 38105 25767 31855 30668 32077 22481 48315 24662 32784 TRUE FALSE 35720.07607 27674.81549 32610.61564 31454.9928 29557.80181 28970.89975 41070.61428 27741.10499 27312.13861 1.307846177 1.013278963 1.193997149 1.151685456 1.082222166 1.060733477 1.503749482 1.015706071 1 14.73725466 DREGPTDHLESACPLNLPLQNNHTAADMYLSPVRS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DREGPTDHLESACPLNLPLQNNHTAADMYLSPVRSPK 37 2 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 DREGPTDHLESACPLNLPLQNNHTAADMYLS(0.026)PVRS(0.974)PK;DREGPTDHLESACPLNLPLQNNHTAADMYLS(0.253)PVRS(0.747)PK;DREGPTDHLESACPLNLPLQNNHT(0.247)AADMY(0.235)LS(0.247)PVRS(0.271)PK 318 3.00E-110 291720000 186006 129764 154659 148188 160681 92357 186755 123317 238715 TRUE FALSE 174364.2165 139371.8616 158327.5845 151990.755 148061.7624 119018.9666 158752.8215 138713.3989 198871.9243 0.876766376 0.700812154 0.796128388 0.764264516 0.74450812 0.598470433 0.798266633 0.697501165 1 17.60148009 -1.377776145 4.877429941 1.000235255 0.745086662 0.537670278 0.073682479 0.000168473 2.15E-05 0.063765216 0.015015854 0.041900949 1.377776145 -0.255148593 DRELDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DRELDLR 7 1 P09661;H0YKK0 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 0 ;; 119.21 0.0044075 1749540000 3935100 4337600 3968600 4009200 4644900 3048410 4477000 3816000 5138800 FALSE TRUE 3688809.115 4658760.417 4062737.066 4112082.86 4280108.291 3928436.48 3805715.412 4292436 4281101.082 0.861649619 1.088215468 0.948993492 0.960519918 0.999768099 0.917622921 0.888957149 1.002647664 1 22.02955047 2.240769724 24.99919929 0.936349108 0.984072119 0 0.065750616 129.9829468 1470965.589 0.022165723 0.017715143 174.0883559 -2.240769724 0.047723011 DRELWVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRELWVQR 8 1 Q9Y3C8 Q9Y3C8 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 0 ; 127.4 0.0010744 943680000 662990 880980 634670 778170 944040 555230 701700 754060 837390 FALSE TRUE 621494.6394 946208.6759 649724.6721 798139.1596 869898.9065 715515.8876 596486.5993 848206.0509 697624.1993 0.890873109 1.356330065 0.931339069 1.144081814 1.246944856 1.025646599 0.855025671 1.215849524 1 19.41209056 2.018635312 24.25069605 0.990721615 1.124516183 0.057741656 0.159929779 321.018812 417749.1162 0.055765133 0.041177706 104.384331 -2.018635312 0.133794568 DRENYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DRENYDR 7 1 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;; 157.91 0.001317 353487000 376054 406005 410702 363756 424878 338729 415627 370770 450591 FALSE TRUE 352517.4514 436066.0326 420444.0454 373090.5948 391509.7958 436514.5635 353307.5898 417061.4507 375384.4512 0.939083785 1.161651825 1.120035857 0.993889314 1.042956879 1.162846682 0.941188663 1.111024842 1 18.51800937 1.856127454 0.622791694 1.012257519 1.087292326 0 0.084766094 2.023219483 1.604298138 0.075427027 0.043564003 71.80049759 -1.856127454 0.075034808 DREPEREER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DREPEREER 9 2 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 0 ; 128.81 0.00022885 84671000 22078 23509 29057 23322 23089 20406 25078 21609 29436 FALSE TRUE 20696.17739 25249.63082 29746.24576 23920.482 21275.68308 26296.88094 21317.78671 24306.93122 24522.94144 0.84395167 1.029633043 1.212996648 0.975432823 0.867582836 1.072337958 0.869299744 0.991191505 1 14.58184441 3.021827548 24.99435023 0.951300358 1.060191638 0.051693779 0.107180381 391.2121661 447967.1813 0.030356748 0.036280706 1051.544237 -3.021827548 0.10889128 DREPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DREPSK 6 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 0 72.138 0.078785 39386000 102770 72970 95199 87126 82429 71646 94020 79452 96373 FALSE TRUE 96337.80915 78372.77473 97457.16524 89361.80066 75955.35884 92329.03712 79922.57384 89371.7571 80287.72371 1.199907093 0.976148919 1.213848902 1.113019482 0.946039511 1.149977018 0.995451984 1.113143492 1 16.29289179 2.944271177 24.99548783 1.044324496 1.115795817 0.190326984 0.085701032 549.3072953 246375.026 0.024151554 0.025616722 879.5715579 -2.944271177 0.071471321 DREPYFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DREPYFDR 8 1 P49750;P49750-1;H0YIQ2;P49750-3;F8VU51;H0YI23 P49750 YLPM1 YLP motif-containing protein 1 0 112.71 0.0027255 387910000 105220 114810 112940 121390 137000 80517 125170 125470 143670 FALSE TRUE 98634.46802 123310.6519 115618.9901 124505.0729 126240.5726 103760.9508 106401.9205 141135.2057 119690.5489 0.824079002 1.030245521 0.965982621 1.040224764 1.054724653 0.866910143 0.888975124 1.179167504 1 16.86894971 4.747452685 24.29129315 0.989849481 0.824078874 0.278584408 0.08830628 1134.502285 3099124.109 0.020518284 0.240763944 55905.26175 -4.747452685 -0.165770607 DREREPEAASSRGS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DREREPEAASSRGSPVR 17 3 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 DREREPEAAS(0.008)S(0.008)RGS(0.985)PVR;DREREPEAAS(0.09)S(0.006)RGS(0.904)PVR 154.34 7.83E-07 866630000 102726 153556 112573 151943 182528 77932 136930 108774 350200 TRUE FALSE 96296.56303 164925.446 115243.2847 155842.1146 168192.9872 100429.7033 116398.6177 122354.6733 291749.3576 0.330066067 0.565298403 0.395007844 0.53416438 0.576498226 0.344232817 0.398967863 0.419382837 1 18.15436995 -1.287852322 3.444039998 1.001936214 0.449894598 0.799510105 0.087246941 45827272.21 69472070.31 925901.7053 0.019874098 0.051540387 1.287852322 -0.552041617 DRESEKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DRESEKDR 8 2 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;; 150.08 0.0002784 207528000 393638 309089 333133 310522 361245 220821 340717 293447 433811 FALSE TRUE 369000.9002 331974.2712 341035.0721 318490.5202 332874.2749 284568.438 289629.6489 330084.5039 361405.1416 1.021017296 0.918565435 0.94363647 0.881256196 0.921055726 0.787394548 0.801398806 0.913336491 1 18.46325751 3.23410137 1.101533322 0.856175322 0.962542026 0.176956771 0.067223173 0.618930284 1.600613733 0.025738062 0.040817968 1714.357413 -3.23410137 0.106366705 DREVGIPPEQSLETAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DREVGIPPEQSLETAK 16 1 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ; 200.71 3.18E-11 237510000 715340 495960 555950 536920 586860 430290 721970 485760 771010 FALSE TRUE 670568.1463 532681.3944 569137.3965 550698.2762 540770.3829 554507.7378 613717.3009 546408.2053 642323.4501 1.0439727 0.829303981 0.886060436 0.857353528 0.841897307 0.863284281 0.955464573 0.85067454 1 19.29294044 -0.897329398 4.718156232 1.000000576 0.886471277 0.217111672 0.064540054 4.40E-07 1.03E-07 0.056879984 0.013406657 0.126669076 0.897329398 -0.113529298 DRFGIDDQDYLVSLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRFGIDDQDYLVSLTR 16 1 Q8TBX8;Q8TBX8-3;F8VNT5;F8VU68 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 156.96 1.03E-07 126320000 110600 126570 114650 105660 137680 92559 132320 108590 148840 FALSE TRUE 103677.7434 135941.3745 117369.5521 108371.4145 126867.1682 119279.2807 112479.8444 122147.7005 123997.6425 0.836126731 1.096322251 0.946546642 0.873979637 1.023141776 0.961947972 0.907112766 0.98508083 1 16.91995317 3.707753891 23.67819868 0.950048227 0.995797254 0 0.076339033 599.3757206 732786.2371 0.018619047 0.028904492 5102.157857 -3.707753891 0.045749027 DRFTDILVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRFTDILVR 9 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 148.32 8.23E-05 83660000 40716 36242 34965 35705 39172 30829 44203 32179 41929 FALSE TRUE 38167.65824 38925.39539 35794.38631 36621.25075 36095.58913 39728.83183 37575.17051 36196.61898 34930.77903 1.092665532 1.114358067 1.02472339 1.048394905 1.033346239 1.137358883 1.075703765 1.036238526 1 15.0922112 0.775682121 0.007291435 3.11E-07 2.102822965 0.265245522 0.036645729 6139.87317 24.27090404 3544.456459 3452.819641 5.965984501 -0.775682121 2.102822654 DRGDAYYDT(ph)DYRHSYEYQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRGDAYYDTDYRHSYEYQR 19 2 B1AVT0;P49760-3;P49760;P49760-2 B1AVT0 CLK2 Dual specificity protein kinase CLK2 1 DRGDAYYDT(0.956)DYRHS(0.044)YEYQR 148.09 4.72E-06 508970000 153410 175680 161650 169650 153530 131520 191080 164310 116920 TRUE FALSE 143808.3419 188687.53 165484.4143 174003.5062 141472.3731 169487.689 162429.3279 184824.4652 97405.29667 1.476391396 1.937138292 1.698926239 1.786386492 1.452409447 1.740025386 1.667561554 1.897478592 1 16.5717126 -1.261314635 4.671804191 0.99974537 1.719302325 0.670824114 0.155441608 0.000377696 5.97E-05 0.137887201 0.032489074 0.05478799 1.261314635 0.719556955 DRGDAYYDTDYRHS(ph)YEYQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRGDAYYDTDYRHSYEYQR 19 2 B1AVT0;P49760-3;P49760;P49760-2 B1AVT0 CLK2 Dual specificity protein kinase CLK2 1 DRGDAYYDT(0.002)DYRHS(0.998)YEYQR 164.05 1.28E-11 629600000 204830 232450 227220 215760 251010 186610 263060 205750 162390 TRUE FALSE 192010.0559 249660.8399 232609.7657 221296.7669 231296.6871 240481.2776 223616.5951 231438.3404 135286.0599 1.41928929 1.84542916 1.719391975 1.635769177 1.709686033 1.77757618 1.652916755 1.710733098 1 17.04565366 -1.072120825 0.937401263 0.905154384 1.702776422 0.783978982 0.112414921 52.13167758 18.90882395 14.49267223 0.031833849 0.084699174 1.072120825 0.797622038 DRGEEDADGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DRGEEDADGSK 11 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;; 110.38 0.0016437 832180000 1512670 896820 1131180 1038450 1011590 882850 1368260 937150 984710 FALSE TRUE 1417994.685 963221.4859 1158012.124 1065098.385 932143.802 1137714.463 1163102.115 1054155.24 820355.5395 1.728512354 1.174151255 1.41159786 1.29833753 1.136268066 1.386855343 1.417802476 1.284998016 1 19.64588978 DRGEQGLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRGEQGLLR 9 1 P55327-2;P55327-4;E5RFR7 P55327-2 TPD52 0 ; 132.25 0.00028303 672900000 245557 351760 295810 315340 381170 209368 255557 258340 358150 FALSE TRUE 230188.0257 377804.6764 302826.7529 323432.1583 351234.4458 269809.1428 217238.6003 290594.3177 298372.4513 0.771478817 1.266218362 1.014928663 1.083988005 1.177167813 0.904269619 0.728078613 0.973931462 1 18.18675481 2.111801262 6.19413015 0.857689578 1.084209813 0.202566598 0.147286278 0.221124956 11.22193346 0.051154908 0.03757912 129.3603739 -2.111801262 0.226520234 DRGEWDSLTPEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRGEWDSLTPEAR 13 1 B7Z7P0;Q14139;Q14139-2 B7Z7P0 UBE4A Ubiquitin conjugation factor E4 A 0 89.992 0.0065621 87743000 41787 58552 55003 53801 63572 46002 59029 53905 53795 FALSE TRUE 39171.62626 62887.251 56307.69713 55181.62474 58579.31156 59282.03062 50178.14945 60635.15791 44816.26697 0.874049289 1.403223768 1.256412034 1.231285613 1.307099308 1.322779308 1.119641435 1.352972079 1 15.45173486 -1.381492349 3.220066383 0.997483401 1.247304261 0.189404751 0.149333755 18640133.53 28607058.47 450049.8211 0.032107316 0.041543937 1.381492349 0.24982086 DRGFGAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DRGFGAPR 8 1 P17844;P17844-2;J3QRQ7;J3KRX8;J3QR02;X6RLV5;J3QKN9 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;; 127.68 0.0010634 550681000 680890 1148830 825240 788320 1229640 809210 728240 1141050 1242050 FALSE TRUE 638274.3103 1233890.569 844815.0825 808549.6258 1133069.035 1042815.791 619047.1726 1283512.604 1034743.831 0.616842827 1.192459942 0.816448533 0.78140077 1.095023716 1.007800925 0.598261284 1.240415807 1 19.98084222 1.201972511 24.99999942 1.120207774 0.894904385 0.20580285 0.198490643 338.6313947 231373.3545 0.18074258 0.045190853 15.9210795 -1.201972511 -0.225303389 DRISPEGLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRISPEGLEK 10 1 Q86US8 Q86US8 SMG6 Telomerase-binding protein EST1A 0 57.492 0.070449 125690000 1607900 985280 1126600 1039000 1210700 904110 1393700 923870 1751500 FALSE TRUE 1507264.409 1058231.156 1153323.484 1065662.499 1115616.506 1165111.88 1184727.623 1039217.203 1459163.335 1.032964832 0.72523146 0.790400537 0.73032434 0.764559031 0.798479411 0.811922555 0.712200737 1 20.47670995 -1.093919723 5.328065344 1.000003153 0.7879876 0.330124034 0.090834745 2.99E-06 5.09E-07 0.077315338 0.018223129 0.080552732 1.093919723 -0.212015553 DRKNS(ph)ASAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRKNSASAER 10 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 DRKNS(0.952)AS(0.048)AER 62.287 0.067781 61476000 57455 49774 51057 67234 74591 41135 57686 47505 81153 TRUE FALSE 53858.99411 53459.31875 52268.09615 68959.33827 68732.92375 53010.00673 49036.51983 53436.10382 67608.04003 0.796635934 0.79072428 0.773104739 1.019987242 1.016638313 0.784078443 0.725306041 0.790380904 1 16.0449072 -2.518986158 2.208304276 3.408325797 0.828001754 0.199948201 0.100951191 2666906.485 351102.6943 32499322.32 0.026625815 0.00302701 2.518986158 -2.580324042 DRKPGS(ph)HASSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRKPGSHASSSAR 13 2 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 DRKPGS(1)HASSSAR 52.172 0.080621 24906000 12248 24473 21662 16857 20963 17839 20329 16573 18774 TRUE FALSE 11481.41954 26285.00638 22175.83287 17289.57916 19316.65054 22988.82971 17280.85518 18642.17553 15640.49812 0.734082729 1.680573482 1.41784697 1.105436606 1.235040623 1.46982721 1.104878825 1.191916996 1 13.93299884 1.185553394 0.749811017 1.000235537 1.339434669 0.046481769 0.257410513 1.219470186 1.584202784 0.235472311 0.093456126 15.33039672 -1.185553394 0.339199132 S(ph)TGDIAGTVVPETNKEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.976)T(0.024)GDIAGTVVPETNKEPR;S(0.984)T(0.016)GDIAGTVVPETNKEPR 169.85 1.04E-11 694330000 266100 204025 248500 220290 338580 166723 414590 277680 627280 TRUE FALSE 249445.276 219131.2233 254394.5374 225943.0144 311989.2926 214853.2236 352426.0784 312348.9592 522582.9156 0.477331479 0.419323359 0.486802247 0.432358211 0.597013954 0.411137098 0.674392652 0.597702202 1 18.99530043 0.282968994 0.415590238 1.062434957 0.437519179 0.860023145 0.065939597 0.904660886 0.255350397 0.159335316 0.038711206 1.918531764 -0.282968994 -0.624915778 DRKPGSHASS(ph)SAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRKPGSHASSSAR 13 2 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 DRKPGSHAS(0.05)S(0.475)S(0.475)AR;DRKPGSHAS(0.043)S(0.478)S(0.478)AR 116.96 0.00028386 61820000 32776 54375 48436 47352 63038 40353 69922 56056 68365 TRUE FALSE 30724.60867 58400.98158 49584.92479 48567.13249 58087.24976 52002.25602 59437.84522 63054.71499 56954.43985 0.539459413 1.025398226 0.870606838 0.852736549 1.019889756 0.913050083 1.043603368 1.107107983 1 15.79752069 4.74297624 24.97476567 0.970911922 0.539459238 0.748877615 0.079876048 235.1887917 1330179.629 0.019116875 0.152192932 55331.98363 -4.74297624 -0.431452683 DRLEFWCTDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRLEFWCTDVK 11 1 Q9UNM6;J3KNQ3;Q9UNM6-2;H0YD73 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 129.71 0.00021833 72460000 150750 121550 136990 123620 148820 86576 165000 135710 161860 FALSE TRUE 141314.8266 130549.6885 140239.4675 126792.2985 137132.2775 111569.0858 140259.7818 152653.6922 134844.5203 1.047983457 0.968149749 1.040008649 0.940285139 1.016965889 0.827390579 1.040159299 1.132071899 1 17.04093737 1.502809421 11.4578417 1.072672838 0.977780203 0.248951637 0.069331759 0.127455974 39.52238147 0.034175321 0.015855546 31.82800528 -1.502809421 -0.094892635 DRLEQLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRLEQLER 8 1 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;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 0 89.886 0.012392 376520000 138000 225280 178820 137790 252010 138590 184270 211890 224970 FALSE TRUE 129362.8263 241959.9656 183061.6948 141325.9247 232218.1512 178598.6832 156640.4242 238344.9329 187421.0536 0.690225691 1.290996721 0.976740293 0.754055758 1.239018492 0.952927538 0.835767493 1.271708425 1 17.5159235 3.688808875 24.23165556 0.984712977 1.063627046 0 0.214698319 891.8032838 564042.8923 0.052771112 0.081755045 4884.373597 -3.688808875 0.078914069 DRLGS(ph)YSGPTSVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRLGSYSGPTSVSR 14 1 V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23;A0A2R8YFI4 V9GYZ0 PANK2 "Pantothenate kinase 2, mitochondrial" 1 DRLGS(0.999)YS(0.001)GPTSVSR;DRLGS(0.699)YS(0.301)GPTSVSR 213.35 7.00E-10 629950000 390020 430970 369080 427590 502140 298250 495800 379530 576710 TRUE FALSE 365609.3444 462879.4672 377834.7519 438562.6833 462703.9499 384349.9333 421459.3928 426915.1559 480453.3753 0.760967376 0.96342224 0.786412941 0.912810079 0.963056924 0.799973427 0.877211847 0.888567295 1 18.87403691 -4.999999975 0.387963464 2.913840438 0.86861702 0.264566382 0.069216717 890.2298 6.483370907 1437.406596 0.040890522 1.00E-05 4.999999975 -2.045223418 DRLIEVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRLIEVER 8 1 Q3V6T2;A0A2U3TZV9;A0A2R8Y4X4;A0A2R8YG73;A0A2R8Y7B1;A0A2R8Y4W8;Q3V6T2-5;Q3V6T2-4;Q3V6T2-2;Q3V6T2-3;H7C2C6;A0A2R8Y820;A0A2R8Y885;A0A2R8YCU9;A0A2R8YGU1;A0A2R8YDS8;A0A2R8Y7D4;H0Y470 Q3V6T2 CCDC88A Girdin 0 81.548 0.02059 115880000 49380 91166 59257 66404 86523 37186 55487 73001 75338 FALSE TRUE 46289.39395 97916.0255 60662.60402 68108.03906 79727.8326 47920.99454 47167.23947 82115.33555 62763.6011 0.737519727 1.560076601 0.966525231 1.085151869 1.270287734 0.763515695 0.751506265 1.308327344 1 15.93764051 2.243537579 24.99980144 0.909326528 1.160165494 0.072602751 0.259786311 206.8807188 1039187.82 0.086892229 0.070586071 175.2014026 -2.243537579 0.250838966 DRLSASSLTMESFAFLWAGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DRLSASSLTMESFAFLWAGGR 21 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRI6;A0A1W2PNG3;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;;; 248.52 1.46E-30 658977300 510469.1 838163.3 578233.8 556615.7 915102 381545.3 602433.2 731373.9 821604 FALSE TRUE 478519.7502 900221.7828 591949.7788 570899.4012 843233.5803 491691.2342 512103.9344 822687.5414 684472.9846 0.699106847 1.315204256 0.864825628 0.834071489 1.231945744 0.718350096 0.748172603 1.201928432 1 19.38463408 2.219803249 24.99951076 0.873925813 1.009528421 0.004233787 0.22471983 660.7231053 880595.4858 0.079726334 0.058982712 165.8835227 -2.219803249 0.135602609 DRNLAPDEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRNLAPDEKR 10 2 O95232;J3KPP4;D6RDI2;C9JL41;O95232-2;E7EN55 O95232 LUC7L3 Luc7-like protein 3 0 62.466 0.047753 42545000 31630 36426 29281 31219 40474 25248 37111 33194 52614 FALSE TRUE 29650.33476 39123.01894 29975.55915 32020.13239 37295.3353 32536.68773 31546.55007 37338.34397 43832.3835 0.676448151 0.892559697 0.683867879 0.730513147 0.850862589 0.742297934 0.719708753 0.851843796 1 15.41970951 0.952919482 4.490835994 0.999853374 0.762812333 0.569728323 0.068062856 0.170233505 10.42515836 0.061708692 0.015678666 8.972624273 -0.952919482 -0.237041042 DRNVATPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRNVATPR 8 1 P11216;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 0 ; 121.83 0.0012918 155464000 94449 159837 108381 109981 181215 104893 123505 137419 183092 FALSE TRUE 88537.60569 171671.4978 110951.8485 112803.2987 166983.1049 135173.9063 104986.5718 154576.0646 152532.7624 0.580449762 1.125472948 0.727396834 0.739534884 1.094735992 0.886195885 0.688288668 1.013395825 1 17.21875963 DRNVIPDT(ph)PPSTPLVPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRNVIPDTPPSTPLVPSR 18 1 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 DRNVIPDT(0.992)PPS(0.004)T(0.004)PLVPSR;DRNVIPDT(0.999)PPS(0.001)T(0.001)PLVPSR 89.721 0.0045895 199394000 195236 193969 212720 231270 244420 180872 220770 168155 250320 TRUE FALSE 183016.5273 208330.6666 217765.8189 237204.7797 225224.2391 233086.8102 187667.588 189149.5219 208539.9749 0.877608849 0.998996316 1.04424017 1.137454725 1.080005113 1.117708057 0.899911819 0.907018053 1 17.66996443 1.688687897 8.94938808 0.928692796 1.042740678 0.304816012 0.075762492 0.141256902 19.62828268 0.036750487 0.019595874 48.83013188 -1.688687897 0.114047882 DRPFFAGLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRPFFAGLVK 10 1 Q32Q12;P22392-2;J3KPD9;E7ERL0;E5RHP0;P15531;P15531-2 Q32Q12;P15531 NME1-NME2;NME2;NME1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Nucleoside diphosphate kinase A 0 ; 162.38 6.19E-06 2327000000 1722350 6132400 1261170 1377340 7763000 922330 1716880 6181500 7176800 FALSE TRUE 1614551.188 6586449.277 1291085.548 1412684.876 7153325.294 1188591.698 1459449.783 6953273.882 5978945.716 0.270039446 1.101607138 0.215938664 0.236276585 1.196419174 0.198796202 0.244098183 1.162959862 1 22.51145968 1.226595244 24.99962238 1.081480361 0.513725024 0.303725674 0.368460886 322.2402996 673245.6949 0.330879917 0.085317399 16.84981914 -1.226595244 -0.567755337 DRPFFPGLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRPFFPGLVK 10 1 Q32Q12;P22392-2;J3KPD9;P22392;F6XY72;O60361 Q32Q12;O60361 NME1-NME2;NME2;NME2P1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Putative nucleoside diphosphate kinase 0 ; 136.48 0.00010642 14039200000 14092200 21106300 12640900 12183200 23827100 8862900 13622600 20759100 21176600 FALSE TRUE 13210194.36 22669032.41 12940748.12 12495841.54 21955815.68 11421475.35 11580017.6 23350919.33 17642088.65 0.748788571 1.284940398 0.733515649 0.708297174 1.244513397 0.647399272 0.656385864 1.323591542 1 24.07251804 5.03173985 16.37673217 0.921249115 0.178024074 0.044534235 0.264699187 15939226.61 225222423.9 0.061011638 333667540.9 107582.0586 -5.03173985 -0.74322504 DRPFMGGQKPNLADLAVYGVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRPFMGGQKPNLADLAVYGVLR 22 2 Q9H7Z7;A6NHH0 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 ; 196.4 1.20E-22 251150000 360560 372260 288050 307260 448120 267330 361470 357100 448730 FALSE TRUE 337993.1932 399822.5177 294882.682 315144.8118 412926.4628 344503.8313 307270.9292 401684.7211 373834.0641 0.904126257 1.069518688 0.788806346 0.843007211 1.104571526 0.921542107 0.821944704 1.074500051 1 18.51203851 DRPGS(ph)PES(ph)PLLDAPFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRPGSPESPLLDAPFSR 17 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 2 DRPGS(1)PES(1)PLLDAPFSR 152.88 1.12E-07 120470000 102270 101530 113900 144120 146210 70254 86191 85100 122310 TRUE FALSE 95869.10326 109047.3868 116601.7618 147818.3632 134727.2564 90535.18932 73267.45971 95724.92233 101895.6708 0.940855509 1.070186652 1.144324983 1.450683449 1.322207855 0.888508693 0.719043892 0.939440523 1 16.63673323 2.139706568 6.775263412 0.843517458 1.175620377 0.472642929 0.154262819 0.185045537 10.94119686 0.060634732 0.044689864 137.9451919 -2.139706568 0.332102919 DRPGS(ph)PESPLLDAPFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DRPGSPESPLLDAPFSR 17 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 DRPGS(0.999)PES(0.001)PLLDAPFSR;DRPGS(0.996)PES(0.004)PLLDAPFSR;DRPGS(0.999)PES(0.001)PLLDAPFSR;DRPGS(0.996)PES(0.004)PLLDAPFSR;DRPGS(1)PESPLLDAPFSR;DRPGS(1)PESPLLDAPFSR 196.11 9.87E-12 3193520000 1499230 1409430 1430550 1191430 1563980 1302880 1821300 1614380 2509610 TRUE FALSE 1405395.871 1513785.664 1464483.322 1222004.111 1441151.32 1679000.306 1548212.973 1815938.897 2090739.878 0.672200251 0.724043043 0.700461754 0.58448405 0.689302067 0.803065136 0.740509611 0.868562807 1 20.99558215 1.079044359 0.86551837 1.000392084 0.683590826 0.824353544 0.048314052 0.244346501 0.407438403 0.045899639 0.016461136 11.99621827 -1.079044359 -0.316801258 DRPHEGTRPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DRPHEGTRPVR 11 2 P31146;H3BRY3;H3BTU6;H3BRJ0 P31146 CORO1A Coronin-1A;Coronin 0 ;;; 148.78 1.95E-05 1175703000 256799 397392 352237 340014 414664 319650 415682 365504 314431 FALSE TRUE 240726.409 426815.3172 360592.228 348739.3349 382097.9621 411927.7659 353354.3431 411137.979 261950.4348 0.91897694 1.629374341 1.376566633 1.331318023 1.458665119 1.572540875 1.348935891 1.569525851 1 17.99893433 -1.094745778 5.304989861 0.999993364 1.421018559 0.28084422 0.199194679 1.36E-05 2.33E-06 0.168175054 0.039638616 0.080399662 1.094745778 0.421025195 DRPMEESLLLFEAMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 DRPMEESLLLFEAMR 15 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A1B0GTT3;A0A0U1RQQ5 P47897 QARS Glutamine--tRNA ligase 0 ;;;;;;;;;;; 246.38 3.28E-18 1189939000 611405 790647 738158 758854 830074 616279 826622 721069 821798 FALSE TRUE 573138.2524 849187.3265 755667.4563 778327.4784 764883.3364 794188.7428 702677.7051 811096.0519 684634.6048 0.837144732 1.24035116 1.103752938 1.136850917 1.117213958 1.160018406 1.02635435 1.184713782 1 19.38497469 -0.636799777 5.681441171 1.000000001 1.111430316 0.070254636 0.109321623 2.78E-09 4.89E-10 0.093201793 0.021967873 0.230781092 0.636799777 0.111430315 DRPPCS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRPPCSPSR 9 1 O95758-1;O95758-6;O95758;O95758-5;O95758-4;O95758-2;X6R242;B1ALY4 O95758-1 PTBP3 Polypyrimidine tract-binding protein 3 1 DRPPCS(0.972)PS(0.028)R 83.573 0.0097369 1017600000 117510 176550 101220 115350 201450 64430 120910 157760 255630 TRUE FALSE 110155.2589 189621.9457 103620.9862 118310.0763 185628.9296 83029.89507 102780.668 177456.6833 212963.7016 0.517248987 0.890395613 0.486566422 0.55554104 0.871645864 0.389878155 0.482620593 0.833271971 1 17.70024803 1.027359247 5.327262824 0.999043724 0.608875655 0.415330655 0.162893953 0.15205578 11.78434313 0.154724639 0.039052477 10.65023639 -1.027359247 -0.390168068 DRPQEADGIDSVIVVDNVPQVGPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DRPQEADGIDSVIVVDNVPQVGPDR 25 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;;;; 299.24 3.59E-63 4974460000 3355180 3026210 3453420 3418170 3136010 2983110 4071350 3040390 3214650 FALSE TRUE 3145185.273 3250273.737 3535336.753 3505886.029 2889720.425 3844285.43 3460888.864 3419989.384 2678104.148 1.174407379 1.213647251 1.320089346 1.309092491 1.079017195 1.435450311 1.292290618 1.277018815 1 21.35278064 -0.882723865 6.403882052 0.999999981 1.268785047 0.430772612 0.094641779 2.34E-08 4.05E-09 0.084952867 0.020023581 0.13100146 0.882723865 0.268785066 DRPVGGS(ph)PGGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRPVGGSPGGPR 12 1 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 DRPVGGS(1)PGGPR 90.754 0.0052583 2723500000 326160 375060 329120 417750 394420 377510 435660 332280 371520 TRUE FALSE 305746.2278 402829.8326 336926.8818 428470.1722 363443.8442 486491.0086 370336.8275 373765.8894 309510.9119 0.987836668 1.301504461 1.088578363 1.384345934 1.174252119 1.571805678 1.196522685 1.207601655 1 18.23963075 4.745472572 24.13391603 1.251476177 0.987836469 0.199903375 0.157569237 756.5580669 2641500.597 0.033912112 0.330657815 55650.94863 -4.745472572 -0.263639708 DRQS(ph)PLHGNHITISHTQATGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DRQSPLHGNHITISHTQATGSR 22 1 Q86VQ1;H7C2L5 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 DRQS(1)PLHGNHITISHTQATGSR;DRQS(1)PLHGNHITISHTQATGSR;DRQS(1)PLHGNHITISHTQATGSR;DRQS(1)PLHGNHITISHTQATGSR 273.32 1.13E-45 2356810000 291696 324833 334998 328646 352255 279796 363586 308357 419001 TRUE FALSE 273439.2681 348883.9733 342944.3108 337079.6128 324590.3132 360568.5631 309069.6547 346856.0502 349067.0263 0.783343162 0.999475594 0.982459771 0.965658706 0.929879619 1.032949365 0.885416357 0.993666042 1 18.41314456 4.744179171 24.81096238 0.969804417 0.783343073 0.677949119 0.04115215 326.5507256 1441967.409 0.009252291 0.08185528 55485.45741 -4.744179171 -0.186461344 DRRPVHLDQAAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRRPVHLDQAAFR 13 2 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 145.81 2.36E-05 138430000 87643 85747 63428 57501 89779 49357 73657 72389 92837 FALSE TRUE 82157.58108 92095.7971 64932.54211 58976.57301 82728.11949 63605.56466 62612.81665 81426.926 77341.90495 1.062264773 1.190761944 0.839551885 0.762543579 1.069641607 0.822394596 0.80955876 1.052817694 1 16.23896268 3.960132885 4.429118239 0.891643516 1.124383465 0.397926767 0.11000974 0.16414625 7.919468929 0.026425686 0.053540519 9122.899389 -3.960132885 0.232739949 DRS(ph)PAAET(ph)PPLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DRSPAAETPPLQR 13 1 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 2 DRS(1)PAAET(1)PPLQR;DRS(1)PAAET(1)PPLQR;DRS(1)PAAET(1)PPLQR 122.49 0.00053727 1456810000 814170 842020 751230 757090 851460 642360 969330 708520 747940 TRUE FALSE 763212.553 904364.0369 769049.5304 776518.2112 784589.7662 827798.9042 823987.9653 796980.2816 623103.9821 1.224855843 1.451385423 1.234223424 1.246209675 1.25916346 1.328508448 1.322392392 1.279048609 1 19.24911341 0.813819708 5.606480513 1.0000004 1.304205726 0.660157632 0.065972755 3.109749554 93.46430186 0.062390296 0.015713967 6.51357934 -0.813819708 0.304205325 DRS(ph)PAAETPPLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DRSPAAETPPLQR 13 1 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 DRS(1)PAAETPPLQR;DRS(1)PAAETPPLQR;DRS(1)PAAETPPLQR 158.29 2.36E-05 1427990000 968760 813590 903820 878040 922950 674220 1074640 664181 824350 TRUE FALSE 908127.0409 873829.0501 925259.0372 900571.9929 850465.23 868856.369 913507.7085 747105.4599 686760.6595 1.322334103 1.272392409 1.347280198 1.311333112 1.238372085 1.265151632 1.330168955 1.08786875 1 19.38944787 1.116477332 3.994596347 1.003841913 1.298959763 0.909015976 0.033934646 0.055696304 1.501797224 0.032344182 0.008366304 13.07607286 -1.116477332 0.29511785 DRS(ph)PHRS(ph)SPSDTRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DRSPHRSSPSDTRPK 15 3 A0A0D9SGE8;Q8IWS0-3;Q5JRC6;Q8IWS0-2;Q8IWS0-4;Q8IWS0-5;Q8IWS0 A0A0D9SGE8;Q8IWS0-5 PHF6 PHD finger protein 6 2 DRS(1)PHRS(0.561)S(0.436)PS(0.003)DTRPK;DRS(0.995)PHRS(0.565)S(0.436)PS(0.003)DTRPK;DRS(0.992)PHRS(0.527)S(0.473)PS(0.008)DTRPK;DRS(0.978)PHRS(0.556)S(0.463)PS(0.003)DTRPK 155.28 3.34E-06 892606000 422299 675762 637547 739791 785386 535807 852829 676159 973576 TRUE FALSE 395868.0594 725796.1216 652669.9159 758775.2895 723704.9517 690485.7828 724955.2087 760578.9396 811079.8761 0.488075307 0.894851596 0.804692528 0.93551241 0.892273342 0.851316625 0.893814814 0.937736174 1 19.62948447 4.739204065 24.98343536 0.887460917 0.488075183 0.853552358 0.053517146 18.29622387 710244.2416 0.011786539 0.070206948 54853.46485 -4.739204065 -0.399385734 DRS(ph)PHRSS(ph)PSDTRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRSPHRSSPSDTRPK 15 3 A0A0D9SGE8;Q8IWS0-3;Q5JRC6;Q8IWS0-2;Q8IWS0-4;Q8IWS0-5;Q8IWS0 A0A0D9SGE8;Q8IWS0-5 PHF6 PHD finger protein 6 2 DRS(0.923)PHRS(0.236)S(0.841)PSDTRPK 119.38 0.00031182 30803000 50549 32023 41420 40698 48077 26780 44910 35040 55455 TRUE FALSE 47385.22832 34394.01624 42402.50196 41742.37958 44301.22635 34510.95126 38176.16242 39414.82113 46199.20225 1.025672003 0.744472081 0.917818921 0.903530311 0.958917561 0.747003186 0.826338131 0.853149388 1 15.49558032 2.252411426 24.99856782 0.837058471 0.888256154 0.029327886 0.094687221 687.5393483 1240901.365 0.03096841 0.025784724 178.8180794 -2.252411426 0.051197683 DRS(ph)PIRGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRSPIRGSPR 10 2 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 2 DRS(1)PIRGS(1)PR 82.651 0.085455 579470000 410050 374010 389340 387540 435010 329400 446660 379560 525040 TRUE FALSE 384385.7025 401702.0896 398575.3287 397484.9325 400846.0693 424492.4326 379687.4796 426948.9015 437407.4321 0.878781827 0.918370517 0.911222122 0.908729261 0.916413485 0.970473754 0.86804076 0.976089728 1 18.73861821 -5 0.164274835 1.329490361 0.893473422 0.477180525 0.030673483 116.1877683 1.081395205 12.39062172 0.110868632 1.00E-05 5 -0.436016939 DRS(ph)PLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DRSPLRR 7 2 Q96PK6;Q9BWF3;E9PB51;Q9BQ04 Q96PK6;Q9BWF3 RBM14;RBM4;RBM4B RNA-binding protein 14;RNA-binding protein 4;RNA-binding protein 4B 1 DRS(1)PLRR;DRS(1)PLRR;DRS(1)PLRR;DRS(1)PLRR 74.841 0.035509 27194430000 2297630 2093715 1952590 2138440 1977240 1771471 2342860 1850010 2281230 TRUE FALSE 2153825.44 2248735.837 1998906.357 2193315.991 1821955.546 2282865.92 1991569.893 2080987.821 1900477.976 1.133307235 1.183247512 1.051791382 1.154086508 0.9586828 1.201206196 1.047931057 1.094981288 1 20.85793088 7.999999999 0.029000603 0.608861435 1.795761341 0.236481478 0.068690083 2018.553017 4.490287955 59.44498236 140.1675405 99999999.74 -7.999999999 1.186899906 DRS(ph)SPPPGYIPDELHQVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 231.29 2.25E-20 1623410000 641384 654601 603805 660631 682467 558888 757231 614529 718926 TRUE FALSE 601240.9203 703068.3392 618127.5397 677583.9099 628868.7948 720229.8928 643691.2413 691254.2984 598932.6062 1.003854047 1.173868866 1.03204857 1.131319122 1.049982566 1.20252243 1.07473067 1.154143707 1 19.19203415 DRS(ph)SSAPNVHINTIEPVNIDDLIR ddPTM_SK-BR-3_Pertuzumab_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 258.24 3.80E-44 1327994000 273407 318196 278774 265941 345065 266518 432269 346800 488773 TRUE FALSE 256294.9439 341755.5629 285386.6509 272765.4963 317964.9868 343457.42 367454.2764 390098.7434 407193.6287 0.629417864 0.839294966 0.70086227 0.669866808 0.780869258 0.843474445 0.902406743 0.958017798 1 18.63535546 1.811459172 1.180509608 0.986633899 0.729470611 0.785034606 0.05644782 0.221228801 0.572735895 0.045613162 0.01866629 64.78271907 -1.811459172 -0.257163288 DRSFS(ph)ENGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRSFSENGDR 10 1 P47974 P47974 ZFP36L2 "Zinc finger protein 36, C3H1 type-like 2" 1 DRSFS(1)ENGDR;DRS(0.246)FS(0.754)ENGDR 104.55 0.0016152 344250000 214385 300030 266630 366000 390350 258930 276980 243360 271750 TRUE FALSE 200967.0255 322244.5334 272954.5895 375392.1796 359693.4856 333678.8876 235449.4204 273744.0317 226393.1694 0.887690322 1.423384523 1.205666188 1.658142693 1.58880008 1.473891145 1.040002315 1.209153228 1 17.78847091 1.718213733 8.3221662 1.096931846 1.378556885 0.279352981 0.218607627 0.154317936 27.96185762 0.103353219 0.05494092 52.26533434 -1.718213733 0.281625039 DRSPAAET(ph)PPLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DRSPAAETPPLQR 13 1 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 DRSPAAET(1)PPLQR;DRSPAAET(1)PPLQR;DRSPAAET(1)PPLQR 141.22 6.42E-05 2297980000 1389120 1607530 1467540 1716810 1565940 1184600 1727200 1257650 1139190 TRUE FALSE 1302177.459 1726553.194 1502350.742 1760866.251 1442957.389 1526574.79 1468222.395 1414670.371 949051.8296 1.372082555 1.819240151 1.583001787 1.855395244 1.520420007 1.60852626 1.547041319 1.49061445 1 19.85612735 0.342542521 0.629740651 0.978718817 1.663417618 0.663578825 0.137558222 1.212417792 0.717429137 0.17763505 0.048649684 2.200607157 -0.342542521 0.684698801 DRSPHRS(ph)S(ph)PSDTRPK ddPTM_SK-BR-3_Pertuzumab_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(0.394)PHRS(0.818)S(0.784)PS(0.004)DT(0.001)RPK;DRS(0.575)PHRS(0.723)S(0.693)PS(0.01)DTRPK 79.311 0.029174 597139000 56474 58340.9 61803 65735 73789 48611.2 78502 57829.8 90513 TRUE FALSE 52939.39315 62660.52094 63268.99635 67421.87139 67993.90959 62644.4643 66731.35388 65049.97783 75405.79556 0.702060004 0.830977519 0.839046865 0.89412055 0.90170668 0.830764583 0.884963197 0.862665493 1 16.20238779 8 0.082801313 1.076682419 0.255226361 0.686635586 0.041812033 115.2340098 0.692417157 0.994625961 10.80183283 100000000 -8 -0.821456058 DRSS(ph)PPPGYIPDELHQVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRSSPPPGYIPDELHQVAR 19 1 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 1 DRS(0.343)S(0.657)PPPGYIPDELHQVAR 198.83 4.37E-16 244340000 165650 169890 186360 175720 188750 159420 212990 151820 189580 TRUE FALSE 155282.2622 182468.8324 190780.5472 180229.2727 173926.3364 205441.966 181054.1268 170775.0612 157937.8733 0.983185723 1.155320308 1.207946791 1.141140304 1.10123261 1.300777083 1.146362953 1.081279985 1 17.26899764 -0.32041519 7.726042841 1.000000025 1.152805125 0.205532164 0.082775809 0 0 0.07431651 0.017516569 0.478172736 0.32041519 0.1528051 DRT(ph)PPLLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DRTPPLLYR 9 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 DRT(1)PPLLYR;DRT(1)PPLLYR;DRT(1)PPLLYR;DRT(1)PPLLYR;DRT(1)PPLLYR;DRT(1)PPLLYR 99.941 0.0080774 6834550000 1868030 1799910 1714014 1643903 2031310 1261010 1849610 1673580 2274400 TRUE FALSE 1751113.337 1933177.209 1754671.221 1686088.334 1871779.107 1625043.116 1572278.151 1882530.147 1894787.947 0.924173779 1.020260453 0.926051501 0.889855953 0.987856773 0.857638513 0.829791088 0.99353078 1 20.85360497 3.668356021 3.768265327 0.910163029 0.978026667 0.042464999 0.062725465 0.375966441 10.70838633 0.016488813 0.027546337 4659.679229 -3.668356021 0.067863638 DRTDIQCLIPCAIDQDPYFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRTDIQCLIPCAIDQDPYFR 20 1 P23381;P23381-2;H0YJP3 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ; 88.755 0.0019845 95623000 116557 108502 117187 107157 112826 97478 147589 96689 136494 FALSE TRUE 109261.9054 116535.601 119966.731 109906.83 103965.1011 125618.3162 125459.3996 108760.8345 113712.2696 0.960862938 1.024828731 1.05500252 0.966534486 0.914282174 1.104703271 1.103305738 0.956456457 1 16.7950284 2.212723156 24.99987626 1.057429424 0.998661773 0.139682327 0.058947228 394.2874016 381503.0904 0.022389005 0.01654073 163.2011281 -2.212723156 -0.058767651 DRVEASSLPEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRVEASSLPEVR 12 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 0 142.1 5.57E-05 158740000 155770 185780 169030 162120 172430 143410 184260 146200 181720 FALSE TRUE 146020.6338 199535.3445 173039.4714 166280.2737 158888.0433 184810.1389 156631.9236 164453.3918 151389.758 0.964534429 1.318024066 1.14300646 1.098358805 1.049529674 1.220757212 1.03462695 1.086291397 1 17.20790808 1.523602753 0.442129689 0.998320966 1.176017303 0.102143649 0.09953232 1.48262871 0.79465151 0.107344157 0.074888654 33.38894931 -1.523602753 0.177696337 DRVGVGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRVGVGIR 8 1 P33992;B1AHB1;B1AHB2 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 67.494 0.053763 117720000 33635 34460 41298 36496 52882 28339 36316 37881 47582 FALSE TRUE 31529.84539 37011.45426 42277.60806 37432.54915 48728.86104 36520.00925 30870.75294 42610.52624 39640.25681 0.795399625 0.933683514 1.066532143 0.944306424 1.229277128 0.92128589 0.778772779 1.07493063 1 15.27467869 4.685968415 2.628908891 0.986775575 0.768502724 0.233453968 0.116677125 0.711692367 7.029818661 0.029969946 0.323803902 48525.32074 -4.685968415 -0.21827285 DRVHHEPQLSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 70.412 0.028451 140570000 299770 326880 293380 291420 304620 224150 335070 282480 294060 FALSE TRUE 281007.9308 351082.5353 300339.1121 298898.3306 280696.374 288858.4662 284829.3641 317748.2498 244979.4863 1.147067189 1.433109933 1.225976577 1.220095344 1.145795422 1.179112874 1.162666183 1.297040232 1 17.90230142 -4.999999997 0.083468286 0.235732847 1.455934809 0.365046398 0.089046875 215.274584 1.265087441 30.03220062 2.545232632 1.00E-05 4.999999997 1.220201963 DRVLDDVSIRS(ph)PETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DRVLDDVSIRSPETK 15 2 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 DRVLDDVS(0.065)IRS(0.934)PETK;DRVLDDVS(0.011)IRS(0.989)PETK;DRVLDDVS(0.04)IRS(0.96)PETK 145.48 2.11E-06 298867000 784420 573590 672480 681760 769000 513350 875350 595520 900880 TRUE FALSE 735324.5524 616059.2004 688431.5432 699255.1158 708605.842 661545.8115 744099.3939 669871.9829 750517.3081 0.979756955 0.820846093 0.917276038 0.931697522 0.944156563 0.881453105 0.991448679 0.892547015 1 19.51752582 1.15180429 0.257743571 1.014022393 0.877351071 0.164214295 0.050238287 2.91948188 0.726749517 0.154676939 0.108060791 14.18418183 -1.15180429 -0.136671322 DRVTDALNATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DRVTDALNATR 11 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;;; 130.65 0.00020034 1493570000 860690 925710 831060 809570 1030920 812030 823270 866140 1214420 FALSE TRUE 806820.9493 994250.5316 850773.1357 830344.9368 949955.7017 1046449.879 699828.3064 974279.4856 1011725.457 0.797470247 0.982727602 0.840913046 0.820721601 0.93894613 1.034321981 0.691717602 0.962988012 1 19.94838642 DRVTNQPIGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRVTNQPIGGR 11 1 Q9H9Y6-4;Q9H9Y6-5;Q9H9Y6-2;Q9H9Y6;Q9H9Y6-3 Q9H9Y6-4 POLR1B DNA-directed RNA polymerase I subunit RPA2 0 112.84 0.0013418 77803000 41121 62780 60202 50222 79424 39940 46705 61380 62361 FALSE TRUE 38547.31001 67428.29652 61630.01987 51510.78155 73186.35942 51470.02963 39702.01884 69043.42811 51952.54623 0.741971526 1.297882422 1.186275252 0.991496765 1.408715544 0.990712359 0.764197748 1.328971015 1 15.66490684 2.038718789 24.98976147 0.973005053 1.155100998 0.023300076 0.224638474 303.6720257 195993.8333 0.077659535 0.057355265 109.3248245 -2.038718789 0.182095945 DRVTSAVEALLSADSASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRVTSAVEALLSADSASR 18 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 153.68 2.87E-08 88963000 84821 108948 98846 99280 110467 96980 107545 85407 101387 FALSE TRUE 79512.20502 117014.6233 101190.6738 101827.6929 101791.3674 124976.5517 91419.62565 96070.25195 84464.85471 0.941364373 1.385364643 1.198021048 1.205562873 1.205132807 1.479627853 1.082339228 1.137399126 1 16.36606355 1.601037437 25 1.082366791 1.248860027 0.220338699 0.142448846 0.844200203 3080.274824 0.06724728 0.032212604 39.90593003 -1.601037437 0.166493236 S(ph)TPDLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STPDLLR 7 0 Q9P2M7;Q9P2M7-2;H0Y4A8 Q9P2M7 CGN Cingulin 1 S(0.984)T(0.016)PDLLR 106.93 0.0079642 37897000 73387 97136 85116 67823 102740 68273 104360 88751 219750 TRUE FALSE 68793.83867 104328.0505 87134.99171 69563.453 94671.21483 87982.30678 88712.18683 99831.75772 183072.3054 0.375774143 0.569873473 0.475959439 0.379978025 0.517124721 0.480587747 0.484574587 0.545313271 1 17.48205404 0.464251007 1.527779796 1.000086953 0.477366119 0.891469455 0.057714001 0.917901353 2.301601863 0.052370439 0.015080876 2.9123999 -0.464251007 -0.522720834 DRWQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DRWQER 6 1 Q09161 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 ;; 128.37 0.015192 732860000 888470 722460 1039460 946670 751430 792200 1142630 671830 852070 FALSE TRUE 832862.2487 775951.6901 1064116.482 970963.1549 692415.7189 1020895.28 971303.2392 755709.4544 709854.0124 1.173286668 1.093114467 1.499063841 1.367834988 0.975433972 1.438176388 1.368314079 1.064598412 1 19.43716283 -1.379177961 6.972599631 0.999987442 1.267703392 0.159911939 0.172821811 3.23E-05 2.88E-06 0.160270515 0.037774353 0.041765919 1.379177961 0.267715949 DRYDS(ph)DRYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DRYDSDRYR 9 2 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 DRYDS(1)DRYR 72.29 0.053436 0 402540 432810 410380 463660 484500 396550 441280 439250 565290 TRUE FALSE 377345.74 464855.7027 420114.4074 475558.3006 446449.3244 511027.5475 375114.1606 494091.3294 470939.4471 0.801261696 0.987081685 0.892077336 1.009807744 0.9479973 1.085123684 0.796523126 1.04916106 1 18.84518205 4.745557031 24.50302663 0.956779694 0.8012616 0.283769733 0.082023284 841.1818109 2945909.559 0.017775508 0.175234998 55661.77241 -4.745557031 -0.155518094 DRYDSDRYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRYDSDRYR 9 2 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 163.38 3.55E-05 451530000 172602 372490 154491 150846 455820 96654 153043 334220 468490 FALSE TRUE 161799.1489 400069.5472 158155.5995 154716.9637 420021.7359 124556.4408 130095.6229 375948.1027 390295.9924 0.414554984 1.025041391 0.405219635 0.396409307 1.076162051 0.319133281 0.333325541 0.96323844 1 18.57420912 1.148470311 8.624236367 0.992295087 0.583168899 0.285224592 0.271996675 0.398260102 33.66546286 0.256148046 0.064153822 14.07571001 -1.148470311 -0.409126189 DRYDSFIELQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRYDSFIELQEK 12 1 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 ; 240.42 3.01E-16 696100000 1196370 904390 1035970 1050800 1102750 754890 1233500 943710 1140580 FALSE TRUE 1121491.337 971351.9766 1060543.698 1077765.307 1016144.463 972814.4884 1048548.126 1061534.271 950209.8296 1.18025651 1.022249977 1.116115267 1.134239274 1.069389551 1.023789123 1.103491138 1.117157745 1 19.85788661 2.539355087 24.98550726 1.068569548 1.098865407 0.160871838 0.051994341 622.7815866 250031.2356 0.016139469 0.015216378 346.2223396 -2.539355087 0.030295859 DRYLPDTLLLEECGLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DRYLPDTLLLEECGLLR 17 1 P21964-2;P21964;E7EMS6 P21964-2 COMT Catechol O-methyltransferase 0 ;;; 202.07 9.96E-12 362683000 281965 331805 321420 311454 387790 292589 387795 336327 540122 FALSE TRUE 264317.314 356372.1874 329044.2342 319446.4369 357334.5377 377054.6945 329648.7399 378318.1663 449972.1489 0.587408164 0.791987211 0.731254668 0.709924909 0.7941259 0.837951183 0.732598097 0.840759072 1 18.77947618 -5 0.123761747 1.823392012 0.639599531 0.70220833 0.058212406 86.99778475 0.691590453 17.77563912 0.483842484 1.00E-05 5 -1.18379248 DRYS(ph)AGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DRYSAGK 7 1 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 1 DRYS(1)AGK;DRY(0.001)S(0.999)AGK;DRYS(1)AGK 98.943 0.0065963 1122130000 1152510 749230 988360 873830 990800 722120 1218470 901890 1770630 TRUE FALSE 1080376.456 804703.7688 1011804.366 896253.9572 912986.5647 930584.3214 1035771.735 1014492.952 1475100.414 0.732408754 0.545524739 0.685922366 0.607588438 0.618931807 0.630861677 0.702170324 0.687745012 1 20.49238174 0.135664413 0.662416392 1.013974058 0.628080486 0.824572952 0.05116044 1.227862624 0.662028016 0.087538695 0.017392494 1.366672365 -0.135664413 -0.385893572 DRYS(ph)AGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRYSAGKR 8 2 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 1 DRY(0.001)S(0.999)AGKR;DRYS(1)AGKR 82.954 0.0098813 204438000 310170 265908 282640 278420 277311 205327 352550 219754 366800 TRUE FALSE 290757.0134 285596.105 289344.3543 285564.7286 255532.1127 264601.5717 299688.4004 247190.7706 305578.7104 0.951496304 0.934607338 0.946873406 0.934504659 0.836223546 0.865903162 0.980724083 0.808926677 1 18.22118451 2.973707842 24.50703188 0.899836276 0.942367394 0.1235572 0.057929132 1236.878133 1152900.03 0.016335547 0.017381802 941.2561838 -2.973707842 0.042531117 DRYSAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRYSAGK 7 1 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ; 109.11 0.0064769 2609900000 2025870 1624940 1750400 1704360 1840740 1484100 2086800 1724620 2542200 FALSE TRUE 1899074.413 1745252.248 1791920.315 1748096.763 1696175.706 1912535.578 1773903.713 1939942.603 2117890.397 0.896682102 0.824052204 0.846087369 0.825395292 0.800879832 0.903038033 0.837580507 0.915978752 1 21.0141965 0.879949936 1.289774616 1.000711645 0.841567282 0.701118271 0.03222785 0.293365136 0.954799938 0.027311635 0.008295045 7.584901333 -0.879949936 -0.159144363 DS(ph)DGVDGFEAEGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSDGVDGFEAEGKK 14 1 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 DS(1)DGVDGFEAEGKK 84.94 0.0048595 161830000 124640 120440 123990 118560 125690 107720 139130 109320 148600 TRUE FALSE 116839.0049 129357.5029 126931.1014 121602.4503 115818.8144 138817.0153 118268.7481 122968.8426 123797.7 0.943789787 1.044910389 1.025310659 0.982267444 0.935549 1.121321441 0.955338816 0.993304743 1 16.91762499 3.253875364 24.82542407 0.99860102 1.016241782 0 0.055133874 1124.779352 1823269.797 0.014290026 0.019276037 1794.218639 -3.253875364 0.017640762 DS(ph)EY(ph)PFKAQNGLCHY(ph)FSGSHSGFSIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSEYPFKAQNGLCHYFSGSHSGFSIK 26 1 P43234 P43234 CTSO Cathepsin O 3 DS(0.31)EY(0.606)PFKAQNGLCHY(0.571)FS(0.498)GS(0.509)HS(0.482)GFS(0.024)IK 47.757 0.0711 672240000 44699 172670 137770 127270 184240 119510 126760 142990 154130 TRUE FALSE 41901.36938 185454.6665 141037.9695 130535.9637 169770.5336 154010.5969 107753.5148 160842.6163 128404.7073 0.326322689 1.444298035 1.098386285 1.016597961 1.322151946 1.199415506 0.839171064 1.252622428 1 16.97033857 -0.409337936 7.47671556 1.000000008 1.093354207 0 0.311089234 0 0 0.270066412 0.063655264 0.38963868 0.409337936 0.093354199 DS(ph)FDDRGPSLNPVLDYDHGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSFDDRGPSLNPVLDYDHGSR 21 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 DS(1)FDDRGPSLNPVLDYDHGSR 183.47 2.60E-17 71617000 39295 48370 58387 61890 64210 50142 68170 54193 82750 TRUE FALSE 36835.59609 51951.36513 59771.96721 63478.20218 59167.20561 64617.18141 57948.54136 60959.11534 68938.49041 0.53432554 0.753590118 0.867033305 0.920794781 0.858260824 0.937316454 0.840583265 0.884253702 1 16.07302209 5.20539188 0.877761931 0.896523289 3.11E-13 0.871098733 0.045630897 1.433170002 0.487120282 0.013249384 1.496870787 160469.2711 -5.20539188 -0.896523289 DS(ph)LGTYSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DSLGTYSSR 9 0 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DS(1)LGTYSSR;DS(1)LGTYSSR;DS(1)LGTYSSR;DS(1)LGTYSSR;DS(1)LGTYSSR;DS(0.998)LGT(0.002)YSSR 242.97 1.88E-10 3326340000 3768630 2901070 3181920 3046830 3063700 2806470 3784050 2793380 2374270 TRUE FALSE 3532758.175 3115868.241 3257396.645 3125016.816 2823089.36 3616652.33 3216666.832 3142139.642 1977988.999 1.7860353 1.575270764 1.646822428 1.579895954 1.427252306 1.828449163 1.626230901 1.588552638 1 20.91560297 0.654490382 3.194164794 1.000008795 1.632533315 0.763998527 0.110745048 2.342516431 21.14565489 0.097657955 0.025375582 4.513260302 -0.654490382 0.63252452 DS(ph)LSPVLHPSDLILTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSLSPVLHPSDLILTR 16 0 Q9HCN4-3;Q9HCN4-2;Q9HCN4-4;Q9HCN4;Q9HCN4-5 Q9HCN4-3 GPN1 GPN-loop GTPase 1 1 DS(0.5)LS(0.5)PVLHPSDLILTR;DS(0.624)LS(0.376)PVLHPSDLILTR 136.49 1.11E-05 135173000 122752 220465 218468 261996 226702 137222 178616 137001 164138 TRUE FALSE 115069.1714 236788.458 223650.1641 268719.2609 208897.7394 176835.7638 151834.189 154105.8764 136742.3074 0.841503801 1.731640064 1.635559384 1.965150844 1.527674524 1.293204474 1.110367317 1.126980225 1 17.06110015 2.072925214 2.402920666 1.094225534 1.601792901 0.343207845 0.286895695 0.301764315 3.376483225 0.136949577 0.080883666 118.2837851 -2.072925214 0.507567367 DS(ph)QDAS(ph)AEQSDHDDEVASLASASGGFGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSQDASAEQSDHDDEVASLASASGGFGTK 29 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 2 DS(0.996)QDAS(0.621)AEQS(0.383)DHDDEVASLASASGGFGTK 89.645 0.000878 65742000 157540 101530 120920 125420 96538 83653 176650 105080 151970 TRUE FALSE 147679.8526 109047.3868 123788.2795 128638.4895 88956.2949 107802.2631 150162.9724 118199.4693 126605.2252 1.166459381 0.861318217 0.977750162 1.016059877 0.702627358 0.851483522 1.186072472 0.933606564 1 16.94997742 -1.366557859 6.97426797 1.000001524 0.960123097 0.006757123 0.143619699 3.31E-06 3.00E-07 0.135116001 0.03184593 0.042997395 1.366557859 -0.039878427 DS(ph)RPLSPILHIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSRPLSPILHIVK 13 1 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 1 DS(0.5)RPLS(0.5)PILHIVK 96.993 0.0024052 19757000 32898 32577 31756 32919 33419 23818 36329 31369 24259 TRUE FALSE 30838.9729 34989.03498 32509.26732 33763.75727 30794.40655 30693.86995 30881.80371 35285.4887 20210.01618 1.525925196 1.731271992 1.608572058 1.670644742 1.523720034 1.518745441 1.528044482 1.745940646 1 14.30278286 -2.468589809 0.454141231 1.81E-33 1.618811519 0.816536861 0.089553126 41.16993648 2.102427424 41.01269217 0.046288271 0.003399462 2.468589809 1.618811519 DS(ph)SQEYTDSTGIDLHEFLVNTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSSQEYTDSTGIDLHEFLVNTLK 23 0 A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5;H0YIX9;Q15032-2;Q15032-4;Q15032;Q15032-3;H7C2F9 A0A0U1RRA6;Q15032-2 R3HDM2;R3HDM1 R3H domain-containing protein 2;R3H domain-containing protein 1 1 DS(0.5)S(0.5)QEYTDSTGIDLHEFLVNTLK;DS(0.5)S(0.5)QEYTDSTGIDLHEFLVNTLK 178.91 3.23E-17 125271000 217306 148880 150835 175294 129784 114179 232450 146227 167181 TRUE FALSE 203705.2054 159903.2301 154412.8774 179792.3408 119591.2882 147140.6238 197596.2805 164483.7628 139277.4111 1.462586099 1.148091632 1.108671365 1.29089376 0.858655307 1.0564572 1.418724536 1.180979468 1 17.08760177 4.738742367 24.95936077 1.149725388 1.462586194 0.309267602 0.153040448 19.75855138 2711368.969 0.036486419 0.212088058 54795.18115 -4.738742367 0.312860806 DSAAPS(ph)PIPGADNLSADPVVSPPTSIPFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSAAPSPIPGADNLSADPVVSPPTSIPFK 29 0 Q5T1M5;Q5T1M5-2;Q5T1M5-3 Q5T1M5 FKBP15 FK506-binding protein 15 1 DS(0.004)AAPS(0.996)PIPGADNLS(0.001)ADPVVSPPTSIPFK;DS(0.001)AAPS(0.999)PIPGADNLSADPVVSPPTSIPFK 108.73 0.00025889 192552000 270090 220193 251890 244700 260980 203132 320100 219900 267760 TRUE FALSE 253185.549 236496.3188 257864.9498 250979.4163 240483.6835 261772.9108 272103.9767 247354.9991 223069.1262 1.135009373 1.060192967 1.15598673 1.125119467 1.078067986 1.173505788 1.219819082 1.108871511 1 17.76713133 3.912110682 6.25961074 1.138140964 1.094356534 0 0.062166474 0.51794314 38.3641586 0.015326296 0.028182727 8167.90508 -3.912110682 -0.04378443 DSAIPVES(ph)DT(ph)DDEGAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSAIPVESDTDDEGAPR 17 0 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 2 DSAIPVES(1)DT(1)DDEGAPR;DSAIPVES(1)DT(1)DDEGAPR 358.85 2.33E-87 881940000 355780 339800 352490 329470 305540 289830 418080 295770 329090 TRUE FALSE 333512.3649 364959.1456 360851.2293 337924.758 281544.1209 373499.216 355392.7853 332697.5356 274162.753 1.216475839 1.33117698 1.316193485 1.232569903 1.026923307 1.362326618 1.296283982 1.213503774 1 18.06467306 -3.546503584 0.3676428 4.40E-09 1.271592102 0.404541981 0.094001175 159.1080503 3.486234695 122.7108059 0.066753819 0.000284116 3.546503584 1.271592098 DSAIPVES(ph)DTDDEGAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSAIPVESDTDDEGAPR 17 0 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 1 DSAIPVES(0.849)DT(0.151)DDEGAPR 128.08 4.00E-05 133870000 76500 86058 93771 96918 84682 81799 116770 77438 94009 TRUE FALSE 71712.00156 92429.82386 95995.2924 99405.07996 78031.41731 105413.0434 99261.42254 87106.30476 78318.29058 0.915648197 1.180181835 1.225707197 1.26924476 0.996337085 1.345956897 1.267410484 1.112208963 1 16.25706166 4.739224224 4.548520369 1.197672154 0.897257919 0.317519177 0.115313532 0.200557157 10.81256569 0.025042741 0.193282094 54856.01112 -4.739224224 -0.300414236 DSAIPVESDT(ph)DDEGAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DSAIPVESDTDDEGAPR 17 0 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 1 DSAIPVES(0.015)DT(0.985)DDEGAPR;DSAIPVES(0.004)DT(0.996)DDEGAPR;DSAIPVES(0.002)DT(0.998)DDEGAPR 394.12 4.91E-121 1504790000 715940 730640 703640 741470 662750 655060 851520 626560 684300 TRUE FALSE 671130.5934 784737.3458 720330.6731 760497.3755 610700.2884 844165.188 723842.4811 704787.3952 570085.9093 1.177244662 1.376524719 1.263547584 1.334004863 1.071242559 1.480768379 1.269707722 1.236282784 1 19.12081982 0.781958583 2.634118489 1.000165218 1.292235921 0.390261911 0.109395345 0.948706195 9.910205389 0.09264469 0.024621241 6.05283149 -0.781958583 0.292070703 DSALAEAPEGLS(ph)PAPPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DSALAEAPEGLSPAPPAR 18 0 C9JPC9;Q9H9J4-2;Q9H9J4 C9JPC9 USP42 Ubiquitin carboxyl-terminal hydrolase 42 1 DSALAEAPEGLS(1)PAPPAR;DSALAEAPEGLS(1)PAPPAR;DSALAEAPEGLS(1)PAPPAR 393.23 9.66E-127 673260000 772660 744040 769780 752950 835130 690560 1003760 759260 1066590 TRUE FALSE 724300.5898 799129.4958 788039.5451 772271.9717 769542.2586 889913.4617 853255.5065 854055.2823 888569.2386 0.81513129 0.899344093 0.88686341 0.869118509 0.866046477 1.001512795 0.96025776 0.961157831 1 19.76112467 2.244298521 24.99944838 0.976441858 0.874420549 0.823250289 0.025966927 57.98525489 252636.4206 0.008757214 0.007141225 175.5086481 -2.244298521 -0.102021309 DSASFNPELLTHILDGS(ph)PEK ddPTM_SK-BR-3_Pertuzumab_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 177.41 4.23E-17 24387000 109380 71532 82330 81898 94433 59726 118440 83530 72249 TRUE FALSE 102534.101 76828.30371 84282.90648 83999.64133 87016.6131 76967.92663 100681.0215 93958.90437 60190.17515 1.703502287 1.276425987 1.40027681 1.395570641 1.445694632 1.278745683 1.672715211 1.561033908 1 15.87724039 DSAYISS(ph)SPLGSHQVFDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSAYISSSPLGSHQVFDFR 19 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 DSAYIS(0.082)S(0.537)S(0.381)PLGSHQVFDFR 219.35 2.03E-19 618970000 747550 762050 861450 949430 1168600 690780 790770 681940 984400 TRUE FALSE 700762.1799 818472.9749 881884.0008 973793.9812 1076822.87 890196.9721 672201.3796 767081.7101 820097.2805 0.854486652 0.998019374 1.075340721 1.187412767 1.313042849 1.085477288 0.81966054 0.935354535 1 19.64543553 1.756155686 25 0.903723579 1.086995295 0.282316856 0.125003354 8.751279437 12447.487 0.060158656 0.033361338 57.03687012 -1.756155686 0.183271717 DSAYISSS(ph)PLGSHQVFDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DSAYISSSPLGSHQVFDFR 19 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 DSAYISS(0.002)S(0.998)PLGSHQVFDFR;DSAYIS(0.02)S(0.162)S(0.818)PLGSHQVFDFR;DSAYIS(0.001)S(0.029)S(0.971)PLGSHQVFDFR 254.24 4.35E-31 1207160000 1210540 1390240 1471070 1660610 1957300 1116900 1233350 1105820 1710620 TRUE FALSE 1134774.462 1493174.816 1505964.475 1703224.064 1803581.553 1439330.899 1048420.617 1243884.061 1425106.471 0.796273461 1.047763691 1.05673822 1.195155659 1.265576706 1.009981309 0.735678799 0.87283588 1 20.44263828 1.95185626 8.375268608 0.847510414 1.077789138 0.313024734 0.135831245 0.371963841 60.51173958 0.05611632 0.0355894 89.50684716 -1.95185626 0.230278724 DSAYPEELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 99.013 0.011407 0 83798 87632 86940 84563 99524 59544 106560 76085 87058 FALSE TRUE 78553.23276 94120.36446 89002.25786 86733.02974 91707.7865 76733.38618 90582.31725 85584.37973 72527.45738 1.083082678 1.297720448 1.227152599 1.195864751 1.264456108 1.057990849 1.248938271 1.1800273 1 16.14623965 -3.360568336 0.267218099 0.480543365 1.225488498 0.378658592 0.076347777 71.7370562 1.550251058 20.63635978 0.089637534 0.000435945 3.360568336 0.744945133 DSAYQSITHYRPVS(ph)ASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DSAYQSITHYRPVSASR 17 1 P50402;Q5HY57 P50402 EMD Emerin 1 DSAYQSITHYRPVS(1)ASR;DSAYQSITHYRPVS(0.994)AS(0.006)R;DSAYQSITHYRPVS(0.932)AS(0.068)R;DSAYQSITHYRPVS(0.996)AS(0.004)R;DSAYQSITHYRPVS(0.96)AS(0.04)R;DSAYQSITHYRPVS(0.779)AS(0.221)R;DSAYQSITHYRPVS(0.917)AS(0.083)R 256.2 2.63E-27 7059270000 1490832 1815025 1417542 1525318 2054697 1081917 2257093 1777044 1587972 TRUE FALSE 1397523.486 1949411.34 1451166.766 1564460.242 1893329.386 1394248.874 1918662.858 1998911.855 1322929.215 1.056385686 1.4735568 1.096934552 1.182572903 1.431164544 1.053910413 1.450314074 1.510974157 1 20.33530444 1.681313784 16.22945437 1.360125348 1.238830249 0.03911294 0.195351601 0.383185788 98.88808146 0.081704543 0.045139947 48.00801883 -1.681313784 -0.121295099 DSCPLDCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSCPLDCK 8 0 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ; 118.74 0.0042524 569450000 823080 640940 682820 659290 771870 624510 970980 581660 924320 FALSE TRUE 771564.892 688395.8645 699016.8129 676208.4976 711250.4438 804795.8989 825390.5631 654281.5314 770045.0207 1.001973744 0.893968334 0.907760967 0.87814151 0.923647871 1.045128372 1.071873126 0.849666596 1 19.55458327 2.320127282 7.010320309 1.007073154 0.912931225 0.197263098 0.066712271 0.257497016 18.40598936 0.02210834 0.01839998 208.9908546 -2.320127282 -0.094141929 DSDAGS(ph)STPTTSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSDAGSSTPTTSTR 14 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3;K7EP28 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 1 DSDAGS(0.41)S(0.326)T(0.261)PT(0.002)TSTR 76.759 0.027865 42477000 146780 127980 133730 130310 135940 114560 175550 135080 171590 TRUE FALSE 137593.3018 137455.7724 136902.1388 133653.9752 125263.8208 147631.6123 149227.9072 151945.0353 142950.5205 0.962523965 0.961561888 0.957688984 0.934966692 0.876273975 1.032746238 1.043913004 1.062920476 1 17.12515635 2.128981617 8.953911893 1.039835729 0.944263765 0.726649295 0.029190904 0.139839445 10.60129525 0.010760342 0.007944158 134.5803388 -2.128981617 -0.095571965 DSDAGSS(ph)TPTTSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSDAGSSTPTTSTR 14 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3;K7EP28 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 1 DSDAGS(0.188)S(0.527)T(0.285)PTTSTR 199.84 2.11E-08 302440000 723520 663460 678360 611220 685860 588020 938800 746720 899980 TRUE FALSE 678236.1747 712583.2687 694451.0195 626904.94 631995.3222 757771.8283 798035.6554 839949.6357 749767.5239 0.904595295 0.95040562 0.926221792 0.836132428 0.842921708 1.010675715 1.064377464 1.120280099 1 19.51608381 2.059129208 4.84698367 1.062269394 0.902497758 0.753599416 0.045034543 0.107032339 5.151706049 0.018813654 0.0133629 114.5853795 -2.059129208 -0.159771636 DSDAGSST(ph)PTTSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.01)S(0.129)T(0.861)PT(0.001)TSTR;DSDAGS(0.405)S(0.18)T(0.413)PT(0.002)TSTR 242.98 1.84E-16 249800000 945680 885110 925580 895900 948750 873220 1303550 975600 1159550 TRUE FALSE 886491.5769 950644.4654 947535.1947 918890.3108 874239.0021 1125304.438 1108094.779 1097405.808 966013.614 0.917680211 0.984090132 0.980871471 0.9512188 0.904996565 1.16489501 1.147079879 1.136014847 1 19.881684 2.235366582 24.9999682 1.12815119 0.957394319 0.710404028 0.051443298 39.7008812 310737.1414 0.01726402 0.013287988 171.9359062 -2.235366582 -0.170756871 DSDEADLVLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSDEADLVLAK 11 0 Q13185 Q13185 CBX3 Chromobox protein homolog 3 0 157.24 7.14E-05 41435000 97376 64131 75615 74915 76036 61735 94083 68722 85254 FALSE TRUE 91281.40998 68879.32597 77408.62351 76837.44573 70064.43927 79556.89232 79976.12757 77302.09298 71024.55664 1.285209149 0.96979593 1.089885346 1.08184337 0.986481896 1.120132192 1.126034872 1.088385435 1 16.1160303 DSDKTDTDWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DSDKTDTDWR 10 1 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;; 115.18 0.001147 3815680000 19322000 13421200 15867300 15197600 16392400 11636500 19645400 13352300 18744200 FALSE TRUE 18112670.51 14414919.61 16243679.85 15587596.15 15105007.03 14995768.65 16699754.65 15019364.05 15615671.93 1.159903371 0.923105946 1.040216516 0.998202077 0.967297923 0.960302491 1.069422739 0.961813498 1 23.89649131 4.754763401 24.66878356 0.994336931 1.159903523 0.617258368 0.041913808 1857.54208 2828057.864 0.009757956 0.254340544 56854.31107 -4.754763401 0.165566592 DSDLSHVQNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSDLSHVQNK 10 0 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ; 98.044 0.0056455 1671060000 720980 744750 842790 802460 832140 632390 869740 746190 825520 FALSE TRUE 675855.1488 799892.0649 862781.3768 823052.4822 766787.0811 814950.727 739330.5613 839353.4641 687735.3789 0.982725579 1.163081164 1.254525219 1.196757514 1.11494494 1.184977176 1.075021853 1.220459918 1 19.39149404 -3.701720068 0.471816479 5.02E-12 1.157575858 0.25353638 0.078366977 597.7471788 11.21488017 605.9462843 0.038381004 0.000198738 3.701720068 1.157575858 DSDPVMAGIGEEIAHFQK ddPTM_SK-BR-3_Pertuzumab_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 0 219.95 7.05E-19 67475000 177300 159540 169070 161950 169020 129680 223580 149690 197910 FALSE TRUE 166203.1095 171352.5076 173080.4202 166105.9112 155745.851 167116.5108 190056.2546 168379.126 164877.5425 1.008039706 1.039271359 1.049751335 1.007450188 0.944615311 1.013579584 1.152711593 1.02123748 1 17.33103538 DSDQVAQS(ph)DGEESPAAEEQLLGEHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSDQVAQSDGEESPAAEEQLLGEHIK 26 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;D6RHZ5;H0Y8V7 D6REX3 SEC31A Protein transport protein Sec31A 1 DSDQVAQS(1)DGEESPAAEEQLLGEHIK;DSDQVAQS(1)DGEESPAAEEQLLGEHIK 222.98 1.53E-34 197441000 297370 196839 231073 225021 185266 172862 295050 195737 125855 TRUE FALSE 278758.1425 211413.1644 236554.1607 230795.4198 170715.9557 222764.4532 250809.9916 220175.1953 104848.9874 2.658663181 2.016358665 2.256141585 2.201217441 1.628207957 2.124621884 2.39210695 2.099926768 1 16.6779534 -1.703340573 2.074449572 0.717529012 2.165163071 0.662852786 0.262675443 581378.1749 349526.0923 851850.4345 0.066114125 0.019799737 1.703340573 1.447634059 DSDQVAQS(ph)DGEESPAAEEQLLGEHIKEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSDQVAQSDGEESPAAEEQLLGEHIKEEK 29 1 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;D6RHZ5;H0Y8V7 D6REX3 SEC31A Protein transport protein Sec31A 1 DSDQVAQS(1)DGEESPAAEEQLLGEHIKEEK 211.25 4.41E-26 127500000 245150 132220 154950 160670 150400 112610 219050 126020 134830 TRUE FALSE 229806.4991 142009.7064 158625.4872 164793.0642 138588.1907 145118.6789 186205.4861 141753.8744 112326.002 2.045888709 1.264263874 1.412188491 1.467096321 1.233803289 1.291941994 1.657723793 1.261986289 1 16.77733241 7.999890192 0.033049015 3.92E-07 3.533892649 0.365258515 0.226104875 1707.550483 4.317738935 140.4597705 372.9664572 99974719.03 -7.999890192 3.533892257 DSDYVYPSLES(ph)DEDNPIFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSDYVYPSLESDEDNPIFK 19 0 O75151;E7ET14;A0A087WW48 O75151 PHF2 Lysine-specific demethylase PHF2 1 DSDYVY(0.001)PS(0.028)LES(0.971)DEDNPIFK;DSDYVYPS(0.005)LES(0.995)DEDNPIFK 100.94 0.00035787 61467000 258160 178797 214016 199565 206893 157275 276030 174670 268690 TRUE FALSE 242002.2264 192035.3159 219092.5606 204686.1758 190644.4583 202677.7394 234641.864 196477.934 223843.9032 1.081120473 0.857898353 0.978773857 0.91441479 0.851684838 0.905442304 1.048238798 0.8777453 1 17.7721335 -0.942601333 5.411712907 1.000000116 0.938912024 0.057549783 0.07702673 9.94E-08 1.95E-08 0.069133679 0.016294934 0.114129698 0.942601333 -0.061088092 DSEDNPQTLLFSATCPHWVFNVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSEDNPQTLLFSATCPHWVFNVAK 24 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 367.58 1.22E-118 573310000 1077960 834120 968030 880700 965270 733540 1185200 805600 961500 FALSE TRUE 1010492.408 895879.1127 990992.1287 903300.253 889461.5879 945301.09 1007490.263 906180.9333 801019.4385 1.261507973 1.118423686 1.237163646 1.127688305 1.110411989 1.180122535 1.257760067 1.131284573 1 19.61147773 0.982997383 23.68013876 0.999999996 1.183234284 0.530022107 0.054962389 423.1493693 589336.422 0.051046563 0.012761641 9.616064849 -0.982997383 0.183234288 DSEGTWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSEGTWR 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 138.37 0.0064966 913530000 1043710 1171780 1165370 1196990 1286400 957800 1356250 973280 1386190 FALSE TRUE 978386.0542 1258539.81 1193013.127 1227706.79 1185371.333 1234301.311 1152892.903 1094796.15 1154825.934 0.847215174 1.089809099 1.033067488 1.063109819 1.026450219 1.068820222 0.998326128 0.948018328 1 20.13924398 1.512288681 5.903219318 0.973513856 1.032538927 0.06194816 0.0677233 0.27566812 21.17736474 0.03513533 0.015677839 32.53034591 -1.512288681 0.059025071 DSEHIDDETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSEHIDDETR 10 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 126.71 0.00037544 676230000 582750 663880 680470 703740 660170 511580 849080 603970 620020 FALSE TRUE 546276.7177 713034.366 696611.0697 721799.1598 608322.9112 659264.8412 721768.3365 679376.984 516534.6565 1.057579992 1.380419217 1.348624068 1.397387669 1.177700089 1.276322572 1.397327996 1.315259248 1 18.97850562 -1.547739102 6.402110684 0.999603413 1.311719 0.415013182 0.107787275 0.00056317 3.98E-05 0.096330007 0.022677128 0.028330934 1.547739102 0.312115588 DSEHIDDETRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DSEHIDDETRR 11 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;; 154.15 2.09E-05 2010945000 1214672 1401271 1334115 1448835 1367633 1080538 1583284 1227074 1346554 FALSE TRUE 1138647.848 1505022.563 1365760.838 1486014.559 1260224.621 1392471.78 1345885.263 1380276.89 1121805.438 1.015013664 1.341607476 1.217466765 1.324663358 1.123389652 1.241277437 1.199749276 1.230406667 1 20.09739105 -2.170617052 0.431077376 0.727672887 1.23003193 0.320482683 0.094131491 67.1810703 4.027767855 17.7834117 0.047695986 0.006751231 2.170617052 0.502359043 DSENLAS(ph)PSEYPENGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.998)PS(0.002)EYPENGER;DSENLAS(0.99)PS(0.01)EYPENGER;DSENLAS(0.996)PS(0.004)EYPENGER;DSENLAS(0.778)PS(0.222)EYPENGER;DSENLAS(0.936)PS(0.064)EYPENGER;DSENLAS(0.999)PS(0.001)EYPENGER 449.72 1.06E-182 4926840000 2947580 2930540 3041320 3200100 3389780 2388660 2818710 2197400 2999990 TRUE FALSE 2763096.229 3147520.231 3113461.547 3282219.984 3123560.353 3078227.365 2396070.603 2471750.227 2499272.288 1.105560303 1.259374677 1.245747237 1.313270266 1.249787935 1.23164946 0.958707306 0.98898797 1 21.25307666 1.755407701 5.687898091 0.981227232 1.242905389 0.832189685 0.053131965 0.059152707 4.757976509 0.024965534 0.013232969 56.93872011 -1.755407701 0.261678157 DSES(ph)PSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DSESPSQK 8 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 DSES(0.998)PS(0.002)QK;DSES(0.996)PS(0.004)QK;DSES(0.972)PS(0.028)QK;DSES(1)PSQK;DSES(0.983)PS(0.017)QK;DSES(1)PSQK;DSES(0.999)PS(0.001)QK 219.5 6.74E-06 1766797000 3123511 1558830 2603036 2240136 2153889 1592895 2841944 1796011 2272490 TRUE FALSE 2928016.022 1674247.395 2664781.243 2297621.682 1984731.246 2052737.928 2415820.881 2020246.927 1893196.738 1.546598916 0.884349398 1.407556431 1.213620136 1.048349179 1.084270793 1.276053794 1.067108814 1 20.85239291 2.894748258 9.071636842 1.12490556 1.22514389 0.148283811 0.183197902 1.057657911 83.79548039 0.053233131 0.056513054 784.7805982 -2.894748258 0.10023833 DSES(ph)PSQKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DSESPSQKK 9 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 DSES(1)PSQKK;DSES(1)PSQKK;DS(0.001)ES(0.95)PS(0.049)QKK;DS(0.259)ES(0.658)PS(0.084)QKK 181.66 2.89E-05 1448075000 7869340 2937840 4818100 4328030 4298260 2845260 5516960 3619850 5166180 TRUE FALSE 7376812.057 3155360.73 4932387.607 4439094.577 3960691.998 3666640.373 4689743.065 4071796.241 4303911.183 1.713978691 0.733137975 1.146024487 1.031409429 0.92025412 0.851932165 1.089646804 0.946068835 1 22.03721688 4.750088491 24.99854011 0.970983815 1.713979129 0.801924223 0.116976534 763.6771051 1656025.718 0.026942555 0.432878763 56245.59184 -4.750088491 0.742995314 DSESPS(ph)QKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSESPSQKK 9 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 DS(0.001)ES(0.301)PS(0.698)QKK 115.29 0.0015895 109700000 255230 110270 179580 159100 153580 100760 187870 128410 185730 TRUE FALSE 239255.6099 118434.5055 183839.7224 163182.7754 141518.4463 129847.7763 159700.6376 144442.2712 154730.4631 1.546273468 0.765424617 1.188128819 1.054626038 0.914612698 0.839186891 1.032121499 0.933508943 1 17.23939774 2.849340815 5.025475495 0.94475599 1.087515629 0.176794786 0.196486942 0.513983367 19.52896088 0.056675232 0.060333744 706.8720584 -2.849340815 0.142759639 DSETGENIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSETGENIR 9 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 155.42 0.00017067 156070000 158910 153800 165110 139080 210590 141790 132580 137890 160040 FALSE TRUE 148964.1068 165187.512 169026.4872 142649.0283 194051.1109 182722.4712 112700.8598 155105.87 133328.2901 1.117273061 1.238953203 1.267746605 1.06990818 1.455438382 1.370470371 0.845288421 1.163338028 1 17.0246234 1.743508591 25 0.997889717 1.254031863 0.442677671 0.132416542 0.807394147 4096.230406 0.057281774 0.031765692 55.39985032 -1.743508591 0.256142147 DSFDDRGPSLNPVLDYDHGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DSFDDRGPSLNPVLDYDHGSR 21 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;; 201.12 4.27E-22 6564160000 4059840 7259330 6847300 7049190 7664740 5804470 8359460 6556160 8264650 FALSE TRUE 3805741.861 7796818.347 7009721.19 7230084.15 7062782.238 7480126.261 7106036.578 7374711.008 6885226.523 0.552740255 1.132398233 1.018081419 1.050086606 1.025787926 1.086402348 1.032070122 1.071091994 1 22.71507269 4.743999896 24.99996854 1.054483827 0.552740042 0.944547855 0.038011813 116.6205144 535994.1325 0.008349548 0.072578709 55462.55797 -4.743999896 -0.501743785 DSFHSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSFHSLR 7 0 Q6V3B1;G3V563;G3V2R5;P61244-2;A0A494C130;P61244-3;P61244-4;P61244;P61244-6;P61244-5 Q6V3B1;P61244-3 MAX Protein max 0 128.57 0.0037452 99925000 68494 125710 107070 91121 131740 75077 111450 127600 119830 FALSE TRUE 64207.08281 135017.6992 109609.751 93459.31913 121393.6718 96750.51113 94739.10715 143531.1409 99829.59887 0.643166792 1.352481636 1.09796846 0.936188467 1.216008811 0.969156565 0.949008192 1.43776137 1 16.60718001 -1.084758891 3.837962015 0.999973823 1.087083993 0.008359187 0.226802498 20368072.75 52505949.12 7175.578764 0.04944285 0.082269927 1.084758891 0.08711017 DSFIENSSSNCTSGSSKPNS(ph)PSIS(ph)PSILSNTEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSFIENSSSNCTSGSSKPNSPSISPSILSNTEHK 34 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 2 DSFIENS(0.002)S(0.002)S(0.003)NCT(0.002)S(0.002)GS(0.002)S(0.013)KPNS(0.973)PS(0.009)IS(0.988)PS(0.003)ILSNTEHK 135.12 3.03E-08 133610000 62399 29292 40261 37687 43252 32994 46100 32409 53385 TRUE FALSE 58493.55798 31460.81016 41216.00993 38654.11222 39855.16239 42518.83219 39187.73297 36455.33499 44474.69862 1.315209766 0.707386697 0.926729381 0.869125895 0.89613114 0.956022941 0.881124194 0.819687061 1 15.44069721 4.752600966 24.90896788 0.875461337 1.31521008 0.746625035 0.079223863 1169.669256 2075071.544 0.018135345 0.385923556 56571.92624 -4.752600966 0.439748742 DSFLKR ddPTM_SK-BR-3_Pertuzumab_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 ;; 98.133 0.064588 3148200000 3830500 4099120 3964380 3891010 4671830 2990370 4877180 3777450 5630110 FALSE TRUE 3590755.843 4402623.11 4058416.966 3990859.904 4304923.317 3853641.274 4145892.137 4249072.948 4690408.269 0.765552941 0.9386439 0.865258786 0.850855549 0.917814201 0.821600392 0.883908585 0.905906843 1 22.16128207 0.827241771 2.114808738 0.999803692 0.870629066 0.443464778 0.048112429 0.587579356 4.78405353 0.041327718 0.011353732 6.718027401 -0.827241771 -0.129174627 DSFPWEVPKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSFPWEVPKK 10 1 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ; 131.82 0.00038489 383300000 1392690 972700 1227800 1242050 1410380 994460 1794860 1210320 2093350 FALSE TRUE 1305524.019 1044719.72 1256923.996 1273923.106 1299614.444 1281544.458 1525737.406 1361431.116 1743956.361 0.748599018 0.599051526 0.720731335 0.730478775 0.745210415 0.734848925 0.874871321 0.780656642 1 20.73393251 1.14106139 0.325732283 1.029458458 0.641677153 0.766639879 0.050800676 0.649266474 0.222117684 0.09520514 0.061745281 13.83761967 -1.14106139 -0.387781306 DSGPPTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSGPPTKK 8 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 74.173 0.059065 0 407000 303790 380430 404480 430540 339920 485970 327500 462600 FALSE TRUE 381526.5965 326282.9277 389453.9793 414859.6416 396727.1251 438049.3859 413103.31 368389.0959 385389.0715 0.989977726 0.846632538 1.010547543 1.076469657 1.029419759 1.13664195 1.071912362 0.955888797 1 18.55595614 3.635338338 2.975054892 1.055267637 0.911785848 0.423913537 0.059172453 0.18802285 3.246430441 0.015320608 0.026130154 4318.553838 -3.635338338 -0.143481789 DSGREDEPGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSGREDEPGSPR 12 1 Q2TAM9 Q2TAM9 TUSC1 Tumor suppressor candidate gene 1 protein 1 DSGREDEPGS(1)PR;DSGREDEPGS(1)PR 122.96 0.00021152 418920000 785440 738360 760850 742530 756190 606340 863110 657570 727600 TRUE FALSE 736280.7125 793028.9427 778897.7213 761584.5769 696801.8877 781380.5149 733694.6682 739669.062 606158.8595 1.214666256 1.308285658 1.284972923 1.256410865 1.149536754 1.289068868 1.210399975 1.220256127 1 19.20933641 -4.620315806 0.206820355 9.38E-10 1.2887353 0.746469613 0.044834972 56.26409284 0.646111958 23.27052993 0.095056914 2.40E-05 4.620315806 1.288735299 DSGRLS(ph)PDLSVCGQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSGRLSPDLSVCGQPR 16 1 Q8TF76;Q8TF76-2 Q8TF76 GSG2 Serine/threonine-protein kinase haspin 1 DS(0.022)GRLS(0.978)PDLSVCGQPR 147.67 6.09E-07 122400000 102760 104270 100040 91430 101010 83564 109200 81660 124630 TRUE FALSE 96328.43503 111990.2593 102412.996 93776.24859 93077.08205 107687.5703 92826.47376 91855.43076 103828.4479 0.927765338 1.078608624 0.986367399 0.903184537 0.896450674 1.037168257 0.894036997 0.884684618 1 16.66384225 3.435802028 5.049725345 0.933603248 1.018411457 0.179195317 0.060801728 0.227168695 13.45873839 0.015787279 0.022132655 2727.734066 -3.435802028 0.084808209 DSGS(ph)ISLQETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSGSISLQETR 11 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 DS(0.001)GS(0.993)IS(0.006)LQETR 121.24 0.00043611 121930000 122080 147420 115210 126840 138550 88565 132960 106270 176830 TRUE FALSE 114439.2307 158335.1302 117942.8356 130094.9291 127668.8419 114132.2778 113023.8823 119538.0434 147315.9306 0.776828617 1.074799782 0.80061155 0.883101567 0.866632966 0.77474498 0.767221046 0.811440032 1 17.16855393 3.739319819 21.83670545 0.828506212 0.944280371 0.087753498 0.098112944 114.6922382 205304.4313 0.022913925 0.040782044 5486.808704 -3.739319819 0.115774159 DSGS(ph)QEVLSELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSGSQEVLSELR 12 0 Q9BVJ6-3;Q9BVJ6;Q9BVJ6-2;X6RJY0 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 1 DS(0.002)GS(0.998)QEVLSELR;DSGS(1)QEVLSELR 162.7 6.45E-05 116634000 126584 110286 118681 112299 121219 111963 135000 108810 136601 TRUE FALSE 118661.3334 118451.6902 121496.1694 115180.7825 111698.9487 144284.9005 114758.0033 122395.168 113801.4106 1.042705295 1.04086311 1.067615671 1.012120868 0.981525168 1.267865659 1.008405807 1.075515386 1 16.79615892 DSGSDGHSVSSRDS(ph)AAPS(ph)PIPGADNLSADPVVSPPTSIPFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSGSDGHSVSSRDSAAPSPIPGADNLSADPVVSPPTSIPFK 41 1 Q5T1M5;Q5T1M5-2;Q5T1M5-3 Q5T1M5 FKBP15 FK506-binding protein 15 2 DS(0.027)GS(0.031)DGHS(0.193)VS(0.225)S(0.244)RDS(0.307)AAPS(0.951)PIPGADNLS(0.022)ADPVVSPPTSIPFK;DS(0.013)GS(0.015)DGHS(0.087)VS(0.11)S(0.118)RDS(0.669)AAPS(0.963)PIPGADNLS(0.025)ADPVVSPPTSIPFK 93.589 0.00023059 236030000 18712.4 25173 22248.5 20253.1 24696 15885.3 30852 18972.3 28084 TRUE FALSE 17541.22429 27036.83511 22776.24493 20772.82883 22756.47578 20471.12823 26226.02902 21341.03342 23396.59897 0.749733938 1.155588261 0.97348529 0.887856772 0.972640332 0.87496171 1.120933391 0.912142549 1 14.51401121 1.744233838 25 1.021805347 0.965019063 0.046726109 0.115077843 3.912094455 17302.29026 0.051447755 0.0285306 55.49244217 -1.744233838 -0.056786284 DSGSDTASAIIPSTTPS(ph)VDSDDESVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSGSDTASAIIPSTTPSVDSDDESVVK 27 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 DSGSDTASAIIPSTT(0.002)PS(0.523)VDS(0.432)DDES(0.043)VVK 148.28 7.10E-14 0 400950 216110 281060 238920 256090 182860 319830 223640 251700 TRUE FALSE 375855.2552 232111.0093 287726.8759 245051.0917 235977.7244 235648.7135 271874.4607 251561.9463 209689.644 1.792435945 1.106926431 1.37215587 1.168637073 1.125366613 1.123797576 1.296556451 1.199687031 1 17.67789609 4.743948653 24.88331894 1.19796449 1.792436214 0.771720873 0.104973622 255.0040989 1177635.207 0.023462488 0.202369262 55456.01435 -4.743948653 0.594471724 DSGSDTASAIIPSTTPSVDS(ph)DDESVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSGSDTASAIIPSTTPSVDSDDESVVK 27 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 DSGSDTASAIIPSTTPS(0.018)VDS(0.967)DDES(0.015)VVK 179.5 1.24E-17 179240000 586530 358960 428430 390970 379510 289280 512330 376790 345560 TRUE FALSE 549820.1343 385537.7719 438592.5619 401002.9521 349704.8155 372790.4399 435510.8727 423833.0609 287883.8036 1.909868243 1.339213138 1.523505513 1.392933354 1.214742931 1.294933703 1.512800885 1.472236561 1 18.1351271 7.999992195 0.034380878 6.42E-08 3.580735287 0.462935399 0.173055067 1137.027661 2.988208272 92.78900846 256.1877787 99998202.77 -7.999992195 3.580735223 DSGSDTASAIIPSTTPSVDS(ph)DDESVVKDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSGSDTASAIIPSTTPSVDSDDESVVKDK 29 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 DSGSDTASAIIPS(0.005)T(0.005)T(0.005)PS(0.041)VDS(0.902)DDES(0.041)VVKDK;DSGSDTASAIIPSTTPSVDS(0.998)DDES(0.002)VVKDK 177.99 7.80E-18 861700000 753716 320737 450761 479379 463053 294446 622355 374807 547048 TRUE FALSE 706542.261 344484.7012 461453.2638 491680.6767 426686.6852 379447.7803 529038.6454 421602.479 455742.1547 1.550311407 0.755876317 1.012531448 1.078857138 0.936245815 0.832593115 1.160828859 0.925089932 1 18.7978583 4.75165316 24.85653432 0.965337638 1.550311814 0.721392633 0.114743013 1129.840335 2144990.262 0.027472633 0.51936305 56448.59802 -4.75165316 0.584974175 DSGSS(ph)SPLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSGSSSPLPK 10 0 Q86VQ1;H7C0B2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 DSGS(0.002)S(0.689)S(0.308)PLPK 105.2 0.0037332 0 489080 303230 373700 368490 393000 281820 485320 327060 506240 TRUE FALSE 458469.3558 325681.4647 382564.3405 377946.0773 362135.3653 363176.859 412550.7715 367894.1609 421745.2736 1.087076452 0.772223153 0.90709811 0.896147748 0.858658977 0.861128463 0.978198921 0.872313655 1 18.68601237 0.649609676 0.645749434 0.999532431 0.884833699 0.0768073 0.084452546 2.555542126 2.038481724 0.085355359 0.030927669 4.462823142 -0.649609676 -0.114698732 DSGSSS(ph)PLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSGSSSPLPK 10 0 Q86VQ1;H7C0B2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 DSGSS(0.079)S(0.921)PLPK 175.97 2.77E-06 174330000 666140 419090 532980 492570 531580 401610 610690 449960 710020 TRUE FALSE 624447.4865 450119.8597 545622.5373 505210.1801 489831.8511 517548.2874 519122.7039 506138.4965 591513.0751 1.055678248 0.7609635 0.922418388 0.854098077 0.828099786 0.874956631 0.877618308 0.85566747 1 19.17405053 -1.100217474 4.476661852 1.000010586 0.870203485 0.195745978 0.075558389 7.94E-06 1.60E-06 0.063329962 0.014925616 0.079393057 1.100217474 -0.1298071 DSHGVAQVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DSHGVAQVR 9 0 P62277;J3KMX5;E9PS50 P62277 RPS13 40S ribosomal protein S13 0 ;;;;;; 213.85 1.21E-06 13716300000 2946323 3664290 3292804 3178287 3901024 2581678 3304073 3283259 3619872 FALSE TRUE 2761917.903 3935597.844 3370910.866 3259847.225 3594653.311 3326966.529 2808657.927 3693181.113 3015691.978 0.915848808 1.30503973 1.117790176 1.0809616 1.191982914 1.103218284 0.931347746 1.22465462 1 21.52405765 1.991618007 23.40969652 1.037600315 1.144980108 0.044111878 0.121499824 315.8652683 882167.076 0.043640445 0.030658055 98.08848044 -1.991618007 0.107379793 DSHS(ph)PDLQLPTPEVIPSSGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSHSPDLQLPTPEVIPSSGSK 21 0 H3BQK9;H3BPE1;H0Y4F5;H0Y6T5 H3BQK9 MACF1 1 DS(0.148)HS(0.852)PDLQLPTPEVIPSSGSK;DS(0.321)HS(0.679)PDLQLPTPEVIPSSGSK 161.2 1.30E-11 243170000 498900 392920 406340 374250 446300 374380 611210 514870 516530 TRUE FALSE 467674.7396 422012.2056 415978.5767 383853.8886 411249.3983 482457.4284 519564.7347 579152.6529 430317.8061 1.086812428 0.980698915 0.966677583 0.892024181 0.955687616 1.121165384 1.207397712 1.345871922 1 18.71504301 2.076842858 3.286733638 1.201702058 0.97177194 0.504732372 0.09545414 0.172320329 3.698542681 0.038347732 0.025182811 119.355616 -2.076842858 -0.229930118 DSIEKEHVEEISELFYDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSIEKEHVEEISELFYDAK 19 1 Q9Y265;H7C4G5 Q9Y265 RUVBL1 RuvB-like 1 0 49.224 0.092198 19917000 20346 21948 18805 21603 31115 12555 25877 15620 61953 FALSE TRUE 19072.58018 23573.05276 19251.06348 22157.36955 28671.35341 16179.42469 21996.98408 17570.19138 51612.64407 0.369533096 0.45673019 0.372991228 0.429301191 0.555510262 0.313477927 0.426193707 0.340424167 1 15.65543692 -1.659720866 3.007983918 1.055768641 0.411171171 0.88315047 0.067662823 36670188.82 37379916.45 15797937.5 0.014527865 0.021891682 1.659720866 -0.64459747 DSIKLDDDSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSIKLDDDSER 11 1 Q86VP6;Q86VP6-2;F5H6I6 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 191.53 1.63E-06 1114810000 2675700 2069070 2341700 2357100 2669900 1694880 3126600 2108670 3833200 FALSE TRUE 2508232.713 2222266.096 2397246.23 2417587.177 2460216.824 2184164.342 2657795.356 2371942.091 3193414.157 0.785439217 0.69589035 0.750684412 0.757054068 0.770403306 0.683958996 0.832273932 0.742760561 1 21.60666824 -3.107842052 0.287935559 1.560752302 0.730785199 0.774205929 0.042003922 29.71482887 0.757593959 10.05562014 0.041839628 0.000780114 3.107842052 -0.829967103 DSITPDIATKPGQPLFLDSIS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSITPDIATKPGQPLFLDSISPK 23 1 Q2TB10 Q2TB10 ZNF800 Zinc finger protein 800 1 DSITPDIATKPGQPLFLDS(0.013)IS(0.987)PK;DSITPDIATKPGQPLFLDSIS(1)PK 201.6 1.35E-24 378930000 1749200 652500 1044060 808510 992930 686760 1230660 703100 1135420 TRUE FALSE 1639720.694 700811.7789 1068825.596 829257.7354 914949.2831 885016.4634 1046133.958 790883.5827 945911.0669 1.733482937 0.740885484 1.129943008 0.876676217 0.967267764 0.935623331 1.10595382 0.836107759 1 19.85134502 4.748720025 24.99706534 0.960624579 1.733483361 0.816299512 0.116831326 575.8786422 1416912.208 0.025929277 0.359779739 56068.64038 -4.748720025 0.772858782 DSIVAELDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DSIVAELDR 9 0 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 0 ;; 155.07 0.00017261 1025240000 1214250 1357360 1282120 1329730 1422190 1048380 1416210 1207020 1235510 FALSE TRUE 1138252.26 1457860.347 1312532.492 1363853.123 1310496.934 1351030.287 1203862.458 1357719.104 1029295.399 1.105855774 1.416367301 1.27517571 1.325035674 1.273198088 1.312577796 1.1695986 1.319076239 1 19.97322565 -0.835828654 0.384843809 0.892696581 1.30455205 0.475224909 0.087928809 9.59097825 1.128702425 1.269432508 0.055920577 0.145938993 0.835828654 0.411855469 DSIVAELDREMSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSIVAELDREMSR 13 1 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 0 102.52 0.0015349 22399000 7794.9 21370 17532 20783 34618 17517 14355 12882 53803 FALSE TRUE 7307.031123 22952.25704 17947.86732 21316.32697 31899.24192 22573.87354 12202.60102 14490.34606 44822.93172 0.163019928 0.512065056 0.400417077 0.475567442 0.711672367 0.503623317 0.272240136 0.323279748 1 15.45194939 -1.263026914 3.437137781 1.001613946 0.429066021 0.596289239 0.149763793 52031312.86 76386534.9 905597.99 0.034967933 0.054572404 1.263026914 -0.572547926 DSKPS(ph)STPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSKPSSTPR 9 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 DS(0.006)KPS(0.331)S(0.331)T(0.331)PR 123.2 0.0014849 280130000 831700 531910 691690 590190 609970 538520 777650 549150 856910 TRUE FALSE 779645.3816 571293.1699 708097.2134 605335.2746 562065.4167 693981.9819 661048.6018 617712.5863 713886.1851 1.092114398 0.800258055 0.991890904 0.847943674 0.78733197 0.97211852 0.925985984 0.865281608 1 19.44533456 DSKPSS(ph)TPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DSKPSSTPR 9 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 DSKPS(0.057)S(0.471)T(0.471)PR;DS(0.034)KPS(0.106)S(0.532)T(0.329)PR;DS(0.006)KPS(0.103)S(0.445)T(0.445)PR 142.19 0.00027599 1568844000 2812730 1752120 2426520 2097150 2066980 1792350 2703870 1886120 2946800 TRUE FALSE 2636686.25 1881848.788 2484078.2 2150966.419 1904647.729 2309772.349 2298449.795 2121606.234 2454960.043 1.0740241 0.766549661 1.01186095 0.876171661 0.775836549 0.940859447 0.936247334 0.864212124 1 21.22726811 -1.53538258 4.713589494 1.000631923 0.90212314 0.088113667 0.094690422 0.00056665 5.59E-05 0.082619576 0.019349597 0.029148581 1.53538258 -0.098508784 DSKPSST(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DSKPSSTPR 9 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 DS(0.004)KPS(0.046)S(0.232)T(0.719)PR;DS(0.003)KPS(0.046)S(0.161)T(0.79)PR;DS(0.001)KPS(0.022)S(0.133)T(0.844)PR 75.479 0.06167 36199000000 35022100 21937400 29507800 23917800 24190400 21530400 31815500 21807500 34077600 TRUE FALSE 32830129.28 23561667.92 30207738.95 24531571.24 22290583.56 27745876.96 27045061.14 24530214.38 28389828.41 1.156404639 0.829933439 1.064033869 0.8640972 0.785160912 0.977317529 0.952632075 0.864049406 1 24.75887079 4.753274942 24.65395781 0.922366365 1.156404839 0.441085863 0.084457523 2182.648319 3656967.289 0.019277445 0.433165706 56659.78761 -4.753274942 0.234038474 DSKPSSTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 DSKPSSTPR 9 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 0 ;;;;;;;;;; 128.91 0.00036865 62426170000 10546371 9794362 9569271 9070444 9769849 7047749 10826140 9005770 10348700 FALSE TRUE 9886292.465 10519546.75 9796258.627 9303206.949 9002564.469 9082319.726 9202860.812 10130160.21 8621435.115 1.146710766 1.220161912 1.136267744 1.079078695 1.044207182 1.053457992 1.067439549 1.174996978 1 23.03949661 3.42792533 2.333248334 1.069616422 1.185902256 0.512465426 0.046713031 0.207545942 2.271347592 0.012819955 0.019837149 2678.707723 -3.42792533 0.116285835 DSLDPSFTHAMQLLTAEIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSLDPSFTHAMQLLTAEIEK 20 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ; 257.22 3.26E-36 774840000 1646840 1326720 1584940 1548060 1556560 1333430 1965680 1377870 1551710 FALSE TRUE 1543767.224 1424951.729 1622535.525 1587785.84 1434314.056 1718369.595 1670944.532 1549900.103 1292719.577 1.194201165 1.102289897 1.255133406 1.228252337 1.109532247 1.329267094 1.292580822 1.198945333 1 20.30197792 3.958124266 7.681617082 1.222898314 1.146218993 0.016383205 0.096942567 0.360067031 108.5684587 0.022823015 0.042960084 9080.803245 -3.958124266 -0.076679321 DSLEEGELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSLEEGELR 9 0 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;A0A087X1I0;A0A087WYI9;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;J3KS35;E7ESP2;E9PFJ2 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 0 ; 102.51 0.0083106 124456000 346470 280650 326450 302110 326150 256890 360090 292600 343570 FALSE TRUE 324785.0612 301429.618 334193.5482 309862.6541 300535.4946 331049.9727 306097.8474 329131.7541 286225.9475 1.134715647 1.053117723 1.167586486 1.082580587 1.049993885 1.15660364 1.069427318 1.149901877 1 18.12679494 -1.154215988 4.126709387 0.999965912 1.105415065 0.378334829 0.043392532 0.229205798 10659727.78 707.659902 0.009072481 0.070110653 1.154215988 0.105449153 DSLGDFIEHYAQLGPS(ph)SPEQLAAGAEEGGGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR 32 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 DSLGDFIEHYAQLGPS(0.5)S(0.5)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.5)S(0.5)PEQLAAGAEEGGGPR 146.03 2.91E-10 448491000 103907 97964 114796 112225 115802 94613 113014 97646 110574 TRUE FALSE 97403.64635 105217.3565 117519.0153 115104.8835 106707.378 121926.2372 96068.59987 109837.318 92118.48506 1.057373515 1.142195906 1.275737603 1.249530791 1.158370961 1.323580572 1.042880805 1.192348289 1 16.49120307 0.806714748 0.938398345 1.004415988 1.196546785 0.280959631 0.089107485 0.998206902 1.713948699 0.080465483 0.026856988 6.407885576 -0.806714748 0.192130796 DSLGDFIEHYAQLGPS(ph)SPEQLAAGAEEGGGPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPRR 33 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 DSLGDFIEHYAQLGPS(0.5)S(0.5)PEQLAAGAEEGGGPRR;DSLGDFIEHYAQLGPS(0.58)S(0.42)PEQLAAGAEEGGGPRR;DSLGDFIEHYAQLGPS(0.861)S(0.139)PEQLAAGAEEGGGPRR 215.43 3.16E-36 520752000 353427 413073 396305 391086 395095 307518 454478 382510 402927 TRUE FALSE 331306.635 443657.3547 405705.5417 401121.9289 364065.8324 396293.4545 386333.2431 430267.2155 335675.8807 0.986983736 1.321683744 1.208622856 1.194967979 1.084575489 1.180583644 1.150911535 1.281793659 1 18.35670935 2.978483607 23.5916381 1.151064531 1.208609944 0 0.109090509 1115.396768 1222978.504 0.030457508 0.032633678 951.6639264 -2.978483607 0.057545412 DSLGDFIEHYAQLGPSS(ph)PEQLAAGAEEGGGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR 32 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 DSLGDFIEHYAQLGPS(0.088)S(0.912)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.218)S(0.782)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.354)S(0.646)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.176)S(0.824)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.034)S(0.966)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.197)S(0.803)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.035)S(0.965)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.189)S(0.811)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.184)S(0.816)PEQLAAGAEEGGGPR 354.57 5.76E-132 13106126000 816630.8 724900.3 828606 822037.9 860879 715307.3 929879 747661 859105 TRUE FALSE 765519.336 778572.6725 848260.9256 843132.7842 793269.036 921804.9055 790452.2765 841008.1217 715714.8255 1.069587088 1.087825269 1.185194012 1.17802895 1.108359095 1.287949994 1.104423506 1.175060362 1 19.44902534 4.201042826 2.923309799 1.157730748 1.073755665 0.126713741 0.07351984 0.422494052 7.17388595 0.01642576 0.048304012 15887.03403 -4.201042826 -0.083975083 DSLGDFIEHYAQLGPSS(ph)PEQLAAGAEEGGGPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPRR 33 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 DSLGDFIEHYAQLGPS(0.368)S(0.632)PEQLAAGAEEGGGPRR;DSLGDFIEHYAQLGPS(0.198)S(0.802)PEQLAAGAEEGGGPRR 292.23 9.68E-90 440400000 343609 457750 392241 419553 514204 353679 508587 364555 775024 TRUE FALSE 322103.126 491642.2863 401545.1417 430319.4403 473820.492 455780.3858 432329.1008 410070.4942 645667.4876 0.49886843 0.761448107 0.621907018 0.666472215 0.733845983 0.70590574 0.669584746 0.635110954 1 19.30043186 -2.142851152 2.338388451 1.709638645 0.671184265 0.683773432 0.072054514 3943557.587 1013200.864 14835344.73 0.015736438 0.007196956 2.142851152 -1.03845438 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR 32 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 0 ;;; 208.34 3.34E-27 595870000 234083 257633 262054 259720 271110 235101 295093 240997 302350 FALSE TRUE 219432.1629 276708.4154 268270.0446 266384.8549 249818.1142 302970.8422 250846.5442 271086.0059 251885.8317 0.871157228 1.098546963 1.065046187 1.057561885 0.991791053 1.202810178 0.995873974 1.076225701 1 17.94241045 4.744746756 24.82761568 1.064678043 0.871157133 0.479560057 0.062040739 506.777006 2033851.255 0.013014286 0.120593585 55558.01957 -4.744746756 -0.19352091 DSLHEKFPDAGEDELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSLHEKFPDAGEDELLK 17 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 62.966 0.034583 204250000 807970 608700 742780 695500 758060 584200 955720 647030 952800 FALSE TRUE 757400.6 653768.7814 760399.0924 713347.7075 698525.0255 752849.0563 812418.6585 727813.1198 793771.5247 0.954179605 0.823623374 0.957957131 0.898681403 0.880007664 0.948445532 1.023491815 0.91690505 1 19.59836428 2.03803525 5.347827488 0.983709123 0.89993862 0.374903482 0.045792617 0.16810245 12.05558538 0.016822125 0.011931356 109.1528927 -2.03803525 -0.083770503 DSLIIIDELGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DSLIIIDELGR 11 0 A0A2R8YFH0;E9PHA6;A0A2R8Y6P0;A0A2R8YG02;P43246;P43246-2;A0A2R8Y713 A0A2R8YFH0 MSH2 DNA mismatch repair protein Msh2 0 ;;;;; 188.04 7.73E-06 108060500 234011 260716 260529 269706 274855 230958 288196 235315 255644 FALSE TRUE 219364.6692 280019.6839 266708.8709 276627.1126 253268.997 297631.8253 244983.6853 264694.5957 212975.3649 1.030000204 1.31479847 1.252299162 1.298869063 1.189193864 1.397494144 1.150291187 1.242841377 1 17.70032704 0.330873945 1.055951396 0.999510714 1.250154355 0.34470679 0.100012625 3.026406017 3.891070443 0.088021602 0.026450226 2.142268712 -0.330873945 0.250643641 DSLITPHVS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSLITPHVSR 10 0 P49792;J3KNE0;A6NKT7;Q7Z3J3;O14715;Q99666;J3KQ37;H7BZ48;F8VYC4;A0A286YES2;P0DJD0;A0A1W2PNU4;P0DJD1 P49792;F8VYC4 RANBP2;RGPD3;RGPD4;RGPD8;RGPD5;RGPD6;RGPD1;RGPD2 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6;RANBP2-like and GRIP domain-containing protein 1;RANBP2-like and GRIP domain-containing protein 2 1 DSLITPHVS(1)R;DSLITPHVS(1)R 130.1 0.00018397 351730000 587270 561150 638470 571340 557780 600480 732680 554230 502370 TRUE FALSE 550513.819 602698.1299 653614.8099 586001.5517 513974.2088 773828.828 622821.4359 623426.8355 418521.2016 1.315378569 1.440065946 1.56172449 1.400171722 1.228072095 1.848959683 1.488147873 1.489594394 1 18.67494118 DSLLDGHFVLATLSDTDS(ph)HSQDLGS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSLLDGHFVLATLSDTDSHSQDLGSPER 28 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 2 DSLLDGHFVLATLS(0.001)DT(0.023)DS(0.781)HS(0.195)QDLGS(1)PER 115.13 0.00019745 39255000 27816 24705 31952 27226 34939 28645 37127 26035 25173 TRUE FALSE 26075.04621 26534.18391 32709.91653 27924.66525 32195.03188 36914.34649 31560.15102 29285.52706 20971.46368 1.243358433 1.265251883 1.559734553 1.331555379 1.535182874 1.760217935 1.504909314 1.3964465 1 14.35613994 4.145286584 3.132302742 1.482507517 1.247364841 0.10785329 0.197109642 0.391364972 7.451162706 0.045879597 0.121410409 13972.90106 -4.145286584 -0.235142676 DSLLDGHFVLATLSDTDSHS(ph)QDLGS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSLLDGHFVLATLSDTDSHSQDLGSPER 28 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 2 DSLLDGHFVLATLSDT(0.006)DS(0.192)HS(0.802)QDLGS(1)PER;DSLLDGHFVLAT(0.407)LS(0.227)DT(0.218)DS(0.265)HS(0.287)QDLGS(0.596)PER 140.34 6.33E-08 51710000 69421 64490 71985 63531 70302 58915 79548 64230 61626 TRUE FALSE 65076.06353 69264.9067 73692.51819 65161.31302 64780.7645 75922.80409 67620.51589 72249.25689 51340.22248 1.267545413 1.349135305 1.435375903 1.269205895 1.261793607 1.478817201 1.317106016 1.407264196 1 15.64780193 -1.052564001 4.719844042 0.999988044 1.354284849 0.684272503 0.074249166 8.69E-06 1.74E-06 0.066888435 0.015765224 0.088600465 1.052564001 0.354296806 DSLLDGHFVLATLSDTDSHS(ph)QDLGSPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSLLDGHFVLATLSDTDSHSQDLGSPER 28 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 1 DSLLDGHFVLAT(0.019)LS(0.016)DT(0.016)DS(0.067)HS(0.851)QDLGS(0.032)PER;DSLLDGHFVLATLSDTDS(0.029)HS(0.966)QDLGS(0.005)PER 244.44 3.06E-45 831490000 98028 100447 102954 101784 108504 85675 116368 96992 93708 TRUE FALSE 91892.60246 107884.2004 105396.1175 104395.9498 99982.53352 110407.9817 98919.69871 109101.6647 78067.52942 1.177091207 1.381934348 1.350063442 1.337251871 1.280718556 1.41426253 1.267104255 1.397529364 1 16.25243499 -1.12130188 4.551674101 0.999966852 1.331138471 0.678088183 0.070447946 4334646.658 1068579.771 1434.24486 0.014396868 0.0756307 1.12130188 0.331171619 DSLLDGHFVLATLSDTDSHSQDLGS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 DSLLDGHFVLATLSDTDSHSQDLGSPER 28 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 1 DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLAT(0.001)LS(0.004)DT(0.014)DS(0.047)HS(0.053)QDLGS(0.881)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDT(0.001)DS(0.044)HS(0.311)QDLGS(0.645)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER 284.73 8.13E-62 1574358000 1058358 1055355 1077448 1072497 1153487 924566 1242639 1021344 1041231 TRUE FALSE 992117.262 1133494.582 1103005.575 1100019.089 1062896.784 1191473.195 1056316.818 1148861.047 867442.8195 1.14372641 1.306708127 1.271559981 1.268117119 1.225322016 1.373546669 1.21773654 1.324422799 1 19.72640914 -1.342802463 4.678203004 0.999772417 1.270175661 0.63804047 0.062999309 0.000128607 1.81E-05 0.052459957 0.012354599 0.045414814 1.342802463 0.270403245 DSLLQDGEFSMDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 22 DSLLQDGEFSMDLR 14 0 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 ;;;;;;;;;;;;;;;;;;;;; 369.05 1.06E-96 13503925000 6889909.9 7990733.8 7442004.6 7460955.3 8142666.5 6665529.3 7965536.8 6690855.6 7723425.6 FALSE TRUE 6458682.738 8582376.045 7618532.463 7652416.044 7503174.319 8589759.403 6771178.505 7526223.65 6434335.972 1.003783882 1.33384021 1.18404331 1.189309367 1.166114787 1.334987704 1.052350784 1.169697026 1 22.61735984 1.027227088 0.982137835 1.006650706 1.209928656 0.224016907 0.103397874 0.696131652 1.44235585 0.087940352 0.029571559 10.64699593 -1.027227088 0.203277951 DSLPLPVRSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSLPLPVRSR 10 1 A0A0A0MSK4;A0A0A0MRC4;Q86YR5-4;Q86YR5 A0A0A0MSK4 GPSM1 G-protein-signaling modulator 1 0 ; 71.614 0.046017 373610000 132951 132951 136948 136052 151075 124401 139900 124352 177557 FALSE TRUE 124629.8342 142794.8304 140196.4712 139543.3247 139210.1789 160313.5492 118923.2938 139877.6209 147921.5896 0.842539852 0.965341373 0.947775586 0.943360094 0.941107916 1.08377384 0.803961707 0.94562005 1 17.17447311 4.745117191 24.00199646 0.946672478 0.842539769 0.200040277 0.068637342 757.9621262 2774577.037 0.015484731 0.146277885 55605.42846 -4.745117191 -0.104132708 DSLRDESQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSLRDESQR 9 1 Q96MW1;Q86WV7 Q96MW1 CCDC43 Coiled-coil domain-containing protein 43 0 ; 130.79 0.00032044 674050000 305500 1063220 934040 973800 1167370 2101130 508650 799080 597080 FALSE TRUE 286379.3003 1141941.915 956195.8699 998789.3566 1075689.469 2707692.122 432382.6546 898846.897 497423.4907 0.575725324 2.295713685 1.922297374 2.007925591 2.162522457 5.443434362 0.869244542 1.807005326 1 18.92411511 4.739673736 22.81841415 2.246807732 0.575723609 0.139999418 1.24881835 54.15015688 1109513.689 0.276474598 1.692349347 54912.81858 -4.739673736 -1.671084122 DSLS(ph)PVLHPSDLILTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DSLSPVLHPSDLILTR 16 0 Q9HCN4-3;Q9HCN4-2;Q9HCN4-4;Q9HCN4;Q9HCN4-5 Q9HCN4-3 GPN1 GPN-loop GTPase 1 1 DS(0.114)LS(0.886)PVLHPSDLILTR;DS(0.032)LS(0.968)PVLHPSDLILTR;DS(0.001)LS(0.999)PVLHPSDLILTR;DS(0.027)LS(0.973)PVLHPSDLILTR;DS(0.022)LS(0.978)PVLHPSDLILTR 208.47 9.51E-12 968343000 769914 1277200 1256430 1510720 1394380 820137 1070395 831131 992611 TRUE FALSE 721726.4571 1371765.217 1286233.113 1549487.633 1284871.019 1056897.238 909899.2068 934899.5349 826937.8116 0.872769931 1.658849309 1.555416979 1.87376561 1.553769826 1.278085514 1.100323621 1.130556037 1 19.65741931 2.034906525 2.750249629 1.092684587 1.54819826 0.360860967 0.255268315 0.27378139 4.017148418 0.118439023 0.070290441 108.369364 -2.034906525 0.455513673 DSLSPGQERPYSTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSLSPGQERPYSTVR 15 1 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 0 ; 110.97 0.00080181 260170000 152967 139645 133373 133004 145929 110051 170486 140806 167807 FALSE TRUE 143393.0685 149984.4611 136536.6705 136417.1078 134468.325 141820.9372 144923.207 158385.9391 139798.9276 1.02570936 1.072858452 0.976664649 0.975809401 0.961869503 1.014463699 1.03665464 1.132955322 1 17.09299377 1.542474103 4.122370706 1.071440144 1.00691255 0.244080023 0.044400332 0.233986356 8.819187901 0.027125437 0.011386128 34.87177898 -1.542474103 -0.064527594 DSLYAQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSLYAQGK 8 0 H0Y5B4;H7BZ11;J3KQN4;P83881;H7BY91;H0Y3V9 H0Y5B4 RPL36A;RPL36A-HNRNPH2 60S ribosomal protein L36a 0 ; 130.27 0.0024544 179823000 233932 248290 225808 220544 284420 171787 238525 244301 289210 FALSE TRUE 219290.6137 266673.6499 231164.2724 226203.5324 262082.8005 221379.1182 202760.3906 274802.5176 240938.9826 0.910149994 1.106809894 0.959430765 0.938841569 1.087755902 0.918818183 0.841542487 1.140548178 1 17.87830831 2.189899002 24.99999593 0.947570847 1.006661121 0 0.09707305 305.7070941 157055.7167 0.034469012 0.025457121 154.8456472 -2.189899002 0.059090275 DSMTVSEVTASISSPS(ph)EEDASEMPEFLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSMTVSEVTASISSPSEEDASEMPEFLDK 29 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 DSMTVSEVTASISS(0.009)PS(0.78)EEDAS(0.21)EMPEFLDK 117.82 7.54E-05 22463000 56991 49915 47269 53970 46624 38197 65708 43431 53459 TRUE FALSE 53424.03504 53610.75854 48390.243 55354.96157 42962.33911 49223.85382 55855.6954 48853.45595 44536.34754 1.199560314 1.203752923 1.086533712 1.242916508 0.964657891 1.105251251 1.25415977 1.096934496 1 15.44269563 -2.468422762 1.317794151 0.386269724 1.148141599 0.212954342 0.086846579 122051.4665 9965.804074 220702.3295 0.023630324 0.00340077 2.468422762 0.761871875 DSNELS(ph)DS(ph)AGEEDSADLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSNELSDSAGEEDSADLKR 19 1 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 2 DS(0.001)NELS(0.999)DS(1)AGEEDSADLKR 110.68 0.00080833 131810000 386210 214140 265640 263570 283000 193950 317810 216710 388080 TRUE FALSE 362037.8055 229995.1484 271941.1062 270333.6524 260774.3216 249940.2165 270157.3409 243766.7205 323306.9409 1.119795958 0.711383269 0.841123625 0.836151713 0.806584359 0.773074082 0.835606375 0.753979237 1 18.30254495 -1.340119241 2.973970424 1.001940316 0.821721657 0.173851498 0.110042951 29498820.59 36904197.92 501591.8658 0.024154839 0.045696271 1.340119241 -0.180218659 DSNNLCLHFNPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DSNNLCLHFNPR 12 0 P09382 P09382 LGALS1 Galectin-1 0 ;;;;; 217.09 3.75E-11 5334110000 3683970 5616900 3618450 3925050 5426170 2670850 3927140 4249570 3542700 FALSE TRUE 3453396.894 6032781.12 3704281.343 4025773.428 5000020.496 3441881.037 3338301.815 4780138.169 2951400.483 1.170087527 2.044040161 1.255092748 1.364021403 1.694117936 1.1661857 1.13109076 1.619616923 1 21.49296827 1.99854038 0.224726744 0.946558992 1.759406544 0.155766592 0.292000189 3.797491331 0.736923361 0.849123209 1.190919627 99.66447414 -1.99854038 0.812847552 DSPAFPDS(ph)PWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DSPAFPDSPWR 11 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 DSPAFPDS(1)PWR;DSPAFPDS(1)PWR;DSPAFPDS(1)PWR 197.38 6.01E-08 234100000 443270 403640 461740 423090 440940 372200 510540 396710 428200 TRUE FALSE 415526.522 433525.9256 472692.6908 433947.2057 406310.3511 479648.0978 433989.2666 446240.1168 356730.6537 1.16481866 1.215275225 1.325068889 1.216456173 1.138983563 1.344566532 1.216574079 1.250916096 1 18.44447567 -1.381705017 4.48122615 0.999592497 1.240353742 0.574128531 0.063153679 0.000241166 3.33E-05 0.057354988 0.013496061 0.041523598 1.381705017 0.240761246 DSPCQLEALKLESCGVTSDNCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSPCQLEALKLESCGVTSDNCR 22 1 P13489 P13489 RNH1 Ribonuclease inhibitor 0 ; 211.17 3.29E-23 860120000 313040 329490 326550 368710 487920 253470 467660 330370 818580 FALSE TRUE 293447.3852 353885.7824 334295.9202 378171.7228 449600.7314 326642.6743 397538.7245 371617.4217 681953.7098 0.430303965 0.518929331 0.490203243 0.554541632 0.659283357 0.478980713 0.582940922 0.544930567 1 19.37931429 -5 0.249879212 3.84024125 0.489692224 0.870521716 0.057372765 58.01444913 0.57537963 84.1160222 0.07745414 1.00E-05 5 -3.350549025 DSPFYQHYDLDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DSPFYQHYDLDLK 13 0 O75582-3;O75582;O75582-2 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 0 ;; 162.41 4.05E-05 367420000 1206610 996260 1113380 1098690 1211690 832050 1431980 1016210 1443010 FALSE TRUE 1131090.434 1070024.127 1139789.899 1126884.245 1116528.755 1072249.328 1217267.893 1143086.055 1202162.309 0.940879967 0.890082911 0.948116482 0.937381115 0.928767062 0.891933909 1.012565345 0.950858338 1 20.19720026 1.733898682 13.10562399 0.985808866 0.922781678 0.610159668 0.024451131 0.050756739 57.83309352 0.010571887 0.005808095 54.18744599 -1.733898682 -0.063027189 DSPNVEAAHLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSPNVEAAHLAR 12 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 ; 142.85 6.17E-05 492510000 778040 832470 899120 870090 880120 727330 908560 722120 885620 FALSE TRUE 729343.8652 894106.945 920447.551 892417.9825 810998.9254 937298.3638 772329.8627 812278.2716 737804.3007 0.988532955 1.211848378 1.247549723 1.209559204 1.099206015 1.270388859 1.046795013 1.100940007 1 19.49287867 1.644417208 8.295620295 1.054925184 1.183075986 0.310890769 0.084012855 0.128839139 17.18437313 0.039235517 0.020316213 44.09782888 -1.644417208 0.128150802 DSPQTIPTYTDALHVYSTVEGYIAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSPQTIPTYTDALHVYSTVEGYIAYR 26 0 P31944 P31944 CASP14 "Caspase-14;Caspase-14 subunit p17, mature form;Caspase-14 subunit p10, mature form;Caspase-14 subunit p20, intermediate form;Caspase-14 subunit p8, intermediate form" 0 91.416 2.18E-06 0 11775 14866 15133 15815 17317 15951 15321 12502 9358.5 FALSE TRUE 11038.02377 15966.69411 15491.96191 16220.83967 15956.99267 20555.79476 13023.75828 14062.90222 7796.505892 1.415765462 2.047929461 1.987039082 2.080526828 2.04668513 2.636539373 1.670460904 1.803744192 1 12.92861199 0.783505214 1.528591705 1.005798063 2.021952682 0.502496959 0.307782099 0.582841625 2.387200219 0.269504719 0.078336267 6.07442555 -0.783505214 1.01615462 DSPSVWAAVPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DSPSVWAAVPGK 12 0 P07737;CON__P02584;I3L3D5 P07737 PFN1 Profilin-1 0 ;; 160.36 0.00015882 578753000 1647060 1396420 1384200 1402840 1518430 1099200 1768520 1403320 1636180 FALSE TRUE 1543973.455 1499812.39 1417033.878 1438839.249 1399178.633 1416521.196 1503346.844 1578527.591 1363090.988 1.132700215 1.100302477 1.039573946 1.05557095 1.026474861 1.039197829 1.102895447 1.158050053 1 20.37845044 -0.932121728 7.183751097 0.999999999 1.077277994 0.257297034 0.043083868 1.24E-09 1.73E-10 0.041634472 0.009813339 0.116917164 0.932121728 0.077277995 DSQDAGGFGPEDR ddPTM_SK-BR-3_Pertuzumab_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 ;; 222.72 3.95E-11 1475970000 648860 642500 659240 724260 687450 554440 784620 600180 495680 FALSE TRUE 608249.0108 690071.3685 674877.4841 742845.7378 633460.45 714497.8274 666973.5151 675113.7942 412947.8058 1.472944044 1.671086173 1.634292457 1.798885301 1.533996406 1.730237617 1.615152098 1.634864709 1 18.65559992 -0.056404128 1.498202251 0.999212 1.644981189 0.828417618 0.090973907 10.4777128 14.17128571 0.109503638 0.021933843 0.878204933 0.056404128 0.645769189 DSQDASAEQS(ph)DHDDEVASLASASGGFGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DSQDASAEQSDHDDEVASLASASGGFGTK 29 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 DSQDAS(0.001)AEQS(0.999)DHDDEVASLASASGGFGTK;DSQDASAEQS(1)DHDDEVASLASASGGFGTK;DSQDAS(0.016)AEQS(0.984)DHDDEVASLASASGGFGTK;DSQDAS(0.046)AEQS(0.954)DHDDEVASLASASGGFGTK;DSQDASAEQS(1)DHDDEVASLASASGGFGTK;DSQDAS(0.012)AEQS(0.988)DHDDEVASLASASGGFGTK 378.37 3.74E-137 4230770000 3051830 2493020 2710150 2634590 3120190 2214136 3543780 2631150 3568750 TRUE FALSE 2860821.408 2677605.795 2774436.038 2702198.04 2875142.864 2853321.12 3012423.088 2959654.869 2973102.57 0.962234346 0.900609963 0.933178716 0.908881539 0.967051353 0.959711632 1.013225416 0.99547688 1 21.50353781 2.229707847 1.415504359 1.004063895 0.923146327 0.71980396 0.019810627 0.184486633 0.72224882 0.010594576 0.006176991 169.7101616 -2.229707847 -0.080917568 DSQQTLINIPSLNDS(ph)DSEIEDISEIESNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSQQTLINIPSLNDSDSEIEDISEIESNR 29 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 DSQQTLINIPS(0.009)LNDS(0.796)DS(0.195)EIEDISEIESNR;DSQQTLINIPS(0.008)LNDS(0.82)DS(0.171)EIEDIS(0.001)EIESNR 190.31 2.45E-18 140455000 349890 302143 376430 346050 372410 349830 348519 307258 418320 TRUE FALSE 327991.0095 324513.9821 385359.0974 354930.2289 343162.4208 450820.242 296261.8114 345619.8377 348499.6895 0.941151511 0.931174379 1.10576597 1.018452066 0.984685012 1.293602995 0.850106386 0.991736429 1 18.41079785 DSQRDLVEAVAHILGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSQRDLVEAVAHILGIR 17 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 85.619 0.0029992 8612700 17974 18012 20194 21871 21025 15308 23971 17649 31023 FALSE TRUE 16849.03942 19345.62722 20673.01122 22432.24689 19373.78131 19727.1711 20376.77109 19852.5165 25845.06088 0.651924927 0.748523182 0.799882473 0.867951017 0.749612524 0.763285921 0.788420317 0.768135799 1 14.65760098 -5 0.248227686 2.357936771 0.750651097 0.670390544 0.051988059 113.5538355 1.127570595 78.25302799 0.075218421 1.00E-05 5 -1.607285673 DSRPLS(ph)PILHIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSRPLSPILHIVK 13 1 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 1 DS(0.15)RPLS(0.85)PILHIVK 123.97 0.0001312 19727000 56087 52256 43902 49762 54489 34327 55855 45966 40275 TRUE FALSE 52576.61479 56125.08861 44943.37617 51038.97717 50209.65374 44236.64765 47480.06128 51704.95628 33552.84231 1.566979462 1.672737233 1.339480446 1.521152118 1.496435183 1.318417296 1.415083135 1.541000783 1 15.03414736 -3.471798371 0.168096428 7.61E-16 1.61246811 0.697745293 0.101786316 42.18045762 0.634783284 15.31450926 0.39606599 0.000337444 3.471798371 1.61246811 DSRPLS(ph)PILHIVKDESPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSRPLSPILHIVKDESPAK 19 2 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 1 DS(0.085)RPLS(0.915)PILHIVKDESPAK 123.65 1.61E-05 141200000 231200 183390 168850 193880 252840 129330 229360 176310 293780 TRUE FALSE 216729.6047 196968.3864 172855.2017 198855.289 232982.9663 166665.4715 194969.5973 198322.6916 244746.2201 0.885527893 0.804786224 0.706263009 0.812495854 0.951936934 0.680972607 0.796619442 0.810319732 1 17.90092705 0.706818062 3.662682226 0.999996951 0.794999637 0.376418331 0.077535568 4.73201879 58.11291 0.071085424 0.018266471 5.091175431 -0.706818062 -0.204997314 DSS(ph)TSPGDYVLSVSENSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSSTSPGDYVLSVSENSR 18 0 P46108-2;P46108;I3L297 P46108-2 CRK Adapter molecule crk 1 DS(0.008)S(0.99)T(0.002)SPGDYVLSVSENSR;DSS(0.999)T(0.001)SPGDYVLSVSENSR 378.5 4.61E-108 297321000 327266 230431 283458 245010 250007 215872 309120 227104 242167 TRUE FALSE 306783.0052 247492.351 290181.7576 251297.3714 230372.4587 278190.742 262770.3257 255458.4343 201747.7632 1.52062655 1.226741487 1.438339404 1.245601772 1.141883583 1.378903724 1.302469586 1.266226848 1 17.62219315 -4.390769763 0.183714341 9.21E-13 1.379678432 0.509025975 0.103124973 89.49800011 1.062963012 33.211859 0.292578056 4.07E-05 4.390769763 1.379678432 DSSDSADGRAT(ph)PSENLVPSSAR ddPTM_SK-BR-3_Pertuzumab_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(0.999)PSENLVPSSAR;DSSDS(0.046)ADGRAT(0.953)PSENLVPSSAR 136.53 7.08E-06 939640000 384760 399270 420790 367530 455860 309820 445200 353180 618450 TRUE FALSE 360678.5584 428832.3662 430771.3375 376961.442 420058.5945 399260.0045 378446.393 397275.3004 515226.6997 0.700038563 0.832317825 0.836081162 0.731641901 0.815288871 0.774921029 0.734524032 0.771068931 1 18.97484783 -0.973427413 6.257002863 1.000000082 0.781624064 0.711127388 0.044966552 5.26E-08 8.72E-09 0.044652657 0.010524728 0.106309625 0.973427413 -0.218376018 DSSEATGWEEPS(ph)PPSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSSEATGWEEPSPPSIR 17 0 A0A1B0GU24;Q9HCJ0-2;Q9HCJ0 A0A1B0GU24 TNRC6C Trinucleotide repeat-containing gene 6C protein 1 DSSEATGWEEPS(1)PPSIR 189.59 9.07E-18 0 72075 72390 78788 71401 75248 63301 86565 64564 67970 TRUE FALSE 67563.95441 77749.83092 80656.88857 73233.27054 69338.32562 81574.97109 73585.38188 72624.95752 56625.3679 1.193174666 1.373056526 1.424394959 1.293294388 1.224509936 1.440608231 1.29951265 1.282551623 1 15.7891609 0.618577318 1.665590496 1.00013464 1.337519181 0.613250834 0.078901712 1.058558076 3.825776067 0.072543278 0.02062427 4.155060175 -0.618577318 0.337384541 DSSFFDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSSFFDK 7 0 O75363;G3XAF7;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 ; 104.75 0.018802 289880000 607150 468570 579920 679530 658670 380300 621420 400990 523150 FALSE TRUE 569149.5653 503263.4103 593675.9763 696967.8902 606940.7151 490086.4363 528243.84 451054.4842 435832.8853 1.305889446 1.154716469 1.362164252 1.599163151 1.392599631 1.124482463 1.212033001 1.034925311 1 18.73341553 1.617072427 1.341012361 1.016490385 1.336475593 0.533898014 0.123084957 0.378911918 1.309486188 0.113410117 0.040814057 41.40687231 -1.617072427 0.319985208 DSSFFDKFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSSFFDKFFK 10 1 O75363;G3XAF7;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 ; 163.34 5.92E-06 879390000 2169720 2791420 2291450 2615700 3965160 1807450 3580150 2671080 6222000 FALSE TRUE 2033921.098 2998099.641 2345804.276 2682823.29 3653752.328 2329231.474 3043339.744 3004570.218 5183508.004 0.392383131 0.578392015 0.452551491 0.517569046 0.704880233 0.449354274 0.587119715 0.579640316 1 22.30549736 -5 0.23577388 3.616709555 0.483204837 0.772332136 0.081761245 73.19010147 0.73152596 91.51952178 0.121762428 1.00E-05 5 -3.133504717 DSSFTEVPRS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSSFTEVPRSPK 12 1 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 DSSFTEVPRS(1)PK 75.911 0.019705 141770000 409160 353850 359980 376340 407310 282610 387500 331540 605000 TRUE FALSE 383551.406 380049.4222 368518.8956 385997.5215 375321.5156 364194.9192 329397.9724 372933.4988 504021.5916 0.760982094 0.754034011 0.731156962 0.76583529 0.744653646 0.722578011 0.653539408 0.73991572 1 18.94312601 0.938734662 23.20074488 1 0.730059751 0.875463267 0.031510793 5705.30066 2160558.694 0.034254346 0.008563586 8.684296885 -0.938734662 -0.269940249 DSSGGDSCAS(ph)EEEPTFDPGYEPDWAVISTVRPQLCHSEPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSSGGDSCASEEEPTFDPGYEPDWAVISTVRPQLCHSEPTR 41 1 M0R2L2 M0R2L2 TBC1D17 1 DS(0.138)S(0.138)GGDS(0.144)CAS(0.579)EEEPT(0.001)FDPGYEPDWAVISTVRPQLCHSEPTR 56.929 0.010983 23369000 12420 9023.9 10119 9976.9 11860 7674.6 12306 7616 13038 TRUE FALSE 11642.65437 9692.038945 10359.02746 10232.92414 10928.56344 9890.132433 10460.82954 8566.874365 10861.87357 1.0718827 0.892299002 0.953705398 0.942095678 1.006139813 0.910536508 0.963077822 0.788710558 1 13.40698536 DSSGQHVDVSPTSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DSSGQHVDVSPTSQR 15 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ;;; 137.79 1.46E-05 2398000000 1738140 2376230 2060090 1983760 2802370 2021700 2032550 2206950 3081250 FALSE TRUE 1629352.92 2552168.542 2108956.308 2034666.64 2582283.164 2605331.97 1727787.997 2482492.566 2566969.469 0.634737943 0.994234085 0.821574363 0.792633751 1.005965671 1.014944666 0.673084747 0.967090803 1 21.29163471 4.753916446 24.46680277 0.890161875 0.634737692 0.349347008 0.115052274 2658.053784 4235043.658 0.026584637 0.629709488 56743.5426 -4.753916446 -0.255424182 DSSGWSSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 144.5 0.002759 0 243270 251660 262390 210030 265850 177813 256080 216430 321700 FALSE TRUE 228044.1649 270293.1683 268614.0147 215419.7254 244971.2134 229144.7265 217683.1813 243451.7619 268006.1917 0.850891405 1.008533297 1.002267944 0.803786375 0.914050574 0.854997883 0.812231911 0.90838111 1 18.03190681 3.250721408 24.99973585 0.868521393 0.972515277 0.151216442 0.071075271 245.0102531 503680.6119 0.018189346 0.024446711 1781.235769 -3.250721408 0.103993884 DSSKGEDSAEET(ph)EAKPAVVAPAPVVEAVSTPSAAFPSDATAENVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSSKGEDSAEETEAKPAVVAPAPVVEAVSTPSAAFPSDATAENVK 45 2 Q12906-7;Q12906-4;Q12906-6 Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 DS(0.229)S(0.229)KGEDS(0.209)AEET(0.252)EAKPAVVAPAPVVEAVS(0.067)T(0.013)PSAAFPSDATAENVK 64.238 0.0018187 119060000 174790 55156 94193 86030 95396 53884 123080 63237 158060 TRUE FALSE 163850.2059 59239.80763 96427.30244 88237.67545 87903.98297 69439.43607 104625.2966 71132.27865 131678.7649 1.244317609 0.449881252 0.732291972 0.670097988 0.667563848 0.527339667 0.794549499 0.540195518 1 17.00666318 -1.164239731 5.103329485 1.000017287 0.681674356 0.147783285 0.218522053 3.72E-05 6.09E-06 0.182970172 0.043124143 0.068510994 1.164239731 -0.318342931 DSSRLPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSSRLPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTR 43 3 P30043;M0R192;A0A2R8YEP4;A0A2R8Y7Y9;M0QZL1 P30043 BLVRB Flavin reductase (NADPH) 0 89.51 9.19E-05 41339000 60622 66281 59439 83565 90993 47060 79796 63984 88828 FALSE TRUE 56827.77723 71188.51421 60848.92115 85709.41938 83846.77683 60645.45804 67831.33059 71972.54325 74002.03295 0.767921839 0.961980521 0.822260129 1.158203578 1.133033425 0.819510703 0.916614421 0.972575217 1 16.17527728 5.683821422 0.928563304 0.967123131 7.73E-13 0.229446223 0.112420349 18.16462466 3.315280591 0.035798059 26.83405097 482860.2134 -5.683821422 -0.967123131 DSSSLSSCTSGILEERS(ph)PAFRGPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSSSLSSCTSGILEERSPAFRGPDR 25 2 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 DSSSLSSCTSGILEERS(1)PAFRGPDR;DSSSLSSCTSGILEERS(1)PAFRGPDR 163.31 9.50E-12 277248000 88785 75706 81313 90819 108497 61922 79565 66070 157136 TRUE FALSE 83228.10534 81311.35101 83241.78276 93149.5693 99976.08328 79797.87618 67634.9669 74318.98494 130908.9865 0.635770756 0.621128871 0.635875237 0.711559778 0.763706801 0.609567596 0.516656409 0.567714921 1 16.99820461 -1.645121181 2.924609274 1.033987118 0.628839234 0.740908585 0.068216579 16746830.26 16749145.22 4299502.366 0.018167458 0.022640125 1.645121181 -0.405147884 DSST(ph)PYQEIAAVPSAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSSTPYQEIAAVPSAGR 17 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 DS(0.001)S(0.034)T(0.965)PYQEIAAVPSAGR 199.33 1.50E-10 119490000 136770 136020 135680 136260 162500 130480 172180 125640 171450 TRUE FALSE 128209.8098 146091.0623 138898.3937 139756.6623 149737.9055 168147.4578 146363.2074 141326.4306 142833.8874 0.89761479 1.022803937 0.972447059 0.978455917 1.048335995 1.177223843 1.024709263 0.989446084 1 17.12397877 2.717607162 5.611030461 1.058609951 0.977555466 0.295038574 0.05958261 0.221389088 23.87530656 0.018502841 0.018002688 521.923873 -2.717607162 -0.081054485 DSTFDLPADSIAPFHICYYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSTFDLPADSIAPFHICYYGR 21 0 Q8N1G2 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 0 ; 135.27 2.43E-08 42373000 62275 71107 64707 61984 74656 58156 74357 64836 70189 FALSE TRUE 58377.31891 76371.83627 66241.8806 63574.61438 68792.81891 74944.69312 63207.85815 72930.91732 58474.00246 0.998346555 1.306081901 1.132843277 1.087228712 1.176468448 1.281675445 1.080956587 1.247236622 1 15.83550772 -1.81303112 2.774620139 0.948403569 1.170496944 0.221426288 0.095843163 22204505.18 15999931.14 7672789.763 0.020840602 0.015380444 1.81303112 0.222093374 DSTLIMQLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 210.01 1.98E-07 1157050000 896200 1320020 790190 713250 1283750 630440 804500 1196600 866860 FALSE TRUE 840108.4418 1417755.654 808933.68 731553.2025 1182929.453 812437.7937 683872.6936 1345998.144 722175.4659 1.163302385 1.963173386 1.120134535 1.012985399 1.638008364 1.124986699 0.946961959 1.8638104 1 19.46198988 3.812940374 5.936867508 1.2246799 1.605272023 0.121522975 0.349109568 0.336393772 18.40306385 0.082401624 0.150113947 6500.404384 -3.812940374 0.380592123 DSVFLSCSEDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSVFLSCSEDNR 12 0 Q9BQA1;Q9BQA1-2;H0Y711 Q9BQA1 WDR77 Methylosome protein 50 0 182.46 3.92E-05 129880000 142010 120340 126380 121670 115050 107880 125740 109730 128290 FALSE TRUE 133121.8476 129250.0988 129377.7933 124792.2582 106014.4371 139023.2047 106886.4543 123430.032 106877.5702 1.245554585 1.209328567 1.21052334 1.16761878 0.991924095 1.300770633 1.000083124 1.154873111 1 16.70559959 7.999999999 0.081155282 0.865599207 1.907750399 0.354404977 0.088346751 182.0884237 1.074786474 2.046209075 21.25908255 99999999.84 -7.999999999 1.042151192 DSVLS(ph)YTSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DSVLSYTSVR 10 0 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 1 DSVLS(0.815)YT(0.184)SVR;DSVLS(0.951)YT(0.049)SVR;DSVLS(0.919)YT(0.081)SVR;DSVLS(0.998)YT(0.002)SVR 238.92 3.36E-12 382179000 431157 477207 419268 480945 455350 340110 584580 349439 336719 TRUE FALSE 404171.653 512539.9028 429213.235 493286.8629 419588.6478 438294.2358 496927.656 393067.2284 280518.4236 1.440802525 1.827116723 1.530071463 1.758482942 1.495761463 1.562443672 1.771461744 1.401217158 1 18.097736 0.953674359 4.760415879 1.000278496 1.638852429 0.713156624 0.127044606 0.11279195 8.033000361 0.109924974 0.02785166 8.98823377 -0.953674359 0.638573933 DSYCSYMGHFDLLNYFAIAENESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSYCSYMGHFDLLNYFAIAENESK 24 0 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 215.79 1.38E-32 61840000 82899 76476 71802 68051 89622 53760 97491 81404 93057 FALSE TRUE 77710.49957 82138.36261 73505.17735 69797.30387 82583.44964 69279.63928 82873.12961 91567.46859 77525.18553 1.002390372 1.059505528 0.948145778 0.900317792 1.06524672 0.893640419 1.068983312 1.181131886 1 16.24237745 1.554149054 7.030945694 1.101161747 0.984111016 0.323972055 0.071324482 0.13052089 12.24483477 0.035697581 0.016570345 35.82193601 -1.554149054 -0.117050731 DSYDSYATHNE ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DSYDSYATHNE 11 0 Q14011 Q14011 CIRBP Cold-inducible RNA-binding protein 0 ; 163.64 5.52E-05 370050000 385940 473070 462040 469050 446510 369420 498160 361370 467460 FALSE TRUE 361784.7043 508096.595 472999.807 481086.6171 411442.9057 476065.557 423465.5327 406487.84 389437.9061 0.928992013 1.304692191 1.214570538 1.235335877 1.056504514 1.222442781 1.087376257 1.043780879 1 18.57103379 1.392716849 1.089146836 0.995651377 1.188709864 0.195099641 0.107251765 0.578597966 1.364759852 0.091573613 0.031666676 24.7011316 -1.392716849 0.193058487 DSYESYGNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DSYESYGNSR 10 0 P38159;P38159-2;H3BUY5;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;;; 262.84 4.54E-17 6420600000 1889270 1927340 1824690 1918860 2095890 1602250 2177650 1582950 2222740 FALSE TRUE 1771023.963 2070042.259 1867972.508 1968101.196 1931287.254 2064793.565 1851131.599 1780584.792 1851750.335 0.95640537 1.117884102 1.008760454 1.06283291 1.042952291 1.115049651 0.999665864 0.9615685 1 20.82045817 1.555240063 7.092722898 0.981033203 1.054078757 0.288242652 0.047533914 0.135725029 12.91956514 0.023247637 0.010800017 35.91203894 -1.555240063 0.073045554 DSYLILETLPTEYDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DSYLILETLPTEYDSR 16 0 P17980;E9PM69;E9PKD5;E9PLG2;R4GNH3;E9PN50;E9PMD8 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ;;;; 256.47 2.84E-26 202545000 328955 321594 317039 318164 340279 274833 373668 303013 351514 FALSE TRUE 308366.2938 345405.1544 324559.3148 326328.6269 313554.86 354172.8256 317639.9524 340844.8401 292844.0425 1.05300518 1.179484996 1.108300896 1.11434272 1.070723028 1.209424725 1.084672748 1.163912495 1 18.15977302 -1.011004489 4.65464749 0.999996973 1.125717854 0.380565588 0.049199802 1.39E-06 2.94E-07 0.041287428 0.009731298 0.097497956 1.011004489 0.125720881 DSYSECNSNRDS(ph)VLSYTSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSYSECNSNRDSVLSYTSVR 20 1 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 1 DSYSECNSNRDS(1)VLSYTSVR 197.54 9.96E-22 105800000 60987 65721 60177 62234 63114 48825 81215 56293 63048 TRUE FALSE 57169.93253 70587.05122 61604.42686 63831.0298 58157.28103 62919.98489 69037.56471 63321.30497 52524.88149 1.08843525 1.343878353 1.172861796 1.21525319 1.107232979 1.197908174 1.314378305 1.205548745 1 15.68071338 0.94823356 22.25670088 0.999999999 1.220026682 0.388151998 0.079593921 4209.264066 1809754.115 0.073454418 0.018363604 8.876332447 -0.94823356 0.220026683 DSYSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DSYSSSR 7 0 P38159;P38159-2;H3BUY5;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 143.11 0.0056859 183130000 73398 89452 85754 74245 96843 78358 97265 76812 98156 FALSE TRUE 68804.1502 96075.11915 87788.12538 76150.2524 89237.34143 100978.6826 82681.01621 86402.14728 81773.12949 0.841402923 1.174898402 1.07355712 0.931238084 1.091279519 1.234863863 1.011102507 1.056608055 1 16.31933923 DSYVGDEAQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 ;;;;;; 370.58 1.73E-85 16049480000 12145800 8336320 9537080 9226520 9805790 7214850 11058790 8232270 9482850 FALSE TRUE 11385616.06 8953549.807 9763304.041 9463288.124 9035682.808 9297660.072 9400627.104 9260087.031 7900101.073 1.441198784 1.133346235 1.23584546 1.197869247 1.143742684 1.176903939 1.189937574 1.172147919 1 22.91343968 -4.999988623 0.033796999 1.42E-09 1.849228499 0.534281678 0.074467176 1024.880383 2.600931176 117.1881133 42.42165144 1.00E-05 4.999988623 1.849228497 DSYVGDEAQSKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 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 ;;;;;;;;; 207.27 1.29E-07 64465802900 23767275 22569422 21939508 21791876 26140429 15589408.5 27527912 19184637 37620446 FALSE TRUE 22279723.68 24240485.49 22459923.49 22351092.43 24087465.15 20089817.66 23400357.15 21579881.16 31341350.53 0.710873122 0.773434619 0.716622708 0.713150265 0.76855224 0.641000382 0.746628871 0.688543435 1 24.90156401 -1.727439915 2.592806688 1.054267279 0.723787892 0.83845284 0.038611441 5724019.397 4357748.877 2002807.261 0.008479084 0.018730962 1.727439915 -0.330479387 DT(ph)HEDHDTSTENTDESNHDPQFEPIVSLPEQEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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;DT(0.167)HEDHDT(0.167)S(0.167)T(0.167)ENT(0.167)DES(0.167)NHDPQFEPIVSLPEQEIK;DT(0.167)HEDHDT(0.167)S(0.167)T(0.167)ENT(0.167)DES(0.167)NHDPQFEPIVSLPEQEIK;DT(0.167)HEDHDT(0.167)S(0.167)T(0.167)ENT(0.167)DES(0.167)NHDPQFEPIVSLPEQEIK 136 1.46E-08 1843690000 592083 465176 561397 535723 581711 433761 711645 489742 669500 TRUE FALSE 555025.5819 499618.1151 574713.602 549470.5592 536025.7646 558980.7592 604940.4388 550887.3668 557756.1249 0.995104414 0.895764462 1.030403032 0.985144823 0.961039674 1.002195645 1.084596676 0.987685015 1 19.08927493 3.291415089 0.637961279 1.027695266 0.941415173 0.178857952 0.043237738 1.167696261 0.996300067 0.02807807 0.057573606 1956.208264 -3.291415089 -0.086280093 DTAAWTVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTAAWTVGR 9 0 Q14974;Q14974-2;J3KTM9;J3QKQ5 Q14974 KPNB1 Importin subunit beta-1 0 ; 182.53 0.00010752 788070000 625630 606660 566560 557790 649740 424030 609560 568550 673180 FALSE TRUE 586472.9351 651577.7376 579999.0707 572103.8357 598712.0413 546440.5774 518162.1369 639534.719 560821.9091 1.045738274 1.161826468 1.034194744 1.020116772 1.06756179 0.974356687 0.923933478 1.140352594 1 19.09718319 3.646497099 2.659643938 1.01017744 1.110055099 0.208874684 0.063247208 0.324357804 4.516067248 0.017240542 0.030370786 4430.952542 -3.646497099 0.099877658 DTATYWPLNWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTATYWPLNWR 11 0 E9PCJ7;Q8N806 E9PCJ7 UBR7 Putative E3 ubiquitin-protein ligase UBR7 0 ; 125.57 0.0007574 284500000 438210 317556 348367 414019 446433 204007 312272 317640 532461 FALSE TRUE 410783.2183 341068.1767 356630.4298 424643.4285 411371.953 262900.5091 265449.7126 357298.0532 443589.8193 0.926042935 0.768881886 0.803964415 0.95728849 0.92737014 0.592665787 0.598412545 0.805469462 1 18.75886673 2.246303411 24.9995551 0.698714826 0.855748681 0.133793066 0.130845547 236.8606093 764764.8488 0.043900918 0.036090879 176.3207447 -2.246303411 0.157033855 DTCVQS(ph)PISSFPCTDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DTCVQSPISSFPCTDLK 17 0 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 DTCVQS(0.997)PIS(0.001)S(0.001)FPCTDLK;DTCVQS(1)PISSFPCTDLK;DTCVQS(0.995)PIS(0.002)S(0.002)FPCTDLK;DTCVQS(0.993)PIS(0.005)S(0.002)FPCTDLK 277.34 9.14E-36 849510000 1624230 1073300 1403850 1406420 1610810 977980 1311310 1030730 1886360 TRUE FALSE 1522572.344 1152768.249 1437149.985 1442511.118 1484303.48 1260306.95 1114691.239 1159418.909 1571514.33 0.968856799 0.733539763 0.914500083 0.917911527 0.944505215 0.801969747 0.709310261 0.737771771 1 20.583724 2.048226959 9.852331839 0.776472645 0.877052218 0.091133977 0.101444878 0.648895234 127.6051949 0.035886298 0.026470282 111.7447065 -2.048226959 0.100579573 DTCYS(ph)PKPSVYLSTPSSASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTCYSPKPSVYLSTPSSASK 20 1 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 DT(0.014)CYS(0.983)PKPS(0.003)VYLSTPSSASK 149.94 5.64E-08 171830000 392520 236260 294460 359680 370340 197020 279550 181950 328900 TRUE FALSE 367952.8739 253752.9362 301444.7303 368909.9977 341254.9903 253896.4756 237634.0727 204666.858 274004.4652 1.342871816 0.926090515 1.100145321 1.346364912 1.245435873 0.926614373 0.867263504 0.746947163 1 18.06383988 2.112559294 5.353553893 0.866368662 1.149581157 0.542314169 0.137602488 0.188290417 8.12380207 0.055238877 0.040332284 129.586361 -2.112559294 0.283212495 DTDAAVGDNIGYITFVLFPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTDAAVGDNIGYITFVLFPR 20 0 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ; 126.88 2.46E-05 39554000 54537 54690 50614 51121 59404 42792 56673 49053 50573 FALSE TRUE 51123.62652 58739.3045 51814.58798 52432.85141 54738.64946 55145.35573 48175.40978 55177.37503 42132.03959 1.213414471 1.394171872 1.229814376 1.244488801 1.299216701 1.308869836 1.143438824 1.309629811 1 15.36263014 -4.542128313 0.197859561 3.17E-10 1.317253829 0.595530727 0.068559254 73.26619554 0.853154607 28.97941901 0.158717887 2.87E-05 4.542128313 1.317253829 DTDFEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTDFEHR 7 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ; 176.66 0.00074355 883900000 1919170 2155050 2024060 2077210 2188320 1622800 2315900 1789240 1876690 FALSE TRUE 1799052.576 2314612.144 2072071.659 2130514.725 2016458.174 2091276.016 1968652.295 2012630.553 1563458.315 1.150687906 1.480443784 1.325313019 1.362693655 1.289742205 1.337596273 1.259165195 1.287294028 1 20.57630932 -0.133951073 0.437919449 0.946647804 1.35599357 0.57765506 0.083340564 3.24465807 0.734477654 0.3657269 0.045251138 0.734596622 0.133951073 0.409345765 DTDIIVWDVINESGLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTDIIVWDVINESGLYR 17 0 Q9UNX4 Q9UNX4 WDR3 WD repeat-containing protein 3 0 ; 178.58 2.24E-09 24381000 45670 48491 46617 53117 60139 41888 62814 47428 51030 FALSE TRUE 42811.59622 52081.32409 47722.77725 54480.07215 55415.92553 53980.38561 53395.62384 53349.4902 42512.76333 1.007029251 1.225075013 1.122551759 1.281499199 1.303512667 1.269745398 1.255990429 1.254905257 1 15.37560842 4.738877648 24.23444703 1.223154427 1.007029231 0.336133027 0.090701636 18.49154795 1412549.076 0.019987449 0.11748853 54812.25232 -4.738877648 -0.216125196 DTDIVDEAIYYFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DTDIVDEAIYYFK 13 0 O15145;C9JZD1;F8VR50 O15145 ARPC3 Actin-related protein 2/3 complex subunit 3 0 ;;; 227.94 1.92E-11 191393000 482910 381898 440092 454270 445981 355590 527061 408886 376761 FALSE TRUE 452685.5251 410174.1253 450531.1901 465927.3373 410955.4513 458243.0605 448033.096 459936.3172 313877.1551 1.442237887 1.306798276 1.435374263 1.484425769 1.309287549 1.459943972 1.427415435 1.465338619 1 18.2598405 -1.186931074 4.720156761 0.999940398 1.410309744 0.819628171 0.061323611 3.67E-05 6.32E-06 0.056670916 0.013355529 0.065023288 1.186931074 0.410369346 DTDSEEEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTDSEEEIR 9 0 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ; 173.73 0.00012845 7105000000 4948100 3575900 4590000 3429900 2770900 2464700 4983400 4518900 2900600 FALSE TRUE 4638407.254 3840663.357 4698876.968 3517917.041 2553284.691 3176218.879 4236185.434 5083094.612 2416471.121 1.919496249 1.589368614 1.944520225 1.455807607 1.056617093 1.314403822 1.753046166 2.103519702 1 21.20447032 3.221759385 24.58481025 1.475500887 1.786950102 0.213970313 0.330114323 354.3729801 518543.5481 0.095394827 0.114319651 1666.323752 -3.221759385 0.311449215 DTDSEEEIREAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DTDSEEEIREAFR 13 1 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ;;;;;; 262.64 3.65E-24 16725490000 5417920 5588680 5257744 5335938 5568810 3168732 6231430 5266084 7452150 FALSE TRUE 5078822.058 6002471.682 5382460.171 5472867.203 5131458.126 4083493.488 5297084.921 5923566.179 6208338.022 0.81806468 0.966840346 0.866972795 0.881534991 0.826542967 0.657743421 0.853221088 0.954130745 1 22.56577568 1.150260021 4.127639608 0.993855189 0.846453019 0.36295396 0.076840129 0.269873482 7.845145054 0.07829921 0.02040892 14.13383512 -1.150260021 -0.14740217 DTDSEEEIREAFRVFDKDGNGYISAAELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTDSEEEIREAFRVFDKDGNGYISAAELR 29 3 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2 P0DP25 CALM2;CALM1 0 ; 172.18 8.38E-13 214650000 182342 195742 193074 217720 257700 233470 208443 109797 225420 FALSE TRUE 170929.5397 210234.9413 197653.8065 223307.0638 237461.2815 300868.9989 177188.9072 123505.3971 187795.9457 0.910187592 1.119486049 1.052492404 1.189094168 1.264464366 1.602105933 0.943518278 0.65765742 1 17.51880639 1.512280551 8.721250345 0.819818029 1.175021801 0.38944985 0.193693924 0.110206516 16.8704714 0.103481939 0.047914675 32.5297369 -1.512280551 0.355203772 DTEAMKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTEAMKR 7 1 P18206;P18206-2 P18206 VCL Vinculin 0 64.803 0.075879 81701000 81888 62088 61496 64795 56972 47668 70635 59525 58250 FALSE TRUE 76762.77625 66685.06012 62954.71416 66457.7494 52497.64893 61428.97777 60043.93749 66956.82728 48527.69869 1.581834258 1.374164898 1.29729445 1.369480754 1.081807923 1.265853923 1.237312692 1.379765146 1 15.56652082 8 0.369006865 1.20116195 5.895324696 0.532139516 0.111096651 52.40217802 0.725539429 0.077807565 174.1693529 100000000 -8 4.694162746 DTEEPLPVKESDQTLAALLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_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 207.54 4.82E-23 381874000 395369 269492 316082 392655 482630 188709 467080 239043 900930 TRUE FALSE 370623.56 289445.4681 323579.6143 402731.1921 444726.1866 243186.2249 397045.6902 268888.0447 750558.9628 0.493796728 0.38563988 0.43111818 0.536575022 0.592526648 0.324006823 0.528999998 0.358250395 1 19.51760589 -1.867794649 2.560528532 1.250462738 0.453906306 0.802885343 0.08464538 15767927.27 9495889.675 24008233.94 0.018975245 0.013558303 1.867794649 -0.796556431 DTEEQNPETVNWEDRPS(ph)TPTILGYEVMEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTEEQNPETVNWEDRPSTPTILGYEVMEER 30 1 A0A0C4DGW2;P57768-2;P57768;E5RGS8;E5RH07;E5RGQ6 A0A0C4DGW2 SNX16 Sorting nexin-16 1 DTEEQNPET(0.016)VNWEDRPS(0.457)T(0.457)PT(0.061)ILGY(0.009)EVMEER 67.459 0.011187 93498000 42360 44291 47239 51687 57683 45868 55143 47715 59109 TRUE FALSE 39708.76321 47570.35172 48359.53139 53013.37593 53152.80986 59109.347 46874.81907 53672.32278 49243.32604 0.806378578 0.966026375 0.982052499 1.076559611 1.079391141 1.200352449 0.95190197 1.089941056 1 15.58764059 5.700393997 0.64851577 1.063179399 0.112262124 0.57937627 0.068050667 7.212030128 0.900777594 0.026540358 6.747268074 501642.1224 -5.700393997 -0.950917274 DTFNHLTTWLEDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DTFNHLTTWLEDAR 14 0 P61019;P61019-2;E9PKL7;H7C125 P61019 RAB2A Ras-related protein Rab-2A 0 ;; 187.37 9.56E-07 520970000 565550 803850 710940 731300 897970 572610 849660 846550 812750 FALSE TRUE 530153.235 863367.8904 727803.8325 750066.3961 827447.0584 737913.2115 722261.3709 952243.631 677096.7744 0.782980004 1.275102649 1.074888938 1.107768379 1.222051396 1.089819416 1.066703311 1.406362675 1 19.36900252 4.750894041 24.71345197 1.151007927 0.782979736 0.492248287 0.118776725 1381.66672 2768495.477 0.025516348 0.43951352 56350.01564 -4.750894041 -0.368028191 DTGIFLDLMHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTGIFLDLMHLK 12 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 163.51 5.98E-05 1125670000 2473100 2731700 2394900 2328100 3168300 1627230 2570700 2703100 2930000 FALSE TRUE 2318313.086 2933957.91 2451708.159 2387842.987 2919474.498 2096984.885 2185247.4 3040587.985 2440964.071 0.949753056 1.201966856 1.004401575 0.978237662 1.196033376 0.859080602 0.895239478 1.245650446 1 21.21901963 2.236147104 24.99947412 0.976253641 1.072205468 0.045033106 0.130819924 142.0798868 1471656.347 0.045307268 0.035057847 172.2451905 -2.236147104 0.095951827 DTGKTPVEPEVAIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DTGKTPVEPEVAIHR 15 1 P60866;P60866-2;E5RJX2;E5RIP1 P60866 RPS20 40S ribosomal protein S20 0 ;;;;; 216.99 1.28E-12 7127420000 12010940 12769040 12847210 13040770 15623620 9888310 16151970 11409700 22245700 FALSE TRUE 11259196.71 13714473.01 13151951.89 13375418.24 14396603.91 12742904.57 13730132.05 12834226.16 18532748.96 0.60752977 0.740012884 0.709660068 0.721717985 0.776819669 0.687588474 0.740857823 0.692516053 1 24.14357356 -2.264472874 2.270919591 2.133861014 0.715588662 0.805348163 0.044783564 2044807.63 329582.4421 11906601.88 0.009538963 0.005439101 2.264472874 -1.418272352 DTHDQLSEPSEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 198.16 1.28E-07 6530930000 4209589 5001407 4826042 5081277 5020169 3884834 5901829 4300621 5007475 FALSE TRUE 3946118.339 5371716.378 4940517.995 5211671.17 4625905.177 5006322.511 5016904.531 4837562.999 4171695.073 0.94592684 1.287657963 1.184295091 1.249293412 1.108879028 1.200069138 1.202605762 1.159615675 1 21.99220228 0.855345836 5.546801897 1.000001219 1.184691048 0.228143576 0.093149465 2.869879814 109.4083945 0.079365782 0.019995755 7.167139148 -0.855345836 0.184689829 DTHEDHDT(ph)S(ph)TENTDESNHDPQFEPIVSLPEQEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 2 DT(0.002)HEDHDT(0.604)S(0.511)T(0.485)ENT(0.394)DES(0.004)NHDPQFEPIVSLPEQEIK;DT(0.02)HEDHDT(0.811)S(0.442)T(0.39)ENT(0.331)DES(0.005)NHDPQFEPIVSLPEQEIK;DT(0.024)HEDHDT(0.472)S(0.495)T(0.493)ENT(0.413)DES(0.104)NHDPQFEPIVSLPEQEIK;DT(0.012)HEDHDT(0.636)S(0.69)T(0.637)ENT(0.021)DES(0.004)NHDPQFEPIVSLPEQEIK 230.43 1.30E-36 1892040000 859141 616706 746523 698955 763285 524947 962278 605474 962809 TRUE FALSE 805368.8984 662367.5539 764230.8781 716891.3686 703339.675 676490.6771 817993.3473 681068.7617 802109.9579 1.00406296 0.825781487 0.952775702 0.893756974 0.876861917 0.843388952 1.01980201 0.849096505 1 19.6134405 -0.368784678 0.455722399 1.016741901 0.902369569 0.133602923 0.06712218 13.40632701 2.74624106 0.437909795 0.034229397 0.427774923 0.368784678 -0.114372331 DTHEDHDT(ph)STENTDESNHDPQFEPIVSLPEQEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 1 DTHEDHDT(0.425)S(0.425)T(0.113)ENT(0.038)DESNHDPQFEPIVSLPEQEIK 273.25 1.91E-73 747480000 517430 414580 522380 467680 512490 402650 604690 455450 619820 TRUE FALSE 485044.9799 445275.9346 534771.1003 479681.4606 472241.1027 518888.5185 514022.3482 512313.9351 516368.0378 0.939339666 0.862322805 1.03563943 0.928952657 0.914543636 1.004881171 0.99545733 0.992148812 1 18.97804018 5.507632072 0.267290286 1.005435137 0.768494934 0.301166933 0.043617347 16.57153161 0.71646071 0.054643782 1.385331958 321834.1105 -5.507632072 -0.236940202 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ; 171.15 4.26E-15 1291310000 514310 493090 567350 550110 565960 439640 699930 477780 701510 FALSE TRUE 482120.2552 529598.8967 580807.8099 564226.7539 521511.7846 566556.931 594981.9943 537431.8847 584423.4491 0.824950224 0.906190362 0.993813323 0.965441676 0.892352601 0.969428814 1.018066601 0.919593294 1 19.15665454 4.624799381 1.691132881 0.966944597 0.794395286 0.602510526 0.037044074 0.518875268 1.753815685 0.009731493 0.135337979 42150.17486 -4.624799381 -0.172549311 DTHLTITPTVLGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTHLTITPTVLGER 14 0 A0A0B4J2A0;Q9UHJ6 A0A0B4J2A0 TRPV1;SHPK Sedoheptulokinase 0 ; 97.417 0.0029828 414490000 120693 156912 137270 141294 148288 108355 154321 119524 146070 FALSE TRUE 113139.0406 168529.9277 140526.1092 144919.8433 136642.0586 139635.3295 131181.9987 134446.8345 121689.9734 0.929731821 1.384912192 1.154787904 1.19089387 1.122870314 1.147467829 1.078001705 1.104830832 1 16.89285078 1.641505142 0.584931394 1.010216004 1.206265825 0.124176565 0.112323582 1.04806966 0.803717387 0.100674892 0.056173752 43.80312977 -1.641505142 0.196049821 DTHPGS(ph)PGSPGPALRPLPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTHPGSPGSPGPALRPLPAR 20 1 Q8N0Y2-2;Q8N0Y2 Q8N0Y2-2 ZNF444 Zinc finger protein 444 1 DTHPGS(0.992)PGS(0.008)PGPALRPLPAR;DTHPGS(0.993)PGS(0.007)PGPALRPLPAR 158.73 1.60E-11 624720000 341460 320390 344520 274968 364930 261318 364790 327244 491810 TRUE FALSE 320088.6281 344112.009 352692.1771 282024.1444 336269.8699 336756.2645 310093.126 368101.1338 409723.7338 0.78123038 0.8398635 0.86080485 0.688327576 0.820723434 0.821910562 0.756834668 0.898413012 1 18.64429194 0.996900629 4.632355183 0.999702694 0.803247789 0.660208783 0.048607571 0.101119367 6.931712662 0.046745495 0.011863956 9.9288884 -0.996900629 -0.196454905 DTHPGSPGS(ph)PGPALRPLPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTHPGSPGSPGPALRPLPAR 20 1 Q8N0Y2-2;Q8N0Y2 Q8N0Y2-2 ZNF444 Zinc finger protein 444 1 DTHPGS(0.22)PGS(0.78)PGPALRPLPAR 148.29 6.77E-08 303000000 247540 224970 251000 210070 271690 205260 266850 272190 350930 TRUE FALSE 232046.9133 241627.0129 256953.8385 215460.7518 250352.5633 264515.2299 226838.3198 306173.5207 292357.5159 0.793709416 0.826477856 0.878902797 0.736976955 0.856323336 0.904766307 0.775893581 1.047257224 1 18.15737415 1.233115183 24.99999975 1.023628724 0.82967446 0.730185961 0.050197325 69.76998714 320297.0973 0.040445113 0.011257379 17.10468901 -1.233115183 -0.193954264 DTIEEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTIEEHR 7 0 P23381;P23381-2 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ; 142.64 0.0024753 813510000 688940 739070 770010 759780 704450 603580 870230 585950 711420 FALSE TRUE 645820.4752 793791.5118 788275.0008 779277.2411 649125.3386 777823.7477 739747.0903 659107.1473 592679.4061 1.089662419 1.339326968 1.330019219 1.314837724 1.095238559 1.312385313 1.248140365 1.112080394 1 19.1768924 1.07389864 2.597652328 1.001636849 1.265860584 0.449598917 0.090909297 0.208868479 2.869774041 0.082523868 0.022399229 11.85492034 -1.07389864 0.264223735 DTIIDVVGAPLT(ph)PNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DTIIDVVGAPLTPNSR 16 0 Q9NPF5 Q9NPF5 DMAP1 DNA methyltransferase 1-associated protein 1 1 DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(0.997)PNS(0.003)R 385.27 3.14E-120 1762985000 3579840 3145920 3558770 3106170 3796130 3382960 4528860 3312500 4523540 TRUE FALSE 3355784.205 3378847.19 3643185.705 3185879.581 3497997.263 4359565.634 3849799.487 3726072.917 3768531.951 0.89047519 0.896595076 0.966738707 0.845390094 0.928212181 1.156833932 1.021564773 0.988733269 1 21.84557119 2.408405095 11.1505233 1.045141952 0.908065265 0.614869961 0.053813786 0.338247277 53.31662026 0.017648469 0.014761376 256.0973559 -2.408405095 -0.137076687 DTLENTIGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DTLENTIGHR 10 0 H3BS70;Q96DC0;P42126-2;P42126 H3BS70 ECI1;DCI "Enoyl-CoA delta isomerase 1, mitochondrial" 0 ;;;;; 208.15 1.19E-07 3120670000 3034040 3829090 2374510 1814350 5033930 2094740 2366310 3981800 3503120 FALSE TRUE 2844144.852 4112599.808 2430834.499 1860909.293 4638585.444 2699457.433 2011503.783 4478936.495 2918426.641 0.974547317 1.40918389 0.832926367 0.637641278 1.589413069 0.924970117 0.689242537 1.534709296 1 21.47675937 3.971241656 24.36700473 0.997082321 1.210179083 0.031892697 0.331853846 475.4651893 1970503.306 0.079738654 0.148927678 9359.263091 -3.971241656 0.213096762 DTLGLFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTLGLFLR 8 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 127.12 0.0027686 30970000 69158 99948 72815 76041 101530 61897 82567 91764 80832 FALSE TRUE 64829.52423 107348.2539 74542.20619 77992.3408 93556.24335 79765.65909 70186.84486 103220.9374 67340.61701 0.962710577 1.594108559 1.106942726 1.158176807 1.389298874 1.184510369 1.042266139 1.532818409 1 16.03918932 -2.318629384 1.897846217 7.21E-05 1.248487724 0.125222285 0.204560742 2672073.736 353507.2143 11418675.93 0.04671831 0.00480143 2.318629384 1.248415662 DTLKETNEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTLKETNEELR 11 1 Q9UJC3;Q9UJC3-2 Q9UJC3 HOOK1 Protein Hook homolog 1 0 97.463 0.005698 120000000 279810 271520 245880 281480 321160 202290 331540 250740 399630 FALSE TRUE 262297.1916 291623.6233 251712.3897 288703.2533 295937.3891 260687.8391 281828.6549 282045.4409 332929.1713 0.787846828 0.875932926 0.756053874 0.867161181 0.888889934 0.78301291 0.846512349 0.847163497 1 18.34485576 -5 0.306854806 2.481557549 0.821922878 0.609382201 0.042784134 189.0663128 1.725024054 180.6785038 0.038585203 1.00E-05 5 -1.65963467 DTLRT(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTLRTPPR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DTLRT(1)PPR;DT(0.002)LRT(0.998)PPR 103.08 0.0078263 3797600000 1674210 1328520 1521820 1504610 1408320 1512700 1723170 1292760 1011340 TRUE FALSE 1569424.185 1426885.003 1557918.289 1543220.84 1297716.228 1949391.933 1464796.656 1454163.932 842540.8205 1.862727771 1.693549996 1.849071583 1.831627385 1.540241371 2.313706216 1.73854681 1.725926977 1 19.68438706 0.668725857 2.324815596 1.000235668 1.82881654 0.637521702 0.195928581 1.24084246 7.931008288 0.170916927 0.046094886 4.663649006 -0.668725857 0.828580872 DTLRT(ph)PPRER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTLRTPPRER 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DTLRT(1)PPRER 132.31 0.01082 3541000000 195340 230660 220020 225490 259880 176930 249760 205380 270440 TRUE FALSE 183114.0181 247738.3064 225238.9783 231276.4552 239470.0731 228006.8188 212310.8067 231022.1451 225301.8169 0.812749851 1.099584148 0.999721092 1.026518376 1.062885672 1.012006126 0.942339523 1.025389623 1 17.78149942 -2.205286541 10.82135818 0.052836468 1.005687805 0 0.077619997 0.495926367 0.009407972 0.02101334 0.016067724 0.006233234 2.205286541 0.952851337 DTLWHLFNTLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTLWHLFNTLQR 12 0 Q7Z434;Q7Z434-5;Q7Z434-2 Q7Z434 MAVS Mitochondrial antiviral-signaling protein 0 109.22 0.0016213 31240000 73608 126020 66492 62368 166100 60531 82995 137280 93390 FALSE TRUE 69001.00667 135350.6519 68069.22164 63968.46847 153055.176 78005.31706 70550.67024 154419.7102 77802.60568 0.886872696 1.739667338 0.874896426 0.822189282 1.967224294 1.002605458 0.906790584 1.984762706 1 16.24753085 -1.150588853 4.67613838 0.999973454 1.248861552 0.030943816 0.462970546 0.000116713 2.12E-05 0.408348536 0.096238415 0.070698654 1.150588853 0.248888097 DTLYEAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DTLYEAVR 8 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;;; 109.01 0.0086081 1495530000 887662 2893510 679523 734679 2764620 532295 664982 2190060 2092160 FALSE TRUE 832104.8199 3107748.491 695641.6065 753532.1069 2547497.897 685959.9254 565274.1225 2463493.812 1742964.98 0.477407653 1.783024058 0.399113932 0.432327738 1.461588687 0.393559213 0.324317544 1.413392604 1 20.73311215 3.92378622 9.850236122 0.715913974 1.206527004 0.062024675 0.519105441 0.80349826 144.3832089 0.123331115 0.223015119 8390.46867 -3.92378622 0.49061303 DTNGENIAESLVAEGLATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DTNGENIAESLVAEGLATR 19 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;; 321.81 1.11E-61 154424800 134848 154697 157573 159122 165443 137373 187738 130403 152045 FALSE TRUE 126408.1044 166150.9268 161310.706 163205.3399 152449.7741 177030.355 159588.4298 146684.1016 126667.7073 0.997950521 1.311707068 1.273495112 1.288452625 1.203540961 1.397596585 1.259898306 1.158022868 1 16.95068924 -0.554669425 7.37287159 1.000000044 1.25460369 0.313134234 0.107001838 0 0 0.092935086 0.02190501 0.278824271 0.554669425 0.254603646 DTNGENIAESLVAEGLATRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTNGENIAESLVAEGLATRR 20 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 144.01 2.59E-07 51388000 19148 34065 24022 29134 52165 26257 45340 30002 124000 FALSE TRUE 17949.56086 36587.20804 24591.81318 29881.62776 48068.17132 33836.96965 38541.68792 33747.81574 103303.5989 0.173755426 0.354171669 0.238053789 0.289260278 0.465309745 0.327548798 0.373091435 0.32668577 1 16.65653099 -5 0.267768845 5.609838821 0.270162177 0.901296057 0.071572394 56.33268516 0.548839736 143.3586575 0.083070844 1.00E-05 5 -5.339676644 DTNYTLNTDSLDWALYDHLMDFLADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DTNYTLNTDSLDWALYDHLMDFLADR 26 0 Q07021;I3L3Q7;I3L3B0 Q07021 C1QBP "Complement component 1 Q subcomponent-binding protein, mitochondrial" 0 ;;; 189.86 6.09E-18 410395000 340855 314110 286583 254790 448367 298022 265126 383607 371101 FALSE TRUE 319521.494 337367.0312 293380.8841 261328.3428 413154.0644 384056.1134 225372.8176 431501.1784 309161.8457 1.033508819 1.091231133 0.948955662 0.845280058 1.336368217 1.242249387 0.72898005 1.395712907 1 18.23800276 4.219539994 22.88503519 1.04564493 1.062369963 0 0.21061863 2236.547658 6751490.62 0.049861039 0.111482931 16578.29999 -4.219539994 0.016725034 DTPDEPWAFPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DTPDEPWAFPAR 12 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;;; 225.87 3.88E-11 3809170000 2357490 2188000 2357170 2353160 2429470 1948694 2679900 2065280 2545050 FALSE TRUE 2209938.909 2350001.797 2413083.186 2413546.069 2238669.226 2511250.323 2278073.874 2323134.754 2120264.713 1.042293868 1.108353019 1.138104676 1.138322991 1.055844212 1.184404149 1.07442899 1.095681468 1 21.01581296 0.623027136 1.330349856 1.00024403 1.111940801 0.381754006 0.041961265 1.277638103 3.29024975 0.035906874 0.010689769 4.197852124 -0.623027136 0.111696771 DTPENNPDTPFDFTPENYKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DTPENNPDTPFDFTPENYKR 20 1 E7EPT4;P19404 E7EPT4 NDUFV2 "NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial" 0 ;; 227.95 5.43E-25 460280000 507952 398365 408772 371273 573110 347289 462220 430178 777250 FALSE TRUE 476160.191 427860.3591 418468.2649 380800.4937 528100.2524 447545.6965 392914.402 483886.6702 647521.9538 0.735357602 0.660765796 0.646261123 0.588088931 0.815571193 0.691166831 0.606797036 0.747289984 1 19.30456958 0.926095855 7.123835541 0.999997472 0.672168891 0.7115239 0.064176155 0.597208138 57.31879069 0.058772414 0.014736265 8.435209134 -0.926095855 -0.327828581 DTPGFIVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTPGFIVNR 9 0 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PQV5;A0A1W2PNM1;A0A1W2PQ78 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 77.282 0.076868 191870000 132930 139260 152550 155380 169260 150720 135320 124430 156110 FALSE TRUE 124610.1486 149570.9553 156168.558 159367.3139 155967.0024 194230.4173 115030.0222 139965.3594 130054.2325 0.958139894 1.150066033 1.200795661 1.225391214 1.199245879 1.493457103 0.884477345 1.076207646 1 16.98875383 1.627742409 24.9999985 0.985281223 1.197758601 0.361814987 0.136038122 0.904809306 1135.156868 0.059493009 0.032934313 42.43677861 -1.627742409 0.212477378 DTPGHGSGWAET(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTPGHGSGWAETPR 14 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 DTPGHGSGWAET(1)PR 117.3 0.0011464 353200000 242890 446210 429240 401760 434550 350680 518280 395020 412740 TRUE FALSE 227687.9485 479247.8527 439421.7755 412069.8418 400422.1959 451915.6232 440568.7255 444339.1165 343851.0276 0.66217033 1.393765946 1.277942307 1.198396424 1.164522319 1.314277367 1.281277908 1.292243096 1 18.39142413 4.74628137 24.99450807 1.262534251 0.662170041 0.738104396 0.107504376 440.9867516 1427579.57 0.023459066 0.253071305 55754.68541 -4.74628137 -0.60036421 DTPGHGSGWAETPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTPGHGSGWAETPR 14 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 152 6.78E-06 1543770000 1059090 1535270 1503550 1475310 1459380 1234040 1660540 1347850 1243830 FALSE TRUE 992803.4474 1648942.988 1539214.916 1513168.952 1344766.182 1590287.315 1411557.443 1516132.039 1036226.738 0.958094799 1.591295542 1.48540359 1.460268199 1.29775283 1.534690486 1.362209053 1.463127696 1 19.98290828 -0.89274223 5.988205813 0.999999901 1.420950094 0.319098993 0.177105325 2.08E-07 3.85E-08 0.153183796 0.036105758 0.128014089 0.89274223 0.420950192 DTPLEHHLYVVSYEAAGEIVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTPLEHHLYVVSYEAAGEIVR 21 0 Q86TI2;Q86TI2-4;Q86TI2-2;M0R1L4 Q86TI2 DPP9 Dipeptidyl peptidase 9 0 ; 154.12 2.13E-08 87705000 83154 88773 93026 93042 101490 79764 108192 88586 88257 FALSE TRUE 77949.53957 95345.84529 95232.62065 95429.61524 93519.38479 102790.5719 91969.61401 99646.1571 73526.33654 1.060158077 1.29675773 1.295217811 1.297897049 1.271916829 1.398010247 1.250839064 1.355244417 1 16.16597348 -1.080748259 4.845193826 0.999989991 1.284666034 0.494665818 0.088173728 0.060016123 25368741.97 537.5010878 0.018389573 0.083033193 1.080748259 0.284676042 DTPRPDHPPHDGHS(ph)PASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DTPRPDHPPHDGHSPASR 18 1 Q9C0J8 Q9C0J8 WDR33 pre-mRNA 3 end processing protein WDR33 1 DTPRPDHPPHDGHS(1)PASR;DTPRPDHPPHDGHS(1)PASR;DTPRPDHPPHDGHS(0.998)PAS(0.002)R;DTPRPDHPPHDGHS(0.995)PAS(0.005)R;DTPRPDHPPHDGHS(0.996)PAS(0.004)R;DTPRPDHPPHDGHS(0.962)PAS(0.038)R 149.18 3.21E-08 2279720000 348605 332743 338994.9 336284.6 366524.3 314883.3 398698.2 340018 460572.5 TRUE FALSE 326786.4353 357379.6379 347036.0191 344914.2322 337738.96 405784.997 338917.1062 382469.9958 383699.9743 0.851671767 0.931403862 0.904446292 0.898916485 0.880216269 1.057558051 0.883286758 0.996794426 1 18.54961914 DTPTSAGPNS(ph)FNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTPTSAGPNSFNK 13 0 Q8WW12;Q8WW12-3 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 1 DTPTSAGPNS(1)FNK 226.62 1.10E-11 104530000 274230 128730 170030 136900 160470 117060 168290 119580 200180 TRUE FALSE 257066.4338 138261.3031 174063.1919 140413.0858 147867.3335 150853.3217 143056.4768 134509.8262 166768.6648 1.54145525 0.829060443 1.043740394 0.841963243 0.886661374 0.904566346 0.857813889 0.806565348 1 17.34748871 4.742300547 24.96066901 0.897954819 1.541455501 0.881607082 0.074298758 111.8370963 746380.7627 0.016887692 0.126649337 55245.96281 -4.742300547 0.643500683 DTQS(ph)PSTCSEGLLGWSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DTQSPSTCSEGLLGWSQK 18 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DTQS(0.664)PS(0.335)T(0.001)CSEGLLGWSQK;DT(0.002)QS(0.514)PS(0.482)T(0.002)CSEGLLGWSQK;DTQS(0.904)PS(0.096)TCSEGLLGWSQK;DTQS(0.971)PS(0.028)TCSEGLLGWSQK;DTQS(0.999)PS(0.001)TCSEGLLGWSQK 322.33 1.04E-61 1952300000 2385820 1755750 2024470 2072720 1890290 1401990 2119520 1422480 1501010 TRUE FALSE 2236495.785 1885747.557 2072491.384 2125909.504 1741834.248 1806721.754 1801717.653 1600079.759 1250481.734 1.78850736 1.508016875 1.657354384 1.700072417 1.392930581 1.444820587 1.440818849 1.279570677 1 20.25405255 1.000544869 0.383091272 0.951908405 1.675334244 0.831333431 0.092390639 0.558243272 0.22827592 0.147616846 0.080221117 10.01255396 -1.000544869 0.723425838 DTRPSSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTRPSSEK 8 1 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A087WT27;A0A494C1E2;A0A494C1Q4;J3KN95;A0A494C099;A0A494C163;D6RCQ8;D6RIS6 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 ; 79.059 0.026465 276830000 614290 612240 696260 657380 649280 551000 789690 636830 700240 FALSE TRUE 575842.6854 657570.8866 712775.616 674249.4837 598288.1679 710064.7553 671283.3156 716339.6273 583365.4203 0.987104592 1.127202374 1.221833848 1.155792682 1.025580446 1.217186913 1.150708102 1.227943245 1 19.15404035 4.725473248 3.355959818 1.154147403 0.967430858 0.271839246 0.077687215 0.3450097 6.577916035 0.016926481 0.163191497 53146.32616 -4.725473248 -0.186716545 DTS(ph)GLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTSGLER 7 0 Q9H307 Q9H307 PNN Pinin 1 DT(0.246)S(0.754)GLER 111.46 0.0068969 274280000 977220 812130 813570 870390 995260 724050 1065200 788350 1106600 TRUE FALSE 916057.5446 872260.9502 832868.2646 892725.681 917096.2943 933071.481 905483.1488 886777.2329 921901.3111 0.99366118 0.946154366 0.903424536 0.968352762 0.994787927 1.012116449 0.982190976 0.961900392 1 19.81425279 3.004869871 24.84565011 0.989489005 0.9404256 0.362883018 0.025168053 114.1602673 582427.2763 0.007393004 0.008807206 1011.276397 -3.004869871 -0.049063404 DTS(ph)PSSGSAVSSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DTSPSSGSAVSSSK 14 0 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8W6A0;Q8NEY8-7;Q8NEY8-6;F8WF16;B7Z8L1;Q8NEY8-3;Q8NEY8-5 F8W0Q9;Q8NEY8-6 PPHLN1 Periphilin-1 1 DTS(1)PSSGSAVSSSK;DTS(0.997)PS(0.001)S(0.001)GSAVSSSK;DTS(0.954)PS(0.001)S(0.045)GSAVSSSK;DTS(0.961)PS(0.019)S(0.019)GSAVSSSK;DT(0.003)S(0.962)PS(0.033)S(0.003)GSAVSSSK;DTS(0.998)PS(0.002)SGSAVSSSK;DTS(0.999)PS(0.001)SGSAVSSSK;DT(0.133)S(0.864)PS(0.002)SGSAVSSSK 360.45 1.80E-82 11908072000 18465540 13245210 15232010 14538660 15100390 11488870 18864200 12811450 16839860 TRUE FALSE 17309814.81 14225899.13 15593320.47 14911746.63 13914466.28 14805520.26 16035688.34 14410987.73 14029178.58 1.233843786 1.014022243 1.111492051 1.06290946 0.991823306 1.055337644 1.143024037 1.027215361 1 23.7419272 4.748318291 24.8442623 1.061038008 1.233843888 0.577611353 0.048504394 968.1021717 2464853.956 0.011408033 0.151354276 56016.79935 -4.748318291 0.17280588 DTS(ph)SDKDLDDALDKLSDSLGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTSSDKDLDDALDKLSDSLGQR 22 2 E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 E7EVY3 CAST 1 DT(0.109)S(0.491)S(0.401)DKDLDDALDKLSDSLGQR 117.96 5.96E-05 38896000 101520 43187 53361 52763 61714 38197 82242 43405 73301 TRUE FALSE 95166.04442 46384.61042 54626.74812 54116.98791 56867.23138 49223.85382 69910.5756 48824.2098 61066.58956 1.558397892 0.759574274 0.894543948 0.886196336 0.931233131 0.806068493 1.144825282 0.799524096 1 15.89809566 4.746458619 24.81280365 0.90462566 1.558398246 0.776870961 0.110424011 420.5631531 1321230.669 0.026247548 0.285886724 55777.44536 -4.746458619 0.653772586 DTSATSQSVNGS(ph)PQAEQPSLESTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTSATSQSVNGSPQAEQPSLESTSK 25 0 C9J0I9;Q86WB0;Q86WB0-2;Q86WB0-3;F8WAU5 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 DTSATSQSVNGS(1)PQAEQPSLESTSK 355.06 2.64E-103 253480000 414820 314000 378800 355820 399480 320040 441040 363950 458920 TRUE FALSE 388857.1567 337248.8867 387785.3149 364950.9436 368106.4522 412430.3526 374910.1464 409389.9587 382323.2873 1.017089907 0.882103963 1.014286411 0.954561116 0.962814624 1.078747663 0.980610282 1.070795247 1 18.54443355 2.330542502 10.83989386 1.027200174 0.960585812 0.325352375 0.046835893 0.436607819 48.18849968 0.01499637 0.012540395 214.0634409 -2.330542502 -0.066614362 DTSEDIEELVEPVAAHGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DTSEDIEELVEPVAAHGPK 19 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;;;; 207.92 2.95E-16 686841000 1459880 1320270 1330730 1367860 1392040 1159289 1764230 1252110 1698490 FALSE TRUE 1368508.717 1418024.165 1362295.544 1402961.603 1282714.794 1493956.915 1499700.09 1408438.69 1415001.046 0.967143254 1.002136478 0.962752323 0.991491566 0.906511551 1.055799159 1.059857937 0.995362296 1 20.43237169 2.207970257 24.99999267 1.036471635 0.971648283 0.45469014 0.032670341 164.941817 134797.8825 0.011496341 0.008491547 161.4247999 -2.207970257 -0.064823352 DTSFEQHVLWHTGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 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 ;;;;;;;;;;;; 295.66 2.73E-44 34415606000 22023734 23106612 25801504 25646537 27661721 21153700 33442548 24193266 32273154 FALSE TRUE 20645307.8 24817449.59 26413527.86 26304670.56 25489281.01 27260429.79 28428148.39 27213848.52 26886556.1 0.767867321 0.923043081 0.982406514 0.978357751 0.948030715 1.0139056 1.057336919 1.012173088 1 24.68038164 5.832107946 0.645184981 1.012051701 1.14E-15 0.87136769 0.02822998 4.315717355 0.46532589 0.012440996 4.438277621 679372.4727 -5.832107946 -1.012051701 DTSLYRPALEELRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DTSLYRPALEELRR 14 2 Q13200;C9JPC0;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;;; 218.68 2.98E-12 2158410000 1049460 1476890 1173410 1173060 1567650 903330 1282440 1258440 1824310 FALSE TRUE 983776.1719 1586240.472 1201243.839 1203162.706 1444533.093 1164106.707 1090150.028 1415559.004 1519820.876 0.647297447 1.043702253 0.790385143 0.791647703 0.950462726 0.765949939 0.717288494 0.931398579 1 20.53546987 3.731449732 24.88600565 0.827909782 0.886783243 0 0.131706893 703.318231 4043586.177 0.031505556 0.054368664 5388.274748 -3.731449732 0.058873461 DTSPDKGELVS(ph)DEEEDT ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTSPDKGELVSDEEEDT 17 1 Q9UPU7 Q9UPU7 TBC1D2B TBC1 domain family member 2B 1 DTSPDKGELVS(0.986)DEEEDT(0.014);DTSPDKGELVS(0.999)DEEEDT(0.001) 189.59 9.10E-10 284640000 659870 517800 509280 531890 651080 393800 669800 523510 612940 TRUE FALSE 618569.9146 556138.4508 521360.3621 545539.1979 599946.8031 507483.6672 569369.7081 588871.3759 510636.3543 1.211370694 1.089108612 1.021001262 1.068351662 1.174900295 0.993825964 1.115019922 1.153210834 1 18.96193673 1.121475186 0.008105086 2.04E-07 2.14476576 0.145669748 0.068276582 5433.858307 33.56896069 4475.380502 4403.271519 13.2274213 -1.121475186 2.144765556 DTSQS(ph)DKDLDDALDKLSDSLGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTSQSDKDLDDALDKLSDSLGQR 23 2 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;A0A0C4DGD1;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5 P20810-6;P20810-5;A0A0C4DGB5 CAST Calpastatin 1 DT(0.301)S(0.301)QS(0.397)DKDLDDALDKLSDSLGQR 63.085 0.021184 40862000 89549 38003 50270 49884 50455 40091 64571 35069 62871 TRUE FALSE 83944.28794 40816.78166 51462.42814 51164.10789 46492.46783 51664.62088 54889.178 39447.44185 52377.42394 1.602680728 0.779281961 0.982530722 0.976835133 0.887643269 0.986391025 1.047954899 0.753138258 1 15.67665749 4.746661323 24.99409283 0.932689236 1.602681058 0.830329301 0.095994994 397.7856356 1227308.315 0.022033729 0.246599708 55803.48517 -4.746661323 0.669991822 DTSQSDKDLDDALDKLS(ph)DSLGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.978)DS(0.022)LGQR;DTSQSDKDLDDALDKLS(0.965)DS(0.035)LGQR 77.522 0.0076553 70631000 217270 93952 126137 129674 135278 89625 173110 103664 158544 TRUE FALSE 203671.4585 100908.3038 129129.0292 133001.6544 124653.8116 115498.2826 147153.7626 116606.6786 132081.9822 1.542007889 0.763982355 0.97764303 1.006962889 0.943760909 0.874443892 1.114109284 0.88283562 1 17.01107415 4.749618613 24.97900445 0.947052077 1.542008236 0.801860448 0.093189052 737.3583546 1665593.34 0.022541085 0.344028396 56184.77075 -4.749618613 0.594956159 DTSQSDKDLDDALDKLSDSLGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 165.85 7.12E-12 680600000 1206160 589830 787810 763780 811330 508900 1001090 625320 1216160 FALSE TRUE 1130668.599 633501.6269 806497.2252 783379.8879 747611.4145 655811.1687 850985.8482 703392.5785 1013175.039 1.115965707 0.625263752 0.796009765 0.773193039 0.737889689 0.647283187 0.839919871 0.694245862 1 19.95045201 -1.927896985 4.80913241 1.105821666 0.764859454 0.199025359 0.137021589 0.08278371 0.001241171 0.070646046 0.027182748 0.011806006 1.927896985 -0.340962212 DTSSDKDLDDALDKLSDSLGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTSSDKDLDDALDKLSDSLGQR 22 2 E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 E7EVY3 CAST 0 89.946 0.0013795 38112000 75647 56394 60113 59551 61775 49956 72559 50620 76548 FALSE TRUE 70912.3893 60569.47044 61538.90875 61079.17948 56923.44069 64377.48623 61679.45155 56940.01843 63771.64428 1.11197367 0.94978687 0.964988585 0.957779593 0.892613658 1.009500178 0.967192429 0.892873613 1 15.96062746 4.739799873 24.83032869 0.955334376 1.111973725 0.628785273 0.038056623 59.10615905 1184132.282 0.008234265 0.050709722 54928.76986 -4.739799873 0.156639349 DTSSS(ph)PTTGSTVQSVDLIFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DTSSSPTTGSTVQSVDLIFTR 21 0 P57060 P57060 RWDD2B RWD domain-containing protein 2B 1 DT(0.011)S(0.009)S(0.104)S(0.868)PT(0.007)T(0.001)GSTVQSVDLIFTR;DTS(0.002)S(0.016)S(0.49)PT(0.49)T(0.003)GSTVQSVDLIFTR;DTS(0.002)S(0.019)S(0.976)PT(0.003)TGSTVQSVDLIFTR 271.64 1.21E-44 110756000 123458 112180 123909 131998 131810 109414 131662 110599 120854 TRUE FALSE 115730.9842 120485.9239 126848.18 135385.2922 121458.1743 141000.0456 111920.5054 124407.5286 100682.6867 1.149462614 1.196689599 1.259880762 1.344673018 1.206346179 1.40043984 1.111616198 1.235639739 1 16.61945609 1.612475741 25 1.130214044 1.253765677 0.352047322 0.091054514 0.505860014 2728.938538 0.040292594 0.021405781 40.97092233 -1.612475741 0.123551633 DTTALSFFHMLNGAALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTTALSFFHMLNGAALR 17 0 P42704 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 162.29 2.86E-09 64716000 36191 73261 40012 42333 86726 32014 34958 71495 61935 FALSE TRUE 33925.86991 78685.32067 40961.10354 43419.33645 79914.8898 41255.9221 29716.37243 80421.30813 51597.64838 0.657508064 1.524978815 0.793856015 0.841498359 1.54880876 0.799569814 0.575924938 1.558623516 1 15.65501769 DTTDKGQQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DTTDKGQQLR 10 1 Q13144;A0A3B3IUB1 Q13144 EIF2B5 Translation initiation factor eIF-2B subunit epsilon 0 ;; 133.81 0.00017087 642090000 1109340 1031540 1106160 1183040 1221330 838370 1364040 1099510 1480810 FALSE TRUE 1039908.39 1107916.295 1132398.638 1213398.809 1125411.668 1080393.809 1159514.865 1236786.244 1233653.245 0.842950314 0.898077559 0.91792296 0.983581744 0.912259319 0.875767817 0.939903389 1.002539611 1 20.23450551 7.999999999 0.088968059 1.052360907 0.551725333 0.526564308 0.036357361 146.2625781 0.936238219 0.698858488 8.942689575 99999999.88 -7.999999999 -0.500635575 DTTINEIEDTFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DTTINEIEDTFR 12 0 Q16864;Q16864-2 Q16864 ATP6V1F V-type proton ATPase subunit F 0 ;;; 312.78 5.64E-46 376611000 393750 403380 403811 366709 418249 343411 462762 377858 460450 FALSE TRUE 369105.8904 433246.6749 413389.5876 376119.3738 385401.4107 442548.1809 393375.1342 425034.4031 383597.9204 0.962220781 1.129429155 1.077663787 0.980504205 1.004701512 1.153677216 1.025488182 1.108020613 1 18.54923537 DTTKLEPAS(ph)PPEDTSAEVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTTKLEPASPPEDTSAEVSR 20 1 E9PFE2;Q9UHL9-2;Q9UHL9;Q9UHL9-3 E9PFE2 GTF2IRD1 General transcription factor II-I repeat domain-containing protein 1 1 DTTKLEPAS(1)PPEDTSAEVSR 112.28 9.44E-05 189310000 213410 188740 207430 213110 258170 112850 223750 174110 319570 TRUE FALSE 200053.049 202714.506 212350.3376 218578.7634 237894.3696 145427.963 190200.7647 195848.0168 266231.7025 0.751424594 0.761421364 0.797614768 0.821009524 0.893561388 0.546245852 0.714418166 0.73562996 1 18.02232285 DTTS(ph)PMELAALEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTTSPMELAALEK 13 0 Q6VY07-2;Q6VY07 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 DTTS(1)PMELAALEK;DTT(0.02)S(0.98)PMELAALEK 275.19 3.58E-32 104346000 582190 426180 525650 505890 540470 361550 590570 396470 549060 TRUE FALSE 545751.7671 457734.8106 538118.6662 518871.9939 498023.6664 465923.6157 502019.5111 445970.1522 457418.3389 1.193113001 1.000691865 1.176425649 1.134348909 1.088770659 1.018594088 1.097506305 0.974972174 1 18.80315468 1.624964636 0.91643909 0.993674159 1.111362208 0.387845004 0.059916369 0.622563999 1.011151227 0.051558851 0.020700186 42.16621671 -1.624964636 0.117688049 DTVTISGPQAPVFEFVEQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 244.17 1.64E-29 132817000 28659.7 48271.1 43156.5 47400.2 50901.4 55452.5 45692.8 48237.6 36668.6 FALSE TRUE 26865.94054 51845.14247 44180.19256 48616.56938 46903.80937 71460.73655 38841.58883 54260.17054 30548.37377 0.87945567 1.697149015 1.446237135 1.591461783 1.535394641 2.339264836 1.271478119 1.776204879 1 14.89880796 4.743179512 24.45434965 1.603500877 0.879455274 0.286514024 0.347037141 416.2109148 2203487.17 0.07263962 0.581477593 55357.88794 -4.743179512 -0.724045603 DTVTISGPQAPVFEFVEQLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTVTISGPQAPVFEFVEQLRK 21 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 292.97 1.43E-54 5372800000 1223250 1252280 1260260 1310410 1559490 1043690 1761500 1173850 1894740 FALSE TRUE 1146688.966 1345000.114 1290153.962 1344037.339 1437013.946 1344986.36 1497379.428 1320407.756 1578495.654 0.726444171 0.852077173 0.817331337 0.851467241 0.910369277 0.85206846 0.948611689 0.836497556 1 20.59011886 8 0.082145203 1.099714698 0.227026678 0.650145705 0.044114546 106.5071796 0.635477482 0.986755503 10.52901691 100000000 -8 -0.87268802 DTWHQVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTWHQVYR 8 0 O60313-10;O60313-9;O60313-2;E5KLJ9;O60313-13;O60313;O60313-11;A0A2R8YDM2;A0A2R8Y3X5;C9JMB8;A0A2R8YE78;A0A2R8YFD1;H7C141 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 68.224 0.057062 176580000 54706 93188 70297 83282 106230 86433 60586 75853 71485 FALSE TRUE 51282.04911 100087.7365 71964.47804 85419.15712 97887.12431 111384.804 51501.69175 85323.41402 59553.69169 0.861106132 1.680630262 1.208396591 1.434321781 1.643678528 1.870325765 0.864794277 1.432714104 1 15.86190332 -0.714176762 6.203293904 0.999999996 1.380568265 0.11361951 0.328336218 1.77E-08 3.56E-09 0.29625858 0.069828816 0.193118215 0.714176762 0.380568269 DTYGVRPLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTYGVRPLFK 10 1 P08243-2;P08243;P08243-3;F8WEJ5;C9J057;C9JT45 P08243-2 ASNS Asparagine synthetase [glutamine-hydrolyzing] 0 ; 119.53 0.0006205 1059550000 1046970 1127030 1092390 1169480 1187970 808220 1370700 1002430 1001300 FALSE TRUE 981442.0166 1210476.474 1118302.007 1199490.837 1094671.628 1041539.994 1165176.26 1127585.592 834176.5614 1.17653991 1.451103435 1.340605884 1.437933997 1.312278094 1.248584583 1.396798129 1.351734926 1 19.66999325 -1.595821507 2.386943422 0.96196672 1.351026382 0.619634121 0.083142298 2544620.526 2073106.174 605813.7237 0.018893117 0.025361708 1.595821507 0.389059662 DTYS(ph)DR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTYSDR 6 0 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 1 DT(0.001)YS(0.999)DR 81.548 0.064604 61654000 167490 116870 164770 136390 128970 155580 186600 132850 114600 TRUE FALSE 157007.0999 125523.1764 168678.4222 139889.9983 118841.2164 200493.4204 158621.0623 149436.6149 95472.51966 1.644526618 1.314757135 1.766774595 1.465238362 1.244768828 2.100011826 1.661431613 1.565231707 1 16.54279791 3.981807914 24.64876227 1.597554115 1.466671774 0 0.305499706 707.4886088 3720864.072 0.070494075 0.144830831 9589.763889 -3.981807914 -0.130882342 DTYS(ph)DRS(ph)GS(ph)SSPDSEITELKFPSINHD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTYSDRSGSSSPDSEITELKFPSINHD 27 2 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 3 DT(0.415)Y(0.13)S(0.451)DRS(0.501)GS(0.508)S(0.496)S(0.47)PDS(0.022)EIT(0.005)ELKFPSINHD 57.78 0.043397 52444000 84013 77596 79254 80129 91769 58004 91184 69855 136730 TRUE FALSE 78754.7763 83341.28858 81133.94231 82185.2458 84561.83292 74748.81318 77511.80571 78576.55052 113908.8797 0.691383995 0.731648742 0.712270567 0.721499904 0.742363836 0.656215858 0.680472022 0.68981936 1 16.79752069 -2.046005141 2.704370934 1.393674749 0.70439301 0.930865649 0.02541705 5528684.541 2584228.532 13451871.2 0.006967608 0.008994869 2.046005141 -0.689281739 DTYSDRS(ph)GSS(ph)SPDSEITELKFPSINHD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTYSDRSGSSSPDSEITELKFPSINHD 27 2 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 2 DTYS(0.002)DRS(0.946)GS(0.052)S(0.636)S(0.363)PDS(0.001)EITELKFPSINHD 169.26 3.43E-12 192360000 88627 120470 106700 105140 148730 72781 117200 106940 270230 TRUE FALSE 83079.99427 129389.7241 109230.9744 107838.0704 137049.3457 93791.6932 99626.94803 120291.6944 225126.8672 0.369036336 0.57474137 0.485197417 0.479010221 0.608764949 0.416617058 0.442536909 0.534328469 1 17.78037872 0.942294125 17.70407794 1.000000001 0.490026326 0.842773457 0.069684141 133.2391971 40878.25062 0.063175601 0.015794023 8.755765571 -0.942294125 -0.509973675 DTYSDRSGSS(ph)S(ph)PDSEITELKFPSINHD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DTYSDRSGSSSPDSEITELKFPSINHD 27 2 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 2 DT(0.005)Y(0.026)S(0.09)DRS(0.374)GS(0.414)S(0.449)S(0.366)PDS(0.246)EIT(0.015)ELKFPS(0.015)INHD 77.31 0.072369 184820000 121190 174030 176180 192150 229380 107130 187130 180380 493690 TRUE FALSE 113604.9342 186915.3623 180359.0728 197080.8943 211365.4201 138056.6919 159071.5937 202900.8401 411289.9496 0.276216169 0.454461293 0.438520496 0.479177511 0.513908546 0.335667555 0.386762657 0.49332798 1 18.64979629 0.801961609 4.200482377 0.999988438 0.419680982 0.875963385 0.068932557 0.693895645 14.41944829 0.063798531 0.016254659 6.33813681 -0.801961609 -0.580307456 DTYYDFDAEAADHKQEEDMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DTYYDFDAEAADHKQEEDMK 20 1 Q7KZ85;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 0 ; 220.36 5.16E-25 168569000 550680 249980 356320 315050 344690 244470 455860 265170 487150 FALSE TRUE 516213.9218 268488.7793 364772.0787 323134.7164 317619.4378 315044.5204 387508.025 298277.0582 405841.5179 1.271959371 0.661560652 0.898804244 0.796209116 0.782619382 0.776274744 0.95482598 0.734959449 1 18.63055694 -0.938068691 7.41198919 1 0.845639974 0.059075725 0.167947798 5.27E-09 7.11E-10 0.141545667 0.033362633 0.115327084 0.938068691 -0.154360026 DVACGANHTLVLDSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVACGANHTLVLDSQK 16 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 124.92 0.00068878 0 113040 88110 107060 89688 108360 72862 113040 89557 99045 FALSE TRUE 105965.0282 94633.75608 109599.5138 91989.54592 99849.8427 93896.07658 96090.70141 100738.3886 82513.74964 1.284210554 1.146884689 1.328257584 1.114838997 1.210099446 1.137944609 1.164541689 1.220867904 1 16.33234692 -4.999999994 0.155612633 0.2620791 1.259303382 0.504924256 0.064295083 105.3302638 0.956398806 23.96245749 0.271406717 1.00E-05 4.999999994 0.997224282 DVAEVDTVRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVAEVDTVRR 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 199.33 4.50E-07 1421840000 1154040 1595280 1428590 1543160 1611730 1079630 1584250 1362970 1729230 FALSE TRUE 1081810.696 1713396.191 1462476.829 1582760.098 1485151.227 1391301.655 1346706.42 1533139.805 1440610.342 0.750939144 1.18935436 1.015178627 1.098673286 1.030918066 0.965772364 0.934816571 1.064229348 1 20.45824874 2.336482412 5.458070216 0.979835865 1.044982347 0 0.115892109 0.598485487 27.41084649 0.037715699 0.031200687 217.0113318 -2.336482412 0.065146482 DVAFTVGEGEDHDIPIGIDK ddPTM_SK-BR-3_Pertuzumab_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" 0 179.95 5.64E-17 103850000 388300 305240 361920 352800 387230 281960 456540 343160 451630 FALSE TRUE 363996.9961 327840.2872 370504.9133 361853.4453 356818.5178 363357.2748 388086.0653 386004.2814 376250.0354 0.967433786 0.87133623 0.984730574 0.961736641 0.948354775 0.96573353 1.031457884 1.025924904 1 18.52133219 2.478881517 0.639969146 1.024396227 0.922604799 0.476541723 0.032569764 0.591445605 0.492729284 0.026579966 0.022342952 301.2184138 -2.478881517 -0.101791428 DVAIKEPLVDVVDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVAIKEPLVDVVDPK 15 1 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ; 147.92 3.31E-06 260270000 952860 560830 760440 706140 765290 541340 991360 672320 1116390 FALSE TRUE 893222.1935 602354.4367 778477.9959 724260.7479 705187.2104 697616.0701 842714.7713 756260.632 930057.2968 0.960394802 0.647653041 0.837021545 0.778727021 0.758219104 0.750078595 0.906089092 0.813133378 1 19.82696007 0.807779913 0.705947379 0.998833352 0.776091247 0.33045013 0.085995921 0.954957091 0.997636088 0.078606111 0.029518499 6.423621053 -0.807779913 -0.222742105 DVAVSYYHFYHMAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVAVSYYHFYHMAK 14 0 P50225;H3BRY5;P50225-2;H3BQX5;P50226;E9PKR8 P50225;P50226 SULT1A1;SULT1A2 Sulfotransferase 1A1;Sulfotransferase;Sulfotransferase 1A2 0 146.79 4.75E-06 180180000 106350 176250 134220 142920 164300 103570 171190 161460 145560 FALSE TRUE 99693.74334 189299.7334 137403.7618 146587.5692 151396.5408 133468.9777 145521.6488 181618.6364 121265.0956 0.822114087 1.561040565 1.133085832 1.208819144 1.248475828 1.100638044 1.200029143 1.497699197 1 16.88780483 3.726106223 24.99964958 1.202867944 1.275169404 0 0.219217388 239.0562922 5888089.875 0.052097585 0.08595855 5322.384227 -3.726106223 0.07230146 DVCLYPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVCLYPR 7 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 97.075 0.028531 499370000 137030 293770 140870 132640 314750 105070 158690 252350 274010 FALSE TRUE 128453.5369 315521.0365 144211.5029 136043.767 290030.8046 135402.0033 134895.9077 283856.453 228275.9608 0.562711625 1.382191254 0.63174196 0.595961863 1.270527144 0.593150513 0.590933479 1.243479392 1 17.80041942 5.006338977 19.24138127 0.88227841 0.139531141 0.105838453 0.308796398 99187751.01 3107884851 0.071603521 1840483865 101470.3076 -5.006338977 -0.742747269 DVCTELLPLIKPQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVCTELLPLIKPQGR 15 1 P16152 P16152 CBR1 Carbonyl reductase [NADPH] 1 0 ; 190.27 2.04E-07 2732300000 3910700 3525900 3906600 3728600 4151900 3244700 4909600 3706300 5121400 FALSE TRUE 3665936.268 3786961.305 3999266.397 3824282.189 3825826.522 4181392.217 4173451.058 4169039.714 4266605.254 0.85921618 0.887581831 0.937341553 0.896329039 0.896690998 0.980027907 0.978166671 0.977132747 1 22.02465721 2.236414979 24.53268778 0.981529492 0.900117174 0.826583482 0.020043907 19.70761183 225326.1686 0.00753624 0.005842841 172.351465 -2.236414979 -0.081412318 DVDASPS(ph)PLSVQDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVDASPSPLSVQDLK 15 0 Q8IWZ8 Q8IWZ8 SUGP1 SURP and G-patch domain-containing protein 1 1 DVDASPS(1)PLSVQDLK 167.71 8.55E-10 0 58209 43337 52747 50278 50069 43052 66310 52831 75145 TRUE FALSE 54565.8026 46545.71657 53998.18375 51568.2186 46136.78271 55480.41351 56367.43109 59427.06665 62602.81404 0.871619007 0.743508375 0.862552021 0.823736431 0.736976179 0.886228748 0.900397721 0.949271491 1 15.93393989 1.550235815 1.281183538 0.989184244 0.807827799 0.667286876 0.047065324 0.232554966 0.731631404 0.038731458 0.013546825 35.50060997 -1.550235815 -0.181356446 DVDDDGEEKELMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVDDDGEEKELMER 14 1 Q5STZ8;Q8NE71;Q8NE71-2;A0A0G2JIC2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 143.38 8.34E-06 432520000 172790 101060 125550 118090 127210 91181 128870 97386 171270 FALSE TRUE 161975.3823 108542.5876 128528.1053 121120.3893 117219.4397 117503.4745 109547.1399 109544.8565 142683.9306 1.135204096 0.760720476 0.900788931 0.848871971 0.821532175 0.823522832 0.767760879 0.767744875 1 17.12246334 4.746177293 24.96457229 0.827109551 1.135204246 0.624631074 0.072488528 547.0586712 1793007.928 0.015642176 0.1655088 55741.32562 -4.746177293 0.308094696 DVDDFFEHER ddPTM_SK-BR-3_Pertuzumab_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 ; 212.82 3.36E-08 422060000 1134920 1072340 1145710 1083820 1115200 980440 1309050 975750 1040730 FALSE TRUE 1063887.383 1151737.169 1172886.782 1111632.656 1027616.691 1263477.112 1112770.105 1097574.535 867025.4396 1.227054403 1.328377596 1.352770898 1.282122306 1.185220921 1.457254948 1.283434204 1.26590811 1 19.7257148 0.689860008 2.268620754 1.000103257 1.311290268 0.62459229 0.072882139 1.021953072 6.657130096 0.064347491 0.017420826 4.896209677 -0.689860008 0.311187012 DVDDGS(ph)GSPHS(ph)PHQLSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVDDGSGSPHSPHQLSSK 18 0 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 2 DVDDGS(0.555)GS(0.445)PHS(1)PHQLSSK 133.68 6.41E-06 224520000 434200 347000 404360 413390 404250 233760 390990 292660 485710 TRUE FALSE 407024.1971 372692.2411 413951.6102 423998.2873 372501.8357 301242.7172 332364.6793 329199.2452 404641.8632 1.005887512 0.921042223 1.023007375 1.04783594 0.92057167 0.744467502 0.821379866 0.813557062 1 18.62628606 2.458756921 7.242280459 0.826289738 0.98985704 0.49737816 0.071898339 0.113319571 27.23251841 0.022626627 0.019237912 287.5788354 -2.458756921 0.163567301 DVDDGSGS(ph)PHS(ph)PHQLSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVDDGSGSPHSPHQLSSK 18 0 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 2 DVDDGS(0.445)GS(0.555)PHS(1)PHQLSSK 138.49 1.01E-06 610970000 586110 447930 539070 583730 592970 388590 501060 379410 667490 TRUE FALSE 549426.4213 481095.2033 551856.995 598709.5001 546400.5281 500769.6248 425930.7046 426780.1737 556081.6068 0.988031998 0.86515216 0.992402892 1.076657621 0.982590543 0.900532617 0.765949996 0.767477594 1 19.08493709 2.001623313 4.550714011 0.82053374 0.969983673 0.35088696 0.082656432 0.19191614 10.18582275 0.034321963 0.022369636 100.3744811 -2.001623313 0.149449933 DVDDGSGS(ph)PHSPHQLSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVDDGSGSPHSPHQLSSK 18 0 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 DVDDGS(0.07)GS(0.89)PHS(0.04)PHQLSSK 130.83 3.05E-05 627480000 273050 216690 245360 201680 278540 284290 446530 339160 508820 TRUE FALSE 255960.2879 232733.9531 251180.0551 206855.4502 256664.592 366359.9079 379576.9719 381504.8726 423894.6549 0.603829949 0.549037244 0.592553013 0.487987871 0.605491456 0.864271119 0.895451187 0.899999253 1 18.69334625 2.229669657 3.350642185 0.912854716 0.560343143 0.942908213 0.042762479 0.04852939 1.145442081 0.01567073 0.01163062 169.6952388 -2.229669657 -0.352511573 DVDDGSGSPHS(ph)PHQLSSK ddPTM_SK-BR-3_Pertuzumab_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(0.002)PHS(0.998)PHQLSSK;DVDDGSGSPHS(1)PHQLSSK 235.25 5.59E-24 1223110000 926990 899920 1044100 1192460 1071450 602550 765610 577320 1028240 TRUE FALSE 868971.3506 966551.0132 1068866.545 1223060.542 987302.639 776496.4034 650813.8881 649399.6728 856620.1013 1.014418584 1.128330997 1.247771963 1.42777474 1.152556002 0.906465307 0.759746225 0.7580953 1 19.70829601 2.199756914 3.478153756 0.817735121 1.206780256 0.655458845 0.122497177 0.133335543 3.351197532 0.048698602 0.035511277 158.4006336 -2.199756914 0.389045135 DVDEAHYAYSFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVDEAHYAYSFK 12 0 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ; 136.27 0.00011297 474850000 1601110 1506630 1557650 1536540 1730630 1193120 1899380 1484080 2178260 FALSE TRUE 1500899.383 1618182.453 1594598.194 1575970.218 1594713.301 1537554.375 1614585.602 1669370.655 1814694.334 0.827081099 0.891710754 0.878714483 0.868449407 0.878777914 0.847280088 0.889728684 0.919918371 1 20.79129513 0.913817961 1.707266247 0.999596802 0.870528671 0.837948692 0.018734062 0.168803102 0.996270854 0.016572211 0.004745793 8.200077574 -0.913817961 -0.129068131 DVDEIEAWISEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DVDEIEAWISEK 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 218.18 8.12E-11 149718000 370219 309300 336457 321133 388128 280208 397574 317222 454348 FALSE TRUE 347047.6536 332200.8938 344437.9189 329373.8165 357645.9925 361099.5008 337961.4696 356827.865 378514.3836 0.916867809 0.877644043 0.909973131 0.870175166 0.94486764 0.95399149 0.892862951 0.942706223 1 18.5299886 -4.545304043 0.139800887 1.283960772 0.874144255 0.577005904 0.025392308 81.9073998 0.791481363 6.532025306 0.152277923 2.85E-05 4.545304043 -0.409816517 DVDELPSLQPS(ph)VGSPSRPSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVDELPSLQPSVGSPSRPSSSR 22 1 O43815-2;O43815 O43815-2 STRN Striatin 1 DVDELPSLQPS(0.496)VGS(0.495)PS(0.009)RPSSSR 192.18 7.03E-18 732680000 321590 254950 313340 340730 355940 289800 352130 257620 463900 TRUE FALSE 301462.256 273826.7633 320772.5728 349473.7087 327985.9082 373460.5555 299331.3755 289784.4241 386472.0931 0.780036286 0.708529201 0.830001903 0.904266349 0.848666473 0.96633253 0.774522613 0.749819791 1 18.56000472 -4.999999956 0.023712262 2.082899002 1.16E-08 0.338447676 0.076282749 2749.344078 4.926812604 307.905747 150.7094946 1.00E-05 4.999999956 -2.082898991 DVDELPSLQPSVGS(ph)PSRPSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVDELPSLQPSVGSPSRPSSSR 22 1 O43815-2;O43815 O43815-2 STRN Striatin 1 DVDELPSLQPS(0.212)VGS(0.761)PS(0.026)RPSSSR 193.06 5.14E-18 805080000 242430 226800 228280 225150 245670 214290 267130 206430 364230 TRUE FALSE 227256.739 243592.508 233694.9094 230927.7302 226376.0692 276152.0443 227076.3364 232203.2399 303437.66 0.748940455 0.802776122 0.770157895 0.761038462 0.746038146 0.910078348 0.748345925 0.765241994 1 18.21104063 -2.211582788 2.297875843 1.66208489 0.783880915 0.665897376 0.048598099 5175141.847 1108282.069 17775527.4 0.01098488 0.006143519 2.211582788 -0.878203975 DVDFELIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DVDFELIK 8 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;;; 131.06 0.0023756 316831000 1090130 931017 953330 906128 1076260 681198 1033370 947252 1039540 FALSE TRUE 1021900.709 999950.4674 975943.4378 929380.7786 991734.881 877848.8043 878425.7618 1065518.497 866034.0583 1.179977507 1.154631804 1.126911151 1.073145761 1.145145357 1.013642357 1.014308564 1.230342487 1 19.72406424 3.649669602 0.643948986 1.062591006 1.189337116 0.222783561 0.068599362 1.590337806 1.170403179 0.03696979 0.125704439 4463.43898 -3.649669602 0.126746109 DVDFELIKVEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DVDFELIKVEGK 12 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;; 171.29 3.54E-05 539920000 849230 804440 789020 924830 1234790 504490 963310 681390 2109570 FALSE TRUE 796078.2102 864001.5746 807735.927 948562.7035 1137814.574 650128.0733 818870.6084 766463.0414 1757469.139 0.452968529 0.491616926 0.45960177 0.539732211 0.647416532 0.369922896 0.465937404 0.436117497 1 20.74506792 -1.890487568 2.860197938 1.251845218 0.48195761 0.834722411 0.07230933 27139819.4 17218247.27 46097165.2 0.017089734 0.012868041 1.890487568 -0.769887608 DVDFMYVELIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVDFMYVELIQR 12 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 164.64 0.00013202 95987000 110383 128115 113545 126288 123978 87528 134538 118374 107289 FALSE TRUE 103474.3251 137600.7679 116238.341 129528.7639 114241.268 112795.9127 114365.2759 133153.2545 89381.77279 1.157666959 1.539472351 1.300470302 1.449163066 1.278127122 1.26195654 1.279514518 1.489713734 1 16.44769304 -2.214173119 2.127642012 2.33E-05 1.350197038 0.461903232 0.116714959 2686260.168 457639.2109 12937472.34 0.026349222 0.006106985 2.214173119 1.350173709 DVDIIDHHDNTYTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVDIIDHHDNTYTVK 15 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 68.944 0.029566 209800000 363590 276340 351710 354240 385160 253690 352140 289620 356490 FALSE TRUE 340833.5509 296800.5011 360052.7273 363330.3981 354911.0873 326926.1847 299339.8761 325779.6945 296989.516 1.147628224 0.999363564 1.21234154 1.223377859 1.19502901 1.100800423 1.00791395 1.09694005 1 18.18005248 1.9696933 5.780019033 1.039347101 1.145468118 0.399444346 0.066857316 0.232164642 23.33411357 0.0307565 0.019513342 93.25954675 -1.9696933 0.106121016 DVDKFGNEITQLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVDKFGNEITQLAR 14 1 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ; 189.37 6.62E-07 377230000 783810 658450 755920 646320 738290 551470 855910 673260 689250 FALSE TRUE 734752.7312 707202.3231 773850.7794 662905.6654 680307.6815 710670.4366 727574.2414 757317.993 574209.7223 1.2795895 1.231609803 1.347679688 1.154466112 1.18477214 1.237649606 1.267087987 1.318887444 1 19.13121823 -1.631747661 2.992854674 0.979876899 1.254625776 0.659491101 0.057054069 9201725.441 11375496.38 1465358.814 0.013736634 0.023348143 1.631747661 0.274748877 DVDKIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVDKIR 6 1 A0A1W2PNZ9;Q15652-3;Q15652;H7BXU7 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 0 85.849 0.049474 309350000 896650 803580 879780 947440 1095300 670520 1032100 785140 1276900 FALSE TRUE 840530.2771 863077.8993 900648.7971 971752.9144 1009279.556 864088.239 877346.1865 883166.4573 1063777.141 0.790137562 0.811333376 0.846651768 0.913492946 0.948769735 0.812283143 0.82474623 0.830217555 1 20.02076451 -2.66301063 2.027100092 4.404327208 0.845816808 0.49352631 0.048626884 1736795.365 80942.08057 27276570.3 0.012634703 0.002172648 2.66301063 -3.558510399 DVDLEFLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DVDLEFLAK 9 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;; 158.07 0.00015607 382777000 1293470 1089591 1161705 1148509 1222290 877824 1396660 1056622 1532220 FALSE TRUE 1212514.022 1170265.451 1189261.191 1177981.685 1126296.274 1131237.539 1187243.799 1188543.583 1276482.583 0.949886851 0.916789204 0.931670519 0.922834123 0.882343628 0.886214629 0.930090088 0.931108343 1 20.28374242 0.69245446 1.805247548 0.999901082 0.916474473 0.626048757 0.020048117 0.841437899 3.937497862 0.019310865 0.005422009 4.925546915 -0.69245446 -0.083426609 DVDNALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVDNALR 7 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 79.451 0.097546 0 307300 344210 299670 311300 398060 258390 355720 344330 402280 FALSE TRUE 288066.6415 369695.6666 306778.3139 319288.485 366797.9733 332982.9984 302383.0883 387320.3585 335136.8692 0.859549241 1.103118459 0.915382168 0.952710711 1.094472161 0.993573161 0.90226745 1.155707993 1 18.35439088 1.23804448 24.99999138 1.077853961 0.981552058 0.197454078 0.085749883 22.82462567 1105033.267 0.062492097 0.019221306 17.29993533 -1.23804448 -0.096301904 DVDREDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DVDREDR 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 160.11 0.0012391 824977000 1310405 1390503 1471963 1405365 1523405 1211324 1566230 1233885 1696435 FALSE TRUE 1228389.09 1493457.289 1506878.657 1441429.045 1403762.916 1561013.575 1331388.352 1387938.258 1413289.039 0.869170464 1.056724596 1.066221145 1.019911006 0.993259608 1.104525353 0.942049584 0.982062565 1 20.43062512 1.650341292 15.35573893 0.971688223 1.027251571 0.082910418 0.063554328 0.270884234 86.83908848 0.027639516 0.015233148 44.70347585 -1.650341292 0.055563348 DVDVSEDS(ph)PPPLPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DVDVSEDSPPPLPER 15 0 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 DVDVSEDS(1)PPPLPER;DVDVS(0.001)EDS(0.999)PPPLPER;DVDVS(0.003)EDS(0.997)PPPLPER 245.26 4.57E-18 1253770000 2342090 1859550 2190960 2162570 1980490 1709370 2278540 1732340 1677290 TRUE FALSE 2195502.768 1997233.017 2242930.606 2218065.207 1824950.304 2202837.37 1936894.08 1948626.462 1397339.463 1.571202149 1.429311251 1.605143678 1.587348862 1.306017866 1.576451126 1.38612995 1.394526179 1 20.41425111 -0.006877786 0.453555771 0.934213187 1.530626316 0.754758843 0.090452283 1.980133543 0.519848589 0.315693128 0.047682331 0.984288053 0.006877786 0.596413129 DVDWGEVDYLIVDTPPGTSDEHLSVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVDWGEVDYLIVDTPPGTSDEHLSVVR 27 0 I3L3A0;I3L531;P53384-2;P53384 I3L3A0 NUBP1 Cytosolic Fe-S cluster assembly factor NUBP1 0 58.812 0.059664 27324000 13247 33175 25161 30833 31325 35006 23385 24862 21492 FALSE TRUE 12417.89392 35631.31152 25757.8308 31624.22698 28864.86086 45111.66393 19878.63635 27966.07543 17904.84636 0.693549314 1.990037268 1.438595467 1.766238389 1.612125582 2.519522537 1.110237751 1.561927697 1 14.12806252 1.019252752 1.515996653 1.035150913 1.660716186 0.120157072 0.486273741 0.743846717 3.486552523 0.40986765 0.121114575 10.45328405 -1.019252752 0.625565273 DVDWTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVDWTAR 7 0 K7ESF4;Q9BRP1 K7ESF4;Q9BRP1 PDCD2L Programmed cell death protein 2-like 0 117.18 0.012306 65723000 93325 133000 120460 130710 132570 107430 137810 110270 123310 FALSE TRUE 87483.95484 142847.4584 123317.3681 134064.2399 122158.487 138443.297 117146.6699 124037.4522 102728.7644 0.851601354 1.390530289 1.200417126 1.305031173 1.189136146 1.347658544 1.140349254 1.207426693 1 16.64848067 0.546486112 1.114012898 1.000452755 1.231179491 0.141163168 0.148508761 2.5553505 4.52162896 0.125387829 0.038806788 3.519541675 -0.546486112 0.230726736 DVDYVCISDNYWLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DVDYVCISDNYWLGK 15 0 Q96KP4;Q96KP4-2;J3QKT2;J3QRH4;J3QRA8;J3KRJ8 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ;; 255.16 2.38E-24 284273000 695230 594730 584610 647210 697840 505590 812960 593410 701470 FALSE TRUE 651716.7953 638764.428 598477.2253 663818.5043 643034.4614 651545.6254 691064.1952 667498.5448 584390.1253 1.115208432 1.093044527 1.024105643 1.135916703 1.100351347 1.114915528 1.182539138 1.142213935 1 19.15657227 3.205715003 24.99938509 1.125312857 1.073172842 0.055946837 0.052362945 302.9241377 230560.4388 0.014324521 0.017122173 1605.887078 -3.205715003 -0.052140016 DVEDEETWIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DVEDEETWIR 10 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 203.19 4.88E-07 1318138000 1120350 1056970 1069893 1044426 1218250 854578 1126603 879156 1307430 FALSE TRUE 1050229.293 1135229.159 1095271.367 1071227.739 1122573.559 1101280.796 957679.339 988920.5619 1089211.487 0.96421063 1.042248611 1.005563548 0.983489205 1.030629564 1.011080776 0.879240947 0.907923368 1 20.05485267 1.754156834 25 0.918586697 1.010354751 0.476709781 0.037405775 3.556408039 5707.766746 0.015496472 0.008593563 56.77495967 -1.754156834 0.091768054 DVEDEILWVGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DVEDEILWVGER 12 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;; 241.03 7.26E-16 343970000 457473 404202 403950 445910 487200 356665 470851 391450 499188 FALSE TRUE 428840.5815 434129.5367 413531.8848 457352.8055 448937.2773 459628.3955 400251.2637 440323.3942 415870.2979 1.03118829 1.04390609 0.994377061 1.099748666 1.079512722 1.105220541 0.962442535 1.058799814 1 18.66577412 1.731337873 25 1.005996005 1.05215348 0.26178894 0.039995441 1.080322926 3715.763915 0.018854212 0.010455613 53.86887089 -1.731337873 0.046157475 DVEDEILWVTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DVEDEILWVTER 12 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 ;;; 188.28 2.19E-05 71906300 138989 131678 136406 137653 151802 114101 153384 115585 168231 FALSE TRUE 130289.9266 141427.5761 139641.6147 141185.409 139880.0833 147040.1064 130385.4931 130016.0417 140152.1593 0.92963196 1.00910023 0.996357212 1.007372343 0.99805871 1.049146208 0.930313838 0.927677764 1 17.09663445 1.666564113 10.37251042 0.947101359 0.999550183 0.268657401 0.034946793 0.12471412 19.23154835 0.015077233 0.008132053 46.40492905 -1.666564113 0.052448824 DVEDMELS(ph)DVEDDGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DVEDMELSDVEDDGSK 16 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 DVEDMELS(1)DVEDDGSK;DVEDMELS(1)DVEDDGSK;DVEDMELS(1)DVEDDGSK;DVEDMELS(1)DVEDDGSK;DVEDMELS(1)DVEDDGSK;DVEDMELS(1)DVEDDGSK;DVEDMELS(1)DVEDDGSK 412.12 4.56E-140 1113784000 4067100 1900822 2681000 2392130 2196261 2047922 3305210 2147818 2021063 TRUE FALSE 3812547.471 2041560.839 2744594.586 2453516.106 2023775.52 2639123.836 2809624.445 2415977.805 1683734.529 2.264340017 1.212519435 1.63006373 1.457187023 1.201956416 1.567422768 1.668686124 1.434892356 1 20.68323326 -2.251985952 1.027689835 0.040614901 1.528455079 0.252562744 0.296874522 6303.799146 726.5549245 13907.38917 0.080384255 0.005597757 2.251985952 1.487840178 DVEDMFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DVEDMFSR 8 0 Q15717;Q15717-2;M0QZR9;M0R055 Q15717 ELAVL1 ELAV-like protein 1 0 ;;;;; 223.06 1.10E-05 1005749000 2308210 2500430 2483000 2394850 2747450 2046156 2886460 2261683 3018730 FALSE TRUE 2163743.256 2685564.439 2541897.933 2456305.905 2531676.36 2636848.021 2453662.12 2544059.101 2514884.461 0.860374816 1.06786792 1.010741436 0.976707258 1.006677006 1.048496685 0.975656002 1.011600787 1 21.26206069 4.751567542 24.8398865 1.013425609 0.86037471 0.739777315 0.028294197 1043.327056 1992448.132 0.006909989 0.126938667 56437.47068 -4.751567542 -0.153050899 DVEPEDPMFLMDPFAIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DVEPEDPMFLMDPFAIHR 18 0 Q15773;F5H7L5;F5H800;F5H0Y3 Q15773 MLF2 Myeloid leukemia factor 2 0 ;; 183.23 6.43E-14 150407000 189387 208376 190379 177780 197511 149420 227425 181679 200275 FALSE TRUE 177533.6057 223804.3759 194894.8798 182342.1358 181999.2828 192555.1284 193324.7326 204362.0231 166847.8087 1.064045175 1.341368386 1.168099727 1.092865032 1.090810147 1.15407646 1.158689072 1.224840918 1 17.34817321 -5 0.161867892 0.38296078 1.217547082 0.225159353 0.082449693 177.8822447 1.644972584 35.62363987 0.340291947 1.00E-05 5 0.834586302 DVES(ph)PSWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DVESPSWR 8 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 1 DVES(0.997)PS(0.003)WR;DVES(0.846)PS(0.154)WR;DVES(0.997)PS(0.003)WR;DVES(0.996)PS(0.004)WR;DVES(0.994)PS(0.006)WR;DVES(0.999)PS(0.001)WR 231.38 7.74E-07 2245990000 2143910 2218730 2187630 2060680 2378760 1864760 2377120 2110590 2889560 TRUE FALSE 2009726.5 2383007.078 2239521.617 2113560.538 2191941.785 2403085.94 2020692.924 2374101.807 2407273.769 0.834855813 0.98991943 0.930314468 0.877989269 0.910549441 0.998260344 0.83941135 0.986220113 1 21.19896879 -1.181279818 4.555145515 1.000014256 0.923547777 0.150102726 0.058831691 7.73E-06 1.39E-06 0.051667185 0.012175802 0.065874932 1.181279818 -0.076466479 DVESCHDMAALNILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVESCHDMAALNILK 15 0 O95793-2;O95793-3;O95793;Q5JW30;A0A087X1A5 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 ; 178.84 6.95E-07 272760000 175974 217407 210427 203159 231484 174212 269552 202634 267880 FALSE TRUE 164960.1015 233504.0405 215418.4278 208372.4039 213304.1804 224504.1763 229135.18 227933.301 223169.0974 0.739170895 1.04630992 0.965269969 0.93369739 0.955796223 1.005982364 1.026733462 1.021347954 1 17.76777774 2.210686362 3.619795861 1.018430552 0.948845462 0.206639585 0.077738471 0.438431205 12.15971196 0.029091923 0.021499693 162.4375245 -2.210686362 -0.06958509 DVESDSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVESDSAK 8 0 P07237;I3L312;I3L3U6;I3L3P5 P07237 P4HB Protein disulfide-isomerase 0 110.81 0.0078046 326110000 827620 575410 645140 554940 528050 410930 736440 557000 601310 FALSE TRUE 775820.7415 618013.9551 660443.0255 569180.6999 486579.0831 529558.8201 626017.6588 626542.6761 500947.4764 1.548706757 1.233690126 1.318387768 1.136208339 0.971317565 1.057114458 1.249667257 1.250715306 1 18.93429982 7.999999998 0.544652402 1.130017618 18.03196534 0.57452138 0.110533845 106.3623603 0.985685388 0.053699174 2098.945043 99999999.47 -7.999999998 16.90194772 DVESYIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DVESYIHR 8 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;;; 170.24 0.00029635 3828880000 3991540 4922280 4729380 4466860 4623150 4100423 4506800 4118650 3746680 FALSE TRUE 3741716.637 5286730.733 4841563.127 4581487.19 4260066.448 5284148.555 3831047.179 4632872.519 3121334.904 1.198755261 1.693740305 1.551119401 1.467797379 1.364821969 1.692913038 1.2273746 1.484259992 1 21.57373173 0.198443527 0.478636177 0.955973214 1.52833681 0.409232039 0.169449215 2.698742204 0.903731702 0.39989173 0.083861642 1.579223242 -0.198443527 0.572363596 DVFERPSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVFERPSAK 9 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 0 ; 116.77 0.0011497 578660000 686790 702420 719750 765850 899550 608090 997720 761720 995470 FALSE TRUE 643805.0399 754427.9077 736822.8099 785503.0076 828902.9716 783635.7115 848121.1484 856822.4188 829319.626 0.776305081 0.909694989 0.888466626 0.947165584 0.999497595 0.944913984 1.022671021 1.03316308 1 19.66156871 7.119251017 0.265540507 1.029599721 6.02E-17 0.814166651 0.032979091 12.5622542 0.264958763 0.037477652 5.368775619 13159852.35 -7.119251017 -1.029599721 DVFFYQADDEHYIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 1115950000 1238590 1342070 1300350 1302960 1424590 1126480 1521560 1244441 1543200 FALSE TRUE 1161068.863 1441438.259 1331194.916 1336396.16 1312708.448 1451676.489 1293416.203 1399812.198 1285629.951 0.903112799 1.12119219 1.035441742 1.039487419 1.021062435 1.12915578 1.006056372 1.088814241 1 20.29404401 DVFHMVVEVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DVFHMVVEVPR 11 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;;;; 155.33 3.16E-05 1198518000 2024840 1917030 1885550 1692590 1817720 1744900 2213410 1848830 1187668 FALSE TRUE 1898108.879 2058968.896 1930276.136 1736024.725 1674963.604 2248624.304 1881529.719 2079660.495 989438.5382 1.918369667 2.080946735 1.950880284 1.754555395 1.692842495 2.272626563 1.901613538 2.101859201 1 19.91625057 -1.583548518 3.051033149 0.948272451 1.964637064 0.764742677 0.167173852 24399040.92 27610893.68 10233851.55 0.038691432 0.026088643 1.583548518 1.016364612 DVFLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DVFLYR 6 0 O14579;M0QXB4;O14579-3;O14579-2;M0R061 O14579 COPE Coatomer subunit epsilon 0 ;;;; 142.53 0.026789 1489610000 1834870 2565060 2301630 2366530 2706180 1974190 2483120 2273410 2049220 FALSE TRUE 1720028.762 2754979.711 2356225.751 2427259.166 2493647.539 2544106.605 2110799.208 2557250.243 1707191.944 1.007519259 1.613749246 1.380176236 1.421784572 1.46067204 1.490228802 1.236415868 1.497927783 1 20.70319384 -1.109201412 4.737792089 1.000026345 1.403223259 0.346881147 0.166480735 3.82E-05 7.17E-06 0.144100326 0.03396273 0.077767581 1.109201412 0.403196915 DVFQHSQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DVFQHSQSR 9 0 Q9NZB2;Q9NZB2-4;Q9NZB2-6;Q9NZB2-2;Q9NZB2-5;A0A0C4DH52 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 ;;;; 146.11 9.56E-05 963560000 1082910 1286180 1116470 1083830 1273960 805120 1031520 1032680 1226180 FALSE TRUE 1015132.596 1381410.105 1142953.196 1111642.913 1173908.321 1037545.074 876853.1522 1161612.371 1021522.637 0.993744592 1.352304938 1.118872118 1.088221517 1.149175044 1.015684858 0.858378582 1.13713816 1 19.96228974 2.566817033 1.171368835 0.974814119 1.190522727 0.209342916 0.11512485 0.490397634 1.372531711 0.059639774 0.046970892 368.8221823 -2.566817033 0.215708608 DVFRDPALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DVFRDPALK 9 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;;;;; 156.48 6.46E-05 6617280000 11398100 10079900 10801000 10558800 10265400 8491560 13714900 9142900 11044900 FALSE TRUE 10684713.27 10826226.28 11057204.82 10829756.68 9459196.893 10942935.52 11658478.07 10284411.19 9201434.837 1.161200775 1.176580226 1.201682674 1.176963906 1.028013246 1.189264035 1.26702827 1.117696465 1 23.13342742 0.987528948 23.9884409 0.999999992 1.176797902 0.458361275 0.05896929 336.3709588 647021.5305 0.057797642 0.01444941 9.716927177 -0.987528948 0.176797909 DVFRDPALKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DVFRDPALKR 10 2 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;; 124.1 0.00024996 4372670000 4641060 4728970 4683500 4551570 4756810 3341740 5655600 4235270 5179780 FALSE TRUE 4350584.339 5079107.859 4794594.832 4668370.992 4383229.331 4306446.089 4807595.284 4764052.782 4315241.255 1.008190292 1.177015967 1.111083842 1.081833139 1.015755336 0.997961837 1.114096524 1.104006126 1 22.04100979 3.09757822 3.584025821 1.05390358 1.117376291 0.119749395 0.05697427 0.370013355 9.270007896 0.016774957 0.020402916 1251.924736 -3.09757822 0.063472711 DVGAQILLHSHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVGAQILLHSHK 12 0 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 135.58 7.24E-05 1878620000 2635600 3406800 2366200 2242620 3825200 1758920 2776900 3280900 2814600 FALSE TRUE 2470642.501 3659043.017 2422327.381 2300169.426 3524784.222 2266691.65 2360529.624 3690527.587 2344825.077 1.053657488 1.560475898 1.033052489 0.980955658 1.503218409 0.966678356 1.006697535 1.573903155 1 21.16104887 3.881145804 7.097199365 1.140786065 1.336453754 0.058881152 0.248201507 0.494678805 31.2528624 0.058691486 0.106654697 7605.815819 -3.881145804 0.195667689 DVGAQILLHSHKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVGAQILLHSHKK 13 1 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 152.74 1.85E-05 1089280000 2670700 2792700 2475700 2536500 3614500 1799990 3457900 2667800 4321500 FALSE TRUE 2503545.654 2999474.414 2534424.773 2601590.884 3330631.75 2319617.893 2939419.997 3000880.703 3600213.732 0.695388063 0.833137874 0.703965087 0.722621232 0.925120562 0.644300051 0.816457082 0.833528486 1 21.77965113 0.83695837 1.594230274 0.999226462 0.762215508 0.476411647 0.079438937 0.502781146 2.39230897 0.067128431 0.019395693 6.870025833 -0.83695837 -0.237010954 DVGRPQPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 DVGRPQPGR 9 1 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ;;;;;;;;; 162.88 5.79E-05 14307940000 4894144 5969696 4742079 4657005 4877465 3397236 5800598 4657422 7151873 FALSE TRUE 4587828.263 6411698.503 4854563.353 4776511.633 4494408.574 4377962.884 4930852.18 5238911.389 5958179.193 0.770005083 1.076117098 0.814772969 0.801673041 0.754325848 0.73478201 0.82757702 0.879280602 1 22.50644008 3.726495891 11.83424188 0.814001929 0.945109685 0.09806265 0.103738376 0.10619232 788.2577544 0.024356971 0.040508885 5327.161841 -3.726495891 0.131107756 DVGRPQPGRENFQNWLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVGRPQPGRENFQNWLK 17 2 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ; 265.73 7.92E-28 1053760000 749890 933390 794710 835910 1069930 575170 1090230 731560 2019710 FALSE TRUE 702955.7235 1002499.167 813560.8965 857360.8658 985902.0137 741212.2419 926760.1327 822896.8764 1682607.353 0.417777637 0.595801014 0.48351203 0.50954304 0.585937065 0.440514087 0.550788115 0.489060549 1 20.68226712 -1.512402461 3.041374188 1.015900851 0.516387812 0.878077722 0.057428383 10580827.98 12094965.75 1394143.619 0.012046229 0.030732475 1.512402461 -0.499513039 DVGSLDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DVGSLDEK 8 0 Q99584 Q99584 S100A13 Protein S100-A13 0 ;;; 140.5 0.0015088 422038000 1405880 1276970 1286220 1185580 1505900 950310 1559760 1203960 1673780 FALSE TRUE 1317888.48 1371518.187 1316729.746 1216003.99 1387632.689 1224649.07 1325888.468 1354277.056 1394415.305 0.945119059 0.983579413 0.944288076 0.872052957 0.995135871 0.878252746 0.950856222 0.971214997 1 20.41122888 1.057048211 2.8687299 0.998977522 0.940586618 0.222434757 0.038756121 0.366922346 6.357006816 0.034474282 0.00919927 11.40376374 -1.057048211 -0.058390904 DVHAAS(ph)SPGMGGAAASWAGWAVTGVSSLTSK ddPTM_SK-BR-3_Pertuzumab_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(0.51)S(0.476)PGMGGAAAS(0.013)WAGWAVTGVSSLTSK 81.429 0.00084515 66380000 68860 55484 66034 67110 70193 52253 70983 50470 52289 TRUE FALSE 64550.17552 59592.09309 67600.35766 68832.15622 64680.32492 67337.59284 60339.75812 56771.2906 43561.6281 1.481812741 1.367995084 1.55183267 1.580109817 1.484800448 1.545800646 1.38515847 1.30324079 1 15.41077025 0.916396873 1.3380236 1.002324271 1.494117785 0.871464629 0.060949757 0.187170055 0.669193843 0.060167339 0.018150429 8.248915846 -0.916396873 0.491793513 DVHEDSLTVVFENNWQPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DVHEDSLTVVFENNWQPER 19 0 B4DXZ6;P51114;C9JAJ4;P51114-2 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 ;; 248.18 7.76E-25 443154000 256063 270807 259887 284811 298688 244577 311119 264922 287456 FALSE TRUE 240036.4739 290857.8321 266051.6424 292119.7324 275230.2493 315182.4095 264469.5942 297998.0949 239477.7366 1.002333149 1.214550614 1.110966081 1.219819999 1.149293681 1.316124054 1.104359838 1.244366592 1 17.86953201 4.746902974 24.40318185 1.174842394 1.002333028 0.265157646 0.087346326 918.558719 2686895.899 0.017740839 0.199457268 55834.54411 -4.746902974 -0.172509367 DVHEDSVTIFFENNWQSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVHEDSVTIFFENNWQSER 19 0 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 0 127.97 2.24E-05 27846000 28595 27447 31384 30884 29729 26447 34574 30026 35636 FALSE TRUE 26805.28999 29479.20444 32128.4433 31676.53573 27394.20426 34081.81957 29389.94967 33774.8122 29688.12138 0.902896133 0.992962945 1.082198597 1.066976765 0.92273283 1.147995157 0.989956531 1.137654072 1 14.85759818 4.648802032 1.929193 1.047828319 0.874580698 0.328447384 0.067500253 0.702180632 3.229649579 0.01526023 0.203679416 44545.31472 -4.648802032 -0.17324762 DVHGEQETEGRS(ph)SPGPDTLVVLEFNPASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVHGEQETEGRSSPGPDTLVVLEFNPASK 29 1 O60303 O60303 KIAA0556 Uncharacterized protein KIAA0556 1 DVHGEQET(0.083)EGRS(0.428)S(0.428)PGPDT(0.061)LVVLEFNPASK 137.35 1.95E-06 43118000 25420 36264 31639 33228 38966 19418 34570 24933 52054 TRUE FALSE 23829.00758 38949.02429 32389.49202 34080.68673 35905.76754 25023.66138 29386.54943 28045.93993 43365.85112 0.549487833 0.898149657 0.746889342 0.785887648 0.827973316 0.577036095 0.677642631 0.646728687 1 15.4042718 2.272992384 24.99972116 0.691917254 0.779371262 0 0.141724653 439.9365635 319421.2695 0.043627517 0.03649974 187.4961629 -2.272992384 0.087454008 DVHMPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVHMPK 6 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 0 ; 69.39 0.071022 412700000 1403000 1204270 1366610 1236340 1300520 986880 1480710 1110380 1283940 FALSE TRUE 1315188.734 1293435.404 1399026.635 1268066.578 1198382.405 1271776.235 1258691.282 1249013.387 1069642.119 1.229559598 1.20922258 1.307938991 1.185505464 1.12035828 1.188973594 1.176740574 1.167692787 1 20.02869675 -4.99999243 0.131130511 0.279133288 1.293541869 0.718502082 0.041769166 78.27725096 0.645971705 14.66842127 0.325479954 1.00E-05 4.99999243 1.014408581 DVHNIYGLYVHMATADGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DVHNIYGLYVHMATADGLR 19 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;; 198.9 4.16E-16 1098475900 242408.5 388320.3 310474.7 295507.9 361241.8 267914.8 339774.7 330697.3 283576.8 FALSE TRUE 227236.5847 417071.9391 317839.3065 303091.133 332871.3262 345257.4535 288828.638 371985.5859 236246.0001 0.961864263 1.765413759 1.34537434 1.282947152 1.409003014 1.461431954 1.222575781 1.574568821 1 17.84993038 -1.766263265 2.75079979 0.909357487 1.398401086 0.232716328 0.212769842 19756095.8 14782115.22 12054702.75 0.049505204 0.017129186 1.766263265 0.489043599 DVHTLLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DVHTLLDR 8 0 E9PI41;Q9NPD3 E9PI41 EXOSC4 Exosome complex component RRP41 0 ;; 133.57 0.0009136 485350000 134903 147033 137461 138301 144571 112813 149408 122504 149139 FALSE TRUE 126459.662 157919.4763 140721.6398 141850.0378 133216.9768 145380.2817 127005.6574 137798.8941 124246.7374 1.017810726 1.271015075 1.13259827 1.141680182 1.072196982 1.170093354 1.022205171 1.109074547 1 16.92284844 1.716502882 0.499106228 1.006553346 1.171400387 0.219637608 0.072411007 0.965878446 0.575610422 0.068077496 0.046135112 52.05984641 -1.716502882 0.164847042 DVIATDKEDVAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DVIATDKEDVAFK 13 1 A0A5K1VW95;P40925;P40925-3;C9JF79;C9JRL4;C9JLV6 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic;Malate dehydrogenase" 0 ;;; 198.23 1.16E-07 3261200000 9939800 6213210 7753510 7901010 8581170 5533330 11681600 7719530 10021400 FALSE TRUE 9317685.661 6673242.533 7937426.919 8103763.293 7907239.523 7130712.545 9930052.527 8683330.313 8348763.599 1.116055755 0.799309078 0.950730827 0.970654301 0.947115034 0.854104019 1.189403965 1.040073804 1 22.99313113 1.74442244 25 1.089967628 0.926222596 0.307062573 0.094767113 1.104003435 4725.147895 0.040077053 0.022224791 55.51654625 -1.74442244 -0.163745033 DVIEEYFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DVIEEYFK 8 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 ;;;;;; 147.04 0.0012649 3401832000 6637870 5659150 5863360 5771560 6495890 4315167 7008260 5299310 7042910 FALSE TRUE 6222417.566 6078159.354 6002441.668 5919668.001 5985729.003 5560885.662 5957436.474 5960940.519 5867402.822 1.060506284 1.035919902 1.023015097 1.00890772 1.020166705 0.947759312 1.01534472 1.015941925 1 22.48429061 4.053697105 0.687686951 0.997405811 1.066879515 0.488448265 0.020477814 1.249925185 0.80257857 0.009227637 0.059515337 11316.10857 -4.053697105 0.069473704 DVIKEIEDFDSLEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DVIKEIEDFDSLEALR 16 1 P46060;B0QYT5;B0QYT4 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ;;; 246.45 3.07E-20 213307000 416839 456083 455766 478889 629878 304500 570763 416782 836586 FALSE TRUE 390749.7911 489851.8599 466576.9847 491178.1025 580409.9227 392404.2069 485182.3869 468818.1502 696954.392 0.560653316 0.702846363 0.669451244 0.704749275 0.83278035 0.563027095 0.696146538 0.6726669 1 19.41070473 -1.273449708 2.983178482 1.002181427 0.679063682 0.639516162 0.076568652 6430186.08 8323030.979 126787.9059 0.017394779 0.053278292 1.273449708 -0.323117745 DVIRPGMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DVIRPGMR 8 1 P25685;P25685-2 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ;;;;; 136.27 0.00082194 1472200000 1940692 2393650 2101850 2108340 2675450 1674040 2370480 2267310 2693610 FALSE TRUE 1819227.552 2570878.337 2151706.875 2162443.574 2465330.949 2157308.172 2015048.53 2550388.644 2244029.09 0.810696956 1.145652857 0.958858726 0.96364329 1.098618089 0.961354816 0.897960075 1.136522096 1 21.09765995 3.72479391 24.9238598 0.992310199 1.01714696 0 0.107027471 780.8709276 8362536.225 0.026233861 0.0428536 5306.325787 -3.72479391 0.024836761 DVITLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 126.24 0.040887 651530000 895770 982720 944120 926040 940920 789330 1065980 871320 963010 FALSE TRUE 839705.3547 1055481.611 966514.9722 949803.7542 867023.9387 1017196.757 906146.1951 980106.22 802277.4097 1.046652124 1.315606795 1.204714181 1.183884455 1.080703418 1.267886575 1.129467419 1.221655014 1 19.61374165 -4.54420112 0.27075667 1.84E-13 1.206543123 0.298082116 0.082787754 179.3041734 2.196762153 99.57342648 0.094012326 2.86E-05 4.54420112 1.206543123 DVKPHNVMIDHEHR ddPTM_SK-BR-3_Pertuzumab_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 ;; 110.35 0.00024035 636420000 911610 918080 868350 736210 966690 586290 1028220 851370 1141460 FALSE TRUE 854553.9574 986055.5985 888947.6721 755102.395 890770.0668 755542.4054 874047.9565 957665.4186 950942.9519 0.89863851 1.036924031 0.934806521 0.794056461 0.936722929 0.794519171 0.919138162 1.007069264 1 19.85899927 -0.87938798 5.508748986 1.000000054 0.919478343 0.104010337 0.077300169 5.20E-08 1.06E-08 0.075856328 0.017879496 0.132011577 0.87938798 -0.080521711 DVKPHNVMIDHEHRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVKPHNVMIDHEHRK 15 2 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 0 182.57 1.74E-07 250020000 384390 325560 369370 364940 405650 278640 462920 321320 502810 FALSE TRUE 360331.7161 349664.8011 378131.6308 374304.9782 373791.8853 359078.8447 393509.4435 361437.5093 418887.7627 0.860210653 0.834745801 0.902703933 0.893568663 0.89234377 0.857219706 0.93941499 0.862850485 1 18.67620421 -5 0.131653985 1.395787168 0.83321356 0.654480007 0.027952461 82.95953376 0.686316812 8.662455372 0.189448438 1.00E-05 5 -0.562573608 DVKPKPIADAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 85.42 0.0085656 721290000 1747900 1193600 1370600 1301500 1662100 990690 1963700 1303800 1898800 FALSE TRUE 1638502.059 1281975.386 1403111.279 1334898.693 1531565.371 1276686.12 1669261.415 1466582.3 1581878.013 1.035795457 0.810413556 0.886990822 0.843869554 0.96819436 0.807069894 1.055240291 0.927114662 1 20.59320692 1.734058489 24.95033153 0.993361658 0.883126083 0.283524083 0.075596827 0.539941993 2962.553086 0.031148857 0.017273537 54.20738894 -1.734058489 -0.110235575 DVKPSNILVNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVKPSNILVNSR 12 1 P36507;G5E9C7;Q02750;Q02750-2 P36507;Q02750 MAP2K2;MAP2K1 Dual specificity mitogen-activated protein kinase kinase 2;Dual specificity mitogen-activated protein kinase kinase 1 0 115.09 0.00090023 536380000 581850 616610 659460 556910 796230 533250 774340 694520 947540 FALSE TRUE 545433.0471 662264.446 675102.7026 571201.2534 733697.3076 687190.6184 658234.9056 781232.3508 789389.4527 0.69095558 0.838957809 0.855221336 0.723598791 0.929449089 0.87053433 0.83385318 0.989666569 1 19.59037772 7.457632088 0.048315255 1.35118942 7.11E-08 0.573133512 0.065215654 379.3577031 1.521881786 10.90678465 40.06313197 28683496.31 -7.457632088 -1.351189349 DVLDGHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DVLDGHLR 8 0 P15924 P15924 DSP Desmoplakin 0 ;; 146.81 0.00081697 736750000 1047320 1401170 1117030 1183990 1467350 851190 1229700 1187090 1103950 FALSE TRUE 981770.1107 1504914.085 1143526.479 1214373.188 1352110.25 1096914.735 1045317.901 1335300.8 919693.6132 1.067496932 1.636321122 1.243377645 1.320410592 1.470174665 1.192695828 1.136593629 1.451897437 1 19.8107938 -0.858237733 0.226304841 0.784418636 1.409387561 0.203902662 0.17529764 20.03227594 1.121619978 3.194209201 0.36576667 0.138599693 0.858237733 0.624968926 DVLDVYIEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DVLDVYIEHR 10 0 P33993;P33993-2 P33993 MCM7 DNA replication licensing factor MCM7 0 ;;; 189.72 9.80E-07 654680000 1050850 1017960 1149610 1133710 1098760 1011848 1243830 1060070 800211 FALSE TRUE 985079.1743 1093330.818 1176879.292 1162802.918 1012467.822 1303952.092 1057329.239 1192422.073 666650.6145 1.477654341 1.640035715 1.765361445 1.744246375 1.518738301 1.955975234 1.586032047 1.788676178 1 19.34657133 -0.915603774 9.247112393 0.99999975 1.689121612 0.702016801 0.140142381 0 0 0.11917199 0.028089107 0.121449638 0.915603774 0.689121862 DVLEVLDDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVLEVLDDSR 10 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 0 ; 166.19 1.31E-05 37871000 79146 85039 92395 91045 79780 75022 100744 68562 64733 FALSE TRUE 74192.39314 91335.37604 94586.65303 93381.36884 73514.40062 96679.63352 85638.37246 77122.11662 53928.64411 1.375751131 1.69363383 1.753922328 1.731572718 1.363179101 1.79273251 1.58799417 1.430077056 1 15.71876414 0.86912948 2.026061255 1.000978777 1.640751135 0.63261534 0.147401111 0.297974229 2.411624083 0.130640307 0.036211057 7.398258136 -0.86912948 0.639772358 DVLFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DVLFLK 6 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ;;; 106.29 0.075031 1679443000 4431410 5447850 4156590 4035000 5148040 2598113 5749240 4350410 5290720 FALSE TRUE 4154055.958 5851214.482 4255186.278 4138544.931 4743733.705 3348146.046 4887194.835 4893568.265 4407664.653 0.94246189 1.327508997 0.965406085 0.938942787 1.076246511 0.759619052 1.108794616 1.110240604 1 22.07158303 3.746240202 10.91019297 0.992473336 1.157800441 0.150926631 0.136412657 0.74550136 416.3300834 0.032211868 0.05691244 5574.94006 -3.746240202 0.165327105 DVLLPWYNAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVLLPWYNAYR 11 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 193.38 2.28E-06 625850000 1058020 1463340 1044490 990370 1515010 754000 1026600 1332440 1091940 FALSE TRUE 991800.4168 1571687.216 1069265.796 1015784.571 1396027.226 971667.5598 872670.8605 1498798.067 909688.1598 1.090264181 1.727720867 1.175420153 1.116629429 1.534621739 1.068132579 0.959307705 1.647595443 1 19.79501255 3.730738113 23.56644399 1.198340007 1.453638836 0.076185679 0.267230461 138.1162513 899902.8999 0.064261914 0.11020779 5379.452944 -3.730738113 0.25529883 DVLLQVDDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVLLQVDDER 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 161.51 1.64E-05 109718000 254910 235852 241570 243750 240490 213383 267600 217650 175203 FALSE TRUE 238955.6381 253314.7275 247300.1545 250005.0377 221602.8855 274983.2081 227475.8643 244824.0816 145960.4874 1.637125515 1.735502066 1.694295208 1.712826821 1.51823887 1.883956493 1.558475641 1.677331214 1 17.15521835 -2.348079514 0.433849364 0.01351818 1.696774204 0.821942252 0.099094946 27.84261035 1.490653343 26.32332682 0.048265844 0.004486632 2.348079514 1.683256024 DVLLQVDDERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DVLLQVDDERR 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 237.67 2.20E-15 5713120000 5488040 5900570 5744590 5679690 5774180 4752790 6390910 5039720 5586210 FALSE TRUE 5144553.373 6337454.342 5880854.388 5825440.461 5320699.195 6124843.318 5432652.376 5668940.136 4653835.463 1.10544376 1.361770177 1.263657565 1.251750413 1.143293363 1.316085059 1.167349473 1.218122166 1 22.14998877 -0.520566665 0.354795081 0.920557491 1.268536988 0.448728614 0.078202381 6.966533351 0.8807872 0.719610139 0.059877 0.301601387 0.520566665 0.347979497 DVLSVAFSSDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DVLSVAFSSDNR 12 0 P63244;J3KPE3;D6RHH4;H0YAF8;D6R9L0;H0Y8W2;D6R9Z1;D6RFX4;E9PD14;D6RFZ9;D6RAU2;H0YAM7 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 ;;;; 270.36 2.54E-27 1389870000 1056400 1395560 1087470 1162000 1399920 910910 1207240 1146140 1205420 FALSE TRUE 990281.8097 1498888.714 1113265.302 1191818.887 1289975.93 1173874.93 1026225.569 1289238.102 1004227.615 0.986112904 1.492578667 1.108578659 1.186801548 1.284545367 1.168933131 1.021905347 1.283810645 1 19.93765487 1.147762034 0.315427892 0.985222179 1.27078091 0.09915145 0.147999371 2.75042527 0.901485814 0.297798801 0.196300322 14.0527731 -1.147762034 0.285558731 DVMQNHLLQMLCLVAMEKPASTNSDDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DVMQNHLLQMLCLVAMEKPASTNSDDVR 28 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;; 207.86 1.56E-25 2027730000 1832270 1603680 1739640 1680660 1824290 1440430 2269570 1661200 1708880 FALSE TRUE 1717591.491 1722418.136 1780905.082 1723788.581 1681017.622 1856258.758 1929269.048 1868604.477 1423656.888 1.206464497 1.209854811 1.250937004 1.210817434 1.18077441 1.303866664 1.355150292 1.3125385 1 20.44117006 2.23066969 24.94033973 1.282462534 1.216806242 0 0.099490728 403.3857934 1274941.711 0.032821647 0.024671976 170.0864396 -2.23066969 -0.065656292 DVMQNHLLQMLCLVAMEKPASTNSDDVRDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVMQNHLLQMLCLVAMEKPASTNSDDVRDEK 31 2 E7EUI8;E7EM57;P11413;P11413-3;P11413-2 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 269.05 1.06E-59 1167320000 695150 475440 573640 550130 710790 428380 705850 507460 1000850 FALSE TRUE 651641.8024 510642.0723 587247.0117 564247.2672 654967.4206 552046.3518 600014.3453 570817.4981 833801.6693 0.78153094 0.612426301 0.704300595 0.676716404 0.78551944 0.662083529 0.71961279 0.684596252 1 19.66934473 -4.999999999 0.412894012 6.340192643 0.691345748 0.754880495 0.052806253 383.3242496 2.557685509 1852.905135 0.028752414 1.00E-05 4.999999999 -5.648846895 DVNFEFPEFQL ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DVNFEFPEFQL 11 0 P62081 P62081 RPS7 40S ribosomal protein S7 0 ;;; 102.52 0.0066466 107150000 405383 461117 469887 454594 492967 400663 523670 415079 503590 FALSE TRUE 380010.8017 495258.5825 481032.9415 466259.6517 454251.3604 516327.9039 445150.545 466902.5269 419537.5757 0.905784901 1.180486829 1.146578923 1.111365653 1.082742969 1.230707173 1.061050478 1.112897995 1 18.67844051 0.531777306 1.324677678 1.000256949 1.118627785 0.10695413 0.086291686 3.545141979 8.006409512 0.074278122 0.022061571 3.402336825 -0.531777306 0.118370835 DVNLRPEQLGDICVGNVLQPGAGAIMAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVNLRPEQLGDICVGNVLQPGAGAIMAR 28 1 P09110;C9JDE9;P09110-2;B4DVF4 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 ; 277.59 1.18E-61 1156880000 873620 921950 959530 877940 1128050 777890 1060300 937060 1034560 FALSE TRUE 818941.6837 990212.1373 982290.5047 900469.4267 1039457.503 1002454.215 901317.8583 1054054.004 861885.2525 0.950174842 1.148890916 1.139699864 1.044767182 1.206027717 1.163094753 1.045751573 1.222963266 1 19.71713628 4.743566116 24.18976532 1.124714213 0.950174726 0.357256617 0.072054898 340.6468912 1646135.555 0.015205902 0.123986207 55407.18878 -4.743566116 -0.174539487 DVNQQEFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DVNQQEFVR 9 0 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ;;;; 241.96 4.66E-10 8356780000 2198870 2407870 2137370 2114190 2390760 1753470 2393140 2005530 2381650 FALSE TRUE 2061246.652 2586151.2 2188069.426 2168443.695 2202999.353 2259668.324 2034310.874 2255924.835 1984137.229 1.038862948 1.303413475 1.102781296 1.092889979 1.110305941 1.138866955 1.025287386 1.136980246 1 20.92008038 2.197829438 0.299817386 1.001535117 1.207257013 0.193452599 0.075417566 2.222203484 0.550908842 0.110705194 0.164701445 157.6991812 -2.197829438 0.205721896 DVPGGGPSSSAPAGAEADGPKAS(ph)PEARPQIPTKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVPGGGPSSSAPAGAEADGPKASPEARPQIPTKPR 35 3 Q8N3F8;B0QY86 Q8N3F8 MICALL1 MICAL-like protein 1 1 DVPGGGPS(0.007)S(0.076)S(0.022)APAGAEADGPKAS(0.741)PEARPQIPT(0.154)KPR 45.665 0.065103 190550000 123920 60210 88355 78603 76307 54739 100970 71216 93444 TRUE FALSE 116164.0684 64668.01105 90450.82232 80620.08605 70314.15603 70541.26069 85830.48586 80107.47437 77847.59273 1.492198594 0.830700203 1.161896202 1.035614375 0.903228392 0.906145691 1.102545151 1.029029564 1 16.24836481 4.751380344 24.97490543 1.003205647 1.492198907 0.717522826 0.097725662 1169.138849 2277631.182 0.022933422 0.423106896 56413.14913 -4.751380344 0.48899326 DVPLVHLDEITLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVPLVHLDEITLFK 14 0 Q96ME1-4 Q96ME1-4 FBXL18 F-box/LRR-repeat protein 18 0 ; 176.91 2.16E-06 89383000 488110 491290 523820 522850 559450 390690 662070 514960 609910 FALSE TRUE 457560.0664 527665.6228 536245.2578 536267.2162 515513.0537 503475.8607 562798.7499 579253.8896 508112.0808 0.900510111 1.038482734 1.055368054 1.055411269 1.014565631 0.990875596 1.107627177 1.14001204 1 18.95478724 1.713151033 8.502015607 1.091972259 1.019943704 0.251560226 0.056807991 0.151449184 26.48373901 0.025806811 0.013736664 51.65959925 -1.713151033 -0.072028554 DVPNETLQVEEDDRPELPWWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DVPNETLQVEEDDRPELPWWK 21 1 O95373 O95373 IPO7 Importin-7 0 ;;; 280.2 5.32E-45 1850855000 1004989 976570 1006330 1075400 1007030 802861 1206907 902415 980960 FALSE TRUE 942088.5324 1048876.259 1030200.623 1102996.585 927941.926 1034633.937 1025942.5 1015083.499 817231.4388 1.152780581 1.283450696 1.260598374 1.349674685 1.135470176 1.266023171 1.255387949 1.242100403 1 19.64038518 -3.062351387 0.564366688 0.00105065 1.251200028 0.604476927 0.061577168 288.3812854 9.692707534 350.856512 0.023289961 0.000866261 3.062351387 1.250149377 DVPPDILLDS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVPPDILLDSPER 13 0 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 DVPPDILLDS(1)PER 176.25 1.77E-05 57950000 32381 43118 41372 40680 41533 37007 50417 34297 40022 TRUE FALSE 30354.33101 46310.50158 42353.36338 41723.91767 38271.16572 47690.32014 42857.4389 38579.05595 33342.06965 0.910391326 1.388951018 1.270267977 1.251389554 1.147834136 1.430334729 1.285386281 1.157068423 1 15.02505604 -0.25082032 7.897444105 0.999999933 1.257242189 0.177927694 0.145531472 0 0 0.126378294 0.02978765 0.561280145 0.25082032 0.257242256 DVPPDILLDS(ph)PERK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DVPPDILLDSPERK 14 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 DVPPDILLDS(1)PERK;DVPPDILLDS(1)PERK;DVPPDILLDS(1)PERK;DVPPDILLDS(1)PERK;DVPPDILLDS(1)PERK;DVPPDILLDS(1)PERK;DVPPDILLDS(1)PERK 194.37 9.25E-08 404476000 673070 523761 562650 544815 560011 435528 701809 492170 645454 TRUE FALSE 630943.7502 562540.8094 575996.3237 558795.8753 516029.995 561257.8634 596579.2557 553618.5079 537723.5576 1.173360812 1.046152435 1.071175543 1.039188013 0.959656663 1.043766552 1.109453449 1.029559706 1 19.03650515 4.738694457 7.984741931 1.04525616 1.17441121 0.524478321 0.04007485 0.084014686 65.27702527 0.009806182 0.058312683 54789.13671 -4.738694457 0.12915505 DVQALWTNDHALAWHLSDDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVQALWTNDHALAWHLSDDFR 21 0 Q9UGT4 Q9UGT4 SUSD2 Sushi domain-containing protein 2 0 90.972 0.001205 45773000 10517 19660 16346 13961 26449 16868 20624 23033 16815 FALSE TRUE 9858.759743 21115.64686 16733.73484 14319.2629 24371.80223 21737.51777 17531.62266 25908.72075 14008.46787 0.70377145 1.507348773 1.194544257 1.022186225 1.739790708 1.551741273 1.251501793 1.849504242 1 13.77401155 2.750221299 24.92524401 1.479665589 1.188290631 0.246688247 0.308394625 1199.355447 2563676.041 0.087398977 0.091995792 562.6279452 -2.750221299 -0.291374958 DVQEIFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DVQEIFR 7 0 O00148;O00148-2;O00148-3;K7EQN7;Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;F6S4E6;A0A0A0MT12;F6TRA5;A0A140T9K1;A0A140T973;A0A140T9L4 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ;;;;;; 152.31 0.0042389 3561987000 4163880 4861580 4759840 4741140 5029030 3911460 5324940 4390640 5092650 FALSE TRUE 3903270.184 5221536.442 4872745.653 4862805.679 4634070.27 5040635.005 4526514.681 4938821.069 4242653.815 0.920006758 1.230724134 1.148513611 1.146170744 1.092257458 1.188085388 1.066906441 1.164087688 1 22.01653553 -1.867330646 0.499652791 0.886197204 1.132671383 0.145343054 0.085307815 105.7873458 9.124126621 14.19650869 0.036634641 0.013572797 1.867330646 0.24647418 DVQFAVEQVLQEEHFDASHVALMGGSHGGFISCHLIGQYPETYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVQFAVEQVLQEEHFDASHVALMGGSHGGFISCHLIGQYPETYR 44 0 C9JIF9;P13798 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 47.518 0.008868 150240000 27355 46283 28017 33041 49267 25494 37700 45937 36364 FALSE TRUE 25642.89938 49709.84148 28681.57647 33888.888 45397.76855 32853.70394 32047.23499 51672.33557 30294.61348 0.846450786 1.640880532 0.94675499 1.118644013 1.49854259 1.084473448 1.057852579 1.70566083 1 14.88677368 3.927237378 24.99982126 1.191603111 1.29958965 0 0.300302224 849.3727832 425671.0123 0.070300626 0.126736507 8457.409862 -3.927237378 0.107986539 DVQGTDASLDEELDRVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DVQGTDASLDEELDRVK 17 1 A0A087WYB4;Q9UJZ1;Q9UJZ1-2 A0A087WYB4 STOML2 "Stomatin-like protein 2, mitochondrial" 0 ;;; 268.55 4.94E-28 530638000 519544 441048 438906 406418 650490 364075 472974 450297 1050550 FALSE TRUE 487026.6685 473703.6528 449317.0576 416847.3739 599403.1394 469177.5422 402055.9396 506517.5717 875206.4182 0.556470632 0.541247919 0.513384098 0.47628464 0.684870594 0.536076441 0.459384131 0.578740696 1 19.73926379 0.956798448 22.56479018 1.000000001 0.534103591 0.851191042 0.06022295 988.3898873 516251.1771 0.056132676 0.014033169 9.053123569 -0.956798448 -0.46589641 DVQIGDIVTVGECRPLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DVQIGDIVTVGECRPLSK 18 1 P62280;M0R1H5 P62280 RPS11 40S ribosomal protein S11 0 ;;; 278.93 3.08E-39 4060140000 6180130 5360020 5501060 5502450 5828630 4537180 6954070 4841060 6592330 FALSE TRUE 5793326.695 5756881.458 5631547.741 5643652.183 5370872.911 5846990.211 5911371.762 5445476.997 5492027.535 1.054861189 1.048225163 1.025404134 1.027608137 0.97793991 1.064632356 1.076355085 0.99152398 1 22.38890743 4.216688726 2.391368648 1.0301656 1.053759969 0.098367651 0.030711044 0.912285828 10.02939373 0.008241513 0.028012151 16469.8152 -4.216688726 0.023594369 DVQIILESCHNQNILGTILHPNGNITELLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DVQIILESCHNQNILGTILHPNGNITELLLK 31 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 396.74 5.89E-156 1318575000 860873 1313203 1252064 1182296 1410656 1019063 1525246 1219685 1132093 FALSE TRUE 806992.4956 1410433.917 1281763.549 1212635.717 1299868.768 1313249.945 1296549.522 1371965.357 943139.3647 0.855645015 1.495467127 1.359039393 1.285743934 1.378236151 1.392424062 1.374716792 1.454679349 1 19.84711144 -1.020140045 4.314853549 0.999981553 1.348355088 0.23915677 0.177411706 10089105.23 2385318.72 1954.90842 0.036677373 0.095468468 1.020140045 0.348373535 DVQIPFVVELEVLDGHDPEPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVQIPFVVELEVLDGHDPEPGR 22 0 Q8N9L9 Q8N9L9 ACOT4 Acyl-coenzyme A thioesterase 4 0 ; 112.58 0.00028807 22781000 23318.3 26580.5 22767.1 25182.6 31170 19893.4 29690.6 25143.2 31501.8 FALSE TRUE 21858.84923 28548.54788 23307.14636 25828.82815 28722.03393 25636.30164 25238.77016 28282.38387 26243.94607 0.832910156 1.087814607 0.888096108 0.984182336 1.094425124 0.976846301 0.961698751 1.077672687 1 14.67969704 2.997302626 24.98575313 1.01400262 0.95864857 0.186837407 0.076234784 247.7520202 2294961.263 0.021120063 0.024824724 993.8083146 -2.997302626 -0.05535405 DVQNFPAATDEKDKFVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVQNFPAATDEKDKFVEK 18 2 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 200.99 8.17E-16 420980000 421040 203370 290820 272300 304530 168420 333630 222760 475300 FALSE TRUE 394687.858 218427.7264 297718.3877 279287.679 280613.4422 217040.1199 283605.2788 250572.0764 395969.3594 0.996763635 0.55162785 0.751872287 0.705326491 0.708674637 0.548123522 0.716230365 0.632806732 1 18.59502927 -1.158146768 5.155675601 1.000014246 0.688098314 0.353807999 0.125665913 1.79E-05 2.92E-06 0.105703194 0.024913345 0.069478948 1.158146768 -0.311915932 DVQNTFYDIVAELGAMEHAQAVDYIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVQNTFYDIVAELGAMEHAQAVDYIK 26 0 E7EMD0;P16435 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 80.102 0.014084 9655500 15396 15329 13727 13769 19882 12143 16851 15224 13998 FALSE TRUE 14432.39184 16463.97511 14052.61092 14122.33585 18320.54792 15648.48697 14324.34899 17124.74991 11661.64337 1.237595027 1.411805745 1.205028355 1.211007351 1.571009106 1.341876653 1.228330222 1.468467983 1 13.50948349 -1.283178737 5.849863535 0.999979107 1.32615335 0.426108233 0.121624722 3.10E-05 3.80E-06 0.110025985 0.025931714 0.052098025 1.283178737 0.326174244 DVRPYIVGAVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVRPYIVGAVVR 12 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 129.34 0.00021516 222770000 63941 118970 51304 54987 144800 43273 61129 97798 129550 FALSE TRUE 59939.04695 127778.6626 52520.95511 56398.05951 133427.9921 55765.21262 51963.27394 110008.2956 107927.2681 0.555365183 1.183933077 0.48663286 0.522556167 1.236276934 0.516692525 0.481465665 1.019281758 1 16.71969989 3.96656148 24.68576395 0.708863195 0.904638858 0.007406531 0.30405021 815.115502 1905515.773 0.072815474 0.133082778 9258.944483 -3.96656148 0.195775663 DVSGFSDPYCLLGIEQGVGVPGGS(ph)PGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DVSGFSDPYCLLGIEQGVGVPGGSPGSR 28 0 Q70J99;Q70J99-3;K7EQ37;Q70J99-2;K7EN81;K7EIH3 Q70J99 UNC13D Protein unc-13 homolog D 1 DVSGFSDPYCLLGIEQGVGVPGGS(0.869)PGS(0.131)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.939)PGS(0.061)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.993)PGS(0.007)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.797)PGS(0.203)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.958)PGS(0.042)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.786)PGS(0.214)R 182.78 8.09E-18 4150420000 1252947 1473361 1414096 1495214 1646918 1333936 1899654 1565017 1516460 TRUE FALSE 1174527.284 1582450.181 1447639.025 1533583.723 1517575.704 1719021.669 1614818.518 1760412.817 1263353.029 0.92969048 1.25257956 1.145870546 1.213899589 1.201228531 1.360681954 1.278200535 1.393444886 1 20.26882641 4.740088829 24.62066009 1.239180592 0.929690353 0.424921937 0.10967414 99.77417444 1607246.057 0.024158122 0.153584043 54965.32868 -4.740088829 -0.309490239 DVSLGDWEFGKRDS(ph)LGAYASQDANEQGQDLGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVSLGDWEFGKRDSLGAYASQDANEQGQDLGKR 33 3 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DVSLGDWEFGKRDS(0.998)LGAYAS(0.002)QDANEQGQDLGKR 113.51 2.87E-05 190230000 74221 75335 58280 81903 106440 40625 95882 59330 210230 TRUE FALSE 69575.6401 80912.88179 59662.42912 84004.76964 98080.63176 52352.77801 81505.38422 66737.4811 175141.2549 0.397254434 0.461986423 0.340653201 0.479640104 0.56000873 0.298917454 0.46536942 0.381049463 1 17.41815943 -1.720030091 2.77271326 1.096642655 0.422611252 0.855672736 0.074458528 18382327.91 15625531.22 12315517.19 0.017004456 0.019053287 1.720030091 -0.674031403 DVSPFDHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVSPFDHSR 9 0 P18031 P18031 PTPN1 Tyrosine-protein phosphatase non-receptor type 1 0 100.48 0.0046337 166110000 219460 511110 425120 480030 491580 504320 382840 430750 288250 FALSE TRUE 205724.3903 548953.1162 435204.0472 492348.3825 452973.2897 649908.997 325436.6961 484530.0857 240139.2128 0.856688035 2.285978661 1.812298966 2.050262332 1.886294556 2.706384307 1.355200145 2.01770498 1 17.87351148 0.171867782 1.005036517 0.995382952 1.923120509 0.221931733 0.500466917 6.340784236 6.494509732 0.515712294 0.135412949 1.485483327 -0.171867782 0.927737557 DVT(ph)PPPETEVVLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.999)PPPET(0.001)EVVLIK;DVT(1)PPPETEVVLIK;DVT(1)PPPETEVVLIK;DVT(1)PPPETEVVLIK 178.67 2.19E-05 3446250000 1580825 947752 1188617 1075056 1025291 953038 1484619 1007216 948198 TRUE FALSE 1481883.985 1017924.544 1216811.557 1102643.757 944768.7807 1228164.599 1262014.163 1132969.135 789937.6282 1.875950622 1.288613819 1.540389409 1.395861797 1.196004275 1.554761484 1.597612417 1.434251382 1 19.59137922 4.748660613 24.41804768 1.415850558 1.875950974 0.406362018 0.184401426 1064.288368 2572982.424 0.040707118 0.545809334 56060.97064 -4.748660613 0.460100416 DVTGPDEESFLYFAYGSNLLTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVTGPDEESFLYFAYGSNLLTER 23 0 O75223;O75223-3;B8ZZK2;O75223-2;O75223-4;A0A0B4J1Y4 O75223 GGCT Gamma-glutamylcyclotransferase 0 82.36 0.0088187 10068000 19007 18370 15984 19692 18102 16330 20321 15883 18301 FALSE TRUE 17817.3858 19730.13391 16363.14803 20197.33006 16680.34194 21044.2059 17274.0547 17866.02751 15246.44487 1.168625601 1.294080953 1.073243511 1.32472391 1.094047962 1.380269701 1.132989024 1.171815965 1 13.89618526 0.74422285 1.522621664 1.000932321 1.211018058 0.309223158 0.098968831 1.008526014 3.877463057 0.082183636 0.023868474 5.549103819 -0.74422285 0.210085737 DVTGS(ph)PPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DVTGSPPAK 9 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 DVTGS(1)PPAK;DVT(0.008)GS(0.992)PPAK;DVT(0.072)GS(0.928)PPAK 155.97 7.56E-05 1395340000 4258130 2926970 3600520 3397710 3634950 2696320 4229760 2911420 3413550 TRUE FALSE 3991621.244 3143685.904 3685926.035 3484900.991 3349475.69 3474703.813 3595546.755 3274917.196 2843806.453 1.403619167 1.105450022 1.296124084 1.225435362 1.177814224 1.221849613 1.264342991 1.151596373 1 21.43939185 0.933837843 4.041681278 1.000127003 1.231445553 0.498721118 0.077379758 0.238819999 10.23783836 0.065981226 0.016864563 8.586928425 -0.933837843 0.23131855 DVTHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVTHPR 6 0 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 103.29 0.080996 238450000 172132 189166 202736 203546 204602 173098 204618 193629 218578 FALSE TRUE 161358.5654 203172.0475 207544.9937 208769.335 188533.3842 223068.5826 173937.4305 217804.0069 182095.9197 0.886118512 1.1157419 1.13975642 1.146480027 1.035352052 1.225005936 0.955196749 1.196094933 1 17.47433907 -0.208243574 7.088356677 1 1.090918539 0.063687191 0.10465871 6055418.845 854276.6964 0.089435756 0.021691357 0.61909376 0.208243574 0.090918539 DVTLENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVTLENR 7 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 97.033 0.028603 407870000 589150 650220 587340 569970 738100 460190 649800 595740 681760 FALSE TRUE 552276.1532 698362.9654 601271.9822 584596.3952 680132.6034 593039.3824 552368.5224 670119.4504 567969.8517 0.972368783 1.229577527 1.058633624 1.029273637 1.197480115 1.044138841 0.972531413 1.179850389 1 19.11545483 1.603784835 0.359853507 1.007467166 1.119460764 0.015472228 0.093460734 3.02138729 1.221949848 0.124134712 0.1083229 40.15917982 -1.603784835 0.111993598 DVTNFTVGGFAPMS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 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 364 4.22E-104 4994502000 3745535 4461556 3877809 4154992 5225631 3036169 4393618 4322618 5218207 TRUE FALSE 3511108.65 4791894.248 3969792.461 4261616.129 4815231.02 3912661.702 3734835.769 4862306.373 4347254.541 0.807661161 1.102280578 0.913172308 0.980300576 1.107648741 0.900030506 0.859125164 1.118477496 1 22.05167314 3.871278967 0.002394753 1.940747383 2.30E-06 0.017350334 0.107522228 1269377.256 643.2792973 257352.8626 263989.3645 7434.965657 -3.871278967 -1.940745085 DVTNNVHYENYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DVTNNVHYENYR 12 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4 E7EPK1 7-Sep Septin-7 0 ;;;;; 248.36 9.56E-17 6417670000 3880210 6057380 3825260 3845560 6511250 2461440 4035940 5511450 7170880 FALSE TRUE 3637354.582 6505874.718 3915996.974 3944243.58 5999882.69 3172017.77 3430788.265 6199566.665 5974013.802 0.608862768 1.089029074 0.655505177 0.660233423 1.004330236 0.530969274 0.574285293 1.037755665 1 22.51026914 3.81276573 8.917724161 0.741859343 0.880928407 0 0.217844945 0.868255973 83.03192378 0.051982684 0.093886983 6497.790874 -3.81276573 0.139069065 DVVEPLLRPQWYVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVVEPLLRPQWYVR 14 1 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 158.81 4.57E-06 591280000 541710 598510 583350 559190 591350 436710 605320 559010 603470 FALSE TRUE 507805.3381 642824.3031 597187.3375 573539.7621 544907.7564 562781.0876 514557.8855 628803.629 502746.9584 1.010061482 1.278623953 1.187848733 1.140811998 1.083860871 1.119412218 1.023492787 1.250735819 1 18.93947292 3.005495759 2.863525247 1.092894945 1.188598123 0.061405944 0.093803024 0.435265627 7.267037097 0.027266772 0.031747026 1012.73486 -3.005495759 0.095703178 DVVFNYLHATAFQGTPLAQAVEGPSENVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVVFNYLHATAFQGTPLAQAVEGPSENVR 29 0 P31930 P31930 UQCRC1 "Cytochrome b-c1 complex subunit 1, mitochondrial" 0 111.82 0.00030493 47648000 27134 26567 28284 26005 34463 28438 27693 30090 38766 FALSE TRUE 25435.73138 28534.04832 28954.90984 26672.33233 31756.415 36647.58895 23540.69174 33846.80274 32295.70416 0.787588691 0.883524576 0.896556077 0.825878643 0.98330152 1.134751197 0.728910929 1.048028015 1 14.97905466 2.735098754 24.5978726 0.956076618 0.86227144 0.250637146 0.10707394 464.2392235 3298583.838 0.033284769 0.032574095 543.3738751 -2.735098754 -0.093805179 DVVICPDASLEDAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DVVICPDASLEDAKK 15 1 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ;;;; 249.13 2.72E-18 3635650000 5866040 3195210 4101060 3894030 4367090 2898680 5344650 3471730 5958070 FALSE TRUE 5498895.028 3431786.673 4198339.08 3993957.402 4024116.367 3735481.86 4543269.35 3905183.133 4963629.626 1.107837498 0.691386532 0.845820377 0.804644525 0.810720515 0.752570627 0.915311917 0.786759574 1 22.24296404 -1.066172197 0.6712561 1.041095378 0.825779288 0.156450474 0.112504616 63.86666145 14.48627367 5.341099517 0.036868905 0.085867299 1.066172197 -0.215316091 DVVLSTS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVVLSTSPK 9 0 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 DVVLS(0.001)T(0.06)S(0.939)PK 137.92 0.00015856 157570000 899130 495710 736380 667900 648210 447660 828090 513530 667730 TRUE FALSE 842855.0583 532412.8842 753847.2813 685039.4448 597302.2014 576892.1748 703925.5921 577645.3509 556281.5493 1.515159112 0.957092474 1.355154206 1.23146174 1.07374081 1.037050709 1.265412439 1.038404656 1 19.08545573 2.748880149 23.38785993 1.109051834 1.228519053 0.227781703 0.156220298 627.4701361 1422075.488 0.04546615 0.047684162 560.893166 -2.748880149 0.119467219 DVVMLDNLPDLPPALVPS(ph)PPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVVMLDNLPDLPPALVPSPPKR 22 1 H3BPY8;H3BPM3;H3BRE8;Q9BWH6-2;Q9BWH6 H3BPY8 RPAP1 RNA polymerase II-associated protein 1 1 DVVMLDNLPDLPPALVPS(1)PPKR 102.27 0.00038066 76848000 52282 42741 47203 44334 49501 33945 54992 35120 44687 TRUE FALSE 49009.76295 45905.58811 48322.67745 45471.6855 45613.39114 43744.37045 46746.46012 39504.80931 37228.45101 1.316459901 1.233078113 1.298003976 1.221422978 1.225229358 1.175025263 1.255664924 1.061145662 1 15.18411797 1.149758718 3.490763989 1.001198888 1.24685242 0.835415351 0.040192809 0.082690174 1.78642613 0.036817563 0.009790809 14.11752997 -1.149758718 0.245653532 DVYEDELVPVFEAVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DVYEDELVPVFEAVGR 16 0 B7Z8Z7;A0AV96;A0AV96-2;D6R9D6;D6RBS9;D6REZ6;D6R9M7;D6RBP6;D6RFL5;D6RA49 B7Z8Z7 RBM47 RNA-binding protein 47 0 126.1 0.00017091 23565000 42887 42221 42607 45119 44270 35222 50917 39834 37716 FALSE TRUE 40202.77923 45347.08677 43617.65816 46276.82993 40793.21278 45390.01962 43282.46854 44807.36259 31420.95595 1.279489373 1.443211558 1.388170947 1.472801464 1.298280448 1.444577934 1.377503238 1.426034353 1 14.93943945 -1.062600945 4.589427691 0.999982221 1.39627951 0.795455735 0.062306023 1.08E-05 2.20E-06 0.051527667 0.012144582 0.086576307 1.062600945 0.396297289 DVYKEHFQDDVFNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DVYKEHFQDDVFNEK 15 1 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;; 252.17 7.36E-25 1325870000 1669990 1489160 1573900 1716870 2131610 1006530 2145730 1381440 3350900 FALSE TRUE 1565468.307 1599418.956 1611233.651 1760927.791 1964201.949 1297098.871 1823997.706 1553915.825 2791613.142 0.560775518 0.572937178 0.577169389 0.630792198 0.703608218 0.46464134 0.65338484 0.556637236 1 21.4126676 -1.430324687 3.04962763 1.007470028 0.590971721 0.802668942 0.063886907 16509450.21 20566456.25 1070187.153 0.01389225 0.037125757 1.430324687 -0.416498307 DVYLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 139.38 0.0028279 32790800000 32123790 35526070 33965650 33500470 40857660 28271460 37540050 33326160 43049800 TRUE FALSE 30113219.33 38156457.19 34771331.26 34360148.78 37648864.2 36432971.55 31911268.01 37487004.44 35864510.27 0.839638381 1.063905708 0.969519199 0.958054314 1.049752636 1.015850245 0.889772864 1.045239546 1 25.0960536 4.756257448 24.43841308 0.993196087 0.839638207 0.482153786 0.051595031 2639.68118 3645183.039 0.012372731 0.375211289 57050.23639 -4.756257448 -0.15355788 DVYLS(ph)PRDDGYSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DVYLSPRDDGYSTK 14 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 1 DVYLS(1)PRDDGYSTK;DVYLS(1)PRDDGYSTK;DVYLS(1)PRDDGYSTK;DVYLS(1)PRDDGYSTK 193.19 1.74E-07 3424730000 2321640 3994540 2597840 4132520 7185800 1170760 2771450 3076650 18985500 TRUE FALSE 2176332.697 4290299.898 2659461.992 4238567.46 6621456.254 1508739.406 2355896.801 3460776.525 15816697.4 0.137597163 0.271251311 0.168142686 0.267980562 0.418637095 0.095389029 0.148949983 0.218805256 1 23.91494505 -1.485297355 2.88261043 1.025807916 0.213903257 0.880276305 0.090881075 12930631.97 14361798.85 2654421.695 0.022536868 0.032711665 1.485297355 -0.811904659 DVYVPEASRPHQWQTDEEGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DVYVPEASRPHQWQTDEEGVR 21 1 P49757-3;P49757;P49757-8;P49757-7;P49757-6;P49757-5;P49757-4;P49757-2;G3V4S6;G3V433;G3V3R1;G3V3M5 P49757-3 NUMB Protein numb homolog 0 ;; 204.55 3.15E-22 413805000 339607 372378 346064 358000 383454 295214 407704 333246 392032 FALSE TRUE 318351.6041 399949.2546 354272.8015 367186.8861 353339.0696 380437.4894 346572.5701 374852.4967 326599.3266 0.974746664 1.224586893 1.084732186 1.124273249 1.081873234 1.164844684 1.061155189 1.147744242 1 18.31716229 -4.343410316 0.397831327 7.98E-08 1.117103989 0.189933084 0.067225597 593.5652517 7.129468796 505.8549832 0.037593149 4.54E-05 4.343410316 1.117103909 DVYVQLYLQHLTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DVYVQLYLQHLTAR 14 0 P42166;P42167;G5E972;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 0 ; 217.16 5.86E-12 549790000 323550 451320 417430 382400 503150 395840 525440 425610 474090 FALSE TRUE 303299.5831 484736.2024 427331.6367 392213.0314 463634.6286 510112.5821 446655.1499 478748.3454 394961.3163 0.767922251 1.227300453 1.081958205 0.993041635 1.173873515 1.291550745 1.130883283 1.212139837 1 18.59135183 2.693734336 14.88193727 1.177223431 1.063249414 0.179559278 0.1363275 9.098363558 3018.917982 0.041252761 0.038901952 494.0084028 -2.693734336 -0.113974017 DWALNHLDDNEVWITR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DWALNHLDDNEVWITR 16 0 Q9H9F9 Q9H9F9 ACTR5 Actin-related protein 5 0 217.88 1.39E-14 54238000 39528 45512 44574 48046 54986 42386 55641 37123 56029 FALSE TRUE 37054.01304 48881.75584 45631.31633 49278.9417 50667.62136 54622.15012 47298.1486 41757.88827 46677.39794 0.793832019 1.047225381 0.977589119 1.05573455 1.08548513 1.17020555 1.013298742 0.894606172 1 15.51043652 4.740358754 24.53699613 1.034983148 0.793831915 0.518415728 0.071577345 102.0364639 1392220.113 0.016902879 0.109384378 54999.50157 -4.740358754 -0.241151233 DWDAWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DWDAWK 6 0 P04181;P04181-2 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ;;; 129.96 0.037149 1207440000 2676380 2209550 2231910 2011750 3098690 1798890 2067610 2252170 3286780 FALSE TRUE 2508870.153 2373147.381 2284851.959 2063374.911 2855331.387 2318200.34 1757591.075 2533358.382 2738195.185 0.916249567 0.86668306 0.834437213 0.753552896 1.042778617 0.846616178 0.641879397 0.925192768 1 21.38479386 1.990294216 24.92645992 0.797986606 0.874475517 0 0.119125215 1159.870573 2978789.671 0.043325931 0.030201724 97.78994829 -1.990294216 0.076488911 DWDDDQND ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DWDDDQND 8 0 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 146.27 0.0012937 558240000 1708510 1556510 1596710 1571810 1648310 1312440 1880210 1387700 1677500 FALSE TRUE 1601577.409 1671755.62 1634584.715 1612145.306 1518858.382 1691320.122 1598289.966 1560957.4 1397514.413 1.146018527 1.196234976 1.169637107 1.15358045 1.08682842 1.210234475 1.143666177 1.116952631 1 20.41443173 0.80000052 1.737625209 1.000196742 1.163200517 0.694914804 0.032943347 0.378853637 2.022460741 0.030030753 0.008521496 6.309580997 -0.80000052 0.163003774 DWEDDS(ph)DEDMSNFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 37 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;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR 475.14 9.21E-200 1.60369E+11 32134825 24314323.4 25804836 24280581.7 24777053.1 21460128.7 30700352 22244777.4 16704063 TRUE FALSE 30123563.67 26114581.2 26416938.9 24903662.53 22831163.3 27655319.48 26097119.23 25022086.83 13916046.97 2.164663839 1.876580415 1.898307684 1.78956442 1.640635688 1.987297077 1.875325606 1.798074329 1 23.73024612 -2.121589482 0.383834699 4.52E-15 1.911211534 0.822475045 0.129604694 19.4285958 1.070748296 17.0741522 0.084185141 0.007558063 2.121589482 1.911211534 DWEDDSDEDMSNFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DWEDDSDEDMSNFDR 15 0 A0A087WYT3;Q15185-4;Q15185;B4DDC6;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ;;;; 401.55 1.88E-132 1079310000 1559860 1199670 1389330 1215710 1312700 1143150 1570370 1193280 963830 FALSE TRUE 1462231.147 1288494.815 1422285.564 1246907.177 1209605.837 1473158.848 1334907.597 1342263.635 802960.5464 1.821049806 1.604680106 1.771301928 1.552887228 1.506432467 1.834659068 1.662482177 1.671643321 1 19.61496958 0.357431663 3.071072802 1.000000073 1.677460139 0.796541319 0.107714728 27.47791409 130.1332515 0.095758459 0.024960363 2.277359867 -0.357431663 0.677460066 DWEQFEYK ddPTM_SK-BR-3_Pertuzumab_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 ;; 190.73 0.00043017 960850000 843960 794960 762635 696093 915280 513175 819470 715330 962100 FALSE TRUE 791138.0501 853819.6656 780725.0623 713955.9249 843397.6009 661320.2918 696598.0811 804640.5251 801519.2946 0.987048042 1.065251543 0.974056479 0.89075326 1.052248656 0.825083434 0.869097083 1.003894143 1 19.61237772 3.556409532 2.995285336 0.926501195 1.028756951 0.177980236 0.071018515 0.323724392 5.69028453 0.019244906 0.031184389 3600.887323 -3.556409532 0.102255756 DWEQFHQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 DWEQFHQPR 9 0 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 ;;;; 191.67 3.56E-05 4312780000 2182350 2776670 2794420 2500280 2915270 2482430 2701650 2502230 2298350 FALSE TRUE 2045760.609 2982257.536 2860704.962 2564441.418 2686316.454 3199067.242 2296562.663 2814638.924 1914740.537 1.068427063 1.557525669 1.494043139 1.339315363 1.402966304 1.670757567 1.199411941 1.469984507 1 20.86871748 -0.927666013 7.906771406 1.000041871 1.416915248 0.343559125 0.172543164 2.27E-09 5.74E-10 0.152383431 0.035917118 0.118122869 0.927666013 0.416873378 DWGEHNQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DWGEHNQR 8 0 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 171.73 0.00028767 141550000 80082 89239 88935 73523 96465 69898 91510 73176 121870 FALSE TRUE 75069.81057 95846.34841 91044.5802 75409.72465 88889.02802 90076.4179 77788.92504 82312.18468 101529.1097 0.739391991 0.944028257 0.896733759 0.742739938 0.875502881 0.887197949 0.766173615 0.810724973 1 16.6315339 DWILPSDYDHAEAEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DWILPSDYDHAEAEAR 16 0 O43852;O43852-3;O43852-15;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;;;;;; 325.09 1.03E-58 5657180000 5001730 4850620 5435820 5144600 4895510 4752940 5828400 4703160 3584140 FALSE TRUE 4688680.648 5209764.952 5564760.217 5276619.146 4511036.392 6125036.62 4954485.528 5290359.879 2985923.88 1.570261278 1.744774871 1.863664461 1.767164656 1.510767379 2.051303673 1.659280587 1.771766492 1 21.50974596 -0.825589443 1.565417133 0.989065271 1.754145543 0.706617616 0.15015844 488.0268509 400.730073 31.08210206 0.036946 0.149420628 0.825589443 0.765080272 DWNEELQTTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DWNEELQTTR 10 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ;;; 213.25 5.97E-08 846010000 968920 973620 1039320 1060700 1016360 773895 1237890 903120 1152410 FALSE TRUE 908277.0268 1045707.838 1063973.161 1087919.358 936539.1854 997305.9234 1052279.887 1015876.52 960065.3261 0.946057525 1.089204879 1.108229963 1.133172221 0.975495271 1.038789649 1.096050298 1.058132704 1 19.87277305 2.754828426 24.98032841 1.044650769 1.079016564 0.054765016 0.058880642 2359.318486 3622886.433 0.017731757 0.01873385 568.6282424 -2.754828426 0.034365795 DWNPKPLDTFLEELAENCVGYCGADIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DWNPKPLDTFLEELAENCVGYCGADIK 27 1 Q6PL18 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 ; 190.19 5.81E-18 244120000 501690 298070 383580 324770 378780 297630 536650 314760 501660 FALSE TRUE 470290.1184 320139.4129 392678.6987 333104.148 349032.1467 383550.9494 456184.3145 354058.4789 417929.7052 1.125285216 0.766012583 0.939580733 0.797033912 0.835145582 0.917740339 1.091533597 0.847172322 1 18.67290078 1.988288698 23.2821642 0.993463542 0.877328061 0.096360924 0.114035752 356.705018 709131.5641 0.040734336 0.027937694 97.33940739 -1.988288698 -0.116135482 DWPDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DWPDAR 6 0 P12532;P12532-2;F8WCN3;P17540;H0YJJ7;P12277;H0YJG0;G3V4N7;P06732 P12532;P12277 CKMT1A;CKMT1B;CKMT2;CKB;CKM "Creatine kinase U-type, mitochondrial;Creatine kinase S-type, mitochondrial;Creatine kinase B-type;Creatine kinase M-type;Creatine kinase M-type, N-terminally processed" 0 ; 132.72 0.034376 975810000 2504100 2492800 2347900 2458500 2877800 2017030 2696900 2285000 2629500 FALSE TRUE 2347372.851 2677369.506 2403593.297 2521589.272 2651789.196 2599313.817 2292524.882 2570287.28 2190619.463 1.071556649 1.222197443 1.097220826 1.151085031 1.210520239 1.186565655 1.046518996 1.173315276 1 21.06290746 0.229951469 0.589343608 0.993745699 1.154599767 0.361602293 0.058864954 2.970602529 1.436808537 0.103975311 0.023524269 1.698053888 -0.229951469 0.160854068 DWQSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DWQSGR 6 0 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 ; 162.21 0.013489 744860000 550430 617360 594460 627380 636350 419190 628000 513170 580180 FALSE TRUE 515979.5688 663069.9768 608560.8719 643479.633 586373.6379 540203.348 533837.2301 577240.4041 483344.2099 1.067519913 1.371838047 1.259063126 1.331307213 1.213159537 1.117636949 1.104465967 1.194263617 1 18.88269143 2.371727649 3.248631523 1.111005441 1.276839808 0.377823635 0.091732878 0.224259402 4.722911286 0.031291509 0.025343622 235.3572866 -2.371727649 0.165834367 DWQSYYYHHPQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DWQSYYYHHPQDR 13 0 Q1KMD3 Q1KMD3 HNRNPUL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;;;; 182.02 6.69E-06 10850940000 2179393 2656580 2404011 2275161 2835008 1964530 2502005 2553795 2770405 FALSE TRUE 2042988.682 2853275.947 2461035.276 2333545.483 2612357.908 2531657.92 2126852.578 2872641.927 2308006.508 0.885174576 1.236251257 1.066303439 1.011065383 1.131867652 1.096902418 0.92151065 1.24464204 1 21.13821586 DWSHYFKIIEDLRAQIFANTVDNAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DWSHYFKIIEDLRAQIFANTVDNAR 25 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 275.33 2.90E-53 445472000 366942 389496 855280 790292 867732 1085224 888014 172519.7 313541 FALSE TRUE 343975.7552 418334.6891 875567.6455 810572.2307 799583.829 1398510.552 754864.5446 194059.1643 261208.9815 1.316860367 1.601532561 3.351981392 3.103156047 3.061088575 5.353991059 2.8898874 0.742926844 1 17.99484498 4.14267246 2.583695681 3.034471104 1.373683208 0.134623079 1.287711779 0.446591203 5.796155438 0.319531718 0.928085562 13889.04739 -4.14267246 -1.660787896 DWTDYDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DWTDYDEK 8 0 Q9NWV4 Q9NWV4 C1orf123 UPF0587 protein C1orf123 0 ;;; 135.83 0.0019006 855290000 1466070 838420 1128660 944590 920500 938340 1338620 946550 843020 FALSE TRUE 1374311.296 900497.4892 1155432.348 968829.7786 848207.6431 1209223.525 1137906.358 1064728.851 702314.5159 1.956831682 1.282185501 1.64517794 1.379481353 1.207731898 1.721769233 1.620223322 1.516028541 1 19.42175773 -1.34637555 2.802827467 0.992249876 1.527522346 0.376320661 0.21832163 7026395.376 8236048.527 448422.5215 0.049195119 0.045042704 1.34637555 0.53527247 DWTISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DWTISR 6 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;;;; 172.52 0.011862 2195110000 1622590 1993120 1705010 1725640 2030020 1612720 1914730 1713920 1865630 FALSE TRUE 1521034.988 2140692.679 1745453.642 1769922.844 1870590.418 2078286.084 1627634.012 1927906.685 1554244.301 0.978633145 1.377320591 1.123023994 1.138767466 1.203536933 1.337168219 1.047218903 1.24041419 1 20.56778186 -0.763755736 0.499531976 0.952891546 1.196510022 0.163837559 0.121924908 22.21378181 4.019534511 1.764276227 0.053903424 0.172283729 0.763755736 0.243618475 DWVLNEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DWVLNEFK 8 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 130.96 0.0023855 208310000 208400 429410 145780 135510 497650 97583 157690 392850 472700 FALSE TRUE 195356.616 461203.9632 149237.9704 138987.416 458566.5764 125753.628 134045.8484 441898.1873 393803.3162 0.496076615 1.171153071 0.378965753 0.352936124 1.164455853 0.319331054 0.34038781 1.122129167 1 18.58711573 1.21974389 24.99743745 1.061065079 0.61960141 0.260296231 0.319883732 409.2794731 543700.6887 0.301623579 0.075922233 16.58608512 -1.21974389 -0.441463669 DWVLNEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DWVLNEFR 8 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2;A0A0U1RQJ0 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;; 184.49 0.00050653 754734000 609012 1596299 489714 483397 1699325 350463 551409 1417691 1315666 FALSE TRUE 570895.026 1714490.639 501330.2473 495801.7854 1565866.869 451635.9788 468730.3395 1594692.842 1096072.845 0.520855004 1.564212312 0.457387709 0.452343827 1.428615695 0.412049236 0.427645244 1.454915017 1 20.06391225 5.003958717 24.96358789 0.854036354 0.10256605 0.054802447 0.461001433 73158.13812 1011726.46 0.103423275 1762890.978 100915.6953 -5.003958717 -0.751470305 DWYDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DWYDVK 6 0 P61247;E9PFI5;D6RG13;H0Y8L7;H0Y9Y4;D6RI02 P61247 RPS3A 40S ribosomal protein S3a 0 ;;;;; 114.94 0.057818 6124770000 14917500 11477980 13351700 12567200 13523400 10685790 16355900 10669640 14615500 FALSE TRUE 13983840.3 12327821.58 13668408.63 12889695.63 12461326.71 13770604.1 13903484.64 12001768.04 12176078.63 1.148468298 1.012462383 1.122562448 1.058608113 1.023426925 1.130955583 1.141868828 0.985684177 1 23.53754624 1.219787077 24.99276182 0.992841959 1.087856371 0.422665051 0.047663814 282.5670786 376164.7744 0.044861686 0.01129353 16.58773455 -1.219787077 0.095014412 DWYPHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 DWYPHSR 7 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;;; 157.58 0.0014664 29140850000 7721620 9372620 6637450 5778070 10270750 3355072 7472220 9378710 12546080 FALSE TRUE 7238337.588 10066578.54 6794893.448 5926345.058 9464126.725 4323626.821 6351829.98 10549662.59 10452058.2 0.692527486 0.963119258 0.650100996 0.567002685 0.90547972 0.41366272 0.607710927 1.009338294 1 23.31728373 1.229015693 24.91877965 1.004669456 0.695094219 0.415935743 0.156851335 225.533725 588775.4993 0.146332398 0.038491132 16.94399024 -1.229015693 -0.309575237 DYAAYNVLDDPELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DYAAYNVLDDPELR 14 0 Q86SX6 Q86SX6 GLRX5 "Glutaredoxin-related protein 5, mitochondrial" 0 ;; 227.57 4.61E-12 147094000 318391 331955 311375 300458 439300 315010 293605 356288 525960 FALSE TRUE 298463.4757 356533.2936 318760.962 308168.261 404799.1501 405948.2732 249581.6559 400771.3411 438173.8782 0.681153055 0.813679937 0.727475959 0.703301306 0.923832228 0.926454756 0.569595013 0.914639966 1 18.74114395 -4.999999965 0.294848977 2.825195694 0.760472997 0.273120043 0.115814084 354.2003387 3.309216717 398.517939 0.115417266 1.00E-05 4.999999965 -2.064722697 DYAFIHFDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 DYAFIHFDER 10 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;;;; 162.36 6.79E-06 2610695000 4011810 4668895 4328247 3988189 4617817 3369998 4660686 4228859 4337510 FALSE TRUE 3760717.973 5014584.844 4430915.063 4090532.682 4255152.28 4342861.715 3961859.402 4756841.355 3613551.56 1.040726253 1.387716423 1.226193951 1.131997874 1.177554052 1.201826415 1.096389338 1.316389507 1 21.78498605 -4.999999999 0.167333698 0.211395371 1.258066218 0.202441784 0.105361001 174.5249893 1.63696056 45.76358688 0.376876133 1.00E-05 4.999999999 1.046670846 DYAFVHFEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DYAFVHFEDR 10 0 O43390;O43390-3;B4DT28;A0A286YEZ8;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;;;; 205.53 1.67E-07 3108840000 3227740 3688130 3356010 3314480 3808690 2763440 3480690 3215950 3705830 FALSE TRUE 3025721.515 3961202.983 3435616.142 3399535.168 3509570.851 3561200.267 2958792.848 3617468.437 3087303.032 0.980053297 1.283062576 1.11282116 1.101134269 1.13677563 1.153498775 0.958374613 1.171724446 1 21.55791567 1.768677388 25 1.040463738 1.143369216 0.146615935 0.091076707 35.50577941 29489.45418 0.038947424 0.02160247 58.70531029 -1.768677388 0.102905478 DYAFVHMEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DYAFVHMEK 9 0 Q96PK6;Q96PK6-2 Q96PK6 RBM14 RNA-binding protein 14 0 ;; 143.89 0.00010086 582400000 2988350 2673190 2896950 2700520 3210660 2288290 3413270 2919230 3530060 FALSE TRUE 2801314.508 2871115.769 2965667.022 2769819.915 2958507.715 2948882.176 2901481.851 3283702.292 2940870.181 0.952546129 0.97628103 1.008431804 0.941836853 1.005997386 1.002724362 0.986606573 1.116575058 1 21.48781167 1.333245979 10.89569361 1.058155755 0.984536319 0.448282908 0.035077816 0.290419387 30.69046083 0.020489283 0.00749261 21.54001389 -1.333245979 -0.073619437 DYAFVHMER ddPTM_SK-BR-3_Pertuzumab_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 ;;; 137.46 0.00016407 1010900000 1137190 1246860 1218740 1169280 1291850 1012220 1292290 1211300 1247340 FALSE TRUE 1066015.308 1339178.812 1247649.088 1199285.704 1190393.312 1304431.482 1098523.112 1362533.471 1039150.896 1.025852272 1.288724108 1.200642845 1.154101593 1.145544229 1.255285914 1.057135317 1.311198861 1 19.98697373 -1.827843965 2.805997389 0.939642115 1.18358248 0.273713316 0.091867584 25030916.06 15604401.8 10116959.8 0.020098122 0.014864696 1.827843965 0.243940365 DYALHWLVLGTHTSDEQNHLVVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DYALHWLVLGTHTSDEQNHLVVAR 24 0 Q16576;E9PC52;Q16576-2;C9J7L0 Q16576 RBBP7 Histone-binding protein RBBP7 0 ;;; 279.96 1.19E-52 649303000 468235.8 695062 654821 636433 738774 546638 798245 695964 689994 FALSE TRUE 438929.7571 746525.1137 670353.6633 652764.9483 680753.6701 704443.5167 678555.5728 782856.6374 574829.5439 0.76358246 1.298689536 1.166178166 1.135580026 1.184270498 1.225482448 1.180446586 1.361893531 1 19.13277469 4.746408937 24.86563905 1.201844901 0.76358223 0.665038649 0.095872867 494.2178364 1565778.98 0.02010394 0.219389144 55771.06491 -4.746408937 -0.438262671 DYAPPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DYAPPPR 7 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ; 120.9 0.010447 788650000 864250 889110 1019930 979590 1030840 916650 1072100 954630 1135550 FALSE TRUE 810158.1352 954940.6295 1044123.221 1004727.938 949881.9846 1181271.974 911348.5579 1073817.657 946019.3691 0.856386414 1.009430315 1.103701737 1.062058527 1.00408302 1.248676309 0.963350844 1.135090562 1 19.8515102 4.78485476 1.745418263 1.073234142 0.765204751 0.422806899 0.08027815 0.938480527 2.615362765 0.018411058 0.498286926 60933.30856 -4.78485476 -0.308029391 DYASHLS(ph)PGSIIQPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DYASHLSPGSIIQPQR 16 0 C9J0Q5;C9JE98;C9J330;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 DYASHLS(1)PGSIIQPQR 147.16 6.79E-07 81792000 61161 62318 62676 52970 69903 67297 78853 69800 86012 TRUE FALSE 57333.04219 66932.08956 64162.70432 54329.29988 64413.10036 86724.55142 67029.72469 78514.68365 71656.04154 0.800114561 0.934074617 0.895426302 0.758195662 0.898920719 1.210289454 0.93543717 1.095716174 1 16.12880073 2.451045399 24.94521921 1.04857987 0.865452615 0.585847692 0.084927166 160.9367367 153957.6783 0.027418295 0.022940431 282.517529 -2.451045399 -0.183127255 DYAVSTVPVADGLHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DYAVSTVPVADGLHLK 16 0 O94760;B4DYP1;O94760-2 O94760 DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1" 0 ; 213.34 2.18E-12 415040000 624790 545500 557370 559280 630660 417920 665160 591550 752090 FALSE TRUE 585685.5092 585889.3876 570591.0796 573632.0717 581130.5076 538566.7196 565425.433 665406.3197 626561.3203 0.934761675 0.935087067 0.910670769 0.915524232 0.927491833 0.859559475 0.90242633 1.061997123 1 19.25709618 1.244917125 24.99997286 1.030998577 0.911869753 0.783361102 0.025968571 58.60141085 230484.6269 0.018074026 0.006242872 17.57588186 -1.244917125 -0.119128823 DYDDMS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 17 DYDDMSPR 8 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR;DYDDMS(1)PR 171.76 0.00030161 70307949000 38459960 33856810 35411790 34059660 37474730 30985710 44751970 33783180 43248150 TRUE FALSE 36052819.76 36363603.44 36251774.38 34933688.54 34531615.87 39930781.47 38041827.56 38001084.39 36029754.37 1.000640176 1.009265927 1.006162129 0.96957887 0.958419408 1.108272376 1.055844766 1.054713946 1 25.10268548 2.245251183 24.99999985 1.060731527 0.993093755 0.532810435 0.030282163 114.3497179 427279.8019 0.010119514 0.008288036 175.8940639 -2.245251183 -0.067637772 DYDDMSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 DYDDMSPR 8 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;;;; 225.57 8.19E-06 18826063000 14978140 15653890 15368990 15200210 16626200 12264370 16465480 13540840 17586380 FALSE TRUE 14040684.95 16812920.3 15733549.7 15590273.12 15320445.32 15804894.52 13996634.13 15231443.68 14651099.57 0.958336601 1.147553481 1.073881836 1.064102599 1.045685701 1.078751424 0.955329944 1.03961096 1 23.80450561 1.755105016 25 0.995717973 1.072270415 0.238702064 0.05059934 6.782669059 10260.93859 0.022004883 0.012202826 56.89905004 -1.755105016 0.076552443 DYDEEEQGYDS(ph)EK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DYDEEEQGYDSEK 13 0 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 DYDEEEQGYDS(1)EK;DYDEEEQGYDS(1)EK 315.47 1.02E-50 538900000 1762810 690840 1082630 979650 838930 865930 1489040 832390 813400 TRUE FALSE 1652478.869 741990.5124 1108310.495 1004789.478 773043.8219 1115909.934 1265772.276 936315.7238 677638.2852 2.438585459 1.094965454 1.635548816 1.482781448 1.140791243 1.646763411 1.867917299 1.381733801 1 19.37015586 -1.923986507 1.388253689 0.563782879 1.55618531 0.185277177 0.381719616 41824.81815 10838.52707 59146.33921 0.098326272 0.01191279 1.923986507 0.992402431 DYDEEEQGYDS(ph)EKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DYDEEEQGYDSEKEK 15 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 DYDEEEQGYDS(1)EKEK 223.51 7.62E-13 1212800000 917250 260840 481570 430520 411050 292970 646970 338260 520460 TRUE FALSE 859840.9598 280152.865 492993.0678 441567.8721 378767.7911 377545.683 549962.8547 380492.5056 433591.8637 1.983065255 0.64612113 1.136997968 1.018395198 0.873558346 0.870739778 1.268388318 0.877536083 1 18.72597816 4.750351012 24.9380612 0.974925904 1.983065881 0.785035374 0.167873438 830.0473425 1755613.571 0.039936889 0.653679617 56279.60122 -4.750351012 1.008139977 DYDEEEQGYDS(ph)EKEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DYDEEEQGYDSEKEKK 16 2 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 DYDEEEQGYDS(1)EKEKK;DYDEEEQGYDS(1)EKEKK;DYDEEEQGYDS(1)EKEKK;DYDEEEQGYDS(1)EKEKK;DYDEEEQGYDS(1)EKEKK;DYDEEEQGYDS(1)EKEKK 208.08 8.24E-12 3794470000 6674690 1299094 2620860 2304040 2270620 1641370 3495400 1650990 2889670 TRUE FALSE 6256933.068 1395280.271 2683028.037 2363165.567 2092294.664 2115206.874 2971297.22 1857119.736 2407365.409 2.599079078 0.57958807 1.114508012 0.981639745 0.869122177 0.878639722 1.234252685 0.771432425 1 21.19902371 4.746298292 24.99619182 0.942488287 2.599079877 0.895268817 0.179497388 288.761583 932808.6933 0.04218004 0.456373813 55756.85799 -4.746298292 1.65659159 DYDEEEQGYDS(ph)EKEKKEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DYDEEEQGYDSEKEKKEEK 19 3 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 DYDEEEQGYDS(1)EKEKKEEK 212.01 5.64E-16 315450000 717560 116680 204640 292690 406860 139280 281710 172000 587540 TRUE FALSE 672649.2005 125319.1086 209494.1574 300200.9209 374906.8568 179487.875 239470.2008 193474.5786 489475.7783 1.37422367 0.256027191 0.427996985 0.613311085 0.765935463 0.36669409 0.489238102 0.395268953 1 18.90087794 -1.40938868 4.545657476 1.000960423 0.535292836 0.127270786 0.316709256 0.002786298 0.000362021 0.277174128 0.065202518 0.038959316 1.40938868 -0.465667587 DYDHLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DYDHLFK 7 0 F5H157;Q15286-2;Q15286;F5H7F8 F5H157 RAB35 Ras-related protein Rab-35 0 89.55 0.017791 118280000 455090 390780 408420 405730 499010 376990 513500 440360 547130 FALSE TRUE 426606.7293 419713.7578 418107.9153 416141.7187 459819.7675 485820.8931 436505.4421 495339.9154 455810.4684 0.935930082 0.920807631 0.917284583 0.912970955 1.008795979 1.0658397 0.957646812 1.086723429 1 18.79807453 2.702299244 5.636245115 1.020120435 0.92073487 0.673444722 0.035297269 0.11079891 10.01456775 0.010439185 0.010011821 503.8476575 -2.702299244 -0.099385565 DYDS(ph)PERER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DYDSPERER 9 1 P52756;C9JR02;C9J9P7;C9JFQ5;P52756-4;P52756-2;P52756-5;F8W910;P52756-3 P52756 RBM5 RNA-binding protein 5 1 DY(0.001)DS(0.999)PERER;DYDS(1)PERER;DYDS(1)PERER 108.9 0.004614 399630000 491052 456702 450177 458911 483534 383987 467587 397361 365920 TRUE FALSE 460317.9319 490516.6913 460855.411 470687.4332 445559.1901 494837.8134 397476.6702 446972.3955 304845.5881 1.510003588 1.609066066 1.511766708 1.544019174 1.461589761 1.623240856 1.303862302 1.466225568 1 18.21771914 -0.086806697 0.379559791 0.893870378 1.571577419 0.818253169 0.077284972 1.84156493 0.342671477 0.355303806 0.052561605 0.818829165 0.086806697 0.67770704 DYDVYAR ddPTM_SK-BR-3_Pertuzumab_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 ;; 120.9 0.010447 820310000 1025610 1180310 1192400 1137570 1276560 1023760 1307420 1090760 1700570 FALSE TRUE 961418.9009 1267701.381 1220684.291 1166761.972 1176304.127 1319302.893 1111384.508 1226943.787 1416733.881 0.678616439 0.894805579 0.86161862 0.823557612 0.830292931 0.931228448 0.784469492 0.866036878 1 20.43413736 -5 0.286296301 2.200949581 0.831638739 0.388388799 0.067075002 262.6870975 2.491427899 188.1686717 0.067776644 1.00E-05 5 -1.369310842 DYDWINAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DYDWINAER 9 0 O95347-2;O95347;A0A0C4DGE5 O95347-2 SMC2 Structural maintenance of chromosomes protein 2 0 ;;; 229.61 2.80E-07 890130000 1128110 1222350 1210530 1165480 1261810 1008970 1344630 1181560 1196410 FALSE TRUE 1057503.609 1312854.066 1239244.343 1195388.19 1162712.532 1300243.26 1143015.214 1329080.367 996721.4419 1.0609821 1.317172492 1.243320642 1.199320231 1.166537092 1.304520205 1.146774983 1.333452167 1 19.92683084 -1.356151607 3.643831939 0.998974909 1.22742484 0.402993806 0.084457471 6001320.644 2272659.437 48162.12549 0.017563983 0.04404011 1.356151607 0.228449931 DYEEIGPSICR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DYEEIGPSICR 11 0 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ;; 234.71 3.88E-15 489820000 518350 555320 544590 527500 605180 476790 671090 516090 638110 FALSE TRUE 485907.3988 596436.4706 557507.932 541036.5431 557651.604 614431.533 570466.2846 580524.9726 531605.3187 0.914037881 1.121953543 1.048725271 1.017741027 1.048995532 1.155803961 1.073101161 1.092022507 1 19.01999601 2.43976191 24.99552988 1.089264848 1.044307201 0.104707352 0.063586221 374.0950619 250289.0281 0.020451291 0.017110823 275.2719185 -2.43976191 -0.044957647 DYEEVGADS(ph)ADGEDEGEEY ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DYEEVGADSADGEDEGEEY 19 0 Q9BQE3;F5H5D3 Q9BQE3 TUBA1C Tubulin alpha-1C chain 1 DYEEVGADS(1)ADGEDEGEEY 189.37 3.21E-21 0 97039 90664 106480 92134 109320 90716 119760 88252 116300 TRUE FALSE 90965.50221 97376.8569 109005.7559 94498.31442 100734.4482 116904.2365 101803.0998 99270.45647 96888.77867 0.938865196 1.00503751 1.125060687 0.975327749 1.039691588 1.206581796 1.050721262 1.024581565 1 16.56404197 4.506457924 2.372103639 1.068031105 0.935044316 0.263148035 0.065603193 0.463850107 4.363514829 0.015931854 0.102699698 32096.51828 -4.506457924 -0.132986789 DYEEVGADSADGEDEGEEY ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DYEEVGADSADGEDEGEEY 19 0 Q9BQE3;F5H5D3 Q9BQE3 TUBA1C Tubulin alpha-1C chain 0 ;; 355.7 1.37E-90 4586100000 6851660 6144170 6857530 6756110 6586120 6209330 8057700 6145710 6896850 FALSE TRUE 6422826.831 6599090.74 7020193.85 6929483.221 6068872.702 8001862.771 6849522.689 6913015.422 5745721.18 1.117845198 1.148522619 1.221812481 1.206024971 1.056242117 1.392664649 1.192108436 1.203158873 1 22.45405655 4.352198685 2.273500846 1.198277669 1.119435417 0.021508744 0.104355276 0.976755253 9.17291009 0.024272419 0.110314676 22500.83757 -4.352198685 -0.078842252 DYEEVGVDSVEGEGEEEGEEY ddPTM_SK-BR-3_Pertuzumab_2h_R1 19 DYEEVGVDSVEGEGEEEGEEY 21 0 P68363;P68363-2 P68363 TUBA1B Tubulin alpha-1B chain 0 ;;;;;;;;;;;;;;;;;; 353.92 4.07E-95 2508058700 4845490 4465299 4741423 4625798 4744973 4210655 5679937 4416857 4541500 FALSE TRUE 4542219.43 4795914.384 4853891.793 4744503.808 4372321.961 5426202.744 4828283.177 4968311.319 3783494.311 1.200535552 1.267588634 1.282912407 1.254000513 1.155630642 1.434177588 1.276143898 1.313154167 1 21.85128785 -1.273618882 5.402017001 0.999967052 1.276533072 0.583544917 0.072429648 2.65E-05 3.56E-06 0.064629406 0.015231485 0.053257542 1.273618882 0.27656602 DYEHQFHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DYEHQFHLR 9 0 Q15276-2;Q15276;A0A087WZZ3 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 ;;; 185.81 2.45E-05 483980000 350169 390624 369464 364542 425251 258512 365239 367605 469840 FALSE TRUE 328252.5474 419546.2074 378227.8606 373896.7649 391853.5018 333140.2178 310474.8027 413501.2934 391420.6687 0.83861833 1.071855017 0.966295065 0.955229999 1.0011058 0.851105331 0.793199817 1.056411494 1 18.57836041 2.247487674 24.99760483 0.893621578 0.980408774 0 0.093948909 332.8692956 932102.8243 0.031106526 0.025668336 176.8022037 -2.247487674 0.086787195 DYEIESQNPLAS(ph)PTNTLLGSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DYEIESQNPLASPTNTLLGSAK 22 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 DYEIESQNPLAS(0.957)PT(0.043)NTLLGSAK;DYEIESQNPLAS(0.997)PT(0.003)NTLLGSAK 317.15 1.32E-67 349570000 612830 472550 579210 624800 600190 315240 450270 323120 509280 TRUE FALSE 574474.0642 507538.0937 592949.1347 640833.4258 553053.4984 406244.6705 382756.1936 363462.2433 424277.8779 1.354004284 1.196239823 1.397549025 1.510409708 1.303517169 0.957496706 0.902135637 0.85666084 1 18.69464993 2.237274416 4.294952858 0.913959854 1.34804927 0.864385796 0.083590981 0.073733368 3.20433485 0.033315733 0.025568111 172.6928736 -2.237274416 0.434089416 DYEIESQNPLASPTNT(ph)LLGSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DYEIESQNPLASPTNTLLGSAK 22 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 DYEIESQNPLAS(0.229)PT(0.127)NT(0.644)LLGSAK 198.68 6.84E-22 639270000 56912 46056 52256 57155 49909 27578 38615 24842 45043 TRUE FALSE 53349.97951 49466.03416 53495.537 58621.69406 45989.34846 35539.32091 32825.03923 27943.57838 37525.03231 1.421717084 1.318214299 1.425596028 1.562202361 1.225564527 0.94708302 0.874750459 0.744665005 1 15.19556569 2.316046575 2.692450334 0.869204515 1.412064439 0.895421076 0.087189939 0.077696128 1.153182226 0.034009114 0.025886016 207.0363369 -2.316046575 0.542859924 DYENDEDVNKQLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DYENDEDVNKQLDK 14 1 A6NKE1;A0A087WWM0;O43617 A6NKE1 TRAPPC3 Trafficking protein particle complex subunit 3 0 ; 204.52 1.23E-08 295010000 788280 427130 567730 582020 651200 385220 756240 431610 938060 FALSE TRUE 738942.9619 458755.1496 581196.8237 596955.6186 600057.3788 496426.7605 642848.8326 485497.4586 781491.7259 0.945554428 0.587024961 0.743701826 0.763866844 0.767835869 0.635229708 0.822591988 0.621244528 1 19.57587107 -1.180429975 4.342549848 1.000075186 0.727621057 0.382260643 0.105052051 6.75E-05 1.27E-05 0.089725157 0.021142599 0.066003965 1.180429975 -0.272454129 DYEVELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DYEVELLR 8 0 E9PKP7;P17480-2;P17480 E9PKP7 UBTF Nucleolar transcription factor 1 0 ; 129.56 0.0025249 74333000 111191 114659 114843 106894 118107 89850 118904 102376 123442 FALSE TRUE 104231.7538 123148.4717 117567.1302 109637.081 108831.3526 115788.2364 101075.4491 115157.869 102838.7327 1.013545685 1.197491144 1.143218387 1.066106885 1.058272012 1.125920491 0.982853895 1.119790821 1 16.65002421 3.203944073 5.476722741 1.056789208 1.138900113 0.135526394 0.063812048 0.231493373 17.71260258 0.017154427 0.021203122 1599.352058 -3.203944073 0.082110905 DYEYNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DYEYNR 6 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 164.78 0.017396 1997360000 1611140 1709990 1657660 1625360 1885380 1285020 1864380 1673400 2216300 FALSE TRUE 1510301.623 1836599.439 1696980.478 1667069.489 1737309.86 1655984.413 1584833.527 1882327.674 1846385.212 0.817977534 0.994700037 0.919082577 0.902882821 0.940924921 0.896879157 0.858343923 1.019466394 1 20.81627214 1.221205443 24.99977086 1.00973331 0.912823847 0.455485194 0.047186362 275.1253527 396301.8194 0.044339486 0.011192053 16.64199715 -1.221205443 -0.096909463 DYFEEYGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 DYFEEYGK 8 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;; 168.23 0.00071658 31022230000 18311490 12124010 14951770 13497390 13497410 11464360 17319420 12435750 12973230 FALSE TRUE 17165406.53 13021684.32 15306433.05 13843755.88 12437377.86 14773934.62 14722533.76 13988380.76 10807914.1 1.588225662 1.204828628 1.416224528 1.280890628 1.150765795 1.366955222 1.362199368 1.294272015 1 23.36558478 -3.416734941 0.334239994 2.42E-20 1.341084714 0.448544254 0.117811211 106.6350747 2.478007485 74.5509132 0.090379016 0.000383058 3.416734941 1.341084714 DYFEEYGKIDTIEIITDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 27 DYFEEYGKIDTIEIITDR 18 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;;;;;;;;;;;;;;;;;; 284.57 1.36E-39 6781819300 7362081.6 6851490.1 7041524.5 7309809.9 9435976.4 4992448.2 9154403 6354328.1 14097338 FALSE TRUE 6901302.054 7358781.556 7208552.786 7497391.998 8694912.876 6433686.95 7781785.255 7147679.951 11744401.22 0.587624854 0.626577841 0.613786319 0.638380098 0.740345354 0.547808852 0.662595318 0.608603182 1 23.48546982 -1.425587684 3.169485595 1.005598645 0.629310693 0.844764007 0.050084763 37125562.8 47290080.88 1868452.999 0.01061167 0.037532917 1.425587684 -0.376287952 DYFEQYGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 175.38 0.00061997 18173850000 8375401 7445656 8037281 7540201 7803483 6201290 9639937 6878181 8690489 FALSE TRUE 7851199.602 7996940.117 8227929.101 7733695.323 7190628.923 7991501.753 8194517.94 7736937.039 7239990.243 1.084421296 1.104551228 1.136455827 1.068191401 0.993182129 1.103800072 1.13184102 1.068639153 1 22.78755632 3.217653504 24.79655682 1.071611175 1.111632173 0.179732464 0.043932208 415.651301 492975.2406 0.013166797 0.015754121 1650.644327 -3.217653504 0.040020998 DYFEQYGKIEVIEIMTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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" 0 137.05 4.54E-06 11324000 15520 36471 24854 34681 87398 16586 23093 27928 164920 FALSE TRUE 14548.6309 39171.35079 25443.54862 35570.97317 80534.11363 21374.10895 19630.41903 31414.87228 137393.7866 0.105890021 0.285102782 0.18518704 0.258897975 0.586155427 0.155568236 0.142877051 0.22864842 1 17.06795724 -1.295760184 2.984383141 1.005983505 0.241429124 0.76089146 0.133262793 8630123.635 11073924.22 463673.5002 0.03243303 0.050610405 1.295760184 -0.764554382 DYFGAHTYELLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DYFGAHTYELLAK 13 0 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;; 202.18 9.60E-08 1641766000 5621590 4992450 4777010 4363020 5674170 3657021 5509190 5436630 4114850 FALSE TRUE 5269744.717 5362096.193 4890322.933 4474982.48 5228543.577 4712743.596 4683138.104 6115405.223 3428054.952 1.537240444 1.564180349 1.426559084 1.305399867 1.525221634 1.374757308 1.366121072 1.783928586 1 21.70895881 -1.919898519 2.724805623 0.715519279 1.470291763 0.559050591 0.134892054 5293799.843 3204904.031 9580992.718 0.030363575 0.012025454 1.919898519 0.754772484 DYGEIFNVQLPDKEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DYGEIFNVQLPDKEER 16 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 262.36 6.39E-27 308940000 515400 375280 465820 410330 442900 329220 540450 378010 380330 FALSE TRUE 483142.034 403066.1217 476869.4704 420859.7625 408116.4206 424260.4696 459414.5398 425205.3806 316850.466 1.524826648 1.272102032 1.505030043 1.328259882 1.288041093 1.338992727 1.449941184 1.341974926 1 18.27344261 0.958183022 21.85560105 0.999999999 1.38366457 0.665665652 0.08544277 955.270401 499272.3872 0.075824859 0.018956215 9.08203187 -0.958183022 0.383664571 DYGHGSYGGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DYGHGSYGGQR 11 0 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-2 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 0 ;; 171.92 1.40E-05 640220000 442250 587750 545270 548300 664510 451820 595680 604220 676000 FALSE TRUE 414570.3619 631267.6216 558204.0619 562370.3063 612322.0651 582253.0993 506363.314 679658.1971 563171.2329 0.736135544 1.120915957 0.991179999 0.998577828 1.087275112 1.033882886 0.899128514 1.206841112 1 19.10321412 4.749294401 24.80418315 1.032743373 0.736135356 0.567664006 0.08358582 1049.837313 2425966.007 0.018675651 0.272589517 56142.84299 -4.749294401 -0.296608017 DYGHSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DYGHSSSR 8 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;;;;; 144.12 0.00059047 325135000 144609 227462 205830 212316 230090 188833 222848 217070 207644 FALSE TRUE 135558.1808 244303.5232 210712.3848 217764.388 212019.6595 243346.0217 189434.0112 244171.6673 172986.875 0.783632752 1.412266238 1.218083076 1.258849193 1.225640151 1.406731127 1.095077365 1.411504008 1 17.40030305 -1.124512984 4.897577923 0.999987601 1.240518864 0.121807407 0.187770098 2.20E-05 3.92E-06 0.156988348 0.037000602 0.075073561 1.124512984 0.240531263 DYGHSSSRDDYPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DYGHSSSRDDYPSR 14 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;;; 186.05 6.65E-07 1520230000 154082 447125 307896 392833 491763 294803 382873 309214 589969 FALSE TRUE 144438.2827 480230.6002 315199.4385 402913.7598 453141.9177 379907.8404 325464.7481 347820.0486 491499.3626 0.293872777 0.977072682 0.641301826 0.819764562 0.921958302 0.772956934 0.662187528 0.707671413 1 18.90683002 -4.999998559 0.028643465 2.011760263 2.71E-06 0.19356802 0.184075582 3736.545011 8.065215574 433.0187868 182.8360374 1.00E-05 4.999998559 -2.011757556 DYGNSPLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DYGNSPLHR 9 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20;A0A087WUW5;K7ELW5 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ;;;;;;; 150.18 8.59E-05 14134930000 4746650 7610460 7304950 7286920 7809680 6307510 8195950 6845970 8193730 FALSE TRUE 4449565.65 8173946.377 7478226.864 7473914.704 7196339.236 8128385.743 6967043.385 7700704.424 6826143.529 0.651841795 1.197447188 1.09552734 1.094895628 1.054232043 1.190772756 1.020641209 1.128119324 1 22.70263932 4.745912029 24.99607602 1.103331551 0.651841582 0.825977472 0.064270351 327.8282229 1114645.817 0.014109584 0.14635062 55707.28963 -4.745912029 -0.451489969 DYGPGSYGGMDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DYGPGSYGGMDR 12 0 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-2 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 0 99.788 0.01279 209830000 49866 46448 51186 47811 45135 42243 59379 44725 44186 FALSE TRUE 46744.97607 49887.05825 52400.15609 49037.9112 41590.27917 54437.86834 50475.6702 50309.0147 36811.07115 1.269861882 1.35521887 1.423489034 1.332151162 1.129830724 1.478844995 1.371208949 1.36668163 1 15.16785211 -0.991989334 4.982244029 0.999996667 1.350729367 0.567692873 0.093144176 3.27E-06 6.62E-07 0.085604597 0.020177005 0.101861641 0.991989334 0.3507327 DYGVLLEGSGLALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DYGVLLEGSGLALR 14 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 ;; 167.2 8.57E-06 152955000 244036 235067 223178 217802 317194 201576 213269 252226 360148 FALSE TRUE 228762.2224 252471.6053 228471.8876 223391.1681 292282.8627 259767.7189 181291.2933 283716.9713 300036.9722 0.762446777 0.841468315 0.761479113 0.744545469 0.974156154 0.865785696 0.604229846 0.945606701 1 18.19478076 1.018017188 24.94641712 1.00000016 0.79249226 0.390578224 0.094503692 187.4404278 259527.2084 0.090369858 0.022592464 10.42358683 -1.018017188 -0.207507901 DYHFVTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 173030000 102790 154730 100960 98851 149390 109160 102590 136360 143440 FALSE TRUE 96356.55739 166186.3702 103354.8189 101387.684 137657.512 140672.7199 87207.5819 153384.8462 119498.9373 0.806338195 1.390693289 0.864901573 0.848440047 1.151955951 1.177188041 0.729777049 1.283566612 1 16.86663826 3.870141775 10.64444111 0.990787672 1.138535892 0.017303012 0.21723068 0.95311056 87.89038977 0.051311373 0.092579904 7415.522807 -3.870141775 0.14774822 DYIHVVDLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DYIHVVDLAK 10 0 Q14376;Q14376-2;Q5QPP4;Q5QPP3;Q5QPP9 Q14376 GALE UDP-glucose 4-epimerase 0 ;; 129.7 0.0002961 512660000 2122280 1829630 1970110 1880520 2075490 1431010 2353130 1823190 2049470 FALSE TRUE 1989450.283 1965097.709 2016841.94 1928777.327 1912489.388 1844119.356 2000300.002 2050819.285 1707400.217 1.165192708 1.150929752 1.181235612 1.129657422 1.120117808 1.080074454 1.171547234 1.201135659 1 20.70336984 -1.580147858 3.278796974 0.993703883 1.149858973 0.656061639 0.034128778 3048998.958 1624672.091 135041.7393 0.008043136 0.026293727 1.580147858 0.156155091 DYIPVDQEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DYIPVDQEELR 11 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 250.94 1.52E-16 1250440000 999890 1222230 1105590 1139380 1363080 937370 1419090 1181750 1131690 FALSE TRUE 937308.6698 1312725.181 1131815.117 1168618.42 1256029.195 1207973.502 1206310.629 1329294.089 942803.628 0.994171683 1.392363311 1.200478109 1.239514131 1.332227792 1.281256739 1.279492985 1.409937392 1 19.84659778 -1.005145378 4.779729869 0.99999715 1.27386695 0.340913239 0.115875547 6483139.854 1363361.087 328.3838378 0.023655588 0.098822224 1.005145378 0.273869799 DYIVVGSDSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DYIVVGSDSGR 11 0 Q15393;Q15393-2;J3QL37;J3QRB2 Q15393 SF3B3 Splicing factor 3B subunit 3 0 153.97 7.50E-05 203530000 108450 119050 119850 107530 113420 104610 126620 98877 112910 FALSE TRUE 101662.3081 127864.5859 122692.8986 110289.4018 104512.4507 134809.2088 107634.5065 111222.0111 94064.59157 1.08077127 1.359327498 1.304347327 1.172485842 1.111071116 1.433155734 1.144261668 1.182400404 1 16.52136414 0.877227216 1.309056269 1.002190038 1.254609905 0.287313572 0.111470962 0.672388031 2.248196291 0.099449901 0.030086123 7.537498099 -0.877227216 0.252419866 DYKVDQEIINIMQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DYKVDQEIINIMQDR 15 1 H3BV16;O96000-2;O96000 H3BV16 NDUFB10 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 0 ;; 194.37 4.94E-08 240674000 362219 272293 276379 261122 438393 290601 284748 352834 519560 FALSE TRUE 339548.3594 292453.857 282934.8404 267822.8326 403963.3822 374492.7912 242052.6809 396886.1016 432842.0795 0.784462453 0.675659486 0.653667593 0.618754149 0.933281216 0.865194973 0.559217073 0.916930494 1 18.72348123 2.758985923 24.94939852 0.806650372 0.676978462 0.269563608 0.127244251 1323.929609 1617170.771 0.038716061 0.041021271 574.0978535 -2.758985923 -0.12967191 DYLGDFIEHYAQLGPSQPPDLAQAQDEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DYLGDFIEHYAQLGPSQPPDLAQAQDEPR 29 0 Q00577 Q00577 PURA Transcriptional activator protein Pur-alpha 0 ;;; 222.66 1.65E-34 350257000 172966 177374 183701 190812 194576 166713 213812 174411 188350 FALSE TRUE 162140.3668 190506.9555 188058.4745 195708.559 179294.7858 214840.3367 181752.8755 196186.5973 156913.1682 1.033312683 1.214091575 1.198487524 1.247241141 1.142636962 1.369167032 1.158302248 1.250287656 1 17.2596069 -1.025006025 4.377408779 0.999989692 1.206047279 0.351192197 0.085972707 8.16E-06 1.82E-06 0.072841834 0.017168059 0.094404778 1.025006025 0.206057587 DYLHLPPEIVPATLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DYLHLPPEIVPATLR 15 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;;;;; 88.507 0.0067586 2917996000 1843947 1837481 1901916 1764864 1886585 1524516 1871802 1720905 1391666 FALSE TRUE 1728537.649 1973530.005 1947030.346 1810153.398 1738420.224 1964619.021 1591142.667 1935763.777 1159387.954 1.490905303 1.702217104 1.67936051 1.56130085 1.499429262 1.694531165 1.372398826 1.669642824 1 20.14493197 -2.710449102 0.27075369 1.45E-14 1.649783687 0.725592771 0.111342699 24.63264856 0.724971156 14.44366553 0.130617796 0.001947829 2.710449102 1.649783687 DYLHYHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DYLHYHIK 8 0 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ; 119.27 0.00099789 491280000 659640 1089570 595370 596820 1333210 366670 601830 1073910 920380 FALSE TRUE 618354.3099 1170242.896 609492.4576 612135.4116 1228505.065 472521.6766 511591.1786 1207990.027 766762.6321 0.806448155 1.526212738 0.794890664 0.798337564 1.602197359 0.616255484 0.667209326 1.575441965 1 19.5484205 DYLHYIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DYLHYIR 7 0 P62280;M0QZC5;M0R1H5 P62280 RPS11 40S ribosomal protein S11 0 ;;;;; 153.15 0.0017657 4347360000 3434980 6488780 3379250 3202000 6691160 2447900 3041610 5520690 4285660 FALSE TRUE 3219990.733 6969216.023 3459407.406 3284168.741 6165663.284 3154568.992 2585548.817 6209960.299 3570355.66 0.90186834 1.951966887 0.968925154 0.919843583 1.726904508 0.883544748 0.724171221 1.7393114 1 21.76763636 3.77417118 8.76525849 1.102836188 1.49096577 0.06587304 0.422669933 0.640790736 111.6752567 0.101383993 0.182461959 5945.264485 -3.77417118 0.388129582 DYLIDGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DYLIDGSR 8 0 P18206;P18206-2;P18206-3 P18206 VCL Vinculin 0 ;;;;; 146.54 0.0012834 2951700000 5746740 6520300 6509740 6318060 6651010 5485750 7293320 5617230 6546480 FALSE TRUE 5387061.802 7003069.796 6664154.107 6480192.116 6128666.503 7069396.971 6199754.374 6318553.531 5453830.196 0.987757522 1.28406451 1.221921818 1.18819103 1.123736215 1.296226086 1.136770701 1.158553403 1 22.37883835 0.669217394 1.269650615 1.000455249 1.196288123 0.268032647 0.088130273 1.28002513 3.246643726 0.07620186 0.022979576 4.668930341 -0.669217394 0.195832873 DYLLCDYNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DYLLCDYNR 9 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ; 140.5 0.00025346 990530000 560560 1815510 406580 401410 1885320 244980 416900 1411850 1467140 FALSE TRUE 525475.5502 1949932.249 416224.2696 411710.8602 1737254.572 315701.7491 354389.7153 1588122.58 1222264.856 0.429919545 1.595343464 0.340535251 0.33684259 1.421340525 0.258292421 0.289945108 1.299327697 1 20.22112551 3.956331465 22.22639065 0.643492941 1.079883735 0.044964895 0.506579912 207.4904015 221828.8189 0.120459628 0.21766003 9043.394264 -3.956331465 0.436390795 DYLLS(ph)ES(ph)EDEGDNDGER ddPTM_SK-BR-3_Pertuzumab_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 316.41 3.87E-58 657590000 649200 606000 643540 621140 600840 523540 698780 468640 548690 TRUE FALSE 608567.7309 650868.8705 658805.0727 637079.504 553652.4501 674677.499 594004.4262 527150.7356 457110.0943 1.331337326 1.423877702 1.441239388 1.3937113 1.21120154 1.475962809 1.299477814 1.153224884 1 18.80218215 1.133004445 1.904129394 1.002918188 1.387167681 0.754439759 0.073006837 0.142748059 0.978953282 0.065426626 0.018778827 13.58327348 -1.133004445 0.384249493 DYNEAYNYYTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DYNEAYNYYTK 11 0 Q99615;A0A6I8PUD4;A0A6I8PU73;A0A6I8PS32;A0A6I8PIK4;A0A6I8PR89;A0A6I8PLE7;A0A6I8PU89;K7EIH8;K7EK03;K7ESP1;K7ELJ8 Q99615 DNAJC7 DnaJ homolog subfamily C member 7 0 ; 152.14 7.70E-05 145018000 204396 183405 207552 199415 219978 142444 236617 202102 204549 FALSE TRUE 191603.2192 196984.497 212475.2315 204532.3265 202701.8152 183565.2704 201138.4775 227334.8796 170408.4505 1.124376278 1.155954981 1.246858538 1.200247558 1.189505653 1.077207556 1.180331591 1.334058722 1 17.37863735 EGRPPEPT(ph)PAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGRPPEPTPAKR 12 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 EGRPPEPT(1)PAKR 116.86 0.037926 562180000 342340 370580 312910 262570 434670 214520 534200 370460 850280 TRUE FALSE 320913.5505 398018.1288 320332.373 269307.9907 400532.7716 276448.4416 454101.6693 416712.7465 708362.775 0.453035594 0.561884592 0.452215142 0.380183714 0.565434528 0.390263932 0.641058064 0.588275896 1 19.43412887 0.578618468 0.834833567 1.001937005 0.476647965 0.830810545 0.073221721 0.503423882 0.580937082 0.066868762 0.022329278 3.78981899 -0.578618468 -0.52528904 DYNPYNYSDSIS(ph)PFNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DYNPYNYSDSISPFNK 16 0 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4X8;H7C5M8;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 DYNPYNYSDS(0.004)IS(0.996)PFNK;DYNPYNYSDSIS(1)PFNK 242.26 6.41E-20 99747000 169098 140663 172369 212628 202179 95024 142250 99122 136531 TRUE FALSE 158514.458 151077.8349 176457.6741 218084.3945 186300.6769 122455.8862 120920.9331 111497.5999 113743.0941 1.393618305 1.328237429 1.551370442 1.91734185 1.637907588 1.076600625 1.063105713 0.980258193 1 16.79541943 2.212735575 9.121328092 1.038719879 1.547346306 0.739764667 0.157641566 0.162216825 52.32885054 0.065379293 0.048934261 163.205795 -2.212735575 0.508626427 DYNVTANSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DYNVTANSK 9 0 P00338;P00338-3;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;;;; 201.21 5.08E-05 4753050000 4499490 4213530 3904750 4104090 4467050 2951320 4815960 3750190 4180040 FALSE TRUE 4217874.953 4525504.145 3997372.514 4209407.898 4116225.912 3803318.173 4093851.507 4218409.477 3482364.32 1.211210133 1.299549309 1.147890383 1.208778724 1.182020471 1.092165501 1.175595409 1.211363628 1 21.73163571 -5 0.088445693 0.399818264 1.35183648 0.620415181 0.049167844 138.8277261 0.856357255 15.96259007 1.173545371 1.00E-05 5 0.952018216 DYPSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DYPSSR 6 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;; 143.37 0.02654 950590000 672690 714030 691460 659060 754290 540410 763380 625570 816710 FALSE TRUE 630587.5337 766897.5241 707861.7577 675972.5954 695051.1061 696417.5942 648918.2559 703673.7915 680395.8249 0.926795125 1.127134377 1.04036758 0.993499035 1.021539346 1.023547718 0.953736387 1.034212389 1 19.37601476 3.350769285 4.628913736 1.001024151 1.055122955 0 0.053759084 0.354381861 12.75062289 0.014177122 0.019433216 2242.690196 -3.350769285 0.054098804 DYPVVSIEDPFDQDDWGAWQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 DYPVVSIEDPFDQDDWGAWQK 21 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;; 283.88 3.40E-45 2567487000 4147590 3940298 3586446 3272987 4493740 2331077 4295940 4022260 4054310 FALSE TRUE 3887999.746 4232041.764 3671518.193 3356977.388 4140819.787 3004021.088 3651803.679 4524448.015 3377619.469 1.151106506 1.252965825 1.087013569 0.993888571 1.225958053 0.889390032 1.081176761 1.339537522 1 21.68757537 3.807208803 3.826885719 1.080782304 1.203392362 0.120821881 0.126481887 0.413868374 11.57640531 0.030999241 0.058157357 6415.179355 -3.807208803 0.122610058 DYQDNKADVILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DYQDNKADVILK 12 1 P47813;O14602;X6RAC9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 ; 131.66 0.00017758 1071640000 1112300 918890 947590 980080 1225730 706700 1238260 794100 1753870 FALSE TRUE 1042683.129 986925.5717 970067.2823 1005230.512 1129466.11 910712.8177 1052594.408 893245.133 1461137.767 0.713610415 0.675450046 0.663912264 0.687977914 0.773004528 0.623290177 0.720393677 0.611335326 1 20.47866078 -1.13330302 4.891746645 1.000007404 0.683941997 0.819618877 0.046644088 8.09E-06 1.43E-06 0.039477103 0.009304307 0.07356936 1.13330302 -0.316065407 DYQGPLKEHEVTIFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DYQGPLKEHEVTIFVR 16 1 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ;;; 263.15 3.79E-27 2205490000 1984240 2190700 2069960 2240240 2863560 1413530 2390240 1888870 4196270 FALSE TRUE 1860049.96 2352901.707 2119060.429 2297728.351 2638667.549 1821593.164 2031845.702 2124699.577 3495885.428 0.532068341 0.673048862 0.606158432 0.657266492 0.754792342 0.521067753 0.58121061 0.607771513 1 21.73722647 -1.123440934 4.726516267 1.000027406 0.619012831 0.757969896 0.068062475 1.88E-05 3.50E-06 0.06318972 0.01489289 0.075259108 1.123440934 -0.381014575 DYQTSPLLETQAEDHPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DYQTSPLLETQAEDHPPR 18 0 Q9Y6U3;Q9Y6U3-3 Q9Y6U3 SCIN Adseverin 0 ;;; 240.07 6.12E-24 2799320000 1175670 1225840 1228390 1065930 1485280 1043960 1418420 1435710 2885620 FALSE TRUE 1102086.913 1316602.469 1257527.991 1093283.568 1368632.1 1345334.305 1205741.089 1614961.554 2403991.38 0.45844046 0.54767354 0.523100042 0.454778489 0.569316559 0.559625261 0.501557992 0.671783421 1 21.19700029 0.875841691 2.59612283 0.999813541 0.520466475 0.938879016 0.039155772 0.100301019 1.366798792 0.034913007 0.009321905 7.51348962 -0.875841691 -0.479347066 DYS(ph)YER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DYSYER 6 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 DYS(1)YER;DYS(1)YER;DYS(1)YER;DYS(0.982)Y(0.018)ER 113.5 0.02736 1821260000 2113590 1622050 1696670 1726240 1814420 1453470 2072430 1490140 2308780 TRUE FALSE 1981304.175 1742148.27 1736915.814 1770538.241 1671922.772 1873063.194 1761688.361 1676187.259 1923429.703 1.030089206 0.905750944 0.903030566 0.920511022 0.869240383 0.973814219 0.915909928 0.87145751 1 20.87524967 -1.153989124 3.995690893 1.000033133 0.92044454 0.199290457 0.047646366 17913868289 3792921142 5705827.529 0.01001951 0.070147287 1.153989124 -0.079588593 DYSDHPSGGSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 136.38 0.00011104 3106970000 1697418 4164390 3292180 3601470 3839600 3086780 3840220 3741540 3737670 FALSE TRUE 1591179.637 4472725.769 3370272.064 3693889.817 3538053.304 3977883.276 3264414.662 4208679.505 3113828.731 0.511004225 1.436407123 1.082356274 1.186285482 1.136238891 1.277489425 1.048360377 1.351609182 1 21.57025816 4.751679744 24.83429631 1.192228903 0.511003742 0.712599298 0.135477258 1027.978493 1945909.01 0.029391524 0.555918803 56452.05339 -4.751679744 -0.681225161 DYSEADGLS(ph)ER ddPTM_SK-BR-3_Pertuzumab_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 209.67 1.61E-08 1186460000 1574280 1429890 1562220 1268430 1578360 1530370 1940520 1617870 2138880 TRUE FALSE 1475748.625 1535760.543 1599276.596 1300980.061 1454401.972 1972162.976 1649557.041 1819864.631 1781887.11 0.828194231 0.861873086 0.897518472 0.730113627 0.81621443 1.106783345 0.925735997 1.02131309 1 20.76497451 2.258056033 24.99998543 1.002087795 0.836819501 0.69610305 0.060884149 148.2541906 190113.5923 0.020873059 0.017440315 181.1573809 -2.258056033 -0.165268293 DYSNFDQEFLNEK ddPTM_SK-BR-3_Pertuzumab_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 0 145 9.67E-05 80149000 158070 134540 145710 149720 163420 114620 179340 142590 183840 FALSE TRUE 148176.6809 144501.4816 149166.31 153562.0687 150585.6524 147708.9333 152449.6319 160392.6754 153155.9163 0.967489108 0.943492651 0.973950687 1.002651888 0.983217991 0.964435046 0.995388461 1.047250927 1 17.22464157 2.885582713 0.429953467 1.013324245 0.947008393 0.449648043 0.020805731 1.271084602 0.464205892 0.020051071 0.034847617 768.3917855 -2.885582713 -0.066315852 DYSPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DYSPSR 6 0 Q9HCM7;A0A3B3IRR3 Q9HCM7 FBRSL1 Fibrosin-1-like protein 0 133.99 0.033099 458610000 225490 252280 224900 255790 276050 223180 302330 256100 300390 FALSE TRUE 211376.9834 270959.0737 230234.7342 262354.0045 254370.1465 287608.443 256998.4232 288074.6487 250252.9684 0.844653251 1.082740698 0.920008005 1.048355215 1.016452065 1.149270855 1.026954545 1.151133793 1 17.93302766 2.836421463 1.942698989 1.07776954 0.97505749 0.304606741 0.07835479 0.432254663 3.230188659 0.025320784 0.026761981 686.1537843 -2.836421463 -0.10271205 DYTYEELLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 DYTYEELLNR 10 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;;; 268 1.40E-17 3418830000 2393460 2696110 2562610 2442870 2942670 2177990 2835570 2260420 2938350 FALSE TRUE 2243657.611 2895732.79 2623396.319 2505558.18 2711564.568 2806740.356 2410402.603 2542638.413 2447920.403 0.916556604 1.182935845 1.071683669 1.023545609 1.107701282 1.146581545 0.984673603 1.038693256 1 21.22312522 1.68705902 9.736061 1.009504484 1.086143859 0.145529353 0.073010931 0.185423984 28.18961432 0.032515336 0.017488402 48.64733118 -1.68705902 0.076639375 DYVAPTANLDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DYVAPTANLDQK 12 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 181.4 0.00027798 0 286120 227250 249970 246750 246220 203510 311380 204930 256280 FALSE TRUE 268212.2599 244075.8265 255899.4064 253082.0227 226882.8744 262260.0333 264691.4597 230515.9616 213505.2124 1.256232843 1.143184392 1.198562806 1.185366952 1.062657309 1.228354242 1.239742378 1.079673695 1 17.70391177 1.026912391 5.098148997 1.000484777 1.184414024 0.578376106 0.05475413 0.108683389 7.529697806 0.05080805 0.012844843 10.63928373 -1.026912391 0.183929247 DYVAVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DYVAVAR 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 88.734 0.042782 363360000 393840 468710 415480 445750 467670 323320 484730 428360 462240 FALSE TRUE 369190.2574 503413.7761 425335.3818 457188.6997 430941.0847 416657.2353 412049.2365 481841.6889 385089.1578 0.958713716 1.307265515 1.104511444 1.187228179 1.11906834 1.081976023 1.070009966 1.251247092 1 18.55483298 2.553314331 5.529952367 1.101612375 1.161316635 0.010372482 0.105599218 0.632018971 34.04160946 0.03191338 0.029731061 357.5315169 -2.553314331 0.05970426 DYVDLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 DYVDLFR 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;;;;; 134.06 0.0074714 1405062000 4872190 4837550 4883940 5037200 4333700 3727484 5230710 4830790 2740433 FALSE TRUE 4567248.325 5195727.235 4999789.363 5166463.08 3993348.683 4803548.12 4446413.595 5433924.765 2283037.028 2.000514345 2.275796306 2.189972962 2.262978224 1.749138815 2.104016738 1.947587157 2.380129931 1 21.12252283 -1.916454066 2.774685392 0.345909135 2.115689481 0.786790298 0.182206939 16999342.84 16793603.56 73150757.02 0.042255145 0.012121209 1.916454066 1.769780346 DYVFIEFCVEDSKDVNVNFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DYVFIEFCVEDSKDVNVNFEK 21 1 A0A087WYT3;Q15185-4;Q15185;Q15185-3;B4DDC6;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ;; 200.35 6.86E-22 54105000 166127 95780.9 120111 118104 131380 93879 161633 93206 150914 FALSE TRUE 155729.4076 102872.6175 122960.0896 121134.7486 121061.9448 120980.3433 137397.6322 104842.9743 125725.4785 1.238646371 0.818232062 0.978004547 0.963486082 0.962907012 0.962257967 1.092838412 0.833903959 1 16.93991752 DYVFYLAVGNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DYVFYLAVGNYR 12 0 Q9Y3D6 Q9Y3D6 FIS1 Mitochondrial fission 1 protein 0 110.14 0.003542 43466000 86413 102080 99059 106440 112700 78642 109740 103980 148490 FALSE TRUE 81004.56458 109638.1094 101408.7263 109171.4306 103848.9966 101344.6688 93285.50578 116962.1319 123706.0597 0.654814847 0.886279214 0.819755528 0.882506733 0.839481888 0.819237707 0.754090026 0.945484256 1 16.91655665 1.076210496 5.397328465 0.998697153 0.818229394 0.515601237 0.066836562 0.144559747 6.753920686 0.059500279 0.015021782 11.91819525 -1.076210496 -0.180467759 DYYINIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DYYINIR 7 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 146.87 0.0050945 1170720000 1401890 1541620 1519480 1596360 1653420 1344650 1701600 1388380 1692580 FALSE TRUE 1314148.207 1655763.149 1555522.783 1637325.3 1523567.063 1732828.626 1446460.877 1561722.299 1410077.464 0.931968804 1.174235595 1.103147042 1.161159825 1.080484656 1.228888959 1.025802422 1.107543621 1 20.42734299 0.837942942 1.160644538 1.002598303 1.115615955 0.117297859 0.082391988 1.223481451 3.159360769 0.068886246 0.021474927 6.885618266 -0.837942942 0.113017652 DYYSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 126.68 0.040453 971300000 678270 853180 758350 795480 836950 584360 822980 694720 880950 FALSE TRUE 635818.2914 916350.3349 776338.4201 815893.3635 771219.3231 753055.2457 699581.7892 781457.3213 733913.7538 0.866339251 1.248580409 1.057806065 1.111701967 1.050830999 1.026081391 0.95322071 1.064780864 1 19.48525101 2.395103508 2.225621281 0.999749783 1.098577582 0.044952809 0.09725645 0.521960607 5.292825989 0.037503224 0.029182399 248.3724997 -2.395103508 0.098827799 EAAAALVEEETRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAAAALVEEETRR 13 1 O75934 O75934 BCAS2 Pre-mRNA-splicing factor SPF27 0 ; 237.3 1.55E-16 507700000 460390 541770 517690 501240 564450 486770 563990 461930 561620 FALSE TRUE 431575.0117 581883.2145 529969.8513 514102.667 520120.3739 627292.5969 479424.9353 519602.9773 467881.9938 0.922401412 1.243653789 1.132699822 1.098787031 1.111648622 1.340706856 1.024670626 1.110542795 1 18.83578518 1.606223999 25 1.050697842 1.151950223 0.141879711 0.109739397 0.294285396 4360.140034 0.050348575 0.025206952 40.38536372 -1.606223999 0.101252381 EAADGYQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAADGYQR 8 0 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 134.08 0.0020747 1009200000 2887690 3515800 3126000 3145640 3555700 2710740 3449000 3002600 3130500 FALSE TRUE 2706954.638 3776113.49 3200150.196 3226362.448 3276449.665 3493286.633 2931854.469 3377481.22 2607999.326 1.037942997 1.447896651 1.227051773 1.237102485 1.256307711 1.339450742 1.124177617 1.295046814 1 21.31451207 -0.81875458 0.375612575 0.900833646 1.278463901 0.293079343 0.113566423 13.3328737 1.530543503 1.599842396 0.075995053 0.151790789 0.81875458 0.377630255 EAADLDAVPMSLS(ph)YEELVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAADLDAVPMSLSYEELVR 19 0 A0A0A6YYG7;Q6IBW4-2;Q6IBW4;Q6IBW4-4;H0YC55 A0A0A6YYG7 NCAPH2 Condensin-2 complex subunit H2 1 EAADLDAVPMS(0.299)LS(0.699)Y(0.002)EELVR 122.22 3.53E-05 18593000 64211 55858 65130 60311 63940 63168 65997 55286 72475 TRUE FALSE 60192.14813 59993.78444 66674.91436 61858.68237 58918.41032 81403.57615 56101.36254 62188.5788 60378.45429 0.99691436 0.993629021 1.104283227 1.024515833 0.975818461 1.348222261 0.929161953 1.029979643 1 15.8817462 4.17433774 4.53151029 1.061709108 0.994656651 0.051235415 0.113072988 0.613668446 26.43973835 0.026342557 0.062912445 14939.55769 -4.17433774 -0.067052457 EAAEIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAAEIYR 7 0 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 79.469 0.075704 203460000 425440 517840 479850 466620 523880 405120 544300 469680 464230 FALSE TRUE 398812.4698 556181.4124 491232.2686 478594.2592 482736.578 522071.5674 462687.268 528320.5819 386747.014 1.031197283 1.438101375 1.270164347 1.237486631 1.248197299 1.349904585 1.196356407 1.366062472 1 18.56103063 -1.239755115 4.337163752 0.999859374 1.278851116 0.364192641 0.109989392 0.000133631 2.34E-05 0.095152947 0.022416505 0.05757645 1.239755115 0.278991742 EAAELEEAS(ph)AESEDEMIHPEGVASLLPPDFQSSLERPELELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAAELEEASAESEDEMIHPEGVASLLPPDFQSSLERPELELSR 43 1 S4R3H4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 EAAELEEAS(0.519)AES(0.481)EDEMIHPEGVASLLPPDFQSSLERPELELSR 64.911 0.0014462 16658000 8274 9256.3 7538.4 7728 9108.5 5744.1 11066 7332.1 8612.9 TRUE FALSE 7756.14511 9941.646083 7717.214408 7926.313563 8393.155152 7402.328422 9406.756032 8247.528825 7175.351349 1.080942902 1.385527426 1.075517286 1.104658598 1.169720442 1.031632886 1.31098194 1.149425084 1 12.80883376 -1.52900491 2.292147731 0.985182815 1.177989943 0.169457567 0.109726757 2382172.844 1956660.675 217742.7693 0.027366437 0.02957979 1.52900491 0.192807127 EAAEMGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EAAEMGK 7 0 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5;P68104;A0A087WVQ9;Q5VTE0;A0A087WV01;A6PW80;Q5JR01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;;;;;; 114.6 0.013652 3678330000 6603600 5504450 6094710 5749950 6091880 4709380 6698060 5187800 6726030 FALSE TRUE 6190292.464 5912005.205 6239279.399 5897503.452 5613448.318 6068901.556 5693748.085 5835508.25 5603412.141 1.104736241 1.055072348 1.113478581 1.052484326 1.001791083 1.083072493 1.016121595 1.041420496 1 22.41787418 3.029089118 8.023800747 1.032310945 1.086278407 0.508999626 0.027794033 0.173568756 40.02892042 0.007291576 0.008662797 1069.274273 -3.029089118 0.053967462 EAAEPLSEPKEDQEAAELLS(ph)EPEEESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAAEPLSEPKEDQEAAELLSEPEEESER 28 1 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 1 EAAEPLSEPKEDQEAAELLS(0.997)EPEEES(0.003)ER;EAAEPLSEPKEDQEAAELLS(1)EPEEESER 186.76 5.22E-18 491710000 419360 369716 367419 413400 495810 242415 468150 348294 452940 TRUE FALSE 393113.0062 397090.1573 376134.3522 424008.5439 456871.0826 312396.2752 397955.2536 391779.2726 377341.3879 1.041796683 1.052336611 0.99680121 1.123673569 1.210763243 0.827887651 1.05462922 1.038262129 1 18.52551082 2.246285384 24.99999217 0.986632414 1.070327279 0.272926084 0.082851723 290.4048798 939850.7561 0.02864984 0.023548774 176.3134259 -2.246285384 0.083694865 EAAEQDVEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAAEQDVEKK 10 1 P26373;P26373-2;J3KS98 P26373 RPL13 60S ribosomal protein L13 0 ; 100.04 0.0068735 800740000 2109390 551160 1595850 1636180 854270 1468360 1580970 686660 611610 FALSE TRUE 1977367.045 591968.4599 1633704.316 1678167.149 787179.0802 1892251.695 1343918.226 772391.0125 509528.3398 3.880779322 1.161796928 3.206307064 3.293569793 1.544917169 3.713731989 2.637573066 1.515894116 1 18.95880287 1.137559898 3.742505017 1.04204779 2.683741152 0.350482467 0.866995561 0.245250217 5.966872608 0.760201259 0.199361155 13.72650264 -1.137559898 1.641693362 EAAEVLQNNRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EAAEVLQNNRR 11 1 P61081;M0QX69 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ;; 151.79 5.33E-05 1922900000 666840 770010 738710 730760 912620 662530 841060 680710 990500 FALSE TRUE 625103.6747 827022.3416 756232.55 749512.5388 840946.5065 853791.6557 714950.861 765698.1419 825179.1511 0.757536923 1.002233685 0.916446506 0.908302806 1.019107797 1.034674294 0.866418959 0.92791746 1 19.65434785 4.747538685 24.46702039 0.953664143 0.757536785 0.570494499 0.054842147 688.2149473 1875467.213 0.012989775 0.156162595 55916.33336 -4.747538685 -0.196127358 EAAFDDAVEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAAFDDAVEER 11 0 Q09028-3;Q09028;E9PNS2;E9PIC4;E9PNS6 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 138.36 0.0001376 109500000 164320 167450 183210 174060 159320 168190 191420 150430 143210 FALSE TRUE 154035.5045 179848.1722 187555.8277 178526.6743 146807.6499 216743.7227 162718.3481 169211.5166 119307.3258 1.291081696 1.507436119 1.572039491 1.4963597 1.230499878 1.816684107 1.363858815 1.418282704 1 16.86432311 0.634886773 1.612764661 1.000630286 1.488155473 0.449602392 0.161265728 1.237945866 4.384577945 0.137650047 0.039386712 4.314065883 -0.634886773 0.487525187 EAAFS(ph)PGQQDWSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EAAFSPGQQDWSR 13 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 EAAFS(1)PGQQDWSR;EAAFS(1)PGQQDWSR;EAAFS(1)PGQQDWSR;EAAFS(1)PGQQDWSR 281.68 1.90E-32 1539230000 1653520 1842270 1888000 1943190 1938990 1582180 2165860 1508980 1896030 TRUE FALSE 1550029.135 1978673.588 1932784.252 1993055.545 1786709.547 2038929.681 1841109.4 1697379.475 1579570.344 0.981297946 1.252665698 1.223613914 1.261770679 1.131136422 1.29081284 1.165576074 1.074583022 1 20.59110076 1.143777885 2.592180319 1.00396325 1.203290547 0.34592532 0.087528065 0.245726127 3.02311436 0.073769788 0.020332977 13.9244447 -1.143777885 0.199327298 EAAFSPGQQDWSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EAAFSPGQQDWSR 13 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ;; 163.9 8.83E-05 338320000 285206 304588 310060 293023 334890 238755 323146 248763 297500 FALSE TRUE 267355.4656 327140.0124 317414.7696 300542.4663 308589.0903 307679.6926 274693.2572 279821.6081 247845.3281 1.078719004 1.319936167 1.280697006 1.212621067 1.24508738 1.241418166 1.108325339 1.129017078 1 17.91908054 1.327778619 0.929058797 1.00834249 1.252411569 0.533909664 0.067961801 0.339424614 0.617512581 0.05931656 0.021575263 21.27054507 -1.327778619 0.244069079 EAAGPAPS(ph)PMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EAAGPAPSPMR 11 0 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 EAAGPAPS(1)PMR;EAAGPAPS(1)PMR;EAAGPAPS(1)PMR;EAAGPAPS(1)PMR 140.16 0.00025851 1466940000 1886190 2177780 2039350 1907900 2096500 1638700 2167400 1870140 1949660 TRUE FALSE 1768136.735 2339025.097 2087724.345 1956859.944 1931849.347 2111766.088 1842418.491 2103631.096 1624249.151 1.088587138 1.440065458 1.285347352 1.204778185 1.189379934 1.30014911 1.13432012 1.295140647 1 20.63134152 -3.667441288 0.16932392 0.378259173 1.328654154 0.323895154 0.102094695 78.2301027 1.11350527 17.10506389 0.371623051 0.00021506 3.667441288 0.950394981 EAALILGVS(ph)PTANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAALILGVSPTANK 14 0 Q96DA6-2;Q96DA6 Q96DA6-2 DNAJC19 Mitochondrial import inner membrane translocase subunit TIM14 1 EAALILGVS(0.998)PT(0.002)ANK 149.3 7.89E-06 19906000 114310 85294 94573 75483 114730 71978 94541 99240 174190 TRUE FALSE 107155.5411 91609.25651 96816.31622 77420.02157 105719.5686 92756.88013 80365.45473 111630.3325 145116.5637 0.738410133 0.631280497 0.667162409 0.533502307 0.728514829 0.639188786 0.553799323 0.769245975 1 17.14685267 0.954214409 5.322444505 0.999907853 0.638856486 0.760501179 0.064329443 0.111584147 10.36850942 0.057402671 0.014482605 8.999417687 -0.954214409 -0.361051367 EAALPPVS(ph)PLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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 177.42 8.38E-06 17936726000 17797220 12279010 15070600 15557650 12131430 7214630 11051270 7007090 9872450 TRUE FALSE 16683323.77 13188160.68 15428081.75 15956885.64 11178676.42 9297376.561 9394234.658 7881940.611 8224674.317 2.028447952 1.603487283 1.875828897 1.940123709 1.359163414 1.13042489 1.142201417 0.958328599 1 22.97152712 2.515250895 2.816644835 1.078567759 1.820990406 0.899752551 0.126165339 0.082379139 1.312110781 0.045477436 0.03982254 327.5298563 -2.515250895 0.742422647 EAALPPVS(ph)PLKAALSEEELEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EAALPPVSPLKAALSEEELEK 21 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 EAALPPVS(1)PLKAALSEEELEK;EAALPPVS(1)PLKAALSEEELEK;EAALPPVS(1)PLKAALSEEELEK 154.69 1.90E-08 226638000 937140 700423 985140 1186740 1209070 493981 793521 448931 1375830 TRUE FALSE 878486.0802 752283.0477 1008507.986 1217193.758 1114114.519 636585.2956 674539.8927 504981.0236 1146195.085 0.766436789 0.656330722 0.879874639 1.061942922 0.972011252 0.555390006 0.588503564 0.440571618 1 20.12842118 2.228051095 24.99799884 0.607310641 0.849106731 0.258145232 0.179630707 264.0248304 628006.2836 0.065328741 0.048758828 169.0639824 -2.228051095 0.241796089 EAALSTALSEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 289.75 6.95E-36 2271800000 2111230 2026520 1976670 2057040 2429880 1508200 2571340 1841290 3425700 FALSE TRUE 1979091.883 2176565.649 2023557.546 2109827.129 2239047.026 1943592.856 2185791.438 2071179.11 2853928.539 0.693462312 0.762655974 0.709042822 0.739271184 0.784549086 0.681023659 0.765888637 0.725729142 1 21.44451778 -4.970231782 0.51442215 9.999999548 0.73307875 0.868859579 0.032627233 845.0836407 3.840366144 8774.276313 0.013048815 1.07E-05 4.970231782 -9.266920798 EAARS(ph)PDKPGGS(ph)PSASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAARSPDKPGGSPSASR 17 2 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 2 EAARS(1)PDKPGGS(0.972)PS(0.025)AS(0.003)R;EAARS(1)PDKPGGS(0.864)PS(0.119)AS(0.017)R 134.66 8.71E-06 1535120000 1230150 750740 937350 905060 890000 697830 1155800 741520 826990 TRUE FALSE 1153157.107 806325.5707 959584.3846 928285.3719 820102.9901 899282.1927 982498.5199 834100.4043 688960.0264 1.673764897 1.170351747 1.392801248 1.347371888 1.190349162 1.305274846 1.426060268 1.210665891 1 19.39406075 -3.888904033 0.233858652 9.66E-14 1.37166953 0.402272452 0.139557989 100.7899421 1.61526061 48.23273077 0.220800366 0.00012915 3.888904033 1.37166953 EAARS(ph)PDKPGGSPS(ph)ASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAARSPDKPGGSPSASR 17 2 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 2 EAARS(0.844)PDKPGGS(0.209)PS(0.872)AS(0.074)R 96.881 0.010881 676360000 723140 469760 599960 621620 540360 377680 756530 480300 565680 TRUE FALSE 677879.9582 504541.5192 614191.3345 637571.8216 497922.3053 486710.0849 643095.3498 540266.5123 471264.3536 1.438428248 1.070612524 1.303284091 1.352896345 1.056566875 1.032775089 1.364617003 1.146419219 1 18.84617703 2.738726437 24.99999995 1.153435542 1.256519634 0.242246796 0.137944989 35.071042 5287822.798 0.043315783 0.043319048 547.9317123 -2.738726437 0.103084092 EAARS(ph)PDKPGGSPSASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EAARSPDKPGGSPSASR 17 2 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 EAARS(1)PDKPGGSPSASR;EAARS(0.998)PDKPGGS(0.001)PS(0.001)ASR;EAARS(1)PDKPGGSPSASR 161.53 1.54E-09 4610500000 3923100 3336760 3455880 3529480 3663670 2590700 4322860 3377660 3995490 TRUE FALSE 3677560.174 3583817.182 3537855.106 3620052.432 3375940.137 3338593.033 3674687.274 3799368.286 3328616.907 1.104831309 1.076668563 1.062860402 1.087554541 1.014217085 1.002997079 1.103968218 1.141425521 1 21.66649141 -0.458358196 6.148843086 1.00000139 1.071342857 0.239129768 0.041359002 0 0 0.039313248 0.009266222 0.348050133 0.458358196 0.071341467 EAARS(ph)PDKPGGSPSASRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAARSPDKPGGSPSASRR 18 3 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 EAARS(0.869)PDKPGGS(0.053)PS(0.039)AS(0.039)RR 89.721 0.015687 48209000 30005 34649 30400 33168 41880 20725 45289 29180 93111 TRUE FALSE 28127.04061 37214.44801 31121.10236 34019.14703 38590.91374 26707.97106 38498.33489 32823.18723 77570.17258 0.362601238 0.479752033 0.401199344 0.438559641 0.497496814 0.344307228 0.496303329 0.423141862 1 16.24321439 -4.461410942 0.486799213 9.998467454 0.429806473 0.922523912 0.051877846 255.8417785 2.228298858 2467.769742 0.021892797 3.46E-05 4.461410942 -9.568660981 EAARSPDKPGGS(ph)PSASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAARSPDKPGGSPSASR 17 2 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 EAARS(0.218)PDKPGGS(0.261)PS(0.261)AS(0.261)R 59.154 0.069781 82935000 69714 52286 55600 57886 53967 44440 72884 43008 64838 TRUE FALSE 65350.72518 56157.30984 56918.85826 59371.45276 49728.64951 57269.10658 61955.72082 48377.64347 54016.11893 1.20983748 1.039639851 1.053738391 1.099143255 0.920626111 1.060222536 1.14698579 0.895614947 1 15.72110237 4.738684436 22.05607784 1.040175737 1.209837547 0.351438005 0.076212924 2.272912849 402133.0339 0.016926365 0.097869953 54787.87246 -4.738684436 0.16966181 EAAS(ph)GTTPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAASGTTPQK 10 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 EAAS(0.373)GT(0.279)T(0.348)PQK;EAAS(0.662)GT(0.189)T(0.148)PQK 73.951 0.045578 166826000 780700 582890 718480 650920 715690 542050 834600 636430 707840 TRUE FALSE 731837.3806 626047.7821 735522.6849 667623.7092 659482.5944 698531.0356 709459.478 715889.6865 589696.9312 1.241039832 1.061643276 1.247289321 1.132147166 1.118341574 1.184559387 1.203091691 1.21399595 1 19.16961416 -1.010970566 4.733634999 0.999996434 1.171338318 0.475290408 0.057741961 2.03E-06 4.25E-07 0.052315882 0.012330715 0.097505572 1.010970566 0.171341883 EAAS(ph)SPAGEPLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAASSPAGEPLRK 13 1 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 EAAS(0.642)S(0.358)PAGEPLRK 85.473 0.0056775 179640000 285960 219030 268260 230980 302850 251440 382570 299080 398000 TRUE FALSE 268062.2741 235247.2091 274623.2539 236907.3378 279065.3826 324026.6462 325207.1801 336420.7964 331571.2288 0.808460598 0.709492226 0.828248141 0.71449908 0.841645349 0.977245967 0.98080639 1.01462602 1 18.3389593 2.337699163 2.857215584 0.993770859 0.766322208 0.89306587 0.037387863 0.072813926 1.209015282 0.013483722 0.010531995 217.6201791 -2.337699163 -0.227448651 EAASGT(ph)TPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAASGTTPQK 10 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 EAAS(0.001)GT(0.499)T(0.499)PQK;EAAS(0.001)GT(0.5)T(0.5)PQK 155.24 0.00014598 4804840000 4464680 3224970 3872690 3328990 3807010 3032040 4646920 3620570 4137650 TRUE FALSE 4185243.648 3463750.134 3964552.036 3414417.519 3508022.791 3907340.727 3950157.486 4072606.134 3447049.485 1.214152471 1.004844911 1.150129133 0.990533363 1.01768855 1.133531951 1.145953229 1.18147597 1 21.71693058 2.19074042 24.97372481 1.129609585 1.072159032 0.041940164 0.081767775 260.3912034 135985.5314 0.027961542 0.02065103 155.1459417 -2.19074042 -0.057450552 EAASGTT(ph)PQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.07)T(0.93)PQK;EAASGT(0.099)T(0.901)PQK;EAASGT(0.14)T(0.86)PQK;EAASGT(0.144)T(0.856)PQK;EAAS(0.001)GT(0.151)T(0.848)PQK 200.67 2.86E-06 10355800000 7268480 5221800 6254380 5467550 6149540 4845070 7292770 5566960 6367290 TRUE FALSE 6813558.811 5608427.505 6402736.847 5607856.59 5666579.934 6243763.056 6199286.841 6262007.21 5304548.165 1.284474869 1.057286564 1.207027752 1.057178937 1.068249313 1.177058415 1.168673872 1.180497757 1 22.33879844 4.755366307 24.20571443 1.126361025 1.284475063 0.365114141 0.068879956 2524.963814 3636685.444 0.015297301 0.418467899 56933.29345 -4.755366307 0.158114038 EAASS(ph)PAGEPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EAASSPAGEPLR 12 0 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 EAAS(0.12)S(0.88)PAGEPLR;EAAS(0.006)S(0.994)PAGEPLR;EAAS(0.004)S(0.996)PAGEPLR 241.35 3.18E-16 1336960000 1454190 1442550 1520990 1396330 1692050 1601410 2022590 1733820 1983400 TRUE FALSE 1363174.844 1549357.903 1557068.601 1432162.192 1559163.218 2063711.07 1719321.406 1950291.244 1652357.727 0.824987726 0.937664937 0.942331419 0.866738581 0.943599073 1.248949327 1.040526139 1.180308121 1 20.65609463 2.384005521 7.613118593 1.116193929 0.908321961 0.666071102 0.075807145 0.131941391 9.381437808 0.023392539 0.019530607 242.1059824 -2.384005521 -0.207871968 EAASSSSGTQPAPPAPAS(ph)PWDSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAASSSSGTQPAPPAPASPWDSKK 24 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 EAASSSSGTQPAPPAPAS(0.99)PWDS(0.01)KK;EAASSSSGTQPAPPAPAS(0.967)PWDS(0.033)KK 174.1 2.04E-12 3272400000 1355130 722050 901000 848620 910410 660880 1259580 773800 1150600 TRUE FALSE 1270314.832 775511.3333 922372.1455 870397.0259 838910.071 851665.3275 1070717.672 870410.6333 958557.4268 1.325236023 0.809040034 0.962250273 0.908028045 0.875179773 0.888486494 1.117009417 0.90804224 1 19.87050534 1.761963094 25 1.019486916 0.938528376 0.004615671 0.147810153 38.03023892 40656.5635 0.062145015 0.03446362 57.80469239 -1.761963094 -0.08095854 EAATLEVERPLPMEVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAATLEVERPLPMEVEK 17 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 226.74 1.80E-15 444640000 414640 284850 346510 333290 327030 300490 452030 330000 329890 FALSE TRUE 388688.4226 305940.5904 354729.3808 341842.7857 301346.383 387236.585 384252.2979 371201.2264 274829.2278 1.414290706 1.113202525 1.290726549 1.243837085 1.096485935 1.409008016 1.39814932 1.350661388 1 18.06817592 2.220460071 24.99623887 1.333809505 1.224147808 0 0.145712193 498.7509042 688754.0061 0.048692205 0.03602963 166.1345927 -2.220460071 -0.109661698 EAATQEDPEQLPELEAHGVS(ph)ES(ph)EGEERPVAEEEILLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAATQEDPEQLPELEAHGVSESEGEERPVAEEEILLR 37 1 Q9BVJ6-3;Q9BVJ6;Q9BVJ6-2;X6RJY0 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 2 EAATQEDPEQLPELEAHGVS(1)ES(1)EGEERPVAEEEILLR 181.84 5.90E-23 113310000 114760 129840 119360 115080 113760 87311 139510 103650 126290 TRUE FALSE 107577.3765 139453.4887 122191.2756 118033.1476 104825.7485 112516.2683 118591.7706 116590.9307 105211.3831 1.022487997 1.325460084 1.161388359 1.121866704 0.996334668 1.069430559 1.127176234 1.108158901 1 16.68293128 3.244076756 2.655842197 1.073332384 1.207895019 0.223288652 0.08486732 0.29795037 4.28491715 0.024123858 0.032500368 1754.190507 -3.244076756 0.134562635 EAATQEDPEQLPELEAHGVS(ph)ESEGEERPVAEEEILLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAATQEDPEQLPELEAHGVSESEGEERPVAEEEILLR 37 1 Q9BVJ6-3;Q9BVJ6;Q9BVJ6-2;X6RJY0 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 1 EAATQEDPEQLPELEAHGVS(0.962)ES(0.038)EGEERPVAEEEILLR;EAATQEDPEQLPELEAHGVS(0.958)ES(0.042)EGEERPVAEEEILLR 347.88 3.58E-145 372930000 130949 135009 154687 135195 152844 125516 147189 131334 151003 TRUE FALSE 122753.1358 145005.2068 158356.2487 138664.3326 140840.2488 161750.4316 125119.3759 147731.339 125799.6238 0.975783012 1.152668048 1.258797474 1.102263492 1.119560175 1.285778341 0.994592608 1.17433848 1 16.94076808 0.753117277 0.790126702 1.003273898 1.152683356 0.119219042 0.099900191 1.753853064 2.143083811 0.092549824 0.032749975 5.663922165 -0.753117277 0.149409458 EAAVGVPPPAQPAPGEPTPPAPPS(ph)PDWTSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EAAVGVPPPAQPAPGEPTPPAPPSPDWTSSSR 32 0 Q8IV56 Q8IV56 PRR15 Proline-rich protein 15 1 EAAVGVPPPAQPAPGEPT(0.001)PPAPPS(0.744)PDWT(0.159)S(0.027)S(0.034)S(0.034)R;EAAVGVPPPAQPAPGEPT(0.005)PPAPPS(0.987)PDWT(0.005)S(0.001)S(0.001)S(0.001)R;EAAVGVPPPAQPAPGEPTPPAPPS(0.981)PDWT(0.011)S(0.003)S(0.003)S(0.003)R;EAAVGVPPPAQPAPGEPTPPAPPS(0.982)PDWT(0.011)S(0.002)S(0.002)S(0.002)R 138.6 4.92E-09 832640000 709971 829427 751708 874082 909690 607522 811882 674077 590575 TRUE FALSE 665535.1824 890838.6381 769538.8687 896512.4239 838246.6169 782903.7391 690147.8312 758236.9973 492004.2172 1.352702191 1.810632118 1.564089985 1.822164105 1.703738683 1.591254123 1.402727471 1.541118898 1 18.90831116 0.650043356 0.665838715 0.995490744 1.66777176 0.635318608 0.14624584 0.744695399 0.626134384 0.145686275 0.052490154 4.467281869 -0.650043356 0.672281015 EAAVSASDILQESAIHS(ph)PGTVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAAVSASDILQESAIHSPGTVEK 23 0 F5H3K2;F5H8B7;E7ENF1;G5EA44;F5H7W8;Q96C57 F5H3K2 C12orf43 Uncharacterized protein C12orf43 1 EAAVSASDILQESAIHS(1)PGTVEK 276.24 1.93E-46 395300000 418730 325580 374860 366040 389590 352470 512200 407000 564730 TRUE FALSE 392522.4368 349686.282 383751.8562 375433.2061 358993.1729 454222.3671 435400.365 457814.8459 470472.9147 0.834314632 0.743265491 0.81567258 0.797991116 0.763047482 0.965459122 0.925452564 0.973095011 1 18.84375214 2.235270779 24.99994862 0.956312962 0.78807632 0.884370914 0.031373226 25.59509548 194497.9752 0.010665604 0.008203869 171.8979822 -2.235270779 -0.168236642 EAAVSHAGSMHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAAVSHAGSMHR 12 0 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 65.234 0.03545 67772000 15207 19828 19902 20865 20943 16798 25817 19292 23819 FALSE TRUE 14255.22102 21296.08575 20374.08484 21400.43122 19298.22126 21647.30991 21945.98052 21700.64867 19843.45502 0.718384021 1.073204526 1.026740798 1.078462959 0.972523244 1.090904275 1.105955616 1.093592252 1 14.27637562 4.74002858 24.84914313 1.058912185 0.718383899 0.855619753 0.043454299 40.8688216 691740.2228 0.01010467 0.063531871 54957.70394 -4.74002858 -0.340528286 EACPELDYFVVFSSVSCGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 226.59 3.41E-19 119442000 116679 128533 118126 126566 151320 116703 152867 130709 156126 FALSE TRUE 109376.2697 138049.7171 120928.0045 129813.8978 139435.9376 150393.2616 129946.0125 147028.3064 130067.562 0.840918889 1.061369299 0.92973223 0.998049751 1.072026995 1.15627032 0.99906549 1.130399495 1 16.98890168 2.845737466 3.773272162 1.072561166 0.966965119 0.382767114 0.072530726 0.270565275 6.956966228 0.021071709 0.022434969 701.0313924 -2.845737466 -0.105596047 EADDIVNWLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EADDIVNWLK 10 0 P07237;I3L312;I3L3P5 P07237 P4HB Protein disulfide-isomerase 0 ;;;;; 204.07 4.51E-07 1393492000 3563370 3268810 3378700 3382820 3304660 2545020 4121230 2729660 3159360 FALSE TRUE 3340345.032 3510836.094 3458844.36 3469628.888 3045125.334 3279725.959 3503289.821 3070464.06 2632042.406 1.269107604 1.3338828 1.31412942 1.318226819 1.156943873 1.246076413 1.331015721 1.166570893 1 21.3277513 -4.461235118 0.195444736 5.15E-11 1.331420213 0.707074102 0.056885297 59.7520208 0.712598777 23.32751023 0.145692349 3.46E-05 4.461235118 1.331420213 EADGSDSLEGFVLCHSIAGGTGSGLGSYLLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EADGSDSLEGFVLCHSIAGGTGSGLGSYLLER 32 0 P23258;K7EIS0;Q9NRH3 P23258 TUBG1;TUBG2 Tubulin gamma-1 chain;Tubulin gamma chain;Tubulin gamma-2 chain 0 ; 270 7.79E-61 172931000 68694 81787 79432 75947 92781 70152 100822 75107 77289 FALSE TRUE 64394.56516 87842.59458 81316.16455 77895.9286 85494.35452 90403.74358 85704.67709 84484.27428 64388.96659 1.000086949 1.364249175 1.262889729 1.209771374 1.327779572 1.404025384 1.33104601 1.312092409 1 15.97452588 -1.331640509 5.56603716 0.999944504 1.291345627 0.368063567 0.11236911 7.05E-05 8.47E-06 0.099181277 0.023372811 0.046597165 1.331640509 0.291401123 EADIDGDGQVNYEEFVQMMTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EADIDGDGQVNYEEFVQMMTAK 22 0 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;M0QZ52 P0DP25 CALM2;CALM3 0 ; 170.91 6.62E-12 36013000 104532 79864 93993 83034 80673 48314 120264 101073 95854 FALSE TRUE 97989.52871 85777.21366 96222.55835 85164.79302 74337.268 62261.46749 102231.5297 113692.1865 79855.34816 1.227087865 1.074157406 1.204960727 1.066488281 0.930899053 0.779678117 1.280208928 1.42372664 1 16.28510141 -0.398750493 6.562025683 0.999999956 1.115733397 0.042615563 0.180592821 0 0 0.172284015 0.040607732 0.399254212 0.398750493 0.11573344 EADKSHPEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EADKSHPEQR 10 1 O14745 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;;;; 159.94 4.53E-06 5014660000 11123110 9540900 10350470 9966570 10810570 8075720 12067510 9325690 14188710 FALSE TRUE 10426934.4 10247318.16 10595988.04 10222329.06 9961551.44 10407049.27 10258098.9 10490022.92 11820522.64 0.882104347 0.86690906 0.896406052 0.864795016 0.842733587 0.880422092 0.867821095 0.887441549 1 23.49479049 0.726184896 3.194548116 0.999997892 0.872673993 0.892691866 0.013874582 0.766125482 8.585748385 0.013266934 0.003448562 5.323348469 -0.726184896 -0.127323898 EADLDHYSAIIMDEAHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EADLDHYSAIIMDEAHER 18 0 Q92620 Q92620 DHX38 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 0 165.8 1.58E-11 29736000 13627 24492 16599 23608 24343 18106 22870 19131 23282 FALSE TRUE 12774.11039 26305.41316 16992.73612 24213.82125 22431.19897 23332.90827 19440.85581 21519.54746 19396.08379 0.658592246 1.356222908 0.876091086 1.248387123 1.156480824 1.20297007 1.002308302 1.10947899 1 14.24347777 4.759407254 24.4941647 1.115047958 0.658591652 0.527781085 0.13681673 3193.827633 3752570.933 0.030239728 1.325199856 57465.50845 -4.759407254 -0.456456306 EAEAAIYHLQLFEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EAEAAIYHLQLFEELR 16 0 P14618;P14618-3;B4DNK4 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;; 239.86 7.67E-20 6385725000 3814922 3755611 3993444 3906785 3891759 3453671 4254634 3607642 2334472 FALSE TRUE 3576152.842 4033680.346 4088170.378 4007039.717 3586115.947 4450689.752 3616691.13 4058064.045 1944833.542 1.838796362 2.074049146 2.102066984 2.060350992 1.84391922 2.288468219 1.859640453 2.086586825 1 20.89121525 -1.980857086 0.682856042 1.28E-14 2.030730121 0.837102512 0.141150197 75.72926903 8.39943528 119.477654 0.045200049 0.010450641 1.980857086 2.030730121 EAEAAIYHLQLFEELRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 28 EAEAAIYHLQLFEELRR 17 1 P14618;P14618-3;B4DNK4 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;; 272.71 7.90E-36 18042448600 4874534.4 5943299.8 5520718.9 5449652.6 6236166.9 4367393 5944545.7 4949184.7 5107535.7 FALSE TRUE 4569445.993 6383347.901 5651672.959 5589499.912 5746403.507 5628188.46 5053216.259 5567101.304 4255054.996 1.073886471 1.500179882 1.328225596 1.313614023 1.350488657 1.322706397 1.187579541 1.308350024 1 22.02074635 0.352685578 0.492039593 0.978808154 1.348403111 0.394305977 0.112162154 2.136038927 0.845540937 0.206890132 0.054696025 2.252607772 -0.352685578 0.369594956 EAEALLQSMGLTPESPIVPPPMS(ph)PSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EAEALLQSMGLTPESPIVPPPMSPSSK 27 0 Q13409-2;Q13409-3;Q13409-6;E7EQL5;E7EV09;E7EQU2;E7ETL8;E9PGG1 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 1 EAEALLQSMGLTPESPIVPPPMS(0.675)PS(0.143)S(0.182)K;EAEALLQSMGLTPESPIVPPPMS(0.921)PS(0.062)S(0.017)K;EAEALLQSMGLTPESPIVPPPMS(0.662)PS(0.266)S(0.071)K;EAEALLQSMGLTPESPIVPPPMS(0.682)PS(0.137)S(0.181)K;EAEALLQSMGLTPESPIVPPPMS(0.824)PS(0.155)S(0.021)K;EAEALLQSMGLTPESPIVPPPMS(0.851)PS(0.129)S(0.02)K;EAEALLQSMGLTPESPIVPPPMS(0.665)PS(0.267)S(0.069)K;EAEALLQSMGLTPESPIVPPPMS(0.924)PS(0.061)S(0.015)K 157.43 4.95E-09 1675080000 3028020 2691020 3014800 3435440 3365800 1584969 2274270 1583273 2183790 TRUE FALSE 2838501.633 2890265.921 3086312.48 3523599.207 3101463.645 2042523.82 1933264.327 1780948.119 1819301.341 1.560215215 1.588668054 1.69642731 1.936787011 1.704755323 1.122696815 1.062641072 0.978918708 1 20.79495309 2.203438915 4.836716355 1.040274311 1.695238101 0.909414117 0.103187388 0.058894482 3.226304879 0.042278518 0.031660295 159.7492821 -2.203438915 0.654963791 EAEAMALLAEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EAEAMALLAEAER 13 0 P54920;M0R0Y2;M0R2M1;M0QZM9;M0QZN5;M0R031 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;; 199.8 1.04E-06 76149000 163277 188123 180240 171900 203493 161674 193480 167518 193831 FALSE TRUE 153057.784 202051.8227 184515.3779 176311.245 187511.4806 208346.6592 164469.4702 188432.9911 161479.3539 0.947847389 1.251254837 1.142656157 1.091850077 1.161210248 1.290237137 1.018517019 1.166916925 1 17.30099019 0.506839245 0.881610054 1.000579696 1.149541196 0.127196943 0.101263852 2.908441825 3.420309002 0.092209174 0.029853079 3.212471217 -0.506839245 0.1489615 EAEDGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAEDGFR 7 0 F6U236;Q9BY11;Q9UNF0-2;Q9UNF0;A0A0U1RR22;B0QYG7;B0QYG8 F6U236;Q9UNF0-2 PACSIN1;PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 1;Protein kinase C and casein kinase substrate in neurons protein 2 0 ; 134.06 0.0074714 399050000 578620 632350 637740 632990 711010 523930 688970 585280 672170 FALSE TRUE 542405.2071 679169.852 652867.494 649233.595 655170.1427 675180.0857 585665.3446 658353.4964 559980.4846 0.968614482 1.212845573 1.16587544 1.159386109 1.169987456 1.205720743 1.04586742 1.175672214 1 19.09501702 0.221295278 0.666520801 0.996124098 1.15244925 0.216743795 0.076912104 3.91131296 2.287462597 0.114695163 0.026740671 1.664543995 -0.221295278 0.156325152 EAEDS(ph)DS(ph)DDNIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAEDSDSDDNIK 12 0 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 EAEDS(1)DS(1)DDNIK 183.58 2.25E-05 76584000 432970 390580 442050 544020 674270 427560 495910 299500 623530 TRUE FALSE 405871.1806 419498.9496 452535.6348 557980.4742 621315.5541 550989.6311 421552.8993 336893.2343 519458.8148 0.781334668 0.807569219 0.871167496 1.074157293 1.196082416 1.060699357 0.811523238 0.648546573 1 18.98664984 3.453218567 9.200397551 0.964028366 0.816736226 0.183294423 0.149348099 0.494334692 175.6068378 0.044180415 0.060558386 2839.347626 -3.453218567 -0.14729214 EAEDS(ph)DS(ph)DDNIKR ddPTM_SK-BR-3_Pertuzumab_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 213.69 2.60E-09 1481910000 5128170 2791700 3556090 3162990 3301020 2221980 4094700 2878790 4180030 TRUE FALSE 4807206.994 2998400.373 3640442.134 3244157.678 3041771.205 2863429.555 3480737.748 3238213.268 3482355.989 1.380446746 0.86102638 1.04539632 0.931598518 0.873480832 0.822267903 0.999535303 0.92989151 1 21.73163226 4.744402621 24.86453381 0.934857394 1.380446955 0.806991003 0.068779385 253.7294018 1079880.532 0.015969064 0.142837646 55514.01284 -4.744402621 0.445589561 EAEDSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAEDSLR 7 0 O43776;K7EIU7;O43776-2;K7EJ19;K7EPK2;K7EMQ6 O43776;REV__H7BZ55 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 120.62 0.01051 62856000 233940 237480 257560 242090 259660 232580 285860 232720 216980 FALSE TRUE 219298.113 255063.2663 263669.4448 248302.4393 239267.351 299722.0704 242997.9468 261775.6043 180764.6363 1.213169332 1.411024145 1.458634002 1.373622874 1.323640265 1.658079128 1.344278128 1.448157171 1 17.46375294 -1.190321838 4.10510023 0.999804344 1.412385187 0.551325085 0.114255882 0.000183686 3.62E-05 0.099321244 0.023399223 0.064517594 1.190321838 0.412580843 EAEDSLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EAEDSLRR 8 1 O43776;K7EIU7;O43776-2;K7EJ19;K7EPK2;K7EMQ6 O43776;REV__H7BZ55 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;;;; 178.94 0.00039597 5567120000 6343610 7248900 6922780 6996110 7695760 5565430 7760980 6088630 9160070 FALSE TRUE 5946574.774 7785616.098 7086991.611 7175642.027 7091366.053 7172079.294 6597293.098 6848808.858 7631195.141 0.779245539 1.020235488 0.928686985 0.940303831 0.929260217 0.939836967 0.864516367 0.897475262 1 22.86347759 EAEDTQVFGDLPRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAEDTQVFGDLPRPR 15 1 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 0 ; 160.8 1.54E-06 214290000 184961 189415 178621 188351 200011 160253 209612 153328 211191 FALSE TRUE 173384.6212 203439.4837 182857.9745 193184.4055 184302.9429 206515.4396 178182.6265 172471.3383 175941.8578 0.985465445 1.156288141 1.039309104 1.098001397 1.047521864 1.173770939 1.012735848 0.980274623 1 17.42473922 1.563096719 7.791692356 0.992798237 1.086490913 0.358041398 0.054568841 0.115117384 12.96172585 0.026262412 0.012270832 36.56762196 -1.563096719 0.093692676 EAEEAEREER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAEEAEREER 10 1 A0A0A0MRX2;Q96HY6-2;Q96HY6 A0A0A0MRX2 DDRGK1 DDRGK domain-containing protein 1 0 ; 152.07 1.70E-05 250180000 250210 251360 215060 208700 263830 191688 239580 233300 262260 FALSE TRUE 234549.8027 269970.9559 220161.3248 214055.5953 243109.856 247025.2138 203657.2032 262428.0186 218487.1117 1.073517796 1.2356379 1.007662754 0.979717264 1.112696553 1.130616867 0.932124561 1.201114411 1 17.73718865 3.916120853 5.805851162 1.047123194 1.160404422 0.18750621 0.088049528 0.262520968 17.77185414 0.020814939 0.038605786 8243.674835 -3.916120853 0.113281228 EAEEEFWYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EAEEEFWYR 9 0 E9PH64;Q9Y6M9;A0A3B3IT57;E7EWZ0;E9PF49 E9PH64 NDUFB9 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 0 ;;; 152.47 0.0022801 160347000 586465 528006 551152 490864 648985 556892 527915 539052 821230 FALSE TRUE 549759.2025 567100.1136 564225.5857 503460.4013 598016.336 717657.68 448759.0467 606353.8288 684161.4077 0.803551905 0.828898133 0.824696598 0.735879568 0.874086625 1.048959605 0.655925695 0.886273067 1 19.3839772 EAEEES(ph)DHN ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 EAEEESDHN 9 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 EAEEES(1)DHN;EAEEES(1)DHN;EAEEES(1)DHN;EAEEES(1)DHN;EAEEES(1)DHN;EAEEES(1)DHN;EAEEES(1)DHN;EAEEES(1)DHN;EAEEES(1)DHN 184.27 4.64E-05 4482069000 7284915 6137504 7905618 7252998 6830190 5849236 7671653 6192714 6795823 TRUE FALSE 6828965.174 6591931.182 8093142.992 7439122.208 6293774.429 7537815.479 6521359.853 6965887.975 5661556.239 1.2061993 1.164332015 1.429490877 1.313971264 1.111668623 1.331403445 1.151867009 1.230383958 1 22.43276724 0.416364157 0.587099161 0.991561584 1.269511051 0.404147884 0.093878851 2.034930272 1.141217047 0.134988684 0.039861872 2.608339732 -0.416364157 0.277949467 EAEEGEDDRDS(ph)ANGEDDS ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 EAEEGEDDRDSANGEDDS 18 1 P07910;G3V2Q1;P07910-3;P07910-2;G3V4C1;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(0.899)ANGEDDS(0.101);EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(0.999)ANGEDDS(0.001);EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(0.85)ANGEDDS(0.15) 289.7 1.02E-48 32454508000 5243830 3476335 4590020 3891632 3493303 4453410 5648120 3870844 2639833 TRUE FALSE 4915628.041 3733726.461 4698897.442 3991497.866 3218953.074 5739037.172 4801236.841 4354127.394 2199227.818 2.235160905 1.697744285 2.136612407 1.814954245 1.463674225 2.609569197 2.183146648 1.979843724 1 21.06856563 0.929867242 20.36939561 0.999999997 2.016363158 0.507649966 0.314393785 3639.444968 1057045.739 0.295891146 0.073972787 8.508778963 -0.929867242 1.016363161 EAEEGEDDRDSANGEDDS ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAEEGEDDRDSANGEDDS 18 1 P07910;G3V2Q1;P07910-3;P07910-2;G3V4C1;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ; 166.62 4.25E-10 86059000 253274 164805 227719 203071 173093 214939 260754 192694 165739 FALSE TRUE 237422.0324 177007.3337 233120.6022 208282.1457 159498.974 276988.4001 221656.3584 216752.2701 138076.0902 1.719501415 1.281954996 1.688348808 1.508459179 1.155152741 2.006056224 1.605320357 1.569803069 1 17.07510399 3.948809541 24.31371562 1.552104247 1.471434342 0 0.29618207 1596.248858 1370837.142 0.069421531 0.125190681 8888.112456 -3.948809541 -0.080669905 EAEEGPTGASESQDS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAEEGPTGASESQDSPR 17 0 H0Y507;Q5TCZ1-2;Q5TCZ1-3;Q5TCZ1 H0Y507 SH3PXD2A SH3 and PX domain-containing protein 2A 1 EAEEGPTGASESQDS(1)PR 178.06 1.04E-09 123820000 71820 90457 73321 86933 100240 49461 74732 64765 36442 TRUE FALSE 67324.9144 97154.5304 75060.20874 89163.84796 92367.55475 63739.58777 63526.63038 72851.05282 30359.59478 2.217582774 3.20012606 2.472371891 2.936924838 3.042450185 2.099487435 2.092472935 2.399605573 1 14.88986491 0.682164084 0.479924219 0.930190136 2.828332163 0.676115405 0.356039517 0.841729559 0.412108162 0.496909151 0.192513325 4.810210527 -0.682164084 1.898142027 EAEEVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAEEVYR 7 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 167.82 0.0024937 485230000 441890 453270 450500 463200 478820 392860 537570 391920 520230 FALSE TRUE 414232.8937 486830.5824 461186.0727 475086.4962 441215.4087 506272.3045 456966.3691 440852.0747 433400.2522 0.955774464 1.123281724 1.064111224 1.096184171 1.018032192 1.168140309 1.05437495 1.017193858 1 18.72534047 1.277409636 3.97965506 1.005505654 1.077555625 0.156040533 0.057214624 0.315750485 9.262905007 0.041691551 0.012837123 18.94129359 -1.277409636 0.072049971 EAEGSSAEYKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EAEGSSAEYKK 11 1 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 ;; 177.93 1.25E-05 2229550000 3122790 2141370 2397030 2358390 2845140 1828950 3201980 2213610 3531290 FALSE TRUE 2927340.148 2299919.263 2453888.684 2418910.28 2621694.181 2356938.174 2721872.825 2489984.081 2941894.886 0.995052598 0.78178159 0.83411841 0.822228657 0.891158346 0.801163286 0.925210767 0.846387848 1 21.48831427 0.196715602 0.573883725 1.007652073 0.844011112 0.292265387 0.064058061 3.257774803 1.468816521 0.118436035 0.02514691 1.572952478 -0.196715602 -0.163640961 EAEHLSSPWGES(ph)SPEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAEHLSSPWGESSPEELR 18 0 Q6PJI9-4;Q6PJI9-3;Q6PJI9;H3BNY4 Q6PJI9-4 WDR59 WD repeat-containing protein 59 1 EAEHLSSPWGES(0.5)S(0.5)PEELR 76.614 0.0096244 90300000 74427 189430 180960 163800 165090 184460 193770 189490 138910 TRUE FALSE 69768.74693 203455.5943 185252.4567 168003.3853 152124.4973 237710.6075 164715.9874 213148.2436 115725.0236 0.602883843 1.758095077 1.600798608 1.451746391 1.314534166 2.054098588 1.423339415 1.841850941 1 16.82034133 4.744579835 24.82639687 1.589933902 0.602883366 0.506115324 0.294018874 445.963535 1839329.442 0.060721875 0.554372742 55536.66985 -4.744579835 -0.987050536 EAELDVNEELDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAELDVNEELDKK 13 1 P43034;I3L495 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ; 179.56 2.19E-05 210052000 571570 282800 372520 369850 409430 274110 550430 339900 614950 FALSE TRUE 535796.454 303738.8063 381356.3503 379340.9772 377275.0194 353241.1072 467898.1314 382337.2632 512310.8723 1.045842443 0.592879876 0.744384652 0.740450765 0.736418139 0.689505389 0.913309002 0.746299335 1 18.96665998 0.689523109 0.658324116 0.999587069 0.737652842 0.206819389 0.126628324 1.54460826 1.313717925 0.124271293 0.045770552 4.892412974 -0.689523109 -0.261934227 EAELTEINRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EAELTEINRR 10 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 0 ;; 180.07 3.27E-06 848880000 659969 792803 672106 635891 814313 630102 762750 644676 883860 FALSE TRUE 618662.7184 851502.959 688048.6717 652209.0396 750360.1418 812002.2185 648382.7185 725165.2177 736338.056 0.840188434 1.156402215 0.934419546 0.885746749 1.019043 1.102757371 0.88055033 0.984826483 1 19.49000874 1.709398878 25 0.946816654 0.999740865 0.018011823 0.098268744 2.490532557 2123.882052 0.043537231 0.024143585 51.21520056 -1.709398878 0.052924211 EAEMEEHR ddPTM_SK-BR-3_Pertuzumab_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 ;;;; 175.91 0.0002634 1795000000 1578718 1506836 1837552 1532571 1431605 1463568 1871850 1522585 1362226 FALSE TRUE 1479908.858 1618403.705 1881139.601 1571899.366 1319172.518 1886076.323 1591183.47 1712683.089 1134861.68 1.304043377 1.426080141 1.657593726 1.385102162 1.162408196 1.66194379 1.402094632 1.509155802 1 20.11408504 -1.071997208 4.78315036 1.000018283 1.453387492 0.454203246 0.150302721 2.51E-05 4.87E-06 0.138147203 0.032560424 0.084723286 1.071997208 0.453369209 EAEMEEHREHIK ddPTM_SK-BR-3_Pertuzumab_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 0 122.42 0.00051545 420520000 426110 439550 421280 444860 516050 327060 524950 405370 733230 FALSE TRUE 399440.5357 472094.7394 431272.9605 456275.8607 475521.5146 421476.9126 446238.6209 455981.3368 610849.1762 0.653910247 0.772849924 0.706022006 0.746953386 0.778459779 0.689985235 0.730521769 0.746471232 1 19.22045668 0.597050699 2.842664191 0.999997464 0.729218583 0.841854676 0.037110262 2.085738749 14.29262374 0.03177899 0.008352804 3.954127777 -0.597050699 -0.270778881 EAENPEGEEKEAATLEVERPLPMEVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EAENPEGEEKEAATLEVERPLPMEVEK 27 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;; 182.95 8.50E-18 651710000 418990 259426 307445 306483 398590 243704 434710 264403 619020 FALSE TRUE 392766.1638 278634.171 314737.7406 314347.8727 367286.3492 314057.3886 369529.2711 297414.2966 515701.563 0.761615229 0.540301195 0.610309844 0.609553849 0.712207167 0.60899057 0.71655643 0.57671785 1 18.97617689 -5 0.3272899 4.624806745 0.620763959 0.706903284 0.071379265 174.938414 1.523216144 440.5904083 0.056238025 1.00E-05 5 -4.004042786 EAEQEAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 74128000 168923 217193 195505 214486 207205 175662 205293 180511 171842 FALSE TRUE 158350.411 233274.1957 200142.4709 219990.0739 190931.9551 226372.7678 174511.2205 203048.1957 143160.4601 1.106104373 1.629459668 1.398028973 1.536667833 1.333691964 1.581252028 1.218990358 1.418325951 1 17.12727356 0.358992704 0.627756729 0.987695986 1.448963262 0.371743704 0.161194502 2.042421135 1.21923536 0.204496811 0.057170357 2.285560405 -0.358992704 0.461267276 EAEQEAARR ddPTM_SK-BR-3_Pertuzumab_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 ; 102.52 0.0057253 299070000 241250 461930 385130 441550 450100 359750 370130 389990 473380 FALSE TRUE 226150.5931 496131.7778 394265.4655 452880.9205 414750.9616 463603.9849 314632.4426 438681.11 394369.8198 0.573448022 1.25803688 0.99973539 1.148366071 1.051680278 1.175556449 0.797810651 1.112359739 1 18.58918962 1.751674561 25 0.951507365 1.061301783 0.008276245 0.198065933 11.47658499 21911.67741 0.082102084 0.045529889 56.45137976 -1.751674561 0.109794418 EAESAKHS(ph)PEKGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAESAKHSPEKGK 13 2 J3KN75;Q0IIM8 J3KN75 TBC1D8B TBC1 domain family member 8B 1 EAES(0.004)AKHS(0.996)PEKGK 52.254 0.080297 26528000 97813 49567 62528 71006 76155 44188 90985 54211 102920 TRUE FALSE 91691.05893 53236.99225 64011.19369 72828.13417 70174.09349 56944.35827 77342.64391 60979.36268 85741.98711 1.069383414 0.620897579 0.746555986 0.849387058 0.818433254 0.664136209 0.902039322 0.711196052 1 16.38771423 -1.66888893 2.89074944 1.024011989 0.782432506 0.188054464 0.128614361 81510474.52 79643655.69 14484302.67 0.028342767 0.021434387 1.66888893 -0.241579482 EAESSPFVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAESSPFVER 10 0 P14625 P14625 HSP90B1 Endoplasmin 0 ; 193.01 1.44E-06 1090360000 517960 628120 569400 613200 547160 463900 650470 496150 428950 FALSE TRUE 485541.8082 674626.6584 582906.4369 628935.7501 504188.2607 597820.3992 552938.0622 558095.4197 357355.4739 1.358708187 1.887830767 1.631166946 1.759972342 1.410887191 1.672901195 1.547305422 1.561737431 1 18.44700036 -1.764730046 0.299469623 0.412616375 1.692736288 0.598139059 0.154834997 16.64556348 0.850020682 7.151874714 0.150407558 0.017189766 1.764730046 1.280119913 EAETDEIKILLEESRAQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAETDEIKILLEESRAQQK 19 2 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 0 49.559 0.090523 1537000000 454790 666050 570680 543770 723090 419860 719940 592320 918960 FALSE TRUE 426325.5057 715365.035 584216.7991 557724.0588 666301.4282 541066.7661 611991.6806 666272.4559 765579.6393 0.556866306 0.934409692 0.763103888 0.728499075 0.870322817 0.706741322 0.799383433 0.870284973 1 19.54619294 0.955009602 2.384751141 0.999197849 0.781405437 0.362433354 0.100345588 0.360841293 4.608793381 0.086449771 0.023470549 9.015910706 -0.955009602 -0.217792412 EAETEPHEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAETEPHEGK 10 0 P41223;P41223-2 P41223 BUD31 Protein BUD31 homolog 0 ; 130.98 0.00026219 424360000 1351540 994800 1118120 1103120 1087120 916430 1402000 992850 958500 FALSE TRUE 1266949.524 1068456.027 1144642.334 1131427.927 1001741.98 1180988.464 1191783.116 1116809.508 798520.1579 1.586621842 1.338045153 1.433454526 1.416905905 1.254498049 1.478971385 1.492489706 1.398599017 1 19.6069693 0.944939811 22.46125991 1 1.421680675 0.695092104 0.088573941 3458.589584 1410899.525 0.080379898 0.020094975 8.809267776 -0.944939811 0.421680676 EAFAQRPSS(ph)APDLMCLSPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAFAQRPSSAPDLMCLSPDR 20 1 P30305;G8JLH2;B4DIG0;P30305-3;P30305-2;P30305-4 P30305 CDC25B M-phase inducer phosphatase 2 1 EAFAQRPS(0.357)S(0.643)APDLMCLSPDR;EAFAQRPS(0.355)S(0.645)APDLMCLSPDR 190.5 1.09E-17 262760000 120529 122935 133229 104498 121872 131546 168727 124172 138874 TRUE FALSE 112985.305 132037.2353 136389.2548 107179.5956 112300.6647 169521.1947 143427.9527 139675.1475 115695.0322 0.976578707 1.141252418 1.178868722 0.92639756 0.970661078 1.465241778 1.239707099 1.207270052 1 16.81996739 2.263041928 24.99977685 1.254896311 1.06672894 0.303833294 0.136175774 269.9333489 275649.1388 0.045749178 0.038259821 183.2491326 -2.263041928 -0.188167372 EAFDEVDMAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAFDEVDMAHR 11 0 Q9NX46 Q9NX46 ADPRHL2 Poly(ADP-ribose) glycohydrolase ARH3 0 108.37 0.0020718 201510000 285140 261500 237680 262460 275890 227590 271120 214490 336650 FALSE TRUE 267293.5964 280861.7321 243317.8818 269195.1679 254222.7123 293291.5384 230468.073 241269.5487 280460.9402 0.95305106 1.001429047 0.867564238 0.959831226 0.906446053 1.045748254 0.821747488 0.860260785 1 18.09744033 1.716826654 24.99999572 0.880128248 0.949057694 0.148338333 0.065703923 1.390732374 1593.170857 0.02778497 0.01540816 52.09867204 -1.716826654 0.068929446 EAFEETHLTSLDPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAFEETHLTSLDPVK 15 0 J3QQZ9;Q9NVS9-3;Q9NVS9;Q9NVS9-4;A0A286YFL3 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 ; 194.59 4.51E-08 412520000 1128390 1179010 1217340 1218070 1391330 898250 1503360 1223510 1403850 FALSE TRUE 1057766.084 1266305.127 1246215.88 1249327.738 1282060.554 1157560.193 1277945.125 1376267.917 1169538.366 0.904430427 1.082739279 1.065562205 1.068222963 1.096210771 0.989758205 1.092691922 1.176761667 1 20.15750776 4.740753173 24.61826911 1.072317857 0.904430356 0.507073596 0.051759557 124.4349175 1397054.02 0.011187168 0.073586117 55049.47397 -4.740753173 -0.167887501 EAFGFIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAFGFIER 8 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0;E9PNG3 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ; 85.161 0.039408 160436000 125747 182795 143393 144029 202767 134340 170155 165660 155494 FALSE TRUE 117876.7197 196329.332 146794.3497 147725.028 186842.4977 173121.7772 144641.8374 186343.0157 129541.0469 0.909956516 1.515576234 1.133187922 1.14037235 1.44234204 1.336424102 1.116571472 1.438486257 1 16.98304978 -0.524997031 7.629240429 1 1.261772843 0.155172743 0.185577826 0 0 0.160168546 0.037752088 0.298540303 0.524997031 0.261772843 EAFNMIDQNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EAFNMIDQNR 10 0 J3QRS3;P19105;O14950;J3KTJ1;P24844-2;P24844 J3QRS3;P24844 MYL12A;MYL12B;MYL9 Myosin regulatory light chain 12A;Myosin regulatory light chain 12B;Myosin regulatory light polypeptide 9 0 ;;;;; 195.58 8.12E-07 2402520000 1738850 1939230 1874880 1848290 1978710 1569910 2098690 1700000 1776500 FALSE TRUE 1630018.482 2082812.607 1919353.039 1895720.251 1823310.098 2023117.532 1784010.918 1912248.742 1479990.673 1.10137078 1.407314684 1.296868334 1.280900133 1.231974046 1.36697992 1.205420379 1.292068103 1 20.49715665 -0.993009445 0.462834137 0.898925596 1.296253165 0.487735392 0.08593887 13.1675019 1.834988557 1.86360337 0.04125518 0.101622659 0.993009445 0.397327569 EAFQLFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EAFQLFDR 8 0 P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;G3V1Y7;P60660-2;G8JLA2 P60660;P60660-2 MYL6 Myosin light polypeptide 6 0 ;;;;;;; 217.66 1.70E-05 8018640000 4081990 5825310 4391750 4416160 6018620 3475060 4666160 4844330 5297730 FALSE TRUE 3826505.532 6256622.014 4495924.384 4529486.142 5545941.863 4478253.409 3966512.627 5449155.264 4413504.638 0.866999323 1.417608573 1.018674444 1.026278777 1.256584578 1.014670602 0.898721753 1.234654931 1 22.07349328 2.828289054 0.810586588 1.026446589 1.165438807 0 0.173213597 1.672778475 2.393421938 0.104090971 0.110059884 673.424719 -2.828289054 0.138992218 EAFSLFDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EAFSLFDK 8 0 P0DP25;P0DP24;P0DP23;E7EMB3;M0QZ52;F8WBR5;G3V479;P27482 P0DP25 CALM2;CALM3;CALM1;CALML3 Calmodulin-like protein 3 0 ;; 122.52 0.0074173 11563000 413613 362094 384069 371429 380835 294970 420902 354118 363470 FALSE TRUE 387725.7007 388903.8165 393179.2981 380960.497 350925.7553 380123.0506 357791.6526 398330.4118 302804.5089 1.280448901 1.284339582 1.298459192 1.258107082 1.158918527 1.255341448 1.181592883 1.315470543 1 18.20802716 -4.791593683 0.193766929 3.71E-14 1.298414536 0.707747073 0.050669294 65.51886728 0.693465473 25.42581659 0.123566228 1.62E-05 4.791593683 1.298414536 EAFSLFDKDGDGTITTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EAFSLFDKDGDGTITTK 17 1 P0DP25;P0DP24;P0DP23;E7EMB3;M0QZ52;F8WBR5;G3V479 P0DP25 CALM2;CALM3;CALM1 0 ;;;;; 264.23 1.70E-27 22435088000 11012440 7070279 8816681 8120522 8772120 6249697 11629500 7758957 11734740 FALSE TRUE 10323191.04 7593769.814 9025816.837 8328908.343 8083193.08 8053883.069 9885764.438 8727679.861 9776136.085 1.055958197 0.776765968 0.923249918 0.851963216 0.826829026 0.823830908 1.011213873 0.892753516 1 23.22083294 1.739815449 24.99999679 0.964073429 0.867485818 0.215084767 0.08114508 0.259273804 5177.647263 0.03376446 0.018724114 54.93073997 -1.739815449 -0.09658761 EAGDEFELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAGDEFELR 9 0 Q5QP56;Q9H1R6;Q5TE64;Q07817-2;Q07817-3;Q07817 Q5QP56 BCL2L1 Bcl-2-like protein 1 0 83.948 0.037223 0 98095 101080 87775 89905 91551 86676 119000 77329 132750 FALSE TRUE 91955.40905 108564.0684 89857.06445 92212.11451 84360.95376 111697.9541 101157.0547 86983.69587 110593.1674 0.831474595 0.981652582 0.812501048 0.833795764 0.762804391 1.009989647 0.914677255 0.786519619 1 16.75490273 2.233847222 24.99991678 0.923231939 0.858315541 0.193636184 0.08160796 254.7861244 1351373.899 0.02965119 0.02261624 171.335447 -2.233847222 -0.064916398 EAGDVCYADVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EAGDVCYADVYR 12 0 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;;; 265.04 3.19E-21 4149100000 2364230 2786510 2261730 2306040 2866550 1875180 2512370 2400040 3062180 FALSE TRUE 2216257.065 2992826.1 2315379.304 2365216.891 2641422.726 2416514.025 2135663.442 2699690.277 2551082.376 0.868751666 1.173159334 0.90760664 0.9271425 1.035412557 0.947250488 0.837159734 1.058252882 1 21.28267805 3.74410947 23.35525409 0.946723258 1.042004202 0.04573206 0.096769562 334.0970704 459307.5754 0.022972958 0.041247942 5547.655312 -3.74410947 0.095280944 EAGELPT(ph)SPLHLLS(ph)PGTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAGELPTSPLHLLSPGTPR 19 0 Q969R5;H7C228;Q969R5-2;Q969R5-3 Q969R5 L3MBTL2 Lethal(3)malignant brain tumor-like protein 2 2 EAGELPT(0.5)S(0.5)PLHLLS(0.976)PGT(0.024)PR;EAGELPT(0.5)S(0.5)PLHLLS(0.883)PGT(0.117)PR 79.013 0.016539 52323000 78132 79544 82346 77317 80229 78519 101343 82479 67183 TRUE FALSE 73241.85759 85433.52053 84299.28601 79301.08512 73928.13797 101186.1607 86147.55797 92776.68471 55969.72328 1.308597815 1.526423851 1.506158706 1.416856837 1.320859451 1.807873163 1.539181417 1.657622716 1 15.77235899 EAGELPT(ph)SPLHLLSPGTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAGELPTSPLHLLSPGTPR 19 0 Q969R5;H7C228;Q969R5-2;Q969R5-3 Q969R5 L3MBTL2 Lethal(3)malignant brain tumor-like protein 2 1 EAGELPT(0.535)S(0.465)PLHLLSPGTPR 70.942 0.076468 24066000 23643 23634 28331 28085 25755 28084 28503 22101 20079 TRUE FALSE 22163.22683 25383.88595 29003.0247 28805.70865 23732.30619 36191.39489 24229.23976 24860.3585 16727.68518 1.324942847 1.517477503 1.733833724 1.722037947 1.418744191 2.16356265 1.448451444 1.486180438 1 14.0299502 0.819160463 1.863231626 1.002889167 1.636944548 0.413619787 0.231654605 0.600441863 3.780206296 0.201972413 0.056649938 6.594174915 -0.819160463 0.634055381 EAGELPTS(ph)PLHLLS(ph)PGTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAGELPTSPLHLLSPGTPR 19 0 Q969R5;H7C228;Q969R5-2;Q969R5-3 Q969R5 L3MBTL2 Lethal(3)malignant brain tumor-like protein 2 2 EAGELPT(0.036)S(0.964)PLHLLS(1)PGTPR 145.65 6.51E-08 27074000 49274 45918 55033 51215 48353 41250 65042 45242 40232 TRUE FALSE 46190.0283 49317.8165 56338.40875 52529.26361 44555.55043 53158.20536 55289.55592 50890.56329 33517.01929 1.378106684 1.471426086 1.680889588 1.567241501 1.329341074 1.586006348 1.649596447 1.518349912 1 15.03260623 0.938654528 22.45580112 1 1.540079502 0.686391951 0.110568059 5481.091447 2006382.395 0.10699392 0.02674848 8.682694652 -0.938654528 0.540079503 EAGELPTS(ph)PLHLLSPGTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EAGELPTSPLHLLSPGTPR 19 0 Q969R5;H7C228;Q969R5-2;Q969R5-3 Q969R5 L3MBTL2 Lethal(3)malignant brain tumor-like protein 2 1 EAGELPT(0.021)S(0.979)PLHLLSPGTPR;EAGELPT(0.033)S(0.967)PLHLLSPGTPR;EAGELPT(0.025)S(0.975)PLHLLSPGTPR;EAGELPT(0.003)S(0.997)PLHLLSPGTPR;EAGELPT(0.009)S(0.991)PLHLLSPGTPR 232.82 1.03E-21 888345000 752045 765146 849622 829015 745953 688694 860189 658434 489999 TRUE FALSE 704975.8459 821798.206 869775.4351 850288.9284 687368.8604 887508.7778 731211.6451 740640.9343 408215.0014 1.726971923 2.013150431 2.130679745 2.082943854 1.683840276 2.174120928 1.791241484 1.814340315 1 18.63896968 0.259548113 0.75874987 0.981293222 1.992638798 0.760939063 0.165299199 1.237995533 0.915343169 0.201759351 0.052924476 1.81780843 -0.259548113 1.011345577 EAGENAPVLS(ph)DDELVSMSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EAGENAPVLSDDELVSMSVR 20 0 O60675 O60675 MAFK Transcription factor MafK 1 EAGENAPVLS(1)DDELVSMSVR;EAGENAPVLS(1)DDELVSMSVR;EAGENAPVLS(1)DDELVSMSVR;EAGENAPVLS(1)DDELVSMSVR 248.52 3.06E-30 240003000 447610 455337 468026 470259 475918 315457 490659 344333 471641 TRUE FALSE 419594.8891 489050.6253 479127.7977 482326.6421 438541.32 406524.3149 417089.238 387323.733 392921.0702 1.067885947 1.244653602 1.219399605 1.227540793 1.116105379 1.034620807 1.061508964 0.985754551 1 18.58388001 2.442755997 2.532061422 1.027519011 1.20392225 0.691457791 0.052754409 0.148535007 1.941989649 0.019413839 0.016010612 277.1762386 -2.442755997 0.17640324 EAGEQGDIEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EAGEQGDIEPR 11 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ;;; 248.09 8.06E-16 2035770000 1606450 1816080 1764470 1707180 1799010 1535500 1930140 1542730 2040200 FALSE TRUE 1505905.162 1950544.453 1806324.062 1750989.129 1657723.011 1978773.923 1640733.426 1735343.236 1699677.44 0.885994676 1.147596836 1.062745212 1.030189075 0.975316241 1.164205559 0.96532047 1.020983862 1 20.69682955 1.620071754 25 0.994863055 1.055867584 0.064506797 0.08012892 1.703500731 3480.773813 0.034601333 0.019008572 41.69382644 -1.620071754 0.061004529 EAGITEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAGITEK 7 0 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3 P60174 TPI1 Triosephosphate isomerase 0 85.212 0.048802 207480000 347400 336360 314630 332860 369920 250010 407830 313920 495450 FALSE TRUE 325656.8541 361264.4444 322093.1722 341401.7511 340867.9754 322183.8284 346679.6776 353113.603 412756.1943 0.788981143 0.875248995 0.780347277 0.827126899 0.825833701 0.780566913 0.839913931 0.855501645 1 18.65493034 0.675517339 1.564287464 0.999855668 0.81772319 0.801579131 0.028608252 0.493040145 1.781419237 0.025452645 0.007334579 4.737152204 -0.675517339 -0.182132478 EAGLAHLCEFIEDCEHTVLATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAGLAHLCEFIEDCEHTVLATK 22 0 Q9UBF2;Q9UBF2-2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 ; 282.75 5.21E-46 112235000 155712 134121 147661 148859 155955 154306 242540 143033 211130 FALSE TRUE 145966.2639 144051.4584 151163.5887 152678.974 143706.9234 198851.6373 206173.3786 160890.9849 175891.039 0.82986754 0.818981224 0.859416088 0.868031565 0.817022426 1.13053876 1.172165335 0.914719623 1 17.42432246 2.242225912 24.99997863 1.081996721 0.840144522 0.678984006 0.072594037 46.44592957 316797.1069 0.024695914 0.019916942 174.6730536 -2.242225912 -0.241852199 EAGS(ph)PAQEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EAGSPAQEFK 10 0 Q5JSZ5;Q5JT00;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 EAGS(1)PAQEFK;EAGS(1)PAQEFK;EAGS(1)PAQEFK;EAGS(1)PAQEFK 202.29 2.37E-07 1509260000 3347690 2138810 2716930 2557150 2884030 2113030 3359820 2529290 3592780 TRUE FALSE 3138164.059 2297169.718 2781376.863 2622770.798 2657529.917 2723027.459 2856046.182 2845077.424 2993121.808 1.048458519 0.767482871 0.929256155 0.876265975 0.887878973 0.909761658 0.954203125 0.95053847 1 21.51321956 1.529988278 0.941959443 0.994222731 0.883663143 0.153976063 0.06936641 0.714385054 1.25229492 0.057532616 0.022030307 33.88350102 -1.529988278 -0.110559587 EAGSQKDENLALYVENQFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAGSQKDENLALYVENQFR 19 1 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ; 183.06 2.55E-14 314360000 380080 348610 343040 331910 430690 239790 361500 371710 547550 FALSE TRUE 356291.4713 374421.4471 351177.0708 340427.3725 396865.3447 309013.4803 307296.431 418118.8117 456160.3677 0.781066258 0.820810999 0.76985441 0.746288798 0.870012769 0.677422903 0.673658767 0.916604864 1 18.79918158 1.050210844 5.649492882 0.99916276 0.764130406 0.669939379 0.058628077 0.103569427 6.84305993 0.05980556 0.01506966 11.22563312 -1.050210844 -0.235032354 EAGVFVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EAGVFVPR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;;; 158.36 0.0008502 1319200000 1533710 1776760 1614330 1617550 1857480 1438950 1788140 1627230 1753930 FALSE TRUE 1437717.829 1908313.159 1652622.67 1659059.072 1711601.014 1854351.506 1520025.007 1830393.247 1461187.752 0.983937777 1.306001338 1.131013224 1.135418134 1.171376513 1.269071345 1.040266732 1.252674918 1 20.47871014 -1.731928897 2.735297898 0.969248286 1.166427559 0.204710629 0.099395127 12796318.23 12063627.77 2704318.31 0.022185898 0.018538351 1.731928897 0.197179273 EAHEPLAVADAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAHEPLAVADAK 12 0 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 0 129.71 0.00022946 630600000 1634200 1237600 1370700 1439200 1528600 997550 1864700 1310500 1887400 FALSE TRUE 1531918.339 1329233.192 1403213.651 1476132.309 1408549.922 1285526.491 1585105.546 1474118.81 1572380.747 0.974266788 0.845363437 0.892413402 0.938788084 0.895807154 0.817566924 1.008092696 0.937507542 1 20.58451917 1.684752173 9.843534748 0.978772024 0.89012989 0.434820651 0.046932493 0.102679991 15.51023023 0.020803117 0.011197447 48.38961567 -1.684752173 -0.088642134 EAHLEKEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAHLEKEEK 9 1 A0A1W2PRI9;E9PNW5 A0A1W2PRI9 C4orf50 0 61.78 0.052234 163490000 1043300 349840 486030 424050 450760 331480 524220 349140 608950 FALSE TRUE 978001.7153 375742.5176 497558.8611 434931.8409 415359.1279 427172.8949 445618.0776 392730.8976 507312.311 1.927809939 0.740653261 0.980774269 0.857325619 0.818744428 0.842031399 0.878390033 0.774140286 1 18.95251465 4.742455438 24.99497136 0.859849974 1.927810352 0.945569913 0.080399043 74.01165456 474950.1108 0.017254405 0.131152762 55265.66976 -4.742455438 1.067960377 EAHLPPGAMAAVGLSWEECK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 232.54 2.36E-26 3233263000 4369251 3695461 4223786 4072627 4760518 3964798 6597570 3939527 5661200 FALSE TRUE 4095787.379 3969076.778 4323976.199 4177137.504 4386646.119 5109370.819 5608325.627 4431385.618 4716309.147 0.868430642 0.841564167 0.916813564 0.885679325 0.93010148 1.083340947 1.189134438 0.939587605 1 22.16922686 2.329689139 3.671582285 1.082993968 0.880723677 0.582500138 0.068246459 0.134875405 3.533019004 0.024391222 0.019592038 213.643232 -2.329689139 -0.202270292 EAHQLFLEPEVLDPESVELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EAHQLFLEPEVLDPESVELK 20 0 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 ;;;;; 229.86 2.07E-25 1219154000 2850930 2177522 2511510 2274030 2662660 1997593 2945960 2216830 3685760 FALSE TRUE 2672495.38 2338747.995 2571084.203 2332385.46 2453545.424 2574265.671 2504240.647 2493606.105 3070582.845 0.870354429 0.761662561 0.837327743 0.759590468 0.799048763 0.838363855 0.81555873 0.812095368 1 21.5500811 -1.797650726 0.463890335 1.15729424 0.80468527 0.752488573 0.033865589 21.77930138 1.80979973 3.802314177 0.015720618 0.015934897 1.797650726 -0.35260897 EAHS(ph)PGPLVKPFETASVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAHSPGPLVKPFETASVK 18 1 P35548;D6RIS4 P35548 MSX2 Homeobox protein MSX-2 1 EAHS(1)PGPLVKPFETASVK;EAHS(1)PGPLVKPFETASVK 249.34 7.25E-25 478020000 732560 558200 624220 582310 730980 527890 856870 634860 893550 TRUE FALSE 686710.3773 599529.7088 639026.7932 597253.0604 673571.7794 680283.2734 728390.2983 714123.6685 744410.7324 0.92248855 0.805374886 0.858433074 0.802316563 0.904838888 0.913854736 0.978479039 0.959314042 1 19.50573933 2.146213196 1.449284797 0.980756805 0.842467583 0.700806873 0.036645758 0.198973735 0.801029116 0.0205762 0.011136173 140.0274551 -2.146213196 -0.138289221 EAIEGTYIDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAIEGTYIDKK 11 1 P62280;M0QZC5 P62280 RPS11 40S ribosomal protein S11 0 99.539 0.007536 3001400000 2626800 1252200 1710400 1852100 2039300 1815900 2850800 1641400 2740100 FALSE TRUE 2462393.277 1344914.191 1750971.496 1899628.022 1879141.604 2340120.851 2423349.006 1846332.403 2282759.608 1.078691452 0.589161551 0.767041562 0.832162973 0.823188564 1.025128026 1.061587474 0.80881596 1 21.12234751 2.360171682 3.921810785 0.989285256 0.774728322 0.210627835 0.137437613 0.248427704 7.123388114 0.048082215 0.039310821 229.1773442 -2.360171682 -0.214556934 EAIHSQLLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EAIHSQLLEK 10 0 O60925;E5RGS4 O60925 PFDN1 Prefoldin subunit 1 0 ;; 168.22 5.00E-06 1092420000 2382890 2463290 2487360 2468780 2926400 1856700 2889870 2421110 3233300 FALSE TRUE 2233749.168 2645674.555 2546361.354 2532133.074 2696572.349 2392699.149 2456560.822 2723390.913 2693641.342 0.82926748 0.982192586 0.945323089 0.940040916 1.001088121 0.888276814 0.91198512 1.01104437 1 21.36112634 -0.899071822 0.00797151 1.951105945 1.41E-06 0.20888023 0.051043552 17964.65141 28.61776587 3661.705868 3346.322895 0.126161888 0.899071822 -1.951104534 EAILAIHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAILAIHK 8 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 94.302 0.010456 301580000 802820 812610 580130 507300 710780 395820 667440 816580 749030 FALSE TRUE 752572.9293 872776.4899 593890.9576 520318.1769 654958.2059 510086.8084 567363.5682 918531.8105 624012.0541 1.206023064 1.398653254 0.951729944 0.833827125 1.049592234 0.817431018 0.909218924 1.471977672 1 19.25121437 3.904626317 3.838473849 0.980983556 1.301549816 0.293304286 0.188562917 0.235912771 6.742405661 0.046245797 0.091340007 8028.350358 -3.904626317 0.32056626 EAILEYILHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAILEYILHQK 11 0 Q9Y314;A0A075B6F9;M0R3B2;A0A075B797;M0R1K2;M0QX85 Q9Y314 NOSIP Nitric oxide synthase-interacting protein 0 152.85 3.27E-05 79136000 283610 266050 292030 278000 343250 256140 344780 293550 492900 FALSE TRUE 265859.3564 285748.6188 298957.0895 285133.9507 316292.5296 330083.4599 293083.4398 330200.3637 410631.8057 0.647439757 0.695875514 0.728041728 0.69437863 0.770258234 0.803842896 0.713737795 0.804127588 1 18.64748585 -5 0.148128771 1.982297664 0.640067275 0.887206437 0.032789702 42.17420006 0.373501572 12.13489524 0.168642182 1.00E-05 5 -1.34223039 EAKPDELMDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAKPDELMDSK 11 1 Q9P0L0-2;Q9P0L0 Q9P0L0-2 VAPA Vesicle-associated membrane protein-associated protein A 0 113.65 0.0012434 116140000 404470 222400 211850 229110 310870 159500 361860 243020 422250 FALSE TRUE 379154.9447 238866.7274 216875.182 234989.3505 286455.5242 205545.0607 307602.4523 273361.582 351773.7472 1.077837524 0.679035117 0.616518952 0.668012756 0.814317517 0.584310405 0.874432657 0.777094892 1 18.42428829 0.842276275 1.02011698 0.996186678 0.722770439 0.199356608 0.144402494 0.989620152 2.02411106 0.127386669 0.041397431 6.95466596 -0.842276275 -0.273416239 EAKPEAPAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAKPEAPAAK 10 1 O75363;G3XAF7;O75363-2 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 76.522 0.032598 325790000 494840 359380 367970 426780 444570 276280 474070 404550 551660 FALSE TRUE 463868.8477 385988.8691 376698.4222 437731.8973 409655.2655 356037.551 402987.6046 455058.958 459584.3821 1.009322479 0.83986507 0.819650181 0.952451637 0.891360284 0.774694626 0.876852261 0.990153225 1 18.80997025 1.239382617 6.122580986 0.997356447 0.868187801 0.329385316 0.066240247 0.146500949 21.28020957 0.051076794 0.015541673 17.35332167 -1.239382617 -0.129168647 EALAEAALES(ph)PRPALVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 275.02 6.32E-36 31241260000 3884320 3741310 4088560 4285930 4564670 3939400 4591080 3620610 4722220 TRUE FALSE 3641207.345 4018320.485 4185542.574 4395914.22 4206179.231 5076640.829 3902690.175 4072651.128 3934050.975 0.925561811 1.021420543 1.063926878 1.117401439 1.069172529 1.290435955 0.99202837 1.035230899 1 21.90758422 4.860285873 0.989138319 1.089124767 0.813428041 0.260601374 0.083478254 3.155253756 2.104722123 0.024432565 0.978688396 72491.29753 -4.860285873 -0.275696726 EALAEAALESPRPALVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EALAEAALESPRPALVR 17 1 O14745;O14745-2;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;; 285.59 2.33E-36 2546100000 1688630 1923630 1783560 1847320 2090500 1568060 2088200 1732850 2336420 FALSE TRUE 1582941.663 2066057.567 1825866.885 1894725.359 1926320.563 2020733.467 1775093.796 1949200.137 1946456.408 0.813242802 1.061445588 0.938046636 0.97342296 0.989655126 1.038160145 0.911961752 1.001409602 1 20.8924186 4.755473247 24.74300843 0.984692916 0.813242645 0.618548981 0.043308721 2062.928945 3017988.032 0.009945505 0.279790718 56947.31427 -4.755473247 -0.171450271 EALAPNSLS(ph)PSPQGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EALAPNSLSPSPQGHR 16 0 B4DF95;Q15735;B5MCL8;B5MBZ3;A0A087WVS7;Q15735-3;Q15735-2 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 EALAPNSLS(1)PSPQGHR;EALAPNS(0.002)LS(0.997)PS(0.001)PQGHR 198.35 2.64E-11 519480000 230541 373580 396670 395960 461150 387790 400000 369800 628820 TRUE FALSE 216111.8503 401240.2519 406079.1997 406121.004 424933.1392 499738.6778 340023.7134 415970.344 523865.8797 0.412532785 0.765921713 0.77515871 0.77523851 0.811148723 0.953943933 0.649066348 0.794039773 1 18.99883797 4.753537053 3.463896807 0.799118258 0.35776126 0.61868034 0.099032909 0.214413752 4.331652327 0.021844675 0.253552616 56693.99392 -4.753537053 -0.441356999 EALAPNSLSPS(ph)PQGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EALAPNSLSPSPQGHR 16 0 B4DF95;Q15735;B5MCL8;B5MBZ3;A0A087WVS7;Q15735-3;Q15735-2 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 EALAPNSLSPS(1)PQGHR 104.35 0.00088126 255620000 57003 60098 61423 58203 74425 51085 60026 55133 101790 TRUE FALSE 53435.28398 64547.71845 62879.98257 59696.58752 68579.96072 65832.4102 51025.65855 62016.47641 84800.59141 0.630128671 0.761170617 0.741504057 0.703964283 0.808720312 0.776320178 0.601713475 0.731321272 1 16.37178671 -1.757494643 2.673928399 1.062693783 0.720944476 0.662398447 0.062956291 9129999.488 7051150.71 3770200.231 0.015865737 0.017478548 1.757494643 -0.341749307 EALASLPSS(ph)PGLLQSLLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EALASLPSSPGLLQSLLER 19 0 P41229-4;P41229-3;P41229-2;P41229-5;P41229 P41229-4 KDM5C Lysine-specific demethylase 5C 1 EALASLPS(0.006)S(0.994)PGLLQSLLER;EALASLPS(0.153)S(0.847)PGLLQSLLER;EALASLPS(0.006)S(0.994)PGLLQSLLER;EALASLPS(0.005)S(0.995)PGLLQSLLER 219.23 3.34E-19 325173000 355542 423185 398265 463358 448107 329902 476396 388008 321212 TRUE FALSE 333289.2609 454518.0577 407712.0339 475248.5507 412914.4838 425139.3519 404964.8424 436451.6529 267599.6421 1.24547723 1.698500245 1.523589608 1.775968559 1.543030778 1.588714202 1.513323558 1.630987431 1 18.02971666 -1.402826888 3.27760246 0.993661679 1.575289554 0.617690263 0.139469184 15055717.62 23248437.76 922817.6635 0.029111598 0.039552425 1.402826888 0.581627875 EALDTIDVQGHPQTGMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EALDTIDVQGHPQTGMR 17 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 175.39 1.23E-09 327600000 147260 163030 169730 141990 173620 132270 167800 129900 153630 FALSE TRUE 138043.2595 175100.9108 173756.0758 145633.7038 159984.5855 170454.2018 142639.9478 146118.3009 127988.1605 1.078562727 1.36810241 1.357594914 1.137868559 1.249995194 1.331796637 1.114477677 1.141654825 1 16.96565083 1.252320769 0.969702318 1.004480972 1.279037724 0.384100321 0.098662804 0.450458562 0.899890736 0.089843902 0.031509174 17.87807556 -1.252320769 0.274556751 EALEALVPVTIEVEVPFDLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EALEALVPVTIEVEVPFDLHR 21 0 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 ;;;; 181.34 5.07E-17 550378000 754244 860316 863299 853517 933580 790156 846959 718846 824459 FALSE TRUE 707037.2144 924014.6918 883776.86 875419.6912 860260.3927 1018261.21 719965.3607 808595.5055 686851.4667 1.029388811 1.345290411 1.286707393 1.274540033 1.252469325 1.482505694 1.048211143 1.177249441 1 19.38963862 1.630922602 12.50995798 1.084616296 1.285232324 0.393343372 0.118516361 0.100198341 40.5250308 0.050913932 0.027455941 42.74866942 -1.630922602 0.200616028 EALEAYRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EALEAYRR 8 1 Q9NRF9 Q9NRF9 POLE3 DNA polymerase epsilon subunit 3 0 80.684 0.039786 251030000 123120 209660 144050 157670 203250 125160 154330 168360 190680 FALSE TRUE 115414.139 225183.4446 147466.934 161716.0791 187287.5649 161291.6602 131189.6492 189380.1166 158854.2762 0.726540964 1.417547264 0.928315797 1.018015272 1.17898976 1.015343522 0.825849026 1.192162535 1 17.2773444 2.007893057 24.37168245 0.970139374 1.085756886 0 0.196693662 373.623131 1153643.323 0.069014236 0.050867073 101.8340595 -2.007893057 0.115617511 EALEEFYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EALEEFYGR 9 0 Q9H2P9-6;Q9H2P9-4;Q9H2P9;Q9H2P9-5;Q9H2P9-3;Q9H2P9-2 Q9H2P9-6 DPH5 Diphthine synthase 0 ; 116.25 0.0031272 209411000 136958 147135 139299 150553 139007 115482 162345 116703 156412 FALSE TRUE 128386.0433 158029.0285 142603.2381 154416.4449 128089.9509 148819.7787 138002.8744 131273.6264 130305.8267 0.985267094 1.212754889 1.094373457 1.185031005 0.982994807 1.142080768 1.059069098 1.007427141 1 16.99154207 1.544662373 0.704983087 0.994227297 1.124504704 0.187124423 0.075382773 0.853241998 0.905208615 0.063993535 0.029340303 35.04793 -1.544662373 0.130277407 EALEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EALEHK 6 0 Q9NYL9 Q9NYL9 TMOD3 Tropomodulin-3 0 ;; 83.287 0.057159 960140000 1240260 1074170 1180130 1206850 1271510 984280 1393720 1066440 1349630 FALSE TRUE 1162634.341 1153702.664 1208123.241 1237819.814 1171650.734 1268425.658 1184744.625 1199587.382 1124368.034 1.034033613 1.026089883 1.074490918 1.100902709 1.042052689 1.128123194 1.053698245 1.066899223 1 20.10068291 3.964002063 3.243160266 1.071730409 1.030469997 0.151926434 0.034095022 0.345814128 7.496933624 0.007838111 0.017139063 9204.539433 -3.964002063 -0.041260412 EALEVDWSSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EALEVDWSSEK 11 0 Q9UBE0;M0QX65;B3KNJ4;Q9UBE0-2;Q9UBE0-3;M0QZS6 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 ; 138.25 0.002223 0 148114 167170 167754 170429 201812 154432 183291 162988 193051 FALSE TRUE 138843.8091 179547.4407 171733.2041 174802.4967 185962.4996 199014.0114 155808.2161 183337.4106 160829.5409 0.863297926 1.116383468 1.067796395 1.08688053 1.156270785 1.237421995 0.968778591 1.139948603 1 17.2951729 4.741624863 24.34909796 1.09640671 0.863297801 0.480929763 0.076198919 173.3704681 1377533.904 0.016975643 0.120007515 55160.07688 -4.741624863 -0.233108908 EALGLGPPAAQLT(ph)PPPAPVGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 238.93 1.60E-29 358522000 391801 380611 410519 466705 551497 365328 399285 339304 436620 TRUE FALSE 367278.8748 408791.8345 420256.7045 478681.4404 508184.6503 470792.263 339415.921 381666.8513 363745.3013 1.009714417 1.123840866 1.155359816 1.315979722 1.39708925 1.294290981 0.933114242 1.049269502 1 18.47256909 1.726680665 9.799608429 0.996150204 1.209144901 0.469160876 0.111011181 0.101111229 32.76246123 0.057403809 0.031012611 53.29428801 -1.726680665 0.212994697 EALLDESRPLFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EALLDESRPLFER 13 1 A0A5F9ZGM7;Q9BU89 A0A5F9ZGM7 DOHH Deoxyhypusine hydroxylase 0 ; 112.72 0.00080099 139872000 153991 182344 186494 176974 184697 174308 208640 169620 254490 FALSE TRUE 144352.9782 195844.9395 190917.7257 181515.4525 170191.6427 224627.8899 177356.3689 190797.4304 212013.9749 0.680865392 0.923735992 0.90049595 0.856148528 0.802737851 1.059495677 0.836531502 0.899928556 1 17.69379984 4.741737828 24.65023604 0.903695316 0.680865292 0.476232283 0.075231853 210.9945626 1636895.333 0.016005234 0.113865014 55174.42649 -4.741737828 -0.222830024 EALLSSAVDHGSDEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EALLSSAVDHGSDEVK 16 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;; 256.18 1.24E-26 2336880000 1641190 1820650 1895340 1880000 2036840 1598840 2235020 1716380 2131030 FALSE TRUE 1538470.848 1955452.82 1940298.36 1928243.983 1876874.803 2060399.153 1899899.5 1930673.821 1775347.326 0.866574571 1.101448033 1.092911979 1.08612211 1.057187388 1.160561161 1.070156511 1.087490765 1 20.75966987 4.74059434 24.95795495 1.088494366 0.866574494 0.737830201 0.040187379 77.90738641 956013.9831 0.008242172 0.054071023 55029.34449 -4.74059434 -0.221919873 EALNIIGDISTSTVSTPVPPPVDDT(ph)WLQSASSHSPTPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EALNIIGDISTSTVSTPVPPPVDDTWLQSASSHSPTPQR 39 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7ENE7 P50570-2 DNM2 Dynamin-2 1 EALNIIGDISTSTVSTPVPPPVDDT(0.192)WLQS(0.192)AS(0.192)S(0.192)HS(0.192)PT(0.041)PQR 135.75 7.06E-09 172520000 28864 47151 42146 46746 53623 39820 51483 43932 46750 TRUE FALSE 27057.45376 50642.1091 43145.72302 47945.5815 49411.66588 51315.38758 43763.60209 49417.00691 38947.12298 0.694722785 1.300278563 1.107802572 1.231042958 1.268685903 1.317565552 1.123667135 1.268823038 1 15.24922914 4.744962013 24.74961398 1.207729621 0.69472252 0.720265511 0.099344719 312.0884551 1206585.024 0.020975757 0.199809651 55585.56352 -4.744962013 -0.513007102 EALNIIGDISTSTVSTPVPPPVDDTWLQSASSHSPT(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EALNIIGDISTSTVSTPVPPPVDDTWLQSASSHSPTPQR 39 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7ENE7 P50570-2 DNM2 Dynamin-2 1 EALNIIGDISTST(0.001)VS(0.001)T(0.016)PVPPPVDDT(0.16)WLQS(0.16)AS(0.16)S(0.16)HS(0.16)PT(0.18)PQR;EALNIIGDISTSTVSTPVPPPVDDT(0.128)WLQS(0.165)AS(0.165)S(0.165)HS(0.165)PT(0.213)PQR;EALNIIGDISTSTVSTPVPPPVDDT(0.158)WLQS(0.158)AS(0.158)S(0.158)HS(0.158)PT(0.209)PQR 138.59 1.44E-09 434720000 166221 261933 258537 271280 282070 243549 314932 247595 294855 TRUE FALSE 155817.5243 281326.7919 264669.6197 278241.5041 259917.36 313857.6426 267710.8703 278507.7808 245641.7957 0.634328225 1.145272494 1.077461671 1.132712384 1.058115372 1.277704561 1.089842506 1.133796388 1 17.90619653 4.74032697 24.99566746 1.120577565 0.634328062 0.813574004 0.072160953 56.93639392 805641.5133 0.015157713 0.097534559 54995.47662 -4.74032697 -0.486249503 EALNSCNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EALNSCNKR 9 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;;; 183.81 7.17E-05 9555990000 5069940 5868610 4997180 4733160 6483040 3773110 6060940 5518260 6705800 FALSE TRUE 4752621.506 6303127.991 5115715.469 4854620.899 5973888.19 4862345.606 5152158.314 6207226.908 5586558.659 0.850724354 1.12826668 0.915718563 0.868982355 1.069332402 0.870365086 0.922241872 1.111100283 1 22.41352842 1.245893021 24.99738251 1.05555015 0.957377337 0.185370993 0.09287888 273.1358594 931188.7567 0.062497576 0.021786748 17.61542074 -1.245893021 -0.098172813 EALNVFGNDYDTEDGTGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EALNVFGNDYDTEDGTGVR 19 0 Q14376;Q14376-2;Q5QPP4;Q5QPP3;Q5QPP9 Q14376 GALE UDP-glucose 4-epimerase 0 178.85 8.62E-14 59291000 47997 61642 55822 48990 52527 48988 64857 42999 50801 FALSE TRUE 44992.95345 66206.03782 57146.1242 50247.16634 48401.7413 63130.04035 55132.29495 48367.5198 42321.98491 1.063110663 1.564341511 1.350270417 1.187259209 1.143654803 1.491660669 1.302686891 1.142846204 1 15.36911967 1.07484566 2.872307262 1.004012805 1.331747335 0.289765202 0.152368968 0.265920465 4.448702133 0.141232569 0.03778155 11.88079932 -1.07484566 0.32773453 EALPESGELLDVWTELQDIHDAHGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EALPESGELLDVWTELQDIHDAHGLR 26 0 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9 Q6ULP2-7 AFTPH Aftiphilin 0 ;;; 151.94 6.32E-08 63018500 59340.7 69438.7 66193.7 66198.7 73918.6 54475.2 82252.4 72683.7 74083.2 FALSE TRUE 55626.67151 74580.0136 67763.84582 67897.47072 68113.33133 70201.30591 69919.41621 81758.41994 61718.23532 0.901300422 1.208395107 1.097955012 1.100120092 1.103617609 1.137448366 1.132881001 1.324704433 1 15.91340919 1.539494157 4.58826419 1.180755342 1.107520945 0.046476649 0.109400012 0.418318774 19.34491957 0.058068037 0.025068292 34.6333225 -1.539494157 -0.073234397 EALPWGLEPQDVQSSDEMRS(ph)PEGYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EALPWGLEPQDVQSSDEMRSPEGYLR 26 1 Q9H5H4 Q9H5H4 ZNF768 Zinc finger protein 768 1 EALPWGLEPQDVQSSDEMRS(1)PEGYLR;EALPWGLEPQDVQS(0.001)S(0.001)DEMRS(0.997)PEGYLR 237.79 3.35E-45 154560000 50677 55548 49716 49524 58308 47353 55169 48904 65549 TRUE FALSE 47505.21703 59660.83172 50895.287 50794.86968 53728.72488 61023.04239 46896.92061 55009.77205 54608.44844 0.869924314 1.092520176 0.932003901 0.930165041 0.98389034 1.11746523 0.858785077 1.007349112 1 15.73683655 EALSVALEEAQAWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EALSVALEEAQAWR 14 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ;;;; 269.91 1.76E-25 345015900 281816 346175 307236 314444 337814 265701 358141 279816 272259 FALSE TRUE 264177.6396 371806.1572 314523.783 322513.1654 311283.4511 342404.5654 304441.0819 314751.6436 226817.214 1.164716006 1.639232537 1.386683918 1.421907798 1.372397825 1.509605727 1.342230938 1.387688518 1 17.79117061 -0.28975266 0.56153489 0.951913883 1.440285438 0.512918661 0.121739032 5.064044591 1.519927436 0.619366684 0.047619954 0.513153553 0.28975266 0.488371555 EALTYDGALLGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EALTYDGALLGDR 13 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;;; 189.17 1.28E-05 1711670000 1656607 1751542 1794827 1800823 1789227 1633194 1940375 1598462 1387030 FALSE TRUE 1552922.925 1881227.992 1837401.144 1847035.167 1648708.329 2104670.595 1649433.782 1798033.499 1155525.732 1.343910292 1.628027779 1.59009972 1.598437071 1.426803647 1.821396561 1.427431459 1.556030687 1 20.14011796 0.097354466 1.104212748 0.997397536 1.567052733 0.627239817 0.132569926 4.022371165 4.348206906 0.140971801 0.03440974 1.251279894 -0.097354466 0.569655197 EAMEDGEIDGNKVTLDWAKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EAMEDGEIDGNKVTLDWAKPK 21 2 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;; 194.25 2.45E-18 2359240000 2379890 1211160 1633860 1550120 1743460 1056500 2162480 1275810 2474040 FALSE TRUE 2230936.933 1300835.547 1672615.931 1589898.704 1606535.684 1361494.399 1838236.199 1435097.687 2061106.741 1.082397572 0.631134487 0.811513493 0.77138106 0.779452928 0.660564721 0.891868511 0.696275287 1 20.97498779 -1.441605294 3.925584068 1.001415069 0.779807235 0.204010127 0.128450165 18983368.41 6972825.186 230125.9513 0.026244257 0.036173848 1.441605294 -0.221607834 EAMFDDDADQFPDDLSLDHSDLVAELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAMFDDDADQFPDDLSLDHSDLVAELLK 28 0 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4X8;H7C5M8;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 0 72.425 0.010494 23176000 9812.5 11925 11561 10256 10366 10934 14409 11066 15050 FALSE TRUE 9198.353141 12807.93941 11835.23238 10519.18632 9551.896174 14090.4683 12248.50422 12447.61446 12538.05777 0.733634611 1.021524995 0.943944636 0.838980527 0.761832203 1.12381587 0.976906028 0.992786497 1 13.61402626 2.231054935 24.99980947 1.020335558 0.892506376 0.408358766 0.093237775 220.8289055 735527.1683 0.035233222 0.02653187 170.2373834 -2.231054935 -0.127829181 EAMQQADDWLGVPQVITPEEIIHPDVDEHSVMTYLSQFPK ddPTM_SK-BR-3_Pertuzumab_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 ; 194.29 2.68E-25 239570000 120552 143931 99825 106885 179908 79831 111564 149926 110712 FALSE TRUE 113006.8655 154587.801 102192.8961 109627.8501 165778.7514 102876.9138 94836.01391 168644.5911 92233.45197 1.225226456 1.676049174 1.107980824 1.188590991 1.797382054 1.11539698 1.028217115 1.828453641 1 16.49300247 -2.216999106 2.119364371 0.00017878 1.346766464 0.128841616 0.297269013 2950824.267 557893.0269 14135620.51 0.070984378 0.006067376 2.216999106 1.346587684 EANEILQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EANEILQR 8 0 P12268;H0Y4R1;E7ETK5;P20839-3;P20839-7;P20839-5;P20839-6;P20839;A0A3B3IRL5;C9J381;P20839-2;P20839-4;C9K0R9 P12268;P20839-3 IMPDH2;IMPDH1 Inosine-5-monophosphate dehydrogenase 2;Inosine-5-monophosphate dehydrogenase 1;Inosine-5-monophosphate dehydrogenase 0 ; 129.42 0.0025391 434390000 1012270 1070940 989090 1009130 1129480 915890 1150440 966300 1244950 FALSE TRUE 948913.8277 1150233.512 1012551.682 1035025.984 1040775.197 1180292.575 977942.2022 1086944.682 1037159.802 0.91491574 1.109022457 0.97627355 0.997942633 1.003485861 1.138004551 0.942904073 1.048001166 1 19.98420677 EANFTVSSMHGDMPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EANFTVSSMHGDMPQK 16 0 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ;;; 225.13 7.16E-15 1146160000 1250750 1815830 1779660 1901900 2063860 1561780 2349390 1893170 2298650 FALSE TRUE 1172467.79 1950275.943 1821874.376 1950705.974 1901772.761 2012640.533 1997120.78 2129536.442 1914990.465 0.612257769 1.018425929 0.951375168 1.018650489 0.99309777 1.050992456 1.042888106 1.11203501 1 20.86890578 4.738579183 10.3659803 1.019129959 0.611464138 0.904532001 0.041959764 0.021237906 90.45725502 0.010433904 0.060414585 54774.59603 -4.738579183 -0.407665821 EANHNVSAPYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EANHNVSAPYGR 12 0 Q7L576;Q7L576-2;Q7L576-3;Q96F07;Q96F07-2;E7EVJ5;H7C229;E7EW33;A0A0G2JR96;A0A0G2JQT1 Q7L576;A0A0G2JR96 CYFIP1;CYFIP2 Cytoplasmic FMR1-interacting protein 1;Cytoplasmic FMR1-interacting protein 2 0 110.38 0.0014962 150090000 48686 88354 67781 77311 86700 55239 75619 78967 72893 FALSE TRUE 45638.83017 94895.82209 69388.79733 79294.93115 79890.93173 71185.60257 64280.63296 88826.20378 60726.68739 0.751544866 1.562670815 1.14264091 1.30576744 1.315581916 1.172229305 1.05852362 1.462721047 1 15.89004305 2.138468289 8.498875231 1.164338387 1.256989478 0 0.234534585 1.03590564 79.00350133 0.080206455 0.059209923 137.5524369 -2.138468289 0.092651091 EANLQQNEEKNHSDSSTSESEVSSVS(ph)PLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EANLQQNEEKNHSDSSTSESEVSSVSPLK 29 1 Q9NY27-2;Q9NY27;Q9NY27-3;H7C559;C9IZ04 Q9NY27-2 PPP4R2 Serine/threonine-protein phosphatase 4 regulatory subunit 2 1 EANLQQNEEKNHSDSSTSESEVS(0.001)S(0.001)VS(0.998)PLK 99.969 0.00047133 130170000 44833 58402 35273 48460 80424 25345 60404 41891 232470 TRUE FALSE 42026.98256 62726.14485 36109.69222 49703.56564 74107.82345 32661.69006 51346.98096 47121.18356 193669.2552 0.217003894 0.323882822 0.186450308 0.256641487 0.382651461 0.168646748 0.265127167 0.243307506 1 17.56323542 -1.354586589 3.025267919 1.008290375 0.256033734 0.933887702 0.062255953 6559753.618 8303884.889 481588.0158 0.014134908 0.044199098 1.354586589 -0.752256641 EANNFLWPFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EANNFLWPFK 10 0 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 142.43 8.32E-05 759820000 1187740 1469290 1218210 1193330 1541060 996280 1346070 1398750 1195630 FALSE TRUE 1113401.474 1578077.76 1247106.516 1223952.868 1420031.364 1283889.863 1144239.3 1573387.017 996071.6289 1.117792578 1.584301485 1.252024935 1.228779972 1.425631775 1.28895335 1.148752024 1.579592241 1 19.92588997 -2.056590322 2.613681663 0.537413499 1.329060727 0.292174337 0.160549286 26607599.19 5382977.786 73791035.54 0.036171516 0.008778285 2.056590322 0.791647228 EANNGSS(ph)PAGSLADAMSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EANNGSSPAGSLADAMSQK 19 0 P51692;C9J4I3 P51692 STAT5B Signal transducer and activator of transcription 5B 1 EANNGS(0.002)S(0.998)PAGSLADAMSQK;EANNGS(0.285)S(0.715)PAGSLADAMSQK 396 2.71E-127 177108000 557260 442630 497220 479900 514910 382330 572250 433200 523590 TRUE FALSE 522382.0913 475402.7858 509014.2932 492215.0465 474471.0456 492702.4644 486446.425 487285.9736 436199.4465 1.197576236 1.089874803 1.166930168 1.128417403 1.087738761 1.129534823 1.115192669 1.117117359 1 18.73462841 -5 0.202304865 0.411699015 1.147540824 0.656776106 0.030573124 85.15521559 0.844704254 20.23707235 0.065145384 1.00E-05 5 0.735841809 EAPADMGAHQGVAVLGIALIAMGEEIGAEMALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAPADMGAHQGVAVLGIALIAMGEEIGAEMALR 33 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 92.49 1.67E-08 0 16978 18534 19124 18418 16485 17791 19745 14651 14160 FALSE TRUE 15915.37729 19906.27664 19577.63031 18890.63706 15190.3346 22926.97289 16784.42055 16480.2096 11796.60452 1.349149008 1.687458167 1.659598766 1.601362242 1.287687026 1.943523057 1.422817941 1.397029931 1 13.52608404 0.909983818 1.656540661 1.004304916 1.596454185 0.483549297 0.185467679 0.361098394 1.993472063 0.157774155 0.045430006 8.128002304 -0.909983818 0.59214927 EAPCVLIYIPDGHTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EAPCVLIYIPDGHTK 15 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;; 158.81 1.80E-06 774140000 1841700 1689680 1804960 1791430 1912730 1479640 2255250 1746240 2469440 FALSE TRUE 1726431.285 1814785.665 1847774.504 1837401.127 1762511.901 1906788.048 1917096.199 1964261.908 2057274.511 0.839183724 0.882131021 0.898166236 0.893123945 0.85672179 0.92685154 0.931862126 0.954788434 1 20.97230288 1.394171076 0.716619284 1.000103891 0.875569475 0.824650666 0.019699059 0.251006817 0.288228678 0.018229079 0.007873545 24.7839815 -1.394171076 -0.124534416 EAPGS(ph)PPLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EAPGSPPLSPR 11 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;E9PNR0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 2 EAPGS(1)PPLS(1)PR;EAPGS(1)PPLS(1)PR;EAPGS(1)PPLS(1)PR 121.86 0.00058876 1349750000 1512130 1597120 1585780 1633470 1541170 1172760 1559790 1163120 1198680 TRUE FALSE 1417488.483 1715372.427 1623395.45 1675387.606 1420132.725 1511316.774 1325913.97 1308338.092 998612.5642 1.419457889 1.717755702 1.625650937 1.677715328 1.422105805 1.513416542 1.327756146 1.310155849 1 19.92956553 1.269872329 0.601601198 1.002516974 1.636713401 0.794355819 0.095241524 0.278331863 0.247763446 0.087183565 0.041462978 18.61539815 -1.269872329 0.634196427 EAPGS(ph)PPLSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EAPGSPPLSPR 11 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;E9PNR0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 EAPGS(0.998)PPLS(0.002)PR;EAPGS(0.998)PPLS(0.002)PR;EAPGS(0.995)PPLS(0.005)PR;EAPGS(0.995)PPLS(0.005)PR 201.38 4.58E-08 2222920000 2909590 3138410 3043880 2991020 3268080 2580500 3512840 2936440 3755120 TRUE FALSE 2727483.956 3370781.142 3116082.271 3067774.637 3011418.18 3325448.459 2986122.254 3303060.998 3128366.213 0.871855713 1.077489307 0.996073368 0.980631559 0.962616898 1.062998458 0.954530912 1.055842179 1 21.57697798 1.22049475 24.99852437 1.027921037 0.997150588 0.056515922 0.059002156 980.9543851 1357354.761 0.050465926 0.012714195 16.61478591 -1.22049475 -0.030770449 EAPIDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 96.253 0.020632 4611600000 8264600 5552810 6724600 6202750 7167200 5144010 8899300 5750010 9081400 FALSE TRUE 7747333.439 5963945.83 6884110.688 6361923.066 6604317.023 6629002.181 7564932.582 6467911.406 7565655.672 1.024013486 0.788291999 0.909915939 0.840895137 0.872933862 0.876196653 0.999904425 0.854904279 1 22.85103369 1.767188656 25 0.950236867 0.874815118 0.149230113 0.071620933 32.01546253 27974.32135 0.029493987 0.016357898 58.50441695 -1.767188656 -0.075421749 EAPNPIHLTVDTSLQNGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAPNPIHLTVDTSLQNGR 18 0 O00303 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 130.56 1.88E-05 562230000 233750 305300 314960 317430 315380 292380 364240 286990 280630 FALSE TRUE 219120.0048 327904.7297 322430.9999 325575.7912 290611.327 376785.3596 309625.5934 322821.3332 233791.0401 0.93724723 1.402554733 1.379141818 1.392593108 1.24303877 1.611633019 1.324368947 1.3808114 1 17.83486011 -1.134289537 4.748985835 0.999972644 1.353423903 0.271135803 0.169398803 4.36E-05 7.95E-06 0.145831969 0.034370268 0.073402434 1.134289537 0.353451258 EAPPMEKPEVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAPPMEKPEVVK 12 1 K7EM56;A0A0B4J2B4;S4R417;K7ELC2;P62841;K7EQJ5;S4R456;K7EJ78 K7EM56 RPS15 40S ribosomal protein S15 0 120.53 0.00036478 251810000 535970 390100 493100 480210 495090 368040 640950 450010 652200 FALSE TRUE 502424.5944 418983.4099 504796.5649 492533.0016 456207.6285 474287.1734 544845.4978 506194.7391 543343.6066 0.924690359 0.77112053 0.929055866 0.906485317 0.839630066 0.872904673 1.002764165 0.931629144 1 19.05150531 1.766938307 9.626388675 0.975015445 0.868345296 0.495111282 0.049322367 0.17064863 50.89749963 0.022295697 0.012316872 58.47070183 -1.766938307 -0.106670148 EAPS(ph)PTCPDLGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EAPSPTCPDLGAK 13 0 O00257 O00257 CBX4 E3 SUMO-protein ligase CBX4 1 EAPS(0.938)PT(0.062)CPDLGAK;EAPS(0.962)PT(0.038)CPDLGAK;EAPS(1)PTCPDLGAK;EAPS(0.996)PT(0.004)CPDLGAK 237.48 1.00E-16 514470000 1251860 832070 1069370 982950 1275900 843260 1255680 970350 1403300 TRUE FALSE 1173508.317 893677.3286 1094735.961 1008174.161 1175695.961 1086695.473 1067402.441 1091500.334 1169080.164 1.003787724 0.764427758 0.936407951 0.862365295 1.005658976 0.929530332 0.913027587 0.933640281 1 20.15694243 3.162635245 1.661047009 0.94349606 0.869205286 0.097806709 0.069619131 0.603739279 3.427646706 0.021759765 0.029489404 1454.237185 -3.162635245 -0.074290774 EAPS(ph)PTLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAPSPTLRR 9 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 EAPS(0.995)PT(0.005)LRR;EAPS(0.997)PT(0.003)LRR 119.74 0.00047632 938470000 337890 321990 353110 360180 349820 301600 358040 329720 537740 TRUE FALSE 316742.0681 345830.4746 361485.936 369422.8286 322346.5483 388667.0239 304355.2259 370886.2678 447987.7201 0.707032925 0.771964184 0.806910368 0.824627132 0.719543268 0.867584102 0.679382966 0.827893827 1 18.77309966 0.980072019 24.41439999 1.000000002 0.771754593 0.625075061 0.056433055 667.4091931 817665.4351 0.048711088 0.012177772 9.551509649 -0.980072019 -0.22824541 EAPSPLMIHS(ph)PQMSQFQSLT(ph)HQSPPQQNVQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPK 32 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 2 EAPS(0.003)PLMIHS(0.997)PQMS(0.001)QFQS(0.087)LT(0.862)HQS(0.05)PPQQNVQPK 150.33 6.16E-10 75531000 43556 48452 45849 43209 53772 40311 61418 43861 62655 TRUE FALSE 40829.90771 52039.43649 46936.55993 44317.81609 49548.96403 51948.13131 52208.94108 49337.1424 52197.47573 0.782219966 0.996972282 0.899211298 0.849041366 0.949259774 0.995223056 1.000219653 0.945201692 1 15.67169242 2.485673618 5.970202538 0.985796604 0.903302917 0.408310037 0.05632985 0.18534849 26.17187558 0.01853952 0.016399677 305.9663166 -2.485673618 -0.082493686 EAPSPLMIHS(ph)PQMSQFQSLTHQS(ph)PPQQNVQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPK 32 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 2 EAPSPLMIHS(1)PQMSQFQSLT(0.001)HQS(0.999)PPQQNVQPK;EAPS(0.017)PLMIHS(0.931)PQMS(0.04)QFQS(0.019)LT(0.041)HQS(0.953)PPQQNVQPK 163.09 3.00E-14 159812000 45958 45663 48059 55114 54350 40799 68350 57929 66149 TRUE FALSE 43081.57082 49043.93603 49198.98218 56528.31855 50081.57024 52577.00898 58101.55203 65161.56317 55108.30456 0.781761863 0.889955451 0.892768931 1.025767695 0.90878445 0.954066894 1.054315724 1.182427289 1 15.74998212 3.27832755 0.432129421 1.07903496 0.783214561 0.601578442 0.069104204 1.146440267 0.380645727 0.060884981 0.153635521 1898.136981 -3.27832755 -0.295820399 EAPSPLMIHSPQMSQFQSLTHQS(ph)PPQQNVQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPK 32 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 1 EAPSPLMIHSPQMSQFQSLTHQS(1)PPQQNVQPK 376.26 4.15E-148 571470000 227700 250540 267200 255770 272070 204090 334990 227560 264120 TRUE FALSE 213448.6635 269090.2423 273538.1102 262333.4912 250702.7197 263007.4699 284761.3594 255971.3669 220036.6657 0.970059525 1.222933648 1.24314786 1.192226261 1.139367927 1.19528929 1.294154129 1.163312333 1 17.74738442 4.74165882 24.64841737 1.202544669 0.970059421 0.3867607 0.079701217 208.3088055 1657144.994 0.017050289 0.120512755 55164.39004 -4.74165882 -0.232485249 EAQLYAAQAHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAQLYAAQAHLK 12 0 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;E9PI86 P49321 NASP Nuclear autoantigenic sperm protein 0 ; 174.05 3.14E-05 500830000 684900 847380 631430 602820 1001000 436240 670270 796480 907940 FALSE TRUE 642033.3316 910120.8969 646407.8178 618289.3818 922385.4978 562175.4062 569769.236 895922.2813 756398.9485 0.848802517 1.203228665 0.854585823 0.817411742 1.219443125 0.743226055 0.753265505 1.184457333 1 19.52878783 2.199006444 24.99968408 0.878401938 0.991877199 0.010778291 0.185172936 420.4895611 265762.3212 0.066289584 0.048958801 158.1271501 -2.199006444 0.113475261 EAQQKVPDEEENEES(ph)DNEKETEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EAQQKVPDEEENEESDNEKETEK 23 2 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 EAQQKVPDEEENEES(1)DNEKETEK;EAQQKVPDEEENEES(1)DNEKETEK;EAQQKVPDEEENEES(1)DNEKETEK;EAQQKVPDEEENEES(1)DNEKETEK;EAQQKVPDEEENEES(1)DNEKETEK 214.91 1.45E-32 5895930000 7225640 1975620 3958630 3792740 3413090 2026880 5850040 2213890 6703790 TRUE FALSE 6773400.091 2121896.96 4052530.573 3890068.129 3145039.679 2612007.352 4972880.811 2490299.04 5584884.141 1.212809419 0.379935717 0.725624824 0.696535153 0.563134275 0.467692308 0.8904179 0.445899857 1 22.41309592 -1.523130094 2.76540011 1.016406955 0.656946739 0.148189158 0.243964923 34087838.18 35662420.41 4218300.206 0.052305797 0.029982642 1.523130094 -0.359460216 EAQTSFLHLGYLPNQLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAQTSFLHLGYLPNQLFR 18 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ; 162.15 3.63E-11 931110000 1347110 1996620 1552860 1326410 2004500 1178950 1616760 1779610 1670990 FALSE TRUE 1262796.79 2144451.822 1589694.573 1360447.926 1847074.656 1519293.726 1374341.847 2001798.226 1392090.974 0.907122317 1.540453794 1.141947331 0.977269411 1.326834733 1.091375316 0.987250024 1.437979459 1 20.40882206 3.675204093 7.783402366 1.126402663 1.290476248 0.004752721 0.212297321 0.539666504 71.97423938 0.051458113 0.080331268 4733.736651 -3.675204093 0.164073585 EARS(ph)PQPNK ddPTM_SK-BR-3_Pertuzumab_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 88.338 0.0077832 6925570000 5552570 7080130 5750280 7057740 10229210 3189990 5485150 5449170 15119370 TRUE FALSE 5205044.555 7604350.192 5886679.357 7238853.557 9425849.109 4110888.328 4662702.679 6129510.87 12595849.47 0.413234897 0.603718726 0.467350723 0.574701498 0.748329768 0.326368486 0.370177707 0.486629416 1 23.58644509 -1.330334887 4.247051762 1.000718389 0.49785473 0.625325456 0.121918155 0.000844461 0.000133153 0.120101986 0.028269265 0.046737461 1.330334887 -0.502863659 EARS(ph)PQPNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EARSPQPNKR 10 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 EARS(1)PQPNKR 60.893 0.07492 120450000 41059 65836 49696 64748 87342 25697 43816 49455 142260 TRUE FALSE 38489.19048 70710.56594 50874.81259 66409.5433 80482.51164 33115.30674 37246.19757 55629.56561 118515.887 0.324759756 0.596633648 0.429265763 0.560342963 0.67908627 0.279416605 0.31427177 0.469384882 1 16.85472094 -1.647663239 4.587578896 1.013115144 0.457817132 0.636559968 0.129024925 0.01775226 0.001363415 0.128138983 0.030058179 0.022507992 1.647663239 -0.555298012 EAS(ph)HVLEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 78.496 0.031056 186684000 121685 566547 430960 428945 497944 902293 226829 379480 245425 TRUE FALSE 114068.9531 608494.7294 441182.5747 439952.4549 458837.4868 1162770.342 192818.0972 426858.9133 204461.982 0.557898109 2.976077623 2.157773149 2.151756775 2.24412129 5.68697579 0.943051101 2.087717771 1 17.64147309 4.74831287 23.27619627 2.48387837 0.557895306 0.16149991 1.312724641 878.6844996 2097082.255 0.2868922 3.55931393 56016.10018 -4.74831287 -1.925983063 EAS(ph)IDILHSIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EASIDILHSIVK 12 0 O00231;O00231-2;J3QRY4 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 1 EAS(1)IDILHSIVK 60.401 0.059394 11679000 37348 27524 38144 33118 27326 28013 38848 25012 34357 TRUE FALSE 35010.45535 29561.9056 39048.79369 33967.86395 25179.92619 36099.89835 33023.10305 28134.80326 28622.59475 1.223175455 1.03281711 1.364264632 1.186749987 0.879721996 1.261237797 1.153742466 0.982957817 1 14.80486684 2.967275766 24.98182347 1.083783253 1.202422999 0.225167903 0.129357533 1157.069865 883312.7754 0.038756981 0.041138671 927.4185244 -2.967275766 0.118639746 EAS(ph)PAPLAQGEPGREDLPTR ddPTM_SK-BR-3_Pertuzumab_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 206.33 4.70E-22 3728220000 2313410 2081740 2243050 2236600 2083680 1862720 2446730 1921690 1865110 TRUE FALSE 2168617.798 2235874.196 2296256.205 2293994.943 1920036.178 2400457.025 2079865.551 2161617.227 1553811.092 1.39567661 1.438961407 1.477821993 1.476366692 1.23569473 1.54488344 1.338557539 1.391171191 1 20.56737968 -3.159719636 0.302648006 0.000194433 1.445750347 0.711905943 0.082999338 38.73512442 0.991258856 24.51699849 0.07434762 0.000692278 3.159719636 1.445555914 EAS(ph)PLPAESASAGATLRPLLLSGHGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EASPLPAESASAGATLRPLLLSGHGAR 27 1 P35548;D6RIS4 P35548 MSX2 Homeobox protein MSX-2 1 EAS(1)PLPAESASAGATLRPLLLSGHGAR;EAS(1)PLPAESASAGATLRPLLLSGHGAR 107.87 0.0010517 187783000 136789 169542 164392 169742 199367 181663 231000 200957 193930 TRUE FALSE 128227.6207 182095.0661 168291.4559 174097.8671 183709.52 234106.159 196363.6945 226046.9238 161561.8302 0.793675217 1.127092123 1.041653562 1.077592813 1.137084916 1.449018984 1.215408951 1.399135697 1 17.30172687 2.456547906 6.38961822 1.284570156 1.041219812 0.390321528 0.147593778 0.154952858 23.47053321 0.045393663 0.038638382 286.1197958 -2.456547906 -0.243350344 EASDGEVRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EASDGEVRR 9 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 ;;; 131.11 0.00054911 845123000 1225154 1326290 1313390 1311135 1496060 1184344 1463170 1138213 1594820 FALSE TRUE 1148473.798 1424489.892 1344544.231 1344780.944 1378565.482 1526244.887 1243781.242 1280321.399 1328634.239 0.864401778 1.072146005 1.011974697 1.012152859 1.03758088 1.148732165 0.936135172 0.963637216 1 20.34151257 1.61487146 25 0.962412975 1.029571208 0.123604342 0.07155119 1.009033627 3588.909368 0.031103961 0.016779841 41.1975567 -1.61487146 0.067158234 EASELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EASELLR 7 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 97.602 0.02763 70306000 155440 154330 173650 149410 172860 133940 156310 144430 174990 FALSE TRUE 145711.2879 165756.7538 177769.06 153244.1136 159284.2729 172606.3037 132872.7666 162462.4034 145783.0385 0.999507826 1.137009871 1.219408388 1.051179308 1.092611833 1.183994417 0.911441879 1.114412246 1 17.15346335 1.748468653 25 1.00367035 1.125545736 0.27693151 0.078628363 2.737845578 6922.507646 0.034625394 0.019201575 56.03619694 -1.748468653 0.121875387 EASEVKPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EASEVKPPR 9 1 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 ;; 81.338 0.019668 260670000 494740 454990 488460 524270 516550 422050 609880 444230 536960 FALSE TRUE 463775.1065 488677.933 500046.5019 537723.6558 475982.2467 543888.9836 518434.1558 499693.0934 447337.9071 1.036744481 1.09241342 1.117827249 1.202052514 1.064032891 1.215834775 1.158931867 1.117037223 1 18.77100549 4.630967357 1.069323986 1.138889015 1.001258334 0.138592235 0.063435779 2.229902779 2.362697216 0.017087727 0.334244018 42753.07502 -4.630967357 -0.137630681 EASQTSSS(ph)PAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EASQTSSSPAPK 12 0 Q5T8J1;P30281-4;P30281-2;P30281-3;P30281 Q5T8J1 CCND3 G1/S-specific cyclin-D3 1 EAS(0.074)QT(0.043)S(0.019)S(0.053)S(0.811)PAPK 83.351 0.010232 0 236110 180410 216400 186210 209190 191520 291070 212950 333010 TRUE FALSE 221332.2966 193767.7441 221533.1102 190988.4639 192761.0612 246808.7149 247426.7557 239537.2763 277428.4797 0.797799479 0.698442151 0.798523318 0.688424145 0.69481353 0.88963006 0.891857808 0.863419922 1 18.08175637 2.217592475 14.02199316 0.900681148 0.736971721 0.734915376 0.052238673 0.864003808 576.4517026 0.017913529 0.013337226 165.041239 -2.217592475 -0.163709427 EASRPPEEPSAPS(ph)PTLPAQFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EASRPPEEPSAPSPTLPAQFK 21 1 A0A0C4DFX9;Q9H3P2;H0Y3X6;Q9H3P2-7 A0A0C4DFX9 NELFA Negative elongation factor A 1 EASRPPEEPSAPS(0.996)PT(0.004)LPAQFK;EASRPPEEPSAPS(0.879)PT(0.12)LPAQFK;EASRPPEEPS(0.001)APS(0.96)PT(0.039)LPAQFK;EASRPPEEPS(0.001)APS(0.98)PT(0.019)LPAQFK 260.14 8.43E-37 2567990000 3247350 2642430 3073420 2815810 3442300 2751220 4020900 3135300 5246280 TRUE FALSE 3044104.16 2838078.267 3146322.974 2888068.452 3171955.644 3545452.552 3418003.373 3526749.107 4370641.976 0.696489023 0.649350435 0.71987662 0.660788156 0.725741358 0.811197204 0.782036916 0.806917868 1 22.05941377 0.705575594 0.328053096 1.042774325 0.65233102 0.914593916 0.02951423 0.593179935 0.155476845 0.076932455 0.032943261 5.076630964 -0.705575594 -0.390443305 EASRS(ph)SPVEFECINEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EASRSSPVEFECINEK 16 1 O75131;H0YB26 O75131 CPNE3 Copine-3 1 EAS(0.092)RS(0.454)S(0.454)PVEFECINEK 153.82 2.51E-07 102560000 160590 161370 139040 126970 254770 114750 201530 184270 281020 TRUE FALSE 150538.9586 173318.0027 142338.0945 130228.2652 234761.3919 147876.4622 171312.4474 207276.5151 234115.9465 0.643010272 0.740308404 0.607981201 0.556255424 1.002756947 0.631637718 0.731741899 0.88535838 1 17.83686368 0.776987005 0.478565021 1.018559731 0.664811498 0.42211936 0.121002526 1.353793 0.704689135 0.158370398 0.066714523 5.983936899 -0.776987005 -0.353748233 EATAQKPTGSVGSTVT(ph)TPPPLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EATAQKPTGSVGSTVTTPPPLVR 23 1 Q86YP4-2;Q86YP4;Q86YP4-3 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 1 EATAQKPTGSVGS(0.012)T(0.038)VT(0.475)T(0.475)PPPLVR 155.09 5.27E-08 482980000 774180 693080 767860 777710 725020 618760 915800 647380 954000 TRUE FALSE 725725.4558 744396.3643 786074.0018 797667.3553 668079.8538 797385.9673 778484.2919 728206.8181 794771.2369 0.913124962 0.936617142 0.989056933 1.003643965 0.8405939 1.003289916 0.97950738 0.916247071 1 19.60018014 EATAQKPTGSVGSTVTT(ph)PPPLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EATAQKPTGSVGSTVTTPPPLVR 23 1 Q86YP4-2;Q86YP4;Q86YP4-3 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 1 EATAQKPTGSVGS(0.001)T(0.014)VT(0.028)T(0.957)PPPLVR 175.86 1.66E-12 565950000 801800 679550 802310 848960 815870 649090 971590 638830 961070 TRUE FALSE 751616.7693 729864.5891 821341.1721 870745.7509 751794.8613 836471.7459 825909.0993 718589.3317 800661.2083 0.938745079 0.911577308 1.025828607 1.087533331 0.93896751 1.044726205 1.031533801 0.897494876 1 19.61083238 3.985060585 3.95013062 1.00935679 0.926362362 0.263043113 0.053862178 0.249346579 8.825160603 0.012930346 0.027685423 9661.856542 -3.985060585 -0.082994428 EATDAIGHLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 188.6 3.08E-06 5295800000 8694600 9597800 9538100 8842700 9759000 7746200 11116600 8592000 10769800 FALSE TRUE 8150420.506 10308431.1 9764348.236 9069618.653 8992567.506 9982402.191 9449769.031 9664730.113 8972250.804 0.908403107 1.148923645 1.088283024 1.01085211 1.002264393 1.112586174 1.053221676 1.077180111 1 23.09703852 3.298439111 24.99998372 1.048749291 1.075726172 0 0.070229444 313.4727735 130874.8383 0.018462917 0.0249989 1988.104052 -3.298439111 0.026976881 EATDEELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EATDEELER 9 0 Q13619;A0A0A0MR50;Q13619-2 Q13619 CUL4A Cullin-4A 0 128.38 0.0029611 0 179410 248400 223780 258430 297260 176680 261100 236010 394190 FALSE TRUE 168181.0484 266791.7945 229088.1673 265061.7513 273914.3987 227684.6478 221950.4789 265476.368 328397.1424 0.512127015 0.812405956 0.697594886 0.807137813 0.834094952 0.693321039 0.675859958 0.80840036 1 18.32508205 -5 0.314835155 3.435237994 0.721619715 0.462712927 0.093762079 284.3141971 2.549473617 460.2116326 0.08034019 1.00E-05 5 -2.713618279 EATDLLHDALQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EATDLLHDALQIR 13 0 Q6P597;Q6P597-3;Q6P597-2;K7ENJ3;K7EL76 Q6P597 KLC3 Kinesin light chain 3 0 129.71 0.00015056 59349000 60283 66118 64466 64789 65385 52612 68362 58674 60372 FALSE TRUE 56509.99464 71013.44552 65995.16396 66451.59543 60249.92585 67800.23032 58111.75274 65999.57806 50295.52318 1.123559137 1.411923786 1.312147877 1.321222869 1.197918265 1.348037082 1.155406069 1.31223564 1 15.61814237 -0.774333802 0.326449801 0.875965463 1.317173405 0.446200725 0.092243167 9.182393994 0.884636526 1.218140766 0.080461403 0.168138124 0.774333802 0.441207943 EATGLS(ph)PQAAQEKDGIVIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EATGLSPQAAQEKDGIVIVK 20 1 P17029;C9JRM9 P17029 ZKSCAN1 Zinc finger protein with KRAB and SCAN domains 1 1 EATGLS(1)PQAAQEKDGIVIVK;EAT(0.002)GLS(0.998)PQAAQEKDGIVIVK 176.53 1.99E-13 531270000 813280 636730 582110 543890 1020910 431260 726450 509760 1661120 TRUE FALSE 762378.2565 683874.1517 595917.9241 557847.1382 940731.8468 555757.7611 617525.5665 573404.6581 1383868.341 0.550903749 0.494175733 0.430617499 0.403107089 0.67978421 0.40159728 0.446231443 0.414349141 1 20.40027526 -1.474643276 3.120647707 1.012071169 0.473265109 0.788073892 0.085110587 29570299.71 35967407.82 3092490.467 0.019766312 0.033524069 1.474643276 -0.53880606 EATNPPVIQEEKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EATNPPVIQEEKPK 14 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 169.09 3.09E-06 232660000 321970 206530 234190 244890 249140 169990 323270 211290 240620 FALSE TRUE 301818.4724 221821.6961 239745.0974 251174.292 229573.5494 219063.3534 274798.6646 237670.0216 200458.9675 1.505637169 1.106569084 1.195980905 1.252996037 1.145239608 1.092808948 1.370847451 1.185629281 1 17.61294743 4.747510077 24.5376747 1.185760662 1.505637385 0.522869949 0.099968053 768.0606027 2105812.976 0.022791996 0.273839878 55912.65013 -4.747510077 0.319876722 EATNTTSEPSAPSQDLLDLSPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EATNTTSEPSAPSQDLLDLSPSPR 24 0 J3KQU4;I3L4I4;O75674;O75674-2;O75674-3;I3NI44 J3KQU4 TOM1L1 TOM1-like protein 1 1 EATNTTSEPSAPSQDLLDLSPS(1)PR;EATNTTSEPSAPSQDLLDLS(0.015)PS(0.985)PR 191.99 5.27E-18 301960000 387550 452560 483760 436550 481540 406260 490260 416780 540470 TRUE FALSE 363293.9373 486068.0133 495235.0156 447752.6121 443721.7908 523540.6669 416750.0644 468815.9004 450262.0654 0.806849977 1.079522462 1.099881721 0.994426683 0.985474516 1.162746558 0.925572231 1.041206747 1 18.78040541 0.013900834 13.11128944 0.999999956 1.023977968 0 0.098648743 0 0 0.087527146 0.020630346 1.032525613 -0.013900834 0.023978012 EATSDPS(ph)RTPEEEPLNLEGLVAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EATSDPSRTPEEEPLNLEGLVAHR 24 1 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7 E9PGF5 TNS1 Tensin-1 1 EATS(0.001)DPS(0.897)RT(0.102)PEEEPLNLEGLVAHR;EAT(0.075)S(0.075)DPS(0.425)RT(0.425)PEEEPLNLEGLVAHR;EAT(0.016)S(0.084)DPS(0.631)RT(0.269)PEEEPLNLEGLVAHR 197.36 1.13E-24 564084000 299689 394855 388604 375552 443352 399763 384419 361093 602796 TRUE FALSE 280932.0005 424090.475 397821.8704 385189.3001 408532.9223 515168.0885 326778.9397 406176.2559 502185.4534 0.559418833 0.844489764 0.792181191 0.767026001 0.813510068 1.025852272 0.650713671 0.808817247 1 18.93786071 -5 0.127971134 1.618311518 0.70683872 0.28826535 0.11734964 224.6155294 1.825119089 36.74398577 0.889861952 1.00E-05 5 -0.911472798 EATSDPSRT(ph)PEEEPLNLEGLVAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EATSDPSRTPEEEPLNLEGLVAHR 24 1 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7 E9PGF5 TNS1 Tensin-1 1 EAT(0.001)S(0.007)DPS(0.232)RT(0.761)PEEEPLNLEGLVAHR;EATSDPS(0.134)RT(0.866)PEEEPLNLEGLVAHR 266.67 2.79E-44 736630000 354340 371030 395700 374640 458060 359360 375850 391590 799300 TRUE FALSE 332162.4919 398501.4473 405086.1909 384253.8967 422085.8153 463101.3983 319494.7817 440480.8735 665891.6663 0.498823621 0.598447867 0.608336478 0.577051668 0.633865592 0.695460571 0.47979994 0.661490293 1 19.34492796 0.972043689 23.84512262 1.000000002 0.588553184 0.816762526 0.061447931 667.8480354 569636.791 0.055180478 0.013795119 9.376563292 -0.972043689 -0.411446818 EATTDFTVDSRPLTQVGGDHIK ddPTM_SK-BR-3_Pertuzumab_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 ;;; 335.24 3.94E-81 3758700000 2640300 2438880 2293330 2253260 2626510 1748350 3235990 2253140 3436750 FALSE TRUE 2475048.336 2619457.213 2347728.871 2311082.466 2420234.499 2253070.263 2750783.341 2534449.489 2863134.223 0.864454176 0.914891517 0.819985613 0.807186212 0.845309479 0.786924429 0.960759478 0.885201074 1 21.44916387 1.302218846 1.323348543 0.981280008 0.8473653 0.495926064 0.047943445 0.344750303 1.16143838 0.043493045 0.013836258 20.05482358 -1.302218846 -0.133914708 EAVCFIPGEGHTLQEHQIVLVEGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAVCFIPGEGHTLQEHQIVLVEGGR 25 0 O15235 O15235 MRPS12 "28S ribosomal protein S12, mitochondrial" 0 ; 182.39 1.29E-17 224006000 131718 151989 137080 130309 176572 134964 138815 133038 210980 FALSE TRUE 123474.0055 163242.4237 140331.6023 133652.9496 162704.7474 173925.9158 118000.9794 149648.0872 175766.075 0.702490543 0.928748188 0.798399818 0.760402424 0.925689143 0.989530635 0.671352418 0.851404841 1 17.42329711 4.761445953 22.96144622 0.849354312 0.702490048 0.182214956 0.103640191 3741.530145 3753788.578 0.02361548 1.109316068 57735.90173 -4.761445953 -0.146864264 EAVELPLTHFELYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EAVELPLTHFELYK 14 0 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;; 220.19 4.73E-12 640334000 2183810 2103810 2107890 2038540 2323850 1695780 2622110 2000790 2703150 FALSE TRUE 2047129.23 2259578.281 2157890.146 2090852.388 2141344.195 2185324.157 2228948.948 2250593.036 2251976.802 0.909036553 1.00337547 0.958220415 0.92845201 0.950873114 0.970402606 0.989774382 0.999385533 1 21.10276054 1.760447032 2.290612538 0.998743517 0.957568654 0.412948586 0.024456091 0.335454531 3.550640746 0.015938345 0.007027734 57.60325596 -1.760447032 -0.041174862 EAVGDLLDAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAVGDLLDAFK 11 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 83.862 0.02877 0 118000 83244 89924 85977 104850 83717 89942 79820 98934 FALSE TRUE 110614.5906 89407.47238 92057.03975 88183.31538 96615.50394 107884.7389 76456.03208 89785.70271 82421.27626 1.34206355 1.084762047 1.116908691 1.069909608 1.172215577 1.308942833 0.927624948 1.089351036 1 16.33072918 8 0.099860047 0.934184294 1.722068168 0.2550288 0.109075649 210.5237384 1.488864381 1.341080361 22.73795531 100000000 -8 0.787883874 EAVILPIKFPHLFTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAVILPIKFPHLFTGK 16 1 O75351;I3L4J1;Q9UN37 O75351;I3L4J1 VPS4B;VPS4A Vacuolar protein sorting-associated protein 4B;Vacuolar protein sorting-associated protein 4A 0 ; 179.14 1.61E-09 116634000 654310 652000 657760 644580 765420 525010 836150 631830 755860 FALSE TRUE 613357.9051 700274.7584 673362.3778 661121.0141 705307.0008 676571.8642 710777.0699 710715.3663 629702.083 0.974044587 1.112073117 1.069334843 1.049894914 1.120064583 1.074431676 1.12875134 1.128653351 1 19.26430991 2.744742178 24.77056652 1.099401595 1.064459237 0.089461191 0.050909493 1032.240648 4136349.725 0.014362404 0.014905199 555.5743389 -2.744742178 -0.034942358 EAVIT(ph)PVASATQSVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EAVITPVASATQSVSR 16 0 P28749;P28749-2;H0YE05 P28749 RBL1 Retinoblastoma-like protein 1 1 EAVIT(1)PVASATQSVSR;EAVIT(1)PVASATQSVSR 232.73 1.61E-15 215738000 340510 436640 312250 287560 467220 307250 501330 444500 425340 TRUE FALSE 319198.0869 468969.2799 319656.7175 294939.2764 430526.4259 395948.0872 426160.2206 499996.8035 354348.0062 0.900803959 1.323470915 0.902098253 0.832343547 1.214981934 1.117398942 1.202660134 1.411033207 1 18.43480741 EAVLDVIPTDIHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EAVLDVIPTDIHQR 14 0 P09467;A0A3B3IUC7 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;;;;; 156.5 5.55E-06 2320154000 2645364 4101418 2117385 1413240 5257757 2508958 2636028 4828536 8467287 FALSE TRUE 2479795.389 4405091.256 2167610.372 1449506.131 4844833.974 3233253.445 2240780.073 5431389.349 7054042.099 0.351542471 0.624477597 0.307286282 0.205485892 0.686816708 0.458354713 0.317659016 0.769968377 1 22.75001876 1.048688562 4.265429401 0.996910891 0.429579861 0.65226815 0.145605238 0.108817121 4.154753003 0.13437745 0.034314991 11.18635407 -1.048688562 -0.56733103 EAVTEILGIEPDREK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EAVTEILGIEPDREK 15 1 E9PGT1;Q15631;H7C1D4 E9PGT1 TSN Translin 0 ;;;; 230.16 3.33E-13 1097608000 1713270 1592420 1489580 1386980 1814110 1145178 1964540 1569070 2185080 FALSE TRUE 1606039.489 1710324.434 1524913.541 1422572.255 1671637.118 1475772.298 1669975.465 1764971.843 1820376.032 0.882256996 0.93954458 0.837691507 0.781471647 0.918292204 0.810696401 0.917379396 0.969564427 1 20.79580507 1.328425289 2.645554087 0.99317992 0.866842306 0.535289393 0.047149724 0.221552526 2.565288571 0.040583445 0.012221237 21.30224079 -1.328425289 -0.126337615 EAVTHIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EAVTHIGR 8 0 D6RBW1;P06730;P06730-3;P06730-2 D6RBW1 EIF4E Eukaryotic translation initiation factor 4E 0 ;;;;; 157.68 0.00037306 3405480000 3803190 4244460 4449010 4156720 4707100 3878600 4593540 3944480 4687260 FALSE TRUE 3565155.127 4558724.235 4554542.618 4263388.473 4337423.354 4998288.856 3904781.321 4436957.011 3904926.025 0.912989159 1.16742909 1.166358233 1.0917975 1.110756856 1.279995786 0.999962943 1.136246111 1 21.89686379 0.698214998 1.055434749 1.002188523 1.12337829 0.083432226 0.099745803 2.130524055 4.080794561 0.08686876 0.02759436 4.991315219 -0.698214998 0.121189767 EAVVDLHADDSRIS(ph)EDETER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EAVVDLHADDSRISEDETER 20 1 Q9UKV3-5;G3V3T3 Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 EAVVDLHADDS(0.001)RIS(0.995)EDET(0.004)ER;EAVVDLHADDS(0.054)RIS(0.933)EDET(0.013)ER;EAVVDLHADDSRIS(1)EDETER;EAVVDLHADDS(0.002)RIS(0.998)EDETER 301.19 4.35E-55 2419130000 1944120 1801990 2016910 1861830 1783450 1760270 2252110 1732890 1547810 TRUE FALSE 1822441 1935411.215 2064752.058 1909607.71 1643385.031 2268431.373 1914427.013 1949245.131 1289470.512 1.413325069 1.500934839 1.601240229 1.480923908 1.274464996 1.759196005 1.484661336 1.511663208 1 20.29834735 0.299097867 2.885018537 1.000000065 1.513998232 0.62014104 0.123543448 47.87448041 195.0096647 0.109158629 0.028628958 1.991121983 -0.299097867 0.513998167 EAVVDLHADDSRIS(ph)EDETERNGDDGTHDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAVVDLHADDSRISEDETERNGDDGTHDK 29 2 Q9UKV3-5;G3V3T3 Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 EAVVDLHADDS(0.023)RIS(0.976)EDETERNGDDGTHDK 237.05 1.30E-45 722370000 152930 111390 132650 154260 145940 89573 163410 123740 238640 TRUE FALSE 143358.3843 119637.4315 135796.5206 158218.5728 134478.4611 115431.271 138908.1875 139189.2114 198809.4423 0.721084384 0.601769363 0.683048647 0.795830273 0.676418884 0.580612619 0.698700152 0.700113686 1 17.60102675 0.510801656 1.939546991 0.999971573 0.672472587 0.739088581 0.059377507 1.993328661 7.310127784 0.056149002 0.015524303 3.241915242 -0.510801656 -0.327498986 EAWPHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EAWPHIK 7 0 P52209-2;P52209;K7EM49;K7EPF6;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;;; 94.262 0.01433 1560300000 2005950 2226200 2139350 2153750 2436530 1651610 2497470 2072920 2805880 FALSE TRUE 1880401.17 2391030.164 2190096.392 2209018.871 2245174.762 2128402.995 2122997.559 2331728.625 2337560.501 0.804428878 1.02287413 0.936915383 0.945010352 0.960477712 0.910523169 0.908210743 0.997505144 1 21.15657227 1.219325636 23.73705356 0.998752777 0.936821212 0.213299513 0.054846043 261.2901984 322430.5699 0.048595434 0.012243429 16.57011931 -1.219325636 -0.061931565 EAYALCHCLPVLSTDKFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAYALCHCLPVLSTDKFK 18 1 Q7L5N1;E7EM64 Q7L5N1 COPS6 COP9 signalosome complex subunit 6 0 101.13 0.00043401 100500000 291590 232170 240020 252580 288510 192350 303610 229440 375750 FALSE TRUE 273339.9024 249360.1084 245713.3877 259061.6304 265851.5884 247878.3225 258086.4991 258086.0891 313034.8976 0.873193067 0.796588848 0.784939282 0.827580671 0.849271409 0.791855235 0.824465582 0.824464272 1 18.25596397 -0.476875892 0.83609876 1.009883145 0.814502479 0.809635703 0.027068975 7.624493973 3.599708888 0.270726012 0.008591431 0.333521709 0.476875892 -0.195380666 EAYPEEAYIADLDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EAYPEEAYIADLDAK 15 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ;;; 243.7 1.27E-17 323577000 443512 315222 364057 361248 383448 280465 437726 329895 497586 FALSE TRUE 415753.3756 338561.3649 372692.604 370518.2353 353333.5408 361430.6925 372093.0499 371083.1169 414535.6821 1.002937488 0.8167243 0.899060371 0.893815059 0.852359775 0.871892839 0.897614044 0.895177745 1 18.66113676 0.382222763 1.199924298 1.000106744 0.88189008 0.329739592 0.047707574 3.041145024 4.944820455 0.04107012 0.012320743 2.411141859 -0.382222763 -0.118216663 EAYPGDVFYLHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 EAYPGDVFYLHSR 13 0 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;;;;;;;; 196.5 1.41E-07 6761450000 5021548 5540805 4977298 4508765 6921834 4545144 4434183 5575532 8236651 FALSE TRUE 4707258.274 5951051.967 5095361.859 4624467.543 6378221.079 5857253.289 3769318.424 6271649.443 6861900.737 0.685999179 0.86725999 0.742558375 0.673933903 0.929512292 0.853590501 0.549311127 0.913981371 1 22.71017683 1.009892601 24.99604116 1.000000103 0.761971815 0.380401744 0.108869627 166.8824813 421666.8985 0.102910924 0.025727731 10.23039967 -1.009892601 -0.238028288 EAYSGCSGPVDSECPPPPS(ph)SPVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAYSGCSGPVDSECPPPPSSPVHK 24 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 EAYSGCSGPVDSECPPPPS(0.629)S(0.371)PVHK 224.91 4.16E-33 266530000 211020 178360 196700 221500 222790 139300 163040 106170 138350 TRUE FALSE 197812.6349 191565.96 201365.8169 227184.065 205292.9721 179513.6487 138593.6656 119425.5582 115258.4912 1.716252163 1.662055072 1.747080104 1.971083107 1.781152693 1.557487407 1.202459481 1.0361541 1 16.81451351 1.741543207 1.916089092 1.017770911 1.765133863 0.939278352 0.08167283 0.077942667 0.576540554 0.063528607 0.026111577 55.14970667 -1.741543207 0.747362952 EAYSGCSGPVDSECPPPPSS(ph)PVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EAYSGCSGPVDSECPPPPSSPVHK 24 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 EAYSGCSGPVDSECPPPPS(0.051)S(0.949)PVHK 198.99 1.09E-24 281430000 179040 143030 179810 190340 182770 129570 163880 99798 118960 TRUE FALSE 167834.206 153620.09 184075.1781 195224.4466 168415.9815 166974.7556 139307.7154 112258 99104.80749 1.693502165 1.550077074 1.857378898 1.969878673 1.69937247 1.684830028 1.405660522 1.132720025 1 16.59666742 1.437846436 1.569413116 1.006009261 1.75106702 0.872410414 0.108415831 0.130774592 0.604796898 0.104322101 0.033520181 27.4060494 -1.437846436 0.745057759 EAYVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 1043690000 2414900 2394100 2240400 2244600 2351800 1697000 2494800 2327600 2814300 FALSE TRUE 2263755.72 2571361.655 2293543.346 2302200.236 2167099.115 2186896.352 2120727.901 2618205.984 2344575.149 0.965529179 1.096728188 0.978234094 0.9819264 0.924303542 0.93274739 0.904525454 1.116708068 1 21.16089509 3.649213054 3.290185207 0.963003402 1.040329181 0.075863785 0.066631846 0.370650931 7.825818369 0.017160723 0.028980239 4458.749297 -3.649213054 0.07732578 ECADLWPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ECADLWPR 8 0 J3KTJ3;P62829 J3KTJ3 RPL23 60S ribosomal protein L23 0 ;;;; 109.86 0.0082276 1446820000 2327580 2839900 2497250 2379240 2885110 1987670 2490190 2254340 2590300 FALSE TRUE 2181900.923 3050169.151 2556485.949 2440295.326 2658525.099 2561478.062 2116809.127 2535799.311 2157962.196 1.011093209 1.413448835 1.184675966 1.130833214 1.231960923 1.186989312 0.980929662 1.175089775 1 21.04123816 2.022714976 0.77560641 1.026634064 1.240751609 0.180598096 0.116836283 0.780246299 0.882116119 0.094976142 0.050532684 105.3695138 -2.022714976 0.214117545 ECFGACLFTCYDLLRPDVVLETAWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ECFGACLFTCYDLLRPDVVLETAWR 25 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5;J3KRF5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 220.69 1.10E-33 665340000 237470 348410 238960 230210 364650 221910 322620 300300 164738 FALSE TRUE 222607.1766 374206.6389 244628.244 236117.5783 336011.8599 285971.8146 274246.1261 337793.116 137242.1636 1.622002822 2.726615708 1.782456919 1.720444885 2.448313632 2.08370232 1.998264374 2.46129256 1 17.06636425 -1.038256258 4.72852569 0.999968243 2.120735291 0.489632164 0.354361274 10762097.06 2363065.68 3555.277103 0.076323003 0.091568003 1.038256258 1.120767048 ECHGLVDALVTSINHALDAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ECHGLVDALVTSINHALDAGK 21 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ; 311.65 8.68E-67 329130000 820660 876750 988060 987540 1016810 822910 1282240 922080 1027100 FALSE TRUE 769296.3555 941665.4823 1011497.25 1012881.948 936953.8442 1060470.758 1089980.016 1037203.718 855670.3747 0.899056901 1.100500275 1.182110869 1.18372913 1.094993904 1.239344951 1.273831662 1.212153358 1 19.70669562 5.526056542 0.938754586 1.19024104 8.96E-12 0.527267729 0.07849324 5.512884125 1.306204221 0.022819342 9.508412765 335781.3276 -5.526056542 -1.19024104 ECHLNADTVSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ECHLNADTVSSK 12 0 P63010;P63010-2;P63010-3;A0A087X253 P63010 AP2B1 AP-2 complex subunit beta 0 ;; 147.18 6.54E-05 1509980000 1897370 2003820 1957830 1922830 2212870 1527380 2314590 1908880 2595910 FALSE TRUE 1778616.999 2152184.918 2004270.652 1972173.073 2039080.116 1968309.811 1967538.717 2147207.87 2162635.851 0.822430183 0.995167502 0.926772138 0.91193026 0.942867989 0.910143892 0.90978734 0.992866122 1 21.04435933 1.228546458 23.754083 0.996433218 0.925244124 0.36219417 0.042742843 141.2987267 335145.5834 0.036294245 0.009549809 16.92569295 -1.228546458 -0.071189094 ECINAAPDS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ECINAAPDSPSK 12 0 J3KNN7;Q7Z569 J3KNN7 BRAP BRCA1-associated protein 1 ECINAAPDS(0.975)PS(0.025)K;ECINAAPDS(0.938)PS(0.062)K;ECINAAPDS(0.997)PS(0.003)K 278.85 6.24E-28 1363150000 3601800 2407970 2791750 2657610 2553420 2075280 3210910 2056970 2248480 TRUE FALSE 3376369.767 2586258.604 2857971.628 2725808.772 2352884.693 2674379.647 2729463.854 2313787.232 1873194.162 1.802466522 1.380667662 1.525720978 1.455166168 1.256081585 1.427710859 1.457117425 1.235209504 1 20.83706902 -2.975400585 0.088811322 2.91E-12 1.877090788 0.672861873 0.119474788 84.9770338 0.819197923 20.04700645 3.296205332 0.001058277 2.975400585 1.877090788 ECINAAPDS(ph)PSKQLPDQISFFSGNPSVEIVHGIMHLYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ECINAAPDSPSKQLPDQISFFSGNPSVEIVHGIMHLYK 38 1 J3KNN7;Q7Z569 J3KNN7 BRAP BRCA1-associated protein 1 ECINAAPDS(0.971)PS(0.029)KQLPDQISFFSGNPSVEIVHGIMHLYK 156.56 2.08E-14 75990000 125070 123780 110750 129060 192400 72183 147450 106790 213800 TRUE FALSE 117242.092 132944.8 113377.0423 132371.8981 177289.6801 93021.06031 125341.2414 120122.9666 178115.3988 0.658236698 0.746397004 0.636537004 0.743180539 0.995364136 0.522251647 0.703708058 0.674410901 1 17.44245272 -1.091450727 4.377137624 1.000030851 0.707507008 0.367544619 0.119508436 15181251.2 3785485.372 4476.192931 0.025945025 0.081011985 1.091450727 -0.292523844 ECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDK 38 0 P68363;P68363-2;F8VVB9;F8VS66;F8W0F6;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;Q9BQE3 TUBA1B;TUBA1C;TUBA1A Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 ;;; 469.64 2.73E-269 1190950000 428306 501301 533415 529024 604964 492210 786966 571229 552866 FALSE TRUE 401499.092 538417.8476 546067.8557 542599.6515 557452.5677 634303.0366 668967.7541 642548.1981 460589.0929 0.871707772 1.168976547 1.185585729 1.178055798 1.210303449 1.377156008 1.452417707 1.395057347 1 18.81312072 5.771981995 0.486339763 1.324670153 7.73E-10 0.415573021 0.135444023 10.47630343 0.883623182 0.074979538 9.848575682 591537.1096 -5.771981995 -1.324670152 ECLIDPDLTQYAIIMLDEAHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ECLIDPDLTQYAIIMLDEAHER 22 0 Q14562;F5H658 Q14562 DHX8 ATP-dependent RNA helicase DHX8 0 ;; 169.84 7.84E-12 58490000 96651 105310 112700 107685 116340 100707 122445 95057 117486 FALSE TRUE 90601.78644 113107.262 115373.2972 110448.3794 107203.1257 129779.4761 104085.509 106925.0757 97876.82761 0.925671465 1.155608173 1.178760081 1.128442575 1.095286068 1.325946899 1.063433619 1.092445253 1 16.57867972 1.04275993 1.977788108 1.005152665 1.140445609 0.127472571 0.099677882 0.553989521 4.466192897 0.086166175 0.024297467 11.03468475 -1.04275993 0.135292944 ECLPLIIFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ECLPLIIFLR 10 0 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ; 123.98 0.0010413 395660000 316562 502559 357553 387227 501770 347328 377358 420794 282194 FALSE TRUE 296748.9495 539768.9913 366034.326 397163.9004 462363.0082 447595.9552 320776.6711 473331.0572 235093.9984 1.262256593 2.295970952 1.556970099 1.689383409 1.96671549 1.903902092 1.364461336 2.013369378 1 17.84287818 -2.278403409 0.346428215 4.36E-12 1.809982098 0.345080708 0.316213776 50.79425458 2.313346701 39.51235183 0.23237674 0.005267404 2.278403409 1.809982098 ECLQALEFLHANQVIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ECLQALEFLHANQVIHR 17 0 Q13177;H7C1X3 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 0 ; 165.9 1.40E-09 612030000 500560 508270 584920 560650 608000 463930 574050 502920 536650 FALSE TRUE 469230.8431 545902.8397 598794.5786 575037.2282 560250.1326 597859.0597 487976.5317 565710.6691 447079.6481 1.049546418 1.221041579 1.339346537 1.286207571 1.253132713 1.337254027 1.09147561 1.265346502 1 18.77017235 0.401411876 0.759697284 0.998440684 1.248705265 0.346908018 0.096161196 2.195587791 1.848222396 0.105177999 0.032257446 2.520065773 -0.401411876 0.250264581 ECPGIEPVCVDLGDWEATER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ECPGIEPVCVDLGDWEATER 20 0 Q7Z4W1;J3KS22;J3QS36 Q7Z4W1 DCXR L-xylulose reductase 0 ;; 255.72 8.46E-36 236679000 233952 250953 236678 227484 246757 225126 299673 234919 296064 FALSE TRUE 219309.3619 269533.8212 242292.1139 233321.6246 227377.7006 290116.2216 254739.8157 264249.1543 246649.0058 0.88915567 1.092782922 0.98233566 0.945966208 0.921867493 1.17623106 1.032802929 1.071357062 1 17.91209995 2.256240703 24.99931494 1.072235482 0.984893007 0.335528315 0.069832105 318.1563231 449866.1361 0.023585008 0.019694765 180.401732 -2.256240703 -0.087342474 ECPPHAEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ECPPHAEQR 9 0 J3QT73;A0A087X1P5;J3KQ34;Q9H9Q2-2;Q9H9Q2 J3QT73 COPS7B COP9 signalosome complex subunit 7b 0 ; 126.39 0.00047492 381040000 172318 298330 213735 221765 278950 210779 240474 275070 254451 FALSE TRUE 161532.924 320418.6636 218804.8951 227455.8653 257042.3922 271627.4756 204417.1562 309413.095 211981.4843 0.762014308 1.511540806 1.032188712 1.072998739 1.212570018 1.28137359 0.96431609 1.459623212 1 17.69357873 -1.109721778 4.095834023 0.999962654 1.170541232 0.047977366 0.224097783 6.97E-05 1.52E-05 0.192097828 0.045267681 0.077674456 1.109721778 0.170578578 ECPSDECGAGVFMASHFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 ECPSDECGAGVFMASHFDR 19 0 P62979;A0A2R8Y422 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ;;;;;;;;;;;;; 333.92 1.72E-75 29818160000 7765007 8354849 8019890 8373983 8621780 7409342 9533910 6961963 8964080 FALSE TRUE 7279009.073 8973450.713 8210125.578 8588873.581 7944660.177 9548298.755 8104388.704 7831179.406 7467917.138 0.974704049 1.201600198 1.099386272 1.150102957 1.063838823 1.278575884 1.085227454 1.04864305 1 22.83227449 1.241593866 3.036059788 1.011110209 1.134174973 0.212732744 0.080772678 0.323093131 5.109664291 0.06428023 0.018385726 17.44190296 -1.241593866 0.123064763 ECREPELGLEELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ECREPELGLEELLR 14 1 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 0 ;;;;; 176.23 2.06E-06 276982000 209030 267723 245957 262163 298533 235692 292985 217860 342776 FALSE TRUE 195947.1854 287545.4895 251791.2162 268890.5464 275087.4224 303732.4543 249054.6192 245060.3006 285564.4712 0.686174945 1.006937202 0.881731593 0.941610647 0.963311091 1.063621301 0.872148479 0.858161029 1 18.12345697 4.747200291 24.95080495 0.944187003 0.686174812 0.615025062 0.065132599 752.2051449 2172270.261 0.014924415 0.176746358 55872.78127 -4.747200291 -0.258012191 ECS(ph)PTSSLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ECSPTSSLER 10 0 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 ECS(0.406)PT(0.185)S(0.378)S(0.031)LER;ECS(0.932)PT(0.067)S(0.001)SLER 194.49 4.81E-07 740100000 1268520 1103650 1214680 1158870 1248670 984130 1355700 999390 1225230 TRUE FALSE 1189125.598 1185365.394 1243492.783 1188608.566 1150604.495 1268232.355 1152425.371 1124166.041 1020731.198 1.164974285 1.161290452 1.218237266 1.164467755 1.127235552 1.242474373 1.129019445 1.101334067 1 19.96117156 1.007162432 1.579870366 1.001645391 1.179365054 0.741929178 0.033616056 0.184351084 0.941565602 0.029323806 0.00858265 10.16628856 -1.007162432 0.177719663 ECS(ph)VEKGTGDSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ECSVEKGTGDSLR 13 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 ECS(0.991)VEKGT(0.009)GDSLR 56.25 0.074841 209040000 178000 143610 146580 170420 213430 89386 180450 150290 384980 TRUE FALSE 166859.2977 154243.0338 150056.9468 174793.2657 196668.0687 115190.2871 153393.1977 169054.0373 320724.3509 0.520257652 0.48092087 0.467868892 0.544995306 0.613199678 0.359156661 0.47827113 0.527100723 1 18.29097437 0.729870055 4.048142912 0.999997061 0.489665991 0.858198306 0.064104461 1.707311624 25.29319406 0.059406609 0.015165486 5.368711357 -0.729870055 -0.51033107 ECSEAMEVETSVISIDS(ph)PQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ECSEAMEVETSVISIDSPQK 20 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 ECSEAMEVETSVISIDS(1)PQK;ECSEAMEVETSVIS(0.001)IDS(0.999)PQK 129.84 1.11E-05 70275000 236280 162836 184735 178741 184912 140132 230600 174777 188204 TRUE FALSE 221491.6566 174892.5469 189117.0014 183327.7967 170389.7574 180585.8335 196023.6708 196598.2932 156791.5366 1.41265059 1.115446348 1.20616843 1.169245488 1.086728029 1.151757534 1.250218443 1.253883325 1 17.25848816 4.745931895 24.76228199 1.166438138 1.412650723 0.522723473 0.076828251 641.4998604 2154925.26 0.017130524 0.17664378 55709.83792 -4.745931895 0.246212586 ECSEAMEVETSVISIDS(ph)PQKLAILDQELEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ECSEAMEVETSVISIDSPQKLAILDQELEHK 31 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 ECSEAMEVET(0.001)S(0.001)VIS(0.01)IDS(0.987)PQKLAILDQELEHK 129.63 2.76E-06 43999000 32659 30020 31991 34051 48861 20363 45070 31906 100840 TRUE FALSE 30614.93149 32242.71204 32749.84163 34924.80631 45023.65416 26241.46753 38312.17191 35889.53433 84009.15255 0.364423763 0.383799992 0.389836591 0.415726207 0.535937488 0.312364388 0.456047594 0.427209813 1 16.35825889 -5 0.359703296 8.289235381 0.39168064 0.913359875 0.057188098 118.2977586 0.942568104 667.4809564 0.038024334 1.00E-05 5 -7.89755474 ECSPT(ph)SSLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ECSPTSSLER 10 0 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 ECS(0.472)PT(0.524)S(0.004)SLER 172 4.30E-05 260520000 639830 474660 542170 532500 598090 436560 665760 485720 627300 TRUE FALSE 599784.1824 509804.3203 555030.5284 546164.8515 551118.424 562587.785 565935.4686 546363.2112 522599.5775 1.147693585 0.975516136 1.062056979 1.045092409 1.054571124 1.076517872 1.082923701 1.045471973 1 18.99534643 2.59785488 3.785343011 1.061812392 1.044648808 0 0.047680262 1.108171915 28.16619201 0.015011516 0.013942675 396.14564 -2.59785488 -0.017163584 ECSPTS(ph)SLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ECSPTSSLER 10 0 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 ECS(0.011)PT(0.011)S(0.977)S(0.001)LER 136.27 0.00012807 375670000 530730 467600 482170 486890 476790 418260 567380 420470 488970 TRUE FALSE 497512.5567 502221.5905 493607.3001 499384.4217 439344.8367 539004.8721 482306.6363 472966.6051 407357.7481 1.221316052 1.232875999 1.211729254 1.22591119 1.078523334 1.323173242 1.183987879 1.161059553 1 18.63593682 0.799563676 2.024148473 1.000340838 1.213948753 0.557457661 0.059148426 0.503560086 3.562484447 0.050391346 0.01392675 6.303237573 -0.799563676 0.213607915 ECSPWMSDFKVEFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ECSPWMSDFKVEFLR 15 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 108.34 0.00099108 88726000 154440 149700 121070 135290 161260 104600 158470 131510 154850 FALSE TRUE 144773.8761 160783.9438 123941.8376 138761.7704 148595.2901 134796.322 134708.8947 147929.313 129004.5346 1.12223866 1.246343349 0.960755666 1.075634828 1.151860983 1.044895998 1.044218291 1.146698551 1 16.97706225 3.989675088 22.14018504 1.062210139 1.18195506 0.385795576 0.064853926 91.12302185 160700.5001 0.014922328 0.031773723 9765.063859 -3.989675088 0.119744921 ECYQSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ECYQSHR 7 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 159.46 0.0013828 534660000 679620 946410 697900 698010 1000810 552810 790550 837800 921880 FALSE TRUE 637083.7974 1016483.181 714454.5176 715922.1183 922210.4197 712397.2729 672014.3666 942401.1742 768012.2724 0.829522939 1.323524659 0.930264454 0.932175362 1.200775629 0.927585793 0.875004724 1.227065254 1 19.55076984 3.747420744 23.72702814 0.999632889 1.116335177 0.007034957 0.165817244 562.433621 657392.8526 0.039183791 0.070505882 5590.115021 -3.747420744 0.116702288 EDAANNYAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 EDAANNYAR 9 0 P68363;P68363-2;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;F8VWV9;F8VX09;P68366-2;P68366;C9JEV8;C9JQ00;C9JJQ8;C9JDL2;Q9BQE3;F5H5D3;A0A1W2PQM2;A6NHL2-2;A6NHL2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA1A;TUBA1C;TUBA4A;TUBAL3 Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain;Tubulin alpha chain-like 3 0 ;;;;;;;;; 232.37 4.46E-08 28652860000 9266484 9619939 9392498 9551923 10397323 7918170 10927437 9603044 10996160 FALSE TRUE 8686511.308 10332209.29 9615292.488 9797041.516 9580759.192 10204017.14 9288969.267 10802005.18 9160829.858 0.94822319 1.127868267 1.04960933 1.069449129 1.045839661 1.113874758 1.013987751 1.179151381 1 23.12704686 EDAEHHPDEDVDESES ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDAEHHPDEDVDESES 16 0 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 ; 161.21 8.51E-09 1073770000 996460 931450 1011660 997180 879060 846110 1143500 867530 716360 FALSE TRUE 934093.3473 1000415.527 1035657.053 1022769.327 810022.1736 1090368.222 972042.7907 975843.0302 596794.8881 1.565183224 1.676313834 1.735365154 1.713770254 1.357287386 1.827040149 1.628771979 1.635139727 1 19.18687565 0.404743581 2.37108157 1.000002296 1.655683649 0.72693836 0.123566105 6.950999646 26.91666337 0.108307605 0.029069029 2.539472891 -0.404743581 0.655681354 EDAGDNDDTEGAIGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDAGDNDDTEGAIGVR 16 0 Q9H0S4;Q9H0S4-2 Q9H0S4 DDX47 Probable ATP-dependent RNA helicase DDX47 0 281.94 3.52E-35 57620000 128100 124560 128230 122920 105560 109890 145610 111440 104220 FALSE TRUE 120082.4497 133782.552 131271.6762 126074.3353 97269.74341 141613.4591 123777.1323 125353.5293 86825.00871 1.38303988 1.540829699 1.51191089 1.452050938 1.120296385 1.631021536 1.425593088 1.443749113 1 16.40582303 0.367456328 2.451977532 1.000000976 1.452804299 0.515662638 0.132979576 16.55069044 62.71819053 0.120194053 0.032117758 2.330538748 -0.367456328 0.452803323 EDAKEDHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDAKEDHER 9 1 P57740;P57740-2;P57740-3 P57740 NUP107 Nuclear pore complex protein Nup107 0 78.342 0.018052 139210000 516410 425530 469370 489280 472620 318640 540950 410270 627150 FALSE TRUE 484088.8199 457036.684 480503.6781 501835.7531 435502.3317 410626.1953 459839.5694 461493.1126 522474.6135 0.926530797 0.874753858 0.919668948 0.96049787 0.833537784 0.785925641 0.880118493 0.883283323 1 18.99500141 2.724863137 24.98205863 0.862654469 0.912645716 0.091580897 0.05802028 1435.682617 2618458.526 0.01733974 0.016424722 530.717169 -2.724863137 0.049991247 EDALDDSVSSSSVHAS(ph)PLASSPVRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDALDDSVSSSSVHASPLASSPVRK 25 1 P49792;J3KNE0;A6NKT7;Q7Z3J3;O14715;Q99666;J3KQ37 P49792 RANBP2;RGPD3;RGPD4;RGPD8;RGPD5 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6 1 EDALDDSVSS(0.001)S(0.005)S(0.021)VHAS(0.325)PLAS(0.325)S(0.325)PVRK 90.907 0.0062596 115320000 20912 45608 46366 47714 38716 35209 23252 25752 19875 TRUE FALSE 19603.15525 48984.86378 47465.82342 48938.42202 35675.40153 45373.26673 19765.57846 28967.19389 16557.7341 1.18392741 2.958427975 2.866685932 2.955623138 2.154606501 2.740306521 1.193736917 1.749466063 1 14.01521764 1.734210813 7.373810782 1.366525484 2.583439558 0.478741011 0.562451682 0.09663391 15.77423951 0.258345321 0.136447494 54.226405 -1.734210813 1.216914074 EDALDDSVSSSSVHASPLAS(ph)SPVRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EDALDDSVSSSSVHASPLASSPVRK 25 1 P49792;J3KNE0;A6NKT7;Q7Z3J3;O14715;Q99666;J3KQ37 P49792 RANBP2;RGPD3;RGPD4;RGPD8;RGPD5 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6 1 EDALDDSVSSSSVHASPLAS(0.5)S(0.5)PVRK;EDALDDSVSSSSVHAS(0.001)PLAS(0.5)S(0.5)PVRK;EDALDDSVSSSSVHASPLAS(0.5)S(0.5)PVRK;EDALDDSVSSSSVHAS(0.014)PLAS(0.493)S(0.493)PVRK 280.71 1.38E-53 3147860000 348869 931350 989177 1115840 961676 744079 933074 686053 471279 TRUE FALSE 327033.912 1000308.123 1012640.746 1144474.344 886149.8462 958882.5282 793168.2159 771708.2272 392619.4903 0.83295384 2.547780097 2.579191228 2.914970784 2.257019501 2.442269301 2.020195725 1.965537235 1 18.58277227 0.77216371 1.094494082 1.005559347 2.352688207 0.316343234 0.555555472 0.883600847 1.937771312 0.490607465 0.154949206 5.917846688 -0.77216371 1.34712886 EDAPIGPHLQSMPSEQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDAPIGPHLQSMPSEQIR 18 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 199.41 1.63E-15 380120000 180399 204912 229290 221212 223787 169683 238296 202539 238747 FALSE TRUE 169108.1486 220083.8977 234728.8671 226888.6744 206211.6717 218667.7275 202565.727 227826.44 198898.5833 0.850222992 1.106513149 1.180143484 1.140725442 1.036767926 1.099393087 1.018437254 1.145440235 1 17.60167347 -1.596512079 8.391210957 0.999966111 1.082377132 0.046602743 0.093020835 5.59E-05 2.69E-06 0.085402884 0.020121384 0.025321412 1.596512079 0.08241102 EDAQVAAEILEIADTPSGDKTSLETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EDAQVAAEILEIADTPSGDKTSLETR 26 1 P08133;P08133-2;E7EMC6 P08133 ANXA6 Annexin A6;Annexin 0 ;; 235.57 5.86E-45 191868000 143856 110843 134474 97734 160399 69294.6 161707 138741 274134 FALSE TRUE 134852.3098 119049.9311 137663.7868 100242.0199 147801.9096 89298.82612 137460.5366 156063.1193 228379.2644 0.590475278 0.521281699 0.60278584 0.438927852 0.647177448 0.391011094 0.601895872 0.683350652 1 17.80107214 0.857461658 1.883258677 0.99885989 0.538599996 0.783491287 0.076682849 0.21547685 1.473863388 0.063298302 0.017753117 7.202141645 -0.857461658 -0.460259894 EDCCPGKPLNVFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDCCPGKPLNVFR 13 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 83.53 0.0092665 389490000 281360 269300 279120 261230 283290 212030 310680 256870 316030 FALSE TRUE 263750.1798 289239.2522 285740.8582 267933.6041 261041.5461 273239.619 264096.4182 288940.7849 263282.5514 1.001776147 1.098588762 1.085301159 1.017665632 0.991488212 1.037818942 1.00309123 1.097455124 1 18.00625239 3.233550491 24.95224155 1.022659182 1.073097632 0.149108153 0.038876784 148.5248236 739707.8546 0.010379425 0.012762353 1712.184224 -3.233550491 0.05043845 EDDDVIVNKPHVS(ph)DEEEEEPPFYHHPFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 EDDDVIVNKPHVSDEEEEEPPFYHHPFK 28 1 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;H7C1M2;H7C2G8;J3QSZ5 P18583-7 SON Protein SON 1 EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;EDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK 282.1 3.94E-62 11805470000 12997840 5929787 8309110 7431110 7192760 6320597 11492640 6933950 7858460 TRUE FALSE 12184328.4 6368834.599 8506206.013 7621804.863 6627869.644 8145250.748 9769425.324 7799668.921 6546832.258 1.861102884 0.972811636 1.299285773 1.164197365 1.012378106 1.244151435 1.492236999 1.191365322 1 22.64236558 4.751048254 24.66388104 1.198416344 1.861103384 0.649555238 0.158006463 1176.479556 2323571.618 0.039315046 0.68899584 56370.02845 -4.751048254 0.66268704 EDDKYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EDDKYR 6 1 P20839-3;P20839-7;P20839-5;P20839-6;P20839;A0A3B3IRL5;C9J381;P20839-2;P20839-4;C9K0R9 P20839-3 IMPDH1 Inosine-5-monophosphate dehydrogenase 1;Inosine-5-monophosphate dehydrogenase 0 ;; 119.22 0.019332 2175950000 5202700 3680760 4078400 3802410 4159000 3076450 4412000 3738300 4193200 FALSE TRUE 4877072.294 3953287.3 4175141.574 3899986.278 3832368.917 3964571.173 3750461.559 4205034.984 3493327.831 1.39611068 1.131667994 1.195175997 1.116410044 1.097053899 1.134898116 1.073607099 1.203733285 1 21.73617061 7.387908708 1.198428366 1.119869413 199.9999997 0.672661191 0.059802656 614.2310957 1.603045844 0.014868028 334967.2484 24429169.81 -7.387908708 198.8801303 EDDKYRLDLLTQAGVDVIVLDSSQGNSVYQIAMVHYIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDDKYRLDLLTQAGVDVIVLDSSQGNSVYQIAMVHYIK 38 2 P20839-3;P20839-7;P20839-5;P20839-6;P20839;A0A3B3IRL5;C9J381;P20839-2;P20839-4 P20839-3 IMPDH1 Inosine-5-monophosphate dehydrogenase 1;Inosine-5-monophosphate dehydrogenase 0 121.82 1.26E-08 47749000 70506 53903 52269 59877 91552 48239 86250 51838 125780 FALSE TRUE 66093.15532 57894.03421 53508.84536 61413.54519 84361.87522 62164.81621 73317.61321 58310.08841 104786.5054 0.630741096 0.552495133 0.510646339 0.586082578 0.805083392 0.593252117 0.699685641 0.556465627 1 16.67709341 -5 0.197373968 2.743772329 0.544824726 0.661037923 0.085385372 81.41741923 0.803908967 55.90741977 0.205250168 1.00E-05 5 -2.198947604 EDDRETLVSQCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDDRETLVSQCR 12 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 0 190.37 6.14E-06 460650000 863030 725930 833050 769080 822040 641060 952010 666100 930900 FALSE TRUE 809014.4929 779678.6125 852810.3394 788815.8948 757480.2943 826123.6153 809264.9385 749264.0513 775526.7762 1.043180607 1.005353569 1.099652992 1.017135603 0.976730034 1.065241898 1.043503543 0.966135631 1 19.56481707 1.246036555 24.98776015 0.983067811 1.038262449 0.29123166 0.034054406 183.5009966 613353.5298 0.023427608 0.008180127 17.62124359 -1.246036555 0.055194638 EDDRVAIHEAMEQQTISIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDDRVAIHEAMEQQTISIAK 20 1 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ; 153.14 3.38E-08 509720000 364800 370360 340540 381470 517640 298400 424970 337530 686060 FALSE TRUE 341967.8192 397781.8398 348617.7696 391259.166 476986.6425 384543.2359 361249.6937 379671.3635 571552.1539 0.598314287 0.695967703 0.609949184 0.684555492 0.834546138 0.672805156 0.632050271 0.664281222 1 19.12452562 -2.171513666 2.356770958 1.831152949 0.672322054 0.712582669 0.065046699 6302150.452 1534869.884 27926781.42 0.015521896 0.006737307 2.171513666 -1.158830895 EDDSDKYCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDDSDKYCK 9 1 P35573-2;P35573-3;P35573 P35573-2 AGL "Glycogen debranching enzyme;4-alpha-glucanotransferase;Amylo-alpha-1,6-glucosidase" 0 ; 113.12 0.0016896 446310000 716100 373158 480710 480510 550300 399987 754800 459017 701460 FALSE TRUE 671280.5793 400787.0066 492112.6682 492840.7001 507081.6578 515456.7537 641624.7472 516326.2829 584381.7944 1.148702074 0.685830754 0.842108144 0.843353959 0.867723229 0.882054778 1.097954716 0.883542725 1 19.15655171 1.928677489 7.395153251 1.002130708 0.847376967 0.134992032 0.124995724 0.38626607 35.29786217 0.049787176 0.031069122 84.85501007 -1.928677489 -0.154753741 EDEDPHRPPTSEELLTAYGYMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EDEDPHRPPTSEELLTAYGYMR 22 1 Q9H089;H7C2X7 Q9H089 LSG1 Large subunit GTPase 1 homolog 0 ;;; 109.85 0.00022618 297035000 606715 617540 607320 580422 701590 476627 662900 594934 827590 FALSE TRUE 568741.7912 663263.3041 621725.9172 595316.6112 646489.9515 614221.4775 563504.2991 669212.8195 689459.8826 0.824909187 0.962004202 0.901757931 0.863453591 0.937675952 0.890873411 0.817312672 0.970633443 1 19.39510708 1.042490477 10.05448797 0.999990811 0.892185214 0.464858033 0.044715909 0.320980797 72.5744757 0.043565932 0.010897333 11.02784052 -1.042490477 -0.107805597 EDEEESLNEVGYDDIGGCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EDEEESLNEVGYDDIGGCR 19 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 482.88 1.08E-239 491384000 569016 446843 474642 423564 414233 390008 636557 446295 524114 FALSE TRUE 533402.3043 479927.7207 485900.7324 434433.3693 381700.8111 502596.9783 541111.1874 502015.9132 436635.9875 1.221617823 1.09914834 1.112827953 0.994955482 0.874185413 1.151066318 1.239272994 1.149735541 1 18.73607152 -0.846119319 8.057527717 0.999999958 1.107174481 0.088562401 0.106070534 0 0 0.107445486 0.025325144 0.142521597 0.846119319 0.107174523 EDEGPPGYPEPLAPGHGS(ph)PFPSLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDEGPPGYPEPLAPGHGSPFPSLSK 25 0 B1AKB5;B0QYS6;B0QYS7;P19484-2;P19484 B1AKB5 TFEB Transcription factor EB 1 EDEGPPGYPEPLAPGHGS(1)PFPSLSK;EDEGPPGYPEPLAPGHGS(1)PFPSLSK 248.69 2.39E-39 374120000 472170 300080 388990 336950 371610 384800 575040 412830 387150 TRUE FALSE 442617.7225 322298.2354 398217.0265 345596.7075 342425.2496 495885.5133 488818.0904 464372.7343 322532.1639 1.372321189 0.999274713 1.234658341 1.071510832 1.061677835 1.537476161 1.515563857 1.439771862 1 18.29908351 2.24234474 24.99999351 1.431148823 1.135983561 0.248532935 0.182072864 91.47740676 604353.9394 0.057647821 0.046530211 174.7208525 -2.24234474 -0.295165262 EDEGWQVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDEGWQVYR 9 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 141.52 0.0002478 274640000 161090 125970 134170 125090 132060 126970 158240 111080 120400 FALSE TRUE 151007.6645 135296.9499 137352.5758 128300.0212 121688.5403 163624.1778 134513.381 124948.5825 100304.4622 1.505492988 1.348862722 1.369356585 1.279105818 1.213191693 1.631275162 1.341050818 1.245693161 1 16.61402626 0.92526597 2.588537038 1.001370637 1.380297493 0.534302659 0.115023664 0.271041514 4.077854839 0.103368649 0.02767432 8.419105853 -0.92526597 0.378926855 EDEIPVLKDELIHELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDEIPVLKDELIHELK 16 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 155.11 1.75E-07 43245000 228450 101504 156170 143157 135061 101952 196048 123576 135402 FALSE TRUE 214151.7223 109019.4618 159874.4261 146830.651 124453.8539 131383.8873 166652.4224 139004.7356 112802.5315 1.898465571 0.966462901 1.417294666 1.301660956 1.103289547 1.164724635 1.477381937 1.232283831 1 16.78343992 7.999999111 0.023750521 2.90E-07 2.9964154 0.185293447 0.245183229 5488.601134 10.02766532 443.0561101 895.0975613 99999795.24 -7.999999111 2.99641511 EDEIS(ph)PPPPNPVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDEISPPPPNPVVK 14 0 P10644;P10644-2;K7EPB2;K7EIE5;K7EID3;K7EJ40;K7EK41;K7EMU2;K7EMZ6 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 1 EDEIS(1)PPPPNPVVK;EDEIS(1)PPPPNPVVK 212.24 2.85E-09 517780000 1840250 995120 1309690 1063910 1092900 1267060 1877210 1173060 1298020 TRUE FALSE 1725072.037 1068799.72 1340756.465 1091211.732 1007068.043 1632839.653 1595739.788 1319519.123 1081372.076 1.595262237 0.9883737 1.239865995 1.009099232 0.931287264 1.509970239 1.475662099 1.22022674 1 20.04443158 2.229762477 24.9984083 1.361551226 1.135703791 0.063836665 0.23269109 312.641962 888311.845 0.079632614 0.059703446 169.7315108 -2.229762477 -0.225847435 EDENSWFNLFVIHQNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDENSWFNLFVIHQNR 16 0 F8W7U8;P49959-2;P49959;P49959-3;F5GXT0 F8W7U8 MRE11A Double-strand break repair protein MRE11A 0 152.34 5.57E-07 31511000 27107 30722 28056 32348 32842 27273 35397 27409 29280 FALSE TRUE 25410.42126 32996.68885 28721.50157 33178.10445 30262.7218 35146.27236 30089.54846 30831.07398 24392.97884 1.041710462 1.35271256 1.177449534 1.360149765 1.240632478 1.440835602 1.233533168 1.263932305 1 14.57417833 0.421256527 2.142063561 1.000009856 1.272613084 0.364016253 0.109169202 8.96035742 31.8049591 0.092074528 0.025059495 2.637889064 -0.421256527 0.272603228 EDERPEGPGAAWPGLEGQAYSQLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EDERPEGPGAAWPGLEGQAYSQLER 25 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 ;;; 218.49 1.30E-33 907276000 170197 145720 143025 152491 161241 116463 183863 135835 149432 FALSE TRUE 159544.6736 156509.2604 146417.6205 156404.1772 148577.7823 150083.9775 156294.4501 152794.2988 124490.8338 1.281577677 1.257195053 1.176131736 1.256350949 1.19348371 1.205582555 1.255469541 1.227353806 1 16.92568 0.902979153 20.95539285 1 1.229458527 0.832446294 0.032648791 12537.83804 2708033.364 0.0304614 0.00761535 7.997958624 -0.902979153 0.229458528 EDEVEEWQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EDEVEEWQHR 10 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;; 189.72 9.80E-07 1118880000 2432890 2302610 2369500 2313830 2776320 1933160 2793780 2230090 2673260 FALSE TRUE 2280619.758 2473097.64 2425705.659 2373206.795 2558279.026 2491231.91 2374878.625 2508521.646 2227075.636 1.024042345 1.110468634 1.089188719 1.065615714 1.148716723 1.118611272 1.066366398 1.126374697 1 21.08671913 -1.029577127 4.057354051 0.999989073 1.094591414 0.405791083 0.035608003 2078027.384 527419.1637 199.2700007 0.007544717 0.093416345 1.029577127 0.094602341 EDFATFDYILCMDESNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDFATFDYILCMDESNLR 18 0 P24666;P24666-3;P24666-2 P24666;P24666-2 ACP1 Low molecular weight phosphotyrosine protein phosphatase 0 ; 224.43 1.07E-18 53130000 51041 50876 48307 47292 50634 54515 73662 44166 57255 FALSE TRUE 47846.43492 54642.91198 49452.86485 48505.59279 46657.40989 70252.59552 62617.06694 49680.22232 47698.77062 1.003095767 1.145583236 1.036774412 1.016914947 0.978167975 1.472838704 1.312760604 1.041540939 1 15.54166446 2.272751459 24.9998867 1.249982079 1.050254373 0.240866509 0.140375056 205.4598905 150228.8049 0.046192129 0.038645299 187.392178 -2.272751459 -0.199727706 EDFEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EDFEEAR 7 0 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ;; 143.56 0.0056153 5768000000 7893230 6605030 7331310 7384720 6648690 5966250 7838630 6384580 4643780 FALSE TRUE 7399206.824 7094073.294 7505212.135 7574224.418 6126528.707 7688609.521 6663300.202 7181708.867 3868703.118 1.912580676 1.833708371 1.939981411 1.95782002 1.58361304 1.987386803 1.722360181 1.856360813 1 21.88341859 -2.149702672 0.377148225 9.08E-13 1.884823719 0.83601568 0.118533601 16.71814627 0.890275405 14.33917664 0.072587677 0.007084306 2.149702672 1.884823719 EDFPQKWPDLLTEMVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDFPQKWPDLLTEMVNR 17 1 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 ; 133.86 1.72E-05 1176210000 773310 812040 816880 836940 903730 628350 1021360 777940 923390 FALSE TRUE 724909.9075 872164.2865 836256.7794 858417.2973 832754.6913 809744.4446 868216.5498 875067.5215 769270.2437 0.942334522 1.133755392 1.087078028 1.115885223 1.082525547 1.052613761 1.128623597 1.137529404 1 19.55313098 4.746641031 24.8846796 1.098284357 0.942334441 0.54937214 0.042358484 644.3424735 1984287.245 0.008947612 0.099242339 55800.87782 -4.746641031 -0.155949916 EDGEGPEATNAVTFDADDDSIIHLLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDGEGPEATNAVTFDADDDSIIHLLHK 27 0 B7Z896;F5H3M2;Q9BVG8-5;Q9BVG8-2;Q9BVG8;Q9BVG8-6;A0A0C4DGM9;Q9BVG8-4 B7Z896 KIFC3 Kinesin-like protein;Kinesin-like protein KIFC3 0 71.091 0.011794 23869000 10942 11014 12337 9393.9 13995 8598 10765 10578 12485 FALSE TRUE 10257.15975 11829.48802 12629.63947 9634.963378 12895.88915 11080.10302 9150.888187 11898.68659 10401.17284 0.986154149 1.137322511 1.214251475 0.92633432 1.23984952 1.065274387 0.879793878 1.143975469 1 13.3444586 1.993111481 24.95097981 0.989058684 1.116579838 0.107989039 0.112757044 446.0703507 1615718.622 0.040216815 0.028587723 98.42637286 -1.993111481 0.127521155 EDGKVFDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDGKVFDEK 9 1 Q9Y5Z4-2;Q9Y5Z4 Q9Y5Z4-2 HEBP2 Heme-binding protein 2 0 ; 103.22 0.0031534 659140000 2232000 1439570 1724410 1725380 1991850 1172480 2324800 1360410 3042000 FALSE TRUE 2092303.104 1546157.261 1765313.82 1769656.172 1835418.136 1510955.942 1976217.822 1530260.183 2534270.548 0.825603685 0.610099526 0.696576702 0.698290154 0.724239224 0.596209408 0.779797494 0.603826685 1 21.27313912 -1.854309324 2.703175741 1.12571048 0.688619292 0.625936323 0.074832066 8742660.735 5799658.387 7081814.527 0.016156048 0.013985908 1.854309324 -0.437091188 EDGLAQQQTQLNLR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 366.53 1.26E-96 3711780000 1023190 1157300 1076990 1162050 1231200 931050 1387910 1066160 1296670 FALSE TRUE 959150.3643 1242987.696 1102536.711 1191870.17 1134506.518 1199829.021 1179805.78 1199272.423 1080247.4 0.887898794 1.150650949 1.020633525 1.103330746 1.050228418 1.110698365 1.092162573 1.110183114 1 20.04293033 4.751141851 24.89659243 1.08314349 0.887898665 0.638849552 0.045264998 1124.64862 2225487.818 0.009555417 0.171508771 56382.17839 -4.751141851 -0.195244825 EDGNEEDKENQGDETQGQQPPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EDGNEEDKENQGDETQGQQPPQR 23 1 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;;;;; 275.2 9.25E-52 6204290000 4126543 2022186 2769674 2542637 2518294 1860684 3522231 2259443 2677508 FALSE TRUE 3868270.04 2171910.756 2835371.975 2607885.37 2320517.348 2397833.265 2994105.16 2541539.432 2230614.617 1.734172281 0.973682652 1.271116917 1.169133094 1.040304017 1.074965279 1.342278104 1.13938975 1 21.08900985 4.749180389 24.725236 1.146203112 1.73417267 0.72713476 0.116451808 726.8970875 1692342.608 0.027339912 0.391917276 56128.1062 -4.749180389 0.587969557 EDGNEEDKENQGDETQGQQPPQRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EDGNEEDKENQGDETQGQQPPQRR 24 2 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;; 249.59 1.54E-38 2067790000 1367090 888320 1018910 1011100 1237680 699630 1519060 867990 2252860 FALSE TRUE 1281526.277 954092.1371 1043079.026 1037046.538 1140477.605 901601.8235 1291291.055 976360.4622 1876843.112 0.682809484 0.508349436 0.555762503 0.552548336 0.6076574 0.480382094 0.688012252 0.520214213 1 20.83987663 -4.999997112 0.388066218 7.392268777 0.561891998 0.781213288 0.070367456 266.2577934 1.938443874 1436.262283 0.040757273 1.00E-05 4.999997112 -6.830376779 EDGSFAGDIWGEIDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDGSFAGDIWGEIDTR 16 0 P53611 P53611 RABGGTB Geranylgeranyl transferase type-2 subunit beta 0 87.363 0.01511 15632000 8336.4 7967.8 8426.1 8074.5 8902.1 7753.4 9913.6 6818 6153.5 FALSE TRUE 7814.639605 8557.744202 8625.971071 8281.70534 8202.964975 9991.680714 8427.147713 7669.242308 5126.441097 1.524379088 1.669334347 1.682643165 1.615488247 1.600128592 1.949048185 1.643859269 1.496016859 1 12.3237419 0.847255232 2.559479967 1.000748185 1.678246616 0.786774056 0.109579909 0.251032554 3.069479952 0.099774618 0.02666423 7.034856318 -0.847255232 0.677498431 EDGSGDRGDGPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EDGSGDRGDGPFR 13 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;; 177.42 1.41E-05 5716240000 5435020 6107600 5781870 5858760 6227320 4713640 6838740 5705260 6395140 FALSE TRUE 5094851.8 6559813.059 5919018.687 6009105.7 5738251.407 6074391.348 5813334.425 6417574.27 5327749.82 0.956285857 1.231253959 1.110979098 1.127888115 1.077049712 1.140142003 1.091142531 1.204556236 1 22.34509491 -1.511674647 3.012577774 0.995791552 1.124655524 0.191625767 0.074477778 13910069.08 13290301.38 467796.5572 0.015943813 0.030784021 1.511674647 0.128863972 EDGTFYEFGEDIPEAPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDGTFYEFGEDIPEAPER 18 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 221.66 1.42E-18 51928000 60761 57768 53626 61589 65714 57773 69647 51280 67940 FALSE TRUE 56958.07747 62045.20283 54898.03404 63169.47801 60553.08752 74451.12723 59204.07892 57682.42088 56600.37509 1.006319788 1.096197732 0.969923502 1.11606112 1.069835446 1.315382223 1.04600153 1.01911729 1 15.78852399 3.207976921 24.84368501 1.107141191 1.031840195 0.102401497 0.092152038 369.3864762 300058.1276 0.02547049 0.030446443 1614.272772 -3.207976921 -0.075300996 EDGVTPYMIFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDGVTPYMIFFK 12 0 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;P13693-2;H0YCX0 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 178.08 5.22E-05 44150000 135190 145990 125240 118140 155990 133260 187900 139820 109980 FALSE TRUE 126728.6992 156799.2515 128210.7519 121171.6724 143739.1746 171729.9987 159726.1394 157276.8348 91623.6275 1.383144312 1.711340795 1.399319755 1.322493725 1.568800304 1.874298185 1.743285479 1.716553241 1 16.48343206 2.473894537 24.89846071 1.671304507 1.483608561 0.002414485 0.256926819 202.3634824 1561476.811 0.080156414 0.067387009 297.7793223 -2.473894537 -0.187695945 EDGWIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDGWIR 6 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ; 130.84 0.036268 1538660000 1744790 1900520 1740350 1690890 1914850 1343500 1937250 1641810 1762990 FALSE TRUE 1635586.708 2041236.478 1781631.924 1734281.1 1764465.405 1731346.64 1646777.347 1846793.593 1468735.58 1.113601884 1.389791673 1.2130379 1.180798725 1.201349943 1.178800775 1.121221117 1.257403728 1 20.48614326 -4.999999939 0.106469346 0.279954487 1.353353271 0.377903137 0.079602781 149.9978296 1.071523828 23.49154964 1.036862233 1.00E-05 4.999999939 1.073398784 EDHLVYADEESSNITDGRIT(ph)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 EDHLVYADEESSNITDGRITPEPAVSNTEEPSTTSTASNYPDVLTRPSLHR 51 2 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 EDHLVYADEESSNIT(0.001)DGRIT(0.999)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEESSNITDGRIT(1)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEESSNIT(0.048)DGRIT(0.952)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEESSNITDGRIT(1)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEESSNIT(0.001)DGRIT(0.999)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEESSNIT(0.03)DGRIT(0.97)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEESSNITDGRIT(0.999)PEPAVS(0.001)NTEEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEESSNITDGRIT(1)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEESSNITDGRIT(1)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR 443.09 3.42E-274 10980490000 353931 545440 525153 544594 569425 503151 633260 519433 514532 TRUE FALSE 331779.0905 585824.9451 537609.8772 558569.204 524704.6574 648402.5257 538308.5419 584285.3535 428653.2852 0.774003377 1.366663841 1.254183499 1.303079256 1.22407707 1.512650312 1.255813406 1.363072146 1 18.70945167 4.742842559 24.94039848 1.302063595 0.774003161 0.598653862 0.130808998 249.900111 1455501.202 0.026563179 0.207805242 55314.9544 -4.742842559 -0.528060434 EDIDAAIETYNLLSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDIDAAIETYNLLSER 16 0 P23921 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ; 237.21 2.19E-19 37934000 46801 40151 46156 37350 32764 38937 45120 35668 34096 FALSE TRUE 43871.80895 43123.82182 47250.84212 38308.46423 30190.8476 50177.47981 38354.67487 40121.22831 28405.15733 1.54450153 1.518168737 1.663459968 1.348644677 1.062865002 1.766491881 1.350271517 1.412462809 1 14.79386527 -3.372116619 0.179524515 5.41E-10 1.592684089 0.385083941 0.187945652 70.80997201 1.159108739 27.12039646 0.605061084 0.000424506 3.372116619 1.592684088 EDINAIEMEEDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDINAIEMEEDKR 13 1 P49756;P49756-2;P49756-3;H0YE46 P49756 RBM25 RNA-binding protein 25 0 ; 109.07 0.0018698 455630000 496470 595240 575210 591900 634970 470950 686720 522460 882630 FALSE TRUE 465396.8289 639312.1889 588854.2528 607089.1561 585102.0175 606905.6198 583752.7112 587690.2811 735313.351 0.632923132 0.869441835 0.800820837 0.825619656 0.79571793 0.825370053 0.793882921 0.799237876 1 19.48799965 -2.256261406 1.970356339 1.632282654 0.802331383 0.52099084 0.061826874 3845067.743 591233.2631 10809317.01 0.013321269 0.00554292 2.256261406 -0.829951271 EDIQGALHNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDIQGALHNYR 11 0 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 0 ; 117.98 0.00078252 734670000 390100 450450 370250 430680 451470 355860 457220 315000 426680 FALSE TRUE 365684.3373 483801.7867 379032.5048 441731.9779 416013.3673 458591.0051 388664.1056 354328.4434 355464.3515 1.028751085 1.361041648 1.066302438 1.242689952 1.170337801 1.290118132 1.093398266 0.996804439 1 18.43934536 1.483566489 4.01505712 1.005268363 1.199050525 0.409790869 0.096815992 0.177626244 5.87053114 0.058728556 0.022661135 30.44854112 -1.483566489 0.193782163 EDIQSVMTEIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDIQSVMTEIRR 12 1 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ; 190.85 9.80E-06 207000000 171433 254340 204221 232580 266690 162449 251640 193128 340570 FALSE TRUE 160703.3145 273171.5982 209065.2186 238548.3966 245745.2432 209345.3892 213908.9181 217240.4559 283726.6668 0.56640187 0.962798461 0.736854314 0.840768332 0.866133754 0.737841781 0.753926025 0.765668093 1 18.11414223 -1.068440679 4.214243153 1.000024259 0.791350446 0.30568768 0.103238737 27756663212 1.09484E+11 12479047.33 0.022551709 0.085419952 1.068440679 -0.208673813 EDITQSAQHALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EDITQSAQHALR 12 0 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;;;;; 275.63 7.83E-28 6197100000 5020210 7470820 6518760 6510660 7293140 6120390 6828280 6266270 7573660 FALSE TRUE 4706004.017 8023967.286 6673388.066 6677734.558 6720366.204 7887247.237 5804442.805 7048627.603 6309567.218 0.745852109 1.271714368 1.057661775 1.058350649 1.065107316 1.250045679 0.919943097 1.117133293 1 22.58910962 1.703858023 25 1.011566888 1.094551282 0.026478274 0.149208154 1.982751666 1417.945015 0.062564428 0.034695103 50.56593282 -1.703858023 0.082984393 EDKLECSEELGDLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 147.17 3.43E-06 283560000 425250 228510 298700 313910 300720 227410 433230 302140 369330 FALSE TRUE 398634.3616 245429.1182 305785.3051 321965.462 277102.6642 293059.5753 368271.1834 339862.8441 307686.437 1.295586394 0.797659853 0.993821203 1.046407717 0.900600842 0.952461792 1.196904183 1.104575318 1 18.23110132 1.753665448 25 1.117605524 0.972348521 0.089321524 0.136127814 7.892852774 13080.15978 0.057824862 0.032067463 56.71075749 -1.753665448 -0.145257004 EDKNGHDGDTHQEDDGEKS(ph)D ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EDKNGHDGDTHQEDDGEKSD 20 2 K7EQH5;Q08117;Q08117-2 K7EQH5 AES Amino-terminal enhancer of split 1 EDKNGHDGDTHQEDDGEKS(1)D;EDKNGHDGDTHQEDDGEKS(1)D;EDKNGHDGDTHQEDDGEKS(1)D 241.59 4.95E-30 2438110000 1379790 601200 798760 771580 955050 562890 1092320 666710 1524350 TRUE FALSE 1293431.407 645713.4735 817706.9644 791380.0491 880044.2255 725387.2052 928536.7566 749950.2111 1269926.137 1.018509163 0.508465378 0.643901201 0.62317014 0.692988513 0.571204249 0.731173829 0.590546323 1 20.27631316 -1.241753726 3.525164239 1.00073052 0.655496548 0.349655941 0.138657129 228424101.7 352528755.5 1806627.197 0.02945449 0.057312094 1.241753726 -0.345233972 EDKPAETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDKPAETK 8 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 63.216 0.068141 126080000 241640 122210 169560 165590 174670 119770 198720 151260 212560 FALSE TRUE 226516.1837 131258.5556 173582.0433 169839.3197 160952.1228 154345.6547 168923.7808 170145.144 177082.3628 1.279157225 0.741228847 0.980233381 0.959097886 0.908911087 0.871603768 0.953927755 0.960824902 1 17.434061 1.025759235 2.22357226 0.998675782 0.932365541 0 0.135151773 1.385539467 14.63221915 0.114391346 0.031596615 10.61107136 -1.025759235 -0.066310241 EDKS(ph)PSEESAPTTSPESVSGSVPSSGSSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EDKSPSEESAPTTSPESVSGSVPSSGSSGR 30 1 P54725-2;P54725;A0A494C0B4;P54725-3 P54725-2;P54725-3 RAD23A UV excision repair protein RAD23 homolog A 1 EDKS(0.904)PS(0.083)EES(0.013)APTTSPESVSGSVPSSGSSGR;EDKS(0.965)PS(0.033)EES(0.002)APTTSPESVSGSVPSSGSSGR;EDKS(0.904)PS(0.093)EES(0.004)APTTSPESVSGSVPSSGSSGR 207.46 6.58E-26 1782040000 820280 436650 546610 523300 545540 360880 699670 433120 574930 TRUE FALSE 768940.139 468980.0203 559575.8473 536728.7639 502695.489 465060.1976 594760.9789 487195.9854 478970.4688 1.60540198 0.979141828 1.168288827 1.120588426 1.049533367 0.970957977 1.241748746 1.017173327 1 18.86957718 4.745628907 24.88472695 1.083422888 1.605402239 0.785083365 0.087983826 355.640784 1252040.705 0.019828899 0.200515821 55670.98524 -4.745628907 0.521979351 EDKSPSEESAPTTS(ph)PESVSGSVPSSGSSGR ddPTM_SK-BR-3_Pertuzumab_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(0.081)T(0.296)S(0.622)PESVSGSVPSSGSSGR 130.19 5.67E-06 365980000 137640 86643 111460 97923 117580 82454 140250 92072 144360 TRUE FALSE 129025.3581 93058.13787 114103.8838 100435.87 108345.7411 106257.1313 119220.8145 103567.3919 120265.3834 1.072838704 0.773773261 0.948767472 0.835118694 0.900888835 0.88352216 0.991314468 0.861157126 1 16.87586192 1.763543636 25 0.948613746 0.890321386 0.054336086 0.085394366 34.98074107 35028.57123 0.035205402 0.019524287 58.01544606 -1.763543636 -0.05829236 EDKVVASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDKVVASR 8 1 Q9BRR0-2;Q9BRR0 Q9BRR0-2 ZKSCAN3 Zinc finger protein with KRAB and SCAN domains 3 0 58.676 0.094339 113100000 176410 73488 250420 355580 117070 308260 252760 77820 386680 FALSE TRUE 165368.813 78929.12798 256360.0807 364704.7848 107875.7944 397249.6578 214860.9845 87535.9983 322140.61 0.513343577 0.245014523 0.795801811 1.132129181 0.334871764 1.233156099 0.666978884 0.271732267 1 18.29733102 3.873483048 3.838963289 0.779588624 0.378947598 0.21637469 0.313471211 0.310326259 8.351491289 0.075179819 0.145632191 7472.794645 -3.873483048 -0.400641026 EDKYEEEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EDKYEEEIK 9 1 P06753-2;P06753-6;P06753-5;P06753-7;A0A494C034;A0A2R8Y6A3;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;P06753;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YE05;K7ENT6;A0A5F9UN72;K7EPB9;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;P67936;P67936-2 TPM3;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-4 chain 0 ;;; 106.62 0.0026507 1442030000 2851700 1313760 1881810 1750530 1600360 1508080 2239690 1342220 1357680 FALSE TRUE 2673217.187 1411032.157 1926447.422 1795451.563 1474674.181 1943438.214 1903869.277 1509799.122 1131074.437 2.363431707 1.247514851 1.703201274 1.587385856 1.303781725 1.71822309 1.683239594 1.334836216 1 20.10926245 -2.850260098 0.205365312 1.39E-13 1.711908014 0.344536729 0.299724632 67.3857466 1.479919357 30.75267378 0.676376336 0.001411692 2.850260098 1.711908014 EDLAAFVEELDKVESQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EDLAAFVEELDKVESQER 18 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 0 ;; 225.6 3.62E-19 105817000 292228 167474 226944 204254 187549 162536 296108 173882 168058 FALSE TRUE 273937.9711 179873.9492 232327.2189 209495.5034 172819.6581 209457.5046 251709.3543 195591.5505 140008.0341 1.956587512 1.284740196 1.659384908 1.496310585 1.234355294 1.496039181 1.797820789 1.397002334 1 17.09515009 -2.001342552 1.33497872 0.462526071 1.535244954 0.372211054 0.220433943 22620.76922 4941.028657 37364.01776 0.058180692 0.009969134 2.001342552 1.072718884 EDLAAFVEELDKVESQEREDVLAGMSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDLAAFVEELDKVESQEREDVLAGMSGK 28 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 0 ; 206.88 1.33E-25 31916000 40793 29306 28996.7 34471.2 38706.7 18447.7 43654.9 25787.8 49047.5 FALSE TRUE 38239.83895 31475.84673 29684.51542 35355.78935 35666.83192 23773.25152 37109.25302 29007.4636 40861.15539 0.935848206 0.770312206 0.726472738 0.865266511 0.872878693 0.581805661 0.908179239 0.709903166 1 15.31844238 -1.367359092 3.553862755 1.00117795 0.791212663 0.264692167 0.106376975 38351479.93 45000924.52 440087.0424 0.022876007 0.042918142 1.367359092 -0.209965286 EDLADNWHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDLADNWHIR 10 0 K7EID2;Q9BT22-2;Q9BT22 K7EID2 ALG1 Chitobiosyldiphosphodolichol beta-mannosyltransferase 0 126.19 0.00038905 71178000 35927 172310 141300 155410 167990 170740 109900 120420 111810 FALSE TRUE 33678.3932 185068.0117 144651.7027 159398.0837 154796.743 220029.8663 93421.51526 135454.7021 93148.18868 0.361557145 1.98681278 1.552920189 1.711231168 1.661833099 2.36214863 1.00293432 1.454185036 1 16.50724009 1.618139232 25 1.1714183 1.652417732 0.140487933 0.519944755 1.276652427 3098.809839 0.221023788 0.120840695 41.50870955 -1.618139232 0.480999432 EDLAYMNHIMVSVS(ph)PPEEHAMPIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDLAYMNHIMVSVSPPEEHAMPIGR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 1 EDLAYMNHIMVS(0.012)VS(0.988)PPEEHAMPIGR 232.38 8.41E-35 81858000 46641 53642 54105 56601 52945 50151 57909 46189 43762 TRUE FALSE 43721.82307 57613.70949 55388.39615 58053.47749 48786.91327 64628.77957 49226.08305 51955.79832 36457.83949 1.199243391 1.580283152 1.519245159 1.592345523 1.338173462 1.772699109 1.350219425 1.425092629 1 15.15394145 0.625251498 1.304576508 1.001035127 1.504590284 0.469630317 0.158510514 1.023921283 2.563408645 0.132236699 0.03954907 4.219407768 -0.625251498 0.503555157 EDLDVLGLTFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDLDVLGLTFR 11 0 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 117.7 0.0019071 8325700 20874 21790 18682 17598 17415 13244 17577 16416 17375 FALSE TRUE 19567.5336 23403.35427 19125.14586 18049.59447 16047.29615 17067.3278 14941.49203 18465.57374 14475.00025 1.351815769 1.616812011 1.321253577 1.24694951 1.108621476 1.179089983 1.03222741 1.275687282 1 13.82127575 3.318143072 1.420682295 1.116197283 1.499629327 0.684107476 0.099852924 0.189470559 0.791424874 0.030621603 0.049189425 2080.381927 -3.318143072 0.383432044 EDLHILFSNHGEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDLHILFSNHGEIK 14 0 P05455 P05455 SSB Lupus La protein 0 ; 164.65 2.36E-06 309289000 365200 503930 504540 520640 562730 413710 624190 492700 614070 FALSE TRUE 342342.7839 541241.5015 516507.9271 534000.5038 518535.4557 533141.361 530598.5042 554214.6796 511577.75 0.669190136 1.057984835 1.0096372 1.043830589 1.013600486 1.04215119 1.037180574 1.083343988 1 18.96459399 4.740652956 24.99323058 1.035931685 0.66919001 0.9574198 0.024308378 31.16007908 372184.7478 0.005179065 0.034172889 55036.77227 -4.740652956 -0.366741676 EDLMGLAIGTHGANIQQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDLMGLAIGTHGANIQQAR 19 0 P51116;A0A087WWR6;Q06787;Q06787-2;R9WNI0;G3V0J0;Q06787-9;Q06787-7;Q06787-6;Q06787-5;Q06787-8;Q06787-3;Q06787-4;A8MQB8;Q06787-10;Q06787-11;A0A087WXI3;Q8IXW7;A0A087WY29 P51116;Q06787 FXR2;FMR1 Fragile X mental retardation syndrome-related protein 2;Fragile X mental retardation protein 1 0 170.5 1.21E-11 162970000 109810 89165 85220 80008 82450 62392 111480 87070 125570 FALSE TRUE 102937.1881 95766.86938 87241.45864 82061.14073 75974.70959 80403.55755 94764.60893 97940.88116 104611.5558 0.983994429 0.915452109 0.83395623 0.784436673 0.726255422 0.768591548 0.905871328 0.936233865 1 16.6746827 1.274462356 2.277230155 0.987374406 0.839208438 0.357295929 0.074216891 0.360227084 3.133414712 0.072324347 0.02110194 18.8131863 -1.274462356 -0.148165968 EDLNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDLNLR 6 0 O76003 O76003 GLRX3 Glutaredoxin-3 0 100.07 0.088599 215190000 347250 373030 345480 370060 348960 304430 346140 283450 297090 FALSE TRUE 325516.2424 400649.5293 353674.9487 379556.3661 321554.0892 392313.999 294239.5204 318839.3565 247503.7597 1.315197162 1.618761387 1.428967985 1.53353778 1.299188706 1.585082988 1.188828488 1.288220255 1 17.91709092 1.154453695 0.712503054 1.002321445 1.49120715 0.59303686 0.120705884 0.389609617 0.464564508 0.102194131 0.041596422 14.27097663 -1.154453695 0.488885705 EDLQELNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EDLQELNDR 9 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;; 186.67 9.64E-05 2978770000 2807210 2514790 2665410 2508290 2369000 2320300 3079870 2440680 2211510 FALSE TRUE 2631511.737 2700987.668 2728634.784 2572656.968 2182948.296 2990132.943 2618072.086 2745404.271 1842394.694 1.428310527 1.466020108 1.481026184 1.396365815 1.184842913 1.622960027 1.421015863 1.49012819 1 20.81315073 -0.973156448 4.450251012 0.999989007 1.441148227 0.614765349 0.108490361 0.101857059 29780130.45 836.5349473 0.023503144 0.106375975 0.973156448 0.44115922 EDLQLDKPASGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDLQLDKPASGVK 13 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 155.28 4.25E-05 417880000 719260 495650 593450 555940 694850 462840 809860 579010 879810 FALSE TRUE 674242.8005 532348.4417 607526.9142 570206.3616 640279.2839 596454.3944 688429.0114 651300.6731 732964.0272 0.919885254 0.726295455 0.828863207 0.777945902 0.873548033 0.813756709 0.939239834 0.888584772 1 19.48338287 1.47725339 0.679684283 0.993283086 0.798848983 0.496804984 0.056992658 0.443891871 0.454679212 0.048354323 0.022294978 30.00912898 -1.47725339 -0.194434103 EDLRLPEGDLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 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 36024210000 70188690 52498350 62358050 56400450 60101460 47221930 74510980 52077310 63997930 FALSE TRUE 65795705.18 56385382.46 63837212.39 57847781.03 55381333.77 60854134.61 63338750.28 58579276.79 53316262.04 1.23406448 1.057564433 1.197330982 1.084993186 1.038732493 1.141380365 1.187981825 1.098713123 1 25.6680723 -2.658403739 1.343958054 1.45E-05 1.130354902 0.298025333 0.062747626 241585.5903 11988.59375 729439.5968 0.016324875 0.002195818 2.658403739 1.13034037 EDLRVECSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDLRVECSK 9 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 82.261 0.017286 260190000 453790 405310 438570 399900 502030 337020 513440 400300 633060 FALSE TRUE 425388.0939 435319.5741 448973.0875 410162.111 462602.5889 434312.2029 436454.4385 450278.3362 527398.1963 0.806578591 0.825409676 0.85129811 0.777708597 0.877141014 0.823499599 0.827561493 0.853772992 1 19.00853311 0.679486879 2.359861907 0.999991638 0.828982054 0.813321185 0.025831216 0.73322292 4.909048264 0.021955135 0.005909795 4.780649223 -0.679486879 -0.171009584 EDLSKS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDLSKSPK 8 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E9PDQ5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 1 EDLS(0.034)KS(0.966)PK;EDLS(0.359)KS(0.641)PK 55.721 0.073968 555710000 1467140 968310 1013960 1117800 1733080 587740 1240650 894460 2436000 TRUE FALSE 1375314.326 1040004.68 1038011.61 1146484.64 1596970.888 757410.9968 1054626.05 1006135.3 2029415.863 0.677689749 0.512465039 0.511482949 0.56493332 0.786911602 0.373216259 0.519669758 0.495775813 1 20.9526331 -1.411305115 5.756529776 1.000185973 0.544697809 0.611065646 0.11122136 0.000246952 2.53E-05 0.100178891 0.023602895 0.038787777 1.411305115 -0.455488164 EDLTEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EDLTEIR 7 0 F8VWS0;P05388;P05388-2;F8VU65;F8VW21;F8VQY6;F8VRK7;G3V210;Q8NHW5;F8VWV4;F8VPE8;F8VZS0;F8VS58 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 0 ;;;; 141.78 0.0058941 2804440000 6771320 6866210 7133230 6765930 6760170 6023060 7951420 6161140 6099970 FALSE TRUE 6347515.168 7374591.333 7302433.584 6939555.218 6229253.517 7761819.646 6759178.388 6930371.891 5081845.6 1.249057069 1.451163989 1.436964867 1.36555806 1.225785671 1.527362352 1.330063705 1.363750975 1 22.27692111 0.195262707 1.266817508 0.999396098 1.385278316 0.616611371 0.090847451 4.057475415 5.752957649 0.08480585 0.024050972 1.567699094 -0.195262707 0.385882217 EDLTEIRDMLLANKVPAAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 77.514 0.0055856 194502000 272870 436850 314270 300530 450110 252950 385760 342380 411640 FALSE TRUE 255791.5538 469194.8285 321724.6328 308242.1086 414760.1763 325972.5587 327918.8692 385126.8967 342934.6247 0.745890136 1.368175724 0.938151501 0.898836357 1.20944386 0.950538485 0.956213942 1.123032989 1 18.38757405 3.737439356 24.59628922 1.00589516 1.11698642 0 0.175619538 802.6084918 1913241.94 0.04100424 0.072851684 5463.102589 -3.737439356 0.111091261 EDLVGPEVGAS(ph)PQSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDLVGPEVGASPQSGR 16 0 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 EDLVGPEVGAS(0.994)PQS(0.006)GR 181.15 1.70E-12 0 412240 388620 371480 338480 423870 308360 463350 404760 376740 TRUE FALSE 386438.6343 417393.8292 380291.681 347165.9698 390580.96 397378.5262 393874.969 455295.177 313859.6602 1.231246583 1.329874087 1.211661546 1.106118479 1.244444602 1.266102582 1.254939768 1.450632989 1 18.25976009 3.876726911 5.738030993 1.230561078 1.285115142 0.037908252 0.117568453 0.778781609 36.63608099 0.027928254 0.051320965 7528.819953 -3.876726911 0.054554064 EDLVGPEVGAS(ph)PQSGRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EDLVGPEVGASPQSGRK 17 1 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 EDLVGPEVGAS(0.983)PQS(0.017)GRK;EDLVGPEVGAS(0.998)PQS(0.002)GRK;EDLVGPEVGAS(1)PQSGRK 213.5 3.75E-13 890670000 771420 601270 651760 663250 727800 504850 896810 618930 886770 TRUE FALSE 723138.1992 645788.6564 667220.055 680270.1179 670641.5238 650591.9994 762341.6661 696204.7729 738762.3582 0.9788509 0.874149379 0.903159247 0.920824011 0.907790599 0.880651257 1.031917311 0.942393403 1 19.49475083 1.744930537 25 0.99111896 0.906031349 0.531426424 0.0354511 0.873861341 3440.893381 0.014728812 0.008167911 55.58153512 -1.744930537 -0.08508761 EDLYLKPIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 EDLYLKPIQR 10 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;; 143.5 3.09E-05 9546990000 17289150 15155170 15939210 15837660 17507130 13018559 18678830 14723400 17612490 FALSE TRUE 16207052.96 16277274.56 16317295.59 16244081.17 16132190.63 16776805.64 15878112.85 16561648.9 14672851.64 1.104560542 1.10934636 1.112073917 1.107084129 1.099458444 1.143390941 1.082142261 1.128727347 1 23.80664595 -1.459222511 3.090054173 0.997661896 1.109766592 0.819765685 0.01632744 456609.0071 328499.4916 6648.311268 0.003294839 0.034735815 1.459222511 0.112104695 EDMAALEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 2776890000 5423290 4430960 4867040 4608030 5237660 3747670 5897450 4717990 5545930 FALSE TRUE 5083855.96 4759032.889 4982488.487 4726279.851 4826315.311 4829561.491 5013182.122 5307041.437 4620278.455 1.100335404 1.030031617 1.078395715 1.022942642 1.044594034 1.045296628 1.085038958 1.148641037 1 22.13954837 1.672206471 5.845516861 1.087997327 1.052277063 0.051670648 0.042009365 0.267629233 19.63304072 0.019296795 0.009580859 47.0117557 -1.672206471 -0.035720263 EDNS(ph)EGEEILEEVGGDLEEEDDHHMEFCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EDNSEGEEILEEVGGDLEEEDDHHMEFCR 29 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR 240.07 3.62E-45 792849000 688580 336930 434014 296461 211381 262566 643008 445936 244778 TRUE FALSE 645483.007 361876.6478 444309.017 304068.6912 194779.9889 338364.5418 546594.9198 501612.0912 203922.9705 3.165327601 1.774575208 2.178808086 1.491095831 0.955164533 1.65927625 2.680398969 2.459811614 1 17.63766477 EDPDGEHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EDPDGEHAR 9 0 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;; 122.44 0.00058567 583730000 1371790 1303360 1369980 1289320 1246210 1135970 1513890 1219920 1079750 FALSE TRUE 1285932.113 1399862.131 1402476.573 1322406.134 1148337.694 1463906.098 1286896.249 1372229.697 899532.7495 1.429555637 1.556210301 1.559116745 1.470103378 1.276593536 1.627407228 1.430627456 1.525491649 1 19.77881628 -1.8717132 2.388620066 0.756739762 1.492657655 0.715495947 0.09586639 3602232.069 1968288.998 4961031.26 0.02183931 0.01343652 1.8717132 0.735917893 EDPVAWAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EDPVAWAR 8 0 Q9UGT4 Q9UGT4 SUSD2 Sushi domain-containing protein 2 0 ;; 143.85 0.0013837 549260000 1046300 1229680 945580 847030 1605610 812770 1198820 1431980 1469860 FALSE TRUE 980813.9507 1320726.787 968009.6041 868766.2238 1479511.867 1047403.505 1019068.07 1610765.855 1224530.87 0.800971192 1.078557363 0.79051466 0.709468618 1.208227496 0.855350837 0.832211008 1.315414657 1 20.22379771 1.250958745 24.99432244 1.157707386 0.902567439 0.304840923 0.163804783 231.4956188 466695.2767 0.102668045 0.03691112 17.82209464 -1.250958745 -0.255139947 EDQEAAELLS(ph)EPEEESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDQEAAELLSEPEEESER 18 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 1 EDQEAAELLS(1)EPEEESER;EDQEAAELLS(1)EPEEESER 347.18 2.95E-90 887850000 1058550 1032060 1126810 1188030 1131320 979380 1344970 1024790 644360 TRUE FALSE 992297.2451 1108474.796 1153538.465 1218516.861 1042470.691 1262111.107 1143304.235 1152737.287 536812.1533 1.848499962 2.064921201 2.148868013 2.269912955 1.941965517 2.351122454 2.129803186 2.14737554 1 19.03405781 -0.846438757 6.007847563 0.999999868 2.122551229 0.855126153 0.143897421 2.31E-07 4.41E-08 0.127003195 0.029934936 0.142416807 0.846438757 1.122551361 EDQINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDQINR 6 0 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 97.068 0.09653 205840000 179070 216130 208920 226120 202970 184970 196580 160740 141740 FALSE TRUE 167862.3283 232132.4901 213875.6811 231922.622 187029.5549 238367.8363 167104.654 180808.7428 118082.6783 1.421566065 1.965847094 1.811236704 1.964069797 1.583886456 2.018652013 1.415149591 1.531204622 1 16.84943782 1.007201147 0.928196714 1.010491927 1.819215783 0.585196119 0.204400702 0.362530573 0.676050641 0.170109568 0.058418442 10.16719485 -1.007201147 0.808723856 EDQIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EDQIYR 6 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;; 160.68 0.020322 12435050000 6060370 6628690 6563780 6308720 7077510 5199920 7338730 6311170 7700820 FALSE TRUE 5681062.26 7119485.105 6719475.961 6470612.436 6521670.914 6701052.49 6238355.566 7099133.467 6415503.393 0.885520888 1.109731329 1.047380938 1.00858998 1.016548588 1.044509227 0.972387541 1.10655907 1 22.61313104 3.24709542 24.41795228 1.020912022 1.039418235 0 0.066287912 805.0335933 2303157.102 0.017163981 0.022863878 1766.425886 -3.24709542 0.018506213 EDQKMS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 108.72 0.0098836 1523070000 5976810 2268790 3306000 3107450 3132350 2189230 4292850 2516560 3829690 TRUE FALSE 5602732.131 2436773.572 3384419.881 3187192.428 2886347.866 2821225.162 3649176.995 2830758.056 3190489.998 1.75607262 0.763761546 1.06078373 0.998966438 0.904672282 0.884260776 1.143766944 0.887248685 1 21.60534658 4.747463935 24.98561898 0.962638315 1.75607303 0.850743093 0.105353612 431.4531088 1210772.166 0.024729093 0.300095434 55906.70993 -4.747463935 0.793434715 EDQTEYLEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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 ;;;;;;;; 295.31 7.08E-32 61428080000 12726780 11390130 11784580 11594370 10831480 10466105 12860250 10242560 8138770 FALSE TRUE 11930233.56 12233467.08 12064115.8 11891901.16 9980819.253 13487499.61 10931974.9 11521366.16 6780356.709 1.759528897 1.804251251 1.779274502 1.753875449 1.472019789 1.989202072 1.612300852 1.699227144 1 22.69292974 -2.314034645 0.359292869 3.67E-14 1.774629842 0.760221956 0.130203948 22.8606846 1.055888728 18.2921617 0.086860611 0.004852498 2.314034645 1.774629842 EDQTEYLEERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 190.1 3.88E-06 1547770000 417120 629530 512660 599820 692900 455600 624510 412800 1010190 FALSE TRUE 391013.2038 676141.0562 524820.5373 615212.3967 638482.429 587124.324 530870.5232 464338.9887 841582.7629 0.46461646 0.803415999 0.62361132 0.731018295 0.758668615 0.697643001 0.630800138 0.55174489 1 19.68274563 -2.07958634 2.559971753 1.525001772 0.671633052 0.531754104 0.100192879 8690416.716 4041764.694 26518844.07 0.022110605 0.008325564 2.07958634 -0.85336872 EDRYEEEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDRYEEEIK 9 1 H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;H0YL42;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 88.576 0.011874 0 309760 200480 249590 229560 245120 204900 289850 205460 240510 FALSE TRUE 290372.6745 215323.7478 255510.3927 235450.8982 225869.264 264051.3037 246389.6833 231112.1333 200367.3272 1.449201716 1.074645007 1.275209867 1.175096267 1.127275924 1.317836133 1.229689924 1.153442213 1 17.61228775 0.902028153 3.313093471 1.000208838 1.222006039 0.339459278 0.10362691 0.460571299 11.16639957 0.089000933 0.023107386 7.980464186 -0.902028153 0.221797201 EDS(ph)CHRLSPVKGEFHQEFQPEPSLLGDSTNSGEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDSCHRLSPVKGEFHQEFQPEPSLLGDSTNSGEER 35 2 Q9Y2L9-2;Q9Y2L9;Q9Y2L9-3 Q9Y2L9-2 LRCH1 Leucine-rich repeat and calponin homology domain-containing protein 1 1 EDS(0.5)CHRLS(0.5)PVKGEFHQEFQPEPSLLGDSTNSGEER 189.39 7.33E-21 59141000 83874 80235 78790 89581 92789 64943 106360 77516 74886 TRUE FALSE 78624.47606 86175.68288 80658.93601 91879.80012 85501.72623 83690.98984 90412.3054 87194.04323 62387.04282 1.26026932 1.381307384 1.292879617 1.472738504 1.370504553 1.341480315 1.449216076 1.39763065 1 15.92895881 -1.674405729 9.688945508 0.999739319 1.372198444 0.769786183 0.063714526 0.000343764 1.16E-05 0.059109674 0.013923004 0.02116383 1.674405729 0.372459125 EDS(ph)GTFSLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EDSGTFSLGK 10 0 O75569;G5E9Q4 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 1 EDS(0.905)GT(0.095)FSLGK;EDS(0.991)GT(0.009)FSLGK;EDS(0.942)GT(0.058)FSLGK;EDS(0.998)GT(0.002)FSLGK;EDS(0.555)GT(0.445)FSLGK 236.16 4.09E-12 1279310000 4803440 2537180 3026110 2765570 2527130 2375210 4056020 2449740 4441700 TRUE FALSE 4502801.265 2725035.447 3097890.758 2836539.208 2328659.404 3060894.569 3447857.455 2755595.432 3700351.576 1.216857688 0.736426091 0.837188223 0.76655938 0.629307609 0.827190202 0.93176483 0.744684762 1 21.81923092 -1.940623018 10.33465881 1.042214423 0.826578991 0.094646961 0.156647876 0.085844588 0.000493213 0.085455524 0.03251158 0.011465077 1.940623018 -0.215635432 EDS(ph)LPEESSAPDFANLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDSLPEESSAPDFANLK 17 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 EDS(1)LPEESSAPDFANLK;EDS(0.994)LPEES(0.005)S(0.001)APDFANLK 202.63 1.09E-11 131248000 232583 138180 140513 176518 134724 80674 232835 127191 208730 TRUE FALSE 218026.0452 148410.991 143846.0347 181047.7507 124143.3205 103963.2742 197923.5533 143071.0763 173891.6146 1.253804249 0.853468359 0.827216626 1.041152854 0.713912058 0.597862493 1.138200676 0.822760066 1 17.40782884 -0.473025506 7.908736176 1.000001488 0.896792985 0.020534595 0.194815618 0 0 0.174119528 0.041040366 0.336491807 0.473025506 -0.103208503 EDSARPGAHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EDSARPGAHAK 11 1 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ;; 87.878 0.0080489 986290000 1627480 1533110 1598910 1577060 1846930 1321480 1929330 1588640 2567040 FALSE TRUE 1525618.932 1646623.06 1636836.9 1617530.03 1701879.568 1702969.824 1640044.878 1786985.201 2138584.44 0.713377926 0.769959338 0.765383339 0.756355465 0.795797227 0.79630703 0.766883386 0.835592538 1 21.02822474 -5 0.203145309 2.066566757 0.737094026 0.930461574 0.020408021 32.96866458 0.327260911 14.23622107 0.044814194 1.00E-05 5 -1.329472731 EDSEKDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDSEKDEK 8 1 P29374;P29374-3;P29374-2;H7C485 P29374 ARID4A AT-rich interactive domain-containing protein 4A 0 68.625 0.033661 2051800000 650390 3048200 2097100 2559700 2418900 2879400 1525000 2074700 1068500 FALSE TRUE 609683.2509 3273891.9 2146844.202 2625386.236 2228929.351 3710636.037 1296340.407 2333730.862 890160.4472 0.684913886 3.677867187 2.411749712 2.949340474 2.503963593 4.168502486 1.456299717 2.621696874 1 19.76370587 0.805683039 1.070840656 1.032769927 2.744974017 0.184080687 0.994648207 1.099971908 2.388242519 0.836524027 0.266667316 6.392681077 -0.805683039 1.712204091 EDSGLFS(ph)PIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDSGLFSPIR 10 0 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 EDSGLFS(1)PIR 124.89 0.0031489 0 100700 115360 99993 121550 141290 73908 83102 81914 132060 TRUE FALSE 94397.36675 123901.3744 102364.8812 124669.1788 130193.6533 95244.0398 70641.62658 92141.14321 110018.3329 0.858014881 1.126188438 0.93043476 1.133167314 1.183381442 0.865710626 0.642089593 0.837507176 1 16.74738442 2.042773373 7.64156372 0.778528967 1.044331215 0.376054737 0.130298927 0.174000618 26.21570244 0.045515745 0.033370312 110.3502632 -2.042773373 0.265802249 EDSGT(ph)FSLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDSGTFSLGK 10 0 O75569;G5E9Q4 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 1 EDS(0.306)GT(0.694)FSLGK 232.56 1.79E-09 428410000 2092300 1047200 1247500 1184700 1009400 910220 1573200 976740 1764200 TRUE FALSE 1961346.678 1124735.778 1277091.289 1215101.408 930125.7957 1172985.738 1337313.265 1098688.139 1469743.623 1.334482183 0.765259845 0.86892113 0.826743786 0.632849009 0.798088673 0.909895606 0.747537272 1 20.48713309 4.741914925 24.97803927 0.815195109 1.334482379 0.731547204 0.098180528 157.2008461 1170551.741 0.021655987 0.156940163 55196.9302 -4.741914925 0.51928727 EDSHPFDLGLYNEAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EDSHPFDLGLYNEAVK 16 0 P35244;B5MC59 P35244 RPA3 Replication protein A 14 kDa subunit 0 ;; 258.23 1.06E-26 707700000 1681690 1300840 1488040 1452940 1503100 1120350 1843190 1261800 1812660 FALSE TRUE 1576436.025 1397155.547 1523337.012 1490224.9 1385052.589 1443776.858 1566820.771 1419338.508 1510115.336 1.043917632 0.925197906 1.008755408 0.986828532 0.917183315 0.956070588 1.0375504 0.939887487 1 20.52622731 EDSQRPGAHLTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 ;;;;;; 116.51 0.00034822 41266870000 29884060 33373880 34734000 32642350 35871400 29060430 42917300 30879220 38582300 FALSE TRUE 28013670.03 35844916.8 35557906.88 33480007.96 33054204.94 37449704.38 36482249.29 34734558.59 32142664.88 0.871541614 1.11518186 1.106252609 1.041606478 1.028359194 1.165108883 1.1350101 1.080637176 1 24.93798621 2.256783625 24.99881349 1.11159632 1.054306144 0.084053244 0.079906685 546.7190386 750002.7388 0.026569814 0.022188284 180.6273978 -2.256783625 -0.057290176 EDSVKPGAHLTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EDSVKPGAHLTVK 13 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 126.95 0.00010973 3383170000 4544760 4199420 4625670 4510630 5032130 3430230 6050400 4466800 6264000 FALSE TRUE 4260311.584 4510349.426 4735393.077 4626380.402 4636926.808 4420481.716 5143198.689 5024489.813 5218497.933 0.816386562 0.864300319 0.907424538 0.886534873 0.888555839 0.847079327 0.985570705 0.962822996 1 22.31520318 1.696586695 6.48464225 0.980523236 0.873992387 0.800176885 0.026787905 0.060715687 5.655655584 0.013466009 0.006883634 49.72636287 -1.696586695 -0.10653085 EDTEEHHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 EDTEEHHLR 9 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;A0A2R8Y4L2;F8VYN5;P22626;P22626-2;A0A087WUI2 F8W6I7;P22626 HNRNPA1;HNRNPA1L2;HNRNPA2B1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2;Heterogeneous nuclear ribonucleoproteins A2/B1" 0 ;;;;;;;;;;;; 218.55 5.26E-07 19878584900 13820068 12452609 13507836 12683420 12384618 11631734 15420766 12107327 11994021 FALSE TRUE 12955094.61 13374613.13 13828248.25 13008898.03 11411980.06 14989626.78 13108565.3 13618953.43 9992141.411 1.29652835 1.338513195 1.383912385 1.301912923 1.142095532 1.500141578 1.311887488 1.362966442 1 23.25236246 -0.944482165 5.64846584 0.999999635 1.33486361 0.576766826 0.088674468 3.72E-07 6.96E-08 0.078336914 0.018464168 0.113636496 0.944482165 0.334863975 EDTEEYNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EDTEEYNLR 9 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 253.21 1.58E-14 2079240000 1957300 1488280 1641700 1481930 1490160 1418040 1961480 1410060 1384000 FALSE TRUE 1834796.087 1598473.8 1680641.899 1519958.833 1373128.845 1827405.128 1667374.283 1586109.095 1153001.459 1.591321566 1.38635887 1.457623393 1.318262714 1.190916832 1.584911375 1.446116369 1.375634942 1 20.13696291 0.81214352 4.820742269 1.00000395 1.421903481 0.563308078 0.116670987 2.153567219 54.77750969 0.106528356 0.026964547 6.488488215 -0.81214352 0.421899531 EDTESLEIFQNEVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDTESLEIFQNEVAR 15 0 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 154.07 5.92E-06 23223000 31728 28959 29659 31763 31574 25699 30535 29101 25963 FALSE TRUE 29742.20112 31103.15449 30362.52549 32578.09235 29094.3054 33117.88411 25956.56022 32734.32391 21629.60757 1.37506892 1.437989773 1.403748329 1.506180463 1.345114806 1.531136614 1.200047672 1.513403505 1 14.40071987 -3.150541897 0.321033146 1.63E-12 1.428666361 0.62605217 0.099282026 51.92021423 1.379363135 34.95337426 0.079038168 0.000707063 3.150541897 1.428666361 EDTGTFDTVLWAIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDTGTFDTVLWAIGR 15 0 A0A096LPK7;A0A182DWF2;D3YTF8;A0A182DWF3;Q9NNW7-3;Q9NNW7-2;Q9NNW7;A0A0U1RQX0;Q9NNW7-4 A0A096LPK7 TXNRD2 "Thioredoxin reductase 2, mitochondrial" 0 90.653 0.013798 13019000 21681 18916 18958 19630 20416 18085 25507 17234 21081 FALSE TRUE 20324.02491 20316.56032 19407.69271 20133.73903 18812.60971 23305.84591 21682.46215 19385.70284 17562.44491 1.157243483 1.156818451 1.10506782 1.146408665 1.071183984 1.327027417 1.234592464 1.103815724 1 14.10020608 EDTHHLVNYIPQGSIDSLFEGTWYLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDTHHLVNYIPQGSIDSLFEGTWYLVR 27 0 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 ; 117.21 0.0003112 120178000 96657 104359 97433 87742 122272 85657 97421 89672 65084 FALSE TRUE 90607.41091 112085.8489 99744.15677 89993.60827 112669.2503 110384.7854 82813.62546 100867.7466 54221.05994 1.671074136 2.067201362 1.839583307 1.659753763 2.077961044 2.035828615 1.527333209 1.860305695 1 15.7265657 -0.023882257 0.574342486 0.936068119 1.897111075 0.671619509 0.184851431 2.518077582 0.954887757 0.541613152 0.074938865 0.946493734 0.023882257 0.961042956 EDTLLLIGHLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EDTLLLIGHLER 12 0 Q92621 Q92621 NUP205 Nuclear pore complex protein Nup205 0 ;;; 165.07 5.56E-05 248856000 392258 468956 425529 452690 431806 350336 506653 418933 304622 FALSE TRUE 367707.272 503677.9902 435622.7488 464306.7918 397893.6986 451472.316 430685.0862 471237.7072 253778.6203 1.448929274 1.984714038 1.716546289 1.829574104 1.567877145 1.779000593 1.697089714 1.856884976 1 17.95321101 -1.419437176 3.174227704 0.989214145 1.751508496 0.703211989 0.14973959 19797575.23 27404027.49 1956430.631 0.032396203 0.038068242 1.419437176 0.762294351 EDTVQSVKPWLTEIMNNYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDTVQSVKPWLTEIMNNYK 19 1 Q9H3G5;H7C0X5 Q9H3G5 CPVL Probable serine carboxypeptidase CPVL 0 153.11 4.47E-08 52684000 126010 102310 123760 106780 114410 85304 120670 107380 107650 FALSE TRUE 118123.259 109885.1389 126695.6456 109520.1556 105424.7001 109929.88 102576.6537 120786.6294 89682.51955 1.317126901 1.225268195 1.412712826 1.221198469 1.175532318 1.225767079 1.143775334 1.346824665 1 16.45253919 3.018559872 24.05319197 1.188525887 1.312529153 0.3067611 0.095353871 185.647125 240592.051 0.02478743 0.029620917 1043.662002 -3.018559872 0.124003267 EDVETGLDPLSLLATECT(ph)GGKTPDSEDKLFSPVIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDVETGLDPLSLLATECTGGKTPDSEDKLFSPVIAR 36 2 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 EDVETGLDPLSLLAT(0.019)ECT(0.49)GGKT(0.49)PDS(0.001)EDKLFSPVIAR 115.27 0.00042632 74133000 63053 23493 34369 31525 41550 27481 60111 31577 49093 TRUE FALSE 59106.62528 25232.44616 35184.24891 32333.98487 38286.8306 35414.31858 51097.91359 35519.45796 40899.06115 1.445182936 0.616944386 0.860270332 0.790580125 0.936129816 0.865895636 1.24936642 0.86846634 1 15.31978011 1.792312195 24.99999632 1.066040417 0.873206204 0.028350406 0.231142099 289.5822863 134721.8246 0.095801607 0.055006391 61.9886524 -1.792312195 -0.192834213 EDVEVAES(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDVEVAESPLR 11 0 Q99567;J3KMX1 Q99567 NUP88 Nuclear pore complex protein Nup88 1 EDVEVAES(1)PLR;EDVEVAES(1)PLR 300.75 8.36E-36 1396130000 1277760 1233680 1245800 1240770 1243450 1050150 1438360 1103060 1122380 TRUE FALSE 1197787.282 1325022.951 1275350.964 1272610.259 1145794.453 1353311.257 1222691.271 1240779.469 935047.5271 1.280990803 1.417064815 1.363942396 1.361011309 1.225386325 1.44731815 1.307624731 1.326969414 1 19.83468017 -3.22874009 0.359402087 2.75E-11 1.362020175 0.738055028 0.063794558 53.29593842 1.424772417 40.21043944 0.04274115 0.000590554 3.22874009 1.362020175 EDVEVAES(ph)PLRVLAETPDSFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDVEVAESPLRVLAETPDSFEK 22 1 Q99567;J3KMX1 Q99567 NUP88 Nuclear pore complex protein Nup88 1 EDVEVAES(1)PLRVLAETPDSFEK;EDVEVAES(1)PLRVLAETPDSFEK 102.57 0.00037046 26430000 25936 35009 28659 40106 49675 17954 40667 23509 89862 TRUE FALSE 24312.71206 37601.10279 29338.80501 41135.18786 45773.72588 23137.02834 34569.36088 26444.1504 74863.45167 0.324760768 0.502262479 0.391897573 0.54946956 0.611429541 0.309056393 0.461765523 0.353231781 1 16.19197395 -1.691587023 2.759617715 1.078376569 0.443694401 0.76489361 0.097877049 19061675.69 16925158.75 10435225.29 0.022461947 0.020342905 1.691587023 -0.634682167 EDVFVHQTAIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 186.81 4.21E-06 1300520000 3104090 3011210 3446330 3115910 3240870 2777190 4035280 3264360 2512040 FALSE TRUE 2909810.548 3234163.122 3528078.575 3195869.526 2986345.143 3578919.669 3430227.226 3671922.532 2092764.296 1.390414847 1.545402475 1.685846123 1.527104382 1.426985901 1.710139874 1.639089138 1.754580074 1 20.9969784 2.241310311 24.99918784 1.590301411 1.543095996 0 0.223511495 525.2192177 4775123.332 0.071174993 0.057153745 174.3051871 -2.241310311 -0.047205415 EDVLWFKPVELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDVLWFKPVELR 12 1 Q2NL82 Q2NL82 TSR1 Pre-rRNA-processing protein TSR1 homolog 0 ; 138.42 6.82E-05 412690000 475460 417810 447020 395320 488500 340890 461480 409950 388780 FALSE TRUE 445701.8073 448745.0871 457623.5255 405464.5805 450135.1805 439299.4091 392285.3582 461133.1599 323890.1064 1.376089601 1.385485627 1.412897512 1.251858493 1.389777494 1.356322408 1.21116808 1.423733392 1 18.30514487 -3.867074521 0.217863019 4.89E-11 1.400616403 0.706949886 0.07019229 44.6640026 0.697652679 19.87200994 0.130406519 0.000135808 3.867074521 1.400616403 EDVRPEEIADQELAEALQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDVRPEEIADQELAEALQK 19 1 Q5TDH0;Q5TDH0-3 Q5TDH0 DDI2 Protein DDI1 homolog 2 0 ; 183.45 2.47E-14 144378000 358530 292220 320790 313100 338900 242460 411140 287960 386760 FALSE TRUE 336090.2473 313856.2729 328399.2903 321134.6761 312284.1611 312454.266 349493.3738 323912.4399 322207.2574 1.043087142 0.974081948 1.019217546 0.996671145 0.969202753 0.96973069 1.084684984 1.005292191 1 18.29762946 1.757472632 25 1.038180815 0.994682458 0.190453628 0.032226977 9.678446398 12806.47588 0.013616745 0.007551107 57.21009009 -1.757472632 -0.043498358 EDVSLHGYKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDVSLHGYKK 10 1 Q12792;Q12792-3;Q12792-4;F8VS81;F8W1Q9 Q12792 TWF1 Twinfilin-1 0 66.92 0.031817 327310000 319460 368110 355690 355380 426480 321460 465900 412590 466110 FALSE TRUE 299465.5689 395365.2474 364127.1348 364499.6525 392985.9811 414260.2835 396042.6202 464102.7697 388313.2298 0.771195895 1.018160642 0.937714986 0.938674308 1.012033459 1.066819907 1.01990504 1.195176301 1 18.56686134 2.489904762 1.085695788 1.080012994 0.928915642 0.451030745 0.079355628 0.509620922 1.212885124 0.044265701 0.031919598 308.9617822 -2.489904762 -0.151097352 EDVSNFDDEFTSEAPILT(ph)PPREPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EDVSNFDDEFTSEAPILTPPREPR 24 1 Q16513-3;Q16513-2;Q16513;Q16513-4;Q16513-5 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 EDVSNFDDEFTSEAPILT(1)PPREPR;EDVSNFDDEFTSEAPILT(0.999)PPREPR 146.94 3.01E-07 158414000 101836 93157 88993 88261 99151 82047 101162 94348 94245 TRUE FALSE 95462.26654 100054.4412 91103.95599 90525.92669 91364.08042 105732.637 85993.69724 106127.5555 78514.90065 1.215849039 1.274336978 1.160339696 1.152977663 1.163652755 1.346656954 1.095253213 1.351686809 1 16.26067886 -1.03527532 4.386288713 0.999987515 1.212806617 0.401450953 0.084041027 0.076086137 21755240.89 603.3399289 0.017420097 0.092198675 1.03527532 0.212819103 EDYDSVEQDGDEPGPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EDYDSVEQDGDEPGPQR 17 0 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 178.84 1.68E-13 0 140080 109700 121000 106920 110800 114000 161760 111510 107130 FALSE TRUE 131312.6428 117822.3021 123870.1771 109663.7482 102098.2149 146909.9494 137505.5897 125432.269 89249.31091 1.471301476 1.320148032 1.38791186 1.228734957 1.143966423 1.646062562 1.540690772 1.405414425 1 16.44555341 2.241162215 24.99982605 1.460804369 1.318595613 0.003004596 0.189387253 143.2739815 1376792.223 0.061830428 0.049521604 174.2457584 -2.241162215 -0.142208756 EEADEYIDIGALNGIFVLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EEADEYIDIGALNGIFVLGR 20 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;; 211.13 1.46E-24 92971000 103779 108963 117952 115984 114515 90814 125055 102546 111436 FALSE TRUE 97283.65764 117030.7339 120749.8771 118960.3458 105521.4538 117030.5276 106304.1637 115349.0938 92836.6117 1.047901855 1.260609707 1.300670877 1.281394739 1.136636203 1.260607485 1.145067251 1.242495732 1 16.50240625 -0.619721433 0.475139305 0.949778882 1.230277622 0.383586356 0.080388439 10.14088572 1.871942574 0.875924234 0.039551504 0.240037208 0.619721433 0.28049874 EEADKLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 88.948 0.012999 345510000 621810 684520 637550 579870 923270 467350 721800 678020 1512640 FALSE TRUE 582892.0221 735202.573 652672.9871 594750.4459 850760.0985 602266.3582 613572.7909 762672.2895 1260170.612 0.462550084 0.583415107 0.517924304 0.471960257 0.675115013 0.477924459 0.486896604 0.605213518 1 20.26518764 0.847604285 4.679627096 0.999987412 0.52945835 0.843835764 0.063732357 0.52206859 15.70211757 0.056664864 0.014361729 7.040512678 -0.847604285 -0.470529062 EEAEKPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EEAEKPER 8 1 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;; 95.358 0.0088526 3069920000 1853890 1221230 1550760 1459320 1439410 1196080 1817770 1345890 1290560 FALSE TRUE 1737858.334 1311651.14 1587544.76 1496768.622 1326364.545 1541368.879 1545212.264 1513927.329 1075157.199 1.616376039 1.219962199 1.476569902 1.39213933 1.233647086 1.433621875 1.437196594 1.408098584 1 20.03611618 -1.143320204 5.158100224 0.999985057 1.391990051 0.551613406 0.113629636 1.76E-05 2.92E-06 0.099033085 0.023341433 0.071891873 1.143320204 0.392004994 EEAIEHNYGGHDDDLSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EEAIEHNYGGHDDDLSVR 18 0 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ;;; 232.51 1.18E-20 1639480000 1301390 1278750 1153110 1016840 1386510 982020 1414840 1203180 1397500 FALSE TRUE 1219938.323 1373429.981 1180462.314 1042933.836 1277619.098 1265513.232 1202697.877 1353399.672 1164248.222 1.047833529 1.1796711 1.013926662 0.895800239 1.097376894 1.086978883 1.033025307 1.1624666 1 20.15096725 3.893185175 5.79336229 1.041697875 1.119490168 0.133387943 0.076291951 0.36269972 19.35934926 0.018853873 0.034719806 7819.611476 -3.893185175 0.077792294 EEALDDAEEPES(ph)PPPPPRS(ph)PS(ph)PEPTVVDTPSHASQSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEALDDAEEPESPPPPPRSPSPEPTVVDTPSHASQSAR 38 1 Q9P2R6;B1AKN3;Q9P2R6-2 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 3 EEALDDAEEPES(0.999)PPPPPRS(0.954)PS(0.952)PEPT(0.086)VVDT(0.004)PS(0.003)HAS(0.001)QS(0.001)AR 71.793 0.015894 87238000 121440 109640 113320 108940 119690 120330 130830 87087 99642 TRUE FALSE 113839.2872 117757.8597 116008.0039 111735.5848 110290.0302 155067.3176 111213.2561 97960.00365 83011.10649 1.371374169 1.418579569 1.39749979 1.346031749 1.328617758 1.868030968 1.339739473 1.180083097 1 16.34101675 1.136347749 2.8705129 1.015436552 1.445344224 0.489273258 0.155592858 0.201005261 3.039309411 0.139594568 0.037882568 13.68824435 -1.136347749 0.429907673 EEALGLYQWIYHTHEDAQEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EEALGLYQWIYHTHEDAQEAR 21 0 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 0 ;;; 282.03 2.68E-45 422133000 374483 425967 412699 444010 411728 359738 522730 362651 304623 FALSE TRUE 351044.7775 457506.0399 422488.4152 455404.0483 379392.5437 463588.5207 444351.4893 407928.7756 253779.4534 1.383267136 1.802770216 1.66478574 1.794487466 1.494969505 1.826737802 1.750935639 1.60741451 1 17.95321574 0.840875751 5.31675012 1.000004794 1.693612134 0.687289355 0.141317952 1.295462649 43.01103944 0.120226582 0.030327587 6.93227449 -0.840875751 0.693607339 EEAPAS(ph)PLRPLYPQIS(ph)PLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 EEAPASPLRPLYPQISPLK 19 1 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 2 EEAPAS(1)PLRPLY(0.006)PQIS(0.994)PLK;EEAPAS(1)PLRPLYPQIS(1)PLK;EEAPAS(1)PLRPLYPQIS(1)PLK;EEAPAS(1)PLRPLYPQIS(1)PLK;EEAPAS(1)PLRPLYPQIS(1)PLK;EEAPAS(1)PLRPLYPQIS(1)PLK;EEAPAS(1)PLRPLYPQIS(1)PLK 213.05 3.03E-17 1843093000 5467554 2984879 4017303 3468702 3833702 3582377 5594302 3742008 3525673 TRUE FALSE 5125349.555 3205882.547 4112595.324 3557714.766 3532618.509 4616551.085 4755488.35 4209205.936 2937215.4 1.74496891 1.091470019 1.400168106 1.211254294 1.20271006 1.571744138 1.619046513 1.433060012 1 21.48601764 2.237344729 24.99992786 1.47893145 1.301721948 0 0.242230185 69.1839283 1422450.83 0.07926826 0.061851983 172.7208352 -2.237344729 -0.177209502 EEAPAS(ph)PLRPLYPQISPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EEAPASPLRPLYPQISPLK 19 1 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 1 EEAPAS(1)PLRPLYPQISPLK;EEAPAS(1)PLRPLYPQISPLK;EEAPAS(1)PLRPLYPQISPLK 205.73 2.41E-16 717090000 1172450 965320 928740 965660 1076730 851940 1354840 1041010 1034940 TRUE FALSE 1099068.447 1036793.297 950770.1514 990440.4705 992167.9691 1097881.248 1151694.32 1170982.39 862201.828 1.274722938 1.202494896 1.102723423 1.148733902 1.150737492 1.273345999 1.335759543 1.358130257 1 19.7176661 2.23136979 23.85989672 1.276984286 1.168301218 0.040686232 0.107630714 146.815417 487141.6084 0.036173058 0.027306219 170.3608469 -2.23136979 -0.108683068 EEAPASPLRPLYPQIS(ph)PLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EEAPASPLRPLYPQISPLK 19 1 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 1 EEAPASPLRPLYPQIS(1)PLK;EEAPASPLRPLYPQIS(1)PLK;EEAPASPLRPLYPQIS(1)PLK 140.66 1.05E-07 824395000 1632320 946103 1219070 1002410 974225 865339 1369924 992285 1054642 TRUE FALSE 1530156.005 1016153.451 1247986.916 1028133.538 897713.2983 1115148.322 1164516.614 1116173.967 878615.437 1.741553745 1.156539491 1.420401764 1.17017468 1.021736314 1.269210937 1.325399674 1.270378279 1 19.74487232 4.743747367 24.95006179 1.231912769 1.741553964 0.618388543 0.131059387 380.1563681 1828624.243 0.030124783 0.257257312 55430.31766 -4.743747367 0.509641195 EEAQAEIEQYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEAQAEIEQYR 11 0 O75348 O75348 ATP6V1G1 V-type proton ATPase subunit G 1 0 ; 206.84 5.82E-08 701240000 406950 468960 415700 442730 444770 391820 482570 383650 549900 FALSE TRUE 381479.7259 503682.2864 425560.6003 454091.2013 409839.5583 504932.0733 410213.1085 431549.547 458118.1375 0.832710375 1.099459386 0.928932006 0.99120983 0.894615438 1.102187475 0.895430839 0.942004936 1 18.80536016 3.744242562 24.58708225 0.963108654 0.993855567 0 0.087875242 1690.678329 2427884.652 0.020251072 0.036385066 5549.35569 -3.744242562 0.030746913 EEAS(ph)DDDMEGDEAVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EEASDDDMEGDEAVVR 16 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 1 EEAS(1)DDDMEGDEAVVR;EEAS(1)DDDMEGDEAVVR;EEAS(1)DDDMEGDEAVVR;EEAS(1)DDDMEGDEAVVR;EEAS(1)DDDMEGDEAVVR 481.23 5.13E-231 5374800000 5278800 3560010 3820230 3404864 2422801 2334729 4374210 4102740 2002850 TRUE FALSE 4948409.331 3823596.845 3910847.66 3492238.575 2232523.983 3008727.361 3718337.819 4614976.12 1668561.396 2.965674109 2.291552983 2.343844026 2.092963785 1.337993308 1.803186486 2.228469283 2.76584136 1 20.67017334 7.999999997 0.462236476 1.915487824 26.57244677 0.320971918 0.490100127 120.2454271 1.404740648 0.270157828 2819.742022 99999999.28 -7.999999997 24.65695895 EEASDYLELDTIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEASDYLELDTIK 13 0 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 ; 276.95 6.94E-32 108559000 335680 247580 282640 264490 255610 207849 338430 232340 165212 FALSE TRUE 314670.388 265911.0808 289344.3543 271277.2612 235535.4217 267851.6322 287685.5633 261348.1604 137637.0499 2.286233164 1.931973121 2.102227231 1.970961027 1.711279208 1.946072169 2.090175309 1.898821289 1 17.07050935 -1.988645724 0.416420102 1.86E-13 2.024926765 0.825047446 0.144700169 19.48632473 1.268131015 18.91976149 0.083974961 0.010264889 1.988645724 2.024926765 EEASLLSHS(ph)PGTSNQS(ph)QPCSPKPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEASLLSHSPGTSNQSQPCSPKPIR 25 1 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 2 EEASLLSHS(1)PGTS(0.012)NQS(0.88)QPCS(0.107)PKPIR 206.95 4.65E-25 356060000 247150 201510 254370 245320 295910 196800 305460 225730 338480 TRUE FALSE 231681.3227 216430.0101 260403.7765 251615.3265 272670.4222 253612.9652 259659.1088 253912.8874 281985.5013 0.821607216 0.767521766 0.923465126 0.892298807 0.966966106 0.899382997 0.920824324 0.900446605 1 18.10526146 3.879036438 2.863722917 0.924522616 0.794684706 0.709504984 0.035578894 0.124110056 1.994436255 0.008325268 0.017429064 7568.963975 -3.879036438 -0.129837911 EEASLLSHS(ph)PGTSNQSQPCSPKPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EEASLLSHSPGTSNQSQPCSPKPIR 25 1 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 1 EEASLLSHS(0.991)PGT(0.009)SNQSQPCSPKPIR;EEASLLSHS(1)PGTSNQSQPCSPKPIR;EEASLLSHS(1)PGTSNQSQPCSPKPIR 269.57 2.17E-46 3692870000 942310 1017810 1018930 1086530 1158390 854690 1264230 922160 1497670 TRUE FALSE 883332.4992 1093169.711 1043099.501 1114412.199 1067414.722 1101425.128 1074670.448 1037293.706 1247699.202 0.707969115 0.876148442 0.836018408 0.89317377 0.855506456 0.882764954 0.861321741 0.831365208 1 20.25083874 -5 0.115999053 1.445923676 0.775812778 0.539538119 0.048516753 131.8968981 1.002949442 14.16878212 0.478794184 1.00E-05 5 -0.670110898 EEASLLSHSPGT(ph)SNQSQPCSPKPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEASLLSHSPGTSNQSQPCSPKPIR 25 1 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 1 EEASLLSHS(0.29)PGT(0.445)S(0.253)NQS(0.011)QPCS(0.001)PKPIR 185.89 2.40E-17 836480000 354750 351190 382390 388220 401670 315070 481100 344130 571570 TRUE FALSE 332546.8307 377192.473 391460.4714 398182.3825 370124.4585 406025.5943 408963.5213 387095.388 476171.2745 0.698376506 0.792136135 0.82210014 0.836216722 0.777292706 0.852688131 0.858858027 0.812933095 1 18.86112107 -5 0.09742691 1.596881111 0.676232987 0.778545779 0.035816528 89.57559974 0.597549327 10.96397507 0.624553428 1.00E-05 5 -0.920648124 EEASNFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EEASNFR 7 0 P25788-2;P25788;G3V4X5 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;; 183.9 0.0014795 2951010000 2022910 2309880 1994270 1965440 2441520 1584070 2248340 2038550 2332880 FALSE TRUE 1896299.674 2480905.919 2041575.026 2015876.518 2249772.868 2041365.294 1911222.29 2293067.455 1943507.257 0.975710107 1.276509727 1.050459173 1.037236424 1.157583981 1.050351259 0.983388296 1.179860506 1 20.89023106 3.727185253 24.99988042 1.061748342 1.152362264 0.049822814 0.094613165 5.282280804 2062001.61 0.022613329 0.037747946 5335.624436 -3.727185253 0.090613923 EEATS(ph)PGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEATSPGAK 9 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 EEAT(0.277)S(0.723)PGAK;EEAT(0.118)S(0.882)PGAK 158.94 6.97E-05 527440000 2919170 1903860 2296330 2133640 2212710 1723830 2467570 1872820 2138190 TRUE FALSE 2736464.361 2044823.775 2350800.032 2188392.815 2038932.682 2221471.737 2097580.786 2106645.7 1781312.276 1.536206985 1.147931109 1.319701247 1.228528453 1.144623944 1.247098427 1.177548044 1.18263694 1 20.76450902 8 0.028759652 0.057907236 2.885893185 0.537266174 0.094368199 1234.745315 2.724278698 86.96898707 203.61967 99999999.97 -8 2.827985949 EEATYGVWAERDS(ph)DDERPSFGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 EEATYGVWAERDSDDERPSFGGK 23 2 Q9UBB9;F6XM96;F6UKU9;F6SQZ1 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(0.999)DDERPS(0.001)FGGK;EEATYGVWAERDS(0.998)DDERPS(0.002)FGGK;EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(1)DDERPSFGGK 220.09 1.03E-32 8414750000 3144730 2753070 2855110 2899600 3121280 2364254 3836520 2879720 3587810 TRUE FALSE 2947906.963 2956910.167 2922834.557 2974008.645 2876147.259 3046775.749 3261269.443 3239259.381 2988981.333 0.986258071 0.989270202 0.977869793 0.994990705 0.962249991 1.019335824 1.091097293 1.08373356 1 21.51122246 1.975751901 4.95948711 1.066276837 0.983384175 0.64126462 0.025805904 0.097156327 6.351915081 0.009936061 0.006268335 94.56967591 -1.975751901 -0.082892662 EEATYGVWAERDSDDERPS(ph)FGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEATYGVWAERDSDDERPSFGGK 23 2 Q9UBB9;F6XM96;F6UKU9;F6SQZ1 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 EEATYGVWAERDS(0.257)DDERPS(0.743)FGGK 227.24 6.90E-33 913270000 1072900 818070 873350 1036900 1048300 720890 1222600 902870 1078800 TRUE FALSE 1005749.104 878640.754 894066.2744 1063508.609 965970.7466 928999.2403 1039282.48 1015595.307 898741.3107 1.119064065 0.977634769 0.99479824 1.183331173 1.07480399 1.033667007 1.156375553 1.130019612 1 19.77754639 3.268677063 24.99991732 1.102310751 1.014070817 0.164385304 0.065755263 246.1397134 204321.1349 0.01701291 0.02303254 1856.423525 -3.268677063 -0.088239934 EEAYHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEAYHSR 7 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 102 0.0086987 56559000 106850 119400 108360 111660 150750 90907 117670 120070 147960 FALSE TRUE 100162.4492 128240.5002 110930.3504 114525.3846 138910.7031 117150.3751 100026.4759 135061.0038 123264.5201 0.812581342 1.040368308 0.899937389 0.929102588 1.126931764 0.950398176 0.81147824 1.09570056 1 16.91139808 4.758426598 22.99487559 0.966253732 0.812580908 0.228967527 0.093802758 2493.729805 2886351.336 0.021917066 0.749066541 57335.89521 -4.758426598 -0.153672825 EECPAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EECPAVR 7 0 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 ; 96.666 0.029229 480630000 737930 724970 718040 747250 688770 642510 842980 650980 679020 FALSE TRUE 691744.2785 778647.5331 735072.2479 766425.7001 634676.7826 827992.2067 716582.9748 732256.286 565687.1754 1.222838892 1.376463118 1.299432407 1.354857832 1.12195717 1.463692731 1.266747782 1.294454458 1 19.10964494 0.378499567 1.747921282 1.000003512 1.309714863 0.515539428 0.091186622 4.631889875 12.16044621 0.076376811 0.021443604 2.39055955 -0.378499567 0.309711351 EEDCHS(ph)PTSKPPKPDQPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EEDCHSPTSKPPKPDQPLK 19 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 EEDCHS(0.918)PT(0.041)S(0.041)KPPKPDQPLK;EEDCHS(0.995)PT(0.004)S(0.001)KPPKPDQPLK;EEDCHS(0.835)PT(0.16)S(0.005)KPPKPDQPLK 173.18 3.60E-12 1488010000 4063410 1466190 2673830 2341330 1896010 2116710 3657020 1798200 1867140 TRUE FALSE 3809088.421 1574748.233 2737254.51 2401412.492 1747105.023 2727769.815 3108683.801 2022709.228 1555502.272 2.44878358 1.012372828 1.759723891 1.543818055 1.123177416 1.753626378 1.998508043 1.300357618 1 20.56894907 4.75919671 24.10621226 1.502128697 2.448785088 0.454000154 0.342222581 3175.033548 3708842.939 0.080882358 3.326414156 57437.6562 -4.75919671 0.946656392 EEDEENDNDNES(ph)DHDEADS ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEDEENDNDNESDHDEADS 19 0 H0YBP8;Q9NRG0 H0YBP8 CHRAC1 Chromatin accessibility complex protein 1 1 EEDEENDNDNES(0.969)DHDEADS(0.031);EEDEENDNDNES(0.999)DHDEADS(0.001) 89.261 0.0025435 47956000 79021 64844 78120 75016 74675 66036 91824 69174 80249 TRUE FALSE 74075.21667 69645.11723 79973.04329 76941.03756 68810.32672 85099.5212 78055.84365 77810.52617 66854.92347 1.107999424 1.041735053 1.196217708 1.150865689 1.029248455 1.272898341 1.167540693 1.163871292 1 16.02874619 3.989016454 9.454983463 1.152348649 1.076114493 0.088370682 0.079850609 0.387247703 266.4537996 0.01825965 0.03755739 9750.26577 -3.989016454 -0.076234157 EEDEEPES(ph)PPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEDEEPESPPEK 12 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EEDEEPES(1)PPEK;EEDEEPES(1)PPEK 291.2 4.18E-36 659350000 2117220 982230 1358910 1245370 1042070 1291230 1959570 1039120 855900 TRUE FALSE 1984706.98 1054955.331 1391143.987 1277328.303 960230.0257 1663987.14 1665750.67 1168856.419 713044.7607 2.783425514 1.479507865 1.950991107 1.791371837 1.346661638 2.333636304 2.336109543 1.639246908 1 19.44363312 0.986663114 22.95376068 0.999999972 1.955135875 0.364109609 0.42134256 270.0609912 464797.3123 0.390603796 0.097650949 9.697574252 -0.986663114 0.955135903 EEDEEPES(ph)PPEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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 284.79 1.11E-32 20221570000 26138690 8792000 13825350 12759000 11423630 12141840 20600790 10692680 11590870 TRUE FALSE 24502716.05 9442968.828 14153293.83 13086417.54 10526464.18 15646992.1 17511892.79 12027684.64 9656278.917 2.537490504 0.977909701 1.465708888 1.355223648 1.090116003 1.620395624 1.813523919 1.245581734 1 23.20303592 4.750715712 24.66537093 1.366707872 2.537491369 0.666175604 0.268896633 1080.206132 2191928.282 0.066904658 1.129298506 56326.88214 -4.750715712 1.170783497 EEDEPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEDEPEER 8 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 193.16 0.00040043 1409290000 1327230 1417090 1388870 1406840 1460420 1279390 1650790 1206710 1404080 FALSE TRUE 1244161.043 1522012.818 1421814.652 1442941.896 1345724.504 1648729.124 1403269.365 1357370.4 1169729.977 1.063630981 1.301165951 1.215506724 1.233568366 1.150457396 1.409495487 1.199652392 1.160413451 1 20.1577441 0.900693921 2.37428824 1.000918515 1.236670743 0.380138215 0.090006095 0.384872632 4.59463922 0.076659264 0.020756879 7.955984356 -0.900693921 0.235752228 EEDEPEERS(ph)GDETPGSEVPGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EEDEPEERSGDETPGSEVPGDK 22 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 EEDEPEERS(1)GDETPGSEVPGDK;EEDEPEERS(1)GDETPGSEVPGDK;EEDEPEERS(1)GDETPGSEVPGDK;EEDEPEERS(1)GDETPGSEVPGDK;EEDEPEERS(1)GDETPGSEVPGDK;EEDEPEERS(1)GDETPGSEVPGDK 394.05 2.99E-132 11843340000 7110360 4363330 4734480 4826070 5502730 3244703 5815360 4645470 7651200 TRUE FALSE 6665335.26 4686395.493 4846784.101 4949915.127 5070567.783 4181396.083 4943400.755 5225467.155 6374165.291 1.045679702 0.735217127 0.760379419 0.776558953 0.795487338 0.65599116 0.775536957 0.819788461 1 22.603805 0.819883113 3.328646854 0.999943928 0.776785955 0.288271694 0.099587538 1.126919377 19.03521788 0.086578734 0.022438022 6.605156509 -0.819883113 -0.223157973 EEDFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEDFTR 6 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 159.19 0.021386 1536560000 1937150 1969780 2025910 1953020 1959890 1795180 2226180 1768050 1601910 FALSE TRUE 1815907.239 2115624.561 2073965.542 2003137.8 1805968.145 2313419.324 1892384.976 1988794.934 1334540.872 1.360698108 1.585282703 1.554066709 1.500993968 1.353250532 1.733494546 1.41800451 1.490246553 1 20.34791206 0.229715391 1.224008716 0.999140409 1.518011695 0.660337182 0.112316199 2.953706753 4.158443718 0.100625323 0.0289888 1.697131098 -0.229715391 0.518871286 EEDGADAS(ph)EEDLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEDGADASEEDLTR 14 0 E5RHA3;Q86X53 E5RHA3 ERICH1 Glutamate-rich protein 1 1 EEDGADAS(1)EEDLTR;EEDGADAS(1)EEDLTR 314.58 8.12E-56 778650000 1073300 1054600 1010090 973500 1097960 801350 1175520 953370 1049810 TRUE FALSE 1006124.069 1132683.681 1034049.812 998481.6581 1011730.651 1032686.736 999261.689 1072400.343 874589.929 1.150395214 1.295102589 1.182325313 1.141656936 1.156805741 1.180766782 1.142548817 1.226175042 1 19.73824721 -4.999999999 0.167236489 0.283738356 1.235479366 0.568688754 0.048834464 91.15441752 0.854781784 21.71798619 0.179325984 1.00E-05 4.999999999 0.95174101 EEDIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEDIGK 6 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3;C9JAX4;A0A0C4DG51;Q9NP80-3;Q9NP80-2;Q9NP80 P22314 UBA1;PNPLA8 Ubiquitin-like modifier-activating enzyme 1;Calcium-independent phospholipase A2-gamma 0 103.29 0.080996 406260000 554820 457680 521240 484600 505760 345420 628030 464190 621590 FALSE TRUE 520094.8066 491567.1034 533604.0589 497035.6564 466039.6497 445137.1466 533862.7318 522145.1433 517842.6134 1.004349185 0.949259661 1.030436749 0.959819921 0.899963884 0.859599297 1.030936269 1.008308567 1 18.98215416 1.610472988 25 1.014719703 0.957130435 0.264632683 0.048275323 0.398284946 3771.795368 0.024898635 0.013008193 40.78241957 -1.610472988 -0.057589268 EEDRPPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EEDRPPLR 8 1 P53618 P53618 COPB1 Coatomer subunit beta 0 ;; 172.25 0.00025962 1875230000 1864790 2322150 2071800 2377890 2371180 1851620 2476780 2129070 2136140 FALSE TRUE 1748076.123 2494084.402 2120944.074 2438910.683 2184957.088 2386152.635 2105409.832 2394889.076 1779604.434 0.982283528 1.401482461 1.191806468 1.3704791 1.227776828 1.340833159 1.183077426 1.345742363 1 20.76312517 -1.405887402 4.468115789 0.999416786 1.263264167 0.298472066 0.122549095 0.000606936 8.07E-05 0.101152231 0.023789977 0.039274675 1.405887402 0.263847381 EEDVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEDVLK 6 0 C9J9K3;A0A0C4DG17;P08865;F8WD59;Q9UBC7;Q68DK2-4;G3V2D8;Q68DK2-5;Q68DK2-2;Q68DK2 C9J9K3;G3V2D8 RPSA;GALP;ZFYVE26 40S ribosomal protein SA;Galanin-like peptide;Zinc finger FYVE domain-containing protein 26 0 99.919 0.088987 188360000 512770 640070 621550 639350 623660 693530 628950 525190 481110 FALSE TRUE 480676.641 687461.4488 636293.4595 655756.8034 574680.2593 893740.8525 534644.7864 590761.1276 400809.6329 1.199264193 1.715181953 1.587520377 1.636080447 1.433798522 2.229838754 1.333912018 1.473919485 1 18.61255766 0.878320223 1.642178114 1.007531272 1.624006834 0.319003866 0.271879708 0.563344443 2.976239604 0.229834729 0.066167378 7.556491925 -0.878320223 0.616475561 EEEADMSS(ph)PTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EEEADMSSPTQR 12 0 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 EEEADMS(0.004)S(0.881)PT(0.115)QR;EEEADMS(0.049)S(0.951)PTQR;EEEADMS(0.012)S(0.956)PT(0.033)QR;EEEADMS(0.008)S(0.981)PT(0.011)QR 246.25 1.66E-16 1211640000 2330730 1894950 2237220 2328710 2000370 1709310 1839920 1394020 1129350 TRUE FALSE 2184853.77 2035254.07 2290287.915 2388468.641 1843269.009 2202760.049 1564041.077 1568066.466 940854.1891 2.322202308 2.16319818 2.43426446 2.538617215 1.95914418 2.341234247 1.662362877 1.666641318 1 19.84361163 1.226272958 0.844332388 1.017747594 2.333358093 0.855218187 0.177183312 0.180942897 0.286493194 0.152549293 0.056981628 16.83731969 -1.226272958 1.315610499 EEECHFYAGGQVYPGEASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEECHFYAGGQVYPGEASR 19 0 Q13162;A6NG45 Q13162 PRDX4 Peroxiredoxin-4 0 128.38 2.16E-05 176240000 150650 138570 134390 142000 133270 130090 185100 127260 127310 FALSE TRUE 141221.0854 148829.867 137577.7943 145643.9604 122803.5118 167644.8712 157345.9734 143148.6911 106061.1385 1.331506406 1.403245986 1.297155548 1.37320759 1.157855869 1.580643707 1.483540301 1.349680883 1 16.69453662 2.239729015 24.99999637 1.410054772 1.325605774 0 0.164508997 94.37697083 2019431.025 0.05308718 0.042131846 173.671684 -2.239729015 -0.084448998 EEEEEEEEDQEGDRETTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEEEEEEEDQEGDRETTIR 19 1 A0A0B4J2E5;Q15269 A0A0B4J2E5 PWP2 Periodic tryptophan protein 2 homolog 0 ; 290.92 1.41E-49 1073190000 369054 505520 466870 523820 523090 455447 558610 473570 509830 FALSE TRUE 345955.5689 542949.2268 477944.3769 537262.108 482008.6214 586927.1553 474851.6164 532696.257 424736.0794 0.814518911 1.278321417 1.125273788 1.264931646 1.134842658 1.381863194 1.117992183 1.254181792 1 18.69620714 4.745497435 24.93984763 1.202124524 0.814518727 0.55383 0.107047301 525.8785009 1890634.847 0.021616798 0.216448167 55654.13477 -4.745497435 -0.387605798 EEEEGISQES(ph)S(ph)EEEQ ddPTM_SK-BR-3_Pertuzumab_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 283.12 1.05E-33 672390000 1173430 1184280 1078980 946150 1179810 814000 1293370 1071550 1549850 TRUE FALSE 1099987.111 1271965.323 1104573.915 970429.8108 1087152.482 1048988.586 1099441.176 1205335.376 1291170.023 0.851930491 0.985126127 0.855482931 0.751589484 0.841990182 0.812432575 0.851507668 0.93352181 1 20.30024756 -0.547129128 15.01133426 1 0.864265796 0.325226452 0.062958999 0 0 0.064344631 0.015166175 0.283707536 0.547129128 -0.135734204 EEEEIS(ph)ELQEDDRDQFSDQLASVGMLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEEEISELQEDDRDQFSDQLASVGMLGR 28 1 F2Z2X4;Q9C0E2 F2Z2X4 XPO4 Exportin-4 1 EEEEIS(1)ELQEDDRDQFSDQLASVGMLGR 67.406 0.0081395 43416000 28921 36241 31824 38605 39005 33842 37857 33240 36794 TRUE FALSE 27110.88624 38924.32135 32578.88031 39595.66966 35941.70464 43611.63602 32180.6943 37390.08717 30652.8437 0.884449303 1.269843729 1.062833864 1.291745394 1.172540629 1.422759873 1.049843682 1.219791793 1 14.9037333 4.748218804 24.53801253 1.18880297 0.884449091 0.359695438 0.126469066 1075.359249 2732031.401 0.026766025 0.348495028 56003.96867 -4.748218804 -0.304353879 EEEERER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEEERER 7 1 Q9H3P7;E9PEW5;A0A0A0MQX1;Q9HD67-3;Q9HD67 Q9H3P7;E9PEW5 ACBD3;MYO10 Golgi resident protein GCP60;Unconventional myosin-X 0 100.45 0.0089232 75947000 14180 21177 18736 17916 19028 13108 15232 18920 17404 FALSE TRUE 13292.49911 22744.96711 19180.42677 18375.75489 17533.61764 16892.06681 12948.10301 21282.20365 14499.15997 0.916777189 1.568709302 1.322864691 1.267366864 1.209285067 1.165037619 0.893024357 1.467823219 1 13.8236817 2.592622221 1.697425532 1.099101733 1.33663554 0.04632191 0.216674702 0.595184691 3.446066098 0.085402626 0.074125798 391.4012619 -2.592622221 0.237533807 EEEGTGVVHQAPYFGAEDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEEGTGVVHQAPYFGAEDYR 20 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 165.1 1.72E-11 503170000 724400 651910 689480 654370 699310 612770 837580 683100 458025 FALSE TRUE 679061.0971 700178.0947 705834.7912 671162.242 644389.0135 789666.7515 711992.6547 768386.5387 381577.6685 1.779614357 1.834955639 1.849780135 1.758913839 1.688749281 2.069478422 1.865918038 2.013709402 1 18.54161722 -0.749093179 12.09358262 1.00000002 1.857062236 0.851261254 0.112664526 0 0 0.103623021 0.024424181 0.17819964 0.749093179 0.857062216 EEEHDCFLEEIMTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEEHDCFLEEIMTK 14 0 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 117.92 0.00027571 39928000 87645 51712 76478 61879 54953 70518 109371 52893 50973 FALSE TRUE 82159.4559 55540.81029 78292.09428 63466.9199 50637.21305 90875.40184 92971.8339 59496.80748 42465.277 1.934744377 1.307911174 1.843673227 1.494560365 1.192438072 2.139993149 2.189361296 1.401069572 1 15.37399604 2.230560644 24.99319197 1.838190736 1.557695227 0 0.412550989 422.0128738 1318424.571 0.142051804 0.106769195 170.0437384 -2.230560644 -0.28049551 EEEITLYPDKHGCVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEEITLYPDKHGCVR 15 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 98.694 0.0017001 76945000 78159 117880 88522 99357 133140 76769 119310 83422 193050 FALSE TRUE 73267.16771 126607.9579 90621.78364 101906.6688 122683.7215 98930.96406 101420.5731 93837.42033 160828.7078 0.455560258 0.787222378 0.56346771 0.633634817 0.762822279 0.615132493 0.630612373 0.583461881 1 17.29516542 -1.775247624 2.571247336 1.095112047 0.640097209 0.600938608 0.094631302 9248143.03 6581290.427 5531735.773 0.021664393 0.016778471 1.775247624 -0.455014838 EEEKLELQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEEKLELQK 9 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 90.108 0.010628 176370000 268100 189160 203390 194240 203720 155000 263320 190760 230470 FALSE TRUE 251320.0996 203165.6032 208214.5068 199224.5272 187720.653 199745.9838 223837.6105 214576.8059 192003.0681 1.308937935 1.058137275 1.084433228 1.037611165 0.977696111 1.040327041 1.165802259 1.117569672 1 17.55076984 4.739963911 24.76320898 1.067782584 1.308938023 0.670250784 0.054600632 71.45356284 1260756.567 0.013726252 0.086715094 54949.52099 -4.739963911 0.24115544 EEEMGEEEEVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEEMGEEEEVER 12 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ; 266.17 3.83E-21 527000000 188512 208803 189826 206670 214467 177492 207716 200355 210900 FALSE TRUE 176713.3704 224262.9914 194328.7624 211973.5021 197623.6269 228731.0591 176570.9141 225369.7628 175699.4275 1.005770895 1.276401378 1.10602957 1.20645528 1.124782418 1.301831556 1.004960099 1.282700609 1 17.42274997 -1.386508419 3.337001999 0.998540772 1.16306871 0.188020324 0.106850803 5050403.253 4278521.09 47919.21502 0.021631535 0.041066868 1.386508419 0.164527937 EEEMMIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEEMMIR 7 0 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 131.04 0.01952 0 171220 174440 175890 183030 203430 151670 179580 164550 228630 FALSE TRUE 160503.6458 187355.7191 180062.1939 187726.8597 187453.4284 195454.6668 152653.6461 185094.4297 190470.176 0.842670749 0.983648585 0.945356368 0.985597135 0.984161575 1.026169403 0.801456949 0.971776441 1 17.53920559 -1.777979789 8.854551027 1.000624332 0.942282824 0.063722716 0.069131 0.000833107 2.09E-05 0.065448921 0.015263801 0.016673248 1.777979789 -0.058341508 EEEMRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEEMRR 6 1 Q15233;Q15233-2;H7C367 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 82.263 0.095732 42840000 51618 59809 56191 53957 62560 44734 58479 53618 81834 FALSE TRUE 48387.32152 64237.32059 57523.87706 55341.62797 57646.78995 57647.9796 49710.61684 60312.32533 68175.37673 0.709747769 0.942236386 0.843763244 0.8117539 0.845566137 0.845583587 0.729157934 0.88466435 1 16.05696315 0.987283634 24.67644401 1.000000007 0.828667067 0.439675446 0.065002183 561.8110173 1090211.595 0.062761394 0.015690349 9.71144005 -0.987283634 -0.17133294 EEEPVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EEEPVKK 7 1 Q14103-3;Q14103;H0Y8G5;H0YA96;Q14103-2;Q14103-4;Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q14103-3;Q14103-2;Q99729-3 HNRNPD;HNRNPAB Heterogeneous nuclear ribonucleoprotein D0;Heterogeneous nuclear ribonucleoprotein A/B 0 ;;;;; 89.298 0.028822 9539440000 15535000 8382900 10925900 9785400 9305500 8327600 14618400 8934100 10200700 FALSE TRUE 14562692.08 9003578.638 11185067.51 10036509.93 8574683.567 10731642.93 12426506.63 10049542.05 8498137.271 1.713633425 1.059476724 1.316178728 1.181024689 1.00900742 1.262822968 1.462262403 1.182558216 1 23.01871522 -4.999999997 0.026781885 1.92E-06 2.027571221 0.177629917 0.198287911 5056.392423 10.2163858 575.4818014 256.9142916 1.00E-05 4.999999997 2.027569302 EEFEHQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EEFEHQQK 8 0 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;; 119.27 0.0017256 1696640000 3457200 2066510 2626280 2237320 1982980 2288160 3684600 2301010 2387050 FALSE TRUE 3240820.023 2219516.551 2688576.602 2294733.419 1827244.75 2948714.647 3132128.436 2588296.164 1988635.934 1.629669849 1.116099992 1.35197024 1.15392334 0.918843273 1.482782543 1.575013497 1.301543495 1 20.92334775 EEFKQEVEATAGLLYVDDPNWSGIGVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEFKQEVEATAGLLYVDDPNWSGIGVVR 28 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ; 145.67 8.53E-08 76037000 226163 168820 189928 186078 199791 152616 227717 154526 202619 FALSE TRUE 212007.8615 181319.6085 194433.1819 190853.0765 184100.2208 196673.7617 193572.9499 173818.9113 168800.5799 1.255966429 1.074164606 1.151851385 1.130642303 1.090637371 1.165124917 1.146755242 1.029729349 1 17.36496034 1.168296622 4.601813021 1.004033762 1.138032551 0.550551886 0.048827715 0.150183187 5.64953231 0.041267673 0.010746491 14.73318431 -1.168296622 0.133998789 EEFTAFLHPEEYDYMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 EEFTAFLHPEEYDYMK 16 0 O43852;O43852-3;O43852-15;O43852-6;H0Y875;O43852-10;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;;;;;;;; 208.39 1.50E-11 3516526000 7914880 6437300 7227980 6973400 7123420 5492166 8858330 6339040 5897520 FALSE TRUE 7419501.789 6913924.39 7399431.099 7152349.25 6563975.328 7077665.166 7530105.653 7130483.098 4913185.813 1.510120332 1.407218179 1.506035265 1.455745726 1.335991672 1.440544982 1.53263197 1.451295223 1 22.22822737 0.913707584 21.94392093 1 1.457060422 0.866515322 0.056116276 11866.75231 3017685.278 0.053827723 0.013456931 8.197993778 -0.913707584 0.457060422 EEFTAFLHPEEYDYMKDIVVQETMEDIDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEFTAFLHPEEYDYMKDIVVQETMEDIDK 29 1 O43852;O43852-3;O43852-15;O43852-6;H0Y875;O43852-10;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ; 209.58 6.89E-26 25645000 15767 14311 14810.6 14772.5 19748.9 10157.3 17988.8 11674.8 24169.4 FALSE TRUE 14780.17161 15370.60133 15161.91443 15151.58736 18197.90106 13089.54762 15291.54644 13132.42448 20135.371 0.734040193 0.763363205 0.75299901 0.752486128 0.903777788 0.6500773 0.759437034 0.65220673 1 14.29744443 -1.097944425 4.243842733 1.000033742 0.749561702 0.566974082 0.069687418 0.997627553 35523765.87 2744.585909 0.014699874 0.079809681 1.097944425 -0.250472041 EEFWEMFDGSLYHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEFWEMFDGSLYHK 14 0 A0A0A0MTI1;Q15392-2;Q15392 A0A0A0MTI1 DHCR24 Delta(24)-sterol reductase 0 148.52 7.74E-06 66688000 167560 157760 135260 113820 211550 115050 196840 201210 149560 FALSE TRUE 157072.7187 169440.7145 138468.4311 116740.8139 194935.7164 148263.0673 167325.6694 226331.5114 124597.4698 1.260641319 1.359904939 1.111326187 0.936943696 1.564523876 1.189936421 1.342929914 1.816501665 1 16.92691525 2.725088091 24.95530997 1.382439149 1.190007861 0.165420413 0.238171166 1514.317829 2804984.026 0.071993918 0.068217162 530.9921379 -2.725088091 -0.192431288 EEGAQTLEEDRAQT(ph)PHEDGGPQPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEGAQTLEEDRAQTPHEDGGPQPHR 25 1 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 1 EEGAQTLEEDRAQT(1)PHEDGGPQPHR 100.68 0.0033157 214880000 47686 79662 72734 71800 80451 73122 64706 91944 75713 TRUE FALSE 44701.41838 85560.25737 74459.28483 73642.50956 74132.70298 94231.13436 55003.936 103423.4108 63076.01118 0.708691269 1.356462715 1.180469143 1.167520079 1.175291551 1.493929825 0.872026226 1.639663144 1 15.94480381 4.747691171 24.59083004 1.225711554 0.708690928 0.356364767 0.222212904 1024.729059 2759773.26 0.046245118 0.567323546 55935.96962 -4.747691171 -0.517020626 EEGDLGPVYGFQWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EEGDLGPVYGFQWR 14 0 P04818;P04818-2 P04818 TYMS Thymidylate synthase 0 ;;; 211.78 7.82E-09 233282000 266143 257075 287752 260257 284156 257068 320087 241086 299589 FALSE TRUE 249485.5847 276109.1005 294577.6133 266935.6352 261839.534 331279.3584 272092.9259 271186.1178 249585.6605 0.999599032 1.106269887 1.180266578 1.06951511 1.049096865 1.327317274 1.09017852 1.086545266 1 17.92917552 0.92607464 2.551161113 1.0009775 1.12693012 0.144264689 0.088312326 0.624180918 9.095556054 0.078911514 0.021171346 8.434797094 -0.92607464 0.125952621 EEGEHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEGEHIR 7 0 Q99567;J3KMX1 Q99567 NUP88 Nuclear pore complex protein Nup88 0 ; 147.34 0.0021582 106905000 124051 130023 131374 139991 126579 117766 160029 120026 137266 FALSE TRUE 116286.8693 139650.0382 134490.2533 143583.4061 116637.9959 151763.1324 136034.1371 135011.5103 114355.4178 1.0168899 1.221193021 1.176072423 1.255589012 1.019960384 1.327117992 1.189573172 1.180630642 1 16.80316519 0.881541088 15.45926131 1 1.183287474 0.240760144 0.095339754 2089.355906 272674.1995 0.08058627 0.020146568 7.612741586 -0.881541088 0.183287474 EEGFPIRPHYFWPLLVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEGFPIRPHYFWPLLVGR 18 1 P42704;B8ZZ38;A0A0C4DG06 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ; 147.56 4.55E-08 286570000 511160 612630 495110 424940 757970 412360 447160 610830 589420 FALSE TRUE 479167.408 657989.7626 506854.243 435844.6798 698442.0937 531401.6379 380112.5092 687093.4701 491041.9942 0.975817575 1.339986743 1.032201419 0.887591459 1.422367337 1.082191837 0.77409369 1.399256027 1 18.90548688 3.736760284 22.99733384 1.063907163 1.184568258 0.008154313 0.218374577 408.7565133 975215.0159 0.053633792 0.094900574 5454.567045 -3.736760284 0.120661095 EEGGENLDQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEGGENLDQAR 11 0 E5RK69;P08133;P08133-2;E7EMC6 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 150.1 7.92E-05 182070000 86028 89580 84386 63465 107250 58769 105180 100820 144720 FALSE TRUE 80643.66104 96212.59641 86387.67577 65093.61935 98827.01763 75734.65626 89409.23544 113407.5989 120565.2971 0.668879545 0.798012353 0.7165219 0.539903446 0.819697044 0.62816298 0.741583504 0.940632186 1 16.87945518 1.210986075 3.442836809 0.995029861 0.706390572 0.669051833 0.079429677 0.132518309 2.846611408 0.067582388 0.018811387 16.25496636 -1.210986075 -0.288639289 EEGGFEYKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEGGFEYKR 9 1 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 74.162 0.067138 188960000 224550 225560 231400 230400 241770 183940 278030 220260 258510 FALSE TRUE 210495.8163 242260.6971 236888.9173 236312.4541 222782.3595 237040.492 236341.9826 247759.9459 215363.011 0.977400044 1.124894642 1.099951734 1.097275029 1.034450431 1.100655544 1.097412139 1.15042943 1 17.71641096 EEGLGFPSFLDPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EEGLGFPSFLDPDR 14 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 0 ;;;;; 172.92 6.47E-06 189996000 230745 221168 234537 198342 215834 218480 262176 232358 156806 FALSE TRUE 216303.0823 237543.5088 240100.3284 203431.7915 198883.2683 281551.6293 222865.1427 261368.4078 130634.0656 1.655793849 1.818388701 1.837961081 1.55726449 1.522445676 2.155269592 1.706026232 2.000767614 1 16.99517163 -0.826837828 10.78492583 1 1.786346699 0.621024665 0.191887987 0 0 0.170654222 0.040223586 0.148991733 0.826837828 0.786346699 EEGS(ph)DIEDEDMEELLNDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EEGSDIEDEDMEELLNDTR 19 0 F5H5U2;Q8NHQ9;Q8NHQ9-2 F5H5U2 DDX55 ATP-dependent RNA helicase DDX55 1 EEGS(1)DIEDEDMEELLNDTR;EEGS(1)DIEDEDMEELLNDTR;EEGS(1)DIEDEDMEELLNDTR 286.57 3.69E-40 160296000 278026 216225 247689 244362 222714 182706 302692 199794 264144 TRUE FALSE 260624.849 232234.524 253564.3 250632.7426 205222.9408 235450.2562 257306.1447 224738.7207 220056.66 1.18435338 1.055339675 1.152268239 1.138946409 0.932591365 1.069952876 1.169272244 1.021276615 1 17.74751551 1.517624978 0.012711934 9.28E-07 2.143105353 0.209882457 0.072481324 1150.901767 14.86163697 1252.57884 1249.723576 32.93252106 -1.517624978 2.143104425 EEGSLS(ph)DTEADAVSGQLPDPTTNPSAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEGSLSDTEADAVSGQLPDPTTNPSAGK 28 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 EEGS(0.02)LS(0.851)DT(0.129)EADAVSGQLPDPTTNPSAGK 257.31 8.95E-54 450610000 863640 475920 674250 594210 468970 578010 797770 504380 454710 TRUE FALSE 809586.314 511157.612 690243.5284 609458.4346 432138.9879 744872.1038 678151.7946 567352.9533 378815.9635 2.137149413 1.34935605 1.822107817 1.608850981 1.140762348 1.966316564 1.790188007 1.497700752 1 18.5311376 0.920829097 5.920311951 1.000029454 1.666172758 0.364902163 0.28507311 0.762673644 55.64132922 0.252735347 0.063574183 8.333531803 -0.920829097 0.666143304 EEGSLSDT(ph)EADAVSGQLPDPTTNPSAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EEGSLSDTEADAVSGQLPDPTTNPSAGK 28 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 EEGS(0.099)LS(0.343)DT(0.558)EADAVSGQLPDPTTNPSAGK;EEGS(0.066)LS(0.311)DT(0.624)EADAVSGQLPDPTTNPSAGK;EEGS(0.288)LS(0.283)DT(0.428)EADAVSGQLPDPTTNPSAGK 217.17 1.20E-33 781190000 1711790 952340 1301630 1174790 1013050 1164760 1657280 1110890 915620 TRUE FALSE 1604652.12 1022852.245 1332505.278 1204937.1 933489.1394 1501007.304 1408786.249 1249587.062 762797.1069 2.103642115 1.340923078 1.746867242 1.579629877 1.223771211 1.967767431 1.846868894 1.638164396 1 19.54093985 0.939030184 21.87077099 0.999999999 1.667710834 0.395163923 0.264588627 6759.058747 2424578.251 0.242547293 0.060636823 8.690208248 -0.939030184 0.667710836 EEGVIDSSDKEIVAEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEGVIDSSDKEIVAEAER 18 1 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 161.35 3.49E-11 153660000 222560 146140 175780 164860 143420 133190 206450 154360 127800 FALSE TRUE 208630.3669 156960.3577 179949.5846 169090.5867 132156.3717 171639.7908 175494.7391 173632.1858 106469.3544 1.959534442 1.474230388 1.690153807 1.588162037 1.241262075 1.612105116 1.648312231 1.630818434 1 16.70007871 -2.067839642 2.362398929 0.140368186 1.59431252 0.531673194 0.178338007 8414500.153 2488587.291 39013563.81 0.042684899 0.008553825 2.067839642 1.453944334 EEGVIDSSDKEIVAEAERLDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEGVIDSSDKEIVAEAERLDVK 22 2 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 61.703 0.025548 31460000 15506 17600 16441 16214 18133 12244 17150 17140 20719 FALSE TRUE 14535.50714 18903.12231 16830.98828 16630.07869 16708.90733 15778.64404 14578.51671 19279.96673 17260.86505 0.842107687 1.095143393 0.975095294 0.963455693 0.968022592 0.914128231 0.844599426 1.116975695 1 14.07521715 3.201435686 2.136170124 0.946173413 1.000388862 0 0.093152636 0.951044534 8.865829679 0.027997359 0.037659749 1590.141186 -3.201435686 0.054215449 EEGWWVVIGDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EEGWWVVIGDAK 12 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;; 180.97 4.36E-05 78514000 372500 343278 370149 376866 404242 303310 475360 337264 400815 FALSE TRUE 349185.8899 368694.6603 378929.1091 386537.0196 372494.464 390870.6732 404084.181 379372.1528 333916.3871 1.045728522 1.10415264 1.134802375 1.157586254 1.115532146 1.170564513 1.21013582 1.136129185 1 18.34912737 5.180880033 0.805523222 1.148823761 0.905258922 0.150019076 0.055620882 6.2661077 1.900154015 0.017412381 1.607855128 151663.1364 -5.180880033 -0.243564839 EEHDKEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEHDKEER 8 1 Q9Y6I3 Q9Y6I3 EPN1 Epsin-1 0 103.7 0.0028373 27980000 115960 82939 96260 95443 88664 69312 104830 88157 101220 FALSE TRUE 108702.2706 89079.88986 98543.33266 97892.22896 81700.68709 89321.24921 89111.71469 99163.59551 84325.72809 1.28907598 1.056378544 1.168603401 1.160882108 0.968870224 1.059240771 1.056755948 1.17595896 1 16.36368525 4.743715367 24.61433169 1.085857073 1.289076086 0.465227975 0.06998072 410.4365216 1959787.799 0.016087548 0.134928194 55426.23352 -4.743715367 0.203219014 EEHETDEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEHETDEKR 9 1 O15042-2;O15042;E7ET15;E7EW00;H0Y8D9;C9JDJ7;C9J5L1 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 ; 161.76 4.17E-05 94790000 168364 141514 172372 179998 161609 171398 190696 139785 171214 FALSE TRUE 157826.3978 151991.8438 176460.7452 184617.0534 148916.881 220877.8202 162102.9051 157237.465 142637.2773 1.106487734 1.065582901 1.237129231 1.294311395 1.044024983 1.548528017 1.136469429 1.10235885 1 17.12199154 3.97926323 3.821130748 1.214607539 1.087711477 0.067510625 0.153915725 0.465600717 15.11869805 0.036193739 0.07741985 9533.738372 -3.97926323 -0.126896062 EEHGGLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EEHGGLIR 8 0 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ;;; 166.68 0.00031706 2002720000 2821710 2894210 2861490 2776940 2835010 2774290 3402780 2666240 2881960 FALSE TRUE 2645104.208 3108500.32 2929365.894 2848200.982 2612359.75 3575182.486 2892564.729 2999125.933 2400942.258 1.10169422 1.294700158 1.220090106 1.186284665 1.08805605 1.489074747 1.204762305 1.249145382 1 21.19516928 -1.489286798 6.345692973 0.999863344 1.237934786 0.292452996 0.111320844 0.000194594 1.57E-05 0.097455477 0.022957383 0.03241255 1.489286798 0.238071442 EEHGGLIRS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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 140.82 2.33E-05 48082450000 10610000 12288550 11425810 11924110 13343160 9426760 12836770 11265720 14679680 TRUE FALSE 9945939.039 13198407.03 11696835.61 12230102.85 12295242.04 12148112.58 10912015.51 12672269.94 12229546.57 0.813271284 1.079222925 0.956440661 1.000045486 1.005371864 0.993341209 0.892266565 1.036201127 1 23.54386758 4.554756969 0.002814844 1.646196372 0.30137939 0.02328127 0.074004163 984877.1101 458.0936942 107325.7681 111559.7326 35872.11381 -4.554756969 -1.344816981 EEHLCTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EEHLCTQR 8 0 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;; 157.91 0.00036932 13262000000 4320440 4733760 4271070 4209480 4466760 3663130 4700450 3897340 3190350 FALSE TRUE 4050031.373 5084252.516 4372381.797 4317502.383 4115958.688 4720616.165 3995661.159 4383931.478 2657859.975 1.523794109 1.912912104 1.645076053 1.624428083 1.54859877 1.776096638 1.503337722 1.649421535 1 21.34183367 -2.523027755 0.261317803 6.81E-12 1.741061639 0.734651581 0.122212168 20.83190906 0.647106645 12.049443 0.156792549 0.002998971 2.523027755 1.741061639 EEHS(ph)KTPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEHSKTPEER 10 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 EEHS(0.62)KT(0.38)PEER 60.196 0.060358 590950000 794740 513470 567970 630720 615110 466810 653850 450480 512290 TRUE FALSE 744998.6421 551487.8531 581442.5166 646905.343 566801.7418 601570.469 555811.2625 506723.4196 426785.4895 1.745604432 1.292189792 1.362376489 1.515762272 1.328071726 1.409538243 1.302319962 1.187302362 1 18.7031516 -3.724323643 0.10292302 1.38E-13 1.671663196 0.623795668 0.119694105 95.30896136 0.881474223 22.1238942 1.956653789 0.000188658 3.724323643 1.671663196 EEHSKT(ph)PEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEHSKTPEER 10 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 EEHS(0.101)KT(0.899)PEER 113.25 0.0024455 505830000 834930 562510 620420 661040 687040 455170 763070 483360 546040 TRUE FALSE 782673.2217 604158.8257 635136.6554 678003.4055 633082.6498 586570.1899 648654.7375 543708.56 454902.3964 1.720530003 1.328106491 1.396204241 1.490437093 1.391688975 1.289441855 1.425920687 1.195220259 1 18.79519751 -3.804975823 0.125057002 4.02E-11 1.607164072 0.665769759 0.108398253 68.25067415 0.733784191 18.34518018 0.948115733 0.000156684 3.804975823 1.607164072 EEIDHAEYYLYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEIDHAEYYLYK 12 0 Q92552;Q92552-2;G5EA06;D6RH20;E5RJ73;D6RJC7 Q92552 MRPS27 "28S ribosomal protein S27, mitochondrial" 0 114.82 0.0010165 186540000 381430 341400 308150 315390 462170 288460 336510 361780 534320 FALSE TRUE 357556.9772 366677.6112 315459.4635 323483.4414 425873.0325 371733.7192 286053.4495 406949.0294 445138.5402 0.803248753 0.823738181 0.708677041 0.72670284 0.956720199 0.835096685 0.642616677 0.914207584 1 18.76389489 1.008233156 23.3191699 1.000000016 0.78071948 0.438031563 0.083978572 57.28346878 162244.8341 0.080683902 0.020170975 10.19138378 -1.008233156 -0.219280536 EEIDSILNKVEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEIDSILNKVEER 13 1 P52788;H7C2R7 P52788 SMS Spermine synthase 0 ; 184.21 8.85E-06 97227000 281160 217580 248100 240540 265960 212241 369140 244580 311360 FALSE TRUE 263562.6975 233689.8496 253985.0492 246712.6636 245072.5744 273511.5313 313790.8839 275116.3514 259392.0045 1.016078726 0.90091385 0.979155274 0.951118999 0.944796178 1.054433161 1.20971687 1.060620014 1 17.98477449 2.091262695 4.314644409 1.117506701 0.953570997 0.487198843 0.060880393 0.131469224 4.485887325 0.022097488 0.015672405 123.3850935 -2.091262695 -0.163935704 EEIEAS(ph)EKSEQAALNAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEIEASEKSEQAALNAAK 18 1 Q9UPV0-2;Q9UPV0 Q9UPV0-2 CEP164 Centrosomal protein of 164 kDa 1 EEIEAS(0.5)EKS(0.5)EQAALNAAK 61.226 0.037117 330700000 237320 203170 214390 196790 214480 163950 240650 188440 232720 TRUE FALSE 222466.5648 218212.9182 219475.432 201839.9646 197635.606 211279.7035 204566.7666 211967.1488 193877.5286 1.147459257 1.125519393 1.132031307 1.041069411 1.01938377 1.089758597 1.055133971 1.093304368 1 17.56478607 8 0.167567545 1.011181755 1.592852909 0.572832605 0.03215252 43.41208692 0.46400588 0.085555394 6.314115716 100000000 -8 0.581671154 EEIFSQNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEIFSQNR 8 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;A1L2Z2 Q7Z406 MYH14 Myosin-14 0 95.815 0.021828 203480000 55833 75553 78761 70909 92727 64494 70171 71772 71343 FALSE TRUE 52338.51219 81147.02273 80629.24811 72728.64499 85444.59546 83112.37083 59649.50999 80732.89219 59435.39241 0.880595047 1.365298006 1.356586452 1.223658868 1.437604633 1.398364972 1.003602527 1.358330263 1 15.85903466 0.599588639 0.751069363 1.004114168 1.283451822 0.125122014 0.184002173 2.395145881 2.365574316 0.178553643 0.061398758 3.977302641 -0.599588639 0.279337654 EEIKDDNPHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEIKDDNPHLK 11 1 Q9HAV7 Q9HAV7 GRPEL1 "GrpE protein homolog 1, mitochondrial" 0 98.353 0.003355 130920000 469820 243060 311260 296190 365880 260250 328740 281090 565810 FALSE TRUE 440414.8049 261056.4153 318643.2342 303790.7368 337145.2607 335379.9502 279448.4889 316184.7053 471372.6557 0.934324042 0.553821721 0.675990069 0.644481035 0.715241448 0.711496405 0.592839838 0.670774389 1 18.84650854 -1.922976971 2.535957824 1.210895335 0.669316912 0.472792609 0.102180836 16603582.94 9232794.219 20791925.02 0.021980113 0.011940514 1.922976971 -0.541578422 EEIQETQTPTHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEIQETQTPTHSR 13 0 Q9BYG3;H7BZL0 Q9BYG3 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 0 176.83 1.60E-05 290610000 208230 220300 220670 247380 220480 207650 236140 193790 191860 FALSE TRUE 195197.256 236611.2412 225904.3966 253728.1896 203164.3902 267595.1841 200732.9992 217985.1081 159837.3265 1.22122448 1.480325318 1.413339434 1.587415125 1.271069747 1.674172047 1.255858088 1.363793507 1 17.28624483 0.671122077 1.115955063 1.001781978 1.435941742 0.457484431 0.142165797 0.863114498 1.766163219 0.116927168 0.036476632 4.689451804 -0.671122077 0.434159764 EEIQPGDIVIIDQFIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 182.57 1.72E-09 30321000 58438 58278.4 62774 59565 57127 52555 66148 52657.8 47437.6 FALSE TRUE 54780.46989 62593.39337 64263.02892 61093.53874 52640.47586 67726.77534 56229.72149 59232.24224 39519.9581 1.386146963 1.583842605 1.626090513 1.545890777 1.331997259 1.713736011 1.422818348 1.498793144 1 15.2702938 -0.478884523 0.584482558 0.929849628 1.54396946 0.664704733 0.11433695 5.61562158 1.566150003 0.925270902 0.043400259 0.331982718 0.478884523 0.614119832 EEISATQIIVCTPEKWDIITR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEISATQIIVCTPEKWDIITR 21 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 123 1.48E-05 0 51709 45676 53872 54135 58818 47931 61864 50467 52585 FALSE TRUE 48472.62599 49057.89857 55149.86928 55524.19575 54198.67154 61767.90161 52588.06752 56767.91604 43808.22379 1.10647321 1.119833089 1.258893069 1.267437731 1.237180302 1.409961333 1.200415424 1.295827841 1 15.4189141 4.039821623 2.234294243 1.255298927 1.107689654 0.192033815 0.102405843 0.402551292 3.914803037 0.02406187 0.066487242 10960.27934 -4.039821623 -0.147609273 EEIVDKYDLFVGSQATDFGEALVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EEIVDKYDLFVGSQATDFGEALVR 24 1 O43852;O43852-3;O43852-15;O43852-6;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4;O43852-8 O43852;O43852-2 CALU Calumenin 0 ;;;;;;; 214.17 3.62E-28 2497933000 3944556 3371906 3663773 3599165 3713845 2943993 4594534 3342411 3689499 FALSE TRUE 3697673.281 3621565.429 3750679.426 3691525.667 3422174.595 3793875.987 3905626.28 3759718.371 3073697.782 1.203004831 1.178243824 1.220249905 1.20100476 1.113373805 1.234303519 1.270660474 1.223190645 1 21.55154389 -1.18583204 5.642000838 0.99999471 1.207501708 0.715764185 0.040681069 2.85E-06 4.11E-07 0.041457598 0.0097714 0.065188046 1.18583204 0.207506999 EEIVYLPCIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEIVYLPCIYR 11 0 Q13228;Q13228-4;Q13228-3;H0Y532;F2Z2W8;F8WCR4;C9JVL0 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 193.1 2.56E-06 1018250000 1296700 1753130 1281170 1199940 1776760 901390 1446900 1432840 1915790 FALSE TRUE 1215541.862 1882933.569 1311559.957 1230732.492 1637220.437 1161606.66 1229950.777 1611733.228 1596032.273 0.761602308 1.179759082 0.821762805 0.771120054 1.025806599 0.727809005 0.770630268 1.009837493 1 20.60605839 3.735063149 24.03630624 0.853696711 1.000612655 0.044559852 0.147276094 325.2931297 984494.5525 0.034656067 0.061009323 5433.293289 -3.735063149 0.146915944 EEKDKDDQEWESPS(ph)PPKPTVFISGVIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEKDKDDQEWESPSPPKPTVFISGVIAR 28 3 P51397 P51397 DAP Death-associated protein 1 1 EEKDKDDQEWES(0.016)PS(0.979)PPKPT(0.005)VFISGVIAR 99.357 0.0086427 239870000 446040 124660 213950 214370 238720 126760 297750 144560 381190 TRUE FALSE 418123.1526 133889.9561 219024.995 219871.0971 219971.8942 163353.5542 253105.1517 162608.6342 317566.9264 1.316645777 0.421611777 0.689697122 0.692361448 0.692678852 0.514390954 0.797013576 0.512045244 1 18.27670114 -1.379727112 5.655857148 1.000100061 0.677567267 0.116765237 0.245587818 0.000269747 2.96E-05 0.207003963 0.048776249 0.04171314 1.379727112 -0.322532794 EEKESEDKPEIEDVGS(ph)DEEEEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEKESEDKPEIEDVGSDEEEEKK 23 3 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 EEKESEDKPEIEDVGS(1)DEEEEKK 213.84 3.28E-25 257130000 1066300 125450 349820 298770 316280 254910 528290 204250 263270 TRUE FALSE 999562.1864 134738.4485 358117.8956 306436.944 291440.6446 328498.3789 449077.8189 229751.0621 219328.5362 4.557374082 0.614322472 1.632792074 1.397159482 1.328785801 1.497745731 2.047512041 1.047520154 1 17.742734 4.74710617 24.97990471 1.379878773 4.557375695 0.871625419 0.389778928 390.2466735 1140722.927 0.095245746 1.119175617 55860.67379 -4.74710617 3.177496923 EEKKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEKKER 6 2 Q8NI08-4;Q8NI08-3;Q8NI08-2;Q8NI08;Q5TF98;Q5TF97;Q5TF96;Q8NI08-6 Q8NI08-4 NCOA7 Nuclear receptor coactivator 7 0 61.837 0.068243 70437000 97363 58886 93626 84923 87668 62947 101110 73700 89959 FALSE TRUE 91269.22363 63245.98071 95846.85293 87102.26795 80782.90892 81118.77704 85949.49416 82901.60723 74944.26174 1.217828043 0.843906915 1.278908494 1.162227313 1.077906527 1.0823881 1.146845564 1.106176848 1 16.1935304 3.971707806 24.98472425 1.129803739 1.011314935 0.091574959 0.11382045 359.3590218 1658563.027 0.025946582 0.048568317 9369.314252 -3.971707806 -0.118488804 EELAQFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EELAQFHR 8 0 E7EMD0;P16435;H0Y4R2 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 ;;;; 188.98 0.00019413 1546470000 1920020 1990430 1615540 1560630 2334850 1731670 2092210 2234360 1923050 FALSE TRUE 1799849.376 2137803.508 1653861.372 1600678.408 2151480.299 2231575.018 1778502.534 2513324.764 1602080.532 1.123445008 1.33439204 1.032320997 0.999124811 1.342928933 1.392923123 1.110120558 1.568788032 1 20.61151524 2.714459464 24.87830475 1.283831557 1.142665955 0.16724635 0.175511303 1451.313797 1498110.203 0.05313622 0.050124156 518.1547265 -2.714459464 -0.141165603 EELDFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EELDFQK 7 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 154.35 0.0039189 284190000 635420 438580 484060 469030 465330 394940 640560 474170 503800 FALSE TRUE 595650.1965 471052.9195 495542.1318 481066.1039 428784.8589 508952.7667 544513.9747 533371.1683 419712.5253 1.419186135 1.122322759 1.180670344 1.146180004 1.021615589 1.212622297 1.297349833 1.27080117 1 18.67904199 2.016981946 24.97866526 1.230563484 1.16497175 0 0.127729515 728.3986023 1071394.162 0.043900974 0.032415366 103.9876935 -2.016981946 -0.065591734 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR 36 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;; 222.66 2.38E-39 260982000 498734 316555 401652 371190 342880 350612 491649 373091 374777 FALSE TRUE 467519.1292 339993.0616 411179.3751 380715.3638 315951.5879 451827.9927 417930.7967 419672.2326 312224.2975 1.497382276 1.088938511 1.316935864 1.219364946 1.011937861 1.447126301 1.338559491 1.344137006 1 18.25222329 2.199729245 24.99998761 1.318530483 1.220029206 0.005287247 0.171871566 431.7150494 277939.7483 0.057740196 0.042644654 158.3905421 -2.199729245 -0.098501277 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 20 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR 37 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;;;;;;;; 399.86 1.79E-180 10210051000 1233180.2 1035040 1165565.6 1102266.9 1235069 970050.3 1475471.3 1070885 1726460.6 FALSE TRUE 1155997.653 1111675.439 1193213.366 1130552.935 1138071.663 1250088.074 1254238.076 1204587.35 1438303.172 0.803723217 0.77290759 0.829597952 0.786032428 0.791259927 0.869140872 0.872026218 0.83750587 1 20.45593638 -0.26116015 0.258712269 1.078640474 0.774500047 0.855459581 0.024928526 2.911693023 0.27026277 0.243034921 0.042348197 0.54807482 0.26116015 -0.304140427 EELEALFLPYDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EELEALFLPYDLK 13 0 Q9H0A0;Q9H0A0-2;A0A087WV29 Q9H0A0 NAT10 N-acetyltransferase 10 0 78.655 0.027327 0 22180 18985 20137 17685 19806 12194 21676 15864 17672 FALSE TRUE 20791.79339 20390.66915 20614.65915 18138.82704 18250.51665 15714.20985 18425.88503 17844.65532 14722.42903 1.41225292 1.385007128 1.400221329 1.232053963 1.239640321 1.067365298 1.251551968 1.212072769 1 13.8457281 5.05706493 0.123890732 0.884472836 2.000776149 0.753837207 0.067090983 19.31447506 0.355384336 0.57747284 3.677447179 114042.0275 -5.05706493 1.116303313 EELEEVIKDI ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EELEEVIKDI 10 1 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ;;;;; 175.73 2.21E-05 470277000 2266860 1762770 1880990 1689460 2039350 1346360 2374480 1713830 2232380 FALSE TRUE 2124981.279 1893287.325 1925607.971 1732814.404 1879187.677 1735032.276 2018448.768 1927805.448 1859781.356 1.142597366 1.018016079 1.035394814 0.931730172 1.010434733 0.932922717 1.085315089 1.036576392 1 20.82670159 5.419298989 1.440486442 1.007614352 1.69022003 0.456972235 0.046384433 7.292721255 3.305130419 0.012212475 11.60119923 262602.5802 -5.419298989 0.682605678 EELEFEVPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EELEFEVPFR 10 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;;;;; 203.35 4.81E-07 772825000 1067317 1054635 1154256 1081916 981553 975335 1405013 1018043 900250 FALSE TRUE 1000515.534 1132721.273 1181635.497 1109679.796 904465.7868 1256898.381 1194344.344 1145147.91 749992.4592 1.334034125 1.510310216 1.575529838 1.479587938 1.205966508 1.675881358 1.592475137 1.526879231 1 19.51651656 -1.132020626 4.868629907 0.999970046 1.503891043 0.564589081 0.133886615 4.21E-05 7.50E-06 0.125348514 0.029543175 0.073786919 1.132020626 0.503920997 EELEQASQAHGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EELEQASQAHGAR 13 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;; 219.97 2.16E-11 1058040000 1000010 1153710 1207330 1121140 1158300 998830 1362850 1029090 1150060 FALSE TRUE 937421.1592 1239131.889 1235968.438 1149910.35 1067331.79 1287176.006 1158503.295 1157574.152 958107.5563 0.978409108 1.293311884 1.290010114 1.200189209 1.113999971 1.34345669 1.209157873 1.208188104 1 19.8698281 0.60458667 2.68186854 1.000009818 1.223901142 0.263091311 0.103597027 5.723201307 37.35844417 0.091764624 0.024279905 4.023339395 -0.60458667 0.223891323 EELFQGDAFHQSDTHIFIIMGASGDLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EELFQGDAFHQSDTHIFIIMGASGDLAK 28 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;; 252.44 1.10E-53 588189000 400952 827446 800001 853685 905517 682334 1044639 857624 931123 FALSE TRUE 375857.13 888710.9628 818977.4015 875592.0024 834401.3475 879312.749 888005.0799 964700.2443 775712.556 0.484531451 1.145670462 1.055774327 1.128758321 1.075657911 1.133554874 1.144760482 1.243631081 1 19.56516263 4.740086794 24.96641048 1.11790401 0.484531239 0.904983011 0.064298353 34.17803631 559059.0802 0.013999341 0.088972428 54965.0711 -4.740086794 -0.633372771 EELGLIEQAYDNPHEALSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EELGLIEQAYDNPHEALSR 19 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;; 306.27 1.35E-50 699730000 822880 929900 937220 899670 998230 760670 1059790 855140 930150 FALSE TRUE 771377.4097 998750.7636 959451.301 922757.0553 919833.0425 980263.0806 900884.3281 961906.1114 774901.956 0.995451623 1.288873716 1.238158316 1.190804912 1.187031515 1.265015623 1.162578467 1.241326214 1 19.56365426 -1.572109327 2.626936499 0.984413621 1.207517316 0.357168466 0.081443344 8920551.59 8297288.387 968909.9655 0.017670863 0.02678494 1.572109327 0.223103695 EELLAEFGSGTLDLPALTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EELLAEFGSGTLDLPALTR 19 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 227.63 2.85E-19 60199000 101820 121340 111550 106210 111150 101860 138680 85870 110010 FALSE TRUE 95447.26795 130324.1399 114196.0187 108935.5284 102420.7274 131265.3284 117886.2214 96591.05852 91648.62031 1.041447952 1.421997837 1.246020052 1.188621586 1.117537035 1.432267371 1.286284737 1.053928125 1 16.48382554 1.182590376 5.215275424 1.011864497 1.268572344 0.356556596 0.121411854 0.19479206 10.4303562 0.106772969 0.02782513 15.22615954 -1.182590376 0.256707847 EELMS(ph)SDLEETAGSTSIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EELMSSDLEETAGSTSIPK 19 0 O00567 O00567 NOP56 Nucleolar protein 56 1 EELMS(0.5)S(0.5)DLEETAGSTSIPK 138.57 4.17E-07 0 37134 34291 28315 31034 29126 22542 35722 27426 29515 TRUE FALSE 34809.84923 36829.94132 28986.64517 31830.38498 26838.56145 29049.50946 30365.81773 30850.19647 24588.75583 1.415681601 1.497836718 1.178857742 1.294509783 1.091497335 1.18141437 1.234947304 1.254646501 1 14.58571112 8 0.229057065 1.098113306 3.304279556 0.631590663 0.087576959 31.93985865 0.417916596 0.123097572 26.39925641 100000000 -8 2.20616625 EELMSS(ph)DLEETAGSTSIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 EELMSSDLEETAGSTSIPK 19 0 O00567 O00567 NOP56 Nucleolar protein 56 1 EELMS(0.288)S(0.712)DLEETAGSTSIPK;EELMS(0.183)S(0.817)DLEETAGSTSIPK;EELMS(0.427)S(0.573)DLEETAGSTSIPK;EELMS(0.027)S(0.973)DLEETAGSTSIPK;EELMS(0.014)S(0.986)DLEETAGSTSIPK;EELMSS(1)DLEETAGSTSIPK;EELMS(0.027)S(0.973)DLEETAGSTSIPK;EELMS(0.038)S(0.962)DLEETAGSTSIPK;EELMS(0.03)S(0.97)DLEETAGSTSIPK;EELMS(0.003)S(0.997)DLEETAGSTSIPK;EELMS(0.026)S(0.974)DLEETAGSTSIPK;EELMS(0.001)S(0.999)DLEETAGSTSIPK;EELMS(0.008)S(0.992)DLEETAGSTSIPK 455.65 6.68E-192 5588075000 6887790 4706943 5674700 5204340 4908820 4510482 7546720 4782000 4712930 TRUE FALSE 6456695.519 5055449.957 5809306.564 5337892.175 4523301.078 5812584.932 6415159.396 5379043.226 3926311.536 1.644468468 1.287582483 1.479583703 1.359518247 1.15204844 1.480418677 1.633889552 1.369999089 1 21.90474322 -1.911794966 2.242692127 0.7297849 1.426137325 0.448196161 0.148527665 4878912.478 2320749.783 6935443.78 0.039046571 0.012251945 1.911794966 0.696352425 EELMSS(ph)DLEETAGSTSIPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EELMSSDLEETAGSTSIPKR 20 1 O00567 O00567 NOP56 Nucleolar protein 56 1 EELMS(0.132)S(0.868)DLEETAGSTSIPKR;EELMS(0.105)S(0.895)DLEETAGSTSIPKR;EELMS(0.006)S(0.994)DLEETAGSTSIPKR;EELMS(0.024)S(0.976)DLEETAGSTSIPKR 225.34 3.16E-25 955950000 776700 808560 718640 742420 874090 569560 1075330 650830 1309760 TRUE FALSE 728087.7334 868426.6237 735686.4802 761471.7541 805442.4973 733982.726 914094.2494 732087.5582 1091152.595 0.667264814 0.795880089 0.674228778 0.697860004 0.738157524 0.672667352 0.837732737 0.670930502 1 20.05742144 -4.999991457 0.323887096 3.653266863 0.71651425 0.690906633 0.058596787 186.176503 1.634610459 339.0408975 0.047133557 1.00E-05 4.999991457 -2.936752613 EELQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EELQDR 6 0 P54577 P54577;REV__M0R2F5 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed" 0 ;; 131.3 0.035801 757490000 885520 891240 929460 916790 899520 796660 1017260 839380 787160 FALSE TRUE 830096.8839 957228.3369 951507.2301 940316.3835 828875.3277 1026642.809 864731.3068 944178.4407 655777.9108 1.265820136 1.459683715 1.450959562 1.433894567 1.263957377 1.565534295 1.318634392 1.439783843 1 19.32284778 -2.622948555 0.623185893 5.52E-12 1.409109786 0.637400933 0.094465111 233.5057267 12.69894081 316.9943837 0.032382444 0.002382602 2.622948555 1.409109786 EELRQEWEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EELRQEWEAK 10 1 Q14320;B0S8I6 Q14320 FAM50A Protein FAM50A 0 131.42 0.0037815 0 234630 217480 203520 218690 246140 167720 234380 212840 309310 FALSE TRUE 219944.9271 233582.4455 208347.5905 224301.9556 226809.1573 216138.0413 199236.8949 239413.5425 257684.1628 0.853544606 0.906467992 0.808538593 0.870453012 0.880182759 0.838771149 0.773182538 0.929096845 1 17.97524435 1.007779702 8.126569012 0.999985576 0.847210164 0.661442499 0.036862066 0.067917716 35.31519993 0.037279964 0.009335224 10.18074835 -1.007779702 -0.152775411 EELSHS(ph)PEPCTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EELSHSPEPCTK 12 0 P41229-4;P41229-3;P41229-2;P41229-5;P41229 P41229-4 KDM5C Lysine-specific demethylase 5C 1 EELS(0.004)HS(0.996)PEPCTK;EELS(0.001)HS(0.999)PEPCTK;EELSHS(1)PEPCTK;EELS(0.003)HS(0.997)PEPCTK 127.32 0.00017506 1983170000 3374280 2726540 2907580 2935700 3160870 2431330 4085660 2884890 2734260 TRUE FALSE 3163089.838 2928415.859 2976549.171 3011035.032 2912628.021 3133215.502 3473053.212 3245074.867 2277894.342 1.388602526 1.285580198 1.306710814 1.321850174 1.278649306 1.375487635 1.524677044 1.424594112 1 21.1192694 2.11474187 6.599012126 1.39290997 1.311361411 0 0.14166792 0.583459667 31.52174399 0.04771396 0.035112829 130.2392449 -2.11474187 -0.081548559 EELSNVLAAMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EELSNVLAAMR 11 0 Q9Y3U8 Q9Y3U8 RPL36 60S ribosomal protein L36 0 123.51 0.00085702 18803000 24967 35519 28950 29905 36691 23578 25672 29823 39520 FALSE TRUE 23404.36004 38148.86372 29636.70767 30672.41293 33809.43686 30384.58584 21822.72193 33546.4672 32923.85669 0.710863258 1.158699726 0.900159053 0.931616646 1.026897826 0.922874441 0.662823986 1.018910619 1 15.00684572 1.989574148 24.63466269 0.840547954 0.968444794 0 0.149370978 792.0755886 1871550.911 0.05391329 0.037342171 97.6279451 -1.989574148 0.12789684 EELTLEGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EELTLEGIR 9 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3KTB5;J3KTN0 P60842;J3KTN0 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;; 175.12 0.00012599 147220000 282466 310152 317532 310361 340508 264535 345446 295202 301993 FALSE TRUE 264786.9573 333115.9768 325064.009 318325.3887 313765.8752 340901.9601 293649.5793 332058.6195 251588.4174 1.052460841 1.324051323 1.292046798 1.265262495 1.247139588 1.354998627 1.167182426 1.319848596 1 17.94070598 -1.137772309 3.612947162 0.999802663 1.260558959 0.447182325 0.087991845 9000704.704 18950029 22414.79745 0.018955879 0.072816146 1.137772309 0.260756297 EEMQSNVEVVHTYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 EEMQSNVEVVHTYR 14 0 Q92597;Q92597-3;Q92597-2 Q92597 NDRG1 Protein NDRG1 0 ;;;;;;;; 295.37 1.32E-43 11513830000 7078490 8079090 7120960 8010770 8010090 5253810 8157250 6668510 3361910 FALSE TRUE 6635459.946 8677274.23 7289872.534 8216339.92 7381009.843 6770499.659 6934146.091 7501088.153 2800785.502 2.369142493 3.098157364 2.602795726 2.933584137 2.635335636 2.417357435 2.475786198 2.678208719 1 21.41740007 -1.321476926 0.355966466 2.94E-19 2.794965743 0.843198939 0.223675701 6.882180759 0.54892608 6.710576519 0.161617973 0.047700516 1.321476926 2.794965743 EENEGVYNGSWGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 202.29 2.47E-07 142240000 190799 202944 227110 221881 229800 171483 237740 208917 254140 FALSE TRUE 178857.2312 217970.1849 232497.1564 227574.8421 211752.435 220987.3583 202093.0941 235000.7473 211722.3922 0.84477239 1.029509362 1.09812266 1.074873752 1.000141897 1.043759973 0.954519227 1.109947535 1 17.69181433 4.737283206 5.210844761 1.039151782 0.836487054 0.626630769 0.047146796 0.106323341 9.926523044 0.011351138 0.07739436 54611.38688 -4.737283206 -0.202664728 EENKGGEDKLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EENKGGEDKLK 11 2 P62258;P62258-2;B4DJF2;I3L3T1;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 ; 100.55 0.0022176 1578000000 6315700 2380900 3513900 3329400 3365200 2111360 4785700 2799200 4233600 FALSE TRUE 5920411.611 2557184.313 3597251.367 3414838.041 3100910.767 2720875.357 4068128.713 3148686.282 3526984.81 1.678604227 0.725034116 1.019922557 0.968203217 0.879195952 0.771445159 1.15342961 0.892741662 1 21.75000393 4.748364807 24.92961117 0.930232167 1.678604647 0.78779017 0.122701379 598.0729795 1520718.491 0.028684136 0.383059142 56022.79952 -4.748364807 0.74837248 EENS(ph)HT(ph)EQPPLMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EENSHTEQPPLMK 13 0 Q03164-2;Q03164;Q03164-3 Q03164-2 KMT2A Histone-lysine N-methyltransferase 2A;MLL cleavage product N320;MLL cleavage product C180 2 EENS(1)HT(1)EQPPLMK 80.31 0.069797 113070000 43347 176260 138860 140470 172510 220150 117330 146240 114360 TRUE FALSE 40633.98865 189310.4738 142153.8248 144074.698 158961.7605 283703.7312 99737.45574 164498.3859 95272.57721 0.426502461 1.987040546 1.492074938 1.512236808 1.668494389 2.977811029 1.046864257 1.726607915 1 16.5397734 2.707722645 5.408398294 1.743271186 1.481986253 0.039250778 0.661259209 0.795060809 68.15299431 0.201341653 0.194222394 510.1790789 -2.707722645 -0.261284933 EENSGLLQELEELRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EENSGLLQELEELRK 15 1 A0A3B3ISJ8;J3KP58;P30622-2;P30622-1;P30622;F5H0N7;A0A3B3ITA2 A0A3B3ISJ8;J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 0 ; 152.34 4.57E-06 74935000 129311 92567 113918 105091 119895 86341 137543 106091 170437 FALSE TRUE 121217.6553 99420.757 116620.1888 107787.813 110478.9303 111266.2451 116919.704 119336.6949 141989.9636 0.853705799 0.700195665 0.821326985 0.759122759 0.778075629 0.783620491 0.823436397 0.840458662 1 17.11542943 0.563649342 0.724547285 1.002889142 0.773016632 0.735698842 0.040212507 0.661862375 0.59679673 0.038480524 0.013094293 3.661418252 -0.563649342 -0.22987251 EENWSFLDWDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EENWSFLDWDSR 12 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 0 ; 164.13 0.0001352 26855000 82616 84002 85541 85716 98699 77221 100055 81910 110761 FALSE TRUE 77445.21203 90221.59548 87570.07292 87915.61768 90947.57867 99513.44912 85052.68162 92136.64381 92274.27356 0.839293652 0.977754601 0.94901937 0.952764127 0.985622267 1.078452805 0.921737754 0.998508471 1 16.49364085 5.507100834 1.52288858 0.980173969 6.19E-14 0.526004752 0.042222301 8.634782735 3.218976635 0.010639517 22.40858768 321440.6767 -5.507100834 -0.980173969 EEPDLDGALLSGPDGDRNVNANLLAEAGT(ph)SQDGGDAGTSHDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEPDLDGALLSGPDGDRNVNANLLAEAGTSQDGGDAGTSHDFK 43 1 Q96DT7-3;Q96DT7-2;Q96DT7;Q96DT7-4 Q96DT7-3 ZBTB10 Zinc finger and BTB domain-containing protein 10 1 EEPDLDGALLSGPDGDRNVNANLLAEAGT(0.5)S(0.5)QDGGDAGT(0.001)SHDFK 77.439 0.0013332 32251000 13782 14267 12103 11062 18579 7926.6 20158 14080 23627 TRUE FALSE 12919.40922 15323.34352 12390.08888 11345.86965 17119.88028 10214.88074 17135.49504 15837.91899 19683.50106 0.65635728 0.778486687 0.629465705 0.576415223 0.869757886 0.518956496 0.870551178 0.804629163 1 14.26469923 1.128546364 1.162907714 0.991095863 0.683599303 0.470890016 0.108908165 0.372522028 1.044091821 0.09044247 0.028983434 13.44455289 -1.128546364 -0.307496561 EEPDSENIPQELLSNLGHPES(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EEPDSENIPQELLSNLGHPESPPR 24 0 D6RF40;D6RAG5;D6R9R7;A0A0A0MTL5;Q13309-2;Q13309 D6RF40 SKP2 S-phase kinase-associated protein 2 1 EEPDSENIPQELLSNLGHPES(1)PPR;EEPDSENIPQELLSNLGHPES(1)PPR;EEPDSENIPQELLSNLGHPES(1)PPR;EEPDSENIPQELLSNLGHPES(1)PPR 150.23 8.44E-08 643949000 366830 335232 398520 339202 352032 411715 541222 394924 362721 TRUE FALSE 343870.7651 360052.9261 407973.0826 347906.4976 324384.8267 530570.4369 460070.7856 444231.1307 302180.5218 1.137964694 1.191515998 1.35009722 1.151320064 1.073480265 1.75580621 1.522503114 1.470085259 1 18.20505114 2.255306498 24.99998362 1.494953274 1.20405884 0.264979479 0.200023832 254.7880532 380373.2468 0.063113765 0.052671691 180.0140893 -2.255306498 -0.290894434 EEPFFPPPEEFVFIHAVPVEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 EEPFFPPPEEFVFIHAVPVEER 22 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;;;;;; 195.36 3.53E-19 1116632000 814256 824159 883559 818731 836742 740406 995562 819428 838776 FALSE TRUE 763293.1704 885180.5899 904517.4367 839741.0236 771027.6586 954149.1927 846286.7204 921735.3896 698778.8669 1.092324348 1.266753521 1.294425861 1.201726416 1.103392926 1.365452274 1.211093753 1.319065921 1 19.41447645 -1.457294583 3.294782176 0.996101154 1.239646537 0.408626205 0.08717298 4320577.473 3825411.769 109292.5339 0.018568835 0.034890357 1.457294583 0.243545384 EEPGPRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EEPGPRPR 8 1 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ;; 94.114 0.009657 264466000 650450 799810 735770 763620 818570 596870 771960 681340 920360 FALSE TRUE 609739.4956 859028.7646 753222.8119 783215.782 754282.8142 769176.6796 656211.7645 766406.7988 766745.9702 0.795230127 1.120356413 0.982362922 1.021480141 0.983745391 1.003170163 0.855839861 0.999557648 1 19.54838915 1.878316938 19.14781077 0.93419215 1.00126931 0 0.089724393 6.944963209 1065.930463 0.033915207 0.021871489 75.56434777 -1.878316938 0.067077159 EEPLDPEEAEGPLSLVTT(ph)ANHSPDFDHDRDYEDEPVNEDME ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEPLDPEEAEGPLSLVTTANHSPDFDHDRDYEDEPVNEDME 41 1 A0A3B3IUB6;Q9H334-8;C9J0F0;Q9H334-3;Q9H334-7;Q9H334-6;Q9H334;Q9H334-4;A0A3B3IRS5;A0A3B3IST0;H0Y882;A0A0B4J2F3;A0A3B3IRW5;A0A3B3IT66 A0A3B3IUB6 FOXP1 Forkhead box protein P1 1 EEPLDPEEAEGPLSLVT(0.079)T(0.461)ANHS(0.461)PDFDHDRDYEDEPVNEDME 170.8 8.44E-20 30516000 24159 29876 27308 27488 33533 21749 32909 26417 28411 TRUE FALSE 22646.93132 32088.05013 27955.75866 28193.38862 30899.45345 28027.58323 27974.60096 29715.2206 23669.02056 0.956817426 1.355698266 1.181111765 1.191151469 1.305480866 1.184146305 1.18190784 1.255447834 1 14.53071239 -1.218037367 3.420596218 0.999557453 1.213148245 0.259839441 0.105234044 10370602.55 14952163.48 48692.01002 0.022209619 0.060528879 1.218037367 0.213590792 EEPLS(ph)EEEPCTSTAIAS(ph)PEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EEPLSEEEPCTSTAIASPEKK 21 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 2 EEPLS(1)EEEPCTSTAIAS(1)PEKK;EEPLS(1)EEEPCTSTAIAS(1)PEKK;EEPLS(1)EEEPCTSTAIAS(1)PEKK 182.09 1.68E-16 1189530000 3243980 1073410 1742940 1482110 1457220 1286720 2782170 1381280 1704940 TRUE FALSE 3040945.082 1152886.393 1784283.36 1520143.452 1342775.819 1658175.176 2365009.437 1553735.849 1420374.5 2.140945985 0.811677761 1.256206275 1.070241301 0.94536745 1.167421111 1.665060473 1.093891681 1 20.43783993 EEPLS(ph)EEEPCTSTAIASPEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EEPLSEEEPCTSTAIASPEKK 21 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 1 EEPLS(1)EEEPCTSTAIASPEKK;EEPLS(0.996)EEEPCT(0.001)S(0.001)T(0.001)AIASPEKK;EEPLS(1)EEEPCTSTAIASPEKK 241.48 3.22E-30 1012480000 1519150 894638 1013225 1048213 997071 764343 1625114 891656 1256780 TRUE FALSE 1424069.113 960877.9284 1037259.175 1075111.92 918765.0657 984996.416 1381443.243 1002981.214 1047015.299 1.360122545 0.917730552 0.990681967 1.026834967 0.87750873 0.94076602 1.319410752 0.957943227 1 19.99785109 EEPPEPVPS(ph)PIIPILPSTAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEPPEPVPSPIIPILPSTAGK 21 0 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37;H0Y765;H7C2V8 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 EEPPEPVPS(1)PIIPILPSTAGK;EEPPEPVPS(1)PIIPILPSTAGK 86.479 0.0017686 47921000 254377 205846 238981 221333 226023 184609 309234 203373 229253 TRUE FALSE 238455.9976 221087.052 244649.7422 227012.7795 208272.0653 237902.6214 262867.2325 228764.5667 190989.1933 1.248531362 1.157589329 1.280961179 1.188615835 1.090491361 1.245633941 1.376346106 1.197788015 1 17.54313148 2.033488069 24.99388983 1.252643473 1.197456668 0 0.107925363 566.9662515 423154.005 0.037517333 0.027708203 108.0159947 -2.033488069 -0.055186805 EEPSQNDIS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEPSQNDISPK 11 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 EEPSQNDIS(1)PK;EEPSQNDIS(1)PK 234.47 1.77E-15 1348850000 2912600 1398890 1947400 1637370 1607110 1520700 2743600 1375810 1900140 TRUE FALSE 2730305.565 1502465.271 1993593.248 1679387.686 1480894.063 1959701.403 2332222.65 1547582.907 1582994.359 1.72477277 0.949128633 1.259381145 1.060893033 0.935501795 1.237971186 1.473298144 0.977630084 1 20.59422468 4.75082318 24.71603174 1.143953229 1.724773191 0.549263444 0.17234482 1437.375194 2897065.643 0.042499777 0.723918134 56340.82218 -4.75082318 0.580819961 EEPVS(ph)S(ph)GPEEAVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EEPVSSGPEEAVGK 14 0 O00567 O00567 NOP56 Nucleolar protein 56 2 EEPVS(1)S(1)GPEEAVGK;EEPVS(1)S(1)GPEEAVGK;EEPVS(1)S(1)GPEEAVGK 186.75 1.50E-06 1126650000 3271370 2242200 2594410 2477660 2394820 1897910 3282500 1940280 2108570 TRUE FALSE 3066620.791 2408214.821 2655950.63 2541240.95 2206740.497 2445805.807 2790319.598 2182528.229 1756636.045 1.745734866 1.370924175 1.511952711 1.446651944 1.25623091 1.392323591 1.588444918 1.242447595 1 20.74438388 -3.45540412 0.198163129 1.02E-13 1.536257975 0.566189093 0.134610277 55.93725483 0.958862553 23.29968426 0.336626276 0.000350426 3.45540412 1.536257975 EEPVS(ph)SGPEEAVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEPVSSGPEEAVGK 14 0 O00567 O00567 NOP56 Nucleolar protein 56 1 EEPVS(0.5)S(0.5)GPEEAVGK 284.91 1.45E-33 1397800000 1309300 950550 1112300 996580 1014800 783360 1406700 846610 923080 TRUE FALSE 1227353.25 1020929.711 1138684.281 1022153.93 935101.7015 1009503.315 1195778.394 952311.1221 769011.9847 1.596013163 1.327586216 1.480710709 1.329178154 1.21597806 1.312727676 1.554954172 1.238356672 1 19.55264656 -3.423477273 0.269263968 6.26E-17 1.423658226 0.517091171 0.121223272 69.42635304 1.463055612 38.89648749 0.150729136 0.000377157 3.423477273 1.423658226 EEPVSS(ph)GPEEAVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EEPVSSGPEEAVGK 14 0 O00567 O00567 NOP56 Nucleolar protein 56 1 EEPVS(0.206)S(0.794)GPEEAVGK;EEPVS(0.011)S(0.989)GPEEAVGK;EEPVS(0.014)S(0.986)GPEEAVGK;EEPVS(0.025)S(0.975)GPEEAVGK;EEPVS(0.015)S(0.985)GPEEAVGK 303.29 4.99E-44 1972420000 4870210 3574560 4013110 3754220 3789730 2846880 5157290 3355190 3720010 TRUE FALSE 4565392.25 3839224.142 4108302.864 3850559.641 3492099.893 3668728.041 4384002.242 3774092.857 3099116.299 1.473127114 1.238812543 1.325636881 1.242470198 1.126805049 1.183798118 1.414597524 1.21779646 1 21.56342546 -3.960177362 0.274138964 7.31E-30 1.300443261 0.438824745 0.101675463 118.4108165 1.942283339 66.95073224 0.121319612 0.000109603 3.960177362 1.300443261 EEQMKEGEET(ph)EGS(ph)EEDDKENDKTEEMPNDSVLENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEQMKEGEETEGSEEDDKENDKTEEMPNDSVLENK 35 3 P49321;P49321-3;P49321-4 P49321 NASP Nuclear autoantigenic sperm protein 2 EEQMKEGEET(1)EGS(1)EEDDKENDKTEEMPNDSVLENK 140.22 5.14E-11 100930000 397000 62997 130890 123680 124770 91270 208850 86125 110490 TRUE FALSE 372152.4787 67661.36343 133994.7726 126853.8382 114971.0675 117618.1674 177534.8814 96877.89583 92048.50521 4.043004043 0.735062055 1.455697432 1.378119481 1.249026991 1.277784654 1.928710097 1.052465715 1 16.49010667 4.745932759 24.99058361 1.30686512 4.043005339 0.883699355 0.316921817 300.7670281 1019535.687 0.07771402 0.812507798 55709.94877 -4.745932759 2.736140219 EEQNGEDEDGGWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEQNGEDEDGGWR 13 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;C9IYH5;C9JH78;Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 0 269.28 1.25E-24 155710000 192460 159350 171450 162160 162080 150790 178160 157260 159730 FALSE TRUE 180414.2722 171148.4398 175516.875 166321.3001 149350.8906 194320.6251 151446.562 176894.2572 133070.0311 1.355784399 1.286153151 1.318981242 1.249877968 1.122348055 1.460288417 1.13809669 1.329332049 1 17.02182617 -4.278807317 0.2250833 3.56E-10 1.314515879 0.445409436 0.09900697 95.28406826 1.282561631 43.44816975 0.160557363 5.26E-05 4.278807317 1.314515878 EEQRS(ph)PFNDRFPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EEQRSPFNDRFPLK 14 2 E9PQ01;E9PKN0;O94913 E9PQ01 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 1 EEQRS(1)PFNDRFPLK;EEQRS(1)PFNDRFPLK;EEQRS(1)PFNDRFPLK 187.39 4.97E-07 325318000 711130 584182 685990 632280 749760 611950 915040 701870 961970 TRUE FALSE 666621.6427 627435.4431 702262.0067 648505.3752 690876.874 788610.0308 777838.2468 789500.0145 801410.9924 0.831809956 0.782913448 0.876281974 0.809204492 0.862075615 0.98402697 0.970585947 0.985137491 1 19.61218277 2.314601689 3.619331209 0.982509066 0.827095367 0.907804579 0.024353001 0.064443762 1.674723377 0.008992463 0.007157969 206.348677 -2.314601689 -0.155413699 EEQT(ph)DTS(ph)DGESVTHHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEQTDTSDGESVTHHIR 17 0 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 2 EEQT(0.963)DT(0.048)S(0.989)DGESVTHHIR;EEQT(0.997)DT(0.017)S(0.986)DGESVTHHIR 149.62 5.64E-07 1046660000 770460 886930 908000 987500 957760 842030 1187540 883440 1031220 TRUE FALSE 722238.2839 952599.22 929538.1888 1012840.922 882541.393 1085110.392 1009479.402 993739.4287 859102.7201 0.84068909 1.108830409 1.081987249 1.17895206 1.027282736 1.263074096 1.175039233 1.156717824 1 19.71247111 5.338633856 1.343831154 1.13920017 3.49E-13 0.554784217 0.078352477 4.031583133 2.056779469 0.019744752 9.308726746 218089.0474 -5.338633856 -1.13920017 EEQTDTS(ph)DGESVTHHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 EEQTDTSDGESVTHHIR 17 0 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 1 EEQTDT(0.203)S(0.796)DGESVTHHIR;EEQTDT(0.004)S(0.981)DGES(0.006)VT(0.009)HHIR;EEQTDT(0.004)S(0.986)DGES(0.003)VT(0.007)HHIR;EEQTDT(0.013)S(0.956)DGES(0.013)VT(0.018)HHIR;EEQTDT(0.009)S(0.986)DGES(0.004)VT(0.001)HHIR;EEQTDT(0.001)S(0.993)DGES(0.004)VT(0.001)HHIR;EEQTDT(0.002)S(0.996)DGES(0.001)VTHHIR 197.92 9.45E-12 5641340000 1615560 1688619 1741000 1833650 1743209 1552520 1882580 1563422 1840450 TRUE FALSE 1514444.983 1813646.108 1782297.342 1880704.563 1606304.397 2000707.321 1600304.606 1758618.678 1533267.005 0.987724237 1.182863847 1.162418115 1.226599514 1.047635142 1.304865568 1.043722066 1.14697484 1 20.54817752 0.634645675 1.033611182 1.001122241 1.151023733 0.167946857 0.093672907 1.850326253 3.203288264 0.078441356 0.024944321 4.3116716 -0.634645675 0.149901492 EEQTPQNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EEQTPQNK 8 0 F5GZQ4;P00338;P00338-3;P00338-4;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2;F5H5J4;F5H6W8;F5GXC7;F5H8H6;F5GXU1;F5GWW2 F5GZQ4;P00338 LDHA L-lactate dehydrogenase A chain 0 ;;; 136.8 0.0018044 1655780000 1392310 1180730 1273340 1260240 1179800 859830 1392440 1092540 1033170 FALSE TRUE 1305167.802 1268152.478 1303544.226 1292579.892 1087143.267 1108048.963 1183656.549 1228946.024 860727.2525 1.516354686 1.473349977 1.514468401 1.501729948 1.263051988 1.287340397 1.375181912 1.427799597 1 19.71519662 -3.742865586 0.132158915 4.19E-13 1.618118293 0.769664084 0.076516824 46.39564926 0.530984241 13.25705065 0.606962145 0.000180773 3.742865586 1.618118293 EEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK 40 0 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ;; 488.36 8.16E-297 3241380000 996781 989172 1065129 1024652 1061890 968482 1321149 962056 864842 FALSE TRUE 934394.2565 1062411.324 1090394.363 1050946.305 978493.4429 1248067.031 1123054.972 1082170.809 720494.2831 1.296879487 1.474558992 1.513397661 1.458646279 1.358086339 1.732237244 1.558728499 1.501983895 1 19.45862746 -0.756392039 9.102655468 1.000000009 1.498870413 0.633702329 0.115994884 0 0 0.108872989 0.02566161 0.175229798 0.756392039 0.498870404 EERLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EERLSPR 7 1 A0A0G2JHC2;Q6NYC8-2;Q6NYC8 A0A0G2JHC2 PPP1R18 Phostensin 1 EERLS(1)PR;EERLS(1)PR 108.15 0.004432 382460000 678270 777880 785890 832420 791430 546820 621590 546680 727210 TRUE FALSE 635818.2914 835475.0446 804531.6819 853781.3065 729274.2803 704678.0571 528388.3501 614934.2014 605833.953 1.049492668 1.379049557 1.327973908 1.40926619 1.203752739 1.163153788 0.872166948 1.015021027 1 19.20856291 2.064414442 2.265654424 0.952847333 1.307319891 0.621853751 0.10882986 0.167580106 1.65207962 0.052625714 0.030218049 115.9883692 -2.064414442 0.354472558 EES(ph)DGEYDEFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EESDGEYDEFGR 12 0 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 EES(1)DGEYDEFGR;EES(1)DGEYDEFGR 323.54 5.40E-47 5299100000 5679800 3313700 4209000 3979100 3466500 3718700 5733200 3224600 3197800 TRUE FALSE 5324311.457 3559049.796 4308839.468 4081210.443 3194255.073 4792228.322 4873559.884 3627198.408 2664066.521 1.998565506 1.335946294 1.617391846 1.531947648 1.199014757 1.798839587 1.829368691 1.361526966 1 21.34519868 4.752813281 23.91889376 1.516141741 1.998566117 0.275478851 0.260742231 1969.96641 3305902.2 0.059207754 1.199786589 56599.58942 -4.752813281 0.482424376 EES(ph)DGEYDEFGRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EESDGEYDEFGRK 13 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 EES(1)DGEYDEFGRK;EES(1)DGEYDEFGRK;EES(1)DGEYDEFGRK;EES(1)DGEYDEFGRK;EES(1)DGEYDEFGRK 164.53 2.26E-05 853051000 1510170 759565 976234 915806 832287 857298 1472960 750646 739389 TRUE FALSE 1415651.155 815803.9829 999390.7315 939307.1324 766922.5363 1104786.016 1252103.322 844365.8055 615980.1993 2.298208866 1.324399687 1.622439703 1.524898257 1.245044138 1.793541443 2.032700603 1.370767772 1 19.23252445 0.995351232 24.76243825 0.999999965 1.655205619 0.344711424 0.311057526 164.9621448 878704.1182 0.291340439 0.07283511 9.893529012 -0.995351232 0.655205654 EES(ph)EEEEDEDDEEEEEEEKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EESEEEEDEDDEEEEEEEKEK 21 1 H0Y993;A0A494C028;P35659;B4DFG0;H0Y8X0;A0A494C198;D6R9L5 H0Y993 DEK Protein DEK 1 EES(1)EEEEDEDDEEEEEEEKEK;EES(1)EEEEDEDDEEEEEEEKEK;EES(1)EEEEDEDDEEEEEEEKEK;EES(1)EEEEDEDDEEEEEEEKEK 319.92 4.01E-67 3278480000 4591000 1195408 2011747 1938600 2065530 1246792 2671220 1371833 2439220 TRUE FALSE 4303657.505 1283917.252 2059466.589 1988347.758 1903311.606 1606720.61 2270695.359 1543109.37 2032098.424 2.117839104 0.631818438 1.013467933 0.978470203 0.93662373 0.790670664 1.117414064 0.759367436 1 20.95453885 4.746649572 24.98672778 0.908299209 2.1178397 0.878430468 0.141963866 322.8880644 997376.3906 0.032464262 0.362861999 55801.97521 -4.746649572 1.209540492 EES(ph)EES(ph)DDDMGFGLFD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EESEESDDDMGFGLFD 16 0 P05387;H0YDD8;P05386-2;P05386 P05387;P05386 RPLP2;RPLP1 60S acidic ribosomal protein P2;60S acidic ribosomal protein P1 2 EES(1)EES(1)DDDMGFGLFD 92.935 0.005446 0 34114 26331 34943 30512 32468 31686 40446 27180 31108 TRUE FALSE 31978.86564 28280.57464 35771.86446 31294.98958 29918.09425 40833.23382 34381.49778 30573.48283 25915.87383 1.233948963 1.091245266 1.380307092 1.207560655 1.154431235 1.575607062 1.326657862 1.179720314 1 14.66154842 3.982511093 23.32181477 1.290392257 1.162825449 0.037722016 0.15735736 212.4661589 919310.84 0.036750401 0.075745434 9605.303527 -3.982511093 -0.127566808 EES(ph)EES(ph)DEDMGFGLFD ddPTM_SK-BR-3_Pertuzumab_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 263.72 1.30E-26 841078000 1857801 1468930 1614567 1578942 1565062 1427265 2146227 1403851 1474056 TRUE FALSE 1741524.552 1577691.106 1652865.292 1619460.325 1442148.344 1839293.236 1824420.186 1579124.888 1228026.531 1.418148963 1.284736987 1.345952429 1.318750275 1.17436253 1.497763436 1.485652093 1.285904537 1 20.2279103 2.23041781 24.99520375 1.376497953 1.310757817 0 0.1522768 657.0958227 2017010.515 0.051266283 0.038519883 169.9878223 -2.23041781 -0.065740135 EES(ph)EES(ph)EAEPVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EESEESEAEPVQR 13 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 EES(1)EES(1)EAEPVQR;EES(1)EES(1)EAEPVQR 301.31 8.68E-41 1486510000 1521110 1180520 1249470 1262730 1316120 1044510 1620330 1105760 1681540 TRUE FALSE 1425906.44 1267926.929 1279108.018 1295133.79 1212757.244 1346043.081 1377376.559 1243816.57 1400880.111 1.017864719 0.905093105 0.91307458 0.924514367 0.865710945 0.960855301 0.983222296 0.887882239 1 20.41790206 2.102936934 20.54795963 0.959636989 0.92017808 0.100134295 0.047308277 6.175033011 1211.254597 0.016316987 0.012050904 126.7467797 -2.102936934 -0.039458909 EES(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EESPLR 6 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 EES(1)PLR;EES(1)PLR;EES(1)PLR;EES(1)PLR;EES(1)PLR;EES(1)PLR 142.08 0.012138 16742230000 13978870 12521160 13823510 12399800 11932770 12628000 15899040 11763090 13267590 TRUE FALSE 13103957.48 13448239.71 14151410.19 12717999.86 10995618.38 16273498.6 13515126.55 13231737.68 11053143.52 1.185541241 1.216689143 1.280306382 1.150622883 0.994795586 1.472295965 1.222740529 1.197101771 1 23.3979534 3.239141024 24.99887853 1.198761874 1.23273502 0.011318193 0.13481357 102.6715708 4422013.959 0.036754903 0.046900306 1734.367091 -3.239141024 0.033973146 EES(ph)S(ph)EDENEVSNILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EESSEDENEVSNILR 15 0 Q01804-5;Q01804-3;Q01804 Q01804-5 OTUD4 OTU domain-containing protein 4 2 EES(1)S(1)EDENEVSNILR;EES(1)S(1)EDENEVSNILR 238.21 1.35E-17 196531000 545660 381470 463370 439800 393790 377420 633040 390840 411980 TRUE FALSE 511508.1146 409714.4357 474361.3552 451086.0126 362863.3219 486375.0271 538121.5289 439637.2343 343217.8765 1.490330631 1.193744451 1.382099791 1.314284725 1.057238992 1.417102839 1.567871506 1.280927552 1 18.38876517 EES(ph)WESGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EESWESGR 8 0 Q9NQ29-3;Q9NQ29;B8ZZ08 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 1 EES(0.99)WES(0.01)GR;EES(1)WESGR 180.27 0.00025172 388790000 665850 568630 575680 590910 648980 530380 776220 594900 725490 TRUE FALSE 624175.6371 610731.9569 589335.4015 606073.751 598011.7287 683492.096 659833.0171 669174.5745 604401.0322 1.032717689 1.010474709 0.975073453 1.002767565 0.989428702 1.130858585 1.091713915 1.107169808 1 19.2051466 2.249880225 24.99860807 1.091710072 0.999581732 0.53558057 0.036686196 130.4617577 288116.2382 0.011425887 0.009478414 177.7789042 -2.249880225 -0.092128341 EESEES(ph)DEDMGFGLFD ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.152)EES(0.848)DEDMGFGLFD;EES(0.001)EES(0.999)DEDMGFGLFD;EESEES(1)DEDMGFGLFD;EESEES(1)DEDMGFGLFD;EESEES(1)DEDMGFGLFD 218.5 1.39E-14 382754000 582523 532291 601429 596491 609215 510719 641392 508609 540106 TRUE FALSE 546063.9253 571702.3795 615695.1799 611797.9689 561369.7114 658155.2845 545221.224 572109.9532 449958.8194 1.213586448 1.270566005 1.368336731 1.359675469 1.247602419 1.462701154 1.211713607 1.271471807 1 18.77943345 0.577101813 1.182678727 1.000542368 1.315018792 0.611449335 0.076276172 0.930795517 1.875395355 0.066621094 0.020356688 3.776607165 -0.577101813 0.314476424 EESEES(ph)EAEPVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EESEESEAEPVQR 13 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 EES(0.49)EES(0.51)EAEPVQR 237.65 9.91E-17 164030000 137580 125640 98568 97064 154930 69893 137730 126040 250230 TRUE FALSE 128969.1134 134942.5163 100906.0795 99554.82657 142762.4228 90069.97448 117078.6651 141776.3714 208464.9965 0.618660761 0.647314986 0.484043275 0.477561357 0.68482683 0.432062821 0.561622657 0.680096773 1 17.66944563 0.859501566 2.682226733 0.999614567 0.555403786 0.758261816 0.078677089 0.254115668 3.517370596 0.071603737 0.019023962 7.236050112 -0.859501566 -0.444210781 EESGKPGAHVTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 EESGKPGAHVTVK 13 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;; 172.57 1.39E-05 31028850000 45028890 38551350 43653970 40647010 45712700 33115370 55224110 40426600 56464680 FALSE TRUE 42210612.15 41405732.07 44689462.78 41690081.09 42122608.94 42675239.74 46943767.38 45473950 47040360.13 0.897327572 0.880217157 0.950023823 0.886261946 0.89545677 0.907204784 0.997946598 0.96670072 1 25.48739577 1.760194306 6.645198139 0.9862058 0.904531393 0.79026994 0.020719719 0.073798136 9.037124833 0.009999854 0.005399515 57.56974502 -1.760194306 -0.081674407 EESHSNDQS(ph)PQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EESHSNDQSPQIR 13 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 EESHSNDQS(1)PQIR 100.04 0.0016641 82788000 162780 203750 185740 233360 290390 128400 195540 196570 428540 TRUE FALSE 152591.8904 218835.862 190145.8405 239348.4127 267583.9408 165466.9956 166220.5923 221112.1972 357013.9055 0.427411616 0.612961732 0.532600657 0.67041762 0.749505654 0.463474932 0.465585765 0.619337773 1 18.44562074 0.962294965 21.76147268 1.000000003 0.561794072 0.659148141 0.098593686 723.8921568 417795.8502 0.094906096 0.023726524 9.168429825 -0.962294965 -0.438205931 EESKKEETPGT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EESKKEETPGTPK 13 2 Q99442 Q99442 SEC62 Translocation protein SEC62 1 EESKKEETPGT(1)PK;EESKKEET(0.001)PGT(0.999)PK;EESKKEETPGT(1)PK 117.18 0.02512 1681830000 6414700 1655750 2626830 2472400 3121100 1918200 4226660 2428880 3267020 TRUE FALSE 6013215.378 1778343.453 2689139.648 2535845.97 2875981.396 2471953.201 3592911.571 2732131.015 2721733.256 2.209333102 0.653386385 0.988024687 0.931702607 1.056672761 0.908227577 1.32008218 1.003820271 1 21.37609425 4.748255622 24.93879995 0.985515248 2.209333781 0.849603393 0.162182514 538.0487412 1384012.354 0.042537904 0.563889245 56008.71675 -4.748255622 1.223818533 EESKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EESKPR 6 1 O75363;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 ; 114.19 0.023257 186432000 297840 256771 348030 339070 358360 278232 342470 317760 360960 FALSE TRUE 279198.7261 275782.592 356285.436 347771.1102 330215.8512 358553.0617 291119.8028 357433.0355 300713.4441 0.928454419 0.917094322 1.18480049 1.156486739 1.098108041 1.192341309 0.968097066 1.188616746 1 18.19802984 4.113121953 3.754384834 1.109310889 0.921942705 0.510553286 0.077056878 0.177358769 4.531887075 0.018507403 0.044492967 12975.4358 -4.113121953 -0.187368184 EESLADDLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EESLADDLFR 10 0 O60934;A0A0C4DG07;A0A087X1V5 O60934 NBN Nibrin 0 ; 246.51 2.99E-12 173110000 339790 390940 395770 384050 405860 330930 453870 346940 365960 FALSE TRUE 318523.1504 419885.6044 405157.8513 393905.3732 373985.3928 426464.1188 385816.407 390256.2227 304878.9118 1.044752976 1.377220884 1.32891399 1.292005967 1.226668616 1.39879835 1.265474233 1.280036787 1 18.21787684 0.393111948 1.867641038 1.000005041 1.294651193 0.43141315 0.098150205 5.981740834 17.35152307 0.084777862 0.023551655 2.472361364 -0.393111948 0.294646152 EESQIPVDEVFFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EESQIPVDEVFFHR 14 0 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 0 ;;; 155.98 5.70E-06 411784000 617249 682500 697627 671343 686580 563848 773505 597322 685620 FALSE TRUE 578616.4869 733033.0101 714175.0419 688570.798 632658.7763 726621.7643 657525.1061 671898.9666 571185.5927 1.013009597 1.283353466 1.250337983 1.205511495 1.107623834 1.272129013 1.151158423 1.176323379 1 19.12360006 0.085831517 0.663294825 0.991613693 1.205914374 0.308386531 0.082361664 4.112112305 2.132569705 0.161991092 0.029068061 1.218516788 -0.085831517 0.214300682 EESSIHCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EESSIHCK 8 0 A0A669KBJ7;Q9H2P0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 ; 98.299 0.0076207 235410000 500200 628670 620520 634040 687890 513980 825270 593770 719020 FALSE TRUE 468893.3749 675217.3809 635239.0274 650310.5398 633865.8942 662357.6822 701528.4249 667903.4915 599010.917 0.782779348 1.127220493 1.060479884 1.085640547 1.058187549 1.105752272 1.17114464 1.115010549 1 19.19222277 4.74177483 24.99744281 1.098132549 0.782779231 0.812392491 0.04633115 125.4870295 975887.3611 0.010871309 0.078029947 55179.12756 -4.74177483 -0.315353317 EETEELKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EETEELKR 8 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;; 183.65 0.00035626 2639610000 2108830 1498760 1912090 1642340 1771250 1654590 2732730 1654600 1867380 FALSE TRUE 1976842.095 1609729.75 1957445.678 1684485.225 1632143.17 2132243.273 2322982.506 1861180.452 1555702.214 1.270707258 1.034728713 1.258239308 1.082781274 1.049135982 1.370598597 1.493205116 1.196360354 1 20.5691345 2.229715757 24.99264671 1.328486046 1.138566494 0.084262727 0.152001837 244.0357637 689559.1429 0.052224435 0.039145093 169.7132526 -2.229715757 -0.189919552 EETKEDAEEKQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EETKEDAEEKQ 11 2 P43487;F6WQW2;P43487-2 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;;;; 163.51 9.48E-05 4684000000 11202750 4435070 6733570 5931970 5930790 4428530 8630840 4995460 6915130 FALSE TRUE 10501589.87 4763447.197 6893293.46 6084194.393 5465009.677 5706974.72 7336725.667 5619154.177 5760950.13 1.822891995 0.826850969 1.196554961 1.05610954 0.948629923 0.990630815 1.273527023 0.975386707 1 22.45787534 4.748988347 24.84649955 1.05061588 1.822892464 0.793773254 0.126187387 632.0919189 1506074.46 0.02991697 0.422776838 56103.29218 -4.748988347 0.772276585 EETNGPSNQKPVKS(ph)PDNSIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EETNGPSNQKPVKSPDNSIK 20 2 Q9UKL0 Q9UKL0 RCOR1 REST corepressor 1 1 EET(0.001)NGPS(0.002)NQKPVKS(0.997)PDNSIK 97.691 0.00047257 405140000 1146300 375100 640790 540560 535380 420240 900320 485860 621370 TRUE FALSE 1074555.129 402872.7943 655989.8414 554431.6848 493333.4144 541556.466 765325.3742 546520.6905 517659.3328 2.075795917 0.778258536 1.267223055 1.071035814 0.953007863 1.046163822 1.478434418 1.055753574 1 18.98164346 4.750822998 24.89551483 1.105799795 2.07579655 0.735779646 0.186787456 1042.059878 2115585.95 0.046060561 0.794895583 56340.79847 -4.750822998 0.969996755 EETPGQRPAVTETHQLAELNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EETPGQRPAVTETHQLAELNEK 22 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1;I3L1C0 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ;; 289.96 1.40E-55 1332310000 1321890 1077840 1158560 1141690 1191010 954360 1467540 1061750 1399070 FALSE TRUE 1239155.265 1157644.395 1186041.59 1170987.698 1097472.879 1229868.239 1247496.001 1194311.825 1165556.179 1.063145035 0.99321201 1.017575654 1.004660024 0.941587286 1.055177144 1.070301049 1.02467118 1 20.15258711 EETQEDKDCPIKEEKGS(ph)PLNAAPYGIESMSQDTEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EETQEDKDCPIKEEKGSPLNAAPYGIESMSQDTEVR 36 3 P18031;B4DSN5 P18031 PTPN1 Tyrosine-protein phosphatase non-receptor type 1;Tyrosine-protein phosphatase non-receptor type 1 EET(0.001)QEDKDCPIKEEKGS(0.999)PLNAAPYGIESMSQDTEVR 304.13 1.05E-92 198190000 527070 182760 243060 227990 322000 156230 335550 211080 503210 TRUE FALSE 494081.6295 196291.7406 248825.498 233840.6094 296711.4189 201331.0648 285237.3926 237433.8026 419221.0001 1.1785708 0.468229742 0.593542542 0.557797938 0.707768501 0.480250428 0.680398626 0.566369057 1 18.67735146 -1.055320042 4.898305151 1.000008799 0.626973289 0.213542559 0.202743619 1.71E-05 3.29E-06 0.17207813 0.040558248 0.088039985 1.055320042 -0.373035509 EETVNDPEEAGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EETVNDPEEAGHR 13 0 O00567 O00567 NOP56 Nucleolar protein 56 0 ; 186.16 8.04E-06 529320000 761120 802710 801010 789440 750080 668490 992000 717970 697940 FALSE TRUE 713482.8578 862143.4836 820010.3355 809698.3669 691171.7425 861472.211 843258.8093 807610.1349 581449.3051 1.227076637 1.482749186 1.410286896 1.392551956 1.188705079 1.481594704 1.45027056 1.38896053 1 19.14929389 0.90591658 20.02605174 1 1.394032306 0.58365883 0.099443154 9381.016384 1996793.754 0.090772422 0.022693106 8.052237578 -0.90591658 0.394032306 EEVFWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEVFWR 6 0 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 126.68 0.040453 86698000 239690 267300 256900 247660 244870 197960 282650 217060 198580 FALSE TRUE 224688.2308 287091.1701 262993.7893 254015.3749 225638.898 255107.8384 240269.2565 244160.4188 165435.7151 1.358160362 1.735363914 1.589703826 1.535432507 1.363906807 1.54203606 1.452342116 1.475862806 1 17.3359112 -2.967664243 0.219130146 3.33E-14 1.619461984 0.678129943 0.109577152 29.56666579 0.656109209 13.86666013 0.216205462 0.001077298 2.967664243 1.619461984 EEVGEEAIVELVENGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEVGEEAIVELVENGKK 17 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 119.47 0.0001896 26185000 112010 66562 83378 80557 69213 67162 120400 66586 75238 FALSE TRUE 104999.494 71490.31974 85355.76553 82624.229 63777.29017 86550.57912 102347.1377 74899.40867 62680.29174 1.675159625 1.140554993 1.361764012 1.318185138 1.017501489 1.380826041 1.632843991 1.194943524 1 15.93572427 4.753945126 24.08608038 1.293979276 1.675160091 0.308819201 0.189667325 2445.53697 3828639.799 0.045560503 1.057667952 56747.28994 -4.753945126 0.381180815 EEVHGEAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEVHGEAQR 9 0 J3KN16;Q5VYK3;R4GMY1 J3KN16 KIAA0368;ECM29 Proteasome-associated protein ECM29 homolog 0 67.726 0.060085 78479000 87921 113400 107490 104110 117580 98917 118970 108030 120770 FALSE TRUE 82418.18155 121796.254 110039.7136 106781.6389 108345.7411 127472.7321 101131.553 121517.7833 100612.7068 0.81916275 1.210545446 1.093695986 1.061313648 1.07685942 1.266964543 1.005156865 1.207777697 1 16.618453 4.749763814 24.72982375 1.118253873 0.819162546 0.523164051 0.088807416 1071.972176 2366209.044 0.018908948 0.285794083 56203.55852 -4.749763814 -0.299091327 EEVILS(ph)PVPSVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEVILSPVPSVLK 13 0 Q4G0A6 Q4G0A6 FAM188B Protein FAM188B 1 EEVILS(1)PVPSVLK;EEVILS(1)PVPSVLK 160.31 4.62E-05 28423000 149239 120902 145220 163278 141958 118149 159767 110525 109324 TRUE FALSE 139898.3974 129853.7099 148664.687 167467.9899 130809.1913 152256.6983 135811.4216 124324.2895 91077.11814 1.536043303 1.425755585 1.632294587 1.838749329 1.436246491 1.671733817 1.491169509 1.365044174 1 16.47480102 0.888646762 1.552853668 1.001372008 1.580390108 0.710963013 0.118836732 0.283855737 1.34787188 0.109382991 0.031860949 7.738321372 -0.888646762 0.5790181 EEVNDRPVRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEVNDRPVRR 10 2 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 106.62 0.0013457 114510000 50371 50927 61122 62613 54376 40777 50213 44514 68920 FALSE TRUE 47218.36902 54697.68807 62571.8427 64219.75558 50105.5283 52548.65794 42684.0268 50071.67089 57416.80676 0.822378876 0.952642461 1.0897827 1.11848358 0.872663095 0.91521387 0.74340649 0.872073417 1 15.80918548 2.584639396 8.157445828 0.855902381 1.004198517 0.220424139 0.101824949 0.353491535 24.20782059 0.032946697 0.031017147 384.2725795 -2.584639396 0.148296137 EEVSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEVSLR 6 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 145.44 0.025929 489690000 375530 487370 396730 437740 455750 309250 441510 413330 435170 FALSE TRUE 352026.2476 523455.3819 406140.6229 448973.1495 419957.2334 398525.4547 375309.6743 464935.1604 362537.3157 0.971006935 1.443866215 1.120272605 1.238419137 1.158383469 1.099267406 1.035230466 1.282447738 1 18.46776997 2.489590229 2.751651956 1.099199738 1.223321627 0.066288778 0.137771146 0.51168126 7.854405606 0.047452648 0.040781533 308.7381013 -2.489590229 0.124121889 EEVTELLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEVTELLAR 9 0 P19388;A0A087WVZ9;A0A0A0MQR7;A0A087WWX0 P19388 POLR2E "DNA-directed RNA polymerases I, II, and III subunit RPABC1" 0 ; 135.83 0.00048809 96494000 170524 182225 201512 189498 206190 143721 198886 161580 210830 FALSE TRUE 159851.2072 195717.1286 206291.9598 194360.8395 189996.6691 185210.9196 169064.8907 181753.6187 175641.111 0.910101322 1.114301359 1.174508398 1.106579424 1.081732335 1.054485015 0.962558764 1.034801122 1 17.42227104 2.02997156 3.091982382 0.996315731 1.097150241 0.174315561 0.070255362 0.32780799 6.223413087 0.032585323 0.019952581 107.1449138 -2.02997156 0.100834511 EEVVGGDDS(ph)DGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEVVGGDDSDGLR 13 0 P25490 P25490 YY1 Transcriptional repressor protein YY1 1 EEVVGGDDS(1)DGLR;EEVVGGDDS(1)DGLR 231.17 3.01E-12 427320000 885220 640570 770340 657050 603190 867910 1045870 664930 533850 TRUE FALSE 829815.6604 687998.4693 788612.8286 673911.0154 555817.8906 1118461.528 889051.5029 747947.9742 444746.9862 1.86581514 1.546943522 1.773171833 1.515268313 1.249739532 2.514826547 1.999005121 1.681738151 1 18.7626253 EEVVLLTHGDSVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEVVLLTHGDSVDK 14 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ; 212.17 2.82E-09 499500000 1297810 877410 1092090 1019810 926830 865550 1333300 895340 848310 FALSE TRUE 1216582.389 942374.3493 1117994.891 1045980.051 854040.5105 1115420.234 1133384.043 1007125.17 706721.5807 1.721445081 1.333444987 1.581945311 1.480045438 1.208453985 1.578302212 1.603720721 1.425066387 1 19.43078244 0.964453584 22.41307431 0.999999997 1.492898982 0.540836262 0.143850804 1089.029661 686667.2623 0.129954277 0.032488569 9.214114062 -0.964453584 0.492898985 EEWYAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EEWYAR 6 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 156.93 0.02254 715340000 939240 1292630 1066500 1065810 1299660 1010330 1224450 1134540 1335270 FALSE TRUE 880454.645 1388337.67 1091797.884 1093160.489 1197589.946 1301995.87 1040855.09 1276189.816 1112404.811 0.791487628 1.248050761 0.981475334 0.982700253 1.07657746 1.170433512 0.935680141 1.147235075 1 20.08525046 -0.978972495 7.517403248 0.999999999 1.051211864 0.00534397 0.130462641 1.67E-09 4.45E-10 0.112241359 0.026455541 0.10496089 0.978972495 0.051211865 EEYHTHLAVLYLEEVLLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EEYHTHLAVLYLEEVLLQR 19 0 Q8WUH2 Q8WUH2 TGFBRAP1 Transforming growth factor-beta receptor-associated protein 1 0 60.768 0.034675 11041000 7655.1 5529.1 7011.8 6653.4 6253.2 5620.7 6911.2 5462.1 4524.9 FALSE TRUE 7175.980956 5938.480317 7178.123207 6824.137508 5762.098896 7243.304846 5874.92972 6144.055209 3769.664958 1.903612399 1.575333719 1.904180686 1.81027693 1.528544038 1.921471782 1.558475298 1.629867714 1 11.88022059 0.157649398 0.623794531 0.965951072 1.766587035 0.736029734 0.141212712 1.558966663 0.778605255 0.250614629 0.050795863 1.437637518 -0.157649398 0.800635963 EEYLLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EEYLLLR 7 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;; 121.29 0.010358 245393000 597840 912200 737610 803510 819290 606890 828190 757060 682870 FALSE TRUE 560422.2616 979740.2371 755106.4575 824129.4269 754946.2683 782089.291 704010.598 851580.6075 568894.5855 0.985107392 1.72218239 1.327322279 1.448650502 1.327040699 1.374752566 1.237506238 1.496904047 1 19.11780182 -3.440422612 0.263324839 1.89E-14 1.421833148 0.232442746 0.192362499 100.370636 2.073742651 54.71942814 0.231887462 0.000362725 3.440422612 1.421833148 EFADFEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EFADFEYR 8 0 Q8ND56-2;Q8ND56;Q8ND56-3;A0A0G2JQ95;A0A096LP11;A0A140TA66 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;;; 131.06 0.0023756 691060000 1569760 1927350 1786830 1724050 1966040 1525290 1871280 1713120 1788280 FALSE TRUE 1471511.524 2070052.999 1829214.451 1768292.042 1811635.149 1965616.462 1590698.936 1927006.803 1489804.515 0.987721214 1.389479612 1.227821793 1.186928905 1.216022056 1.319378779 1.067723262 1.293462856 1 20.50669161 -1.11474059 0.364290658 0.887674731 1.238787009 0.207562744 0.11916196 22.37272432 2.06892265 2.642452406 0.083252132 0.076781998 1.11474059 0.351112278 EFAGEDTSDLFLEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EFAGEDTSDLFLEER 15 0 O14980 O14980 XPO1 Exportin-1 0 ;; 225.97 2.16E-12 266153000 384476 438780 389734 426479 426509 342873 463130 364411 450892 FALSE TRUE 360412.3335 471267.7278 398978.6745 437423.1732 393012.7036 441854.869 393687.956 409908.5155 375635.2123 0.959474303 1.254588793 1.062143967 1.164489267 1.046261614 1.176287138 1.048059242 1.091240922 1 18.51897278 0.818531628 0.608450798 0.998450281 1.124680981 0.114826876 0.082774562 1.77333822 1.439495948 0.079482418 0.0318877 6.584633811 -0.818531628 0.126230701 EFDEDS(ph)DEKEEEEDTYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EFDEDSDEKEEEEDTYEK 18 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 EFDEDS(1)DEKEEEEDTYEK;EFDEDS(1)DEKEEEEDTYEK 270.71 3.71E-39 1061780000 3129400 705860 1336140 1142720 977300 1083740 1820470 1024300 715070 TRUE FALSE 2933536.44 758122.6088 1367833.872 1172044.13 900546.8002 1396598.145 1547507.424 1152186.11 595720.1975 4.92435283 1.272615251 2.296101219 1.967440645 1.511694255 2.344386091 2.597708506 1.93410617 1 19.18427535 4.746824931 24.89835811 1.961637521 4.924354386 0.784398443 0.501740141 463.754558 1397145.957 0.116376044 1.321255865 55824.51139 -4.746824931 2.962716865 EFDEDSEDRLVNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFDEDSEDRLVNEK 14 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 178.23 1.83E-06 135600000 396360 241940 321430 300280 292300 247510 392620 254300 353410 FALSE TRUE 371552.5351 259853.4893 329054.4714 307985.6932 269343.9371 318962.119 333750.2759 286049.9148 294423.5879 1.261965924 0.882583801 1.117622653 1.046063243 0.914817794 1.083344311 1.133571798 0.971559096 1 18.16753373 EFDKHFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EFDKHFGK 8 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 60.973 0.05342 1261260000 1704810 2190480 1807250 2201590 2605050 1241030 2508620 1851420 3584000 FALSE TRUE 1598108.985 2352665.418 1850118.823 2258086.527 2400459.881 1599295.215 2132475.72 2082573.862 2985807.246 0.535235149 0.787949531 0.61963773 0.756273376 0.803956747 0.535632438 0.714204081 0.69749106 1 21.5096896 0.443664918 2.267591786 0.999993494 0.685428264 0.531270908 0.094101797 7.089074041 27.84255934 0.080935516 0.02185589 2.777569396 -0.443664918 -0.31456523 EFDRHS(ph)GSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EFDRHSGSDR 10 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 EFDRHS(0.961)GS(0.039)DR;EFDRHS(0.984)GS(0.016)DR;EFDRHS(0.94)GS(0.06)DR 143.25 2.08E-05 5314380000 2319099 2831490 2835230 3155830 3244520 2356750 2656930 2281290 2836390 TRUE FALSE 2173950.733 3041136.466 2902482.994 3236813.941 2989708.487 3037105.466 2258548.012 2566114.078 2362978.185 0.920004572 1.286993035 1.228315611 1.369802718 1.265228983 1.285287137 0.955805697 1.085966047 1 21.17217488 1.743888921 10.34908174 1.018196708 1.24029796 0.399161465 0.121672756 0.086795112 48.09273038 0.053427084 0.02905036 55.44838751 -1.743888921 0.222101252 EFEDRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EFEDRDR 7 1 Q13951-2;A0A494C0A9;Q13951;J3KS23 Q13951-2 CBFB Core-binding factor subunit beta 0 ;; 96.253 0.016624 500910000 701500 705860 770580 705630 808030 630110 822670 673640 858850 FALSE TRUE 657594.3672 758122.6088 788858.5215 723737.6604 744570.5832 812012.528 699318.2708 757745.4369 715502.3866 0.91906663 1.059566848 1.102523956 1.011509778 1.040626275 1.134884444 0.977380766 1.059039706 1 19.44859705 -1.788581627 3.854686409 0.99320299 1.044388396 0.028292583 0.060832236 0.003779792 0.000207311 0.062653487 0.012847013 0.016271155 1.788581627 0.051185406 EFEFLMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EFEFLMR 7 0 P85037 P85037 FOXK1 Forkhead box protein K1 0 ;; 117.93 0.01191 83684000 128858 174778 136711 131829 182870 101705 145055 157060 180738 FALSE TRUE 120793.0078 187718.745 139953.8495 135211.9553 168508.1279 131065.5825 123305.3494 176669.2867 150571.6602 0.802229368 1.246707015 0.929483339 0.897990732 1.119122467 0.870453193 0.818914723 1.173323629 1 17.20009073 3.727732018 24.99731505 0.953767076 1.065780177 0 0.15228102 67.01017357 2742406.035 0.036987523 0.061975315 5342.34608 -3.727732018 0.1120131 EFEKDKDDDEVFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFEKDKDDDEVFEK 14 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 145.55 4.81E-06 260590000 812520 301100 484120 505590 580010 279770 618220 377980 1005100 FALSE TRUE 761665.8236 323393.7573 495603.555 518564.2954 534458.3542 360535.0573 525523.6503 425171.635 837342.3168 0.909622992 0.386214516 0.591876876 0.619297849 0.638279403 0.430570688 0.627609091 0.507763225 1 19.67545801 -1.387518359 3.631768082 1.00254496 0.570567614 0.446137287 0.142655561 8774915.852 5031387.335 169783.8056 0.029510709 0.040971479 1.387518359 -0.431977346 EFEMWAPDMYVVTYVGDKDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFEMWAPDMYVVTYVGDKDSR 21 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 142.23 1.35E-07 158610000 205160 173440 211800 202410 234800 158990 253160 193960 223720 FALSE TRUE 192319.4018 186281.6781 216823.996 207604.1833 216359.7551 204887.832 215201.0082 218176.333 186379.6867 1.031868897 0.999474145 1.163345641 1.113877735 1.160854806 1.099303447 1.154637675 1.170601458 1 17.50788511 4.020033334 3.996695421 1.130572849 1.017218394 0.430868843 0.050683469 0.163160634 5.530466717 0.011163043 0.024842871 10472.08924 -4.020033334 -0.113354455 EFEPLLKPHVAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFEPLLKPHVAVK 13 1 Q3KQV9;Q3KQV9-2 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 145.6 2.52E-05 402930000 570600 571880 567880 624170 707170 402210 686770 555430 551920 FALSE TRUE 534887.1646 614222.5902 581350.3818 640187.2589 651631.7208 518321.4977 583795.2142 624776.6582 459800.9865 1.163301472 1.335844438 1.264352185 1.3923138 1.417203834 1.127273566 1.269669338 1.358797994 1 18.81065004 -1.736314643 2.76912686 0.945947673 1.290596142 0.494222985 0.092544143 20861848.56 17340439.79 7761693.582 0.02124191 0.018352083 1.736314643 0.344648468 EFEPLLNWMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EFEPLLNWMK 10 0 P14625 P14625 HSP90B1 Endoplasmin 0 ; 185.6 3.33E-06 126311000 437410 738670 384440 412720 720850 260150 417050 583190 433310 FALSE TRUE 410033.2889 793361.8954 393559.0983 423311.0939 664237.3488 335251.0818 354517.2242 656002.5553 360987.7617 1.135864792 2.197752887 1.090228368 1.172646662 1.840055036 0.928704841 0.982075466 1.8172432 1 18.4615904 3.821597227 6.058695641 1.245236332 1.724325889 0.13982131 0.409820276 0.320140127 16.82940612 0.09779395 0.178195526 6631.277872 -3.821597227 0.479089557 EFESVLVDAFSHVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 EFESVLVDAFSHVAR 15 0 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ;;;;;; 251.84 1.25E-24 1081064300 1210762.5 1398044.7 1326779.3 1354417 1494144.7 1182774.9 1548360 1278090.5 1508069.8 FALSE TRUE 1134983.036 1501557.384 1358251.132 1389173.633 1376800.602 1524222.813 1316197.792 1437662.912 1256363.208 0.903387674 1.195161857 1.081097507 1.105710215 1.095861924 1.213202363 1.047625228 1.144305169 1 20.26082217 -1.10815242 3.880485311 0.999966704 1.106340906 0.108755032 0.08572229 5088907.855 1454198.712 1563.507216 0.017439764 0.077955647 1.10815242 0.106374202 EFETAETLLNSEVHMLLEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 EFETAETLLNSEVHMLLEHR 20 0 O15514;E9PHV4 O15514 POLR2D DNA-directed RNA polymerase II subunit RPB4 0 ;;;;;; 248.35 1.78E-30 194912100 80171.2 90852.2 96865.7 97861.5 100659.9 79675.7 107567.4 85796.2 107891.6 FALSE TRUE 75153.4277 97578.99142 99163.40015 100372.7918 92754.4775 102676.7812 91438.66698 96508.04443 89883.79495 0.836117653 1.085612723 1.103240025 1.116695082 1.03193771 1.142328061 1.017298691 1.073697928 1 16.45577342 4.739894308 24.88545292 1.076433762 0.83611757 0.730256045 0.044835902 50.12347153 935152.2646 0.009594145 0.059591381 54940.71518 -4.739894308 -0.240316192 EFFGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFFGGR 6 0 E9PH18;A0A0J9YX62;O75190-3;O75190;C9JDX6;F8WCZ4;C9J2P2;C9J2C4;O75190-2;O75190-4 E9PH18 DNAJB6 DnaJ homolog subfamily B member 6 0 106.29 0.075031 365270000 130000 178680 175460 179990 159290 164520 160290 169380 124810 FALSE TRUE 121863.5321 191909.6531 179621.9941 184608.8481 146780.0059 212014.2532 136256.0026 190527.4659 103978.4047 1.172008095 1.845668374 1.727493267 1.775453746 1.411639334 2.039021986 1.310425977 1.832375351 1 16.6659244 -2.350297191 0.510858423 2.34E-14 1.662947335 0.35130866 0.269483774 128.6284821 7.887477917 145.1580769 0.109964923 0.00446378 2.350297191 1.662947335 EFFNGKEPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EFFNGKEPSR 10 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;; 161.99 6.30E-06 1955620000 3284640 3852900 2965200 3194380 3938500 2103840 4026600 3227270 3625730 FALSE TRUE 3079060.246 4138172.725 3035535.944 3276353.199 3629186.097 2711184.455 3422848.711 3630201.764 3020572.24 1.01936322 1.369996278 1.00495393 1.084679636 1.201489588 0.897573122 1.133178894 1.201825838 1 21.52639046 3.878782283 7.00521967 1.078751888 1.21496056 0.132500359 0.124726767 0.347704901 21.18537661 0.028969658 0.052662415 7564.535813 -3.878782283 0.136208672 EFFQIDGYVTDHIEVVQDHSALFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFFQIDGYVTDHIEVVQDHSALFK 24 0 A0A1B0GUA3;Q96EK5 A0A1B0GUA3 KIAA1279 KIF1-binding protein 0 46.403 0.094066 38153000 159450 140760 155740 164830 171250 118860 183030 133000 186740 FALSE TRUE 149470.3091 151182.0169 159434.2263 169059.8169 157800.7158 153172.9525 155586.3507 149605.3428 155571.8876 0.960779685 0.971782365 1.024826714 1.086699014 1.014326677 0.984579893 1.000092967 0.961647667 1 17.24722186 7.999959864 5.259326246 1.002162111 3.74E-05 0 0.037123059 0 0 0.008354079 0 99990758.82 -7.999959864 -1.002124728 EFFSQYGDVMDVFIPKPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EFFSQYGDVMDVFIPKPFR 19 1 Q13148;A0A087WYY0;A0A087X260;G3V162;B1AKP7;K7EN94;A0A0A0N0M3;A0A087WXQ5;Q13148-4;A0A087WV68;A0A087WXV3;A0A087WX67;A0A087WW61;A0A087WZC9;A0A087WZM1;A0A1W2PNU8;A0A087WYE7 Q13148 TARDBP;TDP43 TAR DNA-binding protein 43 0 ; 134.29 9.15E-06 290290000 542450 513160 544470 514370 561920 558300 621280 546390 400660 FALSE TRUE 508499.0228 551154.9003 557385.0855 527569.605 517789.0699 719472.1468 528124.8317 614607.9943 333787.2576 1.523422513 1.65121612 1.669881257 1.580556456 1.551254753 2.155481164 1.582219871 1.841316528 1 18.34856936 EFFVTS(ph)APWSVIDQQAIHPELNGATYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFFVTSAPWSVIDQQAIHPELNGATYR 27 0 P56545;P56545-3;P56545-2 P56545 CTBP2 C-terminal-binding protein 2 1 EFFVT(0.167)S(0.831)APWS(0.002)VIDQQAIHPELNGATYR 131.03 2.86E-05 38466000 12491 18011 15456 23768 17817 9913.9 12428 10620 14023 TRUE FALSE 11709.21061 19344.55318 15822.62362 24377.92712 16417.72469 12775.88199 10564.53678 11945.93038 11682.47071 1.002288891 1.655861475 1.354390181 2.086709886 1.40532984 1.093594181 0.904306721 1.022551708 1 13.5120578 2.233869789 3.514797412 0.975976959 1.536117371 0.462743668 0.268868086 0.188200165 4.949628488 0.098512137 0.073862023 171.3443502 -2.233869789 0.560140412 EFGIADPDEIMWFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EFGIADPDEIMWFK 14 0 Q15067-2;Q15067;Q15067-3;I3L0T4;I3L4S5;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ;; 169.58 7.70E-06 63198300 264082 277966 241079 258158 306798 178380 310094 247170 206197 FALSE TRUE 247553.579 298546.8919 246797.5077 264782.7713 282703.3226 229875.4102 263598.2835 278029.7186 171781.3886 1.441096623 1.737946667 1.436695265 1.541393823 1.645715668 1.338185773 1.534498502 1.618508971 1 17.39021421 -2.622460926 0.420404795 2.25E-18 1.552907607 0.674163969 0.116323475 55.04113468 2.383373374 50.15844782 0.063679044 0.002385278 2.622460926 1.552907607 EFGYDS(ph)PHDLDS(ph)D ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EFGYDSPHDLDSD 13 0 Q96CW6 Q96CW6 SLC7A6OS Probable RNA polymerase II nuclear localization protein SLC7A6OS 2 EFGYDS(1)PHDLDS(1)D;EFGYDS(1)PHDLDS(1)D 214.47 4.50E-11 328180000 518760 554330 547060 552420 591340 475090 617880 496280 555240 TRUE FALSE 486291.7376 595373.17 560036.5215 566596.0324 544898.5418 612240.7706 525234.6301 558241.6504 462566.857 1.051289625 1.287107282 1.210714761 1.224895437 1.177988724 1.323572498 1.135478304 1.206834519 1 18.81930237 0.298464971 0.974770662 0.999068438 1.216230108 0.407159806 0.075578402 2.695398974 2.993307541 0.0700506 0.0206352 1.988222439 -0.298464971 0.217161669 EFHLNESGDPSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 EFHLNESGDPSSK 13 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;;;;;;;; 185.67 8.46E-06 34807130000 31097500 28347130 30713200 29067180 32128000 24313150 36766900 26971680 35842900 FALSE TRUE 29151162.99 30445981 31441731.61 29813093.05 29604796.48 31331961.71 31254044.67 30339153.62 29860488.44 0.97624535 1.019607602 1.052954364 0.998412773 0.991437114 1.049278272 1.046668903 1.016030052 1 24.83173443 2.221904215 24.99957718 1.034088785 1.015094097 0.079858026 0.025117637 569.1207114 854187.8755 0.009617364 0.007123414 166.6879535 -2.221904215 -0.018994688 EFIEMWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFIEMWR 7 0 Q7L0Y3;C9JVB6 Q7L0Y3 TRMT10C Mitochondrial ribonuclease P protein 1 0 110.61 0.015737 13374000 34636 49209 30107 34159 56958 32567 29910 47133 56046 FALSE TRUE 32468.19459 52852.48556 30821.15226 35035.57777 52484.74844 41968.56422 25425.27317 53017.6588 46691.56053 0.695376086 1.131949435 0.660101138 0.750362108 1.124073555 0.898846895 0.544536805 1.135486975 1 15.51087419 EFITGDVEPT(ph)DAESEWHSENEEEEKLAGDMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFITGDVEPTDAESEWHSENEEEEKLAGDMK 31 1 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 EFITGDVEPT(0.429)DAES(0.429)EWHS(0.142)ENEEEEKLAGDMK 46.034 0.07696 55428000 62550 44278 49318 50060 54597 38942 49876 46153 71402 TRUE FALSE 58635.10715 47556.38919 50487.84625 51344.62435 50309.17185 50183.92323 42397.55683 51915.30365 59484.54493 0.985720026 0.799474708 0.848755695 0.863159068 0.845751983 0.843646418 0.712749116 0.872752808 1 15.86022726 4.74594997 24.4675607 0.831186451 0.985720125 0.23531658 0.072231993 813.6605805 2694097.184 0.015861403 0.164687965 55712.15655 -4.74594997 0.154533674 EFITGDVEPTDAES(ph)EWHSENEEEEKLAGDMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFITGDVEPTDAESEWHSENEEEEKLAGDMK 31 1 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 EFITGDVEPT(0.002)DAES(0.499)EWHS(0.499)ENEEEEKLAGDMK 131.99 1.74E-06 142520000 230520 174500 173510 180680 194940 156480 161140 173430 247960 TRUE FALSE 216092.1647 187420.1616 177625.7391 185316.5547 179630.1988 201653.2358 136978.553 195083.1173 206573.8741 1.046076933 0.907279114 0.859865459 0.897095799 0.869568814 0.976179764 0.663097178 0.944374588 1 17.65629828 EFITGDVEPTDAESEWHS(ph)ENEEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 308.86 1.26E-74 7140410000 6142581 3305984 4558499 4251020 3953527 4210658 5681379 3748845 3148606 TRUE FALSE 5758127.82 3550762.495 4666628.749 4360108.37 3643032.937 5426206.61 4829508.962 4216896.55 2623083.318 2.195175342 1.353659821 1.779062341 1.66220735 1.38883615 2.068636773 1.841157286 1.607610602 1 21.3228322 0.947003052 13.51198648 0.999999993 1.724383501 0.44780377 0.260485684 20.84001847 5314.27456 0.235737186 0.058938771 8.851218294 -0.947003052 0.724383509 EFITGDVEPTDAESEWHS(ph)ENEEEEKLAGDMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 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;EFITGDVEPTDAES(0.001)EWHS(0.999)ENEEEEKLAGDMK 462.09 7.36E-246 12982170000 6946179 3874759 4382760 5297774 5702253 3739846 5996229 4511942 7003179 TRUE FALSE 6511430.056 4161650.188 4486721.137 5433723.85 5254421.051 4819478.829 5097150.128 5075267.891 5834303.183 1.116059596 0.713307152 0.769024337 0.931340673 0.900608159 0.82605903 0.873651911 0.869901294 1 22.47612893 -0.37634457 0.451820279 1.028780077 0.842145586 0.06663654 0.10950564 14.31213878 2.877848227 0.766095905 0.059578606 0.420392956 0.37634457 -0.186634491 EFKEEGEEIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFKEEGEEIPR 11 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 67.519 0.054493 160530000 280810 215890 243140 244680 286320 177890 303730 232450 344730 FALSE TRUE 263234.6034 231874.7202 248907.3956 250958.903 263833.5822 229243.9552 258188.5062 261471.8942 287192.336 0.916579485 0.807384777 0.866692333 0.873835655 0.918665121 0.798224488 0.89900904 0.910441754 1 18.13165772 0.920058637 1.515223615 0.999136535 0.860023999 0.524103005 0.039920784 0.349515589 1.610252025 0.034875064 0.010229943 8.318760807 -0.920058637 -0.139112535 EFLEDYDDDRDDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EFLEDYDDDRDDPK 14 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ;; 165.64 3.59E-06 685520000 2360620 1389780 1747120 1628730 1619500 1301280 2202680 1500590 1794310 FALSE TRUE 2212873.008 1492680.757 1788562.511 1670525.969 1492311.003 1676938.411 1872408.583 1687941.965 1494828.069 1.48035286 0.998563506 1.196500486 1.117537196 0.99831615 1.121826948 1.252591265 1.129188031 1 20.51154813 4.750293682 24.88649897 1.116478564 1.480353092 0.653727818 0.085994198 1166.398895 2473949.533 0.020617423 0.340505724 56272.17243 -4.750293682 0.363874528 EFLHAQEEVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EFLHAQEEVKR 11 1 P43686 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;;; 149.26 2.24E-05 1357730000 2519750 2149470 2330010 2293670 2582700 1810320 2816580 2102380 3321790 FALSE TRUE 2362043.345 2308618.995 2385278.938 2352529.455 2379865.16 2332929.996 2394259.977 2364866.771 2767361.789 0.853536156 0.834231001 0.861932454 0.850098265 0.859976158 0.843015902 0.865177797 0.854556415 1 21.40007984 -5 0.358997897 2.81135053 0.848150829 0.96586769 0.008708253 71.98331611 0.574753344 100.6998042 0.005837461 1.00E-05 5 -1.963199701 EFLHNQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EFLHNQGK 8 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ; 135.83 0.00081697 500560000 1188780 1241680 1180580 1183560 1415520 980430 1470660 1226490 1555640 FALSE TRUE 1114376.382 1333615.279 1208583.915 1213932.153 1304350.769 1263464.225 1250148.186 1379619.976 1295993.634 0.859862543 1.02902919 0.932553898 0.936680645 1.006448438 0.974900024 0.964625252 1.064526816 1 20.3056272 1.257008785 24.71138811 1.032263382 0.964045804 0.286600845 0.048092012 229.5376691 307468.7877 0.028912984 0.010514233 18.07210682 -1.257008785 -0.068217579 EFLLIFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EFLLIFHK 8 0 Q9BUP0;A0A087X1Z2;Q9BUP0-2;Q8WYH2;C9JTV4 Q9BUP0 EFHD1;PP1187 EF-hand domain-containing protein D1 0 ; 98.392 0.0075549 91452000 261440 373570 229170 230100 364030 161371 261400 360580 236570 FALSE TRUE 245076.9371 401229.5115 234606.0206 236004.7556 335440.5522 207956.1881 222205.4967 405599.2067 197084.9387 1.243509213 2.035820262 1.19038026 1.197477378 1.70201008 1.055160224 1.127460567 2.057991896 1 17.588458 3.839172398 5.990518409 1.319809795 1.68194326 0.101293202 0.372700787 0.378069645 17.86741714 0.087698975 0.160126426 6905.138569 -3.839172398 0.362133465 EFLLSLDDSVDETEAVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EFLLSLDDSVDETEAVKR 18 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;A0A286YEP7;H7C0U8 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;;; 244.86 5.74E-24 362917000 601545 484960 548910 533195 581255 453198 659667 502040 738127 FALSE TRUE 563895.3722 520866.943 561930.4044 546877.6864 535605.577 584028.9055 560756.0574 564720.7991 614928.8352 0.917009156 0.847036134 0.913813717 0.88933492 0.871004166 0.949750397 0.911903988 0.918351469 1 19.23005993 -0.263437744 0.247622174 1.046626098 0.87193567 0.617871194 0.025770024 5.251267776 0.457220576 0.248538731 0.045460808 0.545208045 0.263437744 -0.174690428 EFLSEPDLASYSVVMVDEAHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFLSEPDLASYSVVMVDEAHER 22 0 O60231;A0A140T947 O60231 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 0 149.84 6.04E-08 52789000 33457 40906 37824 38966 41005 39730 43546 34486 44763 FALSE TRUE 31362.98609 43934.7228 38721.20314 39965.93353 37784.63271 51199.40604 37016.68156 38791.65301 37291.76612 0.841016379 1.178134676 1.03833117 1.071709326 1.013216499 1.372941305 0.992623451 1.040220323 1 15.1865695 4.750813495 24.22767847 1.094667337 0.841016136 0.315978019 0.114055356 1444.618729 2856370.008 0.024831932 0.412990692 56339.56576 -4.750813495 -0.253651202 EFNAEVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EFNAEVHR 8 0 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;; 214.96 8.60E-06 12528380000 8142020 10667900 8632170 8398270 10548080 6971490 8719820 9409500 8550480 FALSE TRUE 7632425.502 11457762.42 8836929.149 8613783.826 9719676.346 8984045.99 7412363.942 10584296.79 7123349.65 1.071465796 1.608479575 1.240558106 1.209232208 1.364481153 1.261210867 1.040572807 1.485859505 1 22.76412438 -4.999993486 0.108832489 0.038409772 1.468566479 0.148048198 0.178672114 244.6652449 1.77662565 52.27777994 2.159199516 1.00E-05 4.999993486 1.430156708 EFNAEVHRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EFNAEVHRK 9 1 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;; 153.05 5.13E-05 3480500000 3172450 3716420 3367750 3425370 4309110 2628270 4381140 3121880 5928340 FALSE TRUE 2973892.017 3991587.604 3447634.62 3513270.793 3970689.883 3387008.883 3724228.73 3511653.59 4938861.755 0.602141174 0.808199905 0.698062588 0.711352325 0.803968623 0.685787343 0.754066203 0.711024881 1 22.23574716 -1.377800865 2.900685857 1.004233942 0.729771222 0.67975759 0.059783581 8106082.518 9699729.879 288168.6622 0.01272347 0.041898564 1.377800865 -0.27446272 EFNFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFNFEK 6 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 100.45 0.087581 108650000 170860 160370 153920 158000 201140 119750 181860 162260 235990 FALSE TRUE 160166.1776 172243.9617 157571.0551 162054.5475 185343.2758 154319.881 154591.7813 182518.5182 196601.7444 0.814673227 0.876105968 0.801473331 0.824278279 0.942734645 0.784936479 0.786319479 0.928366728 1 17.5849166 1.029179984 4.95837117 0.999487551 0.833236503 0.595323365 0.047014328 0.107180784 6.736426361 0.044223347 0.011193383 10.69498019 -1.029179984 -0.166251049 EFNKYDTDGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EFNKYDTDGSK 11 1 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ;; 150.49 3.09E-05 4131500000 6180500 4632130 5203300 5512200 6427300 4145660 7021600 5088800 8020700 FALSE TRUE 5793673.538 4975097.725 5326724.733 5653652.384 5922525.784 5342444.743 5968776.265 5724147.882 6681993.354 0.867057662 0.744552929 0.797176 0.846102665 0.886341167 0.799528593 0.893262826 0.856652735 1 22.67184712 -0.071766756 0.226071124 1.082301858 0.769123006 0.623984566 0.042046773 4.89312017 0.420328899 0.413612466 0.100656742 0.847682551 0.071766756 -0.313178851 EFPDVLECTVSHAVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EFPDVLECTVSHAVEK 16 0 P48507 P48507 GCLM Glutamate--cysteine ligase regulatory subunit 0 ;;; 211.7 6.41E-12 329738000 750460 635930 717860 656150 760070 595350 867520 695260 1036130 FALSE TRUE 703490.0482 683014.9189 734887.9782 672987.9199 700377.1682 767217.8803 737443.4297 782064.7415 863193.2093 0.814985615 0.791265399 0.851359777 0.779649229 0.811379377 0.888813619 0.85432024 0.906013547 1 19.71932399 0.950513763 0.567227385 1.003605205 0.807485798 0.846095554 0.025500712 0.344413174 0.265321202 0.026573315 0.011691406 8.923058965 -0.950513763 -0.196119407 EFPGFLENQKDPLAVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFPGFLENQKDPLAVDK 17 1 P60903 P60903 S100A10 Protein S100-A10 0 84.653 0.0047432 0 28173 18127 22639 21285 31074 15229 27328 22976 45948 FALSE TRUE 26409.70222 19469.14194 23176.00777 21831.20914 28633.57339 19625.36508 23230.4201 25844.60418 38278.98196 0.689926975 0.508611801 0.605449951 0.570318436 0.748023378 0.512692973 0.606871419 0.675164355 1 15.22426484 0.751544346 2.335462594 0.999878434 0.595712548 0.740829914 0.072568357 0.515369374 4.107930751 0.06344142 0.017126362 5.643445636 -0.751544346 -0.404165887 EFQQNNWHAVGCGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EFQQNNWHAVGCGFR 15 0 Q9NZL9;Q9NZL9-2;Q9NZL9-3;Q9NZL9-4;E5RJR3;Q9NZL9-5 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 0 ; 149.22 3.40E-06 314530000 215340 249260 229180 243920 257230 201017 240090 216470 265400 FALSE TRUE 201862.2538 267715.4698 234616.2578 250179.4002 237028.1934 259047.3447 204090.7334 243496.756 221103.0255 0.912978252 1.210817759 1.061117356 1.131506001 1.072026007 1.171613749 0.923057172 1.101281882 1 17.75435924 1.74332533 25 1.004338036 1.103827947 0.160923925 0.089498907 1.267257791 6677.460595 0.036653024 0.020325877 55.37647794 -1.74332533 0.099489911 EFRPEDQPWLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EFRPEDQPWLLR 12 1 P35269;M0QXD6;M0R0R9;M0R0Z3 P35269 GTF2F1 General transcription factor IIF subunit 1 0 ;;; 227.06 1.26E-11 762660000 615790 750908 704451 706032 799265 619646 826772 695394 833253 FALSE TRUE 577248.8031 806506.0096 721160.9104 724149.9764 736493.951 798527.7411 702805.214 782215.4717 694177.6913 0.831557698 1.161814936 1.038870767 1.043176676 1.06095883 1.150321814 1.012428407 1.12682312 1 19.40494548 4.751324246 24.95012635 1.076003383 0.831557539 0.651777286 0.055748002 1213.264347 2371625.162 0.012115498 0.223463473 56405.8627 -4.751324246 -0.244445844 EFSDIFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EFSDIFR 7 0 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 ;;;;; 133.47 0.0076042 427403000 1117740 1442104 1214460 1151371 1338705 1035001 1291272 1325782 1106116 FALSE TRUE 1047782.649 1548878.881 1243267.565 1180917.129 1233568.509 1333788.987 1097657.751 1491308.801 921498.0938 1.137042665 1.680827004 1.349180832 1.281518798 1.338655519 1.447413723 1.1911666 1.618352562 1 19.81362166 -2.200371439 2.04831589 5.53E-05 1.388658571 0.330691602 0.169779407 4124984.465 734816.5532 19116313.85 0.040718209 0.006304179 2.200371439 1.388603286 EFSEENVLFWLACEDFKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFSEENVLFWLACEDFKK 18 1 O43665;O43665-2;O43665-1 O43665 RGS10 Regulator of G-protein signaling 10 0 104.61 0.00080459 10571000 18727 19418 19684 20808 20305 18129 19702 14831 20202 FALSE TRUE 17554.9105 20855.72892 20150.91378 21341.96851 18710.32721 23362.548 16747.868 16682.683 16830.15569 1.04306287 1.239188116 1.197310004 1.26807909 1.111714446 1.388136178 0.9951107 0.991237592 1 14.0387609 1.61527385 10.21464475 0.993110964 1.208549839 0.550332187 0.090504561 0.061323534 19.91990376 0.039820218 0.020296555 41.23574541 -1.61527385 0.215438875 EFSGGWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFSGGWR 7 0 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 77.741 0.086604 170660000 353080 421020 410100 374660 421390 345720 474020 363570 441700 FALSE TRUE 330981.3531 452192.7589 419827.7657 384274.4099 388295.7292 445523.7517 402945.1016 408962.5148 367977.4165 0.899461049 1.228860084 1.140906335 1.044288026 1.055216195 1.210736669 1.095026715 1.111379385 1 18.4892577 0.446780895 2.205739949 1.000005438 1.114986028 0.075124151 0.093225948 17.79662857 68.09656746 0.082921677 0.022478462 2.797569568 -0.446780895 0.11498059 EFSHIAFLTIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFSHIAFLTIK 11 0 X6R5C5;X6R8A1;P10619-2;P10619 X6R5C5 CTSA Carboxypeptidase;Lysosomal protective protein;Lysosomal protective protein 32 kDa chain;Lysosomal protective protein 20 kDa chain 0 121.08 0.00041914 147070000 186400 242540 175770 174030 308310 144010 201310 250660 307360 FALSE TRUE 174733.5567 260497.914 179939.3474 178495.9044 284096.5763 185583.3492 171125.4344 281955.4528 256059.6304 0.682394005 1.017333008 0.702724389 0.697087253 1.109493815 0.724766137 0.668303059 1.101131999 1 17.96612029 1.225119657 24.99781841 1.050566153 0.808208184 0.320683708 0.151092347 322.5057281 599786.2142 0.135950881 0.034764676 16.79266625 -1.225119657 -0.242357969 EFSITDVVPYPISLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFSITDVVPYPISLR 15 0 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 174.42 2.13E-06 37094000 133890 164160 175070 153610 190180 138840 167770 156050 171630 FALSE TRUE 125510.0639 176314.5772 179222.7431 157551.8927 175244.0299 178920.8541 142614.446 175533.186 142983.8442 0.877791925 1.233108385 1.253447507 1.101885975 1.225621194 1.251336157 0.997416504 1.227643493 1 17.12549262 -1.151085723 3.797219574 0.999907777 1.157290938 0.113447361 0.124813916 4.484002989 29684641.52 5455.072794 0.027456804 0.070617815 1.151085723 0.157383161 EFTELLSQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EFTELLSQDR 10 0 Q92754;Q92754-2 Q92754 TFAP2C Transcription factor AP-2 gamma 0 ;;;; 249.69 1.12E-12 452700000 479019 585583 503900 502836 584098 404539 527198 473501 600810 FALSE TRUE 449038.0559 628940.1746 515852.746 515739.6231 538225.2992 521322.8422 448149.5542 532618.6422 500530.9296 0.897123493 1.256546074 1.030611128 1.030385122 1.075308772 1.041539716 0.895348374 1.064107352 1 18.9330997 2.597238554 0.963953689 0.978953971 1.099411433 0.02417451 0.099500958 0.9129699 1.750298482 0.05809052 0.046613771 395.5838513 -2.597238554 0.120457462 EFTGS(ph)PPSSATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EFTGSPPSSATK 12 0 Q92609;Q92609-2;C9J3F6 Q92609 TBC1D5 TBC1 domain family member 5 1 EFTGS(0.959)PPS(0.04)S(0.001)ATK;EFTGS(0.949)PPS(0.049)S(0.003)ATK;EFTGS(0.921)PPS(0.07)S(0.008)ATK;EFTGS(0.993)PPS(0.006)SATK 203.74 1.27E-07 775920000 2464820 2230250 2216520 2697800 2523940 1588690 2444900 1735860 1348580 TRUE FALSE 2310551.316 2395380.031 2269096.901 2767030.115 2325719.933 2047319.013 2078309.942 1952585.942 1123493.286 2.05657777 2.132082195 2.019679984 2.462880865 2.070079067 1.822279704 1.849864141 1.7379596 1 20.09956007 0.746476832 0.622821008 0.985205471 2.145876614 0.860667818 0.140933629 0.401346999 0.323460524 0.152916659 0.05880871 5.577978451 -0.746476832 1.160671143 EFTGS(ph)PPSSATKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EFTGSPPSSATKK 13 1 Q92609;Q92609-2;C9J3F6 Q92609 TBC1D5 TBC1 domain family member 5 1 EFT(0.189)GS(0.81)PPS(0.001)SATKK;EFT(0.121)GS(0.875)PPS(0.001)S(0.001)AT(0.002)KK 54.501 0.083822 688670000 550600 454880 415020 571890 579640 280900 582160 377360 475480 TRUE FALSE 516138.9288 488559.7885 424864.4704 586565.6656 534117.4126 361991.27 494870.5125 424474.2267 396119.3163 1.302988538 1.233365222 1.072566908 1.480780264 1.348375074 0.913844024 1.249296594 1.071581741 1 18.59557553 1.457508234 0.807992012 1.016261299 1.243908794 0.260953509 0.148298459 0.925763291 1.271065013 0.136126939 0.05530802 28.67531744 -1.457508234 0.227647494 EFTMAEIEHFVDPSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EFTMAEIEHFVDPSEK 16 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 101.39 0.0017326 27287100 118891 109898 82222 75628 109807 75638 112577 115305 90062 FALSE TRUE 111449.8245 118034.9623 84172.34467 77568.74252 101183.2012 97473.46272 95697.12396 129701.0831 75030.07038 1.485402106 1.573168753 1.121848137 1.033835396 1.348568656 1.2991253 1.275450276 1.72865469 1 16.19518129 4.08077205 4.598164701 1.265036286 1.525989593 0.233812578 0.203243056 0.308591846 10.76199183 0.048297719 0.109362088 12044.03614 -4.08077205 0.260953307 EFTMAEIEHFVDPSEKDHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EFTMAEIEHFVDPSEKDHPK 20 1 P41250 P41250 GARS Glycine--tRNA ligase 0 ;;; 258.95 1.83E-36 580427000 1301210 731830 913590 845980 912520 682390 1169360 792590 920530 FALSE TRUE 1219769.589 786015.4547 935260.7862 867689.279 840854.3601 879384.9153 994025.3238 891546.6062 766887.5961 1.590545466 1.024942193 1.219553936 1.131442578 1.096450594 1.146693361 1.296181251 1.162551866 1 19.54865561 7.999999914 0.017324479 1.05E-07 2.645403683 0.207977883 0.148487725 9654.718013 12.90192771 760.1920021 1270.345966 99999980.27 -7.999999914 2.645403578 EFTNHWWNELFNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFTNHWWNELFNK 13 0 A0A0A0MRK1;E9PAV9;Q5T3I0;Q5T3I0-3;F8W895;E9PPY4;F2Z3C6;Q5T3I0-2 A0A0A0MRK1 GPATCH4 G patch domain-containing protein 4 0 172.1 2.40E-05 54658000 239880 254520 261090 226030 304410 201860 254520 262860 252550 FALSE TRUE 224866.339 273364.9256 267283.1781 231830.3125 280502.8665 260133.7051 216357.0888 295678.6496 210397.7735 1.068767674 1.299276704 1.270370754 1.101866758 1.333202638 1.236390009 1.028324042 1.405331648 1 17.68275991 -2.082326656 2.631166648 0.643200916 1.216666599 0.245384853 0.120091976 47022537.27 40097391.16 98942628.73 0.02709347 0.008273197 2.082326656 0.573465683 EFVEAVLELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EFVEAVLELR 10 0 O75367-2;O75367-3;O75367;B4DJC3 O75367-2 H2AFY Core histone macro-H2A.1;Histone H2A 0 ;;; 114.86 0.0030238 116194000 180933 208901 179406 162197 233211 135028 212236 201300 269022 FALSE TRUE 169608.7265 224368.2474 183661.595 166359.2496 214895.5488 174008.3916 180413.1821 226432.7481 224120.4903 0.756774743 1.001105464 0.819477036 0.742275949 0.958839366 0.776405546 0.804982989 1.01031703 1 17.77391503 1.23017142 24.8623858 1.005158661 0.847329027 0.406856729 0.083646259 200.1371358 593105.814 0.073357554 0.019555716 16.98914096 -1.23017142 -0.157829634 EFVISDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EFVISDR 7 0 Q14019;H3BT58 Q14019 COTL1 Coactosin-like protein 0 ;;; 165.11 0.0027282 637576000 1315780 1474940 1525290 1589360 1563020 1272710 1684110 1357910 1342170 FALSE TRUE 1233427.679 1584146.092 1561470.599 1630145.668 1440266.714 1640120.716 1431593.34 1527448.053 1118153.156 1.103093679 1.416752333 1.396472916 1.457891219 1.28807642 1.466812223 1.280319545 1.366045469 1 20.09268638 -0.232654513 0.87073628 0.989567925 1.363498438 0.502333742 0.107432332 8.391869585 5.022947133 0.402574668 0.03088575 0.585255477 0.232654513 0.373930513 EFVISDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EFVISDRK 8 1 Q14019;H3BT58 Q14019 COTL1 Coactosin-like protein 0 ; 104.2 0.0074175 263540000 191142 255640 211614 239650 296670 161465 241180 250000 332670 FALSE TRUE 179178.7634 274567.8516 216633.584 245799.8247 273370.7349 208077.3243 205017.298 281213.0503 277145.2279 0.646515781 0.990700268 0.781660885 0.886898997 0.986380812 0.750788047 0.739746809 1.014677584 1 18.08028264 1.218285513 24.99259498 1.007339066 0.836695013 0.324505684 0.10787209 341.1725259 420543.4717 0.098265691 0.024687536 16.53048186 -1.218285513 -0.170644053 EFVSIS(ph)SPAHVAT ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFVSISSPAHVAT 13 0 P22681;A0A0U1RR39 P22681 CBL E3 ubiquitin-protein ligase CBL 1 EFVS(0.302)IS(0.396)S(0.302)PAHVAT 88.187 0.0084167 51621000 65090 83454 90894 83769 97822 80828 95222 82606 108180 TRUE FALSE 61016.13309 89633.02099 93050.0486 85918.65436 90139.45471 104161.7315 80944.3451 92919.54094 90124.05913 0.677023801 0.994551531 1.032466242 0.953337601 1.000170827 1.155759433 0.89814358 1.031018152 1 16.45962467 4.73868123 5.401606941 1.007120207 0.664223737 0.718898093 0.065127786 0.076550607 8.32128124 0.014347655 0.097348776 54787.46801 -4.73868123 -0.34289647 EFWEIVHSFTDEQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EFWEIVHSFTDEQKR 15 1 A0A1B0GVL3;Q05086-2;Q05086-3;Q05086;A0A0D9SG63;S4R306 A0A1B0GVL3 UBE3A Ubiquitin-protein ligase E3A 0 ; 202.13 3.94E-09 116582000 606290 536130 598850 613230 651830 462378 724470 530551 676670 FALSE TRUE 568343.3912 575825.623 613055.0048 628966.52 600637.9012 595859.0225 615842.4491 596791.4602 563729.4055 1.008184752 1.021457489 1.087498716 1.115724164 1.065472007 1.056994751 1.092443366 1.058648803 1 19.1046433 4.167489177 2.700704294 1.074044304 1.011302007 0.334563765 0.030522079 0.257186418 3.665014879 0.007119717 0.020849517 14705.81767 -4.167489177 -0.062742297 EFYHEVHRPSHFLNFALLQEGEVYSADREDLYA ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFYHEVHRPSHFLNFALLQEGEVYSADREDLYA 33 2 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 133.56 1.40E-08 43946000 37301 56958 38950 37018 66490 35423 47972 53317 35915 FALSE TRUE 34966.39699 61175.22958 39873.91239 37967.94455 61268.14361 45649.04506 40779.04395 59973.74482 29920.55448 1.168641344 2.044588767 1.332659541 1.268958588 2.047694124 1.525675104 1.362910703 2.004432934 1 14.86884929 -1.205094163 4.403462091 0.999818961 1.594746399 0.240806008 0.33170841 0.00055561 0.000100298 0.291589634 0.068706884 0.062359961 1.205094163 0.594927438 EFYILWTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EFYILWTK 8 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 98.392 0.017576 105200000 368110 457720 436180 418050 581470 363200 488480 513830 507560 FALSE TRUE 345070.6522 491610.0651 446526.3956 428777.8708 535803.6917 468049.9439 415236.9588 577982.8066 422844.957 0.816068979 1.162624874 1.056005016 1.014030944 1.267139841 1.106906766 0.982007594 1.366890623 1 18.68976925 4.74486746 24.64536 1.110489169 0.816068818 0.377239945 0.122020124 618.0217858 2414973.493 0.026283268 0.244457158 55573.46296 -4.74486746 -0.294420351 EGAAHAFAQYNMDQFTPVKIEGYEDQVLITEHGDLGNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGAAHAFAQYNMDQFTPVKIEGYEDQVLITEHGDLGNSR 39 1 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 302.54 4.23E-93 78701000 47058 51498 52540 58532 69886 38558 66230 45682 93203 FALSE TRUE 44112.72378 55310.9655 53786.27361 60034.03021 64397.43547 49689.06866 56299.42635 51385.49826 77646.81719 0.56812018 0.712340409 0.692704164 0.773167947 0.829363492 0.639936967 0.725070626 0.661784992 1 16.24463917 -2.130681545 2.410554655 1.608340183 0.70549204 0.635855911 0.071177962 5231804.484 1434140.388 17411231.15 0.016096062 0.007401478 2.130681545 -0.902848143 EGADEEEWVVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGADEEEWVVAK 12 0 Q9H223 Q9H223 EHD4 EH domain-containing protein 4 0 101.95 0.002754 0 40022 55401 54948 55677 61591 49876 54978 52128 60677 FALSE TRUE 37517.09446 59502.94768 56251.39251 57105.76608 56753.89131 64274.39153 46734.55929 58636.29555 50549.61671 0.742183559 1.177119661 1.112795629 1.129697311 1.122736333 1.271510957 0.92452846 1.159975077 1 15.62541253 -1.813705381 7.347587183 0.99612368 1.090622446 0.023815306 0.147971047 0.008717515 0.000221028 0.132926743 0.030173834 0.015356584 1.813705381 0.094498766 EGADMLMVKPGMPYLDIVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGADMLMVKPGMPYLDIVR 19 1 P13716;P13716-2 P13716 ALAD Delta-aminolevulinic acid dehydratase 0 118.52 7.07E-05 132300000 124320 126410 146140 131830 154480 99199 143850 136270 176600 FALSE TRUE 116539.0331 135769.5279 149606.5098 135212.981 142347.7639 127836.1409 122281.0279 153283.6095 147124.3191 0.792112642 0.922821793 1.016871383 0.919038958 0.967533884 0.868898777 0.831140825 1.041864529 1 17.16667621 -4.957883474 0.008883763 1.876268422 0.111686839 0.144826175 0.074905688 59676.01512 40.53466511 4596.542023 3521.318866 1.10E-05 4.957883474 -1.764581583 EGAITFTWVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGAITFTWVER 11 0 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224;J3KPM9;A0A669KBI6;P42224-2;A0A669KB52 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta;Signal transducer and activator of transcription 0 87.298 0.032171 15166000 9961.7 13381 11210 8871.7 12964 11200 11557 10149 11602 FALSE TRUE 9338.214979 14371.74316 11475.90649 9099.362842 11945.85973 14433.25818 9824.13514 11416.12499 9665.551248 0.96613372 1.486903622 1.187299741 0.941422026 1.235921204 1.49326798 1.016407123 1.181114734 1 13.2386363 1.616555194 25 1.074068066 1.237239441 0.12441834 0.186088624 1.318938867 3784.106648 0.08526049 0.046358261 41.35758717 -1.616555194 0.163171375 EGALCEENMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 EGALCEENMR 10 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;;; 204.79 4.20E-07 6957290000 2439257 2774262 2648420 2559947 2788470 2395278 2944580 2384210 2936710 FALSE TRUE 2286588.259 2979671.245 2711241.773 2625639.574 2569474.814 3086755.875 2503067.565 2681883.867 2446554.129 0.934615847 1.217905302 1.108187937 1.073199053 1.050242373 1.261674875 1.023099197 1.096188241 1 21.22231977 0.960320551 1.371494094 1.0037914 1.113924723 0.076774617 0.093135547 0.99110704 3.786457847 0.079822643 0.024011769 9.126842394 -0.960320551 0.110133323 EGAPIEPDPPVSHWKPEAVQYYEDGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGAPIEPDPPVSHWKPEAVQYYEDGAR 27 1 Q96HS1;Q96HS1-2;F5GXG4 Q96HS1 PGAM5 "Serine/threonine-protein phosphatase PGAM5, mitochondrial" 0 ; 73.676 0.010835 315270000 379090 345040 363250 351680 449490 273280 395830 355170 514810 FALSE TRUE 355363.4336 370587.1206 371866.4615 360704.7042 414188.8686 352171.4997 336478.9662 399513.7563 428884.8852 0.828575326 0.864071301 0.867054248 0.841029182 0.965734356 0.821132924 0.784543773 0.931517454 1 18.71023095 1.006817129 7.983380635 0.999984743 0.854027588 0.53103002 0.04652285 0.083496949 42.03324044 0.044864775 0.011236146 10.15820866 -1.006817129 -0.145957155 EGASGRPGS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGASGRPGSPK 11 1 E7EMV7;A0A0A0MRZ4;Q15025-7;Q15025-8;Q15025-5;Q15025-6;Q15025-4;Q15025-3;Q15025-2;Q15025;E7EW15 E7EMV7 TNIP1 TNFAIP3-interacting protein 1 1 EGAS(0.006)GRPGS(0.994)PK;EGAS(0.001)GRPGS(0.999)PK 123.28 0.00098213 474457000 1020220 633120 773417 766995 750017 569813 995210 632979 992314 TRUE FALSE 956366.2513 679996.8636 791762.8165 786677.3902 691113.6902 734308.763 845987.4996 712007.8215 826690.3828 1.15686147 0.822553253 0.957750124 0.951598575 0.836000641 0.888251246 1.023342617 0.861275075 1 19.65698758 -0.506002325 5.897661051 1.000000023 0.930891923 0.034880619 0.098975783 0 0 0.085538717 0.020161669 0.311887289 0.506002325 -0.0691081 EGATVYATGTHAQVEDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGATVYATGTHAQVEDGR 18 0 J3QKT4;J3KQ22;E2QRB3;P32322-2;P32322;P32322-3;J3QR88;J3QLK9;J3QL23;J3QL32;J3QL24 J3QKT4 PYCR1 "Pyrroline-5-carboxylate reductase;Pyrroline-5-carboxylate reductase 1, mitochondrial" 0 220.1 6.97E-19 677900000 323650 352340 355600 303940 504840 280480 288590 342600 449070 FALSE TRUE 303393.3242 378427.6202 364034.9999 311739.615 465191.9028 361450.0228 245318.6086 385374.3642 374117.3159 0.810957717 1.011521264 0.973050389 0.833267004 1.243438577 0.966140853 0.655726421 1.030089621 1 18.51313122 EGDFVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGDFVLR 7 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 131.3 0.0080945 132857000 338380 322450 334710 335960 302380 295770 387160 301630 311840 FALSE TRUE 317201.3998 346324.5335 342649.4793 344581.3024 278632.2945 381153.9976 329108.9522 339289.1695 259791.8894 1.220982689 1.333084471 1.318938324 1.326374365 1.072521144 1.467151259 1.266817655 1.306003702 1 17.98699687 -1.076359443 5.057383336 0.999993942 1.296065437 0.454410348 0.099245061 6.24E-06 1.14E-06 0.084858793 0.020000983 0.08387655 1.076359443 0.296071496 EGDIIPPLTGAT(ph)PPLIGHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGDIIPPLTGATPPLIGHLK 20 0 Q12888;Q12888-2;A6NNK5;Q12888-3;H7C3N7 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 EGDIIPPLTGAT(1)PPLIGHLK;EGDIIPPLTGAT(1)PPLIGHLK 183.86 1.55E-16 155697000 337270 253400 299730 282630 317050 267080 429260 297260 433840 TRUE FALSE 316160.8727 272161.9997 306839.7371 289882.7643 292150.1719 344181.6603 364896.4481 334373.5653 361429.3013 0.874751636 0.75301587 0.848961985 0.802045554 0.808319001 0.952279351 1.009592877 0.925142384 1 18.46335395 2.191651018 4.578090691 0.979171936 0.811742226 0.798931358 0.038533449 0.076532357 3.443542036 0.013504975 0.010018643 155.471582 -2.191651018 -0.16742971 EGDIVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGDIVKR 7 1 P25705;P25705-2;P25705-3;K7EK77;K7ERX7;K7EJP1;K7EQH4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 87.284 0.031195 1029600000 981250 859080 866310 780860 1132000 753760 927860 842960 1779100 FALSE TRUE 919835.3141 922687.1771 886859.2823 800898.1896 1043097.286 971358.2757 788736.0068 948205.4116 1482156.717 0.620605975 0.622530105 0.598357294 0.540359991 0.703769901 0.65536813 0.532154257 0.639747067 1 20.49926657 0.955117392 23.57029213 1.000000001 0.608218057 0.857037181 0.04966469 2030.815618 1066492.675 0.04619628 0.01154907 9.018148701 -0.955117392 -0.391781944 EGDKHTLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EGDKHTLSK 9 1 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;;;; 121.83 0.00036223 55650710000 59008350 62753850 57593030 68578800 73161900 41605590 73966250 45927320 102794200 FALSE TRUE 55315122.71 67400210.35 58959163.87 70338648.11 67416059.49 53616448.42 62875697.48 51661447 85637183.94 0.64592412 0.78704375 0.68847621 0.821356388 0.787228823 0.626088411 0.734210241 0.603259526 1 26.35173402 -1.098105472 4.327115368 1.000033472 0.719182381 0.603159862 0.073268976 24589347944 5125075055 8983559.691 0.015775741 0.079780091 1.098105472 -0.280851091 EGDKHTLSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGDKHTLSKK 10 2 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ; 110.66 0.0011149 5570020000 3861220 5487810 5003570 6228360 7853900 4840540 6342320 2925260 11199900 FALSE TRUE 3619553.133 5894133.162 5122257.043 6388190.262 7237086.375 6237925.318 5391347.995 3290485.15 9330564.336 0.387924353 0.63170168 0.548976124 0.684652078 0.775632225 0.668547485 0.577815853 0.352656606 1 23.15353291 5.114847523 1.711402707 0.637404854 3.04E-15 0.19317621 0.16594935 5.510241276 6.7966196 0.039008379 7.887806232 130270.9328 -5.114847523 -0.637404854 EGDLIAAQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGDLIAAQAR 10 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 169.44 1.08E-05 716640000 843570 1010920 877220 877410 1034440 733950 928050 881100 1039860 FALSE TRUE 790772.4595 1085769.569 898028.0727 899925.8261 953199.2551 945829.4503 788897.5181 991107.2745 866300.6482 0.912815269 1.253340363 1.036624034 1.038814675 1.100309987 1.091802773 0.910650961 1.14406849 1 19.72450827 2.478791826 0.884039717 1.013966371 1.101452629 0 0.103903087 1.45220576 2.284162317 0.068252801 0.049106241 301.1562119 -2.478791826 0.087486257 EGDLPPLWWYIVTRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGDLPPLWWYIVTRPR 16 1 E9PH64;Q9Y6M9 E9PH64 NDUFB9 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 0 ; 179.97 2.32E-09 217890000 351770 355130 358180 299790 475920 369140 360120 378500 568380 FALSE TRUE 329753.3436 381424.1947 366676.1987 307483.1189 438543.163 475704.7255 306123.3492 425756.5582 473513.7061 0.696396618 0.805518805 0.774372936 0.64936477 0.926146714 1.004627151 0.646493111 0.899143051 1 18.85304666 2.725745097 24.66596116 0.864022418 0.75092414 0.33134266 0.109285291 1070.881264 2061116.523 0.035275797 0.033455024 531.7960371 -2.725745097 -0.113098278 EGDNVNYDWIHWDPEHSYEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGDNVNYDWIHWDPEHSYEFK 21 0 Q04446;E9PGM4 Q04446 GBE1 "1,4-alpha-glucan-branching enzyme" 0 ; 287.93 4.18E-46 262100000 278130 264910 298960 300470 311290 209523 383490 270780 359330 FALSE TRUE 260722.3398 284524.212 306051.4724 308180.5689 286842.5391 270008.8888 325989.2346 304587.4791 299355.5016 0.870945543 0.950455931 1.022367956 1.029480224 0.958200325 0.901967351 1.088970247 1.017477472 1 18.19150026 4.668509216 1.600753076 1.004458921 0.833533601 0.435015762 0.048330206 0.879265718 2.411614997 0.013015247 0.224856122 46613.23191 -4.668509216 -0.17092532 EGDPAIYAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGDPAIYAER 10 0 Q9UGI8-2;Q9UGI8;H7BYK1 Q9UGI8-2 TES Testin 0 83.168 0.036818 648610000 454000 437060 458620 417360 452260 396060 526720 377990 494470 FALSE TRUE 425584.9504 469420.3772 469498.683 428070.1642 416741.3239 510396.0925 447743.2258 425182.8836 411939.7626 1.033124231 1.139536456 1.139726546 1.039157185 1.011655979 1.239006619 1.086914317 1.032148198 1 18.65207386 1.199596377 3.760027293 1.006352172 1.108287372 0.211575512 0.065963007 0.302924636 8.005614441 0.057733621 0.015814052 15.83420915 -1.199596377 0.1019352 EGDPVSLSTPLETEFGSPSELS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EGDPVSLSTPLETEFGSPSELSPR 24 0 Q9BUR4;E9PMG4;E9PMR3 Q9BUR4 WRAP53 Telomerase Cajal body protein 1 1 EGDPVSLSTPLETEFGSPS(0.004)ELS(0.996)PR;EGDPVSLSTPLETEFGSPS(0.016)ELS(0.984)PR;EGDPVSLSTPLETEFGSPS(0.006)ELS(0.994)PR 199.31 1.07E-24 113114000 222528 220711 228104 204802 250241 205277 252999 209917 284068 TRUE FALSE 208600.3697 237052.6721 233514.7346 210057.566 230588.0813 264537.1375 215064.1487 236125.5995 236655.2157 0.881452662 1.001679475 0.98672972 0.887610127 0.974362981 1.117816638 0.908765725 0.997762077 1 17.85242719 2.472423831 24.95759879 0.999752207 0.954980824 0.180160934 0.062677064 309.4646472 1644176.288 0.02113598 0.01773932 296.77262 -2.472423831 -0.044771384 EGDQIVGATIYFDNLQSGEVTQLLNTMGHHTVGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGDQIVGATIYFDNLQSGEVTQLLNTMGHHTVGLK 35 0 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2;E9PQE3 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 302.58 9.20E-91 260273000 105555 107845 118233 108387 148392 109731 132186 118649 135283 FALSE TRUE 98948.50097 115829.956 121037.5426 111168.3939 136737.8909 141408.5584 112365.9365 133462.5888 112703.3933 0.87795494 1.027741513 1.073947634 0.986380185 1.213254427 1.254696546 0.997005797 1.184193172 1 16.78217143 5.941260763 0.638621356 1.112774457 1.30E-09 0.374484394 0.092667014 14.46327685 1.37150846 0.035957979 16.64947599 873495.6823 -5.941260763 -1.112774455 EGDVLTLLESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 EGDVLTLLESER 12 0 P62857 P62857 RPS28 40S ribosomal protein S28 0 ;;;;;;;;;; 307.09 3.60E-37 4968441000 2537910 2704594 2651805 2637643 2773510 2279153 2991815 2307526 2918628 FALSE TRUE 2379066.743 2904844.954 2714707.067 2705329.385 2555689.712 2937107.472 2543220.115 2595625.701 2431490.132 0.97843981 1.194676843 1.116478752 1.112621988 1.051079615 1.207945463 1.045951239 1.067504107 1 21.21340931 1.227951574 1.693211385 1.008756681 1.117632645 0.1810679 0.06775348 0.468311122 2.442628795 0.056898742 0.016918273 16.90252449 -1.227951574 0.108875964 EGDVTSGMVKDPPDVLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGDVTSGMVKDPPDVLDR 18 1 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 71.114 0.021942 236840000 187980 158790 176630 171370 189350 152000 215510 169580 292200 FALSE TRUE 176214.6674 170546.9768 180819.747 175767.6443 174479.2148 195879.9325 183196.2762 190752.4363 243429.9323 0.723882497 0.700599861 0.742799972 0.722046146 0.716753331 0.804666586 0.752562655 0.783603045 1 17.89314705 -5 0.197645483 2.187875297 0.696165041 0.936198112 0.021855013 28.94038245 0.285834951 13.50636129 0.049227287 1.00E-05 5 -1.491710256 EGDYVLFHHEGGVDVGDVDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EGDYVLFHHEGGVDVGDVDAK 21 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ;;;;; 208.13 1.90E-22 3543244500 7263387.1 4755120.7 5893126.3 5747942.9 6033516.2 4341701.6 7195818 5095445.4 7268049.4 FALSE TRUE 6808784.667 5107194.784 6032914.039 5895444.846 5559668.176 5595080.37 6116871.894 5731622.975 6054965.002 1.124496123 0.843472222 0.996358201 0.973654653 0.918199886 0.924048342 1.010224154 0.946598861 1 22.52968719 1.735912019 24.99999788 0.984785654 0.952001091 0.004358537 0.073204572 1.204027374 11166.18413 0.030938015 0.017156741 54.43923561 -1.735912019 -0.032784563 EGEDGDQPTT(ph)PPKPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EGEDGDQPTTPPKPLK 16 1 P18858;P18858-3;P18858-2;M0R0Q7;B4E135 P18858 LIG1 DNA ligase 1;DNA ligase 1 EGEDGDQPT(0.165)T(0.835)PPKPLK;EGEDGDQPT(0.162)T(0.838)PPKPLK;EGEDGDQPT(0.137)T(0.863)PPKPLK 80.238 0.026067 1713290000 2335670 867340 1346020 1172010 1057720 967910 1877630 1014130 1086840 TRUE FALSE 2189484.584 931558.7561 1377948.23 1202085.761 974650.9378 1247329.904 1596096.813 1140746.363 905439.3827 2.418145958 1.028847181 1.521855859 1.327626988 1.076439745 1.377596257 1.762787043 1.259881539 1 19.78825853 4.748981832 24.77614722 1.340170428 2.418146641 0.68784526 0.236128688 825.8636591 1963423.689 0.056734981 0.802629431 56102.45057 -4.748981832 1.077976213 EGEELVMDEEAYVLYHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGEELVMDEEAYVLYHR 17 0 Q9BQ67 Q9BQ67 GRWD1 Glutamate-rich WD repeat-containing protein 1 0 ; 196.95 1.55E-11 56573000 116700 94963 106701 101820 105706 89037 118324 92656 118554 FALSE TRUE 109395.9553 101994.1593 109231.9981 104432.8736 97404.27716 114740.5365 100582.4147 104224.3056 98766.57151 1.107621269 1.03267895 1.105961222 1.057370647 0.986206929 1.16173453 1.0183852 1.05525892 1 16.59173521 0.932667936 1.330654034 1.00151377 1.068757688 0.16188084 0.049450404 0.917107547 3.268216973 0.04164145 0.012593402 8.563827992 -0.932667936 0.067243918 EGEEPTKGNS(ph)GSEACTSSFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGEEPTKGNSGSEACTSSFLR 21 1 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2 H3BSS6 ZNF106 Zinc finger protein 106 1 EGEEPTKGNS(0.999)GS(0.001)EACTSSFLR;EGEEPTKGNS(0.997)GS(0.003)EACTSSFLR 181.77 2.98E-17 251670000 265800 140563 182740 179686 173036 133212 242990 138326 180985 TRUE FALSE 249164.0525 150970.4308 187074.6791 184297.047 159446.4506 171668.1419 206555.9053 155596.3056 150777.4343 1.652528799 1.001280009 1.240733933 1.222311865 1.057495449 1.138553277 1.369939118 1.031960162 1 17.202061 7.999995623 0.021072911 3.18E-08 2.735738947 0.21418895 0.178964035 6298.885578 10.22340114 483.9933303 903.5250336 99998992.24 -7.999995623 2.735738915 EGEEPTVYS(ph)DEEEPKDESAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 EGEEPTVYSDEEEPKDESAR 20 1 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 1 EGEEPTVYS(1)DEEEPKDESAR;EGEEPTVYS(1)DEEEPKDESAR;EGEEPTVYS(1)DEEEPKDESAR;EGEEPTVYS(1)DEEEPKDESAR;EGEEPTVYS(1)DEEEPKDESAR;EGEEPTVYS(1)DEEEPKDESAR;EGEEPTVYS(1)DEEEPKDESAR 313.51 1.45E-66 24629470000 14638020 6010530 7009800 6526690 7806370 5224020 10234360 6948540 7445700 TRUE FALSE 13721852.46 6455555.895 7176075.766 6694175.915 7193289.19 6732109.769 8699812.729 7816080.515 6202964.569 2.212144259 1.040721065 1.156878407 1.079189771 1.159653438 1.085305211 1.402524975 1.260055644 1 22.56452645 4.742559521 24.99243319 1.161122825 2.212144668 0.892551593 0.11595086 129.1692078 807253.0976 0.028976749 0.221419909 55278.91631 -4.742559521 1.051021843 EGENNKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGENNKPR 8 1 P45973;F8VNY3 P45973 CBX5 Chromobox protein homolog 5 0 ; 147.19 0.00049371 264340000 699640 488270 566950 569890 553700 408350 612170 519540 640530 FALSE TRUE 655850.7813 524422.0188 580398.3217 584514.3422 510214.6355 526234.016 520380.7916 584405.7126 533621.405 1.229056359 0.982760463 1.087659371 1.095372743 0.956136 0.986156123 0.975187252 1.095169173 1 19.02545701 2.749151023 24.86111579 0.997508219 1.077544798 0.296421293 0.070113078 931.1908747 2185979.917 0.020244995 0.021268371 561.2431108 -2.749151023 0.080036578 EGERPSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EGERPSLR 8 1 Q7L2H7;J3KNJ2;E9PN86;E7ESM3 Q7L2H7 EIF3M Eukaryotic translation initiation factor 3 subunit M 0 ;;; 142.04 0.00056892 3488800000 2641780 2559960 2815510 2735510 2896260 2454270 3214650 2558750 2895370 FALSE TRUE 2476435.706 2749502.102 2882295.227 2805707.818 2668799.423 3162777.907 2732643.076 2878215.57 2412114.042 1.026666095 1.13987235 1.19492494 1.163173784 1.10641511 1.311205794 1.132883035 1.19323362 1 21.20186669 4.753714292 2.431077421 1.168939408 0.990763733 0.202183717 0.078386623 0.768899992 5.443878346 0.016877576 0.291405642 56717.13593 -4.753714292 -0.178175675 EGEVLYIIEEDKGDGWTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EGEVLYIIEEDKGDGWTR 18 1 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 0 ;;; 180.83 6.99E-14 287622000 476574 317555 374398 367197 407867 268421 473511 318941 495558 FALSE TRUE 446746.084 341067.1026 383278.8974 376619.8967 375834.7711 345909.7852 402512.4214 358761.4859 412846.1684 1.082112705 0.82613605 0.928381869 0.912252373 0.910350634 0.837866042 0.974969498 0.868995557 1 18.65524479 -1.165061062 4.729269853 1.000009993 0.911210382 0.106215373 0.073005814 6.71E-06 1.18E-06 0.061674271 0.014535129 0.06838155 1.165061062 -0.088799611 EGGDGEEQDVGDAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGGDGEEQDVGDAGR 15 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 315.09 6.34E-56 759960000 774780 716280 769290 740290 766470 623230 873900 651350 894810 FALSE TRUE 726287.9028 769314.1165 787537.9221 759287.0947 706274.538 803146.3837 742866.8079 732672.4813 745460.4303 0.974280959 1.031998595 1.05644497 1.018547818 0.947433974 1.077382985 0.996520778 0.98284557 1 19.50777225 2.995420046 24.94638317 1.004295408 1.029503256 0.042054682 0.037852921 489.17809 2664513.709 0.010559958 0.012302176 989.509677 -2.995420046 0.025207849 EGGFLLLHTLLR ddPTM_SK-BR-3_Pertuzumab_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 4982446000 4727653 7794720 5134419 4639614 8360353 4392195 5784137 7879498 3027098 FALSE TRUE 4431757.638 8371849.179 5256209.843 4758674.35 7703764.599 5660150.395 4916859.354 8863270.67 2521855.788 1.757339836 3.319717654 2.084262656 1.886973225 3.054799817 2.244438569 1.94969886 3.514582679 1 21.26605435 -1.10800524 4.898161788 0.999937276 2.467501635 0.358010927 0.621258757 0.000387678 7.06E-05 0.548009773 0.129161689 0.07798207 1.10800524 1.467564359 EGGLGPLNIPLLADVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGGLGPLNIPLLADVTR 17 0 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 83.823 0.010846 0 52722 41568 84347 99907 51352 52827 59593 33687 104340 FALSE TRUE 49422.22413 44645.73797 86347.75067 102470.7828 47319.02106 68077.29733 50657.58288 37892.8961 86924.97994 0.568561812 0.51361229 0.993359455 1.178841604 0.544366201 0.783173 0.582773593 0.435926429 1 16.40748321 EGHALGGGMEADGPASLQELPPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EGHALGGGMEADGPASLQELPPSPR 25 0 Q6ZVX7 Q6ZVX7 NCCRP1 F-box only protein 50 1 EGHALGGGMEADGPASLQELPPS(1)PR;EGHALGGGMEADGPASLQELPPS(1)PR;EGHALGGGMEADGPASLQELPPS(1)PR;EGHALGGGMEADGPASLQELPPS(1)PR 202.03 1.97E-24 1364650000 607910 615410 675140 629330 625850 641660 773240 626480 582910 TRUE FALSE 569861.9983 660975.5967 691154.6396 645479.6733 576698.2656 826896.8255 657299.8404 704697.4071 485618.5553 1.173476573 1.361100373 1.423245945 1.329190712 1.187554016 1.702770243 1.353531148 1.45113361 1 18.88946402 -0.949804904 6.797387424 0.999999972 1.382049299 0.386785823 0.147086105 5.81E-08 8.54E-09 0.129922005 0.030622908 0.112252261 0.949804904 0.382049327 EGHDAFELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGHDAFELK 9 0 H3BRF9;Q96K21-2;Q96K21;Q96K21-4;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 0 ; 100.25 0.0047903 293770000 298250 261840 256040 253030 283210 210875 341410 254550 271010 FALSE TRUE 279583.0649 281226.906 262113.3897 259523.1782 260967.829 271751.1892 290218.74 286331.1278 225776.6802 1.238316839 1.245597667 1.160940933 1.149468483 1.155867066 1.203628244 1.285423896 1.268205058 1 17.78453696 1.992367504 24.37422766 1.223324077 1.190798023 0 0.084869259 1073.727983 3428917.722 0.030152059 0.021256851 98.25790583 -1.992367504 -0.032526055 EGHGS(ph)SSFDRELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGHGSSSFDRELER 14 1 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 EGHGS(0.392)S(0.278)S(0.33)FDRELER 77.468 0.01489 567750000 100740 173680 131450 175170 184560 105850 158690 145880 222900 TRUE FALSE 94434.86323 186539.4479 134568.0561 179665.1588 170065.4021 136407.1767 134895.9077 164093.4391 185696.55 0.508543983 1.004539115 0.724666431 0.967520176 0.915824242 0.734570333 0.726431954 0.883664447 1 17.50258749 -2.974339937 1.224136366 3.863549814 0.816277535 0.144432692 0.145527666 309547.8002 7331.209257 2451460.723 0.038214679 0.001060865 2.974339937 -3.047272279 EGHGSS(ph)SFDRELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGHGSSSFDRELER 14 1 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 EGHGS(0.208)S(0.66)S(0.132)FDRELER 90.379 0.0058273 0 75062 130290 96604 105130 132040 98481 117150 108680 156520 TRUE FALSE 70364.00341 139936.8072 98895.4925 107827.8138 121670.111 126910.866 99584.44507 122248.9372 130395.8008 0.53961863 1.073169583 0.758425439 0.826927041 0.933083046 0.973274179 0.763708988 0.93752204 1 16.99253789 -1.428088752 0.019796701 1.91648137 2.29E-06 0.161975745 0.140522911 3846.56361 12.60556699 696.7635699 530.9936746 0.037317389 1.428088752 -1.916479078 EGHGSSSFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGHGSSSFDR 10 0 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 0 78.342 0.025703 0 39103 75193 92309 80365 84298 92661 85937 77197 89155 FALSE TRUE 36655.61303 80760.36796 94498.61307 82427.30196 77677.57512 119410.7265 73051.54465 86835.21538 74274.45454 0.493515749 1.087323609 1.27228956 1.109766507 1.045818183 1.607695771 0.983535256 1.169112798 1 16.18057848 4.747947448 3.098134487 1.179087354 0.379376322 0.583179044 0.178099886 0.248611788 3.587678282 0.039184512 0.492381224 55968.98714 -4.747947448 -0.799711032 EGHILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EGHILK 6 0 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 0 ;;;;;;; 109.88 0.02918 2725465000 11920780 11095060 12037890 11497390 12755980 9467680 14265820 10949330 14381540 FALSE TRUE 11174679.66 11916549.79 12323434.44 11792432.49 11754176.79 12200845.52 12126792.73 12316377.95 11981168.07 0.932686997 0.99460668 1.028567029 0.984247314 0.981054328 1.018335229 1.012154463 1.027978064 1 23.51426523 4.733771329 2.926992988 1.008017082 0.92024534 0.68053965 0.015990798 0.23118131 2.889069918 0.003911441 0.047678624 54171.55839 -4.733771329 -0.087771742 EGHLSPDIVAEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EGHLSPDIVAEQK 13 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ;;; 189.3 5.38E-06 3732580000 5070800 8173600 8216500 8365000 8717800 7034600 10656900 7847600 9183200 FALSE TRUE 4753427.68 8778781.849 8411399.26 8579660.062 8033139.154 9065374.823 9058996.779 8827390.135 7650464.594 0.621325361 1.147483495 1.099462543 1.121456084 1.05001978 1.184944354 1.184110673 1.153837133 1 22.86711593 4.739950992 24.99937072 1.127249004 0.621325197 0.876888481 0.058348264 36.79106657 661448.8309 0.013126143 0.082485803 54947.88639 -4.739950992 -0.505923807 EGHPVTSEPSRPEPAVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGHPVTSEPSRPEPAVFK 18 1 Q16762 Q16762 TST Thiosulfate sulfurtransferase 0 114.99 0.00012155 239380000 368460 331790 339270 316260 450530 223340 331230 384260 420770 FALSE TRUE 345398.7463 356356.0768 347317.6446 324375.767 415147.1912 287814.6324 281565.1365 432235.7069 350540.7687 0.985331172 1.016589534 0.99080528 0.925358178 1.184305017 0.821058941 0.803230784 1.233054028 1 18.41922272 EGHPVYPQLRPGYIPIPVLHEGAENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGHPVYPQLRPGYIPIPVLHEGAENR 26 1 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 0 130.9 4.38E-05 109130000 90789 96030 94535 91452 100750 73019 103520 79188 96658 FALSE TRUE 85106.67855 103140.1611 96777.41484 93798.81315 92837.50141 94098.39994 87998.13703 89074.79611 80525.15537 1.056895552 1.280843988 1.201828353 1.164838649 1.152900618 1.168559061 1.09280307 1.106173539 1 16.29715192 1.289760718 0.575511966 1.001097086 1.20292863 0.460980343 0.057393234 0.564169608 0.466409156 0.054674559 0.02713964 19.48770595 -1.289760718 0.201831544 EGHSLEMENENLVENGADS(ph)DEDDNSFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EGHSLEMENENLVENGADSDEDDNSFLK 28 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK;EGHSLEMENENLVENGADS(1)DEDDNSFLK 443.94 5.73E-211 3330010000 1262388 938777 1118683 1006374 1078701 917775 1265822 1041081 1391527 TRUE FALSE 1183377.389 1008285.026 1145218.689 1032199.261 993984.1747 1182721.744 1076023.742 1171062.255 1159272.154 1.020793421 0.869756961 0.987877338 0.890385624 0.857420901 1.020227855 0.92818907 1.010170261 1 20.14478787 1.503579154 1.257970258 1.002274056 0.929375064 0.159641752 0.058301889 0.715648216 2.172854709 0.047567192 0.016356983 31.88446648 -1.503579154 -0.072898993 EGHSLEMENENLVENGADS(ph)DEDDNSFLKQQS(ph)PQEPK ddPTM_SK-BR-3_Pertuzumab_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(0.984)DEDDNS(0.016)FLKQQS(0.999)PQEPK 161.4 6.45E-17 138320000 35544 23849 24861 36545 44554 20761 34274 24699 71498 TRUE FALSE 33319.36449 25614.80477 25450.71466 37482.80657 41054.90856 26754.36367 29134.93188 27782.72452 59564.52191 0.559382724 0.43003459 0.427279761 0.629280742 0.689251038 0.449166094 0.489132305 0.466430748 1 15.86216566 -1.932664393 2.44089837 1.338513483 0.505748017 0.749698303 0.087383963 5861403.086 2886622.014 11302989.5 0.022130639 0.011677116 1.932664393 -0.832765466 EGIDPTPYYWYTDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EGIDPTPYYWYTDQR 15 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;; 225.23 2.39E-12 1194580000 337441 320745 353353 341103 335152 309578 356235 280846 367402 FALSE TRUE 316321.1702 344493.2935 361734.7 349856.2805 308830.5139 398948.143 302820.8689 315910.2413 306080.2327 1.033458343 1.125499973 1.181829669 1.14302148 1.008985491 1.303410349 0.989351276 1.03211579 1 18.22355035 1.609618955 25 1.008039858 1.134124921 0.352488559 0.080191663 0.177854755 2473.64812 0.035379892 0.018335829 40.70230037 -1.609618955 0.126085063 EGILPERAEEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 156.08 6.65E-05 511200000 1059880 1087640 983800 1103970 1318850 661160 1210790 905420 1840510 FALSE TRUE 993544.0027 1168169.997 1007136.201 1132299.739 1215272.841 852026.159 1029243.28 1018463.68 1533316.991 0.647970386 0.761858118 0.656834958 0.738464222 0.792577692 0.555675157 0.671252772 0.664222523 1 20.54822455 -2.168735289 2.366264507 1.782666722 0.687925923 0.687134765 0.066554312 3688502.781 773497.2161 15507101.45 0.01581531 0.006780547 2.168735289 -1.094740799 EGIPALDNFLDKL ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGIPALDNFLDKL 13 1 P13639 P13639 EEF2 Elongation factor 2 0 ; 174.68 0.00040098 345630000 688890 632090 671390 560050 717130 505460 774410 578710 772330 FALSE TRUE 645773.6046 678890.6013 687315.6879 574421.8312 660809.5026 651378.0965 658294.4098 650963.2174 643423.1336 1.003653072 1.055123084 1.068217246 0.892759059 1.027021672 1.012363502 1.023112747 1.011718702 1 19.29540828 EGIQWEAKEDNS(ph)EGEEILEEVGGDLEEEDDHHMEFCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EGIQWEAKEDNSEGEEILEEVGGDLEEEDDHHMEFCR 37 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 EGIQWEAKEDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EGIQWEAKEDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR;EGIQWEAKEDNS(1)EGEEILEEVGGDLEEEDDHHMEFCR 82.336 0.00059919 70018000 73917 36222 40247 30445.5 25235.3 20418.5 66922 49054 44511 TRUE FALSE 69290.66692 38903.91457 41201.67785 31226.78307 23253.42133 26312.98948 56887.66737 55178.49988 37081.82655 1.868588292 1.049136954 1.111101628 0.842104772 0.627084033 0.709592594 1.534111792 1.488020009 1 15.17842469 1.697532321 10.90789409 1.379796247 1.022258651 0.132096154 0.363866006 0.20582394 41.88862274 0.167796323 0.091194543 49.83475428 -1.697532321 -0.357537595 EGIREETVSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EGIREETVSLR 11 1 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ;;; 219.43 9.01E-12 4102060000 2296200 2658460 2262020 2244330 2744560 1847650 2465190 2209230 2625070 FALSE TRUE 2152484.941 2855295.145 2315676.183 2301923.307 2529013.329 2381036.561 2095557.645 2485057.229 2186928.858 0.984250097 1.305618669 1.058871291 1.05258262 1.156422313 1.088758124 0.958219394 1.136322848 1 21.06047486 2.678325403 0.616967607 1.022711619 1.160073529 0.065369466 0.097500225 1.355878036 1.088523571 0.07495492 0.07742642 476.7880948 -2.678325403 0.13736191 EGIVALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EGIVALR 7 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;;; 113.25 0.026723 665540000 867333 1143070 962900 1061180 1075470 1015210 1042000 961367 752894 FALSE TRUE 813048.1758 1227704.092 985740.4427 1088411.675 991006.9244 1308284.646 885761.7735 1081395.786 627231.1275 1.296249724 1.95733923 1.571574495 1.735264128 1.579970893 2.085809503 1.41217764 1.724078635 1 19.25863763 -0.043542117 0.861122455 0.986026019 1.698161975 0.44259818 0.234248545 5.606371907 3.841425205 0.457219022 0.066383262 0.904602707 0.043542117 0.712135957 EGIVALRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGIVALRR 8 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ; 114.5 0.0042406 259230000 228751 483380 275788 291901 529570 264881 315093 359190 513640 FALSE TRUE 214433.8832 519169.9582 282329.8216 299391.6738 487979.7084 341347.8447 267847.7298 404035.6622 427910.1658 0.501118927 1.213268578 0.659787601 0.69966011 1.140378863 0.797709127 0.625943834 0.944206739 1 18.70694843 2.037590265 24.99923972 0.789321554 0.870814851 0 0.234641083 751.5926692 499840.4691 0.082734977 0.061103718 109.0411103 -2.037590265 0.081493297 EGKPTIVEEDDPELFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGKPTIVEEDDPELFK 16 1 O75937 O75937 DNAJC8 DnaJ homolog subfamily C member 8 0 150.45 6.74E-07 203380000 523640 313780 386760 369700 443990 284710 523790 365560 574980 FALSE TRUE 490866.3071 337012.5977 395934.1298 379187.1279 409120.8164 366901.1551 445252.5521 411200.9707 479012.1235 1.024747147 0.703557553 0.826563902 0.791602361 0.854092822 0.765953798 0.929522512 0.858435414 1 18.86970264 1.01147376 0.80535568 0.996169259 0.811796565 0.227743415 0.088221259 0.787772372 1.143458456 0.076012525 0.027953046 10.26771391 -1.01147376 -0.184372695 EGLDWDLIYVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EGLDWDLIYVGR 12 0 Q8NBJ5;M0QX72 Q8NBJ5 COLGALT1 Procollagen galactosyltransferase 1 0 ;;; 150.61 0.0001588 254074000 402045 488488 469654 484839 505008 419339 524802 417586 348495 FALSE TRUE 376881.7211 524656.1598 480794.4147 497280.7896 465346.7088 540395.3619 446112.8121 469722.5313 290328.9331 1.298119747 1.807109454 1.656033415 1.712818575 1.602825815 1.861321075 1.536577176 1.617897763 1 18.14732883 0.283415443 1.136272884 0.99859464 1.668154408 0.624441931 0.154500834 2.253538462 3.047234046 0.135850547 0.04001883 1.920505004 -0.283415443 0.669559768 EGLELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EGLELLK 7 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;; 119.21 0.011243 1273681000 2633740 2648730 2369920 2202670 3054550 1565580 2956730 2662190 2926280 FALSE TRUE 2468898.915 2844844.725 2426135.622 2259194.241 2814657.964 2017537.531 2513395.785 2994570.282 2437864.964 1.012729971 1.16694106 0.995188683 0.926710164 1.154558602 0.827583792 1.030982365 1.228357734 1 21.21718678 3.82331359 5.558680859 1.015169953 1.097284163 0.049241802 0.115861699 0.520938661 24.20166984 0.027761366 0.05079532 6657.537025 -3.82331359 0.08211421 EGLELPEDEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 233.54 1.24E-15 897690000 3227560 1640840 2234610 1988950 1806010 1852030 2954140 1827960 1541340 FALSE TRUE 3025552.781 1762329.501 2287616.004 2039989.824 1664173.26 2386680.996 2511194.132 2056184.83 1284080.397 2.356201986 1.372444829 1.781520854 1.588677648 1.296003945 1.858669443 1.955636219 1.601289791 1 20.2923041 4.750925346 24.29874104 1.618057555 2.356202668 0.419094693 0.287857484 1371.063581 2694293.54 0.065072136 1.092850779 56354.07764 -4.750925346 0.738145114 EGLELPEDEEEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EGLELPEDEEEKK 13 1 P08238;Q58FF7;Q58FF6;P07900;P07900-2;Q58FG0 P08238;P07900 HSP90AB1;HSP90AB3P;HSP90AB4P;HSP90AA1;HSP90AA5P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 4;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5 0 ;;;;; 185.87 1.33E-05 5373360000 14657800 5432790 8517510 7551580 7774690 5817850 11481930 6649520 8993740 FALSE TRUE 13740394.46 5835039.424 8719549.359 7745366.328 7164097.209 7497368.85 9760321.19 7479727.209 7492626.692 1.833855472 0.778770872 1.163750674 1.03373178 0.956152963 1.00063291 1.302656811 0.998278376 1 22.83704014 4.750803142 24.79427601 1.044064505 1.833856017 0.776284221 0.135538063 867.7810141 1757444.761 0.033284973 0.569809385 56338.22265 -4.750803142 0.789791513 EGLELPEDEEEKKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 147.35 4.53E-06 13422200000 3940110 1437080 2069010 1960750 2112140 1279480 2882330 1638030 2514460 FALSE TRUE 3693505.548 1543482.898 2118087.894 2011066.165 1946261.044 1648845.105 2450151.375 1842541.651 2094780.382 1.763194643 0.736823254 1.011126471 0.960036757 0.929100282 0.78712075 1.169645943 0.879587028 1 20.99836757 4.747272235 24.94470825 0.938861187 1.763195075 0.824359324 0.120242109 445.5639818 1275792.191 0.027993894 0.333174348 55882.03784 -4.747272235 0.824333887 EGLELPEDEEEKKKQEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 186.05 2.19E-14 8392730000 5292950 955082 1913430 1857310 2123070 1044870 2550050 1160156 2838270 FALSE TRUE 4961673.708 1025797.265 1958817.463 1904971.719 1956332.646 1346507.007 2167693.676 1305004.03 2364544.401 2.098363518 0.433824488 0.828412214 0.805640071 0.827361349 0.569457273 0.916748983 0.551905065 1 21.1731308 4.746308681 24.99987442 0.73329393 2.098364175 0.855012894 0.17554502 319.3229431 1030302.271 0.038335846 0.414219684 55758.19174 -4.746308681 1.365070244 EGLEQALPSGKPS(ph)SPVELDLFGDPSPSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EGLEQALPSGKPSSPVELDLFGDPSPSSK 29 1 Q9H201 Q9H201 EPN3 Epsin-3 1 EGLEQALPS(0.092)GKPS(0.454)S(0.454)PVELDLFGDPSPSSK;EGLEQALPS(0.019)GKPS(0.491)S(0.491)PVELDLFGDPSPSSK;EGLEQALPS(0.001)GKPS(0.67)S(0.329)PVELDLFGDPSPSSK 173.23 8.94E-13 1090560000 1885900 1061146 1362062 1269550 1310520 1002492 1815550 1108614 1815370 TRUE FALSE 1767864.885 1139714.354 1394370.754 1302128.802 1207597.046 1291895.166 1543325.132 1247026.898 1512373.019 1.168934425 0.753593419 0.921975423 0.860983888 0.798478305 0.85421728 1.020465925 0.824549818 1 20.52838259 -0.833752297 5.301363848 1.000000071 0.892451525 0.060591552 0.119664992 8.98E-08 2.00E-08 0.104823434 0.024707104 0.146638397 0.833752297 -0.107548546 EGLEQALPSGKPSS(ph)PVELDLFGDPSPSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGLEQALPSGKPSSPVELDLFGDPSPSSK 29 1 Q9H201 Q9H201 EPN3 Epsin-3 1 EGLEQALPS(0.004)GKPS(0.254)S(0.742)PVELDLFGDPSPSSK 152.77 1.55E-08 121100000 656460 383250 491560 459650 484870 352820 637420 422250 649190 TRUE FALSE 615373.3404 411626.2288 503220.0353 471445.3972 446790.2661 454673.4064 541844.7885 474968.842 540835.9951 1.137818758 0.761092517 0.930448491 0.871697523 0.826110448 0.84068629 1.001865248 0.878212335 1 19.04483165 1.741466101 25 0.956342829 0.879845732 0.068544158 0.104234245 1.070419293 9264.72849 0.043515906 0.02413169 55.13991608 -1.741466101 -0.076497097 EGLGVNEVHYVDNQDCIDLIEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGLGVNEVHYVDNQDCIDLIEAK 23 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 113.73 0.00073765 88751000 25856 27550 28004 26202 32940 24445 35724 25796 39541 FALSE TRUE 24237.71911 29589.83067 28668.2681 26874.38768 30353.02527 31501.87467 30367.51785 29016.68738 32941.35166 0.735783989 0.89825794 0.870282082 0.815825287 0.921426224 0.956301824 0.921866175 0.88085904 1 15.00761213 2.637518048 5.902582355 0.933328584 0.848314724 0.490742528 0.052285927 0.237075698 11.53532984 0.016167596 0.015212252 434.0283006 -2.637518048 -0.08501386 EGLHNAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EGLHNAK 7 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;; 110.61 0.0067645 1489150000 5835900 4608190 4945450 4421310 4638890 3373990 4918060 4507460 5254750 FALSE TRUE 5470641.436 4949385.182 5062758.409 4534768.3 4274570.292 4348006.141 4180642.56 5070226.303 4377698.278 1.2496616 1.130590751 1.156488659 1.035879591 0.976442418 0.993217409 0.954986455 1.158194554 1 22.06174109 3.206202327 3.427518456 1.006664009 1.168099279 0.589812728 0.062269567 0.154576822 3.765081944 0.017397013 0.022371867 1607.690062 -3.206202327 0.16143527 EGLLFEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EGLLFEGR 8 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;;;;; 134.81 0.0020022 1783791000 2361010 2669470 2340740 2316450 2746560 1854167 2529880 2284950 3024880 FALSE TRUE 2213238.599 2867120.336 2396263.458 2375894.029 2530856.257 2389434.913 2150547.98 2570231.037 2520007.987 0.878266502 1.137742559 0.950895184 0.942812103 1.004304855 0.948185453 0.853389351 1.019929719 1 21.26499688 3.72000266 21.93059478 0.948516062 1.031872646 0.027417506 0.077998273 91.47786355 281825.3099 0.019293737 0.030724154 5248.106747 -3.72000266 0.083356584 EGLLLWCQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGLLLWCQR 9 0 O43707;P12814-3;P12814;P12814-2;P12814-4;H9KV75;P35609-2;P35609;G3V2N5;A0A494C1A0;G3V2W4;Q08043;A0A494C166;A0A494C033;A0A087WSZ2;G3V2X9 O43707;P12814-3 ACTN4;ACTN1;ACTN2;ACTN3 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2;Alpha-actinin-3 0 ; 155.75 0.0001688 313100000 668450 855160 604830 642720 973900 549980 700680 808850 756930 FALSE TRUE 626612.9077 918476.9362 619176.8532 659213.2833 897413.8225 708750.2978 595619.5388 909836.703 630593.493 0.993687557 1.456527773 0.981895405 1.045385483 1.423125726 1.123941661 0.944538035 1.442826025 1 19.26635076 -2.406075065 1.904475503 4.87E-05 1.168522806 0.07098284 0.198809948 2655930.017 253901.8098 11417456.94 0.047717872 0.003925771 2.406075065 1.168474118 EGLMLDSHEELYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EGLMLDSHEELYK 13 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 187.44 6.96E-06 501970000 902470 839530 893900 930470 1037080 672393 1145560 933710 1067950 FALSE TRUE 845986.0137 901689.6747 915103.7301 954347.4355 955631.9202 866501.9437 973793.9129 1050285.749 889702.2458 0.950864199 1.013473529 1.028550545 1.072659353 1.074103077 0.973923521 1.09451664 1.180491287 1 19.76296307 7.270702931 0.403287312 1.073387976 3.21E-08 0.303945074 0.055337494 49.43001779 1.158602611 0.036597704 38.7770361 18651034.75 -7.270702931 -1.073387944 EGLQNMEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGLQNMEAR 9 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 92.838 0.015815 622810000 928870 1228000 1025020 972390 1288780 774290 1029730 1081110 1256220 FALSE TRUE 870733.6848 1318922.398 1049333.958 997343.1737 1187564.417 997814.9535 875331.546 1216088.963 1046548.767 0.832004884 1.2602589 1.002661311 0.952982991 1.134743507 0.953433787 0.83639824 1.161999328 1 19.99720811 2.207450877 24.69909626 0.958800377 1.058622668 0 0.13747602 395.5971874 314075.6494 0.048941291 0.036149303 161.2318649 -2.207450877 0.099822291 EGLRPGDTTSTFCGTPNYIAPEILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGLRPGDTTSTFCGTPNYIAPEILR 25 1 P41743 P41743 PRKCI Protein kinase C iota type 0 101.41 0.0049537 89818000 23328 27780 27206 31650 36535 25091 35533 31269 33543 FALSE TRUE 21867.94212 29836.86011 27851.33917 32462.19258 33665.68848 32334.36438 30205.15652 35173.00348 27944.4566 0.782550272 1.067720175 0.996667767 1.161668414 1.204735843 1.157094047 1.080899763 1.258675521 1 14.7702745 5.586184988 0.712410374 1.137295542 1.19E-15 0.597446339 0.085138559 5.868192947 0.927321487 0.029530089 7.092879259 385642.5874 -5.586184988 -1.137295542 EGLSGDALSSPSAPEPVVGT(ph)PDDKLDADYIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGLSGDALSSPSAPEPVVGTPDDKLDADYIKR 32 2 K7EJ08;Q92503-3;Q92503;Q92503-2 K7EJ08 SEC14L1 SEC14-like protein 1 1 EGLSGDALSSPSAPEPVVGT(1)PDDKLDADYIKR 108.33 0.00021438 401020000 31612 18489 29022 25828 39228 20774 43632 30661 60676 TRUE FALSE 29633.46135 19857.9448 29710.41555 26490.79021 36147.19112 26771.11656 37089.78666 34489.09334 50548.78362 0.586234905 0.392847135 0.58775728 0.524063851 0.715095172 0.529609511 0.733742417 0.68229324 1 15.62538876 -0.152570483 0.197177818 1.255256986 0.403165263 0.768061046 0.07833962 4.389473385 0.297949971 0.954051953 0.248122275 0.703768003 0.152570483 -0.852091723 EGMAALQSDPWQQELYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGMAALQSDPWQQELYR 17 0 P49748;P49748-3;P49748-2;G3V1M7 P49748 ACADVL "Very long-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 148.57 8.31E-07 66793000 41633 46652 37387 37787 49420 36596 44741 40799 56814 FALSE TRUE 39027.26485 50106.16262 38273.8373 38756.67839 45538.75255 47160.67111 38032.50241 45892.84496 47331.37637 0.824553771 1.058624669 0.808635629 0.818836919 0.9621261 0.996393402 0.803536794 0.969607235 1 15.53050925 EGMNIVEAMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 15 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 ;;;;;;;;;;;;;; 214.82 3.09E-11 12328150000 7186838 8658150 7530833 7114715 8694680 6336988 7832502 8202881 11404780 FALSE TRUE 6737026.638 9299208.435 7709467.915 7297290.632 8011834.905 8166373.563 6658091.038 9227028.75 9501248.54 0.709067509 0.978735415 0.811416298 0.768034917 0.84324022 0.859505309 0.700759591 0.971138552 1 23.17968568 -1.350844377 4.494279387 1.000203268 0.831905018 0.245591479 0.093465834 0.000178825 2.58E-05 0.085012985 0.020013641 0.044581597 1.350844377 -0.16829825 EGMNPSYDEYADS(ph)DEDQHDAYLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 19 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;EGMNPSYDEYADS(1)DEDQHDAYLER 322.08 3.35E-74 1.05275E+11 22481730 24628670 24842970 24417050 24935870 21276950 27629790 22214760 26807320 TRUE FALSE 21074638.65 26452202.35 25432256.98 25043632.84 22977507.36 27419260.06 23486959.49 24988321.69 22333005.11 0.943654405 1.184444378 1.138774511 1.121373175 1.028858734 1.227746106 1.051670359 1.118896519 1 24.41267406 0.166566513 0.925223181 0.999003366 1.114847181 0.118179046 0.080909579 7.577563771 6.889674155 0.091094818 0.02284137 1.467460813 -0.166566513 0.115843815 EGNASGVSLLEALDTILPPTRPTDKPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGNASGVSLLEALDTILPPTRPTDKPLR 28 2 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 229.82 3.57E-35 449510000 518440 429530 432220 415360 457510 347780 517150 417710 324760 FALSE TRUE 485991.7658 461332.8481 442472.4625 426018.8408 421579.0101 448178.4403 439608.1585 469862.013 270555.458 1.796274115 1.705132292 1.635422423 1.574608193 1.558198135 1.656512286 1.624835669 1.736656937 1 18.04556482 -1.607313551 3.030779492 0.957775441 1.654562451 0.893366436 0.071733767 14566282.58 16034547.95 4905293.263 0.017079224 0.024699403 1.607313551 0.69678701 EGNDLYHEMIESGVINLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EGNDLYHEMIESGVINLK 18 0 P06576;H0YH81;F8W079;F8W0P7;H0YI37 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ;;;; 276.46 4.21E-39 1800870000 4316520 3246090 3625660 3191480 4479640 3383880 3659570 3784640 5552920 FALSE TRUE 4046356.718 3486433.881 3711662.367 3273378.78 4127827.144 4360751.223 3110851.452 4257160.635 4626101.779 0.874679571 0.753644007 0.80233046 0.70758901 0.892290603 0.942640571 0.672456336 0.920247941 1 22.14136558 1.007393453 23.83143653 1.000000021 0.800589505 0.392490878 0.082563811 70.02112487 225698.0157 0.074316369 0.018579092 10.17169789 -1.007393453 -0.199410516 EGNNPAENGDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGNNPAENGDAK 12 0 P05204 P05204 HMGN2 Non-histone chromosomal protein HMG-17 0 150.51 0.00015861 158750000 256310 204530 224160 222900 209100 168320 257200 151240 194410 FALSE TRUE 240268.0146 219673.614 229477.1811 228619.9914 192678.1295 216911.2516 218635.2477 170122.6469 161961.7151 1.48348648 1.3563305 1.416860651 1.411568106 1.189652316 1.339274849 1.349919317 1.050388031 1 17.3052933 1.098730884 0.556822087 0.980044303 1.40770929 0.721910043 0.084355302 0.466379117 0.364447787 0.086440262 0.040956967 12.5525189 -1.098730884 0.427664987 EGNTTEDDFPSS(ph)PGNGNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EGNTTEDDFPSSPGNGNK 18 0 Q15007 Q15007 WTAP Pre-mRNA-splicing regulator WTAP 1 EGNTTEDDFPSS(1)PGNGNK;EGNTTEDDFPSS(1)PGNGNK;EGNTTEDDFPS(0.009)S(0.991)PGNGNK 496.73 1.17E-266 963090000 3047510 2196380 2468340 2408050 2432460 1864150 3229800 1999750 2839680 TRUE FALSE 2856771.789 2359002.261 2526890.19 2469844.64 2241424.404 2402299.843 2745521.474 2249423.189 2365719.063 1.207570178 0.997160778 1.068127754 1.044014346 0.947460093 1.015462859 1.160544173 0.950841216 1 21.17384733 4.746314819 24.37212747 1.034281401 1.207570298 0.458345849 0.061994707 659.6923264 2073399.38 0.014637453 0.153955776 55758.97983 -4.746314819 0.173288898 EGPDLDRPGS(ph)DR ddPTM_SK-BR-3_Pertuzumab_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 134.14 0.00039666 638280000 1018210 886550 1035420 888890 886990 957030 1243130 905990 877470 TRUE FALSE 954482.0537 952191.0845 1059980.651 911700.4223 817329.3833 1233309.025 1056734.197 1019104.846 731014.5883 1.305694946 1.302560988 1.450012993 1.247171311 1.118075339 1.68711958 1.445571968 1.394096455 1 19.47954067 4.229616352 22.13489323 1.370495764 1.304127916 0 0.191184633 135.3559174 1200576.86 0.044251919 0.10987786 16967.44116 -4.229616352 -0.066367848 EGPDLDRPGS(ph)DRQER ddPTM_SK-BR-3_Pertuzumab_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 141.31 2.50E-06 993900000 1183930 1198960 1168930 1258480 1526250 879940 1268010 1187700 2050520 TRUE FALSE 1109829.935 1287732.246 1196657.572 1290774.727 1406384.482 1133964.393 1077883.672 1335986.959 1708274.965 0.649678745 0.753820241 0.700506415 0.755601267 0.823277581 0.663806715 0.630977854 0.782067868 1 20.70410878 0.978304814 22.90115603 1.000000002 0.712649626 0.719077175 0.056712829 315.4678005 333004.7473 0.055877586 0.013969397 9.51272219 -0.978304814 -0.287350376 EGPDLDRPGSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGPDLDRPGSDR 12 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WZ99 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 0 ; 93.011 0.0067604 1257720000 1013900 1044120 1062210 1110230 1154910 987280 1163150 910420 1174450 FALSE TRUE 950441.8089 1121427.731 1087406.123 1138720.381 1064208.027 1272291.709 988746.4557 1024087.941 978426.7078 0.971398063 1.146154047 1.111382298 1.163827983 1.087672708 1.300344419 1.010547288 1.046668016 1 19.90010426 1.603634749 25 1.021440106 1.131335188 0.294811499 0.080925441 0.484064277 2843.908666 0.037568585 0.018351059 40.14530383 -1.603634749 0.109895081 EGPEPPEEVPPPTT(ph)PPVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGPEPPEEVPPPTTPPVPK 19 0 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 EGPEPPEEVPPPT(0.164)T(0.836)PPVPK 126.63 0.00027944 75329000 296030 191550 255150 260940 261470 167970 242670 182710 290910 TRUE FALSE 277502.0107 205732.5613 261202.2785 267636.1622 240935.2009 216460.2122 206283.8863 205521.7457 242355.2416 1.1450217 0.848888433 1.077766161 1.104313488 0.994140664 0.893152592 0.851163296 0.848018571 1 17.88676376 2.264710482 4.208465921 0.880729848 1.019667366 0.355242652 0.089265198 0.233382419 9.269451507 0.032577264 0.025563067 183.9545279 -2.264710482 0.138937518 EGPLGWSSDGSLGSVLLDSPSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EGPLGWSSDGSLGSVLLDSPSSPR 24 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 EGPLGWSSDGSLGSVLLDS(0.009)PS(0.184)S(0.807)PR;EGPLGWSSDGSLGSVLLDSPS(0.134)S(0.866)PR;EGPLGWSSDGSLGSVLLDSPS(0.006)S(0.994)PR;EGPLGWSSDGSLGSVLLDSPS(0.041)S(0.959)PR 238.72 1.13E-37 141065000 136525 142821 157593 204867 230110 121020 121246 96878 107170 TRUE FALSE 127980.144 153395.6154 161331.1804 210124.2341 212038.0888 155956.5094 103066.2879 108973.4316 89282.63466 1.433427054 1.718090153 1.806971546 2.353472597 2.37490851 1.746773155 1.154382241 1.220544532 1 16.44609198 1.783258744 3.765154515 1.131264529 1.917901115 0.633540939 0.282377394 0.157506518 4.261887801 0.159009701 0.081861514 60.70979191 -1.783258744 0.786636586 EGPLPAARPAGAT(ph)LERPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EGPLPAARPAGATLERPK 18 2 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 EGPLPAARPAGAT(1)LERPK;EGPLPAARPAGAT(1)LERPK;EGPLPAARPAGAT(1)LERPK 162.65 1.67E-09 2896450000 1306851 1432004 1002885 1055389 2411700 835251 1936956 1888972 3142510 TRUE FALSE 1225057.529 1538031.066 1026673.906 1082472.069 2222294.81 1076374.405 1646527.43 2124814.312 2618004.78 0.467935559 0.587482146 0.392158912 0.413472151 0.848850555 0.411143025 0.628924532 0.811615903 1 21.3200363 1.129110615 1.759716275 0.998978206 0.518605313 0.603054675 0.132140563 0.216091238 1.281063798 0.115939197 0.033689838 13.4620319 -1.129110615 -0.480372893 EGPLSVFGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EGPLSVFGDR 10 0 P17987;E7ERF2;F5GZ03;F5GZI8;F5GYL4 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;; 95.642 0.016943 246512000 776830 645680 721220 673210 712140 589350 858420 646510 701760 FALSE TRUE 728209.597 693486.819 738327.679 690485.7083 656211.397 759485.7777 729707.8902 727228.1966 584631.7225 1.245586869 1.186194304 1.262893631 1.181060969 1.122435495 1.299084105 1.248149668 1.243908205 1 19.15716859 -1.151881143 4.444392967 0.999961793 1.224658343 0.667050885 0.049655768 1.83E-05 3.48E-06 0.046688154 0.011002634 0.070488596 1.151881143 0.22469655 EGPPAPPPVKPPPS(ph)PVNIR ddPTM_SK-BR-3_Pertuzumab_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 183.49 1.63E-14 20091800000 5698280 5315460 5806440 5636230 6425210 4111050 5776900 4653120 6772970 TRUE FALSE 5341634.827 5709022.189 5944171.499 5780865.204 5920599.925 5297843.398 4910707.475 5234072.275 5642517.552 0.946675802 1.011786341 1.053460879 1.024518781 1.049283386 0.938914828 0.870304333 0.927612936 1 22.42790757 2.12628948 5.371112291 0.915253633 1.021419262 0.45591506 0.043405097 0.14284414 6.185016675 0.015653818 0.011453203 133.7486726 -2.12628948 0.106165629 EGPSCPS(ph)PGPFCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGPSCPSPGPFCR 13 0 Q4AC94 Q4AC94 C2CD3 C2 domain-containing protein 3 1 EGPSCPS(1)PGPFCR 136.24 7.82E-05 66202000 97033 100760 96324 93139 111660 87395 125880 91102 118950 TRUE FALSE 90959.87774 108220.3752 98608.85077 95529.10442 102890.674 112624.5178 107005.4626 102476.2852 99096.47655 0.917892148 1.092070869 0.995079282 0.964001019 1.038287915 1.136513847 1.079810971 1.034106245 1 16.59654614 2.473639463 24.94384415 1.074617461 1.008543464 0.227353072 0.056200891 144.4162859 1034589.359 0.018513108 0.015562799 297.604479 -2.473639463 -0.066073997 EGPTDHLESACPLNLPLQNNHTAADMYLS(ph)PVRS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EGPTDHLESACPLNLPLQNNHTAADMYLSPVRSPK 35 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 2 EGPTDHLESACPLNLPLQNNHT(0.003)AADMY(0.247)LS(0.751)PVRS(0.999)PK;EGPTDHLESACPLNLPLQNNHT(0.007)AADMY(0.133)LS(0.862)PVRS(0.998)PK;EGPTDHLESACPLNLPLQNNHT(0.001)AADMY(0.018)LS(0.982)PVRS(1)PK;EGPTDHLESACPLNLPLQNNHT(0.007)AADMY(0.038)LS(0.963)PVRS(0.991)PK 250.31 1.22E-48 624980000 357382 200319 259196 251639 274225 192279 395733 234966 347194 TRUE FALSE 335014.0986 215150.8272 265344.2515 258096.4828 252688.4747 247786.8259 336396.5105 264302.0223 289245.0784 1.158236124 0.743835741 0.91736825 0.892310715 0.87361374 0.856667388 1.163015503 0.913764977 1 18.14193289 1.762729873 25 1.040316507 0.887524193 0.163751301 0.119576247 17.45346924 18066.30274 0.049872177 0.027657488 57.90684094 -1.762729873 -0.152792314 EGPTDHLESACPLNLPLQNNHTAADMYLSPVRS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGPTDHLESACPLNLPLQNNHTAADMYLSPVRSPK 35 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 EGPTDHLESACPLNLPLQNNHTAADMYLS(0.063)PVRS(0.937)PK 339.22 2.57E-118 164290000 86580 64371 72987 69130 79146 48253 91192 61098 104010 TRUE FALSE 81161.11235 69137.09582 74718.28611 70903.99284 72930.19242 62182.85778 77518.60619 68726.21979 86650.05907 0.936653861 0.797888617 0.86229931 0.818279798 0.841663505 0.71763203 0.894616888 0.793146831 1 16.40291311 -1.232819465 4.229487945 1.000095805 0.831667774 0.438397616 0.059470962 7852737.881 2288934.546 6939.364106 0.012136402 0.058503323 1.232819465 -0.168428031 EGPVQFEEDPFGLDKFLEEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGPVQFEEDPFGLDKFLEEAK 21 1 Q13573;G3V4X8 Q13573 SNW1 SNW domain-containing protein 1 0 ; 106.73 0.00032822 28485000 133577 71622 88014 89055 90200 60965 120531 67553 120803 FALSE TRUE 125216.654 76924.9674 90101.73364 91340.30207 83116.05585 78564.60582 102458.4955 75987.14075 100640.1989 1.244201178 0.764356274 0.895285727 0.907592623 0.825873327 0.780648356 1.0180673 0.755037665 1 16.61884715 4.748378498 24.95098519 0.867787067 1.244201387 0.625532017 0.091387668 837.3788725 2128055.539 0.020056788 0.267158363 56024.56559 -4.748378498 0.37641432 EGPYSISVLYGDEEVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGPYSISVLYGDEEVPR 17 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 86.944 0.0092357 0 17384 13740 19096 19014 13060 16589 24107 13093 17427 FALSE TRUE 16295.96647 14757.3239 19548.96614 19501.93143 12034.32028 21377.975 20492.37915 14727.68987 14518.32112 1.122441523 1.01646215 1.34650322 1.343263541 0.828905779 1.472482584 1.411484082 1.014421003 1 13.82558701 4.038040501 5.722121164 1.238812068 1.072986075 0.044667075 0.207645867 0.473971166 31.15753996 0.049722234 0.108708599 10915.42125 -4.038040501 -0.165825992 EGQHYPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGQHYPER 8 0 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 ; 97.277 0.0083456 962220000 377040 454520 409020 425280 483280 344690 411500 406860 512640 FALSE TRUE 353441.7394 488173.1337 418722.1476 436193.4048 445325.1383 444196.4074 349799.3952 457657.3666 427077.0722 0.827583035 1.14305629 0.980436963 1.021345872 1.042727805 1.040084885 0.819054494 1.07160369 1 18.70413692 EGQPSPADEKGNDS(ph)DGEGESDDPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGQPSPADEKGNDSDGEGESDDPEK 25 1 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 EGQPSPADEKGNDS(1)DGEGESDDPEK;EGQPSPADEKGNDS(0.997)DGEGES(0.003)DDPEK 138.84 3.20E-06 756860000 1220870 459300 638480 616720 620050 438120 861280 506290 640000 TRUE FALSE 1144457.926 493307.0499 653625.0471 632546.0793 571353.7742 564598.1317 732139.0597 569501.421 533179.8654 2.146476265 0.925216952 1.225899719 1.186365278 1.071596681 1.058926205 1.373155866 1.068122519 1 19.02426278 4.745805651 24.99071126 1.133388928 2.146476741 0.868093048 0.126317003 303.9918343 1048550.815 0.029952961 0.307286422 55693.64615 -4.745805651 1.013087813 EGQPSPADEKGNDS(ph)DGEGESDDPEKKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGQPSPADEKGNDSDGEGESDDPEKKK 27 3 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 EGQPSPADEKGNDS(1)DGEGESDDPEKKK 229.71 5.07E-35 399000000 270180 61807 105190 133260 152930 79523 173540 66961 243130 TRUE FALSE 253269.9161 66383.25459 107685.1565 136679.6772 140919.4947 102479.9992 147519.2881 75321.22825 202550.0323 1.250406693 0.327737566 0.531647195 0.674794645 0.695726844 0.505949063 0.728310365 0.371864805 1 17.62791879 -1.296437398 4.466383937 1.00024589 0.605213523 0.157378049 0.256292199 0.000648692 0.000102185 0.221782684 0.052237502 0.050531548 1.296437398 -0.395032367 EGQT(ph)IKLCIGNITNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGQTIKLCIGNITNK 15 1 F5H2U7;A0A1W2PNT6;F5GYH1;A0A1W2PRM0;A0A1W2PRL5;A0A1W2PR09;Q8NC96 F5H2U7 NECAP1 Adaptin ear-binding coat-associated protein 1 1 EGQT(1)IKLCIGNITNK 70.802 0.073728 219480000 212970 464860 433980 432910 527580 385390 466990 418910 682580 TRUE FALSE 199640.5879 499278.7181 444274.2105 444019.2035 486145.995 496645.8367 396969.1848 471211.8356 568652.9884 0.351076301 0.878002452 0.781274731 0.780826291 0.854908011 0.87337242 0.69808687 0.828645668 1 19.11718901 4.742899551 24.94367284 0.819887902 0.35107611 0.782016321 0.080162099 189.481928 1089253.585 0.017464418 0.137794582 55322.21382 -4.742899551 -0.468811792 EGRGES(ph)ENAGTNQETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGRGESENAGTNQETR 16 1 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 EGRGES(1)ENAGTNQETR;EGRGES(1)ENAGTNQETR 199.12 2.36E-11 467040000 212701 267610 241680 275040 312220 207647 252180 221660 340240 TRUE FALSE 199388.4241 287424.1228 247412.7637 282097.992 287699.5006 267591.318 214367.9501 249334.7389 283451.746 0.703429867 1.014014297 0.872856729 0.995224041 1.014985812 0.944045404 0.756276697 0.879637337 1 18.11274363 -0.612871029 7.223912748 0.999999996 0.90330537 0.084744515 0.104292709 0 0 0.098130566 0.023129596 0.243853487 0.612871029 -0.096694626 S(ph)TGSIDQLSHFHNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STGSIDQLSHFHNKR 15 1 A0A2R8Y5P9;Q8TF72;Q8TF72-2 A0A2R8Y5P9;Q8TF72-2 SHROOM3 Protein Shroom3 1 S(0.594)T(0.385)GS(0.021)IDQLSHFHNKR 225.54 4.63E-13 147030000 131460 214590 176200 196850 292520 103260 289580 226060 531940 TRUE FALSE 123232.1533 230478.4669 180379.5472 201901.5043 269546.6592 133069.4857 246160.1673 254284.0886 443155.7775 0.278078634 0.520084536 0.407034177 0.455599395 0.608243586 0.300276996 0.555470965 0.573802941 1 18.7574544 0.598165022 1.071000351 1.00054362 0.443029758 0.756480627 0.099516377 0.596884253 1.052535967 0.084235625 0.026442792 3.964286393 -0.598165022 -0.557513862 EGRPPEPTPAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGRPPEPTPAKR 12 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ; 112.95 0.00068525 384900000 497650 453840 449970 455180 495410 392370 593030 431300 624670 FALSE TRUE 466502.9748 487442.7858 460643.5009 466860.6894 456502.497 505640.8494 504110.6569 485148.7544 520408.5415 0.89641683 0.936654084 0.885157456 0.897104202 0.877200239 0.971622887 0.968682519 0.932245949 1 18.98928512 2.227920965 24.99939182 0.966083716 0.901824421 0.704854197 0.022314704 123.473026 290115.6144 0.008032543 0.005993884 169.0133325 -2.227920965 -0.064259295 EGRPSGEAFVELESEDEVK ddPTM_SK-BR-3_Pertuzumab_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 ; 238.68 2.67E-24 385890000 746130 494000 575620 565910 612780 448060 748400 503930 721710 FALSE TRUE 699431.0552 530576.274 589273.9782 580432.2087 564654.7306 577407.6484 636184.3678 566846.7698 601251.9386 1.163291144 0.882452496 0.980078301 0.965372702 0.939131659 0.960342265 1.058099487 0.942777451 1 19.19761011 EGS(ph)PANWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EGSPANWK 8 0 O96019-2;O96019 O96019-2 ACTL6A Actin-like protein 6A 1 EGS(1)PANWK;EGS(1)PANWK;EGS(1)PANWK;EGS(1)PANWK;EGS(1)PANWK 145.46 0.00059692 3770510000 8685230 4635770 5892090 5473200 5840980 4140820 7353230 4895890 7418570 TRUE FALSE 8141636.958 4979007.234 6031853.157 5613651.578 5382252.992 5336207.513 6250681.426 5507152.644 6180362.741 1.317339661 0.805617315 0.975970733 0.908304547 0.870863607 0.86341332 1.01137776 0.891072721 1 22.55926009 4.748334603 24.8881494 0.915345276 1.317339892 0.792942751 0.064479646 557.252653 1418938.842 0.014694002 0.196118858 56018.90334 -4.748334603 0.401994616 EGS(ph)PAPLEPEPGAAQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EGSPAPLEPEPGAAQPK 17 0 Q01167;Q01167-2 Q01167 FOXK2 Forkhead box protein K2 1 EGS(1)PAPLEPEPGAAQPK;EGS(1)PAPLEPEPGAAQPK;EGS(1)PAPLEPEPGAAQPK 357.46 5.87E-88 1272700000 2081290 881820 1283640 1109450 1085640 933360 1773280 1039470 1154340 TRUE FALSE 1951025.774 947110.8703 1314088.547 1137920.365 1000378.214 1202805.88 1507393.126 1169250.118 961673.1967 2.028782523 0.984857302 1.366460614 1.183271375 1.040247578 1.250742856 1.56746921 1.215849752 1 19.87518718 7.999999998 0.023100732 1.23E-05 3.001409359 0.150815326 0.289225106 7160.085446 12.72753085 584.8380435 1159.115278 99999999.57 -7.999999998 3.001397018 EGS(ph)PEPWLPLTDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGSPEPWLPLTDGR 14 0 J3KSM5;Q494U1-3;Q494U1;Q494U1-2 J3KSM5 PLEKHN1 Pleckstrin homology domain-containing family N member 1 1 EGS(1)PEPWLPLTDGR 161.49 2.23E-07 0 96518 73814 78795 80782 76690 55065 98687 66399 74183 TRUE FALSE 90477.11067 79279.26536 80664.05461 82855.00288 70667.07675 70961.37159 83889.80052 74689.06131 61801.37806 1.463998272 1.282807404 1.305214498 1.340665944 1.143454709 1.148216655 1.357409869 1.208533914 1 15.91535139 -5 0.088119665 0.132707336 1.514556426 0.602882672 0.082861913 169.2077203 1.040569519 28.1396128 2.088100028 1.00E-05 5 1.38184909 EGS(ph)PIPHDPEFGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EGSPIPHDPEFGSK 14 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK 195.27 3.11E-08 4004080000 9340930 4362030 5707080 5477060 5621300 4388280 7901680 4740190 6453430 TRUE FALSE 8756297.865 4684999.24 5842454.633 5617610.632 5179825.773 5655105.198 6716896.44 5332013.156 5376310.842 1.628681474 0.871415247 1.086703281 1.044882038 0.963453551 1.051856071 1.249350463 0.991760579 1 22.35818512 4.749125945 24.98000843 1.043844115 1.628681805 0.787556142 0.097162194 763.7545335 1805738.367 0.024864171 0.358652554 56121.0703 -4.749125945 0.58483769 EGSEEDLDALEHMFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EGSEEDLDALEHMFR 15 0 P31944 P31944 CASP14 "Caspase-14;Caspase-14 subunit p17, mature form;Caspase-14 subunit p10, mature form;Caspase-14 subunit p20, intermediate form;Caspase-14 subunit p8, intermediate form" 0 ;;; 214.65 2.45E-12 95253000 165989 189481 170105 164295 232764 132749.2 195865 189497 115574.4 FALSE TRUE 155600.0448 203510.3704 174139.9709 168511.0879 214483.6544 171071.739 166496.8616 213156.1176 96284.286 1.616048176 2.113640541 1.808602194 1.750141117 2.227608089 1.776735812 1.729221543 2.213820411 1 16.55501274 -1.094073261 4.722948215 0.999952561 1.901113573 0.641019385 0.212702704 9.57E-05 1.84E-05 0.185513109 0.043723569 0.080524259 1.094073261 0.901161012 EGSEFSFS(ph)DGEVAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGSEFSFSDGEVAEK 15 0 Q9BVS4-2;Q9BVS4 Q9BVS4-2 RIOK2 Serine/threonine-protein kinase RIO2 1 EGSEFS(0.006)FS(0.994)DGEVAEK 204.13 1.85E-11 0 146020 123570 128370 128310 135420 117100 171040 97113 118020 TRUE FALSE 136880.8689 132719.2514 131414.997 131602.6518 124784.6595 150904.869 145394.1399 109237.7718 98321.69956 1.392173543 1.349847002 1.336581829 1.338490409 1.269146689 1.534807369 1.478759424 1.11102404 1 16.58522223 1.094990884 4.946797381 1.005055546 1.383016661 0.771984434 0.075700129 0.096223466 3.587486516 0.078936623 0.02002183 12.4448849 -1.094990884 0.377961114 EGSGGGGGMDDIFSHIFGGGLFGFMGNQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGSGGGGGMDDIFSHIFGGGLFGFMGNQSR 30 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 141.49 3.93E-08 37595000 31891 41579 32428 28558 40327 23499 28080 32441 43468 FALSE TRUE 29894.99924 44657.55242 33197.20747 29290.84663 37159.88009 30282.77983 23869.66468 36491.33026 36212.90999 0.825534298 1.233194251 0.916723 0.80885095 1.026150069 0.83624265 0.659147931 1.007688426 1 15.14421649 3.616378499 4.038928391 0.861215633 1.063119635 0.099906099 0.148220593 0.292159542 8.4157847 0.038570016 0.062070893 4134.076407 -3.616378499 0.201904003 EGSGIGAIDSNLDWSHNFTNMLGYTDHQFTELTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EGSGIGAIDSNLDWSHNFTNMLGYTDHQFTELTR 34 0 O75390;B4DJV2;A0A0C4DGI3 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ;; 435.24 7.69E-209 867456000 534851.1 545516.7 474048.1 467481.6 647596.4 479488.1 506461.9 536356 583067.1 FALSE TRUE 501375.7244 585907.3241 485292.7448 479477.9693 596736.791 617908.5306 430522.6399 603321.2273 485749.4343 1.032169446 1.206192499 0.999059825 0.987089095 1.228486847 1.272072569 0.886306004 1.242042059 1 18.88985279 -1.571521519 4.550541281 0.998903848 1.097651717 0.058952872 0.12955888 0.001360808 0.000128134 0.118480571 0.027619725 0.026821217 1.571521519 0.098747869 EGSGSSGTGEQKEDQKEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EGSGSSGTGEQKEDQKEEK 19 2 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;; 128.74 1.17E-05 1096570000 4962560 1248670 2061810 1744110 2519590 1568270 2299860 1800050 3032590 FALSE TRUE 4651962.228 1341122.826 2110717.107 1788866.815 2321711.565 2021004.09 1955017.344 2024790.205 2526431.138 1.841317643 0.530836881 0.835454042 0.708060785 0.918968869 0.799944261 0.7738257 0.801442863 1 21.26866943 4.746765937 24.99987566 0.777504304 1.841318169 0.873981675 0.124557967 322.8422875 983610.2701 0.027852783 0.314553353 55816.92878 -4.746765937 1.063813865 EGSGSSGTGEQKEDQKEEKQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EGSGSSGTGEQKEDQKEEKQ 20 3 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;; 177.02 8.20E-17 2822580000 3225010 1178250 1573250 1439500 2288990 1040880 1839340 1348890 3847800 FALSE TRUE 3023162.381 1265488.856 1610568.233 1476440.007 2109221.959 1341365.159 1563548.043 1517301.886 3205577.322 0.943094512 0.394777205 0.502426886 0.460584743 0.657985051 0.418447295 0.487758642 0.473331863 1 21.61215278 -0.994512953 5.116300315 1.000002591 0.518679673 0.439714887 0.160410585 5.58E-06 1.10E-06 0.137074432 0.032308521 0.101271454 0.994512953 -0.481322918 EGSIWNHQPCFLKDWEMHVHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGSIWNHQPCFLKDWEMHVHFK 22 1 Q12907;D6RBV2;D6RDX1;D6RIU4;D6RBH1 Q12907 LMAN2 Vesicular integral-membrane protein VIP36 0 116.94 4.95E-05 59628000 73885 136420 65253 73050 170070 52364 103740 121490 93498 FALSE TRUE 69260.66974 146520.6787 66800.83197 74924.58667 156713.3882 67480.63674 88185.15007 136658.2939 77892.57978 0.88918187 1.881060804 0.857601997 0.961896331 2.011916779 0.866329462 1.132138008 1.754445601 1 16.24919828 -1.265139094 3.721406882 0.999486865 1.28842648 0.042090927 0.440460288 23258752.98 15932785.72 91554.72873 0.094323122 0.054307637 1.265139094 0.288939615 EGSQGELT(ph)PANSQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGSQGELTPANSQSR 15 0 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;J3QQX0 Q13098-7 GPS1 COP9 signalosome complex subunit 1 1 EGSQGELT(1)PANSQSR;EGSQGELT(1)PANSQSR 260.44 7.45E-24 329530000 609360 582750 637280 574300 669730 528320 729240 608520 846780 TRUE FALSE 571221.2453 625897.4164 652396.5825 589037.5103 617132.1074 680837.4074 619897.2319 684495.0615 705446.9476 0.809729558 0.887235275 0.92479893 0.834984845 0.87481009 0.965114967 0.878729767 0.970299842 1 19.42817806 -4.99999974 0.052756353 1.461960653 0.677391095 0.558898895 0.040332485 418.388712 1.627608278 26.04293426 5.377753863 1.00E-05 4.99999974 -0.784569558 EGSTHNWQHITDQIGMFCFTGLKPEQVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGSTHNWQHITDQIGMFCFTGLKPEQVER 29 1 P00505;P00505-2 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 ; 176.01 1.98E-13 568650000 154576 215851 159548 192404 284009 175752 188509 215523 235047 FALSE TRUE 144901.3641 231832.8326 163332.5539 197341.4124 261704.0788 226488.7493 160243.8255 242431.521 195816.1372 0.739986837 1.183931191 0.834111816 1.007789323 1.336478609 1.156639859 0.818338201 1.238056906 1 17.57914014 4.755279081 23.8379138 1.050626724 0.739986368 0.273049161 0.167027952 2568.196179 3661729.894 0.039149967 1.015989703 56921.8598 -4.755279081 -0.310640356 EGSTQQLQTTS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGSTQQLQTTSPK 13 0 A0A087X0H9;Q5T8P6-3;Q5T8P6-2;Q5T8P6;Q5T8P6-5;Q5T8P6-4 A0A087X0H9 RBM26 RNA-binding protein 26 1 EGSTQQLQTT(0.024)S(0.976)PK 109.07 0.0012232 111430000 243320 136010 172400 171790 176290 124430 208710 140690 233160 TRUE FALSE 228091.0355 146080.3219 176489.4094 176198.4222 162444.8945 160350.921 177415.8731 158255.4562 194244.0897 1.174249553 0.752045131 0.908596033 0.907097984 0.836292598 0.825512484 0.913365618 0.814724692 1 17.56751118 -1.656637941 2.714209951 1.014154652 0.878962475 0.074190484 0.113019131 29062764.78 26947551.1 2872285.201 0.023699653 0.022047637 1.656637941 -0.135192176 EGSVIDHIHLISVGDMIEAINGQSLLGCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGSVIDHIHLISVGDMIEAINGQSLLGCR 29 0 O14908;O14908-2;K7ESN1;K7EIT0 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 114.83 0.00012191 149720000 37650 62936 72499 83516 105670 82619 61701 55195 45404 FALSE TRUE 35293.55371 67595.84692 74218.71052 85659.16195 97371.10445 106469.7641 52449.50785 62086.21725 37825.77908 0.933055566 1.787031188 1.962119812 2.264570989 2.574199576 2.814740811 1.386607471 1.641373126 1 15.20708218 4.960358837 1.556476794 2.008964496 7.80E-09 0.252424742 0.535790604 2.661703953 3.965664369 0.137613218 9.574549281 91276.47017 -4.960358837 -2.008964488 EGSVLDILKS(ph)PGFASPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGSVLDILKSPGFASPK 17 1 P49790-3;P49790 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 EGSVLDILKS(1)PGFASPK 188.98 2.30E-10 201460000 530290 330180 444510 595320 720490 289110 453690 330880 609500 TRUE FALSE 497100.0955 354626.8708 455053.9871 610596.9191 663905.6217 372571.3637 385663.3964 372191.0964 507770.5125 0.978985749 0.698399891 0.896180412 1.202505668 1.307491486 0.733739661 0.759523026 0.732990765 1 18.95381709 4.681561407 0.003178893 1.165758827 0.631451557 0 0.208002377 5906064.881 2978.633779 244662.77 256074.6053 48035.39955 -4.681561407 -0.53430727 EGTAPS(ph)ENGETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGTAPSENGETK 12 0 Q15651;A0A087WZE9 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 EGTAPS(0.99)ENGET(0.01)K;EGTAPS(1)ENGETK 150.78 7.18E-05 423790000 1102280 678260 846880 721610 720390 767040 1140840 687260 916180 TRUE FALSE 1033290.262 728479.0761 866968.3935 740127.7343 663813.4753 988471.9961 969781.633 773065.9238 763263.6393 1.353778969 0.954426542 1.135870162 0.969688187 0.869704046 1.295059722 1.270572294 1.012842593 1 19.54182194 2.219117604 24.99987391 1.182813115 1.049590013 0.045933382 0.159995221 471.065361 605693.1091 0.056012733 0.041430584 165.6218395 -2.219117604 -0.133223102 EGTETFADHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGTETFADHR 10 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ; 150.61 2.13E-05 2123400000 1531120 1633760 1670930 1668280 1856700 1413680 1756220 1538790 2064300 FALSE TRUE 1435289.932 1754725.29 1710565.249 1711090.889 1710882.272 1821786.467 1492891.115 1730911.319 1719754.994 0.834589774 1.020334464 0.994656364 0.994962012 0.994840705 1.059329075 0.868083605 1.006487159 1 20.71377161 4.746165356 24.5021651 0.987933045 0.834589676 0.509519486 0.048469151 628.4575645 2024799.952 0.011608925 0.122053126 55739.79362 -4.746165356 -0.153343369 EGTGQQERES(ph)PRPLQLPGAEGPAIS(ph)DGEEGGGEPGAGGGAAGAAGAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EGTGQQERESPRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR 48 2 Q6PKG0;A0A0B4J210 Q6PKG0 LARP1 La-related protein 1 2 EGT(0.118)GQQERES(0.882)PRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR;EGT(0.348)GQQERES(0.652)PRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR 233.69 5.84E-61 584640000 106106 134289 114289 131445 160409 98717 141480 119010 192232 TRUE FALSE 99465.01486 144231.8973 116999.9891 134818.1012 147811.1242 127214.9954 120266.3874 133868.6605 160147.2373 0.6210848 0.900620577 0.73057763 0.841838445 0.922970178 0.794362722 0.75097385 0.835909896 1 17.28903939 -3.515042411 1.096023075 9.999348957 0.803386069 0.344347969 0.086699123 205504.1234 1551.659355 4618676.704 0.023695029 0.000305462 3.515042411 -9.195962888 EGTGQQERES(ph)PRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGTGQQERESPRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR 48 2 Q6PKG0;A0A0B4J210 Q6PKG0 LARP1 La-related protein 1 1 EGT(0.036)GQQERES(0.964)PRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR 247.96 1.15E-61 247610000 44847 52542 54015 54074 66613 36178 62111 52101 84185 TRUE FALSE 42040.10632 56432.26435 55296.26131 55461.63039 61381.48368 46622.0013 52798.03216 58605.92454 70133.97964 0.59942565 0.804635137 0.788437525 0.790795427 0.875203204 0.66475625 0.752816715 0.835628105 1 16.09782597 0.901889186 3.379671951 0.999797735 0.763031912 0.511083286 0.076257165 0.332633658 8.387740847 0.068028937 0.017628612 7.977910982 -0.901889186 -0.236765823 EGTSDPPS(ph)PLLLPSPGGWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGTSDPPSPLLLPSPGGWK 19 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 EGTSDPPS(1)PLLLPSPGGWK 164.01 2.58E-11 51107000 166610 119310 130200 140740 144320 110190 165350 123900 117060 TRUE FALSE 156182.1775 128143.8365 133288.4055 144351.6267 132985.6894 142000.0642 140557.3025 139369.1877 97521.92976 1.601508275 1.314000214 1.366753158 1.480196578 1.363649075 1.456083412 1.441289184 1.429106131 1 16.57343905 -1.274842054 3.160824741 0.997885631 1.417533666 0.744897058 0.078992976 7783796.607 10557676.69 158254.2889 0.018312573 0.053107755 1.274842054 0.419648035 EGTTPKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGTTPKPK 8 1 P61927 P61927 RPL37 60S ribosomal protein L37 0 90.657 0.011894 619810000 712670 493780 570680 612790 626300 439160 731100 525540 787320 FALSE TRUE 668065.2569 530339.985 584216.7991 628515.2289 577112.9244 565938.3628 621478.3422 591154.8259 655911.2057 1.018530025 0.808554543 0.890694951 0.958232187 0.879864407 0.862827709 0.947503773 0.901272643 1 19.323141 0.204842156 0.535931388 1.006760027 0.891548474 0.165111987 0.058441742 4.432179416 1.798429796 0.121276766 0.02578579 1.602662799 -0.204842156 -0.115211553 EGTVSDHIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGTVSDHIER 10 0 Q93100-4;Q93100-2;I3L213;Q93100-3;Q93100 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 0 86.344 0.015916 0 76565 78292 68898 84905 72944 64084 84055 53481 90148 FALSE TRUE 71772.93332 84088.82114 70532.2931 87083.80604 67215.27248 82584.01048 71451.73308 60158.22058 75101.71642 0.955676338 1.11966577 0.939156872 1.159544817 0.894989831 1.099628802 0.951399468 0.801023245 1 16.19655826 1.515532433 5.950699309 0.892662015 1.028209037 0.241201696 0.095270964 0.159188469 12.30008726 0.04686077 0.020993495 32.77422518 -1.515532433 0.135547022 EGVHGGLINK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EGVHGGLINK 10 0 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 ;;;; 150.27 2.19E-05 8998220000 13238640 10951360 12431760 11670950 11286620 9609110 14364980 11179700 11469480 FALSE TRUE 12410057.15 11762210.09 12726647.22 11970446.34 10400214.39 12383104.07 12211084.61 12575510.15 9555149.692 1.298782076 1.230981248 1.331915002 1.252774339 1.08844076 1.295961284 1.277958483 1.31609766 1 23.18784704 -1.133891255 4.556969472 0.999970339 1.262429848 0.59300876 0.068109264 1.98E-05 3.76E-06 0.063553825 0.014978089 0.073469781 1.133891255 0.262459509 EGVHGGLINKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EGVHGGLINKK 11 1 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 ;;; 149.96 2.21E-05 24744930000 51422400 42087000 46206000 44498800 49471200 36316700 60615400 40377400 58240000 FALSE TRUE 48203963.78 45203165.27 47302028.14 45640714.54 45585931.51 46800741.74 51526683.5 45418607.27 48519367.76 0.993499421 0.931651985 0.974910233 0.940670018 0.939540922 0.964578557 1.061981759 0.936092315 1 25.53205742 1.974410231 24.59981493 1.008003715 0.954387241 0.232009218 0.035000573 633.4697922 608962.9976 0.01288858 0.008359857 94.2779719 -1.974410231 -0.053616474 EGVKFDESEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EGVKFDESEK 10 1 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;;; 156.71 9.54E-06 7079370000 12307000 7964700 9006000 9291200 9434800 6018900 12336000 7171710 9376500 FALSE TRUE 11536726.84 8554414.675 9219626.573 9529627.922 8693828.866 7756458.721 10486331.32 8067113.78 7811501.575 1.476889779 1.095105031 1.180263037 1.219948281 1.112952328 0.992953614 1.342421968 1.032722544 1 22.89716847 4.743565043 24.65037777 1.142308396 1.476889949 0.508109251 0.10810051 361.7217426 1781666.109 0.023580939 0.195547183 55407.05192 -4.743565043 0.334581553 EGVKTENDHINLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGVKTENDHINLK 13 1 A8MUA9;A8MU27;P55854;P55854-2 A8MUA9 SUMO3 Small ubiquitin-related modifier 3 0 98.531 0.0019689 137470000 245780 198840 225000 197900 258130 149820 288180 200570 514600 FALSE TRUE 230397.0685 213562.3205 230337.1063 202978.449 237857.511 193070.6019 244970.0843 225611.606 428709.9356 0.537419475 0.498151087 0.537279608 0.473463366 0.55482155 0.450352525 0.571412193 0.526257003 1 18.70964233 -0.588267921 0.745245759 1.043170379 0.512996032 0.946918217 0.035852072 3.352852448 1.241521 0.423606957 0.010558703 0.258066766 0.588267921 -0.530174347 EGVKTENNDHINLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGVKTENNDHINLK 14 1 P61956;P61956-2 P61956 SUMO2 Small ubiquitin-related modifier 2 0 76.588 0.016248 347080000 906080 733220 714790 733400 1086300 534050 1023000 828510 1666000 FALSE TRUE 849370.0702 787508.3717 731745.1563 752220.2856 1000986.38 688221.5654 869610.6471 931951.2973 1387933.837 0.611967262 0.56739619 0.527219048 0.541971285 0.721206122 0.495860499 0.626550505 0.671466659 1 20.40450737 0.577650606 1.157509745 1.00040589 0.57258911 0.81921084 0.061211811 0.545978739 1.06418972 0.053848267 0.016542591 3.781382465 -0.577650606 -0.42781678 EGVVECSFVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGVVECSFVK 10 0 P40926;G3XAL0;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 163.94 0.0072732 0 150970 136900 129130 115770 174350 106060 125920 147930 194620 FALSE TRUE 141521.0572 147036.2184 132193.0246 118740.8542 160657.2543 136677.8003 107039.465 166399.3861 162136.6647 0.872850428 0.906865938 0.815318514 0.732350418 0.990875534 0.84297898 0.660180504 1.026290916 1 17.30685085 -0.668157126 7.525776863 1.000003075 0.842995354 0.137911483 0.10896797 0 0 0.099614466 0.023479355 0.214705354 0.668157126 -0.157007721 EGWLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGWLFK 6 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 104.04 0.079497 118570000 203990 220190 218930 243930 244650 192870 239470 195390 235170 FALSE TRUE 191222.63 236493.0967 224123.123 250189.6568 225436.1759 248548.438 203563.6966 219784.8716 195918.6077 0.976030977 1.2070987 1.14396037 1.27700814 1.150662402 1.268631096 1.03902176 1.121817239 1 17.5798949 1.65432998 9.475365381 1.060669229 1.174763184 0.28012185 0.087775926 0.142308032 21.44561856 0.038399867 0.02041901 45.11593686 -1.65432998 0.114093956 EGWPLDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGWPLDIR 8 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 86.011 0.038005 91515000 302310 318040 279830 267610 414950 268380 257770 320530 436320 FALSE TRUE 283388.9567 341588.0125 286467.6997 274477.3257 382361.5008 345856.9492 219119.7815 360548.8761 363495.3733 0.779621909 0.93973139 0.788091736 0.755105418 1.051901974 0.95147552 0.602813124 0.99189399 1 18.47157748 EGYAWAEDKEHCEEYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EGYAWAEDKEHCEEYGR 17 1 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;;; 248.13 4.75E-21 2984620000 2918670 2332850 2577460 2513180 2744220 2034450 3258670 2362280 3692740 FALSE TRUE 2735995.655 2505576.641 2638598.568 2577672.454 2528700.031 2621762.688 2770062.686 2657215.858 3076397.838 0.889350402 0.814451437 0.857690945 0.837886577 0.821967822 0.85221835 0.900424078 0.863742597 1 21.55281065 0.375812416 0.585120341 1.005642559 0.840600997 0.773230571 0.025160415 0.939078944 0.506354661 0.036139007 0.0101356 2.375813885 -0.375812416 -0.165041563 EGYGGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EGYGGFR 7 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;; 153.26 0.0040899 2124990000 3481410 2712600 2792640 2702740 2800200 2490620 2949860 2078570 2941600 FALSE TRUE 3263514.763 2913443.726 2858882.74 2772096.884 2580283.587 3209621.562 2507555.878 2338084.04 2450627.957 1.331705514 1.18885599 1.166591906 1.131178185 1.052907105 1.309713926 1.023229932 0.954075478 1 21.22472005 8 0.136379121 0.938983866 2.124121586 0.515516881 0.087726585 66.00056204 0.602888947 0.381970229 15.18564773 100000000 -8 1.18513772 EGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPK 34 0 Q16576;E9PC52;Q16576-2;Q5JP01 Q16576 RBBP7 Histone-binding protein RBBP7 0 87.719 0.00031465 75891000 33283 36284 33618 36280 47294 25593 41368 30825 47959 FALSE TRUE 31199.87644 38970.50511 34415.43484 37211.00622 43579.72001 32981.28363 35165.25244 34673.5691 39954.33307 0.78088843 0.975376189 0.861369273 0.93133844 1.090738267 0.825474513 0.880136139 0.867830006 1 15.28606435 EHAALEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EHAALEPR 8 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 85.67 0.016578 392020000 261060 529390 307270 276930 687160 178960 239800 506300 664330 FALSE TRUE 244720.7206 568586.5864 314558.5895 284036.4926 633193.2255 230622.8468 203844.2162 569512.6695 553449.0313 0.442173907 1.027351308 0.568360539 0.513211654 1.144085886 0.416701148 0.36831615 1.029024603 1 19.07809094 1.202706141 24.88863965 1.014513764 0.658204983 0.267543331 0.256232263 280.7532647 194880.4064 0.243160579 0.060798801 15.94799686 -1.202706141 -0.356308781 EHAKS(ph)ESSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EHAKSESSQR 10 1 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 EHAKS(0.705)ES(0.095)S(0.2)QR 60.657 0.058542 87795000 88056 93643 102870 116650 124590 82029 122040 104600 114530 TRUE FALSE 82544.73214 100576.4252 105310.125 119643.4365 114805.204 105709.4407 103741.235 117659.5403 95414.20311 0.865119966 1.054103287 1.103715396 1.253937387 1.20322971 1.107900472 1.087272456 1.233144924 1 16.54191642 5.080582548 1.06938496 1.144493213 0.530079463 0.572987412 0.07532506 2.358304916 1.352074807 0.021184574 1.951847183 120387.8194 -5.080582548 -0.614413749 EHALLAYTLGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EHALLAYTLGVK 12 0 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;P68104;Q5VTE0;A0A087WV01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;; 189.13 8.31E-06 9570867000 12802256 16118970 13716840 13575013 18896650 11925457 16429463 15537408 15998712 FALSE TRUE 12000985.65 17312435.31 14042209.92 13923370.82 17412583.33 15368142.84 13966017.55 17477287.59 13328423.61 0.900405479 1.298910945 1.053553693 1.044637477 1.306424814 1.153035294 1.04783716 1.311279421 1 23.66800282 4.763846873 23.57087156 1.150168449 0.900404794 0.308540976 0.118321038 4327.764018 4034031.707 0.025970234 1.650588072 58055.9683 -4.763846873 -0.249763655 EHALTSGTIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EHALTSGTIK 10 0 E5RHG8;Q15369-2;Q15369;R4GMY8 E5RHG8 TCEB1 Transcription elongation factor B polypeptide 1 0 155.06 1.34E-05 225530000 342660 440190 333210 347310 479430 273280 376590 416090 488860 FALSE TRUE 321213.5223 472782.1256 341113.8986 356222.5626 441777.5017 352171.4997 320123.8256 468039.7524 407266.1078 0.788706735 1.160867837 0.83757006 0.87466783 1.084739175 0.864720862 0.786031097 1.149223428 1 18.63561223 3.912842329 24.96421696 0.923186048 1.001102552 0 0.143621182 318.1559015 123562.1957 0.03421528 0.061682469 8181.676985 -3.912842329 0.077916505 EHAMLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 0.026683 897730000 2391530 3067450 2554210 2527800 3421570 1869220 2651900 3066030 3742780 FALSE TRUE 2241848.406 3294567.19 2614797.067 2592667.628 3152853.694 2408833.47 2254272.214 3448830.595 3118085.839 0.718982261 1.05659926 0.838590469 0.831493346 1.011150384 0.772535971 0.722966695 1.106073012 1 21.57222921 1.221245097 24.99523087 1.053036608 0.863388175 0.352436191 0.113160459 341.2010832 492516.0307 0.107945871 0.027248075 16.64351675 -1.221245097 -0.189648433 EHAPSIIFMDEIDSIGSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EHAPSIIFMDEIDSIGSSR 19 0 P62195-2;P62195;J3QSA9;J3QQM1 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ;;;;; 358.04 4.20E-91 676116000 372320.2 403293 430051 455806 411607 390571.5 445719 359665 425311 FALSE TRUE 349017.3433 433153.2333 440252.0128 467502.7536 379281.0466 503323.1517 378887.5738 404569.967 354323.8465 0.985023579 1.222478356 1.242513077 1.319422213 1.070436129 1.420517294 1.06932564 1.141808464 1 18.43470904 1.151826775 1.629616683 1.014214718 1.211340711 0.188215385 0.126237882 0.502276594 2.546203951 0.105002631 0.031033235 14.1849162 -1.151826775 0.197125993 EHASGSGAQSEAAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EHASGSGAQSEAAGR 15 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 293.29 5.64E-44 668360000 103042 300750 266970 277470 266910 273240 323850 279420 270520 FALSE TRUE 96592.78516 323017.8429 273302.6545 284590.35 245947.9653 352119.9523 275291.699 314306.2021 225368.4644 0.428599385 1.433287678 1.212692535 1.26277805 1.091314909 1.562418918 1.22151828 1.394632576 1 17.78192613 4.744515546 24.89730831 1.288002912 0.428598987 0.724279448 0.163347533 292.4952197 1222873.39 0.034022565 0.307383367 55528.44943 -4.744515546 -0.859403924 EHASIDAQSGAGVPNPSTSAS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EHASIDAQSGAGVPNPSTSASPK 23 0 Q8IXJ6-5;Q8IXJ6-2;Q8IXJ6-3;Q8IXJ6 Q8IXJ6-5 SIRT2 NAD-dependent protein deacetylase sirtuin-2 1 EHASIDAQSGAGVPNPST(0.001)S(0.017)AS(0.982)PK;EHASIDAQSGAGVPNPSTSAS(1)PK;EHASIDAQSGAGVPNPS(0.015)T(0.053)S(0.196)AS(0.736)PK 235.63 2.73E-37 1036090000 518526 713048 781652 813874 864941 626917 1092716 774948 1091613 TRUE FALSE 486072.3833 765842.8158 800193.1546 834759.3847 797012.0229 807897.7608 928873.3801 871701.9637 909415.7382 0.534488642 0.842126196 0.879898072 0.917907344 0.876400077 0.888370111 1.021395761 0.958529666 1 19.79458045 5.171265939 1.00204259 0.93782001 3.14E-33 0.855984659 0.051054395 1.5520886 0.691752943 0.015880736 1.920852342 148342.618 -5.171265939 -0.93782001 EHDPVGQMVNNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EHDPVGQMVNNPK 13 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;;;;;;; 190.1 4.70E-06 2891390000 5054870 4635370 4885660 4955590 5127770 3745800 6335250 4738900 5614600 FALSE TRUE 4738494.71 4978577.618 5001550.162 5082758.829 4725055.629 4827151.652 5385338.076 5330562.097 4677486.988 1.013042842 1.064370169 1.06928147 1.086643072 1.0101697 1.03199681 1.151331493 1.139620935 1 22.15730221 1.750999252 25 1.111586373 1.050933742 0.1806814 0.047217581 4.603691912 9267.69199 0.019942967 0.011059468 56.36366855 -1.750999252 -0.060652631 EHDQLIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EHDQLIEK 8 0 O14980 O14980 XPO1 Exportin-1 0 ;;; 126.82 0.0012026 1703500000 6401300 6121100 6013700 6163700 6292800 4265450 7615800 5675500 5909600 FALSE TRUE 6000654.06 6574312.613 6156347.804 6321870.977 5798588.872 5496816.171 6473881.492 6384098.668 4923249.583 1.218840109 1.335360416 1.250464292 1.284085008 1.177797058 1.116501627 1.31496106 1.296724564 1 22.23117945 -1.886373425 2.659749341 0.873084541 1.254603158 0.584821617 0.06589178 7860508.32 5344020.398 6283655.436 0.016381894 0.012990521 1.886373425 0.381518617 EHDYRDEHFDFIQSHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EHDYRDEHFDFIQSHIR 17 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 ;;;;; 221.85 1.19E-15 4200370000 1163135 1515605 1359368 1488919 1649683 1085758 1481224 1251733 1513825 FALSE TRUE 1090336.457 1627821.971 1391612.851 1527127.182 1520123.552 1399198.709 1259128.212 1408014.62 1261157.828 0.864551948 1.290736128 1.10344068 1.210892997 1.205339663 1.109455675 0.998390673 1.116446007 1 20.2663174 1.971146082 6.467487656 1.041291339 1.155675607 0.113757456 0.115684227 0.316766901 45.6429874 0.044226454 0.02836289 93.57203663 -1.971146082 0.114384268 EHDYRDEHLDFIQSHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EHDYRDEHLDFIQSHLR 17 1 O43237;O43237-2;B4E2E0 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 ;;;; 225.13 8.39E-16 2008579000 627268 757894 786529 769483 885494 592708 818251 723802 712321 FALSE TRUE 588008.4156 814009.2603 805185.8393 789229.2365 815950.8732 763813.1778 695561.8588 814170.273 593430.0233 0.990863948 1.371702186 1.356833675 1.329944906 1.374974034 1.287115831 1.172104261 1.371973512 1 19.17871839 -1.390090602 0.522165769 0.857148299 1.297996087 0.334687876 0.121654873 40.28296006 5.117226365 7.970253518 0.052085571 0.04072953 1.390090602 0.440847789 EHEEAVSVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EHEEAVSVDR 10 0 B4DUC8;Q13126-4;Q13126;Q13126-3;Q13126-2 B4DUC8 MTAP S-methyl-5-thioadenosine phosphorylase 0 ;; 190.86 8.55E-07 799700000 873500 723630 845970 863670 831850 692460 937020 748360 846200 FALSE TRUE 818829.1942 777208.3181 866036.8079 885833.2344 766519.8565 892361.9609 796522.5499 841794.3933 704963.7533 1.161519568 1.102479829 1.228484165 1.256565646 1.087318111 1.265826727 1.129877311 1.194095993 1 19.42718956 -1.363269749 3.482681394 0.998940951 1.17607531 0.459036722 0.060778015 4358611.196 1706316.083 34623.89799 0.012950032 0.04332417 1.363269749 0.17713436 EHEVFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EHEVFQR 7 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ;;; 183.9 0.00063596 2909940000 2783300 2665270 2699110 2522510 2699090 2497310 3359470 2378200 3308530 FALSE TRUE 2609098.221 2862609.364 2763134.164 2587241.877 2487114.359 3218242.857 2855748.661 2675123.505 2756314.969 0.946589287 1.038563951 1.002474026 0.938659735 0.902333147 1.167588934 1.036074866 0.970543474 1 21.39430933 2.26153091 24.9997479 1.049757534 0.979437952 0.258151953 0.062836451 351.2311089 382261.7501 0.02176968 0.018203398 182.6126717 -2.26153091 -0.070319582 EHEVTIFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EHEVTIFVR 9 0 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 142.43 0.00010435 394310000 345360 271500 316250 302660 298340 255850 328780 328300 256960 FALSE TRUE 323744.5341 291602.1425 323751.5993 310426.768 274909.5798 329709.7416 279482.4912 369288.9777 214071.716 1.512318116 1.362170342 1.51235112 1.450106412 1.284193844 1.540183579 1.30555543 1.72507132 1 17.70773467 -1.389212209 4.958764884 0.999583823 1.444663308 0.556861038 0.128602642 0.000509644 6.28E-05 0.107250415 0.025256106 0.040811992 1.389212209 0.445079485 EHFGTFFECLQESLLDLHTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EHFGTFFECLQESLLDLHTK 20 0 O75691 O75691 UTP20 Small subunit processome component 20 homolog 0 177.61 3.75E-17 46327000 89024 134720 98242 113190 120990 106960 134140 113150 110270 FALSE TRUE 83452.14675 144694.809 100572.3466 116094.647 111487.9335 137837.6156 114026.9523 127277.0266 91865.22463 0.90841934 1.575077071 1.094781481 1.263749667 1.213603231 1.500433012 1.241241751 1.385475593 1 16.48723122 -1.123013597 5.052221587 0.999989296 1.288584052 0.16413281 0.190587108 2.01E-05 3.49E-06 0.161497439 0.0380639 0.075333198 1.123013597 0.288594756 EHFGTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EHFGTVK 7 0 E9PGT1;Q15631;H7C1D4;Q15631-2 E9PGT1 TSN Translin 0 117.02 0.0053251 243520000 276440 406610 310950 252220 473060 253090 366090 376620 470430 FALSE TRUE 259138.1139 436715.8275 318325.8808 258692.3922 435907.7758 326152.9744 311198.2031 423641.836 391912.1939 0.661214726 1.114320591 0.812237756 0.660077426 1.112258773 0.832209305 0.794050831 1.0809611 1 18.58017094 1.230312003 24.99720655 1.040480618 0.873453425 0.187949315 0.156578048 359.6990928 1090015.932 0.132088951 0.03523903 16.99464131 -1.230312003 -0.167027193 EHFPEILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EHFPEILK 8 0 O15479 O15479 MAGEB2 Melanoma-associated antigen B2 0 112.17 0.0030923 791350000 1554300 1722000 1326000 1517500 2376400 1612600 1425200 1478600 2597200 FALSE TRUE 1457019.138 1849498.672 1357453.346 1556441.619 2189767.13 2078131.442 1211504.491 1663206.465 2163710.541 0.67338912 0.854781005 0.627372895 0.719339112 1.012042548 0.960447991 0.559919854 0.768682517 1 21.04507608 EHFQDDVFNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EHFQDDVFNEK 11 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;;; 198.55 5.33E-08 2303550000 5256240 4105140 4538410 4297530 4236530 3749820 5457950 3926830 3952790 FALSE TRUE 4927261.321 4409088.837 4646063.228 4407811.896 3903810.023 4832332.161 4639581.067 4417103.37 3293043.813 1.496263518 1.338909862 1.410871975 1.338522093 1.185471632 1.46743634 1.408903534 1.341343638 1 21.65099028 0.892558885 9.26749873 1.000000015 1.375814895 0.660863432 0.08446538 7.147717108 616.9308102 0.076664813 0.019182178 7.808343052 -0.892558885 0.375814881 EHFQSYDLDHMEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EHFQSYDLDHMEK 13 0 Q13564-2;Q13564;Q13564-4;Q13564-3;H3BMR3;J3QRA5 Q13564-2 NAE1 NEDD8-activating enzyme E1 regulatory subunit 0 ;; 202.13 5.57E-08 419643000 571492 523535 555446 544333 582615 415802 691300 491778 624352 FALSE TRUE 535723.3359 562298.0761 568621.4414 558301.5063 536858.7681 535837.2874 587645.9827 553177.5658 520143.6177 1.029952724 1.081043883 1.093200843 1.073360294 1.032135644 1.030171801 1.129776398 1.063509283 1 18.9885505 2.970607017 24.24166696 1.062098703 1.07554294 0 0.037677212 2349.138269 1937444.078 0.011554409 0.012274392 934.5596305 -2.970607017 0.013444238 EHGAVAVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EHGAVAVER 9 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ;;; 110.38 0.0022961 3712130000 1502010 1699930 1739690 1636170 1798290 1525110 1849520 1561700 1963970 FALSE TRUE 1408001.875 1825794.586 1780956.268 1678156.892 1657059.557 1965384.499 1572201.646 1756681.683 1636170.719 0.860547044 1.115894915 1.08849049 1.025661242 1.012766906 1.20120992 0.960903179 1.073654272 1 20.64189186 EHGTVLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EHGTVLLR 8 0 O75382;O75382-3;O75382-4;E9PMK8 O75382 TRIM3 Tripartite motif-containing protein 3 0 123.98 0.0033443 0 35801 44137 60001 55993 56238 63790 83847 42026 131390 FALSE TRUE 33560.27932 47404.9494 61424.25205 57429.87518 51821.29433 82205.13746 71274.92075 47273.03861 109460.1602 0.30659812 0.433079481 0.561156241 0.524664637 0.473426078 0.75100509 0.651149428 0.431874378 1 16.74004635 -5 0.080415693 2.490066905 0.074534249 0.689304523 0.108802422 141.5676782 0.805956605 37.78126069 3.494681468 1.00E-05 5 -2.415532656 EHGVGGVSQCPEPGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EHGVGGVSQCPEPGLR 16 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 83.54 0.0077934 231310000 18776 11607 15074 9934.5 16300 16684 13710 7199.5 14043 FALSE TRUE 17600.84368 12466.39436 15431.5624 10189.43609 15019.86375 21500.39996 11654.31278 8098.373423 11699.13258 1.504457152 1.065582792 1.319034748 0.870956545 1.283844221 1.837777272 0.996168964 0.692219989 1 13.51411395 1.509052291 9.221708268 0.845701138 1.276931739 0.362541654 0.263529384 0.116904923 20.6785274 0.136922961 0.063450935 32.28882874 -1.509052291 0.4312306 EHGVPILISEIHPGQPADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EHGVPILISEIHPGQPADR 19 0 Q9HD26-2;Q9HD26;A0A0J9YVX5 Q9HD26-2 GOPC Golgi-associated PDZ and coiled-coil motif-containing protein 0 85.974 0.0017064 107700000 117710 136500 125870 132350 142830 119580 140620 118930 127380 FALSE TRUE 110342.7412 146606.602 128855.6958 135746.3251 131612.7079 154100.8048 119535.3365 133778.6723 106119.4551 1.039797473 1.381524263 1.21425139 1.279184151 1.24023166 1.452144705 1.126422449 1.260642284 1 16.69532965 -1.28239599 5.972474994 0.999986648 1.257878085 0.31190699 0.115731446 1.82E-05 2.18E-06 0.098875063 0.02330387 0.052192008 1.28239599 0.257891437 EHHFGSSGMTLHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EHHFGSSGMTLHER 14 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ; 117.08 0.00011268 556580000 70580 153375 122800 119381 162471 103243 126354 146494 160190 FALSE TRUE 66162.52379 164731.0446 125712.874 122444.5186 149711.183 133047.5781 107408.3907 164784.0984 133453.2541 0.495773027 1.234372632 0.941999315 0.917508676 1.121824897 0.996960164 0.804839053 1.234770178 1 17.02597496 4.754155729 24.62498849 1.017601155 0.495772555 0.603297154 0.136117835 1774.08769 2801261.894 0.031794463 0.787297171 56774.81514 -4.754155729 -0.5218286 EHHQLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EHHQLQR 7 0 Q13268;H0YJG9;H0YJP4 Q13268;H0YJP4 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;; 154.01 0.0017073 519169000 437514 495326 393817 378375 614701 329164 334326 490437 602681 FALSE TRUE 410130.7797 532000.4524 403158.5252 388084.7431 566424.863 424188.3033 284196.92 551669.139 502089.6476 0.816847712 1.059572638 0.802961238 0.772939145 1.128134917 0.844845747 0.566028241 1.098746293 1 18.93758545 2.011599392 24.97772616 0.806388527 0.919787005 0 0.179347416 562.0491977 1210292.285 0.063386737 0.046778693 102.7068458 -2.011599392 0.113398478 EHIEDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EHIEDFK 7 0 A0A669KBJ7;Q9H2P0;A0A2R8YCL6 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 ; 101.64 0.015854 296830000 1061310 758020 901040 831710 855920 680220 1135560 786040 847370 FALSE TRUE 994884.5016 814144.5895 922413.0943 853053.0867 788699.4958 876588.4716 965293.32 884178.8243 705938.4728 1.409307666 1.153279812 1.306648001 1.208395802 1.117235462 1.241734946 1.367390158 1.252487091 1 19.42918292 4.754873827 23.6655871 1.22866843 1.409307961 0.251983126 0.103743049 2288.989273 3320522.536 0.023387737 0.578479475 56868.769 -4.754873827 0.180639531 EHIEELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EHIEELLR 8 0 P61201;P61201-2;B4DIH5;H0YMC2 P61201 COPS2 COP9 signalosome complex subunit 2 0 ;; 160.88 0.00035078 1202080000 894040 1132060 988200 1015460 1256770 836790 1058640 1064310 1156280 FALSE TRUE 838083.6323 1215878.9 1011640.571 1041518.423 1158068.354 1078357.689 899906.7599 1197191.446 963289.3981 0.870022689 1.262215594 1.050193818 1.081210304 1.202201909 1.119453501 0.934201873 1.242815969 1 19.87760976 -1.605216227 3.143596513 0.994383323 1.097840899 0.053949863 0.124998145 15121779.16 24043789.26 715979.1151 0.028541059 0.024818971 1.605216227 0.103457575 EHIKNPDWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EHIKNPDWR 9 1 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;; 130.41 0.00021745 2067870000 2380400 3118250 2618260 2608490 3533810 2019870 3190490 2940290 3793150 FALSE TRUE 2231415.013 3349128.475 2680366.364 2675428.27 3256278.817 2602973.679 2712105.644 3307391.679 3160048.76 0.706133096 1.059834429 0.848204115 0.846641452 1.03045208 0.823713138 0.858248036 1.046626786 1 21.59151539 1.234871989 24.99842263 1.023313448 0.895119684 0.242696545 0.101794129 146.8011419 994821.9836 0.078700942 0.022652657 17.17402096 -1.234871989 -0.128193764 EHIMQMLQNPDWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EHIMQMLQNPDWK 13 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 108.97 0.0011742 435480000 607280 610280 631160 636260 762750 484320 792220 674840 844950 FALSE TRUE 569271.4288 655465.7662 646131.4133 652587.5088 702846.6918 624135.3217 673433.9656 759095.2595 703922.3864 0.808713347 0.931161984 0.917901498 0.9270731 0.998471856 0.886653605 0.956687809 1.078379199 1 19.42505684 8 0.200160839 1.011786849 0.240638825 0.521198088 0.05002346 47.52463012 0.574514604 0.087458758 11.50842458 100000000 -8 -0.771148024 EHIYDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EHIYDLR 7 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ;;;;; 126.28 0.0039676 1434230000 2137822 2700880 2346243 2265561 2695521 1692529 2577768 2366130 3013810 FALSE TRUE 2004019.537 2900855.965 2401896.992 2323699.131 2483825.654 2181134.646 2191255.619 2661546.539 2510785.641 0.798164329 1.155357876 0.956631643 0.925486865 0.98926233 0.868706038 0.872737036 1.060045308 1 21.25970743 3.567073133 5.904996918 0.937659093 1.017855156 0 0.104252788 0.474847971 24.93361368 0.025935443 0.040397612 3690.397378 -3.567073133 0.080196063 EHKLDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EHKLDGK 7 1 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 ;; 95.531 0.0080502 504660000 1019350 769270 891910 956040 1085040 667880 1185150 775250 2006040 FALSE TRUE 955550.7031 826227.5512 913066.5264 980573.605 999825.3352 860686.1139 1007447.76 872041.669 1671218.964 0.571768705 0.494386175 0.546347634 0.58674155 0.598261123 0.515004995 0.60282212 0.521799769 1 20.67246934 -4.999999999 0.408073086 8.624485782 0.544309158 0.931811105 0.037761452 184.5998663 1.253436741 1257.284358 0.021925822 1.00E-05 4.999999999 -8.080176624 EHKPGPIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EHKPGPIGK 9 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;H7C5N8;A0A2R8YET2;A0A2R8Y7F4 E7EPN9 PRRC2C Protein PRRC2C 0 89.827 0.0071164 122890000 948330 851170 821540 771720 958990 788310 939400 1001400 1155200 FALSE TRUE 888975.7181 914191.5124 841027.3168 791523.6417 883674.7938 1015882.3 798545.691 1126426.994 962389.6571 0.923717032 0.949918264 0.8738948 0.822456513 0.918208947 1.055583144 0.829752985 1.170447943 1 19.87626161 1.239300727 24.99999927 1.085223975 0.911271996 0.472640835 0.076724 15.72701001 531399.5634 0.054221797 0.017134634 17.35004986 -1.239300727 -0.173951979 EHLAMLLSSVLEAKPLLGDQSHAGSELLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EHLAMLLSSVLEAKPLLGDQSHAGSELLQR 30 1 Q12933-4;Q12933-3;Q12933;Q12933-2 Q12933-4 TRAF2 TNF receptor-associated factor 2 0 88.001 0.00077562 43392000 37845 42825 39240 40164 51659 34352 50356 38435 39188 FALSE TRUE 35476.34901 45995.80756 40170.79133 41194.67624 47601.91052 44268.86474 42805.58528 43233.69436 32647.26964 1.086655926 1.408871494 1.230448726 1.261810764 1.458067123 1.355974488 1.311153605 1.324266771 1 14.99467472 -0.673719692 5.733244938 0.999999992 1.312817527 0.468866319 0.101574038 9.22E-09 2.07E-09 0.08842877 0.02084286 0.211972884 0.673719692 0.312817535 EHLASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EHLASK 6 0 Q96TA1;Q96TA1-2;Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q96TA1;Q9P0K7-3 FAM129B;RAI14 Niban-like protein 1;Ankycorbin 0 ;; 99.279 0.038979 818640000 3581270 3418140 3546790 3392120 3872940 2692590 3831410 3362940 3950580 FALSE TRUE 3357124.703 3671222.642 3630921.534 3479167.542 3568774.915 3469897.022 3256925.64 3782810.462 3291202.676 1.020029768 1.115465379 1.103220279 1.057111301 1.084337632 1.054294543 0.989585255 1.149370256 1 21.65018344 2.147485599 4.559391033 1.040061558 1.0842768 0.052995994 0.049828529 0.400891381 14.77830917 0.018040106 0.013130786 140.4383114 -2.147485599 0.044215242 EHLELFWSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EHLELFWSR 9 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 185.6 4.27E-05 583940000 675250 1326340 775410 818320 1404970 521031 738820 1241870 1038130 FALSE TRUE 632987.3079 1424543.594 793803.0914 839319.4766 1294629.324 671444.1915 628040.7999 1396920.203 864859.3964 0.731896202 1.647138945 0.917840628 0.970469281 1.49692462 0.776362255 0.726176766 1.615199198 1 19.72210608 2.214968209 24.99851082 0.968345686 1.179919205 0.013129037 0.356992226 642.5079107 680796.9908 0.126642144 0.093584125 164.0469685 -2.214968209 0.21157352 EHLLLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EHLLLAR 7 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ;;; 103.02 0.0084705 791918000 702360 1275160 576611 583644 1712890 431753 450379 1254000 1448600 FALSE TRUE 658400.5413 1369574.173 590288.4852 598621.2931 1578366.529 556393.0822 382848.8501 1410564.66 1206819.302 0.545566797 1.134862669 0.489127481 0.49603225 1.307873123 0.461040921 0.317237924 1.168828389 1 20.20277825 1.206024082 24.99994135 1.084414947 0.690578461 0.22378957 0.313443763 358.0432065 275099.8869 0.297594037 0.074420645 16.07030362 -1.206024082 -0.393836487 EHLLSYLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EHLLSYLEK 9 0 Q9NYL9 Q9NYL9 TMOD3 Tropomodulin-3 0 129.85 0.00037767 150200000 322960 436020 326680 316550 510570 234650 335370 446580 425290 FALSE TRUE 302746.5101 468303.3745 334429.0039 324673.2089 470471.8917 302389.6458 285084.3819 502336.496 354306.3515 0.854476666 1.321747049 0.943897851 0.916362937 1.327867507 0.853469447 0.804626789 1.417802684 1 18.4346378 EHLLVSIPLLINHLQAESIVVHTYAAHALER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EHLLVSIPLLINHLQAESIVVHTYAAHALER 31 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;; 236.34 2.87E-46 4297160000 174777 303350 192814 184298 326354 180993 260254 292476 146709 FALSE TRUE 163838.0196 325810.3496 197387.6391 189027.3987 300723.4733 233242.7409 221231.3288 328992.2724 122222.3201 1.340491814 2.665718907 1.614988481 1.546586569 2.460462811 1.90834817 1.810073058 2.6917528 1 16.89914825 -1.43625057 5.706144183 0.999387097 2.009781785 0.313259846 0.467497396 0.00327764 0.000323821 0.407015777 0.095882622 0.036622622 1.43625057 1.010394689 EHMDAINHDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EHMDAINHDTK 11 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 137.16 5.89E-05 133980000 121340 113040 138290 135520 128940 102550 156780 120220 140820 FALSE TRUE 113745.546 121409.5992 141570.3041 138997.6726 118813.5725 132154.5202 133272.2945 135229.7316 117316.2323 0.969563579 1.034891736 1.206740972 1.184811939 1.012763283 1.126481116 1.13600899 1.152694124 1 16.84004312 4.404649919 2.835893122 1.125333127 0.975903579 0.357636448 0.066297193 0.272469102 4.120149333 0.015651618 0.065338393 25389.25274 -4.404649919 -0.149429547 EHMGDILYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EHMGDILYK 9 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ;;;;; 107.21 0.0021325 1586060000 5315820 4928400 5412970 5134200 5859790 4288590 6370690 4996380 7334030 FALSE TRUE 4983112.315 5293303.864 5541368.205 5265952.264 5399585.731 5526636.314 5415464.177 5620189.041 6109933.013 0.815575605 0.866344009 0.906944183 0.86186743 0.883738941 0.904533045 0.886337733 0.919844625 1 22.54272513 -5 0.11686049 1.390826756 0.819770555 0.821438429 0.020065858 70.55690722 0.539316069 6.51303794 0.21485815 1.00E-05 5 -0.571056201 EHMQAVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EHMQAVTR 8 0 P15313;C9JL73;C9JNS9 P15313 ATP6V1B1 "V-type proton ATPase subunit B, kidney isoform" 0 ;; 78.934 0.022256 45588000 26616 56689 44723.1 38961.7 52858 41078.3 42724.6 44167 55018 FALSE TRUE 24950.15207 60886.31254 45783.95305 39961.52318 48706.7459 52936.93836 36318.44287 49681.34717 45835.14037 0.544345493 1.328376264 0.99888323 0.871853405 1.062650741 1.154942211 0.79237115 1.083913931 1 15.48416647 1.747545374 24.99999982 0.939495797 1.030748388 0 0.214485957 8.388019773 23393.5823 0.092392336 0.05123634 55.91719452 -1.747545374 0.091252591 EHMQPTHPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 EHMQPTHPIR 10 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;;;;;;;;;;;; 115.29 0.00087006 10020933000 3689030 3704164 3860193 3713359 3919489 3302625 4033907 3602030 3842401 FALSE TRUE 3458140.197 3978424.157 3951758.601 3808650.079 3611668.144 4256039.224 3429060.094 4051751.375 3201079.45 1.080304395 1.242838305 1.234508128 1.189801796 1.128265699 1.329563758 1.071219927 1.265745333 1 21.61012705 -3.591802295 0.440931031 5.69E-09 1.198922336 0.345180678 0.082220704 311.7556353 6.574584867 292.7794486 0.040177134 0.000255975 3.591802295 1.19892233 EHNFFHLDPANVVMFEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EHNFFHLDPANVVMFEQR 18 0 Q3KQV9;Q3KQV9-2 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 ;; 133.54 7.20E-06 320695000 260708 325764 319346 327130 356743 242701 344104 277591 267320 FALSE TRUE 244390.7517 349883.9055 326921.0379 335524.7096 328725.8438 312764.8388 292508.7997 312248.8474 222702.565 1.097386335 1.571081615 1.467971587 1.506604603 1.476075696 1.404406091 1.313450519 1.402089138 1 17.76475865 0.266480786 0.63274403 0.985524369 1.450131511 0.474204922 0.131425689 2.063019349 1.15371425 0.195436976 0.048031451 1.847059076 -0.266480786 0.464607142 EHNGQVTGIDWAPESNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EHNGQVTGIDWAPESNR 17 0 A0A1W2PNV4;C9JEY1;C9K057;O15143;F8VXW2;C9JBJ7;C9JTT6 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 ;;; 247.61 9.09E-21 4664740000 2586350 2720130 2759890 2827890 2965110 2337750 3284990 2641500 3224350 FALSE TRUE 2424474.97 2921531.255 2825355.894 2900458.445 2732242.221 3012620.475 2792436.246 2971297.09 2686185.155 0.9025718 1.087613507 1.051809809 1.079768623 1.017145902 1.12152376 1.039554642 1.10614009 1 21.35712732 4.743369746 24.95233885 1.065276831 0.902571732 0.637712727 0.03795188 270.4168812 1403020.131 0.00758276 0.062111846 55382.14166 -4.743369746 -0.162705099 EHNSMWASLSS(ph)PDAEAVEPDFSSIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 EHNSMWASLSSPDAEAVEPDFSSIER 26 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 EHNS(0.001)MWAS(0.011)LS(0.4)S(0.588)PDAEAVEPDFSSIER;EHNS(0.005)MWAS(0.325)LS(0.325)S(0.346)PDAEAVEPDFSSIER;EHNS(0.006)MWAS(0.028)LS(0.049)S(0.917)PDAEAVEPDFSSIER;EHNSMWASLS(0.226)S(0.773)PDAEAVEPDFSSIER;EHNSMWASLS(0.028)S(0.972)PDAEAVEPDFSSIER;EHNSMWASLS(0.046)S(0.953)PDAEAVEPDFSSIER;EHNSMWASLS(0.249)S(0.751)PDAEAVEPDFSSIER;EHNS(0.001)MWAS(0.016)LS(0.086)S(0.897)PDAEAVEPDFSSIER;EHNSMWAS(0.006)LS(0.218)S(0.776)PDAEAVEPDFSSIER;EHNSMWAS(0.001)LS(0.186)S(0.813)PDAEAVEPDFSSIER 234.07 2.35E-44 1516291000 246595 638998 524472 603597 643488 472344 610336 521242 512677 TRUE FALSE 231161.0591 686310.0768 536912.7235 619086.3209 592951.0482 608702.0449 518821.7829 586320.2111 427107.8967 0.541224035 1.606877518 1.257089199 1.449484605 1.388293339 1.425171601 1.214732359 1.37276837 1 18.70424105 -1.412300956 2.940641483 0.99411528 1.315866375 0.077006207 0.286109159 26360354.53 31373956.58 1304514.647 0.064511233 0.038698938 1.412300956 0.321751096 EHPDAWTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EHPDAWTR 8 0 O14980;C9JKM9;C9J673;C9IYM2;F8WF71;C9IZS4;C9JQ02;C9JV99;H7BZC5 O14980 XPO1 Exportin-1 0 ;;; 89.542 0.013832 3585840000 3443180 4301730 3857610 4126770 4059200 3140210 4425110 3799990 3774850 FALSE TRUE 3227677.51 4620234.565 3949114.331 4232669.905 3740406.806 4046737.65 3761605.836 4274427.116 3144803.149 1.026352798 1.469164951 1.255758833 1.345925231 1.189392986 1.286801577 1.196133958 1.359203395 1 21.58453828 -3.610828171 0.33557463 1.44E-11 1.290451235 0.306090819 0.120397298 146.2537244 3.031354506 102.3025443 0.089956944 0.000245003 3.610828171 1.290451235 EHPFLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EHPFLVK 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 108.09 0.0073318 1177090000 2796260 3063560 2787870 2845480 3084760 1996260 3647920 2991760 3112830 FALSE TRUE 2621247.078 3290389.17 2853999.593 2918499.834 2842495.393 2572547.855 3100948.262 3365287.822 2593278.563 1.010785002 1.268814394 1.100537225 1.125409308 1.096101064 0.992005985 1.195763658 1.297696233 1 21.30634575 -2.327877786 2.468460967 0.092340307 1.140786721 0.157274418 0.098276025 4969710.367 4980947.319 28693240.57 0.022902109 0.004700264 2.327877786 1.048446413 EHPHS(ph)RS(ph)PS(ph)PEPR ddPTM_SK-BR-3_Pertuzumab_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 110.44 0.0017801 751470000 846210 862350 895300 779160 933170 664430 771400 691130 888800 TRUE FALSE 793247.2266 926199.2913 916536.9388 799154.5647 859882.5924 856240.1549 655735.7313 777419.1019 740453.5381 1.071299124 1.250854029 1.237804793 1.079277123 1.16129176 1.156372562 0.8855866 1.049922867 1 19.49804969 1.758344297 25 0.971305597 1.176047922 0.587642055 0.070477273 5.382587261 6808.053615 0.0324086 0.017972595 57.32503083 -1.758344297 0.204742326 EHPVIESHPDNALEDLR ddPTM_SK-BR-3_Pertuzumab_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 89.557 0.0023246 89950000 178000 195710 192210 206170 173470 148160 212370 169780 162500 FALSE TRUE 166859.2977 210200.572 196769.312 211460.6712 159846.3659 190931.3868 180527.09 190977.4067 135377.7002 1.232546405 1.55269717 1.453483932 1.562005197 1.180743695 1.410360691 1.333506846 1.410700628 1 17.04663059 -3.364478973 0.228704597 0.049641637 1.465704493 0.492787571 0.123186118 52.3903128 1.026642569 23.63416863 0.207879217 0.000432037 3.364478973 1.416062857 EHPWEVMPDLYFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EHPWEVMPDLYFYR 14 0 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;; 184.21 1.32E-06 539076000 1027640 982040 1064350 884886 931320 961590 1080700 978890 530466 FALSE TRUE 963321.8468 1054751.263 1089596.885 907593.6729 858177.884 1239185.423 918659.0677 1101106.571 441927.7977 2.179817273 2.386704953 2.46555408 2.053714832 1.941896139 2.804044981 2.078753753 2.49159835 1 18.75345116 -1.649679464 6.954388848 0.995202497 2.31004425 0.721862614 0.253585608 0.017082996 0.000860539 0.222366128 0.052529924 0.022403741 1.649679464 1.314841753 EHPWEVMPDLYFYRDPEEIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EHPWEVMPDLYFYRDPEEIEK 21 1 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;;; 194.18 2.76E-18 407822000 1106910 701960 937700 829780 740960 824490 1297320 739780 692800 FALSE TRUE 1037630.479 753933.8488 959942.6868 851073.5596 682767.9905 1062506.879 1102798.91 832143.1615 577167.2043 1.797798751 1.306265919 1.663196868 1.474570199 1.182963941 1.840899605 1.910709585 1.441771388 1 19.1386298 2.209015531 24.99994966 1.662668786 1.484424308 0 0.304429426 561.2854652 474935.569 0.104593216 0.077257861 161.8137903 -2.209015531 -0.178244478 EHPWEVMPDLYFYRDPEEIEKEEQAAAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 EHPWEVMPDLYFYRDPEEIEKEEQAAAEK 29 2 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;;;;;;;; 229.65 1.74E-33 3442914000 6241243 3164925 4311490 4215881 4616785 2818011 5435066 3520400 5603055 FALSE TRUE 5850614.742 3399259.34 4413760.579 4324067.644 4254201.329 3631525.029 4620128.31 3959929.689 4667868.923 1.253380255 0.728225106 0.945562236 0.926347272 0.911379775 0.777983506 0.989772503 0.848337808 1 22.15433262 -1.116840654 4.250942623 1.000010886 0.906762805 0.017973288 0.141742266 0.376969556 70265213.6 2345.863162 0.029027457 0.076411609 1.116840654 -0.093248081 EHPYLFSQCQAIHCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EHPYLFSQCQAIHCR 15 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 238.22 5.33E-18 860740000 46807 45061 60172 56496 55031 61428 69504 55060 74689 FALSE TRUE 43877.43342 48397.36333 61599.30826 57945.78301 50709.08724 79161.2664 59082.52044 61934.3622 62222.92339 0.705165091 0.777806003 0.989977727 0.931261018 0.81495829 1.272220302 0.949529807 0.995362462 1 15.92515856 4.999310218 0.509264655 1.027633153 0.367355396 0.478231502 0.112092026 4.706754197 0.770925808 0.060886559 1.963962377 99841.298 -4.999310218 -0.660277757 EHQHEEIQNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EHQHEEIQNVR 11 0 Q6DD88;F5H6I7 Q6DD88 ATL3 Atlastin-3 0 ; 150.46 1.96E-05 358370000 340110 366970 284640 292280 360630 269020 371620 326640 417580 FALSE TRUE 318823.1222 394140.8406 291391.7952 299780.3996 332307.5745 346681.7068 315899.031 367421.723 347883.2003 0.916465992 1.132968882 0.837613874 0.861727153 0.955227427 0.996546273 0.90806061 1.056164031 1 18.40824349 -0.471376423 7.666923718 0.999978644 0.957999903 0.021893962 0.08801773 0 0 0.082949581 0.019551404 0.337771947 0.471376423 -0.041978741 EHQISPGDFPSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EHQISPGDFPSLR 13 0 A0A024R571;Q9H4M9;C9JC03;C9J2Z4 A0A024R571 EHD1 EH domain-containing protein 1 0 ;;;; 150.05 4.41E-05 3764320000 2551330 2886290 2854970 2765720 3028040 2726010 3337180 2782970 3404870 FALSE TRUE 2391646.81 3099993.915 2922691.237 2836693.058 2790229.953 3512964.834 2836800.84 3130429.931 2836575.201 0.843145921 1.092865056 1.030359158 1.000041549 0.983661548 1.238452918 1.000079546 1.103594902 1 21.43571868 EHQMAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 76.847 0.065337 220179000 523261 491010 486042 457197 571046 318786 486904 511948 596615 FALSE TRUE 490511.0281 527364.8913 497571.1458 468929.4491 526198.3506 410814.3431 413897.2654 575865.8347 497036.1022 0.986872032 1.061019288 1.001076468 0.943451486 1.058672294 0.826528176 0.832730789 1.158599611 1 18.92299112 3.100688295 1.279712613 0.938273626 1.029036333 0 0.10138361 0.954380173 3.278748495 0.038579143 0.05152989 1260.922213 -3.100688295 0.090762707 EHQTSAYS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EHQTSAYSPPR 11 0 H3BRF9;Q96K21-2;Q96K21;Q96K21-4;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 EHQTSAY(0.021)S(0.978)PPR;EHQTSAYS(1)PPR 138.97 4.87E-05 953600000 1209917 956050 1078920 1036070 1176700 872920 1475670 1070050 1239040 TRUE FALSE 1134190.455 1026836.937 1104512.492 1062657.31 1084286.729 1124917.833 1254406.983 1203648.098 1032236.219 1.098770256 0.994769334 1.070019121 1.029471055 1.050424998 1.089787214 1.215232482 1.166058771 1 19.97734173 1.991170074 5.455831946 1.151885005 1.044922555 0.223472416 0.061144004 0.158484393 15.6617164 0.022841611 0.015035065 97.98736375 -1.991170074 -0.106962449 EHS(ph)PYGPS(ph)PLGWPSSETR ddPTM_SK-BR-3_Pertuzumab_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 2 EHS(0.98)PY(0.02)GPS(1)PLGWPSSETR;EHS(0.991)PY(0.009)GPS(1)PLGWPSSETR 153.57 1.71E-08 254230000 295802 307781 308852 297616 339982 280573 362710 285930 340852 TRUE FALSE 277288.2808 330569.4255 316178.1153 305253.3304 313281.1851 361569.8704 308325.0027 321628.9899 283961.5992 0.976499222 1.164134258 1.113453777 1.074981023 1.10325194 1.273305515 1.085798233 1.132649593 1 18.11533632 4.747526815 24.50575625 1.12688352 0.976499119 0.282327167 0.069984423 1041.731106 2847102.175 0.015029024 0.178069591 55914.80504 -4.747526815 -0.150384401 EHS(ph)PYGPSPLGWPSSETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EHSPYGPSPLGWPSSETR 18 0 Q96PC5;Q96PC5-11;Q96PC5-10;Q96PC5-9;Q96PC5-13;Q96PC5-6;G3V599;Q96PC5-14;Q96PC5-7;Q96PC5-12 Q96PC5 MIA2 Melanoma inhibitory activity protein 2 1 EHS(0.998)PY(0.002)GPSPLGWPSSETR 86.761 0.0021822 121800000 54341 57748 52015 52781 62362 42690 64185 50554 68751 TRUE FALSE 50939.89381 62023.72201 53248.82036 54135.44982 57464.34008 55013.90999 54561.05511 56865.77818 57276.01395 0.889375679 1.082891733 0.929687956 0.9451679 1.003288045 0.960505213 0.952598677 0.992837564 1 15.80564347 3.778875778 24.99699914 0.966267869 1.001856409 0 0.052107038 440.1108211 212566.7916 0.011970365 0.021579866 6010.018079 -3.778875778 0.03558854 KNPTRWS(ph)TTAGFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.976)T(0.023)TAGFLK 92.307 0.0061349 0 106230 135060 86285 98449 179060 57281 149840 121750 319550 TRUE FALSE 99581.25393 145059.9829 88331.72095 100975.368 164997.3499 73817.09482 127372.883 136950.7555 266215.0406 0.374063215 0.544897774 0.331805899 0.379300012 0.619789737 0.277283713 0.478458628 0.514436582 1 18.02223256 0.611650747 1.787376549 0.999848678 0.429513992 0.761432878 0.099742716 0.845165507 3.340104902 0.0860827 0.024164016 4.089316704 -0.611650747 -0.570334686 EHSLQVS(ph)PSLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EHSLQVSPSLEK 12 0 O95235-2;O95235 O95235-2 KIF20A Kinesin-like protein KIF20A 1 EHSLQVS(1)PSLEK;EHSLQVS(1)PSLEK;EHSLQVS(1)PSLEK;EHSLQVS(1)PSLEK 251.04 1.07E-17 1807720000 2895260 2309250 2658500 2622800 2755750 2043710 3220370 2298290 3726240 TRUE FALSE 2714050.845 2480229.273 2721560.875 2690105.488 2539324.511 2633695.9 2737505.415 2585236.566 3104306.472 0.874285728 0.798964051 0.876704958 0.866572136 0.818000585 0.848400738 0.881841223 0.83279038 1 21.56583956 -4.999999974 0.32210639 2.449222982 0.842944994 0.744999848 0.027452734 159.2744416 1.404390391 157.4549718 0.022890484 1.00E-05 4.999999974 -1.606277988 EHSNPNYDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EHSNPNYDK 9 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 147.73 9.17E-05 748000000 1847740 1780040 1709090 1757240 2072940 1345040 2140700 1919570 1957440 FALSE TRUE 1732093.252 1911836.014 1749630.422 1802333.753 1910139.654 1733331.213 1819721.908 2159232.54 1630730.618 1.062157803 1.172380031 1.072911983 1.105230829 1.171339786 1.062916949 1.115893629 1.324089041 1 20.63708705 1.431189448 24.99999989 1.181360083 1.111245231 0.051363644 0.086192719 138.5236192 75402.28463 0.042601447 0.018325881 26.98916497 -1.431189448 -0.070114852 EHSPYGPS(ph)PLGWPSSETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EHSPYGPSPLGWPSSETR 18 0 Q96PC5;Q96PC5-11;Q96PC5-10;Q96PC5-9;Q96PC5-13;Q96PC5-6;G3V599;Q96PC5-14;Q96PC5-7;Q96PC5-12 Q96PC5 MIA2 Melanoma inhibitory activity protein 2 1 EHSPYGPS(1)PLGWPSSETR;EHSPYGPS(1)PLGWPSSETR;EHSPYGPS(1)PLGWPSSETR 175.28 2.41E-12 491555000 284659 284539 286578 272099 364503 268225 324569 302333 327155 TRUE FALSE 266842.7013 305606.5636 293375.7655 279081.521 335876.4047 345657.2032 275902.8916 340079.9406 272550.717 0.979057051 1.121283286 1.076407975 1.023961794 1.232344601 1.268230761 1.012299269 1.247767551 1 18.05616519 4.738672757 24.99993384 1.120825794 0.97905701 0.172385787 0.098889132 16.51810801 3678112.872 0.021791021 0.126819652 54786.39912 -4.738672757 -0.141768784 EHTALLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EHTALLK 7 0 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ;;;;; 121.52 0.0044301 5136830000 8529170 8366640 8481890 8490340 8487270 6809500 10125320 7500920 8031760 FALSE TRUE 7995344.475 8986114.731 8683084.436 8708216.499 7820714.05 8775292.107 8607122.265 8437426.374 6691207.369 1.194903107 1.342973582 1.297685748 1.301441731 1.168804615 1.311466171 1.286333212 1.260972185 1 22.67383513 0.688672249 3.548313737 1.000001647 1.2810413 0.716929264 0.053234085 2.5898664 28.99940416 0.048401003 0.012466403 4.882837254 -0.688672249 0.281039653 EHTLAWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 110.61 0.017923 0 256330 324540 244900 258200 396380 172890 251240 339090 339770 FALSE TRUE 240286.7629 348569.2793 250709.1437 264825.8491 365249.9137 222800.5364 213568.8944 381426.1329 283060.192 0.848889281 1.23143165 0.88570965 0.935581394 1.290361287 0.787113634 0.754499928 1.347508918 1 18.11074935 EHVEEISELFYDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EHVEEISELFYDAK 14 0 Q9Y265;H7C4G5 Q9Y265 RUVBL1 RuvB-like 1 0 ;;;;; 194.12 1.80E-07 952585000 2104980 1634825 1836250 1785170 1906230 1470976 2269260 1636330 2103700 FALSE TRUE 1973233.059 1755869.144 1879806.717 1830980.484 1756522.385 1895622.892 1929005.53 1840629.403 1752578.88 1.125902567 1.001877385 1.072594643 1.044734994 1.002250116 1.081619158 1.100666881 1.050240548 1 20.74104795 EHVIEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EHVIEALR 8 0 P27635;X1WI28;A0A087WV22;H7C123;H7C2C5;F8W7C6 P27635;F8W7C6 RPL10 60S ribosomal protein L10 0 ;;;;;;; 122.52 0.0013871 8077439000 7907740 9076430 8626460 8307500 8334530 6641230 8598660 8038870 6676990 FALSE TRUE 7412808.669 9748458.321 8831083.705 8520684.515 7679969.634 8558445.29 7309370.759 9042540.615 5562557.234 1.332626049 1.752513801 1.587594219 1.531792691 1.380654492 1.538581075 1.314030661 1.625608553 1 22.40731684 -3.058234027 0.198032049 1.56E-10 1.633155305 0.538790797 0.142341748 39.81484133 0.785921105 16.98415377 0.350860644 0.000874512 3.058234027 1.633155305 EHVKPLFNMEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EHVKPLFNMEDK 12 1 Q13867;K7ESE8;J3KSD8;K7ES02 Q13867 BLMH Bleomycin hydrolase 0 ; 123.02 0.00020921 340760000 1348430 1220670 1084690 1000520 1597890 717210 1365170 1396780 1339920 FALSE TRUE 1264034.173 1311049.677 1110419.359 1026195.037 1472398.165 924256.8841 1160475.432 1571171.058 1116278.696 1.132364326 1.174482396 0.994751009 0.919300029 1.319023798 0.827980403 1.039592923 1.407507877 1 20.09026583 -1.297992973 3.825940724 0.99982639 1.084221812 0.024069614 0.174153873 0.0002344 4.30E-05 0.153255801 0.036048511 0.050350876 1.297992973 0.084395422 EHVVAASK ddPTM_SK-BR-3_Pertuzumab_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 ;; 122.13 0.0014034 682040000 1361140 1580030 1278990 1276120 1658000 1028320 1555260 1499070 1839380 FALSE TRUE 1275948.677 1697017.065 1309328.247 1308867.4 1527787.368 1325179.291 1322063.201 1686232.189 1532375.595 0.832660531 1.107441981 0.854443422 0.854142681 0.997005808 0.86478752 0.862754018 1.100403971 1 20.54733852 1.23661 24.99957609 1.050202001 0.920244527 0.301788681 0.087385814 70.6487336 905334.0509 0.07005449 0.020903086 17.24288773 -1.23661 -0.129957474 EHYPNGVCTVYGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EHYPNGVCTVYGK 13 0 P47755;F8W9N7;A0A0D9SET8 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 127.71 0.00017374 378560000 684690 646840 659020 648240 710410 540910 743210 653180 659390 FALSE TRUE 641836.4751 694732.7066 674652.2656 664874.9359 654617.2643 697061.9361 631772.5601 734730.9608 549333.5492 1.168391182 1.264682828 1.228128642 1.210330112 1.191657173 1.268922929 1.150070956 1.337495156 1 19.06732288 -1.065727933 4.539154985 0.999990096 1.225500567 0.63605534 0.054054573 3180954.155 746842.0165 409.7932074 0.011061105 0.085955182 1.065727933 0.225510471 EHYPVSSPSS(ph)PS(ph)PPAQPGGVSR ddPTM_SK-BR-3_Pertuzumab_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(0.151)S(0.85)PS(0.998)PPAQPGGVSR 183.69 2.20E-17 379730000 64179 56613 62643 64060 64790 56194 64871 52665 68222 TRUE FALSE 60162.15095 60804.68543 64128.92154 65703.88805 59701.65475 72416.29557 55144.19578 59240.34118 56835.30747 1.058534802 1.069840001 1.128328928 1.156039986 1.050432511 1.274142761 0.970245403 1.042315839 1 15.79449982 1.616964292 25 1.004709424 1.116339742 0.416607279 0.065908765 0.654713393 1794.092767 0.028150705 0.015330499 41.39656365 -1.616964292 0.111630318 EHYVDLK ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;;;; 141.78 0.0025335 34140870000 30421280 25868930 26513130 26490200 28419790 21258100 35718510 24350880 32403570 FALSE TRUE 28517266.39 27784292.49 27142033.96 27169983.38 26187814.33 27394968.37 30362851.02 27391140.97 26995204.83 1.056382664 1.02923066 1.005439082 1.006474429 0.970091336 1.014808687 1.124749792 1.014666906 1 24.68619983 1.947876353 24.99947962 1.062694835 1.012426523 0.086869844 0.039692125 441.145768 211580.8378 0.015303099 0.009878026 88.69034681 -1.947876353 -0.050268312 EIAATCSGTEWGQSSGAAS(ph)PGLFQAGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EIAATCSGTEWGQSSGAASPGLFQAGHR 28 0 P49757-3;P49757;G3V3Z8 P49757-3 NUMB Protein numb homolog 1 EIAATCSGTEWGQSSGAAS(1)PGLFQAGHR;EIAATCSGTEWGQSSGAAS(1)PGLFQAGHR;EIAATCSGTEWGQSSGAAS(1)PGLFQAGHR;EIAATCSGTEWGQS(0.001)SGAAS(0.999)PGLFQAGHR 298.74 1.27E-71 2110260000 688800 780070 801770 791120 784930 801550 931500 814910 889200 TRUE FALSE 645689.2375 837827.1945 820788.363 811421.4786 723284.7641 1032944.473 791830.2226 916653.3073 740786.7755 0.871626302 1.130996424 1.107995431 1.095350923 0.976373753 1.394388381 1.068904371 1.237405064 1 19.49869882 EIAAVISPELEHLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EIAAVISPELEHLDK 15 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4;Q63HN8-6 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 ;; 187.16 3.52E-07 173281000 281294 274799 287547 291688 330817 229361 379712 300046 298766 FALSE TRUE 263688.3107 295145.4039 294367.7506 299173.2079 304835.9673 295573.7973 322777.7107 337507.4036 248900.0245 1.059414563 1.185799015 1.182674655 1.201981432 1.224732572 1.187520162 1.296816709 1.355995863 1 17.92520685 6.368908999 0.615176952 1.229406058 1.10E-16 0.170813853 0.092822875 32.86176631 1.890217608 0.035084655 44.29113705 2338347.214 -6.368908999 -1.229406058 EIAEAYLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIAEAYLGK 9 0 P11142;E9PKE3;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 138.1 0.00034 188960000 540970 531300 470540 366630 549200 317740 586830 531070 588760 FALSE TRUE 507111.6534 570638.0048 481701.431 376038.3465 506068.0474 409466.3799 498840.2894 597375.2585 490492.1525 1.033883317 1.163398847 0.982077753 0.766655174 1.031755645 0.834807199 1.017019919 1.217909921 1 18.90387053 -0.33905787 6.65133598 0.999999899 1.004781237 0.00013023 0.13267268 0 0 0.126091569 0.029720068 0.458080844 0.33905787 0.004781339 EIAIVHS(ph)DAEKEQEEEEQKQEMEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EIAIVHSDAEKEQEEEEQKQEMEVK 25 2 Q9H307 Q9H307 PNN Pinin 1 EIAIVHS(1)DAEKEQEEEEQKQEMEVK;EIAIVHS(1)DAEKEQEEEEQKQEMEVK;EIAIVHS(1)DAEKEQEEEEQKQEMEVK;EIAIVHS(1)DAEKEQEEEEQKQEMEVK 370.53 4.37E-120 747940000 1732721 352195 689177 605075 544782 576274 1019140 496565 545919 TRUE FALSE 1624273.086 378271.8843 705524.6039 620602.2489 501997.0193 742634.9488 866329.4182 558562.2333 454801.5921 3.571388301 0.831729464 1.551279978 1.364556017 1.103771464 1.632876757 1.904851331 1.22814485 1 18.79487778 4.747399507 24.99426728 1.377902921 3.571389421 0.830175454 0.318261955 498.3692097 1409238.554 0.079235446 0.958265571 55898.41677 -4.747399507 2.1934865 EIAVHIGDRDNAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EIAVHIGDRDNAVR 14 1 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 ; 132.08 3.15E-05 413780000 100095 128846 124612 122504 141688 118970 111667 122832 154069 FALSE TRUE 93830.23262 138385.8919 127567.8555 125647.66 130560.396 153314.7077 94923.57002 138167.8456 128353.8886 0.731027581 1.078158936 0.993876048 0.978915882 1.017190811 1.194468741 0.739545728 1.076460146 1 16.96976748 -0.343615246 6.055902698 1.000000001 0.980047519 0.00206302 0.143883394 0 0 0.126469534 0.029809155 0.453298993 0.343615246 -0.019952482 EIDCLS(ph)PEAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EIDCLSPEAQK 11 0 Q32MZ4-2;Q32MZ4;C9JTC6;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 EIDCLS(1)PEAQK;EIDCLS(1)PEAQK;EIDCLS(1)PEAQK 216.34 1.27E-11 795610000 2262010 1559590 1950970 1780280 2052140 1878700 2888230 1684550 2786660 TRUE FALSE 2120434.832 1675063.666 1997247.93 1825964.999 1890973.202 2421050.192 2455166.725 1894869.776 2321548.443 0.913370918 0.721528629 0.86030853 0.786528924 0.814531012 1.042860078 1.057555672 0.816209449 1 21.14665596 2.248976765 24.93503493 0.993942483 0.810038346 0.481960185 0.081429493 142.3115679 340677.1026 0.026634825 0.022059227 177.4094565 -2.248976765 -0.183904137 EIDLLLGQTDDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EIDLLLGQTDDTR 13 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;; 140.31 9.14E-05 80913000 111171 110451 120819 115336 100957 103461 134531 104994 101800 FALSE TRUE 104213.0056 118628.907 123684.8837 118295.717 93028.24446 133328.5112 114359.3255 118102.732 84808.92235 1.228797663 1.398778615 1.45839471 1.394849902 1.096915771 1.572104768 1.348435074 1.392574375 1 16.37192843 -1.124237574 4.566300537 0.99996251 1.374030087 0.439677958 0.127488875 4.42E-05 8.47E-06 0.112083214 0.026415623 0.075121184 1.124237574 0.374067576 EIDVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EIDVDR 6 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;; 132.96 0.034132 3467720000 6103070 7518300 7512500 7412600 8107100 6752700 8578200 7200500 9522400 FALSE TRUE 5721089.743 8074962.755 7690700.048 7602819.866 7470401.068 8702094.869 7291978.546 8099498.275 7933049.923 0.721171529 1.017888811 0.969450605 0.958372875 0.941680834 1.096941902 0.919189797 1.020981634 1 22.9194442 4.742604146 24.99088886 0.987090881 0.721171425 0.744203861 0.049597854 190.5550721 1177673.859 0.010565562 0.081376884 55284.59679 -4.742604146 -0.265919456 EIEDFDSLEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EIEDFDSLEALR 12 0 P46060;B0QYT5;B0QYT4 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ;;;; 242.59 6.19E-16 816170000 1345660 1260560 1369060 1280800 1256359 1231256 1525660 1245290 1106770 FALSE TRUE 1261437.543 1353893.174 1401534.75 1313667.496 1157689.632 1586699.619 1296901.447 1400767.198 922042.937 1.368089806 1.468362394 1.520031978 1.424735708 1.255570197 1.720852203 1.406552119 1.519199531 1 19.81447441 -1.07808203 5.034127372 0.999989339 1.466481373 0.59165036 0.120117336 1.28E-05 2.35E-06 0.103635952 0.02442667 0.08354452 1.07808203 0.466492034 EIEDPEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EIEDPEDR 8 0 P27824;P27824-2;P27824-3;D6RGY2 P27824 CANX Calnexin 0 ; 119.27 0.0040145 1885260000 6442900 6745100 5745600 6091500 7124100 5454000 7344800 6862300 4281600 FALSE TRUE 6039650.39 7244514.222 5881888.345 6247818.203 6564601.923 7028481.262 6243515.426 7719073.261 3566973.3 1.693214354 2.030997603 1.648985807 1.751574144 1.840384374 1.970432821 1.750367861 2.164040101 1 21.76626899 -1.201161309 4.902949732 0.999897311 1.847596356 0.738236713 0.160162095 0.000161535 2.63E-05 0.139339109 0.03283861 0.062927241 1.201161309 0.847699045 EIEELKELLPEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EIEELKELLPEIR 13 1 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 ;;; 156.5 3.70E-05 660782000 2147260 2005650 2068150 2097460 2609350 1455844 2577310 1936140 3236410 FALSE TRUE 2012866.83 2154150.413 2117207.495 2151284.375 2404422.177 1876122.529 2190866.292 2177871.341 2696232.263 0.74654801 0.798948385 0.785246703 0.797885406 0.891771161 0.695831199 0.812565862 0.807746191 1 21.36251335 0.533812311 2.028314603 0.999976299 0.790540025 0.640661242 0.04914821 2.256670257 9.115081232 0.042143733 0.011574315 3.41831681 -0.533812311 -0.209436274 EIEELKQELIQAEIQNGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EIEELKQELIQAEIQNGVK 19 1 Q12904;Q12904-2;A0A5F9ZHC5;D6R937 Q12904 AIMP1 Aminoacyl tRNA synthase complex-interacting multifunctional protein 1;Endothelial monocyte-activating polypeptide 2 0 ; 266.78 1.35E-31 398690000 1199680 806760 986330 973580 1041660 744180 1320010 917370 1532570 FALSE TRUE 1124594.17 866493.3498 1009726.213 998563.7111 959852.2255 959012.6852 1122086.755 1031905.664 1276774.166 0.880808995 0.678658272 0.79084167 0.782098931 0.751779172 0.751121624 0.878845127 0.808213145 1 20.28407194 0.681439626 0.608110239 1.003502844 0.7593785 0.573667718 0.057990939 0.820775776 0.605228616 0.06078888 0.022698586 4.802193173 -0.681439626 -0.244124344 EIEENSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EIEENSR 7 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ; 143.61 0.0056069 535970000 1184680 1475550 1436900 1442410 1477450 1210670 1485610 1250160 1415520 FALSE TRUE 1110532.994 1584801.257 1470983.947 1479424.683 1361417.037 1560170.775 1262856.572 1406245.228 1179260.567 0.941719773 1.343894048 1.247378219 1.254535871 1.154466684 1.32300767 1.070888493 1.192480497 1 20.1694511 0.91970707 0.802471163 1.004316839 1.228870718 0.179446309 0.120160725 1.004504465 1.40066859 0.104929979 0.038041186 8.312029389 -0.91970707 0.22455388 EIEEYIHKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIEEYIHKPK 10 1 P42285 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 111.91 0.0010162 87930000 84396 81215 84898 83449 83825 72484 108060 77747 101520 FALSE TRUE 79113.80501 87228.2431 86911.82065 85590.44262 77241.72263 93408.95412 91857.40618 87453.88409 84575.65616 0.935420529 1.031363481 1.027622186 1.011998564 0.913285526 1.104442559 1.08609747 1.034031399 1 16.36795484 2.209927538 24.99992131 1.067227079 0.997637475 0.330298476 0.04783248 243.1885409 212329.6757 0.017300975 0.012779876 162.1539521 -2.209927538 -0.069589604 EIEGEEIEIVLAKPPDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EIEGEEIEIVLAKPPDKK 18 2 O43390;O43390-3;B4DT28;A0A286YEZ8;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;; 155.11 1.19E-08 749970000 1979230 1150520 1438930 1368470 1567420 1069510 1953200 1207610 2044700 FALSE TRUE 1855353.527 1235705.698 1473062.099 1403587.257 1444321.156 1378260.175 1660335.793 1358382.767 1703426.361 1.08918916 0.725423609 0.864764179 0.823978828 0.847891749 0.809110512 0.974703592 0.797441438 1 20.70000815 -0.151069438 0.492952649 1.017135882 0.848034295 0.111785259 0.102880348 9.591954227 2.592379551 0.423499798 0.047277053 0.706204632 0.151069438 -0.169101587 EIEHLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIEHLSR 7 0 O95347-2;O95347;Q5T821 O95347-2 SMC2 Structural maintenance of chromosomes protein 2 0 142.64 0.0024753 345780000 111650 230600 234080 224230 256630 217680 244540 229760 222450 FALSE TRUE 104662.0258 247673.8639 239632.4881 229984.1214 236475.315 280520.6823 207873.4972 258446.0418 185321.6579 0.564758739 1.336453962 1.29306251 1.240999698 1.27602633 1.513696162 1.121690252 1.394580885 1 17.49967197 4.741074511 24.97807366 1.284512383 0.564758482 0.714915036 0.140172529 108.1396759 1074414.211 0.028793205 0.195976089 55090.22048 -4.741074511 -0.719753902 EIEIAEQDMSALISLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIEIAEQDMSALISLR 16 0 O43865-2;O43865 O43865-2 AHCYL1 Putative adenosylhomocysteinase 2 0 151.54 1.47E-06 5190000 16346 13791 18018 15117 16229 11888 17579 14402 20727 FALSE TRUE 15322.93304 14812.09999 18445.39547 15504.92781 14954.4398 15319.87261 14943.19215 16200.1214 17267.5298 0.887384195 0.857800749 1.068212749 0.897923907 0.866043955 0.88720696 0.865392579 0.938184071 1 14.07577409 3.059396513 24.99999214 0.896433239 0.94475972 0.013020222 0.067111704 175.2823982 73774.72192 0.019224029 0.022977108 1146.559278 -3.059396513 0.04832648 EIEIDIEPTDKVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EIEIDIEPTDKVER 14 1 Q15843;F8VSA6;E9PS38;S4R3E9;E9PL57 Q15843 NEDD8;NEDD8-MDP1 NEDD8 0 ;;;;; 186.05 1.01E-06 4881380000 9727980 7883240 8701890 8594110 9143160 6679580 10654870 7578500 11509880 FALSE TRUE 9119123.097 8466923.292 8908302.94 8814649.412 8425093.095 8607866.312 9057271.158 8524692.407 9588806.671 0.951017515 0.88300073 0.929031447 0.919264484 0.878638332 0.897699433 0.944567084 0.889025371 1 23.19291985 -1.355668913 3.46381311 1.000516679 0.911630539 0.553577431 0.024967623 2585327.961 2037834.25 9117.539974 0.005399326 0.044089085 1.355668913 -0.08888614 EIELTHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EIELTHR 7 0 O43395;O43395-3 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 0 ;; 152.39 0.001817 159581000 350590 434230 398990 391960 444030 341090 436970 360090 417850 FALSE TRUE 328647.1977 466380.841 408454.2312 402018.3572 409157.6749 439557.1459 371450.4051 405048.0292 348108.1356 0.944095136 1.339758521 1.173354454 1.154866308 1.175375216 1.262702881 1.067054651 1.163569557 1 18.40917601 0.807412748 0.750317322 1.001344637 1.191984648 0.158170576 0.106540253 1.332382884 1.547448415 0.096259223 0.035208315 6.418192644 -0.807412748 0.190640012 EIENEDMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EIENEDMR 8 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 117.89 0.0046344 362240000 556660 623040 606740 626080 706730 528440 683290 609430 782050 FALSE TRUE 521819.6443 669170.5299 621132.1593 642146.2728 651226.2766 680992.0495 580837.0079 685518.677 651520.8028 0.80092553 1.027090044 0.95335737 0.985611311 0.999547941 1.045234544 0.891509535 1.052182331 1 19.31345172 4.746195914 24.8624163 0.987048128 0.800925433 0.623491067 0.046928115 572.427025 1863915.999 0.010400204 0.110020244 55743.71567 -4.746195914 -0.186122695 EIENMILNDPDFQHEDLNFLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EIENMILNDPDFQHEDLNFLTR 22 0 Q15067-2;Q15067;I3L0T4;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ;;;;;;; 309.49 3.73E-67 1185141000 883565 985735 941309 977502 1106385 757239 1196128 962547 878036 FALSE TRUE 828264.2439 1058719.845 963637.294 1002586.356 1019493.985 975841.6066 1016779.711 1082723.112 731486.1193 1.132303433 1.447354662 1.317369214 1.370615696 1.393729776 1.334053485 1.390019146 1.480169047 1 19.48047096 -1.005714542 4.613465273 0.999990561 1.364763571 0.590426555 0.093617362 7.91E-06 1.70E-06 0.078890228 0.018594124 0.098692797 1.005714542 0.36477301 EIENYPHFFLDFENAQPTEGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EIENYPHFFLDFENAQPTEGER 22 0 Q9H0Q0;C9JPE5;C9IYV6 Q9H0Q0 FAM49A Protein FAM49A 0 ; 268.36 5.80E-38 129158000 106793 136626 127532 130636 142611 109562 151815 134251 131268 FALSE TRUE 100109.0168 146741.9312 130557.1193 133988.3409 131410.9073 141190.7708 129051.7501 151012.5329 109358.5228 0.915420346 1.341842661 1.193844942 1.225220838 1.20165218 1.291081547 1.180079493 1.380894045 1 16.73870613 4.750690174 24.57453073 1.235963567 0.915420097 0.46827217 0.103881194 1177.097885 2384749.538 0.021114462 0.353705878 56323.56994 -4.750690174 -0.32054347 EIEQEAAVELSQLRDPQHDLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EIEQEAAVELSQLRDPQHDLDR 22 1 P47985 P47985 UQCRFS1 "Cytochrome b-c1 complex subunit Rieske, mitochondrial;Cytochrome b-c1 complex subunit 11" 0 ;;;; 228.48 2.16E-26 598375000 141154.7 157684.2 134512.9 145877.6 213184 147085.6 130783.3 188006 269013 FALSE TRUE 132320.0793 169359.3022 137703.6095 149621.0662 196441.3886 189546.825 111173.5583 211478.963 224112.9924 0.590416816 0.755687122 0.614438315 0.667614423 0.876528337 0.845764554 0.4960603 0.943626519 1 17.77386676 -5 0.183768208 2.24258592 0.64854169 0.356669599 0.131017489 157.2239516 1.524636331 71.06813617 0.37560241 1.00E-05 5 -1.59404423 EIES(ph)SPQYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIESSPQYR 9 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7;H3BSK9 Q8WWM7 ATXN2L Ataxin-2-like protein 1 EIES(0.839)S(0.161)PQYR 167.12 6.32E-05 174500000 461560 445600 497590 508160 463990 390080 511830 414770 584790 TRUE FALSE 432671.7835 478592.6876 509393.0698 521200.2459 427550.097 502689.7636 435085.8431 466554.9475 487184.7711 0.888106134 0.982363809 1.045584961 1.06982048 0.877593312 1.031825692 0.893061255 0.957655032 1 18.89410951 2.740291743 24.99948874 0.947822088 1.002304022 0.099528732 0.064702003 299.0244157 4318279.81 0.019170234 0.019426117 549.9101588 -2.740291743 0.054481934 EIESEIDS(ph)EEELINK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EIESEIDSEEELINK 15 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 1 EIESEIDS(1)EEELINK;EIESEIDS(1)EEELINK;EIESEIDS(1)EEELINK 259.53 8.76E-17 30446000 238355 211422 230822 234383 231627 168459 253656 205445 235456 TRUE FALSE 223436.786 227075.9049 236297.2068 240397.6646 213435.9498 217090.3786 215622.6376 231095.2605 196156.8725 1.139071923 1.157624008 1.204633841 1.225537813 1.088088054 1.106718189 1.099235703 1.178114524 1 17.58164836 2.724340139 24.68398132 1.101368659 1.181520907 0.440253503 0.048556669 641.1967888 1112991.747 0.014443051 0.013675549 530.078438 -2.724340139 0.080152247 EIESS(ph)PQYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIESSPQYR 9 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7;H3BSK9 Q8WWM7 ATXN2L Ataxin-2-like protein 1 EIES(0.277)S(0.723)PQYR 104.14 0.0034697 219940000 401760 438860 488150 440360 470960 441550 487290 427450 554670 TRUE FALSE 376614.5588 471353.651 499729.1485 451660.3831 433972.7014 569018.317 414225.3883 480818.0734 462091.9937 0.81502074 1.020042886 1.081449485 0.977425251 0.939147848 1.231396183 0.896413255 1.040524571 1 18.81782057 4.738104484 6.364297288 1.025229206 0.81049985 0.346168401 0.089953772 0.130394351 30.27483506 0.019441083 0.12119379 54714.75814 -4.738104484 -0.214729357 EIEVGGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EIEVGGGR 8 0 P62081;B5MCP9 P62081 RPS7 40S ribosomal protein S7 0 ;;; 244.8 1.35E-08 2949110000 2539600 2707910 2773770 2689220 2742980 2505520 2844490 2359050 2513710 FALSE TRUE 2380650.969 2908406.474 2839565.134 2758229.938 2527557.415 3228822.95 2417985.131 2653582.585 2094155.562 1.136807128 1.388820643 1.355947565 1.317108427 1.206957812 1.541825741 1.154634916 1.267137281 1 20.99793718 0.769484471 1.083067169 1.002692214 1.325767547 0.388132688 0.118093992 0.759139464 1.629958797 0.100063629 0.031699291 5.881450834 -0.769484471 0.323075332 EIEVGGGRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EIEVGGGRK 9 1 P62081;B5MCP9 P62081 RPS7 40S ribosomal protein S7 0 ;;;; 134.77 0.00038433 8238910000 5053520 4873030 4812620 4918940 5339870 3972630 6268310 4308280 7003940 FALSE TRUE 4737229.204 5233834.212 4926777.619 5045168.328 4920498.15 5119463.791 5328435.108 4846178.242 5834937.167 0.811873216 0.896982103 0.844358299 0.86464827 0.843282114 0.877381134 0.913194942 0.83054506 1 22.47628569 -5 0.261752028 1.876828032 0.855084006 0.667378914 0.030747202 117.3223229 1.151000767 55.34738337 0.037460798 1.00E-05 5 -1.021744025 EIFDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 EIFDSR 6 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;;;; 159.19 0.021386 43409020000 49608900 64464000 54106400 51143400 68777200 41202400 59851000 56676300 66844700 FALSE TRUE 46503967.5 69236981.63 55389829.36 52455826.23 63375716.15 53096864.01 50876898.18 63752460.81 55687887.74 0.835082266 1.243304145 0.994647698 0.94196114 1.138052074 0.953472401 0.913607972 1.144817363 1 25.73086024 3.714276998 24.23346866 1.002073749 1.083539113 0 0.124714239 683.2338745 1289071.082 0.030569458 0.047719236 5179.370729 -3.714276998 0.081465364 EIFDSRGNPTVEVDLFTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIFDSRGNPTVEVDLFTSK 19 1 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 163.91 2.26E-11 35607000 48316 67389 159630 151680 163290 170240 135460 30782 55986 FALSE TRUE 45291.98781 72378.55168 163416.499 155572.3656 150465.8621 219385.5244 115149.0305 34625.20046 46641.57492 0.971064718 1.551803339 3.503665973 3.335486974 3.226003032 4.703647439 2.468806655 0.742367738 1 15.50932888 4.266184564 2.609097947 2.917789507 1.067110013 0.19936469 1.176335694 0.388630803 5.109021351 0.287285451 0.99846691 18457.99668 -4.266184564 -1.850679494 EIFITFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIFITFR 7 0 Q96EY1-2;Q96EY1;Q96EY1-3 Q96EY1-2 DNAJA3 "DnaJ homolog subfamily A member 3, mitochondrial" 0 101.28 0.021339 51088000 156720 147310 143930 142120 186750 152520 142970 145580 187410 FALSE TRUE 146911.175 158216.9857 147344.0876 145767.0398 172083.4083 196550.048 121532.9758 163755.9835 156130.0603 0.940953809 1.013366583 0.943726578 0.933625719 1.102179862 1.258886647 0.778408562 1.048843401 1 17.25238881 EIGDLWGHLHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EIGDLWGHLHDR 12 0 O75146;O75146-2 O75146 HIP1R Huntingtin-interacting protein 1-related protein 0 ; 144.57 3.65E-05 96898000 133448 182708 173399 172300 204420 152567 200359 186990 192353 FALSE TRUE 125095.7279 196235.8904 177512.1062 176721.5097 188365.6778 196610.6162 170317.028 210336.1131 160248.0417 0.780638107 1.224575904 1.107733388 1.102799809 1.175463212 1.226914315 1.062833756 1.312565888 1 17.2899472 4.745406033 24.88735683 1.152550874 0.780637925 0.627376749 0.089846798 447.1925694 1625779.752 0.018636997 0.183733478 55642.42299 -4.745406033 -0.371912949 EIGDYIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EIGDYIR 7 0 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ; 129.39 0.0085261 406430000 800880 1051580 832400 830080 1062810 712290 938500 857500 1104480 FALSE TRUE 750754.3504 1129440.077 852144.9211 851381.2581 979341.1898 917916.5599 797780.6376 964560.7626 920135.1528 0.815917475 1.227471936 0.926108429 0.925278483 1.064344935 0.99758884 0.867025496 1.048281613 1 19.81148626 3.736073368 24.58980973 0.966902069 1.058801084 0.000364794 0.114973028 592.6428018 1627867.966 0.027109939 0.047965877 5445.946469 -3.736073368 0.091899015 EIGNLLHPSVPISNDEDVDNKVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EIGNLLHPSVPISNDEDVDNKVER 24 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ;;;;; 187.16 1.18E-17 2657780000 1920000 2247260 2446250 2461610 2662730 1935770 3035440 2298780 2613460 FALSE TRUE 1799830.627 2413649.469 2504276.205 2524779.08 2453609.927 2494595.374 2580303.952 2585787.743 2177256.642 0.826650654 1.108573708 1.150197986 1.159614825 1.12692729 1.145751643 1.185117042 1.187635712 1 21.05408004 4.762289758 3.001749163 1.14525169 0.764285831 0.768420373 0.052862094 0.176093834 2.235121752 0.011333465 0.165289325 57848.1877 -4.762289758 -0.380965859 EIGTHKPLPGITVGDIGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIGTHKPLPGITVGDIGPK 19 1 Q15067-2;Q15067;Q15067-3 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 53.779 0.070033 190890000 418740 361650 431680 403740 418310 275970 483950 356530 382100 FALSE TRUE 392531.8109 388426.9423 441919.6535 414100.6519 385457.62 355638.059 411386.1903 401043.5553 318325.0415 1.233116342 1.220221131 1.388265439 1.300873629 1.210893174 1.117216721 1.292346302 1.259855503 1 18.28014113 2.689549487 5.596894245 1.196283492 1.291845741 0.244033879 0.091966134 0.336063247 25.28676745 0.028727734 0.027345121 489.2710139 -2.689549487 0.095562249 EIHKPGYLANDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EIHKPGYLANDR 12 1 A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-3;A0A2R8Y5P0;E9PNV3 A0A2R8Y5S7 RDX Radixin 0 ; 148.72 4.01E-05 669240000 1181640 1414160 1251580 1312410 1525530 1054640 1509960 1358880 1812380 FALSE TRUE 1107683.262 1518865.878 1281268.069 1346088.663 1405721.027 1359097.447 1283555.516 1528539.159 1509882.07 0.73362237 1.005950007 0.848588174 0.891519073 0.93101379 0.900134835 0.850103158 1.012356654 1 20.52600444 1.227988061 24.99713928 1.006178433 0.890446832 0.357210608 0.069227236 260.5326964 615967.9655 0.057402263 0.014960636 16.9039446 -1.227988061 -0.115731601 EIHQDWANR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EIHQDWANR 9 0 Q8WUW1;Q8WUW1-2 Q8WUW1 BRK1 Protein BRICK1 0 ;;;; 185.6 4.27E-05 2619930000 1128690 1635590 1473930 1518460 1658600 1488690 1352250 1486850 1471860 FALSE TRUE 1058047.308 1756690.785 1508892.316 1557426.254 1528340.246 1918450.636 1149492.666 1672486.495 1226197.057 0.862868901 1.43263334 1.230546352 1.270127216 1.246406715 1.564553287 0.937445298 1.363962248 1 20.22575942 -0.642690344 4.897495549 0.999999972 1.247837396 0.112600818 0.209041553 5690427.068 1742859.276 3.258772888 0.043721923 0.227672017 0.642690344 0.247837423 EIIDAS(ph)DKEGMS(ph)PAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EIIDASDKEGMSPAKR 16 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 EIIDAS(1)DKEGMS(1)PAKR;EIIDAS(1)DKEGMS(1)PAKR;EIIDAS(1)DKEGMS(1)PAKR 107.56 0.00059994 1323210000 1673200 693360 985670 975670 988360 673840 1368770 870510 1494520 TRUE FALSE 1568477.399 744697.0958 1009050.558 1000707.344 910738.1925 868366.6691 1163535.646 979195.0897 1245074.957 1.259745359 0.598114267 0.810433582 0.803732609 0.731472581 0.697441278 0.93451052 0.78645473 1 20.24780117 0.543036211 0.903911247 0.998864697 0.795931169 0.058942888 0.178862138 3.411129251 4.325837748 0.158762638 0.051634024 3.491694275 -0.543036211 -0.202933528 EIIDASDKEGMS(ph)PAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EIIDASDKEGMSPAKR 16 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 EIIDASDKEGMS(1)PAKR;EIIDASDKEGMS(1)PAKR;EIIDASDKEGMS(1)PAKR;EIIDASDKEGMS(1)PAKR;EIIDASDKEGMS(1)PAKR;EIIDASDKEGMS(1)PAKR 150.98 3.59E-07 2526334000 4160220 2026140 2738340 2560890 2842240 1849250 3380990 2225660 3428040 TRUE FALSE 3899839.256 2176157.514 2803294.718 2626606.773 2619021.935 2383098.455 2874041.937 2503538.55 2855877.978 1.365548278 0.76199247 0.981587708 0.919719537 0.917063669 0.834453878 1.006360201 0.876626582 1 21.44550291 4.750366739 24.98905779 0.91078014 1.365548553 0.780527443 0.075541595 813.3022655 1721419.113 0.016909644 0.280286441 56281.63937 -4.750366739 0.454768412 EIIDLVLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 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 ;;;;;;;;;; 201.07 5.13E-05 7835470800 3098245 3671034 3442379 3555428 4062896 3387815 3848351 3813056 2963546 FALSE TRUE 2904331.376 3942841.177 3524033.855 3646666.302 3743812.537 4365822.194 3271326.494 4289124.435 2468911.027 1.176361296 1.596996058 1.42736365 1.477034312 1.51638212 1.768318966 1.325007851 1.737253545 1 21.23544342 -1.47658385 8.173557754 0.999973495 1.502934639 0.44635677 0.176084723 7.35E-05 4.71E-06 0.147357747 0.034730732 0.033374606 1.47658385 0.502961144 EIIDTNGAGDAFVGGFLSQLVSDKPLTECIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EIIDTNGAGDAFVGGFLSQLVSDKPLTECIR 31 1 P55263-3;P55263-2;P55263;P55263-4;A0A5F9ZHJ1 P55263-3 ADK Adenosine kinase 0 ; 316.9 7.85E-93 449060000 217654 185269 195962 190203 195762 168671 243698 181518 171374 FALSE TRUE 204031.4247 198986.5095 200610.3112 195083.931 180387.6422 217363.5796 207157.7473 204180.9219 142770.5723 1.42908599 1.393750171 1.405123675 1.366415557 1.263479156 1.522467663 1.450983518 1.430133105 1 17.12333912 -1.048034793 5.095978503 0.999994239 1.408944251 0.792306695 0.065594514 4.25E-06 7.94E-07 0.062867622 0.014817832 0.089529304 1.048034793 0.408950012 EIIKQEESVDPDYWEK ddPTM_SK-BR-3_Pertuzumab_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 ; 186.68 1.33E-09 474250000 1011930 763950 818300 839530 965440 562520 1046850 726780 1300680 FALSE TRUE 948595.1076 820513.6529 837710.4624 861073.7611 889618.2368 724910.3923 889884.561 817520.0828 1083588.105 0.875420377 0.75721914 0.773089385 0.794650437 0.820992988 0.668990725 0.821238768 0.754456494 1 20.04738503 -1.218787074 4.632233839 1.00005305 0.779481304 0.613165423 0.054028988 2.60E-05 4.38E-06 0.045875459 0.010810352 0.060424481 1.218787074 -0.220571745 EIILDDDECPLQIFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EIILDDDECPLQIFR 15 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;H0Y7R8;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 0 ;;; 248.32 5.25E-18 105522000 88368 109955 107505 104392 124545 91282 111948 94732 109128 FALSE TRUE 82837.20462 118096.1826 110055.0694 107070.8755 114763.7381 117633.6316 95162.43667 106559.4987 90913.83181 0.911161734 1.298990267 1.210542633 1.177718212 1.262335288 1.29390247 1.046732216 1.172093362 1 16.47221219 1.120994294 1.144628262 1.014082048 1.203414642 0.150760517 0.11920579 0.697396255 1.902776391 0.102275964 0.032911727 13.21278276 -1.120994294 0.189332594 EIIQDVTLHDLDVANAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EIIQDVTLHDLDVANAR 17 0 Q9Y265;H7C4G5;Q9Y265-2;E7ETR0;H7C4I3 Q9Y265 RUVBL1 RuvB-like 1 0 ; 141.86 6.08E-07 280420000 80913 83744 89681 81802 81314 70874 86993 80991 70750 FALSE TRUE 75848.79976 89944.4929 91808.27567 83901.17781 74927.92644 91334.17326 73949.20725 91102.90463 58941.36794 1.286851704 1.525999413 1.557620376 1.423468453 1.271228155 1.549576748 1.254623193 1.545653042 1 15.84699292 -3.175444129 0.283695521 2.24E-10 1.470256976 0.521218802 0.124544114 54.61409662 1.334742054 32.49554877 0.133062963 0.000667661 3.175444129 1.470256976 EIISHDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EIISHDTR 8 0 P00387-2;P00387;P00387-3;B1AHF3 P00387-2 CYB5R3 NADH-cytochrome b5 reductase 3;NADH-cytochrome b5 reductase 3 membrane-bound form;NADH-cytochrome b5 reductase 3 soluble form 0 ;; 115.71 0.0024106 1230530000 872440 1552130 1272150 1302490 1558760 1389330 1325240 1350000 1280990 FALSE TRUE 817835.5377 1667051.32 1302325.999 1335914.099 1436341.277 1790407.017 1126532.565 1518550.472 1067184.493 0.766348783 1.56210227 1.220338195 1.25181176 1.345916555 1.677692122 1.05561182 1.422950278 1 20.02537818 -1.395077715 3.624518486 0.998052244 1.305803689 0.108632905 0.254547394 2427.8528 54227480.73 148213.3291 0.052547605 0.040264498 1.395077715 0.307751445 EIKDSLAEVEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EIKDSLAEVEEK 12 1 Q32MZ4-2;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ; 179.41 1.89E-05 291340000 674470 430370 528250 517550 606300 372970 685690 448280 943750 FALSE TRUE 632256.1267 462235.0426 540780.3395 530831.2092 558683.6437 480640.3843 582877.1501 504248.7448 786232.0281 0.804159719 0.587911744 0.687812656 0.675158465 0.710583675 0.611321298 0.741355133 0.641348516 1 19.58459561 -4.732473049 0.527586374 9.992552169 0.67462082 0.714068185 0.062885014 1208.256431 6.814399168 12816.40746 0.024998548 1.85E-05 4.732473049 -9.31793135 EIKEEEEGS(ph)EDDSNVKPDFMVTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIKEEEEGSEDDSNVKPDFMVTLK 24 2 E9PGM7;O94988-6;O94988-5;O94988-1;O94988 E9PGM7 FAM13A Protein FAM13A 1 EIKEEEEGS(1)EDDSNVKPDFMVTLK 206.16 4.66E-25 182270000 575620 220910 323170 301210 356880 207310 439370 291010 670330 TRUE FALSE 539592.9717 237266.4063 330835.745 308939.5585 328852.0844 267157.0316 373490.5474 327343.2391 558447.5925 0.966237439 0.424867811 0.592420398 0.553211371 0.5888683 0.478392306 0.668801428 0.586166443 1 19.09106237 -0.079450017 0.979276356 1.005408893 0.582673497 0.409186162 0.145722814 8.207957853 6.498498474 0.288194293 0.039714305 0.83281777 0.079450017 -0.422735396 EILDESLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EILDESLR 8 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 164.53 0.00076672 435170000 729080 881360 834250 875370 917560 762210 915630 807860 803590 FALSE TRUE 683448.1842 946616.8115 854038.804 897833.4762 845498.5389 982247.6536 778339.7818 908723.0993 669465.6376 1.02088613 1.413988647 1.275702226 1.341119582 1.262945387 1.467211457 1.162628428 1.357385724 1 19.35265048 -0.832022331 5.195326969 0.999999746 1.296836905 0.335977749 0.126550468 3.23E-07 7.26E-08 0.106338197 0.025064132 0.14722368 0.832022331 0.296837159 EILFYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EILFYDR 7 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ;;;; 126.28 0.0092303 692526000 624651 956040 718748 686752 1018190 569746 674739 845695 926849 FALSE TRUE 585555.2089 1026826.196 735797.042 704375.219 938225.4646 734222.4211 573568.1509 951281.8824 772151.9142 0.758341977 1.329824064 0.952917461 0.912223626 1.215078856 0.950878198 0.742817754 1.231987987 1 19.55852519 2.032353958 24.99429185 0.933981403 1.059648511 0 0.197420753 475.6775984 367471.5714 0.069548661 0.051364748 107.734291 -2.032353958 0.125667108 EILGTAQSVGCNVDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EILGTAQSVGCNVDGR 16 0 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;; 271.64 8.64E-35 885940000 242625 231785 230709 245736 232145 190575 251095 192151 234592 FALSE TRUE 227439.5343 248946.6026 236181.5264 252042.0018 213913.2681 245590.9088 213445.6358 216141.4753 195437.0797 1.163748122 1.273794118 1.20847859 1.28963246 1.094537784 1.256623918 1.092145033 1.105938933 1 17.57634469 1.328376052 0.684933857 1.000137691 1.233573813 0.593209201 0.059620055 0.383531013 0.4168678 0.049798827 0.021810945 21.29982583 -1.328376052 0.233436122 EILHNTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EILHNTEK 8 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ;; 131.06 0.0010212 1225360000 1849350 2032290 2009400 1958630 2246210 1670920 2354870 1912960 2487280 FALSE TRUE 1733602.485 2182762.866 2057063.917 2008891.762 2069801.727 2153287.479 2001779.105 2151797.267 2072136.9 0.836625459 1.053387383 0.992725875 0.969478301 0.998873061 1.03916275 0.966045779 1.038443583 1 20.98268789 4.748648492 24.80113754 1.005926839 0.836625355 0.773088646 0.029045203 585.8488239 1440282.673 0.006672354 0.089583612 56059.40604 -4.748648492 -0.169301483 EILKEQENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EILKEQENR 9 1 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 74.841 0.036435 565840000 362760 439700 420660 464490 544480 293960 495390 387660 722890 FALSE TRUE 340055.4991 472255.8455 430638.2539 476409.5998 501718.7371 378821.48 421110.8685 436060.2043 602234.989 0.564655833 0.784172049 0.715066812 0.791069281 0.833094633 0.629026023 0.699246766 0.72406986 1 19.199967 -1.158101651 3.40651119 1.000358581 0.723187229 0.562107196 0.078205684 13412066.92 20994139.48 54719.22239 0.017296402 0.069486166 1.158101651 -0.277171352 EILKEQENRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EILKEQENRK 10 2 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 67.776 0.034848 197760000 193450 157170 193690 196370 222620 152550 253900 149200 425040 FALSE TRUE 181342.3098 168807.0303 198284.4183 201409.1867 205136.3232 196588.7086 215830.0521 167827.9484 354098.0781 0.512124524 0.476723938 0.559970332 0.568794916 0.579320634 0.555181518 0.609520541 0.473958936 1 18.43378949 -5 0.334607216 5.735486777 0.527761148 0.905841987 0.046135341 102.2917826 0.874298709 345.2993565 0.036699397 1.00E-05 5 -5.20772563 EILNLIHLEELSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EILNLIHLEELSLR 14 0 Q96CX6 Q96CX6 LRRC58 Leucine-rich repeat-containing protein 58 0 ; 138.39 1.57E-05 106518000 237917 289570 281330 260710 291170 238600 278560 263130 257970 FALSE TRUE 223026.1997 311010.0641 288003.2805 267400.26 268302.6827 307479.9467 236792.514 295982.3597 214913.1405 1.03775041 1.44714308 1.340091536 1.244224804 1.248423815 1.430717294 1.101805658 1.377218532 1 17.71339417 -1.490952815 0.357959207 0.79766885 1.309830448 0.270106004 0.135177453 28.3514687 2.071846388 5.300591271 0.096070257 0.032288449 1.490952815 0.512161598 EILS(ph)PLFPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EILSPLFPR 9 0 A0A2R8YH03;Q5VWN6 A0A2R8YH03 FAM208B Protein FAM208B 1 EILS(1)PLFPR;EILS(1)PLFPR;EILS(1)PLFPR 107.24 0.0029423 40606000 32832.8 37406.3 34653.7 35348 36839.7 34235.7 39579.6 26260.9 38741.8 TRUE FALSE 30777.85366 40175.90137 35475.70213 36255.08952 33946.45857 44118.99082 33645.00642 29539.63117 32275.5433 0.953596764 1.244778469 1.099151199 1.123299124 1.051770322 1.366948045 1.042430366 0.915232655 1 14.97815376 1.492289556 8.936647124 0.964378976 1.147225558 0.318387251 0.111040457 0.104178942 23.20476262 0.054508723 0.025147334 31.06630172 -1.492289556 0.182846582 EILSDDKHDWDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EILSDDKHDWDQR 13 1 E3W994;J3KR49;O75122;A0A0U1RQI6;B3KR06;E7ENG2;O75122-2;C9J668;D6RBU8;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 0 ; 202.25 5.73E-08 445110000 850520 757870 829920 810400 923210 657590 1092670 790080 1104850 FALSE TRUE 797287.4714 813983.4834 849606.0943 831196.236 850704.8106 847425.5579 928834.2774 888723.2272 920443.3974 0.866199349 0.884338446 0.923040023 0.903038947 0.924233704 0.920671016 1.009116128 0.965538163 1 19.81196948 2.074788722 0.775879596 1.00328018 0.889456191 0.798593559 0.02083465 0.273208172 0.309467201 0.017462584 0.009587628 118.7924178 -2.074788722 -0.113823989 EILSDDKHDWEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EILSDDKHDWEQR 13 1 Q7Z460;C9J151;C9JP76;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 0 136.72 4.15E-05 74175000 113970 113610 109770 111510 116570 90148 123210 100830 130460 FALSE TRUE 106836.8211 122021.8026 112373.7962 114371.5354 107415.0624 116172.2642 104735.8043 113418.8475 108685.3832 0.982991622 1.122706651 1.033936606 1.052317543 0.988311945 1.068885813 0.963660441 1.043551986 1 16.7297984 3.058989139 1.506856522 1.010619266 1.064670436 0.087472109 0.045067339 0.572822932 2.67684818 0.014930343 0.018822415 1145.484293 -3.058989139 0.05405117 EILSEVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EILSEVER 8 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;; 174.16 0.00063642 2528820000 2438900 3076110 2627290 2854990 3226220 2318980 3037030 2528380 3141120 FALSE TRUE 2286253.603 3303868.385 2689610.559 2928253.877 2972845.695 2988431.881 2581655.546 2844053.809 2616846.78 0.873667354 1.262537956 1.0278059 1.119000891 1.136041177 1.141997271 0.986552047 1.086824735 1 21.31939802 1.74139633 24.99984555 1.02708879 1.108047178 0.081257269 0.101784979 0.960891872 8521.863811 0.042534372 0.023587607 55.1310584 -1.74139633 0.080958388 EILSPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EILSPLR 7 0 A0A140T9S5;Q9Y334-2;Q9Y334 A0A140T9S5 VWA7 von Willebrand factor A domain-containing protein 7 0 ;; 111.28 0.036031 0 803290 1010840 958180 953090 1051370 840250 1023570 830040 1052420 FALSE TRUE 753013.5128 1085683.645 980908.4821 977547.903 968799.6412 1082816.535 870095.1809 933672.3211 876764.3031 0.858855122 1.238284499 1.118782412 1.114949479 1.104971584 1.235014394 0.992393483 1.06490686 1 19.74182954 1.646034168 11.60173344 1.021820976 1.12676266 0.136260518 0.105344266 0.18302878 42.62916622 0.045431548 0.024609918 44.26231944 -1.646034168 0.104941685 EILVGDVGVTITDPFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EILVGDVGVTITDPFK 16 0 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ; 205.96 4.94E-11 29867000 224924 184111 202347 198914 187229 187846 236552 183540 174328 FALSE TRUE 210846.4083 197742.77 207146.7664 204018.47 172524.7896 242074.0908 201083.2236 206455.373 145231.5306 1.451794989 1.361569139 1.426320893 1.404780829 1.187929294 1.66681498 1.384570023 1.421560264 1 17.14799518 -0.978438786 4.945440683 0.999996345 1.412056916 0.557635739 0.115645645 4.17E-06 8.61E-07 0.100129248 0.023600481 0.105089957 0.978438786 0.412060571 EIPAS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIPASPSR 8 0 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 1 EIPAS(0.987)PS(0.013)R 100.79 0.0061429 240840000 192890 167900 186320 167010 204770 164600 206480 153310 218610 TRUE FALSE 180817.3592 180331.4907 190739.5984 171295.7593 188688.1902 212117.3479 175520.2409 172451.091 182122.5787 0.992833291 0.990165481 1.047314395 0.94055202 1.036050508 1.1646955 0.963747835 0.946895724 1 17.47455027 1.584183877 25 0.966463001 1.026154283 0.17863072 0.058678277 1.541758906 1621.698181 0.030644834 0.014199472 38.38697391 -1.584183877 0.059691282 EIPFNEDPNPNTHSS(ph)GPSTPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIPFNEDPNPNTHSSGPSTPLK 22 0 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 EIPFNEDPNPNT(0.002)HS(0.146)S(0.387)GPS(0.387)T(0.079)PLK 107.19 0.00029783 193590000 173290 172480 157130 165050 177070 128810 191990 140360 228110 TRUE FALSE 162444.0882 185250.5987 160857.1978 169285.4624 163163.6365 165995.3559 163202.8818 157884.255 190036.9674 0.854802571 0.974813486 0.846452141 0.890802799 0.85858893 0.873489818 0.858795444 0.830808117 1 17.53592056 5.086463029 16.49315675 0.886846296 0.000203877 0.036331558 0.05486684 17077310.25 39948259.55 0.01213387 547448048 122028.9935 -5.086463029 -0.886642419 EIPS(ph)ATQS(ph)PISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIPSATQSPISK 12 0 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 2 EIPS(0.996)AT(0.142)QS(0.862)PIS(0.001)K 79.885 0.031912 247660000 180840 174570 183250 175100 168540 124500 201480 148280 203530 TRUE FALSE 169521.5472 187495.3444 187596.7765 179593.3624 155303.5483 160441.1289 171269.9444 166793.0844 169559.5281 0.999776002 1.105778876 1.106377085 1.05917588 0.915923452 0.946223021 1.010087409 0.983684528 1 17.37143233 2.90349064 6.015792747 0.973277563 1.083257881 0.587548018 0.039787402 0.146565411 7.530052379 0.01211381 0.01292582 800.7383704 -2.90349064 0.109980318 EIPSATQS(ph)PISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EIPSATQSPISK 12 0 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 EIPSAT(0.005)QS(0.991)PIS(0.004)K;EIPSAT(0.01)QS(0.99)PISK;EIPSAT(0.018)QS(0.982)PISK 205.2 1.10E-07 5175990000 4228200 2855350 3451100 3255650 3387300 2488050 4417800 2874610 3232650 TRUE FALSE 3963564.51 3066763.085 3532961.722 3339195.491 3121275.122 3206309.645 3755391.903 3233511.386 2693099.831 1.471748081 1.138748386 1.311856947 1.239907801 1.158989758 1.190564719 1.39444957 1.200665252 1 21.36083628 0.97882803 23.98029197 0.999999993 1.263004285 0.407541878 0.102890398 979.6156867 1109557.36 0.091506684 0.022876671 9.524189551 -0.97882803 0.263004292 EIPSHVLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EIPSHVLSK 9 0 E5RHG8;Q15369-2;Q15369 E5RHG8 TCEB1 Transcription elongation factor B polypeptide 1 0 ;; 143.89 0.00010086 1360130000 3147580 3184580 3345060 3340730 3589420 2737760 3566170 3044070 3153700 FALSE TRUE 2950578.586 3420369.617 3424406.403 3426458.788 3307521.432 3528106.868 3031455.915 3424128.84 2627327.096 1.123034353 1.301843848 1.303380309 1.304161477 1.258892141 1.342850258 1.153817475 1.303274665 1 21.32516439 -0.514952603 0.580346448 0.962739386 1.273791912 0.560222744 0.071656592 7.406777427 1.992274586 0.633753037 0.027383114 0.305525453 0.514952603 0.311052526 EIPYTFEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EIPYTFEDR 9 0 P34897-3;P34897-2;P34897;H0YIZ0;G3V2Y4 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial;Serine hydroxymethyltransferase" 0 ;;; 209.84 1.81E-05 1064920000 771480 816380 769300 722975 1033210 704448 699383 813720 1053480 FALSE TRUE 723194.4439 876825.6246 787548.1593 741527.7625 952065.8544 907810.7018 594517.0119 915314.7332 877647.3823 0.824014813 0.999063681 0.897340065 0.844903976 1.084793134 1.034368381 0.67739849 1.042918548 1 19.74328189 EIQAMSQCHHPNIVSYYTSFVVKDELWLVMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIQAMSQCHHPNIVSYYTSFVVKDELWLVMK 31 1 O95747;C9JIG9;F8WBK9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 0 62.683 0.01016 15525000 38256 41460 32747 30490 55110 30931 39763 50409 14994 FALSE TRUE 35861.62525 44529.74154 33523.7743 31272.42502 50781.8829 39860.27758 33800.90729 56702.67461 12491.40454 2.87090416 3.564830633 2.683747389 2.503515512 4.065346115 3.191016468 2.705933284 4.539335385 1 13.60864808 -1.759064985 2.779928947 0.529277185 3.201106679 0.545172893 0.647961541 56309721.12 40469778.59 180260369.1 0.140407768 0.017415463 1.759064985 2.671829494 EIQGHQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIQGHQPR 8 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 157.8 0.00037117 146980000 219080 259200 244620 251580 271720 210420 249040 246410 260700 FALSE TRUE 205368.1739 278391.4377 250422.5019 258035.9687 250380.2073 271164.8381 211698.764 277174.8309 217187.4858 0.945580143 1.281802387 1.153024545 1.188079358 1.152829807 1.248528833 0.974728186 1.276200744 1 17.72858145 1.75302333 25 1.083918275 1.175189745 0.080403952 0.118584318 9.74892173 16874.52076 0.048634403 0.026970587 56.6269708 -1.75302333 0.091271471 EIQNGNLHES(ph)DSESVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EIQNGNLHESDSESVPR 17 0 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 1 EIQNGNLHES(1)DSESVPR;EIQNGNLHES(1)DSESVPR;EIQNGNLHES(0.998)DS(0.002)ESVPR;EIQNGNLHES(1)DSESVPR;EIQNGNLHES(0.998)DS(0.002)ESVPR 287.95 5.14E-37 2655360000 1187539 1281204 1095900 1088058 1428677 1085387 1516780 1343775 1129776 TRUE FALSE 1113213.054 1376065.677 1121895.266 1115979.41 1316474.471 1398720.607 1289352.92 1511548.267 941209.087 1.182747882 1.462019116 1.191972412 1.185687034 1.398705654 1.486089145 1.369890004 1.605964379 1 19.84415572 2.647057381 10.42716239 1.402222266 1.279446749 0.07954468 0.173367176 1.16230302 126.9908738 0.050545045 0.047639506 443.6672591 -2.647057381 -0.122775517 EIQNGNLHESDS(ph)ESVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIQNGNLHESDSESVPR 17 0 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 1 EIQNGNLHES(0.242)DS(0.758)ESVPR 195.53 1.08E-11 264200000 110390 124590 103800 105290 121820 91754 142450 119170 120340 TRUE FALSE 103480.887 133814.7732 106262.185 107991.9197 112252.7486 118241.8903 121090.9449 134048.6368 100254.4766 1.032182208 1.334751103 1.05992459 1.077178031 1.119678167 1.179417562 1.20783579 1.337083803 1 16.61330713 2.035050871 4.957528627 1.202510254 1.142512826 0.033469788 0.115425811 0.621543272 37.49619791 0.04393931 0.0306763 108.4053886 -2.035050871 -0.059997428 EIQSSNLETAMSVIGDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIQSSNLETAMSVIGDRR 18 1 Q9NX55 Q9NX55 HYPK Huntingtin-interacting protein K 0 80.596 0.013376 1793500000 797750 2503800 1921500 2123500 2155600 1894100 1833900 1874500 1932500 FALSE TRUE 747820.2515 2689183.957 1967078.887 2177992.605 1986307.871 2440895.922 1558923.72 2108535.451 1609953.266 0.464498112 1.670349081 1.221823595 1.352829707 1.23376741 1.516128433 0.96830371 1.309687366 1 20.61858738 1.719708587 22.60444684 1.104337467 1.293896145 0.029759074 0.327082807 1.527451039 1815.523915 0.136493409 0.075670871 52.44554306 -1.719708587 0.189558678 EIQSTLEGDRGS(ph)GNWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 216.61 9.10E-15 5205560000 1224100 1315160 1230811 1272880 1593100 1130398 1352072 1243200 1346790 TRUE FALSE 1147485.766 1412535.815 1260006.418 1305544.256 1467984.352 1456725.552 1149341.356 1398416.257 1122002.048 1.022712719 1.258942278 1.122998322 1.163584556 1.308361562 1.298326999 1.024366539 1.246358025 1 20.09764388 -0.671125826 7.011760499 1.000002356 1.179531327 0.236637692 0.101980398 0 0 0.092167736 0.021724144 0.213242701 0.671125826 0.179528971 EIQTAVR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 191.44 0.0012232 23566200000 7267820 9497600 7716650 7719160 9364900 6504620 8463800 7598750 8385700 FALSE TRUE 6812940.12 10200812.19 7899692.582 7917246.714 8629418.53 8382398.2 7194731.764 8547470.664 6986072.496 0.975217495 1.46016409 1.130777355 1.133290088 1.235231746 1.199872776 1.029867893 1.22350157 1 22.73605018 1.251566391 0.343330871 0.99077106 1.250545916 0.102838831 0.133701134 2.183206694 0.836519508 0.217402587 0.151421776 17.84704796 -1.251566391 0.259774855 EIQVQHPAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EIQVQHPAAK 10 0 P49368;B4DUR8;Q5SZX6;E9PRC8;Q5SZX9 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;; 120.06 0.00060965 3515720000 7061500 6341600 6882600 6778100 7351000 5440600 8140100 6375200 8556300 FALSE TRUE 6619533.32 6811138.662 7045858.522 6952037.521 6773682.113 7011212.899 6919567.574 7171157.754 7128198.254 0.928640462 0.955520374 0.988448731 0.97528678 0.950265673 0.98358837 0.970731639 1.006026698 1 22.76510603 6.785884615 0.696348682 0.980445598 4.05E-10 0.562609664 0.015542727 34.01345373 1.126820026 0.005438613 46.6149499 6107797.288 -6.785884615 -0.980445598 EIRPALELLEPIEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EIRPALELLEPIEQK 15 1 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;; 195.2 1.85E-08 1265334000 2882430 2191670 2336140 2336920 2445040 1833720 3024460 2355900 2341360 FALSE TRUE 2702023.852 2353943.527 2391554.344 2396889.324 2253016.421 2363085.196 2570970.301 2650039.301 1950571.89 1.385246996 1.206796601 1.226078544 1.228813629 1.155054286 1.211483262 1.318059751 1.358596068 1 20.89546574 4.743051442 24.19842513 1.226550511 1.385247098 0.231003151 0.095956819 454.6511946 2449706.855 0.020862408 0.165330972 55341.56577 -4.743051442 0.158696586 EIRPVCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EIRPVCR 7 1 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;H0YCC6 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ;;;;; 166.78 0.0010129 5452810000 1493490 1787060 1715710 1572650 1928490 1337590 1773690 1584420 1713750 FALSE TRUE 1400015.127 1919375.782 1756407.451 1613006.861 1777034.175 1723730.519 1507741.651 1782238.325 1427714.054 0.980599107 1.344369888 1.23022355 1.129782856 1.244670927 1.207335961 1.056052959 1.24831602 1 20.44527563 0.235481628 0.399663939 0.976200264 1.21913843 0.167796976 0.107782923 4.637571052 1.183395813 0.320011727 0.07355205 1.719814584 -0.235481628 0.242938166 EIS(ph)DDEAEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EISDDEAEEEK 11 0 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 1 EIS(1)DDEAEEEK;EIS(1)DDEAEEEK 244.72 7.13E-16 1064680000 2929900 1163770 1816520 1469370 1182900 1684200 2858400 1476930 875490 TRUE FALSE 2746522.789 1249936.742 1859608.712 1507076.522 1089999.806 2170401.199 2429809.456 1661327.962 729365.0631 3.765635246 1.713732676 2.5496268 2.066285593 1.494450256 2.975740557 3.331403681 2.277772882 1 19.47628157 0.968056816 23.58257372 0.999999972 2.503274438 0.326954015 0.69416515 2687.159275 1983841.938 0.662673452 0.165668363 9.290879264 -0.968056816 1.503274466 EIS(ph)DDEAEEEKGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EISDDEAEEEKGEK 14 1 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 1 EIS(1)DDEAEEEKGEK;EIS(1)DDEAEEEKGEK;EIS(1)DDEAEEEKGEK;EIS(1)DDEAEEEKGEK 212.32 1.58E-09 4629450000 4619270 1220601 2399770 1831940 1481620 1924980 3552100 1659880 1213640 TRUE FALSE 4330158.136 1310975.568 2456693.678 1878950.682 1365259.542 2480690.477 3019495.581 1867119.672 1011075.644 4.282724209 1.296614726 2.429782275 1.85836806 1.350304055 2.453516206 2.986419068 1.84666665 1 19.94745951 0.987431293 23.53491934 0.999999907 2.275118799 0.205789229 0.854959888 486.6595209 911274.3586 0.760323711 0.190080928 9.714742489 -0.987431293 1.275118892 EIS(ph)LPEVS(ph)LLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EISLPEVSLLK 11 0 Q2M3G0-1;Q2M3G0 Q2M3G0-1 ABCB5 ATP-binding cassette sub-family B member 5 2 EIS(1)LPEVS(1)LLK 67.93 0.085708 131310000 136200 417220 371960 353030 328760 471200 361050 386350 214890 TRUE FALSE 127675.4851 448111.4029 380783.0669 362089.3475 302940.5158 607227.7907 306913.9043 434586.648 179023.4708 0.713177354 2.50308745 2.127000807 2.022580313 1.692183234 3.391889277 1.714378026 2.427540066 1 17.44978922 EIS(ph)SS(ph)PTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EISSSPTSK 9 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 EIS(0.952)S(0.053)S(0.995)PTSK;EIS(0.99)S(0.01)S(1)PTSK;EIS(0.924)S(0.077)S(0.984)PT(0.015)SK;EIS(0.946)S(0.07)S(0.979)PT(0.004)S(0.001)K;EIS(0.92)S(0.083)S(0.992)PT(0.005)S(0.001)K 204 2.53E-05 5076280000 16265000 11032330 12946500 12453300 12924700 9610660 15842100 10676420 14175100 TRUE FALSE 15247002.68 11849175.19 13253597.09 12772872.76 11909646.2 12385101.53 13466724.18 12009394.54 11809184.24 1.291113965 1.003386428 1.12231267 1.081605004 1.008507104 1.048768592 1.140360241 1.016953779 1 23.49340597 4.747958602 24.91353306 1.063339939 1.291114092 0.685881349 0.050244445 736.9472531 1953563.121 0.011485128 0.147918771 55970.42466 -4.747958602 0.227774153 EIS(ph)TPTHWSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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;EIS(0.646)T(0.353)PT(0.001)HWSK;EIS(0.5)T(0.5)PTHWSK 111.94 0.0010868 495720000 1400090 2234800 2134290 2111170 2254130 1808790 2819610 2116570 2464170 TRUE FALSE 1312460.866 2400266.917 2184916.367 2165346.196 2077099.723 2330958.31 2396835.656 2380828.424 2052884.108 0.639325357 1.169216961 1.064315496 1.054782483 1.0117959 1.135455382 1.167545526 1.15974809 1 20.96922075 4.74356213 24.88715519 1.103193685 0.639325154 0.838168373 0.062890659 189.4860816 942835.9751 0.015048834 0.124822777 55406.68035 -4.74356213 -0.463868532 EISDHVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EISDHVLR 8 0 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 ;;;; 217.02 7.62E-06 857920000 664262 939114 944485 889401 875802 904220 1067710 944013 705681 FALSE TRUE 622687.0272 1008646.978 966888.6302 912224.5354 807020.0437 1165253.635 907616.7976 1061875.101 587898.2822 1.059174769 1.715682811 1.644652926 1.551670694 1.372720534 1.982066746 1.543833049 1.806222493 1 19.16520704 EISEVFPDQFIHLGGDEVEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 282.03 4.63E-45 289120000 574380 486470 508170 487730 579480 399450 630070 462400 656850 FALSE TRUE 538430.5811 522488.745 520224.0324 500245.9775 533969.9783 514764.7305 535596.8528 520131.6579 547217.4916 0.983942563 0.954810022 0.950671425 0.914162989 0.975791137 0.940694949 0.978764131 0.950502617 1 19.06175482 0.2170216 0.644560281 1.001414657 0.953296501 0.303618245 0.020521867 3.412903741 1.886064764 0.032101163 0.007328045 1.648244366 -0.2170216 -0.048118156 EISLWFKPEELVDYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EISLWFKPEELVDYK 15 1 Q32Q12;P22392-2;P22392 Q32Q12 NME1-NME2;NME2 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B 0 ;; 208.26 2.72E-09 7288961000 14554610 9928220 10993520 10014430 11584360 7690920 15211140 9377620 14740630 FALSE TRUE 13643662.94 10663315.74 11254291.49 10271417.23 10674571.09 9911163.752 12930370.77 10548436.5 12280323.62 1.111018191 0.868325304 0.916449096 0.836412585 0.869241839 0.807076756 1.05293404 0.858970563 1 23.54984524 -0.463303042 7.824919317 0.99999999 0.912896334 0.071570051 0.095872183 0 0 0.085249858 0.020093584 0.344109734 0.463303042 -0.087103656 EISSS(ph)PTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EISSSPTSK 9 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 EISS(0.012)S(0.986)PT(0.002)SK;EISS(0.134)S(0.865)PTSK;EISSS(0.999)PT(0.001)SK;EISS(0.017)S(0.982)PT(0.001)SK;EISS(0.058)S(0.92)PT(0.022)SK 213.35 2.14E-06 5587840000 17020600 12677700 14296500 13714000 15107600 11447000 16912600 12833700 19241700 TRUE FALSE 15955311.03 13616370.1 14635619.73 14065924.46 13921110.04 14751563.07 14376712.64 14436015.7 16030135.96 0.995332233 0.849423244 0.913006587 0.87746757 0.868433684 0.920239423 0.896855315 0.900554788 1 23.93428333 -0.499068913 0.83809768 1.005692861 0.896805089 0.369546028 0.039349817 19.24758923 8.973040781 0.389348104 0.011342318 0.316906456 0.499068913 -0.108887772 EIST(ph)PTHWSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EISTPTHWSK 10 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 1 EIS(0.06)T(0.94)PTHWSK 123.92 0.001653 300960000 525590 951550 876090 895880 943500 796400 1117800 915890 1039800 TRUE FALSE 492694.2601 1022003.752 896871.2685 918869.7975 869401.3159 1026307.752 950196.2671 1030240.883 866250.6626 0.568766388 1.179801409 1.035348436 1.060743544 1.003637115 1.184769947 1.096906829 1.189310354 1 19.72442503 4.744055043 24.9549263 1.097088347 0.568766159 0.840958613 0.07174531 208.7074245 947891.5366 0.01586354 0.139047026 55469.60109 -4.744055043 -0.528322188 EITALAPS(ph)TMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EITALAPSTMK 11 0 P60709;P63267-2;A0A2R8YFE2;P63261;P68133;P68032;P63267;P62736;A6NL76 P60709;P63261;P68133 ACTB;ACTG2;ACTG1;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 1 EITALAPS(0.977)T(0.023)MK;EITALAPS(0.965)T(0.035)MK;EITALAPS(0.968)T(0.032)MK;EITALAPS(0.958)T(0.042)MK 180.84 6.81E-06 294615000 1256880 1369020 1078720 1139680 1725830 878550 1590270 1109020 2649010 TRUE FALSE 1178214.124 1470383.665 1104307.748 1168926.118 1590290.273 1132173.123 1351823.777 1247483.588 2206873.118 0.533883944 0.666274673 0.500394762 0.529675272 0.720607932 0.513021394 0.612551653 0.565272003 1 21.07357225 -1.530100705 3.047330861 1.015433433 0.582673545 0.780570257 0.069937291 20696677.1 23524867.31 2634079.903 0.015699715 0.02950525 1.530100705 -0.432759889 EITLENKDNIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EITLENKDNIR 11 1 Q9NT62;Q9NT62-2;C9JNW8 Q9NT62 ATG3 Ubiquitin-like-conjugating enzyme ATG3 0 153.54 2.96E-05 242290000 269910 292770 268990 285600 323400 204410 365840 265380 408720 FALSE TRUE 253016.8149 314446.9954 275370.5698 292928.9795 298001.4685 263419.8487 310985.6883 298513.2772 340501.9916 0.74307 0.923480635 0.80871941 0.860285657 0.875182748 0.77362205 0.913315329 0.876685848 1 18.37730371 0.744790665 0.991580516 0.999237823 0.843221088 0.457928212 0.055212933 0.807300372 1.451278466 0.047089206 0.015317507 5.55636369 -0.744790665 -0.156016735 EIVHLQAGQCGNQIGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 EIVHLQAGQCGNQIGAK 17 0 P68371;M0R2D3;M0QY85;M0R0X0;M0QY37;M0QX14;M0QZL7;M0R2T4;P04350;M0QYM7;M0R042;M0R278 P68371;P04350 TUBB4B;TUBB4A Tubulin beta-4B chain;Tubulin beta-4A chain 0 ;;;;;; 256.98 4.09E-27 11002900000 10882160 9428640 10674260 9651210 11204880 8773360 12389320 9699930 12892340 FALSE TRUE 10201065.03 10126746.32 10927458.49 9898876.388 10324893.92 11306086.61 10531656.48 10910987.61 10740525.17 0.949773393 0.942853926 1.017404486 0.921638024 0.961302521 1.052656777 0.980553215 1.01587096 1 23.3565612 2.292806345 24.99825296 1.00892542 0.962787645 0.436603248 0.029982478 97.37599317 44873.60974 0.010113369 0.008461447 196.2484995 -2.292806345 -0.046137775 EIVLADVIDNDSWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EIVLADVIDNDSWR 14 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;; 336.93 2.71E-68 2091270000 1341540 1526090 1477900 1519130 1558750 1356200 1562960 1344300 1217830 FALSE TRUE 1257575.406 1639083.291 1512956.486 1558113.448 1436332.063 1747712.924 1328608.658 1512138.814 1014566.306 1.239520177 1.615550687 1.491234706 1.535743341 1.415710393 1.722620704 1.309533591 1.490428773 1 19.95243172 0.164018429 0.828118844 0.992555886 1.50407956 0.533497893 0.139281836 2.609547716 2.020110597 0.172014493 0.040466198 1.458876165 -0.164018429 0.511523674 EIVVIHQDPEALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EIVVIHQDPEALK 13 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;; 155.98 4.12E-05 804353000 2193440 1644870 1930570 1868420 1757370 1442090 2333890 1649780 1705770 FALSE TRUE 2056156.506 1766657.886 1976364.032 1916366.82 1619353.249 1858397.973 1983944.861 1855758.665 1421065.967 1.44691137 1.243192031 1.390761638 1.348541774 1.139534185 1.307749264 1.396096245 1.30589199 1 20.4385421 0.943314596 22.30539714 1 1.322530966 0.58315085 0.085774452 4472.171 1759777.414 0.078324881 0.01958122 8.776363374 -0.943314596 0.322530966 EIVWLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EIVWLER 7 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 ;;; 110.81 0.015635 435270000 507331 642016 561161 566652 658789 496136 635480 532198 694653 FALSE TRUE 475578.0583 689551.5327 574472.0039 581193.2497 607050.3694 639362.4091 540195.6735 598644.0918 578710.9267 0.821788628 1.191530177 0.992675233 1.004289401 1.048969946 1.104804454 0.933446473 1.034444079 1 19.14248336 1.732144699 24.99999831 0.98561947 1.04223347 0.017809154 0.096640446 1.786599964 6913.08149 0.041074639 0.02277796 53.96904077 -1.732144699 0.056614 EIYDDLQALHTDDPLTWDYVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EIYDDLQALHTDDPLTWDYVAR 22 0 Q9NYH9 Q9NYH9 UTP6 U3 small nucleolar RNA-associated protein 6 homolog 0 ;;; 184.2 3.99E-17 152457000 153437 175975 173117 172760 173911 140749 203819 176928 145167 FALSE TRUE 143833.6521 189004.3721 177223.417 177193.3141 160252.7316 181380.9514 173258.2331 199017.8503 120937.6899 1.18932032 1.562824396 1.465410966 1.465162054 1.325085106 1.499788458 1.432623968 1.645623051 1 16.8839044 -1.211985782 5.214241673 0.999964413 1.4573253 0.562403346 0.124025225 4.53E-05 6.85E-06 0.106053648 0.024995144 0.06137821 1.211985782 0.457360887 EIYDDSFIRPVTFWIVGDFDSPSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EIYDDSFIRPVTFWIVGDFDSPSGR 25 1 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ; 164.83 1.47E-11 303320000 241060 300720 283600 304130 333110 261730 349040 258860 223980 FALSE TRUE 225972.4849 322985.6217 290327.1259 311934.4907 306948.8843 337287.2022 296704.6923 291179.2408 186596.291 1.211023454 1.730932699 1.555910486 1.671707883 1.644989204 1.807577205 1.590088906 1.560477109 1 17.50956078 -0.623981386 19.57771474 0.999995567 1.616164877 0.581721796 0.158211338 0 0 0.135556045 0.031950866 0.237694216 0.623981386 0.616169309 EIYENMAPGENKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIYENMAPGENKR 13 1 Q13200;C9JPC0;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 94.551 0.0081823 190000000 153010 118160 145500 143120 138350 125020 154400 116480 125620 FALSE TRUE 143433.3772 126908.6893 148951.3287 146792.7015 127484.5491 161111.2445 131249.1534 131022.7844 104653.2105 1.370558787 1.212659304 1.423284848 1.402658369 1.218161856 1.539477325 1.254134038 1.251970999 1 16.67525704 0.831976999 1.645542834 1.0016126 1.346498892 0.555186723 0.098603549 0.446423825 2.247703072 0.085702608 0.02460391 6.791676618 -0.831976999 0.344886292 EIYLEVIHNLPDFELLSANTLEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EIYLEVIHNLPDFELLSANTLEDR 24 0 Q8IXB1-2;Q8IXB1 Q8IXB1-2 DNAJC10 DnaJ homolog subfamily C member 10 0 90.468 0.0096602 76186000 30056 39327 30797 33257 41525 28185 35222 27343 32444 FALSE TRUE 28174.84861 42238.812 31527.51938 34110.43092 38263.794 36321.55195 29940.78809 30756.83374 27028.8868 1.042397669 1.56272851 1.166437953 1.261999104 1.415662964 1.343804953 1.107732934 1.137924546 1 14.72221447 1.678077445 4.731394795 1.086200819 1.317108318 0.335541519 0.142386509 0.171983869 8.885491856 0.071994179 0.034656503 47.65159532 -1.678077445 0.2309075 EKAEELAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKAEELAAR 9 1 A0A087WTZ5;Q04323;E9PJ81;Q04323-2;E9PS08 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 0 ; 98.044 0.0057281 774490000 1017040 961560 1045400 1036550 1122610 984330 1219110 934400 1409010 FALSE TRUE 953385.2819 1032754.903 1070197.382 1063149.628 1034444.739 1268490.092 1036315.773 1051061.897 1173837.128 0.812195541 0.879811072 0.91170858 0.90570455 0.881250656 1.080635517 0.882844603 0.895406928 1 20.16280082 7.544588494 0.317008639 0.955830041 1.31E-11 0.349467805 0.059572217 49.932383 0.935642282 0.053113594 26.20434166 35041968.44 -7.544588494 -0.955830041 EKAEGDVAALNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKAEGDVAALNR 12 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;; 168.76 4.16E-05 1905210000 3061990 2894070 3001350 2983630 3498830 2235630 3613490 2901750 3879500 FALSE TRUE 2870345.512 3108349.954 3072543.439 3060194.997 3224046.005 2881020.089 3071680.72 3264039.875 3231986.387 0.888105693 0.961745992 0.950667197 0.946846499 0.997543188 0.891408485 0.950400265 1.009917581 1 21.62398969 -4.999999924 0.064851148 1.188225468 0.875845526 0.289532598 0.035003677 553.0788818 2.603565516 15.9181469 2.308161742 1.00E-05 4.999999924 -0.312379943 EKAEIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKAEIER 7 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 0 66.692 0.061273 188480000 245420 230120 239710 218980 248780 170000 254390 181040 265410 FALSE TRUE 230059.6003 247158.3242 245396.0344 224599.3975 229241.8223 219076.2403 216246.5811 203643.2425 221111.3564 1.0404694 1.117800226 1.10983008 1.015775043 1.036770911 0.990795968 0.977998528 0.920998568 1 17.7544136 2.652887882 1.043910672 0.964455997 1.098282785 0.676055787 0.033440205 0.254324787 0.57482493 0.017894445 0.015225868 449.6637546 -2.652887882 0.133826788 EKDAESVECPDADS(ph)LNIPDVDEEGYSIKPETNQNDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKDAESVECPDADSLNIPDVDEEGYSIKPETNQNDTK 37 2 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 EKDAESVECPDADS(1)LNIPDVDEEGYSIKPETNQNDTK;EKDAESVECPDADS(1)LNIPDVDEEGYSIKPETNQNDTK 263.41 1.05E-62 440610000 474390 175136 264980 295200 321110 199603 412990 231820 359340 TRUE FALSE 444698.7767 188103.2517 271265.4507 302775.3318 295891.3159 257225.1458 351065.9835 260763.2373 299363.8326 1.485479301 0.628343277 0.906139691 1.01139583 0.988400347 0.859239219 1.172706738 0.87105792 1 18.19154041 3.242925125 23.6241645 0.996246645 0.911228263 0 0.229903515 242.1107275 1310469.497 0.060393099 0.078898472 1749.545029 -3.242925125 -0.085018382 EKDDANFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKDDANFK 8 1 Q5VTR2;H3BP71;O75150-4;O75150;O75150-3 Q5VTR2;H3BP71 RNF20;RNF40 E3 ubiquitin-protein ligase BRE1A;E3 ubiquitin-protein ligase BRE1B 0 ; 113.18 0.002644 769390000 1399880 870620 1071660 1080470 1142270 736630 1302640 960230 1419480 FALSE TRUE 1312264.01 935081.6107 1097080.281 1108196.689 1052560.722 949283.1228 1107321.225 1080116.829 1182559.618 1.10968106 0.790726824 0.927716679 0.937116973 0.890069901 0.802735954 0.93637666 0.913371988 1 20.17348149 0.710415487 1.745901069 0.999687016 0.898972067 0.071182081 0.087575985 2.388305783 10.96405787 0.074858631 0.021154282 5.133522698 -0.710415487 -0.100714949 EKDECT(ph)PTR ddPTM_SK-BR-3_Pertuzumab_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(0.974)PT(0.026)R;EKDECT(1)PTR 97.195 0.043663 685560000 1160690 741500 887290 830250 929750 849540 1341250 852970 1184960 TRUE FALSE 1088044.485 796401.4315 908336.9378 851555.6206 856731.1854 1094788.407 1140142.014 959465.1821 987182.5209 1.102171546 0.806741828 0.920130694 0.862612134 0.867854897 1.10900303 1.154945504 0.971922782 1 19.91295732 2.238244079 24.99999863 1.08210568 0.89644376 0.365023654 0.092977939 6.811190506 537872.2049 0.031083629 0.024411398 173.0788811 -2.238244079 -0.18566192 EKDECT(ph)PTRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKDECTPTRK 10 2 O15042-2;O15042;E7ET15;O15042-3;H7C4V2 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 EKDECT(0.999)PT(0.001)RK 134.06 0.00029058 368760000 631410 308360 408910 394080 457600 327580 625450 382220 579060 TRUE FALSE 591891.1752 331191.2952 418609.5383 404192.76 421661.9419 422147.0282 531669.5789 429941.0084 482411.1451 1.22694341 0.686533258 0.867744335 0.837859498 0.874071725 0.875077271 1.102108822 0.891233573 1 18.87990371 1.861015106 8.706068183 1.006087393 0.863924675 0.076549585 0.143958568 0.516104256 34.40795996 0.056156389 0.035314327 72.61312145 -1.861015106 -0.142162718 EKDECTPT(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKDECTPTR 9 1 O15042-2;O15042;E7ET15;O15042-3;H7C4V2 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 EKDECT(0.33)PT(0.67)R 117.79 0.0069683 342060000 591390 385930 467730 436160 530080 449320 786580 469910 692660 TRUE FALSE 554375.9556 414504.6588 478824.7765 447352.604 488449.655 579031.3899 668639.6313 528579.2979 577050.5712 0.960706016 0.718316001 0.829779573 0.77523986 0.84645901 1.00343266 1.158719295 0.916001689 1 19.13833823 2.235141579 3.586164936 1.050621349 0.806270036 0.549955057 0.085629982 0.133683347 3.683069203 0.03080337 0.023179698 171.8468514 -2.235141579 -0.244351314 EKDHSSSRPS(ph)SPRPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKDHSSSRPSSPRPQK 16 3 E9PKU9;B7Z503;Q9BSF8;Q9BSF8-2 E9PKU9 BTBD10 BTB/POZ domain-containing protein 10 1 EKDHS(0.004)S(0.004)S(0.004)RPS(0.494)S(0.494)PRPQK 66.779 0.038265 65386000 132430 242230 251380 271210 292620 232020 323390 225400 284710 TRUE FALSE 124141.4427 260164.9612 257342.8523 278169.7078 269638.8056 299000.4075 274900.6717 253541.6862 237190.0617 0.523383829 1.096862825 1.084964734 1.172771345 1.136804821 1.260594164 1.158988997 1.068938911 1 17.85568404 4.743814461 4.185932536 1.134956763 0.471252048 0.881397653 0.069080134 0.07049133 2.770875895 0.016211975 0.141451586 55438.88162 -4.743814461 -0.663704714 EKDIQEESTFSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKDIQEESTFSSR 13 1 P42704;B8ZZ38;A0A0C4DG06;C9JCA9 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 176.32 1.53E-05 309360000 311060 298310 290820 283850 380030 267250 299550 295510 431490 FALSE TRUE 291591.3099 320397.1828 297718.3877 291134.0716 350183.9768 344400.7366 254635.2584 332405.074 359471.5315 0.811166627 0.891300575 0.828211309 0.809894654 0.97416331 0.958075136 0.708360012 0.924704865 1 18.45551799 -2.595867155 1.364092775 1.92638353 0.857449461 0.223306173 0.079513719 260797.3575 15185.26586 739567.8259 0.021666179 0.002535904 2.595867155 -1.06893407 EKDIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKDIQR 6 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;; 101.69 0.033048 2995420000 3851780 4272080 3861330 3888100 4716050 3033500 4308280 4240310 5266270 FALSE TRUE 3610703.965 4588389.248 3952922.571 3987875.229 4345670.457 3909222.205 3662293.41 4769722.038 4387295.516 0.822990827 1.045835466 0.900993005 0.908959794 0.990512365 0.891032344 0.834749653 1.087166803 1 22.06490045 1.225362436 24.99996297 1.043583427 0.922307836 0.375418076 0.069001567 301.6342437 571338.0463 0.063845417 0.016346682 16.80205633 -1.225362436 -0.121275592 EKDKEPFTFS(ph)SPASGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKDKEPFTFSSPASGR 16 2 Q6P1X5;H0YEX2 Q6P1X5 TAF2 Transcription initiation factor TFIID subunit 2 1 EKDKEPFT(0.001)FS(0.711)S(0.288)PASGR 141.97 8.10E-07 284380000 194860 129970 152720 158590 170580 118780 243330 154790 234310 TRUE FALSE 182664.0604 139593.114 156342.5905 162659.6879 157183.3349 153069.8578 206844.9255 174115.8722 195202.1473 0.935768704 0.715120791 0.800926592 0.833288415 0.805233636 0.784160727 1.059644724 0.891977238 1 17.5746094 1.750324473 25 0.983649817 0.800390716 0.583114768 0.067834763 1.989135532 4234.468511 0.028622257 0.015872552 56.27616224 -1.750324473 -0.1832591 EKDKEPFTFSS(ph)PASGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKDKEPFTFSSPASGR 16 2 Q6P1X5;H0YEX2 Q6P1X5 TAF2 Transcription initiation factor TFIID subunit 2 1 EKDKEPFT(0.003)FS(0.494)S(0.502)PASGR 162.39 4.22E-09 126100000 398980 296350 287630 311300 350090 243070 444370 318710 448100 TRUE FALSE 374008.554 318292.0624 294452.7194 319288.485 322595.3436 313240.3631 377740.8438 358501.6451 373309.2152 1.00187335 0.852623106 0.788763597 0.855292267 0.864150496 0.839090894 1.011871201 0.960334303 1 18.5100116 1.740543315 8.074979658 0.987984441 0.85571034 0.517424258 0.055543803 0.0863628 19.43167434 0.026387261 0.014093206 55.02287958 -1.740543315 -0.132274101 EKDLDLEPLS(ph)DLEEGLEETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKDLDLEPLSDLEEGLEETR 20 1 P29375;P29375-2 P29375 KDM5A Lysine-specific demethylase 5A 1 EKDLDLEPLS(1)DLEEGLEETR 117.36 4.92E-05 33198000 88851 63357 69093 67523 67821 56216 86353 60324 66471 TRUE FALSE 83289.97451 68048.0182 70731.91859 69255.7545 62494.61224 72444.64661 73405.16931 67855.58419 55376.56068 1.504065502 1.228823484 1.277289845 1.250633005 1.128539069 1.308218599 1.325563892 1.225348475 1 15.75698783 -3.992610798 0.270109537 2.94E-21 1.297803938 0.490951913 0.09293537 105.0274676 1.689648963 58.34378766 0.110502276 0.000101716 3.992610798 1.297803938 EKDNIDITLQWLIQHSK ddPTM_SK-BR-3_Pertuzumab_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 ; 286.68 1.05E-36 531410000 1451650 1173220 1309940 1279370 1495540 1093360 1902200 1375890 1844330 FALSE TRUE 1360793.818 1260086.43 1341012.395 1312200.8 1378086.321 1408995.283 1616982.769 1547672.895 1536499.408 0.88564552 0.820102125 0.872771176 0.854019724 0.896900001 0.917016483 1.052380991 1.007272041 1 20.55121578 2.012994861 2.140084754 1.025125473 0.857454555 0.876749442 0.026102198 0.0893456 0.767025863 0.01353192 0.007259378 103.0373928 -2.012994861 -0.167670918 EKDQADFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKDQADFR 8 1 Q96I24;Q96I24-2 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ; 83.948 0.016233 1072580000 3970000 3605200 3756700 3762300 3978200 2975000 4472500 3320400 4357800 FALSE TRUE 3721524.787 3872132.759 3845810.698 3858846.988 3665768.219 3833834.205 3801890.146 3734959.249 3630455.028 1.025084943 1.066569543 1.059319195 1.062910009 1.009726933 1.056020299 1.047221386 1.028785433 1 21.79171895 0.115396658 0.392590585 0.991945231 1.054636333 0.394618641 0.017922497 3.654656878 0.828759395 0.064768331 0.012637447 1.304357554 -0.115396658 0.062691102 EKDRDPEAQFEMPYVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 231.77 2.02E-16 904360000 616310 527120 595590 573240 612680 413380 693510 533030 832510 FALSE TRUE 577736.2572 566148.5133 609717.6761 587950.3089 564562.5842 532716.0953 589524.6137 599579.9688 693558.7028 0.833002679 0.816295017 0.879114736 0.847729697 0.814008363 0.768090853 0.849999591 0.864497794 1 19.40365847 0.739017383 2.044642228 0.999851985 0.831050021 0.777219492 0.028552633 0.522162148 3.281575375 0.028363999 0.007810521 5.4829891 -0.739017383 -0.168801964 EKDRES(ph)EKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKDRESEKDR 10 3 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 EKDRES(1)EKDR;EKDRES(1)EKDR 106.29 0.01346 457660000 1439410 525860 771950 757680 833840 557470 1032770 631640 1087040 TRUE FALSE 1349319.898 564795.2216 790261.0185 777123.3515 768353.5699 718402.5392 877915.7263 710501.6444 905606.0015 1.489963511 0.623665502 0.872632268 0.858125223 0.848441341 0.793283766 0.969423485 0.784559337 1 19.78852399 -0.298891343 7.806335412 1.000013573 0.875808659 0.00256491 0.227482515 0 0 0.193436025 0.045593308 0.502468287 0.298891343 -0.124204914 EKDRQS(ph)PLHGNHITISHTQATGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKDRQSPLHGNHITISHTQATGSR 24 2 Q86VQ1;H7C2L5 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 EKDRQS(1)PLHGNHITISHTQATGSR;EKDRQS(1)PLHGNHITISHTQATGSR;EKDRQS(1)PLHGNHITISHTQATGSR 160.93 1.24E-11 1581440000 489842 520350 496634 521596 557276 411800 605076 503500 782408 TRUE FALSE 459183.6636 558877.2554 508414.393 534981.0364 513509.7909 530679.975 514350.4711 566363.0833 651819.0503 0.704464933 0.857411662 0.779993148 0.820750845 0.787810345 0.814152294 0.78910009 0.868896181 1 19.31411199 0.90861068 2.835725786 0.999861214 0.79952794 0.739434561 0.039158509 0.175872841 3.139408895 0.032799874 0.00866772 8.102344038 -0.90861068 -0.200333274 EKDS(ph)PFKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKDSPFKPK 9 2 Q15291 Q15291 RBBP5 Retinoblastoma-binding protein 5 1 EKDS(1)PFKPK 67.08 0.032305 172780000 601620 190650 316050 274750 329810 222600 449260 271670 480110 TRUE FALSE 563965.6781 204765.9244 323546.8552 281800.5502 303908.053 286861.0064 381897.6337 305588.5975 399976.5394 1.409996894 0.511944837 0.808914582 0.704542698 0.759814697 0.717194581 0.954800085 0.764016305 1 18.60955586 -1.006731909 5.08202711 1.000001796 0.799538938 0.036965561 0.235279494 4.26E-06 8.33E-07 0.202904779 0.047824687 0.098461873 1.006731909 -0.200462858 EKDS(ph)PHMQDPNQADEEAMTQIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKDSPHMQDPNQADEEAMTQIIR 23 1 P23511-2;P23511 P23511-2 NFYA Nuclear transcription factor Y subunit alpha 1 EKDS(1)PHMQDPNQADEEAMTQIIR;EKDS(1)PHMQDPNQADEEAMTQIIR;EKDS(1)PHMQDPNQADEEAMTQIIR;EKDS(1)PHMQDPNQADEEAMTQIIR 267.93 1.46E-44 638600000 835970 581370 690520 630580 752650 563942 912110 657680 954140 TRUE FALSE 783648.1299 624415.2397 706899.4605 646761.7504 693539.905 726742.9006 775347.5731 739792.7957 794887.87 0.985859968 0.78553877 0.889307143 0.813651554 0.8725003 0.914270966 0.975417543 0.930688244 1 19.60039184 2.053056568 2.367576925 0.965766421 0.857221437 0.395107992 0.055075015 0.261755501 2.814956851 0.025638356 0.014769008 112.9943084 -2.053056568 -0.108544984 EKDTAGVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKDTAGVTR 9 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4;A0A3B3ISH4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 0 ; 74.162 0.038187 106126000 236985 197919 222019 229044 247991 177547 282698 199438 300968 FALSE TRUE 222152.5319 212573.1287 227285.3955 234921.6568 228514.7872 228801.9367 240310.0593 224338.2733 250734.4965 0.886007051 0.847801685 0.906478361 0.936933929 0.911381523 0.912526756 0.9584244 0.894724406 1 17.93580097 8 0.04876604 1.17468871 0.434235702 0.648195069 0.024542884 280.5675212 1.033556236 3.762715057 15.78013446 99999999.98 -8 -0.740453008 EKDVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKDVER 6 1 Q13243;Q13243-3;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ;;; 81.297 0.056772 2208550000 3922290 3394660 3788040 3632940 3911560 2595550 3716600 3196210 4449120 FALSE TRUE 3676800.87 3646004.159 3877894.098 3726167.391 3604361.856 3344843.15 3159330.333 3595263.854 3706533.13 0.991978418 0.983669653 1.046232143 1.005297204 0.972434814 0.902418253 0.852368028 0.969980229 1 21.82163898 2.422137929 3.336599419 0.911440692 1.008658129 0.361751768 0.043785447 0.189354024 4.336670463 0.015462549 0.012894038 264.3248104 -2.422137929 0.097217438 EKEAAYQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKEAAYQER 9 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ;; 110.66 0.0020526 1367940000 973460 1006440 950060 1021790 1137260 790020 1064540 948590 1223760 FALSE TRUE 912532.8763 1080957.865 972595.8719 1048010.861 1047944.187 1018085.949 904922.1097 1067023.55 1019506.55 0.895073088 1.060275547 0.953986879 1.027958929 1.02789353 0.99860658 0.887607941 1.046607841 1 19.95943961 -0.178819716 7.64418624 0.999999659 0.986377791 0.00432799 0.059471591 0 0 0.054386823 0.012819097 0.66249146 0.178819716 -0.013621869 EKEAEDGIIAYDDCGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKEAEDGIIAYDDCGVK 17 1 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 160.13 2.85E-09 85789000 280940 126050 189880 170020 196670 157550 282040 151510 256240 FALSE TRUE 263356.4669 135382.8732 194384.0433 174383.001 181224.3315 203032.1274 239750.7203 170426.357 213471.8886 1.233682189 0.634195322 0.910583799 0.816889766 0.848937688 0.951095382 1.123102072 0.798355035 1 17.70368657 2.129822901 4.585239805 0.998240609 0.854042416 0.023526745 0.167669978 0.409844297 14.69074606 0.060084642 0.043532395 134.8412907 -2.129822901 -0.144198193 EKEAENER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKEAENER 8 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 90.108 0.012248 1302800000 1840700 1416100 1596600 1479600 1477200 1087600 1771800 1299400 1562300 FALSE TRUE 1725493.873 1520949.517 1634472.106 1517569.041 1361186.671 1401572.464 1506135.039 1461632.95 1301542.037 1.325730421 1.168575024 1.255796631 1.165977738 1.045826129 1.076855318 1.157192773 1.123000955 1 20.31179048 8 0.13648754 0.984453631 2.00995115 0.651738 0.056347162 51.88734475 0.474267463 0.259487655 10.34008296 99999999.97 -8 1.025497518 EKEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKEALR 6 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;E9PFY5;F8W9I4;P55196-1;Q9UDT6;Q9UDT6-2 P55196-5;P55196-1;Q9UDT6 MLLT4;CLIP2 Afadin;CAP-Gly domain-containing linker protein 2 0 ;; 72.234 0.078556 857400000 685680 815040 713330 740270 883090 550910 836550 810940 817910 FALSE TRUE 642764.5128 875386.4096 730250.5245 759266.5815 813735.6736 709948.7737 711117.0936 912187.6441 681395.5371 0.943306021 1.284696424 1.071698426 1.114281706 1.194219259 1.041904056 1.043618655 1.338705046 1 19.37813297 2.239320253 24.99999949 1.100191578 1.136730526 0 0.125108838 111.3633345 3665065.609 0.041599804 0.032910965 173.5082992 -2.239320253 0.036538948 EKEDFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKEDFEK 7 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;; 73.665 0.04403 1335600000 5756100 3034570 4123000 3859600 3907100 3115470 5781200 3679100 4760700 FALSE TRUE 5395835.976 3259252.72 4220799.507 3958643.87 3600252.126 4014855.614 4914362.73 4138443.734 3966108.415 1.360486253 0.821776003 1.064216876 0.998117917 0.90775434 1.01229094 1.239089358 1.043451994 1 21.91929268 1.957623418 23.65328516 1.12198211 1.001383152 0.012467341 0.152278831 523.3342665 292107.1159 0.056968605 0.03676747 90.70336884 -1.957623418 -0.120598959 EKEEDSSGHTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKEEDSSGHTR 11 1 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;P52701-4 P52701 MSH6 DNA mismatch repair protein Msh6 0 92.856 0.0058182 246120000 217150 201320 191220 215190 232900 147330 253350 206410 240170 FALSE TRUE 203558.9691 216225.9423 195755.8287 220712.1397 214608.9735 189861.7793 215362.5195 232180.7429 200084.0754 1.017367168 1.08067542 0.97836786 1.103096982 1.072593973 0.948909996 1.07636012 1.160415902 1 17.61024682 1.519422422 10.40882621 1.092755842 1.035207877 0.105469437 0.059863888 0.192102972 34.8914307 0.029342397 0.013623291 33.06910357 -1.519422422 -0.057547965 EKEEEEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKEEEEQR 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 101.11 0.0051353 1823100000 5201000 3295180 3959850 3959820 4158080 2922160 4887700 3460460 4980900 FALSE TRUE 4875478.694 3539158.556 4053779.512 4061435.685 3831521.17 3765740.155 4154834.76 3892506.048 4149555.612 1.174939957 0.85290062 0.97691895 0.978764009 0.923356988 0.907504443 1.00127222 0.938053713 1 21.98452541 -0.888292884 4.049770328 1.000001111 0.958809714 0 0.0848385 5.31313E+11 1.07579E+12 9991596.144 0.018020637 0.129332334 0.888292884 -0.041191397 EKEEFAVPENSSVQQFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKEEFAVPENSSVQQFK 17 1 Q9UMX0;Q9UMX0-2;Q9UMX0-4;Q9UHD9 Q9UMX0;Q9UHD9 UBQLN1;UBQLN2 Ubiquilin-1;Ubiquilin-2 0 191.59 2.13E-10 248830000 574140 315440 446240 380020 340780 270340 585890 358680 405970 FALSE TRUE 538205.6023 338795.5058 456825.0235 389771.9566 314016.5134 348382.7694 498041.2336 403461.9876 338210.9843 1.591330936 1.001728275 1.350710192 1.152452092 0.928463379 1.030075265 1.472575572 1.192929876 1 18.36756399 7.501638867 0.016131837 8.84E-07 2.632329671 0.111137942 0.206955697 15941.2121 21.51226849 1404.775383 2183.855953 31742334.71 -7.501638867 2.632328787 EKEELDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKEELDR 7 1 Q16543;K7EKQ2;K7EQA9 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;; 95.099 0.012508 4469900000 6524600 4772200 5489100 5211100 5479500 4273200 6666600 4699500 6778800 FALSE TRUE 6116236.933 5125538.653 5619304.044 5344825.648 5049162.173 5506803.47 5667005.22 5286242.92 5647374.487 1.083023084 0.907596736 0.99502947 0.946426638 0.894072491 0.975108607 1.003476081 0.936053193 1 22.42914887 2.014174941 24.98133181 0.982495102 0.958413825 0.006127604 0.054403353 832.7224124 1467548.908 0.018766965 0.013855563 103.3177502 -2.014174941 -0.024081277 EKEELEEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKEELEEIR 9 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 93.058 0.0088067 637610000 1062770 905520 992860 1013210 1033950 798280 1228580 906640 1362460 FALSE TRUE 996253.1228 972565.643 1016411.108 1039210.684 952747.7378 1028730.477 1044365.835 1019836 1135056.624 0.877712267 0.856843282 0.89547172 0.91555845 0.839383443 0.906325249 0.920100207 0.898489096 1 20.11433284 -5 0.157639434 1.426768019 0.85577487 0.720944092 0.022776846 67.34199114 0.615251741 8.918188459 0.095580469 1.00E-05 5 -0.570993149 EKEELEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKEELEQR 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 99.815 0.0059698 922900000 1364900 1109400 1238700 1117100 1211900 915350 1511600 1112200 1588700 FALSE TRUE 1279473.345 1191541.13 1268082.549 1145766.677 1116722.263 1179596.686 1284949.613 1251060.618 1323535.707 0.966708597 0.900271239 0.958102258 0.865686261 0.843741697 0.89124659 0.970846201 0.945241305 1 20.33596569 1.695380399 6.392686368 0.968531632 0.906288793 0.397923178 0.039065094 0.158427111 14.33526586 0.020404584 0.01040241 49.58843465 -1.695380399 -0.062242839 EKEELETGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKEELETGKK 10 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 60.49 0.054982 179570000 206640 96036 133190 128230 146630 92643 182570 118700 204890 FALSE TRUE 193706.7713 103146.6054 136349.3297 131520.5989 135114.2713 119387.5302 155195.3234 133519.9563 170692.5354 1.134828602 0.604283047 0.798800776 0.770511719 0.791565202 0.699430294 0.909209785 0.782224929 1 17.38104044 0.451979717 0.73971378 1.001632432 0.780557312 0.12324365 0.141080892 3.055556642 2.580712673 0.142207163 0.045205205 2.831259765 -0.451979717 -0.22107512 EKEELMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKEELMER 8 1 A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 A0A2R8Y5S7 RDX;MSN Radixin;Moesin 0 59.426 0.090012 292200000 669710 584830 609210 554210 589890 460930 637260 476910 595080 FALSE TRUE 627794.0466 628131.4217 623660.7489 568431.9669 543562.4189 593993.0084 541708.779 536453.2633 495757.3036 1.26633343 1.267013954 1.257996089 1.146593228 1.096428464 1.198152814 1.092689457 1.082088472 1 18.9192745 2.699400455 0.266883621 0.98411577 1.359689423 0.832439369 0.037147948 1.130904646 0.175656719 0.063288724 0.143220545 500.4958198 -2.699400455 0.375573653 EKEELMLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EKEELMLR 8 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;;;; 141.48 0.00057715 5783330000 7094380 7078850 6255670 5805240 8850040 4585120 6648270 6607770 9012390 FALSE TRUE 6650355.42 7602975.42 6404057.447 5954212.287 8154993.558 5908769.711 5651423.633 7432764.63 7508163.887 0.885749901 1.012627792 0.852945879 0.793031742 1.08615018 0.78697932 0.752703819 0.989957697 1 22.84002871 EKEES(ph)PQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKEESPQPR 9 1 F5H3K2;F5H8B7;E7ENF1;G5EA44;F5H7W8;Q96C57 F5H3K2 C12orf43 Uncharacterized protein C12orf43 1 EKEES(1)PQPR;EKEES(1)PQPR 137.84 9.30E-05 1083090000 2020020 1166890 1490640 1270690 1539790 1279380 2304880 1445430 2037030 TRUE FALSE 1893590.554 1253287.75 1525998.685 1303298.057 1418861.105 1648716.237 1959284.641 1625895.117 1697036.533 1.115821915 0.73851548 0.899213809 0.767984679 0.83608165 0.971526661 1.154532977 0.958079031 1 20.69458619 2.062822394 4.438905324 1.056968027 0.853499131 0.302431878 0.112905361 0.189795286 7.535693685 0.041316734 0.028961468 115.5639543 -2.062822394 -0.203468896 EKEEVAEEAQS(ph)GGD ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKEEVAEEAQSGGD 14 1 O76070 O76070 SNCG Gamma-synuclein 1 EKEEVAEEAQS(1)GGD;EKEEVAEEAQS(1)GGD;EKEEVAEEAQS(1)GGD 201.04 4.84E-08 1135380000 2500270 1764700 1901590 2342880 2518860 2237780 2341580 2135750 1858720 TRUE FALSE 2343782.564 1895360.224 1946696.613 2403002.267 2321038.896 2883790.759 1990481.817 2402403.089 1548487.624 1.513594637 1.224007344 1.257159943 1.551838213 1.498906972 1.862327289 1.285436051 1.551451269 1 20.56242842 3.242616201 24.99817519 1.488903069 1.297901957 0.045802751 0.231297685 195.5192591 1205149.938 0.058590721 0.076538798 1748.300981 -3.242616201 -0.191001112 EKEEVAEEAQSGGD ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKEEVAEEAQSGGD 14 1 O76070 O76070 SNCG Gamma-synuclein 0 ; 157.52 4.30E-05 521220000 1290950 1031920 1094110 1214710 1270060 1047580 1328360 1072710 1239480 FALSE TRUE 1210151.744 1108324.431 1120062.806 1245881.515 1170314.611 1349999.34 1129184.75 1206640.205 1032602.781 1.171943139 1.07333086 1.084698615 1.2065448 1.133363799 1.307375271 1.093532548 1.168542471 1 19.97785396 3.257288383 24.99407898 1.161651586 1.09852196 0.038564824 0.082385455 489.9811016 653924.6831 0.020463433 0.027661769 1808.374535 -3.257288383 -0.063129625 EKEEYISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKEEYISR 8 1 Q08379;Q08379-2;A0A087WYC0 Q08379 GOLGA2 Golgin subfamily A member 2 0 68.657 0.051017 180830000 150120 160950 156880 169120 198000 131510 177020 174420 239300 FALSE TRUE 140724.2572 172866.9055 160601.2677 173459.9055 182449.8787 169474.8021 150477.4944 196196.7209 199359.2841 0.705882637 0.867112391 0.805587101 0.87008692 0.91518125 0.850097365 0.754805552 0.984136364 1 17.60501127 -5 0.118690209 1.530247437 0.756911815 0.436613928 0.069004239 168.2550409 1.30008275 21.40589149 0.671010891 1.00E-05 5 -0.773335623 EKEHASGSGAQSEAAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKEHASGSGAQSEAAGR 17 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;; 233.49 2.48E-20 295757000 159778 424349 372136 401256 431416 316333 473881 393413 487373 FALSE TRUE 149777.7802 455768.2415 380963.2417 411552.9083 397534.3276 407653.2019 402826.9433 442531.4791 406027.2978 0.368885986 1.122506403 0.938270022 1.013608963 0.979082761 1.004004421 0.992117884 1.089905732 1 18.6312172 4.744496164 24.99982146 1.013450135 0.368885706 0.936607068 0.053016916 144.680962 609361.9059 0.011887282 0.107943396 55525.9713 -4.744496164 -0.644564429 EKEHQVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKEHQVVR 8 1 Q9H307 Q9H307 PNN Pinin 0 ;; 93.429 0.0066545 217167000 348063 377908 330788 329654 425190 257335 383025 362794 457720 FALSE TRUE 326278.3581 405888.7015 338634.4476 338113.4797 391797.2925 331623.437 325593.9571 408089.6295 381323.575 0.855646961 1.064420687 0.888050123 0.886683913 1.027466745 0.869664135 0.853852157 1.070192499 1 18.5406562 1.225309178 24.99905008 1.035096281 0.927943486 0.291950397 0.073334131 364.6328351 687865.4926 0.068095297 0.017432403 16.79999597 -1.225309178 -0.107152795 EKEIAETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKEIAETR 8 1 P12270 P12270 TPR Nucleoprotein TPR 0 ;;; 99.653 0.0060746 1122920000 2761680 2395150 2500790 2578950 2706390 2057260 3121350 2400410 2937210 FALSE TRUE 2588831.379 2572489.398 2560109.92 2645130.223 2493841.046 2651157.565 2653332.545 2700106.472 2446970.676 1.05797401 1.051295556 1.046236453 1.080981578 1.019154447 1.083444763 1.084333609 1.103448643 1 21.22256538 EKEIS(ph)DDEAEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKEISDDEAEEEK 13 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 1 EKEIS(1)DDEAEEEK 203.53 6.38E-07 0 992840 230600 472220 388880 369750 350440 692290 306960 341420 TRUE FALSE 930699.9167 247673.8639 483421.2814 398859.3192 340711.3265 451606.3391 588487.5414 345284.6317 284434.7963 3.272102881 0.870757963 1.699585591 1.402287358 1.197853887 1.58773239 2.06897169 1.213932459 1 18.11773844 4.749865901 24.97099672 1.44464135 3.272103965 0.737919131 0.352488437 943.0704156 2083004.595 0.085520138 1.345918779 56216.77151 -4.749865901 1.827462615 EKEIS(ph)DDEAEEEKGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKEISDDEAEEEKGEK 16 2 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 1 EKEIS(1)DDEAEEEKGEK;EKEIS(1)DDEAEEEKGEK;EKEIS(1)DDEAEEEKGEK;EKEIS(1)DDEAEEEKGEK 190.19 7.06E-10 8518070000 18189300 4197600 8041700 6900340 6088710 6754970 12361160 5653610 5295810 TRUE FALSE 17050864.18 4508394.672 8232452.922 7077414.407 5610527.277 8705020.181 10507718.81 6359475.654 4411905.099 3.864739563 1.021870274 1.865963283 1.604162884 1.271679048 1.97307512 2.381673807 1.441435278 1 22.07297033 4.748762593 24.84442802 1.65031908 3.864740898 0.732264834 0.433659881 755.6955787 1840272.494 0.106152817 1.468575527 56074.13637 -4.748762593 2.214421818 EKELETGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKELETGPK 9 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 91.855 0.0095495 376660000 390860 426680 404630 437320 457090 364430 442760 364830 520150 FALSE TRUE 366396.7703 458271.8312 414228.0147 448542.3716 421191.9952 469635.025 376372.2484 410379.8286 433333.6047 0.845530479 1.057549717 0.955910204 1.035097132 0.971980919 1.083772456 0.868550799 0.947029781 1 18.7251186 -0.858823796 4.860118379 1.000000033 0.976132166 0.010096579 0.07571568 5.10E-08 1.20E-08 0.067165112 0.015830924 0.138412784 0.858823796 -0.023867867 EKELGNDAYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKELGNDAYK 10 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;; 96.604 0.0060438 3263620000 3767310 2697470 3181220 3278420 3734980 2364290 4218050 3196720 4284870 FALSE TRUE 3531520.792 2897193.486 3256680.041 3362549.808 3441649.737 3046822.142 3585592.561 3595837.529 3569697.516 0.989305334 0.811607559 0.912312605 0.941970515 0.964129236 0.853523899 1.004452771 1.007322753 1 21.7673704 1.649388843 6.948291167 1.005409219 0.903941303 0.409747224 0.051196567 0.11552451 11.09898643 0.025940334 0.013081508 44.60554427 -1.649388843 -0.101467916 EKELS(ph)PPPGLPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKELSPPPGLPSK 13 1 A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;Q7Z4S6-3;H0YHT2;H0YI78;H0YIM6 A0A1B0GV47 KIF21A Kinesin-like protein KIF21A 1 EKELS(1)PPPGLPSK;EKELS(1)PPPGLPSK;EKELS(1)PPPGLPSK 111.66 0.00058272 913860000 2763770 1495760 2022630 1988990 2093040 1436730 2548230 1672330 2523290 TRUE FALSE 2590790.569 1606507.627 2070607.739 2040030.851 1928661.081 1851490.628 2166146.568 1881124.082 2102136.598 1.23245586 0.764226087 0.985001517 0.970455894 0.917476573 0.880766088 1.030449958 0.894862914 1 21.00342499 -4.33051309 0.540331327 1.984184368 0.945789931 0 0.121173683 10045.14813 86.12881116 11848.52144 0.047412232 4.67E-05 4.33051309 -1.038394437 EKEMNGETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKEMNGETR 9 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;; 102.52 0.0032565 488560000 1144530 984830 1059680 1044770 1140170 840430 1225320 906720 1327800 FALSE TRUE 1072895.91 1057747.838 1084816.11 1071580.567 1050625.647 1083048.498 1041594.641 1019925.988 1106181.602 0.969909379 0.956215359 0.980685367 0.968720294 0.949776823 0.979087426 0.941612697 0.922024002 1 20.07715682 1.71634279 11.16046589 0.949053271 0.967009089 0.054393976 0.021447877 0.202550652 67.43702511 0.008977498 0.004890863 52.04065933 -1.71634279 0.017955817 EKENLSYDLVPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKENLSYDLVPLK 13 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;R4GN69 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 79.466 0.018634 162620000 453520 382000 366310 370530 472870 287660 465110 394290 442760 FALSE TRUE 425134.9928 410283.6775 374999.0462 380038.4271 435732.6977 370702.7722 395371.0734 443517.9744 368860.4957 1.15256309 1.112300402 1.01664193 1.030303954 1.18129402 1.004994508 1.071871556 1.20240031 1 18.49271576 4.479593445 3.010758161 1.071208937 1.150205724 0.127533926 0.069496702 0.541896333 9.362951291 0.015955115 0.075998015 30171.25987 -4.479593445 0.078996787 EKENNPSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKENNPSGK 9 1 I3VM54;Q9Y2K7;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 0 ;; 100.88 0.0039781 135878000 267478 185093 233710 216310 230637 169839 263982 208243 246088 FALSE TRUE 250737.0294 198797.4783 239253.7116 221860.8808 212523.7004 218868.7622 224400.3498 234242.5969 205014.323 1.22302201 0.969676047 1.167009739 1.082172589 1.03662855 1.067577909 1.094559378 1.142566985 1 17.64536518 4.772030565 23.60569324 1.075809456 1.223022622 0.392577721 0.059423515 8146.844565 5745586.569 0.013232811 2.117650043 59160.32683 -4.772030565 0.147213166 EKEPEYTLLTER ddPTM_SK-BR-3_Pertuzumab_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 98.439 0.0039747 132200000 137200 131470 141780 114000 146800 104680 150110 116970 188580 FALSE TRUE 128612.8969 141204.1756 145143.0886 116925.433 135270.9202 134899.4167 127602.3991 131573.962 157104.7797 0.818644074 0.898789813 0.923861698 0.744251277 0.861023582 0.858658896 0.812212074 0.837491782 1 17.26136755 -0.997131128 4.423113947 1.000005233 0.851570764 0.490374495 0.049378559 1.18208E+11 26807637721 6887001.179 0.012094698 0.100662769 0.997131128 -0.148434469 EKEPIVGSTDYGKDEDSAEALLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKEPIVGSTDYGKDEDSAEALLK 23 2 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 142.32 9.77E-08 393710000 1447040 707070 1237250 1103780 768980 1180990 1655160 752690 1227120 FALSE TRUE 1356472.349 759422.1985 1266598.154 1132104.863 708587.4127 1521922.641 1406984.124 846665.0034 1022305.745 1.326875406 0.742852324 1.23896218 1.107403406 0.693126706 1.488715729 1.376285061 0.828191574 1 19.9633953 2.227118034 24.99994103 1.233189 1.017295732 0.054172404 0.266180901 440.4334805 962259.3099 0.09351345 0.069657388 168.7011465 -2.227118034 -0.215893268 EKEPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKEPPK 6 1 Q5STZ8;H7C5Z1;Q8NE71;Q8NE71-2;E9PFR3;Q14738;Q14738-2 Q5STZ8;Q8NE71;E9PFR3 ABCF1;PPP2R5D ATP-binding cassette sub-family F member 1;Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform 0 79.597 0.060858 195180000 296460 259390 247990 301260 268840 226730 287340 257560 255150 FALSE TRUE 277905.0978 278595.5055 253872.4399 308990.8416 247726.3908 292183.2703 244256.0345 289716.933 212563.8167 1.307396067 1.310644069 1.19433516 1.453638001 1.165421259 1.374567294 1.149095073 1.362964485 1 17.69753651 -3.525483878 0.355476935 7.05E-16 1.288580627 0.45698388 0.097987709 122.7998822 2.713307889 91.35406422 0.063972369 0.000298206 3.525483878 1.288580627 EKEPS(ph)RER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKEPSRER 8 2 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477 Q8NI27 THOC2 THO complex subunit 2 1 EKEPS(1)RER;EKEPS(1)RER;EKEPS(1)RER;EKEPS(1)RER 85.963 0.012892 2548760000 4138580 2807720 3232270 3139330 3258860 2387070 3993410 2801780 4120480 TRUE FALSE 3879553.665 3015606.51 3308940.971 3219890.523 3002922.281 3076178.358 3394635.244 3151588.4 3432745.269 1.130160662 0.878482461 0.963934318 0.937992851 0.874787392 0.896127769 0.988898091 0.918095621 1 21.71093137 -1.684900588 6.879659563 1.000392271 0.942275138 0.039661597 0.074012355 0.000397834 1.82E-05 0.064022632 0.014988986 0.02065853 1.684900588 -0.058117133 EKEQEDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EKEQEDRR 8 2 Q14247;Q14247-3;Q14247-2;H0YCD9 Q14247 CTTN Src substrate cortactin 0 ;;;; 166.07 0.00018033 2122239000 3528909 2820352 3017946 2980777 3106695 2312457 3393175 2625234 3726872 FALSE TRUE 3308040.885 3029173.797 3089533.104 3057268.784 2862707.707 2980025.796 2884399.909 2953000.244 3104832.987 1.065448898 0.9756318 0.995072237 0.984680592 0.922016649 0.959802285 0.929003242 0.951097936 1 21.56608424 8 0.521508644 0.95153796 4.74038096 0.564869407 0.026949201 81.82083827 0.814116214 0.012670377 343.1652348 100000000 -8 3.788843 EKEQFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 EKEQFR 6 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;; 138.62 0.011151 63531980000 33770310 31075320 30888880 29897400 32713900 25073580 34585400 29435330 34284230 FALSE TRUE 31656686.58 33376169.03 31621578.82 30664617.9 30144682.26 32311915.51 29399640.35 33110395.75 28561970.53 1.108350929 1.168552744 1.107121751 1.073617028 1.055413254 1.131291536 1.029328152 1.159247599 1 24.76759218 -4.999989388 0.02307822 0.270642079 1.649379361 0.333589638 0.044286788 2344.737554 4.090771814 172.2709456 85.94074879 1.00E-05 4.999989388 1.378737282 EKEQFRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKEQFRK 7 2 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;; 129.4 0.002061 2355280000 3469900 3541710 3339430 3337950 4810140 2662290 4596810 3316570 6948490 FALSE TRUE 3252725.153 3803941.894 3418642.857 3423607.448 4432371.008 3430849.904 3907561.015 3730651.065 5788742.13 0.561905347 0.657127543 0.590567481 0.59142511 0.765688108 0.592676237 0.675027653 0.644466618 1 22.46481846 -5 0.272470509 3.548858828 0.609919891 0.813536952 0.055519848 82.01149129 0.794205793 117.694369 0.060423402 1.00E-05 5 -2.938938937 EKEQMMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 EKEQMMR 7 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;;; 121.62 0.0040315 4198760000 4815380 4683430 4469100 4316370 5769700 3352051 4753700 4517240 6228470 FALSE TRUE 4513993.961 5030196.03 4575109.162 4427135.362 5316571.036 4319733.708 4040926.816 5081227.358 5188898.12 0.869933049 0.969415069 0.881711118 0.853193734 1.024605015 0.832495379 0.778763954 0.979249783 1 22.30699678 EKESFIIEEQSFLLCEDLLYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKESFIIEEQSFLLCEDLLYGR 22 1 H3BNT4;Q99547;H3BU96 H3BNT4 MPHOSPH6 M-phase phosphoprotein 6 0 125.58 1.92E-05 11717000 24507 25700 27385 21947 25965 18658 29637 18003 32172 FALSE TRUE 22973.15062 27602.85474 28034.58513 22510.19718 23925.81364 24044.26171 25193.20699 20250.71418 26802.28536 0.857134021 1.029869445 1.045977414 0.839861112 0.892678117 0.897097445 0.939964882 0.755559233 1 14.7100684 3.239205381 24.99969752 0.889259947 0.998607559 0.203257746 0.08059472 20.40270862 791057.5507 0.021219227 0.027093236 1734.624121 -3.239205381 0.109347612 EKETLAVNYEKEEEFLTNELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKETLAVNYEKEEEFLTNELSR 22 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 250.92 4.33E-32 311390000 448330 306380 354660 341660 394340 235250 411670 297370 511950 FALSE TRUE 420269.8256 329064.694 363072.7027 350427.574 363370.1271 303162.856 349943.9053 334497.2991 426502.2377 0.985387153 0.771542714 0.851279713 0.821631267 0.851977071 0.710811877 0.820497232 0.784280291 1 18.70219379 4.747914036 24.52270733 0.815413362 0.985387271 0.29778388 0.074978079 1029.460277 2698955.955 0.015362342 0.191300256 55964.68138 -4.747914036 0.169973909 EKEVDGLLTSEPMGS(ph)PVSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EKEVDGLLTSEPMGSPVSSK 20 1 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 1 EKEVDGLLTSEPMGS(0.999)PVS(0.001)SK;EKEVDGLLTSEPMGS(1)PVSSK;EKEVDGLLTSEPMGS(1)PVSSK;EKEVDGLLTSEPMGS(1)PVSSK;EKEVDGLLTSEPMGS(1)PVSSK 181.77 7.55E-17 4054710000 5943920 3491880 4798620 4501130 4677170 3169300 5237120 3619670 5786030 TRUE FALSE 5571900.657 3750422.428 4912445.532 4616636.616 4309843.935 4084225.461 4451862.475 4071593.767 4820304.214 1.155923031 0.778046833 1.01911525 0.957747978 0.894102062 0.847296204 0.923564629 0.844675686 1 22.20069277 2.734792065 22.87259561 0.89493175 0.951332531 0.094588818 0.101748899 286.6937863 1740030.055 0.029925594 0.029263085 542.9902917 -2.734792065 0.056400781 EKEWQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKEWQR 6 1 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-4;C9JMV9;A0A1B0GV31 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 ; 88.029 0.047213 385250000 558880 525000 524940 546260 542340 404850 630120 456290 688380 FALSE TRUE 523900.6984 563871.5463 537391.8247 560277.9564 499746.8041 521723.6228 535639.3557 513258.8109 573484.9309 0.913538735 0.983236901 0.937063549 0.976970669 0.871420986 0.909742514 0.934007725 0.89498221 1 19.12939605 EKEYEIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKEYEIER 8 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 87.298 0.014066 130920000 523950 564370 498120 517010 585480 442930 617420 483910 636810 FALSE TRUE 491156.9048 606156.542 509935.6416 530277.3519 539498.7625 570796.7006 524843.6028 544327.2287 530522.2971 0.925798798 1.142565629 0.961195494 0.999538294 1.016920053 1.075914629 0.989296031 1.026021398 1 19.01705386 -1.24607358 0.155105905 0.974407949 1.0345931 0 0.060125332 180.6612244 5.378026571 2.193180083 0.344271054 0.056744846 1.24607358 0.060185151 EKFEPTVFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKFEPTVFR 9 1 E7ETZ4;Q9Y6E2;Q75MG1;E9PFE3;C9JF98;F8WDX8;E7EMS9;Q9Y6E2-2 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 ; 143.5 9.28E-05 669870000 1374750 1408980 1246770 1356240 1746680 1100310 1559240 1409880 1838040 FALSE TRUE 1288706.851 1513302.345 1276343.973 1391043.415 1609502.799 1417951.635 1325446.437 1585906.622 1531259.25 0.841599391 0.988273113 0.833525723 0.908431028 1.051097519 0.926003637 0.865592445 1.035687864 1 20.54628713 -4.9996111 0.056800771 1.323306435 0.783557068 0.178506374 0.07096107 897.0327969 3.739026084 40.41675188 7.413035335 1.00E-05 4.9996111 -0.539749367 EKFPEFCSS(ph)PSPPVEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKFPEFCSSPSPPVEVK 17 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 EKFPEFCS(0.017)S(0.903)PS(0.08)PPVEVK 154.95 7.19E-08 623220000 1430300 871000 1077600 1109400 1017400 854320 1549200 957770 1570200 TRUE FALSE 1340780.076 935489.7463 1103161.181 1137869.082 937497.508 1100948.315 1316911.842 1077349.693 1308123.476 1.024964463 0.715138718 0.843315789 0.869848377 0.71667356 0.841624155 1.0067183 0.823584098 1 20.3190673 1.905933117 7.265317154 0.940625796 0.817381706 0.198868229 0.099290649 0.35660712 24.03797904 0.038658282 0.024006417 80.525442 -1.905933117 -0.12324409 EKFPEFCSSPS(ph)PPVEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKFPEFCSSPSPPVEVK 17 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 EKFPEFCS(0.001)S(0.1)PS(0.898)PPVEVK;EKFPEFCSS(0.004)PS(0.996)PPVEVK;EKFPEFCS(0.001)S(0.036)PS(0.964)PPVEVK 155.17 6.68E-08 1490140000 2647840 1613180 1982640 1907080 1911510 1602190 2955970 1707500 2906470 TRUE FALSE 2482116.421 1732621.526 2029669.157 1956018.901 1761387.715 2064716.244 2512749.74 1920685.134 2421361.38 1.025091273 0.715556769 0.838234711 0.807817832 0.727436941 0.852708836 1.037742553 0.793225311 1 21.20738698 1.986206378 23.55181977 0.947193639 0.807989604 0.212904354 0.104229637 360.8517977 616132.7826 0.037416973 0.025296278 96.87380942 -1.986206378 -0.139204035 EKGPTTGEGALDLSDVHS(ph)PPKSPEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKGPTTGEGALDLSDVHSPPKSPEGK 26 2 O95684;O95684-2 O95684 FGFR1OP FGFR1 oncogene partner 1 EKGPTTGEGALDLSDVHS(0.935)PPKS(0.065)PEGK 81.28 0.0081161 229120000 673790 274260 371430 397390 429160 264220 591230 350940 698700 TRUE FALSE 631618.6866 294566.4958 380240.495 407587.7002 395455.5047 340496.0247 502580.5502 394755.6315 582082.4562 1.085101741 0.506056303 0.653241634 0.700223303 0.679380559 0.58496184 0.863418137 0.678178198 1 19.15086401 0.398397427 0.682158833 1.00491319 0.678208192 0.201534024 0.162157668 2.729397152 1.929247144 0.186191613 0.055733412 2.5026345 -0.398397427 -0.326704999 EKGTWVQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKGTWVQLK 9 1 P46778 P46778 RPL21 60S ribosomal protein L21 0 95.81 0.0071076 330340000 170910 333650 134980 115600 397290 95243 156510 314590 335560 FALSE TRUE 160213.0482 358353.7932 138181.7893 118566.4917 366088.446 122738.108 133042.7785 353867.254 279552.8682 0.573104648 1.281882012 0.494295731 0.424129047 1.309549955 0.439051507 0.475912765 1.265833029 1 18.09276162 1.227512299 24.99809014 1.132916617 0.732138603 0.213156136 0.333206353 400.5168564 906186.0712 0.300432391 0.077970773 16.88543679 -1.227512299 -0.400778014 EKHLAEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKHLAEIK 8 1 H0YC42;P55327-8;H0YC44;P55327-2;P55327-4;P55327-3;E5RFR7 H0YC42;P55327-2 TPD52 0 ; 88.417 0.0087904 514360000 1133620 1496980 818100 811670 1790060 557060 1085200 1549340 2071450 FALSE TRUE 1062668.748 1607817.957 837505.7183 832498.8264 1649475.908 717874.1789 922484.3345 1742778.51 1725711.613 0.615785824 0.931684034 0.485310357 0.482409007 0.955823613 0.415987337 0.534553009 1.009889773 1 20.71875996 1.229143565 24.99334901 1.004945239 0.636865182 0.423161458 0.181115774 215.9903458 573229.1516 0.161742581 0.04259551 16.94897992 -1.229143565 -0.368080056 EKHPDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EKHPDGK 7 1 P53396;P53396-2;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ;;;;; 96.253 0.0077314 4305180000 19282900 10847060 16133800 14267450 14308700 10587120 16384900 12957430 15856300 FALSE TRUE 18076017.71 11650187.61 16516501.35 14633576.92 13184952.42 13643449.68 13928136.35 14575193.66 13209781.09 1.368381321 0.881936462 1.250323623 1.107783454 0.998120433 1.032829354 1.054380558 1.103363754 1 23.65510322 2.899152209 7.018659419 1.042207465 1.125069395 0.156611523 0.125489197 0.635764527 38.46238287 0.036046218 0.038349494 792.7791301 -2.899152209 0.08286193 EKHPNS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKHPNSSPR 9 1 P29374 P29374 ARID4A AT-rich interactive domain-containing protein 4A 1 EKHPNS(0.754)S(0.246)PR 81.92 0.012063 65775000 170850 161080 146450 152630 190280 104440 172710 175380 194460 TRUE FALSE 160156.8035 173006.5308 149923.8632 156546.7442 175336.1764 134590.1326 146813.7389 197276.5791 162003.3697 0.98860168 1.067919335 0.925436696 0.966317827 1.082299563 0.830786006 0.906238797 1.217731331 1 17.3056643 1.250867136 24.99917123 1.108865722 0.966781949 0.304754643 0.089208075 237.9726532 483417.9029 0.058717809 0.021110325 17.81833565 -1.250867136 -0.142083772 EKHPNSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKHPNSSPR 9 1 P29374 P29374 ARID4A AT-rich interactive domain-containing protein 4A 1 EKHPNS(0.386)S(0.614)PR;EKHPNS(0.405)S(0.595)PR;EKHPNS(0.316)S(0.684)PR;EKHPNS(0.415)S(0.585)PR 86.313 0.0086135 489454000 1018750 1045190 962430 941580 1237670 701640 1098100 1123310 1189060 TRUE FALSE 954988.256 1122576.955 985259.2941 965742.5369 1140468.391 904192.0778 933450.0993 1263557.726 990598.2044 0.964052077 1.133231365 0.994610418 0.974908427 1.151292609 0.91277379 0.942309501 1.275550188 1 19.91794048 -1.96882416 3.231031441 0.971786015 1.035579054 0.010138701 0.112924533 0.036277203 0.000350035 0.172827388 0.023592695 0.010744243 1.96882416 0.063793039 EKIDLENTLEQEQEALVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKIDLENTLEQEQEALVNR 19 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ;; 196.31 7.67E-16 520532000 205955 186123 187589 180915 199637 153999 241432 173546 239559 FALSE TRUE 193064.6442 199903.7406 192038.6997 185557.5852 183958.3153 198456.0113 205231.5129 195213.6001 199575.0553 0.967378633 1.001646926 0.962237988 0.929763416 0.921750041 0.994392867 1.028342508 0.978146291 1 17.60657189 2.016737444 24.91646193 1.006826003 0.961912161 0.421647766 0.024916433 237.7817189 353975.8988 0.010152617 0.00749681 103.9291665 -2.016737444 -0.044913842 EKIETELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EKIETELR 8 1 P63104;E7EX29;B0AZS6;E7ESK7;E9PD24;E7EVZ2 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;;;;; 134.68 0.00079016 28078360000 44786700 42302500 41978000 42173100 44011800 32323600 52365400 38528600 43013500 FALSE TRUE 41983580.39 45434621.12 42973737.98 43255333.14 40555290.76 41654898.59 44513694.41 43338980.52 35834268.97 1.17160421 1.267909809 1.199235793 1.207094058 1.131746005 1.162431934 1.242210199 1.209428342 1 25.09483659 -1.266583382 3.2925725 0.999216917 1.204567537 0.719005118 0.038948138 705570816.2 912420538.2 5422824.465 0.009641052 0.054127332 1.266583382 0.20535062 EKINIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKINIR 6 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;; 132.72 0.013476 2791280000 3325080 4860800 3570290 3173120 6614000 3192990 4456590 5547200 6871500 FALSE TRUE 3116969.178 5220698.69 3654978.965 3254547.631 6094563.12 4114754.379 3788365.702 6239780.131 5724602.258 0.544486593 0.911975794 0.638468631 0.568519433 1.064626474 0.718784327 0.661769243 1.089993654 1 22.44874403 1.234754888 24.99999041 1.044996975 0.740037524 0.407617362 0.157593975 99.20078737 651607.4217 0.123048308 0.035316133 17.1693909 -1.234754888 -0.30495945 EKKDELCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKKDELCR 8 2 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 ;; 90.15 0.0075369 793040000 659910 534830 522660 476830 678650 360170 759240 476980 891350 FALSE TRUE 618607.4111 574429.3697 535057.742 489066.2651 625351.5665 464145.2321 645399.0104 536532.003 742577.9267 0.833053864 0.773561062 0.720540866 0.658605983 0.842135948 0.625045824 0.869133039 0.722526194 1 19.50218291 -0.431571771 0.661416042 1.022673304 0.750552125 0.481977698 0.07905489 8.750519126 3.042617409 0.561257164 0.026239009 0.370193022 0.431571771 -0.272121179 EKKEESHSNDQSPQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKKEESHSNDQSPQIR 16 2 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 ; 147.64 6.06E-07 64758000 85973 78017 73654 90162 99218 45115 94093 68921 147453 FALSE TRUE 80592.1034 83793.45986 75401.10766 92475.70956 91425.81851 58138.96812 79984.62817 77525.93856 122842.1417 0.656062344 0.682123078 0.613804893 0.752801183 0.744254514 0.473281948 0.651117174 0.63110214 1 16.90644605 -1.793674241 2.552056325 1.104638991 0.6482277 0.669903079 0.077071123 19455946.75 13604880.03 12639758.93 0.017959372 0.016081471 1.793674241 -0.456411291 EKKEEWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKKEEWDR 8 2 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 0 ;;; 109.66 0.0020106 4585040000 9857230 6980120 8680860 8294550 9014350 5650450 9525280 6989100 11623300 FALSE TRUE 9240283.57 7496935.348 8886774.099 8507402.196 8306399.313 7281643.188 8097052.692 7861704.52 9683296.141 0.954249817 0.774213164 0.917742675 0.878564703 0.85780701 0.75197981 0.836187655 0.811883103 1 23.20706679 2.461669752 24.99204379 0.829774855 0.869327532 0 0.077515444 731.3543756 1182922.226 0.024155889 0.020216088 289.5141215 -2.461669752 0.039552677 EKKPGDGEVS(ph)PSTEDAPFQHSPLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKKPGDGEVSPSTEDAPFQHSPLGK 25 2 O60318 O60318 MCM3AP Germinal-center associated nuclear protein 1 EKKPGDGEVS(0.996)PS(0.003)T(0.001)EDAPFQHSPLGK 105.7 0.0019359 97244000 276990 139120 167170 159980 167640 104110 197200 133050 259880 TRUE FALSE 259653.6903 149420.5896 171135.3513 164085.3576 154474.2306 134164.8669 167631.6907 149661.5854 216504.3491 1.199300113 0.690150522 0.790447638 0.757884811 0.713492506 0.619686706 0.774264773 0.691263644 1 17.72403648 4.742460089 24.90952633 0.741170145 1.199300299 0.655960067 0.100782356 195.7456356 1250355.379 0.020555729 0.156256064 55266.26164 -4.742460089 0.458130154 EKLCYVALDFEQEMATAASSSSLEK ddPTM_SK-BR-3_Pertuzumab_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 ;;; 305.5 9.46E-64 2359875000 2388023 1922595 2181825 2074429 2575883 1777665 3029284 2062335 2936546 FALSE TRUE 2238560.903 2064945.934 2233578.919 2127662.36 2373583.54 2290848.028 2575070.987 2319822.065 2446417.502 0.915036334 0.844069311 0.912999894 0.869705338 0.970228319 0.93640927 1.052588524 0.948252726 1 21.2222392 2.479936404 1.422176696 1.001353307 0.880550681 0.609573193 0.037694974 0.2276519 0.932621281 0.016969608 0.012750603 301.9509527 -2.479936404 -0.120802626 EKLDQLKQEFEFWYPVDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKLDQLKQEFEFWYPVDLR 19 2 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRP1 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 153.58 2.50E-08 381720000 866520 875780 897500 862020 1175850 571260 1143200 796380 1627220 FALSE TRUE 812286.06 940623.6624 918789.1238 884140.8926 1083503.484 736173.4884 971787.7729 895809.796 1355626.47 0.599196075 0.693866403 0.677759799 0.652200966 0.799264036 0.543050394 0.716855118 0.660808723 1 20.37052828 -1.75779443 2.357620624 1.08797068 0.672279477 0.703880523 0.067646272 4116161.297 2720599.039 2099671.566 0.014818712 0.017466487 1.75779443 -0.415691202 EKLDSVIEFSIPDSLLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKLDSVIEFSIPDSLLIR 18 1 F8W1A4;P54819-2;P54819;P54819-6;P54819-3;F8VZG5;A0A5F9ZHP2;F8VY04;A0A5K1VW67;P54819-4 F8W1A4 AK2 "Adenylate kinase 2, mitochondrial;Adenylate kinase 2, mitochondrial;Adenylate kinase 2, mitochondrial, N-terminally processed" 0 ; 168.17 1.95E-11 374330000 1540160 1390140 1310100 1352580 1763190 1178830 1852260 1356490 1719080 FALSE TRUE 1443764.135 1493067.412 1341176.191 1387289.493 1624716.17 1519139.084 1574530.809 1525850.763 1432154.442 1.008106453 1.042532403 0.936474553 0.968673107 1.134455979 1.060736915 1.099414115 1.065423335 1 20.44975565 2.752933329 24.98448044 1.078873984 0.989132242 0.475576572 0.043005483 621.0648401 1079612.842 0.012552014 0.01326057 566.1523686 -2.752933329 -0.089741742 EKLEAEMEAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKLEAEMEAAR 11 1 Q8WXF1;Q8WXF1-2 Q8WXF1 PSPC1 Paraspeckle component 1 0 ;; 139.89 3.54E-05 879540000 1739910 1683820 1702720 1593010 1882630 1237510 1827120 1613330 2600640 FALSE TRUE 1631012.139 1808491.785 1743109.322 1633889.334 1734775.834 1594759.048 1553160.318 1814757.802 2166576.383 0.752806202 0.834723298 0.80454552 0.754134194 0.800699134 0.736073309 0.716873095 0.837615427 1 21.04698567 0.96013527 10.66982155 0.999999923 0.776636222 0.809329093 0.034997357 1.140524112 305.4675539 0.038807628 0.00970555 9.122949473 -0.96013527 -0.223363701 EKLEDFFK ddPTM_SK-BR-3_Pertuzumab_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 63.076 0.068952 100700000 554530 590050 481980 460030 636350 337750 551560 529960 653400 FALSE TRUE 519822.9572 633737.9159 493412.7932 471835.1486 586373.6379 435252.9421 468858.6984 596126.6726 544343.3189 0.954954234 1.164224661 0.906436758 0.866796987 1.077212887 0.799592696 0.861329022 1.095129952 1 19.05415732 3.825222795 4.904739141 0.927746154 1.067934316 0.154518138 0.106853406 0.284567899 11.09372929 0.025847192 0.0476841 6686.868684 -3.825222795 0.140188162 EKLEMEMEAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKLEMEMEAAR 11 1 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;; 155.66 2.87E-05 2359190000 2770910 2627540 2512360 2458930 3082160 1832600 2843510 2583130 3498750 FALSE TRUE 2597483.689 2822085.796 2571954.366 2522030.307 2840099.586 2361641.87 2417152.073 2905639.467 2914786.022 0.891140437 0.968196559 0.882381878 0.865254014 0.9743767 0.810228213 0.829272562 0.996862015 1 21.47495855 1.214292103 24.23871063 0.998431366 0.891036519 0.437980305 0.051627517 194.4326843 194186.4296 0.051889508 0.013002753 16.37917803 -1.214292103 -0.107394847 EKLPANQYTWSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKLPANQYTWSSR 13 1 A0A494C0U1;Q5VZU9;P29144;A0A494C0X4 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 78.902 0.020034 265510000 97464 120210 94543 94607 127100 70921 116460 113060 141000 FALSE TRUE 91363.90222 129110.4735 96785.60461 97034.77579 117118.0787 91394.74139 98997.90416 127175.7899 117466.1891 0.777788936 1.099128817 0.823944365 0.826065581 0.997036505 0.778051472 0.842777866 1.082658685 1 16.84188603 1.23737088 24.99999685 1.041329383 0.889310817 0.301284492 0.1023602 42.43473232 891497.5351 0.080301222 0.024322467 17.27312356 -1.23737088 -0.152018566 EKLQSFDS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EKLQSFDSPER 11 1 P78332;E9PGM9;P78332-2 P78332 RBM6 RNA-binding protein 6 1 EKLQS(0.014)FDS(0.986)PER;EKLQSFDS(1)PER;EKLQS(0.002)FDS(0.998)PER;EKLQSFDS(1)PER;EKLQSFDS(1)PER 124.2 0.00021449 1230396000 2356650 2099310 2343610 2232200 2603610 2117830 2897240 2347010 3525440 TRUE FALSE 2209151.483 2254745.097 2399201.536 2289482.031 2399132.973 2729213.141 2462825.759 2640039.365 2937021.289 0.752174147 0.767697907 0.816882583 0.779525174 0.816859238 0.92924527 0.838545423 0.898883292 1 21.48592229 1.300526824 0.149592025 1.109676563 0.65497495 0.834953328 0.031621621 1.876221552 0.26734672 0.373400657 0.320641246 19.97684153 -1.300526824 -0.454701613 EKMLRAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKMLRAAR 8 2 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 0 ;;; 77.282 0.054069 12719400000 4520890 9582100 3620060 4099870 11737700 3484310 4120390 6720070 10487100 FALSE TRUE 4237935.565 10291568.65 3705929.533 4205079.605 10815868.39 4490173.734 3502575.771 7559085.532 8736735.261 0.485070846 1.177965035 0.424177845 0.481310178 1.237975979 0.513941833 0.40090213 0.865207118 1 23.05866284 3.964857106 24.76557969 0.660294591 0.871018023 0.010266032 0.318113625 884.907742 1786941.279 0.076776269 0.13971616 9222.679269 -3.964857106 0.210723432 EKNEIQNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKNEIQNR 8 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 94.692 0.0092837 173030000 151420 160020 149850 137010 177330 123480 156320 151190 199640 FALSE TRUE 141942.8925 171868.0473 153404.5128 140525.9086 163403.2171 159126.6715 132881.2672 170066.4043 166318.7943 0.853438681 1.033365159 0.922352242 0.844918995 0.982469948 0.956757005 0.79895521 1.022532691 1 17.34359168 3.661549254 7.248231744 0.916890605 0.962632686 0 0.081639102 0.71030356 67.01133277 0.02034208 0.031740768 4587.216671 -3.661549254 0.045742081 EKNGS(ph)EEDDDEKPGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKNGSEEDDDEKPGKR 16 3 Q6ZU65;Q6ZU65-2;H7C4P8 Q6ZU65 UBN2 Ubinuclein-2 1 EKNGS(1)EEDDDEKPGKR;EKNGS(1)EEDDDEKPGKR;EKNGS(1)EEDDDEKPGKR 172.24 2.56E-08 271954000 781810 205807 350943 382535 381416 223078 506020 250643 472610 TRUE FALSE 732877.9077 221045.1644 359267.5337 392351.4957 351461.1259 287476.9972 430146.9987 281936.3303 393728.3378 1.86137963 0.561415431 0.912475682 0.996503066 0.892648794 0.730140479 1.092496926 0.71606817 1 18.58684103 4.749307663 24.99296944 0.861209073 1.861380197 0.799151601 0.157338756 692.5210446 1610472.377 0.036902135 0.546977834 56144.55752 -4.749307663 1.000171124 EKNPDMVAGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKNPDMVAGEK 11 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;;; 108.59 0.0021428 684477000 1506560 1035360 1224860 1153320 1306960 935393 1464920 998340 1621380 FALSE TRUE 1412267.099 1112019.132 1253914.258 1182916.144 1204316.634 1205425.774 1245268.846 1122984.947 1350761.203 1.045534248 0.82325368 0.928301949 0.87574039 0.891583672 0.892404795 0.921901549 0.831371928 1 20.36534122 -1.647360718 6.882926261 1.000384788 0.897100796 0.200973991 0.061376359 0.000312474 1.60E-05 0.051239377 0.012032687 0.022523677 1.647360718 -0.103283993 EKPCVS(ph)PTVGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKPCVSPTVGEK 12 1 Q68DQ2 Q68DQ2 CRYBG3 Very large A-kinase anchor protein 1 EKPCVS(0.952)PT(0.048)VGEK 79.837 0.013299 247350000 315680 201720 235950 257460 243010 145770 260780 166760 284790 TRUE FALSE 295922.1523 216655.5587 241546.8454 264066.8595 223924.9749 187851.4326 221678.46 187580.3531 237256.7092 1.247265687 0.913169366 1.018082255 1.113000599 0.943808821 0.79176447 0.934340111 0.790621912 1 17.85608936 2.483452262 21.35254966 0.876092743 1.03625597 0.415985 0.104911454 45.1477576 152275.5998 0.033027738 0.028672825 304.4053364 -2.483452262 0.160163226 EKPDS(ph)DDDLDIASLVTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKPDSDDDLDIASLVTAK 18 1 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 EKPDS(1)DDDLDIASLVTAK 283.26 1.17E-39 233640000 808580 371070 497570 483340 527070 357970 692700 415610 671410 TRUE FALSE 757972.4212 398544.4089 509372.5954 495743.3227 485676.0483 461310.1278 588836.0657 467499.8234 559347.3335 1.355101519 0.712516866 0.910655267 0.886288882 0.868290629 0.824729287 1.052719894 0.835795212 1 19.09338489 -0.126106901 6.285379629 0.999999977 0.911980064 0.005264071 0.173825353 330906334.8 1949926937 0.149747768 0.037436965 0.747985362 0.126106901 -0.088019913 EKPEEESLAAPTWLVHLQQVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKPEEESLAAPTWLVHLQQVER 22 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 0 155.86 9.62E-09 112350000 62505 59465 57197 59174 60548 43180 65912 50934 56586 FALSE TRUE 58592.92362 63867.85047 58553.73985 60692.50502 55792.80432 55645.36503 56029.1075 57293.22202 47141.43104 1.242917797 1.35481357 1.242086601 1.28745572 1.18351953 1.180391936 1.188532174 1.215347535 1 15.52470793 -4.999999987 0.09221465 0.17119269 1.445237774 0.796148001 0.041284173 79.14195257 0.50517914 12.68444841 0.837681471 1.00E-05 4.999999987 1.274045084 EKPELSEPSHLNGPS(ph)SDPEAAFLSR ddPTM_SK-BR-3_Pertuzumab_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(0.5)S(0.5)DPEAAFLSR;EKPELSEPSHLNGPS(0.827)S(0.173)DPEAAFLSR;EKPELSEPSHLNGPS(0.5)S(0.5)DPEAAFLSR 207.7 1.90E-25 2060990000 1520890 1324310 1481540 1398210 1433230 1266090 1824580 1359580 1638370 TRUE FALSE 1425700.21 1422363.29 1516682.828 1434090.436 1320669.897 1631589.63 1551001.168 1529326.556 1364915.463 1.044533708 1.042088927 1.11119177 1.050680775 0.967583659 1.19537779 1.136334967 1.120455147 1 20.38038017 2.230156572 24.99999222 1.12821641 1.052670878 0.228723486 0.059556654 234.1214704 696448.4015 0.020605531 0.015470983 169.8856014 -2.230156572 -0.075545533 EKPELSEPSHLNGPSS(ph)DPEAAFLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKPELSEPSHLNGPSSDPEAAFLSR 25 1 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 EKPELSEPSHLNGPS(0.377)S(0.623)DPEAAFLSR;EKPELSEPSHLNGPS(0.093)S(0.907)DPEAAFLSR;EKPELSEPSHLNGPS(0.049)S(0.951)DPEAAFLSR 195.35 1.14E-19 2711484000 1037085 839657 936861 839652 963329 853277 1176463 942422 1078426 TRUE FALSE 972175.7011 901826.0779 959083.7853 861198.8918 887673.0262 1099604.218 1000063.295 1060085.461 898429.7337 1.082083178 1.003780311 1.06751118 0.958560096 0.988027213 1.223917883 1.11312355 1.179931409 1 19.77704615 2.254892262 24.99986464 1.138977614 1.021469103 0.394819982 0.066715014 206.3980584 315945.9539 0.020728254 0.01729496 179.8424715 -2.254892262 -0.11750851 EKPEVTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKPEVTDR 8 1 O95104-2;O95104-3;O95104 O95104-2 SCAF4 "Splicing factor, arginine/serine-rich 15" 0 ; 84.17 0.020892 463050000 1261230 1206980 1289180 1286000 1276950 1016840 1436870 1104810 1486860 FALSE TRUE 1182291.866 1296346.055 1319759.958 1319000.937 1176663.498 1310385.201 1221424.683 1242747.96 1238693.461 0.954466866 1.046543068 1.065445165 1.064832405 0.949923073 1.057876902 0.986058877 1.003273207 1 20.24038778 2.771579505 24.96787173 1.002408783 1.040545953 0.129466555 0.04049789 1081.530588 817819.0475 0.01160395 0.012307037 590.9891466 -2.771579505 0.03813717 EKPKEEEWEKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKPKEEEWEKPK 12 3 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 122.45 0.00015698 570410000 1197600 466430 717210 695350 771300 467800 915820 567980 1104700 FALSE TRUE 1122644.354 500964.9625 734222.5599 713193.8582 710725.2093 602846.2659 778501.2931 638893.5533 920318.4334 1.219843386 0.544338725 0.797791866 0.77494249 0.772260104 0.655040955 0.845904271 0.694209232 1 19.8117736 -1.322221038 4.780328999 1.000134523 0.76621971 0.11427091 0.176386835 0.000220796 3.13E-05 0.149113055 0.03512615 0.047618856 1.322221038 -0.233914813 EKPSEDMESNTFFDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKPSEDMESNTFFDPR 16 1 O43395;O43395-3 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 0 67.416 0.041294 0 311520 258440 293540 265470 300460 220260 334100 246420 332910 FALSE TRUE 292022.5193 277575.1665 300502.9074 272282.4096 276863.0836 283845.4864 284004.8066 277186.0794 277345.1703 1.052920875 1.000829278 1.083497892 0.981745632 0.998261781 1.023437639 1.024012087 0.999426379 1 18.08132308 3.220812396 24.9994503 1.007913599 1.04151629 0.398152183 0.023477398 282.5286734 397957.4906 0.006767259 0.008104475 1662.694256 -3.220812396 0.033602691 EKPSYDTETDPSEGLMNVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKPSYDTETDPSEGLMNVLK 20 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 207.82 5.74E-22 166120000 558330 366760 427530 435240 461410 330740 579960 395190 504020 FALSE TRUE 523385.1219 393915.292 437671.2135 446408.9953 425172.7198 426219.2689 493000.3821 444530.3414 419895.8059 1.246464277 0.938126284 1.042332901 1.063142306 1.012567198 1.0150596 1.174101706 1.05866821 1 18.67967185 EKPTHCSECGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKPTHCSECGK 11 1 O75362 O75362 ZNF217 Zinc finger protein 217 0 99.522 0.0028312 67719000 69484 145660 129200 138110 170660 110860 216760 145730 210910 FALSE TRUE 65135.12047 156444.818 132264.685 141654.1364 157257.052 142863.4823 184258.8503 163924.7113 175707.7585 0.370701448 0.890369437 0.752753812 0.8061917 0.894992079 0.813074412 1.048666558 0.932939517 1 17.42281837 4.739111502 24.84943351 0.882306616 0.370701279 0.77080572 0.089248401 21.7705274 981763.0376 0.022655261 0.134624249 54841.77492 -4.739111502 -0.511605337 EKPTTALLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKPTTALLDK 10 1 Q12906;Q12906-5;Q12906-2;Q12906-3;K7EKJ9;K7ER69;K7EKY0;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 88.021 0.011381 947940000 931910 660130 813000 789200 954250 517370 897480 769970 1108300 FALSE TRUE 873583.4166 709006.7121 832284.7439 809452.2081 879307.0543 666726.3202 762911.2058 866102.4494 923317.5701 0.946135376 0.767890415 0.901406808 0.876678008 0.952334368 0.722098595 0.82627173 0.938033107 1 19.81646741 1.050224975 4.265343394 0.998778442 0.848533685 0.311082424 0.072262495 0.200261001 7.570237908 0.065367364 0.016693527 11.22599836 -1.050224975 -0.150244757 EKPYFPIPEEYTFIQNVPLEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 233.66 1.85E-30 6821246000 3879339 3868707 4130858 3825558 4546579 3414063 4709219 3789966 4705593 FALSE TRUE 3636538.097 4155150.092 4228843.902 3923728.295 4189509.025 4399647.565 4003115.329 4263151.598 3920199.129 0.927641167 1.059933426 1.078731912 1.000900252 1.068698014 1.122302062 1.021151017 1.087483431 1 21.90249551 4.739032635 24.08472229 1.058223292 0.927641105 0.513666646 0.038795373 17.26737046 880619.5658 0.008310059 0.048817015 54831.81663 -4.739032635 -0.130582187 EKQDEQVGLPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKQDEQVGLPGK 12 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 ;; 91.032 0.0077757 448300000 1565010 1076820 1303640 1200260 1374880 887080 1758730 1240520 1948170 FALSE TRUE 1467058.818 1156548.873 1334562.956 1231060.704 1266902.471 1143165.595 1495024.764 1395401.653 1623007.841 0.903913574 0.712595986 0.822277578 0.758505703 0.780589248 0.704350014 0.921144511 0.85976273 1 20.63023854 1.260999214 1.296798763 0.98347324 0.778415189 0.500366443 0.066947771 0.293827411 0.963926493 0.055416128 0.017567585 18.23892401 -1.260999214 -0.205058051 EKQDETQTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKQDETQTK 9 1 P35221-2;P35221;P35221-3;E5RGY7 P35221-2 CTNNA1 Catenin alpha-1 0 ; 117.52 0.0010381 129714000 469600 251615 365640 337524 350000 246154 409140 304597 383720 FALSE TRUE 440208.5743 270244.8364 374313.1535 346185.4373 322512.4118 317214.6638 347793.2553 342626.606 319674.6531 1.377051856 0.845374614 1.170919089 1.082930517 1.008877021 0.99230471 1.087960062 1.07179785 1 18.28624483 2.771129911 20.95679896 1.038398685 1.082095028 0.065338414 0.132903046 447.4184254 287888.4931 0.038038644 0.040336959 590.3776536 -2.771129911 0.043696344 EKQDTFALASQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKQDTFALASQQK 13 1 P09110;C9JDE9;H7C131;H0Y4D4;P09110-2 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 ; 198.48 1.14E-07 600840000 1491230 1270030 1144270 1220460 1678920 824020 1631950 1337870 1891670 FALSE TRUE 1397896.576 1364064.343 1171412.625 1251779.07 1547064.396 1061901.197 1387254.248 1504906.015 1575938.056 0.887025077 0.86555708 0.743311338 0.794307279 0.981678429 0.67382166 0.880272065 0.954927136 1 20.5877794 1.280831842 3.294637233 0.988163117 0.822007123 0.361924013 0.082926764 0.239675012 4.429745607 0.065850513 0.019635337 19.09113909 -1.280831842 -0.166155993 EKQEASES(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKQEASESPVK 11 1 Q01167;Q01167-2;E9PPI7;Q01167-3 Q01167 FOXK2 Forkhead box protein K2 1 EKQEAS(0.022)ES(0.978)PVK;EKQEAS(0.003)ES(0.997)PVK 118.55 0.00042741 1421130000 2480100 1135030 1598390 1420960 1479910 1199400 2170600 1351610 1880300 TRUE FALSE 2324874.968 1219068.802 1636304.566 1457424.239 1363683.838 1545647.309 1845138.681 1520361.484 1566465.783 1.484153049 0.77822881 1.044583663 0.930390089 0.870548117 0.986709909 1.177899129 0.97056795 1 20.57908183 -0.356567382 7.808398089 1.000018665 1.011761977 0 0.193004656 0 0 0.169582256 0.039970921 0.439979678 0.356567382 0.011743312 EKQFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKQFQK 6 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 90.986 0.044147 555220000 558860 502570 524600 524830 644270 431310 636540 489330 690460 FALSE TRUE 523881.9502 539780.8057 537043.7597 538298.0263 593671.6331 555822.1953 541096.7363 550423.9276 575217.7655 0.910754121 0.938393836 0.933635559 0.935816066 1.032081533 0.966281344 0.940681545 0.956896606 1 19.13374871 2.963581407 24.99966899 0.972842332 0.931265897 0.464955323 0.025939259 620.7910632 426144.2275 0.007988457 0.008475293 919.5628277 -2.963581407 -0.041576435 EKQLAAENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKQLAAENR 9 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 141.08 9.81E-05 2033620000 2406420 4163770 2318590 2272980 4759860 1634700 2669290 3521340 4815300 FALSE TRUE 2255806.468 4472059.863 2373588.05 2331308.515 4386039.796 2106611.353 2269054.745 3960987.05 4011595.322 0.562321542 1.114783398 0.591681827 0.581142495 1.09334054 0.525130574 0.565624038 0.987384502 1 21.93574465 1.190778851 15.16541463 0.993866516 0.735383887 0.215719667 0.21591473 4.979826496 1574.152557 0.201964719 0.050526892 15.51596715 -1.190778851 -0.258482629 EKQPMVPESLADYITAAYVEMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKQPMVPESLADYITAAYVEMR 22 1 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 136.57 3.94E-06 70005000 84649 94565 89696 91893 102970 63310 96537 77673 86089 FALSE TRUE 79350.97019 101566.691 91823.63148 94251.12995 94883.15156 81586.56925 82062.17306 87370.64503 71720.18974 1.106396546 1.416152012 1.2803038 1.314150594 1.322962919 1.137567672 1.144199051 1.218215475 1 16.13009168 2.235000025 24.97217357 1.13780197 1.305609811 0.420206972 0.093343256 79.02892022 554260.1477 0.030944255 0.023762829 171.7908485 -2.235000025 0.167807841 EKQPPIDNIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKQPPIDNIIR 11 1 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 0 ;;; 196.7 5.44E-08 1899390000 3573300 3733170 3572560 3517070 4014980 2951560 4068080 3473190 4190990 FALSE TRUE 3349653.532 4009577.791 3657302.81 3607323.971 3699659.666 3803627.457 3458109.17 3906825.417 3491486.694 0.95937743 1.14838696 1.04749155 1.033177064 1.059623018 1.089400531 0.990440312 1.118957556 1 21.73541004 -5 0.221872321 0.698282905 1.066712084 0.054635898 0.056720324 379.4793969 3.798872439 51.27460679 0.09829164 1.00E-05 5 0.368429179 EKQPVAGSEGAQYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EKQPVAGSEGAQYR 14 1 Q9UGI8-2;Q9UGI8;F8W7T0 Q9UGI8-2 TES Testin 0 ;;;; 192.78 3.05E-07 6138430000 1814640 1862270 1782380 1805650 1980600 1434280 2105490 1674290 2503040 FALSE TRUE 1701064.922 2000154.408 1824658.895 1851986.036 1825051.665 1848333.352 1789791.321 1883328.792 2085266.454 0.815754226 0.959184091 0.875024337 0.888129204 0.875212691 0.886377541 0.858303416 0.90315978 1 20.99180031 -1.772393777 4.716188904 1.00955917 0.886797997 0.509745662 0.035965107 0.003646939 0.000176004 0.035131883 0.007717041 0.016889089 1.772393777 -0.122761173 EKQS(ph)S(ph)EEEEKETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKQSSEEEEKETR 13 2 Q92504;A2AAT0 Q92504 SLC39A7 Zinc transporter SLC39A7 2 EKQS(1)S(0.999)EEEEKET(0.001)R;EKQS(1)S(1)EEEEKETR 126.25 0.00093806 1701720000 11836300 3690800 4753100 4869100 6092600 3360600 8386900 4493000 6733000 TRUE FALSE 11095487.11 3964070.672 4865845.777 4994049.349 5614111.772 4330750.665 7129362.205 5053960.94 5609218.803 1.978080638 0.706706372 0.867472985 0.890328854 1.000872308 0.772077328 1.271008041 0.901009769 1 22.41936843 4.745898045 24.98759737 0.925620465 1.978081136 0.825977388 0.151737716 382.6725662 1303158.993 0.038500568 0.40021557 55705.4959 -4.745898045 1.052460671 EKQSDDEVYAPGLDIESSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKQSDDEVYAPGLDIESSLK 20 1 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 188.32 2.37E-17 245790000 312700 188150 218210 217820 249740 171090 294980 187930 326270 FALSE TRUE 293128.6652 202080.8218 223386.0442 223409.63 230126.4278 220480.9056 250750.4875 211393.4742 271813.4292 1.078418627 0.743454149 0.821835937 0.821922709 0.846633768 0.811147949 0.922509562 0.777715342 1 18.05225721 -1.004592158 4.228603705 1.000009343 0.84328713 0.191893948 0.092969539 81826452481 3.44397E+11 15354589.1 0.020223252 0.098948187 1.004592158 -0.156722212 EKQSEDTNTESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKQSEDTNTESK 12 1 O95232;J3KPP4;H0YBV7;H0YAR4 O95232 LUC7L3 Luc7-like protein 3 0 76.728 0.027665 221290000 195690 108920 153450 141090 150860 115070 179120 130070 192320 FALSE TRUE 183442.1122 116984.5501 157089.9065 144710.6083 139012.0641 148288.841 152262.6189 146309.5258 160220.5496 1.144934983 0.730146978 0.980460415 0.903196304 0.86762943 0.925529474 0.950331398 0.913175783 1 17.28969967 0.566041487 0.619250651 1.001120797 0.905925263 0.019865664 0.103666155 4.465065973 3.100379171 0.112797073 0.038825597 3.681641415 -0.566041487 -0.095195533 EKS(ph)PSLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EKSPSLGK 8 1 O76021;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 EKS(0.929)PS(0.071)LGK;EKS(0.5)PS(0.5)LGK;EKS(0.791)PS(0.209)LGK;EKS(0.929)PS(0.071)LGK;EKS(0.985)PS(0.015)LGK 128.88 0.0022536 2154290000 6580730 3555640 5009550 4697570 4915050 3248690 5424650 3748160 5097490 TRUE FALSE 6168853.856 3818903.285 5128378.892 4818117.599 4529041.799 4186534.065 4611274.092 4216126.027 4246685.988 1.452627737 0.899266698 1.207619048 1.134559422 1.066488507 0.985835561 1.085852381 0.99280381 1 22.017906 2.591921955 3.686287008 1.028323258 1.133283573 0.20229629 0.137284665 0.52982812 12.97779883 0.043659061 0.040432543 390.7706656 -2.591921955 0.104960316 EKS(ph)PSLGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EKSPSLGKK 9 2 O76021;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 EKS(0.844)PS(0.156)LGKK;EKS(0.95)PS(0.05)LGKK;EKS(0.972)PS(0.028)LGKK 54.198 0.071285 1402685000 5162710 2514560 3487700 3388630 4030280 2261770 4592680 2710720 5527550 TRUE FALSE 4839585.197 2700740.639 3570429.891 3475587.983 3713758.066 2914706.282 3904050.27 3049159.359 4604966.196 1.050949126 0.586484357 0.775343344 0.754747773 0.806468041 0.632948464 0.847791298 0.662145872 1 22.13475914 -1.218722653 4.662030576 1.000056545 0.751839853 0.240111681 0.129846387 6.65E-05 1.11E-05 0.109485181 0.025800036 0.060433444 1.218722653 -0.248216692 EKS(ph)PVREPVDNLSPEER ddPTM_SK-BR-3_Pertuzumab_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 256.58 2.20E-27 1161650000 448260 340851 378317 370734 426127 289035 478503 327914 419473 TRUE FALSE 420204.2068 366087.9627 387290.8579 380247.6621 392660.7043 372474.7124 406755.9174 368854.7847 349460.2464 1.202437791 1.047581138 1.108254406 1.088099908 1.123620522 1.065857179 1.16395476 1.055498554 1 18.41476882 0.998740281 24.81592843 0.999999997 1.107141636 0.413461977 0.044964587 31.10379379 612750.6643 0.039058253 0.009764563 9.97103593 -0.998740281 0.107141639 EKSTFREES(ph)PLR ddPTM_SK-BR-3_Pertuzumab_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(0.003)T(0.002)FREES(0.995)PLR;EKSTFREES(1)PLR;EKSTFREES(1)PLR;EKSTFREES(1)PLR;EKS(0.006)T(0.006)FREES(0.987)PLR;EKS(0.021)T(0.09)FREES(0.888)PLR 186.42 6.15E-06 10448880000 4719000 6227250 5219620 6430800 8935320 3822360 5445560 5351790 14937500 TRUE FALSE 4423646.214 6688322.069 5343431.851 6595825.215 8233576.011 4925813.281 4629048.832 6019972.762 12444334.75 0.355474704 0.53745919 0.429386702 0.530026341 0.661632476 0.395827771 0.371980417 0.483752075 1 23.56898577 -1.126017795 3.146421979 1.000939987 0.469791887 0.768674202 0.091252714 4922681.536 7259925.77 47407.8023 0.022968665 0.074813884 1.126017795 -0.5311481 EKT(ph)PELPEPSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EKTPELPEPSVK 12 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 EKT(0.997)PELPEPS(0.003)VK;EKT(1)PELPEPSVK;EKT(0.996)PELPEPS(0.004)VK;EKT(1)PELPEPSVK;EKT(1)PELPEPSVK;EKT(1)PELPEPSVK 172.43 0.00018051 16511660000 24905520 9964570 14449240 14335300 14701800 10159147 19715740 11361810 18971040 TRUE FALSE 23346727.96 10702357.13 14791982.8 14703168.07 13547179.93 13091927.82 16759547.82 12780356.99 15804650.87 1.477206182 0.677165046 0.935925945 0.930306414 0.857164138 0.828359192 1.060418731 0.808645322 1 23.91384583 -0.616277659 7.249784812 1 0.923497279 0 0.214181582 0 0 0.182604796 0.043040363 0.24194817 0.616277659 -0.076502721 EKT(ph)PPRPQGQRPEPENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKTPPRPQGQRPEPENR 17 3 A9X3U0;Q96GF1 A9X3U0 RNF185 E3 ubiquitin-protein ligase RNF185 1 EKT(1)PPRPQGQRPEPENR;EKT(1)PPRPQGQRPEPENR;EKT(1)PPRPQGQRPEPENR;EKT(1)PPRPQGQRPEPENR 85.945 0.0050516 460679000 524355 312180 337246 331011 418706 283547 481645 349845 449634 TRUE FALSE 491536.5566 335294.132 345245.6344 339505.3027 385822.5197 365402.4159 409426.8036 393523.9184 374587.1807 1.312208698 0.895103061 0.921669647 0.906345225 1.029993923 0.975480301 1.093008049 1.050553619 1 18.514942 1.754243641 25 1.055795456 0.981117629 0 0.121605389 15.15479741 24187.47616 0.053168887 0.029484538 56.78630892 -1.754243641 -0.074677827 EKTIAS(ph)DS(ph)EEEAGKELSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKTIASDSEEEAGKELSDK 19 2 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 EKTIAS(1)DS(1)EEEAGKELSDK 142.21 8.44E-08 135890000 324010 143010 188900 195620 226170 149770 219090 156220 226420 TRUE FALSE 303730.7925 153598.6092 193380.7972 200639.9404 208407.5205 193006.1677 186239.4884 175724.4109 188629.0393 1.610201662 0.814289305 1.02519102 1.063674719 1.104853851 1.023204955 0.98733201 0.931587265 1 17.52519227 4.748844058 24.97470018 0.991947562 1.610202008 0.859376039 0.078362952 555.4541476 1348967.054 0.019810895 0.279566601 56084.65572 -4.748844058 0.618254447 EKTPSPKEEDEEPES(ph)PPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EKTPSPKEEDEEPESPPEK 19 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EKTPSPKEEDEEPES(1)PPEK;EKTPSPKEEDEEPES(1)PPEK;EKTPSPKEEDEEPES(1)PPEK;EKTPSPKEEDEEPES(1)PPEK 160.88 1.60E-11 1102300000 3004890 1147260 1588110 1747180 1964870 1139510 2148550 1289140 2395460 TRUE FALSE 2816819.299 1232204.324 1625780.719 1792015.597 1810557.036 1468468.039 1826394.874 1450091.967 1995642.251 1.411485098 0.617447503 0.814665413 0.89796435 0.907255314 0.735837317 0.915191524 0.726629217 1 20.92842169 4.750563044 24.96460694 0.815318167 1.411485467 0.728711308 0.111903279 947.6449788 1971030.212 0.025789617 0.431761764 56307.08488 -4.750563044 0.596167301 EKTPSPKEEDEEPES(ph)PPEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 165.85 1.15E-11 21898600000 6756200 1814250 2959080 3289520 3506150 1977070 3984030 2247120 4493160 TRUE FALSE 6333341.502 1948578.958 3029270.775 3373934.652 3230791.122 2547818.014 3386661.687 2527677.879 3743222.569 1.691948952 0.520561875 0.809268142 0.901344921 0.8631042 0.680648283 0.904744942 0.675267856 1 21.8358494 4.74882217 24.99717524 0.781795081 1.691949455 0.804056295 0.139128139 609.2300785 1484056.97 0.03200685 0.44689946 56081.82916 -4.74882217 0.910154374 EKVAS(ph)DTEEADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKVASDTEEADR 12 1 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 EKVAS(0.979)DT(0.021)EEADR;EKVAS(0.961)DT(0.039)EEADR 181.86 1.07E-05 1199980000 1913350 1132620 1519040 1391590 1383260 1117270 1826070 1270090 1660500 TRUE FALSE 1793596.839 1216480.363 1555072.346 1427300.555 1274624.339 1439807.712 1552267.756 1428663.532 1383351.823 1.296558699 0.879371642 1.124133659 1.031769744 0.92140287 1.04081094 1.122106271 1.032755015 1 20.39973669 0.984951828 23.24279558 0.999999981 1.047393731 0.019982113 0.114477908 2003.293679 3094220.798 0.099563325 0.024890831 9.659437297 -0.984951828 0.04739375 EKVEPEVLSTDTQTS(ph)PEPGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKVEPEVLSTDTQTSPEPGTR 21 1 P29375;P29375-2 P29375 KDM5A Lysine-specific demethylase 5A 1 EKVEPEVLSTDTQT(0.053)S(0.945)PEPGT(0.002)R 121.72 1.77E-05 107790000 150680 137580 157630 133800 162060 120010 211990 158290 199240 TRUE FALSE 141249.2078 147766.5664 161369.058 137233.5345 149332.4613 154654.9388 180204.0675 178052.8549 165985.5569 0.850972882 0.890237495 0.972187346 0.826779975 0.899671418 0.931737325 1.085661132 1.072700892 1 17.34069819 1.849347335 4.182164324 1.059337652 0.898257611 0.741633663 0.044128839 0.114939065 3.15218664 0.021337639 0.011868304 70.68826714 -1.849347335 -0.161080041 EKVESELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EKVESELR 8 1 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;;;; 138.66 0.00063462 13683200000 19696900 19229500 17800200 17911300 21117100 13423400 20919300 17712100 18641100 FALSE TRUE 18464106.19 20653272.19 18222429.15 18370934.28 19458648.15 17298517.67 17782645.17 19923494.67 15529779.98 1.188948344 1.329914024 1.173386176 1.18294878 1.2529893 1.113893287 1.145067425 1.282921889 1 23.88853405 -5 0.13079029 0.316626491 1.294288334 0.474662224 0.066709304 116.3446928 0.958552511 20.94733755 0.469197743 1.00E-05 5 0.977661843 EKVFDVIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKVFDVIIR 9 1 B3KWE1;P12081-4;P12081;B4DDD8;E7ETE2 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 ; 140.07 0.00010029 1244480000 2847700 2974800 2937800 2952500 3412500 2518400 3415400 2812800 3367100 FALSE TRUE 2669467.54 3195057.287 3007486.003 3028266.149 3144496.015 3245421.197 2903292.477 3163984.272 2805109.258 0.951644765 1.139013491 1.072145762 1.079553725 1.120988784 1.156967839 1.035001567 1.127936198 1 21.41962553 -0.978950931 3.955119955 0.999992026 1.089075898 0.166929044 0.059460804 2788382.428 1410169.772 180.0703171 0.012297355 0.104966102 0.978950931 0.089083872 EKVIET(ph)PENDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKVIETPENDFK 12 1 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 1 EKVIET(1)PENDFK;EKVIET(1)PENDFK 172.24 5.87E-05 654900000 893100 451220 623010 578180 667700 473840 862170 556720 942530 TRUE FALSE 837202.4652 484628.7983 637788.0914 593017.0777 615261.5354 610629.9159 732895.6125 626227.7175 785215.654 1.066207049 0.617191972 0.812245767 0.755228293 0.783557399 0.777658867 0.93336857 0.797523221 1 19.58272941 1.000319758 0.646961129 0.994000867 0.775335388 0.15553467 0.119397064 1.128850962 1.113154337 0.109370369 0.045438 10.00736541 -1.000319758 -0.218665478 EKVLATVTKPVGGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKVLATVTKPVGGDK 15 2 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 0 ; 192.55 7.29E-08 1395730000 4312900 2887800 3570600 3456000 3718300 2621000 4963700 3233400 4918500 FALSE TRUE 4042963.288 3101615.717 3655296.318 3544686.811 3426279.717 3377640.152 4219439.266 3637097.108 4097570.575 0.986673253 0.756940158 0.892064273 0.86507035 0.836173448 0.824303106 1.029741694 0.88762281 1 21.96633737 1.748066085 25 0.970891479 0.851228003 0.374386831 0.067733748 2.125161507 5601.479504 0.028154006 0.015612867 55.98427844 -1.748066085 -0.119663476 EKVPAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKVPAGR 7 1 A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2;A0A087WW69;F8W8L6 A0A087WTA5 EIF2B4 Translation initiation factor eIF-2B subunit delta 0 ; 109.86 0.0063228 337890000 390930 414510 377990 368030 429320 294070 463630 378530 514810 FALSE TRUE 366462.3891 445200.7517 386956.1013 377474.2729 395602.939 378963.2352 394112.9856 425790.3037 428884.8852 0.854453961 1.038042531 0.902237674 0.880129578 0.922398883 0.883601284 0.918924866 0.992784587 1 18.71023095 1.22888593 9.67551117 0.996651712 0.922689831 0.314810423 0.049170228 0.25959756 203.9526393 0.042103367 0.012086179 16.93892832 -1.22888593 -0.07396188 EKVPGGLQGSQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EKVPGGLQGSQDR 13 1 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 88.706 0.0071003 113220000 144780 176100 170540 184240 197260 138720 177270 136910 241560 FALSE TRUE 135718.4782 189138.6272 174585.2893 188967.9103 181767.9953 178766.2121 150690.0092 154003.5149 201242.0755 0.674404087 0.939856274 0.867538704 0.939007958 0.903230574 0.888314293 0.748799717 0.76526499 1 17.61857245 -1.699179087 8.602645447 1.000384013 0.851337333 0.238557034 0.087605311 0.000634956 2.22E-05 0.083473709 0.019625383 0.019990374 1.699179087 -0.14904668 EKVS(ph)SIDLEIDSLSSLLDDMTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 EKVSSIDLEIDSLSSLLDDMTK 22 1 Q15942;H7C3R3;C9IZ41 Q15942 ZYX Zyxin 1 EKVS(0.597)S(0.403)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(0.5)S(0.5)IDLEIDSLSSLLDDMTK;EKVS(0.499)S(0.499)IDLEIDS(0.001)LS(0.001)S(0.001)LLDDMTK;EKVS(0.5)S(0.5)IDLEIDSLSSLLDDMTK 240.68 1.87E-30 1682527500 1959787 996650.1 1352015 1704875 1752065 926725.8 1413274 856637.3 1616234 TRUE FALSE 1837127.43 1070443.11 1384085.434 1748624.979 1614464.882 1194256.494 1201366.684 963590.3526 1346474.104 1.364398635 0.794997176 1.0279332 1.298669595 1.199031513 0.886950956 0.892231555 0.715639721 1 20.36075505 2.14274868 7.556843147 0.865936224 1.082510607 0.342903246 0.172184561 0.335099137 23.05721986 0.067018294 0.049449954 138.9148517 -2.14274868 0.216574382 EKYDTDFYILDKYPLAVRPFYTMPDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EKYDTDFYILDKYPLAVRPFYTMPDPR 27 3 P14868;P14868-2 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ; 86.236 0.0036058 713670000 1561420 1592720 1424410 1262410 1950120 1101540 2050400 1561840 1885680 FALSE TRUE 1463693.509 1710646.646 1458197.678 1294805.578 1796965.442 1419536.716 1742961.555 1756839.162 1570947.826 0.931726366 1.088926454 0.928227949 0.824219338 1.143873407 0.903617989 1.10949678 1.118330687 1 20.58320384 1.676085671 9.066165208 1.084648344 0.980229659 0.205686971 0.095961941 0.181331795 23.8995741 0.04320605 0.023014248 47.43355454 -1.676085671 -0.104418686 EKYEITEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EKYEITEQR 9 1 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ;;;;;;; 165.11 5.63E-05 21203900000 31002060 27528290 29940360 31089810 31510510 27055660 41220360 30309000 31870620 FALSE TRUE 29061696.4 29566513.23 30650559.48 31887627.16 29035801.65 34866189.83 35039749.69 34093145.37 26551207.63 1.094552715 1.113565667 1.154394177 1.200985944 1.093577439 1.313167759 1.319704556 1.284052531 1 24.66227414 2.240362631 24.99996839 1.264758563 1.135276964 0.160549115 0.09682959 54.99546125 762984.3611 0.0309194 0.02465034 173.9252478 -2.240362631 -0.129481599 EKYIDQEELNK ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 188.15 2.99E-06 10493930000 15214160 9823870 11489490 11562500 12963240 8735340 15083840 10133270 14430880 FALSE TRUE 14261932.88 10551239.56 11762026.13 11859213.33 11945159.42 11257090.85 12822158.22 11398431.07 12022272.9 1.186292559 0.877640995 0.978352948 0.986436876 0.993585782 0.936352963 1.066533619 0.948109493 1 23.51920634 1.753986798 25 1.011187627 0.977845645 0 0.083467721 21.91179158 35554.99703 0.035416616 0.019640794 56.75273526 -1.753986798 -0.033341982 ELAAQLNEEAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELAAQLNEEAKR 12 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 144.2 0.00010078 683650000 672400 719650 758060 849840 910980 645880 1039820 778740 1128510 FALSE TRUE 630315.6843 772933.6348 776041.5412 871648.3332 839435.3055 832335.071 883908.6442 875967.4032 940154.3905 0.670438484 0.822134793 0.825440533 0.927133184 0.892869633 0.885317432 0.940173926 0.931727184 1 19.84253817 6.650511625 0.274904852 0.968969668 9.12E-18 0.860930734 0.033651312 8.420987805 0.227321502 0.035912192 3.353633441 4472101.218 -6.650511625 -0.968969668 ELAEAAKEPLPVEQDDDIEVIVDETSDHTEET(ph)SPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELAEAAKEPLPVEQDDDIEVIVDETSDHTEETSPVR 36 1 Q676U5-3;Q676U5;E7EVC7;Q676U5-2;Q676U5-4;Q676U5-5;C9J1B2;C9JAY7;C9JK97 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 1 ELAEAAKEPLPVEQDDDIEVIVDETSDHTEET(0.597)S(0.403)PVR 270.15 9.14E-64 71544000 37157 36980 39314 42878 49557 32781 44169 34884 61262 TRUE FALSE 34831.4097 39718.03768 40246.54665 43978.32207 45664.99312 42244.34254 37546.26849 39239.34419 51036.97643 0.682474005 0.778220821 0.788576234 0.861695287 0.894743308 0.827720322 0.735667963 0.768841474 1 15.63925524 -2.585212196 2.181562242 4.912822239 0.793094398 0.540580253 0.060186792 1870200.059 151854.4739 36428496.38 0.01499563 0.002598889 2.585212196 -4.119727841 ELAEAAKEPLPVEQDDDIEVIVDETSDHTEETS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELAEAAKEPLPVEQDDDIEVIVDETSDHTEETSPVR 36 1 Q676U5-3;Q676U5;E7EVC7;Q676U5-2;Q676U5-4;Q676U5-5;C9J1B2;C9JAY7;C9JK97 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 1 ELAEAAKEPLPVEQDDDIEVIVDETSDHTEET(0.178)S(0.822)PVR 153.02 1.01E-13 56630000 39802 45736 48186 47777 59006 39236 51714 47388 72957 TRUE FALSE 37310.86387 49122.34103 49328.99468 49003.03871 54371.90678 50562.79626 43959.96579 53304.49611 60780.00538 0.6138674 0.808199024 0.811599051 0.806236169 0.894568969 0.831898516 0.723263605 0.877007098 1 15.89130918 -5 0.114760876 1.605451606 0.695020069 0.523339486 0.070400335 155.7258327 1.17517809 22.45646038 0.785570922 1.00E-05 5 -0.910431537 ELAEDGYSGVEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELAEDGYSGVEVR 13 0 P23396;P23396-2;E9PPU1;E9PL09;F2Z2S8;H0YCJ7;H0YEU2;H0YF32;E9PQ96;E9PJH4;E9PK82 P23396 RPS3 40S ribosomal protein S3 0 ;;; 260.08 1.24E-23 1021830000 521709 559797 598647 571240 572960 477854 580180 435096 538177 FALSE TRUE 489056.165 601244.9523 612847.1895 585898.9855 527962.0328 615802.6925 493187.3951 489418.6934 448351.7819 1.09078671 1.341011626 1.366889158 1.306784113 1.177562026 1.373481086 1.10000097 1.09159529 1 18.77427161 1.618845518 5.087285031 1.061535491 1.291063177 0.550158673 0.090305725 0.105911326 5.957241248 0.048000543 0.022468438 41.57626941 -1.618845518 0.229527687 ELAEEAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELAEEAAR 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 97.093 0.019719 171560000 175120 233250 185190 201140 238810 166860 230040 210330 209630 FALSE TRUE 164159.5518 250520.0727 189582.7943 206301.5929 220054.8259 215029.7733 195547.6376 236590.1635 174641.3987 0.939980743 1.434482743 1.085554717 1.181286879 1.260038155 1.231264607 1.119709525 1.354719816 1 17.41403606 -0.977396859 4.783307291 0.999997336 1.207464436 0.171712565 0.137980513 3.46E-06 7.38E-07 0.117720991 0.027746748 0.105342384 0.977396859 0.2074671 ELAEEEPHLVEQFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELAEEEPHLVEQFQK 15 0 Q5QNY5;P40855;E9PS71;P40855-5;B7Z8B3 Q5QNY5 PEX19 Peroxisomal biogenesis factor 19 0 192.65 1.25E-07 90674000 212250 225730 224700 231960 235730 188150 262870 189150 259840 FALSE TRUE 198965.6514 242443.2841 230029.9901 237912.4863 217216.7167 242465.8506 223455.0839 212765.7939 216471.0254 0.919132946 1.119980301 1.062636395 1.099050027 1.003444763 1.120084548 1.032263249 0.982883476 1 17.72381441 1.447367666 5.487386561 0.994708806 1.063344798 0.142229682 0.059886974 0.2802379 17.29218805 0.034576849 0.013617377 28.01351888 -1.447367666 0.068635992 ELAEVAEHVQYMAELIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELAEVAEHVQYMAELIER 18 0 E2QRF9;O75496 E2QRF9 GMNN Geminin 0 ; 155.11 2.12E-08 38965000 57265 61790 68795 65417 70607 69406 83608 60779 76161 FALSE TRUE 53680.88587 66364.99589 70426.84989 67095.71097 65061.81103 89442.38549 71071.75658 68367.39194 63449.23708 0.846044623 1.045954198 1.109971579 1.057470729 1.025415183 1.409668415 1.120135716 1.077513223 1 15.9533152 5.656052766 0.753287449 1.138456624 6.80E-13 0.343497763 0.113592802 10.08724979 1.562737449 0.038553386 13.37206858 452952.61 -5.656052766 -1.138456624 ELAILLGMLDPAEKDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELAILLGMLDPAEKDEK 17 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ; 191.21 2.33E-10 1914080000 6302100 3300000 4355700 4145300 4592000 3085100 5908500 3737800 6793000 FALSE TRUE 5907662.811 3544335.434 4459019.261 4251675.416 4231362.843 3975718.288 5022575.277 4204472.558 5659204.416 1.043903414 0.626295708 0.787923343 0.751285005 0.747695706 0.702522474 0.887505541 0.742944105 1 22.43216782 -0.055546242 0.634082244 1.013012797 0.764789226 0.236494432 0.114459101 6.255702942 2.7030298 0.311905009 0.040212864 0.879941414 0.055546242 -0.248223571 ELAKVEEEIQTLSQVLAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELAKVEEEIQTLSQVLAAK 19 1 H0YC42;P55327-8;H0YC44;P55327-2;P55327-4;P55327-3;E5RFR7 H0YC42;P55327-2 TPD52 0 71.601 0.018101 85032000 36636 37595 27573 35998 38338 21085 35034 25775 42570 FALSE TRUE 34343.01816 40378.57292 28227.04458 36921.76962 35327.08813 27171.89721 29780.97694 28993.06549 35464.79199 0.968369367 1.138553778 0.795917387 1.041082368 0.996117167 0.766165419 0.839733586 0.817516863 1 15.11409987 2.254484994 24.84510757 0.839476021 0.984755308 0.28507162 0.102474247 255.4539647 398556.8568 0.034174823 0.028504232 179.6738999 -2.254484994 0.145279288 ELALGQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELALGQDR 8 0 P30046;J3KQ18;B5MC82;P30046-2;A6NHG4 P30046 DDT;DDTL D-dopachrome decarboxylase;D-dopachrome decarboxylase-like protein 0 ;;; 161.86 0.00080275 1585830000 1117470 1871580 1204110 1161350 1832500 862390 1252690 1608400 1617540 FALSE TRUE 1047529.547 2010153.731 1232672.058 1191152.207 1688582.842 1111347.993 1064860.764 1809212.281 1347562.124 0.777351581 1.491696519 0.914742286 0.883931201 1.253064932 0.824710025 0.790212744 1.342581724 1 20.36192035 3.735518307 23.98784941 0.976050836 1.190849965 0.029994645 0.245589867 380.7035607 1087542.426 0.058417023 0.103029165 5438.99059 -3.735518307 0.214799129 ELAMPGEDLKFNLILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELAMPGEDLKFNLILR 16 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 108.89 0.00092542 63666000 117300 142690 117100 134180 187460 101380 135360 132990 269570 FALSE TRUE 109958.4024 153254.9161 119877.6673 137623.286 172737.6478 130646.7602 115064.0246 149594.0942 224577.0255 0.489624449 0.682415825 0.533793103 0.612811064 0.769168829 0.581745884 0.512358842 0.666114862 1 17.77685082 0.968247034 22.12419407 1.000000002 0.599882082 0.702551573 0.081752144 487.2260831 339480.6629 0.075654739 0.018913685 9.294949493 -0.968247034 -0.40011792 ELAPEPWVERAT(ph)PT ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELAPEPWVERATPT 14 1 Q9BTY7 Q9BTY7 HGH1 Protein HGH1 homolog 1 ELAPEPWVERAT(0.974)PT(0.026) 91.441 0.034102 38464000 67835 97198 78793 101810 128250 65752 95363 84203 164250 TRUE FALSE 63589.32844 104394.6411 80662.00717 104422.617 118177.7623 84733.53501 81064.20346 94715.9299 136835.6139 0.464713291 0.762920106 0.589481092 0.763124555 0.863647693 0.619235977 0.592420359 0.692187708 1 17.06208424 -1.965855951 2.265613763 1.275760411 0.670474242 0.464645021 0.111819795 9755035.086 4092873.548 14122075.4 0.026891069 0.010817927 1.965855951 -0.605286169 ELAPYDENWFYTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ELAPYDENWFYTR 13 0 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ;;;;;;; 268.98 1.62E-24 6944200000 1199625 1073733 1159408 1061893 1075597 1028894 1286370 925339 1213975 FALSE TRUE 1124542.613 1153233.309 1186909.705 1089142.972 991123.9504 1325918.995 1093490.761 1040869.611 1011354.73 1.111917094 1.140285673 1.173583976 1.076914894 0.979996356 1.311032574 1.081213869 1.02918351 1 19.94785768 1.343309269 4.234663883 1.014108061 1.134302773 0.249398726 0.082704217 0.285052032 7.963888871 0.058651142 0.019660175 22.04495767 -1.343309269 0.120194712 ELAQIAGRPTEDEDEKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELAQIAGRPTEDEDEKEK 18 2 O15355 O15355 PPM1G Protein phosphatase 1G 0 ;; 140.97 6.94E-08 999170000 2677390 1102480 1591090 1436680 1361340 1079280 1905580 1177470 1522820 FALSE TRUE 2509816.939 1184108.766 1628831.406 1473547.641 1254425.848 1390850.615 1619855.97 1324479.721 1268651.504 1.978334421 0.933360156 1.283907677 1.16150703 0.988786789 1.096322048 1.276832892 1.044005952 1 20.27486439 4.74620722 24.99862421 1.119396177 1.978334831 0.844902895 0.118210499 353.7960367 1156619.107 0.027295972 0.291786527 55745.16683 -4.74620722 0.858938653 ELAQPSGGHLPQAS(ph)PISVYLFPGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELAQPSGGHLPQASPISVYLFPGER 25 0 H7C3T2;Q2TAZ0-3;Q2TAZ0 H7C3T2;Q2TAZ0 ATG2A Autophagy-related protein 2 homolog A 1 ELAQPSGGHLPQAS(0.998)PIS(0.002)VYLFPGER;ELAQPSGGHLPQAS(0.981)PIS(0.019)VYLFPGER;ELAQPSGGHLPQAS(0.999)PIS(0.001)VYLFPGER 163.15 1.19E-11 274145000 140472 183565 193226 213471 248629 174811 208864 177670 222697 TRUE FALSE 131680.1083 197156.3436 197809.412 218949.0273 229102.6813 225276.0979 177546.7822 199852.4906 185527.432 0.709760852 1.062680281 1.066200345 1.180143685 1.234872271 1.214246839 0.95698399 1.077212617 1 17.50127299 4.79934458 2.64016492 1.102453293 0.591792637 0.658936031 0.088326722 0.419584224 3.323187315 0.022755352 0.503620037 63000.58464 -4.79934458 -0.510660657 ELAQTTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELAQTTR 7 0 P50990-2;P50990;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 127.02 0.0090623 349360000 301320 302860 278530 274780 315280 276470 289130 237850 287200 FALSE TRUE 282460.9191 325284.0695 285136.8631 281831.32 290519.1806 356282.4009 245777.6407 267546.0961 239264.4646 1.180538529 1.359516843 1.191722572 1.177907135 1.214217836 1.489073613 1.027221661 1.11820239 1 17.86824662 1.613455891 25 1.054524128 1.264336448 0.519454566 0.099788985 0.388399895 1729.804885 0.044615506 0.023866667 41.06349321 -1.613455891 0.20981232 ELAVEGMHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELAVEGMHR 9 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 72.325 0.04707 273130000 204090 263720 359820 375880 258960 407450 409860 244540 216150 FALSE TRUE 191316.3712 283246.1032 368355.1003 385525.7172 238622.3262 525074.2006 348405.298 275071.3573 180073.1686 1.062436857 1.57295007 2.045585709 2.140939264 1.32514093 2.915893604 1.934798508 1.527553269 1 17.45822371 4.651016542 1.596886286 1.93525307 0.835302747 0.167805325 0.52002796 1.249049476 3.497837765 0.125441215 2.030193121 44773.03575 -4.651016542 -1.099950323 ELAVQIYEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELAVQIYEEAR 11 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;O15523-2;O15523;O15523-3 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ; 165.63 4.97E-05 141036000 107459 121257 132778 134864 140315 131873 131972 105841 108909 FALSE TRUE 100733.333 130234.9944 135927.5569 138324.8386 129295.2259 169942.5943 112184.0238 119055.4818 90731.38432 1.110236924 1.435390801 1.498131632 1.524553379 1.4250331 1.873029885 1.236441223 1.312175304 1 16.46931405 1.021912304 1.711280478 1.013441732 1.469788545 0.350122097 0.194778634 0.378545844 2.273855366 0.169682711 0.048966517 10.51749476 -1.021912304 0.456346813 ELCEVDEDGDSWLQVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELCEVDEDGDSWLQVTR 17 0 Q5SRE5;Q5SRE5-2 Q5SRE5 NUP188 Nucleoporin NUP188 homolog 0 201.95 2.56E-11 17759000 33924 42750 38157 35626 37315 39528 45800 35269 39552 FALSE TRUE 31800.7574 45915.25448 39062.10206 36540.22347 34384.43042 50939.09192 38932.71519 39672.41229 32950.51568 0.965106516 1.393460877 1.185477716 1.108942386 1.043517217 1.545927002 1.181551013 1.203999739 1 15.00801342 0.681485724 2.695133828 1.000061259 1.225554716 0.118471902 0.166292164 4.82347786 38.46786251 0.146978829 0.038891339 4.802702921 -0.681485724 0.225493457 ELCGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELCGER 6 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 118.69 0.050377 573320000 581860 616890 629760 580050 685250 527630 680490 558340 714750 FALSE TRUE 545442.4212 662565.1775 644698.2046 594935.065 631433.2292 679948.2156 578456.8419 628049.9781 595453.6075 0.916011616 1.112706631 1.08270098 0.999129164 1.060423887 1.141899565 0.971455768 1.054742083 1 19.18362958 1.674805507 16.81576578 1.009950027 1.060921109 0.079691882 0.065081055 0.319722729 81.03134168 0.02822063 0.015600795 47.29394121 -1.674805507 0.050971082 ELCHTQSSHASLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELCHTQSSHASLR 13 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;; 171.26 1.47E-05 378326000 56062.2 219343 152806 166570 202605 140388 194306 205560 162683 FALSE TRUE 52553.36698 235583.3839 156430.6305 170844.4682 186693.2206 180915.7366 165171.6191 231224.6185 135530.1563 0.387761428 1.738235905 1.154212721 1.260564238 1.377503174 1.334874404 1.218707509 1.706075052 1 17.04825437 4.753252125 24.99999998 1.35284637 0.387760757 0.638508281 0.227227676 1656.057149 2818003.691 0.049355338 1.127495882 56656.81087 -4.753252125 -0.965085614 ELCQQIHAECKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELCQQIHAECKR 12 1 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 101.53 0.0016993 124040000 240300 202510 212810 220530 239870 199520 279460 207930 315530 FALSE TRUE 225260.0519 217504.0511 217857.9537 226189.1732 221031.5778 257118.1851 237557.5674 233890.5182 262866.0046 0.856938699 0.827433169 0.828779492 0.86047328 0.840852655 0.978134032 0.903721148 0.889770888 1 18.00396805 2.257583129 24.77193123 0.933089139 0.839661019 0.680163761 0.033740965 122.5894961 159640.9372 0.01083302 0.00904925 180.9602254 -2.257583129 -0.09342812 ELDALDANDELTPLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELDALDANDELTPLGR 16 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 336.8 2.07E-71 189625000 253170 279670 279750 273720 281930 229260 301440 257300 293990 FALSE TRUE 237324.5416 300377.0578 286385.8021 280744.1186 259788.3551 295443.6403 256241.8704 289424.4714 244921.1698 0.968983375 1.226423417 1.16929787 1.146263179 1.06070192 1.206280537 1.046221814 1.181704594 1 17.90195795 -1.715454476 0.339660347 0.88554238 1.144133233 0.160404412 0.0815295 43.6385952 2.645560118 4.171782509 0.06292412 0.019255089 1.715454476 0.258590853 ELDALGHELPVLAPQWEGYDELQTDGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELDALGHELPVLAPQWEGYDELQTDGNR 28 0 P55957;P55957-2;B2ZP78;P55957-3 P55957 BID BH3-interacting domain death agonist;BH3-interacting domain death agonist p15;BH3-interacting domain death agonist p13;BH3-interacting domain death agonist p11 0 ;;; 198.79 4.98E-25 403722000 197148 204368 218710 203819 241487 199291 246297 210767 330108 FALSE TRUE 184808.8586 219499.6194 223897.9045 209049.3406 222521.5851 256823.0765 209367.0514 237081.7239 275010.8422 0.672005718 0.798148966 0.8141421 0.760149451 0.809137499 0.933865277 0.761304717 0.862081371 1 18.06912897 -5 0.091575448 1.626749969 0.646115717 0.629969763 0.0561155 145.070588 0.92078883 17.77400203 1.195320083 1.00E-05 5 -0.980634252 ELDDISQEIAQLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELDDISQEIAQLQR 14 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4;M0R2S2 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 0 152.47 1.55E-05 9484200 18225 20652 17445 15878 20677 19554 22586 17457 18163 FALSE TRUE 17084.32978 22181.09557 17858.80364 16285.45636 19053.11183 25198.92237 19199.43898 19636.54488 15131.47796 1.129058895 1.465890881 1.180241856 1.076263429 1.259170576 1.665331201 1.268840957 1.297728148 1 13.88526529 2.448480204 24.99985672 1.351560574 1.241409546 0.021724775 0.190267815 590.4540151 515385.174 0.06232945 0.052149332 280.8537353 -2.448480204 -0.110151028 ELDDLEQWIQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELDDLEQWIQER 12 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 ;;; 155.97 0.00013874 101500000 194025 186812 192063 189018 220013 173488 219800 173488 250318 FALSE TRUE 181881.3216 200643.7549 196618.8251 193868.5219 202734.0665 223571.1693 186843.0305 195148.3587 208538.3087 0.872172229 0.962143388 0.942842715 0.929654235 0.972167022 1.072086806 0.895965023 0.935791414 1 17.66995291 4.739510517 23.97669905 0.959842083 0.872172188 0.266268976 0.04740808 65.3590832 1649290.733 0.010774917 0.065543825 54892.18484 -4.739510517 -0.087669895 ELDDRDHYGNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELDDRDHYGNK 11 1 P30876;C9J2Y9;C9J4M6 P30876 POLR2B DNA-directed RNA polymerase II subunit RPB2;DNA-directed RNA polymerase 0 ; 77.305 0.019816 357450000 920410 871960 902820 921370 1030160 717870 1092850 869970 1148510 FALSE TRUE 862803.1811 936520.8257 924235.3167 945013.9141 949255.3891 925107.4154 928987.288 978587.6695 956816.2613 0.901743852 0.978788576 0.965948588 0.98766498 0.992097885 0.966860047 0.970915029 1.022754011 1 19.86788238 5.776368831 1.345137596 0.983030036 1.74E-13 0.683299315 0.017685481 11.19990235 1.962254215 0.004522456 28.28172087 597542.5433 -5.776368831 -0.983030036 ELDDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELDDTR 6 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 99.919 0.088987 1513690000 4335800 4817000 4952300 4842900 5036200 3976200 5496200 4408100 4800500 FALSE TRUE 4064430.018 5173655.692 5069770.895 4967177.013 4640677.167 5124064.392 4672095.834 4958460.988 3999265.538 1.016294112 1.293651458 1.267675489 1.242022308 1.160382356 1.281251356 1.168238465 1.239842902 1 21.93130364 -1.532001387 0.573488977 0.879760375 1.223135003 0.377766423 0.082201871 54.91087807 7.143618644 9.653323717 0.03130419 0.029376403 1.532001387 0.343374628 ELDEEGS(ph)DPPLPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELDEEGSDPPLPGR 14 0 C9JQV0;Q9BRJ6;H7C0T1;H7C2R9 C9JQV0 C7orf50 Uncharacterized protein C7orf50 1 ELDEEGS(1)DPPLPGR;ELDEEGS(1)DPPLPGR 167.89 3.75E-06 388110000 582360 597140 592950 631290 599680 567020 689180 493870 601090 TRUE FALSE 545911.1271 641352.8669 607015.054 647489.9702 552583.5518 730709.4692 585843.857 555530.7566 500764.1958 1.090156069 1.280748249 1.212177426 1.293003724 1.103480553 1.459188727 1.169899649 1.109365968 1 18.93377189 1.122705353 2.510170082 1.007890415 1.241537726 0.358384607 0.104183381 0.24996527 2.970547439 0.086009764 0.023682919 13.26494192 -1.122705353 0.233647311 ELDEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELDEGR 6 0 O15541 O15541 RNF113A RING finger protein 113A 0 ; 114.6 0.058509 1284730000 2260700 2381700 2312700 2276700 2401000 2007640 2643300 2076770 2466000 FALSE TRUE 2119206.822 2558043.546 2367558.336 2335123.976 2212435.145 2587213.077 2246961.704 2336059.306 2054408.669 1.031541024 1.245148341 1.152428128 1.136640441 1.076920663 1.259346845 1.093726744 1.137095721 1 20.97029176 0.470532518 0.958037895 0.999593529 1.156916746 0.277426088 0.070074148 2.141655653 2.763821481 0.062849693 0.019881056 2.954830121 -0.470532518 0.157323217 ELDFWQEGWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELDFWQEGWR 10 0 Q5JRX3-3;Q5JRX3;Q5JRX3-2 Q5JRX3-3 PITRM1 "Presequence protease, mitochondrial" 0 ; 116.23 0.0025996 48846000 53416 64020 56851 59165 78636 55653 51047 56903 96434 FALSE TRUE 50072.78791 68760.10741 58199.53257 60683.27407 72460.24576 71719.11765 43392.97625 64007.46481 80338.54241 0.623272298 0.855879449 0.724428535 0.755344474 0.901936276 0.892711213 0.540126506 0.796721759 1 16.29380467 4.756742771 23.34847667 0.783328024 0.623271959 0.152076053 0.125530722 3257.620169 4183077.974 0.029067354 0.850145208 57114.02552 -4.756742771 -0.160056065 ELDGHVLK ddPTM_SK-BR-3_Pertuzumab_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 81.548 0.022576 161230000 373810 389470 372850 357250 464600 280180 434460 381010 506390 FALSE TRUE 350413.8994 418306.764 381694.1781 366417.6398 428112.1901 361063.4177 369316.7563 428579.9372 421870.2376 0.830620101 0.991553153 0.904766784 0.868555321 1.014795906 0.855863689 0.875427379 1.015904653 1 18.68643979 1.227699541 24.97445739 1.00795241 0.912312332 0.345698181 0.057831804 276.2233143 635139.5784 0.050416221 0.013108174 16.89271835 -1.227699541 -0.095640077 ELDLFLAYYVQEQDS(ph)GQSGSPSHNDPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELDLFLAYYVQEQDSGQSGSPSHNDPAK 28 0 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A1B0GWJ4;Q5VW27;O00712-5;Q5VW26;A0A2R8Y7V8;Q5VW30;A0A1B0GWI9 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 ELDLFLAYYVQEQDS(0.312)GQS(0.312)GS(0.312)PS(0.064)HNDPAK 97.346 0.001217 26100000 38217 28853 35582 30482 30830 28909 39207 30032 25523 TRUE FALSE 35825.06619 30989.30614 36426.02184 31264.21973 28408.73616 37254.559 33328.27433 33781.56131 21263.04642 1.684851055 1.457425504 1.713113969 1.470354676 1.336061428 1.75208003 1.56742706 1.588745124 1 14.37606069 -1.221476607 5.309854882 0.999958006 1.571524966 0.667489811 0.126710913 5.81E-05 8.52E-06 0.113242394 0.026689534 0.060051435 1.221476607 0.57156696 ELDLFLAYYVQEQDSGQSGS(ph)PSHNDPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.004)GQS(0.041)GS(0.929)PS(0.026)HNDPAK;ELDLFLAYYVQEQDS(0.006)GQS(0.126)GS(0.686)PS(0.182)HNDPAK;ELDLFLAYYVQEQDS(0.003)GQS(0.153)GS(0.692)PS(0.153)HNDPAK;ELDLFLAYYVQEQDS(0.141)GQS(0.141)GS(0.688)PS(0.03)HNDPAK 226.74 8.19E-35 373320000 303032 197429 263588 237094 244390 194071 306169 227663 232696 TRUE FALSE 284065.768 212046.8486 269840.4318 243178.2334 225196.5952 250096.1472 260261.8008 256087.2267 193857.5343 1.465332617 1.093828255 1.391952254 1.254417241 1.161660268 1.290102797 1.342541582 1.321007345 1 17.56463728 -1.20820753 5.025323217 0.999970476 1.281318174 0.421814196 0.106299401 3.22E-05 5.08E-06 0.094357083 0.022237847 0.061914514 1.20820753 0.281347698 ELDLS(ph)ELDDPDSAYLQEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELDLSELDDPDSAYLQEAR 19 0 Q9UER7-3;Q9UER7;Q9UER7-2;Q9UER7-5;Q9UER7-4 Q9UER7-3 DAXX Death domain-associated protein 6 1 ELDLS(1)ELDDPDSAYLQEAR 104.44 0.00037044 21749000 29128 29259 25393 27278 28834 23189 39821 27363 31032 TRUE FALSE 27304.93047 31425.3668 25995.33395 27977.99966 26569.49395 29883.28786 33850.21073 30779.33078 25852.55873 1.056179033 1.215561181 1.005522673 1.082213949 1.027731693 1.155912193 1.309356304 1.190571932 1 14.65801946 2.005386756 21.001037 1.20892029 1.087113814 0.117578119 0.095297656 25.30897777 98666.77654 0.033519325 0.024613406 101.2480707 -2.005386756 -0.121806476 ELDLYLAYFVHAADSSQSES(ph)PSQPSDADIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELDLYLAYFVHAADSSQSESPSQPSDADIK 30 0 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;A0A590UK73;B1AKN7;S4R3K4 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 1 ELDLYLAYFVHAADS(0.001)S(0.001)QS(0.022)ES(0.808)PS(0.157)QPS(0.012)DADIK 126.25 8.62E-06 17163000 21012 19030 22686 18870 16138 14981 25649 15700 17023 TRUE FALSE 19696.89643 20439.001 23224.12263 19354.23615 14870.58658 19305.7715 21803.17056 17660.17956 14181.75133 1.38889027 1.441218403 1.637606111 1.364728213 1.048571945 1.361310818 1.5374103 1.245274942 1 13.79174808 -3.713761872 0.181987311 1.20E-18 1.503155405 0.388056439 0.154399394 86.23607854 1.27392371 32.53353164 0.52241323 0.000193303 3.713761872 1.503155405 ELDQDMVT(ph)EDEDDPGSHKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELDQDMVTEDEDDPGSHKR 19 1 Q9NRL2;Q9NRL2-2;A0A087WWN7 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 1 ELDQDMVT(1)EDEDDPGSHKR;ELDQDMVT(1)EDEDDPGSHKR;ELDQDMVT(1)EDEDDPGSHKR;ELDQDMVT(1)EDEDDPGSHKR 173.89 4.23E-12 1227158000 1808608 1445723 1622864 1499950 1363337 1115769 2195060 1480693 1588407 TRUE FALSE 1695410.454 1552765.835 1661359.1 1538441.256 1256266.011 1437873.397 1865931.131 1665560.78 1323291.61 1.281206985 1.173411683 1.255474672 1.162586723 0.949349336 1.086588463 1.410067982 1.258649845 1 20.33569959 -0.734349002 10.35638188 1 1.2023793 0.202553021 0.122559799 0 0 0.123339282 0.029071347 0.184353335 0.734349002 0.2023793 ELDRNELFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELDRNELFEK 10 1 O60313-10;O60313-9;O60313-2;E5KLJ9;O60313-13;O60313;O60313-11;A0A2R8YDM2;A0A2R8Y3X5;C9JMB8;A0A2R8YE78;A0A2R8YFD1;A0A2R8YGE5 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 65.563 0.062559 174710000 80218 134400 96431 99325 140190 96691 97079 113680 118870 FALSE TRUE 75197.29857 144351.1158 98718.38886 101873.8477 129180.0429 124604.1221 82522.90519 127873.1982 99029.82907 0.759339881 1.457652883 0.996855087 1.028718807 1.304455881 1.258248381 0.833313618 1.291259406 1 16.59557553 ELDRYS(ph)LDSEDLYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELDRYSLDSEDLYSR 15 1 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 ELDRYS(0.999)LDS(0.001)EDLYSR;ELDRYS(1)LDSEDLYSR 239.56 5.02E-18 307930000 402080 488590 399370 424460 435390 309330 498770 387560 464180 TRUE FALSE 376914.5305 524765.712 408843.245 435352.3622 401196.2257 398628.5494 423984.0689 435947.7191 386705.3593 0.974681425 1.357016911 1.057247424 1.125798626 1.037472629 1.030832751 1.096400809 1.127338188 1 18.56087523 3.728546362 24.92093063 1.072145908 1.197350855 0.124780281 0.09995779 84.71989393 1481457.671 0.023283231 0.039254083 5352.37288 -3.728546362 0.125204947 ELDTVTLEDIKEHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELDTVTLEDIKEHVK 15 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;; 241.66 4.11E-18 649705000 2317100 1671650 1922520 1919740 2095170 1359547 2606420 1766790 2835860 FALSE TRUE 2172076.847 1795420.705 1968123.082 1969003.779 1930623.8 1752026.148 2215611.518 1987377.621 2362536.646 0.919383346 0.759954648 0.833055049 0.833427825 0.817182584 0.741586867 0.937810434 0.841204992 1 21.17190528 0.843704493 0.847140983 0.997309697 0.816101321 0.433759648 0.059609384 0.672521897 0.989123334 0.052030438 0.018179101 6.977574675 -0.843704493 -0.181208376 ELDVEEAHAASTEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELDVEEAHAASTEEK 15 0 Q96C86 Q96C86 DCPS m7GpppX diphosphatase 0 ; 95.57 0.0040344 152730000 499530 407410 453730 464750 444490 364390 567440 431210 423870 FALSE TRUE 468265.309 437575.0603 464492.6899 476676.2718 409581.5484 469583.4776 482357.6399 485047.5177 353123.3587 1.326067215 1.239156373 1.315383643 1.349885982 1.159882342 1.3298001 1.365974887 1.373592275 1 18.42981273 -0.790885205 5.42275518 0.999999916 1.304507061 0.69400363 0.064135453 6.47E-08 1.45E-08 0.061186233 0.014421729 0.161850779 0.790885205 0.304507145 ELEAIFGRPVVDGEEGEPHSIS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ELEAIFGRPVVDGEEGEPHSISPR 24 1 P36507;G5E9C7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 ELEAIFGRPVVDGEEGEPHSIS(1)PR;ELEAIFGRPVVDGEEGEPHSIS(1)PR;ELEAIFGRPVVDGEEGEPHSIS(1)PR;ELEAIFGRPVVDGEEGEPHS(0.001)IS(0.999)PR;ELEAIFGRPVVDGEEGEPHS(0.003)IS(0.997)PR;ELEAIFGRPVVDGEEGEPHS(0.001)IS(0.999)PR 255.25 4.75E-44 2449320000 1458230 1577170 1764670 2002210 1901760 1444430 1447280 1195579 1120814 TRUE FALSE 1366961.987 1693945.308 1806528.806 2053590.098 1752403.441 1861413.493 1230273.8 1344849.67 933742.9027 1.463959708 1.81414531 1.934717577 2.199309995 1.876751551 1.993496804 1.317572317 1.440278332 1 19.83266585 1.675612512 4.972738182 1.270263529 1.890953763 0.661969532 0.211122204 0.094832646 5.343296918 0.109764805 0.053173465 47.38190444 -1.675612512 0.620690234 ELEAIFGRPVVDGEEGEPHSISPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ELEAIFGRPVVDGEEGEPHSISPR 24 1 P36507;G5E9C7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 0 ;;;; 259.44 3.41E-44 551296000 438368 524958 512992 480825 530613 472803 588076 501833 574844 FALSE TRUE 410931.3294 563826.4365 525160.4125 493163.7835 488940.7954 609293.5508 499899.4632 564487.9547 478898.8228 0.858075464 1.177339366 1.096599924 1.029787003 1.020968881 1.272280327 1.043851936 1.178720698 1 18.86936136 ELEAMGLGT(ph)PSEAIEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ELEAMGLGTPSEAIEIR 17 0 O95359-3;E9PBC6;E7EMZ9;O95359-2;Q4VXL4;H0Y911 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 ELEAMGLGT(0.882)PS(0.118)EAIEIR;ELEAMGLGT(0.967)PS(0.033)EAIEIR;ELEAMGLGT(0.889)PS(0.111)EAIEIR;ELEAMGLGT(0.916)PS(0.084)EAIEIR;ELEAMGLGT(0.985)PS(0.015)EAIEIR 258.68 4.00E-26 290030000 665407 725917 748666 733397 1109070 700722 886620 880671 1017130 TRUE FALSE 623760.3637 779664.65 766424.7111 752217.2087 1021968.116 903009.0661 753679.562 990624.7129 847364.4321 0.73611818 0.920105471 0.904480625 0.887713928 1.206055007 1.06566789 0.889439695 1.169065724 1 19.69262305 2.949230912 23.59577559 1.045327922 0.877724019 0.497015797 0.100265221 189.9946504 88302.84917 0.030116734 0.03194423 889.6740269 -2.949230912 -0.167603903 ELEAVLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELEAVLSR 8 0 Q96DP5 Q96DP5 MTFMT "Methionyl-tRNA formyltransferase, mitochondrial" 0 ; 77.072 0.034161 1033930000 517890 1980950 1451810 1568620 1615480 1590630 1091490 1364190 905740 FALSE TRUE 485476.1894 2127621.599 1486247.619 1608873.445 1488606.717 2049819.059 927831.2074 1534512.124 754566.1427 0.643384538 2.819662159 1.969671755 2.132183455 1.972798186 2.716553186 1.229622103 2.033635009 1 19.52528784 0.867032008 0.865180787 1.025463082 2.097081447 0.151530487 0.643707513 1.149706526 1.780502214 0.553764899 0.192392192 7.362613587 -0.867032008 1.071618365 ELEDATETADAMNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELEDATETADAMNR 14 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 235.47 3.51E-09 1582050000 812770 971270 928650 975490 1020050 763610 1117010 905900 1121610 FALSE TRUE 761900.1765 1043183.841 950678.0165 1000522.725 939939.3877 984051.8108 949524.7203 1019003.609 934406.0451 0.815384469 1.11641384 1.01741424 1.070757975 1.005921775 1.053130827 1.016179984 1.090536191 1 19.83369008 4.74933557 24.99768917 1.04685179 0.815384338 0.784276239 0.038058184 677.4727857 1571693.641 0.008291362 0.123268468 56148.1653 -4.74933557 -0.231467452 ELEDYIDNLLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ELEDYIDNLLVR 12 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q7L804;Q7L804-2;Q6WKZ4-1 Q6WKZ4 RAB11FIP1;RAB11FIP2 Rab11 family-interacting protein 1;Rab11 family-interacting protein 2 0 ;;;; 135.66 0.00028781 64586500 191361 204301.7 207149 202490 226319 174992.6 246678 183331 249194 FALSE TRUE 179384.0566 219428.4104 212062.6721 207686.2362 208544.8187 225510.1229 209690.9239 206220.2789 207601.9115 0.864077095 1.056967197 1.021487088 1.000406184 1.0045419 1.086262266 1.010062588 0.993344798 1 17.6634602 4.745532219 24.8813951 1.025209109 0.864077015 0.741110669 0.029197581 376.7754101 1344661.385 0.006658958 0.06638869 55658.59238 -4.745532219 -0.161132094 ELEEEAEEEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELEEEAEEEQR 11 0 Q9H2J4 Q9H2J4 PDCL3 Phosducin-like protein 3 0 ; 199.11 1.19E-07 177093000 204442 200568 200910 212221 221540 183263 261480 185468 230380 FALSE TRUE 191646.3402 215418.2634 205675.6801 217666.9501 204141.142 236168.0531 222273.5015 208624.0881 191928.0897 0.998532005 1.122390494 1.071628861 1.134106792 1.063633481 1.230502807 1.158108236 1.086990906 1 17.55020635 5.641548894 1.435047721 1.119742531 1.14E-20 0.20469991 0.062733088 20.66180147 5.207270224 0.01591056 60.96894148 438075.4276 -5.641548894 -1.119742531 ELEEEEENS(ph)DEDELDSHTMVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ELEEEEENSDEDELDSHTMVK 21 0 A0A087WZ06;Q13188;Q13188-2;E5RFQ9 A0A087WZ06 STK3 Serine/threonine-protein kinase 3;Serine/threonine-protein kinase 3 36kDa subunit;Serine/threonine-protein kinase 3 20kDa subunit 1 ELEEEEENS(1)DEDELDSHTMVK;ELEEEEENS(1)DEDELDSHTMVK;ELEEEEENS(1)DEDELDSHTMVK;ELEEEEENS(1)DEDELDSHTMVK;ELEEEEENS(1)DEDELDSHTMVK;ELEEEEENS(1)DEDELDSHTMVK 273.53 6.60E-45 1005480000 1046810 879566 919410 922140 1044630 681606 1123460 893420 1048760 TRUE FALSE 981292.0307 944689.9818 941218.8394 945803.6736 962588.9736 878374.5873 955007.6027 1004965.454 873715.1808 1.123125765 1.081233339 1.077260485 1.082508001 1.10171941 1.005332867 1.093042245 1.150220891 1 19.73680353 4.793646167 2.605707493 1.07568173 1.137104561 0.110844611 0.04380149 1.465608735 11.38391518 0.009763879 0.208540047 62179.34844 -4.793646167 0.061422831 ELEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 124.89 0.042251 400920000 651870 710870 664950 682800 726870 610290 782170 612820 773710 FALSE TRUE 611070.6203 763503.5545 680722.928 700321.804 669784.5623 786470.8158 664890.8698 689331.926 644572.8026 0.948024207 1.184510968 1.056083852 1.086489844 1.039113905 1.220142725 1.031521757 1.069439981 1 19.29798379 1.000651139 1.700494581 1.003192544 1.093096429 0.087797014 0.076890738 0.762830292 4.549186211 0.064615375 0.018634142 10.01500428 -1.000651139 0.089903885 ELEEKNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELEEKNR 7 1 P32780 P32780 GTF2H1 General transcription factor IIH subunit 1 0 65.038 0.065363 222650000 360530 345230 356160 341830 399340 243890 398590 329590 491930 FALSE TRUE 337965.0709 370791.1884 364608.2834 350601.9365 367977.4473 314297.0838 338825.1298 370740.037 409823.705 0.824659644 0.904757787 0.889671044 0.855494527 0.897892052 0.766908014 0.826758252 0.904632974 1 18.64464391 0.944736834 5.436151338 0.999971254 0.857323354 0.568268724 0.041005304 0.26871995 23.25328202 0.042409496 0.010692479 8.805151518 -0.944736834 -0.142647899 ELEELKEIEADLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELEELKEIEADLER 14 1 K7EJH0;K7EMX1;K7EJV2;K7ESQ2;Q8NBT2 K7EJH0 SPC24 Kinetochore protein Spc24 0 ;; 164.65 3.73E-06 76722000 307768 221579 257506 250298 276032 202094 330736 235310 328198 FALSE TRUE 288505.3503 237984.9397 263614.1639 256721.0704 254353.5602 260435.2571 281145.2072 264688.9715 273419.6336 1.055174226 0.870401795 0.964137654 0.938926979 0.93026809 0.952511177 1.028255373 0.968068635 1 18.06075732 1.889677642 6.401182748 1.000212957 0.941786207 0.159644408 0.047634795 0.325390943 16.34478926 0.019030447 0.011625093 77.56711562 -1.889677642 -0.05842675 ELEELKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELEELKR 7 1 Q8TE76-2;Q8TE76-3;Q8TE76 Q8TE76-2 MORC4 MORC family CW-type zinc finger protein 4 0 ; 104.8 0.01294 1727916000 1236420 1076470 1096320 1082980 1138680 798260 1355320 950480 1451310 FALSE TRUE 1159034.679 1156172.959 1122325.228 1110771.1 1049252.666 1028704.703 1152102.348 1069149.52 1209076.985 0.95861115 0.956244286 0.9282496 0.918693445 0.867812951 0.850818199 0.952877577 0.884269185 1 20.20547468 3.611542434 1.730396194 0.906850446 0.956242272 0.15196432 0.042294736 0.580730773 3.449095035 0.011859885 0.023314245 4088.29696 -3.611542434 0.049391826 ELEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELEELR 6 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5;P06727;Q9BT92;F5GWH6;A0A499FI31;Q15020-4;Q15020;P61129;O94964-2 Q14980;A0A499FI31;P61129;O94964-2 NUMA1;APOA4;TCHP;SART3;ZC3H6;SOGA1 Nuclear mitotic apparatus protein 1;Apolipoprotein A-IV;Trichoplein keratin filament-binding protein;Squamous cell carcinoma antigen recognized by T-cells 3;Zinc finger CCCH domain-containing protein 6;Protein SOGA1;N-terminal form;C-terminal 80 kDa form 0 97.071 0.096521 135110000 312100 340880 318730 315640 364590 278170 369400 316490 348680 FALSE TRUE 292566.2181 366119.1099 326290.4261 323739.8568 335956.5721 358473.1633 314011.8993 356004.4732 290483.0554 1.007171374 1.260380263 1.123268363 1.114487922 1.156544472 1.234058774 1.080999024 1.225560206 1 18.14809448 -1.344418621 3.20147386 0.998774724 1.155082644 0.275547133 0.0762454 17974859.6 28661677.73 216957.2889 0.016301512 0.045246124 1.344418621 0.15630792 ELEELRDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELEELRDK 8 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 85.676 0.015115 85502000 129600 135970 124580 127860 126340 95384 145490 105010 155380 FALSE TRUE 121488.5673 146037.3603 127535.0964 131141.1041 116417.766 122919.8124 123675.1252 118120.7297 129446.0742 0.938526472 1.128171412 0.985237267 1.013094486 0.899353393 0.949583161 0.955418122 0.912509169 1 16.98199169 3.21822716 1.708313443 0.94389225 1.045770517 0.261410236 0.05556684 0.339654132 2.038528441 0.016693409 0.023533338 1652.826092 -3.21822716 0.101878267 ELEELRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELEELRK 7 1 P61129 P61129 ZC3H6 Zinc finger CCCH domain-containing protein 6 0 139.28 0.0043354 659890000 944580 945740 952090 1012200 1101100 812470 1389200 976380 1560700 FALSE TRUE 885460.4239 1015763.574 974674.0244 1038174.766 1014624.048 1047016.9 1180902.357 1098283.192 1300209.087 0.681013871 0.781230945 0.749628682 0.798467551 0.780354527 0.805268099 0.90824035 0.844697367 1 20.31031221 1.270961885 0.262678726 1.042323567 0.695274285 0.855297843 0.033238209 0.686230112 0.185922038 0.09368568 0.072198869 18.662159 -1.270961885 -0.347049282 ELEENKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELEENKR 7 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 0 77.058 0.062659 215630000 312740 301300 287620 297600 326190 224550 363320 267900 355880 FALSE TRUE 293166.1617 323608.5655 294442.4822 305236.9198 300572.3532 289373.9397 308843.5389 301347.9047 296481.3289 0.988818293 1.091497285 0.993123187 1.029531677 1.01379859 0.976027532 1.04169642 1.016414443 1 18.17758173 3.841857117 7.401915916 1.012496523 1.046598307 0.132567339 0.030511379 0.35559443 20.99777014 0.007064448 0.012803942 6947.956925 -3.841857117 0.034101785 ELEEQLENETLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELEEQLENETLHK 13 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 ; 200.21 1.12E-07 127047000 284880 241130 259580 238950 255210 190145 293920 207753 246360 FALSE TRUE 267049.8693 258983.5161 265737.3602 245081.8615 235166.8361 245036.7748 249849.4246 233691.4194 205240.9245 1.301153121 1.261851245 1.294758153 1.194117899 1.145808696 1.193898222 1.217347005 1.13861999 1 17.6469589 -5 0.077432121 0.204764143 1.47669057 0.849287461 0.034190539 101.5873614 0.55979341 13.80015781 1.390721761 1.00E-05 5 1.271926428 ELEEWYAR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 192.11 0.00041331 3052040000 3343590 3755880 3589220 3645270 3821470 2878190 4048300 3308230 3915170 FALSE TRUE 3134320.67 4033969.263 3674357.993 3738813.8 3521347.161 3709076.729 3441294.998 3721269.798 3261702.834 0.960946116 1.236767869 1.126515253 1.146276651 1.079603919 1.137159612 1.05506086 1.140897864 1 21.63719392 0.158887719 0.387269656 0.982393867 1.137469197 0.138118727 0.073455681 5.559003692 1.27247066 0.245358854 0.051260323 1.441742561 -0.158887719 0.155075329 ELEFYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 ELEFYLR 7 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;;;;;;;;; 184.16 0.0014706 5597129000 3312509 5121395 3651848 3582883 5363302 2682135 3491640 4616329 4291793 FALSE TRUE 3105184.975 5500588.415 3738471.559 3674825.844 4942089.895 3456423.834 2968100.997 5192687.837 3575465.022 0.868470242 1.538426017 1.045590304 1.027789622 1.382222974 0.966706096 0.830130061 1.452311183 1 21.76969946 2.206464908 24.99883651 1.021865674 1.198515476 0.030852372 0.244112364 438.8072052 341777.4921 0.086500521 0.063890085 160.866239 -2.206464908 0.176649802 ELEIEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELEIEER 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 84.568 0.049902 254410000 519500 916020 823920 799360 843020 881370 763430 754120 725180 FALSE TRUE 486985.4223 983843.0739 843463.7715 819872.9309 776812.6098 1135807.211 648960.7588 848273.542 604142.7732 0.806076716 1.628494319 1.396133181 1.357084728 1.285809653 1.880031115 1.074184427 1.404094495 1 19.20453001 -1.075738148 6.095035785 0.999999114 1.381055848 0.124014027 0.287784206 3.07E-06 4.66E-07 0.247040793 0.058227938 0.083996628 1.075738148 0.381056734 ELEKPIQSKPQS(ph)PVIQAAAVS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELEKPIQSKPQSPVIQAAAVSPK 23 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 2 ELEKPIQS(0.023)KPQS(0.977)PVIQAAAVS(1)PK 120.18 6.15E-05 209830000 284300 107000 173440 185410 182220 113930 201230 129420 251870 TRUE FALSE 266506.1705 114922.3913 177554.0787 190167.9345 167909.1762 146819.7415 171057.4296 145578.3719 209831.2699 1.270097496 0.547689538 0.846175495 0.906289776 0.800210456 0.699703822 0.815214194 0.693787785 1 17.67887016 2.486138448 23.89736948 0.782119958 0.82994261 0.00297379 0.195123166 1610.052621 4266986.648 0.061475632 0.05402628 306.2939706 -2.486138448 0.047822653 ELEKPIQSKPQSPVIQAAAVS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELEKPIQSKPQSPVIQAAAVSPK 23 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 ELEKPIQSKPQSPVIQAAAVS(1)PK;ELEKPIQSKPQSPVIQAAAVS(1)PK 178.46 2.69E-17 11917600000 8857100 4566400 6178500 5740200 6379800 4327000 9519500 5593400 8715600 TRUE FALSE 8302749.921 4904501.007 6325056.938 5887503.25 5878756.243 5576134.657 8092139.35 6291748.303 7260910.055 1.143486128 0.675466432 0.871110768 0.810849219 0.809644548 0.767966359 1.114480043 0.866523377 1 22.79171895 1.750191351 25 0.999874798 0.826761068 0.203605573 0.133371537 3.988128096 8587.285658 0.055254272 0.030641444 56.25891485 -1.750191351 -0.17311373 ELELAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELELAHR 7 0 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 0 94.262 0.025867 0 195250 276990 282400 275780 289060 282910 273200 232730 244590 FALSE TRUE 183029.651 297498.6278 289098.6614 282856.9817 266358.3936 364581.5243 232236.1963 261786.8528 203766.3489 0.898232962 1.459998814 1.418775293 1.38814374 1.307175572 1.789213608 1.139718101 1.284740362 1 17.63655629 1.004306446 1.589044462 1.01323605 1.381972536 0.178766091 0.226892171 0.585899838 3.029637796 0.193378743 0.05651985 10.09965285 -1.004306446 0.368736487 ELELLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELELLDR 7 0 G3V1A6;P57764 G3V1A6 GSDMD Gasdermin-D 0 ;; 150.17 0.0045767 179197000 523816 595820 581083 603070 565825 472749 628130 513130 331741 FALSE TRUE 491031.2916 639935.1328 594866.5632 618545.7972 521387.3869 609223.9619 533947.7378 577195.41 276371.284 1.776708797 2.315490682 2.152418133 2.238097201 1.886546892 2.20436781 1.931994273 2.08847823 1 18.0762482 -1.853559982 0.391255004 7.84E-15 2.143503982 0.794956265 0.170641402 14.88439008 0.98233668 13.83535102 0.100903888 0.014010061 1.853559982 2.143503982 ELELVQNAFFTDPNDQSAWFYHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELELVQNAFFTDPNDQSAWFYHR 23 0 Q92696;H0YLH3 Q92696 RABGGTA Geranylgeranyl transferase type-2 subunit alpha 0 ; 182.77 3.84E-17 189932000 122851 156669 131574.3 119041 154721 126122 155322 144572 138018 FALSE TRUE 115161.9752 168268.9358 134695.3045 122095.7936 142569.8368 162531.374 132032.908 162622.1324 114981.9042 1.001566082 1.463438417 1.171447851 1.061869644 1.239932821 1.413538723 1.148292934 1.414328051 1 16.8110473 -1.050234621 4.53549903 0.99998777 1.248354035 0.191038652 0.153757771 1.73E-05 3.62E-06 0.135227809 0.031871931 0.089076958 1.050234621 0.248366264 ELESPLT(ph)PGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELESPLTPGK 10 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 ELES(0.012)PLT(0.988)PGK;ELESPLT(1)PGK 182.41 1.99E-05 307370000 1545420 965190 1218920 1049370 1060970 917370 1591200 1117780 1056760 TRUE FALSE 1448694.921 1036653.672 1247833.358 1076298.611 977645.6959 1182199.827 1352614.332 1257337.294 880379.9291 1.645533789 1.177507162 1.417380516 1.222538787 1.110481581 1.342829144 1.53639842 1.428175782 1 19.74776673 4.753404431 24.10703253 1.308863244 1.645534185 0.320049925 0.162752559 2188.019833 3553344.508 0.038318214 0.833789624 56676.68377 -4.753404431 0.33667094 ELESQISELQEDLESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ELESQISELQEDLESER 17 0 P35579 P35579 MYH9 Myosin-9 0 ;;;;; 374.82 1.37E-104 420291000 486012 505267 531432 555061 485627 443849 577427 478849 421375 FALSE TRUE 455593.3765 542677.4944 544037.818 569304.805 447487.8143 571981.001 490847.1819 538634.3517 351044.7903 1.297821216 1.54589246 1.549767531 1.621744064 1.274731392 1.629367582 1.398246593 1.534375005 1 18.42129559 -2.555710558 0.550198388 4.96E-09 1.494882698 0.595931255 0.124028589 135.1968089 7.348516115 162.0204192 0.047317849 0.002781566 2.555710558 1.494882693 ELESVCVVEAGPGTCTFDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELESVCVVEAGPGTCTFDHR 20 0 F6T1Q0;Q6L8Q7-2;Q6L8Q7 F6T1Q0 PDE12 "2,5-phosphodiesterase 12" 0 ; 166.6 1.50E-11 245144000 225984 163886 186984 169476 188582 145034 196693 161351 197015 FALSE TRUE 211840.0648 176020.29 191419.3488 173825.0411 173771.5304 186902.9614 167200.7107 181496.0275 164131.9237 1.290669481 1.072431773 1.166253002 1.059056868 1.058730846 1.138736189 1.018697075 1.10579358 1 17.32449635 7.082991749 1.43026661 1.081409245 199.9993568 0.610011563 0.052255294 891.0084958 2.536148271 0.012998896 580773.3586 12105751.34 -7.082991749 198.9179475 ELEVQHPAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELEVQHPAAK 10 0 P50990-2;P50990;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;; 103.08 0.0028615 6107900000 10567300 9230100 9624600 9387600 9936800 7917600 11857200 8824100 10313900 FALSE TRUE 9905911.556 9913506.208 9852900.057 9628501.709 9156403.811 10203282.59 10079322.94 9925808.309 8592443.46 1.152863164 1.15374704 1.146693616 1.120577837 1.065634456 1.187471601 1.173045011 1.155178775 1 23.03463702 -1.486777729 3.201957158 0.996684495 1.146305241 0.654785713 0.03292523 1778953.047 1653048.268 37125.22792 0.007828916 0.032600351 1.486777729 0.149620746 ELFALHPSPDEEEPIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELFALHPSPDEEEPIER 17 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 0 99.344 0.0016042 50329000 49533 63817 62963 64007 61072 57054 73303 59214 54257 FALSE TRUE 46432.81795 68542.07708 64456.51209 65649.52798 56275.65147 73524.56361 62311.89566 66606.99825 45201.15619 1.027248457 1.516378847 1.425992553 1.452386034 1.245004691 1.62660803 1.3785465 1.473568463 1 15.46407205 -1.726574557 8.336996095 0.997833203 1.412443998 0.359359896 0.16321233 0.005756889 0.000188806 0.138402601 0.032507503 0.018768322 1.726574557 0.414610795 ELFDDPS(ph)YVNVQNLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELFDDPSYVNVQNLDK 16 0 P29353-2;P29353-7;P29353;P29353-6;H0Y539;X6R6D0;P29353-5;P29353-3;Q5T188 P29353-2 SHC1 SHC-transforming protein 1 1 ELFDDPS(0.944)Y(0.056)VNVQNLDK;ELFDDPS(1)YVNVQNLDK;ELFDDPS(0.844)Y(0.156)VNVQNLDK 332.61 1.40E-71 811600000 1332910 1119460 1044680 1277910 1260780 600670 1138660 636470 408150 TRUE FALSE 1249485.542 1202345.983 1069460.303 1310703.334 1161763.425 774073.6779 967928.5038 715934.6805 340027.1283 3.67466428 3.536029579 3.145220525 3.854702243 3.416678635 2.276505648 2.846621412 2.105522239 1 18.37529033 1.133003224 0.541277789 0.959994604 3.578647538 0.865062239 0.320924966 0.293893275 0.220290467 0.333909027 0.163670361 13.58323529 -1.133003224 2.618652934 ELFDDPSY(ph)VNVQNLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELFDDPSYVNVQNLDK 16 0 P29353-2;P29353-7;P29353;P29353-6;H0Y539;X6R6D0;P29353-5;P29353-3;Q5T188 P29353-2 SHC1 SHC-transforming protein 1 1 ELFDDPS(0.245)Y(0.755)VNVQNLDK;ELFDDPS(0.001)Y(0.999)VNVQNLDK;ELFDDPS(0.273)Y(0.727)VNVQNLDK;ELFDDPS(0.011)Y(0.989)VNVQNLDK 289.37 1.79E-44 568862000 1246000 1036451 936660 1180934 1193110 571685 1047802 621554 423331 TRUE FALSE 1168015.084 1113190.91 958878.0175 1211238.766 1099407.953 736721.179 890693.8174 699156.3851 352674.3213 3.31188015 3.156427455 2.718876764 3.434439914 3.117346195 2.088956112 2.525542019 1.982441995 1 18.42797701 1.113042713 0.542619845 0.966521482 3.172482413 0.847984248 0.290668904 0.324405176 0.243416845 0.307751763 0.149321159 12.97306857 -1.113042713 2.205960931 ELFDELVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELFDELVK 8 0 P55263-3;P55263-2;P55263;A0A5K1VW54;A0A5K1VW94;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZH83 P55263-3 ADK Adenosine kinase 0 ;; 131.06 0.0023756 65597000 174094 139576 156888 138258 149406 103526 166125 136047 128846 FALSE TRUE 163197.7673 149910.3523 160609.4574 141805.9344 137672.2554 133412.2756 141216.0985 153032.7674 107340.7702 1.52037075 1.396583534 1.496257732 1.321081767 1.282571898 1.242885395 1.315586782 1.425672343 1 16.71183862 -4.296221162 0.099979991 1.69E-14 1.639697601 0.710295542 0.079508551 85.30456255 0.675161275 18.92832042 1.380480532 5.06E-05 4.296221162 1.639697601 ELFDELVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELFDELVKK 9 1 P55263-3;P55263-2;P55263;A0A5K1VW54;A0A5K1VW94;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZH83 P55263-3 ADK Adenosine kinase 0 ; 138.66 0.00020906 628300000 2211500 1782100 2045000 1967300 2351500 1446800 2699100 1647490 2754900 FALSE TRUE 2073086.163 1914048.538 2093508.366 2017784.249 2166822.675 1864467.673 2294395.012 1853182.753 2295089.393 0.903270334 0.833975593 0.912168551 0.879174578 0.94411254 0.812372572 0.999697449 0.807455587 1 21.13011892 -5 0.186339064 1.454156692 0.869272798 0.225353796 0.060888541 182.6145571 1.778018513 30.8570087 0.152202874 1.00E-05 5 -0.584883894 ELFEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELFEER 6 0 Q9H307 Q9H307 PNN Pinin 0 ;; 122.78 0.044374 1066820000 1530070 1681450 1734440 1682960 1886410 1468320 1916110 1570280 2329230 FALSE TRUE 1434305.65 1805946.308 1775581.736 1726147.603 1738258.968 1892200.148 1628807.094 1766332.915 1940466.466 0.739155082 0.930676381 0.915028302 0.889552916 0.895794387 0.975126436 0.839389457 0.910262015 1 20.88797207 -0.290285759 0.014203619 1.889099193 1.35E-06 0.329511614 0.058911102 2882.813211 10.72529593 756.3955098 670.3861116 0.51252404 0.290285759 -1.889097848 ELFGKDEQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELFGKDEQQR 10 1 G3XA94;Q9NPL8 G3XA94 TIMMDC1 "Complex I assembly factor TIMMDC1, mitochondrial" 0 ;; 52.79 0.088821 26605710000 3229560 11551630 8686790 9822900 11450180 13554140 8278750 8364370 8311770 FALSE TRUE 3027427.605 12406924.7 8892844.761 10074972.24 10550929.05 17467000.18 7037428.294 9408680.007 6924481.891 0.437206372 1.791747729 1.284261393 1.454978496 1.523713863 2.522499222 1.01631117 1.358755811 1 22.7232747 1.597070295 25 1.140622861 1.52817499 0.104633926 0.515982571 1.800851876 4159.060537 0.2522433 0.118596306 39.54306194 -1.597070295 0.387552128 ELFLAEHS(ph)DLEEGGLDLTVSLKPVSFYISDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELFLAEHSDLEEGGLDLTVSLKPVSFYISDKK 32 2 Q9H8G2;A0A3B3ISJ3 Q9H8G2 CAAP1 Caspase activity and apoptosis inhibitor 1 1 ELFLAEHS(1)DLEEGGLDLTVSLKPVSFYISDKK 242.67 3.64E-47 238160000 312240 211140 215950 238060 278700 170950 319720 217610 314580 TRUE FALSE 292697.4558 226773.0253 221072.436 244169.0226 256812.0262 220300.4899 271780.9541 244779.0875 262074.5657 1.116848004 0.865299632 0.843547848 0.931677677 0.979919686 0.840602327 1.037036743 0.934005507 1 17.99961782 1.721721714 18.50154404 0.989015939 0.914301485 0.085147517 0.084277771 0.454611748 480.1168614 0.037286524 0.020643211 52.68921324 -1.721721714 -0.074714455 ELFLAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELFLAGR 7 0 Q7Z4W1;J3KS22;J3KRZ4 Q7Z4W1 DCXR L-xylulose reductase 0 ;; 154.11 0.0039561 187752000 252957 284083 260970 291749 292186 221998 274593 249057 247673 FALSE TRUE 237124.8729 305116.8009 267160.3316 299235.7733 269238.8902 286085.2188 233420.3288 280152.3147 206334.7763 1.149223981 1.478746368 1.294790614 1.45024401 1.304864333 1.386509942 1.131269935 1.357756166 1 17.65462747 0.477037573 0.506664723 0.984965774 1.362660427 0.427684119 0.113955333 1.656143239 0.760623702 0.169500591 0.052786096 2.999422005 -0.477037573 0.377694653 ELFQETLESLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELFQETLESLR 11 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 ;;; 159.09 8.19E-05 78854000 109912 167389 107689 116263 178087 84356 118438 161394 129738 FALSE TRUE 103032.8041 179782.6557 110243.4339 119246.5054 164100.7654 108708.2078 100679.3214 181544.3962 108083.8897 0.95326699 1.663362193 1.019980261 1.103277332 1.518272204 1.005776237 0.931492397 1.679661944 1 16.72179197 3.844872577 9.053706565 1.163025707 1.356197899 0.023966192 0.294162977 0.752845331 54.47524148 0.069785272 0.126058921 6996.366907 -3.844872577 0.193172192 ELFQT(ph)PCTDNPTTDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELFQTPCTDNPTTDEK 16 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 ELFQT(0.993)PCT(0.005)DNPT(0.001)T(0.001)DEK 104.21 0.0070197 0 35915 29640 34383 32181 39345 23312 41360 30938 51837 TRUE FALSE 33667.14426 31834.57644 35198.581 33006.81894 36255.00241 30041.79596 35158.45197 34800.6774 43185.06982 0.779601478 0.737166261 0.815063658 0.764310885 0.839526312 0.695652365 0.814134425 0.805849743 1 15.398245 0.516100603 1.387269375 0.99994376 0.775689824 0.745633617 0.040577288 0.970646223 2.294180722 0.034376862 0.010104796 3.281713039 -0.516100603 -0.224253936 ELFQT(ph)PGHTEEAVAAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELFQTPGHTEEAVAAGK 17 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 ELFQT(1)PGHTEEAVAAGK;ELFQT(1)PGHTEEAVAAGK 269.11 1.36E-27 212770000 532530 424120 509070 494190 471160 316860 685440 449430 780310 TRUE FALSE 499199.8979 455522.2861 521145.3808 506871.7521 434156.9942 408332.3382 582664.6353 505542.3248 650071.22 0.767915703 0.700726739 0.801674285 0.779717262 0.66786066 0.628134773 0.896308923 0.777672214 1 19.31023826 0.859023983 1.022797102 0.99506839 0.737084889 0.558604996 0.07157998 0.523551906 1.08831448 0.065919065 0.021434915 7.228097182 -0.859023983 -0.2579835 ELFQT(ph)PGHTEELVAAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELFQTPGHTEELVAAGK 17 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 ELFQT(1)PGHTEELVAAGK;ELFQT(1)PGHTEELVAAGK 156.74 1.91E-07 324690000 564190 487840 514600 487060 563220 345070 761490 526090 885270 TRUE FALSE 528878.355 523960.1812 526806.555 499558.7842 518986.9731 444686.1073 647311.6438 591773.4946 737512.7179 0.717110827 0.710442232 0.714301655 0.677356162 0.703699015 0.602953815 0.877695568 0.802390901 1 19.4923084 1.163167695 1.163660999 0.98646573 0.695859192 0.737396979 0.057716486 0.210440124 0.586793314 0.049466419 0.015927707 14.56021188 -1.163167695 -0.290606537 ELFQT(ph)PGTDKPTTDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELFQTPGTDKPTTDEK 16 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 ELFQT(0.568)PGT(0.432)DKPTTDEK 100.28 0.0034071 150680000 340910 219650 254420 247400 259090 182880 351730 198440 368460 TRUE FALSE 319573.0516 235913.1145 260454.9625 253748.7028 238742.1165 235674.4872 298991.3518 223215.6708 306961.6457 1.041084631 0.768542643 0.848493505 0.826646281 0.777758785 0.767765258 0.974034887 0.727177724 1 18.22769888 -1.530718289 5.970940785 1.000252529 0.839909993 0.206929799 0.097513431 0.000294208 2.31E-05 0.084739135 0.019941989 0.029463322 1.530718289 -0.160342536 ELFQT(ph)PVCTDKPTTHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELFQTPVCTDKPTTHEK 17 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 ELFQT(1)PVCTDKPTTHEK;ELFQT(0.998)PVCT(0.002)DKPTTHEK;ELFQT(1)PVCTDKPTTHEK 229.78 1.47E-15 292816000 571960 430243 432270 456861 525879 259912 732320 480286 930840 TRUE FALSE 536162.0446 462098.6394 442523.6485 468584.8267 484578.5846 334944.3751 622515.4145 540250.7643 775476.7905 0.691396636 0.595889709 0.570647186 0.604253838 0.624878256 0.431920567 0.802751832 0.69666916 1 19.56472408 0.913891469 1.059372827 0.993626936 0.592814106 0.668216206 0.087161589 0.335057516 0.766962337 0.074507444 0.024054788 8.201465633 -0.913891469 -0.40081283 ELFSPLHALNFGIGGDGTQHVLWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELFSPLHALNFGIGGDGTQHVLWR 24 0 M0R1K3;Q15102;M0R389;M0QZT2;M0QXS6;M0R323 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ;; 307.21 1.52E-63 688511000 560669 1219100 640166 469878 1128890 513388 787747 1075229 491148 FALSE TRUE 525577.7281 1309363.432 655351.0398 481935.865 1040231.533 661594.7814 669631.6504 1209473.708 409172.2259 1.284490234 3.200030084 1.601650841 1.177831325 2.542282852 1.616910288 1.636552063 2.955903727 1 18.64234869 3.739463901 22.96925721 1.801163594 2.385611636 0.053429133 0.737087836 302.3083617 562575.9236 0.170576678 0.304108105 5488.629315 -3.739463901 0.584448042 ELFSPLHALNFGIGGDTTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELFSPLHALNFGIGGDTTR 19 0 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 ; 280.01 1.29E-39 1604800000 1210000 1768840 1616710 1586280 1854330 1406560 1779610 1576430 1784300 FALSE TRUE 1134268.26 1899806.754 1655059.125 1626986.63 1708698.402 1812611.038 1512774.002 1773250.756 1486488.803 0.763052004 1.278049825 1.113401676 1.094516573 1.149486224 1.21939098 1.017682742 1.192912286 1 20.50347717 -1.402235592 5.332264833 0.999922837 1.118809099 0.041036726 0.141152286 0.000114131 1.28E-05 0.120465932 0.028375689 0.039606312 1.402235592 0.118886262 ELGDVLFQMAEVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 190.86 5.55E-07 185705000 497870 574840 582550 540700 642270 505200 573160 569760 519010 FALSE TRUE 466709.2054 617401.7517 596368.3611 554575.2774 591828.705 651043.0388 487219.979 640895.7902 432383.8781 1.079386233 1.427901878 1.379256701 1.282599342 1.368757567 1.505706091 1.126822723 1.482237943 1 18.72195321 -1.585710983 4.841101241 0.996680296 1.33629039 0.35917151 0.139066104 0.004516155 0.000386481 0.122042056 0.028523619 0.025959063 1.585710983 0.339610094 ELGELIPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELGELIPLR 9 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 99.442 0.01241 12897000 28674 36922 27279 28886 38321 24339 31801 33426 39913 FALSE TRUE 26879.34552 39655.7433 27926.07076 29627.26366 35311.42324 31365.27419 27032.73528 37599.30968 33251.26245 0.808370677 1.192608652 0.83984994 0.891011693 1.06195737 0.943280702 0.812983727 1.130763373 1 15.0211215 3.94169401 24.74141028 0.939141731 1.026472087 0.002343827 0.132825776 677.9831553 473484.532 0.031219955 0.056285255 8743.675059 -3.94169401 0.087330355 ELGENLDQILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELGENLDQILR 11 0 Q96P70 Q96P70 IPO9 Importin-9 0 ;;; 202.44 9.31E-08 234411000 354677 398396 393812 407323 386764 349423 441867 368748 326925 FALSE TRUE 332478.3997 427893.6544 403153.4066 417775.5978 356389.1156 450295.7477 375613.1454 414786.9995 272359.1055 1.220735393 1.571064252 1.480227385 1.533914561 1.308526531 1.653316297 1.379109925 1.522941555 1 18.05515057 -1.216694241 4.483010656 0.999855164 1.470377027 0.557930395 0.127953109 8341437.278 2270665.288 11877.92555 0.025816515 0.060716364 1.216694241 0.470521863 ELGEYFLFDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELGEYFLFDPK 11 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 114.5 0.0017806 0 170580 159770 164790 169100 181510 133160 172170 152750 184270 FALSE TRUE 159903.7023 171599.537 168698.8966 173439.3923 167254.9368 171601.1303 146354.7068 171821.1737 153514.1466 1.041621934 1.117809276 1.098914337 1.129794199 1.089508299 1.117819655 0.953362997 1.11925303 1 17.22801208 1.764580742 25 1.020682354 1.102149153 0.361164441 0.046862316 14.90910618 14333.94094 0.018963494 0.010516968 58.15415402 -1.764580742 0.081466799 ELGGLGMLSMGHVLIPQSDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELGGLGMLSMGHVLIPQSDLR 21 0 Q6P2Q9;I3L3Z8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 136.14 5.43E-06 105410000 142700 222200 175100 182100 234270 154690 206560 204250 212000 FALSE TRUE 133768.6617 238651.9192 179253.4547 186772.9943 215871.3792 199346.4918 175588.2456 229751.0621 176615.8304 0.757399047 1.351248745 1.014934246 1.057509929 1.222265177 1.128701155 0.994181808 1.300852033 1 17.43025513 4.76297136 24.35769162 1.12984296 0.757398415 0.472301546 0.12494756 4712.719563 4702369.046 0.028099673 1.778941044 57939.04869 -4.76297136 -0.372444545 ELGITALHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELGITALHIK 10 0 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ; 163.94 6.31E-06 1504980000 4253300 4918400 3733600 3498000 5051300 2812200 4124500 4664800 4233000 FALSE TRUE 3987093.545 5282563.454 3822162.755 3587764.602 4654591.274 3624036.488 3506069.515 5247210.548 3526484.954 1.130614081 1.497968522 1.083844907 1.017376977 1.319895402 1.027662541 0.994210825 1.487943552 1 21.74979945 3.810075209 5.348574542 1.121670098 1.331338623 0.143763813 0.180736486 0.310887098 14.90714267 0.042824684 0.078325644 6457.660493 -3.810075209 0.209668524 ELGIWEPLAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELGIWEPLAVK 11 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 129.85 0.00054992 41072000 257780 218510 250950 250290 284670 209940 285620 230790 251980 FALSE TRUE 241646.01 234688.7078 256902.6525 256712.8651 262313.1665 270546.2699 242793.9326 259604.6395 209922.9101 1.151117855 1.117975678 1.223795213 1.222891132 1.249569027 1.288788678 1.15658616 1.236666543 1 17.6795001 -1.104730146 4.467416261 0.999979799 1.201794225 0.613773152 0.051243515 1.06E-05 2.13E-06 0.051140877 0.012052814 0.07857237 1.104730146 0.201814426 ELGLPEELVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELGLPEELVSR 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;; 194.06 1.58E-06 192734000 252127 304801 283194 290463 301491 256953 325066 252924 286050 FALSE TRUE 236346.8211 327368.7832 289911.4954 297916.7723 277813.113 331131.1598 276325.3711 284502.1182 238306.407 0.991777032 1.373730515 1.216549311 1.250141681 1.165781132 1.389518494 1.159538153 1.193850059 1 17.86245821 0.733249556 1.395116298 1.000991839 1.242080768 0.264540281 0.112436224 1.041442528 3.376374711 0.094568721 0.027971447 5.410651425 -0.733249556 0.241088929 ELGMEERPYSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELGMEERPYSSR 12 1 Q9NX46 Q9NX46 ADPRHL2 Poly(ADP-ribose) glycohydrolase ARH3 0 ; 135.81 0.00011037 313550000 347120 339470 318510 316100 389540 268810 413370 325070 393300 FALSE TRUE 325394.3788 364604.712 326065.2076 324211.6612 358947.0997 346411.0832 351389.006 365655.7051 327655.6892 0.993098516 1.112767835 0.995145875 0.989488881 1.095500892 1.057241167 1.072433709 1.11597545 1 18.32182106 2.718756692 24.7905442 1.071688869 1.03306913 0.177148071 0.046144514 1428.077181 1787663.734 0.014381493 0.013572492 523.3071781 -2.718756692 -0.038619739 ELGNDAYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELGNDAYK 8 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 116.05 0.0054576 1642560000 1017300 840730 916210 924490 1012740 693670 1142410 838150 1156210 FALSE TRUE 953629.0089 902978.524 937942.9339 948213.9786 933203.4856 893921.2682 971116.2261 942794.8725 963231.0816 0.990031392 0.937447453 0.973746541 0.984409657 0.968826176 0.928044459 1.00818614 0.97878369 1 19.87752242 1.668064272 11.44764418 0.994898878 0.962907906 0.35469679 0.020227538 0.124304055 21.23042979 0.008999186 0.004895586 46.56550018 -1.668064272 -0.031990972 ELGSGLALIHHNTHLCFVHTVPWDQLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELGSGLALIHHNTHLCFVHTVPWDQLFR 28 0 P04626-5;P04626-4;P04626;B4DTR1;J3QLU9;P04626-6;F5H1T4 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 0 38.629 0.059612 49971000 15235 33915 12919 12854 38153 16153 14466 36601 8806.6 FALSE TRUE 14281.46855 36426.10189 13225.44478 13183.8554 35156.61728 20816.10888 12296.9576 41170.71542 7336.721567 1.946573604 4.964901769 1.802636867 1.796968207 4.791870178 2.837249402 1.67608345 5.61159573 1 12.84091982 3.961508335 24.45689429 2.777519196 3.635387236 0.026587075 1.598522886 967.0128084 1514782.773 0.37407182 0.677596537 9151.838238 -3.961508335 0.857868041 ELGTVMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELGTVMR 7 0 P0DP25;P0DP24;P0DP23;E7EMB3;M0QZ52;F8WBR5;G3V479;P27482;C9J7T9;P02585 P0DP25 CALM2;CALM3;CALM1;CALML3;TNNC2 "Calmodulin-like protein 3;Troponin C, skeletal muscle" 0 ;; 158.08 0.0045995 1116730000 1369670 1545370 1491470 1449250 1566010 1322280 1642790 1439150 1636980 FALSE TRUE 1283944.8 1659790.803 1526848.373 1486440.209 1443021.892 1704000.771 1396468.89 1618831.045 1363757.463 0.941475911 1.217071839 1.11958938 1.089959358 1.058122086 1.249489603 1.02398625 1.187037351 1 20.37915566 -1.602248212 2.702997685 0.990068171 1.118123902 0.120989505 0.09204994 8423751.512 8550993.345 598073.4151 0.019410157 0.024989167 1.602248212 0.128055731 ELHDLFNLPHDRPYFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELHDLFNLPHDRPYFK 16 1 H0YA18;D6RGX2;Q9NUQ7 H0YA18 UFSP2 Ufm1-specific protease 2 0 204.72 1.58E-11 185420000 159200 179670 162500 151530 247930 141110 203350 198760 267520 FALSE TRUE 149235.9562 192972.9537 166354.5767 155418.5163 228458.5779 181846.1663 172859.5553 223575.6235 222869.1838 0.669612342 0.865857498 0.746422515 0.697353101 1.02507926 0.815932303 0.775609945 1.003169751 1 17.76583762 0.838196347 0.182649972 1.096519456 0.697813975 0.377444826 0.101807972 6.382513655 0.79271028 0.885574286 0.528511225 6.88963711 -0.838196347 -0.398705481 ELHEVCHLLEQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELHEVCHLLEQER 13 0 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 167.89 1.80E-05 42719000 30298 36411 30625 37030 42510 24665 31913 34166 38092 FALSE TRUE 28401.70226 39106.90833 31351.43946 37980.25249 39171.43608 31785.3851 27127.94192 38431.70031 31734.19912 0.894987208 1.232326935 0.987938575 1.196824043 1.234360317 1.00161296 0.854848796 1.211049952 1 14.95375081 2.035527025 24.45952565 0.986436416 1.11387115 0.084336378 0.136280063 232.8067858 160280.9085 0.047441556 0.03503778 108.5243081 -2.035527025 0.127434734 ELHINLIPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELHINLIPNK 10 0 P07900;P07900-2;G3V2J8;Q14568 P07900 HSP90AA1;HSP90AA2P Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2 0 ; 110.84 0.001833 1515090000 7673000 10751600 6140300 5749800 11533900 4461800 7341700 10739500 7945700 FALSE TRUE 7192760.627 11547659.65 6285950.816 5897349.602 10628074.02 5749849.229 6240880.242 12080350.22 6619511.339 1.08659994 1.744488235 0.949609494 0.890904071 1.605567764 0.868621403 0.942800748 1.824961028 1 22.65829329 3.961112994 20.4674923 1.132158774 1.448099907 0.081018987 0.355421772 81.56482368 104287.1688 0.083859018 0.152340905 9143.511046 -3.961112994 0.315941133 ELHINLIPNKQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELHINLIPNKQDR 13 1 P07900;P07900-2;G3V2J8 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 150.34 2.60E-05 40413880000 15743200 15919750 15737910 14949990 17923590 13315820 18757120 15061810 18396190 FALSE TRUE 14757861.21 17098464.85 16111220.66 15333632.05 16515943.54 17159881.07 15944663.99 16942310.13 15325747.05 0.962945635 1.115669259 1.051251897 1.000514494 1.077659934 1.119676647 1.040384129 1.105480215 1 23.86945406 4.75672248 24.31415364 1.066930989 0.962945505 0.350793892 0.042947197 3008.254873 4027199.469 0.009499739 0.308712199 57111.35705 -4.75672248 -0.103985483 ELHIQGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELHIQGNR 8 0 Q15404;Q15404-2 Q15404 RSU1 Ras suppressor protein 1 0 ; 123.98 0.0013243 1002830000 423700 478920 446710 460750 518270 401090 462800 456820 522020 FALSE TRUE 397181.3733 514379.7351 457306.1722 472573.625 477567.1648 516878.1718 393407.4364 513854.9826 434891.4896 0.913288447 1.182777192 1.051540863 1.086647213 1.098129479 1.188522158 0.904610566 1.181570564 1 18.73029595 0.303520562 0.504365073 0.997552177 1.084043697 0.022898066 0.102819916 8.824135333 3.501865656 0.194031028 0.047872294 2.01150243 -0.303520562 0.086491519 ELHSEFSEVMNEIWASDQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 281.5 9.07E-45 643312000 415837.5 423640.1 429486.4 387216.6 552866.1 444017 388503.7 441569.9 592265 FALSE TRUE 389810.9732 455006.8538 439674.0202 397153.2335 509446.2267 572197.4999 330251.1769 496700.874 493412.1453 0.790031167 0.922163871 0.891088767 0.80491175 1.032496325 1.159674534 0.669321134 1.006665277 1 18.9124337 4.739648894 23.18563187 0.918434762 0.790031049 0.092648662 0.133895052 92.70034957 1974185.924 0.03033877 0.185870246 54909.67767 -4.739648894 -0.128403714 ELHSWEPEPDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELHSWEPEPDVR 12 0 Q9BTY7 Q9BTY7 HGH1 Protein HGH1 homolog 0 123.95 0.00033169 258140000 248850 280180 296360 280310 297010 246680 304890 254660 293360 FALSE TRUE 233274.9227 300924.8187 303389.7992 287503.2292 273684.0327 317892.5115 259174.575 286454.8616 244396.3208 0.954494413 1.231298482 1.241384478 1.176381167 1.119836959 1.300725438 1.060468399 1.172091546 1 17.89886304 0.617046261 0.864643261 1.000833255 1.179635872 0.176464777 0.09919995 1.830219937 2.31912438 0.089531627 0.029905792 4.140437763 -0.617046261 0.178802617 ELHWHPQCPGLLVSTALSGFTIFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELHWHPQCPGLLVSTALSGFTIFR 24 0 Q9BQ67 Q9BQ67 GRWD1 Glutamate-rich WD repeat-containing protein 1 0 122.3 7.00E-05 65168000 19433 49599 22119 17751 49140 18695 20646 38110 9687.9 FALSE TRUE 18216.72322 53271.36157 22643.67313 18206.52071 45280.74262 24091.94301 17550.32397 42868.11739 8070.926904 2.257079445 6.600401937 2.805585207 2.255815339 5.610352214 2.985028027 2.174511574 5.311424314 1 12.97851865 -0.497743895 0.237039016 1.01E-12 4.443262779 0.172529128 1.637567322 18.05227141 1.295250056 21.08895362 3.213319298 0.317874804 0.497743895 4.443262779 ELHYLPFPS(ph)P ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELHYLPFPSP 10 0 Q8N565 Q8N565 MREG Melanoregulin 1 ELHYLPFPS(1)P 68.551 0.062556 17741000 25682 39375 25147 28447 50131 21258 27680 40347 44891 TRUE FALSE 24074.60946 42290.36597 25743.49872 29176.99818 46193.91348 27394.83951 23529.64097 45384.41176 37398.40209 0.643733639 1.130806762 0.688358253 0.780166974 1.235184149 0.732513636 0.629161666 1.213538794 1 15.19068901 1.223181687 24.99996702 1.106769422 0.844847925 0.229483143 0.206879886 426.1089127 692662.7499 0.188158618 0.047736456 16.71789861 -1.223181687 -0.261921496 ELIESIKDVIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELIESIKDVIGR 12 1 Q5VZK9;Q5VZK9-2;Q5VZK9-3 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 0 104.24 0.001969 39640000 134370 130950 137740 140400 171180 110220 157120 142230 205170 FALSE TRUE 125960.0216 140645.6743 141007.2578 144002.9017 157736.2133 142038.7247 133561.3146 159987.7286 170925.8016 0.736928073 0.822846364 0.824961805 0.842487795 0.922834422 0.830996394 0.781399376 0.936006894 1 17.38301067 -4.999999999 0.125515207 1.552586794 0.757050955 0.59434614 0.049432559 116.9778832 0.938608449 16.32703583 0.423284794 1.00E-05 4.999999999 -0.795535839 ELIFEETAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELIFEETAR 9 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 ;; 183.65 0.00010452 104450000 183099 212913 208574 202930 198336 171833 220087 184411 196721 FALSE TRUE 171639.1604 228677.3001 213521.4738 208137.5274 182759.4906 221438.3976 187086.9975 207435.1193 163886.9942 1.0473019 1.39533525 1.302857953 1.270006374 1.115155546 1.351165165 1.141560979 1.265720445 1 17.32234184 -0.672175127 0.341115522 0.90291133 1.280511782 0.283797403 0.110650219 11.2871512 1.229101566 1.281350332 0.090682076 0.212728106 0.672175127 0.377600452 ELIIGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ELIIGDR 7 0 P25705;P25705-2;P25705-3;K7EK77;K7ENJ4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;;;; 138.9 0.0063773 1839700000 2171690 2287470 2124690 1961010 2825710 2215840 2023710 2205480 3429960 FALSE TRUE 2035767.799 2456836.659 2175088.65 2011332.837 2603790.135 2855517.037 1720273.473 2480839.033 2857477.518 0.712435281 0.859792122 0.761191868 0.703884046 0.911219815 0.999313912 0.6020252 0.868191969 1 21.44631072 2.737098124 24.99872378 0.841460361 0.77638122 0.151648684 0.119951722 419.7105867 7174156.418 0.03797966 0.037667576 545.8811832 -2.737098124 -0.065079141 ELILGSETPSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELILGSETPSSPR 13 0 R4GNJ5;A0A590TQL1;Q96AP0-2;Q96AP0 R4GNJ5 ACD Adrenocortical dysplasia protein homolog 1 ELILGSETPS(0.003)S(0.996)PR;ELILGSETPS(0.001)S(0.999)PR;ELILGSETPS(0.283)S(0.717)PR;ELILGSETPS(0.002)S(0.998)PR 268.9 7.74E-25 668780000 1624010 1773800 1712880 1746090 1865630 1486700 2046980 1631880 1973070 TRUE FALSE 1522366.113 1905133.998 1753510.322 1790897.626 1719110.945 1915886.155 1740054.352 1835623.81 1643751.87 0.926153235 1.159015562 1.066773127 1.089518228 1.045845773 1.165556791 1.058586994 1.116728043 1 20.64856111 4.753421156 24.58757064 1.092782079 0.926153086 0.500937878 0.050469351 1636.421232 2707490.826 0.0105409 0.238631586 56678.86648 -4.753421156 -0.166628993 ELIPQES(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELIPQESPR 9 0 Q96DF8 Q96DF8 DGCR14 Protein DGCR14 1 ELIPQES(1)PR;ELIPQES(1)PR 93.623 0.0097278 568390000 439700 538120 485610 532150 704690 420520 619510 585220 729200 TRUE FALSE 412179.9619 577962.9647 497128.8985 545805.8699 649346.49 541917.2974 526620.2267 658286.0052 607491.8092 0.678494682 0.951392193 0.818330208 0.89845799 1.068897523 0.892056961 0.866876259 1.083612973 1 19.21250543 4.741807522 24.55034183 0.928508207 0.678494563 0.476197427 0.086647948 224.7879554 1699552.384 0.01977068 0.14121346 55183.28142 -4.741807522 -0.250013644 ELIPTEEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELIPTEEALR 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 123.35 0.00108 96955000 129997 228400 174889 191635 228960 162236 196540 203071 162657 FALSE TRUE 121860.7198 245310.9736 179037.4497 196552.6785 210978.4052 209070.8995 167070.6516 228424.8614 135508.4959 0.89928472 1.810299583 1.32122675 1.450482328 1.55693858 1.54286193 1.232916434 1.685686642 1 17.04802378 -1.686432726 2.736331426 0.937279385 1.452713189 0.22697339 0.252327332 33651067.91 30889801.41 14707089.06 0.053899995 0.020585777 1.686432726 0.515433804 ELISDNQYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELISDNQYR 9 0 P25205;P25205-2 P25205 MCM3 DNA replication licensing factor MCM3 0 ;;; 127.68 0.0010205 442182000 633160 781630 764080 734920 864610 634700 845830 745300 819310 FALSE TRUE 593531.6458 839502.6985 782204.3384 753779.2914 796707.0183 817927.5865 719005.6438 838352.3456 682561.8681 0.869564612 1.229929092 1.14598306 1.104338415 1.167230482 1.198320071 1.053392634 1.228243746 1 19.38060029 -1.312266688 3.255968584 0.999250944 1.13392426 0.115160779 0.105809747 20951167.52 31807410.43 159884.3532 0.022548847 0.04872292 1.312266688 0.134673317 ELISLLHLSLLHLEEDKTTVSQESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELISLLHLSLLHLEEDKTTVSQESR 25 1 Q96R06;J3KTQ0 Q96R06 SPAG5 Sperm-associated antigen 5 0 82.486 0.013024 22065000 33306 68214 61000 62808 73257 55560 83567 62471 62826 FALSE TRUE 31221.43691 73264.63554 62446.94881 64419.75961 67503.69072 71599.27006 71036.90415 70270.64187 52339.93473 0.596512722 1.399784618 1.193103299 1.230795566 1.289716754 1.367966361 1.357221871 1.342581763 1 15.6756245 4.7440736 24.93240565 1.29082078 0.596512415 0.766999325 0.116734539 246.531051 1114899.491 0.025007713 0.218265013 55471.97138 -4.7440736 -0.694308365 ELISNASDALDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELISNASDALDK 12 0 P08238;P14625;Q96GW1;A0A1W2PRR1;F8W026 P08238;P14625 HSP90AB1;HSP90B1 Heat shock protein HSP 90-beta;Endoplasmin 0 ;;; 257.54 7.73E-21 549390000 1614930 1272140 1394140 1351750 1366320 1092560 1632910 1258750 1212690 FALSE TRUE 1513854.414 1366330.569 1427209.659 1386438.194 1259014.739 1407964.336 1388070.305 1415907.708 1010284.205 1.498444108 1.352421985 1.412681355 1.372324923 1.246198577 1.39363194 1.37394042 1.401494452 1 19.94632977 -1.464111197 3.094036382 0.991719134 1.377570716 0.788717021 0.062008277 11791392.52 13402779.82 833842.7997 0.013868892 0.034346999 1.464111197 0.385851582 ELISNASDALDKIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELISNASDALDKIR 14 1 P08238;P14625;Q96GW1;A0A1W2PRR1;F8W026 P08238;P14625 HSP90AB1;HSP90B1 Heat shock protein HSP 90-beta;Endoplasmin 0 ; 209.56 5.90E-09 5122200000 2687030 3740300 2866120 3333970 4784400 2168840 3663200 2844760 5779300 FALSE TRUE 2518853.589 4017235.704 2934105.72 3419525.315 4408652.523 2794948.9 3113937.167 3199934.548 4814697.494 0.523159262 0.834369285 0.609406037 0.71022641 0.915665528 0.580503532 0.646756556 0.664617985 1 22.19901373 -1.126664156 3.461175408 1.000286773 0.691638288 0.419582791 0.116021352 21361716.15 34936891.25 70356.06998 0.025555945 0.074702622 1.126664156 -0.308648485 ELISNSSDALDK ddPTM_SK-BR-3_Pertuzumab_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 0 191.53 1.22E-05 297170000 602490 449190 474930 475540 499500 369530 598800 462290 460060 FALSE TRUE 564781.2264 482448.495 486195.5639 487743.1615 460271.2849 476207.3122 509015.499 520007.9241 383273.0139 1.473574204 1.258759363 1.268535864 1.272573711 1.200896667 1.242475455 1.328075498 1.356755903 1 18.5480129 -1.387900283 3.229240771 0.996946256 1.290116611 0.606139641 0.075663729 18891336.47 28432139.47 552382.3278 0.017123353 0.040935464 1.387900283 0.293170355 ELISNSSDALDKIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELISNSSDALDKIR 14 1 P07900;P07900-2;G3V2J8 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 251.87 3.14E-24 3541470000 2848710 3864270 3294520 3908710 5375780 2850250 4129700 3457460 6888200 FALSE TRUE 2670414.326 4150384.572 3372667.57 4009014.116 4953587.924 3673070.905 3510489.823 3889131.492 5738514.921 0.465349374 0.723250637 0.587724806 0.698615264 0.863217747 0.640073426 0.611741866 0.677724384 1 22.452246 -5 0.344867059 4.769796583 0.649187446 0.535082025 0.100778958 329.3032673 2.738219067 916.2193735 0.075401115 1.00E-05 5 -4.120609137 ELIVVFGGGNEGIVDELHVYNTATNQWFIPAVR ddPTM_SK-BR-3_Pertuzumab_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 81.242 0.00097965 18173000 4735.9 3192.3 4605.5 2515.2 4064.2 2467.2 5305.5 3536.3 2408.3 FALSE TRUE 4439.488473 3428.661214 4714.744635 2579.74429 3745.014126 3179.440588 4509.989529 3977.814839 2006.339172 2.212730796 1.708914057 2.349924031 1.285796702 1.866590743 1.584697459 2.247869948 1.982623325 1 10.9703498 -1.15253865 4.009433824 0.99963432 1.917862888 0.435027005 0.323782815 9739408.029 4199552.68 30009.91336 0.070395934 0.070381959 1.15253865 0.918228567 ELKAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELKAPR 6 1 K7ENH8;A0A0A0MRB7;P15923-2;X6REB3;P15923;P15923-3;K7EMM4;K7EJN4;K7EK65;A0A494C1R3;A0A0A0MTS0;K7EPS2;K7EKB9;K7ERZ7 K7ENH8 TCF3 Transcription factor E2-alpha 0 91.26 0.043863 192560000 465620 417720 434950 404310 527070 377510 412210 435440 704790 FALSE TRUE 436477.6754 448648.4234 445267.2194 414685.2791 485676.0483 486491.0086 350402.9373 489805.6425 587155.9959 0.743376 0.764104304 0.758345691 0.706260827 0.827166974 0.828554953 0.596779969 0.834200189 1 19.16338432 -2.388538709 1.18771631 1.722575282 0.750319596 0.536559402 0.070609715 16769.03517 1618.508143 32092.50619 0.019720373 0.004087533 2.388538709 -0.972255685 ELKELIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELKELIQK 8 1 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ; 113.22 0.0050228 0 757310 1266060 1038060 1323490 1702100 1117990 1334630 682900 2517010 FALSE TRUE 709911.3189 1359800.4 1062683.273 1357452.994 1568423.932 1440735.564 1134514.622 768161.5682 2096904.77 0.338552007 0.648479806 0.506786616 0.647360344 0.747970988 0.68707725 0.541042511 0.366331165 1 20.99982991 -2.232041821 2.359186843 2.499785352 0.574865412 0.517864024 0.132640249 4506979.853 774843.1641 36178295.26 0.030357625 0.005860817 2.232041821 -1.92491994 ELKENGELLPILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELKENGELLPILR 13 1 O76003 O76003 GLRX3 Glutaredoxin-3 0 122.78 0.00016325 0 404780 388760 456820 362410 453130 288800 491400 352100 515380 FALSE TRUE 379445.5424 417544.1949 467655.9861 371710.0542 417542.9976 372171.8717 417719.1319 396060.4601 429359.7485 0.883747356 0.972480994 1.089193823 0.865731023 0.972478205 0.866806618 0.972888431 0.922444317 1 18.71182742 3.222195977 24.99982377 0.932088886 0.995149842 0.097324439 0.065349205 403.3718406 616218.9366 0.01812525 0.021721791 1667.999735 -3.222195977 0.063060956 ELKEQLGEEIDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELKEQLGEEIDSK 13 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;; 153.94 4.19E-05 554620000 1025500 687930 935580 880490 962940 590260 1042110 670570 1384460 FALSE TRUE 961315.7856 738865.053 957772.3994 903084.8641 887314.5767 760658.4799 885855.28 754292.1406 1153384.682 0.833473689 0.640605918 0.830401525 0.782986698 0.769313647 0.659501112 0.768048418 0.65398141 1 20.13744234 -1.793423298 2.734165476 1.070419636 0.741378684 0.572230995 0.070021261 19103438.81 15744072.54 8997592.079 0.01526955 0.016090765 1.793423298 -0.329040952 ELKGELYCLPCHDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELKGELYCLPCHDK 14 1 P48059;P48059-4;P48059-2;P48059-5;P48059-3;A0A0M3HER1;Q7Z4I7-4;Q7Z4I7-3;Q7Z4I7;Q7Z4I7-5;Q7Z4I7-2 P48059 LIMS1;LIMS2 LIM and senescent cell antigen-like-containing domain protein 1;LIM and senescent cell antigen-like-containing domain protein 2 0 105.6 0.00059504 114020000 459700 376040 396850 393840 488400 380750 649160 364940 596690 FALSE TRUE 430928.1976 403882.3929 406263.4694 403946.6012 450043.0341 490666.344 551824.4845 410503.5623 497098.5842 0.866886793 0.812479467 0.817269416 0.812608633 0.905339601 0.987060433 1.110090638 0.825799098 1 18.92317247 2.432412369 2.77269137 1.003194794 0.823779414 0.498322043 0.070960249 0.183415068 2.885266138 0.025394604 0.021018086 270.6527035 -2.432412369 -0.17941538 ELKIDIIPNPQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELKIDIIPNPQER 13 1 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ;;; 144.68 3.78E-05 1482600000 1686590 2134460 1906250 2259340 3397530 1621910 2610760 1806260 5051180 FALSE TRUE 1581029.343 2292497.639 1951467.15 2317318.489 3130701.699 2090129.087 2219300.775 2031775.537 4208105.426 0.375710488 0.544781418 0.463740081 0.550679761 0.743969407 0.496691237 0.527387161 0.482824295 1 22.00473942 -2.34404081 2.285946215 3.898338565 0.526140829 0.722277903 0.092896133 3095329.178 498718.8047 46136289.51 0.0229219 0.00452855 2.34404081 -3.372197736 ELKPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELKPAR 6 1 P36542-2;P36542 P36542-2 ATP5C1 "ATP synthase subunit gamma, mitochondrial" 0 64.803 0.096415 180890000 428290 404850 389460 361250 526200 377810 391420 424590 633100 FALSE TRUE 401484.0934 434825.5152 398698.1751 370520.2866 484874.3746 486877.6138 332730.2048 477600.9961 527431.52 0.761206106 0.824420799 0.755924058 0.702499325 0.919312472 0.923110575 0.630850058 0.905522287 1 19.00862427 1.003849319 24.90317402 1.000000037 0.787709688 0.397641517 0.088555641 78.2670189 506343.8462 0.08185771 0.020464428 10.0890278 -1.003849319 -0.212290348 ELKTDS(ph)SPNQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELKTDSSPNQAR 12 1 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 1 ELKT(0.004)DS(0.534)S(0.462)PNQAR;ELKT(0.006)DS(0.497)S(0.497)PNQAR;ELKT(0.001)DS(0.5)S(0.5)PNQAR;ELKT(0.006)DS(0.497)S(0.497)PNQAR 164.63 3.44E-05 1979040000 1121740 1142001 1010274 1046913 1544347 619258 1347273 1029846 3232800 TRUE FALSE 1051532.296 1226555.942 1034238.176 1073778.56 1423060.216 798027.7318 1145261.921 1158424.54 2693224.795 0.390436141 0.455422787 0.384014798 0.398696225 0.528385235 0.296309366 0.425238147 0.430125455 1 21.36090322 0.458249197 2.666672811 0.999998472 0.411792508 0.90963559 0.058117693 3.777361655 18.19719087 0.050043333 0.013241135 2.872428298 -0.458249197 -0.588205965 ELKTDSS(ph)PNQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELKTDSSPNQAR 12 1 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 1 ELKT(0.009)DS(0.208)S(0.783)PNQAR 96.489 0.0033038 742450000 250950 242540 246360 258120 343950 176610 306850 241860 738720 TRUE FALSE 235243.4875 260497.914 252203.7755 264743.7962 316937.5544 227594.44 260840.6912 272056.7534 615422.8597 0.382246912 0.423282804 0.409805667 0.430181934 0.514991521 0.369817982 0.423839783 0.442064751 1 19.23121851 0.503186472 2.866847331 0.999999171 0.422042478 0.957216901 0.038257367 2.416049612 13.68255734 0.034120347 0.008957095 3.185565006 -0.503186472 -0.577956692 ELLAKPIGPDDAIDALSSDFTCGS(ph)PTAAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELLAKPIGPDDAIDALSSDFTCGSPTAAGK 30 1 P20810-5;E9PCH5;P20810-2;P20810-3;F8W7E0 P20810-5 CAST Calpastatin 1 ELLAKPIGPDDAIDALSSDFT(0.003)CGS(0.969)PT(0.028)AAGK;ELLAKPIGPDDAIDALSSDFTCGS(0.994)PT(0.006)AAGK;ELLAKPIGPDDAIDALSSDFTCGS(0.999)PT(0.001)AAGK;ELLAKPIGPDDAIDALSS(0.001)DFT(0.122)CGS(0.757)PT(0.12)AAGK 259.19 1.85E-58 1146460000 2451694 1759428 2089434 2203032 2508112 1552417 2549326 1548555 2677500 TRUE FALSE 2298246.849 1889697.88 2138996.361 2259565.531 2311135.001 2000574.587 2167078.233 1741895.501 2230607.953 1.030323077 0.847167194 0.958929766 1.012981922 1.036100942 0.896874139 0.971519101 0.780906164 1 21.08900554 -3.042745337 9.543956351 0.999566213 0.943313129 0 0.08370819 0 0 0 0.01707976 0.000906264 3.042745337 -0.056253083 ELLDLAMQNAWFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELLDLAMQNAWFR 13 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ; 229.16 1.45E-11 179873000 204768 310400 247210 255790 341910 240820 246970 254390 248820 FALSE TRUE 191951.9364 333382.339 253073.9379 262354.0045 315057.7678 310340.8246 209939.1413 286151.1515 207290.3346 0.926005242 1.608286945 1.220867044 1.265635491 1.519886436 1.497131187 1.012778245 1.380436536 1 17.66129332 0.912767597 0.845328136 1.014593161 1.345933602 0.132683279 0.219617659 1.231383684 1.876268986 0.194372834 0.068684898 8.180269215 -0.912767597 0.331340442 ELLDMMIAEEESLKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELLDMMIAEEESLKER 16 1 O43663-2;O43663-4;O43663;H0YLA0 O43663-2 PRC1 Protein regulator of cytokinesis 1 0 ;;; 136.17 1.72E-05 74618000 167126 143637 147606 140079 165372 121287 172085 112238 173417 FALSE TRUE 156665.882 154272.0329 151107.284 143673.6643 152384.3502 156300.588 146282.4518 126251.1614 144472.5824 1.08439871 1.067829137 1.045923604 0.994470106 1.054763109 1.081870244 1.012527425 0.87387627 1 17.1404362 1.442682217 5.541021042 0.936688783 1.052370216 0.606072724 0.038837863 0.111756667 6.887705713 0.022972407 0.008972887 27.71291547 -1.442682217 0.115681433 ELLDTELDLHKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELLDTELDLHKR 12 1 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 0 107.09 0.001202 33203000 69232 58576 63383 62274 67604 49213 74050 54788 78301 FALSE TRUE 64898.8927 62913.02799 64886.47469 63872.05627 62294.65454 63419.99419 62946.88995 61628.4024 65232.05726 0.994892625 0.964449546 0.994702259 0.97915134 0.954969951 0.97222128 0.964968646 0.944756382 1 15.99329351 2.912917584 7.568759346 0.965698938 0.982403704 0.18784381 0.016340755 0.432151723 33.30080761 0.004483882 0.004769028 818.309483 -2.912917584 0.016704766 ELLDTS(ph)FEDLSKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELLDTSFEDLSKPK 14 1 P78345 P78345 RPP38 Ribonuclease P protein subunit p38 1 ELLDT(0.157)S(0.843)FEDLSKPK;ELLDT(0.168)S(0.832)FEDLSKPK;ELLDT(0.028)S(0.972)FEDLSKPK;ELLDT(0.009)S(0.991)FEDLSKPK 230.33 5.78E-13 641405000 2098530 871630 1289960 1151180 1120870 985980 1850250 969960 1190230 TRUE FALSE 1967186.753 936166.3921 1320558.46 1180721.228 1032841.392 1270616.42 1572822.189 1091061.641 991572.9238 1.983905274 0.944122585 1.331781484 1.190755818 1.041619196 1.281415002 1.586189126 1.100334242 1 19.91935935 1.996561433 24.95716307 1.328930448 1.242418981 0 0.319094456 817.6972831 5934884.108 0.111396956 0.080532217 99.21136679 -1.996561433 -0.086511467 ELLELASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELLELASR 8 0 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 118.74 0.0042524 52233000 68845 85315 82639 77114 89635 62799 86746 76186 91070 FALSE TRUE 64536.11434 91631.81137 84599.2361 79092.87579 82595.42867 80928.05184 73739.24261 85697.98981 75869.82867 0.850616318 1.20775034 1.115057693 1.042481276 1.088646569 1.066669759 0.971917874 1.129539783 1 16.21123866 1.986326026 21.0722177 1.027847665 1.086661646 0 0.098537624 227.3614156 350371.5315 0.037212935 0.025222084 96.90050169 -1.986326026 0.058813981 ELLELGIDNEDS(ph)EHENDDDTNQSATLNDKDDDSLPAETGQNHPFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELLELGIDNEDSEHENDDDTNQSATLNDKDDDSLPAETGQNHPFFR 46 1 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 ELLELGIDNEDS(1)EHENDDDTNQSATLNDKDDDSLPAETGQNHPFFR;ELLELGIDNEDS(0.998)EHENDDDT(0.001)NQS(0.001)ATLNDKDDDSLPAETGQNHPFFR;ELLELGIDNEDS(0.952)EHENDDDT(0.045)NQS(0.002)AT(0.001)LNDKDDDSLPAETGQNHPFFR 171.82 1.04E-21 1003850000 183754 131971 153405 130742 126821 81751 170240 127693 165278 TRUE FALSE 172253.1652 141742.2702 157043.839 134097.0611 116860.9902 105351.1866 144714.0924 143635.7521 137692.0341 1.251003127 1.029415181 1.140544114 0.973891206 0.848712789 0.76512187 1.050998291 1.043166753 1 17.07108557 3.155370868 4.911003667 0.936691045 1.116467209 0.443282057 0.10122492 0.20738426 8.772541765 0.029787224 0.036290442 1430.114692 -3.155370868 0.179776164 ELLEVVEPEVLQDS(ph)LDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELLEVVEPEVLQDSLDR 17 0 A0A087WUL8;A0A087WVE3;A0A075B762;A0A087WVU4;A0A087WZJ2;A0A087X002;A0A087WYI5;A0A075B757;A0A075B764;P0DPF3-2;A0A087WYQ9;A0A087WWQ1;A0A087WZE1;A0A087WVC7;P0DPF3;A0A494C053;A0A087WY24;A0A075B7A3;A0A087WY62;P0DPF2;A0A087WTW4;H7BY70;A0A075B7F9;H7BZX4;A0A087WU30;A0A087WZB6;A0A087WVG0;A0A087WW93;A0A087WZS8;Q6P3W6-2;Q6P3W6;Q8N660;Q5TAG4;Q3BBV2;B4DH59;A0A075B6G5;Q5TI25 A0A087WUL8 NBPF19;NBPF14;NBPF10;NOTCH2NL;NBPF12;NBPF9;NBPF26;NBPF8;NBPF15 Neuroblastoma breakpoint family member 10;Neuroblastoma breakpoint family member 15;Neuroblastoma breakpoint family member 12;Putative neuroblastoma breakpoint family member 8;Neuroblastoma breakpoint family member 26;Neuroblastoma breakpoint family member 14 1 ELLEVVEPEVLQDS(1)LDR;ELLEVVEPEVLQDS(1)LDR 199.76 1.36E-11 26534000 44687 39673 51730 41139 45412 56006 59994 53156 97753 TRUE FALSE 41890.12044 42610.4302 52957.06003 42194.69639 41845.5247 72174.02302 50998.45666 59792.64361 81437.39279 0.514384351 0.523229302 0.650279414 0.518124352 0.513836743 0.886251641 0.626228995 0.734216084 1 16.31340375 -1.496730338 0.142613957 1.504370792 0.402589375 0.678661448 0.095391232 21.4879496 0.528290933 4.46168684 0.682481184 0.031861753 1.496730338 -1.101781417 ELLFHPALFEVPSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELLFHPALFEVPSLK 15 0 F8W6G1;Q9UHY1 F8W6G1 NRBP1 Nuclear receptor-binding protein 0 ; 157.75 1.90E-06 156579000 652250 564960 648320 609100 690910 525490 713540 578840 876640 FALSE TRUE 611426.8368 606790.2262 663698.4566 624730.5372 636648.7156 677190.4324 606551.3012 651109.4482 730323.1207 0.837200438 0.830851727 0.908773716 0.855416622 0.871735671 0.927247698 0.830524577 0.891536129 1 19.47817538 -5 0.247243356 1.780618738 0.856195323 0.644783855 0.03131006 115.8388659 1.151044479 45.65863431 0.045026952 1.00E-05 5 -0.924423415 ELLHSVHPES(ph)PNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELLHSVHPESPNLK 14 0 Q9Y217 Q9Y217 MTMR6 Myotubularin-related protein 6 1 ELLHSVHPES(1)PNLK;ELLHSVHPES(1)PNLK 232.78 6.61E-14 587470000 186948 227655 250466 329324 306402 197793 275646 193702 267541 TRUE FALSE 175247.2584 244510.8131 256407.1718 337775.0114 282338.4229 254892.6282 234315.4413 217886.1211 222886.6787 0.786261698 1.097018514 1.150392537 1.515456255 1.266735296 1.143597409 1.051276113 0.977564574 1 17.76595087 1.635876896 2.835760989 0.993706228 1.170388365 0.143345581 0.177172359 0.458569603 8.591675605 0.118681451 0.048971088 43.23912487 -1.635876896 0.176682136 ELLKPNASVALHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELLKPNASVALHK 13 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ; 116.84 0.00033272 856770000 1821870 1618940 1755160 1584740 1855180 1392690 2224000 1730410 2274000 FALSE TRUE 1707842.409 1738808.002 1796793.224 1625407.111 1709481.646 1794736.995 1890531.847 1946455.498 1894454.709 0.901495507 0.917840893 0.948448762 0.85798151 0.902360789 0.947363368 0.997929292 1.027448948 1 20.85335122 1.82750521 2.378603838 1.01333523 0.911325631 0.797693755 0.023544221 0.134383493 1.432083574 0.014830416 0.007012664 67.22103731 -1.82750521 -0.102009599 ELLLPNWQGSGSHGLTIAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELLLPNWQGSGSHGLTIAQR 20 0 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2;E9PQE3 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 261.17 2.28E-36 600620000 410630 708650 644350 733920 822900 569360 779960 629140 907990 FALSE TRUE 384929.4013 761119.1833 659634.2863 752753.6297 758272.7534 733724.9892 663012.2388 707689.5139 756440.6032 0.508869301 1.006184993 0.872023902 0.995125892 1.002422068 0.969970393 0.87648949 0.935551993 1 19.52886728 4.743155908 24.99670186 0.948396332 0.508869124 0.886759324 0.05026449 152.9730001 832088.7329 0.011940624 0.096250015 55354.87927 -4.743155908 -0.439527207 ELLLTGPGLEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELLLTGPGLEER 12 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 198.93 4.13E-07 83856000 110884 123780 112257 123955 135625 106195 142729 117238 148904 FALSE TRUE 103943.9684 132944.8 114919.7891 127135.8952 124973.5596 136851.7726 121328.1115 131875.4224 124050.9604 0.837913451 1.071695048 0.926391772 1.024868286 1.007437259 1.103189948 0.978050561 1.063074578 1 16.92057338 3.124819666 8.996561948 1.029350401 0.969788971 0.235174991 0.066854579 0.47434207 35.52730604 0.01773968 0.021229639 1332.967822 -3.124819666 -0.05956143 ELLNPVVEFVSHPSTTCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELLNPVVEFVSHPSTTCR 18 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 286 1.01E-39 202150000 180260 349090 313220 368520 303170 278620 396250 338430 301190 FALSE TRUE 168977.8484 374936.9868 320649.7263 377976.8471 279360.2511 359053.071 336835.9911 380683.7305 250919.4432 0.673434654 1.494252426 1.277899083 1.506367311 1.113346369 1.430949576 1.342406897 1.51715517 1 17.93686474 4.745949546 24.86303993 1.352690822 0.673434308 0.594262694 0.171336346 500.9200908 1685503.898 0.034792011 0.360592882 55712.10223 -4.745949546 -0.679256514 ELLPLIYHHLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELLPLIYHHLLR 12 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 0 89.805 0.0053299 125750000 66532 150540 71712 57830 153910 43492 57966 120500 83767 FALSE TRUE 62367.88088 161686.1382 73413.0425 59314.01571 141822.5294 56047.43437 49274.53643 135544.6903 69785.74654 0.893705147 2.316893438 1.051977605 0.849944561 2.032256391 0.803135843 0.706083102 1.942297632 1 16.09064478 3.735412631 22.9913875 1.154199921 1.700199916 0.073118807 0.565064305 205.1071735 568735.4008 0.135559255 0.23864663 5437.667282 -3.735412631 0.545999995 ELLS(ph)PLS(ph)EPDDRYPLIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELLSPLSEPDDRYPLIVK 18 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 2 ELLS(1)PLS(1)EPDDRYPLIVK 62.684 0.028173 10115000 47227 42451 43006 43501 45870 40303 53114 40467 50255 TRUE FALSE 44271.14637 45594.11621 44026.12263 44617.30931 42267.55523 51937.82184 45150.04879 45519.39403 41867.11584 1.057420495 1.089019754 1.05156808 1.06568863 1.009564533 1.24053976 1.078413162 1.087235008 1 15.35352992 ELLS(ph)PLSEPDDRYPLIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELLSPLSEPDDRYPLIVK 18 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 ELLS(0.786)PLS(0.214)EPDDRYPLIVK;ELLS(0.574)PLS(0.426)EPDDRYPLIVK 234.23 5.59E-24 572030000 483960 456050 458180 459580 488150 401830 600480 450890 582790 TRUE FALSE 453669.8075 489816.4165 469048.246 471373.6009 449812.6681 517831.7978 510443.5986 507184.609 485518.584 0.934402559 1.008852045 0.966076812 0.970866237 0.926458189 1.066554021 1.051336891 1.044624502 1 18.88916699 2.228294939 24.99998734 1.046368972 0.968891832 0.653615381 0.028252859 124.7734837 303858.352 0.009990651 0.0074612 169.1589336 -2.228294939 -0.07747714 ELLSPLS(ph)EPDDRYPLIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELLSPLSEPDDRYPLIVK 18 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 ELLS(0.198)PLS(0.802)EPDDRYPLIVK;ELLSPLS(1)EPDDRYPLIVK 275.5 2.74E-39 647140000 549600 540960 531230 556120 607520 481230 717730 536930 698680 TRUE FALSE 515201.5171 581013.2413 543831.0265 570390.9807 559807.8298 620153.2889 610113.0496 603966.8924 582065.7944 0.885125912 0.998191694 0.934311948 0.97994245 0.961760398 1.065435033 1.048185713 1.037626499 1 19.15082271 2.250320209 23.70339123 1.043351674 0.957065897 0.609464254 0.033916562 70.62029959 142346.459 0.01066393 0.008845602 177.9591033 -2.250320209 -0.086285777 ELLTEFGYKGEETPVIVGSALCALEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELLTEFGYKGEETPVIVGSALCALEGR 27 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 156.27 2.03E-08 99604000 76322 60962 64135 61649 90035 57771 61074 66672 97797 FALSE TRUE 71545.14226 65475.68991 65656.31249 63231.01771 82964.01428 74448.54987 51916.52068 74996.14596 81474.04891 0.87813412 0.803638592 0.805855525 0.776087829 1.018287607 0.913770101 0.637215425 0.920491211 1 16.31405299 1.003415769 24.99877009 1.000000074 0.823706182 0.241415815 0.09815153 103.4139858 756841.9382 0.094131927 0.023532982 10.07896111 -1.003415769 -0.176293892 ELLTLDEKDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ELLTLDEKDPR 11 1 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 ;;;;; 83.397 0.015265 10339590000 33010600 28578400 32706500 32099900 34427400 27391700 39455100 28606600 35565200 FALSE TRUE 30944525.47 30694374.47 33482313.63 32923637.78 31723610.88 35299239.12 33539174.04 32178196.98 29629138.36 1.044395051 1.035952315 1.130046821 1.111191199 1.07068962 1.191369074 1.131965892 1.086032155 1 24.82051334 4.040520212 3.364189121 1.113839227 1.040362284 0.191310915 0.049773657 0.297409747 6.665799713 0.011751841 0.027578339 10977.92381 -4.040520212 -0.073476943 ELLTMQLVDWHQLQADSFIQDER ddPTM_SK-BR-3_Pertuzumab_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 0 207.55 1.17E-24 27198000 18535 23792 21431 24526 29365 17923 25817 21664 21317 FALSE TRUE 17374.92744 25553.58444 21939.35344 25155.37868 27058.79135 23097.07914 21945.98052 24368.79809 17759.05499 0.978370046 1.438904517 1.23538969 1.416481829 1.523661669 1.300580417 1.235762857 1.372190024 1 14.11626719 -1.092599061 5.65067425 0.999997616 1.319647973 0.303050416 0.148679947 4.05E-06 6.51E-07 0.130657027 0.030795927 0.080798061 1.092599061 0.319650357 ELLTSDS(ph)PPHNDIMTPVDPGVAQPNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELLTSDSPPHNDIMTPVDPGVAQPNSR 27 0 Q12778 Q12778 FOXO1 Forkhead box protein O1 1 ELLT(0.027)S(0.024)DS(0.95)PPHNDIMTPVDPGVAQPNSR 116.39 0.00041494 83003000 30511 34805 34559 33671 45732 30633 35236 31505 48299 TRUE FALSE 28601.37097 37381.99841 35378.7558 34535.05486 42140.39319 39476.24981 29952.68891 35438.4686 40237.58488 0.710812318 0.929031862 0.879246503 0.858278522 1.047289327 0.981079007 0.744395793 0.880730509 1 15.29625609 7.9997706 0.015081606 1.626161656 2.23E-06 0.146630903 0.09792214 16651.63432 19.38659023 834.2855599 1304.639211 99947192.68 -7.9997706 -1.626159425 ELLTTMGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 166.82 0.00014064 1175110000 1144730 1342220 1318760 1334190 1373110 1078930 1359120 1197500 1135420 FALSE TRUE 1073083.393 1441599.365 1350041.61 1368427.574 1265271.479 1390399.576 1155332.573 1347010.511 945911.0669 1.134444273 1.524032666 1.42723947 1.446676778 1.337622028 1.469905179 1.221396613 1.424035047 1 19.85134502 -0.301668823 0.47400298 0.937191705 1.411146432 0.469761294 0.120901003 5.169740561 1.179707523 0.678135517 0.058036956 0.499265063 0.301668823 0.473954727 ELLTTMGDRFT(ph)DEEVDELYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELLTTMGDRFTDEEVDELYR 20 1 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 1 ELLTTMGDRFT(1)DEEVDELYR;ELLT(0.002)T(0.002)MGDRFT(0.996)DEEVDELYR 168.65 1.93E-11 96429000 95780 93683 100224 119666 112046 101701 109793 81596 113404 TRUE FALSE 89785.30077 100619.3868 102601.3606 122736.8322 103246.3591 131060.4277 93330.55892 91783.44021 94476.13978 0.950348956 1.065024323 1.086002888 1.299130473 1.092829993 1.387233094 0.98787439 0.971498628 1 16.5276624 1.595320995 25 0.984718807 1.137922138 0.275670018 0.121923466 1.210985889 2406.873223 0.063039432 0.029496671 39.38410628 -1.595320995 0.153203331 ELLTTMGDRFTDEEVDELYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELLTTMGDRFTDEEVDELYR 20 1 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ; 267.7 5.93E-37 147700000 50503 94979 71170 81244 107905 58999 80972 65867 193315 FALSE TRUE 47342.10738 102011.344 72858.18601 83328.85859 99430.57657 76031.05353 68831.00031 74090.63994 161049.4776 0.293960018 0.633416174 0.452396289 0.517411542 0.617391488 0.472097486 0.427390398 0.46004893 1 17.29714446 -1.497177279 3.724265878 1.006781012 0.494199989 0.739383418 0.09606595 18797099.53 7588825.787 1033565.545 0.022193197 0.03182898 1.497177279 -0.512581023 ELLVDCYKPTEAFISGLLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELLVDCYKPTEAFISGLLDK 20 1 B5MC51;P53671-3;F5GXC4;F5H2U0;Q96C90 B5MC51;Q96C90 LIMK2;PPP1R14B LIM domain kinase 2;Protein phosphatase 1 regulatory subunit 14B 0 ; 261.04 2.11E-36 262632000 821990 562710 636270 615780 654400 502760 828870 584650 665470 FALSE TRUE 770543.1132 604373.6339 651362.6249 631581.9573 603006.0637 647898.6504 704588.6384 657644.8395 554398.7579 1.389871644 1.090142475 1.174899142 1.139219647 1.087675712 1.168650978 1.270905875 1.186230723 1 19.0805645 4.748212893 24.66724364 1.153390957 1.389871797 0.531921128 0.072749309 950.0890918 2427975.918 0.017150816 0.223956239 56003.20644 -4.748212893 0.23648084 ELLVHLDDPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELLVHLDDPER 11 0 Q86Y56;H0Y650;Q86Y56-2;E9PGY2;Q86Y56-3 Q86Y56 DNAAF5 "Dynein assembly factor 5, axonemal" 0 ;;; 132.76 0.0001757 302322000 361167 469864 444502 464436 488430 396429 536300 464190 365247 FALSE TRUE 338562.2022 504653.2195 455045.7973 476354.214 450070.678 510871.6168 455886.7938 522145.1433 304284.9161 1.112648653 1.658489109 1.495459595 1.565487439 1.479109395 1.67892521 1.49822344 1.715974456 1 18.21506329 -0.899550234 6.100095095 0.999999896 1.538426146 0.489473165 0.168218823 2.05E-07 3.70E-08 0.140249858 0.033057202 0.126022986 0.899550234 0.53842625 ELLVSQHTVQLVGGLS(ph)PLSSPSDTK ddPTM_SK-BR-3_Pertuzumab_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(0.991)PLS(0.009)SPSDTK;ELLVSQHTVQLVGGLS(0.975)PLS(0.022)S(0.002)PS(0.001)DTK 249.68 1.58E-39 1807260000 2894738 3094266 3394618 3304935 3212819 3062688 4627150 3385996 3213700 TRUE FALSE 2713561.516 3323368.674 3475139.942 3389745.227 2960497.156 3946836.307 3933351.814 3808745.054 2677312.709 1.01353925 1.241307623 1.297995535 1.266099853 1.105771898 1.474178304 1.469141726 1.422599998 1 21.35235422 2.233711771 24.9999103 1.393407397 1.211734172 0.148581237 0.159743461 168.6360805 869452.1715 0.053520464 0.040790882 171.2820178 -2.233711771 -0.181673225 ELNDIRFEFTPGR ddPTM_SK-BR-3_Pertuzumab_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 87.863 0.0074532 225300000 159830 290240 246310 261030 375640 211760 305490 248930 486940 FALSE TRUE 149826.5256 311729.6716 252152.5895 267728.4717 346138.7497 272891.6744 259684.6105 280009.4585 405666.5682 0.369334171 0.768438161 0.621575967 0.659971742 0.853259245 0.672699443 0.640142991 0.69024534 1 18.62993489 -5 0.194470678 2.420319836 0.612711122 0.474935384 0.118235707 129.472967 1.274342305 71.62716615 0.28416197 1.00E-05 5 -1.807608713 ELNEDKLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELNEDKLEK 9 1 O00567;A0A494C128;Q5JXT2 O00567 NOP56 Nucleolar protein 56 0 ; 113.47 0.0016368 621820000 2711600 1605840 2038830 1821590 1860700 1454900 2766100 1647740 2250500 FALSE TRUE 2541885.796 1724738.064 2087192.01 1868335.083 1714568.128 1874906.012 2351348.984 1853463.966 1874877.011 1.355761355 0.919920642 1.113242094 0.996510743 0.91449632 1.000015468 1.254135055 0.98857896 1 20.83836453 -0.601371283 7.629054608 0.99999695 1.063162167 0.0211511 0.141894001 0 0 0.127684891 0.030095617 0.250396767 0.601371283 0.063165217 ELNHMLSDTGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 ELNHMLSDTGNR 12 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;;;;;;;;; 213.18 1.16E-08 10827150000 4193645 4627228 4692190 4251539 5592240 4457549 4995740 4662431 6420990 FALSE TRUE 3931172.245 4969832.776 4803490.963 4360640.689 5153048.028 5744371.034 4246675.165 5244545.774 5349285.288 0.734896726 0.929064821 0.897968739 0.815181927 0.963315238 1.07385767 0.793877114 0.980419905 1 22.35091472 2.721684627 24.56223624 0.946104953 0.867357626 0.285383018 0.087486807 1210.968816 1762507.065 0.027714779 0.026200271 526.8471402 -2.721684627 -0.078747326 ELNHMLSDTGNRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ELNHMLSDTGNRK 13 1 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;;;;;; 138.42 3.20E-05 5571500000 6814590 6289500 6667780 6026600 7983240 5413960 7711140 6469470 10413740 FALSE TRUE 6388076.976 6755181.124 6825942.89 6181252.759 7356268.533 6976882.364 6554926.144 7277197.571 8675619.519 0.736325165 0.778639624 0.786796018 0.712485459 0.847924291 0.804194138 0.755557125 0.838810134 1 23.04853535 -4.999999998 0.242301984 2.282710353 0.759005551 0.78404643 0.037218507 76.16021958 0.759046608 48.10531749 0.053961295 1.00E-05 4.999999998 -1.523704803 ELNHYLEAEKSCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELNHYLEAEKSCR 13 1 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 66.498 0.050805 1631200000 8667.2 0 11730 0 0 0 0 0 10251 FALSE TRUE 8124.735423 0 12008.24114 0 0 0 0 0 8540.041876 0.951369506 0 1.406110335 0 0 0 0 0 1 13.06002743 4.757876697 23.30347958 0.306960664 0.951371004 0.142960806 0.500420127 3780.372331 4560562.645 0.122467916 4.060273108 57263.34285 -4.757876697 0.64441034 ELNLQDFSHLDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELNLQDFSHLDHR 13 0 Q5VZK9;Q5VZK9-2;Q5VZK9-3;A0A0U1RR91;Q5VZK9-4 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 0 ;; 151.54 2.59E-05 319824000 163278 201979 202854 188813 232194 181492 218591 207867 242407 FALSE TRUE 153058.7214 216933.7353 207665.7927 193658.2612 213958.4199 233885.7941 185815.3088 233819.6525 201947.7057 0.757912653 1.074207477 1.028314691 0.95895252 1.059474378 1.158150291 0.920115969 1.157822773 1 17.62362223 4.742818478 24.84974459 1.040012225 0.757912532 0.58335792 0.076061102 271.9725739 1587223.419 0.016354412 0.127411848 55311.88739 -4.742818478 -0.282099694 ELNNYEIRPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELNNYEIRPGR 11 1 B7Z8Z7;A0AV96;A0AV96-2;D6R9D6;D6RBS9;D6REZ6;D6R9M7 B7Z8Z7 RBM47 RNA-binding protein 47 0 ;;; 204.49 3.01E-08 2062530000 1102610 1261950 1121490 1203390 1252340 1076470 1178610 1036940 1289620 FALSE TRUE 1033599.608 1355386.091 1148092.272 1234271.025 1153986.268 1387229.414 1001888.372 1166404.242 1074374.091 0.962048152 1.261558802 1.068615003 1.148827988 1.074100984 1.291197755 0.932532142 1.085659317 1 20.03506499 1.691910653 12.80105847 1.007724825 1.139654741 0.265281065 0.100346806 0.149498942 34.33968238 0.041630826 0.022830547 49.19383191 -1.691910653 0.131929916 ELNS(ph)NHDGADETSEKEQQEAIEHIDEVQNEIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 33 1 Q01105-2 Q01105-2 SET Protein SET 1 ELNS(0.333)NHDGADET(0.333)S(0.333)EKEQQEAIEHIDEVQNEIDR 121.92 6.55E-08 405670000 250720 128170 168120 136130 126910 142870 145990 122040 115690 TRUE FALSE 235027.8827 137659.8402 172107.8858 139623.3263 116943.0005 184114.2497 124100.1548 137276.9626 96380.59161 2.438539532 1.428294202 1.785711033 1.448666416 1.21334595 1.910283457 1.28760524 1.424321643 1 16.55645504 4.740609245 24.75172616 1.48396634 2.438539904 0.582303668 0.263884577 111.7293371 1349814.091 0.056515618 0.37154081 55031.23323 -4.740609245 0.954573565 ELNS(ph)NHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK 44 2 Q01105-2 Q01105-2 SET Protein SET 1 ELNS(0.544)NHDGADET(0.228)S(0.228)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK 96.219 3.12E-05 846750000 358930 228410 285400 277470 384020 224850 398600 257880 442960 TRUE FALSE 336465.212 245321.7141 292169.8228 284590.35 353860.6183 289760.5449 338833.6304 290076.8857 369027.1144 0.911762846 0.664779645 0.791729961 0.771190893 0.958901404 0.785201232 0.918180852 0.786058461 1 18.4933673 2.84241476 8.683319811 0.878698991 0.765461837 0.235954464 0.089612468 0.40513631 30.91584483 0.024488643 0.025993758 695.6883971 -2.84241476 -0.113237154 ELNSNHDGADET(ph)SEKEQQEAIEHIDEVQNEIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 33 1 Q01105-2 Q01105-2 SET Protein SET 1 ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.568)S(0.432)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.56)S(0.44)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.647)S(0.353)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.548)S(0.452)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.557)S(0.443)EKEQQEAIEHIDEVQNEIDR 431.02 6.68E-208 4818071000 1120725 784932 1028065 925029 929309 808268 1239244 908035 1012702 TRUE FALSE 1050580.823 843049.182 1052451.187 948766.8102 856324.8198 1041601.85 1053430.867 1021405.169 843675.4939 1.245242786 0.999257639 1.24745971 1.124563671 1.014993118 1.234600102 1.248620915 1.21066118 1 19.68632867 2.150293675 23.82937894 1.201464566 1.125320991 0.017477871 0.106123326 32.72374651 8824.594724 0.036539414 0.026986158 141.3493041 -2.150293675 -0.076143575 ELNSNHDGADET(ph)SEKEQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK 44 2 Q01105-2 Q01105-2 SET Protein SET 1 ELNS(0.01)NHDGADET(0.495)S(0.495)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNS(0.005)NHDGADET(0.497)S(0.497)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNS(0.046)NHDGADET(0.477)S(0.477)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNS(0.121)NHDGADET(0.439)S(0.439)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNS(0.015)NHDGADET(0.492)S(0.492)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK 175 6.15E-21 2626290000 1218358 822806 1062555 1031502 1139424 783463 1512596 998458 1754908 TRUE FALSE 1142103.148 883727.4124 1087759.306 1057972.088 1049938.235 1009636.05 1285796.272 1123117.679 1462002.518 0.781190958 0.604463673 0.744020132 0.723645873 0.718150771 0.690584344 0.8794761 0.768205024 1 20.47951437 0.857080757 0.460755381 1.012431316 0.682311897 0.669413082 0.061863212 0.690736464 0.354336397 0.079168018 0.035935668 7.195827711 -0.857080757 -0.330119419 ELNSNHDGADETS(ph)EKEQQEAIEHIDEVQNEIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 33 1 Q01105-2 Q01105-2 SET Protein SET 1 ELNSNHDGADET(0.203)S(0.797)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.108)S(0.892)EKEQQEAIEHIDEVQNEIDR 260.28 9.31E-60 1383350000 345740 226040 302220 270580 241240 245720 363500 273540 279210 TRUE FALSE 324100.7506 242776.2368 309388.8011 277523.5409 222293.9835 316655.3751 308996.5496 307692.0711 232608.0472 1.393334214 1.043713834 1.330086404 1.193095184 0.955659042 1.361325968 1.328400084 1.322792031 1 17.82754148 ELNSNHDGADETSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELNSNHDGADETSEK 15 0 Q01105-2 Q01105-2 SET Protein SET 0 ;;; 234.77 1.16E-17 1704730000 2212920 1953550 2251050 2091680 1866220 1899450 2898290 1982470 1814260 FALSE TRUE 2074417.287 2098192.875 2304445.969 2145356.05 1719654.609 2447790.38 2463718.321 2229985.743 1511448.285 1.372469907 1.388200241 1.524660811 1.419404204 1.13775286 1.619499922 1.630038119 1.475396654 1 20.52750019 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 33 1 Q01105-2 Q01105-2 SET Protein SET 0 246.89 1.91E-47 296860000 49576 47453 58735 43980 44461 36895 65826 45019 47146 FALSE TRUE 46473.12666 50966.46949 60128.22194 45108.60126 40969.21241 47545.98756 55956.0024 50639.72125 39277.02803 1.183213929 1.297615223 1.530875042 1.148472874 1.04308331 1.210529155 1.424649603 1.289296156 1 15.26139815 -1.663650401 2.499359732 0.958198218 1.289934743 0.249943566 0.139404046 11597493.91 9312413.296 3094098.74 0.03582388 0.021694498 1.663650401 0.331736525 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK 44 2 Q01105-2 Q01105-2 SET Protein SET 0 ;; 50.322 0.0078432 220574000 214120 193624 214141 207677 243135 144052 290038 197881 332691 FALSE TRUE 200718.6114 207960.1224 219220.5256 213006.3434 224040.1579 185637.4739 246549.4945 222586.8784 277162.7228 0.724190502 0.750317793 0.790945201 0.768524502 0.80833438 0.669777927 0.889547815 0.803090965 1 18.08037371 0.527821949 0.593362155 1.007106088 0.756609208 0.667775924 0.052385267 0.94308352 0.59037404 0.061319513 0.020411445 3.371490564 -0.527821949 -0.25049688 ELNYFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ELNYFAK 7 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;;;; 126.67 0.0091423 2022964000 2864740 3836700 2703450 2871650 3747600 1673720 3720730 3072300 3666570 FALSE TRUE 2685441.037 4120773.26 2767577.111 2945341.401 3453278.613 2156895.793 3162841.078 3455883.418 3054595.78 0.87914776 1.349040448 0.906037103 0.964232787 1.130519015 0.706114965 1.035436865 1.131371765 1 21.54255005 3.795718095 7.73247774 0.975654805 1.14306143 0.093983853 0.164040803 0.440935678 43.82095445 0.038362763 0.069334412 6247.670178 -3.795718095 0.167406625 ELPDVLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELPDVLER 8 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ;;; 151.5 0.0010986 225526000 632540 800580 748170 808750 818040 682110 869730 721230 781570 FALSE TRUE 592950.4505 859855.7762 765916.9457 829503.8942 753794.4382 879024.0839 739322.0607 811277.1531 651120.9179 0.910661037 1.320577719 1.176305237 1.273962902 1.157687332 1.350016656 1.135460466 1.245970035 1 19.31256596 -0.619182965 8.097890249 0.999999266 1.208274983 0.195964274 0.122880075 0 0 0.102047314 0.024052783 0.240335008 0.619182965 0.208275717 ELPDVQGESDSIS(ph)PLLLHLEDDDFSENEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELPDVQGESDSISPLLLHLEDDDFSENEK 29 0 Q8IWI9-3;Q8IWI9 Q8IWI9-3 MGA MAX gene-associated protein 1 ELPDVQGES(0.001)DS(0.031)IS(0.968)PLLLHLEDDDFSENEK 143.83 4.46E-08 20789000 50724 38049 45656 43530 47158 33701 48913 37373 50694 TRUE FALSE 47549.27538 40866.18755 46738.98188 44647.0535 43454.40091 43429.93161 41578.94974 42039.10132 42232.8439 1.125883814 0.967639964 1.106697479 1.057164268 1.028924337 1.028344947 0.984516928 0.995412514 1 15.36607778 2.118913905 1.720377116 0.991960887 1.054081406 0.328202946 0.042152999 0.467047176 2.65918292 0.023162267 0.012816441 131.4964128 -2.118913905 0.062120518 ELPDVQGESDSISPLLLHLEDDDFS(ph)ENEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELPDVQGESDSISPLLLHLEDDDFSENEK 29 0 Q8IWI9-3;Q8IWI9 Q8IWI9-3 MGA MAX gene-associated protein 1 ELPDVQGESDSISPLLLHLEDDDFS(1)ENEK;ELPDVQGESDSISPLLLHLEDDDFS(1)ENEK 151.72 1.98E-08 42471000 62388 40872 44301 43007 48189 42349 74952 45126 53314 TRUE FALSE 58483.24645 43898.20541 45351.84064 44110.63243 44404.43033 54574.46882 63713.64342 50760.08043 44415.54898 1.316729114 0.988352197 1.021080268 0.993134914 0.999749668 1.228724401 1.434489607 1.142844828 1 15.4387772 2.173523985 6.137233647 1.26138374 1.044679044 0.119586716 0.147298041 0.22761781 15.92019039 0.051733467 0.038238766 149.1159105 -2.173523985 -0.216704696 ELPESGIQLGT(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ELPESGIQLGTPR 13 0 A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2;A0A087WW69;F8W8L6 A0A087WTA5 EIF2B4 Translation initiation factor eIF-2B subunit delta 1 ELPESGIQLGT(1)PR;ELPESGIQLGT(1)PR;ELPESGIQLGT(1)PR;ELPESGIQLGT(1)PR;ELPESGIQLGT(1)PR;ELPESGIQLGT(1)PR 194.77 8.20E-06 1131580000 678489 728110 814210 776292 839422 653355 889130 678143 1084280 TRUE FALSE 636023.5846 782020.022 833523.4457 796212.967 773497.1822 841967.9822 755813.2108 762810.6463 903306.6633 0.704105937 0.865730381 0.922746925 0.881442592 0.856295225 0.932095396 0.836718295 0.844464762 1 19.78485633 -0.362361719 0.017823723 1.858019689 3.04E-06 0.404280286 0.05930487 1611.415393 7.262914936 408.5038489 349.0360519 0.434148476 0.362361719 -1.858016647 ELPFGDKDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELPFGDKDTK 10 1 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ; 78.548 0.027061 605780000 1065510 653200 836970 762830 924270 622090 1020900 717290 1142320 FALSE TRUE 998821.6311 701563.6077 856823.3236 782405.5093 851681.5625 801677.2842 867825.5226 806845.2355 951659.4123 1.049557876 0.737200304 0.900346608 0.822148659 0.894943665 0.842399365 0.911907676 0.847829828 1 19.86008582 -1.221821821 0.434359752 1.063730576 0.860640164 0.170762411 0.080403788 32.05442839 3.538061306 2.469955061 0.040877518 0.06000372 1.221821821 -0.203090412 ELPGFLQSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELPGFLQSGK 10 0 P25815 P25815 S100P Protein S100-P 0 ; 159.4 1.79E-05 189723000 552310 596970 519640 570870 573110 501310 720490 474260 417820 FALSE TRUE 517741.903 641170.2799 531966.1062 585519.4907 528100.2524 646030.0589 612459.2132 533472.405 348083.1428 1.487408723 1.842003249 1.528273107 1.682125385 1.517166985 1.855964796 1.75951989 1.532600518 1 18.40907242 0.88306662 4.765935561 1.000048993 1.678665935 0.722679065 0.12914579 0.422190261 16.54088393 0.11620259 0.029431242 7.639529641 -0.88306662 0.678616942 ELPGHTGYLSCCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 257.95 6.44E-24 921098000 377660 877410 326466 341874 1190860 267211 373371 909120 1022720 FALSE TRUE 354022.9347 942374.3493 334209.9277 350647.0656 1097334.659 344350.4779 317387.4848 1022625.633 852021.425 0.415509428 1.106045367 0.392255309 0.41154724 1.287919091 0.404157064 0.372511155 1.200234646 1 19.70053018 1.225126763 24.9890868 1.100117604 0.641537634 0.267598028 0.324632187 365.1873924 679286.0251 0.292538582 0.074805781 16.79294102 -1.225126763 -0.45857997 ELPPAAAIGATSLVAAPHS(ph)SSSSPSKDSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.163)S(0.163)S(0.163)S(0.163)S(0.163)PS(0.163)KDS(0.011)S(0.011)R;ELPPAAAIGATSLVAAPHS(0.186)S(0.186)S(0.186)S(0.186)S(0.186)PS(0.056)KDS(0.007)S(0.007)R;ELPPAAAIGATSLVAAPHS(0.19)S(0.19)S(0.19)S(0.19)S(0.19)PS(0.048)KDS(0.001)S(0.001)R;ELPPAAAIGATSLVAAPHS(0.192)S(0.192)S(0.192)S(0.192)S(0.192)PS(0.04)KDSSR 214.15 2.59E-28 890310000 261297 440144 481737 500575 513802 405477 601045 454276 560562 TRUE FALSE 244942.8872 472732.7197 493164.0291 513420.602 473450.0635 522531.6275 510923.8821 510993.3586 467000.5808 0.524502318 1.012274372 1.056024445 1.09940035 1.013810438 1.118910016 1.094054061 1.094202833 1 18.83306482 4.763911119 3.056796908 1.069560426 0.419659593 0.952006702 0.038035867 0.081778748 1.0914163 0.009152 0.132715916 58064.55728 -4.763911119 -0.649900833 ADYDTLS(ph)LR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ADYDTLSLR 9 0 Q9Y446;Q9Y446-2;E9PQ15;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 1 ADYDTLS(1)LR;ADYDTLS(1)LR;ADYDT(0.002)LS(0.998)LR 116.75 0.0013258 497880000 493277 542906 371883 368345 574660 222526 695610 497533 1219250 TRUE FALSE 462403.6731 583103.3251 380704.2404 377797.3563 529528.5217 286765.6438 591309.7382 559651.0903 1015749.298 0.455234056 0.574062248 0.374801382 0.371939569 0.521318127 0.282319313 0.582141419 0.550973642 1 19.95411294 0.621638424 1.19321958 0.999205308 0.445354848 0.787674308 0.089786994 0.550642615 1.188325617 0.080304425 0.024540254 4.184450393 -0.621638424 -0.55385046 ELPPFWEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELPPFWEQR 9 0 A0A0C4DGA6;Q14527-2;Q14527 A0A0C4DGA6 HLTF Helicase-like transcription factor 0 ; 99.442 0.01241 42427000 54732 54431 61013 52989 54764 50068 52121 50025 59999 FALSE TRUE 51306.42182 58461.12788 62460.25717 54348.78745 50463.05635 64521.81881 44305.93992 56270.73137 49984.77929 1.0264409 1.169578594 1.249585535 1.087306741 1.009568454 1.290829323 0.886388628 1.125757324 1 15.60920123 1.731925668 24.99999992 1.001126137 1.148243384 0.268554408 0.104101952 0.773136365 2893.406399 0.045239892 0.02508778 53.94182895 -1.731925668 0.147117247 ELPPLS(ph)PSLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELPPLSPSLSR 11 0 Q86UU1-3;Q86UU1-2;Q86UU1 Q86UU1-3 PHLDB1 Pleckstrin homology-like domain family B member 1 1 ELPPLS(0.925)PS(0.075)LSR;ELPPLS(0.904)PS(0.095)LSR 162.49 2.63E-05 77870000 178598 223410 196158 212130 234930 175134 226830 184520 209032 TRUE FALSE 167419.87 239951.5089 200810.9604 217573.6149 216479.5455 225692.3427 192818.9473 207557.7282 174143.2088 0.961391898 1.377897597 1.153136903 1.249394774 1.243112189 1.296015758 1.107243565 1.191879543 1 17.40991469 0.735948371 0.934696366 1.002051503 1.223701132 0.221966484 0.112955431 1.20905878 1.946714838 0.096518056 0.032008663 5.444379257 -0.735948371 0.221649629 ELPPS(ph)PEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELPPSPEKK 9 1 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;B5MEG9;P27816-3;P27816-6;P27816;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 ELPPS(1)PEKK;ELPPS(1)PEKK;ELPPS(1)PEKK;ELPPS(1)PEKK 72.34 0.020117 1105040000 5941000 2656710 3860400 3626000 3328160 2555470 4623160 2605530 2793470 TRUE FALSE 5569163.415 2853415.573 3951970.511 3719049.299 3066779.739 3293192.704 3929960.077 2930836.156 2327221.81 2.393052261 1.226103829 1.698149482 1.598063959 1.31778575 1.4150747 1.688691666 1.259371214 1 21.15017729 8 0.044475159 9.25E-10 4.142901668 0.402723408 0.294212131 782.1117021 2.637923629 62.86873891 232.9116036 99999999.97 -8 4.142901667 ELPSFLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELPSFLGK 8 0 P26447 P26447 S100A4 Protein S100-A4 0 ; 148.38 0.0012147 2080200000 3574900 3806800 3560500 3501000 4224600 2769560 4141800 3809400 5268400 FALSE TRUE 3351153.39 4088659.433 3644956.741 3590841.587 3892816.957 3569087.012 3520775.541 4285011.976 4389070.005 0.763522429 0.931554846 0.830462202 0.818132676 0.886934351 0.813176142 0.802168919 0.976291554 1 22.06548385 1.182214598 7.034522634 0.992453978 0.842331633 0.648295649 0.046649619 0.150996603 14.78799757 0.043130573 0.010967555 15.21299063 -1.182214598 -0.150122345 ELPSFLGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELPSFLGKR 9 1 P26447 P26447 S100A4 Protein S100-A4 0 ; 89.029 0.019857 1214420000 1956420 4138000 2958600 3411700 4663200 3008000 4090500 3121200 6196400 FALSE TRUE 1833971.165 4444381.826 3028779.389 3499249.998 4296971.082 3876360.769 3477167.499 3510888.691 5162180.81 0.355270618 0.860950437 0.586724778 0.677862734 0.832394533 0.750915342 0.673584988 0.680117342 1 22.29954924 -5 0.18168664 2.233801085 0.629639796 0.381398459 0.135655587 151.7452922 1.466378938 67.98353395 0.379982544 1.00E-05 5 -1.604161289 ELPSLSPAPDTGLS(ph)PSKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELPSLSPAPDTGLSPSKR 18 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;A0A0A0MSL0 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 ELPSLSPAPDT(0.325)GLS(0.58)PS(0.095)KR;ELPSLSPAPDT(0.007)GLS(0.754)PS(0.239)KR;ELPSLSPAPDT(0.211)GLS(0.667)PS(0.122)KR 151.6 2.85E-08 1176920000 759070 589230 687700 612590 696660 620610 899080 655980 768680 TRUE FALSE 711561.1637 632857.2023 704012.5688 628310.0965 641947.1338 799770.0322 764271.3006 737880.547 640382.3421 1.111150506 0.988248989 1.099362869 0.981148378 1.002443527 1.248894574 1.193460922 1.152249989 1 19.288574 2.250476081 24.99980932 1.170851153 1.035956659 0.332352762 0.076169175 191.75514 402320.5897 0.02401349 0.01994187 178.022986 -2.250476081 -0.134894494 ELPSQASGGLANPPPVNLEDS(ph)LDEDLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELPSQASGGLANPPPVNLEDSLDEDLIR 28 0 Q9NPG3;Q9NPG3-2;K7EJT1 Q9NPG3 UBN1 Ubinuclein-1 1 ELPSQASGGLANPPPVNLEDS(1)LDEDLIR 92.121 0.0017615 18511000 13452 12589 13052 14961 15327 14301 16850 14907 14926 TRUE FALSE 12610.06333 13521.10266 13361.5996 15344.92459 14123.27925 18429.46654 14323.49893 16768.17176 12434.75417 1.014098321 1.087363889 1.074536691 1.234035219 1.135790788 1.482093356 1.151892408 1.348492421 1 13.60209037 3.204185368 1.817373155 1.248544813 1.058454431 0.252600353 0.1301602 0.395771885 2.681821642 0.037608168 0.051890066 1600.240907 -3.204185368 -0.190090383 ELPTAFDYVEFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELPTAFDYVEFTR 13 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 155.48 0.00010867 77202000 43280 51609 44998 46848 51855 42548 53546 40560 65714 FALSE TRUE 40571.18206 55430.18406 46065.37381 48050.19899 47782.51747 54830.91689 45517.2744 45624.00528 54745.90887 0.741081533 1.012499111 0.841439566 0.87769479 0.872805265 1.001552774 0.83142787 0.833377438 1 15.74046354 ELQAHGADELLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELQAHGADELLKR 13 1 O15144;C9JTV5;G5E9J0 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 121.31 0.00016106 517090000 503440 432510 425280 450640 499030 333540 482490 388810 502690 FALSE TRUE 471930.5891 464533.4904 435367.8424 462204.1853 459838.1968 429827.5834 410145.1037 437353.7844 418787.7915 1.126896721 1.109233602 1.039590578 1.103671584 1.098021972 1.026361303 0.979362608 1.044332698 1 18.67585986 2.141234368 4.420527399 1.005136485 1.090087087 0.691577012 0.027538981 0.126480406 4.391548671 0.010851427 0.007863361 138.4313226 -2.141234368 0.084950602 ELQDAQEHDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELQDAQEHDAR 11 0 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 0 147.26 3.54E-05 434470000 388000 421630 396390 469110 507260 340670 506810 416790 525490 FALSE TRUE 363715.7726 452847.9239 405792.558 481148.1568 467421.8458 439015.8987 430818.5455 468827.149 437782.3242 0.830814203 1.034413449 0.926927689 1.09905798 1.067703788 1.00281778 0.984093056 1.070913838 1 18.73985418 4.74210884 24.65187768 1.015841584 0.830814117 0.59259663 0.049807129 214.7106955 1491659.325 0.011867052 0.087178711 55221.58144 -4.74210884 -0.185027467 ELQELVQYPVEHPDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ELQELVQYPVEHPDK 15 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;;; 219.95 1.74E-12 12523108000 14437280 11267870 13033070 11595410 12395780 10451330 15702150 11435830 13115520 FALSE TRUE 13533676.42 12102154.82 13342220.58 11892967.85 11422265.44 13468459.31 13347758.38 12863618.55 10926454.98 1.238615492 1.107601215 1.221093264 1.088456217 1.045377065 1.232646758 1.221600089 1.177291131 1 23.38132207 3.257279143 24.98909786 1.147475478 1.176208541 0.072694487 0.08158853 1187.998245 1585958.82 0.022505679 0.030426789 1808.336061 -3.257279143 0.028733063 ELQQAELPNRS(ph)PGFGIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELQQAELPNRSPGFGIK 17 1 F8VU11;Q6NWY9-2;Q6NWY9-3;Q6NWY9 F8VU11 PRPF40B Pre-mRNA-processing factor 40 homolog B 1 ELQQAELPNRS(1)PGFGIK;ELQQAELPNRS(1)PGFGIK 220.13 2.49E-15 652400000 1943430 1505330 1665010 1660410 2014830 1298690 2068930 1665330 2121750 TRUE FALSE 1821794.185 1616786.199 1704504.823 1703018.932 1856593.379 1673600.721 1758713.154 1873250.116 1767616.218 1.0306503 0.914670381 0.96429576 0.963455141 1.050337375 0.946812268 0.994963237 1.059760652 1 20.75337364 2.963669826 24.09939069 1.003851995 0.958075166 0.174312676 0.041930986 553.5188958 367172.8566 0.01202569 0.012760048 919.7500635 -2.963669826 -0.045776829 ELQQELQEYEVVTESEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELQQELQEYEVVTESEKR 18 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ; 235.7 1.35E-23 188883000 184133 133325 164888 162060 140535 137017 208208 140094 115814 FALSE TRUE 172608.4442 143196.5217 168799.2212 166218.734 129497.948 176571.5836 176989.1433 157585.0443 96483.89521 1.788987103 1.484149468 1.749506701 1.722761437 1.342171641 1.83006276 1.834390526 1.633278216 1 16.55800053 0.946525234 21.88356625 0.999999998 1.67606879 0.650436117 0.155429199 2442.446059 999528.1974 0.146760998 0.03669025 8.841485396 -0.946525234 0.676068792 ELRAPS(ph)PPVEHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELRAPSPPVEHPR 13 1 Q86WR7;Q86WR7-2 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 ELRAPS(1)PPVEHPR;ELRAPS(1)PPVEHPR;ELRAPS(1)PPVEHPR;ELRAPS(1)PPVEHPR 135.27 5.19E-05 507934000 216071 331887 308886 307908 396661 222836 337997 249630 555282 TRUE FALSE 202547.5018 356460.2588 316212.9218 315809.4406 365508.8451 287165.1358 287317.4877 280796.855 462601.8469 0.437844127 0.7705552 0.68355309 0.68268089 0.790115404 0.620760893 0.62109023 0.606994669 1 18.8194115 -1.454082253 3.127324328 1.006561431 0.66554921 0.551572177 0.097991759 38526585.46 47666377.47 2213474.517 0.022616057 0.035149386 1.454082253 -0.341012221 ELS(ph)NS(ph)PLRENSFGSPLEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ELS(0.999)NS(0.992)PLRENS(0.008)FGS(0.001)PLEFR;ELS(0.991)NS(0.988)PLRENS(0.013)FGS(0.008)PLEFR 78.916 0.0053824 579120000 103250 95616 98975 93352 108699 90940 113257 99014 117953 TRUE FALSE 96787.76681 102695.5081 101322.7337 95747.57036 100162.219 117192.9017 96275.16428 111376.1159 98265.88229 0.984957999 1.045077963 1.031107963 0.974372469 1.019298018 1.192610283 0.979741514 1.133415925 1 16.58440298 2.426128943 24.99999882 1.073429374 1.01643762 0.207232361 0.063041164 177.9625966 87248.59165 0.019739992 0.016515665 266.7650581 -2.426128943 -0.056991754 ELS(ph)NSPLRENS(ph)FGSPLEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ELS(0.842)NS(0.158)PLRENS(0.999)FGS(0.001)PLEFR 127.53 1.32E-05 107280000 232390 250090 231220 241390 256200 182140 287520 245570 268630 TRUE FALSE 217845.1247 268606.9238 236704.6476 247584.4761 236079.0855 234720.8612 244409.0452 276229.9551 223793.9176 0.973418434 1.200242289 1.057690263 1.106305653 1.054895003 1.048825919 1.092116568 1.234305016 1 17.7718113 1.445895897 24.99999925 1.132505247 1.085421879 0.027029292 0.079669917 68.12347579 54549.95588 0.038909768 0.017949174 27.91874531 -1.445895897 -0.047083368 ELS(ph)PAALEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ELSPAALEK 9 0 O75683 O75683 SURF6 Surfeit locus protein 6 1 ELS(1)PAALEK;ELS(1)PAALEK;ELS(1)PAALEK;ELS(1)PAALEK;ELS(1)PAALEK;ELS(1)PAALEK;ELS(1)PAALEK 172.61 5.88E-05 2617330000 4960610 3451220 4262010 3762800 3858190 3409440 5265470 3531940 4577970 TRUE FALSE 4650134.275 3706751.92 4363106.89 3859359.818 3555183.321 4393689.98 4475961.656 3972910.484 3813877.232 1.219266901 0.971911704 1.144008216 1.011925551 0.932170362 1.152027114 1.173598777 1.041698577 1 21.86282697 ELS(ph)PAGSISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ELSPAGSISK 10 0 A0A494C0Q6;A0A494C0K5;A0A494C0W0;O95453-2;O95453-3;O95453;O95453-4 A0A494C0Q6 PARN Poly(A)-specific ribonuclease PARN 1 ELS(1)PAGSISK;ELS(1)PAGSISK;ELS(1)PAGSISK;ELS(1)PAGSISK;ELS(1)PAGSISK;ELS(1)PAGSISK 245.78 1.54E-12 8418800000 10144700 8568560 8868620 8627330 9247800 6714350 10478300 8025870 10342000 TRUE FALSE 9509761.336 9202985.098 9078987.854 8848721.894 8521515.092 8652673.847 8907176.191 9027917.537 8615853.388 1.103751527 1.068145508 1.053753754 1.02702791 0.989050615 1.004273571 1.033812414 1.047826272 1 23.03856227 3.868209361 1.006156748 1.017200551 1.09655754 0.702669644 0.018774395 0.415222959 0.732204159 0.006825873 0.02636005 7382.600379 -3.868209361 0.079356988 ELS(ph)PEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELSPEAR 7 0 Q9P0B6 Q9P0B6 CCDC167 Coiled-coil domain-containing protein 167 1 ELS(1)PEAR 79.893 0.032928 101730000 284940 274590 245480 241210 315980 218390 326410 261880 297780 TRUE FALSE 267106.114 294920.9293 251302.9015 247399.857 291164.2054 281435.6477 277467.8507 294576.2945 248078.5943 1.076699563 1.188820544 1.01299712 0.997264023 1.173677262 1.134461635 1.118467523 1.187431327 1 17.92043773 2.703360793 24.99586198 1.129998573 1.07959974 0.112117458 0.071033284 1414.882495 1004725.486 0.022394839 0.021114658 505.0807226 -2.703360793 -0.050398833 ELS(ph)PQHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELSPQHK 7 0 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 ELS(1)PQHK;ELS(1)PQHK 81.547 0.01733 1779980000 2850200 1956290 2342500 2059310 2202100 1747950 2518400 2009770 1977900 TRUE FALSE 2671811.07 2101135.747 2398065.206 2112155.381 2029155.949 2252554.789 2140789.3 2260694.209 1647775.712 1.621465258 1.275134553 1.455334721 1.281822135 1.231451546 1.367027547 1.29919945 1.371967187 1 20.65208845 -4.484567592 0.144082934 4.55E-15 1.47613278 0.574405966 0.103878765 85.52993543 0.857050406 25.36793596 0.551902892 3.28E-05 4.484567592 1.47613278 ELS(ph)PQHKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ELSPQHKR 8 1 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 ELS(1)PQHKR;ELS(1)PQHKR;ELS(1)PQHKR;ELS(1)PQHKR;ELS(1)PQHKR;ELS(1)PQHKR 82.171 0.01284 5448140000 5713380 5094280 5376720 4930290 5814700 4139430 6687620 4774310 8030290 TRUE FALSE 5355789.744 5471465.792 5504258.337 5056809.588 5358036.917 5334416.243 5684873.466 5370393.113 6689982.721 0.800568547 0.81785948 0.822761219 0.755877825 0.800904448 0.797373695 0.849759066 0.802751418 1 22.67357105 -0.672350997 0.572470176 1.033917501 0.804163676 0.872427162 0.023345515 4.752081175 1.122392629 0.331410561 0.009837732 0.212641978 0.672350997 -0.229753824 ELSDDCFQQWGVRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELSDDCFQQWGVRPR 15 1 P42785;P42785-2 P42785 PRCP Lysosomal Pro-X carboxypeptidase 0 147.35 3.40E-06 199910000 94090 119930 107580 111390 129740 93248 139850 116360 109850 FALSE TRUE 88201.07486 128809.742 110131.8484 114248.456 119550.7437 120167.1838 118880.7908 130887.8021 91515.32534 0.963784749 1.407520997 1.203425197 1.248407909 1.306346705 1.313082627 1.299026041 1.430228234 1 16.48172574 4.752098159 24.55166137 1.28886395 0.963784472 0.401039746 0.118994716 1609.933996 2919707.379 0.024513928 0.478309799 56506.46764 -4.752098159 -0.325079478 ELSDFISYLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELSDFISYLQR 11 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;; 199.67 1.15E-07 2559359000 1316938 3028602 1957286 1968074 2890548 1756429 1991530 2258864 1865944 FALSE TRUE 1234513.201 3252842.843 2003713.748 2018578.111 2663536.02 2263481.539 1692918.565 2540888.143 1554505.892 0.79415151 2.092525258 1.288971472 1.298533586 1.71342935 1.456077813 1.089039658 1.634531047 1 20.56802465 -0.018344715 0.335438588 0.896293437 1.527189419 0.077679692 0.361660753 10.15832183 1.62826128 1.846317656 0.331246834 0.958639423 0.018344715 0.630895982 ELSDFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ELSDFLR 7 0 E7ETZ4;Q9Y6E2;Q75MG1;B5MCH7;B5MCE7;E9PFD4 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 ;;;;; 158.38 0.0033101 643133000 1138540 2100350 1200830 1233210 2357020 857383 1211330 1975260 1881600 FALSE TRUE 1067280.814 2255862.099 1229314.255 1264856.256 2171909.157 1104895.554 1029702.312 2221875.559 1567548.804 0.680859703 1.439101668 0.784227101 0.806900718 1.38554484 0.7048556 0.656886924 1.41742034 1 20.58007893 ELSDIAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 16 ELSDIAHR 8 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;;;;;;;;;; 205.77 7.68E-05 1.47483E+11 55238782 73687646 64438154 65697484 68874158 55836407 72522365 58424052 56658498 FALSE TRUE 51781485.24 79143555.98 65966657.44 67383392.67 63465059.46 71955471.27 61648309.63 65718423.5 47201828.66 1.097022864 1.676705294 1.39754453 1.427558944 1.344546626 1.524421263 1.306057655 1.39228554 1 25.49233942 -0.266381371 0.491025185 0.93784889 1.445123453 0.391707726 0.150618963 5.653812217 1.398171304 0.773717585 0.068947786 0.541525147 0.266381371 0.507274563 ELSDIALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELSDIALR 8 0 P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;J3QKK1 P09972 ALDOC Fructose-bisphosphate aldolase C;Fructose-bisphosphate aldolase 0 ;; 107.43 0.0093167 294583000 792940 1303780 1081120 1187550 1237530 934100 1102640 965280 980930 FALSE TRUE 743311.3008 1400313.228 1106764.677 1218024.544 1140339.386 1203759.506 937309.3684 1085797.333 817206.4459 0.909575915 1.713536689 1.354326905 1.49047349 1.395411639 1.473017635 1.146967664 1.328669565 1 19.64034106 1.116710354 0.802304126 1.015365293 1.431087669 0.200627695 0.213782328 0.76599165 1.121026495 0.183266699 0.068869466 13.08309075 -1.116710354 0.415722375 ELSDLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELSDLAR 7 0 P61077-3;P61077-2;P61077;A0A087WY85;D6RA11;D6RGD0;D6R933;D6RIZ3;D6R980;D6R9F6 P61077-3 UBE2D3 Ubiquitin-conjugating enzyme E2 D3 0 ;;; 148.21 0.0048845 810050000 1527870 2207350 1657740 1655270 2211270 1454300 1909000 1951910 1970720 FALSE TRUE 1432243.344 2370784.491 1697062.376 1697747.031 2037605.774 1874132.801 1622763.172 2195610.26 1641794.101 0.872364777 1.444020593 1.033663341 1.034080358 1.241084843 1.141515127 0.988408456 1.33732376 1 20.64684178 -4.745269206 0.304806248 3.23E-37 1.150739473 0.043139012 0.171052283 755.6497223 8.055215601 482.8424918 0.155076247 1.80E-05 4.745269206 1.150739473 ELSDQATAS(ph)PIVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELSDQATASPIVAR 14 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 ELSDQATAS(1)PIVAR;ELSDQAT(0.002)AS(0.998)PIVAR;ELSDQATAS(1)PIVAR;ELSDQATAS(1)PIVAR 230.45 3.80E-12 589700000 976240 984410 1107650 1082980 1129280 969300 1147540 946260 1145810 TRUE FALSE 915138.881 1057296.741 1133923.981 1110771.1 1040590.904 1249121.175 975477.0302 1064402.644 954566.9088 0.958695375 1.10761931 1.187893662 1.163638808 1.090118351 1.308573724 1.021905349 1.115063422 1 19.8644868 1.001004773 1.460012769 1.006374576 1.133888533 0.132030068 0.093891063 0.773180569 3.365472681 0.081695744 0.024300987 10.02316254 -1.001004773 0.127513957 ELSEALGQIFDSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELSEALGQIFDSQR 14 0 Q08380;K7ESM3;K7EKQ5;K7EP36;K7EJY8 Q08380 LGALS3BP Galectin-3-binding protein 0 ;;; 147.18 1.89E-05 83153000 132360 255962 160679 179757 285466 183778 204072 290738 172760 FALSE TRUE 124075.8239 274913.6928 164490.3818 184369.8689 263046.6519 236831.7252 173473.2981 327037.2793 143925.2399 0.862085232 1.910114535 1.142887668 1.281011371 1.827661722 1.645519058 1.205301434 2.272271906 1 17.13496009 2.777137146 24.83472136 1.574099993 1.374850175 0.091216367 0.426157208 1693.269887 1090086.869 0.120072304 0.127353767 598.6005971 -2.777137146 -0.199249818 ELSEALTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELSEALTR 8 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 193.16 0.00040043 372950000 544530 627360 610920 620780 585100 498750 673200 493490 567270 FALSE TRUE 510448.8393 673810.3872 625411.3109 636710.2658 539148.6062 642731.0285 572259.9097 555103.3128 472588.9723 1.080111618 1.425785252 1.323372629 1.347281259 1.14084043 1.360021215 1.210904069 1.174600647 1 18.85022644 0.822028045 0.703933562 0.996283431 1.309583723 0.395674599 0.105084221 0.8239968 0.864442027 0.097241233 0.03671101 6.637859333 -0.822028045 0.313300292 ELSEPMEFQYLPDTDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ELSEPMEFQYLPDTDDR 17 0 Q04206;Q04206-4;Q04206-2;A0A087X0W8;E9PKH5;Q2TAM5;Q04206-3 Q04206 RELA Transcription factor p65 0 ;;;;; 294.52 1.01E-45 320077000 166650 181096 181682 177717 192488 174258 203403 165208 203289 FALSE TRUE 156219.674 194504.5363 185991.5828 182277.5191 177370.7689 224563.4558 172904.6085 185834.5825 169358.7526 0.922418662 1.148476434 1.098210633 1.076280477 1.047307956 1.325963095 1.020936951 1.097283604 1 17.36972302 4.746377764 24.00650359 1.108818756 0.922418501 0.277703184 0.090293991 673.4675188 2068135.14 0.019347827 0.204445206 55767.06191 -4.746377764 -0.186400255 ELSEQIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELSEQIQR 8 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 237.81 2.73E-08 1275340000 724880 992430 858670 838550 1063390 723560 862990 811640 1024610 FALSE TRUE 679511.0547 1065910.55 879038.0579 860068.6127 979875.6389 932440.026 733592.6611 912975.0406 853595.9718 0.796057007 1.248729592 1.029805771 1.007582792 1.147938453 1.092366947 0.85941439 1.069563436 1 19.70319384 1.773086377 25 0.962228264 1.075329625 0.056409412 0.12640471 65.56438116 47496.74561 0.053546644 0.029710654 59.30432636 -1.773086377 0.113101361 ELSESVQQQSTPVPLIS(ph)PKR ddPTM_SK-BR-3_Pertuzumab_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(0.002)PVPLIS(0.998)PKR 256.12 2.17E-36 452230000 337510 383090 343640 414770 558260 198494 358560 335770 852480 TRUE FALSE 316385.8516 411454.3822 351791.3031 425413.7004 514416.5115 255795.9955 304797.2567 377691.6236 710195.5808 0.445491158 0.579353622 0.495344258 0.599009219 0.724330769 0.360176834 0.429173688 0.531813537 1 19.43785686 -1.544667986 2.525499831 1.034111086 0.51818644 0.690267044 0.100913384 3964462.82 3617509.088 915825.5263 0.025965632 0.028531987 1.544667986 -0.515924646 ELSFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ELSFGR 6 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;;;;; 185.89 0.0048112 2787226000 2054058 2604026 1993972 1948320 2100759 1459702 2386894 2005819 2329742 FALSE TRUE 1925498.176 2796830.795 2041269.957 1998317.19 1935773.862 1881094.271 2029001.404 2256249.918 1940893.009 0.99206817 1.441002044 1.051716889 1.029586474 0.997362478 0.96919009 1.045395802 1.162480315 1 20.88828916 3.71052338 5.4903973 1.032143219 1.249143873 0.277123851 0.11848858 0.152052664 14.73343792 0.028366726 0.046907788 5134.798197 -3.71052338 0.217000654 ELSHATIDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELSHATIDSK 10 0 Q9Y263;E5RIM3 Q9Y263 PLAA Phospholipase A-2-activating protein 0 ;;; 107.83 0.0022318 613830000 3343120 3064230 3310080 3174030 3483800 3146150 3932160 2684690 3994660 FALSE TRUE 3133880.087 3291108.778 3388596.661 3255480.983 3210196.401 4054392.432 3342569.112 3019879.456 3327925.44 0.941691797 0.988937053 1.018230944 0.978231346 0.964623895 1.218294251 1.004400241 0.907436032 1 21.66619168 6.132034899 0.602785732 1.025246389 0.551392058 0.064745573 0.080116323 43.40040041 3.210226522 0.033681048 20.7644675 1355298.317 -6.132034899 -0.473854332 ELSKEDLSPAFDHS(ph)PNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELSKEDLSPAFDHSPNK 17 1 K7EIY0;K7ENP9;K7EIE9;D3DUJ3;K7EQG9;P17706-3;P17706-2;P17706-4;P17706 K7EIY0 PTPN2 Protein-tyrosine-phosphatase;Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 2 1 ELSKEDLSPAFDHS(1)PNK;ELSKEDLSPAFDHS(1)PNK;ELSKEDLSPAFDHS(1)PNK 189.78 2.03E-10 616930000 1807610 926200 1240090 1175010 1254490 928370 1680260 1108610 1344820 TRUE FALSE 1694474.917 994776.8117 1269505.52 1205162.746 1155967.416 1196375.348 1428320.612 1247022.399 1120360.854 1.512436739 0.887907506 1.13312199 1.075691588 1.031781333 1.067848224 1.274875507 1.11305424 1 20.09553205 ELSLAGNELGDEGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELSLAGNELGDEGAR 15 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 ; 230.96 1.26E-12 271330000 223260 242890 229990 247070 285910 212040 291740 245470 305240 FALSE TRUE 209286.5551 260873.8283 235445.4714 253410.2345 263455.7819 273252.5058 247996.2954 276117.4698 254293.4721 0.823011906 1.025877016 0.92588091 0.9965267 1.036030456 1.074555723 0.975236577 1.085822092 1 17.9561349 4.741956019 24.81246179 1.007990219 0.823011829 0.62279136 0.046672567 206.1661109 1506517.602 0.01104915 0.079810479 55202.15335 -4.741956019 -0.18497839 ELSNS(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ELSNSPLR 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ELS(0.005)NS(0.995)PLR;ELS(0.084)NS(0.916)PLR;ELS(0.003)NS(0.997)PLR;ELS(0.004)NS(0.996)PLR;ELS(0.053)NS(0.947)PLR;ELS(0.001)NS(0.999)PLR 143.22 0.00063462 15558740000 13492340 13151930 13240380 12872760 12120980 12342160 14660580 11669110 8735890 TRUE FALSE 12647878.52 14125712.58 13554448.07 13203096.82 11169047.12 15905141.23 12462362.13 13126024.07 7277813.523 1.737867903 1.940928074 1.862434098 1.814157064 1.534670693 2.18542852 1.712377226 1.803566968 1 22.79507366 0.245480908 1.379971964 0.999418962 1.84398544 0.706981536 0.166678925 3.272291351 5.450306127 0.145216053 0.041861298 1.759871295 -0.245480908 0.844566478 ELSNS(ph)PLRENS(ph)FGSPLEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ELS(0.014)NS(0.986)PLRENS(1)FGSPLEFR;ELS(0.015)NS(0.985)PLRENS(1)FGSPLEFR;ELS(0.004)NS(0.996)PLRENS(1)FGSPLEFR;ELS(0.449)NS(0.559)PLRENS(0.991)FGSPLEFR;ELS(0.012)NS(0.988)PLRENS(0.975)FGS(0.025)PLEFR 272.18 1.37E-39 1024261000 1183667 1426774 1269024 1275844 1407298 1058346 1529200 1220672 1241383 TRUE FALSE 1109583.395 1532413.832 1299125.849 1308584.317 1296774.492 1363873.309 1299910.656 1373075.586 1034188.158 1.072902824 1.481755346 1.25617939 1.26532518 1.253905764 1.318786431 1.256938253 1.327684499 1 19.98006726 -1.235564781 3.195100595 0.998974041 1.293166486 0.426859203 0.100513564 10146218.11 14180873.81 105383.4532 0.023429383 0.058134671 1.235564781 0.294192445 ELSNS(ph)PLRENSFGS(ph)PLEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ELS(0.003)NS(0.997)PLRENSFGS(1)PLEFR;ELS(0.014)NS(0.986)PLRENSFGS(1)PLEFR;ELS(0.021)NS(0.979)PLRENS(0.001)FGS(0.999)PLEFR;ELS(0.009)NS(0.991)PLRENSFGS(1)PLEFR;ELS(0.001)NS(0.999)PLRENSFGS(1)PLEFR;ELS(0.069)NS(0.931)PLRENS(0.141)FGS(0.859)PLEFR;ELS(0.006)NS(0.994)PLRENSFGS(1)PLEFR 295.25 6.51E-50 4491804000 2114773 2510785 2282750 2304434 2718480 2333710 3170734 2366726 2921614 TRUE FALSE 1982413.133 2696686.134 2336897.908 2363569.678 2504981.547 3007414.192 2695311.872 2662216.951 2433977.749 0.814474633 1.107933766 0.960114738 0.971072837 1.029171917 1.23559642 1.107369151 1.093772099 1 21.21488455 2.462665155 24.79737118 1.122575189 0.9882589 0.345793877 0.090963861 233.6760764 400834.9079 0.028964725 0.02424323 290.1784491 -2.462665155 -0.134316289 ELSNS(ph)PLRENSFGSPLEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ELSNS(1)PLRENSFGSPLEFR;ELS(0.036)NS(0.964)PLRENSFGSPLEFR;ELS(0.026)NS(0.974)PLRENSFGSPLEFR;ELS(0.001)NS(0.999)PLRENSFGSPLEFR;ELS(0.002)NS(0.998)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR 295.17 6.98E-50 20698085000 3051491 4047388 3636142 3925843 4204750 3003483 4066727 3224780 4613632 TRUE FALSE 2860503.625 4347060.819 3722393.005 4026586.778 3874525.896 3870539.785 3456959.04 3627400.882 3843587.014 0.744227623 1.130990609 0.968468514 1.047611714 1.008049481 1.0070124 0.899409595 0.943754068 1 21.8740219 1.75935328 25 0.938211114 1.002812341 0.004149192 0.10103983 24.78258985 29823.01301 0.042265938 0.023439355 57.45836713 -1.75935328 0.064601227 ELSNSPLRENSFGS(ph)PLEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ELSNS(0.004)PLRENS(0.024)FGS(0.972)PLEFR 321.09 1.45E-61 1380900000 571650 712960 626890 656840 680120 528250 736690 566590 823900 TRUE FALSE 535871.4469 765748.3002 641760.1268 673695.6264 626706.1187 680747.1996 626230.1736 637330.0087 686385.7674 0.780714683 1.115623803 0.934984607 0.981511649 0.913052322 0.991785133 0.912358914 0.928530338 1 19.38866011 3.702439057 24.62589744 0.948069532 0.988055216 0 0.086951132 1160.621075 1157974.251 0.020942969 0.032460691 5040.098888 -3.702439057 0.039985684 ELSPDIAHLASLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELSPDIAHLASLK 13 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 147.18 4.27E-05 743520000 2540400 3134400 2891500 2893700 3764800 2276700 3256700 3220200 4331700 FALSE TRUE 2381400.899 3366474.237 2960087.745 2967957.241 3469127.794 2933946.331 2768388.069 3622249.059 3608711.286 0.659903414 0.932874362 0.820261725 0.822442419 0.961320405 0.81301775 0.767140358 1.003751415 1 21.78305229 -5 0.159884132 1.584789892 0.804185229 0.283646603 0.093364117 202.5544542 1.862757376 37.34291216 0.376491739 1.00E-05 5 -0.780604663 ELSPLISLPS(ph)PVPPLS(ph)PIHSNQQTLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELSPLISLPSPVPPLSPIHSNQQTLPR 27 0 A0A669KBI3;F5GXF9;P51825;P51825-3;P51825-2;E7ETI4;E7EMC5 A0A669KBI3 AFF1 AF4/FMR2 family member 1 2 ELSPLIS(0.047)LPS(0.953)PVPPLS(0.921)PIHS(0.042)NQQT(0.036)LPR;ELSPLIS(0.006)LPS(0.994)PVPPLS(0.989)PIHS(0.008)NQQT(0.003)LPR 104.9 0.0011224 195220000 56355 70233 64484 73210 63208 49587 73193 49403 51503 TRUE FALSE 52827.84115 75433.1244 66013.59093 75088.69254 58243.89865 63901.96192 62218.38914 55571.0733 42906.81658 1.231222574 1.75806854 1.538533879 1.750041101 1.357450944 1.489319577 1.450081691 1.29515722 1 15.38891925 0.880490948 0.654509942 0.992977067 1.582119221 0.525948917 0.157944392 0.632586077 0.604631142 0.146392313 0.058213565 7.594355928 -0.880490948 0.589142154 ELSPLISLPSPVPPLS(ph)PIHSNQQTLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELSPLISLPSPVPPLSPIHSNQQTLPR 27 0 A0A669KBI3;F5GXF9;P51825;P51825-3;P51825-2;E7ETI4;E7EMC5 A0A669KBI3 AFF1 AF4/FMR2 family member 1 1 ELSPLISLPSPVPPLS(0.992)PIHS(0.005)NQQT(0.003)LPR 92.865 0.0037424 59691000 30927 28876 30413 34367 30587 23847 32454 23328 24355 TRUE FALSE 28991.33428 31014.00909 31134.41072 35248.9154 28184.8204 30731.24178 27587.82399 26240.55215 20289.99316 1.428848893 1.528537188 1.534471228 1.73725615 1.389099552 1.514600894 1.359676357 1.293275554 1 14.30848076 1.016740664 0.851987829 1.002273 1.540575865 0.777586072 0.090526352 0.268829289 0.431548829 0.07950324 0.028443272 10.3929937 -1.016740664 0.538302865 ELSSTEAGSTVAGAALRPS(ph)HHSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELSSTEAGSTVAGAALRPSHHSQR 24 1 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 ELSSTEAGST(0.008)VAGAALRPS(0.496)HHS(0.496)QR;ELSSTEAGST(0.005)VAGAALRPS(0.498)HHS(0.498)QR 130.21 3.92E-05 388440000 77179 111964 112374 111000 126918 106233 126141 99129 125134 TRUE FALSE 72348.50416 120253.9311 115039.5643 113848.4479 116950.3722 136900.7426 107227.3281 111505.4739 104248.327 0.694001585 1.153533438 1.103514729 1.092088969 1.121844116 1.313217646 1.028576009 1.069614037 1 16.66966471 4.741469433 24.90358652 1.118234636 0.694001422 0.703994497 0.084695368 135.541547 1160365.112 0.018651417 0.131080883 55140.3391 -4.741469433 -0.424233214 ELSSTEAQLHDAQELLQEETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELSSTEAQLHDAQELLQEETR 21 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ;; 329.08 4.90E-80 747920000 452470 552880 521840 571520 585480 433770 623490 551090 582200 FALSE TRUE 424150.7104 593815.8105 534218.2912 586186.1708 539498.7625 558992.3573 530003.4627 619894.7996 485027.0588 0.874488758 1.224294191 1.101419563 1.208563852 1.112306525 1.152497262 1.09272968 1.278062302 1 18.88770571 4.748535364 24.79690021 1.148350225 0.874488591 0.544693263 0.078058856 865.3627607 2151215.545 0.016006677 0.216006511 56044.80519 -4.748535364 -0.273861634 ELSVQDQPSLS(ph)PTSLQNSSSHTTTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ELSVQDQPS(0.001)LS(0.935)PT(0.062)S(0.002)LQNSSSHTTTAK;ELSVQDQPSLS(0.987)PT(0.013)SLQNSSSHTTTAK;ELSVQDQPS(0.001)LS(0.992)PT(0.006)S(0.001)LQNSSSHTTTAK;ELSVQDQPSLS(0.491)PT(0.491)S(0.018)LQNSSSHTTTAK 247.99 9.31E-46 1038040000 612157 1031610 1121860 1386730 1326230 790296 981060 726658 932830 TRUE FALSE 573843.1861 1107991.478 1148471.049 1422315.84 1222073.246 1018441.626 833959.1607 817382.8509 777134.6467 0.73840896 1.425739391 1.477827625 1.830205159 1.572537334 1.310508585 1.073120552 1.051790516 1 19.56780506 1.814614099 2.959890587 1.037709178 1.439620947 0.270692091 0.272451898 0.32083222 5.17173881 0.149374397 0.074404225 65.25504578 -1.814614099 0.401911769 ELT(ph)NRHSLPFSLPSQMEPRPDVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELTNRHSLPFSLPSQMEPRPDVPR 24 2 P22681;A0A0U1RR39;A0A1B0GW38;A0A0U1RQX8 P22681 CBL E3 ubiquitin-protein ligase CBL 1 ELT(0.613)NRHS(0.385)LPFS(0.001)LPS(0.001)QMEPRPDVPR 70.451 0.041877 144710000 66578 50340 58087 49598 61397 46473 70223 50596 75115 TRUE FALSE 62411.00183 54067.22598 59464.85107 50870.76865 56575.12728 59889.00067 59693.71307 56913.02198 62577.82124 0.997334209 0.863999815 0.950254418 0.812920099 0.904076335 0.957032372 0.953911656 0.909475927 1 15.93336381 2.24447712 22.15718824 0.951753954 0.901883482 0.175245439 0.052654728 57.20787674 214244.1598 0.017070522 0.013885542 175.5808392 -2.24447712 -0.049870472 ELTALLHHYYPIEIDPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELTALLHHYYPIEIDPHR 18 0 E5RH64;Q969T7-2;Q969T7;C9J758 E5RH64 NT5C3B 7-methylguanosine phosphate-specific 5-nucleotidase 0 ; 165.9 9.40E-12 345130000 114020 128716 134250 114151 136782 105371 143560 121470 141891 FALSE TRUE 106883.6917 138246.2666 137434.4734 117080.3079 126039.6935 135789.8971 122034.5107 136635.7969 118208.4754 0.904196517 1.169512305 1.162644835 0.99045612 1.066249209 1.148732328 1.032366844 1.155888327 1 16.85097395 3.268407883 24.99998395 1.070515453 1.11020619 0 0.091268157 771.663983 646338.854 0.023857726 0.032299228 1855.273252 -3.268407883 0.039690736 ELTDEEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELTDEEAER 9 0 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 182.73 0.00010699 1041500000 835180 884290 856710 900090 872860 761160 1043600 840030 862500 FALSE TRUE 782907.5746 949763.7517 877031.5658 923187.8332 804309.0965 980894.5356 887121.8683 944909.5946 718543.178 1.089576241 1.321790785 1.220569052 1.284804952 1.119360842 1.365115647 1.234611775 1.315035232 1 19.45471533 -1.701415796 2.563857093 0.957047851 1.250501163 0.436427153 0.086796768 16723357.13 13066764.55 4628963.808 0.018230108 0.019887684 1.701415796 0.293453312 ELTHIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELTHIYR 7 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 ;; 152.39 0.001817 1120080000 700737 976091 758562 888065 944618 679463 922721 818825 924600 FALSE TRUE 656879.122 1048361.793 776555.4489 910854.2514 870431.5127 875612.9379 784367.5522 921057.1037 770278.2869 0.852781564 1.361016935 1.008149213 1.18250023 1.130022133 1.136748826 1.018291137 1.1957459 1 19.55502023 -1.685022325 0.304708073 0.895789757 1.132255372 0.039315986 0.135718874 72.10226246 3.909812941 5.724034907 0.127045216 0.02065274 1.685022325 0.236465616 ELTIGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ELTIGSK 7 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;; 141.78 0.0058941 4855450000 9439500 9152650 8952900 9299920 8770060 6637200 11100600 7776480 9647100 FALSE TRUE 8848698.545 9830321.729 9165267.016 9538571.692 8081294.864 8553251.894 9436168.083 8747390.646 8036936.687 1.101003889 1.22314286 1.140393084 1.186841711 1.005519289 1.064242786 1.174100089 1.088398601 1 22.93821429 -4.999999993 0.07421867 0.53837849 1.287592933 0.327433951 0.060753653 311.1244894 1.652167073 23.9916298 2.652251005 1.00E-05 4.999999993 0.749214443 ELTNRHS(ph)LPFSLPSQMEPRPDVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELTNRHSLPFSLPSQMEPRPDVPR 24 2 P22681;A0A0U1RR39;A0A1B0GW38;A0A0U1RQX8 P22681 CBL E3 ubiquitin-protein ligase CBL 1 ELT(0.298)NRHS(0.702)LPFSLPSQMEPRPDVPR;ELT(0.006)NRHS(0.994)LPFSLPSQMEPRPDVPR;ELT(0.112)NRHS(0.882)LPFS(0.004)LPS(0.002)QMEPRPDVPR 200.52 7.94E-25 498710000 232612 283269 249310 247453 316167 206866 309294 249535 344459 TRUE FALSE 218053.2301 304242.5315 255223.7509 253803.0629 291336.5192 266584.856 262918.236 280689.994 286966.5676 0.759855867 1.060202009 0.889384966 0.884434257 1.015228086 0.92897531 0.916198142 0.978127858 1 18.13052314 -4.944668253 0.008641376 2.03388209 4.36E-08 0.125612044 0.078771085 52431.41894 34.72333009 4647.625874 3588.56182 1.14E-05 4.944668253 -2.033882046 ELTPAS(ph)PTCTNSVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ELTPASPTCTNSVSK 15 0 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;A0A090HNM7 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 1 ELTPAS(1)PTCTNSVSK;ELTPAS(0.987)PT(0.013)CTNSVSK;ELTPAS(0.983)PT(0.017)CTNSVSK;ELTPAS(1)PTCTNSVSK;ELTPAS(0.991)PT(0.009)CTNSVSK;ELTPAS(0.998)PT(0.002)CTNSVSK 391.33 1.64E-114 3147500000 4992430 4182120 4658070 4519220 4800460 4009170 5710320 4183450 6421980 TRUE FALSE 4679962.718 4491768.516 4768561.62 4635190.836 4423451.236 5166552.296 4854110.528 4705762.941 5350110.05 0.874741393 0.83956563 0.891301595 0.866372989 0.826796308 0.965690845 0.907291716 0.879563765 1 22.35113714 -2.637074258 0.142063114 1.212468968 0.825278576 0.558211579 0.03529537 42.93487651 0.718221321 3.06223931 0.228996888 0.002306353 2.637074258 -0.387190392 ELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGSS(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGSSPQR 38 1 O00139-1;O00139-5;O00139;O00139-4;O00139-2;H0Y8H2 O00139-1 KIF2A Kinesin-like protein KIF2A 1 ELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGS(0.004)S(0.996)PQR 144.67 1.89E-13 133990000 50407 46542 57462 49918 59413 62108 68948 52010 41030 TRUE FALSE 47252.11585 49988.01811 58825.02578 51198.98039 54746.94264 80037.57136 58609.88748 58503.56299 34181.82794 1.382375335 1.462415006 1.720944412 1.497842084 1.601638822 2.341524026 1.714650474 1.711539918 1 15.06094193 2.456775204 24.99820346 1.793980821 1.542014276 0.017135971 0.334844362 494.4367175 607486.9277 0.10431226 0.087282506 286.2695821 -2.456775204 -0.251966545 ELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGSS(ph)PQRDDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGSSPQRDDLK 42 2 O00139-1;O00139-5;O00139;O00139-4;O00139-2;H0Y8H2 O00139-1 KIF2A Kinesin-like protein KIF2A 1 ELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGS(0.42)S(0.58)PQRDDLK 283.87 1.72E-81 641360000 334130 236430 289390 238750 293740 215950 353650 266940 394080 TRUE FALSE 313217.3997 253935.5232 296254.4675 244876.7292 270670.8453 278291.2593 300623.4656 300268.0466 328305.5021 0.954042493 0.773473248 0.90237436 0.745880674 0.824448093 0.847659444 0.915682082 0.914599495 1 18.3246794 1.287313718 1.162704966 0.99136453 0.834971573 0.424466106 0.059909894 0.379198551 1.026205267 0.050415162 0.016605549 19.37821266 -1.287313718 -0.156392957 ELVEFAQDDDRLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ELVEFAQDDDRLR 13 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ;;; 253.97 7.77E-24 1534460000 1315360 1504390 1363110 1400730 1447020 1071620 1601360 1238630 1681730 FALSE TRUE 1233033.966 1615776.601 1395443.613 1436675.103 1333376.886 1380979.298 1361250.934 1393275.682 1401038.399 0.880085776 1.153270747 0.996006686 1.025435923 0.951706168 0.98568269 0.971601446 0.994459312 1 20.41806507 3.221992153 1.92191005 0.980172363 1.043713577 0 0.068542523 0.623202446 4.71394284 0.020248986 0.02805619 1667.217087 -3.221992153 0.063541214 ELVEPLT(ph)PSGEAPNQALLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELVEPLTPSGEAPNQALLR 19 0 P00533;E9PFD7;Q504U8 P00533 EGFR Epidermal growth factor receptor;Receptor protein-tyrosine kinase 1 ELVEPLT(0.975)PS(0.025)GEAPNQALLR;ELVEPLT(0.912)PS(0.088)GEAPNQALLR;ELVEPLT(0.987)PS(0.013)GEAPNQALLR 233.49 4.60E-23 148480000 284852 340403 282460 423690 547780 191937 254399 195922 185607 TRUE FALSE 267023.6218 365606.7923 289160.0846 434562.6027 504759.5684 247346.0961 216254.2317 220383.293 154627.9926 1.726877632 2.364428239 1.870037111 2.810374728 3.264347935 1.59962043 1.398545166 1.42524836 1 17.23844199 2.02026724 24.91726236 1.363930997 2.353580914 0.58082387 0.447493037 178.7825848 219800.6679 0.169877801 0.125449256 104.777309 -2.02026724 0.989649916 ELVGDTGSQEGDHEPS(ph)GS(ph)ETEEDTSSSPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELVGDTGSQEGDHEPSGSETEEDTSSSPHR 30 0 P0DJ93 P0DJ93 SMIM13 Small integral membrane protein 13 2 ELVGDT(0.005)GS(0.005)QEGDHEPS(0.64)GS(0.64)ET(0.512)EEDT(0.05)S(0.05)S(0.05)S(0.05)PHR;ELVGDTGSQEGDHEPS(0.999)GS(0.98)ET(0.021)EEDTSSSPHR 124.91 6.97E-06 331330000 102342 152132 135462 128851 151897 123091 151456 141490 151003 TRUE FALSE 95936.59691 163396.0116 138675.2226 132157.5348 139967.6223 158625.3735 128746.5788 159155.338 125799.6238 0.762614339 1.298859302 1.102350058 1.050539984 1.112623537 1.260936788 1.023425786 1.265149554 1 16.94076808 2.464125593 24.91997928 1.138195567 1.100494105 0.024445672 0.156156327 1499.942937 2876217.078 0.050282703 0.042094016 291.1558987 -2.464125593 -0.037701462 ELVGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELVGHK 6 0 K7ER00;Q9Y285;Q9Y285-2 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 91.26 0.048095 221560000 371910 364420 413240 391800 423830 296710 463810 407030 484360 FALSE TRUE 348632.817 391402.036 423042.2479 401854.2513 390544.1014 382365.3603 394265.9963 457848.5915 403517.1869 0.86398505 0.969976122 1.048387186 0.995878898 0.96784998 0.947581349 0.977073614 1.134644586 1 18.6222706 4.714621773 2.581125175 1.003709988 0.838956128 0.435835709 0.052038992 0.454375179 4.095021573 0.012441777 0.159227642 51834.84126 -4.714621773 -0.16475386 ELVGPPLAETVFT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ELVGPPLAETVFTPK 15 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 ELVGPPLAET(0.001)VFT(0.999)PK;ELVGPPLAETVFT(1)PK;ELVGPPLAETVFT(1)PK;ELVGPPLAETVFT(1)PK;ELVGPPLAETVFT(1)PK 242.48 7.02E-17 298432700 339783 219124 280542 223955 209122 239848 411798 256516 226152 TRUE FALSE 318516.5886 235348.169 287196.5887 229702.0645 192698.4017 309088.224 350052.7128 288542.5873 188405.7702 1.690588288 1.249155844 1.524351342 1.219188055 1.02278397 1.640545423 1.857972357 1.53149549 1 17.52348362 ELVGPPLAETVFT(ph)PKT(ph)SPENVQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELVGPPLAETVFTPKTSPENVQDR 24 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 2 ELVGPPLAETVFT(1)PKT(0.675)S(0.325)PENVQDR;ELVGPPLAET(0.004)VFT(0.995)PKT(0.554)S(0.447)PENVQDR 205.32 4.86E-24 124519000 136357 105873 117126 111929 130468 79017 149920 112565 196279 TRUE FALSE 127822.6588 113711.9471 119904.284 114801.2876 120221.5696 101827.9252 127440.8878 126618.988 163518.7669 0.781700237 0.695406095 0.733275368 0.702067963 0.73521573 0.622729287 0.779365514 0.774339181 1 17.3190967 0.6857805 1.362089466 0.999418031 0.714664048 0.800712158 0.043720392 0.41022023 1.196774686 0.036968513 0.010972767 4.850432894 -0.6857805 -0.284753983 ELVGPPLAETVFT(ph)PKTS(ph)PENVQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELVGPPLAETVFTPKTSPENVQDR 24 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 2 ELVGPPLAETVFT(1)PKT(0.271)S(0.729)PENVQDR 134.11 8.55E-05 118310000 149150 119830 133050 119850 155820 91138 162450 131790 230980 TRUE FALSE 139814.9677 128702.3379 136206.0088 122925.5539 143582.5257 117448.0611 138092.1306 148244.2716 192427.9458 0.726583486 0.668833923 0.707828628 0.638813419 0.746162545 0.610348256 0.717630332 0.770388474 1 17.55395881 0.796839114 1.819336888 0.99960048 0.684378541 0.857108334 0.040200993 0.218981717 1.267145404 0.032849296 0.009243492 6.263817763 -0.796839114 -0.315221939 ELVLDNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ELVLDNSR 8 0 P39687;H0YN26;H7BZ09 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;; 158.61 0.00084673 623990000 1053130 1501500 1182550 1175930 1581570 907450 1199100 1322980 1435660 FALSE TRUE 987216.4732 1612672.622 1210600.644 1206106.355 1457359.872 1169416.084 1019306.087 1488156.965 1196039.071 0.825404869 1.348344432 1.012174831 1.008417186 1.218488515 0.977740704 0.852234773 1.244237752 1 20.18983309 2.19250337 24.98899054 0.988721006 1.10583951 0.011110134 0.167521583 288.852632 156719.0999 0.058961791 0.04354632 155.7770123 -2.19250337 0.117118503 ELVPESQAYMDLLAFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELVPESQAYMDLLAFER 17 0 J3KMX2;B9EGA3;Q92925-3;Q92925-2;Q92925;F8VW95;C9JYI7;F8VZ70;F8VUB0;Q6STE5-2;Q96GM5-2;Q6STE5;Q96GM5 J3KMX2 SMARCD2;SMARCD1;SMARCD3 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2;SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3;SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 0 ; 70.412 0.076053 20790900 24015.7 22610.5 25171.6 23082 22182.2 19466.5 25890.5 21898.2 26080.3 FALSE TRUE 22512.60021 24284.60495 25768.68224 23674.3232 20440.09949 25086.16254 22008.45988 24632.23847 21727.32944 1.036142075 1.117698565 1.1860032 1.089610357 0.940755261 1.154590241 1.012939024 1.133698393 1 14.40722324 2.999109443 24.9972596 1.051027365 1.126265455 0.143131645 0.071132452 50.57812766 1419764.475 0.01899084 0.02244181 997.9515184 -2.999109443 0.07523809 ELVSDANQHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELVSDANQHVK 11 0 P30153;B3KQV6;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 145.91 3.60E-05 703470000 808750 861540 834330 871210 957160 709630 992230 830140 988760 FALSE TRUE 758131.7812 925329.318 854120.7016 893566.7236 881988.5146 914488.6611 843454.3229 933784.8064 823729.5684 0.920364899 1.123341147 1.036894552 1.084781654 1.070725816 1.110180691 1.023945668 1.133606031 1 19.65181125 4.75051901 24.75183703 1.073189273 0.920364793 0.552283103 0.043170365 1145.678274 2371309.065 0.008934457 0.150170067 56301.37614 -4.75051901 -0.15282448 ELVVNCCTEFIHLISSEANEICNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELVVNCCTEFIHLISSEANEICNK 24 0 Q01658 Q01658 DR1 Protein Dr1 0 ; 350.85 6.46E-102 222650000 325120 299150 308470 303530 322350 271420 411740 279520 407060 FALSE TRUE 304771.3196 321299.3773 315787.0541 311319.0937 297033.9313 349774.5479 350003.4094 314418.6873 339119.0563 0.898714814 0.94745303 0.931198198 0.918023001 0.875898673 1.031421093 1.032095964 0.927163135 1 18.37143233 2.230609846 24.99999612 1.004856509 0.921265445 0.579991784 0.034751757 125.544593 394752.7895 0.012595822 0.009467268 170.0630038 -2.230609846 -0.083591064 ELWAVLNGWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELWAVLNGWR 10 0 C9J0K6;P30626-3;P30626-2;P30626 C9J0K6 SRI Sorcin 0 ; 204.36 4.38E-07 212790000 224450 489740 249540 259980 520140 192601 240190 399950 289390 FALSE TRUE 210402.0752 526000.8592 255459.2066 266651.5269 479290.3025 248201.7821 204175.7393 449884.6379 241088.9395 0.872715586 2.181771011 1.059605668 1.106029698 1.988022775 1.029502982 0.846889699 1.866052582 1 17.87920594 2.978643385 0.627085133 1.177905965 1.55778958 0 0.497457185 2.605604633 2.235572804 0.349878066 0.490520201 952.0141098 -2.978643385 0.379883615 ELYHEEFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ELYHEEFAR 9 0 Q9Y6U3;Q9Y6U3-2;F8WBX5;C9JGB6 Q9Y6U3 SCIN Adseverin 0 ;;;;; 223.08 3.60E-07 4193290000 1870010 2335710 2020989 1816376 2873250 1618936 2140750 2556850 5068410 FALSE TRUE 1752969.412 2508648.399 2068927.813 1862987.283 2647596.535 2086296.542 1819764.411 2876078.351 4222459.628 0.415153623 0.594120162 0.489981668 0.441209022 0.627027081 0.494095083 0.430972602 0.681138153 1 22.0096522 0.940158778 4.206626069 0.999716644 0.506878336 0.848282874 0.067830106 0.097983534 4.764240481 0.06220449 0.015860382 8.71282072 -0.940158778 -0.492838308 ELYQQLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ELYQQLQR 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 126.04 0.0028764 174879000 164904 226240 174044 168287 236640 135394 185534 182298 205980 FALSE TRUE 154582.953 242991.045 178172.4059 172605.5293 218055.249 174480.0499 157714.8991 205058.3066 171600.6073 0.900829871 1.416026719 1.038297059 1.005856168 1.270713737 1.016779909 0.919081241 1.194974247 1 17.38869513 2.913336904 0.761940642 1.025209316 1.182602358 0 0.162746635 1.515826774 1.94316269 0.099438951 0.118139501 819.0999589 -2.913336904 0.157393043 ELYVAADEASIAPILAEAQAHFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ELYVAADEASIAPILAEAQAHFGR 24 0 Q8NFF5-2;Q8NFF5;Q8NFF5-3;Q5T196;Q8NFF5-4;Q8NFF5-5;Q5T191 Q8NFF5-2 FLAD1 FAD synthase;Molybdenum cofactor biosynthesis protein-like region;FAD synthase region 0 143.98 2.36E-07 84866000 61475 64904 59056 64929 80741 57278 68830 53312 70555 FALSE TRUE 57627.38949 69709.55969 60456.83621 66595.18806 74399.92755 73813.22877 58509.58049 59968.12055 58778.9147 0.980409213 1.185962008 1.028546317 1.132977504 1.265758783 1.255777334 0.995417843 1.020231844 1 15.8430111 1.623019242 11.59861865 1.005523202 1.137680022 0.346776371 0.08803981 0.111123358 47.47797169 0.042940175 0.022653517 41.97775824 -1.623019242 0.132156819 EMADRYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EMADRYDR 8 1 P17812;B4E1E0;P17812-2;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6;A0A3B3ITB8;A0A3B3ISY3 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ; 171.56 0.00026325 1344890000 830120 1008520 947200 904710 1069190 744380 904600 900220 1051200 FALSE TRUE 778164.271 1083191.87 969668.0313 927926.3903 985220.1303 959270.422 768963.6279 1012614.449 875747.929 0.888571066 1.236876314 1.107245589 1.059581598 1.125004237 1.095372755 0.878065026 1.156285291 1 19.74015615 1.961486128 24.45032287 0.995105999 1.106840053 0.065872708 0.10894216 670.5037618 425664.2226 0.041458519 0.026761379 91.51370288 -1.961486128 0.111734054 EMDEAATAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EMDEAATAEER 11 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;; 173.24 2.89E-05 925960000 457324 518532 513697 506907 548648 457905 572804 468416 604580 FALSE TRUE 428700.9072 556924.6488 525882.1354 519915.0918 505559.3992 590094.74 486917.3579 526898.7687 503671.6923 0.851151482 1.105729501 1.044097065 1.032249975 1.003747892 1.171586073 0.966735604 1.046115509 1 18.94212412 4.748889044 24.83073301 1.048963266 0.851151361 0.531583078 0.057516283 1010.439086 2429159.552 0.012586476 0.175124452 56090.46548 -4.748889044 -0.197811905 EMDEEDKAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EMDEEDKAFK 10 1 Q9Y2S6 Q9Y2S6 TMA7 Translation machinery-associated protein 7 0 ;; 113.47 0.001353 1457640000 2442980 1419320 1773880 1848460 1975030 1236390 2269320 1356070 2374290 FALSE TRUE 2290078.243 1524407.93 1815957.271 1895894.613 1819919.111 1593315.722 1929056.533 1525378.325 1978005.661 1.157771329 0.770679255 0.918074861 0.958487961 0.920077807 0.80551626 0.975253293 0.771169848 1 20.91561512 EMDEQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EMDEQIR 7 0 P06753-2;A0A087WWU8;P06753-6;P06753-3;J3KN67;A0A2R2Y2Q3;A0A494C0P6 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;; 158.03 0.0033409 2675540000 4563620 5367750 5048890 4894190 5203510 3849090 5176260 4610170 4347140 FALSE TRUE 4277991.17 5765183.795 5168652.055 5019783.201 4794847.315 4960259.798 4400127.867 5185759.873 3621574.25 1.181251819 1.59189993 1.427183787 1.386077671 1.323967696 1.369641889 1.214976572 1.43190765 1 21.78818552 -0.894516117 0.246127005 0.759127914 1.464086075 0.459949234 0.11930961 11.22454507 0.688809628 2.111244449 0.201259413 0.127492279 0.894516117 0.704958161 EMDRETLIDVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 EMDRETLIDVAR 12 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;;;;;;;;;; 239.03 3.39E-16 8286230000 6281530 7655950 7083170 7288640 8542260 5860660 7684090 6398600 9083580 FALSE TRUE 5888380.25 8222804.504 7251186.137 7475678.842 7871385.357 7552537.402 6531932.04 7197479.295 7567471.816 0.778117236 1.08659863 0.958204578 0.987870061 1.040160512 0.998026499 0.863159084 0.951107513 1 22.85137997 -0.493162035 5.628056941 0.999999996 0.966864168 0.013569484 0.086810421 5.93E-10 0 0.079624098 0.01876758 0.321246175 0.493162035 -0.033135829 EMDTART(ph)PLSEAEFEEIMNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EMDTARTPLSEAEFEEIMNR 20 1 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 1 EMDT(0.189)ART(0.811)PLSEAEFEEIMNR;EMDT(0.17)ART(0.83)PLSEAEFEEIMNR;EMDT(0.157)ART(0.842)PLS(0.001)EAEFEEIMNR;EMDT(0.038)ART(0.953)PLS(0.009)EAEFEEIMNR 196.22 2.87E-21 254223000 226547 220731 221815 224862 240061 211728 274123 215641 278049 TRUE FALSE 212367.8277 237074.1529 227076.5565 230632.3396 221207.5774 272850.4365 233020.801 242564.2535 231640.8256 0.916797922 1.023455828 0.980295921 0.995646337 0.954959372 1.177903056 1.005957393 1.047156747 1 17.82153002 EMEADERDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EMEADERDR 9 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ;;; 105.52 0.0032364 409752000 427962 587145 524637 528470 663643 422901 541945 515319 723730 FALSE TRUE 401176.6224 630617.8267 537081.6374 542031.4349 611523.1558 544985.6535 460685.3784 579657.7115 602934.7875 0.665373156 1.04591382 0.890778984 0.898988491 1.014244274 0.903888223 0.764071651 0.961393709 1 19.20164245 1.008889861 24.93649882 1.000000112 0.897073297 0.116616986 0.109212668 345.6453158 969547.1312 0.099825743 0.024956436 10.20680602 -1.008889861 -0.102926815 EMEAELEDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EMEAELEDER 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;; 223.93 9.79E-09 2729520000 2267990 2547430 2471960 2420450 2524940 2046100 2814790 2216540 2638810 FALSE TRUE 2126040.554 2736044.368 2530596.059 2482562.845 2326641.398 2636775.854 2392738.371 2493279.898 2198375.564 0.967096155 1.244575501 1.151120901 1.129271488 1.058345733 1.199420107 1.088412012 1.134146476 1 21.06800644 -0.853880059 0.407869802 0.951657878 1.14264167 0.167199764 0.077179422 19.0942968 2.417904 1.196968462 0.045526521 0.139997391 0.853880059 0.190983792 EMEAELEDERK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EMEAELEDERK 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;; 198.81 8.40E-08 2592066000 3374400 2425140 2877230 2786810 2970680 1954598 3549730 2314220 2974290 FALSE TRUE 3163202.327 2604699.889 2945479.254 2858324.263 2737374.776 2518858.712 3017480.941 2603155.461 2477861.784 1.276585461 1.051188531 1.188718141 1.153544673 1.104732634 1.016545284 1.217776132 1.05056524 1 21.24066429 -5 0.13009529 0.557670391 1.187614153 0.301768061 0.076164117 204.1033113 1.6759511 23.52875752 0.537254793 1.00E-05 5 0.629943762 EMEHNTVCAAGTS(ph)PVGEIGEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 EMEHNTVCAAGTSPVGEIGEEK 22 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;H7C1M2 P18583-7 SON Protein SON 1 EMEHNTVCAAGT(0.002)S(0.998)PVGEIGEEK;EMEHNTVCAAGT(0.019)S(0.981)PVGEIGEEK;EMEHNTVCAAGT(0.249)S(0.751)PVGEIGEEK;EMEHNTVCAAGT(0.017)S(0.983)PVGEIGEEK;EMEHNTVCAAGT(0.214)S(0.786)PVGEIGEEK;EMEHNTVCAAGT(0.029)S(0.971)PVGEIGEEK;EMEHNTVCAAGT(0.191)S(0.809)PVGEIGEEK;EMEHNTVCAAGT(0.077)S(0.923)PVGEIGEEK;EMEHNTVCAAGT(0.012)S(0.988)PVGEIGEEK;EMEHNTVCAAGT(0.008)S(0.992)PVGEIGEEK;EMEHNTVCAAGT(0.037)S(0.963)PVGEIGEEK;EMEHNTVCAAGT(0.005)S(0.995)PVGEIGEEK 245.53 4.41E-31 12814250000 11951010 10399230 11764320 11609870 12237820 9398370 15236400 10834860 14836960 TRUE FALSE 11203017.62 11169199.81 12043375.23 11907798.92 11276710.98 12111526.85 12951843.27 12187616.12 12360575.53 0.906350808 0.903614867 0.97433774 0.963369294 0.912312777 0.979851369 1.047834969 0.986007172 1 23.55924258 2.020327842 5.585452491 1.016233564 0.935757739 0.633589632 0.027671515 0.105213254 10.25522852 0.011088224 0.007747957 104.7919307 -2.020327842 -0.080475825 EMFEDTVEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EMFEDTVEER 10 0 Q16576;E9PC52 Q16576 RBBP7 Histone-binding protein RBBP7 0 ;;;; 238.51 7.68E-12 2261241000 1705187 1893662 1848952 1839434 1967518 1642281 2056827 1689156 2022378 FALSE TRUE 1598462.39 2033870.705 1892810.015 1886636.991 1812997.073 2116380.864 1748424.886 1900050.845 1684830.047 0.94873806 1.207166686 1.123442699 1.119778813 1.07607119 1.25613908 1.037745551 1.127740361 1 20.68417164 0.510866681 1.024886684 1.000381403 1.125668734 0.130081731 0.085087093 2.926801192 4.373250759 0.073335691 0.023064445 3.242400674 -0.510866681 0.12528733 EMFEVTGLHDVDQGWMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EMFEVTGLHDVDQGWMR 17 0 Q9BWS9-3;Q9BWS9;Q9BWS9-2 Q9BWS9-3 CHID1 Chitinase domain-containing protein 1 0 ;;; 224.86 2.58E-15 339770000 347353 461832 407186 436642 480537 320985 460505 408787 397042 FALSE TRUE 325612.7958 496026.5218 416844.6442 447846.973 442797.5624 413648.1587 391456.5504 459824.9568 330773.1252 0.984399188 1.49959741 1.260213157 1.353940024 1.338674544 1.250549477 1.183459358 1.390152107 1 18.3354825 -3.529191588 0.335808417 2.81E-10 1.307345631 0.271965002 0.138803099 150.4072573 3.274309944 105.2086638 0.104409725 0.000295671 3.529191588 1.307345631 EMFPYEAST(ph)PTGISASCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EMFPYEASTPTGISASCR 18 0 P42167;G5E972;H0YJH7;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 EMFPYEAS(0.038)T(0.961)PT(0.001)GISASCR;EMFPYEAS(0.026)T(0.973)PT(0.001)GISASCR;EMFPYEAS(0.319)T(0.34)PT(0.34)GISASCR;EMFPYEAS(0.324)T(0.676)PTGISASCR;EMFPYEAS(0.152)T(0.844)PT(0.004)GISASCR;EMFPYEAS(0.133)T(0.866)PTGISASCR 439.79 1.64E-189 1157041000 1074150 1083050 1080130 1070240 1132080 1025595 1330700 1095345 1401620 TRUE FALSE 1006920.869 1163240.149 1105751.194 1097704.17 1043171.003 1321667.627 1131173.889 1232101.234 1167680.567 0.86232562 0.996197232 0.946963771 0.940072312 0.893370184 1.131874302 0.968735732 1.055169769 1 20.15521423 2.260991293 24.99999392 1.032508354 0.940288308 0.495796128 0.0547325 217.2328271 242115.0904 0.017508056 0.01463798 182.3859136 -2.260991293 -0.092220046 EMFPYEASTPT(ph)GISASCR ddPTM_SK-BR-3_Pertuzumab_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(0.029)T(0.344)PT(0.627)GISASCR 225.8 4.31E-18 148120000 130540 141680 137760 137800 149160 128900 167890 131720 181720 TRUE FALSE 122369.7344 152170.1346 141027.7323 141336.1813 137445.5753 166111.3375 142716.4531 148165.532 151389.758 0.808309201 1.005154751 0.931553984 0.933591434 0.907892166 1.097242902 0.942708773 0.978702482 1 17.20790808 EMKPVIFLDVFLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EMKPVIFLDVFLPR 14 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 150.57 6.54E-06 246940000 564400 675630 609440 613690 691040 460400 770710 698840 617970 FALSE TRUE 529075.2115 725654.3482 623896.2046 629438.3244 636768.5059 593310.006 655149.1904 786091.7123 514826.8148 1.027676097 1.409511563 1.211856467 1.222621484 1.236859634 1.152445811 1.27256229 1.526905145 1 18.97372767 1.481249049 12.6293655 1.308763505 1.233725471 0 0.157584696 0.261064739 250.5315301 0.075738652 0.035091949 30.28649732 -1.481249049 -0.075038035 EMLMEDVGS(ph)EEEQEEEDEAPFQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EMLMEDVGSEEEQEEEDEAPFQEK 24 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EMLMEDVGS(1)EEEQEEEDEAPFQEK 60.278 0.043843 39376000 29135 25918 29845 24571 22955 29502 33975 21662 21444 TRUE FALSE 27311.49236 27836.99569 30552.93749 25201.53346 21152.2069 38018.74848 28880.76416 24366.54838 17864.85787 1.528783076 1.558198554 1.710225613 1.410676404 1.184012045 2.128130476 1.616624346 1.363937433 1 14.12483682 0.960039655 3.461768569 1.001746269 1.605202327 0.389433482 0.237706771 0.243101352 7.676628252 0.217959888 0.056439079 9.120941179 -0.960039655 0.603456058 EMLQQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EMLQQSK 7 0 P08238;Q58FF7;P07900;P07900-2 P08238;P07900 HSP90AB1;HSP90AB3P;HSP90AA1 Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Heat shock protein HSP 90-alpha 0 ;; 113.71 0.01412 698800000 823640 936770 712810 660690 1022340 522040 800330 832420 936090 FALSE TRUE 772089.8426 1006129.426 729718.1898 677644.4239 942049.5403 672744.4734 680327.9464 936349.4694 779850.5316 0.990048492 1.290156748 0.935715448 0.868941414 1.207987303 0.862658222 0.872382487 1.200678119 1 19.57283811 3.838810029 5.266535534 0.977228009 1.153471664 0.144685915 0.144092329 0.303186348 12.36653605 0.034672524 0.063791283 6899.379427 -3.838810029 0.176243655 EMMSHAEGQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EMMSHAEGQQR 11 0 Q9BXB4 Q9BXB4 OSBPL11 Oxysterol-binding protein-related protein 11 0 ; 51.927 0.07963 52843000 9221.3 14020.5 8297.7 10861.9 14974.8 9014.2 10507.8 11229.8 15396 FALSE TRUE 8644.155293 15058.59241 8494.525362 11140.63474 13798.73961 11616.45321 8932.25294 12631.86525 12826.30814 0.673939469 1.174039501 0.662273608 0.868576883 1.075815384 0.905673954 0.696400932 0.984840307 1 13.64681835 1.034596133 24.99691082 1.000002014 0.873760103 0.090745636 0.166049026 392.1554889 283344.7832 0.151977689 0.037994422 10.82919397 -1.034596133 -0.126241911 EMNDAAMFYTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EMNDAAMFYTNR 12 0 Q01518-2;Q01518;Q5T0R1;Q5T0R9;Q5T0R4;Q5T0R3;Q5T0R2;Q5T0R5;Q5T0R7;Q5T0R6 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 0 ;; 206.1 2.19E-07 693450000 397377 505580 395702 410780 491080 304932 463320 446440 538200 FALSE TRUE 372505.8829 543013.6693 405088.2383 421321.3102 452512.5577 392960.9182 393849.4673 502179.0167 448370.9431 0.830798446 1.21108131 0.903466749 0.939671307 1.009237027 0.876419233 0.878400961 1.120007941 1 18.77433326 3.740829777 24.39404367 0.94773651 1.050854298 0.02049301 0.116527031 587.2580371 1045005.881 0.027230275 0.048736437 5505.918485 -3.740829777 0.103117788 EMNPALGIDCLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EMNPALGIDCLHK 13 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;;;;;; 196.67 1.40E-07 3211720000 3949860 3490260 3630510 3510320 4035790 3054820 4461200 3415870 4486700 FALSE TRUE 3702645.313 3748682.482 3716627.412 3600400.754 3718835.333 3936696.943 3792284.476 3842348.889 3737840.785 0.99058401 1.002900524 0.994324699 0.9632301 0.994915393 1.05320081 1.014565546 1.027959485 1 21.83377369 2.402478811 10.79748678 1.024968305 0.990150932 0.524625426 0.016474354 0.351771695 48.84808604 0.005399158 0.00451554 252.6264451 -2.402478811 -0.034817373 EMPSVFQNVLGSAVLS(ph)PAHKDTQDFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EMPSVFQNVLGSAVLSPAHKDTQDFHK 27 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 EMPSVFQNVLGS(0.001)AVLS(0.821)PAHKDT(0.179)QDFHK 107.29 0.00091061 69805000 123060 109860 126620 123150 152560 77239 145410 98659 217750 TRUE FALSE 115357.8943 117994.1487 129623.4862 126310.2375 140578.553 99536.64543 123607.1204 110976.7933 181406.1183 0.635909612 0.650441947 0.714548591 0.69628433 0.774938323 0.548695085 0.681383415 0.611758823 1 17.46886359 -1.104972409 5.002616889 1.00001107 0.667627106 0.750428273 0.060823255 6.96E-06 1.25E-06 0.05461527 0.012872514 0.078528552 1.104972409 -0.332383964 EMQDVDLAEVKPLVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EMQDVDLAEVKPLVEK 16 1 Q92597;E5RI76;E5RIR1;E5RGM5;E5RIM2;E5RH82;E5RK17;E5RIV1;E5RJ98 Q92597 NDRG1 Protein NDRG1 0 ;;;; 217.09 1.33E-14 1192066000 2528980 2031660 2090260 2301850 2376520 1372450 2826980 1893410 1454833 FALSE TRUE 2370695.656 2182086.22 2139841.954 2360919.368 2189877.706 1768654.035 2403100.593 2129806.406 1212011.974 1.956000194 1.800383385 1.765528725 1.94793403 1.80681194 1.459271091 1.982736677 1.757248651 1 20.20897252 -2.172420961 0.522397039 2.48E-17 1.815751714 0.749337895 0.147439587 51.5610577 3.710654232 60.71400248 0.061856615 0.006723247 2.172420961 1.815751714 EMQPTHPIR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;;;;;;;;;;;;;;;; 142.94 0.00010313 39435210000 12110447 13744563 13674614 13300295 13078229 11519699 14403017 11389627 9862122 FALSE TRUE 11352475.74 14762224.75 13998982.3 13641603.09 12051117.65 14845249.09 12243418.31 12811647 8216070.126 1.381740366 1.796750091 1.703853799 1.660356214 1.466773952 1.806855208 1.490179383 1.559340026 1 22.97001706 0.022265711 0.599158177 0.959587601 1.664108901 0.653845051 0.139135807 2.293761504 0.964083862 0.342008923 0.052269854 1.052605684 -0.022265711 0.704521299 EMSLWESLGESWMRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EMSLWESLGESWMRPR 16 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 297.72 8.62E-46 400930000 402780 525960 480230 482060 581060 417160 530510 439030 504660 FALSE TRUE 377570.7188 564902.6257 491621.2824 494430.4757 535425.8915 537587.32 450964.9505 493843.8619 420428.9858 0.898060628 1.343633871 1.169332513 1.176014244 1.273522782 1.278663789 1.072630494 1.174618969 1 18.68150261 0.897828891 1.040122056 1.005252011 1.202134173 0.142589797 0.124527801 1.020352228 2.23920525 0.106869152 0.034670832 7.903671678 -0.897828891 0.196882162 EMTLDEWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EMTLDEWK 8 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;; 157.33 0.0008809 845855000 2053450 2311910 1644660 1599910 2648140 1025530 1867650 2062150 2683650 FALSE TRUE 1924928.23 2483086.222 1683672.112 1640966.399 2440165.766 1321583.863 1587613.221 2319613.967 2235731.478 0.860983642 1.110637054 0.753074387 0.733972937 1.091439554 0.591119227 0.710109079 1.037519036 1 21.09231549 3.924840449 6.056849205 0.817799049 0.994520103 0.087724082 0.170596451 0.326546785 26.94801618 0.041177328 0.076378699 8410.860869 -3.924840449 0.176721054 EMTPGNILTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EMTPGNILTR 10 0 H3BV81;H3BP25;H3BMC5;H3BPK8;Q9NVC3-2;Q9NVC3 H3BV81 SLC38A7 Putative sodium-coupled neutral amino acid transporter 7 0 ;; 72.006 0.049282 4208020000 1753130 303231 3556910 3980340 259230 3016920 3382130 264738 4182100 FALSE TRUE 1643404.723 325682.5388 3641281.585 4082482.263 238871.1215 3887855.828 2875011.005 297791.1221 3484080.493 0.471689654 0.093477329 1.045119822 1.171753142 0.068560736 1.115891506 0.825185012 0.085471941 1 21.73234652 3.997994591 7.514672542 0.768998078 0.292115196 0.195834051 0.400681758 0.268022237 69.24700851 0.09294903 0.194649498 9953.930202 -3.997994591 -0.476882882 EMVELPLRHPALFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EMVELPLRHPALFK 14 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 142.38 5.66E-06 897310000 1894570 2507460 2196230 2295860 3067900 1684620 2908900 2196840 4737800 FALSE TRUE 1775992.246 2693114.947 2248325.613 2354775.654 2826959.509 2170942.446 2472737.45 2471120.31 3947030.573 0.449956547 0.682314185 0.569624575 0.596594227 0.716224376 0.550019162 0.62648044 0.626070729 1 21.91233626 -5 0.354644596 5.667213544 0.596365267 0.75688735 0.07131233 207.2936191 1.676498961 736.9139942 0.047576957 1.00E-05 5 -5.070848277 ENAEVDGDDDAEEMEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ENAEVDGDDDAEEMEAK 17 0 P05198 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ; 469.35 4.10E-206 409210000 1308360 839660 1018030 984200 1004870 760690 1288520 858820 1105720 FALSE TRUE 1226472.083 901829.3001 1042178.152 1009456.238 925951.5637 980288.8542 1095318.388 966045.5675 921168.1888 1.331431217 0.979006126 1.131365765 1.095843572 1.005192727 1.064180099 1.18905364 1.048717899 1 19.81310507 7.999999996 0.010024688 4.13E-09 2.329643884 0.15344183 0.096837187 36528.60863 28.30556632 2832.359189 3813.101652 99999999.11 -7.999999996 2.32964388 ENAGS(ph)LEAINEPIPQPMPFPPSIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENAGSLEAINEPIPQPMPFPPSIIR 25 0 Q5TCQ9;Q5TCQ9-1;Q5TCQ9-3;Q5TCQ9-2 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 ENAGS(1)LEAINEPIPQPMPFPPSIIR 80.83 2.68E-05 0 15305 18816 17361 18203 17439 13867 17409 14353 16321 TRUE FALSE 14347.08737 20209.15622 17772.81112 18670.1198 16069.41129 17870.17779 14798.68207 16145.00364 13596.91966 1.055171886 1.48630401 1.307120404 1.37311393 1.181842041 1.31428134 1.088384901 1.187401562 1 13.73099223 1.577269752 0.706307698 1.0176625 1.336825613 0.345634837 0.122451549 0.565716013 0.595130383 0.103815564 0.048073111 37.7806784 -1.577269752 0.319163113 ENALSSGTLQEEQRT(ph)PPPGQDTQQFHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENALSSGTLQEEQRTPPPGQDTQQFHEK 28 1 Q12802-2;Q12802;Q12802-4;H0YMW2 Q12802-2 AKAP13 A-kinase anchor protein 13 1 ENALSSGTLQEEQRT(1)PPPGQDTQQFHEK 189.91 8.06E-18 209900000 226500 209220 224020 231370 251890 160450 223470 211100 286930 TRUE FALSE 212323.7693 224710.8665 229333.8602 237307.3459 232107.5755 206769.3103 189962.7481 237456.2997 239039.5294 0.888237062 0.94005735 0.959397221 0.992753569 0.971000805 0.865000491 0.794691776 0.993376704 1 17.86688969 2.238682881 24.99999702 0.884174038 0.952066153 0 0.066668064 5.300804741 1084189.59 0.022940931 0.018067509 173.2538449 -2.238682881 0.067892115 ENAS(ph)PAPGTTAEEAMSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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(1)PAPGTTAEEAMSR;ENAS(1)PAPGTTAEEAMSR;ENAS(1)PAPGTTAEEAMSR;ENAS(1)PAPGTTAEEAMSR;ENAS(1)PAPGTTAEEAMSR;ENAS(1)PAPGTTAEEAMSR 286.86 1.69E-36 2155560000 1981630 1748910 1921650 1833340 1710110 1832050 2248340 1721680 1687640 TRUE FALSE 1857603.316 1878401.116 1967232.445 1880386.608 1575804.859 2360933.094 1911222.29 1936635.538 1405961.981 1.321232964 1.33602554 1.399207426 1.337437735 1.120801899 1.679229684 1.359369823 1.377445168 1 20.42312615 -1.574176634 8.801270104 0.999933602 1.371484954 0.421498936 0.13475966 0.000160517 7.77E-06 0.119290018 0.028111954 0.026657742 1.574176634 0.371551352 ENDFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ENDFDR 6 0 O14579;M0QXB4;O14579-3;O14579-2 O14579 COPE Coatomer subunit epsilon 0 ;;; 155.51 0.022958 3478760000 5431800 5480600 5404700 5449400 5814800 4302060 6431000 4974300 6462700 FALSE TRUE 5091833.334 5886389.327 5532902.036 5589240.83 5358129.064 5543994.884 5466731.252 5595352.305 5384033.619 0.945728369 1.093304712 1.027649979 1.038114028 0.995188634 1.029710302 1.015359791 1.039249139 1 22.36025599 2.877103683 15.91985282 1.017728721 1.037647837 0 0.03812547 4.24485658 531.5664416 0.010777858 0.011431897 753.5354403 -2.877103683 0.019919116 ENDLYVLPPLQEEEKHS(ph)S(ph)EEEDEKEWQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENDLYVLPPLQEEEKHSSEEEDEKEWQER 29 2 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;P28715-3 R4GMW8 BIVM-ERCC5;ERCC5 DNA repair protein complementing XP-G cells 2 ENDLY(0.001)VLPPLQEEEKHS(1)S(1)EEEDEKEWQER 47.191 0.056427 59023000 29823 10446 17707 18431 14716 14239 25052 14653 29225 TRUE FALSE 27956.43167 11219.43271 18127.0184 18903.97066 13560.26472 18349.56815 21295.68517 16482.45931 24347.1587 1.14824206 0.46081076 0.744522949 0.776434363 0.55695471 0.753663636 0.874668188 0.676976706 1 14.5714658 0.245896941 0.55162089 1.013547021 0.706581171 0.118508763 0.18701469 4.773568934 2.099126195 0.341654362 0.078083355 1.761557974 -0.245896941 -0.30696585 ENDPMDS(ph)HQSQESPNLENIANPLEENVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENDPMDSHQSQESPNLENIANPLEENVTK 29 0 Q96JQ2 Q96JQ2 CLMN Calmin 1 ENDPMDS(0.444)HQS(0.304)QES(0.252)PNLENIANPLEENVTK 85.239 0.0068285 69254000 28908 36830 39342 40337 42637 29328 41732 29023 45331 TRUE FALSE 27098.69988 39556.93152 40275.21082 41372.11571 39288.46201 37794.5175 35474.67402 32646.58544 37764.96325 0.717561929 1.04745055 1.066470277 1.095515847 1.040341593 1.000782584 0.939354125 0.864467555 1 15.20476076 1.723030066 3.598715934 0.923889649 1.015491614 0.040830961 0.109963578 0.440926784 12.64308129 0.058611143 0.028095063 52.84818376 -1.723030066 0.091601966 ENDYYTPTGEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENDYYTPTGEFR 12 0 P46977;P46977-2 P46977 STT3A Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A 0 240.41 7.69E-16 99967000 140080 151450 120410 127790 162470 120920 161580 160320 125440 FALSE TRUE 131312.6428 162663.5156 123266.1821 131069.3077 149710.2616 155827.641 137352.579 180336.3049 104503.2536 1.256541192 1.556540203 1.179543964 1.254212699 1.432589478 1.491127172 1.314337825 1.725652539 1 16.67318833 2.70868841 24.24900095 1.411869806 1.330487009 0.029806701 0.20261882 1857.292494 1507669.537 0.05966778 0.056264595 511.3148541 -2.70868841 -0.081382796 ENEFSFEDNAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ENEFSFEDNAIR 12 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3;F2Z2R5;K7EMY3 Q14839-2 CHD4;CHD5 Chromodomain-helicase-DNA-binding protein 4 0 ; 214.82 9.98E-11 604300000 380570 401400 392960 429490 415660 323630 502830 341720 437600 FALSE TRUE 356750.803 431120.0737 402281.1968 440511.4405 383015.7403 417056.7273 427435.3095 384384.4942 364561.733 0.978574466 1.182570837 1.103465231 1.208331541 1.050619705 1.143994801 1.172463456 1.054374224 1 18.47580361 -0.44029173 7.552077734 0.999999865 1.123538661 0.181916924 0.070714743 0 0 0.059775137 0.014089135 0.362834245 0.44029173 0.123538795 ENEVEEVKEEGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENEVEEVKEEGPK 13 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 105.46 0.0013234 146700000 154540 53715 86709 85882 77405 73039 120710 65208 74953 FALSE TRUE 144867.6173 57692.11449 88765.77843 88085.87752 71325.92354 94124.17361 102610.6561 73349.36234 62442.86009 2.320002912 0.923918514 1.421552093 1.410663724 1.142259074 1.507364869 1.643272841 1.17466372 1 15.930249 4.753016676 24.66938058 1.314874419 2.320003751 0.671473937 0.227767292 1414.538892 2413872.278 0.05528933 1.19972033 56626.10319 -4.753016676 1.005129332 ENEYSQFLSEHAGSSNAFTSGEHTNYYFDVSHEHLEGALDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENEYSQFLSEHAGSSNAFTSGEHTNYYFDVSHEHLEGALDR 41 0 A0A3B3ISG5;P14735;Q5T5N3 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 65.048 0.0010394 47049000 5639.4 12553 10454 11288 11552 9091.8 15417 8645 12029 FALSE TRUE 5286.440021 13482.43718 10701.97382 11577.66919 10644.75252 11716.45507 13105.36397 9724.34728 10021.28219 0.527521321 1.345380454 1.067924604 1.15530817 1.062214627 1.169157284 1.307753212 0.970369569 1 13.29077949 4.749236923 24.94529221 1.157926477 0.527520957 0.705395233 0.122519627 775.914401 1812895.523 0.027256323 0.397427315 56135.41306 -4.749236923 -0.63040552 ENFMTVDQDGSGTVEHHELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ENFMTVDQDGSGTVEHHELR 20 0 H7C2Z6;H7BXD5;P28676;C9JIZ3 H7C2Z6 GCA Grancalcin 0 ;; 171.68 4.32E-12 427064000 184325 177938 193829 177204 183335 167779 234083 190418 190655 FALSE TRUE 172788.4273 191112.7147 198426.7154 181751.3546 168936.6086 216214.0736 198984.4273 214192.1065 158833.4488 1.087859192 1.203227129 1.249275369 1.144288914 1.063608515 1.361262853 1.252786669 1.348532743 1 17.27715524 2.23494902 24.99998626 1.264310326 1.170298813 0.110726459 0.111884459 174.7605214 1209703.252 0.037334155 0.028668655 171.7706741 -2.23494902 -0.094011513 ENFQNWLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ENFQNWLK 8 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ;;; 162.25 0.0007975 1207787000 1589996 2176104 1378104 1396464 1949607 957867 1778979 1978708 2716325 FALSE TRUE 1490480.989 2337225.004 1410793.278 1432299.63 1796492.731 1234387.653 1512237.614 2225754.049 2262952.809 0.658644309 1.032820921 0.623430269 0.632933937 0.793871053 0.545476533 0.668258573 0.983561849 1 21.10977507 1.230395683 24.53021756 0.991781268 0.721327124 0.440676985 0.132284254 164.2020664 493293.746 0.123803448 0.033142854 16.99791616 -1.230395683 -0.270454143 ENFS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ENFSPER 7 0 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 ENFS(1)PER;ENFS(1)PER 109.16 0.0074386 1706390000 853030 1137740 982720 946830 1104480 726650 992820 937330 1099620 TRUE FALSE 799640.375 1221979.453 1006030.582 971127.2608 1017738.596 936422.0588 843955.8579 1054357.714 916086.3182 0.872887586 1.333913005 1.098183176 1.060082703 1.110963646 1.022198498 0.921262376 1.150937082 1 19.80512402 2.797143152 1.210914965 1.01076803 1.150989932 0.006487462 0.12718654 0.785165461 2.385343283 0.055601721 0.055423167 626.8204428 -2.797143152 0.140221902 ENFSCLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ENFSCLTR 8 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;C9JF79;C9JRL4 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic;Malate dehydrogenase" 0 ;;;; 170.05 0.00069208 2293390000 1159110 1506900 1130450 1185930 1551290 987850 1493070 1293210 1626240 FALSE TRUE 1086563.374 1618472.444 1157264.808 1216362.972 1429457.941 1273026.259 1269198.014 1454670.115 1354810.038 0.802004225 1.194612085 0.854189721 0.897810717 1.055098428 0.939634504 0.936808836 1.073707807 1 20.36965915 1.241735741 24.99874907 1.036853905 0.967326722 0.079665872 0.10991973 231.4719081 1822571.026 0.076160326 0.025228686 17.4476018 -1.241735741 -0.069527183 ENFTAGS(ph)DCVTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ENFTAGSDCVTLK 13 0 Q1W6H9 Q1W6H9 FAM110C Protein FAM110C 1 ENFTAGS(1)DCVTLK;ENFTAGS(1)DCVTLK;ENFTAGS(1)DCVTLK 218.2 2.57E-11 300493000 775360 644916 649562 655562 727907 512721 954300 636277 1037800 TRUE FALSE 726831.6017 692666.2517 664969.9174 672384.8308 670740.1205 660735.2294 811211.5743 715717.5841 864584.4756 0.840671585 0.801155088 0.769120816 0.77769709 0.775794777 0.76422287 0.938267569 0.827816835 1 19.72164741 1.15129856 0.843866953 0.989529466 0.786107243 0.642770311 0.046812964 0.335818963 0.536219806 0.041994582 0.015456286 14.16767416 -1.15129856 -0.203422224 ENGDKSEAQKPSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENGDKSEAQKPSEK 14 2 A0A494C039;Q9Y4L1 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 104.45 0.00059438 131790000 642770 289510 433200 444360 377580 292670 649460 341580 315530 FALSE TRUE 602540.1731 310945.6216 443475.7086 455763.0299 347926.3899 377159.0779 552079.5023 384227.0149 262866.0046 2.29219512 1.18290542 1.687078971 1.733822639 1.323588383 1.434795947 2.100231649 1.461683931 1 18.00396805 4.758158872 23.88719264 1.548810385 2.292196388 0.386457695 0.309804203 2792.214657 3403169.802 0.071872114 2.563464694 57300.56073 -4.758158872 0.743386003 ENGEEGCHQNGLALPVVEEGEVLS(ph)HSLEAEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ENGEEGCHQNGLALPVVEEGEVLSHSLEAEHR 32 0 Q9HC44 Q9HC44 GPBP1L1 Vasculin-like protein 1 1 ENGEEGCHQNGLALPVVEEGEVLS(0.5)HS(0.5)LEAEHR;ENGEEGCHQNGLALPVVEEGEVLS(0.5)HS(0.5)LEAEHR 72.707 0.0012951 84451000 54947 66221 56201 65416 74787 59835 76043 66086 79002 TRUE FALSE 51507.96535 71124.07174 57534.11426 67094.68531 68913.5307 77108.39316 64641.0581 74336.98257 65816.05583 0.782604863 1.080649256 0.874165331 1.019427319 1.047062602 1.171574203 0.982147248 1.129465776 1 16.00615195 3.028703444 5.355765645 1.064177597 0.942636571 0.352033708 0.092119224 0.223064314 17.53930759 0.025028928 0.029476674 1068.325129 -3.028703444 -0.121541026 ENGFTQHVYHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ENGFTQHVYHK 11 0 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 0 ; 111.94 0.00092138 269610000 2302900 2157740 2279400 2206900 2589100 1659880 2844300 1964700 3402700 FALSE TRUE 2158765.6 2317501.315 2333468.444 2263532.79 2385762.53 2139060.41 2417823.62 2209997.12 2834767.388 0.761531831 0.81752786 0.823160466 0.798489781 0.841607865 0.754580577 0.85291782 0.779604397 1 21.43479893 -1.501754081 3.40468542 1.003840562 0.808738606 0.783092798 0.032374277 12236980.88 17437528.49 442476.4341 0.006745633 0.031495312 1.501754081 -0.195101956 ENGSGHEASLQLRPPPEPST(ph)PVSGQDDLIQHQDMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENGSGHEASLQLRPPPEPSTPVSGQDDLIQHQDMR 35 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 ENGSGHEASLQLRPPPEPS(0.207)T(0.663)PVS(0.13)GQDDLIQHQDMR 74.258 0.0026451 197250000 26174 32454 34093 30938 30771 27470 34421 29696 33446 TRUE FALSE 24535.81606 34856.92793 34901.70206 31731.92146 28354.36978 35400.14306 29259.8906 33403.61097 27863.64653 0.880567302 1.250982275 1.252589176 1.13882874 1.017611595 1.270477754 1.050109883 1.1988241 1 14.76609646 -1.600568618 0.417968877 0.894709199 1.155269582 0.074015173 0.124642993 70.20115417 5.836984201 7.737524022 0.070241111 0.025085998 1.600568618 0.260560383 ENIEKDEDDVDQELANIDPTWIES(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENIEKDEDDVDQELANIDPTWIESPK 26 1 P78362;P78362-2 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 1 ENIEKDEDDVDQELANIDPT(0.002)WIES(0.998)PK 78.588 0.012393 21120000 77833 19716 38911 33805 31321 25529 41855 23997 23387 TRUE FALSE 72961.57147 21175.79315 39833.9873 34672.49353 28861.175 32898.80787 35579.23131 26993.07827 19483.55861 3.74477645 1.08685449 2.044492389 1.779577038 1.481309219 1.688542043 1.82611565 1.385428546 1 14.24996959 4.747178107 24.85270201 1.604209784 3.744777627 0.814835538 0.329419146 411.4795722 1186672.098 0.072173598 0.848165666 55869.92737 -4.747178107 2.140567843 ENIKPNETS(ph)PSFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.067)S(0.895)PS(0.037)FS(0.001)K 161.84 1.19E-05 64254000 212110 109870 148700 149970 131950 108270 190650 125670 109720 TRUE FALSE 198834.4137 118004.8891 152227.2342 153818.4841 121587.1793 139525.7914 162063.8024 141360.1761 91407.02318 2.175264075 1.290982739 1.665377877 1.682786276 1.330173274 1.526423097 1.772990704 1.54649141 1 16.4800174 -1.74554556 1.939466605 0.807631667 1.59932314 0.383297334 0.246940955 494128.2361 256686.6764 453425.8159 0.059264229 0.017966126 1.74554556 0.791691473 ENILHVSENVIFTDVNSILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENILHVSENVIFTDVNSILR 20 0 P07814;V9GYZ6;V9GZ76 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 57.989 0.078269 12885000 13635 16968 17893 15920 13831 14817 20756 16489 10825 FALSE TRUE 12781.60969 18224.32838 18317.43041 16328.53415 12744.76905 19094.42737 17643.83049 18547.68795 9018.237568 1.417306829 2.020830372 2.031154122 1.810612554 1.413221703 2.117312526 1.956461044 2.056686554 1 13.1386298 3.03170133 24.65099538 1.796099935 1.898402541 0 0.371368952 972.8446994 756478.0606 0.100004831 0.119527581 1075.725169 -3.03170133 0.102302605 ENISEWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ENISEWR 7 0 B1ALA9;P60891;A0A2R8Y7H4;P60891-2 B1ALA9 PRPS1 Ribose-phosphate pyrophosphokinase 1 0 ;;;;; 110.12 0.015994 2078800000 3628300 3828920 3935120 3978250 3940640 3465080 4340610 3351200 3774200 FALSE TRUE 3401211.18 4112417.221 4028462.905 4080338.63 3631158.03 4465392.345 3689775.827 3769604.697 3144261.638 1.081720153 1.307911903 1.281211098 1.297709638 1.154852378 1.420172002 1.173495164 1.198883913 1 21.58428984 0.796589709 1.44258209 1.001395186 1.26175296 0.401290075 0.09353023 0.633695433 2.367528391 0.078449829 0.023097562 6.26022164 -0.796589709 0.260357774 ENIVEAIIHSPELIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ENIVEAIIHSPELIR 15 0 O95373;E9PLB2 O95373 IPO7 Importin-7 0 ;;;;; 180.64 6.21E-07 682112000 1072002 1214151 1195985 1256398 1234950 1056705 1373041 1159581 1112218 FALSE TRUE 1004907.308 1304048.003 1224354.329 1288639.3 1137962.009 1361758.579 1167166.249 1304357.24 926581.6306 1.08453187 1.407375195 1.321366935 1.390745572 1.228129256 1.469658511 1.259647515 1.407708935 1 19.82155856 -1.597176073 4.021170814 0.992089839 1.329616643 0.451164119 0.110967083 0.00682044 0.000683243 0.093123396 0.021550804 0.025282728 1.597176073 0.337526804 ENKPSIIFIDEIDSLCGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENKPSIIFIDEIDSLCGSR 19 1 O75351 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 0 111.38 0.00019825 29508000 75812 71024 74719 78729 80383 58905 92558 68467 81214 FALSE TRUE 71067.06225 76282.69086 76491.36996 80749.31943 74070.04343 75909.91726 78679.78717 77015.25566 67658.85874 1.050373352 1.127460502 1.130544786 1.193477409 1.094757506 1.121950897 1.162889659 1.138287833 1 16.04599122 -0.181745604 8.331887454 0.999998314 1.130878531 0.527072064 0.037823477 0 0 0.033956668 0.008003664 0.658043186 0.181745604 0.130880216 ENLATVEGNFASIDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENLATVEGNFASIDER 16 0 Q13561;Q13561-3;Q13561-2;H0YI98 Q13561 DCTN2 Dynactin subunit 2 0 166.9 1.52E-08 46562000 23197 29762 23046 23726 31882 18785 28701 22488 26620 FALSE TRUE 21745.14118 31965.60945 23592.662 24334.84933 29378.11633 24207.92455 24397.5515 25295.6763 22176.95003 0.980528934 1.441388893 1.063837091 1.0973037 1.324714007 1.091580426 1.100131058 1.140629179 1 14.43677335 1.017779743 0.348939729 0.983321916 1.219998402 0.105868065 0.134281928 2.796446624 0.996702786 0.242717088 0.138189415 10.41788942 -1.017779743 0.236676486 ENLISALEEAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ENLISALEEAKK 12 1 P22102;P22102-2 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ; 160.27 0.00010985 441510000 455550 293190 354050 349960 399410 249090 445250 308040 440510 FALSE TRUE 427037.9387 314898.0927 362448.2332 358940.5661 368041.9497 320998.2394 378488.896 346499.4721 366986.0352 1.163635391 0.8580656 0.987634946 0.978076907 1.002877261 0.874687886 1.031344138 0.944176178 1 18.48536564 -1.636837341 2.323031864 1.004237334 0.970276192 0 0.084952035 27928311.09 20436815.68 708784.5271 0.019556289 0.023076113 1.636837341 -0.033961142 ENLSAAFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENLSAAFSR 9 0 P15170-2;P15170-3 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 82.029 0.045623 128530000 147920 151270 122380 140730 168930 96684 135810 146930 168000 FALSE TRUE 138661.9512 162470.1882 125282.9114 144341.3701 155662.9192 124595.1013 115446.5513 165274.5339 139959.7147 0.990727593 1.160835377 0.895135516 1.031306547 1.112198032 0.890221172 0.824855578 1.180872184 1 17.0946521 2.228959242 24.99208334 0.94250689 1.034992205 0.040810554 0.115484103 418.6929985 1089837.386 0.041621128 0.031136361 169.4178796 -2.228959242 0.092485316 ENLVRPGIDHLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ENLVRPGIDHLGR 13 1 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 0 ; 175.29 1.11E-05 160940000 140499 186348 148390 154961 183873 139142 168694 160364 178739 FALSE TRUE 131705.4184 200145.3998 151909.8809 158937.5616 169432.3563 179310.0366 143399.9008 180385.7984 148906.3062 0.884485162 1.344102912 1.020170903 1.067366223 1.137845405 1.204180274 0.963021006 1.211404695 1 17.18404533 -4.99999994 0.214977957 0.44712917 1.12694692 0.032779802 0.133736924 452.0589858 4.518091107 107.8922706 0.248126486 1.00E-05 4.99999994 0.67981775 ENPEDVLS(ph)PTSVATYLSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ENPEDVLSPTSVATYLSSK 19 0 Q5JTU8;B1AMJ5;A0A0A0MRG9;Q96SN8-3;Q96SN8-2;Q96SN8;Q96SN8-4 Q5JTU8 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 1 ENPEDVLS(0.93)PT(0.062)S(0.008)VATYLSSK;ENPEDVLS(0.982)PT(0.015)S(0.002)VATYLSSK 166.61 2.05E-11 36224000 121424 105595 121983 137751 125758 75252 108693 80995 96431 TRUE FALSE 113824.2886 113413.3637 124876.4944 141285.9239 115881.474 96976.03079 92395.49371 91107.40404 80336.04313 1.416852065 1.411736989 1.554426749 1.758686616 1.442459318 1.207129789 1.150112578 1.134078808 1 16.29375978 2.213315472 2.926110396 1.12324161 1.524662182 0.785523691 0.104074213 0.128239769 2.258536858 0.045031011 0.032164982 163.4238628 -2.213315472 0.401420572 ENPEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 148.33 0.017284 714040000 1171710 964910 1092900 1052360 1128400 732920 1076370 1061520 1328810 FALSE TRUE 1098374.763 1036352.94 1118824.104 1079365.339 1039780.016 944502.106 914978.311 1194053.109 1107023.027 0.992187819 0.936162045 1.010660192 0.975016159 0.939257803 0.853191021 0.826521481 1.078616325 1 20.0782538 2.570196621 4.214595988 0.910481424 0.976355226 0 0.074374322 0.444195626 13.9229947 0.024078441 0.022266554 371.703475 -2.570196621 0.065873802 ENPPGPPIAASAPGPSQSLGLNVHNMTPATSPIGAS(ph)GVAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENPPGPPIAASAPGPSQSLGLNVHNMTPATSPIGASGVAHR 41 0 O95155-2;O95155;O95155-4 O95155-2 UBE4B Ubiquitin conjugation factor E4 B 1 ENPPGPPIAASAPGPS(0.169)QS(0.169)LGLNVHNMT(0.169)PAT(0.152)S(0.152)PIGAS(0.188)GVAHR 56.005 0.033411 55387000 12165 17739 20346 14979 14491 13261 13737 11311 12373 TRUE FALSE 11403.61437 19052.41402 20828.61673 15363.3865 13352.93531 17089.23543 11677.26438 12723.20325 10307.86637 1.106302115 1.848337312 2.020652576 1.490452626 1.295412148 1.657882904 1.132849802 1.23431977 1 13.33145812 1.898949981 0.783754012 1.035263614 1.721390462 0.334153623 0.273769071 0.595807958 0.690893094 0.241070539 0.119046581 79.2410061 -1.898949981 0.686126848 ENPPVEDS(ph)SDEDDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ENPPVEDSSDEDDKR 15 1 Q8TCJ2 Q8TCJ2 STT3B Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B 1 ENPPVEDS(0.791)S(0.209)DEDDKR;ENPPVEDS(0.973)S(0.027)DEDDKR 212.26 5.93E-10 975750000 470870 255920 249790 250730 286400 196196 394490 303810 211294 TRUE FALSE 441399.0872 274868.5831 255715.1368 257164.1563 263907.2993 252834.6002 335339.8868 341741.3473 176027.6664 2.507555183 1.561507851 1.452698556 1.460930327 1.499237618 1.436334443 1.905040802 1.94140702 1 17.42544267 4.738604927 23.20287342 1.562642797 2.507554061 0.574967382 0.262397941 0.971898112 504096.2573 0.05950625 0.342829192 54777.843 -4.738604927 0.944911264 ENPPVEDS(ph)SDEDDKRNQGNLYDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENPPVEDSSDEDDKRNQGNLYDK 23 2 Q8TCJ2 Q8TCJ2 STT3B Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B 1 ENPPVEDS(0.993)S(0.007)DEDDKRNQGNLYDK 131.95 1.50E-05 189080000 226870 147060 135820 154710 186840 86319 222710 119480 189810 TRUE FALSE 212670.6117 157948.4754 139041.7145 158680.1205 172166.3401 111237.894 189316.703 134397.341 158129.4848 1.34491434 0.998855309 0.879290252 1.003482183 1.088768109 0.703460801 1.197225826 0.849919553 1 17.27074687 4.737305895 4.179733951 0.966778056 1.375020145 0.445112505 0.133785288 0.191824407 7.56246817 0.028683099 0.234811968 54614.2401 -4.737305895 0.408242089 ENPSATLEDLEKPGVDEEPQHVLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ENPSATLEDLEKPGVDEEPQHVLLR 25 1 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 ; 238.2 1.03E-38 220540000 239990 205815 183336 148124 256190 129029 215100 226420 350290 FALSE TRUE 224969.4543 221053.7568 187684.8165 151925.1126 236069.8708 166277.5777 182847.7519 254689.0354 291824.336 0.770907106 0.757489111 0.643143129 0.520604672 0.808945114 0.569786536 0.626567867 0.872747759 1 18.15474067 1.064696102 4.040297988 0.997097188 0.669960261 0.615953769 0.089970237 0.122911574 3.890517657 0.083126896 0.021334762 11.60636173 -1.064696102 -0.327136927 ENPVYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ENPVYEK 7 0 P46777;A0A2R8Y6J3;A0A2R8Y4A2 P46777 RPL5 60S ribosomal protein L5 0 ;;; 114.5 0.013706 1191900000 1783480 1762940 1800550 1783770 1949210 1392710 2099230 1707620 2208420 FALSE TRUE 1671855.17 1893469.912 1843259.896 1829544.558 1796126.909 1794762.768 1784469.95 1920820.116 1839820.435 0.908705621 1.02916017 1.001869455 0.994414739 0.976251201 0.975509748 0.969915279 1.044025862 1 20.81113354 1.244401932 24.99261215 1.022012932 0.985917844 0.208640521 0.032634803 222.5993975 952442.6123 0.022203036 0.007640765 17.55504441 -1.244401932 -0.036095089 ENPYYDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ENPYYDSR 8 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 200.54 0.00027688 1710770000 1390230 2019190 1606870 1717960 2014100 1297100 1920380 1824120 1983470 FALSE TRUE 1303217.986 2168692.929 1644985.715 1762045.762 1855920.71 1671551.713 1632436.847 2051865.397 1652416.043 0.788674251 1.312437589 0.995503355 1.066345107 1.123155829 1.011580419 0.9879091 1.24173655 1 20.65614554 3.736983448 24.90396817 1.055974436 1.107768438 0 0.147660506 1668.328152 4212820.719 0.034498586 0.06129521 5457.370607 -3.736983448 0.051794001 ENQELNAHNQELNNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENQELNAHNQELNNR 15 0 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 0 157.74 1.03E-08 0 85665 87613 86823 79705 97340 64388 93007 86516 109310 FALSE TRUE 80303.38057 94099.95768 88882.48256 81750.36524 89695.30905 82975.77035 79061.46378 97317.71305 91065.45483 0.881820452 1.033322217 0.976028536 0.897709954 0.984954275 0.911166265 0.868182824 1.068656751 1 16.47461626 3.443606965 24.9215846 0.941162873 0.981123394 0 0.068584105 486.603002 361842.1298 0.017802899 0.024105728 2777.198775 -3.443606965 0.039960521 ENQPENSQT(ph)PTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ENQPENSQTPTKK 13 1 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 ENQPENSQT(0.998)PT(0.002)KK;ENQPENSQT(0.996)PT(0.003)KK;ENQPENSQT(1)PTKK;ENQPENS(0.001)QT(0.999)PTKK;ENQPENS(0.001)QT(0.998)PT(0.001)KK 199.61 6.82E-08 5316710000 4146090 2192270 2872620 2591150 2854740 2051460 3856620 2425600 3612340 TRUE FALSE 3886593.628 2354587.952 2940759.903 2657643.296 2630540.236 2643683.199 3278355.634 2728441.499 3009417.117 1.291477212 0.782406646 0.977185876 0.883108985 0.874102902 0.878470181 1.08936565 0.906634539 1 21.52105265 1.755012052 25 1.006125893 0.92677846 0.012923155 0.141527247 17.3900154 26456.76039 0.059125936 0.032789205 56.88687172 -1.755012052 -0.079347433 ENQPENSQTPT(ph)KK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENQPENSQTPTKK 13 1 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 ENQPENS(0.038)QT(0.34)PT(0.622)KK 135.47 5.37E-06 0 207150 107780 147350 127090 149860 97600 196340 115530 178190 TRUE FALSE 194184.8513 115760.1433 150845.2116 130351.3446 138090.6001 125775.5356 166900.6397 129954.1748 148448.9378 1.308091887 0.779797721 1.016142074 0.878088765 0.930222891 0.847264638 1.124296624 0.875413302 1 17.17960725 ENQRS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 105.2 0.0026846 2167430000 1464700 1972520 1265110 1369960 2073020 941281 1371760 1741430 1750180 TRUE FALSE 1373027.042 2118567.433 1295119.007 1405115.493 1910213.371 1213013.544 1166077.323 1958851.369 1458063.651 0.941678397 1.45300065 0.888245863 0.963685976 1.310102868 0.831934561 0.799743771 1.343460806 1 20.47562227 3.888224582 6.634468302 0.998253647 1.224803548 0.093651506 0.218358973 0.368923615 22.78963695 0.05294331 0.096545428 7730.802567 -3.888224582 0.226549901 ENREDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENREDYR 7 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 61.999 0.080348 47822000 35280 58010 44998 50515 69014 43648 37907 50940 81045 FALSE TRUE 33071.88778 62305.12076 46065.37381 51811.30042 63593.91883 56248.46903 32223.19726 57299.97113 67518.06593 0.489822795 0.922791847 0.682267378 0.76736944 0.941880043 0.833087682 0.477252967 0.848661323 1 16.04298596 4.758514272 23.94270765 0.778362679 0.489822311 0.288658731 0.150805162 3869.298018 4642698.325 0.035809483 1.340308775 57347.4712 -4.758514272 -0.288540369 ENRKRIIS(ph)PS(ph)FDNIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENRKRIISPSFDNIK 15 3 Q6P9A2 Q6P9A2 GALNT18 Polypeptide N-acetylgalactosaminyltransferase 18 2 ENRKRIIS(1)PS(1)FDNIK 69.081 0.072809 1413600000 821820 1903800 1164900 1556000 1602800 620180 1706100 1228600 2681700 TRUE FALSE 770383.7532 2044759.333 1192531.978 1595929.594 1476922.553 799215.8982 1450286.144 1381993.414 2234106.946 0.344828503 0.915246845 0.533784643 0.714347895 0.661079612 0.357733948 0.649156992 0.618588746 1 21.09126682 0.275131063 2.958549732 0.999999979 0.61831849 0.358642754 0.166671895 123.0533246 497.7511304 0.149238528 0.039040259 1.884217629 -0.275131063 -0.381681489 ENS(ph)FGSPLEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ENSFGSPLEFR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ENS(0.975)FGS(0.025)PLEFR;ENS(0.967)FGS(0.033)PLEFR;ENS(0.991)FGS(0.009)PLEFR 158.31 3.15E-05 198588000 346352 278548 294792 296112 261348 202692 285863 213743 242450 TRUE FALSE 324674.4466 299171.9837 301784.6055 303710.7352 240822.7823 261205.89 243000.497 240429.2841 201983.5287 1.607430312 1.481170201 1.494105026 1.5036411 1.192289212 1.293203914 1.203070857 1.190341042 1 17.62387812 2.302623452 0.361112805 0.994468665 1.627606899 0.878330788 0.065950322 0.454599487 0.140947002 0.075436675 0.102548071 200.7351614 -2.302623452 0.633138234 ENS(ph)PSSQSAGLSSINK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ENSPSSQSAGLSSINK 16 0 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2 H3BSS6 ZNF106 Zinc finger protein 106 1 ENS(0.812)PS(0.181)S(0.007)QSAGLSSINK;ENS(0.937)PS(0.063)SQSAGLSSINK 334.98 1.14E-71 278040000 382820 209582 276460 243710 234809 207044 317190 219869 225481 TRUE FALSE 358859.9796 225099.6693 283017.7618 249964.0112 216368.0483 266814.2417 269630.3041 247320.1286 187846.7644 1.910386802 1.198315393 1.506641664 1.330680419 1.151832713 1.420382419 1.435373694 1.316605742 1 17.51919674 -3.48641406 0.061093963 1.34E-30 1.956032316 0.37879836 0.192248958 372.6467621 2.218443272 69.40497032 17.11570118 0.000326277 3.48641406 1.956032316 ENS(ph)REALAEAALESPRPALVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ENSREALAEAALESPRPALVR 21 2 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 ENS(1)REALAEAALESPRPALVR;ENS(1)REALAEAALESPRPALVR 186.84 1.61E-17 214140000 146258 106362 112632 124538 143785 84942 121375 94645 133554 TRUE FALSE 137103.9729 114237.1531 115303.6842 127733.8559 132492.7061 109463.3765 103175.9455 106461.6366 111262.9746 1.232251549 1.026731072 1.03631675 1.148035601 1.190806794 0.983825723 0.927316081 0.956846938 1 16.76361406 2.083759705 7.276520145 0.953877767 1.101491589 0.573504569 0.066631155 0.184355252 13.54084861 0.026088699 0.019209529 121.2717669 -2.083759705 0.147613822 ENS(ph)SPSVTSANLDHTKPCWYWDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENSSPSVTSANLDHTKPCWYWDK 23 1 O75909;G3V5E1;O75909-1;O75909-4;G3V2Q3;O75909-2;G3V235 O75909 CCNK Cyclin-K 1 ENS(0.499)S(0.499)PS(0.002)VTSANLDHTKPCWYWDK 186.56 1.63E-17 47959000 238950 151950 195840 185050 192460 152970 250550 192260 169270 TRUE FALSE 223994.546 163200.5361 200485.4173 189798.6963 177344.9679 197129.9557 212982.3535 216264.0842 141017.7435 1.588413915 1.157304975 1.421703485 1.345920674 1.257607472 1.397908879 1.510323086 1.533594843 1 17.10551717 2.021555017 23.83625467 1.417035428 1.33547138 0 0.184251754 472.7261509 522752.4476 0.061665573 0.045537491 105.0884574 -2.021555017 -0.081564048 ENSFGS(ph)PLEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ENSFGSPLEFR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ENS(0.01)FGS(0.99)PLEFR;ENS(0.004)FGS(0.996)PLEFR;ENS(0.001)FGS(0.999)PLEFR;ENSFGS(1)PLEFR;ENSFGS(1)PLEFR;ENS(0.012)FGS(0.988)PLEFR 228.66 3.26E-12 5638640000 5216270 4422120 4845960 4510000 4369340 5445840 6574260 4637930 3346770 TRUE FALSE 4889792.972 4749538.366 4960908.46 4625734.235 4026189.661 7017965.602 5588510.745 5216985.77 2788172.466 1.753762736 1.703459317 1.779268865 1.659055992 1.444024611 2.5170486 2.004363365 1.871113008 1 21.41088837 ENSS(ph)PENKNWLLAMAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ENSSPENKNWLLAMAAK 17 1 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 1 ENS(0.174)S(0.826)PENKNWLLAMAAK;ENS(0.041)S(0.959)PENKNWLLAMAAK 259.6 1.99E-27 1410210000 2679690 1803230 2240220 2069380 2474930 1532850 2922100 1873360 2940340 TRUE FALSE 2511972.986 1936743.025 2293359.076 2122483.794 2280558.981 1975358.911 2483958.232 2107253.12 2449578.259 1.02547162 0.790643458 0.93622609 0.866469069 0.931000662 0.806407758 1.014035058 0.860251397 1 21.22410195 0.495330406 0.517764361 1.003510082 0.888629979 0.099808898 0.079097416 3.574276621 1.728423607 0.111147511 0.035412352 3.128458556 -0.495330406 -0.114880103 ENTEGEYSGIEHVIVDGVVQSIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ENTEGEYSGIEHVIVDGVVQSIK 23 0 H0YL72;P50213;P50213-2;H0YLI6;H0YMU3 H0YL72 IDH3A "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial" 0 ; 279.74 6.81E-52 211740000 315830 257510 275970 246640 344640 248280 275240 270110 399540 FALSE TRUE 296062.7641 276576.3083 282516.1387 252969.2 317573.3646 319954.4055 233970.3172 303833.8281 332854.1929 0.889466831 0.830923312 0.848768454 0.76000004 0.954091525 0.961244931 0.702921346 0.912813582 1 18.34453082 2.740137956 24.97240661 0.877354713 0.834808406 0.104113969 0.087207365 485.4225586 7685261.873 0.02728675 0.027552036 549.7154662 -2.740137956 -0.042546307 ENTEGEYSSLEHESVAGVVESLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENTEGEYSSLEHESVAGVVESLK 23 0 E9PF84;G5E9Q7;E7EQB8;P51553-2;P51553;H7C1W2 E9PF84 IDH3G "Isocitrate dehydrogenase [NAD] subunit, mitochondrial;Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial" 0 162.01 1.71E-11 35527000 46458 60026 62255 61908 83022 60575 68150 66712 83602 FALSE TRUE 43550.27671 64470.3875 63731.718 63496.66409 76501.78701 78062.01915 57931.54017 75041.14005 69648.28611 0.625288563 0.925656482 0.915050772 0.911675902 1.098401573 1.12080316 0.83177266 1.077429815 1 16.08780023 5.254835539 1.085970865 0.986290618 6.24E-30 0.603603472 0.092059241 3.427062039 1.527843326 0.026380174 5.084668747 179818.9836 -5.254835539 -0.986290618 ENTHQTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ENTHQTLK 8 0 C9JRZ6;Q9NX63 C9JRZ6 CHCHD3 MICOS complex subunit MIC19 0 ; 95.502 0.0096049 312120000 431900 473720 428220 436860 617520 380060 565840 538020 784370 FALSE TRUE 404868.15 508794.7217 438377.5806 448070.5672 569022.4702 489777.1522 480997.545 605192.9813 653453.5798 0.619582113 0.778624125 0.67086262 0.685696094 0.87079249 0.749520957 0.736085255 0.92614533 1 19.31772523 0.825696879 0.440502665 1.021617856 0.696577678 0.658222677 0.06954677 0.905154058 0.421743666 0.100154844 0.044881188 6.694172182 -0.825696879 -0.325040178 ENTLFDIHRS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENTLFDIHRSPAR 13 1 Q9ULI0-2;Q9ULI0;C9JG15 Q9ULI0-2 ATAD2B ATPase family AAA domain-containing protein 2B 1 ENTLFDIHRS(1)PAR 100.45 0.001447 61308000 63061 69961 93943 129510 85112 102990 86655 59966 209150 TRUE FALSE 59114.12458 75140.98523 96171.37232 132833.4459 78427.64685 132721.5411 73661.88722 67452.8871 174241.5138 0.339265444 0.431246168 0.551942934 0.762352455 0.450108847 0.761710216 0.422757388 0.38712294 1 17.41072887 -2.39376279 2.311600922 4.912764722 0.518916848 0.524547707 0.145530389 5924754.532 377679.8163 122619901.5 0.034111059 0.004038659 2.39376279 -4.393847874 ENTVGLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ENTVGLHR 8 0 Q10713;Q10713-2 Q10713 PMPCA Mitochondrial-processing peptidase subunit alpha 0 78.113 0.031467 110140000 69765 71337 65678 65186 83040 65509 62937 67155 96023 FALSE TRUE 65398.53318 76618.86571 67235.91318 66858.78312 76518.37337 84420.38485 53500.18113 75539.44958 79996.14097 0.8175211 0.957782023 0.840489458 0.835775105 0.956525808 1.055305716 0.668784525 0.94428867 1 16.28764279 1.00354474 24.99713134 1.000000118 0.875966921 0.144122375 0.102502217 151.7032719 1069784.612 0.094512313 0.023628078 10.08195465 -1.00354474 -0.124033196 ENVEYIEREES(ph)DGEYDEFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ENVEYIEREESDGEYDEFGR 20 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 ENVEYIEREES(1)DGEYDEFGR;ENVEYIEREES(1)DGEYDEFGR;ENVEYIEREES(1)DGEYDEFGR;ENVEYIEREES(1)DGEYDEFGR;ENVEYIEREES(1)DGEYDEFGR;ENVEYIEREES(1)DGEYDEFGR;ENVEYIEREES(1)DGEYDEFGR;ENVEYIEREES(1)DGEYDEFGR 240.18 6.55E-30 25221580000 5713260 7109590 6407450 6770540 7506010 4650820 6685200 5728490 7013350 TRUE FALSE 5355677.255 7635991.441 6559437.74 6944283.519 6916518.252 5993436.234 5682816.322 6443704.586 5842776.577 0.916632218 1.306911421 1.122657636 1.18852457 1.183772503 1.025785627 0.972622562 1.102849733 1 22.47822269 2.23116844 21.52507469 1.017729944 1.165123966 0.233001802 0.102312093 33.40941095 97279.23392 0.034619191 0.026189749 170.2818814 -2.23116844 0.147394021 ENVEYIEREES(ph)DGEYDEFGRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 188.22 2.04E-17 1323300000 600530 454790 477560 502870 554990 335513 581740 447590 697890 TRUE FALSE 562943.8993 488463.1248 488887.9487 515774.4956 511403.3241 432370.1565 494513.4876 503472.5968 581407.6505 0.96824302 0.840138798 0.84086948 0.887113362 0.879595106 0.743660934 0.850545202 0.865954544 1 19.14919053 0.760198442 3.941837888 0.99999613 0.851255692 0.384232737 0.05536195 3.043716948 49.12355042 0.049808425 0.012736941 5.757029333 -0.760198442 -0.148740437 ENVFQEHQTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ENVFQEHQTLK 11 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;; 145.6 3.62E-05 1750560000 1786370 1908470 1977720 1922300 2039190 1479000 2345310 1875020 2288200 FALSE TRUE 1674564.29 2049775.105 2024632.452 1971629.472 1879040.243 1905963.29 1993652.538 2109120.374 1906284.638 0.878443994 1.07527232 1.062082971 1.034278635 0.985708118 0.999831427 1.045831509 1.106403699 1 20.86233212 4.746022245 24.77419518 1.041156832 0.878443906 0.647371146 0.037124897 519.3216318 1724210.981 0.009051868 0.093738048 55721.42896 -4.746022245 -0.162712926 ENYSHHTQDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ENYSHHTQDDR 11 0 Q92804-2;Q92804;A0A075B7D9;A0A075B7E4;A0A075B7F2 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ; 198.49 3.09E-08 793760000 217998 354450 339580 349560 366180 289960 365010 308567 240895 FALSE TRUE 204353.8943 380693.8468 347634.998 358530.3014 337421.6999 373666.7449 310280.1391 347092.2692 200688.0683 1.018266288 1.896943102 1.732215577 1.786505319 1.681324171 1.861928056 1.546081647 1.729511237 1 17.61459532 -0.899492826 6.613695609 0.999999964 1.688103553 0.402939221 0.248567101 1.18E-07 1.97E-08 0.213149868 0.050239903 0.126039646 0.899492826 0.68810359 ENYSHHTQDDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ENYSHHTQDDRR 12 1 Q92804-2;Q92804;A0A075B7D9;A0A075B7E4;A0A075B7F2 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ; 198.33 1.20E-07 994410000 280825 636400 554004 530940 666597 479107 578225 585575 604823 FALSE TRUE 263248.6645 683519.7182 567145.2365 544564.8193 614245.1605 617417.4132 491525.5292 658685.3278 503874.134 0.522449252 1.356528689 1.125569261 1.080755654 1.219044835 1.225340559 0.97549268 1.307241796 1 18.94270387 4.749508112 24.77360258 1.162830252 0.522448836 0.728496924 0.122553897 734.7382107 1662637.594 0.027943304 0.414593655 56170.47696 -4.749508112 -0.640381416 EPAAAISRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EPAAAISRPR 10 1 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ;;; 178.46 2.02E-06 1575100000 712390 841690 761370 802760 882430 625930 863500 723630 800250 FALSE TRUE 667802.7816 904009.6034 779430.0559 823360.1807 813127.5074 806625.8299 734026.1913 813976.7984 666683.1052 1.001679473 1.35598097 1.169116256 1.235009818 1.219661187 1.209908911 1.101012138 1.220935092 1 19.34664164 0.158375546 0.467004914 0.980628338 1.219109741 0.259851878 0.093993924 3.862737789 1.204136764 0.241507772 0.047631356 1.440043283 -0.158375546 0.238481403 EPAESAAVAHERPPGGTGSADPERPPGATCPES(ph)PGPGPPHPLGVVESGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EPAESAAVAHERPPGGTGSADPERPPGATCPESPGPGPPHPLGVVESGK 49 2 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 EPAESAAVAHERPPGGTGSADPERPPGATCPES(1)PGPGPPHPLGVVESGK;EPAESAAVAHERPPGGTGSADPERPPGAT(0.01)CPES(0.99)PGPGPPHPLGVVESGK;EPAES(0.003)AAVAHERPPGGT(0.01)GS(0.01)ADPERPPGAT(0.069)CPES(0.908)PGPGPPHPLGVVESGK 219.51 3.43E-50 844390000 236066 192632 231747 235481 229600 210621 299751 227834 247725 TRUE FALSE 221291.0504 206894.6737 237244.1483 241523.8411 211568.1422 271423.8636 254806.1203 256279.5764 206378.0971 1.072260349 1.002503059 1.149560693 1.170297839 1.025148236 1.315177663 1.234656797 1.241796392 1 17.65493034 3.460794234 0.842761564 1.202240374 1.027330799 0.178574809 0.098841419 0.858086532 1.25217821 0.042372011 0.098778044 2889.310622 -3.460794234 -0.174909574 EPAHLMSLFGGKPMIIYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EPAHLMSLFGGKPMIIYK 18 1 P06396-2;A0A0A0MS51;A0A0A0MT01;P06396-4;P06396-3;P06396 P06396-2 GSN Gelsolin 0 154.82 1.40E-08 126710000 275190 352460 290890 303790 443400 209720 365740 357940 404710 FALSE TRUE 257966.3491 378556.5051 297790.0482 311585.7657 408577.1526 270262.7595 310900.6824 402629.5969 337161.2865 0.765112602 1.122775717 0.883227287 0.924144551 1.211815143 0.801583012 0.922112635 1.194175052 1 18.36307937 4.762565408 23.88152437 0.99171615 0.765112112 0.234446316 0.134993592 5967.309729 5936490.519 0.030040256 1.735436394 57884.91611 -4.762565408 -0.226604038 EPAITSQNS(ph)PEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 EPAITSQNSPEAR 13 0 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;E5RIS7 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 1 EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR;EPAITS(0.001)QNS(0.999)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR 319.91 6.09E-51 5368160000 1770619 1715742 1780065 1633334 1631652 1668847 1939566 1643236 1620430 TRUE FALSE 1659799.117 1842777.323 1822288.982 1675248.116 1503508.634 2150616.037 1648746.084 1848397.632 1349969.765 1.229508365 1.365050812 1.349873923 1.240952323 1.113735043 1.593084596 1.221320749 1.369214097 1 20.36449566 -1.277356253 3.694038298 0.999343749 1.316405835 0.36853297 0.127448169 21408677.61 28107203.07 152192.9248 0.027498684 0.052801194 1.277356253 0.317062086 EPCITPSGITYDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EPCITPSGITYDRK 14 1 Q9UNE7;Q9UNE7-2;H3BTA3;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 102.9 0.0018388 87798000 148320 118400 113830 113600 128970 88282 140230 120700 171590 FALSE TRUE 139036.916 127166.4592 116530.1014 116515.1683 118841.2164 113767.5803 119203.8133 135769.6607 142950.5205 0.972622663 0.889583744 0.815177874 0.815073411 0.831345112 0.795852858 0.833881632 0.949766816 1 17.12515635 1.104575414 3.961236928 0.997623063 0.845883759 0.521769921 0.050450204 0.161148451 4.352158677 0.048303801 0.012476272 12.72258654 -1.104575414 -0.151739303 EPDCFKDIVNMLMHHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EPDCFKDIVNMLMHHDR 17 1 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;; 190.55 1.89E-10 533656000 475655 558144 537954 564999 700611 429762 685107 518095 943067 FALSE TRUE 445884.6026 599469.5625 550714.5229 579497.8309 645587.8382 553827.3128 582381.5656 582780.3012 785663.0253 0.56752652 0.763011041 0.700955124 0.737590815 0.821710858 0.704917115 0.741261262 0.741768777 1 19.58355114 -5 0.214941527 2.33748017 0.690092384 0.692438603 0.060115984 84.35180288 0.843040637 48.7743363 0.112277178 1.00E-05 5 -1.647387786 EPEAASSRGS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EPEAASSRGSPVR 13 1 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EPEAAS(0.01)S(0.094)RGS(0.896)PVR;EPEAAS(0.002)S(0.018)RGS(0.979)PVR 106.28 0.00083986 844810000 602110 1003490 686270 835300 1063580 469410 867000 709570 1610020 TRUE FALSE 564425.0099 1077789.444 702548.6485 856735.2122 980050.7171 604921.0468 737001.3988 798161.3765 1341297.261 0.42080531 0.803542567 0.523782959 0.638736272 0.730673763 0.450997004 0.5494691 0.595066731 1 20.35519757 -1.506140134 2.775142636 1.017064832 0.598354886 0.549543071 0.116638439 13801809.41 14465339.06 1790397.68 0.026824779 0.031178834 1.506140134 -0.418709945 EPEKEIRPALELLEPIEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EPEKEIRPALELLEPIEQK 19 2 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 99.34 0.0004567 161279000 390210 281440 304580 310820 372390 212864 424530 298990 512810 FALSE TRUE 365787.4526 302278.1104 311804.7814 318796.1674 343143.9915 274314.3812 360875.6676 336319.5597 427218.6981 0.856206562 0.707548878 0.729848162 0.746213049 0.803204525 0.642093575 0.844709441 0.787230431 1 18.70461527 0.584350457 0.935567768 1.000028096 0.745272822 0.586259493 0.062826913 0.850391977 1.187805649 0.054457957 0.017701706 3.840170057 -0.584350457 -0.254755274 EPELFQTVAEGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EPELFQTVAEGLR 13 0 A0A024R571;Q9H4M9;C9JC03;C9JIJ3;C9IZH1 A0A024R571 EHD1 EH domain-containing protein 1 0 74.392 0.07964 28851000 24659 35954 32158 32352 40376 27026 36239 28920 47986 FALSE TRUE 23115.63721 38616.07157 32920.80295 33182.20709 37205.03183 34827.96747 30805.29838 32530.72566 39976.8266 0.578225917 0.965961405 0.823497154 0.830036046 0.930664963 0.871203906 0.770578883 0.813739569 1 15.28687633 4.751394983 24.85453558 0.865100414 0.578225719 0.622093158 0.072448761 1358.196785 2630180.211 0.016768341 0.308355882 56415.05077 -4.751394983 -0.286874695 EPELGLEELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EPELGLEELLR 11 0 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 0 ;; 111.06 0.0039813 34331500 48203 45068 43821 43798 44795 34867.8 44411 38525 47063 FALSE TRUE 45186.06027 48404.88161 44860.45481 44921.93083 41276.98139 44933.56783 37751.98284 43334.93105 39207.88126 1.152473911 1.234570195 1.144169319 1.14573727 1.052772557 1.146034072 0.9628672 1.10526072 1 15.25885606 2.709479654 0.672338659 1.017819375 1.204537821 0.568253371 0.052690882 0.45009423 0.433388524 0.035772938 0.035982189 512.2472723 -2.709479654 0.186718447 EPEQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EPEQLR 6 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;F8W646;P51991;P51991-2 F8W6I7;P51991;P51991-2 HNRNPA1;HNRNPA1L2;HNRNPA3 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2;Heterogeneous nuclear ribonucleoprotein A3" 0 ; 116.11 0.05549 1651170000 885270 809320 858740 842200 808950 862290 998170 787400 644560 FALSE TRUE 829862.531 869242.8949 879109.7183 863812.2778 745418.3301 1111219.125 848503.6751 885708.6233 536978.772 1.545428934 1.618765844 1.637140543 1.608652563 1.388170946 2.069391162 1.580143796 1.649429492 1 19.03450553 -1.481291027 6.194853613 0.999607194 1.64195441 0.579249026 0.170610575 0.000834709 6.99E-05 0.148973499 0.035093027 0.033014823 1.481291027 0.642347215 EPEQLRK ddPTM_SK-BR-3_Pertuzumab_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 90.308 0.027633 1082800000 947190 767340 824610 779170 820130 759680 1043800 776210 662920 FALSE TRUE 887907.0687 824154.652 844170.1386 799164.8213 755720.298 978987.2836 887291.8802 873121.5271 552274.3694 1.607728184 1.492292052 1.528533978 1.447043111 1.368378364 1.772646601 1.606614265 1.580956089 1 19.07502565 -1.068579372 5.09719685 0.999990183 1.549055085 0.720578652 0.107734298 1.21E-05 2.21E-06 0.104842578 0.024711191 0.085392677 1.068579372 0.549064902 EPFELEAFYTNLHEVPYPDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EPFELEAFYTNLHEVPYPDAR 21 0 O95757;E9PDE8;D6RJ96 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 ;;; 219.34 5.09E-25 659980000 420449 476945 466884 478745 537757 386183 519085 449123 482486 FALSE TRUE 394133.8476 512258.5041 477958.709 491030.4072 495523.7344 497667.7629 441253.0232 505196.9952 401955.9696 0.980539854 1.27441447 1.18908225 1.221602475 1.23278113 1.238115118 1.097764573 1.256846604 1 18.61667795 -1.867158412 2.490022902 0.910261079 1.19221937 0.306418472 0.087741747 13079339.57 7718949.763 6941305.486 0.019175503 0.013578181 1.867158412 0.281958291 EPFFHGHDNYDQLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EPFFHGHDNYDQLVR 15 0 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2 P68400 CSNK2A1 Casein kinase II subunit alpha 0 ;;; 255.91 5.62E-25 839610000 543139 611490 559920 500694 589880 440407 626070 597550 566450 FALSE TRUE 509144.8995 656765.3559 573201.5668 513542.6557 543553.2043 567545.3515 532196.6156 672155.4329 471905.8356 1.078912065 1.391729676 1.214652423 1.088231204 1.151825562 1.202666525 1.127760192 1.424342278 1 18.84813949 -2.321293728 2.080684555 4.53E-05 1.214526754 0.243395165 0.11612539 2393830.58 316837.3707 11246867.72 0.02736811 0.004772064 2.321293728 1.214481421 EPFGTEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EPFGTEGR 8 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 110.03 0.0081545 437710000 1117750 1331910 1344890 1321440 1368500 1227640 1521150 1282770 1401900 FALSE TRUE 1047792.023 1430526.002 1376791.426 1355350.388 1261023.53 1582039.739 1293067.679 1442926.658 1167913.833 0.897148396 1.224855774 1.178846749 1.160488342 1.079723088 1.354586009 1.107160171 1.235473557 1 20.15550241 4.744539663 24.50819391 1.1779307 0.897148233 0.435104614 0.096227659 422.1729603 1730428.128 0.019705717 0.178751366 55531.53298 -4.744539663 -0.280782467 EPFPTIYVDSQKENER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EPFPTIYVDSQKENER 16 1 O43776;K7EIU7;O43776-2;K7EJ19;K7EPK2;K7EQ35 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 151.59 5.73E-07 176600000 156190 138050 146020 142690 158340 101970 161440 122890 184530 FALSE TRUE 146414.3467 148271.3656 149483.6634 146351.667 145904.6151 131407.0837 137233.5707 138233.087 153730.7509 0.952407673 0.964487357 0.972373208 0.951999949 0.94909193 0.854787236 0.892687832 0.899189565 1 17.23004625 2.411201947 8.835748092 0.899962924 0.961792162 0.258652882 0.037127811 0.276635921 34.0136311 0.011433557 0.009558945 257.7519426 -2.411201947 0.061829239 EPGS(ph)GTESDTSPDFHNQENEPSQEDPEDLDGSVQGVKPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EPGSGTESDTSPDFHNQENEPSQEDPEDLDGSVQGVKPQK 40 1 Q9HAF1-3;Q9HAF1-2;Q9HAF1;Q9HAF1-4;B1AK63 Q9HAF1-3 MEAF6 Chromatin modification-related protein MEAF6 1 EPGS(0.203)GT(0.203)ES(0.188)DT(0.203)S(0.203)PDFHNQENEPS(0.001)QEDPEDLDGSVQGVKPQK 85.531 0.00025863 49502000 52622 34914 41112 42294 44379 31472 45697 27261 41408 TRUE FALSE 49328.48295 37499.06889 42087.19605 43379.33564 40893.65236 40557.45549 38845.15908 30664.59586 34496.73729 1.429946332 1.087032335 1.220034106 1.25749097 1.185435365 1.175689606 1.126053132 0.888912931 1 15.0741723 1.432625408 2.962629288 0.945636236 1.208143365 0.602046471 0.092116004 0.169479288 2.690569654 0.066523209 0.022170247 27.07855017 -1.432625408 0.262507128 EPGSGTESDT(ph)SPDFHNQENEPSQEDPEDLDGSVQGVKPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EPGSGTESDTSPDFHNQENEPSQEDPEDLDGSVQGVKPQK 40 1 Q9HAF1-3;Q9HAF1-2;Q9HAF1;Q9HAF1-4;B1AK63 Q9HAF1-3 MEAF6 Chromatin modification-related protein MEAF6 1 EPGS(0.253)GT(0.07)ES(0.07)DT(0.3)S(0.3)PDFHNQENEPS(0.007)QEDPEDLDGSVQGVKPQK 67.775 0.0049972 70129000 29306 23988 26541 23142 30290 21031 27155 23457 32457 TRUE FALSE 27471.78977 25764.09648 27170.56505 23735.8629 27911.14558 27102.30829 23083.35984 26385.65809 27039.71702 1.015979189 0.95282419 1.004839105 0.877814767 1.032227725 1.00231479 0.853683484 0.975811177 1 14.72279243 EPHLNYS(ph)PTCLEPPVLSIHPGAID ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EPHLNYSPTCLEPPVLSIHPGAID 24 0 O75054;O75054-2 O75054 IGSF3 Immunoglobulin superfamily member 3 1 EPHLNY(0.001)S(0.897)PT(0.102)CLEPPVLSIHPGAID;EPHLNY(0.002)S(0.973)PT(0.025)CLEPPVLSIHPGAID;EPHLNY(0.016)S(0.87)PT(0.113)CLEPPVLSIHPGAID 126.99 1.23E-05 102371000 55138 100716 88416 121809 138441 58244 68151 58041 60520 TRUE FALSE 51687.011 108173.1174 90513.26927 124934.8252 127568.4023 75058.09729 57932.39023 65287.54661 50418.82103 1.025153107 2.145490815 1.795227802 2.477940234 2.530174243 1.488692035 1.149023104 1.29490427 1 15.62167476 2.031038074 8.115909324 1.202071812 2.011312404 0.464173498 0.418549014 0.190709062 42.8618413 0.152554124 0.111550326 107.4083572 -2.031038074 0.809240592 EPHS(ph)PADQPEQQAESTLTSAETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EPHSPADQPEQQAESTLTSAETR 23 0 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2;H3BS99 H3BSS6 ZNF106 Zinc finger protein 106 1 EPHS(1)PADQPEQQAESTLTSAETR;EPHS(1)PADQPEQQAESTLTSAETR 305.4 1.45E-62 1356910000 315680 267010 293670 280000 241550 280180 338920 269730 239270 TRUE FALSE 295922.1523 286779.6982 300635.9911 287185.274 222579.6374 361063.4177 288102.0924 303406.3842 199334.2913 1.484552158 1.438687224 1.508200065 1.440721876 1.116614888 1.811346233 1.445321277 1.522098292 1 17.60483039 -1.660009025 2.635378899 0.93991249 1.47308187 0.442572879 0.166085577 18270838.61 15988201.99 7415987.616 0.036451131 0.021877162 1.660009025 0.53316938 EPHSFQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EPHSFQSR 8 0 F8VR84;Q9HB07;F8VQQ3;H3BPH3 F8VR84 C12orf10 "UPF0160 protein MYG1, mitochondrial" 0 86.136 0.016248 118900000 25733 34332 34448 21862 33216 21394 20290 26691 33651 FALSE TRUE 24122.41746 36873.977 35265.12283 22423.01593 30607.34935 27570.1005 17247.70286 30023.4301 28034.43071 0.860456833 1.315310355 1.257921846 0.799838462 1.091777096 0.983437145 0.615232856 1.07094845 1 14.77491215 3.243145191 24.99698308 0.899487128 1.197345882 0.211541575 0.184190301 121.2540037 661121.7991 0.050702713 0.06642143 1750.431786 -3.243145191 0.297858754 EPLGPALAHELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 EPLGPALAHELR 12 0 Q13228;Q13228-4;Q13228-2;Q13228-3 Q13228 SELENBP1 Selenium-binding protein 1 0 ;;;;;; 186.76 1.13E-05 2289300000 1565686 1834877 1435874 1391598 1686260 1180261 1598770 1630825 1330830 FALSE TRUE 1467692.508 1970733.202 1469933.609 1427308.761 1553827.942 1520983.191 1359049.281 1834437.091 1108705.876 1.323788879 1.777507674 1.325810246 1.287364658 1.401478946 1.371854542 1.225797852 1.654575061 1 20.08044526 -4.101259241 0.110957868 8.51E-11 1.665259985 0.307461021 0.17902043 143.5236248 1.297237307 35.70067569 2.18342921 7.92E-05 4.101259241 1.665259985 EPLIPAS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EPLIPASPK 9 0 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 EPLIPAS(1)PK;EPLIPAS(1)PK;EPLIPAS(1)PK 100.93 0.0045379 212696000 1036710 794530 961580 1228410 1325010 579710 879130 641340 907740 TRUE FALSE 971824.1717 853357.8279 984389.1317 1259933.08 1220949.059 747062.8662 747312.6179 721412.7108 756232.3298 1.285086783 1.128433412 1.301701994 1.666066142 1.614515819 0.987874806 0.988205064 0.953956453 1 19.52847 2.207792755 23.59830088 0.982467802 1.361085577 0.630479838 0.157003804 89.23121428 68437.47446 0.06720909 0.049645195 161.3588371 -2.207792755 0.378617774 EPNEDCKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 150.61 7.74E-05 915270000 1126690 938290 1007890 1019040 1073740 825900 1278720 924120 1195200 FALSE TRUE 1056172.484 1007761.968 1031797.627 1045190.292 989412.7917 1064323.923 1086987.807 1039498.416 995713.3987 1.060719365 1.012100439 1.036239573 1.049689894 0.993672268 1.068905896 1.09166735 1.043973514 1 19.92537102 2.187470363 24.99998626 1.062661602 1.029634989 0.048115108 0.030127304 148.8572754 72839.21459 0.010273496 0.007587487 153.9821443 -2.187470363 -0.033026613 EPPADVWT(ph)PPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EPPADVWTPPAR 12 0 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 1 EPPADVWT(1)PPAR 119.25 0.0060083 93499000 62794 67820 71610 76448 72720 63369 76148 57689 79281 TRUE FALSE 58863.83563 72841.46337 73308.62302 78409.78511 67008.86454 81662.60159 64730.31432 64891.59864 66048.48893 0.891221534 1.102848295 1.109921275 1.187154867 1.014540463 1.236403783 0.98004232 0.982484228 1 16.01123794 1.605771256 25 0.985932058 1.095814173 0.213856629 0.092535812 0.287158601 3367.633226 0.042471472 0.021166489 40.34328477 -1.605771256 0.109882115 EPPPPYVTPATFET(ph)PEVHAGTGVVGNKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EPPPPYVTPATFETPEVHAGTGVVGNKPR 29 1 Q96DF8;F8WEF8 Q96DF8 DGCR14 Protein DGCR14 1 EPPPPYVTPAT(0.008)FET(0.984)PEVHAGT(0.009)GVVGNKPR;EPPPPYVTPAT(0.002)FET(0.995)PEVHAGT(0.003)GVVGNKPR 133.47 1.38E-05 155227000 86859 79215 86546 83738 99235 73147 113555 94556 77225 TRUE FALSE 81422.65024 85080.16102 88598.91199 85886.85885 91441.48339 94263.35146 96528.48194 106361.5247 64335.64861 1.265591503 1.322441957 1.377135599 1.33498085 1.421319057 1.465180712 1.500388727 1.653228452 1 15.97333074 2.66260782 2.653230899 1.452815241 1.331264021 0.023165973 0.168064902 0.63133983 8.738499938 0.052433066 0.049865683 459.8411367 -2.66260782 -0.121551219 EPPSS(ph)PLQPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EPPSSPLQPQK 11 0 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 EPPS(0.023)S(0.977)PLQPQK;EPPS(0.142)S(0.858)PLQPQK 160.56 2.87E-05 489430000 1439630 1118850 1457620 1654220 1378900 887890 1113110 752490 670590 TRUE FALSE 1349526.128 1201690.818 1492195.435 1696670.086 1270606.756 1144209.429 946209.4891 846440.0329 558664.1968 2.41563024 2.151007394 2.671006023 3.037012387 2.274365824 2.048116625 1.693699891 1.515114156 1 19.09162184 1.587170285 1.064031744 1.09814418 2.517158202 0.824096335 0.244377237 0.204993531 0.444703317 0.2311012 0.086151041 38.65184993 -1.587170285 1.419014022 EPPTVPS(ph)ER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EPPTVPSER 9 0 P27815 P27815 PDE4A "cAMP-specific 3,5-cyclic phosphodiesterase 4A" 1 EPPT(0.001)VPS(0.999)ER 55.806 0.081209 721910000 102830 132220 159450 148410 160800 114100 141380 135980 175570 TRUE FALSE 96394.05386 142009.7064 163232.2293 152218.4519 148171.4166 147038.8177 120181.3815 152957.4023 146266.2328 0.659031494 0.970898776 1.115993939 1.040694417 1.013025452 1.005282046 0.821661837 1.045746509 1 17.15823722 4.735361468 4.316495605 1.000101674 0.634600282 0.681265137 0.073942216 0.139238786 6.178898811 0.020033679 0.155940731 54370.26734 -4.735361468 -0.365501393 EPQLAFHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EPQLAFHQR 9 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;; 98.943 0.0053852 388900000 416101 544190 441783 435115 583960 350770 465362 502100 546010 FALSE TRUE 390057.9812 584482.3938 452262.3014 446280.7875 538098.1372 452031.6047 395585.2883 564788.2903 454877.4036 0.857501336 1.284922903 0.994250973 0.981101246 1.182952006 0.993743811 0.869652537 1.241627493 1 18.79511824 EPS(ph)PALGPNLDGSGLLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EPSPALGPNLDGSGLLPR 18 0 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 1 EPS(1)PALGPNLDGSGLLPR;EPS(1)PALGPNLDGSGLLPR;EPS(1)PALGPNLDGSGLLPR;EPS(1)PALGPNLDGSGLLPR;EPS(1)PALGPNLDGSGLLPR;EPS(1)PALGPNLDGSGLLPR 217.67 8.70E-19 950870000 234942.8 191468.9 227927.1 212969.1 184243.3 218904.1 234058.3 187167.4 146652.1 TRUE FALSE 220238.1495 205645.4566 233333.6384 218434.2477 169773.5744 282098.1601 198963.4308 210535.6619 122174.9171 1.802646196 1.683205207 1.909832591 1.787881284 1.389594349 2.308969523 1.628512918 1.723231469 1 16.8985886 0.528360863 1.721847868 1.000309662 1.793666545 0.532028352 0.230853157 2.037743981 6.611831906 0.195888077 0.055258787 3.375676833 -0.528360863 0.793356883 EPS(ph)PALGPNLDGSGLLPRPIFYCSFPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EPSPALGPNLDGSGLLPRPIFYCSFPTR 28 1 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 1 EPS(1)PALGPNLDGSGLLPRPIFYCSFPTR;EPS(1)PALGPNLDGSGLLPRPIFYCSFPTR 167.56 3.33E-12 222340000 36729 27682 29302 36029 35316 26503 30468 25498 35078 TRUE FALSE 34430.19745 29731.60408 29997.05728 36953.56514 32542.42382 34153.98586 25899.60625 28681.48143 29223.25519 1.178178038 1.017395355 1.026478983 1.264525971 1.113579703 1.168726264 0.886266984 0.981460869 1 14.83482927 1.740194903 14.32046198 0.951271255 1.108319577 0.506500249 0.078486329 0.062529313 145.2853553 0.038388127 0.021154242 54.97875529 -1.740194903 0.157048322 EPS(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 EPSPEK 6 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 EPS(1)PEK;EPS(1)PEK;EPS(1)PEK;EPS(1)PEK;EPS(1)PEK;EPS(1)PEK;EPS(1)PEK 93.162 0.048181 7664900000 22267070 10798460 15337430 13273160 11901370 11365010 17653690 11915740 10381130 TRUE FALSE 20873413.84 11597989.21 15701241.08 13613771.76 10966684.41 14645903.89 15006683.07 13403446.37 8648452.338 2.413543258 1.341047943 1.815497209 1.57412809 1.268051667 1.693471077 1.735187116 1.549808665 1 23.04401055 -2.808473449 0.196418385 1.17E-31 1.786643297 0.366832855 0.299582978 63.65189177 1.364693903 28.81854631 0.763930696 0.00155427 2.808473449 1.786643297 EPS(ph)PEKNSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EPSPEKNSK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 EPS(1)PEKNSK;EPS(1)PEKNSK;EPS(1)PEKNSK;EPS(1)PEKNSK;EPS(1)PEKNSK;EPS(1)PEKNSK 119.39 0.00050607 6974310000 9070320 5285710 6506170 6758860 7827710 4276690 8704880 5229060 11325070 TRUE FALSE 8502624.862 5677069.468 6660499.425 6932303.79 7212953.232 5511300.977 7399664.056 5881919.652 9434842.654 0.901194135 0.601713211 0.705947059 0.734755633 0.764501698 0.58414339 0.784291199 0.623425304 1 23.16956703 -1.904526287 2.740325326 1.161818408 0.704419336 0.473225364 0.094989611 18564840.72 10837330.19 19331654.09 0.021385128 0.012458728 1.904526287 -0.457399072 EPS(ph)PKQDVVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EPSPKQDVVGK 11 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-4;Q9ULU4-2 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 EPS(1)PKQDVVGK 77.776 0.019003 0 349990 328410 312490 324640 458380 186660 329840 262790 840920 TRUE FALSE 328084.7506 352725.8181 319902.4104 332970.812 422380.6838 240545.7118 280383.5541 295599.91 700565.0194 0.468314491 0.503487625 0.456634861 0.475288949 0.602914322 0.343359581 0.400224885 0.421945004 1 19.41815943 -1.408154382 3.746001346 1.003286993 0.458074485 0.863115001 0.067704935 79942662.38 149457202.4 2930951.466 0.016514543 0.039070198 1.408154382 -0.545212507 EPSAPSIPTPAYQSS(ph)PAGGHAPTPPTPAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EPSAPSIPTPAYQSSPAGGHAPTPPTPAPR 30 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 1 EPSAPSIPTPAYQS(0.148)S(0.852)PAGGHAPTPPTPAPR;EPSAPSIPT(0.003)PAY(0.016)QS(0.044)S(0.936)PAGGHAPTPPTPAPR;EPSAPSIPTPAYQS(0.059)S(0.941)PAGGHAPTPPTPAPR;EPSAPSIPTPAYQS(0.029)S(0.971)PAGGHAPTPPTPAPR;EPSAPSIPTPAYQS(0.288)S(0.712)PAGGHAPTPPTPAPR 205.01 9.56E-26 3234740000 646817 702227 764968 723185 722049 683774 882980 661093 856516 TRUE FALSE 606333.8786 754220.6177 783113.4022 741743.1514 665342.1841 881168.4537 750585.3462 743631.9163 713557.9463 0.849733202 1.056985801 1.097476955 1.039499532 0.932429087 1.234894038 1.051891231 1.0421465 1 19.44467107 2.284675194 24.99998702 1.088143456 1.019602955 0.151077545 0.092524987 271.5843631 147232.1165 0.030854474 0.025814612 192.608387 -2.284675194 -0.068540501 EPSEVPT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EPSEVPTPK 9 0 P17096;P17096-3;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 1 EPSEVPT(1)PK 98.754 0.064834 698640000 672900 413400 544720 466430 494130 398360 684750 428570 575060 TRUE FALSE 630784.3902 444008.5661 557641.0156 478399.3835 455323.023 513360.0652 582078.0944 482077.9079 479078.771 1.316661118 0.926796579 1.16398607 0.998581888 0.950413691 1.071556696 1.214994547 1.006260217 1 18.86990336 -0.576343877 7.562828942 1 1.078164371 0.041445369 0.121905357 0 0 0.108522999 0.025579116 0.265250446 0.576343877 0.078164371 EPSTAS(ph)GGGQLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EPSTASGGGQLNR 13 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 EPS(0.001)T(0.054)AS(0.945)GGGQLNR 122.56 0.00016125 0 255690 275750 260580 227990 230210 226860 315460 242910 308290 TRUE FALSE 239686.8193 296166.8169 266761.0807 233840.6094 212130.2352 292350.7992 268159.7016 273237.8482 256834.4074 0.933234849 1.15314307 1.038650091 0.910472284 0.825941654 1.138285178 1.044095705 1.06386777 1 17.97047896 -0.186415294 7.613954173 1.000000002 1.026459229 0 0.101523919 0 0 0.098486723 0.023213543 0.651005573 0.186415294 0.026459227 EPSVPASCAVSATYERS(ph)PS(ph)PAHLPDDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EPSVPASCAVSATYERSPSPAHLPDDPK 28 1 Q92615;H0Y4V9;H0Y641 Q92615 LARP4B La-related protein 4B 2 EPSVPASCAVSAT(0.002)Y(0.001)ERS(0.997)PS(1)PAHLPDDPK;EPSVPASCAVS(0.007)AT(0.034)Y(0.004)ERS(0.955)PS(0.999)PAHLPDDPK 180.47 1.97E-17 373421000 364283 255465 285741 315248 315001 207373 349715 249887 328151 TRUE FALSE 341483.1773 274379.8944 292518.9115 323337.7974 290262.0921 267238.2187 297278.4823 281085.942 273380.4782 1.249113249 1.00365577 1.070006584 1.182739161 1.061751351 0.977532194 1.087416645 1.02818586 1 18.0605507 2.481602312 24.93348624 1.032874706 1.099101094 0.279381975 0.071953397 348.8568808 1941124.265 0.02405217 0.020614533 303.111429 -2.481602312 0.066226388 EPSVPASCAVSATYERS(ph)PSPAHLPDDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EPSVPASCAVSATYERSPSPAHLPDDPK 28 1 Q92615;H0Y4V9;H0Y641 Q92615 LARP4B La-related protein 4B 1 EPSVPAS(0.001)CAVS(0.007)AT(0.075)YERS(0.861)PS(0.055)PAHLPDDPK 69.045 0.0075357 91203000 44390 111140 79542 88765 104080 70546 94837 72755 119090 TRUE FALSE 41611.70914 119368.9212 81428.7738 91042.86018 95905.97664 90911.48498 80617.07227 81838.6219 99213.10965 0.419417447 1.203156737 0.82074611 0.917649497 0.966666371 0.916325325 0.812564716 0.824877097 1 16.59824315 -0.241516029 7.584508127 0.999999869 0.88905928 0.030397514 0.194776745 0 0 0.168354813 0.03968161 0.573434702 0.241516029 -0.110940589 EPTEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EPTEEER 7 0 Q15056;Q15056-2 Q15056;Q15056-2;REV__B4E135 EIF4H Eukaryotic translation initiation factor 4H 0 ;; 157.99 0.003347 2043630000 1675810 1721760 1837250 1763870 1696840 1662840 1940500 1564440 1279810 FALSE TRUE 1570924.044 1849240.902 1880830.438 1809133.89 1563577.031 2142874.914 1649540.04 1759763.778 1066201.443 1.473383903 1.734419808 1.76404792 1.696803078 1.466493073 2.00982181 1.547118558 1.650498402 1 20.02404861 0.312535707 1.300653072 0.999525961 1.691998841 0.636418149 0.158407231 2.543429976 4.245903839 0.13647026 0.040068183 2.053693871 -0.312535707 0.69247288 EPTGVEENKTDSLFVLPS(ph)RDDATPVRDEPMDAESITFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EPTGVEENKTDSLFVLPSRDDATPVRDEPMDAESITFK 38 3 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 EPT(0.001)GVEENKT(0.003)DS(0.01)LFVLPS(0.828)RDDAT(0.157)PVRDEPMDAESITFK 65.377 0.028192 234430000 122090 78225 90335 91580 101950 73387 121200 86372 150650 TRUE FALSE 114448.6048 84016.86039 92477.78886 93930.09784 93943.25825 94572.63556 103027.1852 97155.73433 125505.5418 0.911900807 0.669427495 0.736842275 0.748413947 0.748518806 0.753533543 0.820897498 0.774115095 1 16.93739154 0.075423066 0.551514881 1.01754631 0.744112379 0.553159866 0.06380228 2.477136098 0.95090016 0.155821654 0.026339004 1.189660566 -0.075423066 -0.273433931 EPTGVEENKTDSLFVLPSRDDAT(ph)PVRDEPMDAESITFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EPTGVEENKTDSLFVLPSRDDATPVRDEPMDAESITFK 38 3 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 EPT(0.001)GVEENKT(0.001)DS(0.004)LFVLPS(0.023)RDDAT(0.972)PVRDEPMDAESITFK 90.351 0.00024795 50850000 43220 35970 35114 36059 45921 32862 41468 39962 88785 TRUE FALSE 40514.93735 38633.25623 35946.92066 36984.33499 42314.5499 42348.72593 35250.25837 44951.34367 73966.20993 0.547749268 0.522309528 0.485991113 0.50001663 0.572079466 0.572541516 0.476572457 0.607728092 1 16.17457873 0.848349677 4.342904255 0.999981585 0.522473819 0.953501301 0.032712113 0.231528522 6.404830757 0.031723854 0.008069264 7.052606881 -0.848349677 -0.477507766 EPTPS(ph)IAS(ph)DISLPIATQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EPTPSIASDISLPIATQELR 20 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5 A0A499FIX8 ESYT2 Extended synaptotagmin-2 2 EPT(0.159)PS(0.876)IAS(0.959)DIS(0.006)LPIATQELR 59.9 0.09188 24784000 31177 40839 28786 31090 48189 34401 40445 43922 39211 TRUE FALSE 29225.68722 43862.76205 29468.81751 31887.82204 44404.43033 44332.01025 34380.64772 49405.75838 32666.43079 0.894670355 1.34274731 0.902113173 0.976164866 1.359329111 1.357112154 1.052476408 1.512432096 1 14.99552121 2.743118125 24.94433671 1.250606031 1.060092698 0.249662105 0.192364092 619.0322368 3388113.307 0.056434342 0.058075405 553.5006374 -2.743118125 -0.190513332 EPTPS(ph)IASDISLPIATQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EPTPSIASDISLPIATQELR 20 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5 A0A499FIX8 ESYT2 Extended synaptotagmin-2 1 EPT(0.205)PS(0.795)IASDISLPIATQELR;EPT(0.001)PS(0.999)IASDISLPIATQELR 230.05 2.04E-25 46238000 37967 53808 45164 39007 59673 44474 48611 53644 51692 TRUE FALSE 35590.71324 57792.00031 46235.31141 40007.98566 54986.52329 57312.92182 41322.23183 60341.57149 43064.27126 0.826455718 1.341994155 1.073635059 0.929029669 1.276847876 1.330869423 0.959547918 1.401198017 1 15.3942038 2.690839667 24.99973195 1.183364591 1.097789901 0.104909174 0.189732613 1437.38514 753006.438 0.058589874 0.055239192 490.726676 -2.690839667 -0.08557469 EPTPSIAS(ph)DIS(ph)LPIATQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EPTPSIASDISLPIATQELR 20 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5 A0A499FIX8 ESYT2 Extended synaptotagmin-2 2 EPTPSIAS(1)DIS(1)LPIATQELR;EPTPSIAS(1)DIS(1)LPIATQELR 148.26 1.64E-07 114868000 227363 218234 207515 230579 237034 185832 316210 222524 236843 TRUE FALSE 213132.7557 234392.2724 212437.3538 236496.0475 218418.3058 239478.6817 268797.246 250306.6112 197312.3732 1.080179373 1.187924855 1.076655003 1.19858701 1.106967101 1.213703316 1.362292905 1.268580409 1 17.5901219 2.065892284 5.571650724 1.25940706 1.134673153 0.072113054 0.101161257 0.254088036 14.99822887 0.034707575 0.02516384 116.3837333 -2.065892284 -0.124733908 EPTPSIAS(ph)DISLPIATQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EPTPSIASDISLPIATQELR 20 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5 A0A499FIX8 ESYT2 Extended synaptotagmin-2 1 EPTPSIAS(1)DISLPIATQELR;EPTPSIAS(1)DISLPIATQELR;EPTPSIAS(1)DISLPIATQELR;EPTPSIAS(1)DISLPIATQELR 275.91 1.66E-44 819060000 332681 326538 306271 316663 369165 335134 393754 330262 302060 TRUE FALSE 311859.0901 350715.2133 313535.8928 324789.1087 340172.27 431881.7454 334714.2431 371495.9377 251644.2346 1.239285655 1.393694609 1.245949041 1.290667792 1.351798385 1.716239381 1.330108928 1.476274385 1 17.94102602 -1.52428084 6.124821247 0.999539403 1.37758564 0.428412387 0.138087789 0.000842824 6.55E-05 0.129749915 0.030546383 0.029903303 1.52428084 0.378046237 EPTPSIASDIS(ph)LPIATQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EPTPSIASDISLPIATQELR 20 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5 A0A499FIX8 ESYT2 Extended synaptotagmin-2 1 EPTPSIASDIS(1)LPIATQELR;EPTPS(0.001)IAS(0.035)DIS(0.964)LPIATQELR;EPTPSIAS(0.001)DIS(0.999)LPIATQELR;EPTPSIASDIS(1)LPIATQELR 184.8 4.07E-17 112256000 146088 154457 120950 127763 172918 115344 177769 147990 171178 TRUE FALSE 136944.6129 165893.157 123818.9911 131041.6149 159337.7178 148641.9403 151114.1888 166466.8773 142607.2859 0.960291839 1.163286685 0.868251508 0.918898456 1.117318212 1.042316592 1.059652652 1.167309764 1 17.12168817 2.725603046 24.80870742 1.076244342 0.990377777 0.239341626 0.086952305 1232.775114 2360282.748 0.028471836 0.026998286 531.6221241 -2.725603046 -0.085866564 EPWLLPSQHNDIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EPWLLPSQHNDIIR 14 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 154.6 6.08E-06 698810000 602208 1282780 976920 1013600 1270480 703558 1073050 1131810 1020360 FALSE TRUE 564516.8763 1377758.366 1000093.004 1039610.692 1170701.626 906663.7733 912156.1142 1273118.97 850055.3242 0.664094277 1.620786703 1.176503429 1.222991801 1.377206392 1.066593841 1.073054998 1.497689543 1 19.69719721 2.229592618 24.99583881 1.151996422 1.263618642 0 0.271880756 746.8095577 2081510.308 0.093220445 0.069862716 169.6651392 -2.229592618 0.11162222 EPYGHLGPAELLEAS(ph)PAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EPYGHLGPAELLEASPAAR 19 0 Q9H6W3 Q9H6W3 NO66 Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 1 EPYGHLGPAELLEAS(1)PAAR;EPYGHLGPAELLEAS(1)PAAR;EPYGHLGPAELLEAS(1)PAAR;EPYGHLGPAELLEAS(1)PAAR 234.39 2.52E-24 352663000 192176 206738 216550 211415 231234 188315 260029 218485 269241 TRUE FALSE 180148.0472 222045.0966 221686.6683 216840.2668 213073.8144 242678.4835 221040.0654 245763.3332 224302.9377 0.803146178 0.989933966 0.988336 0.9667295 0.949937689 1.081922894 0.985453279 1.095675945 1 17.77508899 5.408785761 1.443907725 1.007517545 6.06E-09 0.650099755 0.046882877 4.482231224 2.090127547 0.011686215 10.48295546 256321.9278 -5.408785761 -1.007517539 EQAEAEVASLNR ddPTM_SK-BR-3_Pertuzumab_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 ; 196.67 4.74E-07 904490000 526000 607260 627550 565080 567960 473450 610850 482610 486110 FALSE TRUE 493078.5989 652222.1623 642435.7824 579580.9095 523354.7126 610127.3292 519258.7134 542864.9209 404975.1006 1.217552877 1.610524107 1.58635872 1.431151961 1.29231331 1.506579857 1.282199109 1.340489625 1 18.62747368 0.691953332 0.452736371 0.973846637 1.508933227 0.516813218 0.127200418 1.162107542 0.518072595 0.19638344 0.077424582 4.919866656 -0.691953332 0.53508659 EQAEAEVASLNRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 253.16 1.43E-23 899630000 681210 937670 765800 879310 971500 659700 956250 712350 1185940 FALSE TRUE 638574.2821 1007096.062 783965.1376 901874.5833 895202.3088 850144.6807 812869.1899 801288.4656 987998.9525 0.64633093 1.019329079 0.793487823 0.912829493 0.906076172 0.860471237 0.822742967 0.811021574 1 19.91414999 -2.4797979 2.100564871 2.436656752 0.85893857 0.190100335 0.096577906 5290672.551 346035.7274 36271250.28 0.020916544 0.003312853 2.4797979 -1.577718182 EQAEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQAEEER 7 0 Q9UII2;A0A0B4J230;Q9UII2-3;Q9UII2-2 Q9UII2 ATPIF1 "ATPase inhibitor, mitochondrial" 0 ; 166.78 0.0025837 945130000 2273800 2241400 2222000 2037200 2706800 2020700 1920920 2133000 3235400 FALSE TRUE 2131486.917 2407355.588 2274706.889 2089478.001 2494218.847 2604043.287 1632895.879 2399309.745 2695390.839 0.790789553 0.893137854 0.843924694 0.77520409 0.925364445 0.966109719 0.605810429 0.890152816 1 21.36206305 EQAQPPENGKET(ph)SPSHPGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQAQPPENGKETSPSHPGFK 20 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 EQAQPPENGKET(0.636)S(0.364)PS(0.001)HPGFK 152.41 9.48E-08 1391900000 1633500 937820 1191200 1161300 1384300 838860 1529700 1133800 1438600 TRUE FALSE 1531262.151 1007257.169 1219455.827 1191100.924 1275582.662 1081025.264 1300335.686 1275357.426 1198488.366 1.277661256 0.840439671 1.017494922 0.993836033 1.064326278 0.90199062 1.084979815 1.064138344 1 20.19278447 1.624130812 25 1.05591829 0.996644152 0 0.116138317 2.684575604 4116.643045 0.049266086 0.027215002 42.08533727 -1.624130812 -0.059274138 EQAQPPENGKETS(ph)PSHPGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EQAQPPENGKETSPSHPGFK 20 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 EQAQPPENGKET(0.343)S(0.654)PS(0.003)HPGFK;EQAQPPENGKET(0.377)S(0.615)PS(0.009)HPGFK;EQAQPPENGKET(0.035)S(0.96)PS(0.005)HPGFK 213.7 2.94E-23 1623490000 1760510 993440 1378380 1207680 1490090 920770 1616220 1178780 1632370 TRUE FALSE 1650322.822 1066995.331 1411075.825 1238671.113 1373064.342 1186581.352 1373882.815 1325953.278 1359916.901 1.213546813 0.784603331 1.037619154 0.910843238 1.009667826 0.872539602 1.010269682 0.975025221 1 20.37508707 1.609268095 24.99999992 0.99448662 0.95558701 0 0.113034125 0.657008472 11282.15391 0.049636831 0.025636334 40.66943089 -1.609268095 -0.03889961 EQCCYNCGKPGHLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 88.133 0.0041477 983500000 619530 578580 587990 688200 744590 403690 541240 527060 727300 FALSE TRUE 580754.7232 621418.6652 601937.4005 705860.3771 686112.9049 520228.7496 460086.0866 592864.6012 605908.9315 0.958485167 1.025597467 0.993445333 1.164961169 1.132369683 0.858592311 0.759332076 0.978471467 1 19.20874145 2.222651629 24.96249726 0.86548664 1.047575724 0.397747217 0.090979477 203.3469053 319065.7434 0.033781648 0.025029252 166.9750679 -2.222651629 0.182089084 EQDDELRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQDDELRK 8 1 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ; 85.731 0.026513 1432470000 3007500 2231390 2582900 2443500 2740500 1882480 3154900 2207200 2879200 FALSE TRUE 2819265.944 2396604.437 2644167.608 2506204.347 2525272.185 2425921.416 2681852.034 2482773.779 2398642.92 1.17535875 0.999150152 1.102359833 1.044842618 1.052792045 1.011372471 1.118070561 1.035074357 1 21.19378697 1.367442906 0.007267944 2.62E-07 2.100146346 0.193526368 0.051015847 4419.115835 30.53052883 4423.206816 4395.231092 23.30466723 -1.367442906 2.100146083 EQDFFFELDAMDHLQSFIADCDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 EQDFFFELDAMDHLQSFIADCDRR 24 1 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ;;;;;;;;;;; 313.16 1.03E-73 1241407000 816310 1005026 922360 986750 1120394 919256 1127973 900083 1255299 FALSE TRUE 765218.6143 1079439.171 944238.8148 1012071.676 1032402.775 1184630.284 958843.9202 1012460.344 1045781.487 0.731719411 1.032184241 0.902902591 0.967765913 0.987206971 1.132770372 0.916868325 0.968137566 1 19.99615001 4.745414752 24.74409774 0.98361422 0.731719277 0.616416962 0.063550583 476.6515745 1720707.748 0.014572343 0.143281489 55643.5401 -4.745414752 -0.251894943 EQDLPLAEAVRPKT(ph)PPVVIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EQDLPLAEAVRPKTPPVVIK 20 2 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 1 EQDLPLAEAVRPKT(1)PPVVIK;EQDLPLAEAVRPKT(1)PPVVIK;EQDLPLAEAVRPKT(1)PPVVIK;EQDLPLAEAVRPKT(1)PPVVIK 138.78 1.90E-06 2346670000 2554990 1974180 2108280 2267040 2774140 1347820 2672280 1828320 3812770 TRUE FALSE 2395077.737 2120350.341 2158289.397 2325216.084 2556270.235 1736913.754 2271596.422 2056589.777 3176394.056 0.754024121 0.667533783 0.679477848 0.732030108 0.80477113 0.546819357 0.715149438 0.647460529 1 21.59895847 -1.549545729 2.99411608 1.013885624 0.68965938 0.661933932 0.068811965 21726732.95 24533085.96 2435778.715 0.015096623 0.028213325 1.549545729 -0.324226243 EQDLQLEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQDLQLEELR 10 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ; 113.27 0.0051952 168130000 224560 404340 325250 335400 362710 373630 365090 329780 328120 FALSE TRUE 210505.1905 434277.7543 332965.0836 344006.9318 334224.2197 481490.9156 310348.1438 370953.7589 273354.6523 0.770080877 1.58869714 1.218069935 1.25846379 1.222676172 1.761414747 1.135331487 1.357042055 1 18.0604144 -0.952937524 3.824335678 0.999971932 1.314367227 0.099362412 0.263741575 32711212.98 67474966.63 14021.80328 0.056036709 0.111445484 0.952937524 0.314395295 EQDVVTGVS(ph)PLLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EQDVVTGVSPLLFR 14 0 Q6P0Q8;Q6P0Q8-2 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 EQDVVT(0.005)GVS(0.995)PLLFR;EQDVVT(0.097)GVS(0.903)PLLFR;EQDVVT(0.074)GVS(0.926)PLLFR;EQDVVT(0.139)GVS(0.861)PLLFR 139.08 1.22E-05 124790000 162300 167887 167417 169296 200454 166861 253573 196561 199921 TRUE FALSE 152141.9327 180317.5282 171388.2103 173640.422 184711.1514 215031.0619 215552.0827 221102.0735 166552.8936 0.91347517 1.082644224 1.029031719 1.04255422 1.109023971 1.291067704 1.294195964 1.327518657 1 17.34562089 2.412545464 3.360453283 1.258343427 1.031748579 0.479859426 0.10071228 0.172560911 3.974669394 0.033018505 0.027393433 258.5505488 -2.412545464 -0.226594848 EQDYLCHVYVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EQDYLCHVYVR 11 0 O15498;O15498-2 O15498 YKT6 Synaptobrevin homolog YKT6 0 ;; 180.24 6.75E-06 878130000 1038560 1236000 1147570 1158670 1217500 959710 1340060 1152780 994730 FALSE TRUE 973558.3835 1327514.726 1174790.902 1188403.434 1121882.461 1236762.697 1139130.444 1296707.121 828703.1368 1.174797512 1.601918307 1.417625746 1.434052052 1.353780879 1.492407404 1.374594101 1.564742624 1 19.66049586 -1.466354999 3.271193936 0.992142177 1.437869926 0.559450659 0.118644748 13899795.86 22880638.98 1039168.232 0.025278861 0.034170002 1.466354999 0.445727749 EQEELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQEELER 7 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 127.02 0.0090623 134560000 250930 215470 229440 206370 209730 169080 241770 183800 242430 FALSE TRUE 235224.7392 231423.623 234882.4251 211665.8036 193258.6518 217890.6512 205518.833 206747.8346 201966.8668 1.164669943 1.145849449 1.162975041 1.048022415 0.956882952 1.078843548 1.017586875 1.02367204 1 17.62375911 3.172255188 4.552745125 1.020365008 1.156359432 0.821355331 0.030348111 0.075460407 3.045459538 0.008152316 0.010040628 1486.809024 -3.172255188 0.135994423 EQEELRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EQEELRR 7 1 Q8WXF1;Q8WXF1-2;A0A0U1RQF9 Q8WXF1 PSPC1 Paraspeckle component 1 0 ;; 114.28 0.0095247 1225981000 1133740 1613890 1406500 1504610 1621990 1240240 1447960 1422210 1671920 FALSE TRUE 1062781.237 1733384.095 1439862.844 1543220.84 1494605.448 1598277.154 1230851.84 1599776.049 1392865.751 0.763017711 1.244473198 1.033741294 1.107946576 1.073043434 1.147473942 0.883683039 1.148550065 1 20.40962478 -1.714933144 6.610067187 0.999219817 1.059773327 0.008744969 0.138215958 0.001453705 6.27E-05 0.122421651 0.028487178 0.019278217 1.714933144 0.06055351 EQEKGEGS(ph)DSKESPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQEKGEGSDSKESPK 15 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 1 EQEKGEGS(0.997)DS(0.003)KESPK 126.22 4.47E-05 314800000 634920 178030 307770 306040 315840 201460 436470 218270 479320 TRUE FALSE 595181.4906 191211.5264 315070.4497 313893.5045 291035.2004 259618.2316 371025.3755 245521.49 399318.3955 1.490493544 0.478844773 0.789020624 0.786073239 0.728829936 0.650153448 0.929146715 0.614851439 1 18.60718001 -1.171668961 6.960081184 1.000000379 0.778301041 0.036715691 0.271908261 1.41E-06 1.67E-07 0.230608302 0.054354805 0.067348983 1.171668961 -0.221699338 EQELDTLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQELDTLKR 9 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 84.31 0.024979 402920000 462080 517060 420780 349490 560320 288280 497280 477330 554870 FALSE TRUE 433159.2376 555343.6604 430761.1003 358458.5051 516314.7274 371501.7562 422717.4805 536925.7012 462258.6124 0.937049578 1.201370068 0.931861708 0.775450139 1.116939119 0.803666489 0.914461016 1.161526658 1 18.81834067 3.758383036 6.34674188 0.942073423 1.083005469 0.094268463 0.135501662 0.298416077 38.03316023 0.032093649 0.057010244 5733.014448 -3.758383036 0.140932046 EQELQQTLQQEQSVLDQLRGEAEAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 244.71 2.52E-45 257541000 43291.5 67437.8 59759.2 62651 80256 38558.4 65842.6 54363.3 106480 FALSE TRUE 40581.96229 72430.96488 61176.71644 64258.73073 73953.0175 49689.58414 55970.11338 61150.67767 88707.80011 0.457479074 0.816511793 0.689643034 0.724386476 0.83366984 0.560148984 0.630949176 0.6893495 1 16.43677335 -0.653769587 4.41694837 1.000000355 0.686125856 0.45432108 0.111280599 121974543.2 338697560.9 812.9206162 0.025223749 0.221937358 0.653769587 -0.313874499 EQEPIGTDLDAVRT(ph)PEPLEEFPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQEPIGTDLDAVRTPEPLEEFPK 23 1 P10244-2;P10244 P10244-2 MYBL2 Myb-related protein B 1 EQEPIGTDLDAVRT(1)PEPLEEFPK;EQEPIGTDLDAVRT(1)PEPLEEFPK 189.98 2.68E-17 104841000 282130 156503 224690 170644 175331 225030 323010 213140 200703 TRUE FALSE 264471.9869 168090.645 230019.7529 175023.0139 161561.2105 289992.5079 274577.6492 239750.9982 167204.3727 1.58172889 1.005300533 1.375680248 1.046760985 0.966249913 1.734359594 1.642167874 1.433879954 1 17.35125305 2.236997351 24.99992682 1.528844395 1.187130235 0.162730154 0.265954581 51.02620712 815994.0639 0.088018628 0.068489347 172.5827364 -2.236997351 -0.341714159 EQEPMPTVDSHEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EQEPMPTVDSHEPR 14 0 A6NGP5;Q9H910;Q9H910-3;Q9H910-2;H3BU16 A6NGP5;Q9H910-2 HN1L Hematological and neurological expressed 1-like protein 0 ;;;; 172.82 2.80E-06 2896280000 1413330 1605520 1557570 1544290 1683880 1364040 1678130 1426049 1477040 FALSE TRUE 1324872.198 1724394.371 1594516.296 1583919.096 1551634.857 1757816.205 1426509.985 1604094.357 1230512.482 1.076683266 1.401362763 1.295814808 1.287202787 1.26096637 1.428523668 1.159281199 1.303598607 1 20.23082786 0.023458505 0.70906286 0.989599687 1.297246502 0.401793766 0.103728355 4.092858316 2.234163353 0.20954335 0.033473254 1.055500649 -0.023458505 0.307646815 EQEVNILKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQEVNILKK 9 1 P35579 P35579 MYH9 Myosin-9 0 70.1 0.086524 0 538510 443070 477160 523380 588920 407910 675920 472220 898880 FALSE TRUE 504805.6204 475875.3638 488478.4605 536810.8169 542668.5988 525666.9951 574572.0709 531177.7065 748851.121 0.674106783 0.635473929 0.652303838 0.716845848 0.724668206 0.701964623 0.767271431 0.709323511 1 19.5143194 -5 0.161303073 2.176540443 0.609378705 0.926424106 0.027689254 30.37202823 0.2804293 11.37007724 0.110292744 1.00E-05 5 -1.567161738 EQFAWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 ;;;;;; 144.58 0.026183 12124640000 5315530 6890040 5737980 5609490 7045880 4462700 5828860 6032150 5042600 FALSE TRUE 4982840.466 7400185.731 5874087.595 5753439.01 6492525.007 5751009.044 4954876.555 6785277.206 4200957.484 1.186120185 1.7615474 1.398273517 1.369554211 1.545486959 1.368975779 1.179463628 1.615173977 1 22.00228675 -3.534013985 0.173799305 1.56E-10 1.554985749 0.305021183 0.186625464 78.83542404 1.193855869 28.77228528 0.63211211 0.000292406 3.534013985 1.554985749 EQFEGLGST(ph)PDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQFEGLGSTPDAK 13 0 Q8NCN4 Q8NCN4 RNF169 E3 ubiquitin-protein ligase RNF169 1 EQFEGLGS(0.363)T(0.637)PDAK 103.79 0.017692 43402000 172980 162240 175410 149630 194700 132590 227440 168710 206300 TRUE FALSE 162153.4906 174252.4184 179570.808 153469.7591 179409.0474 170866.5806 193337.4834 189773.8149 171867.1973 0.943481323 1.01387828 1.044823043 0.8929555 1.043881847 0.994177966 1.1249237 1.104188687 1 17.39093469 1.752858415 25 1.08718443 0.996635924 0.344786311 0.055524851 4.727573699 8277.550914 0.023896236 0.013251535 56.60547189 -1.752858415 -0.090548505 EQFLDGDGWTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EQFLDGDGWTSR 12 0 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;;;;;; 322.07 1.81E-46 15056470000 11671410 13766010 12726930 13166680 13365310 10545880 15137110 11071880 11314390 FALSE TRUE 10940917.28 14785259.7 13028818.79 13504559.3 12315652.47 13590304.36 12867440.88 12454228.59 9425945.215 1.160723623 1.568570511 1.38222942 1.432700805 1.306569494 1.441797512 1.365108813 1.321271056 1 23.16820587 0.287729192 0.834051045 0.994863334 1.406956958 0.551980761 0.105146497 1.849792314 1.618984563 0.111350763 0.031380767 1.939675998 -0.287729192 0.412093624 EQFLQYAYDITFDPDTAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQFLQYAYDITFDPDTAHK 19 0 H0Y626;O95361;K7ENN8;B3KP96;O95361-2 H0Y626 TRIM16 Tripartite motif-containing protein 16 0 137.73 3.30E-06 75539000 179480 173790 171780 159490 169070 137740 215260 145700 199910 FALSE TRUE 168246.6672 186657.5924 175854.7027 163582.7834 155791.9242 177503.302 182983.7614 163890.9657 166543.7295 1.010225168 1.120772262 1.055907077 0.982221209 0.935441548 1.065805975 1.098713004 0.984071668 1 17.34554151 3.467799359 22.8698847 1.021575875 1.076919211 0.148768128 0.052828464 123.0363595 301849.9756 0.015420644 0.021001346 2936.292791 -3.467799359 0.055343337 EQFVEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EQFVEFR 7 0 O43852;O43852-3;O43852-15;H0Y875;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;;; 169.57 0.002343 3891130000 6462440 8171300 7341890 7215370 8198790 6215160 8248860 6883390 7612050 FALSE TRUE 6057967.416 8776311.554 7516043.098 7400528.61 7554890.106 8009375.797 7012020.022 7742796.394 6341549.679 0.955281867 1.383937996 1.185206058 1.16699056 1.191331849 1.262999772 1.105726577 1.220962822 1 22.596404 -0.576248496 0.421143005 0.94714906 1.213147541 0.183519304 0.111271165 13.13696531 2.077100156 1.065933734 0.062888255 0.265308708 0.576248496 0.265998481 EQFWPAVCEHFGVEATGEESSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQFWPAVCEHFGVEATGEESSIR 23 0 P16435;H0Y4R2 P16435 POR NADPH--cytochrome P450 reductase 0 153.94 4.53E-08 94494000 49598 38424 36780 38914 50419 44031 53910 43923 57098 FALSE TRUE 46493.74971 41268.95294 37652.43897 39912.59912 46459.29512 56742.03492 45826.69598 49406.88324 47567.97493 0.97741705 0.867578513 0.791550177 0.8390645 0.976692726 1.192862109 0.963393881 1.038658537 1 15.53770299 2.581596784 4.403726753 1.046429969 0.856844416 0.55773053 0.074893686 0.155251567 5.027127458 0.024190573 0.022484683 381.5898238 -2.581596784 -0.189585552 EQGDGAEDEEWDD ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQGDGAEDEEWDD 13 0 Q7Z6K5;H0YMP5 Q7Z6K5 ARPIN Arpin 0 ; 219.93 5.04E-11 500260000 973450 1028890 960410 974600 1020510 834950 1039330 832200 969800 FALSE TRUE 912523.5022 1105070.086 983191.3787 999609.886 940363.2611 1075986.511 883492.1152 936102.0019 807934.1149 1.129452867 1.367772527 1.216920242 1.237241834 1.163910824 1.331775068 1.093520002 1.158636558 1 19.62387812 1.068472552 0.644765088 0.998250575 1.25958028 0.459922684 0.079523803 0.58932451 0.587705927 0.072139957 0.03064685 11.70772605 -1.068472552 0.261329705 EQGVEEHETLLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQGVEEHETLLLR 13 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 178.23 5.62E-07 0 203800 379180 239790 233780 382320 201780 261910 343180 404720 FALSE TRUE 191044.5218 407254.8817 245477.932 239779.1906 352294.1294 260030.6104 222639.027 386026.7784 337169.6174 0.566612506 1.207863522 0.728054722 0.711153017 1.04485728 0.77121602 0.660317583 1.144903807 1 18.36311501 -1.182124595 7.591839399 1.000000088 0.857675512 0.04380514 0.213328701 2.94E-07 3.15E-08 0.191253294 0.045078806 0.065746919 1.182124595 -0.142324577 EQGVLSFWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EQGVLSFWR 9 0 P05141;P12236 P05141;P12236 SLC25A5;SLC25A6 "ADP/ATP translocase 2;ADP/ATP translocase 2, N-terminally processed;ADP/ATP translocase 3;ADP/ATP translocase 3, N-terminally processed" 0 ;; 144.65 0.00023043 459396000 776128 1227068 698423 668607 1443584 477104 747322 1239080 1032172 FALSE TRUE 727551.5339 1317921.391 714989.9234 685764.5876 1330210.736 614836.1797 635268.0039 1393781.866 859895.8251 0.846092646 1.53265239 0.831484353 0.797497287 1.546944056 0.715012402 0.738773216 1.62087293 1 19.71380236 3.950225821 21.00263562 1.001042439 1.231369147 0.021171732 0.356243983 149.2572822 116554.897 0.085318556 0.153947981 8917.144851 -3.950225821 0.230326708 EQGVTFPS(ph)GDIQEQLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EQGVTFPSGDIQEQLIR 17 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 EQGVTFPS(1)GDIQEQLIR;EQGVTFPS(1)GDIQEQLIR;EQGVTFPS(1)GDIQEQLIR 247 1.10E-20 194564000 258452 280845 292665 292641 281475 260689 344707 266602 272100 TRUE FALSE 242275.9507 301639.056 299607.152 300150.6635 259369.0889 335945.6824 293021.3855 299887.8466 226684.7522 1.068779211 1.33065437 1.321690803 1.324088456 1.144184099 1.481995058 1.292638268 1.322929062 1 17.79032783 -0.930229099 5.910361677 0.999999858 1.298354842 0.387007107 0.112093182 1.86E-07 3.38E-08 0.09654833 0.022756649 0.117427794 0.930229099 0.298354984 EQGVTFPSGDIQEQLIR ddPTM_SK-BR-3_Pertuzumab_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 0 ; 260.49 7.02E-27 497850000 281600 308580 324840 325310 327670 291780 396040 315590 327450 FALSE TRUE 263975.1587 331427.5843 332545.3582 333658.0053 301936.12 376012.1493 336657.4787 354992.1062 272796.4796 0.967663362 1.214926178 1.219023642 1.223102314 1.106818242 1.378361443 1.234097592 1.301307505 1 18.0574655 4.739244331 5.357821877 1.224226138 0.957364251 0.349633371 0.102136971 0.149654436 15.68702678 0.021408134 0.146997425 54858.55082 -4.739244331 -0.266861887 EQGYDVIAYLANIGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQGYDVIAYLANIGQK 16 0 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 172.1 6.56E-12 0 66500 49492 56542 64134 65246 54537 65111 53056 39138 FALSE TRUE 62337.88371 53156.43918 57883.20294 65779.78702 60121.84235 70280.94657 55348.21001 59680.15839 32605.61496 1.911875724 1.630284822 1.775252606 2.017437398 1.843910701 2.155486 1.697505478 1.830364447 1 14.99283281 0.167713261 1.458936186 0.999482747 1.842552538 0.76228802 0.150385147 5.355581149 8.754356898 0.149920386 0.04215469 1.471340741 -0.167713261 0.843069791 EQGYDVIAYLANIGQKEDFEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQGYDVIAYLANIGQKEDFEEAR 23 1 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 87.72 0.00582 182960000 62020 69884 64482 76812 98374 34004 73576 51951 108620 FALSE TRUE 58138.27891 75058.28407 66011.54349 78783.12596 90648.10286 43820.40279 62543.96185 58437.19671 90490.62029 0.64247851 0.829459273 0.729484927 0.870622013 1.001740319 0.484253535 0.691165136 0.645781812 1 16.46548064 2.23739491 24.99999304 0.673831548 0.807673148 0.092869559 0.155961164 56.9008636 1220263.349 0.051282502 0.040017767 172.7407934 -2.23739491 0.133841601 EQHDAQVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EQHDAQVR 8 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ;; 153.24 0.00044416 319495000 199991 261028 210233 209151 260649 150039 212071 228121 220839 FALSE TRUE 187473.9203 280354.7847 215219.826 214518.1688 240178.6789 193352.8236 180272.9223 256602.409 183979.5442 1.018993286 1.523836717 1.169803018 1.165989239 1.305464039 1.0509474 0.979853076 1.394733366 1 17.48918584 2.875375671 0.974283135 1.099683408 1.300916722 0.052702886 0.176330411 0.939471527 1.918550161 0.087447795 0.094624142 750.5431595 -2.875375671 0.201233314 EQHGVAASCLEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EQHGVAASCLEDLR 14 0 O00273;O00273-2;K7ERT1 O00273 DFFA DNA fragmentation factor subunit alpha 0 ;;; 255.16 2.83E-24 1683650000 1086290 1231020 1162000 1185330 1306290 1083860 1310770 1067770 1304660 FALSE TRUE 1018301.048 1322166.002 1189563.189 1215747.575 1203699.253 1396752.787 1114232.207 1201083.435 1086903.818 0.936882392 1.216451705 1.094451201 1.118542004 1.107457011 1.285074875 1.025143338 1.105050342 1 20.05179285 1.050833321 1.513611303 1.007344819 1.128526906 0.111162892 0.094522428 0.714417705 3.31291377 0.079501253 0.023568462 11.24173443 -1.050833321 0.121182087 EQIEWLIEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQIEWLIEHK 10 0 Q93034 Q93034 CUL5 Cullin-5 0 131.37 0.00025196 31498000 143150 134100 150160 141850 149230 103510 175850 143350 159680 FALSE TRUE 134190.497 144028.9035 153721.8661 145490.1112 137510.0778 133391.6567 149482.925 161247.5631 133028.3764 1.008735885 1.082693087 1.155556959 1.093677267 1.033689815 1.002730848 1.12369202 1.212129076 1 17.0213745 1.597980117 25 1.12594688 1.07499268 0.074609553 0.067914596 1.816478942 4580.972205 0.034957681 0.01648901 39.62598923 -1.597980117 -0.0509542 EQIKGGTGDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQIKGGTGDEK 11 1 Q12904;Q12904-2;A0A5F9ZHC5;D6R937 Q12904 AIMP1 Aminoacyl tRNA synthase complex-interacting multifunctional protein 1;Endothelial monocyte-activating polypeptide 2 0 ; 139.89 3.54E-05 320850000 391920 304270 338370 363180 412360 230433 446380 313880 745890 FALSE TRUE 367390.4268 326798.4674 346396.2962 372499.8137 379974.909 296955.2663 379449.463 353068.6089 621396.1404 0.591233841 0.525910037 0.557448419 0.599456272 0.611485789 0.477883989 0.610640199 0.568186035 1 19.24515376 EQIS(ph)DIDDAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQISDIDDAVR 11 0 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 1 EQIS(1)DIDDAVR;EQIS(1)DIDDAVR 149.35 3.61E-05 362870000 296140 280530 292680 291850 288490 255380 325680 236200 257610 TRUE FALSE 277605.126 301300.7331 299622.5078 299339.3651 265833.1591 329104.0603 276847.3075 265690.0899 214613.2268 1.293513593 1.403924342 1.396104575 1.394785259 1.238661583 1.533475197 1.289982503 1.237994945 1 17.71137947 0.928242606 1.68883762 1.002218878 1.377635678 0.687591032 0.079135753 0.223836336 1.301635983 0.066316882 0.019047482 8.477008262 -0.928242606 0.3754168 EQISDIDDAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQISDIDDAVR 11 0 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 313.5 2.52E-45 499160000 575000 654840 585880 583960 596120 571470 711270 512860 641030 FALSE TRUE 539011.7764 703325.035 599777.3503 598945.4022 549303.1398 736444.112 604621.6666 576891.6999 534037.9518 1.009313616 1.316994481 1.123098739 1.121540895 1.028584463 1.379010817 1.132169848 1.080244762 1 19.02658275 1.095591561 2.816528476 1.004941722 1.174839423 0.168028983 0.114278476 0.366646855 5.680177665 0.099702381 0.026849103 12.46210945 -1.095591561 0.169897701 EQIVPKPEEEVAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQIVPKPEEEVAQK 14 1 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 0 154.82 5.48E-06 599750000 1282800 767450 917330 886910 1003000 663750 1240100 779420 1195100 FALSE TRUE 1202511.838 824272.7965 939089.5008 909669.6121 924228.4259 855363.8499 1054158.518 876732.3027 995630.0894 1.207789771 0.827890604 0.94321125 0.913662234 0.928284948 0.859118119 1.058785315 0.88058036 1 19.92525031 1.741080009 24.99999999 0.983580897 0.930580892 0.005457627 0.110293765 1.38595257 13838.48821 0.046044092 0.025533586 55.09091791 -1.741080009 -0.053000004 EQIVPKPEEEVAQKK ddPTM_SK-BR-3_Pertuzumab_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 99.055 0.0015129 132650000 300250 157850 187050 208240 237530 140200 287430 161730 327880 FALSE TRUE 281457.8885 169537.3782 191486.9143 213583.7909 218875.3519 180673.464 244332.5399 181922.3465 273154.7098 1.030397348 0.620664305 0.701019999 0.781915095 0.801287124 0.661432725 0.894484082 0.666004795 1 18.05935877 -4.999996506 0.370497079 4.223624539 0.750338826 0.237480633 0.123920288 707.3772964 5.452914641 1825.670469 0.079699166 1.00E-05 4.999996506 -3.473285714 EQIVVDLSHPGVSEDDQVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EQIVVDLSHPGVSEDDQVSR 20 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ;; 279.96 1.09E-44 679400000 591900 695200 662420 709410 679810 557090 755060 575150 691080 FALSE TRUE 554854.0356 746673.3314 678132.9152 727614.6616 626420.4648 717912.8394 641845.7626 646958.7436 575734.2835 0.963732839 1.296906147 1.17785745 1.263802908 1.088037456 1.246951693 1.114829846 1.123710646 1 19.1350436 0.888509294 0.943292483 1.000785677 1.189491692 0.212274789 0.09680089 0.88229732 1.613782979 0.081821191 0.027503324 7.735872329 -0.888509294 0.188706015 EQIYDVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EQIYDVYR 8 0 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ;;;;; 144.9 0.0013446 3606210000 2732160 7404440 2670050 2735310 7690460 1547220 2316930 6574090 5607120 FALSE TRUE 2561158.983 7952672.442 2733384.847 2805502.685 7086482.293 1993877.297 1969527.856 7394879.608 4671255.449 0.548280652 1.702470038 0.58514994 0.600588582 1.517040199 0.426839705 0.421627093 1.583060419 1 22.15537891 3.858074192 7.538642521 0.816725298 1.197640677 0.026987684 0.494022273 0.534934994 31.6722459 0.118579396 0.214903986 7212.306793 -3.858074192 0.380915379 EQLEEEEEAKHNLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EQLEEEEEAKHNLEK 15 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;; 295.22 2.94E-44 6851270000 8209800 5134650 6158790 6203570 6560660 4216039 8066840 5194310 8167800 FALSE TRUE 7695963.273 5514824.829 6304879.407 6362764.109 6045412.228 5433141.018 6857292.231 5842831.038 6804541.414 1.131003958 0.81046238 0.926569334 0.935076109 0.888437862 0.798458072 1.007752296 0.858666394 1 22.69806651 -1.551470359 4.590658709 1.00077081 0.911693227 0.058573535 0.09690496 0.000680195 6.65E-05 0.083482417 0.019507991 0.028088571 1.551470359 -0.089077583 EQLEWER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQLEWER 7 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;A0A0U1RQP7;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ; 133.58 0.0075787 849890000 881300 1063740 909940 904230 1181720 688820 958360 924170 1225740 FALSE TRUE 826141.0062 1142500.416 931524.2065 927434.0727 1088912.478 887671.1519 814662.815 1039554.659 1021156.075 0.809025208 1.118830357 0.912225103 0.908219708 1.066352641 0.869280586 0.797784819 1.018017406 1 19.96177196 2.197053703 24.99982368 0.89173928 0.974788671 0 0.106433886 304.2640009 183257.9752 0.03743844 0.027650382 157.4177507 -2.197053703 0.08304939 EQLMFPFHFVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQLMFPFHFVDR 12 0 P82933 P82933 MRPS9 "28S ribosomal protein S9, mitochondrial" 0 ; 111.74 0.0013491 635290000 4610100 3605300 3736600 3570600 4451700 2610240 5404000 3807200 7182300 FALSE TRUE 4321562.07 3872240.163 3825233.917 3662227.641 4102081.439 3363773.914 4593720.368 4282537.301 5983527.731 0.722243176 0.647150032 0.63929409 0.612051587 0.685562368 0.562172361 0.767727764 0.715721142 1 22.51256488 0.614453509 0.919711541 0.999957983 0.646909689 0.802415317 0.05310291 0.480289065 0.67211971 0.045963452 0.015081752 4.115792853 -0.614453509 -0.353048294 EQLNRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQLNRPR 7 1 P82930;C9JJ19 P82930 MRPS34 "28S ribosomal protein S34, mitochondrial" 0 87.251 0.017765 80284000 77543 132260 106250 109420 137190 106740 87914 120700 128270 FALSE TRUE 72689.72205 142052.668 108770.3002 112227.9024 126415.6508 137554.1052 74732.11185 135769.6607 106860.9083 0.680227439 1.329323044 1.01786801 1.050224111 1.182992478 1.287225678 0.699340039 1.27052692 1 16.70537466 EQLQLLEEQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EQLQLLEEQHR 11 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;; 210.79 1.16E-08 2186010000 2333560 2915420 2597000 2774920 2842720 2066010 3025660 2619810 2516980 FALSE TRUE 2187506.645 3131280.73 2658602.066 2846129.145 2619464.238 2662433.548 2571990.372 2946899.045 2096879.778 1.043219868 1.493304844 1.267884833 1.357316321 1.249220039 1.269712063 1.226579797 1.405373392 1 20.99981272 -1.965730317 2.889420991 0.761192772 1.299971013 0.364947014 0.119072492 2703545.871 6430067.504 4174338.203 0.02529318 0.010821057 1.965730317 0.538778241 EQLSAQELMESGLQIQKS(ph)PEPEVLSTQEDLFDQSNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQLSAQELMESGLQIQKSPEPEVLSTQEDLFDQSNK 36 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 EQLSAQELMESGLQIQKS(1)PEPEVLSTQEDLFDQSNK 180.25 3.93E-23 54430000 88097 50577 58543 57782 77765 37058 75085 48900 106310 TRUE FALSE 82583.16603 54321.77371 59931.66761 59264.78394 71657.65059 47756.04301 63826.7013 55005.27264 88566.17421 0.9324459 0.613346734 0.676688004 0.669158225 0.809085988 0.539213119 0.720666799 0.621064115 1 16.43446818 -0.800691565 5.415092283 1.000000101 0.686217827 0.425015478 0.109777054 1.16E-07 2.57E-08 0.092451601 0.021791045 0.158237144 0.800691565 -0.313782274 EQMDNAVYTFETLLHQELGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQMDNAVYTFETLLHQELGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 189.51 1.64E-17 47208000 57370 53134 61264 55703 58264 47589 61332 46291 53047 FALSE TRUE 53779.31411 57068.09665 62717.21101 57132.43328 53688.18047 61327.17176 52135.83598 52070.53325 44193.113 1.216916177 1.291334617 1.419162552 1.292790424 1.214854008 1.387708799 1.179727619 1.178249951 1 15.43153394 1.043898605 0.995695546 1.002255819 1.315045756 0.65182181 0.069679577 0.317713098 0.676383134 0.063658389 0.0213348 11.06365449 -1.043898605 0.312789938 EQMMNSSISSGSGS(ph)LR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 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 EQMMNS(0.001)S(0.001)IS(0.013)S(0.037)GS(0.235)GS(0.713)LR;EQMMNSSISS(0.003)GS(0.061)GS(0.936)LR;EQMMNSSISSGSGS(1)LR;EQMMNSSISSGS(0.048)GS(0.952)LR;EQMMNSSISSGS(0.072)GS(0.928)LR;EQMMNSSISSGS(0.021)GS(0.979)LR;EQMMNSSISSGS(0.009)GS(0.991)LR;EQMMNSSISSGS(0.003)GS(0.997)LR;EQMMNSSISSGS(0.069)GS(0.931)LR;EQMMNSSISSGS(0.006)GS(0.994)LR 277.32 2.63E-35 2278933000 2636097 2825160 2891300 2740700 3522860 2400290 2876510 2691898 4345100 TRUE FALSE 2471108.394 3034337.786 2959883.001 2811031.002 3246188.786 3093214.758 2445204.03 3027987.391 3619874.74 0.68265025 0.838243863 0.817675531 0.776554772 0.896768264 0.854508783 0.6754941 0.83648955 1 21.78750835 0.97515446 24.52274058 1.000000004 0.796286939 0.466554345 0.069600208 1761.98666 1739096.766 0.065450478 0.01636262 9.443966991 -0.97515446 -0.203713065 EQMMNSSMSSGS(ph)GSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQMMNSSMSSGSGSLR 16 0 Q92796-2;Q5JUW8;Q92796 Q92796-2 DLG3 Disks large homolog 3 1 EQMMNSSMS(0.004)S(0.065)GS(0.916)GS(0.015)LR 73.928 0.010239 87747000 152040 159870 160900 160000 165420 162130 192380 148130 203790 TRUE FALSE 142524.0878 171706.9411 164716.624 164105.8709 152428.5805 208934.299 163534.405 166624.3566 169776.1325 0.839482475 1.011372674 0.970198941 0.966601539 0.89782102 1.230645886 0.963235542 0.981435695 1 17.37327413 EQMPLT(ph)PPRFDHDEGDQCSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQMPLTPPRFDHDEGDQCSR 20 1 O76074-2;G5E9C5;O76074;C9JGT3 O76074-2 PDE5A "cGMP-specific 3,5-cyclic phosphodiesterase" 1 EQMPLT(1)PPRFDHDEGDQCSR;EQMPLT(1)PPRFDHDEGDQCSR 140.55 4.01E-07 261629000 138185 160682 151856 148376 196692 143980 190148 170842 275421 TRUE FALSE 129536.2475 172579.0625 155458.096 152183.5794 181244.6037 185544.6887 161637.0726 192171.9998 229451.4558 0.564547508 0.752137579 0.677520635 0.66324957 0.789903917 0.808644635 0.704449976 0.837527917 1 17.80782943 -4.999999987 0.114158094 1.935598714 0.568126943 0.747078822 0.059075949 82.20599802 0.618039369 17.70128968 0.629752156 1.00E-05 4.999999987 -1.36747177 EQMQPTHPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EQMQPTHPIR 10 0 Q04917;A2IDB2 Q04917 YWHAH 14-3-3 protein eta 0 ;;;;;;; 146.71 2.14E-05 2115300000 803490 961498 947860 965981 980545 840908 964808 897615 838673 FALSE TRUE 753200.9952 1032688.312 970343.6868 990769.7079 903536.951 1083664.489 820143.9972 1009684.209 698693.0583 1.078014138 1.478028585 1.388798236 1.418032849 1.29318152 1.550987913 1.173825885 1.445104108 1 19.41429928 -1.200828923 0.552239154 0.866516831 1.369355799 0.367573268 0.143008462 30.52033898 4.767033614 6.368187555 0.054826871 0.062975421 1.200828923 0.502838968 EQMYNILMWIHDNYRDPESETDNDSQEIFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQMYNILMWIHDNYRDPESETDNDSQEIFK 30 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 171.95 7.77E-13 91496000 53519 54208 54347 56445 55534 41354 71121 45405 55800 FALSE TRUE 50169.34132 58221.61672 55636.1365 57893.47426 51172.58365 53292.22847 60457.06631 51073.9142 46486.61952 1.079221114 1.252438171 1.196820442 1.245379313 1.100802428 1.146399309 1.300526193 1.098679894 1 15.5045279 1.000095553 24.40335274 0.999999996 1.197891569 0.451729114 0.068252686 1.513963212 386428.3975 0.061603042 0.01540076 10.00220044 -1.000095553 0.197891573 EQNSALPTS(ph)SQDEELMEVVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQNSALPTSSQDEELMEVVEK 21 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 EQNSALPT(0.111)S(0.552)S(0.337)QDEELMEVVEK;EQNSALPT(0.113)S(0.546)S(0.341)QDEELMEVVEK 139.11 3.39E-07 101823000 224110 160558 196254 179498 191983 159049 237760 169829 225940 TRUE FALSE 210083.3551 172445.8814 200909.2376 184104.2226 176905.4296 204963.8644 202110.0953 191032.5245 188229.1544 1.116104229 0.916148627 1.067365139 0.978085585 0.93984075 1.088906047 1.073744904 1.01489339 1 17.52213058 2.221773738 24.99881092 1.054389155 0.999148161 0.083615445 0.062597809 439.0596024 653837.5124 0.021597204 0.015992762 166.6378824 -2.221773738 -0.055240994 EQPEKEPELQQYVPQLQNNTILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQPEKEPELQQYVPQLQNNTILR 23 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 134.81 1.61E-05 81606000 93821 75967 75297 80910 87053 68323 97749 71449 106930 FALSE TRUE 87948.91109 81591.67572 77083.0804 82986.28758 80216.20853 88046.74097 83092.44491 80369.56493 89082.69221 0.987272712 0.915909406 0.865298056 0.931564657 0.900469065 0.988370903 0.932756328 0.902190571 1 16.44285754 2.269719826 24.99893428 0.949716467 0.912578572 0.138906969 0.040691018 353.990689 284004.398 0.013653404 0.011422192 186.0886246 -2.269719826 -0.037137895 EQPFGEGVPLDGDDPEHIQWIFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQPFGEGVPLDGDDPEHIQWIFQK 24 0 Q8TBC4;F8W8D4;Q8TBC4-2 Q8TBC4 UBA3 NEDD8-activating enzyme E1 catalytic subunit 0 ; 219.38 1.09E-32 390750000 339370 321380 333880 331300 341540 284240 421620 314940 387010 FALSE TRUE 318129.4375 345175.3096 341799.7913 339801.7189 314716.8261 366295.4737 358401.9951 354260.9523 322415.5308 0.986706306 1.070591447 1.060121981 1.053924785 0.976121793 1.136097485 1.11161517 1.098771363 1 18.29856171 2.22111486 24.9999947 1.099038469 1.040384709 0.233488521 0.046947587 312.2946131 447519.1216 0.016233954 0.012016889 166.3852641 -2.22111486 -0.05865376 EQPLDEELKDAFQNAYLELGGLGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQPLDEELKDAFQNAYLELGGLGER 25 1 P05023-4;P05023;P05023-3;P05023-2 P05023-4 ATP1A1 Sodium/potassium-transporting ATPase subunit alpha-1 0 225.3 6.85E-34 133010000 159990 103950 101520 109250 170110 96208 133080 164550 207210 FALSE TRUE 149976.5115 111646.5662 103928.1023 112053.54 156750.2468 123981.6878 113125.8895 185094.4297 172625.3124 0.868797915 0.646756635 0.602044398 0.649114191 0.90803744 0.718212677 0.655326197 1.072232265 1 17.3972845 1.237311634 24.99999994 1.036116288 0.703397842 0.626132462 0.100444116 20.47192133 409690.2202 0.080639022 0.024424084 17.27076735 -1.237311634 -0.332718446 EQPWVSVQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQPWVSVQPR 10 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 159.83 1.76E-05 67410000 87626 76992 86869 89753 91365 71948 97258 76013 97475 FALSE TRUE 82141.64508 82692.56779 88929.5737 92056.21393 84189.56145 92718.21962 82675.0658 85503.39038 81205.79279 1.011524452 1.018308731 1.095113669 1.133616344 1.036743298 1.141768542 1.018093204 1.052922303 1 16.30929502 1.069231674 1.518417506 1.003845171 1.06848755 0.170017091 0.046315109 0.693129564 3.213472003 0.042126842 0.012503168 11.7282084 -1.069231674 0.064642379 EQQAQVEKEDFS(ph)DMVAEHAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQQAQVEKEDFSDMVAEHAAK 21 1 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 1 EQQAQVEKEDFS(1)DMVAEHAAK 71.085 0.01044 221240000 86342 51503 66101 59376 70076 45136 93711 55334 102070 TRUE FALSE 80938.00834 55316.33571 67668.94694 60899.68868 64572.51363 58166.03048 79659.90552 62242.57171 85033.8576 0.951832724 0.650521301 0.795788276 0.716181653 0.759374153 0.684033773 0.936802208 0.731973986 1 16.37574977 0.440642821 0.592529679 1.005539598 0.753601975 0.303713965 0.100596262 2.098847381 1.219668119 0.127604594 0.038831306 2.758308391 -0.440642821 -0.251937623 EQQAQVEKEDFSDMVAEHAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQQAQVEKEDFSDMVAEHAAK 21 1 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ; 173.43 2.59E-12 596390000 772010 522360 615600 672750 700280 448950 794230 555100 929450 FALSE TRUE 723691.2722 561036.0779 630202.3227 690013.904 645282.8336 578554.5769 675142.5848 624405.4569 774318.7905 0.934616699 0.724554389 0.813879671 0.891123801 0.833355514 0.74717879 0.871918121 0.806393264 1 19.56256813 -4.99998519 0.366362511 3.327156926 0.814636744 0.408116882 0.063618753 478.6065852 3.737186351 880.356197 0.042552009 1.00E-05 4.99998519 -2.512520181 EQQEAIEHIDEVQNEIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQQEAIEHIDEVQNEIDR 18 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 220.34 6.84E-19 1312900000 170880 153060 176690 148790 140550 163340 185430 161350 124900 FALSE TRUE 160184.9258 164392.7217 180881.1702 152608.2033 129511.77 210493.6064 157626.4929 181494.9027 104053.3831 1.539449473 1.579888291 1.738349728 1.466633748 1.244666594 2.022938612 1.514861778 1.744247974 1 16.66696435 -1.049156021 5.260762295 0.999993908 1.61224126 0.466051415 0.203890558 1.32E-05 2.38E-06 0.178655377 0.042109058 0.089298462 1.049156021 0.612247352 EQQEAIEHIDEVQNEIDRLNEQAS(ph)EEILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EQQEAIEHIDEVQNEIDRLNEQASEEILK 29 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 1 EQQEAIEHIDEVQNEIDRLNEQAS(1)EEILK;EQQEAIEHIDEVQNEIDRLNEQAS(1)EEILK;EQQEAIEHIDEVQNEIDRLNEQAS(1)EEILK 212.08 3.16E-26 78656000 87669 67117 75599 71438 73680 58325 96093 66177 73048 TRUE FALSE 82181.95378 72086.41252 77392.24398 73271.22002 67893.47001 75162.48067 81684.74673 74439.34412 60855.81689 1.350437115 1.184544325 1.271731248 1.204013417 1.115644707 1.235091147 1.342266868 1.223208362 1 15.89310755 -2.325320769 1.899355215 1.45E-05 1.241044503 0.540757141 0.069758815 1031653.415 133050.912 4412838.556 0.017601541 0.004728019 2.325320769 1.241029958 EQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EQQEAIEHIDEVQNEIDRLNEQASEEILK 29 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 ;; 285.48 5.98E-72 864120000 232854 189879 200328 189086 209825 155099 252461 178522 216231 FALSE TRUE 218280.0838 203937.8387 205079.8748 193938.2669 193346.1909 199873.5635 214606.8168 200810.8647 180140.6492 1.211720313 1.132103385 1.138443076 1.076593583 1.07330684 1.109541707 1.191329207 1.114744871 1 17.45876424 -2.085267929 2.042172054 0.80307539 1.13187569 0.469353623 0.043756595 2068664.739 551630.941 1894283.629 0.011271203 0.008217355 2.085267929 0.3288003 EQQEAIEHIDEVQNEIDRLNEQASEEILKVEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EQQEAIEHIDEVQNEIDRLNEQASEEILKVEQK 33 2 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 ;;; 115.3 2.36E-06 320564000 111953 98832 98689 104911 144596 64278 120454 85989 215519 FALSE TRUE 104946.0616 106149.6241 101029.9497 107603.1939 133240.0134 82834.01513 102393.0409 96724.91594 179547.4866 0.584503095 0.591206405 0.562692086 0.599302145 0.742087879 0.461348787 0.5702839 0.538714954 1 17.45400593 -1.370678164 3.405830984 1.003014894 0.57975656 0.783849284 0.069099652 26253249.9 36261741.78 780171.888 0.01554443 0.042591392 1.370678164 -0.423258334 EQQEVADRLETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EQQEVADRLETK 12 1 O75884 O75884 RBBP9 Putative hydrolase RBBP9 0 ;; 108.97 0.0015033 646250000 633330 560740 582190 571860 653310 478270 665800 490400 1147470 FALSE TRUE 593691.0058 602257.773 595999.8217 586534.8958 602001.6679 616338.7849 565969.471 551627.5195 955949.8441 0.621048279 0.630009803 0.623463485 0.613562416 0.629741897 0.644739668 0.592049337 0.577046508 1 19.8665754 -1.192890232 5.068171947 1.000031014 0.617942811 0.974616025 0.01945134 6.84E-06 1.09E-06 0.018911553 0.004457135 0.064137166 1.192890232 -0.382088203 EQQHVMEELFQSSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EQQHVMEELFQSSFR 15 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;;; 262.36 5.37E-25 1186726000 792727 985559 894331 971958 904084 762560 1085213 877059 785102 FALSE TRUE 743111.6321 1058530.814 915544.9537 996900.0878 833080.8895 982698.6929 922495.3853 986561.7468 654063.4042 1.136146171 1.618391745 1.399780125 1.524164296 1.273700507 1.502451729 1.410406666 1.508357967 1 19.31907097 -1.303243845 3.730421473 0.998899313 1.437563119 0.479626774 0.137149293 6990032.906 4961750.56 57349.26743 0.027979786 0.04974577 1.303243845 0.438663806 EQQILTLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EQQILTLFR 9 0 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ;;; 147.75 0.00021321 262685000 305863 476879 333933 339909 514955 259660 309163 400272 383176 FALSE TRUE 286719.5808 512187.6174 341854.0485 348631.6404 474512.5115 334619.6268 262806.8783 450246.8403 319221.4502 0.898183943 1.604489977 1.070899365 1.092130996 1.486468128 1.04823666 0.823274495 1.410452963 1 18.28419807 2.040054672 24.98554419 1.027643398 1.254563559 0.078436124 0.247751107 260.5091574 162500.868 0.086821722 0.064122007 109.6616238 -2.040054672 0.226920161 EQRERERWQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQRERERWQR 10 3 A0A0J9YYF7;Q86T65-4;Q86T65 A0A0J9YYF7 DAAM2 Disheveled-associated activator of morphogenesis 2 0 ; 66.071 0.039333 91914000 16909.4 9118.1 9922.7 13162.6 11544.9 11731.7 12795.8 7104.3 13439.9 FALSE TRUE 15851.07084 9793.213611 10158.07113 13500.3746 10638.21012 15118.45134 10877.18858 7991.287493 11196.69386 1.415692081 0.874652262 0.907238445 1.205746514 0.950120656 1.350260311 0.971464319 0.713718495 1 13.45078518 1.471874823 16.70461443 0.852096746 1.068969505 0.217080146 0.193538427 0.184760554 520.0761959 0.1004408 0.046512437 29.63976958 -1.471874823 0.216872759 EQS(ph)DDETEESVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQSDDETEESVK 12 0 O94885;A0A1B0GWB9;A0A1B0GVI0 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 EQS(0.982)DDET(0.018)EESVK 272.72 6.10E-15 0 307810 160690 218110 205800 203320 133430 260140 161820 195590 TRUE FALSE 288544.7216 172587.6548 223283.6722 211081.1764 187352.0674 171949.0749 221134.422 182023.5832 162944.7654 1.770813078 1.059178884 1.370302824 1.29541551 1.149788806 1.055259888 1.35711277 1.117087638 1 17.31402348 4.747517053 24.84597323 1.201840625 1.770813396 0.668125142 0.130688614 657.1002867 1822814.042 0.028968866 0.352404952 55913.5482 -4.747517053 0.568972771 EQS(ph)PLLHLDLFNFDCPEAEGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQSPLLHLDLFNFDCPEAEGSR 22 0 Q9NQR7 Q9NQR7 CCDC177 Coiled-coil domain-containing protein 177 1 EQS(1)PLLHLDLFNFDCPEAEGSR 92.121 0.0013666 12027000 8236.5 7364.7 9880.7 8230.5 10388 6015.5 8188.1 8529.4 17348 TRUE FALSE 7720.992168 7909.990051 10115.07487 8441.708564 9572.168383 7752.077197 6960.37042 9594.314366 14452.50673 0.534232041 0.547309211 0.699883768 0.584099957 0.662318902 0.536382881 0.481602988 0.66385123 1 13.81903212 0.973087259 22.85367014 1.000000002 0.582291749 0.813105076 0.063258607 404.3852022 343395.3268 0.065487141 0.016371785 9.399121389 -0.973087259 -0.417708254 EQS(ph)PSQHGKDPASLLASELVQLHMQLEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQSPSQHGKDPASLLASELVQLHMQLEEK 29 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 EQS(0.967)PS(0.027)QHGKDPAS(0.005)LLAS(0.001)ELVQLHMQLEEK;EQS(0.953)PS(0.045)QHGKDPAS(0.001)LLAS(0.001)ELVQLHMQLEEK 130.69 8.33E-06 114425000 130303 110880 133378 147051 149663 99942 158379 124949 205872 TRUE FALSE 122147.5678 119089.6706 136541.7891 150824.5776 137909.0717 128793.633 134631.5393 140549.1577 171510.6332 0.71218656 0.69435736 0.796112676 0.879389078 0.804084675 0.750936724 0.784974883 0.819477808 1 17.3879385 -5 0.142106839 1.760589691 0.6985482 0.711353883 0.04670911 84.46984435 0.731290886 18.26575177 0.299451813 1.00E-05 5 -1.062041491 EQSELDQDLDDVEEVEEEETGEETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQSELDQDLDDVEEVEEEETGEETK 25 0 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VUX1;F8W020;F8VXI6;F8VVB5 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 149.73 1.85E-07 34691000 28804 18365 23239 21004 22271 18548 25373 23017 14943 FALSE TRUE 27001.20906 19724.76371 23790.24005 21542.9982 20521.9255 23902.5065 21568.5542 25890.72312 12448.91676 2.168960526 1.584456229 1.911028928 1.730511868 1.648490859 1.920047097 1.732564737 2.079757107 1 13.60373259 -1.31327395 4.791522834 0.999581548 1.816788687 0.670656363 0.185460631 0.00072302 0.000103624 0.156608615 0.036894905 0.048610048 1.31327395 0.81720714 EQSEVSVS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQSEVSVSPR 10 0 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 EQSEVSVS(1)PR;EQSEVSVS(1)PR 142.12 3.81E-05 6407900000 1406590 1503680 1505630 1449420 1627040 1382670 1683130 1384710 1673210 TRUE FALSE 1318554.043 1615014.032 1541344.255 1486614.571 1499258.842 1781824.383 1430760.282 1557594.092 1393940.442 0.945918494 1.158596152 1.105746134 1.066483565 1.075554447 1.278264358 1.026414213 1.117403617 1 20.41073749 0.231057707 1.353290411 0.999971854 1.104952853 0.102990305 0.086268801 13.86952798 22.18939503 0.075941051 0.021846715 1.702384698 -0.231057707 0.104980999 EQSGTIYLQHADEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQSGTIYLQHADEER 15 0 P37198;M0QXN5 P37198 NUP62 Nuclear pore glycoprotein p62 0 ; 170.11 1.16E-06 575480000 613920 587200 627280 599990 596170 554010 758280 576350 571350 FALSE TRUE 575495.8431 630676.899 642159.3778 615386.7592 549349.213 713943.6934 644582.9535 648308.5662 475987.9939 1.209055376 1.324984888 1.349108351 1.292861936 1.154124096 1.499919541 1.354200025 1.36202714 1 18.86056566 -1.073002116 5.240004649 0.999995471 1.326208033 0.536966287 0.092626944 4.62E-06 8.17E-07 0.084485359 0.019913114 0.084527473 1.073002116 0.326212562 EQSSDLTPS(ph)GDVS(ph)PVKPLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQSSDLTPSGDVSPVKPLSR 20 1 Q8WYQ5-3;Q8WYQ5 Q8WYQ5-3 DGCR8 Microprocessor complex subunit DGCR8 2 EQSSDLT(0.032)PS(0.968)GDVS(1)PVKPLSR 162.07 1.23E-11 206790000 488460 337130 395630 333260 328720 271460 464400 329780 588210 TRUE FALSE 457888.1605 362091.456 405014.5304 341812.0158 302903.6572 349826.0952 394767.5313 370953.7589 490033.951 0.934400891 0.738910958 0.826503 0.697527212 0.6181279 0.713881343 0.805592205 0.756996037 1 18.90252218 -0.874337199 4.528517277 1.000001235 0.760347728 0.443168583 0.084011161 5160894.826 1139643.463 97.35779024 0.019010175 0.133555815 0.874337199 -0.239653506 EQSSDLTPSGDVS(ph)PVKPLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EQSSDLTPSGDVSPVKPLSR 20 1 Q8WYQ5-3;Q8WYQ5 Q8WYQ5-3 DGCR8 Microprocessor complex subunit DGCR8 1 EQSSDLTPSGDVS(1)PVKPLSR;EQSSDLTPSGDVS(1)PVKPLSR;EQSSDLTPSGDVS(1)PVKPLSR;EQSSDLTPSGDVS(1)PVKPLSR 235.73 9.10E-30 4466000000 2454450 1794030 2034260 2055690 2090130 1674220 2589690 1750590 2264370 TRUE FALSE 2300830.356 1926861.848 2082513.608 2108442.486 1925979.621 2157540.135 2201390.026 1969155.015 1886432.019 1.219673083 1.021431904 1.103943099 1.11768803 1.020964234 1.143714756 1.166959638 1.043851565 1 20.84722868 -3.017865122 0.974972261 5.15E-05 1.101754137 0.209870062 0.063681829 28158.9492 797.9370222 61346.41076 0.018552155 0.000959699 3.017865122 1.101702624 EQST(ph)PPKS(ph)PQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EQSTPPKSPQ 10 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 2 EQST(1)PPKS(1)PQ;EQST(1)PPKS(1)PQ;EQST(1)PPKS(1)PQ;EQST(1)PPKS(1)PQ 139.78 0.0010145 2097120000 6745200 4127450 5249170 4934190 5060420 3509530 5486960 3631560 5155800 TRUE FALSE 6323029.973 4433050.693 5373682.791 5060809.669 4662995.026 4522674.339 4664241.286 4084968.26 4295263.672 1.472093556 1.032078827 1.251071692 1.178230268 1.08561322 1.052944518 1.085903368 0.951040162 1 22.03431527 8 0.208948166 0.982853867 2.628188454 0.526213978 0.103111992 46.36279844 0.575770734 0.165731978 25.33296452 100000000 -8 1.645334587 EQSTCNFQAIVISLKEEFYTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQSTCNFQAIVISLKEEFYTK 21 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 196.62 8.71E-22 95690000 112890 95926 92734 100780 117640 78234 119170 83677 125190 FALSE TRUE 105824.4164 103028.4609 94933.69427 103366.1854 108401.0289 100818.8858 101301.5648 94124.25765 104294.9802 1.014664523 0.987856372 0.910242219 0.99109454 1.039369572 0.966670549 0.971298567 0.902481188 1 16.6703102 EQSTPPKS(ph)PQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EQSTPPKSPQ 10 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 EQSTPPKS(1)PQ;EQST(0.001)PPKS(0.999)PQ;EQST(0.055)PPKS(0.945)PQ;EQST(0.003)PPKS(0.997)PQ 157.03 2.60E-05 2402400000 6056400 4489990 5269470 5420710 4697520 3043160 4153890 2737960 3790150 TRUE FALSE 5677340.735 4822433.531 5394464.317 5559814.596 4328595.728 3921670.89 3531052.757 3079800.333 3157549.48 1.798021146 1.52727093 1.708433819 1.760800466 1.37087186 1.241998238 1.118288971 0.975376745 1 21.59037391 2.240577067 1.35334459 1.023067034 1.675156989 0.912718623 0.090488355 0.120327543 0.42998936 0.054621085 0.031844418 174.0111461 -2.240577067 0.652089955 EQTLS(ph)PTITSGLHNIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EQTLSPTITSGLHNIAR 17 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;O94979-7;H7BXG7;H0Y8W8 D6REX3 SEC31A Protein transport protein Sec31A 1 EQT(0.015)LS(0.776)PT(0.207)IT(0.001)SGLHNIAR;EQT(0.005)LS(0.896)PT(0.099)ITSGLHNIAR;EQTLS(0.489)PT(0.489)IT(0.021)SGLHNIAR 261.54 1.74E-27 4193780000 1347200 1916520 1711600 1769670 1926720 1509110 1920200 1637430 1671930 TRUE FALSE 1262881.157 2058421.135 1752199.96 1815082.728 1775403.183 1944765.559 1632283.836 1841866.74 1392874.082 0.906672881 1.477822842 1.257974416 1.30312047 1.274632938 1.39622496 1.171881836 1.322349783 1 20.40963341 -1.023713366 4.423910545 0.999987183 1.281700766 0.222734598 0.151661103 0.165046447 39468010.42 1198.919618 0.031334499 0.094686188 1.023713366 0.281713583 EQTLSPT(ph)ITSGLHNIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQTLSPTITSGLHNIAR 17 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;O94979-7;H7BXG7;H0Y8W8 D6REX3 SEC31A Protein transport protein Sec31A 1 EQT(0.001)LS(0.353)PT(0.633)IT(0.013)SGLHNIAR;EQTLS(0.113)PT(0.821)IT(0.063)S(0.002)GLHNIAR 232.58 3.59E-16 1873640000 602930 867690 859600 856710 825440 689620 916690 772290 831100 TRUE FALSE 565193.6876 931934.6704 879990.1179 878694.629 760613.2721 888702.099 779240.8446 868712.1065 692384.0409 0.816300859 1.345979421 1.270956674 1.269085619 1.098542467 1.283539259 1.125445993 1.25466801 1 19.40121295 -0.746018551 5.19479643 0.999999938 1.204192087 0.113176867 0.151084419 8776091.115 1689400.31 6.23479407 0.03196593 0.179465697 0.746018551 0.20419215 EQTLSPTIT(ph)SGLHNIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQTLSPTITSGLHNIAR 17 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;O94979-7;H7BXG7;H0Y8W8 D6REX3 SEC31A Protein transport protein Sec31A 1 EQTLS(0.001)PT(0.009)IT(0.902)S(0.088)GLHNIAR 302.11 2.07E-45 345040000 213640 303190 267900 286270 308110 252860 317100 250090 304840 TRUE FALSE 200268.6538 325638.5031 274254.7145 293616.1729 283912.2835 325856.5772 269553.7988 281314.287 253960.2347 0.788582724 1.282242094 1.079912038 1.156150187 1.117939916 1.283100788 1.061401598 1.107709982 1 17.95424309 0.839472758 1.645852458 1.001548885 1.132066168 0.042995941 0.137996646 1.545297614 7.857859151 0.115661267 0.033215553 6.909915843 -0.839472758 0.130517283 EQTPEHGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQTPEHGKK 9 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 ; 75.294 0.025102 53620000 110811 86209 104901 97656 108132 83859 115246 86476 141363 FALSE TRUE 103875.5373 92592.00406 107389.3013 100162.0183 99639.7489 108067.732 97965.93219 97272.71896 117768.6021 0.882030826 0.786219777 0.911866995 0.850498491 0.846063782 0.917627704 0.831851024 0.825964792 1 16.84559543 -1.16137616 4.546818342 1.0000222 0.855646163 0.565013401 0.039558929 5377124.862 1373458.292 1190.891013 0.00866123 0.068964222 1.16137616 -0.144376037 EQVANSAFVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 EQVANSAFVER 11 0 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ;;;;;; 255.13 4.34E-20 5941460000 2198740 2348470 2394790 2375220 2430580 2106100 2501980 2077538 2222970 FALSE TRUE 2061124.788 2522353.162 2451595.55 2436172.166 2239692.051 2714096.88 2126831.326 2336923.193 1851941.946 1.11295324 1.362004445 1.323797193 1.315468971 1.209374871 1.465541016 1.148433044 1.261877133 1 20.82060744 0.627882172 0.921825091 1.000757594 1.301241032 0.414209549 0.102634479 1.051785562 1.496873914 0.08844882 0.029062072 4.245043765 -0.627882172 0.300483438 EQVHQGGVELQQLEAGLQEAGEEDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQVHQGGVELQQLEAGLQEAGEEDTR 26 0 K7EJH0;K7EMX1;K7EJV2;K7ESQ2;Q8NBT2 K7EJH0 SPC24 Kinetochore protein Spc24 0 194.81 9.34E-19 45264000 39801 47676 43661 39968 40953 37009 51261 35049 42626 FALSE TRUE 37309.92646 51205.98065 44696.65954 40993.64655 37736.71658 47692.89751 43574.88893 39424.9448 35511.44523 1.050645115 1.441957102 1.258655041 1.154378434 1.062663497 1.343028908 1.227066053 1.110203895 1 15.11599646 -1.324248482 0.218736218 0.792296016 1.291792101 0.205268899 0.123218683 28.68150835 1.238711584 3.611411497 0.281064342 0.047397072 1.324248482 0.499496085 EQVNDLFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EQVNDLFSR 9 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A087WW90;A0A0D9SF80;A0A494C0I1;A0A494C1N8;Q86UP8-3;Q86UP8;Q6EKJ0 A0A494C1K3;A0A087WW90 GTF2I;GTF2IRD2B;GTF2IRD2 General transcription factor II-I;General transcription factor II-I repeat domain-containing protein 2A;General transcription factor II-I repeat domain-containing protein 2B 0 ;; 192.91 7.96E-05 399246000 714740 864530 757310 791810 911790 692360 872420 801760 999920 FALSE TRUE 670005.6992 928540.7007 775273.7508 812129.1851 840181.6914 892233.0925 741608.7202 901861.5009 833026.8923 0.804302605 1.114658734 0.930670736 0.974913526 1.008588917 1.071073576 0.890257838 1.082631917 1 19.66800354 2.749484357 22.17105999 0.999439538 0.97831251 0.050381637 0.091413656 1092.045961 2216430.958 0.02634481 0.027630258 561.6740473 -2.749484357 -0.021127028 EQWDTIEELIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 EQWDTIEELIR 11 0 Q16698-2;Q16698 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 ;;;;;; 290.64 4.54E-35 2282386000 1228535 1207004 1065448 1033004 1473652 1047098 1042665 1155704 1591843 FALSE TRUE 1151643.187 1296371.832 1090720.93 1059512.632 1357917.316 1349378.194 886327.0629 1299996.188 1326154.12 0.868408257 0.977542363 0.822469209 0.798936274 1.023951362 1.01751235 0.668343935 0.980275346 1 20.33881702 1.028184976 24.9984663 1.000001586 0.88034757 0.149013057 0.10747033 326.9591755 289993.0427 0.101833163 0.025458291 10.67050507 -1.028184976 -0.119654016 EQWIQDAEECDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQWIQDAEECDR 12 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ; 233.32 1.26E-15 524380000 561290 621240 615350 581740 688820 666350 832730 574050 707920 FALSE TRUE 526159.8608 667237.256 629946.3926 596668.4333 634722.8558 858714.4277 707869.8672 645721.4061 589763.5787 0.892153873 1.131363957 1.068133766 1.011707835 1.076232712 1.456031635 1.200260397 1.094881796 1 19.1697772 2.447726097 24.99890305 1.21965334 1.049825449 0.2342985 0.130538761 252.8369779 215022.1195 0.041864965 0.035027146 280.366485 -2.447726097 -0.16982789 EQWWLSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQWWLSLR 8 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 106.93 0.009542 89599000 267500 205970 194130 161620 239620 131250 192000 178050 205850 FALSE TRUE 250757.6525 221220.2331 198734.8553 165767.4428 220801.2118 169139.7443 163211.3824 200279.9344 171492.3052 1.462209353 1.289971774 1.158855816 0.966617381 1.287528391 0.986281829 0.95171257 1.167865428 1 17.38778432 7.999999996 0.373037807 1.018205569 7.250095326 0.626457091 0.103467836 39.72811581 0.547480744 0.074276205 177.8547186 99999999.07 -7.999999996 6.231889757 EQYAQEHGLNFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EQYAQEHGLNFQR 13 0 Q15126 Q15126 PMVK Phosphomevalonate kinase 0 ; 167.55 3.17E-05 1059310000 1191800 1038420 1126920 1140720 1140360 883470 1224690 944040 1063860 FALSE TRUE 1117207.365 1115305.697 1153651.075 1169992.806 1050800.726 1138513.447 1041059.104 1061905.472 886294.8932 1.260536842 1.258391203 1.30165601 1.320094266 1.185610719 1.284576337 1.174619319 1.198140123 1 19.75742727 0.594749672 0.536421531 0.989894367 1.28166872 0.825026637 0.038462262 0.579671023 0.3221541 0.048240576 0.017066613 3.933232975 -0.594749672 0.291774353 EQYELVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQYELVHR 8 0 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 0 119.75 0.0041488 0 133820 167020 161400 149680 167060 135840 167860 150890 164700 FALSE TRUE 125444.4451 179386.3346 165228.4842 153521.0422 153939.7815 175054.8028 142690.9513 169728.9486 137210.506 0.914248105 1.307380461 1.204197033 1.118872357 1.121924159 1.275811947 1.039941878 1.23699674 1 17.06603143 -2.958977321 0.359533578 0.620692955 1.171793241 0.120234972 0.117465884 168.0001097 5.305496008 48.5217712 0.080111799 0.001099063 2.958977321 0.551100286 EQYPGIEIESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EQYPGIEIESR 11 0 Q9BRT3;J3KTI2 Q9BRT3 MIEN1 Migration and invasion enhancer 1 0 ;;; 240 2.66E-15 2340200000 1436320 1618840 1501800 1457710 1527880 1374270 1807730 1333100 1622750 FALSE TRUE 1346423.295 1738700.598 1537423.405 1495117.306 1407886.468 1770999.44 1536677.669 1499540.47 1351902.542 0.995947011 1.286113861 1.137229466 1.105935717 1.041411215 1.310005259 1.136677846 1.109207523 1 20.36655972 0.90316058 2.593825622 1.000570974 1.16001257 0.170202898 0.096188305 0.606805237 8.816447295 0.085068146 0.022742946 8.001300479 -0.90316058 0.159441596 EQYQQQQQWGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EQYQQQQQWGSR 12 0 Q14103-3;Q14103;H0Y8G5;H0YA96;Q14103-2;Q14103-4 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 136.7 0.00024503 79196000 95706 77215 77877 86448 101930 67535 93621 74823 122440 FALSE TRUE 89715.9323 82932.07894 79724.27922 88666.40204 93924.82897 87031.25816 79583.40018 84164.81626 102003.973 0.879533705 0.813027929 0.781580137 0.869244593 0.920795791 0.853214395 0.780199024 0.825113118 1 16.63826582 -1.209794823 5.000562556 1.000018723 0.832564162 0.558341164 0.044148116 9.77E-06 1.54E-06 0.045324932 0.010681995 0.061688637 1.209794823 -0.167454562 EQYVPPRS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 83.729 0.0093292 3078720000 5287020 3290840 4099800 4014690 4332620 2817150 4193710 2896890 4838420 TRUE FALSE 4956114.856 3534497.218 4197049.192 4117713.742 3992353.502 3630415.472 3564902.118 3258573.093 4030856.445 1.229543876 0.876860108 1.041230133 1.0215481 0.99044795 0.900656107 0.884403145 0.808407131 1 21.94265497 2.263826437 3.114113038 0.885737436 1.014165473 0.309801234 0.097230881 0.318074394 6.391224583 0.035693161 0.026874249 183.5804528 -2.263826437 0.128428038 ERAS(ph)LDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERASLDK 7 1 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 1 ERAS(1)LDK 97.472 0.0072506 808470000 901670 612910 700820 617100 749280 586390 815260 567210 1095100 TRUE FALSE 845236.0842 658290.4941 717443.7814 632935.8307 690434.5713 755671.2738 693019.3315 638027.4171 912320.7354 0.926468128 0.721555993 0.786394251 0.693764601 0.756789301 0.828295625 0.759622471 0.699345518 1 19.79918158 -1.762263692 7.06863248 1.004850839 0.767572553 0.526060824 0.068059533 0.004686908 0.000157633 0.05936335 0.0137914 0.017287664 1.762263692 -0.237278285 ERAS(ph)SPPDRIDIFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERASSPPDRIDIFGR 15 2 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 ERAS(0.5)S(0.5)PPDRIDIFGR 79.467 0.010362 51382000 26922 29052 23618 27837 34394 27377 29827 25693 47068 TRUE FALSE 25237.00008 31203.04031 24178.23011 28551.34455 31692.83398 35280.29547 25354.71825 28900.82761 39212.04673 0.643603234 0.79575138 0.616602094 0.728126862 0.808242278 0.899731037 0.646605326 0.737039507 1 15.25900933 2.90190493 4.934340699 0.790475106 0.696298342 0.234327289 0.104801017 0.421810237 16.39065742 0.03085112 0.033098552 797.8200204 -2.90190493 -0.094176764 KKYDVDTLDMVFLDHWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKYDVDTLDMVFLDHWK 17 2 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ; 225.11 1.50E-15 702850000 832330 823750 770010 793590 1282930 529440 1017130 856620 2268740 FALSE TRUE 780235.9511 884741.3071 788275.0008 813954.8629 1182173.853 682280.7333 864620.7991 963570.8927 1890072.637 0.412807389 0.468099104 0.417060691 0.430647398 0.625464773 0.360981224 0.457453741 0.509806276 1 20.85001025 0.65118288 2.594148991 0.999976471 0.452139331 0.8620351 0.068219167 0.949627921 6.674002747 0.059693282 0.015863766 4.479018744 -0.65118288 -0.54783714 ERDAEQSGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_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 ERDAEQS(0.005)GS(0.995)PR;ERDAEQS(0.032)GS(0.968)PR;ERDAEQS(0.013)GS(0.987)PR;ERDAEQS(0.003)GS(0.997)PR 135.47 7.23E-05 1510280000 2282440 2405360 2481350 2434360 2424920 1998860 2409830 2073110 2249480 TRUE FALSE 2139586.155 2583455.357 2540208.794 2496829.799 2234476.565 2575898.433 2048498.363 2331942.347 1874027.256 1.141704929 1.378558049 1.355481243 1.33233377 1.192339417 1.374525597 1.093099557 1.244348149 1 20.8377105 1.108086189 0.616107471 1.004985094 1.322826797 0.449382205 0.095808333 0.595561727 0.55283447 0.088277884 0.039136249 12.82585097 -1.108086189 0.317841704 ERDEDSLHQTDLFDSHMLWFLMHHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERDEDSLHQTDLFDSHMLWFLMHHLR 26 1 Q5TAQ9;V9GY98 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 0 ; 175.12 6.12E-13 86434000 90497 130583 79977 64263 133734 57861 88627 107738 57601 FALSE TRUE 84832.95431 140251.5012 81874.09221 65912.09738 123231.0711 74564.53141 75338.20412 121189.3265 47987.02098 1.76783123 2.922696561 1.706171597 1.373540095 2.568008361 1.553847892 1.569970433 2.525460509 1 15.55035663 -1.067070512 0.121863656 1.02E-12 2.665333957 0.216718991 0.532073221 55.39708583 1.348181183 26.39435606 6.537049747 0.085689871 1.067070512 2.665333957 ERDHS(ph)PTPS(ph)VFNSDEERYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERDHSPTPSVFNSDEERYR 19 2 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 2 ERDHS(1)PT(0.006)PS(0.71)VFNS(0.284)DEERYR 98.7 0.00049044 462320000 106460 94447 120390 116160 126940 83781 124640 87802 168190 TRUE FALSE 99796.85864 101439.9542 123245.7077 119140.8623 116970.6445 107967.2146 105951.3891 98764.27298 140118.0025 0.71223438 0.723960893 0.879585103 0.850289472 0.834800971 0.770544917 0.75615829 0.70486498 1 17.0962828 4.219071653 4.4476195 0.814071194 0.715660006 0.232233716 0.080138129 0.295912003 14.73009448 0.018922916 0.048781637 16560.43168 -4.219071653 -0.098411188 ERDHS(ph)PTPSVFNS(ph)DEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ERDHSPTPSVFNSDEER 17 1 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 2 ERDHS(0.333)PT(0.333)PS(0.333)VFNS(1)DEER;ERDHS(1)PT(0.081)PS(0.314)VFNS(0.604)DEER;ERDHS(1)PT(0.001)PS(0.027)VFNS(0.972)DEER 165.4 1.41E-09 618550000 489480 465230 510620 477650 499960 562490 605010 446100 448080 TRUE FALSE 458844.3205 499676.1133 522732.1475 489907.3077 460695.1583 724871.7317 514294.3671 501796.567 373292.5533 1.229181553 1.338564375 1.400328356 1.312395073 1.234139696 1.941832821 1.37772469 1.344244782 1 18.5099472 ERDHS(ph)PTPSVFNS(ph)DEERYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERDHSPTPSVFNSDEERYR 19 2 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 2 ERDHS(1)PT(0.002)PS(0.131)VFNS(0.867)DEERYR 94.003 0.00089348 496800000 261640 269990 285870 255080 298920 241970 336840 254020 403090 TRUE FALSE 245264.4194 289980.3405 292650.9714 261625.7846 275444.029 311822.8109 286333.9691 285734.9562 335811.6749 0.730362991 0.863520724 0.871473487 0.779084839 0.82023363 0.928564532 0.852662342 0.850878565 1 18.35729286 -5 0.145517396 1.550618677 0.79176424 0.563487171 0.048903552 111.6483483 0.979381709 17.76407788 0.265191874 1.00E-05 5 -0.758854437 ERDHS(ph)PTPSVFNSDEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERDHSPTPSVFNSDEER 17 1 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 ERDHS(0.954)PT(0.045)PS(0.001)VFNSDEER;ERDHS(0.96)PT(0.04)PSVFNSDEER 188.86 2.34E-10 3200600000 1238650 907440 949020 953310 978120 814860 1220460 880360 850790 TRUE FALSE 1161125.108 974627.8018 971531.2026 977773.5485 901302.4007 1050096.854 1037463.353 990274.8839 708787.6527 1.638184727 1.375063177 1.37069431 1.379501385 1.271611317 1.481539428 1.46371533 1.397139016 1 19.43499395 0.935365315 20.86189066 1 1.414942667 0.658805587 0.095451657 2587.489114 835156.3629 0.086858238 0.021714559 8.617182978 -0.935365315 0.414942668 ERDHSPT(ph)PSVFNSDEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERDHSPTPSVFNSDEER 17 1 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 ERDHS(0.199)PT(0.794)PS(0.007)VFNSDEER 206.95 9.55E-12 857900000 546340 621880 645480 643130 637980 549170 701070 557200 588130 TRUE FALSE 512145.5546 667924.6423 660791.0904 659633.8046 587875.6243 707706.464 595951.0619 626767.6465 489967.3035 1.045264757 1.363202478 1.348643237 1.346281272 1.199826233 1.444395287 1.216307818 1.279203004 1 18.90232595 0.346661834 1.110748437 0.999508713 1.301665319 0.378373343 0.111042412 2.862854081 4.018171996 0.097979273 0.029496594 2.221579373 -0.346661834 0.302156606 ERDKEVS(ph)DDEAEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERDKEVSDDEAEEK 14 2 P07900;P07900-2;G3V2J8 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 ERDKEVS(1)DDEAEEK 174.02 2.05E-06 206600000 515170 159680 256910 229980 220460 150080 398150 231970 223960 TRUE FALSE 482926.4293 171502.8733 263004.0265 235881.6762 203145.9609 193405.6597 338451.1037 260931.9651 186579.6292 2.58831273 0.919193988 1.409607403 1.264241317 1.088789606 1.036585079 1.81397672 1.398501896 1 17.50943196 4.748196734 24.91537639 1.273610252 2.588313466 0.72224674 0.261829052 735.2335939 1900996.956 0.064360083 0.840749285 56001.12276 -4.748196734 1.314703214 ERDLFFELDAMDHLESFIAECDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERDLFFELDAMDHLESFIAECDRR 24 2 Q9NQ29-3;Q9NQ29;Q9NQ29-2;A8MYV2 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 0 122.3 7.27E-05 3736900 3822.1 5808.4 6154.3 4570.1 8620.4 5322.8 6773.8 6349.9 10962 FALSE TRUE 3582.881584 6238.45998 6300.282902 4687.376503 7943.388557 6859.405952 5758.131575 7142.698993 9132.371383 0.392327626 0.683115011 0.689884657 0.513270465 0.869805686 0.751108958 0.63051877 0.782129711 1 13.15677381 -5 0.051918174 2.268345554 0.049918519 0.575013665 0.111423867 424.642545 1.627272591 73.94812956 15.65088041 1.00E-05 5 -2.218427036 ERDLS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ERDLSR 6 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 ERDLS(1)R;ERDLS(1)R;ERDLS(1)R 80.219 0.03942 1003160000 374420 317744 360470 297064 359130 338440 379220 352780 342790 TRUE FALSE 350985.7206 341270.0964 369020.5186 304687.1652 330925.3785 436142.1339 322359.4815 396825.3596 285576.1345 1.229044301 1.195023166 1.29219663 1.066920966 1.158799138 1.527235932 1.128803995 1.389560652 1 18.12351589 ERDLS(ph)RDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 71.03 0.039218 823330000 471790 545070 465480 531000 770390 321680 472160 527500 780550 TRUE FALSE 442261.5061 585427.5499 476521.4054 544626.359 709886.677 414543.794 401363.9913 593359.5362 650271.1625 0.68011859 0.900282196 0.732804148 0.837537308 1.091677931 0.637493738 0.617225574 0.912480163 1 19.31068192 1.006441569 24.70469282 1.000000059 0.78622579 0.220951811 0.138939496 166.8383724 639853.6873 0.13430012 0.03357503 10.14942805 -1.006441569 -0.213774269 ERDPQQEQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERDPQQEQER 10 1 Q9BZE9;Q9BZE9-2;J3KRY8;Q9BZE9-3;J3QL04;J3QR12;Q9BZE9-4 Q9BZE9 ASPSCR1 Tether containing UBX domain for GLUT4 0 119.74 0.00059451 77272000 49350 46758 48371 46376 47800 44108 47088 45690 45435 FALSE TRUE 46261.27159 50220.01097 49518.38296 47566.08667 44045.98082 56841.26357 40027.59154 51394.49708 37851.60498 1.222174637 1.326760411 1.308224129 1.256646494 1.163648961 1.501687012 1.0574873 1.357789111 1 15.20806685 -4.048376723 0.256960782 3.35E-10 1.298562529 0.331827619 0.119310649 118.5129328 1.833297501 62.03707313 0.14535827 8.95E-05 4.048376723 1.298562529 ERDQGGFGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERDQGGFGDR 10 1 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ; 103.44 0.0025666 560970000 391820 651280 603640 670460 672680 501730 641420 555260 580830 FALSE TRUE 367296.6856 699501.4489 617958.6259 687665.1387 619850.4263 646571.3061 545245.0257 624585.4333 483885.7207 0.759056674 1.445592252 1.277075556 1.42113129 1.280985158 1.336206626 1.126805364 1.290770541 1 18.88430684 0.372201761 0.779439362 0.998191434 1.277285567 0.10909478 0.195521563 4.034818696 3.442747725 0.201675962 0.060617713 2.356143629 -0.372201761 0.279094133 ERDQGGFGDRNEYGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERDQGGFGDRNEYGSR 16 2 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ; 223.65 4.79E-15 412670000 99310 132377 104288 121533 162293 81115 129046 111140 225180 FALSE TRUE 93094.36437 142178.3308 106761.7606 124651.7425 149547.1624 104531.5837 109696.7503 125016.0736 187596.0033 0.496249188 0.757896375 0.569104665 0.664469074 0.797176698 0.557216475 0.584749933 0.666411179 1 17.51726957 0.950208455 21.43359303 1.000000001 0.637863137 0.612960952 0.091045654 1487.277899 640225.0484 0.081651116 0.020412779 8.916788282 -0.950208455 -0.362136864 ERDQRPS(ph)SPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERDQRPSSPIR 11 2 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 ERDQRPS(0.681)S(0.319)PIR 81.703 0.016498 136890000 104620 148100 131190 123630 151840 133190 144010 112270 129110 TRUE FALSE 98072.02095 159065.4781 134301.8888 126802.5551 139915.0989 171639.7908 122417.0374 126287.1566 107560.7069 0.911782971 1.47884374 1.248614783 1.178892913 1.300801221 1.595748073 1.138120425 1.174101215 1 16.71479162 1.148569548 2.003514676 1.018926578 1.29860208 0.169166042 0.184611977 0.45291994 3.370046393 0.158016787 0.045123556 14.07892672 -1.148569548 0.279675502 ERDQRPSS(ph)PIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERDQRPSSPIR 11 2 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 ERDQRPS(0.34)S(0.66)PIR 119.96 0.0004061 1468000000 577220 652940 690900 629600 735360 514200 672460 643340 662430 TRUE FALSE 541092.8306 701284.357 707288.4743 645756.6019 677607.7919 662641.1927 571630.8658 723662.4152 551866.1535 0.980478377 1.270750802 1.281630464 1.170132645 1.227848071 1.20072809 1.035814322 1.311300594 1 19.07395888 1.957029504 21.57886224 1.119330777 1.210348924 0.060583292 0.116218533 203.9822492 102433.6136 0.044266457 0.028567681 90.57941346 -1.957029504 0.091018147 ERDSASFNPELLTHILDGSPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERDSASFNPELLTHILDGSPEK 22 1 Q15067-2;Q15067;I3L0T4;I3L2U4;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 144.01 6.21E-08 81548000 93435 82115 84510 83454 94551 62091 116250 87773 90184 FALSE TRUE 87587.07014 88194.88004 86514.61711 85595.57093 87125.34586 80015.66374 98819.39171 98731.65226 75131.70779 1.16578037 1.173870296 1.151506064 1.139273596 1.159634839 1.065005257 1.315282117 1.314114309 1 16.19713428 1.736011094 25 1.23936816 1.147701132 0.075551763 0.092331075 0.507948214 4889.797646 0.037663336 0.020886208 54.45165628 -1.736011094 -0.091667028 ERDTSPDKGELVS(ph)DEEEDT ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERDTSPDKGELVSDEEEDT 19 2 Q9UPU7 Q9UPU7 TBC1D2B TBC1 domain family member 2B 1 ERDT(0.003)S(0.003)PDKGELVS(0.992)DEEEDT(0.002) 58.284 0.063061 96610000 117250 76341 102030 106690 93926 70014 122150 82633 105790 TRUE FALSE 109911.5318 81993.36707 104450.1998 109427.846 86549.43084 90225.90522 103834.7415 92949.91195 88132.96557 1.24711033 0.930337094 1.18514337 1.241622193 0.982032436 1.023747523 1.178160077 1.054655444 1 16.42739413 2.708689599 24.99918875 1.066489352 1.119948989 0.15700462 0.10390617 2328.437353 1948675.998 0.034111974 0.032167705 511.3162547 -2.708689599 0.053459637 ERDVIMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 150.4 0.0017797 4962860000 834520 929360 940390 1025290 1002060 876440 1090800 903340 906590 FALSE TRUE 782288.8829 998170.7814 962696.4949 1051600.677 923362.2497 1129454 927244.6665 1016123.987 755274.2722 1.035767948 1.321600402 1.274631654 1.392342777 1.222552235 1.495422314 1.227692642 1.345370847 1 19.52664112 -1.0238374 5.005090129 0.999996147 1.296169409 0.362328696 0.120369757 4.50E-06 8.78E-07 0.10143326 0.023907738 0.09465915 1.0238374 0.296173261 ERDVMSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERDVMSR 7 1 E9PER6;O15530-5;O15530-2;O15530;O15530-3;H3BQ10;Q6A1A2 E9PER6;Q6A1A2 PDPK1;PDPK2P 3-phosphoinositide-dependent protein kinase 1;Putative 3-phosphoinositide-dependent protein kinase 2 0 67.897 0.067075 35483000 14436 28831 23912 24755 30626 28037 23238 26972 26670 FALSE TRUE 13532.47653 30965.67724 24479.20393 25390.25521 28220.7575 36130.82676 19753.67763 30339.51357 22218.60471 0.609060592 1.393682351 1.101743528 1.14274751 1.270140851 1.626151923 0.889060222 1.365500398 1 14.4394806 4.748679657 24.78054799 1.221601248 0.609060212 0.458408049 0.209923447 1118.682025 2739481.868 0.045776172 0.625454267 56063.42895 -4.748679657 -0.612541036 ERDVYEELLTQAEIQGNINK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERDVYEELLTQAEIQGNINK 20 1 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 205.68 7.66E-22 80161000 141060 121450 124590 116560 118270 92799 146780 112960 114230 FALSE TRUE 132231.3064 130442.2844 127545.3336 119551.1269 108981.5513 119588.5648 124771.7016 127063.3047 95164.27505 1.38950574 1.370706437 1.340264859 1.256260575 1.145193942 1.256653978 1.311119131 1.335199628 1 16.53813246 -5 0.145281504 1.10E-16 1.400838647 0.663918165 0.068068284 91.0059433 0.797600648 26.67562455 0.400814161 1.00E-05 5 1.400838647 ERDYPFYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERDYPFYER 9 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 0 113.63 0.0016136 64958000 92319 109430 110820 112840 120980 100930 121690 106780 130950 FALSE TRUE 86540.91858 117532.3111 113448.7027 115735.6654 111478.7188 130066.8525 103443.7142 120111.7181 109093.599 0.793272193 1.077352953 1.0399208 1.060884107 1.021863059 1.192250083 0.948210666 1.100996934 1 16.73520693 4.741667017 24.95412366 1.054133916 0.793272095 0.620735702 0.064334669 174.9879519 1405631.952 0.013480297 0.095646871 55165.43122 -4.741667017 -0.260861822 ERECETKTLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERECETKTLEK 11 2 A0A0J9YYF7;Q86T65-4;Q86T65 A0A0J9YYF7 DAAM2 Disheveled-associated activator of morphogenesis 2 0 55.401 0.070625 198440000 405510 280220 288590 310860 355100 200330 394570 263010 348750 FALSE TRUE 380129.853 300967.7804 295435.4911 318837.1939 327211.8784 258162.0189 335407.8915 295847.3775 290541.372 1.308350168 1.03588614 1.016844827 1.097389992 1.126214405 0.888555104 1.154423858 1.018262478 1 18.14838409 4.739968984 24.75865598 1.046398051 1.308350266 0.559400466 0.074149312 75.9240918 1334566.913 0.015888954 0.099625192 54950.16288 -4.739968984 0.261952215 EREDES(ph)EDESDILEESPCGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EREDESEDESDILEESPCGR 20 1 Q9NSY0 Q9NSY0 NRBP2 Nuclear receptor-binding protein 2 1 EREDES(0.999)EDES(0.001)DILEESPCGR;EREDES(0.73)EDES(0.27)DILEESPCGR 285.55 2.54E-45 537330000 482690 515890 489100 525190 501980 354430 576470 394760 342380 TRUE FALSE 452479.2945 554087.0324 500701.683 538667.2645 462556.5157 456748.1873 490033.6752 444046.655 285234.5661 1.586341027 1.942566218 1.755403245 1.888506263 1.62167062 1.60130728 1.718002421 1.55677715 1 18.1217893 -0.513161524 0.342433608 0.745924217 1.825171893 0.808122594 0.112444372 3.299909562 0.3974926 1.049625763 0.092936248 0.306788076 0.513161524 1.079247677 EREDLYAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EREDLYAK 8 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ;; 131.11 0.00092961 781830000 1089300 1045260 1051800 1039910 1171960 766570 1176980 1002810 1420930 FALSE TRUE 1021122.657 1122652.138 1076749.193 1066595.851 1079918.989 987866.3148 1000502.776 1128013.036 1183767.603 0.86260399 0.948372075 0.909595084 0.901017943 0.912272802 0.834510348 0.84518513 0.952900749 1 20.17495445 1.017142594 6.632615511 0.999934082 0.892290939 0.560371756 0.033940976 0.113591902 20.50692916 0.037185381 0.009334121 10.40261664 -1.017142594 -0.107643143 EREDS(ph)GDAEAHAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EREDSGDAEAHAFK 14 1 Q9NPI1-2;Q9NPI1 Q9NPI1-2 BRD7 Bromodomain-containing protein 7 1 EREDS(1)GDAEAHAFK 112.49 0.00035778 410580000 325160 227280 286190 265070 271990 235200 348510 235680 356480 TRUE FALSE 304808.816 244108.0477 292978.5619 271872.145 250629.0026 303098.4218 296254.1609 265105.1668 296981.1851 1.02635733 0.82196469 0.986522301 0.915452421 0.843922158 1.020598062 0.997551952 0.89266654 1 18.18001201 2.220752095 24.99932111 0.981187745 0.914707711 0.154982692 0.067697263 399.2836345 560504.3707 0.02357925 0.017450575 166.2463409 -2.220752095 -0.066480034 EREEIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EREEIEK 7 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ;;; 126.52 0.0035968 5779200000 4296140 3317000 3761710 3649440 3610770 2782250 4613150 3099270 4195570 FALSE TRUE 4027252.266 3562594.131 3850939.538 3743090.809 3327194.689 3585440.409 3921450.984 3486220.682 3495302.263 1.152189986 1.019252089 1.101747216 1.070891879 0.951904711 1.02578837 1.12192042 0.997401775 1 21.73698579 2.971457884 24.80260482 1.032866302 1.078341129 0.249709821 0.054125833 1309.010126 1137507.377 0.016612235 0.017653847 936.3924074 -2.971457884 0.045474827 EREEQETTSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EREEQETTSSK 11 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 69.209 0.050278 503750000 156340 122470 141240 133090 161900 105700 156450 128390 168100 FALSE TRUE 146554.9585 131537.8062 144590.2795 136505.3147 149185.0271 136213.8741 132991.7749 144419.7741 140043.024 1.046499527 0.939267108 1.032470418 0.974738411 1.06527996 0.972657332 0.949649408 1.031252896 1 17.09551059 -2.398592478 8.133656182 9.545804222 0.995105157 0 0.042650424 0.425766053 0.020864813 0.00266021 0.008971342 0.003993995 2.398592478 -8.550699065 EREES(ph)EDELEEANGNNPIDIEVDQNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EREESEDELEEANGNNPIDIEVDQNK 26 1 Q9UKL0 Q9UKL0 RCOR1 REST corepressor 1 1 EREES(1)EDELEEANGNNPIDIEVDQNK;EREES(1)EDELEEANGNNPIDIEVDQNK;EREES(1)EDELEEANGNNPIDIEVDQNK;EREES(1)EDELEEANGNNPIDIEVDQNK 380.94 1.12E-127 2269300000 2796520 1757460 2126690 1986910 2039870 1631460 2608950 1792120 2205540 TRUE FALSE 2621490.805 1887584.167 2177136.091 2037897.474 1879666.839 2102436.017 2217762.168 2015870.127 1837421.126 1.426722904 1.027300786 1.184886829 1.109107458 1.022991851 1.144231983 1.206997208 1.097119272 1 20.80925089 7.999999663 0.015435946 0.0020361 2.506713636 0.239843876 0.107700464 10417.44616 12.41157048 799.5126872 1263.462272 99999922.5 -7.999999663 2.504677536 EREGLENDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EREGLENDLK 10 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 84.507 0.013565 115980000 233160 201780 225260 229650 237350 170720 257910 196600 315940 FALSE TRUE 218566.9318 216720.0012 230603.2736 235543.2078 218709.4884 220004.0926 219238.7898 221145.9428 263207.5729 0.830397581 0.823380569 0.876127047 0.894895254 0.830939194 0.835857761 0.832950159 0.840195973 1 18.00584147 -2.25779073 2.267873692 1.591934875 0.845965274 0.822062644 0.022575603 1640283.667 235341.8472 4996553.1 0.005815435 0.005523435 2.25779073 -0.745969601 EREKEPS(ph)RER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EREKEPSRER 10 3 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477 Q8NI27 THOC2 THO complex subunit 2 1 EREKEPS(1)RER 127.27 0.0019927 910860000 534090 396060 430690 407390 435820 320470 559510 388390 676460 TRUE FALSE 500662.2603 425384.6945 440906.1702 417844.3171 401592.4552 412984.4866 475616.6697 436881.3465 563554.4559 0.888400855 0.754824472 0.782366576 0.741444438 0.712606299 0.732820905 0.843958671 0.775224722 1 19.1041955 0.192609136 0.896555113 1.00212157 0.770808975 0.632938802 0.052732588 2.34861908 2.092056409 0.061959295 0.015926027 1.558149541 -0.192609136 -0.231312595 ERELEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERELEEAR 8 1 Q9Y490;Q9Y4G6;H0YMT1;A0A1B0GVU7 Q9Y490;Q9Y4G6 TLN1;TLN2 Talin-1;Talin-2 0 ; 166.19 0.00029177 236400000 229550 269030 245460 224170 296600 197383 243510 252270 336260 FALSE TRUE 215182.8753 288949.2611 251282.4271 229922.5817 273306.2324 254364.2679 206997.9361 283766.4648 280136.0337 0.768137081 1.031460528 0.897001445 0.820753327 0.975619697 0.908002675 0.738919351 1.012959529 1 18.09576804 3.500047558 22.45351431 0.886310048 0.93201496 0 0.105503745 481.4957722 471559.4317 0.026456072 0.040840769 3162.623966 -3.500047558 0.045704912 ERELEECQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERELEECQR 9 1 Q9UNE7;Q9UNE7-2;H3BTA3;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 138.22 0.00013019 222710000 112210 310200 227190 308230 271130 276170 258650 251150 215090 FALSE TRUE 105186.9764 333167.5308 232579.0541 316139.7036 249836.5435 355895.7958 219867.8337 282506.6303 179190.0895 0.587013359 1.859296637 1.297945968 1.764270025 1.394254248 1.986135488 1.227008895 1.576575084 1 17.45113132 -1.514552978 2.825299203 0.979048429 1.49317991 0.114882962 0.394035909 25822086.85 27232978.08 4158971.718 0.084038949 0.030580672 1.514552978 0.514131482 ERENMDT(ph)DDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERENMDTDDER 11 1 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 1 ERENMDT(1)DDER;ERENMDT(1)DDER 112.96 0.0040207 333480000 392950 361360 422720 442540 346460 402300 470930 287750 187358 TRUE FALSE 368355.9609 388115.4704 432747.118 453896.3256 319250.4292 518437.4792 400318.4184 323676.2209 156086.7394 2.359943979 2.486537113 2.772478429 2.907974933 2.045339856 3.321470364 2.564717668 2.07369455 1 17.25198845 0.915639264 2.580212487 1.00389323 2.654995444 0.707732773 0.335872852 0.185508515 2.728790132 0.290908521 0.077879312 8.23453849 -0.915639264 1.651102214 ERENMDTDDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERENMDTDDER 11 1 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 0 ; 103.91 0.0028029 648940000 647410 683700 692410 715140 715620 564260 801000 646410 620870 FALSE TRUE 606889.7638 734321.8594 708834.2922 733491.7031 659418.0919 727152.702 680897.4861 727115.7114 517242.786 1.173317019 1.419685067 1.370409238 1.418080103 1.27487151 1.405824734 1.316398226 1.405753219 1 18.98048209 -0.992907706 4.755852283 0.999994221 1.355999571 0.662485556 0.077887661 4.17E-06 8.83E-07 0.065911998 0.015535355 0.101646468 0.992907706 0.35600535 EREPEAASSRGS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EREPEAASSRGSPVR 15 2 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EREPEAAS(0.002)S(0.003)RGS(0.995)PVR;EREPEAAS(0.013)S(0.015)RGS(0.972)PVR 146.15 3.10E-06 634470000 213897 328960 250450 319140 342020 162391 271030 230080 562590 TRUE FALSE 200509.5686 353316.5407 256390.7923 327329.6727 315159.1288 209270.6455 230391.5676 258805.9945 468690.0945 0.42780842 0.753838293 0.547036934 0.698392555 0.67242541 0.446501106 0.491564832 0.552190024 1 18.83827478 -1.449618045 3.113455704 1.008058934 0.581705002 0.608398009 0.107309811 28337816.74 34808655.66 1999577.116 0.025730234 0.035512558 1.449618045 -0.426353932 EREQPPR ddPTM_SK-BR-3_Pertuzumab_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 ; 124.08 0.0038134 192398000 90657 100134 102932 96360 109644 89932 103875 89026 100065 FALSE TRUE 84982.9402 107548.0255 105373.5956 98832.76074 101033.0025 115893.9085 88299.90808 100141.0921 83363.50506 1.019426188 1.290109209 1.264025494 1.185563883 1.211957228 1.390223556 1.059215397 1.201258177 1 16.34712832 0.919021256 1.050119824 1.006279536 1.229901439 0.25355244 0.106849934 0.741029018 1.673381254 0.09224292 0.029885636 8.298913853 -0.919021256 0.223621903 ERESLNASIVDAINQAADCWGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERESLNASIVDAINQAADCWGIR 23 1 A0A087WYB4;Q9UJZ1 A0A087WYB4 STOML2 "Stomatin-like protein 2, mitochondrial" 0 167.61 9.67E-12 53457000 135040 139540 131480 126490 197610 124380 139550 139690 223680 FALSE TRUE 126588.0875 149871.6868 134598.7677 129735.9475 182090.5077 160286.4869 118625.773 157130.604 186346.363 0.679316116 0.804264083 0.722304238 0.696208638 0.977161587 0.860153557 0.636587541 0.843217981 1 17.50762714 -5 0.306874292 2.973185045 0.760598857 0.340055522 0.099467708 346.579643 3.162033512 441.5918547 0.094258825 1.00E-05 5 -2.212586188 ERESLQQMAEVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERESLQQMAEVTR 13 1 K7ELL7;P14314-2;P14314;K7EPW7;K7EKX1;K7EJ70 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 214.89 2.74E-11 331640000 206875 326570 224690 252920 371710 188576 263400 256990 348840 FALSE TRUE 193927.063 350749.5826 230019.7529 259410.3554 342517.396 243014.8299 223905.6153 289075.7672 290616.3504 0.667295776 1.206916204 0.791489373 0.892621337 1.178589558 0.836204947 0.770450854 0.994698911 1 18.14875635 EREVDEDS(ph)EPER ddPTM_SK-BR-3_Pertuzumab_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 173.35 2.02E-05 1919560000 767390 746910 764180 697270 705590 687330 894360 659580 617140 TRUE FALSE 719360.4297 802211.9936 782306.7105 715163.1287 650175.8076 885751.0131 760259.0208 741930.0149 514135.3471 1.39916548 1.560312859 1.521596822 1.391001674 1.264600482 1.722797349 1.478713777 1.443063619 1 18.97178868 0.697819199 3.120851817 1.000022547 1.490327559 0.605584892 0.119800999 2.056984916 20.49788463 0.109512157 0.028524619 4.986768405 -0.697819199 0.490305012 EREVDEDS(ph)EPEREVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EREVDEDSEPEREVR 15 2 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EREVDEDS(1)EPEREVR 106.05 0.00066102 488120000 188540 260670 267110 281120 355060 175490 279450 238600 375700 TRUE FALSE 176739.618 279970.278 273445.9753 288334.0151 327175.0198 226151.1142 237549.0668 268389.7352 312993.2429 0.564675506 0.894493042 0.873648175 0.921214824 1.04531017 0.72254312 0.75895909 0.857493704 1 18.25577199 -5 0.016439539 1.977104594 5.62E-17 0.163875865 0.127230042 14138.92153 17.62264839 1354.944207 825.2151938 1.00E-05 5 -1.977104594 EREVEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EREVEER 7 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;;; 182.53 0.00059817 2697997000 2700532 2997734 2949930 2933103 3043667 2522110 3110071 2673228 3158498 FALSE TRUE 2531510.523 3219689.344 3019903.733 3008371.389 2804629.671 3250202.214 2643744.726 3006986.4 2631324.279 0.962067102 1.223600364 1.147674483 1.143291769 1.065862423 1.235196376 1.004720227 1.142765422 1 21.32735762 0.868621762 0.652304448 1.001998114 1.139792312 0.114121288 0.088030896 1.533850375 1.448059623 0.081727237 0.032424198 7.389614138 -0.868621762 0.137794199 EREWQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EREWQK 6 1 O75937;S4R3J5 O75937 DNAJC8 DnaJ homolog subfamily C member 8 0 88.029 0.047213 309270000 141650 151770 118490 137180 153760 102300 160140 138610 201970 FALSE TRUE 132784.3794 163007.2087 121300.6388 140700.271 141684.3098 131832.3493 136128.4937 155915.7636 168259.9022 0.789162347 0.968782262 0.720912334 0.836207969 0.842056295 0.783504255 0.809037043 0.926636481 1 17.36033189 1.053243315 3.696808084 0.998703289 0.824751042 0.488385894 0.062684818 0.17102368 4.870682408 0.05842692 0.015104687 11.30429063 -1.053243315 -0.173952246 ERFS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 100.79 0.0078416 6371890000 1571070 1457366 1596560 1469160 1412490 1542830 1812380 1473060 1299949 TRUE FALSE 1472739.533 1565270.895 1634431.157 1506861.133 1301558.733 1988219.975 1540630.444 1656974.784 1082979.114 1.359896525 1.445338026 1.509199149 1.391403688 1.201831796 1.835880258 1.422585555 1.530015457 1 20.04657399 ERFS(ph)PPRHELS(ph)PPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ERFSPPRHELSPPQK 15 2 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 2 ERFS(1)PPRHELS(1)PPQK;ERFS(1)PPRHELS(1)PPQK;ERFS(1)PPRHELS(1)PPQK 114.46 0.00032416 1233140000 502350 437080 453660 462190 516560 366580 507100 428840 592350 TRUE FALSE 470908.8102 469441.858 464421.0294 474050.5779 475991.4613 472405.6951 431065.0627 482381.618 493482.9583 0.954255466 0.951282816 0.941108546 0.960621983 0.964555013 0.957288772 0.873515601 0.977504106 1 18.91264074 ERFS(ph)PPRHELS(ph)PPQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 103.02 0.0021124 11373900000 802090 742370 794920 758310 982110 571240 858280 701540 1350530 TRUE FALSE 751888.6187 797335.8472 813775.8778 777769.5184 904979.0422 736147.7147 729588.8819 789128.8133 1125117.818 0.668275452 0.708668758 0.723280589 0.691278287 0.804341579 0.654285003 0.64845554 0.701374381 1 20.10164465 -0.954582559 5.15531955 1.000001224 0.699830917 0.82190312 0.043888254 6.16E-07 1.25E-07 0.042395854 0.009992758 0.111024146 0.954582559 -0.300170307 ERFS(ph)PPRHELSPPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ERFSPPRHELSPPQK 15 2 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 ERFS(1)PPRHELSPPQK;ERFS(1)PPRHELSPPQK;ERFS(1)PPRHELSPPQK;ERFS(1)PPRHELSPPQK 146.1 2.06E-06 2069060000 2625530 2369290 2402850 2416680 2550260 2069400 2905890 2225850 2710900 TRUE FALSE 2461202.764 2544714.697 2459846.737 2478696.1 2349972.867 2666802.186 2470178.771 2503752.272 2258433.277 1.089783253 1.126761071 1.089182825 1.097529037 1.040532342 1.180819559 1.093757693 1.10862353 1 21.10689086 -0.915169776 4.963793955 0.999999568 1.104791238 0.461829072 0.035039996 1.50E-07 3.28E-08 0.030438727 0.007174447 0.121571066 0.915169776 0.10479167 ERFS(ph)PPRHELSPPQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ERFSPPRHELSPPQKR 16 3 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 ERFS(1)PPRHELSPPQKR;ERFS(1)PPRHELSPPQKR;ERFS(1)PPRHELSPPQKR;ERFS(1)PPRHELSPPQKR;ERFS(1)PPRHELSPPQKR 173.43 3.01E-09 5265320000 1169840 1332460 1170680 1240720 1429280 1001370 1544860 1126880 2058120 TRUE FALSE 1096621.803 1431116.725 1198449.082 1272558.976 1317030.114 1290449.263 1313222.585 1267573.449 1714606.476 0.63957638 0.834661915 0.698964514 0.742187198 0.768123842 0.752621246 0.765903199 0.739279518 1 20.70944607 -4.999999974 0.41275698 5.411048902 0.744889542 0.724703409 0.049826225 427.0779285 2.851048173 1704.54771 0.026538 1.00E-05 4.999999974 -4.66615936 ERFTEHEVQIYVGEIVLALEHLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERFTEHEVQIYVGEIVLALEHLHK 24 1 O75582-3;O75582;O75582-2;A0A3B3ISL8;G3V2D1 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 0 ; 183.42 9.54E-18 139353000 279605 232478 214880 269773 289016 195811 299643 298344 254886 FALSE TRUE 262105.0222 249690.913 219977.0551 276695.8319 266317.8492 252338.457 254714.3139 335592.9051 212343.88 1.234342248 1.17587996 1.035947234 1.303055364 1.254181892 1.18834815 1.199536874 1.580421838 1 17.696043 3.220954679 24.99806262 1.255099032 1.138431583 0.098086692 0.149762126 482.2439739 684720.0987 0.039884796 0.047767973 1663.239074 -3.220954679 -0.116667448 ERGDYVLAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ERGDYVLAVK 10 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;A0A0A0MT44 O75369-8 FLNB Filamin-B 0 ;; 91.961 0.0089307 921940000 1707070 2337220 1803920 1858410 2401090 1401360 2014250 2138990 2123910 FALSE TRUE 1600227.536 2510270.201 1846709.834 1906099.947 2212518.077 1805909.883 1712231.912 2406047.61 1769415.7 0.904381902 1.418700083 1.043683423 1.077248239 1.250422994 1.020624991 0.967682107 1.359797819 1 20.7548416 3.735597971 24.60999985 1.093699719 1.208152142 0.001692174 0.1715127 688.1773314 1997931.501 0.040521866 0.071565656 5439.98837 -3.735597971 0.114452423 ERGT(ph)PPVDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERGTPPVDPK 10 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 ERGT(1)PPVDPK;ERGT(1)PPVDPK 90.697 0.052919 803430000 1754780 1241790 1468310 1288580 1551600 1226640 1830110 1404310 2155570 TRUE FALSE 1644951.452 1333733.424 1503139.007 1321647.144 1429743.595 1580751.055 1555701.995 1579641.195 1795791.441 0.916003615 0.74269951 0.837034286 0.735969174 0.796163498 0.88025314 0.866304382 0.879635106 1 20.77618838 1.052748193 0.694295606 0.997235832 0.799107133 0.5365543 0.053937445 0.501174641 0.566358973 0.048449637 0.019555893 11.29141042 -1.052748193 -0.198128699 ERGTGDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERGTGDVK 8 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6;C9JDM3;C9JIC6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 92.051 0.010992 108180000 181090 146940 164730 158830 186810 128180 190250 152340 176190 FALSE TRUE 169755.9002 157819.5905 168637.4734 162905.8467 172138.6962 165183.4852 161723.7787 171359.9843 146782.7508 1.156511234 1.075191667 1.148891627 1.10984326 1.172744721 1.125360332 1.10179008 1.167439522 1 17.16332291 -1.529008886 3.332578874 0.996580533 1.12696308 0.637840595 0.03108746 4207688.533 6376624.384 127919.0665 0.006915217 0.029579519 1.529008886 0.130382548 ERHAS(ph)EMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ERHASEMR 8 1 P49754-2;P49754-3;P49754 P49754-2 VPS41 Vacuolar protein sorting-associated protein 41 homolog 1 ERHAS(1)EMR;ERHAS(1)EMR;ERHAS(1)EMR 57.203 0.06829 1485480000 341100 439100 400710 379990 408940 365280 423270 354990 413370 TRUE FALSE 319751.1599 471611.4209 410215.0304 389741.1867 376823.502 470730.4062 359804.5929 399311.2829 344375.8765 0.928494653 1.369467065 1.191183989 1.131731963 1.09422154 1.366908771 1.044801966 1.159521645 1 18.39362456 0.935416917 0.96093699 1.003360484 1.195202675 0.102760906 0.134932407 1.140939929 2.209133106 0.117768924 0.039507527 8.618206909 -0.935416917 0.191842192 ERHPGSFDVVHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ERHPGSFDVVHVK 13 1 P62701;C9JEH7;P22090 P62701 RPS4X;RPS4Y1 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1" 0 ;;;; 202.25 6.15E-08 5985820000 4268991 4964500 4850750 4868560 5725700 3905470 5898660 4679170 6738110 FALSE TRUE 4001802.474 5332076.746 4965812.081 4993495.492 5276026.618 5032915.789 5014210.693 5263374.675 5613475.911 0.712892072 0.949870781 0.884623388 0.889554987 0.939885857 0.896577427 0.89324525 0.937632005 1 22.42046295 4.744464298 24.99196931 0.915741205 0.712891984 0.767133875 0.036291875 294.6129437 1247145.127 0.007671456 0.069859767 55521.89719 -4.744464298 -0.202849221 ERHPS(ph)WR ddPTM_SK-BR-3_Pertuzumab_2h_R1 15 ERHPSWR 7 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR;ERHPS(1)WR 120.45 0.0027579 1.07287E+11 17975758.8 20327311.5 19612986.3 20639911.5 21688454 18607184.2 21756448 17489137.2 21825616 TRUE FALSE 16850688.14 21832366.79 20078215.6 21169566.57 19985130.31 23978776.22 18494270.6 19672694.48 18182779.69 0.926738839 1.200716676 1.104243462 1.164264592 1.099124042 1.318762952 1.017131094 1.08194098 1 24.11606943 1.605615275 25 1.037142141 1.141277215 0.190379033 0.099178422 0.342926718 3750.793444 0.044940714 0.022362264 40.32879772 -1.605615275 0.104135074 ERHPS(ph)WRS(ph)EETQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERHPSWRSEETQER 14 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 ERHPS(1)WRS(0.836)EET(0.164)QER;ERHPS(1)WRS(0.717)EET(0.283)QER 148.44 4.16E-06 1618200000 773570 953970 810680 1014300 1143190 618940 808550 778970 1004750 TRUE FALSE 725153.6346 1024602.931 829909.7124 1040328.655 1053408.469 797617.9303 687315.4337 876226.1192 837050.7341 0.866319812 1.224063118 0.991468831 1.24285018 1.25847625 0.952890784 0.821115621 1.046801685 1 19.67495554 2.09146686 8.574118989 0.923962608 1.11964248 0.258104921 0.132261043 0.288613783 24.07338827 0.046515377 0.034323827 123.4431115 -2.09146686 0.195679872 ERHPS(ph)WRSEET(ph)QER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ERHPSWRSEETQER 14 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 ERHPS(1)WRS(0.395)EET(0.605)QER;ERHPS(0.999)WRS(0.316)EET(0.686)QER;ERHPS(1)WRS(0.076)EET(0.924)QER 107.39 0.0016756 1542950000 595259 762459 658931 767830 865072 530883 648578 592082 790611 TRUE FALSE 558002.8018 818912.2577 674561.1545 787533.8177 797132.7347 684140.3039 551329.75 666004.741 658652.9166 0.847187931 1.243313796 1.024152687 1.195673469 1.210247028 1.038696234 0.837056568 1.01116191 1 19.3291589 1.994362322 23.11757486 0.932945058 1.1170309 0.246816069 0.121138903 98.08806315 402215.9267 0.042313405 0.03021687 98.71026603 -1.994362322 0.184085842 ERHPSWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERHPSWR 7 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 127.02 0.0035526 491010000 366550 416540 391830 405930 431880 366870 397800 357950 425930 FALSE TRUE 343608.2898 447381.055 401124.3926 416346.851 397961.8869 472779.4134 338153.583 402640.8454 354839.5314 0.968348392 1.260798235 1.130438852 1.173338409 1.121526357 1.332375261 0.952976073 1.134712482 1 18.43680722 1.691557258 13.1259806 1.033742915 1.170296049 0.271965497 0.103877051 0.15160765 35.76602348 0.042961243 0.023586027 49.15381809 -1.691557258 0.136553134 ERLDQPMTEIVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ERLDQPMTEIVSR 13 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 162.41 9.83E-07 297260000 123549 163425 172044 193708 178114 158587 198509 147083 158643 FALSE TRUE 115816.2886 175525.157 176124.9649 198678.8752 164125.6449 204368.4925 168744.4183 165446.6363 132164.4584 0.876304341 1.328081385 1.33261973 1.503270074 1.241828907 1.5463196 1.276776074 1.251823965 1 17.01197473 0.795200266 2.359752329 1.000411293 1.32078598 0.209396917 0.179438923 1.170910452 10.69800748 0.156114636 0.042130647 6.24022524 -0.795200266 0.320374687 ERLEHPVLHVSWNDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERLEHPVLHVSWNDAR 16 1 A8MXB9;C9J660;J3KQJ1;Q8NBJ7;A0A494C1B1;H7C3B2;C9JL30;Q8NBJ7-3;Q8NBJ7-2;F8WA42 A8MXB9 SUMF2 Sulfatase-modifying factor 2 0 ; 152.37 3.57E-07 262133000 71615 217709 162227 182119 223097 153188 185893 176863 202902 FALSE TRUE 67132.74499 233828.4009 166075.101 186792.4819 205575.8616 197410.8888 158020.0704 198944.7349 169036.3454 0.397149766 1.38330251 0.982481612 1.105043305 1.216163666 1.167860606 0.934828957 1.176934667 1 17.36697396 4.752034162 24.84431129 1.118351941 0.397149249 0.75386488 0.129946473 1063.435481 1960866.156 0.030373484 0.600784097 56498.1415 -4.752034162 -0.721202692 ERLEQEQLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERLEQEQLER 10 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;A0A0U1RQP7;A0A075B6E5;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 98.105 0.0053871 0 425470 460330 420110 459620 528320 376790 487520 438700 492390 FALSE TRUE 398840.5922 494413.3122 430075.2076 471414.6273 486827.8783 485563.1563 414420.9019 493472.6607 410206.928 0.972291214 1.20527782 1.048434773 1.149211764 1.186786095 1.183702963 1.0102728 1.202984706 1 18.64599233 -0.965130299 7.859894775 0.999999999 1.11875718 0.169527647 0.083346564 1.08E-09 1.37E-10 0.072477652 0.017083146 0.108360176 0.965130299 0.118757181 ERLEQQVPVNQVFGQDEMIDVIGVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERLEQQVPVNQVFGQDEMIDVIGVTK 26 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 141.78 2.66E-07 117890000 114670 114720 102950 114350 140570 83510 136260 98196 153580 FALSE TRUE 107493.0094 123213.9882 105392.0226 117284.4146 129530.1992 107617.9813 115829.078 110455.9868 127946.5058 0.84014025 0.963011747 0.823719428 0.916667586 1.012377778 0.841117001 0.905293015 0.863298189 1 16.96518122 2.311958817 0.008529036 1.811882707 3.01E-06 0.129930879 0.062682585 6763.161358 32.03370208 3350.543288 3451.393977 205.0967681 -2.311958817 -1.811879701 ERLNS(ph)SENGEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERLNSSENGEDR 12 1 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 ERLNS(0.879)S(0.121)ENGEDR;ERLNS(0.954)S(0.046)ENGEDR 186.55 7.04E-06 1740310000 760250 888390 815670 978940 942730 592940 642920 492780 592940 TRUE FALSE 712667.3096 954167.32 835018.0776 1004061.258 868691.7886 764112.1524 546520.1146 554304.6677 493974.4835 1.442720896 1.931612567 1.69040731 2.032617658 1.758576238 1.546865634 1.106373169 1.122132188 1 18.91407699 1.870255348 2.19364654 1.057879577 1.795068462 0.804896457 0.156123034 0.116103274 1.036805178 0.086842358 0.041507014 74.17462305 -1.870255348 0.737188885 ERMSPQEAWLLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERMSPQEAWLLNR 13 1 I3L2X7 I3L2X7 CEP131 0 88.496 0.064282 420750000 165270 168360 192760 201960 201100 138510 217370 184710 230990 FALSE TRUE 154926.0457 180825.5496 197332.3582 207142.6355 185306.4172 178495.5885 184777.3865 207771.4501 192436.2767 0.805077132 0.939664561 1.025442612 1.076421967 0.962949504 0.927556859 0.960200382 1.079689618 1 17.55402127 4.740250808 1.891711391 0.997104009 0.744103122 0.625907731 0.048740156 0.589875066 2.199228334 0.01289815 0.263988139 54985.83289 -4.740250808 -0.253000887 ERNEEEAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERNEEEAKR 9 2 Q96IZ7-2;Q96IZ7;C9J713;H7C5Q0 Q96IZ7-2 RSRC1 Serine/Arginine-related protein 53 0 83.397 0.0091099 45089000 76675 64719 74471 65359 77870 52738 78103 62015 99552 FALSE TRUE 71876.04862 69510.8621 76237.48729 67036.22259 71754.40431 67962.60447 66392.18022 69757.70926 82936.12807 0.866643407 0.838125238 0.91923133 0.808287343 0.865176685 0.819457166 0.80052182 0.841101591 1 16.33971308 -0.985232127 6.117151554 1.000000096 0.845879383 0.672169594 0.034051589 4.76E-08 7.79E-09 0.035128649 0.008279897 0.103458904 0.985232127 -0.154120713 ERNHKPS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ERNHKPSR 8 2 P84103 P84103 SRSF3 Serine/arginine-rich splicing factor 3 1 ERNHKPS(1)R;ERNHKPS(1)R;ERNHKPS(1)R;ERNHKPS(1)R 78.653 0.01569 508786000 411113 293452 282991 338365 323195 338398 497107 335680 296936 TRUE FALSE 385382.1712 315179.4914 289703.6802 347048.0188 297812.5684 436088.0092 422570.4203 377590.3869 247375.4633 1.557883575 1.274093587 1.171109197 1.402920136 1.203888876 1.762858787 1.70821477 1.526385769 1 17.91634288 2.249516879 24.99962327 1.581738896 1.298555196 0.074940325 0.234338467 272.6293351 622076.0209 0.074194291 0.061522251 177.6302304 -2.249516879 -0.283183699 ERPDCLDTVLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERPDCLDTVLAR 12 1 Q9P253 Q9P253 VPS18 Vacuolar protein sorting-associated protein 18 homolog 0 137.4 8.47E-05 148640000 128060 129150 121600 136000 153490 124620 146760 116280 167810 FALSE TRUE 120044.9532 138712.4004 124484.4094 139489.9902 141435.5145 160595.771 124754.7005 130797.814 139801.4269 0.858681888 0.99221019 0.890437331 0.997772293 1.011688634 1.148742002 0.892370723 0.935597131 1 17.09301956 4.743245684 23.55684736 0.97722612 0.858681776 0.219252916 0.073209279 369.075716 1855585.633 0.017340523 0.137158476 55366.32326 -4.743245684 -0.118544344 ERPDLEAPAPGS(ph)PFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 200.74 4.10E-09 3999520000 1094560 1200160 1199120 1176910 1298080 1103340 1416560 1159560 1379000 TRUE FALSE 1026053.443 1289021.095 1227563.693 1207111.503 1196134.033 1421856.347 1204159.979 1304333.619 1148835.991 0.89312439 1.1220236 1.068528234 1.050725702 1.041170404 1.237649549 1.048156558 1.135352329 1 20.13174142 ERPDLPPVQYEPVLCSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERPDLPPVQYEPVLCSR 17 1 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 94.973 0.0024916 0 47490 47273 48728 51878 41782 38500 59131 44648 45847 FALSE TRUE 44517.68567 50773.14211 49883.85117 53209.27731 38500.61026 49614.325 50264.8555 50222.40108 38194.83952 1.165541896 1.329319425 1.306036412 1.393101214 1.008005551 1.2989798 1.316011695 1.314900173 1 15.22109011 ERPEIS(ph)PPSDFEHTIHVGFDAVTGEFTGMPEQWAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ERPEISPPSDFEHTIHVGFDAVTGEFTGMPEQWAR 35 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 ERPEIS(0.326)PPS(0.326)DFEHT(0.326)IHVGFDAVT(0.021)GEFT(0.001)GMPEQWAR;ERPEIS(0.25)PPS(0.25)DFEHT(0.25)IHVGFDAVT(0.25)GEFTGMPEQWAR;ERPEIS(0.471)PPS(0.471)DFEHT(0.058)IHVGFDAVT(0.001)GEFTGMPEQWAR 91.407 0.00027238 77681000 50160 65374 61139 62444 69649 58977 61798 57921 58195 TRUE FALSE 47020.57514 70214.35898 62589.24595 64046.41876 64179.04849 76002.70249 52531.9636 65152.56435 48481.87855 0.969858771 1.448259867 1.290982277 1.321038307 1.323773963 1.567651765 1.083538121 1.343853957 1 15.56515798 -1.565548014 5.976586016 0.999228468 1.304714798 0.230083341 0.167709697 0.001547146 0.000112466 0.145716526 0.034262848 0.027192678 1.565548014 0.30548633 ERPEISPPSDFEHTIHVGFDAVTGEFTGMPEQWAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERPEISPPSDFEHTIHVGFDAVTGEFTGMPEQWAR 35 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 0 140.94 9.14E-11 50028000 14326 17182 14771 13768 18583 13597 17056 14799 15893 FALSE TRUE 13429.36123 18454.17316 15121.3751 14121.31019 17123.56614 17522.23317 14498.61114 16646.68773 13240.35563 1.014274964 1.393782288 1.142067141 1.066535566 1.293285968 1.323395962 1.095031852 1.257268928 1 13.69265425 -3.328783784 0.51225808 2.68E-11 1.20865228 0.202623118 0.121395721 634.082873 16.46506587 698.0068025 0.052261401 0.000469047 3.328783784 1.20865228 ERPES(ph)CDDSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERPESCDDSSK 11 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6 Q8NEY1-5 NAV1 Neuron navigator 1 1 ERPES(0.916)CDDS(0.066)S(0.018)K 82.925 0.017209 0 168040 319010 508330 164430 149500 115430 203190 120950 281140 TRUE FALSE 157522.6764 342629.8323 520387.8277 168649.5522 137758.8731 148752.7672 172723.5458 136050.8737 234215.9178 0.672553249 1.462880216 2.221829467 0.720060164 0.588170413 0.635109554 0.737454343 0.580877999 1 17.8374796 3.147754406 10.49628837 0.687290131 1.563961218 0.437988654 0.389054541 0.282218733 30.41447745 0.113218295 0.135406957 1405.252628 -3.147754406 0.876671087 ERPES(ph)PMVPSEQVVEEAVPLPPQALTTSQDGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 ERPESPMVPSEQVVEEAVPLPPQALTTSQDGHR 33 1 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 ERPES(0.998)PMVPS(0.002)EQVVEEAVPLPPQALTTSQDGHR;ERPES(1)PMVPSEQVVEEAVPLPPQALTTSQDGHR;ERPES(0.998)PMVPS(0.002)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.999)PMVPS(0.001)EQVVEEAVPLPPQALTTSQDGHR;ERPES(1)PMVPSEQVVEEAVPLPPQALTTSQDGHR;ERPES(0.979)PMVPS(0.021)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.997)PMVPS(0.003)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.993)PMVPS(0.007)EQVVEEAVPLPPQALTTSQDGHR;ERPES(1)PMVPSEQVVEEAVPLPPQALTTSQDGHR;ERPES(0.994)PMVPS(0.006)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.998)PMVPS(0.002)EQVVEEAVPLPPQALTTSQDGHR 213.74 2.32E-28 4530123000 1207941 1617251 1656459 1682886 1676347 1468752 1922984 1557120 1709718 TRUE FALSE 1132338.129 1736993.947 1695750.99 1726071.704 1544693.469 1892756.859 1634650.401 1751529.86 1424355.021 0.794983071 1.219495085 1.190539553 1.211826882 1.084486274 1.328851889 1.147642531 1.229700345 1 20.44187735 4.74131631 24.93089236 1.188439235 0.794982925 0.644032716 0.088765604 133.5438094 1208110.758 0.017849126 0.124048318 55120.90128 -4.74131631 -0.39345631 ERPES(ph)PMVPSEQVVEEAVPLPPQALTTSQDGHRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ERPESPMVPSEQVVEEAVPLPPQALTTSQDGHRR 34 2 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 ERPES(0.995)PMVPS(0.005)EQVVEEAVPLPPQALTTSQDGHRR;ERPES(0.999)PMVPS(0.001)EQVVEEAVPLPPQALTTSQDGHRR;ERPES(0.997)PMVPS(0.003)EQVVEEAVPLPPQALTTSQDGHRR;ERPES(0.561)PMVPS(0.439)EQVVEEAVPLPPQALTTSQDGHRR;ERPES(0.993)PMVPS(0.007)EQVVEEAVPLPPQALTTSQDGHRR;ERPES(1)PMVPSEQVVEEAVPLPPQALTTSQDGHRR 176.71 7.82E-17 866680000 175086 300572 255137 277940 308999 231178 340193 270757 374746 TRUE FALSE 164127.6798 322826.6636 261188.9701 285072.411 284731.465 297915.3357 289184.2178 304561.6075 312198.4716 0.525715834 1.034043062 0.836611944 0.913112769 0.912020688 0.954249821 0.926283259 0.975538432 1 18.25210395 4.747089635 24.99145638 0.935462301 0.525715627 0.852775201 0.054515055 388.0174585 1136931.319 0.012262401 0.142873135 55858.54704 -4.747089635 -0.409746674 ERPFYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERPFYGR 7 1 Q13232 Q13232 NME3 Nucleoside diphosphate kinase 3 0 69.198 0.055076 143790000 67403 73350 77836 86689 79340 78061 86764 81004 89083 FALSE TRUE 63184.36655 78780.91032 79682.30668 88913.5865 73108.95644 100595.9435 73754.54368 91117.52771 74214.4718 0.851375278 1.061530297 1.073676127 1.198062647 0.985103776 1.355476109 0.993802716 1.227759566 1 16.17941292 5.521426632 0.979232605 1.122981416 2.38E-13 0.333306882 0.117716581 8.279041636 2.071499896 0.030644103 14.15771635 332220.6567 -5.521426632 -1.122981416 ERPGLGSENMDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ERPGLGSENMDR 12 1 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ;;; 103.67 0.0023305 1991870000 680140 916040 816390 802620 824520 702590 815190 722250 923650 FALSE TRUE 637571.2515 983864.5547 835755.1563 823216.588 759765.5252 905416.3274 692959.8274 812424.5024 769486.848 0.828566795 1.278598273 1.086120131 1.069825417 0.987366486 1.176649516 0.900547981 1.055800375 1 19.55353714 2.295132447 0.914470772 0.99103476 1.107886214 0 0.128752798 1.308970522 2.109888521 0.089118888 0.053878709 197.3024358 -2.295132447 0.116851454 ERPGSEEPPAEPVSFYTQPFSHYGQALCVSFPQPCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERPGSEEPPAEPVSFYTQPFSHYGQALCVSFPQPCR 36 1 Q9H4A4;A6NKB8;A0A087WU27;A0A087WUS4 Q9H4A4 RNPEP Aminopeptidase B 0 421.86 2.18E-220 248350000 224660 247820 220520 237540 305270 220820 286020 261040 276740 FALSE TRUE 210598.9316 266168.8507 225750.8385 243635.6786 281295.3256 284567.1493 243133.9563 293631.4186 230550.3062 0.913461947 1.15449359 0.979182558 1.056757124 1.220103891 1.234295256 1.05458093 1.273611055 1 17.81472206 2.872935761 6.449679852 1.157159201 1.037712538 0.291948337 0.100692667 0.324713018 15.69199805 0.02824223 0.030046172 746.3383552 -2.872935761 -0.119446663 ERPIS(ph)LGIFPLPAGDGLLT(ph)PDAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERPISLGIFPLPAGDGLLTPDAQK 24 1 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9;D6RHI8 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 2 ERPIS(1)LGIFPLPAGDGLLT(1)PDAQK 168.48 2.39E-11 57059000 113800 97468 101260 110760 158770 75140 146430 116020 194910 TRUE FALSE 106677.4611 104684.6321 103661.935 113602.2891 146300.8446 96831.6982 124474.1809 130505.3524 162378.2618 0.656968857 0.6446961 0.638397861 0.699615132 0.900987872 0.596334122 0.766569241 0.803711968 1 17.30899898 -5 0.121026727 2.021872372 0.553160504 0.616041276 0.079085144 96.36840116 0.754648647 23.80826972 0.699277106 1.00E-05 5 -1.468711869 ERPIS(ph)LGIFPLPAGDGLLTPDAQK ddPTM_SK-BR-3_Pertuzumab_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 ERPIS(1)LGIFPLPAGDGLLTPDAQK;ERPIS(1)LGIFPLPAGDGLLTPDAQK;ERPIS(1)LGIFPLPAGDGLLTPDAQK;ERPIS(1)LGIFPLPAGDGLLTPDAQK 213.08 7.38E-26 688947000 1355098 1173435 1114834 1235752 1282752 786445 1550380 1104585 1517000 TRUE FALSE 1270284.835 1260317.348 1141278.389 1267463.488 1182009.832 1013478.905 1317914.912 1242494.869 1263802.9 1.005128913 0.997242013 0.903050934 1.002896487 0.935280203 0.801927978 1.042816813 0.983139751 1 20.26934005 1.614125546 25 1.009735145 0.94358389 0.21231871 0.061338194 0.852360429 3391.641865 0.028192205 0.015144824 41.12685936 -1.614125546 -0.066151256 ERPISLGIFPLPAGDGLLT(ph)PDAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ERPISLGIFPLPAGDGLLTPDAQK 24 1 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9;D6RHI8 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 ERPISLGIFPLPAGDGLLT(1)PDAQK;ERPISLGIFPLPAGDGLLT(1)PDAQK;ERPISLGIFPLPAGDGLLT(1)PDAQK;ERPISLGIFPLPAGDGLLT(1)PDAQK;ERPISLGIFPLPAGDGLLT(1)PDAQK;ERPISLGIFPLPAGDGLLT(1)PDAQK 252.29 1.52E-43 3263994000 3229940 2393611 2778610 2563864 3310842 2315113 3378931 2784195 3780498 TRUE FALSE 3027783.821 2570836.449 2844519.941 2629657.091 3050821.825 2983448.54 2872291.665 3131807.875 3149508.461 0.961351226 0.816265929 0.903163137 0.834942063 0.96866602 0.947274337 0.911980933 0.994379889 1 21.58669526 2.728591063 24.98826963 0.953764857 0.872525236 0.446960335 0.046192449 616.1700611 1544402.408 0.013655194 0.013013139 535.2923824 -2.728591063 -0.081239621 ERPLCPLQPQNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ERPLCPLQPQNR 12 1 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ;; 184.31 1.32E-05 1023330000 486378 533952 535352 552560 589970 445924 647200 506507 590570 FALSE TRUE 455936.4692 573486.3617 548050.8023 566739.6251 543636.136 574655.0198 550158.3683 569745.5139 492000.0518 0.926700043 1.165622564 1.113924278 1.151909686 1.10495138 1.167997885 1.118207948 1.158019215 1 18.90829894 4.744743675 24.88867037 1.129979254 0.926699947 0.605879469 0.049329251 371.1438625 1493922.574 0.009749854 0.0899674 55557.62543 -4.744743675 -0.203279306 ERPLLLEEQPLLLQDLLDQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERPLLLEEQPLLLQDLLDQER 21 1 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 0 96.848 0.0011111 10170000 10953 14369 12300 16055 13848 12568 16395 11798 14408 FALSE TRUE 10267.47128 15432.89571 12591.76181 16466.99848 12760.43394 16196.17758 13936.72195 13271.00627 12003.21172 0.855393666 1.285730525 1.049032717 1.371882698 1.063084967 1.349320328 1.16108274 1.105621277 1 13.55113286 4.749959283 24.57406235 1.183455292 0.855393421 0.378193391 0.127475177 1287.045463 2774638.633 0.026196328 0.406075151 56228.8606 -4.749959283 -0.328061871 ERPLQQVS(ph)PVASVPWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERPLQQVSPVASVPWR 16 1 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 ERPLQQVS(1)PVASVPWR 109.85 0.00056936 191210000 172110 222220 234920 224160 235600 197520 180020 179760 228080 TRUE FALSE 161337.9423 238673.4 240492.4133 229912.3251 217096.9264 254540.8175 153027.6722 202203.4317 190011.9745 0.849093552 1.256096625 1.265669776 1.209988611 1.142543394 1.339604086 0.805358044 1.06416152 1 17.53573081 1.738576472 25 0.94861626 1.196416534 0.334328055 0.144949847 0.035688548 3421.935352 0.061479514 0.034093542 54.77425408 -1.738576472 0.247800274 ERPMYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERPMYGR 7 1 P50402;Q5HY57 P50402 EMD Emerin 0 ; 109.86 0.0063228 186085000 151549 179340 147923 132628 186889 145228 179410 174845 185102 FALSE TRUE 142063.8186 192618.5202 151431.8034 136031.459 172211.4918 187152.966 152509.1361 196674.7831 154207.2804 0.921252345 1.249088368 0.982001648 0.882133831 1.116753317 1.213645462 0.988987911 1.275392333 1 17.23451135 ERPQDRPEDLDVPPALADFIHQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERPQDRPEDLDVPPALADFIHQQR 24 2 Q01780;Q01780-2 Q01780 EXOSC10 Exosome component 10 0 155.49 2.56E-08 97460000 62223 73747 65562 69621 83597 64958 79361 64737 75579 FALSE TRUE 58328.5735 79207.30461 67117.1616 71407.59273 77031.62883 83710.32009 67461.5548 72819.55695 62964.37664 0.926374191 1.257970123 1.065954516 1.134095127 1.223416048 1.329486998 1.071424167 1.156519938 1 15.94224821 0.467318054 1.49878527 1.000202008 1.155048618 0.137604317 0.112257315 5.538115728 13.59630631 0.098080835 0.028349167 2.933040464 -0.467318054 0.15484661 ERPS(ph)SREDT(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERPSSREDTPSR 12 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 2 ERPS(0.708)S(0.292)REDT(0.5)PS(0.5)R 103.88 0.002426 308790000 377140 423930 419970 405990 443220 441000 492560 419250 615880 TRUE FALSE 353535.4806 455318.2183 429931.8867 416408.3907 408411.2891 568309.541 418705.2007 471594.2854 513085.6493 0.689037944 0.88741172 0.837933954 0.811576764 0.795990474 1.107630942 0.816053229 0.91913365 1 18.96884015 ERPS(ph)SREDTPS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERPSSREDTPSR 12 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 2 ERPS(0.667)S(0.333)REDT(0.44)PS(0.56)R 89.459 0.046291 249890000 333010 350960 362210 339610 397500 338920 413630 335090 497530 TRUE FALSE 312167.4985 376945.4436 370801.7922 348324.9676 366281.9534 436760.7021 351610.0215 376926.7241 414489.0288 0.753138146 0.909422005 0.894599776 0.840371984 0.883695172 1.053732841 0.848297535 0.909376842 1 18.66097439 2.456979042 24.9922988 0.938703746 0.866436377 0.318555244 0.068458468 372.2692092 461905.966 0.022554542 0.018872568 286.4039755 -2.456979042 -0.072267369 ERPS(ph)SREDTPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERPSSREDTPSR 12 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 ERPS(0.713)S(0.287)REDTPSR;ERPS(0.959)S(0.041)REDTPSR 140.77 4.72E-05 4074520000 895820 994360 941330 918080 1099050 907320 1106250 926160 1253950 TRUE FALSE 839752.2253 1067983.449 963658.7921 941639.4871 1012735.046 1169248.555 940378.0824 1041793.115 1044657.644 0.803853999 1.02232866 0.922463735 0.901385724 0.969442048 1.119264825 0.900178243 0.997257925 1 19.99459879 2.482212075 24.99111144 0.996805481 0.93276506 0.231176011 0.074590738 435.5294585 2138051.831 0.024215395 0.020806598 303.5373059 -2.482212075 -0.064040421 ERPS(ph)SWSSLDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERPSSWSSLDQK 12 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 ERPS(0.859)S(0.141)WSSLDQK 95.428 0.0036653 348250000 262830 219440 215850 253980 303370 174600 250800 210440 248610 TRUE FALSE 246379.9395 235687.5659 220970.0639 260497.5568 279544.5439 225004.1856 213194.8683 236713.8972 207115.3849 1.189578165 1.137952963 1.066893529 1.257741219 1.349704388 1.086371182 1.029353123 1.142908323 1 17.6600752 2.021971128 24.97428821 1.059976903 1.179748638 0.392662239 0.082300424 289.5147244 329086.1253 0.032979871 0.024355495 105.1891942 -2.021971128 0.119771735 ERPSGPES(ph)PVQGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ERPSGPESPVQGPR 14 1 A0A669KBI7;Q9UMN6 A0A669KBI7 KMT2B Histone-lysine N-methyltransferase 2B 1 ERPSGPES(1)PVQGPR;ERPSGPES(1)PVQGPR;ERPSGPES(1)PVQGPR 160.82 2.84E-06 612010000 633620 700750 649880 706640 779870 652420 844760 721810 807430 TRUE FALSE 593962.8552 752634.2591 665295.4605 724773.5787 718622.156 840763.0628 718096.0804 811929.5674 672664.7168 0.882999867 1.118884699 0.989044681 1.077466323 1.068321465 1.249899158 1.067539388 1.20703457 1 19.35952806 2.750337808 2.269142586 1.133143364 1.024073476 0.252203624 0.091112421 0.424706173 4.314388879 0.028842985 0.02889465 562.7789026 -2.750337808 -0.109069888 ERPSQPEGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERPSQPEGLR 10 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 83.182 0.014393 289220000 421640 477500 493880 459300 537880 352050 460600 379740 560030 FALSE TRUE 395250.305 512854.5968 505595.0668 471086.4156 495637.0745 453681.1199 391537.306 427151.3749 466557.3751 0.847163342 1.099231572 1.083671792 1.00970736 1.062328239 0.972401561 0.839205052 0.915538791 1 18.83169498 2.001798164 5.449543025 0.900975959 1.038240097 0.229211879 0.079982893 0.166093042 16.52391509 0.030940392 0.020825363 100.414901 -2.001798164 0.137264139 ERPSQPEGLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 144.28 2.07E-05 360200000 292790 285530 292390 290160 357180 243450 368430 289930 419830 FALSE TRUE 274464.7965 306670.9383 299325.6289 297605.9968 329128.5236 313730.0629 313187.3418 326128.3987 349757.6608 0.784728477 0.876809782 0.855808642 0.850892004 0.94101877 0.896992684 0.895440978 0.932441045 1 18.41599613 7.999999921 0.035041296 1.389400846 0.113007614 0.771188341 0.027833764 472.4541532 1.264912869 13.60025077 38.28261776 99999981.84 -7.999999921 -1.276393232 ERPSS(ph)AIYPSDSFR ddPTM_SK-BR-3_Pertuzumab_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(0.036)S(0.964)AIYPSDSFR;ERPS(0.002)S(0.998)AIYPSDSFR;ERPS(0.212)S(0.788)AIYPSDSFR;ERPS(0.417)S(0.566)AIYPS(0.004)DS(0.013)FR 214.28 1.82E-11 1323550000 1026290 1166820 1003920 947460 1287010 711600 1042930 857050 1394460 TRUE FALSE 962056.3409 1253212.567 1027733.456 971773.4276 1185933.426 917027.3681 886552.3286 964054.5791 1161715.617 0.82813412 1.078760196 0.88466871 0.836498548 1.02084659 0.789373367 0.763140579 0.829854195 1 20.14782552 2.222484913 24.99978766 0.817831588 0.939704997 0.120130381 0.099543295 320.4793498 498383.4434 0.034937115 0.025882527 166.9109824 -2.222484913 0.121873409 ERPSS(ph)REDTPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.355)S(0.642)REDT(0.002)PS(0.001)R;ERPS(0.154)S(0.846)REDTPSR;ERPS(0.128)S(0.835)REDT(0.003)PS(0.034)R;ERPS(0.192)S(0.808)REDTPSR;ERPS(0.314)S(0.682)REDT(0.003)PS(0.001)R 118.62 0.00047698 4649940000 1432680 1665339 1612483 1649198 1838469 1427733 1745106 1495540 2079871 TRUE FALSE 1343011.116 1788642.432 1650731.858 1691519.213 1694083.061 1839896.34 1483443.556 1682261.461 1732727.094 0.775085194 1.032270136 0.952678506 0.976217905 0.977697565 1.061850044 0.856132256 0.970875025 1 20.72461302 4.749316305 24.76503099 0.973316508 0.775085066 0.582344833 0.053972605 1046.101485 2408601.483 0.012660136 0.184688989 56145.67471 -4.749316305 -0.198231442 ERPT(ph)SPAPHRPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ERPTSPAPHRPPK 13 2 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 ERPT(0.969)S(0.031)PAPHRPPK;ERPT(0.839)S(0.161)PAPHRPPK;ERPT(0.969)S(0.031)PAPHRPPK 131.72 0.0060612 492170000 611360 546820 589840 596480 609720 467550 688190 517390 493850 TRUE FALSE 573096.0689 587307.1218 603831.2833 611786.6866 561835.0507 602524.095 585002.2983 581987.2804 411423.2446 1.392959869 1.42750107 1.467664482 1.487000782 1.365588984 1.464487247 1.421898996 1.414570732 1 18.65026378 -0.399242585 0.885509066 0.983261977 1.43773191 0.934989954 0.035675935 3.841186693 2.076348324 0.260876299 0.010544044 0.39880208 0.399242585 0.454469932 ERPT(ph)SPAPHRPPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ERPTSPAPHRPPKR 14 3 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 ERPT(0.866)S(0.134)PAPHRPPKR;ERPT(0.868)S(0.132)PAPHRPPKR;ERPT(0.612)S(0.388)PAPHRPPKR;ERPT(0.922)S(0.078)PAPHRPPKR 162.79 2.32E-06 1221055000 208066 204942 192687 203912 207120 157215 240676 181507 211829 TRUE FALSE 195043.5205 220116.1189 197257.6266 209144.7271 190853.6307 202600.4183 204588.8681 204168.5485 176473.3714 1.105229185 1.247305002 1.117775589 1.185134763 1.081486851 1.148050931 1.159318635 1.156936862 1 17.42909098 -5 0.25572834 0.028150684 1.168607528 0.504469242 0.046112334 146.9843496 1.450672948 74.92159165 0.059267269 1.00E-05 5 1.140456844 ERPTPSLNNNCTT(ph)SEDSLVLYNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERPTPSLNNNCTTSEDSLVLYNR 23 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 ERPTPSLNNNCT(0.001)T(0.644)S(0.355)EDSLVLYNR 242.45 3.93E-37 182900000 88108 72230 79591 65853 75524 91206 86657 60142 133450 TRUE FALSE 82593.47756 77577.98436 81478.93611 67542.89947 69592.64969 117535.6916 73663.58733 67650.86109 111176.3329 0.742905216 0.697792258 0.732880227 0.607529478 0.625966407 1.057200652 0.662583352 0.608500562 1 16.76249018 ERPTPSLNNNCTTS(ph)EDSLVLYNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ERPTPSLNNNCTTSEDSLVLYNR 23 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 ERPTPSLNNNCT(0.001)T(0.354)S(0.646)EDSLVLYNR;ERPTPSLNNNCTT(0.047)S(0.953)EDSLVLYNR;ERPTPSLNNNCTT(0.017)S(0.983)EDSLVLYNR;ERPTPSLNNNCT(0.001)T(0.038)S(0.961)EDSLVLYNR 310.65 2.21E-73 1046790000 415812 345654 411174 355726 334242 393533 426850 309126 648089 TRUE FALSE 389787.0692 371246.5818 420927.2415 364854.5314 307991.9816 507139.5886 362847.8052 347721.0616 539918.7591 0.721936518 0.687597116 0.779612181 0.675758205 0.570441342 0.939288699 0.672041486 0.644024783 1 19.04238282 -1.401640275 2.914500166 1.005101278 0.716915698 0.465558001 0.097034272 11659015.25 13856916.66 496825.1767 0.021059672 0.039660641 1.401640275 -0.28818558 ERPTPSLNNNCTTSEDSLVLYNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERPTPSLNNNCTTSEDSLVLYNR 23 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 329.43 1.56E-86 1775570000 342860 397010 429630 408030 441860 353750 491420 400500 470230 FALSE TRUE 321401.0046 426405.0335 439821.0265 418500.7406 407158.098 455871.8823 417736.1331 450503.3066 391745.5752 0.820433018 1.088474409 1.122721109 1.068297301 1.039343196 1.163693763 1.066345505 1.149989522 1 18.57955745 4.738467705 6.788123077 1.093239143 0.815857942 0.741438139 0.049438346 0.049153978 15.7473448 0.010219117 0.062719839 54760.53779 -4.738467705 -0.277381201 ERPTS(ph)PAPHRPPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERPTSPAPHRPPKR 14 3 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 ERPT(0.182)S(0.818)PAPHRPPKR;ERPT(0.206)S(0.794)PAPHRPPKR 141.1 6.97E-06 853342000 85832 71137 74326 80394 81034 56849 101843 70976 71052 TRUE FALSE 80459.92833 76404.0575 76089.04782 82457.04615 74669.91652 73260.38343 86572.58761 79837.50984 59192.96219 1.359282005 1.290762528 1.285440786 1.393021114 1.261466123 1.237653612 1.462548661 1.348766929 1 15.85313803 -1.151350754 3.793379732 0.999803134 1.328132626 0.70985543 0.066269012 8043200.33 17039349.13 20270.70912 0.016233879 0.070574733 1.151350754 0.328329491 ERPVQSLKTS(ph)RDT(ph)SPSSGSAVSSSK ddPTM_SK-BR-3_Pertuzumab_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(0.232)LKT(0.354)S(0.401)RDT(0.546)S(0.388)PS(0.057)S(0.016)GS(0.006)AVSSSK 77.522 0.052813 123120000 49082 59676 46098 60133 99625 13780 38438 44592 269040 TRUE FALSE 46010.04523 64094.47313 47191.46633 61676.11458 91800.85437 17758.0623 32674.57874 50159.40936 224135.4859 0.205277826 0.285963077 0.210548839 0.275173359 0.409577511 0.079229142 0.14578048 0.223790575 1 17.77401155 -1.301255598 3.56868329 1.002477748 0.226766776 0.885374869 0.087131415 85412480.11 133031497 2272624.133 0.020906913 0.049974033 1.301255598 -0.775710971 ERPVS(ph)EMFSLEDSIIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ERPVSEMFSLEDSIIER 17 1 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 ERPVS(1)EMFSLEDSIIER;ERPVS(1)EMFSLEDSIIER;ERPVS(1)EMFSLEDSIIER 229.97 5.69E-16 90500000 53737 80489 64438 61751 99132 47963 81428 73598 159571 TRUE FALSE 50373.69709 86448.48931 65966.49979 63335.6352 91346.5726 61809.13949 69218.62734 82786.87231 132937.5692 0.378927472 0.650293892 0.496221649 0.476431422 0.687138881 0.464948621 0.520685219 0.622750008 1 17.02038935 0.802959528 3.138003461 0.999930695 0.53513246 0.735994044 0.088815967 0.521735305 7.564753696 0.076594491 0.019959034 6.352717283 -0.802959528 -0.464798235 ERQELGS(ph)PEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 207.55 1.37E-08 764010000 578630 641260 605590 604940 623780 551890 580840 514950 709790 TRUE FALSE 542414.5812 688739.5576 619954.8808 620463.7846 574790.835 711211.6838 493748.4343 579242.641 591321.4636 0.917292225 1.16474642 1.04842276 1.049283381 0.972044599 1.202749651 0.834991565 0.979573171 1 19.17358312 1.727616178 25 0.929729504 1.066325532 0.273094747 0.09213915 0.905749127 2059.292123 0.038298926 0.021238669 53.40921296 -1.727616178 0.136596028 ERQEQEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERQEQEEAR 9 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ; 126.71 0.00042494 431340000 158250 168077 171680 161290 200488 162294 175089 127788 164043 FALSE TRUE 148345.415 180521.596 175752.3307 165428.9745 184742.4812 209145.6432 148836.0299 143742.6131 136663.1635 1.08548208 1.320923585 1.286025628 1.210486939 1.351808903 1.530373202 1.089072037 1.051802178 1 17.0602649 1.573486412 7.929407082 1.042321167 1.298903695 0.531530255 0.111756923 0.090400161 11.17279846 0.057365471 0.026959772 37.45298286 -1.573486412 0.256582527 ERQEQLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERQEQLER 8 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;A0A0U1RQP7;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ; 190.88 0.0001679 1204460000 549020 633390 590700 537180 640860 456260 564190 554040 751400 FALSE TRUE 514657.8182 680286.8546 604711.6829 550964.9482 590529.4407 587974.8552 479594.9472 623213.1136 625986.4858 0.822154839 1.086743676 0.966013958 0.880154701 0.94335813 0.939277235 0.766142653 0.995569597 1 19.25577199 3.373652745 4.995561651 0.902137853 0.990286262 0 0.093096174 0.372850518 14.99988365 0.024760348 0.033972909 2364.0287 -3.373652745 0.088148409 ERRPDS(ph)PTRPTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERRPDSPTRPTLR 13 3 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 ERRPDS(0.979)PT(0.021)RPTLR 91.657 0.03554 117630000 33595 36281 38816 34586 40132 28055 30690 32163 37370 TRUE FALSE 31492.34892 38967.28299 39736.73385 35473.53531 36980.1946 36154.02307 26088.31941 36178.62135 31132.70558 1.011551946 1.251651029 1.276366224 1.139429891 1.187824634 1.16128754 0.837971481 1.16207765 1 14.92614334 1.916337278 8.664626433 0.985336646 1.194730719 0.359132492 0.105273812 0.309763815 29.8101472 0.041793434 0.026348132 82.47783979 -1.916337278 0.209394073 ERRPS(ph)PGEMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERRPSPGEMR 10 2 A0A0G2JHC2;Q6NYC8-2;Q6NYC8;Q6NYC8-3 A0A0G2JHC2 PPP1R18 Phostensin 1 ERRPS(1)PGEMR;ERRPS(1)PGEMR 63.76 0.027733 0 327978 328200 257354 282723 314543 268329 307575 302927 335790 TRUE FALSE 307450.4424 352500.2695 263458.5584 289978.1508 289840.0616 345791.2263 261456.9841 340748.1028 279744.4797 1.099040248 1.260079448 0.941782868 1.036582209 1.036088583 1.236096693 0.934627859 1.218069086 1 18.09375014 3.986475515 24.23009725 1.054137194 1.179796259 0.182260408 0.107196906 347.0148013 898851.7149 0.023941603 0.050605958 9693.386183 -3.986475515 0.125659066 ERRT(ph)PPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERRTPPGR 8 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 ERRT(1)PPGR 86.923 0.025226 1814400000 425340 578230 472100 440150 629990 239710 400150 446490 863530 TRUE FALSE 398718.7287 621042.7508 483298.4349 451444.9942 580513.1267 308910.3856 340151.2223 502235.2593 719401.2644 0.554236903 0.863277258 0.671806485 0.627528775 0.806939264 0.429399281 0.472825444 0.69812952 1 19.45643717 0.967681558 22.70552146 1.000000008 0.642413285 0.426115523 0.132851328 1476.083739 1037034.101 0.139865976 0.034966494 9.282854814 -0.967681558 -0.357586723 ERS(ph)HERPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERSHERPDR 9 2 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 ERS(1)HERPDR;ERS(1)HERPDR 124.12 0.00028104 122053000 9877.8 10383.6 9685.2 9731.8 9981.6 6689.8 11200.3 7397.5 9040.6 TRUE FALSE 9259.56613 11152.41255 9914.937518 9981.534464 9197.6854 8621.03666 9520.918993 8321.094159 7531.665455 1.229418139 1.48073658 1.316433606 1.325275867 1.221202064 1.14463882 1.26411868 1.104814627 1 12.8787532 1.707423822 0.377331111 0.992220821 1.404856299 0.660691727 0.0768093 0.630387157 0.262023279 0.093608552 0.083916273 50.9828163 -1.707423822 0.412635477 ERS(ph)HERPDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 86.756 0.0095205 2712540000 734920 518960 556280 617490 694770 375499 745880 496011 781550 TRUE FALSE 688922.6691 557384.3384 569475.2243 633335.8388 640205.5668 483899.4656 634042.2184 557939.0652 651104.256 1.058083498 0.856060045 0.87462986 0.972710335 0.983261223 0.74319813 0.97379523 0.856912023 1 19.31252904 ERS(ph)KDKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERSKDKDR 8 3 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 1 ERS(1)KDKDR 95.094 0.054675 563790000 1885500 530290 1045900 994570 895700 719120 1076200 718240 1081100 TRUE FALSE 1767489.921 569553.2234 1070709.242 1020092.35 825355.3351 926718.2701 914833.801 807913.845 900657.4258 1.962444177 0.632374982 1.188808543 1.132608604 0.916392084 1.028935357 1.01574003 0.897026796 1 19.78061894 4.751539079 24.99521984 0.982311433 1.962444804 0.809785737 0.150151363 916.6616651 1765367.306 0.035021666 0.657374171 56433.77197 -4.751539079 0.980133372 ERS(ph)PALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 83 0.013908 48745100000 36633600 25153500 29066900 27321000 28026400 23435600 35149100 25866500 29776500 TRUE FALSE 34340768.37 27015891.31 29756380.59 28022103.11 25825319.6 30201077.27 29878818.76 29095989.46 24806609.79 1.384339443 1.089060196 1.199534352 1.129622442 1.041066063 1.217460892 1.204470059 1.172912773 1 24.56422125 ERS(ph)PALKS(ph)PLQSVVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ERSPALKSPLQSVVVR 16 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 ERS(1)PALKS(0.898)PLQS(0.102)VVVR;ERS(1)PALKS(0.823)PLQS(0.177)VVVR;ERS(1)PALKS(0.987)PLQS(0.013)VVVR 111.67 0.00042826 1199690000 1797440 1534620 1589890 1548460 1779450 1272530 1958740 1468680 1936450 TRUE FALSE 1684941.439 1648244.862 1627602.942 1588196.105 1639699.175 1639888.753 1665045.121 1652047.931 1613243.985 1.044443032 1.02169596 1.008900673 0.984473595 1.016398753 1.016516267 1.03210992 1.024053365 1 20.62153322 1.980719598 20.92890847 1.022794926 1.014038095 0 0.016656964 312.3509094 339051.5121 0.006673552 0.004402272 95.65762599 -1.980719598 -0.008756831 ERS(ph)PALKSPLQS(ph)VVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERSPALKSPLQSVVVR 16 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 ERS(1)PALKS(0.193)PLQS(0.807)VVVR;ERS(1)PALKS(0.412)PLQS(0.588)VVVR 140.67 8.25E-06 991820000 1738490 1180070 1409310 1407150 1424800 1023450 1820670 1169600 1683640 TRUE FALSE 1629681.014 1267443.611 1442739.499 1443259.851 1312901.955 1318903.401 1547677.436 1315627.135 1402629.607 1.161875527 0.903619604 1.02859621 1.028967194 0.936028976 0.940307686 1.103411355 0.937971884 1 20.41970266 ERS(ph)PALKSPLQSVVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ERSPALKSPLQSVVVR 16 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 ERS(1)PALKSPLQSVVVR;ERS(1)PALKSPLQSVVVR;ERS(1)PALKSPLQSVVVR;ERS(1)PALKSPLQSVVVR;ERS(0.982)PALKS(0.016)PLQS(0.002)VVVR;ERS(0.999)PALKS(0.001)PLQSVVVR 171.38 2.58E-09 11554460000 3576560 3946740 3753440 3979560 5000780 2995290 5216230 3493640 9538120 TRUE FALSE 3352709.494 4238960.736 3842473.369 4081682.247 4608038.911 3859981.599 4434104.737 3929828.644 7946146.153 0.421928999 0.533461209 0.483564397 0.513668157 0.579908653 0.485767758 0.558019529 0.494557811 1 22.9218239 -5 0.359924384 7.007591372 0.498861994 0.928268086 0.042949518 105.2770912 0.838268051 489.954491 0.027759146 1.00E-05 5 -6.508729378 ERS(ph)PAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ERSPAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR 40 3 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 ERS(1)PAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR;ERS(1)PAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR;ERS(1)PAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR;ERS(1)PAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR 160.24 1.36E-18 2391430000 200310 207604 234189 199036 200345 181599 234228 207465 180642 TRUE FALSE 187772.9547 222975.2162 239744.0737 204143.6007 184610.7119 234023.6833 199107.6859 233367.4619 150491.6832 1.247729779 1.481644775 1.593071913 1.356510847 1.226717038 1.555060574 1.32304777 1.550700058 1 17.19932423 -1.750319288 2.546927511 0.900758656 1.429195461 0.50413106 0.129395826 8569062.939 6309381.476 5347072.45 0.033069794 0.017769725 1.750319288 0.528436805 ERS(ph)PPVGRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERSPPVGRK 9 2 A6NGG8 A6NGG8 C2orf71 Uncharacterized protein C2orf71 1 ERS(1)PPVGRK 60.045 0.077415 649380000 773800 485400 1020800 1306700 568650 1559800 1298200 460240 1234400 TRUE FALSE 725369.2393 521339.5211 1045013.858 1340232.134 523990.5228 2010088.939 1103546.962 517701.9771 1028370.665 0.70535777 0.506956819 1.016184041 1.303257842 0.509534685 1.954634653 1.073102335 0.503419627 1 19.97192893 3.794994542 2.825334984 1.101611672 0.60968881 0.163368642 0.409695831 0.404729481 6.394006446 0.104649331 0.205364074 6237.269969 -3.794994542 -0.491922862 ERS(ph)PS(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ERSPSPLR 8 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 2 ERS(1)PS(1)PLR;ERS(1)PS(1)PLR;ERS(1)PS(1)PLR 91.961 0.0068942 7375430000 493490 514070 499470 487220 510340 479990 581140 472760 461540 TRUE FALSE 462603.3418 552132.2777 511317.6643 499722.8901 470259.955 618555.321 494003.452 531785.1267 384505.9923 1.203110877 1.435952335 1.32980415 1.29964916 1.223023735 1.608701381 1.284774391 1.383034692 1 18.55264656 -1.247754654 3.065191742 0.998281777 1.354141184 0.467308225 0.115808347 11819907.49 15872446.62 194233.8214 0.026089978 0.056525621 1.247754654 0.355859407 ERS(ph)PS(ph)PLRGNVVPS(ph)PLPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ERSPSPLRGNVVPSPLPTR 19 2 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 3 ERS(1)PS(1)PLRGNVVPS(0.999)PLPT(0.001)R;ERS(1)PS(1)PLRGNVVPS(1)PLPTR;ERS(1)PS(1)PLRGNVVPS(0.936)PLPT(0.064)R;ERS(1)PS(1)PLRGNVVPS(0.93)PLPT(0.071)R;ERS(1)PS(1)PLRGNVVPS(0.903)PLPT(0.097)R 135.8 4.66E-06 13024410000 4195970 5249030 4845520 5325740 6152930 4182060 5591390 4579560 7286410 TRUE FALSE 3933351.728 5637673.643 4960458.023 5462407.505 5669703.698 5389352.832 4753012.977 5151328.147 6070261.099 0.647970765 0.928736598 0.817173749 0.899863682 0.934013151 0.887828834 0.782999759 0.848617228 1 22.53332714 4.747146536 24.75544954 0.874406263 0.647970634 0.583545739 0.062718585 726.9911158 2096052.27 0.014370749 0.167375727 55865.86612 -4.747146536 -0.226435629 ERS(ph)PS(ph)PLRGNVVPS(ph)PLPTRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERSPSPLRGNVVPSPLPTRR 20 3 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 3 ERS(1)PS(1)PLRGNVVPS(1)PLPTRR 76.162 0.022603 534480000 71355 89574 76657 95756 123770 65008 87008 91322 206530 TRUE FALSE 66889.01792 96206.15216 78475.34024 98213.26107 114049.6035 83774.75428 73961.95814 102723.7527 172058.8088 0.388756719 0.559146915 0.456096034 0.570812165 0.662852453 0.48689605 0.429864409 0.59702699 1 17.39254223 0.917340712 8.054925219 0.999999415 0.510061836 0.797354553 0.077490412 1.111310614 108.3306904 0.072722254 0.018211224 8.266862454 -0.917340712 -0.489937579 ERS(ph)PS(ph)PLRGNVVPSPLPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ERSPSPLRGNVVPSPLPTR 19 2 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 2 ERS(1)PS(1)PLRGNVVPSPLPTR;ERS(1)PS(1)PLRGNVVPSPLPTR;ERS(1)PS(1)PLRGNVVPSPLPTR;ERS(1)PS(1)PLRGNVVPSPLPTR;ERS(1)PS(1)PLRGNVVPSPLPTR;ERS(1)PS(1)PLRGNVVPSPLPTR;ERS(1)PS(1)PLRGNVVPSPLPTR 127.41 0.00011544 12309060000 3049770 2906820 2946140 2759830 2935690 2260030 2765070 2118577 3076940 TRUE FALSE 2858890.34 3122043.977 3016023.832 2830651.91 2705132.749 2912463.972 2350473.423 2383086.002 2563378.836 1.115282025 1.21794092 1.176581389 1.104265928 1.055299635 1.136181641 0.916943446 0.929665943 1 21.28961528 2.207205778 0.937365741 0.939467895 1.177730043 0.689526217 0.055419783 0.278568284 0.463380049 0.040354977 0.02256364 161.1408973 -2.207205778 0.238262148 ERS(ph)PS(ph)PLRGNVVPSPLPTRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ERSPSPLRGNVVPSPLPTRR 20 3 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 2 ERS(1)PS(1)PLRGNVVPSPLPTRR;ERS(1)PS(1)PLRGNVVPS(0.001)PLPTRR;ERS(1)PS(1)PLRGNVVPSPLPTRR 103.73 0.00040351 1698850000 279698 398953 327005 295606 404702 256609 362397 271423 767070 TRUE FALSE 262192.2015 428491.8952 334761.713 303191.7504 372918.3374 330687.8526 308058.9342 305310.759 639041.0615 0.410290069 0.670523259 0.523850083 0.474447995 0.583559273 0.517475124 0.482064382 0.477763914 1 19.28554911 -1.328631811 3.403011743 1.002440663 0.528956201 0.820466318 0.070752231 14428616.97 21191679.86 356262.4045 0.017168842 0.0469211 1.328631811 -0.473484462 ERS(ph)PS(ph)PPTIQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERSPSPPTIQSK 12 1 Q14687;Q14687-2;Q14687-3;H0Y613;H7C3B5 Q14687 GSE1 Genetic suppressor element 1 2 ERS(1)PS(0.999)PPT(0.001)IQSK;ERS(1)PS(1)PPTIQSK 147.17 3.72E-05 1291040000 2220040 1712620 1897620 1989670 2029530 1535910 2391100 1741560 1856300 TRUE FALSE 2081091.659 1839424.167 1942632.443 2040728.301 1870138.901 1979302.284 2032576.753 1958997.6 1546471.538 1.345703175 1.189432926 1.256170835 1.319602884 1.209294096 1.279882775 1.314331821 1.26675309 1 20.56054885 0.845142196 18.64105057 1 1.267099072 0.759702515 0.048099992 57944.19679 6975053.722 0.045573153 0.011393288 7.000711751 -0.845142196 0.267099073 ERS(ph)PS(ph)PSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERSPSPSFR 9 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 ERS(1)PS(0.943)PS(0.057)FR 69.602 0.031169 496630000 551400 494320 446950 503290 525840 485980 591090 527420 486800 TRUE FALSE 516888.8583 530919.9671 457551.8651 516205.2735 484542.6475 626274.5368 502461.5419 593269.548 405549.9352 1.274538136 1.30913587 1.128225714 1.272852561 1.19477925 1.544259985 1.238963438 1.462876693 1 18.62952004 ERS(ph)PSPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERSPSPLR 8 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 ERS(0.997)PS(0.003)PLR 94.363 0.006306 986490000 247770 290890 220660 266670 313000 207470 331830 191960 255490 TRUE FALSE 232262.518 312427.7983 225894.1594 273513.2037 288418.2426 267363.221 282075.1721 215926.6286 212847.0685 1.091217838 1.467851075 1.061297959 1.285022179 1.355049166 1.256128275 1.325248095 1.014468417 1 17.69945769 1.230025376 24.90915729 1.007233934 1.269532088 0.447428526 0.11805346 166.3058781 485325.8831 0.098117502 0.026107413 16.98342886 -1.230025376 0.262298154 ERS(ph)PSPSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ERSPSPSFR 9 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 ERS(0.988)PS(0.012)PSFR;ERS(0.824)PS(0.176)PSFR;ERS(0.988)PS(0.012)PSFR 111.12 0.0013177 1224840000 305999 268231 342150 287296 264921 257736 371000 275720 346155 TRUE FALSE 286847.0688 288091.1023 350265.9596 294668.5018 244115.1733 332140.1992 315371.9942 310144.2489 288379.4943 0.99468608 0.998999957 1.214600783 1.021808095 0.846506697 1.151746937 1.093600622 1.075472615 1 18.13760906 ERSDS(ph)GGS(ph)SSEPFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERSDSGGSSSEPFDR 15 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 2 ERS(0.344)DS(0.853)GGS(0.72)S(0.077)S(0.006)EPFDR 152.11 3.45E-05 246900000 255890 269880 272820 301760 326430 211950 273760 218150 320980 TRUE FALSE 239874.3017 289862.196 279291.4192 309503.6725 300793.5046 273136.5243 232712.2295 245386.5077 267406.3644 0.897040361 1.083976429 1.044445669 1.15742822 1.124855443 1.021428659 0.870256884 0.917653954 1 18.02867428 1.925020763 5.408146761 0.919593886 1.067223268 0.391730803 0.074694263 0.19580425 10.10598451 0.031705291 0.01913399 84.14353677 -1.925020763 0.147629383 ERSDS(ph)GGSS(ph)SEPFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERSDSGGSSSEPFDR 15 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 2 ERS(0.021)DS(0.917)GGS(0.434)S(0.612)S(0.016)EPFDR 146.69 4.59E-05 261870000 309760 353460 335530 358460 412380 244170 338090 281910 358910 TRUE FALSE 290372.6745 379630.5462 343488.93 367658.6905 379993.3383 314657.9152 287396.5432 317107.0841 299005.6024 0.971127873 1.269643589 1.148770884 1.229604688 1.270856918 1.052347892 0.961174443 1.060538938 1 18.18981299 2.079054278 6.013792509 1.003770182 1.188258054 0.453762775 0.087587463 0.156966962 9.26013405 0.030552657 0.022342794 119.9649226 -2.079054278 0.184487871 ERSDS(ph)GGSSSEPFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERSDSGGSSSEPFDR 15 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 ERS(0.002)DS(0.998)GGSSSEPFDR;ERSDS(1)GGSSSEPFDR 209.39 1.46E-09 978050000 275400 342590 338530 346100 374720 309680 315510 260740 359720 TRUE FALSE 258163.2056 367955.7201 346560.0915 354981.5119 345291.0027 399079.5888 268202.2046 293293.963 299680.4081 0.861461739 1.227827079 1.156432259 1.184533598 1.152197452 1.331683947 0.894960756 0.978689147 1 18.19306524 1.676009378 9.572666996 0.954282046 1.162433108 0.363434466 0.120511279 0.110410643 15.46065852 0.05260719 0.028195906 47.42522256 -1.676009378 0.208151061 ERSDTFINLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ERSDTFINLR 10 1 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;; 171.67 3.60E-06 1562560000 350278 406514 325025 319622 518394 299644 407280 405659 498585 FALSE TRUE 328354.7252 436612.7195 332734.7465 327824.0416 477681.4263 386146.3585 346212.145 456306.4191 415367.9425 0.790515328 1.051146887 0.801060247 0.789237705 1.150019964 0.929648918 0.833507138 1.098559548 1 18.66403035 ERSDYDRS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ERSDYDRSR 9 2 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;A0A087X0F4 C9JUL9;Q9BXP5-4;REV__Q9BXP5-5 SRRT Serrate RNA effector molecule homolog 1 ERSDYDRS(1)R;ERSDYDRS(1)R;ERSDY(0.001)DRS(0.999)R 145.14 7.71E-05 1925700000 569747 817769 562248 662818 913231 478081 631553 729186 1343009 TRUE FALSE 534087.5523 878317.4676 575584.7881 679827.032 841509.5211 616095.2237 536857.4907 820226.4772 1118852.122 0.477353121 0.785016581 0.514442237 0.607611157 0.752118627 0.550649377 0.479828818 0.733096413 1 20.09358794 0.965600156 9.108087313 0.9999986 0.603387794 0.606742938 0.103802203 0.538218312 142.0807503 0.097387911 0.02436928 9.238472201 -0.965600156 -0.396610806 ERSLS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERSLSR 6 1 P84103 P84103 SRSF3 Serine/arginine-rich splicing factor 3 1 ERS(0.002)LS(0.998)R;ERSLS(1)R 110.55 0.07525 2211500000 2658400 2131800 2625800 2423300 2308400 2570300 2314800 2147600 2728300 TRUE FALSE 2492015.489 2289640.69 2688085.216 2485485.981 2127107.576 3312303.885 1967717.23 2415732.587 2272929.105 1.096389449 1.007352445 1.182652468 1.093516721 0.935844225 1.457284294 0.8657187 1.062827953 1 21.11612125 ERSPALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERSPALK 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 89.752 0.01609 124050000 177040 138120 166340 161060 170000 139670 182130 136860 177810 FALSE TRUE 165959.3824 148346.5485 170285.6634 165193.0723 156648.8857 179990.4616 154821.2973 153947.2723 148132.3623 1.120345209 1.001445911 1.149550717 1.115172064 1.057492659 1.215065087 1.045155123 1.039254825 1 17.17652733 1.531005676 10.01622328 1.02730885 1.102080405 0.318051982 0.056302115 0.151774103 22.90945286 0.029372122 0.01364601 33.9629711 -1.531005676 0.074771555 ERTSTSSSS(ph)VQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERTSTSSSSVQAR 13 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 ERT(0.001)S(0.051)T(0.003)S(0.003)S(0.019)S(0.12)S(0.804)VQAR 135.89 0.00020702 71469000 61359 64393 65384 66847 79998 53544 73159 67269 124160 TRUE FALSE 57518.64972 69160.72472 66934.93936 68562.40719 73715.27978 69001.28359 62189.48712 75667.68273 103436.8939 0.556074796 0.668627238 0.647108946 0.662842866 0.712659449 0.667085805 0.601231193 0.731534754 1 16.65839133 0.892742501 4.769531443 0.999973006 0.649615379 0.874810522 0.042123058 0.226585078 9.582179732 0.038361256 0.009715943 7.811645039 -0.892742501 -0.350357627 ERVDDSTGTVIS(ph)DVEEDAGELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ERVDDSTGTVISDVEEDAGELSR 23 1 S4R403;Q9Y2D8-2;Q9Y2D8-3;Q9Y2D8 S4R403 SSX2IP Afadin- and alpha-actinin-binding protein 1 ERVDDSTGTVIS(1)DVEEDAGELSR;ERVDDSTGTVIS(1)DVEEDAGELSR;ERVDDSTGTVIS(1)DVEEDAGELSR 261.23 5.58E-44 145776000 108913 96682 99909 108790 121511 100188 135822 95287 139976 TRUE FALSE 102096.3297 103840.4359 102278.8887 111581.7356 111968.0162 129110.6492 115456.752 107183.7917 116613.1013 0.875513374 0.890469722 0.877078883 0.956854198 0.960166696 1.107171044 0.990083882 0.919140221 1 16.83137036 2.985837789 2.043929796 1.004894337 0.881537302 0.546084996 0.047238092 0.224681096 1.884786974 0.015518134 0.018128676 967.9162671 -2.985837789 -0.123357034 ERVEAVNMAEGIIHDTETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ERVEAVNMAEGIIHDTETK 19 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;;;; 283.88 4.42E-40 1095976000 1920021 1450628 1548566 1398089 2031625 1385885 1675659 1752455 2492620 FALSE TRUE 1799850.313 1558034.006 1585298.717 1433966.331 1872069.368 1785967.502 1424409.489 1971252.864 2076585.619 0.866735422 0.750286428 0.763416014 0.690540432 0.90151321 0.860050019 0.685938242 0.949275988 1 20.98578193 1.094629399 6.047987693 0.998142135 0.781948879 0.539636053 0.072048781 0.137822065 6.655686147 0.065959099 0.016598533 12.43453071 -1.094629399 -0.216193257 ERVNEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERVNEAR 7 1 P61204;F5H423;P61204-2;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 62.546 0.077342 26984000 19593 23913 22065 26686 24752 21127 22070 19500 24839 FALSE TRUE 18366.7091 25683.5434 22588.39222 27370.80794 22808.07776 27226.02193 18760.80839 21934.61792 20693.21043 0.887571755 1.241157987 1.091584715 1.322695095 1.102201026 1.315698307 0.906616615 1.059991053 1 14.33686987 1.7064098 11.55517949 0.989130486 1.165541804 0.27795052 0.129848466 0.134385896 36.31878474 0.054229732 0.029594856 50.86391673 -1.7064098 0.176411318 ERVPYTDDGLEAIIFTAQGDMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERVPYTDDGLEAIIFTAQGDMR 22 1 P35250;P35250-2;H7C5P4;A0A087WVY3 P35250 RFC2 Replication factor C subunit 2 0 160.69 1.66E-11 26812000 30817 36004 35538 35841 36978 30635 41033 30468 34056 FALSE TRUE 28888.21898 38669.77362 36380.97814 36760.74074 34073.89704 39478.82718 34880.48258 34271.99687 28371.83359 1.018200635 1.3629635 1.282292102 1.2956773 1.200976205 1.391479583 1.2294053 1.207958476 1 14.79217177 0.777015524 1.844576484 1.000484806 1.273183018 0.368090177 0.102337163 0.742987737 4.250395757 0.086736765 0.024329178 5.984329853 -0.777015524 0.272698212 NAMS(ph)LPQLNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 NAMSLPQLNEK 11 0 Q9H3Q1;J3KRZ9 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK;NAMS(1)LPQLNEK 216.83 1.24E-11 1877999000 4959940 4178440 3982780 3741690 5617090 2581790 6498890 5099330 11783130 TRUE FALSE 4649506.209 4487816.045 4077253.422 3837708.1 5175946.41 3327110.861 5524441.777 5735992.576 9816449.481 0.473644388 0.457173039 0.415349096 0.390946656 0.52727276 0.338932204 0.562773922 0.584324565 1 23.22676988 0.676964262 1.059297481 0.999774036 0.436165522 0.901781169 0.057442909 0.268146958 0.505642054 0.047993934 0.015204621 4.752961125 -0.676964262 -0.563608514 ES(ph)ASPTIPNLDLLEAHTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESASPTIPNLDLLEAHTK 18 0 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 ES(0.586)AS(0.404)PT(0.01)IPNLDLLEAHTK;ES(0.551)AS(0.436)PT(0.013)IPNLDLLEAHTK 137.64 2.39E-06 95899000 308820 254760 273020 269220 268370 206200 323290 220870 330280 TRUE FALSE 289491.5075 273622.6955 279496.1633 276128.641 247293.3028 265726.5926 274815.6658 248446.1057 275154.1343 1.052106697 0.994434251 1.015780352 1.003541676 0.898744638 0.965737234 0.998769895 0.9029343 1 18.06988048 2.973298012 24.44955319 0.957318747 1.013821846 0.428431725 0.036277934 571.9022281 523659.9638 0.010409848 0.011077256 940.3683686 -2.973298012 0.056503099 ES(ph)EELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ESEELLK 7 0 O43303-2;O43303 O43303-2 CCP110 Centriolar coiled-coil protein of 110 kDa 1 ES(1)EELLK;ES(1)EELLK;ES(1)EELLK;ES(1)EELLK 146.81 0.0023013 1849020000 3308160 1853720 2056380 2156290 1789630 1604710 3098010 1818140 2385860 TRUE FALSE 3101108.171 1990971.358 2105158.305 2211624.052 1649079.679 2067963.727 2633492.161 2045138.781 1987644.553 1.560192524 1.001673742 1.059122116 1.112685892 0.829665282 1.040409224 1.324931139 1.02892581 1 20.92262835 4.742992472 24.91121747 1.064360182 1.560192732 0.629660378 0.122584579 317.3484004 1783731.213 0.030791243 0.244864189 55334.05173 -4.742992472 0.49583255 ES(ph)GGSGFRSPHLWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESGGSGFRSPHLWK 14 1 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 ES(0.418)GGS(0.371)GFRS(0.21)PHLWK 72.11 0.02388 69460000 190240 217070 209070 226540 261400 166870 245160 215700 279930 TRUE FALSE 178333.218 233142.0887 214029.2391 232353.3999 240870.6984 215042.6601 208400.534 242630.6198 233207.8746 0.764696382 0.999717909 0.91776163 0.996335996 1.032858341 0.922107199 0.89362563 1.040404919 1 17.83125698 4.744725591 24.72994737 0.964928671 0.764696279 0.62769673 0.050420838 419.2169727 1681576.999 0.011885107 0.109447493 55555.31204 -4.744725591 -0.200232393 ES(ph)HTPVSIQEEIVGDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESHTPVSIQEEIVGDFK 17 0 Q12830-4;Q12830;E7ETD6;E9PE19;A0A2R8Y7Q1;A0A0A0MR81;F5H176 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 ES(0.527)HT(0.458)PVS(0.015)IQEEIVGDFK;ES(0.572)HT(0.428)PVSIQEEIVGDFK 195.13 2.29E-11 268930000 319049 264674 278329 269794 329734 223737 381604 302767 436236 TRUE FALSE 299080.2926 284270.7384 284931.0953 276717.3708 303838.0217 288326.2398 324386.0228 340568.1264 363425.3934 0.822948253 0.782198337 0.784015373 0.761414518 0.836039603 0.79335744 0.892579409 0.937106027 1 18.4712997 1.387361213 1.174870877 0.998408743 0.788589688 0.914051881 0.022423792 0.100803009 0.27235587 0.018379223 0.006185512 24.39839245 -1.387361213 -0.209819055 ES(ph)LPIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESLPIK 6 0 Q86V25-3;Q86V25-4;Q86V25-6;Q86V25-2;Q86V25 Q86V25-3 VASH2 Vasohibin-2 1 ES(1)LPIK;ES(1)LPIK 75.109 0.082403 87997000 992710 613110 924450 948660 701320 471800 910400 481280 572100 TRUE FALSE 930578.0531 658505.3023 946378.3906 973004.2217 646241.1562 608001.001 773893.9717 541368.8674 476612.8141 1.952482236 1.381635749 1.985633543 2.041498241 1.355903864 1.275670697 1.623737233 1.13586721 1 18.86245821 2.707705731 19.4982182 1.341464184 1.78808597 0.554811526 0.244620805 43.19918558 27298.1966 0.078210492 0.073771793 510.15921 -2.707705731 0.446621786 ES(ph)PEGSYTDDANQEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESPEGSYTDDANQEVR 16 0 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 ES(0.999)PEGS(0.001)YTDDANQEVR;ES(0.993)PEGS(0.007)YTDDANQEVR 496.57 8.94E-258 2145700000 1025300 645740 759680 717810 653460 821430 994660 691030 472970 TRUE FALSE 961128.3032 693551.2615 777699.9683 736230.2198 602139.8875 1058563.506 845519.967 777306.6166 394028.2515 2.439237033 1.760156179 1.973716264 1.868470642 1.52816425 2.686516772 2.145835898 1.972717981 1 18.58793955 0.939096116 19.65846329 0.999999997 2.034459635 0.503211904 0.327320337 1322.906267 427007.9438 0.305140451 0.076285113 8.691527657 -0.939096116 1.034459637 ES(ph)PGAAATSSSGPQAQQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESPGAAATSSSGPQAQQHR 19 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 ES(1)PGAAATSSSGPQAQQHR;ES(1)PGAAATSSSGPQAQQHR 211.13 1.51E-16 267646000 103627 84243 92981 86268 82672 90387 117117 93230 96982 TRUE FALSE 97141.17105 90480.43937 95186.55323 88481.78293 76179.2746 116480.2596 99556.39311 104869.9707 80795.07767 1.202315461 1.119875641 1.178123172 1.095138287 0.942870244 1.441675198 1.232208644 1.29797475 1 16.30197978 2.238721621 25 1.265495325 1.118368345 0.207247357 0.127213466 5.82253251 904243.1214 0.041362556 0.032574199 173.2693002 -2.238721621 -0.14712698 ES(ph)PGSSEFFQEAVSHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESPGSSEFFQEAVSHGK 17 0 Q8N108-17;Q8N108;Q8N108-13;Q8N108-12 Q8N108-17 MIER1 Mesoderm induction early response protein 1 1 ES(0.998)PGS(0.002)SEFFQEAVSHGK 245.41 9.09E-21 98051000 166500 86177 130060 112760 94583 111980 179380 120270 85192 TRUE FALSE 156079.0622 92557.63475 133145.0846 115653.6125 87154.83271 144306.8082 152483.6343 135285.9742 70972.90484 2.199135889 1.304126342 1.875998804 1.62954599 1.228001487 2.033266195 2.148476727 1.906163691 1 16.11498073 ES(ph)PHFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ESPHFYR 7 0 Q9HDC5 Q9HDC5 JPH1 Junctophilin-1 1 ES(1)PHFYR;ES(1)PHFYR;ES(1)PHFYR 130.75 0.0022758 1559590000 2515540 2471070 2410070 2314470 2534450 2449050 3033530 2494220 2484090 TRUE FALSE 2358096.842 2654030.594 2467237.999 2373863.219 2335404.52 3156050.978 2578680.338 2805628.857 2069479.331 1.139463829 1.282462963 1.19220229 1.147082352 1.128498596 1.525045904 1.246052715 1.355717264 1 20.98083641 ES(ph)PRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESPRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR 40 1 Q6PKG0;A0A0B4J210 Q6PKG0 LARP1 La-related protein 1 1 ES(0.906)PRPLQLPGAEGPAIS(0.094)DGEEGGGEPGAGGGAAGAAGAGR 156.45 2.24E-14 302500000 61908 50483 67980 54810 59639 54863 78046 53110 58686 TRUE FALSE 58033.28879 54220.81385 69592.5177 56216.51739 54955.19351 70701.05747 66343.72684 59740.90041 48890.92747 1.186995048 1.109015857 1.423423962 1.149835364 1.124036633 1.446097694 1.356974193 1.221922011 1 15.57727915 2.266254178 24.99998163 1.299319315 1.21486712 0 0.144686276 593.3537526 535639.9836 0.04794514 0.040105652 184.609556 -2.266254178 -0.084452194 ES(ph)PSLASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESPSLASR 8 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7;H3BSK9 Q8WWM7 ATXN2L Ataxin-2-like protein 1 ES(0.999)PS(0.001)LASR;ES(1)PSLASR 158.57 0.00038207 354320000 794040 681990 777420 674270 652670 756970 879440 665700 539620 TRUE FALSE 744342.4538 732485.2492 795860.7695 691572.9097 601411.9309 975494.9506 747576.1363 748814.1104 449553.9359 1.655735595 1.629360107 1.770334338 1.538353587 1.337797054 2.169917495 1.662928687 1.66568247 1 18.77813469 0.603953129 3.520791613 1.000002864 1.690027064 0.512357997 0.208003249 9.850331851 86.6113428 0.187077895 0.048205117 4.017474502 -0.603953129 0.6900242 ES(ph)PSPAPKPR ddPTM_SK-BR-3_Pertuzumab_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 144.57 1.94E-05 234200000 549770 397950 430200 418110 406670 323040 531940 383420 463850 TRUE FALSE 515360.8771 427414.6321 440404.5472 428839.4105 374731.7786 416296.4039 452180.5353 431290.831 386430.4384 1.333644625 1.106058399 1.139673544 1.109745423 0.96972635 1.077286783 1.170147303 1.11608918 1 18.55984921 ES(ph)PTQISIGAFPSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESPTQISIGAFPSTK 15 0 A0A2R8YH03;Q5VWN6;Q5VWN6-2 A0A2R8YH03 FAM208B Protein FAM208B 1 ES(0.876)PT(0.124)QISIGAFPSTK;ES(0.816)PT(0.184)QISIGAFPSTK 267.62 1.90E-25 165695000 453080 295730 369780 300430 293450 234650 404070 260520 277440 TRUE FALSE 424722.5316 317626.1569 378551.3562 308139.5424 270403.6207 302389.6458 343483.4547 293046.4955 231133.4717 1.837563934 1.37421099 1.637804138 1.33316711 1.169902476 1.308290156 1.486082705 1.267866975 1 17.81836667 8 0.065362917 0.561423515 3.275954642 0.582634917 0.151595366 229.117343 1.111360292 8.625211365 58.00806685 99999999.97 -8 2.714531127 ES(ph)SPEKEAEEGCPEKESEEGCPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESSPEKEAEEGCPEKESEEGCPK 23 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 ES(0.5)S(0.5)PEKEAEEGCPEKESEEGCPK 181.92 2.14E-17 426870000 884580 220080 346430 326220 425260 275850 514450 254580 562250 TRUE FALSE 829215.7168 236374.9522 354647.4832 334591.3575 391861.795 355483.4169 437312.9984 286364.8734 468406.8427 1.770289503 0.504635993 0.757135573 0.714317826 0.836584267 0.758920205 0.933617869 0.611359287 1 18.83740263 4.74732577 24.88867517 0.754521141 1.770290056 0.830256038 0.142848155 420.2997769 1193415.069 0.033367706 0.397897452 55888.92671 -4.74732577 1.015768915 ES(ph)SPKKEETVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESSPKKEETVAR 12 2 Q68DK7;Q68DK7-2;Q68DK7-3;J3KTC2 Q68DK7 MSL1 Male-specific lethal 1 homolog 1 ES(0.77)S(0.23)PKKEETVAR 98.421 0.0022792 445070000 457560 224320 315170 309130 353630 211570 336310 280540 478290 TRUE FALSE 428922.1364 240928.8862 322645.9812 317062.7992 325857.3263 272646.8244 285883.4376 315566.0365 398460.3091 1.076448837 0.604649649 0.809731795 0.795719905 0.81779118 0.684250898 0.7174703 0.791963539 1 18.6040765 0.956875679 20.3224968 1.000000003 0.764319361 0.21116057 0.123572983 951.1105042 448216.8689 0.106114979 0.026528745 9.054733624 -0.956875679 -0.235680642 ES(ph)SPKKEETVASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESSPKKEETVASK 13 2 J3QQY0 J3QQY0 MSL1 1 ES(0.5)S(0.5)PKKEETVASK 75.463 0.016343 616020000 130430 42825 73199 58244 67425 51524 91828 48394 79673 TRUE FALSE 122266.6191 45995.80756 74935.31485 59738.63965 62129.71248 66398.14238 78059.24389 54436.09743 66375.06159 1.842056583 0.692968209 1.128967914 0.900016335 0.936039997 1.000347733 1.176032715 0.820128767 1 16.01835367 4.750050837 24.9985456 0.970970734 1.842057096 0.798834316 0.139448394 786.5546629 1711225.377 0.032578243 0.52326191 56240.71542 -4.750050837 0.871086362 ES(ph)SPKKEETVASKA ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESSPKKEETVASKA 14 3 J3QQY0 J3QQY0 MSL1 1 ES(0.5)S(0.5)PKKEETVASKA;ES(0.5)S(0.5)PKKEETVASKA 136.68 0.00014178 1588850000 2736200 895950 1570090 1407520 1625850 886840 2091900 1129610 2602700 TRUE FALSE 2564946.126 962287.0702 1607333.276 1443639.346 1498162.299 1142856.311 1778239.015 1270644.295 2168292.556 1.182933603 0.443799462 0.741289856 0.665795463 0.690941033 0.52707662 0.82011028 0.586011464 1 21.04812799 -1.148665428 4.597955416 1.000038137 0.686854679 0.167523136 0.200568346 6.81E-05 1.26E-05 0.168592654 0.039732837 0.071012462 1.148665428 -0.313183459 ES(ph)SPSHGLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESSPSHGLLK 10 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 1 ES(0.497)S(0.497)PS(0.005)HGLLK;ES(0.499)S(0.499)PS(0.001)HGLLK 170.04 2.87E-06 347540000 892300 866980 856290 881450 995920 745560 1176420 1005430 1269690 TRUE FALSE 836452.5358 931172.1013 876601.6032 904069.4993 917704.4605 960791.0688 1000026.742 1130960.149 1057770.536 0.790769365 0.880315786 0.828725676 0.854693403 0.867583686 0.908317103 0.945409905 1.069192334 1 20.01259527 1.690041914 1.408091716 1.033440446 0.846215756 0.844937629 0.032427972 0.135087867 0.516128483 0.023858976 0.008969138 48.98260909 -1.690041914 -0.187224691 ES(ph)TGNMVTGQTVCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESTGNMVTGQTVCK 14 0 Q15021;E7EN77 Q15021 NCAPD2 Condensin complex subunit 1 1 ES(0.979)T(0.021)GNMVTGQTVCK 186.94 3.93E-06 36721000 131800 106760 122730 121650 134400 96177 174480 116620 193650 TRUE FALSE 123550.8733 114664.6215 125641.2136 124771.745 123844.7661 123941.7386 148318.3438 131180.2637 161328.564 0.765833838 0.710752136 0.778790875 0.773401448 0.767655542 0.768256628 0.919355755 0.813124846 1 17.29964237 1.110166855 0.425715728 1.00942445 0.731329565 0.780959195 0.039991289 0.472208544 0.238985692 0.050659323 0.028576939 12.88744591 -1.110166855 -0.278094886 ESAAHDYTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ESAAHDYTLR 10 0 Q06124;Q06124-1;Q06124-3;A0A0U1RRI0 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ;; 175.15 2.89E-06 1171850000 800510 1266040 1157620 1218270 1369500 1046320 1317950 1246010 1339090 FALSE TRUE 750407.5081 1359778.919 1185079.293 1249532.871 1261944.994 1348375.598 1120335.633 1401577.091 1115587.228 0.672656955 1.218890719 1.062291915 1.120067386 1.131193476 1.208668909 1.004256417 1.256358137 1 20.08937189 4.746014409 24.97862918 1.123668923 0.672656739 0.730113775 0.08646689 428.7494376 1436760.39 0.018191012 0.19087035 55720.4235 -4.746014409 -0.451012184 ESAAPAAAPTAEAPPPSVVTRPEPQALPS(ph)PAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ESAAPAAAPTAEAPPPSVVTRPEPQALPSPAIR 33 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 1 ESAAPAAAPTAEAPPPSVVTRPEPQALPS(1)PAIR;ESAAPAAAPTAEAPPPSVVTRPEPQALPS(0.999)PAIR;ESAAPAAAPTAEAPPPSVVTRPEPQALPS(1)PAIR;ESAAPAAAPTAEAPPPSVVTRPEPQALPS(1)PAIR 218.27 3.41E-36 1255990000 285372 293995 345903 331183 408819 285187 395696 358904 480541 TRUE FALSE 267511.0759 315762.6957 354107.9825 339681.7165 376712.0048 367515.8573 336365.0583 403713.9544 400335.6027 0.668217051 0.788744977 0.884527831 0.8484924 0.940990515 0.918019419 0.840207706 1.008438799 1 18.6108504 6.109954905 0.405564781 0.937073864 1.07E-26 0.764519213 0.049004536 8.450408609 0.457175251 0.034035333 4.831599712 1288115.793 -6.109954905 -0.937073864 ESADPLGAWLQDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ESADPLGAWLQDAR 14 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;;; 238.01 6.04E-17 395366000 412672 480368 448052 477890 500721 397789 525356 409653 446910 FALSE TRUE 386843.5962 515934.9465 458680.005 490153.4665 461396.3925 512624.2267 446583.745 460799.0788 372317.8339 1.039014415 1.385737936 1.231958191 1.316492045 1.239254074 1.376845749 1.199469121 1.237649763 1 18.5061752 0.521972073 1.197617379 1.000185903 1.27312821 0.390911147 0.098562288 1.615849268 3.101078457 0.082378689 0.025018496 3.326381627 -0.521972073 0.272942307 ESAGADTRPTVRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ESAGADTRPTVRPR 14 2 O75489;E9PS48;O75489-2;G3V194 O75489 NDUFS3 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial" 0 ;;;; 122.66 6.04E-05 2037470000 2389429 2294730 2196720 2054070 2820300 2024770 2280310 2284250 3401560 FALSE TRUE 2239878.904 2464634.197 2248827.236 2106780.914 2598805.015 2609288.23 1938398.685 2569443.641 2833817.661 0.790410383 0.869722223 0.793568078 0.743442651 0.917068536 0.920767862 0.684023786 0.90670747 1 21.4343155 0.999162977 25 1.000000022 0.817803269 0.409793221 0.072965018 22.49713387 671961.7866 0.06756713 0.016891782 9.980745386 -0.999162977 -0.182196753 ESAS(ph)PTIPNLDLLEAHTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ESASPTIPNLDLLEAHTK 18 0 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 ES(0.001)AS(0.996)PT(0.003)IPNLDLLEAHTK;ESAS(0.961)PT(0.039)IPNLDLLEAHTK;ESAS(0.999)PTIPNLDLLEAHTK 325.43 1.59E-62 1349940000 2350060 1981670 2060490 1986700 1992910 1472140 2489400 1749990 2306660 TRUE FALSE 2202973.94 2128394.909 2109365.796 2037682.085 1836394.888 1897122.92 2116137.58 1968480.104 1921663.544 1.146388995 1.107579376 1.097676959 1.060374014 0.955627687 0.987229489 1.101200877 1.024362516 1 20.87392433 3.166552952 3.018356922 1.023398129 1.11436873 0.583321251 0.039387694 0.213731738 3.935421263 0.012704803 0.016146088 1467.414992 -3.166552952 0.090970601 ESAWS(ph)PPPIEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESAWSPPPIEIR 12 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 ESAWS(1)PPPIEIR;ESAWS(1)PPPIEIR 156.24 7.28E-05 100759000 322620 314810 334500 345060 321280 277900 393820 272670 337560 TRUE FALSE 302427.7901 338118.86 342434.498 353914.8238 296047.9648 358125.2187 334770.347 306713.4497 281219.0553 1.075417133 1.202332678 1.217678858 1.258502285 1.052730813 1.273474226 1.190425545 1.09065671 1 18.10133483 1.03112685 3.19976648 1.0013157 1.18992386 0.420101228 0.070438511 0.185367867 4.283800665 0.060737166 0.01592617 10.74303152 -1.03112685 0.18860816 ESCDSALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESCDSALR 8 0 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 ; 79.116 0.058184 80680000 487950 599860 497310 487830 624800 441198 576180 522510 629420 FALSE TRUE 457410.0805 644274.2586 509106.428 500348.5437 575730.7283 568564.7003 489787.158 587746.5237 524365.7358 0.872311155 1.228673452 0.970899495 0.954197633 1.097956424 1.084290337 0.934056374 1.120871338 1 19.00021389 3.746181453 24.78354246 1.019251738 1.083098677 0 0.105710948 1093.659582 1422052.248 0.02475578 0.044538479 5574.185958 -3.746181453 0.063846939 ESCSS(ph)PSTVGSSLTTR ddPTM_SK-BR-3_Pertuzumab_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(0.018)S(0.71)PS(0.211)T(0.061)VGSSLTTR 252.01 1.69E-26 245600000 250050 241470 254670 252210 274260 242880 357610 270350 315620 TRUE FALSE 234399.8169 259348.69 260710.8927 258682.1356 252720.7259 312995.5132 303989.7004 304103.7926 262940.983 0.891454098 0.986338026 0.991518666 0.983803029 0.961130985 1.190364125 1.156113805 1.156547713 1 18.0043795 2.246410496 24.99993681 1.142467397 0.970913953 0.655671008 0.057940307 90.86876666 289395.0975 0.018229786 0.014992154 176.3642259 -2.246410496 -0.171553444 ESDDGTEELEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESDDGTEELEVR 12 0 F5H039;Q9NQX3;Q9NQX3-2 F5H039 GPHN Gephyrin;Molybdopterin adenylyltransferase;Molybdopterin molybdenumtransferase 0 291.33 2.67E-21 0 130840 127860 121460 115340 126840 107900 135130 100960 116030 FALSE TRUE 122650.958 137326.8874 124341.0886 118299.8197 116878.498 139048.9784 114868.511 113565.0782 96663.84342 1.268840071 1.420664465 1.286324691 1.223826981 1.209123225 1.43847972 1.188329648 1.174845467 1 16.56068874 -0.485023882 0.24467151 0.84236939 1.363733617 0.579090947 0.081048952 7.310812273 0.551753501 1.015138539 0.150011449 0.327322695 0.485023882 0.521364227 ESDFYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ESDFYLR 7 0 P61326;P61326-2 P61326 MAGOH Protein mago nashi homolog 0 ;;; 206.1 0.00052492 1437490000 1288990 1516560 1452340 1450840 1638640 1208720 1493510 1329120 1529720 FALSE TRUE 1208314.417 1628847.68 1486790.191 1488071.011 1509947.824 1557657.842 1269572.041 1495063.558 1274399.85 0.948143879 1.278129216 1.166659107 1.167664145 1.18483051 1.222267754 0.9962117 1.173151078 1 20.28138657 1.744478233 25 1.061347401 1.176536469 0.193788286 0.097369238 1.608531625 6819.411154 0.040558526 0.022491679 55.52367879 -1.744478233 0.115189068 ESDGFREEK ddPTM_SK-BR-3_Pertuzumab_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 ; 87.806 0.012049 964320000 904810 823880 849950 837350 956470 608560 983170 766670 1439640 FALSE TRUE 848179.5572 884880.9324 870111.2154 858837.8186 881352.7044 784241.3929 835752.7858 862390.4371 1199354.784 0.707196543 0.737797476 0.725482757 0.716083206 0.734855704 0.653886076 0.69683533 0.719045314 1 20.19382706 -1.593114837 2.256565219 1.034752576 0.712145638 0.935931436 0.023729549 403030.32 305792.9733 82732.58456 0.006588902 0.025520264 1.593114837 -0.322606938 ESDHIHIIALAQALSVSIQVEYMDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESDHIHIIALAQALSVSIQVEYMDR 25 0 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5H3F0;Q96FW1-2 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 220.89 6.87E-34 33237000 23218.8 29398 24151.7 32340.7 28743.5 25849.2 23920.3 21382.7 18118.9 FALSE TRUE 21765.57675 31574.65851 24724.58973 33170.61711 26486.10146 33311.44441 20333.67308 24052.37716 15094.73854 1.441931352 2.091765845 1.637960781 2.197495308 1.754657849 2.20682487 1.347070241 1.593427876 1 13.88175815 1.135794942 1.171905732 1.03833222 1.881205739 0.482361789 0.279383035 0.341647844 0.969489479 0.230067339 0.073619318 13.67083187 -1.135794942 0.842873519 ESDLSHVQNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ESDLSHVQNK 10 0 O43390;O43390-3;O43390-2 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;; 154.85 1.38E-05 2430160000 4848300 5438300 5311600 5049490 6118800 4076040 5635100 5040420 6945500 FALSE TRUE 4544853.557 5840957.391 5437593.66 5179068.462 5638254.13 5252726.579 4790169.069 5669727.532 5786251.18 0.785457357 1.009454517 0.939743798 0.895064576 0.974422636 0.907794428 0.827853634 0.979861979 1 22.46419752 3.290188952 24.76123799 0.91639714 0.936558483 0 0.075209892 571.8209539 274244.0251 0.0199318 0.026987749 1950.693117 -3.290188952 0.020161343 ESDPSDPNKDMVVQLIDDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESDPSDPNKDMVVQLIDDFK 20 1 P78362;P78362-2;C9J2M4;C9JWF7 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 0 59.9 0.057317 15157000 71961 39020 54354 44503 46847 35690 59924 38519 50632 FALSE TRUE 67457.08946 41909.0814 55643.30255 45645.02232 43167.82559 45993.12362 50938.95251 43328.18194 42181.1921 1.599221978 0.993549004 1.319149597 1.082117883 1.023390365 1.090370407 1.207622401 1.027191973 1 15.36431225 4.747546403 24.96826592 1.115730634 1.59922223 0.699092106 0.103432265 675.4268842 1876727.24 0.023642225 0.288486301 55917.32698 -4.747546403 0.483491597 ESDQTLAALLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 ESDQTLAALLSPK 13 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;H7C1M2 P18583-7 SON Protein SON 1 ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK 256.98 7.28E-24 6917202000 4487060 2608874 3287460 3183071 2913634 2189176 3779860 2454680 3062658 TRUE FALSE 4206222.924 2802037.745 3365440.104 3264753.991 2684808.939 2821155.573 3213105.084 2761152.201 2551480.594 1.648542001 1.098200689 1.31901458 1.279552742 1.052255285 1.105693525 1.259310022 1.082176446 1 21.28290324 4.744126564 24.73667073 1.172961125 1.648542238 0.678099086 0.106973982 316.762421 1407734.77 0.024163773 0.212178026 55478.73686 -4.744126564 0.475581113 ESDTKNEVNGTSEDIKS(ph)EGDTQSN ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESDTKNEVNGTSEDIKSEGDTQSN 24 2 O95232 O95232 LUC7L3 Luc7-like protein 3 1 ESDTKNEVNGTSEDIKS(0.709)EGDT(0.145)QS(0.145)N 58.477 0.016845 0 196610 93803 120990 123600 138100 75007 147730 95770 198560 TRUE FALSE 184304.5311 100748.2717 123859.9399 126771.7853 127254.1831 96660.30326 125579.258 107727.0953 165419.0533 1.114167488 0.609048775 0.748764653 0.766367494 0.76928371 0.584335972 0.759158365 0.651237528 1 17.33576589 -1.143948974 4.087339827 1.000077371 0.733071759 0.215801528 0.146356308 18156825.85 5081668.005 13610.46605 0.03005655 0.071787863 1.143948974 -0.267005612 ESDTKNEVNGTSEDIKSEGDT(ph)QSN ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESDTKNEVNGTSEDIKSEGDTQSN 24 2 O95232 O95232 LUC7L3 Luc7-like protein 3 1 ESDTKNEVNGTSEDIKSEGDT(0.5)QS(0.5)N;ESDTKNEVNGTSEDIKSEGDT(0.5)QS(0.5)N 183.12 4.67E-17 624740000 556810 282370 371450 367400 445790 225950 499640 309310 621930 TRUE FALSE 521960.256 303276.9686 380260.9694 376828.106 410779.4516 291178.097 424723.6204 347928.0344 518125.8652 1.007400501 0.585334547 0.733916206 0.727290667 0.792817883 0.561983326 0.819730589 0.671512576 1 18.98294308 -1.172241076 3.661000955 1.0002451 0.724170032 0.295672873 0.125839933 34419476 54559032.83 101205.3582 0.026539779 0.067260319 1.172241076 -0.276075068 ESDVPLKTEEFEVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESDVPLKTEEFEVTK 15 1 Q969H8;M0QXF7;M0QYN0 Q969H8 MYDGF Myeloid-derived growth factor 0 ; 226.25 8.12E-13 393410000 1106630 739390 851720 781630 955100 640570 1215980 786830 1168910 FALSE TRUE 1037368.004 794135.2049 871923.2006 801687.9491 880090.2987 825492.1602 1033655.088 885067.4575 973811.3696 1.065265858 0.815491819 0.895371761 0.823247678 0.903758496 0.847692054 1.06145309 0.908869505 1 19.89328282 1.749936694 25 0.99270222 0.881233669 0.25242586 0.078310192 3.490831138 7685.09978 0.03231021 0.017917628 56.22593602 -1.749936694 -0.111468551 ESEDAELLWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ESEDAELLWR 10 0 E5RH53;Q96DB5-3;Q96DB5-2;Q96DB5;H0YB83;E5RGC8 E5RH53 RMDN1 Regulator of microtubule dynamics protein 1 0 ;;;; 206.38 3.52E-07 1819087000 1457930 1590460 1394230 1455710 1741010 1177430 1570000 1412860 1719900 FALSE TRUE 1366680.764 1708219.313 1427301.794 1493065.983 1604278.097 1517334.927 1334593.075 1589258.681 1432837.579 0.953828113 1.192193266 0.996136488 1.042034355 1.119651048 1.058972035 0.931433607 1.10916876 1 20.45044365 1.972308433 24.41987923 1.003237416 1.070715693 0.062881571 0.077162578 1021.578245 900878.9559 0.029408671 0.019038385 93.82280933 -1.972308433 0.067478277 ESEDDPES(ph)EPDDHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESEDDPESEPDDHEK 15 0 P16383-3;P16383-4;P16383 P16383-3 GCFC2 GC-rich sequence DNA-binding factor 2 1 ESEDDPES(1)EPDDHEK;ESEDDPES(1)EPDDHEK 174.65 5.80E-07 614300000 1780920 1115830 1355940 1223910 1318640 1062210 1663560 1130560 1885090 TRUE FALSE 1669455.396 1198447.214 1388103.537 1255317.603 1215079.334 1368852.783 1414124.622 1271712.905 1570456.301 1.063038427 0.763120383 0.88388549 0.799333036 0.773711012 0.871627426 0.900454614 0.809772869 1 20.58275237 -0.83332036 5.027444148 1.000000202 0.851874142 0.208151293 0.086207196 1.74E-07 4.03E-08 0.074381039 0.017531755 0.146784312 0.83332036 -0.14812606 ESEDKPEIEDVGS(ph)DEEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ESEDKPEIEDVGSDEEEEK 19 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK 290.1 9.80E-50 9451100000 20420400 5009120 9228250 7761510 6389380 7652240 13082100 6476700 4370600 TRUE FALSE 19142323.62 5380000.457 9447148.448 7960683.487 5887583.868 9861317.464 11120560.55 7285330.252 3641118.625 5.25726448 1.477568025 2.594573103 2.186329067 1.616971177 2.708320843 3.054160465 2.000849465 1 21.79595031 4.747108002 24.93379959 2.21048101 5.257266072 0.71594635 0.624177274 599.9782069 1750172.045 0.144445103 1.693201504 55860.90943 -4.747108002 3.046785062 ESEDKPEIEDVGS(ph)DEEEEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 ESEDKPEIEDVGSDEEEEKK 20 2 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK 295.3 7.12E-55 29339210000 33176360 5065764 11682250 10094530 8619130 8693012 17138860 7478038 6451747 TRUE FALSE 31099910.85 5440838.437 11959358.49 10353572.73 7942218.298 11202543.45 14569047.05 8411687.505 5374908.746 5.78612816 1.012266197 2.225034703 1.926278793 1.477647096 2.084229514 2.710566401 1.564991687 1 22.35780883 4.746120398 24.95266489 1.853216632 5.786130085 0.847441626 0.536584463 345.7907091 1141327.884 0.127246213 1.351563286 55734.02366 -4.746120398 3.932913453 ESEDKPEIEDVGS(ph)DEEEEKKDGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 215.92 9.80E-33 28475310000 46116100 5761194 13637720 12760020 12689360 9332190 19075470 8160674 10744180 TRUE FALSE 43229775.62 6187758.798 13961213.16 13087463.72 11692788.85 12026241.76 16215280.36 9179552.113 8950906.948 4.829653115 0.691299645 1.559754027 1.462138283 1.306324479 1.343578011 1.811579593 1.025544357 1 23.09360244 4.744895164 24.96438758 1.322802787 4.829654707 0.92520216 0.317372464 180.7786028 712427.2204 0.075526814 0.710669753 55577.0081 -4.744895164 3.50685192 ESEDSETQPFDTHLEAYGPCLS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ESEDSETQPFDTHLEAYGPCLSPPR 25 0 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 ESEDSETQPFDTHLEAYGPCLS(1)PPR;ESEDSETQPFDTHLEAYGPCLS(1)PPR;ESEDSETQPFDTHLEAYGPCLS(1)PPR;ESEDSETQPFDTHLEAYGPCLS(1)PPR;ESEDSETQPFDTHLEAYGPCLS(1)PPR 280.65 1.90E-53 3501320000 1233440 1140690 1201774 1175580 1326302 1135980 1490450 1076005 1323524 TRUE FALSE 1156241.192 1225147.874 1230280.647 1205747.373 1222139.591 1463918.985 1266970.859 1210346.593 1102619.294 1.04863138 1.11112501 1.115780082 1.093530087 1.108396704 1.327674015 1.149055586 1.097701264 1 20.07250332 2.443960419 24.99986598 1.168489921 1.099491841 0.041158934 0.083093069 356.6752585 268894.6254 0.026394245 0.022083173 277.945994 -2.443960419 -0.068998079 ESEEGNPVRGS(ph)EEDS(ph)PKKESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESEEGNPVRGSEEDSPKKESK 21 3 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 2 ESEEGNPVRGS(1)EEDS(0.999)PKKES(0.001)K 89.272 0.003351 77101000 151840 43493 71700 69980 71859 42622 92625 46445 105710 TRUE FALSE 142336.6054 46713.26697 73400.75786 71775.80528 66215.48401 54926.27949 78736.74114 52243.76049 88066.31809 1.616243401 0.530432837 0.833471405 0.81501994 0.751882053 0.623692243 0.894061917 0.593232028 1 16.42630273 4.747457145 24.96322081 0.747772126 1.616243855 0.782152309 0.142757768 482.5458988 1353970.677 0.030615008 0.372133231 55905.8358 -4.747457145 0.868471729 ESEEGNPVRGSEEDS(ph)PKKESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESEEGNPVRGSEEDSPKKESK 21 3 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 ESEEGNPVRGSEEDS(1)PKKESK 117.03 8.27E-05 364570000 314060 126250 155070 235010 305310 115080 280900 139850 676120 TRUE FALSE 294403.5452 135597.6814 158748.3336 241040.7545 281332.1842 148301.7278 238781.6527 157310.5803 563271.2041 0.522667488 0.240732493 0.281832859 0.427930192 0.499461329 0.263286543 0.42391951 0.279280352 1 19.10347019 -2.078319397 2.566405603 2.025217683 0.354643012 0.794495413 0.100927519 10475453.67 3264880.832 62872174.07 0.023778329 0.008349887 2.078319397 -1.670574671 ESEEQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESEEQKR 7 1 P00367 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 75.38 0.069955 279440000 186770 135050 141430 144510 194810 126540 126960 157340 249430 FALSE TRUE 175080.3991 145049.2425 144784.7864 148218.3713 179510.4084 163070.0438 107923.5266 176984.2453 207798.5216 0.84254882 0.69802827 0.696755613 0.713279238 0.863867592 0.784750741 0.519366191 0.851710801 1 17.66482586 0.998077433 24.99970479 1.000000029 0.718957057 0.458282588 0.095103724 48.16589913 626324.3382 0.091257499 0.022814375 9.955829093 -0.998077433 -0.281042973 ESEIIDFFLGASLKDEVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESEIIDFFLGASLKDEVLK 19 1 P15880;E9PQD7;E9PPT0;E9PMM9;I3L404 P15880 RPS2 40S ribosomal protein S2 0 ; 323.3 2.96E-62 613430000 1203450 863180 946270 935310 1146060 729690 1214560 853270 984200 FALSE TRUE 1128128.213 927090.7453 968715.9713 959311.6381 1056053.071 940339.6575 1032448.003 959802.6378 819930.6618 1.375882456 1.13069408 1.181460843 1.169991175 1.287978508 1.146852656 1.259189406 1.170590005 1 19.64514239 0.970183679 21.90211365 0.999999998 1.208512493 0.463355509 0.073763154 592.8542257 435493.3307 0.064134727 0.016033682 9.336490917 -0.970183679 0.208512495 ESEITDEDIDGILER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ESEITDEDIDGILER 15 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 ;; 369.42 3.70E-97 457905000 1097360 1102210 1175090 1037040 1286540 925450 1363980 1100490 1421500 FALSE TRUE 1028678.196 1183818.775 1202963.69 1063652.202 1185500.338 1192612.392 1159463.862 1237888.599 1184242.467 0.868638159 0.999642226 1.015808606 0.898170967 1.001062174 1.007067746 0.979076409 1.045299956 1 20.17553306 2.525159737 24.99833421 1.003355588 0.964618272 0.25392309 0.046961453 799.7307189 416163.705 0.015042043 0.014181448 335.0886648 -2.525159737 -0.038737316 ESEKQQDS(ph)QPEEVMDVLEMVENVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ESEKQQDSQPEEVMDVLEMVENVK 24 1 Q9H307 Q9H307 PNN Pinin 1 ES(0.163)EKQQDS(0.837)QPEEVMDVLEMVENVK;ES(0.021)EKQQDS(0.979)QPEEVMDVLEMVENVK;ES(0.017)EKQQDS(0.983)QPEEVMDVLEMVENVK;ES(0.235)EKQQDS(0.765)QPEEVMDVLEMVENVK;ES(0.006)EKQQDS(0.994)QPEEVMDVLEMVENVK;ES(0.007)EKQQDS(0.993)QPEEVMDVLEMVENVK;ES(0.004)EKQQDS(0.996)QPEEVMDVLEMVENVK;ES(0.109)EKQQDS(0.891)QPEEVMDVLEMVENVK 191.54 5.59E-18 521344000 303511 209601 218328.7 248055.1 293159 163856.5 308280.1 189775.3 453459 TRUE FALSE 284514.7883 225120.0761 223507.5599 254420.6138 270135.4747 211159.2116 262056.3609 213469.164 377773.7634 0.753135384 0.595912416 0.591643945 0.673473487 0.71507209 0.558956794 0.693685974 0.565071439 1 18.52716298 -1.277293363 4.30973243 1.000278065 0.637908871 0.742863998 0.065870333 0.000159653 2.68E-05 0.057858089 0.013626924 0.052808841 1.277293363 -0.362369193 ESENSGDSGYPS(ph)EK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESENSGDSGYPSEK 14 0 O00418 O00418 EEF2K Eukaryotic elongation factor 2 kinase 1 ESENSGDSGYPS(1)EK;ESENSGDSGYPS(1)EK 260.25 1.97E-24 516740000 1629850 1148920 1153480 1289400 852500 783770 2000510 1012680 798630 TRUE FALSE 1527840.598 1233987.232 1180841.09 1322488.187 785548.0888 1010031.676 1700552.097 1139115.327 665333.4937 2.296353051 1.854689782 1.77481083 1.987707217 1.180683216 1.518083315 2.55593941 1.712096773 1 19.34371814 5.024894918 1.629777022 1.771422482 2.880899543 0.143335055 0.431496279 5.316502544 7.522427518 0.110951929 11.62582659 105899.7459 -5.024894918 1.109477061 ESENVVCHFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESENVVCHFYR 11 0 F8WCJ3;B8ZZX4;O14530-2;O14530 F8WCJ3 TXNDC9 Thioredoxin domain-containing protein 9 0 ; 105.17 0.0025016 222580000 629090 605020 574070 568180 707390 464090 675160 586040 724950 FALSE TRUE 589716.3799 649816.3103 587687.2115 582760.4607 651834.4429 598065.2491 573926.0259 659208.384 603951.1616 0.976430575 1.075941817 0.973070753 0.964913221 1.079283366 0.990254324 0.95028549 1.091492865 1 19.20407237 3.957583192 24.05304197 1.00181317 1.032195661 0.012580667 0.051690617 754.5733966 928946.764 0.012414535 0.022428883 9069.496806 -3.957583192 0.030382491 ESESVDKVMDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 162.72 5.65E-05 1698600000 4118500 3081330 3547740 3718700 4619200 2407370 4840200 3040900 7688700 FALSE TRUE 3860730.437 3309474.879 3631894.068 3814128.138 4256426.665 3102338.639 4114456.944 3420563.059 6405406.299 0.602729984 0.516669002 0.56700448 0.595454521 0.664505336 0.484331281 0.64234129 0.53401188 1 22.61085865 -4.806547878 0.470552939 10 0.569443811 0.850925612 0.05565238 458.8521923 2.968932593 4303.335672 0.02550899 1.56E-05 4.806547878 -9.430556189 ESEVAHVDQLFDDASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESEVAHVDQLFDDASR 16 0 E9PRF4;Q15047-3;Q15047;E9PAP1;X6RHV1;B0QZE6;E9PS59;X6R732;E9PQM8;Q15047-2 E9PRF4 SETDB1 Histone-lysine N-methyltransferase SETDB1 0 ; 165.75 6.92E-09 88316000 114852 144388 132173 133824 155827 112833 161584 134130 165393 FALSE TRUE 107663.6183 155078.6378 135308.206 137258.1504 143588.976 145406.0554 137355.9793 150876.4258 137787.8398 0.781372424 1.125488562 0.982003972 0.996155761 1.042101946 1.055289462 0.996865757 1.094990864 1 17.07208905 4.751624817 24.82351624 1.034971596 0.781372244 0.750477512 0.046244044 966.7176102 1836841.102 0.010443168 0.19654606 56444.91417 -4.751624817 -0.253599352 ESFDGSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESFDGSVR 8 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 151.56 0.0010961 654040000 1452440 1381910 1491290 1397990 1343770 1319440 1600540 1303090 1064670 FALSE TRUE 1361534.373 1484228.054 1526664.103 1433864.79 1238235.725 1700340.909 1360553.886 1465783.655 886969.699 1.535040458 1.673369514 1.721213368 1.616588246 1.396029341 1.917022544 1.533935023 1.652574667 1 19.75852529 -0.377080789 1.150651731 0.991291177 1.642246719 0.677959871 0.136388879 20.1311094 15.49941612 0.975350935 0.035859398 0.419680906 0.377080789 0.650955542 ESFESQFLADTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESFESQFLADTER 13 0 A0A590UJ56;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;Q13616;A0A590UJC4;A0A590UJ50 A0A590UJ56 CUL1 Cullin-1 0 ; 205.09 1.69E-07 109436000 157286 166263 169773 176578 165781 148841 188657 157995 172602 FALSE TRUE 147441.75 178573.2855 173800.0957 181109.2904 152761.229 191808.9805 160369.6343 177721.0235 143793.6111 1.02537066 1.241872181 1.208677453 1.259508604 1.062364508 1.333918656 1.115276492 1.2359452 1 17.13364005 -1.598555862 2.886498621 0.986688243 1.191983125 0.274372139 0.094192637 10752387.19 11351688.36 1089888.453 0.019668182 0.02520253 1.598555862 0.205294882 ESFQIFLDELHEHGQLHSMSSWMELYPTISSDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESFQIFLDELHEHGQLHSMSSWMELYPTISSDIR 34 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ; 126.05 2.48E-08 145992000 199395 341986 214861 186942 381664 202069 254421 301816 135984 FALSE TRUE 186915.2229 367306.9993 219957.6044 191739.2482 351689.649 260403.04 216272.933 339498.392 113287.3919 1.649920788 3.242258411 1.941589445 1.692502978 3.104402379 2.298605658 1.909064454 2.996788842 1 16.78962778 -1.133982185 5.688116168 0.999983836 2.363178261 0.346776098 0.584078108 0.000110174 1.68E-05 0.520402046 0.122658489 0.0734544 1.133982185 1.363194425 ESGADGASTS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESGADGASTSPR 12 0 O75528-2;O75528 O75528-2 TADA3 Transcriptional adapter 3 1 ESGADGASTS(1)PR;ESGADGAST(0.005)S(0.994)PR 164.56 5.98E-05 288110000 346290 347420 340870 331580 372080 315760 391720 306990 342450 TRUE FALSE 324616.327 373143.3383 348955.5974 340088.9042 342858.3377 406914.7861 332985.2226 345318.3773 285292.8827 1.13783535 1.307930765 1.223148626 1.19206936 1.201776695 1.426305424 1.16716975 1.210399552 1 18.12208423 0.669325103 1.572805666 1.00058863 1.246399759 0.453913702 0.080959126 1.042667197 3.761901235 0.07033309 0.020242155 4.670088422 -0.669325103 0.245811129 ESGHSNWLGDPEEPLTGFSWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESGHSNWLGDPEEPLTGFSWR 21 0 Q6DD88;F5H6I7;F5GWF8 Q6DD88 ATL3 Atlastin-3 0 ; 142.99 1.41E-07 208570000 79316 107495 88180 90386 112851 100133 110668 105313 102464 FALSE TRUE 74351.75314 115454.0416 90271.67124 92705.45778 103988.1377 129039.7716 94074.36079 118461.5599 85362.09646 0.871016016 1.352521159 1.057514693 1.086026019 1.218200372 1.511675286 1.102062446 1.387753638 1 16.38130799 2.487931872 24.35525799 1.265333937 1.131778361 0.131519757 0.18167831 805.871186 1815555.576 0.055378254 0.049258342 307.5614306 -2.487931872 -0.133555576 ESGLQAAHPNSIFLIDHAWTCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESGLQAAHPNSIFLIDHAWTCR 22 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 215.79 8.07E-26 1521550000 497930 664560 634620 627170 755250 580390 730950 660330 657870 FALSE TRUE 466765.4501 713764.7139 649673.4861 643264.244 695935.7115 747939.1712 621350.8333 742773.6541 548067.247 0.85165726 1.30233054 1.185390095 1.173695833 1.269799856 1.364685037 1.133712764 1.355260067 1 19.06399339 4.745282707 24.7595391 1.230595857 0.851657061 0.530731836 0.109567767 484.4138572 1784192.869 0.022596678 0.220018475 55626.62454 -4.745282707 -0.378938796 ESGPPHMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 73.26 0.033395 29692000 44377 35884 42604 37847 43691 28446 42123 40116 55553 FALSE TRUE 41599.52279 38540.8887 43614.587 38818.21809 40259.6851 36657.89842 35807.0472 45124.57091 46280.84541 0.898849673 0.832761121 0.942389591 0.838753436 0.869899518 0.792074952 0.77369043 0.975016133 1 15.4981276 1.11367694 6.886428018 0.998282292 0.8511331 0.585878228 0.048319901 0.165578552 8.756420683 0.050778942 0.012745973 12.99202777 -1.11367694 -0.147149192 ESGVVAVS(ph)PEKSES(ph)PQKEDGLSSQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESGVVAVSPEKSESPQKEDGLSSQLK 26 2 Q96T58 Q96T58 SPEN Msx2-interacting protein 2 ES(0.002)GVVAVS(0.533)PEKS(0.521)ES(0.943)PQKEDGLSSQLK;ESGVVAVS(0.999)PEKS(0.009)ES(0.991)PQKEDGLSSQLK 142.05 1.54E-07 462290000 862040 237881 410315 371229 411599 269763 559330 303880 597670 TRUE FALSE 808086.4552 255493.9568 420047.8656 380755.3646 379273.6749 347639.1989 475463.6591 341820.0869 497915.0159 1.622940521 0.513127639 0.843613573 0.764699502 0.761723713 0.698189827 0.954909259 0.686502869 1 18.92554 4.749386534 24.96123228 0.770187538 1.622941016 0.787970855 0.137717777 679.3641777 1566374 0.031139441 0.463788923 56154.7546 -4.749386534 0.852753478 ESHATLVFHNLLGEIDQQYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESHATLVFHNLLGEIDQQYSR 21 0 P40763;P40763-2;P40763-3;K7EP08 P40763 STAT3 Signal transducer and activator of transcription 3 0 ; 359.9 4.03E-96 947630000 530130 696830 714230 720620 795970 689100 812870 640400 836830 FALSE TRUE 496950.1096 748424.0183 731171.8729 739112.3292 733457.727 888031.9834 690987.6898 720355.3497 697157.6669 0.712823129 1.073536237 1.048789833 1.06017959 1.052068652 1.27378931 0.991149811 1.033274658 1 19.41112544 4.738871926 24.68265549 1.070370976 0.712823014 0.669359232 0.078100951 12.01598331 952200.4974 0.017267869 0.100984983 54811.53013 -4.738871926 -0.357547962 ESHPHGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESHPHGVK 8 0 E9PM92;O00193;E9PQA1;E9PRZ9 E9PM92 C11orf58;SMAP Small acidic protein 0 77.058 0.063193 0 14255 10905 13467 12455 15905 9723.1 14148 16640 13331 FALSE TRUE 13362.805 11712.41755 13786.4436 12774.61639 14655.88546 12530.00113 12026.63874 18717.54063 11105.96998 1.203209177 1.054605547 1.241354301 1.150247697 1.319640291 1.128222132 1.082898546 1.685358475 1 13.43904778 3.854546848 5.012046268 1.218711363 1.122825393 0.044405573 0.188206575 0.714286074 27.04631206 0.044419986 0.082272093 7153.965611 -3.854546848 -0.09588597 ESHT(ph)PVS(ph)IQEEIVGDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESHTPVSIQEEIVGDFK 17 0 Q12830-4;Q12830;E7ETD6;E9PE19;A0A2R8Y7Q1;A0A0A0MR81;F5H176 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 2 ES(0.461)HT(0.555)PVS(0.983)IQEEIVGDFK 117.31 0.00098307 0 43876 33683 37881 39304 46899 35815 57788 47640 68463 TRUE FALSE 41129.87948 36176.92437 38779.55521 40312.60718 43215.74172 46154.20909 49123.22588 53587.95887 57036.08301 0.721120338 0.634281361 0.679912665 0.706791299 0.757691262 0.809210708 0.861265769 0.939544864 1 15.79958729 1.798020729 0.684583139 1.001548364 0.661855064 0.960601475 0.023014166 0.108376338 0.101383911 0.019960156 0.010343065 62.8088337 -1.798020729 -0.3396933 ESHT(ph)PVSIQEEIVGDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESHTPVSIQEEIVGDFK 17 0 Q12830-4;Q12830;E7ETD6;E9PE19;A0A2R8Y7Q1;A0A0A0MR81;F5H176 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 ES(0.225)HT(0.773)PVS(0.002)IQEEIVGDFK;ES(0.117)HT(0.877)PVS(0.005)IQEEIVGDFK 164.53 9.50E-09 157327000 278280 221770 246900 231210 288040 200170 340400 261930 340730 TRUE FALSE 260862.9515 238190.0816 252756.5846 237143.24 265418.5003 257955.8295 289360.1801 294632.5371 283859.9618 0.918984664 0.839111229 0.890427037 0.835423349 0.935033242 0.908743269 1.01937652 1.037950316 1 18.11481985 1.928590521 1.527331452 1.028405509 0.872021224 0.785104961 0.03237103 0.148907663 0.647325818 0.020075013 0.009112812 84.83801945 -1.928590521 -0.156384285 ESIESEIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ESIESEIRR 9 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;; 196.32 4.78E-05 8595320000 4771140 5616900 5359890 5232050 6126850 4359690 5909580 5072990 7327390 FALSE TRUE 4472522.864 6032781.12 5487029.122 5366313.261 5645671.916 5618261.729 5023493.341 5706363.969 6104401.272 0.732671832 0.988267457 0.898864422 0.879089205 0.924852686 0.920362453 0.822929738 0.93479503 1 22.54141837 0.992386915 24.46021496 1.000000009 0.892326878 0.235957636 0.067964197 344.937668 1108260.841 0.060619666 0.015154916 9.826229774 -0.992386915 -0.107673131 ESIGNVQVLLEYHIAYLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESIGNVQVLLEYHIAYLK 18 0 B4DXZ6;P51114;P51114-3;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 ; 125.12 3.04E-05 25832000 41848 42723 43449 47902 51180 40702 46011 42033 38653 FALSE TRUE 39228.80838 45886.25537 44479.6308 49131.24642 47160.52925 52452.00666 39112.0777 47280.91258 32201.56459 1.218226781 1.424969748 1.381287877 1.525740971 1.464541548 1.62886516 1.214601781 1.468279979 1 14.97484317 -0.947886737 7.882630787 1.000000003 1.413011087 0.517098477 0.126257055 5.07E-09 6.43E-10 0.113375058 0.026722757 0.112749146 0.947886737 0.413011084 ESILQRPLSLPSLHVFGDTDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESILQRPLSLPSLHVFGDTDK 21 1 Q8WZ82 Q8WZ82 OVCA2 Ovarian cancer-associated gene 2 protein 0 104.44 0.00024891 48027000 154880 176760 177720 172230 182560 147580 223120 179980 193050 FALSE TRUE 145186.3373 189847.4943 181935.6023 176649.7134 168222.474 190183.9502 189665.2273 202450.8992 160828.7078 0.90273894 1.180432877 1.131238351 1.098371775 1.045972925 1.182524891 1.179299578 1.25879827 1 17.29516542 2.218735151 24.92821144 1.171527141 1.09589318 0.118399132 0.097423564 481.9887654 606040.9582 0.033767498 0.024974382 165.4760522 -2.218735151 -0.075633961 ESIWLPFMETELHCDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESIWLPFMETELHCDEK 17 0 O75884;O75884-2 O75884 RBBP9 Putative hydrolase RBBP9 0 ; 215.8 5.50E-15 107804000 213404 170251 188880 185653 204016 175014 249920 163465 323020 FALSE TRUE 200047.4246 182856.5612 193360.3228 190417.1703 187993.4063 225537.7007 212446.8161 183873.9651 269105.8752 0.743378139 0.679496726 0.718528804 0.707592022 0.698585292 0.838100248 0.789454396 0.683277409 1 18.03781436 -5 0.195089593 2.190509865 0.685909789 0.735990911 0.050054779 68.32473466 0.672965123 31.5984463 0.123302307 1.00E-05 5 -1.504600075 ESKDPADETEAD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESKDPADETEAD 12 1 P16949 P16949 STMN1 Stathmin 0 91.313 0.068243 183450000 1162600 775460 899190 921090 1012000 685380 1063600 876010 1110500 FALSE TRUE 1089834.941 832875.8653 920519.2114 944726.7288 932521.6022 883238.0798 904123.054 985381.7768 925150.3759 1.178008429 0.900259987 0.99499415 1.021160185 1.007967598 0.954696774 0.977271455 1.065104444 1 19.81932836 1.255633537 24.74764533 1.032552258 0.991122444 0 0.073045915 591.3844929 857234.5235 0.044608068 0.016201593 18.01496974 -1.255633537 -0.041429814 ESKEETPGTEWEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESKEETPGTEWEK 13 1 P09497-2;P09497;D6RJD1 P09497-2 CLTB Clathrin light chain B 0 74.257 0.031557 207640000 105220 74063 83876 86037 95174 60552 104590 76020 130850 FALSE TRUE 98634.46802 79546.70158 85865.57833 88244.85508 87699.41795 78032.37942 88907.70047 85511.26434 109010.2897 0.904817961 0.729717367 0.787683241 0.809509408 0.80450587 0.715825815 0.815589984 0.784432961 1 16.73410479 -0.161434227 1.418416863 1.000524843 0.786569661 0.609009901 0.051558544 23.04744944 26.77514133 0.108697672 0.01290759 0.689550016 0.161434227 -0.213955182 ESKGS(ph)PVFLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ESKGSPVFLPR 11 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 ES(0.03)KGS(0.97)PVFLPR;ES(0.3)KGS(0.7)PVFLPR;ES(0.061)KGS(0.939)PVFLPR;ES(0.002)KGS(0.998)PVFLPR;ES(0.015)KGS(0.985)PVFLPR;ES(0.001)KGS(0.999)PVFLPR 143.93 2.24E-05 6365760000 9714360 8484570 8911560 8111880 10532250 7916600 12699450 9428230 15874970 TRUE FALSE 9106355.548 9112776.391 9122946.412 8320044.574 9705089.57 10201993.9 10795285.37 10605365.27 13225334.95 0.688553869 0.689039365 0.689808345 0.629098968 0.733825616 0.771397771 0.816257993 0.801897669 1 23.65680093 1.05933719 0.529780372 1.002774214 0.671672587 0.91535223 0.029968894 0.244263241 0.174009365 0.033275355 0.016015252 11.46402674 -1.05933719 -0.331101627 ESLATSEMSAFHQPGPCEDPSCLTHGDYYDNLSLAS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESLATSEMSAFHQPGPCEDPSCLTHGDYYDNLSLASPK 38 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 ESLATSEMSAFHQPGPCEDPSCLTHGDYYDNLSLAS(1)PK 214.11 1.68E-32 216560000 63360 63096 83300 112620 119460 64676 68175 43114 45842 TRUE FALSE 59394.4107 67767.69349 85275.91534 115510.0199 110078.0935 83346.91127 57952.79166 48496.87781 38190.67405 1.555207186 1.774456596 2.232898933 3.02456091 2.882329161 2.182389113 1.517459251 1.269861793 1 15.22093276 1.608288569 2.656826463 1.165604263 2.269328047 0.552556735 0.440074663 0.212521305 3.44001639 0.337613895 0.132424147 40.57780667 -1.608288569 1.103723785 ESLCDS(ph)PHQNLSRPLLENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 184.3 1.52E-14 555930000 310980 256800 293580 264840 323220 248200 374400 260970 444860 TRUE FALSE 291516.3169 275813.7392 300543.8562 271636.2428 297835.605 319851.3108 318262.1958 293552.679 370609.9921 0.786585152 0.744215604 0.810943749 0.732943657 0.803636198 0.863040171 0.858752334 0.792079775 1 18.49954225 -4.999999996 0.134167181 1.708374821 0.717063303 0.772153304 0.036039822 62.88760613 0.52636513 11.83582385 0.241481983 1.00E-05 4.999999996 -0.991311519 ESLIDGIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ESLIDGIKR 9 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;; 119.68 0.0012633 2026120000 3167190 3077250 3134580 3095190 3591030 2363460 3875320 3015030 4498160 FALSE TRUE 2968961.231 3305092.792 3208933.718 3174617.816 3309004.989 3045752.534 3294251.743 3391463.132 3747388.037 0.792274833 0.881972392 0.8563121 0.847154814 0.883016372 0.812766787 0.879079431 0.905020537 1 21.83745394 0.892134032 1.641356503 0.99948431 0.852482535 0.740385071 0.028653971 0.239615284 1.280167112 0.024420745 0.007036745 7.800708187 -0.892134032 -0.147001775 ESLKEEDES(ph)DDDNM ddPTM_SK-BR-3_Pertuzumab_2h_R1 22 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 235.75 4.59E-17 61690980000 60610970 37661360 41720190 38975310 45255610 28922440 51856630 36505990 51593610 TRUE FALSE 56817437.58 40449846.28 42709812.61 39975482.44 41701416.94 37271878.91 44081209.74 41063843.21 42982303.18 1.321879782 0.941081405 0.993660401 0.930045146 0.970199683 0.867144758 1.025566489 0.955366283 1 25.35723946 4.740490258 24.99507029 0.961094545 1.321879905 0.872083326 0.043509481 52.562573 680804.2943 0.009380903 0.061122638 55016.15791 -4.740490258 0.36078536 ESLKELSLAGNELGDEGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESLKELSLAGNELGDEGAR 19 1 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 166.61 1.79E-11 164780000 105330 140400 119270 133610 182280 95345 161080 121800 337670 FALSE TRUE 98737.58332 150795.3621 122099.1407 137038.6588 167964.4641 122869.5537 136927.5494 137006.9981 281310.6956 0.350991217 0.536045605 0.43403661 0.487143436 0.59707813 0.436775265 0.486748465 0.487030889 1 18.10180488 -4.65891155 0.464256885 9.999999684 0.474998196 0.868073999 0.064145362 344.185738 2.636603664 3167.445169 0.029723276 2.19E-05 4.65891155 -9.525001488 ESLLGDMEWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESLLGDMEWR 10 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4;Q63HN8-5 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 ; 134.66 0.00038345 93152000 187458 320950 268390 288620 319430 227479 283960 285770 239660 FALSE TRUE 175725.3384 344713.4719 274756.3375 296026.4778 294343.2563 293148.4945 241382.8342 321449.0136 199659.1977 0.880126437 1.726509351 1.376126623 1.482658857 1.474228383 1.468244377 1.208974277 1.609988506 1 17.60718001 -1.694802535 2.85514107 0.943425396 1.421393552 0.229221676 0.230348723 43825428.61 34870677.83 17705692.28 0.050440287 0.020192843 1.694802535 0.477968156 ESLLVSVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ESLLVSVQR 9 0 J3QRZ1;A6NIZ0;Q9GZM8-3;Q9GZM8;Q9GZM8-2 J3QRZ1 NDEL1 Nuclear distribution protein nudE-like 1 0 ;;; 107.15 0.0028196 1414800000 364331 1819530 1249265 1368350 1571050 1581230 929517 1249511 849960 FALSE TRUE 341528.1731 1954249.894 1278898.156 1403464.178 1447666.07 2037705.432 790144.5551 1405515.199 708096.185 0.4823189 2.759865024 1.806107959 1.982024769 2.04444834 2.877724065 1.115871787 1.984921298 1 19.43358582 0.937301127 1.073140177 1.040331229 2.019488971 0.113531455 0.705401988 1.04683819 2.480974284 0.59828956 0.19273047 8.655678705 -0.937301127 0.979157742 ESLPPAAEPS(ph)PVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ESLPPAAEPSPVSK 14 0 Q9NWT1 Q9NWT1 PAK1IP1 p21-activated protein kinase-interacting protein 1 1 ESLPPAAEPS(1)PVSK;ESLPPAAEPS(1)PVSK;ESLPPAAEPS(1)PVSK 171.15 3.21E-06 458380000 1146410 880800 1048740 972500 1002470 836970 1188570 846110 1041180 TRUE FALSE 1074658.245 946015.3485 1073616.608 997455.9964 923740.05 1078589.652 1010354.963 951748.696 867400.3317 1.238941473 1.090632911 1.237740601 1.149937301 1.064952383 1.243473875 1.164808135 1.097242716 1 19.72633847 0.969626123 2.925518839 1.000607284 1.168171197 0.458860292 0.060151152 0.229478553 4.768670582 0.052755708 0.013927541 9.324512237 -0.969626123 0.167563913 ESNCYDPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ESNCYDPER 9 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 148.5 0.00020907 2053572000 2836080 3605750 3185430 3413180 3826290 2961260 4254950 3372400 3866330 FALSE TRUE 2658574.815 3872723.482 3260989.904 3500767.977 3525788.618 3816127.69 3616959.749 3793451.564 3221014.546 0.825384294 1.20233033 1.012410797 1.086852583 1.09462052 1.184759533 1.122925618 1.177719476 1 21.61908375 2.716216497 2.462538718 1.132210506 1.054373834 0.121809251 0.105177533 0.667979262 8.013977751 0.03386655 0.033255732 520.2552806 -2.716216497 -0.077836672 ESNEEEQVWHFLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ESNEEEQVWHFLGK 14 0 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;Q9H2U2-4;H0YAK2 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 ;;;; 216.54 6.09E-12 850722000 833898 667714 688024 649852 814116 625037 759587 716742 712905 FALSE TRUE 781705.8127 717152.2393 704344.2542 666528.3025 750178.6133 805475.0353 645693.981 806228.8164 593916.55 1.316187961 1.207496641 1.185931347 1.122259184 1.26310441 1.356209109 1.08717964 1.35747828 1 19.17990071 -1.477712014 3.255375056 0.995585983 1.222373612 0.386668857 0.092180387 2828554.653 1988250.58 83409.52399 0.019588302 0.033288022 1.477712014 0.22678763 ESNRLS(ph)APSYLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESNRLSAPSYLAR 13 1 H0YJH0;Q9H4B6 H0YJH0 SAV1 Protein salvador homolog 1 1 ESNRLS(1)APSYLAR 152.89 2.75E-05 337350000 199130 230920 201480 251970 300590 174990 260160 225580 299220 TRUE FALSE 186666.8088 248017.5571 206259.2007 258435.9768 276982.8739 225506.7723 221151.4232 253744.1596 249278.249 0.748829108 0.994942632 0.827425584 1.036736971 1.11113936 0.904638785 0.887166947 1.017915364 1 17.92739748 4.74515652 24.34588912 0.956906202 0.74882897 0.40860358 0.082695871 599.5804458 2213002.755 0.020026297 0.190648269 55610.46417 -4.74515652 -0.208077232 ESNYFGLS(ph)PEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ESNYFGLSPEER 12 0 Q01804-5;Q01804-3;Q01804 Q01804-5 OTUD4 OTU domain-containing protein 4 1 ESNYFGLS(1)PEER;ESNYFGLS(1)PEER;ESNYFGLS(1)PEER 201.72 1.52E-07 609824000 795110 783590 819570 855110 970200 734460 950560 760990 987240 TRUE FALSE 745345.4844 841607.8189 839010.5874 877053.5703 894004.4056 946486.679 808032.3526 856001.2766 822463.2662 0.906235591 1.023277092 1.020119222 1.066374155 1.086983994 1.150795079 0.982454033 1.040777518 1 19.64959172 5.844383334 0.949569683 1.052649894 1.39E-17 0.468420073 0.047309155 12.74802645 1.803695271 0.014268402 22.4269276 698848.9767 -5.844383334 -1.052649894 ESPFSTSAS(ph)PLLSGSQHFDVPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ESPFSTSASPLLSGSQHFDVPPR 23 0 O14980 O14980 XPO1 Exportin-1 1 ESPFS(0.006)T(0.006)S(0.005)AS(0.981)PLLS(0.001)GSQHFDVPPR;ES(0.012)PFS(0.129)T(0.157)S(0.047)AS(0.655)PLLSGSQHFDVPPR;ES(0.002)PFS(0.03)T(0.089)S(0.071)AS(0.806)PLLSGSQHFDVPPR 175.86 6.61E-13 460137000 273941 341360 359164 387553 365888 332714 442004 346422 340184 TRUE FALSE 256795.5218 366634.6496 367683.5397 397498.2661 337152.6324 428763.1306 375729.6036 389673.5493 283405.0927 0.906107647 1.293676998 1.297378026 1.402579828 1.189649167 1.512898468 1.325768708 1.374970173 1 18.11250616 4.743883362 4.112508122 1.321152298 0.869144805 0.445866288 0.136360501 0.185162379 6.829301376 0.02813945 0.249821339 55447.67772 -4.743883362 -0.452007493 ESPFSTSAS(ph)PLLSGSQHFDVPPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESPFSTSASPLLSGSQHFDVPPRR 24 1 O14980 O14980 XPO1 Exportin-1 1 ESPFSTS(0.001)AS(0.999)PLLSGSQHFDVPPRR 128.89 3.50E-05 40890000 25237 28588 27404 38203 34555 19849 36206 22766 44529 TRUE FALSE 23657.46122 30704.68527 28054.03582 39183.35366 31841.18969 25579.08408 30777.24642 25608.38521 37096.82223 0.637722042 0.827690444 0.756238247 1.056245557 0.858326611 0.689522243 0.829646438 0.690312099 1 15.17900799 4.738999727 21.78983284 0.825618022 0.637721717 0.214533188 0.118477292 9.855663078 487955.2171 0.026339663 0.154849195 54827.66202 -4.738999727 -0.187896304 ESPGAAAT(ph)SSSGPQAQQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESPGAAATSSSGPQAQQHR 19 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 ES(0.269)PGAAAT(0.583)S(0.109)S(0.019)S(0.019)GPQAQQHR 344.71 1.02E-75 278930000 131780 96014 114730 110230 92690 120820 151280 103940 116290 TRUE FALSE 123532.125 103122.9765 117451.4498 113058.6884 85410.50129 155698.7727 128596.9684 116917.1378 96880.44774 1.275098618 1.064435383 1.212333887 1.166991803 0.881607211 1.607122761 1.327377932 1.206818719 1 16.56391791 2.245111507 24.99999033 1.324711744 1.127213705 0.155669295 0.180758024 220.1195078 840038.4113 0.057917083 0.04740022 175.8375025 -2.245111507 -0.19749804 ESPRPLQLPGAEGPAIS(ph)DGEEGGGEPGAGGGAAGAAGAGR ddPTM_SK-BR-3_Pertuzumab_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 336.52 2.09E-130 15105670000 1757035 1920978 2009422 1780254 1934152 1666250 2208370 1765080 1821537 TRUE FALSE 1647065.316 2063209.21 2057086.439 1825938.332 1782251.504 2147269.326 1877245.42 1985454.123 1517510.707 1.08537311 1.359601089 1.355566342 1.203245765 1.174457284 1.414994514 1.237055799 1.308362514 1 20.53327527 -1.072919968 4.029098319 0.999951344 1.282064051 0.411735484 0.099040566 0.966300482 18124488.65 2007.421602 0.022343784 0.084543463 1.072919968 0.282112707 ESPRPLQLPGAEGPAIS(ph)DGEEGGGEPGAGGGAAGAAGAGRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ESPRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGRR 41 2 Q6PKG0;A0A0B4J210 Q6PKG0 LARP1 La-related protein 1 1 ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGRR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGRR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGRR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGRR 252.34 8.54E-67 1190200000 223054 410613 330074 342312 423644 265873 413223 299143 952600 TRUE FALSE 209093.4483 441015.2138 337903.5112 351096.3055 390372.7091 342626.219 351264.0473 336491.662 793604.906 0.263472978 0.5557113 0.425783042 0.442406924 0.491898054 0.431733998 0.442618291 0.424004009 1 19.59806142 -1.549235545 2.862546517 1.028355714 0.44627279 0.853353931 0.07350709 18821707.17 19851704.59 4104828.765 0.017144157 0.028233483 1.549235545 -0.582082924 ESQEEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESQEEPR 7 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;H0YD62;H0YF37 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 ; 113.41 0.014274 172541000 773750 890170 869140 914430 896250 711480 827670 716390 672140 FALSE TRUE 725322.3687 956079.113 889756.4112 937895.8219 825862.1403 916872.7261 703568.5672 805832.8685 559955.4918 1.295321466 1.707419834 1.588977025 1.674947091 1.474871043 1.637402864 1.256472305 1.439101643 1 19.09495263 0.981939629 0.692816419 1.0069465 1.596822404 0.587888111 0.141271529 0.466869874 0.51564179 0.125366223 0.049776503 9.592672745 -0.981939629 0.589875904 ESQLAHIKDEPPPLS(ph)PAPLT(ph)PATPSSLDPFFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESQLAHIKDEPPPLSPAPLTPATPSSLDPFFSR 33 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 2 ES(0.016)QLAHIKDEPPPLS(0.984)PAPLT(0.997)PAT(0.002)PSSLDPFFSR 79.29 0.022787 90339000 57057 62029 55557 71114 81701 36271 65109 44997 85699 TRUE FALSE 53485.90422 66621.6917 56874.83828 72938.90564 75284.53303 46741.84889 55346.50989 50614.9745 71395.28326 0.74915179 0.933138558 0.796618988 1.021620789 1.054474884 0.654690993 0.775212414 0.708940033 1 16.12354115 2.227647897 24.99999514 0.762993379 0.903450398 0.187845401 0.126424213 311.7306169 714139.7732 0.043937915 0.032764547 168.9070967 -2.227647897 0.140457019 ESQLAHIKDEPPPLS(ph)PAPLTPATPSSLDPFFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ESQLAHIKDEPPPLSPAPLTPATPSSLDPFFSR 33 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 ESQLAHIKDEPPPLS(1)PAPLTPATPSSLDPFFSR;ES(0.004)QLAHIKDEPPPLS(0.996)PAPLTPATPSSLDPFFSR;ES(0.059)QLAHIKDEPPPLS(0.941)PAPLTPATPSSLDPFFSR;ES(0.038)QLAHIKDEPPPLS(0.962)PAPLTPATPSSLDPFFSR 224 2.07E-36 2126923000 883267 1247892 1207816 1512773 1855066 638421 909847 647854 1385588 TRUE FALSE 827984.8951 1340287.222 1236465.966 1551593.316 1709376.599 822722.7788 773423.889 728739.998 1154324.412 0.7172896 1.161100994 1.071159852 1.344157068 1.480845924 0.712730988 0.670022986 0.631312992 1 20.13861731 2.205442439 24.97991182 0.719544119 1.152936355 0.451358855 0.218472293 157.1508022 118532.607 0.078719291 0.058141701 160.4879536 -2.205442439 0.433392236 ESQNTAEIISPPS(ph)PDRPPHSQTSGSCYYHVISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ESQNTAEIISPPSPDRPPHSQTSGSCYYHVISK 33 1 Q03164-2;Q03164;Q03164-3 Q03164-2 KMT2A Histone-lysine N-methyltransferase 2A;MLL cleavage product N320;MLL cleavage product C180 1 ESQNTAEIIS(0.001)PPS(0.999)PDRPPHSQTSGSCYYHVISK;ESQNTAEIIS(0.001)PPS(0.999)PDRPPHSQTSGSCYYHVISK;ESQNTAEIIS(0.001)PPS(0.999)PDRPPHSQTSGSCYYHVISK 187.96 3.19E-20 736620000 359945 538550 540500 529570 447540 406927 598500 373499 460060 TRUE FALSE 337416.685 578424.8024 553320.9152 543159.6628 412392.0137 524400.219 508760.4812 420131.1723 383273.0139 0.880355968 1.509171743 1.443673035 1.417161248 1.075974563 1.368215867 1.32741013 1.09616685 1 18.5480129 1.136847459 3.494532919 1.004583139 1.328076049 0.206833994 0.1886312 0.286669399 6.208711659 0.168894527 0.044664318 13.70400344 -1.136847459 0.32349291 ESQQQHGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESQQQHGLR 9 0 Q9UHB9;Q9UHB9-4;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ; 145.25 9.76E-05 292080000 183039 254796 195930 229699 262716 176869 226384 214970 344781 FALSE TRUE 171582.9157 273661.361 200577.5521 235593.4652 242083.3451 227928.2091 192439.8208 241809.4777 287234.8237 0.597361119 0.952744369 0.698305134 0.820212056 0.842806391 0.793525681 0.66997385 0.841852929 1 18.13187114 0.983512975 23.84196652 1.000000008 0.777883195 0.355722293 0.098541128 617.1027655 892397.7157 0.087822309 0.021955577 9.627487767 -0.983512975 -0.222116813 ESQSHPGDFVLSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ESQSHPGDFVLSVR 14 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ;; 132.44 5.04E-05 1253460000 437360 681190 575330 622020 668760 539290 671560 599310 710080 FALSE TRUE 409986.4183 731626.0164 588977.0993 637982.0863 616238.2872 694974.2684 570865.8125 674135.1727 591563.0607 0.693056152 1.236767582 0.995628596 1.078468432 1.041711912 1.174810117 0.965012609 1.139582941 1 19.17417244 4.75380071 24.99999999 1.077979249 0.693055874 0.669606436 0.085195459 1637.431239 2686013.279 0.0187388 0.441651695 56728.42296 -4.75380071 -0.384923375 ESRPGLVTVTSSQS(ph)TPAKAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESRPGLVTVTSSQSTPAKAPR 21 2 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 1 ESRPGLVTVTSS(0.005)QS(0.578)T(0.417)PAKAPR 92.833 0.00094427 225420000 334720 289130 333050 296860 369520 253870 430470 332470 442100 TRUE FALSE 313770.4727 310537.486 340950.1033 304477.9302 340499.3898 327158.1478 365925.0198 373979.6114 368310.6539 0.851917992 0.843140112 0.925713388 0.826687816 0.924489656 0.888266859 0.993522766 1.015391782 1 18.4905636 1.76332399 1.900355661 1.013413635 0.873907021 0.775869062 0.032032202 0.141178374 1.012470645 0.020997228 0.008781337 57.98611194 -1.76332399 -0.139506614 ESRPGLVTVTSSQST(ph)PAKAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESRPGLVTVTSSQSTPAKAPR 21 2 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 1 ESRPGLVTVTSSQS(0.286)T(0.713)PAKAPR;ESRPGLVTVTSS(0.001)QS(0.067)T(0.932)PAKAPR 122.51 0.0013323 1718940000 802140 673580 766200 744080 866120 499830 974320 678410 1068070 TRUE FALSE 751935.4893 723452.5641 784374.6258 763174.3525 798098.429 644122.8069 828229.7611 763110.9819 889802.217 0.845059132 0.813048732 0.881515702 0.857689875 0.896939133 0.723894361 0.930802088 0.857618656 1 19.76312517 0.563610521 1.005091351 0.99967735 0.845379799 0.432667816 0.054379682 1.305976422 2.003397675 0.047122097 0.014991167 3.66109098 -0.563610521 -0.154297551 ESRPS(ph)EEREWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESRPSEEREWDR 12 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 ES(0.271)RPS(0.729)EEREWDR 67.902 0.042615 147360000 103940 111830 113610 125270 117480 125730 124880 110810 104210 TRUE FALSE 97434.58094 120110.0096 116304.8829 128484.6403 108253.5947 162026.2099 106155.4033 124644.8724 86816.67778 1.122302574 1.383490046 1.339660602 1.479953433 1.246921645 1.866302813 1.222753577 1.435724974 1 16.4056846 -1.16722568 4.367774832 0.999910091 1.390110949 0.270149318 0.199925839 0.000154494 2.95E-05 0.17085255 0.040261087 0.068041569 1.16722568 0.390200858 ESRPSEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESRPSEER 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 143.7 0.00054464 275020000 232840 287630 295640 275010 311300 276660 328880 257080 281840 FALSE TRUE 218266.96 308926.4245 302652.7204 282067.2222 286851.7537 356527.2508 279567.4972 289177.0039 234799.0832 0.929590342 1.315705412 1.288985954 1.201313132 1.221690263 1.518435446 1.190666903 1.231593411 1 17.84106725 0.644349832 2.057412791 1.000202232 1.258730992 0.200274883 0.144910181 2.797850566 14.35316801 0.126219728 0.034645893 4.409098815 -0.644349832 0.25852876 ESRPSEEREWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESRPSEEREWDR 12 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 114.7 0.00057868 921620000 404960 512970 508420 492790 461160 364080 459450 509140 604710 FALSE TRUE 379614.2765 550950.8325 520479.9625 505435.8257 424942.3538 469183.9857 390559.7378 572707.2498 503779.9944 0.75353186 1.093633806 1.033149328 1.003286814 0.843507798 0.931327148 0.77525853 1.136820152 1 18.94243431 2.775041559 21.83115073 0.910882111 1.001730941 0 0.130545655 294.6825081 176343.9255 0.037205757 0.039459635 595.7191477 -2.775041559 0.09084883 ESRS(ph)PQQSAALPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ESRSPQQSAALPR 13 1 A0A0A6YYG7;Q6IBW4-2;Q6IBW4;Q6IBW4-4;E5RJN3 A0A0A6YYG7 NCAPH2 Condensin-2 complex subunit H2 1 ES(0.086)RS(0.914)PQQSAALPR;ES(0.004)RS(0.996)PQQSAALPR;ES(0.057)RS(0.943)PQQSAALPR;ES(0.347)RS(0.653)PQQSAALPR 127.11 0.00010944 1536500000 928050 1971664 1639286 1562012 2023555 1951421 1606115 1666624 1738650 TRUE FALSE 869965.0071 2117648.054 1678170.638 1602095.872 1864633.153 2514764.564 1365292.966 1874705.675 1448458.083 0.600614555 1.462001613 1.158591096 1.10606989 1.287322826 1.736166613 0.942583691 1.294276788 1 20.4660865 0.099228927 1.216781258 0.999596064 1.223718411 0.03404417 0.300917593 29.30863032 35.87642289 0.305514713 0.078262591 1.256692222 -0.099228927 0.224122348 ESS(ph)KVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESSKVPR 7 1 E5RJ29;Q9NYI0-2;Q9NYI0 E5RJ29 PSD3 PH and SEC7 domain-containing protein 3 1 ES(0.105)S(0.895)KVPR 57.598 0.069412 111080000 298440 136100 157510 141780 185820 113030 205220 124850 205670 TRUE FALSE 279761.1731 146176.9856 161246.2116 145418.3148 171226.4468 145659.9261 174449.1662 140437.7973 171342.3483 1.632761404 0.853128179 0.941076232 0.848700372 0.999323567 0.850110481 1.018132224 0.819632734 1 17.38652224 4.741685575 24.99921033 0.917303423 1.632761666 0.906301476 0.072400844 73.33652366 586653.4765 0.014960503 0.106521948 55167.7885 -4.741685575 0.715458243 ESS(ph)PEKEAEEGCPEKESEEGCPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESSPEKEAEEGCPEKESEEGCPK 23 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 ES(0.082)S(0.918)PEKEAEEGCPEKESEEGCPK;ES(0.024)S(0.976)PEKEAEEGCPEKESEEGCPK 279.02 3.83E-52 598380000 1146940 273263 456150 481120 534600 357350 729910 335514 695020 TRUE FALSE 1075155.073 293495.6768 466970.0934 493466.3537 492614.6725 460511.1439 620466.7717 377403.6615 579016.672 1.856863757 0.506886401 0.806488165 0.852248955 0.850778045 0.795333133 1.071587057 0.651801027 1 19.14324536 4.749022465 24.98945119 0.812164707 1.856864343 0.810381445 0.158081122 666.1855931 1591237.55 0.038945032 0.557886208 56107.69984 -4.749022465 1.044699636 ESS(ph)PIPSPTSDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESSPIPSPTSDRK 13 1 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 ES(0.144)S(0.856)PIPSPTSDRK 57.788 0.06855 1171900000 365890 262630 293410 294080 340720 220810 363450 253520 328570 TRUE FALSE 342989.598 282075.3985 300369.8238 301626.5907 313961.2256 284554.2624 308954.0466 285172.5301 273729.5444 1.253023669 1.030489417 1.097323362 1.101914634 1.146976028 1.039545304 1.128683597 1.041803985 1 18.06239163 -0.139245423 0.012542434 1.98E-05 2.101315708 0.314319046 0.060426611 3479.30854 12.36994054 1086.819687 985.4614494 0.725695745 0.139245423 2.101295928 ESS(ph)PKKEETVASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESSPKKEETVASK 13 2 J3QQY0 J3QQY0 MSL1 1 ES(0.11)S(0.89)PKKEETVASK;ES(0.147)S(0.852)PKKEETVASK 114.96 0.00036607 1070640000 2564750 623980 1233080 1090070 1042160 724870 1534480 835860 1133700 TRUE FALSE 2404226.876 670180.1285 1262329.24 1118043.042 960312.9575 934128.2017 1304398.969 940218.961 944478.146 2.54556115 0.709577168 1.336536208 1.183768038 1.016765673 0.989041626 1.381079038 0.995490436 1 19.84915789 4.748185678 24.99900271 1.100068567 2.54556192 0.851188981 0.192812462 490.7019545 1274465.581 0.044957383 0.589670176 55999.69712 -4.748185678 1.445493353 ESS(ph)PLS(ph)SRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.617)S(0.384)RK;ESS(1)PLS(0.612)S(0.388)RK;ESS(0.999)PLS(0.62)S(0.38)RK;ESS(0.994)PLS(0.612)S(0.393)RK 86.882 0.0085896 6891220000 2140450 3363170 3157830 3227060 3281810 2699010 3052210 2526370 2751410 TRUE FALSE 2006483.055 3612182.606 3232735.219 3309871.823 3024069.881 3478170.372 2594559.446 2841792.856 2292181.896 0.875359437 1.575870838 1.410331014 1.443983058 1.319297516 1.517405917 1.131916909 1.239776329 1 21.1282901 1.292001717 1.255068039 1.028852204 1.388914485 0.205609047 0.200401453 0.51701311 1.59354468 0.168136017 0.054144343 19.58852416 -1.292001717 0.360062281 ESSAAQAGSHATHPGTSVLEGGAAGSMS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESSAAQAGSHATHPGTSVLEGGAAGSMSPSR 31 0 Q5SYE7-2;Q5SYE7 Q5SYE7-2 NHSL1 NHS-like protein 1 1 ESSAAQAGSHATHPGTSVLEGGAAGS(0.23)MS(0.58)PS(0.189)R;ESSAAQAGSHATHPGTSVLEGGAAGS(0.012)MS(0.823)PS(0.165)R 120.19 2.12E-05 338950000 164350 95285 134588 119237 119597 97636 136686 100308 117885 TRUE FALSE 154063.6269 102340.0005 137780.4909 122296.8233 110204.3341 125821.9282 116191.2032 112831.6746 98209.23193 1.568728559 1.042060899 1.402928098 1.245268096 1.122138234 1.281161921 1.183098584 1.148890714 1 16.58357103 -5 0.070006361 0.141445561 1.546883487 0.348517768 0.135992711 387.367823 1.953372753 53.34115928 6.660071654 1.00E-05 5 1.405437926 ESSANNSVS(ph)PSESLR ddPTM_SK-BR-3_Pertuzumab_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;ESSANNS(0.001)VS(0.998)PSESLR;ESSANNS(0.003)VS(0.997)PSESLR;ESSANNSVS(1)PSESLR;ESSANNS(0.015)VS(0.969)PS(0.015)ESLR;ESSANNS(0.027)VS(0.973)PSESLR 421.46 4.09E-153 3747720000 3880820 3954170 4162470 3992310 4796890 4045840 4767660 4005760 5143220 TRUE FALSE 3637926.404 4246940.861 4261205.754 4094759.434 4420161.609 5213808.329 4052793.644 4505887.954 4284783.356 0.849033919 0.991168166 0.994497364 0.955651452 1.031595122 1.216819591 0.945857307 1.051602282 1 22.03079083 6.14380541 0.623106503 1.037477548 7.93E-17 0.356595264 0.074828353 19.81631618 1.476570321 0.029850351 21.7335013 1392532.724 -6.14380541 -1.037477548 ESSIIAPAPAEDVDT(ph)PPR ddPTM_SK-BR-3_Pertuzumab_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 272.21 6.29E-38 542200000 761810 708870 773130 699160 735500 720860 824450 682720 694870 TRUE FALSE 714129.672 761355.4724 791469.0087 717101.6293 677736.7969 928960.5798 700831.3763 767959.0949 578891.708 1.233615307 1.315194987 1.367214278 1.238749181 1.170748842 1.604722554 1.210643315 1.326602341 1 19.14293397 0.047101846 1.510104613 0.999759131 1.314859255 0.390942273 0.120665523 19.34813072 29.08688847 0.116736542 0.030021216 1.114555877 -0.047101846 0.315100124 ESSPSHPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESSPSHPTR 9 0 Q13144;A0A3B3IUB1;A0A3B3ITG6;A0A3B3IRP4;A0A3B3ISX3;A0A3B3ISM8;A0A3B3IUF2;A0A3B3ITQ2;A0A3B3ISV1;A0A3B3IS56;A0A3B3ISS1;A0A3B3ISI2;A0A3B3IST9;A0A3B3ITK8 Q13144 EIF2B5 Translation initiation factor eIF-2B subunit epsilon 0 ; 66.435 0.063739 259166000 94455 146641 128029 133250 136444 109406 143012 129132 162758 FALSE TRUE 88543.23016 157498.4522 131065.9083 136669.4206 125728.2386 140989.7361 121568.6783 145254.4145 135592.6383 0.653009125 1.161556071 0.966615223 1.007941303 0.92724974 1.039803767 0.89657285 1.071255905 1 17.04891933 4.755311388 24.77696951 1.005066797 0.653008813 0.694718359 0.074098622 1763.843624 2608947.834 0.017546439 0.483753485 56926.09429 -4.755311388 -0.352057984 ESSSCGKDT(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ESSSCGKDTPSK 12 1 O43148;O43148-2;K7EPP5 O43148 RNMT mRNA cap guanine-N7 methyltransferase 1 ESS(0.001)S(0.004)CGKDT(0.995)PSK;ESS(0.001)SCGKDT(0.999)PSK;ESSSCGKDT(0.999)PS(0.001)K;ESSSCGKDT(0.999)PS(0.001)K;ES(0.001)S(0.001)S(0.001)CGKDT(0.996)PS(0.001)K;ESSSCGKDT(0.999)PS(0.001)K 193.98 1.35E-05 2300466000 5274650 2339587 3530340 2998830 3222970 2451400 4595520 2842369 4110190 TRUE FALSE 4944519.072 2512812.456 3614081.332 3075785.055 2969850.937 3159079.385 3906464.439 3197245.026 3424172.736 1.444003984 0.733845121 1.055461161 0.898256394 0.867319252 0.922581782 1.140849116 0.933727727 1 21.70732405 1.777501866 25 1.039624507 0.957611422 0 0.192110238 196.3738254 126120.5337 0.080177458 0.044528012 59.91035131 -1.777501866 -0.082013085 ESSTSEGADQKMS(ph)S(ph)PEDDSDTKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESSTSEGADQKMSSPEDDSDTKR 23 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 2 ES(0.001)S(0.001)T(0.001)S(0.001)EGADQKMS(0.997)S(0.996)PEDDS(0.003)DT(0.001)KR;ES(0.003)S(0.003)T(0.003)S(0.003)EGADQKMS(0.991)S(0.998)PEDDSDTKR 63.323 0.0272 452040000 425870 258498 304198 324260 342200 286932 370110 269129 475700 TRUE FALSE 399215.5569 277637.4609 311413.7202 332581.0606 315324.9924 369764.6104 314615.4414 302730.3481 396302.5969 1.007350343 0.700569371 0.785797829 0.839209895 0.795667237 0.933036052 0.79387681 0.763886864 1 18.5962429 ESSTVFELKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ESSTVFELKR 10 1 B8ZZU8;Q15370;Q15370-2;I3L0M9;A0A0B4J296 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 ;;; 172.8 5.78E-06 1307820000 1269440 1393090 1304940 1396600 1811600 1186530 1679210 1470060 2210150 FALSE TRUE 1189988.016 1496235.833 1335893.793 1432439.12 1669324.244 1529061.949 1427428.05 1653600.227 1841261.687 0.646289457 0.812614439 0.725531739 0.777966071 0.906619768 0.830442495 0.775244529 0.898079963 1 20.81226325 -4.999999999 0.050407029 1.872718766 0.363022153 0.668969976 0.057223285 347.7282921 1.295958223 40.42216007 8.94416759 1.00E-05 4.999999999 -1.509696613 ESTAEKDEL ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ESTAEKDEL 9 1 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ;; 104.17 0.026946 665891000 1115980 865600 896900 962990 878270 664270 1197100 748390 647110 FALSE TRUE 1046132.804 929689.9247 918174.8915 987701.9537 809294.217 856033.9655 1017605.968 841828.1389 539103.1605 1.940505789 1.724512102 1.703152493 1.832120503 1.501186185 1.587885266 1.887590433 1.561534416 1 19.04020184 -2.36597883 0.344363863 7.33E-13 1.759376736 0.749589511 0.133164758 25.74695354 1.110726772 19.73979181 0.103882613 0.004305476 2.36597883 1.759376736 ESTLHLVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ESTLHLVLR 9 0 M0R2S1;P62987;P0CG48;Q96C32;Q5PY61;J3QKN0;F5GXK7;F5H747;F5H388;B4DV12;F5H265;F5H2Z3;F5GYU3;F5H6Q2;M0R1M6;J3QTR3;J3QS39;P0CG47;P62979;A0A2R8Y422 M0R2S1;P62979 UBA52;UBC;UBB;RPS27A Ubiquitin-60S ribosomal protein L40;Ubiquitin;60S ribosomal protein L40;Polyubiquitin-C;Ubiquitin;Polyubiquitin-B;Ubiquitin;Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ;;; 133.57 0.00027316 716990000 1045178 1420690 1214600 1136777 1302200 1015365 1404740 1215110 1377280 FALSE TRUE 979762.1747 1525879.366 1243410.886 1165948.622 1199930.465 1308484.392 1194112.278 1366819.158 1147403.07 0.853895375 1.3298547 1.083674009 1.016163066 1.045779374 1.140387738 1.04070863 1.19122843 1 20.12994085 3.57266981 8.79945353 1.073402486 1.149873463 0 0.128609196 0.83520438 69.87687205 0.031175358 0.048348006 3738.262637 -3.57266981 0.076470977 ESTQLS(ph)PADLTEGKPTDPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESTQLSPADLTEGKPTDPSK 20 1 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 ES(0.004)T(0.019)QLS(0.973)PADLT(0.004)EGKPTDPSK;ES(0.002)T(0.007)QLS(0.984)PADLT(0.006)EGKPTDPSK 116.35 5.82E-05 545120000 758190 393630 550840 472480 418940 419630 664000 423610 527930 TRUE FALSE 710736.2413 422774.7748 563906.1849 484604.6367 386038.1423 540770.3689 564439.3643 476498.641 439815.0724 1.615988823 0.961255767 1.282143838 1.101837265 0.877728315 1.229540329 1.283356119 1.083406802 1 18.74653752 4.750767011 24.73270664 1.125265141 1.615989173 0.580160996 0.136073069 1293.673834 2621197.823 0.032210072 0.54709224 56333.53581 -4.750767011 0.490724033 ESTQLS(ph)PADLTEGKPTDPSKLESPSFTGTGDTEIAHATEDLENNGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESTQLSPADLTEGKPTDPSKLESPSFTGTGDTEIAHATEDLENNGSK 47 2 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 ES(0.001)T(0.007)QLS(0.992)PADLTEGKPTDPSKLESPSFTGTGDTEIAHATEDLENNGSK 213.03 7.64E-40 323530000 601290 243380 401810 379050 381150 257500 508540 285050 552620 TRUE FALSE 563656.3322 261400.1084 411341.1229 388777.0647 351216.0165 331836.0698 432289.1481 320639.12 460384.1519 1.224317409 0.567786939 0.893473681 0.844462311 0.762875992 0.720780827 0.938974867 0.696459942 1 18.81247865 -1.264770241 4.047374611 1.000194827 0.815753458 0.078180157 0.175279717 49.75007128 83074754.85 27400.2879 0.036045371 0.054353781 1.264770241 -0.184441369 ESTSSKS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ESTSSKSPPR 10 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 ESTSS(0.001)KS(0.998)PPR;ESTSSKS(1)PPR;ES(0.005)T(0.017)S(0.015)S(0.174)KS(0.79)PPR;ES(0.003)T(0.011)S(0.009)S(0.097)KS(0.881)PPR;ESTSSKS(1)PPR;ESTSS(0.002)KS(0.998)PPR 143.55 2.05E-05 30915520000 5321050 4165270 4607470 4446940 5265670 3563360 5380780 4190010 6672480 TRUE FALSE 4988014.979 4473670.925 4716761.364 4561056.009 4852125.519 4592044.186 4573981.992 4713141.972 5558799.982 0.897318665 0.804790771 0.848521512 0.820510906 0.872872838 0.826085522 0.822836225 0.847870401 1 22.40634204 -2.334389483 1.337482244 1.453381042 0.838107552 0.764995696 0.027316011 25765.82817 2891.452603 34967.87691 0.006848672 0.004630315 2.334389483 -0.61527349 ESTSSKS(ph)PPRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ESTSSKSPPRK 11 2 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 ES(0.016)T(0.155)S(0.285)S(0.057)KS(0.487)PPRK;EST(0.001)S(0.003)S(0.026)KS(0.97)PPRK;ESTS(0.001)S(0.004)KS(0.996)PPRK;ESTSS(0.001)KS(0.999)PPRK;ESTSSKS(1)PPRK 129.17 0.00013075 15523170000 3143640 1916950 2413150 2253300 2410980 1637100 2931800 2145840 3273210 TRUE FALSE 2946885.184 2058882.973 2470391.058 2311123.493 2221631.356 2109704.194 2492203.807 2413752.848 2726890.105 1.080676181 0.755029683 0.905937153 0.847530851 0.814712464 0.773666746 0.913936283 0.885166895 1 21.37882513 0.802033692 1.446391773 0.998772021 0.855665606 0.156261174 0.091038412 1.110126282 4.195361265 0.077050473 0.022678376 6.339188875 -0.802033692 -0.143106415 ESTSYIEEHIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESTSYIEEHIDR 12 0 F5H008;A0A2R8YDQ0;Q9H267-2;Q9H267 F5H008 VPS33B Vacuolar protein sorting-associated protein 33B 0 85.924 0.0091382 0 904430 385200 525570 520310 514140 335810 753940 430950 513370 FALSE TRUE 847823.3408 413720.6088 538036.7686 533662.0355 473761.5183 432752.8956 640893.6962 484755.0561 427685.2305 1.982353564 0.967348366 1.258020456 1.247791594 1.10773411 1.011849053 1.498517252 1.133438851 1 18.70618986 4.747810953 24.94762135 1.176542634 1.982353998 0.730378346 0.15777228 666.1103156 1796422.22 0.037195267 0.469174074 55951.3994 -4.747810953 0.805811364 ESVDHLTIPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ESVDHLTIPSR 11 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;;;; 186.81 3.86E-06 2546430000 1727350 2416890 2195220 2289130 2428040 1861430 2532710 2236200 2484320 FALSE TRUE 1619238.247 2595839.05 2247291.655 2347872.951 2237351.533 2398794.623 2152953.648 2515394.492 2069670.943 0.782365068 1.254227905 1.08582075 1.134418473 1.081017995 1.159022226 1.040239588 1.215359621 1 20.98096998 4.752468928 24.94278103 1.124435484 0.78236483 0.66082173 0.076273267 1345.648999 2413207.252 0.016613174 0.33928333 56554.72926 -4.752468928 -0.342070654 ESVFTVEGGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ESVFTVEGGHR 11 0 Q99623-2;Q99623;F5GY37;J3KPX7;F5H0C5;F5H3X6;F5H2D2;F5GWA7 Q99623-2 PHB2 Prohibitin-2 0 ;;; 196.76 5.94E-08 2003250000 2004680 2127090 1870750 1803530 2955020 1770420 1741030 2385820 2841530 FALSE TRUE 1879210.657 2284581.957 1915125.073 1849811.633 2722944.649 2281511.514 1479978.714 2683694.879 2367260.286 0.793833559 0.965074255 0.809004859 0.781414551 1.150251481 0.96377721 0.625186306 1.133671229 1 21.17478691 ESVPEFPLS(ph)PPK ddPTM_SK-BR-3_Pertuzumab_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 202.13 1.47E-07 2734376000 2527390 1312828 1726650 1712690 1778810 1306974 2150340 1459460 1625580 TRUE FALSE 2369205.171 1410031.151 1767606.953 1756640.525 1639109.438 1684276.177 1827916.48 1641676.794 1354260.196 1.749446065 1.041181861 1.305219601 1.297121875 1.210335682 1.243687278 1.349752791 1.212231444 1 20.36907352 -3.907348759 0.280292931 9.77E-19 1.298642711 0.230799439 0.178068582 190.4035549 3.22347492 109.9764583 0.187567234 0.00012378 3.907348759 1.298642711 ESVPLDDQEKLPFTVVHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESVPLDDQEKLPFTVVHER 19 1 Q96S52-2;Q96S52 Q96S52-2 PIGS GPI transamidase component PIG-S 0 58.107 0.048975 85626000 201820 236070 212120 216840 234930 189340 261380 203130 278940 FALSE TRUE 189188.4465 253548.8684 217151.5866 222404.4815 216479.5455 243999.3843 222188.4955 228491.2276 232383.112 0.814123044 1.091081302 0.93445511 0.957059571 0.931563157 1.049987593 0.956130132 0.983252293 1 17.8261457 2.296549445 24.99992711 0.991677563 0.964478082 0.081526966 0.071085864 328.6326599 141676.6877 0.023339784 0.019527451 197.9472375 -2.296549445 -0.02719948 ESVPSAS(ph)PTGIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESVPSASPTGIPK 13 0 Q5THJ4-2;Q5THJ4;H3BLS7;A0A2R8YD87 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 ESVPS(0.023)AS(0.704)PT(0.273)GIPK 123.79 0.00023003 96684000 249450 212380 227750 243680 224860 147870 221980 159030 177470 TRUE FALSE 233837.3698 228104.8362 233152.3376 249933.2413 207200.4026 190557.6685 188696.1598 178885.2456 147849.1105 1.581594701 1.542821836 1.576961382 1.690461583 1.401431513 1.288865844 1.276275245 1.209917631 1 17.17376604 1.768242128 0.705211106 1.033862843 1.596639267 0.891309274 0.068869468 0.203839374 0.201708076 0.06404075 0.031997268 58.64650393 -1.768242128 0.562776424 ESVQVPDDQDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ESVQVPDDQDFR 12 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5H1Z6;F5GWK5;F5H3G8;F5H5A8 Q9Y365 STARD10 PCTP-like protein 0 ;;; 249.22 1.63E-16 3020250000 1998980 2173750 2010890 2137980 2167400 1734100 2506750 1918030 2390030 FALSE TRUE 1873867.41 2334696.712 2058589.26 2192844.186 1997181.147 2234706.519 2130886.109 2157500.268 1991118.553 0.941112927 1.17255535 1.033885831 1.101312719 1.003044818 1.122337249 1.070195497 1.083561933 1 20.92514769 -0.841844721 4.05535328 0.999998539 1.074074852 0.082598576 0.064303032 11596985.05 15141189.4 219.0403336 0.013493573 0.14393131 0.841844721 0.074076312 ESVSTEDLSPPS(ph)PPLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESVSTEDLSPPSPPLPK 17 0 Q13127-4;Q13127 Q13127-4 REST RE1-silencing transcription factor 1 ESVSTEDLSPPS(1)PPLPK;ESVSTEDLSPPS(1)PPLPK 261.64 2.79E-27 158350000 527330 451320 477390 462800 458770 346500 603170 380720 471680 TRUE FALSE 494325.3566 484736.2024 488713.9162 474676.2315 422740.0548 446528.925 512730.2581 428253.7301 392953.5608 1.257973984 1.233571217 1.243693823 1.207970302 1.075801563 1.136340193 1.304811329 1.089832929 1 18.5839993 -4.999999999 0.14282022 0.28693391 1.276017781 0.505374316 0.067178605 123.0742657 1.068510264 24.93871851 0.400912521 1.00E-05 4.999999999 0.989083871 ESWHGKPLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESWHGKPLPK 10 1 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 98.04 0.0033936 6503300000 6247700 11221300 9612100 7848500 12883300 6433600 11399100 13685500 11585500 FALSE TRUE 5856667.609 12052136.73 9840103.551 8049905.797 11871497.59 8290875.879 9689910.779 15394164.8 9651805.205 0.606795049 1.248692496 1.019509132 0.834031109 1.229976915 0.858997431 1.003948026 1.594951874 1 23.20236737 1.389813725 24.99825714 1.298150124 1.002031742 0.242718662 0.234517432 31.09991549 8899.652333 0.138309265 0.050508211 24.53656284 -1.389813725 -0.296118382 ESWVS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESWVSPR 7 0 Q8IYH5-2;Q8IYH5;Q8IYH5-4 Q8IYH5-2 ZZZ3 ZZ-type zinc finger-containing protein 3 1 ESWVS(1)PR;ESWVS(1)PR 85.716 0.021616 422810000 822980 807250 839240 837300 893170 715440 988930 757830 877820 TRUE FALSE 771471.1509 867019.6299 859147.1691 858786.5355 823024.0311 921975.9138 840649.1273 852446.7437 731306.1711 1.054922249 1.1855768 1.174811868 1.174318732 1.125416499 1.26072492 1.149517344 1.165649597 1 19.48011601 -0.362519709 8.077055867 0.999998727 1.167183222 0.489479007 0.05148776 0 0 0.044153291 0.01040703 0.433990568 0.362519709 0.167184495 ESYDDVSSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESYDDVSSFR 10 0 H7C2Q8;Q99848 H7C2Q8 EBNA1BP2 Probable rRNA-processing protein EBP2 0 ; 223.08 1.07E-08 410090000 736780 738220 765070 741220 735900 675070 857010 649130 839750 FALSE TRUE 690666.255 792878.5769 783217.8217 760240.9601 678105.3825 869951.7502 728509.3066 730175.3094 699590.3 0.987243898 1.133347013 1.119537852 1.086694541 0.969289286 1.243516027 1.041337061 1.043718458 1 19.41615076 1.522681715 14.40986988 1.028793799 1.097001222 0.123529399 0.076601871 0.244442007 66.07623773 0.037706203 0.017482108 33.31821416 -1.522681715 0.068207423 ESYDYLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESYDYLK 7 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ; 87.323 0.07338 318130000 794540 850610 664270 676920 1017980 591850 738150 757780 994890 FALSE TRUE 744811.1597 913590.0495 680026.7981 694290.9132 938031.9571 762707.4871 627471.2601 852390.5011 828836.4318 0.898622613 1.102256144 0.820459589 0.837669396 1.131745567 0.920214723 0.757050772 1.028418236 1 19.66072789 2.002327385 24.98831191 0.885779656 0.959584854 0 0.123779911 206.7619728 2219906.244 0.04511888 0.033110941 100.5373388 -2.002327385 0.073805198 ESYELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ESYELR 6 0 P35268;K7ERI7;K7EMH1 P35268 RPL22 60S ribosomal protein L22 0 ;;; 132.8 0.034289 10176480000 10100420 12441080 11615840 11242900 12431060 10377610 12343570 10514120 11282150 FALSE TRUE 9468252.742 13362230.51 11891373.21 11531411.85 11454774.69 13373457.54 10492766.27 11826831.03 9399086.28 1.00735885 1.421652075 1.265162682 1.226865198 1.218711516 1.422846556 1.116360246 1.258295825 1 23.16408908 0.425244722 0.752518009 0.9972067 1.271836139 0.251509871 0.12554488 2.337414318 1.98066375 0.128278655 0.040041437 2.662224783 -0.425244722 0.274629439 ESYPHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ESYPHIK 7 0 O60664-4;O60664;O60664-3;K7ER39;K7EL96 O60664-4 PLIN3 Perilipin-3 0 73.039 0.049975 230330000 746650 777500 797750 814640 916550 606450 951570 784830 1038400 FALSE TRUE 699918.5093 835066.909 816673.0067 835545.0416 844567.8602 781522.2701 808890.9124 882817.7531 865084.3317 0.809075467 0.96530116 0.944038606 0.965853861 0.976283848 0.903405878 0.935042842 1.020499067 1 19.72248125 4.740593933 24.82290039 0.956730813 0.809075411 0.677209363 0.03325428 97.94878005 1195673.09 0.007427762 0.048790448 55029.29293 -4.740593933 -0.147655402 ESYSIYVYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESYSIYVYK 9 0 Q16778;P33778;P23527;P06899;Q6DRA6;Q6DN03 Q16778 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST2H2BD;HIST2H2BC Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C 0 ; 190.93 8.49E-05 1633910000 1496640 1451750 1468170 1364960 1515670 954520 1807540 1360000 1579770 FALSE TRUE 1402967.974 1559239.081 1502995.686 1399987.184 1396635.392 1230074.429 1536516.157 1529798.994 1316096.181 1.066007176 1.18474554 1.142010521 1.063742304 1.061195536 0.934638704 1.167480143 1.162376288 1 20.3278335 3.243081739 22.93203782 1.070461487 1.144039147 0.140191294 0.07390288 69.08399838 350397.8647 0.02043929 0.026710016 1750.176061 -3.243081739 0.07357766 ESYSVYVYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ESYSVYVYK 9 0 P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053;Q99880 P58876;Q99880 HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS;HIST1H2BL Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S;Histone H2B type 1-L 0 ;;;;;;; 214.25 1.59E-06 13413360000 6076410 6247820 5869300 5773910 6391390 4285110 6836360 5566340 6561190 FALSE TRUE 5696098.345 6710415.094 6008522.568 5922078.306 5889436.011 5522151.694 5811311.284 6261309.802 5466085.002 1.042080089 1.22764558 1.099236943 1.083422286 1.077450499 1.010257194 1.063157869 1.145483431 1 22.38207646 3.410448699 2.167793234 1.061418047 1.151753097 0.189698123 0.059536313 0.357140647 3.382384232 0.016544286 0.025668975 2573.052806 -3.410448699 0.090335049 ESYTEEIVS(ph)EAESHVS(ph)GISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ESYTEEIVSEAESHVSGISR 20 0 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 2 ES(0.031)YT(0.036)EEIVS(0.933)EAESHVS(0.994)GIS(0.006)R;ESYTEEIVS(1)EAESHVS(0.997)GIS(0.003)R 132.35 6.71E-06 93916000 99967 121044 104937 99456 148692 73952 170931 135432 191470 TRUE FALSE 93710.24392 130006.2237 107426.1552 102008.2093 137014.3301 95300.74189 145301.4834 152340.9833 159512.4201 0.587479294 0.815022577 0.673465772 0.639500105 0.858957127 0.597450292 0.910910156 0.955041515 1 17.28330923 1.595754556 5.309106494 0.963384534 0.711129588 0.662352767 0.08771481 0.085673288 5.163169891 0.044037402 0.020421623 39.42344354 -1.595754556 -0.252254946 ESYTEEIVS(ph)EAESHVSGISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ESYTEEIVSEAESHVSGISR 20 0 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR 373.92 1.84E-112 2213275000 1321302 2131572 2188378 2293652 2171324 2143998 2580945 1989989 1603685 TRUE FALSE 1238604.066 2289395.809 2240287.36 2352510.993 2000796.972 2762935.418 2193956.258 2238443.507 1336019.613 0.927085242 1.713594461 1.676837179 1.760835672 1.497580538 2.068035072 1.64215872 1.67545707 1 20.34950976 4.740263696 24.71619018 1.677266547 0.927084947 0.391309805 0.269406061 109.0613024 1582611.81 0.054259617 0.347818561 54987.46461 -4.740263696 -0.750181601 ET(ph)ERASPIKMDLAPSK ddPTM_SK-BR-3_Pertuzumab_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(0.649)ERAS(0.351)PIKMDLAPSK 103.89 0.0018845 810000000 1283000 813520 1013600 989500 1135900 771890 1401400 867700 1364300 TRUE FALSE 1202699.32 873753.8673 1037643.071 1014892.245 1046690.996 994722.1124 1191273.08 976034.255 1136589.516 1.058165066 0.768750595 0.912944432 0.892927685 0.920905024 0.875181495 1.048111973 0.858739449 1 20.11627988 1.770509312 25 0.973028217 0.890213063 0.097193417 0.084380099 47.65279053 37307.34908 0.035692424 0.01979964 58.95346169 -1.770509312 -0.082815155 ET(ph)LS(ph)LT(ph)LAEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETLSLTLAEEK 11 0 H7BZ55 H7BZ55 Putative ciliary rootlet coiled-coil protein-like 3 protein 3 ET(1)LS(1)LT(1)LAEEK;ET(1)LS(1)LT(1)LAEEK 73.435 0.041977 396030000 917380 1724400 1765700 1686300 1569650 2186800 2405600 1955190 1123820 TRUE FALSE 859962.8234 1852076.37 1807583.238 1729573.313 1446376.021 2818093.66 2044902.612 2199299.775 936247.1818 0.918521134 1.978191664 1.930668816 1.847346883 1.544865553 3.009988938 2.184148217 2.3490589 1 19.83652995 4.747222851 3.91817568 2.054982056 0.801232585 0.282471339 0.521488247 0.308276199 9.527320155 0.11616261 1.118166595 55875.68374 -4.747222851 -1.253749471 ET(ph)SPSHPGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETSPSHPGFK 10 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 ET(0.498)S(0.498)PS(0.004)HPGFK;ET(0.494)S(0.494)PS(0.012)HPGFK 106.01 0.0091014 1028360000 1661350 1051880 1383310 1205250 1204950 1182800 1598740 1243950 881690 TRUE FALSE 1557369.069 1129762.29 1416122.766 1236178.755 1110318.088 1524255.159 1359023.779 1399259.896 734530.2431 2.12022457 1.538074573 1.92792983 1.682951474 1.511602957 2.075142818 1.85019445 1.904972476 1 19.48646237 -1.90157581 2.53525934 0.543955595 1.810112432 0.620366469 0.202807792 16878440.3 9226331.562 45887048.37 0.044898147 0.012543658 1.90157581 1.266156837 ET(ph)SSDVALASHILTALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ETSSDVALASHILTALR 17 0 O00273;O00273-2 O00273 DFFA DNA fragmentation factor subunit alpha 1 ET(0.735)S(0.26)S(0.005)DVALASHILTALR;ET(0.748)S(0.245)S(0.007)DVALASHILTALR;ET(0.548)S(0.388)S(0.064)DVALASHILTALR 183.54 2.52E-09 75908000 73760 66622 69853 64227 78091 63458 72961 59301 80976 TRUE FALSE 69143.49327 71554.7622 71509.94615 65875.17356 71958.04786 81777.29445 62021.17539 66704.86039 67460.58248 1.02494658 1.060689955 1.060025626 0.976498737 1.066668049 1.212223367 0.919369106 0.988797575 1 16.04175715 1.624291989 25 0.965565145 1.062154061 0.348797592 0.062477129 0.921966885 1399.905661 0.027541448 0.015216194 42.10095903 -1.624291989 0.096588917 ETAAVIFLHGLGDTGHSWADALSTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETAAVIFLHGLGDTGHSWADALSTIR 26 0 O95372;Q5QPQ3;Q5QPQ2;Q5QPN5;Q5QPN9 O95372 LYPLA2 Acyl-protein thioesterase 2 0 ; 321.7 1.69E-82 667410000 267970 346780 319850 303740 390010 300060 353700 319450 305470 FALSE TRUE 251198.236 372455.952 327436.993 311534.4826 359380.1878 386682.4509 300665.9686 359334.0357 254485.0836 0.987084321 1.463566928 1.286664776 1.224175807 1.412185668 1.519470004 1.181467944 1.412004313 1 17.95722157 -1.378820767 9.679031768 0.999999687 1.321660854 0.280435411 0.155615639 9.36E-07 5.98E-08 0.134026859 0.031590403 0.041800284 1.378820767 0.321661167 ETAENYLGHTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ETAENYLGHTAK 12 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;; 187.44 1.05E-05 3587480000 4204160 3433560 2604930 2058130 4219100 1981520 3332600 3814410 5066300 FALSE TRUE 3941029.13 3687784.355 2666720.17 2110945.1 3887748.905 2553552.657 2832907.568 4290647.485 4220701.8 0.933737875 0.873737243 0.631819137 0.500140782 0.921114329 0.60500665 0.671193489 1.016572051 1 22.00905147 1.232637264 24.98248808 1.00828624 0.726952276 0.392820179 0.141663101 153.0032455 645278.2425 0.120912624 0.033382638 17.08587655 -1.232637264 -0.281333964 ETAIELGYLTAEQFDEWVKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETAIELGYLTAEQFDEWVKPK 21 1 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 215.37 6.01E-25 267560000 422430 262110 327740 284330 374270 246950 386440 309650 509080 FALSE TRUE 395990.8604 281516.8971 335514.1476 291626.3892 344876.3439 318240.4561 328496.9095 348310.4841 424111.2592 0.933695703 0.663780767 0.791099364 0.687617654 0.813174224 0.750370213 0.774553616 0.821271486 1 18.69408326 0.681091692 1.424321053 1.000025539 0.760058025 0.476280268 0.073460002 0.835691869 2.610563849 0.061290028 0.018009427 4.798347443 -0.681091692 -0.239967514 ETAIQTEDSAISES(ph)PEEPLPNLKPKPNLR ddPTM_SK-BR-3_Pertuzumab_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;ETAIQTEDSAISES(1)PEEPLPNLKPKPNLR 277.24 1.73E-71 559850000 329058 274471 272501 266679 336395 201196 344256 257194 496062 TRUE FALSE 308462.8472 294793.1184 278964.8524 273522.4346 309975.8937 259278.0191 292638.0087 289305.2371 413266.0475 0.746402587 0.713325278 0.675024852 0.661855568 0.75006378 0.627387661 0.708110454 0.700045984 1 18.65671132 0.274726311 2.234885881 1.000001867 0.694836676 0.868854899 0.036892587 8.30930913 24.9704485 0.032008345 0.008654557 1.882462403 -0.274726311 -0.305165191 ETAVPGPLGIEDISPNLS(ph)PDDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETAVPGPLGIEDISPNLSPDDK 22 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 ETAVPGPLGIEDISPNLS(1)PDDK 91.725 0.0014054 22528000 72294 41378 50370 57951 47279 48470 70117 39652 37066 TRUE FALSE 67769.24759 44441.67017 51564.80019 59438.12077 43565.89805 62462.50216 59603.60678 44602.63948 30879.44514 2.19463942 1.439199117 1.66987457 1.924844196 1.410838111 2.022785768 1.930203296 1.444411947 1 14.91435921 0.971420699 4.901565938 1.000561167 1.75963879 0.524422404 0.246787937 0.149350013 12.75799648 0.228347676 0.057791135 9.363122368 -0.971420699 0.759077623 ETAVPGPLGIEDISPNLS(ph)PDDKSFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETAVPGPLGIEDISPNLSPDDKSFSR 26 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 ETAVPGPLGIEDISPNLS(0.998)PDDKS(0.001)FS(0.001)R;ETAVPGPLGIEDISPNLS(0.992)PDDKS(0.004)FS(0.004)R 200.4 3.24E-25 472380000 368904 284297 303471 337850 395350 237801 418770 261963 417700 TRUE FALSE 345814.9572 305346.6457 310669.4754 346519.803 364300.8058 306450.2883 355979.3262 294669.6572 347983.1716 0.993769198 0.877475323 0.89277155 0.995794715 1.046892021 0.880646863 1.022978567 0.846792837 1 18.40865801 3.245735785 24.97688265 0.968391989 0.907858371 0.073174798 0.068238881 291.4008557 1014365.926 0.017350931 0.023011373 1760.904425 -3.245735785 -0.060533618 ETCAWFTDNYEQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ETCAWFTDNYEQAR 14 0 Q13630 Q13630 TSTA3 GDP-L-fucose synthase 0 ;; 215.53 1.50E-11 398930000 304103 339580 284748 270805 321631 338620 386180 338815 388870 FALSE TRUE 285069.7361 364722.8565 291502.357 277754.3148 296371.3987 436374.097 328275.8941 381116.7986 323965.0848 0.879939689 1.125809149 0.899795597 0.857358795 0.914825123 1.346978787 1.013306401 1.176413189 1 18.30547881 ETCSLWPGQALSLQVEQLLHHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETCSLWPGQALSLQVEQLLHHR 22 0 P19623;K7EKM4 P19623 SRM Spermidine synthase 0 ; 58.49 0.040622 352590000 337890 425620 393960 379780 397510 329520 427940 371290 327480 FALSE TRUE 316742.0681 457133.3477 403304.9172 389525.7978 366291.1681 424647.0747 363774.3698 417646.3738 272821.4724 1.160986579 1.675576866 1.478274102 1.427768109 1.342603883 1.55650166 1.333378809 1.530841287 1 18.05759767 -2.857692953 0.384605648 4.88E-09 1.470569933 0.464851026 0.143916735 79.65753158 2.786240672 65.35601192 0.08826717 0.001387737 2.857692953 1.470569928 ETCSTLAES(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ETCSTLAESPR 11 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 ETCSTLAES(1)PR;ETCSTLAES(1)PR;ETCSTLAES(1)PR 203.88 3.68E-08 778772000 588190 627830 657840 686500 675260 533880 695800 554870 643340 TRUE FALSE 551376.2378 674315.1865 673444.2755 704116.7522 622227.8035 688002.4892 591471.2495 624146.7409 535962.3979 1.028759182 1.258138984 1.256514036 1.31374282 1.160954212 1.283676788 1.103568556 1.164534571 1 19.03177226 0.997511613 0.931663985 1.005070723 1.227663792 0.357704047 0.085333592 0.576910286 1.080279066 0.073814958 0.025275487 9.9428666 -0.997511613 0.222593068 ETDEFFKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETDEFFKK 8 1 O14745;O14745-2;J3QRA3 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 103.56 0.0076141 571630000 866390 570000 609380 607990 763560 513280 959230 667500 1027700 FALSE TRUE 812164.1965 612203.3931 623834.7814 623592.0527 703593.0777 661455.6036 815402.3666 750838.8443 856170.2308 0.948601303 0.71504868 0.728634048 0.728350543 0.821791102 0.772574869 0.95238346 0.876973781 1 19.70753815 1.752757502 5.95768299 0.935346151 0.769835116 0.492369296 0.073861283 0.12446036 11.47666177 0.034637262 0.018353663 56.59232049 -1.752757502 -0.165511035 ETDLLLDDSLVSIFGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ETDLLLDDSLVSIFGNR 17 0 P30044-2;P30044;P30044-3;P30044-4 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 ;;;; 354.38 1.92E-87 319710000 346104 351742 356725 348952 375876 310841 371786 328997 322270 FALSE TRUE 324441.9685 377785.3437 365186.6855 357906.6991 346356.2152 400575.7506 316040.1408 370072.9997 268481.0551 1.208435241 1.407121048 1.36019536 1.333079904 1.290058306 1.492007511 1.17714131 1.378395208 1 18.03446076 -0.710016256 0.5058713 0.922984459 1.34794711 0.548782787 0.092986628 8.756157502 1.673408687 1.182787957 0.039739723 0.194977162 0.710016256 0.424962652 ETDLLLDDSLVSIFGNRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ETDLLLDDSLVSIFGNRR 18 1 P30044-2;P30044;P30044-3;P30044-4 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 ;;;; 268.93 2.17E-31 2865062000 1698983.3 2132902.3 1927110.6 1945805.6 2512137.5 1573217.9 2104465 1889600.7 2960299 FALSE TRUE 1592646.968 2290824.606 1972822.573 1995738.266 2314844.354 2027380.369 1788920.01 2125521.507 2466205.973 0.645788302 0.928886164 0.799942339 0.80923422 0.938625719 0.822064495 0.725373318 0.861858876 1 21.23386187 -2.426640521 1.655628319 1.907666508 0.821560771 0.305432559 0.086675836 1200003.74 105563.494 4058134.524 0.021609613 0.003744204 2.426640521 -1.086105737 ETDLQELFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ETDLQELFR 9 0 O75821;K7ENA8;K7ER90;K7EL20;K7EP16 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ;; 164.71 0.00014436 77049000 168926 147699 168495 155279 149229 142687 169519 137399 115626 FALSE TRUE 158353.2232 158634.7876 172491.781 159263.722 137509.1563 183878.4206 144101.1997 154553.5676 96327.27363 1.643908493 1.646831491 1.790684761 1.653360632 1.427520484 1.908892608 1.495954305 1.60446322 1 16.55565671 -0.358587865 0.541213642 0.911725684 1.683369476 0.708067038 0.131554288 3.868823838 1.043759898 0.790053294 0.053385289 0.4379375 0.358587865 0.771643792 ETDLQELFRPFGSISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ETDLQELFRPFGSISR 16 1 O75821;K7ENA8;K7EP16 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ;; 234.36 1.03E-19 1395097000 1145375 1270352 1333346 1183456 1328326 1116264 1433713 1134717 1536568 FALSE TRUE 1073688.023 1364410.184 1364973.597 1213825.485 1224004.634 1438511.296 1218741.046 1276388.915 1280104.874 0.838750047 1.065858127 1.066298258 0.948223469 0.956175278 1.123744878 0.952063436 0.997097145 1 20.28783058 3.239866213 24.9999984 0.997902907 1.017349285 0 0.08082804 240.5888505 4606676.98 0.021944528 0.02817734 1737.265572 -3.239866213 0.019446378 ETDPS(ph)PEER ddPTM_SK-BR-3_Pertuzumab_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 134.57 0.00025732 1013130000 2026080 1973770 1985240 1771160 2276900 1832780 1956560 1771030 3657500 TRUE FALSE 1899271.269 2119909.985 2032330.83 1816610.964 2098081.459 2361873.833 1663191.992 1992146.994 3047039.622 0.623316893 0.695727738 0.666985364 0.596188823 0.688563891 0.775137224 0.545838649 0.653797535 1 21.53897683 -1.528419382 6.517446246 1.000289951 0.656579523 0.757430408 0.061232265 0.000247068 1.79E-05 0.056780497 0.013372256 0.029619697 1.528419382 -0.343710428 ETDPVKS(ph)PPLPEHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ETDPVKSPPLPEHQK 15 1 Q96JM3;A0A2R8Y4S6;S4R3K0;A0A2R8Y735 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 ETDPVKS(1)PPLPEHQK;ETDPVKS(1)PPLPEHQK;ET(0.003)DPVKS(0.997)PPLPEHQK;ET(0.076)DPVKS(0.924)PPLPEHQK 149.94 1.97E-06 1328510000 2526900 1368180 1845520 1807050 1855860 1351540 2355930 1617790 2206810 TRUE FALSE 2368745.84 1469481.471 1889296.606 1853421.962 1710108.242 1741707.658 2002680.168 1819774.643 1838479.154 1.288426814 0.799291886 1.027641027 1.008127809 0.930175486 0.947363288 1.089313503 0.989826095 1 20.81008139 1.754570573 24.99999425 1.034505756 0.977776065 0 0.125233026 20.6596582 32299.06433 0.052936143 0.029356053 56.82907318 -1.754570573 -0.056729692 ETDVVNFDDIASSENLLHLTANRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETDVVNFDDIASSENLLHLTANRPK 25 1 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 0 ; 237.32 1.10E-38 217862000 266680 301720 332620 319260 372730 243680 402030 305940 457660 FALSE TRUE 249988.9748 324059.6627 340509.9035 327452.7521 343457.2893 314026.4602 341749.3338 344137.2825 381273.5894 0.655668218 0.849939969 0.893085472 0.858839325 0.900815842 0.823625 0.896336235 0.90259932 1 18.54046707 4.820804583 2.21414416 0.885919571 0.561971941 0.73083847 0.045257311 0.413566179 1.938692158 0.009795318 0.284178938 66191.85967 -4.820804583 -0.32394763 ETEDGHESPLFDFIESCLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ETEDGHESPLFDFIESCLR 19 0 Q9UBF2;Q9UBF2-2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 ;; 260.65 4.06E-31 135729000 58405 95655 87337 91653 90659 96679 119838 90448 81499 FALSE TRUE 54749.53531 102737.3957 89408.67488 94004.97115 83539.00784 124588.6578 101869.4044 101740.6319 67896.2904 0.806370053 1.513151825 1.316841824 1.384537662 1.230391342 1.834984756 1.50036775 1.498471143 1 16.05104513 4.742678811 24.7743817 1.439158639 0.806369771 0.427788528 0.217001487 325.2359952 1956481.409 0.047483782 0.367354898 55294.10215 -4.742678811 -0.632788868 ETEEILADVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETEEILADVLK 11 0 P56537 P56537 EIF6 Eukaryotic translation initiation factor 6 0 ; 224.02 1.52E-11 29594000 173744 113341 135704 114116 118620 116308 167108 128220 93230 FALSE TRUE 162869.6732 121732.8856 138922.963 117044.4098 109304.0637 149884.2315 142051.7068 144228.5492 77669.31071 2.096963031 1.567322852 1.788646786 1.506958266 1.40730055 1.929774194 1.828929669 1.85695673 1 16.24505704 4.746720125 23.83401133 1.662926396 2.096963449 0.214320755 0.276987831 863.6347216 2522571.338 0.059711991 0.650998516 55811.04129 -4.746720125 0.434037052 ETEEILADVLKVEVFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ETEEILADVLKVEVFR 16 1 P56537 P56537 EIF6 Eukaryotic translation initiation factor 6 0 ;; 176.83 2.78E-09 43467500 64417.1 85684.9 81464.1 90020.1 108771.5 51029.7 91100 57544.4 105933 FALSE TRUE 60385.3487 92029.09915 83396.46692 92330.16817 100229.0252 65761.14599 77440.40073 64728.94501 88252.09795 0.684236977 1.042797863 0.944979993 1.046209329 1.135712663 0.745151079 0.877490763 0.733455028 1 16.42934295 2.221120856 24.99959245 0.831042381 0.980516105 0.18305701 0.13700347 351.8669906 504392.0873 0.046840755 0.034673401 166.3875612 -2.221120856 0.149473723 ETEELMAWMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ETEELMAWMR 10 0 Q12931-2;Q12931;I3L0K7 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ;; 199.7 6.37E-07 195329000 268845 278567 237247 223069 345482 235483 217019 296606 269354 FALSE TRUE 252018.4714 299192.3905 242874.6109 228793.3282 318349.2373 303463.1194 184479.0157 333637.912 224397.0773 1.123091594 1.333316789 1.082343022 1.019591391 1.418687093 1.352348805 0.822109708 1.486819329 1 17.77569436 -2.371351856 1.969178479 7.13E-05 1.185666068 0.085185258 0.202462984 4189434.712 370188.9032 18688813.7 0.046391033 0.004252537 2.371351856 1.185594765 ETEELVASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETEELVASR 9 0 Q8TEV9 Q8TEV9 SMCR8 Smith-Magenis syndrome chromosomal region candidate gene 8 protein 0 ; 76.064 0.036489 940910000 409870 1102320 931100 917900 920390 1104250 921240 942280 672780 FALSE TRUE 384216.9683 1183936.92 953186.1317 941454.868 848106.2821 1423029.049 783108.6144 1059925.732 560488.6717 0.68550354 2.112329793 1.700634071 1.679703651 1.513155082 2.53890778 1.397189014 1.891074317 1 19.09632569 4.749909067 24.59136448 1.774109874 0.685502732 0.382511651 0.413214155 1269.147965 2750096.977 0.086009332 1.321594767 56222.35934 -4.749909067 -1.088607142 ETEEQDS(ph)DSAEQGDPAGEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETEEQDSDSAEQGDPAGEGK 20 0 H0Y626;O95361 H0Y626 TRIM16 Tripartite motif-containing protein 16 1 ET(0.083)EEQDS(0.906)DS(0.011)AEQGDPAGEGK 166.85 8.31E-12 0 82275 51744 66241 62644 61454 51203 78040 50050 48138 TRUE FALSE 77125.55462 55575.1796 67812.2678 64251.5511 56627.65073 65984.47489 66338.62649 56298.85267 40103.45682 1.923164753 1.385795241 1.690933231 1.602144957 1.412039141 1.645356289 1.654187239 1.403840395 1 15.29143898 0.915571276 3.6210815 1.000367251 1.596832718 0.632739866 0.149216026 0.219144758 6.762510743 0.128526748 0.033111376 8.233249495 -0.915571276 0.596465467 ETEEQDS(ph)DSAEQGDPAGEGKEVLCDFCLDDTRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETEEQDSDSAEQGDPAGEGKEVLCDFCLDDTRR 33 2 H0Y626;O95361 H0Y626 TRIM16 Tripartite motif-containing protein 16 1 ETEEQDS(0.968)DS(0.032)AEQGDPAGEGKEVLCDFCLDDTRR 163.13 2.41E-14 75097000 13173 16054 14027 16290 21526 13345 22971 15457 33356 TRUE FALSE 12348.52544 17242.65486 14359.72706 16708.02898 19835.43479 17197.48486 19526.7118 17386.84048 27788.66811 0.444372699 0.62049231 0.516747582 0.601253321 0.713795807 0.618866827 0.702686135 0.625680958 1 14.76220907 -5 0.131566512 2.343336792 0.443238015 0.825597794 0.061343132 53.2489108 0.440340894 18.76455595 0.411376024 1.00E-05 5 -1.900098778 ETERAS(ph)PIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETERASPIK 9 1 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 ETERAS(1)PIK;ET(0.014)ERAS(0.986)PIK 80.905 0.013802 1476810000 4420100 2747500 3379800 2935200 3099600 2567700 3990500 2921500 2519400 TRUE FALSE 4143453.831 2950927.759 3459970.452 3010522.201 2856169.919 3308953.307 3392161.571 3286255.706 2098895.864 1.974111199 1.40594291 1.648471709 1.434336144 1.360796392 1.576520953 1.616164779 1.565706885 1 21.00119916 -1.767371159 2.278266594 0.835150932 1.558603435 0.525090856 0.170711922 3262810.547 2028514.333 3000798.082 0.039074423 0.017085545 1.767371159 0.723452503 ETERAS(ph)PIKMDLAPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 ETERASPIKMDLAPSK 16 2 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 ET(0.001)ERAS(0.999)PIKMDLAPSK;ET(0.172)ERAS(0.828)PIKMDLAPSK;ET(0.004)ERAS(0.996)PIKMDLAPSK;ET(0.001)ERAS(0.999)PIKMDLAPSK;ET(0.01)ERAS(0.99)PIKMDLAPSK;ET(0.032)ERAS(0.968)PIKMDLAPSK;ET(0.495)ERAS(0.505)PIKMDLAPSK;ET(0.45)ERAS(0.55)PIKMDLAPSK;ET(0.059)ERAS(0.941)PIKMDLAPSK;ET(0.224)ERAS(0.776)PIKMDLAPSK;ET(0.071)ERAS(0.929)PIKMDLAPSK 151.89 3.13E-07 12675230000 23630390 14441030 17819520 17464770 19816320 12526620 23923830 15056350 23816050 TRUE FALSE 22151406.07 15510258.89 18242207.43 17912945.57 18260026.16 16142851.84 20336673.79 16936168.44 19840997.4 1.116446196 0.781727782 0.919419879 0.902824853 0.920317956 0.813610905 1.024982433 0.85359461 1 24.24198122 0.104596887 0.541566352 1.005730476 0.901852059 0.038689414 0.09850518 9.432934848 3.597067272 0.229112872 0.040874638 1.272321562 -0.104596887 -0.103878417 ETES(ph)APGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ETESAPGSPR 10 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 2 ETES(1)APGS(1)PR;ETES(1)APGS(1)PR;ETES(1)APGS(1)PR;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 200.05 3.91E-07 8451190000 11672100 12183400 11632420 11702540 12308130 9266300 13685010 10606660 13378200 TRUE FALSE 10941564.1 13085471.61 11908346.5 12002846.99 11341499.12 11941330.38 11633069.8 11930924.85 11145291.99 0.981720721 1.174080645 1.06846429 1.076943251 1.017604485 1.071423736 1.043765368 1.07049011 1 23.40993108 3.223138065 2.137578002 1.046490515 1.098473972 0.038985644 0.051937245 0.531077916 4.956360559 0.014906053 0.020345518 1671.621948 -3.223138065 0.051983456 ETESAPGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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;ETES(0.002)APGS(0.998)PR;ETESAPGS(1)PR;ETESAPGS(1)PR 210.44 8.08E-08 7814259000 8016403 7221310 8474164 8324354 8400521 8891610 7540582 6338900 6878089 TRUE FALSE 7514670.646 7755983.306 8675175.172 8537971.017 7740777.967 11458473.46 6409941.732 7130325.619 5730091.512 1.311439901 1.353553131 1.513967998 1.490023501 1.350899536 1.999701652 1.118645613 1.244365051 1 22.45012675 -0.121201859 6.807517017 0.999999997 1.427428947 0.243746496 0.233935061 1281510.221 205362.8575 0.209379946 0.050782096 0.756481202 0.121201859 0.42742895 ETFAS(ph)DTNEALASLDESQEGHAEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETFASDTNEALASLDESQEGHAEAK 25 0 Q9H814 Q9H814 PHAX Phosphorylated adapter RNA export protein 1 ETFAS(0.881)DT(0.119)NEALASLDESQEGHAEAK 335.91 3.11E-88 67500000 99332 62992 80286 67052 78225 72845 99155 69922 75800 TRUE FALSE 93114.98743 67655.99322 82190.42183 68772.66784 72081.52404 93874.16896 84287.62826 78651.91562 63148.49031 1.474540198 1.071379425 1.30154215 1.089062739 1.141460765 1.486562363 1.334752863 1.245507458 1 15.94646062 ETFASDTNEALASLDES(ph)QEGHAEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETFASDTNEALASLDESQEGHAEAK 25 0 Q9H814 Q9H814 PHAX Phosphorylated adapter RNA export protein 1 ETFASDTNEALASLDES(1)QEGHAEAK 265.15 1.62E-45 298730000 276770 185230 218480 207960 232110 171720 288660 177950 201040 TRUE FALSE 259447.4597 198944.6219 223662.4488 213296.6057 213881.0169 221292.7764 245378.1128 200167.4492 167485.1252 1.549077623 1.187834571 1.335416793 1.273525666 1.277014998 1.321268238 1.465074062 1.195135681 1 17.35367345 0.992249371 21.07536231 0.999999993 1.329048754 0.547095778 0.101515433 30.23575046 82218.80777 0.092800772 0.023200193 9.823118236 -0.992249371 0.329048761 ETFLTSPEELYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ETFLTSPEELYR 12 0 O95433;O95433-2;G3V438;H0YJ63;H0YJG7 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ;; 228.2 2.59E-11 629696000 505416 592952 551925 519510 664558 472953 627088 574984 696551 FALSE TRUE 473782.9148 636854.783 565016.9216 532841.5061 612366.2954 609486.8533 533061.976 646772.0181 580292.1382 0.816455857 1.097472706 0.973676678 0.918229752 1.055272431 1.050310375 0.918609681 1.114562779 1 19.14641986 2.714252298 24.91878046 1.01601419 0.979497376 0.12044361 0.085933874 2891.218066 2963821.983 0.026757476 0.025238092 517.9076167 -2.714252298 -0.036516814 ETFS(ph)SAEGTVDKDTTIMELR ddPTM_SK-BR-3_Pertuzumab_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(0.001)FS(0.964)S(0.035)AEGTVDKDTTIMELR;ET(0.002)FS(0.947)S(0.05)AEGTVDKDTTIMELR;ET(0.173)FS(0.781)S(0.045)AEGT(0.001)VDKDTTIMELR 154.86 2.21E-08 243620000 352510 262183 342828 354889 322933 283185 418460 287391 420560 TRUE FALSE 330447.0283 281595.3021 350960.0421 363996.0526 297571.1448 364935.9124 355715.8078 323272.399 350365.8191 0.94314859 0.803717962 1.001696007 1.038902863 0.849315569 1.041585373 1.015269722 0.922671052 1 18.41850251 3.856315809 4.587382255 0.9842234 0.869193161 0.311348422 0.066368027 0.217069736 7.383580462 0.015961788 0.029856182 7183.164447 -3.856315809 -0.115030239 ETGANLAICQWGFDDEANHLLLQNNLPAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ETGANLAICQWGFDDEANHLLLQNNLPAVR 30 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;;; 406.45 7.40E-175 958134000 666293 750038 721252 726234 829359 651370 776878 659083 764598 FALSE TRUE 624590.9105 805571.5939 738360.438 744870.394 764224.4896 839409.9449 660392.3561 741370.9634 636981.6543 0.980547723 1.264670008 1.159154951 1.169374956 1.199759027 1.317792968 1.036752553 1.163881186 1 19.2808923 0.971962956 1.134575613 1.007368424 1.182660522 0.201312242 0.097942683 0.738548209 1.965513907 0.083461997 0.026484295 9.374820388 -0.971962956 0.175292098 ETGEAGWWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETGEAGWWR 9 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 0 ; 131.03 0.00080154 261660000 194669 240685 211737 239748 282284 174036 219927 210095 276613 FALSE TRUE 182485.0148 258505.5678 216759.5016 245900.3396 260114.5533 224277.368 186950.9881 236325.8232 230444.5033 0.791882697 1.121769294 0.940614762 1.067069668 1.12875139 0.973238089 0.811262518 1.025521632 1 17.81405983 1.997037853 24.85451141 0.916530484 1.021103115 0.040616476 0.111943788 191.8072983 1609407.071 0.03899048 0.028251268 99.32026124 -1.997037853 0.104572632 ETGEHLVHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETGEHLVHVK 10 0 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 0 112.83 0.00090691 450640000 249360 271390 263080 255110 284990 238280 280450 256400 252400 FALSE TRUE 233753.0027 291483.998 269320.3818 261656.5545 262608.035 307067.5678 238399.1261 288412.1044 210272.8094 1.111665381 1.386218212 1.280814113 1.244367045 1.248892026 1.460329411 1.133761073 1.371609126 1 17.68190278 -1.696417307 2.716254065 0.957441063 1.28422839 0.399430866 0.107660236 12200014.68 10328658.28 3554028.83 0.023026002 0.020117902 1.696417307 0.326787327 ETGEPYRLS(ph)PEPTPLAEPILEVEVTLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ETGEPYRLS(0.997)PEPT(0.002)PLAEPILEVEVTLSK;ET(0.009)GEPYRLS(0.919)PEPT(0.072)PLAEPILEVEVTLSK;ET(0.155)GEPY(0.126)RLS(0.717)PEPT(0.001)PLAEPILEVEVTLSK;ETGEPYRLS(0.995)PEPT(0.005)PLAEPILEVEVTLSK 328.93 4.73E-96 2537980000 984022 699422 903851 796066 735437 724190 952916 749869 677976 TRUE FALSE 922433.8195 751207.9326 925290.7725 816494.4013 677678.7446 933251.8968 810035.0922 843491.7953 564817.4257 1.633153967 1.330001339 1.638212156 1.445589963 1.199819116 1.652307196 1.434153862 1.493388406 1 19.10742507 -1.68329101 2.434588865 0.919561687 1.474827041 0.526631123 0.1424854 5438818.272 4143919.902 2695570.394 0.03172362 0.020735236 1.68329101 0.555265353 ETGLMYSIMVHALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETGLMYSIMVHALR 14 0 P78527;P78527-2;H0YG84 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 175.28 2.41E-06 57047000 126030 245640 141220 140970 232970 107170 147500 205730 100020 FALSE TRUE 118142.0073 263827.4412 144569.8051 144587.5289 214673.476 138108.2392 125383.7443 231415.8434 83326.01585 1.417828587 3.166207318 1.73499001 1.735202714 2.576307937 1.657444411 1.504737063 2.777233989 1 16.34647938 -1.712045634 0.201989556 2.03E-11 2.351057191 0.18446932 0.610831991 42.83623281 1.43109103 24.33186445 1.579477413 0.019406819 1.712045634 2.351057191 ETGLSHLCEFIEDCEFTVLATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ETGLSHLCEFIEDCEFTVLATR 22 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ;;;;;; 267.78 7.52E-38 1010786000 696644 770855 756986 814532 839473 793631 1080880 804051 656334 FALSE TRUE 653042.2956 827929.9063 774942.0654 835434.2701 773544.1769 1022739.386 918812.0784 904438.5373 546787.6153 1.194325324 1.51417092 1.417263383 1.527895378 1.414706835 1.870450898 1.680382022 1.654094775 1 19.06062104 ETGYVVERPSTTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETGYVVERPSTTK 13 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ; 105.95 0.0012881 504060000 568290 549600 524020 603270 655780 507340 756130 597510 896450 FALSE TRUE 532721.7433 590292.9559 536450.0019 618750.9295 604277.6841 653800.822 642755.3261 672110.4388 746826.7037 0.713313732 0.790401512 0.718305866 0.828506702 0.809127045 0.875438464 0.860648559 0.899955017 1 19.51041399 1.664513263 0.337855819 1.013964947 0.71665656 0.874974499 0.030008045 0.401129996 0.147946785 0.042131774 0.040044908 46.18630963 -1.664513263 -0.297308387 ETHADLWPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ETHADLWPAK 10 0 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 0 ;;; 107.79 0.0022375 1504830000 1766950 2127840 1721440 1791890 2308060 1136920 1909410 1961170 2297510 FALSE TRUE 1656359.754 2285387.488 1762273.37 1837872.931 2126794.278 1465130.348 1623111.697 2206026.392 1914040.739 0.865373302 1.194011936 0.920708392 0.960205754 1.111154133 0.765464558 0.848002691 1.152549341 1 20.86819011 2.260041244 24.99992292 0.914341921 1.020851207 0.040339604 0.136081926 489.543173 569746.2558 0.045094963 0.037697302 181.9873681 -2.260041244 0.106509287 ETHPDSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETHPDSLR 8 0 P56597 P56597 NME5 Nucleoside diphosphate kinase homolog 5 0 ; 95.531 0.0095844 1130640000 995110 1079090 974580 1048790 1143550 843130 1096190 1003140 1169770 FALSE TRUE 932827.8414 1158986.946 997697.4978 1075703.727 1053740.196 1086527.944 931826.486 1128384.237 974527.83 0.957210059 1.189280502 1.023775276 1.103820429 1.081282816 1.114927568 0.95618253 1.1578779 1 19.89434386 -0.275788168 0.296147741 0.976205008 1.087332221 0.041342449 0.07841122 19.37928941 2.173031238 0.610038795 0.089299294 0.529921856 0.275788168 0.111127213 ETHQQVVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ETHQQVVSR 9 0 O14745;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;; 131.52 0.00033091 3343140000 2018050 2247600 2329220 2052850 2134260 1865500 2317940 2050370 2092270 FALSE TRUE 1891743.853 2414014.643 2384470.198 2105529.606 1966643.829 2404039.566 1970386.416 2306363.208 1743056.62 1.085302583 1.384931857 1.367982067 1.207952502 1.128273061 1.379209108 1.130420201 1.323171709 1 20.733188 -4.389936013 0.218787466 2.61E-15 1.302045254 0.286772531 0.115431726 128.3612658 1.637919373 56.49366818 0.216020976 4.07E-05 4.389936013 1.302045254 ETHSIGRD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETHSIGRD 8 1 A0A087WT99;Q9H0W9-4;Q9H0W9-3;Q9H0W9-2;Q9H0W9 A0A087WT99 C11orf54 Ester hydrolase C11orf54 0 93.598 0.017566 156430000 128280 458260 392850 443730 437580 449380 293820 399700 273140 FALSE TRUE 120251.1838 492190.0472 402168.5875 455116.863 403214.2319 579108.7109 249764.4187 449603.4248 227551.1694 0.528457771 2.162986235 1.767376492 2.000063828 1.771971697 2.544960381 1.0976187 1.975834385 1 17.79583148 0.160959311 0.856949837 0.991950158 1.790759398 0.128257688 0.565961841 7.170286407 5.817098287 0.689657131 0.164441747 1.448636125 -0.160959311 0.79880924 ETHVMDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ETHVMDYR 8 0 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;;;;;; 133.58 0.00069273 6885140000 5219960 7268800 4902270 5107130 7522370 3301330 5233280 6185110 6572830 FALSE TRUE 4893252.021 7806989.515 5018554.159 5238187.602 6931593.404 4254370.378 4448598.247 6957334.599 5475782.211 0.893616991 1.425730465 0.916499957 0.956609924 1.265863604 0.776942949 0.812413291 1.27056452 1 22.38463364 3.775354299 7.793281633 0.977603219 1.191023785 0.081591119 0.206777123 0.445248241 63.33328371 0.05017069 0.090295676 5961.48285 -3.775354299 0.213420566 ETIEDVEEMLNNLPGVTSVHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETIEDVEEMLNNLPGVTSVHSR 22 0 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2;H0YD73;E9PL38 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ; 229.59 2.69E-26 346160000 196551 380730 331470 347060 353630 290800 398480 324760 335220 FALSE TRUE 184249.2238 408919.6453 339332.6249 355966.1472 325857.3263 374749.2393 338731.6233 365307.0009 279269.6164 0.659753919 1.464246811 1.215071762 1.274632564 1.16681983 1.341890479 1.212919714 1.308080004 1 18.0912991 4.750492717 24.88392694 1.265037639 0.659753526 0.697063307 0.121399229 882.7009544 1840802.42 0.025832779 0.427346355 56297.96758 -4.750492717 -0.605284113 ETIELVHTEPTDVAQLPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ETIELVHTEPTDVAQLPSR 19 0 Q6IBS0;H0Y858;D6RG15 Q6IBS0 TWF2 Twinfilin-2 0 ;; 176.69 1.62E-13 689120000 2008100 1373190 1541660 1478700 1645930 1321050 1968230 1463830 2193010 FALSE TRUE 1882416.606 1474862.416 1578228.903 1516645.945 1516665.297 1702415.69 1673112.184 1646592.398 1826982.464 1.030341912 0.807266871 0.863844582 0.830137112 0.830147704 0.931818298 0.915779006 0.901263384 1 20.80103136 1.042690723 0.738983499 0.995460776 0.863964774 0.216393538 0.064583886 0.869327463 1.092975252 0.057899824 0.022461834 11.03292646 -1.042690723 -0.131496001 ETIFELEDEVEQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETIFELEDEVEQHR 14 0 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1;C9J8U1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 0 125.53 9.07E-05 16067000 52162 52798 56526 55932 54503 55487 63770 49827 57488 FALSE TRUE 48897.27353 56707.21886 57866.82341 57367.30981 50222.55423 71505.19614 54208.28051 56048.01063 47892.88141 1.020971637 1.184042747 1.208255208 1.1978254 1.048643405 1.493023473 1.13186509 1.170278525 1 15.54752362 0.706129239 2.299420682 1.000212405 1.193269385 0.167426453 0.12666871 2.547366074 17.6121244 0.109567161 0.029614929 5.083106852 -0.706129239 0.193056979 ETIFELEDQVEQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETIFELEDQVEQHR 14 0 Q5M775-4;Q5M775;J3KSG2;Q5M775-5;Q5M775-3;Q5M775-2;J3KRN9;J3QQM0 Q5M775-4 SPECC1 Cytospin-B 0 ; 218.11 5.51E-12 60501000 106765 118496 121012 118094 133220 103451 120484 121095 122176 FALSE TRUE 100082.7692 127269.5671 123882.4618 121124.492 122757.4386 133315.6243 102418.5427 136213.9773 101784.0363 0.983285522 1.25038829 1.217110917 1.190014627 1.206057875 1.309789129 1.00623385 1.338264646 1 16.63515178 -1.323127103 6.347392829 0.999990479 1.188396473 0.210408836 0.114228046 1.38E-05 1.47E-06 0.098830557 0.023293409 0.047519613 1.323127103 0.188405994 ETIPLQETSLYTQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETIPLQETSLYTQDR 15 0 A0A2C9F2P4;A0A286YFF7;P50897;P50897-2;E9PIA8;E9PSE5 A0A2C9F2P4 PPT1 Palmitoyl-protein thioesterase 1 0 ; 226.51 1.99E-12 283990000 25234 27136 38519 26369 31574 36138 24036.5 24580.8 37102 FALSE TRUE 23654.64898 29145.17767 39432.68887 27045.67318 29094.3054 46570.45395 20432.44997 27649.76699 30909.43651 0.76528891 0.942921676 1.275749199 0.87499729 0.941275827 1.506674311 0.661042461 0.894541283 1 14.91575973 1.634466685 25 0.833288297 1.055768777 0.146531754 0.225050476 1.300024216 1217.53924 0.097812735 0.054219606 43.09894952 -1.634466685 0.22248048 ETKPEPMEEDLPENKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ETKPEPMEEDLPENKK 16 2 P31948;P31948-2;P31948-3;F5H783 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;; 173.27 2.41E-09 1461200000 3097440 1349820 1795630 1730570 1900460 1194930 2386200 1422170 2260860 FALSE TRUE 2903576.759 1449762.077 1838223.192 1774979.356 1751205.538 1539886.893 2028411.462 1599731.055 1883507.86 1.541579316 0.769713845 0.975957271 0.942379585 0.929757488 0.817563295 1.076932836 0.849336012 1 20.84499062 4.74726852 24.9981846 0.921853959 1.541579631 0.824895432 0.089968661 445.343336 1278440.163 0.020390286 0.243469635 55881.55983 -4.74726852 0.619725673 ETLAVNYEKEEEFLTNELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETLAVNYEKEEEFLTNELSR 20 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 176.46 3.87E-13 39780000 35515 26151 30016 27633 32716 23512 37509 26273 33915 FALSE TRUE 33292.17955 28087.24725 30727.99369 28342.10956 30146.61733 30299.53271 31884.87367 29553.24188 28254.3674 1.178302068 0.994085157 1.087548458 1.003105437 1.066971945 1.072384042 1.128493631 1.045970751 1 14.78618627 2.479534128 22.82074753 1.077332991 1.055205097 0 0.059865464 133.8115675 1265648.831 0.018712892 0.015948657 301.6713922 -2.479534128 -0.022127894 ETLEQQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ETLEQQKR 8 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITI7 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;; 112.41 0.0048844 1665580000 1314280 1414350 1316130 1408630 1603770 995720 1670230 1310000 1807360 FALSE TRUE 1232021.561 1519069.946 1347349.225 1444777.831 1477816.373 1283168.2 1419794.517 1473556.384 1505699.94 0.818238434 1.008879595 0.894832489 0.959539011 0.981481326 0.852207114 0.942946519 0.978652084 1 20.52200286 1.200069492 3.587076858 0.996137178 0.928218291 0.192181583 0.057208812 0.383884248 9.060543139 0.047391768 0.013025375 15.85146815 -1.200069492 -0.067918888 ETLIAEIEELDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETLIAEIEELDR 12 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 145.55 0.00014888 9221800 29071 24545 25046 27505 22157 18722 27206 25697 18114 FALSE TRUE 27251.498 26362.33734 25640.10295 28210.82487 20416.8786 24126.73747 23126.71287 28905.32702 15090.65638 1.805852398 1.746931126 1.699071419 1.869423314 1.352948347 1.598786485 1.532518685 1.915445312 1 13.88136794 -2.575128344 0.27603995 3.11E-16 1.741631852 0.603786097 0.171722925 32.20936144 1.025988338 19.94144479 0.19709244 0.002659939 2.575128344 1.741631852 ETLIDVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ETLIDVAR 8 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;;; 127.02 0.0027782 396649000 1210770 1163550 1259580 1217750 1187320 1157600 1402060 1143440 940034 FALSE TRUE 1134990.067 1249700.453 1289457.832 1248999.527 1094072.677 1491780.328 1191834.119 1286201.001 783136.2525 1.44928812 1.595763762 1.646530637 1.594868738 1.397040008 1.904879672 1.521873257 1.642371933 1 19.57890381 -1.0961755 5.148976611 0.999986661 1.601073416 0.652210561 0.136250558 1.84E-05 3.22E-06 0.116033482 0.027348748 0.080135417 1.0961755 0.601086755 ETLNPPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETLNPPGR 8 0 Q9H6W3;Q9H6W3-2 Q9H6W3 NO66 Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 0 60.59 0.091333 104050000 61109 473220 160420 198480 332790 167440 117160 267990 94382 FALSE TRUE 57284.29677 508257.7012 164225.2382 203573.3328 306654.0158 215777.2098 99592.94566 301449.1414 78629.03447 0.728538728 6.463995197 2.088608098 2.589035134 3.900009938 2.744243412 1.26661794 3.833814614 1 16.26277452 1.480843401 0.295950858 0.884884225 3.994193621 0.080215234 1.633257783 2.682446138 0.875066772 3.142489028 2.786879907 30.25822171 -1.480843401 3.109309396 ETLPSIWDS(ph)PTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETLPSIWDSPTK 12 0 Q9Y673-2;Q9Y673 Q9Y673-2 ALG5 Dolichyl-phosphate beta-glucosyltransferase 1 ETLPSIWDS(0.986)PT(0.014)K 113.77 0.0011855 30403000 55180 37581 47693 44027 49436 41393 61482 45355 67704 TRUE FALSE 51726.3823 40363.53634 48824.30048 45156.80736 45553.49598 53342.48714 52263.34487 51017.67159 56403.76502 0.917073218 0.715617767 0.865621302 0.800599168 0.807632185 0.945725647 0.926593196 0.904508264 1 15.78350385 2.239735477 24.99999798 0.937130525 0.811997591 0.53557169 0.056328539 22.32265463 475019.7589 0.018545907 0.014716292 173.674268 -2.239735477 -0.125132933 ETLQQHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ETLQQHK 7 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;; 121.52 0.0044304 2386320000 4560870 7609800 3329740 3684920 7562200 2290910 4420850 6006340 4972060 FALSE TRUE 4275413.288 8173237.51 3408723.005 3779481.286 6968295.316 2952258.527 3757984.584 6756244.771 4142191.065 1.032162259 1.973167674 0.822927516 0.912435285 1.682272789 0.712728718 0.907245592 1.631079944 1 21.98196267 3.945125154 10.49792847 1.076900895 1.548290385 0.154084865 0.391488885 0.757389393 245.6775198 0.092299375 0.167826382 8813.028089 -3.945125154 0.47138949 ETLVYLTHLDYVDTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ETLVYLTHLDYVDTER 16 0 O14980 O14980 XPO1 Exportin-1 0 ;;;;; 252.17 1.60E-26 2595040000 1606230 1992460 1849590 1935480 1933130 1621020 2204320 1688610 1818880 FALSE TRUE 1505698.932 2139983.812 1893463.148 1985147.694 1781309.768 2088982.159 1873802.68 1899436.676 1515297.178 0.993665767 1.412253546 1.249565548 1.310071531 1.175551432 1.378595691 1.236590886 1.253507697 1 20.53116933 0.410243982 1.706669753 1.000009348 1.270721902 0.307276915 0.115727672 5.391243362 14.39163479 0.097317154 0.027445192 2.571840207 -0.410243982 0.270712553 ETMQSLNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 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 ;;;;;;;;;;; 258.95 1.05E-14 46801014000 14235563 16287868 15259464 15028846 16674255 13343286 16903538 15171695 18849479 FALSE TRUE 13344584.52 17493838.69 15621425.69 15414511.63 15364726.27 17195276.06 14369009.4 17065914.52 15703379.18 0.849790632 1.114017467 0.994781156 0.981604752 0.978434393 1.09500483 0.915026583 1.086767015 1 23.90457171 -1.590606963 6.033944557 0.99997528 1.0072997 0 0.081900692 2.42E-05 1.64E-06 0.070333998 0.016521928 0.025668059 1.590606963 0.00732442 ETNCESDRER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETNCESDRER 10 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 75.695 0.034859 66429000 31777 42939 33659 36183 44617 29905 36404 37107 37322 FALSE TRUE 29788.13429 46118.24824 34457.40737 37111.51704 41112.9608 38538.08803 30945.55816 41739.89063 31092.71709 0.958042175 1.483249216 1.10821474 1.193575876 1.3222698 1.23945707 0.995267093 1.342433037 1 14.92428907 -0.420988373 0.295275365 0.920263672 1.248557338 0.098461618 0.162370857 16.29509753 1.666742489 1.515508307 0.186383942 0.37932514 0.420988373 0.328293666 ETNGNEDEEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETNGNEDEEGR 11 0 Q9BUQ8;H0YIL9 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ; 211.68 1.98E-08 129879000 169407 178609 176947 185874 171031 167197 213570 165452 147408 FALSE TRUE 158804.1183 191833.3962 181144.2664 190643.8415 157598.9152 215464.0597 181547.1612 186109.0464 122804.6525 1.293144152 1.562102024 1.47506029 1.552415463 1.283330167 1.754526846 1.478341068 1.515488563 1 16.90600569 -1.199200586 4.875725606 0.999937637 1.500502812 0.565804043 0.134388411 7.94E-05 1.30E-05 0.113379155 0.026720407 0.063211983 1.199200586 0.500565175 ETPAAQS(ph)PTRGPSDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETPAAQSPTRGPSDTK 16 1 A0A087WVP4;A0A087X1R1;P53814-5;P53814;P53814-6 A0A087WVP4 SMTN Smoothelin 1 ET(0.136)PAAQS(0.844)PT(0.019)RGPS(0.001)DTK 67.43 0.041579 0 52690 57265 56764 54627 66081 49217 56529 53474 59370 TRUE FALSE 49392.22695 61504.96018 58110.46889 56028.8213 60891.26482 63425.14893 48053.00124 60150.34661 49460.76346 0.998614326 1.243510126 1.174880144 1.132793297 1.231102404 1.28233259 0.971537799 1.216122486 1 15.59399689 0.988771243 0.815658648 1.011011802 1.176480579 0.143982507 0.10426427 1.085288203 1.600538997 0.092425251 0.033634616 9.744762146 -0.988771243 0.165468778 ETPEHPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETPEHPLK 8 0 Q8N163-2;Q8N163;H0YB24;G3V119;E5RHJ4 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ; 77.282 0.033615 667380000 1687890 1591540 1625820 1653230 1744980 1351910 1865520 1493250 1932680 FALSE TRUE 1582247.978 1709379.278 1664385.218 1695654.681 1607936.31 1742184.471 1585802.595 1679685.55 1610103.222 0.982699715 1.061658193 1.033713364 1.053134145 0.998654178 1.082032783 0.98490741 1.043216066 1 20.61872175 1.708062151 25 1.010259438 1.037447002 0.12551679 0.031920686 1.394269806 1136.465249 0.012919239 0.00716436 51.05780623 -1.708062151 0.027187564 ETPHS(ph)PGVEDAPIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 ETPHSPGVEDAPIAK 15 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 ETPHS(1)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK;ET(0.001)PHS(0.999)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK;ET(0.11)PHS(0.89)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK;ET(0.029)PHS(0.971)PGVEDAPIAK;ET(0.027)PHS(0.973)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK 296.25 4.71E-44 56138860000 32467462 27849584 31102818 30448169 33390379 22253214 29058933 24001745 42203104 TRUE FALSE 30435381.51 29911596.18 31840591.53 31229520.57 30768033.32 28677355.63 24701815.77 26998415.7 35159133.3 0.865646523 0.850748962 0.905613664 0.888233515 0.875107844 0.815644555 0.702571806 0.767891958 1 25.06739617 2.142373689 4.305909707 0.783863928 0.877941644 0.034695292 0.078556528 0.293081958 9.81697134 0.027689036 0.02002347 138.7949578 -2.142373689 0.094077716 ETPLDLQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETPLDLQHR 9 0 K7EID2;Q9BT22-2;Q9BT22 K7EID2 ALG1 Chitobiosyldiphosphodolichol beta-mannosyltransferase 0 143.03 0.0016265 0 108850 128750 108770 105260 124920 108380 131380 120670 128970 FALSE TRUE 102037.2728 138282.784 111350.0758 107961.1498 115109.2871 139667.5466 111680.7887 135735.9151 107444.0738 0.949677997 1.287021043 1.036353815 1.004812513 1.071341425 1.299909261 1.039431815 1.263316908 1 16.71322639 ETPPNGNLS(ph)PAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETPPNGNLSPAPR 13 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 ETPPNGNLS(1)PAPR;ETPPNGNLS(1)PAPR 216.98 2.79E-11 773470000 448720 456420 586960 614110 612650 410990 481800 392030 451030 TRUE FALSE 420635.4162 490213.8117 600882.9684 629869.1023 564534.9403 529636.1411 409558.5628 440975.8085 375750.1792 1.119454998 1.304626954 1.599155507 1.676297543 1.502420948 1.409543283 1.089975695 1.173587753 1 18.51941427 1.770151617 4.029742029 1.094931853 1.454383913 0.518513305 0.157447299 0.177815043 5.787608445 0.086061815 0.044338409 58.90492626 -1.770151617 0.35945206 ETQS(ph)PEQVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ETQSPEQVK 9 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 ETQS(1)PEQVK;ETQS(1)PEQVK;ET(0.001)QS(0.999)PEQVK;ETQS(1)PEQVK;ETQS(1)PEQVK;ETQS(1)PEQVK 221.44 4.40E-07 16390490000 23456500 15678900 18624200 17138400 17842600 15412600 23669900 16195400 21596000 TRUE FALSE 21988399.54 16839782.07 19065974.82 17578200.36 16441314.17 19861967.42 20120818.24 18217431.34 17991488.08 1.22215569 0.935986061 1.059721949 0.977028708 0.913838483 1.103964682 1.118352086 1.012558342 1 24.10081118 ETQS(ph)PEQVKSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ETQSPEQVKSEK 12 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 ETQS(1)PEQVKSEK;ETQS(1)PEQVKSEK;ETQS(1)PEQVKSEK;ETQS(1)PEQVKSEK;ET(0.007)QS(0.993)PEQVKSEK 204.05 7.14E-08 7593370000 3802230 2906670 3055730 3488450 4301190 2177830 3854990 2901410 8150880 TRUE FALSE 3564255.211 3121882.871 3128213.359 3577969.533 3963391.888 2806534.167 3276970.037 3263657.425 6790445.471 0.524892693 0.459746402 0.460678666 0.526912343 0.583671853 0.41330634 0.482585428 0.480624937 1 22.69507479 -1.401370032 3.102369758 1.007139344 0.485987178 0.922135703 0.046407295 14621512.89 18709861.11 930078.0114 0.011528964 0.039685327 1.401370032 -0.521152166 ETQTHENMSQLS(ph)EEEQNKDYQDCSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETQTHENMSQLSEEEQNKDYQDCSK 25 1 A0A087X0M4;Q9BWU0 A0A087X0M4 SLC4A1AP Kanadaptin 1 ETQTHENMS(0.001)QLS(0.999)EEEQNKDYQDCSK 145.57 3.50E-07 167540000 112600 52044 77086 64072 72782 53647 93813 59326 104760 TRUE FALSE 105552.567 55897.39191 78914.51632 65716.19599 67065.99531 69134.01801 79746.61157 66732.98169 87274.87922 1.209426675 0.640475156 0.904206537 0.752979512 0.768445581 0.792141091 0.913740727 0.764629894 1 16.41327883 -2.001527886 8.424139699 1.175509416 0.82961581 0.08915353 0.15199185 0.070835046 1.28E-05 0.020806858 0.030199427 0.009964881 2.001527886 -0.345893606 ETS(ph)PSHPGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETSPSHPGFK 10 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 ET(0.427)S(0.569)PS(0.004)HPGFK;ET(0.423)S(0.573)PS(0.004)HPGFK 121.08 0.00033792 876750000 1965690 1246380 1619980 1444270 1523600 1428220 1903620 1486560 1112120 TRUE FALSE 1842660.972 1338663.272 1658406.691 1481332.413 1403942.602 1840523.929 1618189.853 1672160.288 926499.9874 1.988840795 1.44486054 1.789969469 1.598847743 1.515318533 1.986534219 1.746562197 1.804814151 1 19.82143143 ETS(ph)SDVALASHILTALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETSSDVALASHILTALR 17 0 O00273;O00273-2 O00273 DFFA DNA fragmentation factor subunit alpha 1 ET(0.313)S(0.66)S(0.027)DVALASHILTALR 204.5 5.62E-12 22662000 28069 30417 29951 23136 26112 21474 25122 21505 28339 TRUE FALSE 26312.21139 32669.10633 30661.45186 23729.70893 24061.26885 27673.1952 21355.18932 24189.94659 23609.03782 1.114497405 1.383754246 1.298716707 1.005111225 1.019154996 1.172144134 0.904534504 1.024605355 1 14.52705163 3.239909204 24.99762818 1.018879892 1.295685849 0.600921779 0.092938551 19.79537784 366924.3342 0.024966182 0.032044857 1737.437553 -3.239909204 0.276805957 ETSFGS(ph)SENITMTSLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.938)S(0.062)ENITMTSLSK;ETSFGS(0.999)S(0.001)ENITMTSLSK;ETSFGS(0.929)S(0.071)ENITMTSLSK;ETSFGS(0.5)S(0.5)ENITMTSLSK 398.14 2.03E-122 824350000 1512100 1283270 1331680 1375590 1355540 1125620 1765220 1252980 1601280 TRUE FALSE 1417460.36 1378284.646 1363268.078 1410889.968 1249081.356 1450568.221 1500541.648 1409417.311 1334016.023 1.062551225 1.033184476 1.021927814 1.057625953 0.936331599 1.087369414 1.124830304 1.056522026 1 20.34734456 ETSSALTHAGAHLDLSAFSSWEELASLGLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETSSALTHAGAHLDLSAFSSWEELASLGLDR 31 0 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ; 230.12 8.12E-36 80066000 60480 78266 76795 81614 93370 68188 87351 73932 78722 FALSE TRUE 56694.66476 84060.89608 78616.61367 83708.35341 86037.09684 87872.76866 74253.52848 83162.57294 65582.78964 0.864474736 1.28175237 1.198738482 1.276376834 1.311885287 1.339875433 1.132210583 1.268054827 1 16.00102965 -1.470549626 2.705124093 0.991904928 1.219171668 0.18615116 0.136028272 8378066.01 8867617.728 510239.5441 0.03166697 0.03384156 1.470549626 0.22726674 ETSSDVALASHILTALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETSSDVALASHILTALR 17 0 O00273;O00273-2 O00273 DFFA DNA fragmentation factor subunit alpha 0 ; 168.05 2.15E-09 139817000 321930 390750 360980 368250 439020 295990 391060 340280 390250 FALSE TRUE 301780.976 419681.5366 369542.6161 377699.9184 404541.1401 381437.508 332424.1834 382764.707 325114.7539 0.928229102 1.290872012 1.136652864 1.161743397 1.24430262 1.173239613 1.022482614 1.177321861 1 18.3105895 1.128228667 0.804929717 1.012931684 1.170251771 0.112756387 0.105610775 1.008000972 1.483820858 0.092290781 0.034697138 13.43472146 -1.128228667 0.157320087 ETSVSKEDT(ph)DHEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETSVSKEDTDHEEK 14 1 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 ETSVSKEDT(0.999)DHEEK 123.55 0.00014986 483890000 924620 485030 599230 575260 548310 477890 720030 457990 461990 TRUE FALSE 866749.6847 520942.1259 613444.0186 590022.1455 505247.9444 615849.0851 612068.1859 515171.0597 384880.8844 2.251994629 1.353515196 1.593854212 1.53299935 1.312738473 1.600103071 1.590279514 1.338520775 1 18.55405249 2.83595703 0.050402504 3.13E-29 3.073395513 0.477485276 0.231808527 111.3929449 2.080492443 53.66986366 72.04797009 685.4204062 -2.83595703 3.073395513 ETTEAACR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETTEAACR 8 0 Q9Y2Q3-3;Q9Y2Q3;Q9Y2Q3-2;E9PFN5;Q9Y2Q3-4 Q9Y2Q3-3 GSTK1 Glutathione S-transferase kappa 1 0 87.323 0.038216 0 130870 144160 98555 121260 161960 110270 140850 128520 138400 FALSE TRUE 122679.0803 154833.7564 100892.7711 124371.7369 149240.3149 142103.1589 119730.8501 144566.0049 115300.1459 1.063997616 1.342875633 0.875044609 1.078678053 1.294363626 1.232462958 1.038427568 1.253823261 1 16.81503481 -1.131711346 4.50303161 0.999982874 1.139182937 0.09609693 0.140099053 2.33E-05 4.49E-06 0.131086323 0.030893542 0.073839484 1.131711346 0.139200063 ETTGTGPNVYHENDTIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETTGTGPNVYHENDTIAK 18 0 Q4G0F5 Q4G0F5 VPS26B Vacuolar protein sorting-associated protein 26B 0 90.972 0.0025228 0 50264 36546 51116 37752 52419 36408 50484 46906 60451 FALSE TRUE 47118.06596 39251.90387 52328.49566 38720.78023 48302.22319 46918.39857 42914.39287 52762.31735 50361.33757 0.935599971 0.779405507 1.039060878 0.76885925 0.959113191 0.931635275 0.852129728 1.04767506 1 15.62002898 1.233226974 24.99985951 1.023837589 0.895513451 0.300122845 0.081720029 164.2177893 769680.5312 0.064017638 0.017843717 17.1090925 -1.233226974 -0.128324138 ETTSGTSTEPVKNSS(ph)PAPPQPAPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ETTSGTSTEPVKNSSPAPPQPAPGK 25 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 ETTSGTSTEPVKNS(0.21)S(0.79)PAPPQPAPGK;ETTSGTS(0.001)T(0.001)EPVKNS(0.156)S(0.841)PAPPQPAPGK 131.5 4.86E-05 186230000 216730 142568 171429 171751 180284 121862 242830 158361 264100 TRUE FALSE 203165.2562 153123.8831 175495.3768 176158.4214 166125.2219 157041.5811 206419.8958 178132.7194 220020.0038 0.923394476 0.69595437 0.797633732 0.800647297 0.755045991 0.713760469 0.938186948 0.809620563 1 17.74727517 1.011966176 0.836070997 0.993103008 0.775058611 0.390747566 0.077448356 0.575691904 0.892789789 0.067611731 0.024396199 10.27936236 -1.011966176 -0.218044397 ETVQTTEDQILKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ETVQTTEDQILKR 13 1 P18206;P18206-2 P18206 VCL Vinculin 0 ;;;; 211.82 3.02E-08 2085150000 1438180 1377960 1486970 1435840 1745710 1191010 1729130 1318350 1903420 FALSE TRUE 1348166.881 1479985.592 1522241.631 1472686.085 1608608.978 1534835.253 1469863.009 1482948.9 1585726.905 0.850188564 0.93331682 0.95996456 0.928713564 1.014430021 0.96790642 0.926933259 0.935185557 1 20.5967129 5.367360217 1.184200149 0.958467982 0.552149507 0.596388079 0.028720017 4.261470844 1.753496256 0.007846124 3.068034002 233002.3047 -5.367360217 -0.406318475 ETVQTTQS(ph)PTPVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETVQTTQSPTPVEK 14 0 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 ETVQTTQS(1)PTPVEK 240.63 2.20E-17 106960000 300050 230160 249260 237350 206990 207940 312490 220400 152060 TRUE FALSE 281270.4061 247201.2859 255172.5649 243440.8028 190733.8404 267968.9024 265635.0255 247917.4252 126680.2037 2.22031855 1.951380553 2.014304979 1.921695702 1.505632568 2.1153179 2.096894525 1.95703368 1 16.95083157 -1.898263291 2.383029797 0.44233925 1.974648164 0.724242827 0.188647228 2592301.473 1355017.291 8108868.676 0.04449573 0.012639698 1.898263291 1.532308914 ETVSEAPPLLFS(ph)DEEEKEAQLGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETVSEAPPLLFSDEEEKEAQLGVK 24 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 ETVSEAPPLLFS(1)DEEEKEAQLGVK 180.65 2.11E-17 44668000 146550 59222 80809 79049 79680 51564 100970 64243 87139 TRUE FALSE 137377.6971 63606.8585 82725.82764 81077.53117 73422.25421 66449.68973 85830.48586 72263.87997 72594.93796 1.892386728 0.87618862 1.139553665 1.116848274 1.011396335 0.915348805 1.182320535 0.995439655 1 16.14758133 4.745291253 24.99971763 1.039393969 1.892387116 0.888720109 0.095887732 239.6274554 890029.6392 0.022081355 0.21500786 55627.71906 -4.745291253 0.852993147 ETVVEEPVDITPYLDQLDESLRDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ETVVEEPVDITPYLDQLDESLRDK 24 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 0 ;; 100.64 0.0038176 44727000 70097 58087 62077 66217 60379 57527 86135 54944 85764 FALSE TRUE 65709.7539 62387.82192 63549.49575 67916.24033 55637.0769 74134.11103 73219.85639 61803.87935 71449.43434 0.919667937 0.873174469 0.889433154 0.950549727 0.778691636 1.037574499 1.024778671 0.86500166 1 16.12463497 2.216464067 24.99999897 0.990199887 0.885132834 0.374914346 0.06339821 228.2249607 258211.7007 0.021891818 0.016181206 164.6129762 -2.216464067 -0.105067052 ETVVEVPQVTWEDIGGLEDVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ETVVEVPQVTWEDIGGLEDVKR 22 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 276.68 2.84E-45 1429070000 3472040 2776520 3041290 2996830 3271280 2444660 3882350 2658200 4146850 FALSE TRUE 3254731.214 2982096.43 3113430.835 3073733.731 3014366.865 3150393.656 3300227.659 2990082.121 3454713.945 0.942113085 0.863196339 0.901212339 0.889721633 0.872537325 0.911911581 0.955282467 0.865507874 1 21.72013483 -1.695803149 0.287674502 1.089871927 0.888725912 0.472979572 0.031766552 21.10382165 1.064285423 1.361766493 0.035385427 0.020146372 1.695803149 -0.201146015 ETVYCLNDDDETEVLKEDIIQGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ETVYCLNDDDETEVLKEDIIQGFR 24 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;;;; 371.69 8.10E-119 4605074000 1586210 1245525 1331602 1319265 1447725 1095417 1980617 1319297 1916301 FALSE TRUE 1486931.948 1337744.967 1363188.228 1353119.573 1334026.518 1411646.105 1683641.868 1484014.135 1596457.983 0.931394351 0.837945615 0.853882935 0.847576064 0.835616429 0.884236303 1.054610823 0.929566672 1 20.60644315 1.885231884 5.87125967 0.996587534 0.856811535 0.701466274 0.040010748 0.108334636 4.788067134 0.015920545 0.009599892 76.77713186 -1.885231884 -0.139775999 ETWYLSWALDTNQEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ETWYLSWALDTNQEER 16 0 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1;H3BSV8 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ;;; 368.3 7.20E-104 242970000 236424 238603 265214 237328 269237 228425 279122 216858 297113 FALSE TRUE 221626.6439 256269.4144 271505.0013 243418.2383 248092.2121 294367.5893 237270.2473 243933.1987 247522.9209 0.895378267 1.035336095 1.096888322 0.98341696 1.002299953 1.189253861 0.958578892 0.985497415 1 17.9172026 -0.408002724 8.099158612 0.999998988 1.02785188 0 0.0800291 0 0 0.072006513 0.016972098 0.390838444 0.408002724 0.027852892 ETYVEQEQGENANDRNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ETYVEQEQGENANDRNDR 18 1 Q9Y2L1;F2Z2C0 Q9Y2L1 DIS3 Exosome complex exonuclease RRP44 0 68.494 0.024088 0 240330 151060 167230 167720 192420 114680 172720 149430 202600 FALSE TRUE 225288.1743 162244.6396 171196.7746 172023.9791 177308.1094 147786.2543 146822.2395 168086.6644 168784.7512 1.334766161 0.961251763 1.014290529 1.019191473 1.05049839 0.875590083 0.869878579 0.995864042 1 17.36482504 4.739124059 24.70198873 0.967142379 1.334766293 0.785320655 0.059312364 19.86509364 870659.2949 0.015761537 0.093430583 54843.36057 -4.739124059 0.367623914 EVAALCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVAALCR 7 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 90.986 0.038936 108260000 275530 400280 324960 327970 396810 277160 371280 342490 368630 FALSE TRUE 258285.0691 429917.1477 332668.2047 336386.2655 365646.1433 357171.5927 315610.0108 385250.6304 307103.2716 0.841036528 1.399910673 1.083245395 1.095352269 1.190629267 1.163034151 1.02769993 1.254466058 1 18.22836436 -4.850686072 0.286875757 1.17E-10 1.153933124 0.050769379 0.147365362 573.07939 5.897885533 341.4942667 0.147495213 1.41E-05 4.850686072 1.153933124 EVAATEEDVTRLPS(ph)PT(ph)SPFSSLSQDQAATSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVAATEEDVTRLPSPTSPFSSLSQDQAATSK 31 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 2 EVAATEEDVTRLPS(0.964)PT(0.69)S(0.345)PFSSLSQDQAATSK 174.66 5.99E-13 93711000 92123 86307 79062 109140 104930 86204 87292 74265 86686 TRUE FALSE 86357.18587 92697.26008 80937.38798 111940.7172 96689.22107 111089.6954 74203.37498 83537.14873 72217.54659 1.195792296 1.283583623 1.120744082 1.550048741 1.338860507 1.5382646 1.027497866 1.1567431 1 16.14006179 1.638075299 10.83610191 1.069275224 1.313985216 0.461830246 0.138832811 0.109186773 26.6708356 0.067337647 0.036032025 43.45855671 -1.638075299 0.244709992 EVAATEEDVTRLPS(ph)PTS(ph)PFSSLSQDQAATSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVAATEEDVTRLPSPTSPFSSLSQDQAATSK 31 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 2 EVAATEEDVT(0.005)RLPS(0.635)PT(0.516)S(0.844)PFSSLSQDQAATSK 179.58 2.02E-18 58907000 63717 49909 50996 74936 64782 52107 62429 51193 49491 TRUE FALSE 59729.06671 53604.31429 52205.6492 76858.98463 59694.28304 67149.44501 53068.35101 57584.55874 41230.63238 1.448657546 1.300108953 1.266185993 1.864123352 1.447813909 1.628630005 1.287109801 1.396645053 1 15.33142897 -0.560425463 7.932884696 1.000009135 1.433037929 0.380965222 0.180333748 0 0 0.174064654 0.041027432 0.27515318 0.560425463 0.433028794 EVAATEEDVTRLPS(ph)PTSPFSSLSQDQAATSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVAATEEDVTRLPSPTSPFSSLSQDQAATSK 31 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 EVAATEEDVT(0.001)RLPS(0.958)PT(0.038)S(0.002)PFSSLSQDQAATSK;EVAATEEDVTRLPS(0.984)PT(0.006)S(0.006)PFS(0.001)S(0.002)LSQDQAATSK 155.09 2.58E-09 391590000 266570 277960 240497 273458 271329 208270 316768 242541 282253 TRUE FALSE 249885.8595 298540.4476 246201.7024 280475.3952 250019.9148 268394.168 269271.5791 272822.7777 235143.1509 1.062696739 1.269611496 1.047029018 1.192785732 1.063266839 1.141407551 1.145138942 1.160241226 1 17.84317979 -1.874660255 2.640475028 0.934862122 1.139651818 0.284575199 0.067086659 8852987.193 5213238.132 3600473.971 0.014515449 0.01334565 1.874660255 0.204789696 EVADEVTRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVADEVTRPR 10 1 P33992;B1AHA9 P33992 MCM5 DNA replication licensing factor MCM5 0 114.86 0.0011849 165950000 178400 160990 180860 163840 158820 159610 174860 165700 121710 FALSE TRUE 167234.2625 172909.8671 185150.0846 168044.4118 146346.9178 205686.8159 148641.3663 186388.0098 101395.8147 1.649321157 1.7052959 1.826013087 1.657311125 1.443323063 2.028553314 1.465951694 1.838221925 1 16.62963858 -1.522583553 3.184163478 0.978884159 1.701229004 0.620261548 0.172559158 32469412.11 36005994.98 5873273.276 0.036625183 0.030020398 1.522583553 0.722344845 EVADEVTRPRPSGEEVLQDIQVMLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVADEVTRPRPSGEEVLQDIQVMLK 25 2 P33992;B1AHA9 P33992 MCM5 DNA replication licensing factor MCM5 0 70.315 0.021968 48853000 50698 46883 48860 45523 50896 35907 63572 49916 59601 FALSE TRUE 47524.90268 50354.2661 50018.98227 46691.19725 46898.83346 46272.768 54039.96877 56148.12248 49653.20806 0.957136599 1.014119088 1.007366578 0.940346033 0.944527762 0.931919 1.088347982 1.130805534 1 15.59959931 1.679217135 7.034452388 1.082071705 0.974638148 0.578874458 0.042307794 0.092243801 8.988476836 0.021377336 0.010988558 47.77680847 -1.679217135 -0.107433557 EVAEAATGEDAS(ph)SPPPKTEAASDPQHPAASEGAAAAAASPPLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVAEAATGEDASSPPPKTEAASDPQHPAASEGAAAAAASPPLLR 44 1 Q99536-3;Q99536;K7ERT7 Q99536-3 VAT1 Synaptic vesicle membrane protein VAT-1 homolog 1 EVAEAATGEDAS(0.607)S(0.392)PPPKT(0.001)EAASDPQHPAASEGAAAAAASPPLLR 192.7 7.38E-29 80774000 64483 52273 62799 52012 67693 48437 74735 60205 114560 TRUE FALSE 60447.12414 56143.34731 64288.62194 53346.71598 62376.66484 62419.97559 63529.18056 67721.72678 95439.19591 0.633357433 0.588262996 0.673608168 0.558960241 0.65357492 0.654028725 0.665650836 0.709579813 1 16.54229427 0.053083635 0.571871779 1.025585009 0.617630745 0.932495932 0.031238436 0.837114165 0.334712434 0.075852477 0.012300121 1.130013508 -0.053083635 -0.407954264 EVAEMDSVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVAEMDSVKR 10 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 119.27 0.001145 543030000 687770 677760 700950 675340 733840 455070 842110 622870 813640 FALSE TRUE 644723.7034 727942.0556 717576.865 692670.3677 676207.1666 586441.3216 715843.4233 700636.6906 677838.2277 0.951146862 1.073917088 1.058625548 1.021881534 0.997593731 0.865164132 1.056068239 1.033634077 1 19.37058148 2.861381202 3.507006841 0.98872461 1.041795458 0.066746901 0.059248756 0.48527017 10.95148711 0.018455799 0.019769679 726.7435765 -2.861381202 0.053070848 EVAETSMHNLLETDIEQVSQLSALVDAQLDYHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVAETSMHNLLETDIEQVSQLSALVDAQLDYHR 33 0 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 0 ; 250.43 5.14E-48 45006000 13604.4 19626.3 19729.4 20788 21910.9 18526.3 21434 20650 21709 FALSE TRUE 12752.92489 21079.45167 20197.39068 21321.45527 20190.1063 23874.54206 18220.17068 23228.19796 18085.62765 0.705141405 1.165536086 1.116764708 1.178917076 1.116361936 1.320083688 1.007439224 1.284345692 1 14.14255605 4.739940272 24.43219886 1.148344542 0.705141203 0.65256676 0.101708443 47.52375149 841471.6963 0.020677919 0.129249113 54946.53007 -4.739940272 -0.443203338 EVAWVIFDEIHYMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EVAWVIFDEIHYMR 14 0 P42285 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 ;; 198.33 2.22E-08 166112000 362338 446651 384222 391208 471308 354630 460713 426788 343198 FALSE TRUE 339659.9114 479721.5048 393335.9273 401247.0596 434293.3708 457005.9241 391633.3627 480073.4213 285916.0367 1.18797083 1.677840496 1.375704322 1.403373747 1.518954221 1.598392064 1.369749551 1.679071335 1 18.12523202 -1.22427905 3.784396539 0.999444045 1.481613725 0.491345463 0.152243951 4406809.605 2147605.744 19305.93002 0.031196363 0.059665179 1.22427905 0.48216968 EVCGFAPYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EVCGFAPYER 10 0 Q9Y3U8;J3QSB5 Q9Y3U8 RPL36 60S ribosomal protein L36 0 ;;;; 191.45 1.84E-06 6405180000 2044784 2903760 2039920 2050816 2939620 1619922 2124480 2470500 2554760 FALSE TRUE 1916804.619 3118757.412 2088307.866 2103443.411 2708754.103 2087567.184 1805933.947 2778947.363 2128354.052 0.90060421 1.465337691 0.981184434 0.988295819 1.272699014 0.980836427 0.848511997 1.305679082 1 21.02130673 3.738581151 23.96298184 1.037890378 1.223294733 0.058532611 0.193157982 413.5156005 864663.9553 0.046153317 0.082221485 5477.484426 -3.738581151 0.185404355 EVCPVLDQFLCHVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVCPVLDQFLCHVAK 15 0 Q9NY27-2;Q9NY27;C9IZ04;C9IZF4;F8WCA1 Q9NY27-2 PPP4R2 Serine/threonine-protein phosphatase 4 regulatory subunit 2 0 180.62 6.22E-07 75664000 143540 142170 158000 157160 177000 124650 177070 129830 185740 FALSE TRUE 134556.0876 152696.4147 161747.8346 161192.9917 163099.134 160634.4315 150519.9973 146039.5613 154738.7941 0.869569189 0.986801116 1.045295949 1.041710275 1.054028726 1.038100577 0.972736011 0.943781178 1 17.23947541 4.744417998 2.595578814 1.015330509 0.837967812 0.628027739 0.034618541 0.351451755 3.046027118 0.009062215 0.137190765 55515.9784 -4.744417998 -0.177362696 EVDDALVEMHWVEGQNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVDDALVEMHWVEGQNR 17 0 Q86W50 Q86W50 METTL16 Methyltransferase-like protein 16 0 124.2 5.11E-05 43538000 38599 37212 48695 48772 41760 39988 52824 35950 39439 FALSE TRUE 36183.15749 39967.2152 49850.0684 50023.57209 38480.33805 51531.88645 44903.53159 40438.43664 32856.37611 1.101252231 1.216421892 1.5172114 1.52249207 1.171168053 1.568398361 1.366661114 1.230763749 1 15.00388575 0.937125079 3.170610917 1.000780501 1.364478722 0.339496091 0.155867587 0.331135682 8.134695113 0.144104244 0.037623306 8.652170706 -0.937125079 0.363698222 EVDDFFEQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVDDFFEQEK 10 0 Q9Y5X3;Q5QPE5;A0A087WUY5;Q5QPE4 Q9Y5X3 SNX5 Sorting nexin-5 0 185.29 3.41E-06 85647000 173010 109330 143930 124440 130490 105120 153610 116230 139620 FALSE TRUE 162181.6129 117424.907 147344.0876 127633.3411 120241.8418 135466.4375 130577.6065 130741.5714 116316.52 1.394312802 1.009529059 1.266751168 1.097293326 1.033746898 1.164636266 1.122605856 1.1240155 1 16.82769649 8 0.07402943 0.905624004 1.698515308 0.270249992 0.103218155 364.4530493 1.980874003 3.488476556 29.8474197 100000000 -8 0.792891304 EVDDFFEQEKNFLINYYNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVDDFFEQEKNFLINYYNR 19 1 Q9Y5X3;Q5QPE5;A0A087WUY5;Q5QPE4 Q9Y5X3 SNX5 Sorting nexin-5 0 137.69 3.08E-06 77191000 101720 114710 111660 122640 151350 96591 132570 107640 206830 FALSE TRUE 95353.52678 123203.2478 114308.6279 125787.15 139463.5815 124475.2537 112692.3592 121079.0909 172308.7368 0.553387649 0.715014514 0.663394266 0.730010285 0.809381951 0.722396647 0.654014192 0.702686893 1 17.39463633 -5 0.311576398 3.713932756 0.68117435 0.695979513 0.064088031 173.6106284 1.568074999 309.6129448 0.058681775 1.00E-05 5 -3.032758406 EVDDLEQWIAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVDDLEQWIAER 12 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;; 300.35 4.14E-36 384853000 361050 405790 389762 382688 431177 334952 446014 363592 433431 FALSE TRUE 338452.525 435835.1138 399007.3387 392508.422 397314.0977 431647.2049 379138.3413 408987.2616 361088.566 0.937311665 1.207003364 1.105012388 1.087014264 1.10032312 1.195405353 1.049987114 1.132650823 1 18.46199321 -0.917159123 0.750559299 0.982849083 1.111536157 0.139664884 0.075716056 68.13166875 20.19213707 2.883721828 0.023398363 0.121015466 0.917159123 0.128687075 EVDDLGPEVGDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVDDLGPEVGDIK 13 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 176.8 3.72E-05 42399000 171160 115550 133400 127790 144910 115800 156920 122850 196430 FALSE TRUE 160447.4011 124105.4422 136564.311 131069.3077 133529.3531 149229.5801 133391.3028 138188.0929 163644.564 0.980462761 0.758384142 0.834517858 0.800938965 0.815971822 0.911912846 0.815128224 0.844440472 1 17.32020615 -1.871763047 0.44853444 1.147578549 0.831415361 0.3641853 0.062566527 48.14200617 3.664741832 7.521588702 0.030690624 0.013434978 1.871763047 -0.316163188 EVDEDS(ph)EPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVDEDSEPER 10 0 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EVDEDS(1)EPER;EVDEDS(1)EPER 260.57 2.67E-17 1756980000 1395450 1303650 1379110 1295860 1179800 1311250 1672980 1240240 1038970 TRUE FALSE 1308111.275 1400173.602 1411823.14 1329113.961 1087143.267 1689786.589 1422132.18 1395086.694 865559.195 1.511290369 1.617652046 1.631111019 1.535555245 1.256001061 1.952248441 1.643021284 1.611775026 1 19.72327296 -1.686873144 2.521607519 0.901553295 1.606937087 0.547792 0.169530187 10515003.2 8379083.64 6609690.117 0.039927378 0.020564912 1.686873144 0.705383791 EVDEDS(ph)EPEREVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVDEDSEPEREVR 13 1 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EVDEDS(1)EPEREVR;EVDEDS(1)EPEREVR 195.38 1.31E-07 2234700000 1162310 1590560 1254350 1431420 1759520 986810 1653260 1346080 2260540 TRUE FALSE 1089563.092 1708326.717 1284103.774 1468152.661 1621334.397 1271686.027 1405369.011 1514141.051 1883241.27 0.578557357 0.907120476 0.681858344 0.779588194 0.860927605 0.675264528 0.746250113 0.804008002 1 20.84478641 0.832839862 3.663749522 0.99996575 0.757590932 0.416018398 0.093240707 0.98081532 20.06458483 0.08033979 0.020656951 6.80518384 -0.832839862 -0.242374818 EVDEQMLNVQNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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 ;;;;;;;; 286.08 4.01E-28 2328059000 3065436 2577753 2830079 2721864 2989590 2158680 3354742 2676478 3454304 FALSE TRUE 2873575.833 2768612.514 2897209.81 2791711.638 2754799.661 2781855.873 2851729.581 3010642.17 2877758.347 0.998546607 0.962072621 1.006759241 0.970099398 0.957272755 0.966674591 0.990955194 1.046176158 1 21.45651402 1.421186839 5.764182207 1.022786256 0.977829838 0.499358357 0.018849338 0.156535208 9.161823811 0.011884917 0.004474139 26.37465812 -1.421186839 -0.044956417 EVDETRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVDETRK 7 1 Q9UHV9 Q9UHV9 PFDN2 Prefoldin subunit 2 0 89.142 0.029006 318020000 708050 581480 626680 630870 703620 546740 798870 601460 834000 FALSE TRUE 663734.4144 624533.3842 641545.1455 647059.1923 648360.5235 704574.9624 679086.8598 676553.605 694800.0122 0.955288432 0.898867837 0.923352237 0.931288401 0.933161359 1.014068725 0.97738464 0.97373862 1 19.40623825 2.3437424 5.9821053 0.98878117 0.922917303 0.753184657 0.017790872 0.095547362 4.749662517 0.006017017 0.004996702 220.6695452 -2.3437424 -0.065863867 EVDGEGKPYYEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVDGEGKPYYEVR 13 1 G3V1D3;G3V180;Q9NY33-4;Q9NY33;E9PQ14 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ;;; 109.07 0.0010635 1080810000 1296010 1153210 1208130 1193440 1318910 986940 1552690 1159330 1799430 FALSE TRUE 1214895.048 1238594.868 1236787.414 1224065.691 1215328.129 1271853.556 1319878.549 1304074.903 1499093.508 0.810419791 0.826229226 0.825023527 0.81653725 0.810708686 0.848415092 0.880451114 0.869908979 1 20.51565895 0.627292271 0.557066343 1.00536424 0.816373991 0.954514684 0.012124564 0.294138681 0.178909964 0.016127806 0.005861137 4.239281645 -0.627292271 -0.188990249 EVDGLLTSEPMGS(ph)PVSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 EVDGLLTSEPMGSPVSSK 18 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 1 EVDGLLTSEPMGS(1)PVSSK;EVDGLLTSEPMGS(1)PVSSK;EVDGLLTSEPMGS(0.985)PVS(0.014)S(0.001)K;EVDGLLTSEPMGS(0.981)PVS(0.011)S(0.008)K;EVDGLLTSEPMGS(0.995)PVS(0.004)S(0.001)K;EVDGLLTSEPMGS(0.998)PVS(0.002)SK;EVDGLLT(0.001)S(0.01)EPMGS(0.975)PVS(0.009)S(0.004)K;EVDGLLTSEPMGS(1)PVSSK;EVDGLLTSEPMGS(0.996)PVS(0.004)SK;EVDGLLTSEPMGS(1)PVSSK;EVDGLLTSEPMGS(1)PVSSK;EVDGLLTSEPMGS(1)PVSSK 393.34 9.53E-127 3466733000 5698830 4617470 5465870 5086868 5207350 3862672 5939170 4357620 6289860 TRUE FALSE 5342150.403 4959352.283 5595523.018 5217405.645 4798385.736 4977762.701 5048646.595 4901678.449 5240041.732 1.019486232 0.946433738 1.0678394 0.99568017 0.915715176 0.949947148 0.963474501 0.935427369 1 22.32114687 2.94311566 9.560573959 0.951863702 1.008708605 0.369190699 0.035782636 0.546066712 89.40910735 0.010555307 0.011226144 877.2344129 -2.94311566 0.056844903 EVDIGIPDATGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVDIGIPDATGR 12 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 219.35 7.48E-11 350230000 716900 736120 782230 710090 732330 651060 828810 643980 793590 FALSE TRUE 672030.5087 790623.0907 800784.865 728312.1116 674815.7559 839010.4529 704537.6348 724382.3206 661134.7022 1.016480464 1.1958578 1.211228003 1.101609262 1.020693292 1.269046157 1.065649152 1.095665253 1 19.33458472 1.012855404 1.341362415 1.00263827 1.145016632 0.17916814 0.082129224 0.657095923 2.420452553 0.073568295 0.022347898 10.30043115 -1.012855404 0.142378362 EVDILNHVFDDVESFVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVDILNHVFDDVESFVSR 18 0 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 0 83.404 0.0040106 375840000 26379 24592 27777 23828 24884 26166 29288 21101 21253 FALSE TRUE 24727.98548 26412.81727 28435.88356 24439.46682 22929.71102 33719.69943 24896.5363 23735.5063 17705.737 1.396608652 1.491766046 1.606026541 1.380313444 1.295044144 1.904450486 1.406128211 1.34055455 1 14.11192928 0.916897318 2.202632744 1.002946238 1.513233543 0.47427604 0.166555902 0.324520421 3.358600693 0.147254736 0.040374824 8.258426695 -0.916897318 0.510287305 EVDRNEGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVDRNEGLK 9 1 H0Y6T8;Q9NP72;Q9NP72-2;Q5W0J0;A0A087X163;Q9NP72-3 H0Y6T8 RAB18 Ras-related protein Rab-18 0 ; 150.61 7.74E-05 490140000 790090 682230 648590 682000 805860 551340 841840 709390 828630 FALSE TRUE 740639.6773 732743.0191 663974.8611 699501.2746 742571.0063 710502.9077 715613.9073 797958.9031 690326.2998 1.072883472 1.061444449 0.961827561 1.01329078 1.075681176 1.029227639 1.036631383 1.155915548 1 19.39691892 2.748842229 24.19454205 1.057099287 1.022119711 0.087772046 0.049891573 1074.324222 2528085.517 0.014940945 0.015696718 560.8441949 -2.748842229 -0.034979576 EVDRPGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EVDRPGSK 8 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ;;;;;;; 121.05 0.0013223 17786710000 10133040 8782800 9547150 9405200 9649470 7553510 11308630 8202090 10247000 FALSE TRUE 9498831.114 9433087.65 9773612.906 9646553.355 8891639.55 9734085.716 9613005.916 9226138.992 8536709.502 1.112704036 1.10500277 1.144892292 1.130008389 1.041576915 1.140262031 1.126078604 1.080760566 1 23.02524866 0.906053248 3.659983292 1.000064037 1.116081687 0.612772825 0.028702639 0.260869505 7.847578781 0.026372213 0.006787054 8.054771935 -0.906053248 0.11601765 EVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNR 36 1 Q96EK6;G3V4W4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 0 ; 249.13 1.34E-50 526120000 14272.5 13354.3 14444.8 15795.4 13025 12921.3 20693.8 14583.5 17530.7 FALSE TRUE 13379.2097 14343.06627 14787.43748 16200.73671 12002.06904 16651.46955 17590.9568 16404.28208 14604.71292 0.91608851 0.98208478 1.012511342 1.109281421 0.821794246 1.140143572 1.204471249 1.123218386 1 13.83414638 2.076675014 24.9997072 1.142040468 0.982510852 0.388736444 0.089218901 30.40921926 9913.560249 0.030460092 0.022496266 119.3094967 -2.076675014 -0.159529616 EVDYEAGDIPTEWEAWIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVDYEAGDIPTEWEAWIR 18 0 Q8N183 Q8N183 NDUFAF2 "Mimitin, mitochondrial" 0 67.456 0.070074 19145000 28987 28084 25087 23465 34216 22618 28352 29446 46398 FALSE TRUE 27172.75541 30163.36858 25682.07549 24067.15163 31528.81338 29147.44943 24100.88081 33122.39792 38653.87406 0.702976249 0.780345291 0.664411424 0.622632329 0.815670205 0.754062824 0.623504924 0.856897238 1 15.23832539 1.003457549 5.230414794 0.999666571 0.710982602 0.705209842 0.062794433 0.07600764 7.404220502 0.059032101 0.014906298 10.07993077 -1.003457549 -0.28868397 EVDYSGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVDYSGLR 8 0 Q9UKY7;Q9UKY7-2;H0Y8K3 Q9UKY7 CDV3 Protein CDV3 homolog 0 ; 139.88 0.001532 359870000 261400 322130 273400 300760 358770 236130 287450 297800 318850 FALSE TRUE 245039.4406 345980.8404 279885.1771 308478.0108 330593.6514 304296.8977 244349.5411 334980.9855 265631.8752 0.922477547 1.302482393 1.053658101 1.161298924 1.244555651 1.145558671 0.919880345 1.261072247 1 18.01906875 1.955091141 24.94127587 1.046741337 1.153052251 0.061628565 0.132510101 854.7951451 474731.0889 0.049354277 0.031859137 90.17603609 -1.955091141 0.106310914 EVEAVDSEYQLARPSDANRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVEAVDSEYQLARPSDANRK 20 2 O43847;O43847-2;F5H7V1;G3V1R5 O43847 NRD1 Nardilysin 0 60.564 0.032331 51774000 35576 95921 68526 92515 85236 84251 73206 74829 75635 FALSE TRUE 33349.36166 103023.0906 70151.46908 94889.09153 78541.90839 108572.896 62229.43991 84171.56537 63011.02988 0.529262285 1.635000901 1.113320465 1.505912405 1.246478728 1.72307763 0.987595982 1.335822721 1 15.94331677 0.696233729 1.138921714 1.005552651 1.298801793 0.039869351 0.344279367 2.918521263 6.355544438 0.287598628 0.089345849 4.968596495 -0.696233729 0.293249141 EVEDKES(ph)EGEEEDEDEDLSK ddPTM_SK-BR-3_Pertuzumab_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 328.57 5.57E-80 6817170000 10679430 3570550 5262750 5205310 5343880 3479890 7363910 4040700 6004670 TRUE FALSE 10011023.54 3834917.237 5387584.915 5338887.067 4924193.221 4484477.752 6259760.059 4545190.29 5002451.785 2.001223394 0.766607536 1.076988874 1.067254078 0.984355958 0.896455967 1.251338409 0.908592523 1 22.25420393 4.747003636 24.99952594 1.004223579 2.001223892 0.858943765 0.128221405 397.2003719 1176072.489 0.030633519 0.355069367 55847.48709 -4.747003636 0.997000313 EVEEDEYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EVEEDEYK 8 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;; 159.04 0.00084097 2042120000 2767160 1946740 2087630 2231070 2166520 1487970 2651200 1773750 1691540 FALSE TRUE 2593968.395 2090878.655 2137149.569 2288323.033 1996370.259 1917522.784 2253677.173 1995206.592 1409211.046 1.840723859 1.483722868 1.516557492 1.623832739 1.416658111 1.360706609 1.59924745 1.415832353 1 20.42645626 -3.125787629 0.193917588 1.08E-15 1.639011579 0.697656938 0.118599257 35.900213 0.679983938 15.10784055 0.316524625 0.000748535 3.125787629 1.639011579 EVEEEPGIHSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EVEEEPGIHSLK 12 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;;;;; 208.27 6.89E-08 3070570000 5960187 5458990 5513200 6011560 5985630 4189530 7030230 5016573 5489056 FALSE TRUE 5587149.535 5863179.3 5643975.708 6165826.807 5515542.765 5398979.3 5976112.277 5642903.182 4572897.093 1.221796472 1.282158592 1.234223205 1.348341474 1.206137521 1.180647452 1.306854748 1.233988666 1 22.12467702 -3.031287833 0.573136669 2.29E-07 1.25648813 0.719443331 0.049402177 240.4348212 8.348942445 297.6389164 0.018935319 0.000930491 3.031287833 1.256487901 EVEELEQLTQQLMQDMEHPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 EVEELEQLTQQLMQDMEHPQR 21 0 Q15942;Q15942-2;H0Y2Y8;C9JJK5 Q15942 ZYX Zyxin 0 ;;;;;; 122.22 2.16E-05 564493000 152727.1 144640.3 142589.4 141305.8 189648.5 154596.2 150559.2 126640.9 172415.7 FALSE TRUE 143168.1834 155349.6183 145971.6879 144931.9461 174754.2718 199225.6133 127984.2457 142452.2951 143638.4058 0.996726346 1.081532599 1.016244138 1.009005532 1.216626367 1.386994043 0.89101689 0.991742385 1 17.13208202 1.615020648 25 0.956031151 1.104231466 0.271589463 0.119681016 0.863082775 3005.969525 0.057812291 0.031212876 41.2117112 -1.615020648 0.148200315 EVEERPAPTPWGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVEERPAPTPWGSK 14 1 A0A1W2PNV4;C9JEY1;C9K057;O15143 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 ; 199.37 1.89E-08 2136400000 1836130 1662890 1738180 1741570 1768660 1378120 2195600 1665790 1930470 FALSE TRUE 1721209.901 1786012.106 1779410.45 1786261.635 1629756.578 1775960.872 1866390.163 1873767.548 1608262.086 1.070229732 1.110523043 1.106418205 1.110678198 1.013365043 1.104273295 1.160501251 1.16508843 1 20.6170711 1.9935069 24.98611055 1.127869347 1.088032627 0.005258425 0.053799559 656.7298805 2527168.444 0.018967435 0.013530711 98.51602944 -1.9935069 -0.039836721 EVEERS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 52.255 0.088909 99001000 90948 139450 114940 139460 216800 74431 114580 125920 305960 TRUE FALSE 85255.72703 149775.0231 117666.4311 143038.7797 199773.4025 95918.02141 97399.79271 141641.3892 254893.2994 0.33447614 0.587598903 0.461630146 0.561171204 0.783753057 0.376306563 0.382119863 0.555688947 1 17.95953392 0.960404059 22.94860422 1.000000002 0.500859628 0.59493075 0.129110157 1901.251164 1101909.232 0.121484958 0.030371239 9.128597502 -0.960404059 -0.499140374 EVEGERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 137.18 0.0046628 846210000 983500 1455630 1204040 1286780 1512130 971030 1336710 1055290 1616420 FALSE TRUE 921944.4906 1563406.36 1232600.397 1319800.953 1393373.409 1251350.598 1136282.745 1187045.279 1346629.06 0.684631365 1.160977738 0.915322886 0.980077583 1.03471212 0.929246691 0.84379788 0.881493884 1 20.36092107 2.004411884 23.51925399 0.88993666 0.979170992 0.001706568 0.12529233 132.5617627 706663.1168 0.043040214 0.031636159 101.0210513 -2.004411884 0.089234332 EVELVS(ph)E ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVELVSE 7 0 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 EVELVS(1)E;EVELVS(1)E 75.696 0.044865 248890000 791690 1570150 1119820 1219840 1490080 1157090 955410 1172420 1075350 TRUE FALSE 742139.5361 1686405.54 1146382.659 1251143.16 1373055.127 1491123.099 812155.1401 1318799.218 895867.138 0.828403571 1.882428173 1.279634681 1.396572222 1.532654865 1.664446698 0.906557575 1.472092414 1 19.77292526 1.741668519 25 1.132781372 1.46799477 0.172604082 0.306979388 0.777940868 6293.532488 0.128034774 0.071001643 55.16562203 -1.741668519 0.335213398 EVEPEPTEDKDLEADEEDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EVEPEPTEDKDLEADEEDTR 20 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;;;; 219.87 8.13E-25 5642910000 8868830 5430720 6625850 5986660 6385760 4824560 7915520 5283840 6955100 FALSE TRUE 8313745.762 5832816.159 6783018.291 6140287.831 5884248.169 6217332.152 6728661.26 5943539.055 5794248.878 1.434827177 1.006656131 1.170646694 1.059721106 1.015532521 1.073017794 1.16126549 1.025765234 1 22.46619022 4.745622275 24.91602626 1.077970919 1.434827351 0.781783182 0.061167924 374.6885851 1321999.449 0.014001598 0.1415724 55670.1351 -4.745622275 0.356856432 EVESPYEVHDYIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 210.41 3.02E-08 844020000 539990 698660 628110 638810 678730 559600 659130 548987 682090 FALSE TRUE 506192.9898 750389.5134 643009.0658 655202.9461 625425.2837 721147.4357 560299.5756 617529.2354 568244.7725 0.890800962 1.320539228 1.131570578 1.15302943 1.10062655 1.269078873 0.986018003 1.086731045 1 19.11615298 1.683824044 9.740692735 1.028511194 1.161632959 0.181426227 0.115944203 0.165834142 24.57187661 0.050458568 0.027128461 48.28631283 -1.683824044 0.133121764 EVEVEVESMDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVEVEVESMDK 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 166.97 4.60E-05 116502000 214743 162512 176990 201848 199445 145876 218880 166233 225405 FALSE TRUE 201302.619 174544.5576 181188.2864 207027.7614 183781.3942 187988.0331 186060.976 186987.556 187783.4493 1.071993403 0.929499156 0.964878891 1.102481407 0.978687924 1.001089466 0.990827342 0.995761643 1 17.51871039 EVEVIGGADKYHSVCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVEVIGGADKYHSVCR 16 1 P04183 P04183 TK1 "Thymidine kinase, cytosolic" 0 ;;; 233.52 7.10E-20 3064460000 2693250 2424250 2634100 2331220 3112900 2285670 3094170 2611750 4640720 FALSE TRUE 2524684.29 2603743.992 2696582.096 2391043.052 2868425.391 2945505.824 2630227.933 2937832.737 3866153.852 0.653022199 0.673471386 0.697484425 0.618455225 0.741932551 0.76186979 0.680321589 0.759885108 1 21.88246762 -5 0.211712416 2.498382734 0.65179431 0.877890402 0.036836183 46.17683464 0.460884661 29.31113803 0.073495378 1.00E-05 5 -1.846588424 EVFDNDGKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVFDNDGKPR 10 1 Q08209-3;Q08209-2;Q08209;Q08209-4 Q08209-3 PPP3CA Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform 0 ; 96.015 0.0058324 268320000 710100 622380 668860 609940 728430 466730 765320 657900 918140 FALSE TRUE 665656.1086 668461.6628 684725.6751 625592.093 671222.0461 601467.3743 650567.3709 740040.2632 764896.5026 0.870256442 0.873924329 0.895187352 0.817878093 0.877533162 0.786338246 0.850529933 0.967503787 1 19.54490503 1.172038052 4.577454085 0.994977349 0.855244531 0.749104564 0.031628671 0.106604071 4.043167035 0.030539242 0.007980858 14.86065842 -1.172038052 -0.139732818 EVFEDAAEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EVFEDAAEIR 10 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;;; 253.74 1.01E-16 7851980000 6788160 7831830 7438730 7406410 7916930 6486200 8300030 6566490 7871800 FALSE TRUE 6363301.183 8411706.842 7615180.188 7596471.02 7295166.253 8358660.645 7055517.555 7386330.731 6557945.726 0.970319281 1.282674056 1.161214274 1.158361374 1.112416381 1.274585212 1.075873124 1.126317759 1 22.64481253 0.925712147 1.125842618 1.002662314 1.170305814 0.195567579 0.090501571 0.777927945 2.004951533 0.077124635 0.02443122 8.427759757 -0.925712147 0.1676435 EVFEFRPELVNDDDEEADDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EVFEFRPELVNDDDEEADDTR 21 1 Q8WU90;Q8WU90-2 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 0 ;; 283.22 3.50E-45 1042960000 1124410 1205060 1214000 1157110 1146620 1117390 1295520 1059820 852790 FALSE TRUE 1054035.185 1294283.896 1242796.653 1186803.402 1056569.09 1439962.354 1101268.803 1192140.86 710453.8398 1.48360826 1.821770569 1.74929965 1.670486294 1.487174861 2.026820425 1.550091985 1.677999038 1 19.43838139 0.16828095 1.11789409 0.997501006 1.709896379 0.631763209 0.16345092 3.274308875 3.85034492 0.159115794 0.043198882 1.473265265 -0.16828095 0.712395373 EVFNTDECSIQHCLYQFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVFNTDECSIQHCLYQFTR 19 0 Q9Y5T5-4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5 Q9Y5T5-4 USP16 Ubiquitin carboxyl-terminal hydrolase 16 0 149.47 2.10E-08 0 20618 23525 22776 26603 27699 22877 24437 21810 31285 FALSE TRUE 19327.55618 25266.81548 23316.25748 27285.67802 25523.63227 29481.21852 20772.89871 24533.02651 26063.33139 0.741561234 0.969439213 0.894600047 1.046899094 0.979292781 1.131137769 0.797016252 0.941285139 1 14.66973388 4.740208916 24.48341118 0.959327316 0.741561137 0.393065574 0.088319375 119.1873072 1770166.795 0.020383496 0.130092208 54980.52919 -4.740208916 -0.217766179 EVFQIASNDHDAAINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVFQIASNDHDAAINR 16 0 Q9UKG1;C9JAB0 Q9UKG1 APPL1 DCC-interacting protein 13-alpha 0 137.81 9.98E-06 209310000 125140 129960 130140 110720 147870 128450 156150 113650 154010 FALSE TRUE 117307.7108 139582.3736 133226.9823 113561.2626 136256.8867 165531.4298 132736.7571 127839.4527 128304.7361 0.914289795 1.087897282 1.038363714 0.885090186 1.061978621 1.290142787 1.034542927 0.996373607 1 16.9692149 2.485700493 24.99383789 1.096670491 1.005138733 0.157555519 0.100727395 771.7022649 2248203.3 0.033214033 0.029114624 305.9852506 -2.485700493 -0.091531759 EVGKDVSDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVGKDVSDEK 10 1 O75390;B4DJV2;A0A0C4DGI3 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ; 98.105 0.0051108 1635370000 3820900 1857790 2315800 2076670 2913000 1894250 2419800 2289700 3491100 FALSE TRUE 3581756.69 1995342.705 2370731.87 2129960.868 2684224.73 2441089.224 2056973.454 2575574.085 2908412.857 1.231515904 0.686058962 0.815129071 0.732344744 0.922917365 0.83932005 0.707249471 0.885559999 1 21.47180065 0.989887066 23.82281819 1.00000002 0.819855779 0.064663286 0.155894159 497.3962675 1171711.099 0.134038948 0.033509737 9.769831332 -0.989887066 -0.180144241 EVGKDVSDEKLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVGKDVSDEKLR 12 2 O75390;B4DJV2;A0A0C4DGI3 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 119.69 0.00027583 268980000 597280 534420 568350 523530 946040 393660 601940 612890 1805200 FALSE TRUE 559897.311 573989.0129 581831.5304 536964.6661 871741.8345 507303.2515 511684.6851 689410.6656 1503900.458 0.372296789 0.381666891 0.386881676 0.35704801 0.579653946 0.33732502 0.3402384 0.458415091 1 20.52027765 0.848348871 5.989700812 0.999998659 0.391665384 0.883000644 0.068835085 1.080651092 42.60320149 0.062877813 0.01581165 7.052593799 -0.848348871 -0.608333275 EVGSIIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVGSIIGK 8 0 F8VZX2;F8W1G6;F8W0G4;P57721;P57721-4;E9PFP8;P57721-5;P57721-3;P57721-2;F8VTZ0;J3QT27;H3BSP4;C9JZY3;C9J0A4;C9K0A2;C9J5V4;C9JTY5;C9JSA6;C9J7A9;C9IZV9;F8WC71;P57723-2;P57723;Q15366;Q15366-6;Q15366-2;Q15366-3;Q15366-5;Q15366-4;Q15366-8;Q15366-7;Q15365 F8VZX2;Q15366;Q15366-2;Q15366-5;Q15365 PCBP2;PCBP3;PCBP4;PCBP1 Poly(rC)-binding protein 3;Poly(rC)-binding protein 4;Poly(rC)-binding protein 2;Poly(rC)-binding protein 1 0 116.37 0.0053142 105980000 348670 406060 357570 318960 442750 299640 418180 318030 440600 FALSE TRUE 326847.3671 436125.1049 366051.7293 327145.0536 407978.201 386141.2038 355477.7912 357736.7456 367061.0136 0.890444245 1.188154254 0.997250364 0.891255245 1.111472441 1.051980977 0.968443332 0.974597498 1 18.48566037 3.716483034 24.05815378 0.99949257 1.070205667 0.007689993 0.091180521 488.8976968 1105636.069 0.02254502 0.03536641 5205.746717 -3.716483034 0.070713097 EVGVYEALKDDSWLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVGVYEALKDDSWLK 15 1 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 ;;; 215.23 2.16E-12 2186829000 4861130 3811490 3994670 4110880 4796540 3117660 6051600 4077090 6142050 FALSE TRUE 4556880.551 4093696.685 4089425.459 4216372.141 4419839.097 4017677.831 5144218.76 4586123.661 5116902.176 0.890554557 0.80003419 0.799199461 0.824008745 0.863772444 0.785177768 1.0053385 0.89626956 1 22.28683922 1.741472215 11.00902538 0.961599344 0.822073665 0.702678676 0.042801681 0.043091827 30.13488503 0.018257225 0.009956083 55.14069238 -1.741472215 -0.139525679 EVGVYEALKDDSWLKGEFVTTVQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVGVYEALKDDSWLKGEFVTTVQQR 25 2 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 182.4 1.26E-17 44191000 58587 78680 69965 83093 123630 46782 83225 48456 239140 FALSE TRUE 54920.14425 84505.54907 71624.60284 85225.30706 113920.5985 60287.20396 70746.18387 54505.83826 199225.9891 0.27566757 0.424169304 0.359514354 0.427782075 0.571815951 0.302607126 0.355105196 0.273587992 1 17.60404633 -1.488512086 3.463604219 1.010498089 0.379529761 0.832223198 0.088330336 64394099.66 73491152.9 6293602.837 0.020237346 0.032470421 1.488512086 -0.630968328 EVHDELEDLPSPPPPLS(ph)PPPTTSPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVHDELEDLPSPPPPLSPPPTTSPHK 26 0 F5H039;Q9NQX3;Q9NQX3-2;H0YJ30;G3V582 F5H039 GPHN Gephyrin;Molybdopterin adenylyltransferase;Molybdopterin molybdenumtransferase 1 EVHDELEDLPSPPPPLS(0.996)PPPT(0.001)T(0.001)S(0.002)PHK;EVHDELEDLPSPPPPLS(0.995)PPPT(0.002)T(0.002)S(0.002)PHK 144.12 4.18E-07 340510000 372360 345720 334980 279530 381670 367680 576900 407590 544910 TRUE FALSE 349054.6523 371317.4685 342925.8838 286703.213 351695.1778 473823.2472 490399.2007 458478.5087 453961.0007 0.768908897 0.81795015 0.755408247 0.631559126 0.774725532 1.0437532 1.080267247 1.009951313 1 18.79220884 2.250325794 6.018034209 1.04575851 0.753191697 0.88179519 0.051580745 0.05114037 6.595640471 0.019483136 0.015478289 177.9613921 -2.250325794 -0.292566813 EVHELYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVHELYK 7 0 P10155-3;P10155-5;P10155-4;P10155;D6RE09;H0Y9N5 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 ; 91.626 0.016266 427950000 922330 878850 855380 826360 985210 655480 978400 864440 1005450 FALSE TRUE 864603.0117 943920.9684 875670.0175 847565.7966 907835.5807 844706.4352 831698.003 972367.2369 837633.8995 1.032196777 1.126889646 1.045409 1.011857086 1.083809503 1.008443469 0.992913495 1.16084991 1 19.6759603 3.69372367 5.068609325 1.038138049 1.086504004 0.062685894 0.054580655 0.355786633 23.34149887 0.013443711 0.021967158 4939.962698 -3.69372367 0.048365955 EVIEIEDAS(ph)PTKCPITTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVIEIEDASPTKCPITTK 18 1 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 EVIEIEDAS(0.979)PT(0.021)KCPITTK;EVIEIEDAS(0.908)PT(0.092)KCPITTK;EVIEIEDAS(0.5)PT(0.5)KCPITTK;EVIEIEDAS(0.981)PT(0.019)KCPITTK 196.18 1.20E-15 1155670000 2430820 1320180 1803650 1689690 1807530 1369140 2409830 1578600 2255510 TRUE FALSE 2278679.315 1417927.501 1846433.43 1733050.306 1665573.885 1764388.492 2048498.363 1775691.685 1879050.81 1.212675731 0.754597743 0.982641566 0.922300928 0.886391084 0.938978596 1.090177207 0.94499397 1 20.84157265 1.913143567 9.555491342 1.020313307 0.926487963 0.033792261 0.118881774 0.920737705 96.11766081 0.045485671 0.028841818 81.87353966 -1.913143567 -0.093825344 EVIGGLCSLANIPLT(ph)PETQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVIGGLCSLANIPLTPETQR 20 0 Q01664 Q01664 TFAP4 Transcription factor AP-4 1 EVIGGLCSLANIPLT(0.989)PET(0.011)QR 220.16 1.38E-25 0 28332 32592 30716 29039 32175 31292 36772 28980 27691 TRUE FALSE 26558.75069 35005.14559 31444.59803 29784.1899 29648.10529 40325.49242 31258.37997 32598.21679 23069.19321 1.151264825 1.517397911 1.363055818 1.291080691 1.285181715 1.748023524 1.354983665 1.413062715 1 14.49367993 -1.617572169 7.37931244 0.999389094 1.405535296 0.371294744 0.15862828 0.001456366 7.55E-05 0.140302281 0.033023388 0.024122806 1.617572169 0.406146201 EVIITPNSAWGGEGSLGCGIGYGYLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVIITPNSAWGGEGSLGCGIGYGYLHR 27 0 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 0 166.49 8.77E-12 128140000 61271 76480 68743 68844 79480 64306 76604 68427 82187 FALSE TRUE 57436.15748 82142.65878 70373.61642 70610.65359 73237.96141 82870.09828 65117.94136 76970.26158 68469.45875 0.838858062 1.199697796 1.027810322 1.031272262 1.069644229 1.210322088 0.951050914 1.124154667 1 16.06317299 -0.272888885 7.648049467 0.999999997 1.064860619 0.020606719 0.110257011 0 0 0.094107761 0.022181412 0.533471368 0.272888885 0.064860622 EVIKS(ph)PTASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVIKSPTASR 10 1 O94885 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 EVIKS(0.998)PT(0.002)ASR;EVIKS(0.968)PT(0.032)ASR;EVIKS(0.899)PT(0.101)ASR;EVIKS(0.994)PT(0.006)ASR 146.79 1.70E-05 2404370000 1780800 1530070 1585390 1626250 1893100 1270910 1886320 1525660 2093190 TRUE FALSE 1669342.907 1643357.975 1622996.199 1667982.328 1744423.562 1637801.086 1603483.828 1716142.009 1743823.066 0.957289153 0.942388025 0.93071151 0.956508926 1.000344356 0.939201412 0.919522088 0.984126224 1 20.73382224 1.056720001 6.718329346 0.999886555 0.947040125 0.412330681 0.02146683 0.171901267 14.66414954 0.02135877 0.005360848 11.3951488 -1.056720001 -0.05284643 EVIQSDSLWLVEFYAPWCGHCQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVIQSDSLWLVEFYAPWCGHCQR 23 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 158.02 2.10E-10 11380000 17980 28202 17318 24041 22642 16133 22787 16780 10227 FALSE TRUE 16854.6639 30290.10542 17728.79114 24657.93276 20863.78865 20790.3352 19370.30089 18875.01994 8520.047631 1.978235877 3.555156818 2.080832397 2.894107384 2.448787795 2.440166546 2.273496785 2.215365542 1 13.05664578 -0.603013572 0.285013992 0.275681122 2.820143175 0.551847961 0.435894417 6.915149659 0.60525368 4.960118552 0.514124586 0.249451677 0.603013572 2.544462054 EVISKFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVISKFR 7 1 A0A3B3IRK8;Q9BYX4 A0A3B3IRK8 IFIH1 Interferon-induced helicase C domain-containing protein 1 0 66.682 0.061298 680920000 512540 742940 493770 472530 703280 370270 584370 420220 1349900 FALSE TRUE 480461.0363 797948.0506 505482.4576 484655.9198 648047.2257 477160.9382 496749.1435 472685.392 1124592.969 0.427231051 0.709543873 0.449480364 0.430961186 0.576250469 0.424296569 0.441714609 0.420316866 1 20.1009715 -1.539829281 6.003500506 1.00087015 0.496233353 0.752965311 0.092509603 0.001105994 8.48E-05 0.091947109 0.021637919 0.028851654 1.539829281 -0.504636798 EVKPEETTCSEHCLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVKPEETTCSEHCLQK 16 1 Q9Y5J7 Q9Y5J7 TIMM9 Mitochondrial import inner membrane translocase subunit Tim9 0 219.58 7.38E-15 366620000 443550 299780 338380 352910 413720 252050 487560 331110 530850 FALSE TRUE 415788.9973 321976.0231 346406.5334 361966.2681 381228.1001 324812.7433 414454.9043 372449.8124 442247.7056 0.940172198 0.72804453 0.78328622 0.818469522 0.862023918 0.734458855 0.937155578 0.842174663 1 18.75449513 0.959122366 0.646766445 0.999077032 0.796095709 0.359764116 0.071616422 0.770224924 0.748006189 0.066534531 0.02730112 9.101696842 -0.959122366 -0.202981323 EVLAELEALER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVLAELEALER 11 0 Q16822;Q16822-3;H0YML5 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 ; 132.78 0.00040806 17131100 36023 43069 36806 40279 51177 39048 40233 37497 52009 FALSE TRUE 33768.38473 46257.87357 37679.0557 41312.62733 47157.76486 50320.52371 34200.43515 42178.58299 43328.36191 0.779359829 1.067611872 0.869616437 0.953477711 1.088380977 1.161376094 0.789331367 0.973463596 1 15.40302407 4.756772595 23.71599224 0.97679701 0.779359484 0.268771076 0.106714619 2903.644053 3781056.66 0.025310686 0.772734861 57117.94782 -4.756772595 -0.197437526 EVLAGRPLFPHVLCHNCAVEFNFGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVLAGRPLFPHVLCHNCAVEFNFGQK 26 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 145.2 1.49E-07 837440000 525940 619160 477520 428010 753610 366110 701600 551600 706780 FALSE TRUE 493022.3542 665003.2506 488846.9999 438993.4612 694424.5105 471800.0137 596401.5933 620468.4742 588813.852 0.837314463 1.129394712 0.830223335 0.745555594 1.179361709 0.801271934 1.012886486 1.053759982 1 19.16745209 1.555319817 10.45474112 1.028313257 0.935405917 0.100988724 0.138774856 0.296420899 47.79269582 0.069957763 0.03256822 35.91863439 -1.555319817 -0.092907341 EVLAS(ph)PDRLWGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVLASPDRLWGSR 13 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 EVLAS(1)PDRLWGSR;EVLAS(1)PDRLWGSR;EVLAS(1)PDRLWGSR;EVLAS(1)PDRLWGSR 163.02 2.39E-05 882910000 625910 495911 516704 527282 568187 416845 563807 418662 505510 TRUE FALSE 586735.4104 532628.7664 528960.4629 540812.9488 523563.885 537181.3846 479269.3745 470932.8723 421137.1153 1.393217052 1.264739552 1.256029079 1.284173086 1.243214777 1.275549851 1.138036419 1.118241198 1 18.6839305 1.310156362 0.774102406 0.998586178 1.292278202 0.852970517 0.041714337 0.207248257 0.277591459 0.037321246 0.0149582 20.42473177 -1.310156362 0.293692024 EVLDEDT(ph)DEEKETLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVLDEDTDEEKETLK 15 1 Q9Y3P9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 1 EVLDEDT(1)DEEKETLK;EVLDEDT(1)DEEKETLK 286 5.95E-34 694560000 2373200 993960 1350280 1410930 1462640 953030 1980980 1175120 1769100 TRUE FALSE 2224665.648 1067553.833 1382309.279 1447136.852 1347770.154 1228154.29 1683950.44 1321836.319 1473825.781 1.509449541 0.724341945 0.937905482 0.981891395 0.91447047 0.833310358 1.142570893 0.8968742 1 20.49113456 EVLDVAAGMIKPGVTTEEIDHAVHLACIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVLDVAAGMIKPGVTTEEIDHAVHLACIAR 30 1 P53582 P53582 METAP1 Methionine aminopeptidase 1 0 243.04 6.82E-46 165510000 115500 120020 113890 110010 137370 95491 139320 113290 173180 FALSE TRUE 108271.0612 128906.4057 116591.5246 112833.0428 126581.5143 123057.7015 118430.2594 127434.5059 144275.1392 0.750448496 0.893476218 0.808119301 0.782068508 0.877361928 0.852937673 0.820863941 0.883274184 1 17.1384632 0.882671281 2.956770969 0.9999399 0.8322454 0.626156265 0.042431743 0.296862883 5.341064487 0.037235221 0.009781249 7.632578526 -0.882671281 -0.1676945 EVLEALGEVMVSRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVLEALGEVMVSRPR 15 1 Q8NE71;Q8NE71-2;H0YGW7;A0A0G2JIC2 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ; 319.64 1.49E-56 328180000 496080 559590 539380 544820 579800 474700 587270 463670 626120 FALSE TRUE 465031.2383 601022.6259 552174.3483 558801.0036 534264.8468 611738.1839 499214.3154 521560.2202 521616.5271 0.891519371 1.152230795 1.058582924 1.071286998 1.024248311 1.172773776 0.957052335 0.999892053 1 18.99263006 1.621506835 24.99999732 0.983859213 1.070356102 0.174526382 0.076505736 1.157947449 2117.231781 0.032128424 0.017694559 41.83182718 -1.621506835 0.086496889 EVLEGLEYLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EVLEGLEYLHK 11 0 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 0 ;;;;; 193.3 1.01E-06 2030650000 3377950 3459600 3519900 3507970 4050750 2823550 4313070 3490370 4512810 FALSE TRUE 3166530.139 3715752.384 3603393.69 3597990.449 3732620.435 3638663.048 3666365.194 3926150.378 3759592.857 0.842253473 0.988339037 0.95845317 0.957015982 0.992825707 0.967834334 0.975202724 1.04430201 1 21.842145 4.740486975 24.92936012 0.980692839 0.842253424 0.754475806 0.025550046 78.94435424 1021555.778 0.005660363 0.036722434 55015.74201 -4.740486975 -0.138439415 EVLHGNQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EVLHGNQR 8 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;;; 190.26 0.00018736 10110120000 5598230 7285430 6085660 6107390 7093420 5108870 6378450 5876890 6252350 FALSE TRUE 5247846.777 7824850.818 6230014.729 6264115.967 6536331.407 6583717.833 5422060.637 6610632.653 5208792.393 1.007497781 1.50223895 1.196057408 1.202604269 1.254865027 1.263962419 1.040943894 1.269129609 1 22.31251751 1.144160704 0.388011854 0.992972936 1.295715544 0.161170689 0.138284207 1.671997541 0.741275707 0.19329038 0.117121827 13.93672414 -1.144160704 0.302742608 EVLLDEDDDLWIALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVLLDEDDDLWIALR 15 0 A0A1B0GWF2;A0A1B0GVQ5;A0A2R8Y5D4;A0A0D9SG72;A0A1B0GTP9;P61764;P61764-2;A0A1B0GW76 A0A1B0GWF2 STXBP1 Syntaxin-binding protein 1 0 164.11 8.86E-09 0 6122.1 7296.4 8411.9 6819.3 7232.6 7971.8 6207.3 6938 5854.5 FALSE TRUE 5738.928689 7836.633048 8611.43424 6994.294783 6664.580771 10273.12925 5276.572991 7804.224572 4877.346128 1.17664987 1.606741216 1.765598343 1.434036994 1.366435884 2.106294894 1.081853297 1.600096521 1 12.25188064 0.566742831 0.815607735 1.001664634 1.566775736 0.220145779 0.293857394 1.930597017 2.121095358 0.270384303 0.090415039 3.687591716 -0.566742831 0.565111101 EVLPSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVLPSTR 7 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 116.9 0.012449 160850000 215250 338880 274500 329980 346300 271870 332550 259690 383110 FALSE TRUE 201777.8867 363971.0278 281011.2696 338447.8455 319102.9949 350354.4556 282687.2147 292112.8681 319166.466 0.632202654 1.140379916 0.880453618 1.060411671 0.999801135 1.097717 0.885704624 0.915236716 1 18.28394955 4.753535302 24.99986942 0.993596604 0.632202397 0.636998832 0.086610527 1819.38332 3037364.695 0.019728114 0.462841624 56693.76542 -4.753535302 -0.361394206 EVLSEPWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVLSEPWR 8 0 P50416;P50416-2 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 84.097 0.046063 0 168460 196900 161710 162760 235640 166850 175800 198750 221830 FALSE TRUE 157916.3893 211478.6809 165545.8376 166936.6972 217133.7849 215016.8864 149440.422 223564.375 184805.1399 0.85450215 1.144333328 0.895785894 0.903311982 1.17493369 1.16347893 0.808637801 1.209730287 1 17.49564536 2.776642421 24.99194038 1.046508799 0.973008787 0.140293668 0.137347437 1737.087207 1139994.996 0.041507909 0.04402482 597.9190923 -2.776642421 -0.073500012 EVLYDS(ph)EGLS(ph)GEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVLYDSEGLSGEER 14 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 EVLYDS(1)EGLS(1)GEER;EVLYDS(1)EGLS(1)GEER 162.82 6.40E-06 1151450000 988170 1061660 1006970 1032490 1024900 899780 1098980 885220 898890 TRUE FALSE 926322.2036 1140266.411 1030855.804 1058985.441 944408.4882 1159531.879 934198.1514 995741.6656 748859.4519 1.236977381 1.522670787 1.376567794 1.414131101 1.261129156 1.548397201 1.247494639 1.329677636 1 19.51433545 0.377932241 0.663743633 0.989851551 1.404839712 0.550407312 0.105557344 1.421286285 0.9441734 0.123591379 0.035923496 2.387438761 -0.377932241 0.414988161 EVMNADDPDLQRPDEEAIKEITEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVMNADDPDLQRPDEEAIKEITEK 24 2 Q13573;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 0 ; 181.67 1.83E-17 178007000 493640 304590 376820 380670 409380 242230 466530 284670 535920 FALSE TRUE 462743.9536 327142.1605 385758.3483 390438.6367 377228.9462 312157.8687 396578.1576 320211.6761 446471.4898 1.036446815 0.732727997 0.864015636 0.874498474 0.844911612 0.69916641 0.888249679 0.717205204 1 18.76820853 4.753915157 24.55237872 0.820841526 1.036447017 0.337849193 0.091453315 2340.559713 3742545.997 0.019000941 0.448057801 56743.37411 -4.753915157 0.21560549 EVMNGAILQQVFVVDYVVQSQMCGDCHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EVMNGAILQQVFVVDYVVQSQMCGDCHR 28 0 C9JA08;Q96D46;C9J0B9;C9IZW9;C9K0C2 C9JA08 NMD3 60S ribosomal export protein NMD3 0 ;; 244.74 1.75E-45 252918200 490444 540463 551926 566012 584362 534064 649363 472926 442876.6 FALSE TRUE 459747.9855 580479.4429 565017.9454 580536.8262 538468.5657 688239.607 551997.0465 531971.8521 368957.6344 1.246072564 1.573295655 1.531389766 1.573451183 1.459431966 1.865362152 1.496098725 1.441823675 1 18.49309564 0.774001178 2.42654164 1.000414343 1.550055144 0.5508025 0.150510255 0.692207541 6.22878445 0.131422929 0.035306256 5.942937703 -0.774001178 0.549640801 EVMSLHEASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVMSLHEASR 10 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 166.86 5.42E-06 1876520000 952110 1864730 1349090 1410910 1778650 1141390 1537230 1597210 1508260 FALSE TRUE 892519.1347 2002796.549 1381091.052 1447116.339 1638962.004 1470890.764 1306736.632 1796625.184 1256521.662 0.710309389 1.593921227 1.099138275 1.151684354 1.304364304 1.170605178 1.039963474 1.4298402 1 20.26100411 -1.727824683 2.925182329 0.967245134 1.2052923 0.054398673 0.235456261 287201292.4 320517673.1 70066558.86 0.051179584 0.018714375 1.727824683 0.238047166 EVPAHSTEVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVPAHSTEVGR 11 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ;;; 220.5 9.10E-12 2290020000 635030 877770 857140 884440 879440 771680 926660 751720 904900 FALSE TRUE 595284.6059 942761.0041 877471.7656 907136.2278 810372.3299 994451.4888 787715.9357 845573.8967 753866.3441 0.789642104 1.250567838 1.163961984 1.203311747 1.074954912 1.319135012 1.044901317 1.121649618 1 19.52394924 0.925072387 1.435866472 1.003842376 1.147519522 0.046502899 0.14387769 1.207042161 4.992769675 0.12144034 0.036053139 8.415353957 -0.925072387 0.143677146 EVPENETPVDTNLIELDTNDDDIVFEDFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVPENETPVDTNLIELDTNDDDIVFEDFAR 30 0 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 0 105.9 2.96E-11 0 4547.1 7489.6 5647.9 5460.1 7561.6 5095.1 6850.9 5430.1 8127.2 FALSE TRUE 4262.505128 8044.137777 5781.870855 5600.21541 6967.742438 6565.972658 5823.671146 6108.059938 6770.717816 0.62954996 1.188077541 0.853952419 0.827122849 1.029099518 0.969760199 0.860126105 0.902128859 1 12.72509308 1.757778337 24.99999997 0.906185509 0.941346225 0 0.148408217 58.35087575 75979.9711 0.064172677 0.035588048 57.25037517 -1.757778337 0.035160717 EVPEYLNHVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVPEYLNHVSK 11 0 Q13619;A0A0A0MR50;Q13619-2 Q13619 CUL4A Cullin-4A 0 69.03 0.055617 174940000 126970 155870 130730 126690 180350 92558 168570 159380 182360 FALSE TRUE 119023.1743 167410.777 133830.9773 129941.0799 166186.0385 119277.992 143294.4934 179278.9438 151922.9379 0.783444396 1.101945363 0.880913568 0.855309157 1.093883786 0.785121679 0.943205124 1.180065014 1 17.21298018 1.313944638 9.361143123 1.089393281 0.931605191 0.262240719 0.11711584 0.386004735 43.85578679 0.071643671 0.026146027 20.60367251 -1.313944638 -0.15778809 EVPHS(ph)SPPYYEFLWGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVPHSSPPYYEFLWGPR 17 0 Q9UBF1 Q9UBF1 MAGEC2 Melanoma-associated antigen C2 1 EVPHS(0.527)S(0.473)PPYYEFLWGPR;EVPHS(0.793)S(0.207)PPYYEFLWGPR 175.21 8.10E-10 107876000 112939 129841 134623 124423 125219 121565 136868 124648 149249 TRUE FALSE 105870.3496 139454.5627 137816.3211 127615.9048 115384.8048 156658.8421 116345.914 140210.5772 124338.3777 0.851469607 1.121572963 1.108397292 1.026359738 0.927990271 1.259939569 0.935720058 1.127653262 1 16.92391214 EVPHSS(ph)PPYYEFLWGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVPHSSPPYYEFLWGPR 17 0 Q9UBF1 Q9UBF1 MAGEC2 Melanoma-associated antigen C2 1 EVPHS(0.022)S(0.978)PPYYEFLWGPR;EVPHS(0.363)S(0.637)PPYYEFLWGPR 200.6 7.89E-12 209980000 208020 263000 253560 248020 248640 229900 261350 240300 277380 TRUE FALSE 195000.3995 282472.7937 259574.5629 254384.6131 229112.8174 296268.3979 222162.9938 270301.984 231083.4861 0.843852596 1.222384163 1.123293435 1.100834237 0.991472049 1.282083817 0.961397102 1.16971571 1 17.81805464 -3.803771414 0.55658125 0.002724764 1.09889267 0.034726786 0.129129423 3609.259681 54.47766826 4389.012454 0.048783913 0.000157119 3.803771414 1.096167907 EVPIPEHIDIYHLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVPIPEHIDIYHLTR 15 0 Q9UG63;Q9UG63-2;C9JHK9;C9JZV3 Q9UG63 ABCF2 ATP-binding cassette sub-family F member 2 0 ;;; 160.81 9.76E-07 1073930000 686728 835010 835999 743552 839653 739716 910080 737275 838379 FALSE TRUE 643746.9203 896835.0092 855829.2911 762632.8032 773710.0404 953260.0009 773621.9528 829325.4067 698448.1288 0.921681788 1.284039533 1.225329779 1.091896122 1.107755907 1.364825764 1.107629788 1.18738296 1 19.41379345 0.098313183 1.450509687 0.999855999 1.179131444 0.134723077 0.121038002 24.34198277 36.75974142 0.11440753 0.030833632 1.254045178 -0.098313183 0.179275445 EVPVY(ph)IGEDS(ph)T(ph)IARESY(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVPVYIGEDSTIARESYR 18 1 H0YL34;A0A075B7B1;O15061-2;O15061 H0YL34 SYNM Synemin 4 EVPVY(0.956)IGEDS(0.956)T(0.958)IARES(0.501)Y(0.629)R;EVPVY(0.821)IGEDS(0.821)T(0.843)IARES(0.694)Y(0.821)R 62.362 0.020023 1162660000 161149 70793 97842 105574 112288 98516 159000 83399 181536 TRUE FALSE 151062.9717 76034.58738 100162.8584 108283.2076 103469.3534 126955.9699 135159.4261 93811.54873 151236.4688 0.998852809 0.502752993 0.662293025 0.715986087 0.684156105 0.839453413 0.893695992 0.620297138 1 17.20644654 2.246549835 7.330742974 0.837042284 0.677098224 0.118890253 0.153635795 0.210749079 63.90917868 0.051406347 0.040932795 176.4208193 -2.246549835 -0.15994406 EVPWS(ph)PSAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EVPWSPSAEK 10 0 Q5JSZ5;Q5JT00;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 EVPWS(0.995)PS(0.005)AEK;EVPWS(0.999)PS(0.001)AEK;EVPWS(0.998)PS(0.002)AEK 134.75 0.00017023 469900000 1137230 928900 1047680 1201120 1224050 696660 905220 772110 1148520 TRUE FALSE 1066052.804 997676.7225 1072531.464 1231942.773 1127918.051 897774.4327 769490.6647 868509.6331 956824.5923 1.114156986 1.042695527 1.120927987 1.287532514 1.178813818 0.938285282 0.804212884 0.907699948 1 19.86789494 2.138843093 4.904358704 0.880394413 1.136424863 0.686120238 0.078681646 0.120897404 4.809346628 0.031797614 0.023202611 137.6711984 -2.138843093 0.256030451 EVQAEQPSSSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EVQAEQPSSSSPR 13 0 A0A1W2PP04;Q9Y388 A0A1W2PP04 RBMX2 "RNA-binding motif protein, X-linked 2" 1 EVQAEQPSSSS(1)PR;EVQAEQPSSSS(1)PR;EVQAEQPSSSS(1)PR;EVQAEQPSSS(0.002)S(0.998)PR;EVQAEQPS(0.007)S(0.043)S(0.265)S(0.685)PR;EVQAEQPS(0.017)S(0.076)S(0.355)S(0.553)PR;EVQAEQPSSS(0.002)S(0.998)PR;EVQAEQPSSSS(1)PR 299.1 8.37E-41 6222606000 5782602 6553054 6277898 6219121 6260835 5560200 7009069 5289953 5427477 TRUE FALSE 5420679.263 7038248.937 6426812.705 6378714.174 5769134.274 7165339.478 5958124.172 5950415.277 4521596.026 1.198842009 1.556585086 1.421359332 1.41072182 1.275906614 1.584692537 1.317703779 1.315998874 1 22.10840067 0.735750436 1.32108127 1.000925366 1.420867566 0.526554985 0.116738011 0.625381509 1.846616839 0.100164217 0.030005372 5.441898489 -0.735750436 0.4199422 EVQDKDYPLT(ph)PPPS(ph)PTVDEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVQDKDYPLTPPPSPTVDEPK 21 1 Q5THJ4-2;Q5THJ4;H3BLS7 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 2 EVQDKDYPLT(1)PPPS(0.902)PT(0.098)VDEPK 141.78 3.50E-07 178990000 490890 293810 348120 367740 368940 237940 461050 300640 400590 TRUE FALSE 460166.0712 315563.9981 356377.5708 377176.831 339964.9406 306629.4154 391919.8327 338175.5658 333728.9411 1.378861748 0.94556977 1.067865345 1.130189158 1.018685822 0.918797795 1.174365733 1.013324061 1 18.34831728 4.748552328 24.92613295 1.040121019 1.37886194 0.664402508 0.07699219 824.240759 2056175.309 0.017817025 0.237182317 56046.99435 -4.748552328 0.338740921 EVQLEELEAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVQLEELEAAR 11 0 P51570;P51570-2;K7EII7 P51570 GALK1 Galactokinase 0 118.77 0.0015735 102310000 152780 184940 173600 175180 170450 136140 175400 148070 155950 FALSE TRUE 143217.7725 198633.15 177717.874 179675.4154 157063.5446 175441.408 149100.3983 166556.8654 129920.9375 1.10234559 1.52887713 1.367892484 1.382959658 1.208916342 1.350370551 1.147624095 1.281986327 1 16.98727442 1.08396582 0.457794544 0.995957893 1.387017723 0.369773427 0.122783572 0.925299762 0.521665162 0.14136743 0.075315029 12.13293357 -1.08396582 0.39105983 EVQQGEEFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVQQGEEFER 10 0 P00568;Q5T9B7;H0YID2 P00568 AK1 Adenylate kinase isoenzyme 1 0 ;;; 208.75 2.51E-07 1399010000 376511 365954 404719 404803 390265 303599 412395 357688 480202 FALSE TRUE 352945.8486 393049.6149 414319.1258 415190.9303 359615.1612 391243.1028 350560.1982 402346.1342 400053.184 0.882247318 0.982493405 1.035660113 1.037839335 0.898918383 0.977977725 0.876283985 1.005731613 1 18.60983228 2.736399796 24.99277666 0.94080065 0.992732281 0.046366235 0.058886389 363.6194626 4205710.56 0.017794067 0.017542189 545.0041333 -2.736399796 0.051931631 EVQQGEEFERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVQQGEEFERR 11 1 P00568;Q5T9B7;H0YID2 P00568 AK1 Adenylate kinase isoenzyme 1 0 ; 210.44 2.04E-08 1555710000 624900 827870 720510 794840 919880 648100 832270 640350 1158930 FALSE TRUE 585788.6245 889166.3562 737600.8374 815236.9401 847636.3354 835195.949 707478.8399 720299.1071 965497.096 0.606722306 0.920941513 0.763959664 0.844370163 0.877927379 0.865042425 0.73276123 0.746039641 1 19.88091239 4.753806153 24.3984874 0.830548596 0.606722079 0.440683848 0.082763715 1987.927175 3181342.02 0.018479711 0.428378559 56729.1339 -4.753806153 -0.223826517 EVQTNDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EVQTNDLK 8 0 P61247;E9PFI5;D6RG13;D6RAT0;H0Y9Y4;D6RB09;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ;; 122.33 0.0032456 451560000 1145670 939240 1058090 1052220 1163360 847380 1259960 901490 1278360 FALSE TRUE 1073964.56 1008782.307 1083188.394 1079221.747 1071994.398 1092004.85 1071040.695 1014043.011 1064993.457 1.008423622 0.947219253 1.017084553 1.013359978 1.006573694 1.025362966 1.005678192 0.952158911 1 20.02241314 3.875417816 6.00515633 1.004998354 0.974747859 0.147370034 0.024371894 0.295497439 14.5924928 0.005823713 0.010665977 7506.159974 -3.875417816 -0.030250495 EVRPDTQYTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EVRPDTQYTGR 11 1 O43709;O43709-3;H7C0G4 O43709 WBSCR22 Probable 18S rRNA (guanine-N(7))-methyltransferase 0 ;;;;; 194.39 4.85E-07 3084890000 1015475 1134907 1131707 1146682 1132058 1012119 1275710 1023476 1058999 FALSE TRUE 951918.2324 1218936.695 1158551.624 1176107.801 1043150.731 1304301.325 1084429.129 1151259.232 882245.2255 1.078972382 1.381630254 1.313185485 1.333084915 1.182381838 1.478388647 1.229169733 1.304919764 1 19.75082019 0.025372221 1.327790435 0.999402304 1.301583462 0.40039611 0.10946538 12.83987896 16.28262665 0.116408656 0.027166334 1.06016197 -0.025372221 0.302181158 EVS(ph)DSEAGGGPQGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVSDSEAGGGPQGER 15 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 EVS(0.985)DS(0.015)EAGGGPQGER;EVS(0.919)DS(0.081)EAGGGPQGER 318.02 2.12E-56 776590000 886870 631140 788370 683660 598460 779080 879160 627430 455970 TRUE FALSE 831362.3898 677870.2623 807070.5087 701203.873 551459.3657 1003987.749 747338.1197 705766.0166 379865.6613 2.188569472 1.784499973 2.124620862 1.845925927 1.451722074 2.643007386 1.967374774 1.857935814 1 18.53512978 0.7596211 3.170278234 1.000138021 1.996319295 0.511718398 0.304863973 1.38530419 17.26723977 0.270647667 0.070421007 5.749381134 -0.7596211 0.996181274 EVS(ph)PAPAVAGQSK ddPTM_SK-BR-3_Pertuzumab_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 263.12 3.93E-24 1497770000 2694820 2293880 2503680 2462050 2659340 2042420 3104840 2186300 3161700 TRUE FALSE 2526156.027 2463721.262 2563068.472 2525230.371 2450486.164 2632033.498 2639298.066 2459264.368 2633991.845 0.959059927 0.93535645 0.973073807 0.9587085 0.93033172 0.99925651 1.002014517 0.933664382 1 21.32881945 2.228863427 24.99992109 0.986390771 0.95243593 0.330462147 0.022765382 222.4756674 573550.4298 0.008033827 0.006005864 169.3805065 -2.228863427 -0.033954841 EVS(ph)PEVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVSPEVVR 8 0 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 EVS(1)PEVVR;EVS(1)PEVVR;EVS(1)PEVVR;EVS(1)PEVVR 212.63 2.24E-05 2934440000 3257450 3476430 3463260 3404960 3538190 3023400 3817530 2956660 3710710 TRUE FALSE 3053572.019 3733828.494 3545410.163 3492337.038 3260314.83 3896206.499 3245126.817 3325805.509 3091368.529 0.987773535 1.207823803 1.146873991 1.129705826 1.054650974 1.260350056 1.049737935 1.075835986 1 21.55981422 1.601114023 24.99999999 1.047069455 1.140003441 0.226173126 0.076554209 0.80773739 2980.570853 0.036213999 0.017355622 39.91296794 -1.601114023 0.092933986 EVS(ph)PSDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVSPSDVR 8 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 EVS(0.99)PS(0.01)DVR;EVS(0.994)PS(0.006)DVR;EVS(0.978)PS(0.022)DVR;EVS(1)PSDVR 145.89 0.0010047 677600000 2594060 2736470 2667480 2583680 2135840 2248560 3169890 2151570 1599890 TRUE FALSE 2431702.415 2939081.086 2730753.885 2649981.603 1968099.742 2897682.77 2694594.422 2420198.251 1332858.023 1.824427188 2.205096893 2.048795774 1.988194959 1.476601189 2.174037083 2.021666505 1.815795988 1 20.34609168 0.798445192 3.247782317 1.000118803 1.990402796 0.681673863 0.204460314 0.682308225 10.18158185 0.191240703 0.049664097 6.287025066 -0.798445192 0.990283993 EVS(ph)SRPS(ph)TPGLSVVSGISATSEDIPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVSSRPSTPGLSVVSGISATSEDIPNK 27 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 2 EVS(0.5)S(0.5)RPS(0.54)T(0.461)PGLSVVSGISATSEDIPNK 184.15 7.77E-18 481000000 471110 327110 407520 365090 342640 354310 561990 416200 305700 TRUE FALSE 441624.0661 351329.5648 417186.5668 374458.8275 315730.4365 456593.5453 477724.8168 468163.4862 254676.6951 1.734057629 1.37951203 1.638102641 1.470330166 1.239730382 1.792835992 1.875808921 1.838265908 1 17.95830742 2.198472947 24.9999753 1.721905318 1.495834443 0.005294524 0.282875337 295.7723758 184451.6041 0.094551346 0.069831749 157.9330225 -2.198472947 -0.226070875 EVS(ph)SRPS(ph)TPGLSVVSGISATSEDIPNKIEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVSSRPSTPGLSVVSGISATSEDIPNKIEDLR 32 2 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 2 EVS(0.5)S(0.5)RPS(0.499)T(0.5)PGLS(0.002)VVSGISATSEDIPNKIEDLR;EVS(0.5)S(0.5)RPS(0.526)T(0.473)PGLS(0.001)VVSGISATSEDIPNKIEDLR 72.657 0.001539 1788870000 107057 89164 95078 99120 95536 73878 124888 88120 105224 TRUE FALSE 100356.4935 95765.79534 97333.29506 101663.587 88032.98793 95205.37929 106162.2038 99121.97598 87661.43463 1.1448192 1.092450697 1.110331989 1.159729902 1.004238504 1.086057737 1.211047985 1.130736411 1 16.41965467 EVSEDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVSEDRR 7 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 172.15 0.0014613 3862040000 2909740 3532200 3506200 3578720 3644520 3022360 3690120 3101280 2986430 FALSE TRUE 2727624.567 3793727.763 3589368.72 3670556.014 3358294.1 3894866.268 3136820.763 3488481.635 2487975.54 1.096322903 1.524825185 1.442686498 1.475318368 1.349809934 1.565476109 1.260792445 1.402136628 1 21.24654087 0.217114056 0.801477335 0.993810262 1.420106025 0.436505654 0.136754183 2.674299682 2.068246125 0.162590831 0.041089596 1.648595297 -0.217114056 0.426295763 EVSFQSTGESEWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVSFQSTGESEWK 13 0 Q07021;I3L3Q7;I3L3B0 Q07021 C1QBP "Complement component 1 Q subcomponent-binding protein, mitochondrial" 0 122.42 0.00054719 73069000 47265 41671 47131 45089 47924 39211 46859 47300 68447 FALSE TRUE 44306.76802 44756.3642 48248.96958 46246.06008 44160.24236 50530.57916 39832.92797 53205.50912 57022.75352 0.777001553 0.784886058 0.846135386 0.811010644 0.774431953 0.886147652 0.69854445 0.933057522 1 15.79925009 1.045638849 6.713901389 0.99972275 0.800030351 0.68634008 0.048795088 0.087749818 8.993461524 0.043084726 0.01081355 11.10807618 -1.045638849 -0.1996924 EVSHLNALEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVSHLNALEER 11 0 A0A087WYJ2;M0R2B7;P28340;M0R3H8 A0A087WYJ2 POLD1 DNA polymerase;DNA polymerase delta catalytic subunit 0 ; 218.06 1.09E-11 181646000 225620 293840 273890 279080 313050 218690 290910 264910 282600 FALSE TRUE 211498.8469 315596.2193 280386.8001 286241.6653 288464.3158 281822.2529 247290.7462 297984.5966 235432.2343 0.898342776 1.340497066 1.190944821 1.2158134 1.225254123 1.197041916 1.050369109 1.26569158 1 17.84495234 1.771836273 25 1.112227785 1.201502941 0.044531259 0.129999334 75.63316898 56850.4541 0.054341582 0.030148147 59.13386601 -1.771836273 0.089275156 EVSMDDHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVSMDDHK 8 0 P05023-4;P05023;P05023-3;P05023-2;Q5TC02;Q5TC01 P05023-4 ATP1A1 Sodium/potassium-transporting ATPase subunit alpha-1 0 131.22 0.0010143 243070000 299880 244730 264470 229090 355610 187420 292760 327230 481460 FALSE TRUE 281111.0461 262850.0638 270743.3533 234968.8372 327681.8251 241525.1115 248863.3559 368085.3858 401101.2156 0.700848153 0.655321035 0.675000082 0.585809337 0.816955452 0.602155022 0.620450266 0.917687036 1 18.61360681 1.141076033 4.611114039 0.991949605 0.662551879 0.782332253 0.064922008 0.083748071 2.836785618 0.056575281 0.014526274 13.83808624 -1.141076033 -0.329397726 EVSQVDTICECLLEHEEQVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVSQVDTICECLLEHEEQVLR 21 0 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 0 ;;; 255.41 2.04E-36 215704000 158003 188159 168236 181101 192829 171541 223506 179776 180643 FALSE TRUE 148113.8743 202090.4881 172226.6374 185748.3583 177684.9882 221062.102 189993.3502 202221.4293 150492.5163 0.984194284 1.342860716 1.144419946 1.234269735 1.180689861 1.468924219 1.262477065 1.3437308 1 17.19933222 EVSS(ph)RPS(ph)TPGLSVVSGISATSEDIPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.469)S(0.531)RPS(0.53)T(0.468)PGLS(0.002)VVSGISATSEDIPNK;EVS(0.131)S(0.865)RPS(0.541)T(0.463)PGLS(0.001)VVSGISATSEDIPNK 141.69 1.18E-07 521918000 658530 490792 567005 542375 521798 500429 845430 624550 474288 TRUE FALSE 617313.7828 527130.7503 580454.6264 556293.2607 480818.0899 644894.7285 718665.6201 702526.4423 395126.2688 1.56232028 1.334081766 1.46903578 1.407887313 1.216871992 1.632123145 1.818825213 1.777979592 1 18.59195424 2.131256338 9.424367546 1.648414778 1.399659774 0.041626876 0.243898131 0.434112539 35.232557 0.081275821 0.060012825 135.2870846 -2.131256338 -0.248755004 EVSS(ph)RPS(ph)TPGLSVVSGISATSEDIPNKIEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVSSRPSTPGLSVVSGISATSEDIPNKIEDLR 32 2 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 2 EVS(0.093)S(0.907)RPS(0.548)T(0.452)PGLSVVSGISATSEDIPNKIEDLR;EVS(0.477)S(0.523)RPS(0.523)T(0.477)PGLSVVSGISATSEDIPNKIEDLR;EVS(0.476)S(0.524)RPS(0.524)T(0.476)PGLSVVSGISATSEDIPNKIEDLR;EVS(0.361)S(0.636)RPS(0.53)T(0.471)PGLS(0.001)VVSGISATSEDIPNKIEDLR 226.41 1.83E-36 2937930000 255646 228886 239143 249487 264496 180480.9 317191 227378 308842 TRUE FALSE 239645.5732 245832.9576 244815.5849 255889.2588 243723.5511 232582.806 269631.1542 255766.6438 257294.275 0.931406551 0.955454441 0.95150032 0.994539264 0.947256021 0.903956398 1.047948518 0.994062708 1 17.97305983 1.724267632 13.67391087 1.015338754 0.950581661 0.58457806 0.026381076 0.074513378 54.12524121 0.011583382 0.006372493 52.99899476 -1.724267632 -0.064757093 EVSSRPST(ph)PGLSVVSGISATSEDIPNKIEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVSSRPSTPGLSVVSGISATSEDIPNKIEDLR 32 2 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 EVSS(0.002)RPS(0.149)T(0.848)PGLSVVSGISATSEDIPNKIEDLR 190.13 2.94E-18 416530000 162580 135130 135720 143290 145660 130210 164800 131930 177900 TRUE FALSE 152404.408 145135.1658 138939.3425 146967.064 134220.4512 167799.5132 140089.7699 148401.7509 148207.3407 1.028318889 0.979271102 0.937465997 0.991631476 0.905626203 1.132194346 0.945228281 1.001311745 1 17.17725738 EVSTYIKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EVSTYIKK 8 1 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ; 134.91 0.0013731 4993900000 5053000 7034800 5751500 6602400 9339100 5288900 9690900 6479200 16800700 FALSE TRUE 4736741.75 7555663.912 5887928.296 6771828.762 8605644.758 6815719.572 8237839.511 7288142.382 13996554.63 0.338421981 0.539823129 0.420669833 0.483821122 0.614840222 0.486956951 0.588561952 0.520709744 1 23.7385684 -5 0.199129483 3.26659035 0.420139768 0.85213051 0.067678835 46.82476356 0.463156277 42.12629231 0.147580718 1.00E-05 5 -2.846450582 EVTWEVLEGEVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVTWEVLEGEVEK 13 0 P05455 P05455 SSB Lupus La protein 0 205.46 1.62E-07 24794000 76095 56948 55645 56388 52532 48817 66466 49861 44732 FALSE TRUE 71332.34978 61164.48917 56964.92568 57835.01154 48406.34862 62909.67542 56500.04034 56086.25561 37265.94022 1.9141433 1.641297357 1.528605621 1.551953639 1.298943441 1.688127954 1.516130816 1.505027252 1 15.18557004 -3.03541778 0.145327689 5.57E-20 1.798265964 0.678618898 0.136107948 44.37885205 0.672886888 15.14087285 0.826675826 0.000921684 3.03541778 1.798265964 EVTYELDHPGFQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVTYELDHPGFQIR 14 0 A5YKK6-3;A5YKK6-2;A5YKK6;A5YKK6-4 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 ;;; 207.97 8.69E-09 411722000 389350 483857 452427 477993 492773 427378 571410 465508 516859 FALSE TRUE 364981.2785 519682.2757 463158.7821 490259.1096 454072.5963 550755.0907 485732.3752 523627.6985 430591.8939 0.847626915 1.206902134 1.075632841 1.138570225 1.054531223 1.279065163 1.128057407 1.216064924 1 18.71596163 4.746192886 24.91497686 1.14320639 0.847626766 0.549236971 0.082335123 628.4823832 2051583.351 0.017344545 0.186541473 55743.327 -4.746192886 -0.295579625 EVVEEAENGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EVVEEAENGR 10 0 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;; 265.06 3.19E-17 22248700000 19637100 16376100 18057800 17855500 18057400 14155030 21738600 15896520 20931750 FALSE TRUE 18408048.96 17588603.48 18486139.54 18313702.36 16639244.64 18241357.37 18479098.74 17881235.51 17438105.7 1.055622054 1.008630397 1.060100212 1.050211684 0.954188771 1.046063012 1.059696452 1.02541158 1 24.05573999 -0.486772163 6.113486974 1 1.033575012 0.090851788 0.032138187 0 0 0.029629962 0.006983849 0.326007684 0.486772163 0.033575012 EVVESEGERK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVVESEGERK 10 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 0 78.513 0.039151 0 148970 112560 126110 145380 167710 150550 183930 139900 165830 FALSE TRUE 139646.2336 120894.0595 129101.3888 149110.6969 154538.7331 194011.341 156351.404 157366.823 138151.9017 1.010816586 0.875080676 0.934488684 1.079324245 1.118614592 1.404333481 1.131735446 1.139085463 1 17.0758959 3.029040902 2.162694214 1.184874569 0.922237757 0.460233757 0.10593698 0.217390863 2.053015565 0.032489379 0.038935597 1069.155569 -3.029040902 -0.262636812 EVVETPLLHPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVVETPLLHPER 12 0 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ;;; 196.15 2.10E-07 934520000 1187010 1372330 1299920 1187060 1352720 1119480 1320110 1219480 1223180 FALSE TRUE 1112717.163 1473938.741 1330754.716 1217521.969 1246482.828 1442655.703 1122171.761 1371734.762 1019023.356 1.09194471 1.446422923 1.30591189 1.194792997 1.223213208 1.415723883 1.101222807 1.346126911 1 19.95875569 -4.283802111 0.220696294 9.82E-09 1.314920639 0.289960394 0.122454511 121.1192446 1.616328489 53.84572841 0.219010415 5.20E-05 4.283802111 1.314920629 EVVHTVSLHEIDVINSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVVHTVSLHEIDVINSR 17 0 Q9Y230;Q9Y230-2;M0R0Y3 Q9Y230 RUVBL2 RuvB-like 2 0 193.3 7.98E-11 327770000 162330 211830 169870 188310 236350 151690 235320 167690 421370 FALSE TRUE 152170.0551 227514.1136 173899.3966 193142.3534 217788.0244 195480.4405 200035.9506 188626.4656 351040.6248 0.433482749 0.648113345 0.495382541 0.550199435 0.620406896 0.556859881 0.56983704 0.537335147 1 18.42127847 -1.553206497 2.631376707 1.02946169 0.558217424 0.847587758 0.059715054 4472189.681 4265472.352 928113.9483 0.013472794 0.027976508 1.553206497 -0.471244266 EVVKPVPITS(ph)PAVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVVKPVPITSPAVSK 15 1 Q96HC4;A0A0D9SFR4 Q96HC4 PDLIM5 PDZ and LIM domain protein 5 1 EVVKPVPIT(0.287)S(0.713)PAVSK;EVVKPVPIT(0.135)S(0.865)PAVSK;EVVKPVPIT(0.205)S(0.795)PAVSK;EVVKPVPIT(0.203)S(0.797)PAVSK 144.01 2.61E-06 4116650000 6148760 4607030 5409010 5360300 5791760 3753990 7277390 4898330 6945400 TRUE FALSE 5763920.087 4948139.295 5537314.272 5497854.373 5336898.532 4837705.972 6186212.929 5509897.283 5786167.871 0.996155006 0.855166909 0.956991639 0.950171944 0.922354597 0.836081165 1.06913817 0.952253271 1 22.46417675 1.730367196 24.99999738 1.008606858 0.917683056 0.368688438 0.054017849 0.710765438 2156.357398 0.022790708 0.012638639 53.74860491 -1.730367196 -0.090923802 EVWALVQAGIR ddPTM_SK-BR-3_Pertuzumab_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 ; 137.95 0.00015735 56511000 165476 231670 182330 180943 272280 152442 160823 224218 182782 FALSE TRUE 155119.1525 248823.0879 186654.9537 185586.3037 250896.2271 196449.5307 136709.0842 252212.1109 152274.5034 1.01868106 1.63404301 1.225779428 1.21876151 1.647657497 1.290101273 0.897780529 1.656299021 1 17.21631487 -1.465180327 0.237553849 0.727920962 1.379970898 0.086527916 0.266768792 47.673708 2.135156943 8.370324843 0.470730534 0.034262549 1.465180327 0.652049936 EVWDYVFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVWDYVFFK 9 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRP1 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 155.01 0.0030906 0 425440 532200 402870 397830 613060 325960 472310 523160 538470 FALSE TRUE 398812.4698 571604.6418 412426.2666 408038.9913 564912.7406 420059.3605 401491.5002 588477.6776 448595.8784 0.889023928 1.274208412 0.919371502 0.909591485 1.259290974 0.936387026 0.894995963 1.31182141 1 18.77505684 1.245902552 24.99992801 1.155910718 1.023290785 0.118642922 0.160913465 346.1975658 1178861.421 0.106964971 0.037312321 17.61580733 -1.245902552 -0.132619934 EVWYFGLHYVDNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EVWYFGLHYVDNK 13 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;; 233.37 1.24E-16 2312122000 5246192 4430259 4766492 4207610 5873966 3441327 5191768 4651923 4141050 FALSE TRUE 4917842.207 4758279.986 4879555.441 4315584.396 5412648.405 4434782.24 4413310.586 5232725.827 3449882.003 1.425510265 1.379258764 1.414412272 1.250936812 1.568937257 1.285488094 1.279264213 1.516784001 1 21.71811559 -1.990213479 2.887998852 0.643748311 1.380251524 0.59023631 0.101849867 926467.6191 8245139.759 2128761.964 0.021689627 0.010227901 1.990213479 0.736503213 EVYELLDS(ph)PGKVLLQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVYELLDSPGKVLLQSK 17 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 1 EVYELLDS(1)PGKVLLQSK;EVYELLDS(1)PGKVLLQSK;EVYELLDS(1)PGKVLLQSK;EVYELLDS(1)PGKVLLQSK 289.31 3.67E-46 950884000 2613820 1582120 2140300 2014490 2379500 1426155 2808430 1752210 4179830 TRUE FALSE 2450225.672 1699261.811 2191068.927 2066185.224 2192623.668 1837862.797 2387331.994 1970977.276 3482189.37 0.703645153 0.487986617 0.629221646 0.593358087 0.62966813 0.527789445 0.68558362 0.566016683 1 21.73156323 -5 0.362756356 6.056678083 0.586936392 0.774354773 0.066964148 205.9255232 1.625759016 813.8372327 0.042993889 1.00E-05 5 -5.469741691 EVYQQQQYGS(ph)GGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EVYQQQQYGSGGR 13 0 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 1 EVYQQQQYGS(1)GGR 136.81 7.13E-05 81684000 119920 129120 132230 133210 131920 111930 152540 114630 139030 TRUE FALSE 112414.4213 138680.1791 135366.558 136628.3941 121559.5353 144242.374 129668.0431 128941.8078 115824.9948 0.97055408 1.197325149 1.168716288 1.179610621 1.049510389 1.245347554 1.119516934 1.113246826 1 16.82158709 -1.315384206 4.623601729 0.999902715 1.142376181 0.202258297 0.078330249 6.97E-05 1.03E-05 0.067305346 0.015853207 0.048374423 1.315384206 0.142473466 EVYQQQQYGSGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EVYQQQQYGSGGR 13 0 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ;;; 333.92 3.66E-62 1667510000 350066 428935 375448 396666 440632 351122 404015 353723 397214 FALSE TRUE 328155.9939 460693.7937 384353.8039 406845.1211 406026.5401 452485.2214 343436.7014 397886.0952 330916.4173 0.991658246 1.392175696 1.161483032 1.229449794 1.226976115 1.367370121 1.037835186 1.202376414 1 18.33610734 1.106220032 1.027698702 1.013191845 1.234058595 0.196241195 0.124546677 0.681161119 1.538220683 0.105209343 0.035120221 12.7708567 -1.106220032 0.220866749 EWAHATIIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EWAHATIIPK 10 0 P30153;B3KQV6;E9PH38 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 112.75 0.0015796 545770000 1676600 2072600 1991600 1953400 2218600 1518900 2383300 2050200 2104300 FALSE TRUE 1571664.599 2226057.461 2038841.693 2003527.551 2044360.105 1957381.773 2025946.29 2306171.983 1753078.736 0.896516835 1.269798906 1.163006345 1.142862274 1.166154186 1.116539567 1.155650485 1.315498235 1 20.74145936 -1.808424792 2.875007142 0.954293765 1.162484674 0.157259168 0.109658471 244133685 182795843.3 77559875.37 0.02341481 0.015544445 1.808424792 0.208190909 EWAMNVGDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EWAMNVGDKK 10 1 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ;; 90.697 0.017083 2908590000 2325260 1523670 1811540 1613350 2023540 1376160 2224740 1616430 2765430 FALSE TRUE 2179726.127 1636484.112 1854510.584 1654751.292 1864619.331 1773435.052 1891160.89 1818244.844 2303861.868 0.94611841 0.710322149 0.804957368 0.718251088 0.809345108 0.769766225 0.820865572 0.789216085 1 21.13562279 -0.403680566 0.689414699 1.017060874 0.78395822 0.483696889 0.06536837 8.319460766 3.139489068 0.428269788 0.020918103 0.394747542 0.403680566 -0.233102654 EWCISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EWCISR 6 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ;; 122.54 0.04461 858150000 630250 851100 703320 650890 843770 602890 765660 713420 906520 FALSE TRUE 590803.7775 914116.3296 720003.0825 667592.9394 777503.7078 776934.5559 650856.391 802492.0574 755215.9557 0.782297796 1.210403889 0.95337377 0.883976212 1.02951176 1.028758132 0.861814937 1.062599448 1 19.52652972 3.714006095 24.07124273 0.964279426 1.043417543 0 0.121330597 626.7721647 1150363.767 0.029494492 0.046031144 5176.140958 -3.714006095 0.079138117 EWDFDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EWDFDLK 7 0 Q96EY4;H0Y9X1 Q96EY4 TMA16 Translation machinery-associated protein 16 0 ;;; 141.78 0.0058941 270639000 998490 839590 915420 888130 888590 632600 1070590 723600 990450 FALSE TRUE 935996.2933 901754.1172 937134.1947 910920.9194 818803.7258 815221.3506 910064.9684 813943.0528 825137.4964 1.134351908 1.092853156 1.135730952 1.10396258 0.992323982 0.987982432 1.102925236 0.986433239 1 19.65427502 2.837777395 5.777158402 1.02512698 1.117116451 0.658033362 0.036412815 0.16024878 7.677928706 0.011213849 0.011916983 688.2994061 -2.837777395 0.091989471 EWDRDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 81.381 0.056569 305550000 327690 444740 346610 360090 555140 295870 358360 432360 585050 FALSE TRUE 307180.4678 477669.0124 354831.7529 369330.519 511541.5437 381282.866 304627.2449 486341.0977 487401.3754 0.630241282 0.980032139 0.728007287 0.757754364 1.049528314 0.782276959 0.625002842 0.997824631 1 18.8947508 1.144958735 14.58578106 0.999664369 0.8031592 0.286957667 0.134068298 1.419619872 216.2035975 0.124657708 0.031165853 13.96235691 -1.144958735 -0.196505169 EWEEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EWEEAER 7 0 H7C0V9;E9PG40;P05067-7;P05067-11;P05067-8;P05067-9;P05067;A0A0A0MRG2;P05067-10;P05067-3;P05067-4;P05067-5;P05067-6;H7C2L2 H7C0V9 APP Amyloid beta A4 protein;N-APP;Soluble APP-alpha;Soluble APP-beta;C99;Beta-amyloid protein 42;Beta-amyloid protein 40;C83;P3(42);P3(40);C80;Gamma-secretase C-terminal fragment 59;Gamma-secretase C-terminal fragment 57;Gamma-secretase C-terminal fragment 50;C31 0 ; 161.6 0.0030313 518270000 898480 983330 954110 906320 1008560 813540 1059770 876890 973660 FALSE TRUE 842245.7406 1056136.776 976741.9398 929577.7056 929351.7659 1048395.791 900867.3269 986371.6468 811149.8559 1.038335561 1.302024242 1.204144872 1.145999964 1.145721421 1.292481018 1.110605297 1.216016547 1 19.62960894 -3.025625314 0.354858051 0.539487493 1.19931891 0.317660809 0.080758857 102.3883721 3.083178931 35.31564499 0.056219462 0.000942703 3.025625314 0.659831417 EWEFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EWEFQK 6 0 P62877 P62877 RBX1 "E3 ubiquitin-protein ligase RBX1;E3 ubiquitin-protein ligase RBX1, N-terminally processed" 0 96.964 0.096803 151260000 136740 128830 131430 117520 136700 128750 163080 116610 135450 FALSE TRUE 128181.6875 138368.7072 134547.5817 120535.7622 125964.1334 165918.0349 138627.668 131169.0152 112842.52 1.135934287 1.226210716 1.192348254 1.068176803 1.116282528 1.470350316 1.228505602 1.16240771 1 16.78395126 EWFLQAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EWFLQAAK 8 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7ERC6 P06744 GPI Glucose-6-phosphate isomerase 0 148.38 0.0012147 233630000 302550 810140 255630 277650 893780 200180 333690 725390 602840 FALSE TRUE 283613.9356 870123.6085 261693.6643 284774.9691 823586.1241 257968.7163 283656.2823 815956.5383 502222.1095 0.56471814 1.732547397 0.521071572 0.567029933 1.639884244 0.513654639 0.564802459 1.624692587 1 18.93796602 3.958456313 23.95772051 0.868953152 1.218894216 0.023300171 0.506113728 602.5867628 773462.2491 0.120214531 0.217284909 9087.748788 -3.958456313 0.349941064 EWGEELQAVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EWGEELQAVLR 11 0 I3L2C7;P57678 I3L2C7 GEMIN4 Gem-associated protein 4 0 129.16 0.00058361 18501000 19247 23371 23848 23697 30489 21844 21062 23202 24065 FALSE TRUE 18042.36463 25101.41316 24413.68582 24305.10514 28094.51693 28150.00819 17903.94863 26098.82077 20048.39603 0.899940554 1.252040967 1.217737608 1.212321679 1.401334894 1.404102759 0.89303646 1.301790963 1 14.2911992 1.739262498 25 1.062603878 1.237902661 0.174855737 0.169867501 0.172534675 5992.800481 0.073219331 0.040603748 54.86084571 -1.739262498 0.175298783 EWGSGSDTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EWGSGSDTLR 10 0 P16615-5;P16615-2;P16615-3;P16615;H7C5W9;P16615-4 P16615-5 ATP2A2 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 0 136.21 0.00028792 104180000 93638 105130 91474 87131 114270 88691 114200 106650 115970 FALSE TRUE 87777.36473 112913.9346 93643.80648 89366.92897 105295.6951 114294.6519 97076.77018 119965.4873 96613.85781 0.908538037 1.168713652 0.969258537 0.924990793 1.089861201 1.183004742 1.004791366 1.241700621 1 16.55994252 2.506754711 23.94112619 1.104052319 1.017163563 0.21622308 0.100784593 764.4386322 617595.8451 0.030909095 0.029093057 321.1845982 -2.506754711 -0.086888756 EWLKDTCGANAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EWLKDTCGANAK 12 1 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 120.14 0.00021415 0 169600 165890 167720 190470 215570 122610 229000 141270 337280 FALSE TRUE 158985.0387 178172.6682 171698.3976 195357.7827 198640.0018 158005.5166 194663.5759 158907.8705 280985.7891 0.565811671 0.634098503 0.611057229 0.695258587 0.706939673 0.56232565 0.692787975 0.565537037 1 18.10013764 -2.009828912 2.849698458 1.390682469 0.633738134 0.816043121 0.055286934 11825781.69 4170817.126 30331145.77 0.012240421 0.009776223 2.009828912 -0.756944335 EWLSPLPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EWLSPLPDR 9 0 Q96ST2;Q96ST2-3;Q96ST2-2;A0A1B0GW95 Q96ST2 IWS1 Protein IWS1 homolog 0 88.948 0.028938 41422000 83579 86551 74579 85317 88999 76986 97201 86498 106150 FALSE TRUE 78347.93958 92959.3261 76348.0491 87506.37866 82009.37754 99210.60844 82626.61242 97297.46571 88432.87924 0.885959388 1.051185112 0.863344604 0.989523121 0.92736297 1.121874684 0.934342669 1.100240844 1 16.43229524 2.305467475 25 1.026162437 0.949328843 0.290243433 0.072759663 79.01248032 29522.22976 0.022954313 0.01920495 202.0540107 -2.305467475 -0.076833594 EWLTNFMEDR ddPTM_SK-BR-3_Pertuzumab_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 ; 187.99 2.72E-06 169836000 131079 184984 167317 155923 196369 120706 157758 156261 172409 FALSE TRUE 122874.9994 198680.4078 171285.8383 159924.2482 180946.9709 155551.8627 134103.6525 175770.5298 143632.8241 0.855479937 1.383252116 1.192525729 1.113424102 1.259788436 1.082982693 0.933656031 1.223749035 1 17.13202596 2.065563521 6.493929881 1.036134613 1.192597439 0.077178659 0.15197004 0.327123011 25.18630578 0.053816667 0.039411847 116.2956635 -2.065563521 0.156462827 EWNGVVS(ph)ESDS(ph)PVKRPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EWNGVVSESDSPVKRPGR 18 2 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 2 EWNGVVS(1)ESDS(1)PVKRPGR 130.81 9.80E-06 205050000 356420 258670 298120 303860 299380 254740 422530 276520 344200 TRUE FALSE 334112.3084 277822.1959 305191.5472 311657.562 275867.9024 328279.3026 359175.5491 311044.1307 286750.7964 1.165166105 0.968862857 1.064309327 1.086858575 0.962047555 1.14482438 1.252570363 1.084719326 1 18.12943797 2.121377262 8.887864954 1.154853817 1.042321819 0.085528416 0.086832722 0.324284914 23.8181597 0.029900542 0.022073355 132.2443912 -2.121377262 -0.112531998 EWNGVVSESDS(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EWNGVVSESDSPVK 14 0 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 1 EWNGVVSESDS(1)PVK;EWNGVVSES(0.008)DS(0.992)PVK;EWNGVVSESDS(1)PVK 259.4 2.14E-24 898200000 1956290 1076040 1409340 1177120 1190290 1214820 1808200 1257390 1055250 TRUE FALSE 1833849.301 1155711.121 1442770.21 1207326.892 1096809.425 1565518.813 1537077.197 1414377.909 879121.9578 2.08600102 1.314619787 1.641149101 1.373332655 1.24761919 1.780775465 1.748423166 1.608852898 1 19.74570379 4.751322326 24.14495532 1.510593434 2.086001614 0.375275685 0.245711748 1471.513807 2783999.923 0.056021219 0.983105658 56405.61336 -4.751322326 0.575408181 EWNGVVSESDS(ph)PVKRPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EWNGVVSESDSPVKRPGR 18 2 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 1 EWNGVVSES(0.039)DS(0.961)PVKRPGR;EWNGVVSESDS(1)PVKRPGR;EWNGVVSES(0.013)DS(0.987)PVKRPGR;EWNGVVSES(0.013)DS(0.987)PVKRPGR 205.43 5.02E-16 3959790000 3909610 2603500 3231030 2854570 3381610 2817730 4325350 3050800 3854450 TRUE FALSE 3664914.489 2796265.849 3307671.557 2927823.099 3116031.991 3631162.909 3676803.922 3431699.096 3211117.394 1.141320618 0.87080773 1.030068712 0.911777036 0.970388687 1.130809766 1.145023202 1.068693129 1 21.61464398 2.245180131 24.74252074 1.104395804 0.972158828 0.254677052 0.081929414 131.2611561 490630.7207 0.026114874 0.021374967 175.8652895 -2.245180131 -0.132236976 EWNGVVSESDS(ph)PVKRPGRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EWNGVVSESDSPVKRPGRK 19 3 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 1 EWNGVVSES(0.025)DS(0.974)PVKRPGRK 118.32 0.00045081 239470000 90407 61017 66741 62019 79365 47544 85154 56224 120270 TRUE FALSE 84748.58725 65534.76217 68324.12804 63610.51254 73131.99304 61269.18099 72385.94823 63243.69016 100196.16 0.845826699 0.654064608 0.681903658 0.634859784 0.729888182 0.611492306 0.722442339 0.631198742 1 16.61246769 -1.416565581 3.157286027 1.004538274 0.684195167 0.676071399 0.067590975 11409243.52 15219956.12 469407.6205 0.01390085 0.038320787 1.416565581 -0.320343107 EWPSNLDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EWPSNLDLR 9 0 P31327;P31327-3;P31327-2;A0A669KBF2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 ;; 93.649 0.021534 337116000 615700 719940 553450 471260 964870 516480 482640 762580 1265280 FALSE TRUE 577164.4361 773245.1067 566578.0954 483353.3294 889093.0023 665579.3916 410272.6126 857789.7916 1054096.594 0.547544162 0.733561906 0.537501116 0.458547473 0.843464448 0.631421632 0.389217283 0.813767729 1 20.00757565 1.007266977 9.347499412 0.99998945 0.596097257 0.53580329 0.1286044 0.09103934 83.15229195 0.12156957 0.030416742 10.16873612 -1.007266977 -0.403892193 EWPVSSFNRPFPNS(ph)P ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EWPVSSFNRPFPNSP 15 1 Q96H12 Q96H12 MSANTD3 Myb/SANT-like DNA-binding domain-containing protein 3 1 EWPVSSFNRPFPNS(1)P;EWPVSSFNRPFPNS(1)P 149 9.03E-06 117764000 185249 185941 196547 168285 189313 177024 234218 143526 207188 TRUE FALSE 173654.5958 199708.2651 201209.1877 172603.478 174445.1206 228127.9551 199099.1853 161445.537 172606.9843 1.006069346 1.157011496 1.165707103 0.999979686 1.010649258 1.321661206 1.153482787 0.935336062 1 17.39713132 1.24029855 24.99708266 0.967667987 1.129224489 0.274728362 0.098739658 53.27105614 766306.0425 0.073466315 0.023666128 17.38995866 -1.24029855 0.161556502 EWQHEEFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EWQHEEFYR 9 0 Q12931-2;Q12931;I3L0K7;I3L239 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ;;; 215.06 6.53E-07 2768760000 2661310 3063850 2421970 2566630 3667670 2147230 2391250 2631170 3618940 FALSE TRUE 2494743.358 3290700.642 2479420.272 2632494.071 3379625.993 2767100.444 2032704.262 2959677.366 3014915.535 0.827467081 1.091473577 0.822384655 0.873156823 1.120968715 0.917803637 0.67421599 0.98167837 1 21.52368615 1.985051365 24.98417902 0.835827371 0.952494016 0 0.133706568 1301.399419 2175074.02 0.050336155 0.033706864 96.61651424 -1.985051365 0.116666645 EWSGLLEELAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 EWSGLLEELAR 11 0 Q01813;Q01813-2;Q5VSR5;V9GYV7 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ;;;; 185.61 1.02E-05 327460700 322866 445062 369025 412707 429636 278969 412211 343301 246839 FALSE TRUE 302658.3934 478014.8536 377778.4473 423297.7603 395894.1216 359502.8216 350403.7873 386162.8855 205639.9763 1.471787728 2.324522995 1.837086612 2.05844101 1.92518074 1.748214662 1.703967262 1.877859026 1 17.64976123 -0.696450114 0.340173174 0.644872789 1.999780487 0.589269759 0.225833873 6.525186487 0.697667944 2.665299669 0.182943453 0.201163825 0.696450114 1.354907698 EWSLESSPAQNWT(ph)PPQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EWSLESSPAQNWTPPQPR 18 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;F8W1U7;E5RHT6;E5RHC5;Q8N6T3-3 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 EWSLESSPAQNWT(1)PPQPR;EWSLES(0.003)S(0.031)PAQNWT(0.966)PPQPR;EWSLESSPAQNWT(1)PPQPR 210.57 4.44E-15 379742000 370891 363688 400728 389902 392017 379476 451509 359371 445589 TRUE FALSE 347677.5944 390615.8379 410233.4574 399907.5454 361229.5661 489024.5609 383809.4171 404239.2604 371217.3173 0.936587756 1.052256508 1.105103233 1.07728688 0.973094598 1.317353847 1.0339211 1.088955826 1 18.50190449 4.950696779 1.488121624 1.092466312 0.803440321 0.197450451 0.092670063 2.946228438 4.074455487 0.022418188 1.452997771 89268.20026 -4.950696779 -0.289025991 EWSQHINGASHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EWSQHINGASHSR 13 0 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 219.41 1.30E-11 699540000 189414 415530 384140 407520 388100 285470 339010 374640 299400 FALSE TRUE 177558.9159 446296.2736 393251.9822 417977.6531 357620.1915 367880.5548 288178.5977 421414.6287 249428.2058 0.711863822 1.789277488 1.576613924 1.675743334 1.433760029 1.474895566 1.155356896 1.689522752 1 17.92826509 1.918667057 8.334073006 1.301790307 1.510264839 0.024917346 0.335956321 0.911135156 85.91625221 0.13099156 0.082375496 82.9214823 -1.918667057 0.208474532 EWTDGLFTHVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EWTDGLFTHVLR 12 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 218.75 3.36E-11 1317280000 2232927 3015331 2527227 2553315 3543920 2171961 3131530 2994740 2967065 FALSE TRUE 2093172.085 3238589.245 2587174.018 2618837.386 3265594.819 2798970.882 2661986.148 3368639.881 2471842.684 0.846806352 1.310192298 1.04665804 1.059467661 1.321117578 1.132341836 1.076923773 1.362805127 1 21.2371555 4.757157474 24.22908498 1.160596616 0.846805932 0.379468273 0.127294043 2824.675413 3680062.571 0.02767422 0.915533446 57168.58906 -4.757157474 -0.313790683 EWTGIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EWTGIDR 7 0 P56182 P56182 RRP1 Ribosomal RNA processing protein 1 homolog A 0 92.47 0.036399 91351000 245660 286740 271230 302090 291970 241540 304690 246750 327980 FALSE TRUE 230284.5791 307970.528 277663.7037 309842.1408 269039.854 311268.6769 259004.5631 277557.2807 273238.0192 0.84279845 1.12711448 1.016197177 1.133964233 0.984635501 1.139185088 0.947908215 1.015807689 1 18.05979871 1.664541175 14.81731511 0.986628098 1.049175091 0.066542265 0.089285723 0.297680788 69.35484287 0.036734441 0.020240819 46.1892781 -1.664541175 0.062546993 EY(ph)FTFPASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EYFTFPASK 9 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 EY(0.972)FT(0.028)FPASK;EY(1)FTFPASK 122.28 0.0060827 289230000 358970 350450 281840 348860 394430 273890 478900 342240 213522 TRUE FALSE 336502.7085 376397.6826 288525.3779 357812.3382 363453.0589 352957.5968 407093.3909 384969.4174 177883.7988 1.891699586 2.115975065 1.621987949 2.011494811 2.043204954 1.984203166 2.288535514 2.164162335 1 17.44057559 EYADSFGKPPHPIPAGDILSSEGCSQCPGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EYADSFGKPPHPIPAGDILSSEGCSQCPGGR 31 1 Q99447-3 Q99447-3 PCYT2 Ethanolamine-phosphate cytidylyltransferase 0 41.209 0.093043 105810000 40917 36816 38863 41015 37563 32528 48747 34651 48797 FALSE TRUE 38356.07801 39541.89495 39784.84871 42067.51434 34612.9535 41918.30555 41437.83989 38977.25363 40652.46546 0.94351173 0.972681349 0.978657709 1.034808439 0.851435531 1.031138089 1.019319233 0.958791876 1 15.31105523 EYAENIGDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EYAENIGDGR 10 0 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 97.734 0.012006 0 225880 237080 239770 243360 250930 207250 286150 207840 245060 FALSE TRUE 211742.574 254633.6499 245457.4576 249605.0296 231222.97 267079.7106 243244.464 233789.2815 204157.9029 1.037151004 1.247238761 1.202292217 1.222607727 1.132569285 1.308201675 1.191452599 1.145139513 1 17.63932589 -1.101472521 6.340824471 0.999999604 1.197351731 0.381421243 0.0730758 3.62E-07 5.14E-08 0.062662891 0.014769755 0.079163954 1.101472521 0.197352127 EYAENIGDGRS(ph)PEFR ddPTM_SK-BR-3_Pertuzumab_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 199.15 4.58E-09 927020000 765630 846200 755810 875940 869810 702000 927900 798490 754540 TRUE FALSE 717710.585 908853.5285 773738.1701 898418.1034 801498.6312 904656.004 788770.0092 898183.2342 628602.3995 1.141756038 1.445832102 1.230886441 1.429231107 1.275048635 1.439154551 1.254799552 1.42885747 1 19.26178825 -1.735313613 2.764206236 0.938365143 1.332412883 0.495613842 0.104830641 12699153.01 10355932.7 5370429.864 0.022727541 0.018394432 1.735313613 0.39404774 EYCIQAFESFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EYCIQAFESFVR 12 0 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 138.45 0.00017271 99107000 84449 115826 87470 98393 105871 76527 104783 95116 85565 FALSE TRUE 79163.48784 124401.8776 89544.82971 100917.931 97556.31872 98619.10259 89071.76191 106991.442 71283.64873 1.110542028 1.745167086 1.256176294 1.41572342 1.368565168 1.383474392 1.24953988 1.500925442 1 16.12128356 -3.567196324 0.233353658 3.50E-09 1.442445245 0.294858077 0.172969001 86.84865367 1.587439656 41.92509517 0.272828645 0.000270897 3.567196324 1.442445241 EYDSISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EYDSISR 7 0 P54920;M0R0Y2;M0R213 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;; 150.84 0.0044711 368210000 1405120 1460450 1533540 1461160 1443520 1288670 1657630 1381630 1362430 FALSE TRUE 1317176.047 1568583.238 1569916.293 1498655.839 1330151.762 1660688.109 1409083.77 1554129.547 1135031.631 1.160475189 1.381973149 1.383147614 1.320364823 1.171907219 1.463120554 1.2414489 1.369238974 1 20.11430107 -1.486846775 2.944423505 0.990119376 1.321137964 0.503021656 0.096868851 19164244.52 22047459.01 1544321.727 0.021079851 0.032595168 1.486846775 0.331018588 EYEEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EYEEEER 7 0 Q16543;K7EKQ2;K7EQA9;K7EL68;K7EIU0 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ; 181.49 0.0015614 750980000 1287350 1156300 1237920 1149760 1150670 1114770 1429590 1067200 1114680 FALSE TRUE 1206777.061 1241913.655 1267284.047 1179264.788 1060301.02 1436586.002 1215236.251 1200442.269 928632.7069 1.299520308 1.33735722 1.364677377 1.269893661 1.141787288 1.546990529 1.308629604 1.292698674 1 19.82474857 0.701202309 2.802003078 1.000045417 1.330714783 0.508188033 0.099320704 1.822201083 16.12041131 0.088547849 0.023328783 5.025766526 -0.701202309 0.330669365 EYELFEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EYELFEFR 8 0 A0A2R8YE10;Q9NRW7;B7Z7G7;A0A2R8YF01;A0A087WU65;A0A1B0GXI6;A0A2R8YD95;Q9NRW7-2 A0A2R8YE10 VPS45 Vacuolar protein sorting-associated protein 45 0 ;;; 145.63 0.0013173 200799000 291494 416297 295162 305983 419705 214709 311508 374375 360146 FALSE TRUE 273249.9109 447120.063 302163.382 313835.0418 386743.0623 276692.0028 264800.2673 421116.5429 300035.306 0.910725856 1.490224831 1.007092752 1.045993707 1.288991844 0.922198146 0.882563692 1.40355663 1 18.19477275 3.736912335 24.17705763 1.06061086 1.243905381 0.040975117 0.210571168 469.4455904 1159187.489 0.050442147 0.089454222 5456.477075 -3.736912335 0.183294522 EYELRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EYELRK 6 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ; 91.26 0.077118 1036260000 1408680 1579920 1524830 1387650 1775640 1011080 1760660 1369550 2468110 FALSE TRUE 1320513.233 1696898.921 1560999.688 1423259.448 1636188.397 1302962.382 1496665.378 1540541.332 2056166.496 0.642220966 0.825273111 0.759179614 0.692190759 0.795747037 0.633685251 0.727891141 0.749229858 1 20.97152566 0.751395673 4.986980128 0.999999702 0.734911566 0.663902813 0.060707598 5.421958075 108.466869 0.056579377 0.01430223 5.641514041 -0.751395673 -0.265088136 EYFDDS(ph)TEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EYFDDSTEER 10 0 Q8NEF9 Q8NEF9 SRFBP1 Serum response factor-binding protein 1 1 EYFDDS(0.84)T(0.16)EER;EYFDDS(0.817)T(0.183)EER 177.1 0.002642 0 279560 222481 278070 248680 218253 277110 323110 215067 168743 TRUE FALSE 262062.8386 238953.7247 284665.9517 255061.5498 201112.2898 357107.1585 274662.6551 241918.5884 140578.7032 1.86417169 1.699786094 2.024957873 1.814368351 1.430602824 2.540264993 1.953799892 1.720876512 1 17.10101853 4.035997848 20.71904805 1.86720756 1.781752003 0 0.403564469 207.684423 73075.35142 0.091229533 0.197077706 10864.2024 -4.035997848 -0.085455557 EYFSWEGAFQHVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EYFSWEGAFQHVGK 14 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;; 259.7 1.98E-24 10356925000 7911170 8648660 6233682 5038000 6352717 3237781 8811410 6807680 9984190 FALSE TRUE 7416023.992 9289015.785 6381547.881 5167283.609 5853800.232 4172475.814 7490220.872 7657633.834 8317764.189 0.891588632 1.11676835 0.767219139 0.621234684 0.703770881 0.5016343 0.900508923 0.920636082 1 22.98776435 3.796770319 3.813968391 0.751986417 1.008161109 0.265614763 0.156239092 0.251483634 7.165991478 0.039590235 0.073855923 6262.825616 -3.796770319 0.256174692 EYGEQIDPSTHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EYGEQIDPSTHR 12 0 Q9Y2B0;F8VXJ7;F8W031;F8W1K5 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;; 130.1 0.0002225 1288050000 1776630 2077060 2008490 1961410 2168920 1602270 2247530 1932670 1797500 FALSE TRUE 1665433.9 2230847.684 2056132.331 2011743.101 1998581.772 2064819.338 1910533.742 2173968.104 1497485.638 1.112153504 1.489728935 1.373056462 1.343413954 1.334625002 1.378857524 1.275827757 1.451745545 1 20.51411074 -1.642944473 2.644713782 0.95961393 1.355624359 0.526454608 0.102362433 12000383.61 10404788.36 3299710.142 0.02274867 0.022753883 1.642944473 0.39601043 EYGMIYLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EYGMIYLGK 9 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 160.75 0.00015136 205380000 332150 380470 347900 331180 409360 269220 436720 350070 443150 FALSE TRUE 311361.3244 408640.3947 356152.3523 339678.6395 377210.5169 346939.4436 371237.8903 393777.0101 369185.4021 0.843373878 1.106870403 0.964697819 0.920076031 1.021737357 0.939743125 1.005559505 1.066610456 1 18.49398598 1.469376143 8.026326302 1.034401017 0.982006169 0.113650064 0.070341972 0.29195237 58.96186074 0.03735566 0.01673653 29.46972904 -1.469376143 -0.052394849 EYGS(ph)PLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EYGSPLK 7 0 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;Q9UQ88-5;Q9UQ88-10 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 EYGS(1)PLK;EYGS(1)PLK;EYGS(1)PLK;EYGS(1)PLK;EYGS(1)PLK;EYGS(1)PLK;EYGS(1)PLK;EYGS(1)PLK 138.66 0.0028995 17341950000 18603360 11624350 14330980 13128990 13164510 11597630 17708480 12603950 14629840 TRUE FALSE 17439008.91 12485028.97 14670917.61 13465902.11 12130622.49 14945677.51 15053257.82 14177580.9 12188025.19 1.43083138 1.024368491 1.203715728 1.104846921 0.995290238 1.226259158 1.23508588 1.163238562 1 23.53896105 4.752240985 24.50820075 1.133692346 1.430831641 0.532169773 0.090944476 1530.372256 2741578.967 0.021514404 0.423952816 56525.0539 -4.752240985 0.297139295 EYGS(ph)PLKAYT(ph)PVVVTLWYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EYGSPLKAYTPVVVTLWYR 19 1 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12 P21127-2 CDK11B Cyclin-dependent kinase 11B 2 EYGS(1)PLKAYT(0.992)PVVVT(0.008)LWYR;EY(0.001)GS(0.999)PLKAY(0.009)T(0.985)PVVVT(0.006)LWYR;EY(0.001)GS(0.986)PLKAY(0.036)T(0.973)PVVVT(0.003)LWYR 157.24 1.82E-08 1073116000 2044783 1888704 1782431 1894141 2853700 1286936 2375700 1829040 4034690 TRUE FALSE 1916803.682 2028545.609 1824711.105 1942747.865 2629581.913 1658453.532 2019485.84 2057399.67 3361274.174 0.570261033 0.603504952 0.542862918 0.577979589 0.782316996 0.493400254 0.600809614 0.612089215 1 21.6805768 0.552824281 2.833095454 0.999997234 0.592694074 0.745206855 0.073933142 4.125987539 25.52042596 0.065373173 0.017185785 3.571283122 -0.552824281 -0.407303161 EYGS(ph)PLKAYT(ph)PVVVTQWYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EYGSPLKAYTPVVVTQWYR 19 1 Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;Q9UQ88-5;Q9UQ88-10 Q5QPR3 CDK11A Cyclin-dependent kinase 11A 2 EY(0.003)GS(0.997)PLKAYT(0.998)PVVVT(0.002)QWYR;EYGS(1)PLKAYT(1)PVVVTQWYR 138.11 5.84E-06 156454000 440410 414320 372730 439130 579060 268510 539700 402890 904160 TRUE FALSE 412845.5243 444996.6839 381571.3316 450398.8192 533582.9634 346024.4781 458776.9953 453191.7034 753249.8549 0.548085767 0.590769027 0.506566751 0.597940798 0.708374466 0.459375433 0.609063503 0.601648577 1 19.52276896 0.321461562 1.463247754 1.000143481 0.569939813 0.805995101 0.065273342 2.147910676 4.208846235 0.057919841 0.016723837 2.096339233 -0.321461562 -0.430203668 EYGSCSHHYQQLLQSLEQGAQEESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 155.49 3.28E-08 404790000 30100 54414 52090 49906 67369 58765 67358 53472 51198 FALSE TRUE 28216.09473 58442.86918 53325.5994 51186.67245 62078.11049 75729.50153 57258.29322 60148.09691 42652.72305 0.661530911 1.370202533 1.250227315 1.200079826 1.455431355 1.775490429 1.342429958 1.410181874 1 15.38035023 4.738575652 20.87054091 1.369942186 0.661533032 0.541859517 0.198381253 0.103298096 125231.8861 0.045277368 0.260213892 54774.15069 -4.738575652 -0.708409154 EYHPDKNPNAGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EYHPDKNPNAGDK 13 1 O60884;I3L320 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ;;; 180.84 7.55E-06 1117710000 1864400 1015760 1275400 1153410 1070040 976900 1682980 1188120 1314250 FALSE TRUE 1747710.532 1090967.927 1305653.09 1183008.453 986003.3747 1258915.171 1430632.773 1336459.397 1094893.185 1.596238388 0.99641494 1.192493577 1.080478416 0.90054755 1.149806382 1.306641409 1.220629936 1 20.0623587 4.747965203 24.55594408 1.120108421 1.596238713 0.619064379 0.120427184 737.4236269 1925405.728 0.030095214 0.377245601 55971.2754 -4.747965203 0.476130292 EYHTDTTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EYHTDTTVK 9 0 Q02880;Q02880-2;E9PCY5;P11388;P11388-2;P11388-3;P11388-4 Q02880;P11388 TOP2B;TOP2A DNA topoisomerase 2-beta;DNA topoisomerase 2;DNA topoisomerase 2-alpha 0 ; 117.7 0.0011094 1074160000 1101930 1050490 1077750 1023900 1095620 796190 1220350 1004730 1156850 FALSE TRUE 1032962.168 1128269.373 1103314.739 1050175.007 1009574.425 1026037.128 1037369.847 1130172.752 963764.2615 1.071799619 1.170690197 1.144797315 1.089659629 1.04753254 1.06461421 1.076373018 1.17266514 1 19.87832078 3.161874307 4.601799239 1.075643304 1.140313245 0.204768348 0.049135975 0.261505027 10.27279811 0.01335598 0.016372068 1451.691409 -3.161874307 0.064669941 EYINCNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EYINCNR 7 0 J3KMX2;B9EGA3;Q92925-3;Q92925-2;Q92925;J3QWB6 J3KMX2 SMARCD2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 0 111.65 0.015195 135900000 126950 138090 144500 151250 160770 128630 143630 117440 156410 FALSE TRUE 119004.4261 148314.3273 147927.6082 155131.3311 148143.7727 165763.3929 122094.0149 132102.6425 130304.1606 0.91328186 1.13821636 1.135248542 1.190532447 1.136907464 1.272126632 0.936992452 1.013802184 1 16.99152362 1.667522996 10.07249608 0.982575866 1.13459773 0.366869278 0.091035078 0.115937262 17.23479593 0.040648063 0.021864595 46.50750017 -1.667522996 0.152021865 EYIPGQPPLSQS(ph)SDS(ph)SPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 2 EYIPGQPPLS(0.008)QS(0.981)S(0.012)DS(0.533)S(0.414)PT(0.051)R 130.56 2.53E-05 724220000 107080 108200 114510 108220 109320 100510 133170 106610 119850 TRUE FALSE 100378.0539 116211.2406 117226.2313 110997.1084 100734.4482 129525.6054 113202.3948 119920.4932 99846.26074 1.00532612 1.16390178 1.174067315 1.111680173 1.00889555 1.297250437 1.133766993 1.201051419 1 16.60742078 2.252959747 24.99893868 1.169946429 1.114418239 0.078922902 0.092144129 615.9907029 1069445.813 0.029699611 0.024739545 179.0439899 -2.252959747 -0.05552819 EYIPGQPPLSQS(ph)SDSS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 2 EYIPGQPPLSQS(1)SDS(0.012)S(0.987)PTR;EYIPGQPPLSQS(0.999)S(0.001)DS(0.237)S(0.761)PT(0.002)R;EYIPGQPPLSQS(1)SDS(0.039)S(0.958)PT(0.003)R;EYIPGQPPLS(0.001)QS(0.996)S(0.004)DS(0.312)S(0.683)PT(0.005)R 318.43 1.21E-61 2445610000 1609010 1652710 1700610 1593490 1672990 1587820 1985850 1629240 1856820 TRUE FALSE 1508304.936 1775078.368 1740949.272 1634381.651 1541600.114 2046197.858 1688090.228 1832654.2 1546904.746 0.975047067 1.147503343 1.125440514 1.056549639 0.996570809 1.322769138 1.091269667 1.184723367 1 20.56095293 EYIPGQPPLSQSSDS(ph)SPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 EYIPGQPPLS(0.001)QSSDS(0.49)S(0.49)PT(0.019)R;EYIPGQPPLSQSS(0.001)DS(0.641)S(0.356)PT(0.003)R 129.88 1.96E-05 1282318600 218620 247507 247406 256311 260940 216802 281506 227555 251029 TRUE FALSE 204936.9644 265832.6758 253274.5872 262888.3742 240446.825 279389.2179 239296.7887 255965.7427 209130.6382 0.97994711 1.271132141 1.211083127 1.257053373 1.149744614 1.33595546 1.144245486 1.223951425 1 17.67404491 -0.786534271 7.059704355 0.999999999 1.206592469 0.289883401 0.095600383 0 1.70E-10 0.080318327 0.018931211 0.163480414 0.786534271 0.20659247 EYIPGQPPLSQSSDSS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 EYIPGQPPLSQSSDS(0.202)S(0.798)PTR;EYIPGQPPLSQSSDS(0.043)S(0.952)PT(0.005)R;EYIPGQPPLSQSSDS(0.085)S(0.9)PT(0.014)R;EYIPGQPPLSQSSDS(0.006)S(0.977)PT(0.017)R;EYIPGQPPLSQSSDS(0.018)S(0.848)PT(0.133)R;EYIPGQPPLSQSSDS(0.016)S(0.968)PT(0.016)R;EYIPGQPPLS(0.026)QS(0.026)S(0.074)DS(0.202)S(0.482)PT(0.19)R;EYIPGQPPLSQS(0.001)S(0.001)DS(0.38)S(0.616)PT(0.003)R 362.24 1.24E-91 41578350000 3260570 3207210 3311830 3486580 3384350 3047010 3747600 2948820 3675040 TRUE FALSE 3056496.744 3444675.165 3390388.172 3576051.546 3118556.803 3926632.323 3185682.171 3316986.668 3061652.082 0.998316158 1.125103399 1.107372125 1.16801369 1.018586279 1.282520749 1.040510837 1.083397649 1 21.54587892 -0.322291697 6.440778852 0.99999562 1.107792984 0.134385949 0.081323213 0 0 0.068246562 0.016085869 0.476111096 0.322291697 0.107797363 EYLESLQCLESDKSDWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EYLESLQCLESDKSDWR 17 1 P49792;J3KNE0;A6NKT7;Q7Z3J3;O14715;F8W705;F8VYC4;A0A286YES2;P0DJD0;A0A1W2PNU4;P0DJD1 P49792;F8VYC4 RANBP2;RGPD3;RGPD4;RGPD8;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 1;RANBP2-like and GRIP domain-containing protein 2 0 117.2 0.00020905 58205000 163040 163960 176530 163260 197600 122500 208640 152320 217560 FALSE TRUE 152835.6174 176099.769 180717.375 167449.528 182081.2931 157863.7614 177356.3689 171337.4873 181247.8305 0.843241086 0.971596562 0.997073314 0.923870523 1.004598469 0.870982902 0.97852961 0.94532159 1 17.4676042 6.651981196 0.006315452 1.851072989 1.86E-06 0.127547828 0.051442369 76565.04652 47.22851456 6425.151975 7451.205804 4487259.607 -6.651981196 -1.851071126 EYLSEEVQAVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EYLSEEVQAVHK 12 0 Q53GS9;B9A018;A0A087X1B2;Q53GS9-2 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 0 160.67 6.74E-05 195220000 191220 167150 170860 167280 170610 135990 181370 142980 192160 FALSE TRUE 179251.8815 179525.9599 174912.8799 171572.688 157210.9788 175248.1054 154175.2523 160831.3677 160087.2546 1.119713634 1.12142569 1.092609654 1.071744833 0.982033074 1.094703672 0.963070125 1.004648172 1 17.28849893 2.994059085 0.716156849 0.994316274 1.129300692 0.649571357 0.034732027 0.395396798 0.449957092 0.020526315 0.027467211 986.4136754 -2.994059085 0.134984418 EYLY(ph)RYRT(ph)MGNVARR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EYLYRYRTMGNVARR 15 3 Q5FYB1-2;Q5FYB1 Q5FYB1-2 ARSI Arylsulfatase I 2 EYLY(0.511)RY(0.511)RT(0.979)MGNVARR 61.212 0.030578 67492000 78327 83969 93434 92577 90667 77241 102810 83629 100790 TRUE FALSE 73424.65289 90186.15213 95650.2986 94952.68255 83546.37955 99539.2228 87394.59494 94070.26474 83967.49787 0.874441358 1.074060254 1.139134797 1.130826629 0.994984746 1.185449434 1.040814567 1.120317589 1 16.35754338 4.737814348 4.085678599 1.093245315 0.855897554 0.539021474 0.061329542 0.154344201 5.606058772 0.012838472 0.108079631 54678.21743 -4.737814348 -0.237347761 EYPDFNFVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EYPDFNFVGR 10 0 Q96PU8-5;Q96PU8-9;Q96PU8-8;Q96PU8-6;Q96PU8-3;Q96PU8;F5GXS8;F5GYM3;F5H5U6;F5H8C8 Q96PU8-5 QKI Protein quaking 0 91.867 0.022931 50995000 48559 65387 50705 53830 61495 48580 60546 50059 56071 FALSE TRUE 45519.77887 70228.32152 51907.74654 55211.36893 56665.43076 62604.25737 51467.68938 56308.97634 46712.38787 0.974469107 1.503419644 1.111220148 1.181942766 1.213070737 1.340206747 1.101799581 1.205439904 1 15.51151757 0.10829112 0.4339898 0.970373883 1.245290032 0.148550555 0.143440896 5.941394101 1.580150266 0.444595911 0.082422493 1.283190453 -0.10829112 0.274916149 EYS(ph)PPYAPSHQQYPPSHATPLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EYSPPYAPSHQQYPPSHATPLPK 23 0 Q9UPT8 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 EYS(1)PPYAPSHQQYPPSHATPLPK;EYS(1)PPYAPSHQQYPPSHATPLPK;EY(0.001)S(0.993)PPY(0.001)APS(0.004)HQQYPPSHATPLPK;EYS(1)PPYAPSHQQYPPSHATPLPK 265.89 7.49E-44 3041530000 1798760 1681140 1832110 1745860 1865010 1398210 2303710 1643260 2215110 TRUE FALSE 1686178.822 1805613.355 1875568.514 1790661.723 1718539.638 1801850.529 1958290.072 1848424.628 1845393.831 0.913723019 0.978443368 1.016351352 0.970341232 0.931259013 0.976404331 1.061177316 1.001642358 1 20.81549731 1.866226322 8.146808729 1.02639185 0.97063967 0.391735854 0.032429618 0.302871953 18.58442882 0.014033006 0.008779152 73.48967416 -1.866226322 -0.05575218 EYSFDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EYSFDSR 7 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 81.784 0.061099 229860000 473550 623470 569680 596440 685070 535570 645910 602620 581820 FALSE TRUE 443911.3508 669632.3675 583193.0786 611745.6602 631267.3656 690180.3647 549061.7918 677858.4335 484710.4833 0.915827831 1.381509975 1.203178183 1.262084649 1.30235963 1.423902285 1.132762362 1.398481066 1 18.88676376 -1.11264038 4.613684873 0.99997909 1.25962739 0.21921236 0.149232636 2.78E-05 5.35E-06 0.125228388 0.029514239 0.077154208 1.11264038 0.2596483 EYSSELNAPSQESDSHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EYSSELNAPSQESDSHPR 18 0 P49756;P49756-2;P49756-3;E9PQU5 P49756 RBM25 RNA-binding protein 25 0 222.96 5.41E-19 479620000 293700 358350 350400 319160 345470 299950 427420 331600 377870 FALSE TRUE 275317.8413 384882.6069 358711.6535 327350.1859 318338.1798 386540.6957 363332.339 373000.9899 314801.0559 0.874577249 1.222621715 1.139486818 1.039863685 1.011236061 1.227888816 1.154164931 1.184878459 1 18.26408085 2.234129805 24.99888175 1.157153792 1.090433906 0.081531216 0.108413774 305.8941028 1725852.78 0.038470581 0.029407219 171.4469665 -2.234129805 -0.066719885 EYTAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EYTAGR 6 0 P07237;I3L3P5 P07237 P4HB Protein disulfide-isomerase 0 ;;; 177.54 0.0084904 6153120000 3000470 3561990 3262610 3559680 3243820 2660960 3483180 2789420 2885290 FALSE TRUE 2812675.939 3825723.446 3340000.65 3651027.415 2989063.462 3429135.955 2960909.495 3137685.227 2403716.459 1.170136323 1.591586824 1.389515239 1.518909354 1.243517492 1.426597526 1.23180481 1.305347482 1 21.1968353 0.794719226 0.487893293 0.986072407 1.441860436 0.464058148 0.126381583 0.9919521 0.540131899 0.151352819 0.064361437 6.233317168 -0.794719226 0.455788029 EYTINIHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 EYTINIHK 8 0 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 ;;;;; 164.53 0.00032954 6666350000 8194120 7464640 8098190 7888050 8245980 6704710 8825870 7494490 7544420 FALSE TRUE 7681264.656 8017329.713 8290282.891 8090470.717 7598373.993 8640250.935 7502512.729 8430193.574 6285207.563 1.222117898 1.275587104 1.319014974 1.287224111 1.208929684 1.374696197 1.193677799 1.341275286 1 22.58352896 -1.111146508 4.190371192 0.999949541 1.277604666 0.694834488 0.057860834 3500006.028 929022.9668 1667.914979 0.011836034 0.077420058 1.111146508 0.277655125 EYVAYSHTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EYVAYSHTGR 10 0 Q969X5;Q969X5-2 Q969X5 ERGIC1 Endoplasmic reticulum-Golgi intermediate compartment protein 1 0 ; 120.09 0.00060585 661560000 200654 460190 203631 226574 482070 173882 276531 391270 212032 FALSE TRUE 188095.4243 494262.9464 208461.2235 232388.2724 444210.1668 224078.9107 235067.7437 440120.9208 176642.4894 1.064836806 2.798097717 1.180130693 1.315585357 2.514741319 1.268544796 1.330754251 2.491591475 1 17.43047288 -2.045672041 2.623489459 0.015517171 1.746876717 0.119982604 0.634528068 9126129.434 4721456.842 54207837.77 0.142836073 0.009001771 2.045672041 1.731359546 EYVDLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EYVDLER 7 0 Q13951-2;A0A494C0A9;Q13951 Q13951-2 CBFB Core-binding factor subunit beta 0 91.906 0.037363 185720000 373960 417390 404050 425790 446630 379390 445570 412680 496140 FALSE TRUE 350554.5111 448293.9899 413634.2568 436716.4923 411553.4814 488913.7341 378760.915 464204.0064 413331.0288 0.848120481 1.084588281 1.00073362 1.05657805 0.995699458 1.182862403 0.916362161 1.123080471 1 18.65693815 4.746925071 24.40236241 1.040251979 0.848120346 0.406936999 0.0744954 724.0575216 2112290.666 0.015460745 0.173945122 55837.38501 -4.746925071 -0.192131633 EYVEHTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EYVEHTVK 8 0 O75937 O75937 DNAJC8 DnaJ homolog subfamily C member 8 0 ;; 105.57 0.0043629 1346060000 1807920 1677490 1719600 1553000 1917000 1185840 1900790 1656060 2170330 FALSE TRUE 1694765.514 1801693.105 1760389.724 1592852.609 1766446.553 1528172.757 1615784.186 1862822.736 1808087.902 0.937324735 0.996463227 0.973619547 0.880959718 0.9769694 0.845187203 0.893642496 1.03027222 1 20.78603339 3.363851245 11.71240528 0.925465985 0.975958119 0.028812747 0.058255893 0.749782167 73.9504278 0.01509254 0.020437846 2311.272995 -3.363851245 0.050492133 EYVEPELHINDLWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EYVEPELHINDLWR 14 0 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;;; 201.06 1.84E-08 613435000 762110 809740 848210 854300 874110 761240 906900 745720 811580 FALSE TRUE 714410.8955 869693.9921 868329.9418 876222.7843 805460.9266 980997.6303 770918.7642 838824.7835 676122.055 1.056630072 1.286297327 1.284279865 1.29595356 1.191295152 1.450917956 1.140206503 1.240641061 1 19.36692418 0.547642184 1.193612963 1.000644878 1.259682316 0.344501512 0.104592006 1.67858851 3.308482069 0.088998125 0.027089731 3.528923014 -0.547642184 0.259037438 EYVESQLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EYVESQLQR 9 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;; 175.51 0.00012529 890429000 666646 912250 737778 775332 932430 691629 795350 742040 831120 FALSE TRUE 624921.8169 979793.9392 755278.4426 795228.3318 859200.709 891291.0646 676094.6512 834685.3274 692400.7028 0.902543591 1.4150678 1.090811202 1.148508846 1.240900978 1.287247487 0.976449978 1.205494628 1 19.40124766 1.738639876 25 1.065402614 1.198549946 0.124159845 0.145330357 0.067407075 6368.328434 0.061253663 0.033968255 54.7822513 -1.738639876 0.133147333 EYVSNDAAQS(ph)DDEEKLQSQPTDTDGGR ddPTM_SK-BR-3_Pertuzumab_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 272.55 5.23E-61 1850360000 2774280 1627380 1998240 1927810 2056800 1490670 2442770 1719030 2223180 TRUE FALSE 2600642.767 1747872.908 2045639.196 1977280.868 1895267.225 1921002.23 2076499.316 1933654.68 1852116.896 1.404146128 0.943716302 1.104487088 1.067578873 1.023297843 1.037192757 1.121149168 1.044024102 1 20.82074373 4.749220627 24.98695975 1.049257972 1.404146329 0.834487486 0.050515729 623.2379563 1460835.605 0.011975853 0.175595134 56133.30672 -4.749220627 0.354888357 EYVTCHTCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 EYVTCHTCR 9 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;;;;;; 205.09 1.55E-05 1490894000 1292025 2175480 1147127 1145671 2366685 939379 1175169 1866167 1829324 FALSE TRUE 1211159.462 2336554.803 1174337.394 1175070.857 2180815.107 1210562.468 998963.3182 2099162.058 1523998.007 0.794725096 1.533174448 0.770563603 0.771044878 1.430982913 0.794333367 0.655488599 1.377404727 1 20.53942959 3.903394069 8.336102558 0.940528456 1.207972147 0.051255012 0.311222451 0.567882888 58.27145723 0.07489724 0.135631391 8005.603362 -3.903394069 0.267443691 EYWDYEAHVPSWGNQDDYQLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EYWDYEAHVPSWGNQDDYQLVR 22 0 P19784;H3BNI9 P19784 CSNK2A2 Casein kinase II subunit alpha 0 128.05 1.73E-05 117290000 76450 83271 91622 88424 97249 72415 98505 72144 69397 FALSE TRUE 71665.13097 89436.47148 93795.31711 90693.10954 89611.45582 93320.03494 83735.08973 81151.33721 57814.19238 1.239576789 1.546963951 1.622357993 1.568699757 1.549990619 1.614137137 1.448348343 1.403657716 1 15.81913607 0.711862078 1.327800905 1.000847866 1.538499806 0.68306828 0.109214048 0.5181879 1.498089564 0.097641341 0.029183723 5.150650453 -0.711862078 0.53765194 EYWDYESHVVEWGNQDDYQLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 EYWDYESHVVEWGNQDDYQLVR 22 0 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;A0A2R8Y4H0;A0A2R8Y4D6;V9GYA2;A0A2R8YEW1;A0A2R8YDY7;A0A2R8YCK2;V9GY80;A0A2R8Y7T1;A0A2R8YF47;A0A2R8YEL7;A0A2R8Y797;A0A2R8Y3W6 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 ;;; 295.21 1.64E-55 1170500000 858110 937040 867510 856730 956150 729760 1016920 805620 856450 FALSE TRUE 804402.4269 1006419.417 888087.7469 878715.1422 881057.8359 940429.8653 864442.2866 906203.4304 713502.9621 1.127398861 1.41053292 1.244686839 1.231550798 1.234834167 1.318046196 1.211546879 1.27007662 1 19.44455989 -3.848509793 0.297225688 1.70E-11 1.28316949 0.52749046 0.074567601 88.70260851 1.56841546 54.34452133 0.071017738 0.000141739 3.848509793 1.28316949 EYYDHLPELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 EYYDHLPELK 10 0 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;; 115.78 0.0011773 907620000 2860890 2592340 2817990 2757000 3101640 2209300 3608150 2602990 3753230 FALSE TRUE 2681832.002 2784279.551 2884834.054 2827749.288 2858049.706 2847089.045 3067141.404 2927979.031 3126791.666 0.857694496 0.890458927 0.92261793 0.904361272 0.91405185 0.910546448 0.980922854 0.936416411 1 21.57625167 7.99999881 0.074471215 1.088243629 0.51210104 0.801273301 0.018415841 95.65795885 0.522725138 0.660656928 5.7216374 99999726.04 -7.99999881 -0.576142589 EYYS(ph)TESEPLTNGGQKPSSSDTFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 EYYSTESEPLTNGGQKPSSSDTFFR 25 1 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 EYYS(0.838)T(0.16)ES(0.001)EPLTNGGQKPSSSDTFFR;EYYS(0.881)T(0.111)ES(0.007)EPLTNGGQKPSSSDTFFR 291.2 4.64E-63 538087000 360741 332236 319607 357363 202953 194375 523565 319158 436363 TRUE FALSE 338162.8648 356835.0991 327188.229 366533.5396 187013.8901 250487.9071 445061.2888 359005.5789 363531.1963 0.930216906 0.981580406 0.900027927 1.008258833 0.514436978 0.689041022 1.224272616 0.987550952 1 18.47171965 1.734921861 24.99999594 1.081666757 0.855315091 0.319835011 0.158693593 0.550401838 3735.358551 0.075639221 0.041945761 54.31525975 -1.734921861 -0.226351666 EYYSEADASHCIHQILESVNHIHQHDIVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EYYSEADASHCIHQILESVNHIHQHDIVHR 30 0 Q13555-8;Q13555-9;Q13555-10;Q13555-3;Q13555-7;Q13555-4;Q13555-2;A0A2Q3DQE3;Q13555;Q8WU40;Q5SWX3;Q13555-6;Q13555-11;Q13555-5 Q13555-8 CAMK2G Calcium/calmodulin-dependent protein kinase type II subunit gamma 0 225.84 2.28E-35 410950000 284470 347420 323870 361210 423590 377270 404790 301650 419400 FALSE TRUE 266665.5305 373143.3383 331552.3493 370479.2601 390322.9501 486181.7245 344095.4974 339311.6665 349399.4306 0.763211119 1.067956343 0.948920692 1.060331608 1.117125318 1.391478297 0.984819857 0.971128276 1 18.41451773 4.738645177 9.42753081 1.068728763 0.762161047 0.366877721 0.125708769 0.090464431 198.0972763 0.030062079 0.175320565 54782.91995 -4.738645177 -0.306567717 EYYSEADASHCIQQILESVNHCHLNGIVHR ddPTM_SK-BR-3_Pertuzumab_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 58.722 0.012018 42293000 23906 31209 30195 32343 33751 24935 35317 30676 28341 FALSE TRUE 22409.76613 33519.74683 30911.23966 33172.97614 31100.3326 32133.32971 30021.54372 34505.96613 23610.70401 0.949135872 1.419684344 1.309204488 1.404997332 1.317213269 1.360964489 1.271522599 1.461454352 1 14.52715344 -1.597381073 5.824979126 0.998543399 1.322546127 0.322876428 0.14112664 0.002325992 0.000160771 0.119056564 0.027946442 0.025270796 1.597381073 0.324002727 FAAGHDAEGSHSHVHFDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FAAGHDAEGSHSHVHFDEK 19 0 Q9GZN8-2;Q9GZN8;H7BYU9 Q9GZN8-2 C20orf27 UPF0687 protein C20orf27 0 216.29 1.34E-19 391630000 152300 187320 196010 202970 199410 160810 243740 140970 215670 FALSE TRUE 142767.8149 201189.3677 200659.4498 208178.5538 183749.143 207233.2365 207193.4498 158570.4148 179673.2837 0.794596792 1.119751159 1.116801817 1.158650577 1.022684838 1.153389264 1.153167825 0.882548655 1 17.45501638 -0.351304944 6.051300344 0.999999996 1.075243627 0 0.125388316 0 0 0.109777372 0.025874775 0.445343437 0.351304944 0.075243631 FAALDNEEEDKEEEIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FAALDNEEEDKEEEIIK 17 1 Q5STZ8;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ; 171.67 1.55E-09 164218000 590900 228120 336770 297850 304160 235680 435680 282070 351250 FALSE TRUE 553916.6238 245010.2422 344758.3434 305493.3353 280272.5005 303716.9901 370353.8287 317287.0604 292624.1058 1.89292889 0.837286598 1.178161117 1.043978706 0.957790199 1.037908306 1.265629937 1.084282033 1 18.1586891 4.748300579 24.90071236 1.063143337 1.892929361 0.837880221 0.116322609 524.1377919 1339956.17 0.028686276 0.379250901 56014.51483 -4.748300579 0.829786024 FAAQAAHQGTASQYFMLLLLTDGAVTDVEATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FAAQAAHQGTASQYFMLLLLTDGAVTDVEATR 32 0 Q99829;B0QZ18;A6PVH9;H0Y524 Q99829 CPNE1 Copine-1 0 ;; 289.16 2.58E-89 242907000 339271 469340 375382 387593 480270 322374 448372 429336 348268 FALSE TRUE 318036.6337 504090.4219 384286.2383 397539.2926 442551.5315 415438.1405 381142.7811 482939.5447 290139.8209 1.096149549 1.73740516 1.32448637 1.370164534 1.525304352 1.431854956 1.313652086 1.664506248 1 18.14638879 -1.482078447 3.470899882 0.992961944 1.441767386 0.357096641 0.182220257 13617071.08 5837752.109 717082.6002 0.038177063 0.032955018 1.482078447 0.448805442 FACNGTVIEHPEYGEVIQLQGDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 6105300000 2407280 2361320 2551720 2661660 2601450 2257600 2627690 2108000 2038650 FALSE TRUE 2256612.642 2536154.59 2612248.003 2729962.702 2397142.611 2909332.471 2233692.279 2371188.44 1698386.145 1.328680553 1.493273245 1.53807661 1.607386347 1.411423791 1.712998236 1.315185175 1.396142124 1 20.69573308 0.758099607 1.13147682 1.003015486 1.509462852 0.638086464 0.116339199 0.486908577 1.117978509 0.098830714 0.030877002 5.729274187 -0.758099607 0.506447366 FADDQLIIDFDNFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FADDQLIIDFDNFVR 15 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ; 231.52 4.26E-13 121805000 204409 194733 203074 230030 213130 205540 254820 211210 162915 FALSE TRUE 191615.4056 209151.2339 207891.0112 235932.9592 196391.6295 264876.0613 216612.1066 237580.0334 135723.434 1.41180782 1.541010478 1.531725252 1.738336205 1.446998677 1.951586793 1.595981624 1.750471723 1 17.05031031 -0.893522551 5.974211239 0.999999849 1.61735089 0.599468427 0.159497936 2.99E-07 5.51E-08 0.143363629 0.033791123 0.127784285 0.893522551 0.617351041 FADQDDIGNVS(ph)FDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 81.656 0.010127 0 82715 108540 99001 96995 114300 80763 128280 77843 84003 TRUE FALSE 77538.0158 116576.4145 101349.3505 99484.05591 105323.3391 104077.967 109045.6049 87561.8699 69982.35662 1.107965201 1.665797212 1.448212883 1.4215591 1.504998462 1.487202947 1.558187094 1.251199218 1 16.09470363 0.995697512 4.007507211 1.001067055 1.480724436 0.514682991 0.143495445 0.126120382 5.66842833 0.122907135 0.031469357 9.901420661 -0.995697512 0.479657381 FADQDDIGNVSFDR ddPTM_SK-BR-3_Pertuzumab_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 ; 240.37 4.99E-17 355200000 594250 532890 536490 518520 567990 509760 682280 535810 581290 FALSE TRUE 557056.9533 572345.7301 549215.7961 531826.1011 523382.3566 656919.4367 579978.448 602707.058 484268.9437 1.15030493 1.181875769 1.134113189 1.098204021 1.080767956 1.356517789 1.197637089 1.244570947 1 18.88544896 2.315197783 24.99997408 1.219237635 1.135544233 0.11107187 0.091153979 58.36838235 19038.02043 0.028231415 0.023620087 206.6320971 -2.315197783 -0.083693402 FAEAFEAIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FAEAFEAIPR 10 0 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;; 172.23 8.79E-06 400494000 437648 520812 458350 469126 540506 384199 538617 485004 516009 FALSE TRUE 410256.3929 559373.4624 469222.2784 481164.5674 498056.8391 495111.0144 457856.3811 545557.817 429883.7644 0.954342608 1.301220257 1.091509653 1.119289927 1.158584902 1.151732295 1.065070187 1.269082162 1 18.7135871 -1.501200637 3.335082686 0.996900786 1.143856512 0.16424173 0.097860605 1216.948418 14171172.24 50771.96048 0.021105616 0.031535474 1.501200637 0.146955726 FAELPEFRPEEVLPS(ph)PTLQSLAT(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 2 FAELPEFRPEEVLPS(0.845)PT(0.156)LQS(0.101)LAT(0.449)S(0.449)PR;FAELPEFRPEEVLPS(0.999)PT(0.001)LQSLAT(0.89)S(0.11)PR 177.1 6.03E-17 246745000 228908 257853 272421 345454 397698 279701 232527 186751 245090 TRUE FALSE 214581.0569 276944.7044 278882.9548 354318.9345 366464.4033 360446.1381 197661.735 210067.2734 204182.8957 1.050925721 1.356356043 1.36584876 1.735301742 1.794785024 1.76531015 0.96806216 1.028819151 1 17.63950249 1.660327041 7.50825713 0.997802495 1.495119375 0.532323822 0.22557865 0.109001088 11.48187285 0.121167738 0.062386607 45.74325249 -1.660327041 0.497316881 FAELPEFRPEEVLPS(ph)PTLQSLATS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 2 FAELPEFRPEEVLPS(1)PTLQSLAT(0.008)S(0.992)PR 204.47 2.15E-25 186800000 157100 175880 207630 248760 256490 175540 153840 135030 163300 TRUE FALSE 147267.3914 188902.3382 212555.0816 255143.6027 236346.31 226215.5483 130773.1202 151888.7927 136044.175 1.082496854 1.388536761 1.56239752 1.875446727 1.737276219 1.662809512 0.961254829 1.116466712 1 17.05371566 1.723143293 7.504369062 1.034763165 1.553382126 0.570675635 0.214444183 0.094286789 14.43353124 0.110364417 0.05809594 52.86196376 -1.723143293 0.518618961 FAELPEFRPEEVLPSPTLQS(ph)LATSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 1 FAELPEFRPEEVLPSPT(0.004)LQS(0.405)LAT(0.296)S(0.296)PR 121.26 8.78E-05 137010000 63500 64177 58419 53371 54434 48614 67433 59418 82837 TRUE FALSE 59525.64835 68928.73186 59804.72627 54740.59022 50158.97322 62648.07262 57322.04767 66836.4681 69010.96955 0.862553428 0.998808339 0.866597392 0.793215783 0.726826091 0.90779876 0.830622263 0.968490495 1 16.07453808 1.122479049 5.122775316 0.997706978 0.865300954 0.359991921 0.071005549 0.260499482 9.779630297 0.073112758 0.018553808 13.25803158 -1.122479049 -0.132406024 FAELPEFRPEEVLPSPTLQSLAT(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 1 FAELPEFRPEEVLPS(0.001)PT(0.003)LQS(0.017)LAT(0.561)S(0.418)PR 144.28 3.99E-07 118790000 57874 58138 53607 48789 52482 49791 66293 54200 78554 TRUE FALSE 54251.76965 62442.59801 54878.58336 50041.00834 48360.27542 64164.85341 56352.98008 60966.98931 65442.82992 0.82899486 0.954154918 0.838572895 0.764652268 0.738969807 0.980471864 0.861102433 0.93160686 1 15.99794752 1.099607307 1.025812711 0.997037415 0.851193453 0.33487857 0.072168367 0.683269893 1.538279256 0.069180974 0.023088316 12.57787596 -1.099607307 -0.145843962 FAELPEFRPEEVLPSPTLQSLATS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 1 FAELPEFRPEEVLPSPTLQSLAT(0.04)S(0.96)PR;FAELPEFRPEEVLPSPTLQSLAT(0.122)S(0.878)PR 178.59 1.46E-17 346650000 283330 261490 257130 216898 247040 225961 297890 258660 350110 TRUE FALSE 265596.8811 280850.9917 263229.245 222463.9699 227638.4749 291192.2725 253224.16 290954.2704 291674.3792 0.910593799 0.962892224 0.902476404 0.762713443 0.780454134 0.998347107 0.868174163 0.997531121 1 18.15399914 1.230792639 24.72883393 0.998765676 0.890500286 0.304336051 0.071771122 232.2421061 739292.8401 0.065733667 0.017666916 17.0134598 -1.230792639 -0.10826539 FAELVYTGFWHSPECEFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FAELVYTGFWHSPECEFVR 19 0 P00966 P00966 ASS1 Argininosuccinate synthase 0 ;; 287.01 2.89E-40 2758332000 1609431 1934968 1571742 1570148 1983254 1232421 1808478 1770970 1352886 FALSE TRUE 1508699.587 2078235.044 1609024.462 1610440.656 1827497.231 1588200.936 1537313.513 1992079.503 1127080.587 1.338590696 1.843909893 1.427603742 1.428860256 1.621443269 1.409128109 1.363978345 1.767468561 1 20.10415924 -2.829679685 0.324790139 1.40E-15 1.557004449 0.44495773 0.17695519 62.04053177 1.978677761 43.43191976 0.14826783 0.0014802 2.829679685 1.557004449 FAEMEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FAEMEER 7 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ; 82.671 0.055501 593150000 1485590 1341750 1374500 1387050 1591930 1567390 2054500 1274880 1984660 FALSE TRUE 1392609.574 1441094.566 1407103.789 1422644.051 1466906.239 2019870.049 1746446.798 1434051.574 1653407.425 0.842266433 0.871590719 0.851032703 0.860431634 0.887201919 1.221640848 1.056271293 0.867331036 1 20.65701084 2.446071923 24.78714918 1.049754596 0.859573392 0.504770115 0.085543266 133.6322103 106679.856 0.02830944 0.023685592 279.3006351 -2.446071923 -0.190181204 FAEVECLAESHQHLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FAEVECLAESHQHLSK 16 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y4X2;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 228.51 2.34E-15 155760000 117560 218460 220430 228940 236280 187690 311510 216690 273160 FALSE TRUE 110202.1295 234635.0057 225658.7037 234814.988 217723.5219 241873.0561 264801.9674 243744.2235 227567.8313 0.484260578 1.031055243 0.991610732 1.031846139 0.956741208 1.062861366 1.163617748 1.071083826 1 17.79593711 4.739003748 6.110164086 1.04365265 0.47001935 0.90754484 0.05559985 0.040975903 7.779058906 0.015195813 0.09750865 54828.1697 -4.739003748 -0.573633299 FAEWCLEYGEHGCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FAEWCLEYGEHGCR 14 0 O43813;H7C2E3 O43813 LANCL1 LanC-like protein 1 0 ;;; 237.65 2.66E-17 1547620000 1276280 1227450 1234870 1078660 1238680 1385440 1682880 1076760 1625010 FALSE TRUE 1196399.913 1318331.675 1264161.7 1106340.242 1141399.069 1785394.037 1430547.767 1211195.856 1353785.333 0.883744183 0.973811463 0.933797751 0.817219846 0.843116735 1.318816206 1.056702072 0.894673496 1 20.36856756 FAGHSEAGGGS(ph)GDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FAGHSEAGGGSGDR 14 0 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 FAGHSEAGGGS(1)GDR 72.433 0.014807 0 114510 133770 117100 114640 128350 101980 122070 118050 137300 TRUE FALSE 107343.0235 143674.47 119877.6673 117581.8565 118269.9087 131419.9705 103766.7367 132788.8024 114383.743 0.938446502 1.256074213 1.048030639 1.027959511 1.033974808 1.148939238 0.907180811 1.160906252 1 16.8035225 3.678780536 7.219150751 1.039501225 1.129486475 0.015747814 0.104615452 0.423313524 53.0369989 0.025187809 0.039490406 4772.880221 -3.678780536 0.08998525 FAGHSEAGGGSGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FAGHSEAGGGSGDR 14 0 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ; 162.48 4.43E-06 576540000 209867 253400 228712 216905 246610 193196 244958 214822 244014 FALSE TRUE 196731.7991 272161.9997 234137.1566 222471.1495 227242.2454 248968.5489 208228.822 241642.9996 203286.487 0.967756401 1.338810088 1.151759569 1.094372542 1.117842355 1.224717651 1.024312167 1.188682057 1 17.63315479 0.405112486 0.293660685 0.967318742 1.191273612 0.093711896 0.106140567 6.318418596 1.107383625 0.434366585 0.140736335 2.541630924 -0.405112486 0.22395487 FAGVDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FAGVDIR 7 0 P62249;M0R210;M0R3H0;M0R1M5;Q6IPX4;M0QX76 P62249 RPS16 40S ribosomal protein S16 0 ;; 89.903 0.040786 1738160000 4961800 5701500 5614800 5565900 5955500 4773600 6130900 4889500 5289200 FALSE TRUE 4651249.795 6123644.992 5747985.708 5708730.417 5487779.053 6151660.827 5211628.461 5499964.838 4406398.35 1.055567251 1.389716613 1.304463476 1.295554774 1.245411471 1.396074603 1.182741107 1.248176946 1 22.07116849 0.552445103 0.92642176 0.999797887 1.292571761 0.408897008 0.098860529 1.274177333 1.696540622 0.08687808 0.028152822 3.56816643 -0.552445103 0.292773874 FAHEHEEMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FAHEHEEMK 9 0 P48163;P48163-2 P48163 ME1 NADP-dependent malic enzyme 0 ; 117.89 0.00075479 119567000 140171 161731 126788 111018 140335 90904 132207 116899 168215 FALSE TRUE 131397.9473 173705.7315 129795.4712 113866.9098 129313.6552 117146.5091 112383.7877 131494.0975 140138.8298 0.937626977 1.23952606 0.926192058 0.812529333 0.922753925 0.835931835 0.801946098 0.938313083 1 17.09649723 3.669503451 3.567478071 0.869199621 1.105162716 0.426110572 0.09439033 0.155508199 3.963910306 0.023007158 0.038832327 4672.006633 -3.669503451 0.235963095 FAHIDGDHLTLLNVYHAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FAHIDGDHLTLLNVYHAFK 19 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 307.21 1.70E-51 478010000 759430 1047800 841080 724680 1092900 544760 910360 996120 920660 FALSE TRUE 711898.6319 1125380.202 861030.8148 743276.5157 1007068.043 702023.3686 773859.9694 1120487.775 766995.8983 0.928164849 1.467257132 1.12260159 0.969074955 1.313003166 0.915289599 1.008949293 1.460878444 1 19.54885934 3.643616747 5.966052949 1.096642404 1.253213245 0.009345049 0.210101182 0.473622772 26.57565721 0.051617678 0.08098556 4401.662574 -3.643616747 0.156570841 FAHTNVESLVNEYDDNGEGIILFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 FAHTNVESLVNEYDDNGEGIILFR 24 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;; 323.13 3.95E-74 1242840000 758166 792676 808068 794248 718207 636478 811655 712424 407840 FALSE TRUE 710713.7434 851366.5558 827235.7546 814629.7483 661801.9193 820218.8662 689954.8678 801371.7046 339768.8693 2.091756508 2.505722663 2.434701438 2.397599728 1.947800341 2.414049492 2.030659458 2.358578955 1 18.37419415 -1.636025967 0.351338377 2.13E-11 2.375627584 0.807472425 0.194033853 10.50104392 0.692028556 9.305094208 0.142135783 0.023119266 1.636025967 2.375627584 FAHTNVESLVNEYDDNGEGIILFRPSHLTNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FAHTNVESLVNEYDDNGEGIILFRPSHLTNK 31 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 375.46 1.85E-137 2571100000 1308170 1581020 1401660 1546290 1492350 1138400 2010390 1321370 1232910 FALSE TRUE 1226293.975 1698080.366 1434908.037 1585970.419 1375146.851 1467037.6 1708950.683 1486345.953 1027129.356 1.193904125 1.653229319 1.397008107 1.544080509 1.33882538 1.428289038 1.663812521 1.447087404 1 19.97018645 0.95255396 22.94681658 0.999999998 1.483532856 0.503556726 0.141549808 3661.021574 1770620.096 0.124651563 0.031162891 8.965075679 -0.95255396 0.483532858 FAIGS(ph)AR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FAIGSAR 7 0 O96017-13;O96017-4;O96017-12;O96017;O96017-9;B7ZBF2;A0A087X102;H0Y4V6;B7ZBF7;B7ZBF6;O96017-8;O96017-7 O96017-13 CHEK2 Serine/threonine-protein kinase Chk2 1 FAIGS(1)AR;FAIGS(1)AR;FAIGS(1)AR;FAIGS(1)AR 92.439 0.016436 296735000 516540 751910 578690 665860 809180 535093 715990 647120 670380 TRUE FALSE 484210.6835 807582.1988 592416.8001 682947.0949 745630.2669 689565.6626 608633.9464 727914.3565 558489.2472 0.867000906 1.446012081 1.060748802 1.222847348 1.335084374 1.23469819 1.089786329 1.303363243 1 19.09116998 -1.140159738 6.028227922 0.999998665 1.203704203 0.124132868 0.161250498 2.56E-06 3.65E-07 0.138105567 0.032551581 0.072416955 1.140159738 0.203705538 FALNHPELVEGLVLINVDPCAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FALNHPELVEGLVLINVDPCAK 22 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3;Q5TH29 Q5TH30 NDRG3 Protein NDRG3 0 ; 187.86 2.69E-17 261610000 903230 733520 843270 795950 864960 638060 1079160 815690 982240 FALSE TRUE 846698.4466 787830.584 863272.7626 816375.4245 797029.5307 822257.564 917349.9764 917530.6921 818297.7985 1.034706983 0.962767571 1.05496161 0.997650765 0.974009135 1.004839027 1.121046614 1.121267458 1 19.64226645 1.751309913 25 1.091097464 1.004294322 0.407828783 0.042536429 3.026659858 5944.230871 0.017982233 0.009972061 56.40400121 -1.751309913 -0.086803142 FALVT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FALVTPK 7 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 FALVT(1)PK;FALVT(1)PK 105.4 0.088713 170445000 885450 645070 783410 694710 760430 570980 1040600 693690 1082900 TRUE FALSE 830031.2651 692831.654 801992.8552 712537.4347 700708.8952 735812.6569 884571.6905 780298.7235 902156.9942 0.920051909 0.76797238 0.888972607 0.789815342 0.776703944 0.815614867 0.980507491 0.864925649 1 19.78301899 1.754376065 14.63956763 0.941662888 0.823642569 0.489080362 0.05857181 0.2368267 218.6277162 0.024695044 0.013626829 56.80362672 -1.754376065 -0.118020319 FAMEPEEFDSDTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FAMEPEEFDSDTLR 14 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;;; 325.02 2.17E-56 727739000 649617 934040 868727 871210 882070 822509 876690 730048 687443 FALSE TRUE 608958.6316 1003197.293 889333.6147 893566.7236 812795.7803 1059953.996 745238.4733 821196.0998 572704.3222 1.063303712 1.751684516 1.552866951 1.56025839 1.419224107 1.850787492 1.301262177 1.433891919 1 19.12743097 0.788014437 1.157116072 1.004434306 1.549699118 0.33136618 0.219451383 0.777815588 1.913321632 0.185569027 0.057711023 6.137824089 -0.788014437 0.545264812 FAQHGTFEYEYSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FAQHGTFEYEYSQR 14 0 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;; 222.56 3.85E-12 3417820000 1734270 2529240 2264850 2182540 2703040 2017380 2620890 2202710 2728030 FALSE TRUE 1625725.136 2716507.561 2318573.312 2238547.671 2490754.142 2599764.857 2227911.876 2477723.192 2272704.169 0.715326332 1.195275478 1.020182628 0.984970988 1.095942963 1.143908165 0.98029119 1.090209287 1 21.11597847 4.752062016 24.99972769 1.065616031 0.715326102 0.707538593 0.070411018 1285.180857 2379650.861 0.016360037 0.324489046 56501.76519 -4.752062016 -0.350289929 FAQPGSFEYEYAMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FAQPGSFEYEYAMR 14 0 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;;; 224.24 7.50E-12 1287741000 487492 589449 541234 533793 587428 387076 578779 531119 619056 FALSE TRUE 456980.7459 633092.4173 554072.3261 547491.0321 541293.7745 498818.5575 491996.4621 597430.3763 515731.5543 0.886082579 1.22756192 1.074342497 1.061581413 1.049564972 0.967205813 0.953977816 1.158413464 1 18.97626079 2.848919615 1.840821332 1.009572774 1.099213463 0 0.100160231 0.690371637 4.650066439 0.034463642 0.036708339 706.1868319 -2.848919615 0.089640689 FAQPGTFEFEYASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FAQPGTFEFEYASR 14 0 Q8WXF1;Q8WXF1-2 Q8WXF1 PSPC1 Paraspeckle component 1 0 ; 176.87 5.03E-06 190504000 98398 111480 97999 109952 117691 82951 104739 105328 141060 FALSE TRUE 92239.44483 119734.0952 100323.5826 112773.5545 108448.0236 106897.6071 89034.3593 118478.4327 117516.1747 0.784908503 1.018873321 0.853700206 0.95964283 0.922834868 0.90964165 0.757634934 1.008188302 1 16.84249981 1.97752002 24.89133393 0.879668306 0.917904981 0 0.094080653 2925.269268 3239049.398 0.035305634 0.022951762 94.95547715 -1.97752002 0.038236674 FAQSAPGS(ph)PLSSQPVLITVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FAQSAPGSPLSSQPVLITVQR 21 0 Q01167;Q01167-2 Q01167 FOXK2 Forkhead box protein K2 1 FAQSAPGS(0.988)PLS(0.011)SQPVLITVQR;FAQSAPGS(0.915)PLS(0.083)S(0.002)QPVLITVQR;FAQSAPGS(0.993)PLS(0.007)SQPVLITVQR;FAQSAPGS(0.998)PLS(0.002)SQPVLITVQR 291.81 1.01E-54 595632000 622380 615530 627380 638900 716780 655280 899450 661960 759910 TRUE FALSE 583426.3468 661104.4817 642261.7499 655295.2557 660486.9902 844448.6984 764585.8226 744607.1632 633076.1118 0.921573782 1.044273302 1.014509532 1.035097113 1.043297919 1.333881792 1.20773128 1.176173211 1 19.27201943 2.384907084 8.186398927 1.202480304 1.015040664 0.46951634 0.087567229 0.182657545 14.32588908 0.027274271 0.02278348 242.6090983 -2.384907084 -0.18743964 FAQYAEIVHFTLPDGTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FAQYAEIVHFTLPDGTQR 18 0 P15313;C9JL73;C9JNS9 P15313 ATP6V1B1 "V-type proton ATPase subunit B, kidney isoform" 0 97.32 0.0014234 0 68875 83088 78971 80624 86612 73005 87663 73893 96199 FALSE TRUE 64564.2367 89239.92197 80844.22941 82692.94834 79809.8429 94080.35836 74518.74697 83118.70371 80142.76543 0.805615284 1.113511887 1.00875268 1.0318205 0.995845882 1.173909558 0.929825001 1.037132962 1 16.29028467 4.750730024 24.78461787 1.036434424 0.805615125 0.542123649 0.066640724 1289.47375 2626131.022 0.014635816 0.248778016 56328.73837 -4.750730024 -0.2308193 FARPDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FARPDFR 7 1 F8WF90;C9JQU6;F8WF33;O75915 F8WF90 ARL6IP5 PRA1 family protein 3 0 77.674 0.034115 156310000 153870 221570 149260 135080 248200 110160 174230 227900 301350 FALSE TRUE 144239.5514 237975.2733 152800.5177 138546.3815 228707.3732 141961.4037 148105.829 256353.8167 251052.7382 0.574538849 0.947909491 0.60863912 0.551861663 0.910993343 0.565464471 0.58993911 1.021115398 1 17.93763093 1.228435925 24.99885633 1.010558001 0.691051386 0.485923068 0.141543095 204.0504782 503803.4 0.127181496 0.033268581 16.9213857 -1.228435925 -0.319506615 FARS(ph)DDEQSSADKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FARSDDEQSSADKER 15 2 A6NGV6;P27540-3;P27540-4;P27540 A6NGV6 ARNT Aryl hydrocarbon receptor nuclear translocator 1 FARS(1)DDEQSSADKER 133.74 2.06E-05 269430000 148150 130690 131380 149850 171420 89826 139370 138730 192770 TRUE FALSE 138877.556 140366.4236 134496.3956 153695.4047 157957.3647 115757.308 118472.7623 156050.7459 160595.4417 0.864766487 0.874037408 0.837485761 0.957034665 0.983573152 0.720800708 0.737709372 0.971700967 1 17.29307142 2.243213784 24.99999938 0.821093358 0.892831646 0 0.099029662 267.2645776 1435934.464 0.03396044 0.027541302 175.0708273 -2.243213784 0.071738288 FAS(ph)AENIPDLPYDYSSSLESVADETSPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FASAENIPDLPYDYSSSLESVADETSPER 29 0 P50747 P50747 HLCS Biotin--protein ligase;Biotin--[methylmalonyl-CoA-carboxytransferase] ligase;Biotin--[propionyl-CoA-carboxylase [ATP-hydrolyzing]] ligase;Biotin--[methylcrotonoyl-CoA-carboxylase] ligase;Biotin--[acetyl-CoA-carboxylase] ligase 1 FAS(0.999)AENIPDLPYDYSSSLESVADETSPER 76.294 0.0034005 33784000 53214 50896 47268 51882 50532 40127 64432 43636 53942 TRUE FALSE 49883.43073 54664.3928 48389.21928 53213.37996 46563.42056 51711.01349 54771.01976 49084.05065 44938.73172 1.110032011 1.216420462 1.076782041 1.18413177 1.03615342 1.150700332 1.21879318 1.09224379 1 15.45567179 0.990006162 23.93753185 0.999999993 1.145417936 0.381617471 0.05759411 252.9090127 605777.8936 0.052667521 0.01316688 9.772510862 -0.990006162 0.145417943 FAS(ph)DDEHDEHDENGATGPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 284.12 3.81E-45 13409170000 12954680 6957450 8997940 8488130 7719760 6728220 10981960 7292080 6931030 TRUE FALSE 12143869.7 7472586.837 9211375.386 8705949.786 7113481.19 8670547.89 9335317.05 8202512.24 5774196.317 2.103127264 1.29413453 1.595265363 1.507733598 1.231943079 1.501602546 1.616730111 1.420546131 1 22.46118873 -3.245469279 0.205630515 2.77E-15 1.607178352 0.387545764 0.226104033 74.37002673 1.413428476 33.14905393 0.503245969 0.000568239 3.245469279 1.607178352 FAS(ph)DDEHDEHDENGATGPVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 182.39 2.20E-17 9223270000 5853640 3864680 4571730 4752660 4830910 3508140 5705210 3902020 5705750 TRUE FALSE 5487271.121 4150824.928 4680173.595 4874621.302 4451509.816 4520883.068 4849766.725 4389195.786 4753423.464 1.154382975 0.873228518 0.984590081 1.025496958 0.936485009 0.951079386 1.020268184 0.923375714 1 22.1805355 4.757007724 24.52705456 0.964207953 1.154383189 0.62240646 0.046524842 2190.409101 2912280.974 0.011022129 0.368166134 57148.88004 -4.757007724 0.190175236 FASAENIPDLPYDYSSSLES(ph)VADETSPEREGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FASAENIPDLPYDYSSSLESVADETSPEREGR 32 1 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 FASAENIPDLPY(0.01)DY(0.05)S(0.057)S(0.057)S(0.057)LES(0.323)VADET(0.234)S(0.213)PEREGR 48.449 0.051545 29563000 26746 34060 26159 31044 40810 24299 31716 28153 46033 TRUE FALSE 25072.0156 36581.83784 26779.50383 31840.6416 37604.94722 31313.72684 26960.48024 31667.96402 38349.79492 0.65377183 0.953899178 0.698295881 0.830268888 0.980577531 0.816529186 0.703014978 0.82576619 1 15.22693124 -2.317111653 2.050943995 1.852559157 0.809337041 0.249370819 0.104783564 6032340.821 740647.8425 23828412.34 0.024207267 0.004818239 2.317111653 -1.043222117 FASEAEDKIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FASEAEDKIR 10 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 86.344 0.012423 235880000 171430 200120 192770 175010 270460 129550 185110 191180 280130 FALSE TRUE 160700.5023 214937.093 197342.5954 179501.0529 249219.1626 166948.9819 157354.474 215049.2438 233374.4933 0.68859497 0.920996506 0.845604816 0.769154548 1.067893749 0.715369446 0.674257378 0.921477068 1 17.83228736 FASENDLPEWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FASENDLPEWK 11 0 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6;C9JDM3;C9JIC6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 166.69 4.68E-05 121570000 183880 158820 172090 162040 192870 108860 202630 147160 202750 FALSE TRUE 172371.279 170579.1981 176172.0561 166198.2207 177722.7682 140286.1148 172247.5126 165533.2499 168909.7152 1.020493575 1.009883877 1.042995401 0.983947078 1.052176117 0.830539052 1.019760838 0.980010237 1 17.36589278 FATHGAALTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FATHGAALTVK 11 0 Q8WXF1;Q8WXF1-2;X6RDA4 Q8WXF1 PSPC1 Paraspeckle component 1 0 110.93 0.0017281 223900000 347840 499100 365460 340390 569650 285850 398110 476840 628950 FALSE TRUE 326069.3153 536053.8833 374128.8838 349124.9837 524911.9869 368370.2546 338417.1014 536374.5237 523974.1818 0.622300347 1.023054001 0.7140216 0.666301882 1.001789792 0.703031308 0.645865986 1.023665941 1 18.9991362 1.217397586 24.93891355 1.011833359 0.782242475 0.342165097 0.13945212 324.1201038 381938.9986 0.129547409 0.032518373 16.49671937 -1.217397586 -0.229590884 FATLAELVQYYMEHHGQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FATLAELVQYYMEHHGQLK 19 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ; 203.56 2.89E-16 611630000 795630 791270 820540 815420 893950 664540 1007240 795180 906690 FALSE TRUE 745832.9385 849856.4541 840003.5963 836345.0577 823742.773 856381.9101 856213.7128 894459.9734 755357.5816 0.987390551 1.125104818 1.112060853 1.1072174 1.090533534 1.133743714 1.133521042 1.18415436 1 19.52680024 4.740804336 24.27510211 1.11698731 0.987390483 0.402510654 0.046710697 118.5585872 1282568.173 0.009655563 0.063835115 55055.9595 -4.740804336 -0.129596827 FATVEVTDKPVDEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FATVEVTDKPVDEALR 16 1 Q9NRV9;A0A3B3IRV5;F5GWX2 Q9NRV9 HEBP1 Heme-binding protein 1 0 ; 198.95 3.59E-11 267790000 414720 342090 341890 329960 379220 239350 417490 339150 411070 FALSE TRUE 388763.4155 367418.6995 349999.7923 338427.3322 349437.5909 308446.4595 354891.2503 381493.6241 342459.7614 1.135209036 1.072881375 1.022017275 0.988225101 1.020375619 0.900679421 1.036300583 1.113980873 1 18.38557496 4.552572917 1.081136814 1.006667993 1.171587952 0.38004958 0.052150667 1.368763104 1.632688815 0.015455835 0.240261807 35692.16708 -4.552572917 0.164919959 FAVLHGEAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FAVLHGEAPR 10 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;; 148.32 2.53E-05 849080000 862151 1478160 955078 972990 1552740 720850 956831 1278500 1496160 FALSE TRUE 808190.5079 1587604.504 977732.9012 997958.5707 1430794.064 928947.693 813363.0743 1438123.539 1246441.23 0.648398407 1.273709875 0.784419576 0.800646309 1.14790335 0.745279978 0.652548275 1.153783672 1 20.24938343 FAVQDVNDVLDLEWDQHLEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FAVQDVNDVLDLEWDQHLEQK 21 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 0 126.02 1.01E-05 0 31927 34832 29618 28572 35441 22463 36488 29696 35500 FALSE TRUE 29928.74606 37410.99752 30320.55295 29305.20589 32657.60682 28947.70344 31016.96314 33403.61097 29574.82066 1.011967119 1.264961095 1.025215108 0.990883638 1.104236851 0.97879557 1.04876251 1.12946115 1 14.8520818 3.747273758 8.859919323 1.039113425 1.153351005 0.218740092 0.076480552 0.274125973 107.289077 0.017677887 0.03110153 5588.223374 -3.747273758 0.11423758 FAYLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FAYLGR 6 0 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 130.51 0.036597 3904100000 757430 1173410 961210 866150 1391160 643740 988050 1121690 1270320 FALSE TRUE 710023.8084 1260290.497 984010.3551 888376.8754 1281903.905 829577.2878 839901.0751 1261735.466 1058295.385 0.670912694 1.190868367 0.929806903 0.83944132 1.211291217 0.783880662 0.793635772 1.19223374 1 20.01331093 FCFTPHTEEGCLSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 FCFTPHTEEGCLSER 15 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;;;; 294.31 5.25E-44 44458410000 7370630 9251920 8697750 9375320 10511670 8660360 11493480 8712830 10233270 FALSE TRUE 6909315.425 9936941.783 8904064.737 9615906.584 9686125.84 11160465.34 9770139.374 9800646.005 8525271.128 0.810451107 1.1655866 1.044431855 1.127929709 1.13616631 1.30910386 1.146020957 1.149599333 1 23.02331429 4.741178165 24.73441028 1.140993794 0.81045097 0.615037263 0.080527818 139.2181266 1315449.377 0.018649159 0.12803776 55103.37061 -4.741178165 -0.330542824 FCIWTESAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FCIWTESAFR 10 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 200.88 5.87E-07 848240000 47994 217230 37512 49205 237560 35115 39511 195480 162640 FALSE TRUE 44990.14121 233313.9352 38401.80235 50467.6836 218902.9959 45252.13046 33586.69235 219886.1083 135494.3333 0.332044449 1.721946074 0.283419988 0.372470807 1.61558783 0.33397803 0.247882635 1.622843575 1 17.04787299 4.989769656 24.57456159 0.834757279 0.05026847 0.074085262 0.5923652 27535.2284 116316.5799 0.13233373 438264.4358 97671.90459 -4.989769656 -0.784488809 FCLDNGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FCLDNGAK 8 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 131.06 0.0023756 291230000 639470 675190 523950 515840 620270 345770 717090 515900 657350 FALSE TRUE 599446.7142 725181.7701 536378.3414 529077.3277 571556.4962 445588.1859 609569.0116 580311.2506 547634.0384 1.094611862 1.324208722 0.979446681 0.96611476 1.043683293 0.813660501 1.113095551 1.059669798 1 19.06285259 3.843227864 4.209593531 0.997869453 1.215164212 0.462941326 0.095026109 0.169598232 5.16744815 0.022984412 0.043285038 6969.92114 -3.843227864 0.217294759 FCLSS(ph)PTEALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FCLSSPTEALK 11 0 E7EWD6;Q76L83;Q76L83-2 E7EWD6 ASXL2 Putative Polycomb group protein ASXL2 1 FCLS(0.056)S(0.94)PT(0.004)EALK;FCLS(0.063)S(0.926)PT(0.01)EALK 118.77 0.00070945 105859000 319041 229057 263356 273884 305060 225882 305740 264358 328730 TRUE FALSE 299072.7933 246016.6186 269602.9287 280912.3271 281101.8182 291090.4665 259897.1254 297363.6782 273862.8393 1.092053212 0.898320558 0.984445094 1.025740943 1.026432863 1.062906042 0.949004713 1.085812442 1 18.06309399 3.363366685 4.466732276 1.020031957 0.968475259 0.021509791 0.059542305 0.412973727 14.16226446 0.015598655 0.021483499 2308.695653 -3.363366685 -0.051556698 FCNVDDDELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FCNVDDDELR 10 0 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;;;;; 312.24 1.45E-41 3451330000 2648340 2956400 2908910 3077190 2870500 2725600 3470850 2884630 2217310 FALSE TRUE 2482585.127 3175294.932 2977910.719 3156155.905 2645062.509 3512436.474 2950428.264 3244782.405 1847226.637 1.343952646 1.718952547 1.612098191 1.708591595 1.431910117 1.901464825 1.597220507 1.756569736 1 20.81692945 -0.59278779 6.267090754 0.999999999 1.644199526 0.610810116 0.158814832 0 6.28E-10 0.132087715 0.031133373 0.255394894 0.59278779 0.644199526 FCNVDDDELREYCIQAFESFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FCNVDDDELREYCIQAFESFVR 22 1 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 168.75 8.27E-12 71568000 22861 49986 34874 42451 68616 24831 34755 34858 97967 FALSE TRUE 21430.17082 53687.01545 35701.22775 43540.36453 63227.17614 31999.3066 29543.8104 39210.09803 81615.67481 0.262574204 0.657802751 0.437431018 0.533480421 0.774694031 0.392073051 0.361986965 0.480423621 1 16.31655864 -1.459883089 2.771926099 1.016075865 0.494120854 0.548378344 0.146040547 12466330.96 13477646.75 1550967.815 0.036106904 0.03468302 1.459883089 -0.521955011 FCQLLWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FCQLLWR 7 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 79.454 0.075798 71545000 112020 230070 115470 115500 228610 104210 127210 192110 166790 FALSE TRUE 105008.8682 247104.6222 118209.0029 118463.9255 210655.8928 134293.7353 108136.0415 216095.3564 138951.6715 0.755722238 1.778349404 0.850720266 0.852554879 1.516037126 0.966478012 0.778227713 1.555183569 1 17.08422366 3.836840462 8.827414324 1.051077136 1.335640225 0.036857777 0.360007828 0.615978122 45.37376242 0.084994696 0.153567967 6868.160926 -3.836840462 0.284563089 FCSNSGRLS(ph)GPAELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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;FCS(0.001)NS(0.001)GRLS(0.998)GPAELR;FCSNSGRLS(1)GPAELR;FCSNSGRLS(1)GPAELR 171 6.71E-07 4016450000 5483110 4177100 4074060 4023780 5464740 3469600 5032240 4117830 4485710 TRUE FALSE 5139931.933 4486376.83 4170698.627 4127037.007 5035561.364 4471217.196 4277702.329 4631950.14 3737016.022 1.375410729 1.200523841 1.116050507 1.104366955 1.347481877 1.196467227 1.144683968 1.239478266 1 21.83345532 -4.106689599 0.324103146 8.75E-16 1.21003093 0.356339885 0.089781872 217.2650149 3.333959997 146.6890583 0.076532389 7.82E-05 4.106689599 1.21003093 FDADYAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FDADYAEK 8 0 A0A0A6YYL2;P0DMN0;P0DMM9;P0DMM9-3;P50225;P50225-2 A0A0A6YYL2;P50225 SULT1A4;SULT1A3;SULT1A1 Sulfotransferase;Sulfotransferase 1A4;Sulfotransferase 1A3;Sulfotransferase 1A1 0 ;;; 135.83 0.0019006 773920000 1867280 1619940 1594980 1693680 1787450 1199290 2048460 1452290 1681300 FALSE TRUE 1750410.278 1739882.043 1632813.679 1737142.696 1647070.887 1545505.554 1741312.44 1633611.603 1400680.168 1.249685915 1.242169399 1.165729133 1.240213673 1.175907908 1.103396471 1.243190615 1.166298803 1 20.41769614 -5 0.190210845 0.144193323 1.236239546 0.697422735 0.042958774 78.45623449 0.768113369 25.44755434 0.113144023 1.00E-05 5 1.092046223 FDAGELITQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FDAGELITQR 10 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0 P35232 PHB Prohibitin 0 ; 153.05 3.94E-05 193463000 554990 386100 409680 375570 499130 302940 417270 387030 510580 FALSE TRUE 520254.1666 414687.2457 419397.8031 385207.762 459930.3432 390393.8602 354704.2372 435351.5475 425360.8995 1.223088834 0.974906829 0.985981089 0.90560219 1.081270854 0.91779442 0.833890086 1.023487462 1 18.6983279 FDALKDDDSGDHDQNEENSTQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FDALKDDDSGDHDQNEENSTQK 22 1 B9A044;B8ZZ50;O60573-2;O60573;B4E1E4;B9A023;B8ZZL3 B9A044 EIF4E2 Eukaryotic translation initiation factor 4E type 2 0 186.86 1.83E-17 82235000 143120 68853 101530 89920 91652 68567 117290 77747 77285 FALSE TRUE 134162.3747 73950.94776 103938.3395 92227.49943 84454.02163 88361.17981 99703.45337 87453.88409 64385.63422 2.083731508 1.148562853 1.614309478 1.432423561 1.311690452 1.372374146 1.548535703 1.35828256 1 15.97445121 -3.628816035 0.166941968 1.31E-13 1.587842896 0.335271524 0.237228498 104.1447604 1.484384138 37.34025426 0.878034048 0.000235063 3.628816035 1.587842896 FDASFFGVHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FDASFFGVHPK 11 0 P49327;A0A0U1RQF0;A0A0U1RRG3 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 144.28 3.68E-05 27706320000 13948390 15279580 15332250 14601790 16774410 10970983 18718800 15381940 18602730 FALSE TRUE 13075385.17 16410896 15695938.21 14976496.65 15457015.5 14138127.69 15912089.72 17302409.07 15497814.18 0.843692214 1.058916813 1.012783998 0.966361867 0.997367456 0.912265919 1.026731223 1.116441897 1 23.88556142 1.496231907 7.595986296 1.062663771 0.982103048 0.246850729 0.065136287 0.16569783 23.52708974 0.033998294 0.015539752 31.34959303 -1.496231907 -0.080560723 FDDAVVQSDMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FDDAVVQSDMK 11 0 P11142;E9PKE3;E9PNE6;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 83.862 0.038133 41095000 120790 125220 125680 128900 138200 107080 140900 121030 128240 FALSE TRUE 113229.9695 134491.4191 128661.189 132207.7922 127346.3295 137992.2577 119773.3531 136140.8619 106835.9155 1.059849293 1.258859611 1.204287793 1.237484525 1.191980514 1.291627979 1.121096332 1.27429864 1 16.7050372 -1.256805353 3.854994565 0.99972827 1.207709559 0.455221246 0.070397999 0.000148954 2.87E-05 0.059209305 0.01393684 0.055359817 1.256805353 0.207981289 FDDDKVSIVTPEDILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FDDDKVSIVTPEDILR 16 1 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 ;;; 203.89 2.43E-11 533582000 1241220 826835 988080 924310 916500 763638 1179930 841770 900680 FALSE TRUE 1163534.256 888054.7237 1011517.724 948029.3595 844521.787 984087.894 1003010.45 946866.8375 750350.6894 1.550653944 1.183519568 1.348059965 1.263448375 1.12550278 1.311503951 1.336722235 1.26189907 1 19.5172055 -3.519362871 0.346925596 6.38E-27 1.301290185 0.420682989 0.111209882 133.6561806 2.949842336 97.06008185 0.080022304 0.000302439 3.519362871 1.301290185 FDDDVVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FDDDVVSR 8 0 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 149.65 0.0011673 627380000 1673050 1829980 1540580 1386430 1808380 1215390 1897440 1628690 2151830 FALSE TRUE 1568336.787 1965473.623 1577123.285 1422008.141 1666357.129 1566253.363 1612936.487 1832035.532 1792675.672 0.874858075 1.096391084 0.879759407 0.793232241 0.92953631 0.873695888 0.89973692 1.021955929 1 20.77368307 1.236119959 24.98077026 1.01097801 0.917281216 0.232331528 0.076937789 114.6585965 1173433.354 0.066834802 0.01972271 17.22344249 -1.236119959 -0.093696794 FDDGAGGDNEVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FDDGAGGDNEVQR 13 0 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ;; 156.01 0.00010186 535380000 509481 559542 575975 574907 584379 457328 680260 515327 681230 FALSE TRUE 477593.4937 600971.0719 589637.399 589660.0869 538484.2306 589351.1695 578261.3282 579666.7103 567528.3121 0.841532455 1.058927033 1.0389568 1.038996777 0.948823555 1.038452456 1.01891186 1.021388181 1 19.11433284 4.745306936 24.82755751 1.024143328 0.841532363 0.777023809 0.030084421 332.2533607 1222711.666 0.007112703 0.07006141 55629.72794 -4.745306936 -0.182610965 FDDMSS(ph)PGLELPSCELSR ddPTM_SK-BR-3_Pertuzumab_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(0.103)S(0.897)PGLELPSCELSR 87.148 0.0034784 19978000 48395 36739 50597 40455 36277 50342 57536 37958 29529 TRUE FALSE 45366.04334 39459.19379 51797.18473 41493.14379 33427.95075 64874.91817 48909.01094 42697.13986 24600.41914 1.844116683 1.604004939 2.105540741 1.686684424 1.358836635 2.637146864 1.988137302 1.73562652 1 14.58639528 4.053935321 11.03204386 1.873820727 1.72492329 0 0.442360746 3.070957941 428.1723986 0.101937417 0.22038893 11322.3173 -4.053935321 -0.148897438 FDDTNPEKEEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FDDTNPEKEEAK 12 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RQT0;A0A0U1RR66 P47897 QARS Glutamine--tRNA ligase 0 ;; 122.45 0.00032681 638020000 1699420 841655 1156140 1074520 1049460 816750 1463770 942830 1107600 FALSE TRUE 1593056.336 903972.0119 1183564.187 1102094.002 967039.6449 1052532.466 1244291.277 1060544.401 922734.4046 1.72645165 0.97966653 1.282670485 1.194378357 1.04801516 1.140666763 1.348482587 1.149349581 1 19.81555592 4.75035878 24.96995565 1.163577444 1.726451994 0.707070289 0.117371476 1056.814815 2236630.2 0.027563421 0.456600537 56280.6079 -4.75035878 0.56287455 FDDTNPEKEKEDFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FDDTNPEKEKEDFEK 15 2 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 114.23 0.00035031 127720000 886030 310340 461110 505340 548470 283110 664130 382320 889560 FALSE TRUE 830574.9639 333317.8965 472047.747 518307.8799 505395.3786 364839.2611 564549.872 430053.4936 741086.6892 1.120752776 0.449769104 0.636966975 0.699389002 0.681965263 0.492303082 0.76178655 0.580301198 1 19.49928279 -1.514856339 4.605894672 1.002014653 0.654282926 0.222986069 0.184327164 0.00338687 0.000356743 0.158514329 0.037162832 0.030559318 1.514856339 -0.347731726 FDEDDDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FDEDDDK 7 0 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 0 ;; 95.541 0.031151 4578900000 12458100 6007600 7671900 7484200 7313800 5985600 9089200 6412000 8999000 FALSE TRUE 11678369.76 6452408.955 7853881.091 7676257.243 6739403.65 7713545.552 7726358.84 7212552.315 7497008.764 1.557737242 0.860664454 1.047601962 1.023909333 0.898945681 1.028883091 1.030592211 0.962057341 1 22.83788366 4.746169494 24.99396337 0.984257563 1.557737517 0.899347391 0.060568774 272.4049866 894786.451 0.014144562 0.150601597 55740.32471 -4.746169494 0.573479954 FDEILEASDGIMVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FDEILEASDGIMVAR 15 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 270.56 5.22E-33 252265000 556920 522831 571470 531271 524950 484665 633040 482615 395491 FALSE TRUE 522063.3713 561541.9512 585025.5383 544904.3133 483722.5445 624579.9176 538121.5289 542870.5451 329480.9971 1.58450222 1.704322726 1.775597207 1.653826224 1.468134881 1.89564777 1.633239955 1.647653582 1 18.32983573 0.413502485 1.887278186 1.000011078 1.687256246 0.77809639 0.112451774 2.764338537 8.370182921 0.099566984 0.027619726 2.591209246 -0.413502485 0.687245168 FDEISFVNFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FDEISFVNFAR 11 0 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 101.38 0.0077377 100558000 53814 63623 54820 56806 63978 49424 56447 58451 60167 FALSE TRUE 50445.8778 68333.71312 56120.35629 58263.73813 58953.42595 63691.90647 47983.29638 65748.73602 50124.73901 1.006406792 1.363273196 1.119613935 1.162374893 1.176134323 1.270668092 0.95727773 1.311702311 1 15.6132352 -3.13662366 0.181423241 0.657596397 1.217504603 0.107178118 0.129166182 111.861418 1.997462915 14.96953677 0.390246777 0.00073009 3.13662366 0.559908206 FDESEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FDESEK 6 0 P14625 P14625 HSP90B1 Endoplasmin 0 ; 143.37 0.02654 428330000 1241200 864390 977470 1014960 897460 751920 1188970 823400 591900 FALSE TRUE 1163515.508 928390.335 1000656.05 1041005.592 826977.1118 968987.0976 1010694.986 926203.3025 493108.0662 2.359554806 1.882731999 2.029283475 2.111110451 1.677070745 1.965060327 2.049641966 1.8782968 1 18.91154433 -1.986875244 0.384026457 1.05E-14 2.027366072 0.780075473 0.168155643 18.93425652 1.131116519 17.00271449 0.105675505 0.010306822 1.986875244 2.027366072 FDEVLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FDEVLIR 7 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 107.32 0.017459 77766000 128176 146846 127588 132426 152471 102378 131103 140667 134801 FALSE TRUE 120153.693 157718.6306 130614.4476 135824.2754 140496.5427 131932.8666 111445.3223 158229.5846 112301.8423 1.069917381 1.404417127 1.163065939 1.209457233 1.25106178 1.174805898 0.992373055 1.408966954 1 16.77702207 2.004884772 10.56834863 1.120612124 1.234701215 0.065186284 0.13989488 0.298395477 527.6204113 0.049125605 0.035266777 101.1311094 -2.004884772 0.114089091 FDFDSDEDFNAFFNSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FDFDSDEDFNAFFNSSR 17 0 Q9HAV4 Q9HAV4 XPO5 Exportin-5 0 ;;; 351.06 2.60E-87 239110000 315106 351250 334822 360546 333617 295822 435219 298829 325222 FALSE TRUE 295384.0779 377256.9155 342764.136 369798.2208 307416.0666 381221.0091 369961.9513 336138.4585 270940.3472 1.090218127 1.392398435 1.265090783 1.364869517 1.134626385 1.407029308 1.365473822 1.240636406 1 18.04761572 0.962954681 15.86036549 0.999999996 1.302822736 0.413249012 0.106234651 31.1468103 13336.03808 0.091535657 0.022884449 9.182367727 -0.962954681 0.30282274 FDFLCQYHKPASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FDFLCQYHKPASK 13 1 J3KQ32;Q9NTK5;Q9NTK5-3;C9JTK6 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 177.84 9.07E-06 1928780000 6652700 5103500 5918700 5490200 6130700 4705700 8132000 5609800 6053400 FALSE TRUE 6236319.382 5481368.45 6059094.359 5631087.827 5649219.552 6064159.199 6912682.094 6310195.879 5043048.434 1.236616992 1.086915686 1.201474552 1.116603955 1.120199345 1.202478873 1.370734821 1.251266166 1 22.26586465 1.998967811 20.67906146 1.258046533 1.149578383 0 0.102998718 6.210529483 124427.9468 0.034957264 0.025345524 99.76261181 -1.998967811 -0.10846815 FDGGEEVLISGEFNDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FDGGEEVLISGEFNDLR 17 0 Q16698-2;Q16698 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 ;;; 266.97 2.39E-27 141163000 170500 159453 150588 142500 200343 144542 148184 164208 167260 FALSE TRUE 159828.7094 171259.066 154160.0185 146156.7913 184608.8689 186268.929 125965.1849 184709.7303 139343.2255 1.147014567 1.229044795 1.10633307 1.048897718 1.324849976 1.336763437 0.903992171 1.32557381 1 17.08828334 -1.533190398 3.33321108 0.99543461 1.164233764 0.135102385 0.137627604 11282308.4 5582077.518 367940.7059 0.030435127 0.029296086 1.533190398 0.168799154 FDGGEEVLISGEFNDLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FDGGEEVLISGEFNDLRK 18 1 Q16698-2;Q16698 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 ;;; 247.46 3.52E-24 1053307000 1048846 842847 805389 785698 1178530 721731 894313 907862 1313848 FALSE TRUE 983200.6011 905252.2689 824493.2074 805860.3409 1085973.008 930083.0234 760219.068 1021210.569 1094558.281 0.898262448 0.827048029 0.753265698 0.736242514 0.992156404 0.849733668 0.694544166 0.932988756 1 20.06191734 1.015014141 16.66712983 1.000000006 0.813734694 0.348893707 0.084538183 3.8660228 4290.050465 0.080022547 0.020005906 10.35175873 -1.015014141 -0.186265312 FDIYDPFHPTDEAYS(ph)PPPAPEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 FDIYDPFHPTDEAYSPPPAPEQK 23 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(0.999)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPT(0.001)DEAY(0.006)S(0.993)PPPAPEQK 281.11 3.74E-52 10295665000 8263257 6006148 6942725 6687911 7011784 5406244 8557183 5958738 7620780 TRUE FALSE 7746074.495 6450849.447 7107409.716 6859534.119 6461106.769 6966938.88 7274112.85 6702699.556 6348822.586 1.220080478 1.016070202 1.119484695 1.080441929 1.017685828 1.097359201 1.145742026 1.055738992 1 22.59805763 4.754467838 24.42051416 1.076373082 1.220080627 0.496456356 0.047687503 1991.491926 3057235.382 0.011105178 0.271738133 56815.6315 -4.754467838 0.143707546 FDKDHDVMLFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FDKDHDVMLFLK 12 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 86.028 0.0068148 175950000 1086600 1017400 875070 898360 1215700 593690 1018100 1040400 1299200 FALSE TRUE 1018591.646 1092729.355 895827.0736 921413.4385 1120223.826 765078.6652 865445.3566 1170296.23 1082355.127 0.941088207 1.009584865 0.827664647 0.851304175 1.034987314 0.706864731 0.799594639 1.081249768 1 20.0457425 4.000949485 6.579113606 0.878398037 0.973429511 0.04260485 0.116313442 0.382111874 61.9254762 0.027778939 0.05846404 10021.88662 -4.000949485 0.095031474 FDLGQDVIDFTGHALALYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FDLGQDVIDFTGHALALYR 19 0 P50395;P50395-2;Q5SX87;Q5SX91;P31150 P50395;P31150 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 ; 305.63 1.93E-50 2448260000 1538060 1848380 1519460 1480940 1860420 1393360 1723630 1781070 1211100 FALSE TRUE 1441795.57 1985235.978 1555502.309 1518943.428 1714310.118 1795600.413 1465187.683 2003440.51 1008959.586 1.42899239 1.967607034 1.54168941 1.505455173 1.699087002 1.779655437 1.45217678 1.985649909 1 19.94443696 -1.236028463 4.721638984 0.999834516 1.669813778 0.532649295 0.197243731 0.000311613 5.04E-05 0.173200891 0.040813893 0.058072636 1.236028463 0.669979262 FDLLWLIQDRPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FDLLWLIQDRPDR 13 1 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 237.41 8.77E-17 931970000 1026750 1153390 1243290 1198980 1242540 1062860 1399260 1132920 949570 FALSE TRUE 962487.5503 1238788.196 1272781.426 1229747.857 1144955.921 1369690.428 1189453.953 1274367.556 791080.6325 1.216674395 1.565944285 1.608914912 1.55451645 1.447331503 1.731416965 1.503581183 1.610919928 1 19.59346523 -1.07421838 4.436437656 0.999965276 1.544455633 0.603860982 0.13442651 5.05E-05 1.05E-05 0.116318429 0.02741438 0.08429108 1.07421838 0.544490357 FDLLWLIQDRPDRDNDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FDLLWLIQDRPDRDNDLR 18 2 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 133.95 6.51E-06 360290000 372570 571470 506830 566770 711420 378790 620390 455450 949620 FALSE TRUE 349251.5088 613782.2334 518852.2469 581314.2777 655547.9429 488140.5239 527368.2789 512313.9351 791122.2872 0.441463367 0.775837368 0.655843294 0.734796993 0.828630357 0.617022844 0.666607789 0.647578691 1 19.59354119 -2.14903271 2.252664958 1.688838923 0.682051806 0.494701868 0.103970309 7005378.026 1503654.07 24675949.23 0.02262826 0.007095243 2.14903271 -1.006787117 FDLSQNHPLGMAIFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FDLSQNHPLGMAIFLK 16 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 197.88 4.22E-11 3818510000 5802380 9469510 5695390 4847220 10111570 4097610 6956840 10199430 4537190 FALSE TRUE 5439219.393 10170642.37 5830487.34 4971607.872 9317448.08 5280523.488 5913726.426 11472851.29 3779903.678 1.438983598 2.690714696 1.542496274 1.315273694 2.464996168 1.396999484 1.564517758 3.035223187 1 21.84991804 3.811522761 8.340021671 1.75977076 2.146296445 0.032415871 0.659363576 0.827948029 73.71389834 0.153296076 0.277061236 6479.220515 -3.811522761 0.386525685 FDMIWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FDMIWDR 7 0 P51580 P51580 TPMT Thiopurine S-methyltransferase 0 ; 89.298 0.041818 38822000 97332 167298 96713 92352 174658 57913 80703 144029 138989 FALSE TRUE 91240.16386 179684.918 99007.07803 94721.90867 160941.0652 74631.54296 68602.33436 162011.3377 115790.838 0.787973949 1.551806007 0.855051054 0.818043209 1.389929186 0.644537549 0.592467725 1.39917234 1 16.82116158 3.736819456 21.96209939 0.913598139 1.218143523 0.052244805 0.325677463 141.375586 320141.6515 0.079695682 0.140834665 5455.310271 -3.736819456 0.304545385 FDNSYSLWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FDNSYSLWR 9 0 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 85.807 0.033884 91902000 732020 224240 258380 202330 290680 176620 226500 214480 290540 FALSE TRUE 686204.1749 240842.9629 264508.8956 207522.1303 267851.1653 227607.3268 192538.4277 241258.3001 242046.997 2.835003876 0.995025618 1.092799741 0.857362962 1.106608091 0.940343527 0.795458857 0.996741555 1 17.88492767 4.738708355 6.939049629 0.968425449 2.863722123 0.974884164 0.093930798 0.016376754 5.866137409 0.02376732 0.145547326 54790.89005 -4.738708355 1.895296674 FDPETNSDDACTYHPGVPVFHDALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FDPETNSDDACTYHPGVPVFHDALK 25 0 Q9UHD1-2;Q9UHD1;E9PPQ5;E9PIZ4;E9PSD5;E9PL00 Q9UHD1-2 CHORDC1 Cysteine and histidine-rich domain-containing protein 1 0 ; 221.43 6.56E-34 587590000 588250 424960 463140 423310 481190 589660 862710 486040 660960 FALSE TRUE 551432.4826 456424.4806 474125.8995 434172.8513 443399.2784 759885.2697 733354.6445 546723.1639 550641.506 1.001436464 0.828895889 0.861042792 0.788485515 0.805241293 1.379999984 1.331818681 0.992884041 1 19.07075384 2.249194478 24.99999534 1.223832492 0.850618467 0.56263898 0.136924069 124.2186922 292035.6472 0.045249566 0.037492756 177.4984145 -2.249194478 -0.373214025 FDPFGPIGT(ph)SPPGPNPDHLPPPGYDDMYL ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FDPFGPIGTSPPGPNPDHLPPPGYDDMYL 29 0 Q92530 Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 FDPFGPIGT(0.553)S(0.447)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.561)S(0.439)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.534)S(0.466)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.547)S(0.453)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.547)S(0.453)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.527)S(0.473)PPGPNPDHLPPPGYDDMYL 216.14 7.65E-34 554884000 161061 225629 166843 176256 264309 153799 210733 201763 186263 TRUE FALSE 150980.4795 242334.8059 170800.5947 180779.0274 243551.2373 198198.2746 179135.543 226953.5547 155174.502 0.972972219 1.561692178 1.100700131 1.165004721 1.569531297 1.277260581 1.15441352 1.462569892 1 17.24353199 -1.304840662 3.349212078 0.998665387 1.286557534 0.168061119 0.197752893 36098990.84 53263981.08 488868.0249 0.043277338 0.0495632 1.304840662 0.287892147 FDPFGPIGT(ph)SPPGPRPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FDPFGPIGTSPPGPRPDR 18 1 Q5QPM7 Q5QPM7 PSMF1 1 FDPFGPIGT(0.676)S(0.324)PPGPRPDR;FDPFGPIGT(0.598)S(0.402)PPGPRPDR 83.245 0.0065316 375400000 272200 299308 304487 358000 374790 317310 388410 272115 258222 TRUE FALSE 255163.4879 321469.0757 311709.5754 367186.8861 345355.5052 408912.2459 330171.5263 306089.1567 215123.08 1.186127903 1.49434954 1.448982487 1.706868859 1.605385648 1.900829264 1.534802896 1.422855961 1 17.71480279 0.843821519 2.890871531 1.000473801 1.558996631 0.478030727 0.181570142 0.585787619 8.782462698 0.172759263 0.04545476 6.979455122 -0.843821519 0.558522829 FDPFGPIGTS(ph)PPGPNPDHLPPPGYDDMYL ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FDPFGPIGTSPPGPNPDHLPPPGYDDMYL 29 0 Q92530 Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 FDPFGPIGT(0.155)S(0.845)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.068)S(0.932)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.236)S(0.764)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.359)S(0.641)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.202)S(0.798)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.053)S(0.947)PPGPNPDHLPPPGYDDMYL 176.14 8.50E-13 1265984000 248745 361680 247984 262410 428817 237050 343308 309349 295733 TRUE FALSE 233176.4945 388459.1635 253866.2976 269143.8849 395139.4426 305482.4868 291832.1525 347971.9036 246373.2518 0.946435917 1.576709974 1.03041339 1.092423317 1.60382444 1.23991742 1.184512322 1.412376957 1 17.91048611 -1.134837107 4.938557475 0.999985769 1.266628222 0.123511933 0.217873325 3.10E-05 5.43E-06 0.191517911 0.045138796 0.073309945 1.134837107 0.266642454 FDPFGPIGTS(ph)PPGPRPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FDPFGPIGTSPPGPRPDR 18 1 Q5QPM7 Q5QPM7 PSMF1 1 FDPFGPIGT(0.244)S(0.756)PPGPRPDR;FDPFGPIGT(0.102)S(0.898)PPGPRPDR 80.702 0.0049447 373930000 333010 358230 355020 382420 406870 323160 443380 322850 351120 TRUE FALSE 312167.4985 384753.7219 363441.2421 392233.5446 374916.0714 416451.0459 376899.2851 363158.5332 292515.8037 1.067181652 1.315326273 1.242467031 1.340896935 1.281695097 1.423687338 1.288474949 1.241500557 1 18.15815505 0.788683944 3.268453622 1.000043822 1.288270623 0.483030566 0.089985664 1.093230299 15.81728508 0.079131664 0.020535741 6.147293433 -0.788683944 0.288226801 FDPYEHEALFHTPVEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FDPYEHEALFHTPVEGK 17 0 Q9HAV7 Q9HAV7 GRPEL1 "GrpE protein homolog 1, mitochondrial" 0 ; 162.41 1.65E-09 255230000 677920 517020 571370 515250 754480 539970 636200 597510 903770 FALSE TRUE 635490.1973 555300.6988 584923.1662 528472.1873 695226.1842 695850.5733 540807.7162 672110.4388 752924.9484 0.84402861 0.737524636 0.776867824 0.701892252 0.923367177 0.924196462 0.718275729 0.892665916 1 19.52214654 2.738049923 24.99998929 0.864305548 0.762450964 0.351468625 0.080807484 61.81294047 3025852.329 0.024855629 0.024752798 547.0788468 -2.738049923 -0.101854583 FDQKPGLQRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FDQKPGLQRR 10 2 Q0VF96 Q0VF96 CGNL1 Cingulin-like protein 1 0 53.683 0.079878 50507000 197730 64177 102800 101120 85050 61150 105130 74607 112880 FALSE TRUE 185354.4323 68928.73186 105238.4645 103714.9104 78370.51608 78803.01231 89366.73248 83921.84818 94039.59877 1.971025341 0.732975606 1.119086703 1.102885505 0.833377823 0.837976909 0.950309589 0.892409679 1 16.52098076 4.745451689 24.93903134 0.93527292 1.971025833 0.881245955 0.119679132 252.5401689 913927.7064 0.028264292 0.279622676 55648.2728 -4.745451689 1.035752912 FDQLFDDES(ph)DPFEVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FDQLFDDESDPFEVLK 16 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 FDQLFDDES(1)DPFEVLK;FDQLFDDES(1)DPFEVLK;FDQLFDDES(1)DPFEVLK;FDQLFDDES(1)DPFEVLK;FDQLFDDES(1)DPFEVLK;FDQLFDDES(1)DPFEVLK 232.84 4.57E-17 326509000 1046685 795247.2 869352 850877 891472.7 686222.9 1123491.8 762130.7 892365.3 TRUE FALSE 981174.8542 854128.1301 889973.44 872711.9444 821460.0302 884324.3113 955034.6346 857284.3956 743423.7665 1.319805605 1.148911521 1.197128045 1.173909126 1.10496875 1.189529244 1.284643668 1.153157101 1 19.50382528 -2.095536499 1.511000789 0.727763633 1.195252678 0.487538957 0.063303698 89898.31667 18444.83673 84045.75629 0.016830135 0.008025341 2.095536499 0.467489045 FDQLFDDESDPFEVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FDQLFDDESDPFEVLK 16 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;; 185.12 3.98E-09 391998000 1602996 1202144 1354097 1245930 1407698 1073404 1661804 1192038 1394834 FALSE TRUE 1502667.342 1291151.993 1386216.82 1277902.673 1297143.077 1383278.31 1412631.918 1340866.568 1162027.194 1.293143008 1.111120289 1.192929758 1.099718388 1.116276008 1.190400979 1.215661668 1.153902916 1 20.1482124 -2.439022344 1.760598058 1.17E-05 1.16867674 0.467144034 0.057534215 698924.4336 58967.39899 2774177.513 0.013193757 0.003638963 2.439022344 1.16866506 FDREVDIGIPDATGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FDREVDIGIPDATGR 15 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 195.28 1.55E-08 128770000 124960 150080 146380 157170 167910 123360 163910 132960 216840 FALSE TRUE 117138.9767 161192.0794 149852.2027 161203.2483 154723.0259 158972.0294 139333.2172 149560.3487 180648.0032 0.648437705 0.892299259 0.829525929 0.892361086 0.856488991 0.88000989 0.771296747 0.827910334 1 17.46282178 -2.361384568 2.117248794 1.977459441 0.832154778 0.360649913 0.072728578 4416917.482 346718.5747 20778614.75 0.016126085 0.004351264 2.361384568 -1.145304663 FDRPPAR ddPTM_SK-BR-3_Pertuzumab_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 ;;;; 120.62 0.0041199 1478770000 1308478 1551272 1478558 1368977 1621358 860449 1377881 1437673 1868636 FALSE TRUE 1226582.698 1666129.793 1513630.094 1404107.267 1494023.083 1108846.658 1171280.536 1617169.639 1556748.58 0.787913163 1.070262607 0.972302216 0.901948642 0.959707369 0.712283713 0.752389018 1.038812342 1 20.57010453 2.370816086 24.97394702 0.838715397 0.959389593 0.007198472 0.122316646 15.39526295 3570.829775 0.040639838 0.034001727 234.8638012 -2.370816086 0.120674196 FDSEYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 FDSEYER 7 0 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;; 160.03 0.0031676 1177040000 2939160 3469910 3351470 3315720 3420600 3009150 3549970 3340130 2730210 FALSE TRUE 2755203.222 3726825.747 3430968.451 3400806.989 3151959.874 3877842.756 3017684.955 3757152.583 2274520.313 1.211333751 1.638510646 1.508436056 1.495175475 1.385769059 1.704905748 1.326734669 1.651843934 1 21.11713089 -1.308798733 3.573685428 0.998326227 1.499002999 0.503000495 0.152961219 3776165.536 2798606.35 44992.73471 0.031111035 0.049113543 1.308798733 0.500676772 FDSLTDLVEHYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FDSLTDLVEHYK 12 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4;H0YF12 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 176.32 2.53E-05 181430000 612800 495120 586440 543120 626110 446350 690830 579920 631210 FALSE TRUE 574445.9419 531779.2 600350.6337 557057.3787 576937.8462 575203.9991 587246.4549 652324.2886 525856.9732 1.09239959 1.011262049 1.141661448 1.059332494 1.097138339 1.093841155 1.116741785 1.240497553 1 19.00431093 1.699355797 3.442109839 1.13571899 1.080246421 0.051121424 0.065859904 0.414759061 11.21135044 0.03425151 0.015881346 50.04443576 -1.699355797 -0.055472569 FDSPDLLLEAGDPAT(ph)SPCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FDSPDLLLEAGDPATSPCR 19 0 A0A096LNM2;Q969U6-2;Q969U6 A0A096LNM2 FBXW5 F-box/WD repeat-containing protein 5 1 FDSPDLLLEAGDPAT(0.5)S(0.5)PCR;FDSPDLLLEAGDPAT(0.5)S(0.5)PCR 116.96 0.0012099 54044000 58435 58363 65623 62802 61215 54449 66484 51674 52264 TRUE FALSE 54777.65766 62684.25725 67179.60855 64413.60564 56407.42083 70167.54239 56515.34141 58125.61265 43540.80076 1.258076487 1.439667074 1.542911645 1.479384957 1.295507199 1.611535414 1.297985807 1.334968848 1 15.41008032 0.731675675 1.09204257 1.001326072 1.444534831 0.586990861 0.110463601 0.588208975 1.235953985 0.096482766 0.03040789 5.391078735 -0.731675675 0.443208759 FDSSLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 192.28 0.0011947 1249830000 2326240 2490860 2120460 2056690 2317400 1823220 2276620 2426360 1826320 FALSE TRUE 2180644.791 2675285.866 2170758.313 2109468.147 2135400.752 2349554.016 1935261.966 2729296.387 1521495.394 1.433224708 1.758326629 1.426726838 1.386443992 1.403488148 1.54423998 1.271947305 1.793824943 1 20.53705854 -2.924332128 0.325473837 1.69E-22 1.523610062 0.442487388 0.16940535 68.6529058 2.082195884 48.04015031 0.141122691 0.001190331 2.924332128 1.523610062 FDSSLDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 149.65 0.00080453 4622890000 7681980 6706160 6696770 6498790 7736600 5036420 7611400 6714800 6726200 FALSE TRUE 7201178.585 7202691.064 6855620.547 6665559.954 7128998.644 6490352.695 6470141.231 7553157.561 5603553.767 1.285109215 1.28537913 1.223441557 1.18952369 1.272228115 1.158256522 1.154649621 1.347922742 1 22.41791064 -5 0.193687718 0.008961647 1.272787817 0.558799081 0.064392345 100.6282274 0.989527784 38.7102351 0.156821097 1.00E-05 5 1.26382617 FDSSLLS(ph)S(ph)DDETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FDSSLLSSDDETK 13 0 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;A0A090HNM7 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 2 FDS(0.001)S(0.004)LLS(0.998)S(0.997)DDETK 97.904 0.0052109 51998000 349480 230470 263520 282110 288480 195470 318510 209560 368020 TRUE FALSE 327606.6706 247534.2386 269770.8188 289349.4202 265823.9445 251899.0158 270752.3824 235724.0273 306595.0845 1.068532039 0.80736532 0.879892837 0.943751009 0.86701959 0.821601612 0.883094335 0.76884477 1 18.22597504 2.500354162 23.37069258 0.857986245 0.898558441 0.053774741 0.087981279 1139.599683 1146357.664 0.026329171 0.024645543 316.485751 -2.500354162 0.040572196 FDSSLLSS(ph)DDETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FDSSLLSSDDETK 13 0 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;A0A090HNM7 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 1 FDSSLLS(0.013)S(0.987)DDETK;FDSSLLS(0.175)S(0.825)DDETK 256.51 7.54E-24 271800000 970320 692520 799690 763680 782370 596190 974800 645260 1168200 TRUE FALSE 909589.4033 743794.9014 818659.0244 783277.3217 720925.8161 768300.3747 828637.7896 725822.1314 973219.8731 0.934618608 0.764261933 0.841186095 0.804830792 0.740763558 0.789441724 0.851439446 0.745794606 1 19.89240625 -1.216378595 4.28046921 1.000075458 0.808103053 0.521983081 0.057423053 4.13E-05 7.56E-06 0.049382176 0.011634353 0.060760509 1.216378595 -0.191972405 FDVNTSAVQVLIEHIGNLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FDVNTSAVQVLIEHIGNLDR 20 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 180.63 5.39E-17 110120000 108970 155650 160350 188710 207780 232280 167730 146020 90345 FALSE TRUE 102149.7622 167174.488 164153.5777 193552.6181 191461.7969 299335.4652 142580.4436 164250.9184 75265.83585 1.357186313 2.22112046 2.18098392 2.571586642 2.54380749 3.977042995 1.894358071 2.182277212 1 16.19970753 5.125952627 1.08029845 2.450474669 7.45E-15 0.128003383 0.740350034 6.526989378 3.553552793 0.199744624 22.30341261 133644.9727 -5.125952627 -2.450474669 FDVQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FDVQLK 6 0 P62244;I3L3P7;H3BVC7 P62244 RPS15A 40S ribosomal protein S15a 0 ; 112.75 0.062188 333050000 1387450 1246860 1356620 1349100 1477910 1035050 1673630 1213240 1757790 FALSE TRUE 1300611.981 1339178.812 1388799.667 1383720.19 1361840.91 1333852.132 1422684.719 1364715.685 1464403.493 0.888151378 0.914487583 0.948372271 0.944903639 0.929962894 0.910850144 0.971511421 0.931925996 1 20.48188169 FDWFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FDWFLK 6 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 101.52 0.084748 70659000 267740 263440 239030 224400 309500 162570 255460 235950 289540 FALSE TRUE 250982.6313 282945.3717 244699.9045 230158.4839 285193.1185 209501.3199 217156.1446 265408.8769 241213.9035 1.040498196 1.173006065 1.014451907 0.954167569 1.182324544 0.868529205 0.900263797 1.100305053 1 17.87995354 3.443156998 0.886490055 0.973798027 1.118339746 0.121865413 0.0979622 0.982808658 1.600360596 0.042147758 0.093890029 2774.322846 -3.443156998 0.14454172 FDYEGLDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FDYEGLDPK 9 0 Q15124 Q15124 PGM5 Phosphoglucomutase-like protein 5 0 ;; 105.78 0.0070764 129233000 469813 385404 430070 419553 488191 332231 543916 418848 536840 FALSE TRUE 440408.243 413939.7132 440271.4635 430319.4403 449850.4481 428140.6964 462360.8453 471142.0948 447237.9359 0.984729174 0.925546963 0.984423342 0.962171153 1.005841437 0.957299598 1.033814013 1.053448415 1 18.77068304 1.703434916 5.974810614 1.032795733 0.96763049 0.55619114 0.024680342 0.093361128 7.799264357 0.012108362 0.006136698 50.5166934 -1.703434916 -0.065165243 FEAFEHENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FEAFEHENK 9 0 Q9UBQ0;F8VXU5;Q9UBQ0-2;Q05DG7 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ; 140.45 0.00010908 1146330000 1396740 1111680 1221750 1090910 1180520 1016640 1441700 1153460 1030990 FALSE TRUE 1309320.537 1193989.944 1250730.487 1118904.598 1087806.721 1310127.464 1225530.469 1297472.02 858911.1086 1.524395858 1.390120505 1.456181524 1.302701276 1.266495113 1.525335336 1.426842029 1.510601047 1 19.7121493 -1.813191845 2.827478729 0.875112783 1.421423018 0.697558416 0.087982809 9772874.038 7649707.17 8341131.408 0.020613804 0.015374753 1.813191845 0.546310234 FEAHPNDLYVEGLPENIPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FEAHPNDLYVEGLPENIPFR 20 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 ;; 197.31 1.67E-21 1817680000 1068550 1274080 1185660 1206000 1347570 987230 1276830 1064520 1444740 FALSE TRUE 1001671.363 1368414.209 1213784.415 1236948.002 1241737.288 1272227.275 1085381.195 1197427.665 1203603.561 0.832226985 1.136931008 1.008458644 1.027703841 1.031682963 1.057015214 0.901776324 0.994868829 1 20.19892885 1.752796751 25 0.95711065 1.029908277 0.058296152 0.08031999 8.244201243 14497.47119 0.033765769 0.018724893 56.59743515 -1.752796751 0.072797627 FEAHPNDLYVEGLPENIPFRS(ph)PSWYGIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FEAHPNDLYVEGLPENIPFRSPSWYGIPR 29 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 1 FEAHPNDLYVEGLPENIPFRS(0.836)PS(0.164)WYGIPR;FEAHPNDLYVEGLPENIPFRS(0.835)PS(0.159)WY(0.006)GIPR 162.08 3.71E-12 98375000 62856 60662 66600 65453 79183 56003 70015 62966 99023 TRUE FALSE 58921.95516 65153.4776 68179.78345 67132.63479 72964.28659 72170.15697 59516.90074 70827.44371 82495.42159 0.714245155 0.789782952 0.826467483 0.813774068 0.884464679 0.874838331 0.721457017 0.858562116 1 16.33202643 -5 0.254867056 2.182897382 0.792155254 0.551884534 0.055447045 155.0421703 1.531390601 95.91967557 0.077592046 1.00E-05 5 -1.390742128 FEALEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FEALEK 6 0 P21266 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 108.24 0.07115 704200000 1197770 1008970 1147440 1087760 1261980 928640 1331050 1056860 1867340 FALSE TRUE 1122803.714 1083675.189 1174657.819 1115673.763 1162869.181 1196723.293 1131471.409 1188811.297 1555668.891 0.721749802 0.696597583 0.755082155 0.717166596 0.747504298 0.769266069 0.727321486 0.764180157 1 20.5691036 -5 0.279972575 2.944506454 0.717942078 0.952761428 0.018595915 42.9600449 0.411578014 48.50875201 0.020541165 1.00E-05 5 -2.226564375 FEAWLAEVEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FEAWLAEVEGR 11 0 Q96RU3-5;Q96RU3-2;Q96RU3;H0Y7W6;Q96RU3-3;B7ZL14;Q96RU3-4 Q96RU3-5 FNBP1 Formin-binding protein 1 0 111.65 0.0037955 9428700 14362 18591 17803 17497 18294 13435 17444 16939 16181 FALSE TRUE 13463.10806 19967.49698 18225.29557 17946.00264 16857.26303 17313.4664 14828.43414 19053.87144 13480.28657 0.998725657 1.481236833 1.351996152 1.331277533 1.250512217 1.284354477 1.100008822 1.413461898 1 13.71856355 -0.44532524 0.320417126 0.901174324 1.332470436 0.209019171 0.147143083 10.69280312 1.215804864 1.333142439 0.142340731 0.358653242 0.44532524 0.431296112 FEDEDS(ph)DDVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FEDEDSDDVPR 11 0 P49756 P49756 RBM25 RNA-binding protein 25 1 FEDEDS(1)DDVPR;FEDEDS(1)DDVPR 199.4 5.28E-08 188530000 575410 447290 480060 435740 392420 496130 675590 472410 394890 TRUE FALSE 539396.1152 480407.817 491447.2499 446921.8261 361600.9161 639354.677 574291.5514 531391.4284 328980.3079 1.639600007 1.460293536 1.493850051 1.358506316 1.09915672 1.943443609 1.745671512 1.615268196 1 18.3276417 2.231934621 24.99985743 1.66064637 1.426143499 0.043409955 0.276591538 291.8112474 1100992.704 0.093193371 0.070408065 170.5825575 -2.231934621 -0.234502871 FEDEDSDDVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FEDEDSDDVPR 11 0 P49756 P49756 RBM25 RNA-binding protein 25 0 120.22 0.0011182 318570000 665660 564300 679460 611210 561530 653200 860380 585910 494380 FALSE TRUE 623997.5288 606081.3592 695577.1121 626894.6834 517429.6989 841768.2362 731374.0064 659062.1532 411864.7842 1.51505434 1.471554215 1.688848231 1.522088577 1.25630964 2.043797548 1.775762421 1.600190593 1 18.65181125 4.229904305 0.824557974 1.622947745 1.457045399 0 0.287078669 6.561040849 5.556091881 0.102709722 0.86760948 16978.69491 -4.229904305 -0.165902346 FEDENFILK ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;;; 230.7 1.87E-07 8406470000 8279950 6035920 6800400 5881610 5888890 5978150 9040770 6392260 10967730 FALSE TRUE 7761722.71 6482825.797 6961708.699 6032542.07 5426400.334 7703944.858 7685190.469 7190347.732 9137145.009 0.84946914 0.709502344 0.761912905 0.660221772 0.593883574 0.843145736 0.841093193 0.786935933 1 23.12331202 0.968771799 0.783850442 0.992200153 0.725931637 0.507029836 0.079435959 0.579343903 0.791090789 0.075315928 0.027872129 9.306187522 -0.968771799 -0.266268515 FEDFEPSDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FEDFEPSDSR 10 0 Q5T447-2;Q5T447 Q5T447-2 HECTD3 E3 ubiquitin-protein ligase HECTD3 0 94.85 0.0182 54371000 59906 71486 67069 68613 71248 60619 81034 68253 73367 FALSE TRUE 56156.5904 76778.89782 68659.90835 70373.72574 65652.46948 78118.72123 68883.70398 76774.53729 61121.57373 0.918768725 1.2561669 1.123333451 1.151372935 1.074129239 1.278087531 1.126994934 1.256095559 1 15.89939407 FEDHEGLPTVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FEDHEGLPTVVK 12 0 P49589-3;P49589;B4DKY1;P49589-2 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 0 182.35 1.70E-05 188470000 455010 437290 450670 449190 460600 305900 559750 379470 445380 FALSE TRUE 426531.7363 469667.4066 461360.1052 460716.9759 424426.334 394208.3641 475820.684 426847.6648 371043.2007 1.149547372 1.265802488 1.243413447 1.241680147 1.143873094 1.062432524 1.28238621 1.150398832 1 18.50122764 2.738702149 23.95320715 1.150938124 1.234943235 0.241994963 0.079096454 11.15414272 1887818.247 0.023672247 0.023673771 547.9010708 -2.738702149 0.084005111 FEDRFDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FEDRFDK 7 1 Q9HD45;Q5TB53 Q9HD45 TM9SF3 Transmembrane 9 superfamily member 3 0 84.476 0.019624 182390000 368150 446000 288730 350010 516710 235810 388180 480000 306350 FALSE TRUE 345108.1487 479022.3041 295578.8119 358991.8492 476129.6809 303884.5189 329976.0127 539929.0566 255218.2059 1.352208192 1.876912748 1.158141563 1.406607526 1.865578826 1.190685115 1.292917218 2.115558546 1 17.96137172 -1.135924847 4.46318538 0.999929767 1.504763867 0.207583637 0.322891752 0.00020823 4.03E-05 0.288484711 0.067987076 0.073126562 1.135924847 0.5048341 FEDYLNAESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FEDYLNAESR 10 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1;A0A5F9ZGZ7 E7EPK1 7-Sep Septin-7 0 ;;; 282.51 8.38E-24 1295530000 1409010 1510450 1551620 1451830 1482730 1352150 1634670 1362480 1304950 FALSE TRUE 1320822.579 1622285.29 1588425.159 1489086.416 1366282.367 1742493.755 1389566.409 1532588.627 1087145.415 1.214945638 1.492243142 1.461097235 1.36972147 1.256761376 1.602815715 1.278178972 1.409736551 1 20.0521135 -0.688730235 0.606536035 0.93479999 1.407496424 0.507221164 0.118063382 11.72408271 2.985775528 1.662792049 0.042859452 0.204771619 0.688730235 0.472696434 FEEAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FEEAKR 6 1 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 151.7 0.016599 1154240000 1082280 1235750 1128700 1120390 1434070 897140 1159600 1193850 1226900 FALSE TRUE 1014542.027 1327246.216 1155473.297 1149141.104 1321443.927 1156129.754 985728.7452 1342904.8 1022122.464 0.992583631 1.298519759 1.130464634 1.124269493 1.292843053 1.131106883 0.964393974 1.313839435 1 19.96313663 1.999193717 24.99995057 1.078528785 1.181300598 0.060038413 0.125696996 57.33596333 1777814.075 0.043161705 0.031485128 99.81451863 -1.999193717 0.102771813 FEEEIKAEQEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FEEEIKAEQEER 12 1 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 0 ; 152.99 6.41E-05 286610000 619470 468030 527110 558940 596090 358260 651480 434820 667080 FALSE TRUE 580698.4785 502683.4282 539613.2981 573283.3467 549275.4959 461683.8461 553796.622 489108.2342 555740.0385 1.044910279 0.904529804 0.970981503 1.031567472 0.988367686 0.830755055 0.996503012 0.880102566 1 19.08405066 FEEESKEPVADEEEEDS(ph)DDDVEPITEFR ddPTM_SK-BR-3_Pertuzumab_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 368.76 1.11E-127 11603270000 8329490 5423786 6056480 5928220 6002400 4116303 7557830 5848551 8225050 TRUE FALSE 7808162.089 5825368.759 6200142.566 6080348.162 5530995.717 5304612.854 6424603.555 6578755.467 6852236.019 1.139505713 0.850141289 0.90483494 0.887352412 0.807181145 0.774143336 0.937592275 0.96008886 1 22.70814341 -0.873036416 5.549993666 1.000000058 0.89575494 0.066898954 0.100095515 6.64E-08 1.34E-08 0.089131882 0.021008574 0.133956436 0.873036416 -0.104245118 FEEFLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FEEFLQR 7 0 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;E9PFG7;Q02218-3 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 ; 114.6 0.013652 114716000 178001 282060 191908 185182 337510 181308 176335 291510 294910 FALSE TRUE 166860.2352 302944.0159 196460.1484 189934.0836 311003.326 233648.6763 149895.2038 327905.6652 245687.6158 0.679156068 1.233045528 0.799633908 0.773071459 1.265848606 0.950998997 0.610104841 1.334644663 1 17.90646561 FEEHKNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FEEHKNEK 8 1 E9PH64;Q9Y6M9;A0A3B3IT57;E7EWZ0;E9PF49 E9PH64 NDUFB9 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 0 53.751 0.080876 97803000 121620 65058 82961 74670 111430 71338 95234 78655 140340 FALSE TRUE 114008.0213 69874.96201 84928.8741 76586.15862 102678.7373 91932.12252 80954.54581 88475.24989 116916.3474 0.975124727 0.597649205 0.726407179 0.6550509 0.878223958 0.78630683 0.692414257 0.756739771 1 16.83511714 -4.999999167 0.425696956 6.005198711 0.735267456 0.309435055 0.109355635 1089.309418 6.930258585 5107.22731 0.058181777 1.00E-05 4.999999167 -5.269931255 FEEHVQSVDIAAFNKI ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FEEHVQSVDIAAFNKI 16 1 P29692;P29692-2;E9PRY8;P29692-4;E9PQZ1;H0YE72;P29692-3 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 ; 185.02 2.77E-09 254310000 720090 544781 664860 588782 512805 570154 860480 567168 532050 FALSE TRUE 675020.8523 585117.1521 680630.7932 603891.1429 472531.3639 734748.2041 731459.0123 637980.1733 443247.4178 1.522898555 1.320068947 1.53555501 1.362424503 1.066066817 1.657648019 1.650227351 1.439331957 1 18.7577527 FEELCSDLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 FEELCSDLFR 10 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;P17066;P48741 A0A0G2JIW1;P17066 HSPA1B;HSPA1A;HSPA6;HSPA7 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 6;Putative heat shock 70 kDa protein 7 0 ;;;;;; 211.45 1.37E-07 1385234000 1444643 1854264 1147641 989497 1829603 828908 1405729 1868765 1532907 FALSE TRUE 1354225.373 1991555.636 1174863.586 1014889.168 1685913.361 1068200.283 1194952.987 2102084.424 1277054.919 1.060428454 1.559490987 0.919978906 0.794710669 1.32015729 0.836456027 0.935709944 1.64604074 1 20.28438914 3.917695794 6.522458707 1.042516275 1.331735624 0.112972485 0.278693385 0.340257 29.32921642 0.066009203 0.121221825 8273.624265 -3.917695794 0.289219349 FEELNADLFR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;;;; 325.34 1.14E-42 6456832000 3309123 4397477 2917333 2548138 4120193 2024925 3290014 4120459 3613450 FALSE TRUE 3102010.898 4723070.773 2986533.516 2613527.535 3796609.662 2609487.976 2796706.944 4634907.376 3010341.851 1.030451375 1.568948314 0.992091152 0.868182972 1.261188878 0.866841078 0.929033008 1.539661475 1 21.5214959 3.795064665 5.734167793 1.04341186 1.326511596 0.133641068 0.240385884 0.302594671 18.55727752 0.056936597 0.103468296 6238.277141 -3.795064665 0.283099736 FEELNMDLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 FEELNMDLFR 10 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;; 145.89 6.89E-05 180081000 268366 490468 298623 322485 406173 217365 311604 381896 270600 FALSE TRUE 251569.4511 526782.7611 305706.4786 330760.5111 374273.811 280114.7469 264881.873 429576.5563 225435.1119 1.115928433 2.336737861 1.356073045 1.467209382 1.660228559 1.242551547 1.174980556 1.90554414 1 17.78235271 3.728674515 24.9028576 1.398018385 1.823395358 0.098844442 0.384310033 104.4815281 1675070.76 0.090514231 0.152876849 5353.952516 -3.728674515 0.425376973 FEFTPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FEFTPGR 7 0 O95747;C9JIG9;Q9UEW8-2;Q9UEW8 O95747;Q9UEW8-2 OXSR1;STK39 Serine/threonine-protein kinase OSR1;STE20/SPS1-related proline-alanine-rich protein kinase 0 ;; 139.54 0.0062458 701840000 1136520 1232900 1233440 1232140 1208020 1080630 1370150 1072620 1191680 FALSE TRUE 1065387.242 1324185.199 1262697.779 1263758.798 1113146.982 1392590.338 1164708.727 1206538.968 992780.9095 1.073134296 1.333814124 1.271879593 1.272948328 1.121241325 1.402716677 1.173178006 1.215312419 1 19.92111585 0.582617125 1.215582653 1.000307132 1.253716247 0.358771239 0.097081241 1.42472079 3.017355079 0.082489618 0.02504386 3.824873931 -0.582617125 0.253409115 FEGGDRDLEHLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FEGGDRDLEHLSK 13 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;;; 180.84 7.55E-06 2817650000 2654730 4151160 3711820 4060470 4007330 2685350 4748180 3584920 3576710 FALSE TRUE 2488575.188 4458516.206 3799866.123 4164668.535 3692610.467 3460566.952 4036234.489 4032505.153 2979733.995 0.835166895 1.496279941 1.275236692 1.397664537 1.239241648 1.161367746 1.354562017 1.35331045 1 21.50675211 FEGGVVIAADMLGSYGSLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FEGGVVIAADMLGSYGSLAR 20 0 P28070 P28070 PSMB4 Proteasome subunit beta type-4 0 59.306 0.067802 0 4481 3897.8 4979.4 3403.5 2681.6 3356.5 4799.8 4347.4 2702.2 FALSE TRUE 4200.542209 4186.397168 5097.513719 3490.839572 2470.997953 4325.467062 4080.114549 4890.18246 2251.185363 1.865924627 1.859641252 2.26436872 1.550667319 1.097643043 1.921417549 1.812429405 2.172270014 1 11.13646914 3.221331772 24.9031015 1.644278362 2.005533273 0.203601445 0.367316852 383.8425855 554816.6807 0.103010245 0.123404303 1664.683871 -3.221331772 0.361254911 FEGKPLLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FEGKPLLQR 9 1 Q9H3K6;A0A087WZT3;H3BV85;Q9H3K6-2;H3BTW0;A0A0B4J295;H3BVE0 Q9H3K6 BOLA2;BOLA2B BolA-like protein 2 0 ; 150.35 7.79E-05 4676600000 4899800 7232400 4468800 4331900 7503800 2894000 5681100 6384400 8305700 FALSE TRUE 4593130.264 7767894.421 4574802.046 4443063.888 6914481.817 3729450.82 4829271.796 7181506.394 6919425.013 0.663802304 1.122621375 0.661153497 0.642114609 0.999285606 0.538982764 0.697929638 1.037876179 1 22.72222073 1.229902546 24.81201575 1.018938295 0.775805087 0.269479351 0.175326546 276.5549845 792509.3529 0.157310071 0.04179317 16.97862615 -1.229902546 -0.243133209 FEGLS(ph)PLQR ddPTM_SK-BR-3_Pertuzumab_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 127.17 0.00047525 398742000 511264 548050 551045 577230 619720 489304 659030 515685 773550 TRUE FALSE 479264.8989 588628.1922 564116.0476 592042.699 571049.691 630558.1216 560214.5696 580069.4074 644439.5077 0.743692609 0.913395571 0.875359193 0.918693984 0.886118378 0.978459753 0.869305129 0.900114596 1 19.29768542 4.739385402 24.75051847 0.909499219 0.74369255 0.61569371 0.042767476 38.48437195 1154631.241 0.008907292 0.054163596 54876.37337 -4.739385402 -0.16580667 FEHCNFNDVTTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FEHCNFNDVTTR 12 0 E9PNW4;A0A2U3TZL5;P13987;P13987-2 E9PNW4 CD59 CD59 glycoprotein 0 ; 148.96 6.69E-05 558510000 396780 462210 412630 338010 526770 375240 441610 513310 843410 FALSE TRUE 371946.2481 496432.5093 422417.7785 346683.9088 485399.6091 483565.6965 375394.6802 577397.8834 702639.4224 0.529355792 0.706525272 0.601187131 0.493402303 0.690823193 0.688213159 0.534263618 0.821755605 1 19.422425 1.019951938 4.305364308 0.99890256 0.615645901 0.763979162 0.073858819 0.07817395 3.725155681 0.067345673 0.017170382 10.47012673 -1.019951938 -0.383256659 FEHLLED ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 150.07 0.0045919 855744000 1809240 2317810 2219450 2224710 2512340 1917070 2637020 2160790 2447020 FALSE TRUE 1696002.898 2489423.064 2272096.402 2281799.825 2315030.951 2470496.988 2241623.332 2430569.388 2038596.554 0.831946319 1.221145528 1.114539509 1.119299364 1.135600346 1.211861652 1.099591446 1.192275825 1 20.95914486 4.747359616 24.98818743 1.143838865 0.831946159 0.688887833 0.064226624 588.1873553 1670350.896 0.013318057 0.161117702 55893.28253 -4.747359616 -0.311892706 FEIGEGENLDLPYGLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 FEIGEGENLDLPYGLER 17 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;; 297.03 8.20E-46 656157000 505926 514354 553765 552519 591648 481596 619005 501220 555699 FALSE TRUE 474260.9948 552437.3053 566900.5673 566697.573 545182.3527 620624.9471 526190.9468 563798.4203 462949.2469 1.024434099 1.193299933 1.224541504 1.224103024 1.177628771 1.340589603 1.136606119 1.217840668 1 18.82049451 -1.138773106 4.301354744 0.999960914 1.197910749 0.3665287 0.079186638 2.67E-05 5.35E-06 0.069050035 0.016272038 0.07264854 1.138773106 0.197949836 FEIINAIYEPTEEECEWKPDEEDEISEELKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FEIINAIYEPTEEECEWKPDEEDEISEELKEK 32 2 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8VV59;F8W543;F8W118;H0YH88;F8VRJ2 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 58.398 0.01987 91990000 19435 18157 20216 20254 23258 19730 23023 17871 22828 FALSE TRUE 18218.59804 19501.36317 20695.53307 20773.75193 21431.4105 25425.73071 19570.91489 20102.23369 19017.85933 0.95797312 1.025423674 1.088215698 1.092328615 1.126909718 1.336939677 1.029080852 1.057018739 1 14.21506724 4.34098716 0.991310008 1.118936033 0.933661062 0.220604484 0.091095015 1.606881321 1.924885454 0.028684195 0.276589396 21927.40106 -4.34098716 -0.185274971 FEIWDTAGQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 226.2 1.14E-11 418270000 722770 750950 605680 612110 621910 543480 850070 776250 651760 FALSE TRUE 677533.1159 806551.1194 620047.0156 627817.7789 573067.6973 700373.8533 722609.8952 873166.5212 542977.0455 1.247811711 1.485423972 1.141939647 1.15625105 1.055417908 1.289877462 1.330829546 1.608109456 1 19.05053168 1.831046061 3.927132864 1.349771248 1.237059026 0.036077505 0.182842651 0.66563012 17.04910626 0.088430904 0.047884113 67.77133823 -1.831046061 -0.112712222 FEKEAAEMGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FEKEAAEMGK 10 1 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5;P68104;A0A087WVQ9;Q5VTE0;A0A087WV01;A6PW80;Q5JR01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ; 90.614 0.0097686 166520000 391890 403960 386120 393780 510030 285550 532110 337260 847360 FALSE TRUE 367362.3044 433869.6187 395278.9487 403885.0615 469974.3012 367983.6495 452325.0454 379367.6534 705930.1418 0.5203947 0.614607017 0.559940602 0.57213177 0.665751855 0.521274879 0.640750435 0.537401126 1 19.4291659 -1.535297072 3.122918035 1.014696357 0.584502001 0.878495777 0.049164045 12876405.43 15340573.06 1601676.269 0.010474844 0.029154321 1.535297072 -0.430194356 FEKPLEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FEKPLEEK 8 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 113.71 0.0025508 177510000 620420 354190 474710 448900 427150 360930 655390 444830 486250 FALSE TRUE 581589.0197 380414.5961 485970.3454 460419.534 393603.362 465124.6318 557120.3538 500368.0047 405091.7337 1.435697081 0.939082594 1.199655053 1.136580917 0.971640074 1.148195811 1.375294304 1.235196779 1 18.62788912 1.980860139 24.18298175 1.249333587 1.113358207 0 0.163495837 966.5924375 1221276.279 0.060132138 0.039537715 95.68858637 -1.980860139 -0.13597538 FELAVDAVHR ddPTM_SK-BR-3_Pertuzumab_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 0 120.09 0.00060585 78389000 59273 77818 66157 71682 81455 57660 74181 66170 82826 FALSE TRUE 55563.20874 83579.72569 67726.27528 73521.48148 75057.85287 74305.50597 63058.24771 74431.47016 69001.80552 0.805242824 1.211268677 0.981514538 1.065500836 1.087766506 1.076863213 0.913863735 1.078688733 1 16.07434649 FELLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FELLDR 6 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YGP5;A0A2R8YFV8;F6VDE0;P51531-2;P51531;A0A0U1RQZ9 A0A2R8Y4P4;F6VDE0 SMARCA4;SMARCA2 Transcription activator BRG1;Probable global transcription activator SNF2L2 0 ; 110.34 0.066976 102927000 239440 256320 250300 251190 244650 198109 287380 239990 215640 FALSE TRUE 224453.8778 275298.1995 256237.2342 257635.9607 225436.1759 255299.8523 244290.0369 269953.2798 179648.2909 1.249407254 1.532428714 1.426327147 1.434113063 1.254875149 1.421109274 1.359823885 1.502676582 1 17.45481568 -1.771359527 2.803741824 0.907115706 1.406632296 0.646898715 0.092100719 12878673.18 9798012.673 8199303.479 0.020777909 0.016929357 1.771359527 0.499516589 FELSENCSERPGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FELSENCSERPGLR 14 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 ; 199.38 1.89E-08 522930000 320150 319020 328060 335950 370300 323390 378080 323670 379860 FALSE TRUE 300112.383 342640.5727 335841.7381 344571.0458 341218.1317 416747.4432 321390.4139 364080.912 316458.912 0.948345493 1.082733207 1.061249108 1.08883344 1.078238339 1.316908538 1.015583388 1.150483991 1 18.27165867 6.084398975 0.746188528 1.111274939 3.80E-10 0.217257445 0.088157918 25.67220861 2.253316625 0.028429318 37.55536892 1214504.071 -6.084398975 -1.111274939 FENAFLSHVVSQHQALLGTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FENAFLSHVVSQHQALLGTIR 21 0 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;; 285.82 1.23E-45 1381338000 320000.4 542830 399547 338247.2 602630 351271 392530.4 508348 497986 FALSE TRUE 299972.1462 583021.698 409024.4435 346927.1958 555301.8707 452677.2353 333674.1106 571816.3668 414868.9195 0.72305283 1.40531544 0.985912476 0.836233276 1.338499571 1.09113316 0.804288041 1.378306111 1 18.66229605 3.726929753 24.9999011 1.04327964 1.137726209 0 0.247295329 40.25728222 5256066.644 0.06011 0.100025085 5332.486359 -3.726929753 0.094446569 FENLCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FENLCK 6 0 P08238;Q58FF7;P07900;P07900-2;Q58FG0;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AB3P;HSP90AA1;HSP90AA5P;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5;Putative heat shock protein HSP 90-beta 2 0 ;; 122.79 0.04436 1836120000 2468110 2249500 2105570 2074610 2512250 1757000 2858450 2105780 2330140 FALSE TRUE 2313635.401 2416055.321 2155515.115 2127848.005 2314948.019 2264217.377 2429851.959 2368691.268 1941224.581 1.191843244 1.244603713 1.110389357 1.096136957 1.192519424 1.166386105 1.251710896 1.220204654 1 20.8885356 4.048208956 7.059468786 1.163173685 1.217234648 0.113519176 0.072468932 0.594341177 49.520514 0.017495795 0.03806158 11174.00744 -4.048208956 0.054060963 FEPES(ph)PGFESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 260.83 1.22E-20 1861690000 2426080 2616140 2504500 2424580 2410240 2047460 2741440 2045050 2664740 TRUE FALSE 2274235.983 2809841.728 2563907.923 2486798.828 2220949.473 2638528.464 2330386.522 2300378.994 2219977.679 1.024440923 1.265707198 1.154925091 1.120190915 1.000437749 1.188538285 1.049734213 1.036217173 1 21.08211374 3.106176813 3.045568085 1.067798877 1.175631716 0.196753347 0.079346154 0.3147039 5.856521043 0.022455522 0.027629513 1276.958588 -3.106176813 0.107832839 FEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIK 34 2 P63279;H3BQQ9;B0QYN7 P63279 UBE2I SUMO-conjugating enzyme UBC9 0 266.81 2.51E-60 169600000 333110 238200 239020 186840 277310 190030 340860 248460 195550 FALSE TRUE 312261.2397 255836.5758 244689.6673 191634.6307 255531.1912 244888.5761 289751.2074 279480.7779 162911.4417 1.916754505 1.570402749 1.501979632 1.176311674 1.568528205 1.503200595 1.778581077 1.715538056 1 17.31372841 -1.410444453 3.130504332 0.991782865 1.579364725 0.471994335 0.196214491 27074873.44 34374411.33 1998402.298 0.048560354 0.03886472 1.410444453 0.58758186 FEPYANPTKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FEPYANPTKR 10 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 84.31 0.024065 449360000 958710 1190700 1090200 1166300 1506700 999110 1216400 1013300 1377400 FALSE TRUE 898706.0524 1278860.667 1116060.059 1196229.233 1388369.86 1287536.838 1034012.113 1139812.736 1147503.042 0.783184026 1.114472573 0.97259878 1.042462799 1.209905167 1.122033486 0.901097492 0.993298226 1 20.13006655 1.732383924 24.99999999 0.959572789 1.047983068 0.086247593 0.114574582 1.370784025 5508.203447 0.050410413 0.027955064 53.99877699 -1.732383924 0.08841028 FESILPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FESILPR 7 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 119.57 0.011058 113820000 158700 210950 214450 217280 221190 159080 204800 185220 262880 FALSE TRUE 148767.2503 226568.9575 219536.8553 222855.7727 203818.6296 205003.8136 174092.1413 208345.1247 219003.6297 0.679291254 1.034544303 1.002434779 1.017589402 0.930663249 0.936074958 0.794928109 0.951331834 1 17.74059526 1.983793452 22.35656564 0.885851052 0.95786813 0 0.113216572 470.4807641 649014.8056 0.042888069 0.028606047 96.3370742 -1.983793452 0.072017078 FESPATGILS(ph)PR ddPTM_SK-BR-3_Pertuzumab_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 190.24 7.24E-06 1536430000 1304542 1559065 1567741 1556360 1737159 1479540 1686105 1317683 1864300 TRUE FALSE 1222893.045 1674499.795 1604928.557 1596298.833 1600729.54 1906659.18 1433289.208 1482198.623 1553136.286 0.787370082 1.078140927 1.033346894 1.027790572 1.030643321 1.22761872 0.92283544 0.954326183 1 20.566753 1.60584254 25 0.953932468 1.039217826 0.086252221 0.107376995 0.421114764 5106.860291 0.049934011 0.02490339 40.34990717 -1.60584254 0.085285358 FESPEVAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FESPEVAER 9 0 A0A087X0X3;P52272-2;P52272 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 194.22 7.60E-05 858230000 833020 967020 947120 881750 1036700 824590 1014270 846270 962440 FALSE TRUE 780882.7652 1038619.167 969586.1337 904377.1978 955281.7638 1062635.747 862189.6295 951928.6724 801802.5464 0.973909061 1.295355286 1.209257988 1.127930064 1.191417723 1.325308521 1.075314157 1.187235781 1 19.61288747 0.557853585 0.941411404 1.00058403 1.19427793 0.202741303 0.102198889 2.002691547 2.750903363 0.091140384 0.029449659 3.612880402 -0.557853585 0.193693899 FESVIHEFDPYFNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FESVIHEFDPYFNYR 15 0 P46977;A0A0C4DH80;E9PN73;E9PI32 P46977 STT3A Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A 0 63.709 0.070671 34492000 77654 135890 84190 101360 143100 87327 106010 137280 125000 FALSE TRUE 72793.77476 145951.437 86187.02656 103961.0692 131861.5032 112536.8873 90114.78465 154419.7102 104136.6925 0.699021383 1.401537091 0.827633608 0.998313531 1.266234793 1.080665082 0.865350939 1.482855913 1 16.66811896 FEVGDIMLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FEVGDIMLIR 10 0 P00491;G3V5M2;G3V393 P00491 PNP Purine nucleoside phosphorylase 0 ; 175.51 6.46E-06 256040000 344030 599430 303670 322540 654680 291600 358190 537020 335550 FALSE TRUE 322497.7764 643812.4209 310873.1958 330816.9225 603264.0737 375780.1863 304482.7348 604068.1291 279544.5373 1.153654368 2.30307638 1.112070366 1.183414012 2.158024906 1.344258736 1.089210105 2.160901211 1 18.09271863 -3.055325163 0.242511891 3.82E-32 1.616882384 0.088498631 0.485607534 146.0156652 3.386139143 77.61198369 0.741404174 0.000880389 3.055325163 1.616882384 FEWELPLDEAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FEWELPLDEAQR 12 0 Q9BSJ8-2;Q9BSJ8 Q9BSJ8-2 ESYT1 Extended synaptotagmin-1 0 ;;; 208.33 1.58E-07 113513000 215380 246519 210283 216017 280259 200018 263419 247749 239190 FALSE TRUE 201899.7503 264771.5233 215271.0121 221560.3619 258248.5887 257759.9496 223921.7664 278681.008 199267.6438 1.013208901 1.32872311 1.080310922 1.111873246 1.29598857 1.293536395 1.123723662 1.398526137 1 17.60434794 2.751183106 24.38096462 1.226941006 1.157191706 0.087236967 0.132881946 1630.631168 3149644.187 0.037350688 0.039364264 563.8753456 -2.751183106 -0.0697493 FFAPECGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FFAPECGR 8 0 Q96HC4;Q96HC4-4;Q96HC4-7;H0Y8Y3;A0A0A0MSP3;Q96HC4-6 Q96HC4;Q96HC4-6 PDLIM5 PDZ and LIM domain protein 5 0 ; 95.352 0.022592 332740000 426850 540980 462440 518650 571660 439000 570820 470540 581720 FALSE TRUE 400134.2204 581034.7221 473409.2952 531959.4371 526764.1296 565732.1734 485230.8402 529287.9548 484627.1739 0.825653702 1.198931371 0.976852559 1.097667373 1.086947158 1.167355451 1.00124563 1.092154925 1 18.88651578 4.757109037 24.66836383 1.077371927 0.82565344 0.553772722 0.071088083 2519.787624 3351112.549 0.015609077 0.521240094 57162.21335 -4.757109037 -0.251718487 FFDANYDGKDYDPVAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FFDANYDGKDYDPVAAR 17 1 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ;; 164.2 2.39E-09 1287890000 3758740 3529920 3607750 3491680 4239430 2535159 4489270 3250480 5551140 FALSE TRUE 3523487.173 3791278.95 3693327.534 3581282.42 3906482.269 3267018.248 3816145.64 3656309.583 4624618.872 0.761897849 0.819803546 0.798623116 0.774395149 0.844714424 0.706440539 0.825180571 0.790618575 1 22.14090304 -0.101497643 1.456053366 1.000354316 0.792844933 0.746338393 0.038404935 15.01394511 18.89863235 0.057366198 0.009366875 0.79159375 0.101497643 -0.207509383 FFDDDLLVSTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FFDDDLLVSTSR 12 0 O43924 O43924 PDE6D "Retinal rod rhodopsin-sensitive cGMP 3,5-cyclic phosphodiesterase subunit delta" 0 82.417 0.034919 13889000 27582 34893 32387 38490 36330 26136 35080 34756 31510 FALSE TRUE 25855.69186 37476.51403 33155.23493 39477.71856 33476.78835 33681.03892 29820.07967 39095.36311 26250.77744 0.984949566 1.427634443 1.263019163 1.503868549 1.275268454 1.283049197 1.135969391 1.489303058 1 14.68007253 1.972778026 12.03241424 1.220010922 1.31244687 0.035149737 0.179188396 4.089315206 1799.992226 0.066039245 0.043094599 93.92431281 -1.972778026 0.092435947 FFDEESYSLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FFDEESYSLLR 11 0 A6NLM8;P51571 A6NLM8 SSR4 Translocon-associated protein subunit delta 0 ; 197.27 1.34E-07 160211000 308480 438950 329450 354600 489680 277740 396100 428670 383850 FALSE TRUE 289172.7875 471450.3147 337264.7096 363699.6363 451222.5081 357919.0293 336708.4822 482190.3931 319782.9552 0.904278301 1.474282187 1.054667561 1.137332776 1.411027388 1.119256119 1.052928171 1.507867712 1 18.28673352 -2.06573863 2.914387763 0.679111486 1.206425963 0.097527036 0.198531742 9140262.845 34765672.61 20779804.41 0.043112077 0.008595307 2.06573863 0.527314477 FFDHSGTLVMDAYEPEISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FFDHSGTLVMDAYEPEISR 19 0 E9PL01;A0A087WUC6;E9PI68;Q15005;E9PRB9 E9PL01 SPCS2 Signal peptidase complex subunit 2 0 ; 153.36 4.65E-08 197278000 152815 196312 164443 155923 219537 151102 207473 187267 172865 FALSE TRUE 143250.5819 210847.1447 168343.6656 159924.2482 202295.4496 194722.6945 176364.3497 210647.6972 144012.7147 0.994707878 1.464087009 1.168950019 1.110487004 1.40470548 1.352121546 1.224644296 1.462702078 1 17.13583667 -1.23682174 4.439887094 0.999885845 1.279203127 0.235689229 0.154004669 0.000155334 2.67E-05 0.133101592 0.031359568 0.057966658 1.23682174 0.279317282 FFDS(ph)EDEDFEILSL ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FFDSEDEDFEILSL 14 0 Q9Y4P1;Q9Y4P1-4 Q9Y4P1 ATG4B Cysteine protease ATG4B 1 FFDS(1)EDEDFEILSL;FFDS(1)EDEDFEILSL 140.75 1.03E-05 106266000 307166 339288 344233 331788 370627 306040 384819 300037 438820 TRUE FALSE 287941.0284 364409.2365 352398.3693 340302.2418 341519.4505 394388.7799 327118.9634 337497.2799 365578.1071 0.787632035 0.996802679 0.96394823 0.930860561 0.934190106 1.078808529 0.894799106 0.923187886 1 18.47982015 4.745161105 24.83026523 0.963926547 0.787631947 0.538954152 0.051635328 534.4777317 2010583.977 0.011563183 0.110420841 55611.05122 -4.745161105 -0.1762946 FFEDLEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 FFEDLEQR 8 0 Q5VV41;Q5VV41-2;B0QZD3 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 0 ;;;; 134.81 0.0020022 436091000 907800 1101540 1081320 1046860 1229940 897350 1160850 1059320 1118750 FALSE TRUE 850982.4185 1183099.168 1106969.421 1073724.2 1133345.474 1156400.378 986791.3193 1191578.434 932023.3976 0.913048343 1.26938784 1.187705613 1.152035671 1.216005389 1.240741789 1.058762389 1.278485537 1 19.83000665 -1.769449558 2.597830604 0.956672965 1.172107161 0.179297947 0.109555843 14470009.68 11268245.13 4009039.742 0.024301884 0.017003974 1.769449558 0.215434196 FFEDYGLFMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FFEDYGLFMR 10 0 Q12931-2;Q12931;I3L0K7 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ; 191.78 1.76E-06 314810000 272800 461680 333210 337040 513170 343390 279080 411530 392550 FALSE TRUE 255725.935 495863.2676 341113.8986 345689.017 472867.6982 442521.1185 237234.5449 462910.4264 327030.869 0.781962681 1.516258294 1.043063303 1.057053171 1.44594209 1.353147854 0.725419425 1.415494592 1 18.3190673 FFEEVLLFEDELHDHGVSSLSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FFEEVLLFEDELHDHGVSSLSVK 23 0 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 157.85 1.17E-09 36380000 40323 44973 45495 48275 46716 34580 52881 41767 37212 FALSE TRUE 37799.25541 48302.84771 46574.16288 49513.81823 43047.1138 44562.68464 44951.98497 46981.70189 31001.0768 1.219288467 1.558102256 1.502340167 1.597164465 1.388568342 1.437456025 1.450013664 1.515486129 1 14.92003071 -1.597450312 2.889896366 0.967703498 1.470931579 0.654146776 0.10444095 16460147.38 16877878.46 4046034.352 0.023712965 0.025266768 1.597450312 0.503228081 FFEHFIEGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FFEHFIEGGR 10 0 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8;F5H3F0;Q96FW1-2 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ;;;;; 254.42 4.15E-17 2855260000 2245101 3060028 2446164 2573811 3165885 1829414 2463244 2756951 2813101 FALSE TRUE 2104584.136 3286595.657 2504188.165 2639859.348 2917249.163 2357536.124 2093903.43 3101162.401 2343576.27 0.898022464 1.402384765 1.068532822 1.126423484 1.244785246 1.005956646 0.893465025 1.323260711 1 21.16028032 2.225503981 24.9799268 1.028906257 1.170891938 0.050706503 0.167435854 436.0484953 834241.6073 0.05837652 0.043374171 168.0753333 -2.225503981 0.141985681 FFEHHPIPQEEASLAETALTS(ph)GSSPSAPASDSIGPQILTSPSPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FFEHHPIPQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSK 45 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5 P15056 BRAF Serine/threonine-protein kinase B-raf 1 FFEHHPIPQEEAS(0.015)LAET(0.056)ALT(0.056)S(0.217)GS(0.217)S(0.217)PS(0.217)APAS(0.004)DS(0.001)IGPQILTSPSPSK 55.767 0.023819 191370000 37417 32517 34666 35334 37415 27478 42205 34267 34098 TRUE FALSE 35075.13676 34924.59251 35488.29389 36240.73026 34476.57682 35410.45253 35876.75206 38545.31038 28406.82352 1.234743362 1.229443781 1.249287653 1.275775528 1.21367237 1.246547419 1.262962472 1.356903223 1 14.7939499 -1.792125928 2.841738123 0.934702773 1.254468804 0.811434255 0.039141079 18222054.03 12549037.38 8175869.533 0.008867389 0.016138905 1.792125928 0.31976603 FFEHHPIPQEEASLAETALTSGS(ph)SPSAPASDSIGPQILTSPSPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FFEHHPIPQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSK 45 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5 P15056 BRAF Serine/threonine-protein kinase B-raf 1 FFEHHPIPQEEASLAETALT(0.015)S(0.089)GS(0.404)S(0.404)PS(0.089)APASDSIGPQILTSPSPSK 146.37 5.42E-14 134070000 43833 40264 40945 47358 45735 46920 54996 39518 47345 TRUE FALSE 41089.57077 43245.18845 41916.23474 48573.28646 42143.15759 60465.04232 46749.86036 44451.90929 39442.81364 1.041750499 1.09640222 1.062709043 1.231486346 1.068462255 1.532979946 1.185256731 1.126996408 1 15.26747485 3.23973759 24.97993044 1.216664512 1.072657839 0.128924231 0.141353546 49.28399016 1045976.789 0.03720552 0.047701559 1736.751131 -3.23973759 -0.144006673 FFEVILIDPFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FFEVILIDPFHK 12 0 P61313;A0A2R8YEM3;E7EQV9;E7ENU7 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 185.25 1.33E-05 2392000000 5079600 5001800 5223900 5026900 5588800 4143100 6198900 4910900 4711400 FALSE TRUE 4761676.903 5372138.476 5347813.375 5155898.765 5149878.192 5339145.712 5269432.493 5524036.675 3925036.903 1.213154684 1.368684832 1.362487413 1.31359243 1.312058541 1.360279112 1.342517949 1.407384647 1 21.90427479 -0.727070752 6.328193171 0.999999997 1.340454446 0.806419086 0.051523952 1.34E-09 4.24E-10 0.04500771 0.010608419 0.187468907 0.727070752 0.340454449 FFFDPSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FFFDPSAR 8 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 112.37 0.0071052 486780000 2198700 2956900 2557100 2675300 3004000 2047610 2870600 2575100 2514000 FALSE TRUE 2061087.292 3175831.953 2617755.62 2743952.727 2768077.958 2638721.767 2440180.179 2896606.903 2094397.159 0.984095726 1.516346572 1.249885013 1.310139634 1.321658572 1.259895601 1.165099069 1.383026563 1 20.99810361 -3.786348735 0.288712004 3.30E-08 1.306322395 0.246225642 0.141036831 140.408374 2.547339733 83.44241416 0.140464659 0.00016355 3.786348735 1.306322361 FFGNS(ph)WAETYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FFGNSWAETYR 11 0 O43488;H3BLU7 O43488 AKR7A2 Aflatoxin B1 aldehyde reductase member 2 1 FFGNS(1)WAETYR;FFGNS(0.996)WAET(0.004)YR 159.66 2.98E-05 66585000 92885 109007 106616 118313 117954 93285 121047 97117 119023 TRUE FALSE 87071.49365 117077.9917 109144.9819 121349.1119 108690.3686 120214.8651 102897.1261 109242.2712 99157.29238 0.878114878 1.180730019 1.100725718 1.22380421 1.09614095 1.212365347 1.037716174 1.10170688 1 16.59743126 -0.90252537 5.323456301 0.999999842 1.113085093 0.091938638 0.098967967 1.69E-07 3.48E-08 0.084689846 0.019961559 0.125162616 0.90252537 0.113085251 FFHLAFEEEFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FFHLAFEEEFGR 12 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ; 155.15 6.11E-05 324810000 369070 479780 430410 419900 514130 311040 431100 453790 457020 FALSE TRUE 345970.5675 515303.4104 440619.5285 430675.3449 473752.3037 400832.1987 366460.5571 510446.6804 380740.4095 0.908678351 1.353424532 1.157270196 1.131152182 1.244292152 1.052770309 0.962494518 1.340668518 1 18.53844817 2.225013594 24.89179871 1.071458653 1.183985848 0.031367886 0.149610013 472.8588902 868842.3522 0.05188698 0.038533932 167.8856569 -2.225013594 0.112527195 FFIGQFSDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FFIGQFSDDR 10 0 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;P52701-4 P52701 MSH6 DNA mismatch repair protein Msh6 0 208.35 2.68E-07 94000000 165860 251120 187490 197020 251690 144940 192660 254790 192820 FALSE TRUE 155479.1187 269713.1861 191937.3513 202075.8668 231923.2827 186781.8251 163772.4216 286601.0924 160637.0963 0.967890495 1.679021797 1.194850727 1.257965136 1.443771632 1.162756483 1.019518065 1.784152596 1 17.29344557 3.730746949 24.90260288 1.253219637 1.393056747 0 0.281087545 534.987956 3674452.451 0.06675432 0.114649964 5379.562397 -3.730746949 0.13983711 FFMT(ph)PPR ddPTM_SK-BR-3_Pertuzumab_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 109.11 0.079388 136614000 338930 380180 406050 368390 446810 382750 477200 432220 452880 TRUE FALSE 317716.9763 408328.9228 415681.6978 377843.5111 411719.3449 493243.7116 405648.2901 486183.6184 377291.4023 0.842099699 1.082264055 1.101752373 1.001463348 1.091250271 1.307328258 1.075159115 1.288615684 1 18.5253197 2.47037282 24.93003973 1.172090612 1.036375055 0.293272792 0.11363682 218.1616361 805923.625 0.03569592 0.02993126 295.3743781 -2.47037282 -0.135715557 FFPASADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FFPASADR 8 0 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ;;; 168.45 0.00071364 672890000 461161 1348750 400057 371913 1309690 289854 408288 1018600 926550 FALSE TRUE 432297.7562 1448612.853 409546.541 381456.9172 1206832.23 373530.1444 347069.0048 1145774.452 771902.8193 0.560041686 1.876677759 0.53056749 0.494177386 1.563450995 0.483908253 0.44962785 1.484350651 1 19.5580597 3.875824615 7.157493191 0.806247996 1.296192142 0.0676033 0.511476708 0.411424161 25.13918626 0.121586051 0.220818989 7513.194209 -3.875824615 0.489944146 FFPKPYDDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FFPKPYDDSR 10 1 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 ; 106.4 0.0022085 519640000 1627150 1808340 1607590 1755190 2131700 1281780 2213600 1911410 1965870 FALSE TRUE 1525309.586 1942231.375 1645722.794 1800231.147 1964284.881 1651809.078 1881691.23 2150053.746 1637753.597 0.931342535 1.185911836 1.004865932 1.099207567 1.19937754 1.008582171 1.14894648 1.312806609 1 20.64328689 2.999451241 24.99623347 1.13464815 1.064868857 0.12042456 0.108647524 50.98991012 2322857.028 0.029277737 0.034623283 998.7372329 -2.999451241 -0.069779293 FFPLESWQIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FFPLESWQIGK 11 0 P30046;J3KQ18;H7C342 P30046 DDT D-dopachrome decarboxylase 0 179.8 1.62E-05 160010000 270210 267420 256880 226940 316310 186830 315060 293700 368240 FALSE TRUE 253298.0384 287220.0551 262973.3149 232763.6646 291468.2885 240764.7881 267819.6779 330369.0915 306778.3651 0.825671127 0.936246123 0.857209454 0.758735593 0.950094015 0.784816713 0.873007058 1.076898273 1 18.22683722 1.260124026 12.01585839 1.038434842 0.860380974 0.60384233 0.061622505 0.404439479 225.7608778 0.038935659 0.0138833 18.20220602 -1.260124026 -0.178053868 FFQGS(ph)QEFLASASASAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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(1)QEFLASASASAER;FFQGS(1)QEFLASASASAER;FFQGS(1)QEFLASASASAER 266.45 3.98E-31 323938000 314592 335005 325696 321796 334657 284380 393640 330315 356516 TRUE FALSE 294902.2483 359809.1188 333421.6629 330053.8302 308374.3892 366475.8895 334617.3364 371555.5549 297011.1764 0.992899499 1.211432927 1.122589617 1.11125054 1.038258536 1.233879122 1.126615303 1.250981729 1 18.18015769 2.234478805 24.99973458 1.161993282 1.115573256 0.065631583 0.088733913 311.963344 1910643.71 0.029670735 0.022727703 171.5847969 -2.234478805 -0.046420026 FFQTSGLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FFQTSGLSK 9 0 P0CE72;P0CE71 P0CE72 OCM;OCM2 Oncomodulin-1;Putative oncomodulin-2 0 61.78 0.050272 410710000 385310 2074600 1369700 1886100 1944500 1560700 1226300 1428800 1231100 FALSE TRUE 361194.1349 2228205.543 1402189.931 1934500.519 1791786.814 2011248.754 1042427.699 1607188.825 1025621.457 0.352171001 2.172541855 1.367161267 1.886173994 1.747025476 1.961004951 1.016386399 1.567039003 1 19.96806692 1.719093645 12.68301105 1.222126863 1.642650754 0.102135976 0.516872954 0.217731647 105.4906598 0.216893945 0.118965974 52.37133505 -1.719093645 0.420523891 FFSDCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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" 0 114.54 0.058621 643100000 1854000 1729900 1766100 1699900 2059000 1602000 2401100 1777100 2290400 FALSE TRUE 1737961.449 1857983.596 1807992.726 1743522.312 1897294.446 2064471.394 2041077.346 1998974.847 1908117.443 0.910825199 0.973726016 0.947526963 0.913739517 0.994327918 1.081941471 1.069681194 1.047616253 1 20.86371854 2.447907064 4.395530029 1.057388918 0.944883659 0.777061865 0.028285107 0.085807246 3.886628874 0.00939214 0.007994539 280.4833361 -2.447907064 -0.11250526 FFSGYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FFSGYGR 7 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;; 133.47 0.0076042 1309485000 2625001 3094984 2713439 2629987 3539060 2196698 3315101 3168741 4285835 FALSE TRUE 2460706.873 3324139.836 2777803.054 2697476.919 3261116.503 2830849.052 2818032.381 3564365.289 3570501.451 0.68917683 0.931000836 0.777986816 0.755489658 0.913349721 0.792843552 0.789253952 0.998281429 1 21.76769527 1.233251257 24.98868751 0.99914086 0.816132892 0.557228998 0.070838375 100.5021855 472991.3785 0.056360622 0.015728762 17.11004916 -1.233251257 -0.183007968 FFSLSSVDKLEQIYECTDTEDVCIVER ddPTM_SK-BR-3_Pertuzumab_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 0 123.64 7.63E-05 28865000 26533 21620 23015 23118 33058 17664 35175 23312 26687 FALSE TRUE 24872.34689 23220.7673 23560.92667 23711.24702 30461.75803 22763.31005 29900.8353 26222.55452 22232.7673 1.118724744 1.044438912 1.059738824 1.066500031 1.370128946 1.0238631 1.344899396 1.179455268 1 14.44039991 2.915920656 25 1.204486021 1.065475652 0.167091011 0.118100772 108.7650611 32338.42864 0.031500809 0.033411644 823.987561 -2.915920656 -0.139010369 FFT(ph)TPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 FFTTPSK 7 0 O76021;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 FFT(0.872)T(0.128)PSK;FFT(0.869)T(0.131)PSK;FFT(0.898)T(0.102)PSK;FFT(0.87)T(0.13)PSK;FFT(0.734)T(0.266)PSK 157.2 0.016678 2092230000 10002410 8724780 9286680 7900340 9937400 4878830 12760100 7082920 15586800 TRUE FALSE 9376377.013 9370771.789 9506964.435 8103076.1 9156956.69 6287269.02 10846841.46 7967238.153 12985262.39 0.722078364 0.721646703 0.732134951 0.624020975 0.705180721 0.484184981 0.835319391 0.613560043 1 23.63037183 -1.357615963 4.553713744 1.000368914 0.689430583 0.538055345 0.092867614 2832085282 399517828.4 11173031.23 0.019613965 0.043891865 1.357615963 -0.310938331 FFTDYGCDMEQGSVCTYHPGAVHCVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FFTDYGCDMEQGSVCTYHPGAVHCVR 26 0 Q9UGT4 Q9UGT4 SUSD2 Sushi domain-containing protein 2 0 ; 170.56 4.00E-12 197804000 28597 34275 29838 33293 45046 25756 37380 35031 41833 FALSE TRUE 26807.16482 36812.75666 30545.77145 34147.35474 41508.26887 33191.33909 31775.21602 39404.69746 34850.80205 0.769197931 1.056295824 0.876472553 0.979815463 1.19102765 0.952383794 0.911749921 1.13066831 1 15.08890424 4.747832711 24.66411602 0.99753069 0.769197786 0.379636339 0.096027558 1192.870353 3172998.85 0.022225188 0.277937046 55954.20263 -4.747832711 -0.228332905 FFTEEVDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FFTEEVDSR 9 0 Q9H845 Q9H845 ACAD9 "Acyl-CoA dehydrogenase family member 9, mitochondrial" 0 ; 110.22 0.0054034 106694000 179654 170480 161982 144294 212769 166511 160117 178450 293680 FALSE TRUE 168409.7768 183102.5166 165824.2895 147996.8283 196058.981 214580.0226 136108.9423 200729.8753 244662.9108 0.688333905 0.748386897 0.677766356 0.604900955 0.801343287 0.877043529 0.556312119 0.820434428 1 17.90043589 0.991690012 24.49113735 1.000000011 0.708051317 0.519651184 0.09059032 199.7253152 588631.3821 0.082430033 0.020607508 9.810474468 -0.991690012 -0.291948695 FFTESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 FFTESR 6 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;;;; 151.14 0.024247 5443100000 5379960 6859570 6406240 6488070 7084030 5590590 6817620 5746180 6983990 FALSE TRUE 5043237.907 7367459.7 6558199.038 6654564.86 6527678.859 7204502.577 5795381.173 6463603.222 5818316.951 0.866786383 1.266252726 1.12716428 1.143726771 1.121918746 1.238245121 0.996058005 1.110906002 1 22.47217046 1.693482935 10.98987094 1.041077086 1.143702336 0.120510085 0.110566509 0.203399933 39.07753449 0.047241194 0.025682044 49.37225174 -1.693482935 0.10262525 FFTGDVFGYHGYTFANLGEHEFVEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FFTGDVFGYHGYTFANLGEHEFVEEK 26 0 Q9UBE0;M0QX65;B3KNJ4;Q9UBE0-2;Q9UBE0-3;A0A590UK93;A0A590UKC5;M0QYM8;M0R054 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 148.09 1.03E-07 24712000 52738 49666 45786 38504 57951 35311 60185 49745 47038 FALSE TRUE 49437.22272 53343.32232 46872.06554 39492.07783 53399.76222 45504.71247 51160.81798 55955.77275 39187.05392 1.261570283 1.361248601 1.196110982 1.007783793 1.36268887 1.161218002 1.305554076 1.427914761 1 15.25808949 3.926047314 5.354497517 1.222028777 1.313673125 0.080065707 0.138934544 0.504797352 32.23110245 0.033374184 0.062899276 8434.266403 -3.926047314 0.091644348 FFTT(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FFTTPSK 7 0 O76021;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 FFT(0.372)T(0.627)PSK 120.15 0.051653 206140000 1269600 1186500 1188100 1050700 1279200 593580 1636600 884380 1997800 TRUE FALSE 1190138.002 1274349.695 1216282.293 1077662.741 1178736.792 764936.91 1391207.023 994796.7898 1664354.274 0.715074922 0.765672138 0.730783291 0.647496004 0.708224691 0.459599811 0.835883949 0.597707354 1 20.66653113 -1.72276152 5.928078435 1.006940338 0.694597863 0.485332657 0.102066501 0.008664064 0.000405192 0.091455823 0.021266642 0.01893383 1.72276152 -0.312342475 FFTVEPQHIPCVLMAFLDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FFTVEPQHIPCVLMAFLDHR 20 0 O43592 O43592 XPOT Exportin-T 0 149.94 5.39E-08 23499000 81022 128270 86761 87116 130670 60679 85733 111890 60993 FALSE TRUE 75950.97765 137767.2443 88819.01189 89351.54405 120407.7053 78196.04226 72878.13256 125859.7128 50812.87427 1.494719178 2.71126651 1.747962759 1.758443019 2.369629883 1.538902166 1.434245427 2.476925673 1 15.63290645 -1.818766612 0.190677485 3.05E-11 2.212020296 0.248794992 0.460481679 39.65733642 1.191297396 20.33572577 1.377109432 0.015178658 1.818766612 2.212020296 FFVGGNWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FFVGGNWK 8 0 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 0 ; 104.11 0.010802 775550000 1167150 2302800 1281800 1189770 2590600 1169770 1333030 2041440 2561500 FALSE TRUE 1094100.165 2473301.708 1312204.901 1220301.512 2387144.726 1507463.609 1133154.527 2296318.278 2133969.102 0.512706657 1.15901477 0.614912793 0.571845914 1.118640717 0.706413044 0.531007935 1.076078503 1 21.02510786 -0.795059468 7.689597906 0.999905156 0.785313365 0.06811342 0.248354557 0 0 0.224302257 0.052868549 0.160302587 0.795059468 -0.214591791 FFYSDQNVDSRDPVQLNLLYVQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FFYSDQNVDSRDPVQLNLLYVQAR 24 1 Q9Y490;Q9Y4G6 Q9Y490;Q9Y4G6 TLN1;TLN2 Talin-1;Talin-2 0 126.26 8.48E-05 115400000 111690 106490 110370 116200 133900 92982 133330 117900 100030 FALSE TRUE 104699.5223 114374.6304 112988.0285 119181.8887 123384.0341 119824.394 113338.4043 132620.0745 83334.34678 1.256378988 1.372478874 1.355839853 1.430165272 1.480590403 1.437875241 1.360044311 1.59142154 1 16.34662361 -1.061924492 4.553699339 0.999978444 1.402972748 0.68100448 0.088178501 1.79E-05 3.69E-06 0.079269613 0.018683028 0.086711262 1.061924492 0.402994304 FGAVFLWDSGSSVGEITGHNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FGAVFLWDSGSSVGEITGHNK 21 0 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ;; 269.61 9.65E-38 261446000 764177 791920 839510 851150 905887 640721 963513 740433 950419 FALSE TRUE 716348.5257 850554.5808 859423.5736 872991.95 834742.2892 825686.7515 819043.1705 832877.6899 791787.929 0.904722716 1.074220192 1.085421414 1.102557791 1.05424983 1.042813007 1.034422401 1.051894907 1 19.59475455 -0.396011373 9.800434057 0.99999744 1.051025408 0.046872054 0.05388816 0 0 0.048617872 0.011459342 0.40178029 0.396011373 0.051027968 FGAVWTGDNTAEWDHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FGAVWTGDNTAEWDHLK 17 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 334.04 4.13E-72 1659760000 2333400 2382300 2254800 2203000 2594000 1568950 2584400 2164810 1749150 FALSE TRUE 2187356.659 2558687.971 2308284.921 2259532.71 2390277.704 2021880.395 2196893.212 2435091.294 1457205.565 1.501062521 1.755886769 1.584048933 1.550592973 1.640316069 1.387505266 1.507606933 1.67106917 1 20.47477298 -2.78482676 0.263494334 4.38E-18 1.641977223 0.736868562 0.10619157 25.79478018 0.717753303 14.7615751 0.136409608 0.001641244 2.78482676 1.641977223 FGDES(ph)PLLTMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FGDESPLLTMR 11 0 H0YJ41;Q9P203-5;Q9P203 H0YJ41 BTBD7 BTB/POZ domain-containing protein 7 1 FGDES(1)PLLTMR 85.522 0.011111 0 27944 29099 26993 28103 28840 22598 28892 20838 26224 TRUE FALSE 26195.03492 31253.52024 27633.28671 28824.17056 26575.02273 29121.67575 24559.91282 23439.67017 21847.04499 1.19901959 1.430560529 1.264852374 1.319362439 1.216412689 1.332980079 1.124175505 1.072898883 1 14.41515053 1.483741519 1.349713044 1.002374244 1.310955986 0.716037489 0.068476505 0.190357116 0.663000349 0.056486249 0.018976448 30.46081501 -1.483741519 0.308581741 FGDILHVINASDDEWWQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FGDILHVINASDDEWWQAR 19 0 A0A590UJD9;A0A0C4DFT3;A0A590UJ18;A0A590UK02;E7EQD7;A0A590UK70;A0A590UJ08;Q12959-4;Q12959-2;A0A590UJC5;A0A590UJL2;A0A590UJ25;Q12959;Q12959-3;Q12959-5;Q12959-7;Q12959-6;A0A590UKA8;A0A590UJR5;A0A590UJ68;A0A590UJS9;A0A590UK48;A0A590UJ81;C9JUA9;Q12959-8;A0A590UJX2;A0A590UJ64;A0A590UK81;A0A590UJ29;Q12959-9;A0A590UJR4 A0A590UJD9;A0A590UJ08;Q12959 DLG1 Disks large homolog 1 0 ; 219.66 3.08E-19 315790000 558620 588240 599940 546140 716710 505690 628540 598440 776920 FALSE TRUE 523656.9714 631793.9017 614170.8601 560154.877 660422.4877 651674.4938 534296.2621 673156.5513 647247.0329 0.809052718 0.976124833 0.948897143 0.865442171 1.020356145 1.00684045 0.825490477 1.040030339 1 19.30395692 FGDRFPAMSDAYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FGDRFPAMSDAYDR 14 1 P00491;G3V5M2 P00491 PNP Purine nucleoside phosphorylase 0 ;;; 204.82 1.20E-08 1184450000 1480700 1190090 1482170 1204090 1406390 1319230 1647760 979080 1317480 FALSE TRUE 1388025.63 1278205.502 1517327.772 1234988.988 1295937.803 1700070.285 1400693.685 1101320.293 1097584.077 1.264618957 1.164562724 1.382425096 1.125188506 1.18071848 1.548920325 1.276160719 1.003404037 1 20.06590003 1.23957523 10.01465318 1.001139985 1.28171086 0.475745176 0.120314687 0.074035503 147.8982916 0.091282377 0.028586639 17.36101971 -1.23957523 0.280570875 FGDSHHSHAGGHCGGCCH ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FGDSHHSHAGGHCGGCCH 18 0 F5H2C9;Q86UY6-4;Q86UY6-3;Q86UY6 F5H2C9 NAA40 N-alpha-acetyltransferase 40 0 ; 85.976 0.0012283 192121000 22209.4 107951 97776 87371 112279 173574 80198 101692 92934 FALSE TRUE 20819.3533 115943.8044 100095.2929 89613.08778 103461.0603 223681.9961 68173.05442 114388.4701 77422.71502 0.268904976 1.497542476 1.292841421 1.157452148 1.336314029 2.889100389 0.880530402 1.477453613 1 16.24046928 2.46845018 24.99431213 1.600783775 1.175756879 0.114256933 0.623132435 471.5395545 1359198.375 0.202347023 0.169536544 294.0696332 -2.46845018 -0.425026896 FGDYNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FGDYNK 6 0 P15311;E7EQR4 P15311 EZR Ezrin 0 111.81 0.064042 373430000 1012500 877980 905470 877470 1096200 697370 1014100 795500 1007200 FALSE TRUE 949129.4324 942986.5527 926948.176 899987.3658 1010108.874 898689.3981 862045.1194 894819.9261 839091.8132 1.13113895 1.123818083 1.104704111 1.07257317 1.203812095 1.071026298 1.02735494 1.066414798 1 19.67846915 2.0077403 24.98278742 1.038019657 1.122546563 0.594373184 0.036302342 123.3687328 398186.1347 0.012467677 0.009192127 101.7982471 -2.0077403 0.084526907 FGEEIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FGEEIAR 7 0 Q8WUM4;Q8WUM4-2;F8WDK9 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;; 132.09 0.0079152 807860000 1370730 1301670 1366700 1377210 1371060 1104390 1572100 1168110 1392330 FALSE TRUE 1284938.456 1398047.001 1399118.769 1412551.54 1263382.478 1423209.465 1336378.2 1313951.105 1159941.128 1.107761786 1.205274102 1.206198087 1.217778649 1.089178104 1.226966981 1.152108643 1.13277396 1 20.14562015 0.661975826 1.156325897 0.99987984 1.181981245 0.579204422 0.045869125 0.726059482 1.560938564 0.039981039 0.0123448 4.591724534 -0.661975826 0.182101405 FGEENIEVYHSYFWPLEWTIPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FGEENIEVYHSYFWPLEWTIPSR 23 0 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 ; 198.99 2.69E-24 508270000 470940 516610 398260 350660 602110 330110 473360 487520 379820 FALSE TRUE 441464.7061 554860.3419 407706.9153 359658.5293 554822.7094 425407.3981 402384.0625 548387.9452 316425.5883 1.395161208 1.753525513 1.288476439 1.136629093 1.753406583 1.344415287 1.271654624 1.733070793 1 18.27150674 -1.845255668 2.54528583 0.817897679 1.451133879 0.301099664 0.219697579 31808114.62 20155411.65 35261055.91 0.050093133 0.01428053 1.845255668 0.6332362 FGEILKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FGEILKR 7 1 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZHJ1;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZGZ8 P55263-3 ADK Adenosine kinase 0 92.925 0.024552 374820000 425960 493370 448150 460760 513270 374160 521530 392200 564410 FALSE TRUE 399299.924 529899.6282 458780.3296 472583.8817 472959.8446 482173.918 443331.4181 441167.0333 470206.3248 0.849201516 1.126951298 0.975700039 1.005056412 1.005855982 1.025451791 0.942844438 0.938241385 1 18.84293442 1.733263628 9.147497001 0.956136216 1.010893781 0.039277783 0.069567792 0.212818586 64.95704283 0.030589637 0.016454563 54.1082674 -1.733263628 0.054757565 FGESEEVEMEVES(ph)DEEDDKQEK ddPTM_SK-BR-3_Pertuzumab_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 248.47 2.14E-31 1082500000 3307730 1008230 1617420 1604540 1643130 1105670 2105990 1169970 1897350 TRUE FALSE 3100705.084 1082880.398 1655785.966 1645715.213 1514085.198 1424858.98 1790216.351 1316043.33 1580670.028 1.961639703 0.685076821 1.047521581 1.041150388 0.957875566 0.901427214 1.132568037 0.832585743 1 20.5921048 4.748174278 24.90559522 0.955585921 1.961640269 0.866388745 0.124860564 438.4597945 1135869.557 0.029568786 0.386155842 55998.22723 -4.748174278 1.006054348 FGEVVDCTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FGEVVDCTLK 10 0 Q14103-3;Q14103;H0Y8G5;H0YA96;D6RAF8;D6RD83;D6RF44;Q14103-2;Q14103-4;D6RBQ9 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 119.68 0.0015359 36914000 87485 72504 71981 78464 88124 56746 89044 70451 92569 FALSE TRUE 82009.47002 77872.2716 73688.42331 80477.51908 81203.09652 73127.64901 75692.67884 79246.96243 77118.63588 1.063419614 1.00977242 0.955520316 1.043554754 1.052963341 0.948248736 0.981509566 1.027598083 1 16.23479191 2.23713151 24.99999469 0.985711969 1.014323828 0.159589244 0.035926123 87.05752868 1522906.756 0.013635981 0.010604971 172.6360579 -2.23713151 0.028611859 FGEYNSNMS(ph)PEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FGEYNSNMSPEEK 13 0 P78316;E9PFK5;P78316-2 P78316 NOP14 Nucleolar protein 14 1 FGEYNS(0.013)NMS(0.987)PEEK 90.561 0.0072738 89758000 244000 142690 178390 166560 171780 130220 212000 142690 181930 TRUE FALSE 228728.4756 153254.9161 182621.495 170834.2116 158289.0917 167812.4001 180212.5681 160505.1606 151564.7077 1.509114352 1.011151728 1.204907777 1.127137143 1.044366424 1.107199708 1.189014058 1.058987696 1 17.20957433 4.747134206 24.93582517 1.107945842 1.509114561 0.776520498 0.069764045 498.6959261 1450397.419 0.01567118 0.18478805 55864.28005 -4.747134206 0.401168719 FGFPEGSVELYAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FGFPEGSVELYAEK 14 0 P23396;E9PPU1;F2Z2S8;H0YCJ7;H0YF32 P23396 RPS3 40S ribosomal protein S3 0 151.55 1.61E-05 90593000 112370 110810 110590 102530 122620 65425 124720 103680 116270 FALSE TRUE 105336.9623 119014.4877 113213.247 105161.0934 112989.9198 84312.13541 106019.3938 116624.6762 96863.78587 1.087475173 1.228678878 1.16878817 1.085659542 1.16648259 0.870419576 1.094520443 1.204007 1 16.56366977 2.94418562 1.65549258 1.054520108 1.177346069 0.167113056 0.096017826 0.523237772 2.896526358 0.033401415 0.038179804 879.3982957 -2.94418562 0.122825961 FGGAFCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FGGAFCR 7 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 0 110.24 0.015932 188390000 348120 376760 370760 318580 434430 282980 438970 338230 484390 FALSE TRUE 326331.7906 404655.7024 379554.6023 326755.3022 400311.6202 364671.7322 373150.5237 380458.76 403542.1797 0.808668355 1.002759371 0.940557447 0.80971784 0.991994494 0.903676866 0.924687783 0.942798 1 18.62235995 0.824889169 2.383003815 0.99995008 0.922459193 0.144764059 0.064659183 1.438365195 14.50392153 0.05721876 0.015434395 6.681733798 -0.824889169 -0.077490887 FGHEFLEFEFRPDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FGHEFLEFEFRPDGK 15 1 P61326;Q96A72;F5H6N1;P61326-2 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ;; 192.46 8.01E-08 881985000 2748844 2188051 2590245 2452586 2519470 2017659 2916684 2256842 2509936 FALSE TRUE 2576798.761 2350056.573 2651686.835 2515523.509 2321600.989 2600124.399 2479354.311 2538613.692 2091011.467 1.232321679 1.123885072 1.26813596 1.203017558 1.110276546 1.243476873 1.185720093 1.214060148 1 20.99576954 -1.552425545 2.624109745 0.986893712 1.196154295 0.614085743 0.049219794 4613551.213 4422749.284 425632.4211 0.011501847 0.028026861 1.552425545 0.209260583 FGHGSDYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FGHGSDYSR 9 0 Q9NWH9;Q9NWH9-3;H7C3F4;H0YMM0 Q9NWH9 SLTM SAFB-like transcription modulator 0 76.827 0.034331 132490000 33089 97693 63422 80649 101730 74186 66927 85561 106840 FALSE TRUE 31018.01856 104926.2914 64926.39979 82718.58988 93740.53616 95602.29389 56891.91767 96243.47919 89007.71379 0.348486858 1.178844921 0.729446888 0.92934181 1.053173171 1.074089984 0.639179631 1.081293689 1 16.44164275 4.754171854 24.60495206 0.93510999 0.348486318 0.569225711 0.166047805 1855.127756 2923815.857 0.038304382 0.935848992 56776.92316 -4.754171854 -0.586623672 FGINIPS(ph)PEHSNTIDVCNTVDIK ddPTM_SK-BR-3_Pertuzumab_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(1)PEHSNTIDVCNTVDIK 291.51 1.01E-61 224460000 375150 296190 320540 319580 369070 277300 462140 283050 370810 TRUE FALSE 351670.0312 318120.2158 328143.3602 327780.9638 340084.731 357352.0084 392846.3973 318389.4156 308919.4155 1.138387597 1.02978382 1.062229642 1.061056533 1.100884936 1.15678067 1.271679207 1.030655244 1 18.23687102 2.436463527 3.479778175 1.151940887 1.064625816 0 0.080883212 0.371448472 9.423883834 0.027707277 0.023344909 273.1892006 -2.436463527 -0.087315071 FGIYDIDNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FGIYDIDNK 9 0 Q99829;B0QZ18;F2Z2V0;A6PVH9;E7ENH5;Q5JX45;Q5JX60;Q5JX52;Q5JX44;Q5JX61;Q5JX59;Q5JX58;Q5JX56;Q5JX54;Q5JX55;E7EV27;Q5JX57 Q99829 CPNE1 Copine-1 0 99.802 0.010624 0 130980 121800 107360 126210 137650 85344 127980 108910 122000 FALSE TRUE 122782.1956 130818.1987 109906.6299 129448.7623 126839.5243 109981.4274 108790.5871 122507.6532 101637.4118 1.208041344 1.287106749 1.081359982 1.273633005 1.247960982 1.082095907 1.070379353 1.20534015 1 16.63307202 -4.999955428 0.055418729 0.256164799 1.511371078 0.424477221 0.074599443 437.2016242 1.780958502 45.02449056 8.598643816 1.00E-05 4.999955428 1.255206279 FGKPNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FGKPNKR 7 2 P51858;P51858-2;P51858-3;Q5TGJ6 P51858 HDGF;HDGFL1 Hepatoma-derived growth factor;Hepatoma-derived growth factor-like protein 1 0 59.205 0.059019 1612000000 610950 772700 644170 694460 1092300 500110 814540 900930 1133200 FALSE TRUE 572711.7301 829911.512 659450.0166 712281.0193 1006515.164 644483.6384 692407.2888 1013413.094 944061.5992 0.606646569 0.879086187 0.698524352 0.754485745 1.066154121 0.682671172 0.733434438 1.073460773 1 19.84852147 -5 0.066499675 1.787279486 0.506381278 0.272271685 0.142232502 515.9307689 2.484472906 62.10563674 8.584218787 1.00E-05 5 -1.280898208 FGLGT(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FGLGTPEK 8 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 FGLGT(1)PEK;FGLGT(1)PEK;FGLGT(1)PEK 134.57 0.0097379 624862000 1840710 1281310 1474160 1393350 1573290 1127490 1832780 1512430 1799210 TRUE FALSE 1725503.247 1376179.526 1509127.771 1429105.72 1449730.15 1452978.06 1557971.654 1701260.215 1498910.228 1.151171841 0.918120045 1.006816648 0.953429828 0.967189444 0.969356292 1.039402911 1.13499807 1 20.51548255 1.56772262 4.571159638 1.073165035 0.984731283 0.153845465 0.069497287 0.216476285 9.958178791 0.036374955 0.016078698 36.95920493 -1.56772262 -0.088433752 FGLSVGHHLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FGLSVGHHLGK 11 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ; 161.17 1.54E-05 2637000000 4621000 8544800 7326300 6899000 8057800 6267200 8909200 7561000 8563200 FALSE TRUE 4331779.859 9177465.883 7500083.296 7076040.02 7424972.892 8076438.901 7573348.169 8505007.494 7133946.6 0.607206656 1.286450039 1.051323162 0.991882953 1.040794571 1.132113731 1.061593056 1.192188275 1 22.76626899 2.263409182 22.68006762 1.098408892 1.042644245 0.040569401 0.17406031 395.4109396 360900.6243 0.056836629 0.047520437 183.4041598 -2.263409182 -0.055764648 FGNDVQHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FGNDVQHFK 9 0 P62993;J3KT38 P62993 GRB2 Growth factor receptor-bound protein 2 0 73.067 0.044971 397860000 1063200 998810 997070 935180 1199000 744710 1085100 972860 1265300 FALSE TRUE 996656.2099 1072762.932 1020720.971 959178.3021 1104835.377 959695.6876 922399.3286 1094323.713 1054113.256 0.945492531 1.017692288 0.968321919 0.909938564 1.048118284 0.910429389 0.875047651 1.038146239 1 20.00759845 FGNWLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FGNWLK 6 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 106.75 0.074111 182110000 383310 342740 329820 326550 375790 257460 381170 340900 413490 FALSE TRUE 359319.3113 368116.8262 337643.4862 334929.8258 346276.9693 331784.5225 324017.0971 383462.1154 344475.8478 1.043089998 1.068628842 0.98016592 0.972288269 1.005228586 0.963157576 0.940609042 1.11317562 1 18.39404331 3.950459157 3.653644442 0.988558701 1.055185834 0.204362138 0.046653424 0.285291884 8.096666288 0.011389634 0.023775959 8921.937103 -3.950459157 0.066627133 FGQAATMEGIGAIGGT(ph)PPAFNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 FGQAATMEGIGAIGGTPPAFNR 22 0 Q15233;Q15233-2 Q15233 NONO Non-POU domain-containing octamer-binding protein 1 FGQAATMEGIGAIGGT(1)PPAFNR;FGQAATMEGIGAIGGT(1)PPAFNR;FGQAATMEGIGAIGGT(1)PPAFNR;FGQAATMEGIGAIGGT(1)PPAFNR;FGQAATMEGIGAIGGT(1)PPAFNR;FGQAATMEGIGAIGGT(1)PPAFNR;FGQAATMEGIGAIGGT(1)PPAFNR;FGQAATMEGIGAIGGT(1)PPAFNR 333.54 8.59E-80 1621280000 2193370 2085310 2404640 2135050 2504210 2202830 2800900 2293210 3602650 TRUE FALSE 2056090.887 2239708.522 2461679.196 2189838.998 2307539.448 2838751.261 2380931.047 2579522.316 3001344.441 0.685056623 0.746235084 0.820192165 0.729619356 0.768835265 0.945826551 0.793288173 0.85945561 1 21.51717746 -4.999999999 0.040651063 2.027758589 0.207484954 0.693882196 0.053715241 463.3570171 1.406414807 57.18846255 16.88354809 1.00E-05 4.999999999 -1.820273635 FGQYNKEDPTSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FGQYNKEDPTSFR 13 1 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ; 93.649 0.0050316 655930000 1163490 1426880 1335720 1373690 1582630 971310 1786630 1235410 2155900 FALSE TRUE 1090669.238 1532527.68 1367403.909 1408941.211 1458336.624 1251711.429 1518741.418 1389653.658 1796066.362 0.60725442 0.853268962 0.76133262 0.784459439 0.811961437 0.696918252 0.845593153 0.773720664 1 20.77640923 -5 0.254734249 2.395707886 0.758154899 0.527655251 0.070531359 148.7332491 1.469249391 108.2676201 0.087882824 1.00E-05 5 -1.637552987 FGTFGGLGS(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FGTFGGLGSK 10 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 FGTFGGLGS(1)K;FGTFGGLGS(1)K 128.57 0.0034236 142740000 713450 434530 428160 414050 494760 262610 536020 303200 931290 TRUE FALSE 668796.438 466703.0533 438316.1574 424675.224 455903.5454 338421.2439 455648.7772 341055.1874 775851.6826 0.862015838 0.601536433 0.564948388 0.547366505 0.58761688 0.43619322 0.587288508 0.439588126 1 19.56542136 -1.671616088 6.327228676 1.003567997 0.573239184 0.564095844 0.116418367 0.005392005 0.000279846 0.103728139 0.02431189 0.021300211 1.671616088 -0.430328812 FGTVLTEHVAAAELGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FGTVLTEHVAAAELGAR 17 0 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 106.36 0.00075696 63331000 89061 96604 95729 92243 100260 90446 109200 90315 113370 FALSE TRUE 83486.83099 103756.6607 97999.73709 94610.11155 92385.98403 116556.2919 92826.47376 101591.0266 94447.8146 0.883946668 1.098560736 1.037607249 1.001718377 0.978169632 1.234081407 0.982833474 1.07563131 1 16.52722979 FGVEQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FGVEQDR 7 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 151.29 0.0043996 3760360000 4109070 4626350 4439260 4520920 4722720 3812690 4847040 3938530 4664370 FALSE TRUE 3851890.644 4968889.768 4544561.344 4636934.461 4351816.622 4913351.709 4120271.35 4430264.14 3885856.514 0.991259103 1.278711592 1.169513421 1.193285044 1.119911815 1.264419232 1.060325139 1.140099776 1 21.8898012 0.967676638 0.87144779 1.003314008 1.180299629 0.230351734 0.086109389 0.78865993 1.298519497 0.07340439 0.025787135 9.282749641 -0.967676638 0.176985621 FGVEQDVDMVFASFIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FGVEQDVDMVFASFIR 16 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 76.728 0.060256 305230000 191660 160360 191250 195220 243080 161890 158140 142120 202380 FALSE TRUE 179664.3427 172233.2213 195786.5403 200229.6757 223989.4773 208625.0149 134428.3751 159863.9948 168601.4706 1.065615514 1.021540445 1.161238628 1.187591514 1.328514375 1.2373855 0.797314369 0.948176753 1 17.36325759 1.743508296 18.75211555 0.904967275 1.156542157 0.593847363 0.097796802 0.134509636 504.993207 0.048675154 0.026952927 55.39981266 -1.743508296 0.251574883 FGVLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FGVLFR 6 0 Q9P1F3 Q9P1F3 ABRACL Costars family protein ABRACL 0 ; 108.69 0.070243 267850000 403140 623580 448380 437190 620190 384180 513720 549670 636280 FALSE TRUE 377908.187 669750.512 459015.7853 448409.0356 571482.7791 495086.5294 436692.4551 618297.5095 530080.7575 0.712925685 1.26348769 0.865935575 0.845925888 1.078105121 0.933983214 0.823822501 1.166421344 1 19.01585264 3.748540353 24.44358686 0.943351641 1.038686286 0 0.169195246 977.3893793 1115393.082 0.039486651 0.071094419 5604.544907 -3.748540353 0.095334645 FGVQMDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FGVQMDR 7 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 113.89 0.014024 330880000 356690 471900 396630 381400 523120 301630 423690 419050 502060 FALSE TRUE 334365.4096 506839.967 406038.2509 391187.3697 482036.2654 388705.6844 360161.6178 471369.3149 418262.9426 0.799414377 1.211773541 0.970772712 0.935266623 1.152471846 0.929333309 0.861088997 1.126968868 1 18.67405066 FGVQSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FGVQSER 7 0 Q14247 Q14247 CTTN Src substrate cortactin 0 120.92 0.010442 246260000 187340 281710 211550 216720 281420 192680 211210 242280 268690 FALSE TRUE 175614.7238 302568.1015 216568.0659 222281.4021 259318.4084 248303.5881 179541.0213 272529.1913 223843.9032 0.784541019 1.351692395 0.967495933 0.993019684 1.158478764 1.109271169 0.802081355 1.217496601 1 17.7721335 FGVQTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FGVQTDR 7 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;; 109.01 0.016573 1011900000 1129870 1585630 1391190 1393930 1482920 1244950 1484410 1274340 1473420 FALSE TRUE 1059153.454 1703031.695 1424189.684 1429700.604 1366457.445 1604346.855 1261836.501 1433444.154 1227496.683 0.862856469 1.387402278 1.16023913 1.16472869 1.113206629 1.307007079 1.027975487 1.167778434 1 20.2272877 0.926987039 0.731448204 1.00284788 1.187766772 0.063367061 0.144285921 1.573383955 1.869855405 0.128795804 0.048995249 8.452536199 -0.926987039 0.184918892 FGVYDIDNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FGVYDIDNK 9 0 O75131;A0A087WYQ3;E5RHZ0;A0A087WXR6;A0A087WUS8 O75131 CPNE3 Copine-3 0 99.802 0.011843 39393000 78149 65802 63160 46099 110960 38067 69025 88447 114390 FALSE TRUE 73257.79359 70674.04855 64658.18503 47281.97839 102245.6492 49056.32493 58675.34205 99489.80265 95297.57001 0.768726774 0.741614383 0.678487238 0.496150934 1.072909301 0.514769946 0.615706592 1.043990971 1 16.54015181 1.232608528 24.99977866 1.021995713 0.693442975 0.414366438 0.159883747 139.9029134 587586.7947 0.127745965 0.035246653 17.08474607 -1.232608528 -0.328552737 FGWDCHGLPVEYEIDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FGWDCHGLPVEYEIDK 16 0 A0A0A0MSX9;P41252;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;; 195.6 4.80E-11 1092520000 1845760 1744850 1653290 1602620 2209060 1124200 1957870 1844220 2183090 FALSE TRUE 1730237.176 1874040.51 1692506.82 1643745.942 2035569.339 1448738.29 1664305.569 2074474.927 1818718.176 0.951349802 1.03041831 0.930604226 0.903793652 1.119232966 0.796571074 0.915098112 1.140624729 1 20.79449057 1.248995511 24.9973461 1.070312384 0.950462571 0.238768097 0.089610526 257.8419336 617683.6578 0.057842264 0.020621098 17.74171141 -1.248995511 -0.119849813 FGYVDFESAEDLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FGYVDFESAEDLEK 14 0 P19338 P19338 NCL Nucleolin 0 ;;; 240.12 5.10E-17 309975000 653767 470702 549266 526400 540421 424806 652851 477827 596806 FALSE TRUE 612848.8905 505553.2658 562294.8489 539908.3152 497978.5146 547440.5961 554962.0533 537484.7528 497195.2231 1.232612185 1.016810384 1.130933731 1.08590809 1.00157542 1.101057634 1.116185409 1.081033622 1 18.92345291 -0.507982464 0.010092508 1.11E-05 2.095293264 0.229248099 0.061371445 8212.398944 19.52772734 2124.978531 1930.506027 0.310468494 0.507982464 2.095282199 FHDFDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 521700000 781410 993480 761480 745390 1000510 617010 835920 791890 1087200 FALSE TRUE 732502.943 1067038.293 779542.6652 764517.9693 921933.9805 795130.7707 710581.5563 890759.2097 905739.2964 0.80873486 1.178085457 0.860670028 0.844081705 1.017880072 0.877880394 0.784532104 0.983460929 1 19.78873633 3.737087801 23.94823634 0.89406263 1.01966801 0.060796516 0.115473127 333.2107572 800650.556 0.027343851 0.048499177 5458.682073 -3.737087801 0.12560538 FHDFLGDSWGILFSHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FHDFLGDSWGILFSHPR 17 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;; 268.13 3.88E-28 3350713000 480764 1333496 720749 593959 1327527 199457.9 440270.4 1167002 832888 FALSE TRUE 450673.8394 1432229.431 737845.5066 609200.9935 1223268.384 257038.1578 374255.9408 1312704.769 693873.6121 0.64950422 2.064107074 1.063371619 0.877971122 1.76295562 0.370439448 0.539371918 1.891849965 1 19.40431338 3.673686834 5.850818674 0.999396868 1.489312446 0.018320897 0.581008587 0.402378206 30.39018884 0.147496298 0.233825371 4717.227635 -3.673686834 0.489915577 FHDIDDVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FHDIDDVKK 9 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;H0Y9D8;D6R967 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 127.4 0.00028989 220500000 832720 720560 646670 685960 857690 422690 690220 597610 945430 FALSE TRUE 780601.5416 773911.0121 662009.3178 703562.8949 790330.4872 544713.7412 586727.9187 672222.924 787631.6253 0.991074402 0.982579911 0.840506268 0.893263897 1.003426553 0.691584395 0.744926816 0.853473759 1 19.58716151 2.245555941 24.99994756 0.791290293 0.931594339 0.253553572 0.094622613 176.2199306 629777.377 0.031387452 0.025734798 176.0175374 -2.245555941 0.140304046 FHDIISDAEIEIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FHDIISDAEIEIVK 14 0 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ;;; 157.52 5.28E-06 463095000 1328840 1382400 1219260 1381940 1561710 789818 1606910 1172181 880753 FALSE TRUE 1245670.276 1484754.334 1248181.423 1417402.92 1439059.596 1017825.635 1365968.763 1318530.378 733749.6344 1.697677543 2.023516285 1.701099891 1.931725555 1.961240631 1.387156582 1.861627862 1.796975857 1 19.48492835 -2.231481615 0.320670744 1.86E-19 1.859345361 0.66285139 0.178400539 23.99736612 1.040339563 17.4941458 0.151304375 0.005868382 2.231481615 1.859345361 FHDLLSQLDDQYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FHDLLSQLDDQYSR 14 0 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224;J3KPM9;A0A669KBI6;P42224-2;A0A669KB52;E7EPD2;A0A669KB75;D2KFR9;A0A669KB17;E7ENM1 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta;Signal transducer and activator of transcription 0 ;;; 173.44 2.70E-06 318830000 309141 354388 365049 395675 378794 312081 453303 315236 375100 FALSE TRUE 289792.4166 380627.2563 373708.1347 405828.6904 349045.0472 402173.7185 385334.4234 354593.9085 312493.3868 0.927355358 1.218032996 1.195891339 1.298679292 1.116967789 1.286983135 1.23309625 1.134724521 1 18.25346613 4.740473813 24.59359729 1.203109663 0.92735524 0.445464396 0.088627063 104.6847353 1345563.943 0.018059148 0.117282004 55014.07476 -4.740473813 -0.275754423 FHDPDSAVVAQHLTNTVFVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FHDPDSAVVAQHLTNTVFVDR 21 0 Q05519-2;Q05519;B4DWT1;Q5T760 Q05519-2;Q5T760 SRSF11 Serine/arginine-rich splicing factor 11 0 ;;; 349.55 1.45E-95 952360000 405046 589585 590983 552124 629654 539256 638817 520586 662630 FALSE TRUE 379694.8939 633238.4869 605001.3958 566292.4366 580203.5147 694930.4531 543032.3213 585582.3081 552032.7722 0.687812233 1.147103068 1.095951955 1.025831192 1.051030924 1.258857242 0.983695803 1.060774536 1 19.07439439 4.744095777 24.92910456 1.084593639 0.687812057 0.703393142 0.079503698 307.6548487 1385564.55 0.01770287 0.155407174 55474.80407 -4.744095777 -0.396781582 FHDTS(ph)SPLLISGTSAAELPWAVKPEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FHDTSSPLLISGTSAAELPWAVKPEDK 27 1 P42566;B1AUU8 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 FHDT(0.076)S(0.526)S(0.398)PLLISGTSAAELPWAVKPEDK;FHDT(0.094)S(0.514)S(0.393)PLLISGTSAAELPWAVKPEDK 221.3 1.56E-34 805590000 1480000 836270 1039200 871770 898200 543210 1545400 864900 2973100 TRUE FALSE 1387369.442 898188.3009 1063850.315 894141.0941 827658.9952 700025.9087 1313681.617 972884.6689 2476870.403 0.560130009 0.362630318 0.429513919 0.360996317 0.334155148 0.282625166 0.530379634 0.392787878 1 21.24008695 -0.197301808 0.881939897 1.015361478 0.39686506 0.82759574 0.085001961 3.886732002 2.433136758 0.289384223 0.025242326 0.634889569 0.197301808 -0.618496418 FHDTSS(ph)PLMVTPPSAEAHWAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 FHDTSSPLMVTPPSAEAHWAVR 22 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 FHDTS(0.121)S(0.878)PLMVTPPSAEAHWAVR;FHDT(0.003)S(0.107)S(0.89)PLMVTPPSAEAHWAVR;FHDTS(0.006)S(0.994)PLMVTPPSAEAHWAVR;FHDTS(0.005)S(0.995)PLMVTPPSAEAHWAVR;FHDTS(0.09)S(0.91)PLMVTPPSAEAHWAVR;FHDTS(0.012)S(0.988)PLMVTPPSAEAHWAVR;FHDTS(0.017)S(0.983)PLMVTPPSAEAHWAVR;FHDTS(0.05)S(0.95)PLMVTPPSAEAHWAVR;FHDTS(0.036)S(0.963)PLMVTPPSAEAHWAVR;FHDTS(0.011)S(0.989)PLMVTPPSAEAHWAVR 267.18 1.56E-37 9264530000 873417 1029237 1081406 1011991 977173 794753 1354416 908930 1355633 TRUE FALSE 818751.3891 1105442.778 1107057.461 1037960.402 900429.7743 1024185.289 1151333.895 1022411.911 1129369.095 0.724963515 0.97881444 0.980244161 0.919062163 0.797285651 0.906864987 1.019448735 0.905294749 1 20.10708563 1.765422055 24.99999995 0.975682832 0.904431823 0.182212788 0.083433732 37.65628356 35068.74869 0.038668567 0.02144557 58.26691914 -1.765422055 -0.071251009 FHEVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FHEVFK 6 0 Q09161 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 ; 74.743 0.079523 799080000 2091190 1975360 2098200 2201100 2160740 1586700 2626000 2017800 1857010 FALSE TRUE 1960306.151 2121617.71 2147970.295 2257583.952 1991044.196 2044754.532 2232255.679 2269726.772 1547063.034 1.267114595 1.371384141 1.388418085 1.459270826 1.28698324 1.321700853 1.442898983 1.467119776 1 20.56110055 -1.380132475 3.361729471 0.996881306 1.37861475 0.745944155 0.068869605 16744915.37 24721932.66 514139.8337 0.015922944 0.041674224 1.380132475 0.381733443 FHFPPLDTHS(ph)PTNDVQPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FHFPPLDTHSPTNDVQPGR 19 0 P41162 P41162 ETV3 ETS translocation variant 3 1 FHFPPLDT(0.043)HS(0.944)PT(0.012)NDVQPGR 124.86 1.83E-05 94236000 66490 74224 75304 101150 86636 59844 61970 35962 59131 TRUE FALSE 62328.50959 79719.62219 77090.24644 103745.6802 79831.95803 77119.99131 52678.1738 40451.93486 49261.6541 1.265254095 1.618289594 1.564913884 2.106012925 1.620569985 1.565517698 1.069354547 0.82116477 1 15.58817745 1.690553393 2.846033588 0.911817359 1.642669006 0.699697168 0.205998218 0.124281585 2.263282594 0.125568196 0.055053021 49.04033097 -1.690553393 0.730851647 FHGILDQGEGVLIIFDEPPVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FHGILDQGEGVLIIFDEPPVDK 22 0 O00231 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 139.83 1.34E-07 21149000 32911 27825 28803 28082 28076 27437 33048 25853 23934 FALSE TRUE 30851.15926 29885.19195 29486.22076 28802.63166 25871.02421 35357.6165 28092.7592 29080.80396 19939.26078 1.547256922 1.498811429 1.478802102 1.44451853 1.297491642 1.773266165 1.408916785 1.458469513 1 14.2833243 0.479741509 1.784778236 1.000087873 1.4933165 0.623743268 0.119654528 2.404190861 7.545062738 0.103082293 0.028878784 3.018154789 -0.479741509 0.493228627 FHGTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FHGTVK 6 0 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 130.84 0.015589 3633730000 3916300 8787340 7945640 8793570 7971890 8215330 5591760 5778560 3743290 FALSE TRUE 3671185.774 9437963.797 8134114.333 9019227.894 7345809.916 10586962.41 4753327.499 6500025.936 3118510.716 1.177224037 3.026433017 2.608332975 2.892158698 2.355550641 3.394877674 1.524229971 2.084336572 1 21.57242579 1.222414859 1.310074053 1.116320135 2.61569954 0.336000287 0.650141897 0.393124079 1.324916462 0.540143464 0.169527753 16.68840608 -1.222414859 1.499379406 FHGVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FHGVLK 6 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 87.758 0.052076 118750000 553460 491800 526040 576200 487460 393280 620510 549520 335150 FALSE TRUE 518819.9266 528213.3837 538517.9172 590986.2675 449176.8579 506813.5516 527470.286 618128.7816 279211.2998 1.858162355 1.891805181 1.928711043 2.116627328 1.608734525 1.81516132 1.889143764 2.213838702 1 18.0909978 2.736305011 24.98488328 1.779235362 1.935970349 0.10556524 0.312556341 607.1151223 6724854.433 0.088675452 0.087408827 544.8851987 -2.736305011 0.156734988 FHHTIGGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FHHTIGGSR 9 0 P61313;E7ERA2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 117.89 0.0010783 637440000 341480 465967 426292 471372 507671 400241 511333 410006 498824 FALSE TRUE 320107.3764 500467.6815 436403.8475 483468.2036 467800.5675 515784.0793 434663.3636 461196.1516 415567.0519 0.770290558 1.204300676 1.050140635 1.163393973 1.125692149 1.241157298 1.04595242 1.109799609 1 18.66472175 4.746865605 24.95782432 1.121942255 0.77029038 0.687409123 0.073541174 548.4858158 1648250.128 0.01573191 0.17912604 55829.74001 -4.746865605 -0.351651876 FHINWEDNTEKLEDAES(ph)SNPNLQSLLSTDALPSASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FHINWEDNTEKLEDAESSNPNLQSLLSTDALPSASK 36 1 Q9Y294 Q9Y294 ASF1A Histone chaperone ASF1A 1 FHINWEDNT(0.007)EKLEDAES(0.47)S(0.47)NPNLQS(0.015)LLS(0.019)T(0.019)DALPSASK;FHINWEDNT(0.006)EKLEDAES(0.486)S(0.486)NPNLQS(0.02)LLSTDALPSASK 102.01 1.88E-05 177454000 389640 217697 289710 243560 333620 204133 379190 276420 639670 TRUE FALSE 365253.1279 233815.5124 296582.058 249810.1619 307418.831 263062.8833 322333.9797 310931.6455 532904.9446 0.685400148 0.438756508 0.556538386 0.468770584 0.57687367 0.493639412 0.604862055 0.583465492 1 19.02351869 -0.022723161 0.691495849 1.02016726 0.525074113 0.803928522 0.069941077 1.817580103 0.920334302 0.157739485 0.022323367 0.949023221 0.022723161 -0.495093146 FHKPGENYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FHKPGENYK 9 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RQT0;C9J165;A0A0U1RR66;A0A0U1RQJ6 P47897 QARS Glutamine--tRNA ligase 0 111.06 0.0013138 958120000 192600 153290 158680 140150 207980 139510 224710 181380 242640 FALSE TRUE 180545.5098 164639.7511 162443.9645 143746.4863 191646.0898 179784.2722 191016.8216 204025.6923 202141.8165 0.893162597 0.81447646 0.803613856 0.711117021 0.94807741 0.889396738 0.944964406 1.009319575 1 17.62500827 2.038772759 1.123394171 0.996145915 0.81173683 0.620273164 0.057332067 0.31499834 0.736780554 0.041277355 0.019796771 109.3384113 -2.038772759 -0.184409084 FHMVDGNVSGEFTDLVPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FHMVDGNVSGEFTDLVPEK 19 0 O95433;O95433-2;G3V438;H0YJ63 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ; 135.04 8.55E-06 735840000 1733550 1461090 1590540 1592060 1729650 1265140 2074100 1608060 1855800 FALSE TRUE 1625050.2 1569270.624 1628268.36 1632914.955 1593810.266 1630365.38 1763107.96 1808829.831 1546054.991 1.051094695 1.015016046 1.053176225 1.056181678 1.030888471 1.054532594 1.140391493 1.169964743 1 20.5601602 1.860193061 5.356436845 1.116796297 1.040299868 0.269466396 0.045126464 0.216527118 8.274096537 0.01826643 0.010763355 72.47580722 -1.860193061 -0.076496429 FHMYEGYPLWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FHMYEGYPLWK 11 0 P00491;G3V5M2;G3V393 P00491 PNP Purine nucleoside phosphorylase 0 ; 132.32 0.00018499 816840000 2963300 4385400 2399530 1997470 5427800 2016500 2816100 4703100 2354300 FALSE TRUE 2777832.343 4710099.579 2456447.985 2048728.462 5001522.483 2598630.815 2393851.948 5290292.388 1961352.121 1.416284365 2.401455368 1.252425793 1.044549033 2.550038022 1.324918044 1.220511056 2.697268039 1 20.90341713 -1.803047213 2.814934629 0.804068017 1.703256511 0.126172943 0.604451966 136919059.3 101278398.2 183056192.7 0.135885835 0.015738118 1.803047213 0.899188494 FHNLEGFLEEFADIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FHNLEGFLEEFADIAK 16 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ; 114.91 0.00054685 237360000 475060 356700 421310 403010 403660 309900 472730 348120 344480 FALSE TRUE 445326.8426 383110.4391 431303.6722 413351.9189 371958.1719 399363.0992 401848.5251 391583.5483 286984.0626 1.551747643 1.33495371 1.502883708 1.440330572 1.296093478 1.391586333 1.400246834 1.364478378 1 18.13061109 -3.356699355 0.259483451 7.22E-19 1.449902372 0.78833592 0.068649255 32.60265086 0.693955391 17.58084708 0.088325454 0.000439846 3.356699355 1.449902372 FHNWFDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FHNWFDDR 8 0 P46977;A0A0C4DH80;E9PN73;E9PI32 P46977 STT3A Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A 0 ;; 169.12 0.00030285 363900000 312163 448971 300443 293691 498346 243700 352719 455685 367239 FALSE TRUE 292625.2751 482213.28 307569.6498 301227.6083 459207.9154 314052.2339 299832.0604 512578.2753 305944.4384 0.956465418 1.576146579 1.005312113 0.984582723 1.500951995 1.026500875 0.980021281 1.675396611 1 18.22291015 3.939356507 23.79417916 1.15320268 1.308089054 0.014244791 0.28066006 493.6395093 311023.529 0.06605054 0.119079683 8696.740413 -3.939356507 0.154886373 FHPEPYGLEDDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FHPEPYGLEDDQR 13 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 0 ;;;;; 169.62 2.82E-05 3506360000 3150840 3504230 3441880 3395190 3792900 3009340 3935490 3199600 4142390 FALSE TRUE 2953634.549 3763686.835 3523523.019 3482316.323 3495020.934 3878087.605 3345399.81 3599077.103 3450998.348 0.855878285 1.090608124 1.021015562 1.009075048 1.012756478 1.123758175 0.969400583 1.042908961 1 21.71858235 4.749803908 24.91605049 1.034817705 0.855878176 0.610552846 0.044621872 1072.952459 2377703.19 0.009917943 0.154517887 56208.74748 -4.749803908 -0.178939529 FHPLQEHVVKEELLNALYCEFINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FHPLQEHVVKEELLNALYCEFINR 24 1 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ; 149.32 9.44E-08 217630000 298110 414970 366440 386740 589800 252160 418520 364280 779840 FALSE TRUE 279451.8272 445694.8106 375132.1298 396664.4031 543479.4871 324954.4985 355766.8113 409761.1599 649679.666 0.430137869 0.686022411 0.577410914 0.610553822 0.83653455 0.500176495 0.547603427 0.630712613 1 19.30936903 0.945063457 20.90912306 1.000000001 0.604490957 0.571670576 0.108411967 1656.536737 630488.2004 0.097108467 0.024277117 8.811776174 -0.945063457 -0.395509044 FHQLDIDDLQSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FHQLDIDDLQSIR 13 0 O75828;P16152;E9PQ63;A8MTM1;P16152-2 O75828;P16152 CBR3;CBR1 Carbonyl reductase [NADPH] 3;Carbonyl reductase [NADPH] 1 0 ;;;;; 255.85 7.53E-24 12343520000 7132640 8087260 7416000 7369590 8138750 6580100 8757920 7031110 9690290 FALSE TRUE 6686220.795 8686049.145 7591911.022 7558706.156 7499565.405 8479668.051 7444751.201 7908959.561 8072917.997 0.828228504 1.075949136 0.94041721 0.936304092 0.928978271 1.050384514 0.922188384 0.979690313 1 22.94465881 FHS(ph)PS(ph)TTWSPNKDTPQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FHSPSTTWSPNKDTPQEK 18 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 2 FHS(0.995)PS(0.824)T(0.066)T(0.002)WS(0.112)PNKDTPQEK 170.91 1.94E-11 250700000 594090 264780 401610 371100 362790 290960 509130 297610 399290 TRUE FALSE 556906.9674 284384.5867 411136.3789 380623.0543 334297.9368 374955.4287 432790.683 334767.2636 332645.9195 1.674173452 0.854916805 1.23595798 1.144228839 1.004966294 1.127190826 1.301055139 1.006377184 1 18.34362781 4.754964271 24.79096401 1.103953122 1.674173946 0.67032269 0.129349416 1852.076958 2799005.911 0.030750129 0.818818729 56880.61336 -4.754964271 0.570220824 FHS(ph)PSTTWS(ph)PNKDTPQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FHSPSTTWSPNKDTPQEK 18 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 2 FHS(0.995)PS(0.005)TTWS(1)PNKDTPQEK;FHS(0.974)PS(0.025)T(0.009)T(0.001)WS(0.992)PNKDTPQEK 235.25 1.15E-23 1499940000 1162260 498100 735300 661380 766070 609810 1090560 591050 842310 TRUE FALSE 1089516.221 534979.8423 752741.6632 678352.1305 705905.9524 785852.2476 927040.6523 664843.8936 701723.0195 1.552630014 0.762380352 1.072704817 0.966694995 1.005960946 1.119889509 1.321091979 0.947444897 1 19.42054216 2.15581702 5.659940637 1.147315903 1.02534756 0 0.222446593 0.615642836 32.19795703 0.078123705 0.057496591 143.1584607 -2.15581702 -0.121968343 FHS(ph)PSTTWSPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FHSPSTTWSPNK 12 0 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 FHS(0.851)PS(0.102)T(0.034)T(0.012)WSPNK;FHS(0.876)PS(0.112)T(0.011)T(0.001)WSPNK 88.224 0.0065095 693670000 1613030 1490930 1369230 1395340 1823090 1024320 1583000 1516670 1664630 TRUE FALSE 1512073.332 1601320.009 1401708.782 1431146.787 1679911.865 1320024.556 1345643.846 1706029.588 1386792.499 1.090338557 1.154693301 1.010755959 1.031983363 1.211364978 0.95185441 0.970328183 1.230198165 1 20.40332051 2.209438889 24.99540097 1.025635075 1.092079269 0.086819914 0.093916831 488.8190667 419554.4918 0.033721911 0.024909208 161.9716063 -2.209438889 0.066444194 FHS(ph)PSTTWSPNKDTPQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FHSPSTTWSPNKDTPQEK 18 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 FHS(0.956)PS(0.034)T(0.01)TWSPNKDTPQEK 195.03 2.58E-15 424140000 563050 422020 499230 519950 583200 358100 668260 404510 729130 TRUE FALSE 527809.7056 453266.7999 511071.9714 533292.7973 537397.8245 461477.6567 568060.6168 455013.9639 607433.4926 0.868917687 0.746199881 0.841362845 0.877944341 0.884702327 0.759717175 0.935181586 0.749076186 1 19.21236693 -5 0.225656689 1.862985533 0.813040198 0.362973088 0.065851501 159.3034981 1.595058805 62.79678452 0.108959101 1.00E-05 5 -1.049945334 FHS(ph)SDS(ph)EEEEHKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FHSSDSEEEEHKK 13 1 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 FHS(0.502)S(0.502)DS(0.996)EEEEHKK 83.54 0.010356 289220000 677330 329120 433220 453380 478450 366830 531960 375240 561950 TRUE FALSE 634937.1244 353488.3872 443496.183 465014.4984 440874.467 472727.866 452197.5365 422089.54 468156.9147 1.356248524 0.755063903 0.947323791 0.993287686 0.941723711 1.009763716 0.965910194 0.901598432 1 18.83663264 FHSGWEPPVDVLQEAPWEVEGLASAPIEEVS(ph)PVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FHSGWEPPVDVLQEAPWEVEGLASAPIEEVSPVSR 35 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 FHSGWEPPVDVLQEAPWEVEGLASAPIEEVS(0.847)PVS(0.152)R;FHSGWEPPVDVLQEAPWEVEGLASAPIEEVS(0.865)PVS(0.135)R;FHSGWEPPVDVLQEAPWEVEGLASAPIEEVS(0.999)PVS(0.001)R;FHSGWEPPVDVLQEAPWEVEGLASAPIEEVS(0.978)PVS(0.022)R 185.96 4.04E-20 150402000 108931 111828 113871 110351 123620 104791 128207 96919 105858 TRUE FALSE 102113.2032 120107.8615 116572.0739 113182.7935 113911.3839 135042.4606 108983.5506 109019.5505 88189.61593 1.157882389 1.361927481 1.321834466 1.283402726 1.29166436 1.531273939 1.235786656 1.236194867 1 16.42832117 0.850625289 1.78659535 1.001769624 1.325099826 0.518143329 0.094790207 0.415311183 2.527217494 0.082193629 0.023260092 7.089658056 -0.850625289 0.323330201 FHSPPDKDEAEAPSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FHSPPDKDEAEAPSQK 16 1 F5H8D7;P18887;M0QYS5;M0QZ96;M0R0D2;M0R1U8 F5H8D7 XRCC1 DNA repair protein XRCC1 0 139.6 1.07E-06 89465000 225030 145020 165990 165660 186550 109660 212910 136840 239220 FALSE TRUE 210945.774 155757.4317 169927.3612 169911.1161 171899.1155 141317.0618 180986.1221 153924.7752 199292.6366 1.058472494 0.781551363 0.852652482 0.852570968 0.862546246 0.709093242 0.908142544 0.772355556 1 17.60452888 -1.168672859 3.746865202 1.000116861 0.842885546 0.201896422 0.093064311 5172905.099 2422370.383 4822.909236 0.018943796 0.067815215 1.168672859 -0.157231314 FHTEALTALLSDDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FHTEALTALLSDDSK 15 0 B7Z7P8;P62495-2;P62495;I3L492;D6RJE8 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 228.25 6.22E-13 258830000 742430 491450 588060 565700 668950 486760 697530 543590 370320 FALSE TRUE 695962.6316 527837.4694 602009.0609 580216.8197 616413.3654 627279.7101 592941.8521 611458.4081 308511.1996 2.25587477 1.710918339 1.951336164 1.880699373 1.998025894 2.033247775 1.921945954 1.981965027 1 18.23496334 -0.968545343 4.403620246 0.999974061 1.942285145 0.83005197 0.137077913 6973265.166 3167060.481 1708.790674 0.029543728 0.107511435 0.968545343 0.942311084 FHTVSGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FHTVSGSK 8 0 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ; 109.71 0.0035651 1729120000 5320900 5627600 5553400 5961700 7118600 4178400 6272000 5372900 8830300 FALSE TRUE 4987874.367 6044273.36 5685129.271 6114687.315 6559533.871 5384636.249 5331571.826 6043718.392 7356465.884 0.678025895 0.821627321 0.772807128 0.831199031 0.891669176 0.731959658 0.724746354 0.821551882 1 22.81058142 0.971089526 22.6964222 1.000000002 0.782165654 0.567519955 0.060279724 733.8516187 576118.11 0.056775872 0.014193968 9.355985186 -0.971089526 -0.217834348 FHVDISLTDFIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FHVDISLTDFIQK 13 0 Q15046;Q15046-2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 131.13 0.00013401 49060000 99160 101640 99721 97412 117750 79099 112660 94364 98582 FALSE TRUE 92953.75261 109165.5314 102086.4292 99911.75684 108502.39 101933.5972 95767.67888 106145.5531 82128.02734 1.131815236 1.329211658 1.243015722 1.216536669 1.321137174 1.241154823 1.166077915 1.292440067 1 16.32558703 -3.74614615 0.338729728 0.00019462 1.256348875 0.579394846 0.063877965 101.5732298 1.941508883 71.62909031 0.048175503 0.000179413 3.74614615 1.256154255 FHVEEEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 FHVEEEGK 8 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ;;;;;;; 182.39 0.00022882 17651290000 23123600 18491810 16639710 16046750 18056390 10132690 24965260 16520660 18811490 FALSE TRUE 21676335.15 19860962.85 17034411.78 16458536.77 16638313.97 13057833.11 21221951.03 18583300.77 15671730.79 1.383148769 1.267311385 1.086951531 1.05020543 1.061676862 0.833209381 1.354154899 1.185784839 1 23.90166118 4.350123707 1.557528039 1.094853056 1.397540521 0.381297994 0.132105133 0.656829995 2.460202459 0.036870401 0.243188451 22393.58922 -4.350123707 0.302687465 FHVEEEGKGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 FHVEEEGKGK 10 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;;;;;; 196.27 2.02E-07 6267750000 14291910 12703320 11303570 12545410 16096920 6260170 16435600 10237930 24826040 FALSE TRUE 13397404.86 13643887.03 11571696.02 12867346.46 14832732.84 8067379.454 13971234.36 11516158.1 20682413.54 0.647767962 0.659685438 0.559494471 0.622139502 0.717166437 0.390059866 0.675512765 0.556809198 1 24.30190122 -1.314482834 3.143113781 1.002764847 0.604350674 0.656002901 0.090214376 10928721.92 14829803.16 283983.1567 0.01993705 0.048474927 1.314482834 -0.398414173 FHVGS(ph)AESMLHVRPGGYTPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FHVGSAESMLHVRPGGYTPQR 21 1 O75140;O75140-9;O75140-4;O75140-1;A0A2R8Y7U0;O75140-8;H0Y770;A0A2R8Y6H3;A0A2R8Y5T1;A0A2R8Y721;A0A2R8Y5K9;A0A5F9UWT1;A0A2R8Y842;A0A2R8Y6V4;A0A2R8YEW8;H7C1T0;O75140-6;O75140-5;A0A2R8Y7U6;A0A2R8Y6H8;A0A2R8Y5E9;A0A2R8YF97;A0A2R8YF50 O75140 DEPDC5 DEP domain-containing protein 5 1 FHVGS(1)AESMLHVRPGGYTPQR 223.97 2.03E-25 270070000 81282 85249 93200 92085 103900 85249 125660 94509 115700 TRUE FALSE 76194.70471 91560.92466 95410.74801 94448.057 95740.11311 109859.0024 106818.4496 106308.6567 96388.92255 0.790492338 0.949911279 0.989851795 0.979864226 0.993268838 1.139747177 1.108202548 1.102913632 1 16.55657973 6.282287477 0.374632854 1.092708851 1.08E-13 0.717015479 0.052738408 9.82504701 0.439187174 0.041908017 6.122242369 1915523.466 -6.282287477 -1.092708851 FHVLVASQDFVESVLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FHVLVASQDFVESVLVR 17 0 O60784;O60784-4;O60784-2;O60784-3;V9GYF4;B0QY02;V9GZ68;Q6UW50;B0QY01;H7BYN7 O60784 TOM1 Target of Myb protein 1 0 ; 211.7 2.23E-12 105813000 102898 121756 115585 129179 142620 111283 130259 102338 122077 FALSE TRUE 96457.79786 130770.9409 118326.7308 132493.9518 131419.2005 143408.5956 110727.8722 115115.1246 101701.5601 0.948439707 1.285830236 1.163470164 1.302772069 1.292204372 1.410092387 1.088752937 1.131891433 1 16.63398228 1.603775759 25 1.082711441 1.237508511 0.270370698 0.123697073 0.526107017 3196.609394 0.059254419 0.028979419 40.15834059 -1.603775759 0.154797071 FICEQDHQNFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FICEQDHQNFLR 12 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;;;; 318.64 1.38E-46 4757780000 2030880 2548940 2300770 2153780 2668640 1926300 2364110 2258580 2460270 FALSE TRUE 1903770.846 2737666.17 2355345.351 2209049.641 2459055.779 2482391.539 2009633.653 2540568.685 2049635.043 0.928834064 1.335684701 1.149153533 1.077777065 1.199752994 1.211138318 0.980483652 1.239522467 1 20.96693562 0.304922699 0.365978168 0.979885387 1.17570699 0.061348881 0.124372188 6.70747523 1.558003106 0.386294786 0.100524033 2.018007142 -0.304922699 0.195821603 FICHVVGITYQHIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FICHVVGITYQHIDR 15 0 Q9UBQ5;A0A087WVB9;Q9UBQ5-2;K7EQM4;K7EK53;B4DQ48 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 0 75.764 0.017846 38580000 75242 151700 110780 124520 142420 133020 109070 132340 75101 FALSE TRUE 70532.73753 162932.0258 113407.7539 127715.394 131234.9077 171420.7146 92715.96606 148862.9403 62566.15793 1.127330491 2.604155845 1.812605371 2.041285549 2.097538223 2.739831249 1.48188684 2.379288504 1 15.93309489 -1.293773762 5.716850036 0.999903011 2.057092711 0.308680814 0.486049775 0.000525888 6.50E-05 0.411903199 0.09707777 0.050842423 1.293773762 1.0571897 FICVTPTTCSNTIDLPMS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 FICVTPTTCSNTIDLPMSPR 20 0 P40763;P40763-2;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 1 FICVTPTTCSNTIDLPMS(1)PR;FICVTPTTCSNTIDLPMS(1)PR;FICVTPTTCSNTIDLPMS(1)PR;FICVTPTTCSNTIDLPMS(1)PR;FICVTPTTCSNT(0.001)IDLPMS(0.999)PR;FICVTPTTCSNTIDLPMS(1)PR;FICVTPTTCSNTIDLPMS(1)PR;FICVTPTTCSNTIDLPMS(1)PR 206.63 7.37E-22 711850000 474801 555296 579752 716130 747106 454425 463911 388372 431162 TRUE FALSE 445084.053 596410.6936 593503.9912 734507.1082 688431.3084 585610.1205 394351.8523 436861.0991 359198.2768 1.239104087 1.660394084 1.652301889 2.044851425 1.916577425 1.630325529 1.097866771 1.216211567 1 18.4544209 1.772132216 4.353981717 1.114326916 1.709966267 0.627288108 0.213085565 0.134709493 5.167137711 0.109510112 0.057373956 59.17417556 -1.772132216 0.595639351 FIEEHATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FIEEHATK 8 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;; 143.12 0.00060653 3718060000 9907200 10951500 10555200 11085300 11491800 8017400 13447000 9376200 11155900 FALSE TRUE 9287126.037 11762360.46 10805574.33 11369767.57 10589280.38 10331893.23 11430747.19 10546839.21 9293908.22 0.999270255 1.265598947 1.162651284 1.223356988 1.139378627 1.111684448 1.229918234 1.134812068 1 23.14785397 0.976248822 22.53334219 0.999999997 1.17412345 0.30516752 0.074323503 591.4789205 561152.9538 0.063831252 0.015957813 9.467794484 -0.976248822 0.174123453 FIEIAAR ddPTM_SK-BR-3_Pertuzumab_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 ; 135.87 0.0070624 337580000 688350 890220 763050 709010 989320 585010 813870 728700 893590 FALSE TRUE 645267.4022 956132.8151 781149.9063 727204.397 911622.7979 753892.8902 691837.7491 819679.7991 744444.0562 0.86677756 1.284358183 1.049306392 0.976842237 1.224568576 1.01269247 0.929334775 1.101062991 1 19.50580391 2.027388168 24.99405286 0.994464002 1.100860689 0.054570835 0.123578186 394.6311011 360133.1305 0.04333527 0.032004597 106.5094564 -2.027388168 0.106396688 FIGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 86.833 0.055729 101280000 239800 316760 267860 334200 372320 284670 334870 295620 246250 TRUE FALSE 224791.3461 340213.24 274213.7657 342776.1378 343079.4891 366849.6078 284659.3523 332528.8077 205149.2842 1.095745213 1.65836913 1.336654753 1.670861973 1.672340659 1.788208081 1.387571755 1.620911372 1 17.64631459 -1.294127805 4.780223029 0.999775029 1.532541795 0.396716229 0.204901723 0.000444895 6.57E-05 0.17966562 0.042329976 0.050800992 1.294127805 0.532766766 FIHQQPQSS(ph)SPVYGSSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FIHQQPQSSSPVYGSSAK 18 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 FIHQQPQS(0.026)S(0.742)S(0.232)PVYGSSAK 197.68 1.17E-15 1149000000 1578200 1486100 1628600 1632900 1750000 1239200 1713200 1266900 1675600 TRUE FALSE 1479423.279 1596132.39 1667231.161 1674802.978 1612562.059 1596936.923 1456321.565 1425075.254 1395931.535 1.059810773 1.143417388 1.194350238 1.199774442 1.155187069 1.14399373 1.043261455 1.020877613 1 20.41279675 1.682098101 2.471414783 1.011626458 1.15804528 0.716437339 0.03823873 0.134327241 1.812741521 0.02569441 0.010716522 48.09479753 -1.682098101 0.146418822 FIHQQPQSSS(ph)PVYGSSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FIHQQPQSSSPVYGSSAK 18 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 FIHQQPQSS(0.002)S(0.998)PVYGSSAK 277.84 2.41E-39 1242600000 1333900 1142300 1348800 1329000 1337600 984280 1369000 1053000 1387100 TRUE FALSE 1250413.58 1226877.081 1380794.173 1363104.39 1232550.292 1268425.658 1163731.159 1184469.368 1155584.049 1.082061994 1.061694371 1.194888571 1.179580482 1.06660376 1.097648984 1.00705021 1.024996294 1 20.14019076 1.940519421 1.591072103 1.006499885 1.125727018 0.555386024 0.043718774 0.299625174 1.4129651 0.031044587 0.014360849 87.20058956 -1.940519421 0.119227134 FIIGSVSEDNS(ph)EDEISNLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FIIGSVSEDNSEDEISNLVK 20 0 Q13085;Q13085-4;A0A0C4DGT1;A0A087X2F8;A0A087X126;A0A087WYK6 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 1 FIIGSVSEDNS(1)EDEISNLVK 196.11 1.15E-21 42082000 50051 46079 50067 55872 65230 45242 70452 55225 65692 TRUE FALSE 46918.39725 49490.73711 51254.61288 57305.77011 60107.09893 58302.63096 59888.37664 62119.96282 54727.58081 0.85730808 0.904310703 0.93654081 1.047109506 1.098296289 1.065324469 1.094299725 1.135075987 1 15.73998046 3.285756182 1.801185981 1.085697867 0.891186978 0.836947931 0.0367894 0.1145237 0.760884447 0.010782593 0.015860931 1930.883992 -3.285756182 -0.194510889 FIIHAPPGEFNEVFNDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FIIHAPPGEFNEVFNDVR 18 0 P47755;F8W9N7;C9JUG7;A0A0D9SET8;P47755-2 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 ;;; 243.29 4.42E-24 1849740000 1678540 1992080 1842300 1770050 2079740 1618730 2052220 1774000 2040420 FALSE TRUE 1573483.178 2139575.676 1886000.226 1815472.48 1916405.61 2086031.073 1744508.663 1995487.805 1699860.72 0.925654178 1.258677049 1.109502798 1.068012489 1.127389784 1.227177643 1.026265648 1.173912534 1 20.69698511 -3.961845777 0.459707303 0.000302136 1.125354185 0.111001759 0.096605897 1016.131719 15.24962701 1007.099684 0.045652229 0.000109183 3.961845777 1.125052049 FIILFS(ph)LDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FIILFSLDLK 10 0 Q5T6F7;F1DAM0;Q13285 Q5T6F7 NR5A1 Steroidogenic factor 1 1 FIILFS(1)LDLK 66.962 0.041482 643450000 1296400 1079300 1020500 1216700 1431900 1165200 1283200 911320 1552900 TRUE FALSE 1215260.638 1159212.495 1044706.742 1247922.582 1319444.35 1501574.325 1090796.073 1025100.308 1293710.958 0.939360242 0.896036698 0.807527165 0.96460695 1.019891145 1.160672185 0.843152843 0.792371976 1 20.30308389 3.205238214 24.02348318 0.964130406 0.873709782 0.122439209 0.103467618 242.7508859 175007.927 0.030766343 0.036775676 1604.125024 -3.205238214 -0.090420624 FIIVSAFDHFASVHSVSAEGTVVSNLSS ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FIIVSAFDHFASVHSVSAEGTVVSNLSS 28 0 Q9Y547 Q9Y547 HSPB11 Intraflagellar transport protein 25 homolog 0 107.17 0.00084248 9408900 5073.4 7295 8246.4 7437.2 8426.8 5498.5 7803.4 6898.1 5514.6 FALSE TRUE 4755.86495 7835.12939 8442.008502 7628.051143 7764.99312 7085.827689 6633.352613 7759.34297 4594.177634 1.035193963 1.705447637 1.837545079 1.660373575 1.690181299 1.542349524 1.443860717 1.688951448 1 12.16559092 -1.462718674 4.584771129 0.997924467 1.603178301 0.398400932 0.219917434 0.004521221 0.000529834 0.206342468 0.048492178 0.034457307 1.462718674 0.605253834 FIKDNWEELYNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FIKDNWEELYNR 12 1 E9PLK3;P55786;P55786-2;H0YDG0 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 164.64 5.18E-05 422960000 374590 452600 426920 454890 627400 328930 497130 524850 698070 FALSE TRUE 351145.0806 486110.9749 437046.744 466563.2475 578126.5348 423886.7513 422589.9716 590378.6778 581557.6073 0.603801027 0.835877596 0.751510665 0.802264886 0.994100202 0.728881793 0.726651954 1.015168008 1 19.14956258 -4.524092651 0.030455424 2.152153822 6.32E-06 0.38331019 0.107654248 1634.571481 4.048278199 217.1521424 92.82913531 2.99E-05 4.524092651 -2.1521475 FILHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FILHAK 6 0 P61221 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 74.949 0.078979 115850000 122150 381180 94184 101630 410020 64214 106790 341760 342980 FALSE TRUE 114504.8495 409402.9638 96418.08896 104237.9979 377818.6831 82751.53937 90777.83089 384429.4883 285734.4223 0.40073873 1.432809392 0.337439529 0.364807282 1.3222722 0.289609977 0.317700017 1.345408387 1 18.12431532 -1.369954599 0.002279537 0.446898052 1.002956708 0 0.47836844 20590825.43 8034.928617 994676.9009 965473.1464 0.042662412 1.369954599 0.556058657 FINYVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FINYVK 6 0 P06748;P06748-2 P06748 NPM1 Nucleophosmin 0 ; 106.84 0.073935 846950000 1625670 1856640 1665260 1581490 2035590 1254840 1898710 1707450 2009570 FALSE TRUE 1523922.217 1994107.557 1704760.754 1622073.711 1875722.973 1617091.937 1614016.062 1920628.891 1674159.785 0.910260914 1.19110946 1.018278404 0.96888823 1.120396625 0.965912544 0.964075279 1.147219584 1 20.6750058 3.712788548 23.43573649 1.019332828 1.080930231 0 0.092293639 458.2043153 749221.6554 0.022546527 0.035147975 5161.64994 -3.712788548 0.061597403 FIPHENGVHTIDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FIPHENGVHTIDVK 14 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;;; 232.53 7.60E-14 2670650000 3386340 3670450 3627600 3514920 4436200 2964090 4139840 3576030 4226940 FALSE TRUE 3174395.024 3942213.937 3713648.385 3605118.798 4087798.747 3819774.665 3519109.424 4022505.217 3521436.407 0.901448914 1.119490311 1.054583402 1.023763709 1.160832761 1.084720615 0.999339195 1.142291029 1 21.7477326 4.74842227 24.77452758 1.07258292 0.901448809 0.480389812 0.056110116 1068.353315 2683864.442 0.012440327 0.169355926 56030.21259 -4.74842227 -0.171134111 FIQELSGS(ph)SPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FIQELSGSSPKR 12 1 Q01664;I3L254 Q01664 TFAP4 Transcription factor AP-4 1 FIQELS(0.019)GS(0.49)S(0.49)PKR;FIQELS(0.005)GS(0.497)S(0.497)PKR 85.469 0.0071397 250310000 126391 91295 114059 106396 123847 89174 125477 99812 113185 TRUE FALSE 118480.4129 98054.57679 116764.5333 109126.3015 114120.5562 114917.0862 106662.8887 112273.7479 94293.6923 1.256504121 1.039884794 1.238306938 1.157302242 1.210267128 1.218714459 1.131177347 1.190681425 1 16.52487365 -0.725722278 5.584603097 0.999999987 1.171852083 0.44816338 0.062262932 9.98E-09 2.08E-09 0.055800842 0.013152384 0.188051898 0.725722278 0.171852096 FIQELSGSS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FIQELSGSSPK 11 0 Q01664;I3L254 Q01664 TFAP4 Transcription factor AP-4 1 FIQELSGS(0.07)S(0.93)PK 203.87 3.69E-08 69656000 417520 251510 277300 267760 313200 212270 395510 248870 291690 TRUE FALSE 391388.1685 270132.0621 283877.687 274631.1749 288602.5354 273548.9031 336206.9472 279941.9673 243005.0546 1.610617397 1.111631454 1.168196634 1.130145936 1.187640051 1.125692235 1.383538905 1.152000594 1 17.8906268 7.74990818 0.018235595 4.65E-06 2.704499238 0.237763451 0.149369091 8108.724413 11.86493821 676.8009514 1137.764908 56222244.52 -7.74990818 2.704494591 FIQENIFGICPHMTEDNKDLIQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FIQENIFGICPHMTEDNKDLIQGK 24 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 279.74 2.10E-52 797820000 1129640 1035380 1063660 1090850 1414520 667610 1419360 862160 1507160 FALSE TRUE 1058937.849 1112040.613 1088890.517 1118843.058 1303429.305 860338.1693 1206540.145 969802.5738 1255605.259 0.84336844 0.885661002 0.867223603 0.891078665 1.03808844 0.685197966 0.960923137 0.772378553 1 20.25995155 2.700063037 0.008469458 1.759679069 3.16E-07 0.05315474 0.101054145 14764.84276 50.28112803 5105.338823 5338.074508 501.2599847 -2.700063037 -1.759678753 FIQENVFVAANHNGS(ph)PLSIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FIQENVFVAANHNGSPLSIK 20 0 P11172-2;P11172-3;P11172;P11172-4;E9PFD2 P11172-2 UMPS Uridine 5-monophosphate synthase;Orotate phosphoribosyltransferase;Orotidine 5-phosphate decarboxylase 1 FIQENVFVAANHNGS(0.99)PLS(0.01)IK;FIQENVFVAANHNGS(1)PLSIK 230.8 9.22E-26 1193180000 1019150 795900 949500 891320 1023910 801870 1219580 875830 1092420 TRUE FALSE 955363.2207 854829.2641 972022.5884 914192.7802 943496.2389 1033356.852 1036715.301 985179.3034 910088.0447 1.049748127 0.93928194 1.068053354 1.004510262 1.03670875 1.135447123 1.139137369 1.082509884 1 19.7956466 2.382993136 5.054199864 1.105760489 1.012270174 0.295524106 0.051307438 0.189784647 8.029156805 0.017004291 0.014119298 241.5422656 -2.382993136 -0.093490315 FISADVHGIWSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FISADVHGIWSR 12 0 A0AVT1;A0AVT1-4;A0AVT1-3 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 92.19 0.0078746 131010000 112860 198400 133040 136260 211620 116140 151910 174940 194940 FALSE TRUE 105796.2941 213089.7424 136195.7716 139756.6623 195000.2188 149667.7326 129132.5058 196781.6441 162403.2546 0.651441957 1.31210266 0.838627107 0.860553334 1.2007162 0.92158087 0.795134962 1.211685348 1 17.30922102 3.822853221 21.0068269 0.95817156 1.042885258 0 0.21142181 32.93141569 7206.285142 0.04996268 0.090071468 6650.48351 -3.822853221 0.084713698 FISDKDASIVGFFDDSFSEAHSEFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FISDKDASIVGFFDDSFSEAHSEFLK 26 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;; 349.68 4.06E-110 4679460000 2228130 2196640 2267830 2326520 2497620 1641520 2885610 1941950 2316340 FALSE TRUE 2088675.321 2359281.511 2321623.999 2386222.442 2301467 2115400.176 2452939.569 2184406.732 1929727.89 1.082367795 1.222598027 1.203083611 1.236559027 1.192638098 1.096216823 1.271132361 1.131976557 1 20.879966 0.986043313 23.82082843 0.999999996 1.193357714 0.502354607 0.05832902 296.8872904 506719.3858 0.050559093 0.012639773 9.683744286 -0.986043313 0.193357718 FISDRES(ph)RR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FISDRESRR 9 2 F8VX12;F8VX04;Q9H2H9 F8VX12 SLC38A1 Sodium-coupled neutral amino acid transporter 1 1 FISDRES(1)RR 73.881 0.033602 402610000 244870 299300 222330 221890 445650 208500 279250 397100 514940 TRUE FALSE 229544.0238 321460.4834 227603.7726 227584.0731 410650.4467 268690.5653 237379.0549 446678.8091 428993.1874 0.535076152 0.749337036 0.53055335 0.530507429 0.95724235 0.62632828 0.553339918 1.04122588 1 18.71059521 1.232246048 24.9947146 1.020613216 0.642002393 0.590255375 0.131714661 109.5259077 433511.7046 0.110250506 0.030237579 17.0704924 -1.232246048 -0.378610823 FISETLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FISETLRR 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 0 174.52 0.00052319 0 83599 157940 111680 122940 184360 92948 111800 144170 139020 FALSE TRUE 78366.68782 169634.0419 114329.1023 126094.8485 169881.1093 119780.5787 95036.6279 162169.9419 115816.6639 0.67664432 1.464677329 0.987155894 1.088745301 1.466810591 1.034225773 0.820578185 1.40022978 1 16.82148332 -1.08595021 4.702402582 0.999993946 1.1203067 0.018971166 0.264537685 1.55E-05 3.02E-06 0.236763121 0.055802795 0.08204456 1.08595021 0.120312754 FITEIWHPNVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FITEIWHPNVDK 12 0 P62253;K7EPR7;I3L2H7 P62253 UBE2G1 "Ubiquitin-conjugating enzyme E2 G1;Ubiquitin-conjugating enzyme E2 G1, N-terminally processed" 0 ; 111.39 0.0013872 430870000 1356010 1441330 1320100 1362280 1691160 1006190 1620850 1400220 1432130 FALSE TRUE 1271139.755 1548047.573 1351413.395 1397238.411 1558343.115 1296660.719 1377818.59 1575040.549 1193098.251 1.065410794 1.297502173 1.132692462 1.171100879 1.306131422 1.08680129 1.15482408 1.320126442 1 20.18628142 -1.382749059 3.546435507 0.998773059 1.19135686 0.30939907 0.090063171 341.1653276 19176443.9 33742.62094 0.018991528 0.041423896 1.382749059 0.192583801 FITHAPPGEFNEVFNDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FITHAPPGEFNEVFNDVR 18 0 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 ;;;;; 234.48 9.09E-24 2997320000 1933410 2240800 2085440 2123040 2274730 1878850 2338720 2024270 2196410 FALSE TRUE 1812401.319 2406711.164 2134907.622 2177520.801 2096081.882 2421243.494 1988050.648 2277004.565 1829814.982 0.990483375 1.315275691 1.166734147 1.190022392 1.14551575 1.323217658 1.08647632 1.244390601 1 20.80326635 -1.5821744 2.668074754 0.985360482 1.190803689 0.245749351 0.099745051 10959710.24 10516148.56 1134295.412 0.021327878 0.026171318 1.5821744 0.205443207 FITIFGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FITIFGTR 8 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ; 134.08 0.0020747 200130000 476659 420830 380767 381236 437573 310144 488970 376948 525420 FALSE TRUE 446825.7641 451988.6911 389798.9731 391019.1612 403207.7817 399677.538 415653.4879 424010.7876 437724.0077 1.020793368 1.032588305 0.890513123 0.893300697 0.921146144 0.913081145 0.949578914 0.968671538 1 18.73966199 4.094047897 3.864077985 0.929264988 1.026504915 0.563410798 0.033731646 0.149460542 3.990695475 0.008198538 0.019326887 12417.89254 -4.094047897 0.097239926 FITLLLPGGAQTAVRPGS(ph)PSTSTMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FITLLLPGGAQTAVRPGSPSTSTMR 25 1 H0Y4W2;F2Z2U4;Q9Y4A5-2;Q9Y4A5 H0Y4W2 TRRAP Transformation/transcription domain-associated protein 1 FITLLLPGGAQT(0.003)AVRPGS(0.992)PS(0.004)T(0.001)STMR;FITLLLPGGAQT(0.02)AVRPGS(0.922)PS(0.039)T(0.013)S(0.003)T(0.003)MR 176.94 1.92E-17 376520000 388019 421166 401588 434525 423352 360075 451820 413010 377335 TRUE FALSE 363733.5834 452349.5689 411113.857 445675.6471 390103.6416 464022.8072 384073.7855 464575.2076 314355.3508 1.157077754 1.438975248 1.307799775 1.417744746 1.240963898 1.476109142 1.221782243 1.47786639 1 18.26203679 -1.061545283 4.242478957 0.99996481 1.343961406 0.48259011 0.111372537 6242741.01 1563143.621 2068.237122 0.021941605 0.086787008 1.061545283 0.343996597 FIVLNSLNQNAKPEGPEQAELGRLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FIVLNSLNQNAKPEGPEQAELGRLSPR 27 2 P41182-2;P41182 P41182-2 BCL6 B-cell lymphoma 6 protein 1 FIVLNSLNQNAKPEGPEQAELGRLS(1)PR 175.34 6.29E-13 112710000 206010 189950 172960 200810 191590 133470 210870 155930 251660 TRUE FALSE 193116.2018 204014.0956 177062.6929 205963.1246 176543.2942 172000.6223 179252.0011 175398.2037 209656.3202 0.92110842 0.973088221 0.844537826 0.982384525 0.842060445 0.820393214 0.854980193 0.836598694 1 17.6776668 2.710332172 24.89666537 0.85722988 0.923124185 0.162953678 0.061993854 990.5117958 873601.3278 0.018082768 0.017051684 513.253798 -2.710332172 0.065894304 FIVS(ph)PVPESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 FIVSPVPESR 10 0 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4;H0YH68 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 FIVS(1)PVPESR;FIVS(1)PVPESR;FIVS(1)PVPESR;FIVS(1)PVPESR;FIVS(1)PVPESR 153.54 1.69E-05 578292000 731816 955788 959768 951826 1006040 906886 936612 900480 1008160 TRUE FALSE 686012.9429 1026555.538 982534.1502 976251.4666 927029.6766 1168689.266 796175.7257 1012906.91 839891.583 0.816787496 1.222247679 1.1698345 1.162354149 1.103749216 1.39147634 0.947950595 1.205997215 1 19.67984358 0.041041818 0.863761388 0.998089936 1.140906758 0.051150931 0.156271381 15.31125859 11.3113146 0.24510969 0.045214653 1.099111666 -0.041041818 0.142816822 FIY(ph)VDVLPEEAVGHARPS(ph)RR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FIYVDVLPEEAVGHARPSRR 20 2 O75995 O75995 SASH3 SAM and SH3 domain-containing protein 3 2 FIY(1)VDVLPEEAVGHARPS(1)RR 62.765 0.065172 119560000 2450.6 4684.4 3115.5 5917.1 5410.5 2070.4 4189.4 1559.2 2803.5 TRUE FALSE 2297.22132 5031.23785 3189.401131 6068.942804 4985.581155 2668.09087 3561.238362 1753.869552 2335.577739 0.983577332 2.15417272 1.365572671 2.598476044 2.134624368 1.142368685 1.524778346 0.750936063 1 11.18956375 1.686347698 1.522485042 0.936659791 1.831126259 0.342158335 0.488074019 0.412806751 1.873477788 0.366910861 0.13800709 48.56771795 -1.686347698 0.894466468 FIYVDVLS(ph)EDEEKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FIYVDVLSEDEEKPK 15 1 O94885;A0A087WW74 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 FIYVDVLS(1)EDEEKPK;FIYVDVLS(1)EDEEKPK 229.96 2.38E-13 133990000 207264 102237 134646 136170 145557 91125 174358 117746 171215 TRUE FALSE 194291.7162 109806.7339 137839.8667 139664.3527 134125.5404 117431.3082 148214.6366 132446.8473 142638.1104 1.362130469 0.769827457 0.966360717 0.979151731 0.940320508 0.823281435 1.039095626 0.928551612 1 17.12199997 -1.551208413 2.288269362 1.004199928 0.955190459 0 0.158475146 14508600.35 11710679.08 372791.2626 0.036701931 0.028105518 1.551208413 -0.049009469 DLMTDLKSEISGDLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 DLMTDLKSEISGDLAR 16 1 E5RK69;P08133;P08133-2;E7EMC6 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ;; 112.3 0.00068378 373585000 449773 430968 452923 398150 630319 252146 538382 475597 1209870 FALSE TRUE 421622.5108 462877.3191 463666.5474 408367.2031 580816.2883 324936.457 457656.6172 534976.3324 1007934.881 0.418303324 0.459233357 0.460016372 0.405152367 0.576243862 0.322378423 0.454053755 0.530764777 1 19.942971 0.72301452 2.538223249 0.99991202 0.443805482 0.886080346 0.062396359 0.443724001 3.679248498 0.05329174 0.014215084 5.284629197 -0.72301452 -0.556106539 FKDELWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FKDELWR 7 1 Q8IUF8-2;Q8IUF8-4;Q8IUF8 Q8IUF8-2 MINA Bifunctional lysine-specific demethylase and histidyl-hydroxylase MINA 0 ; 99.442 0.0095993 518460000 657870 665740 677350 658800 763340 494390 733100 590350 691530 FALSE TRUE 616695.091 715032.0823 693417.0619 675705.9233 703390.3556 637112.3672 623178.4608 664056.497 576109.1755 1.070448306 1.241139896 1.20362093 1.172878253 1.220932395 1.105888249 1.081702023 1.152657387 1 19.13598271 1.266887331 0.591051712 1.00878756 1.196144055 0.44271371 0.05622601 0.585695382 0.506875798 0.05342351 0.025743553 18.48788925 -1.266887331 0.187356495 FKDIFQEIFDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FKDIFQEIFDK 11 1 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 181.98 5.46E-06 1039710000 2831500 2464000 2172000 1985200 3666200 1693690 2178100 2639800 3783200 FALSE TRUE 2654281.469 2646437.124 2223520.866 2036143.593 3378271.441 2182630.808 1851514.125 2969384.841 3151759.48 0.842158638 0.839669759 0.70548558 0.646033939 1.071868416 0.692511856 0.587454131 0.94213561 1 21.58772601 -1.936478068 6.223081943 1.091188569 0.773409035 0.161788099 0.144770025 0.090589533 0.00092469 0.06932923 0.031475967 0.011575025 1.936478068 -0.317779534 FKDIFQEIFDKHYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FKDIFQEIFDKHYK 14 2 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 152.89 3.93E-06 48682000 57187 81315 54256 81930 182100 34736 73219 67542 552040 FALSE TRUE 53607.76775 87335.64721 55542.97794 84032.46251 167798.6006 44763.71931 62240.49068 75974.76738 459900.9577 0.116563723 0.18990099 0.120771607 0.182718607 0.364858124 0.09733339 0.135334553 0.165198106 1 18.81096368 -1.617802022 2.491182357 1.092764723 0.168943543 0.92375213 0.074794 2014620.569 1692320.544 1210433.773 0.018495993 0.024110043 1.617802022 -0.92382118 FKDIFQEIYDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FKDIFQEIYDK 11 1 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 179.93 6.28E-06 1011690000 3700700 3346400 3186900 3204300 4346200 2226900 3601000 3726400 4874100 FALSE TRUE 3469079.793 3594170.938 3262494.773 3286527.763 4004866.984 2869769.879 3061063.48 4191649.243 4060581.222 0.854330847 0.885137063 0.80345512 0.809373728 0.986279245 0.706738696 0.753848603 1.032278143 1 21.95325482 1.227848784 24.95418069 1.016139236 0.826556261 0.51926675 0.075060785 187.445554 436656.5187 0.06898704 0.017950951 16.89852444 -1.227848784 -0.189582975 FKDPGLVDQLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FKDPGLVDQLVK 12 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 130.07 0.00020341 517280000 1233930 945890 1004560 1002410 1223780 744650 1346910 1083490 1383860 FALSE TRUE 1156700.524 1015924.68 1028388.638 1028133.538 1127669.255 959618.3666 1144953.35 1218766.112 1152884.826 1.003309696 0.88120223 0.892013334 0.891792063 0.978128283 0.832362735 0.993120322 1.057144724 1 20.13681696 1.555363193 6.03909489 1.02731462 0.908581396 0.494477996 0.050133307 0.096816918 7.18018895 0.025095393 0.011527886 35.92222203 -1.555363193 -0.118733225 FKDPLKDGEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FKDPLKDGEAK 11 2 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 59.57 0.055766 882330000 3220700 1663600 2266900 2209600 2472200 1698300 3049600 2069100 3826200 FALSE TRUE 3019122.136 1786774.675 2320671.939 2266302.077 2278043.384 2188571.64 2592340.791 2327431.69 3187582.502 0.947151057 0.560542252 0.728035098 0.710978328 0.71466178 0.68659294 0.813262336 0.730155749 1 21.60403125 0.083162136 0.539967902 1.021261978 0.702630825 0.395282855 0.09928599 3.234397017 1.207091751 0.241790516 0.041447463 1.211050172 -0.083162136 -0.318631154 FKDPNAPK ddPTM_SK-BR-3_Pertuzumab_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 ; 111.17 0.0029964 5399200000 22326000 16970200 18777200 18046400 20638000 12972200 23248000 16307300 25166000 FALSE TRUE 20928655.51 18226691.27 19222604.05 18509501.18 19017174.73 16717063.55 19762178.22 18343302.3 20965632.02 0.998236328 0.869360449 0.916862608 0.882849664 0.907064223 0.797355574 0.942598735 0.874922458 1 24.32152299 -1.407101517 7.396259255 1.000004269 0.896357316 0.272788487 0.051881052 3.19E-06 2.56E-07 0.043859043 0.01033725 0.039165032 1.407101517 -0.103646953 FKDPNCVGTVLASRPHTLDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FKDPNCVGTVLASRPHTLDGR 21 2 K7EQ55;K7EK33;Q96EP5;Q96EP5-2;K7EQ02 K7EQ55 DAZAP1 DAZ-associated protein 1 0 ; 168.78 6.22E-12 3269300000 2425200 2548600 2567500 2490000 2858600 1985170 3033400 2361700 3383600 FALSE TRUE 2273411.061 2737300.996 2628402.312 2553897.616 2634097.087 2558256.352 2578569.831 2656563.444 2818855.301 0.806501512 0.97106829 0.932436054 0.906005219 0.934456297 0.907551498 0.914757785 0.942426326 1 21.42667799 -4.999999994 0.281219842 1.587001202 0.915420357 0.299295917 0.042313822 317.8181911 3.039022675 108.9138468 0.044669413 1.00E-05 4.999999994 -0.671580845 FKEANNFLWPFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FKEANNFLWPFK 12 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 138.89 6.05E-05 722460000 2753100 4855000 2475800 2003520 5880800 1803060 3620400 4116100 3377400 FALSE TRUE 2580788.385 5214469.252 2534527.145 2054933.715 5418945.69 2323574.152 3077554.63 4630004.146 2813690.121 0.91722552 1.853249301 0.900784037 0.730334055 1.925921284 0.825810253 1.093778809 1.645527384 1 21.42403202 7.999997562 0.02068578 3.24E-09 2.805947406 0.00018948 0.438721367 15555.57045 24.78764939 1233.313262 2276.204911 99999438.61 -7.999997562 2.805947403 FKEEGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FKEEGVR 7 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;;;; 114.89 0.0052918 2966600000 4424280 5124690 4868120 5177640 6023870 4110390 6076700 5687450 5970880 FALSE TRUE 4147372.212 5504127.38 4983594.105 5310507.008 5550779.549 5296992.866 5165555.248 6397540.652 4974301.555 0.833759708 1.106512607 1.001868112 1.067588474 1.115891244 1.064871683 1.038448351 1.286118379 1 22.24606254 4.742782836 24.47875377 1.077630421 0.833759578 0.48433949 0.081192894 269.7250319 1563679.713 0.017494254 0.135556777 55307.34819 -4.742782836 -0.243870843 FKEIAEAYDVLSDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FKEIAEAYDVLSDPR 15 1 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ;;; 101.67 0.001534 540836000 1776933 1705209 1824370 1821367 1788838 1348747 2250310 1655929 2523770 FALSE TRUE 1665717.935 1831464.449 1867644.918 1868106.361 1648349.879 1738108.364 1912896.906 1862675.381 2102536.483 0.792242108 0.871073802 0.888281813 0.888501282 0.783981583 0.826672154 0.909804382 0.885918221 1 21.0036994 0.799469345 1.107320823 0.998624066 0.852669767 0.589606851 0.03978267 0.587881881 1.348988544 0.038059625 0.012000716 6.301868629 -0.799469345 -0.145954299 FKEMELPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FKEMELPAK 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 91.936 0.0081891 0 452140 425830 398080 405750 547310 293050 550850 405280 534080 FALSE TRUE 423841.3645 457358.8963 407522.6456 416162.2319 504326.4803 377648.7777 468255.1563 455880.1001 444938.5977 0.952583945 1.027914635 0.915907605 0.935325085 1.133474333 0.848766054 1.052403992 1.024591039 1 18.76324673 1.608546552 25 1.028874375 0.972976411 0.110450385 0.075058059 0.16651739 5329.189423 0.03357358 0.01721499 40.60191822 -1.608546552 -0.055897965 FKFPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FKFPGR 6 1 P27635;X1WI28;A0A087WV22;H7C123;H7C2C5;Q96L21;F8W7C6 P27635;F8W7C6 RPL10;RPL10L 60S ribosomal protein L10;60S ribosomal protein L10-like 0 124.12 0.016864 3067100000 3826200 3706800 3931100 3887800 4161500 2761800 4263800 3850100 4472700 FALSE TRUE 3586724.972 3981255.329 4024347.548 3987567.53 3834672.577 3559086.826 3624482.773 4330793.46 3726177.475 0.962574916 1.068455637 1.080020363 1.070149652 1.029116998 0.955157625 0.972708036 1.162261725 1 21.82926496 2.482252855 24.82182388 1.010250359 1.054414822 0.003259196 0.06428418 515.5363827 2493701.064 0.02103017 0.018096164 303.5658092 -2.482252855 0.044164463 FKGPEFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FKGPEFVR 8 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 116.52 0.0020569 255440000 464350 720110 464240 452710 954210 356680 611030 807120 1181900 FALSE TRUE 435287.1624 773427.6937 475251.992 464327.305 879270.1957 459647.7258 519411.724 907890.7087 984633.2546 0.442080501 0.785498245 0.482669044 0.47157386 0.892992585 0.466821249 0.527517958 0.922059766 1 19.90922694 1.170785597 5.521663373 0.984089815 0.589780097 0.531649835 0.148423534 0.156905677 8.490403418 0.130395141 0.033442025 14.81786375 -1.170785597 -0.394309717 FKGPGDTSNFDDYEEEEIRVS(ph)INEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 265.72 1.17E-45 1709630000 1524810 907848 1045238 1315910 1259400 900620 1490880 1134580 1237430 TRUE FALSE 1429374.864 975066.0105 1070031.539 1349678.478 1160491.804 1160614.374 1267336.385 1276234.811 1030894.939 1.386537861 0.945844211 1.037963713 1.309229901 1.125712971 1.125831867 1.229355521 1.237987269 1 19.97546588 3.284908832 24.99980299 1.180555356 1.073178311 0 0.140034905 258.7276357 139553.562 0.035991297 0.048732287 1927.120326 -3.284908832 -0.107377045 FKGQILMPNIGYGSNKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FKGQILMPNIGYGSNKK 17 2 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ; 118.53 9.24E-05 864580000 907800 758810 768790 771920 1003840 567480 1105470 783440 1299210 FALSE TRUE 850982.4185 814993.0819 787026.0618 791728.7741 925002.4557 731302.2637 939715.0362 881254.2086 1082363.458 0.786226117 0.752975423 0.727136579 0.731481434 0.85461353 0.675653135 0.868206543 0.814194347 1 20.04575361 0.671153529 0.652697642 1.003498516 0.749829631 0.65470873 0.053888225 0.681604729 0.563188205 0.05178849 0.018941378 4.689791429 -0.671153529 -0.253668886 FKIDSNIS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FKIDSNISPK 10 1 Q9H501 Q9H501 ESF1 ESF1 homolog 1 FKIDSNIS(1)PK;FKIDSNIS(1)PK 170.95 1.10E-05 668240000 2016620 908050 1311760 1196140 1375070 988000 1846080 1088250 1775410 TRUE FALSE 1890403.354 975282.9668 1342875.567 1226834.977 1267077.549 1273219.561 1569277.442 1224120.408 1479082.601 1.278091806 0.659383706 0.907911137 0.829456703 0.856664494 0.860817077 1.060980259 0.827621396 1 20.49627119 1.781537555 24.99991886 0.968764038 0.86788383 0.009803492 0.164788853 189.9415346 110528.8734 0.068959678 0.038382436 60.46966388 -1.781537555 -0.100880209 FKIPGS(ph)PPESMGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FKIPGSPPESMGR 13 1 P50395;P50395-2;Q5SX87;V9GYF8;Q5SX90;V9GYJ7;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 1 FKIPGS(0.978)PPES(0.022)MGR;FKIPGS(0.976)PPES(0.024)MGR 75.239 0.019337 330000000 1164080 1170170 1217410 1216490 1393850 828800 1421170 1103900 1852650 TRUE FALSE 1091222.311 1256810.604 1246287.54 1247707.193 1284382.644 1068061.106 1208078.752 1241724.345 1543430.746 0.707010867 0.814296726 0.807478757 0.80839856 0.832160851 0.692004554 0.782723005 0.804522229 1 20.55770932 -1.879695476 2.669398519 1.102813846 0.784624634 0.688498266 0.046223541 6956907.607 4273365.966 4515125.214 0.010912531 0.013191814 1.879695476 -0.318189212 FKIPGSPPESMGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FKIPGSPPESMGR 13 1 P50395;P50395-2;Q5SX87;V9GYF8;Q5SX90;V9GYJ7;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 0 ;;; 146.96 3.88E-05 5790820000 3176300 3524760 3290100 3394170 4088940 2691280 3822400 3114690 4524160 FALSE TRUE 2977501.053 3785736.898 3368142.726 3481270.149 3767811.146 3468208.847 3249266.605 3503565.903 3769048.469 0.789987467 1.004427757 0.893632107 0.923646957 0.999671715 0.920181546 0.862092019 0.929562443 1 21.84576892 FKLDLDFPNLPYLLDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FKLDLDFPNLPYLLDGK 17 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 188.6 3.67E-10 1934470000 5561100 4284100 5224500 4807900 6064100 4048700 6229700 4782700 9377100 FALSE TRUE 5213040.678 4601299.222 5348427.607 4931278.854 5587850.047 5217493.965 5295614.319 5379830.623 7812001.432 0.667311792 0.589003889 0.684642425 0.631243977 0.715290454 0.66788185 0.677881893 0.688662268 1 22.89726078 -5 0.255924175 3.143856381 0.63225354 0.923214855 0.030659988 44.1162681 0.435330461 49.57594911 0.039018872 1.00E-05 5 -2.511602841 FKLPPGEYILVPSTFEPNKDGDFCIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FKLPPGEYILVPSTFEPNKDGDFCIR 26 2 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ; 141.5 1.67E-07 278030000 975050 878730 792090 801820 1221970 687140 1293130 943950 1636920 FALSE TRUE 914023.361 943792.0835 810878.7489 822396.0587 1126001.405 885506.1632 1099237.161 1061804.235 1363707.477 0.670248845 0.692078103 0.594613407 0.603058994 0.825691304 0.649337324 0.806065215 0.778615835 1 20.37910278 0.869702169 0.496868589 1.010373142 0.643217602 0.725584224 0.064369034 0.583545049 0.343299986 0.075751261 0.033827915 7.408020398 -0.869702169 -0.36715554 FKMPDLHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FKMPDLHLK 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 100.15 0.0029172 221650000 1845500 1883700 1684100 1699300 2802000 1147000 2081400 2081400 3273000 FALSE TRUE 1729993.449 2023171.108 1724047.647 1742906.915 2581942.223 1478120.28 1769313.393 2341267.372 2726715.156 0.634460642 0.741981099 0.632280069 0.639196548 0.946905737 0.542088262 0.648880903 0.858640246 1 21.37873257 1.036133475 3.875336455 0.998033292 0.683636512 0.504398141 0.106206273 0.146448438 4.962451355 0.09435585 0.024259945 10.86759573 -1.036133475 -0.31439678 FKMPEMHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FKMPEMHFK 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 100.15 0.0029172 278560000 670350 1178100 488970 515800 1612600 217120 583490 1188300 1834500 FALSE TRUE 628393.9901 1265327.75 500568.5993 529036.3012 1485952.901 279799.0194 496001.0914 1336661.871 1528310.099 0.411169167 0.827926054 0.32753078 0.346157695 0.972284945 0.183077387 0.32454218 0.874601216 1 20.54350587 1.103646875 5.534997628 0.992736843 0.492647144 0.382587153 0.24119705 0.204887879 8.552086043 0.223779581 0.056493669 12.6954142 -1.103646875 -0.5000897 FKMPEMNIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FKMPEMNIK 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 90.142 0.010607 735340000 424760 617450 337310 352290 832960 251740 441550 604290 872650 FALSE TRUE 398175.0298 663166.6405 345311.1525 361330.3578 767542.6816 324413.2513 375343.6766 679736.9367 726999.0775 0.547696747 0.912197362 0.474981555 0.497016254 1.05576844 0.446236125 0.51629182 0.934990095 1 19.47159401 1.137684363 6.161866857 0.990963584 0.641512003 0.325278042 0.199180552 0.250575924 12.43073993 0.181924318 0.045856112 13.73043711 -1.137684363 -0.34945158 FKMPFLSISS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FKMPFLSISSPK 12 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 FKMPFLSIS(0.005)S(0.995)PK;FKMPFLSIS(0.133)S(0.867)PK 132.59 0.00010796 323470000 920860 736460 845960 910070 1305610 471290 958060 875620 1781480 TRUE FALSE 863225.0164 790988.2647 866026.5707 933423.9369 1203072.657 607343.7722 814407.7972 984943.0845 1484139.479 0.581633349 0.532960868 0.583521012 0.628932759 0.810619672 0.40922284 0.548740741 0.663645903 1 20.50119525 0.855780554 4.102052222 0.999950758 0.579327104 0.631517047 0.098927328 0.593387541 15.96482133 0.091751609 0.023413768 7.174316859 -0.855780554 -0.420623654 FKNELER ddPTM_SK-BR-3_Pertuzumab_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 ;;;; 128.61 0.003412 1541030000 3805530 3413040 3665550 3574580 3775100 2717580 3977350 3083290 3645130 FALSE TRUE 3567348.67 3665745.033 3752498.577 3666309.775 3478618.874 3502101.23 3380983.291 3468245.544 3036734.255 1.174731923 1.207133956 1.235701995 1.207319926 1.145513101 1.153245868 1.113361594 1.142097152 1 21.53408923 0.992331983 0.417754423 0.991877594 1.2188455 0.851622139 0.025143929 0.448558982 0.210088045 0.037413448 0.019545397 9.824986971 -0.992331983 0.226967906 FKPES(ph)SSPVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FKPESSSPVKK 11 2 Q5TCQ9;Q5TCQ9-1 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 FKPES(0.333)S(0.333)S(0.333)PVKK 50.145 0.082896 452120000 360420 200420 294570 301830 292790 188420 357460 238830 479390 TRUE FALSE 337861.9556 215259.3053 301557.3395 309575.4688 269795.4545 242813.7953 303862.1915 268648.4512 399376.712 0.845973101 0.538988125 0.755069914 0.775146521 0.675541278 0.607981858 0.760841036 0.672669295 1 18.60739068 FKPNQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FKPNQTR 7 1 Q9NZJ9;A0A024RBG1;Q9NZJ9-2 Q9NZJ9 NUDT4 Diphosphoinositol polyphosphate phosphohydrolase 2 0 ; 86.953 0.017964 596500000 595410 689860 625200 595980 792510 629460 785020 648570 896100 FALSE TRUE 558144.3509 740937.9522 640030.0392 611273.8558 730269.4614 811174.8836 667313.5388 729545.3922 746535.121 0.747646474 0.992502471 0.857334131 0.818814599 0.978211796 1.086586365 0.893880971 0.977241889 1 19.50985061 2.704418893 17.63103989 0.98179818 0.877689456 0.410876126 0.076774361 22.74096809 11742.5915 0.024147573 0.022776752 506.3127842 -2.704418893 -0.104108724 FKRPQFS(ph)PTGDCQAEAAAAANGTGGEEDDGPAAELLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FKRPQFSPTGDCQAEAAAAANGTGGEEDDGPAAELLEK 38 2 Q7Z4Q2 Q7Z4Q2 HEATR3 HEAT repeat-containing protein 3 1 FKRPQFS(0.937)PT(0.063)GDCQAEAAAAANGTGGEEDDGPAAELLEK;FKRPQFS(0.959)PT(0.041)GDCQAEAAAAANGTGGEEDDGPAAELLEK 326.4 1.46E-112 447583000 262730 198274 235760 237210 260910 171741 307510 215730 371920 TRUE FALSE 246286.1983 212954.4133 241352.3385 243297.2102 240419.1811 221319.8387 261401.7303 242664.3654 309844.1493 0.794871224 0.687295254 0.778947542 0.785224477 0.775935843 0.714294071 0.843655531 0.783182016 1 18.2411832 -4.268241159 0.203880297 1.792204305 0.726716471 0.764155772 0.040745586 44.47393218 0.57873078 14.41160828 0.087806608 5.39E-05 4.268241159 -1.065487835 FKYDDAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 174.41 0.00024818 6220540000 11724070 11491860 10693900 10606490 13200140 8176940 13344510 11007190 13867110 FALSE TRUE 10990281.39 12342729.27 10947564.36 10878670.49 12163454.25 10537489.84 11343624.61 12381461.9 11552599.76 0.951325383 1.068394087 0.947627771 0.941664276 1.052875933 0.912131473 0.981910985 1.071746807 1 23.46171421 1.266822324 24.30018574 1.035873388 0.982858075 0.170434266 0.051346619 243.5890568 209445.0648 0.032404397 0.011826022 18.48512214 -1.266822324 -0.053015313 FKYDDAERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 154.35 4.27E-05 1345250000 2145330 2396450 2094190 2142450 2720390 1593650 2784780 2185500 4029800 FALSE TRUE 2011057.625 2573885.652 2143865.176 2197428.894 2506741.543 2053710.884 2367228.092 2458364.486 3357200.346 0.599028183 0.766676214 0.638587202 0.654542079 0.746676184 0.611733192 0.705119697 0.732266243 1 21.6788272 0.626812314 1.727348347 0.999902972 0.679037144 0.782434226 0.053603191 0.708821531 2.742150065 0.046129138 0.013031064 4.234599224 -0.626812314 -0.320865829 FLAADGDPARPDGSWTFAQRPTEQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLAADGDPARPDGSWTFAQRPTEQELR 27 2 Q9ULW3 Q9ULW3 ABT1 Activator of basal transcription 1 0 ; 101.47 0.0015 175953000 379200 352620 367560 350330 381380 304970 395140 314690 374040 FALSE TRUE 355466.5489 378728.3517 376278.6968 359320.0609 351427.9532 393009.8882 335892.4253 353979.7392 311610.3076 1.140740663 1.215390963 1.207529686 1.153107109 1.127780258 1.261222362 1.077924629 1.135969288 1 18.24938343 0.84753498 0.66267529 0.998469768 1.190783419 0.565458112 0.048308527 0.623516395 0.597869365 0.045509507 0.017795545 7.039389242 -0.84753498 0.192313651 FLAAGTHLGGTNLDFQMEQYIYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FLAAGTHLGGTNLDFQMEQYIYK 23 0 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 ;; 322.4 9.36E-74 2203693000 1734260 1689060 1526673 1270237 1886090 1324164 1954340 1662423 1180343 FALSE TRUE 1625715.762 1814119.76 1562886.405 1302833.432 1737964.1 1706428.651 1661304.86 1869980.171 983336.128 1.653265568 1.844862309 1.589371488 1.324911589 1.767416095 1.735346238 1.689457768 1.901669346 1 19.90732512 -1.892445886 2.757578502 0.652853789 1.687238724 0.655214736 0.156909911 5331617.239 2917539.286 11941781.97 0.036764359 0.012810147 1.892445886 1.034384935 FLAAGTHLGGTNLDFQMEQYIYKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLAAGTHLGGTNLDFQMEQYIYKR 24 1 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 142.04 1.74E-07 275650000 217830 308830 230040 230930 388680 194621 308620 276250 319600 FALSE TRUE 204196.4091 331696.0945 235496.6574 236856.0548 358154.6407 250804.9233 262345.2961 310740.4206 266256.6953 0.766915585 1.245775601 0.884472246 0.889577836 1.345147923 0.941966635 0.985309668 1.167070823 1 18.02245828 FLASSGHDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLASSGHDQR 10 0 Q9H6Y2;G3V1J0;Q9H6Y2-2 Q9H6Y2 WDR55 WD repeat-containing protein 55 0 121.6 0.00051065 250780000 56704 132760 109430 106430 143470 114550 107600 129040 114060 FALSE TRUE 53154.99786 142589.6885 112025.7313 109161.174 132202.4449 147618.7254 91466.37891 145150.9281 95022.64914 0.559392927 1.500586332 1.178937151 1.148791104 1.391272987 1.553510945 0.962574499 1.527540322 1 16.53598381 4.749477197 24.7696171 1.282482083 0.559392456 0.535476061 0.211777395 1081.195789 2453169.359 0.046023306 0.690336636 56166.4787 -4.749477197 -0.723089627 FLATEGAPDFLCPEELEHVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLATEGAPDFLCPEELEHVSR 21 0 A0A494C1T9;Q6ZRV2 A0A494C1T9 FAM83H Protein FAM83H 0 ; 214.26 7.00E-25 305400000 161866 277590 273850 278350 307320 262160 314660 268130 316300 FALSE TRUE 151735.096 298143.0524 280345.8513 285492.9322 283184.3269 337841.3362 267479.6542 301606.6207 263507.4866 0.575828406 1.131440538 1.063900897 1.083433856 1.074672794 1.282093881 1.015074211 1.144584636 1 18.00748443 4.740525615 24.99122038 1.101738807 0.575828227 0.814168115 0.07860365 65.12381508 828196.3585 0.016642637 0.108815185 55020.63708 -4.740525615 -0.52591058 FLCADYAEQDELDYHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FLCADYAEQDELDYHR 16 0 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ;;; 248.67 1.91E-20 821700000 989010 1181260 1163630 1095080 1296060 1091240 1278230 1154360 1347870 FALSE TRUE 927109.6295 1268721.719 1191231.853 1123181.607 1194272.676 1406263.273 1086571.278 1298484.387 1122901.789 0.825637325 1.129859914 1.060851327 1.000249191 1.063559331 1.252347522 0.967645869 1.156365053 1 20.09880032 4.745679584 24.64537113 1.079304498 0.82563718 0.470925443 0.084349206 592.5817038 2051413.543 0.018153381 0.183892031 55677.4817 -4.745679584 -0.253667318 FLDAGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 FLDAGHK 7 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;; 105.39 0.0079373 3501400000 7425120 7538550 6894310 7161720 7531410 5134970 8336010 6404650 5916070 FALSE TRUE 6960394.993 8096712.086 7057846.289 7345501.86 6939923.439 6617352.48 7086102.688 7204284.651 4928639.698 1.412234495 1.642788392 1.432006948 1.490371038 1.408080904 1.34263263 1.437740051 1.461718667 1 22.23275809 -3.338456856 0.207561688 2.12E-15 1.546220823 0.780737218 0.075953059 28.69289288 0.530655359 12.5549773 0.168563319 0.000458715 3.338456856 1.546220823 FLDFWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLDFWR 6 0 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 104.25 0.079083 109690000 287500 714950 314700 285880 732470 201440 331330 620580 674740 FALSE TRUE 269505.8882 767885.6419 322164.8326 293216.1648 674944.7608 259592.4579 281650.1424 698060.7791 562121.535 0.479444162 1.366049144 0.573123093 0.521624144 1.200709667 0.46180842 0.501048483 1.241832479 1 19.10052256 5.001158907 20.83281363 0.821200488 0.118216044 0.101426986 0.338745423 4868.874129 37879.11575 0.07647166 84411.1041 100267.2047 -5.001158907 -0.702984444 FLDGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLDGDR 6 0 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 120.9 0.046264 317600000 502770 639820 562750 626100 515670 464400 683140 529680 293670 FALSE TRUE 471302.5232 687192.9385 576098.6957 642166.786 475171.3583 598464.7411 580709.499 595811.714 244654.5798 1.926399757 2.808829244 2.354743149 2.624789556 1.942213216 2.44616202 2.373589325 2.435318049 1 17.90038676 -1.537110208 2.74079755 0.924596946 2.399918602 0.714215266 0.27031151 9378504.589 9377130.782 5216573.755 0.059008411 0.029032858 1.537110208 1.475321656 FLDKPEDVLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLDKPEDVLLK 11 1 Q9H4G0-2;Q9H4G0-3;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 0 ; 153.34 2.97E-05 301580000 1908690 1140790 1548920 1382000 1925010 1239490 1990740 1562820 3726800 FALSE TRUE 1789228.5 1225255.279 1585661.114 1417464.46 1773827.48 1597310.642 1692247.018 1757941.517 3104773.004 0.576283193 0.394636026 0.510717245 0.456543669 0.571322759 0.51446938 0.545046938 0.566206133 1 21.56605636 -4.789092678 0.245961263 3.627865768 0.458274435 0.899303448 0.051363698 40.70465229 0.445988801 53.42031667 0.069061349 1.63E-05 4.789092678 -3.169591333 FLDNFDSSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLDNFDSSEK 10 0 Q13938-4;Q13938 Q13938-4 CAPS Calcyphosin 0 111.73 0.0039878 126400000 439020 268760 336980 289400 313710 232910 355130 261890 250800 FALSE TRUE 411542.5219 288659.27 344973.3247 296826.494 289072.482 300147.336 301881.5534 294587.543 208939.8598 1.969669752 1.381542375 1.651065168 1.420631249 1.383520035 1.436525019 1.444825098 1.409915481 1 17.67272822 -1.542857259 0.073320608 1.47E-13 2.206361861 0.631423972 0.146561923 81.41160927 0.968847518 23.32119184 8.365685411 0.028651195 1.542857259 2.206361861 FLDNFSSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLDNFSSGR 9 0 Q9HAB8;Q5VVM3 Q9HAB8 PPCS Phosphopantothenate--cysteine ligase 0 120.31 0.0038316 0 36843 57811 46324 54779 57144 41464 50877 47615 55648 FALSE TRUE 34537.0624 62091.38659 47422.82716 56184.72188 52656.14075 53433.98369 43248.46617 53559.83756 46359.9893 0.744975633 1.33933134 1.022925757 1.211922667 1.135810028 1.152588352 0.932883437 1.155303061 1 15.50059261 -0.992132583 4.310573553 0.99999603 1.099522665 0.022552491 0.162181472 0.019625717 42034983.83 439.2924628 0.03424993 0.101828048 0.992132583 0.099526635 FLEEHPGGEEVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FLEEHPGGEEVLR 13 0 P00167-2;P00167;P00167-3 P00167-2 CYB5A Cytochrome b5 0 ;;; 168.31 3.04E-05 562933000 869240 891590 835720 828690 1198330 843340 1001130 1005760 1604490 FALSE TRUE 814835.82 957604.2513 855543.6731 849955.5884 1104217.996 1086798.568 851019.8505 1131331.35 1336690.254 0.609592101 0.716399516 0.640046316 0.635865778 0.826083674 0.813051913 0.63666197 0.846367621 1 20.35023376 -5 0.140066872 2.051206135 0.597151076 0.658765561 0.072929881 86.94454781 0.746533483 25.28780082 0.438496308 1.00E-05 5 -1.454055059 FLEESVSMS(ph)PEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLEESVSMSPEER 13 0 A0A087WTB8;P15374;Q5TBK7 A0A087WTB8;Q5TBK7 UCHL3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L3 1 FLEESVS(0.001)MS(0.999)PEER;FLEESVSMS(1)PEER 177.38 1.63E-05 271630000 421960 431120 395430 405330 455790 347460 489200 405070 516860 TRUE FALSE 395550.2768 463040.5734 404809.7863 415731.454 419994.092 447766.0615 415849.0015 455643.8812 430592.727 0.91861811 1.075356234 0.940122211 0.965486475 0.975385941 1.039883011 0.965759465 1.058178303 1 18.71596443 2.288594355 24.99914501 1.008986293 0.983492199 0.135514848 0.047425149 323.802585 161784.6127 0.015809363 0.013227035 194.3543902 -2.288594355 -0.025494094 FLEFQYLTGGLVDPEVHGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLEFQYLTGGLVDPEVHGR 19 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 228.01 1.14E-19 525720000 461120 496990 488440 525700 567680 417730 568900 502170 465930 FALSE TRUE 432259.3223 533787.6567 500026.0275 539190.352 523096.7027 538321.8697 483598.7264 564867.0299 388163.273 1.113601807 1.375162706 1.288184798 1.389081321 1.347620291 1.386843906 1.245864202 1.45523049 1 18.56630409 -0.725944618 8.00194001 0.999999966 1.325734412 0.539526542 0.094415188 0 0 0.079287398 0.018688219 0.187955648 0.725944618 0.325734446 FLEGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FLEGVR 6 0 F8VWS0;P05388;F8VU65;F8VW21;Q8NHW5;F8VZS0 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 0 ;;; 139.01 0.028046 2250810000 2714510 3917440 2872100 2871850 3445770 2436810 3040120 3044280 3024880 FALSE TRUE 2544613.665 4207491.334 2940227.568 2945546.533 3175153.124 3140277.489 2584282.229 3424365.059 2520007.987 1.009764127 1.669634127 1.166753274 1.168863967 1.259977405 1.246137911 1.025505571 1.358870717 1 21.26499688 2.269674363 0.27570311 1.008820225 1.420628851 0.085724462 0.190969203 3.538693584 0.747201905 0.318852788 0.522904342 186.0691455 -2.269674363 0.411808626 FLEHLSGAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLEHLSGAGK 10 0 Q01813 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 135.55 0.00014123 227520000 256650 660300 498710 605830 695810 390430 652620 551910 509670 FALSE TRUE 240586.7346 709189.299 510539.6367 621376.6235 641163.8894 503140.8029 554765.6896 620817.1784 424602.7844 0.566616008 1.670241753 1.20239352 1.463430402 1.51003223 1.184968214 1.306552171 1.462112829 1 18.69575431 FLEIGKFDLSQNHPLGMAIFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 222.51 5.09E-26 567610000 901140 2160960 1000910 846050 3002900 662750 1564180 2000060 1280180 FALSE TRUE 844739.256 2320959.727 1024652.058 867761.0754 2767064.347 854075.1662 1329645.73 2249771.894 1066509.688 0.792059618 2.176220013 0.960752696 0.813645751 2.594504653 0.800813322 1.24672635 2.109471597 1 20.02446564 -0.684488243 5.431695259 0.999999969 1.433880177 0.042586459 0.650710343 2.19E-07 5.28E-08 0.566323111 0.133483627 0.206781536 0.684488243 0.433880209 FLELGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FLELGK 6 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 0 ;; 102.98 0.081604 1165354000 2687050 2413650 2736830 2517510 2709760 2225250 3300550 2560040 1997564 FALSE TRUE 2518872.337 2592359.157 2801748.9 2582113.569 2496946.38 2867643.551 2805663.168 2879666.629 1664157.664 1.513601981 1.55776055 1.68358381 1.551603929 1.500426573 1.723180209 1.685935912 1.730404932 1 20.66636069 -0.706542144 6.957687286 0.999999987 1.622643538 0.838295752 0.085325037 1.24E-09 8.91E-11 0.08320754 0.019612205 0.196543124 0.706542144 0.622643551 FLENGS(ph)QEDLLHGNPGSTYLASNSTSAPNWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLENGSQEDLLHGNPGSTYLASNSTSAPNWK 31 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 FLENGS(1)QEDLLHGNPGSTYLASNSTSAPNWK 328.64 8.43E-106 319810000 331120 274860 319970 269860 297330 285650 449860 296300 383540 TRUE FALSE 310395.7903 295210.9204 327559.8395 276785.0645 273978.9012 368112.5179 382407.6693 333293.7072 319524.6962 0.971429733 0.923906427 1.025147174 0.866239974 0.857457669 1.152062805 1.196801605 1.043092165 1 18.28556792 2.228284414 24.99998162 1.124564689 0.938451984 0.553103478 0.073574079 139.7474107 339975.5743 0.026933395 0.020112583 169.1548344 -2.228284414 -0.186112705 FLENHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FLENHEK 7 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;; 114.93 0.0057939 811660000 1184902 1121925 1186796 1215324 1309350 853874 1355901 1095421 1600535 FALSE TRUE 1110741.099 1204993.494 1214947.362 1246511.271 1206518.933 1100373.562 1152596.233 1232186.723 1333395.369 0.833017067 0.903703075 0.911168128 0.934839959 0.9048471 0.825241776 0.864406957 0.924097047 1 20.34667319 0.941354022 5.043111297 0.999966669 0.886199594 0.541919871 0.034436134 0.265711024 19.24348574 0.034659289 0.00876046 8.736832743 -0.941354022 -0.113767075 FLEPTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLEPTLR 7 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ; 118.69 0.011517 46594000 165983 209445 195300 192542 218752 152591 196648 180559 192207 FALSE TRUE 155594.4203 224952.5257 199932.6082 197482.9537 201572.1003 196641.5446 167162.458 203102.1886 160126.41 0.971697425 1.404843372 1.248592335 1.233294081 1.258831072 1.228039426 1.043940584 1.268386574 1 17.28885175 1.885701399 6.503074486 1.112916647 1.251291866 0.146603836 0.126431601 0.368086755 18.45243185 0.050627278 0.030969835 76.86018026 -1.885701399 0.138375219 FLEQS(ph)MDIEDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLEQSMDIEDLK 12 0 O95239;O95239-2;Q2VIQ3 O95239 KIF4A;KIF4B Chromosome-associated kinesin KIF4A;Chromosome-associated kinesin KIF4B 1 FLEQS(1)MDIEDLK 154.65 7.52E-05 24312000 25346 23017 23559 24154 24788 15619 31756 22151 30236 TRUE FALSE 23759.6391 24721.20263 24117.83061 24773.83253 22841.25047 20127.95175 26994.48261 24916.60111 25189.41627 0.943238972 0.981412287 0.957458893 0.983501653 0.906779666 0.799063842 1.071659713 0.989169453 1 14.62053007 1.628815044 25 1.022809466 0.938989605 0.359269591 0.056565073 0.997867279 1187.696362 0.026082847 0.014444291 42.5417199 -1.628815044 -0.083819861 FLEQVHQLYDDSFPMEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLEQVHQLYDDSFPMEIR 18 0 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224;J3KPM9;A0A669KBI6;P42224-2;A0A669KB52;E7EPD2;A0A669KB75;D2KFR9;A0A669KB17;E7ENM1;E9PH66;Q67C41 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta;Signal transducer and activator of transcription 0 ; 200.26 1.53E-15 129867000 244330 289210 288120 297090 318080 262840 335870 273140 262180 FALSE TRUE 229037.8214 310623.4093 294954.3425 304713.8324 293099.2799 338717.6411 285509.4116 307242.1303 218420.4643 1.048609718 1.422135103 1.350397013 1.395079135 1.341903932 1.550759643 1.307155044 1.406654506 1 17.73674851 -0.936076302 5.516114644 0.999999507 1.364352466 0.431354338 0.126703406 6.75E-07 1.30E-07 0.107782204 0.025404475 0.115857379 0.936076302 0.364352959 FLESAAADFS(ph)DEDEDDDVDGREK ddPTM_SK-BR-3_Pertuzumab_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 237.98 2.19E-37 1094690000 362496 340625 339018 377190 457824 269436 419489 307525 700464 TRUE FALSE 339808.0224 365845.2294 347059.6671 386869.334 421868.3498 347217.7993 356590.5188 345920.1732 583552.0332 0.582309722 0.626928206 0.594736454 0.662956021 0.722931848 0.595007436 0.611068934 0.592783768 1 19.15450178 -1.781589848 2.531062269 1.105478985 0.623256456 0.887965766 0.042018352 10832050.82 7474994.164 7056130.26 0.010269853 0.016535227 1.781589848 -0.482222529 FLEVDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLEVDER 7 0 Q92696;H0YLH3 Q92696 RABGGTA Geranylgeranyl transferase type-2 subunit alpha 0 ; 120.52 0.010558 243510000 900920 1102300 1120130 1140430 1178110 993360 1269590 1043730 1145060 FALSE TRUE 844533.0254 1183915.439 1146700.013 1169695.365 1085585.993 1280126.906 1079226.766 1174041.988 953942.0886 0.885308485 1.241076846 1.202064597 1.226170203 1.137999891 1.341933563 1.13133363 1.230726689 1 19.86354216 4.743030491 24.93427404 1.200813775 0.885308354 0.528196 0.089551014 301.8015957 1683476.589 0.017990236 0.14456698 55338.89606 -4.743030491 -0.31550542 FLEVQYLTGGLIEPDTPGRVPLDEALQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 257.19 1.28E-53 211196000 42312 48776 44729 46673 60954 50598 53782 40512 46627 FALSE TRUE 39663.76745 52387.42579 45789.993 47870.7082 56166.91872 65204.82121 45717.88839 45570.01238 38844.65248 1.021086943 1.348639322 1.178797855 1.23236289 1.44593696 1.678604828 1.176941624 1.173134768 1 15.24542838 1.088555581 2.306607246 1.012465334 1.309433434 0.239013625 0.175278356 0.399156426 4.21066136 0.162004145 0.044863187 12.26183819 -1.088555581 0.2969681 FLGDIEVWDQAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLGDIEVWDQAEK 13 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 164.04 8.77E-05 35421000 50132 35794 38524 32364 39540 34540 56203 39012 65750 FALSE TRUE 46994.32761 38444.225 39437.80747 33194.51503 36434.6879 44511.13729 47775.88191 43882.73408 54775.90024 0.857938024 0.701845608 0.719984652 0.606005833 0.665159089 0.812604395 0.872206239 0.801132138 1 15.74125367 2.047249621 3.808081748 0.871702412 0.706015491 0.5172999 0.079427393 0.18515695 5.594317109 0.031932942 0.021244674 111.4935185 -2.047249621 -0.165686921 FLGGDMEHTHLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLGGDMEHTHLVK 13 0 Q13123;E7EQZ7;D6REL4 Q13123 IK Protein Red 0 168.31 1.76E-05 108880000 238470 200030 238020 245830 278810 173580 241080 218830 262230 FALSE TRUE 223544.5884 214840.4293 243665.9468 252138.414 256913.3873 223689.7282 204932.2921 246151.4072 218462.1189 1.023264763 0.983421887 1.115369328 1.154151645 1.176008859 1.023929134 0.938067859 1.126746405 1 17.73702361 -1.605302158 7.345248489 0.999925352 1.059179921 0.061495793 0.076978378 0.00010021 5.38E-06 0.07937234 0.0186847 0.024814061 1.605302158 0.059254569 FLGTEPEPDAVGLDSGHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLGTEPEPDAVGLDSGHIR 19 0 Q16762 Q16762 TST Thiosulfate sulfurtransferase 0 ; 172.56 8.12E-12 195063000 171191 250225 185768 193659 311456 193223 205813 229654 267069 FALSE TRUE 160476.4609 268751.9194 190174.5047 198628.6178 286995.5021 249003.3434 174953.2513 258326.8074 222493.4586 0.721263726 1.207909307 0.854742004 0.892739135 1.289905348 1.119149053 0.786329865 1.161053494 1 17.7634034 4.764985173 23.77877126 1.021844756 0.721262944 0.270321805 0.161884651 6761.623408 6084414.955 0.037757328 2.845734394 58208.33454 -4.764985173 -0.300581812 FLGVAEQLHNEGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLGVAEQLHNEGFK 14 0 P31327;P31327-3;P31327-2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 ; 230.06 1.05E-12 256640000 1361380 1054130 1093890 950500 1714700 962650 1048110 1303400 2969420 FALSE TRUE 1276173.656 1132178.882 1119837.587 974891.4392 1580034.379 1240551.428 890955.6357 1466132.359 2473804.619 0.515874878 0.457667058 0.452678267 0.394085867 0.638706213 0.501475104 0.360156024 0.592662956 1 21.23830013 0.929964655 7.416848545 0.999996874 0.469569962 0.830300545 0.074442803 0.457097274 48.26104872 0.069395 0.017391497 8.510687713 -0.929964655 -0.530426912 FLHKHDLDLICR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLHKHDLDLICR 12 1 F8W0W8;P36873;P36873-2;F8VYE8;F8VR82;P62136;P62136-2;P62136-3;E9PMD7 F8W0W8;P62136 PPP1CC;PPP1CA Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit;Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 107.37 0.0010942 323080000 197830 236230 166240 179970 273650 112690 233520 200440 369700 FALSE TRUE 185448.1734 253720.715 170183.2913 184588.3349 252158.6329 145221.7736 198505.8439 225465.3752 307994.6816 0.602114856 0.82378278 0.552552695 0.599323124 0.818710997 0.471507407 0.644510622 0.73204308 1 18.23254591 0.851726164 3.289357235 0.999843934 0.649518946 0.516022579 0.10798577 0.553928447 10.60144955 0.097623207 0.025339298 7.107652125 -0.851726164 -0.350324988 FLHNPDAAQGFVGCALSSTIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLHNPDAAQGFVGCALSSTIQR 22 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 302.06 7.42E-56 3957000000 1744510 2092550 1872800 1811460 2137710 1551090 2150240 1788950 2022080 FALSE TRUE 1635324.233 2247484.579 1917223.7 1857945.13 1969822.88 1998864.503 1827831.474 2012304.345 1684581.785 0.970759774 1.334149876 1.138100695 1.102911801 1.169324575 1.186564239 1.085035758 1.194542386 1 20.68395904 -4.999999996 0.217620989 0.190792143 1.180836563 0.158670314 0.094560822 227.5111075 2.27571803 80.42475156 0.172474651 1.00E-05 4.999999996 0.99004442 FLIATGERPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLIATGERPR 10 1 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881;E9PKD3 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 ; 233.09 4.26E-12 4433900000 3372000 3850500 3541300 3416600 3929600 2862100 3979600 3128800 5262800 FALSE TRUE 3160952.539 4135595.026 3625301.308 3504275.74 3620985.067 3688341.808 3382895.925 3519437.567 4384404.681 0.720953646 0.943251211 0.82686284 0.799259191 0.825878387 0.841241189 0.771574745 0.802717318 1 22.06394953 -1.116180896 3.97476765 1.000049678 0.825597055 0.500855401 0.056935382 18481604.28 30150795.85 12068.48574 0.013707325 0.076527778 1.116180896 -0.174452622 FLIDGFPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLIDGFPR 8 0 P30085;P30085-3;A0A494BXC7;P30085-2;Q5T0D2 P30085 CMPK1 UMP-CMP kinase 0 ; 91.626 0.02874 359760000 675460 1102730 789610 785780 1124310 570330 821870 922610 1079660 FALSE TRUE 633184.1643 1184377.277 808339.9221 805944.4451 1036011.228 734975.0125 698638.2234 1037799.889 899457.7711 0.703962081 1.316768074 0.898696913 0.896033667 1.15181753 0.817131205 0.776732656 1.153806129 1 19.77869602 2.223508813 24.99470195 0.899529116 1.02019382 0 0.192088086 623.0953395 1034691.97 0.068129916 0.050512636 167.3049585 -2.223508813 0.120664704 FLKNEVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLKNEVER 8 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 90.108 0.012248 488370000 940570 1199360 967260 1092070 1444260 884300 1318980 1022030 1918730 FALSE TRUE 881701.4027 1288161.862 990203.864 1120094.365 1330833.645 1139583.055 1121211.194 1149632.695 1598481.568 0.551586844 0.805865947 0.6194653 0.700723979 0.832561146 0.712915981 0.70142266 0.719202973 1 20.60827068 -5 0.280393763 3.125233453 0.690799908 0.589541416 0.078378996 159.4748857 1.526864606 197.2962276 0.082648898 1.00E-05 5 -2.434433546 FLKS(ph)PPLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLKSPPLHK 9 1 Q9NYF8-4;E9PJA7 Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 FLKS(1)PPLHK;FLKS(1)PPLHK 87.001 0.008308 591310000 1199220 872490 979770 994410 1167110 769800 1284570 986920 1482570 TRUE FALSE 1124162.961 937090.0674 1003010.607 1019928.244 1075449.888 992028.7633 1091960.654 1110139.134 1235119.489 0.910165349 0.758703976 0.812075767 0.825772934 0.870725382 0.803184447 0.884093129 0.898811122 1 20.23621919 0.929265844 0.67647038 1.002011946 0.813901383 0.6130093 0.042097006 0.493409011 0.511807554 0.039283504 0.015585927 8.497004415 -0.929265844 -0.188110564 FLLDHQGELFPSPDPSGL ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLLDHQGELFPSPDPSGL 18 0 Q07960 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 61.038 0.096154 0 59599 45640 42612 45306 53364 34961 66388 38823 82996 FALSE TRUE 55868.80498 49019.23309 43622.77676 46468.62866 49173.0067 45053.67316 56433.73572 43670.13701 69143.43143 0.808013196 0.708949962 0.630902688 0.672061362 0.711173942 0.651597299 0.816183614 0.631587645 1 16.07730458 -4.056189812 0.423291343 3.240917941 0.69786976 0.662024256 0.065948077 236.3520042 3.441433545 480.1578481 0.036387285 8.79E-05 4.056189812 -2.543048182 FLLESFNNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLLESFNNDR 10 0 Q13618;Q13618-2;Q13618-3 Q13618 CUL3 Cullin-3 0 ; 153.97 3.56E-05 537620000 334760 441440 387480 389780 428380 310160 473130 364970 398350 FALSE TRUE 313807.9692 474124.6769 396671.2086 399782.4147 394736.7628 399698.157 402188.5488 410537.3079 331862.8116 0.945595464 1.428676731 1.195286711 1.204661688 1.189457659 1.204407795 1.211912076 1.237069336 1 18.34022744 -3.5855802 0.408496995 4.24E-13 1.225697505 0.207027113 0.116857223 305.8846376 6.544509854 264.333466 0.06488352 0.000259669 3.5855802 1.225697505 FLLSLPEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLLSLPEHR 9 0 Q15008;Q15008-4;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 142.92 0.00010317 750250000 1136580 1689610 1344690 1342910 1702560 1131100 1530010 1440970 1600340 FALSE TRUE 1065443.487 1814710.482 1376586.682 1377371.344 1568847.805 1457630.208 1300599.204 1620878.276 1333232.915 0.799142801 1.361135374 1.032517774 1.033106315 1.176724477 1.093304997 0.975522873 1.21575027 1 20.34649741 -3.34805915 0.21498488 0.782375991 1.114671762 0.001611403 0.151728479 262.1041533 4.953690953 25.7145428 0.29742639 0.000448684 3.34805915 0.332295771 FLMECRNS(ph)PVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 FLMECRNSPVTK 12 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 FLMECRNS(0.795)PVT(0.205)K;FLMECRNS(0.995)PVT(0.005)K;FLMECRNS(0.854)PVT(0.146)K;FLMECRNS(0.989)PVT(0.011)K;FLMECRNS(1)PVTK 132.84 0.0001053 3164540000 1193744 1221738 1043005 1201040 2344850 1027896 1799790 1367900 6260450 TRUE FALSE 1119029.694 1312196.753 1067745.571 1231860.72 2160694.94 1324632.889 1529928.198 1538685.326 5215540.451 0.214556805 0.25159363 0.20472386 0.236190426 0.414280161 0.253978068 0.293340299 0.295019345 1 22.31438533 -5 0.315069832 7.741946664 0.233122409 0.946758654 0.054611433 62.20193976 0.557476841 278.888183 0.048399191 1.00E-05 5 -7.508824255 FLMPEAYPS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 72.29 0.04436 24144000 50894 61137 67797 70011 75865 54256 65238 65916 58851 TRUE FALSE 47708.63539 65663.64709 69405.17686 71807.60079 69906.86892 69918.82643 55456.16754 74145.7577 49028.38791 0.97308187 1.339298514 1.415612053 1.464612724 1.425844738 1.426088628 1.131103222 1.512302584 1 15.58132971 -1.09148652 4.263876932 0.99996308 1.338497588 0.291392765 0.16462188 10547770.73 2700066.995 4431.718454 0.036165217 0.081005308 1.09148652 0.338534508 FLMPEAYPSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FLMPEAYPSSPR 12 0 O43166-3;O43166-2;O43166 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 FLMPEAYPS(0.101)S(0.899)PR;FLMPEAYPS(0.197)S(0.803)PR;FLMPEAYPSS(1)PR 226.51 1.59E-11 168341000 399235 493091 452264 434870 510732 395847 480564 417517 403753 TRUE FALSE 374247.594 529599.9707 462991.9157 446029.5004 470621.1689 510121.6029 408507.8895 469644.9165 336364.016 1.112626727 1.574484623 1.376460899 1.326032153 1.399142437 1.516576027 1.214481544 1.396240068 1 18.35966385 -0.051171138 0.579489877 0.971257799 1.399386018 0.405951707 0.134751493 4.192355201 1.578919014 0.400508132 0.052227467 0.888850789 0.051171138 0.428128219 FLNEHPGGEEVLLEQAGVDASESFEDVGHSSDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLNEHPGGEEVLLEQAGVDASESFEDVGHSSDAR 34 0 D6RFH4;H3BUX2;O43169 D6RFH4 CYB5B Cytochrome b5 type B 0 ; 217.93 2.15E-36 50580000 29746 57384 44879 48291 62792 48885 58865 68853 65700 FALSE TRUE 27884.25096 61632.77107 45943.55107 49530.22882 57860.56961 62997.30592 50038.73973 77449.44861 54734.24556 0.509447982 1.126036733 0.839393155 0.904922107 1.057118245 1.150966918 0.914212651 1.415008973 1 15.74015615 4.745213589 24.84308025 1.028448579 0.509447724 0.517081177 0.163178502 580.0062112 2165758.131 0.035949534 0.348302397 55617.77226 -4.745213589 -0.519000855 FLPLFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLPLFDR 7 0 P61604;B8ZZL8;S4R3N1 P61604;S4R3N1 HSPE1;HSPE1-MOB4 "10 kDa heat shock protein, mitochondrial" 0 ; 163.84 0.0028377 1761960000 853030 1353200 779880 670990 1634880 680310 718650 1286840 1476130 FALSE TRUE 799640.375 1453392.336 798379.1219 688208.7394 1506483.12 876704.4531 610895.1041 1447504.807 1229754.367 0.650243981 1.181855804 0.649218367 0.55963106 1.225027664 0.712910217 0.49676189 1.177068239 1 20.22993875 3.953071743 23.74882722 0.790090547 0.949211528 0 0.277177042 641.6722875 633650.0579 0.066907356 0.120720343 8975.770573 -3.953071743 0.159120981 FLPLNIRNS(ph)PFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FLPLNIRNSPFTR 13 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 FLPLNIRNS(1)PFTR;FLPLNIRNS(0.847)PFT(0.153)R;FLPLNIRNS(0.999)PFT(0.001)R 222.64 1.04E-11 655008000 628230 930860 735140 754840 1169330 568880 913180 843040 1584970 TRUE FALSE 588910.2057 999781.843 752577.868 774210.4723 1077495.539 733106.421 776257.1365 948295.3998 1320428.268 0.445999393 0.757164829 0.569949831 0.586332852 0.816019745 0.555203519 0.587882853 0.718172598 1 20.3325745 0.884833655 4.201816657 0.999936662 0.627376527 0.572354907 0.103912012 0.444683951 14.86347558 0.090568508 0.02308304 7.67067629 -0.884833655 -0.372560134 FLQDYFDGNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLQDYFDGNLK 11 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 123.67 0.00084938 195445000 711660 665140 674690 667220 695170 543540 766330 619060 537390 FALSE TRUE 667118.4709 714387.6577 690693.9654 684341.9948 640574.1524 700451.1744 651425.9308 696351.0037 447696.1373 1.490114422 1.595697613 1.542774011 1.528585882 1.430823496 1.564568277 1.455062656 1.555409899 1 18.77216035 -2.707471563 0.380508047 1.39E-16 1.541657664 0.907337668 0.052069208 21.46741816 0.820620668 17.57419651 0.032686467 0.00196123 2.707471563 1.541657664 FLQDYFDGNLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLQDYFDGNLKR 12 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 166.62 8.25E-05 4672600000 2126830 2354840 2058170 2260150 2406270 1567140 2629380 1848330 2265310 FALSE TRUE 1993715.507 2529194.804 2106990.764 2318149.275 2217291.261 2019547.878 2235128.879 2079098.069 1887215.127 1.05643256 1.340173024 1.116455 1.228343946 1.17490117 1.07012065 1.184352991 1.101675183 1 20.84782746 0.599540736 0.323326769 0.970849649 1.216807714 0.303021045 0.080909305 2.858536636 0.675892528 0.226212517 0.086952425 3.976863972 -0.599540736 0.245958065 FLQEHGSDS(ph)FLAEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLQEHGSDSFLAEHK 15 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 1 FLQEHGS(0.248)DS(0.752)FLAEHK;FLQEHGS(0.049)DS(0.951)FLAEHK 167.45 2.19E-06 330290000 368190 374910 386780 393640 424940 299660 468970 361870 493990 TRUE FALSE 345145.6451 402668.7265 395954.6043 403741.4688 391566.9265 386166.9774 398652.3022 407050.2661 411539.8777 0.838668775 0.978444006 0.962129372 0.98105066 0.951467762 0.938346436 0.968684504 0.989090701 1 18.65067271 4.741367496 24.99307516 0.968019583 0.838668728 0.840999312 0.01805797 96.01259081 854871.2499 0.004036242 0.028040714 55127.39825 -4.741367496 -0.129350855 FLQEHGSDSFLAEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FLQEHGSDSFLAEHK 15 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ;;; 236.81 5.89E-18 752000000 392569 768218 660504 679229 793733 535458 795021 736576 939263 FALSE TRUE 367998.807 825097.6601 676171.4668 696659.1661 731396.4119 690036.0322 675814.9817 828539.135 782493.9374 0.470289659 1.054446074 0.864123585 0.890306152 0.934699142 0.881842017 0.86366801 1.058844159 1 19.57772005 4.748137121 24.92681683 0.930940843 0.470289403 0.799989421 0.074123145 545.2951403 1419325.932 0.016877759 0.218123557 55993.43626 -4.748137121 -0.460651439 FLQESNVLYQHNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLQESNVLYQHNLR 14 0 P40763;P40763-2;P40763-3 P40763 STAT3 Signal transducer and activator of transcription 3 0 194.48 1.39E-07 873520000 1305600 1417500 1135200 1165500 1440500 876090 1341800 1253500 1240900 FALSE TRUE 1223884.827 1522453.175 1162127.48 1195408.703 1327368.941 1129002.961 1140609.547 1410002.234 1033785.773 1.183886312 1.472696969 1.124147294 1.156340834 1.283988399 1.092105337 1.103332601 1.363921105 1 19.97950582 7.999999963 0.061199709 0.762089432 2.15163055 0.219139675 0.123975701 411.8638727 1.879587472 8.486135828 50.76023697 99999991.42 -7.999999963 1.389541118 FLQPVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLQPVHK 7 0 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ; 97.071 0.012267 994650000 1817730 1833170 1817660 1758680 1885440 1559600 2332600 1704080 2069390 FALSE TRUE 1703961.524 1968899.814 1860775.754 1803810.706 1737365.148 2009831.202 1982848.285 1916838.139 1723995.44 0.988379368 1.142056277 1.079339139 1.04629668 1.007755071 1.165798444 1.150147059 1.11185801 1 20.71732453 2.226231835 24.99862013 1.124405516 1.068271016 0.107405635 0.061558177 411.2931754 833958.2367 0.021964715 0.016337816 168.3572544 -2.226231835 -0.056134499 FLRPHYGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLRPHYGK 8 1 Q13200;C9JPC0;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 108.46 0.002287 1092940000 2302390 2620800 2355200 2277080 2873700 1566880 2716000 2572800 3438900 FALSE TRUE 2158287.52 2814846.759 2411066.456 2335513.728 2648011.194 2019212.82 2308761.014 2894019.743 2864925.374 0.7533486 0.982520098 0.841580894 0.815209272 0.924286272 0.704804683 0.805871258 1.010155367 1 21.45006613 1.231706007 24.92794059 1.005077818 0.842521112 0.45183891 0.078417982 167.0820459 607593.7999 0.070252857 0.01912109 17.04927857 -1.231706007 -0.162556706 FLRT(ph)AEADGGLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLRTAEADGGLAR 13 1 Q8NC60 Q8NC60 NOA1 Nitric oxide-associated protein 1 1 FLRT(1)AEADGGLAR;FLRT(1)AEADGGLAR 76.522 0.045977 263880000 4102.4 10950.4 6975.8 6902.5 14265 10363.2 7359.8 9509 8862.4 TRUE FALSE 3845.638107 11761.17901 7141.26927 7079.629836 13144.68444 13354.88761 6256.266315 10696.21958 7383.208187 0.520862748 1.59296321 0.967231194 0.958882596 1.780348611 1.808819049 0.847364202 1.448722467 1 12.85003212 FLS(ph)DPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLSDPAR 7 0 Q6P1Q9;F8WAS9 Q6P1Q9 METTL2B Methyltransferase-like protein 2B 1 FLS(1)DPAR 89.698 0.018548 72174000 456470 498690 484870 459800 535660 378380 546110 440380 592660 TRUE FALSE 427900.3575 535613.5265 496371.3454 471599.2464 493591.4243 487612.1635 464225.8753 495362.4124 493741.2173 0.866649051 1.084806185 1.005326936 0.955154704 0.999696617 0.987586506 0.940221029 1.003283492 1 18.91339556 3.375837027 8.060895218 0.976867342 1.010327217 0 0.057615212 0.678151367 48.06698391 0.014923802 0.020237899 2375.948525 -3.375837027 0.033459875 FLSAIVSSVDKIPYGMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLSAIVSSVDKIPYGMR 17 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 134.44 1.55E-05 152475000 160801 198132 159913 189768 212928 143024 196423 160077 173157 FALSE TRUE 150736.7524 212801.8994 163706.2119 194637.7682 196205.4938 184312.707 166971.1947 180062.9658 144255.9781 1.044925517 1.475168671 1.134831388 1.349252702 1.360120367 1.277678121 1.157464646 1.248218398 1 17.13827158 0.61884554 0.738483923 0.999583003 1.284767479 0.295614069 0.123627168 1.476477316 1.441395314 0.11630973 0.040439261 4.157627156 -0.61884554 0.285184476 FLSAQSHSTS(ph)PQGLDSPLPLEGSGAHQVLHNESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNESK 34 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 FLS(0.002)AQS(0.026)HS(0.062)T(0.208)S(0.702)PQGLDSPLPLEGSGAHQVLHNESK;FLSAQSHST(0.003)S(0.997)PQGLDSPLPLEGSGAHQVLHNESK 244.5 4.81E-47 471540000 175372 217683 225984 218434 223598 189881 244256 201757 259108 TRUE FALSE 164395.7796 233800.4758 231344.4472 224039.3862 206037.515 244696.5622 207632.0804 226946.8056 215861.2009 0.761580955 1.083105601 1.071727787 1.037886315 0.954490729 1.133582882 0.961877723 1.051355244 1 17.71974443 4.744001971 24.89611364 1.040027034 0.76158083 0.715167618 0.054540761 292.3818681 1337707.132 0.012171518 0.106973906 55462.82299 -4.744001971 -0.278446204 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNES(ph)KGSPTSAYPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNESKGSPTSAYPER 44 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNES(0.856)KGS(0.142)PT(0.003)SAYPER 402.52 3.22E-214 572030000 32182 72239 54140 64051 97485 36938 73810 66132 120640 TRUE FALSE 30167.78607 77587.65072 55424.22637 65694.6571 89828.92134 47601.40096 62742.87572 74388.72577 100504.4046 0.30016382 0.771982591 0.55146067 0.653649532 0.893780941 0.473625023 0.624279861 0.740153887 1 16.6168992 -5 0.210823199 2.764529391 0.580380143 0.38793959 0.157767645 161.0524011 1.606737131 120.2185493 0.308626707 1.00E-05 5 -2.184149248 FLSDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLSDFR 6 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 98.03 0.093984 57567000 219830 328210 237240 254120 358720 185120 257690 302180 353980 FALSE TRUE 206071.2327 352511.0099 242867.4448 260641.1494 330547.5782 238561.1388 219051.7768 339907.8382 294898.4512 0.698787097 1.19536406 0.823562972 0.883833565 1.120886111 0.808960298 0.742804094 1.152626732 1 18.16985872 FLSDPQVHTVLVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FLSDPQVHTVLVER 14 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 136.81 2.49E-05 308690000 1114150 1523260 1377370 1437830 1661090 1165980 1680600 1527100 1537880 FALSE TRUE 1044417.34 1636043.755 1410041.867 1474727.152 1530634.692 1502579.498 1428609.632 1717761.797 1281197.893 0.81518815 1.276964132 1.10056524 1.15105337 1.194690298 1.17279267 1.115057744 1.340746661 1 20.2890619 4.749383357 24.74418737 1.170700334 0.815187917 0.586809699 0.093290046 893.303821 2042328.13 0.019480006 0.28601586 56154.34392 -4.749383357 -0.355512417 FLSHS(ph)TDSLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FLSHSTDSLNK 11 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;A0A087WY36 Q12802-2 AKAP13 A-kinase anchor protein 13 1 FLS(0.014)HS(0.978)T(0.008)DSLNK;FLS(0.003)HS(0.996)T(0.001)DSLNK;FLS(0.002)HS(0.993)T(0.006)DSLNK;FLS(0.002)HS(0.995)T(0.003)DSLNK;FLS(0.003)HS(0.978)T(0.02)DSLNK;FLSHS(0.999)T(0.001)DSLNK 202.13 2.65E-08 2279450000 3706110 3720080 3920750 3829970 4584030 2849130 5028530 3887720 6589730 TRUE FALSE 3474151.191 3995518.594 4013752.042 3928253.514 4224018.775 3671627.579 4274548.609 4373110.4 5489861.492 0.63283039 0.727799526 0.731120821 0.715546926 0.769421739 0.668801496 0.778625948 0.796579368 1 22.38833832 -5 0.19003496 2.198502268 0.67737731 0.853769017 0.037741636 47.53312018 0.465255721 21.44847664 0.095814067 1.00E-05 5 -1.521124957 FLSLYGDQIDMHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLSLYGDQIDMHR 13 0 Q96CN7;D6RGE2 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 ; 195.71 1.48E-07 445000000 790680 884830 848560 787760 905560 678170 833530 861310 738940 FALSE TRUE 741192.7502 950343.7339 868688.2439 807975.2553 834440.9705 873946.6698 708549.9146 968846.4495 615606.1403 1.204004804 1.543752851 1.411110428 1.312487323 1.355478635 1.419652295 1.150979284 1.573808944 1 19.2316481 -3.541092052 0.258564872 3.12E-12 1.410627315 0.388763382 0.137289443 79.61828652 1.556304778 42.66942348 0.175539829 0.000287679 3.541092052 1.410627315 FLSNGHVTIPGQQDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLSNGHVTIPGQQDK 15 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 97.579 0.0032594 403880000 733990 733510 843800 809510 771360 728140 1058700 751790 587480 FALSE TRUE 688050.8761 787819.8436 863815.3345 830283.3971 710780.4971 938342.1976 899957.7635 845652.6364 489425.7927 1.405832889 1.609681907 1.764956705 1.696443893 1.452274293 1.917230787 1.838803301 1.727846487 1 18.90073061 2.252281686 24.99947082 1.714804742 1.618542282 0 0.272425857 1006.350718 1833545.482 0.085577777 0.071234136 178.7646679 -2.252281686 -0.09626246 FLSNGHVTIPGQQDKDMFQETMEAMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLSNGHVTIPGQQDKDMFQETMEAMR 26 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 158.94 1.20E-11 1483830000 1118620 1508090 1418490 1494330 1726150 1089170 1861280 1413070 1673090 FALSE TRUE 1048607.571 1619750.553 1452137.253 1532677.038 1590585.142 1403595.698 1582198.343 1589494.9 1393840.47 0.752315343 1.162077431 1.041824573 1.099607215 1.141152934 1.006998812 1.13513589 1.140370748 1 20.41063402 4.745487103 24.99804998 1.094712633 0.752315185 0.772946762 0.057637498 349.2945497 1260590.429 0.012248472 0.122887175 55652.81076 -4.745487103 -0.342397448 FLSPVVPNYDNVHPNYHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLSPVVPNYDNVHPNYHK 18 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ; 146.76 4.71E-08 624230000 1345680 1271240 1357830 1359170 1357800 1164580 1653640 1279020 1173090 FALSE TRUE 1261456.291 1365363.932 1390038.369 1394048.603 1251163.865 1500775.341 1405692.034 1438708.462 977293.7005 1.290764783 1.397086599 1.422334318 1.426437725 1.280233224 1.535644136 1.438351678 1.472135205 1 19.89843267 -1.41381301 3.059717294 0.99336908 1.412590059 0.73872529 0.07618573 7896678.619 10022722.15 458816.864 0.017130411 0.038564437 1.41381301 0.41922098 FLSQIESDR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 166.09 0.00014193 1914450000 1692220 1871510 1811440 1694570 1776920 1430050 1756680 1724310 1735290 FALSE TRUE 1586306.971 2010078.548 1854408.212 1738055.535 1637367.871 1842882.22 1493282.142 1939593.899 1445658.889 1.097289951 1.390423815 1.28274258 1.202258395 1.132610109 1.27476975 1.032942248 1.341667744 1 20.46329575 3.122677732 3.150895547 1.158080227 1.290144112 0.102837033 0.122909033 0.379826079 7.51441255 0.033641129 0.041654248 1326.409832 -3.122677732 0.132063886 FLSQPFQVAEVFTGHMGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FLSQPFQVAEVFTGHMGK 18 0 P06576 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 ;; 372.18 1.12E-107 854880000 2126180 2011250 1843760 1720060 2717910 1731440 2057830 2210860 3504320 FALSE TRUE 1993106.189 2160165.043 1887494.858 1764199.652 2504456.312 2231278.62 1749277.495 2486890.738 2919426.353 0.682704733 0.739927911 0.646529362 0.60429668 0.857859048 0.764286661 0.599185348 0.851842258 1 21.47725349 1.003698743 5.54237406 0.99973079 0.699119853 0.630132678 0.07693283 0.083989924 10.01328127 0.07188163 0.018116727 10.08553042 -1.003698743 -0.300610937 FLTAVNLEHPEMLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLTAVNLEHPEMLEK 15 0 Q9Y2Q3-3;Q9Y2Q3;Q9Y2Q3-2;E9PFN5;Q9Y2Q3-4;C9JNT3 Q9Y2Q3-3 GSTK1 Glutathione S-transferase kappa 1 0 129.05 6.82E-05 228680000 761420 796270 698990 744280 841010 544970 812950 740260 760510 FALSE TRUE 713764.0814 855226.6593 715570.3729 763379.4849 774960.4671 702293.9922 691055.6946 832683.0905 633575.9679 1.126564323 1.349840749 1.12941527 1.204874433 1.223153191 1.108460591 1.090722707 1.314259272 1 19.27315809 -5 0.12450143 0.385435083 1.27847353 0.272995318 0.089727189 174.7373104 1.394582772 27.1206338 0.723189187 1.00E-05 5 0.893038447 FLTPIYHPNIDSAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLTPIYHPNIDSAGR 15 0 Q9NPD8 Q9NPD8 UBE2T Ubiquitin-conjugating enzyme E2 T 0 ; 182.35 5.50E-07 756400000 596510 763490 732180 675130 840380 731730 828480 735190 823410 FALSE TRUE 559175.5039 820019.594 749547.6554 692454.9788 774379.9447 942968.5724 704257.1152 826980.0899 685977.5516 0.815151316 1.195402958 1.092670822 1.009442623 1.128870679 1.374634739 1.026647466 1.205549785 1 19.38780184 2.488690575 24.44080185 1.161121061 1.067026878 0.126767044 0.139642568 1003.784823 2120554.432 0.043428356 0.038799944 308.0992033 -2.488690575 -0.094094183 FLTWILNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLTWILNR 8 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 150.84 0.0011231 74752000 107162 253750 124953 125012 277790 106840 131662 200460 129961 FALSE TRUE 100454.9217 272537.914 127916.9442 128220.0196 255973.494 137682.9736 111920.5054 225487.8723 108269.6695 0.927821449 2.517213872 1.1814661 1.184265364 2.364221624 1.271667072 1.033719839 2.082650416 1 16.72426962 -2.75343009 0.144262021 1.86E-12 1.831807755 0.050898307 0.578067038 154.084228 2.524960232 52.8069547 3.530075842 0.00176429 2.75343009 1.831807755 FLVHNVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLVHNVK 7 0 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ; 107.74 0.0074086 4249200000 11399300 11436200 10686200 10672700 11645900 9065500 13250100 10046300 11931700 FALSE TRUE 10685838.16 12282948.15 10939681.71 10946579.55 10731277.99 11682562.68 11263370.51 11300602.67 9940222.188 1.075009991 1.235681448 1.100547 1.101240932 1.0795813 1.175281846 1.133110538 1.136856144 1 23.24484667 -1.272028679 3.037506142 0.999175257 1.136031508 0.412069813 0.048142956 5154298.241 6789735.864 39647.28278 0.011962801 0.053452906 1.272028679 0.136856252 FLVYVANFDEKDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLVYVANFDEKDPR 14 1 P50395;P50395-2;Q5SX87;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 0 ; 105.17 0.00092592 5836700000 22219900 20388700 19786200 19926300 22850900 15450100 24855000 20028800 23414900 FALSE TRUE 20829196.12 21898300.56 20255538.01 20437642.59 21056282.49 19910293.06 21128223.49 22529439.77 19506801.92 1.06779144 1.122598192 1.038383333 1.047718774 1.079432834 1.020684638 1.08312083 1.154953019 1 24.21747394 3.975658451 24.84768761 1.06277625 1.096782234 0.095659561 0.043753265 143.9817199 2445771.394 0.010270558 0.019876908 9454.932903 -3.975658451 0.034005984 FLYDDNQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 FLYDDNQR 8 0 Q02880;Q02880-2;E9PCY5;P11388;P11388-2;P11388-3;P11388-4 Q02880;P11388 TOP2B;TOP2A DNA topoisomerase 2-beta;DNA topoisomerase 2;DNA topoisomerase 2-alpha 0 ;;;; 172.97 0.00065247 2489820000 2082760 2429990 2359220 2260150 2510090 1849270 2603060 2145340 2476970 FALSE TRUE 1952403.769 2609908.988 2415181.813 2318149.275 2312957.657 2383124.229 2212755.319 2413190.421 2063547.705 0.946139391 1.264767944 1.170402703 1.123380511 1.12086464 1.154867524 1.072306355 1.169437671 1 20.97669536 -0.501700612 0.365175312 0.957622797 1.155128198 0.1406767 0.083886681 12.87799596 1.720213045 0.756066554 0.062115023 0.314991902 0.501700612 0.1975054 FLYQLHETEKEDLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FLYQLHETEKEDLIR 15 1 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 240.04 4.78E-18 311410000 761260 751980 806710 762170 763290 550380 1019430 725640 1057340 FALSE TRUE 713614.0955 807657.3816 825845.5422 781728.5726 703344.2824 709265.7713 866575.9354 816237.7513 880863.1233 0.810130515 0.91689317 0.937541282 0.887457486 0.798471708 0.805194079 0.983780468 0.926634036 1 19.74855833 1.664846322 8.954427249 0.965966983 0.873896563 0.494633643 0.051277111 0.127737928 16.71392246 0.027097181 0.014363721 46.22174341 -1.664846322 -0.09207042 FLYTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FLYTGR 6 0 U3KQ56;Q9UBQ7;Q9UBQ7-2 U3KQ56 GRHPR Glyoxylate reductase/hydroxypyruvate reductase 0 99.228 0.090816 408360000 370990 387880 370560 330010 430160 319010 368840 371690 483250 FALSE TRUE 347770.3981 416599.0388 379349.8582 338478.6153 396376.9688 411103.0083 313535.8661 418096.3147 402592.4531 0.863827415 1.034790979 0.942267684 0.840747542 0.984561349 1.021139381 0.77879221 1.038510065 1 18.6189606 3.486679999 24.02862804 0.926563253 0.968919283 0 0.091175939 707.9523982 1779630.775 0.023074638 0.034377777 3066.761477 -3.486679999 0.04235603 FMADCPHTIGVEFGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FMADCPHTIGVEFGTR 16 0 P61106;X6RFL8 P61106 RAB14 Ras-related protein Rab-14 0 142.45 1.51E-06 68191000 70902 73337 81677 83330 90931 63278 93140 76173 94039 FALSE TRUE 66464.37038 78766.94779 83614.41701 85468.38888 83789.64606 81545.33137 79174.52167 85683.36673 78343.28338 0.848373562 1.005407795 1.067282521 1.090947241 1.069519204 1.040872017 1.010610205 1.093691291 1 16.25752197 4.830954678 1.84785176 1.05202769 0.748426816 0.814315518 0.030639414 0.460356741 1.34170214 0.007752849 0.260863492 67757.07945 -4.830954678 -0.303600874 FMDQHPEMDFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FMDQHPEMDFSK 12 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 87.498 0.010514 205740000 294170 259000 262790 275830 341850 145340 264900 300410 395670 FALSE TRUE 275758.4248 278176.6295 269023.5029 282908.2648 315002.48 187297.2986 225180.7042 337916.8498 329630.1209 0.836569255 0.843905371 0.8161375 0.858259749 0.955624077 0.568204441 0.683131455 1.025139477 1 18.33048855 1.222186432 24.9934652 1.012570012 0.792390997 0.42827013 0.104704011 284.1069374 433647.395 0.104776991 0.026509951 16.67963075 -1.222186432 -0.220179015 FMEQSRS(ph)PSVS(ph)PSKQPVSTSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FMEQSRSPSVSPSKQPVSTSSK 22 2 Q96JG6;Q96JG6-3;H0Y7Q2 Q96JG6 CCDC132 Coiled-coil domain-containing protein 132 2 FMEQS(0.202)RS(0.797)PS(0.135)VS(0.731)PS(0.135)KQPVSTSSK 97.771 0.0006766 128310000 123970 91644 108100 122920 138280 67919 136070 101050 183980 TRUE FALSE 116210.939 98429.41712 110664.183 126074.3353 127420.0466 87526.11273 115667.5667 113666.3149 153272.5494 0.758197991 0.642185554 0.722009149 0.822549998 0.831329857 0.571048848 0.754652853 0.741596035 1 17.22573981 -4.999998907 0.495752278 9.585054261 0.720418494 0.543138803 0.077393397 1758.454686 8.394631769 16738.49711 0.035969976 1.00E-05 4.999998907 -8.864635767 FMEQSRS(ph)PSVSPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FMEQSRSPSVSPSK 14 1 Q96JG6;Q96JG6-3;H0Y7Q2 Q96JG6 CCDC132 Coiled-coil domain-containing protein 132 1 FMEQSRS(1)PSVSPSK;FMEQS(0.004)RS(0.993)PS(0.003)VSPSK;FMEQS(0.156)RS(0.831)PS(0.013)VSPSK 167.14 2.24E-06 311330000 771070 856820 767480 856650 1006130 519430 955210 797560 1118210 TRUE FALSE 722810.1051 920259.8443 785684.988 878633.0893 927112.6083 669381.0088 811985.1282 897137.1216 931573.5271 0.775902367 0.987855298 0.843395572 0.943170951 0.995211415 0.718548766 0.871627525 0.963034152 1 19.82931012 1.10894532 4.456383812 0.99716427 0.882302225 0.205854804 0.086580839 0.328829454 10.37550905 0.078170141 0.019990389 12.85124847 -1.10894532 -0.114862045 FMERDPDELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 FMERDPDELR 10 1 A0A087WTB8;P15374;Q5TBK7 A0A087WTB8;Q5TBK7 UCHL3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L3 0 ;;;;;; 175.49 2.54E-06 1650510000 1876719 2336324 2137680 2175930 2403940 1843286 2314199 1960476 2644030 FALSE TRUE 1759258.508 2509307.86 2188386.779 2231768.048 2215144.249 2375412.745 1967206.344 2205245.744 2202724.312 0.798673941 1.139183804 0.993491 1.01318537 1.005638444 1.078397661 0.893078781 1.001144688 1 21.07085751 1.740798941 24.99999993 0.956147739 1.019329723 0.022166701 0.091506699 0.847433435 9525.105682 0.038397806 0.021293521 55.05527559 -1.740798941 0.063181984 FMFNIADGGFTELHSLWQNEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FMFNIADGGFTELHSLWQNEER 22 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y4X2;A0A2R8Y7I0;A0A2R8Y7M9 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ; 239.56 1.36E-30 218931000 219933 299451 258490 260697 320518 229166 285845 243003 267054 FALSE TRUE 206167.7861 321622.6636 264621.5049 267386.9264 295345.8092 295322.504 242985.1959 273342.4595 222480.9622 0.926676081 1.445618809 1.189411904 1.201841829 1.327510481 1.32740573 1.092161745 1.22861056 1 17.76332236 0.773250225 0.868073234 1.003493327 1.251132246 0.167555601 0.142544434 1.331187812 1.944036602 0.125118065 0.042839789 5.932670459 -0.773250225 0.247638919 FMLQDVLDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FMLQDVLDLR 10 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C044 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 147.75 6.13E-05 321650000 631570 1028430 724510 731890 1045500 564000 768220 894970 964950 FALSE TRUE 592041.1611 1104576.027 741695.7193 750671.5365 963390.6473 726817.6442 653032.5428 1006708.975 803893.6112 0.736467056 1.374032598 0.9226292 0.933794629 1.198405652 0.904121682 0.812337023 1.252291299 1 19.61664506 3.734813341 24.83576583 0.984229377 1.115052434 0 0.202944293 759.1784505 2451171.554 0.048438626 0.085319832 5430.168935 -3.734813341 0.130823057 FMQASEDLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FMQASEDLLK 10 0 Q32Q12;P22392-2;J3KPD9;E7ERL0;E5RHP0;P15531;P15531-2 Q32Q12;P15531 NME1-NME2;NME2;NME1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Nucleoside diphosphate kinase A 0 ; 117.67 0.0021554 121887000 371450 437720 308430 313590 436270 186047 385560 370070 452560 FALSE TRUE 348201.6076 470129.2442 315746.1053 321637.2503 402007.114 239755.7487 327748.8574 416274.0541 377024.8124 0.923550907 1.246945105 0.837467707 0.853093059 1.066261691 0.63591504 0.869303151 1.104102543 1 18.52429995 3.863741933 5.155975949 0.890856004 1.098428016 0.176040659 0.153042737 0.27059301 10.70019422 0.03666615 0.06784613 7307.047538 -3.863741933 0.207572012 FMSVQRPGPYDRPGTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FMSVQRPGPYDRPGTAR 17 2 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ;; 267.51 4.83E-28 5890140000 1861570 2059350 1940380 2017630 2187400 1614080 2287130 1976670 2428040 FALSE TRUE 1745057.657 2211826.417 1986406.73 2069405.802 2015610.428 2080038.694 1944196.089 2223461.601 2022784.438 0.862700752 1.093456314 0.982016023 1.023048113 0.996453398 1.028304675 0.961148431 1.099208378 1 20.94791115 4.756819059 24.60945188 1.019079301 0.862700587 0.562533389 0.044295842 2406.893514 3244041.555 0.009804404 0.31916097 57124.05904 -4.756819059 -0.156378714 FMTDPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FMTDPIR 7 0 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 94.407 0.052815 0 108800 212930 146900 141310 219750 117510 146580 184600 208950 FALSE TRUE 101990.4022 228695.5588 150384.5374 144936.2538 202491.7214 151433.2294 124601.6898 207647.7164 174074.8951 0.585899547 1.3137768 0.863907097 0.832608595 1.163244828 0.86993147 0.715793565 1.192864234 1 17.40934863 FMVGEVSYGSWYQHVQEWWELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FMVGEVSYGSWYQHVQEWWELSR 23 0 P50225;H3BRY5;P50225-2;H3BQX5 P50225 SULT1A1 Sulfotransferase 1A1;Sulfotransferase 0 ; 225.3 1.18E-32 62873000 21994.9 37708 15824.8 18890.8 34207 12933 22320.1 31166 12584.4 FALSE TRUE 20618.27847 40499.93956 16200.17173 19375.56991 31520.5202 16666.54715 18973.40821 35057.1437 10483.98234 1.966645669 3.863030119 1.545230734 1.848111651 3.006540757 1.589715302 1.809752019 3.343876646 1 13.35589921 3.939975863 9.328749192 2.050693061 3.00656074 0.167422076 0.82138329 0.515559725 125.062393 0.189096004 0.344082185 8709.15186 -3.939975863 0.955867679 FNADEFEDMVAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 FNADEFEDMVAEK 13 0 P27635;X1WI28;A0A087WV22;F8W7C6 P27635;F8W7C6 RPL10 60S ribosomal protein L10 0 ;;;;;;; 249.2 3.79E-17 846691000 1895459 1445830 1670943 1612680 1596244 1245954 1921980 1428972 1543900 FALSE TRUE 1776825.605 1552880.758 1710578.557 1654064.099 1470881.435 1605640.693 1633796.942 1607382.3 1286213.116 1.381439501 1.207327727 1.329934002 1.28599536 1.143575211 1.248347318 1.270238129 1.249701375 1 20.29469828 -4.230506043 0.245222603 1.61E-13 1.289724843 0.657484509 0.061394527 72.02408735 1.013927773 35.9543297 0.088524164 5.88E-05 4.230506043 1.289724843 FNADEFEDMVAEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 FNADEFEDMVAEKR 14 1 P27635;X1WI28;A0A087WV22;F8W7C6 P27635;F8W7C6 RPL10 60S ribosomal protein L10 0 ;;;;;;; 207.55 1.49E-08 3602483000 3283833 3340225 3337399 3359015 4055078 2400453 4327199 3233705 5768381 FALSE TRUE 3078303.754 3587538.735 3416563.68 3445213.012 3736608.531 3093424.813 3678375.682 3637440.188 4805600.946 0.640565829 0.746532801 0.710954513 0.716916167 0.777552813 0.643712378 0.765435109 0.75691682 1 22.19628542 0.379644207 1.029815258 1.000894038 0.714740241 0.807105621 0.043783149 0.972771807 1.270706854 0.038199503 0.011687055 2.396868493 -0.379644207 -0.286153798 FNADSGYSIHS(ph)DSESQAETVHGLDGCASLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FNADSGYSIHSDSESQAETVHGLDGCASLLR 31 0 A0A0A0MR27;J3QT39;Q49A88-5;Q49A88-6;Q49A88 A0A0A0MR27 CCDC14 Coiled-coil domain-containing protein 14 1 FNADSGYSIHS(0.985)DS(0.008)ES(0.008)QAETVHGLDGCASLLR 181.05 5.38E-18 83820000 17917 20711 20394 21014 20932 20458 25578 19587 22086 TRUE FALSE 16795.60695 22244.46399 20877.75531 21553.25482 19288.08516 26363.89249 21742.81635 22032.48007 18399.70392 0.912819414 1.208957714 1.134678873 1.171391394 1.048282366 1.432843301 1.181693817 1.197436663 1 14.16739493 FNDEHIPESPYLVPVIAPSDDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FNDEHIPESPYLVPVIAPSDDAR 23 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;;;;; 162.03 1.71E-11 6350440000 5090620 5583450 5148940 5271510 6126300 4346560 6073730 5037720 5395010 FALSE TRUE 4772007.181 5996854.448 5271075.288 5406785.871 5645165.11 5601341.311 5163030.572 5666690.431 4494547.978 1.061732393 1.334250847 1.172770947 1.202965437 1.256002859 1.246252424 1.148731885 1.260792066 1 22.0997446 -3.23448194 0.537076205 9.76E-08 1.217402341 0.439817623 0.07400193 395.6559233 11.19366943 457.7820225 0.029335245 0.000582798 3.23448194 1.217402244 FNDFDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FNDFDHR 7 0 Q9NWH9;Q9NWH9-3;H7C3F4;H0YMM0 Q9NWH9 SLTM SAFB-like transcription modulator 0 ;; 153.71 0.0017277 632940000 1369240 1503460 1473220 1365470 1576160 1219200 1574860 1307570 1967740 FALSE TRUE 1283541.713 1614777.743 1508165.474 1400510.272 1452374.752 1571163.248 1338724.363 1470822.993 1639311.482 0.782976101 0.98503412 0.919999336 0.854328349 0.885966314 0.958428746 0.816638191 0.897219966 1 20.64465857 FNDIHVPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FNDIHVPVR 9 0 Q29RF7;Q29RF7-3 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 0 63.283 0.07708 50862000 78091 102310 79032 86411 98281 61207 94977 93888 83723 FALSE TRUE 73203.42371 109885.1389 80906.67636 88628.45255 90562.40671 78876.46729 80736.08057 105610.1235 69749.09043 1.049525137 1.575434721 1.159967476 1.270675388 1.298402691 1.130860156 1.157521626 1.514143379 1 16.08988678 3.740716405 24.47546817 1.221303251 1.355341795 0.031941088 0.182904729 726.8676776 1308576.104 0.042131989 0.075409992 5504.48136 -3.740716405 0.134038544 FNDILGR ddPTM_SK-BR-3_Pertuzumab_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 ; 135.77 0.0070847 145684000 489010 545940 477090 473710 564330 417780 575710 472810 616240 FALSE TRUE 458403.737 586361.9657 488406.8001 485866.2006 520009.7982 538386.3039 489387.6301 531841.3693 513385.5629 0.892903444 1.142147361 0.951345023 0.946396307 1.012903042 1.048697787 0.953255536 1.035949212 1 18.9696832 3.754657457 24.81485385 0.990812516 1.038753853 0.000878096 0.069012073 864.0670894 778667.3296 0.01605709 0.028938894 5684.044338 -3.754657457 0.047941337 FNDS(ph)EGDDT(ph)EETEDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FNDSEGDDTEETEDYR 16 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 2 FNDS(1)EGDDT(1)EETEDYR;FNDS(1)EGDDT(1)EETEDYR 205.84 1.14E-10 1206420000 3545300 2804600 3355200 3099100 2953300 3253700 4182500 3055300 3344700 TRUE FALSE 3323406.002 3012255.502 3434786.928 3178628.153 2721359.731 4192990.371 3555372.953 3436760.931 2786447.962 1.192703415 1.081037774 1.232675785 1.140745564 0.976641146 1.504779715 1.275951678 1.233384214 1 21.40999578 2.253948217 24.99997433 1.284615511 1.134240837 0.158285737 0.138642618 337.830044 548865.887 0.043773253 0.0364991 179.4519646 -2.253948217 -0.150374673 FNDS(ph)EGDDTEETEDYR ddPTM_SK-BR-3_Pertuzumab_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(1)EGDDTEETEDYR;FNDS(1)EGDDTEETEDYR;FNDS(1)EGDDTEETEDYR;FNDS(0.999)EGDDT(0.001)EETEDYR 497.23 8.60E-258 16742110000 1463374 1345464 1360353 1390382 1444154 1202789 1587486 1167548 1524854 TRUE FALSE 1371784.034 1445083.555 1392621.216 1426061.556 1330735.97 1550014.659 1349457.212 1313318.938 1270346.016 1.079850699 1.137551136 1.09625346 1.122577264 1.047538193 1.220151548 1.062275313 1.03382773 1 20.27679008 1.499094878 7.805199875 1.026800268 1.116464317 0.459288841 0.045341985 0.095882435 14.02540674 0.022229474 0.010198968 31.55693959 -1.499094878 0.089664048 FNDSEGDDT(ph)EETEDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FNDSEGDDTEETEDYR 16 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 FNDS(0.245)EGDDT(0.755)EETEDYR 427.24 4.20E-159 468560000 179500 155530 175410 171230 164720 136600 181470 145610 188880 TRUE FALSE 168265.4154 167045.603 179570.808 175624.0517 151783.5556 176034.2025 154260.2582 163789.729 157354.7078 1.069338298 1.061586306 1.141184846 1.116102938 0.964594945 1.118709475 0.98033456 1.040895003 1 17.26366082 2.761243547 24.9890713 1.02458347 1.098497261 0.394846747 0.046704228 789.7698969 870063.4647 0.01323962 0.014035177 577.089997 -2.761243547 0.073913791 FNEEHIPDSPFVVPVAS(ph)PSGDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FNEEHIPDSPFVVPVASPSGDAR 23 0 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5C6 Q60FE5 FLNA Filamin-A 1 FNEEHIPDSPFVVPVAS(0.918)PS(0.082)GDAR;FNEEHIPDSPFVVPVAS(0.903)PS(0.097)GDAR;FNEEHIPDSPFVVPVAS(0.963)PS(0.037)GDAR;FNEEHIPDSPFVVPVAS(0.902)PS(0.098)GDAR 184.19 2.20E-17 609770000 775340 782330 796860 790800 829720 710560 876130 700220 1010390 TRUE FALSE 726812.8534 840254.5272 815761.8955 811093.2668 764557.1381 915687.137 744762.4401 787644.0084 841749.3816 0.863455168 0.99822411 0.969126813 0.963580472 0.908295456 1.087838206 0.884779314 0.935722705 1 19.68303123 4.75017379 23.76283131 0.966532688 0.863455043 0.259479973 0.055657013 1215.414934 2486882.301 0.012130587 0.185165315 56256.63996 -4.75017379 -0.103077645 FNEEHIPDSPFVVPVASPSGDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 FNEEHIPDSPFVVPVASPSGDAR 23 0 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5C6 Q60FE5 FLNA Filamin-A 0 ;;;; 180.42 4.56E-17 1173860000 1131312 1219200 1212704 1204267 1299728 935803 1309973 1057302 1296990 FALSE TRUE 1060505.201 1309470.837 1241469.912 1235170.53 1197652.606 1205954.135 1113554.71 1189308.482 1080513.99 0.981482157 1.211896235 1.148962367 1.143132381 1.108410087 1.116093031 1.030578706 1.100687722 1 20.04328632 1.733520079 0.866672307 1.021857022 1.142030125 0.203371165 0.063525145 0.662119378 0.94600288 0.052517391 0.022662553 54.14022785 -1.733520079 0.120173103 FNEGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FNEGER 6 0 P35579 P35579 MYH9 Myosin-9 0 ;; 145.88 0.025799 4066330000 3571510 4173690 3712670 4021950 4091710 3216040 4417240 3500300 4103320 FALSE TRUE 3347975.564 4482714.35 3800736.286 4125160.046 3770363.602 4144458.54 3754915.87 3937320.16 3418449.384 0.979384273 1.311329743 1.1118305 1.206734277 1.102945569 1.212379671 1.09842664 1.15178542 1 21.70491063 -0.005506903 0.487356242 0.982319281 1.170680292 0.194738444 0.088567723 5.72926682 1.692139711 0.276669221 0.040826716 0.987399941 0.005506903 0.188361012 FNFLAPELPAVSEFSTSETMGHSADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FNFLAPELPAVSEFSTSETMGHSADR 26 0 P55084-2;P55084;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ;; 239.34 4.91E-45 432637000 773299 825534 794759 729048 1067495 775691 745236 835248 1149805 FALSE TRUE 724899.596 886657.3963 813611.0588 747756.606 983658.2488 999620.3994 633494.7802 939530.5514 957895.1175 0.756763014 0.92563098 0.849373845 0.780624718 1.026895566 1.043559343 0.661340442 0.980828208 1 19.86950817 4.749133018 23.25504509 0.889128034 0.756762811 0.118336377 0.120232857 1371.760695 3017160.939 0.027488881 0.368407696 56121.98433 -4.749133018 -0.132365223 FNFLNPNDPYHAYYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FNFLNPNDPYHAYYR 15 0 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 ; 210.36 1.92E-09 1252150000 1092070 1294510 1075920 1058470 1282620 832830 1229670 1166740 1328020 FALSE TRUE 1023719.288 1390356.867 1101441.33 1085632.132 1181888.199 1073254.501 1045292.399 1312410.057 1106364.883 0.925299875 1.256689261 0.995549794 0.981260477 1.068262576 0.97007282 0.944798968 1.186236185 1 20.07739584 3.72984007 24.58538658 1.011737388 1.118101541 0.054201552 0.104120284 164.4828103 1487336.543 0.024564855 0.041889645 5368.340697 -3.72984007 0.106364153 FNGGHS(ph)PTHS(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FNGGHSPTHSPEK 13 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 2 FNGGHS(0.86)PT(0.14)HS(1)PEK;FNGGHS(0.975)PT(0.025)HS(1)PEK 127.62 9.23E-05 1258250000 1926820 1243820 1470470 1452330 1634610 1154210 1870070 1335420 1796010 TRUE FALSE 1806223.776 1335913.727 1505350.243 1489599.247 1506234.324 1487411.69 1589670.364 1502150.127 1496244.328 1.207171677 0.892844639 1.006085847 0.995558826 1.006676714 0.994096794 1.062440361 1.003947081 1 20.51291435 FNGGHS(ph)PTHSPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FNGGHSPTHSPEK 13 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 FNGGHS(0.559)PT(0.439)HS(0.003)PEK;FNGGHS(0.843)PT(0.157)HSPEK;FNGGHS(0.88)PT(0.12)HSPEK;FNGGHS(0.758)PT(0.241)HSPEK 148.97 2.80E-05 3961680000 3089540 3190920 3031790 2986780 3895510 2069950 3253880 2954880 4059080 TRUE FALSE 2896171.206 3427179.037 3103705.491 3063425.831 3589572.358 2667510.962 2765990.902 3323803.272 3381593.325 0.856451657 1.013480542 0.917823402 0.905911958 1.061503266 0.788832573 0.817954921 0.982910407 1 21.68927174 2.22730735 24.99990353 0.872028412 0.952969843 0.053722354 0.086103038 371.6565295 825654.5458 0.029765344 0.022181988 168.7747019 -2.22730735 0.080941431 FNGGHSPT(ph)HSPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FNGGHSPTHSPEK 13 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 FNGGHS(0.231)PT(0.766)HS(0.002)PEK;FNGGHS(0.067)PT(0.932)HS(0.001)PEK 135.08 0.00032436 2630930000 2091350 2101500 1911600 1901620 2469200 1337560 1952890 1993080 2628100 TRUE FALSE 1960456.137 2257097.247 1956944.055 1950418.789 2275278.992 1723691.859 1660072.274 2241920.425 2189453.132 0.895409044 1.030895439 0.893804954 0.890824636 1.039199679 0.787270498 0.758213204 1.023963652 1 21.06213914 2.231493095 24.99969474 0.85696504 0.950696686 0.0265484 0.098375414 283.3487939 1002270.463 0.034571538 0.026068953 170.4092224 -2.231493095 0.093731646 FNGST(ph)EALDKLDADAVSPTVSQLSAVFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FNGSTEALDKLDADAVSPTVSQLSAVFEK 29 1 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 1 FNGS(0.118)T(0.882)EALDKLDADAVSPTVSQLSAVFEK;FNGS(0.139)T(0.861)EALDKLDADAVSPTVSQLSAVFEK 241.83 2.97E-45 449600000 995140 572020 596620 647330 636980 414040 1025320 576240 783540 TRUE FALSE 932855.9638 614372.956 610772.1081 663941.5837 586954.1603 533566.6266 871582.7846 648184.8325 652762.1121 1.42909024 0.941189669 0.935673344 1.01712641 0.899185399 0.817398278 1.335222692 0.992987829 1 19.3161978 -0.583656393 7.698123585 1.000001652 1.033741016 0.002043932 0.192128861 0 0 0.177121797 0.041748008 0.260821631 0.583656393 0.033739364 FNHDGEEEEEDDDYGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FNHDGEEEEEDDDYGSR 17 0 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;Q6PJT7-9;Q6PJT7-2;H0YJA2;Q6PJT7-3;Q6PJT7-11;G3V5I6 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 0 ; 193.19 1.44E-10 517780000 147163 205426 193659 181882 196290 161006 204707 148848 195183 FALSE TRUE 137952.3305 220635.9548 198252.6829 186549.4 180874.1752 207485.8185 174013.0858 167432.0005 162605.6964 0.848385595 1.356877156 1.21922348 1.147250092 1.112348332 1.276005842 1.070153689 1.029681027 1 17.31101827 1.561670236 5.252548413 1.02522073 1.187219704 0.154647432 0.13354333 0.216845378 12.72299082 0.071577027 0.032390103 36.44770905 -1.561670236 0.161998975 FNHPEIVQLVSELEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FNHPEIVQLVSELEAER 17 0 Q7Z4H3-2;Q7Z4H3 Q7Z4H3-2 HDDC2 HD domain-containing protein 2 0 ; 145.91 4.57E-07 111900000 101907 102671 106688 101469 123040 91845 123597 97439 117292 FALSE TRUE 95528.82278 110272.8677 109218.6897 104072.8663 113376.9347 118359.1605 105064.7773 109604.4736 97715.20746 0.977624929 1.128512854 1.117724585 1.065063147 1.160279323 1.211266533 1.075214186 1.121672629 1 16.57629549 4.741504839 24.31070155 1.117049325 0.977624853 0.342995171 0.056815731 196.9815567 1626366.579 0.012191347 0.086198899 55144.83464 -4.741504839 -0.139424472 FNHWELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FNHWELK 7 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 141.78 0.0025335 2900300000 8182700 7604500 7756200 7179800 8351500 5833900 9685800 7324200 9006300 FALSE TRUE 7670559.414 8167545.092 7940180.727 7364045.823 7695606.878 7518052.225 8233504.209 8238642.493 7503090.347 1.022320012 1.088557476 1.058254714 0.981468366 1.025658298 1.001994095 1.097348403 1.098033225 1 22.8390535 -0.854693296 7.262468511 1 1.050411921 0.112097543 0.04012039 0 8.11E-11 0.039538206 0.009319244 0.139735484 0.854693296 0.050411921 FNLILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FNLILR 6 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 115.83 0.056065 68531000 124840 231430 112990 114210 278940 91998 122680 244390 238860 FALSE TRUE 117026.4872 248565.318 115670.1762 117140.822 257033.1776 118556.3291 104285.2729 274902.6295 198992.7229 0.588094306 1.249117628 0.581278423 0.588668873 1.291671242 0.595782235 0.524065762 1.381470767 1 17.60235615 1.231871194 24.99913631 1.190735355 0.790854236 0.258548606 0.292256564 245.7110171 918208.4948 0.249572278 0.068050247 17.05576461 -1.231871194 -0.399881119 FNLLAHLADDLGHVVPNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FNLLAHLADDLGHVVPNSR 19 0 Q8N5N7;Q8N5N7-2 Q8N5N7 MRPL50 "39S ribosomal protein L50, mitochondrial" 0 ; 161.04 1.75E-11 115649000 139184 175679 144191 135165 228440 132160 148841 176103 237000 FALSE TRUE 130472.7219 188686.456 147611.2786 138633.5627 210499.2439 170312.4466 126523.6738 198089.8472 197443.1689 0.660811527 0.955649451 0.747614007 0.702144133 1.066125736 0.862589714 0.640810591 1.003275263 1 17.59107793 1.184974385 24.93535846 1.001639882 0.813762338 0.275850223 0.131803395 145.8572016 67868.04846 0.120908259 0.030227142 15.30997159 -1.184974385 -0.187877544 FNLTYVSHDGDDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FNLTYVSHDGDDK 13 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ; 170.56 2.66E-05 370140000 829610 485700 569420 524050 550680 478260 889030 591260 1023070 FALSE TRUE 777686.191 521661.7334 582926.9113 537498.0102 507431.8141 616325.8981 755728.2048 665080.1125 852313.0077 0.912442007 0.612054173 0.683935252 0.630634527 0.595358524 0.723121544 0.886679187 0.780323785 1 19.70102382 1.825289437 3.710962651 0.876512984 0.672772302 0.446481295 0.102296159 0.198387066 4.674517491 0.047839945 0.025447469 66.87894861 -1.825289437 -0.203740683 FNPFVTSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 169.44 0.00013602 2818600000 2277580 2897980 2542120 2692550 2838960 2206340 2794100 2588040 2723640 FALSE TRUE 2135030.333 3112549.455 2602420.287 2761645.391 2615999.533 2843274.541 2375150.644 2911162.491 2269046.889 0.940937071 1.371743118 1.146922217 1.217094898 1.152906776 1.253069981 1.046761376 1.282989129 1 21.11365499 -4.477800731 0.285160994 6.62E-12 1.197370162 0.147016754 0.122537799 283.0803794 3.571115806 166.3109711 0.122005785 3.33E-05 4.477800731 1.197370162 FNSLNELVDYHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FNSLNELVDYHR 12 0 P62993;P62993-2 P62993 GRB2 Growth factor receptor-bound protein 2 0 ;;; 180.48 1.94E-05 668270000 745770 806850 794750 760940 875040 609350 862990 732390 879120 FALSE TRUE 699093.5869 866590.0135 813601.8453 780467.0087 806317.8881 785259.453 733592.6611 823830.5037 732389.1927 0.954538371 1.183237031 1.11088729 1.065645174 1.100941816 1.07218875 1.001643209 1.124853441 1 19.48225098 1.999780496 6.151245616 1.04088401 1.098888111 0.045565524 0.066227913 0.290229145 47.25640638 0.025235184 0.017187021 99.94947004 -1.999780496 0.058004101 FNVLHWHIVDDQSFPYQSITFPELSNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FNVLHWHIVDDQSFPYQSITFPELSNK 27 0 P07686;Q5URX0 P07686 HEXB Beta-hexosaminidase subunit beta;Beta-hexosaminidase subunit beta chain B;Beta-hexosaminidase subunit beta chain A 0 144.4 9.98E-08 71784000 74832 91456 56249 46168 112760 40992 73640 85303 38799 FALSE TRUE 70148.3987 98227.4974 57583.25284 47352.74904 103904.2845 52825.72495 62598.36564 95953.26733 32323.19625 2.170218507 3.038916592 1.781483873 1.464977308 3.214542388 1.63429769 1.936639098 2.968557521 1 14.98028224 -1.941491798 2.877154649 0.150479612 2.251740675 0.29870197 0.613529699 50319075.87 45681620.1 288276498.2 0.138251711 0.011442165 1.941491798 2.101261063 FNVWDTAGQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FNVWDTAGQEK 11 0 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 143.97 8.59E-05 92356000 209670 205250 204780 182480 226360 186810 239210 210880 248950 FALSE TRUE 196547.129 220446.9236 209637.4783 187162.7457 208582.5987 240739.0144 203342.6812 237208.8322 207398.6367 0.947678018 1.062914043 1.010794871 0.902429971 1.005708629 1.160755047 0.980443673 1.143733806 1 17.66204689 2.447099797 24.99764917 1.065796772 0.995035743 0.271051778 0.06862136 321.2219456 267466.8655 0.02250673 0.018830721 279.9624574 -2.447099797 -0.070761029 SKDDQVTVIGAGVTLHEALAAAELLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKDDQVTVIGAGVTLHEALAAAELLKK 27 2 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 273.41 4.92E-61 571020000 1052600 817240 801410 699280 1448700 579770 1150000 1040700 2370700 FALSE TRUE 986719.6449 877749.2999 820419.8237 717224.7087 1334924.946 747140.1872 977568.1761 1170633.686 1975014.855 0.499601126 0.444426683 0.415399318 0.36314902 0.675906281 0.378295984 0.494967506 0.592721459 1 20.91343207 0.723435691 1.631268718 0.999867317 0.457217221 0.789305339 0.086362036 0.399697387 1.676608794 0.074962538 0.021460682 5.289756621 -0.723435691 -0.542650097 FPAMSDAYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FPAMSDAYDR 10 0 P00491;G3V5M2 P00491 PNP Purine nucleoside phosphorylase 0 ;;; 101.65 0.0074206 532523000 292286 704521 291138 327440 710216 299569 323196 650382 342210 FALSE TRUE 273992.341 756684.4679 298043.9308 335842.6648 654438.5002 386049.7072 274735.7602 731583.6244 285092.9402 0.961063227 2.65416768 1.045427258 1.178011158 2.295526854 1.35411879 0.963670865 2.566123257 1 18.12107279 -2.085987322 2.471236783 0.00015546 1.612972368 0.082266727 0.656873643 6512793.672 2660947.054 36779020.02 0.147933482 0.008203755 2.085987322 1.612816908 FPDSVEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FPDSVEELR 9 0 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 ;; 137.06 0.00040751 225357000 254746 291663 297797 297297 307277 247431 306770 279695 323727 FALSE TRUE 238801.9026 313258.032 304860.8855 304926.1443 283144.7039 318860.313 260772.6864 314615.5364 269694.8723 0.885452143 1.161527578 1.130391849 1.130633822 1.04987055 1.182300243 0.96691748 1.166561061 1 18.04096857 1.737402745 24.99999943 1.044197369 1.102954617 0.035972728 0.096763843 0.433319145 8888.653588 0.040509325 0.022464269 54.62642073 -1.737402745 0.058757248 FPEFCSSPS(ph)PPVEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FPEFCSSPSPPVEVK 15 0 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 FPEFCS(0.035)S(0.02)PS(0.944)PPVEVK;FPEFCS(0.002)S(0.023)PS(0.975)PPVEVK;FPEFCS(0.001)S(0.006)PS(0.994)PPVEVK;FPEFCS(0.344)S(0.275)PS(0.381)PPVEVK 155.1 2.48E-06 267229000 659120 556310 608350 589070 560980 469007 783520 520900 852570 TRUE FALSE 617866.8558 597499.7712 622780.3493 604186.5335 516922.8937 604401.7072 666038.4498 585935.5116 710270.5592 0.869903515 0.841228407 0.876821292 0.850642795 0.727783078 0.850945741 0.937724986 0.824946922 1 19.43800916 0.270710236 0.666493856 1.003460243 0.843894331 0.444435151 0.052749792 2.608503108 1.590830443 0.080058595 0.020203935 1.865134848 -0.270710236 -0.159565912 FPEHELTFDPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FPEHELTFDPQR 12 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2;J3QL06;J3KTF1;Q9BST8;J3QQH7;J3QLE9 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;;; 148.13 6.62E-05 1574660000 1364040 1647550 1812820 2132580 1594600 1401900 1831360 1408260 1975530 FALSE TRUE 1278667.171 1769536.316 1855820.946 2187305.613 1469366.548 1806605.772 1556764.57 1584084.361 1645801.281 0.77692683 1.075182245 1.127609371 1.329021698 0.892797062 1.097705898 0.945900692 0.962500382 1 20.65035872 FPGLALRPS(ph)SR ddPTM_SK-BR-3_Pertuzumab_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(0.5)S(0.5)R 60.157 0.057792 290390000 115010 114410 125140 117670 142180 114960 126210 122430 261370 TRUE FALSE 107811.7294 122881.0354 128108.3799 120689.6114 131013.7563 148147.0858 107285.9822 137715.655 217745.6585 0.495126884 0.564332884 0.588339537 0.554268738 0.601682519 0.680367576 0.492712383 0.632461083 1 17.73228443 -5 0.359373277 6.230959373 0.562093531 0.859430211 0.054282665 161.0505918 1.284476688 651.4730154 0.037416342 1.00E-05 5 -5.668865841 FPGLALRPSS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FPGLALRPSSR 11 1 B4DF95;Q15735;B5MCL8;B5MBZ3;A0A087WVS7;Q15735-3;Q15735-2 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 FPGLALRPS(0.246)S(0.754)R;FPGLALRPS(0.252)S(0.748)R;FPGLALRPS(0.009)S(0.991)R 97.716 0.0036693 2967250000 1616960 1882110 1700500 1514690 2056840 1393460 1867260 1863020 3718140 TRUE FALSE 1515757.36 2021463.383 1740836.663 1553559.51 1895304.083 1795729.281 1587281.698 2095622.148 3097558.414 0.489339395 0.652598955 0.562002852 0.501543249 0.611870328 0.579724106 0.512429948 0.676539993 1 21.56270006 0.892705411 4.327519969 0.999937051 0.567075414 0.88302255 0.05052212 0.184373524 6.799255461 0.047007394 0.011961511 7.810977938 -0.892705411 -0.432861637 FPGQLNADLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 85.764 0.03261 397540000 121322 436970 99076 100732 474200 80295 119264 369310 311500 FALSE TRUE 113728.6726 469323.7135 101426.1295 103316.9537 436958.2448 103474.863 101381.4704 415419.1665 259508.6376 0.438246193 1.808509026 0.390839127 0.398125298 1.683790755 0.398733792 0.390667036 1.600791289 1 17.98542303 3.957162573 24.19232587 0.776287052 1.206056097 0.027431179 0.585825623 635.6469576 770481.6311 0.139273825 0.251557596 9060.717151 -3.957162573 0.429769045 FPGQLNADLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FPGQLNADLRK 11 1 Q13509;A0A0B4J269;Q13509-2;G3V2A3;Q5JP53;P07437;Q5ST81;A6NNZ2;CON__ENSEMBL:ENSBTAP00000025008;Q9H4B7;P68371;M0R2D3;Q13885;Q3ZCM7;A0A075B736;Q5SQY0;Q9BVA1;P04350;K7ESM5;Q9BUF5 Q13509;Q5JP53;P68371;Q13885;Q3ZCM7;Q9BVA1;P04350;K7ESM5 TUBB3;TUBB;TUBB1;TUBB4B;TUBB4A;TUBB2A;TUBB8;TUBB2B;TUBB6 Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-8 chain-like protein LOC260334;Tubulin beta-1 chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-8 chain;Tubulin beta-2B chain;Tubulin beta-4A chain;Tubulin beta-6 chain 0 ; 153.34 5.21E-05 2456800000 857410 1463710 878430 982680 2204420 643420 1302010 1796710 2850300 FALSE TRUE 803746.2386 1572084.611 899266.7744 1007897.232 2031293.745 829164.9089 1106785.688 2021033.199 2374566.516 0.338481248 0.6620512 0.378707763 0.424455253 0.855437711 0.3491858 0.466100099 0.851116692 1 21.17923274 1.12074491 4.043400245 0.990852597 0.501512214 0.567562021 0.158152116 0.143662506 3.934504922 0.138746541 0.03587841 13.20519776 -1.12074491 -0.489340384 FPHHDNELAQSEAYFENDCWVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FPHHDNELAQSEAYFENDCWVR 22 0 P49589-3;P49589;B4DKY1;P49589-2 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 0 ;;; 204.31 6.84E-23 480620000 622715 683596 675499 684806 665694 560121 805929 542033 579815 FALSE TRUE 583740.3797 734210.1591 691522.1553 702379.2813 613413.0785 721818.8399 685087.4283 609707.0132 483040.1308 1.208471807 1.51997756 1.431603942 1.454080596 1.269900862 1.494324786 1.418282633 1.262228487 1 18.88178353 0.928190175 2.74295864 1.000691155 1.416943272 0.632734399 0.096373703 0.191484958 3.303083533 0.083936819 0.022296787 8.475984909 -0.928190175 0.416252117 FPLDYYSIPFPTPTT(ph)PLTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FPLDYYSIPFPTPTTPLTGR 20 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;H0Y5H6;H7C2T8 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 FPLDYYSIPFPTPT(0.234)T(0.756)PLT(0.01)GR;FPLDYYSIPFPTPT(0.151)T(0.78)PLT(0.068)GR 305.64 2.58E-54 447540000 1033760 1320800 1397130 1877960 2430870 778470 979070 765830 1161400 TRUE FALSE 969058.8069 1418593.406 1430270.583 1926151.633 2239959.276 1003201.652 832267.5427 861445.5613 967554.8371 1.001554403 1.466163314 1.478232064 1.990741567 2.31507217 1.036842165 0.860176096 0.890332546 1 19.8839839 2.027008281 24.98679838 0.913102218 1.622130778 0.511454625 0.342711455 181.5073057 167921.2939 0.132301459 0.097708918 106.4163309 -2.027008281 0.70902856 FPLGDGQSLLLADALHTHSPLFLEGSSRDS(ph)PPLLDAPASPPQASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FPLGDGQSLLLADALHTHSPLFLEGSSRDSPPLLDAPASPPQASR 45 1 Q9BZ71;Q9BZ71-3;Q9BZ71-2 Q9BZ71 PITPNM3 Membrane-associated phosphatidylinositol transfer protein 3 1 FPLGDGQSLLLADALHTHSPLFLEGS(0.034)S(0.163)RDS(0.803)PPLLDAPASPPQASR 103.95 6.59E-07 117440000 38441 45403 33352 39088 53807 33899 42448 41106 39847 TRUE FALSE 36035.04643 48764.68536 34143.12519 40091.06426 49581.21527 43685.091 36083.31647 46238.17459 33196.27828 1.085514651 1.468980497 1.028522683 1.207697559 1.493577529 1.315963513 1.086968731 1.392872243 1 15.01873389 -0.794914361 5.259331672 0.999999884 1.253484554 0.20199663 0.16195383 2.07E-07 4.76E-08 0.147518484 0.034770424 0.160356157 0.794914361 0.25348467 FPPEASGYLHIGHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FPPEASGYLHIGHAK 15 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 220.21 9.84E-13 529700000 492080 547940 570380 565290 585450 412370 661900 529220 688720 FALSE TRUE 461281.5912 588510.0477 583909.683 579796.2984 539471.1186 531414.5247 562654.2398 595294.282 573768.1827 0.803951152 1.025693068 1.017675257 1.010506187 0.940224876 0.926183328 0.980629907 1.037517067 1 19.13010844 4.744968379 24.98552133 0.991508289 0.803951067 0.734128043 0.035619637 426.9475826 1664734.111 0.009284526 0.088103008 55586.3784 -4.744968379 -0.187557222 FPPEDFRHS(ph)PEDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FPPEDFRHSPEDFR 14 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR 108.71 0.00048898 225207000 158525 201219 188860 186159 210919 167398 218475 174225 234447 TRUE FALSE 148603.2032 216117.4641 193339.8484 190936.1551 194354.2725 215723.0851 185716.702 195977.3748 195316.2811 0.760833671 1.106499995 0.98988086 0.977574189 0.995074611 1.104480814 0.950851106 1.003384734 1 17.57545269 4.751267828 24.99940416 1.016834684 0.76083351 0.713059891 0.050860653 1115.544346 2194615.813 0.01181422 0.209601675 56398.53566 -4.751267828 -0.256001174 FPQGPPSQMGS(ph)PMGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FPQGPPSQMGSPMGSR 16 0 Q8WXF1 Q8WXF1 PSPC1 Paraspeckle component 1 1 FPQGPPSQMGS(0.997)PMGS(0.003)R 107.34 0.0011912 108980000 27464 36155 31865 32846 48419 41326 44495 41668 64758 TRUE FALSE 25745.07726 38831.95382 32620.85285 33688.88397 44616.36705 53256.14533 37823.38782 46870.34152 53949.47145 0.47720722 0.719783768 0.604655652 0.624452531 0.827002858 0.987148602 0.701089127 0.868782219 1 15.7193212 2.710258701 4.954539611 0.856783696 0.624312472 0.631086756 0.101832899 0.141965379 9.541410829 0.031187328 0.030243397 513.1669765 -2.710258701 -0.232471224 FPQLDSTSFANSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FPQLDSTSFANSR 13 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 186.36 1.83E-05 1350360000 119583 193153 148474 179064 190418 149579 178222 168167 194185 FALSE TRUE 112098.5135 207454.2491 151995.8734 183659.0854 175463.3384 192760.0291 151499.2656 189163.0201 161774.269 0.692931664 1.282368638 0.939555309 1.135279958 1.084618336 1.191537012 0.936485552 1.169302271 1 17.30362263 4.757808884 24.59260515 1.086742999 0.692931219 0.562338372 0.110651326 2617.148217 3343739.753 0.024272225 0.882370669 57254.40219 -4.757808884 -0.393811781 FPRLLT(ph)RILQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FPRLLTRILQK 11 2 D6RC04;D6RJ90;Q9Y6G5 D6RC04 COMMD10 COMM domain-containing protein 10 1 FPRLLT(1)RILQK 74.944 0.063412 327030000 353310 433380 490870 470590 454040 259180 370370 413960 315430 TRUE FALSE 331196.9578 465467.9061 502513.6682 482666.1361 418381.5299 334001.0586 314836.4568 465643.8172 262782.6952 1.260345387 1.771303494 1.912278386 1.836750078 1.592119791 1.271016184 1.198086718 1.77197291 1 18.00351075 2.389835256 3.870651662 1.312002112 1.742544174 0.329095786 0.257432424 0.229012967 6.633215527 0.0883636 0.072969238 245.377793 -2.389835256 0.430542062 FPS(ph)SPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FPSSPLR 7 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 FPS(0.5)S(0.5)PLR 86.833 0.020755 47982000 102980 294770 87246 92327 266390 74474 109100 277840 202130 TRUE FALSE 96534.66562 316595.0775 89315.51632 94696.26713 245468.804 95973.43482 92741.46783 312528.9356 168393.1972 0.573269391 1.880094225 0.530398602 0.562352094 1.457712117 0.569936532 0.550743554 1.855947513 1 17.36147433 3.95522125 23.45561476 0.877455018 1.30567887 0.037451679 0.537130833 399.8200442 428220.7092 0.126363143 0.228130914 9020.305563 -3.95522125 0.428223852 FPSLLTHNENMVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FPSLLTHNENMVAK 14 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ; 242.07 1.82E-17 1920260000 1713420 1619100 1655060 1643020 1619220 1271360 1895840 1506970 1356520 FALSE TRUE 1606180.101 1738979.849 1694318.805 1685182.675 1492052.993 1638380.993 1611576.392 1695118.522 1130108.049 1.421262421 1.538773085 1.499253816 1.491169519 1.320274636 1.449756061 1.426037443 1.499961463 1 20.10802928 -2.949873258 0.338407457 1.76E-15 1.483625288 0.837772895 0.062561268 30.47833931 0.933884575 21.91236733 0.050733238 0.001122346 2.949873258 1.483625288 RPS(ph)RPSNSNISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPSRPSNSNISK 12 2 Q6P158-2;Q6P158 Q6P158-2 DHX57 Putative ATP-dependent RNA helicase DHX57 1 RPS(0.962)RPS(0.019)NS(0.019)NISK 61.11 0.068657 100780000 66705 80736 61104 46401 79363 36578 104980 85048 215260 TRUE FALSE 62530.05312 86713.77745 62553.41574 47591.72822 73130.15011 47137.47481 89239.22359 95666.43001 179331.7154 0.348683739 0.483538438 0.348814015 0.265383778 0.40779262 0.262850744 0.497620978 0.533460742 1 17.45227113 0.724355337 1.232567512 0.998738523 0.368357858 0.886015753 0.07145806 0.286907007 0.739494318 0.066387903 0.020221615 5.30096988 -0.724355337 -0.630380664 FPTTATKIS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FPTTATKISPK 11 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 FPTTATKIS(1)PK;FPTTATKIS(1)PK 98.439 0.0033428 1237450000 2005130 1300600 1550220 1515600 1816000 926400 1776660 1265390 2240890 TRUE FALSE 1879632.493 1396897.777 1586991.95 1554492.862 1673378.685 1193836.641 1510266.327 1423376.727 1866870.982 1.006835775 0.748256195 0.850081214 0.832672893 0.896354757 0.639485349 0.808982699 0.762439794 1 20.8321908 FQAPS(ph)PSTLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FQAPSPSTLLR 11 0 Q6P9B9 Q6P9B9 INTS5 Integrator complex subunit 5 1 FQAPS(0.946)PS(0.023)T(0.031)LLR 62.14 0.086917 31923000 31807 41980 33763 38917 39351 39667 35726 33627 37530 TRUE FALSE 29816.25665 45088.24288 34563.8743 39915.67611 36260.53119 51118.21896 30369.21796 37825.40497 31266.00055 0.953631936 1.442085399 1.105477954 1.276647969 1.159743189 1.634945886 0.971317643 1.209793524 1 14.93230707 1.618367406 25 1.067911883 1.264398761 0.194615015 0.193188575 1.15397709 2740.252898 0.080704276 0.044152994 41.5305235 -1.618367406 0.196486878 FQDADPLEQDELHTFTDTMLPGCFHLLDELPDTVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FQDADPLEQDELHTFTDTMLPGCFHLLDELPDTVYR 36 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 145.9 2.34E-13 20805000 5983.2 6379.3 8097.6 6638.6 10148 6701.9 8493.9 7205.4 7699 FALSE TRUE 5608.722192 6851.63001 8289.678896 6808.957715 9351.017015 8636.629734 7220.318549 8105.010051 6413.987163 0.874451733 1.068232573 1.292437712 1.061579567 1.457910154 1.346530561 1.125714531 1.263646129 1 12.64700575 4.644831739 1.455491942 1.23244819 0.769835752 0.410857976 0.134891047 0.907826596 2.023852386 0.033935 0.579201352 44139.94002 -4.644831739 -0.462612438 FQDLGAAYEVLSDSEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FQDLGAAYEVLSDSEKR 17 1 Q9UBS4 Q9UBS4 DNAJB11 DnaJ homolog subfamily B member 11 0 ; 116.29 0.00043806 97249000 135341 105558 112977 121481 130059 86625 162440 109720 173459 FALSE TRUE 126870.2484 113373.6242 115656.8678 124598.4081 119844.6908 111632.2313 138083.63 123418.7835 144507.5723 0.877948791 0.784551441 0.800351607 0.862227537 0.829331563 0.772500911 0.955545981 0.854064473 1 17.14078557 1.100459914 0.674675328 0.99679076 0.81259599 0.528074772 0.049610485 0.495428354 0.536652581 0.045262613 0.018833667 12.60259309 -1.100459914 -0.184194769 FQDNFEFVQWFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FQDNFEFVQWFK 12 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ; 229.64 1.80E-11 378890000 596710 602490 577280 549310 663350 429510 629600 636540 596920 FALSE TRUE 559362.9863 647098.9865 590973.3542 563406.2246 611253.1668 553502.5645 535197.3249 716013.4202 497290.1957 1.124822068 1.30125024 1.188387302 1.132952609 1.229167943 1.113037356 1.076227381 1.439830156 1 18.92372846 3.537203926 4.695453989 1.161747433 1.230563231 0.02061725 0.122362152 0.617688534 27.34301546 0.030305953 0.046989216 3445.116604 -3.537203926 0.068815798 FQEAEERPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FQEAEERPK 9 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 101.38 0.0045011 0 384090 351280 382280 374060 418160 298930 485540 374400 467810 FALSE TRUE 360050.4925 377289.1367 391347.8621 383659.0129 385319.4004 385226.2383 412737.7845 421144.6642 389729.4888 0.923847188 0.968079521 1.004152555 0.984423873 0.988684232 0.988445189 1.059036579 1.080607643 1 18.57211357 1.795586758 4.438229178 1.052397107 0.978575379 0.56539469 0.028921524 0.145567706 5.254024607 0.013699173 0.007398421 62.45781089 -1.795586758 -0.073821728 FQEHLQLQNLGINPANIGFSTLTMESDKFICIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FQEHLQLQNLGINPANIGFSTLTMESDKFICIR 33 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;J3KSQ2;J3QL20 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 85.412 0.00024869 612050000 42839 62759 24856 22149 67871 24322 42750 57440 15222 FALSE TRUE 40157.78346 67405.74166 25445.59606 22717.38084 62540.68544 31343.36657 36340.03437 64611.51044 12681.34986 3.166680511 5.315344375 2.00653687 1.791400843 4.931705703 2.471611217 2.865628247 5.095002594 1 13.6304207 -1.839156433 2.839739187 0.160865346 3.402554688 0.267471703 1.274393628 106761703.6 105863278.5 618720022.3 0.288792645 0.014482501 1.839156433 3.241689342 FQEKPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 FQEKPDR 7 1 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 ;;;; 107.69 0.0067671 3066330000 3476110 3043870 3309340 3222840 3576000 2601680 3853990 3200530 4944190 FALSE TRUE 3258546.48 3269241.302 3387839.108 3305543.531 3295155.385 3352742.781 3276119.978 3600123.216 4118972.748 0.791106589 0.793703067 0.822496121 0.802516485 0.799994461 0.813975471 0.795373065 0.87403424 1 21.97385315 0.91498947 2.754557611 0.999841067 0.803696307 0.974972475 0.010112926 0.051183284 0.869802275 0.009715464 0.002577744 8.22222714 -0.91498947 -0.19614476 FQELIFEDFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 FQELIFEDFAR 11 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ;;;;;;; 189.57 6.17E-06 463030600 616167.8 738491 658392.8 655357.7 741677.2 551063.8 675140.2 598808.1 603738.5 FALSE TRUE 577602.9573 793169.642 674010.1881 672175.2881 683428.8645 710146.9733 573909.1947 673570.6094 502970.6441 1.14838304 1.576970051 1.340058701 1.336410576 1.358784797 1.41190541 1.141039147 1.339184737 1 18.94011467 0.709833719 0.447498461 0.980664957 1.405690052 0.410561177 0.124103571 1.345351033 0.595437045 0.1826569 0.073406061 5.126650587 -0.709833719 0.425025095 FQELLAS(ph)PAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FQELLASPAYR 11 0 Q9NSI2-2;Q9NSI2 Q9NSI2-2 FAM207A Protein FAM207A 1 FQELLAS(1)PAYR;FQELLAS(1)PAYR 151.74 3.49E-05 61156000 129861 142727 150934 131822 158328 132784 156930 127330 193738 TRUE FALSE 121733.2318 153294.6556 154514.2258 135204.7757 145893.5575 171116.5852 133399.8034 143227.4308 161401.8762 0.754224391 0.949769973 0.957326082 0.837690236 0.90391488 1.060189567 0.826507142 0.887396319 1 17.30029782 4.743877164 24.25888303 0.924648769 0.754224281 0.373763675 0.070521238 415.2211945 1894521.256 0.015905103 0.134754799 55446.88646 -4.743877164 -0.170424489 FQEMIETTLDMDQVENHEFLVKPSFDPNLSELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FQEMIETTLDMDQVENHEFLVKPSFDPNLSELR 33 1 A0A2R8YFH0;E9PHA6;A0A2R8Y6P0;A0A2R8YG02;P43246;P43246-2;A0A2R8Y7S8 A0A2R8YFH0 MSH2 DNA mismatch repair protein Msh2 0 131.78 3.42E-08 66870000 84027 82160 76677 81360 88058 70932 82512 68550 74243 FALSE TRUE 78767.90006 88243.21189 78495.81465 83447.83534 81142.27989 91408.91692 70140.0916 77108.6184 61851.36367 1.273503046 1.42669792 1.269104026 1.349167268 1.311891526 1.477880381 1.134010431 1.246676125 1 15.91651778 1.050880906 1.019363885 1.009215296 1.346155121 0.603957418 0.085816207 0.328801027 0.730632169 0.072896254 0.024228364 11.24296621 -1.050880906 0.336939825 FQESEERPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FQESEERPK 9 1 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;; 150.18 7.83E-05 2977930000 1998050 1564430 1641400 1707080 1884440 1381760 2082020 1642110 2271350 FALSE TRUE 1872995.617 1680262.025 1680334.783 1750886.563 1736443.684 1780651.681 1769840.43 1847131.048 1892247.012 0.989826173 0.887971821 0.888010272 0.925294928 0.917662268 0.941024967 0.935311521 0.976157466 1 20.851669 1.271425143 0.883843687 1.000901736 0.911870332 0.427693271 0.029340635 0.438354661 0.743325878 0.026431442 0.009730379 18.68207635 -1.271425143 -0.089031403 FQETEFLS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FQETEFLSPPR 11 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 FQETEFLS(1)PPR;FQETEFLS(1)PPR;FQETEFLS(1)PPR;FQETEFLS(1)PPR 135.24 0.00013022 938770000 1087690 1026500 1129760 1096410 1116230 1026670 1221440 961320 1676040 TRUE FALSE 1019613.424 1102503.128 1156558.441 1124545.737 1028565.798 1323052.962 1038296.411 1081342.918 1396298.096 0.73022618 0.789590082 0.828303386 0.805376545 0.736637686 0.94754334 0.743606551 0.774435574 1 20.41317555 -1.65933199 2.734386952 1.023592025 0.798421778 0.51458189 0.062631621 26657613.96 24601434.18 4416244.998 0.014224126 0.021911293 1.65933199 -0.225170247 FQFDGDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FQFDGDKK 8 1 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 75.378 0.061803 2798800000 5312700 3508900 3934800 4066300 4489400 2680200 5298900 3756200 5492700 FALSE TRUE 4980187.59 3768702.607 4028135.314 4170648.142 4136820.633 3453930.231 4504379.138 4225169.838 4575932.886 1.08834367 0.823592194 0.880287236 0.911431231 0.904038747 0.754803516 0.984363025 0.923346112 1 22.12563446 1.609762127 25 0.965396035 0.884060745 0.139424443 0.086013411 0.321973988 4153.615557 0.038377784 0.019916981 40.71572078 -1.609762127 -0.081335291 FQGEDTVVIASKPYAFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FQGEDTVVIASKPYAFDR 18 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 176.46 7.40E-13 243840000 167320 166040 174460 174740 196960 146610 201620 156630 228980 FALSE TRUE 156847.7399 178333.7744 178598.2736 179224.1242 181491.5561 188933.927 171388.9527 176185.6003 190761.7587 0.822217938 0.934850756 0.936237298 0.939518095 0.951404292 0.990418249 0.898445023 0.923589725 1 17.54141246 4.742992279 4.217314044 0.94248033 0.812243792 0.630467494 0.029874253 0.14513493 5.870131161 0.006684048 0.057421474 55334.02719 -4.742992279 -0.130236538 FQGIKHECQANGPEDLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FQGIKHECQANGPEDLNR 18 1 P60981;P60981-2 P60981 DSTN Destrin 0 ;;; 300.97 8.72E-50 3107110000 1436600 1964460 1621310 1850770 2673730 1244990 2318880 1513460 6367500 FALSE TRUE 1346685.77 2109910.662 1659768.239 1898263.892 2463746.031 1604398.402 1971185.471 1702418.813 5304723.114 0.253865422 0.397741902 0.31288499 0.357844104 0.464443851 0.302447153 0.371590643 0.320925103 1 22.33884602 -1.886698082 2.605445984 1.328231482 0.352279039 0.927032452 0.057498931 8576578.811 5020790.066 17318097.48 0.012685257 0.012980814 1.886698082 -0.975952443 FQNDRTEDEQFNDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FQNDRTEDEQFNDEK 15 1 Q9Y376;A0A087X0K1 Q9Y376 CAB39 Calcium-binding protein 39 0 132.4 4.35E-05 112570000 189640 138870 142090 158890 195330 108580 192140 151540 236430 FALSE TRUE 177770.7709 149152.0793 145460.4419 162967.3864 179989.5697 139925.2834 163330.3907 170460.1026 196968.3056 0.902534905 0.757238982 0.738496691 0.827378729 0.913799655 0.710394918 0.829221687 0.865418942 1 17.58760398 0.884905355 1.940407793 0.999377183 0.797981941 0.446052721 0.065545933 0.409965816 3.098478136 0.060135664 0.016804022 7.671942776 -0.884905355 -0.201395242 FQNVADLHLYLYSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FQNVADLHLYLYSAK 15 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;; 145.1 4.12E-06 606134000 1514820 1585880 1598660 1504750 1806720 1170230 1835530 1520250 1610650 FALSE TRUE 1420010.12 1703300.205 1636580.97 1543364.433 1664827.499 1508056.404 1560309.317 1710056.559 1341822.11 1.058270027 1.269393456 1.219670594 1.150200478 1.240721469 1.123886984 1.162828743 1.274428664 1 20.35576199 -1.841236151 2.709230725 0.928328106 1.193033825 0.42957389 0.067601079 12179401.39 5768473.871 5592653.061 0.016108016 0.014413314 1.841236151 0.264705719 FQPFESYDSRPCLPEHNPYRPSYSYDYEFDLGSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FQPFESYDSRPCLPEHNPYRPSYSYDYEFDLGSDR 35 2 O43823 O43823 AKAP8 A-kinase anchor protein 8 0 109.27 9.58E-06 56335000 73751 67310 69351 68362 83179 58873 81231 62919 100130 FALSE TRUE 69135.05656 72293.70244 70996.03847 70116.28466 76646.45687 75868.67938 69051.16566 70774.57565 83417.65614 0.828782056 0.866647491 0.851091265 0.840544891 0.918827745 0.90950385 0.827776383 0.848436397 1 16.34806516 -1.538605086 2.775518678 1.007244569 0.861697662 0.666342182 0.030810651 10966924.81 11562335.77 596978.6823 0.007266138 0.028933096 1.538605086 -0.145546906 FQPGETLTEILETPATSEQEAEHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 FQPGETLTEILETPATSEQEAEHQR 25 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;;; 303.76 1.84E-63 745929000 398996 467355 457878 458121 481664 389480 488940 403091 415598 FALSE TRUE 374023.5526 501958.4505 468739.0824 469877.1605 443836.0524 501916.5533 415627.9861 453417.7987 346232.0089 1.080268557 1.449774826 1.353829427 1.357116466 1.281903582 1.449653817 1.200432009 1.309577933 1 18.40137958 0.3647939 0.750801808 0.995398809 1.341755523 0.424753176 0.111454651 1.864175038 1.490122818 0.118704233 0.035144167 2.316295163 -0.3647939 0.346356714 FQPLDQVVVDNVFPNCILLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FQPLDQVVVDNVFPNCILLLK 21 0 Q5TBB1;A0A2R8YEC1;A0A2R8YEH2;A0A2R8Y6Y1;A0A2R8YGP2;A0A2R8Y6Q6;A0A2R8YCJ4;A0A087WZJ6;A0A2R8Y761;A0A087WXR7;A0A2R8YCX2;A0A2R8Y7Q3;A0A2R8Y883;A0A2R8Y6M7;A0A2R8YCP1;A0A2R8YE60;A0A2R8Y687;A0A2R8Y4S2;A0A2R8Y7R8;Q5TBB1-2 Q5TBB1 RNASEH2B Ribonuclease H2 subunit B 0 ; 68.82 0.011519 313130000 77823 339660 185539 237280 292530 339030 123403 233230 61587 FALSE TRUE 72952.19735 364808.7798 189940.0727 243369.0065 269555.8738 436902.4573 104899.8658 262349.2789 51307.73183 1.421855824 7.110210621 3.701977576 4.743320311 5.253708636 8.515333688 2.044523545 5.113250372 1 15.64688863 3.780377003 24.96838367 4.538361343 4.892467311 0 2.429056324 1970.437106 923806.1491 0.571449882 1.030194856 6030.828841 -3.780377003 0.354105968 FQPQLNPDVVAPLPTHTAHEDFTFGES(ph)RPELGSEGLGSAAHGSQPDLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGSQPDLRR 49 2 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 FQPQLNPDVVAPLPT(0.015)HT(0.015)AHEDFT(0.057)FGES(0.246)RPELGS(0.246)EGLGS(0.21)AAHGS(0.21)QPDLRR 98.098 2.45E-06 873910000 100270 147570 163980 174040 165770 118150 171220 138670 229730 TRUE FALSE 93994.27969 158496.2363 167869.683 178506.161 152751.0929 152257.987 145547.1505 155983.2548 191386.5789 0.491122629 0.828147079 0.877123589 0.932699472 0.798128551 0.79555206 0.760487759 0.815016683 1 17.54613014 7.999999996 0.041222884 1.301437664 2.13E-08 0.328452891 0.109431672 1234.366361 3.869500428 32.83406991 110.683134 99999998.99 -7.999999996 -1.301437643 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGS(ph)QPDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGSQPDLR 48 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 FQPQLNPDVVAPLPT(0.143)HT(0.143)AHEDFT(0.143)FGES(0.143)RPELGS(0.055)EGLGS(0.055)AAHGS(0.317)QPDLR 55.185 0.0047056 675560000 21610 21003 20276 21067 26742 15319 25903 19243 40079 TRUE FALSE 20257.46867 22558.08397 20756.9563 21607.61489 24641.79119 19741.34662 22019.08562 21645.53091 33389.55598 0.606700751 0.675602994 0.621660147 0.647136934 0.738008951 0.591243161 0.659460271 0.648272499 1 15.02710929 -0.94557889 2.292580173 1.001340543 0.649352026 0.882505706 0.040304448 14337.65011 16683.22773 155.8218385 0.009341874 0.113349892 0.94557889 -0.351988517 FQPVHDLTIGVEFGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FQPVHDLTIGVEFGAR 16 0 P61019;E9PKL7;A0A3B3ITL1;Q8WUD1;E9PE37;H0YD31 P61019 RAB2A;RAB2B Ras-related protein Rab-2A;Ras-related protein Rab-2B 0 ; 151.62 6.26E-07 424250000 331270 370000 337380 371220 396810 309140 455560 357300 363780 FALSE TRUE 310536.402 397395.185 345382.8129 380746.1337 365646.1433 398383.6995 387253.0072 401909.6915 303062.7679 1.024660351 1.311263629 1.139641188 1.256327646 1.206503015 1.314525378 1.277798028 1.326159905 1 18.2092571 2.437587985 23.72397944 1.258014877 1.20056113 0 0.117765069 284.0136483 170434.2973 0.036070329 0.030178685 273.8974473 -2.437587985 -0.057453748 FQQENLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FQQENLK 7 0 Q6ZUJ8-3;Q6ZUJ8-2;Q6ZUJ8 Q6ZUJ8-3 PIK3AP1 Phosphoinositide 3-kinase adapter protein 1 0 ;; 99.919 0.02367 109049000 104483 363384 288399 296900 335203 469420 206310 311987 183165 FALSE TRUE 97943.59554 390289.3295 295239.9605 304518.9567 308877.5085 604933.9336 175375.7308 350939.2637 152593.5782 0.641859223 2.557704813 1.934812486 1.995621049 2.02418419 3.96434726 1.14929955 2.299829835 1 17.21933472 2.464131986 24.9934161 2.192773441 1.94436706 0.00960146 0.927176672 1389.515271 2673631.736 0.297398273 0.248948709 291.1601848 -2.464131986 -0.248406381 FQSGDFHVINGVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FQSGDFHVINGVLR 14 0 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 153.14 6.47E-06 1001200000 837130 1697200 995320 1079300 1668600 758260 1110000 1429800 1138400 FALSE TRUE 784735.5276 1822862.454 1018929.46 1106996.665 1537554.887 977157.3527 943565.8047 1608313.677 948393.6857 0.827436474 1.922052499 1.07437394 1.167233272 1.62122008 1.030328826 0.994909413 1.695829171 1 19.85512653 3.743390497 24.50688222 1.214342468 1.466515971 0.013947401 0.359487294 818.5190078 1232952.116 0.084455644 0.151638738 5538.478787 -3.743390497 0.252173503 FQSPQIQATIS(ph)PPLQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FQSPQIQATISPPLQPK 17 0 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 1 FQSPQIQAT(0.007)IS(0.993)PPLQPK;FQSPQIQATIS(1)PPLQPK 259.55 3.47E-27 165185000 759900 591050 680440 676950 723360 549210 836850 588840 777190 TRUE FALSE 712339.2155 634811.957 696580.3581 694321.6831 666550.2235 707758.0113 711372.1114 662357.9702 647471.9682 1.100185414 0.980447013 1.075846357 1.072357905 1.029465763 1.093109889 1.098691753 1.02299096 1 19.30445821 3.737400725 24.04421578 1.06406176 1.030678425 0 0.042937619 497.2947948 1163184.965 0.010121688 0.017966454 5462.616661 -3.737400725 -0.033383334 FQSSHHPTDITSLDQYVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FQSSHHPTDITSLDQYVER 19 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;;; 251.75 4.51E-31 5178830000 1041157 3275490 2587980 3082250 2956110 2508940 3135030 2735190 1879460 FALSE TRUE 975992.8419 3518010.688 2649368.108 3161345.753 2723949.045 3233230.249 2664961.356 3076684.492 1565765.984 0.623332511 2.246830448 1.692058797 2.019041022 1.739691035 2.064951137 1.702017659 1.964970834 1 20.57843718 -1.434297533 5.982410496 0.999666495 1.807959749 0.216948672 0.442281825 0.001694584 0.000160242 0.368846185 0.086903857 0.036787686 1.434297533 0.808293254 FQVDKVNFHMFDVGGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FQVDKVNFHMFDVGGQR 17 1 P63092-4;P63092;P63092-3;A0A590UJ58;B0AZR9;A0A590UJF0;A0A590UJY2;A0A590UJR6;A0A590UJI6;A0A590UJQ9;A0A590UKB4;A0A590UJQ2;A0A590UJG5;P38405-2;P38405;K7EPE2;K7EQ80;P63092-2;A0A590UJB0;A0A590UJS2;A0A590UJJ0;Q5JWF2 P63092-4;P63092-2;Q5JWF2 GNAS;GNAL Guanine nucleotide-binding protein G(s) subunit alpha isoforms short;Guanine nucleotide-binding protein G(olf) subunit alpha;Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas 0 112.89 0.0002636 155660000 232410 319470 243830 290200 455320 200790 334360 281070 516240 FALSE TRUE 217863.873 343123.8912 249613.7627 297647.0233 419561.0039 258754.8134 284225.822 316162.2082 430076.209 0.50657039 0.79782114 0.580394259 0.692079722 0.975550368 0.60164875 0.660873157 0.735130662 1 18.7142328 -5 0.311500085 3.729111128 0.680012049 0.369788385 0.127669012 329.0238457 2.972284815 589.7360475 0.11198999 1.00E-05 5 -3.049099079 FQVPTAHSEMQPLDPAAASIS(ph)DGDCDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FQVPTAHSEMQPLDPAAASISDGDCDAR 28 0 Q5T586;A0A0A0MRW2;Q5T593;A0A0A0MRW3;Q8IW50-5;Q8IW50-6;Q8IW50;A0A0A0MRV9;Q8IW50-7 Q5T586 FAM219A Protein FAM219A 1 FQVPTAHSEMQPLDPAAAS(0.023)IS(0.977)DGDCDAR 162.86 5.37E-12 44708000 36601 34585 34950 34242 35612 37849 49327 35374 29474 TRUE FALSE 34310.20874 37145.70939 35779.0305 35120.70769 32815.17717 48775.39187 41930.87428 39790.52177 24554.59899 1.397302752 1.512780127 1.457121353 1.430310782 1.336416741 1.986405557 1.707658687 1.620491615 1 14.58370564 2.328737692 22.81015404 1.658275697 1.442809445 0.041782061 0.25022846 17.3782198 4386.486615 0.077015415 0.064435655 213.1756972 -2.328737692 -0.215466252 FQVWDYEEGEVEALLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FQVWDYEEGEVEALLDR 17 0 O43598;H0Y8X4 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ;; 146.2 1.04E-06 92338000 73550 90936 77876 79831 90753 69493 84234 79909 96119 FALSE TRUE 68946.63679 97668.99606 79723.2555 81879.59861 83625.62546 89554.50098 71603.89369 89885.81455 80076.11795 0.861013727 1.219701936 0.995593412 1.022522079 1.044326668 1.118367165 0.894197865 1.122504648 1 16.28908441 FQWDLNAWTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FQWDLNAWTK 10 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 160.36 1.72E-05 154019000 350550 553240 352310 331800 661680 245436 349410 539090 564760 FALSE TRUE 328609.7012 594202.4652 360666.9596 340314.5497 609714.3219 316289.3889 297019.2143 606396.5732 470497.9075 0.698429676 1.262922652 0.766564428 0.723307255 1.295891676 0.672243986 0.631287004 1.288840106 1 18.84382878 FRDGPPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 FRDGPPLR 8 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;;;;;; 125.82 0.0011361 5981610000 3012470 3517520 3298340 3380010 3568170 2844900 3953230 3179720 3789350 FALSE TRUE 2823924.88 3777960.841 3376578.182 3466746.779 3287940.322 3666176.447 3360479.861 3576715.041 3156883.005 0.89452947 1.196737679 1.069592436 1.098154976 1.041514784 1.161327943 1.064493 1.132989419 1 21.59006936 -0.919954433 7.681546074 0.999991804 1.092219546 0.080324284 0.081874232 5.11E-10 6.66E-11 0.068648636 0.016180639 0.120239059 0.919954433 0.092227742 FRDQDLASCDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FRDQDLASCDR 11 1 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ; 248.19 3.07E-16 1059190000 763030 951060 807340 774230 994620 722400 788850 867960 928570 FALSE TRUE 715273.3143 1021477.472 826490.4861 794098.0526 916506.5573 930945.1528 670569.2658 976326.7166 773585.6682 0.92462069 1.320445187 1.068389087 1.026515983 1.184751211 1.203415719 0.866832587 1.262079634 1 19.56120154 FRDQDLASCDRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FRDQDLASCDRDR 13 2 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ;; 220.4 1.17E-11 1355940000 426540 641110 456900 515260 739180 360776 532200 530620 933990 FALSE TRUE 399843.6228 688578.4515 467737.8838 528482.4439 681127.7845 464926.1745 452401.5507 596869.075 778101.0352 0.513871084 0.884947353 0.601127441 0.679195143 0.875371904 0.597513888 0.58141749 0.767084283 1 19.56959797 -2.027715741 2.179543768 1.355469312 0.690671977 0.386307761 0.123701825 7570958.281 2515905.863 13449559.81 0.030557118 0.009381759 2.027715741 -0.664797335 FRDQDLASCDRDRSS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FRDQDLASCDRDRSSR 16 3 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 1 FRDQDLASCDRDRS(0.002)S(0.998)R;FRDQDLASCDRDRS(0.007)S(0.993)R;FRDQDLASCDRDRS(0.119)S(0.881)R;FRDQDLASCDRDRS(0.107)S(0.893)R 147.25 5.78E-06 4028470000 643755 865010 691690 781930 1135120 482154 873960 662990 2547800 TRUE FALSE 603463.5237 929056.2404 708097.2134 801995.6476 1045972.254 621344.0327 742917.8114 745765.7609 2122555.721 0.284309862 0.437706408 0.333605948 0.377844332 0.492789067 0.292733909 0.350010982 0.351352737 1 21.017371 -1.612096301 2.878939593 1.048256867 0.368326624 0.911012724 0.062358478 19901229.19 20137839.11 7236910.24 0.01393967 0.024428888 1.612096301 -0.679930243 FRDSILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 4568390000 1108228 1562850 1236040 1496430 1759550 1155100 1889580 1590180 2423540 FALSE TRUE 1038865.988 1678565.04 1265359.453 1534830.927 1621362.041 1488558.619 1606255.021 1788717.473 2019035.517 0.514535767 0.831369743 0.626714806 0.760180251 0.803037899 0.737262225 0.795555604 0.8859267 1 20.94523486 -4.999999997 0.063453895 2.015063732 0.344592712 0.622684098 0.081579169 242.93022 1.121151464 36.76246013 5.551791471 1.00E-05 4.999999997 -1.67047102 FRDYEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FRDYEEK 7 1 Q9UJC3;Q9UJC3-2 Q9UJC3 HOOK1 Protein Hook homolog 1 0 ; 123.72 0.0038452 636210000 645040 577540 631450 628370 775140 533750 791730 635530 902290 FALSE TRUE 604668.0978 620301.6625 646428.2922 644495.038 714263.6312 687834.9603 673017.4366 714877.3195 751691.97 0.804409415 0.825207249 0.859964344 0.857392474 0.950207877 0.915048967 0.895336738 0.951024287 1 19.51978207 8 0.106338707 1.058157847 0.272826485 0.865106072 0.022351371 39.14862404 0.291992253 0.225882793 4.5026258 100000000 -8 -0.785331362 FREDHPDLIQNAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FREDHPDLIQNAK 13 1 E9PKP7;P17480-2;P17480 E9PKP7 UBTF Nucleolar transcription factor 1 0 ;; 117.93 0.00028085 584320000 764010 729180 694090 664970 760600 516127 864870 652680 851930 FALSE TRUE 716191.9779 783169.2459 710554.1426 682034.256 700865.5441 665124.4863 735190.7726 734168.5347 709737.3793 1.009094348 1.103463434 1.001150796 0.960967079 0.987499834 0.937141689 1.035863115 1.034422811 1 19.43692576 3.726231808 4.407909937 0.99242581 1.060943113 0.330151423 0.036958538 0.191356341 9.300099405 0.00951926 0.016441139 5323.923513 -3.726231808 0.068517303 FREGERPSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FREGERPSLR 10 2 Q7L2H7;J3KNJ2;E9PN86;E7ESM3 Q7L2H7 EIF3M Eukaryotic translation initiation factor 3 subunit M 0 63.624 0.043518 139750000 58039 124160 108390 121760 134400 117680 102600 113990 114000 FALSE TRUE 54406.44259 133352.9356 110961.062 124884.5677 123844.7661 151652.3056 87216.08249 128221.9024 94972.66353 0.572864239 1.40411915 1.168347373 1.314952778 1.304004348 1.596799542 0.918328277 1.350092728 1 16.53522469 4.746088566 24.85791815 1.258623241 0.572863886 0.550356952 0.194355864 623.7980482 2059780.356 0.042498385 0.447977948 55729.93874 -4.746088566 -0.685759356 FRELAEEAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 190.53 8.13E-07 934800000 418986 994570 375186 478398 1136950 227034 426313 883800 1107560 FALSE TRUE 392762.4142 1068208.998 384085.5891 490674.5026 1047658.533 292575.0302 362391.3233 994144.3755 922701.0809 0.425665931 1.157697785 0.416262208 0.531780566 1.135425714 0.317085388 0.392750514 1.077428428 1 19.81550382 1.217600075 24.77405078 1.038714841 0.643245127 0.25016589 0.296332222 375.616908 443942.7503 0.278268282 0.069872946 16.5044127 -1.217600075 -0.395469714 FRFS(ph)GR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FRFSGR 6 1 Q9H329-2;Q9H329;H7C3Q2 Q9H329-2;H7C3Q2 EPB41L4B;HECW1 Band 4.1-like protein 4B 1 FRFS(1)GR;FRFS(1)GR 85.642 0.032995 227274000 119893 137854 102552 97521 144249 86135 122951 111635 147462 TRUE FALSE 112389.1111 148060.8536 104984.5819 100023.554 132920.2654 111000.7762 104515.639 125572.8755 122849.6396 0.914850964 1.20522009 0.854577858 0.814194932 1.081975217 0.903549873 0.850760648 1.022167228 1 16.9065341 3.907744344 6.559373435 0.922240518 1.073910863 0.185866349 0.108442576 0.259097397 19.64732091 0.025626006 0.046905039 8086.1975 -3.907744344 0.151670345 FRIDELEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 FRIDELEPR 9 1 Q14697;F5H6X6;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;;;; 148.56 8.18E-05 2015861000 1484830 1872180 1658410 1739970 1887220 1351828 1962620 1569140 1594320 FALSE TRUE 1391897.141 2010798.155 1697748.268 1784620.576 1739005.354 1742078.799 1668343.351 1765050.583 1328217.692 1.047943533 1.51390707 1.27821537 1.343620542 1.30927736 1.311591322 1.256076742 1.328886517 1 20.34106019 -1.825132831 0.383732471 0.71870806 1.328857918 0.382803069 0.115324976 33.15653536 2.17678846 8.549765594 0.070495097 0.014957781 1.825132831 0.610149857 FRKVQHELDEAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FRKVQHELDEAEER 14 2 P13533;P12883 P13533 MYH6;MYH7 Myosin-6;Myosin-7 0 54.524 0.078727 551680000 51229 276910 162970 224760 229240 224570 132780 167940 132090 FALSE TRUE 48022.66834 297412.7045 166835.7254 230527.7221 211236.4151 289399.7134 112870.8717 188907.6787 110043.3257 0.436397828 2.702687353 1.51609127 2.094881454 1.919574984 2.629870659 1.025694843 1.716666391 1 16.74771212 1.669325974 11.04898149 1.283036015 1.943948035 0.167979965 0.655104192 0.184025268 30.1122035 0.276979539 0.150295373 46.70097779 -1.669325974 0.66091202 FRLEAPDADELPKGEFDPGQDTYQHPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FRLEAPDADELPKGEFDPGQDTYQHPPK 28 2 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 121.86 2.86E-05 64157000 133080 88150 82406 80225 136370 67424 100840 94950 224050 FALSE TRUE 124750.7604 94676.71772 84360.70923 82283.70932 125660.0503 86888.21426 85719.97815 106804.7165 186654.6076 0.668350822 0.50722947 0.451961569 0.440834065 0.673222333 0.465502649 0.459243837 0.57220509 1 17.5100116 0.881013592 7.152103112 0.999999534 0.511953278 0.755086025 0.084383987 1.779260865 106.9667904 0.076622583 0.019210795 7.603500735 -0.881013592 -0.488046255 FRLS(ph)LFSDLPEDTELQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 FRLSLFSDLPEDTELQR 17 1 Q9BST9 Q9BST9 RTKN Rhotekin 1 FRLS(1)LFSDLPEDTELQR;FRLS(1)LFSDLPEDTELQR;FRLS(1)LFSDLPEDTELQR;FRLS(1)LFSDLPEDTELQR;FRLS(1)LFSDLPEDTELQR 287.67 6.10E-37 1847403000 847417 990604 851827 811835 1137237 610328 915084 813521 874129 TRUE FALSE 794378.6827 1063949.351 872032.7387 832668.0605 1047922.993 786519.7858 777875.6494 915090.8876 728231.2228 1.090833046 1.461004853 1.197466837 1.143411645 1.438997616 1.080041285 1.068171242 1.256593866 1 19.47403707 1.660450882 0.461308898 1.014813417 1.301554519 0.190053692 0.139065217 1.208132143 0.658863395 0.141554171 0.101476441 45.75629818 -1.660450882 0.286741102 FRNS(ph)VEGLNQEIEIIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FRNSVEGLNQEIEIIIK 17 1 Q6P1L5 Q6P1L5 FAM117B Protein FAM117B 1 FRNS(1)VEGLNQEIEIIIK;FRNS(1)VEGLNQEIEIIIK 288.95 3.45E-38 200930000 264454 223536 237321 242762 261420 192073 292909 225387 282781 TRUE FALSE 247902.2962 240086.838 242950.3662 248991.6839 240889.1277 247521.3571 248990.0147 253527.0631 235583.0243 1.052292698 1.019117735 1.031272805 1.056916918 1.022523284 1.050675692 1.056909832 1.076168641 1 17.84587606 2.154913219 10.0227395 1.051417377 1.03430281 0.012895898 0.022361701 0.731026933 81.77553765 0.007567338 0.005588807 142.8608464 -2.154913219 -0.017114567 FRPAGAAPRPPPKPM ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FRPAGAAPRPPPKPM 15 3 P62854;Q5JNZ5 P62854 RPS26;RPS26P11 40S ribosomal protein S26;Putative 40S ribosomal protein S26-like 1 0 ; 134.04 4.60E-05 1010760000 1012420 915970 914950 986010 1127460 834510 1109330 994670 1482550 FALSE TRUE 949054.4394 983789.3719 936653.0461 1011312.686 1038913.84 1075419.49 942996.265 1118856.739 1235102.827 0.768401155 0.796524265 0.758360377 0.818808494 0.841155746 0.870712516 0.763496159 0.905881449 1 20.23619973 -5 0.148396704 1.713747217 0.74328127 0.74086787 0.038214237 66.96122954 0.593585711 13.96201142 0.192615431 1.00E-05 5 -0.970465947 FRPDMEEEEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 FRPDMEEEEAK 11 1 Q99436 Q99436 PSMB7 Proteasome subunit beta type-7 0 ;;;;;; 208.27 1.84E-08 2647170000 3976934 2799226 2982665 2805931 3255008 2098615 3526324 2781016 3074528 FALSE TRUE 3728024.8 3006483.606 3053415.222 2877935.94 2999372.802 2704451.082 2997584.453 3128231.969 2561369.415 1.455481111 1.173779771 1.192102633 1.123592686 1.171003599 1.055861395 1.170305398 1.221312299 1 21.28848391 7.485610948 1.126360259 1.139509117 199.987888 0.69077365 0.066470087 533.4635776 1.430149753 0.01678543 273138.125 30592216.75 -7.485610948 198.8483789 FRPLNESEVNRGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FRPLNESEVNRGDK 14 2 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 171.46 1.69E-06 297330000 305920 293440 298750 306220 368640 232360 380020 310610 558890 FALSE TRUE 286773.0133 315166.6029 305836.4911 314078.1236 339688.5014 299438.56 323039.5289 349390.3422 465607.6484 0.615911303 0.676893097 0.656854526 0.674555336 0.729559539 0.64311349 0.693802024 0.750396484 1 18.82875523 0.644949799 1.31431545 1.000111493 0.667660191 0.928278428 0.028870153 0.276974172 0.72059896 0.025327987 0.007567714 4.41519408 -0.644949799 -0.332451302 FRPPETTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FRPPETTER 9 1 Q96P70 Q96P70 IPO9 Importin-9 0 ; 93.556 0.0084992 1236200000 912700 983360 1099530 1107470 1050530 937540 1115070 891250 1023050 FALSE TRUE 855575.7362 1056168.998 1125611.371 1135889.555 968025.6114 1208192.578 947875.6053 1002524.524 852296.3458 1.003847711 1.239203949 1.320680742 1.332740145 1.135785242 1.417573341 1.112143223 1.176262845 1 19.70099562 0.982755387 1.330461235 1.005718184 1.246529062 0.25907989 0.118827641 0.572246342 2.068962939 0.102548109 0.031134387 9.610708093 -0.982755387 0.240810878 FRQDLMNIAGTTLSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FRQDLMNIAGTTLSSK 16 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 172.97 4.00E-09 631960000 1356360 1344680 1303570 1296230 1673200 1073060 1614480 1273500 1796180 FALSE TRUE 1271467.849 1444241.506 1334491.296 1329493.456 1541793.621 1382835.002 1372403.712 1432499.278 1496385.954 0.849692451 0.965153076 0.891809558 0.888469617 1.03034489 0.924116535 0.917145545 0.957306017 1 20.5130509 -1.821334987 0.010819662 1.975205345 1.59E-06 0.285418495 0.045833892 8527.430682 13.5181541 1340.955658 1133.304381 0.015089158 1.821334987 -1.975203757 FRRS(ph)ET(ph)PPHWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FRRSETPPHWR 11 2 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 FRRS(1)ET(1)PPHWR 75.911 0.069551 1349400000 350130 429910 284590 357050 475910 252820 282010 282780 424370 TRUE FALSE 328215.9883 461740.9837 291340.6092 366212.5075 438533.9483 325805.0298 239725.2186 318085.7055 353539.9055 0.928370414 1.306050538 0.824067113 1.035844898 1.240408626 0.921550933 0.678071173 0.899716554 1 18.43151354 2.005777584 24.89224464 0.81757228 1.066349285 0.260815473 0.158433581 151.9946199 654852.5918 0.056767163 0.041802805 101.3392263 -2.005777584 0.248777005 FRS(ph)FSELPSCDGNESWAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FRSFSELPSCDGNESWAYR 19 1 Q8NEV8-2;Q8NEV8 Q8NEV8-2 EXPH5 Exophilin-5 1 FRS(0.988)FS(0.012)ELPSCDGNESWAYR 148.02 6.03E-08 214950000 46287 66341 48969 85568 99043 40209 70648 53998 82823 TRUE FALSE 43389.97929 71252.95667 50130.5678 87763.81975 91264.5623 51816.68556 60054.98826 60739.76916 68999.30624 0.628846602 1.032661929 0.726537273 1.271952205 1.322688115 0.750974008 0.8703709 0.880295361 1 16.07429424 4.746415631 23.80474432 0.962011872 0.628846282 0.236428881 0.196538329 829.7074009 2514321.193 0.047623863 0.501642723 55771.92447 -4.746415631 -0.33316559 FRTPS(ph)FLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FRTPSFLKK 9 2 P35611;P35611-3;P35612;Q9UEY8-2;Q9UEY8 P35611;Q9UEY8-2 ADD1;ADD2;ADD3 Alpha-adducin;Beta-adducin;Gamma-adducin 1 FRT(0.007)PS(0.993)FLKK;FRT(0.006)PS(0.994)FLKK 79.466 0.021155 639090000 1207760 1003920 991340 1143900 1500370 705480 1650190 1239970 2526200 TRUE FALSE 1132168.458 1078251.281 1014855.053 1173254.411 1382536.992 909140.6235 1402759.329 1394782.984 2104560.9 0.537959466 0.512340261 0.482217004 0.557481806 0.656924203 0.431985895 0.666533018 0.66274299 1 21.00508783 0.447067055 0.591278824 1.017622793 0.515229549 0.835218065 0.064290006 0.677820656 0.394601671 0.082697146 0.025338718 2.799413514 -0.447067055 -0.502393244 FRYS(ph)GK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FRYSGK 6 1 Q9HCM4-2;Q9HCM4-4;Q9HCM4-3;Q9HCM4;Q5JV61;A2A2Y4-3;A2A2Y4-5;A2A2Y4-2;A2A2Y4 Q9HCM4-2 EPB41L5;FRMD3 Band 4.1-like protein 5;FERM domain-containing protein 3 1 FRYS(1)GK;FRYS(1)GK 78.516 0.042137 466660000 558490 469830 424040 370390 456460 264159 412430 288720 612360 TRUE FALSE 523535.1078 504616.7021 434098.429 379894.8345 420611.4729 340417.415 350589.9503 324767.3276 510153.16 1.026231236 0.989147459 0.850917848 0.744668198 0.824480775 0.667284733 0.687224892 0.636607499 1 18.96057092 3.725093223 0.983123684 0.726368827 1.037041349 0.475977504 0.103655998 0.462150961 0.832822856 0.034360747 0.108157095 5309.984132 -3.725093223 0.310672522 FRYS(ph)GR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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;FRY(0.001)S(0.999)GR;FRYS(1)GR;FRYS(1)GR;FRYS(1)GR;FRYS(1)GR;FRYS(1)GR 98.299 0.02428 4549326000 2647360 2572800 2428870 1984070 2243700 1693911 1833671 1371733 3456840 TRUE FALSE 2481666.463 2763292.789 2486483.943 2034984.595 2067488.853 2182915.607 1558729.057 1542996.885 2879871.072 0.861728321 0.959519617 0.863401132 0.706623507 0.717910212 0.757990741 0.541249597 0.535786793 1 21.45757279 3.253994388 1.758648475 0.671713216 0.920112501 0.281655495 0.132509322 0.332721872 2.112284422 0.039956749 0.057617783 1794.710435 -3.253994388 0.248399286 FS(ph)GGFGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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;FS(1)GGFGAR;FS(1)GGFGAR 158.57 0.00038207 2781170000 2796770 2605160 2682640 2428280 2903820 2064910 2780720 2251350 2699200 TRUE FALSE 2621725.158 2798048.757 2746273.488 2490593.776 2675765.691 2661015.996 2363776.851 2532436.003 2248686.083 1.16589202 1.244303853 1.221279177 1.107577352 1.189924068 1.183364818 1.051181341 1.126184763 1 21.10065084 1.544016303 0.440702651 0.997236902 1.225084225 0.645728301 0.044876549 0.532169322 0.282558517 0.049174237 0.034779752 34.99583042 -1.544016303 0.227847323 FS(ph)PDSQYIDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSPDSQYIDNR 11 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 FS(1)PDSQYIDNR 108.56 0.0021462 103040000 191030 169070 176170 164310 178680 157580 205710 158240 166480 TRUE FALSE 179073.7733 181588.1187 180348.8356 168526.4728 164647.1936 203070.7879 174865.6952 177996.6123 138693.4125 1.291148369 1.309277171 1.300341756 1.215100773 1.187130597 1.46417039 1.260807504 1.283381879 1 17.08153974 0.443340755 2.313711525 1.000006491 1.293190543 0.607572615 0.072963355 6.61417035 26.55716199 0.065656157 0.017681627 2.775496954 -0.443340755 0.293184052 FS(ph)PGAPGGSGSQPNQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 FSPGAPGGSGSQPNQK 16 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK 292.44 1.51E-45 1368090000 1557380 905080 1300470 1132480 1104500 1014550 1361890 950020 994250 TRUE FALSE 1459906.366 972093.0649 1331317.763 1161541.354 1017757.025 1307434.115 1157687.238 1068632.088 828303.2519 1.762526421 1.173595616 1.607283032 1.40231413 1.228725135 1.578448608 1.397661104 1.290145953 1 19.65979953 0.886892332 2.192622885 1.000893941 1.435439076 0.40764434 0.173258552 0.443056436 4.355851082 0.147309364 0.040350078 7.707123753 -0.886892332 0.434545135 FS(ph)PPEPGDTPTDEPDALYVACQGQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSPPEPGDTPTDEPDALYVACQGQPK 26 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 FS(0.973)PPEPGDT(0.026)PT(0.001)DEPDALYVACQGQPK 83.606 0.0093152 24260000 27577 15961 20368 16820 26401 15988 27880 16842 25639 TRUE FALSE 25851.0048 17142.76905 20851.13858 17251.62968 24327.57196 20603.47606 23699.65283 18944.76077 21359.68527 1.210270867 0.80257592 0.976191284 0.807672466 1.138948053 0.964596425 1.109550657 0.886940071 1 14.38260277 2.734512124 24.99776706 1.0289376 0.929246292 0.055550605 0.131548669 719.4685441 4442406.099 0.037590464 0.036655121 542.6404003 -2.734512124 -0.099691307 FS(ph)PPRHELS(ph)PPQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FSPPRHELSPPQKR 14 2 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 2 FS(1)PPRHELS(1)PPQKR;FS(1)PPRHELS(1)PPQKR 56.719 0.065711 1577080000 1438140 1107470 1281680 1211860 1329700 944020 1528610 1095170 1728650 TRUE FALSE 1348129.385 1189468.231 1312082.055 1242958.379 1225270.726 1216543.249 1299409.121 1231904.385 1440127.147 0.936118305 0.825946676 0.911087647 0.863089333 0.850807325 0.844747112 0.902287776 0.855413626 1 20.45776476 -1.396747636 3.89833166 1.000566543 0.872675921 0.581305489 0.033679906 0.000147939 2.29E-05 0.029090828 0.006826576 0.040109972 1.396747636 -0.127890622 FS(ph)PTMGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FSPTMGR 7 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 FS(0.865)PT(0.135)MGR;FS(0.998)PT(0.002)MGR;FS(0.999)PT(0.001)MGR;FS(0.72)PT(0.28)MGR;FS(0.941)PT(0.059)MGR;FS(0.987)PT(0.013)MGR 145.16 0.0024185 1564502000 3067930 3055150 3179730 3046570 3010800 2788310 3670340 3088690 2145690 TRUE FALSE 2875913.738 3281356.485 3255154.697 3124750.144 2774343.913 3593249.833 3120006.591 3474319.746 1787560.477 1.608848357 1.835661801 1.821003954 1.748052826 1.552028 2.010141686 1.74539918 1.943609623 1 20.76956062 -0.578013785 6.264670776 0.999999999 1.790084024 0.763947434 0.136751703 4.02E-09 50961909.22 0.269541908 0.028571386 0.264232489 0.578013785 0.790084024 FS(ph)PVLGR ddPTM_SK-BR-3_Pertuzumab_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 180.87 0.00071347 2832112000 4125341 4746270 4026279 3852234 4958500 3010780 4701070 4428296 4606730 TRUE FALSE 3867143.271 5097688.769 4121784.239 3951088.846 4569079.412 3879943.31 3996188.196 4981178.503 3837837.002 1.007636142 1.328271306 1.073986268 1.02950929 1.190535035 1.010971364 1.041260531 1.297912991 1 21.87186201 3.729177409 24.65161757 1.087391503 1.193938014 0.055596153 0.118718686 150.2994841 1801924.288 0.028021338 0.047524614 5360.155753 -3.729177409 0.106546511 FS(ph)PVTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FSPVTPK 7 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 FS(1)PVTPK;FS(1)PVTPK 125.83 0.0042075 1225680000 3635900 2275570 3000100 2869510 2761020 2130120 2996410 2138320 2268990 TRUE FALSE 3408335.509 2444055.571 3071263.789 2943146.485 2544180.627 2745051.064 2547126.138 2405293.959 1890280.911 1.803084129 1.292958923 1.624765807 1.556988947 1.34592727 1.452192131 1.34748551 1.272453182 1 20.85016922 0.823031391 0.419168278 0.962697542 1.55229169 0.634190084 0.132625301 0.99571266 0.425674813 0.199702697 0.090435345 6.653212441 -0.823031391 0.589594147 FS(ph)RS(ph)PIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSRSPIR 7 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 FS(1)RS(1)PIR 53.237 0.080169 109070000 63813 47279 63341 56974 45243 51707 67891 45890 38836 TRUE FALSE 59819.05824 50779.58635 64843.47843 58436.0493 41689.79728 66633.97151 57711.37482 51619.46752 32354.02071 1.848891017 1.569498481 2.004186095 1.806144894 1.288550739 2.059526762 1.783746612 1.595457578 1 14.98165739 0.8399379 3.205843498 1.000273384 1.7692065 0.552816348 0.215694146 0.549701988 9.591747857 0.192574806 0.050100962 6.917320532 -0.8399379 0.768933116 FSALQQAVPTESTDNRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FSALQQAVPTESTDNRR 17 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C044 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;;;; 225.01 4.06E-15 3900220000 1932850 2159680 2202150 2259170 2362280 2029500 2681260 2043320 2623490 FALSE TRUE 1811876.369 2319584.954 2254386.038 2317144.127 2176756.058 2615383.704 2279229.955 2298433 2185612.571 0.829001623 1.061297407 1.031466449 1.060180637 0.995947812 1.196636467 1.042833476 1.051619592 1 21.05960626 4.738961291 24.68982109 1.058679607 0.829001549 0.622536577 0.055238147 16.95897156 1044595.342 0.012061197 0.070769746 54822.80993 -4.738961291 -0.229678058 FSCPETDSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FSCPETDSHR 10 0 P50416 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 ;; 110.54 0.0018724 872310000 469010 564160 508230 564500 800790 662040 606230 662710 640780 FALSE TRUE 439655.5013 605930.9934 520285.4556 578986.0257 737899.1836 853160.2007 515331.4395 745450.8023 533829.6784 0.823587596 1.135064268 0.974628194 1.084589428 1.38227456 1.598188027 0.965348051 1.39642068 1 19.02601999 2.92298809 5.3952055 1.267758631 1.01270258 0.310344658 0.198448814 0.286383312 14.68176199 0.057745826 0.06203222 837.5063148 -2.92298809 -0.255056051 FSCPPNFTAKPPASES(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSCPPNFTAKPPASESPR 18 1 O15446;O15446-2 O15446 CD3EAP DNA-directed RNA polymerase I subunit RPA34 1 FSCPPNFTAKPPAS(0.023)ES(0.977)PR 189.07 2.10E-14 361490000 249980 178200 226160 205030 226240 191010 262810 192370 318430 TRUE FALSE 234334.198 191394.1134 231524.622 210291.4169 208472.023 246151.4862 223404.0803 216387.818 265281.9759 0.883340066 0.721474246 0.872749162 0.792709027 0.785850687 0.927886206 0.84213818 0.815689861 1 18.01716713 -5 0.17202255 1.692476936 0.785649504 0.458503146 0.057704387 109.262281 1.036042471 25.73775041 0.1866912 1.00E-05 5 -0.906827431 FSDAGQPMSFVLEFHFEPNEYFTNEVLTK ddPTM_SK-BR-3_Pertuzumab_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 0 243.9 1.45E-45 154810000 192590 177190 176780 154470 197040 147730 222310 160500 168520 FALSE TRUE 180536.1357 190309.332 180973.3051 158433.9617 181565.2732 190377.2528 188976.6793 180538.7783 140392.9233 1.285934728 1.355547897 1.289048627 1.128503902 1.293265137 1.356031688 1.346055591 1.285953551 1 17.09911069 0.93860333 21.25778612 1 1.300113568 0.665358098 0.065090298 2786.731589 964871.4583 0.064644779 0.016161195 8.681671121 -0.93860333 0.300113568 FSDFLGLHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FSDFLGLHSK 10 0 O60749;O60749-2;D6RC15 O60749 SNX2 Sorting nexin-2 0 ; 77.744 0.032081 6424300000 439320 2646900 1786300 1888610 2020120 3027600 779100 1391250 515020 FALSE TRUE 411823.7454 2842879.23 1828671.88 1937074.93 1861467.924 3901618.971 662281.1878 1564950.625 429059.8348 0.959828238 6.625833973 4.262043965 4.514696489 4.33848096 9.093414611 1.543563704 3.647394834 1 18.71081933 1.612611842 25 2.19647684 5.05500387 0.290215096 2.132953116 0.512679204 2686.934536 0.9212212 0.489902191 40.983764 -1.612611842 2.85852703 FSDHVALLSVFQAWDDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 FSDHVALLSVFQAWDDAR 18 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;; 269.59 7.12E-32 1044236000 866637 1527916 1225206 1256486 1582603 1034888 1435571 1379952 1339112 FALSE TRUE 812395.7372 1641044.49 1254268.465 1288729.558 1458311.744 1333643.366 1220320.456 1552242.045 1115605.556 0.728210551 1.470989886 1.124293849 1.155183883 1.307192974 1.19544346 1.093863731 1.391389668 1 20.08939559 -1.361931208 7.303946639 0.999995644 1.199326572 0.071192732 0.200829013 1.25E-05 1.09E-06 0.170395888 0.040161818 0.043457906 1.361931208 0.199330928 FSDIQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FSDIQIR 7 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ;; 100.45 0.022762 226921000 513990 591240 589520 595380 659830 491730 621050 551200 713540 FALSE TRUE 481820.2834 635016.0248 603503.6928 610658.4588 608009.6134 633684.4684 527929.318 620018.5333 594445.5644 0.810537267 1.068249244 1.015237944 1.027273977 1.022817983 1.066009247 0.888103722 1.043019867 1 19.18118518 -2.882492697 9.439695534 0.999995824 0.998515117 0 0.082073738 0 0 0 0.01668061 0.001310712 2.882492697 -0.001480707 FSDQAGPAIPTSNS(ph)YSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSDQAGPAIPTSNSYSK 17 0 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 FSDQAGPAIPT(0.01)S(0.028)NS(0.934)YS(0.028)K 107.91 0.0013677 0 38507 38085 39781 39252 39775 29898 40278 30557 43264 TRUE FALSE 36096.91561 40904.85303 40724.62411 40259.27277 36651.23194 38529.06725 34238.68782 34372.10871 36042.9589 1.001497011 1.134891648 1.129891256 1.116980237 1.016876335 1.068976256 0.949941094 0.953642813 1 15.13742983 2.164776026 1.30919103 0.964103262 1.106162116 0.525818516 0.047607521 0.289507516 0.948331516 0.029443409 0.015869086 146.1423296 -2.164776026 0.142058855 FSEAEHWLDYFPPLAIQDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FSEAEHWLDYFPPLAIQDLK 20 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRU9 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 130.56 1.59E-05 341100000 1002330 836500 960040 893060 1012830 724470 1217750 916410 796130 FALSE TRUE 939595.9545 898435.3304 982812.6022 915977.4315 933286.4174 933612.7282 1035159.693 1030825.806 663250.7598 1.416652662 1.354593745 1.481811498 1.381042416 1.407139613 1.4076316 1.560736535 1.554202224 1 19.3391949 FSEAEHWLDYFPPLAIQDLKR ddPTM_SK-BR-3_Pertuzumab_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 ; 134.9 4.86E-06 205870000 472660 594370 494050 514190 726860 365990 701370 568480 710970 FALSE TRUE 443077.0543 638377.7732 505769.0993 527384.9859 669775.3476 471645.3716 596206.0797 639455.9794 592304.514 0.748056184 1.07778644 0.853900464 0.890395014 1.130795616 0.796288667 1.006587094 1.079606797 1 19.17597956 1.518692204 8.91673686 1.040735155 0.932816707 0.1641942 0.117469298 0.203693888 29.80949699 0.057479105 0.026651404 33.01354825 -1.518692204 -0.107918448 FSEEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FSEEQR 6 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;; 168.82 0.014504 2996050000 4278730 4800800 4571170 4720910 4939230 3903740 5118960 4312690 4613290 FALSE TRUE 4010931.927 5156256.227 4679600.311 4842056.543 4551322.8 5030686.366 4351419.47 4851138.84 3843302.096 1.043616095 1.341621371 1.217598876 1.259868837 1.184221975 1.308948982 1.132208544 1.262231987 1 21.87391495 -1.230159782 0.462989946 0.896934711 1.234781531 0.3703972 0.087209939 22.57226512 2.70536987 2.99349519 0.040669857 0.058862705 1.230159782 0.33784682 FSEGVLQS(ph)PSQDQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FSEGVLQSPSQDQEK 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 FSEGVLQS(1)PSQDQEK;FSEGVLQS(1)PSQDQEK;FSEGVLQS(0.961)PS(0.039)QDQEK;FSEGVLQS(0.724)PS(0.276)QDQEK 437.12 3.80E-154 1229520000 3261210 2264160 2614190 2787540 2687350 1848080 2968780 1935490 2388260 TRUE FALSE 3057096.688 2431800.762 2676199.821 2859072.996 2476296.371 2381590.695 2523639 2177140.187 1989643.977 1.536504381 1.222229097 1.345064671 1.436977182 1.244592701 1.196993393 1.268387223 1.09423606 1 20.92407887 1.263870764 0.559129175 0.99142168 1.358425261 0.647809935 0.091893264 0.528508332 0.418576834 0.090554093 0.045593487 18.35991914 -1.263870764 0.367003581 FSEGVLQSPS(ph)QDQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSEGVLQSPSQDQEK 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 FSEGVLQS(0.106)PS(0.894)QDQEK 165.45 1.49E-06 58224000 411960 276080 310080 334800 257850 182100 442850 245170 227030 TRUE FALSE 386176.159 296521.2505 317435.244 343391.5348 237599.5011 234669.3139 376448.7537 275780.0142 189137.2263 2.041777637 1.567757211 1.678332976 1.815568207 1.256228114 1.240735726 1.990347226 1.458094842 1 17.52907382 -2.801406155 0.215394776 1.10E-18 1.743015458 0.398384622 0.260461352 58.45418033 1.363108193 28.44980902 0.555447418 0.00157977 2.801406155 1.743015458 FSEVLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FSEVLKR 7 1 P12277;H0YJG0;H0YJK0 P12277 CKB Creatine kinase B-type 0 ; 120.65 0.0072397 1306090000 1600940 1757100 1722290 1437660 1073620 816450 1437560 857950 748130 FALSE TRUE 1500740.023 1887197.512 1763143.532 1474552.79 989302.216 1052145.861 1222011.224 965066.9461 623262.2699 2.407878827 3.027934793 2.828895021 2.365862432 1.587296815 1.688126992 1.96066934 1.54841227 1 19.24947985 2.934602642 2.698756594 1.650900523 2.823634602 0.781492252 0.291416042 0.117643863 1.692232045 0.088318585 0.098800811 860.2063453 -2.934602642 1.172734078 FSFSGNTLVSSSADPEGHFETPIWIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FSFSGNTLVSSSADPEGHFETPIWIER 27 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 223.44 2.11E-34 891019000 680486 870950 801036 837032 826283 628007 937665 743235 635087 FALSE TRUE 637895.596 935436.0442 820036.9522 858511.6582 761390.0662 809302.4261 797070.8381 836029.5258 529086.8769 1.205653785 1.768019743 1.549909832 1.622628902 1.439064357 1.529621054 1.506502756 1.580136576 1 19.01314511 -2.577824071 0.440917156 1.34E-12 1.557883777 0.555260505 0.145287049 71.56412852 3.305460195 68.4628017 0.072832494 0.002643479 2.577824071 1.557883777 FSFSPEPTLEDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSFSPEPTLEDIR 13 0 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 108.47 0.0028236 16886000 57231 45580 58911 49498 63014 43934 67829 60283 79272 FALSE TRUE 53649.01387 48954.79063 60308.39674 50768.20248 58065.13463 56617.03259 57658.67114 67809.46525 66040.99108 0.812359309 0.741278861 0.913196422 0.768737744 0.879228698 0.857301377 0.873073983 1.026778432 1 16.01107415 1.365263428 2.445876711 1.018582277 0.827726995 0.682121183 0.050968846 0.161584527 1.644392907 0.042716117 0.013076379 23.18800728 -1.365263428 -0.190855282 FSFSPEPTLEDIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FSFSPEPTLEDIRR 14 1 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 ;;; 302.37 9.22E-44 1964410000 1598480 2101640 1805130 1728350 2256140 1535360 1874380 1895640 2340790 FALSE TRUE 1498433.99 2257247.612 1847948.536 1772702.387 2078951.865 1978593.508 1593334.12 2132314.827 1950097.027 0.768389454 1.157505284 0.947618765 0.909032916 1.066076116 1.014612853 0.817053766 1.093440376 1 20.89511448 FSFWDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FSFWDK 6 0 P78406;E9PQ57 P78406 RAE1 mRNA export factor 0 ; 105.2 0.077189 236710000 1005680 1248780 878320 844340 1270420 631440 967630 1184920 963990 FALSE TRUE 942736.284 1341240.971 899154.1652 866007.1939 1170646.338 813726.4774 822542.8645 1332859.87 803093.8414 1.173880604 1.670092462 1.119612826 1.078338731 1.45767067 1.013239594 1.024217622 1.659656446 1 19.61520905 3.818040123 5.507154109 1.180215551 1.446023524 0.129053319 0.242744122 0.332616743 15.75916341 0.057581547 0.105323657 6577.185986 -3.818040123 0.265807973 FSGDLDDQTCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FSGDLDDQTCR 11 0 P05455 P05455 SSB Lupus La protein 0 ;;; 280.25 5.64E-27 2956550000 4820200 4438260 4541740 4456370 4890400 4434600 5990100 4251950 4824600 FALSE TRUE 4518512.286 4766873.388 4649472.218 4570727.999 4506327.711 5714797.03 5091940.114 4782815.317 4019343.092 1.124191736 1.185983202 1.156774157 1.137182842 1.121160251 1.421823641 1.266858787 1.189949504 1 21.9385283 FSGEEGEIEDDES(ph)GTENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FSGEEGEIEDDESGTENR 18 0 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 FSGEEGEIEDDES(0.977)GT(0.023)ENR;FSGEEGEIEDDES(1)GTENR 369.44 1.48E-107 1061950000 1627550 1206480 1510860 1317580 1071240 1552860 1925910 1270740 737300 TRUE FALSE 1525684.551 1295809.035 1546698.313 1351391.333 987109.1316 2001145.473 1637137.675 1429394.686 614239.8669 2.483857908 2.10961402 2.518068911 2.200103586 1.607041784 3.257921834 2.665306769 2.327095266 1 19.22844263 0.945195199 21.54394778 0.999999997 2.414505384 0.523630002 0.419087921 2812.182977 1105481.054 0.397948924 0.099487232 8.814449602 -0.945195199 1.414505388 FSGEEGEIEDDES(ph)GTENREEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FSGEEGEIEDDESGTENREEK 21 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 FSGEEGEIEDDES(0.965)GT(0.035)ENREEK;FSGEEGEIEDDES(0.949)GT(0.051)ENREEK 272.18 6.75E-45 772070000 836330 409830 582520 559670 492200 516370 709400 478530 426270 TRUE FALSE 783985.5982 440174.2396 596337.6495 574032.0797 453544.5974 665437.6364 603032.0557 538275.5239 355122.7832 2.207646581 1.239498732 1.679243568 1.616432701 1.27714869 1.873824119 1.69809453 1.515744833 1 18.4379584 0.888365761 6.294677887 1.00000435 1.617808113 0.351003546 0.275451579 2.112053145 118.6482806 0.240724917 0.060473851 7.733316079 -0.888365761 0.617803763 FSGEEGEIEDDES(ph)GTENREEKDNIQPTTE ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FSGEEGEIEDDESGTENREEKDNIQPTTE 29 2 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 FSGEEGEIEDDES(0.98)GT(0.02)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.997)GT(0.003)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.938)GT(0.062)ENREEKDNIQPTTE 268.23 6.80E-59 1439810000 1568320 1097390 1285520 1329630 1421310 899590 1634940 1167110 1582270 TRUE FALSE 1470161.651 1178641.897 1316013.141 1363750.557 1309686.046 1159287.029 1389795.925 1312826.253 1318178.915 1.115297502 0.894144098 0.998356996 1.034571666 0.993557119 0.879461063 1.054330265 0.995939351 1 20.33011477 1.631381198 25 1.018867967 0.978054345 0.035298896 0.067973597 2.234124829 2368.226538 0.029282162 0.016225575 42.79383405 -1.631381198 -0.040813621 FSGFSAKPNNSGEAPS(ph)SPTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSGFSAKPNNSGEAPSSPTPK 21 1 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 FSGFSAKPNNSGEAPS(0.496)S(0.496)PT(0.008)PK 146.57 6.52E-08 485640000 1016200 549020 716440 678540 736340 521030 997490 619220 927050 TRUE FALSE 952597.856 589670.0121 733434.2951 695952.4852 678510.8267 671442.9028 847925.6347 696530.9801 772319.366 1.233424795 0.763505407 0.949651566 0.901120075 0.878536596 0.86938504 1.097895083 0.901869111 1 19.55883802 1.757328525 25 1.008080392 0.911768999 0.040233878 0.128800725 16.99456091 22659.9991 0.053791633 0.02983087 57.1911099 -1.757328525 -0.096311393 FSGFSAKPNNSGEAPSS(ph)PTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSGFSAKPNNSGEAPSSPTPK 21 1 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 FSGFSAKPNNSGEAPS(0.164)S(0.725)PT(0.111)PK 124.51 1.49E-05 438850000 743030 408110 519010 505600 473340 372900 694330 439670 587710 TRUE FALSE 696525.0786 438326.889 531321.1623 518574.552 436165.7858 480550.1765 590221.6623 494563.7673 489617.4042 1.422590522 0.895243685 1.085176217 1.059142399 0.890829823 0.981480994 1.205475249 1.010102507 1 18.90129532 4.750604441 24.54304866 1.025419133 1.422590837 0.661059283 0.091286858 985.3643809 2007939.538 0.022613712 0.374071056 56312.45242 -4.750604441 0.397171704 FSGWYDADLSPAGHEEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FSGWYDADLSPAGHEEAK 18 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ; 258.61 1.15E-30 1260020000 1903490 1744410 1939760 1940920 2009810 1455300 2577800 1782940 1972790 FALSE TRUE 1784353.959 1873567.931 1985772.023 1990727.293 1851967.63 1875421.485 2191282.821 2005543.984 1643518.604 1.085691366 1.139973668 1.208244323 1.21125936 1.12683095 1.141101464 1.333287506 1.220274586 1 20.64835636 4.547285405 1.447739725 1.196539914 1.063676135 0.073130507 0.085821303 1.609437179 4.041937849 0.022604533 0.278789178 35260.25149 -4.547285405 -0.132863779 FSGWYDADLSPAGHEEAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FSGWYDADLSPAGHEEAKR 19 1 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;; 213.99 5.82E-18 4140090000 3145950 3562860 3475180 3733560 3770090 2503310 4198040 3205000 3298370 FALSE TRUE 2949050.605 3826657.862 3557612.911 3829369.471 3474002.339 3225974.959 3568582.875 3605151.305 2747850.739 1.073220814 1.392600336 1.294689286 1.393587147 1.264261661 1.173999342 1.298681484 1.311989496 1 21.38987221 -1.150348538 4.339467534 0.999940976 1.287125252 0.446047352 0.095651825 5.03E-05 9.84E-06 0.085254708 0.020090605 0.070737786 1.150348538 0.287184276 FSHDADPEVSYNSIFAMGMVGSGTNNAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSHDADPEVSYNSIFAMGMVGSGTNNAR 28 0 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 139.47 1.40E-07 13868000 17271 20880 16753 19799 20984 13717 20332 15606 18745 FALSE TRUE 16190.03894 22425.97693 17150.38907 20307.07586 19336.00129 17676.87522 17283.40535 17554.44345 15616.3384 1.036737199 1.436058591 1.098233698 1.300373707 1.238190464 1.131947501 1.106751462 1.124107521 1 13.9307686 1.543875976 0.685912856 1.010855029 1.245690204 0.274878523 0.110456068 0.719906186 0.730856626 0.095175045 0.044556584 34.98452456 -1.543875976 0.234835174 FSHDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSHDLK 6 0 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 102.98 0.035077 127610000 362010 320280 349110 358970 381820 264980 445830 348270 418820 FALSE TRUE 339352.4403 343993.8645 357391.0541 368181.7779 351833.3974 341475.4244 378981.9304 391752.2761 348916.2363 0.972589994 0.985892397 1.024288975 1.055215377 1.008360634 0.978674504 1.086168802 1.122768835 1 18.41252121 1.693692944 7.453418208 1.077865953 1.00660457 0.384785735 0.038362282 0.114189503 12.91457761 0.017887526 0.009324695 49.39613215 -1.693692944 -0.071261383 FSHEEIAMATVTALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 FSHEEIAMATVTALR 15 0 P04075;J3KPS3;P04075-2;H3BQN4;H3BU78;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;;;;;;; 254.45 1.07E-24 9271142000 6430484 7409255 6437852 6222553 7313372 4727176 6595404 6383320 4766779 FALSE TRUE 6028011.485 7957843.95 6590560.89 6382234.245 6739009.264 6091834.972 5606484.399 7180291.553 3971172.79 1.517942382 2.003902718 1.659600636 1.607140908 1.696982131 1.534014079 1.411795632 1.808103533 1 21.9211337 -2.482099311 0.175687049 1.71E-14 1.866987767 0.583105253 0.169891021 29.84223391 0.646169359 12.37894743 0.600855982 0.003295343 2.482099311 1.866987767 FSHEEIAMATVTALRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FSHEEIAMATVTALRR 16 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BU78;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;; 228.73 2.49E-15 9919000000 2376510 2763260 2830980 3127290 2859250 1900770 3168800 1998090 2740010 FALSE TRUE 2227768.481 2967854.646 2898132.182 3207541.556 2634696.039 2449491.443 2693667.858 2247555.935 2282684.63 0.975942297 1.300159736 1.269615673 1.405161937 1.154209392 1.073074839 1.180043806 0.984610798 1 21.12230012 2.487912284 18.06093321 1.089193803 1.256067068 0.310733744 0.120292966 15.80338168 26452.65507 0.037742358 0.033610281 307.5475589 -2.487912284 0.166873265 FSHQGVQLIDFSPCER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FSHQGVQLIDFSPCER 16 0 P55884;P55884-2;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;; 204.9 2.40E-11 1097620000 1270000 1623740 1380130 1358550 1661580 1135350 1583700 1498820 1579950 FALSE TRUE 1190512.967 1743963.399 1412867.335 1393412.693 1531086.209 1463107.114 1346238.887 1685950.976 1316246.138 0.904475943 1.324952339 1.073406633 1.058626235 1.163221806 1.111575618 1.022786581 1.280878194 1 20.32799787 3.720029027 24.78413402 1.09914089 1.161077565 0 0.128214818 863.2432671 3016652.295 0.030663089 0.048647228 5248.425385 -3.720029027 0.061936675 FSHVDSPNSECKGEDATDDQFES(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSHVDSPNSECKGEDATDDQFESPK 25 1 Q5T5P2;Q5T5P2-3;A0A0U1RRK8 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 FSHVDSPNSECKGEDATDDQFES(1)PK 248.82 2.14E-39 101100000 238370 134540 183420 174730 199320 131340 186060 125830 168570 TRUE FALSE 223450.8472 144501.4816 187770.809 179213.8676 183666.2112 169255.7259 158162.0303 141540.1525 140434.578 1.591138382 1.028959418 1.337069628 1.276137759 1.3078418 1.205228287 1.126232816 1.007872523 1 17.09953868 1.564723769 1.657134128 0.995739289 1.272168776 0.439805943 0.136677288 0.351492491 1.912852753 0.106589875 0.036769287 36.70487667 -1.564723769 0.276429487 FSKEEPVSS(ph)GPEEAVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FSKEEPVSSGPEEAVGK 17 1 O00567 O00567 NOP56 Nucleolar protein 56 1 FSKEEPVS(0.179)S(0.821)GPEEAVGK;FSKEEPVS(0.06)S(0.94)GPEEAVGK;FSKEEPVS(0.033)S(0.967)GPEEAVGK;FSKEEPVS(0.037)S(0.963)GPEEAVGK 203.71 5.71E-12 1213880000 2264530 1713380 1915410 1922890 2125250 1224760 2463340 1576580 2564730 TRUE FALSE 2122797.11 1840240.438 1960844.43 1972234.613 1958341.438 1578328.33 2093985.036 1773419.483 2136659.994 0.99351189 0.861269665 0.917714767 0.923045603 0.916543317 0.738689513 0.980027258 0.82999611 1 21.02692592 -0.960356388 3.995476142 1.000007171 0.89491775 0.167834482 0.073406973 17461930.4 34317687.33 1777.962648 0.015520835 0.109557878 0.960356388 -0.10508942 FSKPIGDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSKPIGDFK 9 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 0 69.349 0.050609 271910000 659550 425940 494760 502140 543350 296800 494580 423620 630000 FALSE TRUE 618269.9428 457477.0408 506495.9408 515025.7625 500677.4828 382481.3419 420422.3205 476509.8895 524848.93 1.177996005 0.871635655 0.965031863 0.981283819 0.953945896 0.728745587 0.80103492 0.907899135 1 19.0015427 2.387033478 9.269519357 0.834464937 0.971646458 0.258013107 0.104251329 0.363655217 34.04205209 0.033609042 0.028093812 243.7998745 -2.387033478 0.137181521 FSLAHSMLAISGHLDS(ph)DDDSGSGSLVGIDNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSLAHSMLAISGHLDSDDDSGSGSLVGIDNK 31 0 Q9Y3Q8;Q9Y3Q8-2 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 FSLAHSMLAIS(0.003)GHLDS(0.837)DDDS(0.127)GS(0.017)GS(0.017)LVGIDNK 140.55 4.23E-08 80057000 114710 135720 142940 153920 180760 102470 160500 130980 204050 TRUE FALSE 107530.5059 145768.85 146330.6043 157869.8478 166563.8388 132051.4255 136434.515 147333.1413 169992.7368 0.632559413 0.85750046 0.860805038 0.928685841 0.97982915 0.77680628 0.802590261 0.866702567 1 17.37511358 7.999999969 0.028117245 1.454154834 9.88E-07 0.31118791 0.087721067 2676.183045 5.77484498 97.90856118 224.9442548 99999992.93 -7.999999969 -1.454153846 FSLCS(ph)DNLEGISEGPSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 202.61 1.34E-15 45324000 29502 28304 27366 32179 31607 28096 35802 26217 29065 TRUE FALSE 27655.52248 30399.65761 28015.13444 33004.76762 29124.71372 36206.8591 30433.82247 29490.25016 24213.86373 1.142135877 1.255464966 1.156987367 1.363052505 1.202811498 1.495294576 1.256875929 1.217907662 1 14.56354568 0.808779972 3.24219027 1.000086753 1.266362932 0.402240854 0.101869518 1.10837996 17.21682414 0.093879034 0.024386697 6.438429904 -0.808779972 0.26627618 FSLCSDNLEGIS(ph)EGPSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSLCSDNLEGISEGPSNR 18 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-5;Q14C86;C9IZ08;H0Y7I9;B4DGD8;A0A0A0MQV8 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 FSLCS(0.008)DNLEGIS(0.991)EGPS(0.001)NR 275.19 4.86E-39 92616000 115820 115320 130280 120450 122620 130730 155130 119530 119770 TRUE FALSE 108571.0329 123858.4128 133370.3031 123540.9509 112989.9198 168469.6288 131869.6967 134453.5836 99779.61326 1.088108376 1.241319832 1.336648828 1.238138202 1.132394846 1.688417336 1.321609619 1.34750556 1 16.60645746 5.881081493 0.754714137 1.330155645 1.30E-09 0.096159932 0.177804268 24.66036904 2.865058871 0.057714985 41.25362867 760468.9609 -5.881081493 -1.330155643 FSLYFLAYEDKNDIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FSLYFLAYEDKNDIPK 16 1 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ; 209.66 1.07E-11 173910000 357350 274203 228832 248642 302353 158975 385010 260460 685140 FALSE TRUE 334984.1014 294505.2754 234260.0031 255022.5747 278607.415 204868.5018 327281.3248 292979.0043 570785.7078 0.586882427 0.515964698 0.410416729 0.446792152 0.488112108 0.358923671 0.573387386 0.513290715 1 19.12258969 0.240348 1.03732605 1.002236915 0.471484281 0.851421119 0.067628012 1.35221241 1.545716854 0.067791053 0.01932899 1.739193887 -0.240348 -0.530752634 FSMPGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSMPGFK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 106.42 0.01793 211610000 712600 674980 684820 610610 815550 556430 784860 697040 718650 FALSE TRUE 667999.638 724956.2215 701064.2538 626279.2864 751499.9928 717062.3081 667177.5293 784066.9784 598702.6723 1.115745209 1.210878546 1.170972314 1.046060616 1.255214028 1.197693515 1.114372058 1.309609953 1 19.19148018 -1.23020689 5.702068982 0.999992872 1.174748232 0.357775993 0.074681332 6.03E-06 8.14E-07 0.064424818 0.015184456 0.058856321 1.23020689 0.17475536 FSPDGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FSPDGNR 7 0 O75083;O75083-3;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ; 107.66 0.039632 0 777260 860960 740790 821230 914990 678650 943660 786510 865770 FALSE TRUE 728612.684 924706.3742 758361.8886 842304.1521 843130.3763 874565.238 802166.9435 884707.5048 721267.3939 1.010183866 1.282057642 1.051429602 1.167811216 1.168956733 1.212539546 1.112163048 1.226601275 1 19.46017468 -0.887810641 7.093721292 0.999999998 1.156435428 0.264321304 0.080632112 2.03E-09 4.29E-10 0.068151726 0.016063516 0.129476025 0.887810641 0.15643543 FSPPS(ph)PLPQAVFSTSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FSPPSPLPQAVFSTSSR 17 0 Q99594;A0A1X7SBS4 Q99594 TEAD3 Transcriptional enhancer factor TEF-5 1 FSPPS(1)PLPQAVFSTSSR;FSPPS(1)PLPQAVFSTSSR;FSPPS(1)PLPQAVFSTSSR;FSPPS(1)PLPQAVFSTSSR 197.94 1.54E-11 414908000 356559 334519 326865 343855 396888 279961 387349 306994 469118 TRUE FALSE 334242.6087 359287.1348 334618.3922 352678.9014 365718.0174 360781.1959 329269.6134 345322.8767 390819.1752 0.85523595 0.919318083 0.856197478 0.90240941 0.935772963 0.923140979 0.842511408 0.883587343 1 18.57614173 -1.916638717 2.628128269 1.066914137 0.88917333 0.549364885 0.0313704 9260686.298 5688359.574 3821727.96 0.007440139 0.012116056 1.916638717 -0.177740807 FSQMLQDKPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSQMLQDKPLR 11 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 0 59.739 0.089448 356540000 107350 174230 121040 116820 224950 85953 138550 158650 253070 FALSE TRUE 100631.1551 187130.1705 123911.126 119817.799 207283.3344 110766.2358 117775.7137 178457.8017 210830.9821 0.477307245 0.88758383 0.58772731 0.568312104 0.983173025 0.525379309 0.558626216 0.846449606 1 17.68572736 1.013515583 5.50504598 0.999531483 0.668585045 0.34359014 0.160870113 0.157322474 16.2002057 0.145142589 0.036590676 10.31610095 -1.013515583 -0.330946438 FSS(ph)PTEELDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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(0.032)S(0.966)PT(0.002)EELDYR;FSS(0.999)PT(0.001)EELDYR;FSS(1)PTEELDYR;FSS(1)PTEELDYR;FS(0.12)S(0.86)PT(0.019)EELDYR;FS(0.018)S(0.968)PT(0.014)EELDYR;FS(0.003)S(0.997)PTEELDYR 326.85 2.36E-57 7203260000 4667410 4980450 4752310 4591670 5472660 3089700 4357640 4067380 4156550 TRUE FALSE 4375285.14 5349207.7 4865037.037 4709500.026 5042859.359 3981646.233 3704252.336 4575201.346 3462794.953 1.263512625 1.54476594 1.404945168 1.360028558 1.456297421 1.149835981 1.069729045 1.321245239 1 21.72350553 2.23148226 21.37019437 1.133690252 1.422627831 0.610497923 0.106979767 16.0118005 48338.45536 0.036282087 0.027486469 170.4049711 -2.23148226 0.288937579 FSSELEQIELHNSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSSELEQIELHNSIR 15 0 Q96EY4;H0Y9X1;D6RA57 Q96EY4 TMA16 Translation machinery-associated protein 16 0 172.43 1.03E-06 131600000 26967 88309 85488 87342 85908 59665 84555 73782 79339 FALSE TRUE 25279.18361 94847.49025 87515.81573 89583.34359 79161.13222 76889.31692 71876.76272 82993.84511 66096.80835 0.382456948 1.434978369 1.324055093 1.355335391 1.197654383 1.163283354 1.0874468 1.255640736 1 16.01229299 2.113201394 3.419304282 1.124434868 1.214505899 0 0.299477977 1.383531146 31.57502845 0.119010647 0.081486768 129.7780948 -2.113201394 0.09007103 FSSETWQNLGTLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FSSETWQNLGTLHR 14 0 F8W9U3;Q96IU4;B4DQI4 F8W9U3 ABHD14B Alpha/beta hydrolase domain-containing protein 14B 0 ; 256.57 2.56E-24 1426710000 1186080 1596220 1335690 1317140 1732840 1087870 1499900 1492270 1216950 FALSE TRUE 1111845.37 1714405.79 1367373.198 1350940.042 1596749.736 1401920.409 1275003.919 1678583.194 1013833.183 1.096674866 1.691013688 1.34871616 1.332507226 1.574962985 1.382791994 1.257607208 1.655679871 1 19.95138886 -1.491143133 3.235211978 0.990428066 1.424020216 0.341325156 0.182064944 39020571.38 50120450.48 3340800.528 0.039916203 0.032274303 1.491143133 0.43359215 FSSGYYDFLVEVEGDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FSSGYYDFLVEVEGDNR 17 0 P04844-2;P04844 P04844-2 RPN2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 0 ; 196.58 3.69E-11 47374000 60173 60732 55105 61689 66884 49352 74557 65038 52146 FALSE TRUE 56406.87934 65228.66047 56412.11662 63272.04418 61631.20044 63599.12124 63377.87 73158.13747 43442.49572 1.298426308 1.501494318 1.298546865 1.456455094 1.418684618 1.463984059 1.458891091 1.684022436 1 15.40681937 -0.83813434 5.242905588 0.999999643 1.44055504 0.628592494 0.10799852 0.000143143 34806640.67 33.23928189 0.023317068 0.145166251 0.83813434 0.440555397 FSSPTEELDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSSPTEELDYR 11 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 152.37 0.0036619 0 167760 177140 176570 178340 198500 129410 203790 180590 177450 FALSE TRUE 157260.2011 190255.6299 180758.3238 182916.5063 182910.6107 166768.5662 173233.5814 203137.059 147832.4486 1.063773228 1.286967994 1.222724276 1.237323118 1.237283238 1.128091754 1.171823798 1.374103324 1 17.17360344 2.283777459 24.99964392 1.17968975 1.223209814 0.022194647 0.106818591 481.0052528 265937.9536 0.033620022 0.028128405 192.2106553 -2.283777459 0.043520064 FSSVSS(ph)PQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSSVSSPQPR 10 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 FS(0.002)S(0.112)VS(0.029)S(0.857)PQPR 121.68 0.00053353 523890000 840950 829600 886190 863320 988570 801280 882930 827160 1053500 TRUE FALSE 788316.4406 891024.4472 907210.8453 885474.2528 910931.6999 1032596.528 750542.8432 930432.7468 877664.0441 0.898198401 1.015222685 1.033665275 1.008898859 1.037904772 1.176528234 0.855159612 1.060124034 1 19.74330928 4.738419439 5.730055181 1.019160522 0.89436484 0.202558113 0.077726783 0.235160609 33.22691528 0.017535337 0.114867242 54754.45227 -4.738419439 -0.124795682 FSTELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FSTELER 7 0 Q9UH65;E7EMB1 Q9UH65 SWAP70 Switch-associated protein 70 0 ; 143.11 0.0056859 230580000 237900 299290 293060 280040 317970 251670 340440 257256 322940 FALSE TRUE 223010.2637 321449.743 300011.5216 287226.3005 292997.9188 324323.0435 289394.1825 289374.9779 269039.2277 0.828913559 1.194806221 1.115121851 1.067600078 1.08905278 1.205486078 1.075657944 1.075586562 1 18.03745702 0.849076082 2.239712327 1.000395445 1.101146394 0.035918103 0.10317175 1.428773073 13.6251707 0.088655384 0.02415982 7.064413019 -0.849076082 0.100750949 FSTLTDDPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSTLTDDPSPR 11 0 Q14C86-2;Q14C86-6;Q14C86-4;Q14C86-5;Q14C86 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 FSTLTDDPS(1)PR 125.03 0.00035323 122440000 353820 429810 435660 520540 500660 350590 415220 338770 471010 TRUE FALSE 331675.0378 461633.5796 445994.0609 533897.9377 461340.1832 451799.6416 352961.6157 381066.1802 392395.3882 0.845257227 1.176450064 1.136593534 1.360612163 1.175702358 1.151388766 0.899505005 0.971128081 1 18.58194856 1.762854673 10.12822192 0.952539577 1.154425062 0.315182366 0.126840551 0.210320092 76.92198744 0.056767871 0.031197556 57.92348365 -1.762854673 0.201885485 FSVCVLGDQQHCDEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FSVCVLGDQQHCDEAK 16 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;;; 274.17 3.17E-35 6089690000 7800750 5878740 6557510 6541540 6418940 5050280 8545580 5344280 7220950 FALSE TRUE 7312514.982 6314008.026 6713057.234 6709406.991 5914822.345 6508213.852 7264249.612 6011525.122 6015726.796 1.215566336 1.049583573 1.115917903 1.11531112 0.983226557 1.081866593 1.207543138 0.999301552 1 22.52030762 -5 0.279776602 0.281052404 1.10497867 0.161758827 0.074835109 462.7674206 4.434853598 193.1737424 0.082211448 1.00E-05 5 0.823926266 FSWFAGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FSWFAGEK 8 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 155.1 0.00096394 1145800000 1345020 2158340 1192920 1218480 2585300 770110 1195960 2132560 2818200 FALSE TRUE 1260837.599 2318145.739 1221216.626 1249748.26 2382260.967 992428.2553 1016636.901 2398814.81 2347824.214 0.53702385 0.987359158 0.520148237 0.532300609 1.014667518 0.422701261 0.433012359 1.021718234 1 21.16289296 1.216674022 24.94252965 1.010859794 0.646709373 0.359848755 0.207807454 311.4941675 354977.3146 0.198409065 0.049773364 16.46925757 -1.216674022 -0.36415042 FSWNVWPSSR ddPTM_SK-BR-3_Pertuzumab_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 ; 181.87 4.28E-06 699120000 570400 1008810 649230 647910 989100 415440 698410 822890 835200 FALSE TRUE 534699.6822 1083503.342 664630.0422 664536.4675 911420.0758 535370.7839 593689.9042 925629.6279 695799.7244 0.768467798 1.557205765 0.955203083 0.955068598 1.309888527 0.769432302 0.85324826 1.330310426 1 19.40831258 3.730448525 24.89575033 1.002756912 1.230283998 0.027708565 0.258867092 281.0102669 2102583.942 0.062226776 0.106602354 5375.867121 -3.730448525 0.227527087 FSWPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSWPFR 6 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 0 158.08 0.022184 43287000 141520 146780 153210 140120 137500 112680 156820 120160 117320 FALSE TRUE 132662.5158 157647.7439 156844.2136 143715.7164 126701.3046 145208.8868 133306.2968 135162.2405 97738.53408 1.357320499 1.612953841 1.604732617 1.470409985 1.296329087 1.485687177 1.363907266 1.38289613 1 16.57663985 -0.249581084 0.27821765 0.818170675 1.571660293 0.69406667 0.096448191 4.073523098 0.423190849 0.858629948 0.139341442 0.562884016 0.249581084 0.753489618 FSYDTFVDYDVDEEDMMNQVLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FSYDTFVDYDVDEEDMMNQVLQR 23 0 Q9Y508 Q9Y508 RNF114 E3 ubiquitin-protein ligase RNF114 0 83.776 0.0076332 15362000 16932 18071 16188 16873 17352 15546 16873 17385 21594 FALSE TRUE 15872.25634 19408.99564 16571.987 17305.98975 15989.24391 20033.87783 14343.05029 19555.55552 17989.8219 0.882290911 1.078887593 0.92118683 0.961987831 0.888793897 1.113622911 0.797286953 1.087034415 1 14.13489328 3.759750315 24.07950885 0.954775837 0.99625351 0 0.102698271 917.1788148 676850.0784 0.023376219 0.042136821 5751.091999 -3.759750315 0.041477673 FT(ph)DTRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FTDTRK 6 1 P13639 P13639 EEF2 Elongation factor 2 1 FT(0.999)DT(0.001)RK;FT(1)DTRK;FT(1)DTRK;FT(1)DTRK;FT(1)DTRK;FT(1)DTRK 93.429 0.026739 7145140000 4519370 3421280 2932950 3471260 1889850 1598040 6952830 2979040 2569350 TRUE FALSE 4236510.699 3674595.131 3002520.959 3560338.408 1741428.804 2059368.206 5910317.688 3350979.702 2140508.886 1.979207246 1.716692304 1.402713616 1.663314005 0.813558316 0.962092808 2.761174096 1.565506092 1 21.02952239 FT(ph)DTRKDEQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FTDTRKDEQER 11 2 P13639 P13639 EEF2 Elongation factor 2 1 FT(0.973)DT(0.027)RKDEQER 118.16 0.0012177 1664000000 2061700 2071900 1425900 2088300 1367300 667840 3327500 1530800 2844000 TRUE FALSE 1932661.877 2225305.632 1459723.021 2141889.313 1259917.773 860634.5665 2828572.266 1721923.75 2369318.027 0.815703867 0.939217786 0.616094169 0.904010896 0.531763891 0.363241471 1.193833936 0.726759232 1 21.17604043 -1.332330373 6.398885611 1.000012014 0.775084263 0.093365315 0.230216222 3.80E-05 3.96E-06 0.214523924 0.050561075 0.046523205 1.332330373 -0.224927751 FT(ph)GSFDDDPDPHRDPYGEEVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FTGSFDDDPDPHRDPYGEEVDR 22 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 FT(0.587)GS(0.413)FDDDPDPHRDPYGEEVDR 166.23 1.75E-11 97946000 29908 41887 45438 37517 26863 37579 49359 28279 19354 TRUE FALSE 28036.11167 44988.35706 46515.81082 38479.74974 24753.28834 48427.44726 41958.07618 31809.6954 16123.69237 1.738814598 2.790201899 2.884935395 2.386534601 1.535212145 3.003496107 2.602262262 1.972854274 1 13.97689454 3.003977373 24.75808094 2.213706057 2.603362695 0.046430477 0.634895065 279.5614832 1740166.577 0.174850454 0.208115926 1009.200305 -3.003977373 0.389656638 FT(ph)GSFDDDPDPHRDPYGEEVDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FTGSFDDDPDPHRDPYGEEVDRR 23 2 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 FT(0.577)GS(0.423)FDDDPDPHRDPYGEEVDRR;FT(0.601)GS(0.399)FDDDPDPHRDPYGEEVDRR 164.05 7.03E-10 482520000 125328 145491 130641 164544 91093 85268 173852 104288 105419 TRUE FALSE 117483.9442 156263.305 133739.8662 168766.4776 83938.92323 109883.4874 147784.5066 117308.5864 87823.88787 1.337721969 1.779280203 1.522818785 1.921646624 0.955764147 1.251179947 1.682737011 1.33572527 1 16.42232578 2.74807297 24.99047951 1.319990635 1.643927743 0.356707207 0.252872369 873.6006855 2295088.895 0.075832686 0.079469631 559.8516601 -2.74807297 0.323937108 FTASAGIQVVGDDLTVTNPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FTASAGIQVVGDDLTVTNPKR 21 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 288.98 4.28E-47 311360000 107290 117080 83618 90246 150130 81856 122990 95322 227480 FALSE TRUE 100574.9104 125748.725 85601.45845 92561.86515 138339.3954 105486.4984 104548.7913 107223.1615 189512.1184 0.530704375 0.663539229 0.45169385 0.48842188 0.729976513 0.556621388 0.551673382 0.565785251 1 17.53193058 -1.271570597 2.97379071 1.002953869 0.566485016 0.744816586 0.079594301 5915698.381 7606213.146 157478.61 0.018873864 0.053509316 1.271570597 -0.436468853 FTATMST(ph)PDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FTATMSTPDKK 11 1 C9J5J4;H7C4T7;H0Y322;Q5TKA1-3;Q5TKA1;Q5TKA1-2;B1B047 C9J5J4 LIN9 Protein lin-9 homolog 1 FTATMS(0.229)T(0.771)PDKK 107.17 0.0020465 0 761890 376610 525180 462250 574380 373640 697280 407210 741210 TRUE FALSE 714204.6649 404494.5963 537637.5176 474112.1176 529270.5117 481503.8025 592729.3372 458051.0649 617497.2626 1.156611872 0.655054882 0.870671904 0.767796307 0.857122037 0.7797667 0.959889822 0.741786389 1 19.23607322 -1.325929956 4.715823791 1.000107888 0.837154807 0.102653221 0.137031343 0.000136933 1.96E-05 0.116884151 0.027531656 0.047213918 1.325929956 -0.162953081 FTDDDKTDHLSWEWNLTIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FTDDDKTDHLSWEWNLTIK 19 1 P52565;J3KRE2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;; 265.22 1.28E-31 1625829000 3472560 3350640 3910060 3857020 4141150 2729540 5289980 3583820 4075050 FALSE TRUE 3255218.668 3598724.872 4002808.47 3955997.663 3815920.784 3517513.888 4496796.609 4031267.816 3394897.829 0.958856152 1.060039227 1.17906596 1.165277385 1.124016384 1.036117746 1.324574946 1.187448936 1 21.69493673 4.602113304 1.311202211 1.162398675 0.901071126 0.305485262 0.089037828 1.18419744 2.149646205 0.024283442 0.387322366 40004.91062 -4.602113304 -0.261327549 FTDEESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FTDEESR 7 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ;; 240.12 1.01E-07 1066200000 1912230 2143020 2178320 2133450 2254360 2054570 2430590 1923910 2841640 FALSE TRUE 1792546.938 2301691.431 2229990.779 2188197.939 2077311.659 2647691.006 2066145.594 2164114.399 2367351.926 0.757194956 0.972264159 0.941976879 0.924323044 0.877483249 1.118418844 0.872766559 0.914149846 1 21.17484276 4.742704623 24.4574469 0.94988111 0.757194852 0.431881381 0.070394439 287.7425456 1698133.532 0.015190376 0.117352515 55297.38871 -4.742704623 -0.192686257 FTDEEVDELYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FTDEEVDELYR 11 0 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ;;;;; 318.23 1.60E-45 15504760000 9129760 9842520 9326990 9594470 9611590 8153370 10417440 8752850 8643990 FALSE TRUE 8558344.619 10571270.42 9548230.607 9840680.344 8856734.493 10507115.56 8855441.583 9845662.59 7201252.227 1.188452279 1.467976692 1.325912537 1.366523493 1.22988811 1.459067844 1.229708571 1.367215351 1 22.77981637 -3.375234947 0.32840127 4.84E-11 1.354182544 0.534744822 0.095102842 73.7373552 1.744393886 50.47856555 0.072199239 0.000421468 3.375234947 1.354182544 FTDFDEVR ddPTM_SK-BR-3_Pertuzumab_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 ; 117.72 0.0047089 143525000 315200 402820 343710 357400 405160 275710 369240 375480 360000 FALSE TRUE 295472.1946 432645.2119 351862.9635 366571.4891 373340.3679 355303.0012 313875.8899 422359.5045 299913.6743 0.985190806 1.442565808 1.17321414 1.222256671 1.244826095 1.184684233 1.046554115 1.408270248 1 18.19418778 2.079289014 5.076077702 1.147386725 1.23905563 0.017683643 0.152977526 0.55710365 25.50681706 0.054465775 0.039307219 120.0297811 -2.079289014 0.091668905 FTDKDQQPS(ph)GS(ph)EGEDDDAEAALKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FTDKDQQPSGSEGEDDDAEAALKK 24 2 Q9NXG2;H3BNW0 Q9NXG2 THUMPD1 THUMP domain-containing protein 1 2 FT(0.003)DKDQQPS(0.997)GS(1)EGEDDDAEAALKK;FTDKDQQPS(1)GS(1)EGEDDDAEAALKK;FTDKDQQPS(1)GS(1)EGEDDDAEAALKK 151.67 5.25E-07 612080000 2039320 754789 1127260 1080530 1146210 667927 1679850 908404 1732540 TRUE FALSE 1911682.601 810674.3629 1153999.14 1108258.229 1056191.29 860746.682 1427972.087 1021820.239 1443367.881 1.324459707 0.561654706 0.799518373 0.767827969 0.731754741 0.596346013 0.989333424 0.70794165 1 20.46100763 -1.722573864 6.502937889 1.003320029 0.788540674 0.062684625 0.217616722 0.009407808 0.000401352 0.189243579 0.044024075 0.018942013 1.722573864 -0.214779355 FTDLFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FTDLFEK 7 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 126.28 0.0092303 251110000 816440 889040 852140 868010 1018450 696810 1066190 836870 1057180 FALSE TRUE 765340.4778 954865.4466 872353.1632 890284.6061 938465.0452 897967.7352 906324.7075 941355.0617 880729.8284 0.868984396 1.08417521 0.99048895 1.010848705 1.065553834 1.019572298 1.029060988 1.068835222 1 19.74834 4.749759665 24.99718221 1.03305401 0.8689843 0.738047881 0.030813131 850.8524316 1899135.473 0.006841139 0.107624997 56203.02162 -4.749759665 -0.16406971 FTDLLQLVEFHQLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FTDLLQLVEFHQLNR 15 0 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ; 304.28 1.35E-44 1297610000 1568380 2209500 1685600 1681610 2187370 1321110 1980080 1863160 1359270 FALSE TRUE 1470217.895 2373093.679 1725583.228 1724762.96 2015582.784 1702493.011 1683185.386 2095779.627 1132399.056 1.298321372 2.095633749 1.523829625 1.523105261 1.779922699 1.503439094 1.486388899 1.850743001 1 20.11095102 -2.560219916 0.312050611 6.82E-10 1.692210928 0.400228634 0.23278077 50.19878857 1.790066894 34.54952303 0.209182964 0.002752834 2.560219916 1.692210927 FTDYQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FTDYQLR 7 0 Q15911;Q15911-2;E7EVZ1;Q86UP3;Q86UP3-4;Q86UP3-2;Q86UP3-5 Q15911;E7EVZ1 ZFHX3;ZFHX4 Zinc finger homeobox protein 3;Zinc finger homeobox protein 4 0 ;; 100.67 0.022387 483308000 814280 688110 1167890 1526300 715300 762950 1032520 643780 3788780 FALSE TRUE 763315.6683 739058.3804 1195592.902 1565467.442 659123.2234 983201.2795 877703.2114 724157.3501 3156408.142 0.241830471 0.234145379 0.378782733 0.495964835 0.208820657 0.311493709 0.278070253 0.229424497 1 21.58985234 -1.695888765 2.820532876 1.0969373 0.3011551 0.868739165 0.085827557 42578647.85 39190307.05 29473722.35 0.020060044 0.020142401 1.695888765 -0.7957822 FTEDLVGSVVHVLSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FTEDLVGSVVHVLSHR 16 0 Q6P9B6;H3BUB0;H3BM75 Q6P9B6 TLDC1 TLD domain-containing protein 1 0 ; 110.84 0.00049905 88991000 139835 201969 144569 144908 190329 113769 174229 167231 164379 FALSE TRUE 131082.977 216922.9949 147998.245 148626.5846 175381.3281 146612.2634 148104.9789 188110.1585 136943.083 0.957207725 1.584037618 1.080728152 1.085316479 1.280687745 1.070607293 1.081507556 1.373637532 1 17.06321687 3.736203018 24.42990123 1.138197627 1.320492272 0.066240574 0.185636192 435.0784779 1170348.178 0.04281386 0.075751839 5447.572484 -3.736203018 0.182294645 FTENDSEKVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FTENDSEKVDR 11 1 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 ; 112.95 0.0013289 642310000 628020 569060 577370 587460 677130 441980 724500 546920 888430 FALSE TRUE 588713.3492 611193.7945 591065.4891 602535.2182 623950.9412 569572.4511 615867.9509 615204.1659 740145.2935 0.795402409 0.825775425 0.798580352 0.814076943 0.843011429 0.769541408 0.832090613 0.831193782 1 19.49744898 0.38913527 1.323101626 1.000092816 0.810625816 0.894491901 0.020259285 0.898683831 1.682584656 0.017194966 0.005074088 2.449826171 -0.38913527 -0.189467 FTGS(ph)FDDDPDPHRDPYGEEVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FTGSFDDDPDPHRDPYGEEVDR 22 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 FT(0.158)GS(0.842)FDDDPDPHRDPYGEEVDR 130.78 7.91E-06 70486000 30974 26566 25897 36138 22570 30326 39607 24069 19880 TRUE FALSE 29035.39263 28532.97428 26511.28907 37065.36226 20797.44324 39080.6239 33668.29804 27074.06763 16561.89957 1.753143865 1.722808073 1.600739635 2.237989797 1.25574021 2.359670383 2.032876597 1.63471995 1 14.01558053 FTGS(ph)FDDDPDPHRDPYGEEVDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 FTGSFDDDPDPHRDPYGEEVDRR 23 2 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 FT(0.037)GS(0.963)FDDDPDPHRDPYGEEVDRR;FT(0.045)GS(0.955)FDDDPDPHRDPYGEEVDRR;FT(0.191)GS(0.809)FDDDPDPHRDPYGEEVDRR;FT(0.006)GS(0.994)FDDDPDPHRDPYGEEVDRR;FT(0.178)GS(0.822)FDDDPDPHRDPYGEEVDRR 250.82 1.08E-38 9467710000 2165110 2716670 2305460 2831870 1653500 1628120 2972540 1850540 1814190 TRUE FALSE 2029599.63 2917815.073 2360146.6 2904540.579 1523640.78 2098131.814 2526835.223 2081583.993 1511389.969 1.342869591 1.930550774 1.561573551 1.921767802 1.008105659 1.388213404 1.671861846 1.377264661 1 20.52744452 2.754286927 24.9991299 1.366572831 1.708147662 0.348332974 0.25962949 1005.011184 1597601.738 0.075605618 0.079947507 567.9196914 -2.754286927 0.34157483 FTGSFDDDPDPHRDPYGEEVDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FTGSFDDDPDPHRDPYGEEVDRR 23 2 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 172 3.31E-12 452880000 179910 209120 215280 211680 242090 191240 229510 199470 224590 FALSE TRUE 168649.7542 224603.4624 220386.5433 217112.0672 223077.2279 246447.8835 195097.1062 224374.2686 187104.4781 0.901366744 1.200417353 1.177879576 1.160378786 1.192260229 1.31716721 1.04271746 1.199192402 1 17.51348456 -1.9640213 1.027556948 0.855991114 1.156821444 0.149309765 0.110255916 3895.808367 682.1227529 1335.626962 0.030208665 0.010863723 1.9640213 0.30083033 FTIGDHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FTIGDHSR 8 0 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ;;;;; 199.7 0.00012575 3884280000 3469430 4830680 3776050 3773050 4732990 2893600 4121130 4248100 4559290 FALSE TRUE 3252284.569 5188348.574 3865619.689 3869872.851 4361280.057 3728935.346 3503204.815 4778484.636 3798315.045 0.856244027 1.365960567 1.017719606 1.018839355 1.148214407 0.981734085 0.922304963 1.25805379 1 21.85692814 3.724040445 24.89891494 1.037923685 1.160809465 2.28E-05 0.154273917 279.1096523 2255771.515 0.037203126 0.060470655 5297.12773 -3.724040445 0.12288578 FTISDHPQPIDPLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FTISDHPQPIDPLLK 15 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 99.069 0.0026847 266780000 304730 371040 364220 371270 419510 283060 459880 382880 429720 FALSE TRUE 285657.4933 398512.1877 372859.4704 380797.4168 386563.3768 364774.8269 390925.2633 430683.4108 357996.9559 0.797932744 1.113172001 1.041515757 1.06368898 1.07979515 1.018932762 1.091979294 1.203036517 1 18.44958779 4.743229031 24.90648686 1.076149536 0.797932625 0.710105284 0.055938578 235.5305724 1256534.914 0.01218362 0.097943786 55364.20029 -4.743229031 -0.278216911 FTLDCTHPVEDGIMDAANFEQFLQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 20 FTLDCTHPVEDGIMDAANFEQFLQER 26 0 P35268 P35268 RPL22 60S ribosomal protein L22 0 ;;;;;;;;;;;;;;;;;;; 326.37 5.18E-84 7814294000 2608742 2840163.2 2740576.6 2711096.2 3004856 2637064.6 3096289 2460301.6 2804049 FALSE TRUE 2445465.495 3050451.839 2805584.371 2780667.518 2768866.731 3398342.341 2632029.209 2767475.671 2336035.107 1.046844496 1.305824484 1.201002657 1.190336357 1.185284726 1.454747975 1.1267079 1.184689246 1 21.15563053 0.813043218 1.624866014 1.001867552 1.230181415 0.281299206 0.107329003 0.782623353 3.748188544 0.091930465 0.026432762 6.501943894 -0.813043218 0.228313863 FTLRDEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FTLRDEGK 8 1 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ;;; 130.56 0.00095083 1530100000 1716390 1817910 1747180 1801770 2373820 1305950 2141820 1765830 3430990 FALSE TRUE 1608964.214 1952509.948 1788623.935 1848006.469 2187389.753 1682956.565 1820673.975 1986297.763 2858335.604 0.562902485 0.683093317 0.625757148 0.646532362 0.765266944 0.588789001 0.636969981 0.694914117 1 21.44674389 0.766081192 3.402395353 0.999983413 0.647455498 0.807704854 0.05411497 0.753907639 10.5011135 0.047445134 0.012266317 5.835541905 -0.766081192 -0.352527915 FTLTQSEADADILFNFSHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FTLTQSEADADILFNFSHFK 20 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 256.92 3.34E-36 354617000 634571 682572 634305 616970 818399 565770 759835 660313 711287 FALSE TRUE 594854.3339 733110.3411 649351.0141 632802.4947 754125.2438 729098.6145 645904.7957 742754.5316 592568.6046 1.003857324 1.237173781 1.095824195 1.067897438 1.272637865 1.230403718 1.090008466 1.253449011 1 19.17662267 -0.974642519 4.284434122 0.999993897 1.157330871 0.22678088 0.090747989 4.98E-06 1.19E-06 0.079254085 0.018679611 0.106012599 0.974642519 0.157336975 FTPGTFTNQIQAAFREPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FTPGTFTNQIQAAFREPR 18 1 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 272.13 5.16E-39 483350000 199670 375230 261970 274990 477890 198917 339630 250080 952200 FALSE TRUE 187173.0111 403012.4196 268184.0521 282046.709 440358.4471 256341.1088 288705.6345 281303.0385 793271.6686 0.235950707 0.508038337 0.338073403 0.355548698 0.555116821 0.323144162 0.363942954 0.354611225 1 19.5974555 -1.648219666 2.862321387 1.060286067 0.38741259 0.820462835 0.091179207 31006310.3 30550373.37 13812405.82 0.020124672 0.022479173 1.648219666 -0.672873476 FTPNGSSFSISWQSPPVT(ph)FTGIPVSPTHHPVGTGEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FTPNGSSFSISWQSPPVTFTGIPVSPTHHPVGTGEQR 37 0 Q6ZNC4 Q6ZNC4 ZNF704 Zinc finger protein 704 1 FTPNGSSFSISWQS(0.002)PPVT(0.254)FT(0.254)GIPVS(0.191)PT(0.191)HHPVGT(0.108)GEQR 116.36 1.14E-05 83170000 21282 18647 20219 20202 30058 13995 25577 22014 26302 TRUE FALSE 19949.99761 20027.64328 20698.60423 20720.41752 27697.36593 18035.12931 21741.9663 24762.49636 21912.02628 0.910458821 0.914002339 0.94462301 0.945618504 1.264025772 0.823069901 0.992238966 1.130087014 1 14.41943528 2.974413013 24.98630306 1.027655565 0.926796629 0.200356294 0.111048505 1315.079285 1284207.095 0.032091523 0.034159031 942.7857578 -2.974413013 -0.100858936 FTPVASKFS(ph)PGAPGGSGSQPNQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FTPVASKFSPGAPGGSGSQPNQK 23 1 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 FTPVAS(0.003)KFS(0.997)PGAPGGSGSQPNQK;FTPVAS(0.001)KFS(0.999)PGAPGGSGSQPNQK 250.24 2.18E-38 2465600000 3820600 2671200 3444900 3396200 3842400 2494000 3973500 2804300 5099300 TRUE FALSE 3581475.466 2868978.427 3526614.655 3483352.242 3540633.403 3213977.313 3377710.563 3154423.028 4248193.887 0.843058382 0.675340746 0.830144468 0.819960749 0.8334444 0.756551466 0.795093316 0.742532735 1 22.01841818 -1.099639107 4.444888699 1.000020464 0.782800002 0.627738967 0.051453758 0.290728342 29313653.31 1313.878044 0.011581452 0.079498859 1.099639107 -0.217220462 FTQDTQPHYIYSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FTQDTQPHYIYSPR 14 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 162.79 4.38E-06 418290000 376250 711920 363420 421620 804380 286070 444040 668710 721570 FALSE TRUE 352701.1841 764631.2976 372040.494 432439.483 741207.2395 368653.765 377460.3243 752199.9155 601135.3055 0.58672512 1.271978689 0.618896429 0.719371295 1.233012323 0.613262541 0.62791242 1.251298848 1 19.19733023 1.2296627 24.99942448 1.125649434 0.82813274 0.204726734 0.256611764 360.0216224 1011472.775 0.22459052 0.059485923 16.96925203 -1.2296627 -0.297516694 FTRPLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FTRPLFK 7 1 P09960-4;P09960 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 62.659 0.076725 398050000 715960 893790 656690 727850 924150 589830 989610 880720 1212400 FALSE TRUE 671149.3416 959967.1416 672266.9969 746527.8632 851570.9868 760104.3459 841227.1676 990679.8307 1010042.608 0.664476267 0.950422422 0.66558281 0.739105319 0.843104024 0.752546814 0.832863051 0.980829742 1 19.94598472 1.296155333 2.841314781 1.00284318 0.780114178 0.539713141 0.083041535 0.204167977 2.721725435 0.069113904 0.020502325 19.77676862 -1.296155333 -0.222729003 FTSGAFLS(ph)PSVSVQECR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FTSGAFLSPSVSVQECR 17 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;H7C3P6 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 FTSGAFLS(1)PSVSVQECR;FTSGAFLS(1)PSVSVQECR 307.02 2.47E-47 430380000 540380 548280 561980 583860 532350 580070 776990 594130 711820 TRUE FALSE 506558.5804 588875.2217 575310.431 598842.8361 490541.3784 747526.7924 660487.5627 668308.4383 593012.6435 0.854212108 0.993023046 0.970148676 1.009831481 0.827202225 1.260557933 1.113783273 1.126971652 1 19.17770334 2.239004618 24.99999566 1.137048258 0.948299972 0.55973694 0.084630306 8.335399165 469369.7598 0.027552877 0.021751468 173.3822433 -2.239004618 -0.188748285 FTVETASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FTVETASR 8 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 ; 78.324 0.060113 0 139500 264610 222393 238409 249148 192578 221157 209670 193499 FALSE TRUE 130768.944 284201.9997 227668.267 244526.9786 229580.9211 248172.1424 187996.561 235847.761 161202.7668 0.811207813 1.76300944 1.412309921 1.516890704 1.424174818 1.539502995 1.166211751 1.463050329 1 17.29851698 0.472472662 0.629685734 0.993266223 1.451260423 0.152098949 0.257309092 2.708429529 1.789066337 0.296024539 0.094043828 2.968059906 -0.472472662 0.457994199 FTVHTK ddPTM_SK-BR-3_Pertuzumab_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 93.593 0.045443 291230000 994550 1011400 1073900 1017300 1192900 765220 1225400 963270 1335900 FALSE TRUE 932302.8908 1086285.108 1099373.415 1043405.64 1099214.446 986126.5917 1041662.646 1083536.38 1112929.66 0.837701541 0.976059088 0.987819316 0.937530626 0.987676477 0.886063718 0.935964494 0.973589274 1 20.08593098 -4.673396851 0.005726512 1.914029885 0.072359943 0.155252237 0.047017144 121462.8077 55.61504549 9706.294537 8235.454433 2.12E-05 4.673396851 -1.841669942 FVAFSGEGQS(ph)LR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FVAFSGEGQSLR 12 0 Q92890;Q92890-1 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 1 FVAFSGEGQS(1)LR 124.62 0.00033534 69906000 249690 309840 236880 212400 257980 174000 300440 163180 522280 TRUE FALSE 234062.3486 332780.876 242498.9055 217850.5436 237719.2914 224230.9753 255391.8111 183553.3822 435108.0939 0.537940691 0.764823456 0.557330256 0.500681432 0.546345367 0.515345447 0.586961757 0.42185697 1 18.73101433 -1.148717837 4.860652478 1.000031254 0.570771295 0.714024957 0.088149871 3.08E-05 5.40E-06 0.088188831 0.020784796 0.071003893 1.148717837 -0.429259959 FVCYCEGEESGEGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FVCYCEGEESGEGDR 15 0 Q9BUH6;Q9BUH6-2 Q9BUH6 C9orf142 Protein PAXX 0 264.17 9.64E-25 142610000 60648 53395 49927 41048 56826 50599 72651 46639 39656 FALSE TRUE 56852.14994 57348.42136 51111.29202 42101.36117 52363.11519 65206.10989 61757.65701 52461.98182 33037.15741 1.720854771 1.735876384 1.547085041 1.274363912 1.584976411 1.97372035 1.869339309 1.587969 1 15.01180194 2.427792027 24.99993401 1.719499493 1.577136341 0 0.290686471 360.3084277 182601.3937 0.093864555 0.078532737 267.7885646 -2.427792027 -0.142363151 FVDGEWYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 FVDGEWYR 8 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;;;;;; 181.49 0.00054335 11721244000 6978500 9481080 7882300 7844230 9648840 6237650 8100860 7854660 9116990 FALSE TRUE 6541728.142 10183069.03 8069271.878 8045526.222 8891059.028 8038358.295 6886211.248 8835331.591 7595305.471 0.86128572 1.340705659 1.062402547 1.059276187 1.170599268 1.058332456 0.90664046 1.163262179 1 22.85667656 2.007862947 12.1989862 1.005316793 1.124200342 0.03970454 0.133706851 0.745032554 1134.856439 0.047525636 0.034521195 101.8269995 -2.007862947 0.118883549 FVDGLMIHSGDPVNYYVDTAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 FVDGLMIHSGDPVNYYVDTAVR 22 0 P23396;P23396-2;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 0 ;;;;;;;; 287.67 1.94E-46 6688140000 6349742 7303580 7085780 6966960 7048120 6216669 7574470 6190819 6331659 FALSE TRUE 5952322.983 7844344.663 7253858.048 7145743.989 6494589.086 8011320.421 6438748.541 6963756.38 5274864.209 1.12843151 1.487117839 1.375174367 1.354678283 1.231233417 1.518772826 1.22064726 1.320177374 1 22.33070252 0.270302569 0.709368415 0.991656232 1.362936045 0.423257988 0.11925588 2.281535982 1.534577399 0.150749939 0.039013463 1.863384888 -0.270302569 0.371279812 FVDILGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FVDILGLR 8 0 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 ; 126.28 0.0028522 49232000 173496 224861 210529 207614 251230 173942 240340 218836 256750 FALSE TRUE 162637.1951 241509.9424 215522.8473 212941.7267 231499.4092 224156.2317 204303.2482 246158.1563 213896.7663 0.760353688 1.129095809 1.007602176 0.995535044 1.08229504 1.047964565 0.95514884 1.150826918 1 17.70655515 4.749690286 24.99716022 1.041883892 0.760353526 0.682138702 0.061232912 962.2573968 2161182.468 0.013791877 0.209898526 56194.04385 -4.749690286 -0.281530367 FVDKYSIS(ph)LSPPEQQKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FVDKYSISLSPPEQQKK 17 2 Q15057;A0A0U1RQT1;A0A087X1H5;H7C3K3 Q15057 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 1 FVDKYS(0.123)IS(0.462)LS(0.414)PPEQQKK 95.957 0.0012732 116510000 448420 316740 344540 401400 440090 250040 536460 324940 782920 TRUE FALSE 420354.1927 340191.7592 352712.6515 411700.6036 405527.1066 322222.4889 456022.8033 365509.4743 652245.5941 0.644472261 0.521570038 0.540766629 0.631204882 0.621739894 0.494020185 0.69915812 0.560386268 1 19.31505577 -5 0.286460089 4.185362084 0.559023949 0.803135977 0.063580555 93.99921809 0.891281611 178.4613144 0.064011474 1.00E-05 5 -3.626338135 FVEDTKNEVHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FVEDTKNEVHER 12 1 O75828 O75828 CBR3 Carbonyl reductase [NADPH] 3 0 ; 149.57 3.73E-05 205447000 430730 400570 419260 422770 476750 352150 534910 351020 519010 FALSE TRUE 403771.3782 430228.6196 429205.0452 433618.9939 439307.9781 453809.9883 454705.2114 394845.6197 432383.8781 0.933826164 0.995015405 0.992648123 1.002856526 1.016013779 1.049553444 1.05162388 0.91318303 1 18.72195321 6.475224046 0.744100968 1.012739005 4.53E-18 0.214926153 0.038680916 42.50332183 2.139506481 0.013108454 62.02578267 2986923.129 -6.475224046 -1.012739005 FVEGLPINDFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FVEGLPINDFSR 12 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 ;;;;; 252.16 1.10E-20 1003643000 1282893 1574388 1187412 1290632 1662109 990010 1378432 1310618 1552462 FALSE TRUE 1202599.017 1690957.326 1215577.973 1323751.802 1531573.664 1275809.816 1171748.918 1474251.542 1293346.063 0.929835449 1.307428363 0.939870626 1.023509361 1.184194786 0.986441179 0.905982515 1.139873994 1 20.30267692 3.870977438 7.822993749 1.019185171 1.142318711 0.081749477 0.122377291 0.423441326 27.69941006 0.029381359 0.05321757 7429.805379 -3.870977438 0.12313354 FVEVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FVEVGR 6 0 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ;;;;; 159.65 0.021057 2506980000 2306100 2811390 2789990 2973350 3106170 2980200 2879520 2424570 2535110 FALSE TRUE 2161765.318 3019548.241 2856169.88 3049651.195 2862223.938 3840535.36 2447762.708 2727282.902 2111983.764 1.023570993 1.429721333 1.35236356 1.443974735 1.355230086 1.818449283 1.158987465 1.291337059 1 21.01016731 0.985023396 1.652191375 1.011744466 1.394034803 0.248805986 0.203295621 0.511938864 2.877080304 0.174611652 0.05056729 9.661029223 -0.985023396 0.382290337 FVFDRPLPVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FVFDRPLPVSR 11 1 P25786;P25786-2;F5GX11;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ; 208.27 1.84E-08 3447400000 2355800 3258200 2360500 2130750 3097900 1630820 2344900 2761100 2701500 FALSE TRUE 2208354.683 3499440.518 2416492.175 2185428.652 2854603.43 2101611.26 1993304.014 3105829.413 2250602.198 0.981228351 1.554890741 1.073709151 0.97104173 1.268373164 0.933799524 0.88567585 1.37999928 1 21.10187965 3.711797161 6.292500985 1.052785441 1.311484118 0.123479426 0.203736095 0.204101876 33.15782359 0.049761868 0.081487591 5149.880612 -3.711797161 0.258698677 FVFLLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FVFLLDR 7 0 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 0 ; 91.041 0.038841 58013000 95730 269340 114342 122793 289560 107081 113295 229300 197535 FALSE TRUE 89738.43018 289282.2138 117054.2462 125944.0763 266819.1256 137993.5464 96307.46653 257928.6098 164565.1324 0.545306462 1.757858482 0.711294334 0.765314465 1.6213588 0.838534533 0.585224009 1.567334502 1 17.32829917 3.900431229 24.90762222 0.975734412 1.237744419 0.003079546 0.447577006 169.4997786 55048.07209 0.106993696 0.192885669 7951.173471 -3.900431229 0.262010008 FVGHTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 85.909 0.054178 3845020000 6086270 5749880 6214710 5986360 6304710 4939240 6919590 5548950 5412840 FALSE TRUE 5705341.225 6175607.098 6362125.856 6139980.132 5809563.509 6365118.406 5882061.718 6241748.622 4509402.036 1.26521015 1.369495789 1.410857982 1.361595192 1.288322368 1.411521607 1.30439949 1.38416326 1 22.10450471 -1.690751698 2.795868495 0.951627491 1.354332154 0.828484229 0.049924032 4973878.207 4554611.156 1705206.839 0.012142637 0.020382071 1.690751698 0.402704663 FVGQDVEGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FVGQDVEGER 10 0 P17812;B4E1E0;P17812-2;A0A3B3IRI2 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ;;; 205.73 3.80E-07 938480000 1154050 1269480 1232550 1133260 1308060 1160380 1314280 1121470 1368310 FALSE TRUE 1081820.071 1363473.62 1261786.668 1162341.37 1205330.244 1495362.869 1117215.915 1261487.998 1139930.221 0.949023063 1.196102704 1.106898163 1.019660106 1.057371953 1.311802109 0.98007395 1.106636156 1 20.12051408 1.616831222 25 1.032513208 1.114303723 0.110596959 0.102508438 1.404325889 3905.251085 0.044635769 0.024295863 41.38388152 -1.616831222 0.081790515 FVHLLDQSDQDFQEELDLMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FVHLLDQSDQDFQEELDLMK 20 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 254.72 3.89E-36 127298000 125121 99558 113220 114351 115579 92493 132024 99869 103239 FALSE TRUE 117289.9 106929.3779 115905.6319 117285.4403 106501.8916 119194.2276 112228.2269 112337.8645 86007.74395 1.363713249 1.24325291 1.347618558 1.363661397 1.238282586 1.3858546 1.304861884 1.306136626 1 16.39217894 0.399762187 2.289916584 1.000001027 1.317022631 0.806084022 0.049223276 5.174005671 19.12834711 0.042798972 0.011539765 2.510511339 -0.399762187 0.317021603 FVHSENQHLVSPEALDFLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 128.38 1.15E-05 798334000 1128486 1109858 1048295 1027080 1244765 829848 1377935 1118618 1547913 FALSE TRUE 1057856.076 1192033.041 1073161.052 1053436.612 1147006.178 1069411.646 1171326.439 1258279.92 1289556.32 0.82032561 0.924374548 0.832194015 0.816898491 0.889457994 0.829286499 0.908317396 0.975746386 1 20.29844335 1.333655264 2.382643621 0.997486858 0.858226436 0.731081455 0.033774115 0.150822782 1.435708535 0.028860748 0.008658751 21.56032305 -1.333655264 -0.139260422 FVIFPIEYHDIWQMYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FVIFPIEYHDIWQMYK 16 0 P31350;P31350-2;A0A286YFD6;C9JXC1 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 0 178.07 2.85E-09 84301000 150400 254720 143930 120540 282340 99772 167840 243320 170880 FALSE TRUE 140986.7325 273579.7338 147344.0876 123633.2605 260166.1553 128574.5567 142673.9502 273699.0376 142359.0241 0.990360347 1.921758987 1.035017545 0.868461 1.827535395 0.903171103 1.002212196 1.922597035 1 17.11917442 3.829545983 7.406544381 1.201755195 1.514384906 0.042971623 0.429546354 0.565541718 35.9456756 0.101283937 0.183510719 6753.765585 -3.829545983 0.312629712 FVIKPIDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FVIKPIDK 8 1 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 ; 138.1 0.0014615 0 7450000 5426100 6022000 5645200 7182200 4561900 6938700 5389100 7649800 FALSE TRUE 6983717.799 5827854.09 6164844.684 5790065.389 6618138.984 5878846.474 5898306.351 6061940.998 6372998.96 1.095829113 0.914460229 0.967338097 0.908530729 1.038465411 0.922461546 0.925515034 0.951191274 1 22.60354099 4.746955313 24.62287822 0.948802875 1.095829204 0.542345331 0.04088905 611.9251265 1794815.781 0.008807652 0.099591064 55841.27334 -4.746955313 0.14702633 FVIKPIDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FVIKPIDKK 9 2 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 86.898 0.0077766 1346800000 4339700 2868300 3354000 3100500 4194800 2397300 4368700 3140200 5400400 FALSE TRUE 4068085.924 3080671.916 3433558.464 3180064.079 3865357.329 3089361.593 3713653.992 3532260.882 4499038.352 0.904212324 0.684740088 0.763176082 0.706831956 0.859151896 0.68667154 0.825432837 0.785114641 1 22.10118523 0.023812358 0.656359461 1.011186568 0.757712063 0.475799979 0.072949004 3.290778254 1.596935241 0.156600705 0.024425719 1.056360999 -0.023812358 -0.253474506 FVINYDYPNSSEDYIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FVINYDYPNSSEDYIHR 17 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;;;; 241.68 2.26E-20 8598240000 5016520 5467840 5790990 5617720 5975540 5266520 6326330 5139530 6412620 FALSE TRUE 4702544.968 5872684.563 5928355.018 5761880.206 5506245.193 6786878.829 5377755.547 5781211.634 5342312.295 0.88024524 1.099277661 1.109698327 1.078536762 1.030685757 1.27040099 1.00663444 1.082155313 1 22.34903288 4.73996997 24.4639808 1.090918479 0.880245147 0.415281808 0.075912656 80.85185098 1403256.151 0.016083209 0.100601829 54950.2876 -4.73996997 -0.210673333 FVINYDYPNSSEDYVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FVINYDYPNSSEDYVHR 17 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;; 278.22 8.06E-36 3001510000 2042780 2323860 2368330 2390950 2703750 2111900 2531050 2328970 2651140 FALSE TRUE 1914926.046 2495921.012 2424507.906 2452305.825 2491408.381 2721571.246 2151542.55 2619747.031 2208647.607 0.867012936 1.13006756 1.097734151 1.110320097 1.128024395 1.232234258 0.974144786 1.186131741 1 21.07473182 4.741904007 24.57876181 1.107393132 0.867012821 0.496235511 0.076095793 202.8919689 1491462.156 0.016240029 0.117576554 55195.54257 -4.741904007 -0.240380311 FVKEPAFEDITLESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FVKEPAFEDITLESER 16 1 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 210.75 8.09E-12 162960000 101820 103940 106880 111800 128450 83890 133750 93869 163570 FALSE TRUE 95447.26795 111635.8257 109415.2441 114668.9773 118362.0551 108107.6812 113695.4292 105588.7513 136269.1103 0.700432165 0.819230606 0.802935044 0.841489146 0.868590504 0.793339598 0.834344841 0.774854632 1 17.05609904 -5 0.270218652 2.291808175 0.796076003 0.646792437 0.045359806 131.3206639 1.275495375 94.80957976 0.05157828 1.00E-05 5 -1.495732172 FVLCPECENPETDLHVNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FVLCPECENPETDLHVNPK 19 0 P55010;H0YLZ1;H0YN40 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 170.89 1.13E-11 456170000 673290 503330 534720 530880 560410 446730 740100 465200 556820 FALSE TRUE 631149.9808 540597.0769 547403.8109 544503.2796 516397.6592 575693.6989 629128.8758 523281.244 463883.1448 1.36057968 1.165373398 1.180046779 1.173794059 1.113206343 1.241031724 1.356222753 1.128045392 1 18.8234019 -2.425072113 1.280884207 0.247723277 1.214734426 0.386437986 0.085059456 57255.4443 5174.963345 123228.6656 0.024364097 0.00375775 2.425072113 0.967011148 FVLINWTGEGVNDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FVLINWTGEGVNDVR 15 0 Q9UJU6-2;Q9UJU6-3;Q9UJU6-6;F8WBG8;Q9UJU6 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ; 188.29 7.10E-07 99793000 170362 176472 177937 169824 211916 154422 202461 173434 204596 FALSE TRUE 159699.3465 189538.1705 182157.7497 174181.9714 195272.9722 199001.1246 172103.8526 195087.6167 170447.6059 0.936940978 1.112002539 1.068702307 1.02190917 1.145648079 1.167520797 1.009717043 1.144560616 1 17.37896881 4.745133549 24.5819468 1.084806609 0.936940893 0.375141756 0.059534792 619.317414 2316092.604 0.012955537 0.123703413 55607.52287 -4.745133549 -0.147865716 FVLINWTGEGVNDVRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FVLINWTGEGVNDVRK 16 1 Q9UJU6-2;Q9UJU6-3;Q9UJU6-6;F8WBG8;Q9UJU6 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 125.89 0.0001196 77301000 82295 85426 91748 94239 105750 81338 112390 80163 132290 FALSE TRUE 77144.30285 91751.02993 93924.30589 96657.33229 97444.82157 104818.9602 95538.16288 90171.52701 110209.9444 0.69997588 0.832511353 0.852230771 0.877029136 0.884174492 0.951084412 0.86687425 0.818179589 1 16.74989488 5.945416822 0.632219772 0.895560539 1.56E-20 0.60184418 0.050125296 9.269379862 0.867781484 0.018795094 8.488133374 881894.8824 -5.945416822 -0.895560539 FVLMAT(ph)PNLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(1)PNLSR 126.5 0.0028291 257200000 495420 584810 600190 513610 690880 437950 596430 561970 745970 TRUE FALSE 464412.5465 628109.9409 614426.7902 526790.1021 636621.0717 564379.0555 507000.8585 632133.1915 621462.7878 0.747289388 1.010695979 0.988678328 0.847661537 1.024391298 0.908146178 0.815818531 1.017169819 1 19.24530848 FVMQEEFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FVMQEEFSR 9 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;; 238.31 6.43E-10 1121150000 485664 1001495 460177 506481 926952 289389 508004 687305 696593 FALSE TRUE 455267.1572 1075646.732 471092.6158 519478.1599 854152.9291 372930.9065 431833.5163 773116.5422 580327.1281 0.784500905 1.853517921 0.811770798 0.895147124 1.471847321 0.642621874 0.744120851 1.332208171 1 19.14650685 3.797142653 6.977659869 0.957497784 1.381685732 0.120931077 0.358477927 0.341744919 28.43045904 0.085449494 0.154677431 6268.197223 -3.797142653 0.424187947 FVNDYDKDNDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FVNDYDKDNDGR 12 1 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 ; 90.731 0.0079304 513680000 966050 665020 826280 762520 715350 643790 911980 688830 619860 FALSE TRUE 905586.6549 714258.7728 845879.7518 782087.5541 659169.2966 829641.7219 775237.0654 774831.9418 516401.3616 1.753648852 1.383146572 1.638027733 1.514495531 1.276467 1.606583142 1.501229708 1.500445195 1 18.97813328 -2.711200673 0.391325499 1.08E-12 1.530966327 0.617111332 0.129923765 57.23218557 2.22456476 48.20270498 0.076714809 0.001944461 2.711200673 1.530966327 FVNKGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FVNKGEK 7 1 D6RC52;D6RCB9;Q9NX24;H0YC83;J3QSY4 D6RC52 NHP2 H/ACA ribonucleoprotein complex subunit 2 0 66.258 0.062347 261150000 429180 359410 375440 352800 463080 250570 498740 345080 520700 FALSE TRUE 402318.3899 386021.0904 384345.6141 361853.4453 426711.5648 322905.4913 423958.5671 388163.9976 433791.8061 0.927445803 0.889876399 0.886014002 0.834163855 0.98367825 0.744378955 0.977331893 0.894816343 1 18.72664328 0.820575035 1.155873196 0.997917821 0.885714845 0.201769028 0.068208085 1.042379928 2.633877668 0.055693034 0.017362401 6.615688292 -0.820575035 -0.112202976 FVPAENDSILMNPAQDGEVQLS(ph)QNDDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FVPAENDSILMNPAQDGEVQLSQNDDK 27 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 FVPAENDSILMNPAQDGEVQLS(1)QNDDK 162.1 8.06E-12 56637000 11267 40996 37328 37452 33440 47671 27368 35522 13419 TRUE FALSE 10561.81858 44031.3865 38213.43779 38413.08173 30813.75729 61432.84383 23264.42247 39956.99989 11179.28221 0.944767149 3.938659537 3.418237152 3.436095539 2.756326991 5.495240452 2.081030073 3.574200843 1 13.44853994 4.747487491 24.35511712 3.349095904 0.94476533 0.261397209 1.178236046 972.5646171 2653356.472 0.242926977 2.887129608 55909.74231 -4.747487491 -2.404330574 FVPDKEFSGSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FVPDKEFSGSDR 12 1 Q13573;G3V4X8 Q13573 SNW1 SNW domain-containing protein 1 0 86.467 0.010118 143130000 276520 262970 281490 272580 309380 220600 325780 278450 282060 FALSE TRUE 259213.1068 282440.5724 288167.0757 279574.8643 285082.5428 284283.6389 276932.3134 313215.0954 234982.3638 1.103117283 1.201964981 1.226334909 1.189769563 1.213208252 1.209808405 1.178523821 1.332930227 1 17.84219296 -1.055982689 4.532755181 0.999989164 1.205996444 0.574341376 0.055986914 5.42E-06 1.13E-06 0.047888598 0.011286857 0.087905756 1.055982689 0.206007279 FVPDKEFSGSDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FVPDKEFSGSDRR 13 2 Q13573;G3V4X8 Q13573 SNW1 SNW domain-containing protein 1 0 112.08 0.00052233 74638000 108690 120560 109910 112530 128350 86423 129700 106840 140610 FALSE TRUE 101887.2869 129486.3878 112517.1171 115417.7103 118269.9087 111371.9171 110252.6891 120179.2092 117141.2826 0.869781213 1.105386461 0.960524886 0.98528638 1.009634743 0.950748657 0.941194143 1.025933868 1 16.83789007 3.723453817 24.97894716 0.976692211 1.01297565 0 0.062686196 477.2716201 3250721.775 0.015138356 0.024472054 5289.977405 -3.723453817 0.036283439 FVPYLIAGIQHGCQDIGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FVPYLIAGIQHGCQDIGAR 19 0 P20839-3;P20839-7;P20839-5;P20839-6;P20839;A0A3B3IRL5;C9J381;P20839-2;P20839-4 P20839-3 IMPDH1 Inosine-5-monophosphate dehydrogenase 1;Inosine-5-monophosphate dehydrogenase 0 ; 222.3 2.47E-19 469120000 478410 431890 431310 367830 527440 471670 574640 466640 561600 FALSE TRUE 448467.1721 463867.585 441540.8769 377269.1405 486016.99 607833.4721 488478.0667 524901.0312 467865.3319 0.95853901 0.991455347 0.943734974 0.806362675 1.038796758 1.299163307 1.044056983 1.121906231 1 18.83573381 2.480003174 24.99958671 1.124566489 0.937550312 0.498165394 0.090113781 91.81638037 796484.3915 0.02865017 0.024391646 301.997379 -2.480003174 -0.187016177 FVPYLIAGIQHSCQDIGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FVPYLIAGIQHSCQDIGAK 19 0 P12268;H0Y4R1 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 206.8 3.48E-16 80977000 309270 282770 305600 279760 351910 315930 456830 298920 411740 FALSE TRUE 289913.3428 303706.585 312848.9763 286939.1152 324272.4081 407133.8623 388332.5825 336240.82 343017.9341 0.845184213 0.885395645 0.912048454 0.836513449 0.945351178 1.186917131 1.13210577 0.980242683 1 18.38792448 2.413845114 5.816567681 1.09339267 0.880332028 0.696076403 0.063352935 0.100285453 6.554484837 0.021214913 0.017729658 259.3254342 -2.413845114 -0.213060641 FVS(ph)EGDGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FVSEGDGGR 9 0 Q53EL6;Q53EL6-2 Q53EL6 PDCD4 Programmed cell death protein 4 1 FVS(1)EGDGGR;FVS(1)EGDGGR;FVS(1)EGDGGR;FVS(1)EGDGGR 184.9 4.56E-05 815290000 1634500 2059590 1821110 2552470 3275660 1885940 2607760 2346570 3163410 TRUE FALSE 1532199.563 2212084.187 1864307.589 2617970.702 3018402.877 2430380.262 2216750.597 2639544.43 2635416.435 0.581388028 0.839367987 0.707405314 0.993380275 1.145322932 0.922199706 0.841138641 1.001566354 1 21.32959952 3.237625202 24.99999994 0.970104239 0.736957016 0.627069175 0.098667231 18.76076938 501408.5784 0.028898552 0.036488595 1728.324163 -3.237625202 -0.233147223 FVSEDDRNS(ph)FTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FVSEDDRNSFTLK 13 1 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 1 FVSEDDRNS(0.984)FT(0.016)LK 96.163 0.0016798 0 111620 89697 101650 98817 107800 73781 119430 100270 136660 TRUE FALSE 104633.9034 96338.25921 104061.186 101352.8115 99333.82284 95080.37697 101522.5802 112788.9302 113850.5631 0.919045989 0.846181666 0.914015558 0.890226703 0.87249303 0.835133128 0.891717857 0.990675207 1 16.7967819 1.246297371 4.668622288 0.999347563 0.87858195 0.772013498 0.025866685 0.079453701 4.072664573 0.020399223 0.006123602 17.63182922 -1.246297371 -0.120765614 FVSEDDRNSFTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FVSEDDRNSFTLK 13 1 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 153.81 4.19E-05 525730000 740030 768650 751890 757530 927860 611390 893730 705990 1063100 FALSE TRUE 693712.8433 825561.6458 769725.1859 776969.5023 854989.6184 787888.3679 759723.4835 794134.4056 885661.7421 0.783270644 0.932141027 0.869096122 0.877275675 0.965368128 0.889604157 0.857803208 0.896656554 1 19.75639627 FVSELWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FVSELWK 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 117.17 0.01231 182659000 547030 832090 457750 479930 834950 334250 538480 864750 584600 FALSE TRUE 512792.3688 893698.8094 468608.0462 492245.8163 769376.395 430742.5489 457739.923 972715.941 487026.4833 1.052904485 1.835010703 0.962181857 1.010716733 1.579742419 0.884433524 0.939866596 1.997254717 1 18.8936407 3.958567019 22.22646393 1.169647734 1.48716891 0.058547955 0.393547752 219.1596811 262536.4802 0.092786637 0.167873061 9090.065641 -3.958567019 0.317521176 FVSISDLLVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FVSISDLLVPK 11 0 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 99.013 0.011846 32565000 286810 260610 267870 305700 372990 193540 346470 258360 394880 FALSE TRUE 268859.0741 279905.8356 274224.0029 313544.7795 343696.87 249411.8561 294520.04 290616.8147 328971.977 0.817270445 0.850850088 0.833578609 0.953104828 1.044760326 0.758155325 0.895273946 0.883409029 1 18.32760517 -3.977269125 0.016150048 2.011510868 3.35E-06 0.208047381 0.07702082 7232.925518 10.49688511 801.2370646 531.1147747 0.000105373 3.977269125 -2.01150752 FVVPKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FVVPKPR 7 1 F8VVM2;Q00325-2;Q00325 F8VVM2 SLC25A3 "Phosphate carrier protein, mitochondrial" 0 132.22 0.0030921 273860000 360910 338190 270040 213720 339970 238080 223600 363490 409130 FALSE TRUE 338321.2873 363229.9395 276445.4763 219204.417 313270.1276 306809.8311 190073.2558 408872.5266 340843.5599 0.992599911 1.065679339 0.811062636 0.643123247 0.919102381 0.900148535 0.557655412 1.199590002 1 18.3787502 3.929950224 3.544936751 0.82363511 1.026802283 0.101685539 0.180724222 0.367480117 9.426346126 0.043830556 0.090254423 8510.404926 -3.929950224 0.203167174 FVYVWDTTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FVYVWDTTSR 10 0 Q96DI7;Q96DI7-2;Q9NSS8 Q96DI7 SNRNP40;DKFZp434D199 U5 small nuclear ribonucleoprotein 40 kDa protein 0 ; 129.42 0.00070619 268450000 293610 403400 352040 356030 471350 325310 419060 408320 302390 FALSE TRUE 275233.4742 433268.1557 360390.555 365166.3326 434332.0723 419221.716 356225.8434 459299.6508 251919.1555 1.092546828 1.719869832 1.430580197 1.449537777 1.724093079 1.664112105 1.41404826 1.823202566 1 17.9426013 -1.060656837 5.502766051 0.999996309 1.544728936 0.393825469 0.210365587 8.33E-06 1.42E-06 0.178121157 0.041983275 0.086964732 1.060656837 0.544732627 FWAWDPEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 115.71 0.0027597 30950000 115341 137712 126462 123873 147599 114827 148303 121494 149940 FALSE TRUE 108122.0127 147908.3398 129461.7384 127051.7909 136007.1699 147975.6908 126066.3419 136662.7933 124914.0454 0.865571301 1.184080936 1.036406579 1.017113732 1.088806063 1.184620116 1.009224716 1.094054659 1 16.93057618 4.757397185 24.36328789 1.080182755 0.865571032 0.50149786 0.066103593 2449.195388 3167726.161 0.014914295 0.506680001 57200.15225 -4.757397185 -0.214611723 FWEGDFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FWEGDFHR 8 0 P49589-3;P49589;B4DKY1;P49589-2 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 0 ;; 117.04 0.0021563 244260000 433150 654030 492090 501910 650620 373739 496980 537410 488990 FALSE TRUE 406039.9147 702455.0617 503762.6072 514789.8603 599522.9297 481631.3822 422462.4627 604506.8215 407374.41 0.996724155 1.72434754 1.236608375 1.263677462 1.471675478 1.182281877 1.037037311 1.483909658 1 18.63599583 1.41609542 0.333731415 1.000736983 1.427132376 0.092026809 0.225365546 2.204001086 0.832149641 0.357357285 0.286301456 26.06726218 -1.41609542 0.426395393 FWETLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FWETLDR 7 0 A0A1B0GUB2;Q6P1J9 A0A1B0GUB2 CDC73 Parafibromin 0 ;;; 189.62 0.0012852 361803000 540100 671810 627900 600770 699570 513720 673240 598850 637550 FALSE TRUE 506296.1051 721551.5114 642794.0845 616186.7753 644628.5941 662022.6245 572293.9121 673617.7407 531138.7863 0.953227515 1.358499003 1.210218687 1.160123853 1.213672605 1.246421164 1.077484693 1.268251836 1 19.01872936 -1.87983347 0.345497351 0.810090647 1.210183903 0.184708217 0.11217263 48.63737032 2.75030911 7.588454428 0.083910403 0.013187623 1.87983347 0.400093256 FWEVISDEHGIDPTGSYHGDSDLQLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FWEVISDEHGIDPTGSYHGDSDLQLER 27 0 Q13885;Q9BVA1 Q13885;Q9BVA1 TUBB2A;TUBB2B Tubulin beta-2A chain;Tubulin beta-2B chain 0 ;; 272.91 4.89E-61 57677660000 222643 350337 358076 330711 383612 306683 403931 352097 415911 FALSE TRUE 208708.1721 376276.316 366569.7318 339197.6042 353484.6609 395217.4035 343365.2965 396057.0855 346492.7672 0.60234496 1.085957202 1.057943387 0.978945699 1.020179047 1.140622376 0.990973922 1.143045752 1 18.40246571 4.741146141 24.98553433 1.052536471 0.6023448 0.856619493 0.05784066 77.39252256 747849.7332 0.01242514 0.084973523 55099.30759 -4.741146141 -0.450191671 FWEVISDEHGIDPTGTYHGDS(ph)DLQLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FWEVISDEHGIDPTGTYHGDSDLQLDR 27 0 Q5JP53;P07437 Q5JP53 TUBB Tubulin beta chain 1 FWEVISDEHGIDPT(0.006)GT(0.006)Y(0.025)HGDS(0.963)DLQLDR 77.439 0.024395 39102000 11641 13933 13359 11285 14428 10922 13564 12610 13188 TRUE FALSE 10912.41059 14964.61382 13675.88179 11574.59221 13294.88308 14075.0041 11530.20412 14184.38626 10986.8376 0.993225802 1.362049241 1.244751427 1.053496249 1.210073686 1.281078742 1.049456135 1.291034488 1 13.42348857 -4.971121832 0.221434628 2.37E-09 1.222386335 0.146493896 0.12283133 246.7564894 2.499417696 110.005861 0.219650339 1.07E-05 4.971121832 1.222386333 FWEVISDEHGIDPTGTYHGDSDLQLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 29 FWEVISDEHGIDPTGTYHGDSDLQLDR 27 0 Q5JP53;P07437 Q5JP53 TUBB Tubulin beta chain 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;; 370.62 4.26E-127 66300487400 2539209.6 3239270.5 3148063.7 2979091.6 3308335.2 2769230.9 3514274.8 3055048.2 3718758.8 FALSE TRUE 2380285.004 3479109.458 3222737.258 3055540.134 3048511.899 3568662.906 2987341.919 3436477.693 3098073.932 0.768311233 1.122991102 1.040238977 0.98627089 0.984002308 1.15189727 0.964257789 1.10923037 1 21.56294014 FWEVISDEHGIDPTGTYHGDSDLQLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 FWEVISDEHGIDPTGTYHGDSDLQLER 27 0 P68371;M0R2D3;M0QY85;M0R0X0;M0QY37;M0QX14;M0QZL7;P04350;M0QYM7;M0R278 P68371;P04350 TUBB4B;TUBB4A Tubulin beta-4B chain;Tubulin beta-4A chain 0 ;;;;;;;;;;;; 386.18 2.46E-145 30662068100 3327859 4428839.7 4442101.61 4317293 4648162.1 3776505.57 4846265.5 3961647.3 4809608 FALSE TRUE 3119574.246 4756755.6 4547470.358 4428082.048 4283114.198 4866721.422 4119612.979 4456267.686 4006853.354 0.778559625 1.187154902 1.134923082 1.105127055 1.068947082 1.214599336 1.02814169 1.112161413 1 21.93403828 -1.589026761 8.06517652 0.999953939 1.095038996 0.025256463 0.120222447 8.86E-05 4.51E-06 0.103546056 0.024394234 0.025761624 1.589026761 0.095085057 FWTHWNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FWTHWNR 7 0 Q15428 Q15428 SF3A2 Splicing factor 3A subunit 2 0 139.31 0.0027006 234220000 51040 166040 72857 87112 175500 62707 63891 142980 90077 FALSE TRUE 47845.49751 178333.7744 74585.20245 89347.4414 161716.9379 80809.49294 54311.13768 160831.3677 75042.56678 0.637578105 2.376434896 0.993905268 1.190623472 2.155002752 1.076848733 0.72373774 2.143201847 1 16.19542155 FYAFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 FYAFGR 6 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;; 138.97 0.02809 11638508000 5109902 7133346 5645598 5131161 6942069 4123409 6051138 6165679 6754905 FALSE TRUE 4790082.355 7661506.36 5779514.251 5262835.278 6396866.904 5313770.24 5143826.033 6935477.595 5627467.717 0.851196772 1.361448301 1.027018642 0.935204881 1.136722097 0.944256015 0.91405696 1.23243312 1 22.42405444 3.680126094 7.394358277 1.012766165 1.158070798 0.013798127 0.156299251 0.406367459 54.60255291 0.038035254 0.059599677 4787.69079 -3.680126094 0.145304633 FYAGGSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FYAGGSER 8 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 92.467 0.027353 282870000 83943 153990 141330 149350 185620 179260 129390 120050 174930 FALSE TRUE 78689.15747 165391.5798 144682.4143 153182.5738 171042.154 231009.452 109989.1707 135038.5068 145733.0529 0.539954087 1.134894086 0.992790664 1.05111758 1.173667542 1.585154825 0.754730437 0.926615507 1 17.1529686 4.742452677 24.47122151 1.076306345 0.539953806 0.384418925 0.213720725 312.5871075 1965274.549 0.049475922 0.37323784 55265.31842 -4.742452677 -0.536352538 FYALSASFEPFSNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FYALSASFEPFSNK 14 0 P27797 P27797 CALR Calreticulin 0 164.9 9.42E-06 41085000 160130 187710 131840 114920 212130 109310 177960 176500 118760 FALSE TRUE 150107.7491 201608.2437 134967.3071 117869.0418 195470.1655 140866.0225 151276.5501 198536.4135 98938.18878 1.517187155 2.037719168 1.364157852 1.191340202 1.975679643 1.42377806 1.529000601 2.006671195 1 16.59423987 -1.901101147 2.61431903 0.655997797 1.624095031 0.318299546 0.289924209 41722089.54 29854700.96 88750937.98 0.067055858 0.012557375 1.901101147 0.968097234 FYCDYCDTYLTHDS(ph)PSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 FYCDYCDTYLTHDSPSVR 18 0 A0A0A0MRR7;P09234 A0A0A0MRR7 SNRPC U1 small nuclear ribonucleoprotein C 1 FYCDYCDTYLTHDS(1)PSVR;FYCDYCDTYLTHDS(1)PSVR;FYCDYCDTYLTHDS(0.998)PS(0.002)VR 312.43 2.18E-61 1297132000 1501950 1604730 1665840 1511640 1631440 1627960 2136220 1602940 1943330 TRUE FALSE 1407945.631 1723545.879 1705354.511 1550431.242 1503313.283 2097925.624 1815913.643 1803070.588 1618975.669 0.869652125 1.064590353 1.053354009 0.957661855 0.928558293 1.295835178 1.121643566 1.113710739 1 20.62664987 2.259807857 24.99999261 1.146114018 0.99695204 0.409052465 0.091649945 235.1813016 276719.0178 0.030272203 0.025304474 181.8895955 -2.259807857 -0.149161978 FYCDYCDTYLTHDSPSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 FYCDYCDTYLTHDSPSVR 18 0 A0A0A0MRR7;P09234 A0A0A0MRR7 SNRPC U1 small nuclear ribonucleoprotein C 0 ;;; 340.2 2.35E-75 2356370000 435083 1589250 1273890 1383170 1447900 1366510 1677400 1466160 1275360 FALSE TRUE 407851.9317 1706919.724 1304107.272 1418664.484 1334187.775 1760999.254 1425889.442 1649213.303 1062494.177 0.383862745 1.606521486 1.227401807 1.33522095 1.255713023 1.657420146 1.342020948 1.552209263 1 20.0190235 4.746232912 24.76320488 1.389908468 0.383862191 0.714073949 0.196229663 402.3369172 1298552.902 0.041239271 0.440965834 55748.46476 -4.746232912 -1.006046277 FYEAFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FYEAFSK 7 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 141.78 0.0058941 3688100000 6319900 6717900 6565800 6470300 7665300 4716600 7109800 6547000 7062900 FALSE TRUE 5924348.74 7215300.306 6721543.877 6636338.852 7063298.258 6078205.852 6043751.494 7364407.362 5884056.362 1.006847721 1.226245954 1.142331661 1.127851 1.200413086 1.032995858 1.027140313 1.251586815 1 22.48837964 2.234792423 24.99824629 1.072822693 1.152029641 0.102137548 0.088530154 172.8572381 1146720.942 0.029947472 0.022969396 171.7087485 -2.234792423 0.079206948 FYEDDENGWQAFGDFSPTDVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 287.37 2.37E-46 201379000 235405 206648 226557 215868 238068 182993 261328 196030 242412 FALSE TRUE 220671.4213 221948.4329 231931.039 221407.5383 219371.0996 235820.1085 222144.2925 220504.777 201951.8712 1.092693125 1.099016472 1.148447091 1.096338138 1.086254355 1.167704499 1.099986305 1.091867957 1 17.62365199 0.744341872 1.960919245 1.000127682 1.115765405 0.650560534 0.025856498 0.585025883 3.477253154 0.023297258 0.006460067 5.550624797 -0.744341872 0.115637723 FYEEEENGGVWEGFGDFSPTDVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FYEEEENGGVWEGFGDFSPTDVHR 24 0 P19838;P19838-2;P19838-3;A0A494C1E9;D6RF93 P19838 NFKB1 Nuclear factor NF-kappa-B p105 subunit;Nuclear factor NF-kappa-B p50 subunit 0 ; 185.5 2.35E-17 112835000 59623 68899 58214 68020 78152 56848 75879 63353 80805 FALSE TRUE 55891.30286 74000.35365 59594.86357 69765.50836 72014.25717 73259.09475 64501.64838 71262.76151 67318.12348 0.8302564 1.099263465 0.885272204 1.036355512 1.069760318 1.088252182 0.958161711 1.058596969 1 16.03870734 FYEEVHDLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 FYEEVHDLER 10 0 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W543;F8W118;F8VUX1;H0YHC3;H0YH88;F8W020;P55209-3;F8VXI6;F8VRJ2;F8VVB5;Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8;E9PS34;E9PNW0;E9PJJ2 P55209;Q99733 NAP1L1;NAP1L4 Nucleosome assembly protein 1-like 1;Nucleosome assembly protein 1-like 4 0 ;;;;;; 242.49 2.30E-12 14577080000 11266150 14285270 12633850 12655520 15344280 10440970 12125940 12630020 13163790 FALSE TRUE 10561021.78 15342966.25 12933530.89 12980282.07 14139202.14 13455108.54 10307767.87 14206905.8 10966668.41 0.963010952 1.399054452 1.179349134 1.183612159 1.289288745 1.226909399 0.939917894 1.295462329 1 23.38662198 1.784269892 25 1.072953604 1.228145684 0.143461851 0.141476906 129.6430432 70929.41454 0.058676224 0.032762481 60.85130442 -1.784269892 0.15519208 FYEQFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FYEQFSK 7 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 157.58 0.0075864 1929500000 5462100 5752100 5172100 5467000 6731700 4100400 6492300 5283400 5975200 FALSE TRUE 5120236.911 6177991.469 5294784.654 5607292.476 6203019.436 5284118.916 5518839.887 5943044.12 4977900.519 1.028593659 1.241083755 1.06365819 1.126437231 1.246111571 1.061515572 1.108668176 1.193885675 1 22.24710597 -1.754045136 2.882760269 0.973639987 1.135016109 0.242428326 0.074271277 31539142.91 43220916.85 6163990.74 0.016586272 0.017617929 1.754045136 0.161376122 FYFHDGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FYFHDGVR 8 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ; 155.75 0.00040391 982050000 564260 1119100 571540 595130 1109090 376860 683680 1034910 1019540 FALSE TRUE 528943.9738 1201959.328 585097.1987 610402.0434 1021986.545 485653.3642 581168.531 1164120.792 849372.1875 0.622746991 1.415115006 0.688858438 0.718650849 1.203225818 0.571779217 0.68423306 1.370566177 1 19.69603734 5.011169958 17.96166543 0.927280355 0.139405031 0.103129202 0.298467072 27405670.39 715444409.2 0.069177517 538955663.5 102605.3385 -5.011169958 -0.787875325 FYGAEIVSALDYLHSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FYGAEIVSALDYLHSEK 17 0 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 0 205.68 7.67E-12 57061000 278120 237570 266540 269840 282620 205030 331560 235670 231600 FALSE TRUE 260712.9657 255159.93 272862.4547 276764.5512 260424.1652 264218.8326 281845.6561 265093.9183 192944.4638 1.351233202 1.322452715 1.414202042 1.434425978 1.349736396 1.369403544 1.460760524 1.373938972 1 17.55782612 0.938950132 23.50794023 1 1.387668099 0.894061751 0.041614378 5897.364097 2270848.72 0.042153092 0.010538273 8.688606559 -0.938950132 0.387668099 FYGDEEKDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 FYGDEEKDK 9 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;;;;;; 157.95 6.14E-05 9413250000 27921210 13882410 17038490 17603030 18096260 10759170 23094520 14661480 18766300 FALSE TRUE 26173671.31 14910278.08 17442651.03 18054753.55 16675052.74 13865167.72 19631711.13 16491998.05 15634083.3 1.674141733 0.95370338 1.115681086 1.154832887 1.066583337 0.886855178 1.255699535 1.054874644 1 23.89819129 4.745397798 24.9948164 1.070884939 1.67414201 0.776216922 0.103337846 369.3373135 1350159.124 0.023595006 0.232438844 55641.36782 -4.745397798 0.603257071 FYGDEEKDKGLQTSQDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FYGDEEKDKGLQTSQDAR 18 2 P27797 P27797 CALR Calreticulin 0 ; 142.26 6.41E-08 662580000 1532420 1515110 1578950 1961580 2357210 1033740 2053900 1180450 3060750 FALSE TRUE 1436508.568 1627290.321 1616403.44 2011917.464 2172084.235 1332163.957 1745936.762 1327831.781 2549891.052 0.563360763 0.638180333 0.633910786 0.789020951 0.851834134 0.522439559 0.684710337 0.520740594 1 21.28200418 -2.26931243 2.405520143 2.535351714 0.654587666 0.51458731 0.106605765 4917783.389 747156.7597 41347516.02 0.024359387 0.005378827 2.26931243 -1.880764048 FYHDWNDKEIEVLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FYHDWNDKEIEVLNK 15 1 J3KQ32;Q9NTK5;Q9NTK5-3;Q9NTK5-2;C9JCJ9 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 312.78 1.97E-56 1484120000 6302000 4327800 4862900 4712300 5362100 3354400 6318000 4226700 5920900 FALSE TRUE 5907569.069 4648234.815 4978250.284 4833225.596 4940982.296 4322760.826 5370674.553 4754412.799 4932663.54 1.19764282 0.9423377 1.009241811 0.979840923 1.001686463 0.876354284 1.088798072 0.963863187 1 22.23393545 4.745867382 24.73147644 0.985788886 1.197642936 0.611799837 0.053743917 499.5468069 1690787.131 0.011777022 0.120685231 55701.56297 -4.745867382 0.21185405 FYIDPYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FYIDPYK 7 0 Q9NY12-2;Q9NY12 Q9NY12-2 GAR1 H/ACA ribonucleoprotein complex subunit 1 0 ; 107.66 0.017281 221930000 1311400 1168520 1283250 1199350 1248010 968630 1448010 1070010 1534420 FALSE TRUE 1229321.815 1255038.437 1313689.296 1230127.351 1149996.329 1248257.757 1230894.343 1203603.104 1278315.389 0.961673328 0.981790916 1.027672284 0.962303483 0.899618622 0.976486528 0.962903485 0.941554106 1 20.28581239 3.023486557 24.28936509 0.953779941 0.994006445 0.210681466 0.030085212 206.4584989 213513.6598 0.008339688 0.00996716 1055.568828 -3.023486557 0.040226504 FYIGEMVLAIDSIHQLHYVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FYIGEMVLAIDSIHQLHYVHR 21 0 Q9Y5S2;A0A0U1RRC3 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 0 112.74 7.57E-05 18314000 10526 21730 11363 11520 24336 8071.9 13819 23173 11031 FALSE TRUE 9867.196449 23338.91181 11632.53573 11815.6227 22424.74873 10402.12649 11746.96924 26066.20006 9189.854837 1.073705366 2.539638789 1.265801901 1.285724629 2.440163542 1.131914125 1.278254058 2.836410425 1 13.16582636 3.91174526 24.71036733 1.589382373 1.910300705 0.009305126 0.685178622 314.0673432 118707.6495 0.160640896 0.289599605 8161.035375 -3.91174526 0.320918332 FYNELTEILVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FYNELTEILVR 11 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 199.08 1.20E-07 254120000 337930 423070 368520 442090 388850 280150 343510 335360 331400 FALSE TRUE 316779.5645 454394.543 377261.4684 453434.7779 358311.2895 361024.7571 292003.8645 377230.4342 276087.1991 1.147389541 1.645837056 1.366457662 1.642360745 1.297819279 1.307647578 1.057650863 1.366345254 1 18.07476447 2.249423618 2.036882302 1.155523275 1.467093957 0.346600153 0.173743682 0.306626954 2.578409111 0.073692127 0.049077468 177.5920899 -2.249423618 0.311570682 FYQNNKDFIDSLGLLHEQNMAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FYQNNKDFIDSLGLLHEQNMAK 22 1 Q7L2H7;Q7L2H7-2;H0YCQ8 Q7L2H7 EIF3M Eukaryotic translation initiation factor 3 subunit M 0 ; 190.79 9.95E-18 272970000 501810 385510 449080 448850 524370 292654 551140 422950 447580 FALSE TRUE 470402.6079 414053.5615 459732.3897 460368.2509 483188.0954 377138.459 468501.6735 475756.2385 372876.0065 1.261552365 1.1104323 1.232936369 1.234641658 1.29584121 1.011431286 1.256454332 1.275910035 1 18.50833644 -1.157829838 6.318403987 0.999999038 1.201568619 0.363645399 0.086641185 1.07E-06 1.44E-07 0.076827718 0.01810838 0.069529669 1.157829838 0.201569582 FYS(ph)TSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FYSTSLK 7 0 A0A0C4DH43 A0A0C4DH43 1 FY(0.001)S(0.333)T(0.333)S(0.333)LK;FYS(0.333)T(0.333)S(0.333)LK 73.616 0.050779 143860000 315809 1042870 761420 875920 954090 1071010 783060 871710 639910 TRUE FALSE 296043.0784 1120085.18 779481.242 898397.5901 879159.62 1380193.201 665647.4226 980544.9124 533104.887 0.555318635 2.101059674 1.462153623 1.685217322 1.649130671 2.588971203 1.248623749 1.839309555 1 19.02405988 3.110071675 5.876234618 1.716139015 1.542197034 0.026374555 0.558348466 1.087986442 52.38305306 0.150107955 0.180523958 1288.462178 -3.110071675 -0.173941981 FYSTS(ph)LK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FYSTSLK 7 0 A0A0C4DH43 A0A0C4DH43 1 FYS(0.27)T(0.27)S(0.46)LK 81.784 0.027549 148310000 82387 542070 364310 388800 460400 549330 331070 442850 310440 TRUE FALSE 77230.54473 582205.4268 372951.6052 398777.2662 424242.0412 707912.6534 281429.127 498140.7973 258625.5585 0.298619151 2.251151937 1.442052392 1.541909735 1.640371677 2.737210729 1.088172138 1.926108155 1 17.98050533 4.752114762 24.6657772 1.726997616 0.298618011 0.422192233 0.515804918 1767.726907 3216834.441 0.11068599 2.171594036 56508.62781 -4.752114762 -1.428379604 FYTAEIVSALEYLHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FYTAEIVSALEYLHGK 16 0 E9PER6;O15530-5;O15530-2;O15530;O15530-3;Q6A1A2 E9PER6;Q6A1A2 PDPK1;PDPK2P 3-phosphoinositide-dependent protein kinase 1;Putative 3-phosphoinositide-dependent protein kinase 2 0 110.35 0.0009016 92330000 102190 115960 115150 118410 133260 94359 113580 107030 106980 FALSE TRUE 95794.11031 124545.7991 117881.4124 121448.6011 122794.2971 121598.9115 96549.73343 120392.9311 89124.34688 1.074836604 1.397438561 1.322662286 1.362687137 1.377786222 1.364373662 1.083314906 1.350842226 1 16.44353198 0.635958784 0.649092845 1.000872842 1.324786629 0.34359224 0.120618683 1.350688621 1.075212807 0.12510845 0.044943048 4.324727863 -0.635958784 0.323913787 FYTLIPHDFGMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FYTLIPHDFGMK 12 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 134.13 0.00015092 296590000 1135280 2131040 1000990 946480 2494600 573790 1314340 2040920 2460200 FALSE TRUE 1064224.851 2288824.419 1024733.956 970768.2792 2298684.179 739433.8583 1117266.919 2295733.355 2049576.727 0.519241284 1.116730293 0.499973454 0.473643297 1.121540926 0.360773934 0.545120807 1.120101202 1 20.96689457 1.231785422 24.99047328 1.060050811 0.678600294 0.284632607 0.261088997 230.8277257 851375.2956 0.223070343 0.060737047 17.0523965 -1.231785422 -0.381450518 FYTQQWEDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FYTQQWEDYR 10 0 A0A590UJ56;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;Q13616;A0A590UJC4;A0A590UK34;A0A590UJ50;A0A590UJM8;A0A590UJA0 A0A590UJ56 CUL1 Cullin-1 0 ; 126.67 0.00087568 229473000 145132 387790 155231 153467 387190 107631 147304 316890 300170 FALSE TRUE 136048.4472 416502.3751 158913.1526 157405.223 356781.6592 138702.3225 125217.1327 356454.4141 250069.6878 0.544042136 1.665545227 0.635475471 0.629445433 1.426728934 0.554654679 0.500728952 1.425420318 1 17.93197067 3.81549839 8.254544227 0.833283328 1.177862027 0.029601092 0.426781978 0.599368262 50.15482092 0.101770548 0.183978985 6538.805053 -3.81549839 0.344578699 FYWGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FYWGHK 6 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 120.78 0.019935 2898300000 3855700 4645500 4091200 3823000 5045500 3008400 4690400 4427300 5752300 FALSE TRUE 3614378.62 4989457.654 4188245.196 3921104.652 4649246.783 3876876.243 3987118.064 4980058.151 4792203.969 0.754220531 1.041161371 0.873970562 0.818225743 0.970168802 0.808996501 0.83200091 1.039199955 1 22.19225788 1.230057324 24.99617103 1.019600062 0.88410999 0.346032728 0.083341199 252.2713917 741545.5893 0.073829172 0.019645473 16.98467824 -1.230057324 -0.135490072 GAAAADLLSS(ph)SPESQHGGTQSPGGGQPLLQPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 33 0 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 GAAAADLLS(0.011)S(0.761)S(0.228)PESQHGGTQSPGGGQPLLQPTK 363.56 1.44E-133 596010000 289140 339670 338530 397470 358120 373370 463270 401890 436470 TRUE FALSE 271043.2435 364819.5202 346560.0915 407669.7531 329994.6998 481155.8578 393806.9643 452066.8512 363620.3373 0.745401771 1.003297898 0.953082256 1.121141232 0.907525421 1.323236927 1.083016883 1.243238633 1 18.47207337 5.937863812 0.394257449 1.146779044 4.59E-12 0.439585074 0.123453272 12.45472835 0.732088543 0.083351564 8.174998452 866690.0533 -5.937863812 -1.146779044 GAAAADLLSSS(ph)PESQHGGTQSPGGGQPLLQPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 33 0 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 GAAAADLLS(0.023)S(0.137)S(0.84)PESQHGGTQSPGGGQPLLQPTK;GAAAADLLS(0.015)S(0.114)S(0.87)PESQHGGTQSPGGGQPLLQPTK;GAAAADLLS(0.023)S(0.137)S(0.834)PES(0.007)QHGGTQSPGGGQPLLQPTK 209.48 1.27E-27 1828900000 1044640 1404450 1405540 1449680 1520410 1307040 1730780 1532190 1508870 TRUE FALSE 979257.8471 1508436.939 1438880.073 1486881.243 1401003.132 1684361.23 1471265.607 1723487.294 1257029.849 0.779025134 1.200000891 1.144666591 1.182852773 1.114534498 1.339953248 1.170430127 1.371079052 1 20.26158748 4.738970068 24.28168854 1.195233702 0.77902496 0.600812302 0.105326033 13.84161599 820419.8168 0.021945642 0.128832606 54823.91789 -4.738970068 -0.416208742 GAAAHPDSEEQQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GAAAHPDSEEQQQR 14 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;;;;;; 257.95 2.31E-24 2131922000 2076579.5 2410879 2412429.7 2453013 2741063 2247916 2514059 2290073 2990290 FALSE TRUE 1946610.096 2589382.99 2469653.672 2515961.467 2525790.969 2896852.857 2137099.192 2575993.655 2491191.281 0.781397282 1.039415564 0.991354494 1.009943109 1.013888812 1.16283839 0.857862344 1.034040892 1 21.24840437 4.743345306 24.73970316 1.008637378 0.781397174 0.496086151 0.073413809 369.3525958 1909699.099 0.016437985 0.133850463 55379.02504 -4.743345306 -0.227240204 GAADEVEVEPPEPPGPVAS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GAADEVEVEPPEPPGPVASR 20 0 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 GAADEVEVEPPEPPGPVAS(1)R 287.54 1.58E-40 0 54301 50500 54232 46632 36490 51977 52442 41301 33938 TRUE FALSE 50902.39734 54239.07255 55518.40865 47828.65607 33624.22259 66981.91612 44578.80895 46457.52076 28273.52855 1.800355313 1.918369419 1.963617967 1.691640857 1.18924748 2.369068155 1.576697753 1.643145484 1 14.78716432 -2.21412604 0.265033737 3.06E-18 1.890083878 0.40924565 0.296779461 34.756345 1.257237527 21.16669766 0.377165107 0.006107647 2.21412604 1.890083878 GAADVEKVEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GAADVEKVEEK 11 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ;; 144.57 0.0010349 292410000 817470 633200 644370 694860 729770 475710 789880 582310 942450 FALSE TRUE 766306.0119 680082.7868 659654.7607 712691.284 672456.808 613039.7545 671444.8269 655012.6853 785149.0065 0.976000741 0.866183083 0.840165058 0.907714686 0.856470304 0.780794154 0.8551814 0.834252709 1 19.58260695 4.739388462 4.141051031 0.856670254 0.985953515 0.244022971 0.057429633 0.26457634 10.06876071 0.012113964 0.102128426 54876.76002 -4.739388462 0.129283262 GAAEEAELEDS(ph)DDEEKPVKQDDFPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GAAEEAELEDSDDEEKPVKQDDFPK 25 2 Q9UBB9;F6XM96 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 GAAEEAELEDS(1)DDEEKPVKQDDFPK;GAAEEAELEDS(1)DDEEKPVKQDDFPK;GAAEEAELEDS(1)DDEEKPVKQDDFPK 341.88 8.96E-89 854100000 2302370 694430 1115280 1113860 1169680 747530 1592720 872400 1569740 TRUE FALSE 2158268.772 745846.3198 1141734.968 1142443.533 1077818.051 963329.7759 1353906.422 981321.0604 1307740.253 1.650380316 0.570332157 0.873059436 0.87360126 0.824183586 0.736636938 1.035302247 0.750394475 1 20.31864459 4.749809589 24.99216184 0.827687319 1.650380797 0.79037866 0.132275266 763.0067317 1695161.819 0.031139135 0.485200286 56209.48274 -4.749809589 0.822693478 GAAEEEQQDS(ph)GS(ph)EPRGDEDDIPLGPQSNVSLLDQHQHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GAAEEEQQDSGSEPRGDEDDIPLGPQSNVSLLDQHQHLK 39 1 Q9UJV9;D6RGI7;A0A499FJW5 Q9UJV9 DDX41 Probable ATP-dependent RNA helicase DDX41 2 GAAEEEQQDS(1)GS(1)EPRGDEDDIPLGPQSNVSLLDQHQHLK 95.205 0.00032092 155600000 15660 18130 16920 13529 14501 13496 20084 16099 21499 TRUE FALSE 14679.86855 19472.36406 17321.35039 13876.17704 13362.14995 17392.07611 17072.59065 18108.99559 17910.67801 0.819615458 1.087193017 0.967096297 0.774743259 0.746043782 0.971045099 0.953207391 1.011072589 1 14.12853233 -3.094208231 9.166356043 0.999729038 0.934561707 0 0.110786675 0 0 0 0.025274407 0.000804992 3.094208231 -0.065167331 GAAEEEQQDS(ph)GSEPRGDEDDIPLGPQSNVSLLDQHQHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GAAEEEQQDSGSEPRGDEDDIPLGPQSNVSLLDQHQHLK 39 1 Q9UJV9;D6RGI7;A0A499FJW5 Q9UJV9 DDX41 Probable ATP-dependent RNA helicase DDX41 1 GAAEEEQQDS(0.971)GS(0.029)EPRGDEDDIPLGPQSNVSLLDQHQHLK 313.95 2.29E-110 110980000 33545 30596 30885 30995 34051 26974 44429 35577 41967 TRUE FALSE 31445.47833 32861.35968 31617.60678 31790.38417 31376.77182 34760.95591 37767.28391 40018.86676 34962.43658 0.899407519 0.939904735 0.904330758 0.909272559 0.897442366 0.994237225 1.080224595 1.144624651 1 15.09351811 1.955854334 2.710246967 1.083630267 0.913428897 0.804430467 0.037032608 0.103406578 1.401080848 0.017571284 0.009578525 90.33464323 -1.955854334 -0.17020137 GAAS(ph)PVLQEDHCDSLPSVLQVEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GAASPVLQEDHCDSLPSVLQVEEK 24 0 Q8N9B5-2;Q8N9B5 Q8N9B5-2 JMY Junction-mediating and -regulatory protein 1 GAAS(1)PVLQEDHCDSLPSVLQVEEK;GAAS(1)PVLQEDHCDSLPSVLQVEEK;GAAS(1)PVLQEDHCDSLPSVLQVEEK;GAAS(1)PVLQEDHCDSLPSVLQVEEK;GAAS(1)PVLQEDHCDSLPSVLQVEEK;GAAS(1)PVLQEDHCDSLPSVLQVEEK 366.62 8.38E-119 790194000 969699 673214 818692 771007 843807 722709 1010251 760778 878747 TRUE FALSE 909007.2706 723059.465 838111.7609 790792.3449 777537.802 931343.3561 858773.2413 855762.808 732078.4488 1.24168014 0.987680304 1.144838729 1.080201645 1.062096287 1.272190648 1.17306177 1.168949597 1 19.48163873 2.285239972 24.99997728 1.172240691 1.092147704 0.044704878 0.092354366 211.6173814 113334.6429 0.028689099 0.02400294 192.8590271 -2.285239972 -0.080092987 GAASTLVPGVSETSASPGS(ph)PSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GAASTLVPGVSETSASPGSPSVR 23 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 GAASTLVPGVSETSAS(0.029)PGS(0.971)PSVR;GAASTLVPGVSETSASPGS(1)PSVR 334.14 1.25E-86 319550000 313600 352300 352010 313040 376530 383990 423690 366220 490090 TRUE FALSE 293972.3358 378384.6586 360359.8434 321073.1364 346958.8526 494841.6794 360161.6178 411943.3731 408290.8129 0.720007226 0.926752811 0.88260581 0.786383446 0.849783639 1.21198338 0.882120309 1.008945977 1 18.63923758 2.381356665 23.37392428 1.011395028 0.850420239 0.485162313 0.097214973 9.061121611 2202.967397 0.031524134 0.026374985 240.6338195 -2.381356665 -0.160974789 GACHGQTGMFPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GACHGQTGMFPR 12 0 P62993;P62993-2 P62993 GRB2 Growth factor receptor-bound protein 2 0 83.617 0.0096321 26008000 21191 27904 18663 20709 27694 16919 22839 22548 33280 FALSE TRUE 19864.69314 29970.04119 19105.69517 21240.428 25519.02495 21803.24064 19414.50398 25363.16743 27725.353 0.716481162 1.080961573 0.68910557 0.766101265 0.920422003 0.786400831 0.700243707 0.914800523 1 14.75891821 GADDDRPSWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GADDDRPSWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 148.56 2.27E-05 4234620000 5573000 6460800 6644000 6252000 6416700 6392900 7277500 5931800 6018200 FALSE TRUE 5224195.878 6939164.354 6801598.818 6412436.905 5912758.266 8238426.45 6186306.436 6672398.288 5013723.541 1.041979247 1.384034101 1.356596303 1.278976962 1.179314778 1.643175253 1.233874661 1.330826926 1 22.25745102 0.080581938 1.88257261 0.999963863 1.322084449 0.272510773 0.155183772 48.85082727 97.06433856 0.136168171 0.037012986 1.203876504 -0.080581938 0.322120586 GADELPYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GADELPYLR 9 0 O60825;O60825-2 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 0 123.69 0.003467 0 65973 78086 80173 76489 75113 68670 83415 68308 66533 FALSE TRUE 61843.8677 83867.56869 82074.74142 78451.83724 69213.92797 88493.91424 70907.69514 76836.40416 55428.21248 1.115747107 1.513084491 1.48073946 1.415377363 1.248712973 1.596550029 1.279270826 1.386232764 1 15.75833286 0.090769206 0.802953483 0.991690486 1.410500089 0.408336788 0.140727258 3.891370884 2.701915493 0.215412982 0.042877909 1.232449707 -0.090769206 0.418809603 GADIMYTGTVDCWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GADIMYTGTVDCWR 14 0 P12236;P12235 P12236;P12235 SLC25A6;SLC25A4 "ADP/ATP translocase 3;ADP/ATP translocase 3, N-terminally processed;ADP/ATP translocase 1" 0 140.14 2.61E-05 0 80716 60012 63157 73523 82297 67923 83424 68117 106620 FALSE TRUE 75664.12964 64455.35092 64655.11386 75409.72465 75833.72559 87531.26746 70915.34567 76621.55739 88824.43321 0.85183915 0.725648885 0.727897849 0.848975017 0.853748488 0.985441328 0.798376563 0.862618028 1 16.43866896 3.078706743 3.442775626 0.88561115 0.753655982 0.410959777 0.069619981 0.213420166 5.064926204 0.019874387 0.024001248 1198.689615 -3.078706743 -0.131955168 GADNDGS(ph)GS(ph)ESGYTTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 2 GADNDGS(1)GS(0.996)ES(0.004)GYTTPK;GADNDGS(1)GS(0.996)ES(0.003)GY(0.001)TTPK 148.15 5.45E-07 302560000 1214870 956070 1074650 1027100 1124530 889010 1329290 1024230 1419150 TRUE FALSE 1138833.455 1026858.418 1100141.205 1053457.125 1036213.95 1145652.755 1129975.305 1152107.37 1182284.697 0.963248072 0.86853735 0.930521395 0.891035068 0.876450446 0.969015972 0.955755672 0.974475415 1 20.17314605 2.222953045 24.70520878 0.969402769 0.903526744 0.578887832 0.028977176 145.4698466 230262.39 0.009899172 0.007337143 167.0909948 -2.222953045 -0.065876026 GADNDGS(ph)GSESGYTTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 GADNDGS(0.898)GS(0.102)ESGYTTPK;GADNDGS(0.992)GS(0.008)ESGYTTPK;GADNDGS(0.989)GS(0.011)ESGYTTPK;GADNDGS(0.999)GS(0.001)ESGYTTPK 337.71 2.90E-72 2532050000 3811330 3052730 3382820 3313260 3380760 3056530 4061790 2936870 3969590 TRUE FALSE 3572785.659 3278757.306 3463062.088 3398283.861 3115248.747 3938900.592 3452762.297 3303544.684 3307039.784 1.080357628 0.991447796 1.047178841 1.027590861 0.942005222 1.191065378 1.044064336 0.998943133 1 21.65710897 GADNDGSGS(ph)ESGYTTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 GADNDGS(0.227)GS(0.773)ESGYTTPK 301.34 2.21E-46 777460000 923500 703110 841410 789620 818720 715510 992890 668790 879890 TRUE FALSE 865699.7835 755168.996 861368.6425 809882.986 754421.0338 922066.1217 844015.362 752289.9037 733030.6747 1.180987117 1.030201084 1.175078578 1.104841876 1.029180715 1.257882042 1.151405243 1.026273428 1 19.48351405 -0.904095101 6.696408923 0.999999995 1.121743 0.195301702 0.076096447 6.15E-09 9.19E-10 0.068809022 0.016218441 0.124711039 0.904095101 0.121743005 GADNDGSGSESGYTT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 GADNDGSGSESGYT(0.002)T(0.998)PK 210.98 3.23E-11 259310000 401510 263010 349990 311810 342870 247750 375370 269070 420660 TRUE FALSE 376380.2058 282483.5341 358291.9281 319811.5725 315942.3733 319271.4031 319086.7533 302663.9818 350449.1284 1.073993842 0.806061454 1.022379281 0.91257631 0.901535623 0.911034947 0.910508052 0.863645982 1 18.41884551 3.050393354 24.99962734 0.910854565 0.944075103 0.060218156 0.076245761 384.3344821 190661.626 0.020332023 0.024301413 1123.035162 -3.050393354 0.033220537 GADPES(ph)PRREEMGCNADQESQSGPGVPQTQGGEVKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GADPESPRREEMGCNADQESQSGPGVPQTQGGEVKPK 37 3 Q68DA7-5;Q68DA7-3 Q68DA7-5 FMN1 Formin-1 1 GADPES(1)PRREEMGCNADQESQSGPGVPQTQGGEVKPK 95.657 0.001881 132250000 38647 29597 31843 36941 38621 22315 37382 28794 40682 TRUE FALSE 36228.15326 31788.39268 32598.331 37888.9686 35587.86245 28756.97825 31776.91614 32388.99428 33891.91138 1.068932137 0.937934492 0.96183218 1.117935432 1.050039995 0.848490896 0.93759587 0.955655582 1 15.04865338 2.256970809 24.99906352 0.928104405 1.010329913 0.318881248 0.063717828 328.9892423 446731.1048 0.02304785 0.019250676 180.705266 -2.256970809 0.082225508 GADS(ph)GEEKEEGINR ddPTM_SK-BR-3_Pertuzumab_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 236.27 1.77E-17 6973200000 10084580 5936650 7410940 6621570 6476740 5643460 8478950 6022290 6565070 TRUE FALSE 9453404.139 6376205.743 7586730.996 6791490.696 5968082.966 7272635.288 7207610.162 6774186.163 5469317.405 1.728443138 1.165813807 1.387144032 1.241743749 1.091193384 1.329715346 1.317826271 1.238579819 1 22.38292936 8 0.029207516 1.15E-15 3.12112989 0.39321317 0.152889598 1795.696879 4.022561313 138.6097506 328.8253357 100000000 -8 3.12112989 GADS(ph)GEEKEEGINREDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GADSGEEKEEGINREDK 17 2 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 1 GADS(1)GEEKEEGINREDK;GADS(1)GEEKEEGINREDK;GADS(1)GEEKEEGINREDK 206.34 3.69E-12 1166150000 4703560 1943350 2785680 2743560 2569720 2001610 3478150 2107810 2828010 TRUE FALSE 4409172.576 2087237.656 2851757.645 2813964.394 2367904.557 2579442.314 2956633.697 2370974.718 2355996.861 1.871467933 0.885925482 1.210425061 1.194383762 1.005054207 1.09484115 1.254939574 1.006357333 1 21.16790619 4.748390082 24.89248963 1.098175132 1.871468377 0.823725118 0.114616605 529.2820516 1340344.144 0.026821563 0.356677951 56026.05995 -4.748390082 0.773293245 GADS(ph)GEEKEEGINREDKTDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GADSGEEKEEGINREDKTDK 20 3 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 1 GADS(1)GEEKEEGINREDKTDK;GADS(1)GEEKEEGINREDKTDK;GADS(0.987)GEEKEEGINREDKT(0.013)DK;GADS(1)GEEKEEGINREDKTDK;GADS(1)GEEKEEGINREDKTDK 155.39 1.68E-07 1962170000 3143780 1038719 1620184 1674179 1774160 1000985 2130500 1111049 2738540 TRUE FALSE 2947016.422 1115626.836 1658615.53 1717141.268 1634824.63 1289953.12 1811051.304 1249765.913 2281459.982 1.291723916 0.48899689 0.726997424 0.75265018 0.716569496 0.565406858 0.793812435 0.54779217 1 21.12152592 -1.103545951 4.380879768 1.000028309 0.711158114 0.114759686 0.221905289 2.745641019 113070513.2 7970.217046 0.04532543 0.078786906 1.103545951 -0.288870195 GADSLEDFLYHEGYACTSIHGDR ddPTM_SK-BR-3_Pertuzumab_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 ;;;; 280.2 3.74E-52 1100532000 540569 936238 946680 898901 928560 954153 1005604 839866 869762 FALSE TRUE 506735.7512 1005558.036 969135.6967 921968.3215 855634.6432 1229601.482 854823.0158 944725.1189 724593.1033 0.699338358 1.38775546 1.33748954 1.272394558 1.18084845 1.696954437 1.179728336 1.303800871 1 19.46681155 4.742544722 24.67625888 1.318026183 0.699338067 0.517272386 0.179566429 239.3656182 1482482.757 0.037637997 0.287174773 55277.03278 -4.742544722 -0.618688116 GADVWFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GADVWFK 7 0 P05109 P05109 S100A8 "Protein S100-A8;Protein S100-A8, N-terminally processed" 0 110.35 0.015875 146670000 534480 579650 513940 473720 517050 330840 658580 477340 832450 FALSE TRUE 501027.8509 622567.8891 526130.8995 485876.4572 476442.9787 426348.1373 559832.043 536936.9498 693508.7172 0.722453573 0.897707374 0.758650737 0.700606128 0.68700359 0.614769687 0.807245863 0.774232445 1 19.40355449 0.554159983 1.727412216 0.999845664 0.751552426 0.534488227 0.074977344 2.265577282 7.710986251 0.077677492 0.021909933 3.582283751 -0.554159983 -0.248293238 GADYMDCLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GADYMDCLYR 10 0 A0A0A0MTN0;Q13617;Q13617-2;Q5T2B5 A0A0A0MTN0 CUL2 Cullin-2 0 143.86 7.73E-05 86956000 95001 117780 118390 122830 124340 110040 120130 106510 130500 FALSE TRUE 89055.05699 126500.5537 121198.2667 125982.0258 114574.838 141806.7616 102117.6217 119808.008 108718.7069 0.819132783 1.163558299 1.114787603 1.158788853 1.05386498 1.30434555 0.939282894 1.101999935 1 16.73024068 1.63690166 24.99999999 1.015454252 1.111970844 0.094933659 0.126724605 1.536713611 1317.684596 0.052764748 0.029253287 43.34127265 -1.63690166 0.096516592 GAEADQIIEYLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GAEADQIIEYLK 12 0 Q12904;Q12904-2;A0A5F9ZHC5;D6R937 Q12904 AIMP1 Aminoacyl tRNA synthase complex-interacting multifunctional protein 1;Endothelial monocyte-activating polypeptide 2 0 ; 176.8 5.60E-05 43551000 138058 122932 131199 123824 140977 111781 166393 124714 177301 FALSE TRUE 129417.1962 132034.0132 134311.1022 127001.5335 129905.2351 144050.3601 141443.9144 140284.8174 147708.3177 0.876167289 0.8938834 0.909299519 0.859813012 0.87947136 0.975235263 0.957589367 0.949742165 1 17.17239154 2.238920385 24.99990381 0.966377969 0.887512062 0.845602702 0.018375002 3.834357488 266470.0868 0.006547906 0.005165017 173.3486186 -2.238920385 -0.078865907 GAEDDELEEEADWIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GAEDDELEEEADWIYR 16 0 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;;; 266.74 7.33E-27 622560000 419874 442400 443830 443391 441928 398252 513432 398190 478898 FALSE TRUE 393594.8358 475155.7563 454357.8572 454769.1637 407220.7575 513220.8873 436447.6381 447904.898 398966.83 0.986535236 1.190965566 1.138836171 1.139867101 1.020688255 1.286374828 1.093944672 1.122661997 1 18.60590928 0.599407118 1.969559191 1.00008782 1.133750509 0.166536734 0.083403096 3.720326063 16.40454264 0.070649878 0.019510565 3.975640606 -0.599407118 0.133662688 GAEDDRGPWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GAEDDRGPWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 98.943 0.00459 1626600000 1747760 2083410 2102070 1980890 2086070 1955890 2245730 1969790 1742770 FALSE TRUE 1638370.821 2237667.844 2151932.093 2031722.991 1922238.477 2520523.692 1909003.635 2215722.618 1451890.428 1.128439715 1.54120986 1.482158744 1.399363858 1.32395561 1.736028865 1.314840017 1.526094927 1 20.46950115 -0.884365674 10.76266631 1.000000002 1.445578985 0.409973001 0.161907165 0 0 0.137497514 0.032408475 0.130507156 0.884365674 0.445578982 GAEEEPPPPLQAVLVADSFDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 258.43 5.66E-37 493244000 409013 533631 515902 511417 563801 463165 602322 477861 646752 FALSE TRUE 383413.6064 573141.5945 528139.4391 524540.826 519522.3437 596873.2166 512009.4078 537522.9978 538804.913 0.711600056 1.063727484 0.980205314 0.973526435 0.964212336 1.107772409 0.950268632 0.997620817 1 19.03940348 4.745676564 24.99442079 1.004562947 0.711599919 0.789509306 0.047556119 363.0690553 1275230.696 0.010591283 0.107561086 55677.09458 -4.745676564 -0.292963027 GAEEMETVIPVDVMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GAEEMETVIPVDVMR 15 0 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ;;;; 339.5 6.69E-69 368044000 544421 632328 641009 628162 678628 558381 656347 584871 700841 FALSE TRUE 510346.6614 679146.2231 656214.0362 644281.7004 625331.2943 719576.5301 557933.8606 657893.4318 583866.1095 0.874081666 1.163188293 1.123911845 1.103475077 1.071018311 1.232434146 0.955585281 1.126788182 1 19.15527805 1.708678545 25 1.02963266 1.10539586 0.084504791 0.100174081 1.645326939 1369.015884 0.041865225 0.023216377 51.13032402 -1.708678545 0.0757632 GAEETSWS(ph)GEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GAEETSWSGEER 12 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 GAEETSWS(1)GEER;GAEETSWS(1)GEER 268.93 3.76E-22 2621300000 917000 1074190 991860 1018370 1045970 969350 1095480 840390 900440 TRUE FALSE 859606.6069 1153724.145 1015387.388 1044503.098 963823.7354 1249185.609 931222.9439 945314.5414 750150.7469 1.145911819 1.537989731 1.353577787 1.392390933 1.284840066 1.665246104 1.241381079 1.2601661 1 19.51682102 0.97932571 1.615986275 1.006431697 1.400882728 0.408298582 0.144315522 0.353903869 1.897947018 0.120883411 0.035143304 9.535110056 -0.97932571 0.394451031 GAEFLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GAEFLLR 7 0 Q9BXT2 Q9BXT2 CACNG6 Voltage-dependent calcium channel gamma-6 subunit 0 ;;; 153.61 0.0048727 392380000 805220 950090 867590 894450 954110 707460 996120 821490 805720 FALSE TRUE 754822.7176 1020435.652 888169.6445 917403.1013 879178.0493 911692.2173 846761.0535 924054.8348 671240.1268 1.124519658 1.520224449 1.323177219 1.366728633 1.309781722 1.358220674 1.261487536 1.376638252 1 19.35646944 -3.430675209 0.308511315 2.00E-09 1.362948734 0.496672125 0.10164313 73.75008702 1.650730943 47.24687577 0.088742546 0.000370958 3.430675209 1.362948732 GAEILEVLHSLPAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GAEILEVLHSLPAVR 15 0 Q15008;Q15008-4;Q15008-3;Q15008-2;H7C531 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 224.16 1.17E-12 346490000 479810 587500 578360 662150 570250 613910 582880 508270 445250 FALSE TRUE 449779.5486 630999.1113 592078.9723 679141.89 525464.8653 791135.851 495482.5552 571728.6283 370934.8986 1.212556571 1.701104732 1.596180286 1.830892409 1.416595924 2.132815904 1.335766888 1.541317979 1 18.50080648 0.721551161 1.314751164 1.004076151 1.635332523 0.350458926 0.257672211 0.93426779 2.687663772 0.21413357 0.064178934 5.266852558 -0.721551161 0.631256372 GAEQDNPNQYSWGENYAGSSGLMSAS(ph)PELGPAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GAEQDNPNQYSWGENYAGSSGLMSASPELGPAQR 34 0 H0YA26;E9PHT6;Q9NVE7;H0YA31 H0YA26 PANK4 Pantothenate kinase 4 1 GAEQDNPNQYSWGENYAGSSGLMS(0.001)AS(0.999)PELGPAQR;GAEQDNPNQYSWGENYAGSSGLMS(0.015)AS(0.985)PELGPAQR 280.8 3.44E-74 374840000 212479 240040 278340 263310 291120 242310 280590 225772 248540 TRUE FALSE 199180.3187 257812.8114 284942.3562 270066.9804 268256.6095 312260.9634 238518.1344 253960.1312 207057.0684 0.961958557 1.245129246 1.376153727 1.304311814 1.295568471 1.5080913 1.151943936 1.226522394 1 17.65966893 0.834797062 1.504156976 1.003122145 1.284875983 0.24979305 0.141322093 0.816585381 3.455289231 0.126446744 0.036966378 6.835921425 -0.834797062 0.281753838 GAEVHLVPWNHDFTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GAEVHLVPWNHDFTK 15 0 P31327;P31327-3;Q5R211 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 170.45 6.59E-07 21316000 87981 75983 75336 66004 110480 67191 67665 84190 169330 FALSE TRUE 82474.42626 81608.86038 77123.0055 67697.77438 101803.3465 86587.95095 57519.26142 94701.30683 141067.7291 0.584644176 0.578508358 0.54670906 0.479895543 0.7216629 0.613804103 0.407742166 0.671318008 1 17.10602847 0.980783598 24.15726753 1.000000004 0.558455553 0.740361694 0.081521803 438.4356802 551166.0354 0.076927997 0.019231999 9.567172353 -0.980783598 -0.441544452 GAFGKPQGTVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GAFGKPQGTVAR 12 1 P27635;X1WI28;A0A087WV22;H7C123;H7C2C5;Q96L21;F8W7C6 P27635;F8W7C6 RPL10;RPL10L 60S ribosomal protein L10;60S ribosomal protein L10-like 0 ; 154.67 6.19E-05 4378600000 5707400 6763400 6527100 6319000 7275600 5337700 7506200 6733600 7143500 FALSE TRUE 5350184.022 7264169.173 6681925.894 6481156.238 6704203.724 6878607.34 6380714.994 7574304.782 5951203.701 0.89900872 1.220621833 1.122785613 1.089049638 1.126529029 1.155834632 1.072172171 1.272734923 1 22.50475007 4.751785507 24.60101105 1.135839559 0.899008527 0.485321216 0.07548399 1433.82649 2667152.562 0.016032713 0.304603806 56465.8028 -4.751785507 -0.236831033 GAGAELKDTQS(ph)PSTCSEGLLGWSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GAGAELKDTQSPSTCSEGLLGWSQK 25 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GAGAELKDT(0.01)QS(0.989)PS(0.001)TCSEGLLGWSQK;GAGAELKDT(0.002)QS(0.956)PS(0.036)T(0.006)CSEGLLGWSQK 167.22 7.82E-12 309680000 320510 210020 265550 259180 274050 161159 258830 175283 300320 TRUE FALSE 300449.8512 225570.0993 271848.9714 265830.9976 252527.2185 207682.9871 220020.8444 197167.4684 250194.6519 1.200864403 0.901578422 1.08654989 1.062496723 1.009323007 0.830085638 0.879398671 0.788056287 1 17.93269143 2.321619014 5.23522717 0.865002092 1.039204713 0.485668219 0.090515151 0.172615596 8.037825815 0.029485857 0.024282057 209.7099388 -2.321619014 0.174202621 GAGATS(ph)GSPPAGRN ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GAGATSGSPPAGRN 14 1 B4DEE8;P16455 B4DEE8 MGMT Methylated-DNA--protein-cysteine methyltransferase 1 GAGAT(0.037)S(0.482)GS(0.482)PPAGRN;GAGAT(0.02)S(0.49)GS(0.49)PPAGRN 105.6 0.0010491 529640000 418460 495060 397960 442650 537280 410390 466770 389130 528120 TRUE FALSE 392269.3356 531714.7575 407399.7991 454009.1484 495084.1961 528862.9309 396782.1718 437713.7371 439973.3602 0.891575198 1.2085158 0.925964697 1.03190145 1.125259484 1.202033984 0.901832265 0.994864182 1 18.74705665 1.67363476 13.33958606 0.961825532 1.065925416 0.162675587 0.105252009 0.211402859 41.97964319 0.04655853 0.025563065 47.16662046 -1.67363476 0.104099884 GAGDGS(ph)DEEVDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GAGDGSDEEVDGK 13 0 P35579;P35579-2 P35579 MYH9 Myosin-9 1 GAGDGS(1)DEEVDGK;GAGDGS(1)DEEVDGK 232.78 1.87E-13 2207200000 4394800 2501800 3243300 2963700 2478000 2521000 3611700 2709000 2097200 TRUE FALSE 4119737.313 2687035.875 3320232.608 3039753.56 2283387.876 3248771.775 3070159.114 3047224.613 1747163.772 2.357957153 1.537941616 1.900355686 1.739821767 1.306911185 1.859454636 1.757224574 1.74409787 1 20.73658342 -2.38517055 0.290952903 1.04E-18 1.82039773 0.475017839 0.261803924 39.40777019 1.440862655 26.1494458 0.267810045 0.004119357 2.38517055 1.82039773 GAGDGS(ph)DEEVDGKADGAEAKPAE ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GAGDGSDEEVDGKADGAEAKPAE 23 2 P35579;P35579-2 P35579 MYH9 Myosin-9 1 GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE 210.61 4.98E-25 4249310000 12520400 6274900 8271000 8185000 8019900 5185700 10554800 6740200 10656000 TRUE FALSE 11736770.51 6739500.125 8467192.026 8395040.957 7390049.405 6682727.407 8972205.726 7581728.807 8877444.76 1.322088825 0.75917117 0.95378707 0.945659611 0.832452311 0.752776006 1.010674352 0.854044042 1 23.08171305 4.749117648 24.75999037 0.886451737 1.322089106 0.691823988 0.090921117 744.2346506 1745455.669 0.020447552 0.292965369 56119.99817 -4.749117648 0.435637369 GAGGEENKENERPSAGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GAGGEENKENERPSAGSK 18 2 Q9UHB9;Q9UHB9-4;Q9UHB9-2;K7EN53;K7EQC2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;; 208.17 3.72E-16 543650000 1099250 674150 837750 823850 871990 631058 1159920 784320 1132610 FALSE TRUE 1030449.905 724064.7675 857621.8256 844991.3858 803507.4228 813234.2002 986000.7642 882244.0785 943570.0741 1.092075653 0.767367244 0.908911642 0.895525843 0.851560944 0.861869428 1.044968245 0.935006422 1 19.84777014 1.748679383 24.99999493 0.993836672 0.881071301 0.209941516 0.085497542 3.172476417 7854.029723 0.03591012 0.019913941 56.06339367 -1.748679383 -0.112765371 GAGGS(ph)PVGVEEGLVNVGTGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GAGGSPVGVEEGLVNVGTGQK 21 0 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 GAGGS(1)PVGVEEGLVNVGTGQK;GAGGS(1)PVGVEEGLVNVGTGQK;GAGGS(1)PVGVEEGLVNVGTGQK 340.32 1.55E-80 574590000 440000 373350 386641 391626 369644 311255 464312 327955 418445 TRUE FALSE 412461.1854 400993.2225 395812.3071 401675.7862 340613.6513 401109.2657 394692.7261 368900.9037 348603.8262 1.183180316 1.15028348 1.13542158 1.152241473 0.977079497 1.15061636 1.132209965 1.058223909 1 18.41122888 -5 0.020785991 3.41E-08 1.888070117 0.449067763 0.051729605 2890.623675 4.547299519 281.5346112 150.4568126 1.00E-05 5 1.888070083 GAGHMVPTDKPLAAFTMFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GAGHMVPTDKPLAAFTMFSR 20 1 X6R5C5;X6R8A1;P10619-2;P10619 X6R5C5 CTSA Carboxypeptidase;Lysosomal protective protein;Lysosomal protective protein 32 kDa chain;Lysosomal protective protein 20 kDa chain 0 70.897 0.010849 221500000 338820 421840 348850 352200 461120 314860 446240 399110 487830 FALSE TRUE 317613.861 453073.4725 357124.8867 361238.0483 424905.4953 405754.9707 379330.4547 448939.762 406408.0215 0.781514744 1.114824139 0.878734838 0.888855606 1.045514539 0.998393115 0.933373444 1.104652808 1 18.63256935 2.731153286 24.84780164 1.004268052 0.942914717 0.190973717 0.09398664 1352.31255 4536307.109 0.029145377 0.027975375 538.459801 -2.731153286 -0.061353335 GAGHPCYLDKPEEWHTGLLDFLQGLQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GAGHPCYLDKPEEWHTGLLDFLQGLQ 26 1 F8W9U3;Q96IU4;Q96IU4-2 F8W9U3 ABHD14B Alpha/beta hydrolase domain-containing protein 14B 0 ; 130.15 4.44E-05 612180000 945410 938730 866010 820560 1019060 674070 1083820 849530 1131400 FALSE TRUE 886238.4757 1008234.546 886552.1662 841616.9588 939027.1383 868663.0664 921311.2527 955595.6905 942562.0309 0.940244193 1.069674475 0.940576999 0.892903524 0.996249698 0.921597771 0.977454239 1.013827907 1 19.84622804 1.333713349 5.712224364 1.006426801 0.967827795 0.124457012 0.047795147 0.504789895 23.16466585 0.034519404 0.012208247 21.56320686 -1.333713349 -0.038599007 GAGSIAGASAS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GAGSIAGASASPK 13 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GAGSIAGASAS(1)PK 186.29 3.33E-07 0 335520 223760 260310 262160 289570 193890 351350 228990 260660 TRUE FALSE 314520.4021 240327.4232 266484.6761 268887.4694 266828.3403 249862.8955 298668.3293 257579.9056 217154.1621 1.448373815 1.10671341 1.227168172 1.238233092 1.228750753 1.150624483 1.375374648 1.186161495 1 17.72836008 0.977383517 23.9822637 0.999999993 1.239555252 0.389341643 0.098815014 1196.002484 1268229.64 0.088737415 0.022184354 9.492563623 -0.977383517 0.239555259 GAGSVFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GAGSVFR 7 0 P62917;E9PKZ0;G3V1A1;E9PKU4;E9PP36 P62917 RPL8 60S ribosomal protein L8 0 86.512 0.046579 254260000 191390 284680 247350 258740 307800 234860 284110 301960 297590 FALSE TRUE 179411.2415 305758.0034 253217.2588 265379.7064 283626.6296 302660.2694 241510.343 339660.3707 247920.3065 0.723664972 1.233291487 1.021365544 1.070423436 1.14402339 1.220796609 0.974145065 1.370038524 1 17.91951692 4.748883266 24.44580216 1.120998122 0.723664668 0.521237058 0.121934253 832.4114143 1971239.291 0.0257851 0.357367678 56089.71921 -4.748883266 -0.397333454 GAGTDDHTLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GAGTDDHTLIR 11 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;;;; 189.58 2.65E-06 5491060000 7048780 9211570 7006820 6676000 6985980 5916490 8732760 7191370 10524810 FALSE TRUE 6607609.442 9893604.227 7173025.079 6847317.462 6437329.311 7624484.617 7423363.709 8089228.375 8768151.218 0.753592095 1.128356934 0.818077255 0.780930585 0.734171794 0.869565821 0.846628157 0.922569442 1 23.06384125 3.732231327 24.62234759 0.840455793 0.969385554 0.07151351 0.115595826 277.5682503 1337417.693 0.027105193 0.047024081 5397.980697 -3.732231327 0.128929762 GAGWTGHVAGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GAGWTGHVAGTR 12 0 Q15274 Q15274 QPRT Nicotinate-nucleotide pyrophosphorylase [carboxylating] 0 ;;; 140.24 5.95E-05 1515060000 799070 1213670 897560 844310 1303310 746853 891760 1145330 1464970 FALSE TRUE 749057.6351 1303531.39 918850.5471 865976.424 1200953.29 962457.337 758048.8667 1288326.972 1220457.043 0.613751741 1.068068227 0.75287414 0.709550925 0.984019304 0.788604025 0.621118843 1.055610256 1 20.21899009 1.206220684 24.99121768 1.027805685 0.808904412 0.313273284 0.143816262 293.9464656 227145.3469 0.135637936 0.033920091 16.07758018 -1.206220684 -0.218901274 GAGYTFGQDISETFNHANGLTLVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 342.55 1.36E-88 197270000 142330 161930 170090 159110 178690 145140 177640 135130 166640 FALSE TRUE 133421.8194 173919.4657 174124.6151 163193.032 164656.4082 187039.5618 151004.5311 152001.278 138826.7075 0.961067375 1.252781031 1.254258768 1.175516116 1.186057144 1.347288035 1.087719603 1.094899395 1 17.08292561 1.574873683 8.268798891 1.063002022 1.209067602 0.283860611 0.100687509 0.136624818 18.49669529 0.050244994 0.023638867 37.57281056 -1.574873683 0.14606558 GAHNGQGLGNAFLSHISACDGIFHLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GAHNGQGLGNAFLSHISACDGIFHLTR 27 0 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 374.44 1.74E-127 851320000 52906 136676 81333 78815 123427 70684 99650 105820 96025 FALSE TRUE 49594.7079 146795.6333 83262.25717 80837.52633 113733.5413 91089.32334 84708.40761 119031.8599 79997.80715 0.619950842 1.834995714 1.040806744 1.010496777 1.421708236 1.138647753 1.05888412 1.487939034 1 16.28767283 3.734011176 24.94175894 1.163955189 1.351353903 0 0.336243752 833.7715863 3018258.079 0.078427749 0.137539678 5420.148383 -3.734011176 0.187398714 GAHVTINAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GAHVTINAR 9 0 Q9UJU6-2;Q9UJU6-3;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ; 151.44 8.28E-05 217260000 187863 311570 205650 196633 316680 160560 193420 277310 288250 FALSE TRUE 176104.9902 334638.967 210528.1151 201678.9357 291809.2302 206911.0655 164418.4666 311932.7639 240139.2128 0.733345413 1.393520713 0.876691951 0.839841746 1.215166931 0.861629648 0.684679793 1.29896638 1 17.87351148 3.7361233 24.22068641 0.938080075 1.117943851 0.003572681 0.239950075 530.7070412 1427892.844 0.057660306 0.101973972 5446.572643 -3.7361233 0.179863776 GAILSEEELAAMS(ph)PTAAAVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GAILSEEELAAMSPTAAAVAK 21 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 GAILSEEELAAMS(0.998)PT(0.002)AAAVAK;GAILSEEELAAMS(0.973)PT(0.027)AAAVAK;GAILSEEELAAMS(0.996)PT(0.004)AAAVAK;GAILSEEELAAMS(0.991)PT(0.009)AAAVAK;GAILSEEELAAMS(0.997)PT(0.003)AAAVAK;GAILSEEELAAMS(0.985)PT(0.015)AAAVAK 315.28 1.19E-66 493779000 958824 834823 932273 913611 981890 777744 1131213 855485 1127659 TRUE FALSE 898812.9174 896634.1636 954386.9558 937055.805 904776.3202 1002266.067 961598.1123 962294.1854 939445.4279 0.956748408 0.954429216 1.015904626 0.997456347 0.963096198 1.066869919 1.023580597 1.024321538 1 19.84144983 4.162682443 0.54445471 1.02528755 0.925482198 0.444088367 0.026287124 2.052141186 0.719230052 0.015561129 0.120929602 14543.95233 -4.162682443 -0.099805352 GAKEEHGGLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GAKEEHGGLIR 11 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 143.17 2.24E-05 517960000 1187150 1382690 1366650 1365430 1556350 1062280 1519320 1226560 2075900 FALSE TRUE 1112848.401 1485065.806 1399067.583 1400469.245 1434120.549 1368942.991 1291512.071 1379698.716 1729418.879 0.643481122 0.858707988 0.808981329 0.809791811 0.829249967 0.791562419 0.746789622 0.79778169 1 20.72185591 -1.74945577 2.491498527 1.049122633 0.793207366 0.567813125 0.058413704 14367189.71 10199903.99 4338001.663 0.01318862 0.017805092 1.74945577 -0.255915268 GAKEEHGGLIRS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 124.2 5.14E-05 41276330000 8344620 10486140 9044080 10444130 14660350 6523640 10371360 9341270 22680000 TRUE FALSE 7822345.13 11262544.72 9258609.849 10712144.06 13508985.25 8406908.966 8816270.851 10507548.12 18894561.48 0.413999824 0.596073358 0.49001454 0.566943248 0.714966858 0.44493803 0.466603623 0.55611495 1 24.1714677 0.9439825 21.88375368 1 0.529730095 0.747420705 0.085793274 2263.583951 884291.6558 0.079243258 0.019810814 8.789870963 -0.9439825 -0.470269905 GALHTVS(ph)HEDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GALHTVSHEDIR 12 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2;H0YD72 Q13136-2 PPFIA1 Liprin-alpha-1 1 GALHT(0.057)VS(0.943)HEDIR;GALHTVS(1)HEDIR;GALHTVS(1)HEDIR;GALHT(0.007)VS(0.993)HEDIR;GALHT(0.028)VS(0.972)HEDIR;GALHT(0.018)VS(0.982)HEDIR 232.53 5.39E-13 12592640000 7787810 8945000 8998260 8595440 10433710 8971760 9592170 8873200 12288940 TRUE FALSE 7300384.874 9607297.107 9211702.976 8816013.542 9614288.504 11561761.47 8153913.158 9981038.552 10237836.52 0.713078867 0.938410873 0.89977047 0.861120757 0.939093771 1.129316867 0.796448853 0.974916774 1 23.28740754 4.739658917 24.17156604 0.931725893 0.713078762 0.395754356 0.088175385 61.44770803 1352063.699 0.019426365 0.119207462 54910.94494 -4.739658917 -0.218647131 GALKEEVASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GALKEEVASR 10 1 Q9P2M7;Q9P2M7-2 Q9P2M7 CGN Cingulin 0 ; 82.417 0.010861 122132000 210796 450980 359940 374140 479780 353560 331870 389420 447030 FALSE TRUE 197602.6546 484371.0284 368477.9468 383741.0658 442100.0141 455627.0324 282109.1744 438039.9442 372417.8051 0.530594005 1.300611898 0.989420865 1.030404724 1.18710762 1.223429778 0.757507215 1.176205698 1 18.50656252 -1.996597295 7.722403976 0.963332385 1.038954687 0 0.231769198 0.18066517 7.96E-05 0.277091731 0.047635175 0.010078658 1.996597295 0.075622302 GALQNIIPAS(ph)TGAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GALQNIIPASTGAAK 15 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 GALQNIIPAS(0.701)T(0.299)GAAK;GALQNIIPAS(0.5)T(0.5)GAAK;GALQNIIPAS(0.939)T(0.061)GAAK;GALQNIIPAS(0.987)T(0.013)GAAK 266.71 2.55E-25 1285790000 3421380 3201650 3200240 3179180 4188850 2599300 3937090 2768740 6054740 TRUE FALSE 3207241.933 3438703.497 3276151.204 3260763.141 3859874.618 3349675.714 3346759.905 3114423.284 5044164.779 0.63583211 0.681719105 0.649493295 0.646442629 0.765215806 0.664069447 0.663491391 0.617430917 1 22.26618397 -1.840059137 2.816799199 1.117816674 0.667533677 0.876153981 0.039520641 14336935.73 11599653.14 11456540.49 0.009212629 0.01445243 1.840059137 -0.450282997 GALQNIIPASTGAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GALQNIIPASTGAAK 15 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 245.92 9.09E-18 481040000 1368520 1326770 1378250 1417350 1474890 1144590 1688640 1291650 1543090 FALSE TRUE 1282866.776 1425005.431 1410942.741 1453721.601 1359058.089 1475014.552 1435444.109 1452915.346 1285538.31 0.997921856 1.108489276 1.097550131 1.130827132 1.057189878 1.147390584 1.116609359 1.130199959 1 20.29394117 4.739673384 24.31766278 1.105147772 0.997921808 0.342134254 0.042982902 61.360715 1340677.255 0.00873013 0.053420859 54912.77413 -4.739673384 -0.107225964 GALVAINPGDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GALVAINPGDRK 12 1 P51580 P51580 TPMT Thiopurine S-methyltransferase 0 80.245 0.033449 429520000 891650 636800 746530 761350 890940 610200 976550 661360 1275800 FALSE TRUE 835843.2181 683949.3346 764238.0441 780887.53 820969.1663 786354.8342 830125.3933 743932.2518 1062860.738 0.78640897 0.643498541 0.719038738 0.734703524 0.772414614 0.739847476 0.781029314 0.699933891 1 20.01952115 -5 0.236370358 2.514296122 0.700862232 0.773472038 0.044491903 72.36527574 0.723132891 52.55226372 0.068835078 1.00E-05 5 -1.81343389 GANDFMCDEMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GANDFMCDEMER 12 0 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;;;;;; 274.43 1.98E-27 3430000000 1911899 2221744 2168623 2109353 2439389 2052585 2270239 2025372 1973100 FALSE TRUE 1792236.654 2386244.237 2220063.762 2163482.569 2247809.228 2645132.969 1929837.738 2278244.153 1643776.863 1.090316268 1.451683796 1.35058706 1.316165605 1.367466156 1.60918007 1.174026585 1.385981397 1 20.64858304 -0.700434312 6.803546629 1.000000172 1.35209727 0.367694304 0.140998505 1.82E-09 1.59E-18 0.122356209 0.028839635 0.199326797 0.700434312 0.352097098 S(ph)SLSASHPMVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSLSASHPMVGK 12 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 S(0.604)S(0.374)LS(0.006)AS(0.016)HPMVGK 82.543 0.0097411 0 71227 77632 58547 56902 93625 28460 110020 75695 173900 TRUE FALSE 66769.02921 83379.95406 59935.76249 58362.20165 86272.07017 36675.93999 93523.52238 85145.68738 144874.9666 0.460873475 0.575530446 0.413706825 0.402845316 0.595493288 0.253155813 0.645546464 0.587718426 1 17.1444488 0.728584973 1.177951975 0.997906593 0.468593696 0.705249222 0.107374485 0.465341324 1.11291561 0.091341483 0.028165576 5.352848759 -0.728584973 -0.529312896 GANPVEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GANPVEIR 8 0 P10809;E7EXB4;E7ESH4;P10809-2 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 84.916 0.039812 108840000 108070 161430 124850 131010 199850 123630 124190 158850 170980 FALSE TRUE 101306.0916 173382.4452 127811.501 134371.9384 184154.5872 159319.974 105568.8624 178682.7722 142442.3334 0.711207751 1.217211492 0.897285925 0.943342721 1.292836074 1.118487532 0.741134043 1.254421827 1 17.12001845 4.760919155 23.97109324 1.03785837 0.711207136 0.278390442 0.172805088 4983.326262 5342586.187 0.040069148 1.956930759 57665.91066 -4.760919155 -0.326651234 GAPHSS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GAPHSSPAR 9 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 GAPHS(0.243)S(0.757)PAR 77.593 0.020716 21183000 10067 33055 12445 11754 31530 8895 14743 25876 34614 TRUE FALSE 9436.92444 35502.42659 12740.20128 12055.62754 29053.76099 11462.8421 12532.42402 29106.67556 28836.69979 0.327253968 1.231154288 0.441805108 0.418065438 1.007527255 0.397508806 0.434599802 1.009362229 1 14.81561844 1.216685454 24.47315136 1.004682006 0.639574323 0.23538789 0.29282783 345.7635662 386814.803 0.274105049 0.068786274 16.46969113 -1.216685454 -0.365107683 GAPPS(ph)TFKGTPTAENPEYLGLDVPV ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GAPPSTFKGTPTAENPEYLGLDVPV 25 1 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 GAPPS(0.268)T(0.268)FKGT(0.231)PT(0.231)AENPEYLGLDVPV 51.175 0.080228 122810000 196470 176930 153320 159020 305700 175810 249710 248010 372550 TRUE FALSE 184173.2934 190030.0813 156956.8228 163100.7224 281691.5551 226563.493 212268.3037 278974.5944 310368.9982 0.593401063 0.612271465 0.505710376 0.525505844 0.907602102 0.729981069 0.683922379 0.898848132 1 18.24362493 1.543840683 0.419833874 1.009145041 0.541032051 0.64398802 0.101082967 0.65788674 0.327698262 0.121716364 0.090054393 34.98168164 -1.543840683 -0.46811299 GAPPSTFKGT(ph)PTAENPEYLGLDVPV ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GAPPSTFKGTPTAENPEYLGLDVPV 25 1 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 GAPPS(0.122)T(0.122)FKGT(0.65)PT(0.105)AENPEYLGLDVPV;GAPPS(0.129)T(0.097)FKGT(0.632)PT(0.141)AENPEYLGLDVPV 194.75 1.95E-18 153729000 373101 349776 313016 306577 647410 343663 509150 526790 744360 TRUE FALSE 349749.2744 375673.779 320440.8873 314444.2849 596565.0301 442872.9292 432807.6842 592560.8911 620121.5073 0.5640012 0.605806724 0.516738871 0.507068826 0.962013127 0.714171213 0.697940128 0.955556103 1 19.2421914 1.807359229 0.442444789 1.006130935 0.527828911 0.610041991 0.117160215 0.689601254 0.339240084 0.126219776 0.102035266 64.1740176 -1.807359229 -0.478302025 GAPS(ph)PGVLGPHASEPQLAPPACTPAAPAVPGPPGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GAPSPGVLGPHASEPQLAPPACTPAAPAVPGPPGPR 36 0 O96013;O96013-4;O96013-3;M0R0L9 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 GAPS(0.996)PGVLGPHAS(0.004)EPQLAPPACTPAAPAVPGPPGPR;GAPS(1)PGVLGPHASEPQLAPPACTPAAPAVPGPPGPR 204.16 1.94E-30 373020000 49144 126818 107862 122039 108952 113720 119615 108905 92457 TRUE FALSE 46068.16476 136207.7367 110420.5376 125170.7274 100395.3494 146549.1179 101679.8412 122502.029 77025.3294 0.59809111 1.768349941 1.433561381 1.625059293 1.303406947 1.902609428 1.320083172 1.59041227 1 16.23304533 -1.049401689 4.957983626 0.999990689 1.480917858 0.125522789 0.354684584 3.15E-05 6.03E-06 0.295922341 0.069748215 0.089247963 1.049401689 0.48092717 GAPS(ph)SPATGVLPSPQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GAPSSPATGVLPSPQGK 17 0 Q5SRE5;Q5SRE5-2 Q5SRE5 NUP188 Nucleoporin NUP188 homolog 1 GAPS(0.859)S(0.141)PATGVLPSPQGK 176.25 1.18E-09 134570000 275490 260200 278830 277830 276480 198210 277100 210080 284110 TRUE FALSE 258247.5727 279465.4787 285443.9793 284959.5882 254766.3761 255430.0093 235551.4275 236308.9504 236690.2056 1.091078408 1.180722616 1.205981374 1.203934854 1.076370589 1.079174395 0.99518874 0.998389223 1 17.85264048 2.274740562 1.496770054 0.998953641 1.177295673 0.78604229 0.037893503 0.164562521 0.731623312 0.020633634 0.012775247 188.2524177 -2.274740562 0.178342032 GAPSS(ph)PATGVLPSPQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GAPSSPATGVLPSPQGK 17 0 Q5SRE5;Q5SRE5-2 Q5SRE5 NUP188 Nucleoporin NUP188 homolog 1 GAPS(0.037)S(0.963)PATGVLPSPQGK;GAPS(0.038)S(0.962)PATGVLPSPQGK;GAPS(0.009)S(0.99)PATGVLPSPQGK 235.78 3.78E-20 580157000 797760 771200 823820 885550 781460 589840 836040 641800 803990 TRUE FALSE 747829.6256 828300.4504 843361.3994 908274.7122 720087.2839 760117.2327 710683.5634 721930.1428 669798.875 1.116498778 1.236640552 1.25912633 1.356040964 1.075079865 1.134843997 1.061040246 1.077831226 1 19.35336843 2.710515013 24.41956502 1.077847332 1.244012248 0.629157376 0.065567493 347.0243006 302156.7206 0.020122894 0.018976447 513.4699276 -2.710515013 0.166164916 GAPVGGHILSYLLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GAPVGGHILSYLLEK 15 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 164.33 1.49E-06 236840000 1176680 1211750 1136130 1088420 1453030 886970 1289640 1182680 1427690 FALSE TRUE 1103033.699 1301469.231 1163079.54 1116350.7 1338914.885 1143023.84 1096270.454 1330340.201 1189399.316 0.927387198 1.094223961 0.977871371 0.938583607 1.125706789 0.961009331 0.921700929 1.118497534 1 20.18180172 GAPVNIS(ph)SSDLTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GAPVNISSSDLTGR 14 0 P48730-2;H7BYT1;P48730;J3KRM8 P48730-2 CSNK1D Casein kinase I isoform delta 1 GAPVNIS(0.333)S(0.333)S(0.333)DLTGR;GAPVNIS(0.893)S(0.096)S(0.012)DLTGR;GAPVNIS(0.479)S(0.479)S(0.042)DLTGR;GAPVNIS(0.479)S(0.479)S(0.041)DLTGR;GAPVNIS(0.488)S(0.488)S(0.025)DLTGR;GAPVNIS(0.498)S(0.498)S(0.004)DLTGR 291.02 1.88E-43 3776560000 1994810 2344970 2336600 2224870 2404200 2290850 2770330 2266060 2750100 TRUE FALSE 1869958.403 2518594.019 2392025.255 2281963.931 2215383.83 2952181.206 2354944.735 2548982.579 2291090.544 0.816187037 1.099299207 1.044055313 0.996016477 0.966956036 1.288548466 1.027870654 1.112563005 1 21.12760304 GAPVNISS(ph)S(ph)DLTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GAPVNISSSDLTGR 14 0 P48730-2;H7BYT1;P48730;J3KRM8 P48730-2 CSNK1D Casein kinase I isoform delta 2 GAPVNIS(0.502)S(0.583)S(0.884)DLT(0.031)GR 69.729 0.067525 91154000 212860 238120 259260 244220 309190 249250 312160 315440 391790 TRUE FALSE 199537.4726 255750.6526 265409.7696 250487.0987 284907.4646 321204.4288 265354.506 354823.3784 326397.7179 0.611332315 0.783555272 0.813148362 0.767429075 0.872884365 0.984089076 0.812979048 1.087089029 1 18.31627144 6.442983019 0.178492809 1.047292367 2.10E-15 0.683557633 0.076715055 19.64995615 0.35704458 0.176741474 5.017576851 2773211.67 -6.442983019 -1.047292367 GAPVNISSS(ph)DLTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GAPVNISSSDLTGR 14 0 P48730-2;H7BYT1;P48730;J3KRM8 P48730-2 CSNK1D Casein kinase I isoform delta 1 GAPVNIS(0.002)S(0.096)S(0.901)DLTGR;GAPVNIS(0.002)S(0.348)S(0.65)DLTGR;GAPVNISS(0.011)S(0.988)DLTGR;GAPVNIS(0.001)S(0.069)S(0.931)DLTGR 177.76 2.16E-06 775470000 1017860 1221690 1207190 1177500 1570670 1151750 1407850 1192200 1584190 TRUE FALSE 954153.9595 1312145.199 1235825.117 1207716.644 1447315.914 1484241.528 1196755.962 1341048.794 1319778.455 0.722965249 0.99421626 0.93638831 0.915090437 1.096635506 1.124614152 0.906785497 1.016116599 1 20.33186434 4.738840848 23.87115648 0.992139672 0.722965141 0.5967681 0.071055528 8.969141468 763271.408 0.01696888 0.099140096 54807.60801 -4.738840848 -0.26917453 GAQASS(ph)GSPALPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GAQASSGSPALPR 13 0 P42684-2;P42684-6;P42684-3;P42684;P42684-4;P42684-7;P42684-10;P42684-5 P42684-2 ABL2 Abelson tyrosine-protein kinase 2 1 GAQAS(0.107)S(0.746)GS(0.146)PALPR 121.76 0.00017548 0 206210 156340 172410 175630 169910 146340 204760 139830 186810 TRUE FALSE 193303.6842 167915.5763 176499.6466 180136.9631 156565.954 188585.9824 174058.1389 157288.0833 155630.2042 1.242070492 1.07893951 1.134096351 1.157467884 1.006012649 1.211756955 1.118408472 1.010652682 1 17.24776256 -5 0.111957092 0.585956748 1.19135812 0.330497697 0.06918538 217.1067042 1.609536631 20.25494694 0.766394392 1.00E-05 5 0.605401372 GAQASSGS(ph)PALPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.018)S(0.061)GS(0.921)PALPR;GAQASS(0.022)GS(0.978)PALPR 190.28 4.77E-06 834900000 535220 644610 600280 642330 690990 566940 728250 555840 588310 TRUE FALSE 501721.5356 692337.5951 614518.9251 658813.2753 636722.4327 730606.3745 619055.6732 625237.8476 490117.2604 1.023676528 1.412595824 1.253820207 1.344195213 1.299122647 1.490676688 1.263076662 1.275690326 1 18.90276743 -0.552996203 7.288792012 1 1.309023192 0.364215294 0.121450779 0 0 0.10323085 0.024331745 0.279900579 0.552996203 0.309023193 GAQEVGER ddPTM_SK-BR-3_Pertuzumab_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 ; 121.05 0.007988 0 557300 754350 688790 723930 777520 646190 789370 704710 725090 FALSE TRUE 522419.5878 810202.8589 705128.4241 742507.2694 716456.7156 832734.563 671011.2967 792694.5948 604067.7947 0.864836021 1.341244916 1.167300144 1.229178705 1.186053489 1.378544876 1.110821174 1.312260977 1 19.20435095 -1.060126208 4.50924 0.999987869 1.209901626 0.15379299 0.144457405 1.51E-05 3.15E-06 0.120159033 0.028320119 0.087071052 1.060126208 0.209913757 GAQGEPHDVAPNGPSAGGLAIPQSSSSSSRPPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GAQGEPHDVAPNGPSAGGLAIPQSSSSSSRPPTR 34 1 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ; 174.14 3.43E-15 269270000 119130 141672 137975 135500 143074 127832 149659 117014 128018 FALSE TRUE 111673.866 152161.5423 141247.8322 138977.1594 131837.5452 164735.0232 127219.0223 131623.4555 106650.9688 1.047096592 1.426724427 1.324393334 1.303102644 1.236158909 1.544618161 1.192853884 1.234151522 1 16.70253755 0.881128994 1.517185938 1.003321861 1.3215792 0.328619227 0.131944438 0.546671312 2.460340287 0.111744969 0.032691433 7.605521426 -0.881128994 0.318257339 GAQPGRHS(ph)VTGYGDCAVGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GAQPGRHSVTGYGDCAVGAR 20 1 Q96IF1;H0YJL9 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 GAQPGRHS(1)VTGYGDCAVGAR;GAQPGRHS(0.996)VT(0.004)GYGDCAVGAR;GAQPGRHS(0.992)VT(0.008)GYGDCAVGAR 272.79 1.18E-44 1814630000 426223 587701 498317 533787 594238 408440 631020 518941 557240 TRUE FALSE 399546.4633 631214.9935 510137.3146 547484.8781 547568.9445 526349.9975 536404.4091 583731.9262 464233.0441 0.860659249 1.359694235 1.098881954 1.179331987 1.179513073 1.133805541 1.155463653 1.257411409 1 18.82448969 -1.89968961 2.775488624 0.91223919 1.166617344 0.117670976 0.127038782 2019356.329 5814721.108 1014727.049 0.025977691 0.012598255 1.89968961 0.254378154 GAQQIHSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GAQQIHSIR 9 0 Q86YP4-2;Q86YP4;Q86YP4-3 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 0 68.335 0.05836 49120000 38371 72982 45345 46184 68347 50796 54920 55803 63917 FALSE TRUE 35969.4276 78385.66322 46420.60481 47369.15963 62979.30232 65459.9806 46685.25585 62770.12739 53248.83978 0.675496926 1.472063308 0.871767441 0.889581066 1.182735672 1.229322195 0.876737522 1.178807419 1 15.70046247 -4.999999864 0.287453137 0.520897721 1.066869007 0 0.230006272 2319.484924 21.9562252 666.192866 0.232968988 1.00E-05 4.999999864 0.545971286 GAS(ph)PLGPGSAAGSGAAASGGLGLGLGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GASPLGPGSAAGSGAAASGGLGLGLGGR 28 0 A0A6I8PS01;Q6P1R3-3;Q6P1R3;B4E1M0;E9PPE2 A0A6I8PS01 MSANTD2 Myb/SANT-like DNA-binding domain-containing protein 2 1 GAS(0.912)PLGPGS(0.088)AAGSGAAASGGLGLGLGGR;GAS(1)PLGPGSAAGSGAAASGGLGLGLGGR 275.63 1.59E-61 109320000 56938 56953 49993 56523 59665 51424 68433 51502 70645 TRUE FALSE 53374.35222 61169.85938 51178.85757 57973.47587 54979.15158 66269.274 58172.10695 57932.13807 58853.89312 0.906895863 1.039351114 0.86959171 0.985040629 0.934163378 1.125996438 0.988415615 0.984338249 1 15.84485023 GAS(ph)PPISAIEEFSIIPEAPMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 GASPPISAIEEFSIIPEAPMR 21 0 A0A2R8YF49;C9J591;A0A2R8YFR7;Q12774;A0A5F9ZH52 A0A2R8YF49;A0A2R8YFR7;A0A5F9ZH52 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 GAS(1)PPISAIEEFSIIPEAPMR;GAS(1)PPISAIEEFSIIPEAPMR;GAS(0.975)PPIS(0.025)AIEEFSIIPEAPMR;GAS(0.798)PPIS(0.202)AIEEFSIIPEAPMR;GAS(1)PPISAIEEFSIIPEAPMR;GAS(1)PPISAIEEFSIIPEAPMR;GAS(0.997)PPIS(0.003)AIEEFSIIPEAPMR;GAS(0.98)PPIS(0.02)AIEEFSIIPEAPMR;GAS(0.8)PPIS(0.2)AIEEFSIIPEAPMR;GAS(0.995)PPIS(0.005)AIEEFSIIPEAPMR 249.47 1.16E-30 917201000 214314.2 236552.8 237822 230165.2 242171.1 217283.9 253367.8 202137 240677.8 TRUE FALSE 200900.6568 254067.4154 243463.2501 236071.6287 223151.9587 280010.2346 215377.6505 227374.2494 200507.1203 1.001962706 1.267124155 1.214237428 1.177372795 1.112937826 1.39651018 1.074164599 1.133995885 1 17.61329394 1.099628987 1.638032708 1.010019145 1.199112916 0.214471662 0.106956628 0.462057953 2.440848243 0.090180516 0.0264483 12.57850384 -1.099628987 0.189093771 GASDEEIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GASDEEIKR 9 1 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ;;; 123.35 0.00089802 2343260000 3835890 3084130 3412650 3101510 3186890 2487810 4245140 3014660 4398770 FALSE TRUE 3595808.492 3312482.194 3493599.67 3181099.997 2936604.515 3206000.361 3608620.667 3391046.937 3664586.87 0.981231615 0.903916952 0.953340661 0.868065108 0.801346678 0.87485997 0.984727827 0.925355861 1 21.80521913 1.728742678 9.839490943 0.965428902 0.899612897 0.304435451 0.05166128 0.142993595 49.45435838 0.025493723 0.013780643 53.54792887 -1.728742678 -0.065816005 GASFEELCHNYTQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GASFEELCHNYTQDR 15 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 215.48 2.34E-12 916500000 376390 468800 396730 419860 508000 417750 446290 425130 490920 FALSE TRUE 352832.4218 503510.4398 406140.6229 430634.3184 468103.7292 538347.6434 379372.9577 478208.4163 408982.2805 0.862708334 1.231130207 0.993051881 1.052941262 1.144557482 1.316310435 0.927602431 1.169264389 1 18.64167881 -1.182684338 4.403479435 0.99997723 1.090450444 0.037940537 0.137122048 2.74E-05 5.08E-06 0.118602522 0.027947848 0.065662235 1.182684338 0.090473215 GASIVEDKLVEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GASIVEDKLVEDLR 14 1 P00367 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ; 112.72 0.00052624 120898000 384770 443830 370790 349530 675650 321290 392340 382790 1308950 FALSE TRUE 360687.9325 476691.635 379585.3139 358499.5316 622587.1744 414041.2073 333512.2593 430582.1741 1090477.789 0.330761375 0.43714016 0.348090826 0.328754547 0.570930633 0.379687887 0.305840488 0.394856437 1 20.05652895 -1.623961196 2.502799599 1.070348944 0.385491604 0.867226733 0.075376241 2838507.483 2384210.519 1296278.794 0.018685004 0.023770527 1.623961196 -0.68485734 GASQEEEKGAEYVASVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GASQEEEKGAEYVASVLK 18 1 Q9Y6U3;Q9Y6U3-3 Q9Y6U3 SCIN Adseverin 0 178.75 7.95E-14 99466000 127620 83767 92533 105300 134970 73929 131750 105230 278880 FALSE TRUE 119632.492 89969.19584 94727.92646 108002.1763 124370.0006 95271.10216 111995.3106 118368.1971 232333.1264 0.514917928 0.387242221 0.40772458 0.464859136 0.535308944 0.410062498 0.482046243 0.509476195 1 17.82583534 -4.999999313 0.305451427 5.737917619 0.425554932 0.926757806 0.047517935 66.41371093 0.607725583 201.8747039 0.044670958 1.00E-05 4.999999313 -5.312362687 GASWIDTADGSANHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GASWIDTADGSANHR 15 0 A8MXB9;C9J660;J3KQJ1;Q8NBJ7;A0A494C1B1;H7C3B2;C9JL30;Q8NBJ7-2;E9PBT8;J3QT17;Q8NBJ7-5 A8MXB9 SUMF2 Sulfatase-modifying factor 2 0 ;;; 291.51 6.34E-44 2336600000 1694510 2507450 2327470 2491630 2512970 2264570 2535890 2166900 2315740 FALSE TRUE 1588453.644 2693104.207 2382678.688 2555569.444 2315611.473 2918314.597 2155656.837 2437442.235 1929228.034 0.823362307 1.395949136 1.235042538 1.324659086 1.200278781 1.51268515 1.117367568 1.263428787 1 20.87959225 -0.644647981 7.72825501 1.000000811 1.2527411 0.133113051 0.182307295 0 0 0.153913637 0.036277792 0.226648067 0.644647981 0.252740289 GATKES(ph)SEKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GATKESSEKDR 11 2 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BTY0;H3BUG0;H3BNU7;H3BNI3;H3BTR6;H3BP82 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 1 GATKES(0.5)S(0.5)EKDR;GAT(0.003)KES(0.499)S(0.499)EKDR;GAT(0.001)KES(0.932)S(0.067)EKDR 164.81 1.17E-05 1026360000 2482240 1143050 1537130 1484180 1570880 1115410 1929750 1264850 2056850 TRUE FALSE 2326881.029 1227682.611 1573591.449 1522266.572 1447509.421 1437410.76 1640401.902 1422769.307 1713548.447 1.357931276 0.716456318 0.918323291 0.888370897 0.844743797 0.838850376 0.957312824 0.830305854 1 20.70855555 4.749809944 24.98583958 0.869283674 1.357931562 0.793640178 0.077466108 721.4039317 1602277.13 0.017553243 0.272833298 56209.52877 -4.749809944 0.488647888 GATQQILDEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GATQQILDEAER 12 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;;;; 290.25 9.80E-36 1446960000 1785696 1847577 1784596 1872967 1996994 1701480 1879482 1678511 1666537 FALSE TRUE 1673932.475 1984373.523 1826927.46 1921030.504 1840158.147 2192669.655 1597671.122 1888076.793 1388381.208 1.205672091 1.429271378 1.31586876 1.383647728 1.325398338 1.579299433 1.150743839 1.35991238 1 20.40497231 0.421626613 0.869571654 0.998923196 1.360902722 0.457596379 0.116990486 1.669354371 1.767699341 0.107548342 0.033747598 2.640137908 -0.421626613 0.361979526 GATS(ph)PGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GATSPGQK 8 0 Q15061 Q15061 WDR43 WD repeat-containing protein 43 1 GAT(0.001)S(0.999)PGQK 84.817 0.018024 139300000 276130 185270 300690 240810 243380 186030 299980 220610 262680 TRUE FALSE 258847.5162 198987.5836 307822.5088 246989.5923 224265.9165 239733.8411 255000.7839 248153.6441 218837.011 1.182832442 0.909295839 1.406629104 1.128646343 1.024807986 1.095490383 1.165254372 1.133965607 1 17.73949723 3.001069053 24.99893435 1.09841903 1.160793294 0.074910596 0.126936524 132.0564742 3087904.447 0.037417377 0.044391545 1002.464617 -3.001069053 0.062374264 GATYGKPVHHGVNQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GATYGKPVHHGVNQLK 16 1 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 145.52 7.82E-07 4601300000 4315400 3898300 4325800 4294200 4812700 3250600 4921300 4056000 4863200 FALSE TRUE 4045306.817 4186934.188 4428410.019 4404396.442 4434729.955 4188995.451 4183396.752 4562400.528 4051500.503 0.998471261 1.033428031 1.093029611 1.087102529 1.094589511 1.033936797 1.032554914 1.126101435 1 21.95002489 4.499936453 2.342091949 1.066705418 0.996642108 0.275186769 0.036707197 0.491224062 4.504763567 0.008844355 0.056670777 31618.14986 -4.499936453 -0.07006331 GAVAAEGAS(ph)DTEREEPTESQGLAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.997)DT(0.003)EREEPTESQGLAAR;GAVAAEGAS(0.837)DT(0.163)EREEPTESQGLAAR;GAVAAEGAS(0.9)DT(0.1)EREEPTESQGLAAR;GAVAAEGAS(0.999)DT(0.001)EREEPTESQGLAAR 304.17 1.00E-63 5558470000 1865600 2102800 1958310 1884130 2317480 1853960 2112770 1782490 2274030 TRUE FALSE 1748835.426 2258493.5 2004762.038 1932479.966 2135474.469 2389168.155 1795979.752 2005037.8 1894479.702 0.923121754 1.19214447 1.058212466 1.020058417 1.127208946 1.26112101 0.948006859 1.058358027 1 20.85337025 1.627878022 25 1.002390749 1.101906802 0.180918655 0.094752395 1.326091904 1652.397807 0.040870842 0.022626566 42.45003202 -1.627878022 0.099516053 GAVAAEGASDT(ph)EREEPTESQGLAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.195)DT(0.805)EREEPTESQGLAAR 333.23 1.01E-87 1944200000 738050 884200 747910 823800 909420 739190 882400 755470 867390 TRUE FALSE 691856.768 949667.088 765650.7784 844940.1027 837997.8216 952582.1533 750092.3118 849792.0925 722617.0054 0.95743217 1.314205286 1.059552671 1.169277911 1.159670773 1.318239325 1.038021948 1.175992381 1 19.46287168 0.407486287 0.977148695 1.000114191 1.160863191 0.135977191 0.113400235 4.022926394 5.010004165 0.10090487 0.031285697 2.555561206 -0.407486287 0.160749 GAVAEDGDELRTEPEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 217.88 4.40E-15 1104340000 1365190 1223920 1273000 1279450 1432750 891200 1592030 1225050 1817320 FALSE TRUE 1279745.195 1314540.31 1303196.161 1312282.853 1320227.594 1148474.973 1353319.881 1378000.189 1513997.552 0.845275604 0.868257884 0.860765039 0.866766826 0.872014352 0.758571222 0.893871909 0.910173327 1 20.52993144 0.986713067 1.940625504 0.998172166 0.851488806 0.65910072 0.034805372 0.206029327 1.643012394 0.030952715 0.008709614 9.698689742 -0.986713067 -0.146683361 GAVDGGLSIPHSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GAVDGGLSIPHSTK 14 0 P46777;A0A2R8Y6J3;Q5T7N0 P46777 RPL5 60S ribosomal protein L5 0 ;;;;; 194.3 1.60E-07 4553560000 6859440 8272030 8638680 8771020 9088430 7693210 10676080 8467520 9807680 FALSE TRUE 6430119.895 8884499.708 8843593.569 8996099.223 8374661.369 9914114.838 9075300.916 9524708.511 8170714.848 0.786971521 1.087358924 1.082352491 1.101017401 1.02496067 1.213371782 1.110710762 1.165712999 1 22.96203087 4.74148771 4.547301318 1.104228983 0.765692225 0.720563324 0.060900887 0.097350263 5.226518743 0.013380822 0.105888376 55142.65972 -4.74148771 -0.338536758 GAVEALAAALAHISGATSVDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GAVEALAAALAHISGATSVDQR 22 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;; 266.62 1.10E-37 730101000 224692 680932 539936 584033 602191 499044 572425 478202 689670 FALSE TRUE 210628.9288 731348.9138 552743.5369 599020.2755 554897.348 643109.9015 486595.1854 537906.5724 574559.6216 0.366591944 1.272886027 0.962029903 1.042572873 0.965778532 1.119309254 0.846901117 0.936206709 1 19.13209708 -1.716341247 9.036809687 1.000072412 0.973504026 0 0.236081966 0.000306242 9.61E-06 0.203247055 0.047775323 0.019215813 1.716341247 -0.026568386 GAVEKGEELSCEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GAVEKGEELSCEER 14 1 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 176.29 2.05E-06 616280000 343300 386980 408510 407080 536710 316420 455330 391790 919870 FALSE TRUE 321813.4658 415632.4019 418200.0501 417526.362 494558.9616 407765.3174 387057.4936 440705.8439 766337.7544 0.419936854 0.542361902 0.545712446 0.544833345 0.645353773 0.532096083 0.505074285 0.575080428 1 19.54762086 -5 0.409041535 8.890220643 0.531605258 0.877420121 0.054382903 263.2647207 1.781345216 1860.507469 0.031693152 1.00E-05 5 -8.358615385 GAVIVVSHDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GAVIVVSHDAR 11 0 Q8NE71;Q8NE71-2;H0YGW7;A0A0G2JIC2 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ;;;; 187.97 3.35E-06 1815020000 1691460 1953710 1846180 1782270 2081270 1643810 1935150 1762770 1901670 FALSE TRUE 1585594.538 2098364.721 1889972.261 1828006.066 1917815.45 2118351.262 1644992.223 1982855.715 1584268.992 1.000836693 1.324500279 1.19296172 1.153848289 1.210536506 1.337115902 1.038328864 1.251590308 1 20.59538588 -0.164655557 0.55522525 0.981130273 1.206110618 0.206608792 0.109371215 7.907104751 2.555393198 0.428031742 0.043952746 0.684454279 0.164655557 0.224980346 GAYQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GAYQDR 6 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 102.81 0.08195 200920000 286030 374010 312440 308290 370220 293830 335610 309750 295850 FALSE TRUE 268127.8929 401702.0896 319851.2243 316201.2433 341144.4146 378653.9511 285288.3962 348422.9693 246470.7237 1.087869134 1.629816651 1.297725018 1.282916034 1.384117389 1.536303969 1.15749405 1.413648502 1 17.91105677 -0.846580279 0.39820885 0.866206116 1.387672372 0.293025189 0.163261398 14.53770948 1.78590418 2.467132457 0.099732036 0.142370405 0.846580279 0.521466256 GCDVVVIPAGVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GCDVVVIPAGVPR 13 0 P40926;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial" 0 ; 148.32 0.0001001 160717000 296490 325770 326340 281420 393440 312940 320300 319580 406920 FALSE TRUE 277933.2201 349890.3498 334080.9389 288641.7136 362540.8095 403280.6978 272273.9885 359480.2665 339002.4232 0.819856146 1.032117548 0.985482451 0.851444397 1.069434271 1.189610074 0.803162367 1.060406186 1 18.37093606 4.747402706 23.73854087 0.991436883 0.819855965 0.207883306 0.108996363 950.5257061 2551778.454 0.024616782 0.283715778 55898.82842 -4.747402706 -0.171580918 GCEVVVSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GCEVVVSGK 9 0 P23396;P23396-2;E9PL09;H0YEU2;E9PSF4;E9PJN9 P23396 RPS3 40S ribosomal protein S3 0 ; 161.92 0.00014929 243670000 448730 398200 415220 400940 431690 377750 483540 359890 439580 FALSE TRUE 420644.7903 427683.1423 425069.2145 411228.7992 397786.8088 486800.2927 411037.666 404823.0587 366211.2582 1.148639701 1.167859078 1.160721319 1.122927791 1.086222228 1.329288169 1.12240587 1.105435864 1 18.48231662 0.955591354 2.279198255 1.001575393 1.165706616 0.401888692 0.063861556 0.321434767 3.697218642 0.056228601 0.015373822 9.027995911 -0.955591354 0.164131223 GCFQAEIVPVTTTVHDDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GCFQAEIVPVTTTVHDDK 18 0 P09110;C9JDE9;H7C131;H0Y4D4;P09110-2 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 ;;;; 214.66 9.93E-19 3230430000 7328450 4962210 5759820 5686540 5778080 4937520 7751110 5621570 5530510 FALSE TRUE 6869775.396 5329617.192 5896445.65 5832466.244 5324292.904 6362901.87 6588903.013 6323435.389 4607432.153 1.491020414 1.156743499 1.279768308 1.265882177 1.155587913 1.381008262 1.430059694 1.372442432 1 22.13553149 2.207590217 24.99685273 1.344013188 1.255564632 0 0.15048759 526.0690646 424598.2006 0.050479689 0.037285643 161.2836031 -2.207590217 -0.088448555 GCFQAEIVPVTTTVHDDKGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GCFQAEIVPVTTTVHDDKGTK 21 1 P09110;C9JDE9;H7C131;H0Y4D4;P09110-2 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 128.38 1.10E-05 472790000 1037900 702130 799280 861960 1033000 534050 1046100 769550 1178900 FALSE TRUE 972939.6917 754116.4358 818239.299 884079.3529 951872.3469 688221.5654 889247.0165 865630.0115 982133.974 0.990638464 0.767834588 0.833123913 0.900161665 0.969187883 0.700741023 0.905423333 0.881376711 1 19.90556031 0.77836124 1.743254457 0.999364832 0.851972534 0.17430362 0.086984639 1.183957954 6.131723611 0.076526361 0.021683053 6.00290182 -0.77836124 -0.147392298 GCGDLCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GCGDLCR 7 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 102.98 0.019726 235290000 311100 541780 340200 343470 637610 284510 385290 515320 545840 FALSE TRUE 291628.8063 581893.9549 348269.7047 352284.0217 587534.6826 366643.4184 327519.3414 579658.8364 454735.7777 0.641314848 1.279630905 0.765872671 0.774700472 1.292035312 0.806277923 0.720240978 1.274715702 1 18.79466899 1.229030168 24.99968859 1.137357753 0.916663873 0.1536087 0.230906186 449.6031166 1179329.564 0.199738363 0.052553197 16.94455501 -1.229030168 -0.22069388 GCHLLVATPGR ddPTM_SK-BR-3_Pertuzumab_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 ;; 102.52 0.002857 1076200000 1050740 1106630 938770 1007420 1324610 758970 1106600 1035350 1521460 FALSE TRUE 984976.059 1188566.037 961038.0677 1033272.103 1220580.474 978072.3182 940675.6032 1164615.727 1267518.497 0.777090087 0.937710999 0.758204373 0.815192918 0.962968569 0.771643428 0.742139547 0.918815567 1 20.27357537 1.007131103 8.17019352 0.99998447 0.826112853 0.397939436 0.073288116 0.109433353 59.95854285 0.069597767 0.01742715 10.1655552 -1.007131103 -0.173871618 GCIVDANLSVLNLVIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GCIVDANLSVLNLVIVK 17 0 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 142.57 2.09E-05 0 15364 16866 15907 15289 19238 10514 17064 17195 15692 FALSE TRUE 14402.39467 18114.77619 16284.32155 15681.34162 17727.12508 13549.22112 14505.41161 19341.8336 13072.90383 1.101698204 1.385673484 1.245654506 1.199530099 1.356020462 1.036435462 1.109578393 1.479536135 1 13.67429202 2.248838153 24.99821131 1.154915249 1.270874727 0.098753203 0.14916276 419.4195825 1020160.614 0.048339944 0.040025513 177.3528425 -2.248838153 0.115959478 GCLAGGGS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GCLAGGGSPK 10 0 Q9H257;Q9H257-2 Q9H257 CARD9 Caspase recruitment domain-containing protein 9 1 GCLAGGGS(1)PK;GCLAGGGS(1)PK 115.29 0.00243 154960000 352050 231550 269610 274820 259570 212490 331390 233990 242450 TRUE FALSE 330015.8189 248694.2029 276005.2765 281872.3465 239184.4193 273832.4135 281701.146 263204.1666 201983.5287 1.633874906 1.231259819 1.366474179 1.395521448 1.184177843 1.355716554 1.394673852 1.30309718 1 17.62387812 -3.296445172 0.344617379 3.66E-16 1.361522372 0.485531387 0.117668127 96.71087871 2.440584254 69.9203769 0.085354966 0.000505306 3.296445172 1.361522372 GCLDEETSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GCLDEETSR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 148.99 0.00020636 306610000 437560 489850 521390 518810 582790 469140 596600 473950 468010 FALSE TRUE 410173.9007 526119.0037 533757.617 532123.5429 537020.0243 604573.1021 507145.3686 533123.7008 389896.1075 1.052008196 1.34938255 1.368973957 1.364782907 1.377341332 1.550600507 1.30071924 1.367348097 1 18.57273023 -1.275876068 4.976077158 0.999912285 1.351898972 0.435052835 0.121740167 0.000108748 1.58E-05 0.108191706 0.025494701 0.052981461 1.275876068 0.351986687 GCLTTPNS(ph)PSMHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GCLTTPNSPSMHSR 14 0 O75128-3;O75128;O75128-7;A0A0J9YWK3;A0A3B3IU00;O75128-5;O75128-4 O75128-3 COBL Protein cordon-bleu 1 GCLTTPNS(0.996)PS(0.004)MHSR;GCLTTPNS(0.996)PS(0.004)MHSR;GCLTTPNS(0.964)PS(0.035)MHS(0.001)R;GCLTTPNS(0.962)PS(0.038)MHSR;GCLTTPNS(0.984)PS(0.015)MHSR;GCLTTPNS(0.952)PS(0.046)MHS(0.001)R 147.09 6.16E-06 1177000000 710561 1000292 898688 935002 1089473 903904 1040221 963580 940480 TRUE FALSE 666088.2554 1074354.66 920005.3038 958995.7343 1003910.185 1164846.411 884249.518 1083885.084 783507.8123 0.850136074 1.371211166 1.174213313 1.223977246 1.281302075 1.486706824 1.128577794 1.383374954 1 19.57958813 4.747965493 24.53618685 1.26382166 0.850135789 0.457354609 0.138771948 813.2145223 2121520.523 0.028956636 0.364400445 55971.31276 -4.747965493 -0.41368587 GCNPSGHTQSVT(ph)TPEPAKEGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GCNPSGHTQSVTTPEPAKEGTK 22 1 O75363;G3XAF7;O75363-2;H0Y542;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 GCNPSGHTQS(0.002)VT(0.604)T(0.394)PEPAKEGTK;GCNPSGHTQS(0.048)VT(0.832)T(0.12)PEPAKEGTK 178.95 8.57E-17 835930000 965250 1029920 1050290 1140320 1413770 877680 1457760 985740 2393130 TRUE FALSE 904836.7255 1106176.348 1075203.375 1169582.542 1302738.207 1131051.968 1239182.421 1108811.809 1993701.143 0.453847724 0.554835589 0.539300175 0.586638848 0.653427025 0.567312695 0.621548734 0.556157483 1 20.92701773 -5 0.230774743 3.325693226 0.520538514 0.893130769 0.047698948 46.41508474 0.4645126 50.43049926 0.076490313 1.00E-05 5 -2.805154712 GCNPSGHTQSVTT(ph)PEPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GCNPSGHTQSVTTPEPAK 18 0 O75363;G3XAF7;O75363-2;H0Y542;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 GCNPSGHTQSVT(0.054)T(0.946)PEPAK;GCNPSGHTQSVT(0.248)T(0.751)PEPAK;GCNPSGHTQS(0.001)VT(0.208)T(0.791)PEPAK 141.08 4.51E-07 1820770000 1868720 1786080 2021840 2006070 2011600 1858420 2540180 1889860 2256240 TRUE FALSE 1751760.151 1918323.222 2069799 2057549.152 1853617.05 2394915.685 2159303.591 2125813.181 1879658.968 0.931956371 1.020569824 1.101156664 1.094639606 0.986145403 1.274122448 1.148774127 1.130956848 1 20.8420395 5.649194442 0.52748208 1.131897366 0.506443895 0.324647827 0.080434579 10.57512081 1.087001273 0.039474068 5.019306333 445855.8222 -5.649194442 -0.625453471 GCNPSGHTQSVTT(ph)PEPAKEGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GCNPSGHTQSVTTPEPAKEGTK 22 1 O75363;G3XAF7;O75363-2;H0Y542;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 GCNPSGHTQSVT(0.119)T(0.881)PEPAKEGTK 168.26 1.41E-11 631860000 975250 1171500 1241300 1304100 1598800 1036400 1618200 1245700 2581000 TRUE FALSE 914210.8434 1258239.079 1270744.222 1337565.414 1473236.697 1335591.855 1375565.933 1401228.387 2150214.426 0.425171942 0.585169118 0.590984884 0.622061408 0.685158038 0.621143566 0.639734306 0.651669141 1 21.03604911 -5 0.153567968 2.431950357 0.486497774 0.873183375 0.050862885 44.77551347 0.403937097 19.54101939 0.234030207 1.00E-05 5 -1.945452583 GCQLLVYPGAFNLTTGPAHWELLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GCQLLVYPGAFNLTTGPAHWELLQR 25 0 Q9NQR4 Q9NQR4 NIT2 Omega-amidase NIT2 0 ; 264.08 3.04E-45 177110000 614500 953820 456330 344530 968000 387830 582290 830550 306140 FALSE TRUE 576039.5419 1024441.825 467154.3631 353371.2231 891977.1847 499790.2251 494981.0202 934245.9958 255043.2563 2.258595465 4.016737554 1.831667184 1.385534471 3.497356479 1.95962925 1.940772822 3.663088409 1 17.96038243 -1.513832998 0.209990883 3.56E-37 2.879887202 0.179070792 0.913577463 43.89232883 1.663835355 31.18928258 2.218211788 0.030631411 1.513832998 2.879887202 GCRLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GCRLSPR 7 1 P17812;B4E1E0;P17812-2;A0A3B3IRI2 P17812 CTPS1 CTP synthase 1;CTP synthase 1 GCRLS(1)PR;GCRLS(1)PR;GCRLS(1)PR;GCRLS(1)PR 64.711 0.04394 3422770000 1055164 2902530 941000 975380 3198060 767490 823450 2269590 3443820 TRUE FALSE 989123.1688 3117436.341 963320.9644 1000409.902 2946897.268 989051.9038 699981.317 2552953.307 2869024.194 0.344759438 1.086584194 0.335766065 0.348693435 1.027142704 0.344734599 0.243978883 0.889833314 1 21.4521287 1.052668967 9.221696085 0.999873449 0.554045365 0.254609988 0.294584555 0.39818102 63.81901888 0.280532505 0.070194262 11.28935077 -1.052668967 -0.445828085 GCRPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GCRPGK 6 1 P62140;C9JP48;C9J9S3 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatase 0 72.62 0.077627 297560000 808460 670420 768640 737280 794140 602270 763300 774800 820570 FALSE TRUE 757859.9317 720058.5944 786872.5038 756199.853 731771.4478 776135.572 648850.2511 871535.4855 683611.5659 1.108611922 1.053315406 1.151052064 1.106183527 1.070449191 1.135345876 0.949150488 1.274898684 1 19.38281728 GCSVSLWDLLLSEYVGADKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GCSVSLWDLLLSEYVGADKR 20 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 87.49 0.0037774 76367000 84496 138070 132840 130640 151040 128760 133680 118140 84880 FALSE TRUE 79207.54619 148292.8465 135991.0275 133992.4436 139177.9277 165930.9218 113635.925 132890.0391 70712.97965 1.120127402 2.097109289 1.923140959 1.894877634 1.968209066 2.346541223 1.607002358 1.879287787 1 16.10968743 -0.583173 19.2567075 0.999980062 1.888056084 0.407581207 0.321523524 0 0 0.279278667 0.065826613 0.261112102 0.583173 0.888076022 GCTALHYAVLADDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GCTALHYAVLADDYR 15 0 Q9H078-5;Q9H078-3;Q9H078-2;H0YGM0;Q9H078-4;Q9H078;A0A2R8Y602;A0A2U3TZY2;A0A2R8YDH5;F5H7A5;F5H392;A0A2R8Y6R5 Q9H078-5 CLPB Caseinolytic peptidase B protein homolog 0 119.31 0.00022243 191170000 118250 132530 115520 125070 182970 104300 118710 148110 161230 FALSE TRUE 110848.9436 142342.6591 118260.189 128279.5079 168600.2743 134409.7168 100910.5375 166601.8595 134319.6714 0.825262171 1.059730549 0.880438343 0.955031431 1.255216548 1.000670381 0.751271474 1.240338498 1 17.03531108 4.7540426 23.35663296 0.99347941 0.825261859 0.120042215 0.151602698 2765.874233 4172511.665 0.035056831 0.773925964 56760.0278 -4.7540426 -0.168217551 GCTSSSSLS(ph)PPRGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GCTSSSSLSPPRGDR 15 1 Q96LT9-2;Q96LT9;X6RLP6 Q96LT9-2 RNPC3 RNA-binding protein 40 1 GCTSS(0.002)S(0.008)SLS(0.99)PPRGDR 87.157 0.0044084 470260000 97052 104690 105440 110170 120670 93915 105310 103410 124680 TRUE FALSE 90977.68856 112441.3565 107941.0866 112997.1487 111193.065 121026.7359 89519.74315 116320.9661 103870.1025 0.875879453 1.082518971 1.03919303 1.08786981 1.070501157 1.165173933 0.861843215 1.119869561 1 16.66442093 -1.577164395 6.634127271 0.999941949 1.037067314 0.014586393 0.097594181 7.69E-05 4.90E-06 0.086765067 0.020418757 0.026474978 1.577164395 0.037125365 GCWDSIHVVEVQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GCWDSIHVVEVQEK 14 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;; 222.74 3.78E-12 1507320000 3430900 3808620 3826130 3853130 4223780 3157990 4354960 3829310 3840580 FALSE TRUE 3216166.093 4090614.188 3916887.61 3952007.839 3892061.357 4069650.447 3701974.177 4307407.783 3199562.387 1.005189368 1.278491773 1.224194792 1.235171364 1.216435527 1.271939708 1.157025158 1.346249037 1 21.60944317 -1.030649346 7.83204486 0.999999995 1.22122859 0.364807541 0.089753985 8.69E-09 8.58E-10 0.075162863 0.017716056 0.093185996 1.030649346 0.221228595 GDAASS(ph)PAPAASVGSSQGGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GDAASSPAPAASVGSSQGGAR 21 0 E7EXA6;A0A0D9SF58;Q8WVB6;Q8WVB6-2;F8WCC1 E7EXA6 CHTF18 Chromosome transmission fidelity protein 18 homolog 1 GDAAS(0.003)S(0.997)PAPAASVGSSQGGAR;GDAAS(0.002)S(0.998)PAPAASVGSSQGGAR;GDAAS(0.016)S(0.984)PAPAASVGSSQGGAR;GDAAS(0.002)S(0.998)PAPAASVGSSQGGAR 464.87 1.46E-223 1902640000 1084700 1223080 1233500 1121870 1304090 1278610 1474390 1153250 1109890 TRUE FALSE 1016810.563 1313638.116 1262759.203 1150659.084 1201672.032 1647723.951 1253318.907 1297235.801 924642.1888 1.099680044 1.420698873 1.365673357 1.244437143 1.299607617 1.782012513 1.355463683 1.402959779 1 19.81853566 GDAAVRDELMAAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDAAVRDELMAAVR 14 1 Q15008;Q15008-4;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 154.13 5.66E-06 346080000 204992 292238 239842 267044 306820 222703 238441 227818 311831 FALSE TRUE 192161.9166 313875.6056 245531.1655 273896.8011 282723.5949 286993.7408 202688.9856 256261.5788 259784.3916 0.739697699 1.208215796 0.945134402 1.054323547 1.08830093 1.104738199 0.780220029 0.986439475 1 17.98695523 1.753867785 25 0.902269702 1.039381321 0.096797335 0.135653831 8.358833015 13669.00768 0.056378836 0.031265213 56.73718504 -1.753867785 0.137111619 GDACDDDIDGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDACDDDIDGDR 12 0 G3XAP6;P49747-2;P49747 G3XAP6 COMP Cartilage oligomeric matrix protein 0 80.782 0.045161 233780000 141040 187470 174880 181120 178770 203630 174230 138390 125140 FALSE TRUE 132212.5582 201350.4739 179028.2362 185767.8458 164730.1253 262414.6753 148105.829 155668.2961 104253.3256 1.268185523 1.931357803 1.71724245 1.781888921 1.580094682 2.517086855 1.420634097 1.493173434 1 16.66973388 1.048305876 1.838591099 1.023875893 1.791771033 0.350729358 0.329076411 0.333118505 2.2925751 0.277675452 0.079312327 11.17650139 -1.048305876 0.76789514 GDADQASNILASFGLSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDADQASNILASFGLSAR 18 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 112.24 0.00046525 0 117920 97136 111720 138930 206210 101850 205610 258390 146090 FALSE TRUE 110539.5977 104328.0505 114370.0512 142495.179 190015.0984 131252.4416 174780.6893 290650.5603 121706.6352 0.908246272 0.857209225 0.939719112 1.170808631 1.561255046 1.078432917 1.436081845 2.388124195 1 16.8930483 2.831336488 0.854712634 1.568939983 0.846595312 0.347357945 0.370355686 0.629326531 0.997973358 0.207225089 0.217179664 678.1667419 -2.831336488 -0.722344671 GDARPAEIDSLWEISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDARPAEIDSLWEISK 16 1 B4DE93;G3V0I5;P49821-2;P49821 B4DE93 NDUFV1 "NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial" 0 95.954 0.0032626 112470000 285180 251990 235790 229240 328890 181800 267560 284750 517960 FALSE TRUE 267331.0929 270647.6018 241383.0501 235122.6865 303060.3061 234282.7087 227441.8619 320301.6643 431509.1299 0.619525925 0.627211762 0.559392684 0.544884616 0.702326521 0.542938011 0.527084704 0.742282474 1 18.71903156 0.949047621 4.106728462 0.999662889 0.587904928 0.865323366 0.052043832 0.082743396 3.965346708 0.04944855 0.012628283 8.892986262 -0.949047621 -0.411757961 GDASKEDIDTAMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GDASKEDIDTAMK 13 1 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0D9SFP2;A0A1W2PNM1;A0A1W2PQ78 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 ;;;;; 90.412 0.0070906 1936380000 2683390 1752400 1848170 1803320 2771740 1469000 2059520 1932060 4539540 FALSE TRUE 2515441.41 1882149.519 1892009.465 1849596.244 2554058.721 1893076.453 1750714.096 2173281.944 3781861.447 0.665133148 0.497678073 0.500285241 0.489070335 0.675344339 0.500567374 0.462923912 0.574659324 1 21.85066508 0.953913476 21.20214481 1.000000001 0.529827395 0.791297399 0.073320081 628.4191191 289105.6779 0.066830719 0.01670768 8.993183926 -0.953913476 -0.470172606 GDCFIIDLGTEIYQWCGSSCNKYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GDCFIIDLGTEIYQWCGSSCNKYER 25 1 Q9Y6U3;Q9Y6U3-2 Q9Y6U3 SCIN Adseverin 0 ;; 242.64 1.04E-38 178423000 175578 190546 196600 194097 333623 197957 212556 221971 464605 FALSE TRUE 164588.8864 204654.2241 201263.4448 199077.8576 307421.5954 255103.9723 180685.2011 249684.568 387059.424 0.425228986 0.528741096 0.519980738 0.514334093 0.79424909 0.659082189 0.466815145 0.64508071 1 18.56219555 -5 0.186908324 2.836827094 0.478260538 0.675943002 0.098185196 85.93895057 0.83745529 58.79866661 0.285629293 1.00E-05 5 -2.358566556 GDDALEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GDDALEKR 8 1 Q9Y617 Q9Y617 PSAT1 Phosphoserine aminotransferase 0 ;; 97.635 0.012975 1037830000 874320 956930 772290 783460 988670 599270 1147450 836930 1387720 FALSE TRUE 819597.8719 1027782.093 790609.0835 803564.91 911023.8463 772269.5207 975400.5249 941422.5528 1156100.567 0.708933025 0.889007516 0.6838584 0.695064887 0.788014358 0.667995106 0.843698682 0.81430853 1 20.14083547 0.804668392 1.163369968 0.998174343 0.752526559 0.569644078 0.068829868 0.561387233 1.41589123 0.06319466 0.019643706 6.377763224 -0.804668392 -0.245647785 GDDDEES(ph)DEEAVKK ddPTM_SK-BR-3_Pertuzumab_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 202.5 1.00E-08 1974900000 2105780 820890 1348620 1225330 1123070 1000350 1494360 873290 840480 TRUE FALSE 1973982.989 881669.5497 1380609.903 1256774.042 1034868.612 1289134.806 1270294.591 982322.1788 700198.4583 2.819176428 1.259170938 1.97174085 1.794882618 1.477964712 1.841099178 1.814192214 1.402919654 1 19.41740436 -2.103664446 0.154491285 2.79E-21 2.073928194 0.367353662 0.392312611 57.12682413 1.23530021 23.31551404 2.048037282 0.007876541 2.103664446 2.073928194 GDDGIFDDNFIEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GDDGIFDDNFIEER 14 0 O60493-4;O60493;O60493-2 O60493-4 SNX3 Sorting nexin-3 0 ;;;;; 364.95 1.38E-96 2729590000 2202540 2549890 2526750 2356900 2577150 2599420 2855080 2390740 2588520 FALSE TRUE 2064686.953 2738686.509 2586685.703 2417382.044 2374751.035 3349830.356 2426987.259 2689229.152 2156479.29 0.957434167 1.269980436 1.199494804 1.120985514 1.101216713 1.553379331 1.125439633 1.24704613 1 21.04024643 4.746064809 24.30630986 1.216380685 0.957433985 0.209272208 0.147241444 888.0159967 2876206.12 0.031595907 0.326789991 55726.89035 -4.746064809 -0.2589467 GDDLLPAGTEDYIHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GDDLLPAGTEDYIHIR 16 0 K7EM18;P41567;O60739 K7EM18 EIF1;EIF1B Eukaryotic translation initiation factor 1;Eukaryotic translation initiation factor 1b 0 ;;;;;;; 235.88 1.03E-19 4990505000 8132100 8187400 9442660 8712570 8005890 8659660 9215970 7373770 5535454 FALSE TRUE 7623126.377 8793603.615 9666644.354 8936149.297 7377139.694 11159563.26 7834120.855 8294401.416 4611550.967 1.653050445 1.90686467 2.096180748 1.937775243 1.599709023 2.419915413 1.698803919 1.798614279 1 22.13682061 0.589990922 1.405776063 1.001060005 1.933172336 0.5882206 0.235629383 1.023201829 2.740418762 0.202081382 0.059368029 3.890370133 -0.589990922 0.93211233 GDDQLELIKDDEKEAEEGEDDRDS(ph)ANGEDDS ddPTM_SK-BR-3_Pertuzumab_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 74.527 0.01896 325110000 670350 264030 363220 333870 365830 275310 457420 289290 303080 TRUE FALSE 628393.9901 283579.0559 371835.7499 342437.6694 337099.1875 354787.5277 388834.1175 325408.4933 252493.99 2.488748307 1.123112102 1.472651883 1.35622107 1.335078064 1.405132564 1.539973753 1.288777183 1 17.94588952 4.745550393 24.99854791 1.349292704 2.488748833 0.839803747 0.160475053 307.1559855 1098498.847 0.035574482 0.357827499 55660.92159 -4.745550393 1.139456128 GDDSFGDKYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDDSFGDKYR 10 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 150.46 1.96E-05 677530000 757220 811140 747190 740960 933030 513280 715740 796980 827140 FALSE TRUE 709826.9519 871197.6496 764913.6996 759974.288 859753.5875 661455.6036 608421.4316 896484.7074 689084.9905 1.03010073 1.264281854 1.110042608 1.102874534 1.247674234 0.959904239 0.88294106 1.300978428 1 19.39432241 2.228973253 24.99996173 1.008483985 1.158671359 0.15267082 0.126854937 275.9202573 719482.499 0.044289237 0.033129456 169.4233453 -2.228973253 0.150187374 GDDSRPGPWRPLVKPGGWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDDSRPGPWRPLVKPGGWR 19 3 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 69.605 0.0099364 479950000 330570 308920 358950 322140 322410 314130 413300 322390 278470 FALSE TRUE 309880.2138 331792.7582 367464.4635 330406.6578 297089.2191 404814.2315 351329.5019 362641.1012 231991.558 1.335739181 1.430193241 1.583956186 1.424218453 1.280603577 1.744952424 1.514406407 1.563165075 1 17.82371278 GDDTPLHLAASHGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDDTPLHLAASHGHR 15 0 A0A0A0MTH3;Q13418;Q13418-2;A0A087WWY6 A0A0A0MTH3 ILK Integrin-linked protein kinase 0 ; 214.18 1.45E-12 434590000 274980 458720 399860 426150 435470 398240 463340 426580 450820 FALSE TRUE 257769.4927 492684.1061 409344.868 437085.7305 401269.9428 513205.4231 393866.4684 479839.452 375575.2296 0.686332517 1.311812035 1.089914445 1.163776778 1.068414291 1.366451732 1.048701931 1.277612085 1 18.51874239 4.749133977 24.83531159 1.169912964 0.686332219 0.609850095 0.120491532 864.7806074 2031202.473 0.02499258 0.362075619 56122.1083 -4.749133977 -0.483580745 GDDWNDREWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDDWNDREWDR 11 1 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 131.17 0.00019048 774240000 652370 917960 770740 733920 910480 735870 772360 794430 904500 FALSE TRUE 611539.3262 985926.7135 789022.3168 752753.6297 838974.5735 948303.7231 656551.7882 893616.3343 753533.1067 0.811562652 1.308405304 1.047097081 0.99896557 1.113387807 1.258476522 0.871297867 1.185901888 1 19.52331137 1.734461488 25 1.010781534 1.107408427 0.035069449 0.155069229 1.229788719 7419.664702 0.065859099 0.036522038 54.25771348 -1.734461488 0.096626893 GDEELDSLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GDEELDSLIK 10 0 Q71UI9;P0C0S5;C9J0D1;A0A494C189;Q71UI9-4;Q71UI9-2;Q71UI9-3;C9J386 Q71UI9 H2AFV;H2AFZ Histone H2A.V;Histone H2A.Z;Histone H2A 0 ;;;;; 242.08 5.59E-12 1864610000 5104050 4126300 4531510 4360630 4574110 3563460 5443070 3742920 4572700 FALSE TRUE 4784596.621 4431815.545 4638999.557 4472531.148 4214877.852 4592173.054 4626932.184 4210231.801 3809486.829 1.255968805 1.163362874 1.217749205 1.174050823 1.106416176 1.205457128 1.214581489 1.105196576 1 21.86116524 0.980093823 3.836097097 1.000352857 1.18916379 0.714626586 0.039526644 0.104774407 4.337858687 0.03610451 0.00927111 9.551989199 -0.980093823 0.188810933 GDEGIFEESFIEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GDEGIFEESFIEER 14 0 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 0 ;; 263.29 3.05E-24 223385000 255161 251762 272919 272972 278689 242556 323763 240825 293160 FALSE TRUE 239190.9285 270402.7204 279392.7676 279976.9237 256801.8901 312577.9796 275217.7438 270892.5314 244229.7021 0.979368711 1.107165583 1.143975385 1.146367216 1.0514769 1.279852438 1.126880725 1.109171116 1 17.89787914 4.811852676 2.170710122 1.134452926 0.918058052 0.264015701 0.072331329 1.000677514 4.561728503 0.016253288 0.448976026 64841.44379 -4.811852676 -0.216394874 GDEVWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDEVWLR 7 0 E9PGA6;Q9BXJ4-2;Q9BXJ4;Q9BXJ4-3 E9PGA6 C1QTNF3-AMACR;C1QTNF3 Complement C1q tumor necrosis factor-related protein 3 0 79.116 0.077928 22944000 61373 103420 87219 86249 103450 75200 86635 91488 103030 FALSE TRUE 57531.77348 111077.3244 89287.87587 88462.29536 95325.4543 96909.01923 73644.88603 102910.4782 85833.6274 0.670270793 1.294100317 1.040243534 1.030625153 1.110584012 1.129033249 0.857995733 1.19895292 1 16.38925535 GDFCIQVGR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;; 185.55 9.94E-05 10827580000 5282230 7251010 5875260 6057430 7141950 5193490 6933430 6052870 7670280 FALSE TRUE 4951624.653 7787882.325 6014623.942 6212873.909 6581050.056 6692766.254 5893826.538 6808584.144 6390060.716 0.774894774 1.218749347 0.941246759 0.972271499 1.029888502 1.047371309 0.922342807 1.065496002 1 22.60739821 3.738128048 24.89754103 0.992881714 1.043967577 0 0.11579563 1378.235258 3117573.261 0.026926959 0.047953437 5471.772696 -3.738128048 0.051085864 GDFDENLNYPEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDFDENLNYPEQK 13 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ; 226.04 2.66E-11 293840000 548770 431470 502480 464990 528210 410870 613860 460850 582770 FALSE TRUE 514423.4653 463416.4877 514399.0629 476922.4306 486726.5173 529481.4991 521817.3918 518388.137 485501.9222 1.059570399 0.954510099 1.059520137 0.982328615 1.002522328 1.090585794 1.074799847 1.067736529 1 18.88911748 2.249476429 24.9953382 1.066547074 1.009080631 0.245154174 0.039307738 225.1794458 515621.941 0.012474819 0.010343222 177.6136867 -2.249476429 -0.057466443 GDFFPPERPQQLPHGLGGIGMGLGPGGQPIDANHLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDFFPPERPQQLPHGLGGIGMGLGPGGQPIDANHLNK 37 1 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R019;M0R0N3 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 231.28 3.08E-40 301630000 377300 356150 318470 310470 381600 261840 401130 324930 417970 FALSE TRUE 353685.4665 382519.7166 326024.2588 318437.1858 351630.6753 337428.9574 340984.2804 365498.2258 348208.1068 1.015730133 1.098537653 0.936291409 0.914502505 1.009829089 0.969043945 0.979254284 1.049654556 1 18.40959027 3.976895396 24.05622322 0.976980943 1.057344456 0.367074355 0.042092914 5.942654104 633189.8484 0.010065172 0.01973993 9481.900547 -3.976895396 0.080363513 GDFIHVMDNSDPNWWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDFIHVMDNSDPNWWK 16 0 P62993;P62993-2 P62993 GRB2 Growth factor receptor-bound protein 2 0 ; 202.63 2.99E-11 558020000 1217640 1019440 1187270 1118850 1150010 978910 1381460 1130450 1030400 FALSE TRUE 1141430.086 1094920.398 1215432.605 1147561.585 1059692.854 1261505.426 1174322.898 1271589.171 858419.5834 1.329687845 1.275507246 1.41589571 1.336830622 1.234469569 1.469567389 1.368005717 1.481314261 1 19.71132346 -1.394819341 7.020293648 0.99997962 1.361214153 0.684626887 0.077602252 2.33E-05 2.01E-06 0.070818323 0.016691099 0.040288459 1.394819341 0.361234533 GDFIPGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDFIPGLR 8 0 P08559-3;P08559;P08559-2;P08559-4 P08559-3 PDHA1 "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial" 0 79.597 0.064268 31239000 60117 64309 68161 62512 77800 64863 62454 62835 91849 FALSE TRUE 56354.38428 69070.50527 69777.81111 64116.16375 71689.90183 83587.89514 53089.60249 70680.08807 76518.80853 0.736477545 0.902660491 0.911904046 0.837913775 0.936892552 1.092383647 0.693811149 0.923695617 1 16.22352679 4.739259744 23.19630784 0.899609612 0.736477433 0.215243472 0.103026457 35.46781852 1176068.817 0.023208677 0.138961788 54860.49775 -4.739259744 -0.163132178 GDFYTAHGEDALLAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDFYTAHGEDALLAAR 16 0 A0A2R8YFH0;E9PHA6;A0A2R8Y6P0;A0A2R8YG02;P43246;A0A2R8Y7S8 A0A2R8YFH0 MSH2 DNA mismatch repair protein Msh2 0 ; 171.15 5.02E-09 1593860000 1477700 1275040 1413900 1571990 1687420 999400 1426780 1205480 1603320 FALSE TRUE 1385213.395 1369445.288 1447438.376 1612329.925 1554896.84 1287910.556 1212847.585 1355986.832 1335715.534 1.037057187 1.025252199 1.083642691 1.207090794 1.164092803 0.96421021 0.908013386 1.015176358 1 20.34918136 2.197108417 13.09220782 0.958110251 1.094771238 0.528862008 0.060797351 1.058250286 332.7266677 0.024761295 0.018303985 157.4375842 -2.197108417 0.136660988 GDGDVAWQHTQLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDGDVAWQHTQLFR 14 0 Q96IV0-5;Q96IV0;A0A0C4DFP4;Q96IV0-2;Q96IV0-4 Q96IV0-5 NGLY1 Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase 0 76.759 0.026564 142570000 68189 135730 113940 91708 108180 101360 100560 84077 121050 FALSE TRUE 63921.17221 145779.5904 116642.7106 94061.38254 99683.97918 130620.9866 85481.96155 94574.19853 100845.973 0.633849526 1.4455668 1.156642225 0.932723239 0.988477539 1.29525238 0.847648736 0.93780838 1 16.62179395 1.683834733 10.35012441 0.92134531 1.118442864 0.067419981 0.220625756 0.226099356 35.94735327 0.101502459 0.054878504 48.28750131 -1.683834733 0.197097553 GDGGITHSEEINGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GDGGITHSEEINGK 14 0 O75363;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 ;;;; 240.37 2.14E-17 1985770000 5183920 4365880 4683950 4563200 4998310 3911370 5563570 4193210 5487910 FALSE TRUE 4859467.701 4689134.298 4795055.506 4680299.437 4605762.895 5040519.023 4729364.328 4716741.499 4571942.368 1.062889098 1.025632854 1.048800514 1.023700445 1.007397409 1.102489624 1.034432184 1.03167125 1 22.12437579 GDGPVQGIINFEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDGPVQGIINFEQK 14 0 P00441 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ; 180.48 4.07E-06 98668000 212783 199918 211088 202438 216112 156846 228630 186660 228650 FALSE TRUE 199465.2919 214720.1367 216095.107 207632.9018 199139.4353 202124.894 194349.054 209964.9119 190486.8379 1.047134249 1.127217708 1.134435898 1.090011804 1.045423597 1.06109638 1.020275501 1.102254173 1 17.53933179 2.865363858 3.338133056 1.045845729 1.112703374 0.357037899 0.035302399 0.223150958 4.636527004 0.010497034 0.011269848 733.4387604 -2.865363858 0.066857645 GDHRYPSSNPESPVVIFYSEIGSEEFSNFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GDHRYPSSNPESPVVIFYSEIGSEEFSNFHR 31 1 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ;; 152.49 5.18E-09 388435000 88170 111585 111939 105776 113970 91773 125654 92487 100046 FALSE TRUE 82651.59709 119846.8695 114594.2459 108490.3912 105019.2559 118266.3753 106813.3492 104034.2055 83347.67628 0.991648487 1.437914947 1.374894311 1.301660659 1.260014203 1.41895228 1.281539618 1.248195633 1 16.34685436 0.742655923 1.767614535 1.000355902 1.321801618 0.339530051 0.124731025 0.926957077 4.613585654 0.108710976 0.030684938 5.529118815 -0.742655923 0.321445716 GDHSPVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDHSPVTR 8 0 Q9H3U1;A0A1W2PNX8;Q9H3U1-3;Q9H3U1-2 Q9H3U1;Q9H3U1-2 UNC45A Protein unc-45 homolog A 0 ; 99.802 0.0065549 163354000 85746 124844 99274 113326 124111 96212 114917 102712 118171 FALSE TRUE 80379.31092 134087.5797 101628.8262 116234.137 114363.8227 123986.8425 97686.26269 115535.8193 98447.49669 0.816468815 1.362021221 1.032314986 1.180671332 1.161673243 1.259420978 0.992267614 1.173578031 1 16.5870669 0.672239768 0.815851781 1.002677217 1.143916824 0.039212774 0.151742394 3.095468551 3.740543379 0.133745707 0.045989401 4.701536018 -0.672239768 0.141239607 GDHWTTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDHWTTR 7 0 O75821;K7ENA8;K7ER90;K7EL20 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 89.296 0.017977 121600000 209770 238500 240790 235490 257540 227050 268170 201770 202730 FALSE TRUE 196640.8702 256158.7882 246501.6525 241533.0721 237313.8473 292595.6492 227960.3981 226961.4287 168893.0533 1.164292233 1.516692268 1.45951327 1.430094769 1.405113133 1.73243152 1.349732233 1.343817429 1 17.36575046 0.811966924 1.837342561 1.001604695 1.457214529 0.48586231 0.140483599 0.518287905 3.137468697 0.1210073 0.034012975 6.485850349 -0.811966924 0.455609835 GDIDHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GDIDHVK 7 0 P42704;B8ZZ38;A0A0C4DG06;C9JCA9 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ;; 117.16 0.0052935 967460000 1645640 1312300 1347610 1286900 1671950 1380720 1375250 1430680 1849020 FALSE TRUE 1542642.33 1409464.057 1379575.946 1319924.033 1540641.791 1779311.45 1169044.03 1609303.547 1540406.617 1.001451379 0.914994809 0.895592067 0.856867283 1.00015267 1.155092058 0.758919117 1.044726457 1 20.55487979 2.719552292 24.23315702 0.972589265 0.913248727 0.09727136 0.103789559 1621.208317 2066827.585 0.032888012 0.031059855 524.266722 -2.719552292 -0.059340538 GDIFLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GDIFLVR 7 0 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 119.57 0.011058 180305000 292985 400714 339395 329176 378899 286148 370135 351670 408963 FALSE TRUE 274647.5918 430383.2815 347445.6097 337623.2135 349141.8009 368754.2824 314636.6929 395576.7736 340704.4333 0.806116871 1.263215971 1.019785995 0.990956326 1.024764479 1.082328982 0.923488696 1.161055551 1 18.37816119 3.691008706 22.76797441 1.021349014 1.089571749 0 0.126800677 330.2588413 208218.2796 0.030620002 0.047439795 4909.177172 -3.691008706 0.068222735 GDKHDDLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDKHDDLQR 9 1 Q9BY42;A2A2L6;A2A2L5;A0A0A0MQR2 Q9BY42 RTFDC1 Protein RTF2 homolog 0 87.568 0.0080351 256980000 317370 327810 336260 277000 356230 203280 375390 352900 378680 FALSE TRUE 297506.3782 352081.3935 344236.246 284108.289 328253.1328 261963.636 319103.7544 396960.3418 315475.8616 0.943040069 1.11603275 1.091165087 0.900570609 1.040501581 0.830376165 1.011499748 1.258290697 1 18.2671701 -2.041250734 8.112854247 0.945289306 1.025316929 0.003856069 0.119068903 0.177464484 0.000902339 0.173640055 0.026134776 0.009093881 2.041250734 0.080027622 GDKSELNEIKENQRS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_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 171.29 9.73E-12 5492090000 1782070 1519080 1456530 1636680 1952600 1029560 1820530 1390460 2940770 TRUE FALSE 1670533.42 1631554.264 1491079.579 1678679.98 1799250.672 1326777.258 1547558.427 1564061.992 2449936.489 0.681868051 0.665957779 0.608619687 0.685193264 0.734407068 0.541555777 0.631672876 0.638409199 1 21.22431292 -1.837578158 3.078713396 1.112441532 0.644386102 0.822422601 0.051305073 8445829.617 17423337.51 7339932.644 0.011922861 0.014535228 1.837578158 -0.46805543 GDKVDILYNNIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDKVDILYNNIK 12 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 197.56 1.76E-07 702290000 1488180 1387140 1307390 1387920 1790910 963020 1579310 1536000 1743720 FALSE TRUE 1395037.47 1489845.289 1338401.908 1423536.377 1650259.153 1241028.241 1342507.127 1727772.981 1452681.867 0.960318637 1.025582629 0.921331737 0.97993677 1.13600864 0.85430146 0.924157696 1.189367762 1 20.47028736 1.253005492 24.9997197 1.094683945 0.969665308 0.260834531 0.08604632 264.0014732 456911.4006 0.054616828 0.019745206 17.90628499 -1.253005492 -0.125018637 GDLAGR ddPTM_SK-BR-3_Pertuzumab_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" 0 132.01 0.065311 0 299730 356680 294180 323980 358440 286620 319630 306330 318400 FALSE TRUE 280970.4343 383088.9583 301158.0885 332293.8753 330289.5683 369362.5411 271704.4488 344575.9748 265256.9831 1.059238596 1.444218184 1.13534462 1.252724326 1.245168231 1.392470565 1.024306488 1.299026969 1 18.01703121 0.107073316 0.450387783 0.972861033 1.259957463 0.206806985 0.134699068 5.129489235 1.448792172 0.393525808 0.072002264 1.279597303 -0.107073316 0.28709643 GDLEEYGQDLLHTVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GDLEEYGQDLLHTVFK 16 0 P43490 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;; 218.98 1.28E-14 108678000 289210 265607 290756 266483 255727 256544 349016 252590 197369 FALSE TRUE 271108.8624 285272.8186 297652.8696 273321.4049 235643.233 330604.0882 296684.2909 284126.4175 164426.8388 1.648811497 1.734952886 1.810245041 1.662267589 1.433119037 2.010645528 1.804354405 1.727980782 1 17.32708628 0.915995168 19.6864101 1 1.744088318 0.710773071 0.145914402 3271.58878 766694.8653 0.135724239 0.03393106 8.241289447 -0.915995168 0.744088318 GDLGIEIPAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GDLGIEIPAEK 11 0 P14618;P14618-3;B4DNK4;P30613;P30613-2;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM;PKLR Pyruvate kinase PKM;Pyruvate kinase;Pyruvate kinase PKLR 0 ;;;;; 205.18 7.14E-08 1204548000 4143320 3664040 3840740 3749840 4054160 3067630 4638960 3435250 4356160 FALSE TRUE 3883996.997 3935329.334 3931844.167 3846067.243 3735762.627 3953204.982 3943391.014 3864148.524 3629088.754 1.070240289 1.084384979 1.083424637 1.059788697 1.029394121 1.089310637 1.086606386 1.064771017 1 21.79117591 -2.454620662 1.321578682 0.706722486 1.07352493 0.607610855 0.017825641 55474.9647 4678.163435 48074.07959 0.005171527 0.003510584 2.454620662 0.366802444 GDLGPAS(ph)PSQELGSQPVPGGDGAPALGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDLGPASPSQELGSQPVPGGDGAPALGK 28 0 H3BLU1;Q4KMQ1;Q4KMQ1-2;Q4KMQ1-4;Q4KMQ1-3 H3BLU1 TPRN Taperin 1 GDLGPAS(0.498)PS(0.498)QELGS(0.005)QPVPGGDGAPALGK;GDLGPAS(0.854)PS(0.146)QELGSQPVPGGDGAPALGK 143.47 7.09E-08 145591000 103867 100909 104156 125994 114386 69455 98503 69260 79986 TRUE FALSE 97366.14988 108380.4074 106626.6295 129227.2193 105402.585 89505.53099 83733.38961 77907.26346 66635.81987 1.461168334 1.626458676 1.60013983 1.939305611 1.581770663 1.343204468 1.256582267 1.16914992 1 16.02401028 1.881663921 1.446471905 1.099611437 1.650021244 0.764762013 0.129357191 0.197384347 0.771969757 0.094120787 0.04076997 76.14895033 -1.881663921 0.550409807 GDLS(ph)DVEEEEEEEMDVDEATGAVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDLSDVEEEEEEEMDVDEATGAVKK 25 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 GDLS(1)DVEEEEEEEMDVDEATGAVKK;GDLS(1)DVEEEEEEEMDVDEATGAVKK 304.59 8.92E-64 152290000 154810 112857 128794 125795 133772 87052 167974 112463 180792 TRUE FALSE 145120.7184 121213.0497 131849.0545 129023.1127 123266.0867 112182.4992 142787.8581 126504.2531 150616.6472 0.963510482 0.804778568 0.875394964 0.856632484 0.818409445 0.744821381 0.948021754 0.839908838 1 17.20052171 0.405210648 0.958364318 0.999989203 0.849211548 0.319074015 0.064729193 2.491874769 3.007822149 0.059336573 0.018412425 2.542205464 -0.405210648 -0.150777655 GDLSSIR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 185.22 0.0014344 3446510000 3197950 6093020 3591840 3628040 6335370 3044050 3687480 5275880 4653020 FALSE TRUE 2997796.018 6544153.541 3677040.141 3721141.649 5837815.596 3922817.819 3134576.607 5934585.232 3876400.902 0.773345197 1.688203492 0.948570654 0.959947576 1.505988607 1.01197423 0.808630657 1.530952391 1 21.88628635 3.751573489 23.58305214 1.088602552 1.302801247 0.010130592 0.320937988 537.0778361 517980.5834 0.076190579 0.137244814 5643.824349 -3.751573489 0.214198695 GDLSYLDQGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDLSYLDQGHR 11 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 0 130.56 0.001211 0 143970 164300 158490 161410 195750 144290 169630 159820 215020 FALSE TRUE 134959.1747 176464.943 162249.4576 165552.0539 180376.5846 185944.1806 144195.5563 179773.8788 179131.7729 0.75340724 0.985112468 0.905754769 0.924191455 1.00694914 1.038030147 0.804969179 1.003584545 1 17.45066173 4.745733076 24.25072229 0.946878622 0.7534071 0.465175202 0.068117962 537.7956844 1818264.814 0.015691518 0.15776028 55684.33995 -4.745733076 -0.193471522 GDMEQNDSDNRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GDMEQNDSDNRR 12 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ;;;;;; 168.76 7.32E-05 2131371000 1703510 1511612 1615102 1654384 1651588 1363585 1842545 1395057 2226333 FALSE TRUE 1596890.35 1623533.325 1653412.982 1696838.294 1521878.941 1757229.854 1566272.483 1569232.937 1854743.64 0.860976318 0.875341093 0.891450951 0.914864059 0.820533312 0.947424655 0.844468448 0.846064601 1 20.82278836 -1.157599323 4.027377647 1.000044063 0.876984776 0.534088778 0.036613592 6838728.915 17341591.43 4476.945155 0.007780943 0.069566584 1.157599323 -0.123059287 GDMS(ph)DEDDENEFFDAPEIITMPENLGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 29 GDMSDEDDENEFFDAPEIITMPENLGHK 28 0 P22059 P22059 OSBP Oxysterol-binding protein 1 1 GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(0.999)DEDDENEFFDAPEIIT(0.001)MPENLGHK;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 271.58 1.27E-61 4416489800 3358765 2952563 3134687 3258626 3326098.6 2525506.7 3926518 3026879.3 3147725.7 TRUE FALSE 3148545.894 3171173.837 3209043.256 3342247.86 3064880.233 3254579.486 3337773.078 3404791.844 2622349.946 1.200658173 1.209287053 1.223728077 1.274523969 1.168753331 1.241092743 1.272817567 1.298374326 1 21.32242879 -0.879714977 5.559879937 0.999999861 1.234825318 0.787092898 0.038593903 6.57E-08 1.33E-08 0.037034127 0.008729022 0.131912218 0.879714977 0.234825456 GDMS(ph)DEDDENEFFDAPEIITMPENLGHKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 214.99 1.36E-34 652623000 195936 302994 229238 282664 361737 167023.4 333540 232061 705535 TRUE FALSE 183672.7155 325427.991 234675.6336 289917.6368 333327.6352 215240.3442 283528.7734 261034.3267 587776.6506 0.312487261 0.55365927 0.399259878 0.493244562 0.567099144 0.366194104 0.48237502 0.444104621 1 19.16490852 -1.715696939 2.421296273 1.110831704 0.459155582 0.82558647 0.079057943 3564438.138 2571239.938 2389139.303 0.018057422 0.019244342 1.715696939 -0.651676122 GDMVTLPAGIYHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDMVTLPAGIYHR 13 0 Q9BV57;Q9BV57-2;A0A0G2JQN5 Q9BV57 ADI1 "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase" 0 85.554 0.0092319 131690000 27647 32270 35137 33178 32077 31450 33554 28291 37954 FALSE TRUE 25916.62362 34659.30438 35970.46623 34029.40365 29557.80181 40529.10445 28522.8892 31823.19363 31619.23221 0.819647468 1.096146299 1.137613526 1.076224857 0.93480454 1.281786483 0.902074061 1.006450549 1 14.94851472 1.622280525 25 0.965690437 1.069106058 0.096531559 0.123766466 1.611651907 2788.660203 0.052700894 0.029055887 41.90641646 -1.622280525 0.103415621 GDNIYEWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GDNIYEWR 8 0 R4GN77;R4GND1;A0A1B0GX65;Q969T4;A0A087X283;H7C061;B7Z306;P51965-2;C9J180;Q96LR5;C9J2P0;P51965-3;P51965 R4GN77;C9J180;C9J2P0 UBE2E3;UBE2E2;UBE2E1 Ubiquitin-conjugating enzyme E2 E3;Ubiquitin-conjugating enzyme E2 E1;Ubiquitin-conjugating enzyme E2 E2 0 ;;; 105.94 0.0099854 1156950000 1537010 1970300 1847920 1821450 1961200 1606670 1986670 1750490 2160310 FALSE TRUE 1440811.288 2116183.062 1891753.535 1868191.491 1807175.263 2070489.547 1688787.277 1969042.53 1799740.305 0.800566217 1.175826899 1.051125837 1.038033924 1.004131128 1.15043795 0.938350534 1.094070364 1 20.77935732 1.714488449 24.99999398 1.007997468 1.053218304 0 0.107126771 3.339005087 3452.722917 0.045175501 0.025052121 51.81893091 -1.714488449 0.045220836 GDNPFPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDNPFPK 7 0 P14550;Q5T621;V9GYP9 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 77.058 0.090912 51814000 177700 216790 189610 201640 240600 155650 222680 185480 261180 FALSE TRUE 166578.0742 232841.3572 194107.6387 206814.4238 221704.2465 200583.6282 189291.2013 208637.5863 217587.3707 0.765568671 1.07010511 0.892090557 0.950489098 1.018920564 0.921853266 0.869954909 0.958868089 1 17.7312353 2.052412049 24.99984988 0.920343352 0.952890491 0 0.086448078 400.9201549 191231.589 0.029662075 0.021906891 112.8267424 -2.052412049 0.032547138 GDNRLDLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDNRLDLLK 9 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 143.89 9.20E-05 256270000 559280 1235390 440650 469340 1393620 287430 584330 1133150 1333050 FALSE TRUE 524275.6631 1326859.561 451102.4261 481384.059 1284170.707 370406.375 496715.1412 1274626.272 1110555.343 0.472084229 1.194771219 0.406195359 0.433462467 1.156332023 0.333532568 0.447267346 1.147737733 1 20.08284986 1.227300436 24.99951494 1.073869139 0.652963424 0.260667052 0.306229482 355.0826956 788318.5138 0.277018067 0.071772541 16.8772015 -1.227300436 -0.420905715 GDPESPWWEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDPESPWWEGR 11 0 P52735-3;P52735-2;P52735 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 0 166.19 4.82E-05 90115000 36815 45939 43356 46380 54799 41005 42465 42379 44339 FALSE TRUE 34510.81487 49340.37136 44384.42479 47570.18932 50495.30759 52842.47784 36097.76748 47670.11144 36938.53446 0.934276776 1.335742527 1.201575142 1.287820159 1.36700896 1.430551553 0.977238756 1.290525251 1 15.17283901 1.020336799 1.032793813 1.020167361 1.252131351 0.135058916 0.162730282 0.955780555 2.165215619 0.142211993 0.046855007 10.4794092 -1.020336799 0.231963991 GDPIVQHRPMLEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GDPIVQHRPMLEER 14 1 P40763;P40763-2;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 ;; 133.14 2.78E-05 778320000 752950 922930 801530 868520 1001200 673020 905060 823630 1014060 FALSE TRUE 705824.2036 991264.6975 820542.6701 890807.6936 922569.7906 867309.9484 769354.6552 926462.0185 844806.8349 0.835485906 1.173362545 0.971278446 1.054451333 1.092048209 1.026636993 0.910687063 1.096655449 1 19.68826198 1.981968649 24.5079475 0.986558389 1.041122454 0 0.097457459 1685.103 2290364.308 0.035969254 0.023729 95.93313763 -1.981968649 0.054564065 GDPPRLS(ph)PDPVAGSAVSQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GDPPRLSPDPVAGSAVSQELR 21 1 Q9BUR4;E9PMG4;E9PMR3 Q9BUR4 WRAP53 Telomerase Cajal body protein 1 1 GDPPRLS(1)PDPVAGSAVSQELR;GDPPRLS(1)PDPVAGSAVSQELR;GDPPRLS(1)PDPVAGSAVSQELR 130.57 8.87E-06 1313700000 536517 545215 590450 531846 533701 546372 570872 494811 514085 TRUE FALSE 502937.3587 585583.2859 604455.7528 545494.0688 491786.2763 704100.7268 485275.0433 556589.2426 428280.8924 1.174316594 1.367287909 1.411353538 1.273682946 1.148279751 1.644016204 1.133076567 1.299589247 1 18.70819779 0.65670058 1.078291031 1.001792661 1.332123118 0.289517796 0.15020316 1.304774628 2.481081871 0.129231318 0.040669645 4.536287591 -0.65670058 0.330330457 GDQCCYSHS(ph)PPTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GDQCCYSHSPPTPR 14 0 Q9NXH9-2;Q9NXH9 Q9NXH9-2 TRMT1 tRNA (guanine(26)-N(2))-dimethyltransferase 1 GDQCCYS(0.002)HS(0.952)PPT(0.046)PR;GDQCCYSHS(0.974)PPT(0.026)PR;GDQCCYSHS(0.994)PPT(0.006)PR;GDQCCYS(0.001)HS(0.998)PPT(0.001)PR 149.74 3.21E-07 797950000 538300 600320 578440 577370 642530 550490 659510 555540 733940 TRUE FALSE 504608.7639 644768.3174 592160.87 592186.2917 592068.2856 709407.5265 560622.5981 624900.3919 611440.6726 0.825278374 1.054506752 0.968468237 0.968509813 0.968316817 1.160222992 0.916887972 1.022013124 1 19.221853 GDQENVHPDVMLVQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GDQENVHPDVMLVQPR 16 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;;;; 149.57 8.23E-07 1879770000 1776380 1924950 1977990 1910620 1780090 1912690 2158130 1837282 1469807 FALSE TRUE 1665199.547 2067475.301 2024908.857 1959649.744 1640288.912 2464852.553 1834538.442 2066670.702 1224486.716 1.359916383 1.688442409 1.653679725 1.600384649 1.339572647 2.012967981 1.498210162 1.687785318 1 20.22374569 -1.244723373 5.389630863 0.999947466 1.618171636 0.498609669 0.190300735 0.000104907 1.47E-05 0.160910129 0.037923675 0.056921538 1.244723373 0.618224171 GDQPAASGDS(ph)DDDEPPPLPR ddPTM_SK-BR-3_Pertuzumab_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 287.26 2.23E-45 264830000 198097 191234 168449 196085 229885 192846 230371 249805 213996 TRUE FALSE 185698.4624 205393.1643 172444.6898 201116.8731 211830.7594 248517.5096 195829.0072 280993.7041 178278.6851 1.041618981 1.152090415 0.96727598 1.128103861 1.188200144 1.393983299 1.098443188 1.576148623 1 17.4437747 2.724458057 2.764107317 1.261855985 1.062951625 0.247100826 0.160804875 0.360430362 5.512304103 0.049013048 0.048479871 530.2223831 -2.724458057 -0.19890436 GDQVLNFS(ph)DAEDLIDDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GDQVLNFSDAEDLIDDSK 18 0 F8W126;Q96EZ8-4;Q96EZ8-3;Q96EZ8;Q96EZ8-2 F8W126 MCRS1 Microspherule protein 1 1 GDQVLNFS(1)DAEDLIDDSK;GDQVLNFS(1)DAEDLIDDSK;GDQVLNFS(1)DAEDLIDDSK;GDQVLNFS(1)DAEDLIDDSK 276.79 4.30E-39 169291000 248800 174061 217894 196153 209622 172524 269608 193297 220856 TRUE FALSE 233228.0521 186948.6576 223062.5486 201186.6181 193159.1337 222328.8781 229182.7833 217430.5559 183993.7068 1.267587116 1.016060064 1.212337924 1.093442931 1.049813806 1.208350448 1.245601207 1.181728222 1 17.4892969 2.200469196 24.99846539 1.187515591 1.122561768 0 0.097512702 384.8673548 252577.0145 0.033183999 0.024508584 158.660638 -2.200469196 -0.064953822 GDQVLNFS(ph)DAEDLIDDSKLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDQVLNFSDAEDLIDDSKLK 20 1 F8W126;Q96EZ8-4;Q96EZ8-3;Q96EZ8;Q96EZ8-2 F8W126 MCRS1 Microspherule protein 1 1 GDQVLNFS(1)DAEDLIDDSKLK 147.28 7.49E-08 25279000 56748 39886 44982 51529 56358 36444 69182 39965 119060 TRUE FALSE 53196.24398 42839.20094 46048.99428 52851.32138 51931.87002 46964.79118 58808.80135 44954.71822 99188.11684 0.536316705 0.431898521 0.464259185 0.532839246 0.523569473 0.473492115 0.592901682 0.453226855 1 16.59787967 -5 0.306216846 5.351214036 0.473357663 0.905963641 0.05024903 74.66992122 0.682190165 209.1265743 0.045387538 1.00E-05 5 -4.877856372 GDREEEVERPVS(ph)SPGDPEQK ddPTM_SK-BR-3_Pertuzumab_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 98.121 0.00044068 299760000 373720 266960 291170 333970 367530 277250 389480 303140 265650 TRUE FALSE 350329.5323 286725.9962 298076.6899 342540.2356 338665.6763 357287.5742 331081.0898 340987.6963 221311.2988 1.582971742 1.295577757 1.346866118 1.547775633 1.530268351 1.614411809 1.495997229 1.54076045 1 17.75571758 -1.16577266 5.022264561 0.999969436 1.473079824 0.695663944 0.101895215 3.98E-05 6.62E-06 0.112706624 0.026563493 0.068269597 1.16577266 0.473110388 GDREEEVERPVSS(ph)PGDPEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDREEEVERPVSSPGDPEQK 20 2 O43149 O43149 ZZEF1 Zinc finger ZZ-type and EF-hand domain-containing protein 1 1 GDREEEVERPVS(0.181)S(0.819)PGDPEQK 131.94 7.02E-06 231510000 397630 326040 356120 388190 377760 311940 467520 343080 335970 TRUE FALSE 372743.0481 350180.3408 364567.3346 398151.6126 348092.2534 401992.0141 397419.7162 385914.2932 279894.4366 1.331727249 1.25111576 1.30251726 1.422506347 1.243655493 1.43622724 1.419891446 1.378785152 1 18.09452329 -1.035471016 5.099721786 0.999995851 1.344178006 0.718504181 0.068471053 3.46E-06 6.55E-07 0.071108462 0.016760224 0.092157139 1.035471016 0.344182155 GDRS(ph)PEPGQTWTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GDRSPEPGQTWTR 13 1 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GDRS(0.998)PEPGQT(0.001)WT(0.001)R;GDRS(0.97)PEPGQT(0.027)WT(0.003)R;GDRS(0.997)PEPGQT(0.002)WT(0.002)R 132.21 0.0003196 614890000 641120 581940 657820 674500 703020 483810 623040 495690 728520 TRUE FALSE 600993.4436 625027.4431 673423.801 691808.8119 647807.645 623478.093 529620.936 557577.9876 606925.3056 0.990226372 1.029825973 1.109566193 1.139858242 1.067359754 1.027273187 0.872629517 0.918692931 1 19.21115945 1.91836977 4.621656625 0.920290533 1.069904979 0.600084698 0.050758165 0.140388093 5.176828962 0.023520655 0.01383291 82.86473963 -1.91836977 0.149614447 GDRWEDLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GDRWEDLSR 9 1 Q9NR50-3;Q9NR50-2;Q9NR50;H0Y580 Q9NR50-3 EIF2B3 Translation initiation factor eIF-2B subunit gamma 0 ;; 184.71 3.99E-05 1126800000 914430 1250650 924330 933040 1238730 775540 952280 1018540 1174220 FALSE TRUE 857197.4586 1343249.427 946255.5441 956983.386 1141445.143 999425.8082 809494.4545 1145706.961 978235.0962 0.876269377 1.373135591 0.96730893 0.978275457 1.166841332 1.021662187 0.827505022 1.171197972 1 19.8998217 3.73426274 24.41953137 1.005567127 1.163201762 0.057953942 0.154218474 368.4252105 1259776.285 0.037091203 0.065096365 5423.288903 -3.73426274 0.157634635 GDS(ph)ES(ph)EEDEDLEVPVPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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;GDS(1)ES(1)EEDEDLEVPVPSR;GDS(1)ES(1)EEDEDLEVPVPSR;GDS(1)ES(1)EEDEDLEVPVPSR 360.92 7.27E-91 1903618000 1265319 1078698 1166379 1078655 1029812 1083164 1312876 1022588 839202 TRUE FALSE 1186124.942 1158565.922 1194046.061 1106335.113 948934.7196 1395855.863 1116022.432 1150260.363 699133.7647 1.696563665 1.657144857 1.707893569 1.582436966 1.357300659 1.996550494 1.596293139 1.645265071 1 19.41520899 0.378708563 2.252655587 1.000005762 1.661466358 0.635620744 0.155844905 8.559847579 30.07854928 0.136250926 0.036815344 2.391710241 -0.378708563 0.661460596 GDS(ph)ES(ph)EEDEQDSEEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDSESEEDEQDSEEVR 16 0 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 2 GDS(1)ES(1)EEDEQDSEEVR 229.69 8.24E-14 0 208340 224410 219260 211190 221170 203560 231740 191910 198360 TRUE FALSE 195300.3713 241025.5499 224460.9507 216609.4929 203800.2004 262324.4675 196992.7384 215870.3859 165252.4345 1.181830524 1.458529495 1.35829134 1.310779436 1.233265948 1.587416659 1.192071626 1.306306842 1 17.334312 0.622436229 1.052408571 1.000949801 1.355839721 0.417891063 0.122177406 1.085503186 1.91065667 0.105029058 0.033194436 4.192144359 -0.622436229 0.35488992 GDS(ph)ETDLEALFNAVMNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GDSETDLEALFNAVMNPK 18 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 1 GDS(0.981)ET(0.019)DLEALFNAVMNPK;GDS(0.5)ET(0.5)DLEALFNAVMNPK;GDS(0.863)ET(0.137)DLEALFNAVMNPK 164.02 1.06E-10 199572500 101215 95182 94324 106590 109283 77612 126236 84064 104412 TRUE FALSE 94880.13382 102229.3743 96561.40982 109325.2799 100700.354 100017.3245 107308.0837 94559.57545 86984.96267 1.090764782 1.175253414 1.110093134 1.256829646 1.157675429 1.149823158 1.233639475 1.087079566 1 16.4084784 -0.820010791 7.53527731 1.000010162 1.162857167 0.439325533 0.055692574 0 0 0.049234146 0.0116046 0.151352364 0.820010791 0.162847005 GDS(ph)IGSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDSIGSSK 8 0 A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5;H0YIX9;H7C0E9;Q9Y2K5-3;Q9Y2K5-2 A0A0U1RRA6 R3HDM2 R3H domain-containing protein 2 1 GDS(0.957)IGS(0.037)S(0.006)K 67.207 0.062616 107980000 282140 289480 238330 315220 220750 184360 381400 265300 217540 TRUE FALSE 264481.361 310913.4004 243983.3001 323309.0789 203413.1855 237581.7392 324212.6107 298423.289 181231.1686 1.459359132 1.71556252 1.346254631 1.783959577 1.122396258 1.310932004 1.788945098 1.6466444 1 17.46747157 3.979025019 24.66909983 1.472131275 1.596404512 0.038305848 0.268347917 287.7163997 3728106.417 0.063924947 0.127970147 9528.510551 -3.979025019 0.124273237 GDS(ph)LILEHQWELEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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;GDS(1)LILEHQWELEK;GDS(1)LILEHQWELEK;GDS(1)LILEHQWELEK 271.31 3.82E-33 993127000 2217964 1635759 2009860 1935520 1813273 1796588 2515637 1746247 1812823 TRUE FALSE 2079145.592 1756872.298 2057534.828 1985188.72 1670865.853 2315233.79 2138440.586 1964269.782 1510251.13 1.376688652 1.163298119 1.362379268 1.314475904 1.106349679 1.533012454 1.41595033 1.300624607 1 20.52635704 2.242939139 24.99805702 1.361081714 1.266412896 0 0.15865375 288.1422666 1645082.282 0.05080206 0.041127131 174.9601485 -2.242939139 -0.094668818 GDS(ph)LILEHQWELEKLELLHEVEK ddPTM_SK-BR-3_Pertuzumab_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 245.28 8.40E-38 75344000 117393 103009 103104 137957 158850 80069 115974 101916 229092 TRUE FALSE 110045.5817 110635.8935 105549.6756 141497.2102 146374.5618 103183.6205 98584.77535 114640.4369 190855.0652 0.576592408 0.579685393 0.553035758 0.741385669 0.766940933 0.540638627 0.51654262 0.600667511 1 17.54211795 -1.173163109 3.692411364 1.000352214 0.600979758 0.687492353 0.082579612 27438205.9 43176520.79 111309.262 0.02113018 0.067117673 1.173163109 -0.399372456 GDS(ph)LKEPTSIAESSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GDSLKEPTSIAESSR 15 1 Q9C0B5;Q9C0B5-2;H0YEF4 Q9C0B5 ZDHHC5 Palmitoyltransferase ZDHHC5;Palmitoyltransferase 1 GDS(1)LKEPTSIAESSR;GDS(1)LKEPTSIAESSR;GDS(1)LKEPTSIAESSR;GDS(1)LKEPTSIAESSR 170.38 6.93E-07 458934000 542439 384673 371775 367061 547111 315937 494579 455682 526695 TRUE FALSE 508488.7113 413154.5892 380593.6786 376480.4067 504143.109 407142.8831 420421.4704 512574.9008 438786.2019 1.158853011 0.94158519 0.867378411 0.858004206 1.148949322 0.927884426 0.958146515 1.168165495 1 18.74315863 2.760169115 24.98853432 1.022035039 0.939130749 0.103584523 0.111008906 1783.723467 2062733.017 0.032975124 0.034951997 575.6640588 -2.760169115 -0.08290429 GDS(ph)PELKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDSPELKPR 9 1 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 GDS(1)PELKPR;GDS(1)PELKPR 131.43 0.00025539 344610000 1217560 965540 1064610 899910 1079240 1077840 1285810 1193170 1597990 TRUE FALSE 1141355.093 1037029.586 1089863.052 923003.2141 994480.8438 1388994.911 1093014.727 1342139.901 1331275.146 0.857339744 0.778974647 0.818661007 0.693322652 0.747013754 1.043356751 0.821028419 1.008161164 1 20.34437735 2.254026737 24.98057861 0.942277757 0.780552935 0.611935561 0.07354199 171.5971197 277159.9286 0.024099305 0.020095333 179.4844122 -2.254026737 -0.161724823 GDS(ph)PENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GDSPENR 7 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 GDS(1)PENR;GDS(1)PENR;GDS(1)PENR 152.38 0.0019065 321365000 814198 801812 965596 980509 830529 796017 929997 770986 671358 TRUE FALSE 763238.8006 861178.9948 988500.3931 1005670.521 765302.6025 1025814.186 790552.5835 867245.2992 559304.0127 1.364622429 1.539733267 1.767375829 1.798074926 1.368312376 1.834090517 1.413457736 1.550579434 1 19.09327316 0.339701186 0.852664961 0.994925744 1.614947525 0.530346634 0.172040567 1.820149028 1.728933223 0.174418031 0.051894372 2.186256866 -0.339701186 0.620021781 GDS(ph)RS(ph)PSHKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GDSRSPSHKR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GDS(1)RS(0.985)PS(0.015)HKR;GDS(1)RS(0.99)PS(0.01)HKR;GDS(1)RS(0.993)PS(0.007)HKR 97.273 0.0033097 1385205000 299719 223659 267866 225355 227641 171443 294791 215867 231675 TRUE FALSE 280960.1228 240218.9451 274219.908 231137.9908 209762.9941 220935.811 250589.8263 242818.4701 193006.9458 1.455699543 1.244612954 1.420777407 1.197563071 1.086815779 1.144703938 1.298346156 1.258081512 1 17.55829324 7.999999858 0.028234953 1.56E-06 3.021992407 0.494542044 0.099021847 1428.93418 3.096159344 108.4423794 250.0085934 99999967.23 -7.999999858 3.021990847 GDS(ph)RSPSHKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDSRSPSHKR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GDS(0.996)RS(0.004)PSHKR;GDS(0.989)RS(0.011)PSHKR 72.705 0.024621 274310000 96274 179201 131016 179427 148559 89997 147745 95637 193530 TRUE FALSE 90248.38219 192469.2285 134123.7614 184031.4006 136891.7754 115977.6729 125592.0088 107577.49 161228.5927 0.559754202 1.193766101 0.831885704 1.141431538 0.849053962 0.71933688 0.778968586 0.667235806 1 17.29874809 2.484529174 23.56332125 0.77325648 0.962397678 0.094411829 0.191581887 256.6952498 816511.5183 0.057819313 0.050365957 305.1611015 -2.484529174 0.189141198 GDSEPLSEAAQAHTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDSEPLSEAAQAHTR 15 0 H3BP71;O75150-4;O75150;O75150-3;H3BS50 H3BP71 RNF40 E3 ubiquitin-protein ligase BRE1B 0 164.63 3.84E-09 0 197200 279720 248790 248220 270240 265280 254780 242760 261140 FALSE TRUE 184857.604 300430.7598 254691.4163 254589.7454 249016.4405 341862.0295 216578.1043 273069.1204 217554.047 0.849708873 1.380947696 1.170704107 1.170236771 1.144618746 1.571388969 0.995514022 1.255178307 1 17.73101433 -1.053033463 7.876168124 0.999999999 1.206404775 0.083294165 0.195551813 2.12E-08 2.84E-09 0.166553355 0.039257 0.088504741 1.053033463 0.206404777 GDSFFIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDSFFIR 7 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 0 ; 109.11 0.016523 66764000 164440 243050 173897 183914 272890 152100 184618 209700 260460 FALSE TRUE 154147.9939 261045.6749 178021.919 188633.5446 251458.3202 196008.8009 156936.2448 235881.5066 216987.5434 0.710400199 1.20304452 0.820424602 0.86932891 1.158860625 0.903318217 0.723250019 1.087073953 1 17.7272527 2.020601946 24.99024125 0.882839403 0.970337135 0 0.173475775 747.2809127 906450.9065 0.060948552 0.04500916 104.8580907 -2.020601946 0.087497733 GDSGAAPDVDDKLCLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDSGAAPDVDDKLCLR 16 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 0 ; 132.44 3.57E-05 369020000 348120 251990 292800 296260 287900 236240 413180 268990 318990 FALSE TRUE 326331.7906 270647.6018 299745.3543 303862.5332 265289.4953 304438.653 351227.4948 302573.9936 265748.5082 1.227972239 1.018435075 1.127928643 1.143421407 0.998272755 1.14558932 1.321653683 1.138572689 1 18.01970207 1.998728866 24.99504856 1.200266446 1.094769371 0 0.102737916 73.58724102 1447000.1 0.035198464 0.025655671 99.70773842 -1.998728866 -0.105497075 GDSIEEILADS(ph)EDEEDNEEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDSIEEILADSEDEEDNEEEER 22 0 Q5JTH9-2;Q5JTH9-3;Q5JTH9 Q5JTH9-2 RRP12 RRP12-like protein 1 GDSIEEILADS(1)EDEEDNEEEER 106.49 0.00031229 31765000 42768 52630 49204 46670 41993 41366 54167 40331 41263 TRUE FALSE 40091.22722 56526.77996 50371.14212 47867.63121 38695.03917 53307.69268 46045.16121 45366.41413 34375.93873 1.166258398 1.644370512 1.465302301 1.392474882 1.125643127 1.550726893 1.33945902 1.31971419 1 15.06911149 -2.796149695 0.216881619 0.289488993 1.47907733 0.342908096 0.159236906 50.33542566 1.183230236 16.83500822 0.322466303 0.001599007 2.796149695 1.189588336 GDT(ph)PGHATPGHGGATSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDTPGHATPGHGGATSSAR 19 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 GDT(0.991)PGHAT(0.009)PGHGGATSSAR;GDT(0.989)PGHAT(0.011)PGHGGATSSAR 248.7 2.42E-24 1065010000 305210 391020 384210 381850 321610 391710 408770 357200 268780 TRUE FALSE 286107.4509 419971.5277 393323.6426 391648.9175 296352.0479 504790.3181 347478.7333 401797.2063 223918.8816 1.277728117 1.875552096 1.756545227 1.749066066 1.323479493 2.254344584 1.55180631 1.79438734 1 17.77261666 -1.020247437 5.338828 0.999995758 1.721627719 0.37992815 0.278718139 1.22E-05 2.24E-06 0.234360064 0.055238872 0.095444864 1.020247437 0.72163196 GDTNIKPILQVINIRPITTGNS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDTNIKPILQVINIRPITTGNSPPR 25 2 P27694;I3L524;I3L2M5 P27694 RPA1 "Replication protein A 70 kDa DNA-binding subunit;Replication protein A 70 kDa DNA-binding subunit, N-terminally processed" 1 GDTNIKPILQVINIRPIT(0.114)T(0.365)GNS(0.521)PPR 121.19 9.66E-05 123370000 261400 273160 256640 280760 281750 250600 325670 237100 362310 TRUE FALSE 245039.4406 293385.0506 262727.622 287964.7769 259622.4915 322944.1518 276838.8069 266702.4569 301838.1204 0.811824034 0.971994691 0.870425583 0.954037139 0.86013818 1.069925003 0.917176421 0.883594347 1 18.2034155 GDTPGHAT(ph)PGHGGATSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDTPGHATPGHGGATSSAR 19 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 GDT(0.005)PGHAT(0.995)PGHGGATSSAR 114.63 0.0005657 15582000 9470.3 11470 10158 9765.9 10703 8828.2 9131.1 8564.8 7883 TRUE FALSE 8877.570828 12319.25073 10398.95256 10016.50953 9862.429554 11376.75803 7761.976324 9634.134133 6567.276374 1.351788827 1.87585386 1.583449815 1.525215166 1.501753389 1.732340377 1.181917112 1.466990817 1 12.68107945 1.086941787 0.501375236 0.989814956 1.664132744 0.49899913 0.177868134 0.684807791 0.448323135 0.18764466 0.09479787 12.21635901 -1.086941787 0.674317789 GDTPGHATPGHGGAT(ph)SSARK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDTPGHATPGHGGATSSARK 20 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 GDTPGHATPGHGGAT(0.333)S(0.333)S(0.333)ARK 163.64 1.47E-11 45852000 40918 48535 47839 47338 62002 42640 49866 42193 49931 TRUE FALSE 38357.01542 52128.5819 48973.76367 48552.77322 57132.61302 54949.4758 42389.05623 47460.88893 41597.19353 0.922105848 1.253175454 1.177333361 1.167212716 1.37347278 1.320989979 1.019036445 1.140963726 1 15.34419858 1.684636651 9.338636638 1.061368588 1.210378099 0.239323698 0.124186345 0.166373668 23.59713929 0.056628994 0.030317444 48.37674578 -1.684636651 0.14900951 GDTPGHATPGHGGATSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDTPGHATPGHGGATSSAR 19 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 50.226 0.084042 86731000 46156 69988 65564 65944 61244 60962 75803 67238 70302 FALSE TRUE 43267.17835 75169.98434 67119.20904 67636.23468 56434.14329 78560.73976 64437.04387 75632.81231 58568.14203 0.738749376 1.283461994 1.146002019 1.154829782 0.963563831 1.341356189 1.100206386 1.291364378 1 15.83782851 2.244125156 24.99967322 1.187141057 1.104683798 0.082259677 0.172314499 447.5006776 2010482.742 0.056235882 0.045796199 175.4386011 -2.244125156 -0.082457259 GDTSGDYKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDTSGDYKK 9 1 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 121.6 0.00097687 1232900000 4266500 3373900 2710400 2285200 2798500 1691200 3810400 2683000 6334100 FALSE TRUE 3999467.381 3623707.067 2774691.968 2343842.101 2578717.099 2179421.986 3239065.894 3017978.456 5276897.79 0.757920191 0.686711627 0.525818782 0.444170457 0.488680509 0.413011976 0.613820093 0.571922856 1 22.33125861 0.294447029 1.769911824 1.000019037 0.559731466 0.631429906 0.105040143 7.196143178 17.11012324 0.104840145 0.029334272 1.969912922 -0.294447029 -0.440287571 GDTVSAS(ph)PCSAPLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDTVSASPCSAPLAR 15 0 Q15477 Q15477 SKIV2L Helicase SKI2W 1 GDTVSAS(0.999)PCS(0.001)APLAR 218.63 7.05E-12 0 105690 119280 128940 124850 141620 108680 138830 116120 171510 TRUE FALSE 99075.05156 128111.6153 131998.5177 128053.8624 130497.7365 140054.1517 118013.7303 130617.8376 142883.873 0.693395619 0.896613541 0.923816768 0.896209346 0.913313264 0.980195657 0.82594157 0.914153815 1 17.12448357 4.740638285 4.273556093 0.91164145 0.67634141 0.689527725 0.047432657 0.120363852 5.127921231 0.010468865 0.086696784 55034.91308 -4.740638285 -0.23530004 S(ph)FTGGLGQLVVPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFTGGLGQLVVPSK 14 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 S(0.993)FT(0.007)GGLGQLVVPSK;S(0.998)FT(0.002)GGLGQLVVPSK 205.52 1.27E-08 251740000 599430 475700 493390 375860 679650 429290 651470 670550 1490870 TRUE FALSE 561912.7463 510921.323 505093.4438 385505.2039 626273.0306 553219.0541 553788.1215 754269.6436 1242034.166 0.452413276 0.411358509 0.406666304 0.310382125 0.504231726 0.445413717 0.44587189 0.607285745 1 20.24427343 0.729989791 1.237404849 1.000762961 0.412961185 0.934173137 0.048488203 0.195961526 0.511872681 0.043055778 0.013105173 5.370191719 -0.729989791 -0.587801775 GDVDMSEVEHFMPILMEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDVDMSEVEHFMPILMEK 18 0 E7ENJ6;Q9BXS5;Q9BXS5-2;K7ENA7 E7ENJ6 AP1M1 AP-1 complex subunit mu-1 0 131.51 1.68E-05 13204000 45534 42798 46341 43764 45356 44326 59968 43551 36424 FALSE TRUE 42684.10822 45966.80845 47440.2304 44887.05833 41793.92272 57122.19663 50976.35512 48988.43822 30344.59909 1.406645976 1.514826685 1.563383001 1.479243743 1.377310097 1.8824502 1.679915261 1.61440387 1 14.88915214 GDVEEDEAVPDSEQDIKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDVEEDEAVPDSEQDIKPR 19 1 O14787-2;O14787;A0A075B780 O14787-2 TNPO2 Transportin-2 0 150.91 6.47E-08 85026000 94731 89339 90499 86406 93141 70118 110570 92833 96220 FALSE TRUE 88801.95581 95953.75252 92645.67902 88623.32425 85826.08157 90359.92833 93991.05498 104423.4044 80160.2604 1.107805231 1.197023962 1.155755714 1.105576801 1.070681172 1.127240953 1.172539292 1.302682949 1 16.29059957 1.653661569 5.965595049 1.178895511 1.135778871 0.004640757 0.079929284 0.434051865 32.36506665 0.038734207 0.019078629 45.04655356 -1.653661569 -0.043116641 GDVEEDETIPDSEQDIRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GDVEEDETIPDSEQDIRPR 19 1 Q92973-2;Q92973;Q92973-3 Q92973-2 TNPO1 Transportin-1 0 ;;;;; 322.43 3.78E-62 5202380000 1800232 2205973 2004617 2094109 2337610 1995647 2490983 2005470 2280522 FALSE TRUE 1687558.693 2369305.536 2052167.462 2147847.382 2154023.54 2571757.892 2117483.224 2255857.344 1899888.145 0.888241077 1.24707633 1.080151727 1.130512545 1.133763346 1.353636475 1.114530468 1.18736324 1 20.85748305 4.749580508 24.73809816 1.163434323 0.888240893 0.436075395 0.095305364 1230.999075 2763357.85 0.020544102 0.303303482 56179.84131 -4.749580508 -0.275193431 GDVEGSQS(ph)QDEGEGSGESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDVEGSQSQDEGEGSGESER 20 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 1 GDVEGSQS(1)QDEGEGSGESER;GDVEGSQS(1)QDEGEGSGESER 382.04 1.91E-113 458760000 221471 256730 252365 248434 258730 219186 263580 228401 244060 TRUE FALSE 207609.5254 275738.5563 258351.217 254809.237 238410.3895 282461.44 224058.626 256917.3676 203324.8093 1.021073258 1.356148112 1.270633022 1.253212719 1.172559267 1.389212861 1.101973865 1.263581009 1 17.63342674 0.087839451 0.615587129 0.987798909 1.253066435 0.274537313 0.111536599 4.255885637 1.966781618 0.229655217 0.040438666 1.22416357 -0.087839451 0.265267525 GDVEHTIR ddPTM_SK-BR-3_Pertuzumab_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 80.165 0.026154 66862000 79688 101190 101680 88180 89236 100440 89900 91632 73223 FALSE TRUE 74700.47033 108682.2129 104091.8976 90442.84809 82227.76452 129435.3975 76420.32959 103072.4569 61001.60826 1.224565589 1.781628649 1.706379562 1.482630551 1.347960601 2.12183582 1.252759259 1.68966786 1 15.89655966 -0.679736738 0.610005746 0.904997847 1.608770155 0.296693322 0.272994791 17.87312127 4.619515262 3.741977869 0.097841558 0.209056301 0.679736738 0.703772308 GDVIHVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDVIHVTR 8 0 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E7EUY6;E7EU80;C9JAD7;C9JDI6;B1ANY6;E7ENL8 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 0 ; 99.802 0.0065549 401450000 449070 530930 532730 535150 574180 442450 546040 469930 541770 FALSE TRUE 420963.5103 570240.6096 545366.6072 548882.855 529086.2189 570178.1324 464166.3712 528601.7949 451345.087 0.93268659 1.263424874 1.208314044 1.216104641 1.172243222 1.263286449 1.028406832 1.171169932 1 18.78387138 1.137851356 0.944161757 1.012744432 1.188002777 0.153353351 0.105328862 0.771100736 1.498276421 0.090318055 0.031391311 13.73571769 -1.137851356 0.175258345 GDVPTKRPPVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDVPTKRPPVLR 12 2 P62424;Q5T8U2;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 ; 137.55 5.07E-05 1143870000 1449840 2121400 1915710 1989720 2509100 1500970 2283800 1709320 3636500 FALSE TRUE 1359097.102 2278470.663 1961151.546 2040779.584 2312045.407 1934275.673 1941365.392 1922732.365 3029544.657 0.448614315 0.752083538 0.647342016 0.673625846 0.763165977 0.638470758 0.640810951 0.634660512 1 21.53066954 -2.058721355 2.469507262 1.473586008 0.660864547 0.621530362 0.085487256 13657458.36 5478221.082 36428634.29 0.018910865 0.008735317 2.058721355 -0.812721461 GDVSVQEHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDVSVQEHER 10 0 Q9P232 Q9P232 CNTN3 Contactin-3 0 ; 66.595 0.065498 1097380000 985940 1101910 1172600 1252990 1164340 964740 1362430 1031450 1388000 FALSE TRUE 924231.7754 1183496.563 1200414.626 1285143.845 1072897.433 1243244.777 1158146.27 1160228.803 1156333.833 0.799277638 1.023490387 1.038121165 1.111395177 0.927844021 1.075160772 1.001567399 1.003368378 1 20.14112653 4.738541241 7.957089609 1.025408403 0.797398873 0.675730185 0.048590341 0.04957536 37.90426876 0.010245367 0.060781284 54769.81081 -4.738541241 -0.22800953 GDVTAEEAAGAS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDVTAEEAAGASPAK 15 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 GDVTAEEAAGAS(1)PAK;GDVTAEEAAGAS(1)PAK 232.68 2.95E-14 1099890000 2287520 1401390 1873750 1669640 1676040 1531290 2220450 1538860 1559450 TRUE FALSE 2144348.207 1505150.374 1918196.235 1712485.789 1544410.579 1973348.565 1887514.136 1730990.058 1299167.721 1.650555331 1.158549701 1.47648083 1.318140654 1.188769206 1.518932878 1.452864096 1.332383826 1 20.30915626 0.958866522 20.33287931 0.999999996 1.380818352 0.407764185 0.14771981 635.7418386 314258.336 0.131112103 0.032778026 9.096336592 -0.958866522 0.380818356 GDVTAEEAAGAS(ph)PAKANGQENGHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GDVTAEEAAGASPAKANGQENGHVK 25 1 P49006 P49006 MARCKSL1 MARCKS-related protein 1 GDVTAEEAAGAS(1)PAKANGQENGHVK;GDVTAEEAAGAS(1)PAKANGQENGHVK;GDVTAEEAAGAS(1)PAKANGQENGHVK 238.6 1.00E-38 758790000 783060 497480 655450 597540 736930 426062 769110 533060 1014170 TRUE FALSE 734049.6724 534313.9368 670997.5835 612873.888 679054.4904 549059.1829 653789.0956 599613.7144 844898.4752 0.868802222 0.632400167 0.794175399 0.725381695 0.803711346 0.649852259 0.773807877 0.709687296 1 19.68841847 -1.991488951 3.344770248 1.244763713 0.738654794 0.55782892 0.071243098 0.047975922 0.000122079 0.025450383 0.014014387 0.010197907 1.991488951 -0.506108918 GDVTDTEQLAQEMLIISHHPSLVAVQSGLWPALLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDVTDTEQLAQEMLIISHHPSLVAVQSGLWPALLAR 36 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 177.21 4.51E-23 61014000 19614 52821 32653 39633 63354 30204 43714 47568 35111 FALSE TRUE 18386.39475 56731.9218 33427.54458 40650.04988 58378.4324 38923.40448 37159.49152 53506.96951 29250.74727 0.628578634 1.939503332 1.142792841 1.389709791 1.995792854 1.330680687 1.270377511 1.829251369 1 14.83618586 -1.33416625 4.634983245 0.99962675 1.455122695 0.102298892 0.408458016 0.00139229 0.000200008 0.349514176 0.082315106 0.046326954 1.33416625 0.455495946 GDVVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 102.98 0.081604 660470000 1361000 1034200 1235300 1170900 1188700 982260 1429200 1081500 1395200 FALSE TRUE 1275817.439 1110773.244 1264601.899 1200947.276 1095344.297 1265822.516 1214904.728 1216527.656 1162332.107 1.097635893 0.955641884 1.087986723 1.033222148 0.942367754 1.089036867 1.045230293 1.046626561 1 20.14859091 GDYLAVVLATQGHTQVLIHQLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDYLAVVLATQGHTQVLIHQLSR 23 0 Q14137;Q14137-2 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 115.5 0.00032758 33078000 87539 199910 142450 136590 202510 167500 132310 193000 97724 FALSE TRUE 82060.09025 214711.5444 145828.9813 140095.1306 186605.6815 215854.5309 112471.3438 217096.4748 81413.23308 1.007945357 2.637305218 1.79121963 1.720790655 2.292080469 2.651344538 1.381487254 2.666599355 1 16.31297569 -1.287929928 7.631425809 0.999996199 2.032652723 0.244351134 0.562451463 3.21E-05 2.99E-06 0.480376213 0.113225343 0.051531178 1.287929928 1.032656524 GDYPLEAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GDYPLEAVR 9 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;; 227.62 4.50E-07 5184910000 3387650 5968020 2438590 2548680 5782490 1844888 2761840 4913740 4442710 FALSE TRUE 3175623.034 6409898.411 2496434.506 2614083.444 5328356.561 2377477.216 2347727.732 5527231.255 3701193 0.857999849 1.731846572 0.67449455 0.706281311 1.439632184 0.642354294 0.634316484 1.493364776 1 21.81955894 3.937355262 9.057793733 0.904699916 1.337800177 0.125556398 0.374396801 0.496743102 108.2900736 0.088924217 0.161758105 8656.757706 -3.937355262 0.433100261 GDYPQAMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GDYPQAMK 8 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 73.665 0.084541 0 241390 225370 253960 222700 274400 186260 283730 227700 286250 FALSE TRUE 226281.8308 242056.6293 259984.0511 228414.859 252849.7309 240030.2383 241187.3205 256128.8462 238473.0258 0.948878097 1.015027291 1.09020318 0.957822623 1.060286504 1.006529932 1.011381978 1.074036971 1 17.86346656 4.709032018 3.568736161 1.030331596 0.941835292 0.290724103 0.038745014 0.306595667 7.052358301 0.008669563 0.069353945 51171.95598 -4.709032018 -0.088496304 GEAAAERPGEAAVAS(ph)SPSKANGQENGHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEAAAERPGEAAVASSPSKANGQENGHVK 29 2 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 GEAAAERPGEAAVAS(0.499)S(0.499)PS(0.001)KANGQENGHVK 205.96 1.07E-25 677620000 97396 61107 73039 77176 81719 56405 102220 67617 92836 TRUE FALSE 91300.15822 65631.42586 74771.51957 79156.46682 75301.11938 72688.20784 86893.05996 76059.13129 77341.07186 1.180487366 0.848597314 0.966776355 1.023472586 0.973623944 0.939839675 1.123504729 0.983424841 1 16.23894714 1.761884253 25 1.04759382 0.97083104 0.026333872 0.091164076 25.20524767 27037.06782 0.039359293 0.021828035 57.79419952 -1.761884253 -0.07676278 GEAAAERPGEAAVASS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GEAAAERPGEAAVASSPSK 19 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 GEAAAERPGEAAVAS(0.077)S(0.901)PS(0.022)K;GEAAAERPGEAAVAS(0.084)S(0.898)PS(0.017)K;GEAAAERPGEAAVAS(0.181)S(0.818)PSK;GEAAAERPGEAAVAS(0.169)S(0.821)PS(0.01)K 241.06 1.45E-24 3823360000 4159500 2331120 3072090 2930740 2500380 2631520 3724050 2457770 1691170 TRUE FALSE 3899164.32 2503718.55 3144961.426 3005947.75 2304010.241 3391197.105 3165663.275 2764627.995 1408902.802 2.767518324 1.777069751 2.232206098 2.13353806 1.63532235 2.406977331 2.246899695 1.962256013 1 20.42614065 0.857554926 5.207881877 1.000017392 2.135643089 0.577670894 0.311562875 1.223451555 44.23775036 0.271790734 0.068606679 7.203688517 -0.857554926 1.135625697 GEAAAERPGEAAVASS(ph)PSKANGQENGHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GEAAAERPGEAAVASSPSKANGQENGHVK 29 2 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 GEAAAERPGEAAVAS(0.163)S(0.822)PS(0.015)KANGQENGHVK;GEAAAERPGEAAVAS(0.025)S(0.974)PS(0.002)KANGQENGHVK;GEAAAERPGEAAVAS(0.015)S(0.871)PS(0.114)KANGQENGHVK;GEAAAERPGEAAVAS(0.03)S(0.581)PS(0.389)KANGQENGHVK 222.98 8.32E-35 3563840000 2082400 1221950 1596160 1534940 1556410 1099150 2067280 1212580 1395810 TRUE FALSE 1952066.301 1312424.449 1634021.669 1574329.159 1434175.837 1416456.762 1757310.556 1363973.282 1162840.294 1.678705418 1.128636887 1.4051987 1.353865331 1.233338615 1.21810086 1.51122262 1.172966993 1 20.14922154 0.99935443 24.16357993 0.999999995 1.33982623 0.370597218 0.156149536 12.05083895 451091.3287 0.135649109 0.033912277 9.985146236 -0.99935443 0.339826235 GEAASLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEAASLR 7 0 Q9H2J1 Q9H2J1 ARRDC1-AS1 Uncharacterized protein ARRDC1-AS1 0 90.986 0.038936 219300000 182850 149640 181680 168360 146600 162210 219460 135580 167050 FALSE TRUE 171405.7449 160719.5013 185989.5354 172680.4026 135086.6274 209037.3937 186554.0104 152507.4614 139168.2758 1.231643806 1.154857315 1.336436298 1.240802917 0.970671129 1.502047737 1.340492359 1.095849327 1 17.08647085 2.232693217 24.99964521 1.279815833 1.205359924 0 0.163967043 510.1512724 2173617.392 0.057014332 0.043245853 170.8807797 -2.232693217 -0.074455909 GEADRDTYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GEADRDTYR 9 1 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;;;; 182.16 4.25E-05 20286680000 10676390 13705960 11873580 11657910 13662800 10007300 12601810 11109030 11693380 FALSE TRUE 10008173.81 14720763.54 12155226.92 11957071.71 12589778.8 12896245.06 10712285.58 12496016.85 9741679.336 1.027356112 1.511111486 1.247754777 1.227413806 1.292362268 1.323821552 1.099634386 1.282737444 1 23.21573906 0.541485342 0.414039105 0.976694141 1.31264483 0.236199807 0.132031035 2.537014289 0.86723562 0.257237765 0.087174513 3.479247645 -0.541485342 0.335950689 GEADRDTYRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GEADRDTYRR 10 2 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;;;;;; 183.85 9.13E-07 10488521000 1784957 3069927 2277357 2458471 2932914 1895449 2670647 2200084 4028347 FALSE TRUE 1673239.728 3297227.589 2331376.983 2521559.528 2702574.765 2442634.356 2270208.275 2474769.33 3355989.862 0.49858307 0.982490331 0.694691307 0.75136089 0.805298847 0.727843187 0.676464581 0.737418596 1 21.67830693 -1.414673964 8.18967633 1.000004024 0.749821758 0.31978948 0.119904201 8.15E-06 5.83E-07 0.107412682 0.025317005 0.038488061 1.414673964 -0.250182265 GEAERGS(ph)GGS(ph)S(ph)GDELREDDEPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEAERGSGGSSGDELREDDEPVK 23 2 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WT54 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 3 GEAERGS(1)GGS(1)S(1)GDELREDDEPVK 57.009 0.0061298 0 270760 202040 227160 229610 218200 152520 238450 174410 218550 TRUE FALSE 253813.6149 216999.2518 232548.3425 235502.1813 201063.4522 196550.048 202696.6362 196185.4724 182072.5931 1.394024277 1.191828205 1.277228706 1.293452119 1.104303777 1.07951474 1.113273737 1.077512376 1 17.47415425 2.690993588 5.354293507 1.083114438 1.271055045 0.769683691 0.057806208 0.10380983 7.157271865 0.017625301 0.016811271 490.9006287 -2.690993588 0.187940607 GEAGVPAEFSIWTR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 248.32 1.45E-17 698490000 719060 899400 821930 893250 946490 767510 885470 770670 863200 FALSE TRUE 674055.3182 965992.5118 841426.5677 916172.3073 872156.4934 989077.6775 752701.9938 866889.846 719126.3435 0.937325303 1.343286226 1.170067785 1.274007434 1.212800089 1.375387908 1.046689501 1.205476414 1 19.45588573 0.911856832 1.048208964 1.007130844 1.22184225 0.168808816 0.130438463 0.930913092 2.087665976 0.10969317 0.035537729 8.163132249 -0.911856832 0.214711406 GEAHLAVNDFELAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GEAHLAVNDFELAR 14 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;;; 226.19 2.50E-12 2675450000 3017610 2990260 3402830 3243640 3049740 3602500 3354600 2902380 2003310 FALSE TRUE 2828743.177 3211661.962 3483546.735 3326877.294 2810225.722 4642483.268 2851608.873 3264748.532 1668944.619 1.694929325 1.924367007 2.087275213 1.993401852 1.683834017 2.781688029 1.708630017 1.956175474 1 20.67050465 0.438330181 1.584438795 1.000335668 2.002173507 0.486403008 0.31621826 2.99739905 7.591970983 0.270982771 0.077466236 2.743659302 -0.438330181 1.001837839 GECEESWIHFI ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GECEESWIHFI 11 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 0 ;;; 188.76 7.00E-06 241586000 534181 726770 620433 636468 757700 589535 717840 645542 839870 FALSE TRUE 500747.5648 780580.807 635149.9637 652800.8464 698193.2984 759724.1842 610206.5561 726139.3397 699690.2712 0.715670326 1.115609062 0.907758747 0.932985456 0.997860521 1.085800697 0.872109534 1.037801109 1 19.41635691 2.732048328 23.06657064 0.988316136 0.949231901 0.083665547 0.110503858 823.3802001 2916404.109 0.033412107 0.032243077 539.570662 -2.732048328 -0.039084235 GEDEEENNLEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GEDEEENNLEVR 12 0 P04843;F8WF32 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ; 203.8 2.81E-07 633190000 324980 337310 298670 317610 388630 285240 394750 323440 280160 FALSE TRUE 304640.0819 362284.7834 305754.5934 325760.4103 358108.5675 367584.1575 335560.9022 363822.196 233399.4861 1.305230303 1.552209002 1.310005427 1.395720341 1.534316007 1.574914168 1.437710544 1.558796046 1 17.83244186 -1.472198097 5.381918336 0.999339202 1.457778688 0.679788701 0.09891758 0.000742571 7.28E-05 0.090680955 0.021344341 0.033713349 1.472198097 0.458439486 GEDGKPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEDGKPVR 8 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 76.827 0.031733 156790000 347950 389720 333400 334480 405970 298550 403520 342840 326100 FALSE TRUE 326172.4306 418575.2743 341308.4054 343063.3231 374086.7538 384736.5384 343015.9221 385644.3287 271671.8033 1.200612013 1.540738749 1.256326204 1.262785902 1.37698042 1.41618134 1.262611423 1.419522836 1 18.05150531 -1.455194327 2.965103899 0.991572863 1.347751068 0.528745724 0.101329351 13249422.3 16198104.07 933731.104 0.02269843 0.035059496 1.455194327 0.356178204 GEDIFLDMFEDEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEDIFLDMFEDEYR 14 0 Q2KHT3;Q2KHT3-2 Q2KHT3 CLEC16A Protein CLEC16A 0 161.62 1.06E-05 6548200 9236.5 16358 9978.7 9247.5 14330 10406 10208 12936 8863 FALSE TRUE 8658.403953 17569.16334 10215.39948 9484.806506 13204.5796 13410.04327 8677.405166 14551.08808 7383.708043 1.172636283 2.379449897 1.383505336 1.284558714 1.788339887 1.816166511 1.17520968 1.970701982 1 12.85012979 -2.739942038 0.192585446 1.47E-12 1.785507988 0.155969325 0.396471437 81.71157745 1.76375871 36.03049454 1.080209841 0.001819944 2.739942038 1.785507988 GEDLTEEEDGGIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GEDLTEEEDGGIIR 14 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;; 274.71 1.11E-32 318230000 632680 457100 551610 471340 428190 547150 640610 511310 346923 FALSE TRUE 593081.6882 490944.1596 564694.4497 483435.3824 394561.6846 705103.3228 544556.4776 575148.179 289019.3101 2.052048661 1.698655219 1.953829485 1.672675027 1.365174128 2.439640876 1.884152576 1.989999142 1 18.14080636 -1.564008153 7.058289173 0.999267002 1.875935316 0.496295348 0.27919436 0.003010163 0.000185938 0.252673114 0.059514304 0.027289266 1.564008153 0.876668314 GEDS(ph)AEETEAKPAVVAPAPVVEAVSTPSAAFPSDATAENVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEDSAEETEAKPAVVAPAPVVEAVSTPSAAFPSDATAENVK 41 1 Q12906-7;Q12906-4;Q12906-6 Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 GEDS(0.5)AEET(0.5)EAKPAVVAPAPVVEAVSTPSAAFPSDATAENVK 112.68 2.79E-06 117670000 231490 110700 148040 127550 124660 122340 209430 118220 154900 TRUE FALSE 217001.4541 118896.3432 151551.5787 130823.1489 114869.7065 157657.572 178027.9158 132980.0272 129046.1893 1.681579714 0.921347184 1.174397939 1.01376995 0.890144119 1.221714278 1.379567399 1.030483953 1 16.97752801 GEDSVPDTVHHVVVPVNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GEDSVPDTVHHVVVPVNPK 19 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ; 117.67 5.46E-05 1101450000 1255280 985860 1238980 1121310 1057430 1096950 1420380 1054220 1107490 FALSE TRUE 1176714.266 1058854.1 1268369.191 1150084.713 974383.7133 1413621.658 1207407.205 1185841.688 922642.7643 1.275373645 1.147631717 1.374713204 1.246511388 1.056079071 1.532144089 1.308639976 1.285266339 1 19.81541264 2.257012847 24.99908317 1.315416122 1.23247615 0.014326049 0.15202209 683.6371041 926189.7417 0.048241531 0.040292658 180.7227585 -2.257012847 -0.082939972 GEDVPS(ph)EEEEEEENGFEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GEDVPSEEEEEEENGFEDR 19 0 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 1 GEDVPS(1)EEEEEEENGFEDR;GEDVPS(1)EEEEEEENGFEDR 233.09 4.41E-24 3856800000 314110 265450 292910 253460 272000 302840 343180 266370 256370 TRUE FALSE 294450.4158 285104.1942 299857.9635 259964.2127 250638.2172 390264.9918 291723.3449 299626.8809 213580.1908 1.378641037 1.33488126 1.40395962 1.217173801 1.173508724 1.827252754 1.365872668 1.402877672 1 17.70441832 GEEAAGGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEEAAGGDR 9 0 O43598;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 78.192 0.070883 115510000 101900 91195 94136 96797 94251 84799 93900 81804 90310 FALSE TRUE 95522.2609 97947.17269 96368.95037 99280.9749 86848.90665 109279.0947 79820.56672 92017.40947 75236.67758 1.269623593 1.30185404 1.280877273 1.319582125 1.154342662 1.452471032 1.060926257 1.223039247 1 16.19914852 1.083516408 0.822044382 1.006490237 1.291307923 0.455071084 0.096591572 0.490815072 0.747997336 0.079849405 0.029427087 12.1203848 -1.083516408 0.284817687 GEEDTGQEEGGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEEDTGQEEGGSR 13 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 83.214 0.023976 32596000 24468 32167 28465 29935 33756 28258 33171 27750 27627 FALSE TRUE 22936.59156 34548.67815 29140.20324 30703.18278 31104.93993 36415.62587 28197.31649 31214.64859 23015.87522 0.996555262 1.501080355 1.266091468 1.334000227 1.351455881 1.582196007 1.225124668 1.356222533 1 14.49034168 -1.452639508 9.588876466 0.999998078 1.340590457 0.295987608 0.156977975 5.66E-06 3.23E-07 0.133514534 0.0314695 0.035266348 1.452639508 0.340592379 GEEDWLYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GEEDWLYER 9 0 J3QQZ9;Q9NVS9-3;Q9NVS9;Q9NVS9-4 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 ;; 201.07 5.13E-05 811560000 826200 903390 782020 773830 919970 613430 826610 751070 736690 FALSE TRUE 774489.6168 970277.9356 800569.8837 793687.7879 847719.2672 790517.2828 702667.5044 844842.7428 613731.6798 1.261935211 1.580948104 1.304429786 1.29321626 1.381253885 1.288050314 1.144909946 1.376566944 1 19.22724853 -0.65749861 0.1350701 0.634777057 1.572213236 0.493775708 0.107794616 19.60781707 0.63981597 3.673876049 1.014032883 0.220039875 0.65749861 0.937436179 GEEGHDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GEEGHDPK 8 0 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 90.657 0.013041 476990000 1720740 925950 1314370 1142470 998610 1124520 1512850 1052030 786870 FALSE TRUE 1613041.955 994508.3015 1345547.477 1171787.714 920183.1988 1449150.669 1286012.187 1183378.261 655536.3136 2.460644699 1.517091091 2.052590298 1.787525252 1.403710488 2.210633704 1.961771088 1.805206267 1 19.32231618 0.886801639 8.841387 1.000000054 1.885563602 0.460881252 0.306895039 9.371127487 732.4455695 0.267760544 0.067011438 7.705514443 -0.886801639 0.885563548 GEEGRPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GEEGRPGK 8 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ;; 85.67 0.015119 634990000 1643140 1445730 1529750 1427490 1414570 1207900 1620180 1340890 1405080 FALSE TRUE 1540298.8 1552773.353 1566036.392 1464121.81 1303475.378 1556601.121 1377249.05 1508303.068 1170563.071 1.315861434 1.326518316 1.337848794 1.250784214 1.113545618 1.329788339 1.176569708 1.288527808 1 20.15877124 -4.999999995 0.119938509 0.111900894 1.405288128 0.617830078 0.068628163 94.81594837 0.737927325 20.41642699 0.618108643 1.00E-05 4.999999995 1.293387234 GEEGRPGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GEEGRPGKK 9 2 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ;;; 71.425 0.027906 451094000 1092570 888110 978900 953370 1030010 726100 1196040 857170 1328910 FALSE TRUE 1024187.994 953866.5885 1002119.97 977835.0883 949117.1695 935713.2828 1016704.905 964189.5614 1107106.336 0.925103543 0.86158534 0.905170477 0.883235021 0.8572954 0.845188265 0.918344402 0.870909623 1 20.07836237 -1.545967558 3.898894345 1.001977932 0.883470486 0.66081453 0.026263293 0.000423977 4.94E-05 0.023876646 0.005535576 0.028446736 1.545967558 -0.118507447 GEEGS(ph)DDDETENGPKPK ddPTM_SK-BR-3_Pertuzumab_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 297.67 2.01E-46 1476500000 2862340 1305720 1699920 1645320 1654510 1241670 2309660 1445650 2070780 TRUE FALSE 2683191.249 1402396.867 1740242.905 1687541.697 1524571.459 1600119.972 1963347.925 1626142.585 1725153.44 1.555334839 0.812911382 1.008746738 0.97819803 0.883730933 0.927523277 1.138071478 0.942607508 1 20.71829325 4.747756776 24.99498632 0.965465399 1.555335147 0.828344538 0.084941981 529.0430948 1437899.041 0.021289004 0.266336227 55944.42003 -4.747756776 0.589869748 GEEHCGHLIEAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GEEHCGHLIEAHK 13 0 H7C4E5;C9J8T6;Q14061 H7C4E5 COX17 Cytochrome c oxidase copper chaperone 0 ;; 184.21 3.37E-06 1064561000 1358310 1089300 1214470 1189030 1305740 963720 1277800 1160410 1081120 FALSE TRUE 1273295.802 1169952.905 1243277.802 1219542.523 1203192.448 1241930.319 1086205.753 1305289.743 900674.0877 1.41371426 1.298974758 1.38038589 1.354033095 1.335879941 1.378889807 1.205992009 1.449236478 1 19.78064563 -3.250216797 0.364941666 6.05E-17 1.352528215 0.717615144 0.068468187 62.24160949 1.650844198 47.78796389 0.044737747 0.000562061 3.250216797 1.352528215 GEEHCGHLIEAHKECMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GEEHCGHLIEAHKECMR 17 1 H7C4E5;C9J8T6;Q14061 H7C4E5 COX17 Cytochrome c oxidase copper chaperone 0 ; 107.98 0.00022797 296690000 114882 154189 140101 139551 191176 121278 174716 130641 242510 FALSE TRUE 107691.7407 165605.314 143424.2619 143132.1149 176161.8081 156288.9898 148518.9578 146951.8164 202033.5143 0.533038991 0.81969229 0.709903317 0.708457284 0.871943493 0.773579524 0.7351204 0.727363561 1 17.62423511 -5 0.217108906 2.251765468 0.710756936 0.497695662 0.085855011 131.9784593 1.319953865 72.38131395 0.157340242 1.00E-05 5 -1.541008532 GEEKPAGHRT(ph)SPVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GEEKPAGHRTSPVAK 15 2 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 GEEKPAGHRT(0.696)S(0.304)PVAK;GEEKPAGHRT(0.562)S(0.438)PVAK;GEEKPAGHRT(0.5)S(0.5)PVAK 127.01 0.0038508 2504390000 5827310 3959360 4759080 4688880 4697870 3584410 6194600 4306870 4613460 TRUE FALSE 5462589.069 4252515.134 4871967.625 4809204.599 4328918.24 4619170.979 5265777.238 4844592.2 3843443.722 1.421274634 1.106433564 1.267604778 1.251274884 1.126312379 1.201831304 1.370067476 1.260482148 1 21.87396811 GEEVEGAGWMPGREPTTHAEAQGDEGDGEEGLQRT(ph)RIT(ph)EEQDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEEVEGAGWMPGREPTTHAEAQGDEGDGEEGLQRTRITEEQDK 43 3 Q8IVF2;Q8IVF2-3 Q8IVF2 AHNAK2 Protein AHNAK2 2 GEEVEGAGWMPGREPT(0.347)T(0.347)HAEAQGDEGDGEEGLQRT(0.653)RIT(0.653)EEQDK 42.782 0.046492 62816000 67971 39126 51938 50655 67973 25067 59947 41235 103270 TRUE FALSE 63716.81644 42022.92975 53169.99389 51954.89306 62634.67477 32303.43597 50958.50387 46383.28052 86033.56985 0.740604122 0.488448054 0.618014503 0.603890936 0.728025989 0.375474783 0.592309536 0.539130023 1 16.39261208 -1.484653325 3.26698987 1.008772777 0.57647179 0.597780296 0.106551459 22344132.2 30311390.59 1786745.707 0.022776962 0.03276021 1.484653325 -0.432300987 GEFKDEEETVTTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEFKDEEETVTTK 13 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 153.24 4.16E-05 315840000 258090 165720 205000 204720 229370 156230 257990 207350 307240 FALSE TRUE 241936.6076 177990.0812 209862.6968 209973.4618 211356.2054 201331.0648 219306.7946 233238.1039 255959.6592 0.945213822 0.695383334 0.819905361 0.820338105 0.825740299 0.786573421 0.856802182 0.911229936 1 17.96555692 1.102909247 1.320846107 0.999453346 0.801328959 0.484163888 0.061341363 0.312156438 1.103932788 0.053257347 0.016393191 12.67386996 -1.102909247 -0.198124388 GEFSAS(ph)PMLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 GEFSASPMLK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GEFSAS(1)PMLK;GEFSAS(1)PMLK;GEFS(0.001)AS(0.999)PMLK;GEFSAS(1)PMLK;GEFSAS(1)PMLK;GEFSAS(1)PMLK;GEFSAS(1)PMLK;GEFSAS(1)PMLK;GEFS(0.001)AS(0.999)PMLK;GEFSAS(1)PMLK 228.12 2.35E-09 15760800000 24106340 19812010 22207000 20238090 23661390 20755030 31685620 22881010 28495960 TRUE FALSE 22597567.21 21278911.83 22733760.53 20757433.65 21803119.87 26746670.23 26934655.44 25737754.47 23739800.19 0.951885316 0.89633913 0.957622236 0.87437272 0.91842053 1.12665945 1.134578018 1.084160535 1 24.50080446 2.242932837 24.96428188 1.102569211 0.919644367 0.775651551 0.044146455 40.98983806 234042.9233 0.014259802 0.011548258 174.9576097 -2.242932837 -0.182924845 GEFVTTVQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GEFVTTVQQR 10 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 ; 163.16 1.52E-05 245610000 252010 283740 232570 209130 291690 184291 248700 244790 277130 FALSE TRUE 236237.144 304748.4048 238086.6702 214496.6299 268781.844 237492.82 211409.7438 275352.5703 230875.2127 1.02322437 1.319970218 1.031235304 0.929058721 1.164186666 1.028663135 0.915688356 1.192646743 1 17.81675376 3.736983803 5.995952296 1.026984094 1.188928089 0.190265542 0.112352752 0.183165556 25.91623749 0.027026667 0.046522296 5457.37507 -3.736983803 0.161943995 GEGDAPFSEPGTTSTQRPS(ph)S(ph)PETATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEGDAPFSEPGTTSTQRPSSPETATK 26 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GEGDAPFSEPGTTSTQRPS(1)S(0.988)PET(0.012)ATK 148.76 9.47E-08 373340000 706290 513990 598810 552150 533530 515450 720250 514260 485000 TRUE FALSE 662084.5697 552046.3544 613014.056 566319.1038 491628.706 664252.0474 612255.199 578466.493 404050.3668 1.638618905 1.366281038 1.517172378 1.401605221 1.216751045 1.64398328 1.515294254 1.431669268 1 18.62417562 0.944252101 19.65084239 0.999999999 1.466285758 0.576871999 0.125927004 789.1682686 278179.3184 0.113781469 0.028445367 8.795329228 -0.944252101 0.46628576 GEGDAPFSEPGTTSTQRPS(ph)SPETATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEGDAPFSEPGTTSTQRPSSPETATK 26 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GEGDAPFS(0.003)EPGT(0.016)T(0.016)S(0.014)T(0.012)QRPS(0.515)S(0.417)PET(0.007)AT(0.001)K 68.269 0.020224 538280000 493740 370860 431250 440580 399320 328680 515540 376440 421440 TRUE FALSE 462837.6948 398318.8603 441479.4537 451886.0287 367959.018 423564.5803 438239.563 423439.3626 351098.9414 1.318254316 1.134491772 1.257421774 1.287061781 1.04802087 1.206396632 1.248193917 1.206039987 1 18.42151812 -0.966520469 3.85521073 0.999980564 1.209959616 0.430586445 0.076980961 9489623.104 18214441.94 2768.813417 0.017075107 0.108013871 0.966520469 0.209979052 GEGDAPFSEPGTTSTQRPSS(ph)PETATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GEGDAPFSEPGTTSTQRPSSPETATK 26 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GEGDAPFSEPGTTSTQRPS(0.003)S(0.997)PETATK;GEGDAPFSEPGT(0.001)T(0.004)S(0.003)T(0.002)QRPS(0.155)S(0.835)PETATK;GEGDAPFSEPGTTSTQRPS(0.015)S(0.984)PET(0.001)ATK;GEGDAPFSEPGTTSTQRPS(0.034)S(0.966)PETATK;GEGDAPFSEPGTTSTQRPS(0.007)S(0.985)PET(0.007)ATK;GEGDAPFSEPGTTSTQRPS(0.087)S(0.911)PET(0.001)ATK 240.21 2.76E-45 23010500000 20424500 15828930 17640630 17048750 15897630 15004880 20922300 15749230 15968840 TRUE FALSE 19146167 17000920.45 18059074.07 17486249.79 14649094.27 19336545.27 17785195.35 17715556.03 13303537.44 1.439178646 1.277924802 1.35746407 1.314406027 1.101142785 1.453488995 1.33687716 1.331642513 1 23.66530658 -1.747437006 2.432752878 0.921192939 1.324458806 0.532284677 0.09617179 6694857.89 4638761.593 3168910.236 0.022455375 0.01788805 1.747437006 0.403265867 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(ph)PVAPAPVPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPSPVAPAPVPSR 42 1 Q9UK76;Q9UK76-3 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(1)PVAPAPVPSR;GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(1)PVAPAPVPSR;GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(1)PVAPAPVPSR 250.97 4.02E-56 4797550000 971784 647272 897386 835919 800882 769329 1010073 651892 585808 TRUE FALSE 910961.7741 695196.6924 918672.4197 857370.0967 737983.9583 991421.7933 858621.9307 733282.1512 488032.8603 1.866599256 1.424487466 1.882398696 1.75678764 1.512160386 2.031465243 1.7593527 1.502526184 1 18.89661877 0.905631429 3.266478565 1.000756952 1.73518326 0.648767867 0.174745463 0.240509093 5.746313066 0.160293941 0.041679498 8.046952345 -0.905631429 0.734426308 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPSPVAPAPVPSR ddPTM_SK-BR-3_Pertuzumab_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" 0 ; 243.01 5.44E-55 541005000 402651 285306 350192 323390 294459 311584 433565 308460 229260 FALSE TRUE 377449.7927 306430.3531 358498.7196 331688.7349 271333.3779 401533.2427 368555.9533 346971.91 190995.0249 1.976228401 1.604389189 1.877005539 1.73663547 1.420630606 2.102323046 1.929662584 1.816654178 1 17.54317553 -0.8731255 4.10764209 0.999981528 1.804713286 0.636547675 0.191848877 235975976 510028184.5 67253.30049 0.044889609 0.133928961 0.8731255 0.804731758 GEGERPAQNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GEGERPAQNEK 11 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;; 203.61 3.29E-08 11986430000 8727720 7649160 7949470 7973760 8807060 6843060 9665000 7209560 10390100 FALSE TRUE 8181467.585 8215511.765 8138035.182 8178380.181 8115389.034 8818540.334 8215822.975 8109689.436 8655925.187 0.945186957 0.949120006 0.940169307 0.944830276 0.937553047 1.01878657 0.949155959 0.936894585 1 23.0452566 GEGGS(ph)EDGS(ph)EDGLPEGIHLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEGGSEDGSEDGLPEGIHLDK 21 0 O75362 O75362 ZNF217 Zinc finger protein 217 2 GEGGS(1)EDGS(1)EDGLPEGIHLDK 51.956 0.065373 101730000 195870 107900 158030 116800 110600 138510 181040 129190 108010 TRUE FALSE 183610.8463 115889.0283 161778.5462 119797.2857 101913.9221 178495.5885 153894.7327 145319.6559 89982.43323 2.040518796 1.287907252 1.797890326 1.331340812 1.13259798 1.983671502 1.710275297 1.614978065 1 16.45735576 -1.99652198 2.614100404 0.41052909 1.60194631 0.298735241 0.294485375 17796765.73 8472459.352 63184180.15 0.066260447 0.010080406 1.99652198 1.191417219 GEGGTTNPHIFPEGSEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GEGGTTNPHIFPEGSEPK 18 0 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5H3F0;Q96FW1-2 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ;;; 141.86 1.17E-07 851810000 2328900 1734130 2067540 2004160 1930360 1650100 2434510 1752590 1799730 FALSE TRUE 2183138.306 1862526.79 2116583.025 2055590.139 1778757.312 2126457.083 2069477.826 1971404.719 1499343.436 1.456062869 1.242228261 1.411673252 1.370993522 1.186357488 1.41825884 1.380256035 1.314845333 1 20.51589945 0.9299761 14.08351311 0.999999998 1.347336792 0.645351388 0.081374262 42.85387795 8619.772187 0.071929519 0.017983479 8.51091199 -0.9299761 0.347336794 GEGPAIPGDT(ph)PPPTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GEGPAIPGDTPPPTPR 16 0 O75145-2;O75145 O75145-2 PPFIA3 Liprin-alpha-3 1 GEGPAIPGDT(1)PPPTPR;GEGPAIPGDT(1)PPPTPR;GEGPAIPGDT(1)PPPTPR;GEGPAIPGDT(1)PPPTPR 274.02 3.59E-34 1453960000 2089920 2506020 2331190 2470720 2383920 2139720 2660540 2024630 2142400 TRUE FALSE 1959115.638 2691568.328 2386486.928 2534122.858 2196696.539 2757422.429 2261616.726 2277409.512 1784819.6 1.097654709 1.508033825 1.3371026 1.419820165 1.230766706 1.544930608 1.267140235 1.275988628 1 20.76734683 0.776954896 1.438576727 1.001321104 1.367831048 0.400476318 0.130678723 0.669361913 2.428269373 0.108608318 0.031967388 5.983494501 -0.776954896 0.366509944 GEGPDVHMTLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GEGPDVHMTLPK 12 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 136.96 0.00010074 392820000 1354590 1501750 1519190 1452700 1863730 1248780 1773390 1489510 2038400 FALSE TRUE 1269808.63 1612941.133 1555225.904 1489978.741 1717360.164 1609282.514 1507486.633 1675478.602 1698177.871 0.747747719 0.949806943 0.91582038 0.877398514 1.011295809 0.947652505 0.887708324 0.986633162 1 20.69555615 4.740660141 24.7915779 0.938396056 0.747747645 0.65289039 0.045279057 103.3571029 1220365.986 0.009971586 0.065639605 55037.68278 -4.740660141 -0.190648411 GEGPGEAGGPLT(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 173.19 3.06E-05 874100000 489456 634630 690210 803270 852340 510990 431924 320919 499600 TRUE FALSE 458821.8227 681618.6655 706582.1071 823883.2681 785400.6546 658504.5178 367161.006 360986.4436 416213.5325 1.102371227 1.637665795 1.697643282 1.979472564 1.88701374 1.582131446 0.882145767 0.867310684 1 18.66696435 1.769929327 4.426148749 0.902512167 1.6804296 0.688292425 0.231814742 0.109455726 4.397709787 0.117529376 0.061590174 58.87478402 -1.769929327 0.777917433 GEGQLGPAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GEGQLGPAER 10 0 P13639 P13639 EEF2 Elongation factor 2 0 ;; 200.78 5.91E-07 2894070000 1760400 2319940 1951100 1862700 2420460 1693890 1991530 2029180 2098040 FALSE TRUE 1650219.706 2491710.771 1997381.013 1910500.036 2230366.835 2182888.545 1692918.565 2282527.59 1747863.57 0.944135306 1.425575093 1.142755675 1.093048719 1.276053162 1.248889549 0.968564477 1.30589574 1 20.73716115 -0.035891611 0.300564471 0.948946707 1.221424739 0.069340052 0.153099837 11.88066514 1.586834185 0.928380929 0.178857373 0.920679321 0.035891611 0.272478031 GEGS(ph)DSKESPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GEGSDSKESPK 11 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 1 GEGS(0.988)DS(0.012)KESPK;GEGS(0.989)DS(0.01)KES(0.001)PK 92.935 0.005829 519730000 1147640 530330 755830 691380 720100 538000 989750 643360 941640 TRUE FALSE 1075811.261 569596.185 773758.6445 709121.9813 663546.2507 693311.8663 841346.1759 723684.9122 784474.2008 1.371378765 0.726086574 0.986340461 0.903945573 0.845848404 0.8837918 1.072496935 0.922509512 1 19.58136648 1.751531499 24.99999999 1.003565522 0.924586329 0 0.170770618 13.64692459 26343.28721 0.071588786 0.039700293 56.43278701 -1.751531499 -0.078979193 GEGSDSKES(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GEGSDSKESPK 11 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 1 GEGSDS(0.03)KES(0.969)PK;GEGSDS(0.013)KES(0.987)PK 76.588 0.021161 478040000 2465340 730340 1331250 1104810 993030 963870 1755770 993500 874220 TRUE FALSE 2311038.77 784415.1335 1362827.879 1133161.295 915041.4295 1242123.622 1492508.588 1117540.662 728307.0343 3.173165521 1.077039074 1.871227126 1.555884046 1.256395155 1.705494473 2.049284873 1.534436178 1 19.47418725 4.749629876 24.9993465 1.570905162 3.173166446 0.707468748 0.334574944 959.8785596 2167794.805 0.078175725 1.191427936 56186.22789 -4.749629876 1.602261284 GEGYAKPNEGAIVEVALEGYYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GEGYAKPNEGAIVEVALEGYYK 22 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;; 185.5 3.22E-17 494860000 1754040 1230490 1499990 1418430 1563700 1184100 1861270 1410600 1542720 FALSE TRUE 1644257.767 1321596.76 1535570.471 1454829.315 1440893.31 1525930.448 1582189.843 1586716.515 1285230.066 1.279348975 1.028295863 1.194782562 1.131960226 1.121117027 1.187281942 1.231055735 1.234577806 1 20.2935952 2.223315716 23.48822041 1.187859096 1.139441344 0 0.091117643 342.4231545 527573.1355 0.030645 0.022738034 167.2305876 -2.223315716 -0.048417752 GEHPEGDPGEVPAPS(ph)PQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEHPEGDPGEVPAPSPQER 19 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 GEHPEGDPGEVPAPS(1)PQER 67.979 0.016097 206120000 112980 108060 117070 111310 125270 96543 96354 91984 90633 TRUE FALSE 105908.7835 116060.8748 119846.9557 114166.403 115431.7995 124413.3969 81906.61221 103468.4049 75505.76679 1.402658207 1.537112724 1.58725566 1.512022298 1.528781237 1.647733705 1.084772934 1.370337781 1 16.20429921 1.731112522 9.169133725 1.175503455 1.540702704 0.724723379 0.111171079 0.049162758 14.49852693 0.046996156 0.025273187 53.8409262 -1.731112522 0.36519925 GEHSIVYLKPSYAFGSVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEHSIVYLKPSYAFGSVGK 19 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 217.26 2.19E-19 1739300000 2393000 1795500 2162500 1974700 2152300 1711600 2666200 2057100 2064600 FALSE TRUE 2243226.402 1928440.688 2213795.521 2025374.145 1983267.04 2205711.134 2266428.062 2313933.463 1720004.922 1.304197664 1.121183238 1.287086736 1.177539738 1.153058933 1.282386525 1.317686963 1.345306303 1 20.71398126 2.212472975 24.66504589 1.269396459 1.205979458 0 0.10947475 510.0270838 482210.6747 0.036516489 0.026978482 163.1071408 -2.212472975 -0.063417001 GEKPNPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GEKPNPLR 8 1 P68402;J3KNE3 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 ;;;;; 92.439 0.010741 4460550000 6671030 6883710 6886670 7011050 8043600 6005320 8469940 6777870 9139310 FALSE TRUE 6253502.14 7393387.051 7050025.065 7190965.413 7411888.102 7738958.396 7199951.128 7624101.989 7613900.119 0.821327052 0.971038093 0.925941364 0.944452291 0.973467998 1.016424996 0.945632464 1.001339901 1 22.86020421 5.456171726 1.630776872 0.968263585 5.11E-10 0.709371948 0.029774464 5.61745194 2.510365707 0.007600457 15.24979175 285872.0695 -5.456171726 -0.968263585 GELS(ph)EEELPYYVELPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GELSEEELPYYVELPDR 17 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 GELS(1)EEELPYYVELPDR;GELS(1)EEELPYYVELPDR 233.52 4.32E-20 99816000 178541 188602 187732 192619 160011 185124 232940 170597 140887 TRUE FALSE 167366.4375 202566.2883 192185.0917 197561.9296 147444.3815 238566.2936 198012.8095 191896.411 117372.0495 1.425947985 1.725847756 1.637400833 1.683211041 1.256213742 2.032564776 1.687052499 1.634941298 1 16.84072937 0.915700519 17.75516358 1 1.655156109 0.496453038 0.200345728 1288.590346 271405.7808 0.175317725 0.043829431 8.235700013 -0.915700519 0.65515611 GELWDTCNIGVPWYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GELWDTCNIGVPWYDR 16 0 P13807 P13807 GYS1 "Glycogen [starch] synthase, muscle" 0 ; 150.26 1.76E-06 84980000 98491 107260 105222 96242 96568 102010 118264 94930 74818 FALSE TRUE 92326.62412 115201.642 107717.9155 98711.73266 88983.93882 131458.631 100531.4111 106782.2195 62330.39246 1.481245673 1.848241884 1.728176437 1.583685402 1.427617175 2.1090615 1.612879482 1.713164562 1 15.92764818 0.052823944 2.035035005 0.999954023 1.707612343 0.55459537 0.193049216 47.2018242 99.11421732 0.172779214 0.04647779 1.129338006 -0.052823944 0.707658319 GEMMDLQHGSLFLQTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GEMMDLQHGSLFLQTPK 17 0 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50;C9J7H8;F5H793 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 ;; 217.88 4.83E-15 1490490000 1055210 2013020 2008760 1981170 2071900 1898090 2154830 1966500 1620020 FALSE TRUE 989166.2897 2162066.095 2056408.736 2032010.176 1909181.332 2446037.77 1831733.246 2212021.854 1349628.196 0.732917623 1.60197164 1.523685369 1.505607383 1.414597988 1.812378977 1.357213232 1.6389861 1 20.36413059 4.742691242 24.73338366 1.510886136 0.732917267 0.545518752 0.213356051 231.9968662 1389090.812 0.042763127 0.328998995 55295.6849 -4.742691242 -0.777968869 GEMMDLQHGSLFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 18 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 ;;;;;;;;;;;;;;;;; 238.03 2.59E-17 20610405000 10982324 31214550 25195876 26973429 26957289 23252751 27762637 26587586 15830809 FALSE TRUE 10294959.94 33525707.76 25793534.08 27665612.85 24840172.26 29965442.74 23599887.32 29907104.64 13188544.71 0.780598631 2.542032385 1.955752864 2.097700199 1.883465751 2.272081068 1.789423158 2.267657676 1 23.65278204 -0.561407293 8.809166524 1.000000703 2.003398233 0.27961801 0.47125379 0 0 0.39630267 0.093409435 0.274531831 0.561407293 1.00339753 GENHPHFEGGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GENHPHFEGGVK 12 0 F6WE04;Q5SRH9-5;Q5SRH9-6;Q5SRH9-4;Q5SRH9;A0A0A0MRQ0;A0A0A0MSH8;E9PAZ4;A0A0A0MSW9;Q5SRH9-3 F6WE04 TTC39A Tetratricopeptide repeat protein 39A 0 ; 89.231 0.0055167 468010000 430840 430660 395690 426470 472890 333700 527960 353780 430830 FALSE TRUE 403874.4935 462546.5145 405075.9537 437413.9422 435751.1269 430033.7728 448797.2993 397950.2118 358921.6897 1.125244044 1.288711515 1.128591459 1.218689075 1.214056267 1.198127015 1.250404509 1.108738266 1 18.45330958 0.993245574 4.443618737 1.000331098 1.206637587 0.649003357 0.049184844 0.093216229 5.71755683 0.042884653 0.010907407 9.845676771 -0.993245574 0.206306489 GENLEHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GENLEHLR 8 0 C9JXZ5;Q9BV40;B8ZZT4 C9JXZ5 VAMP8 Vesicle-associated membrane protein 8 0 ;; 177.97 0.00025206 877990000 1238310 2428500 1181060 1292220 2464000 892920 1449310 2266160 2263760 FALSE TRUE 1160806.388 2608308.667 1209075.301 1325380.553 2270487.379 1150691.509 1231999.42 2549095.064 1885923.832 0.615510748 1.383040303 0.641105055 0.702775229 1.203912555 0.610147393 0.653260434 1.351642639 1 20.84683998 5.016233307 17.69986447 0.910574172 0.043726743 0.099810627 0.295159211 32645009.49 736004338 0.067962242 745012466.7 103808.5935 -5.016233307 -0.866847429 GEPAAAAAPEAGAS(ph)PVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GEPAAAAAPEAGASPVEK 18 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 GEPAAAAAPEAGAS(1)PVEK;GEPAAAAAPEAGAS(1)PVEK;GEPAAAAAPEAGAS(1)PVEK;GEPAAAAAPEAGAS(1)PVEK 290.94 3.78E-49 774200000 3050410 2169370 2883250 3662600 2320040 1347110 1644610 1023400 862520 TRUE FALSE 2859490.283 2329992.412 2951642.052 3756588.517 2137833.417 1735998.788 1398015.998 1151173.743 718559.8399 3.979474115 3.242586466 4.107719201 5.227941096 2.975164069 2.415941849 1.94558048 1.602056891 1 19.45474878 2.141278484 1.649268415 1.555546018 3.977406523 0.79885672 0.571002812 0.180013052 0.945802749 0.339590371 0.189535522 138.4453851 -2.141278484 2.421860504 GEPNVS(ph)YICSR ddPTM_SK-BR-3_Pertuzumab_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(0.758)Y(0.241)ICS(0.001)R;GEPNVS(0.638)Y(0.362)ICSR;GEPNVS(0.954)Y(0.046)ICSR;GEPNVS(0.902)Y(0.098)ICSR 285.55 1.01E-27 14434430000 1255830 1381920 1261290 1397910 1288390 1290970 1545410 1118020 1438690 TRUE FALSE 1177229.842 1484238.795 1291208.394 1433782.737 1187205.047 1663652.082 1313690.117 1257607.258 1198563.345 0.982200772 1.238348229 1.077296749 1.196251115 0.990523406 1.388038512 1.096053974 1.049262239 1 20.19287473 1.276446836 3.90045942 1.017528478 1.150890678 0.141817108 0.119112548 0.360241203 10.0640529 0.087210162 0.026695822 18.89934862 -1.276446836 0.1333622 GEPNVSY(ph)ICSR ddPTM_SK-BR-3_Pertuzumab_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(0.39)Y(0.61)ICSR;GEPNVS(0.392)Y(0.608)ICSR;GEPNVS(0.194)Y(0.806)ICSR;GEPNVS(0.47)Y(0.53)ICSR 173.24 0.00012799 4732800000 624000 708514 684644 702515 757462 638877 770660 667074 846487 TRUE FALSE 584944.9539 760973.1138 700884.079 720542.7243 697973.99 823310.4186 655106.6875 750359.6573 705202.8512 0.829470489 1.079084 0.993875844 1.021752426 0.989749246 1.167480275 0.928962052 1.064033783 1 19.42767878 4.747862141 24.43669028 1.028227518 0.829470345 0.495215752 0.063781548 737.9859714 1938758.465 0.013565111 0.168924667 55957.99453 -4.747862141 -0.198757174 GEQGLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GEQGLLR 7 0 P55327-2;P55327-4;P55327-3;E5RFR7 P55327-2 TPD52 0 ;;; 140.12 0.0061558 1471980000 1764670 2963360 1850900 1918570 3038930 1582030 1800900 2589430 1919180 FALSE TRUE 1654222.455 3182770.258 1894804.222 1967803.754 2800264.696 2038736.379 1530871.764 2912726.036 1598856.46 1.034628496 1.990654157 1.185099645 1.230756984 1.751417195 1.275121582 0.957479175 1.821755804 1 20.60860899 -3.810023544 0.104747415 9.78E-11 1.688474312 0.064807464 0.355483797 272.2519872 2.506762554 64.84843462 5.286258552 0.000154873 3.810023544 1.688474312 GEQGYGFHLHGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEQGYGFHLHGEK 13 0 Q15599;Q15599-2 Q15599 SLC9A3R2 Na(+)/H(+) exchange regulatory cofactor NHE-RF2 0 116.78 0.00032287 307060000 591820 568410 558340 596540 795510 453910 598820 613240 766150 FALSE TRUE 554779.0426 610495.6678 571584.0885 611848.2263 733033.8535 584946.4484 509032.5002 689804.3639 638274.6155 0.869185503 0.956478063 0.895514367 0.958597148 1.148461549 0.916449494 0.797513308 1.080732881 1 19.28381775 6.199352505 0.877189102 0.955190709 3.26E-12 0.071765555 0.097610733 88.01304676 6.641825692 0.031664228 141.0877189 1582532.015 -6.199352505 -0.955190709 GES(ph)ENAGTNQETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GESENAGTNQETR 13 0 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 GES(1)ENAGTNQETR;GES(1)ENAGTNQETR 292.85 1.44E-40 504870000 611680 559640 580150 606610 561380 506210 731430 530130 503070 TRUE FALSE 573396.0407 601076.3279 593911.432 622176.6396 517291.4793 652344.6094 621758.8618 596317.8975 419104.367 1.368146185 1.434192471 1.417096739 1.48453867 1.234278428 1.556520668 1.483541835 1.422838663 1 18.67695003 -1.226283327 4.296321435 0.999795616 1.431105036 0.713775912 0.084533018 0.000152749 2.75E-05 0.075547056 0.017798249 0.059390458 1.226283327 0.43130942 GESAADS(ph)DGWDSAPSDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GESAADSDGWDSAPSDLR 18 0 I3L4Q4;Q9BUL5-4;Q9BUL5;I3L0Y2;A0A087WVQ2;Q9BUL5-2 I3L4Q4 PHF23 PHD finger protein 23 1 GESAADS(1)DGWDSAPSDLR 221.85 6.31E-19 63009000 62442 68398 60498 69971 60051 63022 76395 63313 51069 TRUE FALSE 58533.86668 73462.25909 61933.04113 71766.57432 55334.83669 81215.42832 64940.27897 71217.76742 42545.25398 1.375802497 1.72668517 1.455698 1.686829143 1.300611267 1.908918639 1.526381274 1.673929775 1 15.37671058 -1.518626319 6.209457421 0.999396714 1.588291343 0.510430129 0.17898589 0.001273638 9.87E-05 0.147656852 0.034770001 0.03029519 1.518626319 0.588894629 GESAEDKEHEEGRDS(ph)EEGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GESAEDKEHEEGRDSEEGPR 20 2 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;K7EPS6;A0A087WX58 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 1 GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR;GESAEDKEHEEGRDS(1)EEGPR 250.99 3.03E-31 4144511000 3774938 2187898 2742801 2652922 2559323 2424139 3270583 2462505 2383785 TRUE FALSE 3538671.369 2349892.244 2807861.535 2721000.47 2358324.095 3123948.577 2780189.442 2769954.17 1985915.884 1.781883814 1.183278841 1.413887445 1.370148903 1.187524665 1.573051811 1.399953273 1.394799343 1 20.92137309 -1.16670088 4.604257716 0.999942873 1.392283823 0.3534649 0.173556406 9.08E-05 1.64E-05 0.14985493 0.035316016 0.06812384 1.16670088 0.39234095 GESDDFHMDFDSAVAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GESDDFHMDFDSAVAPR 17 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 ;;; 175.65 1.20E-09 394682000 606270 760790 739600 726520 747570 631270 846650 699000 792190 FALSE TRUE 568324.6429 817119.6832 757143.6613 745163.7332 688858.8678 813507.4012 719702.6924 786271.6887 659968.3713 0.861139212 1.23811946 1.147242344 1.129090068 1.043775577 1.232646043 1.090510885 1.191377834 1 19.33203736 -0.959637058 4.409909675 0.999996624 1.130719489 0.089193045 0.109406669 0.00786034 28350234.2 229.3414042 0.022579318 0.109739491 0.959637058 0.130722865 GESEDDFWWCIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GESEDDFWWCIDR 13 0 O43865-2;O43865;H0Y8B3;Q96HN2-4;Q96HN2-3;Q96HN2-2;Q96HN2 O43865-2 AHCYL1;AHCYL2 Putative adenosylhomocysteinase 2;Adenosylhomocysteinase;Putative adenosylhomocysteinase 3 0 ;;;; 307.96 3.82E-50 1170210000 674801 739128 741822 717429 817188 854084 944277 729599 789186 FALSE TRUE 632566.41 793853.8062 759418.3682 735839.4427 753009.3509 1100644.186 802691.4301 820691.0412 657465.7583 0.962128296 1.207445097 1.155069079 1.119205728 1.145321017 1.674070736 1.22088705 1.24826431 1 19.32655623 2.429242451 24.99999954 1.321144449 1.13417831 0.168544356 0.17596831 170.1783846 88857.96322 0.055170224 0.046158731 268.6843993 -2.429242451 -0.186966138 GESEFDSFRQSLPVFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GESEFDSFRQSLPVFEK 17 1 Q9H6S0;D6RA70 Q9H6S0 YTHDC2 Probable ATP-dependent RNA helicase YTHDC2 0 ; 74.816 0.014028 293260000 501880 629540 651890 687470 861430 448190 780900 625620 1278120 FALSE TRUE 470468.2267 676151.7966 667353.1386 705111.6441 793776.7626 577575.1772 663811.2945 703730.0342 1064793.515 0.441839869 0.635007433 0.62674418 0.662205051 0.745474828 0.542429278 0.62341786 0.660907513 1 20.02214226 -5 0.292235544 3.993089972 0.599405169 0.717830138 0.076650516 135.6640233 1.273532984 247.8085907 0.076707715 1.00E-05 5 -3.393684804 GESFYQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GESFYQDR 8 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;; 180.87 0.00055093 1508160000 1211520 1666970 1437570 1474240 1726670 1274880 1584660 1449230 1727000 FALSE TRUE 1135693.126 1790394.193 1471669.839 1512071.494 1591064.303 1642917.16 1347054.944 1630169.556 1438752.543 0.789359596 1.244407318 1.022879053 1.050960084 1.105863764 1.141903914 0.9362659 1.133043735 1 20.45638705 GESVCLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GESVCLDR 8 0 P62072 P62072 TIMM10 Mitochondrial import inner membrane translocase subunit Tim10 0 79.596 0.064272 236510000 249380 327290 294840 320670 359570 268980 324300 290400 312740 FALSE TRUE 233771.751 351522.8921 301833.744 328898.9351 331330.8226 346630.1595 275674.2257 326657.0792 260541.6736 0.897252818 1.349200254 1.158485473 1.262365941 1.271699909 1.330421175 1.058081119 1.253761345 1 17.99115462 0.151009828 0.799228628 0.996829606 1.213620178 0.156819054 0.136677394 6.197399132 4.502298458 0.183412474 0.041284099 1.415825818 -0.151009828 0.216790572 GETDEEYLWCIEQTLYFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GETDEEYLWCIEQTLYFK 18 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 95.654 0.0017382 11013000 35762 29759 35274 34427 38948 28534 43300 32469 36031 FALSE TRUE 33523.72026 31962.38732 36110.71594 35310.4551 35889.18119 36771.30259 36807.56698 36522.82612 30017.19333 1.116817282 1.064802661 1.203001078 1.176340996 1.195620816 1.225008021 1.226216141 1.216730216 1 14.87350147 3.920961332 3.642359483 1.192275754 1.091290569 0.194998742 0.068011707 0.258456456 6.909549325 0.015568961 0.031566793 8336.069606 -3.920961332 -0.100985185 GETITGLLQEFDVQEQDIETLHGSVHVTLCGTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 GETITGLLQEFDVQEQDIETLHGSVHVTLCGTPK 34 0 Q92597;E5RI76;E5RIR1;E5RGM5;E5RIM2;E5RH82;E5RK17;E5RIV1 Q92597 NDRG1 Protein NDRG1 0 ;;;;;;;; 425.62 2.89E-208 875843000 355178.3 978503 753284 912951 993655 617066.8 956930 815783 466900.7 FALSE TRUE 332948.3242 1050952.38 771152.2522 936378.8683 915617.3445 795203.9679 813447.2302 917635.3033 388971.9569 0.855969996 2.701871849 1.982539457 2.407317164 2.35394179 2.044373518 2.091274746 2.359129719 1 18.56930662 -1.614546175 8.65468187 0.999468199 2.152735965 0.325956467 0.491656238 0.004380821 0.000195109 0.413370036 0.097398282 0.024291472 1.614546175 1.153267766 GEVFSVLEFAPSNHSFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEVFSVLEFAPSNHSFK 17 0 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 0 188.44 4.11E-10 147740000 104670 186010 158360 169250 190640 125170 206810 170330 182710 FALSE TRUE 98118.89154 199782.3739 162116.374 173593.2415 175667.9034 161304.547 175800.7604 191596.0754 152214.5206 0.644609273 1.312505358 1.065051963 1.140451258 1.154081113 1.059718523 1.154953941 1.258724034 1 17.21574647 4.750451257 24.80518593 1.147885886 0.644608934 0.743835803 0.091913899 798.4440169 1665607.884 0.020188861 0.33536313 56292.59336 -4.750451257 -0.503276953 GEVPGGSAHYGGPS(ph)PEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GEVPGGSAHYGGPSPEKK 18 1 O94762-4;O94762;J3KS37 O94762-4 RECQL5 ATP-dependent DNA helicase Q5 1 GEVPGGSAHYGGPS(1)PEKK;GEVPGGSAHYGGPS(1)PEKK;GEVPGGSAHYGGPS(1)PEKK;GEVPGGSAHYGGPS(1)PEKK 190.63 1.25E-14 1333920000 2484280 1485110 1907730 1923700 2007110 1337940 2742860 1650140 2328720 TRUE FALSE 2328793.349 1595069.09 1952982.256 1973065.399 1849479.677 1724181.558 2331593.606 1856163.611 1940041.588 1.20038321 0.822182936 1.006670305 1.017022218 0.953319603 0.888734329 1.201826611 0.956764856 1 20.88765615 1.757264714 25 1.072282772 0.966224348 0.059739544 0.116101798 13.90053312 18597.83696 0.048800981 0.027062572 57.18270741 -1.757264714 -0.106058424 GEVPPKET(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GEVPPKETPK 10 1 P49006 P49006 MARCKSL1 MARCKS-related protein 1 GEVPPKET(1)PK;GEVPPKET(1)PK;GEVPPKET(1)PK;GEVPPKET(1)PK 97.463 0.0097672 2232840000 5789900 2628830 3635690 3599050 3904430 2200130 4119930 2576690 4232150 TRUE FALSE 5427520.494 2823471.308 3721930.284 3691407.716 3597791.818 2835271.815 3502184.744 2898395.418 3525776.824 1.539382883 0.80080829 1.055634111 1.046977134 1.020425284 0.804155214 0.993308686 0.822058673 1 21.74950973 2.419486204 10.33843357 0.910302172 1.048269447 0.17048945 0.193355334 1.017746782 176.463085 0.062107569 0.051949021 262.7158067 -2.419486204 0.137967274 GEVQVSDKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GEVQVSDKER 10 1 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ;;; 183.99 1.47E-06 3849040000 3448540 3924340 3197530 3278220 4632940 2514540 3645070 3644620 5188390 FALSE TRUE 3232702.037 4214902.217 3273376.922 3362344.675 4269087.581 3240446.878 3098525.593 4099658.83 4322414.191 0.747892704 0.975126869 0.757302928 0.777885813 0.987662772 0.74968449 0.716850689 0.948465059 1 22.04340589 1.052071905 7.590627532 0.999824053 0.822100934 0.336433442 0.093590363 0.228857646 26.70566682 0.088807705 0.022252924 11.27384099 -1.052071905 -0.177723118 GEVTAADLFNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GEVTAADLFNSR 12 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 166.87 0.00011804 115815000 235910 268960 276610 253210 265780 228189 279440 232634 246930 FALSE TRUE 221144.8142 288874.0783 283171.3198 259707.7973 244906.7109 294063.46 237540.5662 261678.867 205715.7878 1.075001664 1.404238738 1.376517198 1.262459241 1.190510041 1.429464715 1.154702654 1.27204076 1 17.65029299 0.320040298 0.564760234 0.985998523 1.311606369 0.341937387 0.113950579 2.421802876 1.176015865 0.184293623 0.047447087 2.089490003 -0.320040298 0.325607846 GEWGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEWGGR 6 0 H3BNR6 H3BNR6 VWA9 0 99.511 0.090068 386340000 253840 301060 291190 296630 303600 271530 310400 284290 256900 FALSE TRUE 237952.6075 323350.7957 298097.1643 304242.028 279756.4807 349916.3031 263858.4016 319784.2323 214021.7304 1.111815175 1.510831611 1.39283597 1.42154737 1.307140542 1.634956892 1.232857996 1.494167119 1 17.70739776 -1.632159693 2.525417985 0.95324827 1.397020256 0.404969032 0.147570335 10276660.25 8689732.753 3138250.494 0.031851951 0.023326002 1.632159693 0.443771986 GEWIKPGAIVIDCGINYVPDDKKPNGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GEWIKPGAIVIDCGINYVPDDKKPNGR 27 3 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ; 248.64 4.23E-46 956750000 1453650 848510 1101580 1054630 1205420 831240 1576180 989770 1641380 FALSE TRUE 1362668.641 911334.5633 1127709.998 1081693.591 1110751.176 1071205.494 1339846.442 1113344.963 1367423.074 0.996523071 0.666461303 0.824697213 0.791045297 0.812295182 0.783375324 0.979833138 0.814192026 1 20.38302824 1.444982483 0.72807055 0.981180066 0.788705828 0.207952666 0.096462738 0.726020591 0.84115909 0.082824213 0.035911058 27.86008792 -1.444982483 -0.192474237 GEWKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GEWKPR 6 1 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;;;; 106.29 0.029414 6982690000 10558130 12562850 10119820 10384480 12732010 7541200 11896540 10710950 10547670 FALSE TRUE 9897315.49 13493016.49 10359866.91 10650963.34 11732089.29 9718222.019 10112764.27 12048235.69 8787195.736 1.126333791 1.535531572 1.178973044 1.212100385 1.335134626 1.105952605 1.150852282 1.371112702 1 23.0669714 -4.999999979 0.080918154 0.150912661 1.514043646 0.218677778 0.135731711 304.5612631 1.743164905 46.12874561 4.205746272 1.00E-05 4.999999979 1.363130985 GEYVLLEAALTDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GEYVLLEAALTDLR 14 0 Q9UGT4 Q9UGT4 SUSD2 Sushi domain-containing protein 2 0 ;;; 203.51 3.47E-08 44757900 73137 104364 71336 67724 128382 70781 87890 115555 120386 FALSE TRUE 68559.48572 112091.2192 73028.12361 69461.9125 118299.3956 91214.32567 74711.71043 129982.2961 100292.7989 0.683593304 1.117639755 0.728149223 0.692591226 1.179540275 0.909480309 0.74493594 1.296028205 1 16.6138585 1.240627248 24.99677213 1.148014099 0.876841029 0.288048285 0.184177926 66.2735636 801691.919 0.129288202 0.041900442 17.40312534 -1.240627248 -0.27117307 GEYWECK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GEYWECK 7 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 108.09 0.017057 180940000 201200 205350 190040 201930 212390 158530 253590 174070 238510 FALSE TRUE 188607.2512 220554.3277 194547.8385 207111.8657 195709.7461 204295.0375 215566.5337 195803.0227 198701.1402 0.949200649 1.109980182 0.979097746 1.042328522 0.98494526 1.028152316 1.084878192 0.985414691 1 17.60024063 1.991475431 24.91214775 1.038775215 1.021638208 0 0.050675442 1890.30485 5524202.29 0.018559138 0.012949273 98.05628401 -1.991475431 -0.017137007 GFAFVEYESHR ddPTM_SK-BR-3_Pertuzumab_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 0 138.71 0.0015073 0 31525 60690 35795 37021 58395 26969 33520 51544 50269 FALSE TRUE 29551.90652 65183.55075 36644.0743 37971.02154 53808.89225 34754.51249 28493.98718 57979.38186 41878.77915 0.705653487 1.556481638 0.875003404 0.906688836 1.284872514 0.829883612 0.680392021 1.384457308 1 15.35393176 3.738130867 24.28089762 0.962356151 1.199011521 0.01621905 0.291084639 565.3698118 1246870.626 0.069766072 0.124178806 5471.808215 -3.738130867 0.236655371 GFAFVQYVNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFAFVQYVNER 11 0 B4DY08;G3V4W0;G3V5X6;G3V3K6;G3V251;B4DSU6;G3V4M8;P07910;G3V2Q1;G3V576;G3V555;G3V575;P07910-2;G3V4C1;B2R5W2;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ; 202.2 9.50E-08 894780000 245860 805270 187682 181679 966740 122063 205196 711040 723590 FALSE TRUE 230472.0615 864893.0287 192133.9057 186341.1907 890816.14 157300.6066 174428.7647 799814.9092 602818.1544 0.382324354 1.434749472 0.318726144 0.309116753 1.477752675 0.260942053 0.289355527 1.326793003 1 19.20136334 1.222704173 24.98411748 1.163396667 0.665363825 0.179170211 0.463974086 507.2395321 799206.9315 0.427180184 0.108227858 16.69952709 -1.222704173 -0.498032842 GFAFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFAFVR 6 0 Q01130;Q01130-2;J3KP15;J3QL05;Q9BRL6-2;Q9BRL6 Q01130;Q9BRL6-2 SRSF2;SRSF8 Serine/arginine-rich splicing factor 2;Serine/arginine-rich splicing factor 8 0 ; 106.05 0.075504 771620000 688310 1562930 733370 654780 1584540 611500 896070 1357110 1390540 FALSE TRUE 645229.9058 1678650.963 750765.8827 671582.7633 1460096.62 788030.1231 761712.6222 1526548.171 1158449.891 0.556976966 1.449049266 0.648077995 0.579725346 1.260388241 0.680245326 0.657527467 1.317750714 1 20.14376421 5.002521694 20.56746578 0.920304332 0.147687752 0.129218798 0.31204069 99612239.17 3665665362 0.071964755 1922374170 100582.3306 -5.002521694 -0.77261658 GFAFVTFDDHDSVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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 ;;;;;;;; 286.09 3.57E-34 6258649000 7977480 9048070 10345420 9234700 9303620 9931260 11005130 8646050 7961700 FALSE TRUE 7478183.767 9717998.517 10590818.25 9471678.036 8572951.214 12798253.54 9355012.923 9725528.375 6632840.835 1.127448095 1.465133682 1.596724316 1.427997184 1.292500669 1.929528216 1.410408173 1.466268921 1 22.66119548 0.525837564 2.431667968 1.000030038 1.48790544 0.328143699 0.20681577 7.209400221 35.56208258 0.182447483 0.048836037 3.356120642 -0.525837564 0.487875402 GFAFVTFDDHDSVDKIVIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 334.21 3.65E-80 1392069000 1166155 1907374 1816737 2175481 2811471 1257109 2494113 1785073 4267944 FALSE TRUE 1093167.44 2048597.956 1859830.86 2231307.526 2590669.409 1620015.961 2120143.91 2007943.293 3555596.574 0.307449796 0.576161528 0.523071395 0.627548002 0.728617365 0.455624233 0.596283596 0.564727536 1 21.76166021 -5 0.220410594 3.248360007 0.497202299 0.657861173 0.105255825 94.73611754 0.948183215 94.71431633 0.188699019 1.00E-05 5 -2.751157708 GFAFVTFDDHDTVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GFAFVTFDDHDTVDK 15 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;;; 304.42 1.30E-44 3328070000 4752960 3790780 4249270 4033410 4089690 3445550 5184930 3908550 4233460 FALSE TRUE 4455480.718 4071453.296 4350064.691 4136914.129 3768502.244 4440224.351 4407497.881 4396541.071 3526868.177 1.26329664 1.154410398 1.233407225 1.17297101 1.068512362 1.258970885 1.249691698 1.24658503 1 21.74995622 -1.116918913 4.463510916 0.999977312 1.204476599 0.532687537 0.060616675 1.38E-05 2.73E-06 0.057468222 0.013543841 0.076397841 1.116918913 0.204499287 GFAFVTFDDHDTVDKIVVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GFAFVTFDDHDTVDKIVVQK 20 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 324.19 2.51E-67 136123000 164513.3 258374 233942 279593 361626 208307 238928 201716 385800 FALSE TRUE 154216.7062 277504.2798 239491.2147 286767.8297 333225.3527 268441.8493 203102.9645 226900.6866 321407.4876 0.479816781 0.863403282 0.745132655 0.892225106 1.036769103 0.835207205 0.63191734 0.705959554 1 18.29404401 4.74323195 24.30180821 0.819283698 0.479816574 0.44174019 0.125133586 350.0834852 1821153.545 0.030730953 0.246828628 55364.57243 -4.74323195 -0.339467124 GFAFVTFES(ph)PADAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFAFVTFESPADAK 14 0 P38159;H3BT71;H0Y6E7;H3BR27;P38159-3;O75526;Q8N7X1;Q96E39;A0A1B0GUK8 P38159;Q96E39 RBMX;RBMXL2;RBMXL3;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA-binding motif protein, X-linked-like-2;RNA-binding motif protein, X-linked-like-3;RNA binding motif protein, X-linked-like-1" 1 GFAFVT(0.001)FES(0.999)PADAK;GFAFVTFES(1)PADAK 154.72 6.34E-06 61766000 246490 134522 155599 144646 170197 127971 190457 138282 207242 TRUE FALSE 231062.6309 144482.1489 159289.8818 148357.8612 156830.4142 164914.1503 161899.741 155546.8121 172651.9714 1.338314466 0.836840424 0.922606794 0.859288545 0.908361561 0.95518255 0.937723095 0.900926939 1 17.39750728 4.744580057 24.99915865 0.910265369 1.338314654 0.892978804 0.046015453 196.4513987 815854.0628 0.01055023 0.096344521 55536.69825 -4.744580057 0.428049285 GFAFVYFENVDDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFAFVYFENVDDAK 14 0 P62995;P62995-3;H7BXF3 P62995 TRA2B Transformer-2 protein homolog beta 0 ; 191.29 1.18E-06 91940000 302480 260030 288080 270750 307340 218370 334500 280170 324130 FALSE TRUE 283548.3167 279282.8918 294913.3936 277697.9034 283202.7561 281409.8741 284344.8303 315149.8412 270030.609 1.050059909 1.034263829 1.092148015 1.028394167 1.0487802 1.042140649 1.053009625 1.167089325 1 18.04276343 1.422578322 24.99990969 1.092379641 1.051316134 0.087455116 0.043064775 140.9609315 64613.00753 0.02352397 0.009085249 26.45929826 -1.422578322 -0.041063507 GFAVLEYETAEMAEEAQQQADGLSLGGSHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GFAVLEYETAEMAEEAQQQADGLSLGGSHLR 31 0 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 0 ;; 190.48 1.11E-18 55404000 24185.2 32656.1 37201.4 34466.2 36457.5 32919.3 38473.8 32750.2 35632 FALSE TRUE 22671.4915 35073.99162 38083.83478 35350.66104 33594.27501 42422.56751 32705.01086 36839.13456 29684.78901 0.763741036 1.181547614 1.282941063 1.190867856 1.131699976 1.429101197 1.10174308 1.24101049 1 14.85743624 4.738400624 4.534784666 1.210960017 0.734632207 0.584080589 0.113914375 0.119688748 6.383503507 0.023766921 0.182302489 54752.08025 -4.738400624 -0.476327809 GFAVSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GFAVSER 7 0 Q96CN7;D6RGE2 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 110.34 0.015881 223670000 187730 214390 191080 209930 244950 181080 238730 215870 258060 FALSE TRUE 175980.3144 230263.6587 195612.5078 215317.1592 225712.6151 233354.8564 202934.6528 242821.8447 214988.1189 0.818558325 1.071052949 0.909875899 1.001530505 1.049884134 1.085431407 0.943934269 1.129466344 1 17.71389741 3.005518468 23.1481527 1.033277303 0.95892363 0.26072785 0.07889431 101.6932298 426556.3856 0.021167477 0.025203941 1012.787816 -3.005518468 -0.074353673 GFAYVQFEDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GFAYVQFEDVR 11 0 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 0 ;; 120.09 0.0011599 164368000 169127 375980 144844 146243 397331 104015 150342 319815 334135 FALSE TRUE 158541.643 403817.9504 148279.7681 149995.843 366126.226 134042.442 127799.6128 359744.6067 278365.7099 0.569544442 1.450674189 0.532679719 0.53884454 1.31527057 0.481533598 0.459106881 1.292345264 1 18.08662198 3.953296922 21.98142591 0.753852644 1.062875621 0.032701361 0.382345825 194.0976032 179083.5801 0.09115116 0.164539811 8980.425664 -3.953296922 0.309022977 GFAYVQFEDVRDAEDALHNLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 247.85 2.55E-31 308415000 88919 147855 108222 116931 172866 77714.6 107462 112949 224177 FALSE TRUE 83353.71851 158802.338 110789.0769 119931.6474 159289.8017 100149.5434 91349.07073 127050.9313 186760.4105 0.44631364 0.850299791 0.593215 0.642168472 0.852909893 0.536246109 0.489124384 0.680288349 1 17.51082914 -2.074597631 2.277364301 1.528870783 0.642347209 0.416058301 0.135235716 11899128.12 3450497.652 32686995.7 0.032199059 0.00842175 2.074597631 -0.886523574 GFAYVQFEDVRDAEDALHNLDRK ddPTM_SK-BR-3_Pertuzumab_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 ; 219.04 1.29E-32 51687000 56207 98211 62918 71874 142100 38508 75793 67518 287140 FALSE TRUE 52689.1042 105482.6446 64410.44467 73718.40852 130940.0392 49624.63447 64428.54328 75947.77093 239214.479 0.220258842 0.440954264 0.269258136 0.308168673 0.547375058 0.207448289 0.269333794 0.317488186 1 17.86794519 -1.490158657 3.481115901 1.011330642 0.325320655 0.812316606 0.10233075 74421960.28 110182684.1 8219037.492 0.02393043 0.032347546 1.490158657 -0.686009987 GFCFITFKEEEPVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GFCFITFKEEEPVKK 15 2 Q14103-3;Q14103;H0Y8G5;H0YA96;Q14103-2;Q14103-4 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 222.45 7.87E-13 473900000 1292900 831180 1052100 1090800 1225900 686500 1284400 865510 1835000 FALSE TRUE 1211979.697 892721.432 1077056.309 1118791.775 1129622.759 884681.4056 1091816.144 973570.8287 1528726.645 0.79280341 0.583964069 0.704544735 0.731845538 0.73893051 0.578704773 0.714199721 0.636850827 1 20.54389903 -1.291462843 3.499359749 1.001059156 0.678760824 0.675646796 0.068409633 14305403.83 24354178.98 164742.5976 0.01478962 0.051113681 1.291462843 -0.322298332 GFCFLEYEDHK ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;; 251.43 1.66E-17 9504974000 12667420 10963090 12324120 11113120 13040880 9424040 13914540 10223930 14987680 FALSE TRUE 11874588.79 11774808.59 12616453.95 11398301.47 12016701.89 12144607.36 11828183.9 11500410.17 12486139.38 0.951021643 0.943030366 1.010436738 0.91287636 0.962403311 0.972647108 0.947305131 0.921054124 1 23.57382414 1.647660392 12.04187345 0.950673786 0.961236771 0 0.031000248 0.565938625 135.200151 0.013816265 0.007512521 44.42837122 -1.647660392 0.010562985 GFCYVEFDEVDSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFCYVEFDEVDSLK 14 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ; 256.19 6.13E-24 132067000 449890 327820 370390 327960 365950 324300 442810 339530 334360 FALSE TRUE 421732.188 352092.1339 379175.8257 336376.0088 337209.7632 417920.1454 376414.7513 381921.0679 278553.156 1.514009728 1.264003392 1.361233278 1.207582832 1.210575992 1.500324575 1.351321079 1.37108864 1 18.08759314 -1.937323322 2.537741336 0.763874421 1.340641027 0.523121175 0.104091535 7836041.868 4437365.158 10962667.62 0.024999629 0.011552519 1.937323322 0.576766607 GFCYVEFDEVDSLKEALTYDGALLGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFCYVEFDEVDSLKEALTYDGALLGDR 27 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ; 327.17 3.66E-95 1724530000 1653330 2023450 1892880 1987960 2621400 1527320 2492600 1770780 3415800 FALSE TRUE 1549851.027 2173268.343 1937780.007 2038974.419 2415525.818 1968232.49 2118857.77 1991865.781 2845680.913 0.544632752 0.763707671 0.680954776 0.716515478 0.848839308 0.691656075 0.744587266 0.699961043 1 21.44034247 -5 0.221147508 2.422120596 0.682802371 0.611122868 0.073805795 103.0526303 1.03153741 65.4379729 0.127862326 1.00E-05 5 -1.739318225 GFDILGIKPVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFDILGIKPVQR 12 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 197.3 1.79E-07 1148690000 2758000 3150900 2883100 2898800 3270200 2426600 3475200 2946700 3420000 FALSE TRUE 2585381.703 3384195.915 2951488.493 2973188.116 3013371.683 3127120.027 2954126.022 3314601.981 2849179.906 0.907412585 1.187778949 1.035908083 1.043524177 1.057627732 1.09755092 1.036833798 1.163352997 1 21.44211529 -0.479084324 7.538276103 1.000002179 1.072238656 0.063758816 0.076790582 0 0 0.06533666 0.015399998 0.331830022 0.479084324 0.072236476 GFDLASFNPHGISTFIDNDDTVYLFVVNHPEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GFDLASFNPHGISTFIDNDDTVYLFVVNHPEFK 33 0 A0A0J9YXF2;Q15165-1;Q15165;A0A0J9YYF0;A0A0J9YYF3;A0A0J9YXU7;G3XAK4 A0A0J9YXF2 PON2 Serum paraoxonase/arylesterase 2 0 171.23 1.08E-14 61658000 49039 58481 39721 42431 72001 38989 53038 55571 37839 FALSE TRUE 45969.73653 62810.99409 40663.20088 43519.8513 66346.3319 50244.49137 45085.44428 62509.16168 31523.42645 1.458272203 1.992517983 1.289935945 1.380555866 2.104667524 1.593877856 1.430220295 1.982943122 1 14.94413674 -1.070522367 4.628645601 0.999972574 1.638831252 0.342331703 0.284231075 18048179.28 4174219.663 5842.791874 0.062381023 0.085011491 1.070522367 0.638858678 GFDPLLNLVLDGTIEYMRDPDDQYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GFDPLLNLVLDGTIEYMRDPDDQYK 25 1 Q9UK45 Q9UK45 LSM7 U6 snRNA-associated Sm-like protein LSm7 0 82.885 0.020536 99199000 62100 54722 48740 65867 63481 43895 64443 54311 64104 FALSE TRUE 58213.27185 58773.67382 49896.13582 67557.25873 58495.45833 56566.77392 54780.37041 61091.8479 53404.62827 1.090041701 1.100535211 0.934303588 1.265007564 1.095325634 1.059211079 1.025760729 1.143942948 1 15.70467716 -1.095868139 6.68552041 0.999999931 1.076679261 0.082995518 0.08449587 8.45E-08 1.12E-08 0.078687831 0.018546883 0.080192151 1.095868139 0.07667933 GFDQDMANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GFDQDMANK 9 0 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 118.71 0.0021985 152020000 282420 257630 265770 275790 293390 187720 309890 261090 332470 FALSE TRUE 264743.8363 276705.1933 272074.1899 282867.2383 270348.3329 241911.7166 263424.8714 293687.6612 276978.6092 0.955827734 0.999012863 0.982293148 1.021260231 0.976062136 0.873394943 0.95106576 1.060326146 1 18.07941504 2.473032283 24.99775595 0.957386229 0.990821122 0 0.049213765 296.4732679 1812454.116 0.016380492 0.01376096 297.1886934 -2.473032283 0.033434893 GFDQELNVDWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GFDQELNVDWR 11 0 Q8N1G2;Q5T7F5 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 0 115.7 0.0025313 43615000 68249 93612 80132 94591 99048 73627 88756 97280 90666 FALSE TRUE 63977.41692 100543.1299 82032.76888 97018.3652 91269.16962 94881.91967 75447.86177 109425.6221 75533.25888 0.847009885 1.33111071 1.08604832 1.284445642 1.208330886 1.25616081 0.998869411 1.448707811 1 16.20482441 4.753309961 24.28391414 1.195164068 0.847009517 0.378383347 0.142656525 1830.469884 3013683.118 0.03014648 0.656908582 56664.35651 -4.753309961 -0.348154551 GFDQTINLILDESHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GFDQTINLILDESHER 16 0 F2Z2Y6;C9JIZ0;C9JNV3;O95777 F2Z2Y6 LSM8 U6 snRNA-associated Sm-like protein LSm8 0 ;; 285.31 7.93E-36 1015340000 671760 897160 839130 785770 849790 732050 939620 786090 830120 FALSE TRUE 629715.7407 963586.6599 859034.5599 805934.1885 783050.9213 943380.9512 798732.704 884235.0669 691567.6092 0.910562803 1.393336887 1.242155573 1.165372955 1.132283975 1.36411963 1.154959679 1.27859526 1 19.39951077 -1.171370611 4.444989322 0.999953563 1.223940923 0.172092493 0.135998118 5.61E-05 1.05E-05 0.11810131 0.027830981 0.067395266 1.171370611 0.22398736 GFEDDRIEALLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFEDDRIEALLHK 13 1 Q5JRX3-3;Q5JRX3;Q5JRX3-2;H0Y4F7 Q5JRX3-3 PITRM1 "Presequence protease, mitochondrial" 0 ; 115.12 0.00041416 133793000 248553 214969 240990 210781 300896 223101 229580 251689 391430 FALSE TRUE 232996.5114 230885.5284 246706.3966 216189.9973 277264.8419 287506.637 195156.6103 283112.9257 326097.8043 0.714498866 0.7080254 0.756541116 0.662960604 0.850250564 0.88165769 0.598460363 0.868184091 1 18.3149452 -5 0.236319628 2.430667473 0.717981639 0.456536964 0.087941825 152.7856856 1.526786977 104.7586734 0.13739957 1.00E-05 5 -1.712685834 GFEGSFEELCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GFEGSFEELCR 11 0 E7EPM6;P33121-2;P33121;P33121-3;B7Z3Z9;H0Y9U7 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 ;;; 198.61 1.23E-07 356667000 323318 325101 301765 299737 376108 279476 361672 302067 491677 FALSE TRUE 303082.1035 349171.8163 308923.0083 307428.7589 346569.9948 360156.1843 307442.6412 339780.7299 409612.9323 0.73992318 0.85244334 0.754182751 0.750534797 0.846091438 0.879259798 0.750568688 0.829516607 1 18.64390174 -5 0.319270612 2.885331741 0.791618188 0.62739396 0.04903183 211.7634542 1.879719943 269.5908827 0.042088698 1.00E-05 5 -2.093713553 GFEKPTENSSAVLLQWHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GFEKPTENSSAVLLQWHEK 19 1 Q9BPX5 Q9BPX5 ARPC5L Actin-related protein 2/3 complex subunit 5-like protein 0 90.718 0.0013169 278010000 799080 429720 470390 435440 524550 404460 575730 390260 683340 FALSE TRUE 749067.0092 461536.9159 481547.8729 446614.1276 483353.9589 521221.0361 489404.6313 438984.8201 569286.1395 1.315800539 0.810729234 0.845880199 0.784516075 0.849052744 0.915569518 0.85968127 0.771114541 1 19.11879445 4.741318425 24.9931197 0.84778988 1.315800708 0.828145673 0.06596702 90.66711179 821641.8623 0.01399086 0.097390499 55121.16968 -4.741318425 0.468010828 GFENVIHDKLPLQES(ph)EEEEREER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 221.72 9.03E-33 202100000 114810 126850 105790 123730 140870 90128 138750 125240 196560 TRUE FALSE 107624.247 136242.106 108299.3888 126905.1213 129806.6384 116146.4905 117945.7256 140876.4897 163752.8662 0.657235806 0.831998298 0.661358737 0.774979542 0.792698421 0.70927913 0.720266633 0.860299383 1 17.32116063 0.991236883 3.324477373 0.999253704 0.738874003 0.716445309 0.054835253 0.110932713 3.096706138 0.048296317 0.012573905 9.800243882 -0.991236883 -0.260379701 GFESPSDNSSAMLLQWHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GFESPSDNSSAMLLQWHEK 19 0 B1ALC0;O15511;O15511-2 B1ALC0 ARPC5 Actin-related protein 2/3 complex subunit 5 0 ;; 275.68 1.91E-39 1143550000 1518180 1442400 1656780 1470130 1708370 1290010 1834500 1440280 1799110 FALSE TRUE 1423159.824 1549196.797 1696079.604 1507856.025 1574201.511 1662414.945 1559433.756 1620102.128 1498826.918 0.949515789 1.033606201 1.131604713 1.006024115 1.050289058 1.109144041 1.040436182 1.080913419 1 20.51540236 4.677807967 2.926725793 1.064999199 0.93760067 0.409767785 0.04108865 0.29969028 3.968169696 0.009275941 0.083414369 47622.03689 -4.677807967 -0.12739853 GFFDPNTEENLTYLQLMER ddPTM_SK-BR-3_Pertuzumab_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 0 127.32 5.50E-05 49886000 8232.4 12197 9316.9 10044 10734 9140.4 12575 8788.8 7580.4 FALSE TRUE 7717.148779 13100.07857 9537.901268 10301.74604 9890.994939 11779.0851 10689.49549 9886.101027 6315.182269 1.221999374 2.074378539 1.510312903 1.631266622 1.566224777 1.865201129 1.692666187 1.565449833 1 12.62460866 0.786053106 3.045839279 1.000112962 1.685707436 0.448685085 0.222743948 1.006506018 13.12337082 0.192514152 0.050307976 6.110167357 -0.786053106 0.685594474 GFFDPNTHENLTYLQLLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 303.73 3.67E-50 4357090000 3485210 4761570 4165810 4143310 4630570 3840290 4781530 3951590 3432490 FALSE TRUE 3267076.927 5114121.597 4264624.98 4249634.349 4266903.711 4948919.381 4064583.966 4444954.71 2859585.244 1.142500275 1.788413759 1.491343889 1.48610165 1.492140764 1.730642369 1.421389334 1.554405388 1 21.44737448 -0.439836291 0.931224655 0.981010377 1.539523222 0.451188119 0.175741704 18.86242189 10.59357246 1.498429146 0.049164884 0.363214944 0.439836291 0.558512845 GFFDPNTHENLTYLQLLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFFDPNTHENLTYLQLLQR 19 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 241.79 2.23E-24 1357450000 887320 1269930 1019860 990670 1232380 869830 1141740 1007790 872990 FALSE TRUE 831784.2251 1363956.939 1044051.561 1016092.269 1135593.846 1120935.8 970546.6864 1133614.8 727282.3293 1.14368821 1.87541603 1.435551943 1.397108425 1.561420923 1.541266377 1.334484075 1.558699771 1 19.472156 -2.979886685 0.26402489 8.85E-10 1.555442738 0.359024949 0.192750449 58.68938416 1.497886825 32.8320027 0.238399335 0.001047402 2.979886685 1.555442737 GFFDPNTHENLTYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GFFDPNTHENLTYR 14 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 216.15 6.24E-12 3834680000 4664660 6649100 5546600 5911800 6382800 4794160 6529500 5678500 5836900 FALSE TRUE 4372707.257 7141406.282 5678167.971 6063506.797 5881520.635 6178156.165 5550462.092 6387473.225 4862683.682 0.899237446 1.468614195 1.167702516 1.246946582 1.209521536 1.270523968 1.141440088 1.313569552 1 22.21332132 -1.897870468 2.746700695 0.879516072 1.22992978 0.17269808 0.144291332 14318919.36 11085881.32 11200807.61 0.030790965 0.012651136 1.897870468 0.350413708 GFFDPNTHENLTYVQLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GFFDPNTHENLTYVQLLR 18 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;; 296.17 2.48E-49 7149758000 7626664 10044854 8365218 8601387 9612614 7562374 9481301 8341914 7473147 FALSE TRUE 7149324.714 10788585.44 8563644.921 8822113.153 8857678.072 9745508.609 8059667.935 9383420.326 6225830.487 1.148332697 1.732874909 1.375502423 1.417017885 1.422730363 1.565334718 1.294553064 1.507175684 1 22.56983487 -2.981718803 0.334549637 6.48E-09 1.471114537 0.411048496 0.158400304 72.64738263 2.17090952 51.37713306 0.120275176 0.001042993 2.981718803 1.471114531 GFGDGYNGYGGGPGGGNFGGS(ph)PGYGGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GFGDGYNGYGGGPGGGNFGGSPGYGGGR 28 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 GFGDGYNGYGGGPGGGNFGGS(1)PGYGGGR;GFGDGYNGYGGGPGGGNFGGS(1)PGYGGGR;GFGDGYNGYGGGPGGGNFGGS(1)PGYGGGR;GFGDGYNGYGGGPGGGNFGGS(1)PGYGGGR 305.74 2.82E-72 2700720000 1842500 1960440 2050680 2050960 2276790 2013580 2362260 2037400 2055750 TRUE FALSE 1727181.214 2105593.017 2099323.098 2103591.106 2097980.098 2594867.858 2008061.043 2291773.875 1712632.044 1.00849521 1.22944857 1.225787585 1.22827966 1.225003412 1.515134478 1.172499983 1.338158936 1 20.70778379 5.479635904 1.265267751 1.259613135 8.21E-12 0.233328158 0.129385578 10.44256798 3.66194303 0.031570893 26.98167111 301742.0965 -5.479635904 -1.259613135 GFGEYSRS(ph)PTF ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GFGEYSRSPTF 11 1 D6REL5;Q6UWZ7-2;Q6UWZ7 D6REL5 FAM175A BRCA1-A complex subunit Abraxas 1 GFGEYSRS(1)PTF;GFGEYS(0.002)RS(0.998)PTF;GFGEYS(0.022)RS(0.978)PTF 127.52 0.0009311 205143000 277635 454611 342590 413200 543442 213977 318339 371957 787880 TRUE FALSE 260258.3209 488270.8715 350716.3966 423803.4115 500762.2575 275748.6863 270607.0223 418396.6502 656377.7381 0.396506929 0.743887008 0.53432098 0.645669996 0.762917796 0.420106701 0.412273309 0.637432725 1 19.32416678 0.969813824 23.63699522 1.000000004 0.567309879 0.528550341 0.129764435 1575.436443 1233632.284 0.126609191 0.031652298 9.328543133 -0.969813824 -0.432690125 GFGFGQGAGALVHS(ph)E ddPTM_SK-BR-3_Pertuzumab_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 252.46 1.26E-24 11304780000 9021390 10731150 9782910 10042340 10360640 9139350 10528990 8114340 10348880 TRUE FALSE 8456757.304 11525695.51 10014965.25 10300043.45 9546957.127 11777731.98 8950265.696 9127433.211 8621585.072 0.980881965 1.336841824 1.161615313 1.19468095 1.10733201 1.366075018 1.038122993 1.05867229 1 23.0395217 1.607062011 17.63485762 1.036081726 1.20162122 0.319052825 0.108734257 0.058616392 286.7619714 0.048948978 0.02473424 40.4633663 -1.607062011 0.165539495 GFGFILFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFGFILFK 8 0 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ; 168.43 0.00078183 25300000 235050 422890 221580 201093 476160 193254 278020 434030 316890 FALSE TRUE 220338.6401 454201.2156 226835.9822 206253.3868 438764.3143 249043.2926 236333.482 488219.6009 263999.0118 0.834619185 1.72046559 0.859230422 0.781265753 1.66199226 0.943349336 0.895205934 1.849323592 1 18.010173 3.953020762 24.62827401 1.114874163 1.334446075 0.011406393 0.408943276 1022.132133 1044516.493 0.096602728 0.174274943 8974.716982 -3.953020762 0.219571912 GFGFITFEDEQSVDQAVNMHFHDIMGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GFGFITFEDEQSVDQAVNMHFHDIMGK 27 0 K7EQ55;K7EK33;Q96EP5;Q96EP5-2;K7EQ02 K7EQ55 DAZAP1 DAZ-associated protein 1 0 ;;; 370.26 4.39E-127 701766000 872816 824203 836660 822847 948747 661435 977699 840142 1072574 FALSE TRUE 818188.0046 885227.8477 856505.9703 843962.6471 874236.2377 852380.547 831102.1115 945035.5781 893554.4703 0.915655432 0.990681461 0.958538062 0.944500503 0.978380464 0.953921194 0.930107944 1.057613844 1 19.76919615 1.239664079 24.99990754 1.02880693 0.956623074 0.60212887 0.025456647 18.89667533 428208.4546 0.018219674 0.005804345 17.36457183 -1.239664079 -0.072183855 GFGFITFTNPEHASVAMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFGFITFTNPEHASVAMR 18 0 P98179 P98179 RBM3 RNA-binding protein 3 0 ; 213.99 1.59E-17 421090000 205490 504300 388440 386880 433540 371080 441940 362480 408120 FALSE TRUE 192628.7477 541638.8967 397653.9802 396807.9958 399491.5172 478204.772 375675.1998 407736.4259 340002.1354 0.566551582 1.593045573 1.169563184 1.16707501 1.174967671 1.40647579 1.104920118 1.19921725 1 18.37518428 0.646231396 1.220956554 1.001116604 1.220506004 0.015413213 0.262657591 3.612128058 8.341808276 0.224982094 0.068436028 4.428242505 -0.646231396 0.2193894 GFGFVDFNS(ph)EEDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GFGFVDFNSEEDAK 14 0 P19338;H7BY16 P19338 NCL Nucleolin 1 GFGFVDFNS(1)EEDAK;GFGFVDFNS(1)EEDAK;GFGFVDFNS(1)EEDAK;GFGFVDFNS(1)EEDAK 189.1 7.94E-07 136551000 424341 299886 364341 341534 378657 283383 448655 314246 477147 TRUE FALSE 397782.2543 322089.8715 372983.3406 350298.3407 348918.8066 365191.0718 381383.3479 353480.3048 397508.0832 1.000689725 0.810272508 0.938303789 0.881235767 0.877765312 0.918700995 0.959435453 0.889240546 1 18.60062467 0.470558471 0.429776443 1.007298457 0.891088556 0.199070041 0.052585944 3.039954864 1.048752583 0.102788238 0.031839067 2.955006706 -0.470558471 -0.1162099 GFGFVDFNSEEDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GFGFVDFNSEEDAK 14 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;; 322.07 6.65E-56 925050000 2224735 1650322 1905101 1833325 1909618 1496705 2255653 1542691 2202424 FALSE TRUE 2085492.808 1772513.558 1950290.895 1880371.223 1759644.305 1928779.437 1917438.773 1735299.367 1834825.206 1.136616611 0.966039464 1.062930076 1.024823082 0.959025579 1.051206093 1.045025306 0.945757319 1 20.8072112 4.753036847 24.37844891 1.013485618 1.136616733 0.493901769 0.04079338 1617.423426 2723729.338 0.00918177 0.195612621 56628.73328 -4.753036847 0.123131115 GFGFVEFEDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GFGFVEFEDPR 11 0 Q13243;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ;;; 145.17 8.46E-05 500345000 934900 1032610 1087280 1007750 967390 1085360 1177280 953830 725430 FALSE TRUE 876386.2778 1109065.519 1113070.795 1033610.571 891415.0917 1398685.813 1000757.793 1072917.775 604351.0465 1.45012784 1.835134605 1.841762005 1.710281759 1.474995529 2.314359875 1.655921338 1.77532211 1 19.20502728 0.270537592 2.085520367 0.999995129 1.779737787 0.495766521 0.239061326 16.25780397 45.06044418 0.206486618 0.056364591 1.864393551 -0.270537592 0.779742658 GFGFVEFEDPRDADDAVYELDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFGFVEFEDPRDADDAVYELDGK 23 1 Q13243;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ; 177.03 5.09E-17 299760000 453420 522740 475020 490250 651160 306480 554090 425310 910590 FALSE TRUE 425041.2516 561444.2135 486287.6987 502830.645 600020.5203 394955.8007 471009.3484 478410.8897 758606.6464 0.560292022 0.740099255 0.641027469 0.662834484 0.790950782 0.520633193 0.620887453 0.630644211 1 19.53299249 -2.109640469 2.376183192 1.63607779 0.650901122 0.671984915 0.077675261 3198898.514 896986.6397 10994525.06 0.018260084 0.0077689 2.109640469 -0.985176668 GFGFVSFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 168.23 0.00013814 1448690000 840440 1793710 871040 809980 1843950 706760 1006250 1526510 1497450 FALSE TRUE 787838.3606 1926518.155 891701.4801 830765.4581 1699133.605 910790.1387 855372.1541 1717098.134 1247515.921 0.631525696 1.544283421 0.714781643 0.665935756 1.362013563 0.730082978 0.685660311 1.376413803 1 20.2506268 3.85131453 9.138903552 0.901841605 1.149388583 0.021151828 0.339550349 0.675766031 48.61671127 0.08016925 0.144807508 7100.918532 -3.85131453 0.247546978 GFGFVTFDDHDPVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 GFGFVTFDDHDPVDK 15 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;;; 339.5 6.69E-69 38720081000 50226160 37477415 42002304 39656836 44295176 34355723 51938985 40240010 45069347 FALSE TRUE 47082594.3 40252281.8 42998618.49 40674497.55 40816411.56 44273662.51 44151216.38 45264063.83 37546981.83 1.25396482 1.072051064 1.14519507 1.083296062 1.0870757 1.179153699 1.175892555 1.205531354 1 25.16219361 2.226207381 24.91732659 1.157931498 1.120899205 0 0.075440929 687.3041732 1386331.012 0.025113671 0.018681623 168.3477752 -2.226207381 -0.037032293 GFGFVTFDDHDPVDKIVLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFGFVTFDDHDPVDKIVLQK 20 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ; 313.12 1.48E-66 2289700000 1290040 1772800 1546800 1659270 2654050 1043163 2084150 1545770 4680130 FALSE TRUE 1209298.699 1904059.957 1583490.826 1701849.677 2445611.619 1344307.224 1771651.056 1738762.787 3898986.068 0.310157225 0.488347463 0.406128875 0.436485191 0.627242974 0.344783798 0.454387634 0.445952552 1 21.89466757 0.246205393 2.749289665 1.000000311 0.442459695 0.811812301 0.08484655 34.36903104 123.9330815 0.073047408 0.019255756 1.762809545 -0.246205393 -0.557540616 GFGFVTFSSMAEVDAAMAARPHS(ph)IDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GFGFVTFSSMAEVDAAMAARPHSIDGR 27 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 GFGFVTFS(0.001)S(0.001)MAEVDAAMAARPHS(0.998)IDGR;GFGFVTFSSMAEVDAAMAARPHS(1)IDGR;GFGFVTFSSMAEVDAAMAARPHS(1)IDGR;GFGFVTFSSMAEVDAAMAARPHS(1)IDGR;GFGFVTFSSMAEVDAAMAARPHS(1)IDGR 164.65 6.24E-12 74622700 22540.8 26241.7 24572 25721.21 35591.7 27416.3 34588.3 24814.2 31653.4 TRUE FALSE 21130.01156 28184.66277 25154.85944 26381.25979 32796.47145 35330.94074 29402.10552 27912.30749 26370.24305 0.801282397 1.068805574 0.953910792 1.000417772 1.243692422 1.339803379 1.114972868 1.058477445 1 14.68662325 2.843224415 5.730537836 1.16992078 0.971736461 0.412399145 0.114351927 0.223660957 10.25840045 0.033722954 0.035854399 696.9865787 -2.843224415 -0.198184319 GFGFVTFSSMAEVDAAMAARPHSIDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GFGFVTFSSMAEVDAAMAARPHSIDGR 27 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;; 271.94 5.38E-61 1652018000 124600.2 217276.6 183036.2 184923 219953.6 179589.3 205326.2 176819.8 195769.4 FALSE TRUE 116801.6959 233363.9855 187377.9051 189668.4373 202679.3315 231433.8155 174539.4425 198896.1413 163094.2224 0.716160844 1.430853785 1.14889358 1.162937806 1.242713129 1.419019093 1.070175509 1.219516782 1 17.31534615 0.330296471 1.198152075 1.000055653 1.203036248 0.056197272 0.200025204 8.945976051 13.67644819 0.173786562 0.051707582 2.139422066 -0.330296471 0.202980594 GFGFVTYATVEEVDAAMNAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 209.21 3.06E-25 8513100 19922.3 21580 22880.3 20619.1 22702.7 21609.5 23172.9 16440.3 17044.1 FALSE TRUE 18675.39881 23177.80565 23423.03152 21148.22101 20919.72152 27847.81185 19698.33877 18492.90764 14199.3296 1.315231024 1.632316898 1.649587141 1.489381655 1.473289381 1.961206101 1.387272451 1.302378927 1 13.7935352 1.098421209 1.994549384 1.015525009 1.591032398 0.539656171 0.172243041 0.211631985 1.644246855 0.148398805 0.042074076 12.54357149 -1.098421209 0.575507389 GFGFVTYATVEEVDAAMNARPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 306.82 5.33E-63 3917140000 3206952 3636269 3650047 3666951 4458379 3299368 4664528 3321831 5043004 FALSE TRUE 3006234.599 3905502.14 3736627.839 3761051.171 4108235.898 4251841.981 3965125.33 3736568.913 4201294.053 0.715549676 0.929595046 0.889399264 0.895212552 0.977850121 1.012031514 0.943786671 0.889385238 1 22.00240233 5.359856999 1.401950482 0.942873246 2.26E-22 0.707126565 0.04530699 3.656653944 1.865279756 0.012369176 7.464394176 229011.3458 -5.359856999 -0.942873246 GFGFVTYATVEEVDAAMNARPHKVDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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" 0 115.55 0.00045119 86565000 44164 46035 43725 53019 70726 37569 48147 39471 124940 FALSE TRUE 41399.85407 49443.4793 44762.17765 54379.5573 65171.46525 48414.56042 40927.80432 44399.04124 104086.7069 0.397743913 0.475022035 0.430047016 0.522444786 0.62612669 0.465136826 0.393208754 0.426558228 1 16.66742631 -1.878500907 3.192544686 1.218856663 0.465371403 0.858162154 0.068091461 109544166.4 130838451.6 184166626.6 0.016963515 0.013228149 1.878500907 -0.75348526 GFGFVTYSCVEEVDAAMCARPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GFGFVTYSCVEEVDAAMCARPHK 23 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 214.26 1.73E-32 530315000 629137 750739 631793 663112 950894 723576 1074354 665595 1338983 FALSE TRUE 589760.4382 806324.4967 646779.4283 680128.5766 876214.621 932460.6449 913264.5915 748696.0009 1115498.087 0.528696952 0.722838081 0.579812225 0.60970842 0.785491818 0.835914159 0.818705654 0.671176409 1 20.08925661 2.676749964 4.480121159 0.816004169 0.623663077 0.565444415 0.092208573 0.168891038 6.918363978 0.027598701 0.026283514 475.0616399 -2.676749964 -0.192341092 GFGFVYFQNHDAADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFGFVYFQNHDAADK 15 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ; 226.19 8.99E-13 1294580000 1892930 1523210 1766250 1581470 1824300 1419710 2056500 1640960 2278240 FALSE TRUE 1774454.89 1635990.053 1808146.284 1622053.198 1681026.837 1829557.23 1748146.917 1845837.468 1897987.026 0.934914131 0.861960609 0.95266525 0.854617642 0.885689319 0.96394612 0.921053143 0.972523754 1 20.8560387 1.327265333 0.877147759 0.999330205 0.900239378 0.486850923 0.034352099 0.442127235 0.728831592 0.029916355 0.011200276 21.24542057 -1.327265333 -0.099090827 GFGS(ph)EEGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 226.4 2.49E-07 3868950000 3135220 3721480 3341780 3323120 3398830 3125100 3686470 2893740 3312760 TRUE FALSE 2938992.177 3997022.251 3421048.6 3408396.885 3131899.602 4027265.638 3133718.047 3255029.809 2759838.955 1.064914375 1.448280975 1.239582692 1.23499847 1.134812449 1.459239363 1.135471344 1.179427446 1 21.39615265 1.011819468 1.336432021 1.005139928 1.274186749 0.273153183 0.126353537 0.516409079 1.888678882 0.108750342 0.033062678 10.27589051 -1.011819468 0.269046821 GFGS(ph)VEELCTNSSLGMEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GFGSVEELCTNSSLGMEK 18 0 Q2NKX8;B5MDQ0 Q2NKX8 ERCC6L DNA excision repair protein ERCC-6-like 1 GFGS(1)VEELCTNSSLGMEK;GFGS(1)VEELCTNSSLGMEK;GFGS(1)VEELCTNSSLGMEK 335.46 4.81E-75 268439000 294659 250186 270976 258804 274552 226695 374561 251627 310905 TRUE FALSE 276216.8192 268710.0318 277403.6787 265445.3488 252989.7934 292138.1664 318399.0553 283043.1848 259012.947 1.066420897 1.03743861 1.071003137 1.024834287 0.976745743 1.127890207 1.229278532 1.092776203 1 17.98266469 2.104262842 7.672003877 1.144037487 1.040222747 0.204101298 0.06374465 0.230667986 15.17510302 0.022248347 0.016405151 127.1343309 -2.104262842 -0.10381474 QAVRVS(ph)PCHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QAVRVSPCHSR 11 1 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-2;Q674X7;Q674X7-5 A0A1B0GWK2 KAZN Kazrin 1 QAVRVS(0.818)PCHS(0.182)R 95.236 0.0047895 170530000 90793 124770 87395 94911 127230 74315 122600 108500 251990 TRUE FALSE 85110.4282 134008.1006 89468.05067 97346.57694 117237.869 95768.5341 104217.2682 122046.4638 209931.2411 0.405420497 0.638342821 0.426177877 0.463706957 0.558458419 0.456190006 0.49643525 0.58136399 1 17.67955735 0.732430592 2.576572929 0.999944748 0.499487084 0.848727911 0.066873493 0.526388556 4.577362637 0.059925824 0.015956179 5.400457993 -0.732430592 -0.500457664 GFGSEEGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFGSEEGSR 9 0 Q9Y5S9 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ; 160.54 0.00015173 1522350000 1035700 1193450 1092410 1113600 1165300 1036430 1162910 1026650 1241220 FALSE TRUE 970877.3858 1281814.28 1118322.481 1142176.861 1073782.039 1335630.516 988542.4414 1154829.512 1034052.363 0.938905437 1.239602872 1.08149502 1.104563852 1.038421338 1.291646887 0.955988765 1.116799838 1 19.97987781 1.640576417 25 1.027298462 1.122802781 0.142320515 0.104864959 1.168322529 887.9923552 0.043391304 0.024059574 43.7095582 -1.640576417 0.09550432 GFGSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GFGSFR 6 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;; 126.05 0.041086 3494710000 2344210 3449080 2622200 2584640 3399840 2267200 3031530 2917380 3369770 FALSE TRUE 2197490.081 3704453.472 2684399.822 2650966.238 3132830.281 2921703.835 2576980.22 3281621.315 2807333.617 0.782767701 1.319562965 0.956209766 0.944300393 1.115945131 1.040739803 0.917945842 1.168945969 1 21.42076909 3.73641546 24.61024126 1.013403097 1.104021407 0 0.149983648 798.3619732 2113973.561 0.035015964 0.06203716 5450.237909 -3.73641546 0.09061831 GFGSSAPEGLEPDSMAS(ph)AASALHLLSPRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GFGSSAPEGLEPDSMASAASALHLLSPRPR 30 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDS(0.01)MAS(0.33)AAS(0.33)ALHLLS(0.33)PRPR;GFGSSAPEGLEPDS(0.071)MAS(0.31)AAS(0.31)ALHLLS(0.31)PRPR;GFGSSAPEGLEPDS(0.072)MAS(0.309)AAS(0.309)ALHLLS(0.309)PRPR 117.21 0.00011044 308679000 144859 227855 223428 296733 308103 158977 162153 144248 184711 TRUE FALSE 135792.5338 244725.6213 228727.8177 304347.6711 283905.8332 204871.0791 137839.663 162257.6803 153881.5408 0.882448493 1.590350733 1.486388923 1.977804937 1.844963546 1.331355782 0.895751773 1.054432387 1 17.23146066 1.942080329 4.465275335 0.990220496 1.57285762 0.452490213 0.286558119 0.194566872 7.689397934 0.129001248 0.076835646 87.51456316 -1.942080329 0.582637125 GFGSSAPEGLEPDSMASAAS(ph)ALHLLSPRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFGSSAPEGLEPDSMASAASALHLLSPRPR 30 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDSMAS(0.132)AAS(0.61)ALHLLS(0.258)PRPR;GFGSSAPEGLEPDS(0.003)MAS(0.093)AAS(0.452)ALHLLS(0.452)PRPR 189.2 1.80E-18 618570000 138047 213088 211547 256930 279587 148480 132994 131197 169992 TRUE FALSE 129406.8847 228865.2572 216564.9947 263523.2588 257629.3648 191343.7656 113052.7844 147577.2343 141619.237 0.913766289 1.616060516 1.529206055 1.860787167 1.819169276 1.351114225 0.798286919 1.042070536 1 17.11165772 1.924655315 4.685780092 0.943514121 1.570699041 0.52097722 0.262089307 0.1641357 6.447958824 0.115681921 0.068441147 84.07276191 -1.924655315 0.62718492 GFGSSAPEGLEPDSMASAASALHLLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GFGSSAPEGLEPDSMASAASALHLLSPR 28 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR 257.87 8.57E-54 1073046000 687660 1019737 1161999 1310867 1292535 886639 764141 686480 706202 TRUE FALSE 644620.5881 1095239.389 1189562.165 1344506.067 1191024.515 1142597.286 649565.151 772188.5391 588332.324 1.095674268 1.861599888 2.021922163 2.285283354 2.024407748 1.942095036 1.104078638 1.312504018 1 19.16627178 1.735316518 6.174646524 1.159966259 1.910568148 0.54395631 0.314286819 0.10761736 10.97756473 0.153671583 0.079948823 54.36464023 -1.735316518 0.750601889 GFGTDEQAIVDVVANR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GFGTDEQAIVDVVANR 16 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;;; 216.81 3.45E-14 146828000 178721 238540 202971 180253 202661 112466 230080 189156 290965 FALSE TRUE 167535.1716 256201.7498 207785.568 184878.5971 186744.8226 144933.1085 195581.64 212772.543 242401.0618 0.691148671 1.056933282 0.857197433 0.762697142 0.770396058 0.597906244 0.806851416 0.877770672 1 17.88703649 3.431293103 4.054074308 0.779193749 0.916709844 0.010972867 0.134622243 0.350935552 12.14280747 0.035032768 0.050112405 2699.560737 -3.431293103 0.137516094 GFHCESSAHWPIFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GFHCESSAHWPIFK 14 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 146.5 4.79E-06 608820000 909100 1415100 1373500 1441900 1570400 1277700 1672900 1516000 1500700 FALSE TRUE 852201.0538 1519875.476 1406080.069 1478901.595 1447067.119 1646551.248 1422064.175 1705275.937 1250223.475 0.68163898 1.215683041 1.124662988 1.182909795 1.157446767 1.317005544 1.137447987 1.363976898 1 20.25375457 4.740316013 24.95161359 1.190065858 0.681638805 0.713437726 0.100720406 72.73537934 1033791.899 0.020673921 0.133445406 54994.08914 -4.740316013 -0.508427053 GFHLDVEDYLSGVLILASELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GFHLDVEDYLSGVLILASELSR 22 0 E9PGT1;Q15631;H7C1D4 E9PGT1 TSN Translin 0 ;; 248.35 3.67E-31 1214300000 359372 460765 347104 380862 487060 349805 424191 422492 389177 FALSE TRUE 336879.548 494880.52 355337.4708 390635.5637 448808.2723 450788.0249 360587.4975 475241.0562 324220.8445 1.03904346 1.526368611 1.095973553 1.204844076 1.384267174 1.39037336 1.112166302 1.46579427 1 18.30661732 -1.806118552 2.529155671 0.910427572 1.277183499 0.218924026 0.164640181 11188372.12 7758019.416 6147576.06 0.038190673 0.01562721 1.806118552 0.366755927 GFHQVPFAPIVFIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFHQVPFAPIVFIER 15 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RRC8 P47897 QARS Glutamine--tRNA ligase 0 ; 111.43 0.00084286 631340000 766410 1251470 964430 835540 1195780 745640 942090 1086940 929640 FALSE TRUE 718441.7662 1344130.141 987306.735 856981.371 1101868.262 960894.1635 800832.3504 1222646.852 774477.0783 0.927647553 1.735532501 1.274804333 1.106529031 1.422725466 1.240700584 1.034029764 1.578674032 1 19.56286302 3.57027534 6.00149512 1.225168003 1.422209447 0 0.259994975 0.475277482 24.91654 0.063393155 0.09874793 3717.708546 -3.57027534 0.197041443 GFIYVHKPPVHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GFIYVHKPPVHIR 13 1 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 0 144.65 2.67E-05 995320000 566160 645840 639920 608990 675310 526420 718930 588930 755100 FALSE TRUE 530725.0562 693658.6656 655099.2046 624617.7144 622273.8767 678388.9083 611133.1207 662459.2069 629068.9319 0.843667569 1.102675129 1.041379047 0.992924118 0.989198234 1.078401545 0.971488321 1.053078881 1 19.26285859 3.251349424 24.63916166 1.013217934 1.025282035 0 0.073010865 1913.357563 3686295.06 0.018956249 0.025510154 1783.813406 -3.251349424 0.012064101 GFKDQIYDIFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFKDQIYDIFQK 12 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;J3QR64;J3KTN0 P60842;J3KTN0 EIF4A1 Eukaryotic initiation factor 4A-I 0 ; 166.6 4.69E-05 3336300000 8839100 9732700 8215500 8673100 12122000 6434400 10845600 9694100 13284200 FALSE TRUE 8285876.509 10453319.23 8410375.54 8895666.43 11169987.02 8291906.826 9219402.966 10904429.72 11066981.2 0.748702502 0.944550194 0.759952094 0.803802434 1.00930749 0.749247394 0.833054904 0.985312031 1 23.39975841 1.229344711 9.050446358 0.993401157 0.838890647 0.374721913 0.084309637 0.162048264 107.8815304 0.064900718 0.018767384 16.95683175 -1.229344711 -0.15451051 GFKDQIYEIFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GFKDQIYEIFQK 12 1 Q14240;Q14240-2;E7EQG2 Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 166.6 4.69E-05 235600000 925320 1036900 858120 948310 1379400 674390 997990 1159900 1551900 FALSE TRUE 867405.8729 1113673.155 878475.0116 972645.2401 1271067.488 869075.4452 848350.6644 1304716.068 1292877.864 0.670910917 0.861390844 0.679472544 0.752310227 0.983130366 0.672202278 0.656172317 1.009156475 1 20.30215456 1.22463504 24.999703 1.004578536 0.755542539 0.513354696 0.1015555 217.2222749 389954.066 0.093012926 0.023731906 16.77393826 -1.22463504 -0.249035997 GFNGCDS(ph)PEPDGEDSLEQSPLLEDKYR ddPTM_SK-BR-3_Pertuzumab_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 209.47 1.01E-25 472980000 703360 635170 653300 686030 711510 580820 964650 621720 747750 TRUE FALSE 659337.9531 682198.6477 668796.5845 703634.6912 655630.8747 748493.3052 820009.6879 699343.1106 622945.6944 1.058419633 1.095117366 1.07360335 1.12952814 1.052468747 1.201538612 1.316342171 1.122638967 1 19.24874688 2.228650499 24.4547577 1.200941757 1.084686455 0.097877602 0.084193479 179.9387177 444022.6432 0.028742947 0.021496501 169.297482 -2.228650499 -0.116255302 GFNS(ph)RS(ph)NLRSHMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GFNSRSNLRSHMR 13 2 Q9H4Q4 Q9H4Q4 PRDM12 PR domain zinc finger protein 12 2 GFNS(0.98)RS(0.988)NLRS(0.032)HMR 65.276 0.033476 163800000 8161.5 7369.8 11252 13148 11706 4805.4 9954.3 11073 12440 TRUE FALSE 7650.686284 7915.46766 11518.90275 13485.39994 10786.65798 6192.640971 8461.745126 12455.48842 10363.68363 0.738220748 0.763769712 1.111468003 1.301216866 1.040813128 0.597532807 0.816480455 1.201839892 1 13.33924926 4.196929985 3.9585299 0.982702446 0.744822303 0.223042784 0.196030882 0.380299754 13.00443335 0.053534603 0.137596606 15737.29136 -4.196929985 -0.237880143 GFPGYMYTDLATIYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFPGYMYTDLATIYER 16 0 P21281;P15313;C9JL73 P21281;P15313 ATP6V1B2;ATP6V1B1 "V-type proton ATPase subunit B, brain isoform;V-type proton ATPase subunit B, kidney isoform" 0 ; 180.2 4.16E-12 0 92633 113597 97148 91117 115617 101859 118450 94781 118707 FALSE TRUE 86835.26588 122007.8401 99452.39644 93455.21648 106536.9072 131264.0398 100689.5221 106614.6165 98894.03482 0.878063738 1.233722947 1.00564606 0.945003575 1.077283452 1.327320096 1.018155668 1.078069235 1 16.59359588 2.472423572 24.97760005 1.117767953 1.046385134 0.077722575 0.126774265 396.8037863 2109786.318 0.042361208 0.035574285 296.772443 -2.472423572 -0.071382819 GFPTDATLDDIKEWLEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFPTDATLDDIKEWLEDK 18 1 P05455;E7ERC4;E9PGX9 P05455 SSB Lupus La protein 0 ; 151.57 4.26E-08 248480000 1405990 703570 763460 750790 791300 590930 1057660 700100 967410 FALSE TRUE 1317991.596 755663.0549 781569.6317 770056.5425 729154.49 761521.8981 899073.7018 787509.0261 805943.0213 1.635340912 0.937613497 0.969757925 0.955472685 0.904722134 0.944883047 1.115554919 0.977127421 1 19.62031832 4.740722166 24.99410146 0.978420649 1.635341139 0.932278852 0.05587315 51.1834398 591797.1898 0.014682881 0.097003241 55045.54377 -4.740722166 0.65692049 GFPTIYFSPANKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFPTIYFSPANKK 13 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 192.63 4.09E-06 726260000 1248490 1302080 1168270 1255680 1401790 954660 1454480 1121760 1211440 FALSE TRUE 1170349.24 1398487.358 1195981.916 1287902.875 1291699.068 1230254.844 1236394.227 1261814.205 1009242.838 1.159630959 1.385679745 1.185028886 1.276108015 1.279869442 1.218987937 1.225071093 1.250258271 1 19.94484192 -4.094277136 0.269455635 2.93E-13 1.273821106 0.608578973 0.062002192 75.30136691 1.152427024 41.47583172 0.070282905 8.05E-05 4.094277136 1.273821106 GFPTWLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFPTWLK 7 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 124.37 0.009661 280960000 516790 809090 498010 481770 998990 402790 529520 743750 670290 FALSE TRUE 484445.0364 868995.8655 509823.0324 494133.0338 920533.3551 519068.9343 450123.3918 836608.8247 558414.2688 0.867536994 1.556184922 0.912983534 0.884886117 1.648477495 0.929540958 0.806074302 1.49818669 1 19.09097628 3.939698044 22.31846401 1.076102483 1.257741827 0.014236218 0.318059202 255.8378944 152576.0602 0.076824284 0.138507384 8703.582369 -3.939698044 0.181639344 GFQFVSS(ph)SLPDICYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.199)S(0.602)S(0.199)LPDICYR;GFQFVS(0.374)S(0.42)S(0.206)LPDICYR 160.78 1.77E-06 59142000 98837 101977 91148 98174 117182 106481 120641 90929 114074 TRUE FALSE 92650.9686 109527.4832 93310.0736 100693.311 107978.9984 137220.3361 102552.002 102281.6858 95034.31245 0.974921228 1.15250461 0.98185667 1.059546899 1.136210655 1.443903077 1.079105003 1.076260596 1 16.53616088 2.684452479 4.774995089 1.172244301 1.050243622 0.132049251 0.125981677 0.368152698 18.26186124 0.0393038 0.037495795 483.56235 -2.684452479 -0.122000679 GFQQILAGEYDHLPEQAFYMVGPIEEAVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFQQILAGEYDHLPEQAFYMVGPIEEAVAK 30 0 P06576 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 ; 279.45 1.73E-71 214110000 320540 286990 282540 248340 400920 258210 284670 298900 457080 FALSE TRUE 300477.9736 308239.0382 289241.9822 254712.8248 369433.3604 332751.0353 241986.3762 336218.323 380790.3952 0.789090212 0.809471673 0.759583188 0.668905592 0.970175102 0.873843037 0.635484454 0.882948539 1 18.53863756 2.763073309 24.98784576 0.832601664 0.766017609 0.173942396 0.106422778 2128.858546 2170120.93 0.032827632 0.034805883 579.526513 -2.763073309 -0.066584056 GFRDDFLGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GFRDDFLGGR 10 1 Q15056-2 Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 170.89 3.82E-06 175150000 62192 78579 63811 79453 88927 56550 86914 63854 69517 FALSE TRUE 58299.51374 84397.07092 65324.62705 81491.89849 81943.03213 72875.06699 73882.05257 71826.31246 57914.1636 1.006653815 1.457278594 1.127955978 1.407115176 1.41490487 1.258328921 1.275716474 1.240220146 1 15.8216286 0.553312487 1.411453267 1.000047705 1.29035836 0.288716012 0.135366227 2.198522516 5.617259917 0.115515042 0.03387005 3.575299985 -0.553312487 0.290310655 GFS(ph)FVATGLMEDDGKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GFSFVATGLMEDDGKPR 17 1 E9PGT3;Q15418-4;Q15418;Q15418-2;Q15418-3;Q5SVM6 E9PGT3 RPS6KA1 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1 1 GFS(0.908)FVAT(0.092)GLMEDDGKPR;GFS(1)FVATGLMEDDGKPR;GFS(1)FVATGLMEDDGKPR 141.83 3.69E-07 111151000 87282 102342 86374 99254 103015 58543 107554 71244 159205 TRUE FALSE 81819.17542 109919.5082 88422.83207 101801.0257 94924.61744 75443.41373 91427.27618 80138.97023 132632.657 0.616885594 0.82875146 0.666674664 0.767541177 0.715695663 0.568814766 0.689327035 0.604217483 1 17.01707652 -0.904053489 5.125415012 1.000000743 0.692216069 0.62150664 0.077584434 6.42E-07 1.37E-07 0.073181611 0.017249029 0.124722989 0.904053489 -0.307784674 GFS(ph)LEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFSLEELR 8 0 P26373;P26373-2;J3QSB4 P26373 RPL13 60S ribosomal protein L13 1 GFS(1)LEELR;GFS(1)LEELR 140.75 0.00067605 81778000 351770 241940 239920 198014 389870 277620 213110 192397 391930 TRUE FALSE 329753.3436 259853.4893 245611.0157 203095.3745 359251.1829 357764.3872 181156.1339 216418.189 326514.351 1.009919909 0.795840944 0.752221196 0.62201056 1.10026154 1.095708002 0.55481829 0.662813712 1 18.31678688 1.719216749 24.99999609 0.703254947 0.865172305 0.110764192 0.187907945 1.861818286 2396.639812 0.085598374 0.047468586 52.38618223 -1.719216749 0.161917357 GFSDKLDFLEGDQKPLAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GFSDKLDFLEGDQKPLAQR 19 2 H7C2Q8;Q99848 H7C2Q8 EBNA1BP2 Probable rRNA-processing protein EBP2 0 143.14 8.34E-08 391380000 1134800 800640 990500 907670 966210 685670 1241600 820580 1205800 FALSE TRUE 1063774.894 859920.2187 1013995.128 930962.3489 890327.7641 883611.7981 1055433.606 923031.2193 1004544.19 1.058962765 0.856030254 1.009408185 0.926751016 0.886300247 0.879614662 1.050659211 0.918855764 1 19.9381096 1.741375958 24.99999967 0.992435034 0.933098306 0.12027851 0.067951443 0.881187107 7871.749023 0.028827816 0.015986486 55.12847235 -1.741375958 -0.059336729 GFSEEHNTWEPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GFSEEHNTWEPEK 13 0 P45973;F8VNY3 P45973 CBX5 Chromobox protein homolog 5 0 ;;; 162.48 4.04E-05 992030000 2315580 2019310 2229460 2160300 2204120 1588390 2521580 2078920 1777290 FALSE TRUE 2170651.981 2168821.813 2282343.844 2215736.955 2031017.306 2046932.408 2143492.488 2338477.738 1480648.817 1.466014058 1.464778 1.541448463 1.49646353 1.371707648 1.382456382 1.447671091 1.57936015 1 20.49779807 -1.205380081 3.995028844 0.999689415 1.467483634 0.845697628 0.062921181 28.31588171 17197067.37 9841.473058 0.015118835 0.06231892 1.205380081 0.467794219 GFSLEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GFSLEELR 8 0 P26373;P26373-2;J3QSB4 P26373 RPL13 60S ribosomal protein L13 0 ;;;;; 178.6 0.00057867 977561000 618683 5479790 351454 365560 5415800 232848 303111 4090880 4007210 FALSE TRUE 579960.7354 5885519.353 359790.6548 374940.8885 4990464.914 300067.4376 257662.3195 4601635.373 3338380.763 0.173725161 1.762986241 0.107774002 0.1123122 1.49487589 0.089884126 0.077181825 1.378403394 1 21.67071708 3.955645171 23.42263723 0.52712188 1.063562459 0.033791032 0.658903839 389.2256197 424504.8593 0.156119646 0.28189367 9029.114718 -3.955645171 0.536440579 GFSLLATEDKEALKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFSLLATEDKEALKK 15 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 217.01 1.20E-12 1343780000 3906180 2288260 2928950 2837540 3218820 2065300 4078160 2473980 4348300 FALSE TRUE 3661699.167 2457685.151 2998426.077 2910356.08 2966026.861 2661518.583 3466677.768 2782861.849 3622540.639 1.010809686 0.678442396 0.827713579 0.803401913 0.818769796 0.734710483 0.956974155 0.768207213 1 21.78857044 0.109571484 0.484631632 1.01690126 0.80051782 0.202586841 0.099869998 4.777413574 1.525142734 0.264260615 0.047814862 1.286979071 -0.109571484 -0.21638344 VQVEYKGETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 137.16 8.99E-05 3198320000 3711410 3627700 3013370 3135200 5149660 1874750 4129030 3573640 8760300 FALSE TRUE 3479119.473 3896298.683 3084848.559 3215654.54 4745226.476 2415959.891 3509920.284 4019816.821 7298149.336 0.476712563 0.533874891 0.422689153 0.440612324 0.650195859 0.331037333 0.480932922 0.550799475 1 22.79909924 0.733071066 2.802691604 0.999938066 0.475225526 0.802881828 0.080872148 0.687188085 6.69598435 0.070657701 0.018621656 5.408428164 -0.733071066 -0.524712541 GFSQYGVSGS(ph)PTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GFSQYGVSGSPTK 13 0 Q9NXC5 Q9NXC5 MIOS WD repeat-containing protein mio 1 GFSQYGVS(0.036)GS(0.797)PT(0.168)K;GFSQYGVSGS(0.999)PT(0.001)K;GFSQYGVSGS(0.972)PT(0.028)K 274.1 3.87E-32 1737690000 3033940 2143490 2516730 2474040 2591580 2157010 3214630 2283530 3039640 TRUE FALSE 2844051.111 2302196.23 2576428.024 2537528.055 2388047.761 2779703.771 2732626.075 2568633.747 2532304.447 1.123107893 0.909130903 1.017424278 1.002062788 0.943033435 1.097697306 1.079106455 1.01434634 1 21.27201943 2.234928373 24.99870851 1.058576075 0.98936392 0.11178529 0.062146201 134.1364383 923171.0891 0.020945774 0.016076757 171.7625082 -2.234928373 -0.069212155 GFSVLHTYQDHLWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFSVLHTYQDHLWR 14 0 Q5SY38;P41214 Q5SY38 EIF2D Eukaryotic translation initiation factor 2D 0 ; 221.86 2.38E-12 337450000 290190 461220 361890 354550 428040 270590 367670 371100 354690 FALSE TRUE 272027.5259 495369.2087 370474.2017 363648.3533 394423.465 348704.9403 312541.2968 417432.6519 295489.9476 0.920598241 1.67643337 1.253762453 1.23066235 1.334811787 1.180090704 1.057705344 1.412679705 1 18.17274953 2.599117091 0.93228136 1.147030313 1.363521009 0.021840822 0.214928124 1.119822286 2.011412529 0.126599013 0.101998996 397.2986514 -2.599117091 0.216490695 GFSVVADT(ph)PELQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GFSVVADTPELQR 13 0 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 1 GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR;GFSVVADT(1)PELQR 295.16 1.30E-39 3080390000 4310610 4695710 4838080 4829000 5069420 4915990 6058290 4737820 6961240 TRUE FALSE 4040816.615 5043385.254 4952841.542 4952920.315 4671288.202 6335156.509 5149905.657 5329347.256 5799364.073 0.696768915 0.869644532 0.854031835 0.854045418 0.805482833 1.092388136 0.888012132 0.918953732 1 22.46746328 2.277248128 24.99996641 0.961735051 0.830226978 0.536824 0.072196395 137.9885464 89168.01971 0.023387878 0.019567352 189.3425092 -2.277248128 -0.131508073 GFTDADNTWEPEENLDCPELIEAFLNSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GFTDADNTWEPEENLDCPELIEAFLNSQK 29 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 0 ;;; 375.13 1.03E-136 249115000 474525 395402 428020 383287 432966 387007 539661 387138 453167 FALSE TRUE 444825.3273 424677.9755 438172.8365 393122.7933 398962.5969 498729.6384 458743.843 435473.0315 377530.5001 1.178250041 1.124883884 1.160628973 1.041300751 1.05676918 1.321031382 1.215117303 1.153477749 1 18.52623368 2.275021586 24.99999888 1.197656908 1.117424485 0.069274455 0.089220186 298.1319339 204417.4574 0.028770363 0.024070254 188.3742715 -2.275021586 -0.080232423 GFTECEMTKSS(ph)PLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GFTECEMTKSSPLK 14 1 Q9NQW6 Q9NQW6 ANLN Actin-binding protein anillin 1 GFTECEMTKS(0.108)S(0.892)PLK;GFTECEMT(0.002)KS(0.107)S(0.89)PLK;GFTECEMTKS(0.01)S(0.99)PLK;GFTECEMTKS(0.075)S(0.925)PLK;GFTECEMTKS(0.035)S(0.965)PLK 244.97 7.67E-18 2370110000 3542010 2291110 2771940 2828900 3424770 1679890 3505630 2485530 5626200 TRUE FALSE 3320321.917 2460746.168 2837691.726 2901494.363 3155802.379 2164846.972 2979993.326 2795853.892 4687150.873 0.708388103 0.524998285 0.605419327 0.61903157 0.673287988 0.461868421 0.635779263 0.596493257 1 22.1602798 0.05033917 1.699170754 1.000130604 0.594668298 0.760171412 0.069911016 13.24823445 22.81016171 0.063700697 0.016914699 1.122895056 -0.05033917 -0.405462306 GFTIPEAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GFTIPEAFR 9 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ;;;; 152.63 0.00018614 1609416000 2198817 3854070 2206330 2156901 3681010 1626264 2341216 3232227 3288814 FALSE TRUE 2061196.969 4139429.353 2258665.19 2212250.731 3391918.323 2095740.017 1990172.396 3635777.656 2739889.697 0.752291952 1.51080146 0.824363547 0.807423282 1.237976232 0.764899411 0.726369532 1.326979572 1 21.38568638 3.747696133 20.3837824 0.925873541 1.180284112 0.054681822 0.267967099 82.44242581 81671.69652 0.063304861 0.113742232 5593.66088 -3.747696133 0.254410571 GFVEFAAKPPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFVEFAAKPPAR 12 1 Q8WXF1;Q8WXF1-2;X6RDA4 Q8WXF1 PSPC1 Paraspeckle component 1 0 ; 147.33 5.46E-05 1229290000 2118070 2360000 2537800 2377300 2801400 2076340 2815600 2332800 3516700 FALSE TRUE 1985503.78 2534736.856 2597997.814 2438305.543 2581389.344 2675745.651 2393426.919 2624055.215 2929740.051 0.677706467 0.865174661 0.886767348 0.83226003 0.881098425 0.9133048 0.816941734 0.895661448 1 21.48234123 -3.417073008 0.021389601 2.019597736 2.16E-20 0.533606455 0.056068293 2073.99765 4.431784025 266.2089437 163.2403191 0.00038276 3.417073008 -2.019597736 GFVEPDHYVVVGAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GFVEPDHYVVVGAQR 15 0 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ;;; 185.95 4.02E-07 1432150000 906150 1146920 990980 901170 1233860 874940 1121360 1133610 1272740 FALSE TRUE 849435.689 1231839.15 1014486.514 924295.5479 1136957.613 1127520.975 953222.4782 1275143.704 1060311.472 0.801119022 1.16177103 0.956781607 0.871720784 1.072286439 1.063386566 0.899002325 1.202612381 1 20.0160567 GFVLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFVLHK 6 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ; 105.82 0.032648 3606700000 3387200 4275400 3165400 2960500 4404100 2493500 3775700 3785200 4553300 FALSE TRUE 3175201.198 4591955.065 3240484.783 3036471.442 4058219.751 3213332.971 3209568.837 4257790.552 3793324.815 0.837049647 1.210535688 0.85425977 0.800477573 1.069831862 0.847101983 0.846109678 1.122442912 1 21.85503148 3.822656718 7.330673747 0.918525409 1.04697933 0.053247088 0.13759645 0.438719676 29.19910065 0.03223273 0.058400993 6647.475078 -3.822656718 0.128453921 GFVPSPTSQPGGHESLVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFVPSPTSQPGGHESLVDR 19 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ; 184.2 2.54E-14 2442000000 315610 801180 673290 716740 801300 725520 752710 727050 854640 FALSE TRUE 295856.5335 860500.2008 689260.7568 735132.7618 738369.1303 934965.8462 639848.1233 817823.7929 711995.0628 0.415531721 1.208576078 0.968069573 1.032496994 1.037042486 1.313163384 0.898669326 1.148636888 1 19.44150771 4.745976033 24.86759415 1.071390677 0.415531387 0.746521964 0.120893871 395.1989101 1325265.067 0.026222403 0.273271273 55715.50005 -4.745976033 -0.65585929 GFVQVDDGRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GFVQVDDGRK 10 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;;; 140.07 6.40E-05 1329130000 1752360 1681040 1788850 1735920 1970170 1412210 2218550 1701920 2497310 FALSE TRUE 1642682.916 1805505.951 1831282.367 1780466.646 1815440.795 1819892.102 1885899.024 1914408.458 2080492.828 0.789564325 0.867826087 0.88021566 0.855790812 0.872601324 0.874740868 0.906467448 0.92017066 1 20.98849388 -4.999999995 0.085348788 1.442590147 0.751351037 0.855172701 0.020241117 88.24527141 0.528411305 7.121012463 0.57190702 1.00E-05 4.999999995 -0.69123911 GGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAAIDAR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 355.59 1.86E-154 555174000 278776 345528 332299 313894 395119 308546 338492 324537 290033 FALSE TRUE 261327.9078 371111.2526 340181.2892 321949.0515 364087.9476 397618.2214 287738.267 365056.1588 241624.6186 1.08154504 1.535900004 1.407891676 1.332434804 1.506832994 1.6456031 1.190848303 1.510840083 1 17.88240793 -0.502220201 6.228085097 1 1.409773785 0.360856181 0.167599228 0 0 0.146203377 0.034460466 0.314615271 0.502220201 0.409773785 GGAAPEGPNEAEVTSGKPEQEVPDAEEEKS(ph)VSGTDVQEECR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGAAPEGPNEAEVTSGKPEQEVPDAEEEKSVSGTDVQEECR 41 2 P49321;P49321-3;P49321-4;E9PPR5 P49321 NASP Nuclear autoantigenic sperm protein 1 GGAAPEGPNEAEVTSGKPEQEVPDAEEEKS(0.822)VS(0.121)GT(0.058)DVQEECR 78.439 0.00060664 379790000 66301 36275 38680 41247 45939 35320 60492 31902 39747 TRUE FALSE 62151.33876 38960.83874 39597.50787 42305.46785 42331.13625 45516.31063 51421.78618 35885.03492 33112.96892 1.876948542 1.176603609 1.195830792 1.27761023 1.278385407 1.374576551 1.552919833 1.083715417 1 15.01510875 1.07388825 7.080599373 1.001054788 1.351390307 0.321627049 0.206313467 0.249605736 18.2798924 0.191881131 0.04812446 11.85463672 -1.07388825 0.350335519 GGAAVDPDSGLEHSAHVLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GGAAVDPDSGLEHSAHVLEK 20 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;;;; 245.22 3.50E-30 6094550000 6250270 7039640 7373750 7371600 7864940 6264950 9180950 7085490 8469880 FALSE TRUE 5859076.758 7560862.27 7548658.832 7560767.736 7247259.338 8073539.362 7804351.779 7970129.024 7056202.31 0.830344213 1.071520053 1.06979059 1.071506655 1.027076467 1.144176287 1.106027213 1.129521047 1 22.75046049 4.740169656 4.904019938 1.082900435 0.816870102 0.763743418 0.043148443 0.079183989 5.731075302 0.009772477 0.071878826 54975.55925 -4.740169656 -0.266030333 GGAEGELQALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGAEGELQALR 11 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 163.16 5.65E-05 101520000 108060 157690 117460 140660 158160 106430 141000 136400 121300 FALSE TRUE 101296.7175 169365.5317 120246.2067 144269.5737 145738.7516 137154.6133 119858.359 153429.8403 101054.2464 1.002399415 1.675986292 1.189917406 1.427644843 1.44218335 1.357237505 1.186079391 1.518291866 1 16.62477042 -2.95327628 0.464274089 9.93E-11 1.362624105 0.242408242 0.190553074 249.6889043 8.920392313 247.9511892 0.088453344 0.001113586 2.95327628 1.362624104 GGAEPRPLPLSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGAEPRPLPLSYR 13 1 Q8NFV4;Q8NFV4-6;H0YC52;C9J7Q4;H7BZ58;Q8NFV4-3;Q8NFV4-2 Q8NFV4 ABHD11 Alpha/beta hydrolase domain-containing protein 11 0 ; 83.226 0.0093941 180096000 256430 235710 200556 200780 268110 178548 229890 206600 316740 FALSE TRUE 240380.504 253162.2137 205313.283 205932.3547 247053.7221 230091.9091 195420.1287 232394.4648 263874.0478 0.910966827 0.959405503 0.778073042 0.78041913 0.936256234 0.871976274 0.740581085 0.880702239 1 18.00948994 4.064943414 5.151257359 0.838935361 0.933535949 0.12360499 0.079076419 0.320487702 14.01420137 0.018604702 0.041354963 11612.97294 -4.064943414 0.094600588 GGAEQFMEETER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GGAEQFMEETER 12 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;; 290.07 9.91E-36 3118200000 1233080 1480720 1388970 1376200 1449400 1299440 1431830 1252390 1370670 FALSE TRUE 1155903.724 1590354.049 1421917.024 1411515.622 1335569.971 1674567.233 1217140.384 1408753.648 1141896.322 1.012266789 1.392730687 1.245224279 1.236115394 1.169607034 1.466479225 1.065893952 1.233696633 1 20.12300024 0.804261142 0.941693241 1.003691841 1.258500031 0.208545676 0.134835202 1.081796978 1.865566713 0.115259212 0.038409543 6.371785429 -0.804261142 0.254808189 GGAFDGTMNGPFGHGYGEGAGEGIDDVEWVVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GGAFDGTMNGPFGHGYGEGAGEGIDDVEWVVGK 33 0 A0A024R571;Q9H4M9 A0A024R571 EHD1 EH domain-containing protein 1 0 ;; 289.21 1.89E-89 268717000 222947 209499 206899 209101 245445 185466 269397 216821 290545 FALSE TRUE 208993.1452 225010.5239 211806.742 214466.8857 226168.7398 239007.0234 229003.4208 243891.5791 242051.1625 0.863425497 0.929599022 0.875049472 0.886039478 0.934384026 0.987423572 0.946095108 1.00760342 1 17.8849525 2.476081204 3.064720671 0.977387072 0.89333923 0.778646284 0.024034801 0.126343254 2.447699372 0.008379095 0.00719899 299.2824178 -2.476081204 -0.084047842 GGAGGS(ph)PGSSSGSGSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GGAGGSPGSSSGSGSSR 17 0 Q8TAE6 Q8TAE6 PPP1R14C Protein phosphatase 1 regulatory subunit 14C 1 GGAGGS(0.998)PGS(0.001)S(0.001)SGSGSSR;GGAGGS(0.99)PGS(0.009)SSGSGSSR;GGAGGS(0.965)PGS(0.017)S(0.017)S(0.001)GSGSSR 266 1.39E-27 364489000 378715 421627 378851 396517 418339 333846 422799 353310 250480 TRUE FALSE 355011.9042 452844.7018 387837.5246 406692.2975 385484.3424 430221.9207 359404.215 397421.5312 208673.2698 1.701281168 2.170113605 1.85858747 1.948942947 1.847310596 2.061701151 1.722329915 1.904515761 1 17.67088628 -2.044550847 0.355468951 9.50E-13 1.965400638 0.800445058 0.141264205 15.3417124 0.816831021 12.5755793 0.096434982 0.00902504 2.044550847 1.965400638 GGAVERPLT(ph)PAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGAVERPLTPAPR 13 1 H9KVB4;O15417 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 GGAVERPLT(1)PAPR;GGAVERPLT(1)PAPR 136.63 0.00011333 921170000 484930 578900 560090 561240 567030 427410 618730 482370 680530 TRUE FALSE 454579.0969 621762.3583 573375.5993 575642.3686 522497.7511 550796.3286 525957.1805 542594.9563 566945.1466 0.801804371 1.09668874 1.011342284 1.0153405 0.921601947 0.971516084 0.927703824 0.957050183 1 19.11284963 2.75191084 23.65855262 0.950563877 1.005534491 0 0.077625398 866.3807685 1535350.248 0.022124289 0.023320924 564.8210055 -2.75191084 0.054970613 GGCGS(ph)PGLQCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGCGSPGLQCK 11 0 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 GGCGS(1)PGLQCK 72.705 0.047795 73669000 168830 161060 149050 158570 210290 142580 186740 149620 204560 TRUE FALSE 158263.2317 172985.05 152585.5364 162639.1747 193774.6717 183740.5314 158740.0706 168300.3864 170417.6145 0.928678835 1.015065552 0.895362471 0.954356597 1.137057764 1.078178051 0.931476896 0.987576237 1 17.37871494 2.951604981 24.99750182 1.022012036 0.950184849 0.285774247 0.0614045 586.283938 302833.1443 0.019607797 0.020797655 894.5507434 -2.951604981 -0.071827187 GGCWPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GGCWPR 6 0 Q9Y4W6 Q9Y4W6 AFG3L2 AFG3-like protein 2 0 ;;;; 128.65 0.038468 3181370000 2685360 2682840 2550950 2560300 2883480 1483870 2731730 2486640 3000970 FALSE TRUE 2517288.111 2881480.265 2611459.739 2626001.633 2657023.112 1912239.18 2322132.447 2797102.478 2500088.72 1.006879512 1.152551204 1.044546827 1.050363378 1.062771529 0.764868529 0.928820017 1.118801287 1 21.25354786 2.433967203 24.99999086 0.935599466 1.073372929 0.243577251 0.093663883 154.1745428 89315.57424 0.03112572 0.026041661 271.6234135 -2.433967203 0.137773464 GGDAKS(ph)PVLQEK ddPTM_SK-BR-3_Pertuzumab_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 164.8 3.41E-05 4437800000 8333870 5107080 6168590 5872180 6316350 4744360 7340170 5116610 8914830 TRUE FALSE 7812267.953 5485213.517 6314911.868 6022870.08 5820289.35 6113979.714 6239579.651 5755430.022 7426887.281 1.051889931 0.738561568 0.850277058 0.810954826 0.783678159 0.823222365 0.840133883 0.774945115 1 22.82432625 -1.274936681 5.22577858 1.000028368 0.825480718 0.270763922 0.084434753 2.42E-05 3.36E-06 0.070842671 0.016695066 0.053096185 1.274936681 -0.17454765 GGDEYDNHCGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GGDEYDNHCGK 11 0 P20645;F5GX30;F5H4U1;H0YGE9 P20645 M6PR Cation-dependent mannose-6-phosphate receptor 0 ;; 126.71 0.00030182 908700000 1152650 1371690 1070650 1071950 1466330 845560 1534420 1346060 1636750 FALSE TRUE 1080507.694 1473251.355 1096046.324 1099458.052 1351170.357 1089659.445 1304347.966 1514118.554 1363565.851 0.792413284 1.080440196 0.803808868 0.806310932 0.990909501 0.799124915 0.956571305 1.110411025 1 20.37895294 1.445040209 5.795216145 1.051518246 0.893991556 0.350805521 0.097459147 0.208409108 14.57519617 0.059138794 0.023422434 27.86379131 -1.445040209 -0.157526689 GGDISVCEWYQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GGDISVCEWYQR 12 0 P14854 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 ;;;;;; 307.55 1.06E-37 6110763000 2292985 2560623 2222892 1975359 2965539 1987424 2435625 2344571 2892273 FALSE TRUE 2149471.162 2750214.191 2275620.048 2026050.056 2732637.529 2561161.046 2070425.642 2637295.85 2409533.952 0.892069257 1.141388437 0.944423317 0.840847275 1.134093806 1.062927976 0.859263942 1.094525291 1 21.2003227 3.750785645 23.72484901 0.98175914 1.037047948 0 0.1110576 794.4919608 796512.8546 0.026961165 0.048559306 5633.595292 -3.750785645 0.055288808 GGDLMAYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GGDLMAYDR 9 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;; 172.94 0.00012984 3276930000 2543140 4257930 2648110 2669690 4360800 2047700 2265000 3844580 3104240 FALSE TRUE 2383969.407 4573191.568 2710924.42 2738198.765 4018320.359 2638837.748 1925384.277 4324584.276 2586122.29 0.921831661 1.768358591 1.048258402 1.058804828 1.553801371 1.020383977 0.744506277 1.672227293 1 21.30235907 3.737650886 23.22307772 1.126861322 1.406385642 0.038561923 0.338289089 318.0994048 701555.9715 0.081848977 0.145293402 5465.764129 -3.737650886 0.279524321 GGDLMAYDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 GGDLMAYDRR 10 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;;; 175.41 4.50E-06 9603990000 2725040 5905960 2811690 2937440 6494310 2174410 2686870 4970120 5437980 FALSE TRUE 2554484.611 6343243.424 2878384.615 3012819.683 5984273.089 2802126.868 2283998.787 5590650.423 4530346.007 0.563860819 1.40016754 0.635356463 0.665030812 1.320930693 0.618523809 0.504155485 1.234044908 1 22.11118981 GGDS(ph)PEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GGDSPEAK 8 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;H0YD62;H0YF37 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 GGDS(1)PEAK;GGDS(1)PEAK;GGDS(1)PEAK;GGDS(1)PEAK;GGDS(1)PEAK;GGDS(1)PEAK 152.67 0.00047549 2800350000 8630420 5362370 9006350 7451450 6721210 5822750 9220720 5881420 7025750 TRUE FALSE 8090257.418 5759405.454 9219984.875 7642666.822 6193353.279 7503683.401 7838158.637 6615728.234 5853106.937 1.382215891 0.983991155 1.575229186 1.305745291 1.058130894 1.282000053 1.339144957 1.130293416 1 22.48077121 GGDSIGET(ph)PT(ph)PGASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGDSIGETPTPGASK 15 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 GGDSIGET(1)PT(1)PGASK 325.29 4.33E-57 234800000 835760 678620 708370 765870 793580 590410 962840 712540 599450 TRUE FALSE 783451.2735 728865.7309 725172.8709 785523.5208 731255.4279 760851.7825 818471.0806 801502.1875 499397.9224 1.568791616 1.459488913 1.452094289 1.572941107 1.464274069 1.523538141 1.63891567 1.604936968 1 18.92983029 -1.452438792 6.574722908 0.999867388 1.528041763 0.874784958 0.063627834 0.00013929 1.16E-05 0.069377988 0.016348509 0.035282651 1.452438792 0.528174375 GGDSIGET(ph)PTPGASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGDSIGETPTPGASK 15 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 GGDSIGET(0.977)PT(0.023)PGASK;GGDSIGET(1)PTPGASK 284.53 6.11E-33 696540000 984900 707330 820490 833070 821380 720770 1049770 725920 699910 TRUE FALSE 923256.8671 759701.4492 839952.4103 854447.9866 756872.1281 928844.5983 892366.7341 816552.7099 583090.4994 1.5833852 1.302887716 1.440518086 1.465377994 1.298035432 1.592968157 1.530408633 1.400387608 1 19.15336029 0.95751417 21.65129491 0.999999998 1.448536363 0.671193853 0.099977671 954.0253613 486184.2609 0.095623597 0.023905899 9.068055517 -0.95751417 0.448536365 GGDVS(ph)PSPYSSSSWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GGDVSPSPYSSSSWR 15 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YFE7 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 GGDVS(1)PSPYSSSSWR;GGDVS(0.986)PS(0.014)PYSSSSWR;GGDVS(0.974)PS(0.026)PYS(0.001)SSSWR;GGDVS(0.835)PS(0.165)PYSSSSWR;GGDVS(0.709)PS(0.291)PYSSSSWR;GGDVS(0.999)PS(0.001)PYSSSSWR;GGDVS(0.997)PS(0.003)PYSSSSWR 385.62 2.58E-114 6833920000 2987230 3239150 3189400 3141260 3280470 2985110 3508570 2745770 3094010 TRUE FALSE 2800264.607 3478980.036 3265054.074 3221870.05 3022835.119 3846862.798 2982492.5 3088585.429 2577599.743 1.086384577 1.349697542 1.26670329 1.249949709 1.17273255 1.492420539 1.157081315 1.198240897 1 21.29759682 0.891971535 1.581914752 1.00309225 1.271810098 0.341446805 0.110552224 0.511954568 2.532512173 0.093448656 0.027122937 7.797790001 -0.891971535 0.268717848 GGET(ph)PGSEQWK ddPTM_SK-BR-3_Pertuzumab_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(0.998)PGS(0.002)EQWK;GGET(0.998)PGS(0.002)EQWK;GGET(1)PGSEQWK;GGET(1)PGSEQWK;GGET(1)PGSEQWK 257.75 1.73E-19 2555470000 4589390 3850890 4273670 3947300 5193100 3620570 5611680 4473350 6365990 TRUE FALSE 4302148.272 4136013.902 4375043.471 4048594.401 4785254.874 4665769.784 4770260.68 5031857.595 5303465.143 0.811195729 0.779870102 0.824940553 0.763386633 0.902288361 0.879758735 0.899461117 0.948786776 1 22.33850386 1.787452019 0.548496266 0.99924288 0.787047916 0.847097346 0.029158697 0.272492376 0.181545521 0.026254741 0.01664457 61.29880649 -1.787452019 -0.212194964 GGEYGFGAAFDADGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGEYGFGAAFDADGDR 16 0 Q15124;Q15124-2 Q15124 PGM5 Phosphoglucomutase-like protein 5 0 117.03 0.00088816 115780000 101160 120580 90139 93263 127000 93996 115180 131640 73315 FALSE TRUE 94828.57618 129507.8687 92277.13965 95656.28647 117025.9323 121131.1193 97909.82828 148075.5438 61078.25287 1.552575127 2.120359745 1.510801886 1.566126763 1.915999997 1.983211923 1.60302274 2.424357882 1 15.89837117 2.703630432 24.63354375 1.820119525 1.730170612 0.005714189 0.391499116 3410.43414 2405109.914 0.114221791 0.107696044 505.394408 -2.703630432 -0.089948913 GGFCNFMHLKPISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGFCNFMHLKPISR 14 1 P0DN76;Q01081;Q01081-2;Q01081-4 P0DN76;Q01081-2;Q01081-4 U2AF1 Splicing factor U2AF 35 kDa subunit 0 ; 182.57 9.06E-07 803890000 1140510 1566740 1115650 1072360 1714550 865330 1354310 1478450 1823350 FALSE TRUE 1069127.515 1682743.06 1142113.745 1099878.573 1579896.159 1115136.724 1151243.788 1663037.737 1519021.106 0.703826636 1.107781224 0.751874836 0.724070633 1.040075186 0.734115358 0.757885314 1.094808842 1 20.53471048 1.231654113 24.99792399 1.047404501 0.845000078 0.289810058 0.139329039 237.5511997 859772.6652 0.119645042 0.032499034 17.04724147 -1.231654113 -0.202404423 GGFDGEYQDDSLDLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGFDGEYQDDSLDLLR 16 0 Q5F1R6;Q5F1R6-3;Q5F1R6-2 Q5F1R6 DNAJC21 DnaJ homolog subfamily C member 21 0 107.18 0.0026715 21917000 30076 32379 35881 33420 36741 31821 38422 32764 31517 FALSE TRUE 28193.59685 34776.37485 36732.11426 34277.61378 33855.51007 41007.20613 32660.97779 36854.65752 26256.60909 1.073771436 1.324480809 1.398966414 1.30548517 1.289409076 1.561786063 1.243914539 1.403633553 1 14.68039299 -1.212946943 5.140805912 0.999969968 1.333945626 0.400675601 0.124576913 3.85E-05 5.89E-06 0.108295953 0.025523309 0.061242521 1.212946943 0.333975658 GGFDS(ph)PFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGFDSPFYR 9 0 A0A2R8YFV7;A0A2R8Y5N2;A0A2R8Y5S3;Q92574-2;Q92574;A0A2R8Y6S1;A0A2R8YEH9 A0A2R8YFV7 TSC1 Hamartin 1 GGFDS(1)PFYR;GGFDS(1)PFYR;GGFDS(1)PFYR;GGFDS(1)PFYR 146.11 0.00010025 1132770000 1908600 2257400 2045910 2092910 2530540 2066990 2502190 2158490 2343550 TRUE FALSE 1789144.133 2424540.245 2094439.951 2146617.614 2331801.596 2663696.458 2127009.839 2427982.228 1952396.365 0.916383663 1.241827883 1.072753458 1.099478391 1.194327974 1.364321562 1.089435463 1.243590836 1 20.89681454 4.74956874 24.2324027 1.167147064 0.916383438 0.354230993 0.104617773 1134.490872 2497303.389 0.022874421 0.334962479 56178.31902 -4.74956874 -0.250763626 GGFGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GGFGFR 6 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;;; 142.14 0.026902 4147830000 2769840 3374830 3293640 3081220 3325210 2870300 3376230 2934280 3134190 FALSE TRUE 2596480.659 3624705.925 3371766.696 3160289.322 3064061.42 3698909.015 2869995.655 3300631.317 2611073.441 0.994411194 1.388205275 1.291333535 1.210341031 1.173487261 1.41662389 1.099163129 1.264089805 1 21.31621161 0.140090347 0.611408231 0.98816855 1.259417026 0.219839493 0.127618949 4.375389689 2.086484717 0.243793453 0.047496676 1.380671457 -0.140090347 0.271248476 GGGAPWPGGAQTYS(ph)PSSTCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGGAPWPGGAQTYSPSSTCR 20 0 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 GGGAPWPGGAQTYS(0.966)PS(0.026)S(0.006)T(0.001)CR 153.36 5.64E-08 193180000 54643 54362 62158 54383 64787 54432 61960 62053 82180 TRUE FALSE 51222.99217 58387.01904 63632.41711 55778.55985 59698.89036 70145.63477 52669.67321 69800.45365 68463.6271 0.748178184 0.85281808 0.929433917 0.814718153 0.871979661 1.024567902 0.769308835 1.019526084 1 16.06305011 8 0.072370774 1.110189158 0.340332648 0.349952192 0.080870672 318.5334314 1.696088457 3.039717431 24.84588442 100000000 -8 -0.76985651 GGGCCHREPSQDHHESQEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGGCCHREPSQDHHESQEHR 20 1 P52943-2 P52943-2 CRIP2 Cysteine-rich protein 2 0 70.335 0.0063032 12581000 1160.4 7598.5 5710.5 4990.4 8245.2 5426.6 6602 4972.3 16903 FALSE TRUE 1087.772635 8161.100846 5845.955757 5118.462113 7597.655252 6993.171327 5612.09139 5593.1026 14081.7801 0.077246813 0.579550368 0.415143236 0.363481185 0.539537984 0.496611314 0.39853565 0.397187185 1 13.7815421 -2.084657195 2.418064185 1.915594516 0.4286177 0.644914643 0.137228824 12948321.36 4210602.012 65255344.49 0.02962624 0.008228919 2.084657195 -1.486976816 GGGDRYEDRYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GGGDRYEDRYDR 12 2 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;; 188.29 5.28E-06 3525270000 1075702 1677520 1343190 1285870 1956030 1073743 1455110 1295060 2685590 FALSE TRUE 1008375.732 1801725.326 1375051.101 1318867.601 1802411.294 1383715.173 1236929.764 1456751.092 2237347.679 0.4507014 0.805295191 0.614589817 0.589478163 0.805601789 0.618462292 0.552855408 0.651106265 1 21.09335804 0.919105644 21.63152475 1 0.644900764 0.533576792 0.106680386 15591.82951 4169334.032 0.096656826 0.024164207 8.300526569 -0.919105644 -0.355099237 GGGEAAQSPGPLPQS(ph)KPDGGETLYVTADLTLEDNRR ddPTM_SK-BR-3_Pertuzumab_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(0.449)PGPLPQS(0.551)KPDGGETLYVTADLTLEDNRR 78.542 0.0012989 34636000 30849 28361 27524 36811 38552 29392 32166 29534 34802 TRUE FALSE 28918.21616 30460.87795 28176.88228 37755.63258 35524.28143 37876.99326 27343.00691 33221.38491 28993.32137 0.997409568 1.050617056 0.971840443 1.302218263 1.225257396 1.306404078 0.943079496 1.145828879 1 14.82343299 3.277390495 24.99997806 1.150496985 1.011080864 0.261644949 0.116379922 232.6977663 149817.1223 0.032517638 0.044028273 1894.045882 -3.277390495 -0.139416121 GGGESLQEAS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGGESLQEASPR 12 0 P98175-5 P98175-5 RBM10 RNA-binding protein 10 1 GGGESLQEAS(1)PR 120.29 0.00020648 0 66084 106770 104550 108400 106770 90809 117470 101130 97781 TRUE FALSE 61947.9204 114675.3619 107029.9754 111181.7275 98384.71489 117024.0841 99856.46404 113756.3031 81460.71941 0.760463704 1.407738143 1.313884485 1.364850793 1.207756519 1.436570718 1.225823498 1.396455911 1 16.31381693 4.74469156 24.84007891 1.312011534 0.760463437 0.625169095 0.129208543 351.8591727 1425546.734 0.025940834 0.239109612 55550.95889 -4.74469156 -0.551548097 GGGEYGETWHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGGEYGETWHK 11 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ;;; 176.95 8.20E-06 2230760000 1492440 1753530 1704840 1721670 1931560 1558680 2176840 1721440 1829350 FALSE TRUE 1399030.844 1883363.186 1745279.61 1765850.967 1779863.069 2008645.613 1850443.051 1936365.573 1524019.667 0.917987395 1.235786668 1.145181816 1.158679908 1.167874082 1.317991924 1.214185808 1.270564688 1 20.53945009 4.743123606 24.81280819 1.199321175 0.917987269 0.493416856 0.085641185 327.1680356 1779017.359 0.018336518 0.146852213 55350.76226 -4.743123606 -0.281333906 GGGFGDRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGGFGDRDR 9 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;; 126.31 0.00043503 2289270000 1082970 2011600 1338980 1315530 2202440 1031310 1379140 1675570 2462090 FALSE TRUE 1015188.841 2160540.957 1370741.238 1349288.727 2029469.247 1329032.455 1172350.76 1884768.603 2051151.273 0.494936114 1.053330871 0.668278959 0.657820193 0.989429338 0.647944631 0.571557435 0.918883277 1 20.96800246 1.015500622 21.11648306 1.000000058 0.746519287 0.2389981 0.173445612 44.98925797 61287.15034 0.161317802 0.040329451 10.3633609 -1.015500622 -0.253480772 GGGFGGNDNFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGGFGGNDNFGR 12 0 F8W6I7;P09651-2;P09651;A0A2R8Y4L2;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 ; 148.56 0.00015477 78404000 136331 169390 158492 176900 186979 121457 163190 137024 108397 FALSE TRUE 127798.2861 181931.8119 162251.5051 181439.5535 172294.4236 156519.6642 138721.1745 154131.748 90304.84043 1.415187552 2.014640754 1.79670884 2.009189681 1.907920138 1.733236707 1.536143288 1.706793869 1 16.4625157 0.572363288 0.639817969 0.988658434 1.855269958 0.636636383 0.184452145 0.866109339 0.638888105 0.198635738 0.068622263 3.735625126 -0.572363288 0.866611524 GGGGEGGGEAS(ph)PDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGGGEGGGEASPDR 14 0 A0A0D9SGD0;A0A0D9SGA5 A0A0D9SGD0 SLC12A5 1 GGGGEGGGEAS(1)PDR;GGGGEGGGEAS(1)PDR;GGGGEGGGEAS(1)PDR;GGGGEGGGEAS(1)PDR 232.98 3.73E-17 690620000 804549 847516 804053 820969 866245 764289 865863 784516 586710 TRUE FALSE 754193.7143 910266.9665 823125.5169 842036.4544 798213.612 984926.8271 736034.8814 882464.5495 488784.3107 1.542999024 1.86230807 1.68402606 1.722715799 1.633058988 2.015054095 1.50584801 1.805427323 1 18.89883845 -2.243775322 0.558378196 9.60E-05 1.730967257 0.693815711 0.150215992 76.2715797 5.50306508 95.04013534 0.055945549 0.005704593 2.243775322 1.730871264 GGGGEGGGEAS(ph)PDRQGSLPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGGGEGGGEASPDRQGSLPSR 21 1 A0A0D9SGD0;A0A0D9SGA5 A0A0D9SGD0 SLC12A5 1 GGGGEGGGEAS(1)PDRQGSLPSR;GGGGEGGGEAS(1)PDRQGSLPSR;GGGGEGGGEAS(1)PDRQGSLPSR;GGGGEGGGEAS(1)PDRQGSLPSR 288.67 1.44E-46 2491760000 719248 953217 763447 933297 1079915 573511 854353 776994 1182940 TRUE FALSE 674231.5516 1023794.179 781556.3234 957246.9811 995102.8321 739074.3155 726250.6991 874003.4113 985499.6719 0.68415198 1.03885796 0.793055894 0.971331608 1.009744458 0.749948819 0.73693652 0.886863219 1 19.91049587 2.222247426 24.9911093 0.80989726 0.907204519 0.014637139 0.127245009 500.701512 767048.4726 0.043696084 0.032367394 166.8197345 -2.222247426 0.09730726 GGGGGQDNGLEGLGNDS(ph)R ddPTM_SK-BR-3_Pertuzumab_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 306.43 2.95E-50 1901860000 1940960 1895190 2215510 1896700 2121690 2338610 2518410 2225740 2657110 TRUE FALSE 1819478.778 2035511.84 2268062.943 1945372.533 1955061.026 3013728.743 2140797.8 2503628.538 2213621.175 0.821946771 0.919539378 1.024593986 0.878819084 0.883195846 1.361447377 0.967102151 1.131010385 1 21.07797692 GGGGNFGPGPGS(ph)NFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GGGGNFGPGPGSNFR 15 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 GGGGNFGPGPGS(1)NFR;GGGGNFGPGPGS(1)NFR;GGGGNFGPGPGS(1)NFR 98.552 0.0030254 395140000 291571 321171 296696 302469 369737 245053 380001 300113 450447 TRUE FALSE 273322.0916 344950.835 303733.7692 310230.8666 340699.3475 315795.823 323023.3778 337582.7687 375264.4857 0.728345212 0.919220572 0.809385862 0.826699244 0.907891262 0.841528669 0.860788564 0.899586243 1 18.51754824 -5 0.162267342 1.569882078 0.812407001 0.52400261 0.050382874 109.9471816 1.017851734 20.04791198 0.189438339 1.00E-05 5 -0.757475077 GGGGNFGPGPGSNFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGGGNFGPGPGSNFR 15 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;; 343.57 1.88E-69 1913910000 838800 962220 911470 886230 978160 790850 1007090 857740 1065860 FALSE TRUE 786301.0053 1033463.77 933090.4988 908972.1622 901339.2593 1019155.557 856086.2039 964830.7271 887961.0803 0.885512916 1.163861562 1.050823645 1.023662165 1.015066177 1.147748003 0.964103296 1.086568712 1 19.76013692 0.395860258 0.505650059 0.997831486 1.056365034 0 0.082735248 9.064822825 3.888970215 0.138751203 0.038991704 2.48805661 -0.395860258 0.058533548 GGGHILPYDQPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGGHILPYDQPLR 13 0 Q9H3G5;H7C0X5;H7C218 Q9H3G5 CPVL Probable serine carboxypeptidase CPVL 0 69.352 0.047942 321790000 153890 187450 177920 167230 188000 160760 190200 166070 234140 FALSE TRUE 144258.2996 201328.993 182140.3464 171521.4049 173235.2384 207168.8023 161681.2757 186804.2051 195060.5214 0.739556618 1.032136034 0.93376325 0.879324036 0.888110198 1.062074482 0.828877492 0.957673053 1 17.57356229 -1.79139188 2.403100146 1.023687727 0.924860638 0.067117755 0.093372659 35019238.27 22520149.63 4846515.024 0.021726477 0.016166206 1.79139188 -0.098827089 GGGHVAQIYAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGGHVAQIYAIR 12 0 P62249;M0R210;M0R3H0;M0R1M5;M0QX76 P62249 RPS16 40S ribosomal protein S16 0 ;;; 152.62 6.78E-05 2057340000 1412010 2190670 1409140 1261490 2055920 1097290 1549130 1779130 1527700 FALSE TRUE 1323634.815 2352869.486 1442565.466 1293861.969 1894456.336 1414059.81 1316852.338 2001258.297 1272717.001 1.040007177 1.848698088 1.133453443 1.016614038 1.488513421 1.111055961 1.034678045 1.572429924 1 20.27948023 3.734378035 23.22098959 1.185716955 1.498804281 0.120123901 0.272510589 171.1750467 547732.699 0.063532795 0.111352496 5424.728851 -3.734378035 0.313087326 GGGPGKS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGGPGKSPTR 10 1 H7BZ50;H7C173;A0A494C0V9;B8ZZ87;Q6NZ67 H7BZ50 MZT2B Mitotic-spindle organizing protein 2B 1 GGGPGKS(0.5)PT(0.5)R;GGGPGKS(0.763)PT(0.237)R;GGGPGKS(0.65)PT(0.35)R;GGGPGKS(0.958)PT(0.042)R 98.105 0.0033938 9801210000 2359520 1957370 2073390 1984170 2135090 1691510 2410730 1980800 2558490 TRUE FALSE 2211841.855 2102295.711 2122571.79 2035087.161 1967408.644 2179821.478 2049263.417 2228107.24 2131461.491 1.037711385 0.986316535 0.995829293 0.95478486 0.923032695 1.022688652 0.961435816 1.04534248 1 21.02341156 1.23979886 24.99993052 1.022671238 0.982682483 0.18622963 0.034368086 51.75577812 1045126.316 0.024390143 0.007790906 17.36996165 -1.23979886 -0.039988755 GGGPGKSPT(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GGGPGKSPTR 10 1 H7BZ50;H7C173;A0A494C0V9;B8ZZ87;Q6NZ67 H7BZ50 MZT2B Mitotic-spindle organizing protein 2B 1 GGGPGKS(0.213)PT(0.787)R;GGGPGKS(0.125)PT(0.875)R;GGGPGKS(0.391)PT(0.609)R 100.38 0.0065565 4133230000 1762510 1529690 1596140 1519880 1737760 1259300 1871490 1484680 1894170 TRUE FALSE 1652197.645 1642949.839 1634001.195 1558882.694 1601283.339 1622839.467 1590877.449 1670045.566 1578020.79 1.04700626 1.041145877 1.035475074 0.987872089 1.014741599 1.028401829 1.008147331 1.05831658 1 20.58968478 3.456187184 24.9971922 1.016395751 1.041193283 0.292815976 0.01852472 276.4642992 330122.516 0.004734851 0.006412613 2858.822449 -3.456187184 0.024797532 SETDLLDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SETDLLDIR 9 0 P50995;P50995-2;H0Y6E1 P50995 ANXA11 Annexin A11 0 101.64 0.0089423 37649000 97854 125610 110910 75602 162170 59808 136090 122760 315010 FALSE TRUE 91729.49281 134910.2951 113540.8376 77542.07531 149433.8224 77073.5987 115684.5679 138086.8562 262432.796 0.349535173 0.514075593 0.432647288 0.295474028 0.569417484 0.293688898 0.440815971 0.526179877 1 18.0015885 0.73338713 2.333435526 0.999843037 0.421680131 0.815529584 0.08709638 0.48906395 3.707575913 0.075361743 0.020338344 5.412365658 -0.73338713 -0.578162907 GGGPQAQSHGEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GGGPQAQSHGEAR 13 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 0 ;; 155.66 4.68E-05 714020000 274651 293231 292867 281169 282816 264194 288702 241661 335859 FALSE TRUE 257461.0842 314942.1283 299813.9435 288384.2726 260604.7722 340462.519 245413.8153 271832.9078 279801.9632 0.920154674 1.125589416 1.071521944 1.030672799 0.931390078 1.216798178 0.877098261 0.971518944 1 18.09404656 1.657340435 15.31678486 0.943574385 1.055296241 0.209427544 0.090627065 0.182371029 49.67096085 0.038355812 0.021148572 45.42975923 -1.657340435 0.111721856 GGGPVTLQDYRLPDS(ph)DDDEDEETAIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGGPVTLQDYRLPDSDDDEDEETAIQR 27 1 Q96K21-3 Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 GGGPVTLQDYRLPDS(1)DDDEDEETAIQR;GGGPVTLQDYRLPDS(1)DDDEDEETAIQR 267.26 9.13E-54 525990000 133180 242350 205682 230440 226200 165956 228340 135074 322320 TRUE FALSE 124844.5015 260293.8462 210560.8742 236353.4805 208435.1644 213864.8031 194102.5368 151938.2862 268522.7097 0.464930887 0.969355055 0.784145499 0.880199223 0.776229186 0.796449594 0.722853337 0.565830303 1 18.03468458 1.801476891 5.154184883 0.733596481 0.805623783 0 0.166346935 0.796762033 37.87259773 0.071504206 0.040070318 63.31066736 -1.801476891 0.072027302 GGGQEERPFVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGGQEERPFVAR 12 1 Q9HA64;I3L2G3 Q9HA64 FN3KRP Ketosamine-3-kinase 0 164.81 5.13E-05 531330000 287260 394710 322550 373610 401820 301430 405180 319790 341650 FALSE TRUE 269280.9094 423934.7391 330201.0383 383197.4651 370262.6781 388447.9477 344427.0205 359716.4854 284626.4079 0.946085472 1.489442748 1.160120878 1.346317329 1.30087254 1.364764256 1.210102123 1.263819785 1 18.11871 0.315871301 1.123767907 0.999528892 1.281016602 0.235619869 0.143937853 4.375392678 6.035133115 0.124712492 0.037178545 2.069527972 -0.315871301 0.281487709 GGGQLDLLGVSLAS(ph)LKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGGQLDLLGVSLASLKK 17 1 E7EXA6;A0A0D9SF58;Q8WVB6;Q8WVB6-2;F8WCC1;H0Y7D3 E7EXA6 CHTF18 Chromosome transmission fidelity protein 18 homolog 1 GGGQLDLLGVSLAS(1)LKK 122.53 3.47E-05 76423000 168320 122120 136720 139740 159240 99060 214680 144750 224510 TRUE FALSE 157785.1517 131161.8919 139963.063 143325.965 146733.9327 127657.0139 182490.727 162822.3561 187037.8306 0.843600202 0.701258625 0.748314191 0.766293987 0.784514728 0.682519753 0.975688856 0.870531676 1 17.51297058 1.713761094 8.083755859 0.94013639 0.749329872 0.733660636 0.054948071 0.054171253 8.647056243 0.024007492 0.012709539 51.73221735 -1.713761094 -0.190806518 GGGQSVQFTDIETLKQES(ph)PNGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGGQSVQFTDIETLKQESPNGSR 23 1 Q02241;A0A2U3TZL8;Q02241-2;Q02241-3 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23 1 GGGQSVQFTDIETLKQES(1)PNGSR;GGGQSVQFTDIETLKQES(1)PNGSR 210.73 3.70E-25 1367670000 1046660 784880 950470 925430 1034390 771670 1119310 815740 1105270 TRUE FALSE 981151.4189 842993.3319 973015.5972 949178.1005 953153.1819 994438.602 951479.8567 917586.9347 920793.2967 1.065550132 0.915507677 1.056714466 1.030826467 1.035143485 1.07998028 1.03332622 0.996517826 1 19.81251781 3.779591847 8.22442523 1.037160345 0.981401951 0.132290433 0.043124615 0.380973315 54.3388928 0.009946406 0.017924194 6019.935627 -3.779591847 -0.055758394 GGGSCSGSAGGGGS(ph)GSLPSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGGSCSGSAGGGGSGSLPSQR 21 0 O15234 O15234 CASC3 Protein CASC3 1 GGGSCSGSAGGGGS(1)GSLPSQR;GGGSCSGSAGGGGS(0.999)GS(0.001)LPSQR 314.43 1.28E-66 391250000 301830 342480 320580 335320 321820 351600 342600 298530 306820 TRUE FALSE 282938.9991 367837.5756 328184.309 343924.8789 296545.5554 453101.2123 291230.3105 335802.1276 255609.7599 1.106917824 1.439059196 1.283927144 1.345507617 1.160149579 1.772628762 1.139355206 1.313729678 1 17.9635834 0.669308005 1.445661812 1.001807742 1.339540987 0.217262958 0.190150672 1.6313083 5.133262335 0.159310947 0.046643729 4.669904566 -0.669308005 0.337733245 GGGSQHYPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGGSQHYPEER 11 0 Q9NWH9;Q9NWH9-3;H7C3F4;H0YKH2 Q9NWH9 SLTM SAFB-like transcription modulator 0 66.498 0.062546 196740000 136980 241780 228750 246290 277710 216730 318350 246390 267790 FALSE TRUE 128406.6663 259681.6428 234176.058 252610.2184 255899.7768 279296.4327 270616.3729 277152.3339 223094.119 0.575571722 1.164000396 1.049673829 1.13230335 1.14704851 1.251921987 1.213014373 1.24231125 1 17.76729296 4.73910559 24.95503399 1.154929837 0.575571542 0.839236408 0.078990319 16.92137081 774653.4221 0.019032298 0.112947115 54841.02839 -4.73910559 -0.579358295 GGGT(ph)PDANSLAPPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGGTPDANSLAPPGK 15 0 Q9BRQ0;Q5T171 Q9BRQ0 PYGO2 Pygopus homolog 2 1 GGGT(1)PDANSLAPPGK;GGGT(1)PDANSLAPPGK 232.26 9.46E-13 1821170000 2910700 2587570 2731390 2523660 2953140 2633790 3784180 2797360 3191710 TRUE FALSE 2728524.483 2779156.375 2796179.861 2588421.388 2721212.297 3394122.417 3216777.34 3146616.554 2658992.982 1.026149562 1.045191316 1.051593547 0.973459278 1.023399579 1.276469115 1.209772783 1.183386558 1 21.34244854 2.257501551 24.9900458 1.190825127 1.028326941 0.47490878 0.073051508 164.132439 216550.3891 0.022799901 0.019046933 180.9262372 -2.257501551 -0.162498186 GGGTSSGGSSTNS(ph)LTGSRPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGGTSSGGSSTNSLTGSRPPK 21 1 Q5T9C2-3;Q5T9C2;Q5T9C2-2 Q5T9C2-3 FAM102A Protein FAM102A 1 GGGTSSGGSST(0.001)NS(0.999)LTGSRPPK 164.79 9.41E-12 248750000 106120 93966 99327 96262 132400 76821 118230 107000 204740 TRUE FALSE 99478.13863 100923.3404 101683.0833 98732.24589 122001.8381 98997.97562 100502.5091 120359.1855 170567.5713 0.583218357 0.591691255 0.59614546 0.578845352 0.715269832 0.580403267 0.589224014 0.705639323 1 17.37998386 0.847283481 2.907695254 0.999860213 0.603911786 0.904419933 0.040350059 0.171267549 2.626769192 0.036821453 0.009682342 7.035313923 -0.847283481 -0.395948428 GGHDILVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGHDILVR 8 0 Q9Y678;H0Y8X7 Q9Y678 COPG1 Coatomer subunit gamma-1 0 108.46 0.0038063 373260000 172380 141920 197750 193880 163760 174540 218740 140980 165720 FALSE TRUE 161591.0435 152427.9045 202440.7234 198855.289 150898.9502 224926.8646 185941.9677 158581.6633 138060.2614 1.170438487 1.104067911 1.466321455 1.440351387 1.092993369 1.629193385 1.346817439 1.148640903 1 17.0749386 1.035861488 3.82485384 1.002608296 1.325890344 0.293941462 0.167769544 0.238722047 7.880859608 0.156494927 0.040281869 10.86079179 -1.035861488 0.323282048 GGHFAAFEEPELLAQDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGHFAAFEEPELLAQDIR 18 0 P07099 P07099 EPHX1 Epoxide hydrolase 1 0 ;;; 217.11 8.60E-19 275161000 168097 440920 108543 110927 502830 162160 139689 455970 287816 FALSE TRUE 157576.1088 473566.1756 111117.6912 113773.5746 463339.7601 208972.9596 118743.9313 512898.8582 239777.6502 0.657175966 1.975022172 0.463419719 0.474496161 1.932372595 0.871528098 0.495225185 2.139060324 1 17.87133767 GGHGAASPSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGHGAASPSEK 11 0 Q07065 Q07065 CKAP4 Cytoskeleton-associated protein 4 0 81.017 0.022826 44016000 31495 33888 29278 30560 40074 27923 36449 36180 34828 FALSE TRUE 29523.78417 36397.10278 29972.48799 31344.22134 36926.74969 35983.91681 30983.81083 40697.15264 29014.9818 1.01753585 1.254424457 1.033000406 1.080277132 1.272678713 1.240184021 1.067855601 1.402625475 1 14.8245104 2.762086211 24.73873491 1.193330373 1.11211045 0.130674049 0.125559111 1679.405183 1766003.757 0.035363862 0.037487638 578.2108153 -2.762086211 -0.081219923 GGHMDDGGYSMNFNMSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 235.24 3.72E-24 909040000 394160 674050 522670 524830 696120 468700 520282 587650 631580 FALSE TRUE 369490.2292 723957.3633 535067.9792 538298.0263 641449.5432 604006.0813 442270.5442 661019.3961 526165.2178 0.702232334 1.37591262 1.016920087 1.023058933 1.219102901 1.147939964 0.840554505 1.256296261 1 19.00515636 GGIDNPAITS(ph)DQELDDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGIDNPAITSDQELDDKK 18 1 Q13017-2;Q13017;H0YK04;A0A0A0MSK6 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 1 GGIDNPAIT(0.043)S(0.957)DQELDDKK;GGIDNPAIT(0.045)S(0.955)DQELDDKK;GGIDNPAIT(0.179)S(0.821)DQELDDKK;GGIDNPAIT(0.142)S(0.858)DQELDDKK 222.46 3.48E-19 2394990000 4543000 2010490 2794860 2762690 3013820 1960460 3848820 2316440 4171030 TRUE FALSE 4258661.739 2159348.772 2861155.399 2833585.303 2777126.734 2526412.977 3271725.172 2605652.633 3474858.147 1.225564198 0.621420697 0.823387683 0.815453519 0.799205785 0.727054996 0.941542081 0.749858706 1 21.72852265 -2.566657594 0.57821379 1.385962784 0.818466033 0.078850668 0.16107179 599.6188857 33.21279773 291.5767246 0.059345931 0.002712329 2.566657594 -0.56749675 GGIHTADTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGIHTADTK 9 0 O00442;O00442-2 O00442 RTCA RNA 3-terminal phosphate cyclase 0 ;;; 108.81 0.0025514 533904000 596880 588550 535400 561740 571060 449107 611750 555890 567320 FALSE TRUE 559522.3463 632126.8544 548099.9408 576155.1994 526211.2511 578756.9003 520023.7667 625294.0902 472630.627 1.183846992 1.337464858 1.159679271 1.219039069 1.113366805 1.224543792 1.100275219 1.323007978 1 18.85035359 -5 0.140050208 0.329450191 1.277366055 0.358950618 0.081033656 137.0838442 1.176964407 25.9884714 0.450852598 1.00E-05 5 0.947915864 GGKDPLS(ph)SPGGPGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGKDPLSSPGGPGSR 15 1 G3V1D0;B7WPE2;H0Y3M3;Q32P44;Q32P44-2 G3V1D0 EML3 Echinoderm microtubule-associated protein-like 3 1 GGKDPLS(0.58)S(0.42)PGGPGSR 83.063 0.0055541 376440000 738460 724890 857880 1027500 975660 597980 734850 620380 889470 TRUE FALSE 692241.1068 778561.6098 878229.3187 1053867.39 899035.5992 770607.1186 624666.0645 697835.8086 741011.7108 0.934183761 1.050673827 1.185176032 1.422200721 1.213254239 1.03993919 0.842990813 0.941733846 1 19.49913682 2.000832978 4.804345009 0.915757634 1.159973562 0.407113237 0.128445097 0.188261604 11.93674384 0.056990366 0.037483325 100.1919843 -2.000832978 0.244215928 GGKNIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGKNIR 6 1 Q9NYT6 Q9NYT6 ZNF226 Zinc finger protein 226 0 92.279 0.042807 975480000 2207600 1687100 2097500 2066700 2116200 1412400 1799800 1756800 1977900 FALSE TRUE 2069430.257 1812014.639 2147253.691 2119735.021 1950002.188 1820136.952 1529936.699 1976140.347 1647775.712 1.255893166 1.099673108 1.303122552 1.286422057 1.183414814 1.104602367 0.928486011 1.199277506 1 20.65208845 2.175854098 3.166963069 1.031907345 1.224152164 0.488164169 0.086958541 0.198311323 4.034464339 0.034771181 0.02450717 149.9181099 -2.175854098 0.192244819 GGLHDFRS(ph)PPPGMGLNQNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGLHDFRSPPPGMGLNQNR 19 1 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 1 GGLHDFRS(1)PPPGMGLNQNR 69.152 0.014087 115570000 53941 168780 79120 106900 153560 75192 88888 138400 130510 TRUE FALSE 50564.9291 181276.6468 80996.76376 109643.235 141500.017 96898.70976 75560.0696 155679.5447 108727.0379 0.465063061 1.667263731 0.744955122 1.00842658 1.301424372 0.891210794 0.694951974 1.43183837 1 16.73035122 GGLLTSEEDSGFSTS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGLLTSEEDSGFSTSPK 17 0 Q9UQR1 Q9UQR1 ZNF148 Zinc finger protein 148 1 GGLLTSEEDSGFST(0.009)S(0.991)PK;GGLLTSEEDSGFST(0.001)S(0.999)PK;GGLLTSEEDSGFSTS(1)PK;GGLLTSEEDSGFST(0.044)S(0.956)PK 325.61 2.32E-59 615050000 2269150 1221920 1599120 1404590 1324050 1258040 2069070 1175600 1239310 TRUE FALSE 2127127.952 1312392.228 1637051.882 1440634.157 1220064.454 1621215.725 1758832.162 1322376.248 1032461.155 2.060249862 1.271129884 1.585582057 1.395339816 1.181704947 1.570243798 1.703533497 1.280800001 1 19.97765607 -2.772229478 0.378631007 2.58E-16 1.51453282 0.299770323 0.250669805 115.139725 4.211867385 93.48663399 0.159599934 0.001689548 2.772229478 1.51453282 GGLMNSWKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGLMNSWKR 9 1 E9PEW5;A0A0A0MQX1;Q9HD67-3;Q9HD67 E9PEW5 MYO10 Unconventional myosin-X 0 78.334 0.048206 218910000 238350 198810 204950 219150 243130 168660 260060 202630 259340 FALSE TRUE 223432.099 213530.0993 209811.5108 224773.76 224035.5505 217349.404 221066.4173 227928.8015 216054.4786 1.034147037 0.988316006 0.971104659 1.040356865 1.03694009 1.005993513 1.023197569 1.054959856 1 17.72103561 3.231185129 24.99999835 1.026739454 0.99199003 0.2616928 0.022287835 176.8231031 599359.3193 0.006209514 0.007561411 1702.884251 -3.231185129 -0.034749423 GGLNTPLHESDFSGVT(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGLNTPLHESDFSGVTPQR 19 0 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 1 GGLNTPLHESDFSGVT(1)PQR 263.83 1.00E-30 181640000 48104 103280 79800 81415 118820 103460 100240 99551 90836 TRUE FALSE 45093.25651 110926.9587 81692.89368 83504.24674 109488.3565 133327.2225 85209.94258 111980.1615 75674.88478 0.595881403 1.465835845 1.07952452 1.103460507 1.446825546 1.761842424 1.126000295 1.479753313 1 16.20752695 2.743594163 24.29549013 1.383390508 1.131677095 0.189325717 0.292883904 532.8927697 2572123.655 0.084280163 0.08687746 554.107671 -2.743594163 -0.251713413 GGLNTPLHESDFSGVTPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGLNTPLHESDFSGVTPQR 19 0 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 0 117.84 9.10E-05 98451000 59001 76035 71939 86500 80615 53622 77372 68278 87623 FALSE TRUE 55308.23273 81664.71051 73645.42705 88719.73644 74283.82309 69101.80092 65770.78689 76802.6586 72998.15523 0.757666171 1.118722936 1.008866961 1.215369569 1.017612333 0.946623935 0.900992452 1.052117802 1 16.15557239 2.36582949 5.487554795 0.959605348 1.045153379 0.019514732 0.121240133 0.484688405 21.56307803 0.039724246 0.032975878 232.1825037 -2.36582949 0.085548031 GGLRPGS(ph)LDAEIDLLSSTLAELNGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGLRPGSLDAEIDLLSSTLAELNGGR 26 1 Q15654 Q15654 TRIP6 Thyroid receptor-interacting protein 6 1 GGLRPGS(1)LDAEIDLLSSTLAELNGGR;GGLRPGS(1)LDAEIDLLSSTLAELNGGR 218.01 2.17E-34 2467980000 275109 405654 290046 369204 384123 371059 372309 326326 436720 TRUE FALSE 257890.4188 435689.0442 296926.0281 378678.3997 353955.5291 478177.7097 316484.7218 367068.5194 363828.6107 0.708823911 1.197511772 0.816115114 1.040815342 0.972863372 1.314293862 0.869873101 1.008905041 1 18.47289947 GGLS(ph)PANDTGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGLSPANDTGAK 12 0 P30419;B7Z8J4;K7EN42 P30419 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 1 GGLS(1)PANDTGAK;GGLS(1)PANDTGAK;GGLS(1)PANDTGAK;GGLS(1)PANDTGAK 198.16 1.96E-07 4100570000 9321830 7000050 8281020 7293330 7922520 6806720 9769390 6800450 8945550 TRUE FALSE 8738393.3 7518340.986 8477449.705 7480489.195 7300317.237 8771709.566 8304560.664 7649501.152 7452479.915 1.172548387 1.00883747 1.137534056 1.003758384 0.979582276 1.177018881 1.114335196 1.026437004 1 22.82928915 4.762657854 23.01584489 1.067867471 1.172548751 0.212237277 0.067196218 4071.852013 3888935.206 0.015630852 0.848097438 57897.23909 -4.762657854 0.10468128 GGLVS(ph)DAYGEDDFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGLVSDAYGEDDFSR 15 0 X6R3T8;J3QLH3;J3QQJ0;Q9UHR5-2;Q9UHR5;J3KS14;F5H478;J3KRU5 X6R3T8 SAP30BP SAP30-binding protein 1 GGLVS(1)DAYGEDDFSR;GGLVS(1)DAYGEDDFSR 120.7 0.00012539 155429000 257090 213370 225230 223610 270010 172875 274470 202227 271530 TRUE FALSE 240999.1958 229168.1368 230572.562 229348.2112 248804.5038 222781.2061 233315.7716 227475.4861 226209.8888 1.065378693 1.013077448 1.019285952 1.013873497 1.099883409 0.984842914 1.031412785 1.005594792 1 17.78730247 1.48370212 1.323175827 1.002647066 1.031648808 0.140778854 0.031181168 0.942252136 3.156861124 0.025903073 0.008736535 30.45805174 -1.48370212 0.029001743 GGLWDDDDAPRPSQFEEDLALMEEMEAEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGLWDDDDAPRPSQFEEDLALMEEMEAEHR 30 1 A0A087WYJ2;M0R2B7;P28340;M0QZR8;A0A2R8Y7K6;M0R2J2 A0A087WYJ2 POLD1 DNA polymerase;DNA polymerase delta catalytic subunit 0 ;;; 229.82 1.93E-35 101793000 93146 116610 111946 114517 121909 95551 120472 103070 101022 FALSE TRUE 87316.15813 125243.9257 114601.412 117455.7001 112334.7589 123135.0226 102408.342 115938.5164 84160.77557 1.037492318 1.488150803 1.361696244 1.395610952 1.334763827 1.463092774 1.216817945 1.377583745 1 16.36086038 -0.227364212 0.674492785 0.977567562 1.358644037 0.380714201 0.130615543 6.898445391 2.870852962 0.527157116 0.043346339 0.592428288 0.227364212 0.381076476 GGMGS(ph)GGLATGIAGGLAGMGGIQNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGMGSGGLATGIAGGLAGMGGIQNEK 26 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 GGMGS(0.997)GGLAT(0.003)GIAGGLAGMGGIQNEK 206.31 1.97E-25 38373000 109430 87081 95166 97028 100010 91922 124760 90215 130810 TRUE FALSE 102580.9716 93528.56785 97423.38246 99517.90275 92155.61802 118458.3892 106053.3962 101478.5413 108976.9659 0.941308751 0.858241621 0.893981417 0.913201261 0.845643088 1.08700392 0.97317259 0.931192573 1 16.7336637 2.255238751 24.99981414 0.996467218 0.88759085 0.570914885 0.046207461 160.9913645 241318.7711 0.014940262 0.012468281 179.9860108 -2.255238751 -0.108876368 GGNFGFGDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 GGNFGFGDSR 10 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;; 236.89 8.64E-12 36573200000 31809220 38769400 35000000 35031400 40809600 32997720 37880900 34058700 39776800 FALSE TRUE 29818337.7 41639926.72 35830216.53 35930365.03 37604578.63 42523626.09 32201010.71 38311003.67 33137795.11 0.899828658 1.25656902 1.081249263 1.084271446 1.134794228 1.283236436 0.971730636 1.156112033 1 24.98197428 0.645734885 0.88708106 1.00229283 1.12353836 0.058079625 0.116397461 2.901556127 3.940406839 0.102571039 0.034187137 4.423182764 -0.645734885 0.12124553 GGNFGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GGNFGGR 7 0 F8W6I7;P09651-2;P09651;P09651-3;Q32P51;H0YH80;P51991;P51991-2 F8W6I7;P51991;P51991-2 HNRNPA1;HNRNPA1L2;HNRNPA3 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2;Heterogeneous nuclear ribonucleoprotein A3" 0 ;;;;; 144.29 0.0054992 4837200000 4212370 5603410 4528070 4688180 5581410 3967500 4758590 4627010 5411130 FALSE TRUE 3948725.281 6018292.307 4635477.959 4808486.636 5143068.573 5112852.843 4045083.606 5204702.384 4507977.446 0.875941668 1.335031592 1.028283308 1.066661645 1.140881611 1.134178887 0.897316736 1.154553776 1 22.10404887 1.780906679 25 1.006872833 1.116939423 0.061626797 0.129426835 132.6167168 78321.35509 0.055196473 0.030708503 60.38188667 -1.780906679 0.11006659 GGNFPSFPHDEVTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGNFPSFPHDEVTDR 15 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 ; 131.56 5.29E-05 720520000 613540 678660 700840 688540 672810 571380 726040 582550 700680 FALSE TRUE 575139.6266 728908.6925 717464.2558 706209.1021 619970.2166 736328.1304 617177.0422 655282.6499 583731.9814 0.985280308 1.248704398 1.229098762 1.20981739 1.062080263 1.261414748 1.057295235 1.122574522 1 19.15494659 1.139711038 0.799900355 1.003611638 1.184283453 0.203278352 0.091871828 0.76399731 1.112337763 0.080571903 0.030467889 13.79466118 -1.139711038 0.180671814 GGNIGDGGGAADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGNIGDGGGAADR 13 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 176.87 3.71E-05 1780840000 1916560 2226790 2176460 2112490 2219810 2016400 2383700 2005210 2349370 FALSE TRUE 1796605.931 2391663.849 2228086.659 2166700.07 2045475.077 2598501.946 2026286.314 2255564.883 1957244.969 0.917925941 1.22195427 1.138379045 1.107015271 1.045078725 1.327632456 1.035274759 1.152418281 1 20.9003929 -0.228581763 1.137846552 0.998764377 1.129819842 0.092801961 0.110477354 47.04908425 39.9598478 0.370282197 0.028801123 0.590769734 0.228581763 0.131055465 GGNLPPVS(ph)PNDSGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GGNLPPVSPNDSGAK 15 0 Q9UK61-3;Q9UK61;Q9UK61-2;A0A087X0F1;Q9UK61-4 Q9UK61-3 FAM208A Protein FAM208A 1 GGNLPPVS(1)PNDSGAK;GGNLPPVS(1)PNDSGAK;GGNLPPVS(1)PNDSGAK 189.81 2.55E-07 356290000 662780 569050 626860 625000 608840 402506 621030 469903 652370 TRUE FALSE 621297.7829 611183.0541 641729.4152 641038.5581 561024.1623 518702.9481 527912.3169 528571.4239 543485.2325 1.143173256 1.124562394 1.180766977 1.179495817 1.032271217 0.954401182 0.971346203 0.972558944 1 19.05188131 2.573764416 3.562526956 0.972594927 1.155238915 0.946778574 0.020481355 0.051129974 1.207746779 0.007322799 0.006724402 374.7696525 -2.573764416 0.182643989 GGNLYHTDVSLFGEPTEFEYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGNLYHTDVSLFGEPTEFEYLR 22 0 Q13439-5;Q13439-3;Q13439-4;Q13439;H0Y6I0 Q13439-5 GOLGA4 Golgin subfamily A member 4 0 114.39 0.0002297 70394000 58439 117810 89097 91439 104470 102450 81687 80628 63854 FALSE TRUE 54781.40731 126532.775 91210.42291 93785.47955 96265.34761 132025.6519 69438.79269 90694.58328 53196.35489 1.02979626 2.378598595 1.714599113 1.76300575 1.809623005 2.481855235 1.305329902 1.704902215 1 15.69903977 0.94907069 1.174915625 1.022898386 1.879092246 0.242106883 0.428613395 0.667789123 1.883272532 0.3640146 0.114036353 8.893458655 -0.94907069 0.856193861 GGNRFEPYANPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGNRFEPYANPTK 13 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 123.38 0.00015215 0 217905 235075 224588 231207 282800 171128 269140 218448 351950 FALSE TRUE 204266.715 252480.1976 229915.3334 237140.1631 260590.0288 220529.8756 228784.9556 245721.7137 293207.2713 0.696663197 0.861098009 0.784139262 0.808779953 0.888757047 0.752129627 0.780284045 0.838047817 1 18.16156136 0.86918545 4.936918935 0.999992901 0.801733071 0.588921692 0.053151175 0.821543223 30.32590379 0.046679053 0.011805532 7.399211641 -0.86918545 -0.198259831 GGNRFEPYANPTKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGNRFEPYANPTKR 14 2 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 107.61 0.00049145 394290000 359760 441620 375760 419520 544350 304410 423660 370490 724310 FALSE TRUE 337243.2638 474318.0043 384673.2046 430285.5934 501598.9468 392288.2253 360136.1161 416746.492 603417.9818 0.558888323 0.786052154 0.637490456 0.713080496 0.831262843 0.650110267 0.596826954 0.690643144 1 19.20279816 -1.732278048 2.632324425 1.062080967 0.685424106 0.599635845 0.081371929 23396723.09 18373325.82 9507333.756 0.01886494 0.018523453 1.732278048 -0.376656861 GGNVFAALIQDQS(ph)EEEEEEEKHPPKPAKPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGNVFAALIQDQSEEEEEEEKHPPKPAKPEK 31 3 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 GGNVFAALIQDQS(1)EEEEEEEKHPPKPAKPEK 269.6 7.03E-60 3801200000 9660700 3121600 5038200 4910700 5174900 3480100 7111200 3941300 7705100 TRUE FALSE 9056054.032 3352726.512 5157708.483 5036716.876 4768484.229 4484748.375 6044941.577 4433379.981 6419069.033 1.410804898 0.522307284 0.803497899 0.784649121 0.742862275 0.69866025 0.941716244 0.690657782 1 22.61393265 -1.713268887 6.904089069 1.002127349 0.797018755 0.041289442 0.235053693 0.006853686 0.000284638 0.20265778 0.047325485 0.019352234 1.713268887 -0.205108594 GGNVGINSFGFGGSNVHIILRPNTQPPPAPAPHATLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGNVGINSFGFGGSNVHIILRPNTQPPPAPAPHATLPR 38 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 332.62 1.86E-129 1626440000 122963 294181 131199 101868 315390 166143 246466 282271 128448 FALSE TRUE 115266.9653 315962.4673 134311.1022 104482.1053 290620.5416 214105.787 209510.7114 317513.1557 107009.199 1.077168752 2.952666409 1.25513604 0.976384333 2.715846342 2.000816649 1.957875709 2.967157578 1 16.7073753 2.719022157 24.91240606 2.156722288 1.744859507 0.100645795 0.753235257 2343.183405 2987659.188 0.232998551 0.219970586 523.6271501 -2.719022157 -0.411862781 GGPAS(ph)PGGLQGLETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGPASPGGLQGLETR 15 0 C9JWC4;Q8NCD3-3;Q8NCD3-2;Q8NCD3 C9JWC4 HJURP Holliday junction recognition protein 1 GGPAS(1)PGGLQGLETR;GGPAS(1)PGGLQGLETR;GGPAS(1)PGGLQGLETR;GGPAS(1)PGGLQGLETR 232.62 3.75E-14 826280000 684775 688592 748211 736081 714669 712940 815153 621588 809195 TRUE FALSE 641916.1551 739576.0682 765958.9183 754970.0846 658541.7796 918754.2044 692928.3752 699194.6301 674135.1269 0.952206953 1.097073923 1.136209771 1.119909132 0.976869107 1.362863568 1.027877569 1.037172819 1 19.36267828 1.526570541 25 1.023185678 1.11158704 0.119162909 0.109701734 0.827736172 405.0510972 0.053935734 0.024969306 33.61789688 -1.526570541 0.088401363 GGPASVPSS(ph)SPGTSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGPASVPSSSPGTSVK 16 0 O43237;O43237-2;J3KRI4;J3KRZ2 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 GGPASVPS(0.045)S(0.471)S(0.471)PGT(0.012)S(0.002)VK;GGPASVPS(0.002)S(0.909)S(0.089)PGTSVK 239.89 8.03E-20 271990000 855950 643210 767720 781600 783380 641150 933880 693770 960640 TRUE FALSE 802377.6174 690833.9377 785930.6809 801657.1792 721856.4948 826239.5968 793853.3637 780388.7117 800302.978 1.002592317 0.863215503 0.98204143 1.001692111 0.901979019 1.0324085 0.991941034 0.975116591 1 19.61018675 3.722643171 7.831464671 0.984202106 0.922737338 0.161343796 0.046790483 0.152205612 77.70382611 0.011211875 0.018554772 5280.112438 -3.722643171 -0.061464768 GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(ph)PGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGPEGVAAQAVASAASAGPADAEMEEIFDDASPGK 35 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 1 GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(1)PGK 121.55 3.78E-08 104680000 57243 37763 50335 42385 41615 40558 60497 40623 42212 TRUE FALSE 53660.26281 40559.01181 51528.96997 43472.67086 38346.72577 52266.4362 51426.03648 45694.87097 35166.5445 1.525889551 1.153340835 1.465283857 1.236193987 1.090432009 1.486254534 1.462356828 1.299384731 1 15.10191596 -2.219461444 2.003119852 0.065377747 1.33958845 0.343611378 0.147634793 2420639.655 418396.7382 10237888.73 0.034695095 0.006033073 2.219461444 1.274210703 GGPEVQQVPAGERPLWFICSGMGTQWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 286.44 1.24E-61 12417226000 1882615 2381476 2165781 1989049 2610881 2146211 2739143 2249171 2063766 FALSE TRUE 1764785.488 2557802.961 2217154.348 2040091.365 2405832.938 2765787.275 2328433.936 2529984.95 1719310.122 1.026449775 1.487691446 1.289560458 1.186575556 1.399301329 1.608661078 1.354283853 1.471511694 1 20.71339837 -1.230577811 5.744839346 0.999986079 1.366345539 0.313465651 0.163120768 2.68E-05 3.58E-06 0.145304506 0.0342473 0.058806074 1.230577811 0.366359461 GGPGAAPGGASPAS(ph)SSSAASSPSSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGPGAAPGGASPASSSSAASSPSSGR 26 0 Q9BXK1 Q9BXK1 KLF16 Krueppel-like factor 16 1 GGPGAAPGGAS(0.011)PAS(0.354)S(0.181)S(0.26)S(0.181)AAS(0.011)S(0.002)PSSGR 182.98 1.88E-17 91800000 92210 98426 106290 93621 109980 117760 138390 102300 106640 TRUE FALSE 86438.7407 105713.5635 108811.249 96023.47336 101342.6144 151755.4003 117639.7042 115072.3802 88841.09508 0.972958974 1.189917384 1.224785094 1.080845225 1.140717754 1.708166701 1.324158647 1.295260713 1 16.43893956 2.382379673 20.68696316 1.374775079 1.143082307 0.226359815 0.183242087 5.609036355 1217.006189 0.057607715 0.048197932 241.2013162 -2.382379673 -0.231692772 GGPGGGFRPFVPHIPFDFYLCEMAFPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGPGGGFRPFVPHIPFDFYLCEMAFPR 27 1 Q12905;A0A0A0MRL0 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 156.05 1.51E-08 63505000 54912 173990 27667 14459 177840 31949 29050 139990 19466 FALSE TRUE 51475.15594 186872.4006 28323.27431 14830.04242 163873.1638 41172.15765 24694.22219 157468.0597 16216.99884 3.174148092 11.5232419 1.746517625 0.914475148 10.10502408 2.538827193 1.522736878 9.710061718 1 13.98521924 8 0.089488265 3.35E-10 19.0452241 0.046339693 4.048856882 394.2306845 2.536385694 71.0848384 922.1488548 100000000 -8 19.0452241 GGPGKLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GGPGKLSPR 9 1 Q12888;Q12888-2;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 GGPGKLS(1)PR;GGPGKLS(1)PR;GGPGKLS(1)PR;GGPGKLS(1)PR;GGPGKLS(1)PR;GGPGKLS(1)PR;GGPGKLS(1)PR 96.756 0.0043319 16152040000 14944030 18205950 12755290 12645420 20718500 8087120 15001930 17447180 23360400 TRUE FALSE 14008709.84 19553937.48 13057851.5 12969922.89 19091352.58 10421740.26 12752529.87 19625498.83 19461398.33 0.719820313 1.004755011 0.670961628 0.666443524 0.980985655 0.535508296 0.655273052 1.008432102 1 24.21411204 -1.272289306 8.998017519 1.000000064 0.773404525 0.146812949 0.165733074 2.04E-07 1.65E-08 0.15324307 0.036119728 0.053420838 1.272289306 -0.226595539 GGPNIITLADIVKDPVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGPNIITLADIVKDPVSR 18 1 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YF43;A0A2R8Y4H0;A0A2R8Y4D6;V9GYA2;A0A2R8YEW1 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 114.9 0.00018667 136360000 364420 361900 367280 339090 430710 304730 470500 357480 540860 FALSE TRUE 341611.6027 388695.4526 375992.055 347791.6235 396883.774 392700.6041 399952.8929 402112.1649 450586.9719 0.75814798 0.862642457 0.834449459 0.77186347 0.880815023 0.8715312 0.887626403 0.892418534 1 18.78144608 0.61394415 0.306955684 1.030625462 0.803931094 0.738700983 0.034392006 1.520891878 0.334418874 0.111833876 0.044451905 4.110968512 -0.61394415 -0.226694368 GGPNYQEGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGPNYQEGLR 10 0 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ; 137.13 0.00023109 787710000 559260 772650 576370 606260 742390 494280 609440 661570 744810 FALSE TRUE 524256.9149 829857.8099 590041.7686 621817.658 684085.6841 636970.612 518060.1298 744168.4708 620496.3993 0.844899206 1.33740955 0.950918924 1.002129357 1.102481311 1.026550054 0.834912387 1.199311505 1 19.24306331 3.738450009 24.47118176 1.003101051 1.131682882 0.01955682 0.150744132 591.734058 1278191.244 0.035567167 0.063380345 5475.830664 -3.738450009 0.128581831 GGPPCKPPAPEDEDEAWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGPPCKPPAPEDEDEAWR 18 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 0 ; 168.32 1.92E-11 369270000 205336 201367 207780 199432 231830 176120 252550 187513 286860 FALSE TRUE 192484.3863 216276.4222 212708.6397 204549.7628 213623.007 226962.9849 214682.4721 210924.4108 238981.2128 0.805437315 0.904993408 0.890064274 0.85592403 0.893890379 0.949710575 0.898323636 0.882598294 1 17.86653768 -5 0.112041629 1.347037027 0.829050398 0.590107221 0.032910901 124.5967278 0.924212469 9.954079877 0.375745509 1.00E-05 5 -0.517986629 GGPPFAFVEFEDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GGPPFAFVEFEDPR 14 0 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;; 79.659 0.04297 262511000 213862 224933 235103 226845 216093 246651 271246 215967 174573 FALSE TRUE 200476.7592 241587.2734 240679.7542 232666.2267 199121.9275 317855.1397 230575.1804 242930.9554 145435.6385 1.378456898 1.661128426 1.654888421 1.599788258 1.369141219 2.185538173 1.585410445 1.670367441 1 17.15002131 GGPPFAFVEFEDPRDAEDAVYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GGPPFAFVEFEDPRDAEDAVYGR 23 1 J3KTL2;Q07955;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;; 199.7 2.34E-24 2122137000 271034 456713 352375 375088 478844 294606 374737 359654 568006 FALSE TRUE 254070.4657 490528.5057 360733.5014 384713.3931 441237.5238 379653.9697 318548.6657 404557.5936 473202.1291 0.536917419 1.03661517 0.762324341 0.813000131 0.932450419 0.802308245 0.673176738 0.854936123 1 18.85209704 2.019276133 24.54185486 0.789228512 0.841187485 0 0.152142194 885.092775 1126870.417 0.052258614 0.038589143 104.5384683 -2.019276133 0.051958973 GGPPS(ph)PTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGPPSPTK 8 0 Q5TCQ9;Q5TCQ9-1;Q5TCQ9-3;Q5TCQ9-2 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 GGPPS(0.994)PT(0.006)K;GGPPS(0.857)PT(0.143)K;GGPPS(0.992)PT(0.008)K;GGPPS(0.997)PT(0.003)K 109.83 0.0037163 1239380000 1650660 1205140 1320570 1366840 1546550 1066156 1502100 1133680 1630790 TRUE FALSE 1547348.137 1294369.82 1351894.544 1401915.428 1425090.201 1373937.93 1276874.05 1275222.444 1358600.614 1.138927895 0.952722829 0.995063987 1.031881934 1.04893976 1.011289054 0.939845041 0.938629374 1 20.37368998 1.789044384 6.768014673 0.954443268 1.017929068 0.27944768 0.050710361 0.299109701 29.05991575 0.022661274 0.01300377 61.52397458 -1.789044384 0.0634858 GGPRPVS(ph)SSIDPSLLSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.94)S(0.043)S(0.017)IDPSLLSTK 112.47 0.00016645 160990000 257090 326730 271720 279480 431420 177060 401450 292760 532590 TRUE FALSE 240999.1958 350921.4292 278165.3267 286651.93 397538.0135 228174.3477 341256.2994 329311.7304 443697.2883 0.5431613 0.790902803 0.626925911 0.646052923 0.895966741 0.5142568 0.769119642 0.742199105 1 18.75921621 0.604511459 1.269678629 0.99973366 0.686727864 0.436053102 0.113273624 1.257209366 2.932733248 0.094863066 0.028529039 4.022642699 -0.604511459 -0.313005796 GGPRPVSS(ph)SIDPSLLSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.353)S(0.529)S(0.118)IDPSLLSTK 113.73 0.00014439 153410000 106790 143430 125380 107210 177670 72932 161970 121180 223110 TRUE FALSE 100106.2045 154049.7064 128354.0728 109961.1901 163716.5149 93986.28445 137684.1022 136309.5898 185871.4997 0.538577483 0.828796812 0.690552737 0.591597907 0.880804831 0.50565194 0.740748864 0.733353903 1 17.50394605 0.642038833 2.047068556 0.999866635 0.694959907 0.411228595 0.117992643 1.89961718 9.630426343 0.100421704 0.027585046 4.385699111 -0.642038833 -0.304906728 GGPTVDPEELFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGPTVDPEELFR 12 0 Q96EY1-2;Q96EY1 Q96EY1-2 DNAJA3 "DnaJ homolog subfamily A member 3, mitochondrial" 0 112.75 0.0028854 39137000 29609 31506 26502 27748 37418 33683 30871 26553 39423 FALSE TRUE 27755.82554 33838.73702 27130.63996 28460.06066 34479.34122 43406.7353 26242.18014 29868.2005 32843.04662 0.84510508 1.030316627 0.826069526 0.866547522 1.049821645 1.321641558 0.799017839 0.909422346 1 15.00330034 2.738590133 24.9999575 1.012206506 0.904070818 0.156735248 0.141513685 6.061920461 5135554.636 0.044874265 0.044874858 547.7597703 -2.738590133 -0.108135688 GGQGDPAVPAQQPADPST(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.029)T(0.971)PER;GGQGDPAVPAQQPADPS(0.043)T(0.957)PER 300.34 4.98E-54 1614150000 1034780 1141570 1092110 1087960 1093520 1068770 1203250 960560 884710 TRUE FALSE 970014.9669 1226093.031 1118015.365 1115878.896 1007639.35 1377306.549 1022833.833 1080488.03 737046.1856 1.316084373 1.663522659 1.516886441 1.513987749 1.367131898 1.868684183 1.387747271 1.465970589 1 19.4913955 0.609845393 1.448441806 1.000826045 1.541104779 0.511910283 0.158050212 1.101242027 3.179384407 0.133618847 0.039031583 4.07235278 -0.609845393 0.540278734 GGQS(ph)DDDEDEGVPASYHTVSLQLLDLMHTLHTR ddPTM_SK-BR-3_Pertuzumab_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 286.61 4.06E-74 1966051000 308842.5 611582 500795.05 611545 631404.2 473242 665665 588517 526454.56 TRUE FALSE 289512.5992 656864.1676 512674.1451 627238.28 581816.2611 609859.283 565854.713 661994.6429 438585.8929 0.660104677 1.497686493 1.168925297 1.430137837 1.326573131 1.390512766 1.290179922 1.509384259 1 18.74249988 4.747073507 24.97047472 1.33559641 0.660104334 0.651442781 0.153107669 591.6787728 1735505.648 0.031139151 0.363006268 55856.47279 -4.747073507 -0.675492076 GGQS(ph)DDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGQSDDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR 37 0 A0A669KBG8;A0A669KB10;Q92538 A0A669KBG8 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 GGQS(1)DDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR 57.068 0.015253 60488000 3672.9 5116.7 7924.6 5842.7 5167.8 5612.2 3888.6 5628.9 6424.9 TRUE FALSE 3443.019745 5495.545792 8112.575254 5992.633574 4761.941834 7232.351034 3305.54053 6331.680556 5352.542684 0.643249377 1.026716855 1.515648867 1.119586321 0.889659759 1.351199133 0.617564534 1.182929484 1 12.38600868 1.747665929 25 0.900351851 1.125944672 0.054926134 0.27306276 4.617341693 12706.5148 0.123204326 0.068323203 55.93271871 -1.747665929 0.225592821 GGRT(ph)PPQQGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGRTPPQQGGR 11 1 A0A2R8Y4Z8;M0QYB4;Q9Y3X0 A0A2R8Y4Z8;Q9Y3X0 CCDC9 Coiled-coil domain-containing protein 9 1 GGRT(1)PPQQGGR;GGRT(1)PPQQGGR 86.498 0.023322 663650000 160085 190759 186661 177059 199529 169003 199055 154490 163877 TRUE FALSE 150065.5656 204882.9948 191088.6871 181602.6337 183858.7972 217791.4226 169208.5507 173778.4166 136524.87 1.099181165 1.500700897 1.399662106 1.330179869 1.346705528 1.595250906 1.239397266 1.272870039 1 17.05880426 0.90218875 1.436197826 1.004258302 1.388175942 0.41635988 0.133404101 0.450619727 1.841552203 0.114334053 0.03389118 7.983415813 -0.90218875 0.383917641 GGS(ph)DDSSKDPIDVNYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGSDDSSKDPIDVNYEK 17 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 1 GGS(1)DDSSKDPIDVNYEK;GGS(1)DDSSKDPIDVNYEK 119.87 5.99E-05 245898000 378220 219409 284764 256970 291990 207889 335630 254911 434070 TRUE FALSE 354547.8853 235654.2707 291518.7366 263564.2852 269058.2832 267903.1795 285305.3973 286737.1995 361620.9128 0.980440768 0.651661069 0.806144574 0.72884138 0.74403408 0.740839841 0.78896266 0.792922061 1 18.46411859 0.422044099 1.259311627 1.000121115 0.762786881 0.397938965 0.084343205 2.425958493 4.423197207 0.071025639 0.021204402 2.642677087 -0.422044099 -0.237334234 GGS(ph)GSHNWGTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GGSGSHNWGTVK 12 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 GGS(0.562)GS(0.438)HNWGTVK;GGS(0.96)GS(0.04)HNWGTVK;GGS(0.808)GS(0.192)HNWGTVK 138.55 4.67E-05 564280000 1154570 1086840 1095860 1044790 1208270 1015180 1182970 1104900 1068420 TRUE FALSE 1082307.525 1167310.764 1121854.317 1071601.08 1113377.348 1308245.986 1005594.631 1242849.197 890093.7997 1.215947718 1.311446911 1.260377633 1.203919273 1.250853953 1.469784405 1.129762538 1.396312611 1 19.76359785 -1.37947088 3.399027923 0.997865486 1.275404026 0.451399185 0.096831338 10352763.12 17239887.89 223731.7043 0.020724111 0.041737758 1.37947088 0.27753854 GGS(ph)GYHS(ph)RS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGSGYHSRSPAR 12 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 GGS(0.998)GY(0.003)HS(1)RS(1)PAR;GGS(0.998)GY(0.002)HS(1)RS(1)PAR 70.802 0.077897 510367000 745450 809290 733690 736020 786110 607390 798830 649760 664670 TRUE FALSE 698793.6152 869210.6737 751093.4733 754907.5193 724372.0916 782733.6328 679052.8575 730883.9663 553732.2831 1.261970155 1.569730897 1.356419873 1.363307761 1.308163013 1.413559687 1.226319791 1.319922982 1 19.07882911 -0.363674359 0.248367317 0.821652906 1.461840058 0.627286677 0.088375696 5.371473657 0.443141193 0.926107195 0.152160117 0.432838258 0.363674359 0.640187152 GGS(ph)LESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGSLESR 7 0 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 GGS(0.995)LES(0.005)R 95.605 0.022647 0 464330 525060 502620 509120 466040 408800 512610 420810 449370 TRUE FALSE 435268.4142 563935.9887 514542.3838 522184.8811 429439.0983 526813.9237 435748.8893 473349.0548 374367.244 1.162677614 1.506371078 1.374432171 1.39484661 1.147106498 1.407211588 1.163961047 1.264397627 1 18.51409468 0.920848136 0.408705674 0.981103398 1.394558261 0.419575432 0.116922387 1.143051457 0.497267895 0.168085975 0.083528784 8.333897133 -0.920848136 0.413454862 GGS(ph)LPKVEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGSLPKVEAK 10 1 P06748;P06748-2 P06748 NPM1 Nucleophosmin 1 GGS(1)LPKVEAK;GGS(1)LPKVEAK 88.282 0.0074494 324740000 1157960 664120 846160 827360 1016980 600540 1081120 736840 1682710 TRUE FALSE 1085485.351 713292.1358 866231.3148 848591.4583 937110.4931 773906.149 919016.0926 828836.096 1401854.83 0.774320798 0.508820258 0.617917987 0.605334761 0.668478984 0.552058696 0.655571513 0.591242458 1 20.41890553 -1.711183204 2.458659537 1.075573127 0.612285595 0.732708016 0.071602285 4430578.327 3293947.601 2061227.199 0.016566197 0.019445396 1.711183204 -0.463287533 GGS(ph)PDLWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGSPDLWK 8 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 GGS(1)PDLWK 146.11 0.00058599 327700000 1366100 1084000 1269400 1155400 1324700 1025900 1506200 1125500 1541900 TRUE FALSE 1280598.24 1164260.488 1299510.767 1185049.52 1220663.406 1322060.676 1280359.293 1266021.153 1284546.929 0.996926006 0.906358858 1.011649118 0.9225428 0.950267661 1.029203874 0.99673999 0.985577968 1 20.29282817 2.254688789 24.99497453 1.002929817 0.95635454 0.326112342 0.032355146 264.8018733 410381.3643 0.010532318 0.008788296 179.7582324 -2.254688789 -0.046575277 GGS(ph)PLAAPQGGSPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGSPLAAPQGGSPTK 15 0 E7EPC8;Q9UQB3-2;Q9UQB3 E7EPC8 CTNND2 Catenin delta-2 1 GGS(1)PLAAPQGGSPTK 205.95 1.95E-11 0 124810 113030 109430 101760 122450 93093 143590 105110 129020 TRUE FALSE 116998.3649 121398.8588 112025.7313 104371.3339 112833.2709 119967.4379 122060.0125 118233.2149 107485.7285 1.08850139 1.129441652 1.042238191 0.971025041 1.049751186 1.116124341 1.135592736 1.099989892 1 16.71378559 2.239959515 24.99970476 1.103726068 1.060406223 0.042493538 0.053676078 81.17525216 1450716.51 0.019645341 0.015622225 173.7638837 -2.239959515 -0.043319845 GGS(ph)PQMDDIK ddPTM_SK-BR-3_Pertuzumab_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 174.72 3.17E-06 16570700000 40398600 26741630 32243770 30319170 28726860 28075220 41547800 28860700 26918300 TRUE FALSE 37870123.74 28721608.11 33008607.45 31097211.23 26470768.29 36180080.25 35318093.1 32464021.93 22425461.83 1.688710985 1.280758823 1.471925426 1.386692121 1.180388992 1.613348279 1.574910402 1.447641175 1 24.41863436 -0.845612478 5.877684836 0.999999927 1.447654469 0.472540661 0.15105085 1.41E-07 2.76E-08 0.141569904 0.033368341 0.142688024 0.845612478 0.447654543 GGS(ph)PQMDDIKVFQNEVLGTLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGSPQMDDIKVFQNEVLGTLQR 22 1 Q13144;A0A3B3IUB1;A0A3B3ITG6 Q13144 EIF2B5 Translation initiation factor eIF-2B subunit epsilon 1 GGS(1)PQMDDIKVFQNEVLGTLQR;GGS(1)PQMDDIKVFQNEVLGTLQR 186.84 1.85E-17 532760000 220763 290436 257819 306163 365925 181081 368850 249480 749550 TRUE FALSE 206945.8379 311940.1836 263934.5884 314019.6609 337186.7266 233356.1451 313544.3667 280628.1272 624445.2627 0.331407491 0.499547682 0.422670495 0.502877802 0.539978036 0.373701522 0.502116655 0.449403885 1 19.25221559 -4.655451223 0.457683561 10 0.451472544 0.879748434 0.063614984 298.0917702 2.340429243 2699.731608 0.029534049 2.21E-05 4.655451223 -9.548527456 GGS(ph)SKDLLDNQSQEEQRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGSSKDLLDNQSQEEQRR 18 2 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-4 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 GGS(0.942)S(0.058)KDLLDNQSQEEQRR 46.353 0.094688 102830000 42618 55969 48176 50751 56395 40438 54484 45464 53328 TRUE FALSE 39950.61546 60113.003 49318.75747 52053.35658 51965.96419 52111.79414 46314.63 51140.28048 44427.21229 0.899237503 1.353067183 1.110102456 1.171654801 1.16968771 1.172970156 1.04248337 1.15110262 1 15.439156 1.097733981 0.638575291 1.00543584 1.172048088 0.081218938 0.116287254 1.335623586 1.316123884 0.105753445 0.045606631 12.52373823 -1.097733981 0.166612248 GGS(ph)TEDASQYYCDKNDNGDSYLVLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGSTEDASQYYCDKNDNGDSYLVLIR 26 1 J3KN34;P26045-2;P26045;P26045-3 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 GGS(1)TEDASQYYCDKNDNGDSYLVLIR 304.89 3.18E-71 152160000 170520 172680 175370 236340 192450 92339 155250 93745 88870 TRUE FALSE 159847.4576 185465.4069 179529.8592 242404.8845 177335.7533 118995.7703 131971.7038 105449.2696 74037.02288 2.1590206 2.50503599 2.424865996 3.274103619 2.395230743 1.60724683 1.782509596 1.424277551 1 16.17595926 2.262704744 4.058332111 1.536739101 2.573732275 0.717727377 0.3423548 0.12102583 4.410440491 0.123949848 0.096735546 183.1069142 -2.262704744 1.036993174 GGS(ph)WIQEINVAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGSWIQEINVAEK 13 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 1 GGS(1)WIQEINVAEK;GGS(1)WIQEINVAEK 166.35 7.97E-07 21703000 84316 70485 76852 81588 79813 61355 95695 69725 82943 TRUE FALSE 79038.81207 75703.78274 78674.96573 83681.68621 73544.80893 79067.19248 81346.42314 78430.31973 69099.27747 1.143844262 1.095579947 1.138578703 1.211035618 1.064335426 1.144254982 1.177239851 1.135038203 1 16.076383 -0.935547572 7.275547621 0.999999998 1.137973613 0.54670149 0.039696911 1.10E-09 2.26E-10 0.036840928 0.00868349 0.115998515 0.935547572 0.137973616 GGSAAATSNPHHDNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGSAAATSNPHHDNVR 16 0 Q9GZY8-5;Q9GZY8-2;Q9GZY8 Q9GZY8-5 MFF Mitochondrial fission factor 0 60.55 0.053509 6377900 6144.3 7257 6719.3 5673.3 7633.4 5898.2 5975.9 6326.2 7335.2 FALSE TRUE 5759.739231 7794.315831 6878.684969 5818.886483 7033.903556 7600.914591 5079.869273 7116.039996 6110.907733 0.942534151 1.275475948 1.125640456 0.952213114 1.151040707 1.243827419 0.831279001 1.164481662 1 12.57717098 1.748603167 25 0.985614405 1.129954449 0.138689602 0.13222247 3.911782453 9757.977633 0.057358969 0.031808411 56.05355577 -1.748603167 0.144340043 GGSDDSSKDPIDVNYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGSDDSSKDPIDVNYEK 17 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;; 187.39 4.28E-10 4424420000 7005320 4225510 4976390 5302920 5455450 3539720 6978380 4484460 6867880 FALSE TRUE 6566869.526 4538371.157 5094432.321 5439001.905 5027000.963 4561579.701 5932036.703 5044354.703 5721586.46 1.147735785 0.793201534 0.890388069 0.950610804 0.878602639 0.797257847 1.036781799 0.881635668 1 22.4479838 1.723548292 24.99999993 0.970921211 0.894359052 0.061404702 0.105643351 2.04948946 3399.115989 0.044763027 0.024823337 52.91128293 -1.723548292 -0.076562159 GGSDGYGSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GGSDGYGSGR 10 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;; 219.19 1.50E-08 11964825000 3647700 4377389 4153666 4400792 4436158 3687861 4435359 3893759 4513034 FALSE TRUE 3419396.968 4701495.436 4252192.919 4513723.773 4087760.045 4752486.603 3770318.094 4379903.382 3759779.47 0.909467429 1.250471064 1.130968705 1.200528863 1.087233993 1.264033341 1.00280299 1.164936246 1 21.84221661 0.727964301 0.769313305 1.00260539 1.146796987 0.088980366 0.109931661 2.004519074 2.294464959 0.096883247 0.034429548 5.345204197 -0.727964301 0.144191596 GGSFGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGSFGGR 7 0 P51991;H7C1J8;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 89.427 0.041599 182830000 238610 262860 243760 233600 308050 222940 243350 227600 317810 FALSE TRUE 223675.826 282322.4279 249542.1023 239594.5715 283856.9956 287299.1589 206861.9267 256016.361 264765.4579 0.84480743 1.066311407 0.942502486 0.904931381 1.072107358 1.08510816 0.781302547 0.966955293 1 18.01435539 1.746046861 24.99999996 0.895931118 0.990415484 0.094006764 0.09499698 2.723895538 9121.783622 0.04066024 0.022548208 55.72458734 -1.746046861 0.094484366 GGSGSHNWGTVKDELTES(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGSGSHNWGTVKDELTESPK 20 1 Q8NC51;Q8NC51-2 Q8NC51 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 GGSGSHNWGTVKDELT(0.286)ES(0.714)PK;GGSGSHNWGTVKDELT(0.476)ES(0.524)PK;GGSGSHNWGT(0.002)VKDELT(0.089)ES(0.909)PK;GGSGSHNWGTVKDELT(0.466)ES(0.534)PK 152.5 3.85E-08 1848910000 919834 788152 1020712 1318730 1110220 521068 821582 516591 815705 TRUE FALSE 862263.2319 846507.5942 1044923.771 1352570.844 1023027.8 671491.8728 698393.4063 581088.5235 679558.5658 1.268857866 1.24567276 1.537650797 1.990366853 1.505429923 0.98812951 1.027716287 0.855097048 1 19.37423837 2.235339987 9.49729953 0.976409339 1.499507265 0.632846242 0.204961657 0.081102255 98.74399147 0.08034774 0.062626265 171.9253777 -2.235339987 0.523097926 GGSGYHS(ph)RS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGSGYHSRSPAR 12 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GGS(0.001)GY(0.001)HS(0.999)RS(0.999)PAR;GGSGYHS(1)RS(1)PAR;GGS(0.002)GY(0.001)HS(0.998)RS(1)PAR;GGS(0.001)GYHS(0.999)RS(1)PAR 65.511 0.034456 3334400000 1041070 1410770 1416320 1418690 1414760 1291490 1321720 1220780 1364020 TRUE FALSE 975911.2871 1515224.879 1449915.779 1455095.987 1303650.456 1664322.197 1123540.356 1373197.07 1136356.25 0.858807515 1.33340656 1.275934179 1.280492792 1.147219859 1.464613054 0.98872194 1.208421276 1 20.11598376 1.657857282 13.67521882 1.074630302 1.243450789 0.16759495 0.165862173 0.197514879 46.17843088 0.0699376 0.038401609 45.48385664 -1.657857282 0.168820487 GGSISVQVNSIKFDS(ph)E ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 GGSISVQVNSIKFDSE 16 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 GGSISVQVNSIKFDS(1)E;GGSISVQVNS(0.328)IKFDS(0.672)E;GGSISVQVNS(0.028)IKFDS(0.972)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNS(0.004)IKFDS(0.996)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNS(0.002)IKFDS(0.998)E;GGSISVQVNS(0.01)IKFDS(0.99)E 260.56 2.26E-26 3569037000 5810060 4180450 4794058 4662903 4992310 3762510 6207470 3886882 6229800 TRUE FALSE 5446418.716 4489974.868 4907775.32 4782560.985 4600234.111 4848685.558 5276717.501 4372167.774 5190006.134 1.049405063 0.865119376 0.945620331 0.921494284 0.886363906 0.934235034 1.016707373 0.842420541 1 22.30730481 1.983186595 24.13319854 0.96004206 0.924096715 0.003750709 0.066430188 1380.448469 1981429.486 0.024270898 0.016112997 96.20255244 -1.983186595 -0.035945345 GGSMEDYCDSPHGETTSVEDSTQDVT(ph)AEHHTSDDECEPIEAIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGSMEDYCDSPHGETTSVEDSTQDVTAEHHTSDDECEPIEAIAK 44 0 B7ZM87;O75044;A0A075B7B5;Q5VZB4;A0A075B7E6 B7ZM87 SRGAP2 SLIT-ROBO Rho GTPase-activating protein 2 1 GGS(0.001)MEDYCDS(0.001)PHGET(0.014)T(0.014)S(0.014)VEDS(0.065)T(0.065)QDVT(0.275)AEHHT(0.275)S(0.275)DDECEPIEAIAK 80.859 0.00030561 95688000 22660 22483 22433 24779 25323 23459 38249 22912 27380 TRUE FALSE 21241.75105 24147.66471 22965.12135 25414.87109 23334.23373 30231.23247 32513.91754 25772.61364 22810.10112 0.931243178 1.058639091 1.006796122 1.114193706 1.022978092 1.32534408 1.42541751 1.12987722 1 14.47738522 2.244262355 24.99093098 1.276295172 1.032365873 0.333212101 0.12506636 111.8182485 490105.0165 0.040889485 0.033338348 175.4940331 -2.244262355 -0.243929299 GGSMEDYCDSPHGETTSVEDSTQDVTAEHHTS(ph)DDECEPIEAIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGSMEDYCDSPHGETTSVEDSTQDVTAEHHTSDDECEPIEAIAK 44 0 B7ZM87;O75044;A0A075B7B5;Q5VZB4;A0A075B7E6 B7ZM87 SRGAP2 SLIT-ROBO Rho GTPase-activating protein 2 1 GGS(0.04)MEDY(0.013)CDS(0.035)PHGET(0.031)T(0.031)S(0.031)VEDS(0.031)T(0.031)QDVT(0.124)AEHHT(0.124)S(0.508)DDECEPIEAIAK 78.961 0.00020375 229860000 30471 20031 26946 28190 26620 31470 47869 24775 28721 TRUE FALSE 28563.8745 21514.11608 27585.17184 28913.40313 24529.37258 40554.87813 40691.48784 27868.21329 23927.27956 1.193778609 0.899145932 1.152875394 1.208386564 1.025163455 1.694922234 1.700631605 1.16470463 1 14.54636876 2.252563318 24.99454547 1.484272549 1.081931775 0.238373526 0.235229229 217.9492483 389034.5757 0.07720305 0.06429277 178.8806311 -2.252563318 -0.402340774 GGSREYDTGGGS(ph)SSSR ddPTM_SK-BR-3_Pertuzumab_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(0.005)REYDT(0.01)GGGS(0.777)S(0.064)S(0.019)S(0.125)R;GGS(0.01)REYDT(0.127)GGGS(0.391)S(0.04)S(0.04)S(0.391)R 191.44 1.83E-09 575320000 410370 624630 499680 534590 730240 340730 496690 500300 1058420 TRUE FALSE 384685.6742 670878.2551 511532.6456 548308.4845 672889.896 439093.2197 422215.9455 562763.5563 881762.8643 0.436268854 0.760837502 0.580124959 0.621832135 0.763118887 0.497972003 0.478831625 0.638225513 1 19.75003119 -1.852974247 3.56941972 1.11877839 0.60231972 0.574101409 0.108963538 0.067672162 0.002787442 0.069320116 0.024555581 0.014028969 1.852974247 -0.516458671 GGSSVEAPCPSDVT(ph)PEDDRSFQTVWATVFEHHVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGSSVEAPCPSDVTPEDDRSFQTVWATVFEHHVER 35 1 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 GGSSVEAPCPS(0.004)DVT(0.992)PEDDRS(0.002)FQT(0.002)VWATVFEHHVER;GGSSVEAPCPS(0.001)DVT(0.993)PEDDRS(0.003)FQT(0.003)VWATVFEHHVER;GGSSVEAPCPS(0.045)DVT(0.952)PEDDRS(0.002)FQT(0.002)VWATVFEHHVER;GGSSVEAPCPS(0.07)DVT(0.89)PEDDRS(0.02)FQT(0.02)VWATVFEHHVER 156.17 2.27E-11 265333000 27996.2 31305 32348.5 31162 33279 31012 33207.3 27893 41458 TRUE FALSE 26243.96782 33622.85477 33115.8217 31961.66968 30665.40158 39964.66096 28228.17365 31375.50245 34538.39197 0.759849151 0.973492188 0.958811914 0.925395418 0.887864195 1.157108327 0.817298433 0.90842395 1 15.0759133 4.742961218 24.4803412 0.950022695 0.759849049 0.322584683 0.088082428 400.9317005 2230255.376 0.01926702 0.151541166 55330.06977 -4.742961218 -0.190173646 GGST(ph)EDASQYYCDKNDNGDSYLVLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGSTEDASQYYCDKNDNGDSYLVLIR 26 1 J3KN34;P26045-2;P26045;P26045-3 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 GGS(0.118)T(0.881)EDAS(0.001)QYYCDKNDNGDSYLVLIR 199.04 9.52E-25 182510000 125890 138700 147380 175800 138340 71150 107590 74517 64499 TRUE FALSE 118010.7696 148969.4923 150875.9232 180311.3256 127475.3344 91689.84998 91457.87832 83820.61148 53733.70022 2.196215208 2.772366163 2.807845404 3.35564692 2.372353549 1.706375135 1.702058074 1.559926287 1 15.71353957 2.303380542 2.855167581 1.541173797 2.792216604 0.767938686 0.33650991 0.122613649 2.045332302 0.127042678 0.096906466 201.0854012 -2.303380542 1.251042806 GGTLGGGTLGPPS(ph)PPGAPS(ph)PPEPGGEIELVFRPHPLLVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGTLGGGTLGPPSPPGAPSPPEPGGEIELVFRPHPLLVEK 40 1 Q06587;Q06587-2 Q06587 RING1 E3 ubiquitin-protein ligase RING1 2 GGTLGGGTLGPPS(1)PPGAPS(1)PPEPGGEIELVFRPHPLLVEK 139.16 2.00E-10 144060000 207420 175590 191050 189600 202900 165040 226920 173790 173870 TRUE FALSE 194437.9525 188590.8663 195581.7962 194465.457 186965.0525 212684.3688 192895.4526 195488.0641 144849.9738 1.342340267 1.301973769 1.350237015 1.34253015 1.290749647 1.468307955 1.331691319 1.349589917 1 17.1441999 -0.778089419 8.703677351 1 1.345940625 0.841272702 0.047389995 0 0 0.042882013 0.010107388 0.166690397 0.778089419 0.345940625 GGTLGGGTLGPPS(ph)PPGAPSPPEPGGEIELVFRPHPLLVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGTLGGGTLGPPSPPGAPSPPEPGGEIELVFRPHPLLVEK 40 1 Q06587;Q06587-2 Q06587 RING1 E3 ubiquitin-protein ligase RING1 1 GGTLGGGTLGPPS(1)PPGAPSPPEPGGEIELVFRPHPLLVEK;GGTLGGGTLGPPS(1)PPGAPSPPEPGGEIELVFRPHPLLVEK 199.78 2.43E-31 639780000 507420 424600 511300 453370 518800 432640 570170 460040 516580 TRUE FALSE 475661.488 456037.8258 523428.2775 465004.2418 478055.5407 557536.1447 484678.3017 517477.0067 430359.4608 1.105265554 1.059667249 1.216258326 1.080501962 1.110828469 1.295512695 1.126217374 1.202429722 1 18.71518266 4.085058077 5.52641125 1.156968376 1.083556851 0.090138237 0.081245159 0.40814692 17.72817704 0.01826795 0.040497769 12163.4865 -4.085058077 -0.073411525 GGTPAFLPSSLS(ph)PQSSLPASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GGTPAFLPSSLSPQSSLPASR 21 0 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;B3KPU0;H0YBP7;E5RGS7 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 GGTPAFLPSSLS(1)PQSSLPASR;GGTPAFLPS(0.007)S(0.03)LS(0.963)PQS(0.001)SLPASR;GGTPAFLPSS(0.003)LS(0.996)PQS(0.001)SLPASR;GGTPAFLPS(0.001)S(0.017)LS(0.982)PQSSLPASR 427.18 6.45E-174 1452110000 815850 948430 926900 985000 1039820 782030 958690 827700 699022 TRUE FALSE 764787.4048 1018652.744 948886.5057 1010276.768 958156.7316 1007789.366 814943.3345 931040.167 582350.7123 1.313276328 1.749208376 1.629407307 1.734825332 1.645325937 1.730554019 1.399403001 1.598761961 1 19.15152873 0.284294847 0.704279137 0.986498819 1.644690758 0.632379212 0.143332389 1.507743025 1.015028407 0.180149455 0.04742365 1.92439778 -0.284294847 0.658191939 GGVDHAAAFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GGVDHAAAFGR 11 0 Q9HC38-2;F6TLX2;Q9HC38;I3L3Q4 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ;; 147.75 3.52E-05 1881540000 903840 1075370 782530 774070 942650 906250 1019360 801070 1058810 FALSE TRUE 847270.2678 1154991.514 801091.9811 793933.9467 868618.0715 1167869.663 866516.4313 901085.3529 882087.7708 0.960528301 1.309383887 0.908177177 0.900062299 0.984729752 1.32398351 0.982347177 1.021537065 1 19.75056269 3.966179198 24.82475103 1.025217989 1.153487624 0.099740779 0.143095532 659.0559518 1495235.795 0.035364605 0.064524905 9250.798003 -3.966179198 0.128269635 GGVILVSHDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GGVILVSHDER 11 0 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 ;; 126.71 0.00030186 1038820000 1087900 1248970 1180850 1301780 1222410 1178880 1222710 1057680 1167090 FALSE TRUE 1019810.281 1341445.038 1208860.32 1335185.879 1126406.85 1519203.518 1039375.987 1189733.676 972295.1393 1.048869052 1.379668564 1.243305937 1.373231054 1.158503014 1.562492146 1.068992268 1.223634294 1 19.89103478 1.099613078 1.368514145 1.016733011 1.289722761 0.23135042 0.151969867 0.513339305 1.938325685 0.124022799 0.037818648 12.5780431 -1.099613078 0.27298975 GGVTGS(ph)PEASIS(ph)GSKGDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GGVTGSPEASISGSKGDLK 19 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 GGVT(0.004)GS(0.996)PEAS(0.006)IS(0.544)GS(0.45)KGDLK;GGVT(0.435)GS(0.564)PEAS(0.266)IS(0.435)GS(0.3)KGDLK 187.16 1.08E-14 995460000 3713000 1317690 2021750 1347280 1995390 1891340 3323700 2437120 5953300 TRUE FALSE 3480609.958 1415253.139 2069706.865 1381853.486 1838680.118 2437339.155 2825342.041 2741399.797 4959655.77 0.701784583 0.285353098 0.417308572 0.27861883 0.370727366 0.491433129 0.569664947 0.552739933 1 22.24180856 0.677539112 0.71030049 1.00309595 0.390710776 0.674864526 0.122286087 0.625911426 0.600614831 0.116426538 0.041804159 4.7592565 -0.677539112 -0.612385174 GGVTGS(ph)PEASISGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 GGVTGSPEASISGSK 15 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GGVT(0.004)GS(0.961)PEAS(0.035)ISGSK;GGVTGS(0.999)PEAS(0.001)ISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK 383.34 2.95E-114 17807970000 18087570 13060240 15472110 13338110 16059580 14781530 18901810 15304650 20536760 TRUE FALSE 16955501.28 14027233.76 15839115.76 13680388.48 14798325.37 19048717.75 16067659.07 17215469.24 17109042.08 0.991025751 0.819872538 0.925774551 0.799599908 0.864941783 1.113371378 0.939132594 1.006220521 1 24.02825565 2.272128771 24.99053372 1.005763671 0.874553778 0.492194353 0.067447404 145.5531876 108359.6603 0.021221423 0.017754143 187.1236889 -2.272128771 -0.131209894 GGVTGSPEASISGS(ph)KGDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GGVTGSPEASISGSKGDLK 19 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GGVTGSPEASIS(0.002)GS(0.998)KGDLK;GGVTGSPEASIS(0.002)GS(0.998)KGDLK;GGVTGSPEASIS(0.003)GS(0.997)KGDLK 272.51 1.43E-39 2042720000 3877600 1614890 2156750 1837870 2492310 1585960 3129450 2012350 4201800 TRUE FALSE 3634907.938 1734458.136 2207909.128 1885032.856 2296574.026 2043800.906 2660218.025 2263596.327 3500492.435 1.038399027 0.495489754 0.630742437 0.538505051 0.656071701 0.583860969 0.75995537 0.646650827 1 21.73912646 0.141786978 0.740173719 1.008581333 0.636077423 0.3041093 0.151998626 3.90941443 2.512621539 0.226741973 0.048055733 1.386075791 -0.141786978 -0.372503909 GGVVGIKVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGVVGIKVDK 10 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 88.596 0.01227 0 784430 614980 747260 832800 810410 599260 926560 572080 1037800 FALSE TRUE 735333.9265 660513.7591 764985.3601 854171.0579 746763.6676 772256.6338 787630.9298 643505.4473 864584.4756 0.850505587 0.763966712 0.884801175 0.987955581 0.863725511 0.893211312 0.910993607 0.744294474 1 19.72164741 -0.36879684 0.017614476 1.856272709 4.28E-06 0.184134675 0.073860928 1994.186499 8.854928082 503.1834638 430.5058943 0.427762944 0.36879684 -1.85626843 GGYFDEFGIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 GGYFDEFGIIR 11 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;;; 268 6.60E-21 2067921000 1660095 2856503 1921595 2004342 3057279 1628843 1840317 2585978 2633508 FALSE TRUE 1556192.617 3068001.454 1967176.141 2055776.809 2817172.64 2099063.532 1564378.551 2908843.046 2193958.502 0.709308137 1.398386274 0.89663325 0.93701718 1.284059219 0.956747145 0.713039262 1.325842327 1 21.06510481 2.039047571 24.99974368 0.944529526 1.072462285 0 0.243631333 472.6393768 302599.9117 0.085479992 0.063131067 109.4076201 -2.039047571 0.127932759 GGYIGSTYFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GGYIGSTYFER 11 0 P61081 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ;; 166.19 4.82E-05 725640000 457070 658090 575450 579160 648830 493920 600190 526630 732720 FALSE TRUE 428462.8046 706815.6683 589099.9457 594022.2261 597873.5091 636506.6859 510197.0814 592380.9148 610424.2984 0.701909812 1.157908802 0.965066344 0.973130047 0.979439237 1.042728292 0.835807295 0.970441243 1 19.21945287 1.755417357 25 0.919385145 0.991617199 0 0.120867871 17.33777345 25742.20977 0.051164143 0.02837343 56.93998615 -1.755417357 0.072232055 GGYLS(ph)DGDSPELTTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GGYLSDGDSPELTTK 15 0 Q5VT97-2;Q5VT97 Q5VT97-2 SYDE2 Rho GTPase-activating protein SYDE2 1 GGYLS(1)DGDSPELTTK;GGYLS(1)DGDSPELTTK;GGYLS(0.997)DGDS(0.003)PELTTK 285.04 5.08E-34 376681000 1352710 1309750 1283880 1359940 1437880 975910 1607160 1150300 1318230 TRUE FALSE 1268046.296 1406725.253 1314334.24 1394838.363 1324954.705 1257639.374 1366181.278 1293917.487 1098208.897 1.154649447 1.280926841 1.196798026 1.270102953 1.206468741 1.14517318 1.244008569 1.17820707 1 20.06672107 -2.851061296 0.308457498 0.578226985 1.230561197 0.689960962 0.044425192 33.42097274 1.016112333 9.246353971 0.0392036 0.00140909 2.851061296 0.652334212 GHAAPILYAVWAEAGFLAEAELLNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GHAAPILYAVWAEAGFLAEAELLNLR 26 0 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 ;; 180.32 2.17E-17 1234670000 116366 193781 146170 125170 207939 135421 136505 161046 101834 FALSE TRUE 109082.8598 208128.7469 149637.2214 128382.0741 191608.3097 174514.8443 116037.3425 181152.9476 84837.24753 1.285789709 2.453270856 1.763815138 1.513274863 2.258539914 2.05705453 1.367764112 2.135299681 1 16.37241019 -2.1023809 0.327257681 4.72E-11 1.934523845 0.300030087 0.391970446 44.87802931 2.124797036 33.81185786 0.32631629 0.007899855 2.1023809 1.934523845 GHALLILRPEELGFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GHALLILRPEELGFLR 16 1 Q9NVP1;H7C452 Q9NVP1 DDX18 ATP-dependent RNA helicase DDX18 0 ; 156.17 1.13E-07 343280000 157313 214480 156199 177421 204898 142871 164779 177422 188011 FALSE TRUE 147467.0601 230360.3224 159904.114 181973.9232 188806.1376 184115.5384 140071.9187 199573.5273 156630.7495 0.941494953 1.470722212 1.020898607 1.161802033 1.205421912 1.175475052 0.894281098 1.274165692 1 17.25700794 2.382562468 0.633383462 1.038600224 1.212708637 0.020581432 0.169969438 1.745953588 1.403911436 0.136451537 0.10705401 241.3028591 -2.382562468 0.174108412 GHAVGDIPGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GHAVGDIPGVR 11 0 D6RD47;P62266 D6RD47 RPS23 40S ribosomal protein S23 0 ;;;;; 134.57 0.00013819 5417970000 1535480 1539710 1656670 1625570 1499050 1524470 1695100 1404000 1205338 FALSE TRUE 1439377.048 1653711.73 1695966.995 1667284.878 1381320.66 1964559.741 1440935.492 1579292.491 1004159.301 1.433415043 1.646861936 1.688942176 1.660378863 1.375599129 1.956422392 1.434967032 1.572750946 1 19.93755673 0.367077335 1.112743793 0.99911105 1.622037067 0.56287555 0.165315086 1.897799035 2.730952963 0.142311364 0.043046887 2.328505859 -0.367077335 0.622926016 GHAVNLLDVPVPVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GHAVNLLDVPVPVAR 15 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 ; 85.734 0.0078284 300600000 399460 419070 380820 401160 425620 327550 452240 404740 474940 FALSE TRUE 374458.5117 450098.3788 389853.2302 411454.4448 392193.5221 422108.3677 384430.8104 455272.6799 395669.4458 0.946392287 1.137561628 0.985300317 1.03989441 0.991215082 1.066820732 0.971595898 1.150638961 1 18.59393614 -0.579786943 5.448969638 0.999999999 1.036032614 0.027474064 0.067639102 8.57E-10 7.86E-11 0.057518021 0.013557127 0.263155867 0.579786943 0.036032615 GHAYSVTGAEEVESNGSLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHAYSVTGAEEVESNGSLQK 20 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 221.24 4.54E-26 0 56773 57092 61409 66854 58201 49067 71631 56957 84365 FALSE TRUE 53219.67927 61319.15108 62865.65048 68569.58682 53630.12823 63231.84636 60890.59654 64068.20683 70283.93648 0.757209712 0.872449014 0.894452611 0.975608229 0.76304958 0.899662847 0.866351539 0.911562585 1 16.10090738 -5 0.160770413 1.477589791 0.836381355 0.347683713 0.062610251 163.9652553 1.511666033 25.00780873 0.246122069 1.00E-05 5 -0.641208436 GHDDLGDHYLDCGDLSNALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GHDDLGDHYLDCGDLSNALK 20 0 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;Q13098-6;J3KSA5;J3KRJ4;J3QLT0 Q13098-7 GPS1 COP9 signalosome complex subunit 1 0 ;; 146.86 7.44E-08 917220000 1516950 1385320 1476290 1394470 1500260 1283320 1902660 1345140 1857290 FALSE TRUE 1422006.807 1487890.534 1511308.296 1430254.461 1382435.631 1653793.651 1617373.796 1513083.69 1547296.3 0.919026826 0.961606729 0.976741362 0.92435719 0.893452425 1.068828026 1.045290289 0.977888779 1 20.56131806 2.233768286 24.99999962 1.030261502 0.943861593 0.616887113 0.033839752 82.82640686 432073.0836 0.01268549 0.009670487 171.3043085 -2.233768286 -0.086399909 GHDGGHSHGGDMSNRPVCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GHDGGHSHGGDMSNRPVCR 19 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 0 ;;;;;; 189.87 8.43E-15 823093000 112288.7 161173 149270.1 152926 167673 144320 165331 140843.9 161868 FALSE TRUE 105260.7507 173106.4166 152810.8573 156850.3401 154504.6389 185982.8412 140541.1514 158428.571 134851.1851 0.780569712 1.2836848 1.133181419 1.163136534 1.145741796 1.37917098 1.042194411 1.174840035 1 17.04100867 0.218995858 1.296932717 0.99991869 1.155580965 0.059902045 0.156767198 15.98133189 23.93311184 0.137786122 0.039536434 1.655754171 -0.218995858 0.155662275 GHDLNEDGLVSWEEYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHDLNEDGLVSWEEYK 16 0 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-13;O43852-14;O43852-11 O43852 CALU Calumenin 0 186.43 1.50E-09 189070000 544850 414020 469110 429380 418080 366690 531750 407500 307600 FALSE TRUE 510748.8111 444674.4716 480237.5107 440398.6177 385245.6833 472547.4503 452019.024 458377.272 256259.5728 1.993091635 1.735250187 1.874027594 1.718564551 1.503341627 1.844018723 1.763910784 1.788722532 1 17.96724637 -1.41184264 3.014052639 0.986975963 1.774675765 0.792140379 0.125176756 24122205.61 30139003.06 2721977.506 0.028166386 0.038739799 1.41184264 0.787699802 GHDWGAPPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GHDWGAPPFR 10 0 Q9UGT4 Q9UGT4 SUSD2 Sushi domain-containing protein 2 0 ;; 128.27 0.00033406 1001740000 339355 598210 431090 354812 696530 485540 427910 605140 647460 FALSE TRUE 318115.3763 642502.0908 441315.6584 363917.0766 641827.3435 625707.5159 363748.868 680693.0611 539394.7432 0.589763583 1.191153786 0.81816826 0.674676721 1.189902852 1.160017823 0.674364874 1.261957165 1 19.04098194 2.730192981 24.81923956 1.015814819 0.880514063 0.183932385 0.225046737 1591.999005 4722018.48 0.071559991 0.06848191 537.2704817 -2.730192981 -0.135300755 GHEDDSYEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GHEDDSYEAR 10 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 ; 185.33 1.46E-06 232780000 71966 89939 97651 110837 112021 109523 111531 95852 117733 FALSE TRUE 67461.77652 96598.17714 99967.32783 113681.2651 103223.3225 141140.5121 94807.96195 107819.3332 98082.60172 0.687805741 0.984865567 1.019215703 1.159035987 1.052412158 1.438996414 0.966613449 1.09927073 1 16.58170963 5.295540564 0.815704713 1.120241451 6.29E-18 0.496149452 0.132008377 4.443413813 1.197350132 0.04140133 5.559364356 197487.9329 -5.295540564 -1.120241451 GHEFYNPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHEFYNPQK 9 0 P78406 P78406 RAE1 mRNA export factor 0 124.23 0.00053548 111550000 289020 337390 288590 283320 364330 217550 288940 348520 306210 FALSE TRUE 270930.7541 362370.7067 295435.4911 290590.4709 335716.9914 280353.1534 245616.1294 392033.4892 255101.5728 1.062050505 1.420495776 1.15810925 1.139116736 1.316013021 1.098986377 0.962816994 1.536774097 1 17.96071227 3.722463382 23.54004232 1.159465418 1.273604223 0.012552024 0.182991967 254.8524389 1287995.654 0.044764577 0.072062159 5277.927036 -3.722463382 0.114138805 GHEGPVWQVAWAHPMYGNILASCSYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHEGPVWQVAWAHPMYGNILASCSYDR 27 0 P55735;P55735-4;P55735-3;P55735-2;A8MXL6;E7ERC8 P55735 SEC13 Protein SEC13 homolog 0 212.86 2.70E-26 209470000 137390 163190 113260 103390 187730 118870 160650 144550 81420 FALSE TRUE 128791.0051 175272.7574 115946.5807 106043.1624 172986.4431 153185.8393 136562.0239 162597.3857 67830.47601 1.898718876 2.583982418 1.709358205 1.563355717 2.550276119 2.25836303 2.013284175 2.39711403 1 16.049646 -1.70688206 2.59698274 0.805843549 2.120493517 0.519369109 0.339145107 14935909.53 11992169.73 18912714.75 0.081301268 0.019638935 1.70688206 1.314649967 GHEGPVWQVAWAHPMYGNILASCSYDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHEGPVWQVAWAHPMYGNILASCSYDRK 28 1 P55735;P55735-4;P55735-3;P55735-2;A8MXL6;E7ERC8 P55735 SEC13 Protein SEC13 homolog 0 95.212 0.00090892 100890000 148300 171430 154600 144510 193850 127750 195960 146220 174840 FALSE TRUE 139018.1677 184122.8556 158267.185 148218.3713 178625.803 164629.3512 166577.6172 164475.8889 145658.0745 0.954414427 1.264075859 1.086566506 1.017577445 1.226336429 1.13024528 1.143620893 1.129191701 1 17.15222615 -1.675910553 2.046967037 0.971656762 1.130731893 0.136080377 0.090019711 1097869.452 672146.847 161035.6511 0.021448538 0.021090625 1.675910553 0.159075131 GHELVPLEQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHELVPLEQER 11 0 A0A0M3HER3;Q96LD4 A0A0M3HER3;Q96LD4 TRIM47 Tripartite motif-containing protein 47 0 77.387 0.032756 76383000 47923 67950 55273 59648 89294 42445 51228 62181 68579 FALSE TRUE 44923.58497 72981.0887 56584.10166 61178.66866 82281.20943 54698.18246 43546.83698 69944.43473 57132.72186 0.786302201 1.277395621 0.990397443 1.07081663 1.440176605 0.957388003 0.762204837 1.224244749 1 15.80202964 2.041041638 24.99998203 0.941743705 1.123626104 0.069109918 0.203745554 257.9089797 157100.8565 0.07077326 0.052269471 109.9111213 -2.041041638 0.181882398 GHFEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHFEEEK 7 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 158.08 0.0014338 308900000 705460 516620 586480 564070 634520 502020 717790 553700 734480 FALSE TRUE 661306.5179 554871.0823 600391.5826 578544.9912 584687.3587 646945.0244 610164.0531 622830.6638 611890.5431 1.080759501 0.90681428 0.981207488 0.945504057 0.955542401 1.05728881 0.997178433 1.017879212 1 19.22291408 2.262396241 24.99761091 1.017045004 0.964502376 0.163155109 0.046986276 316.2086606 331622.9776 0.014835168 0.012405498 182.9768898 -2.262396241 -0.052542629 GHFGPINSVAFHPDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHFGPINSVAFHPDGK 16 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 211.78 3.59E-12 899010000 1084200 1151500 1010300 911420 1284000 766970 1301700 1191200 1371100 FALSE TRUE 1016341.857 1236758.258 1034264.793 934808.5802 1183159.819 988381.7883 1106522.169 1339923.942 1142254.552 0.88976827 1.082734366 0.905459112 0.818389017 1.035810991 0.865290304 0.968717671 1.173051961 1 20.12345276 1.384062729 7.807923958 1.084692473 0.944301281 0.333487903 0.087640274 0.278164465 19.85662491 0.055422004 0.020312926 24.21378764 -1.384062729 -0.140391192 GHGDSVDQLCWHPSNPDLFVTASGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHGDSVDQLCWHPSNPDLFVTASGDK 26 0 Q96J01;Q96J01-2 Q96J01 THOC3 THO complex subunit 3 0 111.67 0.0011285 61327000 58367 79178 84348 88155 89906 82790 114720 85623 96480 FALSE TRUE 54713.91366 85040.4215 86348.77439 90417.20655 82845.14542 106690.129 97518.80101 96313.22003 80376.86472 0.680717192 1.058021133 1.074298863 1.124915818 1.030708845 1.327373609 1.213269532 1.198270427 1 16.29449268 5.223247819 0.947596443 1.162122107 5.91E-32 0.665686804 0.098974334 2.723961923 1.025625022 0.029866371 4.035494758 167204.4452 -5.223247819 -1.162122107 GHHVT(ph)DSENDEPLNLNAS(ph)DS(ph)ESEELHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHHVTDSENDEPLNLNASDSESEELHR 27 0 Q96ST2;B8ZZB6 Q96ST2 IWS1 Protein IWS1 homolog 3 GHHVT(0.908)DS(0.092)ENDEPLNLNAS(1)DS(0.935)ES(0.065)EELHR 150.59 1.27E-07 165880000 60311 75538 75336 75789 80547 68323 71409 59555 86991 TRUE FALSE 56536.24217 81130.91212 77123.0055 77733.87405 74221.16353 88046.74097 60701.88338 66990.57285 72471.64012 0.780115395 1.119484974 1.06418187 1.07261094 1.024140801 1.214913045 0.837595 0.924369488 1 16.14512892 1.687451599 11.98532122 0.911853791 1.056600706 0.201590041 0.115634758 0.155038523 30.49220624 0.04921874 0.026896203 48.69132571 -1.687451599 0.144746914 GHHVTDS(ph)ENDEPLNLNAS(ph)DS(ph)ESEELHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHHVTDSENDEPLNLNASDSESEELHR 27 0 Q96ST2;B8ZZB6 Q96ST2 IWS1 Protein IWS1 homolog 3 GHHVT(0.128)DS(0.872)ENDEPLNLNAS(0.992)DS(0.859)ES(0.149)EELHR 146.06 7.36E-08 145910000 24684 24880 20026 26526 22966 20278 26707 17918 21782 TRUE FALSE 23139.0725 26722.14109 20501.02618 27206.70207 21162.343 26131.92941 22702.53329 20155.10174 18146.44348 1.275129891 1.472582829 1.1297545 1.499285637 1.166197829 1.440057907 1.25107343 1.110691567 1 14.1473992 1.176123684 2.375017193 1.006099733 1.325143425 0.470716102 0.121454701 0.221828291 2.219090777 0.10006152 0.028128339 15.00111996 -1.176123684 0.319043692 GHHVTDSENDEPLNLNAS(ph)DS(ph)ESEELHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHHVTDSENDEPLNLNASDSESEELHR 27 0 Q96ST2;B8ZZB6 Q96ST2 IWS1 Protein IWS1 homolog 2 GHHVTDSENDEPLNLNAS(0.999)DS(0.87)ES(0.131)EELHR 173.25 1.42E-12 102050000 56194 40897 46538 48752 52559 40669 59003 38060 64523 TRUE FALSE 52676.91785 43925.05643 47641.90334 50003.05886 48431.22815 52409.48009 50156.04791 42811.87478 53753.69447 0.979968324 0.817154186 0.886300073 0.930225529 0.900984177 0.974993079 0.933071641 0.796445253 1 15.71407629 3.335135198 4.858859967 0.922828191 0.875379306 0.01451998 0.066366501 0.485613344 19.17879633 0.017296888 0.023592258 2163.391892 -3.335135198 -0.047448885 GHKGS(ph)FKDDPQLYQEIQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GHKGSFKDDPQLYQEIQER 19 2 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 GHKGS(1)FKDDPQLYQEIQER;GHKGS(1)FKDDPQLYQEIQER;GHKGS(1)FKDDPQLYQEIQER;GHKGS(1)FKDDPQLYQEIQER 134.03 5.50E-06 3452120000 3955600 2268140 2645070 2582180 2601410 1559250 2761600 1501850 3013340 TRUE FALSE 3708026.057 2436075.446 2707812.309 2648443.11 2397105.752 2009380.163 2347523.717 1689359.278 2510394.087 1.477069308 0.970395628 1.078640331 1.054990977 0.954872291 0.800424194 0.935121593 0.672945848 1 21.25948243 8 0.552246837 0.893134596 23.73699164 0.633325447 0.126113523 90.53458823 0.818900746 0.055731908 2455.684804 100000000 -8 22.84385705 GHLEIGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHLEIGEK 8 0 M0QWZ7;Q9NP81;Q9NP81-2;M0R2C6;M0R259 M0QWZ7 SARS2 "Serine--tRNA ligase, mitochondrial" 0 84.476 0.017425 33497000 50660 48386 43892 43453 61311 40946 45041 47297 74984 FALSE TRUE 47489.28103 51968.54979 44933.13897 44568.07755 56495.88138 52766.4455 38287.52019 53202.13456 62468.68598 0.76020938 0.831913605 0.719290606 0.713446695 0.904387222 0.844686336 0.612907405 0.851660856 1 15.93084556 0.990208325 24.95159719 1.000000013 0.767144972 0.457483251 0.080314624 381.3982451 971899.128 0.076813404 0.019203351 9.777061004 -0.990208325 -0.232855041 GHLENNPALEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 180.2 6.77E-06 9317000000 20314500 18488100 18888800 18578500 20669100 14520800 21977800 18309600 21809600 FALSE TRUE 19043051.71 19856978.16 19336851.26 19055255.76 19045832.26 18712719.23 18682432.92 20595593.86 18169436.86 1.048081559 1.092878019 1.064251545 1.048753239 1.048234593 1.029900892 1.02823401 1.133529565 1 24.11501037 3.365126022 2.791629675 1.04655926 1.074954049 0.065403653 0.035580552 0.567100185 8.848243046 0.009608135 0.013847499 2318.067198 -3.365126022 0.028394789 GHLSRPEAQSLS(ph)PYTTSANR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GHLSRPEAQSLSPYTTSANR 20 1 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 1 GHLS(0.002)RPEAQS(0.002)LS(0.996)PYTTSANR;GHLSRPEAQSLS(1)PYTTSANR;GHLSRPEAQSLS(1)PYTTSANR;GHLSRPEAQSLS(0.985)PYT(0.014)T(0.001)SANR;GHLSRPEAQSLS(1)PYTTSANR 236.59 8.59E-30 2801310000 760886 1223290 1214390 1199940 1312750 1737750 1596750 1177440 1466850 TRUE FALSE 713263.5035 1313863.664 1243195.904 1230732.492 1209651.91 2239410.215 1357332.161 1324445.976 1222023.259 0.583674245 1.075154384 1.017325894 1.007126896 0.98987634 1.832543038 1.110725308 1.083814049 1 20.22084031 2.43316957 24.99999779 1.287297067 0.966212292 0.265660879 0.261386483 173.7685634 98839.75749 0.084056202 0.0703265 271.1250031 -2.43316957 -0.321084774 GHMLADVVAIIGTQDIVFGEVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GHMLADVVAIIGTQDIVFGEVDR 23 0 O75306 O75306 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" 0 ; 181.85 4.12E-17 90688000 85260 86108 77937 79310 123754 91705 69010 88771 105658 FALSE TRUE 79923.72879 92483.52592 79785.70244 81345.22887 114034.86 118178.7448 58662.59116 99854.25476 88022.99722 0.907986905 1.050674583 0.906418833 0.924136094 1.295512123 1.34258942 0.66644619 1.134410982 1 16.42559288 GHNCPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHNCPK 6 0 P17844;J3KTA4;J3QRQ7;J3KRX8;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 69.439 0.0935 33934000 91799 64692 103230 78563 70036 66195 78177 80178 65548 FALSE TRUE 86053.46446 69481.86299 105678.6643 80579.05959 64535.65507 85304.42191 66455.08461 90188.39979 54607.61534 1.575850986 1.272384127 1.935236756 1.475601142 1.181806872 1.562134171 1.216956357 1.651571841 1 15.73681454 2.997652863 24.99695971 1.344020377 1.590554947 0.209510828 0.241114187 148.4507762 1581027.29 0.065411913 0.076963205 994.6100958 -2.997652863 0.24653457 GHNCPKPVLNFYEANFPANVMDVIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHNCPKPVLNFYEANFPANVMDVIAR 26 1 P17844;J3KTA4;J3QRQ7;J3KRX8;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 138.08 6.19E-06 94698000 108670 129140 98430 78972 146460 85471 134200 125400 146920 FALSE TRUE 101868.5387 138701.66 100764.8061 80998.55522 134957.6224 110145.0902 114077.9559 141056.466 122398.1029 0.832272203 1.133201061 0.82325464 0.661763159 1.102612044 0.899892136 0.932023889 1.15243997 1 16.90122167 1.302000448 9.135573034 1.075718856 0.922749315 0.190155185 0.139464432 0.493659579 65.83130574 0.090366546 0.032916304 20.04474095 -1.302000448 -0.152969541 GHNGWVTQIATTPQFPDMILSASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GHNGWVTQIATTPQFPDMILSASR 24 0 P63244;J3KPE3;D6RHH4;D6RAC2;D6REE5;E9PD14;D6RFZ9;D6RAU2;D6RBD0;D6R909;D6RGK8;D6RHJ5;D6RDI0 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 ; 252.47 9.30E-44 1810280000 1441860 1978130 1465250 1228620 2004780 1489730 1735810 1722740 925840 FALSE TRUE 1351616.556 2124592.803 1500006.422 1260148.469 1847332.666 1919790.867 1475541.405 1937827.881 771311.3228 1.752361876 2.754520439 1.944748349 1.633774109 2.395054514 2.488996091 1.913029618 2.512380959 1 19.55695376 -1.178385319 4.28021586 0.999643437 2.189647251 0.506678052 0.363890532 12457695.43 3429795.663 42098.66296 0.079890398 0.066315444 1.178385319 1.190003814 GHNTNVGAIVFHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHNTNVGAIVFHPK 14 0 O43172-2;O43172 O43172-2 PRPF4 U4/U6 small nuclear ribonucleoprotein Prp4 0 106.42 0.00054505 178110000 72275 123350 110790 113270 138060 88291 113270 116710 136430 FALSE TRUE 67751.43676 132482.9623 113417.9911 116176.7 127217.3245 113779.1784 96286.21505 131281.5004 113658.9516 0.596094155 1.165618374 0.997879969 1.022151782 1.11928997 1.001057785 0.847150301 1.15504761 1 16.79435179 4.749905205 24.83157214 1.029716711 0.596093875 0.688866948 0.093277484 973.0709906 2129860.215 0.022883515 0.354714657 56221.85937 -4.749905205 -0.433622836 GHNVAEVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHNVAEVQK 9 0 A0A087WYV5;X6R3P0;O94813-3;O94813-2;O94813 A0A087WYV5 SLIT2 Slit homolog 2 protein;Slit homolog 2 protein N-product;Slit homolog 2 protein C-product 0 78.334 0.030064 190570000 250940 146070 181010 208950 185890 236910 389300 126840 128260 FALSE TRUE 235234.1133 156885.1748 185303.6427 214312.0108 171290.9492 305302.0711 330928.0791 142676.2532 106852.5774 2.201482819 1.4682395 1.734199092 2.005679376 1.603058657 2.857227018 3.097052847 1.335262627 1 16.70526218 2.26103561 24.99082606 2.359991166 1.756862339 0 0.671417945 412.7363615 458936.3341 0.218748307 0.182892918 182.4045261 -2.26103561 -0.603128826 GHPEFSTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GHPEFSTNR 9 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;; 104.01 0.003329 849420000 248798 455972 311687 378636 357984 376475 360723 321203 287021 FALSE TRUE 233226.1773 489732.6413 319080.3628 388352.4408 329869.3807 485157.2209 306635.9349 361305.9016 239115.3409 0.975371034 2.04810214 1.334420291 1.624121812 1.37954085 2.028967356 1.282376672 1.511010964 1 17.86734717 0.655263254 1.154452408 1.002874634 1.577889454 0.193790435 0.327750441 1.618190786 3.442707838 0.275587798 0.085097275 4.521299263 -0.655263254 0.57501482 GHPHSASS(ph)PSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GHPHSASSPSER 12 0 C9J470;E9PHA2;Q15003;C9JZP1 C9J470 NCAPH Condensin complex subunit 2 1 GHPHSAS(0.064)S(0.935)PS(0.001)ER;GHPHSAS(0.079)S(0.919)PS(0.002)ER 182.37 1.09E-05 753320000 139061 228970 237239 261400 232023 167546 170987 144112 176125 TRUE FALSE 130357.4202 245923.177 242866.4211 268107.9665 213800.8495 215913.8103 145349.0867 162104.7004 146728.5997 0.888425437 1.676041191 1.655208471 1.827237274 1.457117767 1.471518237 0.9905982 1.1047928 1 17.16279058 1.817448699 3.558428515 1.030989254 1.555424316 0.423110095 0.250326449 0.199274295 4.435679182 0.124572971 0.065196589 65.68235244 -1.817448699 0.524435062 GHPHSASSPS(ph)ER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GHPHSASSPSER 12 0 C9J470;E9PHA2;Q15003;C9JZP1 C9J470 NCAPH Condensin complex subunit 2 1 GHPHS(0.058)AS(0.111)S(0.185)PS(0.647)ER;GHPHS(0.02)AS(0.138)S(0.138)PS(0.703)ER;GHPHS(0.027)AS(0.296)S(0.296)PS(0.381)ER;GHPHS(0.002)AS(0.132)S(0.132)PS(0.734)ER 100.11 0.00074653 60945000 59858 72649.3 63147.6 76337 73952 49656.4 60849.4 47042.3 52504.2 TRUE FALSE 56111.59463 78028.32976 64645.49089 78295.93666 68144.10823 63991.39658 51725.59737 52915.63471 43740.90983 1.282817272 1.783875326 1.477918295 1.789993326 1.55790331 1.462964461 1.182545072 1.209751578 1 15.41669561 1.768628135 1.584386706 1.086416093 1.60627513 0.649991941 0.151374667 0.20310017 0.986402334 0.102570405 0.041328382 58.69865295 -1.768628135 0.519859037 GHQFSCVCLHGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GHQFSCVCLHGDR 13 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;;; 214.65 1.76E-11 1443940000 149122 233943 193126 196983 265249 196960 200735 187503 250821 FALSE TRUE 139788.7202 251264.3831 197707.0399 202037.9173 244417.4135 253819.1546 170636.6503 210913.1623 208957.3547 0.668982053 1.202467286 0.946159757 0.966885887 1.169699979 1.214693567 0.816609927 1.009359841 1 17.67284901 1.718338905 24.9999992 0.930990857 1.041896117 0.050725707 0.166606574 2.245936512 2765.510799 0.071150931 0.03945676 52.28040043 -1.718338905 0.11090526 GHQQLYWSHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GHQQLYWSHPR 11 0 A0A2R8Y851;P62273;P62273-2 A0A2R8Y851 RPS29 40S ribosomal protein S29 0 ;;;;; 170.52 9.03E-06 3929800000 2007541 3534380 1868254 1733324 3682600 1142566 2133254 3034370 3484630 FALSE TRUE 1881892.592 3796069.173 1912569.867 1777804.028 3393383.451 1472406.256 1813392.367 3413217.774 2903022.741 0.64825279 1.307626399 0.658820146 0.612397555 1.168913837 0.507197631 0.624656618 1.175746137 1 21.46912444 5.021174674 16.97934117 0.856039495 0.172783789 0.058233282 0.278536572 20112460.58 387706751.6 0.065143033 364891799.1 104996.464 -5.021174674 -0.683255706 GHS(ph)PAQKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GHSPAQKPK 9 1 Q14966;Q14966-3;Q14966-4;A0A096LPI0;Q14966-2;Q14966-6;A0A096LPB4 Q14966 ZNF638 Zinc finger protein 638 1 GHS(1)PAQKPK;GHS(1)PAQKPK 124.1 0.00032554 317500000 991630 545210 724470 605110 668330 591060 948200 691940 840700 TRUE FALSE 929565.6484 585577.9157 741654.7705 620638.147 615842.0577 761689.4269 806026.2127 778330.2321 700381.7389 1.327227135 0.836083929 1.058929337 0.886142674 0.879294852 1.087534675 1.150838418 1.111294297 1 19.41778194 2.074993333 9.76327278 1.107886185 0.978940218 0.076668738 0.141480104 0.603282228 73.56962605 0.048433183 0.035754815 118.8483981 -2.074993333 -0.128945967 GHSAQIAKPIRPGQHPAAS(ph)PTHPSAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHSAQIAKPIRPGQHPAASPTHPSAIR 27 2 P33176 P33176 KIF5B Kinesin-1 heavy chain 1 GHSAQIAKPIRPGQHPAAS(0.973)PT(0.027)HPSAIR 110.43 0.00087903 1052100000 333030 519260 580990 531350 460700 424490 589020 457190 492030 TRUE FALSE 312186.2468 557706.5507 594771.3572 544985.3406 424518.4804 547033.372 500701.9192 514271.1779 409907.0144 0.761602597 1.360568449 1.450990923 1.329534069 1.035645806 1.3345304 1.221501223 1.254604483 1 18.64493715 GHSHFVSDVVISSDGQFALSGSWDGTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GHSHFVSDVVISSDGQFALSGSWDGTLR 28 0 P63244;D6RHH4;D6R9L0;D6RAC2;D6R9Z1;D6RFX4;D6REE5;E9PD14;D6RFZ9;D6RAU2;D6RBD0;D6R909 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 ; 81.839 0.0028742 27606000 34114 37491 31812 33187 37150 32295.3 33308 34896 28565 FALSE TRUE 31978.86564 40266.87265 32566.59566 34038.63461 34232.38886 41618.42884 28313.77462 39252.84242 23797.31696 1.343801307 1.692076158 1.36849863 1.430355979 1.438497832 1.748870635 1.189788524 1.649465042 1 14.53851131 -2.756141369 0.412645682 8.04E-10 1.490642099 0.424942418 0.17373683 97.24870735 3.795493992 86.17333915 0.094172871 0.00175331 2.756141369 1.490642098 GHSVEEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GHSVEEALR 9 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 177.7 5.18E-05 516360000 134011 428420 150477 142697 411760 126234 142141 340645 286999 FALSE TRUE 125623.4907 460140.6626 154046.3855 146358.8466 379422.0306 162675.7066 120828.2766 383175.2781 239097.0128 0.525408031 1.924493565 0.644284024 0.61213164 1.586895738 0.68037532 0.505352514 1.602593331 1 17.86723658 3.821565385 8.370645839 0.899533055 1.316950736 0.035933868 0.508149525 0.585353785 46.55747578 0.120532469 0.217883343 6630.79169 -3.821565385 0.417417681 GHTAS(ph)ESDEQQWPEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHTASESDEQQWPEEK 16 0 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 GHT(0.013)AS(0.92)ES(0.067)DEQQWPEEK 177.61 1.88E-09 480610000 762090 641930 681360 872550 937550 571300 825200 585720 774040 TRUE FALSE 714392.1473 689459.1651 697522.181 894941.1102 863918.6049 736225.0357 701468.9208 658848.4313 644847.7235 1.107846273 1.069181359 1.08168511 1.387833247 1.339724982 1.141703706 1.087805532 1.02171165 1 19.29859899 1.543568578 2.381869034 1.012762558 1.175794836 0.335348975 0.104200534 0.40559513 4.888280459 0.090823689 0.032172289 34.95977089 -1.543568578 0.163032278 GHTDSVQDISFDHSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GHTDSVQDISFDHSGK 16 0 P43034 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ;;;; 318.18 3.61E-58 2196110000 2211700 2412430 2162060 2218720 2607240 1956850 3051660 2464020 2819440 FALSE TRUE 2073273.645 2591048.827 2213345.084 2275656.111 2402477.888 2521760.828 2594091.913 2771658.321 2348857.25 0.882673328 1.103110386 0.942307194 0.968835425 1.022828394 1.073611787 1.104405946 1.180002881 1 21.16352761 2.232390936 2.3556598 1.103990902 0.990686517 0.366638558 0.069867539 0.318921988 3.608043245 0.029257242 0.020068565 170.7618832 -2.232390936 -0.113304384 GHTDTEGRPPS(ph)PPPTSTPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GHTDTEGRPPSPPPTSTPEK 20 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 1 GHTDT(0.007)EGRPPS(0.992)PPPTSTPEK;GHTDT(0.002)EGRPPS(0.996)PPPT(0.001)ST(0.001)PEK;GHTDTEGRPPS(1)PPPTSTPEK;GHTDTEGRPPS(1)PPPTSTPEK;GHT(0.02)DT(0.017)EGRPPS(0.958)PPPT(0.005)STPEK;GHT(0.024)DT(0.024)EGRPPS(0.917)PPPT(0.016)S(0.016)T(0.002)PEK 194.77 1.52E-18 11143620000 3953380 2433310 2807780 2845780 2971070 2217057 3517290 2430930 3338880 TRUE FALSE 3705945.003 2613474.804 2874381.868 2918807.533 2737734.147 2857085.365 2989905.017 2734436.962 2781599.358 1.332307254 0.939558314 1.033355814 1.04932708 0.98423022 1.027137627 1.07488701 0.983044864 1 21.40748321 4.747004955 24.99909819 1.015155533 1.332307413 0.874291183 0.038213542 384.7537638 1139021.622 0.009410054 0.109783882 55847.6566 -4.747004955 0.31715188 GHTESCSCPLQQS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHTESCSCPLQQSPR 15 0 O76074-2;G5E9C5;O76074;C9JGT3 O76074-2 PDE5A "cGMP-specific 3,5-cyclic phosphodiesterase" 1 GHTESCSCPLQQS(1)PR 75.215 0.02093 1142000000 138730 157420 168130 165130 191320 156220 175930 164920 192990 TRUE FALSE 130047.1369 169075.5406 172118.123 169367.5154 176294.4989 201318.178 149550.9298 185510.625 160778.7222 0.808857883 1.051603958 1.070527994 1.053419961 1.096503919 1.252144408 0.930166179 1.153825721 1 17.29471696 4.749786315 3.540420543 1.075282387 0.77387566 0.49539282 0.085087961 0.252371341 5.519706393 0.01879738 0.205966363 56206.4706 -4.749786315 -0.301406728 GHTGGHHS(ph)PVK ddPTM_SK-BR-3_Pertuzumab_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;GHTGGHHS(1)PVK;GHTGGHHS(1)PVK 191.01 3.37E-06 1912600000 1611500 1418230 1320740 1399730 1877400 975640 1542630 1532160 1685250 TRUE FALSE 1510639.092 1523237.225 1352068.576 1435649.442 1729956.577 1257291.43 1311326.953 1723453.549 1403970.888 1.075976079 1.084949295 0.963031775 1.02256354 1.232188354 0.895525285 0.934012923 1.227556471 1 20.42108159 GHTSERPYECEECGKCFS(ph)QK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GHTSERPYECEECGKCFSQK 20 2 M0QX82;J3KQR4;Q8TF45 M0QX82 ZNF418 Zinc finger protein 418 1 GHTSERPYECEECGKCFS(1)QK;GHTSERPYECEECGKCFS(0.999)QK 51.645 0.067558 3034200000 270392 911910 774150 815430 801700 887200 763730 760580 429020 TRUE FALSE 253468.6474 979428.7652 792513.2036 836355.3143 738737.7159 1143320.238 649215.7766 855540.0872 357413.7904 0.709174224 2.740321698 2.217354855 2.34001971 2.066897629 3.19886996 1.81642621 2.393696355 1 18.44723577 4.748591831 24.60859546 2.299992792 0.709173129 0.39835494 0.577083933 989.4593029 2427282.605 0.118112176 1.583740915 56052.09259 -4.748591831 -1.590819663 GHVDILAPTVQELAALEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHVDILAPTVQELAALEK 18 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 126.19 2.81E-05 133650000 297690 268760 269740 258930 311310 233360 326240 254190 343400 FALSE TRUE 279058.1143 288659.27 276138.3602 265574.5822 286860.9684 300727.2437 277323.3407 285926.181 286084.3216 0.975440083 1.009000663 0.965234161 0.928308761 1.002714748 1.051183938 0.969376229 0.999447224 1 18.12608091 2.531735131 24.99993446 1.003934758 0.974383942 0.27717831 0.027625413 492.3987053 225398.4186 0.009084704 0.008565067 340.2006433 -2.531735131 -0.029550817 GHVFEESQVAGTPMFVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHVFEESQVAGTPMFVVK 18 0 P13639 P13639 EEF2 Elongation factor 2 0 178.99 8.60E-14 1102700000 1697500 1689000 1720500 1649700 1863800 1428500 2151700 1652100 2082100 FALSE TRUE 1591256.505 1814055.317 1761311.072 1692034.095 1717424.666 1840884.76 1829072.56 1858368.322 1734584.059 0.91737065 1.045815743 1.015408313 0.975469644 0.990107488 1.061283107 1.05447329 1.071362504 1 20.72615833 2.238399378 24.99999983 1.052012969 0.999620784 0.342551377 0.037996827 5.190877958 804610.0479 0.013156043 0.010337977 173.1407831 -2.238399378 -0.052392184 GHVQPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHVQPIR 7 0 P62854;Q5JNZ5 P62854 RPS26;RPS26P11 40S ribosomal protein S26;Putative 40S ribosomal protein S26-like 1 0 88.591 0.069487 0 38760 45693 39217 41227 42423 36597 37224 31533 42368 FALSE TRUE 36334.08079 49076.15726 40147.24576 42284.95462 39091.26871 47161.9598 31642.60677 35469.96446 35296.50709 1.029395931 1.390396991 1.137428292 1.197992609 1.107510967 1.336165068 0.896479833 1.004914293 1 15.1072378 1.712429348 9.287482122 0.966081536 1.210827367 0.505284768 0.107989567 0.0805137 16.56803128 0.047645429 0.025584143 51.57382565 -1.712429348 0.244745831 GHWDDVFLDSTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GHWDDVFLDSTQR 13 0 Q9H6T3;Q9H6T3-3 Q9H6T3 RPAP3 RNA polymerase II-associated protein 3 0 ;; 212.68 1.20E-08 289435000 388730 460910 446503 470923 532034 425898 489095 434387 538070 FALSE TRUE 364400.0832 495036.256 457094.262 483007.6815 490250.1958 548847.8387 415759.7453 488621.1732 448262.6409 0.812916469 1.104344219 1.01970189 1.077510453 1.093667308 1.224388982 0.927491402 1.090033227 1 18.77398474 4.744131414 24.62825911 1.064873422 0.812916335 0.516465718 0.077278579 405.6533202 1793309.059 0.017258622 0.152349078 55479.35637 -4.744131414 -0.251957087 GHYEVT(ph)GSDDETGKLQGSGVSLASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GHYEVTGSDDETGKLQGSGVSLASK 25 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GHY(0.014)EVT(0.43)GS(0.43)DDET(0.126)GKLQGSGVSLASK;GHYEVT(0.5)GS(0.5)DDETGKLQGSGVSLASK 261.79 6.10E-45 6033000000 2198630 1208190 1631730 1493940 1528070 1145710 1823540 1241050 1599170 TRUE FALSE 2061021.673 1297645.645 1670435.406 1532277.03 1408061.546 1476457.878 1550117.106 1395997.824 1332258.196 1.547013694 0.974019637 1.25383759 1.150135187 1.056898393 1.108237039 1.163526042 1.0478433 1 20.34544228 4.749819375 24.91324662 1.11033082 1.547013961 0.742310394 0.083350704 820.3789612 1815288.53 0.018685419 0.288953685 56210.74932 -4.749819375 0.43668314 GHYEVTGS(ph)DDETGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GHYEVTGSDDETGK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GHYEVTGS(1)DDETGK;GHYEVTGS(1)DDETGK;GHYEVTGS(1)DDETGK;GHYEVTGS(1)DDETGK;GHYEVTGS(1)DDETGK;GHYEVTGS(1)DDETGK 274.81 3.06E-33 2625730000 4168270 2388060 2993970 2639220 2782640 2271540 3347960 2551330 2254410 TRUE FALSE 3907385.421 2564874.447 3064988.382 2706946.853 2564102.679 2927296.723 2845964.479 2869869.167 1878134.407 2.080461019 1.365650103 1.631932396 1.441295598 1.365239181 1.5586194 1.515314595 1.528042485 1 20.84086888 -3.245194363 0.174608176 1.48E-23 1.678780966 0.487641452 0.192131642 61.2852661 1.022589991 23.77972243 0.645241676 0.000568598 3.245194363 1.678780966 GHYEVTGS(ph)DDETGKLQGSGVSLASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GHYEVTGSDDETGKLQGSGVSLASK 25 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GHYEVT(0.156)GS(0.844)DDETGKLQGSGVSLASK;GHY(0.015)EVT(0.196)GS(0.788)DDETGKLQGSGVSLASK;GHYEVT(0.004)GS(0.996)DDETGKLQGSGVSLASK;GHYEVT(0.145)GS(0.83)DDET(0.026)GKLQGSGVSLASK;GHYEVT(0.072)GS(0.928)DDETGKLQGSGVSLASK 292.37 4.31E-63 4856610000 2509650 1370297 1809020 1769340 1905550 1338864 2209740 1505420 1879110 TRUE FALSE 2352575.486 1471755.216 1851930.809 1814744.26 1755895.79 1725372.302 1878410.001 1693375.001 1565474.401 1.502787579 0.940133684 1.18298377 1.159229597 1.121638136 1.102140221 1.199898254 1.081700856 1 20.57816849 -2.632574948 0.017797825 5.54E-06 2.051331197 0.172474091 0.136295049 6737.816091 14.2154084 969.9912309 688.3860514 0.002330371 2.632574948 2.05132566 GHYNNVSCAVFHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GHYNNVSCAVFHPR 14 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 53.051 0.087721 198980000 153130 188260 136980 139010 207820 108170 167490 176770 244580 FALSE TRUE 143545.8666 202198.9663 140229.2303 142577.2319 191498.6555 139396.923 142376.4294 198840.1236 203758.018 0.704491868 0.992348514 0.688214538 0.69973802 0.939833718 0.684129756 0.698752524 0.975864045 1 17.63649731 1.205055287 12.77176057 0.988220445 0.780574621 0.400569386 0.109215587 1.390199109 523.2963588 0.10221138 0.025814739 16.03449503 -1.205055287 -0.207645824 GHYTEGAELVDAVLDVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GHYTEGAELVDAVLDVVR 18 0 P04350;M0R278;M0R1I1;K7ES63;K7ESM5;Q9BUF5;K7EL29 P04350;K7ESM5 TUBB4A;TUBB6 Tubulin beta-4A chain;Tubulin beta-6 chain 0 ; 172.2 1.14E-11 53555000 49871 73562 67486 62829 75145 60404 67848 64298 72240 FALSE TRUE 46749.66313 79008.60702 69086.79979 64441.29851 69243.41482 77841.65422 57674.82227 72325.74684 60182.67731 0.776796002 1.312813098 1.147951585 1.070761578 1.150553912 1.29342292 0.958329288 1.201770178 1 15.87706067 0.176982361 0.660230746 0.996511243 1.136761345 0.024152772 0.159041869 9.839021113 5.461832836 0.25822209 0.055442355 1.503080917 -0.176982361 0.140250102 GHYTEGAELVDSVLDVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 16 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 ;;;;;;;;;;;;;;; 375.57 7.53E-108 27898681100 6734281.8 8905298 8321468.8 8327126 9601481 7775929.7 8882838.8 8229904 9224274.3 FALSE TRUE 6312795.123 9564655.53 8518857.97 8540814.151 8847419.413 10020714.37 7550939.586 9257425.631 7684683.328 0.821477588 1.244638864 1.108550295 1.11140743 1.15130566 1.303985336 0.982596063 1.204659351 1 22.87355438 -1.139334133 4.279082966 0.999973937 1.125572514 0.063381138 0.135945761 2.97E-05 5.98E-06 0.11577295 0.027282285 0.072554753 1.139334133 0.125598577 GHYTEGAELVDSVLDVVRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 308.36 1.21E-61 1444134000 971476 1498623 1289656 1353808 2035322 1019353 1837604 1231465 4111256 FALSE TRUE 910673.0513 1609582.606 1320247.249 1388549.005 1875476.02 1313623.663 1562072.34 1385216.116 3425060.814 0.265885221 0.469942782 0.385466805 0.40540857 0.547574517 0.383532946 0.456071417 0.404435481 1 21.70769817 -5 0.380021528 9.157182291 0.407767051 0.869559628 0.071324549 184.0890891 1.376451862 1237.586494 0.042759151 1.00E-05 5 -8.749415239 GHYTIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GHYTIGK 7 0 P68363;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;F8VWV9;P68366-2;P68366;C9JEV8;C9JQ00;C9JJQ8;C9JDL2;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA1A;TUBA1C;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 ;;;;; 123.96 0.0041931 23443100000 45210700 48419500 52377800 50396900 54493500 48361400 64848800 52607200 45807900 FALSE TRUE 42381042.99 52004530.16 53620226.15 51690169.78 50213800.33 62322551.1 55125324.47 59175324.72 38162265.56 1.110548401 1.362721248 1.405058776 1.354483782 1.315797152 1.633093586 1.444498215 1.550623996 1 25.18564349 5.473565609 1.182158879 1.417936647 1.03E-11 0.187687224 0.168202713 10.4052821 3.464714607 0.041954602 27.6941803 297553.8738 -5.473565609 -1.417936647 GHYTIGKEIIDLVLDR ddPTM_SK-BR-3_Pertuzumab_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 ; 278.08 1.41E-35 206060000 262870 424090 384230 417180 542810 307980 502870 333380 708020 FALSE TRUE 246417.4359 455490.0649 393344.117 427885.5451 500179.8922 396888.8264 427469.3119 375003.2269 589846.888 0.417765086 0.772217459 0.666858002 0.725417992 0.847982591 0.672867543 0.724712329 0.635763678 1 19.16998098 -5 0.22263417 2.515173888 0.66023347 0.452053664 0.110627237 147.2074659 1.473771826 100.6196516 0.189049285 1.00E-05 5 -1.854940418 GHYTIGKEIIDLVLDRIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GHYTIGKEIIDLVLDRIR 18 2 P68363;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 ; 270.42 3.74E-39 65578000 180264 277190 239750 300660 328120 142342 251990 213770 451880 FALSE TRUE 168981.598 297713.436 245436.9832 308375.4446 302350.7788 183433.8247 214206.4389 240459.6551 376458.3087 0.448872011 0.790827109 0.651963252 0.819148993 0.803145453 0.48726199 0.569004413 0.638741793 1 18.52213058 -0.97312948 4.743729506 1.000003399 0.659193461 0.424392751 0.12738198 3.21364E+11 69569522441 16846809.7 0.029582043 0.10638258 0.97312948 -0.340809938 GIAFPTSISVNNCVCHFSPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIAFPTSISVNNCVCHFSPLK 21 0 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7;F8VZ69 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 205.68 4.62E-22 141600000 173400 317500 256780 242670 321370 207070 314620 322830 295940 FALSE TRUE 162547.2035 341008.0304 262870.9429 248897.323 296130.8965 266847.7475 267445.6518 363136.0361 246545.7022 0.659298467 1.383143277 1.06621588 1.009538276 1.201119687 1.082345971 1.084771097 1.472895422 1 17.91149558 GIAPAS(ph)PMLGNASNPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 277.69 4.47E-27 0 119670 105540 104790 107810 112490 93011 142270 97140 91708 TRUE FALSE 112180.0683 113354.2914 107275.6683 110576.5871 103655.4892 119861.7658 120937.9343 109268.1428 76401.34234 1.468299704 1.483668846 1.404107114 1.447312099 1.356723403 1.568843716 1.582929443 1.430186165 1 16.22131037 0.95829719 23.59582377 0.999999999 1.474817404 0.829327551 0.066959912 2018.534659 1142106.441 0.070253346 0.017563336 9.084419692 -0.95829719 0.474817405 GIAPAS(ph)PMLGNASNPNKADIPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GIAPASPMLGNASNPNKADIPER 23 1 H0YIY6;P27448-6;P27448-7;H0YKP9;J3KNR0;P27448-8;P27448-3;P27448-4;P27448-2;P27448 H0YIY6;J3KNR0 MARK3 MAP/microtubule affinity-regulating kinase 3 1 GIAPAS(1)PMLGNASNPNKADIPER;GIAPAS(1)PMLGNASNPNKADIPER;GIAPAS(0.772)PMLGNAS(0.228)NPNKADIPER 196.22 1.93E-24 646920000 1130040 1080180 1100440 1106700 1383080 979820 1576360 1123460 1714050 TRUE FALSE 1059312.814 1160157.651 1126542.956 1135099.796 1274458.476 1262678.128 1339999.452 1263726.454 1427963.982 0.741834407 0.812455822 0.788915526 0.794907862 0.892500436 0.884250684 0.938398636 0.884984825 1 20.44552816 2.214223496 0.397394916 0.995840042 0.751106517 0.850265429 0.029842209 0.43070366 0.159689953 0.031727972 0.036680698 163.7659075 -2.214223496 -0.244733525 GIAYIEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIAYIEFK 8 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 135.16 0.0019674 197335000 502180 1061900 372700 389670 1210610 246960 439030 1011970 1134510 FALSE TRUE 470749.4502 1140524.181 381540.62 399669.5919 1115533.574 318253.3429 373201.5273 1138316.682 945152.9518 0.498066952 1.206708585 0.40368135 0.422862343 1.180267778 0.336721525 0.394858342 1.204372985 1 19.85018829 1.226101401 24.9960775 1.102186739 0.651911564 0.270517614 0.31815712 364.2851146 730818.1953 0.292548558 0.075203078 16.83066987 -1.226101401 -0.450275174 GIDIHGVPYVINVTLPDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GIDIHGVPYVINVTLPDEK 19 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;; 196.06 8.53E-16 495460000 1443250 1142570 1281600 1232140 1420320 1131140 1640090 1186930 1690350 FALSE TRUE 1352919.559 1227167.072 1312000.157 1263758.798 1308773.796 1457681.755 1394173.73 1335120.823 1408219.665 0.960730483 0.871431569 0.931672941 0.897415957 0.929381849 1.035123846 0.99002575 0.948091307 1 20.42544096 2.388928965 6.390372822 0.993394094 0.910983824 0.596907978 0.03077376 0.129103604 7.674617928 0.010008528 0.008344355 244.8662695 -2.388928965 -0.08241027 GIDLLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIDLLKK 7 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 98.299 0.036712 0 868220 856340 798670 810830 1083510 628970 931550 834110 1192010 FALSE TRUE 813879.66 919744.3046 817614.8296 831637.2705 998415.4953 810543.4285 791872.7256 938250.4696 993055.8303 0.819570899 0.926175827 0.823332188 0.837452684 1.005397144 0.816211339 0.797410076 0.9448114 1 19.9215153 1.0263372 6.792302233 0.999900628 0.862365366 0.374393816 0.062245426 0.151055315 23.63269656 0.057939365 0.014538376 10.62520212 -1.0263372 -0.137535263 GIDPFSLDALSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIDPFSLDALSK 12 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 103.43 0.0024331 0 183760 182520 175490 183550 199080 157290 199380 178310 205530 FALSE TRUE 172258.7896 196033.9707 179652.7057 188260.2037 183445.0599 202697.0696 169484.82 200572.396 171225.7152 1.006033407 1.144886272 1.049215683 1.099485574 1.071363957 1.183800397 0.989832746 1.171391784 1 17.38553986 -1.280988996 5.164226692 0.999983054 1.087540759 0.158468844 0.064677751 1.08E-05 1.51E-06 0.053839046 0.012687529 0.05236137 1.280988996 0.087557705 GIEEEEILPGFILCDPNNLCHSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GIEEEEILPGFILCDPNNLCHSGR 24 0 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ;;;;;; 300.06 3.80E-62 1811330000 1871426 1790365 1967183 1958316 1917975 1980622 2235752 1744127 1800380 FALSE TRUE 1754296.787 1922925.487 2013845.51 2008569.704 1767344.98 2552395.419 1900521.743 1961885.095 1499884.947 1.169620904 1.282048661 1.342666658 1.339149185 1.178320366 1.701727472 1.267111685 1.308023725 1 20.51642041 0.61236419 2.426884719 1.00006784 1.332643896 0.325032855 0.146616807 3.903292965 23.05423653 0.129120359 0.034594795 4.096040009 -0.61236419 0.332576055 GIEESLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIEESLR 7 0 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PQV5;A0A1W2PQC2;A0A1W2PRT2;A0A1W2PP40;A0A1W2PQ55 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 114.19 0.013869 145480000 283110 322520 295720 268850 416710 280880 247810 332240 405390 FALSE TRUE 265390.6505 346399.7164 302734.618 275749.1462 383983.2775 361965.4963 210653.1911 373720.8954 337727.7901 0.785812297 1.025677266 0.89638646 0.816483435 1.136960857 1.071766988 0.623736622 1.106574307 1 18.36550137 GIEESLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIEESLRK 8 1 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PQV5;A0A1W2PQC2;A0A1W2PRT2;A0A1W2PP40;A0A1W2PQ55 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 ; 105.14 0.0071289 594410000 332960 410370 331550 327680 590450 294020 362430 405510 791250 FALSE TRUE 312120.628 440754.2218 339414.5226 336088.8236 544078.4388 378898.801 308086.9861 456138.8161 659185.2633 0.473494547 0.668634823 0.514900046 0.50985488 0.825380161 0.574798652 0.467375415 0.691973625 1 19.33032446 0.972174145 15.75942876 1.000000004 0.579756242 0.613070883 0.106075767 12.11426891 6861.815926 0.09737469 0.024344182 9.379380285 -0.972174145 -0.420243762 GIEFEDESS(ph)DRDARPALETQPQQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIEFEDESSDRDARPALETQPQQEK 25 2 D6RB01;Q9Y6X4 D6RB01 FAM169A Soluble lamin-associated protein of 75 kDa 1 GIEFEDES(0.136)S(0.864)DRDARPALETQPQQEK;GIEFEDES(0.244)S(0.756)DRDARPALETQPQQEK 219.65 6.84E-34 246240000 276874 228652 247767 233936 282770 202332 274590 241359 448940 TRUE FALSE 259544.9506 245581.632 253644.1502 239939.1938 260562.3848 260741.9638 233417.7787 271493.2024 374009.0137 0.693953731 0.656619555 0.67817657 0.641533185 0.696674078 0.697154224 0.624096666 0.725900159 1 18.51271351 0.886682859 5.992441977 0.999997096 0.66863353 0.948394497 0.024043348 0.303011737 15.92282666 0.021535198 0.005415423 7.703407272 -0.886682859 -0.331363566 GIEGHS(ph)PGNLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GIEGHSPGNLPK 12 0 Q96GY0;H0YAP0 Q96GY0 ZC2HC1A Zinc finger C2HC domain-containing protein 1A 1 GIEGHS(1)PGNLPK;GIEGHS(1)PGNLPK;GIEGHS(1)PGNLPK;GIEGHS(1)PGNLPK 183.81 9.75E-06 2474830000 4768820 4014360 4390080 4635700 4832800 3387240 4868390 3107200 4513720 TRUE FALSE 4470348.069 4311587.391 4494214.771 4754659.91 4453251.383 4365081.201 4138420.115 3495140.76 3760350.972 1.188811391 1.146591747 1.195158325 1.264419185 1.184264824 1.160817496 1.100540919 0.929471952 1 21.84243589 1.477118058 2.465614632 0.964656398 1.189081451 0.862718565 0.036621254 0.093956525 1.113301512 0.029321962 0.009793676 29.99977919 -1.477118058 0.224425053 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLS(ph)VHTPTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLSVHTPTLR 41 0 Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha 1 GIEHQDSQHSFLAFLNTPTDALDQFET(0.008)VDS(0.115)T(0.115)PLS(0.389)VHT(0.302)PT(0.07)LR 115.41 1.37E-06 62655000 22247 45046 36878 37228 37476 30779 38181 47214 48048 TRUE FALSE 20854.59998 48381.25271 37752.76358 38183.33351 34532.78613 39664.39764 32456.11351 53108.77183 40028.4784 0.520994073 1.208670793 0.943147606 0.953904196 0.862705442 0.990904457 0.810825562 1.326774685 1 15.28873916 1.244874795 24.99972524 1.163387353 0.932753637 0.23806497 0.189378314 204.186789 808461.0431 0.122542896 0.042308812 17.57416888 -1.244874795 -0.230633716 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLSVHT(ph)PTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLSVHTPTLR 41 0 Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha 1 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLSVHT(0.996)PT(0.004)LR;GIEHQDSQHSFLAFLNTPTDALDQFETVDS(0.028)T(0.021)PLS(0.005)VHT(0.926)PT(0.02)LR 402.35 3.68E-213 259810000 41325 101217 88389 86440 124567 81838 102835 105532 108294 TRUE FALSE 38738.54202 108711.212 90485.62882 88658.19674 114784.0103 105463.3021 87415.84642 118707.9025 90219.03179 0.42938326 1.204969837 1.002954998 0.982699492 1.272281558 1.168969562 0.968929113 1.315774512 1 16.46114418 4.743711798 24.88275411 1.105861771 0.429382958 0.746806557 0.125290753 250.9171199 1212012.698 0.027617698 0.23474709 55425.77804 -4.743711798 -0.676478812 GIEHSLIEENCGVVVESIQVTLECGLGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIEHSLIEENCGVVVESIQVTLECGLGHR 29 0 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 0 88.517 0.001017 17419000 5268 5663.5 5591.9 5653.9 6968.5 4967.1 6167.5 5610 6078.7 FALSE TRUE 4938.285284 6082.831433 5724.542509 5798.988646 6421.22212 6401.021136 5242.740631 6310.420849 5064.1257 0.975150614 1.201161226 1.130410825 1.145111514 1.267982372 1.263993336 1.035270635 1.246102728 1 12.3060975 -1.165884585 4.106103884 0.999941166 1.157986844 0.212516703 0.095672703 4.75E-05 9.64E-06 0.084553661 0.019922007 0.068252005 1.165884585 0.158045677 GIEILTDMSRPVELSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 GIEILTDMSRPVELSDR 17 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;;;;;;;;;; 283.31 3.88E-36 8472873000 5703769 6279686 6356927 6169234 6143137 6297582 6857443 5872619 4960173 FALSE TRUE 5346780.28 6744640.485 6507716.31 6327546.989 5660679.8 8115591.691 5829233.084 6605828.409 4132288.082 1.293903081 1.632180611 1.574845747 1.531245369 1.369865723 1.963946252 1.410655058 1.598588549 1 21.9785094 -1.016570863 4.771448065 0.999988651 1.558901065 0.468794419 0.182562267 1.93E-05 3.97E-06 0.15459954 0.036438722 0.096256294 1.016570863 0.558912414 GIEILTDMSRPVELSDRETLLNSATTSLNSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIEILTDMSRPVELSDRETLLNSATTSLNSK 31 2 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 77.791 0.0013662 25371000 14370 20972 18715 18818 27586 14843 22690 16604 34725 FALSE TRUE 13470.60735 22524.7887 19158.92864 19300.90174 25419.50684 19127.93314 19287.84514 18677.04595 28929.17317 0.465640939 0.778618475 0.662270177 0.667177787 0.878680724 0.66119875 0.666726457 0.64561285 1 14.82023747 -2.08821493 2.444204868 1.510967999 0.689025477 0.48111672 0.104480764 8539759.249 2445248.766 24310049.9 0.024234069 0.008161783 2.08821493 -0.821942521 GIEKPPFELPDFIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIEKPPFELPDFIKR 15 2 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 0 76.391 0.01631 146710000 564140 449390 507660 485840 591400 379280 631540 478080 765890 FALSE TRUE 528831.4844 482663.3032 519701.9349 498307.4769 544953.8296 488771.9789 536846.4399 537769.3404 638058.0112 0.828814113 0.756456772 0.814505775 0.780975191 0.854081949 0.766030628 0.841375597 0.842822018 1 19.28332807 -0.213070925 0.449811266 1.032952479 0.790835282 0.804290266 0.030182943 2.146208152 0.479586747 0.143597483 0.015154502 0.612250397 0.213070925 -0.242117197 GIELAVRPHSAPEYEDETMTVYQIPIHSEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIELAVRPHSAPEYEDETMTVYQIPIHSEQR 31 1 Q9BQ52;G5E9D5;Q9BQ52-2;V9GYS7;J3QRS2;V9GYU5;J3QL08 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 0 ; 179.74 2.26E-18 282960000 72662 82773 76270 77856 101992 77552 93126 81265 123967 FALSE TRUE 68114.21513 88901.59905 78079.16042 79853.91677 93981.95974 99940.00345 79162.62084 91411.11414 103276.1068 0.659535077 0.860814779 0.756023468 0.773208046 0.910006802 0.967697239 0.766514378 0.885113865 1 16.656147 2.744895281 24.26692509 0.886434926 0.777736595 0.434704096 0.078743225 408.8239315 1566128.296 0.02339263 0.024250678 555.7702316 -2.744895281 -0.108698331 GIEQAVQSHAVAEEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIEQAVQSHAVAEEEAR 17 0 C9J406;B9A067;Q16891-2;Q16891-4;Q16891;H7C463;Q16891-3 C9J406 IMMT MICOS complex subunit MIC60 0 103.73 0.00088505 86374000 23153 50792 39469 39194 44616 38549 32099 38068 37229 FALSE TRUE 21703.89506 54552.69253 40405.22332 40199.7844 41112.03933 49677.47051 27286.05294 42820.8736 31015.23939 0.699781639 1.758899612 1.302753876 1.29613007 1.325543189 1.601711658 0.879762771 1.38063979 1 14.92068964 1.736640042 25 1.090146898 1.375428238 0.117338769 0.299181332 0.428300706 5431.242192 0.125573725 0.069636984 54.53057054 -1.736640042 0.28528134 GIEYSRVS(ph)PQPMISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIEYSRVSPQPMISR 15 1 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 GIEYSRVS(1)PQPMISR;GIEYS(0.002)RVS(0.998)PQPMISR 191.61 1.02E-07 536790000 345030 386160 367940 361050 476050 339570 383400 329590 658560 TRUE FALSE 323435.1882 414751.6882 376667.7106 370315.1543 438662.9533 437598.3465 325912.7293 370740.037 548642.0815 0.589519468 0.755960401 0.686545424 0.674966735 0.799543032 0.797602592 0.594035238 0.675741161 1 19.06550576 -1.287160716 3.589671318 1.000825998 0.700146149 0.632691588 0.07257571 1029819852 1716867609 9381625.369 0.01693889 0.05162253 1.287160716 -0.300679849 GIFEALRPLETLPVEGLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIFEALRPLETLPVEGLIR 19 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 169.39 1.30E-11 280650000 116810 171280 150770 170840 170630 141840 174670 155260 143320 FALSE TRUE 109499.0706 183961.7494 154346.3356 175224.0436 157229.4081 182786.9054 148479.8551 174644.5528 119398.9661 0.917085584 1.54073151 1.292694071 1.467550761 1.316840616 1.530891861 1.243560643 1.462697362 1 16.86543082 -0.530251319 8.268451343 1.000000007 1.361279576 0.258970077 0.182694432 0 0 0.151195101 0.035637027 0.29495019 0.530251319 0.361279569 GIFEPFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIFEPFGR 8 0 Q14498-2;Q14498;G3XAC6;H0Y4X3;A0A0U1RQH7;A0A0U1RQW2;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 0 ; 157.21 0.00088539 704720000 1242430 1508480 1366990 1311590 1500200 1303350 1559260 1315760 1681130 FALSE TRUE 1164668.524 1620169.429 1399415.648 1345247.62 1382380.344 1679605.987 1325463.438 1480035.532 1400538.542 0.8315862 1.15681888 0.999198241 0.96052167 0.987034845 1.19925724 0.946395546 1.056761729 1 20.41755026 GIFGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIFGFR 6 0 Q9UHB9;Q9UHB9-4;Q9UHB9-2;Q9UHB9-3 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 159.55 0.021132 104570000 148100 269290 181120 204760 256720 165590 207540 229220 221880 FALSE TRUE 138830.6854 289228.5118 185416.2519 210014.4883 236558.2468 213393.1449 176421.3037 257838.6216 184846.7946 0.751058116 1.564693142 1.003080699 1.136154342 1.279753037 1.154432487 0.954419059 1.394877429 1 17.4959705 -5 0.23951486 0.073943587 1.182235812 0.022191556 0.230515968 614.6662719 6.134453647 277.876251 0.335236015 1.00E-05 5 1.108292225 GIFLGDDEWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GIFLGDDEWR 10 0 Q8TB72-3;Q8TB72;Q8TB72-2;C9JW01 Q8TB72-3 PUM2 Pumilio homolog 2 0 ;; 157.91 1.94E-05 138488000 169791 213193 225524 193526 213898 165708 206684 169355 222165 FALSE TRUE 159164.0844 228978.0315 230873.5358 198492.2048 197099.3139 213545.2096 175693.653 190499.3445 185084.2263 0.859954884 1.237155841 1.247397147 1.072442578 1.064916865 1.153773144 0.949263244 1.029257589 1 17.49782242 1.75091728 11.95661916 0.99302939 1.134540014 0.156907202 0.111068551 0.18191092 143.4792149 0.052113127 0.028573008 56.35303099 -1.75091728 0.141510624 GIFPVLCKDPVQEAWAEDVDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GIFPVLCKDPVQEAWAEDVDLR 22 1 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;; 246.22 5.54E-31 20321232000 9010815 9852968 8871417 9130640 10671625 7598989 11409041 8357788 10382112 FALSE TRUE 8446844.174 10582492 9081851.201 9364947.681 9833518.62 9792693.765 9698361.218 9401276.23 8649270.436 0.976596146 1.223512674 1.050013555 1.082744233 1.136918853 1.132198818 1.121292401 1.086944419 1 23.04414702 0.864852211 3.927850635 1.000017583 1.111999236 0.194169454 0.063762921 1.073898311 28.72692227 0.054963863 0.014065587 7.325751986 -0.864852211 0.111981653 GIGEFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIGEFFR 7 0 H0YKX3;H0YMA4;A0A0U1RQM0;Q15004 H0YKX3 KIAA0101 PCNA-associated factor 0 104.11 0.019134 81175000 254190 220420 189570 195080 231110 123100 280830 173820 263880 FALSE TRUE 238280.7016 236740.1261 194066.6899 200086.0831 212959.5529 158636.9716 238722.1486 195521.8096 219836.7233 1.083898532 1.076890715 0.882776485 0.910157685 0.968716917 0.721612701 1.085906599 0.889395578 1 17.74607288 4.107886568 3.151430195 0.925145112 1.083189924 0.330014025 0.093229279 0.277681638 5.271818941 0.022124399 0.056227849 12819.95698 -4.107886568 0.158044812 GIGEFFRLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIGEFFRLSPK 11 1 H0YKX3;H0YMA4;A0A0U1RQM0;Q15004 H0YKX3 KIAA0101 PCNA-associated factor 1 GIGEFFRLS(1)PK;GIGEFFRLS(1)PK 93.823 0.0054279 650430000 438830 400460 403780 360540 581920 265110 444600 435870 944870 TRUE FALSE 411364.4136 430110.4751 413357.8523 369792.0668 536218.3506 341642.9533 377936.3575 490289.329 787165.0929 0.522589756 0.546404406 0.525122183 0.469777014 0.681201892 0.4340169 0.48012337 0.622854511 1 19.58630672 0.863170025 4.167342972 0.999950237 0.523115795 0.839746974 0.065224331 0.308474601 8.861277502 0.058413512 0.014892985 7.297431474 -0.863170025 -0.476834443 GIGIENIHYLNDGLWHMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIGIENIHYLNDGLWHMK 18 0 Q9ULC4-2;Q9ULC4;Q9ULC4-3;A0A3B3IRV3 Q9ULC4-2 MCTS1 Malignant T-cell-amplified sequence 1 0 ; 207.56 4.22E-16 414220000 754330 911110 760520 761280 1141740 686700 920130 822080 1070340 FALSE TRUE 707117.8318 978569.5324 778559.8935 780815.7336 1052072.346 884939.1424 782165.0486 924718.4976 891693.3393 0.793005623 1.09742833 0.873125164 0.875655003 1.179858926 0.992425426 0.877168208 1.037036453 1 19.76618812 GIGLDESELDS(ph)EAELMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIGLDESELDSEAELMR 17 0 Q96RS0 Q96RS0 TGS1 Trimethylguanosine synthase 1 GIGLDESELDS(1)EAELMR 409.05 2.56E-109 0 152450 188050 166610 162110 182560 157150 207660 154700 176700 TRUE FALSE 142908.4266 201973.4177 170562.0679 166270.0171 168222.474 202516.6539 176523.3108 174014.6355 147207.6285 0.970794979 1.372030918 1.158649655 1.129493212 1.142756498 1.37572119 1.19914513 1.182103382 1 17.16749291 0.750940962 3.044043185 1.000039097 1.21105464 0.195083411 0.117825501 2.501693663 28.73367624 0.103472881 0.027030322 5.635610403 -0.750940962 0.211015543 GIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK 33 1 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;; 276.19 1.01E-73 1336680000 856100 1035770 785780 670381 1221660 762940 963890 1036060 710695 FALSE TRUE 802518.2292 1112459.489 804419.0727 687584.1114 1125715.752 983188.3927 819363.6428 1165414.372 592075.4132 1.355432452 1.878915192 1.358642927 1.161311711 1.901304676 1.660579667 1.383883918 1.968354614 1 19.17542142 -1.17209278 5.704968612 0.999989107 1.575865153 0.312963168 0.271510621 3.46E-05 5.02E-06 0.241715807 0.056971886 0.06728329 1.17209278 0.575876046 GIHDADAEAR ddPTM_SK-BR-3_Pertuzumab_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 88.596 0.012086 99897000 99573 68959 55898 64761 84260 54322 72918 55041 77699 FALSE TRUE 93340.90367 74064.79611 57223.92696 66422.8769 77642.55949 70003.87956 61984.62284 61912.99001 64730.53495 1.441991847 1.144201823 0.884032968 1.026144415 1.199473472 1.081466106 0.957579339 0.956472707 1 15.98215881 4.689889121 2.303737338 1.016583639 1.520550194 0.723133006 0.083619687 0.29323156 2.019775709 0.021949165 0.286024334 48965.3791 -4.689889121 0.503966555 GIHNSIGDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIHNSIGDYR 10 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 102.52 0.0029357 378980000 799800 927540 858820 841030 945330 839820 1034030 711700 941030 FALSE TRUE 749741.9457 996216.0267 879191.616 862612.2537 871087.5951 1082262.401 878986.801 800557.3116 783966.0137 0.95634496 1.270738794 1.121466493 1.10031843 1.111129283 1.38049658 1.121205238 1.021163287 1 19.58043159 1.289159374 4.526239583 1.007155027 1.168343208 0.215424584 0.111260728 0.260052724 10.08997983 0.080025584 0.025892558 19.46074106 -1.289159374 0.161188181 GIHPTIISESFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIHPTIISESFQK 13 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 269.04 6.62E-25 1814700000 2549500 3213100 2940600 3029600 3657300 2351600 3448800 3368800 3680000 FALSE TRUE 2389931.346 3451001.267 3010352.421 3107344.665 3370070.411 3030468.745 2931684.457 3789402.096 3065784.226 0.779549756 1.125650409 0.981919208 1.013556218 1.099252316 0.988480767 0.956259228 1.236030267 1 21.54782473 4.750407755 24.71206095 1.040784747 0.779549571 0.499584725 0.084650699 1329.958396 2774113.036 0.018627993 0.305357462 56286.95503 -4.750407755 -0.261235176 GIIRPGTAFELLEAQAATGYVIDPIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIIRPGTAFELLEAQAATGYVIDPIK 26 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 145.2 2.10E-07 76236000 139450 147640 154690 158360 163870 108510 195500 142540 119380 FALSE TRUE 130722.0734 158571.4192 158359.3198 162423.7857 151000.3112 139835.0755 166186.5899 160336.4328 99454.70678 1.314388003 1.594408393 1.59227577 1.633143277 1.518282202 1.406017674 1.670977627 1.612155301 1 16.60175203 -0.849487287 7.823191181 0.999999999 1.556191482 0.707856694 0.109265326 1.46E-09 1.87E-10 0.098092138 0.023120539 0.141420612 0.849487287 0.556191483 GIITDS(ph)FGR ddPTM_SK-BR-3_Pertuzumab_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 179.57 5.21E-05 745161000 1029880 1291830 1215040 1135150 1407970 1082770 1285030 1216370 1510410 TRUE FALSE 965421.6492 1387478.437 1243861.323 1164279.871 1297393.716 1395348.122 1092351.681 1368236.472 1258312.813 0.767235014 1.102649852 0.988515184 0.925270615 1.031058177 1.108904008 0.868108208 1.087357975 1 20.26305919 4.752945714 24.79262899 1.008717429 0.767234826 0.505321804 0.076567 1988.637267 3427338.534 0.017520802 0.380342086 56616.85144 -4.752945714 -0.241482603 GILAADES(ph)TGSIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GILAADESTGSIAK 14 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 GILAADES(0.837)T(0.155)GS(0.008)IAK;GILAADES(0.958)T(0.042)GSIAK;GILAADES(0.945)T(0.055)GSIAK;GILAADES(0.862)T(0.137)GSIAK;GILAADES(0.87)T(0.13)GSIAK 306.15 1.78E-44 888747000 2153544 2421773 1606596 1524266 2449200 1305403 2370836 2074654 2486537 TRUE FALSE 2018757.525 2601083.593 1644705.216 1563381.246 2256849.712 1682251.655 2015351.152 2333679.119 2071517.911 0.974530567 1.255641372 0.793961378 0.754703224 1.089466666 0.812086464 0.972886182 1.126555125 1 20.98225686 3.976940602 24.99927912 0.927223383 1.121369842 0.221661566 0.138967081 10.6026713 1467616.129 0.032655844 0.064071873 9482.887584 -3.976940602 0.194146458 GILAADEST(ph)GSIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GILAADESTGSIAK 14 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 GILAADES(0.143)T(0.463)GS(0.394)IAK 198.16 2.51E-07 106670000 418440 405160 319480 312340 430870 256270 507940 356700 475130 TRUE FALSE 392250.5873 435158.468 327058.2165 320355.1732 397031.2082 330250.9888 431779.1125 401234.7802 395827.7335 0.990962871 1.099363261 0.826264025 0.809329782 1.0030404 0.834330091 1.090825821 1.013660101 1 18.59451317 1.701545216 11.93635805 1.038291995 0.933853945 0.228043976 0.092670189 0.19307644 48.96761823 0.04466517 0.024415966 50.29736295 -1.701545216 -0.10443805 GILAADESTGS(ph)IAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GILAADESTGSIAK 14 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 GILAADES(0.001)T(0.053)GS(0.945)IAK;GILAADES(0.002)T(0.005)GS(0.992)IAK 156.96 5.69E-06 152409000 458680 461320 369660 369460 507030 289460 511450 373090 524260 TRUE FALSE 429972.0376 495476.6128 378428.5098 378940.9691 467209.9091 373022.403 434762.8206 419671.1078 436757.6192 0.984463736 1.134442975 0.866449704 0.86762303 1.069723546 0.854071885 0.99543271 0.960878733 1 18.73647335 3.978300928 24.99189505 0.943445391 1.061451197 0.277625129 0.076790521 60.89041345 1289935.152 0.017478649 0.034765493 9512.637066 -3.978300928 0.118005806 GILAADESTGS(ph)IAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GILAADESTGSIAKR 15 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 GILAADESTGS(1)IAKR;GILAADES(0.007)T(0.174)GS(0.819)IAKR;GILAADEST(0.001)GS(0.999)IAKR;GILAADESTGS(1)IAKR 244.27 3.09E-18 1144900000 1267041 1196168 1078128 1132674 1358550 857968 1563159 1003192 1838180 TRUE FALSE 1187739.166 1284733.523 1103701.705 1161740.332 1251854.963 1105649.434 1328777.82 1128442.729 1531375.883 0.775602632 0.838940679 0.720725537 0.758625198 0.817470731 0.721997418 0.867701937 0.736881612 1 20.54639701 -4.999994432 0.406563836 4.650963474 0.779777868 0.656460558 0.049774429 476.6414024 3.254021718 1547.912475 0.028001221 1.00E-05 4.999994432 -3.871185606 GILAADESTGSIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GILAADESTGSIAK 14 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ; 240.8 4.80E-17 177884000 445330 441040 420490 417250 477540 332510 513200 408780 430280 FALSE TRUE 417457.5902 473695.0605 430464.2214 427957.3414 440035.9347 428500.2392 436250.4243 459817.0828 358463.4883 1.164574926 1.321459719 1.200859322 1.193865918 1.227561381 1.195380431 1.217001002 1.282744541 1 18.45146665 -1.427564475 2.993907635 0.995580975 1.228730536 0.704888123 0.045796267 4917247.239 5734704.268 183113.9318 0.010918726 0.037362465 1.427564475 0.233149562 GILAADESTGSIAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GILAADESTGSIAKR 15 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ; 211.94 1.81E-09 1588060000 1141460 1181520 1406420 1661060 1222630 1045520 1595070 861410 1908470 FALSE TRUE 1070018.056 1269000.97 1439780.947 1703685.612 1126609.572 1347344.651 1355904.061 968958.9347 1589934.028 0.672995255 0.798146934 0.905560181 1.071544845 0.70858888 0.847421734 0.852805234 0.609433422 1 20.60053547 -0.450368998 8.032951328 0.999999998 0.824830284 0.166704652 0.130107696 0 0 0.117568629 0.027711192 0.35451205 0.450368998 -0.175169714 GILADEDSSRPVWLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 240.2 7.16E-18 54528850000 30427200 31178510 34573640 34368400 37198850 29423960 44145930 33165890 40090960 FALSE TRUE 28522815.87 33486999.32 35393743.07 35250351.33 34277402.37 37918179.59 37526657.63 37306724.37 33399519.78 0.853988801 1.002619186 1.059708143 1.055414915 1.026284288 1.135291161 1.123568778 1.116983855 1 24.99332402 5.917742576 0.639930822 1.091412967 3.71E-16 0.714574232 0.043759802 6.702180886 0.653287565 0.017225136 7.537553389 827451.5542 -5.917742576 -1.091412967 GILFVGSGVSGGEEGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GILFVGSGVSGGEEGAR 17 0 P52209-2;P52209;K7EM49;K7EPF6;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 133.32 4.71E-05 0 57334 58488 50970 58579 59452 47145 65732 48964 62243 FALSE TRUE 53745.56728 62818.51238 52179.03247 60082.23631 54782.87974 60754.99616 55876.09683 55077.26318 51854.24119 1.036473894 1.211444058 1.006263543 1.158675451 1.056478284 1.171649508 1.077560785 1.062155417 1 15.66217437 1.006947736 1.920214934 1.001337322 1.10757428 0.218640093 0.063240966 0.474272724 3.67018424 0.05333554 0.015061173 10.16126403 -1.006947736 0.106236958 GILGYTEHQVVSSDFNSDTHSSTFDAGAGIALNDHFVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 36 GILGYTEHQVVSSDFNSDTHSSTFDAGAGIALNDHFVK 38 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 352.05 1.07E-145 8160653300 1585105.6 3880446 3453011.6 3789455.5 3899252.1 3386487.7 3697266.1 3270372.8 2887770.4 FALSE TRUE 1485896.67 4167758.259 3534918.666 3886699.344 3593020.569 4364111.724 3142895.372 3678686.043 2405782.865 0.617635403 1.732391697 1.469342357 1.615565312 1.493493291 1.814008982 1.306391952 1.52910144 1 21.19807501 -0.398489194 1.234529211 0.994892279 1.485409671 0.145475013 0.328908074 89.06520775 73.48834319 2.692869547 0.083718488 0.399494502 0.398489194 0.490517392 GILHLS(ph)PDVYQEMEASR ddPTM_SK-BR-3_Pertuzumab_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 257.96 2.44E-27 444228000 493323 544990 568810 540190 607080 482002 569040 490450 625730 TRUE FALSE 462446.794 585341.6267 582302.4418 554052.1899 559402.3856 621148.1528 483717.7347 551683.7621 521291.6206 0.88711726 1.122867899 1.117037794 1.062844995 1.07310834 1.191555989 0.927921562 1.058301611 1 18.99173114 1.722357047 24.99999906 0.994608734 1.08535668 0.165782272 0.083118244 1.374706542 2112.504416 0.035309249 0.019580727 52.7663492 -1.722357047 0.090747946 GILHTDSQSQS(ph)LR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GILHTDSQSQSLR 13 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 GILHTDS(0.009)QS(0.04)QS(0.952)LR;GILHTDS(0.001)QS(0.144)QS(0.855)LR 153.72 2.95E-05 422210000 465850 777220 700530 680390 878160 686630 842140 847690 988380 TRUE FALSE 436693.2801 834766.1775 717146.9024 697849.9593 809192.8559 884848.9345 715868.925 953525.9625 823412.9928 0.530345384 1.013787959 0.87094436 0.847509045 0.98273025 1.074611334 0.869392311 1.158016658 1 19.65125669 4.742752984 24.99310606 0.961971234 0.530345214 0.672167607 0.097548876 248.5286952 1481567.361 0.02150838 0.167046242 55303.54664 -4.742752984 -0.431626019 GILLEDGSES(ph)PAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GILLEDGSESPAKR 14 1 Q08999;Q08999-2 Q08999 RBL2 Retinoblastoma-like protein 2 1 GILLEDGS(0.001)ES(0.999)PAKR 139.49 6.25E-06 73462000 147740 120480 118890 130920 141710 108260 184570 127570 159510 TRUE FALSE 138493.2171 129400.4646 121710.1269 134279.6288 130580.6682 139512.9045 156895.442 143497.3953 132886.7505 1.042189809 0.973764984 0.91589362 1.010481694 0.982646259 1.049863165 1.180670318 1.079847274 1 17.01983774 2.092826212 3.728089335 1.108684449 0.975156087 0.393359208 0.055259069 0.164800245 4.422475079 0.021762364 0.014996223 123.8300967 -2.092826212 -0.133528361 GILRT(ph)PDTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GILRTPDTIR 10 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 1 GILRT(1)PDTIR;GILRT(1)PDTIR 147.33 4.38E-05 552050000 219120 400600 321170 372940 436840 240450 323830 294450 439780 TRUE FALSE 205405.6703 430260.8408 328788.3041 382510.2718 402532.3485 309864.0116 275274.6978 331212.7307 366377.8769 0.560638847 1.174363595 0.897402176 1.044032121 1.098680826 0.845749788 0.751340938 0.904019461 1 18.48297287 2.143134846 12.36372116 0.842849625 0.981096475 0.02314198 0.175037488 1.059383748 130.8966707 0.05985505 0.044206153 139.0384269 -2.143134846 0.13824685 GILSGTSDLLLTFDEAEVRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GILSGTSDLLLTFDEAEVRK 20 1 P18206;P18206-2;P18206-3 P18206 VCL Vinculin 0 ; 146.18 2.19E-07 132090000 205084 173137 182623 195300 211828 156804 225555 161372 223951 FALSE TRUE 192248.1585 185956.2436 186954.9038 200311.7286 195191.8834 202070.7693 191735.1217 181519.6494 186572.1313 1.030422696 0.99669893 1.002051606 1.073642281 1.046200641 1.083070488 1.027672892 0.972919418 1 17.50937398 3.302225697 24.99996649 1.03865992 1.005836969 0.091001355 0.033153424 105.7208064 41512.98116 0.008864944 0.012003188 2005.513996 -3.302225697 -0.032822951 GILSLPHQAS(ph)PVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GILSLPHQASPVSR 14 0 O75925;O75925-2 O75925 PIAS1 E3 SUMO-protein ligase PIAS1 1 GILSLPHQAS(1)PVSR;GILSLPHQAS(1)PVSR;GILSLPHQAS(0.997)PVS(0.003)R 193.27 1.79E-07 550240000 563580 677080 696010 660090 789500 678420 788500 646010 682890 TRUE FALSE 528306.5338 727211.7077 712519.6859 677029.0269 727495.8547 874268.8408 670271.7451 726665.7705 568911.2474 0.928627332 1.278251592 1.252426787 1.190043315 1.27875105 1.5367403 1.178165748 1.277291975 1 19.11784408 4.740011819 23.69156186 1.264944569 0.928627096 0.360921189 0.132449638 59.67496465 974008.084 0.028222099 0.177096825 54955.58298 -4.740011819 -0.336317474 GILTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GILTLK 6 0 C9JTX5;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6;Q6S8J3;A5A3E0;P0CG38;P0CG39 C9JTX5;P60709;P63261;P68133;Q6S8J3 ACTB;ACTG1;ACTA1;ACTC1;ACTG2;ACTA2;POTEE;POTEF;POTEI;POTEJ "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, gamma-enteric smooth muscle;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I;POTE ankyrin domain family member J" 0 ; 142.63 0.026758 1765340000 4151000 4277300 4081700 4069800 4546100 3571600 5020700 4067000 4547600 FALSE TRUE 3891196.32 4593995.743 4178519.852 4174237.958 4189067.644 4602662.94 4267892.645 4574773.903 3788576.181 1.02708673 1.212591623 1.102926179 1.101795967 1.105710284 1.214879342 1.126516253 1.207517992 1 21.85322433 -1.210502515 5.464928402 0.999993148 1.141381734 0.339074674 0.060045721 4.46E-06 6.44E-07 0.051698067 0.012184761 0.061588196 1.210502515 0.141388586 GIMVLAGDTLPIEVYCHLPVMCEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIMVLAGDTLPIEVYCHLPVMCEDR 25 0 D6RC52;D6RCB9;Q9NX24;H0YC83 D6RC52 NHP2 H/ACA ribonucleoprotein complex subunit 2 0 ; 265.23 2.48E-45 353640000 184847 242260 191395 190644 233980 173729 240550 184824 226420 FALSE TRUE 173277.7562 260197.1825 195934.9798 195536.2478 215604.1546 223881.742 204481.7607 207899.6832 188629.0393 0.918616544 1.379412117 1.038731791 1.036617949 1.143006164 1.186889054 1.084041786 1.102161597 1 17.52519227 -4.662996048 0.164483883 0.553662662 1.163325335 0.046354217 0.12109388 273.2567403 2.815672417 39.80271191 0.455689504 2.17E-05 4.662996048 0.609662673 GIPAPEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIPAPEEER 9 0 O95433;G3V438;H0YJU2 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ; 115.49 0.0034126 708880000 352480 473250 442360 446490 479500 453420 518410 448080 501700 FALSE TRUE 330418.906 508289.9224 452852.9881 457947.6893 441842.0042 584314.9933 440679.2332 504023.7743 417963.0289 0.790545774 1.216112161 1.083476185 1.095665544 1.057131788 1.39800641 1.054349793 1.205905163 1 18.67301581 4.74580401 24.75972718 1.144125749 0.790545582 0.481473494 0.113470899 613.3894459 2096658.825 0.024121712 0.246173293 55693.43563 -4.74580401 -0.353580167 GIPHLVTHDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 188.28 1.86E-06 10429630000 7033380 10363130 7915100 7536580 10708140 6208890 8205030 9066870 9343620 FALSE TRUE 6593173.301 11130426.93 8102849.91 7729981.402 9867165.879 8001295.75 6974761.923 10198888.68 7784109.46 0.847004187 1.429890855 1.040947581 0.993046339 1.267603691 1.027901238 0.896025674 1.310219073 1 22.89210057 3.722842496 24.84965854 1.06345372 1.196683367 0 0.187976903 414.2455324 2405821.368 0.045822766 0.073781874 5282.536376 -3.722842496 0.133229646 GIPILSLDWLHQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIPILSLDWLHQSR 14 0 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 0 ; 185.02 1.23E-06 83216000 43748 74166 65262 66123 69844 60139 62459 59806 48481 FALSE TRUE 41009.89077 79657.32781 66810.04546 67819.82813 64358.73398 77500.15302 53093.85279 67272.91075 40389.2079 1.015367543 1.972242882 1.654155873 1.679157172 1.593463634 1.9188332 1.314555436 1.665615996 1 15.30168223 0.255432131 0.688102122 0.984180515 1.66665606 0.296343364 0.279447113 2.983091489 1.888519847 0.372941768 0.093166401 1.800661716 -0.255432131 0.682475545 GIPLATGDT(ph)SPEPELLPGAPLPPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIPLATGDTSPEPELLPGAPLPPPK 25 0 O75821;K7ENA8;K7ER90;K7EL20;K7EL60 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 1 GIPLAT(0.052)GDT(0.522)S(0.426)PEPELLPGAPLPPPK;GIPLAT(0.095)GDT(0.5)S(0.405)PEPELLPGAPLPPPK 153.21 3.96E-07 216867000 410750 336720 370920 366950 397470 306790 443300 344890 439810 TRUE FALSE 385041.8907 361651.0992 379718.3976 376366.5582 366254.3095 395355.2927 376831.2804 387950.2757 366402.8697 1.050870292 0.987031295 1.036341221 1.02719326 0.999594544 1.079018003 1.028461597 1.058807962 1 18.48307128 2.266474681 24.99988998 1.043537613 1.018200128 0.132480014 0.026687151 338.295541 302976.5483 0.00825786 0.006908006 184.7033109 -2.266474681 -0.025337485 GIPLATGDTS(ph)PEPELLPGAPLPPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIPLATGDTSPEPELLPGAPLPPPK 25 0 O75821;K7ENA8;K7ER90;K7EL20;K7EL60 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 1 GIPLATGDT(0.034)S(0.966)PEPELLPGAPLPPPK 182.48 1.43E-17 163220000 393460 317210 356260 340890 370890 316820 445650 323960 409670 TRUE FALSE 368834.0409 340696.5585 364710.6554 349637.8145 341761.7955 408280.7909 378828.9197 364407.1191 341293.4304 1.080694816 0.998251147 1.068613172 1.024449296 1.001372324 1.196274978 1.109980111 1.067723802 1 18.38065312 2.275012128 24.99972275 1.10678778 1.033872021 0.206821898 0.054529303 195.9912885 134416.9625 0.017208775 0.014397523 188.3701694 -2.275012128 -0.07291576 GIPNERPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIPNERPTR 9 1 Q96F86;H3BPW9;H3BSQ0;H3BPN4 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 0 77.14 0.030502 93156000 22642 37880 31545 29946 34151 30208 32895 34512 41146 FALSE TRUE 21224.87764 40684.67461 32293.2623 30714.46506 31468.91822 38928.55921 27962.70013 38820.89917 34278.46679 0.619189819 1.186887234 0.94208596 0.896027971 0.918037508 1.135656372 0.815751192 1.132515623 1 15.06501496 1.207855611 24.99984833 1.066257697 0.95840625 0.090401045 0.161109606 641.3381175 522159.3535 0.139232602 0.034824175 16.13821925 -1.207855611 -0.107851447 GIPVLVGLLDHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIPVLVGLLDHPK 13 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 0 141.73 4.05E-06 0 215020 202800 216500 213600 236840 176760 275160 222220 257620 FALSE TRUE 201562.282 217815.523 221635.4822 219081.3376 218239.5418 227787.7425 233902.3125 249964.6562 214621.5577 0.939152079 1.014881848 1.032680429 1.020779739 1.016857505 1.06134605 1.089836058 1.164676367 1 17.71143547 2.094192928 2.157718198 1.094291604 1.009382621 0.386134747 0.046572248 0.304619252 2.747033431 0.022214894 0.012925652 124.2204014 -2.094192928 -0.084908983 GIPVVEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 98.629 0.0073866 351200000 990810 863850 925140 881030 932700 681200 1160180 862800 1045980 FALSE TRUE 928796.9707 927810.3528 947084.7577 903638.7214 859449.5043 877851.3816 986221.7796 970522.4793 871399.1807 1.065868538 1.064736315 1.086855231 1.036997442 0.986286794 1.007404415 1.131768082 1.113751884 1 19.73297423 -0.351505637 6.550067675 1 1.06387755 0.16008814 0.044173056 0 0 0.044818314 0.010563778 0.445137685 0.351505637 0.06387755 GIQLS(ph)PGVGSSAGPPGDLEDDEGLKHLQQEAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIQLSPGVGSSAGPPGDLEDDEGLKHLQQEAEK 33 1 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 GIQLS(1)PGVGSSAGPPGDLEDDEGLKHLQQEAEK;GIQLS(0.955)PGVGS(0.023)S(0.023)AGPPGDLEDDEGLKHLQQEAEK 242.32 3.53E-47 178400000 258760 161907 197184 243600 263900 124312 195864 144992 250180 TRUE FALSE 242564.6735 173894.7627 201861.2976 249851.1884 243174.3585 160198.8564 166496.0115 163094.5704 208423.3418 1.163807621 0.834334395 0.96851579 1.198767788 1.166732845 0.768622435 0.798835726 0.782515859 1 17.66915733 2.222438703 24.99405477 0.816523001 1.02744518 0.423955909 0.127165392 264.3348159 409799.7894 0.050009875 0.037047229 166.8932233 -2.222438703 0.210922179 GIQYIDLSSDS(ph)EDVVSPNCSNTVQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIQYIDLSSDSEDVVSPNCSNTVQEK 26 0 D6RAY8;Q9H4L7;Q9H4L7-2 D6RAY8 SMARCAD1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 1 GIQYIDLS(0.061)S(0.367)DS(0.572)EDVVSPNCSNTVQEK 177.41 1.67E-17 119300000 40147 38179 37485 40039 40752 32055 51024 35167 39126 TRUE FALSE 37634.27093 41005.81289 38374.1619 41066.46853 37551.50231 41308.75813 43373.42488 39557.67736 32595.61784 1.15458069 1.258016126 1.177279783 1.259876979 1.152041434 1.267310175 1.330652025 1.213588819 1 14.9923904 0.95715024 23.76422528 0.999999999 1.234066524 0.620297218 0.055722038 3882.67139 2153309.139 0.054250324 0.013562581 9.060459853 -0.95715024 0.234066525 GIRDDIEEEDDQEAYFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIRDDIEEEDDQEAYFR 17 1 A0A0A0MSJ0;Q86XP3-2;Q86XP3;J3KRE3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 148.55 3.27E-07 89004000 21238 26412 23467 27976 26641 20581 28528 22604 26950 FALSE TRUE 19908.75149 28367.57196 24023.64832 28693.91152 24548.72332 26522.4006 24250.49124 25426.15916 22451.8709 0.886730179 1.263483658 1.070006523 1.27801873 1.093393216 1.181300245 1.080110043 1.132473961 1 14.45454805 0.412632529 0.860028497 0.999478712 1.139312958 0.096804983 0.110691288 4.091156867 4.22229646 0.100822733 0.031493276 2.586023866 -0.412632529 0.139834246 GIRPAINVGLSVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIRPAINVGLSVSR 14 1 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 132.65 4.49E-05 184430000 146450 173740 149250 151750 211600 135880 142970 163610 213780 FALSE TRUE 137283.9559 186603.8904 152790.2805 155644.1619 194981.7896 175106.3502 121532.9758 184037.0687 178098.7369 0.770830598 1.047755271 0.857896485 0.873920639 1.094796027 0.983198158 0.682391003 1.033342919 1 17.44231776 GIRPFPSEETTENDDDVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIRPFPSEETTENDDDVYR 19 1 P52735-3;P52735-2;P52735 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 0 189.34 1.30E-14 201090000 65300 82965 80454 82295 88309 78398 82526 79269 80117 FALSE TRUE 61212.98956 89107.81493 82362.40687 84406.82903 81373.56736 101030.2299 70151.99243 89165.90914 66744.95512 0.917117847 1.335049439 1.233986999 1.264617361 1.219171804 1.513675898 1.051045615 1.335919831 1 16.02637118 -1.67087276 6.429359321 0.998149971 1.241688354 0.170302527 0.161367696 0.003765844 0.000192778 0.137499269 0.032186833 0.021336699 1.67087276 0.243538383 GIS(ph)PIVFDR ddPTM_SK-BR-3_Pertuzumab_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 206.27 1.43E-05 9884030000 6268290 6109040 6847760 6282800 5499640 7199900 7480850 5430580 4784990 TRUE FALSE 5875968.918 6561359.678 7010192.101 6444027.285 5067720.459 9278394.249 6359165.991 6108599.867 3986344.257 1.474024454 1.645959118 1.758551608 1.616525536 1.271270149 2.32754465 1.595237536 1.532381419 1 21.92663487 -0.838142141 19.92954367 1.000009293 1.673478391 0.360142635 0.272156897 0 0 0.239199662 0.056379901 0.145163643 0.838142141 0.673469098 GIS(ph)PVVSEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GISPVVSEHR 10 0 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 GIS(1)PVVSEHR;GIS(1)PVVSEHR 134.56 0.00010781 238770000 112143 140678 145504 132216 138038 131538 156003 134128 109313 TRUE FALSE 105124.1698 151093.9455 148955.4236 135608.8864 127197.0523 169510.8853 132611.7984 150874.1761 91067.95411 1.154348649 1.659134072 1.635651367 1.489095563 1.396726802 1.861367008 1.456185106 1.656720825 1 16.47465585 -1.098756671 4.398414662 0.999939259 1.559177226 0.441136993 0.189287617 3.834149072 49441177.74 6232.315067 0.039479946 0.079660555 1.098756671 0.559237967 GIS(ph)PVVSEHRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GISPVVSEHRK 11 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 GIS(1)PVVSEHRK 99.941 0.0026948 321120000 238070 345630 287180 291770 341970 246030 367120 294940 339630 TRUE FALSE 223169.6237 371220.8048 293992.0452 299257.3122 315113.0556 317054.867 312073.7642 331763.9082 282943.5589 0.788742548 1.311995955 1.039048375 1.05765727 1.113695809 1.120558702 1.102954121 1.17254448 1 18.11015477 GISCLVDAFLGISRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GISCLVDAFLGISRPR 16 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 0 ; 139.66 1.62E-06 42216000 36795 64702 53519 63469 69954 57713 60797 57608 51744 FALSE TRUE 34492.06663 69492.6034 54788.49595 65097.72199 64460.09502 74373.80621 51681.05426 64800.48561 43107.59212 0.800139023 1.612073419 1.270970919 1.510121971 1.495330448 1.725306438 1.198885201 1.50322675 1 15.39565436 -1.146740544 4.377600645 0.999937601 1.405220017 0.181144103 0.258347991 0.000164936 3.21E-05 0.219490786 0.051724989 0.071327903 1.146740544 0.405282415 GISDLAQHYLMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GISDLAQHYLMR 12 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;; 156.36 6.71E-05 1586960000 1765840 3246520 1658150 1647870 3179310 1156950 1343340 2564500 1825890 FALSE TRUE 1655319.227 3486895.719 1697482.101 1690157.134 2929619.817 1490942.683 1141918.638 2884683.47 1521137.163 1.088211679 2.292295398 1.115929676 1.111114221 1.925940598 0.980150061 0.750700637 1.896399312 1 20.53671882 3.767370023 7.274619492 1.220259923 1.758358516 0.119695772 0.47605661 0.345210411 51.00814984 0.115462332 0.206915092 5852.885433 -3.767370023 0.538098593 GISEETTTGVHNLYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GISEETTTGVHNLYK 15 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;; 273.61 1.87E-33 7089610000 6015780 6772840 6574250 6335030 7405370 5537550 7759480 6846190 8613440 FALSE TRUE 5639263.068 7274308.121 6730194.315 6497597.595 6823782.112 7136150.79 6596018.009 7700951.892 7175801.219 0.785872253 1.013727652 0.937901443 0.905487401 0.950943582 0.994474425 0.919203 1.073183559 1 22.7747085 1.244053483 24.99990143 1.036591791 0.940770735 0.315591305 0.063857538 146.9779481 668970.9689 0.041027265 0.014018995 17.54096506 -1.244053483 -0.095821056 GISHVIVDEIHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GISHVIVDEIHER 13 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;;;; 255.16 4.57E-24 11278300000 2921942 3442517 3189282 3167619 3329014 2977474 3399410 2954548 3091704 FALSE TRUE 2739062.866 3697404.541 3264933.275 3248905.466 3067566.669 3837022.409 2889700.029 3323429.822 2575678.629 1.063433471 1.435506937 1.267601182 1.26137843 1.190974151 1.489713183 1.121917927 1.290312302 1 21.29652117 0.189574061 0.706077281 0.992457055 1.289853217 0.281127101 0.129291748 3.655489136 2.277008572 0.185672357 0.042054148 1.547298344 -0.189574061 0.297396162 GISQDRS(ph)PLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GISQDRSPLVK 11 1 Q5T5U3;E7ESW5;A0A1B0GV73;Q5T5U3-3 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 GIS(0.004)QDRS(0.996)PLVK 65.895 0.038876 100460000 120840 84892 110420 98391 115170 87903 120580 110710 132790 TRUE FALSE 113276.8401 91177.49201 113039.2145 100915.8796 106125.0128 113279.1691 102500.1484 124532.3872 110626.4911 1.023957634 0.824192208 1.021809635 0.912221644 0.959309219 1.023978687 0.926542525 1.125701321 1 16.75533738 1.972339769 0.753042278 1.033610615 0.932004503 0.178455334 0.073634637 1.037817171 1.113664959 0.059359091 0.031260761 93.82957926 -1.972339769 -0.101606113 GISQEQMQEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GISQEQMQEFR 11 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 100.55 0.014011 121100000 48270 53146 49602 45556 47649 37131 48714 48880 51786 FALSE TRUE 45248.86686 57080.98514 50778.58286 46725.04409 43906.83975 47850.11693 41409.78794 54982.7756 43142.58205 1.048821483 1.323077628 1.176994525 1.083037729 1.017714695 1.109115743 0.959835642 1.274443322 1 15.3968249 3.292201153 3.204833573 1.06261071 1.218207194 0.170157362 0.107171374 0.279927641 5.81926592 0.028511404 0.038873192 1959.752164 -3.292201153 0.155596484 GISTKPVYIPEVELNHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GISTKPVYIPEVELNHK 17 1 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 127.83 2.34E-05 315910000 583930 590710 535340 593590 530800 437460 700940 537440 613480 FALSE TRUE 547382.8636 634446.783 548038.5176 608822.5243 489113.1091 563747.6004 595840.5542 604540.5671 511086.2248 1.071018621 1.241369366 1.072301485 1.191232506 0.957007028 1.103038143 1.165831762 1.182854356 1 18.96320718 -2.477849382 1.867464812 6.74E-05 1.128120808 0.187393572 0.079938702 833653.608 58544.34378 3528337.341 0.018501173 0.003327749 2.477849382 1.128053408 GITGVEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GITGVEDK 8 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ;;; 124.98 0.0029812 734186000 1394250 1423790 1239330 1182510 1683360 1052180 1499210 1590370 1602540 FALSE TRUE 1306986.381 1529208.893 1268727.493 1212855.209 1551155.696 1355927.285 1274417.378 1788931.195 1335065.721 0.978967822 1.145418438 0.950310889 0.908461051 1.161857182 1.015625871 0.954572766 1.339957402 1 20.34847933 1.268415682 24.99967991 1.169979715 1.020576443 0.238074438 0.113993566 241.8000077 202475.8569 0.068983356 0.025181992 18.55306568 -1.268415682 -0.149403272 GITGVEDKESWHGKPLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GITGVEDKESWHGKPLPK 18 2 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 185.55 3.16E-14 5954200000 1317890 1475920 1626720 1628760 2372270 1186060 2108850 1743630 4138600 FALSE TRUE 1235405.617 1585198.652 1665306.567 1670556.739 2185961.483 1528456.268 1792647.52 1961326.044 3447840.924 0.358312824 0.4597656 0.482999826 0.484522568 0.634008799 0.443308233 0.519933361 0.568856304 1 21.71726178 -5 0.217610848 3.559747222 0.424649829 0.882336431 0.060054561 46.99243442 0.470049049 52.59971529 0.112833288 1.00E-05 5 -3.135097393 GITINAAHVEYSTAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GITINAAHVEYSTAAR 16 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ;; 149.86 7.95E-07 1301630000 529783 598941 503470 461286 694410 547324 483693 566060 822930 FALSE TRUE 496624.8277 643287.2148 515412.5462 473123.3797 639873.8397 705327.5537 411167.725 636733.8371 685577.6667 0.724388865 0.938314134 0.751793081 0.69010909 0.933335304 1.028807658 0.599739089 0.928755221 1 19.38696059 2.714453853 24.89230935 0.86191504 0.799118692 0.12928144 0.135116424 2724.12075 2812886.518 0.043972786 0.041478252 518.1480324 -2.714453853 -0.062796348 GIVEFASKPAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIVEFASKPAAR 12 1 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 175.57 2.49E-05 3206800000 2434610 3263800 2916070 2930230 3819500 2446640 3383800 3277700 4478200 FALSE TRUE 2282232.106 3505455.148 2985240.557 3005424.663 3519531.877 3152945.25 2876430.604 3686928.06 3730759.49 0.611733914 0.939608988 0.800169661 0.805579848 0.943382142 0.845121552 0.771004031 0.988251339 1 21.83103793 -5 0.070174083 1.540055387 0.645159783 0.339051332 0.096010665 442.8690343 2.238018207 38.90756795 4.834402014 1.00E-05 5 -0.894895604 GIVEFSGKPAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIVEFSGKPAAR 12 1 Q15233;Q15233-2;H7C367;C9IZL7 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 191.79 4.49E-06 1401900000 1828700 2023800 1845500 1725200 2085400 1429300 2192900 1753000 2491000 FALSE TRUE 1714244.931 2173644.258 1889276.132 1769471.553 1921621.096 1841915.707 1864095.003 1971865.909 2075236.008 0.826048182 1.047420269 0.910390975 0.852660394 0.925977137 0.88756927 0.898256871 0.95018875 1 20.98484399 0.964771569 5.287816589 0.999966395 0.918170014 0.196735869 0.05863676 0.384990712 39.26346589 0.056667408 0.014300728 9.220862995 -0.964771569 -0.081796382 GIVQNLHSMLPIQQLQEWGVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GIVQNLHSMLPIQQLQEWGVER 22 0 A0A0B4J2A0 A0A0B4J2A0 TRPV1 0 208.39 6.94E-23 82404000 57190 79629 58577 56907 72355 46132 55800 59601 61606 FALSE TRUE 53610.57999 85524.81401 59966.4741 58367.32996 66672.53017 59449.55951 47433.30802 67042.31605 51323.56061 1.044560809 1.666385048 1.168400504 1.137242414 1.299062835 1.158328822 0.924201428 1.306267828 1 15.64733364 3.68314281 4.942617117 1.130975584 1.406028265 0.172142537 0.188065196 0.226185987 12.74213728 0.046833538 0.076028285 4821.063039 -3.68314281 0.275052681 GIWHNDNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIWHNDNK 8 0 P12277;H0YJG0;P06732 P12277 CKB;CKM "Creatine kinase B-type;Creatine kinase M-type;Creatine kinase M-type, N-terminally processed" 0 ; 125.01 0.0012804 1235460000 2266790 2270190 2308330 2598000 2139270 1652730 2649500 1605370 1172290 FALSE TRUE 2124915.66 2438277.23 2363084.678 2664669.078 1971260.364 2129846.321 2252232.072 1805803.978 976627.2257 2.175769428 2.496630409 2.419638338 2.728440298 2.018436832 2.18081809 2.306132793 1.849020722 1 19.89744847 0.481447821 0.612810139 0.955092377 2.426853137 0.829458363 0.193719768 0.65762304 0.418281211 0.236711086 0.075599419 3.030036226 -0.481447821 1.47176076 GIWHNNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GIWHNNEK 8 0 P12532;P12532-2;F8WCN3 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ;;;;; 188.98 0.00019413 6152660000 9888120 9469320 8366800 8847870 12265200 7227210 10046420 9504020 11599500 FALSE TRUE 9269240.22 10170438.31 8565264.447 9074921.324 11301940.67 9313588.203 8540052.587 10690617.82 9663468.514 0.959204266 1.052462508 0.886355084 0.939095658 1.169553215 0.963793506 0.883746097 1.106291991 1 23.20410968 GIYAYGFEKPSAIQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GIYAYGFEKPSAIQQR 16 1 P60842;J3KT12;P60842-2;J3QS69;J3QL43;J3KTB5;J3QR64;J3QLN6;J3KS25;J3QKZ9;J3QQP0;J3KSN7;J3KT04;J3KS93;Q14240;Q14240-2;E7EQG2;E9PBH4;F8WE11;E7EMV8;P38919;I3L3H2 P60842;Q14240;P38919 EIF4A1;EIF4A2;EIF4A3 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed;Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ; 262.42 6.34E-27 8884700000 1409400 1830850 1572850 1404050 1920380 1256980 1762220 1748480 2047410 FALSE TRUE 1321188.17 1966408.039 1610158.745 1440080.3 1769561.101 1619849.721 1497991.471 1966781.577 1705684.044 0.774579662 1.152855973 0.9439959 0.844283151 1.037449525 0.949677478 0.878235026 1.153074969 1 20.701919 1.237601363 24.99999546 1.076537462 0.958043352 0.19641661 0.11015661 46.03529665 1199461.424 0.083866294 0.025547352 17.28229296 -1.237601363 -0.118494109 GIYETPAGTILYHAHLDIEAFTMDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 GIYETPAGTILYHAHLDIEAFTMDR 25 0 P00966 P00966 ASS1 Argininosuccinate synthase 0 ;;;;;;;;;; 369.64 5.71E-120 2162933400 1304750.5 1534631.8 1364044.2 1422657.7 1714353.7 1312702.1 1545250.4 1377929.5 1106847.9 FALSE TRUE 1223088.495 1648257.535 1396399.973 1459165.505 1579715.276 1691657.886 1313554.448 1549967.031 922107.835 1.326405057 1.787488917 1.514356477 1.582423931 1.713156765 1.834555376 1.424512837 1.680895631 1 19.81457595 -0.93712598 0.836860397 0.920473964 1.616752669 0.593404091 0.157754798 38.27613307 13.05875208 8.402205585 0.046696408 0.115577693 0.93712598 0.696278706 GKAEEQAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 153.12 7.19E-05 1413810000 1943960 2819480 1689120 1945590 3096780 1193570 1943570 2651190 2649270 FALSE TRUE 1822291.014 3028237.233 1729186.724 1995517.133 2853571.391 1538134.283 1652149.722 2982196.907 2207089.722 0.825653346 1.3720499 0.783469157 0.904139561 1.292911367 0.696906097 0.748564821 1.351189704 1 21.07371385 2.226200736 24.99993572 0.900703462 1.041153074 0.012008238 0.254289017 680.3924175 1376198.533 0.091269284 0.067887948 168.3451993 -2.226200736 0.140449613 GKAS(ph)PFEEDQNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 178.01 1.37E-05 3356960000 2121430 1796740 1940510 2026130 2243550 1610310 2311920 1954820 2474260 TRUE FALSE 1988653.483 1929772.499 1986539.814 2078123.926 2067350.633 2075180.356 1965269.059 2198883.58 2061290.022 0.964761612 0.936196498 0.9637362 1.008166684 1.002940203 1.006738661 0.953417053 1.066751188 1 20.97511607 3.371482115 3.912900949 1.000448985 0.949754361 0.419569962 0.028190394 0.213390067 6.072684626 0.007577208 0.010561577 2352.242624 -3.371482115 -0.050694624 GKDANPQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GKDANPQER 9 1 Q9Y6U3;Q9Y6U3-3;Q9Y6U3-2 Q9Y6U3 SCIN Adseverin 0 ;;;;; 169.99 5.29E-05 1534222000 771862 677732 712334 662155 861541 609135 798729 828793 1721141 FALSE TRUE 723552.5352 727911.9825 729230.8989 679147.0183 793879.0451 784982.386 678967.0015 932269.6304 1433871.448 0.504614647 0.507654981 0.50857481 0.473645681 0.553661241 0.547456599 0.473520135 0.650176577 1 20.45148426 0.880298788 3.218261632 0.99982708 0.510313501 0.970868625 0.02679083 0.072375955 1.514826496 0.024882432 0.006475836 7.590996453 -0.880298788 -0.489513579 GKDCAVIVTQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKDCAVIVTQK 11 1 G3V5Z7;P60900;G3V3I1;G3V295;P60900-2;G3V3U4 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ; 111.79 0.0014706 586630000 1468240 1275450 1303220 1207260 1495480 1016620 1627190 1227740 1526000 FALSE TRUE 1376345.479 1369885.645 1334132.994 1238240.335 1378031.033 1310101.691 1383207.966 1381026.042 1271300.742 1.082627764 1.077546485 1.049423594 0.973994819 1.083953614 1.030520669 1.088025768 1.086309475 1 20.27787393 1.73916204 25 1.067030017 1.051271264 0 0.040073469 0.397463302 15847.18616 0.01750624 0.009707796 54.8481571 -1.73916204 -0.015758753 GKDETDSPTVHLGLDS(ph)DS(ph)ESELVIDLGEDHSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GKDETDSPTVHLGLDSDSESELVIDLGEDHSGR 33 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;Q9ULU4-2 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 2 GKDETDSPTVHLGLDS(0.993)DS(0.979)ES(0.028)ELVIDLGEDHSGR;GKDETDSPTVHLGLDS(1)DS(0.995)ES(0.005)ELVIDLGEDHSGR;GKDETDSPTVHLGLDS(1)DS(0.887)ES(0.113)ELVIDLGEDHSGR 237.1 1.21E-46 270205000 251246 229360 244180 246821 259732 180726 279543 214715 306910 TRUE FALSE 235520.9613 246342.053 249972.0649 253154.8447 239333.6964 232898.6624 237628.1223 241522.6404 255684.7383 0.921138129 0.963460137 0.977657355 0.990105418 0.936049989 0.910882143 0.929379375 0.944611094 1 17.96400652 2.693970686 23.104537 0.936252161 0.965579755 0.056814684 0.028966456 291.8569783 151226.6158 0.008700588 0.008203086 494.2773227 -2.693970686 0.029327594 GKDETDSPTVHLGLDS(ph)DSES(ph)ELVIDLGEDHSGR ddPTM_SK-BR-3_Pertuzumab_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 GKDETDS(0.016)PT(0.019)VHLGLDS(0.905)DS(0.495)ES(0.565)ELVIDLGEDHSGR 74.474 0.0036667 213760000 32252 27307 26312 33044 32206 23327 36576 26396 31241 TRUE FALSE 30233.40489 29328.83869 26936.13307 33891.96498 29676.67067 30061.12622 31091.76835 29691.5987 26026.67528 1.161631464 1.126876114 1.034943295 1.302201093 1.140240555 1.155012152 1.194611606 1.140814122 1 14.66770341 4.777461955 19.75116819 1.141299065 1.161632172 0.006368916 0.081925503 10460.39087 5309341.658 0.018627933 2.613447227 59904.84589 -4.777461955 0.020333107 GKDIGKPIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKDIGKPIEK 10 2 O60869 O60869 EDF1 Endothelial differentiation-related factor 1 0 ; 62.088 0.049137 1326430000 2945150 2167490 2528210 2522520 3130780 2004940 3327260 2368220 3641620 FALSE TRUE 2760818.319 2327973.215 2588180.335 2587252.134 2884901.168 2583733.631 2828368.252 2663897.48 3033810.096 0.910016854 0.76734309 0.853112177 0.852806224 0.950916859 0.851646461 0.932282563 0.87806995 1 21.53269935 1.290507394 0.234060453 1.028256543 0.796308497 0.431548847 0.04858998 1.863367668 0.441567921 0.174169993 0.139620387 19.52123971 -1.290507394 -0.231948046 GKDILYIGDHIFGDILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKDILYIGDHIFGDILK 17 1 P49902-2;P49902;Q5JUV6 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 131.56 1.60E-05 29424000 164380 175590 165820 178070 206920 124520 224480 151340 201260 FALSE TRUE 154091.7492 188590.8663 169753.3287 182639.5777 190669.3379 160466.9026 190821.308 170235.1321 167668.4058 0.919026745 1.124784752 1.012434799 1.089290357 1.137181074 0.957049134 1.138087447 1.015308348 1 17.35525134 4.754027118 24.30859757 1.06519251 0.919026588 0.324268942 0.063109102 2130.013344 3347645.587 0.013150517 0.314111682 56758.00444 -4.754027118 -0.146165922 GKDS(ph)TEMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GKDSTEMR 8 1 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 1 GKDS(0.8)T(0.2)EMR;GKDS(0.991)T(0.009)EMR;GKDS(0.735)T(0.265)EMR;GKDS(0.976)T(0.024)EMR 121.08 0.00087737 2590665000 5256730 3856590 4798540 4368880 4624170 3401460 5370190 4290380 4808430 TRUE FALSE 4927720.653 4142135.936 4912363.635 4480992.857 4261006.341 4383406.284 4564979.864 4826043.387 4005871.969 1.23012435 1.034016056 1.226290723 1.118606109 1.063690096 1.094245227 1.139572083 1.204742294 1 21.93368488 3.019473341 24.99808473 1.108967143 1.148176232 0.113429685 0.074610127 743.8316951 954856.0916 0.020363376 0.024334394 1045.859488 -3.019473341 0.039209089 GKDSLYAQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKDSLYAQGK 10 1 H0Y5B4;H7BZ11;J3KQN4;P83881;H7BY91;H0Y3V9 H0Y5B4 RPL36A;RPL36A-HNRNPH2 60S ribosomal protein L36a 0 ; 96.103 0.0063556 1539280000 1347230 1974530 1733870 1440060 2182600 1180980 2052660 1901070 2843950 FALSE TRUE 1262909.279 2120726.256 1774998.215 1477014.378 2011187.4 1521909.754 1744882.689 2138422.774 2369276.372 0.533035864 0.895094502 0.749173138 0.62340316 0.84886146 0.642352143 0.736462284 0.902563668 1 21.17601507 1.095439777 3.393007116 0.996514816 0.735806428 0.461696037 0.105994146 0.197732145 4.273796617 0.093799515 0.024621363 12.45775475 -1.095439777 -0.260708387 GKDSLYAQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GKDSLYAQGR 10 1 Q969Q0 Q969Q0 RPL36AL 60S ribosomal protein L36a-like 0 ;; 118.9 0.0017637 408280000 590535 874710 593797 610433 935420 449999 654710 707160 968830 FALSE TRUE 553574.4685 939474.4385 607882.1453 626097.7442 861955.8865 579906.4062 556542.3135 795450.4827 807126.0141 0.685858786 1.163974921 0.753144038 0.775712507 1.067932233 0.718483107 0.689535839 0.985534438 1 19.62243441 2.200382419 24.99990304 0.804553067 0.903043256 0 0.174074259 473.1690255 309838.4917 0.061995657 0.0457877 158.6289387 -2.200382419 0.098490189 GKDSTEMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GKDSTEMR 8 1 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 0 ;;; 80.239 0.02368 990470000 2214110 2239970 2257050 2142390 2417240 1772730 2471210 2170350 2723870 FALSE TRUE 2075532.807 2405819.709 2310588.292 2197367.354 2227399.721 2284488.373 2100675.002 2441322.975 2269238.5 0.91463846 1.060188124 1.01822188 0.968328078 0.981562635 1.00672026 0.925718034 1.075833578 1 21.11377682 3.255701844 24.76873371 0.985473902 1.014010975 0 0.052421673 644.8323887 931762.8059 0.013479211 0.018204255 1801.780343 -3.255701844 0.028537074 GKDYYQTLGLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKDYYQTLGLAR 12 1 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 178.22 2.03E-05 534050000 408030 622400 412890 379880 682070 369860 448070 573480 642330 FALSE TRUE 382492.1307 668483.1436 422683.9458 389628.3639 628502.9735 476632.5778 380886.0632 645080.2404 535120.9734 0.714776938 1.249218732 0.789884842 0.728112676 1.174506336 0.890700611 0.711775621 1.205484876 1 19.02950555 3.867119252 21.13677169 0.90459625 1.0200946 0 0.210787434 14.05945647 2652.176103 0.050112507 0.090341742 7364.092789 -3.867119252 0.11549835 GKEALESEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKEALESEFR 10 1 A0A0A0MRE1;B4DJ07;A0A0A0MSB8;Q9UPT5-2;Q9UPT5-5;Q9UPT5-1;Q9UPT5-6;Q9UPT5;Q9UPT5-4;C9JKC2;C9JME6 A0A0A0MRE1 EXOC7 Exocyst complex component 7 0 60.255 0.090546 378350000 253090 370810 331630 351480 433090 279150 351440 341530 450790 FALSE TRUE 237249.5487 398265.1582 339496.4202 360499.5719 399076.8584 359736.0734 298744.8346 384170.7723 375550.2368 0.631738514 1.060484375 0.903997354 0.959923697 1.062645738 0.957890684 0.795485678 1.022954414 1 18.51864638 4.749975881 24.74525973 0.957977243 0.631738293 0.639529405 0.079423126 1074.131128 2328380.381 0.019546399 0.307710555 56231.00959 -4.749975881 -0.32623895 GKEDALVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKEDALVTK 9 1 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ; 77.674 0.029122 784650000 1959330 1643940 1807530 1786650 2053300 1506190 2575800 1865640 2778400 FALSE TRUE 1836699.033 1765659.028 1850405.465 1832498.464 1892042.101 1941002.602 2189582.703 2098569.261 2314667.091 0.793504621 0.76281338 0.799426178 0.791689859 0.817414352 0.838566639 0.945960096 0.906639779 1 21.14237328 1.75537729 0.817788403 0.98900635 0.778174397 0.919564181 0.021734539 0.134188881 0.171839525 0.017780116 0.007995099 56.93473319 -1.75537729 -0.210831953 GKEGTHATCASEEGGTESSESGSSLQPLSADSTPDVNQS(ph)PR ddPTM_SK-BR-3_Pertuzumab_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 124.91 6.64E-09 356750000 24688 39530 32262 38478 47440 31728 47838 39190 62594 TRUE FALSE 23142.82215 42456.84233 33027.26988 39465.41062 43714.25376 40887.35854 40665.13601 44082.95777 52146.65703 0.443802603 0.814181479 0.633353541 0.756815736 0.838294461 0.784083983 0.779822491 0.845364982 1 15.67028715 5.295758022 0.084512117 1.215142967 6.52E-12 0.623213289 0.089330678 67.42750161 0.766548889 2.584177701 10.60631263 197586.8431 -5.295758022 -1.215142967 GKEKCSEKSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKEKCSEKSR 10 3 Q5VUJ6-2;Q5VUJ6 Q5VUJ6-2 LRCH2 Leucine-rich repeat and calponin homology domain-containing protein 2 0 ; 77.379 0.04057 1813940000 1104740 3570800 2373000 2731000 3465500 2872800 3339900 3211900 3391100 FALSE TRUE 1035596.295 3835185.747 2429288.681 2801082.084 3193333.609 3702130.724 2839113.001 3612912.785 2825103.503 0.366569329 1.357538138 0.859893692 0.991497154 1.130342165 1.31044074 1.004958933 1.278860326 1 21.42987229 2.754003064 4.553430568 1.148427015 0.963681272 0.166140986 0.260052338 0.461787892 25.49428754 0.076919978 0.07816074 567.5486096 -2.754003064 -0.184745743 GKEKDS(ph)PFKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKEKDSPFKPK 11 3 Q15291 Q15291 RBBP5 Retinoblastoma-binding protein 5 1 GKEKDS(1)PFKPK 92.265 0.055947 347820000 1216400 349190 613880 579600 689280 428200 813960 507710 1191900 TRUE FALSE 1140267.695 375044.3909 628441.5235 594473.5173 635146.7292 551814.3888 691914.2544 571098.7111 992964.19 1.148347248 0.377701829 0.632894449 0.598685756 0.639647165 0.55572436 0.696816926 0.575145324 1 19.92138216 -1.332083633 3.179590457 1.002810162 0.625573326 0.224643608 0.19669632 36009770.67 48863552.96 953911.3407 0.041655072 0.046549644 1.332083633 -0.377236835 GKELNEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKELNEFR 8 1 Q9UHV9 Q9UHV9 PFDN2 Prefoldin subunit 2 0 ; 83.948 0.016233 347290000 679300 1063950 722950 796580 1236730 562010 896920 963140 1353270 FALSE TRUE 636783.8256 1142725.965 740098.7154 817021.5914 1139602.215 724253.1635 762435.1726 1083390.149 1127400.495 0.564824859 1.013593635 0.656464778 0.72469508 1.01082288 0.642409833 0.676277132 0.960962989 1 20.10456867 1.135330963 6.461259219 0.994730017 0.768858544 0.280685789 0.148904687 0.289066791 15.03241503 0.134203043 0.03376744 13.6562344 -1.135330963 -0.225871473 GKEQERPPEAVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKEQERPPEAVSK 13 2 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 0 ; 124.78 0.00011691 252560000 514040 451150 449110 445080 507410 358470 583460 451130 685760 FALSE TRUE 481867.154 484553.6154 459763.1013 456501.5063 467560.0654 461954.4697 495975.5896 507454.5736 571302.2258 0.843454011 0.848156358 0.804763364 0.799054311 0.818411069 0.808599107 0.868149234 0.888241898 1 19.12389463 0.910811349 1.171763823 0.998952245 0.820961753 0.909383785 0.017836985 0.167287131 0.461408198 0.017578874 0.005494119 8.14350466 -0.910811349 -0.177990492 GKEVDNFVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKEVDNFVDK 10 1 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 ; 155.99 1.07E-05 471420000 2178600 1715280 1817820 1774640 1884570 1249720 2212200 1657390 2177000 FALSE TRUE 2042245.315 1842281.116 1860939.549 1820180.267 1736563.474 1610493.876 1880501.147 1864318.79 1813644.636 1.126044912 1.015789466 1.026077277 1.00360359 0.957499303 0.887987561 1.036863071 1.027940509 1 20.79046037 8 0.736641968 0.986866246 22.64509197 0.479980411 0.043386597 322.8727148 1.459710393 0.015516957 11584.73789 100000000 -8 21.65822573 GKFEDMAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 95.523 0.0087459 2549400000 3145600 5779800 2420980 2594240 7918700 1652010 3335300 6468800 8511200 FALSE TRUE 2948722.511 6207742.406 2478406.789 2660812.59 7296797.244 2128918.469 2835202.728 7276443.92 7090625.736 0.4158621 0.875485837 0.349532874 0.375257797 1.029076631 0.30024409 0.39985226 1.026206176 1 22.75748152 1.228721524 24.98866862 1.013103533 0.542670933 0.411291238 0.237645312 222.1560536 564197.3238 0.207944761 0.054537957 16.93251715 -1.228721524 -0.4704326 GKFGHEFLEFEFRPDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKFGHEFLEFEFRPDGK 17 2 P61326;Q96A72;F5H6N1;P61326-2 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ; 154.12 9.00E-08 863910000 1858830 1746770 1865250 1784940 2233950 1452000 2351570 1732620 2493350 FALSE TRUE 1742489.148 1876102.668 1909494.611 1830744.582 2058504.578 1871168.829 1998973.909 1948941.421 2077193.777 0.838866921 0.903190973 0.919266479 0.88135474 0.991002669 0.90081573 0.96234349 0.938256913 1 20.98620438 8 0.126778947 1.014392291 0.519663828 0.604921325 0.031046457 57.44794293 0.495125834 0.157092844 5.06407231 100000000 -8 -0.494728464 GKFNTSDVSAIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKFNTSDVSAIEK 13 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 162.87 3.62E-05 1243260000 3897000 3378300 3376200 3165000 3729000 2323200 3997100 3378700 5283900 FALSE TRUE 3653093.726 3628432.847 3456285.058 3246219.258 3436139.382 2993870.126 3397771.962 3800538.132 4401982.955 0.829874573 0.824272353 0.78516548 0.737444759 0.780588979 0.680118519 0.771873039 0.86336957 1 22.06972213 0.953227387 3.084401225 0.999413548 0.773820146 0.751242422 0.042249824 0.144786262 3.405367051 0.04291617 0.011247087 8.978987917 -0.953227387 -0.225593402 GKGAYQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GKGAYQDR 8 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;; 66.692 0.055656 1522870000 1279300 1864550 1347740 1433530 2151910 1087770 1700960 1639290 2837660 FALSE TRUE 1199230.897 2002603.222 1379709.029 1470316.807 1982907.669 1401791.541 1445916.839 1843958.965 2364036.214 0.507281102 0.847111906 0.583624321 0.621951897 0.838780581 0.592965341 0.611630579 0.780004534 1 21.17282071 0.937876662 4.627296881 0.99987139 0.668545222 0.504496893 0.108181919 0.247375574 14.6039753 0.096427282 0.02446082 8.667156962 -0.937876662 -0.331326167 GKGEKEPPS(ph)PGMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKGEKEPPSPGMER 14 2 P56182 P56182 RRP1 Ribosomal RNA processing protein 1 homolog A 1 GKGEKEPPS(1)PGMER;GKGEKEPPS(1)PGMER 89.483 0.0031992 580850000 512390 375360 417520 443010 503190 265160 536260 375780 771920 TRUE FALSE 480320.4245 403152.045 427423.7716 454378.3866 463671.4872 341707.3875 455852.7914 422696.9602 643081.5652 0.746904359 0.626906549 0.664649392 0.706564161 0.72101505 0.531359327 0.708856879 0.657299141 1 19.29464221 -1.44374008 1.786642596 1.033913727 0.665612218 0.745937501 0.060385049 20450.17577 13160.00348 3424.628187 0.014651236 0.035996471 1.44374008 -0.368301509 GKGEQIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKGEQIAR 8 1 P61026 P61026 RAB10 Ras-related protein Rab-10 0 116.3 0.0020949 265080000 448140 516830 416960 415400 604370 381900 508630 555870 533220 FALSE TRUE 420091.7174 555096.631 426850.4881 426059.8673 556905.2181 492148.3304 432365.6534 625271.5931 444222.1373 0.945679385 1.249592455 0.960894229 0.959114442 1.253663812 1.107887899 0.973309561 1.407565136 1 18.76092176 2.753051235 24.98570093 1.129021398 1.054294543 0.119084536 0.149882575 2628.20564 4531727.995 0.044004945 0.046489888 566.306094 -2.753051235 -0.074726854 GKGGVTGS(ph)PEASISGS(ph)KGDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKGGVTGSPEASISGSKGDLK 21 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 GKGGVT(0.136)GS(0.864)PEAS(0.369)IS(0.163)GS(0.468)KGDLK 114.61 9.30E-05 364070000 615560 189160 323130 201690 321890 307220 495270 326370 1051400 TRUE FALSE 577033.1984 203165.6032 330794.7962 206865.7069 296610.0578 395909.4267 421008.8614 367118.0129 875914.5477 0.658777959 0.231946831 0.37765647 0.236171105 0.338628989 0.451995492 0.48065061 0.419125375 1 19.7404306 -0.124126171 0.554364526 1.057888752 0.350985286 0.699878643 0.123388558 2.647061012 0.879525969 0.444993491 0.049952811 0.751404565 0.124126171 -0.706903466 GKGGVTGS(ph)PEASISGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKGGVTGSPEASISGSK 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GKGGVT(0.005)GS(0.995)PEAS(0.001)ISGSK;GKGGVTGS(0.998)PEAS(0.001)ISGSK 219.95 2.22E-17 192380000 387960 281100 325380 296770 370630 287890 419290 287990 546410 TRUE FALSE 363678.2761 301912.9365 333098.1673 304385.6206 341522.2148 370999.1695 356421.357 323946.1854 455210.6411 0.798923055 0.663237871 0.731745125 0.668669827 0.750250948 0.815005485 0.782981163 0.711640186 1 18.79617476 -5 0.210549983 2.283642903 0.698410306 0.713940669 0.051315878 74.21860435 0.740336729 40.13772426 0.10379111 1.00E-05 5 -1.585232597 GKGGVTGSPEAS(ph)ISGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKGGVTGSPEASISGSK 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GKGGVTGS(0.455)PEAS(0.543)IS(0.001)GS(0.001)K 262.54 6.28E-27 333000000 316600 219260 261610 261890 329320 233320 356080 284260 551970 TRUE FALSE 296784.5711 235494.2385 267815.5127 268610.5408 303456.5356 300675.6964 302689.1097 319750.4867 459842.6411 0.645404633 0.512119185 0.582406869 0.584135782 0.659913867 0.653866496 0.658244979 0.695347621 1 18.81078073 -1.136530171 0.25576176 1.275127091 0.540454368 0.916068032 0.037457976 4.119057746 0.235752562 0.835576882 0.056823324 0.073024708 1.136530171 -0.734672724 GKGS(ph)PRPQAPK ddPTM_SK-BR-3_Pertuzumab_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 86.944 0.011099 11133820000 11066920 7336910 8642980 7598180 9606450 7090340 11490680 8290460 11849380 TRUE FALSE 10374261.23 7880142.45 8847995.567 7793162.162 8851998.168 9137206.056 9767759.208 9325542.181 9871641.928 1.050915472 0.798260564 0.896304346 0.789449437 0.896709811 0.925601447 0.989476652 0.944679948 1 23.23485863 2.086437607 2.446968183 0.9755554 0.870251862 0.236409592 0.072504316 0.34788914 4.065980808 0.032621899 0.01965193 122.0218504 -2.086437607 -0.105303538 GKHDELADSLPCAEGEFIFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKHDELADSLPCAEGEFIFLR 21 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 126.91 1.24E-05 108034000 182957 182834 153058 153966 211536 149293 205139 182285 202560 FALSE TRUE 171506.048 196371.2196 156688.608 157917.0282 194922.8159 192391.4655 174380.3114 205043.6835 168751.4274 1.016323539 1.163671458 0.928517231 0.935796696 1.155088397 1.14008793 1.033356067 1.215063402 1 17.36454018 2.720987021 24.62308524 1.106906077 1.022749592 0.231938331 0.087114173 1189.273135 1666337.306 0.027979788 0.026436368 526.001547 -2.720987021 -0.084156485 GKHQPWQS(ph)PERPLSR ddPTM_SK-BR-3_Pertuzumab_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 193.06 5.65E-08 2622100000 481590 515150 522470 548410 616940 513680 638880 495040 800760 TRUE FALSE 451448.1416 553292.242 534863.2351 562483.1291 568488.021 661971.0771 543085.8751 556846.8337 667107.9829 0.676724238 0.829389329 0.801764105 0.843166539 0.852167918 0.992299739 0.814089906 0.834717689 1 19.34756078 8 0.120301587 1.008798177 0.156609357 0.550250131 0.062069818 77.60303099 0.641029545 0.398818116 11.0958332 100000000 -8 -0.85218882 GKHS(ph)LDSDEEEDDDDGGSSKYDILASEDVEGQEAATLPSEGGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKHSLDSDEEEDDDDGGSSKYDILASEDVEGQEAATLPSEGGVR 44 2 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 GKHS(0.409)LDS(0.379)DEEEDDDDGGS(0.083)S(0.083)KY(0.024)DILAS(0.02)EDVEGQEAAT(0.002)LPSEGGVR 44.945 0.019473 117640000 58211 39406 46402 43099 53175 28912 62528 34090 87436 TRUE FALSE 54567.67742 42323.66124 47502.67735 44204.99331 48998.85 37258.42505 53152.50688 38346.21154 72842.36674 0.74912005 0.581030836 0.65212979 0.606858279 0.672669659 0.511493884 0.729692201 0.526427315 1 16.15249018 -1.57130613 3.29930123 1.01427093 0.629409644 0.693623916 0.077555261 20695307.25 28245596.72 2622950.951 0.016058328 0.026834522 1.57130613 -0.384861286 GKHSLDS(ph)DEEEDDDDGGSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GKHSLDSDEEEDDDDGGSSK 20 1 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 GKHS(0.001)LDS(0.999)DEEEDDDDGGSSK;GKHS(0.149)LDS(0.851)DEEEDDDDGGSSK;GKHS(0.006)LDS(0.994)DEEEDDDDGGSSK 247.13 2.56E-30 274360000 763270 400178 530330 507047 529511 442398 695110 421290 555930 TRUE FALSE 715498.2932 429807.5955 542909.678 520058.6844 487925.342 570111.1209 590884.7086 473888.9839 463141.6916 1.544879907 0.928026138 1.17223236 1.122893261 1.053512026 1.230964802 1.275818436 1.023205193 1 18.82109411 -2.266380989 0.012885252 8.93E-07 2.137456424 0.10915507 0.165495935 19314.68633 32.29269697 2995.928049 2388.229604 0.005415256 2.266380989 2.137455531 GKHSYNS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKHSYNSR 8 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 GKHS(0.007)YNS(0.993)R 55.401 0.075196 64769000 62392 74713 67166 78525 101420 53184 89305 68443 124270 TRUE FALSE 58486.99609 80244.82826 68759.20924 80540.08444 93454.88231 68537.35743 75914.54432 76988.25921 103528.5342 0.564936001 0.775098661 0.664157083 0.777950592 0.902696856 0.662014178 0.733271701 0.743642898 1 16.65966893 -5 0.226906832 2.408478672 0.698365687 0.508824584 0.086247929 134.228388 1.343934944 86.84512659 0.145810912 1.00E-05 5 -1.710112984 GKIEVLDS(ph)PASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKIEVLDSPASK 12 1 Q8N5I9 Q8N5I9 C12orf45 Uncharacterized protein C12orf45 1 GKIEVLDS(0.998)PAS(0.002)K;GKIEVLDS(1)PASK 125.18 0.00018769 596640000 1364180 813880 1140400 985140 1090900 812540 1378810 934310 986710 TRUE FALSE 1278798.409 874140.522 1167450.827 1010420.36 1005225.114 1047107.108 1172070.241 1050960.66 822021.7266 1.555674707 1.063403185 1.420218942 1.22918936 1.222869277 1.27381926 1.425838518 1.278507156 1 19.648817 0.952641923 23.11207856 0.999999998 1.300876375 0.341802952 0.134631231 6120.469236 2986965.283 0.118632402 0.0296581 8.966891664 -0.952641923 0.300876377 GKKPDIDITGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKKPDIDITGPK 12 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 121.28 0.00021321 258900000 1126000 639770 856900 840280 1023400 614090 1090000 793290 1367000 FALSE TRUE 1055525.67 687139.2365 877226.0727 861843.0074 943026.2922 791367.8141 926564.6191 892334.0027 1138838.869 0.926843734 0.603368269 0.770281114 0.756773439 0.828059454 0.694890064 0.813604667 0.783547196 1 20.11913221 -0.831614031 0.370294424 1.096710358 0.737319486 0.398173875 0.085663456 10.80071604 1.205350574 1.2314593 0.058902505 0.147362157 0.831614031 -0.359390872 GKLDDYQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GKLDDYQER 9 1 Q14444-2;Q14444;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ;;;; 129.88 0.00034377 3052200000 3052890 3024780 3125810 2866250 3521960 2602340 3525760 2930930 3996140 FALSE TRUE 2861815.064 3248737.858 3199955.689 2939802.828 3245359.469 3353593.313 2997105.02 3296863.062 3329158.418 0.859621173 0.975843577 0.961190574 0.883046842 0.974828789 1.007339661 0.900259057 0.990299243 1 21.66672609 GKLDGNQDLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GKLDGNQDLIR 11 1 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;; 158.4 2.73E-05 1468010000 2432230 3163280 2067440 1903740 4186380 1613610 1899370 3049310 3938510 FALSE TRUE 2280001.066 3397492.543 2116480.653 1952593.191 3857598.602 2079433.012 1614577.101 3430023.066 3281147.237 0.69487923 1.035458727 0.645042877 0.595094658 1.175685918 0.633751814 0.492077004 1.045373102 1 21.6457689 GKLEAIIT(ph)PPPAK ddPTM_SK-BR-3_Pertuzumab_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 113.28 0.0013494 1321620000 3515300 2163400 2837600 2336400 3246400 2081500 3954400 2864000 4842700 TRUE FALSE 3295283.648 2323580.387 2904909.212 2396355.98 2991440.839 2682395.26 3361474.431 3221576.704 4034422.085 0.816791991 0.575938843 0.72003106 0.593977509 0.741479393 0.6648772 0.8331985 0.798522474 1 21.9439306 1.097743726 0.755645645 0.996132454 0.665778634 0.632158781 0.075397908 0.355473383 0.468299927 0.063473274 0.024592122 12.52401923 -1.097743726 -0.33035382 GKLEEQRPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GKLEEQRPER 10 2 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;E9PJF7;P13693-2 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 ;;;;;; 168.22 2.81E-06 14806920000 15397980 14708910 15115310 14914580 15624080 12960720 17648050 13253180 16907280 FALSE TRUE 14434247.92 15797973 15473852.29 15297313.37 14397027.78 16702269.46 15001888.74 14907868.7 14085345.74 1.024770579 1.121589295 1.098578095 1.086044578 1.022128107 1.185790521 1.065070678 1.058395652 1 23.74769164 0.969801359 2.168819941 1.00109286 1.09289041 0.251361425 0.046881983 0.406505724 4.178416112 0.040087942 0.011059611 9.328275397 -0.969801359 0.09179755 GKLPES(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GKLPESPK 8 1 E9PKP7;P17480-2;P17480;E9PLT2 E9PKP7 UBTF Nucleolar transcription factor 1 1 GKLPES(1)PK;GKLPES(1)PK;GKLPES(1)PK;GKLPES(1)PK 103.21 0.0029166 1650990000 6355300 2816950 3933130 3631270 3666420 2716340 5349300 3339760 4254610 TRUE FALSE 5957533.118 3025519.909 4026425.701 3724454.536 3378474.163 3500503.262 4547222.125 3756736.388 3544488.105 1.680788012 0.853584444 1.13596818 1.050773603 0.953162788 0.987590636 1.28289953 1.059881223 1 21.75714586 4.749951796 24.96983487 1.052330172 1.680788388 0.757227791 0.113764237 914.3038459 2004145.681 0.028353496 0.44728932 56227.89127 -4.749951796 0.628458216 GKLPIVNDCDELVAIIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKLPIVNDCDELVAIIAR 18 1 P20839-3;P20839-7;P20839-5;P20839-6;P20839;A0A3B3IRL5;C9J381;P20839-2;P20839-4;C9K0R9 P20839-3 IMPDH1 Inosine-5-monophosphate dehydrogenase 1;Inosine-5-monophosphate dehydrogenase 0 162.33 3.27E-11 197490000 1135700 1041700 1074600 1029100 1213400 1008100 1532100 1082600 1418300 FALSE TRUE 1064618.564 1118828.552 1100090.019 1055508.448 1118104.459 1299122.105 1302375.828 1217764.993 1181576.567 0.901015299 0.946894668 0.931035745 0.893305163 0.946281849 1.099481947 1.102235661 1.030627237 1 20.17228169 2.305554114 5.705584537 1.071430944 0.925015003 0.785822598 0.03465274 0.07853636 4.736167048 0.01156834 0.009533824 202.0943231 -2.305554114 -0.146415941 GKLPIVNEDDELVAIIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKLPIVNEDDELVAIIAR 18 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 216.17 8.31E-19 123594000 163102 180888 192615 194218 204005 143804 221042 169728 222742 FALSE TRUE 152893.737 194281.1357 197183.9188 199201.9627 187983.2702 185317.8803 187898.8042 190918.9144 185564.9212 0.823936636 1.04697124 1.062614192 1.073489329 1.013032361 0.998668709 1.012577177 1.028852399 1 17.50156449 4.740983939 24.83546418 1.032540267 0.823936555 0.86627706 0.025360416 75.6797306 775553.8171 0.006710261 0.044849453 55078.73275 -4.740983939 -0.208603711 GKLS(ph)AEENPDDSEVPSSSGINSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKLSAEENPDDSEVPSSSGINSTK 24 1 A0A494C1S7;Q9Y5Q9;Q9Y5Q9-2 A0A494C1S7 GTF3C3 General transcription factor 3C polypeptide 3 1 GKLS(1)AEENPDDSEVPSSSGINSTK 85.004 7.37E-05 0 277350 195020 210050 217120 226790 144020 286750 177940 267480 TRUE FALSE 259991.1586 209459.4837 215032.4852 222691.6668 208978.8282 185596.236 243754.4996 200156.2007 222835.86 1.166738417 0.939972066 0.964981512 0.999352917 0.937815073 0.832883164 1.093874655 0.898222578 1 17.76562189 4.742315368 24.58839487 0.961687467 1.166738517 0.478076097 0.068337913 253.6788306 1661156.328 0.015044694 0.111591923 55247.84823 -4.742315368 0.20505105 GKNDGTVQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 163.9 5.77E-06 273770000 348270 358390 368790 385430 442860 332870 448190 373800 482890 FALSE TRUE 326472.4024 384925.5685 377537.873 395320.7863 408079.562 428964.1653 380988.0703 420469.7528 402292.5394 0.811529846 0.956829995 0.938466007 0.982669942 1.01438511 1.066299082 0.947042346 1.045184068 1 18.61788546 6.227155159 0.557721136 1.00723792 9.36E-13 0.696982702 0.038771456 10.53618548 0.673642318 0.017378858 9.909650312 1687155.683 -6.227155159 -1.00723792 GKNENESEKR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 175.86 1.50E-06 4258130000 3990531 2708736 3153172 3052385 3036532 2182729 3612086 2565511 3616096 FALSE TRUE 3740770.788 2909293.632 3227966.729 3130714.367 2798055.026 2812847.429 3070487.237 2885820.696 3012546.217 1.241730589 0.965725809 1.071507787 1.03922534 0.928800697 0.933710963 1.019233239 0.957934082 1 21.52255194 4.742644874 24.80883884 0.994443066 1.241730697 0.75038366 0.045637162 196.1596102 1191474.398 0.011194975 0.08600103 55289.7815 -4.742644874 0.247287631 GKNNTVGLIQLNRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKNNTVGLIQLNRPK 15 2 P30084 P30084 ECHS1 "Enoyl-CoA hydratase, mitochondrial" 0 103.6 0.00082087 312300000 306960 411860 323330 343120 490390 349010 415460 401360 655230 FALSE TRUE 287747.9215 442354.5429 330999.5403 351925.0401 451876.7475 449763.5213 353165.6299 451470.6795 545867.8801 0.527138401 0.810369247 0.606372993 0.64470736 0.827813403 0.823942089 0.646980053 0.827069509 1 19.05819228 -5 0.146812592 2.040665163 0.616331916 0.531180221 0.095603189 113.0838096 0.996737103 34.14550492 0.491956352 1.00E-05 5 -1.424333247 GKPDAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GKPDAAK 7 1 P09429 P09429 HMGB1 High mobility group protein B1 0 ;;; 92.439 0.01429 1384170000 2784980 2237450 2551100 2362060 2818260 1549540 2520980 2686060 2968950 FALSE TRUE 2610673.073 2403113.126 2611613.297 2422674.459 2596925.228 1996867.043 2142982.453 3021420.504 2473413.065 1.055494171 0.97157776 1.055874303 0.9794864 1.049935922 0.807332617 0.866407024 1.221559208 1 21.23807176 GKPELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GKPELR 6 1 J3KTJ3;P62829;J3KT29;J3QQT9;C9JD32;B9ZVP7 J3KTJ3 RPL23 60S ribosomal protein L23 0 ;;; 100.82 0.033949 5402630000 13043200 13012100 13540900 12825000 14001200 11950300 15131000 11187700 14542400 FALSE TRUE 12226849.39 13975529.42 13862096.54 13154111.21 12901602.23 15400157.61 12862247.02 12584508.97 12115179.49 1.009217354 1.153555292 1.14419242 1.085754546 1.064912182 1.271145642 1.061663761 1.038738962 1 23.53031244 1.508891434 10.00476347 1.029607573 1.127028943 0.278564172 0.068451106 0.127482082 26.20392929 0.034250086 0.015888666 32.27687157 -1.508891434 0.097421371 GKPLPEYHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKPLPEYHVR 10 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 102.52 0.0017639 868320000 2136010 2761300 2191100 2490500 2652800 1755890 2880700 2771900 2696100 FALSE TRUE 2002320.947 2965749.525 2243073.927 2554410.446 2444459.789 2262786.939 2448765.778 3117977.817 2246103.493 0.891464242 1.32039754 0.99865119 1.137263022 1.08831129 1.007427728 1.090228383 1.388171928 1 21.09899297 GKPNWEHLNEDLHVLITVEDAQNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKPNWEHLNEDLHVLITVEDAQNR 24 1 Q96PU8-5;Q96PU8-9;Q96PU8-8;Q96PU8-6;Q96PU8-3;Q96PU8;F5GXS8;F5GYM3;H0YG47 Q96PU8-5 QKI Protein quaking 0 58.015 0.053866 7916500 9374.8 12548 9559.9 10529 13099 7745.2 10788 10478 14268 FALSE TRUE 8788.048002 13477.06698 9786.665343 10799.19197 12070.25738 9981.113507 9170.439551 11786.20136 11886.57863 0.739325274 1.133805395 0.823337451 0.908519794 1.015452618 0.839696083 0.771495301 0.991555412 1 13.5370459 2.208760141 24.98244379 0.868344759 0.938239626 0 0.124977808 592.0908117 496360.1593 0.043938368 0.032454816 161.7186625 -2.208760141 0.069894866 GKPSEQLT(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKPSEQLTPTR 11 1 Q14687;Q14687-2;Q14687-3;H0Y613 Q14687 GSE1 Genetic suppressor element 1 1 GKPSEQLT(0.984)PT(0.016)R 119.32 0.00097421 320250000 396920 306560 368250 359660 364520 296260 447930 328570 332270 TRUE FALSE 372077.4857 329258.0214 376985.0639 368889.4845 335892.0696 381785.4526 380767.0549 369592.6878 276811.9905 1.344152344 1.189464448 1.361881266 1.332635497 1.213430347 1.379222959 1.375543936 1.335175861 1 18.07854691 -0.95892687 6.173173834 0.999999882 1.313953257 0.70254546 0.064691034 1.06E-07 1.79E-08 0.063633859 0.014998639 0.109919091 0.95892687 0.313953374 GKPYLTLEQLMDFINQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKPYLTLEQLMDFINQK 17 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 0 117.18 0.00020994 67392000 100340 134140 110790 92647 156010 72715 107900 126990 138210 FALSE TRUE 94059.89851 144071.8652 113417.9911 95024.47887 143757.6039 93706.64007 91721.39669 142844.981 115141.8581 0.816904469 1.251255343 0.98502832 0.825281791 1.248526003 0.813836441 0.796594724 1.240599929 1 16.81305287 3.618768652 5.946120322 0.960800653 1.080229955 0 0.190968145 0.589183333 27.97399279 0.048073553 0.075210747 4156.891143 -3.618768652 0.119429301 GKQS(ph)PPGPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKQSPPGPGK 10 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 GKQS(1)PPGPGK;GKQS(1)PPGPGK 53.448 0.086934 742700000 2322090 1464460 1733160 1738410 1748150 1342150 2089180 1421050 1561740 TRUE FALSE 2176754.532 1572890.142 1774271.374 1783020.544 1610857.351 1729606.917 1775926.854 1598471.221 1301075.505 1.673042436 1.208915345 1.363695932 1.3704205 1.238096747 1.329367059 1.364968326 1.228576831 1 20.31127326 -4.299168058 0.172071356 1.06E-13 1.419307892 0.507729831 0.119213348 91.31809168 1.078363175 31.8654571 0.399435795 5.02E-05 4.299168058 1.419307892 GKS(ph)DSEDGEKENEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKSDSEDGEKENEK 14 2 O00203;O00203-3 O00203 AP3B1 AP-3 complex subunit beta-1 1 GKS(0.824)DS(0.176)EDGEKENEK;GKS(0.992)DS(0.008)EDGEKENEK 112.56 0.00030601 306820000 876240 219860 389300 426060 413550 280940 585220 295580 512560 TRUE FALSE 821397.7025 236138.6632 398534.3798 436993.4209 381071.4512 362042.8173 497471.6939 332483.8137 427010.4247 1.923601053 0.553004446 0.933312998 1.023378811 0.892417208 0.847854751 1.165010653 0.778631608 1 18.70391177 4.750870142 24.86531988 0.899614241 1.923601732 0.799127226 0.161407673 853.2660424 1723569.177 0.04019281 0.697328991 56346.91489 -4.750870142 1.02398749 GKS(ph)SPICSTTGDDKLCADSACQQNTVTSSGDLVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKSSPICSTTGDDKLCADSACQQNTVTSSGDLVAK 35 2 Q12802-2;Q12802;Q12802-4;H0YMW2 Q12802-2 AKAP13 A-kinase anchor protein 13 1 GKS(0.425)S(0.425)PICS(0.05)T(0.05)T(0.05)GDDKLCADSACQQNTVTSSGDLVAK;GKS(0.41)S(0.41)PICS(0.06)T(0.06)T(0.06)GDDKLCADSACQQNTVTSSGDLVAK 102.36 1.34E-05 287100000 211682 97035 143682 132708 157884 101881 193147 125502 254371 TRUE FALSE 198433.2015 104219.5724 147090.2049 136113.512 145484.4275 131292.3908 164186.4004 141171.201 211914.8368 0.936381824 0.491799319 0.694100551 0.642302889 0.686523085 0.619552613 0.774775391 0.6661695 1 17.69312507 -0.340254537 0.514805313 1.047278956 0.657168305 0.402809196 0.115487557 6.355660634 1.606841612 0.66962653 0.049241407 0.456820372 0.340254537 -0.390110652 GKTPEEIR ddPTM_SK-BR-3_Pertuzumab_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 520360000 1595790 2013460 1749130 1729480 2260300 1489310 1988170 1937790 2296800 FALSE TRUE 1495912.352 2162538.673 1790620.19 1773861.385 2082785.156 1919249.62 1690062.366 2179727.347 1913449.242 0.781788364 1.130178228 0.93580752 0.927049093 1.08849773 1.003031373 0.88325435 1.139161311 1 20.8677442 4.762279228 23.80974254 1.00343963 0.781787875 0.413185358 0.086012953 3810.401331 3824922.897 0.019659818 1.120218444 57846.78518 -4.762279228 -0.221651755 GKTPQVGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GKTPQVGDR 9 1 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H2E6;F5H3E1 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ; 77.288 0.03012 227200000 237639 242231 240906 240855 308520 202099 271800 266537 373910 FALSE TRUE 222765.5992 260166.0353 246620.4041 247035.7471 284290.0837 260441.7005 231046.1133 299814.7312 311502.0054 0.715133756 0.835198589 0.791713696 0.793047052 0.912642868 0.836083543 0.741716295 0.962480902 1 18.24888193 -4.99999996 0.145949774 1.667574603 0.754464467 0.513280704 0.063948177 119.0804169 1.046260856 22.88217038 0.337570449 1.00E-05 4.99999996 -0.913110136 GKVEEVELPVEK ddPTM_SK-BR-3_Pertuzumab_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 0 102.64 0.0021273 154030000 495200 314880 440600 370020 444230 330580 509690 397720 475930 FALSE TRUE 464206.316 338194.0428 451051.2401 379515.3396 409341.9677 426013.0795 433266.7162 447376.2175 396494.2084 1.170777041 0.852960865 1.137598559 0.957177511 1.032403397 1.074449691 1.092744124 1.128329766 1 18.59694027 2.266731099 3.822123939 1.08357152 1.016314887 0.039170175 0.093031748 0.504029021 15.81202176 0.03235995 0.025160574 184.8123965 -2.266731099 -0.067256633 GKYGQFSGLNPGGRPIT(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKYGQFSGLNPGGRPITPPR 20 2 P62136;P62136-2;P62136-3 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 1 GKYGQFSGLNPGGRPIT(1)PPR 101.58 0.016843 311270000 444180 492930 435660 457860 502790 358010 666970 434390 664480 TRUE FALSE 416379.5667 529427.0501 445994.0609 469609.4628 463302.9016 461361.6752 566964.0403 488624.5477 553573.9953 0.752166052 0.956379914 0.805662955 0.848322838 0.836930393 0.833423678 1.024188356 0.88267251 1 19.07841665 1.751238812 25 0.967361918 0.848847574 0.489971525 0.062023662 3.214767741 6349.139627 0.026331279 0.014602104 56.39476772 -1.751238812 -0.118514344 GKYS(ph)PTVQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKYSPTVQTR 10 1 O60437;K7EKI8 O60437 PPL Periplakin 1 GKY(0.001)S(0.826)PT(0.173)VQTR 66.004 0.040739 444290000 459210 406980 403110 393700 460710 340900 449770 348720 726930 TRUE FALSE 430468.8658 437113.2227 412671.9596 403803.0085 424527.695 439312.296 382331.164 392258.4596 605600.6869 0.710813041 0.721784556 0.681425845 0.666780962 0.701002664 0.725415782 0.631325512 0.64771799 1 19.20800732 -2.0622051 2.629149172 1.457324537 0.686184759 0.911499898 0.03076962 4129640.132 1311386.256 11358945.96 0.007902522 0.008665525 2.0622051 -0.771139778 GKYSPT(ph)VQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GKYSPTVQTR 10 1 O60437;K7EKI8 O60437 PPL Periplakin 1 GKYS(0.02)PT(0.98)VQTR 90.861 0.017044 413860000 433800 365960 433770 449780 440780 349710 420810 360020 724210 TRUE FALSE 406649.2324 393056.0592 444059.2292 461322.1163 406162.9168 450665.5999 357713.4471 404969.2895 603334.6724 0.674002757 0.651472685 0.736008139 0.764620595 0.673196711 0.7469579 0.5928939 0.671218327 1 19.20259897 -1.060261024 5.160249059 1.000004428 0.687056789 0.790948513 0.050273437 2.59E-06 4.71E-07 0.049212213 0.011599266 0.087044027 1.060261024 -0.312947638 GLAGPPAS(ph)PGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GLAGPPASPGK 11 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 GLAGPPAS(1)PGK;GLAGPPAS(1)PGK;GLAGPPAS(1)PGK;GLAGPPAS(1)PGK 168.98 1.83E-05 2263460000 4797800 3251260 3769590 3395080 4034110 2897210 4156650 3291260 5072300 TRUE FALSE 4497514.262 3491986.673 3859006.455 3482203.501 3717287.273 3733587.495 3533398.921 3702181.056 4225700.362 1.064323988 0.826368738 0.913222927 0.824053578 0.879685485 0.883542886 0.836168828 0.876110642 1 22.01075904 4.746860463 24.92207015 0.871451205 1.064324089 0.552478207 0.051671188 653.8836353 1963380.068 0.010486757 0.119182116 55829.07889 -4.746860463 0.192872884 GLAPDLPEDLYHLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GLAPDLPEDLYHLIK 15 0 P62277;J3KMX5 P62277 RPS13 40S ribosomal protein S13 0 ;;;;; 225.32 1.01E-12 4167492000 6084191 5914915 6499737 6365805 6592968 5494567 7548968 5814928 6303156 FALSE TRUE 5703392.346 6352861.461 6653913.831 6529162.334 6075182.888 7080759.296 6417070.33 6540934.561 5251118.544 1.086129041 1.209811092 1.267142186 1.243385058 1.156931202 1.348428766 1.222038748 1.245626909 1 22.32419333 -0.936478233 4.747375796 0.999997953 1.229094309 0.508104947 0.068503132 1.36E-06 3.04E-07 0.060743176 0.014317176 0.115750205 0.936478233 0.229096356 GLAPEVADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLAPEVADR 9 0 B3KWE1;P12081-4;P12081;B4DDD8;P12081-3;P12081-2;B4E1C5;E7ETE2;A0A2R8Y3N3;A0A2R8Y5P7;P49590-2;P49590;D6RJE6;A0A2R8Y6I1;D6RB22;B4DQ67 B3KWE1;A0A2R8Y3N3 HARS;HARS2 "Histidine--tRNA ligase, cytoplasmic;Probable histidine--tRNA ligase, mitochondrial" 0 126.41 0.0011033 132820000 211500 278030 285900 280810 272130 232710 272340 255680 283530 FALSE TRUE 198262.5925 298615.6305 292681.683 288016.06 250758.0075 299889.5993 231505.1453 287602.2108 236207.0113 0.839359473 1.264211544 1.239089735 1.219337472 1.061602728 1.269604986 0.980094299 1.21758541 1 17.84969226 0.845804514 0.62743759 1.006059581 1.169265601 0.03546847 0.14377467 2.317408331 2.017724596 0.140021541 0.056093237 7.011396285 -0.845804514 0.16320602 GLAPNT(ph)PGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLAPNTPGK 9 0 O43663-2;O43663-4;O43663;O43663-3;H0YL53;G3V3N7 O43663-2 PRC1 Protein regulator of cytokinesis 1 1 GLAPNT(1)PGK 97.911 0.071212 263800000 626230 609400 551430 491010 742550 268140 890030 505600 1306900 TRUE FALSE 587035.3822 654520.6101 564510.18 503610.1479 684233.1183 345547.6651 756578.2641 568725.273 1088769.947 0.539173022 0.601156022 0.518484352 0.462549641 0.628446 0.31737436 0.694892678 0.522355778 1 20.05426772 -0.096111848 0.872426808 1.009955994 0.534254868 0.675526937 0.101093898 4.276095798 2.85800492 0.23188905 0.028674556 0.801471626 0.096111848 -0.475701127 GLAPPPPTSAS(ph)PSLLSNRPPPPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLAPPPPTSASPSLLSNRPPPPAR 24 1 Q8TF74;Q8TF74-2 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 1 GLAPPPPT(0.001)S(0.009)AS(0.972)PS(0.018)LLSNRPPPPAR;GLAPPPPT(0.05)S(0.192)AS(0.749)PS(0.008)LLSNRPPPPAR 151.41 6.73E-08 537630000 77101 75820 79944 75770 81098 74119 78118 76699 71733 TRUE FALSE 72275.38604 81433.79169 81840.30943 77714.38648 74728.89021 95515.95208 66404.93111 86275.03899 59760.29889 1.209421428 1.362673768 1.36947624 1.300435037 1.250477183 1.598317844 1.111188069 1.443684864 1 15.86689974 -1.800156003 2.602112735 0.900520707 1.329439792 0.382130429 0.132148634 24054201.97 16026079.03 15070731.24 0.029228324 0.01584324 1.800156003 0.428919086 GLAPPPPTSAS(ph)PSLLSNRPPPPARDPPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLAPPPPTSASPSLLSNRPPPPARDPPSR 29 2 Q8TF74;Q8TF74-2 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 1 GLAPPPPT(0.059)S(0.184)AS(0.726)PS(0.03)LLS(0.001)NRPPPPARDPPSR;GLAPPPPT(0.06)S(0.168)AS(0.634)PS(0.099)LLS(0.035)NRPPPPARDPPS(0.003)R 76.478 0.0027118 653250000 225450 285330 247130 280070 332180 255090 318450 257710 366440 TRUE FALSE 211339.4869 306456.1301 252992.0403 287257.0704 306091.9227 328730.342 270701.3788 289885.6608 305278.7967 0.692283543 1.003856584 0.828724573 0.940966335 1.002663552 1.076820092 0.886734951 0.949576793 1 18.21976786 3.045670226 6.053726108 0.976292527 0.874964981 0.320464913 0.089595514 0.282343881 24.81693812 0.024941793 0.029711276 1110.887874 -3.045670226 -0.101327546 GLATFCLDKDALRDEYDDLSDLNAVQMESVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLATFCLDKDALRDEYDDLSDLNAVQMESVR 31 2 U3KQM0;O15173;O15173-2 U3KQM0 PGRMC2 Membrane-associated progesterone receptor component 2 0 137.88 3.95E-07 65346000 47777 55519 45069 53626 84572 37922 64599 60605 88744 FALSE TRUE 44786.72285 59629.68453 46138.05796 55002.13395 77930.05627 48869.46579 54912.97966 68171.66766 73932.05309 0.605782215 0.80654712 0.624060283 0.743955181 1.054076723 0.661005122 0.742749286 0.922085412 1 16.17391236 -4.999999874 0.07654022 1.842279579 0.490369785 0.352389189 0.124016512 323.2839277 1.763601072 46.20383589 4.777283726 1.00E-05 4.999999874 -1.351909795 GLCNFLMSDEEYDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLCNFLMSDEEYDDR 15 0 Q9UKN8 Q9UKN8 GTF3C4 General transcription factor 3C polypeptide 4 0 ; 242.48 1.46E-17 109003000 106976 142799 146863 134039 133635 120985 154991 126009 130572 FALSE TRUE 100280.5631 153371.9865 150346.6597 137478.6677 123139.8462 155911.4055 131751.5384 141741.501 108778.6897 0.921876917 1.409945156 1.382133395 1.26383824 1.132021782 1.433289976 1.211188872 1.303026369 1 16.73103643 -2.238913159 0.749086743 0.574771795 1.281642468 0.206619719 0.151714506 773.4267853 71.80322204 550.5979048 0.048296541 0.005768818 2.238913159 0.706870673 GLDDDRGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLDDDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 111.65 0.0019062 1354230000 2472700 2934500 2932900 2918800 2975800 2885000 3175700 2731700 3035400 FALSE TRUE 2317938.121 3151773.433 3002469.773 2993701.35 2742092.672 3717852.666 2699533.267 3072758.758 2528772.131 0.916625936 1.246365141 1.187323182 1.183855719 1.08435736 1.470220516 1.067527293 1.21511888 1 21.27000561 -1.169873627 4.012600551 0.999917344 1.182155809 0.121955919 0.141982243 9.44E-05 1.95E-05 0.120156381 0.028307937 0.067627973 1.169873627 0.182238466 GLDDDRGPWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GLDDDRGPWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;;; 131.28 0.00023183 3621530000 1341000 1752530 1612070 1543090 1885320 1424650 1734470 1590740 1675230 FALSE TRUE 1257069.204 1882289.145 1650309.062 1582688.302 1737254.572 1835923.328 1474402.326 1789347.391 1395623.291 0.900722431 1.348708607 1.182488909 1.134036894 1.244787604 1.315486306 1.056447206 1.282113449 1 20.41247815 -1.257844401 3.78500854 0.999710901 1.19392052 0.154724089 0.132364735 40.31049197 29879010.09 15367.53301 0.027725745 0.055227527 1.257844401 0.194209619 GLDDS(ph)TGGTPLTPAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLDDSTGGTPLTPAAR 16 0 Q9NXR1;Q9NXR1-1;I3L533;I3L2R9;I3L2T8;I3L2R3;I3L522 Q9NXR1 NDE1 Nuclear distribution protein nudE homolog 1 1 GLDDS(0.722)T(0.27)GGT(0.004)PLT(0.004)PAAR 57.525 0.075739 207670000 61310 204930 185620 177920 173480 220080 145190 168170 90589 TRUE FALSE 57472.71654 220103.2304 190022.9941 182485.7284 159855.5806 283613.5233 123420.1074 189166.3947 75469.11067 0.761539602 2.91646779 2.517890994 2.4180188 2.118159061 3.758008022 1.635372489 2.506540663 1 16.20359865 1.605839701 25 1.803164956 2.4893983 0.131966389 0.82253573 0.392141787 4749.05609 0.373654368 0.186345877 40.34964337 -1.605839701 0.686233344 GLDEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLDEDR 6 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 114.59 0.058529 296100000 598030 731160 742620 722420 761650 702390 813140 725430 739690 FALSE TRUE 560600.3698 785295.8472 760235.2971 740958.5203 701833.0813 905158.5907 691217.2058 816001.5324 616230.9604 0.909724447 1.27435312 1.233685657 1.202403916 1.138912399 1.468862567 1.121685294 1.324181329 1 19.23311164 4.743212669 24.6244533 1.232083516 0.909724284 0.373940892 0.125586571 368.6952732 1951509.626 0.025605828 0.206883698 55362.11452 -4.743212669 -0.322359232 GLDFSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GLDFSDR 7 0 Q13561;Q13561-3;Q13561-2;F8W1I6;F8VW18;F8VX93;F8VRV7;H0YHL1 Q13561 DCTN2 Dynactin subunit 2 0 ;;;; 167.24 0.0025446 1542900000 2194270 2928990 2811910 2839630 2973710 2697480 2852490 2527550 2965250 FALSE TRUE 2056934.558 3145855.467 2878609.833 2912499.713 2740166.812 3476198.686 2424785.606 2843120.181 2470330.619 0.832655573 1.273455238 1.165273106 1.178991869 1.109230801 1.407179533 0.981563191 1.150906749 1 21.23627271 1.622033684 25 1.04967247 1.174775385 0.114352012 0.150021554 1.578432653 2778.760227 0.062700401 0.034557815 41.88260484 -1.622033684 0.125102915 GLDGIPFTVDATSQIHCIEDFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GLDGIPFTVDATSQIHCIEDFHR 23 0 Q15654;H7BZE2 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 ;; 211.03 3.22E-25 353034000 259255 339234 326322.9 314040 384786 356231 416901 324506 485265 FALSE TRUE 243028.6923 364351.2383 334063.4333 322098.7981 354566.4597 459069.1068 354390.5654 365021.2884 404271.1366 0.601152717 0.901254642 0.826335108 0.796739537 0.877051136 1.13554757 0.876616046 0.902912069 1 18.62496368 2.471046578 24.99240416 0.969821239 0.811650283 0.43949119 0.102369787 168.8740875 694773.6479 0.033382564 0.028001873 295.8329728 -2.471046578 -0.158170956 GLDHDFGPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GLDHDFGPSR 10 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6 Q9UDY2-7 TJP2 Tight junction protein ZO-2 0 ;; 148.56 2.49E-05 872680000 479390 763080 503940 453320 874580 399190 418240 705480 705750 FALSE TRUE 449385.8356 819579.2372 515893.6948 464952.9587 805894.0147 514429.6727 355528.7947 793560.731 587955.7657 0.764319124 1.393947105 0.877436237 0.790795815 1.370671166 0.874946217 0.604686297 1.349694615 1 19.16534809 GLDHLLDENRVPDLAQMYQLFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLDHLLDENRVPDLAQMYQLFSR 23 1 Q13619;A0A0A0MR50;Q13619-2 Q13619 CUL4A Cullin-4A 0 ; 302.66 2.94E-62 332470000 233667 322400 268270 249468 345470 269657 326800 281427 301763 FALSE TRUE 219042.1996 346270.8315 274633.4911 255869.7712 318338.1798 347502.5984 277799.3739 316563.7804 251396.8058 0.871300647 1.377387554 1.092430312 1.017792451 1.266277742 1.382287246 1.105023482 1.259219581 1 17.93960679 -1.712287083 6.463055859 0.997449259 1.184574178 0.097456411 0.159614159 0.005364986 0.000238831 0.141334647 0.032906072 0.019396033 1.712287083 0.187124919 GLDIESYDS(ph)LERPLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLDIESYDSLERPLRK 16 2 Q9H792 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 1 GLDIESYDS(1)LERPLRK 93.776 0.0022525 78923000 52017 62012 54492 56717 74721 51538 63991 57091 83301 TRUE FALSE 48761.34882 66603.433 55784.57597 58172.45424 68852.71407 66416.18395 54396.14361 64218.93702 69397.52495 0.702638154 0.959737873 0.803841002 0.838249697 0.992149419 0.957039664 0.783834058 0.925377916 1 16.08259659 -4.207726264 0.017092461 2.030292758 1.61E-06 0.255493743 0.085984219 6976.692859 10.28565811 764.4700547 485.8765496 6.20E-05 4.207726264 -2.030291143 GLDIPEVDLVIQSS(ph)PPKDVESYIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLDIPEVDLVIQSSPPKDVESYIHR 25 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 GLDIPEVDLVIQS(0.183)S(0.812)PPKDVES(0.003)Y(0.001)IHR 85.881 0.010316 22569000 77426 54993 69365 75993 68016 54046 90774 51927 77277 TRUE FALSE 72580.04487 59064.73894 71010.37056 77943.10904 62674.29772 69648.20284 77163.2814 58410.20026 64378.96947 1.127387491 0.917453936 1.103005704 1.210692089 0.973521295 1.081847122 1.198579009 0.907286972 1 15.97430186 3.736815126 22.76164114 1.085701081 1.00826671 0.00558789 0.106914181 267.4277042 627918.3542 0.025413575 0.044961046 5455.255877 -3.736815126 -0.077434371 GLDIPEVDLVIQSSPPKDVESYIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLDIPEVDLVIQSSPPKDVESYIHR 25 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 216.65 9.66E-34 353737000 243769 294317 270931 296141 342333 236178 330223 229281 438117 FALSE TRUE 228511.9334 316108.5369 277357.6113 303740.4794 315447.5471 304358.7546 280709.1268 257907.2376 364992.4424 0.626073055 0.866068719 0.759899601 0.832182928 0.86425775 0.833876868 0.769082025 0.706609802 1 18.47750707 -2.505803008 2.242493686 3.830018632 0.792278285 0.450141906 0.074906323 4259751.362 313133.7134 61541800.64 0.016474242 0.003120305 2.505803008 -3.037740347 GLDIPEVDLVIQSSPPQDVESYIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLDIPEVDLVIQSSPPQDVESYIHR 25 0 Q9BQ39;A0A087WVC1 Q9BQ39 DDX50 ATP-dependent RNA helicase DDX50 0 191.41 6.93E-18 26320000 27254 35421 33188 34422 31442 29338 35165 30661 29760 FALSE TRUE 25548.22079 38043.6077 33975.23503 35305.3268 28972.67215 37807.40434 29892.33471 34489.09334 24792.86374 1.030466712 1.534457983 1.37036348 1.42401165 1.168589174 1.524930913 1.205683015 1.391089537 1 14.5976373 -1.263332123 0.441272829 0.828799918 1.362840159 0.279663012 0.160716667 26.44967852 2.906970049 5.485865996 0.080071167 0.054534066 1.263332123 0.53404024 GLDIPHVDVVVNFDIPTHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLDIPHVDVVVNFDIPTHSK 20 0 Q9H0S4;Q9H0S4-2 Q9H0S4 DDX47 Probable ATP-dependent RNA helicase DDX47 0 205.68 4.86E-22 119990000 192970 189450 206670 192460 193770 153140 232530 181950 219280 FALSE TRUE 180892.3522 203477.0751 211572.31 197398.8494 178552.0858 197349.032 197664.2852 204666.858 182680.7514 0.990210248 1.11383971 1.158153272 1.080567317 0.977399559 1.080294615 1.082020321 1.120352618 1 17.4789651 3.001660822 24.99889271 1.058183046 1.105197249 0.043748027 0.05862733 119.0554056 1791987.955 0.01672024 0.01986099 1003.831505 -3.001660822 0.047014203 GLDISHISQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLDISHISQR 10 0 H3BVG0;Q8N1F7;H3BM93;H3BNN5;H3BV11;H3BRI8 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 178.84 0.0031311 0 96163 305450 200550 206200 288270 184770 237460 266030 235680 FALSE TRUE 90144.32949 328065.8358 205307.1407 211491.4411 265630.437 238110.0995 201855.0775 299244.4311 196343.4854 0.459115459 1.670877111 1.045652929 1.077150284 1.35288643 1.212722179 1.028071173 1.524086376 1 17.58302021 4.76090951 24.55418062 1.236245588 0.459114403 0.54750133 0.222785605 3774.59761 4146972.743 0.050607739 2.620784264 57664.63004 -4.76090951 -0.777131185 GLDIYVWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLDIYVWR 8 0 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 0 98.418 0.017533 127030000 201090 333890 249130 251320 340360 216420 263800 275750 255350 FALSE TRUE 188504.1359 358611.563 255039.4812 257769.2967 313629.4985 278896.9407 224245.639 310177.9945 212730.4354 0.886117379 1.685755789 1.19888572 1.211717995 1.474304784 1.311034503 1.054130494 1.458080006 1 17.69866693 -1.185288718 0.291270395 0.807849594 1.340487638 0.097498638 0.229331492 32.57438873 2.151646636 5.211595927 0.251482255 0.06526965 1.185288718 0.532638044 GLDQDHAR ddPTM_SK-BR-3_Pertuzumab_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 0 120.15 0.0015563 70194000 208220 307360 249990 243870 338590 249230 232110 250390 311450 FALSE TRUE 195187.8819 330117.2542 255919.8809 250128.1171 311998.5072 321178.6551 197307.2603 281651.7427 259466.983 0.752264815 1.272290025 0.986329274 0.964007498 1.202459379 1.237840173 0.760433016 1.085501282 1 17.98519144 1.742126673 24.99999952 0.929737899 1.084151304 0.091375333 0.17160314 1.134625206 7996.281406 0.072987232 0.040475122 55.22384908 -1.742126673 0.154413405 GLDVDSLVIEHIQVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GLDVDSLVIEHIQVNK 16 0 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2;J3KRB3;A0A087WWH0;J3QS96 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 0 ;;;;; 296.04 1.10E-45 2357077000 2781519 2720702 2919557 2799849 2974291 2519733 3392363 2541173 3097125 FALSE TRUE 2607428.691 2922145.607 2988810.271 2871697.865 2740702.183 3247139.013 2883709.661 2858444.043 2580194.829 1.010554963 1.132529053 1.158366119 1.112977141 1.062207455 1.258485978 1.117632525 1.107840389 1 21.29904858 0.781584047 2.908558522 1.000060657 1.129882468 0.255280202 0.063769168 1.504327864 18.10980722 0.05636295 0.014801671 6.047613763 -0.781584047 0.129821811 GLDVEDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 147.04 0.0012649 367473000 1737250 1297630 1550930 1423920 1599340 1260650 1834690 1356450 1920760 FALSE TRUE 1628518.624 1393707.875 1587718.792 1460460.198 1473734.288 1624579.19 1559595.267 1525805.768 1600172.747 1.01771426 0.870973386 0.992217118 0.912689083 0.920984494 1.01525238 0.974641813 0.953525656 1 20.60979623 2.249533783 24.99666756 0.983892165 0.938454345 0.190286203 0.043392163 317.4530427 723152.0263 0.013930014 0.011549537 177.6371445 -2.249533783 -0.04543782 GLDWVKEEAPDILCLQETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLDWVKEEAPDILCLQETK 19 1 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;H7C4A8;G3V5M0;G3V359;G3V5D9 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 213.45 3.14E-17 220310000 574570 533150 502910 557820 713750 362010 644670 510120 1051840 FALSE TRUE 538608.6893 572624.9807 514839.2627 572134.6056 657694.9541 466516.4103 548007.7183 573809.6049 876281.1089 0.61465286 0.653471785 0.587527515 0.652912176 0.750552474 0.532382138 0.625378903 0.654823662 1 19.74103423 0.694576666 3.641143978 0.999997129 0.62892118 0.814508155 0.055002578 2.054290004 24.09980108 0.049555307 0.012739076 4.9496748 -0.694576666 -0.37107595 GLEDHESVVEVQAAWPVGGDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GLEDHESVVEVQAAWPVGGDSR 22 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ;; 238.87 1.44E-30 1314800000 606150 1087260 927860 1062190 1037790 976650 1116410 825180 719220 FALSE TRUE 568212.1535 1167761.862 949869.2774 1089447.594 956286.1596 1258593 949014.6847 928205.5394 599177.5357 0.948320188 1.948941327 1.585288534 1.818238383 1.595998018 2.100534358 1.583862258 1.549132743 1 19.19262401 0.771430445 2.068776616 1.001063704 1.697060935 0.3042403 0.304528649 0.93968465 6.486323664 0.255426578 0.070274444 5.907863399 -0.771430445 0.695997232 GLEFPMTDLDMLS(ph)PIHTPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GLEFPMTDLDMLSPIHTPQR 20 0 O60784;O60784-4;O60784-2;V9GYF4;B0QY02;B0QY01 O60784 TOM1 Target of Myb protein 1 1 GLEFPMTDLDMLS(1)PIHTPQR;GLEFPMTDLDMLS(1)PIHTPQR;GLEFPMTDLDMLS(1)PIHTPQR;GLEFPMTDLDMLS(1)PIHTPQR 198.64 9.89E-22 110339000 139025 148178 177570 209379 201346 144960 140160 124116 133544 TRUE FALSE 130323.6734 159149.2533 181782.0443 214752.0196 185533.0974 186807.5988 119144.3092 139612.1558 111254.6437 1.171399855 1.430495376 1.633927702 1.930274661 1.667643626 1.67909934 1.070915382 1.254888346 1 16.76350603 1.721251959 7.180505077 1.12650112 1.589465579 0.550059594 0.20267564 0.101318695 13.74493606 0.102875782 0.053848314 52.63225275 -1.721251959 0.462964459 GLEFPMTDLDMLSPIHT(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLEFPMTDLDMLSPIHTPQR 20 0 O60784;O60784-4;O60784-2;V9GYF4;B0QY02;B0QY01 O60784 TOM1 Target of Myb protein 1 1 GLEFPMTDLDMLSPIHT(1)PQR 161.53 8.25E-11 9292300 14010 19404 16573 24286 25907 12778 19102 12174 12131 TRUE FALSE 13133.13911 20840.69235 16966.11939 24909.21988 23872.36872 16466.80117 16237.83243 13693.9507 10106.25773 1.299505659 2.06215722 1.678773671 2.464732301 2.362137337 1.629366834 1.6067107 1.354997177 1 13.30296126 1.342270542 1.33167472 1.045941753 1.95287709 0.469661432 0.337688071 0.349929858 1.185949779 0.301928257 0.096864992 21.99229449 -1.342270542 0.906935336 GLEGERPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GLEGERPAR 9 1 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;;;;; 173.39 5.06E-05 32883100000 4746750 5799160 5235590 4877410 5401690 4980330 5399730 4690110 5478930 FALSE TRUE 4449659.391 6228535.84 5359780.667 5002572.598 4977463.057 6418070.422 4590090.615 5275680.558 4564461.188 0.974848774 1.36457198 1.174241701 1.09598316 1.090482064 1.406095957 1.005614995 1.15581672 1 22.12201314 1.620181459 25 1.060537836 1.197627048 0.171360358 0.132950227 1.271789717 2575.524219 0.057853911 0.031789636 41.70435984 -1.620181459 0.137089212 GLEPS(ph)PAAVAALPPEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLEPSPAAVAALPPEVR 17 0 Q9P265 Q9P265 DIP2B Disco-interacting protein 2 homolog B 1 GLEPS(1)PAAVAALPPEVR 113.01 0.00045398 18687000 18659 29882 23302 24745 27692 23862 26431 22919 32377 TRUE FALSE 17491.1665 32094.49437 23854.73444 25379.99859 25517.18202 30750.57203 22467.91692 25780.4876 26973.06954 0.648467779 1.189871784 0.884390796 0.940938463 0.946024404 1.140047186 0.832975902 0.955786199 1 14.71923209 4.764740679 24.27160362 0.981838039 0.648467127 0.493513286 0.107459572 5271.61768 4887211.024 0.024802084 1.914767014 58175.57428 -4.764740679 -0.333370912 GLESLPPLRPQQNPVLPVAGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLESLPPLRPQQNPVLPVAGER 22 1 P56192;P56192-2 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ; 195.13 1.07E-18 397970000 227242 253090 250389 274370 269310 237690 287230 229914 284880 FALSE TRUE 213019.3289 271829.0469 256328.3453 281410.7987 248159.4789 306307.2444 244162.528 258619.269 237331.6876 0.897559576 1.14535505 1.080042652 1.18572788 1.045623033 1.290629361 1.028781831 1.089695487 1 17.85654521 4.743785964 24.47191975 1.113754516 0.897559453 0.379958894 0.084314983 396.5396008 1857038.616 0.017477105 0.147433452 55435.24409 -4.743785964 -0.216195063 GLESTTLADKDGEIYCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GLESTTLADKDGEIYCK 17 1 P21291;E9PP21;E9PND2 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ;;; 231.44 4.23E-16 3689340000 5905480 4024390 4926960 4592900 5295430 4430830 6992170 4544700 8174610 FALSE TRUE 5535866.548 4322360.023 5043829.818 4710761.59 4879548.289 5709938.692 5943759.021 5112115.799 6810214.781 0.812876939 0.634687769 0.740627129 0.691719974 0.716504317 0.838437388 0.872771155 0.750654122 1 22.69926887 1.096441111 0.414211425 1.005507042 0.690060823 0.601229051 0.065453806 0.724766836 0.349739031 0.087219885 0.04942489 12.48651121 -1.096441111 -0.315446219 GLEVTAYSPLGSSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLEVTAYSPLGSSDR 15 0 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 147.33 1.04E-05 0 37872 42375 41363 39892 41883 32603 45109 37524 46075 FALSE TRUE 35501.65912 45512.48909 42344.14989 40915.69626 38593.67813 42014.95683 38345.32422 42208.954 38384.78484 0.92488884 1.185690874 1.103149335 1.065935277 1.005442086 1.094573201 0.998971972 1.099627214 1 15.22824694 3.062939788 4.249606229 1.040326539 1.09988735 0 0.073826526 0.437476566 15.97830439 0.020375388 0.024363796 1155.951966 -3.062939788 0.059560812 GLEYLYLNVHDEDRDDQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GLEYLYLNVHDEDRDDQTR 19 1 Q9Y6G9;C9JGM7;C9JLW1 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 ;;;;; 264.71 1.41E-31 3183690000 1757760 2145990 2078020 2107500 2141740 1904580 2262120 1898760 2265160 FALSE TRUE 1647744.939 2304881.333 2127311.616 2161582.018 1973536.38 2454401.328 1922936.106 2135824.366 1887090.163 0.873167044 1.221394387 1.127297284 1.145457732 1.045809267 1.300627483 1.018995353 1.13180833 1 20.84773192 -1.14824726 6.663907207 0.999999746 1.120262285 0.070913785 0.115677339 3.81E-07 4.86E-08 0.097924971 0.023081089 0.071080871 1.14824726 0.120262539 GLEYLYLSVHDEDRDDHTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GLEYLYLSVHDEDRDDHTR 19 1 O43237 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 ;;; 203.19 3.34E-16 448433000 220567 395235 326969 370177 414772 302146 338562 339037 376951 FALSE TRUE 206762.1052 424498.6106 334724.8591 379676.3685 382197.4802 389370.6453 287797.7712 381366.5158 314035.4429 0.658403724 1.351753823 1.065882424 1.20902394 1.217052052 1.239893948 0.916449967 1.214405967 1 18.26056787 1.749053481 25 1.03872175 1.150193374 0.023581411 0.19801348 7.803204667 18627.98006 0.082397562 0.045693465 56.11170697 -1.749053481 0.111471624 GLFDDEDEESDLFTEAPQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLFDDEDEESDLFTEAPQDR 20 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 0 194.85 1.49E-21 0 17941 19133 16866 20795 16937 15098 18415 17429 21254 FALSE TRUE 16818.10484 20549.62723 17266.06948 21328.63491 15606.83634 19456.5475 15653.84171 19605.04902 17706.57009 0.949822848 1.160565096 0.975122194 1.204560499 0.881414992 1.098832095 0.884069677 1.107218897 1 14.11199716 2.726626342 24.99730442 0.987390529 1.070959661 0.119224654 0.10465836 1406.703326 2946449.787 0.029631301 0.028135064 532.8762222 -2.726626342 0.083569132 GLFDEYGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GLFDEYGSK 9 0 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ;;; 147.51 0.00021457 642391000 1074090 1176210 1132600 1144120 1175170 790840 1296750 1004250 826270 FALSE TRUE 1006864.624 1263297.812 1159465.807 1173480.056 1082876.889 1019142.67 1102314.376 1129632.823 688360.1991 1.462700234 1.835227856 1.684388215 1.704747104 1.573125364 1.480536892 1.601362742 1.64104901 1 19.39280416 -2.583345733 0.267658083 4.64E-13 1.70970456 0.754927432 0.110652927 21.54785663 0.665527419 12.67551539 0.140046488 0.002610083 2.583345733 1.70970456 GLFIIDDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 GLFIIDDK 8 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5;Q13162;H7C3T4 Q06830;Q13162 PRDX1;PRDX4 Peroxiredoxin-1;Peroxiredoxin-4 0 ;;;;;;;; 181.81 0.00053946 6215682000 7147719 5719039 6376521 6332087 6618965 5123827 7770200 5424358 8001348 FALSE TRUE 6700356.027 6142482.598 6527775.089 6494579.073 6099138.189 6602992.677 6605130.645 6101601.037 6665871.328 1.005173322 0.921482323 0.979283093 0.974303096 0.914979886 0.990567077 0.99088781 0.915349357 1 22.66836204 GLFIIDDKGILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLFIIDDKGILR 12 1 Q06830;A0A0A0MSI0;A0A0A0MRQ5;Q13162;H7C3T4 Q06830;Q13162 PRDX1;PRDX4 Peroxiredoxin-1;Peroxiredoxin-4 0 ; 158.4 6.13E-05 1608720000 1311740 2751200 1972420 2447690 3756100 1422560 2494900 1835630 7957800 FALSE TRUE 1229640.535 2954901.711 2019206.734 2510501.869 3461111.057 1833229.979 2120812.907 2064812.446 6629591.771 0.185477564 0.445713976 0.304574822 0.378681215 0.522070012 0.276522302 0.31990098 0.311453935 1 22.66048861 -1.61045446 2.764074208 1.054465573 0.349981607 0.833582656 0.092202451 11644164.71 11189932.56 4583577.021 0.021859516 0.024521416 1.61045446 -0.704483966 GLFIIDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLFIIDGK 8 0 P32119 P32119 PRDX2 Peroxiredoxin-2 0 91.065 0.029109 0 190020 215520 201040 205950 220390 207810 226010 184170 248350 FALSE TRUE 178126.9874 231477.325 205808.7637 211235.0257 203081.4584 267801.3735 192121.8987 207164.0299 206898.7806 0.860937831 1.118795018 0.994731642 1.020958292 0.981549808 1.294359361 0.928579173 1.001282025 1 17.65856562 4.754136041 24.01532234 1.044354292 0.860937595 0.24101481 0.101228316 2410.375287 3716383.733 0.022170414 0.518886128 56772.24141 -4.754136041 -0.183416697 GLFITIHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLFITIHDR 9 0 P48163;P48163-2 P48163 ME1 NADP-dependent malic enzyme 0 ; 153.24 7.85E-05 542630000 577870 825780 642050 633620 880220 564200 726380 709720 937960 FALSE TRUE 541702.1482 886921.6104 657279.7292 649879.7619 811091.0718 727075.381 617466.0624 798330.1043 781408.4165 0.69323818 1.135029508 0.841147491 0.831677453 1.037986096 0.930467814 0.790196329 1.021655369 1 19.57571727 GLFS(ph)DEEDSEDLFSSQSASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GLFSDEEDSEDLFSSQSASK 20 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 1 GLFS(0.984)DEEDS(0.016)EDLFSSQSASK;GLFS(0.854)DEEDS(0.136)EDLFS(0.005)S(0.005)QS(0.001)ASK;GLFS(0.998)DEEDS(0.002)EDLFSSQSASK;GLFS(0.994)DEEDS(0.006)EDLFSSQSASK 221.48 5.03E-25 223051000 197563 156303 174647 164044 167537 138037.9 183785 136437 213503 TRUE FALSE 185197.8845 167875.8368 178789.7093 168253.6468 154379.3198 177887.2009 156228.1454 153471.4598 177867.97 1.041209862 0.943822751 1.005182154 0.945946855 0.867943339 1.000108119 0.87833771 0.862839216 1 17.44044721 3.032023157 6.005472947 0.916876651 0.985828459 0.27963628 0.053599456 0.222111811 23.27340793 0.014344629 0.016974212 1076.522612 -3.032023157 0.068951808 GLFYFDNSFRPVPLEQTYVGITEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLFYFDNSFRPVPLEQTYVGITEK 24 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 66.853 0.032996 121580000 92382 101220 93826 100800 131330 72391 117320 92010 126690 FALSE TRUE 86599.97553 108714.4341 96051.59703 103386.6987 121015.8716 93289.10653 99728.95515 103497.651 105544.6206 0.820505821 1.030032924 0.910056775 0.979554411 1.146584932 0.883883101 0.944898514 0.980605648 1 16.68749352 4.751299643 23.79974328 0.977391039 0.820505624 0.336815728 0.071691722 1289.817655 2409622.025 0.016395666 0.281360768 56402.66737 -4.751299643 -0.156885415 GLGAFVIDSDHLGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLGAFVIDSDHLGHR 15 0 Q13057;Q13057-2;K7EQ60 Q13057 COASY Bifunctional coenzyme A synthase;Phosphopantetheine adenylyltransferase;Dephospho-CoA kinase 0 ; 76.262 0.01699 252870000 141076 224307 195214 220659 215203 186616 222315 180798 155153 FALSE TRUE 132246.305 240914.9237 199844.5683 226321.4835 198301.8245 240489.0097 188980.9296 203371.0283 129256.962 1.023127133 1.863844856 1.546102935 1.750942309 1.534167456 1.860549761 1.462056099 1.573385489 1 16.97988246 0.360663187 1.189347229 0.999502269 1.617745719 0.353350951 0.24145612 3.081572299 4.828112197 0.204628435 0.061278455 2.294368584 -0.360663187 0.618243451 GLGGEVPGSHQGPDPYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLGGEVPGSHQGPDPYR 17 0 K7EM09;K7EPR0;K7ELQ9;Q6UW68 K7EM09 TMEM205 Transmembrane protein 205 0 91.616 0.0035116 244060000 225880 259150 196940 213800 290080 188370 265400 239290 251530 FALSE TRUE 211742.574 278337.7356 201611.5098 219286.47 267298.2869 242749.3611 225605.7339 269165.8832 209548.0181 1.010472807 1.328276632 0.962125587 1.046473605 1.275594441 1.158442649 1.076630244 1.284506939 1 17.67692135 -1.491068295 5.379005609 0.999743286 1.140280083 0.117163166 0.123028386 0.000351562 3.33E-05 0.110569309 0.026014094 0.032279865 1.491068295 0.140536797 GLGHPPSS(ph)PLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GLGHPPSSPLLK 12 0 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 GLGHPPS(0.071)S(0.929)PLLK;GLGHPPS(0.026)S(0.974)PLLK;GLGHPPS(0.013)S(0.987)PLLK 106.17 0.0012563 641260000 1705220 1394580 1653600 1753110 2045110 1428500 1698320 1329460 1720120 TRUE FALSE 1598493.324 1497836.154 1692824.173 1798097.771 1884495.31 1840884.76 1443672.682 1495446.008 1433020.86 1.115471079 1.045229833 1.181297649 1.254760361 1.315050857 1.284618258 1.007433125 1.043561925 1 20.45062818 1.656090896 7.771469128 1.0187774 1.185713152 0.531950599 0.079807511 0.1217644 13.6427513 0.046184129 0.023857028 45.29923796 -1.656090896 0.166935753 GLGKPGGQGDAIQLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLGKPGGQGDAIQLSPK 17 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 GLGKPGGQGDAIQLS(1)PK;GLGKPGGQGDAIQLS(1)PK 202.62 6.31E-12 413060000 627270 387446 463360 492600 534050 318993 621640 430608 606700 TRUE FALSE 588010.2904 416132.905 474351.118 505240.95 492107.8673 411081.1007 528430.853 484370.3567 505437.8506 1.163368137 0.823311718 0.93849544 0.999610436 0.97362686 0.813316811 1.045491256 0.95831833 1 18.94717418 1.629835774 24.99999992 1.001435764 0.93758856 0.039375631 0.099122983 2.114678942 2399.768098 0.042525067 0.023556238 42.64182409 -1.629835774 -0.063847204 GLGLDDALEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GLGLDDALEPR 11 0 Q9Y230;X6R2L4;M0R0Z0;A0A1W2PS48 Q9Y230 RUVBL2 RuvB-like 2 0 ;; 142 8.81E-05 161011000 388858 492370 442391 456950 519960 398314 487890 425095 506070 FALSE TRUE 364520.0719 528825.5871 452884.7234 468676.1106 479124.439 513300.7857 414735.4238 478169.0465 421603.6477 0.864603696 1.254319288 1.074195458 1.111650986 1.136433334 1.217496074 0.983709287 1.134167243 1 18.68552782 1.036936973 0.987474582 1.008881784 1.117288901 0.037526908 0.112410151 1.397254209 2.92797464 0.095622925 0.032125108 10.88772075 -1.036936973 0.108407117 GLGLGANLTEAQALT(ph)PTGPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLGLGANLTEAQALTPTGPSR 21 0 Q92917 Q92917 GPKOW G patch domain and KOW motifs-containing protein 1 GLGLGANLTEAQALT(0.997)PT(0.002)GPSR 170.53 9.04E-11 41529000 51108 55625 62037 61687 68008 65775 81144 59186 84606 TRUE FALSE 47909.24151 59743.53288 63508.54694 63269.99286 62666.92601 84763.17473 68977.2105 66575.50238 70484.71202 0.679711105 0.847609803 0.901025841 0.897641361 0.889085366 1.202575315 0.978612362 0.944538191 1 16.10502275 5.938007577 0.373737104 1.027496146 9.99E-18 0.586834119 0.084264471 10.23045127 0.564706536 0.066636772 5.652697152 866977.0008 -5.938007577 -1.027496146 GLGLPGCIPGLLPENS(ph)MDCI ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLGLPGCIPGLLPENSMDCI 20 0 K7ES22;Q9NVP2 K7ES22 ASF1B Histone chaperone ASF1B 1 GLGLPGCIPGLLPENS(1)MDCI 65.395 0.097005 8242600 13925 15833 16172 17034 22812 16471 31788 22546 31496 TRUE FALSE 13053.45911 17005.29179 16555.60748 17471.12128 21020.43754 21225.91032 27021.68451 25360.91773 26239.11413 0.497480938 0.648089402 0.630951464 0.66584265 0.801110793 0.808941575 1.029824573 0.96653102 1 14.67943139 2.321732005 0.896646529 1.023295826 0.595114355 0.913376043 0.051844639 0.147047505 0.229191659 0.035997082 0.022365397 209.7645066 -2.321732005 -0.428181471 GLGMEVFPVDLIYRPWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLGMEVFPVDLIYRPWK 17 1 A5YKK6-3;A5YKK6-2;A5YKK6;A5YKK6-4 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 145.69 4.24E-07 77226000 82323 81848 68297 74072 103990 70778 72152 82227 66718 FALSE TRUE 77170.55038 87908.11108 69917.03709 75972.81292 95823.04488 91210.45962 61333.47743 92493.22195 55582.33479 1.388400661 1.581583635 1.257900327 1.366851774 1.723983803 1.64099727 1.103470692 1.664075867 1 15.76233882 -1.627918081 2.627139022 0.953243221 1.444757007 0.355089058 0.195487196 20680216.67 18355153.11 6594808.293 0.048023171 0.023554935 1.627918081 0.491513786 GLGPPS(ph)PPAPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 179.67 2.14E-05 2087844000 727590 804340 785700 815250 902250 735139 890460 716160 882220 TRUE FALSE 682051.4407 863894.1705 804337.175 836170.6952 831390.9245 947361.6953 756943.7896 805574.1525 734971.7826 0.92799677 1.175411344 1.094378307 1.137690881 1.131187542 1.288976962 1.029895035 1.096061334 1 19.48732934 1.100929983 1.737557078 1.009311546 1.125953445 0.120090338 0.092914268 0.623649027 3.68636394 0.079030112 0.022931925 12.6162412 -1.100929983 0.1166419 GLGS(ph)SPDLELLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLGSSPDLELLLR 13 0 Q9NQQ7-2;Q9NQQ7;Q9NQQ7-3 Q9NQQ7-2 SLC35C2 Solute carrier family 35 member C2 1 GLGS(0.99)S(0.01)PDLELLLR;GLGS(0.975)S(0.025)PDLELLLR 148.62 4.55E-05 64845000 100308 110818 85952 93733 86726 59822 109565 81979 76934 TRUE FALSE 94029.90133 119023.08 87990.82203 96138.34747 79914.8898 77091.64027 93136.7454 92214.25861 64093.21839 1.467080351 1.857030791 1.372856977 1.499976907 1.246854064 1.202804949 1.453145087 1.438752195 1 15.96788409 8 0.064127798 0.504158317 3.45957279 0.513548765 0.156018342 224.8664013 1.071686721 9.40108273 61.07129359 99999999.9 -8 2.955414473 GLGTDEDS(ph)LIEIICSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLGTDEDSLIEIICSR 16 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;A6NMY6;H0YL33;H0YNP5;H0YN28;H0YKS4;H0YNA0;H0YMM1;H0YN52;H0YLE2 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 1 GLGTDEDS(1)LIEIICSR;GLGTDEDS(1)LIEIICSR 219.53 5.97E-13 13581000 50550 39207 39634 39375 47974 43396 45879 41709 57342 TRUE FALSE 47386.16573 42109.92707 40574.1372 40385.42916 44206.31556 55923.72072 38999.86987 46916.46046 47771.24976 0.991939 0.881491007 0.849342176 0.845391933 0.925374902 1.170656431 0.816387892 0.982106616 1 15.543855 2.473578402 24.99994642 0.976861363 0.883387923 0.196160549 0.093250508 177.4280848 1251990.866 0.03079196 0.025880443 297.562639 -2.473578402 -0.09347344 GLGTDEDSLIEIICSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GLGTDEDSLIEIICSR 16 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;A6NMY6;H0YL33;H0YNP5;H0YN28;H0YKS4;H0YNA0;H0YMM1;H0YN52;H0YLE2 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 ;;; 307.55 4.02E-47 209811000 234858 247700 249841 216100 269285 155597 334347 267025 547131 FALSE TRUE 220158.657 266039.9657 255767.3465 221645.4919 248136.4423 200515.328 284214.7713 300363.659 455811.3015 0.483003945 0.583662504 0.561125504 0.486265898 0.544384138 0.439908636 0.623536034 0.658964923 1 18.79807717 0.761056757 1.342394665 0.998887021 0.530962379 0.904818764 0.048357365 0.228595678 0.716325285 0.044533212 0.013305418 5.768418445 -0.761056757 -0.467924642 GLGTDEDTIIDIITHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GLGTDEDTIIDIITHR 16 0 E5RK69;P08133;P08133-2 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ;;;;;;; 300.98 6.37E-46 3339798000 2214978 2207931 2277089 1741137 2989312 1543065 2609470 2567951 4386048 FALSE TRUE 2076346.481 2371408.509 2331102.626 1785817.523 2754543.494 1988522.816 2218204.199 2888565.335 3653988.254 0.568241148 0.648991826 0.637961171 0.488731052 0.753845744 0.544206133 0.607063856 0.790523979 1 21.80104057 0.989971234 2.902417497 0.998725305 0.611485107 0.772637093 0.070171056 0.10560065 2.125753594 0.060009271 0.015880004 9.771724941 -0.989971234 -0.387240198 GLGTDEESILTLLTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLGTDEESILTLLTSR 16 0 P08758;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 ; 234.92 2.54E-19 41872000 40278 49240 31735 33017 41717 26591 46984 31868 63435 FALSE TRUE 37757.07188 52885.78083 32487.76919 33864.27212 38440.7151 34267.39003 39939.18538 35846.78995 52847.28869 0.714456178 1.000728365 0.614748079 0.640794882 0.72739238 0.648422859 0.755747104 0.67830897 1 15.68954184 -0.618668826 8.986420981 0.999999772 0.733839853 0.390159231 0.108190502 0 0 0.107336554 0.025299468 0.240619696 0.618668826 -0.266159919 GLHQSIEEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 2836910000 882700 2591060 1856200 2136080 2349680 2061700 2465320 2144560 1736760 FALSE TRUE 827453.3827 2782904.778 1900229.941 2190895.429 2165145.611 2656879.321 2095668.153 2412313.037 1446883.536 0.571886653 1.923378564 1.31332612 1.514216849 1.496420104 1.83627725 1.448401409 1.667247554 1 20.46451737 3.03311558 19.4487434 1.536554956 1.415630209 0.018458364 0.392196775 88.94417017 52230.94481 0.103666932 0.123901377 1079.233903 -3.03311558 -0.120924747 GLHSENREDEGWQVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GLHSENREDEGWQVYR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 ;;; 236.43 5.96E-20 905370000 295423 391274 350956 349795 427127 293486 365417 345164 503954 FALSE TRUE 276933.0018 420244.3341 359280.8421 358771.3319 393582.1684 378210.6439 310626.1132 388258.4852 419840.8217 0.659614281 1.000961108 0.855754904 0.854541325 0.937455693 0.900842949 0.73986639 0.924775451 1 18.67948292 2.130755317 0.010125965 1.757215693 5.79E-06 0.128371593 0.100349605 5816.469078 39.01769238 3337.745294 3428.270305 135.1311015 -2.130755317 -1.757209905 GLHVVEVTYDDVPIPNS(ph)PFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLHVVEVTYDDVPIPNSPFK 20 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 1 GLHVVEVTYDDVPIPNS(1)PFK;GLHVVEVTYDDVPIPNS(1)PFK 172.42 4.11E-12 224590000 499980 355330 463750 451810 510040 318280 487470 363550 609360 TRUE FALSE 468687.1443 381639.0029 474750.369 463404.2095 469983.5158 410162.2692 414378.3989 408940.0178 507653.8794 0.92324153 0.751770091 0.935185149 0.912834962 0.925795182 0.807956535 0.816261661 0.805548887 1 18.95348567 -2.427455615 2.277800869 2.362758684 0.855218523 0.323060899 0.063458207 4788786.45 520691.5394 33738284.89 0.01619647 0.003737183 2.427455615 -1.507540161 GLIAAICAGPTALLAHEIGFGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLIAAICAGPTALLAHEIGFGSK 23 0 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ; 227.25 8.73E-33 384640000 636900 697370 679480 639820 753430 583600 766640 655440 675230 FALSE TRUE 597037.5659 749004.0004 695597.5865 656238.8644 694258.647 752075.846 651689.4491 737273.1268 562529.7508 1.061343982 1.331492244 1.23655253 1.166585169 1.234172319 1.336953014 1.158497747 1.310638461 1 19.10156987 -1.00606459 6.298186143 0.99999987 1.236535336 0.412008694 0.085811346 1.39E-07 2.20E-08 0.073915893 0.017422133 0.098613281 1.00606459 0.236535466 GLIHPDDSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLIHPDDSVK 10 0 Q16401-2;Q16401 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 125.48 0.0035547 0 832330 1863200 1405300 1454700 1597700 1165100 1234700 1720600 1309900 FALSE TRUE 780235.9511 2001153.267 1438634.38 1492030.065 1472223.087 1501445.456 1049568.197 1935420.698 1091269.228 0.714980255 1.833785115 1.318312973 1.367242864 1.34909246 1.375870792 0.961786671 1.773550145 1 20.05757564 1.955125093 24.98004673 1.222856914 1.387447808 0 0.346277748 1493.957947 831623.7829 0.130844309 0.084463015 90.18308616 -1.955125093 0.164590894 GLKEGMNPSYDEYADS(ph)DEDQHDAYLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLKEGMNPSYDEYADSDEDQHDAYLER 27 1 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 1 GLKEGMNPSYDEYADS(1)DEDQHDAYLER;GLKEGMNPSYDEYADS(1)DEDQHDAYLER 222.71 1.37E-34 640360000 117926 281760 117839 184472 455300 112692 221930 187234 857540 TRUE FALSE 110545.2222 302621.8036 120634.1967 189205.8638 419542.5746 145224.351 188653.6568 210610.5771 714411.0341 0.154736163 0.423596206 0.16885825 0.264841743 0.587256572 0.203278427 0.264068789 0.294803085 1 19.44639484 -1.508805413 2.594992969 1.037338357 0.296635234 0.749177277 0.128163267 3685631.573 3570477.417 973829.77 0.030257611 0.030988074 1.508805413 -0.740703123 GLKPSCTIIPLMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLKPSCTIIPLMK 13 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 147.26 3.89E-05 1340760000 4348600 4096900 4177100 4366800 4987800 3630500 6179700 4793700 5926600 FALSE TRUE 4076428.888 4400238.739 4276182.785 4478859.481 4596078.308 4678566.414 5253111.355 5392203.997 4937412.173 0.825620537 0.891203445 0.866077742 0.907126917 0.930867861 0.94757461 1.063940212 1.092111375 1 22.23532365 2.096438414 1.349404174 1.062851057 0.873693678 0.836357221 0.034055742 0.148191921 0.509081189 0.021001319 0.010703676 124.8643366 -2.096438414 -0.189157379 GLKYELISETGGSHDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLKYELISETGGSHDKR 17 2 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6;Q96SI9;Q96SI9-2 Q12906;Q12906-7;Q96SI9 ILF3;STRBP Interleukin enhancer-binding factor 3;Spermatid perinuclear RNA-binding protein 0 95.767 0.0014937 556280000 244560 258290 222320 260760 343820 203650 312730 231550 513060 FALSE TRUE 229253.4262 277414.0604 227593.5354 267451.5431 316817.7641 262440.449 265839.0397 260459.5272 427426.9715 0.536356949 0.649032651 0.5324735 0.625724535 0.741220805 0.614000675 0.621951953 0.609366148 1 18.70531842 -5 0.316230996 4.547700111 0.598437708 0.816127503 0.057380524 127.1762006 1.13680869 301.416638 0.050800401 1.00E-05 5 -3.949262403 GLLALGDYMNVQCHACIGGTNVGEDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLLALGDYMNVQCHACIGGTNVGEDIR 27 0 P38919 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ; 188.22 8.74E-18 83669000 37627 44021 40412 37975 47016 39615 44660 42235 44983 FALSE TRUE 35271.99324 47280.36064 41370.59172 38949.50279 43323.55301 51051.2074 37963.6476 47508.13272 37475.0467 0.941212789 1.261649145 1.103950371 1.03934501 1.156064017 1.362272016 1.013038033 1.267727112 1 15.19364266 -1.200514363 5.005908447 0.99998534 1.147332949 0.108913554 0.12819346 1.86E-05 2.97E-06 0.110002329 0.025925219 0.06302105 1.200514363 0.14734761 GLLAQGLRPES(ph)PPPAGPLLNGAPAGES(ph)PQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GLLAQGLRPESPPPAGPLLNGAPAGESPQPK 31 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 2 GLLAQGLRPES(1)PPPAGPLLNGAPAGES(1)PQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGES(1)PQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGES(1)PQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGES(1)PQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGES(1)PQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGES(1)PQPK 244.02 2.63E-46 1517450000 1783650 1288967 1575450 1498390 1517670 1214278 1794790 1219311 1634750 TRUE FALSE 1672014.53 1384403.458 1612820.418 1536841.224 1398478.32 1564820.346 1525677.902 1371544.662 1361899.664 1.227707572 1.016523826 1.184243201 1.128454074 1.026858554 1.148998262 1.120257198 1.007082018 1 20.37718899 1.233757869 12.3194421 1.003458695 1.11627564 0.372990498 0.063458116 0.279764152 657.0287328 0.047125335 0.013935888 17.13001995 -1.233757869 0.112816945 GLLAQGLRPES(ph)PPPAGPLLNGAPAGESPQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GLLAQGLRPESPPPAGPLLNGAPAGESPQPK 31 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK 285.14 1.95E-72 10908860000 8724940 7129550 7628300 7885380 8501070 6427360 9231190 6957180 8680820 TRUE FALSE 8178861.58 7657429.3 7809246.878 8087732.201 7833430.254 8282834.493 7847058.758 7825799.238 7231935.062 1.130936812 1.058835462 1.079828125 1.118335844 1.083172095 1.145313726 1.085056585 1.082116912 1 22.78595029 0.685691015 2.229048615 1.000039554 1.095758315 0.588522053 0.025985098 1.271438604 8.001739842 0.024597381 0.006675799 4.849433579 -0.685691015 0.095718761 GLLASDLNTDGDMRVT(ph)PEPGAGPTQGLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.997)PEPGAGPT(0.003)QGLLR 176.96 2.21E-17 1338520000 646620 743964 697277 664286 834115 817881 978179 817975 1099690 TRUE FALSE 606149.2084 799047.8687 713816.7397 681332.7034 768606.9726 1053989.968 831510.1399 920100.9793 916144.6347 0.661630473 0.872185284 0.77915289 0.743695567 0.838958111 1.150462413 0.90761885 1.004318472 1 19.80521585 2.422107205 8.782348635 1.001962916 0.785298152 0.694220658 0.078589438 0.174598407 25.6800362 0.025213475 0.02108946 264.3061113 -2.422107205 -0.216664764 GLLDDLRNDLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLLDDLRNDLDR 12 1 Q07065 Q07065 CKAP4 Cytoskeleton-associated protein 4 0 75.045 0.031802 13266000 14376 27304 16990 21716 30009 19358 19242 23952 23013 FALSE TRUE 13476.23182 29325.61657 17393.01082 22273.26933 27652.21419 24946.34035 16356.84073 26942.45992 19171.98163 0.702912828 1.529608005 0.907209863 1.161761458 1.442324259 1.30118737 0.853163802 1.405303867 1 14.22671184 -1.013944547 7.44572972 0.999999993 1.164156784 0.034334718 0.271487899 3.15E-08 3.81E-09 0.238076079 0.056115068 0.09684015 1.013944547 0.164156792 GLLEDVQEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLLEDVQEGR 10 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 178.55 5.13E-06 339940000 564350 742350 690070 698610 717640 616660 767650 615630 640180 FALSE TRUE 529028.3409 797314.3664 706438.7863 716537.5153 661279.4492 794679.7314 652548.009 692492.7607 533329.8223 0.991934669 1.494974279 1.324581444 1.343516686 1.23990713 1.490034306 1.223535572 1.298432474 1 19.02466848 0.424232286 1.061855984 0.999606752 1.3306539 0.290410936 0.143573254 2.490020197 3.568657848 0.124608599 0.038385979 2.65602578 -0.424232286 0.331047147 GLLEFEHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GLLEFEHQR 9 0 Q14697;F5H6X6;Q14697-2;E9PKU7;E9PNH1 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;; 234.05 3.65E-10 2449240000 3290620 6659090 3318900 3595390 6532220 2229330 3243370 5299080 4541400 FALSE TRUE 3084665.968 7152135.952 3397625.875 3687653.794 6019205.791 2872901.381 2757056.778 5960681.803 3783411.001 0.815313474 1.890393602 0.898032456 0.974690245 1.590946844 0.759341605 0.728722515 1.575478266 1 21.85125608 3.772057157 9.680459403 1.042695522 1.419906247 0.069702976 0.391254923 0.815651937 169.5753875 0.093903007 0.16897961 5916.394947 -3.772057157 0.377210726 GLLGLEPVPS(ph)SPCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLLGLEPVPSSPCR 14 0 E7EX78;O14901-2;O14901 E7EX78 KLF11 Krueppel-like factor 11 1 GLLGLEPVPS(0.73)S(0.27)PCR 147.18 8.50E-06 64674000 120750 118330 127420 127280 141500 118570 132810 127350 125930 TRUE FALSE 113192.473 127091.2763 130442.4626 130546.2203 130387.1608 152799.2342 112896.3734 143249.9278 104911.4695 1.078933253 1.21141451 1.243357502 1.244346504 1.242830374 1.456458812 1.076110877 1.365436292 1 16.67881288 -1.11457527 4.571135683 0.999978872 1.235642297 0.304673783 0.113719125 2.17E-05 4.21E-06 0.097765304 0.023041438 0.076811232 1.11457527 0.235663425 GLLGLEPVPSS(ph)PCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLLGLEPVPSSPCR 14 0 E7EX78;O14901-2;O14901 E7EX78 KLF11 Krueppel-like factor 11 1 GLLGLEPVPS(0.1)S(0.9)PCR 139.77 1.06E-05 59150000 141720 142000 140020 148190 173100 123740 157120 125950 134940 TRUE FALSE 132849.9982 152513.8278 143341.3405 151992.8063 159505.4243 159461.7292 133561.3146 141675.1348 112417.6423 1.181753998 1.356671646 1.275078694 1.352036951 1.4188647 1.418476015 1.188081443 1.260257126 1 16.77850894 0.800226228 1.136131287 1.003521856 1.32723589 0.610438716 0.079472874 0.49719571 1.196156794 0.072247269 0.022606569 6.312861018 -0.800226228 0.323714035 GLLGLPEEETELDNLTEFNTAHNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLLGLPEEETELDNLTEFNTAHNKR 25 1 Q12972;A0A0A0MT09;Q12972-2 Q12972 PPP1R8 Nuclear inhibitor of protein phosphatase 1;Activator of RNA decay 0 ; 226.51 4.10E-34 157361000 173916 166598 182862 174963 190266 141832 219438 168311 208023 FALSE TRUE 163030.908 178933.0893 187199.573 179452.8468 175323.2759 182776.5959 186535.3091 189324.9988 173302.6174 0.940729635 1.032489249 1.080188954 1.035488381 1.011659711 1.054667256 1.076355983 1.092453199 1 17.40293392 4.739697169 2.717005233 1.053909216 0.918585313 0.573671976 0.029276565 0.31725927 3.160768192 0.006963148 0.096849944 54915.78159 -4.739697169 -0.135323904 GLLPGGTQVLDGTSGFS(ph)PAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GLLPGGTQVLDGTSGFSPAPK 21 0 Q96S94;Q96S94-3 Q96S94 CCNL2 Cyclin-L2 1 GLLPGGTQVLDGTSGFS(1)PAPK;GLLPGGTQVLDGTSGFS(1)PAPK;GLLPGGTQVLDGTSGFS(1)PAPK;GLLPGGTQVLDGTSGFS(1)PAPK 364.36 3.47E-112 573570000 847590 620226 733400 621715 805640 685810 1096590 783160 1188860 TRUE FALSE 794540.8549 666148.1784 750796.5943 637669.2595 742368.2842 883792.2138 932166.5097 880939.2499 990431.5857 0.802216798 0.672583738 0.75804993 0.643829689 0.749540195 0.892330401 0.941172034 0.889449875 1 19.9176978 2.218448627 3.176285046 0.933354531 0.715858642 0.80751269 0.050431743 0.093525139 1.959534238 0.018304598 0.013346736 165.3669159 -2.218448627 -0.217495889 GLLS(ph)PPMGQSGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GLLSPPMGQSGLR 13 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 GLLS(0.999)PPMGQS(0.001)GLR;GLLS(1)PPMGQSGLR;GLLS(1)PPMGQSGLR;GLLS(1)PPMGQSGLR;GLLS(1)PPMGQSGLR;GLLS(1)PPMGQSGLR 186.62 8.03E-06 2263110000 2182810 2568740 2525470 2425590 2476580 2096040 2567810 2043760 1976400 TRUE FALSE 2046191.819 2758932.182 2585375.341 2487834.746 2282079.397 2701132.722 2182790.729 2298927.935 1646526.072 1.242732717 1.675607954 1.570200062 1.510959825 1.385996515 1.64050407 1.325694604 1.396229294 1 20.65099393 0.601616681 0.654441811 0.991023176 1.536948904 0.557810261 0.133568916 0.92508542 0.726258358 0.137919522 0.048491902 3.995919041 -0.601616681 0.545925728 GLLSDS(ph)MTDVPVDTGVAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 GLLSDSMTDVPVDTGVAAR 19 0 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;A0A087WZ51;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 1 GLLSDS(0.875)MT(0.125)DVPVDTGVAAR;GLLSDS(0.984)MT(0.016)DVPVDTGVAAR;GLLSDS(0.945)MT(0.055)DVPVDTGVAAR;GLLSDS(0.899)MT(0.101)DVPVDTGVAAR;GLLS(0.004)DS(0.593)MT(0.403)DVPVDTGVAAR;GLLSDS(0.999)MT(0.001)DVPVDTGVAAR;GLLSDS(0.999)MT(0.001)DVPVDTGVAAR;GLLSDS(0.987)MT(0.013)DVPVDTGVAAR;GLLSDS(0.773)MT(0.227)DVPVDTGVAAR 322.37 4.42E-62 994771000 1546181 1475743 1450558 1411057 1459360 1294215 1599519 1418484 1822931 TRUE FALSE 1449408.291 1585008.547 1484965.921 1447267.112 1344747.752 1667833.861 1359685.975 1595584.85 1518672.04 0.954391899 1.043680601 0.977805531 0.952981996 0.885476072 1.098218587 0.895312444 1.050644779 1 20.53437892 -3.047779519 9.359776108 0.999957556 0.983264768 0 0.06729976 0 0 0 0.013243617 0.000895819 3.047779519 -0.016692788 GLLSDSMT(ph)DVPVDTGVAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLLSDSMTDVPVDTGVAAR 19 0 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;A0A087WZ51;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 1 GLLSDS(0.3)MT(0.7)DVPVDTGVAAR 297.73 1.03E-48 151000000 166670 159540 143480 144690 155090 130880 178780 146530 200810 TRUE FALSE 156238.4222 171352.5076 146883.4134 148402.9904 142909.857 168662.9313 151973.5987 164824.5931 167293.5137 0.933917991 1.024262709 0.877998256 0.887081555 0.854246252 1.008185719 0.908424931 0.985241982 1 17.35202198 1.11855942 5.477214006 0.999107064 0.931519876 0.201360563 0.053609177 0.35089723 14.24102601 0.050805661 0.01284362 13.13891249 -1.11855942 -0.067587188 GLLSNHTGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GLLSNHTGSPR 11 0 Q13111 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 GLLSNHT(0.017)GS(0.983)PR;GLLSNHT(0.031)GS(0.969)PR;GLLSNHT(0.013)GS(0.987)PR 97.203 0.0041491 861140000 968780 1525210 1511600 1282870 1428370 1631470 1869250 1413750 1727720 TRUE FALSE 908145.7891 1638138.135 1547455.866 1315790.616 1316191.582 2102448.904 1588973.316 1590259.8 1439352.371 0.630940559 1.138107783 1.07510565 0.914154618 0.914433192 1.460690896 1.103950185 1.104843979 1 20.45698839 GLLTDS(ph)PAATVLAEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLLTDSPAATVLAEAR 16 0 Q86UU1-3;Q86UU1-2;Q86UU1 Q86UU1-3 PHLDB1 Pleckstrin homology-like domain family B member 1 1 GLLTDS(0.987)PAAT(0.013)VLAEAR 96.673 0.0034963 13124000 24193 26194 25211 28492 35054 23688 28035 26979 34494 TRUE FALSE 22678.80332 28133.43101 25809.01683 29223.15296 32301.00024 30526.34106 23831.41201 30347.38754 28736.72856 0.789192245 0.979006046 0.898119519 1.016926923 1.124031922 1.062276139 0.829301497 1.056048794 1 14.81060821 5.604023233 1.048354608 0.98872769 3.39E-14 0.354206297 0.084883305 12.46866683 2.892126288 0.02588867 21.22895545 401812.3053 -5.604023233 -0.98872769 GLLYDS(ph)DEEDEERPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 GLLYDSDEEDEERPAR 16 1 P49736 P49736 MCM2 DNA replication licensing factor MCM2 1 GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLY(0.002)DS(0.998)DEEDEERPAR 348.1 2.38E-87 40701660000 25162120 24068160 25765570 24240540 26502320 21815060 28497980 22435170 23129560 TRUE FALSE 23587267.82 25850191.61 26376741.49 24862593.3 24420934.69 28112713.68 24224972.46 25236250.36 19269087.01 1.22409888 1.341536918 1.368863064 1.290283929 1.267363351 1.458954109 1.257193579 1.309675458 1 24.19978488 0.249881124 1.228531406 0.999530803 1.325931574 0.691016142 0.066004755 2.626201986 3.796214068 0.059643591 0.017326302 1.777792724 -0.249881124 0.326400771 GLLYDS(ph)DEEDEERPARK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GLLYDSDEEDEERPARK 17 2 P49736 P49736 MCM2 DNA replication licensing factor MCM2 1 GLLYDS(1)DEEDEERPARK;GLLYDS(1)DEEDEERPARK;GLLYDS(1)DEEDEERPARK;GLLYDS(1)DEEDEERPARK;GLLYDS(1)DEEDEERPARK;GLLYDS(1)DEEDEERPARK;GLLYDS(1)DEEDEERPARK;GLLYDS(1)DEEDEERPARK 316.14 1.42E-58 4973480000 2351055 2431024 2273899 2462753 2765930 1773669 3026330 2183819 4166800 TRUE FALSE 2203906.664 2611019.546 2327836.958 2525951.411 2548705.015 2285698.447 2572559.912 2456473.609 3471334.161 0.634887499 0.752166004 0.670588555 0.727660114 0.734214828 0.658449559 0.741086796 0.707645388 1 21.72705882 -5 0.397500792 5.658314401 0.700843028 0.859571789 0.037759048 229.3346431 1.616570588 926.3858402 0.020885509 1.00E-05 5 -4.957471373 GLMAGGRPEGQYS(ph)EDEDT(ph)DTDEYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLMAGGRPEGQYSEDEDTDTDEYK 24 1 Q9NPQ8-4;Q9NPQ8;Q9NPQ8-3;Q9NPQ8-2;H0YE35;H0YC88 Q9NPQ8-4 RIC8A Synembryn-A 2 GLMAGGRPEGQYS(1)EDEDT(0.997)DT(0.003)DEYK 223.65 1.71E-32 434630000 730230 441230 526660 521140 473660 452610 717420 498080 417640 TRUE FALSE 684526.2078 473899.1283 539152.6239 534513.3347 436460.6543 583271.1595 609849.5312 560266.3844 347933.1859 1.967407064 1.362040609 1.549586661 1.53625281 1.254438127 1.676388407 1.752777705 1.610270038 1 18.40845076 -1.949390519 2.558837353 0.576446044 1.570821776 0.467149315 0.196757738 10706162.18 5027603.368 26964628.77 0.046009433 0.011235942 1.949390519 0.994375732 GLMAGGRPEGQYS(ph)EDEDT(ph)DTDEYKEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GLMAGGRPEGQYSEDEDTDTDEYKEAK 27 2 Q9NPQ8-4;Q9NPQ8;Q9NPQ8-3;Q9NPQ8-2;H0YE35;H0YC88 Q9NPQ8-4 RIC8A Synembryn-A 2 GLMAGGRPEGQY(0.001)S(0.999)EDEDT(0.967)DT(0.033)DEYKEAK;GLMAGGRPEGQY(0.058)S(0.937)EDEDT(0.599)DT(0.405)DEYKEAK;GLMAGGRPEGQYS(1)EDEDT(0.98)DT(0.02)DEYKEAK;GLMAGGRPEGQYS(1)EDEDT(1)DTDEYKEAK;GLMAGGRPEGQY(0.003)S(0.997)EDEDT(0.897)DT(0.103)DEYKEAK 193.44 9.86E-18 2214540000 2236081 1188693 1404052 1645849 1833274 1028397 2112829 1383455 2267240 TRUE FALSE 2096128.682 1276705.067 1437356.776 1688084.272 1689296.055 1325278.519 1796029.906 1556182.402 1888822.997 1.109753897 0.675926261 0.760980134 0.89372285 0.894364405 0.701642516 0.950872532 0.823890012 1 20.84905608 0.518127936 0.592345495 1.004217573 0.815639457 0.07640103 0.128960817 3.261907939 2.019934063 0.158381072 0.052236794 3.297068242 -0.518127936 -0.188578116 GLMAGGRPEGQYS(ph)EDEDTDTDEYKEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLMAGGRPEGQYSEDEDTDTDEYKEAK 27 2 Q9NPQ8-4;Q9NPQ8;Q9NPQ8-3;Q9NPQ8-2;H0YE35;H0YC88 Q9NPQ8-4 RIC8A Synembryn-A 1 GLMAGGRPEGQYS(1)EDEDTDTDEYKEAK 225.53 8.58E-35 194920000 282960 131690 192940 182500 218930 126470 205900 163810 265210 TRUE FALSE 265250.0387 141440.4646 197516.6279 187183.259 201736.1209 162979.8359 175027.2065 184262.0391 220944.7377 1.200526618 0.640162179 0.893963939 0.847194918 0.913061443 0.737649775 0.792176398 0.833973423 1 17.75332604 2.264008647 24.97652992 0.817190186 0.86064999 0 0.1523236 1217.075513 1194521.255 0.048945224 0.040937035 183.657491 -2.264008647 0.043459804 GLNNDS(ph)PERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLNNDSPERR 10 1 G5EA48;Q7Z6B7-2;Q7Z6B7 G5EA48 SRGAP1 SLIT-ROBO Rho GTPase-activating protein 1 1 GLNNDS(1)PERR;GLNNDS(1)PERR 175.21 1.76E-06 546480000 322470 405590 317860 332140 423370 316320 380350 372070 412780 TRUE FALSE 302287.1783 435620.3056 325399.7893 340663.2747 390120.228 407636.449 323320.0485 418523.7585 343884.3513 0.879037319 1.266763969 0.946247737 0.990633256 1.134451819 1.18538819 0.940199946 1.21704799 1 18.39156394 2.727974277 24.52444047 1.086658101 1.049282328 0.055749841 0.128378988 3133.144423 7258279.314 0.039753805 0.037835254 534.5326983 -2.727974277 -0.037375773 GLNPDGTPALSTLGGFS(ph)PASKPSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLNPDGTPALSTLGGFSPASKPSSPR 26 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 2 GLNPDGTPALSTLGGFS(0.997)PAS(0.003)KPS(0.084)S(0.916)PR 154.23 3.88E-08 413410000 567330 389020 483410 513120 571520 456160 602250 458100 415120 TRUE FALSE 531821.828 417823.4456 494876.7135 526287.5279 526635.1246 587845.9869 511948.2035 515294.7934 345833.7902 1.537796025 1.208162584 1.43096692 1.521793251 1.522798348 1.699793379 1.480330199 1.490007073 1 18.39971931 3.520857566 3.864122552 1.495678897 1.341852249 0 0.195904601 0.461601541 14.28829116 0.047902488 0.074047637 3317.856253 -3.520857566 -0.153826647 GLNPDGTPALSTLGGFSPASKPSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLNPDGTPALSTLGGFSPASKPSSPR 26 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 1 GLNPDGTPALSTLGGFSPAS(0.023)KPS(0.339)S(0.638)PR 159.27 1.18E-11 324730000 350400 282300 322420 348170 343800 243520 329790 213620 246770 TRUE FALSE 328469.0895 303201.7857 330067.9547 357104.6317 316799.3348 313820.2708 280341.0511 240290.9272 205582.4928 1.597748354 1.474842442 1.605525598 1.737038144 1.540984013 1.526493168 1.36364263 1.168829719 1 17.64935789 1.319327338 1.31820439 1.003817519 1.584733436 0.912496433 0.064811289 0.114577286 0.38247491 0.062680809 0.020042692 20.86062603 -1.319327338 0.580915917 GLNSESMTEETLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLNSESMTEETLKR 14 1 P31327;P31327-3;P31327-2;A0A669KBF2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 196.8 3.90E-08 312160000 278490 232710 233530 205550 318020 190980 236370 244960 582680 FALSE TRUE 261059.808 249940.0905 239069.4419 210824.761 293043.992 246112.8257 200928.5129 275543.7952 485426.9437 0.537794227 0.51488714 0.492493144 0.434307909 0.603682997 0.507002812 0.41392122 0.567631852 1 18.88889466 0.964382079 22.28227743 1.000000001 0.498098193 0.899905823 0.051931008 372.8777527 233269.8394 0.04852689 0.012131723 9.212597116 -0.964382079 -0.501901808 GLPPS(ph)MER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 123.86 0.0013945 2256630000 2181260 2090350 2055370 2076000 2253720 1816330 2604220 1942160 2511840 TRUE FALSE 2044738.83 2245121.689 2104124.347 2129273.675 2076721.922 2340674.985 2213741.387 2184642.951 2092597.677 0.977129456 1.072887404 1.005508307 1.01752654 0.992413375 1.11854993 1.057891544 1.04398613 1 20.99686353 2.268311501 24.99993733 1.061806312 1.020414052 0.21074535 0.038026779 296.9426176 249522.4366 0.012314858 0.010302161 185.4861561 -2.268311501 -0.041392259 GLPQLGTLGAGNHYAEIQVVDEIFNEYAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLPQLGTLGAGNHYAEIQVVDEIFNEYAAK 30 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 195.51 3.02E-25 137770000 181470 160340 173650 169970 174140 143080 163600 164830 177440 FALSE TRUE 170112.1166 172211.7404 177769.06 174331.718 160463.7468 184384.8733 139069.6988 185409.3883 147824.1177 1.150773766 1.164977293 1.202571426 1.179318508 1.085504513 1.247326053 0.940778142 1.254256688 1 17.17352214 1.753921071 25 1.061997364 1.171495845 0.244953117 0.088282971 6.658685656 10850.96442 0.035633004 0.019760467 56.74414683 -1.753921071 0.109498481 GLPSPYNMSS(ph)APGS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 2 GLPSPYNMS(0.034)S(0.966)APGS(1)R;GLPSPYNMS(0.024)S(0.976)APGS(1)R;GLPSPYNMS(0.009)S(0.991)APGS(1)R;GLPSPYNMS(0.003)S(0.997)APGS(1)R;GLPSPYNMS(0.017)S(0.983)APGS(1)R;GLPSPYNMS(0.002)S(0.998)APGS(1)R;GLPSPYNMS(0.001)S(0.999)APGS(1)R;GLPSPYNMS(0.066)S(0.934)APGS(1)R;GLPSPYNMS(0.007)S(0.993)APGS(1)R;GLPSPYNMS(0.003)S(0.997)APGS(1)R;GLPSPYNMS(0.041)S(0.959)APGS(1)R;GLPSPYNMS(0.025)S(0.975)APGS(1)R;GLPSPYNMS(0.03)S(0.97)APGS(1)R 243.01 8.65E-18 7485380000 6596130 9669410 7785370 8386320 10420870 6242440 10565850 8295700 7737860 TRUE FALSE 6183289.998 10385343.18 7970042.653 8601527.169 9602456.906 8044531.09 8981598.881 9331436.406 6446361.178 0.959190748 1.611039607 1.236363032 1.334322873 1.489593375 1.247918146 1.393281982 1.447550975 1 22.62005359 -1.849522167 2.785080006 0.863714087 1.357749683 0.265507022 0.175455309 35974052.45 26326095.91 32672201.11 0.036886301 0.014140925 1.849522167 0.494035595 GLPSPYNMSS(ph)APGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GLPSPYNMS(0.001)S(0.982)APGS(0.017)R;GLPSPYNMS(0.03)S(0.962)APGS(0.009)R 189.91 2.50E-07 3804400000 1257070 1353450 1309160 1352380 1497460 1197770 1507700 1195920 1284320 TRUE FALSE 1178392.233 1453660.846 1340213.893 1387084.36 1379855.532 1543546.755 1281634.382 1345233.245 1069958.695 1.101343667 1.358613985 1.252584702 1.296390568 1.289634393 1.44262275 1.197835382 1.257275866 1 20.02912367 -0.804022737 6.124065232 0.999999987 1.282417987 0.476076478 0.090174512 1.39E-08 2.84E-09 0.077939851 0.018370598 0.157028059 0.804022737 0.282418001 GLPSPYNMSSAPGS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GLPSPYNMS(0.003)S(0.034)APGS(0.962)R;GLPSPYNMSSAPGS(1)R;GLPSPYNMSS(0.002)APGS(0.998)R;GLPSPYNMSSAPGS(1)R;GLPSPYNMSSAPGS(1)R;GLPSPYNMSS(0.011)APGS(0.988)R;GLPSPYNMSSAPGS(1)R 154.36 9.74E-06 3444479000 2528540 3123870 2817660 2922860 3096850 2767010 3069440 2700200 2157550 TRUE FALSE 2370283.195 3355164.585 2884496.226 2997865.536 2853635.893 3565800.868 2609205.967 3037325.914 1797440.967 1.318698772 1.866634091 1.604779394 1.667852014 1.587610356 1.983820851 1.451622621 1.689805657 1 20.77751296 -0.143146463 0.906989611 0.986333919 1.669947719 0.53339627 0.188666423 6.736301064 4.57170235 0.493360567 0.052544731 0.719206389 0.143146463 0.6836138 GLPSTAS(ph)GR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLPSTASGR 9 0 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GLPSTAS(1)GR;GLPSTAS(1)GR 152.04 8.54E-05 987890000 1403540 1786890 1675200 1543630 2056310 1447510 1995750 1725290 2047360 TRUE FALSE 1315694.937 1919193.195 1714936.535 1583242.159 1894815.707 1865382.639 1696505.815 1940696.254 1705642.39 0.771377954 1.125202567 1.005449059 0.928238046 1.110910305 1.09365401 0.994643324 1.137809582 1 20.70188377 2.729611369 24.98605227 1.063230053 0.993486541 0.195820635 0.099188439 1520.924953 4246368.242 0.030414731 0.029053149 536.5514454 -2.729611369 -0.069743512 GLPVTCEVAPHHLFLSHDDLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLPVTCEVAPHHLFLSHDDLER 22 0 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 ; 202.53 4.85E-23 501500000 115428 150421 141836 156633 178913 124662 162510 161862 210907 FALSE TRUE 108203.5675 161558.3274 145200.4169 160652.468 164861.8947 160649.8957 138143.1342 182070.827 175705.2592 0.615824296 0.91948487 0.826386288 0.914329308 0.938286625 0.914314668 0.786220827 1.03622867 1 17.42279785 4.741297781 24.87160844 0.897456544 0.615824187 0.608391269 0.0744748 162.1756587 1473545.275 0.016316578 0.112713056 55118.54955 -4.741297781 -0.281632356 GLPWSCS(ph)VEDVQNFLSDCTIHDGAAGVHFIYTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR 33 0 P52597;A0A1B0GW42 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 1 GLPWS(0.029)CS(0.971)VEDVQNFLSDCTIHDGAAGVHFIYTR;GLPWS(0.003)CS(0.997)VEDVQNFLSDCTIHDGAAGVHFIYTR 265.68 1.43E-59 152504000 43420 39879 33768 41667 54212 39952 46977 36591 40578 TRUE FALSE 40702.41971 42831.68265 34568.99291 42736.24576 49954.4082 51485.49383 39933.23496 41159.4669 33805.26966 1.204025885 1.26701201 1.02259184 1.264188873 1.477710686 1.523002016 1.181272487 1.217545883 1 15.04496053 0.771500569 2.021987698 1.000842984 1.265176256 0.271600237 0.141680645 1.401037611 9.304214001 0.146871414 0.040557396 5.908817396 -0.771500569 0.264333271 GLPWSCSADEVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GLPWSCSADEVQR 13 0 P31943;G8JLB6;E9PCY7;D6RBM0;D6RIT2;D6RIU0;E7EN40;D6R9T0;D6RFM3;E5RGV0;D6RDU3;D6RJ04;D6RIH9;D6RAM1;D6RDL0;D6RF17;D6R9D3;E7EQJ0 P31943;E7EQJ0 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 ;;;; 252.42 2.17E-23 1402710000 461677 498663 474066 455399 558209 459533 610547 479842 626900 FALSE TRUE 432781.4607 535584.5274 485311.0694 467085.3093 514369.5168 592192.7172 519001.1454 539751.33 522266.3401 0.828660451 1.025500758 0.929240566 0.894343122 0.984879701 1.133890262 0.993748028 1.033479067 1 18.9944262 2.473733594 24.99908348 1.040839835 0.938834069 0.446835701 0.061751216 102.5296567 756600.1075 0.020083625 0.016881318 297.6689898 -2.473733594 -0.102005767 GLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR 33 0 P52597;A0A1B0GW42 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 300.5 4.27E-90 59376000 16245 15176 17205 14972 18942 15399 16954 15283 16694 FALSE TRUE 15228.25445 16299.64683 17613.11072 15356.20687 17454.37173 19844.44132 14411.90509 17191.11619 13907.66355 1.094954188 1.171990304 1.26643204 1.104154325 1.255018261 1.426870965 1.03625638 1.23608945 1 13.76359245 -0.615138142 7.747411425 0.999999997 1.199463465 0.245708619 0.109556737 0 0 0.098186881 0.02314287 0.242583835 0.615138142 0.199463469 GLQEFLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GLQEFLDR 8 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ;; 154.28 0.00099468 300613000 500963 671960 583788 638296 667100 549612 652040 554589 579700 FALSE TRUE 469608.6201 721712.6176 597635.727 654675.756 614708.657 708276.0622 554272.6552 623830.6575 482944.325 0.972386662 1.49440128 1.237483693 1.355592606 1.272835449 1.466579118 1.147694727 1.291723756 1 18.88149736 0.502442618 0.899957733 0.999933489 1.30889186 0.241626986 0.150898825 2.050624943 2.480359964 0.132259892 0.042620901 3.180113479 -0.502442618 0.308958371 GLQEVGLPLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLQEVGLPLHR 11 0 P11172-2;P11172-3;P11172 P11172-2 UMPS Uridine 5-monophosphate synthase;Orotate phosphoribosyltransferase;Orotidine 5-phosphate decarboxylase 0 106.49 0.0023242 139990000 93638 101540 93776 90443 104610 81021 100020 83101 83564 FALSE TRUE 87777.36473 109058.1273 96000.411 92763.9205 96394.35258 104410.4474 85022.92954 93476.34278 69616.62856 1.260867792 1.566552841 1.378986788 1.332496595 1.384645516 1.499791783 1.221302027 1.342730102 1 16.08714433 0.250344914 0.449362575 0.958844429 1.431428718 0.594045521 0.098660825 1.881834874 0.590431897 0.24052307 0.05497349 1.779692268 -0.250344914 0.472584289 GLQLT(ph)PGIGGMQQHFFDDEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GLQLTPGIGGMQQHFFDDEDR 21 0 P12270 P12270 TPR Nucleoprotein TPR 1 GLQLT(1)PGIGGMQQHFFDDEDR;GLQLT(1)PGIGGMQQHFFDDEDR;GLQLT(1)PGIGGMQQHFFDDEDR;GLQLT(1)PGIGGMQQHFFDDEDR 236.08 2.97E-29 549067000 458296 570130 690940 1242650 1131590 499580 361172 227768 251553 TRUE FALSE 429612.0714 612343.0184 707329.4231 1274538.503 1042719.486 643800.636 307017.6116 256205.3362 209567.1792 2.049996918 2.921941407 3.375191792 6.081765798 4.975585824 3.072048965 1.465008083 1.222545139 1 17.67705327 1.782560175 3.126049096 1.188061887 3.792167701 0.549586397 1.093495436 0.205998581 3.880364414 0.660352783 0.324899421 60.61221777 -1.782560175 2.604105815 GLQPS(ph)TPPPKPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLQPSTPPPKPPR 13 1 A0A1B0GTL5 A0A1B0GTL5 1 GLQPS(0.84)T(0.16)PPPKPPR 62.377 0.046693 271610000 349440 302170 332530 302830 325800 251420 375190 294840 353970 TRUE FALSE 327569.1742 324542.9812 340417.7686 310601.1305 300212.9822 324000.8725 318933.7426 331651.423 294890.1203 1.110817731 1.100555627 1.154388517 1.053277506 1.018050323 1.098717286 1.081534174 1.124661019 1 18.16981796 3.226801351 24.99981775 1.068121933 1.121980684 0.339264298 0.038463071 255.8005232 543822.5326 0.010679699 0.012863531 1685.781763 -3.226801351 0.053858752 GLQQITGHGGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLQQITGHGGLR 12 0 Q9UI09;H0YID5;F8VXI1;F8VRD8;Q9UI09-2 Q9UI09 NDUFA12 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 0 97.463 0.0018212 0 134210 167290 147050 161260 201500 140500 185440 165530 196600 FALSE TRUE 125810.0357 179676.3257 150538.0954 165398.2046 185675.0028 181060.0692 157634.9935 186196.7849 163786.1899 0.768135798 1.097017555 0.919113483 1.009842189 1.133642604 1.10546603 0.962443742 1.136828355 1 17.32145419 2.998249511 23.5501981 1.061146771 0.963189712 0.279120064 0.096797265 52.34794221 704299.4563 0.026470317 0.031161235 995.9774634 -2.998249511 -0.097957059 GLQSIFQEQGMAESVHTWQDHGYLATYTNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLQSIFQEQGMAESVHTWQDHGYLATYTNK 30 0 P52788;H7C2R7;P52788-2 P52788 SMS Spermine synthase 0 248.92 1.91E-46 196740000 268740 367120 352440 343830 406450 324320 405000 362370 417070 FALSE TRUE 251920.0431 394301.9468 360800.0432 352653.2599 374529.0565 417945.9191 344274.0098 407612.6922 347458.3226 0.725036722 1.134817966 1.038398046 1.014951253 1.077910737 1.202866335 0.990835411 1.173126863 1 18.40648041 4.744189427 24.9693982 1.078170588 0.725036568 0.702939559 0.072335129 315.8417389 1401031.824 0.01548375 0.13661825 55486.76774 -4.744189427 -0.35313402 GLQSLPTHDPSPLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLQSLPTHDPSPLQR 15 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 0 87.647 0.0070904 155850000 115770 138360 117610 125970 158200 138010 169090 118040 130910 FALSE TRUE 108524.1624 148604.3184 120399.7647 129202.6035 145775.6101 177851.2466 143736.5243 132777.5538 109060.2753 0.995084251 1.36258888 1.103974517 1.184689871 1.336651771 1.630761028 1.3179549 1.217469454 1 16.73476618 2.729308605 7.201272839 1.347503089 1.185302321 0.092016086 0.180456259 0.26223166 90.5032025 0.053476173 0.052566373 536.1775239 -2.729308605 -0.162200767 GLQTSQDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GLQTSQDAR 9 0 P27797 P27797 CALR Calreticulin 0 ;; 172.59 0.00013045 377605000 874120 1233750 843880 931350 1165940 722230 1002200 991740 888230 FALSE TRUE 819410.3895 1325098.134 863897.2321 955250.0178 1074371.776 930726.0766 851929.414 1115560.922 739978.6748 1.107343248 1.790724758 1.167462336 1.290915604 1.451895591 1.257774188 1.151289142 1.507558204 1 19.49712417 -4.511839148 0.107093404 8.16E-12 1.570938899 0.168648428 0.209591008 218.4429142 1.745106779 49.82602061 2.739565233 3.08E-05 4.511839148 1.570938899 GLQVDLQS(ph)DGAAAEDIVASEQSLGQK ddPTM_SK-BR-3_Pertuzumab_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 206.93 1.81E-25 101258000 85979 79286 83304 84750 101581 74899 103907 87262 121857 TRUE FALSE 80597.72787 85156.41794 85280.01022 86924.82848 93603.23802 96521.12542 88327.10998 98156.85279 101518.2795 0.793923304 0.83882842 0.840045858 0.856248046 0.922033337 0.95077582 0.87006114 0.966888459 1 16.63138 4.956603624 0.12766875 1.057062859 0.551333751 0.804580269 0.028920862 15.93277137 0.313278867 0.223824474 1.412628633 90490.63263 -4.956603624 -0.505729108 GLQVLMGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLQVLMGR 8 0 Q7L576;Q96F07;Q96F07-2;E7EVJ5;H7C229;E7EW33;A0A087WVZ5;A0A0G2JQH3;A0A0G2JR96;A0A0G2JQT1 Q7L576;A0A0G2JR96 CYFIP1;CYFIP2 Cytoplasmic FMR1-interacting protein 1;Cytoplasmic FMR1-interacting protein 2 0 ; 88.643 0.033662 270970000 597790 606210 617750 613370 625520 485470 607860 507970 747460 FALSE TRUE 560375.391 651094.4192 632403.3217 629110.1126 576394.1824 625617.3081 516717.0361 571391.1727 622704.0972 0.899906382 1.045591995 1.015575977 1.010287415 0.925630946 1.004678323 0.829795465 0.917596616 1 19.24818725 2.329565066 1.552969861 0.907436277 1.00411961 0.109108508 0.062983091 0.461711102 2.239001238 0.030693063 0.020311961 213.5822053 -2.329565066 0.096683333 GLS(ph)GEEEDDEPDCCNDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLSGEEEDDEPDCCNDER 18 0 Q6P158-2;Q6P158;A0A087WW12;A0A087WZ11;Q6P158-3 Q6P158-2 DHX57 Putative ATP-dependent RNA helicase DHX57 1 GLS(1)GEEEDDEPDCCNDER;GLS(1)GEEEDDEPDCCNDER 437.88 5.97E-170 1087400000 1088870 1060010 1088520 1018820 1092000 1319160 1625220 914570 802320 TRUE FALSE 1020719.57 1138494.243 1114340.208 1044964.646 1006238.725 1699980.077 1381533.349 1028756.078 668407.6088 1.527091489 1.703293362 1.667156678 1.563364379 1.505426796 2.543328434 2.066902487 1.539114852 1 19.35036863 GLS(ph)LDSFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GLSLDSFLR 9 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 GLS(1)LDSFLR;GLS(1)LDSFLR;GLS(1)LDSFLR;GLS(0.952)LDS(0.048)FLR;GLS(1)LDSFLR 168.46 6.21E-05 212942000 440913 588632 460205 504841 519310 390751 667612 533513 605303 TRUE FALSE 413317.0424 632214.9258 471121.2799 517796.0748 478525.4874 503554.4704 567509.7784 600123.2725 504274.0189 0.819627875 1.253713065 0.9342565 1.026814897 0.948939405 0.9985731 1.125399599 1.19007375 1 18.94384837 1.711338783 6.853140529 1.117591943 1.018730504 0.136548189 0.11858675 0.265696586 30.00244306 0.056089857 0.029074673 51.44448014 -1.711338783 -0.09886144 GLS(ph)LEHQK ddPTM_SK-BR-3_Pertuzumab_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 123.96 0.00085372 2071770000 4437860 3919160 3815560 4165100 3313660 2743020 5386800 3691740 4308730 TRUE FALSE 4160102.264 4209338.684 3906066.885 4271983.517 3053418.51 3534885.345 4579099.349 4152661.866 3589575.128 1.158940018 1.172656522 1.088169699 1.190108402 0.850635076 0.984764274 1.275666113 1.156867239 1 21.77538166 3.867409269 1.573365329 1.087344813 1.168349892 0.08383023 0.117883371 1.353865916 6.419900566 0.036450191 0.100416015 7369.012084 -3.867409269 0.081005079 GLS(ph)SAGGGSPHREDAQPEHSASAR ddPTM_SK-BR-3_Pertuzumab_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(0.4)S(0.344)AGGGS(0.256)PHREDAQPEHSASAR 108.75 0.0013722 1761900000 356570 477020 453720 434960 490570 465210 554760 486970 476440 TRUE FALSE 334252.9202 512339.0571 464482.4527 446121.81 452042.6111 599508.5749 471578.8881 547769.2765 396919.0861 0.842118537 1.290789673 1.170219495 1.123961597 1.138878494 1.510405007 1.188098292 1.38005275 1 18.59848541 GLSAS(ph)LPDLDSENWIEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 GLSASLPDLDSENWIEVK 18 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 1 GLSAS(1)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK;GLS(0.104)AS(0.896)LPDLDSENWIEVK;GLS(0.011)AS(0.989)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK;GLS(0.008)AS(0.992)LPDLDSENWIEVK;GLS(0.016)AS(0.984)LPDLDSENWIEVK;GLS(0.011)AS(0.989)LPDLDSENWIEVK;GLS(0.001)AS(0.999)LPDLDSENWIEVK;GLS(0.008)AS(0.992)LPDLDSENWIEVK;GLS(0.012)AS(0.988)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK 389.59 1.40E-126 9846499700 4963747.3 4007779.2 4414455 4070549 4486942 3349062.3 5681916 3861739.4 5579073 TRUE FALSE 4653075.217 4304519.342 4519167.957 4175006.179 4134555.675 4315882.219 4829965.444 4343886.065 4647889.674 1.001115677 0.92612339 0.972305342 0.898258451 0.889555468 0.928568129 1.039173858 0.934593196 1 22.14814439 -1.029620506 5.105812428 1.000000542 0.951193541 0.109076122 0.045577569 2.87E-07 5.46E-08 0.045033649 0.010614415 0.093407015 1.029620506 -0.048807001 GLSAS(ph)LPDLDSENWIEVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLSASLPDLDSENWIEVKK 19 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 1 GLS(0.001)AS(0.999)LPDLDSENWIEVKK;GLS(0.001)AS(0.999)LPDLDSENWIEVKK 175.71 1.25E-12 425090000 673480 615150 562570 627430 830960 400940 900480 511180 1700010 TRUE FALSE 631328.089 660696.3461 575914.4261 643530.916 765699.7535 516684.8693 765461.3836 575001.9482 1416267.349 0.445769007 0.466505386 0.406642451 0.454385196 0.540646337 0.364821564 0.540478028 0.405998168 1 20.4336622 -4.415264183 0.502928064 10 0.450757466 0.903115613 0.056211069 330.197302 2.878277312 3298.506238 0.023178721 3.84E-05 4.415264183 -9.549242534 GLSDHVS(ph)LDGQELGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GLSDHVSLDGQELGTR 16 0 Q7L8J4;Q7L8J4-2 Q7L8J4 SH3BP5L SH3 domain-binding protein 5-like 1 GLSDHVS(1)LDGQELGTR;GLSDHVS(1)LDGQELGTR;GLSDHVS(1)LDGQELGTR;GLSDHVS(1)LDGQELGTR 274.82 3.49E-35 291260000 914100 1118450 1098740 1123650 1174130 1061570 1252440 1001510 1321300 TRUE FALSE 856888.1127 1201261.202 1124802.632 1152484.761 1081918.566 1368028.026 1064648.249 1126550.728 1100766.494 0.778446762 1.091295209 1.021835819 1.046983868 0.982877451 1.242795846 0.967188096 1.023423891 1 20.07007703 4.743962839 24.85998938 1.049685994 0.778446637 0.541595906 0.077626858 390.9924565 1799213.351 0.016659395 0.1435809 55457.82572 -4.743962839 -0.271239357 GLSEDTTEETLKESFDGSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GLSEDTTEETLKESFDGSVR 20 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;; 297.87 9.87E-55 3168910000 2516950 2463400 2583570 2553390 2932190 1940180 3257590 2308480 3837570 FALSE TRUE 2359418.592 2645792.699 2644853.5 2618914.31 2701907.625 2500278.47 2769144.621 2596698.81 3197054.775 0.73799755 0.827571901 0.827278131 0.819164667 0.84512397 0.782056813 0.866154888 0.812215927 1 21.60831203 -5 0.235295455 2.003533974 0.800183923 0.762298404 0.033064826 76.15152838 0.761245247 36.46473333 0.049126242 1.00E-05 5 -1.203350051 GLSFHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLSFHPK 7 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1;A0A3B3ITX2;A0A3B3IS23;A0A3B3IU84 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 81.297 0.027584 199920000 350990 1135700 540370 569460 1126100 298570 707860 1190100 1013100 FALSE TRUE 329022.1624 1219788.41 553187.8316 584073.3077 1037660.648 384762.3121 601722.9645 1338686.605 844007.0651 0.389833422 1.445234833 0.655430333 0.692024192 1.229445453 0.455875701 0.712935933 1.586108292 1 19.68689555 1.252191439 24.99783321 1.293054274 0.834969417 0.251360177 0.351064251 290.9196039 533528.8233 0.224028516 0.080843997 17.87275242 -1.252191439 -0.458084857 GLSHS(ph)PWAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLSHSPWAVK 10 0 Q96KB5;Q96KB5-2;E5RFX4 Q96KB5 PBK Lymphokine-activated killer T-cell-originated protein kinase 1 GLS(0.018)HS(0.982)PWAVK 93.011 0.0058466 127180000 351240 340260 334900 356820 368200 272620 457400 315890 566990 TRUE FALSE 329256.5154 365453.2044 342843.9862 365976.6053 339283.0572 351320.9684 388817.1163 355329.5619 472355.7061 0.697052054 0.773682205 0.725817391 0.77479027 0.718278731 0.743763574 0.823144743 0.752249962 1 18.84951416 -5 0.235407599 2.381742635 0.727998903 0.859997396 0.032047595 55.38363131 0.55361966 36.47037967 0.048989734 1.00E-05 5 -1.653743732 GLSLVDKENT(ph)PPALSGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLSLVDKENTPPALSGTR 18 1 P31350;P31350-2;A0A286YFD6 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 GLSLVDKENT(1)PPALSGTR;GLSLVDKENT(1)PPALSGTR 106.58 0.00071922 656540000 592000 443550 519540 520650 508960 435050 672950 439000 587280 TRUE FALSE 554947.7768 476390.9035 531863.7341 534010.7605 468988.3346 560641.8726 572047.3949 493810.1164 489259.174 1.134261361 0.973698458 1.087079737 1.091468058 0.9585683 1.145899561 1.169211382 1.009301701 1 18.90023938 GLSQNQQIPQNSVT(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLSQNQQIPQNSVTPR 16 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 GLSQNQQIPQNS(0.002)VT(0.998)PR 140.81 1.86E-05 114060000 61135 65585 68906 61894 66087 50788 80594 50590 74294 TRUE FALSE 57308.66948 70440.98164 70540.48286 63482.30483 60896.7936 65449.67113 68509.6779 56906.27286 61893.85144 0.925918619 1.138093365 1.139700975 1.025664155 0.983890842 1.057450289 1.106889882 0.919417221 1 15.91750848 3.209437585 24.56283964 1.028055787 1.093201497 0.046510351 0.07730576 335.6976733 283131.6661 0.021901579 0.026182004 1619.7112 -3.209437585 0.06514571 GLSSAGGGS(ph)PHREDAQPEHSASAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GLSSAGGGSPHREDAQPEHSASAR 24 1 Q92994-9;Q92994-3;Q92994-7;Q92994-8;Q92994-5;Q92994 Q92994-9 BRF1 Transcription factor IIIB 90 kDa subunit 1 GLS(0.007)S(0.035)AGGGS(0.958)PHREDAQPEHSASAR;GLSSAGGGS(1)PHREDAQPEHSASAR;GLSSAGGGS(0.999)PHREDAQPEHSASAR;GLS(0.142)S(0.142)AGGGS(0.716)PHREDAQPEHSASAR 225.65 3.54E-33 3255910000 755458 892190 889969 835677 975360 894029 1120936 937663 961448 TRUE FALSE 708175.2323 958248.6759 911079.485 857121.8866 898759.16 1152120.659 952862.0531 1054732.29 800976.1176 0.884140259 1.196351121 1.137461486 1.070096683 1.122079848 1.438395769 1.189626048 1.316808662 1 19.6113997 2.443429136 24.99420277 1.255514472 1.102888018 0.230131048 0.135682639 252.9202226 187625.3858 0.042137969 0.0352553 277.6061836 -2.443429136 -0.152626454 GLSSDNKPMVNLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLSSDNKPMVNLDK 14 1 F8VZQ9;H0YHG0;P82979 F8VZQ9 SARNP SAP domain-containing ribonucleoprotein 0 116.96 0.00099156 0 156940 116920 128860 127520 160110 92549 151550 130160 178440 FALSE TRUE 147117.4055 125576.8785 131916.6201 130792.3791 147535.6065 119266.3939 128826.4844 146410.7625 148657.2112 0.989641904 0.84474125 0.887387964 0.879825324 0.992455093 0.802291345 0.866600977 0.984888397 1 17.18162992 1.218505609 11.58368426 0.992634379 0.886276431 0.314672751 0.05895452 0.69092262 386.6790047 0.049450519 0.013043025 16.53886145 -1.218505609 -0.106357949 GLSTS(ph)LPDLDSEPWIEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GLSTSLPDLDSEPWIEVK 18 0 A0A3B3ISF0;Q659C4;Q659C4-9;Q659C4-2;H0Y9K3;D6R9W6;D6RJB0;Q659C4-4 A0A3B3ISF0 LARP1B La-related protein 1B 1 GLS(0.005)T(0.04)S(0.955)LPDLDSEPWIEVK;GLST(0.002)S(0.997)LPDLDSEPWIEVK;GLS(0.018)T(0.178)S(0.804)LPDLDSEPWIEVK;GLS(0.01)T(0.112)S(0.878)LPDLDSEPWIEVK 238.83 7.11E-24 228678000 774590 667909 692870 722043 765739 545050 920470 608438 699687 TRUE FALSE 726109.7946 717361.6773 709305.2036 740571.8458 705600.9478 702397.0869 782454.0687 684402.8236 582904.7195 1.245674928 1.230667128 1.216845875 1.270485246 1.210491053 1.204994681 1.342336136 1.174124691 1 19.15290056 0.983988785 24.43189101 0.999999997 1.244866404 0.796338944 0.039321348 316.6822623 483233.9608 0.038047169 0.009511792 9.638041344 -0.983988785 0.244866407 GLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSR 33 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;; 319.36 5.97E-105 7359380000 1799677 2773596 2163740 2244532 2991240 2142833 2404732 2604416 2429359 FALSE TRUE 1687038.429 2978955.934 2215064.935 2302130.491 2756320.076 2761434.101 2044164.761 2929583.071 2023883.289 0.833565077 1.471901048 1.094462782 1.137481842 1.361896752 1.364423589 1.010021068 1.447505934 1 20.94869467 -1.057078784 4.423862973 0.999985148 1.220387012 0.099066433 0.203368597 0.259489423 53180865.06 1715.127968 0.042221879 0.087684174 1.057078784 0.220401864 GLTLAPGLS(ph)PARPLFGSDFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLTLAPGLSPARPLFGSDFEK 21 1 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 GLTLAPGLS(1)PARPLFGSDFEK;GLTLAPGLS(1)PARPLFGSDFEK 205 3.02E-22 383710000 1000460 794920 933050 792350 883890 864470 1172810 888110 1040390 TRUE FALSE 937842.9945 853776.7039 955182.3866 812683.0424 814472.8448 1114028.456 996958.0283 998992.4885 866742.1878 1.082032244 0.98504113 1.102037492 0.937629498 0.939694475 1.285305447 1.150235955 1.152583205 1 19.7252434 2.249907804 24.99930729 1.163044047 1.015371363 0.381298339 0.085926427 198.6406438 437630.407 0.027811878 0.023075188 177.790194 -2.249907804 -0.147672684 GLTMLDHEQVTPEDPGAQFLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GLTMLDHEQVTPEDPGAQFLIR 22 0 Q9UBE0;M0QX65;B3KNJ4;Q9UBE0-2;Q9UBE0-3;A0A590UK93;A0A590UKC5;M0QZS6;A0A590UKA0 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 ;;; 162.39 1.63E-11 569010000 567687 593690 599950 592360 623650 532940 648280 529030 664120 FALSE TRUE 532156.484 637647.4253 614181.0973 607560.9605 574671.0447 686791.1264 551076.4323 595080.56 553274.0816 0.96183158 1.152498276 1.110084708 1.098119324 1.038673352 1.241321705 0.996027919 1.075561968 1 19.07763482 1.615965976 25 1.026844533 1.106056076 0.187283824 0.074475468 0.958383889 2949.250381 0.031469881 0.017068351 41.30151435 -1.615965976 0.079211543 GLVAAYSGDS(ph)DNEEELVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLVAAYSGDSDNEEELVER 19 0 P52756 P52756 RBM5 RNA-binding protein 5 1 GLVAAYSGDS(1)DNEEELVER 249.42 5.19E-25 318450000 246020 279280 236370 295160 301710 240400 284620 228970 222230 TRUE FALSE 230622.0474 299958.1818 241976.808 302734.3053 278014.9136 309799.5774 241943.8733 257557.4085 185138.3773 1.245673915 1.620183703 1.307005125 1.63517856 1.501660097 1.673340676 1.306827232 1.391161639 1 17.49824446 0.73772258 1.208298655 1.002959663 1.48729748 0.510683309 0.145490603 0.67221562 1.698237556 0.124453541 0.038132701 5.466666496 -0.73772258 0.484337817 GLVAAYSGES(ph)DS(ph)EEEQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GLVAAYSGESDSEEEQER 18 0 P98175-5;P98175-2;P98175;P98175-4;P98175-3 P98175-5 RBM10 RNA-binding protein 10 2 GLVAAYS(0.002)GES(0.998)DS(1)EEEQER;GLVAAYSGES(1)DS(1)EEEQER;GLVAAYSGES(1)DS(1)EEEQER 329.59 1.08E-74 376144000 657888 744070 724685 743740 777750 685281 796930 653572 749060 TRUE FALSE 616711.9644 799161.717 741874.8704 762825.6275 716668.6523 883110.5001 677437.7448 735171.9029 624037.0469 0.988261783 1.280631849 1.188831455 1.222404393 1.148439273 1.415157168 1.085572961 1.178090158 1 19.25127215 0.79064832 1.371691666 1.002367765 1.207217464 0.212885177 0.112600575 0.999105729 3.372232842 0.094482879 0.028126972 6.175161503 -0.79064832 0.204849699 GLVDRPLALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLVDRPLALR 10 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 153.97 1.40E-05 997630000 803520 1274990 797180 827370 1260160 642420 832200 1068280 967620 FALSE TRUE 753229.1175 1369391.586 816089.4861 848601.7149 1161192.117 827876.2252 707419.3358 1201657.11 806117.9709 0.934390678 1.698748366 1.012369796 1.052701646 1.440474172 1.026991402 0.877563038 1.490671531 1 19.62063146 3.745861737 21.76407188 1.112687978 1.366484779 0.070324125 0.265917312 159.3896061 185099.9517 0.063062039 0.113263647 5570.0839 -3.745861737 0.253796801 GLVGEIIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLVGEIIKR 9 1 Q32Q12;P22392-2;J3KPD9;P22392;E7ERL0;E5RHP0;F6XY72;C9K028;P15531;P15531-2 Q32Q12;P15531 NME1-NME2;NME2;NME1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Nucleoside diphosphate kinase A 0 ; 177.3 8.38E-05 11558200000 6304500 7125900 7055200 7100500 8248400 5932600 9095200 6381000 9351500 FALSE TRUE 5909912.599 7653509.05 7222552.676 7282710.851 7600603.936 7645245.312 7731459.196 7177681.896 7790674.237 0.758588078 0.982393669 0.927076715 0.934798533 0.975602843 0.981332948 0.99239924 0.921317164 1 22.89331676 4.741800225 24.99637724 0.963358229 0.758588003 0.84465734 0.027730501 116.918249 902084.0154 0.006505623 0.046830136 55182.35427 -4.741800225 -0.204770227 GLVGPELHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GLVGPELHDR 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 182.71 1.75E-06 1733120000 1873100 2601430 2224650 2365690 2454290 1988940 2573850 2190530 2045250 FALSE TRUE 1755866.015 2794042.584 2277419.749 2426397.611 2261539.964 2563114.69 2187925.087 2464022.492 1703884.562 1.030507614 1.639807441 1.336604485 1.424038731 1.327284731 1.504277195 1.284080586 1.446120557 1 20.70039617 -2.794873124 0.505724928 1.31E-08 1.396511178 0.342768213 0.159729831 211.9546915 8.935443069 230.707299 0.06611474 0.001603714 2.794873124 1.396511165 GLVLDHGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GLVLDHGAR 9 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;;;;; 193.41 3.36E-05 10758750000 7148690 9688800 8108740 7714970 10436900 7004380 8372210 8198620 8087350 FALSE TRUE 6701266.254 10406168.83 8301083.142 7912949.192 9617227.974 9026430.799 7116874.834 9222235.754 6737519.039 0.994619268 1.54451049 1.232068228 1.174460383 1.427413848 1.339726203 1.056304968 1.368788081 1 22.68378601 -0.007054782 0.400240645 0.953915846 1.312347806 0.163215633 0.169838342 6.895614939 1.477510256 0.693668545 0.111636231 0.98388699 0.007054782 0.35843196 GLVMVKPGSIKPHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLVMVKPGSIKPHQK 15 2 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ; 174.62 5.42E-07 1900500000 2443720 2248030 2081590 2122690 3370800 1935120 2516020 2702340 4512300 FALSE TRUE 2290771.927 2414476.48 2130966.298 2177161.819 3106070.965 2493757.73 2138766.159 3039733.098 3759167.979 0.609382698 0.642290127 0.566871794 0.579160557 0.826265541 0.663380233 0.568946685 0.808618586 1 21.84198195 -1.8639453 0.270789615 1.369725911 0.598723949 0.652551095 0.083357616 17.9355855 0.779389872 4.321358998 0.109225791 0.013679011 1.8639453 -0.771001962 GLVQALQTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLVQALQTK 9 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 123.35 0.0013029 60782000 115380 159710 84280 110180 185840 88708 134670 141470 188990 FALSE TRUE 108158.5718 171535.0946 86279.1614 113007.4053 171244.876 114316.5595 114477.4837 159132.8409 157446.3481 0.6869551 1.089482841 0.547990871 0.717751836 1.087639556 0.726066758 0.727088847 1.01071154 1 17.26450077 1.22603401 24.42989816 1.005356069 0.801452295 0.204722054 0.170128419 319.2827965 622652.8797 0.152330805 0.039211108 16.82805837 -1.22603401 -0.203903774 GLVRPDQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLVRPDQPR 9 1 K7EIH1;O60304-2;O60304 K7EIH1 ZNF500 Zinc finger protein 500 0 ; 74.464 0.037407 428120000 309120 403760 333030 319390 438240 302530 365850 430030 748630 FALSE TRUE 289772.731 433654.8105 340929.6289 327586.0881 403822.3982 389865.4998 310994.1889 483720.1921 623678.8167 0.464618524 0.695317524 0.546642951 0.525248059 0.64748455 0.625106208 0.498644784 0.775591826 1 19.25044373 0.988721202 4.321358191 0.999369795 0.582036928 0.800158119 0.070510966 0.071704692 4.109227183 0.063700616 0.016226635 9.743639381 -0.988721202 -0.417332866 GLVYETSVLDPDEGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GLVYETSVLDPDEGIR 16 0 O75390;B4DJV2;A0A0C4DGI3;F8VPA1;F8VX68;F8VPF9;F8W1S4;H0YH82;F8VRP1;F8VZK9;F8VTT8;F8W4S1;F8VX07;F8W642 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ;;;; 264.84 1.12E-26 382234000 525413 577534 540507 493743 706769 571804 480004 537933 789301 FALSE TRUE 492528.3382 620295.2183 553328.0813 506413.2813 651262.2137 736874.5323 408031.8563 605095.1192 657561.564 0.749022396 0.943326454 0.841484831 0.770138203 0.990420136 1.120616795 0.620522668 0.920210597 1 19.32676645 4.757338436 22.39606529 0.883060484 0.749021894 0.095519646 0.137457935 2547.309569 3037932.725 0.031563006 0.909330093 57192.41507 -4.757338436 -0.134038589 GLWHEEMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GLWHEEMK 8 0 P23921;E9PL69 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ;;; 153.78 0.00043559 418300000 907370 888450 818200 785980 979460 578490 935510 794290 999520 FALSE TRUE 850579.3314 954231.7624 837608.0904 806149.5775 902537.1626 745490.672 795238.9603 893458.8549 832693.6549 1.0214793 1.145957768 1.005901853 0.968122638 1.083876594 0.895276033 0.955019839 1.072974256 1 19.66742631 3.709527244 3.713219734 0.988248885 1.089672997 0.245576691 0.061902246 0.241900376 7.214084671 0.015812277 0.027426043 5123.034072 -3.709527244 0.101424113 GLWSTDS(ph)AEEDKETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GLWSTDSAEEDKETK 15 1 Q99549-2;Q99549;A0A0A0MT47 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 GLWST(0.003)DS(0.997)AEEDKETK 154.26 1.52E-06 204120000 386890 196190 229720 225300 290550 163330 333240 186610 434760 TRUE FALSE 362675.2455 210716.1117 235169.0669 231081.5794 267731.375 210480.7196 283273.7556 209908.6693 362195.7473 1.001323865 0.581774119 0.649287212 0.638001912 0.739189725 0.581124216 0.782101275 0.57954482 1 18.46641008 -1.448065911 3.187265317 1.00552967 0.68206546 0.355193326 0.12865555 153867042 193148860.7 7609579.24 0.027331825 0.035639704 1.448065911 -0.32346421 GLYGIKDDVFLSVPCILGQNGISDLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLYGIKDDVFLSVPCILGQNGISDLVK 27 1 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 167.51 7.20E-12 1590920000 905410 775360 817765 727798 961250 545408 953540 754620 824900 FALSE TRUE 848742.0043 832768.4612 837162.772 746474.5288 885757.3025 702858.4356 810565.5292 848835.9681 687218.8609 1.235038868 1.211795119 1.218189458 1.086225322 1.288901328 1.022757779 1.179486733 1.235175599 1 19.39041011 -5 0.142256759 0.387735727 1.245811015 0.354891864 0.077626347 143.0216417 1.238935443 25.01988244 0.408494033 1.00E-05 5 0.858075288 GLYNEHTVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GLYNEHTVDR 10 0 Q6P6C2-3;Q6P6C2;Q6P6C2-1 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 0 ; 96.171 0.0062212 0 212329 297960 259180 273020 311000 235740 268790 250869 314460 FALSE TRUE 199039.7069 320021.2684 265327.872 280026.1554 286575.3145 303794.3111 228487.4348 282190.5469 261974.5945 0.759767211 1.221573676 1.01280001 1.068905769 1.093904984 1.159632718 0.872174018 1.077167606 1 17.99906738 1.742820671 24.99999988 0.973610298 1.069834783 0.047881446 0.130287428 1.682756651 9921.140672 0.054222332 0.03006904 55.31216667 -1.742820671 0.096224485 GMDDDRGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GMDDDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;; 109.44 0.00257 4115361000 7285140 8398160 8039650 7884660 8264940 7967970 8623190 7879110 8349930 FALSE TRUE 6829176.092 9019968.505 8230354.295 8086993.724 7615844.952 10268193.59 7330222.713 8862834.228 6956272.74 0.981729203 1.296666885 1.183155779 1.16254696 1.094816899 1.476105664 1.053757233 1.274078024 1 22.72988307 -0.520065232 7.325550178 1.000000043 1.197609816 0.155590142 0.138452695 0 0 0.11636914 0.027428469 0.301949815 0.520065232 0.197609772 GMGEAVQEFVDKEEKDAIEELVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GMGEAVQEFVDKEEKDAIEELVK 23 2 F8W7U8;P49959-2;P49959;P49959-3 F8W7U8 MRE11A Double-strand break repair protein MRE11A 0 124.86 3.16E-05 9040600 52640 24873 36697 30932 36410 23470 49557 28323 61549 FALSE TRUE 49345.35637 26714.6228 37567.47017 31725.76749 33550.50547 30245.408 42126.38791 31859.1889 51276.07428 0.962346612 0.520995867 0.73265106 0.618724579 0.654311118 0.589854204 0.821560318 0.6213266 1 15.64599819 -0.864851979 0.57939252 1.071317748 0.674619246 0.359100246 0.127494062 19.59546605 4.12880449 2.647576737 0.047022113 0.136504831 0.864851979 -0.396698503 GMGGAFVLVLYDELKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GMGGAFVLVLYDELKK 16 1 P12236 P12236 SLC25A6 "ADP/ATP translocase 3;ADP/ATP translocase 3, N-terminally processed" 0 ; 205.61 3.56E-11 231463000 427140 335410 356330 371750 587710 390680 395280 493930 657050 FALSE TRUE 400406.0699 360244.1054 364782.3159 381289.7344 541553.6273 503462.9738 336011.4336 555598.2478 547384.1103 0.731490122 0.658119406 0.66641013 0.696567049 0.989348461 0.919761762 0.613849447 1.015006167 1 19.06219403 2.871908392 7.610034638 0.862380601 0.67748537 0.432398414 0.118732887 0.301296824 17.28085985 0.036346371 0.038613851 744.5749002 -2.871908392 -0.184895231 GMGPGT(ph)PAGYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GMGPGTPAGYGR 12 0 P23246 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 1 GMGPGT(1)PAGYGR 110.92 0.014988 234430000 377590 418740 401500 405030 472770 366610 507430 392110 486980 TRUE FALSE 353957.3159 449743.9453 411023.7696 415423.7555 435640.5513 472444.3556 431345.5822 441065.7966 405699.892 0.872460957 1.108563138 1.013122699 1.02396812 1.073800018 1.164516838 1.063213451 1.087172576 1 18.63005339 2.687126827 4.65032216 1.088152602 1.023127746 0.185578676 0.070237604 0.375445953 17.87897846 0.021323361 0.020388384 486.5492718 -2.687126827 -0.065024856 GMGS(ph)LDAMDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GMGSLDAMDK 10 0 P12268;H0Y4R1 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 1 GMGS(1)LDAMDK;GMGS(1)LDAMDK;GMGS(1)LDAMDK 140.63 4.09E-05 308339000 890166 699018 782179 739239 765343 617447 898624 654361 881702 TRUE FALSE 834452.0991 750774.02 800732.6553 758209.1243 705236.048 795693.9255 763883.6736 736059.4113 734540.2402 1.136019585 1.0221006 1.090114076 1.032222719 0.960105396 1.08325437 1.039948027 1.002068193 1 19.486482 4.743478489 24.52318427 1.035913626 1.136019639 0.419613916 0.038846885 424.502995 2116707.558 0.008875673 0.074536022 55396.01054 -4.743478489 0.100106013 GMKDDKEEEEDGT(ph)GSPQLNNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GMKDDKEEEEDGTGSPQLNNR 21 2 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 GMKDDKEEEEDGT(0.786)GS(0.214)PQLNNR;GMKDDKEEEEDGT(0.619)GS(0.381)PQLNNR 180.26 7.32E-17 1795900000 892780 380660 518240 529280 582590 416690 701490 469270 787880 TRUE FALSE 836902.4935 408844.4625 530532.8975 542862.2209 536835.7315 536981.6386 596308.0868 527859.3925 656377.7381 1.275031807 0.622879843 0.808273753 0.827057637 0.817876202 0.818098493 0.908483107 0.804200633 1 19.32416678 -0.249651034 0.593711962 1.015031692 0.828978095 0.035554855 0.166466832 17.46047298 5.883280534 0.7618636 0.062327314 0.562793361 0.249651034 -0.186053597 GMKDDKEEEEDGTGS(ph)PQLNNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GMKDDKEEEEDGTGSPQLNNR 21 2 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 GMKDDKEEEEDGT(0.003)GS(0.997)PQLNNR;GMKDDKEEEEDGT(0.102)GS(0.898)PQLNNR;GMKDDKEEEEDGT(0.047)GS(0.953)PQLNNR;GMKDDKEEEEDGT(0.296)GS(0.704)PQLNNR;GMKDDKEEEEDGT(0.021)GS(0.979)PQLNNR;GMKDDKEEEEDGT(0.213)GS(0.787)PQLNNR;GMKDDKEEEEDGT(0.287)GS(0.713)PQLNNR 250.71 2.41E-31 7558440000 3398880 1365440 2021010 1956120 2245730 1650260 2500030 1813740 3240470 TRUE FALSE 3186150.168 1466538.598 2068949.312 2006317.351 2069359.425 2126663.272 2125173.711 2040189.432 2699614.623 1.180224074 0.543239982 0.766386911 0.743186577 0.766538826 0.787765503 0.787213735 0.755733583 1 21.36432204 -1.363243468 0.553251995 1.105549778 0.762291592 0.125112828 0.157862791 68.53838516 9.59035091 10.71772917 0.061185348 0.043326792 1.363243468 -0.343258186 GMLPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GMLPHK 6 0 P40429;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 93.595 0.04544 1368980000 1263470 2159400 1320710 1288330 2373170 981630 1689220 2105610 2461890 FALSE TRUE 1184391.668 2319284.223 1352037.865 1321390.729 2186790.801 1265010.646 1435937.143 2368500.044 2050984.655 0.577474661 1.130815005 0.659214033 0.644271387 1.066215096 0.616782111 0.700120861 1.154811197 1 20.96788527 1.23720663 24.99944898 1.077405675 0.788768978 0.306641508 0.190234501 46.10934454 851188.3011 0.145401379 0.043965755 17.26659213 -1.23720663 -0.288636697 GMPQEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GMPQEER 7 0 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;H0Y400 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ; 134.06 0.0095001 595210000 1282140 1466160 1310430 1374370 1512350 1097880 1474560 1269920 1513140 FALSE TRUE 1201893.146 1574716.012 1341514.018 1409638.661 1393576.132 1414820.133 1253463.417 1428472.307 1260587.159 0.953439148 1.24919249 1.06419775 1.118239743 1.105497642 1.122350108 0.99434887 1.13318012 1 20.26566444 1.414650044 0.527203991 1.008141432 1.123668438 0.063494425 0.082441841 1.478192046 1.042391469 0.078271492 0.043999655 25.9806519 -1.414650044 0.115527005 GMSNNT(ph)PQLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GMSNNTPQLNR 11 0 Q9NZN8;Q9NZN8-5;F8VP97;F8VV52;F8VUB4;Q9NZN8-4;F8VX63;F8VVY1;F8VQD8;A0A087X050;F8VWH8;F8W145 Q9NZN8 CNOT2 CCR4-NOT transcription complex subunit 2 1 GMS(0.2)NNT(0.8)PQLNR 61.082 0.085253 0 178680 158170 167350 170900 184050 148930 204290 175850 222750 TRUE FALSE 167496.7378 169881.0714 171319.621 175285.5833 169595.4554 191923.6733 173658.611 197805.2596 185571.586 0.902599053 0.915447645 0.923199638 0.944571241 0.91390853 1.034229849 0.935803885 1.065924282 1 17.5016163 2.214337977 0.780084011 1.01561936 0.911895179 0.545989151 0.03752245 0.482323371 0.559746024 0.027225635 0.016374847 163.8090823 -2.214337977 -0.103724181 GMTPGEAEIHFLENAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GMTPGEAEIHFLENAK 16 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;Q4VXN0 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 0 ; 174.59 3.82E-09 93914000 443320 371540 427200 365330 468250 350860 451170 400820 753710 FALSE TRUE 415573.3925 399049.2082 437333.3857 374704.9863 431475.5338 452147.5863 383521.247 450863.2593 627910.9318 0.661834938 0.63551881 0.696489524 0.596748627 0.687160411 0.720082361 0.61078925 0.718036964 1 19.2602004 0.895863566 6.559590344 0.999998396 0.659614169 0.889609729 0.037567087 0.518916376 32.59265503 0.032995545 0.00828296 7.867985768 -0.895863566 -0.340384227 GMWSEGNGSHTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GMWSEGNGSHTIR 13 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;;;; 247.95 2.47E-17 6751730000 2679716 3480360 3343810 3259550 3348760 2897490 3539310 3128420 3134920 FALSE TRUE 2511997.359 3738049.476 3423126.752 3343195.571 3085761.898 3733948.326 3008623.323 3519010.124 2611681.6 0.961831396 1.431280703 1.310698346 1.280093091 1.181523007 1.429710393 1.151987028 1.347411616 1 21.31654759 -1.867607038 2.355076636 0.864640886 1.277658146 0.249267777 0.140421844 9289461.771 5119970.106 7032152.824 0.030169678 0.013564162 1.867607038 0.413017261 GNAEGS(ph)S(ph)DEEGKLVIDEPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GNAEGSSDEEGKLVIDEPAK 20 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 2 GNAEGS(1)S(1)DEEGKLVIDEPAK;GNAEGS(1)S(1)DEEGKLVIDEPAK;GNAEGS(1)S(1)DEEGKLVIDEPAK;GNAEGS(1)S(1)DEEGKLVIDEPAK;GNAEGS(1)S(1)DEEGKLVIDEPAK;GNAEGS(1)S(1)DEEGKLVIDEPAK;GNAEGS(1)S(1)DEEGKLVIDEPAK 201.66 7.04E-22 12355720000 25163080 9084000 14136450 12498730 12359690 10150730 18689870 11617260 12482190 TRUE FALSE 23588167.74 9756588.812 14471773.27 12819468.57 11389009.8 13081080.97 15887497.5 13067700.48 10398831.85 2.268347837 0.938238924 1.391672976 1.232779677 1.095220114 1.257937541 1.527815598 1.256650811 1 23.30991814 4.74910762 24.98787374 1.240790848 2.268348415 0.780747648 0.175267157 741.7366398 1757281.847 0.042269606 0.609213377 56118.70236 -4.74910762 1.027557567 GNAEGS(ph)S(ph)DEEGKLVIDEPAKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GNAEGSSDEEGKLVIDEPAKEK 22 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 2 GNAEGS(1)S(1)DEEGKLVIDEPAKEK;GNAEGS(1)S(1)DEEGKLVIDEPAKEK;GNAEGS(1)S(1)DEEGKLVIDEPAKEK;GNAEGS(1)S(1)DEEGKLVIDEPAKEK;GNAEGS(1)S(1)DEEGKLVIDEPAKEK;GNAEGS(1)S(1)DEEGKLVIDEPAKEK;GNAEGS(1)S(1)DEEGKLVIDEPAKEK;GNAEGS(1)S(1)DEEGKLVIDEPAKEK 145.67 4.89E-08 4389840000 4247760 1549650 2195830 2331945 2659510 1581752 3137960 1789795 3600900 TRUE FALSE 3981900.284 1664387.698 2247916.125 2391786.657 2450642.813 2038378.125 2667452.029 2013254.846 2999886.527 1.327350301 0.554816885 0.749333718 0.797292376 0.816911837 0.679485076 0.889184309 0.671110333 1 21.5164765 -1.874287695 5.025999296 1.05041401 0.784036081 0.063672191 0.206809592 0.095243893 0.002382278 0.163247952 0.041779521 0.013357104 1.874287695 -0.266377929 GNAEGS(ph)SDEEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GNAEGSSDEEGK 12 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.5)S(0.5)DEEGK 108.36 0.00059866 0 166850 93963 127860 113300 88046 102790 129530 97582 67512 TRUE FALSE 156407.1563 100920.1183 130892.8996 116207.4698 81131.22232 132463.8043 110108.179 109765.3275 56243.81106 2.780877636 1.794332859 2.327240938 2.066137903 1.442491552 2.355171207 1.957694134 1.951598326 1 15.77940673 -1.814310851 0.264558077 5.28E-13 2.208471065 0.521078175 0.341604208 22.70500586 0.98363578 15.25161516 0.438410582 0.01533519 1.814310851 2.208471065 GNAEGS(ph)SDEEGKLVIDEPAKEK ddPTM_SK-BR-3_Pertuzumab_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(0.893)S(0.107)DEEGKLVIDEPAKEK 214 1.14E-24 1039250000 2410200 863750 1305520 1387100 1530220 935180 1793190 1081870 1919320 TRUE FALSE 2259349.884 927702.9487 1336487.551 1422695.334 1410042.694 1205151.285 1524317.807 1216943.851 1598973.093 1.413000566 0.580186717 0.835841176 0.889755644 0.881842665 0.753703293 0.95331048 0.76107838 1 20.60871423 -2.018612663 2.867983671 1.165230197 0.853879719 0.011770542 0.215626287 9173953.642 31190973.28 9789244.73 0.04496998 0.009580482 2.018612663 -0.311350478 GNAEGSS(ph)DEEGKLVIDEPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GNAEGSSDEEGKLVIDEPAK 20 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.384)S(0.616)DEEGKLVIDEPAK;GNAEGS(0.194)S(0.806)DEEGKLVIDEPAK 260.32 1.51E-36 1491740000 2825300 1164190 1669240 1488770 1431990 1226000 2031970 1303410 1242030 TRUE FALSE 2648469.516 1250387.839 1708835.161 1526974.359 1319527.282 1579926.298 1727294.962 1466143.608 1034727.169 2.559582463 1.208422738 1.651483804 1.475726553 1.275241746 1.526901337 1.669324063 1.416937383 1 19.98081899 4.746259211 24.80342726 1.448765886 2.559583062 0.75188137 0.207324741 413.0689635 1330795.481 0.045584226 0.488368587 55751.84077 -4.746259211 1.110817176 GNAEGSS(ph)DEEGKLVIDEPAKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GNAEGSSDEEGKLVIDEPAKEK 22 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.351)S(0.649)DEEGKLVIDEPAKEK;GNAEGS(0.354)S(0.646)DEEGKLVIDEPAKEK 209.68 2.82E-23 1778760000 3055300 1111700 1567870 1670580 1840050 1159850 2209100 1316200 2286840 TRUE FALSE 2864074.227 1194011.425 1605060.617 1713449.911 1695539.895 1494679.866 1877865.963 1480530.467 1905151.63 1.503331379 0.626727766 0.842484446 0.899377185 0.889976351 0.784546407 0.985677955 0.777119492 1 20.8614744 -0.51181688 7.482795413 0.999999999 0.882381323 0 0.231947776 0 0 0.199001962 0.046905212 0.307739412 0.51181688 -0.117618676 GNAGQSNYGFANSAMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 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 ;;;;;;;;;; 377.09 9.66E-105 3183650000 667666 992937 823261 856604 996461 743734 953904 903415 945614 FALSE TRUE 625877.9769 1066455.089 842789.1397 878585.9089 918202.9726 958437.9323 810874.9508 1016208.351 787784.9145 0.794478246 1.353738906 1.069821374 1.115261149 1.165550337 1.216623871 1.029310077 1.289956602 1 19.58744227 -0.545673741 7.488114399 1.000010189 1.140386806 0.061527457 0.153455418 0 0 0.129449732 0.030511595 0.284659878 0.545673741 0.140376617 GNAMVEEGHFAAEDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GNAMVEEGHFAAEDVK 16 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 131.48 4.43E-05 178750000 414030 329600 359340 313190 362690 273860 416900 303750 448970 FALSE TRUE 388116.6014 354003.9269 367863.7145 321226.9856 334205.7904 352918.9363 354389.7153 341673.8561 374034.0065 1.037650573 0.946448507 0.983503393 0.858817594 0.893517126 0.943547726 0.947479933 0.9134834 1 18.51280992 7.999994416 0.831298918 0.930678495 33.30201133 0.369521771 0.041115247 654.2936741 1.947232774 0.012913675 40003.55237 99998714.18 -7.999994416 32.37133284 GNDKGDESQSQSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GNDKGDESQSQSVR 14 1 Q96GM8;Q96GM8-2 Q96GM8 TOE1 Target of EGR1 protein 1 0 68.257 0.045872 170750000 78228 69846 77731 73362 95716 54371 85278 71683 100450 FALSE TRUE 73331.84912 75017.47051 79574.81603 75244.59312 88198.85146 70067.02506 72491.35558 80632.78034 83684.24607 0.876292164 0.896434802 0.950893624 0.899148844 1.053948092 0.83727856 0.866248535 0.96353596 1 16.35266843 4.380812806 2.700299243 0.927154947 0.878226581 0.089231047 0.063121726 0.852402942 11.611737 0.01554798 0.064454043 24033.26671 -4.380812806 -0.048928366 GNDPLTSS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GNDPLTSSPGR 11 0 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 GNDPLTSS(1)PGR;GNDPLTSS(1)PGR;GNDPLTSS(1)PGR;GNDPLTS(0.006)S(0.994)PGR;GNDPLT(0.001)S(0.054)S(0.945)PGR;GNDPLTSS(1)PGR;GNDPLTS(0.001)S(0.999)PGR 198.03 5.77E-08 16486050000 9074820 10349740 10186380 10094430 11126470 9963930 11301400 9635560 10363770 TRUE FALSE 8506843.215 11116045.52 10428005.74 10353470.16 10252641.93 12840354.84 9606859.987 10838580.88 8633989.834 0.985273712 1.287474937 1.20778527 1.199152462 1.187474403 1.487186699 1.112679094 1.255338619 1 23.04159596 -1.13062758 4.032386623 0.999930185 1.223666135 0.217950184 0.127292241 7883036.509 2210300.14 4801.205642 0.026413441 0.074023978 1.13062758 0.22373595 GNDS(ph)DGEGESDDPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GNDSDGEGESDDPEK 15 0 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 GNDS(1)DGEGESDDPEK;GNDS(1)DGEGESDDPEK 254.59 1.11E-24 173110000 786830 469040 607760 527940 487540 500930 648370 497470 319580 TRUE FALSE 737583.7148 503768.2096 622176.3542 541487.8342 449250.575 645540.3591 551152.9377 559580.2246 266240.0334 2.770371177 1.892158002 2.336900075 2.033833256 1.687389268 2.424655491 2.070135473 2.10178844 1 18.02236799 -1.848626609 0.428041735 1.59E-15 2.179398214 0.6106414 0.294289822 28.86292258 2.115346116 29.54454559 0.152920121 0.014170116 1.848626609 2.179398214 GNEEKPAS(ph)PSAAVPPGTDHDPHGLVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GNEEKPASPSAAVPPGTDHDPHGLVVK 27 1 Q52LW3 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 GNEEKPAS(0.856)PS(0.144)AAVPPGTDHDPHGLVVK 147.35 8.17E-08 211910000 98774 60166 77362 80119 102300 57317 83608 67593 144380 TRUE FALSE 92591.91166 64620.75324 79197.06317 82174.98918 94265.77066 73863.48744 71071.75658 76032.13484 120282.0453 0.769789967 0.537243552 0.658427972 0.683185832 0.783706084 0.614085729 0.590875857 0.632115414 1 16.87606178 -1.674376471 2.638799843 1.048927742 0.646125441 0.66351313 0.075921583 11400486.1 9916331.179 3753117.331 0.017970722 0.021165256 1.674376471 -0.402802301 GNEFFCEVDEDYIQDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GNEFFCEVDEDYIQDK 16 0 P67870;Q5SRQ3;Q5SRQ6;N0E472;A0A0G2JM12;N0E644;A0A0G2JM58 P67870 CSNK2B;CSNK2B-LY6G5B-1181;CSNK2B-LY6G5B--991;CSNK2B-LY6G5B-562 Casein kinase II subunit beta 0 ; 197.2 1.02E-10 46780000 77842 68900 50736 44313 69066 52110 90297 66596 80539 FALSE TRUE 72970.00817 74001.42769 51939.48188 45450.1466 63641.83496 67153.31106 76757.80313 74910.6572 67096.5206 1.087537886 1.102910062 0.774100973 0.677384553 0.948511702 1.0008464 1.143990813 1.11646113 1 16.03395033 2.046210434 3.078049059 1.099088515 0.912831538 0.254183105 0.131247589 0.359983977 6.77811623 0.06520556 0.040613499 111.2270539 -2.046210434 -0.186256977 GNEFFCEVDEDYIQDKFNLTGLNEQVPHYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GNEFFCEVDEDYIQDKFNLTGLNEQVPHYR 30 1 P67870;Q5SRQ3;Q5SRQ6;N0E472;A0A0G2JM12;N0E644;A0A0G2JM58 P67870 CSNK2B;CSNK2B-LY6G5B-1181;CSNK2B-LY6G5B--991;CSNK2B-LY6G5B-562 Casein kinase II subunit beta 0 387.63 4.03E-155 284150000 360600 470980 346180 318250 507230 344830 547030 425360 619790 FALSE TRUE 338030.6897 505851.8493 354391.5531 326416.8338 467394.2019 444376.8232 465007.9299 478467.1323 516343.045 0.654663005 0.979681733 0.68634904 0.632170486 0.905200925 0.860623238 0.900579439 0.926645835 1 18.97797035 2.55359402 24.70705639 0.906945919 0.769702465 0.417489246 0.102427037 138.2654397 44670.28389 0.033321475 0.031415778 357.7618439 -2.55359402 -0.137243454 GNEPGSDRS(ph)PS(ph)PSKNDSFFTPDSNHNSLSQSTTGHLSLPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GNEPGSDRSPSPSKNDSFFTPDSNHNSLSQSTTGHLSLPQK 41 2 Q5VT52-2;Q5VT52-3;Q5VT52 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 2 GNEPGS(0.012)DRS(0.986)PS(0.534)PS(0.402)KNDS(0.036)FFT(0.031)PDSNHNSLSQSTTGHLSLPQK;GNEPGS(0.478)DRS(0.526)PS(0.967)PS(0.027)KNDSFFTPDSNHNSLSQSTTGHLSLPQK;GNEPGS(0.174)DRS(0.793)PS(0.491)PS(0.43)KNDS(0.089)FFT(0.021)PDSNHNSLSQSTTGHLSLPQK 232.29 4.08E-45 975290000 59332.1 379269 320109 400556 402811 297104 501054 403908 435122 TRUE FALSE 55618.60977 407350.4714 327702.1366 410834.9451 371175.8489 382873.1017 425925.6043 454336.8029 362497.3272 0.153431779 1.123733724 0.90401256 1.133346136 1.023940926 1.056209448 1.174975848 1.253352146 1 18.46761083 4.740287082 24.9864459 1.077860552 0.153431468 0.90038714 0.097224361 45.2605792 654984.27 0.023529244 0.151023629 54990.42575 -4.740287082 -0.924429084 GNEPGSDRS(ph)PSPSKNDS(ph)FFTPDSNHNSLSQSTTGHLSLPQK ddPTM_SK-BR-3_Pertuzumab_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(0.151)DRS(0.768)PS(0.115)PS(0.14)KNDS(0.453)FFT(0.363)PDS(0.007)NHNSLSQS(0.001)T(0.001)T(0.001)GHLSLPQK 80.859 0.0013429 201430000 42025 147520 127910 153860 169060 122840 205850 158900 186310 TRUE FALSE 39394.73027 158442.5343 130944.0856 157808.3081 155782.7096 158301.9139 174984.7035 178739.0148 155213.6574 0.25380969 1.020802789 0.843637653 1.016716639 1.003666251 1.019896809 1.127379552 1.151567573 1 17.24389598 4.738850845 24.8895 1.014476405 0.253809452 0.895759185 0.082413483 7.654370333 656098.0228 0.022268016 0.130273765 54808.86965 -4.738850845 -0.760666953 GNFGGSFAGSFGGAGGHAPGVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GNFGGSFAGSFGGAGGHAPGVAR 23 0 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 283.64 3.95E-52 1397020000 525540 708930 713290 769890 769110 652960 768200 677980 815460 FALSE TRUE 492647.3895 761419.9148 730209.5756 789646.6808 708707.203 841458.9521 653015.5416 762627.2954 679354.4579 0.725169878 1.120799173 1.074858003 1.162348567 1.043206819 1.238615486 0.961229494 1.12257642 1 19.37380498 4.7413797 24.89410654 1.091283139 0.725169738 0.677580158 0.079187027 132.4330135 1169393.584 0.016629225 0.114958921 55128.94737 -4.7413797 -0.366113401 GNFNYIEFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GNFNYIEFTR 10 0 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ;;;;;;; 218.47 1.57E-08 4330700000 1901255 2764775 1945580 1991482 2765208 1591592 2130463 2331361 2501262 FALSE TRUE 1782258.843 2969481.818 1991730.076 2042586.8 2548039.718 2051058.773 1811019.851 2622436.553 2083785.213 0.855298728 1.425042177 0.955823116 0.98022905 1.222793838 0.984294715 0.869101019 1.258496574 1 20.99077515 3.742455059 23.89675827 1.025555096 1.183736356 0.036253522 0.180436199 480.66259 749074.2728 0.042616591 0.076411354 5526.562161 -3.742455059 0.15818126 GNFTLPEVAECFDEITYVELQKEEAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GNFTLPEVAECFDEITYVELQKEEAQK 27 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;; 239.15 3.71E-45 159511000 350513 246995 289271 291213 354120 236456 407720 232038 512690 FALSE TRUE 328575.017 265282.7668 296132.6447 298686.0186 326308.8437 304717.0087 346586.1711 261008.4551 427118.7269 0.769282629 0.621098421 0.693326296 0.699304432 0.763976906 0.713424604 0.811451592 0.611091106 1 18.70427763 -5 0.241907688 2.67190826 0.680460227 0.640040067 0.066140116 101.9165301 1.015957311 83.94428752 0.09513711 1.00E-05 5 -1.991448032 GNHECASINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 163.84 6.34E-06 887160000 439350 647050 448960 469840 682350 393880 476220 534200 580950 FALSE TRUE 411851.8678 694958.2553 459609.5432 481896.8898 628760.9835 507586.7619 404815.232 600896.0459 483985.6919 0.850958767 1.435906612 0.949634567 0.995684166 1.299131346 1.048763983 0.836419834 1.241557459 1 18.88460487 2.005861964 24.92890891 0.991510603 1.128922892 0.019247934 0.193511265 342.5240723 1456627.577 0.068519497 0.050461746 101.3589177 -2.005861964 0.137412289 GNIETTSEDGQVFS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GNIETTSEDGQVFSPK 16 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 GNIETTSEDGQVFS(1)PK;GNIETTSEDGQVFS(1)PK;GNIETTSEDGQVFS(1)PK;GNIETTSEDGQVFS(1)PK 351.98 3.11E-87 838450000 1984500 1243290 1527690 1428490 1455190 1092190 1874740 1234500 1596620 TRUE FALSE 1860293.687 1335344.485 1563927.528 1465147.472 1340905.247 1407487.523 1593640.141 1388630.042 1330133.807 1.398576352 1.003917409 1.175767069 1.101503821 1.008098012 1.058154837 1.198105132 1.043977707 1 20.34313995 4.748243465 24.95093251 1.088111909 1.398576521 0.67654465 0.06996919 817.3547246 2106129.442 0.016170834 0.215059142 56007.14892 -4.748243465 0.310464612 GNIIISTPEKWDILSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GNIIISTPEKWDILSR 16 1 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 203.59 2.50E-11 664390000 626690 756560 726940 783340 861090 615610 964340 736530 972710 FALSE TRUE 587466.5916 812576.4896 744183.3601 803441.8306 793463.4649 793326.6134 819746.1695 828487.3918 810358.4171 0.724946615 1.00273715 0.918338533 0.991464781 0.97915126 0.978982382 1.011584692 1.022371551 1 19.62820062 4.741135812 24.99993757 0.983600953 0.724946524 0.893932012 0.028447863 77.93210441 756520.7188 0.007147446 0.049042864 55097.99709 -4.741135812 -0.258654429 GNILIPGINEAVAAVTEEEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GNILIPGINEAVAAVTEEEHK 21 0 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ;; 230.77 7.96E-26 860760000 3873750 2969300 3351010 3241730 3540830 2573610 4085200 3085820 3088570 FALSE TRUE 3631298.902 3189150.062 3430497.54 3324918.28 3262747.495 3316569.428 3472662.185 3471091.42 2573067.714 1.411272188 1.239434953 1.333232515 1.29220007 1.268037944 1.288955362 1.349619431 1.349008967 1 21.29505799 -0.992913 4.282865707 0.99998513 1.310583509 0.806232143 0.048682048 2855368.576 666695.8083 401.8200716 0.010575468 0.101645229 0.992913 0.310598379 GNIWS(ph)AEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GNIWSAEK 8 0 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 GNIWS(1)AEK;GNIWS(1)AEK 75.229 0.040837 520550000 285410 249710 279300 274540 297550 185791 287690 245670 333240 TRUE FALSE 267546.6976 268198.7882 285925.1279 281585.1612 274181.6233 239425.8456 244553.5553 276342.4403 277620.0912 0.963715185 0.966064045 1.029915114 1.01428236 0.987614485 0.862422617 0.880892857 0.995397844 1 18.08275245 2.364205161 8.652700507 0.917973853 0.995548909 0.233339794 0.04784791 0.266130831 19.20223908 0.016108319 0.013458105 231.315727 -2.364205161 0.077575056 GNKHDDGTQS(ph)DSENAGAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GNKHDDGTQSDSENAGAHR 19 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 GNKHDDGTQS(1)DSENAGAHR;GNKHDDGT(0.008)QS(0.992)DSENAGAHR 264.63 1.44E-31 172652000 131251 98728 123590 118590 123921 99526 142300 131071 138507 TRUE FALSE 123036.2342 106037.9238 126521.6132 121633.2202 114188.7445 128257.5405 120963.436 147435.5029 115389.2869 1.06627086 0.918958135 1.096476255 1.054111897 0.989595721 1.11152035 1.048307337 1.277722628 1 16.81614976 1.898287098 1.670178325 1.125659629 1.022229535 0.167235298 0.086031388 0.56774696 2.962522255 0.053431466 0.02416884 79.1201493 -1.898287098 -0.103430094 GNKPWISLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GNKPWISLPR 10 1 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ; 147.72 2.41E-05 1652670000 983500 5474500 602410 459040 5200100 328540 753630 4341000 4310600 FALSE TRUE 921944.4906 5879837.676 616699.4497 470819.7436 4791705.122 423384.1646 640630.1779 4882983.406 3591133.012 0.256728026 1.63732105 0.171728379 0.131106183 1.33431569 0.117897099 0.178392217 1.359733374 1 21.77600766 -1.132638644 7.661772815 1.000000081 0.641029511 0.034044825 0.587407824 7.75E-07 8.87E-08 0.542758279 0.127929325 0.073681991 1.132638644 -0.35897057 GNLELRPGGAHPGTCS(ph)PSRPGS ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GNLELRPGGAHPGTCSPSRPGS 22 2 Q5JTU8;B1AMJ5;A0A0A0MRG9;Q96SN8-3;Q96SN8-2;Q96SN8;Q96SN8-4 Q5JTU8 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 1 GNLELRPGGAHPGT(0.005)CS(0.987)PS(0.008)RPGS 137.9 1.20E-06 635260000 349420 373460 393090 371830 385120 371040 433210 315200 345010 TRUE FALSE 327550.4259 401111.367 402414.2804 381371.7873 354874.2287 478153.2247 368254.1822 354553.4138 287425.6022 1.13960073 1.395531101 1.400064147 1.326853921 1.234664644 1.663572142 1.281215659 1.233548477 1 18.13282905 0.947173025 2.213045108 1.002949715 1.366750437 0.399546201 0.135879922 0.319920825 3.427467415 0.117719428 0.032316939 8.854683143 -0.947173025 0.363800722 GNLELRPGGAHPGTCSPS(ph)RPGS ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GNLELRPGGAHPGTCSPSRPGS 22 2 Q5JTU8;B1AMJ5;A0A0A0MRG9;Q96SN8-3;Q96SN8-2;Q96SN8;Q96SN8-4 Q5JTU8 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 1 GNLELRPGGAHPGT(0.019)CS(0.36)PS(0.62)RPGS(0.001) 90.37 0.0012461 685130000 480090 509320 484560 497570 503090 522800 554510 429470 487870 TRUE FALSE 450042.0239 547030.5827 496053.992 510338.4886 463579.3408 673723.8731 471366.3733 483090.2749 406441.3452 1.107274221 1.345902894 1.220481129 1.255626413 1.140581159 1.657616483 1.159740216 1.188585464 1 18.63268764 -0.547717161 6.22678729 1.000035068 1.269683506 0.211031999 0.156570353 0 3.25E-10 0.135775943 0.032002697 0.283323657 0.547717161 0.269648437 GNLLHFPSS(ph)QGEEEKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GNLLHFPSSQGEEEKEK 17 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 GNLLHFPS(0.004)S(0.996)QGEEEKEK;GNLLHFPS(0.003)S(0.997)QGEEEKEK 226.45 1.25E-15 660540000 2341100 945170 1437600 1293060 1234180 1089010 2010350 1200080 1295540 TRUE FALSE 2194574.73 1015151.37 1471700.551 1326242.109 1137252.481 1403389.508 1708916.681 1349912.63 1079306.004 2.033320227 0.940559365 1.363561904 1.22879156 1.053688645 1.300270269 1.583347701 1.250722802 1 20.04167252 4.752869643 24.70967336 1.244879006 2.033320864 0.646760946 0.188896749 1541.806519 2662429.121 0.046878163 1.006193302 56606.93527 -4.752869643 0.788441858 GNLLHFPSS(ph)QGEEEKEKLEGDHTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GNLLHFPSSQGEEEKEKLEGDHTIR 25 2 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 GNLLHFPS(0.034)S(0.966)QGEEEKEKLEGDHTIR;GNLLHFPS(0.272)S(0.727)QGEEEKEKLEGDHT(0.001)IR;GNLLHFPS(0.268)S(0.732)QGEEEKEKLEGDHTIR 145.65 1.31E-07 698270000 1054880 596910 656770 771330 913240 402020 896620 617430 1306030 TRUE FALSE 988856.9438 641105.8375 672348.8945 791123.6337 841517.8142 518076.6478 762180.1548 694517.4946 1088045.156 0.908838148 0.589227234 0.617942087 0.727105515 0.773421774 0.476153627 0.700504157 0.638316793 1 20.053307 -1.387958052 6.041018936 1.000067572 0.663390391 0.425622782 0.115969617 9.54E-05 9.66E-06 0.101463014 0.023910283 0.040930019 1.387958052 -0.33667718 GNLYSFGCPEYGQLGHNSDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GNLYSFGCPEYGQLGHNSDGK 21 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 231.37 5.70E-26 452640000 201025 371400 375520 393020 402930 327730 451390 369880 372550 FALSE TRUE 188443.2041 398898.8424 384427.5117 403105.5586 371285.5031 422340.3307 383708.26 416060.3322 310368.9982 0.607158592 1.285240616 1.238614404 1.298794534 1.19627123 1.360768418 1.236296995 1.340534443 1 18.24362493 4.740000523 24.95421055 1.258319046 0.607158374 0.797936486 0.100592796 43.70957472 757430.9532 0.019855621 0.125091755 54954.1535 -4.740000523 -0.651160672 GNPGLHSPMLDLDNDT(ph)RPSVLGHLSQTASLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GNPGLHSPMLDLDNDTRPSVLGHLSQTASLKR 32 2 Q96KP1 Q96KP1 EXOC2 Exocyst complex component 2 1 GNPGLHSPMLDLDNDT(0.225)RPS(0.194)VLGHLS(0.194)QT(0.194)AS(0.194)LKR 91.538 0.00012363 129970000 35847 78367 62694 66291 89808 45482 99906 74347 102740 TRUE FALSE 33603.40026 84169.37422 64181.13129 67992.13929 82754.84195 58611.91506 84926.02278 83629.38661 85592.03027 0.39259964 0.983378639 0.749849385 0.794374652 0.96685219 0.68478239 0.992218814 0.977069785 1 16.38518885 4.746047566 24.89001159 0.880318544 0.392599393 0.654619129 0.11399734 527.3109648 1752975.807 0.025238742 0.265720441 55724.6778 -4.746047566 -0.487719152 GNPS(ph)PPAAGEGQRPPPPLCVPGGGGGAPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GNPSPPAAGEGQRPPPPLCVPGGGGGAPAR 30 1 Q92623 Q92623 TTC9 Tetratricopeptide repeat protein 9A 1 GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR;GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR;GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR 247.66 2.95E-46 1488750000 101985 101560 97643 104509 96996 91173 109646 84024 121215 TRUE FALSE 95601.9409 109079.6081 99959.13807 107190.8779 89378.32542 117493.165 93205.6002 94514.58136 100983.4334 0.946709155 1.080173296 0.989856798 1.061469929 0.885079091 1.163489506 0.922979117 0.935941453 1 16.62375911 1.609294272 25 0.947091789 1.022267125 0.145443621 0.077402675 0.230857373 3896.498482 0.033136377 0.017118607 40.67188233 -1.609294272 0.075175335 GNRES(ph)DGFREEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GNRESDGFREEK 12 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 GNRES(1)DGFREEK 67.646 0.04316 375510000 837680 512990 650440 617970 593080 439150 689810 563220 766760 TRUE FALSE 785251.1041 550972.3134 665868.744 633828.1564 546501.8892 565925.476 586379.3944 633539.2568 638782.8025 1.229292807 0.862534669 1.042402427 0.992243614 0.855536322 0.885943507 0.917963652 0.991791348 1 19.28496595 4.748166762 24.93202673 0.940268458 1.229292966 0.668010751 0.063268405 788.6074334 2046728.147 0.015021737 0.196139071 55997.25804 -4.748166762 0.289024508 GNRGS(ph)GGGGGGGGQGSTNYGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GNRGSGGGGGGGGQGSTNYGK 21 1 Q99729-3;Q99729-4 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 1 GNRGS(0.992)GGGGGGGGQGS(0.008)TNYGK;GNRGS(1)GGGGGGGGQGSTNYGK;GNRGS(1)GGGGGGGGQGSTNYGK;GNRGS(1)GGGGGGGGQGSTNYGK;GNRGS(1)GGGGGGGGQGSTNYGK 199.57 4.81E-22 1726980000 731689 693906 713873 764020 811536 569177 856193 627564 1098948 TRUE FALSE 685893.8916 745283.5222 730806.4047 783626.0467 747801.2361 733489.1601 727814.8082 705916.7468 915526.4793 0.749179742 0.814049117 0.798236229 0.855929418 0.816799135 0.801166516 0.794968605 0.77105006 1 19.80424209 -1.432679063 3.399336965 1.002322811 0.802858121 0.832776702 0.028118286 15763679.4 26285938.22 365890.2413 0.006401428 0.036925037 1.432679063 -0.19946469 GNRPVILTYHDIGLNHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GNRPVILTYHDIGLNHK 17 1 Q5TH30;Q9UGV2;Q9UGV2-2;Q5TH29 Q5TH30 NDRG3 Protein NDRG3 0 ; 282.19 3.29E-36 3970100000 1193220 1014320 1199260 1058520 1325450 968920 1284440 1194960 1285540 FALSE TRUE 1118538.49 1089421.308 1227707.014 1085683.415 1221354.504 1248631.475 1091850.146 1344153.386 1070975.069 1.044411324 1.01722378 1.146345091 1.013733603 1.140413572 1.165882858 1.019491655 1.255074395 1 20.03049347 4.083835815 4.725836681 1.103554168 1.031728766 0.133596395 0.079091687 0.407944563 14.63872371 0.017667282 0.039881996 12129.30215 -4.083835815 -0.071825402 GNRPVILTYHDIGMNHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GNRPVILTYHDIGMNHK 17 1 Q92597;E5RI76;E5RIR1;E5RGM5;E5RIM2;E5RH82;E5RK17;E5RIV1 Q92597 NDRG1 Protein NDRG1 0 ;; 292.8 3.17E-46 8984700000 4305680 4979070 4150640 4470550 5441200 2782430 5051480 4275980 2544180 FALSE TRUE 4036195.175 5347725.524 4249095.141 4585271.882 5013870.101 3585672.372 4294057.47 4809845.516 2119539.922 1.904278911 2.523059589 2.004725222 2.163333577 2.365546432 1.691722026 2.025938471 2.269287531 1 21.01531971 -1.802525198 0.330736917 1.17E-09 2.210283025 0.671816664 0.242373334 16.90839918 0.948776795 13.7703899 0.199167119 0.015757046 1.802525198 2.210283024 GNS(ph)PPSSGEACR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GNSPPSSGEACR 12 0 P41227-2;P41227 P41227-2 NAA10 N-alpha-acetyltransferase 10 1 GNS(0.998)PPSS(0.001)GEACR;GNS(1)PPSSGEACR;GNS(1)PPSSGEACR;GNS(1)PPSSGEACR;GNS(0.992)PPS(0.005)S(0.003)GEACR;GNS(0.992)PPS(0.005)S(0.003)GEACR 166.79 5.35E-05 2784380000 1660668 1652826 1747520 1597811 1675930 1774710 1953630 1490115 1536559 TRUE FALSE 1556729.754 1775202.957 1788972 1638813.535 1544309.218 2287039.967 1660701.318 1676159.138 1280097.376 1.216102605 1.386771811 1.397528057 1.280225681 1.2063998 1.786614057 1.29732421 1.309399714 1 20.28782213 0.773883469 2.328070191 1.000577337 1.379609309 0.330243341 0.16288109 1.053758252 8.882256942 0.143887985 0.038883458 5.941327183 -0.773883469 0.379031973 GNS(ph)PPSSGEACREEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GNSPPSSGEACREEK 15 1 P41227-2;P41227 P41227-2 NAA10 N-alpha-acetyltransferase 10 1 GNS(1)PPSSGEACREEK;GNS(0.998)PPS(0.001)S(0.001)GEACREEK;GNS(0.999)PPS(0.001)SGEACREEK;GNS(0.999)PPS(0.001)SGEACREEK 198.05 4.92E-09 1627920000 1556860 1520960 1412490 1597000 2287320 1099880 1666680 1287770 3789870 TRUE FALSE 1459418.912 1633573.461 1445994.93 1637981.724 2107683.114 1417397.501 1416776.807 1448550.919 3157316.214 0.462234003 0.517393049 0.457982296 0.518789254 0.667555282 0.448924785 0.448728195 0.458791841 1 21.59026733 -1.488953058 5.57291227 1.000715453 0.495802065 0.852462568 0.065687885 0.000577181 5.29E-05 0.06286841 0.014798486 0.032437468 1.488953058 -0.504913388 GNS(ph)RPGTPS(ph)AEGGSTSSTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 2 GNS(0.959)RPGT(0.042)PS(0.725)AEGGS(0.241)T(0.027)S(0.006)S(0.001)TLR 190.09 2.33E-16 459420000 859620 750140 823970 754620 733510 857490 1009400 761830 618700 TRUE FALSE 805817.9187 805681.1461 843514.9575 773984.8268 675903.0834 1105033.443 858049.8408 856946.1525 515434.973 1.563374549 1.563109196 1.636510911 1.501614883 1.311325616 2.143885263 1.664710168 1.662568893 1 18.9754309 GNSRPGT(ph)PSAEGGS(ph)TSSTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 2 GNS(0.163)RPGT(0.837)PS(0.137)AEGGS(0.758)T(0.084)S(0.017)S(0.002)T(0.002)LR 146.15 3.43E-06 421940000 865260 794530 926140 825280 670780 912740 1114200 811220 644060 TRUE FALSE 811104.9211 853357.8279 948108.4782 846458.082 618099.6446 1176233.221 947136.0537 912502.6027 536562.2252 1.511669818 1.590417267 1.76700564 1.577558095 1.151962653 2.192165541 1.765193316 1.700646374 1 19.03338596 4.525661941 3.087480209 1.656231275 1.513876466 0 0.334094082 1.519777032 26.62755655 0.075966737 0.403855274 33547.63747 -4.525661941 -0.142354808 GNSRPGT(ph)PSAEGGSTSSTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 GNSRPGT(0.976)PS(0.024)AEGGSTSSTLR 224.24 9.57E-25 921020000 256820 204390 241680 262370 266190 330080 333730 269390 196170 TRUE FALSE 240746.0946 219523.2483 247412.7637 269102.8584 245284.5112 425368.7376 283690.2847 303023.9345 163427.9597 1.473102247 1.343241687 1.513894955 1.646614563 1.500872382 2.60279048 1.735873624 1.854174372 1 17.3182953 2.423969945 24.99999964 1.895203866 1.482465123 0.107279037 0.391087093 138.0114976 64913.50699 0.12052753 0.100840578 265.4421858 -2.423969945 -0.412738743 GNSRPGTPSAEGGSTS(ph)STLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 GNSRPGT(0.014)PS(0.016)AEGGS(0.017)T(0.069)S(0.295)S(0.295)T(0.295)LR 85.087 0.0070961 75306000 94158 96537 105700 112030 110460 134400 124420 98346 79452 TRUE FALSE 88264.81886 103684.6999 108207.2539 114904.8795 101784.9172 173199.0982 105764.3761 110624.7146 66190.94792 1.33348776 1.566448331 1.6347742 1.735960627 1.537746782 2.616658375 1.597867675 1.671296727 1 16.01434631 4.508923594 0.833554173 1.766821709 1.218005874 0.048728503 0.396153078 4.204720646 2.828834557 0.129654718 1.991217232 32279.26176 -4.508923594 -0.548815835 GNTAEGCVHETQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GNTAEGCVHETQEK 14 0 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 0 68.919 0.048448 220090000 83475 82625 92366 80096 92606 72781 110730 94457 100730 FALSE TRUE 78250.44876 88742.64097 94556.96514 82151.39896 85333.09831 93791.6932 94127.06447 106250.1644 83917.51226 0.932468643 1.057498472 1.126784655 0.978954175 1.01686878 1.11766532 1.12166176 1.266126241 1 16.35668429 2.126423037 4.686874993 1.137478757 1.039700634 0.27277104 0.081249589 0.30236134 11.11311389 0.030174018 0.021883664 133.78981 -2.126423037 -0.097778124 GNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK 49 1 P68104;A0A087WVQ9;A0A087WV01 P68104 EEF1A1 Elongation factor 1-alpha 1;Elongation factor 1-alpha 0 ; 409.35 1.92E-230 979870000 798550 808510 774200 788780 976980 612820 1092510 701480 1607550 FALSE TRUE 748570.181 868372.9217 792564.3896 809021.4302 900251.9317 789731.1857 928698.2679 789061.3221 1339239.52 0.558951681 0.64840748 0.591801823 0.604090171 0.672211295 0.589686291 0.693451958 0.589186109 1 20.35298258 -5 0.329903321 4.809999835 0.608748386 0.891618116 0.041778645 96.56783146 0.835365679 257.9675746 0.030840758 1.00E-05 5 -4.201251449 GNVDEELSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GNVDEELSKK 10 1 P41236;E7EMN6;E7EUI7 P41236 PPP1R2 Protein phosphatase inhibitor 2 0 ; 128.85 0.00051112 362650000 850220 504200 580080 610180 648010 444280 786930 496930 777720 FALSE TRUE 797006.2479 541531.4926 593839.7715 625838.2518 597117.9085 572536.4237 668937.152 558972.8044 647913.5077 1.230112103 0.835808308 0.916541737 0.965928699 0.921601265 0.883661811 1.032448227 0.862727506 1 19.30544171 GNVVPS(ph)PLPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GNVVPSPLPTR 11 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 GNVVPS(0.986)PLPT(0.014)R;GNVVPS(0.999)PLPT(0.001)R;GNVVPS(0.976)PLPT(0.024)R;GNVVPS(0.983)PLPT(0.017)R;GNVVPS(1)PLPTR;GNVVPS(0.92)PLPT(0.08)R;GNVVPS(0.998)PLPT(0.002)R;GNVVPS(0.995)PLPT(0.005)R 140.31 4.06E-05 77347500000 10670060 10283730 10907230 10393910 9796280 11074400 11833180 10173980 7149710 TRUE FALSE 10002239.99 11045148.07 11165954.65 10660635.33 9026919.685 14271399.5 10058904.51 11444223.8 5956377.212 1.679248918 1.854339924 1.874621813 1.789785124 1.51550504 2.395986519 1.688762171 1.921339665 1 22.50600369 -1.269943548 5.884657926 0.999957205 1.846300781 0.569406066 0.229491354 0.000113198 1.40E-05 0.195211897 0.046009575 0.053710161 1.269943548 0.846343576 GNVVPS(ph)PLPTRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 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(0.999)PLPT(0.001)RR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(0.997)PLPT(0.003)RR;GNVVPS(0.961)PLPT(0.039)RR 135.55 7.70E-05 48626000000 7153690 8927790 8190180 8206620 8981330 8097930 9695340 7928800 9552720 TRUE FALSE 6705953.313 9588812.861 8384454.937 8417215.763 8275972.571 10435670.93 8241613.774 8918728.133 7958309.319 0.84263542 1.204880644 1.053547255 1.057663811 1.039915922 1.311292451 1.035598573 1.120681262 1 22.92403054 4.752078258 24.33961574 1.1086664 0.842635165 0.434753805 0.093078325 1447.371456 2606044.396 0.020220472 0.393700517 56503.87826 -4.752078258 -0.266031235 GNWAHSGFPEIAFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GNWAHSGFPEIAFGR 15 0 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;P52701-4 P52701 MSH6 DNA mismatch repair protein Msh6 0 133.48 4.11E-05 106310000 226130 286130 255590 245480 296230 213910 285880 266630 222150 FALSE TRUE 211976.927 307315.3629 261652.7155 251779.4324 272965.2907 275662.3445 243014.948 299919.3424 185071.7299 1.145377131 1.660520292 1.413790835 1.360442422 1.47491619 1.489489209 1.313085192 1.620557298 1 17.49772501 -1.59344407 3.085405416 0.975280205 1.444715958 0.461166757 0.147345841 36574463.43 44090745.23 7449463.949 0.032007578 0.025500925 1.59344407 0.469435753 GNWEQPQNQNQTQHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GNWEQPQNQNQTQHK 15 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;Q5VU81;Q5VU80;Q5VU79;Q5VU78;Q5VU77 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 0 ;;; 259.53 7.28E-25 1469440000 1072980 984490 992770 958810 1081310 871960 1243040 958630 1235460 FALSE TRUE 1005824.097 1057382.664 1016318.973 983414.6879 996388.2744 1123680.697 1056657.692 1078317.066 1029253.745 0.977236277 1.027329431 0.987432864 0.955463794 0.968068642 1.091743122 1.026625064 1.047668829 1 19.97316727 2.257780628 24.99999949 1.043610396 0.988470166 0.491770429 0.029186316 212.4380944 276323.5087 0.009968869 0.008329514 181.0425373 -2.257780628 -0.05514023 GNYAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GNYAER 6 0 Q99878;Q96KK5;Q6FI13;P0C0S8;Q16777;Q9BTM1;Q9BTM1-2;Q96QV6;H0YFX9;Q8IUE6 Q99878 HIST1H2AJ;HIST1H2AH;HIST2H2AA3;HIST1H2AG;HIST2H2AC;H2AFJ;HIST1H2AA;HIST2H2AB Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-A;Histone H2A type 1;Histone H2A type 2-C;Histone H2A.J;Histone H2A type 1-A;Histone H2A;Histone H2A type 2-B 0 ;;; 131.3 0.035801 3988190000 3561410 4832110 3550340 3322610 4294960 2717670 3479970 3773780 4287850 FALSE TRUE 3338507.705 5189884.452 3634555.741 3407873.798 3957651.167 3502217.211 2958180.805 4244944.74 3572180.134 0.934585486 1.45286191 1.017461495 0.954003905 1.107909181 0.980414503 0.828116359 1.188334457 1 21.7683734 3.70395853 5.552407221 0.99235311 1.233122873 0.177225955 0.155628583 0.186734645 17.75359547 0.038059035 0.062292065 5057.763646 -3.70395853 0.240769763 GNYDEGFGHRPHK ddPTM_SK-BR-3_Pertuzumab_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 ; 180.48 7.73E-06 413530000 446200 437900 463980 420890 505380 371110 501000 435090 714310 FALSE TRUE 418273.1385 470322.5716 474985.8247 431690.75 465689.4934 478243.4325 425879.7011 489411.9443 595087.0464 0.702877236 0.790342479 0.798178733 0.725424545 0.782556932 0.803652903 0.715659505 0.822420766 1 19.18274119 0.933393394 7.472435666 0.999998522 0.766003971 0.816611745 0.035726273 0.451852137 50.51808003 0.032670144 0.008187008 8.578145217 -0.933393394 -0.233994551 GPAAEEALNVFYYCTYEGAVDLDHVTDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GPAAEEALNVFYYCTYEGAVDLDHVTDER 29 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7;H7C408 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 0 ;; 131.94 1.18E-05 55431000 39678.8 44188.8 43675.1 44893.7 43489.7 46538.1 48710.4 36648.3 41956 FALSE TRUE 37195.37474 47460.58473 44711.094 46045.74835 40074.19439 59972.89399 41406.72773 41223.92093 34953.27255 1.064145701 1.357829504 1.279167607 1.317351566 1.14650765 1.715801972 1.184630929 1.179400895 1 15.09313992 -0.727374796 19.43566947 1 1.295684397 0.194223156 0.177269931 0 0 0.153194199 0.036108219 0.187337709 0.727374796 0.295684397 GPAFNMAS(ph)PESDFGINLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GPAFNMASPESDFGINLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GPAFNMAS(0.999)PES(0.001)DFGINLK;GPAFNMAS(1)PESDFGINLK;GPAFNMAS(0.999)PES(0.001)DFGINLK;GPAFNMAS(0.983)PES(0.017)DFGINLK;GPAFNMAS(0.991)PES(0.009)DFGINLK 275.69 4.68E-39 430489000 1079429 920307 1012050 1022254 1080283 901667 1299225 968816 1417529 TRUE FALSE 1011869.466 988447.4879 1036056.304 1048486.768 995441.9308 1161963.626 1104418.273 1089774.81 1180934.252 0.856838104 0.837004673 0.877319209 0.887845167 0.842927478 0.983935916 0.935207248 0.922807352 1 20.17149722 2.113288375 0.435177924 0.994674949 0.835843294 0.680147357 0.031737095 0.579068451 0.253272437 0.031419327 0.030734272 129.8040894 -2.113288375 -0.158831655 GPAGEAGAS(ph)PPVR ddPTM_SK-BR-3_Pertuzumab_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 93.649 0.0057872 850900000 835550 917510 910980 850600 950080 853580 980510 859610 874890 TRUE FALSE 783254.417 985443.3951 932588.8758 872427.8361 875464.5492 1099994.689 833491.6281 966934.2007 728865.207 1.074621767 1.352024195 1.279508017 1.196967324 1.201133681 1.50918809 1.14354701 1.326629659 1 19.47529251 -1.14702815 4.052597851 0.9999062 1.268505737 0.312908005 0.120768458 9.06E-05 1.91E-05 0.103479366 0.024381823 0.071280683 1.14702815 0.268599537 GPAGEAGAS(ph)PPVRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GPAGEAGASPPVRR 14 1 Q13425;Q13425-2;A0A140TA73 Q13425 SNTB2 Beta-2-syntrophin 1 GPAGEAGAS(1)PPVRR;GPAGEAGAS(1)PPVRR;GPAGEAGAS(1)PPVRR;GPAGEAGAS(1)PPVRR;GPAGEAGAS(1)PPVRR 133.28 2.79E-05 3206090000 1306888 1628130 1508943 1520809 1807440 1288840 1617680 1597290 1829520 TRUE FALSE 1225092.213 1748678.439 1544735.841 1559835.534 1665490.953 1660907.185 1375123.902 1796715.173 1524161.293 0.803781213 1.147305372 1.013498931 1.023405817 1.092726184 1.089718781 0.902216785 1.178822203 1 20.53958415 4.753604093 24.30940514 1.049542406 0.803780954 0.501373199 0.078804536 1641.619088 2652697.093 0.017889095 0.408312238 56702.74627 -4.753604093 -0.245761452 GPAGNNDCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPAGNNDCR 9 0 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ; 125.49 0.0011633 67946000 304080 346960 344190 321860 362740 321730 362940 317410 374140 FALSE TRUE 285048.1756 372649.2794 352354.3493 330119.4725 334251.8636 414608.2281 308520.5164 357039.3372 311693.617 0.914513997 1.195562755 1.130450963 1.05911528 1.072373143 1.330178758 0.989819809 1.14548171 1 18.24976909 0.17978907 1.040173617 0.999636242 1.115729979 0.067633715 0.1131825 11.95067209 12.91979283 0.114424348 0.030753239 1.512826315 -0.17978907 0.116093738 GPAHCLLLGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPAHCLLLGER 11 0 Q15274 Q15274 QPRT Nicotinate-nucleotide pyrophosphorylase [carboxylating] 0 127.42 0.00028694 168930000 149160 412060 247590 207320 407900 217060 261320 348700 419910 FALSE TRUE 139824.3419 442569.3511 253462.9517 212640.1822 375865.1794 279721.6983 222137.492 392235.9626 349824.3083 0.399698759 1.26511892 0.724543566 0.607848503 1.074439856 0.799606236 0.634997302 1.121237013 1 18.41627102 1.217883335 24.98016148 1.060618691 0.822560613 0.167145132 0.24423987 543.6976291 656822.1142 0.220177563 0.055291535 16.51518088 -1.217883335 -0.238058078 GPALTPIRDEEWGGHS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GPALTPIRDEEWGGHSPR 18 1 S4R3V8;Q86X29-6;Q86X29-5;Q86X29-2;Q86X29-3;Q86X29-4;Q86X29 S4R3V8 LSR Lipolysis-stimulated lipoprotein receptor 1 GPALTPIRDEEWGGHS(1)PR;GPALTPIRDEEWGGHS(1)PR;GPALTPIRDEEWGGHS(1)PR 171.84 7.42E-12 406372000 310145 381240 335429 297595 475610 351108 394080 430410 453330 TRUE FALSE 290733.5781 409467.4063 343385.5343 305231.7915 438257.5091 452467.1798 334991.3625 484147.6359 377666.2944 0.769816058 1.084204263 0.909230025 0.808205011 1.160435855 1.198060792 0.887003599 1.281945578 1 18.52675251 2.727948946 24.88236969 1.088718758 0.927481605 0.360837222 0.136209035 936.235992 2195293.01 0.042200278 0.040164721 534.5015215 -2.727948946 -0.161237153 GPAPAPQQCS(ph)EPETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPAPAPQQCSEPETK 15 0 Q3YEC7;Q3YEC7-2;G3V154 Q3YEC7 RABL6 Rab-like protein 6 1 GPAPAPQQCS(1)EPETK;GPAPAPQQCS(0.998)EPET(0.002)K 171.26 1.15E-06 292950000 778510 696950 714670 697530 784270 576160 880900 631860 833440 TRUE FALSE 729784.4488 748552.9032 731622.3099 715429.8007 722676.5978 742488.0388 748817.2229 710749.1119 694333.4798 1.051057554 1.078088447 1.053704497 1.030383557 1.040820613 1.069353647 1.078469129 1.023642288 1 19.40526921 1.036982795 5.26949348 1.000178364 1.059025238 0.623524079 0.015286229 0.106653846 7.119222531 0.015772172 0.003982849 10.88886955 -1.036982795 0.058846874 GPAS(ph)DS(ph)ETEDASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPASDSETEDASR 13 0 Q96ST2;Q96ST2-3 Q96ST2 IWS1 Protein IWS1 homolog 2 GPAS(1)DS(0.978)ET(0.022)EDASR;GPAS(0.985)DS(0.957)ET(0.058)EDASR 158.31 1.53E-06 0 527270 442130 492190 457430 446540 459690 549850 417089 336085 TRUE FALSE 494269.1119 474865.7652 503864.9792 469168.4282 411470.5497 592395.0406 467405.0971 469163.4798 279990.2423 1.765308347 1.696008266 1.799580496 1.675659924 1.469588891 2.115770306 1.669362093 1.675642251 1 18.09501702 0.592726432 2.204685059 1.000109109 1.745342143 0.678012786 0.159538705 1.72062096 8.652455733 0.138759789 0.037665838 3.914951911 -0.592726432 0.745233034 GPAS(ph)TPTYSPAPTQPAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPASTPTYSPAPTQPAPR 18 0 Q6P1N0-2;Q6P1N0;K7EJY5 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 GPAS(0.499)T(0.499)PT(0.002)YSPAPTQPAPR 88.561 0.0032034 105520000 63819 59888 62978 62610 71541 56467 69298 57025 77836 TRUE FALSE 59824.68271 64322.16983 64471.8679 64216.6786 65922.45844 72768.10623 58907.40823 64144.69678 64844.66876 0.922584445 0.991942299 0.994250863 0.99031547 1.016621099 1.122191039 0.908438725 0.989205404 1 15.98470035 4.784045531 2.792319895 0.999859269 0.902989051 0.189446039 0.051483377 0.98087753 9.499954413 0.012216323 0.22828947 60819.87607 -4.784045531 -0.096870218 GPASQFYITPSTSLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GPASQFYITPSTSLSPR 17 0 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 1 GPASQFYITPS(0.001)T(0.002)S(0.025)LS(0.973)PR;GPASQFYITPSTS(0.003)LS(0.997)PR;GPASQFYITPSTSLS(1)PR 145.71 4.87E-07 558400000 607820 610970 619870 596380 720710 633010 722540 633510 893010 TRUE FALSE 569777.6312 656206.8545 634573.6091 611684.1205 664108.3438 815749.7109 614201.8347 712605.118 743960.8619 0.765870438 0.88204486 0.852966388 0.822199328 0.8926657 1.096495465 0.82558353 0.957852966 1 19.5048672 2.473346008 24.99115742 0.952572722 0.84445708 0.438054714 0.072475096 123.0802134 814746.6159 0.023583477 0.019814648 297.4034538 -2.473346008 -0.108115643 GPASTPT(ph)YSPAPTQPAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPASTPTYSPAPTQPAPR 18 0 Q6P1N0-2;Q6P1N0;K7EJY5 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 GPAST(0.002)PT(0.858)Y(0.001)S(0.139)PAPTQPAPR 213.02 1.44E-15 111900000 89139 104040 112620 113210 124320 114620 116220 99449 121880 TRUE FALSE 83559.94911 111743.2299 115291.3996 116115.1603 114556.4087 147708.9333 98793.88993 111865.4266 101537.4406 0.822947167 1.100512571 1.135457018 1.143569895 1.128218399 1.454723818 0.972979911 1.101716036 1 16.63165228 4.786530249 2.639101744 1.139365046 0.735157426 0.361947063 0.12838619 0.627758928 5.152340088 0.029433569 0.588708562 61168.84062 -4.786530249 -0.404207621 GPAVGIDLGTTYSCVGVFQHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GPAVGIDLGTTYSCVGVFQHGK 22 0 P11142;E9PKE3;E9PNE6;P11142-2;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;; 314.21 2.69E-67 2881749000 3891800 4028050 3383940 3074780 4243270 2446536 4671800 4045680 5164980 FALSE TRUE 3648219.185 4326291.013 3464208.655 3153684.06 3910020.691 3152811.227 3971306.961 4550792.054 4302911.471 0.847848999 1.005433424 0.805084808 0.732918649 0.908691875 0.732715801 0.922934852 1.057607642 1 22.03688173 1.434099418 5.069424915 1.022791353 0.851158908 0.478021833 0.081080466 0.186339224 8.887949063 0.055165887 0.020851752 27.17061182 -1.434099418 -0.171632445 GPAWVGSHGVLQHTQGLPADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPAWVGSHGVLQHTQGLPADR 21 0 Q15654 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 ; 193.07 4.96E-18 503970000 236070 231587 248679 244160 271930 193389 231672 223827 256520 FALSE TRUE 221294.8001 248733.9424 254577.7833 250425.559 250573.7147 249217.2649 196934.9343 251772.2937 213705.1548 1.035514563 1.163911758 1.191257102 1.171827414 1.172520686 1.16617339 0.921526364 1.178129249 1 17.70526218 1.771294072 25 1.02643829 1.158210421 0.343332293 0.075533749 28.26882901 21600.74149 0.031441431 0.017442584 59.06008563 -1.771294072 0.131772131 GPDETLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPDETLR 7 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 83.801 0.051212 240530000 336310 714900 627790 808610 693910 799730 515370 532760 343170 FALSE TRUE 315260.9574 767831.9399 642681.4753 829360.3016 639413.1077 1030599.068 438095.053 599276.2587 285892.71 1.102724716 2.685734588 2.247981333 2.900949456 2.236549185 3.604845567 1.532375739 2.096157886 1 18.12511431 0.998836516 1.400244871 1.048542308 2.439855365 0.277127834 0.681819395 0.517196627 2.07128783 0.573757163 0.172274544 9.97324564 -0.998836516 1.391313056 GPDPSS(ph)PDKAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPDPSSPDKAK 11 1 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 GPDPS(0.168)S(0.832)PDKAK 73.927 0.027645 0 657310 328710 418400 379160 387340 287760 558680 349240 558470 TRUE FALSE 616170.1404 353048.0304 428324.6456 388889.8875 356919.8789 370831.6406 474911.1205 392843.3828 465257.7491 1.324362983 0.758822461 0.920617972 0.835859023 0.767144404 0.797045597 1.020748438 0.844356453 1 18.82767065 -0.865963355 7.561472796 0.999999999 0.894323228 0.022492188 0.167173073 1.08E-09 0 0.144577614 0.03407727 0.136155956 0.865963355 -0.105676771 GPEEEHPSVTLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPEEEHPSVTLFR 13 0 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-3;Q03154-4;A0A1B0GV31;C9JYZ0;A0A1B0GVA5;F8WC59;A0A1B0GTG3;A0A1B0GVZ3;A0A1B0GVG0;A0A1B0GU36;A0A1B0GUT4 A0A1B0GW23 ACY1 Aminoacylase-1 0 ; 235.73 1.08E-16 491770000 500050 1002470 899130 929410 815760 802490 963850 764630 800390 FALSE TRUE 468752.7631 1076693.922 920457.7882 953260.2341 751693.5002 1034155.836 819329.6404 860095.7387 666799.7383 0.702988823 1.614718573 1.380411142 1.429604991 1.12731523 1.550924178 1.228749193 1.289886137 1 19.34689401 0.591939821 1.198603903 1.000486143 1.342456431 0.089977432 0.256571052 2.702843087 5.664312431 0.219717918 0.066967492 3.907867416 -0.591939821 0.341970288 GPELLTMWFGESEANVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GPELLTMWFGESEANVR 17 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 135.26 5.05E-05 130883500 305295 445774 392050 417529 485019 398558 417283 366933 498187 FALSE TRUE 286187.1309 478779.5708 401349.6111 428243.501 446927.5642 513615.2246 354715.288 412745.3928 415036.3713 0.689547111 1.153584611 0.967022745 1.03182162 1.076839514 1.237518589 0.85466073 0.994480054 1 18.66287825 1.649529121 25 0.943283105 1.036876139 0.052685166 0.147086709 1.316438991 779.3165125 0.062017542 0.034390634 44.61995428 -1.649529121 0.093593034 GPESESEDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GPESESEDHR 10 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;; 190.96 8.44E-07 1273104000 1047825 1428755 1262531 1360329 1305821 1065030 1552258 1242106 1150849 FALSE TRUE 982243.5037 1534541.507 1292478.832 1395237.345 1203267.086 1372486.872 1319511.323 1397185.668 958764.8671 1.02448842 1.600539986 1.348066534 1.455244547 1.255017917 1.431515608 1.376261656 1.457276665 1 19.87081752 -1.133407928 4.747203464 0.999970105 1.388590099 0.360887161 0.15207152 4.20E-05 7.68E-06 0.128670181 0.030325523 0.073551591 1.133407928 0.388619995 GPEVDIRDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GPEVDIRDPK 10 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 90.827 0.0096359 923890000 4056430 2740200 3319730 3111760 3535630 2627280 3834580 3005520 3516400 FALSE TRUE 3802545.287 2943087.259 3398475.563 3191613.03 3257955.882 3385733.086 3259620.327 3380765.788 2929490.123 1.298022908 1.004641468 1.160091149 1.089477314 1.112123866 1.155741424 1.112692035 1.154045805 1 21.48221816 -1.09595531 3.629530933 0.999940161 1.124212477 0.237595059 0.0739099 6262498.675 14183881.7 5243.859969 0.015845286 0.080176056 1.09595531 0.124272315 GPFLVSAPLSTIINWER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPFLVSAPLSTIINWER 17 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3;Q12873-3;Q12873;Q12873-2;A0A5F9ZHX5 Q14839-2;Q12873-3 CHD4;CHD3 Chromodomain-helicase-DNA-binding protein 4;Chromodomain-helicase-DNA-binding protein 3 0 ; 122.39 0.00013276 24855000 85525 107708 78922 76419 115659 64967 74782 93948 60869 FALSE TRUE 80172.14292 115682.8124 80794.06711 78380.04092 106575.6087 83721.91825 63569.13334 105677.6146 50709.57067 1.581006146 2.281281637 1.593270581 1.545665638 2.101686275 1.651008225 1.253592419 2.083977703 1 15.62997044 -2.101537845 0.163466608 1.93E-12 2.038790035 0.331975613 0.320383383 44.40018014 1.019249363 18.65042809 1.44570391 0.007915205 2.101537845 2.038790035 GPGAPAASS(ph)PTQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPGAPAASSPTQK 13 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 GPGAPAAS(0.049)S(0.947)PT(0.004)QK 255.34 8.18E-24 78394000 284140 231200 286950 307580 271800 170130 217440 166100 250660 TRUE FALSE 266356.1846 248318.2886 293756.5895 315473.0235 250453.9244 219243.7692 184836.8906 186837.9506 208823.2267 1.275510339 1.189131556 1.406723736 1.510718077 1.19935856 1.049901262 0.885135689 0.894718244 1 17.67192266 2.220614589 2.458698767 0.922600537 1.330266188 0.801550931 0.091917735 0.126841987 1.56356421 0.042655784 0.029312261 166.1937124 -2.220614589 0.407665651 GPGAPGLAHLQESQAGS(ph)DT(ph)DVEEGKAPQAVPLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPGAPGLAHLQESQAGSDTDVEEGKAPQAVPLEK 34 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 2 GPGAPGLAHLQESQAGS(1)DT(1)DVEEGKAPQAVPLEK 129.72 7.90E-07 96538000 155130 102930 120810 121520 121670 86619 179090 106970 151540 TRUE FALSE 145420.6902 110551.0443 123675.6703 124638.4089 112114.529 111624.4992 152237.1171 120325.44 126246.995 1.151874468 0.875672679 0.979632586 0.987258421 0.888057011 0.884175494 1.205867253 0.953095477 1 16.94588952 1.759688366 24.99999962 1.072772537 0.951586087 0.139097516 0.102116599 13.80907696 16353.82352 0.042652931 0.023654044 57.50271702 -1.759688366 -0.12118645 GPGAPGLAHLQESQAGS(ph)DTDVEEGKAPQAVPLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPGAPGLAHLQESQAGSDTDVEEGKAPQAVPLEK 34 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 GPGAPGLAHLQES(0.002)QAGS(0.997)DT(0.001)DVEEGKAPQAVPLEK;GPGAPGLAHLQESQAGS(0.969)DT(0.031)DVEEGKAPQAVPLEK 252.15 1.31E-59 2769500000 694710 385150 475020 485370 533760 358680 586920 388230 502860 TRUE FALSE 651229.3412 413666.9067 486287.6987 497825.4159 491840.6427 462225.0933 498916.7947 436701.3701 418929.4174 1.554508502 0.987438193 1.160786707 1.188327664 1.174041789 1.103348378 1.190932825 1.042422308 1 18.67634767 GPGASVHDR ddPTM_SK-BR-3_Pertuzumab_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 ; 185.81 4.24E-05 237450000 287300 613170 483450 548010 560160 495060 549440 520570 606430 FALSE TRUE 269318.4058 658569.7448 494917.6623 562072.8644 516167.2932 637975.7854 467056.5728 585564.3104 505212.9153 0.53307902 1.303548909 0.979621952 1.112546507 1.021682696 1.262785978 0.924474729 1.159044618 1 18.946532 4.752284755 24.94851739 1.09343161 0.533078639 0.679023934 0.121507704 1322.97177 2404930.433 0.026461881 0.546253365 56530.75098 -4.752284755 -0.560352971 GPGDLMGPQGLS(ph)PEEMAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GPGDLMGPQGLSPEEMAR 18 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 GPGDLMGPQGLS(1)PEEMAR;GPGDLMGPQGLS(1)PEEMAR;GPGDLMGPQGLS(1)PEEMAR;GPGDLMGPQGLS(1)PEEMAR 140.06 1.36E-07 277038000 699581 725006 802166 766480 779177 825709 928495 704123 750974 TRUE FALSE 655795.474 778686.1986 821193.7563 786149.1744 717983.5815 1064077.784 789275.7945 792034.3065 625631.5879 1.048213496 1.244640158 1.312583591 1.256568865 1.14761402 1.700805721 1.261566407 1.265975571 1 19.25495383 5.558637755 1.082854582 1.307361994 4.29E-11 0.123974692 0.176841549 15.20371527 3.946104099 0.046826595 34.90801093 361940.9776 -5.558637755 -1.307361994 GPGGSQGSQGPS(ph)PQGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPGGSQGSQGPSPQGAR 17 0 Q96MG7 Q96MG7 NDNL2 Melanoma-associated antigen G1 1 GPGGSQGSQGPS(1)PQGAR;GPGGSQGSQGPS(1)PQGAR 314.24 3.38E-58 320910000 331220 351050 359980 355400 344750 331600 420290 311580 303080 TRUE FALSE 310489.5314 377042.1073 368518.8956 364520.1657 317674.7257 427327.5369 357271.4163 350481.4489 252493.99 1.22969078 1.493271611 1.459515514 1.443678583 1.258147672 1.692426568 1.414969981 1.388078381 1 17.94588952 0.703475675 2.708476656 1.000071022 1.442725651 0.521593776 0.127071453 1.531532929 13.07199355 0.109559256 0.02897991 5.052143466 -0.703475675 0.442654629 GPGLLES(ph)PSIFNFTADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GPGLLESPSIFNFTADR 17 0 Q92615 Q92615 LARP4B La-related protein 4B 1 GPGLLES(0.989)PS(0.011)IFNFTADR;GPGLLES(0.978)PS(0.022)IFNFTADR;GPGLLES(0.878)PS(0.122)IFNFTADR;GPGLLES(0.967)PS(0.032)IFNFT(0.001)ADR 188.04 4.55E-10 192298000 222659 267031 268135 278975 309971 235648 303033 227782 293030 TRUE FALSE 208723.1706 286802.2531 274495.2888 286133.9708 285627.128 303675.7522 257596.0149 256221.0841 244121.4 0.854997434 1.174834542 1.124421246 1.172097042 1.170020851 1.243953837 1.055196369 1.049564209 1 17.89723924 1.556177125 8.448988617 1.034466967 1.134223539 0.138088865 0.103224902 0.208716825 25.58248956 0.051783279 0.024147387 35.9896087 -1.556177125 0.099756572 GPGPTVKPSGHLFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPGPTVKPSGHLFFR 15 1 F5GXQ0;Q5VW32-2;Q5VW32 F5GXQ0 BROX BRO1 domain-containing protein BROX 0 154.6 1.47E-06 327010000 384420 415430 343800 337790 443060 307490 451910 422890 441120 FALSE TRUE 360359.8384 446188.8695 351955.0984 346458.2633 408263.8548 396257.3713 384150.2908 475688.7474 367494.2223 0.980586405 1.214138461 0.957716005 0.942758395 1.11093952 1.078268303 1.045323348 1.2944115 1 18.48736204 GPGQPSS(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPGQPSSPQR 10 0 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 GPGQPS(0.008)S(0.992)PQR;GPGQPS(0.001)S(0.999)PQR 123.2 0.00049133 347810000 794010 936910 801610 781250 906160 729530 880160 901340 696500 TRUE FALSE 744314.3314 1006279.791 820624.5677 801298.1977 834993.8489 940133.4681 748188.179 1013874.283 580249.6504 1.282748436 1.734218694 1.414261201 1.38095421 1.439025165 1.620222377 1.28942461 1.747307012 1 19.14631422 -1.525029134 3.182651836 0.984953328 1.490105535 0.462795074 0.165401737 17692460.4 23228495.98 2331120.014 0.037302902 0.029851824 1.525029134 0.505152207 GPGQVPTATSALSLELQEVEPLGLPQAS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GPGQVPTATSALSLELQEVEPLGLPQASPSR 31 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GPGQVPTATSALSLELQEVEPLGLPQAS(0.865)PS(0.135)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.816)PS(0.184)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.814)PS(0.186)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.837)PS(0.163)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.826)PS(0.174)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.966)PS(0.034)R 250.38 4.80E-47 1572916000 1030036 1344836 1367362 1424585 1452778 1138370 1363306 1145098 1379448 TRUE FALSE 965567.8854 1444409.057 1399796.472 1461142.263 1338682.676 1466998.939 1158890.922 1288066.006 1149209.217 0.840202002 1.256872147 1.218051902 1.271432774 1.164872902 1.27652904 1.008424666 1.12082812 1 20.13221004 1.702458081 9.348416667 1.050077656 1.190069351 0.167368579 0.129855925 0.174831957 30.51425785 0.057257574 0.030730854 50.40319664 -1.702458081 0.139991695 GPGS(ph)PPRT(ph)PPAPGPPSFEEQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 114.24 0.00053735 877050000 613000 678480 679460 733280 768570 561100 663960 534700 717590 TRUE FALSE 574633.4242 728715.3652 695577.1121 752097.2062 708209.6125 723080.4613 564405.3619 601458.472 597819.5932 0.961215442 1.218955306 1.163523444 1.258067174 1.184654402 1.209529546 0.944106497 1.006086918 1 19.18935066 1.738364926 8.573207324 0.983783218 1.176072478 0.529456901 0.080673326 0.075387981 20.14877902 0.035726913 0.019149621 54.74757995 -1.738364926 0.19228926 GPHGGAASAQDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPHGGAASAQDGR 13 0 O75638-2;O75638 O75638-2 CTAG2 Cancer/testis antigen 2 0 ; 160.18 4.43E-05 158930000 49105 72060 53301 67158 67482 56212 68824 65222 55439 FALSE TRUE 46031.6057 77395.39738 54565.32489 68881.38798 62182.23593 72439.49187 58504.48013 73365.11027 46185.87275 0.996659865 1.675737466 1.181428901 1.491395179 1.346347535 1.568433973 1.266718082 1.588475131 1 15.49516401 -1.270425132 4.171093355 0.999640973 1.396507677 0.261815488 0.205177863 13566150.34 4132030.203 44286.55881 0.040984538 0.053650635 1.270425132 0.396866704 GPHHLDNSS(ph)PGPGSEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GPHHLDNSSPGPGSEAR 17 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 1 GPHHLDNS(0.002)S(0.998)PGPGSEAR;GPHHLDNS(0.023)S(0.977)PGPGSEAR;GPHHLDNS(0.013)S(0.987)PGPGSEAR 189.98 2.09E-10 1301610000 552950 619770 663050 698410 696400 622980 602840 527320 599980 TRUE FALSE 518341.8465 665658.4157 678777.8591 716332.383 641707.5531 802824.2128 512449.7385 593157.0628 499839.462 1.037016654 1.331744423 1.357991737 1.433124908 1.283827312 1.606164126 1.025228653 1.186695145 1 18.93110528 1.633762995 12.43174685 1.079726499 1.342714906 0.427459144 0.147555441 0.09906874 36.07740914 0.064212871 0.034716954 43.02917255 -1.633762995 0.262988408 GPHHLDNSSPGPGSEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 137.61 3.70E-06 351071000 240252 312607 291178 289703 293380 273978 292279 265352 269507 FALSE TRUE 225215.0562 335752.7475 298084.8797 297137.2694 270339.1182 353071.0009 248454.4773 298481.7813 224524.5406 1.003075457 1.49539443 1.327627166 1.323406647 1.204051537 1.572527439 1.106580495 1.329394909 1 17.77651362 0.432487671 0.756833656 0.997172793 1.329592682 0.215582439 0.16874795 2.513964836 2.163946117 0.16814865 0.052804276 2.706996358 -0.432487671 0.332419889 GPHVDVSGPDIDIEGPEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPHVDVSGPDIDIEGPEGK 19 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 258.82 4.82E-31 522020000 1885340 1289360 1509410 1500690 1599440 1266230 1738430 1384750 1531690 FALSE TRUE 1767339.935 1384825.556 1545213.918 1539200.246 1473826.434 1631770.045 1477768.56 1557639.086 1276041.044 1.385018094 1.085251578 1.210943743 1.206230986 1.154999239 1.278775517 1.15808858 1.220681022 1 20.2832433 -1.494373674 2.797179495 0.992357386 1.198976867 0.399290124 0.080405492 10230294.33 11415432.77 606710.8137 0.017046355 0.032035118 1.494373674 0.206619481 GPIAQWADGAIS(ph)PNGHRPQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 168.25 6.67E-12 257750000 176330 255100 240080 265430 274750 215720 210880 176670 217820 TRUE FALSE 165293.8201 273987.8694 245774.811 272241.3832 253172.2433 277994.8621 179260.5017 198727.6384 181464.4348 0.910888242 1.509870899 1.354396586 1.5002465 1.395161777 1.531952321 0.987854738 1.095132711 1 17.4693273 1.694335483 7.528994671 1.033577324 1.387829466 0.442503476 0.178033207 0.10229219 11.7919646 0.079944075 0.04174224 49.46926792 -1.694335483 0.354252142 GPIKFNVWDTAGQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPIKFNVWDTAGQEK 15 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 173.58 8.77E-07 1141200000 616850 722550 679770 712820 944920 538250 899070 626400 1271200 FALSE TRUE 578242.4596 776048.3538 695894.4654 731112.168 870709.7948 693634.0372 764262.8001 704607.4189 1059028.508 0.546012176 0.732792695 0.657106452 0.690361178 0.822177863 0.654972016 0.721664048 0.66533376 1 20.01430999 -5 0.292664183 3.427106558 0.674928292 0.671108239 0.069273415 144.9915065 1.360042858 215.2194868 0.065896228 1.00E-05 5 -2.752178266 GPKPEPPGS(ph)GSPAPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPKPEPPGSGSPAPPR 16 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 GPKPEPPGS(0.604)GS(0.396)PAPPR;GPKPEPPGS(0.5)GS(0.5)PAPPR 108.71 0.0006232 538130000 920370 840860 836410 824490 918290 715370 1021110 795810 981930 TRUE FALSE 862765.6846 903118.1493 856250.0402 845647.8093 846171.2076 921885.7059 868004.035 895168.6303 818039.5395 1.054674796 1.104003053 1.046709846 1.03374931 1.03438913 1.126945168 1.061078338 1.094285285 1 19.64181105 3.963360499 23.32305977 1.061599623 1.081924128 0.04842206 0.03666809 535.3329124 907338.745 0.008848853 0.016072766 9190.952014 -3.963360499 0.020324505 GPKPEPPGSGS(ph)PAPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPKPEPPGSGSPAPPR 16 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 GPKPEPPGS(0.183)GS(0.817)PAPPR 100.28 0.0012763 1604500000 461060 388920 405380 399320 432860 344080 454940 416470 497770 TRUE FALSE 432203.0776 417716.0415 414995.805 409567.2272 398864.9217 443410.3103 386725.9705 468467.1963 414688.9713 1.042234319 1.007299616 1.000739913 0.987649192 0.961841161 1.069259954 0.932568738 1.129683278 1 18.66167015 1.23749838 24.99999695 1.064841598 0.999410337 0.234344671 0.048537881 36.77188749 865226.7508 0.033537136 0.010168511 17.27819537 -1.23749838 -0.065431261 GPKPEPPGSGS(ph)PAPPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPKPEPPGSGSPAPPRR 17 2 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 GPKPEPPGS(0.221)GS(0.779)PAPPRR 71.527 0.015823 177700000 141110 148720 153980 157360 178790 136500 178600 146900 211090 TRUE FALSE 132278.177 159731.3835 157632.4783 161398.124 164748.5546 175905.3341 151820.588 165240.7884 175857.7153 0.752188647 0.908298981 0.896363734 0.917776759 0.936828699 1.00027078 0.863314912 0.939627744 1 17.42404911 5.535635329 1.190438279 0.929109759 5.21E-17 0.637681064 0.042615772 5.688925478 1.678739249 0.011163576 10.34591022 343269.5879 -5.535635329 -0.929109759 GPLINSEFYTGWLDHWGQPHSTIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPLINSEFYTGWLDHWGQPHSTIK 24 0 P16278-3;P16278;E7EQ29;P16278-2;C9J4G9 P16278-3 GLB1 Beta-galactosidase 0 172.3 3.24E-12 85368000 79573 127250 99060 91189 134020 75805 118870 121040 123570 FALSE TRUE 74592.66797 136671.7224 101409.75 93529.06412 123494.6098 97688.67291 101046.547 136152.1104 102945.3687 0.72458498 1.327614094 0.985083168 0.908531052 1.19961307 0.948937035 0.981555055 1.32256664 1 16.6515194 1.282441196 24.99956329 1.161287933 1.036554036 0.095266522 0.179627537 304.5563526 173510.954 0.110617739 0.040393316 19.16201589 -1.282441196 -0.124733897 GPLLVQDVVFTDEMAHFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GPLLVQDVVFTDEMAHFDR 19 0 P04040 P04040 CAT Catalase 0 ;;;;;; 234.11 3.97E-24 686332000 556193 760172 632107 679385 930176 557019 746382 733756 613947 FALSE TRUE 521381.873 816455.9258 647100.8765 696819.1693 857123.7291 717821.3429 634468.9482 825367.0518 511475.2795 1.019368665 1.596276416 1.265165498 1.362371159 1.675787205 1.403433111 1.240468452 1.613698814 1 18.96430499 -0.030324848 8.96936431 0.999999964 1.39884758 0.285807111 0.197243618 11645042.32 1298313.013 0.170731818 0.041408548 0.932556496 0.030324848 0.398847616 GPLS(ph)PFNSR ddPTM_SK-BR-3_Pertuzumab_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 132.62 0.0003145 606610000 618740 727580 705760 767660 829890 653880 856840 716940 877130 TRUE FALSE 580014.1679 781450.7802 722500.9605 787359.4552 764713.787 842644.5411 728364.7965 806451.5372 730731.3365 0.793744758 1.069409154 0.988736796 1.077495128 1.046504712 1.153152327 0.996761409 1.10362249 1 19.47898155 4.740951996 24.97903778 1.051697256 0.793744667 0.71848129 0.051262008 110.6222688 1155428.07 0.011098305 0.075335432 55074.68177 -4.740951996 -0.257952589 GPPASS(ph)PAPAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GPPASSPAPAPK 12 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 GPPASS(1)PAPAPK;GPPAS(0.195)S(0.805)PAPAPK;GPPAS(0.05)S(0.95)PAPAPK;GPPAS(0.045)S(0.955)PAPAPK;GPPAS(0.022)S(0.978)PAPAPK 203.88 1.26E-07 8607400000 8715570 7608500 8714480 8383540 9620190 7409610 9643200 8211780 10557800 TRUE FALSE 8170078.031 8171841.257 8921191.581 8598675.83 8864659.083 9548644.122 8197291.683 9237038.809 8795634.974 0.928878706 0.929079172 1.014274877 0.977607172 1.007847541 1.085611687 0.931972701 1.05018442 1 23.0683563 4.03986675 2.477237786 1.00578798 0.927060011 0.40261181 0.040501319 0.290149483 3.493098614 0.010030891 0.026273438 10961.41827 -4.03986675 -0.078727969 GPPASSPAPAPKFS(ph)PVTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPPASSPAPAPKFSPVTPK 19 1 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 GPPASSPAPAPKFS(0.998)PVT(0.002)PK;GPPASSPAPAPKFS(1)PVTPK 207.13 2.01E-16 884850000 1082480 821700 960320 1048720 1317330 533550 1047330 740620 1792470 TRUE FALSE 1014729.509 882539.523 983099.2439 1075631.931 1213872.216 687577.2235 890292.5894 833088.0373 1493295.177 0.67952373 0.591001388 0.658342208 0.720307644 0.812881629 0.460442941 0.596193307 0.557885708 1 20.51006794 -1.546505284 6.057953619 1.000661541 0.630336206 0.592771214 0.095129853 0.000833982 6.24E-05 0.090377085 0.021265848 0.028411536 1.546505284 -0.370325336 GPPDFS(ph)S(ph)DEEREPT(ph)PVLGSGAAAAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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" 3 GPPDFS(1)S(1)DEEREPT(1)PVLGSGAAAAGR 109.49 0.0020012 237580000 207740 204960 174380 168860 228730 210060 291390 213470 252010 TRUE FALSE 194737.9242 220135.4517 178516.3759 173193.2335 210766.4685 270700.912 247698.7746 240122.1994 209947.903 0.927553557 1.048524175 0.850288921 0.824934334 1.003898898 1.289371831 1.179810663 1.143722781 1 17.67967185 2.423787375 6.430266397 1.172459414 0.923857195 0.603155304 0.091389999 0.125796756 11.23708152 0.030943943 0.025906 265.3306218 -2.423787375 -0.248602219 GPPDFS(ph)S(ph)DEEREPTPVLGSGAAAAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GPPDFSSDEEREPTPVLGSGAAAAGR 26 1 P42166;P42167;G5E972;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 2 GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR;GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR;GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR;GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR;GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR;GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR 181.81 1.11E-17 11861080000 4908050 5317640 4806070 5224850 5151270 4481660 5696340 4308960 5038780 TRUE FALSE 4600863.912 5711363.599 4920072.25 5358928.497 4746710.033 5775442.488 4842226.699 4846943.141 4197775.066 1.096024403 1.360569232 1.172066672 1.276611636 1.130768076 1.375834197 1.153522193 1.15464575 1 22.00119343 0.953393109 1.528640586 1.002675078 1.239096496 0.376351987 0.092118458 0.411025014 1.954318966 0.076122759 0.022338396 8.982414855 -0.953393109 0.236421418 GPPDFS(ph)SDEEREPTPVLGSGAAAAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GPPDFSSDEEREPTPVLGSGAAAAGR 26 1 P42166;P42167;G5E972;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 GPPDFS(0.979)S(0.021)DEEREPTPVLGSGAAAAGR;GPPDFS(0.993)S(0.007)DEEREPTPVLGSGAAAAGR;GPPDFS(0.933)S(0.067)DEEREPTPVLGSGAAAAGR;GPPDFS(0.988)S(0.012)DEEREPTPVLGSGAAAAGR;GPPDFS(0.867)S(0.133)DEEREPTPVLGSGAAAAGR;GPPDFS(0.92)S(0.08)DEEREPTPVLGSGAAAAGR 324.62 6.79E-83 13282200000 1811340 1759180 1711780 1667910 1776520 1639970 1889620 1500590 1759550 TRUE FALSE 1697971.463 1889431.518 1752384.23 1710711.394 1636999.285 2113402.716 1606289.023 1687941.965 1465869.738 1.15833721 1.288949126 1.195456994 1.16702825 1.11674267 1.441739782 1.095792472 1.151495198 1 20.48332548 1.03417364 1.616052252 1.007147384 1.222245111 0.328479332 0.096789569 0.404702263 2.150529599 0.082821342 0.02418902 10.81866417 -1.03417364 0.215097727 GPPDFSSDEEREPT(ph)PVLGSGAAAAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GPPDFSSDEEREPTPVLGSGAAAAGR 26 1 P42166;P42167;G5E972;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 GPPDFSSDEEREPT(1)PVLGSGAAAAGR;GPPDFSSDEEREPT(0.997)PVLGS(0.003)GAAAAGR;GPPDFSSDEEREPT(1)PVLGSGAAAAGR;GPPDFSSDEEREPT(1)PVLGSGAAAAGR;GPPDFSSDEEREPT(1)PVLGSGAAAAGR;GPPDFSSDEEREPT(1)PVLGSGAAAAGR 277.24 1.81E-60 7070770000 4517700 4409260 3689390 3291740 5134560 4294140 7182080 6201270 5319210 TRUE FALSE 4234945.221 4735726.198 3776904.073 3376211.621 4731312.369 5533788.508 6105193.779 6975512.21 4431399.488 0.95566767 1.068675079 0.85230503 0.761883832 1.067679044 1.248767692 1.377712345 1.574110443 1 22.07933096 2.269527664 2.639936767 1.349146314 0.926140484 0.56391745 0.160638355 0.180461091 2.584483637 0.062679425 0.045807918 186.0063041 -2.269527664 -0.42300583 GPPDFSSDEEREPTPVLGSGAAAAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GPPDFSSDEEREPTPVLGSGAAAAGR 26 1 P42166;P42167;G5E972;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 0 ;; 250.82 2.83E-46 965850000 266389 299605 287214 269887 271061 252958 324574 277720 354134 FALSE TRUE 249716.188 321788.0659 294026.8517 276812.7573 249772.9625 325982.8682 275907.1419 312393.9533 295026.7476 0.846418808 1.090708109 0.99661083 0.938263258 0.846611246 1.104926488 0.935193653 1.058866546 1 18.17048623 GPPHSDSCPGLTLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPPHSDSCPGLTLHR 15 0 Q9BVJ7 Q9BVJ7 DUSP23 Dual specificity protein phosphatase 23 0 124.81 5.45E-05 152610000 72628 137130 133850 149220 170850 124700 101770 109310 110340 FALSE TRUE 68082.34312 147283.2479 137024.9852 153049.2378 157432.1302 160698.8657 86510.53329 122957.5941 91923.54118 0.740640996 1.602236446 1.490640846 1.664962379 1.712642139 1.748179668 0.941114019 1.337607239 1 16.48814676 1.726701344 11.72157878 1.108603057 1.520477484 0.278047946 0.301467241 0.115762595 63.07616421 0.132399368 0.072360736 53.29682571 -1.726701344 0.411874427 GPPHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPPHSK 6 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ; 72.021 0.086696 80606000 144365 115775 163610 152571 133917 128651 160595 120133 159878 FALSE TRUE 135329.4523 124347.1015 167490.9065 156486.2302 123399.699 165790.4552 136515.2706 135131.8695 133193.3289 1.016037766 0.933583554 1.257502217 1.174880389 0.926470567 1.244735427 1.024940751 1.014554337 1 17.0231623 -0.508805913 7.363980339 1.00000393 1.080060509 0.035704544 0.117410829 0 0 0.108025873 0.025461942 0.309880385 0.508805913 0.080056579 GPPLREGEELVMDEEAYVLYHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GPPLREGEELVMDEEAYVLYHR 22 1 Q9BQ67 Q9BQ67 GRWD1 Glutamate-rich WD repeat-containing protein 1 0 ;; 126.22 1.20E-05 36073200 18530.4 35735.6 27861 28229.1 50261 24494.1 33091.7 26156.5 93839 FALSE TRUE 17370.61534 38381.50101 28521.87608 28953.5065 46313.7038 31565.14904 28129.90679 29422.1966 78176.66468 0.222196936 0.490958538 0.364838743 0.370359961 0.592423634 0.403766894 0.359824852 0.37635523 1 16.25445041 -1.965029237 3.203257574 1.459774594 0.404932285 0.797889444 0.095219719 4878882.697 22196646.72 17367032.69 0.020435075 0.010838539 1.965029237 -1.054842309 GPPPPPTASEPTRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPPPPPTASEPTRR 14 1 O14776;O14776-2 O14776 TCERG1 Transcription elongation regulator 1 0 191.48 7.75E-07 150990000 29536 32461 38104 35735 33033 26400 34038 22255 45250 FALSE TRUE 27687.39448 34864.44622 39007.84487 36652.0206 30438.72143 34021.25143 28934.31789 25033.58574 37697.48267 0.734462689 0.924848126 1.034759939 0.972267059 0.807447057 0.902480723 0.767539789 0.664065183 1 15.20218057 2.730876065 24.19746281 0.81650937 0.937657647 0.111033235 0.114919395 596.0257893 1876787.493 0.035504403 0.034085756 538.1161975 -2.730876065 0.121148277 GPPPSWGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GPPPSWGR 8 0 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;; 113.7 0.0065116 364236000 276211 325990 311202 270633 288048 242557 299499 266979 318713 FALSE TRUE 258923.4466 350126.6388 318583.8584 277577.901 265425.872 312579.2683 254591.9054 300311.9158 265517.7413 0.975164391 1.318656287 1.199859026 1.045421295 0.999653999 1.177244378 0.958850825 1.131042748 1 18.01844874 3.240387564 22.73962623 1.049967581 1.202623369 0.171333432 0.106109263 17.04135952 212097.9198 0.027498154 0.035365887 1739.352334 -3.240387564 0.152655788 GPPPTDPYGRPPPYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPPPTDPYGRPPPYDR 16 1 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 0 66.022 0.050826 476690000 439770 470440 461990 426180 495370 429240 458500 462610 403120 FALSE TRUE 412245.5807 505271.8671 472948.621 437116.5003 456465.6384 553154.6199 389752.1815 520367.8768 335836.6677 1.227518077 1.504516676 1.408269753 1.301574671 1.359189398 1.647094177 1.160540879 1.549467127 1 18.35740023 -1.603673429 3.140321888 0.977505415 1.395711919 0.41831453 0.146295053 33162129.07 27350894.51 5949512.074 0.031476977 0.024907295 1.603673429 0.418206505 GPPQEEEEEEDEEEEATKEDAEAPGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GPPQEEEEEEDEEEEATKEDAEAPGIR 27 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;;;; 212.38 5.83E-26 5429000000 4523460 3061440 3503180 3303580 3668300 2684310 4138020 3009450 4568630 FALSE TRUE 4240344.713 3288112.203 3586277.084 3388355.456 3380206.515 3459226.721 3517562.316 3385186.457 3806096.139 1.114092908 0.863906765 0.942245533 0.890244317 0.888103293 0.908864778 0.924191662 0.889411705 1 21.85988057 4.746468509 24.98820146 0.909634653 1.114093007 0.736369444 0.03768504 442.6273491 1398628.479 0.007755342 0.085777207 55778.71557 -4.746468509 0.204458354 GPPQQHGHHNEFDDEFEDDDPLPAIGHCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GPPQQHGHHNEFDDEFEDDDPLPAIGHCK 29 0 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 0 ;; 212.38 1.38E-26 371413000 509495 489677 508257 484557 554065 432634 630125 494959 661135 FALSE TRUE 477606.6174 525933.1946 520313.0961 496991.553 510550.9699 557528.4126 535643.606 556755.7207 550787.2974 0.867134409 0.954875316 0.944671561 0.902329366 0.926947612 1.012239053 0.972505373 1.010836167 1 19.07113576 2.247921661 24.99847929 0.994580339 0.92676566 0.683945023 0.026576067 128.009359 341846.373 0.009083217 0.007505135 176.9789693 -2.247921661 -0.067814679 GPPQRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPPQRPK 7 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 72.234 0.047569 88541000 212370 202340 208190 171970 216890 146460 221450 202260 273080 FALSE TRUE 199078.1408 217321.4641 213128.3651 176383.0413 199856.3343 188740.6244 188245.6283 227512.6062 227501.1838 0.875064197 0.955254212 0.936823104 0.775306037 0.87848481 0.829624801 0.827449006 1.000050208 1 17.79551453 1.223918498 24.95331358 1.000025269 0.876551628 0.517787435 0.052383806 262.0156363 446518.0202 0.056140756 0.014284154 16.74628579 -1.223918498 -0.123473641 GPPQS(ph)PVFEGVYNNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 GPPQSPVFEGVYNNSR 16 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7;H3BSK9 Q8WWM7 ATXN2L Ataxin-2-like protein 1 GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR 277.32 2.63E-35 9856652000 3500371 3754260 4180914 4521180 3812340 2953206 3424488 2577758 3125065 TRUE FALSE 3281289.027 4032229.317 4280087.254 4637201.133 3512934.195 3805748.631 2911017.816 2899596.761 2603471.463 1.260351448 1.54878952 1.643992383 1.781160731 1.349326945 1.461797713 1.118129335 1.113742479 1 21.31200516 1.793394971 1.408391072 1.028547304 1.560442502 0.665015906 0.144715838 0.227057366 0.852800012 0.108447506 0.043842651 62.14339428 -1.793394971 0.531895198 GPPS(ph)PPAPVMHS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 GPPSPPAPVMHSPSR 15 0 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 2 GPPS(1)PPAPVMHS(0.689)PS(0.311)R;GPPS(1)PPAPVMHS(0.923)PS(0.077)R;GPPS(1)PPAPVMHS(0.997)PS(0.003)R;GPPS(1)PPAPVMHS(0.742)PS(0.258)R;GPPS(1)PPAPVMHS(0.987)PS(0.013)R;GPPS(1)PPAPVMHS(0.978)PS(0.022)R;GPPS(1)PPAPVMHS(0.987)PS(0.013)R;GPPS(1)PPAPVMHS(0.664)PS(0.336)R;GPPS(1)PPAPVMHS(0.999)PS(0.001)R 200.26 1.02E-08 4964250000 2543300 2994170 2825410 2840900 3110900 2550510 3056170 2446580 2577000 TRUE FALSE 2384119.393 3215861.462 2892430.059 2913802.304 2866582.463 3286800.833 2597925.681 2752040.899 2146882.052 1.110503202 1.497921816 1.347270129 1.357225145 1.335230531 1.530964791 1.210092412 1.281878013 1 21.0338115 0.825443021 1.136394101 1.00338593 1.37100141 0.441330657 0.120391538 0.579998119 1.426069281 0.101984957 0.031964513 6.690260389 -0.825443021 0.36761548 GPPS(ph)PPAPVMHS(ph)PSRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GPPSPPAPVMHSPSRK 16 1 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 2 GPPS(1)PPAPVMHS(0.968)PS(0.032)RK;GPPS(1)PPAPVMHS(0.562)PS(0.438)RK;GPPS(1)PPAPVMHS(0.708)PS(0.292)RK;GPPS(1)PPAPVMHS(0.953)PS(0.047)RK;GPPS(1)PPAPVMHS(0.793)PS(0.207)RK;GPPS(1)PPAPVMHS(0.9)PS(0.1)RK 92.932 0.002387 3556550000 2151245 2011963 1972200 1972784 2239610 1604307 2454330 1838610 2582880 TRUE FALSE 2016602.416 2160930.834 2018981.515 2023408.977 2063720.065 2067444.387 2086326.001 2068164.506 2151780.642 0.937178435 1.004252381 0.938284078 0.940341658 0.959075486 0.960806295 0.969581174 0.961140957 1 21.03709958 0.07670128 0.813523241 1.000757165 0.960125798 0.304956955 0.019506903 6.337157773 4.430871686 0.033048089 0.00641827 1.193167127 -0.07670128 -0.040631367 GPPS(ph)PPAPVMHSPS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GPPSPPAPVMHSPSR 15 0 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 2 GPPS(1)PPAPVMHS(0.469)PS(0.531)R;GPPS(1)PPAPVMHS(0.001)PS(0.999)R;GPPS(1)PPAPVMHS(0.351)PS(0.649)R 199.91 1.05E-08 1520180000 567740 649830 636340 660060 690300 581950 687070 536510 594020 TRUE FALSE 532206.1668 697944.0893 651434.2853 676998.2571 636086.6225 749949.5178 584050.2319 603494.4545 494874.2245 1.075437233 1.410346417 1.316363337 1.36802085 1.285350077 1.515434591 1.180199338 1.219490579 1 18.91670238 1.004818571 1.439667762 1.007164528 1.332588387 0.410927539 0.118047869 0.368144559 1.558019238 0.098727562 0.029469201 10.11156949 -1.004818571 0.325423859 GPPS(ph)PPAPVMHSPS(ph)RK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GPPSPPAPVMHSPSRK 16 1 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 2 GPPS(1)PPAPVMHS(0.458)PS(0.542)RK;GPPS(1)PPAPVMHS(0.133)PS(0.867)RK;GPPS(1)PPAPVMHS(0.163)PS(0.837)RK 87.802 0.022208 2323870000 2089280 1919520 1954870 2001730 2158470 1657260 2399320 1892510 2578820 TRUE FALSE 1958515.694 2061643.258 2001240.44 2053097.781 1988952.473 2135684.059 2039564.24 2128794.039 2148398.282 0.911616673 0.959618743 0.931503463 0.955641139 0.925783869 0.994081999 0.949341776 0.99087495 1 21.03483004 1.544883453 0.537238246 1.001330622 0.936465101 0.538145515 0.020412855 0.607122459 0.424271935 0.018247968 0.010629984 35.06577591 -1.544883453 -0.06486552 GPPS(ph)PPAPVMHSPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GPPSPPAPVMHSPSR 15 0 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 1 GPPS(1)PPAPVMHSPSR;GPPS(1)PPAPVMHSPSR;GPPS(1)PPAPVMHSPSR;GPPS(1)PPAPVMHSPSR;GPPS(1)PPAPVMHSPSR;GPPS(1)PPAPVMHSPSR;GPPS(1)PPAPVMHSPSR;GPPS(1)PPAPVMHSPSR 170.61 7.28E-07 3746170000 2403552 2493490 2549500 2604370 2350240 2165190 2495530 1851765 2498639 TRUE FALSE 2253117.971 2678110.594 2609975.344 2671202.543 2165661.631 2790245.204 2121348.444 2082961.936 2081600.009 1.082397176 1.2865635 1.253831347 1.283244875 1.040383177 1.340432932 1.019095136 1.00065427 1 20.98926144 1.628852249 6.785578742 1.003004542 1.22281442 0.532112436 0.091705134 0.088287687 8.571880489 0.043869312 0.02163595 42.54536454 -1.628852249 0.219809878 GPQLFHMDPSGTFVQCDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GPQLFHMDPSGTFVQCDAR 19 0 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ;;; 220.04 2.99E-19 2838650000 1977930 2461820 1957360 1784505 2345380 1713219 2229720 2158800 1511141 FALSE TRUE 1854134.892 2644095.714 2003789.504 1830298.419 2161183.316 2207797.514 1895394.186 2428330.932 1258921.805 1.472795916 2.100285899 1.59167114 1.453861878 1.716693847 1.753720926 1.505569431 1.928897349 1 20.26375725 -1.731165932 2.829392525 0.878586802 1.70031725 0.528340056 0.204825357 15977098.23 12390218.94 13569172.82 0.049147648 0.018570948 1.731165932 0.821730448 GPQPPTVS(ph)PIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GPQPPTVSPIR 11 0 P46087-2;P46087;P46087-4 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 GPQPPTVS(1)PIR;GPQPPT(0.013)VS(0.987)PIR;GPQPPT(0.002)VS(0.998)PIR;GPQPPTVS(1)PIR 152.4 3.46E-05 5863530000 1933200 2342210 2111880 2045340 2384730 1885290 2217920 1989470 2008480 TRUE FALSE 1812204.463 2515629.665 2161974.791 2097826.887 2197442.925 2429542.618 1885363.486 2237859.709 1673251.713 1.083043543 1.503437675 1.292079831 1.253742561 1.313276962 1.451988723 1.126766207 1.337431596 1 20.67422306 -0.038843621 0.483485637 0.963945423 1.331862084 0.319932431 0.129703766 4.704226641 1.337994927 0.447847891 0.062349255 0.914442451 0.038843621 0.367916661 GPREPGPAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GPREPGPAGR 10 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;; 126.71 0.00034241 2136560000 668520 1587779 1375933 1295957 1573093 1376353 1319137 1272195 1630648 FALSE TRUE 626678.5265 1705339.809 1408570.781 1329213.451 1449548.621 1773683.768 1121344.653 1431031.346 1358482.314 0.461307829 1.255327207 1.0368709 0.978454733 1.067035328 1.30563626 0.825439272 1.053404473 1 20.37356435 4.749832916 24.90236663 1.066332771 0.461307456 0.663859111 0.135060889 998.1118571 2204949.636 0.031601654 0.489876909 56212.50194 -4.749832916 -0.605025315 GPRT(ph)PPITTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPRTPPITTK 10 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 GPRT(1)PPITTK;GPRT(1)PPITTK 79.633 0.042713 539300000 1311230 1232420 1278110 1335080 1403140 1042660 1497910 1262100 1444260 TRUE FALSE 1229162.455 1323669.659 1308427.373 1369340.413 1292943.044 1343659.016 1273312.301 1419675.963 1203203.676 1.021574717 1.100121023 1.087452938 1.138078648 1.074583689 1.116734467 1.058268294 1.179913253 1 20.19844945 4.740589785 24.1285012 1.095926253 1.021574686 0.18686682 0.047642755 169.2878138 2012718.852 0.009572674 0.062078385 55028.76744 -4.740589785 -0.074351567 GPS(ph)LDIDTPDVNIEGPEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPSLDIDTPDVNIEGPEGK 19 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GPS(1)LDIDTPDVNIEGPEGK 200.6 1.06E-21 0 68362 35915 45121 36445 38928 34343 43621 35345 40749 TRUE FALSE 64083.34445 38574.18397 46191.29143 37380.2404 35870.75191 44257.26659 37080.43601 39757.90105 33947.72865 1.887706394 1.136281734 1.360659262 1.101111676 1.056646596 1.303688593 1.092280323 1.171150549 1 15.05102743 4.740321276 24.98239288 1.172470268 1.887706636 0.814527025 0.109862694 63.34253179 898708.5011 0.024794131 0.160572956 54994.75549 -4.740321276 0.715236368 GPS(ph)PAPAS(ph)SPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPSPAPASSPKR 12 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 GPS(1)PAPAS(0.646)S(0.354)PKR 90.754 0.030385 466060000 1537100 1222500 1276600 1287500 1342700 987820 1568700 1090200 1281000 TRUE FALSE 1440895.655 1313015.172 1306881.555 1320539.43 1237249.758 1272987.598 1333487.998 1226313.87 1067192.824 1.350173672 1.230344828 1.224597397 1.237395342 1.159349772 1.192837479 1.24952864 1.149102432 1 20.02538944 -5 0.136629539 0.232458073 1.310730317 0.777767324 0.042228721 69.29550779 0.586391552 14.50056924 0.276415034 1.00E-05 5 1.078272245 GPS(ph)PAPASS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPSPAPASSPK 11 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 GPS(1)PAPAS(0.114)S(0.886)PK;GPS(1)PAPAS(0.116)S(0.884)PK 113.86 0.0019512 647460000 2007920 1335000 1510880 1509560 1451120 1181700 1867270 1321170 1429260 TRUE FALSE 1882247.871 1433844.789 1546718.787 1548297.865 1337154.889 1522837.607 1587290.198 1486120.983 1190707.273 1.580781368 1.204195878 1.298991635 1.300317803 1.122992124 1.278935337 1.333065007 1.248099358 1 20.18338735 -4.853830947 0.171077309 5.68E-25 1.351453297 0.44510627 0.111401678 131.6906805 1.304152046 45.37307641 0.378353256 1.40E-05 4.853830947 1.351453297 GPS(ph)PAPASS(ph)PKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPSPAPASSPKR 12 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 GPS(1)PAPAS(0.262)S(0.738)PKR 94.007 0.023979 915770000 1808500 1459900 1516100 1611300 1658900 1130800 1764500 1347700 1684800 TRUE FALSE 1695309.213 1567992.515 1552062.608 1652648.686 1528616.686 1457243.603 1499929.606 1515963.312 1403595.996 1.207832751 1.117125241 1.105775888 1.177439014 1.089071706 1.038221545 1.068633432 1.080056737 1 20.42069631 2.50211261 5.312841708 1.054406455 1.138421458 0.640097894 0.036459297 0.135670101 11.12879819 0.011765269 0.010593272 317.769792 -2.50211261 0.084015003 GPS(ph)PEPPPS(ph)PLQVPTYPQLTLEVPQAPEVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPSPEPPPSPLQVPTYPQLTLEVPQAPEVLR 31 0 H7C1V4;Q9HCH0-2;Q9HCH0 H7C1V4 NCKAP5L Nck-associated protein 5-like 2 GPS(1)PEPPPS(1)PLQVPTYPQLTLEVPQAPEVLR 100.72 0.00011654 18287000 10147 10889 13151 14447 16135 10051 8571.4 5979.4 8419.5 TRUE FALSE 9511.917383 11695.23289 13462.94793 14817.73448 14867.82219 12952.56054 7286.198143 6725.941252 7014.231058 1.356088401 1.667357803 1.919376168 2.112524432 2.119665301 1.846611614 1.038773614 0.9588993 1 12.77606924 1.712134124 4.58314832 0.985260106 1.850646989 0.766935666 0.217659919 0.084610122 4.186909218 0.123042499 0.060616596 51.53877877 -1.712134124 0.865386884 GPS(ph)PEPPPSPLQVPTYPQLTLEVPQAPEVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPSPEPPPSPLQVPTYPQLTLEVPQAPEVLR 31 0 H7C1V4;Q9HCH0-2;Q9HCH0 H7C1V4 NCKAP5L Nck-associated protein 5-like 1 GPS(0.986)PEPPPS(0.014)PLQVPTYPQLTLEVPQAPEVLR 139.33 1.74E-08 45422000 68640 76975 77146 60555 67283 77107 95958 81876 115890 TRUE FALSE 64343.94493 82674.30909 78975.93955 62108.94382 61998.86459 99366.53917 81569.98873 92098.39883 96547.21032 0.666450586 0.856309663 0.81800333 0.643301278 0.642161119 1.029201557 0.844871524 0.95392087 1 16.55894695 2.235318439 24.99999916 0.936482957 0.752041736 0.627315226 0.086778636 72.26549796 557221.3466 0.033429206 0.025722819 171.9168478 -2.235318439 -0.184441221 GPS(ph)PRPPATAYDAPASAFGSSLLGSGGSAFAPPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLR 35 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 GPS(0.998)PRPPAT(0.002)AYDAPASAFGSSLLGSGGSAFAPPLR;GPS(0.998)PRPPAT(0.002)AYDAPASAFGSSLLGSGGSAFAPPLR 268.38 6.54E-61 471760000 117832 131382 122933 110703 116925 102217 121886 105029 91530 TRUE FALSE 110457.1055 141109.66 125849.0288 113543.8264 107742.1822 131725.3885 103610.3258 118142.1018 76253.05169 1.448559802 1.850544429 1.650413013 1.489039768 1.412955675 1.727476942 1.358769564 1.549342606 1 16.21850746 -2.715890664 0.172655038 1.10E-09 1.763804776 0.59787586 0.146439998 32.37076758 0.636680171 12.62700021 0.536183776 0.001923576 2.715890664 1.763804775 GPS(ph)PSPVGSPASVAQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GPSPSPVGSPASVAQSR 17 0 O14497;H0Y488;A0A1B0GTU5;O14497-3;O14497-2;A0A087WUV6 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 GPS(0.984)PS(0.016)PVGSPASVAQSR;GPS(0.947)PS(0.053)PVGSPASVAQSR;GPS(0.962)PS(0.038)PVGSPASVAQSR;GPS(0.997)PS(0.003)PVGSPASVAQSR;GPS(0.999)PS(0.001)PVGSPASVAQSR;GPS(0.999)PS(0.001)PVGSPASVAQSR 318.72 2.14E-58 4662620000 1338150 1452790 1509520 1486160 1368160 1318910 1642930 1177090 1386940 TRUE FALSE 1254397.58 1560356.083 1545326.527 1524297.382 1260710.232 1699657.906 1396587.899 1324052.278 1155450.754 1.085634828 1.350430624 1.337423098 1.319223149 1.091098195 1.470991213 1.208695303 1.145918398 1 20.14002434 1.068581638 2.107131222 1.004978926 1.28775298 0.35467473 0.117403337 0.283807181 2.549236519 0.100266402 0.028072272 11.71066717 -1.068581638 0.282774053 GPS(ph)PSS(ph)PTPPAAAAPAEQAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPSPSSPTPPAAAAPAEQAPR 21 0 Q86VQ1 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 2 GPS(1)PSS(0.918)PT(0.082)PPAAAAPAEQAPR 256.11 4.64E-38 0 115030 121850 117430 114800 134270 116910 135110 108060 153740 TRUE FALSE 107830.4776 130871.9008 120215.4951 117745.9624 123724.9758 150660.0191 114851.5098 121551.5289 128079.8008 0.841900729 1.02179969 0.938598392 0.919317188 0.965999127 1.176298044 0.896718367 0.949029653 1 16.96668344 2.466217334 24.99781652 1.002398738 0.946567901 0.141916343 0.082787865 543.2280279 1245370.738 0.027587167 0.023099982 292.5616079 -2.466217334 -0.055830837 GPS(ph)PTPEDVSMKEENLCQAFSDALLCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPSPTPEDVSMKEENLCQAFSDALLCK 27 1 H1UBN3;O95067 H1UBN3 CCNB2V;CCNB2 G2/mitotic-specific cyclin-B2 1 GPS(0.929)PT(0.068)PEDVS(0.003)MKEENLCQAFSDALLCK;GPS(0.987)PT(0.013)PEDVSMKEENLCQAFSDALLCK 309.09 3.56E-82 100979000 136257 94722 110956 100487 123819 93572 165896 107796 158953 TRUE FALSE 127728.9176 101735.3154 113587.9287 103065.6665 114094.7552 120584.7174 141021.4349 121254.5679 132422.7174 0.964554421 0.768261801 0.857767692 0.778308047 0.86159503 0.910604462 1.064933855 0.915662888 1 17.01479112 2.062955517 3.144855989 0.999216482 0.833582865 0.5112458 0.0647063 0.164554048 3.240207069 0.02633332 0.016818204 115.5993831 -2.062955517 -0.165633617 GPS(ph)WDPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GPSWDPFR 8 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR;GPS(1)WDPFR 133.99 0.00093948 6352800000 6155170 6231370 5113470 4418660 6350160 3928050 5599470 6676770 7516570 TRUE FALSE 5769928.897 6692747.119 5234763.923 4532050.296 5851444.049 5062014.268 4759881.456 7510379.432 6262005.908 0.921418629 1.068786459 0.835956401 0.723737787 0.934436047 0.808369449 0.760120882 1.19935681 1 22.57819344 -0.905639541 6.636524862 1.000000006 0.895605727 0.035803403 0.142787071 1.09E-08 1.93E-09 0.132403311 0.031207758 0.124268329 0.905639541 -0.104394278 MGPSGGEGMEPERRDSQDGS(ph)SYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MGPSGGEGMEPERRDSQDGSSYR 23 2 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 1 MGPSGGEGMEPERRDS(0.001)QDGS(0.864)S(0.135)YR;MGPSGGEGMEPERRDS(0.144)QDGS(0.429)S(0.427)YR;MGPSGGEGMEPERRDS(0.07)QDGS(0.584)S(0.345)YR;MGPSGGEGMEPERRDS(0.01)QDGS(0.557)S(0.434)YR 215.59 2.11E-32 4212730000 2043600 2422650 2191960 2230050 2620060 1997900 2609260 2391420 5855860 TRUE FALSE 1915694.724 2602025.527 2243954.326 2287276.858 2414291.056 2574661.297 2218025.686 2689994.051 4878479.136 0.392682775 0.533368178 0.459970057 0.468850393 0.494886006 0.527759005 0.454655155 0.551400134 1 22.21800003 0.768991579 3.482974687 0.999988617 0.482045543 0.943448146 0.03997776 0.378560853 5.485239294 0.034145991 0.008810865 5.874779616 -0.768991579 -0.517943074 GPSAGGGPGSGTS(ph)PQVEWTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GPSAGGGPGSGTSPQVEWTAR 21 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43;A0A2R8Y4C3;A0A2R8Y454 Q7Z406 MYH14 Myosin-14 1 GPSAGGGPGSGT(0.378)S(0.622)PQVEWTAR;GPSAGGGPGSGT(0.025)S(0.975)PQVEWTAR;GPSAGGGPGSGT(0.038)S(0.962)PQVEWTAR;GPSAGGGPGSGT(0.126)S(0.874)PQVEWTAR 404.07 1.75E-151 1462820000 1425000 1666090 1648930 1686700 1853770 1437320 1800890 1648980 1862270 TRUE FALSE 1335811.794 1789449.037 1688043.398 1729983.578 1708182.382 1852250.951 1530863.263 1854858.783 1551445.106 0.861011317 1.153407897 1.088045843 1.115078819 1.101026633 1.19388752 0.98673376 1.195568425 1 20.56518122 4.745709149 24.87171228 1.10429327 0.861011194 0.545204427 0.069808339 574.1442521 1997553.587 0.014688689 0.150379047 55681.27217 -4.745709149 -0.243282076 GPSFPEPLREEQDLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GPSFPEPLREEQDLER 16 1 A0A1B0GVZ4;A0A494C085;P06132;A0A1B0GVN9;H0Y5R6;Q5T446;A0A494BZY8;A0A494C0Q8;A0A494C1D8;A0A494C0S8 A0A1B0GVZ4 UROD Uroporphyrinogen decarboxylase 0 ;;; 214.82 1.52E-14 1008400000 1039360 1266040 1179940 1172710 1372230 1070390 1274020 1150010 1192530 FALSE TRUE 974308.3129 1359778.919 1207928.734 1202803.724 1264460.591 1379394.217 1082992.528 1293591.28 993489.039 0.980693571 1.368690409 1.215845054 1.210686456 1.2727474 1.388434258 1.090090062 1.302069001 1 19.92214452 -0.891655529 5.071711645 0.999999442 1.237019039 0.254915328 0.122113128 6.97E-07 1.53E-07 0.105332494 0.024827047 0.12833481 0.891655529 0.237019597 GPSLNPVLDYDHGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GPSLNPVLDYDHGSR 15 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;; 155.1 2.36E-06 836690000 581677 1051390 960150 970120 1002830 923030 973090 979750 712950 FALSE TRUE 545270.8749 1129236.01 982925.2114 995014.9216 924071.777 1189493.777 827184.1882 1102073.944 593954.0392 0.918035469 1.90121783 1.654884295 1.675238917 1.555796772 2.002669733 1.392673732 1.855486909 1 19.17999177 -0.631158215 5.879884592 0.999999994 1.645917832 0.28559568 0.305391633 17220281.03 2928676.647 1.516938692 0.062231104 0.233798535 0.631158215 0.645917838 GPSPAPAS(ph)SPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPSPAPASSPKR 12 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 GPSPAPAS(0.549)S(0.451)PKR;GPS(0.002)PAPAS(0.554)S(0.443)PKR 73.466 0.011269 364110000 388520 321880 368130 360350 335590 259173 400430 324340 398310 TRUE FALSE 364203.2267 345712.3301 376862.2174 369597.1911 309234.1151 333992.0378 340389.2389 364834.563 331829.4878 1.097561368 1.041837277 1.135710452 1.113816597 0.931906676 1.006517052 1.025795631 1.099463961 1 18.34008257 2.776357572 24.99992522 1.014739655 1.094412248 0.450317109 0.04631143 546.0645044 361181.0676 0.013994507 0.014843134 597.5270526 -2.776357572 0.079672593 GPSPAPASS(ph)PKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GPSPAPASSPKR 12 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 GPSPAPAS(0.048)S(0.952)PKR;GPSPAPAS(0.128)S(0.872)PKR;GPSPAPAS(0.041)S(0.959)PKR 115.63 0.00056914 769400000 777530 621797 613240 571260 626519 464620 649190 502062 662050 TRUE FALSE 728865.7852 667835.4969 627786.3424 585919.4987 577314.725 598748.2515 551849.9863 564745.5459 551549.578 1.321487341 1.210834934 1.138222868 1.062315197 1.046714109 1.085574671 1.000544662 1.023925261 1 19.07313105 8 0.288030285 0.992817031 3.668255994 0.955345809 0.021473496 9.120521596 0.129661497 0.021555694 12.39770064 100000000 -8 2.675438963 GPSQEEEDNHS(ph)DEEDRASEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPSQEEEDNHSDEEDRASEPK 21 1 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 GPSQEEEDNHS(1)DEEDRASEPK 90.468 0.0013033 225950000 111160 77285 81793 92175 91885 79452 106130 71255 102030 TRUE FALSE 104202.694 83007.26181 83733.16859 94540.36655 84668.72275 102388.5026 90216.79176 80151.3436 85000.53386 1.225906348 0.976549888 0.985089914 1.112232621 0.996096364 1.204563053 1.061367355 0.942951061 1 16.37518428 1.251901588 23.29729049 0.971475572 1.064923807 0.197256542 0.087058844 162.0811751 283049.5759 0.058017561 0.020860378 17.860828 -1.251901588 0.093448235 GPSS(ph)VEDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPSSVEDIK 9 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 GPS(0.035)S(0.965)VEDIK;GPS(0.194)S(0.806)VEDIK 100.69 0.0047115 1724660000 2592100 1767190 2100910 2054840 2254430 1693870 2603510 1847860 2534020 TRUE FALSE 2429865.088 1898034.586 2150744.577 2107570.673 2077376.162 2182862.771 2213137.845 2078569.389 2111075.692 1.151008037 0.899084099 1.01879084 0.9983397 0.984036797 1.034004977 1.048346042 0.984602019 1 21.00954688 2.236277333 24.99512891 1.024194766 0.995715588 0 0.064084696 219.3249876 2400913.578 0.021648923 0.016758585 172.296848 -2.236277333 -0.028479178 GPSSHEMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPSSHEMR 8 0 Q9H0L4 Q9H0L4 CSTF2T Cleavage stimulation factor subunit 2 tau variant 0 64.265 0.051642 11452000 4049.9 13225 7431.1 9972.4 10956 7633.5 7520.2 9094.7 10119 FALSE TRUE 3796.423988 14204.19276 7607.369201 10228.30867 10095.55995 9837.16753 6392.615824 10230.19331 8430.073529 0.450342927 1.684942926 0.902408404 1.213311916 1.197564875 1.16691361 0.758310803 1.213535479 1 13.0413295 GPSSVEDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPSSVEDIK 9 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ; 125.82 0.0011421 719120000 1032780 783040 868540 854880 894450 691670 1049480 810610 1132730 FALSE TRUE 968140.1434 841017.0964 889142.179 876817.6681 824203.505 891343.9007 892120.2169 911816.4429 943670.0453 1.025930778 0.891219447 0.942217233 0.929157042 0.873402212 0.944550381 0.945373037 0.966244979 1 19.84792298 1.117461772 1.42512676 0.998802931 0.928111746 0.212992017 0.039986461 0.516644687 2.088389614 0.033940521 0.010271161 13.10574675 -1.117461772 -0.070691184 GPSWDPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GPSWDPFR 8 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;; 97.093 0.019719 3248110000 3271210 12073700 2441500 2363870 10735100 1686170 3860580 11470100 8973050 FALSE TRUE 3066470.805 12967649.31 2499413.533 2424530.906 9892008.549 2172939.906 3281721.869 12902167.23 7475389.987 0.410208807 1.73471208 0.33435226 0.324335039 1.323276587 0.290679136 0.439003433 1.725952393 1 22.83371742 -0.841835162 6.321864138 1.000000009 0.809330309 0.008778029 0.576091409 6.64E-08 1.36E-08 0.524226849 0.123561448 0.143934478 0.841835162 -0.1906697 GPSWDPFRDWYPHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GPSWDPFRDWYPHSR 15 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;; 174.59 5.43E-07 8280734000 2034045 4034189 2158654 2132079 3909985 935225 3048302 3508615 6347870 FALSE TRUE 1906737.754 4332884.551 2209858.292 2186791.757 3602910.55 1205209.275 2591237.414 3946673.306 5288369.488 0.360553051 0.81932334 0.417871387 0.413509639 0.68128949 0.227898084 0.489987967 0.746293033 1 22.33439155 1.008802185 3.391992324 0.997356073 0.504463512 0.516425905 0.164786159 0.174878328 4.916357682 0.153555619 0.039930272 10.20474567 -1.008802185 -0.492892561 GPTEADELMKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPTEADELMKR 11 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 106.49 0.0037267 193290000 219650 231980 235710 257550 282930 178310 293240 200730 544250 FALSE TRUE 205902.4986 249156.0406 241301.1525 264159.169 260709.8191 229785.2024 249271.3843 225791.5824 453411.159 0.454118728 0.549514576 0.532190591 0.582604031 0.574996477 0.50679212 0.549768967 0.497984176 1 18.79046037 -1.565715302 2.870706943 1.026307465 0.535589876 0.937378196 0.038079973 6336113.817 6785324.668 1280517.45 0.008435449 0.027182206 1.565715302 -0.490717589 GPTEQLVSPEPEVHDIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPTEQLVSPEPEVHDIER 18 0 P35813;P35813-3;P35813-2 P35813 PPM1A Protein phosphatase 1A 0 ; 202.49 1.29E-15 451760000 370640 419710 387930 372780 436790 385400 434810 390530 432080 FALSE TRUE 347442.304 450785.7651 397131.8828 382346.1659 402486.2753 496658.7236 369614.2771 439288.5302 359963.0567 0.965216562 1.252311194 1.103257336 1.062181685 1.118132175 1.379749156 1.026811697 1.220371152 1 18.45748932 -1.036012434 4.662503271 0.999996023 1.146326814 0.119936631 0.119264575 5.16E-06 1.07E-06 0.102519236 0.024163242 0.092042322 1.036012434 0.146330791 GPTS(ph)SPCEEEGDEGEEDRT(ph)SDLRDEASSVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPTSSPCEEEGDEGEEDRTSDLRDEASSVTR 31 2 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 2 GPT(0.105)S(0.448)S(0.448)PCEEEGDEGEEDRT(0.531)S(0.469)DLRDEASSVTR 98.625 0.00054169 118780000 56123 44924 46924 47147 41807 43579 62667 40509 47144 TRUE FALSE 52610.36161 48250.2197 48037.05944 48356.87184 38523.64686 56159.54985 53270.66512 45566.63782 39275.36184 1.339525829 1.228511144 1.223083816 1.231226641 0.980860393 1.429892615 1.356337985 1.160183782 1 15.26133695 GPTSS(ph)PCEEEGDEGEEDRT(ph)SDLRDEAS(ph)SVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPTSSPCEEEGDEGEEDRTSDLRDEASSVTR 31 2 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 3 GPT(0.032)S(0.272)S(0.695)PCEEEGDEGEEDRT(0.5)S(0.5)DLRDEAS(0.519)S(0.478)VT(0.003)R 89.119 0.0038396 189580000 37205 40920 36630 39085 40579 34521 45298 36821 40041 TRUE FALSE 34876.40546 43949.75938 37498.8809 40087.98727 37392.08903 44486.6523 38505.98543 41418.1829 33357.89843 1.045521664 1.31752183 1.12413799 1.201753982 1.120936594 1.333616756 1.154328877 1.241630464 1 15.02574078 -1.308741648 3.266239287 0.99891211 1.19867394 0.314058516 0.088950637 767790595.2 952994747.3 8000322.335 0.018618093 0.049119999 1.308741648 0.19976183 GPTSS(ph)PCEEEGDEGEEDRTSDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPTSSPCEEEGDEGEEDRTSDLR 23 1 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 GPT(0.027)S(0.165)S(0.808)PCEEEGDEGEEDRTSDLR 174.4 1.65E-12 218410000 103080 116900 107640 118890 106410 130680 157800 102630 98700 TRUE FALSE 96628.4068 125555.3976 110193.2716 121940.9187 98052.98784 168405.1946 134139.3549 115443.5814 82226.33237 1.175151609 1.526948777 1.340121448 1.482991095 1.192476729 2.048068906 1.631343039 1.403973375 1 16.32731286 6.073291 0.622064967 1.519292336 9.54E-10 0.026274777 0.28471461 42.8374732 3.44627449 0.112661221 67.43361283 1183834.52 -6.073291 -1.519292335 GPTSTSIDNIDGT(ph)PVRDER ddPTM_SK-BR-3_Pertuzumab_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;GPTSTSIDNIDGT(1)PVRDER;GPTSTSIDNIDGT(1)PVRDER;GPTSTSIDNIDGT(1)PVRDER 220.47 4.68E-19 3080630000 1565040 1607470 1775250 1520750 2035160 2080500 2317210 2016410 2582540 TRUE FALSE 1467086.94 1726488.751 1817359.768 1559775.02 1875326.743 2681106.576 1969765.872 2268163.227 2151497.39 0.681891108 0.802459143 0.844695316 0.724971839 0.871637935 1.246158414 0.915532541 1.054225414 1 21.03690966 2.465255763 24.8252055 1.042341064 0.785006256 0.683335015 0.092891914 119.4401351 249893.0277 0.029487451 0.024688124 291.9145642 -2.465255763 -0.257334809 GPTTGEGALDLSDVHS(ph)PPKS(ph)PEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GPTTGEGALDLSDVHSPPKSPEGK 24 1 O95684;O95684-2 O95684 FGFR1OP FGFR1 oncogene partner 2 GPTTGEGALDLSDVHS(1)PPKS(1)PEGK 133.4 5.62E-05 53088000 304830 116090 185850 180790 188340 132760 194550 131200 183010 TRUE FALSE 285751.2344 124685.4244 190258.4498 185429.3775 173548.5361 171085.6568 165379.0336 147580.6088 152464.4487 1.87421551 0.817799988 1.247887303 1.216213872 1.138288549 1.122134755 1.084705549 0.967967353 1 17.21811335 4.75086386 24.97837099 1.085697721 1.874215999 0.801695983 0.124903589 874.0205266 1774427.404 0.029410969 0.516815687 56346.09983 -4.75086386 0.788518278 GPVEGYEENEEFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GPVEGYEENEEFLR 14 0 F5GYQ2;Q9UI30;Q9UI30-2;F5GX77 F5GYQ2 TRMT112 Multifunctional methyltransferase subunit TRM112-like protein 0 ;;; 326.24 3.17E-57 1155530000 924240 1005240 1020420 976040 1028110 911050 1221680 842540 1359500 FALSE TRUE 866393.4682 1079669.016 1044624.844 1001086.839 947366.3878 1174055.345 1038500.426 947732.9737 1132590.667 0.764966102 0.953273806 0.922332202 0.883891125 0.836459645 1.036610471 0.91692476 0.836783315 1 20.11119512 2.277037531 24.999631 0.941541607 0.890612685 0.184345965 0.072826396 372.7130272 242161.8233 0.024312056 0.020340564 189.2507157 -2.277037531 -0.050928922 GPVS(ph)PSVSFQPLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GPVSPSVSFQPLAR 14 0 Q7Z434;Q7Z434-4 Q7Z434 MAVS Mitochondrial antiviral-signaling protein 1 GPVS(0.999)PS(0.001)VSFQPLAR;GPVS(0.998)PS(0.002)VSFQPLAR;GPVS(0.995)PS(0.005)VSFQPLAR;GPVS(0.991)PS(0.009)VSFQPLAR 257.81 4.67E-13 306393000 557540 687380 566736 718805 872240 495847 445487 535689 597987 TRUE FALSE 522644.5666 738274.3304 580179.2456 737250.7532 803737.7888 638989.9795 378690.36 602570.9508 498179.1066 1.049109767 1.481945591 1.164599715 1.479890954 1.613351058 1.282651101 0.760149021 1.209546813 1 18.92630499 1.912458985 7.366718722 0.973873534 1.361434553 0.436826638 0.191595174 0.231928429 17.11352275 0.076834378 0.047810207 81.74458345 -1.912458985 0.387561019 GPVTIPYPLFQSHVEDLYVEGLPEGIPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPVTIPYPLFQSHVEDLYVEGLPEGIPFR 29 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 234.52 3.21E-45 504430000 172113 222619 202982 172453 253061 191795 223340 214542 207781 FALSE TRUE 161340.7546 239101.9424 207796.8289 176878.4359 233186.6099 247163.103 189852.2404 241328.041 173101.0088 0.932061319 1.381285667 1.200436845 1.021822098 1.347112946 1.427854781 1.096771427 1.39414578 1 17.40125461 -1.097166946 4.90521021 0.9999913 1.233396831 0.1492911 0.167920749 1.43E-05 2.64E-06 0.145750822 0.034352518 0.079952685 1.097166946 0.23340553 GPWALEEESLVGREPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GPWALEEESLVGREPEER 18 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63 O00515 LAD1 Ladinin-1 0 ; 255.32 1.34E-30 311500000 315120 380850 411420 386270 431680 351720 401680 371250 494240 FALSE TRUE 295397.2017 409048.5303 421179.0767 396182.3422 397777.5941 453255.8543 341451.813 417601.3797 411748.1511 0.717422048 0.993443514 1.022904597 0.962195801 0.96607014 1.100808475 0.829273458 1.014215555 1 18.65140265 4.740130954 24.77026445 0.981617585 0.71742195 0.607951964 0.067724231 83.61808093 1318842.563 0.015492905 0.098549185 54970.66029 -4.740130954 -0.264195635 GQAALDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQAALDR 7 0 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 133.6 0.0075747 385760000 348390 524350 370640 358600 516150 311940 395090 446900 474920 FALSE TRUE 326584.8918 563173.4196 379431.7558 367802.2831 475613.661 401992.0141 335849.9223 502696.4487 395652.7839 0.825433069 1.423403152 0.95900186 0.929608733 1.202098609 1.016022205 0.848850143 1.270549505 1 18.59387538 3.736835528 24.36115389 1.017548429 1.174351967 0.020361268 0.18908249 531.9403774 1333971.201 0.044555384 0.079011283 5455.512152 -3.736835528 0.156803538 GQAGASRPHAPGTPAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQAGASRPHAPGTPAGR 17 1 Q8TDD1-2 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 0 54.281 0.077091 16220000 20183 24365 21919 20044 20821 15390 16416 21518 20366 FALSE TRUE 18919.78206 26169.00995 22438.92903 20558.36297 19185.80265 19832.84316 13954.5732 24204.56967 16966.78303 1.115107208 1.542367219 1.322521128 1.211683024 1.130786114 1.168921836 0.822464292 1.426585678 1 14.05042543 2.976329237 1.516762381 1.069526373 1.380847083 0.208503959 0.182520578 0.410906503 1.930208082 0.063705458 0.074932191 946.9547728 -2.976329237 0.31132071 GQAS(ph)SPTPEPGVGAGDLPGPTSAPVPS(ph)GS(ph)QSGGRGSPVSPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQASSPTPEPGVGAGDLPGPTSAPVPSGSQSGGRGSPVSPRR 42 2 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 3 GQAS(0.447)S(0.408)PT(0.144)PEPGVGAGDLPGPTSAPVPS(0.537)GS(0.481)QS(0.447)GGRGS(0.333)PVS(0.201)PRR 132.06 3.18E-09 94115000 14322 26260 16872 17595 35785 14725 17047 18564 44885 TRUE FALSE 13425.61159 28204.31772 17272.21181 18046.51749 32974.59045 18975.86846 14490.96061 20881.75626 37393.40353 0.359036897 0.754259176 0.461905314 0.482612327 0.881829075 0.507465667 0.38752719 0.558434223 1 15.19049617 -1.616458109 2.648978441 1.042988116 0.553393357 0.440828429 0.159519382 31597727.21 28471491.37 9377372.42 0.039874233 0.024184766 1.616458109 -0.489594759 GQAVTLLPFFTSLTGGSLEELRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GQAVTLLPFFTSLTGGSLEELRR 23 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 166.43 1.92E-11 314460000 693320 760980 695620 747120 823960 646300 668040 796630 274490 FALSE TRUE 649926.3388 817323.751 712120.4349 766292.3641 759249.5053 832876.3182 567873.6038 896091.0091 228675.8457 2.842129376 3.574158645 3.114104302 3.350998273 3.320199835 3.642170058 2.483312577 3.918608046 1 17.80294446 -1.618684038 3.14525863 0.857568008 3.254015745 0.755829919 0.4071354 35355836.45 38107785.73 41211162.12 0.09027084 0.024061127 1.618684038 2.396447737 GQDHCGIESEVVAGIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GQDHCGIESEVVAGIPR 17 0 P07858;R4GMQ5 P07858 CTSB Cathepsin B;Cathepsin B light chain;Cathepsin B heavy chain 0 ; 198.42 1.61E-17 443850000 239140 326750 281540 288740 331040 261800 339180 288620 296650 FALSE TRUE 224172.6543 350942.91 288218.2618 296149.5572 305041.4538 337377.41 288323.1078 324654.8423 247137.1986 0.907077751 1.420032727 1.166227761 1.198320443 1.234300039 1.365142164 1.166652003 1.313662388 1 17.91495265 -1.43204939 10.05692501 0.999999543 1.235277528 0.193099317 0.13972302 1.24E-06 7.03E-08 0.117639309 0.027727797 0.036978612 1.43204939 0.235277985 GQDS(ph)PLLQRPQHLMDQGQMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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;GQDS(1)PLLQRPQHLMDQGQMR;GQDS(1)PLLQRPQHLMDQGQMR 221.5 4.71E-25 2479970000 949695 1276490 1087783 1243970 1270080 998730 1341650 1141108 948129 TRUE FALSE 890255.2852 1371002.648 1113585.726 1275892.376 1170333.04 1287047.138 1140482.038 1283577.846 789880.1448 1.127076419 1.735709724 1.409816076 1.615298707 1.481659019 1.629420801 1.443867206 1.625028625 1 19.59127423 -0.940142827 8.256428064 1.000004053 1.521971224 0.474610854 0.167599523 4.11E-09 3.50E-18 0.137918089 0.032507605 0.114777609 0.940142827 0.521967172 GQDTPKPAGQHGSLS(ph)PAAAHTAS(ph)PEPPTQSGPLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GQDTPKPAGQHGSLSPAAAHTASPEPPTQSGPLTR 35 1 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 2 GQDTPKPAGQHGS(0.042)LS(0.958)PAAAHTAS(1)PEPPTQSGPLTR;GQDTPKPAGQHGS(0.002)LS(0.998)PAAAHTAS(1)PEPPTQSGPLTR;GQDTPKPAGQHGS(0.005)LS(0.995)PAAAHT(0.016)AS(0.984)PEPPTQSGPLTR;GQDTPKPAGQHGS(0.026)LS(0.974)PAAAHTAS(1)PEPPTQSGPLTR;GQDTPKPAGQHGS(0.14)LS(0.86)PAAAHT(0.065)AS(0.781)PEPPT(0.115)QS(0.023)GPLT(0.016)R;GQDTPKPAGQHGS(0.436)LS(0.564)PAAAHT(0.033)AS(0.966)PEPPT(0.001)QSGPLTR 311.33 1.46E-104 2386033000 691492 938450 899650 926574 987564 852641 1277243 1006256 948869 TRUE FALSE 648212.7501 1007933.814 920990.1228 950351.4575 910004.7071 1098784.615 1085732.269 1131889.277 790496.634 0.820006971 1.275064018 1.165077855 1.202220752 1.151181002 1.389992782 1.373481205 1.43187109 1 19.59239979 2.248670487 24.7368196 1.336766758 1.152877151 0.186963741 0.168310682 253.3168283 619815.1944 0.052988573 0.043847558 177.2843858 -2.248670487 -0.183889607 GQDTPKPAGQHGSLS(ph)PAAAHTASPEPPTQSGPLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQDTPKPAGQHGSLSPAAAHTASPEPPTQSGPLTR 35 1 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 GQDTPKPAGQHGS(0.012)LS(0.988)PAAAHTASPEPPTQSGPLTR 217.39 9.00E-37 812530000 121980 202310 171050 193130 189380 136180 215090 182950 167510 TRUE FALSE 114345.4895 217289.2429 175107.3868 198086.0428 174506.8587 175492.9553 182839.2513 205791.7102 139551.4988 0.819378441 1.557054168 1.254786858 1.419447619 1.250483586 1.25754977 1.310191956 1.474664994 1 17.09043809 GQDTPKPAGQHGSLSPAAAHTAS(ph)PEPPTQSGPLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQDTPKPAGQHGSLSPAAAHTASPEPPTQSGPLTR 35 1 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 GQDTPKPAGQHGSLSPAAAHTAS(1)PEPPTQSGPLTR 255.06 5.13E-60 258910000 37124 117980 111250 123660 108990 84601 129480 106230 107690 TRUE FALSE 34800.47511 126715.362 113888.9025 126833.325 100430.365 109023.9353 110065.676 119493.0493 89715.8433 0.38789665 1.412407857 1.26944025 1.413722708 1.119427309 1.21521385 1.226825408 1.33190577 1 16.45307516 4.744460438 24.90261662 1.265382364 0.387896247 0.820269916 0.126402108 232.6876866 982124.2619 0.027596677 0.250231353 55521.40381 -4.744460438 -0.877486117 GQECVEECR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GQECVEECR 9 0 P04626-5;P04626-4;P04626;B4DTR1;J3QLU9;P04626-6;F5H1T4 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 0 ; 137.69 0.00036641 338510000 283630 334860 246590 254970 427130 297010 369530 362070 293210 FALSE TRUE 265878.1046 359653.3828 252439.2312 261512.9619 393584.9328 382751.9654 314122.407 407275.2365 244271.3568 1.088453874 1.472351845 1.033437709 1.070583818 1.611261091 1.566913004 1.285956778 1.667306564 1 17.89812518 2.744897031 24.98295215 1.442198543 1.195102803 0.246818398 0.222271644 722.9298664 2850339.342 0.063788796 0.066198245 555.7724705 -2.744897031 -0.24709574 GQEETPSWEHILFTCCHNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GQEETPSWEHILFTCCHNR 19 0 Q8TCD5;J3KSY6 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 0 ;;; 266.78 8.59E-32 625110000 499890 665850 667150 678820 610820 651770 729450 541930 568080 FALSE TRUE 468602.7772 715150.2268 682975.1131 696239.6704 562848.6611 839925.4184 620075.7444 609591.1534 473263.7781 0.990151368 1.511102814 1.443117231 1.471145063 1.189291653 1.774751116 1.310211711 1.288057911 1 18.85228498 -0.566596397 7.149506133 1.000002066 1.399839983 0.22968321 0.208859051 0 0 0.17877865 0.042138532 0.271271147 0.566596397 0.399837917 GQETSTNPIASIFAWTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQETSTNPIASIFAWTR 17 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 119.45 0.00027834 37957000 39952 40222 57658 63965 51869 45525 57429 38832 72771 FALSE TRUE 37451.47564 43200.07873 59025.67499 65606.45019 47795.41797 58667.32846 48818.05459 43680.26068 60625.04998 0.61775579 0.712578031 0.973618579 1.082167358 0.788377378 0.967707713 0.805245597 0.720498551 1 15.88762641 4.294233325 2.468558958 0.89829717 0.630583828 0.462893174 0.109495014 0.279871019 3.231063923 0.027632845 0.104767771 19689.43824 -4.294233325 -0.267713342 GQFQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GQFQGR 6 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 148.4 0.025056 811510000 576730 644350 609410 565480 541050 508610 592200 542731 382110 FALSE TRUE 540633.4988 692058.3444 623865.493 579991.1742 498558.1155 655437.4504 503405.1077 610492.16 318333.3725 1.698324918 2.174005003 1.959786648 1.82196158 1.566150956 2.05896556 1.581377107 1.917776183 1 18.28017888 -2.047934949 0.238415788 6.34E-12 2.01219165 0.639159272 0.19821012 18.7057686 0.652314914 10.73705095 0.323542292 0.008954989 2.047934949 2.01219165 GQFQGRPVSVWDVLFSSYLSEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GQFQGRPVSVWDVLFSSYLSEAR 23 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 252.84 1.62E-43 964580000 335520 1821640 830660 775260 1401950 296500 403450 1307500 722500 FALSE TRUE 314520.4021 1956516.121 850363.6475 795154.4841 1291846.502 382094.7367 342956.4179 1470744.253 601910.0825 0.522537188 3.250512291 1.412775217 1.321051943 2.146244995 0.634803682 0.569780151 2.443461733 1 19.19918846 3.645784689 5.216780455 1.276396617 2.153878364 0.035075478 0.880221867 0.357830242 16.67344573 0.222249684 0.352020628 4423.690041 -3.645784689 0.877481746 GQFSTDELVAEVEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GQFSTDELVAEVEKR 15 1 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;;;;; 282.52 1.27E-33 2520232000 2366230 2432156 2533224 2711934 2947564 2089562 3522920 2624787 3428733 FALSE TRUE 2218131.888 2612235.361 2593313.27 2781526.818 2716074.213 2692784.628 2994690.851 2952497.435 2856455.312 0.776533026 0.914502443 0.907878117 0.973768715 0.950854789 0.942701472 1.048394084 1.033622834 1 21.44579453 7.067022351 0.2794463 1.028928458 3.27E-17 0.785350715 0.035525876 13.89321037 0.312650125 0.039281944 6.293079953 11668696.68 -7.067022351 -1.028928458 GQGESDPLDHEPAVS(ph)PLLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GQGESDPLDHEPAVSPLLPR 20 0 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 GQGESDPLDHEPAVS(1)PLLPR;GQGESDPLDHEPAVS(1)PLLPR;GQGESDPLDHEPAVS(1)PLLPR 226.9 2.64E-25 866330000 626030 861270 793320 828420 787480 723750 953400 750430 743390 TRUE FALSE 586847.8998 925039.327 812137.925 849678.6597 725634.4973 932684.8759 810446.5209 844122.8374 619313.4065 0.947578227 1.493652999 1.311352082 1.371968782 1.171675746 1.505998201 1.308620986 1.362997843 1 19.24031015 -0.978787209 4.418708557 0.999992505 1.330854 0.258558751 0.160905536 0.102159943 41314463.25 987.7003084 0.032839054 0.10500568 0.978787209 0.330861496 GQGGAGAGDDEEED ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GQGGAGAGDDEEED 14 0 P46781 P46781 RPS9 40S ribosomal protein S9 0 ; 90.653 0.012366 0 22876.6 31132 28930 29960 26322.7 26415.4 29495 25191 26783.2 FALSE TRUE 21444.79444 33437.04567 29616.23326 30728.82432 24255.42132 34041.09716 25072.49857 28336.1518 22312.91089 0.961093537 1.498551481 1.327313742 1.377176849 1.087057688 1.525623318 1.123676722 1.269944201 1 14.44559112 0.628087159 0.705208836 0.997519614 1.318711958 0.168479607 0.179327271 1.877254143 1.709126669 0.169495724 0.059732834 4.247047899 -0.628087159 0.321192344 GQGPRS(ph)PHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GQGPRSPHK 9 1 Q86U38;Q86U38-2 Q86U38 NOP9 Nucleolar protein 9 1 GQGPRS(1)PHK;GQGPRS(1)PHK 73.632 0.026193 861290000 412610 786200 295119 267896 845920 178414 406850 748740 916610 TRUE FALSE 386785.4766 844411.066 302119.362 274770.6649 779484.8555 229919.2255 345846.6195 842221.8372 763621.8695 0.506514405 1.105797385 0.395640007 0.359825558 1.020773352 0.301090415 0.452902979 1.102930483 1 19.5424989 1.230293192 24.89325601 1.051465558 0.607610417 0.331724506 0.27051997 234.4354978 705857.375 0.240612471 0.064213632 16.99390523 -1.230293192 -0.443855141 GQGPRS(ph)PHKVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GQGPRSPHKVGR 12 2 Q86U38;Q86U38-2 Q86U38 NOP9 Nucleolar protein 9 1 GQGPRS(1)PHKVGR;GQGPRS(1)PHKVGR;GQGPRS(1)PHKVGR 79.337 0.012161 1454860000 630540 808510 681890 708590 1042480 557740 969140 715820 1899420 TRUE FALSE 591075.6269 868372.9217 698064.7528 726773.619 960607.826 718750.4838 823826.4541 805191.7027 1582394.531 0.3735324 0.548771438 0.441144569 0.459287241 0.607059622 0.454216992 0.520620135 0.508843836 1 20.59367791 -5 0.337299302 6.391465032 0.474401158 0.873668465 0.061398106 116.1892067 0.986101812 450.5012026 0.044767285 1.00E-05 5 -5.917063874 GQGT(ph)FDGEENAVLYQNYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GQGTFDGEENAVLYQNYK 18 0 Q96DR7;Q96DR7-4;Q96DR7-3 Q96DR7 ARHGEF26 Rho guanine nucleotide exchange factor 26 1 GQGT(1)FDGEENAVLYQNYK;GQGT(1)FDGEENAVLYQNYK 199.41 1.82E-14 147203000 151856 157399 141805 161878 115302 102276 215153 126247 185435 TRUE FALSE 142351.604 169052.9857 145168.6816 166032.0635 106246.646 131801.4209 182892.805 142009.2159 154484.7005 0.921460854 1.094302446 0.939696171 1.074747615 0.687748662 0.853168116 1.183889436 0.919244529 1 17.23710444 -0.220868142 6.948001144 0.999999511 0.975747024 0 0.138478879 17714149.33 2549531.822 0.130919105 0.031752547 0.60135629 0.220868142 -0.024252488 GQHHQQQQAAGGSESHPVPPTAPLT(ph)PLLHGEGASQQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GQHHQQQQAAGGSESHPVPPTAPLTPLLHGEGASQQPR 38 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 GQHHQQQQAAGGSESHPVPPT(0.001)APLT(0.999)PLLHGEGASQQPR;GQHHQQQQAAGGSESHPVPPT(0.002)APLT(0.997)PLLHGEGAS(0.001)QQPR;GQHHQQQQAAGGSESHPVPPT(0.061)APLT(0.938)PLLHGEGAS(0.001)QQPR 236.19 6.01E-50 1924510000 111977 182822 147856 167374 133178 126868 226434 141458 171429 TRUE FALSE 104968.5595 196358.3311 151363.2141 171669.1002 122718.7371 163492.7321 192482.3238 159119.3427 142816.3924 0.734989574 1.374900512 1.059844823 1.202026583 0.859276271 1.144775675 1.347760719 1.114153214 1 17.12380206 1.997474474 24.9879016 1.206025606 1.091809507 0.017771 0.195981337 281.0826272 2781089.318 0.070064022 0.050823217 99.42016362 -1.997474474 -0.114216098 GQHPNPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GQHPNPLR 8 0 M0R1K3;Q15102;M0R389;M0QZT2 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ;;; 106.04 0.0042717 1400810000 1168090 1862300 1115970 1084050 1869850 965263 1284460 1679070 2080090 FALSE TRUE 1094981.332 2000186.63 1142441.335 1111868.558 1722999.524 1243918.758 1091867.147 1888705.586 1732909.541 0.63187449 1.15423603 0.659261957 0.641619503 0.994281284 0.717820942 0.630077405 1.089904315 1 20.72476492 1.220838765 24.9998401 1.044952388 0.793304899 0.287630367 0.174509176 392.8754583 554206.2122 0.164541755 0.041496548 16.62795209 -1.220838765 -0.251647489 GQICWYQKPGVGLDAINDANLLEACIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GQICWYQKPGVGLDAINDANLLEACIYR 28 1 P14324-2;P14324;A0A087WVN4;A0A087X090 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 ; 306.76 1.95E-72 134815000 173508 211264 180703 171923 229715 199770 283378 203445 176053 FALSE TRUE 162648.444 226906.2064 184989.3605 176334.8352 211674.1105 257440.356 240888.0997 228845.5561 146668.617 1.108951917 1.547067199 1.261274323 1.202266981 1.443213381 1.755251814 1.642397022 1.560289862 1 17.16220068 2.476975129 24.96030299 1.565993752 1.321459298 0.112912594 0.229957698 7.611969315 1299718.217 0.071732428 0.06058037 299.8990771 -2.476975129 -0.244534455 GQKPALDCSQVS(ph)PPRPAT(ph)SPENNASLSDTSPMDSSPSGIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQKPALDCSQVSPPRPATSPENNASLSDTSPMDSSPSGIPK 41 2 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 2 GQKPALDCS(0.024)QVS(0.973)PPRPAT(0.533)S(0.47)PENNASLSDTSPMDSSPSGIPK 189.85 2.71E-27 282970000 83884 57960 72564 67044 72523 53103 89540 71511 99705 TRUE FALSE 78633.85018 62251.41871 74285.25235 68764.46255 66827.33612 68432.97404 76114.30825 80439.30577 83063.59138 0.946670483 0.749442899 0.894317849 0.827853232 0.804532227 0.823862452 0.916337796 0.968406307 1 16.34192863 1.461285791 2.190809122 0.990324997 0.834594512 0.559599656 0.052712187 0.198354539 1.808506626 0.040432567 0.013096478 28.92582742 -1.461285791 -0.155730485 GQKPALDCSQVS(ph)PPRPATSPENNASLSDTSPMDSSPSGIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQKPALDCSQVSPPRPATSPENNASLSDTSPMDSSPSGIPK 41 2 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 1 GQKPALDCS(0.211)QVS(0.712)PPRPAT(0.038)S(0.038)PENNAS(0.001)LSDTSPMDSSPSGIPK 150.19 8.11E-14 276580000 396820 296060 344680 334970 366750 297860 454150 311970 459510 TRUE FALSE 371983.7445 317980.5905 352855.9724 343565.8973 337946.9344 383847.3466 386054.4236 350920.1412 382814.8125 0.971706769 0.830638157 0.921740646 0.897472841 0.882794822 1.002697216 1.008462607 0.916683811 1 18.54628713 2.240584209 24.99999435 0.986145438 0.893984945 0.460639098 0.04314079 40.09261323 495322.6803 0.014370128 0.011467991 174.0140076 -2.240584209 -0.092160494 GQKPEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQKPEQR 7 1 Q92522 Q92522 H1FX Histone H1x 0 66.682 0.061298 41923000 110750 92535 99557 100220 125620 75311 96911 99122 63751 FALSE TRUE 103818.3552 99386.38768 101918.5391 102791.8149 115754.3119 97052.06313 82380.09523 111497.5999 53110.54625 1.954759695 1.87131172 1.918988718 1.935431324 2.179497672 1.827359535 1.551106156 2.099349522 1 15.69671075 -2.082445677 0.350722513 4.15E-10 1.942886252 0.734992749 0.171231255 21.65239462 1.113025903 17.47491527 0.133005811 0.00827093 2.082445677 1.942886252 GQLGHGDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GQLGHGDTK 9 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;;;; 119.53 0.00081249 1941650000 3472410 2859310 3148440 2994400 3375570 2639050 3619280 2872860 3534070 FALSE TRUE 3255078.057 3071016.288 3223122.484 3071241.374 3110466.349 3400900.894 3076602.564 3231542.895 2944210.886 1.105585905 1.043069402 1.094732208 1.043145852 1.056468599 1.155114571 1.044966778 1.097592197 1 21.48944958 -1.272704784 5.23141497 0.999987895 1.077225961 0.330969544 0.035577492 4.48E-06 6.23E-07 0.030725496 0.007240934 0.053369756 1.272704784 0.077238067 GQLGHGDTKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQLGHGDTKR 10 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 105.13 0.001681 70291000 96306 97250 104790 103990 113940 71730 107050 93845 137290 FALSE TRUE 90278.37937 104450.4912 107275.6683 106658.5595 104991.612 92437.28656 90998.8463 105561.7548 114375.4121 0.78931632 0.913225048 0.937925961 0.932530493 0.917956142 0.808191943 0.795615462 0.922940979 1 16.80341742 2.26860173 24.9975616 0.855241368 0.907220262 0 0.072221348 449.0329465 373643.9931 0.023569684 0.019717385 185.6101533 -2.26860173 0.051978894 GQLTNIVS(ph)PTAATTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GQLTNIVSPTAATTPR 16 0 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;H0Y6F6;Q8NEY1-6 Q8NEY1-5 NAV1 Neuron navigator 1 1 GQLTNIVS(0.928)PT(0.072)AATTPR;GQLTNIVS(0.937)PT(0.063)AATTPR 186.73 1.53E-09 250960000 296800 324600 337260 343340 386970 325660 343510 285680 404350 TRUE FALSE 278223.8178 348633.7217 345259.9665 352150.6857 356578.9372 419672.7554 292003.8645 321347.7769 336861.3728 0.825929716 1.034947162 1.024931899 1.045387551 1.058533171 1.24583223 0.866836889 0.953946646 1 18.36179548 1.625059474 25 0.932787308 1.039396927 0.165281991 0.104420327 1.387570715 2012.777698 0.04558741 0.025200941 42.1754256 -1.625059474 0.106609618 GQNHNVQGFHPYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQNHNVQGFHPYR 13 0 K7EQ55;K7EK33;Q96EP5 K7EQ55 DAZAP1 DAZ-associated protein 1 0 96.745 0.002369 47036000 26960 39183 34656 29885 43475 28760 35579 32689 44091 FALSE TRUE 25272.62172 42084.15009 35478.05669 30651.8997 40060.64887 37062.54512 30244.25925 36770.29361 36731.92726 0.688028743 1.145710373 0.965864286 0.834475672 1.090622024 1.009000831 0.823377958 1.001044496 1 15.16474697 GQNQDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GQNQDYR 7 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;; 158.2 0.0033253 1556420000 2753890 3463000 3034960 3023790 3469820 2641280 3071720 2980120 3371280 FALSE TRUE 2581528.941 3719404.123 3106950.684 3101385.571 3197314.334 3403774.658 2611144.102 3352194.542 2808591.589 0.919154266 1.324295116 1.106230859 1.104249398 1.138404867 1.211915136 0.929698755 1.193550018 1 21.42141542 1.753782811 25 1.03702731 1.151807229 0.105979902 0.119907752 8.879882552 14602.25161 0.050664638 0.028096215 56.72608499 -1.753782811 0.114779919 GQPDVVVKEDEEYKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GQPDVVVKEDEEYKR 15 2 A0A5F9ZHD4;A0A5F9ZI66;A0A5F9ZHJ0;A0A5F9ZHL1;P24752;A0A5F9ZHJ7 A0A5F9ZHD4 ACAT1 "Acetyl-CoA acetyltransferase, mitochondrial" 0 ;;; 193.64 4.75E-08 2215660000 2734530 1536940 1742620 1607590 2629640 1295890 1905150 1779960 4101150 FALSE TRUE 2563380.649 1650736.637 1783955.769 1648843.481 2423118.682 1669992.406 1619490.444 2002191.924 3416641.571 0.750263262 0.483145979 0.522137231 0.482591881 0.709210677 0.488781855 0.474000685 0.586011697 1 21.70414748 0.954355653 21.41674337 1.000000001 0.542418606 0.662986357 0.097798389 923.140197 433147.0486 0.08651358 0.021628395 9.002345006 -0.954355653 -0.457581396 GQPEGPLPSSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_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 GQPEGPLPSS(0.014)S(0.986)PR 159.02 4.86E-05 90424000 121900 148870 130780 157550 169720 141630 184760 146570 147850 TRUE FALSE 114270.4966 159892.4897 133882.1634 161592.9997 156390.8758 182516.2818 157056.9532 164869.5871 123172.8799 0.927724486 1.298114405 1.086945142 1.311920286 1.269685957 1.481789514 1.27509362 1.338521819 1 16.91032511 3.227526856 24.89993762 1.305051751 1.143327544 0.208232498 0.149529299 286.527708 646607.3148 0.038696196 0.046669962 1688.600278 -3.227526856 -0.161724207 GQPEPAKDQQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GQPEPAKDQQQK 12 1 Q9NW13;Q9NW13-2 Q9NW13 RBM28 RNA-binding protein 28 0 ; 84.479 0.0096978 0 86375 57468 75665 76143 87449 74054 82777 63271 87812 FALSE TRUE 80968.94293 61722.99052 77459.80953 78096.95829 80581.10829 95432.18763 70365.35731 71170.52363 73155.60991 1.106804291 0.843721904 1.058836221 1.06754572 1.101502788 1.304509493 0.961858665 0.97286488 1 16.15868088 3.684504573 4.794191891 1.075361138 0.954413007 0.091479667 0.114420776 0.327746435 17.28604599 0.029527358 0.048173918 4836.203571 -3.684504573 -0.120948131 GQPIYIQFSNHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GQPIYIQFSNHK 12 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;K7ES59;K7EKJ7 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ; 280.21 5.15E-28 3248700000 1451630 3134600 1969380 1837530 3287100 1736270 2607600 2936500 2912400 FALSE TRUE 1360775.07 3366689.046 2016094.624 1884684.131 3028944.426 2237502.963 2216614.588 3303128.489 2426301.625 0.560843324 1.387580592 0.830933221 0.776772398 1.248379177 0.922186648 0.913577506 1.361384114 1 21.21032748 1.261042033 24.99970486 1.180692416 0.979848669 0.122674237 0.247285566 455.0081708 505978.6365 0.151942231 0.055393622 18.24072234 -1.261042033 -0.200843746 GQPSNKEDVDDLVSQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GQPSNKEDVDDLVSQLR 17 1 P12270 P12270 TPR Nucleoprotein TPR 0 ;;; 179.78 8.18E-10 1448580000 1494400 1232200 1358470 1361480 1454010 1076240 1616170 1269490 1619330 FALSE TRUE 1400868.172 1323433.37 1390693.55 1396417.882 1339817.92 1386933.017 1373840.312 1427988.621 1349053.362 1.038408273 0.981008912 1.030866228 1.035109449 0.993154131 1.028078693 1.018373588 1.058511592 1 20.36351598 1.790105041 2.437378805 1.029375852 1.014114816 0.022541042 0.023012112 0.753604061 8.725764446 0.013079282 0.006036747 61.67441526 -1.790105041 -0.015261036 GQPSSSNAGNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQPSSSNAGNKR 12 1 Q9H0H5;F8VRD2;F8W1E5;F8VQZ5;F8W1T4;F8VZ66;F8VV37;F8VV47;F8VWY4;F8VVE5 Q9H0H5 RACGAP1 Rac GTPase-activating protein 1 0 68.44 0.08444 17348000 16022 11603 13491 13567 15424 14191 17059 12774 19657 FALSE TRUE 15019.21162 12462.09819 13811.01289 13915.15219 14212.66126 18287.71133 14501.16132 14368.86202 16376.11971 0.91714105 0.760992128 0.843362966 0.849722183 0.867889433 1.116730437 0.885506553 0.877427759 1 13.99930593 2.460226008 24.99944616 0.962234128 0.832216568 0.392043066 0.075343944 231.3184202 342273.6957 0.024859354 0.020803036 288.5532751 -2.460226008 -0.13001756 GQS(ph)PLAPLLETLEDPSASHGGQTDAYLTLTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GQSPLAPLLETLEDPSASHGGQTDAYLTLTSR 32 0 Q5UIP0-2;Q5UIP0 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 GQS(0.997)PLAPLLET(0.003)LEDPSASHGGQTDAYLTLTSR;GQS(1)PLAPLLETLEDPSASHGGQTDAYLTLTSR;GQS(0.989)PLAPLLET(0.011)LEDPSASHGGQTDAYLTLTSR;GQS(1)PLAPLLETLEDPSASHGGQTDAYLTLTSR 179.5 1.19E-19 269219000 93369.1 111545 108346 116635 113908 90023 114245 84717 95789 TRUE FALSE 87525.2947 119803.9079 110916.0183 119628.0516 104962.1252 116011.1787 97115.02285 95294.10394 79801.19708 1.096791751 1.501279583 1.389904191 1.499075903 1.315295121 1.453752361 1.216961981 1.19414379 1 16.28412277 1.197980472 1.202738669 1.009230345 1.396849784 0.498063893 0.120735759 0.30659575 0.898138959 0.100649724 0.032245884 15.77540332 -1.197980472 0.387619439 GQS(ph)QLS(ph)NPTDDSWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQSQLSNPTDDSWK 14 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 2 GQS(1)QLS(0.968)NPT(0.032)DDSWK 133.52 6.44E-05 63136000 446670 389680 417330 449650 468620 353310 578980 419200 434410 TRUE FALSE 418713.722 418532.3127 427229.2647 461188.7803 431816.4755 455304.8615 492167.324 471538.0428 361904.1646 1.156974036 1.156472773 1.180503864 1.274339522 1.193179073 1.258081299 1.359938271 1.302936216 1 18.46524818 3.336276662 4.511227446 1.256591688 1.162265472 0.060125862 0.096132298 0.360815598 12.81580722 0.025112164 0.034338669 2169.085455 -3.336276662 -0.094326216 GQS(ph)QTSPDHRS(ph)DT(ph)SSPEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQSQTSPDHRSDTSSPEVR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 GQS(0.325)QT(0.356)S(0.322)PDHRS(0.848)DT(0.42)S(0.38)S(0.349)PEVR 70.107 0.018388 337880000 294820 380910 329790 346020 387090 338420 370010 338470 376710 TRUE FALSE 276367.7425 409112.9727 337612.7745 354899.459 356689.5128 436116.3602 314530.4355 380728.7246 313834.6674 0.880615723 1.303593947 1.07576635 1.130848488 1.136552299 1.389637301 1.002216989 1.21315063 1 18.2596452 -1.295087684 3.84813666 0.999709666 1.149795147 0.08517327 0.143543928 39.16978577 32310367.98 15226.02171 0.029490034 0.050688836 1.295087684 0.150085481 GQSLGYAFAEFQEHEHALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQSLGYAFAEFQEHEHALK 19 0 Q9NW13;Q9NW13-2 Q9NW13 RBM28 RNA-binding protein 28 0 156.92 6.44E-09 89377000 134290 120240 136770 139920 162620 141670 135950 113390 128840 FALSE TRUE 125885.0286 129142.6947 140014.249 143510.5841 149848.4812 182567.8292 115565.5596 127546.9911 107335.7717 1.172815238 1.203165475 1.304450947 1.337024758 1.396072147 1.700903868 1.076673301 1.188299009 1 16.71177144 1.603197993 25 1.099329985 1.334889632 0.406318249 0.149280854 0.508974802 2712.311866 0.077766727 0.037846286 40.10495125 -1.603197993 0.235559647 GQSQLS(ph)NPTDDSWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GQSQLSNPTDDSWK 14 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 GQSQLS(1)NPTDDSWK;GQSQLS(1)NPTDDSWK 278.85 3.57E-33 337960000 1017760 939760 989160 1063890 1097940 835630 1253070 903920 1145830 TRUE FALSE 954060.2184 1009340.808 1012623.342 1091191.219 1011712.221 1076862.816 1065183.786 1016776.402 954583.5707 0.999451748 1.057362435 1.060801142 1.14310706 1.059846673 1.128096951 1.115862266 1.065151793 1 19.86451198 4.924215593 0.858628549 1.092780281 0.927223005 0.249246526 0.041924914 3.430302192 1.580768553 0.012592651 0.576948234 83987.68152 -4.924215593 -0.165557276 GQSQTS(ph)PDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GQSQTSPDHR 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GQSQT(0.043)S(0.957)PDHR;GQSQT(0.005)S(0.995)PDHR;GQSQT(0.003)S(0.997)PDHR 152.16 1.19E-05 360849000 660616 698779 713160 716974 660515 671202 696820 613491 551972 TRUE FALSE 619269.2238 750517.3242 730076.492 735372.7667 608640.8163 864967.1213 592338.31 690086.7018 459844.3073 1.346693248 1.632111809 1.587660172 1.599177711 1.323580191 1.880999955 1.288127961 1.500696411 1 18.81078596 0.471463345 0.834503407 0.997071825 1.55845884 0.469255411 0.174564428 1.385954392 1.444180905 0.157713579 0.05072944 2.961170031 -0.471463345 0.561387015 GQSQTS(ph)PDHRS(ph)DTS(ph)S(ph)PEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQSQTSPDHRSDTSSPEVR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 4 GQS(0.083)QT(0.446)S(0.471)PDHRS(0.936)DT(0.297)S(0.767)S(1)PEVR 100.59 0.00046092 614300000 359750 423010 365320 367540 404820 311660 405780 318300 390810 TRUE FALSE 337233.8897 454330.1005 373985.5629 376971.6986 373027.0702 401631.1826 344937.0561 358040.4557 325581.2863 1.035790151 1.395442919 1.148670328 1.157842034 1.145726385 1.233581903 1.059449884 1.099696054 1 18.31265825 1.550488238 0.471201765 0.99512661 1.235145622 0.265401518 0.096028718 0.961027302 0.557475638 0.09735639 0.064733797 35.52124982 -1.550488238 0.240019012 GQSQTS(ph)PDHRS(ph)DTS(ph)SPEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQSQTSPDHRSDTSSPEVR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 GQS(0.11)QT(0.413)S(0.476)PDHRS(0.704)DT(0.367)S(0.494)S(0.435)PEVR 68.835 0.040001 399170000 295470 384570 353550 358980 361940 318140 342100 296470 358370 TRUE FALSE 276977.0601 413043.9629 361936.373 368192.0346 333514.6924 409981.8534 290805.2809 333484.9321 298555.7318 0.927723137 1.383473566 1.21229082 1.233243898 1.117093584 1.373217157 0.974040187 1.116993903 1 18.18764074 1.689084727 9.726233438 1.03601806 1.22589206 0.275693346 0.133112806 0.132380186 20.49614416 0.057584692 0.030976941 48.87477006 -1.689084727 0.189873999 GQSS(ph)PPPAPPICLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GQSSPPPAPPICLR 14 0 O43379-4;O43379;H7C3R4;O43379-3;O43379-2 O43379-4 WDR62 WD repeat-containing protein 62 1 GQS(0.021)S(0.979)PPPAPPICLR;GQS(0.003)S(0.997)PPPAPPICLR;GQS(0.032)S(0.968)PPPAPPICLR;GQS(0.007)S(0.993)PPPAPPICLR 234.28 3.47E-17 1221870000 1026360 1066770 1071520 1010700 1068010 1013490 1145900 975480 1026790 TRUE FALSE 962121.9597 1145754.761 1096936.96 1036636.273 984132.8027 1306068.11 974082.933 1097270.825 855412.1157 1.124746706 1.339418439 1.282349104 1.211855963 1.15047798 1.5268291 1.138729409 1.282739401 1 19.70626012 0.094887841 1.115963304 0.998886608 1.268142404 0.311771324 0.118794469 8.019472422 8.767297208 0.128448753 0.031384966 1.244193251 -0.094887841 0.269255796 GQSSLFPMEDGFLDDGRGDQPLHS(ph)GLGSPHCFSHQNGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQSSLFPMEDGFLDDGRGDQPLHSGLGSPHCFSHQNGER 39 1 E5RJM0;B7ZLQ8;Q17RY0-2;Q17RY0;Q17RY0-3 E5RJM0 CPEB4 Cytoplasmic polyadenylation element-binding protein 4 1 GQSSLFPMEDGFLDDGRGDQPLHS(0.49)GLGS(0.49)PHCFS(0.02)HQNGER 56.186 0.013679 54417000 27321 25634 27251 28559 35357 27247 28602 23450 33057 TRUE FALSE 25611.02738 27531.96803 27897.40659 29291.87229 32580.20384 35112.76658 24313.39563 26377.78412 27539.57314 0.929971835 0.999723848 1.012993427 1.063628406 1.183032274 1.274993131 0.882853031 0.957813833 1 14.74921858 1.620593765 25 0.940249257 1.065568144 0.268104473 0.100179316 1.194037912 2339.779393 0.049065529 0.026981708 41.74397149 -1.620593765 0.125318886 GQSSLFPMEDGFLDDGRGDQPLHSGLGS(ph)PHCFSHQNGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GQSSLFPMEDGFLDDGRGDQPLHSGLGSPHCFSHQNGER 39 1 E5RJM0;B7ZLQ8;Q17RY0-2;Q17RY0;Q17RY0-3 E5RJM0 CPEB4 Cytoplasmic polyadenylation element-binding protein 4 1 GQSSLFPMEDGFLDDGRGDQPLHS(0.003)GLGS(0.994)PHCFS(0.003)HQNGER 144.35 1.77E-13 152600000 26560 32520 35042 33741 38150 30829 33269 29145 39736 TRUE FALSE 24897.65701 34927.81464 35873.21279 34606.85118 35153.85289 39728.83183 28280.6223 32783.81741 33103.8049 0.75210862 1.055099701 1.083658296 1.045404034 1.061927866 1.200128866 0.854301262 0.990333815 1 15.01470943 -3.357453779 8.219409412 1.000180206 1.015485256 0 0.124535626 0 0 0 0.025991258 0.000439083 3.357453779 0.01530505 GQTEHDEGMLEYLEDIIGCGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GQTEHDEGMLEYLEDIIGCGR 21 0 Q9NTJ3;E9PD53;Q9NTJ3-2;C9JR83;C9J578 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 0 ;;;; 179.36 5.78E-17 355212000 266896 309930 316234 314974 311352 314297 343073 286211 303988 FALSE TRUE 250191.4558 332877.5397 323735.2198 323056.7661 286899.6699 405029.4417 291632.3886 321945.0734 253250.439 0.987921114 1.314420386 1.278320469 1.275641485 1.132869388 1.59932375 1.151557288 1.271251788 1 17.95020524 0.319522337 1.648917229 1.000025643 1.265716454 0.1970027 0.157024831 10.89042249 24.61928713 0.133515847 0.037804566 2.086999462 -0.319522337 0.265690811 GQVEFFEPFWDSGEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GQVEFFEPFWDSGEPR 16 0 H0YJT0;Q9H7Z3 H0YJT0 NRDE2 Protein NRDE2 homolog 0 ; 123.64 0.00020195 44582000 19527.2 27811 22230.2 23741.1 24227 20234.5 27803 22035.6 27149 FALSE TRUE 18305.02741 29870.15538 22757.51084 24350.33682 22324.30915 26075.87167 23634.19826 24786.79317 22617.65651 0.809324671 1.320656513 1.006183414 1.07660742 0.987030161 1.152898916 1.04494461 1.095904571 1 14.46516183 3.731638051 24.80266559 1.057540568 1.120085987 0 0.132835964 646.9589056 3552543.914 0.030885882 0.053467922 5390.611717 -3.731638051 0.062545419 GQVLFDLVCEHLNLLEK ddPTM_SK-BR-3_Pertuzumab_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 ; 241.74 2.25E-20 371600000 1073460 882560 1071460 868390 1166610 903320 1179130 1047020 1410340 FALSE TRUE 1006274.055 947905.6607 1096875.537 890674.3576 1074989.156 1164093.82 1002330.403 1177742.752 1174945.143 0.856443436 0.806765887 0.93355468 0.758056121 0.914927104 0.9907644 0.85308698 1.002381055 1 20.16416197 1.730081837 0.444494342 1.00536918 0.835654862 0.424273671 0.063472409 0.987040068 0.501155293 0.065685996 0.050730894 53.71330022 -1.730081837 -0.169714318 GQVLNSDELQELYEGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GQVLNSDELQELYEGLR 17 0 O00764;F2Z2Y4;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;;;; 321.85 2.82E-58 356638000 283444 303626 293609 282902.7 303288 277443 352842 277883.3 308815 FALSE TRUE 265703.746 326106.785 300573.5441 290162.4622 279468.9839 357536.2902 299936.6177 312577.6417 257271.7815 1.032774541 1.267557534 1.168311357 1.127844105 1.086279196 1.389722138 1.165835662 1.214970565 1 17.9729337 -0.798915883 5.33139121 0.999999925 1.19113299 0.247332271 0.098366984 6.15E-06 31772027.03 6.660738411 0.020930915 0.158885446 0.798915883 0.191133065 GQVQEVGWHDVAGWLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GQVQEVGWHDVAGWLGR 17 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ;;; 189.9 3.29E-10 2481950000 2549530.6 3042394.7 2678422.1 2799185 2842438.3 2425163.8 3008211.4 2479840 2406170.9 FALSE TRUE 2389960.031 3267656.769 2741955.537 2871016.826 2619204.662 3125269.22 2557158.027 2789453.483 2004565.432 1.192258428 1.630107312 1.367855343 1.432239018 1.306619689 1.559075683 1.275667028 1.391550227 1 20.93485808 -0.629293085 0.411821755 0.880405818 1.440278252 0.471476887 0.129543996 7.67628005 1.134272788 1.327922187 0.073821735 0.23480477 0.629293085 0.559872435 GQVYILGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GQVYILGR 8 0 P00966 P00966 ASS1 Argininosuccinate synthase 0 ;;; 135.6 0.0019237 1362360000 1256516 1850620 1460870 1545900 1827960 1403790 1598780 1559310 1422960 FALSE TRUE 1177872.907 1987641.83 1495522.526 1585570.411 1684399.395 1809041.384 1359057.781 1753993.286 1185458.783 0.993600894 1.676685734 1.261555903 1.337516271 1.420883981 1.526026387 1.146440349 1.479590274 1 20.17701407 -2.276858279 0.396352211 0.510106598 1.381001265 0.232569505 0.195438104 80.52546409 4.164530001 34.85682284 0.113287764 0.005286177 2.276858279 0.870894667 GQYISPFHDIPIYADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GQYISPFHDIPIYADK 16 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 174.23 3.94E-09 1180430000 2358620 3518400 3871500 3609400 3490950 3875400 4971100 3881900 2650520 FALSE TRUE 2210998.184 3778905.997 3963333.808 3702023.315 3216784.869 4994165.068 4225729.704 4366563.76 2208131.089 1.001298426 1.711359446 1.794881576 1.676541458 1.456790715 2.261715843 1.913713242 1.977492995 1 21.07439439 2.279705517 24.99972158 1.883852941 1.596267251 0.062144284 0.389617599 305.2862287 185491.2749 0.122584812 0.102560794 190.4169115 -2.279705517 -0.28758569 GQYISPFHDIPIYADKDVFHMVVEVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GQYISPFHDIPIYADKDVFHMVVEVPR 27 1 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;;;; 265.45 1.55E-53 8421850000 2937111 6858950 4897550 4261264 7338060 4570729 6173900 6097820 4088298 FALSE TRUE 2753282.465 7366793.795 5013722.199 4370615.249 6761758.368 5890224.263 5248181.011 6859146.25 3405934.652 0.808377948 2.162928696 1.472054725 1.283235204 1.98528717 1.729400257 1.540893043 2.013880755 1 21.69961932 2.746689057 24.74906618 1.680817596 1.560263376 0.022942554 0.434887872 3051.710052 9291694.883 0.124312033 0.129697721 558.0704879 -2.746689057 -0.12055422 GQYTHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GQYTHK 6 0 F5GWE5;Q00169;I3L4H1;I3L471;I3L4U7;A0A0A0MSW4;P48739;P48739-3;P48739-2;B3KYB7 F5GWE5;A0A0A0MSW4 PITPNA;PITPNB Phosphatidylinositol transfer protein alpha isoform;Phosphatidylinositol transfer protein beta isoform 0 ; 72.234 0.086135 234190000 313490 453000 294360 277090 471850 240900 297440 469290 324300 FALSE TRUE 293869.2205 486540.5913 301342.3582 284200.5985 434792.8044 310443.9193 252841.6333 527881.8895 270172.2349 1.087710662 1.800853413 1.115371305 1.05192378 1.609317125 1.149059301 0.935853506 1.953871721 1 18.04351989 3.824267486 7.193798971 1.237716551 1.488137361 0.039551095 0.351863959 0.568711972 36.43306562 0.08289559 0.15026797 6672.175876 -3.824267486 0.25042081 GRAEGEWEDQEALDYFS(ph)DK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRAEGEWEDQEALDYFSDK 19 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 GRAEGEWEDQEALDYFS(1)DK 162.82 1.63E-11 47228000 77567 43477 51800 47572 45433 47862 73653 45698 51798 TRUE FALSE 72712.21993 46696.08232 53028.72046 48792.77806 41864.87545 61678.98243 62609.41641 51403.49589 43152.57917 1.685002874 1.082115675 1.228865608 1.130703633 0.970159287 1.429323197 1.450884689 1.191203327 1 15.39715917 2.168427348 24.99999988 1.325435537 1.197886424 0 0.225702984 134.6346916 47989.61102 0.078222481 0.057771143 147.376198 -2.168427348 -0.127549112 GRAEGEWEDQEALDYFS(ph)DKESGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GRAEGEWEDQEALDYFSDKESGK 23 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 GRAEGEWEDQEALDYFS(0.999)DKES(0.001)GK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(0.969)DKES(0.031)GK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(0.999)DKES(0.001)GK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDY(0.004)FS(0.995)DKES(0.002)GK;GRAEGEWEDQEALDYFS(1)DKESGK 250.52 2.25E-38 7369580000 5290870 2574103 3174568 3237442 3531514 2343733 4236650 2830904 5857260 TRUE FALSE 4959723.891 2764692.264 3249870.252 3320520.243 3254163.136 3020330.67 3601403.664 3184348.596 4879645.467 1.016410705 0.566576462 0.666005404 0.680483913 0.666885158 0.618965187 0.738046173 0.65257786 1 22.2183449 -1.153836494 4.056986739 1.000115834 0.684348069 0.36810074 0.121545528 22778072.61 58374848.26 35224.35965 0.026000866 0.070171944 1.153836494 -0.315767766 GRAEGSEKEESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GRAEGSEKEESR 12 2 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 92.856 0.004218 189568000 154075 179010 156948 173073 215376 129649 190924 157654 333480 FALSE TRUE 144431.7208 192264.0867 160670.8807 177514.3462 198461.2377 167076.5616 162296.7187 177337.4489 277820.0336 0.519875111 0.692045437 0.578327195 0.638954448 0.714351788 0.601384139 0.584179321 0.638317715 1 18.08379111 0.93721642 21.4908913 1 0.622135841 0.820899929 0.055699375 2148.572921 735460.6114 0.049567981 0.012391995 8.653990626 -0.93721642 -0.377864159 GRAEGSEKEESRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GRAEGSEKEESRR 13 3 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ;; 85.457 0.0040637 77269000 54115 76871 60801 67571 102255 42316.8 81777 59503 202691 FALSE TRUE 50728.03875 82562.60882 62243.22843 69304.98626 94224.30478 54532.9732 69515.29803 66932.08053 168860.5627 0.300413773 0.488939558 0.368607255 0.410427309 0.558000656 0.322946769 0.411672785 0.396374852 1 17.3654729 -1.606351807 2.557421563 1.057900361 0.411856084 0.862589393 0.074338985 3577849.695 3141659.139 1384953.572 0.017202878 0.02475416 1.606351807 -0.646044277 GRAS(ph)PGGVSTSSSDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRASPGGVSTSSSDGK 16 1 P54259 P54259 ATN1 Atrophin-1 1 GRAS(1)PGGVSTSSSDGK 143.58 8.47E-07 485080000 821330 568320 764350 678870 671720 533170 901210 645020 741810 TRUE FALSE 769924.4214 610399.0041 782480.743 696290.9535 618965.8208 687087.5237 766081.9269 725552.1669 617997.1187 1.245838206 0.987705259 1.266155973 1.126689644 1.001567486 1.111797293 1.239620548 1.174038106 1 19.23724059 GRAS(ph)PGGVSTSSSDGKAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GRASPGGVSTSSSDGKAEK 19 2 P54259 P54259 ATN1 Atrophin-1 1 GRAS(1)PGGVSTSSSDGKAEK;GRAS(1)PGGVSTSSSDGKAEK 127.53 1.21E-05 375156000 356810 304300 298160 357640 438950 209645 391580 279469 783050 TRUE FALSE 334477.899 326830.6886 305232.496 366817.6479 404476.6376 270166.1082 332866.2143 314361.3198 652353.8963 0.512724613 0.501002125 0.467894034 0.562298547 0.6200264 0.414140407 0.510254045 0.481887702 1 19.3152953 -1.719463254 2.494188664 1.098713036 0.505459514 0.889043965 0.054526104 4862326.738 3663029.498 2990718.168 0.013006814 0.019078171 1.719463254 -0.593253521 GRAS(ph)S(ph)HS(ph)SQTQGGGSVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRASSHSSQTQGGGSVTK 18 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 3 GRAS(0.999)S(0.983)HS(0.901)S(0.111)QT(0.006)QGGGSVTK 71.54 0.03929 179880000 210490 202820 183380 194910 200740 117630 228890 135330 133760 TRUE FALSE 197315.8066 217837.0038 187729.8602 199911.7206 184974.6901 151587.8714 194570.0694 152226.2484 111434.5919 1.77068721 1.954841851 1.684664134 1.793982615 1.659939585 1.360330476 1.74604731 1.366059191 1 16.76583762 -1.642925149 0.133987007 3.86E-15 2.120733365 0.784870981 0.129028437 18.0974112 0.394100792 6.885063211 1.069565655 0.022754896 1.642925149 2.120733365 GRAS(ph)S(ph)HSSQTQGGGSVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRASSHSSQTQGGGSVTK 18 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 GRAS(0.9)S(0.583)HS(0.27)S(0.246)QTQGGGSVTK 71.54 0.013288 435650000 160090 183680 167030 189270 185450 137270 188400 151880 165400 TRUE FALSE 150070.2527 197279.8583 170992.0305 194126.9886 170885.5051 176897.6206 160151.169 170842.5523 137793.6715 1.089093941 1.431704782 1.240928039 1.408823689 1.24015496 1.283786249 1.162253442 1.239843242 1 17.0721501 0.772449558 0.590554623 0.997514214 1.307700704 0.413271381 0.099917758 0.959914748 0.71798662 0.099761951 0.039544791 5.921743037 -0.772449558 0.31018649 GRAS(ph)SHS(ph)SQTQGGGSVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GRASSHSSQTQGGGSVTK 18 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 GRAS(0.701)S(0.339)HS(0.763)S(0.181)QT(0.016)QGGGSVTK;GRAS(0.712)S(0.368)HS(0.832)S(0.083)QT(0.006)QGGGSVTK 63.268 0.025488 701280000 339130 376200 336260 362760 349570 254130 374270 275680 288080 TRUE FALSE 317904.4587 404054.2394 344236.246 372069.0358 322116.1823 327493.2055 318151.6881 310099.2548 239997.5869 1.324615229 1.683576258 1.434332113 1.550303236 1.342164254 1.364568743 1.325645362 1.29209322 1 17.87266037 0.97820831 0.371537893 0.962847773 1.553632428 0.688241011 0.098968716 0.743900663 0.286255837 0.159235575 0.085783046 9.510608614 -0.97820831 0.590784656 GRAS(ph)SHSSQT(ph)QGGGSVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRASSHSSQTQGGGSVTK 18 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 GRAS(0.781)S(0.204)HS(0.036)S(0.016)QT(0.617)QGGGS(0.328)VT(0.017)K 96.723 0.0035286 200550000 218530 378160 378310 401320 496030 301380 511660 462550 832290 TRUE FALSE 204852.5974 406159.3599 387283.6919 411618.5506 457073.8047 388383.5135 434941.333 520300.3857 693375.4222 0.295442542 0.58577121 0.558548341 0.593644565 0.659201048 0.560134526 0.627281151 0.750387696 1 19.40327717 -5 0.094364854 2.386016498 0.252733191 0.810249275 0.076458132 87.51436415 0.569123479 24.03124018 1.493020234 1.00E-05 5 -2.133283307 GRAS(ph)SHSSQTQGGGS(ph)VTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GRASSHSSQTQGGGSVTK 18 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 GRAS(0.756)S(0.244)HSSQT(0.002)QGGGS(0.997)VT(0.001)K;GRAS(0.754)S(0.246)HSSQT(0.002)QGGGS(0.976)VT(0.021)K 140.26 7.31E-08 531810000 432730 770090 727000 795330 927470 560940 1043320 922260 1520520 TRUE FALSE 405646.2017 827108.2649 744244.7833 815739.5143 854630.2474 722874.2719 886883.8517 1037406.191 1266735.389 0.320229627 0.652944784 0.587529795 0.643969941 0.674671486 0.570659254 0.700133476 0.818960455 1 20.27268376 -5 0.06874449 2.385734363 0.119068324 0.751871119 0.086530657 165.4360334 0.820792082 36.19609486 4.687609127 1.00E-05 5 -2.266666039 GRAS(ph)SHSSQTQGGGSVTK ddPTM_SK-BR-3_Pertuzumab_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 1 GRAS(0.918)S(0.063)HS(0.017)S(0.002)QTQGGGSVTK;GRAS(0.416)S(0.416)HS(0.059)S(0.107)QT(0.001)QGGGSVTK;GRAS(0.673)S(0.16)HS(0.16)S(0.006)QTQGGGSVTK;GRAS(0.849)S(0.137)HS(0.013)S(0.001)QTQGGGSVTK;GRAS(0.2)S(0.2)HS(0.2)S(0.2)QT(0.2)QGGGSVTK 184.01 3.65E-14 1372308000 610220 1358967 1157013 1143746 1335767 977759 1391731 1214958 1740872 TRUE FALSE 572027.4195 1459586.331 1184457.895 1173096.459 1230861.248 1260022.151 1183053.857 1366648.181 1450309.217 0.394417558 1.006396646 0.816693351 0.808859549 0.848688841 0.86879552 0.815725256 0.942315035 1 20.4679291 4.748262628 24.85075114 0.876039728 0.394417277 0.814197079 0.073955744 509.969131 1306207.101 0.016758602 0.220504379 56009.6202 -4.748262628 -0.481622451 GRASS(ph)HSS(ph)QTQGGGSVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRASSHSSQTQGGGSVTK 18 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 GRAS(0.149)S(0.85)HS(0.026)S(0.973)QT(0.001)QGGGSVTK 92.518 0.0013201 98319000 51209 59149 37056 57361 69890 30340 66462 54538 151530 TRUE FALSE 48003.9201 63528.4535 37934.98582 58832.98037 64401.12132 39098.66547 56496.6401 61347.18935 126238.6641 0.380263214 0.503240857 0.300502117 0.466045651 0.510153698 0.309720209 0.447538324 0.485961966 1 16.94579432 0.558044429 1.817618064 0.999937586 0.414064473 0.867314767 0.071165164 0.839324585 3.079008745 0.063477178 0.017749584 3.614468374 -0.558044429 -0.585873112 GRASS(ph)HSSQTQGGGS(ph)VTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRASSHSSQTQGGGSVTK 18 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 GRAS(0.307)S(0.362)HS(0.291)S(0.03)QT(0.01)QGGGS(0.998)VT(0.001)K 87.991 0.001798 138170000 177220 277720 299080 293810 366560 217250 388500 355180 638670 TRUE FALSE 166128.1165 298282.6778 306174.3188 301349.662 337771.8562 279966.5482 330248.0317 399525.0048 532071.851 0.312228727 0.560606011 0.575437919 0.56637024 0.634823766 0.526181845 0.620683148 0.750885438 1 19.02126155 -5 0.116270887 2.452794457 0.336683319 0.825548114 0.072816879 66.26154593 0.504687213 22.53684682 0.755808801 1.00E-05 5 -2.116111139 GRASSHSS(ph)QTQGGGSVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRASSHSSQTQGGGSVTK 18 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 GRAS(0.061)S(0.008)HS(0.401)S(0.516)QT(0.014)QGGGSVTK 77.287 0.0083737 36206000 19485 29302 30900 30743 34392 21622 36907 34433 44055 TRUE FALSE 18265.46863 31471.55057 31632.96259 31531.91743 31690.99105 27863.9204 31373.13798 38732.03585 36701.93589 0.497670441 0.857490206 0.861888122 0.859134993 0.863469195 0.759194841 0.854808805 1.055313157 1 15.16356854 4.739536964 5.152566043 0.872588504 0.480578355 0.679844629 0.083783715 0.093378709 8.28892205 0.018448133 0.130219763 54895.5277 -4.739536964 -0.392010149 GRDEVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GRDEVSK 7 1 Q9UKY7;H0Y8K3;D6R9V8 Q9UKY7 CDV3 Protein CDV3 homolog 0 ; 73.208 0.04516 290320000 737000 656740 712500 691230 741400 585130 748600 594420 693020 FALSE TRUE 690872.4856 705365.7129 729400.8365 708968.132 683173.4347 754047.5322 636354.3797 668634.6455 577350.4849 1.196625799 1.221728796 1.263358836 1.227968367 1.183290657 1.306048149 1.102197705 1.158108745 1 19.13908786 1.032430203 0.939034293 1.004131129 1.23350341 0.69421853 0.047327732 0.290232567 0.555543542 0.040165673 0.013771999 10.77532067 -1.032430203 0.229372281 GRDIVVLGVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRDIVVLGVEK 11 1 O14818;O14818-4 O14818 PSMA7 Proteasome subunit alpha type-7 0 115.34 0.0010361 223550000 300200 458380 306000 292590 572470 201220 342430 450310 527100 FALSE TRUE 281411.0179 492318.9321 313258.4645 300098.3548 527510.5154 259308.9475 291085.8005 506532.1948 439123.6048 0.640846939 1.121139758 0.713371955 0.683402922 1.201280254 0.590514708 0.662878965 1.153507097 1 18.74426756 1.228097639 24.99838391 1.076753637 0.815894224 0.231092558 0.207202391 366.5519586 875744.9134 0.183340924 0.047816958 16.90821023 -1.228097639 -0.260859413 GRDNPHINNEQHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRDNPHINNEQHER 14 1 Q8IVM0-2 Q8IVM0-2 CCDC50 Coiled-coil domain-containing protein 50 0 113.59 0.00033995 12904000 9685.1 14471 10964 11332 12612 10153 11459 10542 11863 FALSE TRUE 9078.926879 15542.4479 11224.07126 11622.79831 11621.50439 13084.00628 9740.82933 11858.19191 9882.988662 0.918641839 1.572646537 1.135696057 1.176040842 1.175909919 1.323891661 0.985615755 1.1998589 1 13.27073167 1.697365359 0.480080633 1.005939999 1.280996478 0.073832819 0.179709889 1.527318715 0.868438095 0.175193072 0.12262139 49.81559926 -1.697365359 0.275056479 GRDPDAHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GRDPDAHPK 9 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;B1AP61 Q641Q2 FAM21A WASH complex subunit FAM21A 0 ; 62.271 0.050298 72095000 184444 190376 197689 184057 216091 164251 217692 187506 271704 FALSE TRUE 172899.9793 204471.6371 202378.2764 188780.2142 199120.0845 211667.5973 185051.1056 210916.5369 226354.8471 0.763844828 0.903323431 0.894075294 0.8340012 0.879681116 0.935114048 0.817526587 0.931795981 1 17.78822667 -5 0.211855977 1.6198474 0.854626544 0.443721588 0.049847652 149.4972944 1.492213034 39.36080645 0.098319292 1.00E-05 5 -0.765220856 GRDPVNPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRDPVNPEK 9 1 O60568;C9JIX5 O60568 PLOD3 "Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3" 0 67.726 0.054798 204680000 102710 105000 89708 114220 113690 69846 107940 98848 83571 FALSE TRUE 96281.56444 112774.3093 91835.91612 117151.0786 104761.246 90009.40634 91755.39907 111189.3904 69622.46021 1.38290954 1.61979782 1.319055889 1.68266215 1.504704742 1.292821398 1.317899408 1.597033343 1 16.08726517 -3.191128202 0.257043735 4.66E-12 1.504388378 0.509848424 0.140322374 54.65694972 1.2454217 29.52468834 0.18811764 0.000643979 3.191128202 1.504388378 GRDS(ph)PYQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 GRDSPYQSR 9 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 GRDS(0.998)PYQS(0.002)R;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(0.999)PYQS(0.001)R;GRDS(0.998)PY(0.002)QSR;GRDS(1)PYQSR;GRDS(1)PYQSR 146.08 5.79E-05 14317762000 1942202 2143453 2004691.5 2077178 2113366 2042742.1 2460182 1869216.3 1920435 TRUE FALSE 1820643.044 2302156.49 2052243.729 2130481.904 1947390.759 2632448.583 2091300.548 2102592.07 1599901.992 1.137971609 1.438935948 1.282730904 1.331632759 1.217193784 1.645381152 1.307142912 1.314200545 1 20.6095521 0.668491421 2.602596237 1.000066252 1.349755495 0.375734279 0.135111924 2.543477761 18.76395357 0.116736595 0.031016418 4.661132203 -0.668491421 0.349689243 GRDVIAQSQSGTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GRDVIAQSQSGTGK 14 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ; 178.03 1.85E-06 485620000 348130 424330 382990 387150 463980 354710 469630 380530 533590 FALSE TRUE 326341.1647 455747.8347 392074.7037 397084.9244 427540.8824 457109.0188 399213.3413 428040.0081 444530.3819 0.734125671 1.02523439 0.881997541 0.893268358 0.961781016 1.028296462 0.898056371 0.962903832 1 18.7619225 2.727428823 21.70528895 0.963372174 0.906976318 0.207134643 0.077817331 277.7749986 541614.9866 0.023652182 0.02255778 533.8617712 -2.727428823 -0.056395856 GRDWNVDLIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 140.14 3.53E-05 10100970000 27111540 26344170 25444510 25992230 31174610 19671396 33548030 24449700 38744730 FALSE TRUE 25414677.11 28294719.76 26048065.79 26659234.63 28726281.88 25350208.69 28517814.35 27502298.87 32277984.26 0.787368781 0.876595004 0.806991712 0.825926254 0.889965174 0.785371493 0.883506669 0.852045117 1 24.94404715 -0.626370662 0.443759346 1.041476147 0.831063406 0.669948705 0.036379684 5.669981657 0.939514251 0.369491314 0.018332529 0.236390129 0.626370662 -0.210412741 GRECS(ph)PTSSLER ddPTM_SK-BR-3_Pertuzumab_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(0.747)PT(0.018)S(0.154)S(0.081)LER;GRECS(0.983)PT(0.01)S(0.003)S(0.003)LER 144.8 0.00016668 600530000 436990 569380 467770 484420 622090 511080 616910 479620 715340 TRUE FALSE 409639.5759 611537.4876 478865.7253 496851.0373 573233.5608 658620.4993 524410.0726 539501.6128 595945.1327 0.687378004 1.026164078 0.803539955 0.833719432 0.961889827 1.105169693 0.879963681 0.905287388 1 19.18481999 2.723732498 20.6802122 0.967477637 0.863417602 0.280609363 0.101935721 133.5149767 186206.002 0.031690816 0.030075942 529.3373003 -2.723732498 -0.104060035 GREDVSNFDDEFTSEAPILT(ph)PPREPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GREDVSNFDDEFTSEAPILTPPREPR 26 2 Q16513-3;Q16513-2;Q16513;Q16513-4;Q16513-5 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 GREDVSNFDDEFTSEAPILT(1)PPREPR;GREDVSNFDDEFTSEAPILT(1)PPREPR;GREDVSNFDDEFTSEAPILT(1)PPREPR;GREDVSNFDDEFTSEAPILT(1)PPREPR;GREDVSNFDDEFTSEAPILT(1)PPREPR;GREDVSNFDDEFTSEAPILT(1)PPREPR 235.67 3.04E-43 6653300000 811668 979150 943880 957420 1094940 885330 1022364 868812 1096540 TRUE FALSE 760867.1487 1051647.285 966269.2793 981989.0181 1008947.829 1140910.399 869070.0094 977285.0907 913520.3901 0.832895639 1.151202859 1.057742432 1.074950301 1.104461203 1.248916183 0.951341665 1.06980107 1 19.80107741 1.628985983 25 1.007916176 1.086328048 0.086587552 0.107104066 1.85135558 2185.674797 0.045337038 0.025108249 42.55846775 -1.628985983 0.078411872 GREETVAEDVCIDLTCDSGSQAVPS(ph)PATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GREETVAEDVCIDLTCDSGSQAVPSPATR 29 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 GREETVAEDVCIDLTCDSGSQAVPS(0.999)PAT(0.001)R;GREETVAEDVCIDLTCDSGSQAVPS(0.999)PAT(0.001)R 169.75 1.78E-12 307660000 243310 234090 252900 244040 328370 355000 425700 304000 391290 TRUE FALSE 228081.6614 251422.2672 258898.9074 250302.4796 302581.1448 457482.7371 361870.237 341955.0692 325981.1712 0.69967741 0.771278495 0.794214299 0.767843365 0.928216632 1.403402336 1.110095518 1.049002517 1 18.31442911 2.456822909 7.360648901 1.156946528 0.773978969 0.734065413 0.108165795 0.077781092 18.65301888 0.034979916 0.029675431 286.3010288 -2.456822909 -0.382967558 GREEYEGPNKKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GREEYEGPNKKPR 13 3 P23246 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 130.1 6.40E-05 225200000 416710 325180 369030 335670 392080 255490 439010 325880 474390 FALSE TRUE 390628.8649 349256.6655 377783.5659 344283.8605 361287.6184 329245.8155 373184.5261 366566.8354 395211.2443 0.98840524 0.88372148 0.955902878 0.871138829 0.914163308 0.833088178 0.944265963 0.92752127 1 18.59226447 0.78517497 1.693716155 0.999494113 0.910141453 0.278611616 0.043990302 0.928747904 4.614440865 0.037791447 0.010767771 6.097825191 -0.78517497 -0.089352659 GREGS(ph)LTGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 99.498 0.0028187 934760000 653290 589850 637710 616030 685880 562990 991080 710200 1426080 TRUE FALSE 612401.7451 633523.1077 652836.7823 631838.3727 632013.7515 725516.0736 842476.7547 798870.0333 1188058.035 0.515464503 0.53324256 0.549499067 0.531824502 0.53197212 0.610673934 0.709120876 0.672416675 1 20.18017388 0.688433551 0.499473936 1.019233945 0.518117668 0.961967017 0.028596631 0.261842447 0.138007783 0.040729167 0.015784303 4.88015427 -0.688433551 -0.501116277 GRELEPELEPGPGPGSALEPGEEFEIVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRELEPELEPGPGPGSALEPGEEFEIVDR 29 1 Q96T51-3;Q96T51 Q96T51-3 RUFY1 RUN and FYVE domain-containing protein 1 0 100.98 0.00063277 22018000 11293 12587 11808 12942 13534 13520 13224 11953 16463 FALSE TRUE 10586.19129 13518.95458 12088.09134 13274.11363 12471.09423 17423.00452 11241.18397 13445.35836 13715.21894 0.771857258 0.98569003 0.881363352 0.967838259 0.909288746 1.270340969 0.819613891 0.980324005 1 13.74349003 2.878861414 2.225935105 0.99521029 0.904308281 0.145567902 0.124239745 0.737723299 7.207481294 0.039887174 0.043375768 756.5914232 -2.878861414 -0.090902009 GRES(ph)PAAGPR ddPTM_SK-BR-3_Pertuzumab_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 82.774 0.044732 211357000 320359 347471 312243 333205 360374 324909 373401 339160 418510 TRUE FALSE 300308.302 373198.1144 319649.5514 341755.6044 332071.6797 418704.9538 317412.9865 381504.8726 348657.9773 0.861326347 1.070384556 0.916799764 0.980203026 0.952428171 1.200904557 0.910384982 1.094209504 1 18.41145297 GRKDDDS(ph)DDESQSSHTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GRKDDDSDDESQSSHTGK 18 2 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 GRKDDDS(0.998)DDES(0.002)QSSHTGK;GRKDDDS(0.993)DDES(0.006)QS(0.001)SHTGK;GRKDDDS(0.987)DDES(0.013)QSSHTGK;GRKDDDS(1)DDESQSSHTGK;GRKDDDS(1)DDESQSSHTGK;GRKDDDS(1)DDESQSSHTGK;GRKDDDS(0.974)DDES(0.02)QS(0.005)SHTGK 258.55 6.03E-31 2442184000 1710810 1345433 1503128 1638550 1598550 975922 2093010 1342465 1989340 TRUE FALSE 1603733.456 1445050.259 1538782.906 1680597.967 1473006.331 1257654.839 1779182.581 1510074.71 1657306.302 0.967674746 0.871927089 0.928484314 1.014053929 0.888795468 0.758854798 1.073538777 0.911162112 1 20.66040883 1.700614206 24.99999187 0.994465175 0.907437773 0.23565987 0.076264601 0.913490329 596.2124075 0.033190731 0.018405924 50.18965447 -1.700614206 -0.087027402 GRLDS(ph)SEMDHS(ph)ENEDYTMSSPLPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GRLDSSEMDHSENEDYTMSSPLPGK 25 1 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 GRLDS(0.827)S(0.173)EMDHS(1)ENEDYTMSSPLPGK;GRLDS(0.508)S(0.508)EMDHS(0.962)ENEDY(0.018)T(0.003)MS(0.001)S(0.001)PLPGK 227.58 2.99E-34 346140000 327700 321820 324590 342470 328640 212951 303690 237510 349560 TRUE FALSE 307189.842 345647.8877 332289.4281 351258.36 302829.9401 274426.4967 258154.5038 267163.6463 291216.1778 1.054851569 1.186911697 1.141040414 1.206177358 1.03988021 0.942346331 0.886470339 0.91740661 1 18.15173098 2.424601368 2.857364427 0.921789828 1.152389107 0.798296312 0.04950209 0.094576143 1.580713246 0.017099752 0.014122428 265.8283946 -2.424601368 0.23059928 GRLDS(ph)SEMDHSENEDYTMSSPLPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRLDSSEMDHSENEDYTMSSPLPGK 25 1 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 GRLDS(0.327)S(0.327)EMDHS(0.327)ENEDY(0.011)T(0.003)MS(0.003)S(0.003)PLPGK 58.457 0.064838 92733000 106980 105060 106900 99697 121410 88917 176230 127360 160420 TRUE FALSE 100284.3128 112838.7517 109435.7185 102255.3938 111874.9483 114585.8945 149805.9475 143261.1764 133644.8656 0.750379091 0.844317896 0.818854641 0.765127738 0.83710622 0.857390921 1.120925573 1.07195421 1 17.02804489 1.837603809 4.468180434 1.072497767 0.812053963 0.88935945 0.042115431 0.062432095 1.937636042 0.018979148 0.010638012 68.80243507 -1.837603809 -0.260443803 GRLDSS(ph)EMDHS(ph)ENEDYTMSSPLPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRLDSSEMDHSENEDYTMSSPLPGK 25 1 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 GRLDS(0.143)S(0.586)EMDHS(0.607)ENEDY(0.24)T(0.257)MS(0.077)S(0.089)PLPGK 59.678 0.079244 75088000 60724 63997 55623 64276 62522 43126 56819 45763 69273 TRUE FALSE 56923.39324 68735.40447 56942.40383 65925.43098 57611.77432 55575.77611 48299.51843 51476.61129 57710.88878 0.986354472 1.19103008 0.986683883 1.142339555 0.998282569 0.963003296 0.836922103 0.891973982 1 15.81655593 2.29044019 2.232258082 0.894826502 1.08022649 0.47198727 0.075340528 0.212217034 2.165915879 0.030362866 0.021620332 195.1821916 -2.29044019 0.185399988 GRLDSS(ph)EMDHS(ph)ENEDYTMSSPLPGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GRLDSSEMDHSENEDYTMSSPLPGKK 26 2 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 GRLDS(0.438)S(0.566)EMDHS(0.956)ENEDY(0.012)T(0.01)MS(0.01)S(0.009)PLPGKK;GRLDS(0.445)S(0.559)EMDHS(0.97)ENEDY(0.002)T(0.01)MS(0.011)S(0.003)PLPGKK 56.041 0.047998 363300000 149529 123593 127077 132446 143202 92402 129808 97126 192073 TRUE FALSE 140170.2468 132743.9543 130091.3265 135844.7886 131955.4926 119076.9574 110344.4955 109252.3949 160014.7755 0.875983148 0.829573106 0.812995713 0.848951531 0.824645675 0.744162263 0.689589415 0.682764417 1 17.2878456 2.266490967 5.517478075 0.745824961 0.834852261 0.043569625 0.090787767 0.282849113 23.56785508 0.02897081 0.023311933 184.7102377 -2.266490967 0.0890273 GRLDSSEMDHS(ph)ENEDYTMSSPLPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GRLDSSEMDHSENEDYTMSSPLPGK 25 1 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 GRLDS(0.026)S(0.198)EMDHS(0.737)ENEDY(0.024)T(0.007)MS(0.007)S(0.001)PLPGK;GRLDS(0.007)S(0.007)EMDHS(0.985)ENEDYT(0.002)MSSPLPGK;GRLDS(0.183)S(0.183)EMDHS(0.603)ENEDY(0.027)T(0.003)MSSPLPGK 103.85 0.0027609 334629000 215277 195925 200327 209819 237170 216200 339450 265534 313089 TRUE FALSE 201803.1969 210431.4909 205078.851 215203.3108 218543.6249 278613.4303 288552.6238 298686.5044 260832.4233 0.773689077 0.806768914 0.78624754 0.825063495 0.837869856 1.068170233 1.1062759 1.145127974 1 17.99276369 2.253203434 3.480134552 1.095451692 0.799713199 0.926602842 0.038428478 0.049554864 1.270528368 0.01350347 0.010265538 179.1444815 -2.253203434 -0.295738493 GRLGS(ph)VDSFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GRLGSVDSFER 11 1 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 GRLGS(1)VDSFER;GRLGS(1)VDSFER 181.75 3.69E-06 282950000 274580 312320 287400 378740 500720 242310 335290 307960 415530 TRUE FALSE 257394.5279 335444.4978 294217.2637 388459.1096 461395.471 312260.9634 285016.3772 346409.4839 346175.3586 0.743537983 0.969001662 0.849908165 1.122145468 1.332837418 0.902031169 0.823329478 1.00067632 1 18.40114351 5.538750015 0.951625159 0.993394453 4.05E-17 0.223829348 0.146381361 14.91065691 3.51594563 0.048164427 21.94728406 345740.3085 -5.538750015 -0.993394453 GRLPLLLVANAGTAAVGHTDK ddPTM_SK-BR-3_Pertuzumab_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 0 179.58 3.42E-17 242020000 185860 190680 158010 150140 205000 148140 191720 172110 183890 FALSE TRUE 174227.3544 204798.1456 161758.0718 153992.8466 188900.1269 190905.6131 162973.3658 193598.3124 153197.571 1.137272303 1.336823712 1.055878828 1.005191176 1.233049099 1.246139948 1.063811683 1.263716592 1 17.2250339 -2.433032129 1.801860608 7.48E-05 1.165853849 0.201641582 0.10483082 1703382.658 134610.9689 6933787.664 0.025096769 0.003689503 2.433032129 1.165779047 GRLPNNSS(ph)RPS(ph)TPTINVLESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GRLPNNSSRPSTPTINVLESK 21 2 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 2 GRLPNNS(0.441)S(0.556)RPS(0.554)T(0.44)PT(0.008)INVLESK;GRLPNNS(0.446)S(0.55)RPS(0.554)T(0.45)PTINVLESK;GRLPNNS(0.475)S(0.515)RPS(0.479)T(0.442)PT(0.089)INVLESK;GRLPNNS(0.444)S(0.556)RPS(0.852)T(0.145)PT(0.002)INVLESK 161.68 1.05E-11 1355410000 964620 699950 685400 650160 794510 487292 881970 633100 1238830 TRUE FALSE 904246.1561 751775.0263 701658.0117 666844.2063 732112.3895 627965.2899 749726.7863 712143.9286 1032061.27 0.876155498 0.728420926 0.679860811 0.646128506 0.709369115 0.608457374 0.726436316 0.69002098 1 19.97709719 -1.72847789 9.67191441 1.000702739 0.702879674 0.631293631 0.070004266 0.000989937 2.78E-05 0.06325365 0.014877493 0.018686248 1.72847789 -0.297823065 GRLPNNSSRPS(ph)TPTINVLESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GRLPNNSSRPSTPTINVLESK 21 2 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 GRLPNNS(0.057)S(0.057)RPS(0.442)T(0.442)PT(0.002)INVLESK;GRLPNNS(0.003)S(0.003)RPS(0.497)T(0.497)PTINVLESK;GRLPNNS(0.002)S(0.002)RPS(0.498)T(0.498)PTINVLESK 158.77 1.22E-11 650050000 982050 685900 802850 820720 914540 779300 1011320 788700 938890 TRUE FALSE 920585.2435 736684.7497 821893.9811 841781.0647 842715.7175 1004271.259 859681.9546 887170.9311 782183.1935 1.176943267 0.941831473 1.050769165 1.076194262 1.07738919 1.283933569 1.099080064 1.134223975 1 19.57714701 2.77866905 2.255901737 1.139490362 1.033820948 0.065606091 0.090591703 0.451057365 4.523930588 0.029330791 0.029929269 600.7157939 -2.77866905 -0.105669413 GRLPNNSSRPST(ph)PTINVLESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRLPNNSSRPSTPTINVLESK 21 2 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 GRLPNNS(0.254)S(0.254)RPS(0.208)T(0.283)PT(0.001)INVLESK 107.19 0.016639 278150000 464340 335320 386020 395890 452160 378620 522510 384030 522030 TRUE FALSE 435277.7883 360147.4417 395176.5767 406049.2076 416649.1775 487921.4476 444164.4762 431976.9909 434899.8206 1.000869091 0.828115866 0.908661163 0.933661474 0.958034834 1.121916875 1.021302965 0.993279303 1 18.73032359 2.585077804 2.726127262 1.037353039 0.899624756 0.466338936 0.056228529 0.196031621 2.843514539 0.019136422 0.017425285 384.6606877 -2.585077804 -0.137728283 GRLS(ph)PVPVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 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 99.844 0.0026757 79395033900 5794188.6 6140754.6 6390815.2 5317732.4 7069478.1 5808482.8 7406422.4 6136729.4 8522288.4 TRUE FALSE 5431540.678 6595422.46 6542408.355 5454194.416 6514269.807 7485297.492 6295898.119 6902913.574 7099863.41 0.765020447 0.928950612 0.921483693 0.768211176 0.917520441 1.054287535 0.886763274 0.972260053 1 22.75935984 2.476996196 24.99999941 0.965987038 0.869401613 0.430695958 0.068850219 5.444752933 1087945.973 0.023178855 0.019572442 299.9136249 -2.476996196 -0.096585425 GRLT(ph)PS(ph)PDIIVLS(ph)DNEASSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 3 GRLT(1)PS(1)PDIIVLS(1)DNEASSPR;GRLT(1)PS(1)PDIIVLS(1)DNEASSPR;GRLT(1)PS(1)PDIIVLS(1)DNEASSPR;GRLT(1)PS(1)PDIIVLS(1)DNEASSPR 172.03 5.14E-12 1136630000 1061350 1217120 1216530 1208690 1297790 926470 1150690 924960 1337270 TRUE FALSE 994921.9981 1307236.831 1245386.666 1239707.032 1195866.808 1193926.849 978154.717 1040443.292 1114070.998 0.893050802 1.173387364 1.117870107 1.112772017 1.073420644 1.07167932 0.878000342 0.933911119 1 20.08740975 1.828702999 5.837803607 0.928341623 1.09312631 0.385492906 0.078702898 0.183380376 9.012046666 0.033539479 0.019769856 67.40668962 -1.828702999 0.164784687 GRLT(ph)PS(ph)PDIIVLSDNEAS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 3 GRLT(1)PS(1)PDIIVLSDNEAS(0.642)S(0.358)PR;GRLT(1)PS(1)PDIIVLS(0.038)DNEAS(0.481)S(0.481)PR 160.27 1.79E-11 260340000 100045 102257 115683 120338 117266 132554 134561 101532 172569 TRUE FALSE 93783.36204 109828.2147 118427.0554 123426.0768 108056.4014 170820.188 114384.8273 114208.4937 143766.1191 0.652332849 0.763936701 0.823748016 0.858519918 0.751612425 1.188181117 0.795631321 0.794404791 1 17.13336419 6.236104737 0.337963483 0.927791007 5.44E-13 0.323433106 0.122549809 22.34195387 0.924015929 0.104105016 10.36051474 1722283.88 -6.236104737 -0.927791007 GRLT(ph)PS(ph)PDIIVLSDNEASSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 GRLT(1)PS(1)PDIIVLSDNEASSPR;GRLT(1)PS(1)PDIIVLSDNEASSPR;GRLT(1)PS(1)PDIIVLSDNEASSPR 242.45 1.09E-29 1420450000 885860 1016660 1020660 1070670 1064680 817190 923650 831590 1179950 TRUE FALSE 830415.6039 1091934.564 1044870.537 1098145.205 981064.3275 1053099.487 785157.2572 935415.8421 983008.7222 0.844769314 1.110808622 1.062931095 1.117126613 0.998021996 1.071302282 0.798728678 0.951584478 1 19.90684469 1.758205402 25 0.898468759 1.048125048 0.249427853 0.092128344 8.656233407 11026.15697 0.038674447 0.021447222 57.30670025 -1.758205402 0.149656289 GRLT(ph)PSPDIIVLS(ph)DNEAS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 3 GRLT(0.996)PS(0.004)PDIIVLS(0.994)DNEAS(0.536)S(0.47)PR 92.822 0.00029847 0 39682 45615 47096 42391 45769 38200 47194 45410 59333 TRUE FALSE 37198.37445 48992.38206 48213.13936 43478.82483 42174.48736 49227.71987 40117.69783 51079.53846 49429.93899 0.752547448 0.991147937 0.975383347 0.879605068 0.853217467 0.995908975 0.81160727 1.033372476 1 15.59309751 1.203375784 24.99782433 1.016686531 0.91006067 0.273093211 0.079882693 301.5801381 214257.4676 0.073111724 0.018280806 15.97260617 -1.203375784 -0.106625861 GRLT(ph)PSPDIIVLS(ph)DNEASS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 3 GRLT(0.955)PS(0.045)PDIIVLS(1)DNEAS(0.135)S(0.865)PR;GRLT(0.998)PS(0.002)PDIIVLS(1)DNEAS(0.098)S(0.902)PR 176.5 2.65E-13 347870000 333830 362020 339160 346180 414610 327480 438800 370510 490260 TRUE FALSE 312936.1762 388824.3375 347205.0354 355063.5649 382048.2031 422018.1598 373006.0136 416768.9891 408432.4388 0.76618835 0.951991812 0.850091722 0.869332431 0.935401224 1.03326308 0.91326246 1.020411088 1 18.63973793 2.561848978 3.859341648 0.979363313 0.873735825 0.545771574 0.055635615 0.206181264 5.713405918 0.017656858 0.016203507 364.6271287 -2.561848978 -0.105627488 GRLT(ph)PSPDIIVLS(ph)DNEASSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 GRLT(1)PSPDIIVLS(1)DNEASSPR 228.76 3.56E-25 215530000 220390 265950 237410 275200 285260 196590 280300 244540 292380 TRUE FALSE 206596.1833 285641.2147 243041.4773 282262.0979 262856.8303 253342.3416 238271.6172 275071.3573 243579.8892 0.848166012 1.172679796 0.997789588 1.158807071 1.079140118 1.040079058 0.978207265 1.129285994 1 17.8940355 -0.229037822 7.546592992 1.000000001 1.054651578 0.025080681 0.095959874 0 0 0.082450462 0.01943376 0.590149683 0.229037822 0.054651576 GRLT(ph)PSPDIIVLSDNEASS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 GRLT(0.885)PS(0.115)PDIIVLSDNEAS(0.09)S(0.91)PR 205.29 1.11E-21 87705000 112340 127680 108150 125370 136070 118550 165300 134640 186570 TRUE FALSE 105308.8399 137133.5601 110715.3691 128587.2065 125383.6111 152773.4605 140514.7996 151450.1004 155430.2617 0.677531124 0.882283531 0.7123154 0.827298398 0.806687254 0.982906796 0.904037592 0.974392623 1 17.24590789 2.300245204 5.55446055 0.952485137 0.786066855 0.684552736 0.061855196 0.11898883 7.185876397 0.020201789 0.016596575 199.6389166 -2.300245204 -0.166418282 GRLT(ph)PSPDIIVLSDNEASSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 GRLT(0.993)PS(0.007)PDIIVLSDNEASSPR 247.08 3.80E-30 177280000 137590 165520 149050 155280 169310 132750 157210 139890 179760 TRUE FALSE 128978.4875 177775.273 152585.5364 159264.7477 156013.0756 171072.77 133637.82 157355.5744 149756.8947 0.861252417 1.18709241 1.018888223 1.063488583 1.041775578 1.14233652 0.892365058 1.050740099 1 17.1922629 1.739877202 24.99999987 0.973899987 1.064143264 0.105664136 0.093200919 0.334322023 6368.453535 0.038664273 0.021441352 54.93855118 -1.739877202 0.090243277 GRNDLMEYAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRNDLMEYAK 10 1 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 84.687 0.013453 264990000 89412 269620 72235 70595 340460 60983 88308 258740 315130 FALSE TRUE 83815.86252 289582.9453 73948.44831 72406.58722 313721.6449 78587.80212 75067.03521 291044.2586 262532.7672 0.319258672 1.103035436 0.281673214 0.275800191 1.19498091 0.299344737 0.285933966 1.108601649 1 18.00213797 1.222483713 24.99180326 1.05430135 0.555715824 0.280303153 0.343509423 374.6288706 582350.5245 0.313977451 0.079498801 16.6910521 -1.222483713 -0.498585527 GRNDS(ph)GEENVPLDLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GRNDSGEENVPLDLTR 16 1 Q6R327-3;Q6R327;Q6R327-4 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 GRNDS(1)GEENVPLDLTR;GRNDS(1)GEENVPLDLTR;GRNDS(1)GEENVPLDLTR 123.55 5.28E-05 561023000 368660 414233 385636 424172 407402 341062 459063 378402 401592 TRUE FALSE 345586.2287 444903.2423 394783.468 435056.9716 375406.2903 439521.0627 390230.7649 425646.3227 334563.7008 1.032945977 1.329801294 1.179994922 1.300371112 1.122077169 1.313714135 1.166387041 1.272242989 1 18.3519214 -1.80288819 2.725149903 0.935609637 1.221971657 0.338383764 0.093855035 26407897.54 17755890.3 11192783.67 0.019163133 0.015743881 1.80288819 0.28636202 GRNS(ph)ATSADEQPHIGNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.432)AT(0.174)S(0.394)ADEQPHIGNYR;GRNS(0.984)AT(0.015)S(0.001)ADEQPHIGNYR;GRNS(0.744)AT(0.246)S(0.01)ADEQPHIGNYR 229.89 9.89E-20 2104530000 275877 347238 371173 383855 411465 271543 325738 275032 391664 TRUE FALSE 258610.351 372947.8628 379977.3988 393705.3692 379150.1987 349933.056 276896.6109 309370.3506 326292.7482 0.792571556 1.142985448 1.164529095 1.206601653 1.161993948 1.07245122 0.848614051 0.948137378 1 18.3158074 1.889882654 5.595235089 0.921370034 1.115321289 0.266879542 0.120291685 0.24765241 10.50413882 0.051409629 0.030806612 77.60374041 -1.889882654 0.193951255 GRPPAEKLS(ph)PNPPNLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GRPPAEKLSPNPPNLTK 17 2 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3;K7EP28;A0A2R8YF38 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 1 GRPPAEKLS(1)PNPPNLTK;GRPPAEKLS(1)PNPPNLTK;GRPPAEKLS(1)PNPPNLTK;GRPPAEKLS(1)PNPPNLTK 174.2 7.21E-10 5886940000 4678450 2767450 3455740 3153940 2921580 2439130 4386170 2885720 3775990 TRUE FALSE 4385634.166 2972354.878 3537711.785 3234875.44 2692130.892 3143267.235 3728504.528 3246008.494 3145752.875 1.394144531 0.944878697 1.124599396 1.028331076 0.855798595 0.999209843 1.185250296 1.031870151 1 21.58497391 4.747368166 24.53169998 1.032924703 1.394144773 0.626701165 0.090046932 643.9942229 1793668.521 0.022241376 0.262481837 55894.38293 -4.747368166 0.36122007 GRPPAEKLS(ph)PNPPNLTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRPPAEKLSPNPPNLTKK 18 3 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)PNPPNLTKK 93.583 0.0015145 243750000 768660 452860 627740 632310 663650 462940 883800 516850 1104600 TRUE FALSE 720550.9427 486390.2256 642630.2892 648536.1451 611529.606 596583.2628 751282.3948 581379.8602 920235.124 0.783007434 0.528549947 0.698332711 0.70475048 0.664536258 0.648294384 0.816402651 0.631773169 1 19.811643 -5 0.19880368 2.470611965 0.625178579 0.58568935 0.08170587 89.07459263 0.880781979 51.83906483 0.183192041 1.00E-05 5 -1.845433386 GRPPEEEPFITHGFTMTTEVPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRPPEEEPFITHGFTMTTEVPLR 23 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 0 83.245 0.0046876 89495000 69132 56728 59809 62535 78134 48450 59122 47218 56127 FALSE TRUE 64805.15152 60928.20015 61227.69772 64139.75397 71997.67082 62436.72848 50257.20496 53113.27124 46759.04111 1.385938419 1.303025013 1.30943014 1.371708069 1.539759352 1.33528676 1.074812566 1.13589308 1 15.51295772 1.755650081 4.593837439 1.077277953 1.366483788 0.795320574 0.072695635 0.091942408 4.25718523 0.039075497 0.020229181 56.9705066 -1.755650081 0.289205834 GRPS(ph)KTPS(ph)PSQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRPSKTPSPSQPK 13 2 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 GRPS(0.701)KT(0.301)PS(0.945)PS(0.054)QPK 68.845 0.026452 369300000 385900 196760 257800 245790 279520 144550 326270 199300 309550 TRUE FALSE 361747.2079 211328.3151 263915.1377 252097.3875 257567.6267 186279.2384 277348.8424 224183.0437 257884.1052 1.402751083 0.819470106 1.0233866 0.977560782 0.998772788 0.722337029 1.075478623 0.869317027 1 17.97636333 4.747732338 24.89654678 0.938723663 1.402751339 0.658234886 0.10572534 675.04295 1832356.3 0.02274243 0.283240511 55941.27207 -4.747732338 0.464027675 GRPSKT(ph)PS(ph)PSQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GRPSKTPSPSQPK 13 2 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 GRPS(0.228)KT(0.773)PS(0.772)PS(0.227)QPK;GRPS(0.065)KT(0.935)PS(0.769)PS(0.232)QPK 128.64 0.00017984 291760000 895720 443550 582650 584030 621340 390720 760660 470090 680250 TRUE FALSE 839658.4841 476390.9035 596470.7331 599017.1986 572542.4628 503514.5212 646606.0946 528781.7713 566711.8804 1.481632048 0.840622757 1.052511433 1.057004837 1.010288442 0.888484146 1.140978541 0.933069854 1 19.11225592 4.750128552 24.87190215 0.995886051 1.481632358 0.759626457 0.086798542 812.600291 1747115.051 0.0200557 0.322247892 56250.78042 -4.750128552 0.485746307 GRPVS(ph)PQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GRPVSPQSR 9 1 Q9C0D5;Q9C0D5-2 Q9C0D5 TANC1 Protein TANC1 1 GRPVS(1)PQSR;GRPVS(0.998)PQS(0.002)R;GRPVS(0.996)PQS(0.004)R 80.469 0.01455 494780000 146842 307322 261818 267662 270378 223747 246088 263571 233014 TRUE FALSE 137651.4213 330076.4406 268028.4466 274530.6601 249143.6025 288339.1267 209189.389 296478.4195 194122.4581 0.709095808 1.700351644 1.380718384 1.414213805 1.283435235 1.485346567 1.077615599 1.527275218 1 17.56660751 1.745916803 24.99999999 1.217374924 1.37924465 0.021776429 0.286102932 4.587925308 15636.47649 0.120304391 0.066714961 55.70790207 -1.745916803 0.161869726 GRPVSLWELLFSEAISSEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRPVSLWELLFSEAISSEQR 20 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 164.35 1.67E-11 85803000 72259 251090 158840 163390 217420 63175 78735 193530 120000 FALSE TRUE 67736.43818 269680.9649 162607.7598 167582.864 200344.7102 81412.59694 66929.41769 217692.6465 99971.22477 0.677559351 2.697585885 1.62654564 1.676311003 2.004023765 0.814360303 0.669486823 2.177553061 1 16.60922528 2.2434222 24.97601909 1.076078383 1.849762901 0.146926535 0.636781928 158.3600644 813566.3398 0.211529244 0.171734059 175.1548631 -2.2434222 0.773684518 GRPYDYNGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GRPYDYNGPR 10 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;;; 158.79 7.19E-06 3074170000 1102120 1406480 1161210 1140850 1479450 926140 1384610 1156750 1313190 FALSE TRUE 1033140.277 1510617.243 1188754.45 1170126.142 1363259.965 1193501.583 1177000.585 1301172.784 1094010.105 0.944360817 1.380807394 1.086602805 1.06957526 1.246112772 1.09094201 1.075858969 1.189360845 1 20.06119463 -1.278854456 0.199490784 0.866878226 1.192607209 0.069682436 0.120484456 44.35520938 1.749234239 3.420974628 0.334383189 0.052619358 1.278854456 0.325728983 GRRPS(ph)GPDGAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GRRPSGPDGAAR 12 2 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;H7C528 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 GRRPS(1)GPDGAAR;GRRPS(1)GPDGAAR;GRRPS(1)GPDGAAR;GRRPS(1)GPDGAAR;GRRPS(1)GPDGAAR 132.05 0.00014792 1812752000 780241 1164972 795573 923584 1258435 605375 859659 839556 1272864 TRUE FALSE 731407.1086 1251227.739 814444.3673 947284.7291 1159602.591 780136.9351 730761.1136 944376.4147 1060414.775 0.689736814 1.179941819 0.768043209 0.893315287 1.093536811 0.735690367 0.689127623 0.890572667 1 20.01619725 2.208401127 24.99744863 0.788345415 0.936863434 0.051650957 0.164305551 363.4712372 301258.0649 0.057366646 0.042373322 161.5850313 -2.208401127 0.148518019 GRS(ph)IDQDYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GRSIDQDYER 10 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 GRS(1)IDQDYER;GRS(1)IDQDYER;GRS(1)IDQDYER;GRS(1)IDQDYER;GRS(1)IDQDYER;GRS(1)IDQDYER 229.48 9.71E-10 5497100000 2014720 2472680 2106700 2316970 2860480 1645150 2288200 2423200 3291080 TRUE FALSE 1888622.272 2655759.8 2156671.919 2376427.373 2635829.439 2120078.098 1945105.653 2725741.854 2741777.487 0.688831344 0.968627036 0.786596261 0.866746986 0.961357897 0.77324951 0.709432353 0.994151373 1 21.38668006 1.175316879 13.35416334 0.997467495 0.830708418 0.37803134 0.09279053 1.432216345 298.6559218 0.087777106 0.021951255 14.9732777 -1.175316879 -0.166759077 GRS(ph)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 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(0.992)PQPPAEEDEDDFDDT(0.008)LVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;GRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK 381.53 2.50E-149 14379075000 793061.3 684078.5 701821.2 528406.6 841947.8 575159 817597.7 770133.6 1177101.3 TRUE FALSE 743425.0089 734728.3839 718468.7303 541966.4079 775824.616 741198.0664 695006.5151 866286.4752 980635.4887 0.758105349 0.749236992 0.732656261 0.552668565 0.791144747 0.755834431 0.70873074 0.883392948 1 19.90335745 1.056915044 3.078478581 0.998907512 0.722169937 0.686040508 0.064527353 0.123898596 2.467947865 0.058442396 0.01544341 11.40026755 -1.056915044 -0.276737575 GRS(ph)PSQYHDFAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GRSPSQYHDFAEK 13 1 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 GRS(0.964)PS(0.036)QYHDFAEK;GRS(0.977)PS(0.023)QYHDFAEK 123.14 0.0001374 328510000 283560 287280 300220 291510 351410 284950 399580 316460 334920 TRUE FALSE 265812.4858 308550.5101 307341.3602 298990.6401 323811.6761 367210.4392 339666.6885 355970.7276 279019.6883 0.952665697 1.105837771 1.101504206 1.071575421 1.160533431 1.316073577 1.217357422 1.275790715 1 18.0900074 2.568385009 3.836845912 1.225048513 1.073677363 0.331491543 0.093418253 0.232571801 6.284509858 0.028341151 0.026068194 370.1561841 -2.568385009 -0.15137115 GRS(ph)RT(ph)PPTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GRSRTPPTSR 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GRS(0.997)RT(0.983)PPT(0.016)S(0.004)R;GRS(0.984)RT(0.874)PPT(0.064)S(0.077)R 65.956 0.074401 3338260000 1459980 1796360 1559000 1690820 1746240 1373940 1575840 1442640 1877080 TRUE FALSE 1368602.458 1929364.364 1595980.216 1734209.304 1609097.354 1770574.174 1339557.421 1622756.78 1563783.222 0.875186816 1.233779936 1.020589167 1.108983189 1.028977247 1.132237608 0.856613246 1.037712106 1 20.5766091 1.751511092 25 0.953400814 1.08078217 0.169179289 0.102239042 5.004795273 9676.238903 0.042461767 0.023547162 56.43013529 -1.751511092 0.127381356 GRSPGQLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRSPGQLQR 9 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7;Q9C040;Q9C040-2 O75382 TRIM3;TRIM2 Tripartite motif-containing protein 3;Tripartite motif-containing protein 2 0 76.221 0.032872 371760000 105620 134670 111860 128620 121400 100430 110460 107510 120930 FALSE TRUE 99009.43274 144641.1069 114513.372 131920.607 111865.7337 129422.5107 93897.54846 120932.8602 100746.0018 0.982762899 1.435700717 1.136654259 1.309437642 1.110373928 1.284641657 0.93202258 1.200373792 1 16.62036306 1.749218108 25 1.043748953 1.227522974 0.233751062 0.139095154 3.386481802 7959.139186 0.057497767 0.031885624 56.13298126 -1.749218108 0.183774021 GRVPKS(ph)EK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRVPKSEK 8 2 Q9NRJ4-2;Q9NRJ4 Q9NRJ4-2 TULP4 Tubby-related protein 4 1 GRVPKS(1)EK 51.346 0.078175 289880000 25806 53050 34166 39881 58149 18803 31437 50357 54132 TRUE FALSE 24190.84853 56977.8772 34976.43365 40904.41398 53582.2121 24231.12086 26723.3137 56644.1823 45097.01949 0.536417901 1.263451063 0.775581935 0.907031428 1.188154177 0.537310916 0.592573833 1.256051574 1 15.46074447 2.240496328 24.99990563 0.779135679 0.956183597 0 0.284599977 133.1514575 1719692.333 0.095583239 0.076229818 173.9787987 -2.240496328 0.177047919 GRVS(ph)VPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GRVSVPLR 8 1 Q6A1A2 Q6A1A2 PDPK2P Putative 3-phosphoinositide-dependent protein kinase 2 1 GRVS(1)VPLR;GRVS(1)VPLR 77.674 0.019744 3551200000 5089300 4499200 5431300 6237700 4913400 6511000 5819700 3693200 6733400 TRUE FALSE 4770769.798 4832325.449 5560133.001 6397769.942 4527521.384 8390620.003 4947090.012 4154304.15 5609552.041 0.850472509 0.861445872 0.991190199 1.14051352 0.807109258 1.495773627 0.881904647 0.740576809 1 22.41945414 3.900985641 2.269132162 1.022935987 0.855505376 0.083351395 0.206750232 0.724516478 7.33460619 0.053323653 0.124339546 7961.330284 -3.900985641 -0.167430611 GRWESQQDVS(ph)QTTVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GRWESQQDVSQTTVSR 16 1 Q9NQT8;H0YBA8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 GRWES(0.079)QQDVS(0.433)QT(0.061)T(0.061)VS(0.366)R 192.24 1.47E-12 0 70597 79798 71712 74375 87095 54919 86106 64269 118360 TRUE FALSE 66178.45979 85706.32695 73413.0425 76283.58842 80254.91002 70773.22376 73195.20467 72293.12612 98604.95137 0.671147431 0.869188877 0.744516796 0.773628376 0.813903449 0.717745131 0.742307599 0.733159188 1 16.58937247 -1.050216797 5.815854799 1.000000702 0.765495169 0.661582259 0.054126219 4.68E-07 7.64E-08 0.04979467 0.011736681 0.089080614 1.050216797 -0.234505533 GRYPDHS(ph)VDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GRYPDHSVDRR 11 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 GRYPDHS(1)VDRR;GRYPDHS(1)VDRR;GRYPDHS(1)VDRR 158.31 1.56E-05 961050000 232197 241207 303710 357392 422610 289291 361260 204183 104323 TRUE FALSE 217664.2043 259066.2173 310914.1446 366563.2838 389419.9153 372804.6155 307092.4168 229675.697 86910.81735 2.504454692 2.980828223 3.577392943 4.217694586 4.480684076 4.289507645 3.53341996 2.642659499 1 16.40724813 4.328245221 1.674187735 3.615525169 2.496451768 0.040688551 1.020937331 1.046581163 4.784640456 0.251887152 1.464256973 21293.41023 -4.328245221 -1.119073401 GRYPDHSVDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GRYPDHSVDRR 11 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 ;; 142.97 2.10E-05 139017000 83706 167934 92154 94628 172987 76720 92642 136921 187264 FALSE TRUE 78466.99088 180368.0081 94339.9364 97056.31468 159401.2988 98867.81855 78751.19215 154015.8883 156008.4286 0.502966356 1.156142714 0.60471051 0.62212225 1.021747993 0.633733827 0.504788061 0.987227995 1 17.25126445 3.771238531 23.34152986 0.729978167 0.877475405 0 0.242539765 330.2595539 174729.8536 0.057578741 0.103800214 5905.253307 -3.771238531 0.147497238 GS(ph)DESIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSDESIGK 8 0 Q8NHV4-2;Q8NHV4;Q8NHV4-3 Q8NHV4-2 NEDD1 Protein NEDD1 1 GS(0.5)DES(0.5)IGK 72.234 0.048969 100440000 83313 336050 267140 282720 286590 315500 225530 283510 173340 TRUE FALSE 78098.58805 360931.4917 273476.687 289975.0738 264082.3774 406579.7283 191713.8702 318906.8476 144408.4342 0.540817359 2.499379581 1.893772261 2.008020345 1.828718516 2.81548464 1.327580839 2.208367187 1 17.13979548 -1.383524312 2.988905934 0.986568163 1.942355436 0.163037309 0.624075774 46581883.39 57444088 5444044.472 0.133151275 0.041350017 1.383524312 0.955787273 GS(ph)FKDDPQLYQEIQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSFKDDPQLYQEIQER 16 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 GS(1)FKDDPQLYQEIQER 121.33 6.02E-05 418100000 632770 453250 477620 450450 461710 273330 440430 281470 481030 TRUE FALSE 593166.0552 486809.1016 488949.3719 462009.3096 425449.159 352235.9339 374391.6103 316612.1491 400742.9854 1.480165784 1.21476637 1.220107125 1.152881838 1.06165092 0.878957204 0.934243702 0.79006286 1 18.61231774 2.970401191 0.707756204 0.870956664 1.348926165 0.810927392 0.08644177 0.290516223 0.322340173 0.053815969 0.070346956 934.1168176 -2.970401191 0.477969502 GS(ph)FSSENYWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSFSSENYWR 10 0 Q6P6C2-3;Q6P6C2;Q6P6C2-1;K7ER58 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 GS(0.961)FS(0.039)SENYWR;GS(0.977)FS(0.011)S(0.011)ENYWR 158.06 8.50E-06 289230000 305500 325460 307210 324250 348160 317630 406540 304460 298600 TRUE FALSE 286379.3003 349557.397 314497.1663 332570.804 320816.918 409324.6247 345583.1011 342472.5012 248761.731 1.151219278 1.405189599 1.264250595 1.336905008 1.289655434 1.645448531 1.389213284 1.376708949 1 17.92440504 -0.704129113 7.323053759 0.999999812 1.365329418 0.440761823 0.126205328 8.70E-10 0 0.116828986 0.027536856 0.197638199 0.704129113 0.365329606 GS(ph)GDTSSLIDPDTSLSELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSGDTSSLIDPDTSLSELR 19 0 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 GS(1)GDTSSLIDPDTSLSELR 132.59 6.35E-07 0 62731 68911 58780 57758 59577 61264 60268 60079 46647 TRUE FALSE 58804.77869 74013.24214 60174.28936 59240.16806 54898.06274 78949.92226 51231.3729 67579.9954 38861.31435 1.513195827 1.904548093 1.548436803 1.524399497 1.412666135 2.03158137 1.318312923 1.739004368 1 15.24604708 -2.579473036 0.312123078 1.44E-15 1.671901851 0.434701314 0.219948038 47.61701165 1.681533748 32.50969195 0.191361692 0.002633461 2.579473036 1.671901851 GS(ph)GFSLDVIDGPISQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSGFSLDVIDGPISQR 16 0 O43166-3;O43166-2;O43166 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 GS(1)GFSLDVIDGPISQR 169.92 5.72E-09 82370000 203500 223310 212710 198680 220780 219640 250100 200750 156440 TRUE FALSE 190763.2983 239844.1048 217755.5816 203778.4652 203440.8294 283046.5024 212599.8268 225814.0794 130329.1534 1.463703963 1.840295119 1.670812524 1.563567781 1.560977142 2.171781947 1.631253034 1.732644413 1 16.99180031 -0.97419549 5.566152281 0.999998597 1.719410587 0.560544626 0.195600384 3.11E-06 5.74E-07 0.173186869 0.040820456 0.106121776 0.97419549 0.71941199 GS(ph)GGGGGGGGQGSTNYGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GSGGGGGGGGQGSTNYGK 18 0 Q99729-3;Q99729-4 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 1 GS(1)GGGGGGGGQGSTNYGK;GS(1)GGGGGGGGQGSTNYGK;GS(1)GGGGGGGGQGSTNYGK;GS(1)GGGGGGGGQGSTNYGK 325.6 2.15E-62 1169880000 1249700 1013860 1107660 1071850 1071920 942120 1208800 884623 1004910 TRUE FALSE 1171483.508 1088927.249 1133934.218 1099355.486 987735.7271 1214094.75 1027551.662 995070.1288 837184.029 1.399314209 1.300702368 1.354462315 1.313158693 1.179831068 1.450212507 1.227390426 1.188591868 1 19.67518526 0.987466544 1.449336137 1.002351166 1.325427148 0.673795264 0.073384833 0.238082319 1.020724043 0.06187934 0.01841628 9.715531047 -0.987466544 0.323075982 GS(ph)GGLFS(ph)PSTAHVPDGALGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSGGLFSPSTAHVPDGALGQR 21 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 GS(1)GGLFS(0.909)PS(0.048)T(0.043)AHVPDGALGQR 58.272 0.039039 45968000 50234 59561 60679 66023 62292 59841 60147 45955 52322 TRUE FALSE 47089.94361 63970.95841 62118.33453 67717.26196 57399.83759 77116.12526 51128.51573 51692.58291 43589.12019 1.080314157 1.467590035 1.425088056 1.553535875 1.316838637 1.76915994 1.172965077 1.185905627 1 15.41168046 1.575602767 9.076586276 1.124538494 1.44046941 0.412981124 0.178342638 0.104753518 17.17545975 0.085908843 0.0404061 37.63593995 -1.575602767 0.315930916 GS(ph)GGLFSPSTAHVPDGALGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GSGGLFSPSTAHVPDGALGQR 21 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GS(1)GGLFSPSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(0.999)GGLFS(0.001)PSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(0.999)GGLFS(0.001)PSTAHVPDGALGQR 280.66 3.56E-45 6646963000 2536336 3381534 3284579 3371783 3536270 3570813 3904178 3245637 2474710 TRUE FALSE 2377591.257 3631906.296 3362490.765 3458308.66 3258545.619 4601648.746 3318782.754 3650861.924 2061664.914 1.153238454 1.761637535 1.630958912 1.677434891 1.580540852 2.23200614 1.609758565 1.770831865 1 20.97537844 4.742496855 24.50116457 1.70105999 1.15323817 0.206977675 0.30004811 394.5083497 2455490.74 0.061729677 0.467735945 55270.94051 -4.742496855 -0.547821821 GS(ph)GSPTHSLSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSGSPTHSLSQK 12 0 I3L2R2;I3L419;I3L156;Q9BSJ6-2;Q9BSJ6 I3L2R2 FAM64A Protein FAM64A 1 GS(0.487)GS(0.487)PT(0.026)HSLSQK;GS(0.446)GS(0.446)PT(0.108)HSLSQK 79.885 0.01406 1256730000 718040 1092700 906010 1024450 1092300 860850 1157640 999050 1108790 TRUE FALSE 673099.1581 1173604.645 927500.985 1050739.121 1006515.164 1109363.42 984062.629 1123783.592 923725.7859 0.728678541 1.270511945 1.004086926 1.137501126 1.089625492 1.200966171 1.065318998 1.21657705 1 19.81710512 4.752266823 24.78852693 1.123497679 0.728678247 0.662241898 0.088516874 1187.309978 2147282.086 0.018741591 0.376682457 56528.41684 -4.752266823 -0.394819432 GS(ph)GVFCANCLTTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSGVFCANCLTTK 13 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 GS(1)GVFCANCLTTK;GS(1)GVFCANCLTTK 185.86 3.42E-07 0 278029 322545 243741 260320 344213 179661 357053 267205 420597 TRUE FALSE 260627.6612 346426.5674 249522.6516 267000.2519 317179.8995 231526.2141 303516.2174 300566.1324 350396.6435 0.743807528 0.988669766 0.712114845 0.761994319 0.905202448 0.660754657 0.866207548 0.857788275 1 18.41862943 0.828082452 1.824585352 0.999097028 0.810788278 0.293540806 0.095558746 0.818455405 5.021907147 0.085413232 0.024054767 6.731044356 -0.828082452 -0.18830875 GS(ph)HSPQRPQLHSPAQSEGPSSLCGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSHSPQRPQLHSPAQSEGPSSLCGK 25 1 Q5SY21;Q5SY20;P10074 Q5SY21 ZBTB48 Zinc finger and BTB domain-containing protein 48 1 GS(0.498)HS(0.498)PQRPQLHS(0.003)PAQSEGPSSLCGK 91.615 0.0077186 104500000 53320 44529 44314 40694 63214 50169 50267 38321 78422 TRUE FALSE 49982.79638 47825.97349 45365.14901 41738.27693 58249.42743 64651.97587 42729.93001 43105.4612 65332.86157 0.765048326 0.732035492 0.69436954 0.638855791 0.891579307 0.989578205 0.654034264 0.659782232 1 15.99552121 2.739878249 24.99824994 0.81690972 0.709452365 0.217908948 0.119694867 227.869294 4323178.175 0.037438157 0.037771916 549.386836 -2.739878249 -0.107457356 GS(ph)IDEVDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSIDEVDKR 9 1 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 1 GS(1)IDEVDKR 54.982 0.080533 1181700000 1961000 1375600 1521900 1557400 1467400 972690 1462900 1323800 1397600 TRUE FALSE 1838264.51 1477450.855 1558000.187 1597365.521 1352156.323 1253489.813 1243551.726 1489079.344 1164331.531 1.578815364 1.26892626 1.338107012 1.371916398 1.161315559 1.076574652 1.068039208 1.278913526 1 20.15107048 2.655731106 3.648209963 1.106763556 1.361798354 0.620007201 0.105618708 0.167549181 4.258521864 0.033325992 0.031591436 452.6172541 -2.655731106 0.255034798 GS(ph)IGLLLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSIGLLLGK 9 0 Q8IY63-2;Q8IY63 Q8IY63-2 AMOTL1 Angiomotin-like protein 1 1 GS(1)IGLLLGK;GS(1)IGLLLGK 123.51 0.00058281 132457000 465480 475930 481610 487580 542380 458670 697320 541620 742790 TRUE FALSE 436346.4377 511168.3524 493034.0166 500092.1283 499783.6627 591080.5831 592763.3396 609242.4493 618813.5504 0.705133941 0.826045829 0.796740822 0.808146699 0.80764822 0.955183646 0.957902973 0.984533142 1 19.23914526 2.231524448 3.692204617 0.972582061 0.793875625 0.882178378 0.033783117 0.072251732 2.129705039 0.01236897 0.009313558 170.4215252 -2.231524448 -0.178706436 GS(ph)KSPDLLMYQGPPDTAEIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSKSPDLLMYQGPPDTAEIIK 21 1 P82909 P82909 MRPS36 "28S ribosomal protein S36, mitochondrial" 1 GS(0.596)KS(0.404)PDLLMYQGPPDTAEIIK 153.84 2.39E-08 74056000 113110 70729 79118 80470 114210 61868 92329 79748 135740 TRUE FALSE 106030.647 75965.84875 80994.71632 82534.99644 105240.4073 79728.28726 78485.12359 89704.71335 113084.1171 0.937626342 0.671764088 0.716234237 0.729854895 0.930638272 0.705035237 0.694041972 0.793256521 1 16.78703679 0.96738824 21.44157391 1.000000003 0.751940795 0.356843804 0.09437241 643.2273373 422910.8197 0.085799255 0.021449814 9.276587381 -0.96738824 -0.248059208 GS(ph)LAS(ph)LDSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSLASLDSLR 10 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 2 GS(1)LAS(1)LDSLR 79.466 0.039356 50897000 93065 99002 102910 83822 111340 109640 100700 89291 109650 TRUE FALSE 87240.22778 106332.2111 105351.0738 85973.01443 102595.8055 141291.2881 85600.96985 100439.1779 91348.70663 0.955024225 1.16402536 1.153284788 0.941151962 1.123122694 1.546724561 0.937079166 1.099513957 1 16.47909668 GS(ph)LDESSLGFGYPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GSLDESSLGFGYPK 14 0 Q9BUZ4;Q2KJU6 Q9BUZ4 TRAF4 TNF receptor-associated factor 4 1 GS(0.892)LDES(0.101)S(0.007)LGFGYPK;GS(1)LDESSLGFGYPK;GS(0.668)LDES(0.315)S(0.016)LGFGYPK;GS(0.995)LDES(0.004)S(0.001)LGFGYPK;GS(1)LDESSLGFGYPK;GS(1)LDESSLGFGYPK 331.8 1.98E-68 1965502000 2449930 2145870 2258220 2152730 2420480 1871470 2642460 2006120 2561680 TRUE FALSE 2296593.255 2304752.448 2311786.045 2207972.696 2230385.265 2411733.008 2246247.654 2256588.498 2134119.059 1.076131739 1.079954953 1.083250738 1.034606147 1.04510817 1.130083628 1.052540928 1.057386414 1 21.02520923 0.786618786 1.758731697 1.000267755 1.07374048 0.43074894 0.025892403 0.700369021 3.739184034 0.023440811 0.006633289 6.118131196 -0.786618786 0.073472725 GS(ph)LPSGTTIEWLEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSLPSGTTIEWLEPK 15 0 Q9BXB4 Q9BXB4 OSBPL11 Oxysterol-binding protein-related protein 11 1 GS(1)LPSGTTIEWLEPK 153.09 2.85E-06 19529000 28925 21101 24087 25269 26849 19731 31193 21970 31118 TRUE FALSE 27114.63588 22663.34 24658.35501 25917.44532 24740.38784 25427.01939 26515.89923 24713.00286 25924.20477 1.045919677 0.874215437 0.951171125 0.999739261 0.954335458 0.980821577 1.022824016 0.95327911 1 14.66201211 3.380980457 5.038103903 0.98690238 0.936462336 0.023494328 0.046822559 0.32076376 13.33022116 0.012253779 0.016829136 2404.254606 -3.380980457 -0.050440044 GS(ph)LQDSVMNLTQSIVLLEQHTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSLQDSVMNLTQSIVLLEQHTR 22 0 Q5THJ4-2;Q5THJ4 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 GS(1)LQDSVMNLTQSIVLLEQHTR;GS(0.997)LQDS(0.003)VMNLTQSIVLLEQHTR 169.13 5.56E-12 179294000 126189 146196 165040 170935 147796 159344 191525 135520 154120 TRUE FALSE 118291.0557 157020.504 168954.8267 175321.4815 136188.6983 205344.0261 162807.6043 152439.9703 128396.3763 0.921295905 1.222935634 1.315884697 1.365470635 1.060689579 1.599297674 1.268007781 1.18726069 1 16.97024496 4.777739646 2.450521423 1.283510225 0.816889659 0.273943005 0.165723884 0.716823189 4.906660657 0.036528094 0.731803276 59943.16164 -4.777739646 -0.466620567 GS(ph)LSNAGDPEIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSLSNAGDPEIVK 13 0 O43847;O43847-2;F5H7V1 O43847 NRD1 Nardilysin 1 GS(1)LSNAGDPEIVK;GS(0.999)LS(0.001)NAGDPEIVK 207.4 5.68E-08 129569000 716260 598480 666410 639970 580680 629970 878990 650990 653200 TRUE FALSE 671430.5652 642792.0819 682217.5599 656392.7137 535075.7352 811832.1123 747193.6096 732267.5345 544176.7002 1.233846589 1.181219412 1.253669184 1.206212455 0.983275717 1.491853863 1.373071668 1.34564294 1 19.05371566 2.226136826 24.99999833 1.34359362 1.185706713 0.138537356 0.145015801 324.5665903 653110.434 0.04871119 0.036225185 168.3204277 -2.226136826 -0.157886907 GS(ph)LTLTISGESPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GSLTLTISGESPK 13 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(0.949)LT(0.051)LTISGESPK;GS(1)LTLTISGESPK;GS(0.951)LT(0.049)LTISGESPK 321.67 4.45E-51 882044000 1910970 1544890 1714200 1770340 1846840 1428530 2226120 1559410 2354810 TRUE FALSE 1791365.799 1659275.263 1754861.634 1815769.922 1701796.636 1840923.421 1892333.972 1754105.771 1961776.998 0.913134266 0.845802181 0.894526562 0.92557407 0.867477108 0.938395864 0.964601978 0.894141267 1 20.90372962 1.424597665 0.283256619 1.010609193 0.85921805 0.503358692 0.031726414 1.196057712 0.369691237 0.069577236 0.059816893 26.58261275 -1.424597665 -0.151391143 GS(ph)PDGSLQTGKPSAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GSPDGSLQTGKPSAPK 16 1 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 GS(0.997)PDGS(0.003)LQTGKPSAPK;GS(0.996)PDGS(0.004)LQTGKPSAPK;GS(0.934)PDGS(0.005)LQT(0.061)GKPSAPK;GS(0.997)PDGS(0.003)LQTGKPSAPK;GS(0.98)PDGS(0.02)LQTGKPSAPK;GS(0.989)PDGS(0.009)LQT(0.002)GKPSAPK 244.64 1.20E-19 4854700000 5983210 4113140 4742790 4575340 4668770 4144553 6206120 4389367 5022590 TRUE FALSE 5608731.566 4417681.165 4855291.219 4692750.97 4302103.637 5341018.17 5275569.921 4937389.132 4184287.282 1.34042698 1.055778647 1.160362779 1.121517395 1.028156851 1.276446336 1.260804903 1.179983304 1 21.99655048 2.220960821 24.99996507 1.210138473 1.13130313 0 0.112075114 540.2828155 767450.0694 0.037997354 0.028125272 166.3262597 -2.220960821 -0.078835343 GS(ph)PEEELPLPAFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 279.24 3.44E-33 1160310000 1528089 1431866 1490692 1451926 1591187 1227436 1633723 1402468 1769285 TRUE FALSE 1432448.637 1537882.848 1526051.918 1489184.879 1466221.592 1581776.847 1388761.403 1577569.217 1473979.903 0.971823723 1.043354014 1.035327493 1.010315592 0.994736487 1.073133252 0.942184761 1.070278647 1 20.49128542 GS(ph)PHYFS(ph)PFRPY ddPTM_SK-BR-3_Pertuzumab_2h_R1 19 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)PHY(0.008)FS(0.992)PFRPY;GS(0.999)PHY(0.189)FS(0.812)PFRPY;GS(0.894)PHY(0.107)FS(1)PFRPY;GS(1)PHY(0.006)FS(0.994)PFRPY;GS(1)PHYFS(1)PFRPY;GS(0.999)PHY(0.007)FS(0.994)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHY(0.015)FS(0.985)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHY(0.003)FS(0.997)PFRPY;GS(0.999)PHY(0.169)FS(0.832)PFRPY;GS(0.998)PHY(0.182)FS(0.82)PFRPY;GS(1)PHY(0.001)FS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY 181.51 1.03E-05 4893598300 1569386.2 1837493.1 1644643.5 1724377.2 1978207.4 1653711 1958719.6 1721815.8 2061156.4 TRUE FALSE 1471161.119 1973543.001 1683655.22 1768627.638 1822846.971 2131110.52 1665027.78 1936788.293 1717136.081 0.856752785 1.149322423 0.980501918 1.029986882 1.061562325 1.241084235 0.969653948 1.127917766 1 20.71157295 2.661844365 4.741403863 1.083656332 1.02437805 0.109224211 0.101451989 0.620039293 25.75348823 0.030954987 0.029279652 459.0334831 -2.661844365 -0.059278282 GS(ph)PHYFSPFRPY ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GSPHYFSPFRPY 12 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 GS(1)PHYFSPFRPY;GS(0.998)PHYFS(0.002)PFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY 196.38 5.45E-07 11810198000 2507772 4439113 2577761 2666955 4784485 2124230 2399051 3641617 3967591 TRUE FALSE 2350815.027 4767789.545 2638906.708 2735393.58 4408730.848 2737460.717 2039335.574 4096280.899 3305374.43 0.711209903 1.442435538 0.798368464 0.82755937 1.333806787 0.828184756 0.616975661 1.239278933 1 21.65638228 GS(ph)PLAEGPQAFFPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 213.49 3.64E-10 543465000 198180 233800 249788 328488 283043 207530 218331 170080 170166 TRUE FALSE 185776.2676 251110.7953 255713.0893 336917.5582 260813.9445 267440.542 185594.2934 191314.8624 141764.1953 1.310459719 1.771327342 1.803791774 2.376605443 1.83977304 1.886516842 1.30917608 1.349528786 1 17.11313368 1.666072711 3.679244297 1.214594917 1.844202054 0.538548073 0.267723587 0.150682404 4.796301874 0.153541154 0.069915133 46.35245182 -1.666072711 0.629607137 GS(ph)PLNAAPYGIESMSQDTEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GSPLNAAPYGIESMSQDTEVR 21 0 P18031;B4DSN5 P18031 PTPN1 Tyrosine-protein phosphatase non-receptor type 1;Tyrosine-protein phosphatase non-receptor type 1 GS(1)PLNAAPYGIESMSQDTEVR;GS(1)PLNAAPYGIESMSQDTEVR;GS(1)PLNAAPYGIESMSQDTEVR 227.7 2.04E-25 246357000 127149 112885 104238 116102 116431 109144 118756 100345 91445 TRUE FALSE 119190.9711 121243.1229 106710.5746 119081.3739 107286.9789 140652.101 100949.6403 112873.2941 76182.23874 1.564550649 1.591488054 1.400727733 1.56311203 1.408293858 1.846258437 1.325107295 1.481622173 1 16.21716706 0.502764744 1.109618344 1.000384741 1.53276716 0.587247579 0.139497049 1.216468702 2.033660446 0.120202055 0.037098268 3.18247312 -0.502764744 0.532382419 GS(ph)PLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSPLPK 6 0 H7C1J2;F2Z2A4;H7C1M5;Q9H147 H7C1J2;H7C1M5 DNTTIP1 Deoxynucleotidyltransferase terminal-interacting protein 1 1 GS(1)PLPK;GS(1)PLPK 85.212 0.057662 503640000 2235380 1572210 1915490 1687170 1765440 1727510 2362430 1851170 1614280 TRUE FALSE 2095471.556 1688618.064 1960926.327 1730465.639 1626789.464 2226214.093 2008205.553 2082292.649 1344846.239 1.558149545 1.255621658 1.458104481 1.286738653 1.209647182 1.655367006 1.49326034 1.548349981 1 20.3590098 2.249719789 24.99990983 1.475126199 1.351486477 0.001971765 0.197624805 515.9354318 1155849.942 0.060987582 0.050590764 177.7132416 -2.249719789 -0.123639722 GS(ph)PMMNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSPMMNR 7 0 O75376;O75376-2;A0A088AWL3;E7EVK1 O75376 NCOR1 Nuclear receptor corepressor 1 1 GS(1)PMMNR 52.937 0.095025 22734000 45746 56309 55499 45826 60944 53213 66366 56063 59158 TRUE FALSE 42882.83952 60478.17695 56815.46249 47001.97274 56157.70408 68574.72926 56415.03441 63062.58896 49284.14762 0.870114258 1.227132453 1.152814145 0.95369353 1.139467898 1.391415548 1.144689259 1.279571465 1 15.58883605 2.467653446 24.99619985 1.220958952 1.092213205 0.179965188 0.140444581 364.6574047 962733.3995 0.04541839 0.038045126 293.5306432 -2.467653446 -0.128745747 GS(ph)PNTASAEATLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSPNTASAEATLPR 14 0 Q6PJG6;Q6PJG6-3 Q6PJG6 BRAT1 BRCA1-associated ATM activator 1 1 GS(0.993)PNT(0.007)AS(0.001)AEATLPR 77.24 0.012435 0 25787 48283 35836 45287 65852 36060 38973 34028 103970 TRUE FALSE 24173.0377 51857.92356 36686.04684 46449.14109 60680.24955 46469.93661 33129.36046 38276.4707 86616.73533 0.279080453 0.598705589 0.423544558 0.536260584 0.70056034 0.536500671 0.382482211 0.441906181 1 16.40235818 -1.475392548 3.21773786 1.010358748 0.493379157 0.65392676 0.117124999 61960849.33 78220298.6 5750563.882 0.027406336 0.033466281 1.475392548 -0.516979591 GS(ph)PPFEMLSPSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSPPFEMLSPSFR 13 0 H3BMK1;P13631 H3BMK1 RARG Retinoic acid receptor gamma 1 GS(1)PPFEMLSPSFR;GS(1)PPFEMLSPSFR 102.73 0.0017479 52355000 20058.7 23176 20494.9 21103 30934 20915.1 21662 21977 31584 TRUE FALSE 18803.26177 24891.97515 20981.04871 21644.53871 28504.56842 26952.94984 18413.9842 24720.87683 26312.42636 0.714615274 0.946015955 0.797381755 0.822597597 1.083312046 1.024343003 0.699820836 0.939513388 1 14.68345667 4.749356322 23.65995793 0.894561974 0.714615055 0.211071793 0.115855278 1312.78298 2876984.431 0.027434085 0.381831574 56150.84836 -4.749356322 -0.179946918 GS(ph)PPRPPPPPPLLGTVS(ph)SPSSS(ph)PTHLWTGEVSAAPPPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSPPRPPPPPPLLGTVSSPSSSPTHLWTGEVSAAPPPAR 39 1 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 3 GS(1)PPRPPPPPPLLGT(0.318)VS(0.396)S(0.284)PS(0.172)S(0.155)S(0.583)PT(0.093)HLWT(0.001)GEVSAAPPPAR 117.01 1.59E-05 47745000 11039 15101 16673 15076 16778 14444 14757 12410 16179 TRUE FALSE 10348.0887 16219.09375 17068.49143 15462.87568 15460.32356 18613.74832 12544.32485 13959.41582 13478.62038 0.767740941 1.203320021 1.266338168 1.147215015 1.147025669 1.380983201 0.930683148 1.035670968 1 13.71838521 1.632192394 15.63837119 0.987575229 1.170061623 0.186725001 0.157607242 0.209840499 123.291536 0.06921839 0.037966105 42.87384113 -1.632192394 0.182486394 GS(ph)PQAISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSPQAISR 8 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 GS(1)PQAISR 75.416 0.040329 156540000 133050 163230 151460 156310 134970 155780 178010 131150 99775 TRUE FALSE 124722.638 175315.719 155052.7027 160321.1792 124370.0006 200751.1571 151319.0531 147524.3662 83121.90793 1.500478527 2.109139737 1.865365059 1.928747586 1.496236116 2.415141352 1.820447302 1.774795236 1 16.34294115 0.705428789 2.367516889 1.000330194 1.9083019 0.509193859 0.267131991 1.182253007 8.496452656 0.227104496 0.061130667 5.074915186 -0.705428789 0.907971706 GS(ph)PRPQAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSPRPQAPK 9 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 GS(1)PRPQAPK 100.55 0.012052 111520000 140080 112500 113010 105580 131890 95418 136330 111410 144730 TRUE FALSE 131312.6428 120829.6171 115690.6506 108289.3615 121531.8914 122963.6276 115888.5821 125319.7837 120573.628 1.089066034 1.002123093 0.959502111 0.898118132 1.007947537 1.01982191 0.961143693 1.039363133 1 16.87955487 -0.241702967 7.739034161 1.000003662 0.990410842 0 0.051390398 0 50412966.31 0.047166518 0.011439561 0.573187925 0.241702967 -0.00959282 GS(ph)PRY(ph)SPRHS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSPRYSPRHSR 11 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 3 GS(1)PRY(0.556)S(0.445)PRHS(0.999)R 98.062 0.010352 1353500000 346530 573020 358870 465340 662130 267880 397840 426850 933250 TRUE FALSE 324841.3059 615446.997 367382.5659 477281.4122 610128.9807 345212.6073 338187.5854 480143.1621 777484.546 0.417810627 0.791587434 0.472527162 0.61387897 0.784747406 0.444012179 0.434976601 0.61755975 1 19.56845447 -1.53962492 2.195613806 1.041512973 0.57432574 0.49470011 0.135881166 729363.408 562458.7398 177847.234 0.034803132 0.028865234 1.53962492 -0.467187232 GS(ph)PRYS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GSPRYSPR 8 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 2 GS(1)PRY(0.053)S(0.947)PR;GS(1)PRY(0.085)S(0.916)PR;GS(1)PRY(0.014)S(0.986)PR;GS(1)PRY(0.008)S(0.992)PR 87.184 0.008822 1944120000 1550260 2076910 1614350 1865540 2167540 1328030 1637710 1800610 2227030 TRUE FALSE 1453231.994 2230686.577 1652643.144 1913412.915 1997310.152 1711410.702 1392150.589 2025420.122 1855324.306 0.783276535 1.202316258 0.890757017 1.03130914 1.076528856 0.922432104 0.75035431 1.09167983 1 20.82323996 2.083353397 7.767223188 0.89910423 1.011526226 0 0.140282668 0.480072968 38.66408837 0.048908973 0.036049477 121.1583631 -2.083353397 0.112421995 GS(ph)PRYS(ph)PRHS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GSPRYSPRHSR 11 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 3 GS(0.999)PRY(0.212)S(0.789)PRHS(1)R;GS(1)PRY(0.054)S(0.947)PRHS(0.999)R;GS(0.996)PRY(0.139)S(0.873)PRHS(0.992)R 78.441 0.019726 984844000 526356 882510 645020 769300 1017450 454821 598030 587380 1494980 TRUE FALSE 493412.3175 947851.9587 660320.179 789041.5404 937543.5812 586120.4393 508360.9533 660715.686 1245458.18 0.396169318 0.761046797 0.530182538 0.633535154 0.752770022 0.470606279 0.408171837 0.530500098 1 20.24824515 -1.87456667 2.385998211 1.216980676 0.567646615 0.545036921 0.126074287 8408877.959 4669474.686 10318555.85 0.03344513 0.013348527 1.87456667 -0.649334062 GS(ph)PSPASVSSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GSPSPASVSSGR 12 0 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 GS(0.933)PS(0.067)PASVSSGR;GS(0.995)PS(0.005)PASVSSGR;GS(0.559)PS(0.433)PAS(0.008)VS(0.001)SGR 232.7 4.61E-13 1110590000 471590 551550 534550 572250 630510 536830 518620 459890 412330 TRUE FALSE 442074.0237 592387.3359 547229.7784 586934.9038 580992.288 691804.1063 440857.7456 517308.2788 343509.4592 1.286934062 1.724515352 1.593055922 1.708642624 1.691342909 2.013930294 1.283393321 1.505950608 1 18.3899903 0.943185484 1.233500223 1.015651286 1.655303008 0.47265221 0.207548041 0.428106009 1.321710252 0.178765144 0.055195263 8.773754608 -0.943185484 0.639651722 GS(ph)PSSHLLGADHGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSPSSHLLGADHGLR 15 0 F8VU11;Q6NWY9-2;Q6NWY9-3;Q6NWY9 F8VU11 PRPF40B Pre-mRNA-processing factor 40 homolog B 1 GS(0.994)PS(0.004)S(0.002)HLLGADHGLR 136.39 1.49E-05 333150000 141810 216360 209160 242790 245300 184580 210910 202200 251700 TRUE FALSE 132934.3652 232379.5195 214121.374 249020.4024 226035.1275 237865.2496 179286.0035 227445.1151 209689.644 0.633957704 1.108206944 1.021134711 1.187566528 1.077950838 1.134368131 0.855006476 1.084675003 1 17.67789609 4.743196152 24.99527047 1.052680287 0.633957535 0.688315299 0.089726719 294.2192519 1586405.544 0.021635843 0.17543606 55360.00903 -4.743196152 -0.418722753 GS(ph)PTGGAQLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSPTGGAQLLK 11 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 GS(0.922)PT(0.078)GGAQLLK 86.592 0.015058 414620000 407070 361580 379520 344720 414020 361030 405230 356280 449660 TRUE FALSE 381592.2153 388351.7594 388522.3936 353566.0988 381504.5393 465253.5002 344469.5235 400762.3423 374608.8411 1.018641776 1.036686049 1.037141549 0.943827428 1.018407729 1.241971489 0.919544564 1.069815494 1 18.51502542 4.751896771 19.08375507 1.032677449 1.01864156 0.002816814 0.086399617 1129.971658 1616087.33 0.018929551 0.262498432 56480.27087 -4.751896771 -0.014035888 GS(ph)PTSAYPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GSPTSAYPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(0.999)PT(0.001)SAYPER;GS(0.94)PT(0.06)SAYPER;GS(0.999)PTSAYPER;GS(0.998)PT(0.002)SAYPER;GS(0.659)PT(0.27)S(0.071)AYPER;GS(0.968)PT(0.014)S(0.018)AYPER;GS(0.886)PT(0.084)S(0.03)AYPER;GS(0.96)PT(0.037)S(0.003)AYPER 220.74 5.98E-09 10634940000 2954590 3283150 3136730 3056120 3438270 3027080 3123650 2966330 2901280 TRUE FALSE 2769667.486 3526237.842 3211134.717 3134545.213 3168242.144 3900948.855 2655287.681 3336682.83 2417037.625 1.14589341 1.458908958 1.328541469 1.296854125 1.310795542 1.613937994 1.098571099 1.380484439 1 21.2048085 0.263187191 0.753676898 0.994667013 1.349703329 0.322563782 0.146482517 3.020936821 2.21791376 0.175041018 0.046017966 1.833104364 -0.263187191 0.355036316 GS(ph)PTSAYPERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSPTSAYPERR 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(0.855)PT(0.126)S(0.019)AYPERR;GS(0.526)PT(0.447)S(0.027)AYPERR 149.69 2.10E-05 370960000 110490 155138 130811 140318 172159 111694 154912 115730 229906 TRUE FALSE 103574.6281 166624.5789 133913.8987 143918.7974 158638.3266 143938.2446 131684.3837 130179.1453 191533.2034 0.540765916 0.869951403 0.699168063 0.751403908 0.828254965 0.751505442 0.687527705 0.679668814 1 17.54723499 -1.460553928 3.349948019 1.004088526 0.737717593 0.47606717 0.089582322 3967025.741 2308782.864 113405.2523 0.019150702 0.034629488 1.460553928 -0.266370933 GS(ph)PTTGFIEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSPTTGFIEQK 11 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(0.684)PT(0.243)T(0.072)GFIEQK 121.69 0.00091844 0 81347 69129 80361 71858 77678 62765 78278 63484 84177 TRUE FALSE 76255.63648 74247.38309 82267.20087 73701.99794 71577.48322 80884.2366 66540.9406 71410.11715 70127.3149 1.08738851 1.058751261 1.173112089 1.05097419 1.02067908 1.153391324 0.948859096 1.018292476 1 16.09768887 1.72038446 10.92196001 0.988832466 1.092282429 0.497086511 0.048154043 0.083049874 29.83408612 0.022116638 0.012034753 52.52722524 -1.72038446 0.103449964 GS(ph)PVFLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GSPVFLPR 8 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 GS(1)PVFLPR;GS(1)PVFLPR;GS(1)PVFLPR;GS(1)PVFLPR;GS(1)PVFLPR;GS(1)PVFLPR;GS(1)PVFLPR;GS(1)PVFLPR 134.77 0.0009048 2225975000 1620840 1853890 1595840 1445900 1853800 1612970 1861970 1858350 1763550 TRUE FALSE 1519394.518 1991153.945 1633694.078 1483004.242 1708210.026 2078608.255 1582784.884 2090369.088 1469202.112 1.034163037 1.355262103 1.111960067 1.009394303 1.162678716 1.41478714 1.077309154 1.422792052 1 20.48660144 2.438046658 24.999688 1.232674781 1.155303353 0.072103503 0.15825861 516.3673456 330365.8856 0.051193063 0.042831218 274.1868724 -2.438046658 -0.077371428 GS(ph)PVPPVPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GSPVPPVPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(1)PVPPVPER;GS(1)PVPPVPER;GS(1)PVPPVPER 112.13 0.0017436 872580000 571470 613250 649300 603080 621220 585000 655100 558230 594940 TRUE FALSE 535702.7128 658655.6681 664701.7026 618556.0538 572431.8871 753880.0033 556873.8367 627926.2443 495640.6705 1.080828803 1.328897541 1.341095964 1.247992932 1.154933243 1.521021272 1.123543466 1.266898141 1 18.91893505 0.501521666 1.029948882 1.000349341 1.279514161 0.284058469 0.12632919 2.033507117 3.030579386 0.11022243 0.034582796 3.173376972 -0.501521666 0.279164821 GS(ph)QHSPTRPPVAAAAASLGSLPGPGAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSQHSPTRPPVAAAAASLGSLPGPGAAR 28 1 Q86VQ1 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 GS(0.333)QHS(0.333)PT(0.333)RPPVAAAAASLGSLPGPGAAR 67.832 0.0079655 361130000 203490 183330 202130 174150 219210 182550 191830 179130 278940 TRUE FALSE 190753.9241 196903.944 206924.6191 178618.9838 201994.1309 235249.2215 163066.8724 201494.7748 232383.112 0.820859668 0.847324671 0.890446028 0.768640123 0.86922896 1.012333554 0.701715675 0.867080112 1 17.8261457 0.967580171 23.91646561 1.000000004 0.844785209 0.269060333 0.080000487 3562.758956 2628290.029 0.072056141 0.018014035 9.280687964 -0.967580171 -0.155214795 GS(ph)QSFDDKIGAFYDDVFVSGPNAPVPQSGHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSQSFDDKIGAFYDDVFVSGPNAPVPQSGHPR 32 1 F5H212 F5H212 HIVEP1 1 GS(0.5)QS(0.5)FDDKIGAFYDDVFVSGPNAPVPQSGHPR 88.838 9.26E-05 92389000 75104 86468 84688 84520 92749 71681 100750 80037 88918 TRUE FALSE 70403.3747 92870.18069 86696.83935 86688.92629 85464.86767 92374.14106 85643.47282 90029.79563 74077.01137 0.950407872 1.253697726 1.170360922 1.1702541 1.153729964 1.247001456 1.156141038 1.215354048 1 16.17673827 -0.985278047 4.376067968 0.999994541 1.175218226 0.264943186 0.084548713 4680012.695 1069594.153 283.7931971 0.017294776 0.103447965 0.985278047 0.175223685 GS(ph)SGSVDETLFALPAASEPVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSSGSVDETLFALPAASEPVIR 22 0 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 GS(0.889)S(0.111)GSVDETLFALPAASEPVIR;GS(0.886)S(0.112)GS(0.002)VDETLFALPAASEPVIR 209.66 5.69E-23 33069000 35032 37998 34138 36416 35402 28560 41927 33591 36163 TRUE FALSE 32839.40965 40811.41146 34947.76948 37350.49621 32621.66972 36804.80837 35640.43558 37784.91029 30127.16168 1.090026668 1.354638445 1.160008694 1.239761535 1.082799305 1.221648716 1.18300011 1.254180885 1 14.87877714 -2.355717796 1.929073519 2.57E-05 1.205963047 0.376525966 0.079629279 1797776.592 175816.4481 7842722.222 0.018446023 0.004408412 2.355717796 1.205937377 GS(ph)SPLGPAGLGAEEPAAGPQLPSWLQPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSSPLGPAGLGAEEPAAGPQLPSWLQPER 29 0 O43482;H0YKL4 O43482 OIP5 Protein Mis18-beta;Protein yippee-like 1 GS(0.5)S(0.5)PLGPAGLGAEEPAAGPQLPSWLQPER;GS(0.5)S(0.5)PLGPAGLGAEEPAAGPQLPSWLQPER 186.3 4.35E-18 103325000 60661 65661 77636 63229 70296 81205 77878 56651 74817 TRUE FALSE 56864.33629 70522.60876 79477.56258 64851.56319 64775.23572 104647.5652 66200.91688 63724.00205 62329.55936 0.912317316 1.131447254 1.275118313 1.040462404 1.039237825 1.678939596 1.0621111 1.022372093 1 15.92762889 1.496935749 25 1.021491398 1.190200471 0.111424045 0.203421261 1.739072963 2188.909216 0.104314843 0.048292045 31.40044109 -1.496935749 0.168709073 GS(ph)SPQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSSPQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK 38 1 Q27J81-2;Q27J81 Q27J81-2 INF2 Inverted formin-2 1 GS(0.535)S(0.465)PQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK;GS(0.559)S(0.441)PQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK 399.05 2.10E-180 5397300000 202102 173644 199952 207321 223637 150814 244412 168644 229158 TRUE FALSE 189452.7966 186500.7824 204694.9559 212641.2079 206073.4521 194351.5535 207764.6896 189699.5746 190910.0494 0.992366809 0.976903956 1.07220629 1.113829306 1.079426949 1.018026836 1.088285767 0.99365945 1 17.54253352 4.002560622 3.619126063 1.058900637 0.985492643 0.324036401 0.039509069 0.22333262 6.203097688 0.009489809 0.021096785 10059.13466 -4.002560622 -0.073407994 GS(ph)SSSSPEHSASSDSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSSSSSPEHSASSDSTK 17 0 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 GS(0.21)S(0.21)S(0.21)S(0.184)S(0.184)PEHS(0.001)ASSDSTK 58.671 0.05961 26923000 18582 21489 19347 17503 24145 16721 25237 18733 25942 TRUE FALSE 17418.98579 23080.06792 19805.91998 17952.15661 22248.7491 21548.08126 21452.94614 21071.85629 21612.11261 0.805982557 1.067922805 0.916426836 0.830652558 1.029457393 0.997037247 0.992635312 0.975002151 1 14.39955248 GS(ph)VHS(ph)LDAGLLLPSGDPFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSVHSLDAGLLLPSGDPFSK 20 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 2 GS(1)VHS(1)LDAGLLLPSGDPFSK 66.386 0.012464 27732000 162480 118360 135620 120540 123700 113170 177260 126640 97465 TRUE FALSE 152310.6668 127123.4976 138836.9704 123633.2605 113985.101 145840.3418 150681.5086 142451.2828 81197.46185 1.875805762 1.565609252 1.709868354 1.522624694 1.403801281 1.796119466 1.85574161 1.754380981 1 16.30914701 -0.586307913 10.24504426 1.000004037 1.681617951 0.672718917 0.150240574 0 0 0.149021798 0.035124775 0.259234075 0.586307913 0.681613914 GS(ph)VSDEEMMELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSVSDEEMMELR 12 0 P13796;Q5TBN3;Q5TBN5 P13796 LCP1 Plastin-2 1 GS(1)VSDEEMMELR;GS(0.999)VS(0.001)DEEMMELR 252.04 5.65E-16 243180000 178783 282673 286513 364499 371356 218586 177165 156885 166038 TRUE FALSE 167593.2912 303602.403 293309.2237 373852.6614 342191.1977 281688.2298 150600.753 176472.4376 138325.1852 1.211589133 2.194845448 2.12043254 2.702708556 2.473817023 2.036420406 1.088744272 1.275779515 1 17.07770433 1.776338232 4.412579602 1.13215624 2.175840658 0.597488621 0.387029562 0.135770376 5.274518029 0.191354204 0.101002629 59.75004432 -1.776338232 1.043684417 GS(ph)WACSIFDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSWACSIFDLK 11 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GUE9;Q96N67-7;A0A0C4DGY6;A0A1B0GVW2 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 GS(1)WACSIFDLK 154.28 3.36E-05 80275000 162090 178610 159740 157320 225730 119080 172360 167250 150200 TRUE FALSE 151945.0762 191834.4702 163529.1082 161357.0975 208002.0764 153456.4629 146516.2181 188131.5307 125130.6497 1.214291436 1.533073398 1.306866932 1.289508989 1.662279201 1.226369905 1.170905917 1.503480811 1 16.93307568 -3.64918349 0.24018908 2.33E-11 1.404162183 0.314688059 0.161330758 96.22736849 1.72717578 47.380657 0.246717167 0.000224293 3.64918349 1.404162183 GS(ph)YGDLGGPIITTQVTIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GSYGDLGGPIITTQVTIPK 19 0 P61978;P61978-2;S4R359;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 GS(1)YGDLGGPIITTQVTIPK;GS(1)YGDLGGPIITTQVTIPK;GS(1)YGDLGGPIITTQVTIPK;GS(1)YGDLGGPIITTQVTIPK;GS(1)YGDLGGPIITTQVTIPK;GS(1)YGDLGGPIITTQVTIPK 304.52 3.10E-50 1243699000 753460 571658 597872 532601 628402 564610 842123 662185 577150 TRUE FALSE 706302.2836 613984.1531 612053.8062 546268.4434 579049.8418 727603.7413 715854.474 744860.2549 480819.9365 1.468953822 1.276952361 1.272937663 1.136118538 1.204296656 1.513256182 1.488820283 1.549145945 1 18.87513719 2.241200019 24.99785733 1.43802472 1.266525711 0.066807761 0.174629465 108.775129 1030224.867 0.056118409 0.044957857 174.2609266 -2.241200019 -0.171499009 GSAADSEESPAIEAIHLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GSAADSEESPAIEAIHLLR 19 0 P13716;P13716-2;B7ZBK6 P13716 ALAD Delta-aminolevulinic acid dehydratase 0 ;;; 237.59 3.18E-24 768880000 378276 443070 417078 435057 499868 419138 476855 400749 516984 FALSE TRUE 354600.3804 475875.3638 426971.2871 446221.2992 460610.3837 540136.3365 405355.0197 450783.3948 430696.0306 0.82331936 1.10489842 0.991351805 1.036046928 1.069455837 1.254101032 0.941162655 1.046639307 1 18.7163105 4.746365899 24.62960586 1.054540623 0.823319222 0.432632123 0.083539246 758.90648 2394663.455 0.01876217 0.202598431 55765.53836 -4.746365899 -0.2312214 GSALGDLAPSRPPS(ph)FSPCPAEDLFPGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSALGDLAPSRPPSFSPCPAEDLFPGHR 28 1 O75427 O75427 LRCH4 Leucine-rich repeat and calponin homology domain-containing protein 4 1 GSALGDLAPS(0.078)RPPS(0.461)FS(0.461)PCPAEDLFPGHR 47.006 0.069018 90763000 36090 43701 41975 48001 51008 49360 55344 42941 43180 TRUE FALSE 33831.19132 46936.66751 42970.66682 49232.78693 47002.03744 63609.43071 47045.68099 48302.27837 35972.97905 0.940461208 1.304775661 1.194526224 1.368604665 1.306592856 1.768255852 1.307806088 1.34273779 1 15.13462602 5.579239335 0.725426271 1.372851341 4.08E-13 0.242844073 0.195271314 10.97666959 1.78732057 0.066118701 16.32751545 379524.0788 -5.579239335 -1.372851341 GSALGDLAPSRPPSFS(ph)PCPAEDLFPGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSALGDLAPSRPPSFSPCPAEDLFPGHR 28 1 O75427 O75427 LRCH4 Leucine-rich repeat and calponin homology domain-containing protein 4 1 GSALGDLAPS(0.092)RPPS(0.045)FS(0.863)PCPAEDLFPGHR 123.41 2.63E-05 171080000 135590 128250 129940 127620 146520 151780 168680 122190 137830 TRUE FALSE 127103.6639 137745.7634 133022.2382 130894.9453 135012.9102 195596.4221 143387.9999 137445.6905 114825.2826 1.106930992 1.199611796 1.158475165 1.139948819 1.175811696 1.703426438 1.248749376 1.196998495 1 16.80908081 2.437161851 24.99996784 1.331271655 1.160244912 0.099305818 0.175716466 246.950999 154499.7561 0.055614767 0.046530708 273.6288283 -2.437161851 -0.171026744 GSASYS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GSASYSPPR 9 0 A0A087WTY1;P0DPB5 A0A087WTY1 POLR1D 1 GSAS(0.001)YS(0.999)PPR;GSASYS(1)PPR;GSASYS(1)PPR;GSAS(0.001)YS(0.999)PPR 117.71 0.0018039 1227680000 2394060 3068270 2810250 2723030 3154290 2292060 2932210 2618430 2759330 TRUE FALSE 2244220.058 3295447.903 2876910.457 2792907.56 2906564.787 2953740.514 2492552.332 2945346.749 2298779.997 0.976265698 1.43356385 1.251494471 1.214952089 1.264394501 1.284916572 1.084293554 1.281265172 1 21.13243697 0.315936797 0.451950592 0.979864312 1.267576654 0.198196309 0.126219672 3.535235409 1.178154617 0.277423288 0.069694025 2.069840101 -0.315936797 0.287712342 GSAVHQLSEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GSAVHQLSEELR 12 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;;;; 192.15 4.46E-06 25228500000 12588580 21693180 18409170 19374590 20807540 15853820 19707190 17845120 17212220 FALSE TRUE 11800683.25 23299365.62 18845844.21 19871774.78 19173399.74 20430560.47 16752279.81 20073122.51 14339389.29 0.822955777 1.624850623 1.314271049 1.385817372 1.33711411 1.424785956 1.168270104 1.399858956 1 23.77348025 -0.418666086 0.544243133 0.95293323 1.348471811 0.15314592 0.210175892 13.39916931 3.494780149 1.436595643 0.084165231 0.381358924 0.418666086 0.395538582 GSCFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 2683520000 1493530 2670910 2008100 1969590 2539650 1963600 2253810 2477600 3143190 FALSE TRUE 1400052.623 2868666.955 2055733.08 2020133.014 2340196.133 2530459.444 1915872.114 2786933.814 2618571.283 0.534662788 1.095508445 0.785059049 0.771463823 0.893691972 0.966351178 0.731647875 1.064295569 1 21.32034845 1.220815644 24.99801575 1.032147953 0.849656625 0.236300417 0.149629544 425.5272755 599440.3811 0.129313313 0.032613561 16.6270669 -1.220815644 -0.182491328 GSCLESGGHSNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSCLESGGHSNDR 13 0 A0A096LP25;Q6ZSR9 A0A096LP25 AAK1 Uncharacterized protein FLJ45252 0 ; 186.16 8.04E-06 699450000 194296 290960 268120 281450 314620 290740 308080 265630 337310 FALSE TRUE 182135.3602 312502.9811 274479.933 288672.4835 289911.0143 374671.9182 261886.2641 298794.4902 281010.7819 0.648143672 1.112067583 0.976759437 1.027264796 1.03167221 1.333300864 0.931943829 1.06328479 1 18.10026596 4.743206923 24.80390671 1.058001235 0.648143487 0.586082085 0.108645075 302.1905619 1613156.109 0.024013711 0.195428894 55361.38205 -4.743206923 -0.409857748 GSDALS(ph)ETSS(ph)VSHIEDLEK ddPTM_SK-BR-3_Pertuzumab_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 2 GS(0.001)DALS(0.548)ET(0.461)S(0.293)S(0.694)VS(0.004)HIEDLEK;GSDALS(0.761)ET(0.22)S(0.205)S(0.811)VS(0.003)HIEDLEK 170.56 6.32E-12 341910000 1096380 960430 940050 995160 956760 799560 1402710 906720 751670 TRUE FALSE 1027759.533 1031541.237 962348.4299 1020697.49 881619.929 1030379.992 1192386.658 1019925.988 626211.421 1.641234092 1.647273112 1.53677879 1.629956683 1.407863063 1.645418716 1.904127931 1.628724667 1 19.2562903 0.91745503 22.29934345 1 1.637797173 0.724286627 0.122123639 20688.33025 5588915.542 0.128453621 0.032113405 8.269038813 -0.91745503 0.637797173 GSDALS(ph)ETSSVSHIEDLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GSDALSETSSVSHIEDLEK 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 GSDALS(0.994)ET(0.005)SSVSHIEDLEK;GSDALS(0.985)ET(0.014)S(0.001)SVSHIEDLEK;GSDALS(0.348)ET(0.348)S(0.151)S(0.151)VS(0.002)HIEDLEK 384.56 8.57E-127 658757000 608660 531064 558866 599170 568267 497960 707440 472223 383376 TRUE FALSE 570565.0571 570384.5311 572122.5654 614545.7166 523637.6021 641712.9683 601365.9396 531181.081 319388.0689 1.78643197 1.785866745 1.791308509 1.924134858 1.639502702 2.009195179 1.882869143 1.66312124 1 18.28495089 0.843702075 3.772911166 1.00010746 1.829564305 0.876326263 0.097640286 0.290350306 6.531774098 0.088618561 0.022737908 6.977535831 -0.843702075 0.829456845 GSDALSET(ph)SS(ph)VSHIEDLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSDALSETSSVSHIEDLEK 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 2 GS(0.001)DALS(0.334)ET(0.503)S(0.325)S(0.832)VS(0.006)HIEDLEK 126.45 4.50E-05 184970000 322090 275000 273760 299310 283410 232610 411850 277270 214980 TRUE FALSE 301930.9618 295361.2861 280253.7165 306990.8013 261152.1218 299760.7309 350096.9159 311887.7698 179098.4492 1.685837947 1.649156023 1.564802586 1.714089668 1.458148426 1.673720416 1.954773576 1.741431996 1 17.45039332 0.113622692 17.80321867 0.99998106 1.681597511 0.740730434 0.126475336 0 0 0.134788798 0.031770024 1.299040502 -0.113622692 0.681616452 GSDALSETSS(ph)VSHIEDLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GSDALSETSSVSHIEDLEK 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 GSDALSET(0.002)S(0.02)S(0.978)VSHIEDLEK;GSDALSETS(0.019)S(0.98)VSHIEDLEK;GSDALS(0.002)ET(0.012)S(0.129)S(0.841)VS(0.016)HIEDLEK 327.19 2.34E-75 1077670000 1170740 1028990 1060040 1070330 1129310 854820 1559420 1096480 1128400 TRUE FALSE 1097465.473 1105177.49 1085184.649 1097796.48 1040618.548 1101592.657 1325599.448 1233377.942 940062.7503 1.167438528 1.175642254 1.154374694 1.167790639 1.106967112 1.171828856 1.410118045 1.312016609 1 19.84239754 1.962735324 23.46216304 1.287453643 1.156386535 0.06958719 0.106117755 345.8246015 217733.0059 0.038634853 0.024941775 91.77730989 -1.962735324 -0.131067107 GSDFDCELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GSDFDCELR 9 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;; 225.08 6.66E-07 17605710000 11068600 13572970 12015550 12189560 13974690 11541210 13860730 11558850 13002800 FALSE TRUE 10375836.08 14577926.82 12300564.52 12502364.75 12877174.22 14872969.97 11782442.21 13001997.87 10832548.68 0.957838861 1.345752256 1.13551897 1.154148033 1.188748336 1.372988981 1.087688831 1.200271354 1 23.36886938 0.373363141 1.153893263 1.000037948 1.195733554 0.174157294 0.119123729 4.535588415 6.914992995 0.103869208 0.031306991 2.362452804 -0.373363141 0.195695607 GSDHSASLEPGELAELVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GSDHSASLEPGELAELVR 18 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 0 ;;;;; 258.34 1.18E-30 6515980000 2792570 5652310 5089590 5480730 5416980 4940740 5795930 4820670 5089770 FALSE TRUE 2617788.029 6070812.914 5210317.478 5621374.811 4991552.242 6367051.432 4926884.103 5422541.261 4240254.506 0.61736578 1.43170956 1.228774705 1.32571637 1.177182227 1.501572942 1.161931223 1.278824479 1 22.01571943 4.74665306 24.97438341 1.280204819 0.617365449 0.672064319 0.141339965 525.9916964 1623244.841 0.02916465 0.326398304 55802.42343 -4.74665306 -0.662839371 GSDIDNPTLTVMDISPPSRS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSDIDNPTLTVMDISPPSRSPR 22 1 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 1 GSDIDNPTLTVMDISPPS(0.023)RS(0.977)PR 174.86 1.30E-12 122820000 50977 64337 54691 71041 71384 45435 53221 42678 40368 TRUE FALSE 47786.44057 69100.57842 55988.29635 72864.03233 65777.78859 58551.34692 45241.00513 48006.44225 33630.32001 1.420933269 2.054710701 1.664816045 2.166617276 1.955907305 1.741028539 1.345244562 1.427475035 1 15.03747489 1.583165567 1.440719699 1.136488065 1.872458559 0.607155832 0.224001266 0.242354315 0.97555306 0.177007596 0.062051545 38.29707161 -1.583165567 0.735970494 GSDRT(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSDRTPER 8 1 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 GSDRT(1)PER;GSDRT(1)PER 87.363 0.02486 288600000 235130 274020 251540 251790 265060 239520 268150 222180 269620 TRUE FALSE 220413.633 294308.7259 257506.6476 258251.3577 244243.2568 308665.5357 227943.3969 249919.6621 224618.6802 0.981279174 1.31025935 1.146416885 1.149732326 1.087368409 1.374175716 1.014801604 1.112639705 1 17.77711839 1.613578891 25 1.047785338 1.183713582 0.234399406 0.111892031 0.65941081 2873.856433 0.048207669 0.025808982 41.07512474 -1.613578891 0.135928244 GSDS(ph)DSEGDNPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSDSDSEGDNPEK 13 0 I3L4J1;Q9UN37 I3L4J1 VPS4A Vacuolar protein sorting-associated protein 4A 1 GSDS(0.996)DS(0.004)EGDNPEK;GSDS(1)DSEGDNPEK 361.48 1.15E-76 204570000 1349180 922500 1017480 979270 1067860 883520 1266220 929720 1073970 TRUE FALSE 1264737.232 990802.8599 1041615.106 1004399.726 983994.5831 1138577.881 1076362.066 1045797.589 894717.4689 1.413560455 1.10739188 1.164183267 1.122588707 1.099782465 1.272555774 1.203018946 1.168857908 1 19.77107266 4.745009004 24.92302185 1.15474184 1.413560576 0.578569317 0.072065267 530.7638142 2051345.602 0.016255325 0.155129659 55591.5783 -4.745009004 0.258818736 GSEEDPLLS(ph)PVETWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSEEDPLLSPVETWK 15 0 Q13017-2;Q13017;H0YK04;A0A0A0MSK6 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 1 GSEEDPLLS(0.795)PVET(0.205)WK 74.769 0.035474 17400000 50433 39224 46122 47124 54754 45476 55211 45645 66408 TRUE FALSE 47276.48856 42128.18577 47216.03562 48333.28162 50453.84171 58604.18296 46932.6231 51343.87873 55324.07579 0.85453734 0.761480154 0.853444634 0.873639206 0.911968993 1.059288965 0.848321864 0.928056691 1 15.75561982 3.114679068 1.534470317 0.942157114 0.805210489 0.494966769 0.059496222 0.30974905 1.504624017 0.020195928 0.026622895 1302.20413 -3.114679068 -0.136946625 GSEEDS(ph)PKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GSEEDSPKK 9 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 GSEEDS(1)PKK;GSEEDS(1)PKK;GSEEDS(1)PKK;GSEEDS(1)PKK 119.39 0.0005118 1703920000 9226300 2660000 5029620 4221840 3717780 3291750 5364760 3663300 3397970 TRUE FALSE 8648842.352 2856949.168 5148924.962 4330179.562 3425800.556 4242024.788 4560364.042 4120671.069 2830826.855 3.055235376 1.009227803 1.818876683 1.529651859 1.210176648 1.498510861 1.610965373 1.455642213 1 21.43279208 4.747998447 24.99126572 1.437919065 3.055236233 0.798912151 0.261383129 547.6626676 1450174.305 0.058086126 0.749163197 55975.56004 -4.747998447 1.617317169 GSEEDS(ph)PKKESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GSEEDSPKKESK 12 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 GSEEDS(1)PKKESK;GSEEDS(1)PKKESK;GSEEDS(1)PKKESK;GSEEDS(1)PKKESK;GSEEDS(1)PKKESK;GSEEDS(1)PKKESK;GSEEDS(1)PKKESK 157.58 3.87E-05 6125010000 11574050 3551120 5700010 5475150 5697430 3683590 7615650 4116800 7755210 TRUE FALSE 10849650.87 3814048.62 5835216.929 5615651.618 5249976.83 4746982.635 6473753.983 4630791.542 6460815.35 1.679300565 0.590335494 0.90317036 0.869186212 0.812587351 0.734734299 1.002002631 0.716750331 1 22.62328481 4.748381904 24.99796088 0.825451874 1.679301025 0.815954605 0.126965022 544.6898448 1386362.118 0.028689231 0.382571461 56025.00498 -4.748381904 0.853849151 GSEGYLAATYPTVGQTS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GSEGYLAATYPTVGQTSPR 19 0 H0Y465;P21359-2;P21359-6;P21359;J3QSG6 H0Y465 NF1 Neurofibromin;Neurofibromin truncated 1 GSEGYLAATYPTVGQT(0.078)S(0.922)PR;GSEGYLAATYPTVGQT(0.011)S(0.989)PR;GSEGYLAATYPTVGQT(0.002)S(0.998)PR;GSEGYLAATYPTVGQT(0.001)S(0.999)PR;GSEGYLAATYPTVGQT(0.001)S(0.999)PR;GSEGYLAATYPTVGQT(0.003)S(0.997)PR 474.21 1.93E-215 1649776000 2475580 3166670 3000730 3216750 3478510 2874310 3692000 3177950 2812900 TRUE FALSE 2320637.867 3401133.542 3071908.733 3299297.251 3205321.856 3704076.636 3138418.875 3574724.053 2343408.818 0.99028298 1.451361587 1.310871884 1.407905111 1.367803104 1.580636126 1.339253676 1.525437655 1 21.16017723 4.743994234 24.45788818 1.390586558 0.990282747 0.366769362 0.156476355 405.9645708 1827257.942 0.031471598 0.271922298 55461.83494 -4.743994234 -0.400303811 GSELSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSELSER 7 0 P49770;G3V5E5 P49770 EIF2B2 Translation initiation factor eIF-2B subunit beta 0 97.473 0.027851 310000000 341130 344270 407230 360620 450960 327860 422910 340540 470020 FALSE TRUE 319779.2822 369760.109 416889.6879 369874.1197 415543.4207 422507.8596 359498.5716 383057.1686 391570.6256 0.816657996 0.944299916 1.06466027 0.944591079 1.061222149 1.079008056 0.91809382 0.978258183 1 18.57891302 4.677828519 2.245660133 1.004364382 0.783049961 0.575151702 0.051868336 0.394899708 2.590912154 0.012955322 0.164718516 47624.29058 -4.677828519 -0.221314421 GSESATYVPVAPPTPAWQPEIKPEPAWHDQDET(ph)SSVKSDGAGGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSESATYVPVAPPTPAWQPEIKPEPAWHDQDETSSVKSDGAGGAR 45 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 GSESATYVPVAPPT(0.029)PAWQPEIKPEPAWHDQDET(0.243)S(0.243)S(0.243)VKS(0.243)DGAGGAR;GSESATYVPVAPPT(0.037)PAWQPEIKPEPAWHDQDET(0.241)S(0.241)S(0.241)VKS(0.241)DGAGGAR 58.131 0.010831 1529930000 362490 217188 260580 259500 305120 170080 355410 223129 377450 TRUE FALSE 339802.398 233268.8255 266761.0807 266159.2093 281157.106 219179.335 302119.57 250987.1468 314451.1566 1.080620601 0.741828486 0.848338685 0.846424647 0.89412012 0.697021876 0.960783777 0.798175302 1 18.26247642 -0.975488322 4.300329057 1.000004868 0.848902195 0.139595861 0.10820128 13765.08222 54453101.93 763.321713 0.022238272 0.105806337 0.975488322 -0.151102673 GSET(ph)PGAT(ph)PGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GSETPGATPGSK 12 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 GSET(1)PGAT(1)PGSK;GSET(1)PGAT(1)PGSK;GS(0.02)ET(0.98)PGAT(0.999)PGS(0.001)K 179.21 3.27E-05 812810000 1746900 1539300 1469440 1543040 1567270 946130 2233550 1501210 1890450 TRUE FALSE 1637564.647 1653271.374 1504295.811 1582637.019 1444182.936 1219262.372 1898649.913 1688639.373 1574921.682 1.039775289 1.04974831 0.955155947 1.00489887 0.916987145 0.774173335 1.205551955 1.072205299 1 20.58684866 1.69560618 16.64631753 1.103797274 0.967657905 0.321237719 0.091663351 0.199652013 70.73338231 0.041505011 0.022943793 49.61422138 -1.69560618 -0.136139369 GSET(ph)PGATPGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GSETPGATPGSK 12 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 GSET(1)PGATPGSK;GSET(1)PGATPGSK;GSET(1)PGATPGSK;GSET(1)PGATPGSK;GS(0.004)ET(0.992)PGAT(0.004)PGSK;GSET(0.998)PGAT(0.002)PGSK 293.43 3.85E-35 4086570000 11080570 9402340 9993230 9857860 9613660 7897450 12333340 8922890 9803610 TRUE FALSE 10387056.9 10098499.04 10230274.13 10110829.38 8858641.923 10177315.61 10484070.16 10036932.46 8167324.157 1.271782129 1.236451357 1.252585784 1.237961073 1.08464434 1.246101589 1.283660347 1.228913199 1 22.96143206 -1.122798096 3.264799337 0.999682602 1.233175545 0.638055267 0.054463384 3951973.256 6323879.929 13545.97228 0.013857031 0.075370588 1.122798096 0.233492943 GSEVGFHGAAPDISVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSEVGFHGAAPDISVK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 135.45 2.28E-05 394620000 888250 843180 893830 847610 1100080 757070 1056070 831660 1274860 FALSE TRUE 832656.0181 905609.9245 915032.0697 869361.1076 1013684.154 975623.819 897722.1076 935494.5817 1062077.63 0.783987907 0.852677713 0.861549141 0.818547612 0.954435086 0.918599348 0.845250933 0.880815635 1 20.01845779 -5 0.062486054 1.452979295 0.676891487 0.583162298 0.041238627 296.735335 1.350399243 20.61845601 3.202777126 1.00E-05 5 -0.776087808 GSFKDDPQLYQEIQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSFKDDPQLYQEIQER 16 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 0 ; 126.91 6.30E-05 614510000 636080 706850 702520 718410 866360 614290 924340 760070 888760 FALSE TRUE 596268.8882 759185.9095 719184.1062 736845.6169 798319.5803 791625.5508 785743.7982 854966.4126 740420.2144 0.805311466 1.025344655 0.971318843 0.995172204 1.078197981 1.069157129 1.061213326 1.15470431 1 19.49798476 6.206829985 0.503737275 1.06885118 9.20E-20 0.626052207 0.055864372 11.77521796 0.71617452 0.028206372 10.26089843 1610015.234 -6.206829985 -1.06885118 GSFMLGLETHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSFMLGLETHDR 12 0 Q92905 Q92905 COPS5 COP9 signalosome complex subunit 5 0 117.2 0.00075932 133450000 92549 120780 111870 113630 123040 109660 124120 104100 135560 FALSE TRUE 86756.52329 129722.6769 114523.6092 116545.9382 113376.9347 141317.0618 105509.3583 117097.1142 112934.1602 0.76820444 1.148657559 1.01407412 1.03198127 1.003920643 1.251322554 0.934255482 1.036861778 1 16.78512241 4.750560936 24.74246591 1.054449474 0.768204239 0.50648914 0.088218795 1319.427151 2720359.993 0.019369768 0.324509815 56306.81165 -4.750560936 -0.286245235 GSFS(ph)DTGLGDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GSFSDTGLGDGK 12 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 GSFS(0.998)DT(0.002)GLGDGK;GSFS(1)DTGLGDGK;GSFS(1)DTGLGDGK;GSFS(0.995)DT(0.005)GLGDGK;GSFS(0.841)DT(0.159)GLGDGK;GSFS(0.991)DT(0.009)GLGDGK 383.41 1.20E-102 5262570000 14119500 11001240 11856580 11897800 12900600 9678320 14816600 10721820 15430500 TRUE FALSE 13235785.7 11815783.26 12137823.68 12203117.69 11887438.91 12472293.87 12594988.38 12060462.83 12855049.87 1.029617608 0.919154992 0.944206658 0.949285909 0.924729117 0.970225242 0.979769702 0.938188724 1 23.61583187 2.086600383 14.30007871 0.971552738 0.947291 0.0550162 0.033469326 2.075649292 336.2254536 0.011516679 0.008505648 122.0675935 -2.086600383 -0.024261738 GSFSEQGINEFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GSFSEQGINEFLR 13 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;; 262.39 9.60E-24 778810000 497000 697290 500090 506080 597010 397716 580010 549000 603250 FALSE TRUE 465893.6572 748918.0771 511952.371 519066.8696 550123.2428 512530.1528 493042.885 617543.8585 502563.6779 0.927034081 1.490195392 1.018681599 1.032838011 1.094633908 1.019831268 0.981055549 1.228787287 1 18.93894688 3.731463491 24.7587745 1.047590017 1.250519964 0.140308796 0.151161622 211.4749924 1205783.556 0.0349136 0.060240192 5388.445453 -3.731463491 0.202929947 GSGDGEMGKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSGDGEMGKPR 11 1 O60547 O60547 GMDS "GDP-mannose 4,6 dehydratase" 0 59.542 0.090586 102350000 186710 131470 159270 149450 161700 80594 137650 122630 125530 FALSE TRUE 175024.1544 141204.1756 163047.9596 153285.14 149000.7343 103860.1795 117010.6604 137940.6254 104578.232 1.673619366 1.350225308 1.559100364 1.465746141 1.424777713 0.993133824 1.118881607 1.319018526 1 16.67422306 2.341760023 5.625204087 1.114589925 1.48798503 0.720770018 0.120108583 0.109397376 5.098249828 0.039344943 0.032605666 219.6645742 -2.341760023 0.373395105 GSGEKPVSAPGDDT(ph)ESLHS(ph)QGEEEFDMPQPPHGHVLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSGEKPVSAPGDDTESLHSQGEEEFDMPQPPHGHVLHR 38 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 GSGEKPVSAPGDDT(0.674)ES(0.326)LHS(1)QGEEEFDMPQPPHGHVLHR 111.24 7.08E-06 484380000 101470 99255 93647 111020 114620 78788 113920 99886 117260 TRUE FALSE 95119.17383 106603.9435 95868.35106 113868.9612 105618.2076 101532.8166 96838.75358 112356.987 97688.54847 0.973698303 1.091263461 0.981367341 1.165632645 1.081172862 1.03935229 0.991300977 1.150155149 1 16.57590183 4.755326463 23.48759953 1.056219102 0.973698151 0.157161139 0.063164977 2915.17362 4083765.235 0.014159323 0.367105087 56928.0703 -4.755326463 -0.082520951 GSGEKPVSAPGDDTES(ph)LHS(ph)QGEEEFDMPQPPHGHVLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GSGEKPVSAPGDDTESLHSQGEEEFDMPQPPHGHVLHR 38 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 GSGEKPVSAPGDDT(0.137)ES(0.863)LHS(1)QGEEEFDMPQPPHGHVLHR;GSGEKPVSAPGDDT(0.036)ES(0.964)LHS(1)QGEEEFDMPQPPHGHVLHR;GS(0.001)GEKPVS(0.003)APGDDT(0.126)ES(0.928)LHS(0.942)QGEEEFDMPQPPHGHVLHR;GSGEKPVSAPGDDT(0.17)ES(0.891)LHS(0.938)QGEEEFDMPQPPHGHVLHR;GSGEKPVSAPGDDT(0.067)ES(0.933)LHS(1)QGEEEFDMPQPPHGHVLHR;GS(0.003)GEKPVS(0.01)APGDDT(0.174)ES(0.865)LHS(0.949)QGEEEFDMPQPPHGHVLHR;GSGEKPVSAPGDDT(0.142)ES(0.857)LHS(1)QGEEEFDMPQPPHGHVLHR 175.09 5.09E-19 2376440000 827732 763798 800240 836916 865093 637251 997639 758129 1056100 TRUE FALSE 775925.7317 820350.3987 819222.0707 858392.6815 797152.0854 821215.0188 848052.2936 852783.0745 879830.0873 0.881904066 0.932396392 0.931113953 0.975634607 0.906029581 0.933379104 0.963881897 0.969258823 1 19.74686541 8 0.037482452 1.18710982 0.551765944 0.602260004 0.021928252 620.8437738 1.77483599 8.557535872 25.86902154 99999999.92 -8 -0.635343875 GSGEKPVSAPGDDTES(ph)LHSQGEEEFDMPQPPHGHVLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSGEKPVSAPGDDTESLHSQGEEEFDMPQPPHGHVLHR 38 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 GSGEKPVSAPGDDT(0.224)ES(0.6)LHS(0.175)QGEEEFDMPQPPHGHVLHR;GS(0.007)GEKPVS(0.012)APGDDT(0.059)ES(0.647)LHS(0.275)QGEEEFDMPQPPHGHVLHR 112.95 3.29E-06 401300000 249392 228750 265203 279520 285810 243726 273090 224420 301140 TRUE FALSE 233782.9999 245686.888 271493.7404 286692.9564 263363.6355 314085.7396 232142.6897 252439.331 250877.7886 0.931860095 0.979309047 1.082175277 1.142759421 1.049768642 1.251947179 0.925321811 1.006224315 1 17.93662522 4.27431764 2.046674716 1.067163219 0.935901154 0.221411023 0.087556143 0.562309259 4.295869395 0.022537485 0.096033369 18806.9184 -4.27431764 -0.131262065 GSGEKPVSAPGDDTESLHS(ph)QGEEEFDMPQPPHGHVLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSGEKPVSAPGDDTESLHSQGEEEFDMPQPPHGHVLHR 38 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 GS(0.002)GEKPVS(0.005)APGDDT(0.081)ES(0.404)LHS(0.508)QGEEEFDMPQPPHGHVLHR 106.97 5.85E-06 259950000 75223 70193 81552 82720 84478 68921 77967 66086 85148 TRUE FALSE 70514.92671 75390.16276 83486.45195 84842.73524 77843.43865 88817.37386 66276.57216 74336.98257 70936.24872 0.994060554 1.062787561 1.176922285 1.196042035 1.097371796 1.252073171 0.934311771 1.047940706 1 16.11423542 1.695715378 11.12217364 0.994602853 1.128772473 0.413852534 0.07609691 0.114708922 23.25158225 0.034798788 0.01893603 49.62669778 -1.695715378 0.134169621 GSGIFDEST(ph)PVQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSGIFDESTPVQTR 14 0 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BTV5;Q9H910-2;H3BU16;H3BMT0 A6NGP5;Q9H910-2 HN1L Hematological and neurological expressed 1-like protein 1 GSGIFDES(0.068)T(0.932)PVQTR 169.67 3.68E-05 67957000 259600 294170 289500 298610 344140 265200 367860 289030 359010 TRUE FALSE 243352.0994 315950.6529 296367.0767 306272.8381 317112.6326 341758.9348 312702.808 325116.0317 299088.9117 0.813644672 1.056377019 0.990899579 1.024019367 1.060262083 1.142666684 1.045517891 1.087021347 1 18.1902149 4.739422537 24.90450664 1.050524147 0.813644593 0.748696297 0.04318786 35.94453632 1038413.974 0.010513641 0.063583164 54881.06587 -4.739422537 -0.236879554 GSGNLEAIHIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSGNLEAIHIIK 12 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 113.65 0.001143 257420000 541270 504920 519140 529380 539270 481050 569580 511240 475770 FALSE TRUE 507392.8769 542304.8022 531454.246 542964.787 496917.9095 619921.3258 484176.7667 575069.4394 396360.9134 1.280128438 1.368209588 1.340834144 1.369874699 1.253700586 1.564032438 1.22155528 1.450873232 1 18.59645517 -1.786361033 8.242261555 0.993882504 1.352729682 0.563572016 0.098455021 0.009369365 0.000242853 0.080700125 0.018948976 0.016354564 1.786361033 0.358847178 GSGPQRPHS(ph)FSEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GSGPQRPHSFSEALR 15 1 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 GSGPQRPHS(0.919)FS(0.081)EALR;GSGPQRPHS(0.995)FS(0.005)EALR;GSGPQRPHS(0.993)FS(0.007)EALR 149.94 1.98E-06 2813580000 467260 619070 540850 564930 685170 521300 698360 608600 695830 TRUE FALSE 438015.0307 664906.5869 553679.2174 579427.0602 631359.512 671790.8474 593647.4013 684585.0497 579691.4778 0.755600259 1.147000797 0.955127406 0.999543865 1.089130229 1.158876529 1.024074743 1.180947238 1 19.14492575 2.745086233 5.81149952 1.092381271 0.992833631 0.231489084 0.109009885 0.286187869 40.03186309 0.031727029 0.032031623 556.0146486 -2.745086233 -0.09954764 GSGPQRPHSFS(ph)EALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSGPQRPHSFSEALR 15 1 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 GSGPQRPHS(0.211)FS(0.789)EALR;GSGPQRPHS(0.152)FS(0.848)EALR 164.99 8.78E-07 618210000 299260 364560 330620 337863 365930 259572 335849 324690 393810 TRUE FALSE 280529.8508 391552.4017 338462.4625 346533.1366 337191.3339 334506.2226 285491.5603 365228.2612 328080.5669 0.855063905 1.193464171 1.031644348 1.056244019 1.027769908 1.019585603 0.870187354 1.113227354 1 18.32369062 2.223959192 2.864874331 0.974767013 1.057892401 0 0.10122672 0.549931519 9.291526696 0.039499356 0.028330423 167.4785498 -2.223959192 0.083125388 GSGS(ph)PTHSLSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GSGSPTHSLSQK 12 0 I3L2R2;I3L419;I3L156;Q9BSJ6-2;Q9BSJ6 I3L2R2 FAM64A Protein FAM64A 1 GSGS(0.997)PT(0.003)HSLSQK;GSGS(1)PTHSLSQK;GSGS(0.999)PTHSLSQK;GS(0.151)GS(0.837)PT(0.011)HSLSQK;GSGS(0.995)PT(0.005)HSLSQK 301.07 1.69E-36 2115140000 2642250 2592410 2654900 2538740 2955160 2152600 3119250 2574080 3535430 TRUE FALSE 2476876.289 2784354.734 2717875.482 2603888.366 2723073.654 2774020.675 2651547.42 2895459.554 2945343.893 0.840946381 0.945341133 0.922770169 0.884069386 0.924535047 0.941832525 0.900250537 0.983063323 1 21.49000466 1.157950805 5.034325058 0.997874202 0.914235882 0.555097857 0.030660096 0.152581248 6.372947447 0.026621772 0.006828922 14.38635606 -1.157950805 -0.08363832 GSGS(ph)QSSVPSVDQFTGVGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GSGSQSSVPSVDQFTGVGIR 20 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 1 GS(0.024)GS(0.976)QSSVPSVDQFTGVGIR;GS(0.041)GS(0.959)QS(0.001)SVPSVDQFTGVGIR;GS(0.001)GS(0.852)QS(0.133)S(0.014)VPSVDQFTGVGIR;GS(0.005)GS(0.991)QS(0.004)SVPSVDQFTGVGIR 245.82 5.74E-30 401410000 460646 497420 508096 490221 537505 479634 565493 511925 625683 TRUE FALSE 431814.9891 534249.4944 520148.2771 502800.9008 495291.5255 618096.5496 480702.5744 575839.9631 521252.4652 0.828418124 1.024934231 0.997881663 0.964601483 0.950195075 1.18579113 0.922206812 1.104723721 1 18.99162278 GSGTAEVELKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GSGTAEVELKK 11 1 P14618;P14618-3;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;; 158.04 4.86E-05 5190570000 7165500 5177130 5893020 6090000 6693070 4602110 7652730 5069000 7873060 FALSE TRUE 6717024.146 5560450.092 6032805.217 6246279.71 6167423.281 5930664.448 6505274.181 5701875.808 6558995.424 1.024093434 0.84775941 0.919775793 0.952322621 0.940299982 0.904203169 0.991809532 0.86932151 1 22.64504344 -5 0.213549762 1.355124811 0.916976664 0.097525074 0.053636667 281.618952 2.813090893 42.92322407 0.102514997 1.00E-05 5 -0.438148147 GSGTAS(ph)DDEFENLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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;GSGTAS(1)DDEFENLR 370.76 4.18E-97 15275450000 3580870 4297500 3948380 4213010 4228190 3603480 4558440 3867180 3827580 TRUE FALSE 3356749.739 4615691.372 4042037.438 4321122.969 3896125.013 4643746.178 3874944.24 4350005.936 3188732.171 1.052691025 1.447500487 1.267600169 1.355122581 1.22184141 1.456298594 1.21519903 1.364180402 1 21.6045515 -1.876474392 2.444833082 0.846377901 1.307944795 0.375104913 0.120032671 8298512.411 4461184.075 7371181.461 0.025381843 0.013290019 1.876474392 0.461566894 GSHQIS(ph)LDNPDYQQDFFPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSHQISLDNPDYQQDFFPK 19 0 P00533;E9PFD7 P00533 EGFR Epidermal growth factor receptor;Receptor protein-tyrosine kinase 1 GS(0.027)HQIS(0.972)LDNPDYQQDFFPK 153.34 3.01E-08 212330000 123280 161620 116440 139780 159600 104970 166280 130440 121450 TRUE FALSE 115564.1249 173586.513 119202.0118 143366.9914 147065.6598 135273.135 141347.8577 146725.7211 101179.2104 1.14217263 1.715634193 1.178127516 1.416960963 1.453516579 1.336965711 1.397004949 1.450156811 1 16.62655336 -1.569219414 2.601956294 0.969890158 1.397815052 0.36952303 0.157951069 9407832.896 8678823.958 1956644.873 0.037767561 0.026963768 1.569219414 0.427924893 GSHS(ph)LDDLLDRPGNSTPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSHSLDDLLDRPGNSTPSR 19 1 Q6UXY1-2 Q6UXY1-2 1 GS(0.001)HS(0.999)LDDLLDRPGNSTPSR 135.64 4.46E-06 80578000 28539 29151 30376 33211 30666 28282 33388 24066 22574 TRUE FALSE 26752.79493 31309.37037 31096.53306 34063.25049 28257.61606 36446.55428 28381.77936 27070.69308 18806.25357 1.422547816 1.664838255 1.653520886 1.81127253 1.502564876 1.938001854 1.509167111 1.439451669 1 14.19892485 0.896266004 1.691838255 1.003649595 1.662398637 0.660979406 0.147502914 0.262236619 1.498292054 0.123406353 0.035362604 7.87528 -0.896266004 0.658749042 GSIDEVDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GSIDEVDKR 9 1 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ;;;;; 125.48 0.00080236 5105460000 4792560 4121480 4492520 4411540 4520460 3581460 5280490 3885650 4709620 FALSE TRUE 4492602.225 4426638.668 4599084.696 4524747.585 4165441.306 4615369.362 4488729.546 4370781.956 3923553.997 1.145033872 1.128221676 1.172173162 1.153226791 1.061650052 1.176323651 1.144046839 1.113985422 1 21.90372962 0.804823263 3.050849085 1.000029526 1.141631727 0.659776931 0.03140369 0.592718303 8.320092991 0.028282645 0.007391503 6.380037969 -0.804823263 0.141602201 GSIHDFPGFDPNQDAEALYTAMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSIHDFPGFDPNQDAEALYTAMK 23 0 E5RK69;P08133;E7EMC6;E5RFF0;E5RIU8;E5RJR0;E5RI05 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ; 244.16 1.97E-37 182805000 148109 175340 181516 139669 234123 111003 233252 225616 336600 FALSE TRUE 138839.1221 188322.356 185821.6452 143253.143 215735.924 143047.7641 198278.028 253784.6542 280419.2855 0.495112602 0.671574195 0.662656439 0.510853391 0.769333406 0.510120992 0.707077003 0.905018547 1 18.09722605 1.229098192 2.61243162 0.993333384 0.619879884 0.731985503 0.086693966 0.12677888 1.466202442 0.070385243 0.020022547 16.94720925 -1.229098192 -0.3734535 GSKPS(ph)PLSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GSKPSPLSVK 10 1 Q96S94;Q96S94-3;A0A0A0MSF3 Q96S94 CCNL2 Cyclin-L2 1 GSKPS(1)PLSVK;GSKPS(0.999)PLS(0.001)VK;GS(0.002)KPS(0.997)PLSVK;GSKPS(1)PLSVK 148.41 1.52E-05 8283810000 13537870 8809670 10689090 9569720 10870080 8731530 14024530 10120780 15601220 TRUE FALSE 12690558.88 9461947.133 10942640.26 9815295.217 10016387.76 11252180.97 11921681.92 11384381.66 12997275.59 0.976401461 0.727994653 0.841917999 0.755180972 0.770652872 0.865733814 0.917244682 0.875905229 1 23.63170591 1.935666037 2.757129395 0.923255737 0.803910441 0.332402926 0.073800508 0.291829759 4.039189214 0.035416315 0.019042169 86.23151917 -1.935666037 -0.119345296 GSKS(ph)PLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GSKSPLKR 8 2 K7EMM8;Q49A26-4;Q49A26-2;Q49A26-3;Q49A26;K7EPU6 K7EMM8 GLYR1 Putative oxidoreductase GLYR1 1 GS(0.149)KS(0.851)PLKR;GS(0.336)KS(0.664)PLKR;GS(0.005)KS(0.995)PLKR 85.958 0.0085435 3243150000 4111930 2476630 3020400 2539590 3100000 1969450 3751770 2575540 3362600 TRUE FALSE 3854571.641 2660002.262 3092045.314 2604760.179 2856538.505 2537998.244 3189226.918 2897101.838 2801360.337 1.375964238 0.949539489 1.10376565 0.929819754 1.019696919 0.905987784 1.138456512 1.034176789 1 21.41769614 4.745348744 24.74242029 1.017921888 1.375964428 0.713971744 0.072612906 370.6224576 1350861.539 0.016348546 0.160117948 55635.08347 -4.745348744 0.35804254 GSLAEAVGSPPPAAT(ph)PTPTPPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GSLAEAVGSPPPAATPTPTPPTR 23 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 GSLAEAVGSPPPAAT(0.997)PT(0.002)PTPPTR;GSLAEAVGSPPPAAT(0.99)PT(0.008)PT(0.002)PPTR;GSLAEAVGSPPPAAT(1)PTPTPPTR 235.92 4.65E-36 348076000 337134 419432 397326 388127 450608 391576 529860 483392 606470 TRUE FALSE 316033.3847 450487.1817 406750.7604 398086.9959 415219.0653 504617.6345 450412.412 543744.5553 505246.2391 0.625503686 0.89161907 0.805054504 0.787906896 0.821815252 0.998755845 0.891471083 1.076197136 1 18.94662715 2.069270375 1.008899771 1.015589934 0.793786871 0.601016007 0.081399649 0.403858276 0.762198364 0.059437566 0.029485906 117.2925358 -2.069270375 -0.221803063 GSLAPQDS(ph)DSEVSQNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.967)DS(0.033)EVSQNR;GSLAPQDS(0.826)DS(0.174)EVSQNR;GSLAPQDS(0.995)DS(0.005)EVSQNR 335.64 1.39E-57 377200000 588157 688091 581119 595323 666984 575437 764766 618743 560138 TRUE FALSE 551345.3033 739037.9736 594903.4171 610599.9961 614601.7671 741556.3205 650096.438 695994.4256 466647.3492 1.181503129 1.583718358 1.274845808 1.308482727 1.317058306 1.589115039 1.393121464 1.491478365 1 18.83197317 -0.861315715 5.082730519 0.999999344 1.402379982 0.464437656 0.13204623 8.98E-07 2.01E-07 0.116995765 0.027576122 0.137620866 0.861315715 0.402380638 GSLAS(ph)LDSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GSLASLDSLR 10 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 1 GSLAS(1)LDSLR;GSLAS(1)LDSLR;GSLAS(1)LDSLR 170.02 4.67E-06 269296000 367144 461340 398170 406610 548140 431170 507440 489740 657260 TRUE FALSE 344165.1124 495498.0936 407614.7804 417044.301 505091.2955 555641.7795 431354.0828 550885.1171 547559.0599 0.628544275 0.904921733 0.74442158 0.761642591 0.922441673 1.014761366 0.787776359 1.006074335 1 19.06265506 2.73218778 22.99640915 0.926930255 0.781478913 0.481419637 0.093746166 178.5008562 644118.1904 0.028395783 0.027430023 539.7439461 -2.73218778 -0.145451342 GSLDESS(ph)LGFGYPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSLDESSLGFGYPK 14 0 Q9BUZ4;Q2KJU6 Q9BUZ4 TRAF4 TNF receptor-associated factor 4 1 GS(0.011)LDES(0.263)S(0.726)LGFGYPK;GS(0.024)LDES(0.318)S(0.658)LGFGYPK 340.11 7.51E-69 1540180000 2116540 1831700 1964410 1743170 1915540 1704260 2302770 1717290 2194680 TRUE FALSE 1984069.54 1967320.974 2011006.733 1787902.693 1765101.215 2196252.196 1957491.016 1931697.437 1828373.73 1.085155353 1.07599499 1.099888223 0.977865009 0.965394102 1.20120529 1.070618651 1.056511262 1 20.80212956 GSLDYRPLTTADPIDEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSLDYRPLTTADPIDEHR 18 1 O00139-1;O00139-5;O00139;O00139-4;O00139-2;D6R9M0 O00139-1 KIF2A Kinesin-like protein KIF2A 0 ; 140.95 7.42E-08 672020000 863840 986370 987230 983680 1040930 961450 1087400 924800 1153970 FALSE TRUE 809773.7964 1059401.861 1010647.562 1008922.894 959179.5567 1239005.007 924354.4649 1040263.316 961364.9521 0.842316744 1.101976787 1.051263165 1.049469186 0.997726779 1.288797771 0.961502146 1.082069108 1 19.87472468 4.743778602 24.5328573 1.068832528 0.84231662 0.384029522 0.089228694 429.2799997 2018216.945 0.018943101 0.16147403 55434.30431 -4.743778602 -0.226515908 GSLESPATDVFGSTEEGEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSLESPATDVFGSTEEGEKR 20 1 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ; 191.14 2.52E-17 535650000 503240 392580 424850 418360 431220 307510 503410 347450 542580 FALSE TRUE 471743.1067 421647.0317 434927.6426 429095.8259 397353.7207 396283.145 427928.3439 390829.8973 452019.8928 1.043633509 0.932806362 0.962186951 0.94928527 0.879062464 0.876694038 0.946702459 0.864629862 1 18.78602674 7.999999999 0.736852577 0.918709514 19.56385035 0.402549121 0.043430591 341.3614281 1.543024943 0.014095898 10547.35342 99999999.71 -7.999999999 18.64514083 GSLEVLNLKDVEEGDEKFE ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSLEVLNLKDVEEGDEKFE 19 2 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 149.36 3.43E-07 29968000 79434 42563 61096 51034 65955 33509 69273 38553 104130 FALSE TRUE 74462.36773 45714.40881 62545.22597 52343.61884 60775.16035 43182.50433 58886.15675 43366.42692 86750.03029 0.858355524 0.526967064 0.72098218 0.603384445 0.700577973 0.497780856 0.678802723 0.499901 1 16.40457664 -1.311469896 4.845579622 1.00016964 0.631992876 0.509502281 0.112232009 0.000174965 2.49E-05 0.092440365 0.021778443 0.048812394 1.311469896 -0.368176764 GSLLFTAGPLEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSLLFTAGPLEEER 14 0 P53004 P53004 BLVRA Biliverdin reductase A 0 167.44 3.86E-07 0 39641 57044 48212 47733 49102 43816 53558 42855 55845 FALSE TRUE 37159.94057 61267.59711 49355.61141 48957.90959 45245.72699 56464.96791 45527.47511 48205.54109 46524.10873 0.798724394 1.316899964 1.060860976 1.052312681 0.972522166 1.213671136 0.978578125 1.036141098 1 15.50569089 3.508777685 20.0132625 1.046346728 1.123346811 0 0.142661375 109.5183623 69233.74094 0.034659452 0.053636126 3226.841885 -3.508777685 0.077000083 GSLLGDFLTAYHGLEKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSLLGDFLTAYHGLEKPR 18 1 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 0 84.653 0.0022705 32182000 67654 71677 67932 71608 72451 55150 76141 67830 73403 FALSE TRUE 63419.65691 76984.03966 69543.37912 73445.58251 66760.99071 71070.90971 64724.36391 76298.72481 61151.5651 1.037089677 1.258905468 1.137229751 1.201041746 1.091729878 1.16220917 1.058425304 1.247698643 1 15.9001018 2.73482516 24.92547412 1.114975889 1.171733643 0.059405408 0.08470965 723.8280786 4829846.443 0.024028376 0.023457038 543.0316718 -2.73482516 0.056757754 GSLS(ph)PVTKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSLSPVTKPR 10 1 F5H4N6;Q9Y3R0-3;Q9Y3R0-2;Q9Y3R0;F5H4P8;H0YFK8;F5H4Q7 F5H4N6 GRIP1 Glutamate receptor-interacting protein 1 1 GS(0.002)LS(0.998)PVTKPR;GS(0.23)LS(0.769)PVTKPR 137.4 5.59E-05 841760000 1017510 1004720 974910 965680 1158390 759320 1068320 1045050 1310070 TRUE FALSE 953825.8654 1079110.514 998035.3256 990460.9837 1067414.722 978523.3575 908135.3338 1175526.793 1091410.854 0.873938409 0.988729873 0.914445117 0.907505162 0.978013659 0.896567369 0.832074677 1.077070829 1 20.05776287 1.224332726 24.99999971 1.038535457 0.917557171 0.531701206 0.048821309 228.1448419 400864.6419 0.047171394 0.012019132 16.76226593 -1.224332726 -0.120978286 GSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVK 41 0 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 119.77 2.89E-07 24181000 42308 42603 43374 49111 51859 42818 57574 44701 54624 FALSE TRUE 39660.0178 45757.37045 44402.85176 50371.2714 47786.20333 55178.86151 48941.31319 50282.01825 45506.90152 0.87151655 1.005503977 0.97573885 1.106893015 1.050086948 1.212538311 1.075470128 1.104931704 1 15.47379774 3.748219948 0.839371867 1.105556307 0.909266605 0.50180805 0.064400209 0.620202717 0.779311892 0.024442256 0.087391229 5600.411614 -3.748219948 -0.196289702 GSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKR 42 1 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 196.62 1.20E-35 43949000 33903 36181 36323 36474 40399 26390 45879 36355 47335 FALSE TRUE 31781.07175 38859.87889 37184.59871 37409.98459 37226.2255 34008.36459 38999.86987 40894.00178 39434.4827 0.805920848 0.985428899 0.942946279 0.94866173 0.944001872 0.862401692 0.988978863 1.037011239 1 15.2671701 1.540219027 6.365990254 1.016708752 0.928378902 0.413444142 0.051838231 0.136600291 11.10194789 0.027065848 0.012407052 34.69117637 -1.540219027 -0.088329851 GSNEEQVNGS(ph)PLER ddPTM_SK-BR-3_Pertuzumab_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 315.05 7.80E-56 1452990000 1057980 1116870 1151170 1120980 1235640 1206400 1276680 1127610 1427260 TRUE FALSE 991762.9203 1199564.217 1178476.296 1149746.245 1138597.819 1554668.096 1085253.686 1268394.591 1189041.086 0.834086334 1.008850099 0.991114866 0.966952495 0.957576515 1.307497373 0.912713361 1.066737395 1 20.18136714 GSNMDFREPTEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GSNMDFREPTEEER 14 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;; 182.02 1.43E-06 3479600000 4332490 7226230 5256950 6093150 8090660 4163210 5749620 5161890 10305380 FALSE TRUE 4061327.185 7761267.588 5381647.337 6249510.545 7455252.2 5365061.143 4887517.858 5806363.329 8585345.503 0.473053435 0.904013424 0.62684109 0.72792767 0.868369502 0.624909171 0.5692861 0.676310968 1 23.03344476 -0.789224179 4.249181141 1.000002055 0.693377051 0.370805379 0.128897453 149098795.4 351784277.2 5358.77598 0.029943861 0.162470988 0.789224179 -0.306625004 GSNPLDGRDS(ph)PSAGGPVGQLEPIPIPAPAS(ph)PGTRPTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSNPLDGRDSPSAGGPVGQLEPIPIPAPASPGTRPTLK 38 2 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 2 GS(0.001)NPLDGRDS(0.966)PS(0.033)AGGPVGQLEPIPIPAPAS(0.977)PGT(0.019)RPT(0.004)LK 90.109 0.00027578 70754000 56979 57566 56404 58684 64938 44886 59264 47027 56370 TRUE FALSE 53412.7861 61828.24654 57741.92952 60189.93079 59838.03143 57843.85954 50377.91338 52898.42447 46961.48284 1.137374352 1.316573558 1.229559333 1.281687186 1.274193825 1.231729836 1.072749631 1.126421511 1 15.51919034 1.76976255 3.603863976 1.071131008 1.256319877 0.696198777 0.055516773 0.110723051 2.849378619 0.026830293 0.013499394 58.85217942 -1.76976255 0.185188869 GSNWVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSNWVPR 7 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C044 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 82.716 0.055217 177910000 162600 228510 188340 161090 214270 109190 210290 198430 214460 FALSE TRUE 152423.1562 245429.1182 192807.5137 165223.8421 197442.0985 140711.3804 178758.9667 223204.4223 178665.2405 0.85312149 1.373681402 1.079155146 0.924767692 1.105095193 0.787569983 1.000524591 1.249288455 1 17.44689946 3.491587168 5.858554101 0.99933438 1.171296968 0.035056947 0.172014997 0.274572085 32.86206805 0.043500196 0.064573697 3101.609857 -3.491587168 0.171962588 GSNYWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GSNYWR 6 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 130.05 0.037058 6264470000 5268860 7737850 5732900 5921090 7127690 4489920 6030590 5927540 5123800 FALSE TRUE 4939091.458 8310768.465 5868887.095 6073035.194 6567909.979 5786087.016 5126359.015 6667606.417 4268604.679 1.157073992 1.946952011 1.374895905 1.422721393 1.538655011 1.355498448 1.200944899 1.562010755 1 22.02533313 0.363759027 0.214814316 0.813532401 1.663581581 0.253001393 0.224309508 6.938283791 0.740420217 1.735722445 0.651836693 2.310782274 -0.363759027 0.85004918 GSPFPEVAESVQQELESYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSPFPEVAESVQQELESYR 19 0 Q8WVM8;Q8WVM8-2;Q8WVM8-3 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 103.85 0.0015551 0 8555.3 6973.4 8894.6 9979.2 7578.5 6715.2 7678.6 8813 9656.8 FALSE TRUE 8019.839045 7489.717792 9105.584112 10235.28317 6983.31518 8653.769228 6527.265215 9913.32245 8045.017695 0.99687028 0.930975925 1.131828973 1.272251169 0.86802981 1.075668141 0.811342555 1.23223128 1 12.97387988 GSPHSEGGKRS(ph)PEPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GSPHSEGGKRSPEPNK 16 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 GSPHSEGGKRS(1)PEPNK;GS(0.001)PHS(0.006)EGGKRS(0.993)PEPNK;GSPHSEGGKRS(1)PEPNK;GSPHSEGGKRS(1)PEPNK;GSPHSEGGKRS(1)PEPNK;GSPHSEGGKRS(1)PEPNK 161.22 4.44E-09 4737220000 3300050 2614050 2903330 3143450 3286110 1738730 3226320 2296940 3700710 TRUE FALSE 3093505.761 2807596.982 2972198.359 3224116.249 3028032.176 2240673.125 2742563.268 2583718.015 3083037.593 1.003395407 0.910659341 0.964048692 1.045759629 0.982158694 0.726774506 0.889565302 0.838042981 1 21.55592105 2.320843267 24.9999922 0.853582843 0.972180607 0.377306027 0.074082273 26.75438264 8126.259698 0.023628802 0.019769267 209.3356848 -2.320843267 0.118597764 GSPQQIDHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GSPQQIDHAK 10 0 A0A087WTP3;Q92945;M0R3J3 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;;;;; 155.98 1.18E-05 1931230000 2544720 2418510 2504370 2344530 2627660 2038730 2874010 2261590 3098770 FALSE TRUE 2385450.518 2597578.997 2563774.839 2404694.609 2421294.183 2627278.255 2443078.882 2543954.49 2581565.268 0.92403262 1.006203108 0.993108666 0.931487047 0.93791709 1.017707469 0.946355652 0.985431018 1 21.29981464 0.999776034 24.99893593 1.000000008 0.971048699 0.100141889 0.032287943 16.34164996 1824167.636 0.030035443 0.007508861 9.994844332 -0.999776034 -0.028951309 GSPSSYNSSSSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSPSSYNSSSSSPR 14 0 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 GSPSSYNSS(0.004)S(0.028)S(0.197)S(0.771)PR 103.14 0.0025101 0 98355 121250 120760 130190 124920 119850 119280 90632 120620 TRUE FALSE 92199.13612 130227.4762 123624.4842 133530.8958 115109.2871 154448.7494 101395.0713 101947.6047 100487.7428 0.917516242 1.295953841 1.230244414 1.328827697 1.14550575 1.536990932 1.009029246 1.014527761 1 16.61666001 1.604264263 25 1.008791931 1.248721657 0.340810007 0.15367686 0.359733126 2479.229378 0.070349964 0.034556565 40.20353701 -1.604264263 0.239929726 GSPSVAASS(ph)PPAIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSPSVAASSPPAIPK 15 0 Q92610;H0YM74 Q92610 ZNF592 Zinc finger protein 592 1 GSPSVAAS(0.142)S(0.858)PPAIPK 167.32 1.38E-06 107040000 271710 207110 252510 262710 241300 187030 261300 199530 239910 TRUE FALSE 254704.1561 222444.6399 258499.6564 269451.5834 222349.2714 241022.5248 222120.4908 224441.7597 199867.4711 1.274365232 1.112960697 1.293355317 1.348151262 1.112483538 1.205911715 1.111338876 1.122952917 1 17.60868416 1.31720246 0.780672807 1.008119852 1.231424899 0.523446088 0.072751556 0.487887821 0.661584657 0.067386257 0.026913036 20.75881027 -1.31720246 0.223305048 GSQNSSEHRPPASSTSEDVKAS(ph)PSSANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSQNSSEHRPPASSTSEDVKASPSSANK 28 2 O15014 O15014 ZNF609 Zinc finger protein 609 1 GSQNSSEHRPPAS(0.101)S(0.101)T(0.101)S(0.101)EDVKAS(0.576)PS(0.016)S(0.003)ANK 54.326 0.037857 69446000 47796 32836 49173 34959 33152 34504 66154 46239 56105 TRUE FALSE 44804.53368 35267.21161 50339.40678 35856.10713 30548.37565 44464.74467 56234.82184 52012.04093 46740.71305 0.95857617 0.754528746 1.076992701 0.767127945 0.653571023 0.951306511 1.203122892 1.11277808 1 15.51239212 1.958995176 6.843214802 1.117119589 0.854209881 0.479784131 0.124512413 0.194764013 25.67583103 0.05278535 0.033348483 90.99031646 -1.958995176 -0.262909708 GSQQYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 137.83 0.029234 1933654000 1534860 2190520 1703870 1654280 2259070 1308859 1590700 2012290 2247190 FALSE TRUE 1438795.852 2352708.38 1744286.601 1696731.625 2081651.755 1686705.346 1352189.302 2263528.836 1872119.472 0.76853848 1.256708461 0.931717568 0.90631589 1.111922496 0.900960313 0.722277249 1.209072856 1 20.83624107 2.201909281 24.96599906 0.910935926 1.018054724 0 0.176532799 455.1443145 310030.5299 0.062767342 0.046358012 159.1876169 -2.201909281 0.107118798 GSQS(ph)PKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GSQSPKR 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 GS(0.013)QS(0.987)PKR;GS(0.004)QS(0.996)PKR;GS(0.001)QS(0.999)PKR;GS(0.041)QS(0.959)PKR;GS(0.005)QS(0.995)PKR 85.533 0.012704 853745000 1447749 954035 1571470 1309745 1277185 991051 1513590 1085148 1556380 TRUE FALSE 1357136.974 1024672.744 1608746.011 1343355.274 1176880.042 1277151.335 1286641.231 1220631.117 1296610.123 1.046680841 0.79027051 1.240732261 1.036051817 0.90765915 0.984992568 0.992311573 0.94140181 1 20.30631331 2.787618684 24.96706222 0.968742279 1.02412305 0.074452571 0.109814488 1295.03484 659077.6801 0.034395818 0.036482177 613.2233503 -2.787618684 0.055380771 GSRPAS(ph)PAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.004)RPAS(0.996)PAAK;GS(0.227)RPAS(0.773)PAAK;GS(0.074)RPAS(0.926)PAAK 68.168 0.036813 674320000 756720 602030 720060 653310 732450 631020 903780 696780 935620 TRUE FALSE 709358.246 646604.9276 737140.1632 670075.0407 674926.3316 813185.2302 768266.5793 783774.5168 779458.9777 0.910064886 0.829556072 0.945707451 0.859666846 0.865890766 1.043268797 0.985640812 1.005536583 1 19.57211357 2.244271707 24.99959986 1.006362505 0.8826416 0.777012451 0.033646002 61.6324405 269789.2036 0.011372282 0.009269274 175.4978125 -2.244271707 -0.123720905 GSRPIDTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GSRPIDTSR 9 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C044 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;;;; 137.85 0.0001396 3469360000 1616220 2080160 1925100 1978020 2117790 1728930 2125170 1871280 2169320 FALSE TRUE 1515063.675 2234177.211 1970764.281 2028779.342 1951467.316 2228044.024 1806520.488 2104913.427 1807246.478 0.838327087 1.23623271 1.090478972 1.122580327 1.079801422 1.232839046 0.999598289 1.164707445 1 20.78536185 -0.963547374 5.043154551 0.99999937 1.106235194 0.056357428 0.115809826 7.16E-07 1.47E-07 0.097794596 0.023050271 0.10875585 0.963547374 0.106235824 GSRPPLILQSQSLPCS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSRPPLILQSQSLPCSSPR 19 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 GSRPPLILQSQSLPCS(0.5)S(0.5)PR 147.26 6.49E-08 355530000 122350 140420 127190 105730 127180 115730 162780 111900 127120 TRUE FALSE 114692.3319 150816.8429 130207.0069 108443.2108 117191.7958 149139.3723 138372.6502 125870.9613 105902.8508 1.082995699 1.424105601 1.229494824 1.023987645 1.106597178 1.408265889 1.306599862 1.188551209 1 16.6923819 3.491550465 23.50089147 1.201707683 1.290175499 0.016270294 0.147580075 575.0224 936533.4639 0.039447877 0.060078495 3101.347742 -3.491550465 0.088467816 GSRPPLILQSQSLPCSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSRPPLILQSQSLPCSSPR 19 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 GSRPPLILQSQSLPCS(0.155)S(0.845)PR 124.81 1.73E-05 467550000 104490 119860 101970 121320 122770 95206 143550 110740 120310 TRUE FALSE 97950.15742 128734.5591 104388.7766 124433.2766 113128.1394 122690.4267 122026.0102 124566.1328 100229.4838 0.977258924 1.284398106 1.041497697 1.241483762 1.128691231 1.224095167 1.217466214 1.242809282 1 16.61294743 3.210656111 24.99954789 1.18964254 1.131832237 0.065326378 0.106710578 598.8137607 536473.7279 0.027859603 0.033305173 1624.262103 -3.210656111 -0.057810303 GSS(ph)FQSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GSSFQSGR 8 0 Q96KP1 Q96KP1 EXOC2 Exocyst complex component 2 1 GSS(1)FQSGR;GS(0.001)S(0.999)FQSGR;GS(0.039)S(0.961)FQSGR;GS(0.001)S(0.999)FQSGR 188.49 0.00020635 2401100000 3348830 4210650 3908400 4005690 4136690 3422590 4259890 3699280 3572240 TRUE FALSE 3139232.708 4522410.907 4001109.094 4108482.787 3811811.054 4410636.172 3621159.041 4161143.251 2976010.066 1.054846132 1.519622181 1.344454153 1.380533901 1.280846156 1.482063593 1.216783196 1.39822889 1 21.50494798 -1.40683426 0.499027679 0.819714261 1.356819848 0.369676145 0.134116195 32.80633736 3.87830488 7.775350187 0.057084983 0.039189141 1.40683426 0.537105587 GSS(ph)GSPAHAESYSSGGGGQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSSGSPAHAESYSSGGGGQQK 21 0 P15408 P15408 FOSL2 Fos-related antigen 2 1 GS(0.094)S(0.554)GS(0.352)PAHAESYSSGGGGQQK 301.9 2.26E-55 380020000 294170 316600 306420 325840 357880 267450 387830 317350 359050 TRUE FALSE 275758.4248 340041.3934 313688.4271 334201.606 329773.5484 344658.4733 329678.4919 356971.8461 299122.2354 0.921892097 1.136797446 1.048696452 1.117274366 1.102470861 1.152232875 1.102153076 1.193397895 1 18.19037563 4.74395065 24.82956761 1.108300895 0.92189201 0.54391958 0.053143052 370.3199728 1705847.601 0.011194436 0.095316651 55456.2693 -4.74395065 -0.186408885 GSS(ph)LSGTDDGAQEVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GSSLSGTDDGAQEVVK 16 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 GS(0.001)S(0.999)LSGTDDGAQEVVK;GSS(0.993)LS(0.007)GTDDGAQEVVK;GS(0.041)S(0.959)LSGTDDGAQEVVK;GS(0.023)S(0.977)LSGTDDGAQEVVK 378.74 8.82E-88 695750000 3229900 2760880 3023320 3409390 2978040 2203350 3210570 2229790 2273470 TRUE FALSE 3027746.325 2965298.428 3095034.578 3496880.719 2744156.751 2839421.377 2729174.834 2508184.19 1894013.17 1.598587788 1.565616583 1.634114602 1.8462811 1.448858326 1.499156089 1.440948182 1.324269667 1 20.85301493 1.020655427 0.697490573 0.999404434 1.632255817 0.816866758 0.094261556 0.299698168 0.338884522 0.090175241 0.036009991 10.48710044 -1.020655427 0.632851383 GSS(ph)PGPRPVEGTPASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GSSPGPRPVEGTPASR 16 1 Q13112 Q13112 CHAF1B Chromatin assembly factor 1 subunit B 1 GS(0.114)S(0.886)PGPRPVEGTPASR;GS(0.137)S(0.863)PGPRPVEGTPASR;GS(0.039)S(0.961)PGPRPVEGTPASR;GS(0.045)S(0.955)PGPRPVEGTPASR;GS(0.027)S(0.973)PGPRPVEGTPASR;GS(0.047)S(0.949)PGPRPVEGT(0.004)PASR;GS(0.116)S(0.884)PGPRPVEGTPASR 127.37 4.03E-05 14846263000 6601620 7068400 7215530 6868190 7359120 7053030 7925520 6334850 7643630 TRUE FALSE 6188436.388 7591751.691 7386685.779 7044439.383 6781164.4 9089125.265 6737161.853 7125769.967 6367858.773 0.971823749 1.192198502 1.159995226 1.106249311 1.064904961 1.42734404 1.05799486 1.119021357 1 22.60237691 0.925009629 1.928670882 1.00305716 1.153940367 0.114230034 0.119318635 0.799778928 6.202503615 0.102750459 0.028811337 8.414137964 -0.925009629 0.150883206 GSS(ph)PLPTATTPKPLIPTEASIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GSSPLPTATTPKPLIPTEASIR 22 1 Q9BUK6-2;Q9BUK6;A0A3B3IUD2;Q9BUK6-7;Q9BUK6-3 Q9BUK6-2 MSTO1 Protein misato homolog 1 1 GS(0.054)S(0.946)PLPTATTPKPLIPTEASIR;GS(0.024)S(0.968)PLPT(0.006)AT(0.002)TPKPLIPTEASIR;GS(0.026)S(0.974)PLPTATTPKPLIPTEASIR 147.18 4.85E-08 587150000 528809 480608 571505 610151 597779 445671 618325 433858 587342 TRUE FALSE 495711.7886 516192.7164 585061.3685 625808.5076 550831.8487 574328.9828 525612.9065 488026.1263 489310.8258 1.013081588 1.054938271 1.195684497 1.278959047 1.125729944 1.17375082 1.074190226 0.997374472 1 18.90039168 1.449813633 3.025032562 0.998918261 1.141451186 0.393048835 0.072548783 0.272468036 4.648210498 0.058654288 0.019987838 28.17173747 -1.449813633 0.142532925 GSS(ph)PQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSSPQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK 38 1 Q27J81-2;Q27J81 Q27J81-2 INF2 Inverted formin-2 1 GS(0.145)S(0.855)PQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK 299.87 1.03E-92 1346200000 229540 181560 214490 201250 210070 184010 298250 209890 264160 TRUE FALSE 215173.5011 195002.8913 219577.8041 206414.4157 193571.9496 237130.6998 253530.1813 236095.2285 220069.9895 0.977750313 0.886094882 0.997763505 0.937948951 0.87959267 1.077524021 1.152043411 1.07281883 1 17.7476029 2.159302279 6.778104805 1.09666859 0.937831888 0.631312925 0.052081616 0.116867027 8.171523474 0.018314716 0.013515692 144.3119447 -2.159302279 -0.158836703 GSS(ph)PTPPCS(ph)PVQPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSSPTPPCSPVQPSK 15 0 E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3;H0YBY0 E7EPX0 STAU2 Double-stranded RNA-binding protein Staufen homolog 2 2 GS(0.004)S(0.89)PT(0.107)PPCS(1)PVQPSK 265.56 4.69E-25 274310000 820250 685840 762120 938090 1029300 657410 847840 564400 807870 TRUE FALSE 768912.0167 736620.3072 780197.8463 962162.9776 948462.93 847193.5948 720714.263 634866.5824 673031.278 1.142461044 1.094481537 1.1592297 1.42959623 1.409240493 1.258772991 1.070848097 0.943294321 1 19.36031403 1.571068827 3.542489915 0.978237359 1.233436292 0.539116094 0.10832802 0.187004028 5.372221348 0.080048921 0.032995584 37.24507277 -1.571068827 0.255198933 GSS(ph)PTPPCSPVQPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GSSPTPPCSPVQPSK 15 0 E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3;H0YBY0 E7EPX0 STAU2 Double-stranded RNA-binding protein Staufen homolog 2 1 GS(0.01)S(0.99)PTPPCSPVQPSK;GS(0.005)S(0.995)PTPPCSPVQPSK;GS(0.003)S(0.997)PT(0.001)PPCSPVQPSK;GS(0.017)S(0.982)PTPPCSPVQPSK 309.14 4.35E-56 977540000 2094720 1865080 2065340 1805980 1898390 1686760 2448680 1940610 2142740 TRUE FALSE 1963615.214 2003172.464 2114330.84 1852324.504 1749298.107 2173700.23 2081523.166 2182899.43 1785102.851 1.100001164 1.122160811 1.184430823 1.03765702 0.979942475 1.217689069 1.166052233 1.222842386 1 20.76757577 GSSAGFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSSAGFDR 8 0 G3V5Z7;P60900;G3V3I1;G3V295;G3V3U4;G3V4S5;G3V2S7 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ; 103.35 0.011141 2005400000 767250 1045110 917830 825260 1033220 853760 983600 869300 926710 FALSE TRUE 719229.1921 1122491.032 939601.361 846437.5688 952075.069 1100226.652 836118.3113 977834.0186 772036.1142 0.931600451 1.453935912 1.217043275 1.096370433 1.233200172 1.425097391 1.083004144 1.266565126 1 19.55830881 -0.214426867 0.656137336 0.984251194 1.238244753 0.136178599 0.156896977 12.20964033 4.921843675 0.639707763 0.054954821 0.610341826 0.214426867 0.253993559 GSSCFECTHYQSFLEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GSSCFECTHYQSFLEYR 17 0 P21964-2;P21964 P21964-2 COMT Catechol O-methyltransferase 0 ;;;; 230.93 6.28E-16 3573670000 1757873 2345462 2281324 1979346 2434357 2277671 2240100 2241214 2731887 FALSE TRUE 1647850.867 2519122.447 2335438.083 2030139.369 2243172.421 2935197.643 1904217.801 2521034.501 2275917.411 0.724038077 1.10686022 1.026152386 0.892009244 0.9856124 1.289676694 0.836681416 1.107700345 1 21.11801678 2.445257612 24.9991332 1.04462528 0.976191558 0.102177436 0.148884425 693.6487231 544209.6696 0.04912302 0.041099532 278.7774313 -2.445257612 -0.068433722 GSSDGRGS(ph)DS(ph)ESDLPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSSDGRGSDSESDLPHR 17 1 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3;D6RJ93;D6R8Y0;Q9UPQ0-7;Q6NVB9 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 2 GSSDGRGS(1)DS(0.999)ES(0.001)DLPHR;GSSDGRGS(1)DS(0.863)ES(0.137)DLPHR 143.91 3.02E-07 465680000 566870 693450 641530 670640 746060 562690 752260 620900 760960 TRUE FALSE 531390.6186 744793.7595 656747.3946 687849.7578 687467.4571 725129.4685 639465.5966 698420.7318 633950.86 0.838220519 1.174844624 1.035959466 1.085020624 1.084417579 1.143825988 1.008698997 1.101695377 1 19.27401149 4.752631678 24.99993739 1.081408243 0.838220354 0.656288161 0.054812345 1454.76365 2584621.974 0.01206326 0.252906757 56575.92692 -4.752631678 -0.243187888 GSSDGRGS(ph)DSESDLPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GSSDGRGSDSESDLPHR 17 1 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3;D6RJ93;D6R8Y0;Q9UPQ0-7;Q6NVB9 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 GSSDGRGS(0.999)DS(0.001)ESDLPHR;GS(0.001)SDGRGS(0.989)DS(0.01)ESDLPHR;GSSDGRGS(0.999)DS(0.001)ESDLPHR;GS(0.002)S(0.002)DGRGS(0.995)DS(0.001)ESDLPHR 198.1 8.78E-12 902940000 736600 917900 839390 831850 969280 765480 887590 800030 1095270 TRUE FALSE 690497.5209 985862.2711 859300.7272 853196.6793 893156.6587 986461.6495 754504.1195 899915.5066 912462.3613 0.756740826 1.080441575 0.941738272 0.935048628 0.978842193 1.081098455 0.826887937 0.986249455 1 19.79940552 -2.127854066 6.747895251 1.317849324 0.956401109 0.020262636 0.099799137 0.144160054 0.002731438 0.029190376 0.020640008 0.007449823 2.127854066 -0.361448215 GSSERGS(ph)PIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GSSERGSPIEK 11 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 GSSERGS(1)PIEK;GS(0.001)S(0.001)ERGS(0.997)PIEK;GS(0.011)S(0.011)ERGS(0.978)PIEK;GSSERGS(1)PIEK;GS(0.002)S(0.002)ERGS(0.995)PIEK;GS(0.005)S(0.005)ERGS(0.99)PIEK;GS(0.187)S(0.187)ERGS(0.626)PIEK 103.6 0.0016424 18275410000 16109960 13455180 14579957 14788640 15989070 11977541 16381880 12076842 18655040 TRUE FALSE 15101666.36 14451415.53 14925800.47 15168141.54 14733352.94 15435262.65 13925569.18 13584662.31 15541393.31 0.971706079 0.929866148 0.960390112 0.975983378 0.948007212 0.993171097 0.896030935 0.874095523 1 23.88961251 1.70539383 10.72255129 0.914272097 0.958904155 0.190685279 0.036359431 0.148100301 34.32503724 0.015465041 0.008398528 50.74506697 -1.70539383 0.044632058 GSSGCSEAGGAGHEEGRAS(ph)PLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GSSGCSEAGGAGHEEGRASPLRR 23 2 Q9C0C9 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 GSSGCSEAGGAGHEEGRAS(1)PLRR;GSSGCSEAGGAGHEEGRAS(1)PLRR;GSSGCSEAGGAGHEEGRAS(1)PLRR;GSSGCSEAGGAGHEEGRAS(1)PLRR 196.68 1.62E-24 1404733000 414314 490928 492502 547808 571456 470262 591150 479294 444495 TRUE FALSE 388382.8263 527276.8199 504184.38 561865.6807 526576.1509 606019.0053 502512.5455 539134.911 370305.913 1.048816162 1.423895221 1.361534781 1.517301402 1.422003086 1.636536129 1.357020042 1.45591764 1 18.49835806 -0.991519589 4.112049063 0.999971747 1.41144506 0.416782687 0.149468941 4003088.048 1460253.214 1012.374294 0.031861343 0.101971876 0.991519589 0.411473313 GSSGENNNPGS(ph)PTVSNFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSSGENNNPGSPTVSNFR 18 0 D6RD37;D6RAX8;D6RBL1;D6RDZ9;D6RCK9;Q99576-3;D6R8Z7;D6RDZ7 D6RD37 TSC22D3 1 GSSGENNNPGS(0.995)PT(0.005)VSNFR;GSSGENNNPGS(0.969)PT(0.031)VSNFR 456.64 7.02E-192 537350000 624950 856280 825520 1028020 1024460 592100 586070 462350 814890 TRUE FALSE 585835.4951 919679.8622 845101.7242 1054400.734 944003.0441 763029.6581 498194.2443 520075.4153 678879.5946 0.862944622 1.354702468 1.244847733 1.553148367 1.390530886 1.123954327 0.733847722 0.766079021 1 19.3727962 1.923175533 3.945057942 0.815134599 1.297239564 0.541972292 0.186856259 0.158559381 4.415352876 0.084720152 0.048687568 83.7867863 -1.923175533 0.482104964 GSSGGSGAKPSDAASEAARPATSTLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GSSGGSGAKPSDAASEAARPATSTLNR 27 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C044 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;; 190.28 3.52E-18 2669590000 607151 596530 667760 652220 687450 556276 755900 585020 892360 FALSE TRUE 569150.5027 640697.7019 683599.5825 668957.0694 633460.45 716863.8508 642559.8124 658061.0348 743419.3511 0.765584729 0.86182543 0.919534286 0.899838117 0.852090343 0.964279245 0.864330221 0.885181471 1 19.50381672 7.999999155 0.022673813 1.559885285 7.10E-09 0.515508406 0.044616269 2274.71444 3.969542202 97.20834441 190.2501363 99999805.43 -7.999999155 -1.559885278 GSSGPQPAKPCSGATPTPLLLVGDRS(ph)PVPSPGSS(ph)SPQLQVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSSGPQPAKPCSGATPTPLLLVGDRSPVPSPGSSSPQLQVK 41 2 Q8N3F8 Q8N3F8 MICALL1 MICAL-like protein 1 2 GSSGPQPAKPCSGATPTPLLLVGDRS(1)PVPSPGS(0.139)S(0.601)S(0.26)PQLQVK 239.79 8.66E-55 98980000 123000 88495 105950 99331 112790 89390 141420 112880 155810 TRUE FALSE 115301.6496 95047.26188 108463.184 101880.0016 103931.9284 115195.4419 120215.3839 126973.3165 129804.3044 0.888272928 0.732235054 0.835590041 0.78487383 0.800681679 0.887454714 0.926127869 0.978190338 1 16.9859787 1.774650852 1.239597841 0.994904729 0.798050239 0.765318622 0.041044921 0.185070265 0.532541223 0.030569169 0.012179485 59.51834574 -1.774650852 -0.19685449 GSSGPTQINQVVSHPNQPLTITAHDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSSGPTQINQVVSHPNQPLTITAHDDR 27 0 F5GYK2;Q9NRL3;Q9NRL3-3;M0R317 F5GYK2 STRN4 Striatin-4 0 ; 332.9 1.58E-95 719930000 77042 105171 96984 104155 108522 98181 117467 77187 107842 FALSE TRUE 72220.07874 112957.9703 99284.50628 106827.7936 99999.11988 126524.2609 99853.91386 86823.96686 89842.47351 0.803852297 1.257289185 1.105095423 1.189056684 1.113049496 1.408290043 1.111433267 0.966402231 1 16.45511003 1.330197993 5.379767441 0.984930334 1.162648567 0.153553292 0.151257347 0.307002301 13.12811219 0.097782174 0.034196995 21.38937002 -1.330197993 0.177718233 GSSGS(ph)PAHAESYSSGGGGQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSSGSPAHAESYSSGGGGQQK 21 0 P15408 P15408 FOSL2 Fos-related antigen 2 1 GS(0.02)S(0.131)GS(0.849)PAHAESYSSGGGGQQK 301.19 2.54E-55 301080000 180650 182210 206430 197650 240320 169210 261210 213430 235230 TRUE FALSE 169343.439 195701.018 211326.6171 202722.0336 221446.2366 218058.1801 222043.9855 240077.2053 195968.5934 0.864135605 0.998634601 1.078369822 1.03446185 1.130008808 1.112720035 1.133059036 1.225080005 1 17.58026294 6.088399758 0.501423331 1.126408671 2.52E-16 0.638569979 0.059054232 8.977169244 0.602500725 0.028771708 7.987980242 1225743.948 -6.088399758 -1.126408671 GSSMGVRNS(ph)PQALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSSMGVRNSPQALR 14 1 Q7L7X3-3;Q7L7X3 Q7L7X3-3 TAOK1 Serine/threonine-protein kinase TAO1 1 GSSMGVRNS(1)PQALR 124.43 5.88E-05 340450000 55461 102570 73307 80479 121950 64378 87254 70601 179230 TRUE FALSE 51989.79501 110164.3895 75045.87666 82544.22739 112372.5389 82962.88351 74171.07273 79415.69026 149315.3551 0.348187867 0.737796789 0.50259986 0.552818076 0.752585284 0.555621915 0.496741093 0.531865528 1 17.18800301 -1.608219551 3.253168835 1.022828233 0.570459115 0.582850796 0.116731594 46990451.5 51034073.05 9062538.939 0.025973545 0.02464793 1.608219551 -0.452369118 GSSPS(ph)HSATSVHTSV ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GSSPSHSATSVHTSV 15 0 F8WA39;Q13613 F8WA39 MTMR1 Myotubularin-related protein 1 1 GSS(0.012)PS(0.987)HS(0.001)ATSVHTSV;GSS(0.011)PS(0.759)HS(0.198)AT(0.032)SVHTSV;GSS(0.082)PS(0.916)HS(0.002)ATSVHTSV 201.38 1.85E-11 754270000 167113 518470 443580 502680 532730 464900 529540 490500 454190 TRUE FALSE 156653.6956 556858.0583 454101.9271 515579.6198 490891.5347 599109.083 450140.393 551740.0047 378382.7548 0.41400855 1.471679275 1.200112641 1.362587521 1.297341193 1.583341406 1.189642993 1.458153147 1 18.52948681 4.743952227 24.98918027 1.330627044 0.414008159 0.745964553 0.166124925 254.8784368 1181281.245 0.033980548 0.293864963 55456.47069 -4.743952227 -0.916618885 GSSPT(ph)PPCS(ph)PVQPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSSPTPPCSPVQPSK 15 0 E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3;H0YBY0 E7EPX0 STAU2 Double-stranded RNA-binding protein Staufen homolog 2 2 GSS(0.236)PT(0.764)PPCS(1)PVQPSK;GSS(0.001)PT(0.999)PPCS(1)PVQPSK 226.06 4.86E-12 366140000 483100 395760 442540 532390 598740 363550 459670 298203 464310 TRUE FALSE 452863.6334 425062.4822 453037.2578 546052.0287 551717.3756 468500.9833 390746.7509 335434.301 386813.6614 1.170753979 1.098881773 1.171202837 1.411666865 1.426313056 1.211180033 1.010167918 0.867172839 1 18.56127922 1.662331707 3.473624208 0.935969824 1.236400257 0.621066238 0.107420625 0.152699583 4.336749499 0.072480434 0.032468115 45.95488744 -1.662331707 0.300430433 GSSSNEPSSDSLSS(ph)PTLLAL ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSSSNEPSSDSLSSPTLLAL 20 0 G3V2V7;P01100-2;P01100-3;P01100 G3V2V7 FOS Proto-oncogene c-Fos 1 GSSSNEPS(0.001)S(0.001)DS(0.001)LS(0.055)S(0.796)PT(0.147)LLAL 57.434 0.086799 10331000 31153 42061 49375 54103 29376 17651 20136 16548 27008 TRUE FALSE 29203.18934 45175.2402 50546.19832 55491.37458 27068.92746 22746.55716 17116.79373 18614.05423 22500.19032 1.297908548 2.00777147 2.246478701 2.466262453 1.203053266 1.010949545 0.760739953 0.827284301 1 14.45764958 2.56136098 4.363457241 0.891320925 2.042204155 0.747735095 0.304808018 0.106384697 3.643012768 0.102360455 0.094546169 364.2176432 -2.56136098 1.15088323 GSSSS(ph)SPEHSASSDSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSSSSSPEHSASSDSTK 17 0 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 GSSS(0.002)S(0.99)S(0.007)PEHSASSDSTK 278.33 8.36E-36 241870000 471830 413030 474850 407300 514740 448660 701160 566860 647000 TRUE FALSE 442299.0025 443611.171 486113.6662 417752.0076 474314.3968 578180.8586 596027.5673 637633.7188 539011.5202 0.820574303 0.823008701 0.901861367 0.775033542 0.879970796 1.072668833 1.105778902 1.182968628 1 19.03995658 2.246490566 3.545492719 1.104351055 0.839518075 0.844991625 0.053596451 0.077676743 2.082524039 0.019190245 0.014549779 176.3967447 -2.246490566 -0.26483298 GSSSSS(ph)PEHSASSDSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSSSSSPEHSASSDSTK 17 0 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 GS(0.003)S(0.002)S(0.017)S(0.138)S(0.839)PEHSASSDSTK;GSSS(0.001)S(0.005)S(0.994)PEHSASSDSTK 192.6 1.14E-10 1594600000 1923800 1692840 1910570 1710480 2035600 1879860 2958700 2286500 2527900 TRUE FALSE 1803392.792 1818179.635 1955889.623 1754373.813 1875732.187 2422545.065 2515070.402 2571974.558 2105977.159 0.856321154 0.863342523 0.928732591 0.833045033 0.890670717 1.150318775 1.194253409 1.221273719 1 21.00605836 2.238956284 5.721369141 1.163061465 0.877311089 0.812547645 0.063416644 0.056827564 6.299174941 0.020914111 0.01631996 173.3629482 -2.238956284 -0.285750376 GSTAPVGGGAFPTIVEREPWDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GSTAPVGGGAFPTIVEREPWDGR 23 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;; 263.31 6.47E-44 1243870000 875030 1287980 986110 1052710 1224500 607720 1021620 937340 1593760 FALSE TRUE 820263.4343 1383343.379 1009500.995 1079724.321 1128332.709 783158.8985 868437.5653 1054368.962 1327751.16 0.617784009 1.041869456 0.760308878 0.813197799 0.849807361 0.58983861 0.654066508 0.79410133 1 20.34055336 2.306326615 24.99978456 0.717432143 0.839483917 0 0.150257255 100.4605438 37059.80916 0.048096782 0.04024064 202.4541181 -2.306326615 0.122051774 GSTDDKGPVAGWINALEAYQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSTDDKGPVAGWINALEAYQK 21 1 Q96KP4;J3QKT2;J3QRH4;A0A087WYZ1;J3KSV5;A0A087WVS2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 229.97 1.00E-25 660320000 1702490 1230760 1435650 1349180 1597180 1092970 1822530 1369510 1784230 FALSE TRUE 1595934.19 1321886.751 1469704.296 1383802.243 1471743.926 1408492.696 1549258.546 1540496.338 1486430.486 1.073668903 0.889302771 0.988747412 0.930956581 0.990119578 0.947567148 1.042267742 1.036372943 1 20.50342057 1.732947744 8.491654302 1.028626728 0.962176847 0.215096415 0.048881349 0.129118291 31.1828186 0.021212533 0.011339336 54.06892616 -1.732947744 -0.06644988 GSTDNLMDDIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GSTDNLMDDIER 12 0 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;; 322.27 1.72E-46 2225240000 1580150 2010890 1882280 1815870 2016810 1576060 1899250 1723810 1868660 FALSE TRUE 1481251.232 2159778.388 1926928.57 1862468.298 1858417.878 2031042.937 1614475.094 1939031.473 1556768.574 0.951490965 1.387347114 1.237774582 1.196368124 1.193766311 1.304653094 1.037068143 1.245548957 1 20.57012306 0.730717883 0.536286087 0.997594588 1.236984218 0.145283003 0.12750383 1.923938303 1.182472384 0.146972712 0.058214803 5.379202365 -0.730717883 0.23938963 GSTFEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSTFEER 7 0 P05019-4 P05019-4 0 100.82 0.022129 466430000 1834600 1577900 2044000 2120400 1641200 1887400 2138700 1418300 1499600 FALSE TRUE 1719775.661 1694729.358 2092484.645 2174813.054 1512306.772 2432261.741 1818021.79 1595377.877 1249307.072 1.376583627 1.356535471 1.674916193 1.740815451 1.210516458 1.946888635 1.455224124 1.277010202 1 20.2526967 1.040385332 2.58896488 1.006981754 1.547087652 0.42009615 0.210237874 0.23445425 3.387758173 0.184119079 0.049764656 10.97451489 -1.040385332 0.540105898 GSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNK 40 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 202.68 2.25E-31 535860000 545590 636000 452170 385060 726560 438740 622740 643340 280274 FALSE TRUE 511442.4958 683090.1018 462895.6859 394941.2915 669498.9084 565397.1157 529365.9182 723662.4152 233494.4588 2.190383868 2.925508834 1.982469684 1.691437534 2.867301057 2.421458388 2.267145529 3.099270188 1 17.83302879 -1.827536346 2.776080209 0.530576768 2.41437919 0.514234269 0.43672515 39296364.85 37026217.54 124852274.6 0.097713299 0.014875229 1.827536346 1.883802422 GSVFLESDS(ph)SPPSSSDAGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSVFLESDSSPPSSSDAGLR 20 0 Q8TBP0 Q8TBP0 TBC1D16 TBC1 domain family member 16 1 GSVFLES(0.002)DS(0.739)S(0.259)PPSSSDAGLR;GSVFLES(0.012)DS(0.64)S(0.346)PPS(0.001)S(0.001)SDAGLR 222.28 7.62E-25 151042000 317950 367750 348950 369340 348120 311960 357830 288930 225580 TRUE FALSE 298050.0771 394978.5926 357227.2588 378817.8897 320780.0594 402017.7878 304176.7134 325003.5465 187929.2407 1.585969676 2.101741013 1.900860438 2.015747461 1.706919361 2.139197638 1.618570438 1.729393176 1 17.51983003 0.539603156 0.777152553 0.992459185 1.929648567 0.688381739 0.183949689 0.749318504 0.742163579 0.16723382 0.055795925 3.464201585 -0.539603156 0.937189381 GSVILDSGHLST(ph)ASS(ph)SDDLKGEEGSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSVILDSGHLSTASSSDDLKGEEGSFR 27 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 2 GSVILDSGHLS(0.151)T(0.769)AS(0.278)S(0.67)S(0.132)DDLKGEEGSFR 110.44 0.021514 68455000 54728 59263 66899 60344 70037 56901 78678 58957 84864 TRUE FALSE 51302.67217 63650.89418 68485.87587 61892.5292 64536.57654 73327.39499 66880.96431 66317.91123 70699.65016 0.725642518 0.900299988 0.96868762 0.875429073 0.912827382 1.03716772 0.945987203 0.938023188 1 16.10941546 5.425561103 1.171050125 0.953514375 2.57E-13 0.722981369 0.044257108 3.564747004 1.292561368 0.012161317 6.141589577 266416.4906 -5.425561103 -0.953514375 GSVILDSGHLSTAS(ph)SSDDLKGEEGSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSVILDSGHLSTASSSDDLKGEEGSFR 27 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 GSVILDSGHLSTAS(0.38)S(0.38)S(0.239)DDLKGEEGSFR 198.02 3.47E-25 230960000 142220 194610 213010 230770 223420 184080 241020 175260 259700 TRUE FALSE 133318.7041 209019.1269 218062.6978 236691.9489 205873.4944 237220.9077 204881.2885 197141.5968 216354.3923 0.616205212 0.966096064 1.007895867 1.094001127 0.951556806 1.096445999 0.946970784 0.911197571 1 17.72303688 4.746914836 3.616396138 1.00086624 0.569092083 0.805777814 0.058953151 0.118026058 2.784217205 0.013375708 0.139527373 55836.06904 -4.746914836 -0.431774157 GSVLPNSDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSVLPNSDKK 10 1 H0YF61;P22307-6;P22307-2;P22307-4;P22307-7;P22307-8;P22307 H0YF61 SCP2 Non-specific lipid-transfer protein 0 ; 96.64 0.0093892 327940000 938230 751030 830960 809380 855440 638820 1042900 701940 991900 FALSE TRUE 879507.8591 806637.0426 850670.7636 830150.0611 788257.1931 823236.9636 886526.8268 789578.7542 826345.4821 1.064334323 0.976149879 1.029437181 1.004604102 0.953907549 0.996238234 1.07282831 0.955506833 1 19.65638555 GSVPLS(ph)SSPPATHFPDETEITNPVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSVPLSSSPPATHFPDETEITNPVPK 26 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 GS(0.067)VPLS(0.348)S(0.288)S(0.288)PPAT(0.009)HFPDETEITNPVPK 124.17 0.0002035 444230000 384600 304050 330280 295130 324320 247330 406890 333380 333180 TRUE FALSE 360528.5725 326562.1784 338114.3976 302703.5355 298849.2154 318730.1559 345880.6219 375003.2269 277570.1056 1.298873925 1.17650342 1.218122524 1.090548043 1.07666211 1.148287044 1.246101849 1.351021667 1 18.08249267 7.101595713 1.262801402 1.171741216 58.56760603 0.151152397 0.097735771 1444.052258 6.704310017 0.025937732 238692.7842 12635595.45 -7.101595713 57.39586481 GSVPLSS(ph)S(ph)PPATHFPDETEITNPVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSVPLSSSPPATHFPDETEITNPVPK 26 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 2 GS(0.024)VPLS(0.473)S(0.54)S(0.962)PPAT(0.001)HFPDETEITNPVPK;GS(0.023)VPLS(0.461)S(0.548)S(0.955)PPAT(0.013)HFPDETEITNPVPK 135.02 1.84E-05 193643000 200884 168927 188775 169921 193722 144782 240500 206242 286580 TRUE FALSE 188311.029 181434.5308 193252.8321 174281.4605 178507.8556 186578.2131 204439.2577 231991.7677 238747.9466 0.788744078 0.759941744 0.809442908 0.729980982 0.747683312 0.781486148 0.856297449 0.971701625 1 17.8651288 1.38145426 1.936550427 1.001276215 0.769723174 0.943785061 0.021754599 0.070518847 0.47071206 0.019951708 0.006133457 24.06879014 -1.38145426 -0.231553041 GSVPLSS(ph)SPPATHFPDETEITNPVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSVPLSSSPPATHFPDETEITNPVPK 26 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 GS(0.018)VPLS(0.069)S(0.437)S(0.437)PPAT(0.039)HFPDETEITNPVPK 155.16 8.62E-08 446590000 377570 308130 344630 332740 346270 259210 425050 336410 320010 TRUE FALSE 353938.5677 330944.2658 352804.7863 341278.6717 319075.351 334039.7191 361317.6985 378411.529 266598.2637 1.327610176 1.241359419 1.323357405 1.280123385 1.196839569 1.252970348 1.355289016 1.419407328 1 18.02430786 -2.241274624 2.195753026 1.99E-05 1.295268377 0.691930243 0.062770187 738702.4361 153175.9307 3665372.731 0.015278605 0.005737535 2.241274624 1.295248429 GSVPLSSS(ph)PPATHFPDETEITNPVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GSVPLSSSPPATHFPDETEITNPVPK 26 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 GSVPLS(0.004)S(0.026)S(0.969)PPAT(0.001)HFPDETEITNPVPK;GSVPLS(0.003)S(0.022)S(0.975)PPATHFPDETEITNPVPK;GSVPLS(0.001)S(0.005)S(0.992)PPAT(0.002)HFPDETEITNPVPK;GSVPLSS(0.042)S(0.946)PPAT(0.012)HFPDETEITNPVPK;GS(0.002)VPLS(0.008)S(0.158)S(0.833)PPATHFPDETEITNPVPK 260.82 5.48E-53 17491260000 2522790 2123310 2420530 2175580 2349980 1996600 3037850 2236430 2418220 TRUE FALSE 2364893.077 2280522.082 2477946.115 2231409.066 2165422.05 2572986.008 2582352.595 2515653.208 2014603.46 1.173875219 1.131995515 1.229991988 1.107617013 1.074862668 1.277167472 1.281816817 1.248708869 1 20.94206447 2.223306374 24.99973185 1.233300368 1.152209383 0.042014033 0.090580727 423.8734761 694669.0997 0.031008658 0.022987282 167.2269905 -2.223306374 -0.081090985 GSVSSVS(ph)PKPPSSFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GSVSSVSPKPPSSFK 15 1 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 1 GSVS(0.012)S(0.157)VS(0.831)PKPPSSFK;GSVS(0.04)S(0.033)VS(0.926)PKPPSSFK 90.718 0.0035767 1016350000 2058400 1075420 1504310 1226310 1300330 1146700 1737330 1236540 1433530 TRUE FALSE 1929568.418 1155045.216 1539992.944 1257779.191 1198207.327 1477733.675 1476833.495 1390924.741 1194264.582 1.615695925 0.967160237 1.289490593 1.05318303 1.0033014 1.237358704 1.236604951 1.164670511 1 20.18769106 4.75154288 24.84320384 1.137121631 1.615696258 0.650222452 0.113804134 1291.64371 2471676.306 0.026381009 0.490395109 56434.26585 -4.75154288 0.478574627 GSYGS(ph)DAEEEEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 385.89 5.63E-108 10453250000 4271050 4182510 4602140 4177010 4340890 4559560 4840800 3862500 3796610 TRUE FALSE 4003732.605 4492187.392 4711304.934 4284199.148 3999974.01 5875830.954 4114966.98 4344741.627 3162931.264 1.265829786 1.420260833 1.489537565 1.354502767 1.264641459 1.857716929 1.300997915 1.373644023 1 21.59283077 0.695729135 1.851583693 1.000834756 1.43597683 0.372566727 0.170818773 1.247900592 6.114635014 0.148473272 0.041509501 4.96282698 -0.695729135 0.435142074 GSYGS(ph)DAEEEEYRQQLSEHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GSYGSDAEEEEYRQQLSEHSK 21 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 GS(0.001)YGS(0.999)DAEEEEYRQQLSEHSK;GSYGS(1)DAEEEEYRQQLSEHSK;GS(0.002)YGS(0.998)DAEEEEYRQQLSEHSK;GS(0.008)YGS(0.992)DAEEEEYRQQLSEHSK;GSYGS(1)DAEEEEYRQQLSEHSK;GS(0.014)YGS(0.986)DAEEEEYRQQLSEHSK;GS(0.002)YGS(0.998)DAEEEEYRQQLSEHSK;GS(0.004)YGS(0.996)DAEEEEYRQQLSEHSK 326.21 1.47E-68 16871800000 2661760 3219050 3011470 3184640 3793300 2459580 3468850 2976600 5215220 TRUE FALSE 2495165.193 3457391.811 3082903.491 3266363.254 3495389.519 3169620.818 2948728.146 3348235.062 4344766.09 0.574292181 0.795760172 0.709567196 0.751792659 0.8045058 0.729526228 0.678685132 0.770636438 1 22.05084708 0.965027088 21.0100605 1.000000002 0.728420778 0.645107236 0.064511591 363.1180835 218145.1112 0.056553495 0.014138374 9.226289716 -0.965027088 -0.271579224 GSYSLSHVYTPNDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSYSLSHVYTPNDVR 15 0 P07686;Q5URX0 P07686 HEXB Beta-hexosaminidase subunit beta;Beta-hexosaminidase subunit beta chain B;Beta-hexosaminidase subunit beta chain A 0 157.38 1.96E-06 170250000 152250 279280 214290 235220 281190 168090 243020 238770 238980 FALSE TRUE 142720.9443 299958.1818 219373.06 241256.1434 259106.4717 216614.8543 206581.4071 268580.9601 199092.6941 0.716856763 1.506625761 1.101863938 1.211777984 1.301436363 1.088010061 1.037614203 1.349024691 1 17.60308076 2.205234657 24.97811039 1.111570485 1.206951447 0 0.217268065 671.7964645 503513.7074 0.074576941 0.055082443 160.4111885 -2.205234657 0.095380962 GSYVSIHSSGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GSYVSIHSSGFR 12 0 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 98.902 0.0040979 457440000 304620 432260 412190 411650 444000 382880 407130 373450 372420 FALSE TRUE 285554.378 464264.9802 421967.3415 422213.6359 409130.031 493411.2405 346084.6361 420076.0546 310260.6961 0.920369166 1.496370588 1.360041239 1.36083507 1.318665355 1.590311782 1.115463997 1.35394544 1 18.24312142 -1.10956211 4.909272252 0.999985861 1.332524208 0.214473693 0.186337988 2.59E-05 4.69E-06 0.161883687 0.038154729 0.077703018 1.10956211 0.332538346 GT(ph)GQSDDSDIWDDTALIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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;GT(0.5)GQS(0.5)DDSDIWDDTALIK 92.977 0.0082229 161834000 162233 117385 139132 124319 137057 121908 153625 118886 144512 TRUE FALSE 152079.1261 126076.3075 142432.2767 127509.236 126293.0961 157100.8606 130590.3574 133729.1788 120392.0136 1.263199456 1.047214875 1.183070807 1.059117064 1.049015564 1.304910981 1.084709471 1.110781146 1 16.87738017 0.785772186 1.926702574 1.000575257 1.136265448 0.200659652 0.088605456 1.275265854 8.022922384 0.076389791 0.021274586 6.106216325 -0.785772186 0.13569019 GT(ph)PGPPPAHGAALQPHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTPGPPPAHGAALQPHPR 18 0 Q15654 Q15654 TRIP6 Thyroid receptor-interacting protein 6 1 GT(1)PGPPPAHGAALQPHPR 80.545 0.015727 152270000 49161 70227 64122 77479 79202 58477 75014 74265 99699 TRUE FALSE 46084.10076 75426.68015 65643.00412 79467.24231 72981.79441 75358.36061 63766.3471 83537.14873 83058.59282 0.554838448 0.908114111 0.79032165 0.956761241 0.878678436 0.907291564 0.767727275 1.005761666 1 16.34184181 4.741500193 24.8279895 0.880789892 0.554838317 0.640745302 0.080292322 158.6700897 1340070.892 0.017360276 0.122122116 55144.2447 -4.741500193 -0.325951575 GT(ph)PPPVFTPPLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTPPPVFTPPLPK 13 0 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 GT(1)PPPVFTPPLPK 102.33 0.018979 17947000 37696 40104 44325 41871 44807 36238 54505 47537 62308 TRUE FALSE 35336.67465 43073.34189 45376.40993 42945.48075 41288.03896 46699.32233 46332.48125 53472.09909 51908.39227 0.680750705 0.829795338 0.87416327 0.82733213 0.795401999 0.89964879 0.892581704 1.030124355 1 15.66368018 1.556125873 1.297150247 1.018373943 0.816718054 0.680753078 0.056112379 0.254190409 0.820067924 0.04745279 0.016606954 35.98536177 -1.556125873 -0.201655888 GT(ph)PSQS(ph)PVVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GTPSQSPVVGR 11 0 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 2 GT(0.999)PS(0.005)QS(0.996)PVVGR;GT(0.999)PS(0.001)QS(1)PVVGR;GT(0.998)PS(0.002)QS(1)PVVGR;GT(1)PSQS(1)PVVGR;GT(0.999)PS(0.056)QS(0.944)PVVGR 220.48 4.83E-11 2229180000 1598720 1599050 1684923 1600015 1425888 1756081 2098900 1651121 1078358 TRUE FALSE 1498658.969 1717445.326 1724890.169 1641074.094 1313904.508 2263033.077 1784189.43 1857267.091 898373.0833 1.668192199 1.911728387 1.920015416 1.82671779 1.462537706 2.519034819 1.986022804 2.067367251 1 19.77695518 4.740053778 21.91796863 1.902842355 1.668192125 0 0.398447252 96.89110002 1421356.248 0.083892319 0.523930738 54960.89273 -4.740053778 -0.23465023 GT(ph)PSQSPVVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTPSQSPVVGR 11 0 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 1 GT(0.735)PS(0.265)QSPVVGR;GT(0.997)PS(0.003)QSPVVGR 156.08 0.00034908 312810000 143480 162550 159334 163151 161764 135403 170465 149334 125870 TRUE FALSE 134499.8429 174585.3711 163113.4777 167337.7309 149059.708 174491.648 144905.3558 167978.6786 104861.4838 1.282642949 1.664914177 1.555513729 1.595797854 1.4214915 1.664020397 1.381873977 1.601910182 1 16.67812534 -2.60576296 0.439343162 8.26E-11 1.542475195 0.619097655 0.127128711 63.84553371 2.883392877 60.70749753 0.062296766 0.002478775 2.60576296 1.542475195 GT(ph)PTAENPEYLGLDVPV ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTPTAENPEYLGLDVPV 17 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 GT(0.903)PT(0.097)AENPEYLGLDVPV 103.88 0.0098092 100630000 91745 89965 81448 72266 112970 115210 109460 115540 80942 TRUE FALSE 86002.84422 96626.10221 83379.98502 74120.46791 104097.7919 148469.2567 93047.48918 129965.4233 67432.25729 1.275396193 1.432935899 1.236499983 1.099184142 1.543738799 2.201754215 1.379866149 1.927347957 1 16.04115127 2.488570847 24.71383681 1.676433739 1.289163924 0.218662872 0.323893025 617.4677458 1332801.409 0.095821596 0.085605193 308.0142767 -2.488570847 -0.387269816 GT(ph)RESGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GTRESGQK 8 1 A0A1W2PQW7;A8K830-4;A8K830-2 A0A1W2PQW7 1 GT(0.688)RES(0.312)GQK;GT(0.5)RES(0.5)GQK;GT(0.651)RES(0.349)GQK 73.931 0.068369 1203320000 370900 1261420 834560 721840 1366500 1086890 700260 1129780 1102970 TRUE FALSE 347686.0311 1354816.849 854356.1573 740363.6365 1259180.602 1400657.499 595262.5139 1270835.52 918877.1815 0.378381396 1.474426481 0.929782755 0.805726436 1.370347014 1.52431416 0.647815101 1.383030883 1 19.80951252 4.757079243 23.88572245 1.12431211 0.378380191 0.394410035 0.296627675 2333.886541 3010206.926 0.067643835 2.148317045 57158.29198 -4.757079243 -0.745931918 GT(ph)SPRPPEGGLGYSQLGDDDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTSPRPPEGGLGYSQLGDDDLK 22 1 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12;Q9UQ88-8;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;Q9UQ88-5;Q9UQ88-10 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 GT(0.5)S(0.5)PRPPEGGLGYSQLGDDDLK 179.47 9.16E-17 168760000 410930 230830 300650 260790 276630 259680 366990 262130 261520 TRUE FALSE 385210.6248 247920.8934 307781.56 267482.3129 254904.5957 334645.4004 311963.2565 294857.5075 217870.6225 1.76807052 1.137927135 1.412680408 1.227711703 1.169981491 1.535982211 1.431873893 1.353360559 1 17.73311215 -1.724009077 2.445831618 0.923416842 1.362387164 0.29012608 0.184900348 9635069.408 7041125.005 4498112.297 0.044171629 0.018879519 1.724009077 0.438970322 GT(ph)SPRPPEGGLGYSQLGDDDLKETGFHLTTTNQGASAAGPGFSLKF ddPTM_SK-BR-3_Pertuzumab_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(0.464)S(0.464)PRPPEGGLGY(0.029)S(0.032)QLGDDDLKET(0.01)GFHLT(0.001)TTNQGASAAGPGFSLKF 74.757 0.00027768 481340000 230060 272170 248990 251760 362700 176420 354730 253020 591160 TRUE FALSE 215660.9553 292321.75 254896.1604 258220.5878 334215.0051 227349.5901 301541.5297 284610.104 492491.577 0.437897754 0.593556852 0.517564507 0.524314729 0.678620754 0.461631428 0.612277537 0.57789842 1 18.90973952 -5 0.293217345 4.564778762 0.528587709 0.817517819 0.067514046 94.26856189 0.883369405 205.7488805 0.062115386 1.00E-05 5 -4.036191053 GT(ph)SPTQIWCNNSQLPVDHILAGSFETAMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTSPTQIWCNNSQLPVDHILAGSFETAMR 29 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 1 GT(0.445)S(0.445)PT(0.11)QIWCNNS(0.001)QLPVDHILAGSFETAMR;GT(0.458)S(0.458)PT(0.076)QIWCNNS(0.007)QLPVDHILAGSFETAMR 82.62 0.0090695 95835000 17532.6 19638.3 18033.9 19398.7 20544.3 18155.7 21486.1 18836.8 19634.9 TRUE FALSE 16435.26586 21092.34017 18461.67262 19896.50348 18930.83355 23396.95586 18264.45877 21188.61594 16357.70834 1.004741344 1.289443467 1.128622191 1.216338075 1.157303526 1.430332132 1.116565865 1.295329119 1 13.99768303 -0.947385667 4.252378715 0.999993448 1.207799405 0.233354599 0.116569449 5517061.488 2595081.33 331.3881459 0.023662862 0.112879307 0.947385667 0.207805957 GTADVTHDLQEMKEESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTADVTHDLQEMKEESR 17 1 P11166 P11166 SLC2A1 "Solute carrier family 2, facilitated glucose transporter member 1" 0 184.01 3.96E-10 195390000 159410 180820 140920 151730 276720 107590 180150 192460 392760 FALSE TRUE 149432.8127 194208.1009 144262.6889 155623.6487 254987.5274 138649.4864 153138.1799 216489.0547 327205.8187 0.456693629 0.593534986 0.440892798 0.47561394 0.779287876 0.423737839 0.468017899 0.661629599 1 18.31983888 0.907537589 3.967451007 0.999809951 0.520061527 0.681186887 0.103887316 0.234465487 8.281988128 0.093883915 0.024018609 8.082348797 -0.907537589 -0.479748424 GTAPPYVGVRPCSAS(ph)PSSEMVTLEEFLEESNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTAPPYVGVRPCSASPSSEMVTLEEFLEESNR 32 1 Q9P219;Q9P219-2;A0A0A0MR69;Q9P219-3 Q9P219 CCDC88C Protein Daple 1 GTAPPYVGVRPCS(0.172)AS(0.801)PS(0.022)S(0.005)EMVTLEEFLEESNR 141.65 3.74E-10 36900000 6650.9 7154.7 7094.6 9009.3 7425.7 8332.6 10598 6472.8 8284.2 TRUE FALSE 6234.632041 7684.441432 7262.887262 9240.493891 6842.515476 10738.08635 9008.928287 7280.943328 6901.513502 0.903371708 1.113442933 1.052361523 1.338908326 0.991451437 1.555903114 1.305355453 1.054977771 1 12.75269706 3.968059893 0.805955752 1.246213149 0.935986912 0.148333332 0.182719365 1.592693081 1.574539751 0.069816119 0.36646035 9290.945072 -3.968059893 -0.310226237 GTCADRDNLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTCADRDNLTR 11 1 P55212;D6RBM3;D6RHU3 P55212 CASP6 Caspase-6;Caspase-6 subunit p18;Caspase-6 subunit p11 0 79.23 0.025275 156600000 103190 93305 106830 105480 124450 85628 124270 111640 138050 FALSE TRUE 96731.5221 100213.3993 109364.058 108186.7954 114676.199 110347.4135 105636.8672 125578.4997 115008.5632 0.841081042 0.87135598 0.950921001 0.940684697 0.997110092 0.959471282 0.918513059 1.091905649 1 16.81138176 7.604786028 0.269245845 1.005629033 2.17E-07 0.624313151 0.042868494 28.21181541 0.478413272 0.047954732 12.64097815 40251866.88 -7.604786028 -1.005628816 GTCSGFEPHSWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTCSGFEPHSWR 12 0 Q9NZU5;F8WB09;C9IYS1;H7C3D2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 100.04 0.0015483 0 69127 91943 79438 82105 96171 69931 86782 73110 74409 FALSE TRUE 64800.46447 98750.55539 81322.30687 84211.9533 88618.1176 90118.94447 73769.84474 82237.94443 61989.6572 1.045343165 1.593016639 1.311868956 1.358483933 1.429562956 1.45377388 1.190034726 1.326639768 1 15.91973991 0.68763387 0.778789727 1.000847627 1.384199504 0.331442979 0.148658247 1.119869744 1.267140259 0.134275459 0.047037909 4.871176542 -0.68763387 0.383351876 GTCSRPDTECK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 182.71 5.17E-06 717310000 1454700 1171630 1302120 1312870 1548720 1259180 1786840 1307300 2110930 FALSE TRUE 1363652.924 1258378.704 1333006.901 1346560.467 1427089.778 1622684.825 1518919.93 1470519.283 1758602.146 0.775418662 0.71555622 0.757992309 0.76569932 0.81149098 0.922712865 0.863708676 0.836186449 1 20.7459977 2.528480156 2.201837892 0.892905911 0.745793079 0.700052886 0.046313262 0.16500112 1.603706599 0.01636454 0.014080694 337.6604196 -2.528480156 -0.147112832 GTDIMYTGTLDCWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTDIMYTGTLDCWR 14 0 P05141 P05141 SLC25A5 "ADP/ATP translocase 2;ADP/ATP translocase 2, N-terminally processed" 0 199.19 4.88E-08 97902000 61064 70360 47111 52461 103070 53501 54779 87964 96796 FALSE TRUE 57242.11324 75569.52761 48228.49517 53807.23808 94975.29796 68945.87018 46565.39749 98946.49903 80640.12227 0.709846558 0.937120697 0.59807071 0.667251445 1.177767286 0.854982213 0.57744701 1.227013256 1 16.29921021 GTDLWLGVDALGLNIYEKDDKLTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTDLWLGVDALGLNIYEKDDKLTPK 25 2 P15311;E7EQR4 P15311 EZR Ezrin 0 97.623 0.0046538 164520000 424310 260660 325410 315050 469660 228120 415230 241150 551450 FALSE TRUE 397753.1945 279959.5376 333128.8789 323134.7164 432774.7981 293974.5408 352970.1163 271258.1083 459409.4325 0.865792399 0.609390051 0.72512416 0.703369791 0.942024189 0.639896615 0.768312732 0.590449584 1 18.80942095 -1.547890343 5.772728114 1.000677739 0.723962276 0.37262319 0.109584373 0.000861247 6.75E-05 0.095602319 0.022480324 0.02832107 1.547890343 -0.276715463 GTDTQTPAVLS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GTDTQTPAVLSPSK 14 0 P46087-2;P46087;P46087-4 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 GTDTQTPAVLS(1)PSK;GTDTQTPAVLS(0.937)PS(0.063)K;GTDTQTPAVLS(0.922)PS(0.078)K;GTDTQTPAVLS(0.999)PS(0.001)K 306.92 9.22E-45 4694170000 6548200 4159750 4972550 4425920 4711650 4182130 5673690 4220090 4273690 TRUE FALSE 6138359.851 4467742.218 5090501.234 4539496.6 4341616.015 5389443.04 4822972.856 4746977.526 3560383.53 1.724072645 1.25484858 1.429762044 1.275002134 1.219423688 1.513725416 1.354621719 1.333277015 1 21.76360123 -3.483602128 0.270395283 3.15E-19 1.408362801 0.434463395 0.143432861 83.2501183 1.709143038 46.79899302 0.164952787 0.000328396 3.483602128 1.408362801 GTDTQTPAVLS(ph)PSKTQATLKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTDTQTPAVLSPSKTQATLKPK 22 2 P46087-2;P46087;P46087-4 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 GTDTQTPAVLS(0.994)PS(0.006)KTQATLKPK;GTDTQTPAVLS(0.931)PS(0.068)KT(0.001)QATLKPK 208.26 3.70E-23 4930300000 1917780 905540 1317760 1271990 1304580 995210 1684110 925660 1685420 TRUE FALSE 1797749.573 972587.1238 1349017.889 1304631.417 1202123.549 1282510.971 1431593.34 1041230.689 1404112.514 1.28034581 0.692670362 0.960761959 0.929150196 0.856144744 0.913396155 1.01957167 0.741557873 1 20.42122712 1.972756174 24.25443671 0.9335343 0.909008599 0 0.163043043 5464.003524 4864447.907 0.061405911 0.039781795 93.919587 -1.972756174 -0.024525701 GTEAPAVVT(ph)EEEDDDEETAPPVIAPRPDHTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GTEAPAVVTEEEDDDEETAPPVIAPRPDHTK 31 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 GTEAPAVVT(1)EEEDDDEETAPPVIAPRPDHTK;GTEAPAVVT(1)EEEDDDEETAPPVIAPRPDHTK;GTEAPAVVT(1)EEEDDDEETAPPVIAPRPDHTK;GTEAPAVVT(1)EEEDDDEETAPPVIAPRPDHTK;GTEAPAVVT(1)EEEDDDEETAPPVIAPRPDHTK 242.12 8.49E-46 1518870000 1897633 1598663 1715925 1734127 1951773 1377107 2147609 1690975 2073128 TRUE FALSE 1778863.538 1717029.672 1756627.551 1778627.635 1798488.622 1774655.435 1825594.968 1902096.951 1727109.544 1.02996567 0.994163733 1.017090987 1.029829081 1.041328634 1.02752917 1.057023264 1.101318071 1 20.71992816 2.762509289 1.009083236 1.053638126 1.008410701 0.226767744 0.026563804 0.591066421 1.271489145 0.013209674 0.012616521 578.7743679 -2.762509289 -0.045227426 GTEAS(ph)PPQNNSGSSSPVFTFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GTEASPPQNNSGSSSPVFTFR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 GT(0.002)EAS(0.995)PPQNNS(0.002)GSSSPVFTFR;GTEAS(1)PPQNNSGSSSPVFTFR;GTEAS(1)PPQNNSGSSSPVFTFR;GTEAS(1)PPQNNSGSSSPVFTFR;GTEAS(1)PPQNNSGSSSPVFTFR 373.26 1.77E-112 820072000 319268 347399 382956 368556 370903 318809 357094 310776 368019 TRUE FALSE 299285.5858 373120.7834 392039.8972 378013.7709 341773.7745 410843.9829 303551.0698 349577.0677 306594.2514 0.976161766 1.216985582 1.278692915 1.232944744 1.114742931 1.340025069 0.990074238 1.140194463 1 18.22597112 1.689036766 10.4541472 1.050319715 1.204214702 0.306427253 0.105076127 0.131597405 22.2909128 0.046140275 0.024980157 48.86937288 -1.689036766 0.153894986 GTEASPPQNNS(ph)GSSS(ph)PVFTFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTEASPPQNNSGSSSPVFTFR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 GT(0.001)EAS(0.405)PPQNNS(0.581)GS(0.014)S(0.012)S(0.988)PVFTFR;GTEASPPQNNS(0.888)GS(0.112)S(0.011)S(0.988)PVFTFR 246.77 3.67E-30 181583000 256627 313710 285240 275130 297160 281880 340280 285770 368690 TRUE FALSE 240565.1742 336937.4148 292006.0275 282190.3016 273822.2523 363254.1801 289258.173 321449.0136 307153.2572 0.783208931 1.096968393 0.950685108 0.918728013 0.891484124 1.182647983 0.941738908 1.046542747 1 18.22859916 GTEASPPQNNSGSSS(ph)PVFTFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTEASPPQNNSGSSSPVFTFR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 GTEASPPQNNSGSS(0.003)S(0.997)PVFTFR;GTEASPPQNNSGSSS(1)PVFTFR 392.09 3.03E-131 369760000 282810 327230 279810 279467 359010 333990 396820 366880 355050 TRUE FALSE 265109.4269 351458.4497 286447.2253 286638.5964 330814.8028 430407.4911 337320.5249 412685.7756 295789.8613 0.896276248 1.188203166 0.968414617 0.9690616 1.118411569 1.455112387 1.140405974 1.395199192 1 18.17421308 2.468975948 24.96407506 1.257765516 1.031159657 0.377287943 0.144798493 185.6382651 568946.818 0.04464328 0.037410948 294.4258572 -2.468975948 -0.226605859 GTEDELDKYSEALKDAQEK ddPTM_SK-BR-3_Pertuzumab_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 0 169.39 8.00E-12 90939000 365400 161230 227340 222970 227080 190530 309260 182780 263690 FALSE TRUE 342530.2663 173167.637 232732.6122 228691.7877 209246.0528 245532.918 262889.334 205600.4853 219678.4355 1.559234822 0.788277814 1.059424024 1.041029754 0.952510666 1.117692401 1.196700684 0.935915648 1 17.74503373 GTEDFIVESLDASFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTEDFIVESLDASFR 15 0 C9J3L8;C9J5W0;A0A3B3IRT8;E9PAL7;C9IZQ1;P43307-2;P43307 C9J3L8 SSR1 Translocon-associated protein subunit alpha 0 ; 117.23 0.00089821 24635000 41920 51814 37950 43638 52163 38022 54240 47041 42016 FALSE TRUE 39296.30203 55650.36247 38850.19192 44757.82496 48066.3284 48998.33416 46107.21554 52914.1724 35003.25817 1.122646979 1.589862355 1.109902162 1.278675966 1.373195837 1.399822095 1.317226394 1.511692773 1 15.0952016 -1.305087287 4.695558786 0.999814246 1.340362171 0.335300272 0.149469515 0.000264501 3.91E-05 0.131699909 0.031025162 0.049535062 1.305087287 0.340547925 GTEDITSPHGIPLDLLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GTEDITSPHGIPLDLLDR 18 0 Q9Y265;H7C4G5;Q9Y265-2;E7ETR0;J3QLR1 Q9Y265 RUVBL1 RuvB-like 1 0 ;;;; 206.74 8.19E-16 1456916000 1471120 2105490 2011270 2027910 2231070 1920030 2115200 1941780 2027630 FALSE TRUE 1379045.225 2261382.67 2058978.274 2079949.604 2055850.762 2474311.492 1798045.397 2184215.507 1689205.454 0.816386913 1.338725651 1.218903402 1.231318309 1.217051932 1.464778299 1.064432626 1.29304313 1 20.68791338 -1.130044204 3.307887396 0.999716642 1.219817422 0.118830843 0.172094409 10509463.11 15953451.2 32593.4582 0.036542577 0.074123479 1.130044204 0.22010078 GTEPS(ph)PGGTPQPSRPVS(ph)PAGPPEGVPEEAQPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTEPSPGGTPQPSRPVSPAGPPEGVPEEAQPPR 33 1 I3L1Q2;Q8WUZ0;Q8WUZ0-2 I3L1Q2 BCL7C B-cell CLL/lymphoma 7 protein family member C 2 GT(0.002)EPS(0.998)PGGT(0.002)PQPS(0.043)RPVS(0.956)PAGPPEGVPEEAQPPR;GT(0.001)EPS(0.998)PGGT(0.001)PQPS(0.001)RPVS(0.999)PAGPPEGVPEEAQPPR 188.49 3.36E-20 771500000 270417 478654 488363 481951 490331 470119 439168 440876 302711 TRUE FALSE 253492.0827 514094.0402 499947.201 494318.6786 451822.3812 605834.7236 373318.8354 495920.3391 252186.5785 1.005176739 2.038546394 1.982449676 1.960130795 1.791619458 2.402327384 1.480327929 1.966481888 1 17.94413197 0.036668238 11.42515221 0.999995618 1.861117504 0.326159327 0.371555469 0 0 0.320508141 0.075544493 1.088098566 -0.036668238 0.861121886 GTEPSPGGTPQPSRPVS(ph)PAGPPEGVPEEAQPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GTEPSPGGTPQPSRPVSPAGPPEGVPEEAQPPR 33 1 I3L1Q2;Q8WUZ0;Q8WUZ0-2 I3L1Q2 BCL7C B-cell CLL/lymphoma 7 protein family member C 1 GTEPSPGGTPQPSRPVS(1)PAGPPEGVPEEAQPPR;GTEPSPGGT(0.001)PQPS(0.022)RPVS(0.978)PAGPPEGVPEEAQPPR;GTEPSPGGTPQPS(0.001)RPVS(0.999)PAGPPEGVPEEAQPPR;GTEPSPGGTPQPS(0.002)RPVS(0.998)PAGPPEGVPEEAQPPR 314.78 1.71E-104 1483180000 155540 186789 166336 225533 256830 201318 194066 165490 148416 TRUE FALSE 145805.029 200619.0519 170281.5685 231320.5586 236659.6078 259435.2385 164967.6049 186151.7908 123644.4108 1.179228629 1.622548489 1.377187755 1.870853338 1.914034013 2.098236684 1.334209964 1.505541493 1 16.9158375 0.857778647 1.537187884 1.008616864 1.638625447 0.338207716 0.279108112 0.700860849 3.171693321 0.264644749 0.077112229 7.207400364 -0.857778647 0.630008583 GTEVQVDDIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTEVQVDDIKR 11 1 Q9Y230;Q9Y230-2 Q9Y230 RUVBL2 RuvB-like 2 0 ; 198.32 8.67E-08 1098130000 1009650 822820 929210 997780 1094600 806920 1167640 925860 1070330 FALSE TRUE 946457.8088 883742.4489 951251.3 1023384.724 1008634.531 1039864.705 992563.2218 1041455.659 891685.0084 1.061426176 0.99109264 1.066801944 1.147697577 1.131155646 1.166179419 1.113132118 1.16796363 1 19.76617464 3.453856392 3.201967812 1.12905671 1.024433769 0.375638707 0.050345913 0.188816743 3.971120133 0.012446233 0.018627511 2843.520686 -3.453856392 -0.104622941 GTFHDDRDDGVDYWAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GTFHDDRDDGVDYWAK 16 1 E9PK91;Q9NYF8-3;H0YF63 E9PK91 BCLAF1 Bcl-2-associated transcription factor 1 0 ;;;;; 92.977 0.002757 2189212000 2464140 2196355 2421332 2281900 2483687 2050373 2754918 2176833 3578587 FALSE TRUE 2309913.876 2358975.41 2478767.138 2340457.417 2288628.242 2642282.4 2341843.621 2448615.392 2981297.711 0.774801479 0.791257915 0.831438984 0.785046528 0.767661758 0.886285992 0.785511495 0.821325352 1 21.50750902 -4.999999984 0.291200872 2.524649804 0.795217106 0.774201266 0.033413431 111.1693426 1.045520341 102.9753494 0.032727142 1.00E-05 4.999999984 -1.729432698 GTFIADSHQNFALFFQLVDVNTGAELTPHQTFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GTFIADSHQNFALFFQLVDVNTGAELTPHQTFVR 34 0 P04844-2;P04844 P04844-2 RPN2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 0 ;;; 373.88 9.32E-149 269643000 228837.5 440197.9 185167.8 172484.1 449731.7 183643.3 290847.3 419697.8 118308.4 FALSE TRUE 214514.9694 472790.6105 189560.0677 176910.334 414411.5864 236658.1395 247237.4475 472097.9942 98561.96374 2.176447802 4.796887081 1.923257821 1.794914867 4.204579238 2.401110231 2.50844685 4.789859864 1 16.58874338 -1.804668581 2.781330254 0.413562386 3.050533959 0.245627299 1.141820751 82513228.09 81391061.1 331554740.2 0.255290616 0.015679471 1.804668581 2.636971573 GTGGVDTAATGGVFDISNLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GTGGVDTAATGGVFDISNLDR 21 0 P12532;P12532-2 P12532 CKMT1A "Creatine kinase U-type, mitochondrial" 0 ;; 162.67 4.26E-11 303551000 98495 100938 99604 102586 127300 90487 103007 97939 116949 FALSE TRUE 92330.37377 108411.5545 101966.6539 105218.5304 117302.3715 116609.128 87562.05662 110166.8997 97429.45638 0.94766385 1.112718459 1.046569053 1.079945782 1.203972349 1.196857011 0.898722623 1.130735035 1 16.5720704 1.74047034 24.99999963 1.003488615 1.097114856 0.172410036 0.090661457 0.495801614 6530.70341 0.039757536 0.022047532 55.01363478 -1.74047034 0.093626241 GTGHVSSGYVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTGHVSSGYVER 12 0 Q6IN85-2;Q6IN85;G3V5Z3;G3V231;H0YIY8;Q6IN85-5;Q6IN85-4;G3V4R3;G3V5A2 Q6IN85-2 SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3A 0 ; 99.732 0.0015807 167830000 92483 176019 167038 165079 184663 150250 175265 163817 157036 FALSE TRUE 86694.65412 189051.6299 171000.2202 169315.2066 170160.3129 193624.7359 148985.6403 184269.9131 130825.6771 0.662673078 1.445065174 1.307084542 1.294204703 1.300664492 1.480020896 1.13881039 1.408514881 1 16.9972862 -1.397792703 3.503229187 0.997851013 1.278596948 0.098463797 0.232284922 2500.334584 47744102.31 143229.0872 0.047866868 0.04001357 1.397792703 0.280745935 GTGLVLDGDTSYTYHLVCMGPEASGWGQDEPQTWPTDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTGLVLDGDTSYTYHLVCMGPEASGWGQDEPQTWPTDHR 39 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 193.44 1.55E-24 56605000 52521 42370 49483 35673 44452 68026 103300 37069 47387 FALSE TRUE 49233.80436 45507.11889 50656.76013 36588.42957 40960.91923 87664.00189 87811.12399 41697.14625 39477.80357 1.247126231 1.152726717 1.283170682 0.926810163 1.037568343 2.220589647 2.224316351 1.056217481 1 15.2687541 2.256877075 24.96769198 1.7981755 1.144395733 0.206408236 0.426387049 249.4199687 339990.7904 0.14061311 0.117436873 180.6662685 -2.256877075 -0.653779767 GTGQS(ph)DDS(ph)DIWDDTALIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GTGQSDDSDIWDDTALIK 18 0 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 2 GT(0.022)GQS(0.978)DDS(1)DIWDDTALIK;GT(0.128)GQS(0.872)DDS(1)DIWDDTALIK;GT(0.093)GQS(0.907)DDS(1)DIWDDTALIK 218.38 1.40E-18 90959000 416980 329907 354690 337297 378470 293658 416210 341010 387840 TRUE FALSE 390881.9661 354333.6575 363103.4143 345952.6121 348746.4929 378432.2975 353803.1744 383585.8492 323106.9985 1.209760135 1.096644948 1.123786907 1.070706031 1.079352953 1.171229033 1.095003129 1.187179018 1 18.30165247 4.742632368 24.51357028 1.108257853 1.209760188 0.286272115 0.052399125 386.5698753 2327184.499 0.010812747 0.081427158 55288.18949 -4.742632368 0.101502335 GTGQS(ph)DDSDIWDDTALIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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;GT(0.004)GQS(0.996)DDSDIWDDTALIK 337.95 3.58E-75 481220000 846505 623211 713223 645336 726750 632826 817564 656183 730747 TRUE FALSE 793523.7631 669354.1909 730140.9864 661896.4143 669673.9866 815512.5931 694977.8681 738108.892 608780.6049 1.303464264 1.099499862 1.199349947 1.08724951 1.100025167 1.339583729 1.141590029 1.212438251 1 19.21556287 -1.791221494 2.56953422 0.94836826 1.177688252 0.315245338 0.085201572 13317927.6 9729010.489 4311339.132 0.019405448 0.01617255 1.791221494 0.229319992 GTHDRDPSEKPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GTHDRDPSEKPPR 13 2 Q969S3 Q969S3 ZNF622 Zinc finger protein 622 0 ;;; 175.21 1.12E-05 259817000 305614 315140 298209 302128 342086 250186 352620 289033 379382 FALSE TRUE 286486.1653 338473.2935 305282.6583 309881.116 315219.9455 322410.6368 299747.9046 325119.4063 316060.6933 0.906427694 1.07091233 0.965898844 0.980448131 0.997339917 1.020090899 0.948387164 1.028661308 1 18.2698421 GTHTGVWVGVSGSETSEALSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 290.94 1.01E-54 6282150000 2020168 2316290 2371950 2344510 2443358 2269430 2927570 2202558 2182120 FALSE TRUE 1893729.291 2487790.522 2428213.774 2404674.096 2251466.519 2924577.6 2488608.057 2477552.215 1817910.075 1.041706802 1.36848932 1.33571721 1.322768452 1.238491689 1.608758123 1.368939031 1.362857409 1 20.79384941 4.740609821 22.92537786 1.351733509 1.041706445 0.244970841 0.150701271 68.76058667 769059.7955 0.03163709 0.205753009 55031.30621 -4.740609821 -0.310027064 GTHTGVWVGVSGSETSEALSRDPETLVGYSMVGCQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 336.14 2.33E-129 505874000 162692 244016 235529 239786 275067 212223 289227 224399 300387 FALSE TRUE 152509.3981 262083.1985 241115.8591 245939.3147 253464.3474 273488.3349 245860.0964 252415.7091 250250.4691 0.609427022 1.047283545 0.96349813 0.982772642 1.012842646 1.092858431 0.982456086 1.008652291 1 17.93301325 4.741783627 24.99961677 1.010211649 0.609426874 0.92271006 0.036551148 77.39541379 600298.0243 0.008486707 0.061031492 55180.24527 -4.741783627 -0.400784775 GTINFLHADCDKFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTINFLHADCDKFR 14 1 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 98.281 0.0015864 258340000 536330 1253000 805530 868940 1226400 652380 833990 1051400 877720 FALSE TRUE 502762.0627 1345773.424 824637.552 891238.4715 1130083.491 840711.5155 708940.9419 1182669.604 731222.8617 0.68756338 1.840442216 1.127751326 1.218832887 1.545470677 1.14973363 0.969527868 1.617385979 1 19.47995165 GTITDAPGFDPLRDAEVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTITDAPGFDPLRDAEVLR 19 1 P50995;P50995-2 P50995 ANXA11 Annexin A11 0 142.35 1.42E-07 86885000 31231 34907 29555 25902 46866 18328 41073 31550 92781 FALSE TRUE 29276.30746 37491.5506 30256.05856 26566.68917 43185.33341 23618.99607 34914.48495 35489.08695 77295.25171 0.378759456 0.485043386 0.391434893 0.343704026 0.558706162 0.305568525 0.451702843 0.459136702 1 16.23809217 0.409053437 1.786449893 1.000005563 0.41890441 0.867536101 0.071220113 1.747002923 4.921212677 0.060065623 0.016809958 2.5647996 -0.409053437 -0.581101152 GTKT(ph)PINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GTKTPINR 8 1 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 1 GT(0.163)KT(0.837)PINR;GT(0.157)KT(0.843)PINR;GT(0.038)KT(0.962)PINR 87.568 0.024625 281852000 383874 419940 325620 286422 505760 247566 593440 288836 1515900 TRUE FALSE 359848.0116 451032.7945 333343.8602 293772.0734 466039.6497 319034.2853 504459.1812 324897.8104 1262886.497 0.284940897 0.357144364 0.263953935 0.232619538 0.369027344 0.252623087 0.399449343 0.257266042 1 20.26829355 -4.274225195 0.488199459 9.99999994 0.301582855 0.937178547 0.056721982 197.3674224 2.072682774 1899.916254 0.024917065 5.32E-05 4.274225195 -9.698417085 GTLDEEDEEADS(ph)DTDDIDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTLDEEDEEADSDTDDIDHR 20 0 Q9HCN4-3;Q9HCN4-2;Q9HCN4-4;Q9HCN4;Q9HCN4-5 Q9HCN4-3 GPN1 GPN-loop GTPase 1 1 GTLDEEDEEADS(1)DTDDIDHR;GTLDEEDEEADS(1)DTDDIDHR 362.25 3.35E-96 14683500000 4616300 5033900 4989700 5221900 5361100 4584800 5541100 4652000 4721600 TRUE FALSE 4327374.023 5406615.194 5108058.04 5355902.795 4940060.832 5908357.332 4710263.496 5232812.44 3933534.457 1.100123584 1.374492903 1.298592423 1.361600579 1.255883452 1.502047941 1.197463387 1.330308021 1 21.90739479 -0.914764141 6.183792315 0.999999941 1.309583535 0.438153549 0.107414024 7.80E-08 1.35E-08 0.090257339 0.021273855 0.121684667 0.914764141 0.309583594 GTLDPVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTLDPVEK 8 0 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 113.91 0.0064179 508790000 1607260 2141400 1786920 1590440 2212400 1831800 2048900 2052210 2543700 FALSE TRUE 1506664.466 2299951.484 1829306.586 1631253.383 2038647.028 2360610.923 1741686.466 2308432.936 2119140.037 0.710979189 1.085323029 0.863230629 0.769771395 0.962016192 1.113947583 0.821883611 1.089325337 1 21.0150475 2.496116691 24.85717158 0.985194763 0.893268061 0.213865868 0.124979203 1600.474732 2094359.973 0.039633403 0.036808977 313.4127726 -2.496116691 -0.091926702 GTLS(ph)DSEIETNSATSTIFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GTLSDSEIETNSATSTIFGK 20 0 A0A0A0MRB5;Q8WXG6-6;Q8WXG6-8;Q8WXG6-5;Q8WXG6-4;Q8WXG6-7;Q8WXG6-3;Q8WXG6-2;Q8WXG6;F8W8U2 A0A0A0MRB5 MADD MAP kinase-activating death domain protein 1 GT(0.013)LS(0.987)DSEIETNSATSTIFGK;GT(0.033)LS(0.967)DSEIETNSATSTIFGK;GTLS(0.994)DS(0.005)EIETNSATSTIFGK;GTLS(1)DSEIETNSATSTIFGK;GTLS(0.999)DSEIETNSATSTIFGK;GT(0.007)LS(0.982)DS(0.011)EIETNSATSTIFGK 510.4 8.22E-277 1124944000 1152021 1088321 1126281 1156303 1225375 973841 1388520 1060336 1381207 TRUE FALSE 1079918.062 1168901.419 1152996.917 1185975.693 1129138.99 1254973.088 1180324.316 1192721.284 1150674.629 0.938508624 1.015840091 1.002018197 1.03067858 0.981284337 1.090641139 1.025767221 1.036540873 1 20.13404852 6.517274998 0.700736586 1.029757302 1.43E-12 0.425741934 0.029789955 28.14411813 1.353706325 0.010155858 38.93228602 3290599.278 -6.517274998 -1.029757302 GTLTLCPYHSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GTLTLCPYHSDR 12 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;; 193.23 3.07E-06 1757110000 1221890 2047090 1255870 1216310 1993230 1352130 1938840 1657790 2400150 FALSE TRUE 1145414.086 2198658.674 1285659.829 1247522.574 1836689.756 1742467.981 1648128.941 1864768.731 1999549.459 0.572836086 1.099577039 0.642974758 0.623901833 0.9185518 0.871430298 0.82425015 0.932594451 1 20.93124354 1.159858982 0.856474642 1.000043606 0.795178134 0.197323455 0.153806546 1.101298703 1.803250106 0.141189338 0.051645953 14.44970503 -1.159858982 -0.204865472 GTMTTGHNVADLVVILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTMTTGHNVADLVVILK 17 0 Q12905;B4DY09;A0A0A0MRL0;X6R6Z1 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 96.208 0.0025632 0 129340 128410 131050 128300 152100 108530 142450 109300 161740 FALSE TRUE 121244.8403 137917.61 134158.5679 131592.3952 140154.6795 139860.8492 121090.9449 122946.3456 134744.5491 0.899812579 1.023548714 0.995651169 0.976606446 1.040151015 1.037970367 0.898670453 0.912440217 1 17.03986739 1.731487331 13.19440506 0.92968386 0.999825449 0.244161774 0.047621288 0.095613955 96.12432419 0.020458394 0.011241867 53.88741254 -1.731487331 0.070141589 GTPGPDSSGSLGS(ph)GEFTGVK ddPTM_SK-BR-3_Pertuzumab_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 GTPGPDS(0.07)S(0.025)GS(0.218)LGS(0.687)GEFTGVK 147.84 1.23E-07 60360000 62515 38310 46425 42391 47967 38787 50631 37318 46191 TRUE FALSE 58602.29774 41146.51226 47526.22292 43478.82483 44199.86531 49984.17725 43039.35159 41977.23445 38481.42369 1.522872392 1.069256496 1.235043259 1.129865287 1.148602652 1.298917047 1.118444887 1.090844112 1 15.23187455 8 0.052491843 0.70517078 2.075892746 0.361770026 0.117482095 591.9369107 2.338670175 13.84136797 64.61055984 100000000 -8 1.370721965 GTPGPPPAHGAALQPHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTPGPPPAHGAALQPHPR 18 0 Q15654 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 ; 193.69 6.42E-15 533660000 446890 546480 510220 490650 572640 472190 566450 487530 689340 FALSE TRUE 418919.9526 586941.9478 522322.6593 503240.9097 527667.1643 608503.5876 481516.0812 548399.1937 574284.7007 0.729463892 1.022040021 0.909518674 0.876291688 0.918825042 1.059585232 0.838462318 0.954925655 1 19.1314066 2.456352485 24.99455927 0.947704866 0.910086731 0.107496166 0.090393368 940.770652 1132180.678 0.029806889 0.024940259 285.991078 -2.456352485 -0.037618135 GTPKPPGPPAQPPGPPNAS(ph)SNPDLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GTPKPPGPPAQPPGPPNASSNPDLRR 26 2 Q8N4C8;Q8N4C8-4 Q8N4C8 MINK1 Misshapen-like kinase 1 1 GTPKPPGPPAQPPGPPNAS(0.56)S(0.44)NPDLRR;GTPKPPGPPAQPPGPPNAS(0.559)S(0.441)NPDLRR;GTPKPPGPPAQPPGPPNAS(0.5)S(0.5)NPDLRR 162 8.61E-12 1006150000 204611 190585 198358 186673 236218 179522 252280 225584 425460 TRUE FALSE 191804.7628 204696.1117 203063.1454 191463.3452 217666.3911 231347.0871 214452.9561 253748.659 354447.9774 0.54113657 0.577506784 0.572899716 0.540173333 0.614099685 0.652696875 0.605033657 0.715898172 1 18.43521437 0.035824298 0.45329524 1.053150862 0.557786144 0.960610777 0.026886405 0.686632992 0.18585403 0.090701342 0.014729684 1.085986178 -0.035824298 -0.495364719 GTPKPPGPPAQPPGPPNASS(ph)NPDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTPKPPGPPAQPPGPPNASSNPDLR 25 1 Q8N4C8;Q8N4C8-4 Q8N4C8 MINK1 Misshapen-like kinase 1 1 GTPKPPGPPAQPPGPPNAS(0.186)S(0.814)NPDLR;GTPKPPGPPAQPPGPPNAS(0.026)S(0.974)NPDLR 118.47 0.00045409 940410000 443530 394770 422140 381330 455190 400020 536110 479420 711150 TRUE FALSE 415770.249 423999.1816 432153.3601 391115.5734 419441.2135 515499.2802 455725.2825 539276.6423 592454.4708 0.701775866 0.715665427 0.729428811 0.660161401 0.707972062 0.870107841 0.769215703 0.910241494 1 19.17634476 1.276236498 0.708434271 1.00084946 0.703651104 0.824490884 0.045410212 0.245264166 0.285424537 0.041132386 0.017333375 18.89019746 -1.276236498 -0.297198356 GTPLGTPAT(ph)SPPPAPLCHSDDYVHISLPQATVTPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTPLGTPATSPPPAPLCHSDDYVHISLPQATVTPPR 36 0 A0A2R8YFV7;A0A2R8Y5N2;A0A2R8Y5S3;Q92574-2;Q92574;A0A2R8Y6W1;Q59IT9 A0A2R8YFV7 TSC1 Hamartin 1 GTPLGT(0.003)PAT(0.497)S(0.497)PPPAPLCHS(0.002)DDYVHISLPQATVTPPR;GTPLGT(0.001)PAT(0.5)S(0.5)PPPAPLCHSDDYVHISLPQATVTPPR 125.59 3.83E-08 200006000 54918 128056 103624 137479 142237 110593 126937 105344 102468 TRUE FALSE 51480.78041 137537.3995 106082.0102 141006.9439 131066.2798 142519.4038 107903.9753 118496.4303 85365.42883 0.603063572 1.611160412 1.242681161 1.651803849 1.53535549 1.669521324 1.264024287 1.388107949 1 16.38136431 0.459646983 1.503166081 1.000300375 1.403400229 0.115126945 0.312419142 6.038308908 14.72007818 0.267529076 0.07726877 2.881688163 -0.459646983 0.403099854 GTPLISPLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 101.65 0.010175 0 178140 147300 138700 144680 159480 112900 161260 142660 156710 FALSE TRUE 166990.5354 158206.2453 141990.0295 148392.7337 146955.0841 145492.3972 137080.5601 160471.415 130554.0886 1.279090813 1.211806133 1.087595425 1.136637966 1.125626058 1.114422373 1.049990556 1.229156564 1 16.99428811 4.414067261 1.4179507 1.106191718 1.300784626 0.504504554 0.0592191 0.540490346 1.498013825 0.014799487 0.126398638 25945.81165 -4.414067261 0.194592908 GTPQQIDYAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTPQQIDYAR 10 0 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 ; 125.75 0.00093265 324270000 233860 289470 277880 251620 305630 253500 283300 271960 328340 FALSE TRUE 219223.1201 310902.66 284471.4448 258076.9952 281627.0527 326681.3348 240821.795 305914.8047 273537.9328 0.801435902 1.136597973 1.039970734 0.943477903 1.029572205 1.194281654 0.88039634 1.118363371 1 18.06138139 2.489606306 24.57225081 1.037569327 1.01336019 0.036190175 0.116853347 3873.63266 7623864.427 0.037251812 0.033414942 308.7495309 -2.489606306 -0.024209137 GTPS(ph)QSPVVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTPSQSPVVGR 11 0 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 1 GT(0.003)PS(0.525)QS(0.472)PVVGR 105.65 0.0025563 43479000 48727 78693 69430 79482 82610 64925 70361 65033 61541 TRUE FALSE 45677.26405 84519.5116 71076.91239 81521.64268 76122.14383 83667.79353 59811.02125 73152.51321 51269.40953 0.890926275 1.648536864 1.386341544 1.590064006 1.484747816 1.631924266 1.166602498 1.42682574 1 15.64581066 0.713551121 0.919858604 1.005775575 1.450989919 0.21586302 0.232016639 1.318185494 2.024653906 0.200231872 0.066595521 5.170721193 -0.713551121 0.445214344 GTPSQS(ph)PVVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GTPSQSPVVGR 11 0 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 1 GTPSQS(1)PVVGR;GTPS(0.013)QS(0.987)PVVGR;GTPS(0.001)QS(0.999)PVVGR;GTPSQS(1)PVVGR;GTPS(0.112)QS(0.888)PVVGR;GTPS(0.001)QS(0.999)PVVGR 273.02 4.64E-27 10338740000 5407950 6403280 6203300 6321310 7110230 5421000 6362750 5188510 6335410 TRUE FALSE 5069476.063 6877385.514 6350445.205 6483525.517 6551821.217 6985954.697 5408714.706 5836306.895 5277989.143 0.960493841 1.303031387 1.203194064 1.228408271 1.241347991 1.323601567 1.024768062 1.105782285 1 22.33155695 1.673530664 8.096971619 1.049724915 1.221543272 0.369453779 0.101395702 0.117158448 13.4802817 0.045219131 0.023706586 47.15531653 -1.673530664 0.171818357 GTPT(ph)AENPEYLGLDVPV ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTPTAENPEYLGLDVPV 17 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 GT(0.474)PT(0.526)AENPEYLGLDVPV;GT(0.438)PT(0.562)AENPEYLGLDVPV 103.75 0.0098795 84815000 132683 127652 111225 104848 158879 168001 160763 177682 101598 TRUE FALSE 124378.6079 137103.4869 113863.3095 107538.5772 146401.2842 216500.1614 136658.0806 199865.9888 84640.63745 1.469490444 1.61983051 1.345255813 1.270531277 1.729680785 2.557874893 1.614568188 2.361347868 1 16.36906287 2.481217361 24.96102698 1.950267878 1.450539719 0.198492326 0.425099022 223.8895389 1364360.778 0.127146848 0.108743814 302.842875 -2.481217361 -0.49972816 GTPTAENPEY(ph)LGLDVPV ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTPTAENPEYLGLDVPV 17 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 GTPTAENPEY(1)LGLDVPV;GTPTAENPEY(1)LGLDVPV 152.4 2.21E-06 340980000 576430 808840 470180 607260 1098830 389310 768190 815830 406390 TRUE FALSE 540352.2753 868727.3552 481332.8916 622843.3197 1012532.324 501697.4771 653007.041 917688.1714 338560.8836 1.596026893 2.565941304 1.421702609 1.839678917 2.990694948 1.481853047 1.928772852 2.710555814 1 18.36905577 -1.120052841 7.318269749 0.999999622 2.040102679 0.28105953 0.534734404 3.00E-06 3.60E-07 0.471311055 0.111089041 0.075848528 1.120052841 1.040103057 GTQEVAPPTPLT(ph)PTSHTANTSPRPVSGMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLT(0.995)PT(0.005)S(0.001)HTANTSPRPVSGMER 116.73 0.00014251 275860000 122010 168080 151660 199420 194690 146710 166330 136830 142420 TRUE FALSE 114373.6119 180524.8181 155257.4468 204537.4548 179399.8327 189062.7954 141390.3606 153913.5267 118649.1819 0.963964606 1.52150074 1.308542076 1.72388424 1.512019129 1.593460589 1.191667387 1.297215237 1 16.85634263 1.11956973 1.354567567 1.022659382 1.438157921 0.276513172 0.211349075 0.495966932 1.827493035 0.183743881 0.05630687 13.16951343 -1.11956973 0.415498539 GTQEVAPPTPLTPT(ph)SHTANTSPRPVSGMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLTPT(0.293)S(0.293)HT(0.293)ANT(0.054)S(0.054)PRPVS(0.013)GMER;GTQEVAPPTPLT(0.002)PT(0.19)S(0.19)HT(0.19)ANT(0.19)S(0.19)PRPVS(0.046)GMER 92.589 0.0018679 1164980000 185757 161360 159345 160547 184288 145686 166245 158850 142676 TRUE FALSE 174130.801 173307.2623 163124.7386 164666.9078 169814.7639 187743.1832 141318.1056 178682.7722 118862.4539 1.464977335 1.458048834 1.372382391 1.385356792 1.428666146 1.579499472 1.18892132 1.503273459 1 16.85893354 -3.210644224 0.297039309 7.39E-13 1.439963989 0.62011582 0.103033808 51.03414108 1.258839729 31.69658803 0.098616135 0.000615681 3.210644224 1.439963989 GTQEVAPPTPLTPTSHT(ph)ANTSPRPVSGMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLTPT(0.021)S(0.078)HT(0.299)ANT(0.299)S(0.299)PRPVS(0.006)GMER;GTQEVAPPTPLT(0.002)PT(0.09)S(0.09)HT(0.32)ANT(0.245)S(0.245)PRPVS(0.008)GMER;GTQEVAPPTPLTPT(0.063)S(0.063)HT(0.291)ANT(0.291)S(0.291)PRPVSGMER 124.79 2.18E-05 801570000 66000.5 61664.5 61116.3 64505.9 72539 52277.3 91848 53326.1 67292.3 TRUE FALSE 61869.64652 66230.20374 62566.0075 66161.2306 66842.07955 67368.90786 78076.24508 59983.98097 56060.78041 1.10361729 1.18139996 1.116038825 1.180169632 1.192314468 1.201711916 1.392707067 1.069981198 1 15.77470421 2.826341738 2.166513076 1.216533561 1.141956386 0 0.107443467 0.798114879 7.380079561 0.035513692 0.0373479 670.4119357 -2.826341738 -0.074577174 GTQEVAPPTPLTPTSHTANT(ph)SPRPVSGMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLTPT(0.02)S(0.08)HT(0.252)ANT(0.299)S(0.299)PRPVS(0.051)GMER;GTQEVAPPTPLTPT(0.003)S(0.003)HT(0.19)ANT(0.402)S(0.402)PRPVSGMER;GTQEVAPPTPLTPT(0.047)S(0.047)HT(0.156)ANT(0.375)S(0.375)PRPVSGMER;GTQEVAPPTPLTPTS(0.001)HT(0.007)ANT(0.887)S(0.105)PRPVSGMER 181.35 1.09E-17 2376160000 305233 337466 310768 341530 382821 315134 397568 308095 317222 TRUE FALSE 286129.0114 362452.3338 318139.5637 350294.238 352755.7829 406108.07 337956.3692 346561.339 264275.5989 1.082691753 1.371493756 1.203817398 1.32548839 1.3348027 1.536683946 1.278802775 1.311363366 1 18.0116837 0.296457814 2.696802504 1.000000123 1.312054961 0.407781356 0.115526811 53.73625155 203.2088867 0.103574373 0.027362496 1.979054774 -0.296457814 0.312054838 GTQSIPNDS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTQSIPNDSPAR 12 0 Q9NQ92;H9KV77;J3QRX6 Q9NQ92 COPRS Coordinator of PRMT5 and differentiation stimulator 1 GTQSIPNDS(1)PAR;GTQSIPNDS(1)PAR 246.85 1.47E-16 1044900000 1211810 1114110 1199170 1090170 960160 1279100 1378600 1085420 835110 TRUE FALSE 1135964.975 1196599.864 1227614.879 1118145.608 884752.9067 1648355.406 1171891.728 1220937.076 695724.746 1.632779317 1.719932877 1.76451231 1.607166648 1.271699637 2.369263728 1.684418637 1.75491397 1 19.40815711 3.319489964 24.09680119 1.686252388 1.717176751 0 0.354282497 404.1998138 120309.5041 0.090727241 0.122845213 2086.843898 -3.319489964 0.030924363 GTQSTEGS(ph)PVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTQSTEGSPVSK 12 0 A0A087WXK8;Q9H4H8-2;Q9H4H8 A0A087WXK8 FAM83D Protein FAM83D 1 GTQST(0.012)EGS(0.988)PVSK 159.02 7.54E-05 159930000 348020 315790 354330 340010 332520 288140 430930 285700 300160 TRUE FALSE 326238.0494 339171.4202 362734.8749 348735.2322 306405.2205 371321.3404 366316.0471 321370.2739 250061.3569 1.304632005 1.356352794 1.450583487 1.394598656 1.225320155 1.484920921 1.46490466 1.285165681 1 17.9319226 0.92392575 5.661789824 1.000025986 1.390400052 0.707063916 0.077412839 0.30994338 22.15769098 0.073689756 0.018556838 8.393164795 -0.92392575 0.390374067 GTS(ph)PRPPEGGLGYSQLGDDDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GTSPRPPEGGLGYSQLGDDDLK 22 1 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12;Q9UQ88-8;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;Q9UQ88-5;Q9UQ88-10 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 GT(0.139)S(0.861)PRPPEGGLGYSQLGDDDLK;GT(0.02)S(0.98)PRPPEGGLGYSQLGDDDLK;GT(0.04)S(0.96)PRPPEGGLGYSQLGDDDLK;GTS(1)PRPPEGGLGYSQLGDDDLK;GT(0.022)S(0.978)PRPPEGGLGYSQLGDDDLK 215.2 8.75E-26 2083050000 3000060 1575330 2122010 1870230 1841190 1867750 2618610 1819050 1827970 TRUE FALSE 2812291.6 1691969.072 2172345.079 1918223.268 1696590.364 2406939.105 2225973.74 2046162.397 1522869.998 1.846704974 1.111039731 1.426480975 1.25961065 1.114074325 1.580528284 1.461696496 1.343622502 1 20.53836136 -2.150470582 2.047067913 0.240889035 1.373404323 0.238944987 0.217932113 3690831.544 802221.4415 12994957.24 0.049042398 0.007071791 2.150470582 1.132515288 GTS(ph)PSSSSRPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GTSPSSSSRPQR 12 1 H3BVG0;Q8N1F7;Q8N1F7-2 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 GT(0.201)S(0.797)PS(0.002)SSSRPQR;GT(0.358)S(0.642)PSSSSRPQR;GT(0.02)S(0.453)PS(0.049)S(0.177)S(0.177)S(0.124)RPQR 110.14 0.00092193 3623214000 1700480 2007212 1882484 1921270 1883345 1834030 2290298 1845782 1518830 TRUE FALSE 1594049.992 2155828.065 1927137.409 1970573.041 1735434.681 2363484.688 1946889.077 2076231.946 1265327.461 1.259792458 1.703770867 1.523034526 1.557362107 1.371530086 1.867883817 1.538644451 1.640865317 1 20.27107937 -1.250181691 5.948844686 0.99998014 1.573511003 0.522117344 0.16713253 3.87E-05 4.87E-06 0.142169282 0.033508463 0.056210611 1.250181691 0.573530864 GTSDLLAWDPLFGPSLDSSSSSSLTSSSS(ph)ARPTTPLSVGTIVPPPRPASRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTSDLLAWDPLFGPSLDSSSSSSLTSSSSARPTTPLSVGTIVPPPRPASRPK 52 3 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 GTSDLLAWDPLFGPSLDSS(0.001)S(0.005)S(0.005)S(0.005)S(0.005)LT(0.005)S(0.043)S(0.043)S(0.037)S(0.314)ARPT(0.264)T(0.264)PLS(0.007)VGT(0.001)IVPPPRPAS(0.001)RPK 146.98 2.11E-18 101540000 131560 150870 134890 139180 179780 111170 167290 141070 188850 TRUE FALSE 123325.8944 162040.5718 138089.6545 142751.5944 165660.804 143262.9743 142206.4175 158682.9 157329.715 0.783869051 1.029942575 0.877708668 0.907340323 1.052953055 0.910590694 0.903875136 1.00860095 1 17.26343165 GTSDLLAWDPLFGPSLDSSSSSSLTSSSSARPTT(ph)PLSVGTIVPPPRPAS(ph)RPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTSDLLAWDPLFGPSLDSSSSSSLTSSSSARPTTPLSVGTIVPPPRPASRPK 52 3 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 2 GTSDLLAWDPLFGPSLDS(0.022)S(0.023)S(0.025)S(0.027)S(0.029)S(0.031)LT(0.036)S(0.039)S(0.042)S(0.046)S(0.049)ARPT(0.302)T(0.327)PLS(0.026)VGT(0.378)IVPPPRPAS(0.597)RPK 119.17 5.39E-11 127600000 70821 57888 63695 62856 84228 55742 99666 75532 117550 TRUE FALSE 66388.44003 62174.08775 65205.87548 64468.99137 77613.07264 71833.8105 84722.00855 84962.33647 97930.1456 0.67791628 0.634882011 0.665840688 0.658316098 0.792535048 0.73352092 0.865126954 0.867581029 1 16.57946541 1.643330868 0.555031544 0.999332012 0.639364879 0.922308667 0.032616488 0.168309286 0.119397655 0.028468063 0.016731149 43.98766087 -1.643330868 -0.359967133 GTSGS(ph)LADVFANTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTSGSLADVFANTR 14 0 Q9P265 Q9P265 DIP2B Disco-interacting protein 2 homolog B 1 GTS(0.016)GS(0.984)LADVFANTR 170.92 3.25E-06 126110000 206360 225100 229360 187870 214880 188650 279890 237000 311860 TRUE FALSE 193444.296 241766.6382 234800.5275 192691.0623 198004.1916 243110.1925 237923.0929 266589.9717 259808.5513 0.744564777 0.930556893 0.903744416 0.741665589 0.76211576 0.935728217 0.915763133 1.026101606 1 17.98708939 1.623296356 1.740255369 1.008485901 0.843821201 0.522899694 0.07075797 0.325154433 2.001265649 0.059611607 0.021601293 42.00455186 -1.623296356 -0.1646647 GTSPSSSS(ph)RPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GTSPSSSSRPQR 12 1 H3BVG0;Q8N1F7;Q8N1F7-2 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 GTS(0.011)PS(0.107)S(0.045)S(0.045)S(0.793)RPQR;GT(0.002)S(0.282)PS(0.052)S(0.03)S(0.03)S(0.604)RPQR;GTS(0.043)PS(0.05)S(0.05)S(0.05)S(0.807)RPQR 133.18 0.00044162 2254280000 1997450 2429010 2276360 2442010 2318020 2100490 2664360 2051650 1793690 TRUE FALSE 1872433.17 2608856.428 2330356.334 2504676.111 2135972.06 2706867.364 2264863.953 2307803.019 1494311.551 1.253040685 1.745858436 1.559484923 1.6761405 1.429402093 1.811447795 1.515657127 1.544392143 1 20.51104954 0.449582647 1.627986303 1.000054361 1.593938087 0.555052974 0.158797357 2.458664481 6.554584123 0.131799328 0.037501528 2.815675795 -0.449582647 0.593883726 GTSS(ph)PDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTSSPDYR 8 0 Q66K14-2;Q66K14;G3V133 Q66K14-2 TBC1D9B TBC1 domain family member 9B 1 GT(0.007)S(0.061)S(0.932)PDYR;GT(0.004)S(0.045)S(0.951)PDYR 114.89 0.0026941 707300000 560800 650030 592780 645880 649860 553580 653730 538610 587420 TRUE FALSE 525700.5291 698158.8976 606841.0215 662454.3743 598822.617 713389.5594 555709.2554 605856.6441 489375.8071 1.07422664 1.42663141 1.240030694 1.353672095 1.223645731 1.457754039 1.135547053 1.238019198 1 18.90058326 0.84596622 1.036830147 1.003808224 1.299617828 0.346479837 0.117896728 0.689998276 1.457185022 0.097690781 0.031579958 7.014007407 -0.84596622 0.295809604 GTSYQSPHGIPIDLLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GTSYQSPHGIPIDLLDR 17 0 Q9Y230;Q9Y230-2;M0R0Y3 Q9Y230 RUVBL2 RuvB-like 2 0 ;;; 167.92 2.16E-09 2012280000 991880 1388960 1318250 1306860 1460360 1270230 1335040 1225610 1028570 FALSE TRUE 929800.0014 1491800.044 1349519.513 1340396.24 1345669.216 1636924.781 1134863.146 1378630.106 856895.0222 1.085080409 1.74093676 1.574894798 1.564247901 1.570401486 1.910297922 1.324389939 1.60886698 1 19.70875895 -0.917327651 7.754057614 0.999999998 1.566553177 0.373987429 0.221336674 5.68E-09 1.47E-09 0.190597013 0.044924146 0.120968515 0.917327651 0.566553179 GTTGTQASFLQLFEGDDHKVEQLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTTGTQASFLQLFEGDDHKVEQLDK 25 1 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A1B0GTG9;A0A1B0GWF8;P30566-2;A0A096LNY5;A0A096LNY6;A0A096LP92;A0A096LPA2 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 0 51.234 0.079374 17531000 24479 20484 27243 30101 30077 16418 25353 21392 29796 FALSE TRUE 22946.90309 22000.65667 27889.21683 30873.44262 27714.87374 21157.61008 21551.55302 24062.83829 24822.85511 0.92442642 0.886306453 1.123529775 1.243750668 1.116506285 0.852343938 0.868214108 0.969382377 1 14.59938144 2.235848411 24.99690597 0.90475203 1.052582646 0.271478817 0.109070646 99.11340045 913457.95 0.043519039 0.033613613 172.1267667 -2.235848411 0.147830615 GTTITLVLKEEASDYLELDTIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GTTITLVLKEEASDYLELDTIK 22 1 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 ;;;;; 287.93 1.43E-46 158582300 180843.6 204032.6 187455.5 244879.9 304954.4 120198.6 218369.9 161621.1 302300.5 FALSE TRUE 169524.9219 219139.386 191902.033 251163.9328 281004.5116 154897.9846 185627.3607 181799.8501 251844.5936 0.67313306 0.870137345 0.761985915 0.997297298 1.115785364 0.615053841 0.737071057 0.72187315 1 17.94217424 -0.525858968 7.164938758 1 0.812547831 0.133805706 0.150671616 0 1.50E-10 0.144009733 0.03394342 0.297948382 0.525858968 -0.187452168 GTVGEPTYDAEFQHFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GTVGEPTYDAEFQHFLR 17 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 301.48 2.06E-46 1557910000 1511130 2016710 1829850 1864690 2073570 1657620 2079510 2010780 1678360 FALSE TRUE 1416551.071 2166029.307 1873254.906 1912541.102 1910720.177 2136147.985 1767706.781 2261830.309 1398230.873 1.013102412 1.549121356 1.339732187 1.367829261 1.366526954 1.527750549 1.264245279 1.617637225 1 20.41517116 -1.311026484 4.404506438 0.999641113 1.388638654 0.332777326 0.169102909 0.000510941 7.99E-05 0.140378203 0.033057382 0.048862256 1.311026484 0.388997541 GTVIIIANHGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTVIIIANHGDR 12 0 A0A087WYS1;E7EUC7;Q16851;Q16851-2 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 ; 137.62 8.89E-05 449540000 447080 462550 511020 501070 502370 467930 502550 465630 463960 FALSE TRUE 419098.0609 496797.6833 523141.6357 513928.3045 462915.8867 603013.7948 427197.2929 523764.9305 386522.0787 1.084279745 1.285302213 1.353458611 1.329622117 1.197644099 1.560101811 1.10523387 1.355071183 1 18.5601913 -0.53048073 6.438471452 1.000009289 1.287748246 0.298991399 0.136469689 0 0 0.116517635 0.02746347 0.294794428 0.53048073 0.287738957 GTVLLADNVICPGAPDFLAHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTVLLADNVICPGAPDFLAHVR 22 0 P21964-2;P21964 P21964-2 COMT Catechol O-methyltransferase 0 ; 195.39 2.43E-19 2083000000 1140670 1178770 1260820 1181590 1287640 1264050 1211240 1143330 1221060 FALSE TRUE 1069277.501 1266047.357 1290727.246 1211911.6 1186513.948 1628960.715 1029625.807 1286077.267 1017257.198 1.051137808 1.244569574 1.268830782 1.191352199 1.166385405 1.60132631 1.012158782 1.264259688 1 19.95625306 -0.607882183 7.116191636 1.000063728 1.228621854 0.165934951 0.158348774 0 0 0.136691457 0.032218485 0.246670842 0.607882183 0.228558126 GTVQALHATGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GTVQALHATGAR 12 0 Q7Z4W1;J3KS22;J3QS36 Q7Z4W1 DCXR L-xylulose reductase 0 ;;; 206.03 9.49E-08 2955160000 1677620 2557140 2238480 2319410 2713020 2131830 2354690 2134360 2332340 FALSE TRUE 1572620.759 2746473.306 2291577.803 2378929.987 2499950.353 2747254.714 2001626.094 2400839.544 1943057.387 0.809353738 1.413480284 1.179367022 1.224323071 1.286606546 1.413882437 1.030142552 1.235598887 1 20.88989708 0.81119508 1.042248546 1.006134468 1.229884886 0.086874524 0.179561459 1.543868217 3.206812618 0.153570389 0.049410941 6.474333703 -0.81119508 0.223750417 GTVRPANDFNPDADAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GTVRPANDFNPDADAK 16 1 E5RK69;P08133;P08133-2 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ;;;; 164.93 6.57E-09 2887410000 2725720 1716070 2098760 1614810 2555760 1238930 2736050 2331690 4059560 FALSE TRUE 2555122.051 1843129.608 2148543.578 1656248.758 2355040.919 1596588.979 2325804.703 2622806.629 3381993.21 0.755507741 0.544983237 0.635289146 0.489725631 0.696347028 0.472085211 0.687702357 0.775520962 1 21.68944233 1.002087934 1.737440505 0.996834448 0.596479985 0.677150428 0.088182704 0.18621089 1.162129055 0.071732045 0.020606944 10.04819221 -1.002087934 -0.400354463 GTVSFHSHSDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GTVSFHSHSDHR 12 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 118.87 0.00033504 243590000 121200 195460 145850 146060 202080 158550 206440 179870 206170 FALSE TRUE 113614.3083 209932.0618 149309.6309 149808.1469 186209.452 204320.8112 175486.2385 202327.1654 171758.8951 0.661475543 1.222248558 0.869297807 0.872200225 1.084132801 1.189579212 1.021701021 1.177971978 1 17.39002529 2.633418824 7.204801045 1.098926005 0.953069822 0.25841511 0.149567734 0.443967562 26.78559415 0.046087737 0.043389638 429.9508622 -2.633418824 -0.145856183 GTVTDFPGFDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GTVTDFPGFDER 12 0 P08758;D6RBE9;E9PHT9;D6RCN3 P08758 ANXA5 Annexin A5;Annexin 0 ;;;;; 215.87 9.40E-11 2716860000 3207630 4241320 2765560 2583880 3074190 2260990 3883320 2874770 6001660 FALSE TRUE 3006870.164 4555351.746 2831160.389 2650186.735 2832755.518 2913701.109 3301052.217 3233691.363 4999944.174 0.601380747 0.911080522 0.5662384 0.530043265 0.566557429 0.582746728 0.660217815 0.646745494 1 22.25348056 0.104002312 2.27059608 1.000005841 0.645524677 0.536061838 0.106709542 78.02456827 194.2818027 0.109910991 0.029571407 1.270580871 -0.104002312 -0.354481164 GTVTDFPGFDERADAETLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTVTDFPGFDERADAETLR 19 1 P08758;D6RBE9;E9PHT9;D6RCN3 P08758 ANXA5 Annexin A5;Annexin 0 ; 179.78 3.20E-14 220815000 232741 244981 328750 341810 394290 287520 311620 292930 118264 FALSE TRUE 218174.1563 263119.6481 336548.1052 350581.4233 363324.0539 370522.3565 264895.4739 329502.9553 98524.97439 2.214404598 2.670588344 3.41586595 3.55830007 3.687634086 3.760694776 2.688612462 3.344359716 1 16.58820185 -1.159752927 3.832539213 0.998707082 3.163590288 0.649576718 0.500319943 45831863.16 87808925.91 747416.2005 0.122199732 0.069222467 1.159752927 2.164883206 GTWERPGGAAPLGYDFWYQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GTWERPGGAAPLGYDFWYQPR 21 1 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 217.42 5.31E-25 7199900000 1462140 1924880 1470320 1299940 1934720 943190 1657550 1517690 1885700 FALSE TRUE 1370627.267 2067400.118 1505196.685 1333298.661 1782774.895 1215473.642 1409015.765 1707176.937 1570964.488 0.872475016 1.316006908 0.958135398 0.848713431 1.134828259 0.773711724 0.896911277 1.086706256 1 20.58321914 3.706731427 6.512613564 0.941131141 1.129699199 0.110998321 0.149704501 0.210315068 35.71873676 0.036115536 0.05850211 5090.159918 -3.706731427 0.188568058 GTWESHPETTELVVLQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GTWESHPETTELVVLQGR 18 0 P36915;A0A140T8Y2;P36915-2 P36915 GNL1 Guanine nucleotide-binding protein-like 1 0 ;;; 254.72 1.53E-30 612110000 663670 770680 733120 746900 821200 696300 814220 705490 821130 FALSE TRUE 622132.0794 827741.9491 750509.9526 766066.7185 756706.2646 897310.5065 692135.2698 793571.9795 684078.0983 0.909445984 1.210010891 1.097111506 1.119852719 1.106169407 1.311707696 1.011778146 1.160060498 1 19.38380152 -1.787234121 1.053343105 0.926667878 1.122886799 0.100001224 0.107232557 3531.486607 791.8013075 656.5924988 0.028416777 0.016321718 1.787234121 0.196218921 GTYVPSS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GTYVPSSPTR 10 0 Q9Y4P8-4;Q9Y4P8 Q9Y4P8-4 WIPI2 WD repeat domain phosphoinositide-interacting protein 2 1 GTYVPS(0.004)S(0.586)PT(0.41)R;GTYVPS(0.003)S(0.992)PT(0.005)R;GTYVPS(0.001)S(0.998)PT(0.001)R;GTYVPSS(1)PTR 199.8 2.85E-07 5084580000 3937030 5898100 4622460 5573290 7050100 3409320 4046350 4369330 5402470 TRUE FALSE 3690618.32 6334801.461 4732106.934 5716310.057 6496413.585 4393535.338 3439637.382 4914850.469 4500762.856 0.819998395 1.407495055 1.051401082 1.270075816 1.443402773 0.976175702 0.764234307 1.092003873 1 22.10173812 2.026663196 21.06000449 0.911963657 1.21014511 0.268283508 0.193319192 38.11960931 30108.04595 0.066464611 0.049082586 106.3318075 -2.026663196 0.298181454 GVAGAHGLLCLLSDHVDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GVAGAHGLLCLLSDHVDKR 19 1 U3KQ56;Q9UBQ7 U3KQ56 GRHPR Glyoxylate reductase/hydroxypyruvate reductase 0 ; 214.82 1.71E-19 1184000000 942140 1222590 1250340 1212420 1467540 1049640 1365010 1226750 1617280 FALSE TRUE 883173.1392 1313111.836 1279998.655 1243532.75 1352285.328 1352654.029 1160339.423 1379912.438 1347345.52 0.655491206 0.974591756 0.950015149 0.92295015 1.003666326 1.003939976 0.861204053 1.02417117 1 20.36168844 4.740347106 24.97999918 0.959011218 0.655491103 0.802742833 0.04845261 66.2543997 926343.5997 0.010915207 0.070288609 54998.02645 -4.740347106 -0.303520115 GVAINMVTEEDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GVAINMVTEEDKR 13 1 P60842 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;; 190.34 7.21E-06 1036010000 794930 557590 690680 701290 705050 530620 814930 648000 839550 FALSE TRUE 745176.7503 598874.5438 707063.2558 719286.2887 649678.217 683801.3801 692738.8119 728904.2264 699423.6813 1.065415384 0.856240016 1.010922671 1.028398534 0.928876494 0.977664037 0.990442318 1.042149767 1 19.41580712 1.524081523 3.064868942 1.020664359 0.967813929 0.064854674 0.057832153 0.480939577 9.682951321 0.039444297 0.014675894 33.42577788 -1.524081523 -0.05285043 GVAPADS(ph)PEAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVAPADSPEAPR 12 0 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 GVAPADS(1)PEAPR 119.39 0.0005488 610960000 286570 366940 331490 313720 346520 339220 353750 265450 308430 TRUE FALSE 268634.0952 394108.6194 339353.0993 321770.5863 319305.717 437147.3072 300708.4716 298592.0168 256951.0405 1.045468019 1.533788766 1.320691672 1.252264189 1.24267143 1.701286387 1.17029482 1.162058018 1 17.97113397 1.538238676 9.116394302 1.110058124 1.364436284 0.287200205 0.178905351 0.137760101 17.99853177 0.089001071 0.041369418 34.53334729 -1.538238676 0.25437816 GVAPADS(ph)PEAPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GVAPADSPEAPRR 13 1 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 GVAPADS(1)PEAPRR;GVAPADS(1)PEAPRR 236.17 6.40E-17 1951330000 1286240 1535980 1429550 1376910 1532090 1333420 1439140 1314740 1752490 TRUE FALSE 1205736.534 1649705.557 1463459.601 1412243.842 1411765.832 1718356.708 1223354.317 1478888.183 1459988.097 0.825853674 1.129944525 1.002377762 0.967298188 0.966970781 1.176966244 0.837920747 1.01294537 1 20.47752518 1.71083532 25 0.939773509 1.020766249 0.062682726 0.10528033 1.70455932 1529.446464 0.044190286 0.024505733 51.38487683 -1.71083532 0.080992739 GVCLIDEFDKMNDQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GVCLIDEFDKMNDQDR 16 1 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 ;; 147.35 9.45E-07 372980000 359878 322635 334484 341695 380483 280034 392575 306061 417701 FALSE TRUE 337353.8784 346523.2311 342418.1184 350463.4722 350601.4 360875.2698 333712.0232 344273.3896 347984.0046 0.969452256 0.995802182 0.984005339 1.007125234 1.007521597 1.037045568 0.958986674 0.989336823 1 18.40866147 6.367885786 1.146027659 0.996372165 7.93E-06 0.156711615 0.019828836 134.1312496 5.855351003 0.005639475 326.4342047 2332844.472 -6.367885786 -0.996364234 GVDDLDFFIGDEAIEKPTYATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GVDDLDFFIGDEAIEKPTYATK 22 1 B4DXW1;P61158;F8WDR7 B4DXW1 ACTR3 Actin-related protein 3 0 ;;; 319.02 1.49E-67 1367570000 2452220 1911545 2144567 2040438 2346642 1664823 2652710 1979360 2819820 FALSE TRUE 2298739.928 2053077.781 2195437.142 2092799.094 2162346.203 2145430.374 2254960.762 2226487.453 2349173.825 0.978531219 0.873957371 0.934557127 0.890866002 0.920470925 0.913270168 0.959895235 0.947774673 1 21.16372204 1.199460894 0.907970481 0.997255703 0.912902645 0.430237618 0.028971453 0.426194687 0.768327888 0.024162314 0.008647144 15.82927025 -1.199460894 -0.084353058 GVDFES(ph)S(ph)EDDDDDPFMNTSSLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GVDFESSEDDDDDPFMNTSSLRR 23 1 F8W7U8;P49959-2;P49959;P49959-3 F8W7U8 MRE11A Double-strand break repair protein MRE11A 2 GVDFES(1)S(1)EDDDDDPFMNTSSLRR;GVDFES(1)S(1)EDDDDDPFMNTSSLRR 83.202 0.0037943 157377000 107718 160533 130292 144351 170241 107934 151655 128186 270340 TRUE FALSE 100976.1227 172419.0304 133382.5878 148055.291 156870.9586 139092.7936 128915.7406 144190.3043 225218.5075 0.448347357 0.765563329 0.592236354 0.6573851 0.696527831 0.617590424 0.572402961 0.640224047 1 17.78096586 0.923951835 21.31778476 1 0.631620279 0.670359147 0.082772205 6746.008663 1891041.707 0.072919051 0.018229763 8.39366893 -0.923951835 -0.368379721 GVDLDAPGSINGVPLLEVDLDSFEDKPWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GVDLDAPGSINGVPLLEVDLDSFEDKPWR 29 1 Q6UN15;Q6UN15-5;Q6UN15-3;A0A0B4J203;Q6UN15-4 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 0 ; 208.57 1.28E-25 160555000 193449 189688 193111 172151 201499 155738 212828 174248 208185 FALSE TRUE 181341.3724 203732.6969 197691.6841 176568.6861 185674.0813 200697.0324 180916.4172 196003.2464 173437.5786 1.045571403 1.174674477 1.139843428 1.018053224 1.070552777 1.157171554 1.043121212 1.130108296 1 17.40405699 -4.999999981 0.150255482 0.628688208 1.136119333 0.199083996 0.054595985 184.6766869 1.647756219 20.45110048 0.268141429 1.00E-05 4.999999981 0.507431125 GVDLLLEGVQGESS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVDLLLEGVQGESSPTR 17 0 F5H7T0;F6RJM5;Q96S38-2;Q96S38 F5H7T0 RPS6KC1 Ribosomal protein S6 kinase delta-1 1 GVDLLLEGVQGES(0.064)S(0.934)PT(0.002)R 244.27 1.75E-20 19378000 67643 58595 64686 64779 59884 60776 70097 53093 50139 TRUE FALSE 63409.34538 62933.43477 66220.38247 66441.33881 55180.9522 78321.04458 59586.6056 59721.77792 41770.47699 1.518042166 1.506648698 1.585339389 1.590629162 1.321051522 1.875033522 1.426524423 1.429760497 1 15.350196 0.763326867 1.719527186 1.001376547 1.55318927 0.602175536 0.139791827 0.518725543 2.55364693 0.117161424 0.033260534 5.798649614 -0.763326867 0.551812723 GVDLVLNSLAEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GVDLVLNSLAEEK 13 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 206.69 1.39E-07 171749000 370580 358803 393903 401353 400404 352911 452990 375032 421486 FALSE TRUE 347386.0593 385369.1475 403246.5652 411652.3975 368957.885 454790.6767 385068.3549 421855.5707 351137.2637 0.989316986 1.09748861 1.148401514 1.172340392 1.050751154 1.295193429 1.096631986 1.201397899 1 18.42167558 5.047116145 1.215640957 1.146161436 0.809519437 0.244551258 0.080967117 3.515190183 2.707755649 0.019642834 1.777324794 111459.2573 -5.047116145 -0.336641999 GVEEEEEDGEMRE ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GVEEEEEDGEMRE 13 1 P62306 P62306 SNRPF Small nuclear ribonucleoprotein F 0 ;;; 268.91 1.50E-23 4969200000 2887280 4401640 3077600 3040690 4399440 2806880 3528740 3744250 4125690 FALSE TRUE 2706570.299 4727542.006 3150602.125 3118719.253 4053925.729 3617180.69 2999638.196 4211727.855 3437085.686 0.787460816 1.375450727 0.916649282 0.907373146 1.179466007 1.052397589 0.872727209 1.225377613 1 21.71275439 3.755915762 24.51696824 1.011893292 1.130233594 8.80E-05 0.180254734 774.4243112 659374.8075 0.042161453 0.075989689 5700.53691 -3.755915762 0.118340303 GVEFPMADLDALS(ph)PIHT(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVEFPMADLDALSPIHTPQR 20 0 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-5 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 2 GVEFPMADLDALS(1)PIHT(1)PQR 65.833 0.043079 12412000 4981.1 7289.2 8052.1 6768.3 6282.4 8057.8 6352.9 6509 7497.1 TRUE FALSE 4669.341843 7828.899952 8243.099614 6941.986037 5789.005646 10383.95605 5400.341622 7321.662978 6245.785577 0.747598806 1.253469216 1.31978588 1.111467237 0.926865896 1.662554041 0.864637691 1.172256538 1 12.60866733 GVEFVHVYCVDNILVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GVEFVHVYCVDNILVR 16 0 Q3KQV9;Q3KQV9-2 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 ; 128.9 5.83E-05 160368000 192168 231683 223161 229685 267921 179220 225750 201543 158173 FALSE TRUE 180140.5479 248837.0504 228454.4843 235579.106 246879.5654 230957.9046 191900.8833 226706.0872 131772.9045 1.367053027 1.888377974 1.733698481 1.787765906 1.873522986 1.752696471 1.456300019 1.720430221 1 17.00769422 0.206449816 0.626164926 0.97216495 1.753412277 0.625268078 0.168295564 1.78654266 0.934499289 0.281786566 0.062471147 1.60860649 -0.206449816 0.781247327 GVEITGFPEAQALGLEVFHAGTALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVEITGFPEAQALGLEVFHAGTALK 25 0 P22102;P22102-2 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 250.71 1.14E-39 66227000 206390 205820 223800 219210 236410 184040 255450 219970 243480 FALSE TRUE 193472.4183 221059.127 229108.6417 224835.2997 217843.3122 237169.3604 217147.644 247433.7387 202841.6151 0.953810283 1.089811511 1.129495255 1.108427872 1.073957689 1.169234234 1.070528076 1.219837155 1 17.62999414 4.757640032 2.840637698 1.112654093 0.92099104 0.408063788 0.058659123 0.401720363 4.382250038 0.012193046 0.182155852 57232.14623 -4.757640032 -0.191663053 GVELCFPENET(ph)PPEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVELCFPENETPPEGK 16 0 A0A590UJ01;Q13535-2;Q13535-3;Q13535 A0A590UJ01 ATR Serine/threonine-protein kinase ATR 1 GVELCFPENET(1)PPEGK 250.1 1.09E-19 28526000 96303 74368 80304 80817 74587 76438 111640 69178 99190 TRUE FALSE 90275.56714 79874.2841 82208.8488 82890.90104 68729.23789 98504.40973 94900.61841 77815.02558 82634.54821 1.092467607 0.96659673 0.994848409 1.003102248 0.831725221 1.192048748 1.148437554 0.941676663 1 16.33445746 2.222321991 24.99994172 1.093829038 0.9797117 0.174533373 0.094366687 325.5539986 501199.087 0.033189864 0.024586043 166.8483787 -2.222321991 -0.114117338 GVEPSPS(ph)PIKPGDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GVEPSPSPIKPGDIK 15 1 Q92890;Q92890-1;Q92890-3;C9JNP9 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 1 GVEPS(0.016)PS(0.984)PIKPGDIK;GVEPS(0.031)PS(0.969)PIKPGDIK;GVEPS(0.002)PS(0.998)PIKPGDIK;GVEPS(0.01)PS(0.99)PIKPGDIK 125.73 5.78E-05 965070000 3524110 1488910 2388510 2035490 1943400 1763490 2782490 1835770 2314190 TRUE FALSE 3303542.246 1599150.446 2445166.585 2087724.119 1790773.203 2272580.935 2365281.456 2064969.926 1927936.739 1.713511745 0.829462095 1.268281545 1.082879992 0.928854753 1.178763229 1.226845989 1.071077637 1 20.87862628 4.754175721 24.79998507 1.090272331 1.713512258 0.692428612 0.133674612 1637.564742 2600739.88 0.031450037 0.792732172 56777.4288 -4.754175721 0.623239927 GVEPSPS(ph)PIKPGDIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GVEPSPSPIKPGDIKR 16 2 Q92890;Q92890-1;Q92890-3 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 1 GVEPSPS(1)PIKPGDIKR;GVEPS(0.01)PS(0.99)PIKPGDIKR;GVEPS(0.004)PS(0.996)PIKPGDIKR;GVEPSPS(1)PIKPGDIKR;GVEPSPS(1)PIKPGDIKR 201.67 1.69E-11 1575750000 3813130 2048060 2841910 2523310 3024690 2076350 3697380 2341370 4329240 TRUE FALSE 3574473 2199700.493 2909321.447 2588062.407 2787143.048 2675758.538 3142992.194 2633695.198 3606661.876 0.991075161 0.609899283 0.80665212 0.71757833 0.772776363 0.741893371 0.871440768 0.730230692 1 21.78223275 -0.745099224 0.422051738 1.071121431 0.756000094 0.291511617 0.102469613 12.80679636 1.824558957 1.291978319 0.055963424 0.179845997 0.745099224 -0.315121336 GVESVFDIMEMEDEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GVESVFDIMEMEDEER 16 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;;; 262.07 1.69E-26 133601000 138807 157945 153372 154480 146996 147491 177634 146677 115557.5 FALSE TRUE 130119.3176 169639.4121 157010.0563 158444.2183 135451.5271 190069.2574 150999.4308 164989.9463 96270.20672 1.351605259 1.76211746 1.630930914 1.645828172 1.406993209 1.97433104 1.568495965 1.713821461 1 16.55480177 -0.720043939 6.469368182 1.000000006 1.646585373 0.561182531 0.175133867 6.59E-09 1.36E-09 0.147499112 0.034765874 0.190526795 0.720043939 0.646585367 GVFPEGEGDGS(ph)LPEDHFSELPQVDTILFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVFPEGEGDGSLPEDHFSELPQVDTILFK 29 0 Q8IWZ3-6;Q8IWZ3;Q8IWZ3-4;E9PDP5 Q8IWZ3-6 ANKHD1 Ankyrin repeat and KH domain-containing protein 1 1 GVFPEGEGDGS(0.999)LPEDHFS(0.001)ELPQVDTILFK 66.902 0.0060918 9200000 11896 15393 17132 13926 17003 12395 19585 17615 14908 TRUE FALSE 11151.45059 16532.71374 17538.37913 14283.36474 15667.65297 15973.23528 16648.41107 19814.27153 12419.75849 0.897879826 1.331162256 1.41213528 1.15005173 1.261510276 1.286114806 1.340477843 1.595382997 1 13.6003495 1.886879663 3.155145102 1.348308588 1.252812312 0.021248209 0.197367936 0.927860833 16.0727155 0.096134513 0.051351672 77.06898923 -1.886879663 -0.095496277 GVGDDQLGEESEERDDHLLPM ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GVGDDQLGEESEERDDHLLPM 21 1 P20645;F5GX30;H0YF90 P20645 M6PR Cation-dependent mannose-6-phosphate receptor 0 ; 67.866 0.022067 336588000 270935 364155 293779 290968 379747 234093 350844 321211 392215 FALSE TRUE 253977.662 391117.4151 300747.5766 298434.7315 349923.2024 301671.8489 298238.1993 361314.9004 326751.7827 0.777280111 1.196986324 0.920416024 0.91333773 1.07091444 0.923244692 0.912736258 1.105777901 1 18.31783558 4.794182356 23.02417043 0.998130007 0.777276088 0.357011037 0.095778724 33828.75754 14001859.01 0.022653712 33.97017698 62256.16372 -4.794182356 -0.22085392 GVGDGTVSWGLEDDEDMTLTR ddPTM_SK-BR-3_Pertuzumab_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 ; 296.04 1.64E-54 69909000 41840 42431 44740 41316 42297 42839 47241 38785 32871 FALSE TRUE 39221.30909 45572.63539 45801.25393 42376.23851 38975.16424 55205.92387 40157.65061 43627.39263 27384.61775 1.432238691 1.664169126 1.672517555 1.547446778 1.423250257 2.015946484 1.466430935 1.593134987 1 14.74107812 0.377548343 1.49668209 1.000031148 1.621427846 0.548997131 0.171131074 3.098953382 6.71188648 0.147200217 0.042451069 2.3853293 -0.377548343 0.621396697 GVGQADWT(ph)PDLGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVGQADWTPDLGLR 14 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GVGQADWT(1)PDLGLR 126.91 0.00092355 109480000 268120 296950 279780 312690 286860 297130 349470 266800 278990 TRUE FALSE 251338.8478 318936.487 286416.5137 320714.1548 264331.1727 382906.6075 297070.2178 300110.5673 232424.7667 1.081377219 1.372213863 1.232297736 1.379862221 1.137276275 1.647443226 1.278134951 1.291215956 1 17.82640428 0.65089971 2.900185632 1.000025141 1.314684046 0.275533681 0.153575703 4.878663107 39.09689916 0.131124478 0.034400652 4.476099272 -0.65089971 0.314658905 GVGTDEACLIEILASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVGTDEACLIEILASR 16 0 P50995;P50995-2 P50995 ANXA11 Annexin A11 0 153.75 9.80E-07 10913000 10492 12843 16600 14195 16986 13497 17563 12843 27521 FALSE TRUE 9835.324449 13793.90908 16993.75984 14559.26773 15651.98808 17393.36479 14929.5912 14446.47682 22927.56731 0.428973747 0.601629859 0.741193325 0.635011449 0.682671121 0.758622341 0.651163335 0.630092004 1 14.48479567 -5 0.143494884 2.152064757 0.536660466 0.677353726 0.081839055 89.85275803 0.782141783 29.90976766 0.471997765 1.00E-05 5 -1.615404291 GVHIHQAGGS(ph)PPASSTSSSSLTNDVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GVHIHQAGGSPPASSTSSSSLTNDVAK 27 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 1 GVHIHQAGGS(0.398)PPAS(0.111)S(0.111)T(0.111)S(0.111)S(0.111)S(0.046)S(0.002)LTNDVAK;GVHIHQAGGS(0.17)PPAS(0.17)S(0.17)T(0.17)S(0.17)S(0.065)S(0.065)S(0.019)LTNDVAK;GVHIHQAGGS(0.462)PPAS(0.313)S(0.031)T(0.192)S(0.002)SSSLTNDVAK;GVHIHQAGGS(0.985)PPASST(0.011)S(0.003)S(0.001)SSLTNDVAK 274.76 4.82E-61 3655980000 476617 492830 554171 564860 581074 468414 676380 488380 685080 TRUE FALSE 446786.3928 529319.646 567316.1978 579355.2639 535438.792 603637.5177 574963.0982 549355.3181 570735.7222 0.782825352 0.927433881 0.994008568 1.01510251 0.938155386 1.05764804 1.007406889 0.962538872 1 19.12246334 5.613958544 0.901305801 1.001007791 9.72E-13 0.819327717 0.031771708 3.371307777 0.667953022 0.009327285 4.827010149 411110.4763 -5.613958544 -1.001007791 GVHIHQAGGSPPAS(ph)STSSSSLTNDVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVHIHQAGGSPPASSTSSSSLTNDVAK 27 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 1 GVHIHQAGGS(0.006)PPAS(0.829)S(0.105)T(0.059)SSSSLTNDVAK 264.36 1.90E-53 702630000 217890 255050 252500 275970 309670 215370 340630 260100 355140 TRUE FALSE 204252.6538 273934.1674 258489.4192 283051.8574 285349.7673 277543.8228 289555.6938 292574.0576 295864.8397 0.690357983 0.925876044 0.873674004 0.956693123 0.964459878 0.938076397 0.978675581 0.988877414 1 18.17457873 5.56726087 0.840208985 0.960417615 3.13E-62 0.810058927 0.039251773 3.581022332 0.704010688 0.012491715 4.428912354 369199.3009 -5.56726087 -0.960417615 GVHPHIVEMDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVHPHIVEMDR 11 0 O76041-2;O76041 O76041-2 NEBL Nebulette 0 88.441 0.0090833 140620000 65531 74089 71918 86903 68876 80989 84936 64734 62311 FALSE TRUE 61429.53169 79574.62665 73623.92892 89133.07811 63466.75679 104369.2096 72200.63531 72816.1824 51910.89156 1.18336499 1.53290811 1.418275177 1.717040017 1.222609647 2.010545503 1.390857162 1.402714926 1 15.66374965 0.79501727 2.191259094 1.001158606 1.509541445 0.301044445 0.23665718 0.893039585 7.193440235 0.198797806 0.054245936 6.237596397 -0.79501727 0.508382838 GVIDYDRDRFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVIDYDRDRFDR 12 2 P49750;P49750-1;H0YIQ2;P49750-3;F8VU51;H0YI23 P49750 YLPM1 YLP motif-containing protein 1 0 123.84 0.00018767 124820000 86216 151710 116990 105790 173420 95368 108540 110910 219280 FALSE TRUE 80819.89446 162942.7663 119765.058 108504.7505 159800.2927 122899.1934 92265.43464 124757.3576 182680.7514 0.442410565 0.891953668 0.655597577 0.593958311 0.874751672 0.67275393 0.505063801 0.682925577 1 17.4789651 -1.095622492 5.496811818 1.000003461 0.676149984 0.358011066 0.140298797 5.76E-06 9.48E-07 0.131507169 0.030996206 0.080237522 1.095622492 -0.323853477 GVILTSDRPGVFSAGLDLTEMCGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GVILTSDRPGVFSAGLDLTEMCGR 24 1 H3BS70;Q96DC0;P42126-2;P42126 H3BS70 ECI1;DCI "Enoyl-CoA delta isomerase 1, mitochondrial" 0 ; 248.21 4.21E-38 614990000 263490 348930 193917 173095 480780 211686 203454 329280 327670 FALSE TRUE 246998.6312 374765.1403 198516.8028 177536.9107 443021.4782 272796.3118 172947.9615 370391.3328 272979.7602 0.904823973 1.372867864 0.727221691 0.650366572 1.622909618 0.999327978 0.633555987 1.356845403 1 18.05843446 1.635351593 0.009965144 3.71E-07 2.000897906 0 0.332784813 11585.94181 116.2182186 11637.57997 11679.4195 43.18685643 -1.635351593 2.000897536 GVIS(ph)TPVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVISTPVIR 9 0 Q9NZB2;Q9NZB2-4;Q9NZB2-6;A0A0C4DG79;A0A494C0Y9 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 1 GVIS(0.5)T(0.5)PVIR 148.52 9.42E-05 87215000 171160 240790 215060 212000 281980 161420 303110 231320 330780 TRUE FALSE 160447.4011 258618.3421 220161.3248 217440.2789 259834.4283 208019.3336 257661.4694 260200.8112 275570.6811 0.582236835 0.938482792 0.798928696 0.789054474 0.942895765 0.754867436 0.935010461 0.944225308 1 18.07206288 8 0.084449875 1.118197951 0.125725832 0.40611848 0.096796825 201.9634511 1.234914858 2.052411302 23.29598303 100000000 -8 -0.992472119 GVITDQNS(ph)DGYCQTGTMSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVITDQNSDGYCQTGTMSR 19 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GVITDQNS(1)DGYCQTGTMSR 176.1 5.46E-15 0 104420 131140 111400 114020 112570 102790 149450 99644 82869 TRUE FALSE 97884.5386 140849.7421 114042.4606 116945.9462 103729.2063 132463.8043 127041.3599 112084.7727 69037.62855 1.417843293 2.040188011 1.651888441 1.693945008 1.502502454 1.918718924 1.840175606 1.623531618 1 16.07509529 0.874021065 5.413600867 1.000013499 1.752597942 0.596271797 0.184462364 0.935279523 39.71921291 0.165639846 0.041761754 7.482057911 -0.874021065 0.752584442 GVIVDKDFSHPQMPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GVIVDKDFSHPQMPK 15 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;; 198.16 4.84E-09 6055400000 14440800 11166850 12817920 12289200 14447500 9631790 15740700 11887600 17439800 FALSE TRUE 13536976.11 11993655.19 13121967.12 12604561.68 13312851.63 12412331.41 13380528.16 13371793.03 14528984.71 0.931722097 0.825498507 0.903157886 0.867545938 0.916296072 0.854315126 0.920954108 0.920352887 1 23.79243056 0.723380678 0.68720887 1.001682851 0.876479419 0.558275182 0.031835415 0.726885055 0.682929239 0.029494374 0.010883222 5.289086599 -0.723380678 -0.125203432 GVKPVFSIGDEEEYDT(ph)DEIDSSSMSDDDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVKPVFSIGDEEEYDTDEIDSSSMSDDDRK 30 2 Q9NUY8-2;Q9NUY8;E9PGE5 Q9NUY8-2 TBC1D23 TBC1 domain family member 23 1 GVKPVFSIGDEEEYDT(1)DEIDSSSMSDDDRK 178.8 3.78E-16 111820000 300240 169270 204680 226390 227930 177940 285950 219750 238920 TRUE FALSE 281448.5143 181802.9269 209535.1063 232199.5507 210029.2972 229308.3894 243074.4521 247186.2712 199042.7085 1.414010674 0.91338652 1.052714303 1.166581546 1.055197142 1.152056215 1.221217567 1.241875541 1 17.6027185 2.081759277 5.395340648 1.180791246 1.085416542 0 0.143080385 0.510209948 25.18273019 0.051807682 0.037633532 120.7144547 -2.081759277 -0.095374704 GVLFHSGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVLFHSGGK 9 0 P43034;I3L3N5 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 107.57 0.0034151 0 506170 549490 437710 487250 574300 390730 616460 550390 590970 FALSE TRUE 474489.7232 590174.8113 448092.6879 499753.6599 529196.7946 503527.408 524027.5459 619107.4031 492333.2892 0.963757141 1.198730259 0.910140951 1.015071844 1.074875102 1.022736872 1.064375612 1.257496531 1 18.90927577 1.441169928 12.42517268 1.139513836 1.03880954 0.142416911 0.096188852 0.875151962 295.8868273 0.050697829 0.022031167 27.61658212 -1.441169928 -0.100704296 GVLRPGTALVLLEAQAATGFVIDPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GVLRPGTALVLLEAQAATGFVIDPVR 26 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;; 253.39 1.38E-52 2912446000 1540122 1971740 1748540 1708132 2062543 1652954 1928604 1620112 1269198 FALSE TRUE 1443728.513 2117729.681 1790016.195 1751965.559 1900559.193 2130134.986 1639427.734 1822386.55 1057360.654 1.365407827 2.002845171 1.692909781 1.656923351 1.797455943 2.014577502 1.55049058 1.72352408 1 20.01203612 0.221864005 0.990305844 0.995774116 1.762909685 0.578083455 0.193612193 2.554731655 2.690274171 0.193988688 0.053779651 1.666725214 -0.221864005 0.767135569 GVLTGPEYEALDALPDAERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GVLTGPEYEALDALPDAERR 20 1 H3BM67;H3BUP2;H3BUN4;O60936;O60936-3;O60936-1;H3BQJ5 H3BM67 NOL3 Nucleolar protein 3 0 ; 230.07 3.09E-25 107686000 66325 80589 79907 73278 75397 69117 72292 62313 76347 FALSE TRUE 62173.83664 86555.89341 81802.43177 75158.43754 69475.62376 89069.95588 61452.48573 70092.91522 63604.19248 0.977511611 1.360852014 1.286116977 1.181658545 1.092312017 1.400378692 0.966170363 1.102017218 1 15.95683424 1.679912323 9.566782096 1.027355431 1.234749932 0.332767514 0.127223078 0.120995281 17.16241866 0.0573564 0.030761388 47.85334742 -1.679912323 0.207394501 GVMAVTAVTATAAS(ph)DR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVMAVTAVTATAASDR 16 0 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WT54 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 1 GVMAVTAVTAT(0.001)AAS(0.999)DR 144.29 1.40E-06 63525000 147090 106190 134070 132780 121560 169440 166520 110820 105080 TRUE FALSE 137883.8995 114052.4181 137250.2037 136187.3596 112013.1679 218354.5774 141551.8719 124656.1209 87541.46916 1.575069516 1.302838748 1.56783071 1.555689674 1.279544072 2.494298753 1.616969343 1.423966517 1 16.41767898 GVMLAVDAVIAELKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GVMLAVDAVIAELKK 15 1 P10809;E7EXB4;E7ESH4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;; 221.91 2.36E-12 409470000 452181 409473 416869 361171 505670 326211 416255 389726 584200 FALSE TRUE 423879.7984 439790.807 426757.3295 370439.2593 465956.718 420382.8201 353841.4271 438384.149 486693.2459 0.870938321 0.903630389 0.876850733 0.761134991 0.957393023 0.863753141 0.727031719 0.900740153 1 18.89265323 3.461410646 24.97572564 0.847447792 0.888762494 0 0.082296723 762.1308168 1211583.999 0.021632145 0.02932121 2893.414447 -3.461410646 0.041314702 GVNADKVGIEAAEMLLANLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GVNADKVGIEAAEMLLANLR 20 1 O00442;O00442-2 O00442 RTCA RNA 3-terminal phosphate cyclase 0 ; 164.98 2.01E-11 72674000 394200 386870 390210 418670 469940 339180 466810 365150 475730 FALSE TRUE 369527.7257 415514.2573 399465.9655 429413.781 433032.808 437095.7599 396816.1742 410739.7813 396327.5897 0.932379515 1.048411133 1.007918641 1.083481928 1.092613331 1.10286483 1.001232779 1.036364341 1 18.59633388 4.739240469 24.17456137 1.046256285 0.932379459 0.481717416 0.037235408 32.47983807 1154545.638 0.008952347 0.053126091 54858.06303 -4.739240469 -0.113876826 GVNAIVYMIDAADREK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVNAIVYMIDAADREK 16 1 Q9NVJ2;Q9NVJ2-2 Q9NVJ2 ARL8B ADP-ribosylation factor-like protein 8B 0 84.859 0.006699 50079000 186350 164650 164490 174780 190860 127520 179520 155990 181800 FALSE TRUE 174686.6861 176840.8573 168391.7805 179265.1507 175870.6255 164332.9539 152602.6426 175465.6949 151456.4055 1.153379321 1.167602365 1.111816829 1.183608908 1.161196351 1.085018183 1.007568099 1.158522773 1 17.20854307 2.115277968 4.424490897 1.054097859 1.152293732 0.507005993 0.046010411 0.165710019 5.643747153 0.01649804 0.011856688 130.4001132 -2.115277968 0.098195873 GVNCIDYYSGGDKPYLISGADDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GVNCIDYYSGGDKPYLISGADDR 23 1 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ;;; 283.72 3.55E-52 3114240000 3001077 3023829 3208610 3331373 3360070 2659866 4031777 2905148 3726880 FALSE TRUE 2813244.948 3247716.445 3284719.744 3416861.671 3096183.656 3427726.135 3427249.468 3267862.123 3104839.651 0.906083812 1.046017447 1.057935389 1.100495373 0.997212096 1.103994576 1.103841052 1.052505923 1 21.56608733 4.855425791 2.166808243 1.066152114 0.827002504 0.598220234 0.038788316 0.660881406 2.675209172 0.009127938 0.340992719 71684.58766 -4.855425791 -0.23914961 GVNIGGAGS(ph)YIYEKPLAEGPQVTGPIEVPAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVNIGGAGSYIYEKPLAEGPQVTGPIEVPAAR 32 1 P52943;H0YFA4;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 1 GVNIGGAGS(1)YIYEKPLAEGPQVTGPIEVPAAR 189.02 4.52E-20 63751000 49003 42619 43372 36687 49512 33678 51432 37074 67469 TRUE FALSE 45935.9897 45774.55511 44400.80432 37628.45053 45623.52724 43400.29188 43720.24907 41702.77051 56207.98803 0.817250204 0.814378111 0.789937621 0.66945023 0.811691164 0.772137438 0.777829817 0.741936724 1 15.77848755 -1.216179449 4.149725269 1.000124507 0.777241756 0.724139791 0.043741145 4.84E-05 9.14E-06 0.040661294 0.009578619 0.060788377 1.216179449 -0.222882751 GVNTFS(ph)PEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GVNTFSPEGR 10 0 P28066 P28066 PSMA5 Proteasome subunit alpha type-5 1 GVNT(0.003)FS(0.997)PEGR;GVNT(0.007)FS(0.993)PEGR;GVNT(0.032)FS(0.968)PEGR;GVNT(0.05)FS(0.95)PEGR 135.1 0.0025419 339867000 667005 727270 732240 733160 787680 679757 810920 650210 1005100 TRUE FALSE 625258.3477 781117.8275 749609.0786 751974.1268 725818.7901 875991.811 689330.0742 731390.1498 837342.3168 0.746717722 0.932853639 0.895224168 0.898048638 0.866812504 1.04615734 0.823235683 0.873466126 1 19.67545801 4.743437615 24.6827067 0.910322367 0.746717642 0.399395429 0.065162241 432.0363461 2186468.759 0.01398623 0.114190845 55390.79715 -4.743437615 -0.163604725 GVNTGAVGSYIYDRDPEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GVNTGAVGSYIYDRDPEGK 19 1 P52943;H0YFA4;H0YHD8;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 ;;;; 302.74 4.18E-50 11862130000 6506550 5440000 6087560 5876740 6313980 4637590 7547170 5506990 7413350 FALSE TRUE 6099316.65 5842783.26 6231959.798 6027547.098 5818105.48 5976386.948 6415541.923 6194549.824 6176013.993 0.987581417 0.946044369 1.009058562 0.975960726 0.942048623 0.967677041 1.03878358 1.003001261 1 22.55824459 1.753205262 25 1.016738066 0.971862671 0.462533157 0.021538742 4.070827224 6958.565947 0.009758265 0.005411481 56.65069757 -1.753205262 -0.044875395 GVNWAAFHPTMPLIVSGADDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GVNWAAFHPTMPLIVSGADDR 21 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1;A0A3B3IU78 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;; 206.28 4.30E-22 1467550000 1224640 1854520 1570200 1592830 1763540 1273540 1731480 1521600 1632960 FALSE TRUE 1147991.968 1991830.59 1607445.886 1633704.714 1625038.682 1641190.324 1471860.648 1711575.109 1360408.427 0.843858319 1.464141615 1.181590656 1.200892822 1.194522652 1.206395294 1.08192556 1.258133275 1 20.37560842 -0.150250999 0.372129971 0.957783035 1.224318457 0.068175519 0.157387418 10.94394101 1.889928816 0.835072121 0.114256848 0.707536748 0.150250999 0.266535422 GVPAGNS(ph)DTEGGQPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.987)DT(0.013)EGGQPGR;GVPAGNS(0.975)DT(0.025)EGGQPGR;GVPAGNS(0.958)DT(0.042)EGGQPGR;GVPAGNS(0.983)DT(0.017)EGGQPGR;GVPAGNS(0.936)DT(0.064)EGGQPGR;GVPAGNS(0.997)DT(0.003)EGGQPGR 244.27 5.02E-20 2440030000 712077 812253 819214 847308 801559 809347 880436 689402 844857 TRUE FALSE 667509.3717 872393.0573 838646.1429 869051.3578 738607.7895 1042992.34 748422.7954 775475.3573 703844.9087 0.948375648 1.239467739 1.191521218 1.23471996 1.049389973 1.481849662 1.063334814 1.101770216 1 19.42489804 1.586146998 25 1.061848108 1.198504796 0.173478977 0.138861595 1.498051666 1718.653074 0.066507439 0.030831848 38.56088544 -1.586146998 0.136656688 GVPEKS(ph)PVLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 143.97 2.24E-05 5771260000 7891000 4579330 6028200 5688570 5743580 4083330 6702450 4438960 6052820 TRUE FALSE 7397116.396 4918388.358 6171191.751 5834548.337 5292502.395 5262121.084 5697479.845 4993173.927 5042565.239 1.46693519 0.975374264 1.223819913 1.157059564 1.049565478 1.043540506 1.12987727 0.990205122 1 22.26572641 4.748984409 24.94449585 1.086093047 1.466935408 0.70347854 0.080230325 830.2846061 1986859.661 0.018270531 0.260175004 56102.78346 -4.748984409 0.380842361 GVPHPEDDHSQVEGPESLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GVPHPEDDHSQVEGPESLR 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ;;; 233.65 2.36E-24 3793320000 1031280 1343310 1225190 1315610 1313670 1131590 1384990 1129880 1270060 FALSE TRUE 966734.0257 1442770.07 1254252.085 1349370.78 1210499.657 1458261.663 1177323.607 1270948.005 1058078.781 0.91366923 1.36357528 1.185405196 1.275302751 1.144054374 1.378216527 1.112699383 1.201184664 1 20.01301562 0.578714364 1.116121101 1.000701954 1.220248407 0.163650374 0.133389868 2.164882212 3.988759017 0.111780246 0.034660683 3.790655907 -0.578714364 0.219546453 GVPLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 GVPLYR 6 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90;A0A2R8YEM5;P13929-3;P13929-2;P13929;E5RGZ4;E5RI09;E5RG95;K7EPM1;K7EKN2 P06733 ENO1;ENO3 Alpha-enolase;Enolase;Beta-enolase 0 ;;;;;;;;; 148.49 0.02503 8941699000 4217160 5611030 4489750 4235040 5864640 3551560 4906190 4955270 5944140 FALSE TRUE 3953215.483 6026476.499 4596248.99 4343718.296 5404054.831 4576837.717 4170552.356 5573946.367 4952024.633 0.798302871 1.216972238 0.928155518 0.877160074 1.091281896 0.924235652 0.842191359 1.125589386 1 22.23958706 3.727934303 24.98810184 0.954850595 1.048048923 0 0.133786607 92.34256312 2837888.178 0.032125824 0.054005682 5344.835002 -3.727934303 0.093198328 GVQDIVVGEGTHFLIPWVQKPIIFDCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GVQDIVVGEGTHFLIPWVQKPIIFDCR 27 1 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 ; 245.68 1.16E-45 1944810000 2119610 2339720 1976700 1658230 3146300 1767040 2213780 2548070 2578660 FALSE TRUE 1986947.394 2512955.303 2023588.257 1700782.989 2899202.29 2277155.763 1881844.241 2866202.148 2148264.987 0.924907963 1.169760397 0.941963989 0.791700744 1.349555249 1.059997615 0.875983294 1.33419395 1 21.03474053 2.762403944 24.99683981 1.0910637 0.990009625 0.167213784 0.169846627 2212.150219 2319168.59 0.051252263 0.054336583 578.633994 -2.762403944 -0.101054075 GVQKPAGPSTS(ph)PDGNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GVQKPAGPSTSPDGNSR 17 1 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 GVQKPAGPS(0.015)T(0.037)S(0.948)PDGNSR;GVQKPAGPS(0.061)T(0.173)S(0.766)PDGNSR;GVQKPAGPS(0.083)T(0.248)S(0.669)PDGNSR;GVQKPAGPS(0.016)T(0.061)S(0.923)PDGNSR 177.32 6.27E-10 957680000 535102 508289 528270 534521 558480 418905 545678 468068 585340 TRUE FALSE 501610.921 545923.2464 540800.8139 548237.7138 514619.2336 539836.0731 463858.6497 526507.3201 487642.9726 1.028643801 1.119514229 1.109009756 1.124260462 1.055319696 1.107031381 0.95122595 1.079698365 1 18.89546574 1.758041308 25 1.007312691 1.096018929 0.4383573 0.042523681 6.570722232 8440.253001 0.017712247 0.009822232 57.28505153 -1.758041308 0.088706238 GVQLQTHPNVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVQLQTHPNVDK 12 0 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 110.8 0.00040744 0 188500 166930 188010 190100 192510 147360 230060 174790 194290 FALSE TRUE 176702.1215 179289.6709 192469.686 194978.2878 177391.0411 189900.4398 195564.6388 196612.9163 161861.7438 1.091685517 1.107671687 1.189099298 1.204597722 1.09594174 1.173226207 1.208220263 1.214696639 1 17.30440252 -1.332582998 3.323138346 0.999021514 1.161851656 0.536033245 0.0469569 1291318.688 1048772.777 8103.215058 0.011183844 0.046496151 1.332582998 0.162830142 GVQLQTHPNVDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVQLQTHPNVDKK 13 1 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 136.3 4.80E-05 1232100000 1341200 965890 1143100 1124800 1266700 861600 1453000 1031300 1557400 FALSE TRUE 1257256.686 1037405.501 1170214.872 1153664.272 1167218.492 1110329.933 1235136.139 1160060.075 1297459.879 0.969013922 0.799566536 0.901927598 0.889171443 0.899618178 0.855772075 0.951964804 0.894100923 1 20.3072585 0.539652561 0.426842424 1.009439771 0.871380714 0.319452995 0.047027039 2.089210296 0.751204882 0.086195517 0.029037637 3.464595689 -0.539652561 -0.138059056 GVQVETISPGDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GVQVETISPGDGR 13 0 P62942;A0A087WZM5;Q1JUQ3;A0A087WTS4;A0A087WV48 P62942 FKBP1A;FKBP12-Exin Peptidyl-prolyl cis-trans isomerase FKBP1A;Peptidyl-prolyl cis-trans isomerase 0 ;; 191.29 8.58E-06 602720000 543780 562710 570650 586800 574580 546980 615260 527880 623870 FALSE TRUE 509745.7805 604373.6339 584186.0875 601858.2815 529454.8045 704884.2465 523007.4748 593786.98 519742.0666 0.980766833 1.162833784 1.123992313 1.157994167 1.018687612 1.356219348 1.006282747 1.14246473 1 18.98743631 -0.82277105 8.760133271 1 1.123192238 0.107690904 0.106630396 0 0 0.088944795 0.020964489 0.15039346 0.82277105 0.123192238 GVQYLNEIKDSVVAGFQWATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVQYLNEIKDSVVAGFQWATK 21 1 P13639 P13639 EEF2 Elongation factor 2 0 339.22 1.65E-80 858890000 1757300 1705500 1758900 1857800 2094900 1401200 2225000 1557000 2790500 FALSE TRUE 1647313.73 1831776.995 1800621.939 1905474.293 1930375.004 1805703.693 1891381.906 1751394.877 2324747.523 0.708598983 0.787946638 0.774545159 0.819647843 0.83035899 0.776731097 0.813585943 0.75336993 1 21.14864261 -4.99999999 0.311943797 2.905193776 0.776851909 0.785195152 0.035529083 130.7197775 1.179729957 163.8668117 0.030771383 1.00E-05 4.99999999 -2.128341867 GVS(ph)CFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GVSCFR 6 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 GVS(1)CFR;GVS(1)CFR;GVS(1)CFR;GVS(1)CFR 130.04 0.016714 3033740000 2348270 4033600 4062480 4002730 4549070 4017540 4331270 3751420 2624860 TRUE FALSE 2201295.972 4332251.941 4158843.944 4105446.828 4191804.392 5177338.579 3681836.273 4219793.045 2186753.909 1.006650069 1.981133736 1.901834462 1.877416024 1.916907237 2.367590865 1.683699413 1.929706415 1 21.06035944 -1.27583899 4.064651975 0.999015033 1.866629926 0.367816106 0.340744946 23682149.28 7434443.627 206554.4443 0.071618273 0.052985985 1.27583899 0.867614894 GVS(ph)FDQANNLLIEPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVSFDQANNLLIEPAR 16 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 GVS(1)FDQANNLLIEPAR 57.159 0.082833 0 12096 12947 11081 11092 11102 9975.7 12890 8096.7 10929 TRUE FALSE 11338.93295 13905.60935 11343.84655 11376.6395 10230.0937 12855.52265 10957.26416 9107.590818 9104.879296 1.245368838 1.527270038 1.245908505 1.249510194 1.123583671 1.411937735 1.20344969 1.00029781 1 13.15242418 1.663225659 0.283259753 0.94813096 1.435008788 0.468514181 0.118950165 1.399394751 0.421290666 0.238915786 0.248086965 46.04957843 -1.663225659 0.486877827 GVSAVAGPHDIGAS(ph)PGDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVSAVAGPHDIGASPGDKK 19 1 Q8IYB7;Q8IYB7-3;Q8IYB7-2;Q8IYB7-4;Q8IYB7-5;C9JGP4 Q8IYB7 DIS3L2 DIS3-like exonuclease 2 1 GVSAVAGPHDIGAS(1)PGDKK 118.16 3.99E-05 94583000 314670 151980 213270 210040 206290 141270 283640 169460 275030 TRUE FALSE 294975.3664 163232.7573 218328.8651 215429.982 190088.8155 182052.3557 241110.8152 190617.454 229125.7162 1.287395283 0.712415699 0.952878047 0.940226115 0.829626716 0.79455226 1.052307961 0.831933915 1 17.80577987 -1.207916558 5.134990369 1.00000763 0.910898343 0.014343217 0.159910138 1.24E-05 1.91E-06 0.137228485 0.032342295 0.06195601 1.207916558 -0.089109287 GVSDSLLFDTS(ph)DDEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVSDSLLFDTSDDEELR 17 0 F8W6C0;G3V0F5;Q9UHY8;Q9UHY8-2;F8WB37 F8W6C0 FEZ2 Fasciculation and elongation protein zeta-2 1 GVSDSLLFDT(0.059)S(0.941)DDEELR 164.93 2.61E-09 0 50438 44115 49154 46824 40494 46988 54203 43873 35756 TRUE FALSE 47281.17561 47381.3205 50319.95609 48025.58311 37313.76458 60552.67281 46075.76335 49350.64063 29788.09261 1.58725086 1.59061277 1.689264122 1.612240963 1.252640277 2.032781139 1.546784615 1.656723755 1 14.86244813 -1.329197307 5.047478629 0.999742658 1.625709463 0.517870069 0.188270025 0.000482313 6.41E-05 0.161260874 0.037994272 0.046860044 1.329197307 0.625966805 GVSFYEVPPHLFAVADTVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GVSFYEVPPHLFAVADTVYR 20 0 O00159-3;F5H6E2;O00159-2;O00159;I3L3F5;I3L501;I3L3Y6 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 150.98 8.11E-08 258570000 721160 819140 735860 677820 882010 633780 727500 818980 660720 FALSE TRUE 676023.8829 879789.9779 753314.9467 695214.0087 812740.4925 816741.9974 618418.1288 921231.4558 550441.5636 1.228148322 1.59833493 1.368564797 1.263011471 1.476524569 1.483794196 1.123494608 1.673622627 1 19.07022989 -2.013188576 2.998950731 0.564211138 1.397809711 0.361925119 0.167641179 3713294.029 25595548.28 11512416.41 0.036454627 0.009700887 2.013188576 0.833598572 GVSMSLPSS(ph)PLLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GVSMSLPSSPLLPR 14 0 Q9C0D5;Q9C0D5-2 Q9C0D5 TANC1 Protein TANC1 1 GVSMSLPS(0.427)S(0.573)PLLPR;GVS(0.001)MS(0.009)LPS(0.308)S(0.682)PLLPR 110.25 0.0007557 233237000 353410 398080 437480 422690 432110 408040 433270 355910 341570 TRUE FALSE 331290.699 427554.2574 447857.2322 433536.941 398173.8236 525834.524 368305.1858 400346.147 284559.7604 1.164221879 1.502511307 1.573860027 1.523535655 1.399262577 1.847887851 1.2942982 1.406896556 1 18.11837214 -0.6214356 7.179665725 0.999996745 1.480469767 0.392667749 0.180351044 0 0 0.158717202 0.037410003 0.239091645 0.6214356 0.480473022 GVSSESSGDREK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVSSESSGDREK 12 1 Q13435;E9PPJ0;H0YCG1;E9PJ04 Q13435 SF3B2 Splicing factor 3B subunit 2 0 77.674 0.02534 106820000 45398 53811 46587 58657 73738 56716 58359 47530 74868 FALSE TRUE 42556.62022 57795.22243 47692.06564 60162.23793 67946.91492 73088.98849 49608.60973 53464.22513 62372.04713 0.682302765 0.926620579 0.764638453 0.96457052 1.089380869 1.171822825 0.795366066 0.857182465 1 15.92861199 5.904988388 0.539584268 0.96281759 8.38E-15 0.291079626 0.125690935 19.42394268 1.638363207 0.065098539 15.51796186 803504.6379 -5.904988388 -0.96281759 GVTDHTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GVTDHTQR 8 0 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 147.29 0.00053968 171410000 214820 301520 265770 271580 289230 251450 313210 266650 259720 FALSE TRUE 201374.7997 323844.8545 272074.1899 278549.2026 266515.0425 324039.5331 266247.0682 299941.8395 216371.0541 0.930691956 1.49671062 1.257442642 1.287368145 1.231749984 1.497610364 1.23051149 1.386238287 1 17.72314798 -1.131922086 3.799353794 0.999867584 1.307201184 0.23537391 0.161458285 5886543.881 5261253.508 6336.319349 0.032856323 0.073803663 1.131922086 0.3073336 GVTECYECHPKPTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GVTECYECHPKPTQR 15 1 Q9UBT2;Q9UBT2-2;K7EPL2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 ;;; 266.15 1.69E-25 2117450000 2122150 2082390 2215840 2122370 2297460 1947400 2670830 2079960 2837060 FALSE TRUE 1989328.42 2236572.322 2268400.771 2176833.607 2117026.759 2509582.767 2270363.836 2339647.585 2363536.358 0.841674558 0.946282174 0.959748626 0.921007033 0.895703065 1.06179148 0.960579188 0.989892784 1 21.17251563 2.256840068 24.99702867 0.997795314 0.924197534 0.537055151 0.040731701 219.2770258 299859.2583 0.013713558 0.01145353 180.6508743 -2.256840068 -0.07359778 GVTIPYRPKPSS(ph)SPVIFAGGQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GVTIPYRPKPSSSPVIFAGGQDR 23 2 Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3 Q15366;Q15366-2 PCBP2 Poly(rC)-binding protein 2 1 GVTIPYRPKPS(0.16)S(0.501)S(0.339)PVIFAGGQDR;GVTIPYRPKPS(0.131)S(0.544)S(0.325)PVIFAGGQDR;GVT(0.001)IPYRPKPS(0.124)S(0.514)S(0.361)PVIFAGGQDR;GVT(0.003)IPYRPKPS(0.045)S(0.476)S(0.476)PVIFAGGQDR 203.75 1.46E-24 5942400000 3946640 3518110 3863930 3430480 4050680 3303320 4930080 3776590 4146890 TRUE FALSE 3699626.847 3778594.525 3955584.244 3518511.925 3732555.932 4256934.859 4190860.273 4248105.575 3454747.269 1.070882053 1.093739782 1.144970655 1.018457111 1.0804136 1.232198632 1.213072895 1.229642936 1 21.72014874 2.250077449 24.975857 1.190966067 1.089089894 0.230458422 0.073554861 240.2783162 521076.7963 0.023234347 0.019281919 177.8596564 -2.250077449 -0.101876173 GVVDSDDLPLNVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GVVDSDDLPLNVSR 14 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;;; 333.92 3.70E-68 5634740000 5408100 7129680 6102470 6572630 6520130 5228900 7010720 5241480 4427330 FALSE TRUE 5069616.675 7657568.926 6247223.47 6741294.813 6008065.291 6738398.546 5959527.62 5895890.316 3688380.021 1.374483281 2.076133392 1.693758082 1.827711563 1.628917101 1.826926322 1.615757483 1.598504027 1 21.81455588 0.215981748 0.590148399 0.961584981 1.787866677 0.605228359 0.180682725 1.728496255 0.828362822 0.309256637 0.068368521 1.644302618 -0.215981748 0.826281696 GVVDSEDLPLNISR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;; 352.27 1.35E-81 5449554000 6594750 7906070 7601860 7613350 8349680 6906660 7929930 6927680 6944270 FALSE TRUE 6181996.369 8491443.649 7782179.709 7808721.45 7693929.814 8900500.622 6740910.614 7792616.098 5785226.475 1.068583295 1.46778068 1.345181514 1.349769362 1.32992716 1.538487847 1.165193903 1.346985486 1 22.46394201 0.398242977 0.864328647 0.998504553 1.352804552 0.358067864 0.134469278 2.091784474 2.145354083 0.126321443 0.039154159 2.501744637 -0.398242977 0.354299999 GVVIPTWNIS(ph)PIKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GVVIPTWNISPIKK 14 1 A4PB68;Q3T8J9-3;Q3T8J9;A0A087WUE6;Q3T8J9-2 A4PB68;Q3T8J9-3 GON4L GON-4-like protein 1 GVVIPTWNIS(1)PIKK;GVVIPTWNIS(1)PIKK 216.19 3.81E-12 329980000 1085410 635590 801820 712520 875080 654420 1132440 749580 937710 TRUE FALSE 1017476.126 682649.7449 820839.549 730804.4695 806354.7467 843340.4304 962641.1351 843166.713 781200.1432 1.302452559 0.87384744 1.050741678 0.935489421 1.032199947 1.079544644 1.232259292 1.079322272 1 19.57533269 2.116503105 3.831595509 1.134642191 1.013230158 0.01060003 0.125640727 0.390635064 10.78738531 0.046557705 0.032748394 130.7684887 -2.116503105 -0.121412033 GVVPLAGTDGETTTQGLDGLSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GVVPLAGTDGETTTQGLDGLSER 23 0 P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5 P09972 ALDOC Fructose-bisphosphate aldolase C;Fructose-bisphosphate aldolase 0 ;;; 356.82 1.58E-101 439965000 280379 343481 273185 250143 324064 226135 277263 227128 300554 FALSE TRUE 262830.5789 368912.6906 279665.0772 256562.0929 298613.3207 291416.5035 235689.9871 255485.4308 250389.5957 1.049686502 1.473354712 1.11691972 1.024651572 1.192594763 1.163852286 0.941293053 1.020351624 1 17.93381509 2.92364437 0.57114159 0.989029552 1.296257717 0.271550625 0.127647626 0.965257233 0.672112727 0.099172095 0.13899947 838.7728616 -2.92364437 0.307228165 GVVPLAGTNGETTTQGLDGLSER ddPTM_SK-BR-3_Pertuzumab_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 ;;; 419.37 3.08E-158 1031880000 235671 252216 187194 209122 225059 201755 240900 220927 183451 FALSE TRUE 220920.7728 270890.3351 191634.3301 214488.4246 207383.774 259998.3933 204779.2814 248510.2223 152831.843 1.445515336 1.77247313 1.253890069 1.403427587 1.35694087 1.70120564 1.339899313 1.62603694 1 17.22158564 -1.214077559 3.553904622 0.999265719 1.484421707 0.459445723 0.166125939 29614902.97 50259674.42 259682.2303 0.037713957 0.061083293 1.214077559 0.485155988 GVVTEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 68.422 0.062495 322290000 187500 508090 402650 456960 525750 364520 403100 504580 422120 FALSE TRUE 175764.7097 545709.5123 412201.0481 468686.3672 484459.7158 469751.0065 342658.8972 567577.9237 351665.445 0.499806598 1.551785994 1.172139754 1.332762072 1.377615352 1.335789493 0.974388875 1.613971267 1 18.42384406 4.750607927 24.88079672 1.289570101 0.499806082 0.594700887 0.206216455 1208.98283 2496812.227 0.045429036 0.762266826 56312.90443 -4.750607927 -0.789764019 GVYSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GVYSGR 6 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ; 111.69 0.064292 490200000 307300 524440 371760 415360 523880 319300 375120 429140 404460 FALSE TRUE 288066.6415 563270.0833 380578.3228 426018.8408 482736.578 411476.7266 318874.2384 482719.0737 336953.0131 0.854916354 1.671657654 1.129470009 1.264327144 1.432652504 1.221169453 0.946346304 1.432600555 1 18.3621879 1.995650179 24.12332729 1.111205029 1.307525144 0.056241071 0.242558996 233.5231632 1295081.489 0.084829308 0.061051539 99.00341585 -1.995650179 0.196320114 GWAFGSNS(ph)LPIAGSVGMGVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GWAFGSNSLPIAGSVGMGVAR 21 0 M0QZ22;Q5PRF9;A0A087WZT0 M0QZ22 SAMD4B Protein Smaug homolog 2 1 GWAFGSNS(1)LPIAGSVGMGVAR;GWAFGSNS(1)LPIAGSVGMGVAR 313.1 1.42E-66 187556000 202314 275150 207641 220650 278980 181810 213250 227607 213729 TRUE FALSE 189651.5279 295522.3923 212566.3426 226312.2526 257070.0362 234295.5956 181275.1422 256024.235 178056.2492 1.065121436 1.659713679 1.193815682 1.2710155 1.443757449 1.315851573 1.018077956 1.437884018 1 17.44197354 0.619056719 0.289413551 0.941601105 1.400658422 0.157430378 0.192648832 4.529197728 0.911049508 0.677037823 0.276643106 4.159649322 -0.619056719 0.459057317 GWDDLFNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GWDDLFNK 8 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 172.14 0.00066367 499160000 1046860 1145370 1125640 1173150 1340540 911870 1386960 1161850 1322220 FALSE TRUE 981338.9013 1230174.387 1152340.712 1203255.015 1235259.396 1175112.066 1178998.224 1306909.53 1101532.94 0.890884753 1.116784021 1.046124605 1.092345922 1.121400324 1.066797027 1.070324982 1.186446163 1 20.07108121 4.74393263 24.62224942 1.087128391 0.89088465 0.61066198 0.049344203 290.9746087 1333611.056 0.010358694 0.088211157 55453.96828 -4.74393263 -0.196243741 GWDLVDAVT(ph)PGPQPTLEQLEEGGPRPLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GWDLVDAVTPGPQPTLEQLEEGGPRPLER 29 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 GWDLVDAVT(0.999)PGPQPT(0.001)LEQLEEGGPRPLER 136.79 6.64E-06 76783000 57013 82444 77738 104160 100820 65646 91131 70737 71318 TRUE FALSE 53444.6581 88548.23954 79581.98207 106832.9219 92902.00389 84596.93453 77466.75257 79568.67016 59414.56507 0.899521153 1.490345666 1.339435574 1.798093141 1.563623394 1.423841686 1.303834379 1.339211523 1 15.85852902 0.745852697 1.121089338 1.003346245 1.431101406 0.237546808 0.225334432 1.22317828 2.729722887 0.20233457 0.063334714 5.569967956 -0.745852697 0.427755161 GWEEGVAQMSVGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GWEEGVAQMSVGQR 14 0 P62942;Q5W0X3;Q1JUQ5 P62942 FKBP1A;FKBP12-Exip2 Peptidyl-prolyl cis-trans isomerase FKBP1A;Peptidyl-prolyl cis-trans isomerase 0 ; 239.48 5.38E-17 336790000 244590 240520 244640 256020 295580 209005 273270 258513 325350 FALSE TRUE 229281.5485 258328.3511 250442.9763 262589.9066 272366.3391 269341.3506 232295.7004 290788.9171 271046.9832 0.845910719 0.953075913 0.923983633 0.968798485 1.004867628 0.993707244 0.857031123 1.072835837 1 18.04818342 5.900696887 0.979179274 0.963939733 8.91E-13 0.311260534 0.05701568 21.98016537 2.845014049 0.016396029 37.59461673 795603.8702 -5.900696887 -0.963939733 GWEFMWNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 GWEFMWNER 9 0 P12532;P12532-2;P17540 P12532 CKMT1A;CKMT2 "Creatine kinase U-type, mitochondrial;Creatine kinase S-type, mitochondrial" 0 ;;;;;;; 148.52 0.00020894 4489444000 1632104 2392437 1493247 1705348 2865008 1277850 1574925 2136528 2329972 FALSE TRUE 1529953.524 2569575.525 1528667.524 1749110.117 2640001.829 1646744.551 1338779.617 2403278.224 1941084.621 0.788195171 1.323783362 0.787532654 0.901099364 1.360065295 0.848363092 0.689706983 1.238111001 1 20.88843158 GWGS(ph)PGRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GWGSPGRPK 9 1 S4R3H3;S4R393;S4R410;A7E2V4-5;A7E2V4;A7E2V4-3;A7E2V4-4;A7E2V4-2;H7BZ52;H0YCW2;S4R3B3;H7C453;S4R3U7 S4R3H3 ZSWIM8 Zinc finger SWIM domain-containing protein 8 1 GWGS(1)PGRPK;GWGS(1)PGRPK 92.611 0.0060312 883530000 810400 741020 847660 862440 1017450 702070 1110600 918130 1274320 TRUE FALSE 759678.5106 795885.8918 867766.8955 884571.6705 937543.5812 904746.2118 944075.8403 1032760.552 1061627.76 0.715578981 0.749684515 0.817392808 0.833222062 0.88311894 0.852225466 0.889271999 0.972808541 1 20.01784657 7.498634442 0.119821022 1.077570498 5.05E-09 0.93944004 0.021587663 17.64028684 0.163177041 0.147336683 3.125709263 31523500.86 -7.498634442 -1.077570493 GWLRDPSAS(ph)PGDAGEQAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GWLRDPSASPGDAGEQAIR 19 1 P18206;P18206-2 P18206 VCL Vinculin 1 GWLRDPS(0.098)AS(0.902)PGDAGEQAIR 81.89 0.0031702 90953000 38148 46499 42285 44545 48267 38988 49522 47817 59610 TRUE FALSE 35760.38478 49941.83434 43288.02017 45688.10011 44476.30452 50243.20268 42096.63584 53787.05771 49660.7059 0.72009417 1.005660984 0.87167549 0.920005048 0.89560355 1.011729531 0.847685007 1.083090881 1 15.59981715 4.749209855 24.72993985 0.940738685 0.720094024 0.491614643 0.073731071 1121.042037 2603254.02 0.015530707 0.226169912 56131.91453 -4.749209855 -0.220644662 GWMDPQSK ddPTM_SK-BR-3_Pertuzumab_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 59604000 120760 133560 107880 110720 110980 84069 157710 111230 167440 FALSE TRUE 113201.8472 143448.9214 110438.9645 113561.2626 102264.0785 108338.3556 134062.8496 125117.3103 139493.1823 0.811522436 1.028357938 0.791715858 0.814099017 0.73311166 0.776656993 0.961070981 0.896942118 1 17.08983509 1.669220428 8.16247416 0.94638087 0.841513507 0.334184051 0.082090623 0.184512893 21.4050711 0.0436895 0.022895203 46.6896295 -1.669220428 -0.104867363 GWQDVTATSAYKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GWQDVTATSAYKK 13 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 0 ; 222.45 2.79E-11 4959200000 6514900 7011300 6211300 6535200 9069700 4561200 8101800 6993800 10753200 FALSE TRUE 6107144.038 7530423.947 6358634.969 6702904.296 8357402.347 5877944.395 6887010.303 7866991.325 8958421.452 0.681721001 0.840597195 0.709794131 0.748223817 0.932910155 0.656136176 0.768774983 0.878167138 1 23.09481311 1.007769719 3.044669465 0.998693623 0.765164575 0.498091923 0.078986727 0.182899881 4.008846869 0.068560989 0.018054711 10.18051432 -1.007769719 -0.233529048 GWS(ph)QEGPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GWSQEGPVK 9 0 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GWS(1)QEGPVK;GWS(1)QEGPVK;GWS(1)QEGPVK;GWS(1)QEGPVK;GWS(1)QEGPVK;GWS(1)QEGPVK;GWS(1)QEGPVK 133.05 0.00030196 5765210000 7283560 5775430 5881900 5814990 3941280 4156770 7789090 4037820 5475190 TRUE FALSE 6827694.981 6203048.847 6021421.446 5964212.488 3631747.767 5356762.019 6621188.265 4541950.715 4561345.418 1.496859886 1.359916489 1.320097667 1.307555544 0.796200997 1.174382014 1.451586683 0.99574803 1 22.12102799 2.981477472 24.50465759 1.137402471 1.367388825 0.38625554 0.174641893 793.0903928 1049232.371 0.054870677 0.059193741 958.2470081 -2.981477472 0.229986354 RRS(ph)QVIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RRSQVIEK 8 2 A0A494BZV2;A0A1W2PPU9 A0A494BZV2 1 RRS(1)QVIEK;RRS(1)QVIEK;RRS(1)QVIEK;RRS(1)QVIEK 129 0.0008737 2361880000 1095450 1153320 972960 949260 1382900 675230 1281760 1171180 2620770 TRUE FALSE 1026887.74 1238713.013 996039.0707 973619.6187 1274292.612 870157.9396 1089571.987 1317404.401 2183346.556 0.470327414 0.567346036 0.456198338 0.445929949 0.583641937 0.398543207 0.499037583 0.603387674 1 21.05810971 0.789970482 2.469393567 0.999802846 0.490923571 0.896173236 0.054522359 0.249057527 2.413558111 0.048675893 0.0130502 6.165530951 -0.789970482 -0.508879275 GWVTFDR ddPTM_SK-BR-3_Pertuzumab_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 ; 108.98 0.016588 81078000 206307 304690 203765 209670 311650 178977 250850 262220 296230 FALSE TRUE 193394.6131 327249.5646 208598.402 215050.4872 287174.2661 230644.7545 213237.3713 294958.7442 246787.2993 0.783648971 1.326038923 0.845255824 0.87140014 1.163650913 0.93458924 0.864053263 1.195194182 1 17.91290862 3.927591593 24.68334844 0.969657121 1.092593939 0.015395844 0.175396962 386.4859546 192606.7469 0.041039478 0.07398511 8464.31063 -3.927591593 0.122936817 GYADS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.998)PS(0.002)K;GYADS(0.967)PS(0.033)K;GYADS(0.884)PS(0.116)K;GYADS(0.862)PS(0.138)K;GYADS(0.993)PS(0.007)K 191.4 0.00019025 14609000000 24507800 15382400 18600300 16916600 17856500 16030500 24316300 16422100 19950800 TRUE FALSE 22973900.55 16521328.9 19041507.9 17350708.6 16454122.52 20658245.12 20670296.56 18472435.33 16620882.59 1.382231083 0.994010325 1.145637591 1.043910183 0.989966834 1.242909033 1.243634112 1.111399183 1 23.98649366 2.218051419 24.99958475 1.180311883 1.096823675 0 0.130732331 597.5863912 728420.7821 0.044884363 0.033187243 165.2157397 -2.218051419 -0.083488208 GYADSPS(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.346)PS(0.654)K;GYADS(0.325)PS(0.675)K 126.29 0.0014144 268480000 810740 549170 658830 604980 683520 571340 831260 599990 745950 TRUE FALSE 759997.2306 589831.1182 674457.7587 620504.811 629839.0964 736276.5831 706620.28 674900.0722 621446.126 1.222949503 0.949126712 1.085303666 0.998485283 1.013505548 1.184779424 1.137057985 1.086015415 1 19.2452698 2.257586797 24.99696251 1.118470965 1.041358567 0.047245287 0.085542779 409.3323892 537787.3955 0.026921656 0.022490336 180.9617541 -2.257586797 -0.077112399 GYAFIEYEHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GYAFIEYEHER 11 0 P08621;P08621-2;M0QYR1;P08621-3 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;;;;;; 186.72 3.90E-06 5664240000 4244455 7312830 4848103 5080229 8005730 3390494 4257732 6658920 7577860 FALSE TRUE 3978802.138 7854279.542 4963102.293 5210596.277 7376992.259 4369274.578 3619324.613 7490300.82 6313066.211 0.630248758 1.244130709 0.78616351 0.825366962 1.168527624 0.69210023 0.573306931 1.186475885 1 22.58990945 2.20428722 24.99998259 0.79535483 0.949071516 0 0.243477825 472.9343861 344968.9954 0.086047798 0.06355359 160.0616243 -2.20428722 0.153716686 GYAFNHSADFETVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GYAFNHSADFETVR 14 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ;;; 204.28 1.39E-08 2129550000 902391 1712160 901914 994660 1771270 557187 845723 1562820 1202470 FALSE TRUE 845911.9581 1838930.108 923307.826 1020184.66 1632161.599 718037.8417 718914.6875 1757941.517 1001769.989 0.844417349 1.835680973 0.921676469 1.018382135 1.629277796 0.716769168 0.717644465 1.754835478 1 19.93411987 2.227390861 24.9998049 0.980017459 1.274489066 0.043114364 0.415628376 506.0613473 1132643.035 0.148082417 0.11036305 168.807159 -2.227390861 0.294471607 GYAVLGGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 130.27 0.00085117 337380000 132076 872750 199552 221717 852090 212998 204678 691040 469690 FALSE TRUE 123809.5989 937369.3181 204285.4677 227406.6336 785170.2886 274487.0649 173988.434 777317.8652 391295.7047 0.316409297 2.395552281 0.522074393 0.581163123 2.006590615 0.701482438 0.444646931 1.986522867 1 18.57789975 3.885898777 11.99345373 0.980248983 1.498538716 0.019458376 0.745519768 1.457457074 184.8095038 0.176481165 0.318281217 7689.511966 -3.885898777 0.518289733 GYAYVEFENPDEAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GYAYVEFENPDEAEK 15 0 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BV80;H3BPG5 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 0 ; 238.87 2.04E-17 98810000 274960 203956 234788 212189 255270 197520 284030 220135 305150 FALSE TRUE 257750.7444 219057.1145 240357.2822 217634.129 235222.1239 254540.8175 241442.3383 247619.3393 254218.4937 1.013894547 0.86168835 0.945475204 0.85609086 0.925275422 1.001267901 0.949743407 0.974041407 1 17.95570946 2.370030698 6.306219013 0.974671755 0.911868312 0.289869964 0.046140978 0.246376399 12.93072833 0.014570031 0.012132679 234.4394521 -2.370030698 -0.062803443 GYDDRDYYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GYDDRDYYSR 10 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 ;;;; 158.05 7.39E-06 21700400000 14998300 19385300 17104900 16993400 19574600 15080300 19134200 16168300 20687500 FALSE TRUE 14059583.18 20820607.78 17510636.31 17429479.41 18037289.88 19433737.8 16265204.34 18186947.85 17234622.6 0.815775518 1.20806868 1.016015071 1.011306126 1.046572953 1.127598686 0.943751698 1.055256518 1 24.03880637 1.726009123 25 0.997637035 1.054083767 0.012611838 0.102994825 2.623845435 5203.410477 0.043859992 0.024322587 53.21194367 -1.726009123 0.056446733 GYDELVPHQISVVSEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYDELVPHQISVVSEER 17 0 P35573-2;P35573-3;P35573 P35573-2 AGL "Glycogen debranching enzyme;4-alpha-glucanotransferase;Amylo-alpha-1,6-glucosidase" 0 118.24 0.00017844 174060000 169990 245600 207680 267310 262150 215100 264820 225490 267620 FALSE TRUE 159350.6293 263784.4795 212606.2677 274169.6272 241561.7965 277195.8781 225112.6995 253642.9229 222952.4931 0.714729076 1.183142094 0.953594484 1.229722186 1.083467572 1.24329571 1.009689088 1.137654571 1 17.76637681 4.74610711 24.66521615 1.101503554 0.714728853 0.61296648 0.09744061 488.0045679 1594964.25 0.020897443 0.219454446 55732.31849 -4.74610711 -0.386774701 GYDKVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYDKVDR 7 1 O60828-2;O60828;A0A5H1ZRR1;O60828-3 O60828-2 PQBP1 Polyglutamine-binding protein 1 0 64.836 0.065862 222430000 561300 714170 644250 660360 766130 440520 749060 637410 1108500 FALSE TRUE 526169.2349 767047.8899 659531.9142 677305.9556 705961.2402 567690.9728 636745.4069 716992.0416 923484.1888 0.569765288 0.830602082 0.714177809 0.733424528 0.764454063 0.614727333 0.689503312 0.776398828 1 19.81672774 0.868899685 4.175639311 0.999961256 0.714248173 0.618761134 0.072924595 0.544614017 16.25866198 0.067176432 0.017125716 7.394344583 -0.868899685 -0.285713084 GYDRYEDYDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GYDRYEDYDYR 11 1 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 0 ; 104.87 0.0023188 307540000 691860 1189300 871520 878040 1426640 687360 909490 894380 2338090 FALSE TRUE 648557.7176 1277357.009 892192.866 900571.9929 1314597.449 885789.6736 773120.4178 1006045.312 1947847.674 0.33296121 0.655778697 0.458040368 0.462342104 0.674897461 0.454753051 0.396910101 0.516490753 1 20.89344943 -1.497949274 3.271341647 1.011385034 0.5002673 0.696750096 0.104833046 120944724.5 142344165.3 12245211.31 0.024833675 0.031772452 1.497949274 -0.511117734 GYDS(ph)EDDTWEPEQHLVNCEEYIHDFNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 GYDSEDDTWEPEQHLVNCEEYIHDFNR 27 0 Q9Y232;Q9Y232-2 Q9Y232 CDYL Chromodomain Y-like protein 1 GYDS(1)EDDTWEPEQHLVNCEEYIHDFNR;GYDS(1)EDDTWEPEQHLVNCEEYIHDFNR;GYDS(1)EDDTWEPEQHLVNCEEYIHDFNR;GYDS(1)EDDTWEPEQHLVNCEEYIHDFNR;GYDS(1)EDDTWEPEQHLVNCEEYIHDFNR;GYDS(1)EDDTWEPEQHLVNCEEYIHDFNR;GYDS(1)EDDTWEPEQHLVNCEEYIHDFNR 391.27 4.71E-145 2486498000 475048.5 432059 472994.4 426480.5 430254.1 457733.7 533922.4 402938 344001.3 TRUE FALSE 445316.0624 464049.0979 484214.0505 437424.7117 396463.6785 589873.9885 453865.6928 453245.6963 286585.2607 1.553869384 1.619235744 1.689598584 1.526333596 1.383405684 2.05828446 1.583702148 1.581538755 1 18.12860489 0.646546966 2.61855557 1.000070092 1.640453083 0.566062855 0.172248881 2.214789182 15.56013995 0.153126254 0.040645291 4.431461353 -0.646546966 0.640382991 GYDS(ph)EDDTWEPEQHLVNCEEYIHDFNRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GYDSEDDTWEPEQHLVNCEEYIHDFNRR 28 1 Q9Y232;Q9Y232-2 Q9Y232 CDYL Chromodomain Y-like protein 1 GYDS(1)EDDTWEPEQHLVNCEEYIHDFNRR;GYDS(1)EDDTWEPEQHLVNCEEYIHDFNRR;GYDS(1)EDDTWEPEQHLVNCEEYIHDFNRR;GYDS(0.965)EDDT(0.034)WEPEQHLVNCEEYIHDFNRR 274.22 7.90E-62 506132000 61293 70911 67426.8 73384.8 75495.6 68954.3 78039 61475 89923.9 TRUE FALSE 57456.78054 76161.32422 69026.19554 75267.97821 69566.48011 88860.28703 66337.77643 69150.28907 74915.02016 0.766959422 1.016636237 0.921393272 1.004711446 0.928605238 1.186147809 0.885507022 0.923049729 1 16.19296738 4.744722733 24.43605509 0.980056192 0.766959291 0.396791301 0.083729271 514.8543828 2041591.033 0.018288278 0.168434775 55554.94641 -4.744722733 -0.213096901 GYDVDFPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GYDVDFPR 8 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9;O94808 Q06210-2 GFPT1;GFPT2 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1;Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 2 0 ;;; 188.81 0.00045366 1197170000 3162140 3985860 3819410 3972100 3861550 3431250 4267800 3249990 3146760 FALSE TRUE 2964227.302 4280977.222 3910008.209 4074030.811 3558279.44 4421796.173 3627883.01 3655758.406 2621545.427 1.130717504 1.632997535 1.491489779 1.554056919 1.357321297 1.686713542 1.383871884 1.394505076 1 21.32198611 0.672127164 1.415922813 1.000798899 1.492129981 0.456864688 0.15597121 0.901078266 2.751369347 0.130839606 0.038482794 4.700317169 -0.672127164 0.491331082 GYDYGPHFQGILEASLEGDSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 15 GYDYGPHFQGILEASLEGDSGR 22 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;;;;;;;;; 342.19 1.96E-81 11560397000 5661111 6857290 7066749 7134268 7135210 6648313 7980728 6856665 5877797 FALSE TRUE 5306792.168 7365010.887 7234375.623 7317345.395 6574839.389 8567573.037 6784091.926 7712734.719 4896754.709 1.083736573 1.504059591 1.477381665 1.494325493 1.342693228 1.749643089 1.38542613 1.57507067 1 22.2233945 -1.06760672 5.039208873 0.99999071 1.46406616 0.407090064 0.17066368 1.56E-05 2.88E-06 0.144623061 0.034087301 0.085584138 1.06760672 0.464075451 GYEEWLLNEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GYEEWLLNEIR 11 0 O43707;O43707-2;F6THM6;A0A494C060;P12814-3;P12814;P12814-2;P12814-4;H9KV75;P35609-2;P35609;A0A494C1A0 O43707;P12814-3 ACTN4;ACTN2;ACTN1 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2 0 ;;;;; 266.99 9.49E-21 1240667000 1675937 1731786 1414906 1291104 1370809 1177067 1492110 1613298 1365321 FALSE TRUE 1571043.095 1860009.237 1448468.238 1324235.914 1263151.191 1516867.135 1268381.958 1814721.807 1137440.105 1.381209514 1.635259061 1.273445725 1.164224744 1.11052106 1.333579789 1.115119778 1.595443838 1 20.11735915 3.733755276 3.291009779 1.220916633 1.514981294 0.322406601 0.170408875 0.236406358 5.308448042 0.041079026 0.07430468 5416.955602 -3.733755276 0.29406466 GYEEWLLNEIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 152.47 0.00011197 295360000 318320 317890 290610 270100 313300 243090 309830 301340 224999 FALSE TRUE 298396.9194 341426.9064 297503.4064 277031.2233 288694.6818 313266.1368 263373.8678 338962.9623 187445.2134 1.591915387 1.821475728 1.587148592 1.477931702 1.540154996 1.671241058 1.405071184 1.808330852 1 17.51610946 -2.686284132 0.292228945 6.54E-16 1.659517664 0.64813733 0.137959227 32.83973409 1.040912711 21.0492828 0.14247667 0.002059282 2.686284132 1.659517664 GYELLFQPEVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYELLFQPEVVR 12 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30 O60716-13 CTNND1 Catenin delta-1 0 112.13 0.0030409 20238000 31628 42361 38717 43717 47476 36491 40984 34787 54757 FALSE TRUE 29648.45994 45497.45252 39635.38552 44838.85223 43747.42647 47025.35932 34838.82968 39130.23353 45617.70296 0.649933206 0.997363952 0.86885974 0.982926569 0.959001081 1.030857677 0.763712932 0.857786144 1 15.47730618 4.748462419 24.52872722 0.922950821 0.649933011 0.537159718 0.08201862 899.0330975 2227024.074 0.019600954 0.259608906 56035.39264 -4.748462419 -0.273017809 GYESPT(ph)LSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GYESPTLSK 9 0 Q68DQ2 Q68DQ2 CRYBG3 Very large A-kinase anchor protein 1 GYES(0.096)PT(0.904)LSK;GYES(0.21)PT(0.79)LSK;GYES(0.498)PT(0.501)LS(0.001)K 142 0.001178 456824000 888780 860500 880520 880070 941900 780300 1096000 846230 877890 TRUE FALSE 833152.8463 924212.3153 901406.3502 902654.0862 867926.9734 1005559.943 931664.9748 951883.6783 731364.4876 1.139175966 1.263682242 1.232499479 1.234205518 1.186722883 1.374909447 1.273872317 1.301517498 1 19.48023105 -0.884167706 8.087342692 1 1.254896516 0.60791305 0.0632302 0 0 0.057777696 0.013618334 0.13056666 0.884167706 0.254896516 GYEVIYLTEPVDEYCIQALPEFDGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GYEVIYLTEPVDEYCIQALPEFDGKR 26 1 P14625 P14625 HSP90B1 Endoplasmin 0 ; 196.81 1.08E-24 312910000 463380 445330 404570 426960 461730 376090 600140 382000 387460 FALSE TRUE 434377.873 478302.6966 414166.5915 437916.5164 425467.5883 484661.0777 510154.5784 429693.5409 322790.4229 1.345696285 1.481774745 1.283082031 1.356658951 1.318092354 1.501472916 1.580451408 1.331184293 1 18.30023825 2.258448175 24.99221401 1.42437083 1.363961032 0 0.163975802 1008.024517 1266757.78 0.052254696 0.043665268 181.321029 -2.258448175 -0.060409798 GYFDEEMNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 267.39 2.70E-15 10935470000 6339300 9966390 7035940 7643700 9919100 5559650 7124440 8139150 7834640 FALSE TRUE 5942534.529 10704311.89 7202835.819 7839850.283 9140093.898 7164630.702 6056196.362 9155340.794 6526987.97 0.910455873 1.640007908 1.103546667 1.20114367 1.400354028 1.09769326 0.927870005 1.402690006 1 22.63798595 2.144369373 8.262890956 1.080548398 1.281486757 0.079144744 0.224136108 0.460510297 35.82167449 0.078648788 0.058059186 139.4342206 -2.144369373 0.200938359 GYFEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYFEDR 6 0 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 113.25 0.061181 335810000 679490 779030 846980 764300 947940 769290 878230 803440 1176600 FALSE TRUE 636961.9338 836710.1918 867070.7656 783913.232 873492.6162 991371.5346 746547.5646 903751.2526 980217.8589 0.649816699 0.853596151 0.884569443 0.799733676 0.891120896 1.011378772 0.761613919 0.921990193 1 19.90274291 4.762159067 3.002989366 0.880158351 0.604798424 0.48694129 0.077489896 0.369705206 4.699933897 0.017226513 0.250858391 57830.78233 -4.762159067 -0.275359927 GYFEDRRPS(ph)ANCDPFSVTEALIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYFEDRRPSANCDPFSVTEALIR 23 2 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 1 GY(0.02)FEDRRPS(0.98)ANCDPFSVTEALIR 84.762 0.0038197 27283000 7700.5 9426.2 8131.9 11082 11601 9770.9 13002 11017 46121 TRUE FALSE 7218.539451 10124.12566 8324.792508 11366.38288 10689.90426 12591.60021 11052.4708 12392.4967 38423.10715 0.187869748 0.263490551 0.216661096 0.295821544 0.278215508 0.327709057 0.287651667 0.322527188 1 15.22968657 -5 0.291262541 6.763065786 0.2275442 0.983396086 0.029979706 26.45871246 0.248810195 92.64481189 0.029397597 1.00E-05 5 -6.535521586 GYFEHREDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 150.61 5.10E-05 412000000 348431 618460 404773 434500 700140 343487 441330 496670 774760 FALSE TRUE 326623.3257 664251.4219 414374.4067 445650.0056 645153.8286 442646.1209 375156.6636 558680.3428 645447.5509 0.506041622 1.029133074 0.641995475 0.690451153 0.999544932 0.685797196 0.581234932 0.865570474 1 19.29994034 GYFEYIEENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GYFEYIEENK 10 0 Q00839;Q5RI18;A0A1W2PRI6;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;; 208.03 2.82E-07 593698000 1399990 965910 1147290 1073020 1101810 971400 1340180 1004640 1011440 FALSE TRUE 1312367.125 1037426.981 1174504.261 1100555.51 1015278.287 1251827.411 1139232.451 1130071.515 842624.1298 1.557476315 1.23118594 1.393864974 1.306104906 1.204900561 1.485629673 1.352005491 1.34113358 1 19.6845297 0.658742063 4.49192333 1.000000138 1.350928872 0.532244948 0.105579322 14.99229041 196.7406334 0.091247076 0.023164485 4.557661466 -0.658742063 0.350928734 GYFEYIEENKYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GYFEYIEENKYSR 13 1 Q00839;Q5RI18;A0A1W2PRI6;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;;; 236.92 9.08E-17 6488880000 7225020 7744080 7691480 7509970 9131630 5963670 8956140 7081180 11400530 FALSE TRUE 6772818.895 8317459.741 7873925.538 7702688.545 8414468.615 7685284.717 7613249.952 7965280.911 9497707.893 0.713100358 0.87573337 0.829034292 0.811004995 0.885947295 0.809172571 0.801588134 0.838652968 1 23.17914796 0.948670816 20.79250128 1 0.824834714 0.591473689 0.046909595 1156.745755 468577.9937 0.04101575 0.010253937 8.885273808 -0.948670816 -0.175165286 GYGFVHFETQEAAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GYGFVHFETQEAAER 15 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;H0YBN4;E5RGH3 P11940-2 PABPC1 Polyadenylate-binding protein 1;Polyadenylate-binding protein 0 ;;;;; 248.68 2.01E-18 6094870000 3149450 4022090 3719880 3893620 4100500 3428140 4120830 3644670 4196230 FALSE TRUE 2952331.546 4319889.729 3808117.31 3993536.881 3778463.271 4417788.367 3502949.797 4099715.072 3495852.104 0.844524156 1.235718674 1.08932449 1.142364368 1.080841854 1.263722902 1.002030318 1.172736989 1 21.73721272 -1.722080347 6.653587518 0.998391008 1.113688531 0.06440458 0.119396734 0.002499972 0.000104423 0.101416699 0.02358478 0.018963551 1.722080347 0.115297523 GYGTVIPPQASLVFHVLLIDVHNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYGTVIPPQASLVFHVLLIDVHNPK 25 0 Q96AY3 Q96AY3 FKBP10 Peptidyl-prolyl cis-trans isomerase FKBP10 0 161.51 1.19E-11 90477000 93491 127460 101140 108590 135380 75527 108640 93787 75357 FALSE TRUE 87639.5652 136897.271 103539.0886 111376.6032 124747.8009 97330.41882 92350.44056 105496.5134 62779.42988 1.395991734 2.180607108 1.649251813 1.774093895 1.987080818 1.550355252 1.471030252 1.680431211 1 15.93800431 0.582791782 0.435587335 0.94644734 1.854765702 0.496120378 0.229112047 1.439283174 0.553685241 0.395077788 0.139536342 3.826412462 -0.582791782 0.908318362 GYIFLEYASPAHAVDAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYIFLEYASPAHAVDAVK 18 0 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 226.67 1.63E-19 0 263340 296500 310180 302560 361970 253960 362090 313140 404590 FALSE TRUE 246858.0195 318453.1685 317537.6161 310324.2018 333542.3363 327274.1293 307797.966 352236.2183 337061.3152 0.732383125 0.944792992 0.942076713 0.920675817 0.989559826 0.970963188 0.913180932 1.045021195 1 18.36265153 4.742744514 4.311379024 0.958215994 0.714711711 0.773049813 0.039625938 0.096850573 4.248263133 0.008670253 0.07281345 55302.46817 -4.742744514 -0.243504282 GYIWNYGAIPQTWEDPGHNDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GYIWNYGAIPQTWEDPGHNDK 21 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;; 309.59 1.71E-66 10675830000 5561740 4762280 4956230 4538630 5199690 3878860 6233980 4432360 5362240 FALSE TRUE 5213640.621 5114884.166 5073794.116 4655098.93 4791327.322 4998623.914 5299252.572 4985749.903 4467247.503 1.16708121 1.144974431 1.135776362 1.042050821 1.07254575 1.1189494 1.186245573 1.116067534 1 22.09095476 3.460943078 24.99434515 1.104249507 1.14820163 0.20567348 0.050758388 487.475725 753119.985 0.014506399 0.019659552 2890.301035 -3.460943078 0.043952123 GYIWNYGTLPQTWEDPHEKDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYIWNYGTLPQTWEDPHEKDK 21 1 Q9H2U2-2;Q9H2U2;H0Y9D8;D6RGV9;D6RGI1 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 135.73 3.67E-06 206070000 322790 196310 217520 199330 297940 150370 253680 207860 372400 FALSE TRUE 302587.1501 210844.9967 222679.6771 204445.1453 274540.9942 193779.3779 215643.039 233811.7786 310244.0342 0.975319802 0.679610157 0.717756516 0.658981714 0.884919496 0.624603076 0.695075538 0.753638274 1 18.24304394 0.947795882 20.05806617 1.000000001 0.731559748 0.343080103 0.107427425 1144.993716 439936.0881 0.092608884 0.023152221 8.867391484 -0.947795882 -0.268440253 GYKIPVIENLGATLDQFDAIDFSDNEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYKIPVIENLGATLDQFDAIDFSDNEIR 28 1 P09661;H0YKK0 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 0 126.99 3.08E-05 9860500 7835.8 12785 8717.1 10011 13131 7966.1 10848 8063.6 15853 FALSE TRUE 7345.371265 13731.6147 8923.873729 10267.89921 12099.74423 10265.78375 9221.443108 9070.35821 13207.03189 0.556171237 1.039719963 0.675691087 0.777456986 0.916159235 0.77729681 0.698222219 0.686782487 1 13.68901865 2.008656445 24.8987244 0.755542889 0.813030899 0 0.154883802 788.7694729 2268744.109 0.053192958 0.039228537 102.0132174 -2.008656445 0.05748801 GYLPSHYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GYLPSHYER 9 0 Q6P2Q9;I3L1T8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 125.82 0.00049093 431770000 313480 639710 515440 455850 577920 454200 410230 508850 409030 FALSE TRUE 293859.8464 687074.794 527666.4802 467547.8828 532532.4944 585320.1667 348719.8199 572381.0426 340760.2506 0.86236539 2.016299709 1.548497747 1.372072834 1.562777623 1.717689096 1.023358268 1.679717754 1 18.37839753 0.640053705 0.447314026 0.977594586 1.586861138 0.107815523 0.344258327 2.891755843 1.215570001 0.542907119 0.203432576 4.365698157 -0.640053705 0.609266552 GYNDDYYEESYFTTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GYNDDYYEESYFTTR 15 0 P50402;Q5HY57 P50402 EMD Emerin 0 ;;; 302.63 4.64E-44 494590000 529240 565750 466080 517375 595840 491497 649750 548350 547190 FALSE TRUE 496115.8131 607638.7187 477135.6377 530651.7184 549045.1299 633384.2051 552326.0195 616812.7046 455860.454 1.08830632 1.332948961 1.046670387 1.164066139 1.204414915 1.389425644 1.211612051 1.35307351 1 18.79823273 2.468319046 24.98463134 1.261244819 1.170165712 0.06701175 0.126518662 433.9135618 1231633.219 0.039585884 0.033166763 293.9808533 -2.468319046 -0.091079107 GYNFEDLTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYNFEDLTDR 10 0 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y9R3 A0A499FIZ0 WDR26 WD repeat-containing protein 26 0 142.83 8.16E-05 145970000 155020 183220 187970 201290 197110 190730 202590 178520 214310 FALSE TRUE 145317.5749 196785.7994 192428.7372 206455.4422 181629.7757 245790.6548 172213.5103 200808.615 178540.2765 0.813920409 1.102192756 1.07778895 1.156352204 1.017304214 1.376667829 0.964563927 1.124724454 1 17.44589004 4.738632214 7.935858906 1.104456946 0.811470515 0.389402236 0.113524729 0.090075693 67.64685424 0.023751287 0.141208515 54781.28489 -4.738632214 -0.292986431 GYNHGQGSYSYSNSYNS(ph)PGGGGGSDYNYESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GYNHGQGSYSYSNSYNSPGGGGGSDYNYESK 31 0 Q12906;Q12906-7 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 GYNHGQGSYSYSNSYNS(1)PGGGGGSDYNYESK;GYNHGQGSYSYSNSYNS(1)PGGGGGSDYNYESK 241.61 3.93E-46 1408220000 395530 395720 414260 415740 451740 417950 572630 442080 571360 TRUE FALSE 370774.4833 425019.5205 424086.4428 426408.5922 416262.1626 538605.3801 486769.4475 497274.6611 475996.3249 0.778944004 0.892905046 0.890944784 0.895823287 0.874507094 1.131532644 1.022632785 1.044702732 1 18.86059091 2.255502332 24.99920768 1.051353758 0.874852018 0.786242856 0.047326471 100.7477457 148663.1319 0.015134054 0.012631954 180.0952804 -2.255502332 -0.176501741 GYNPGLLVHPDLAYLQAEGGGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GYNPGLLVHPDLAYLQAEGGGDR 23 0 P19838;P19838-2;A0A494C1E9;A0A494C157;D6RH30 P19838 NFKB1 Nuclear factor NF-kappa-B p105 subunit;Nuclear factor NF-kappa-B p50 subunit 0 ; 197.37 2.98E-24 448490000 487040 574330 553590 579340 596960 529510 575440 513640 594220 FALSE TRUE 456557.0358 616853.9908 566721.4162 594206.8452 550077.1696 682370.9411 489158.1141 577769.0847 495040.8432 0.922261349 1.246066864 1.144797291 1.200318829 1.111175325 1.378413419 0.988116679 1.167113972 1 18.91718803 1.055153571 1.242036839 1.01263216 1.165249456 0.094355301 0.127775104 0.895080297 2.84820751 0.106409522 0.033131142 11.35412238 -1.055153571 0.152617296 GYPEVALHFVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYPEVALHFVK 11 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 121.83 0.0010255 0 530280 615300 488810 471140 660980 364280 573780 693010 527390 FALSE TRUE 497090.7214 660857.4522 500404.804 483230.25 609069.2971 469441.7224 487747.0157 779533.824 439365.2019 1.131383913 1.504118782 1.138926801 1.099837329 1.386248375 1.068454489 1.110117537 1.7742275 1 18.74506109 3.866230073 7.549378428 1.215572335 1.34086306 0.022037136 0.23811481 0.767348182 46.86269284 0.055912973 0.101349567 7349.030889 -3.866230073 0.125290725 GYPHLCSICDLPVHSNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYPHLCSICDLPVHSNK 17 0 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 200.71 7.02E-12 395260000 771710 665070 693940 624310 710670 611610 892700 591840 650890 FALSE TRUE 723410.0486 714312.4748 710400.5845 640330.8516 654856.8449 788171.8783 758847.9224 665732.5268 542252.2541 1.334083986 1.317306603 1.310092451 1.180872641 1.207660899 1.453515172 1.399437101 1.227717399 1 19.04860462 0.949753642 8.056955757 1.000002084 1.317331895 0.611653459 0.07907239 0.641337143 102.4269771 0.080801454 0.020234466 8.907455095 -0.949753642 0.317329811 GYPHWPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GYPHWPAR 8 0 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;M0R0J3;H3BPQ6;P51858;O75475;O75475-3;O75475-2;Q9Y3E1 Q7Z4V5-2;P51858;O75475;Q9Y3E1 HDGFRP2;HDGFRP3;HDGF;PSIP1 Hepatoma-derived growth factor-related protein 2;Hepatoma-derived growth factor;PC4 and SFRS1-interacting protein;Hepatoma-derived growth factor-related protein 3 0 ;;; 121.29 0.0014395 1184350000 517329 1977190 376760 403068 1935040 299669 483850 1667900 1689790 FALSE TRUE 484950.3013 2123583.205 385696.9251 413411.4073 1783069.764 386178.5756 411301.1843 1876140.987 1407753.133 0.344485329 1.508491195 0.273980513 0.293667546 1.266606852 0.274322654 0.292168545 1.332720165 1 20.42496293 -1.440548143 3.726009961 1.002553284 0.689136757 0.035245375 0.493986361 2863811123 233808212.2 62910510.84 0.113391739 0.036262009 1.440548143 -0.313416527 GYS(ph)FSLTTFSPSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYSFSLTTFSPSGK 14 0 A0A024RA52;P25787;H3BT36 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 1 GYS(0.997)FS(0.003)LTTFSPSGK 237.59 2.80E-17 136180000 85791 108900 82795 77317 104370 51582 102880 87158 125960 TRUE FALSE 80421.49445 116963.0693 84758.9365 79301.08512 96173.20121 66472.88604 87454.09909 98039.86816 104936.4623 0.766382749 1.114608467 0.807716733 0.755705723 0.916489837 0.633458424 0.83340049 0.934278382 1 16.67915653 3.731521667 22.65758807 0.82111665 0.964107078 0.071722934 0.13143275 87.41102389 450059.0538 0.030643815 0.052788147 5389.167313 -3.731521667 0.142990427 GYSDRDGYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 167.09 4.88E-06 2536200000 1043860 1760910 1290710 1351140 1781760 1099360 1596960 1251820 2750190 FALSE TRUE 978526.6659 1891289.609 1321326.251 1385812.54 1641827.757 1416727.385 1357510.673 1408112.483 2291165.522 0.42708685 0.825470526 0.576704842 0.604850469 0.716590635 0.618343534 0.592497862 0.614583481 1 21.12765026 -1.918847827 2.344681668 1.235416271 0.635141987 0.574597947 0.101653888 10452885.63 5037928.94 13507057.29 0.022887755 0.012054582 1.918847827 -0.600274283 GYSEQDLEAILDVVHLHHILQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GYSEQDLEAILDVVHLHHILQR 22 0 P33897 P33897 ABCD1 ATP-binding cassette sub-family D member 1 0 ; 156.85 3.03E-09 127957000 85896 85338 105913 94461 91680 92653 111053 88031 85091 FALSE TRUE 80519.92269 91656.51431 108425.3064 96885.02918 84479.82262 119400.417 94401.63362 99021.86413 70888.76239 1.135863005 1.29296254 1.529513321 1.366719151 1.191723762 1.684334907 1.331686863 1.396862645 1 16.11326932 -1.443858429 6.030382432 0.999831834 1.379738572 0.348268568 0.156467266 0.000327118 3.02E-05 0.140089952 0.033005083 0.035986663 1.443858429 0.379906738 GYSFTTTAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 GYSFTTTAER 10 0 P60709;A0A2R8Y793;A0A2R8YEA7;P63261;I3L3I0;I3L1U9;I3L4N8 P60709;P63261 ACTB;ACTG1 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 ;;;;;;;;;; 206.38 3.52E-07 43771370000 7045340 8180315 6789429 7332975 9884746 5406321 7051059 7298496 7899876 FALSE TRUE 6604384.746 8785994.034 6950477.462 7521151.553 9108437.922 6967038.108 5993818.162 8209729.292 6581335.66 1.00350219 1.334986466 1.056089192 1.142800176 1.383980151 1.058605497 0.910729747 1.247426011 1 22.64994897 2.025257179 24.99838171 1.028266548 1.188445338 0.168696006 0.139904146 306.4399111 303298.6069 0.048534249 0.035843743 105.9881176 -2.025257179 0.160178791 GYSSLDQSPDEKPLVALDT(ph)DS(ph)DDDFDMSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYSSLDQSPDEKPLVALDTDSDDDFDMSR 29 1 Q5T586;A0A0A0MRW2;Q5T593;A0A0A0MRW3;Q8IW50-5;Q8IW50-6;Q8IW50;A0A0A0MRW1;A0A0A0MRW0;Q8IW50-3;Q8IW50-2;Q8IW50-4 Q5T586 FAM219A Protein FAM219A 2 GYSSLDQSPDEKPLVALDT(1)DS(1)DDDFDMSR 89.559 0.00085255 51037000 118620 96311 93235 90308 123200 83988 139670 104580 129760 TRUE FALSE 111195.7859 103441.9667 95446.57823 92625.45617 113524.369 108233.9722 118727.7801 117637.0432 108102.2177 1.028617065 0.956890329 0.882928956 0.856832155 1.050157632 1.001218795 1.098291808 1.088201942 1 16.72203659 2.712318374 22.28918609 1.053398321 0.927514654 0.525821856 0.054650234 144.9355396 123102.1573 0.01781616 0.016806384 515.6064882 -2.712318374 -0.125883667 GYSYDDIPDFDD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYSYDDIPDFDD 12 0 Q96A57;Q96A57-2 Q96A57 TMEM230 Transmembrane protein 230 0 99.855 0.0082853 37114000 243630 292430 278920 287870 304330 243930 337010 278970 293670 FALSE TRUE 228381.6332 314081.8215 285536.1141 295257.2316 280429.1494 314348.6311 286478.4791 313800.0186 244654.5798 0.933486033 1.283776587 1.167098995 1.206833045 1.146224811 1.284867144 1.170950813 1.282624747 1 17.90038676 4.749440004 24.6648814 1.203050417 0.933485846 0.470428183 0.085854265 1024.294418 2322144.568 0.017303256 0.258300212 56161.66876 -4.749440004 -0.26956457 GYSYDLEVEQAYDLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GYSYDLEVEQAYDLAR 16 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;; 285.54 1.73E-35 409766000 467839 613975 559172 549190 613290 461659 597784 573978 541903 FALSE TRUE 438557.7921 659434.3478 572435.8239 563283.1452 565124.6773 594932.4589 508151.8388 645640.4168 451455.8885 0.971429996 1.4606839 1.267977312 1.247703617 1.251782714 1.317808614 1.125584695 1.430129572 1 18.7842255 -1.88862359 2.560765971 0.860351427 1.269317942 0.251688719 0.139445567 12207211.45 6564634.014 10283833.81 0.030679871 0.012923389 1.88862359 0.408966515 GYT(ph)SDSEVYTDHGRPGK ddPTM_SK-BR-3_Pertuzumab_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 176.11 1.68E-09 859040000 766580 761360 740960 831760 793090 629050 1024200 708310 772510 TRUE FALSE 718601.1262 817731.8866 758535.9211 853104.3698 730803.9106 810646.5232 870630.7182 796744.0627 643573.0904 1.116580443 1.270612303 1.178632128 1.325574954 1.135541435 1.259602888 1.352807834 1.238000896 1 19.29574448 -0.73448359 4.903871199 0.999999849 1.242009229 0.485161106 0.075636359 4613333.778 940753.5245 7.422649909 0.016876907 0.184296213 0.73448359 0.24200938 GYTS(ph)DDDTWEPEIHLEDCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GYTSDDDTWEPEIHLEDCK 19 0 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 GYT(0.089)S(0.91)DDDT(0.001)WEPEIHLEDCK;GYT(0.123)S(0.877)DDDTWEPEIHLEDCK;GYT(0.109)S(0.891)DDDTWEPEIHLEDCK;GYT(0.231)S(0.769)DDDTWEPEIHLEDCK 391.06 3.22E-127 1449680000 2792106 1894761 2125758 1859884 2010647 1886978 3479708 1757841 2309063 TRUE FALSE 2617353.07 2035051.076 2176181.984 1907611.772 1852738.895 2431717.916 2957958.089 1977311.318 1923665.468 1.360607191 1.057902795 1.131268414 0.991654632 0.963129466 1.264106445 1.537667613 1.027887307 1 20.8754265 2.112956514 8.543298011 1.285986116 1.094544211 0.002356188 0.186527562 0.403321023 28.6516505 0.065877045 0.048620828 129.7049392 -2.112956514 -0.191441905 GYTS(ph)DSEVYTDHGRPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.002)S(0.992)DS(0.006)EVYTDHGRPGK;GYT(0.001)S(0.995)DS(0.004)EVYTDHGRPGK;GYT(0.411)S(0.589)DSEVYTDHGRPGK;GYT(0.077)S(0.922)DS(0.001)EVYTDHGRPGK;GYT(0.073)S(0.925)DS(0.002)EVYTDHGRPGK 297.67 2.01E-46 8739040000 3488270 3629260 3545730 3789660 3582790 3105690 4964350 3409860 3512070 TRUE FALSE 3269945.407 3897974.187 3629836.39 3886909.091 3301412.126 4002252.286 4219991.804 3835588.527 2925882.828 1.11759274 1.332238649 1.240595268 1.328456852 1.128347347 1.367878525 1.442296924 1.310916654 1 21.48044056 GYWAGLDASAQTTSHELTIPNDLIGCIIGR ddPTM_SK-BR-3_Pertuzumab_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 ;; 265.23 1.40E-58 769088000 381115 503566 429638 396159 533394 433202 513168 459577 382306 FALSE TRUE 357261.6925 540850.5506 439829.2162 406325.1106 491503.3868 558260.385 436223.2224 516956.2001 318496.6588 1.121712528 1.698135712 1.380953941 1.275759413 1.543197937 1.752798246 1.369632021 1.623113417 1 18.28091871 -1.429218806 6.137962666 0.999848313 1.483483705 0.36575836 0.194127786 0.000362971 3.38E-05 0.169310713 0.039894586 0.037220414 1.429218806 0.483635392 GYWAS(ph)LDASTQTTHELTIPNNLIGCIIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYWASLDASTQTTHELTIPNNLIGCIIGR 29 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 GY(0.001)WAS(0.959)LDAS(0.009)T(0.009)QT(0.01)T(0.012)HELTIPNNLIGCIIGR 68.326 0.0056835 73691000 36270 45762 32332 32327 43143 28398 47895 42986 64354 TRUE FALSE 33999.92544 49150.2661 33098.93031 33156.56555 39754.72281 36596.0416 40713.58939 48352.89672 53612.90166 0.63417432 0.916761909 0.617368754 0.61844378 0.741514105 0.682597667 0.759399102 0.901889195 1 15.7102926 1.147455161 2.27028545 0.998034267 0.714848627 0.58671714 0.086976285 0.210940574 1.995907271 0.081847485 0.022970269 14.04284689 -1.147455161 -0.28318564 GYWASLDASTQTTHELTIPNNLIGCIIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 GYWASLDASTQTTHELTIPNNLIGCIIGR 29 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ;;;; 301.19 4.54E-81 650913000 775130 1016005 818844 767096 1101388 802974 995226 998598 830122 FALSE TRUE 726615.9969 1091231.067 838267.3664 786780.9821 1014889.429 1034779.559 846001.1005 1123275.158 691569.2754 1.050677095 1.57790565 1.212123494 1.137674865 1.467516654 1.496277518 1.223306371 1.624240981 1 19.39951425 2.700147374 24.9818104 1.374261448 1.294734776 0.045427483 0.216069861 2321.669976 1509881.281 0.064736044 0.061034804 501.3573356 -2.700147374 -0.079526672 GYWGNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GYWGNK 6 0 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 ; 135.81 0.031271 4661500000 4505800 4792600 4872100 4460400 5011200 4017400 5603300 4258200 5114900 FALSE TRUE 4223790.021 5147449.091 4987668.513 4574861.415 4617640.566 5177158.163 4763137.183 4789845.643 4261190.146 0.99122308 1.2079839 1.170487198 1.073611188 1.083650437 1.214955913 1.117795034 1.124062874 1 22.022825 0.572633937 2.063067747 1.000027825 1.136409472 0.230868427 0.067145143 4.059459035 18.03140361 0.060698943 0.016635203 3.73795387 -0.572633937 0.136381647 GYYS(ph)PYSVSGSGST(ph)AGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYYSPYSVSGSGSTAGSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 2 GYYS(0.994)PY(0.004)S(0.002)VSGSGS(0.208)T(0.734)AGS(0.057)R 163.22 1.79E-10 198510000 324590 348810 372740 300740 301190 366220 447410 386980 514550 TRUE FALSE 304274.4913 374636.2553 381581.5688 308457.4976 277535.7523 471941.7689 380325.0241 435295.3048 428668.2809 0.709813403 0.873953759 0.890155829 0.719571546 0.647437109 1.100948659 0.887224553 1.015459562 1 18.70950214 2.232392471 24.99892751 0.984245271 0.797031601 0.605978042 0.091183625 129.2159542 523695.1732 0.034851759 0.026389491 170.7624869 -2.232392471 -0.18721367 GYYS(ph)PYSVSGSGSTAGS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYYSPYSVSGSGSTAGSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 2 GYYS(1)PYSVSGSGS(0.007)T(0.006)AGS(0.987)R 339.39 3.99E-75 230690000 287160 324790 313140 255970 255000 330280 391810 299660 416120 TRUE FALSE 269187.1682 348837.7895 320567.8287 262538.6236 234973.3286 425626.4744 333061.7279 337073.2106 346666.8838 0.77650096 1.006262224 0.924714311 0.757322478 0.677807254 1.227767907 0.960754383 0.97232596 1 18.4031905 2.240036262 25 1.035593878 0.86263974 0.42846882 0.117830875 47.59039505 806281.7169 0.043731885 0.034758747 173.7945936 -2.240036262 -0.172954138 GYYS(ph)PYSVSGSGSTAGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GYYSPYSVSGSGSTAGSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 GYYS(0.998)PYS(0.002)VSGSGSTAGSR;GYYS(0.842)PYS(0.148)VS(0.01)GSGSTAGSR;GYYS(0.5)PYS(0.5)VSGSGSTAGSR;GYYS(0.549)PYS(0.45)VS(0.002)GSGSTAGSR 354.71 1.62E-90 1796818000 710622 763221 775681 713284 757764 812506 873529 774771 1004639 TRUE FALSE 666145.4375 819730.677 794080.5196 731588.075 698252.2721 1047063.292 742551.4359 871502.8648 836958.2607 0.795912376 0.979416436 0.948769559 0.874103416 0.834273709 1.251034062 0.88720247 1.041273987 1 19.67479615 GYYSPYS(ph)VSGSGSTAGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 GYYSPYSVSGSGSTAGSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 GYYS(0.01)PYS(0.985)VS(0.005)GSGSTAGSR;GYYS(0.411)PYS(0.589)VSGSGSTAGSR;GYYS(0.137)PYS(0.859)VS(0.004)GSGSTAGSR 391.86 1.13E-126 3042050000 833930 932860 914570 820320 927200 1030080 1129800 1001440 1226710 TRUE FALSE 781735.8099 1001929.925 936264.0323 841370.8 854381.4521 1327447.374 960396.9785 1126471.988 1021964.176 0.764934651 0.980396327 0.916141734 0.823287958 0.836018984 1.298917717 0.939756012 1.102261718 1 19.96291319 2.299128318 24.99999992 1.072983491 0.885237949 0.500154271 0.108383912 64.22167017 26507.71019 0.034967199 0.029255646 199.1261595 -2.299128318 -0.187745543 GYYSPYSVS(ph)GSGS(ph)TAGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GYYSPYSVSGSGSTAGSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 2 GYYSPYS(0.015)VS(0.985)GSGS(0.523)T(0.112)AGS(0.365)R;GYYSPYSVS(1)GS(0.004)GS(0.578)T(0.032)AGS(0.386)R 281.53 3.67E-39 663010000 898230 1117680 1002900 947080 983650 907400 1377080 1081430 1355770 TRUE FALSE 842011.3877 1200434.19 1026689.262 971383.6762 906398.0969 1169351.65 1170599.638 1216448.916 1129483.228 0.745483746 1.062817189 0.908990267 0.860024878 0.802489204 1.035297931 1.036402851 1.076995997 1 20.10723142 2.146475031 10.6065057 1.040159858 0.905278207 0.447497257 0.085617954 0.420967974 45.3139496 0.032450447 0.023965603 140.1119028 -2.146475031 -0.13488165 GYYSPYSVS(ph)GSGSTAGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GYYSPYSVSGSGSTAGSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 GYYSPYSVS(0.989)GS(0.011)GSTAGSR;GYYSPYS(0.002)VS(0.943)GS(0.055)GSTAGSR;GYYSPYSVS(0.996)GS(0.004)GSTAGSR;GYYSPYS(0.006)VS(0.992)GS(0.002)GSTAGSR 358.04 1.03E-90 1512370000 1120600 1184250 1219010 1164610 1107010 1334590 1398980 1219430 1537760 TRUE FALSE 1050463.646 1271933.102 1247925.493 1194495.864 1020069.9 1719864.468 1189215.936 1371678.52 1281097.922 0.819971392 0.992846121 0.97410625 0.932400127 0.796246628 1.342492591 0.928278718 1.070705445 1 20.28894932 GYYSPYSVSGSGS(ph)TAGS(ph)R ddPTM_SK-BR-3_Pertuzumab_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 2 GYYSPYSVSGS(0.001)GS(0.998)T(0.001)AGS(1)R;GYYSPYSVSGSGS(0.999)T(0.004)AGS(0.997)R;GYYSPYSVSGSGS(1)TAGS(1)R;GYYSPYSVSGSGS(0.999)T(0.001)AGS(1)R;GYYSPYSVSGSGS(0.992)T(0.007)AGS(1)R 283.49 1.11E-33 2706980000 3572350 4930330 3941930 4230620 4380990 3164250 6808290 4606140 4864430 TRUE FALSE 3348762.99 5295376.763 4035434.441 4339184.872 4036924.717 4077717.608 5787450.12 5181226.718 4052525.208 0.82633983 1.306685706 0.995782687 1.070736059 0.996150427 1.00621647 1.428109592 1.278518073 1 21.95038973 1.755410812 25 1.276515641 1.06076992 0.241505988 0.158588259 7.692464612 11425.80401 0.067853276 0.037628681 56.93912797 -1.755410812 -0.215745721 GYYSPYSVSGSGS(ph)TAGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYYSPYSVSGSGSTAGSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 GYYSPYS(0.004)VS(0.022)GS(0.098)GS(0.355)T(0.26)AGS(0.26)R 80.361 0.0091587 99303000 97945 104620 88712 99670 106360 90029 124810 96149 105390 TRUE FALSE 91814.79729 112366.1737 90816.29053 102227.7009 98006.91464 116018.9108 106095.8992 108153.4143 87799.72815 1.045729858 1.279800929 1.034357309 1.164328217 1.116255331 1.321403987 1.208385281 1.231819467 1 16.42192885 2.344546656 19.6606808 1.212822849 1.137639162 0.059096089 0.10433172 5.154189456 932.8015991 0.03267617 0.027338736 221.0785746 -2.344546656 -0.075183688 GYYSPYSVSGSGST(ph)AGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GYYSPYSVSGSGSTAGSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 GYYSPYSVSGSGS(0.067)T(0.693)AGS(0.24)R 361.02 5.36E-90 2602200000 276580 347980 315660 351970 391770 322690 453130 326930 362660 TRUE FALSE 259269.3515 373744.8013 323147.6043 361002.1461 361001.9645 415845.3646 385187.3632 367747.9302 302129.7031 0.858139232 1.237034285 1.069565822 1.194858176 1.194857575 1.376380277 1.274907297 1.21718562 1 18.2048085 3.001142582 2.1072098 1.248080777 1.094500488 0.186059607 0.133316382 0.471079988 4.207331431 0.040923412 0.048222511 1002.634357 -3.001142582 -0.153580289 GYYSPYSVSGSGSTAGS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 GYYSPYSVSGSGSTAGSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 GYYSPYSVSGSGS(0.319)T(0.319)AGS(0.362)R;GYYSPYSVSGSGS(0.122)T(0.122)AGS(0.757)R;GYYSPYSVSGSGS(0.001)T(0.262)AGS(0.737)R;GYYSPYSVSGSGS(0.002)T(0.009)AGS(0.989)R 420.4 1.29E-168 4847453000 1693635 2043670 1946480 2047500 2104130 1879366 2612900 1962660 2069280 TRUE FALSE 1587633.409 2194985.453 1992651.425 2100042.316 1938880.117 2421908.455 2221119.902 2207702.421 1723903.8 0.920952439 1.273264467 1.155894792 1.218189969 1.124703198 1.404897684 1.288424506 1.28064131 1 20.71724784 2.279095335 24.9999929 1.274672081 1.162940074 0.094855326 0.136594311 278.047588 171486.0749 0.04251067 0.035566563 190.1495644 -2.279095335 -0.111732007 HAAENPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 HAAENPGK 8 0 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;;;; 127.56 0.0011709 4711062000 7754070 5707614 6563754 6118170 6258309 5025837 7085986 5815638 6298867 FALSE TRUE 7268756.6 6130211.679 6719449.345 6275172.6 5766806.656 6476714.554 6023508.182 6541733.206 5247545.405 1.385172693 1.168205552 1.280493798 1.195830072 1.09895317 1.234236972 1.14787157 1.246627271 1 22.32321131 -5 0.08618232 0.356113827 1.39204372 0.515250487 0.07260385 186.2478194 1.124362864 22.73189562 1.78269567 1.00E-05 5 1.035929892 HAAQCVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HAAQCVGR 8 0 P18074;E7EVE9;A8MX75 P18074 ERCC2 TFIIH basal transcription factor complex helicase XPD subunit 0 80.229 0.027096 0 9422.3 17362 10388 14130 17854 12469 14302 13252 15082 FALSE TRUE 8832.575062 18647.50055 10634.40827 14492.59972 16451.81886 16068.59788 12157.54787 14906.54137 12564.71677 0.702966507 1.484116267 0.846370711 1.153436245 1.309366472 1.278866701 0.967594264 1.18638101 1 13.61709053 0.124965628 0.932918419 0.999185544 1.12992969 0.019504969 0.229411803 21.90213122 19.39418368 0.279203527 0.065363835 1.333415894 -0.124965628 0.130744146 HAASYS(ph)SDSENQGSYSGVIPPPPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HAASYSSDSENQGSYSGVIPPPPGR 25 0 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;F2Z3L2;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 HAAS(0.085)Y(0.009)S(0.4)S(0.4)DS(0.106)ENQGSYSGVIPPPPGR 172.06 4.09E-12 531600000 406940 495100 429650 500240 536950 388180 588260 460410 500560 TRUE FALSE 381470.3518 531757.7192 439841.5009 513077.0053 494780.113 500241.2644 500055.8741 517893.202 417013.3023 0.914767826 1.27515769 1.054742135 1.230361244 1.186485204 1.199581073 1.199136506 1.241910508 1 18.66973388 4.751860093 24.85446229 1.179138945 0.91476764 0.479689139 0.084472664 1635.405902 3056238.557 0.017773186 0.337727014 56475.50104 -4.751860093 -0.264371305 HAASYSSDS(ph)ENQGSYSGVIPPPPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HAASYSSDSENQGSYSGVIPPPPGR 25 0 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;F2Z3L2;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 HAAS(0.046)Y(0.041)S(0.292)S(0.292)DS(0.328)ENQGSYSGVIPPPPGR 73.036 0.022441 120300000 99594 131250 113810 132330 128460 97540 155780 122620 144830 TRUE FALSE 93360.58932 140967.8866 116509.6269 135725.8118 118371.2698 125698.2146 132422.2352 137929.3769 120656.9374 0.77376893 1.168336356 0.965627253 1.124890245 0.981056476 1.041781909 1.09751033 1.143153307 1 16.88055134 4.751492166 24.88468366 1.065088749 0.773768732 0.636645623 0.069214077 1236.537982 2379473.172 0.015151634 0.279483775 56427.67627 -4.751492166 -0.291320017 HACVPVDFEEVHVSSNADEEDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HACVPVDFEEVHVSSNADEEDIR 23 0 E9PF84;G5E9Q7;E7EQB8;P51553-2;P51553 E9PF84 IDH3G "Isocitrate dehydrogenase [NAD] subunit, mitochondrial;Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial" 0 208.08 6.25E-25 73940000 24016 34257 36064 34972 41384 38171 32689 36007 46564 FALSE TRUE 22512.88143 36793.42392 36919.45511 35869.44073 38133.86758 49190.34805 27787.58792 40502.55321 38792.16759 0.580346055 0.948475587 0.951724469 0.924656779 0.983030079 1.268048452 0.716319547 1.044091004 1 15.24347777 4.740560718 4.714839635 0.967914047 0.557082153 0.464347523 0.134405107 0.16759063 10.36633543 0.029907007 0.227538128 55025.08454 -4.740560718 -0.410831894 HADGEKEDQFNGS(ph)PPRPQPR ddPTM_SK-BR-3_Pertuzumab_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 215.68 6.15E-25 4434820000 1624120 1282600 1389930 1426280 1445740 1037810 1697410 1198150 1568330 TRUE FALSE 1522469.228 1377565.039 1422899.796 1462880.759 1332197.412 1337408.9 1442899.128 1347741.665 1306565.591 1.165245158 1.054340515 1.089038167 1.11963821 1.019617707 1.023606399 1.104344962 1.031514739 1 20.31734812 8 0.065901574 0.922166147 1.401258454 0.431452904 0.03921042 322.4030902 1.575732258 2.123630662 14.49951417 99999999.95 -8 0.479092307 HADIVTTTTHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HADIVTTTTHK 11 0 P34897-3;P34897-2;P34897;H0YIZ0;G3V2Y4 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial;Serine hydroxymethyltransferase" 0 ; 120.96 0.00024379 385760000 598350 782290 649790 638870 856830 552290 659220 722050 937860 FALSE TRUE 560900.3416 840211.5656 665203.3257 655264.4858 789538.0281 711727.1573 560376.0809 812199.5319 781325.1072 0.717883422 1.075367421 0.851378408 0.838657916 1.010511528 0.910923188 0.717212433 1.039515465 1 19.57556345 3.73398232 24.58113109 0.888968543 0.934523859 0 0.129297844 1134.210465 4063491.519 0.031401021 0.055053418 5419.788258 -3.73398232 0.045555315 HADNS(ph)SDTEMEDMIAEETLEEMDSELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HADNSSDTEMEDMIAEETLEEMDSELLK 28 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 HADNS(0.453)S(0.453)DT(0.094)EMEDMIAEETLEEMDSELLK;HADNS(0.332)S(0.332)DT(0.332)EMEDMIAEET(0.005)LEEMDSELLK;HADNS(0.322)S(0.322)DT(0.322)EMEDMIAEET(0.035)LEEMDSELLK;HADNS(0.333)S(0.333)DT(0.333)EMEDMIAEET(0.001)LEEMDSELLK;HADNS(0.456)S(0.456)DT(0.088)EMEDMIAEETLEEMDSELLK 238.37 2.18E-45 160843800 175448.6 143075.7 140423.7 152053.2 156107.3 105456.6 173062.1 125379.9 159784.4 TRUE FALSE 164467.5853 153669.1737 143754.6165 155955.1425 143847.2624 135900.2085 147113.0447 141033.8565 133115.3514 1.235526809 1.1544061 1.079925155 1.171578942 1.080621137 1.020920631 1.105154614 1.05948604 1 17.02231743 8 0.202212145 1.02035461 1.938462297 0.70657282 0.038364731 31.68502146 0.385537236 0.06791991 9.256844049 100000000 -8 0.918107687 HADNSSDT(ph)EMEDMIAEETLEEMDSELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HADNSSDTEMEDMIAEETLEEMDSELLK 28 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 HADNS(0.289)S(0.289)DT(0.422)EMEDMIAEET(0.001)LEEMDSELLK 128.89 0.00010507 27849000 47871 38594 41752 42308 43596 31723 44675 34168 41818 TRUE FALSE 44874.83956 41451.53992 42742.37716 43393.69491 40172.14602 40880.91512 37976.39849 38433.95001 34838.30565 1.288089037 1.189826519 1.226878758 1.245574206 1.153102749 1.173447283 1.090075932 1.103209507 1 15.08838684 1.554483394 0.55543599 1.000685098 1.238309717 0.86196129 0.03106854 0.256804303 0.187811223 0.028981916 0.016409752 35.84952403 -1.554483394 0.237624619 HAEATLGSGNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HAEATLGSGNLR 12 0 Q9H8S9;Q7L9L4;Q7L9L4-2;D6RCK3;Q9H8S9-2 Q9H8S9 MOB1A;MOB1B MOB kinase activator 1A;MOB kinase activator 1B 0 ;;; 160.22 6.38E-05 824060000 482260 533830 510520 487160 529220 392083 514920 458100 536580 FALSE TRUE 452076.2075 573355.3286 522629.7755 499661.3504 487657.196 505270.9972 437712.5263 515294.7934 447021.3316 1.011307908 1.282612905 1.169138335 1.117757286 1.090903636 1.130306233 0.979175926 1.152729763 1 18.76998415 2.697427068 1.110371314 1.050176859 1.184218496 0.159899128 0.083425989 0.580109124 1.484154531 0.040540697 0.036280372 498.2267803 -2.697427068 0.134041637 HAEELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HAEELER 7 0 Q9UHB9;Q9UHB9-4;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 135.84 0.0030379 444910000 70306 91683 84192 76684 73053 70426 88563 72827 75001 FALSE TRUE 65905.67296 98471.30472 86189.074 78651.84127 67315.71206 90756.84293 75283.80033 81919.61126 62482.84858 1.054780223 1.575973358 1.379403724 1.258774897 1.077347042 1.452508088 1.204871449 1.311073569 1 15.93117261 -4.293618718 0.163771543 0.04423918 1.4066774 0.203223208 0.162918745 131.9169243 1.514978921 41.5739554 0.637957197 5.09E-05 4.293618718 1.36243822 HAEMVHTGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HAEMVHTGLK 10 0 Q01518-2;Q01518;Q5T0R1;Q5T0R9;Q5T0R4;Q5T0R3;Q5T0R2;Q5T0R5;Q5T0R7;Q5T0R6 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 0 ;;; 162.36 3.93E-06 1801700000 1568296 1470422 1313186 1208248 1579926 803637 1617325 1415980 1877280 FALSE TRUE 1470139.153 1579293.575 1344335.392 1239253.689 1455844.985 1035633.956 1374822.131 1592768.22 1563949.84 0.940016818 1.009810887 0.859577051 0.792387107 0.930877032 0.662191286 0.879070476 1.018426665 1 20.57676281 3.860625031 3.581539318 0.859290569 0.974697746 0.113529676 0.103537909 0.377080414 8.997186472 0.025456507 0.049657204 7254.793102 -3.860625031 0.115407177 HAEVMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HAEVMK 6 0 Q9NT62;Q9NT62-2 Q9NT62 ATG3 Ubiquitin-like-conjugating enzyme ATG3 0 69.39 0.071022 30008000 95346 120400 115730 115170 124830 112030 135400 113280 114630 FALSE TRUE 89378.46406 129314.5413 118475.1703 118125.4572 115026.3553 144371.2423 115098.027 127423.2574 95497.51246 0.935924526 1.354114238 1.240610014 1.236948001 1.204495828 1.511780136 1.205246336 1.334309702 1 16.54317553 4.746780003 24.3489844 1.276905917 0.93592428 0.373025402 0.130975597 674.279587 1997409.011 0.027018627 0.299723834 55818.73667 -4.746780003 -0.340981637 HAFSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HAFSLK 6 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 106.76 0.031846 604960000 1823390 2136380 1860990 1871120 2398490 1334770 2201480 2126950 2732700 FALSE TRUE 1709267.275 2294559.798 1905133.562 1919136.107 2210122.27 1720096.431 1871388.512 2392504.389 2276594.716 0.750799983 1.007891208 0.836834746 0.8429854 0.97080181 0.755556718 0.822012147 1.050913618 1 21.11844605 1.234787495 24.99912942 1.025456884 0.864842634 0.42119751 0.08234894 101.7349674 674004.6383 0.067091357 0.019264894 17.17068 -1.234787495 -0.16061425 HAGVQTSRPIS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HAGVQTSRPISR 12 1 Q86X02 Q86X02 CDR2L Cerebellar degeneration-related protein 2-like 1 HAGVQTSRPIS(1)R;HAGVQTSRPIS(1)R;HAGVQTSRPIS(0.999)R;HAGVQTSRPIS(1)R 145.49 3.87E-05 1536210000 210493 233110 207834 233939 230816 190994 240955 197873 325751 TRUE FALSE 197318.6189 250369.707 212763.9206 239942.2708 212688.6424 246130.8673 204826.0347 222577.8796 271381.0537 0.727090621 0.922576221 0.784004328 0.884152624 0.783726939 0.906956709 0.754754364 0.82016735 1 18.04996048 -1.153395756 4.169022489 1.000051005 0.82736749 0.423087943 0.064797563 2.70E-05 5.47E-06 0.055044581 0.012970303 0.070243193 1.153395756 -0.172683514 HAGVYSTGLAMVGAICDFCEAWVCHGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HAGVYSTGLAMVGAICDFCEAWVCHGR 27 0 Q9Y3S2;D6RBR7;D6R8Y9;D6R9C8 Q9Y3S2 ZNF330 Zinc finger protein 330 0 138.62 2.29E-06 77613000 63876 89293 67432 56241 91717 68475 95036 78514 70765 FALSE TRUE 59878.11518 95904.34663 69031.51888 57684.23928 84513.91679 88242.6209 80786.23407 88316.64573 58953.86434 1.015677528 1.62676947 1.170941373 0.978464091 1.433560255 1.496808087 1.370329748 1.498063727 1 15.84729876 HAHGDQYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HAHGDQYK 8 0 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;;;; 185.55 0.00021217 243158000 743374 997906 490354 498802 1383030 313332 482610 975927 1560810 FALSE TRUE 696847.5483 1071791.999 501985.4284 511602.1038 1274412.403 403785.8619 410247.1108 1097773.634 1300300.728 0.535912603 0.824264707 0.386053332 0.393449064 0.980090509 0.310532674 0.315501716 0.844245958 1 20.31041389 1.046982982 6.492877358 0.999124405 0.537847695 0.366530591 0.216783356 0.180691694 16.82929213 0.206126969 0.051765227 11.1425087 -1.046982982 -0.461276711 HAHLTDTEIMTLVDETNMYEGVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HAHLTDTEIMTLVDETNMYEGVGR 24 0 O60925;E5RGS4 O60925 PFDN1 Prefoldin subunit 1 0 ;;; 248.89 2.13E-38 743751000 269140 356741 311802 334419 347438 298343 340956 287779 320518 FALSE TRUE 252295.0078 383154.4748 319198.0907 343000.7577 320151.621 384469.7809 289832.8131 323708.8416 267021.4752 0.944849127 1.434920074 1.195402319 1.284543715 1.198973306 1.439845917 1.085428851 1.212295159 1 18.02659625 0.925124852 1.115478963 1.00614328 1.258397384 0.178529737 0.147469286 0.832854965 2.109184574 0.123306824 0.039173671 8.416370628 -0.925124852 0.252254104 HAIGLSCELVVEHIQSFLHSDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HAIGLSCELVVEHIQSFLHSDIR 23 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 0 114.75 0.00022229 49759000 143020 45974 59819 55021 68005 52641 70784 46244 95994 FALSE TRUE 134068.6335 49377.9628 61237.93493 56432.93201 62664.16162 67837.60214 60170.59633 52017.6652 79971.98126 1.676445067 0.617440784 0.765742376 0.705658796 0.783576456 0.848267119 0.752395969 0.650448624 1 16.28720701 4.743624713 24.99980678 0.75133308 1.67644545 0.877596794 0.106807642 157.7917319 778941.9415 0.022922588 0.192293611 55414.66513 -4.743624713 0.92511237 HAIPIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HAIPIIK 7 0 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 88.591 0.018495 366850000 616620 572340 613840 622360 710930 539650 781200 594970 841810 FALSE TRUE 578026.8549 614716.6491 628400.5747 638330.8113 655096.4256 695438.1945 664066.3123 669253.3142 701306.4727 0.824214345 0.876530694 0.896042742 0.910202367 0.934108626 0.991632363 0.946898878 0.954295077 1 19.41968552 8 0.18340291 1.008391252 0.21248939 0.891124788 0.017404894 16.25771093 0.185351388 0.036919795 3.629500525 100000000 -8 -0.795901861 HAIPS(ph)AERGPGLLESPSIFNFTADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HAIPSAERGPGLLESPSIFNFTADR 25 1 Q92615 Q92615 LARP4B La-related protein 4B 1 HAIPS(1)AERGPGLLESPSIFNFTADR;HAIPS(1)AERGPGLLESPSIFNFTADR 184.25 1.16E-17 49830000 21681.5 33082 29237 31608 39607 16816.3 40601 34038 50095 TRUE FALSE 20324.49362 35531.4257 29930.51545 32419.11479 36496.42599 21670.89282 34513.25697 38287.71923 41733.82087 0.487002944 0.851382044 0.717176497 0.776806775 0.874504783 0.519264529 0.826985314 0.917426644 1 15.34892939 1.276065932 2.944290943 0.980204939 0.729504793 0.396612943 0.127121062 0.259643744 3.759366537 0.10172717 0.029829024 18.88277995 -1.276065932 -0.250700146 HAIVICNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HAIVICNR 8 0 P53621;A0A3B3IT15;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 117.17 0.0021307 151790000 169710 190396 184178 187015 189727 150138 220377 185763 185443 FALSE TRUE 159088.154 204493.1179 188546.7891 191814.1215 174826.6067 193480.4033 187333.5147 208955.9195 154491.3653 1.029754341 1.323654028 1.220435775 1.241584739 1.131627042 1.252370338 1.212582427 1.352541089 1 17.23716668 -1.149581472 4.418127287 0.999964987 1.228031725 0.365413719 0.090876242 3.15E-05 6.05E-06 0.077538196 0.018272736 0.070862836 1.149581472 0.228066738 HALFQPCDGEMIIVLHFHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HALFQPCDGEMIIVLHFHLK 20 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 200.39 4.74E-22 100157000 150536 124667 127998 131609 117958 87245 140520 88596 103044 FALSE TRUE 141114.2205 133897.4744 131034.173 134986.3098 108694.0545 112431.2152 119450.3305 99657.40562 85845.29071 1.643820171 1.559753287 1.526399083 1.572436981 1.266162111 1.309695783 1.391460493 1.160895429 1 16.38945137 1.795821964 0.244692645 0.9130266 1.740257118 0.863024937 0.075122827 0.735500458 0.178257501 0.199101687 0.237549886 62.49164601 -1.795821964 0.827230518 HALIIYDDLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HALIIYDDLSK 11 0 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;;; 166.97 1.98E-05 1168612000 2678540 1896580 1983240 1859870 2706560 1668030 2081490 2165230 3429210 FALSE TRUE 2510894.963 2037004.757 2030283.389 1907597.413 2493997.695 2149563.183 1769389.898 2435563.732 2856852.697 0.878902495 0.713024077 0.710671359 0.667726906 0.87298785 0.752423527 0.619349363 0.852533886 1 21.44599522 0.991064831 10.97151063 0.999999582 0.734869864 0.509191279 0.08099819 0.227735486 274.3358568 0.074358679 0.018595561 9.796362133 -0.991064831 -0.265129717 HAPEHHPGHGDRLS(ph)PGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HAPEHHPGHGDRLSPGER 18 1 C9JPC9;Q9H9J4-2;Q9H9J4 C9JPC9 USP42 Ubiquitin carboxyl-terminal hydrolase 42 1 HAPEHHPGHGDRLS(1)PGER;HAPEHHPGHGDRLS(1)PGER;HAPEHHPGHGDRLS(1)PGER;HAPEHHPGHGDRLS(1)PGER 138.44 1.01E-06 971260000 149748 201884 204782 195740 182363 189251 196249 193911 181573 TRUE FALSE 140375.54 216831.7014 209639.5257 200763.0198 168040.9456 243884.6915 166823.2843 218121.2152 151267.2933 0.92799664 1.433434133 1.385887995 1.327207061 1.110887502 1.612276429 1.10283777 1.441958869 1 17.20674056 -1.171499689 4.470478287 0.999939023 1.308306367 0.1718057 0.199477354 0.000106109 1.97E-05 0.169040264 0.039835309 0.067375238 1.171499689 0.308367344 HAPEHHPGHGDRLS(ph)PGERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HAPEHHPGHGDRLSPGERR 19 2 C9JPC9;Q9H9J4-2;Q9H9J4 C9JPC9 USP42 Ubiquitin carboxyl-terminal hydrolase 42 1 HAPEHHPGHGDRLS(1)PGERR;HAPEHHPGHGDRLS(1)PGERR;HAPEHHPGHGDRLS(1)PGERR;HAPEHHPGHGDRLS(1)PGERR;HAPEHHPGHGDRLS(1)PGERR 134.81 5.60E-06 601596000 236645 381838.6 328503 346889 362939 281063 329885 325520.7 464562 TRUE FALSE 221833.8119 410110.3272 336295.2463 355790.759 334435.235 362201.3254 280421.8068 366162.676 387023.601 0.573179029 1.059651985 0.868926973 0.919299903 0.864121036 0.935863664 0.724559965 0.946099088 1 18.56206202 HAPHCLS(ph)EEEGEQDRPR ddPTM_SK-BR-3_Pertuzumab_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 224.86 1.56E-15 5507620000 1173072 1282838 1290001 1351884 1521480 1346023 1753460 1210613 1737990 TRUE FALSE 1099651.518 1377820.66 1320600.433 1386575.632 1401989.098 1734597.989 1490544.951 1361760.698 1447908.241 0.759475971 0.951593907 0.912074671 0.957640542 0.968285875 1.198002705 1.029447108 0.94050207 1 20.46553875 2.843154253 1.847132484 1.047473575 0.89531694 0.407686352 0.083302677 0.344438758 2.334655119 0.029276499 0.031057449 696.8739868 -2.843154253 -0.152156635 HAPINSAQHLDNVDQTGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HAPINSAQHLDNVDQTGPK 19 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 0 66.335 0.015802 92423000 97511 90763 93408 91415 98571 70745 120480 75850 116510 FALSE TRUE 91407.96057 97483.18696 95623.68187 93760.86367 90829.63128 91167.93305 102415.1425 85320.03947 97063.72832 0.941731398 1.004321477 0.985163908 0.965972205 0.935773155 0.939258512 1.055132996 0.879010532 1 16.56664466 -0.927058089 4.439902153 1.000000461 0.97322262 0.019761482 0.047487132 5568912.346 1254287.08 24.8333925 0.01027578 0.118288333 0.927058089 -0.026777841 HAPS(ph)LHGS(ph)TELLPLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HAPSLHGSTELLPLSR 16 0 Q9H5N1;B4DHR0;Q9H5N1-2;H3BU67;H3BNR2;H3BT64 Q9H5N1 RABEP2 Rab GTPase-binding effector protein 2 2 HAPS(1)LHGS(0.855)T(0.145)ELLPLSR 130.25 2.69E-05 73389000 76476 74638 78725 76586 69395 63360 92800 67546 70182 TRUE FALSE 71689.50367 80164.27518 80592.39418 78551.32642 63944.99663 81651.00344 78885.50151 75979.26679 58468.17081 1.226128724 1.371075477 1.378397734 1.343488694 1.09367192 1.39650347 1.349204198 1.299497927 1 15.83536384 0.937743161 18.23042769 0.999999999 1.3214193 0.529507497 0.090405342 507.641457 148652.308 0.083586769 0.020896692 8.664493125 -0.937743161 0.321419301 HAPS(ph)PEPAVQGTGVAGVPEESGDAAAIPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HAPSPEPAVQGTGVAGVPEESGDAAAIPAK 30 0 P13051 P13051 UNG Uracil-DNA glycosylase 1 HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAK;HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAK;HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAK 248.08 2.80E-46 2168060000 1175670 819870 983960 874350 1176100 826910 1309470 1002010 1306890 TRUE FALSE 1102086.913 880574.0279 1007299.996 896787.3013 1083733.85 1065625.493 1113127.13 1127113.154 1088761.616 1.012238948 0.808784967 0.925179563 0.823676449 0.995382124 0.978750056 1.022379108 1.035224917 1 20.05425668 2.636356713 6.491605464 1.007887833 0.884214581 0.493624673 0.057116092 0.177961653 9.675010496 0.01687762 0.015884424 432.8692277 -2.636356713 -0.123673252 HAPS(ph)PEPAVQGTGVAGVPEESGDAAAIPAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HAPSPEPAVQGTGVAGVPEESGDAAAIPAKK 31 1 P13051 P13051 UNG Uracil-DNA glycosylase 1 HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAKK 190.48 5.23E-19 313980000 362530 225470 281750 242330 313870 223760 363100 305460 416410 TRUE FALSE 339839.8944 242164.0334 288433.2431 248548.5981 289219.9163 288355.8796 308656.5259 343597.3534 346908.4809 0.97962406 0.698063169 0.831439008 0.716467344 0.833706675 0.831215999 0.889734737 0.990455329 1 18.40419559 1.485268535 1.438348255 1.007729522 0.794930572 0.477252493 0.076542533 0.284825235 1.125070331 0.060980089 0.020276781 30.56810633 -1.485268535 -0.21279895 HAPSLHGS(ph)TELLPLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HAPSLHGSTELLPLSR 16 0 Q9H5N1;B4DHR0;Q9H5N1-2;H3BU67;H3BNR2;H3BT64 Q9H5N1 RABEP2 Rab GTPase-binding effector protein 2 1 HAPSLHGS(0.956)T(0.044)ELLPLSR;HAPSLHGS(0.5)T(0.5)ELLPLSR 265.42 2.77E-27 883380000 428890 527540 536420 529270 485970 487800 566370 410230 447540 TRUE FALSE 402046.5405 566599.6105 549144.1357 542851.9643 447803.8765 628619.9412 481448.0764 461448.1185 372842.6828 1.07832756 1.519674749 1.472857484 1.455981274 1.201053144 1.686019252 1.29129013 1.237648316 1 18.5082075 1.025873009 1.909674645 1.006271647 1.419103576 0.347762971 0.169794412 0.320644368 2.427274034 0.144044468 0.040786152 10.61385154 -1.025873009 0.41283193 HAPTYT(ph)IPLSPVLSPTLPAEAPTAQVPPSLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HAPTYTIPLSPVLSPTLPAEAPTAQVPPSLPR 32 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 HAPT(0.124)YT(0.437)IPLS(0.437)PVLS(0.001)PTLPAEAPTAQVPPSLPR 111.42 1.26E-05 54888000 45951 39659 46432 47300 45900 35514 41288 30490 43638 TRUE FALSE 43075.00893 42595.39363 47533.38897 48513.79808 42295.19915 45766.31528 35097.2477 34296.74362 36354.53589 1.184859272 1.17166655 1.307495414 1.334463414 1.163409135 1.258888724 0.96541592 0.943396547 1 15.14984776 1.712866222 5.401590196 0.964448794 1.238640133 0.827652871 0.057351561 0.059619844 4.205673059 0.030241802 0.015219527 51.62573198 -1.712866222 0.274191339 HAPTYTIPLS(ph)PVLS(ph)PTLPAEAPTAQVPPSLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HAPTYTIPLSPVLSPTLPAEAPTAQVPPSLPR 32 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 2 HAPT(0.008)Y(0.001)T(0.012)IPLS(0.979)PVLS(0.939)PT(0.061)LPAEAPTAQVPPSLPR;HAPTYTIPLS(0.997)PVLS(0.969)PT(0.034)LPAEAPTAQVPPSLPR 193.13 1.42E-20 228330000 125423 132730 147062 208871 173208 93317 108647 81258 106532 TRUE FALSE 117572.9983 142557.4673 150550.3801 214230.9835 159604.9424 120256.103 92356.39098 91403.24017 88751.12098 1.324749446 1.606261034 1.696320885 2.413839748 1.798342833 1.35498123 1.040622248 1.029882656 1 16.43747772 2.013726894 2.888127173 1.037163389 1.764028084 0.616257336 0.269355762 0.19324168 3.125983174 0.137251849 0.080812036 103.2112158 -2.013726894 0.726864696 HAPTYTIPLS(ph)PVLSPTLPAEAPTAQVPPSLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HAPTYTIPLSPVLSPTLPAEAPTAQVPPSLPR 32 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 HAPTYTIPLS(0.999)PVLS(0.001)PTLPAEAPTAQVPPSLPR 184.54 8.14E-20 114400000 99850 111590 115950 124100 132670 83479 112180 94795 111740 TRUE FALSE 93600.56674 119852.2397 118700.3888 127284.6161 122250.6334 107578.0321 95359.65043 106630.3644 93089.87213 1.005486038 1.287489573 1.275116036 1.367330443 1.313253854 1.155636265 1.024382656 1.145456127 1 16.5063366 2.014814061 4.415182117 1.064237506 1.263014112 0.425976571 0.101672215 0.176608792 8.40652576 0.040738311 0.026970604 103.4699076 -2.014814061 0.198776606 HAQGGTWYGVDINNEDIADNFEAFVWEPAMVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HAQGGTWYGVDINNEDIADNFEAFVWEPAMVR 32 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;;;; 397.02 1.17E-166 738092000 368863.4 409722.4 360099.7 354660.1 422640.4 317316.1 397100.4 373864.6 299184.3 FALSE TRUE 345776.8982 440058.6728 368641.4349 363761.2786 389447.9278 408920.1069 337558.8815 420542.4183 249248.5075 1.387277708 1.765541857 1.479011604 1.459432123 1.562488505 1.640612058 1.354306531 1.68724147 1 17.92722534 -2.626668088 0.408875688 1.99E-10 1.559365032 0.615287946 0.132751864 57.84672998 2.449637482 51.22623564 0.075076473 0.002362283 2.626668088 1.559365031 HAQPTCPGAQLCTVYYASLNFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HAQPTCPGAQLCTVYYASLNFR 22 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 268.36 5.80E-38 1759790000 627270 751240 668280 580090 857880 571320 889730 774410 573280 FALSE TRUE 588010.2904 806862.5913 684131.9172 594976.0915 790505.5653 736250.8094 756323.2463 871096.7932 477595.8645 1.231187986 1.689425414 1.432449416 1.245773123 1.655176739 1.54157702 1.583605099 1.823920302 1 18.86543082 HAS(ph)APSHVQPSDSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HASAPSHVQPSDSEK 15 0 O60343-2;O60343-3;O60343;A0A3B3IRT3 O60343-2 TBC1D4 TBC1 domain family member 4 1 HAS(0.998)APS(0.002)HVQPSDSEK;HAS(1)APSHVQPSDSEK;HAS(0.997)APS(0.003)HVQPSDSEK;HAS(0.993)APS(0.007)HVQPSDSEK;HAS(0.999)APS(0.001)HVQPSDSEK 231.21 1.45E-13 2520937000 3133850 2450150 2525780 2838440 3648260 1710240 3665010 2484260 3735940 TRUE FALSE 2937707.923 2631561.655 2585692.694 2911279.176 3361740.376 2203958.525 3115475.775 2794425.33 3112387.479 0.943876025 0.845512223 0.830774674 0.935384555 1.080116277 0.708124724 1.000992259 0.897839793 1 21.56959025 -0.733986657 0.182428587 1.083151302 0.854947298 0.072613108 0.100561753 40.79921852 1.844200231 2.135543208 0.381176692 0.18450721 0.733986657 -0.228204004 HAS(ph)PDKWNDKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HASPDKWNDKPK 12 2 Q96JM3;A0A2R8Y4S6;S4R3K0;A0A2R8Y735 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 HAS(1)PDKWNDKPK;HAS(1)PDKWNDKPK 140.74 3.13E-05 320680000 2874500 872380 1496520 1358940 1482960 1054460 2222650 1245780 2488730 TRUE FALSE 2694590.176 936971.9229 1532018.161 1393812.701 1366494.304 1358865.484 1889384.267 1401318.375 2073344.885 1.299634323 0.451913201 0.738911395 0.672253184 0.659077182 0.655397707 0.911273508 0.675873264 1 20.98352869 0.361776336 0.685153685 1.003603953 0.715311136 0.0720405 0.226454046 4.610623103 3.178854708 0.266327285 0.076664725 2.30025687 -0.361776336 -0.288292817 HAS(ph)PILPITEFSDIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 HASPILPITEFSDIPR 16 0 P42167;G5E972;H0YJH7 P42167 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 HAS(1)PILPITEFSDIPR;HAS(1)PILPITEFSDIPR;HAS(1)PILPITEFSDIPR;HAS(1)PILPITEFSDIPR;HAS(1)PILPITEFSDIPR;HAS(1)PILPITEFSDIPR;HAS(1)PILPITEFSDIPR;HAS(1)PILPITEFSDIPR;HAS(1)PILPITEFSDIPR 261.31 5.11E-27 3003929000 695011 657119 664406 651047 700063 561643 790694 677829 812584 TRUE FALSE 651511.5021 705772.7745 680166.0241 667753.9682 645082.8759 723780.2166 672136.7751 762457.4427 676958.4809 0.962409838 1.042564344 1.004738168 0.986403136 0.952913501 1.069164856 0.992877398 1.126298679 1 19.36870783 1.285474625 24.99981182 1.063150951 1.006484386 0.235356155 0.045473032 146.9181258 78290.33044 0.026967501 0.009847891 19.29632587 -1.285474625 -0.056666565 HAS(ph)S(ph)SPESPKPAPAPGSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HASSSPESPKPAPAPGSHR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 HAS(0.909)S(0.662)S(0.429)PESPKPAPAPGSHR;HAS(0.986)S(0.557)S(0.457)PESPKPAPAPGSHR 141.53 2.18E-07 160124000 197240 155721 190748 165756 198596 126692 189725 166587 262430 TRUE FALSE 184895.1005 167250.7449 195272.6326 170009.5796 182999.0713 163265.9237 161277.4976 187385.7537 218628.7376 0.845703554 0.764998905 0.893170014 0.777617716 0.837031185 0.746772476 0.737677486 0.857095712 1 17.73812352 0.981529793 21.80898303 1.000000003 0.800574026 0.63459369 0.047822564 152.0564451 179544.2008 0.047272901 0.011818225 9.58362459 -0.981529793 -0.199425977 HAS(ph)SSPESPKPAPAPGSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HASSSPESPKPAPAPGSHR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HAS(0.287)S(0.287)S(0.287)PES(0.138)PKPAPAPGSHR;HAS(0.263)S(0.263)S(0.237)PES(0.237)PKPAPAPGSHR;HAS(0.333)S(0.333)S(0.333)PESPKPAPAPGSHR;HAS(0.312)S(0.312)S(0.312)PES(0.065)PKPAPAPGSHR 139.26 1.91E-07 559481000 411120 420699 462086 459859 501723 396219 472123 403998 496946 TRUE FALSE 385388.7331 451847.9917 473046.8981 471659.7605 462319.6994 510600.9932 401332.5391 454438.0396 414002.5022 0.930885033 1.091413673 1.142618452 1.139267898 1.1167075 1.233328278 0.969396409 1.09766979 1 18.65927996 1.677255979 14.35244384 1.025544975 1.112287671 0.202711249 0.080747647 0.203970662 44.28817069 0.035467858 0.019530687 47.56154775 -1.677255979 0.086742695 HASS(ph)SPESPKPAPAPGSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HASSSPESPKPAPAPGSHR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HAS(0.325)S(0.408)S(0.267)PESPKPAPAPGSHR 107.56 0.00017637 81679000 43900 39383 42491 50075 55755 26398 46530 38468 45168 TRUE FALSE 41152.37736 42298.9583 43498.90659 51360.00928 51376.2272 34018.67406 39553.25846 43270.81448 37629.169 1.093629715 1.12410025 1.15598903 1.364898844 1.365329838 0.904050633 1.051132925 1.149927453 1 15.19956381 2.231432113 24.99998617 1.02822793 1.205318626 0.44315062 0.10756188 183.70231 644246.2954 0.04202261 0.031687052 170.385296 -2.231432113 0.177090696 HASSSPES(ph)PKPAPAPGSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HASSSPESPKPAPAPGSHR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HASS(0.001)S(0.004)PES(0.995)PKPAPAPGSHR;HAS(0.001)S(0.003)S(0.003)PES(0.993)PKPAPAPGSHR;HASS(0.001)S(0.001)PES(0.998)PKPAPAPGSHR;HASSSPES(1)PKPAPAPGSHR 211.71 7.02E-17 1911250000 556240 911880 938790 991590 986680 806850 1244710 951050 1031890 TRUE FALSE 521425.9313 979396.544 961058.5421 1017035.878 909190.1329 1039774.497 1058077.291 1069790.686 859660.8927 0.606548391 1.139282422 1.117950753 1.183066354 1.057614858 1.209517038 1.230807752 1.244433352 1 19.71340815 4.739423573 5.450127606 1.157502933 0.585566896 0.83162504 0.076480827 0.055624419 6.275046016 0.017438661 0.1188565 54881.1968 -4.739423573 -0.571936038 HASTSS(ph)PADKAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HASTSSPADKAK 12 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5;A0A0A0MSW0 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 HAS(0.008)T(0.068)S(0.089)S(0.835)PADKAK;HAS(0.036)T(0.257)S(0.07)S(0.637)PADKAK 109.83 0.00094171 195157000 103751 181184 176003 178209 241140 148795 365780 247490 367960 TRUE FALSE 97257.41011 194599.0519 180177.8743 182782.1446 222201.8371 191749.701 310934.6847 278389.6713 306545.0989 0.3172695 0.634813776 0.587769548 0.596265102 0.724858554 0.62551873 1.014319543 0.908152413 1 18.22573981 1.985803079 0.836264857 1.02319788 0.540030752 0.74893072 0.107084718 0.291002458 0.378441464 0.085070172 0.042515027 96.78389111 -1.985803079 -0.483167128 HATAEEVEEEERDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HATAEEVEEEERDR 14 1 Q8TDN6 Q8TDN6 BRIX1 Ribosome biogenesis protein BRX1 homolog 0 238.47 1.51E-17 647660000 20501 29227 25267 22104 17254 18929 27510 24842 22300 FALSE TRUE 19217.87901 31390.99749 25866.34517 22671.22606 15898.94044 24393.49501 23385.13089 27943.57838 18577.98594 1.034443619 1.68968787 1.392311592 1.220327442 0.855794621 1.313032268 1.258754903 1.504123132 1 14.18130649 3.290371452 4.227959235 1.200397898 1.449552337 0.090564361 0.235191485 0.341709828 12.6016947 0.06395324 0.086072749 1951.513016 -3.290371452 0.249154439 HATAEEVEEEERDRIPGPVCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HATAEEVEEEERDRIPGPVCK 21 2 Q8TDN6 Q8TDN6 BRIX1 Ribosome biogenesis protein BRX1 homolog 0 ;; 251.75 1.53E-36 324200000 200936 239652 236536 248794 302966 180039 325763 221795 406810 FALSE TRUE 188359.7744 257396.0834 242146.7456 255178.4752 279172.2725 232013.3366 276917.8624 249486.594 338910.7829 0.555779822 0.75948036 0.714485221 0.752937021 0.823733816 0.68458529 0.817081888 0.736142391 1 18.37054601 -5 0.126357799 1.852962256 0.622476076 0.655106196 0.066385798 89.75582006 0.723343503 19.52887744 0.494590523 1.00E-05 5 -1.23048618 HATLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HATLQK 6 0 Q13263;Q13263-2;M0R3C0 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 82.263 0.059704 233540000 599110 1182700 1008500 1092400 1430200 963430 996080 1136100 1236000 FALSE TRUE 561612.7745 1270268.339 1032422.096 1120432.833 1317877.861 1241556.601 846727.0512 1277944.586 1029703.615 0.545412064 1.23362521 1.002640062 1.088111974 1.279861352 1.205741713 0.822301717 1.241080023 1 19.97379771 4.74730909 24.90677556 1.097870499 0.54541177 0.612111407 0.140781967 771.2940406 2195812.711 0.032987325 0.393830674 55886.78025 -4.74730909 -0.552458729 HAVGDDAQFEMDI ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HAVGDDAQFEMDI 13 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 0 96.89 0.0093753 53947000 111330 109230 117990 94836 118570 86179 123660 89558 131970 FALSE TRUE 104362.054 117317.5029 120788.7785 97269.65232 109257.9905 111057.4783 105118.331 100739.5134 109943.3544 0.949234763 1.067072252 1.098645563 0.884725164 0.993766208 1.010133617 0.956113551 0.916285609 1 16.74640088 3.251683221 24.99993365 0.962832852 1.053097539 0.307406934 0.053692183 229.3995234 437027.5551 0.01438972 0.019369514 1785.184967 -3.251683221 0.090264687 HAVS(ph)DPSILDSLDLNEDEREVLINNINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HAVSDPSILDSLDLNEDEREVLINNINR 28 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 1 HAVS(0.958)DPS(0.039)ILDS(0.003)LDLNEDEREVLINNINR 95.302 0.0013445 22401000 9001.9 7825.8 7677.3 9119.5 8788.5 5943.5 8299.3 7276.9 9658.1 TRUE FALSE 8438.487148 8405.230375 7859.409181 9353.521809 8098.286661 7659.291965 7054.897012 8185.436983 8046.100716 1.048767278 1.044634 0.976797266 1.162491266 1.006485868 0.951925937 0.876809434 1.017317241 1 12.97407408 2.344291124 4.134500469 0.943237736 1.045643202 0.34049335 0.059513459 0.221542478 6.898699693 0.020901345 0.017060104 220.9485338 -2.344291124 0.102405466 HAVSDPSILDSLDLNEDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HAVSDPSILDSLDLNEDER 19 0 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ;;; 328.8 3.31E-75 1298430000 1072110 1026440 1203670 939630 896460 995250 1460510 1011890 862150 FALSE TRUE 1005008.549 1102438.686 1232221.621 963742.4966 826055.6477 1282562.518 1241520.084 1138226.694 718251.5953 1.399243044 1.534892081 1.715584941 1.341789566 1.150092326 1.785673052 1.728530911 1.584718644 1 19.45412977 4.738094486 8.581979488 1.536285247 1.398471424 0 0.259962096 0.421722231 516.6460501 0.058894538 0.342665104 54713.4986 -4.738094486 -0.137813823 HAVSDPSILDSLDLNEDEREVLINNINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HAVSDPSILDSLDLNEDEREVLINNINR 28 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ;;;;; 416.44 9.55E-167 1978791000 665032 749473 760543 749653 840561 530082 835399 654223.1 908043 FALSE TRUE 623408.8342 804964.7607 778583.4391 768890.3651 774546.7297 683108.0682 710138.6754 735904.2942 756484.7571 0.824086445 1.064085896 1.02921233 1.016399019 1.023876188 0.903003083 0.938734943 0.97279461 1 19.52895149 2.254628524 24.94153407 0.945852621 1.007694248 0.036620973 0.069311744 416.9523721 647216.4096 0.022586111 0.018838706 179.7332898 -2.254628524 0.061841628 HAVSDPSILDSLDLNEDEREVLINNINRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HAVSDPSILDSLDLNEDEREVLINNINRR 29 2 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ;; 203.66 1.58E-25 407690000 88610 108320 95196 119950 150685 84599 112450 93791 186277 FALSE TRUE 83064.05827 116340.1255 97454.09407 123028.1201 138850.8079 109021.3579 95589.16643 105501.0128 155186.1653 0.535254274 0.749681038 0.627981843 0.792777628 0.894737025 0.702519827 0.615964485 0.679835168 1 17.24364042 -2.521958176 2.129031412 4.87271814 0.700290219 0.474180975 0.099332504 2606654.045 160012.4181 48915872.54 0.023741469 0.003006366 2.521958176 -4.17242792 HAVSEGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 15 HAVSEGTK 8 0 Q16778;P33778;P23527;P06899;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053;A0A2R8Y619;Q99880;Q96A08 Q16778;P58876;Q99880 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS;HIST1H2BL;HIST1H2BA Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S;Histone H2B type 1-L;Histone H2B type 1-A 0 ;;;;;;;;;;;;;; 182.68 0.00033272 1.98227E+11 163991558.9 151378928.9 139800951.1 130484486.7 159731650.8 83590019 160885307.4 141186322.5 174490356.2 FALSE TRUE 153727620 162587182.3 143117095.7 133832939.5 147186971.3 107721100.5 136762049.1 158813745.7 145366788.5 1.057515417 1.118461679 0.984524025 0.920656918 1.012521311 0.741029651 0.940806704 1.092503641 1 27.11512246 3.678708007 2.138125683 0.936027469 1.08861222 0.259738134 0.091245766 0.358015527 3.229094809 0.025222418 0.048569836 4772.0832 -3.678708007 0.152584752 HAVTGEAVELR ddPTM_SK-BR-3_Pertuzumab_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 97.911 0.0059134 281590000 39466 70080 60037 64346 67131 60875 66829 66958 51961 FALSE TRUE 36995.89351 75268.79612 61461.10599 65997.2273 61858.80205 78448.62428 56808.61186 75317.85369 43288.37342 0.854638107 1.738776262 1.419806316 1.52459476 1.428993449 1.812233126 1.312329556 1.739909536 1 15.40169197 -1.012267999 5.051362725 0.999994898 1.497843135 0.229413213 0.273893664 1.35E-05 2.63E-06 0.227015424 0.053507501 0.097214714 1.012267999 0.497848236 HAYGDQYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HAYGDQYR 8 0 O75874;C9J4N6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 145.16 0.00057389 410760000 385906 847760 250853 245817 875160 170730 217007 715010 843400 FALSE TRUE 361752.8323 910529.0325 256803.3516 252125.0804 806428.4638 220016.9794 184468.8149 804280.5724 702631.0914 0.514854576 1.295884915 0.36548817 0.358829951 1.1477267 0.313132997 0.262540069 1.144669774 1 19.42240789 5.024133233 17.1561257 0.688788567 0.063653648 0.017726839 0.39722246 92679028.93 1647902217 0.093099889 1610640259 105714.1769 -5.024133233 -0.625134919 HAYGLGEHYNSVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HAYGLGEHYNSVTR 14 0 A0A087X0W9;Q8N6M0;Q8N6M0-2 A0A087X0W9 OTUD6B OTU domain-containing protein 6B 0 ; 182.02 9.09E-07 970000000 73158 87528 76973 99200 117406 76563 96433 80147 93684 FALSE TRUE 68579.17137 94008.66419 78798.83591 101745.6399 108185.4064 98665.4952 81973.76689 90153.52938 78047.53518 0.878684653 1.204505228 1.009626194 1.303636812 1.386147636 1.264171828 1.050305646 1.155110526 1 16.25206545 3.251810947 24.96085972 1.199376686 1.065086877 0.22240857 0.137898475 403.1317077 759411.2582 0.038150461 0.051351052 1785.710068 -3.251810947 -0.134289809 HCAPS(ph)PDRS(ph)PELSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 HCAPSPDRSPELSSSR 16 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 2 HCAPS(1)PDRS(1)PELSSSR;HCAPS(1)PDRS(1)PELSSSR;HCAPS(1)PDRS(1)PELSSSR;HCAPS(1)PDRS(1)PELSSSR;HCAPS(1)PDRS(1)PELSSSR;HCAPS(1)PDRS(1)PELSSSR;HCAPS(0.999)PDRS(0.911)PELS(0.085)S(0.004)S(0.001)R;HCAPS(1)PDRS(0.999)PELS(0.001)SSR 160.77 4.93E-09 16324050000 4303690 4504820 4471290 4538650 4602190 3800270 5193340 4036660 5336510 TRUE FALSE 4034329.725 4838361.56 4577351.11 4655119.443 4240752.562 4897346.257 4414646.88 4540645.887 4445812.006 0.907444966 1.088296481 1.029587194 1.047079687 0.953875818 1.101563955 0.992990004 1.02133106 1 22.08401551 1.60042741 25 1.005371149 1.029739631 0.003934441 0.057770621 2.494106447 8355.757721 0.027355619 0.013055282 39.84991597 -1.60042741 0.024368482 HCAPS(ph)PDRSPELSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HCAPSPDRSPELSSSR 16 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 HCAPS(0.993)PDRS(0.007)PELSSSR;HCAPS(0.953)PDRS(0.047)PELSSSR;HCAPS(0.991)PDRS(0.009)PELSSSR 205.24 1.40E-11 719790000 288262 326765 326480 320770 321017 254187 346785 238802 299127 TRUE FALSE 270220.196 350959.0206 334224.2598 329001.5013 295805.6197 327566.6605 294787.8086 268616.9554 249200.7713 1.08434735 1.408338421 1.341184692 1.320226657 1.187017272 1.314468887 1.182932971 1.07791382 1 17.92694901 1.306376099 1.144172876 0.994508757 1.30530921 0.525562684 0.091300887 0.305618406 0.801062857 0.080066821 0.02662576 20.24771874 -1.306376099 0.310800453 HCAPSPDRS(ph)PELSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HCAPSPDRSPELSSSR 16 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 HCAPS(0.402)PDRS(0.598)PELSSSR 149.36 5.30E-06 0 114590 119080 129880 132790 128450 99771 140750 93182 118840 TRUE FALSE 107418.0164 127896.8071 132960.8149 136197.6162 118362.0551 128573.2681 119645.8442 104815.9778 99004.83626 1.084977467 1.291823833 1.342972929 1.375666294 1.195517912 1.298656438 1.208484845 1.058695532 1 16.59521138 1.260086118 2.104207674 0.999097983 1.279258774 0.586432613 0.080890943 0.196253065 1.48217561 0.071151154 0.020753993 18.2006173 -1.260086118 0.280160791 HCDLQVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HCDLQVR 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 150.84 0.0019219 599951000 232023 308557 241102 224499 357840 197786 224415 287124 347116 FALSE TRUE 217501.0946 331402.8813 246821.0533 230260.0244 329736.6899 254883.6074 190766.0541 322972.0634 289180.0971 0.752130236 1.146008611 0.853520196 0.796251287 1.140246833 0.881400933 0.659679058 1.116854398 1 18.14160874 2.019826419 24.99418061 0.858408185 0.953373195 0 0.174331344 700.9551632 883655.7193 0.061456696 0.045383663 104.671011 -2.019826419 0.09496501 HCECAEEGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HCECAEEGTR 10 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;;; 160.18 7.46E-06 2421250000 859890 970640 976796 914960 851070 835769 1068200 844110 685176 FALSE TRUE 806071.0198 1042507.196 999966.0624 938439.4226 784230.3953 1077041.943 908033.3267 949498.9916 570815.6992 1.412138841 1.826346397 1.751819482 1.644032258 1.373876711 1.886847093 1.590764459 1.663407284 1 19.12266549 -2.341325624 0.500131681 1.84E-12 1.675695298 0.600666324 0.163440949 74.95945953 4.548978201 82.88332742 0.072272621 0.004556951 2.341325624 1.675695298 HCGLSLSS(ph)TPPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HCGLSLSSTPPGK 13 0 Q09GN1;Q71F23-3;Q71F23;D6R9S4 Q09GN1 MLF1IP;CENPU Centromere protein U 1 HCGLS(0.063)LS(0.246)S(0.41)T(0.281)PPGK 54.812 0.086628 418570000 343350 792420 339110 354640 814700 297130 465140 750260 579650 TRUE FALSE 321860.3364 851091.6013 347153.8493 363740.6628 750716.7483 382906.6075 395396.5751 843931.6125 482902.6703 0.666511817 1.762449565 0.718889894 0.753238044 1.554592249 0.792927087 0.818791445 1.747622584 1 18.88137292 3.949674171 24.69053415 1.023640788 1.286250569 0.013073591 0.431874776 873.7102006 785962.6412 0.1016156 0.183247665 8905.825288 -3.949674171 0.26260978 HCGLSLSST(ph)PPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HCGLSLSSTPPGK 13 0 Q09GN1;Q71F23-3;Q71F23;D6R9S4 Q09GN1 MLF1IP;CENPU Centromere protein U 1 HCGLS(0.002)LS(0.02)S(0.129)T(0.849)PPGK;HCGLSLSS(0.197)T(0.803)PPGK;HCGLSLS(0.001)S(0.151)T(0.849)PPGK 145.69 0.00015426 1165810000 1240030 1640210 1305050 1244990 1776450 1215540 1601360 1511370 1534070 TRUE FALSE 1162418.736 1761652.855 1336006.402 1276938.551 1636934.783 1566446.665 1361250.934 1700067.871 1278023.807 0.909543883 1.378419436 1.045368948 0.999150833 1.280832778 1.225678784 1.065121735 1.330231771 1 20.28548328 -0.877465725 7.725421222 1 1.159880994 0.092022577 0.151412718 9.83E-10 1.27E-10 0.131970222 0.03110568 0.132597176 0.877465725 0.159880995 HCNGVDWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HCNGVDWR 8 0 O15371-2;O15371;O15371-3 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ;;; 117.89 0.001992 2485990000 1335350 1689910 1569690 1509270 1738290 1299430 1842300 1515640 1758290 FALSE TRUE 1251772.827 1815032.695 1606923.788 1548000.423 1601771.715 1674554.347 1566064.218 1704870.99 1464820.04 0.854557415 1.239082375 1.097011062 1.056785394 1.093493857 1.143180937 1.069117144 1.163877435 1 20.482292 -0.901675687 4.43462209 0.999998618 1.102706686 0.061000612 0.099393021 1.21E-06 2.99E-07 0.085427399 0.02013516 0.125407732 0.901675687 0.102708068 HCPYLDTINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HCPYLDTINR 10 0 Q53GS9;B9A018;Q53GS9-3;F8WC91;A0A087X1B2;C9JIU2 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 0 ; 129.85 0.00029216 323510000 417510 488170 464430 484160 491630 360490 527370 439300 506020 FALSE TRUE 391378.7944 524314.6147 475446.4989 496584.3653 453019.3629 464557.6109 448295.7644 494147.572 421561.993 0.928401518 1.243742613 1.127821072 1.177962847 1.074620982 1.10199121 1.063415991 1.172182455 1 18.68538528 2.721111512 24.10191941 1.086008814 1.141581958 0.013912328 0.090132372 1308.102866 1806838.614 0.026592971 0.025133754 526.1523476 -2.721111512 0.055573144 HCSQVDSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HCSQVDSVR 9 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 157.75 6.78E-05 1191530000 207035 481870 403040 413227 433389 306997 391405 415867 468692 FALSE TRUE 194077.0489 517548.1562 412600.2991 423831.1044 399352.3761 395622.0502 332717.4539 467788.9104 390464.2773 0.497041753 1.325468644 1.056691542 1.085454237 1.022762899 1.013209334 0.852107281 1.198032541 1 18.57483104 2.368035895 3.141323369 0.987393626 1.057381301 0 0.223644911 1.360446888 26.93783625 0.079205409 0.063810899 233.3650935 -2.368035895 0.069987674 HCVTFVLHEEDHTLGNSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HCVTFVLHEEDHTLGNSLR 19 0 A0A0R4J2F3;P0DPB6 A0A0R4J2F3 0 ; 300.97 2.16E-50 333900000 89359 180816 149093 146844 183278 178820 143057 119652 124618 FALSE TRUE 83766.1797 194203.8048 152629.5564 150612.2656 168884.0852 230442.4311 121606.9309 134590.8156 103818.4507 0.806852531 1.870609737 1.470158293 1.450727347 1.626725153 2.219667405 1.171342185 1.296405549 1 16.66370334 1.600305261 25 1.175313917 1.600895054 0.227119633 0.360840879 0.9150154 3016.071134 0.17332127 0.082658559 39.8387094 -1.600305261 0.425581137 HDAATCFVDAGNAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HDAATCFVDAGNAFK 15 0 P54920;M0R2M1;M0R058;M0R0I4 P54920 NAPA Alpha-soluble NSF attachment protein 0 ; 194.85 3.46E-08 731360000 1027820 838470 941300 920640 956930 728510 1148740 769610 1064890 FALSE TRUE 963490.5809 900551.1912 963628.0805 944265.181 881776.5779 938819.0106 976497.1014 865697.5026 887152.9795 1.086047844 1.015102482 1.086202834 1.064376948 0.993939713 1.058238018 1.100708811 0.975815358 1 19.75882338 1.221102945 24.98885356 0.987907616 1.056703215 0.439227796 0.032814975 265.0701746 379410.5023 0.030460742 0.007685399 16.63806991 -1.221102945 0.068795599 HDADGQATLLNLLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HDADGQATLLNLLLR 15 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;; 238.88 8.75E-18 54179500 88506 100183 97861 85267 105622 79223 101716 87176 99001 FALSE TRUE 82966.56745 107600.6536 100182.3091 87455.09558 97326.87418 102093.394 86464.63009 98060.1155 82477.09353 1.005934665 1.304612577 1.214668278 1.060356177 1.180047332 1.237839376 1.0483472 1.188937574 1 16.33170587 0.251734615 0.365124937 0.972954434 1.196145319 0.164838975 0.095614791 4.969164435 1.105440875 0.323635045 0.078686949 1.785396235 -0.251734615 0.223190885 HDDPALTLVAGLTSNKPTDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HDDPALTLVAGLTSNKPTDK 20 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q86XE2;Q6P996-2;J3KNK7;Q6XYB5;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ; 240.59 6.27E-30 465120000 1070710 663660 829910 811680 876270 569640 1057580 700390 956010 FALSE TRUE 1003696.172 712798.0769 849595.8571 832509.083 807451.2889 734085.8207 899005.6971 787835.2332 796445.7549 1.260219125 0.894973791 1.066734114 1.045280332 1.01381831 0.92170222 1.128772037 0.989188816 1 19.60321658 4.757014986 24.38389324 1.012798263 1.260219424 0.583678534 0.066930663 2172.610768 2870621.781 0.015498984 0.511545435 57149.83564 -4.757014986 0.247421161 HDDSSDNFCEADDIQSPEAEYVDLLLNPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HDDSSDNFCEADDIQSPEAEYVDLLLNPER 30 0 Q96HE7;G3V3E6;G3V5B3 Q96HE7 ERO1L ERO1-like protein alpha 0 ; 142.38 4.90E-08 43499000 11350.9 12114.6 11497.5 15737.1 13556.1 11886.3 11527.3 7869.2 8010.5 FALSE TRUE 10640.46743 13011.57759 11770.22613 16140.94063 12491.45859 15317.68185 9798.888379 8851.686942 6673.4958 1.594436821 1.949739384 1.76372721 2.418663488 1.871801371 2.29530104 1.468329145 1.326394323 1 12.70422698 1.476733841 2.881412523 1.161851011 1.964908506 0.652877681 0.251842685 0.150997984 2.457260103 0.180709689 0.06255113 29.97325037 -1.476733841 0.803057494 HDDYLVMLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HDDYLVMLK 9 0 Q9Y224;G3V4C6;H0YJB9 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ;; 93.551 0.0079969 251290000 889380 955940 839670 853970 1133650 554540 882560 894270 1236900 FALSE TRUE 833715.2934 1026718.792 859587.3689 875884.316 1044617.702 714626.6958 750228.3213 1005921.578 1030453.399 0.809076174 0.996375763 0.834183641 0.849998958 1.013745699 0.693507049 0.728056525 0.976193177 1 19.97484783 2.241065318 24.99975102 0.811440379 0.902355341 0.000364055 0.11590064 134.7111945 1344585.394 0.038800111 0.031063222 174.2068861 -2.241065318 0.090914962 HDEES(ph)HSLSPPGENTVMADSFQIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HDEESHSLSPPGENTVMADSFQIK 24 0 Q96JQ2 Q96JQ2 CLMN Calmin 1 HDEES(0.332)HS(0.332)LS(0.332)PPGENT(0.003)VMADSFQIK;HDEES(0.385)HS(0.307)LS(0.307)PPGENT(0.001)VMADSFQIK;HDEES(0.412)HS(0.327)LS(0.26)PPGENT(0.001)VMADSFQIK 153.82 1.18E-07 497930000 566080 438108 494956 503700 535132 358344 570091 405397 545139 TRUE FALSE 530650.0633 470545.9722 506696.5901 516625.7948 493104.8913 461792.0956 484611.147 456011.7078 454151.7792 1.16844211 1.036098489 1.115698789 1.137561975 1.085771132 1.016823266 1.067068697 1.00409539 1 18.79281501 2.347776819 4.994407998 1.031641204 1.102440825 0.548767429 0.038667219 0.196935478 7.856111207 0.013335757 0.011010111 222.7290268 -2.347776819 0.070799622 HDGGS(ph)PSIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HDGGSPSIK 9 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 HDGGS(0.919)PS(0.081)IK;HDGGS(1)PSIK;HDGGS(0.766)PS(0.234)IK 102.46 0.0037558 784390000 937390 689980 815070 708020 765300 620080 1000930 688800 1019380 TRUE FALSE 878720.4332 741066.8371 834403.8453 726188.9919 705196.4251 799087.0298 850849.8387 774798.1962 849238.8926 1.03471525 0.872624704 0.982531361 0.85510567 0.830386398 0.940944929 1.001896929 0.912344221 1 19.69581092 -1.075332814 6.123740217 1.000000154 0.929410233 0.105553055 0.065099159 1.32E-07 2.00E-08 0.060880493 0.014349639 0.08407506 1.075332814 -0.070589921 HDGGSPSIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HDGGSPSIK 9 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 0 76.035 0.085084 378650000 967980 942580 912080 865180 1168100 718600 1162800 1020200 1335500 FALSE TRUE 907395.8597 1012369.604 933714.9683 887381.9835 1076362.138 926048.1545 988448.9349 1147574.216 1112596.422 0.815566041 0.909916286 0.839221617 0.797577599 0.967432679 0.832330696 0.888416424 1.031437988 1 20.08549894 1.29846163 4.92697264 1.016335 0.865468273 0.620808111 0.049396005 0.116005969 5.187551413 0.033552071 0.01123371 19.88207145 -1.29846163 -0.150866727 HDGKDEIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HDGKDEIIK 9 1 Q7L576;Q7L576-2;Q7L576-3;H0YL50 Q7L576 CYFIP1 Cytoplasmic FMR1-interacting protein 1 0 58.978 0.063265 123390000 147230 90919 135920 155990 110790 91782 165370 94336 252200 FALSE TRUE 138015.1371 97650.73736 139144.0866 159992.9675 102089.0003 118277.9734 140574.3037 106114.0573 210106.1907 0.656882773 0.464768492 0.662256005 0.761486213 0.485892395 0.562943781 0.669063121 0.505049646 1 17.68075915 -1.502866973 3.078069536 1.011890867 0.59584869 0.645869635 0.094004042 30369957.42 37603086.46 3078475.236 0.021765279 0.031414708 1.502866973 -0.416042177 HDGSEPCVDVLFGDGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HDGSEPCVDVLFGDGHR 17 0 Q96EL3 Q96EL3 MRPL53 "39S ribosomal protein L53, mitochondrial" 0 ; 254.72 2.77E-27 96561000 87348 126504 103365 88645 151505 117946 110710 112577 196649 FALSE TRUE 81881.0446 135870.4878 105816.8666 90919.78078 139606.4084 151995.0955 94110.06328 126632.4863 163827.0115 0.499801857 0.829353393 0.645906103 0.554974298 0.85215745 0.92777799 0.574447781 0.772964636 1 17.32181372 2.723335093 24.78269203 0.789434998 0.667549184 0.282302636 0.141955626 1414.147329 2301814.847 0.045185207 0.042752457 528.8531472 -2.723335093 -0.121885815 HDLDLICR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;; 150.24 0.0004923 4731230000 3655820 4183160 3532170 3349880 4269420 2807050 4124560 3798130 3772710 FALSE TRUE 3427008.752 4492885.519 3615954.74 3435843.592 3934116.975 3617399.766 3506120.519 4272334.891 3143020.328 1.090355261 1.429480261 1.150471318 1.093166201 1.251699501 1.150931075 1.11552588 1.359308705 1 21.58372017 -5 0.159500411 0.271438834 1.264025572 0.177576034 0.118371249 202.2665089 1.858064213 47.27011079 0.481581346 1.00E-05 5 0.992586738 HDLINQLQHNHALVTLVAENLATYMESMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HDLINQLQHNHALVTLVAENLATYMESMR 29 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 ; 193.14 5.94E-19 286110000 162605 218828 220422 192437 222409 146835 235357 194842 159977 FALSE TRUE 152427.8433 235030.2528 225650.5139 197375.2592 204941.8943 189223.8808 200067.4028 219168.4526 133275.8052 1.143702288 1.763487772 1.693109365 1.480953418 1.537727677 1.419791691 1.50115321 1.64447292 1 17.02405537 -2.628186876 0.398200218 4.19E-09 1.567067373 0.451823786 0.174806302 73.85863118 3.066390771 63.67333758 0.107203993 0.002354036 2.628186876 1.567067368 HDMAAAGFTEALTFALCSQEDIADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HDMAAAGFTEALTFALCSQEDIADK 25 0 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 72.145 0.036221 5943500 10599 7097.8 8995.2 7052.2 7302.5 6539.9 10978 7166.9 5463.2 FALSE TRUE 9935.62751 7623.328497 9208.570392 7233.171391 6728.991107 8427.862964 9331.950815 8061.703241 4551.356626 2.183003514 1.674957408 2.023258371 1.589234153 1.478458328 1.851725465 2.050366864 1.771274788 1 12.15208092 -1.906664077 2.107474712 0.471472261 1.831463465 0.591772923 0.216050239 1934827.795 843908.3175 5058674.588 0.053612906 0.012397552 1.906664077 1.359991204 HDMLAWINESLQLNLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HDMLAWINESLQLNLTK 17 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ;; 272.71 1.22E-35 275994000 843108 793394 764608 707261 889865 568586 855666 782690 622179 FALSE TRUE 790339.3753 852137.7173 782744.8628 725410.5147 819978.5924 732727.548 727366.8269 880410.5694 518333.3055 1.524770581 1.643995684 1.510118788 1.399505891 1.581952353 1.413622355 1.403280127 1.698541383 1 18.98352057 -2.758867575 0.370389328 1.07E-28 1.535561931 0.69995301 0.105336492 45.74243378 1.662906248 36.52984351 0.071707923 0.001742338 2.758867575 1.535561931 HDPLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HDPLAK 6 0 Q9BYN8 Q9BYN8 MRPS26 "28S ribosomal protein S26, mitochondrial" 0 69.39 0.09363 51947000 374200 244290 260720 233170 338130 210180 276100 290990 497190 FALSE TRUE 350779.49 262377.4858 266904.4015 239153.537 311574.6338 270855.554 234701.3682 327320.742 414205.777 0.846872519 0.633447191 0.644376337 0.577378565 0.752221845 0.653915443 0.566629876 0.790237028 1 18.65998815 0.964992675 5.561930609 0.999905811 0.657438619 0.627064847 0.081902578 0.121171776 14.12959668 0.072884744 0.018364775 9.225558665 -0.964992675 -0.342467192 HDS(ph)DT(ph)SPPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HDSDTSPPRR 10 1 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 HDS(0.999)DT(0.554)S(0.447)PPRR 77.527 0.028333 115600000 263220 230420 242290 237370 233240 161490 240260 186350 237790 TRUE FALSE 246745.5301 247480.5366 248037.2332 243461.3161 214922.2712 208109.5414 204235.2435 209616.2077 198101.3128 1.24555222 1.249262476 1.252072637 1.228973764 1.084910888 1.050520759 1.030963604 1.058126293 1 17.59587892 2.675589022 2.370571229 1.037048837 1.250582208 0.977313817 0.015261011 0.035715173 0.395697453 0.004957837 0.004736544 473.7934167 -2.675589022 0.213533371 HDS(ph)DTS(ph)PPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HDSDTSPPRR 10 1 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 HDS(1)DT(0.084)S(0.917)PPRR;HDS(1)DT(0.252)S(0.748)PPRR 116.51 0.0037816 310390000 533530 429340 458190 418000 472670 322810 461300 353260 495280 TRUE FALSE 500137.3097 461128.7803 469058.4832 428726.5877 435548.4049 416000.0066 392132.3475 397365.2886 412614.5684 1.212117429 1.117577555 1.136795739 1.039048595 1.055581742 1.008204844 0.950359918 0.963042314 1 18.65443523 2.987860444 0.683578035 0.961016607 1.174822704 0.855938707 0.031029427 0.247829415 0.255976942 0.019873358 0.02693417 972.4346908 -2.987860444 0.213806097 HDS(ph)LKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HDSLKK 6 1 G5EA48;Q7Z6B7-2;Q7Z6B7 G5EA48 SRGAP1 SLIT-ROBO Rho GTPase-activating protein 1 1 HDS(1)LKK;HDS(1)LKK 85.676 0.033347 389690000 1152040 474810 710320 662090 669360 336420 818660 512800 1068120 TRUE FALSE 1079935.873 509965.4264 727169.1258 679080.3503 616791.1657 433538.9927 695909.5331 576824.2088 889843.8717 1.213623993 0.573095396 0.817187317 0.763145504 0.693145377 0.487207932 0.782058016 0.648230804 1 19.7631927 4.74802027 24.81706088 0.706829753 1.21362429 0.548485896 0.140118239 807.986305 2119674.219 0.029639969 0.380715805 55978.37279 -4.74802027 0.506794537 HDS(ph)PDLAPNVTYSLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HDSPDLAPNVTYSLPR 16 0 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 HDS(1)PDLAPNVTYSLPR;HDS(1)PDLAPNVTYSLPR;HDS(1)PDLAPNVTYSLPR;HDS(1)PDLAPNVTYSLPR;HDS(1)PDLAPNVTYSLPR 238.68 5.44E-20 1701996000 1493287 1186274 1399682 1355832 1279834 1080525 1561234 1093199 1358643 TRUE FALSE 1399824.832 1274106.961 1432883.118 1390624.945 1179321 1392455.027 1327141.455 1229687.302 1131876.706 1.236729075 1.125658788 1.265935689 1.228601081 1.041916486 1.230217937 1.172514151 1.086414532 1 20.11028539 1.049422439 2.468295359 1.001031561 1.187378402 0.488668973 0.064286125 0.218224177 2.807714177 0.057241388 0.015601133 11.20527292 -1.049422439 0.186346841 HDS(ph)PDPS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HDSPDPSPPR 10 0 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 HDS(1)PDPS(1)PPR 111.96 0.002462 150500000 342020 272470 280750 267240 271060 238270 325940 238210 247860 TRUE FALSE 320613.5787 292643.9623 287409.5226 274097.8308 249772.041 307054.681 277068.3229 267951.0429 206490.5648 1.552679073 1.4172268 1.391877265 1.327410921 1.209605104 1.487015551 1.341796528 1.297643034 1 17.65571634 -4.066239573 0.160799208 2.67E-11 1.490886063 0.703296204 0.083190379 55.04032343 0.668535199 18.27954891 0.355469695 8.59E-05 4.066239573 1.490886063 HDS(ph)PDPS(ph)PPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HDSPDPSPPRR 11 1 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 HDS(1)PDPS(1)PPRR 81.703 0.07331 239720000 348040 318300 361690 329670 322840 262380 382690 279500 344060 TRUE FALSE 326256.7977 341867.2632 370269.4576 338129.8903 297485.4487 338124.8466 325309.1872 314396.1903 286634.1633 1.138234166 1.192695453 1.29178411 1.179656627 1.037857614 1.179639031 1.134928173 1.096855262 1 18.12885105 2.989451137 24.51234763 1.108606664 1.218827285 0.422122194 0.062519483 376.3877599 874613.9145 0.017801401 0.020041513 976.0029659 -2.989451137 0.110220621 HDS(ph)PDPS(ph)PPRRPQHNS(ph)SGASPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HDSPDPSPPRRPQHNSSGASPR 22 2 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 3 HDS(1)PDPS(0.997)PPRRPQHNS(0.399)S(0.354)GAS(0.25)PR;HDS(1)PDPS(0.992)PPRRPQHNS(0.388)S(0.353)GAS(0.267)PR;HDS(1)PDPS(0.98)PPRRPQHNS(0.378)S(0.353)GAS(0.289)PR;HDS(1)PDPS(0.885)PPRRPQHNS(0.41)S(0.386)GAS(0.318)PR 70.983 0.012481 636212000 194854 533935 403013 444177 545058 317466 458361 380092 606534 TRUE FALSE 182658.436 573468.103 412572.6587 455575.3338 502251.3433 409113.2806 389634.0233 427547.3229 505299.557 0.361485446 1.134907195 0.816491234 0.901594564 0.993967512 0.809645041 0.771095121 0.846126455 1 18.94677939 7.999943729 0.016316608 1.569229515 4.18E-07 0.06742187 0.197037579 25389.19837 31.96572434 1204.389114 1953.53034 99987043.99 -7.999943729 -1.569229097 HDS(ph)PEDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HDSPEDVK 8 0 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 1 HDS(1)PEDVK;HDS(1)PEDVK;HDS(1)PEDVK;HDS(1)PEDVK;HDS(1)PEDVK 141.91 0.00056112 1672270000 4386860 2322960 3028170 2824920 3106100 2080610 3702470 2516180 4108630 TRUE FALSE 4112294.263 2494954.375 3099999.622 2897412.23 2862159.435 2681248.331 3147318.996 2830330.612 3422873.11 1.201415925 0.728906476 0.905671792 0.846485434 0.836186251 0.78333267 0.919496252 0.82688739 1 21.70677638 -1.12772305 3.296015583 1.000176016 0.866813686 0.070174404 0.127006968 24256661.23 35314537.86 45277.97853 0.02753636 0.074520704 1.12772305 -0.13336233 HDS(ph)PEDVKR ddPTM_SK-BR-3_Pertuzumab_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 167.44 3.67E-05 2645430000 4330920 2451810 3149020 2854470 3236790 2162770 3792280 2675020 4343160 TRUE FALSE 4059855.448 2633344.564 3223716.241 2927720.533 2982585.57 2787126.589 3223662.82 3009002.135 3618258.538 1.122046809 0.727793367 0.890957959 0.809151834 0.824315216 0.770295036 0.890943194 0.831616122 1 21.78686407 -1.06006764 4.490880551 1.000009226 0.846496672 0.14078076 0.106398322 8.51E-06 1.78E-06 0.089257962 0.021037039 0.087082795 1.06006764 -0.153512554 HDS(ph)VDSGVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HDSVDSGVSK 10 0 Q9HC44 Q9HC44 GPBP1L1 Vasculin-like protein 1 1 HDS(1)VDSGVSK 89.301 0.011049 0 163440 158610 140020 161330 148860 105230 221760 146850 221060 TRUE FALSE 153210.5821 170353.6494 143341.3405 165470.0009 137169.1361 135608.1927 188509.1467 165184.5458 184163.6579 0.831926255 0.925012304 0.778336737 0.898494322 0.744821957 0.736346108 1.0235958 0.896944314 1 17.49062887 1.715726904 10.73858335 0.968611843 0.826906291 0.533195001 0.067727366 0.089069637 26.79074435 0.03126095 0.016987678 51.96691116 -1.715726904 -0.141705552 HDSEQDNSDNNTIFVQGLGENVTIESVADYFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HDSEQDNSDNNTIFVQGLGENVTIESVADYFK 32 0 P35637-2;P35637 P35637-2 FUS RNA-binding protein FUS 0 ; 168.96 2.09E-14 127829000 39086 92161 86398 74264 103026 105986 64887 82534 89642 FALSE TRUE 36639.67703 98984.69633 88447.40136 76169.73997 94934.75355 136582.4377 55157.79673 92838.55158 74680.17109 0.490621225 1.325448173 1.184349206 1.019945976 1.271217676 1.828898296 0.738586909 1.243148619 1 16.18843761 4.744771865 24.15436241 1.203520797 0.490620706 0.389550414 0.27963629 448.5999789 1744440.223 0.06246849 0.56976462 55561.23168 -4.744771865 -0.712900091 HDSIPAADTFEDLS(ph)DVEGGGSEPTQR ddPTM_SK-BR-3_Pertuzumab_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 348.11 4.83E-110 873730000 175441 589500 480640 572100 499520 406017 654310 440120 298335 TRUE FALSE 164460.461 633147.1934 492041.0078 586781.0546 460289.7142 523227.5168 556202.2898 495069.9508 248540.9612 0.661703649 2.547456123 1.979717973 2.360902814 1.851967225 2.10519632 2.237869714 1.991904869 1 17.92312411 0.939324024 20.04519779 0.999999996 2.05215314 0.247976723 0.511710277 2318.47717 765946.2871 0.431673549 0.107918388 8.696089954 -0.939324024 1.052153144 HDSPEDVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HDSPEDVKR 9 1 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 107.15 0.0018304 122999000 153449 299260 291320 266650 336630 311000 249720 235880 254700 FALSE TRUE 143844.901 321417.5218 298230.248 273492.6904 310192.4377 400780.6513 212276.8043 265330.1372 212188.9246 0.677909562 1.514770492 1.405493942 1.288911243 1.461869126 1.888791567 1.000414158 1.250442914 1 17.69498983 1.613158979 25 1.094060695 1.396940133 0.164539041 0.30383859 0.7748613 3643.566973 0.13443746 0.071772452 41.03542912 -1.613158979 0.302879438 HDVDALLWQPHSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HDVDALLWQPHSSK 14 0 Q96RS6-2;Q96RS6;Q96RS6-3 Q96RS6-2 NUDCD1 NudC domain-containing protein 1 0 108.71 0.00046824 74013000 93718 187710 194750 190380 210100 147930 236790 188870 234910 FALSE TRUE 87852.35767 201608.2437 199369.562 195265.4731 193599.5935 190634.9896 201285.5378 212450.8353 195702.0034 0.448908831 1.030179764 1.018740526 0.997769413 0.989257085 0.974108523 1.028530798 1.085583344 1 17.578299 4.7394951 24.99998484 1.014959001 0.448908653 0.971848074 0.030306896 11.6012816 310320.39 0.007107564 0.043168998 54890.23627 -4.7394951 -0.566050348 HDVTCTVSGGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HDVTCTVSGGGR 12 0 P82933 P82933 MRPS9 "28S ribosomal protein S9, mitochondrial" 0 ; 166.04 5.30E-05 248140000 174396 176689 161778 146844 209110 146361 145785 166248 242490 FALSE TRUE 163480.8657 189771.2374 165615.4506 150612.2656 192687.3441 188613.0447 123925.8927 187004.4288 202016.8525 0.809243703 0.9393832 0.819810073 0.745543076 0.953818168 0.933650052 0.61344334 0.925687271 1 17.62411612 HDVVFLITK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HDVVFLITK 9 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 131.44 0.00033308 332230000 523800 564950 476570 516520 633460 352250 532430 602020 462690 FALSE TRUE 491016.293 606779.4858 487874.4655 529774.7777 583710.6069 453938.8567 452597.0643 677183.5222 385464.0499 1.273831614 1.574153247 1.265680848 1.374381808 1.514306216 1.177642524 1.174161545 1.756800725 1 18.55623679 2.235237154 24.99811094 1.275002839 1.404588418 0.076712945 0.212262715 224.9098482 1691683.345 0.071523765 0.055011227 171.8846737 -2.235237154 0.129585579 HDWDYCEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HDWDYCEHR 9 0 P17568 P17568 NDUFB7 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 0 163.64 3.64E-05 292740000 57778 61310 70385 61267 70345 56647 62133 67088 79840 FALSE TRUE 54161.77812 65849.45619 72054.56544 62839.21494 64820.38746 73000.06931 52816.73346 75464.08448 66514.18821 0.814289095 0.990006162 1.083296171 0.944749032 0.974534745 1.097511242 0.794067174 1.134556198 1 16.0213745 4.737526449 6.22692258 0.995463798 0.81009877 0.27716226 0.094907774 0.169982806 35.56606309 0.021459216 0.133766685 54641.98262 -4.737526449 -0.185365027 HEALLYTWLAEHKPLVLCGPPGSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HEALLYTWLAEHKPLVLCGPPGSGK 25 1 Q14204;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 92.833 0.0076561 180840000 306480 329480 295210 268060 361540 209860 415120 322340 322110 FALSE TRUE 287297.9639 353875.042 302212.5206 274938.8734 333146.1068 270443.1752 352876.6098 362584.8586 268347.7601 1.070618081 1.318718077 1.126197292 1.024561835 1.241471539 1.007808581 1.314997411 1.351175275 1 18.03374432 1.66958792 15.43708901 1.249485765 1.152715091 0.067749835 0.132156647 0.308655291 71.9518718 0.05692079 0.031405549 46.72915416 -1.66958792 -0.096770675 HEAMITDLEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HEAMITDLEER 11 0 P35579 P35579 MYH9 Myosin-9 0 ;;;; 162.68 3.87E-05 491950000 1421570 2263400 1968750 2090270 2197920 1860970 2079640 1920950 1717920 FALSE TRUE 1332596.471 2430984.491 2015449.68 2143909.867 2025304.229 2398201.829 1767817.288 2160784.836 1431188.054 0.93111207 1.698577964 1.408235399 1.497993126 1.415120972 1.675672056 1.235209645 1.509784008 1 20.44878182 -0.683401647 6.409070802 0.999999998 1.44306117 0.262040314 0.219634479 5.57E-09 8.68E-10 0.18674394 0.044015969 0.207299547 0.683401647 0.443061171 HEANNPQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HEANNPQLK 9 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;; 118.18 0.0010317 634292000 1276630 917338 1027110 1012172 939150 814612 1263720 922234 834569 FALSE TRUE 1196728.007 985258.66 1051473.534 1038146.047 865392.9473 1049777.26 1074236.918 1037376.945 695274.0424 1.72123211 1.417079597 1.512315246 1.493146564 1.244678925 1.509875526 1.545055406 1.492040378 1 19.4072222 -1.173311738 3.163574097 0.998829706 1.484992589 0.635301579 0.117028645 6744921.983 9706901.19 79506.31386 0.026791525 0.067094707 1.173311738 0.486162884 HEAPSS(ph)PISGQPCGDDQNASPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HEAPSSPISGQPCGDDQNASPSK 23 0 O75376;O75376-2;A0A088AWL3;E7EVU5;E7EW50;J3KS51;O75376-3 O75376 NCOR1 Nuclear receptor corepressor 1 1 HEAPS(0.182)S(0.818)PISGQPCGDDQNASPSK 249.09 4.30E-38 497560000 322300 297660 320110 340770 346620 234160 384490 298540 434870 TRUE FALSE 302127.8183 319699.0561 327703.1604 349514.7351 319397.8634 301758.1907 326839.2939 335813.3762 362287.3876 0.833945173 0.882446 0.904539246 0.964744419 0.881614636 0.832924913 0.902154767 0.926925385 1 18.46677506 0.915024344 2.291242741 0.999571155 0.887745482 0.494327708 0.036992103 0.347782572 3.921551052 0.034954352 0.009523726 8.222887407 -0.915024344 -0.111825673 HECQANGPEDLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 HECQANGPEDLNR 13 0 P60981;P60981-2 P60981 DSTN Destrin 0 ;;;;;;;;;;; 320.94 1.14E-50 11779126000 3838781 3826697 4012536 3763815 3804649 3451274 4216437 3537541 4659048 FALSE TRUE 3598518.55 4110029.628 4107715.249 3860400.865 3505847.215 4447600.777 3584221.415 3979210.781 3881422.79 0.927113263 1.05889769 1.05830142 0.994583964 0.903237654 1.145868672 0.923429786 1.025193852 1 21.88815416 3.201957738 24.14987155 0.995798003 1.030445227 0 0.074141034 393.145283 259387.7672 0.01975307 0.023610268 1592.053793 -3.201957738 0.034647224 HEDEQALLDQNSQT(ph)PPPSPFSVQAFNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HEDEQALLDQNSQTPPPSPFSVQAFNK 27 0 A0A499FJI4;O75592-2;O75592;A0A087WY34 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 HEDEQALLDQNS(0.124)QT(0.876)PPPSPFSVQAFNK;HEDEQALLDQNS(0.031)QT(0.968)PPPSPFSVQAFNK;HEDEQALLDQNS(0.031)QT(0.969)PPPSPFSVQAFNK;HEDEQALLDQNS(0.014)QT(0.986)PPPSPFSVQAFNK 218.4 1.19E-33 996440000 773640 770910 728180 699620 721390 499483 760440 458554 861630 TRUE FALSE 725219.2534 827988.9785 745452.7735 717573.4337 664734.9393 643675.6337 646419.0816 515805.4763 717818.3867 1.010310222 1.153479757 1.038497742 0.999658754 0.926048917 0.896710987 0.900532911 0.718573787 1 19.45325935 2.873474892 1.118048445 0.867453856 1.093672181 0.55173674 0.076102229 0.299928908 0.790466838 0.032430771 0.034828984 747.2654315 -2.873474892 0.226218325 HEDGDSNGTFFVYHAIYLEELTAVELTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HEDGDSNGTFFVYHAIYLEELTAVELTEK 29 0 F8VX55;Q12800-2;Q12800-3;Q12800-4;Q12800;F8VWL0 F8VX55 TFCP2 Alpha-globin transcription factor CP2 0 106.63 0.00027033 19041000 17393 15263 15240 15832 17866 14486 17990 14993 17785 FALSE TRUE 16304.40318 16393.0884 15601.5 16238.27592 16462.87643 18667.87304 15292.56651 16864.90905 14816.5686 1.100416946 1.10640249 1.052976598 1.095953885 1.111112624 1.259932278 1.032126056 1.138246615 1 13.85492375 -1.127940409 3.884487122 0.999959481 1.106858883 0.248770163 0.060629724 0.507124412 14730553.88 1295.002234 0.013318927 0.074483417 1.127940409 0.106899402 HEDGEFWMSFSDFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HEDGEFWMSFSDFLR 15 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;;;; 193.16 1.04E-07 212779500 312127 395173 348077 321152 430333 267769 339790 403673 318189 FALSE TRUE 292591.5282 424432.0201 356333.5508 329393.304 396536.3821 345069.5634 288841.644 454072.4626 265081.2003 1.103780758 1.601139649 1.344243011 1.242612843 1.495905336 1.301750418 1.089634586 1.712956113 1 18.01607483 -2.043585116 2.73633178 0.527309578 1.359095732 0.245227496 0.199274154 34316621.36 28148922.36 100896756.3 0.044787333 0.009045131 2.043585116 0.831786154 HEDLKDMLEFPAQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HEDLKDMLEFPAQELR 16 1 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 0 105.6 0.00076363 35548000 52983 45346 54020 50184 55888 36039 61432 43234 65183 FALSE TRUE 49666.88861 48703.46502 55301.37991 51471.8064 51498.78192 46442.87426 52220.84191 48631.86007 54303.5362 0.914616102 0.89687465 1.018375299 0.947853676 0.94835043 0.855245855 0.96164717 0.895556044 1 15.72875853 HEDPCAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HEDPCAK 7 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ;;; 98.299 0.011364 853870000 2274740 1747110 2070140 2040960 1956220 1779500 2678620 1995360 1834970 FALSE TRUE 2132368.084 1876467.842 2119244.698 2093334.489 1802586.372 2293212.762 2276985.798 2244485.088 1528701.653 1.394888323 1.227491211 1.386303661 1.369354501 1.179161656 1.500104849 1.489489983 1.468229647 1 20.54387544 2.219996692 24.99963898 1.417660735 1.312833457 0 0.159663254 568.0430575 764966.5814 0.053032216 0.039236603 165.9574266 -2.219996692 -0.104827278 HEEAPGHRPTTNPNASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HEEAPGHRPTTNPNASK 17 1 P21291;E9PS42;E9PP21;E9PND2 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ;;;;; 134.76 1.03E-05 3942880000 1085739 905313 929937 955328 1009161 746371 1138096 911156 1241251 FALSE TRUE 1017784.534 972343.3165 951995.5448 979843.3338 929905.5658 961836.1914 967449.0704 1024915.832 1034078.189 0.984243304 0.940299608 0.9206224 0.947552462 0.8992604 0.930138747 0.935566653 0.99113959 1 19.97991384 1.214248777 4.691197601 0.998729925 0.934156038 0.563141241 0.021479947 0.130081565 6.517501247 0.018015702 0.005002336 16.37754407 -1.214248777 -0.064573886 HEEEAFTAFTPAPEDSLASVPYPPLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HEEEAFTAFTPAPEDSLASVPYPPLLR 27 0 P82930;C9JJ19 P82930 MRPS34 "28S ribosomal protein S34, mitochondrial" 0 53.475 0.090991 22467000 19470 23177 20456 20896 25284 23375 24656 21894 28634 FALSE TRUE 18251.40745 24893.0492 20941.22598 21432.22674 23298.29663 30122.98304 20959.0617 24627.51409 23854.80042 0.765104178 1.043523683 0.877862133 0.898445024 0.976671203 1.262763993 0.878609811 1.032392377 1 14.541992 2.476186072 24.99900388 1.036789997 0.919703922 0.256427791 0.114936287 52.05468577 1391430.856 0.037313746 0.031463473 299.3546937 -2.476186072 -0.117086075 HEEEEWT(ph)DDDLVESL ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HEEEEWTDDDLVESL 15 0 D6RHI7;P51946 D6RHI7 CCNH Cyclin-H 1 HEEEEWT(1)DDDLVESL;HEEEEWT(1)DDDLVESL;HEEEEWT(1)DDDLVESL;HEEEEWT(1)DDDLVESL 236.92 1.13E-16 438918000 694066 627933 708255 673966 664705 617018 819793 599771 694957 TRUE FALSE 650625.648 674425.8127 725055.1431 691261.1086 612501.7506 795141.0801 696872.6502 674653.7296 578964.1871 1.123775291 1.164883472 1.252331594 1.193961775 1.057926836 1.373385605 1.203654156 1.165277136 1 19.14311458 0.827221784 3.671397424 1.000039355 1.201911552 0.355799548 0.081805051 1.159923384 23.14638397 0.073333953 0.018851785 6.717718238 -0.827221784 0.201872197 HEEEFDLFMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HEEEFDLFMR 10 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 0 ;; 208.6 1.11E-07 232365000 126642 149422 144132 140370 137695 115272 154383 127766 151411 FALSE TRUE 118715.7033 160485.3604 147550.8791 143972.1318 126880.9901 148549.1551 131234.7024 143717.8663 126139.5259 0.941145944 1.272284473 1.169743409 1.14137207 1.005878127 1.177657471 1.040393179 1.139356322 1 16.94466089 2.980372023 22.40035015 1.080228715 1.163561116 0.039357525 0.098808154 372.4406421 425047.7937 0.027508013 0.029643271 955.8109973 -2.980372023 0.083332401 HEENLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HEENLK 6 0 P42766 P42766 RPL35 60S ribosomal protein L35 0 ;; 139.92 0.011846 1996060000 2763690 2393420 2339070 2395720 2637620 1607760 2565750 2332760 2555000 FALSE TRUE 2590715.576 2570631.307 2394553.845 2457198.231 2430471.965 2071894.212 2181039.607 2624010.221 2128553.994 1.217124669 1.207689029 1.124967396 1.154397886 1.141841819 0.973381093 1.024657872 1.232766577 1 21.02144226 2.416457474 7.972333751 1.052961788 1.170407717 0.370388954 0.07316002 0.263660193 30.42628672 0.024500853 0.020484653 260.890025 -2.416457474 0.117445928 HEGALETLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HEGALETLLR 10 0 Q8WUM4;Q8WUM4-2;A0A3B3IT07;Q8WUM4-3;C9IZF9;F8WEQ7;F8WBR8 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;; 149.96 2.24E-05 646278000 754321 1473320 1017570 1037510 1495540 1256770 1032910 1014510 1237400 FALSE TRUE 707109.3951 1582406.146 1041707.241 1064134.263 1378086.321 1619579.097 878034.7346 1141173.807 1030869.946 0.68593463 1.535020156 1.010512766 1.032268199 1.336818797 1.571079944 0.85174152 1.107000753 1 19.9754309 1.63128271 25 0.98454842 1.212298917 0.119411115 0.264878496 1.56536536 1666.328074 0.114331186 0.063351105 42.78413043 -1.63128271 0.227750497 HEGVFICR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HEGVFICR 8 0 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ;;; 131.06 0.0010211 2121190000 1125740 1085660 1061080 1001520 953010 853900 1139910 1008060 930100 FALSE TRUE 1055281.943 1166043.396 1086249.319 1027220.699 878164.4389 1100407.068 968991.0779 1133918.51 774860.3013 1.361899611 1.504843381 1.401864719 1.325685026 1.133319693 1.420136076 1.250536485 1.463384442 1 19.56357671 -4.392304881 0.147997859 9.77E-13 1.481552417 0.497506134 0.109634312 87.9461918 0.919994687 26.87543211 0.563916264 4.05E-05 4.392304881 1.481552417 HEHQVMLMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HEHQVMLMR 9 0 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 67.726 0.033303 62607000 44925 70512 48899 44812 85640 32818 38471 65072 80275 FALSE TRUE 42113.22444 75732.78185 50058.90737 45961.95179 78914.17986 42292.02384 32702.6307 73196.38244 66876.5839 0.629715544 1.132425992 0.748526681 0.687265244 1.179997172 0.632389117 0.488999718 1.094499422 1 16.02921354 HEIEGTGLPQAQLLWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HEIEGTGLPQAQLLWR 16 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 195.2 9.08E-11 353930000 327930 340310 326790 339180 361200 285200 375940 315120 299890 FALSE TRUE 307405.4467 365506.9065 334541.6131 347883.933 332832.809 367532.6102 319571.2871 354463.4257 249836.4216 1.230426872 1.462984877 1.339042606 1.392446829 1.332202914 1.471092997 1.279122095 1.418782031 1 17.93062429 -1.385864269 3.00578616 0.994744761 1.369818907 0.69607989 0.075912191 8933779.083 10833348.93 406710.1011 0.01641176 0.041127824 1.385864269 0.375074145 HEILSVAEVTTCEYEVVILTPLLCSHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HEILSVAEVTTCEYEVVILTPLLCSHPK 28 0 Q96DZ1;Q96DZ1-3;Q96DZ1-2 Q96DZ1 ERLEC1 Endoplasmic reticulum lectin 1 0 205.38 1.65E-25 27817000 37874 29632 32921 34239 35859 28126 44030 28458 31041 FALSE TRUE 35503.53395 31825.98411 33701.90167 35117.63071 33042.77879 36245.51961 37428.11025 32011.04394 25860.05657 1.372910142 1.230700483 1.303241607 1.357987389 1.277753539 1.401602488 1.447332884 1.237856687 1 14.65843781 0.983181252 23.27395878 0.999999996 1.334433709 0.754247368 0.061679505 240.2723223 332492.4946 0.067527721 0.01688193 9.620136891 -0.983181252 0.334433713 HEIS(ph)PGHDGTWNDNQLQEMAQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HEISPGHDGTWNDNQLQEMAQLR 23 0 Q676U5-3;Q676U5;E7EVC7;Q676U5-2;C9J1B2 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 1 HEIS(0.996)PGHDGT(0.004)WNDNQLQEMAQLR;HEIS(0.5)PGHDGT(0.5)WNDNQLQEMAQLR 232.44 1.15E-33 109999000 108833 90702 107635 116491 109424 71941 107574 81966 110209 TRUE FALSE 102021.3368 97417.67046 110188.153 119480.3563 100830.2804 92709.19884 91444.27737 92199.63553 91814.40592 1.111169165 1.061028163 1.200118347 1.301324722 1.098196731 1.00974567 0.995968731 1.004195743 1 16.48643291 2.35497809 3.945791278 1.00149454 1.159201237 0.611782144 0.061888681 0.169547883 4.903964173 0.024199749 0.019757755 226.4530059 -2.35497809 0.157706697 HEIVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HEIVPK 6 0 P25788-2;P25788;G3V4X5;H0YJ03 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ; 76.592 0.07465 1343920000 5685000 4413100 4804300 4481600 5042900 3350400 5925100 4586000 5279900 FALSE TRUE 5329185.998 4739850.516 4918260.265 4596605.443 4646850.976 4317606.091 5036686.261 5158572.195 4398650.581 1.211550202 1.077569229 1.118129339 1.045003544 1.056426486 0.981575147 1.145052595 1.172762442 1 22.06862957 HEIVQTLSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HEIVQTLSLK 10 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 159.94 7.53E-06 1848460000 7347300 6864000 6158600 6494100 7879400 4274700 7449500 6426600 7111800 FALSE TRUE 6887445.608 7372217.702 6304684.9 6660749.6 7260583.708 5508736.496 6332516.633 7228975.157 5924794.636 1.16247837 1.24429928 1.064118723 1.124216114 1.225457447 0.929776783 1.068816224 1.220122485 1 22.49833372 7.999999973 0.159130724 1.013882818 1.77196852 0.194023957 0.092023111 92.58306518 0.952389736 0.261330332 16.44885085 99999993.8 -7.999999973 0.758085702 HEKEDGAISTIVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HEKEDGAISTIVLR 14 1 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;; 192.65 2.10E-07 1392059000 1852690 1448500 1549760 1526790 1598660 1275440 1879420 1351810 1615020 FALSE TRUE 1736733.44 1555748.447 1586521.039 1565970.016 1473107.692 1643638.823 1597618.419 1520586.454 1345462.729 1.290807544 1.156292489 1.179163871 1.163889555 1.09487068 1.22161602 1.187411873 1.130158734 1 20.359671 -5 0.228636676 0.059183215 1.196920136 0.589187881 0.049073829 117.6098945 1.177379356 51.16154504 0.082080693 1.00E-05 5 1.137736921 HELIEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HELIEFR 7 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5;J3KRF5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 156.4 0.001546 1210240000 1334180 1634250 1432540 1443490 1591450 1114770 1579550 1506710 1216310 FALSE TRUE 1250676.055 1755251.57 1466520.525 1480532.397 1466463.937 1436586.002 1342711.141 1694826.06 1013300.003 1.234260388 1.73221313 1.447271805 1.461099765 1.44721596 1.417730186 1.325087474 1.672580731 1 19.95062994 -2.925446135 0.338609189 1.38E-13 1.497753719 0.467248956 0.150798361 66.91533772 2.079917725 48.36179211 0.115905085 0.001187282 2.925446135 1.497753719 HELLQPFNVLYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HELLQPFNVLYEK 13 0 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 162.37 4.00E-05 1493720000 1775040 1651970 1625550 1571460 1780230 1267620 1899900 1491260 2011990 FALSE TRUE 1663943.415 1774283.578 1664108.814 1611786.324 1640417.917 1633561.316 1615027.633 1677447.094 1676175.871 0.992702164 1.058530676 0.992800841 0.961585447 0.978666944 0.974576322 0.963519199 1.000758406 1 20.6767421 3.63343318 3.452564977 0.976712036 1.029374762 0.445791828 0.020437583 0.154959237 3.519997942 0.005005518 0.008300697 4299.650747 -3.63343318 0.052662726 HELQANCYEEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HELQANCYEEVK 12 0 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;;; 194.3 1.71E-06 4699030000 10887080 5969830 7564880 6705060 6502460 6352360 10029960 6652010 5436170 FALSE TRUE 10205677.1 6411842.425 7744322.526 6877123.191 5991783.021 8186183.21 8526060.612 7482528.091 4528838.108 2.253486844 1.415780885 1.710002067 1.518518222 1.32302875 1.807568081 1.882615454 1.652195975 1 22.11070954 4.74827177 24.53644499 1.592651 2.253487308 0.414625054 0.259977721 1079.04861 2726278.653 0.058464619 0.759141521 56010.79927 -4.74827177 0.660836307 HELQANCYEEVKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 HELQANCYEEVKDR 14 1 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;;;;;; 297.72 6.44E-44 78160900000 61041800 41061880 47421600 45331540 47546500 37601370 61711400 42353620 54308100 FALSE TRUE 57221302.7 44102144.32 48546462.75 46494824.06 43812389.68 48456275.11 52458348.47 47641562.69 45243727.27 1.264734498 0.97476815 1.072998749 1.027652381 0.968363845 1.071005376 1.159461248 1.052998185 1 25.43121445 1.999616006 24.99999906 1.095211628 1.047328135 0 0.091157492 42.34518415 2756929.899 0.031573178 0.023072712 99.91162113 -1.999616006 -0.047883493 HELQVEMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HELQVEMK 8 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 72.79 0.045243 121800000 132980 184950 153230 172830 180770 155990 168460 156740 175780 FALSE TRUE 124657.0192 198643.8904 156864.688 177265.1104 166573.0534 201021.7807 143200.9869 176309.334 146441.1824 0.851242916 1.356475598 1.071178786 1.210486746 1.137474108 1.37271345 0.977873741 1.203960055 1 17.1599618 0.610372748 0.892633039 1.00240722 1.166829822 0.061038092 0.159353519 3.110824638 4.128244459 0.13762117 0.045506202 4.077300757 -0.610372748 0.164422601 HELS(ph)PPQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 HELSPPQKR 9 1 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR 161.99 3.02E-05 16207560000 3265030 2180311 2687960 2423770 2362730 2281773 3431220 2376330 2546360 TRUE FALSE 3060677.601 2341743.495 2751719.681 2485968.042 2177170.717 2940483.824 2916740.415 2673020.031 2121356.066 1.442792961 1.103889881 1.297151254 1.171876839 1.026310836 1.386134026 1.374941464 1.260052508 1 21.01655536 HELSTEYIPDPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HELSTEYIPDPER 13 0 A0A3B3IUD7;Q14690 A0A3B3IUD7 PDCD11 Protein RRP5 homolog 0 ; 116.51 0.00057955 176662000 335270 392090 374850 387620 391230 305650 464710 363550 417980 FALSE TRUE 314286.0492 421120.7516 383741.619 397566.9854 360504.3739 393886.1932 395031.0497 408940.0178 348216.4377 0.902559486 1.209364941 1.102020403 1.141723774 1.035288214 1.131153359 1.134441132 1.174384588 1 18.40962478 HELTEISNVDVETQSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HELTEISNVDVETQSGK 17 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 256.08 4.37E-27 532340000 389060 310930 372640 362840 404600 276980 434370 321420 471090 FALSE TRUE 364709.4291 333951.5807 381479.1968 372151.0887 372824.3481 356939.6296 369240.251 361549.9945 392462.0356 0.929285882 0.850914357 0.972015538 0.948247359 0.949962835 0.9094883 0.940830494 0.921235589 1 18.58219358 -1.902068273 0.010125852 1.964648606 1.12E-06 0.329624725 0.032253804 7811.420262 11.32361725 1189.766623 1012.617523 0.012529442 1.902068273 -1.964647491 HEMLPASLIQAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HEMLPASLIQAQR 13 0 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ; 177.42 1.55E-05 941210000 1021050 1200640 1030890 1022490 1217690 786570 1112260 1091260 1108680 FALSE TRUE 957144.3031 1289536.635 1055343.198 1048728.824 1122057.539 1013639.99 945486.9387 1227506.213 923634.1457 1.036280769 1.396155221 1.142598725 1.135437477 1.214828993 1.097447507 1.023659577 1.328996139 1 19.81696198 3.681187319 6.217359291 1.129600697 1.250123676 0.052745952 0.126144205 0.336525353 32.27534467 0.030763932 0.048738542 4799.404112 -3.681187319 0.120522979 HEMPPHIYAITDTAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HEMPPHIYAITDTAYR 16 0 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 ;; 196.95 2.58E-11 537188000 461530 550270 543115 522639 579797 481299 585770 539851 564983 FALSE TRUE 432643.6612 591012.5634 555997.9443 536050.8016 534262.0824 620242.2081 497939.2265 607252.5857 470683.6874 0.919181337 1.255647007 1.181256031 1.138876948 1.135076691 1.317747406 1.057906275 1.290150056 1 18.84439833 -0.944836161 4.115794161 0.999992645 1.169265966 0.158792546 0.116094238 5451818.982 2649218.492 347.6365692 0.023669535 0.113543908 0.944836161 0.169273321 HENEALWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HENEALWR 8 0 E9PMQ6;Q00613-2;Q00613;E9PI02 E9PMQ6 HSF1 Heat shock factor protein 1 0 122.13 0.0014034 63884000 18876 22039 21277 21984 24875 20021 21834 19794 25467 FALSE TRUE 17694.58485 23670.79049 21781.70049 22548.14666 22921.41784 25800.73769 18560.1944 22265.32447 21216.39318 0.834005323 1.115684004 1.026644836 1.062770023 1.08036355 1.216075582 0.874804414 1.049439661 1 14.3728918 1.710819661 25 0.969260095 1.060653716 0.118463956 0.103493934 1.485123173 1331.796321 0.043459934 0.02410072 51.38302414 -1.710819661 0.091393621 HEPLVLFCESCDTLTCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HEPLVLFCESCDTLTCR 17 0 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;; 339.21 2.21E-72 1371960000 875720 825690 850100 761633 893280 1037420 1331310 784830 916780 FALSE TRUE 820910.2484 886824.9467 870264.7734 781177.7922 823125.3921 1336906.313 1131692.425 882817.7531 763763.4954 1.074822577 1.161125076 1.139442745 1.02280064 1.077722878 1.750419234 1.481731494 1.155878434 1 19.54276644 2.33995104 21.34593856 1.410985359 1.106894024 0.252214844 0.201985035 4.494378447 934.1588256 0.065209677 0.054558232 218.7515002 -2.33995104 -0.304091335 HEPVGVCGQIIPWNFPLLMQAWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HEPVGVCGQIIPWNFPLLMQAWK 23 0 P05091;P05091-2;F8VP50 P05091 ALDH2 "Aldehyde dehydrogenase, mitochondrial" 0 179.36 4.88E-17 106760000 150620 261660 83786 63783 338370 53979 96331 281880 77184 FALSE TRUE 141192.9631 281033.5787 85773.44349 65419.77976 311795.7851 69561.86102 81887.06084 317073.3385 64301.49177 2.195796072 4.37056079 1.333926183 1.017391323 4.848966587 1.081807888 1.273486176 4.931041719 1 15.97256459 7.999999997 0.056169503 5.07E-11 7.29561253 0.035239376 1.614633362 1278.559398 5.384858419 149.9792629 777.7203677 99999999.27 -7.999999997 7.29561253 HEQILVLDPPTDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HEQILVLDPPTDLK 14 0 Q9P0L0-2;Q9P0L0;J3QKM9 Q9P0L0-2 VAPA Vesicle-associated membrane protein-associated protein A 0 ; 75.764 0.029342 206856000 174724 124767 119672 121720 151864 105608 161500 129811 202468 FALSE TRUE 163788.3367 134004.8785 122510.6764 124843.5413 139937.214 136095.3152 137284.5743 146018.1891 168674.7828 0.97103037 0.794457098 0.726312934 0.740143483 0.829627356 0.806850395 0.813900999 0.865678833 1 17.36388478 0.75740052 1.20607706 1.000124972 0.796216007 0.434720842 0.066434848 0.741498976 1.907041723 0.061321214 0.018818269 5.72005915 -0.75740052 -0.203908965 HEQISDLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HEQISDLER 9 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ; 176.95 5.27E-05 331170000 222840 271170 213710 217060 263500 148386 210340 222160 221570 FALSE TRUE 208892.8422 291247.709 218779.3021 222630.1271 242805.7729 191222.6294 178801.4697 249897.165 184588.5356 1.131667476 1.577821223 1.185226923 1.206088592 1.315389236 1.035939901 0.968648834 1.353806531 1 17.49395343 2.961132705 0.863684935 1.078868765 1.374040718 0.208407249 0.16379027 0.690308878 1.133446191 0.086848275 0.105531386 914.3926048 -2.961132705 0.295171953 HEQNIDCGGGYVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HEQNIDCGGGYVK 13 0 P27797 P27797 CALR Calreticulin 0 ;;;; 208.15 4.82E-08 11425050000 9784800 8245490 8439630 8642170 8471880 6524870 11167350 7534800 7986770 FALSE TRUE 9172386.834 8855994.659 8639822.009 8863942.713 7806532.719 8408494.047 9492909.54 8475536.366 6653726.49 1.378533796 1.330982671 1.298493712 1.332177198 1.173257231 1.263727035 1.426705704 1.27380294 1 22.66573113 -1.953238859 1.805625855 0.741818658 1.313590783 0.671502891 0.068028811 306609.2906 101292.5606 331935.8496 0.018229174 0.011136818 1.953238859 0.571772125 HERGS(ph)PSHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HERGSPSHSK 10 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 HERGS(0.5)PS(0.5)HSK 102.87 0.001745 67515000 69643 59937 62746 58995 60982 45907 69692 49761 67446 TRUE FALSE 65284.16895 64374.79784 64234.36475 60508.91158 56192.71971 59159.60566 59242.33159 55973.77039 56188.82688 1.161871008 1.14568681 1.143187504 1.07688512 1.000069281 1.052871344 1.054343628 0.996172611 1 15.77799566 3.099304041 2.910991893 1.02926627 1.149509643 0.877893703 0.021900463 0.084099538 1.437815971 0.006555809 0.008057221 1256.909594 -3.099304041 0.120243373 HERGSPS(ph)HSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HERGSPSHSK 10 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 HERGS(0.052)PS(0.948)HSK;HERGS(0.083)PS(0.917)HSK;HERGS(0.071)PS(0.929)HSK 139.78 2.44E-05 1056020000 1558930 1138690 1387560 1286870 1403640 883070 1408320 1086090 1898340 TRUE FALSE 1461359.354 1222999.792 1420473.578 1319893.263 1293403.776 1137997.974 1197155.49 1221690.727 1581494.79 0.92403678 0.773318888 0.898184166 0.834585906 0.817836255 0.719571118 0.756977195 0.772491149 1 20.59285737 2.61035258 3.466496186 0.784506136 0.850432715 0.01225185 0.085447698 0.517616818 11.45026662 0.026138666 0.024326974 407.7111422 -2.61035258 0.065926579 HERPAGPGT(ph)PPPDSGPLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HERPAGPGTPPPDSGPLAK 19 1 Q9P2K8-2;Q9P2K8;H0YME5 Q9P2K8-2 EIF2AK4 Eukaryotic translation initiation factor 2-alpha kinase 4 1 HERPAGPGT(1)PPPDSGPLAK;HERPAGPGT(1)PPPDSGPLAK;HERPAGPGT(0.999)PPPDS(0.001)GPLAK 149.07 1.44E-07 611460000 1205190 993550 1089860 1165290 1165870 795740 1440990 1039030 1054270 TRUE FALSE 1129759.309 1067113.476 1115711.994 1195193.314 1074307.273 1025457.22 1224926.927 1168755.183 878305.5262 1.286294206 1.214968418 1.270300551 1.360794483 1.223158959 1.16754044 1.394647865 1.33069319 1 19.74436336 -1.103394247 12.40862738 1 1.278413472 0.622586025 0.068742131 0 0 0.066647537 0.015708975 0.078814432 1.103394247 0.278413473 HESGASIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HESGASIK 8 0 P61978;P61978-2;S4R359;P61978-3 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;; 175.91 0.0002634 5567170000 2892260 7216780 6497530 6839960 7301440 5423210 8348120 7027800 7018030 FALSE TRUE 2711238.609 7751117.9 6651654.48 7015484.954 6728014.355 6988802.689 7096396.906 7905236.3 5846675.455 0.463723124 1.325730829 1.137681496 1.199910104 1.150741889 1.19534644 1.213749072 1.352090835 1 22.47918508 4.744272962 24.99986307 1.204950077 0.463722806 0.847479345 0.097696587 206.5642653 903994.4907 0.02059221 0.182680899 55497.44152 -4.744272962 -0.741227271 HESGASIKIDEPLEGSEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HESGASIKIDEPLEGSEDR 19 1 P61978;P61978-2;S4R359;P61978-3 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 162.39 1.66E-11 191870000 34852 104980 66853 94559 145280 52456 106430 74573 329780 FALSE TRUE 32670.67553 112752.8284 68438.78473 96985.54403 133870.2948 67599.19565 90471.80955 83883.60321 274737.5875 0.118915929 0.410401902 0.249106012 0.353011559 0.487266035 0.246050045 0.329302628 0.305322632 1 18.06769478 -1.902872949 2.52393327 1.386860503 0.319701752 0.825997597 0.09912734 16487186.12 8864206.873 37834368.34 0.021288998 0.012506248 1.902872949 -1.067158751 HETWSGHVISS ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HETWSGHVISS 11 0 Q9Y2V2 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 0 ;;; 200.71 4.59E-08 1612780000 891730 1646630 1467120 1432650 1623060 1300740 1703470 1417590 1754170 FALSE TRUE 835918.2111 1768548.199 1501920.779 1469414.224 1495591.415 1676242.522 1448050.488 1594579.232 1461387.695 0.572003045 1.210184132 1.027736024 1.005492403 1.02340496 1.147021101 0.990873601 1.091140454 1 20.47890753 4.749082667 24.99804597 1.065227863 0.57200277 0.826179795 0.07061656 607.4508428 1443139.752 0.016443296 0.238261055 56115.47807 -4.749082667 -0.493225094 HEWAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HEWAQK 6 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 86.086 0.053976 87336000 153150 185320 148200 162020 212600 107770 184680 165530 196600 FALSE TRUE 143564.6149 199041.2856 151715.374 166177.7075 195903.2536 138881.4495 156988.9485 186196.7849 163786.1899 0.876536752 1.215250722 0.926301381 1.014601461 1.196091402 0.847943588 0.958499301 1.136828355 1 17.32145419 2.230254994 24.99999324 0.975002468 1.051163775 0.050493566 0.124087522 488.0256594 1468950.596 0.04329226 0.032508534 169.924106 -2.230254994 0.076161306 HEWQVNGLDDIKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HEWQVNGLDDIKDR 14 1 Q9Y281;Q9Y281-3 Q9Y281 CFL2 Cofilin-2 0 ; 165.33 2.39E-06 209420000 411700 271940 333030 326580 341300 269410 370780 303620 444160 FALSE TRUE 385932.4319 292074.7206 340929.6289 334960.5957 314495.6747 347184.2935 315184.9812 341527.6254 370026.8266 1.042985006 0.789333906 0.921364626 0.905233274 0.849926687 0.9382679 0.851789542 0.922980716 1 18.49727034 0.981978175 20.09155746 1.000000007 0.889523924 0.168200328 0.066847054 122.6506113 136738.993 0.056351478 0.01408787 9.593524188 -0.981978175 -0.110476083 HFCCFDCDSILAGEIYVMVNDKPVCKPCYVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HFCCFDCDSILAGEIYVMVNDKPVCKPCYVK 31 2 Q9UGI8-2;Q9UGI8;H7BYK1 Q9UGI8-2 TES Testin 0 ;; 230.8 6.37E-36 1074681000 2368223 1782074 1718652 1478744 2133728 1592502 2853722 1899804 2036226 FALSE TRUE 2220000.15 1914020.613 1759419.237 1516691.075 1966153.61 2052231.475 2425832.879 2136998.711 1696366.726 1.308679377 1.128305916 1.037169151 0.89408207 1.159038066 1.209780553 1.430016777 1.259750429 1 20.69401666 2.239076414 3.258674274 1.283250197 1.085807012 0.101864842 0.148112552 0.315263957 7.008190489 0.056113733 0.041771913 173.4109087 -2.239076414 -0.197443184 HFCPNVPIILVGNKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HFCPNVPIILVGNKK 15 1 Q5JR08;P08134;E9PQH6;Q5JR07;C9JNR4;C9JX21;Q5JR05;P61586 Q5JR08;P61586 RHOC;RHOA Rho-related GTP-binding protein RhoC;Transforming protein RhoA 0 196.5 5.78E-09 415420000 2127700 1889000 1745400 1851600 2482700 1596500 2614200 2095400 2593300 FALSE TRUE 1994531.055 2028863.526 1786801.712 1899115.191 2287718.757 2057383.633 2222224.979 2357015.303 2160461.477 0.923196769 0.939088036 0.827046319 0.879032193 1.058902823 0.952288969 1.028588106 1.090977705 1 21.04290808 2.745764374 24.94013366 1.021787586 0.88908294 0.675420008 0.046103318 323.0622304 1118474.285 0.014212168 0.014782572 556.8835299 -2.745764374 -0.132704646 HFDETVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HFDETVNR 8 0 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ; 146.81 0.00054736 615340000 347720 373590 414660 358660 431990 319750 472860 390920 436900 FALSE TRUE 325956.8259 401250.9923 424495.931 367863.8228 398063.248 412056.6343 401959.0328 439727.2225 363978.5675 0.895538515 1.102402801 1.166266283 1.010674407 1.093644746 1.132090379 1.104348082 1.208112954 1 18.47349398 4.737884163 5.787210882 1.109805577 0.889034266 0.513867191 0.062826543 0.100715963 14.90928214 0.013583213 0.08790803 54687.00803 -4.737884163 -0.220771311 HFEANNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HFEANNGK 8 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 62.582 0.078727 48253000 191420 201910 195750 198420 232810 164260 243900 195780 199300 FALSE TRUE 179439.3639 216859.6265 200393.2824 203511.7931 214526.0417 211679.1955 207329.4593 220223.564 166035.5425 1.080728627 1.306103641 1.206930031 1.225712219 1.29204891 1.274902905 1.248705284 1.326363986 1 17.34113258 -1.044523829 4.57161089 0.999989317 1.249318515 0.556846345 0.068652078 6.55E-06 1.37E-06 0.058269986 0.013733779 0.090256018 1.044523829 0.249329197 HFEELETIMDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HFEELETIMDR 11 0 Q92922;F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 Q92922;F8VXC8 SMARCC1;SMARCC2 SWI/SNF complex subunit SMARCC1;SWI/SNF complex subunit SMARCC2 0 ;;;; 248.05 3.50E-16 837212000 792516 827811 885113 835533 893875 761833 899096 772324 861924 FALSE TRUE 742913.8382 889102.9878 906108.2983 856974.1913 823673.6632 981761.8198 764284.9016 868750.3515 718063.3162 1.034607703 1.238195808 1.261877996 1.193452126 1.14707665 1.367235727 1.064369791 1.209852017 1 19.45375154 0.504235012 0.85605337 1.000038431 1.207672515 0.2639628 0.096143412 1.980618296 2.217471174 0.088139625 0.028638806 3.193265378 -0.504235012 0.207634084 HFELGGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HFELGGDK 8 0 H0Y5B4;H7BZ11;J3KQN4;P83881;R4GN19;Q969Q0 H0Y5B4;Q969Q0 RPL36A;RPL36A-HNRNPH2;RPL36AL 60S ribosomal protein L36a;60S ribosomal protein L36a-like 0 ;;; 155.07 0.00041492 4693940000 10868900 10366400 9174300 9109200 11517200 6414120 9864600 10031400 10458700 FALSE TRUE 10188634.95 11133939.04 9391918.728 9342957.494 10612685.57 8265772.319 8385494.808 11283842.37 8713075.404 1.169350026 1.277842613 1.077910874 1.072291592 1.218018332 0.948663008 0.962403562 1.295047024 1 23.0547506 3.817904663 3.254763475 1.06999308 1.224851807 0.215122257 0.110439816 0.326873335 6.71513803 0.0285108 0.055212167 6575.134827 -3.817904663 0.154858727 HFEQMKDDAIVCNIGHFDVEIDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HFEQMKDDAIVCNIGHFDVEIDVK 24 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 109.08 0.0014281 27046000 118950 65117 84475 85755 85254 61470 109300 72889 99035 FALSE TRUE 111505.1318 69938.33043 86478.78689 87955.61848 78558.49474 79215.39112 92911.47969 81989.3521 82505.41871 1.351488588 0.847681662 1.048158875 1.066058689 0.952161639 0.960123497 1.126125788 0.993745058 1 16.33220125 -0.196194833 6.58465378 1.000000039 1.027718696 0 0.133435035 7801421.156 1184788.308 0.115580571 0.028032406 0.636509906 0.196194833 0.027718657 HFFHHADEDDEEEDDS(ph)PPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HFFHHADEDDEEEDDSPPER 20 0 A0A087WZV0;O43314-2;O43314;D6RFG4 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 HFFHHADEDDEEEDDS(1)PPER;HFFHHADEDDEEEDDS(1)PPER 198.98 2.51E-21 1031020000 389880 430070 391370 367450 378340 289360 382550 328980 428770 TRUE FALSE 365478.1068 461912.8303 400653.4812 376879.3891 348626.7026 372893.5346 325190.1789 370053.8772 357205.517 1.023159188 1.293129048 1.121632959 1.055077179 0.975983533 1.043918744 0.910372778 1.035969098 1 18.44639484 3.197384806 1.895399666 0.985103262 1.184918338 0.455295719 0.074898026 0.218879621 1.611008672 0.022375723 0.030517409 1575.378107 -3.197384806 0.199815076 HFGAEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HFGAEYR 7 0 P04818;P04818-2 P04818 TYMS Thymidylate synthase 0 79.597 0.032193 124460000 16459 17399 13000 16722 25970 15413 17469 17403 23055 FALSE TRUE 15428.86057 18687.24006 13308.36614 17151.11483 23930.42096 19862.48289 14849.68562 19575.80286 19206.97156 0.80329481 0.972940477 0.692892479 0.892962994 1.245923694 1.034128823 0.773140397 1.019202991 1 14.22934244 2.991812235 24.97547918 0.992005931 0.831115313 0.30560243 0.131211528 579.3715414 1767288.781 0.04063689 0.046497834 981.3235803 -2.991812235 -0.160890617 HFGAGGNQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HFGAGGNQR 9 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;;;;; 138.54 0.00013359 809554000 443338 341060 295871 292066 381146 264308 345669 305539 370232 FALSE TRUE 415590.266 366312.4373 302889.1998 299560.908 351212.3306 340609.4289 293839.1425 343686.2167 308437.8874 1.347403425 1.187637616 0.982010357 0.971219556 1.138680898 1.104304765 0.952668769 1.114280154 1 18.23462047 4.525569359 1.759615854 1.036158729 1.383489952 0.715891814 0.064470597 0.313186906 1.343384563 0.016709279 0.158210589 33540.48659 -4.525569359 0.347331222 HFHPLFEYFDYESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HFHPLFEYFDYESR 14 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 150.21 4.21E-06 71845000 91301 143329 126658 132032 137104 101837 133397 121211 111631 FALSE TRUE 85586.63339 153941.2283 129662.3876 135420.1646 126336.4049 131235.6887 113395.3582 136344.4602 92999.06494 0.920295634 1.655298668 1.394233239 1.456145443 1.358469625 1.411150626 1.219317187 1.466084205 1 16.50492859 -0.8989163 0.417681412 0.861025935 1.405730418 0.225447183 0.19457258 17.86534951 2.277523506 3.258680819 0.108822035 0.126207075 0.8989163 0.544704483 HFIDVGAGVIDEDYR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 207.52 3.35E-09 2100400000 2180950 2240060 2346400 2050472 2523490 2213410 2467790 2285220 2913600 FALSE TRUE 2044448.233 2405916.373 2402057.716 2103090.583 2325305.275 2852385.535 2097767.799 2570534.747 2427301.337 0.842272116 0.991189819 0.989600129 0.866431601 0.957979645 1.175126257 0.864238719 1.059009324 1 21.21092179 2.456533627 24.9975516 1.011024268 0.941763038 0.20950486 0.088947065 503.5051602 611353.8444 0.029333789 0.024544487 286.1103883 -2.456533627 -0.069261229 HFIEITDDQFDFHTYCMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HFIEITDDQFDFHTYCMR 18 0 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ;; 260.24 5.72E-31 282944000 187616 233737 209553 225651 220823 221137 259749 197227 180210 FALSE TRUE 175873.4495 251043.1307 214523.6961 231441.5867 203480.4523 284975.662 220802.0488 221851.2251 150131.7868 1.171460443 1.672151754 1.428902571 1.541589504 1.355345571 1.898170055 1.470721514 1.477709883 1 17.19586994 0.642190479 2.563379601 1.000068947 1.525806913 0.404243594 0.190660338 2.809894404 19.03187915 0.162204594 0.043166885 4.38723077 -0.642190479 0.525737966 HFILDECDK ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 182.65 4.61E-05 2005400000 8062040 6001590 6396140 6148120 6749390 5007610 8695650 5907490 7021730 FALSE TRUE 7557451.308 6445953.968 6547859.461 6305891.168 6219320.135 6453225.715 7391818.009 6645053.13 5849757.901 1.291925484 1.101918075 1.119338539 1.077974726 1.063175646 1.103161161 1.263610928 1.135953529 1 22.47994549 HFIMQVVCEATQCPDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HFIMQVVCEATQCPDTR 17 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ; 284.25 3.56E-36 1136460000 735240 755300 715690 781450 816530 597650 909430 750230 871720 FALSE TRUE 689222.6408 811223.1979 732666.5048 801503.33 752403.0275 770181.853 773069.4142 843897.867 726224.3005 0.949049268 1.11704221 1.008870819 1.103658098 1.036047716 1.060528892 1.064505021 1.162034741 1 19.47005568 4.754146281 24.46496541 1.067956501 0.949049149 0.37065747 0.049136075 2259.126248 3546093.509 0.010387614 0.248154274 56773.57999 -4.754146281 -0.118907352 HFKDEDEDEDVAS(ph)PDGLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HFKDEDEDEDVASPDGLGR 19 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 HFKDEDEDEDVAS(1)PDGLGR;HFKDEDEDEDVAS(1)PDGLGR 297.95 5.44E-50 1689580000 2988500 1770000 2188400 1869920 2525400 1743430 2557900 1916050 3678500 TRUE FALSE 2801455.12 1901052.642 2240309.881 1917905.313 2327065.271 2246729.939 2174366.641 2155273.06 3064534.586 0.914153533 0.620339757 0.731044085 0.625839017 0.759353568 0.733139038 0.709525894 0.703295394 1 21.54723656 -1.628596647 2.452174458 1.035109361 0.713970499 0.528034348 0.081280994 4862566.561 3967887.193 1083593.595 0.018679431 0.023518161 1.628596647 -0.321138862 HFLLDPLMPELLVFPAQTDLHEHPLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HFLLDPLMPELLVFPAQTDLHEHPLYR 27 0 Q96P11-2;Q96P11-5;Q96P11;Q96P11-4;Q96P11-3 Q96P11-2 NSUN5 Probable 28S rRNA (cytosine-C(5))-methyltransferase 0 100.88 0.0010023 68772000 78130 79842 67978 64002 100770 64211 70961 83505 69249 FALSE TRUE 73239.98277 85753.58476 69590.47026 65644.39968 92855.93069 82747.67332 60321.05682 93930.78307 57690.89453 1.269524131 1.486431879 1.206264365 1.137864133 1.609542224 1.434328138 1.045590596 1.628173455 1 15.81605601 -1.745945818 3.038089862 0.943426087 1.334558904 0.241923399 0.193713752 6967266.643 4682046.111 2602505.565 0.043443414 0.017949575 1.745945818 0.391132817 HFLLEEDKPEEPTAHAFVSTLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 272.1 8.01E-52 4020900000 2404490 1922770 2040010 2004800 2343230 1669850 2764230 1949730 2557490 FALSE TRUE 2253997.263 2065133.891 2088400.001 2056246.562 2159202.168 2151908.587 2349759.373 2193158.082 2130628.397 1.057902573 0.969260475 0.980180309 0.96508925 1.013410959 1.009987753 1.10284805 1.029348002 1 21.02284756 1.955168715 8.173041624 1.055886625 0.991356937 0.224878377 0.03689633 0.316317969 53.2220545 0.014473496 0.009190134 90.19214495 -1.955168715 -0.064529688 HFLPLDFSTQVNSSLTS(ph)PTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HFLPLDFSTQVNSSLTSPTGR 21 0 P19793 P19793 RXRA Retinoic acid receptor RXR-alpha 1 HFLPLDFSTQVNSSLT(0.003)S(0.996)PTGR;HFLPLDFSTQVNSSLTS(1)PTGR 259.53 9.50E-37 848450000 730280 794070 801570 849680 1152400 696810 981400 953580 1145820 TRUE FALSE 684573.0784 852863.769 820583.6189 871484.2273 1061895.153 897967.7352 834248.1809 1072636.562 954575.2397 0.717149419 0.893448451 0.859632206 0.912954989 1.112426877 0.94069875 0.873947015 1.123679431 1 19.86449939 6.326514587 0.373899468 0.997931147 1.33E-17 0.509462046 0.08429767 17.98773971 0.780481213 0.066074621 10.28516428 2120872.627 -6.326514587 -0.997931147 HFLQQATQVNAWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HFLQQATQVNAWDR 14 0 P37198 P37198 NUP62 Nuclear pore glycoprotein p62 0 ; 230.16 1.02E-12 1255100000 626980 783180 670970 682200 817620 536920 751380 671140 798360 FALSE TRUE 587738.441 841167.4621 686885.7253 699706.407 753407.4233 691920.0878 638717.5445 754933.3064 665108.5584 0.883672949 1.264707019 1.032742274 1.052018348 1.132758576 1.040311509 0.960320742 1.135052762 1 19.34323031 2.056206729 8.03679946 1.020680824 1.092519694 0.012545528 0.103951713 0.587305499 74.15962054 0.036567863 0.026920834 113.8168937 -2.056206729 0.07183887 HFLVEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HFLVEDK 7 0 P53992;P53992-2 P53992 SEC24C Protein transport protein Sec24C 0 111.01 0.0066756 149710000 626850 504250 590260 582130 655210 461300 766470 535880 708280 FALSE TRUE 587616.5775 541585.1947 604261.2459 597068.4413 603752.4496 594469.8214 651544.9391 602785.7976 590063.4923 0.995853133 0.917842235 1.0240614 1.011871517 1.023199126 1.007467551 1.104194629 1.021560909 1 19.17051067 3.543079941 1.157223038 1.041549679 0.951817191 0.36667841 0.035740574 0.421875855 1.139224756 0.012287987 0.027424363 3492.045877 -3.543079941 -0.089732489 HFNALGGWGELQNSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HFNALGGWGELQNSVK 16 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 170.92 5.10E-09 257430000 1101000 1260300 1092700 1110700 1348300 860210 1304100 1199100 1404200 FALSE TRUE 1032090.375 1353613.923 1118619.36 1139202.442 1242409.957 1108538.663 1108562.312 1348810.275 1169829.949 0.882256756 1.157103154 0.956223904 0.973818839 1.062043213 0.947606671 0.947626886 1.152996875 1 20.1578674 -1.667425076 2.764740071 0.998648616 1.011259703 0.001019958 0.090130809 210732886.3 25349405.82 1843950.843 0.019429182 0.021506757 1.667425076 0.012611087 HFPNIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HFPNIDR 7 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 136.16 0.0030076 1022670000 809320 1055140 992340 1029930 1084650 839920 1131610 1043210 1119650 FALSE TRUE 758666.1059 1133263.663 1015878.773 1056359.747 999465.9643 1082391.269 961935.5859 1173457.065 932773.1818 0.813344681 1.214940229 1.089095177 1.132493695 1.071499464 1.16040136 1.031264197 1.258030449 1 19.83116678 4.749666112 24.89402874 1.120385158 0.813344492 0.600783661 0.07848483 996.813455 2234407.363 0.016493933 0.251160477 56190.91607 -4.749666112 -0.307040666 HFRHDT(ph)PDS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HFRHDTPDSSPR 12 1 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 HFRHDT(1)PDS(0.692)S(0.308)PR 84.859 0.027498 250270000 162210 216870 182640 202390 252950 129400 212130 164200 305500 TRUE FALSE 152057.5657 232927.2805 186972.307 207583.67 233084.3274 166755.6794 180323.0758 184700.7314 254510.0764 0.597452045 0.915198658 0.734636167 0.815620635 0.915815714 0.655202661 0.708510556 0.72571088 1 17.95736325 2.22367058 24.99979228 0.740510765 0.804604337 0 0.12840183 738.6460765 1240150.044 0.042931503 0.031835646 167.3672886 -2.22367058 0.064093572 HFRHDT(ph)PDS(ph)SPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HFRHDTPDSSPRR 13 2 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 HFRHDT(1)PDS(0.541)S(0.459)PRR 83.418 0.019304 119610000 70458 72937 73424 68285 89717 50513 90145 57294 139550 TRUE FALSE 66048.15955 78337.33137 75165.65195 70037.30871 82670.98872 65095.28309 76628.59412 64447.28202 116258.2035 0.568116121 0.673821967 0.646540629 0.602428961 0.71109811 0.559919912 0.659124189 0.554346103 1 16.82697299 -1.515952342 3.421387207 1.0081603 0.630235921 0.8356823 0.052572188 14445705.73 20993650.99 1111439.374 0.01108795 0.030482295 1.515952342 -0.377924379 HFRHDT(ph)PDSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HFRHDTPDSSPR 12 1 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 HFRHDT(1)PDS(0.39)S(0.61)PR 108.77 0.025481 180560000 57004 83459 79740 82798 101770 54997 75853 67104 143010 TRUE FALSE 53436.2214 89638.3912 81631.47046 84922.73686 93777.39472 70873.7411 64479.54683 75482.08211 119140.7071 0.448513549 0.752374175 0.685168591 0.712793628 0.787114639 0.594874269 0.541205004 0.633554089 1 16.8623069 -1.060912092 4.640728527 1.000011803 0.65346262 0.552176237 0.100336453 79229012107 16033110065 13390433.85 0.023515825 0.086913634 1.060912092 -0.346549183 HFRPELEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HFRPELEER 9 1 B4DE93;G3V0I5;P49821-2;P49821 B4DE93 NDUFV1 "NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial" 0 ; 179.1 3.02E-05 755560000 394200 490230 351300 324160 631500 248680 318300 496900 746290 FALSE TRUE 369527.7257 526527.1393 359633.0019 332478.4944 581904.5373 320469.879 270573.87 558939.0588 621729.3778 0.594354616 0.846875117 0.578439776 0.534764009 0.935945056 0.51544915 0.435195568 0.899006994 1 19.24592722 1.057281003 7.265167412 0.999454811 0.641033646 0.436931233 0.150925773 0.182443758 17.88196862 0.14628925 0.036675282 11.40987805 -1.057281003 -0.358421165 HFS(ph)ESTSIDNALSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HFSESTSIDNALSR 14 0 Q8NEV8-2;Q8NEV8 Q8NEV8-2 EXPH5 Exophilin-5 1 HFS(0.985)ES(0.01)T(0.004)S(0.001)IDNALSR;HFS(0.878)ES(0.093)T(0.015)S(0.015)IDNALSR;HFS(0.994)ES(0.006)TSIDNALSR;HFS(0.999)ES(0.001)TSIDNALSR;HFS(0.976)ES(0.024)TSIDNALSR 212.41 1.60E-09 828240000 459764 572316 471184 592515 666380 334794 642097 457619 553893 TRUE FALSE 430988.1919 614690.8721 482360.707 607719.938 614045.2028 431443.5929 545820.5158 514753.7395 461444.68 0.933997531 1.332100897 1.045327269 1.316994137 1.330701663 0.934984434 1.182851465 1.115526436 1 18.81579818 0.938554892 0.693182119 1.004453862 1.179233285 0.091740368 0.148852878 1.787588068 1.94316395 0.135633796 0.05324179 8.680702884 -0.938554892 0.174779423 HFS(ph)QSEETGNEVFGALNEEQPLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HFSQSEETGNEVFGALNEEQPLPR 24 0 Q6GYQ0-2;A0A1B0GUI1;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5;Q6GYQ0-6;Q6GYQ0-3 Q6GYQ0-2 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 1 HFS(0.589)QS(0.244)EET(0.167)GNEVFGALNEEQPLPR;HFS(0.997)QS(0.003)EETGNEVFGALNEEQPLPR;HFS(0.955)QS(0.039)EET(0.005)GNEVFGALNEEQPLPR;HFS(0.984)QS(0.016)EETGNEVFGALNEEQPLPR 307.74 1.43E-73 3080540000 1045951 1212930 1229480 1237150 1393440 977090 1509650 1092541 1228340 TRUE FALSE 980486.794 1302736.599 1258643.846 1268897.363 1284004.843 1259160.021 1283291.997 1228947.149 1023322.119 0.958140918 1.273046459 1.229958606 1.239978439 1.254741611 1.230463017 1.254045011 1.200938714 1 19.96482891 0.95039522 20.26190288 0.999999999 1.220782457 0.324869094 0.090993361 1118.622457 456922.1384 0.078010582 0.019502646 8.920623704 -0.95039522 0.220782458 HFSEHPSTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HFSEHPSTSK 10 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 ; 108.43 0.0012445 118801000 82009 274610 211060 224600 261370 214030 289220 271060 282700 FALSE TRUE 76876.20308 294942.4101 216066.4429 230363.6162 240843.0545 275816.9865 245854.146 304902.4377 235515.5437 0.326416685 1.252326728 0.917419035 0.978124894 1.022620634 1.171120098 1.043897749 1.294617047 1 17.84546275 4.74678262 24.89049888 1.078366447 0.326416289 0.794745169 0.121114829 424.1593524 1284028.341 0.027291977 0.309570246 55819.07305 -4.74678262 -0.751950158 HFSGLEEAVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HFSGLEEAVYR 11 0 P50990-2;P50990;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;; 242.97 8.52E-16 4938380000 1340391 5505030 3116920 3585830 5057560 2683764 3247270 4672800 3768630 FALSE TRUE 1256498.32 5912628.149 3190854.814 3677848.469 4660359.639 3458523.1 2760372.01 5256209.366 3139621.307 0.400206967 1.883229718 1.016318372 1.171430599 1.484369987 1.101573331 0.879205401 1.674153935 1 21.58215912 HFSQSEET(ph)GNEVFGALNEEQPLPR ddPTM_SK-BR-3_Pertuzumab_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(0.185)QS(0.288)EET(0.527)GNEVFGALNEEQPLPR 147.55 6.48E-07 180700000 48599 57070 55148 61019 62133 44900 68216 57256 63605 TRUE FALSE 45557.27534 61295.52218 56456.1366 62584.85084 57253.32481 57861.90111 57987.64409 64404.53764 52988.9146 0.859751057 1.156761233 1.065432969 1.181093278 1.080477403 1.091962376 1.094335382 1.215434174 1 15.69340296 4.744849477 24.89484541 1.111813663 0.859750938 0.622810096 0.061366072 403.6532875 1597841.338 0.01268405 0.119141778 55571.16183 -4.744849477 -0.252062726 HFSTLKDDDLVEFS(ph)DLES(ph)EDDERPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HFSTLKDDDLVEFSDLESEDDERPR 25 2 Q9HCK8-2;Q9HCK8;H0YJG4;A0A2R8Y840 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 2 HFSTLKDDDLVEFS(1)DLES(1)EDDERPR;HFSTLKDDDLVEFS(1)DLES(1)EDDERPR;HFSTLKDDDLVEFS(1)DLES(1)EDDERPR;HFSTLKDDDLVEFS(1)DLES(1)EDDERPR 189.76 5.22E-18 586014000 222904 425939 408771 442938 476939 292606 570135 400707 533724 TRUE FALSE 208952.8365 457475.9667 418467.2412 454304.539 439482.1348 377076.6021 484648.5496 450736.151 444642.0164 0.469934979 1.028863557 0.941132924 1.021731016 0.988395425 0.848045367 1.089974703 1.01370571 1 18.76228476 4.741111764 24.99582633 0.990700101 0.469934794 0.871333123 0.062984266 75.53073522 739998.2607 0.014145331 0.096690811 55094.94631 -4.741111764 -0.520765307 HFSVEGQLEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 185.18 4.58E-06 1578221000 670653 1726276 1354831 1477004 1754735 1189037 1519671 1445378 1419374 FALSE TRUE 628678.0259 1854091.271 1386968.231 1514906.423 1616925.191 1532292.679 1291810.441 1625836.625 1182471.31 0.531664507 1.567979921 1.172940282 1.281135881 1.367411774 1.295839203 1.092466625 1.374948053 1 20.17337375 -1.326303591 3.701368566 0.999233404 1.23887201 0.046638458 0.273720591 461.0759166 59347276.89 70571.34067 0.056314778 0.047173316 1.326303591 0.239638606 HFTEDIQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HFTEDIQTR 9 0 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;A8MPP7;A8MPY5;E7ETV6;Q9UPE1-2;Q9UPE1-3;Q9UPE1-4;Q9UPE1;H7C2I2;P78362;P78362-2;H7C521 H3BLV9;P78362 SRPK1;SRPK3;SRPK2 SRSF protein kinase 1;SRSF protein kinase 3;SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 0 ;;; 160.53 6.52E-05 1823780000 331318 525980 438014 458107 536640 451606 486740 422085 442374 FALSE TRUE 310581.3978 564924.1065 448403.8989 469862.8012 494494.4591 581977.321 413757.8557 474783.2414 368538.9216 0.842737034 1.532875019 1.216707036 1.274933999 1.341769974 1.579147512 1.122697852 1.288285208 1 18.49145747 0.658847287 1.254681997 1.002186163 1.30652354 0.136812983 0.206418057 1.962958774 4.8176102 0.175713852 0.053118665 4.558765858 -0.658847287 0.304337377 HFTEFVPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HFTEFVPLR 9 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 134.77 0.00023969 251630000 129480 178780 146090 149330 164070 120470 152470 193370 131990 FALSE TRUE 121376.0779 192017.0572 149555.3238 153162.0606 151184.604 155247.7333 129608.539 217512.6702 109960.0163 1.103820116 1.74624435 1.360088228 1.392888668 1.374905253 1.411856223 1.178687884 1.978106929 1 16.7466195 3.715200364 23.84710738 1.381611437 1.495593662 0 0.290683976 876.1820143 1752760.026 0.068951614 0.107877175 5190.394455 -3.715200364 0.113982225 HFTILDAPGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HFTILDAPGHK 11 0 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1;H3BSV8 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ; 168.22 1.06E-05 1892240000 978030 1616720 1498490 1390300 1677060 1599300 1664290 1548230 2058590 FALSE TRUE 916816.8481 1736423.631 1534034.89 1425977.452 1545350.473 2060991.948 1414745.165 1741529.924 1714998.03 0.534587698 1.012493076 0.894482013 0.831474688 0.901080028 1.201745956 0.824925242 1.01547051 1 20.70977549 2.461470599 24.9988542 0.993277321 0.86362958 0.240037936 0.150832518 455.5919174 727714.1935 0.049124255 0.041112101 289.3813905 -2.461470599 -0.12964774 HFVALSTNTTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HFVALSTNTTK 11 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90 P06744 GPI Glucose-6-phosphate isomerase 0 ; 172.21 1.36E-05 4410900000 4433700 5267600 4483400 4496200 5244300 2879500 5625600 4864700 5817800 FALSE TRUE 4156202.631 5657618.585 4589748.365 4611580.104 4832433.832 3710764.905 4782093.506 5472068.504 4846771.596 0.857519805 1.167296307 0.94697022 0.951474608 0.997041791 0.765615798 0.986655429 1.129013075 1 22.20859267 6.465307685 10.57133025 0.981872088 0.533810442 0 0.115943786 0 0 0.024830022 0 2919494.656 -6.465307685 -0.448061647 HFVDSELECNDVVLFWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HFVDSELECNDVVLFWR 17 0 O60313-10;O60313-9;O60313-2;E5KLJ9;O60313-13;O60313;O60313-11;A0A2R8YDM2;A0A2R8Y3X5;C9JMB8;A0A2R8YE78;A0A2R8YFD1;H7C141 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 ; 175.65 1.20E-09 71084000 86969 81969 70752 75058 105554 80695 97826 84308 74459 FALSE TRUE 81525.76553 88038.07005 72430.27085 76984.11535 97264.21462 103990.3365 83157.89947 94834.03938 62031.31188 1.314267957 1.419252106 1.167640481 1.241052511 1.567985775 1.676416851 1.34057941 1.528809185 1 15.92070902 2.75306922 24.42049291 1.455969309 1.288184269 0.101209288 0.189233736 1037.080436 1745584.24 0.052848905 0.055810058 566.3295465 -2.75306922 -0.16778504 HFVDSHHQKPVNAIIEHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HFVDSHHQKPVNAIIEHVR 19 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;; 218.88 1.10E-19 6443340000 1674629 2331619 2349416 2239032 2324027 1784547 2852054 2089669 2694692 FALSE TRUE 1569816.96 2504254.497 2405145.257 2296489.352 2141507.294 2299716.749 2424414.98 2350568.775 2244930.497 0.699271965 1.11551538 1.071367359 1.022966793 0.953930332 1.024404431 1.07995102 1.047056369 1 21.09823935 4.745475249 24.99863547 1.047179096 0.699271805 0.847932183 0.045160286 326.4628489 1180239.319 0.011633654 0.11696326 55651.29173 -4.745475249 -0.347907291 HFVGMLPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HFVGMLPEK 9 0 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;; 95.502 0.0060697 1155430000 1949560 5305600 1426560 1482240 6185100 916260 1720700 5389900 5755800 FALSE TRUE 1827540.52 5698432.144 1460398.677 1520276.788 5699347.195 1180769.388 1462697.009 6062840.88 4795119.796 0.381125102 1.188381602 0.304559373 0.317046675 1.188572432 0.246243981 0.305038679 1.264377354 1 22.19313543 1.229250744 24.99922981 1.13218892 0.581383416 0.305098139 0.357050754 282.9072938 759646.3317 0.318026302 0.083851531 16.95316324 -1.229250744 -0.550805504 HFVGMLPEKDCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HFVGMLPEKDCR 12 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;;;; 134.08 9.13E-05 6910204000 5590773 6860200 5463762 5230647 8708660 4496769 7154760 6248110 13783290 FALSE TRUE 5240856.498 7368136.346 5593365.015 5364874.257 8024716.973 5794913.211 6081970.16 7028200.287 11482769.86 0.45641048 0.641668904 0.48710939 0.467210815 0.698848542 0.504661618 0.529660547 0.612064892 1 23.45296735 0.77209507 3.327597117 0.999976243 0.546130699 0.77911939 0.076215355 0.732106136 10.15491587 0.066855199 0.017318946 5.916911451 -0.77209507 -0.453845544 HFVLDECDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HFVLDECDK 9 0 O00148;O00148-2;O00148-3;K7EQN7;K7EPJ3;A0A0D9SEM9 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ;;; 182.65 4.61E-05 1375330000 3185980 2521570 2489870 2356210 2981360 1811300 3189270 2632840 3208990 FALSE TRUE 2986575.199 2708269.666 2548930.892 2416674.338 2747216.012 2334192.906 2711068.571 2961555.87 2673388.838 1.117149573 1.013047421 0.953445625 0.903974126 1.027615576 0.873121363 1.014094371 1.107790916 1 21.35023826 -0.42402947 6.308200584 1 0.991852881 0 0.07793068 0 0 0.070402146 0.016593945 0.376678238 0.42402947 -0.008147119 HFWTAES ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HFWTAES 7 0 Q14157-4;Q14157-1 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 0 124.32 0.0096722 188860000 154340 218140 171860 180430 254670 125330 267770 212100 339950 FALSE TRUE 144680.1349 234291.3126 175936.6004 185060.1393 234669.2455 161510.7364 227620.3744 238581.1519 283210.1488 0.510857875 0.827270186 0.621222795 0.653437527 0.828604647 0.570285836 0.803715458 0.842417381 1 18.11151344 1.106807117 1.471584743 0.995348458 0.686695401 0.523381053 0.103050263 0.295035377 1.27006837 0.086257146 0.025881324 12.7881322 -1.106807117 -0.308653057 HFYWYLTNEGIQYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HFYWYLTNEGIQYLR 15 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ; 228.25 6.22E-13 241558000 76397 169096 74903 56309 158123 34384 64440 145988 56919 FALSE TRUE 71615.44814 181616.0438 76679.73453 57753.98427 145704.6574 44310.10262 54777.82023 164214.9232 47418.85119 1.510273791 3.830038882 1.617072801 1.217954101 3.072715888 0.93444066 1.155190791 3.463072576 1 15.53317309 3.747890162 8.146943823 1.7290683 2.805617895 0.112177463 1.016920375 0.327980021 105.0456859 0.241093513 0.423748238 5596.1605 -3.747890162 1.076549595 HGAGS(ph)GCLGTMEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HGAGSGCLGTMEVK 14 0 Q9BYG5-2;Q9BYG5 Q9BYG5-2 PARD6B Partitioning defective 6 homolog beta 1 HGAGS(1)GCLGTMEVK;HGAGS(1)GCLGTMEVK;HGAGS(1)GCLGTMEVK;HGAGS(1)GCLGTMEVK;HGAGS(1)GCLGTMEVK;HGAGS(1)GCLGTMEVK 195.6 1.68E-08 2150180000 3222790 2307740 2749248 2405493 3054723 1824683 3122011 2300638 3998900 TRUE FALSE 3021081.327 2478607.471 2814461.461 2467222.023 2814817.378 2351439.361 2653894.434 2587877.719 3331457.756 0.90683465 0.744000871 0.844813792 0.740583313 0.844920627 0.705828959 0.796616565 0.7768004 1 21.66772217 -1.189972038 5.783652594 1.000004313 0.791206398 0.542038463 0.059110097 2.82E-06 3.95E-07 0.049052416 0.011561526 0.06456958 1.189972038 -0.208797916 HGAPAAPS(ph)PPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HGAPAAPSPPPR 12 0 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 HGAPAAPS(1)PPPR;HGAPAAPS(1)PPPR 58.079 0.069996 439620000 538400 545550 565770 531270 544360 467020 639420 571580 645490 TRUE FALSE 504702.5051 585943.0896 579190.3316 544903.2876 501608.1614 601841.0926 543544.9071 642943.0212 537753.549 0.938538678 1.089612687 1.07705534 1.013295568 0.932784474 1.119176421 1.01076954 1.195609071 1 19.03658562 HGAPS(ph)PSHPISAPQAAAAAALRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGAPSPSHPISAPQAAAAAALRR 23 1 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;H0YF36 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 HGAPS(0.999)PS(0.001)HPISAPQAAAAAALRR 126.59 2.33E-05 40333000 36572 48348 46411 50480 51535 37494 58533 41248 77045 TRUE FALSE 34283.0238 51927.73623 47511.89084 51775.40226 47487.64898 48317.90914 49756.52004 46397.9036 64185.69177 0.534122526 0.80902355 0.740225579 0.806650218 0.739847896 0.75278318 0.775196444 0.722869885 1 15.96996411 -5 0.253875604 2.557331839 0.725121621 0.550835627 0.075914531 142.618284 1.409903702 115.6107289 0.095957611 1.00E-05 5 -1.832210219 HGAVSVS(ph)LFIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGAVSVSLFIR 11 0 Q9BT04-2 Q9BT04-2 1 HGAVS(0.177)VS(0.823)LFIR 57.347 0.072936 105180000 22749 102680 65735 77902 79213 86911 60524 70857 43069 TRUE FALSE 21325.1807 110282.534 67294.26524 79901.09721 72991.93051 112000.7948 51448.98808 79703.65243 35880.50566 0.594338912 3.073605904 1.875510503 2.226866532 2.034306071 3.121494325 1.433898077 2.221363689 1 15.1309126 0.410077741 0.953901562 0.999233095 2.183527315 0.158890256 0.736519115 3.441794028 4.146162623 0.654344842 0.203466507 2.570855938 -0.410077741 1.18429422 HGDLPDIQIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HGDLPDIQIK 10 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 152.97 1.71E-05 518590000 1763420 1443110 1502470 1614170 1522580 1045560 2011300 1377650 1606360 FALSE TRUE 1653050.69 1549959.366 1538109.298 1655592.335 1403002.709 1347396.199 1709724.237 1549652.635 1338248.139 1.235234814 1.158200278 1.149345367 1.237134047 1.048387566 1.006835848 1.277583871 1.157971075 1 20.35191422 -2.029016498 2.475174195 0.812398734 1.159012517 0.267326525 0.08263897 9120922.283 3749487.369 9707242.027 0.01908502 0.009353701 2.029016498 0.346613783 HGDPGDAAQQEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HGDPGDAAQQEAK 13 0 O14737;O14737-2;Q3HM38;X6R2P6;K7ESJ4 O14737 PDCD5 Programmed cell death protein 5 0 ;;; 168.76 2.97E-05 2520070000 5620070 3970460 4564640 4590640 4904920 3210700 5594970 3865660 5282040 FALSE TRUE 5268319.851 4264436.99 4672915.416 4708443.594 4519707.369 4137576.969 4756056.19 4348296.16 4400433.401 1.197227494 0.969094769 1.061921632 1.069995422 1.02710505 0.940265786 1.080815401 0.988151794 1 22.06921419 2.485833837 24.34296204 1.010452582 1.054243387 0.183310973 0.065392421 718.0237321 2006164.063 0.020738154 0.018217173 306.0792137 -2.485833837 0.043790805 HGEAQVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 HGEAQVK 7 0 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 0 ;;;;;;; 143 0.002451 7799462000 15165720 11349960 12561990 12733880 12888520 8391080 13796330 11270020 13758460 FALSE TRUE 14216524.66 12190322.85 12859966.34 13060652.92 11876307.63 10813448.58 11727698.4 12677106.81 11462084.14 1.240308872 1.06353458 1.121957069 1.139465804 1.036138584 0.94341033 1.023173295 1.106003642 1 23.45036606 2.661772642 4.916839151 1.014972001 1.125075521 0.496981863 0.058827057 0.199332043 8.814699378 0.018536267 0.017522329 458.9576805 -2.661772642 0.11010352 HGESAWNLENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 HGESAWNLENR 11 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;;;;; 221.6 8.29E-12 14596240000 7692080 8357810 7720020 8054490 8015330 5784650 8632030 7046170 7301300 FALSE TRUE 7210646.444 8976630.949 7903142.52 8261181.85 7385838.314 7454584.549 7337737.237 7925899.835 6082665.862 1.185441812 1.475772491 1.299289275 1.358151514 1.214243636 1.225545627 1.206335742 1.303030614 1 22.53627232 -0.798604342 0.19119719 0.770040089 1.404971541 0.523603536 0.085569087 12.05861189 0.560501457 1.790708506 0.283248815 0.158999463 0.798604342 0.634931452 HGEVCPAGWKPGSDTIKPDVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HGEVCPAGWKPGSDTIKPDVQK 22 2 Q06830;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ; 209.01 3.72E-23 11006300000 9514800 4896200 6743100 5963300 6168400 4511400 8792600 5054100 8406500 FALSE TRUE 8919285.652 5258719.742 6903049.516 6116328.374 5683958.746 5813767.944 7474231.256 5685115.51 7003400.842 1.273564923 0.750880874 0.985671058 0.873336899 0.811599803 0.830134969 1.067228826 0.811764975 1 22.73962423 -1.042623608 6.358677636 1.000000068 0.917233722 0.020095397 0.154064453 1.31E-07 1.95E-08 0.132027625 0.031119184 0.090651792 1.042623608 -0.082766346 HGFCGIPITDTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGFCGIPITDTGR 13 0 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 100.38 0.00243 362520000 652940 785830 694100 755380 847130 602980 856840 659160 868890 FALSE TRUE 612073.6509 844013.6709 710564.3798 774764.3297 780599.827 777050.5374 728364.7965 741457.577 723866.6458 0.84556134 1.165979502 0.98162332 1.07031362 1.078375184 1.073471947 1.00621406 1.024301342 1 19.46536442 1.657924029 8.71528943 1.011525127 1.047511804 0.007944451 0.082760197 0.436094068 56.93452915 0.03645803 0.019196405 45.49084762 -1.657924029 0.035986678 HGFSDNQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HGFSDNQK 8 0 Q8WW12;Q8WW12-3 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 0 ; 147.29 0.00053968 565670000 752330 800200 614890 609110 869220 503770 794880 775150 843920 FALSE TRUE 705243.0082 859447.6406 629475.4812 624740.7938 800954.9675 649200.221 675695.1233 871929.1838 703064.3001 1.003098875 1.222431064 0.895331311 0.888596952 1.139234302 0.923386696 0.961071588 1.240184125 1 19.42329711 3.976803336 24.99993616 0.996900628 1.11973777 0.111870157 0.121261845 25.55837989 2010092.05 0.028328393 0.055511024 9479.89083 -3.976803336 0.122837141 HGFSGIPITETGTMGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGFSGIPITETGTMGSK 17 0 P20839-3;P20839-7;P20839-5;P20839-6;P20839;A0A3B3IRL5;C9J381;P20839-2;P20839-4;C9K0R9;C9J029;H7C5T1;H7C511 P20839-3 IMPDH1 Inosine-5-monophosphate dehydrogenase 1;Inosine-5-monophosphate dehydrogenase 0 126.63 4.30E-05 275810000 256520 234840 250150 263250 303800 223140 327130 248530 359060 FALSE TRUE 240464.8711 252227.798 256083.6761 270005.4407 279940.7735 287556.8956 278079.8934 279559.5176 299130.5664 0.803879303 0.843203023 0.856093308 0.90263407 0.935848104 0.961308967 0.929627142 0.934573557 1 18.19041581 5.10697403 0.219535042 1.001640471 0.598828358 0.913089158 0.017306341 3.989838932 0.15004324 0.032178944 0.451607079 127930.4803 -5.10697403 -0.402812112 HGGPGPGGPEPELS(ph)PITEGSEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HGGPGPGGPEPELSPITEGSEAR 23 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 HGGPGPGGPEPELS(1)PITEGSEAR;HGGPGPGGPEPELS(0.996)PIT(0.003)EGS(0.001)EAR 246.63 8.49E-38 758260000 296544 286260 328090 385930 327530 227100 270970 228120 295930 TRUE FALSE 277983.8404 307454.9883 335872.4497 395833.6172 301807.115 292660.0833 230340.5641 256601.2842 246537.3712 1.127552545 1.247092831 1.362359175 1.605572475 1.22418404 1.187082031 0.934302832 1.040821044 1 17.91144683 2.034893353 2.406476492 0.98866967 1.326827568 0.57760389 0.125284622 0.210828929 2.326958351 0.065379616 0.037179465 108.3660773 -2.034893353 0.338157898 HGGPKDEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HGGPKDEER 9 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;;; 163.38 3.79E-05 2330160000 3655230 2917300 2974650 2825630 3160700 1950810 3170530 2754350 3864050 FALSE TRUE 3426455.679 3133299.927 3045210.103 2898140.45 2912471.372 2513977.178 2695138.46 3098236.661 3219115.092 1.064409187 0.973342002 0.945977393 0.900291032 0.904742853 0.780952873 0.837229606 0.962449795 1 21.61823273 4.285925324 0.744851141 0.875879359 1.093298082 0.374580647 0.063756138 1.499028177 0.95473805 0.025138052 0.245374528 19316.36146 -4.285925324 0.217418724 HGGS(ph)PQPLAT(ph)TPLSQEPVNPPSEAS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 HGGS(1)PQPLAT(0.5)T(0.5)PLSQEPVNPPS(0.144)EAS(0.714)PT(0.141)R;HGGS(1)PQPLAT(0.592)T(0.408)PLSQEPVNPPS(0.047)EAS(0.797)PT(0.156)R;HGGS(1)PQPLAT(0.782)T(0.218)PLSQEPVNPPS(0.045)EAS(0.802)PT(0.153)R 174.79 3.47E-12 781990000 553640 486730 508900 508220 491110 451780 603820 436401 473460 TRUE FALSE 518988.6607 522767.9956 520971.3483 521261.7856 452540.2016 582201.552 513282.7966 490886.6255 394436.4673 1.31577251 1.325354116 1.320799144 1.321535479 1.147308221 1.476033785 1.301306647 1.244526473 1 18.58943342 0.818863123 2.635681673 1.000240614 1.318248187 0.617747066 0.077761533 0.463220096 5.457183123 0.067360581 0.017916035 6.589661753 -0.818863123 0.318007573 HGGS(ph)PQPLATT(ph)PLSQEPVNPPSEAS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 HGGS(0.96)PQPLAT(0.236)T(0.804)PLSQEPVNPPSEAS(0.992)PT(0.007)R 223.29 5.86E-34 265860000 162590 149480 149610 152100 147780 146000 173340 128570 133840 TRUE FALSE 152413.7821 160547.6547 153158.8199 156003.1435 136173.9549 188147.8299 147349.2762 144622.2475 111501.2394 1.366924556 1.439873275 1.373606435 1.39911578 1.221277501 1.687405727 1.321503483 1.297046099 1 16.76670022 0.843233627 2.009214695 1.001408555 1.407583794 0.541535906 0.116766445 0.408362185 3.108693321 0.099379506 0.0275496 6.970013624 -0.843233627 0.406175239 HGGS(ph)PQPLATTPLSQEPVNPPS(ph)EASPTRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HGGSPQPLATTPLSQEPVNPPSEASPTRDR 30 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 HGGS(1)PQPLATTPLSQEPVNPPS(0.333)EAS(0.333)PT(0.333)RDR;HGGS(1)PQPLATT(0.001)PLS(0.013)QEPVNPPS(0.435)EAS(0.276)PT(0.276)RDR 95.252 0.0010374 263050000 81302 76658 86784 80872 63082 71678 106733 70996 59474 TRUE FALSE 76213.45295 82333.83808 88842.55746 82947.31244 58127.79418 92370.275 90729.37751 79860.00688 49547.40518 1.538192619 1.661718465 1.793081941 1.674100029 1.173175345 1.864280776 1.831163048 1.611789893 1 15.59652188 0.954195541 22.18379886 0.999999997 1.670733292 0.515610946 0.195331931 2163.330896 1047736.35 0.184511356 0.046127839 8.999026714 -0.954195541 0.670733295 HGGS(ph)PQPLATTPLSQEPVNPPSEAS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 HGGS(1)PQPLATTPLSQEPVNPPS(0.154)EAS(0.735)PT(0.111)R;HGGS(0.999)PQPLAT(0.001)TPLSQEPVNPPSEAS(0.996)PT(0.004)R;HGGS(0.998)PQPLAT(0.001)TPLSQEPVNPPS(0.004)EAS(0.972)PT(0.024)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.009)EAS(0.855)PT(0.136)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.006)EAS(0.954)PT(0.04)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.022)EAS(0.975)PT(0.003)R 273.25 9.45E-62 11148840000 1355344 1143708 1289920 1255770 1171428 1138470 1573210 1116963 1003954 TRUE FALSE 1270515.438 1228389.33 1320517.512 1287995.184 1079428.77 1467127.807 1337321.765 1256418.289 836387.5916 1.519051037 1.468684307 1.578834412 1.539950135 1.290584391 1.754124311 1.598925879 1.502196233 1 19.67381213 0.945618741 20.68431454 0.999999999 1.539830943 0.680076211 0.114771579 1106.950066 421038.2016 0.105686563 0.026421641 8.823050004 -0.945618741 0.539830944 HGGSPQPLATTPLSQEPVNPPS(ph)EASPTRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGGSPQPLATTPLSQEPVNPPSEASPTRDR 30 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HGGSPQPLATTPLS(0.008)QEPVNPPS(0.331)EAS(0.331)PT(0.331)RDR 72.792 0.003247 121130000 38865 38054 44976 42384 39409 32627 44459 32821 34684 TRUE FALSE 36432.50903 40871.55776 46042.85196 43471.6452 36313.97611 42045.88524 37792.78569 36918.7741 28895.01633 1.26085788 1.414484674 1.593453052 1.504468615 1.256755687 1.455125851 1.307934394 1.277686563 1 14.81853306 0.797179471 0.684770151 0.996546695 1.447311324 0.609799746 0.102807087 0.647299218 0.636844151 0.104984423 0.039803779 6.268728641 -0.797179471 0.45076463 HGGSPQPLATTPLSQEPVNPPSEAS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HGGSPQPLATTPLSQEPVNPPSEAS(0.752)PT(0.248)R;HGGSPQPLATTPLSQEPVNPPSEAS(0.996)PT(0.004)R;HGGSPQPLATTPLSQEPVNPPSEAS(0.956)PT(0.043)R;HGGSPQPLATTPLSQEPVNPPSEAS(0.988)PT(0.012)R;HGGSPQPLATTPLSQEPVNPPS(0.015)EAS(0.898)PT(0.087)R;HGGSPQPLATTPLSQEPVNPPS(0.001)EAS(0.781)PT(0.219)R 299.15 1.21E-71 6227280000 2172450 2213060 2414450 2403500 2061250 1988710 2541820 1968460 1650778 TRUE FALSE 2036480.232 2376917.265 2471721.894 2465177.879 1899367.74 2562818.293 2160697.688 2214226.564 1375252.487 1.480804617 1.72834973 1.797285893 1.792527483 1.381104748 1.863525655 1.571127999 1.610050943 1 20.39126508 -0.252713018 0.62634498 0.94421919 1.694319097 0.652594763 0.149827619 4.069778988 1.485472149 0.679261209 0.053718692 0.558839354 0.252713018 0.750099907 HGGSPQPLATTPLSQEPVNPPSEASPT(ph)RDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGGSPQPLATTPLSQEPVNPPSEASPTRDR 30 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HGGSPQPLATTPLS(0.009)QEPVNPPS(0.299)EAS(0.299)PT(0.394)RDR 90.974 0.0015095 92059000 45176 46774 47660 54528 46586 48053 56719 42788 49551 TRUE FALSE 42348.5148 50237.19563 48790.51771 55927.2808 42927.32348 61925.12102 48214.5125 48130.17599 41280.61799 1.025869206 1.216968109 1.181923142 1.354807256 1.039890524 1.500101598 1.167969736 1.165926731 1 15.33317695 0.848335874 2.445352745 1.000687548 1.219927424 0.189051463 0.137688142 0.881304397 9.928843252 0.11621229 0.031257334 7.052382746 -0.848335874 0.219239876 HGGTIPIVPTAEFQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HGGTIPIVPTAEFQDR 16 0 P00367;P00367-2;P00367-3 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ; 121.82 9.67E-05 535320000 622780 592060 549240 525420 731100 519200 529430 599250 883280 FALSE TRUE 583801.3115 635896.7384 562268.2322 538903.1667 673682.3551 669084.6115 450046.8865 674067.6816 735854.8618 0.793364754 0.864160545 0.764102082 0.732349808 0.915509824 0.909261658 0.611597354 0.916033469 1 19.48906172 1.006000306 24.9970799 1.000000075 0.797429547 0.37806446 0.088693365 120.9791005 503991.8591 0.083713544 0.020928386 10.139121 -1.006000306 -0.202570528 HGGVCAPAAVATS(ph)PPGAIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HGGVCAPAAVATSPPGAIPK 20 0 Q9Y6A5;A0A494BZT8;E7EMT0 Q9Y6A5 TACC3 Transforming acidic coiled-coil-containing protein 3 1 HGGVCAPAAVAT(0.006)S(0.994)PPGAIPK;HGGVCAPAAVAT(0.027)S(0.973)PPGAIPK;HGGVCAPAAVAT(0.003)S(0.997)PPGAIPK;HGGVCAPAAVAT(0.241)S(0.759)PPGAIPK 180.8 3.43E-17 1730000000 1280190 866770 1073130 1006510 1085700 773860 1229210 853310 1528800 TRUE FALSE 1200065.193 930946.5527 1098585.15 1032338.751 1000433.502 997260.8194 1044901.372 959847.6319 1273633.404 0.942237531 0.730937607 0.862559939 0.810546228 0.785495653 0.783004604 0.820409836 0.753629442 1 20.28051865 -1.006630296 4.762457011 1.000003578 0.807459126 0.503176917 0.058889883 0.01042134 32449132.28 265.606041 0.011965363 0.098484913 1.006630296 -0.192544452 HGHFGWPGWEMGPPGNWS(ph)PRPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HGHFGWPGWEMGPPGNWSPRPPR 23 1 Q13501;Q13501-2;E7EMC7;C9JRJ8;E9PFW8 Q13501 SQSTM1 Sequestosome-1 1 HGHFGWPGWEMGPPGNWS(1)PRPPR;HGHFGWPGWEMGPPGNWS(1)PRPPR 107.23 0.0017224 660780000 205446 205011 195741 161847 216413 184744 215500 170982 190353 TRUE FALSE 192587.5016 220190.2278 200384.069 166000.268 199416.7959 238076.5937 183187.7756 192329.4791 158581.8546 1.214435927 1.388495729 1.263600237 1.046779712 1.257500718 1.501285216 1.155162273 1.212808865 1 17.27486818 0.8452233 1.520145087 1.002665012 1.276564756 0.313621238 0.121356633 0.717268143 3.133963073 0.112336927 0.032786543 7.00201924 -0.8452233 0.273899744 HGIVEDWDLMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 HGIVEDWDLMER 12 0 B4DXW1;P61158;F8WDR7 B4DXW1 ACTR3 Actin-related protein 3 0 ;;;;;;;;; 246.26 1.58E-16 3445204000 2687328 2965818 2871279 2867642 3139335 2306501 3050622 2660274 2960387 FALSE TRUE 2519132.937 3185410.251 2939387.094 2941230.549 2892784.293 2972350.396 2593209.552 2992415.065 2466279.285 1.021430522 1.291585373 1.191830589 1.192578053 1.172934594 1.205196189 1.051466299 1.213331792 1 21.23390475 0.514355498 0.444875351 0.989100054 1.200835983 0.259259925 0.081104123 2.334125252 0.883503986 0.144207467 0.046977438 3.268552751 -0.514355498 0.21173593 HGLAHDEMKS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 HGLAHDEMKSPR 12 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR;HGLAHDEMKS(1)PR 181.26 1.11E-05 9683290000 12739800 8888230 10068520 9894820 10274630 6950860 12118950 8279370 10872470 TRUE FALSE 11942438.66 9546323.797 10307350.05 10148737.83 9467702.006 8957460.444 10301825.95 9313067.57 9057784.518 1.318472374 1.053935847 1.137954875 1.120443726 1.045255822 0.988923994 1.137345002 1.028183829 1 23.11072679 4.741580685 24.95658527 1.075009223 1.318472465 0.681304477 0.054233262 166.6717339 1377235.745 0.012223441 0.08665913 55154.46605 -4.741580685 0.243463243 HGLEAISIMDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HGLEAISIMDSR 12 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ;;;;; 218.62 3.39E-11 886230000 1200784 1455398 1312237 1227081 1632917 1001695 1331715 1360462 1693290 FALSE TRUE 1125629.073 1563157.182 1343363.881 1258569.976 1504674.286 1290868.085 1132036.699 1530318.675 1410668.96 0.797939917 1.10809639 0.952288538 0.892179534 1.066638828 0.915075132 0.802482178 1.084817713 1 20.42794804 HGLEVIYMIEPIDEYCVQQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HGLEVIYMIEPIDEYCVQQLK 21 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 303.14 2.77E-55 3046355000 2478636 1867688 2177903 2014371 2323643 1806153 2758884 1938129 1995182 FALSE TRUE 2323502.597 2005973.563 2229563.888 2066063.17 2141153.452 2327560.051 2345214.956 2180108.672 1662173.235 1.397870299 1.206837844 1.341354704 1.242989074 1.28816504 1.400311353 1.410932932 1.311601358 1 20.66463932 0.934326898 21.90199741 1 1.322956348 0.697495506 0.067299482 5533.639882 1845474.109 0.068743606 0.017185901 8.596603531 -0.934326898 0.322956348 HGLLVPNNTTDQELQHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HGLLVPNNTTDQELQHIR 18 0 P56537;B7ZBH1 P56537 EIF6 Eukaryotic translation initiation factor 6 0 ;;; 149.97 3.37E-08 3367089000 1212551 1190509 1289874 1293140 1245762 1070500 1405148 1074139 1276439 FALSE TRUE 1136659.597 1278655.525 1320470.42 1326324.162 1147924.878 1379535.972 1194459.102 1208247.619 1063393.085 1.068898805 1.202429791 1.241751935 1.247256711 1.079492517 1.297296354 1.123252652 1.13621918 1 20.02024356 0.862266808 1.277278489 1.001296264 1.194372098 0.376903435 0.073029937 0.582687702 1.837466738 0.062573225 0.019030713 7.282270525 -0.862266808 0.193075834 HGLQLGAQS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 HGLQLGAQSPGR 12 0 Q8N1G0;A6PVV7 Q8N1G0 ZNF687 Zinc finger protein 687 1 HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR 189.8 4.80E-06 6625860000 4588225 4893723 4717686 4553501 5438834 3560955 5336330 4901362 5988280 TRUE FALSE 4301056.187 5256059.343 4829591.74 4670351.545 5011689.917 4588944.901 4536196.857 5513307.835 4988797.382 0.862142889 1.053572422 0.968087371 0.936167815 1.004588788 0.919849926 0.909276627 1.105137654 1 22.25026065 1.239362459 24.99992747 1.052568822 0.959702605 0.337584112 0.058334667 25.70978172 801811.8375 0.043727224 0.013834281 17.35251621 -1.239362459 -0.092866217 HGLTEPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGLTEPER 8 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 0 75.825 0.037388 926040000 1164800 807330 1440000 1361500 873680 1455600 1824400 859870 1304200 FALSE TRUE 1091897.247 867105.5532 1474157.48 1396438.395 805064.6971 1875808.09 1550848.157 967226.6623 1086520.595 1.004948505 0.798057172 1.356769018 1.285238772 0.740956684 1.726435835 1.427352748 0.890205549 1 20.05128409 3.978175023 5.04753304 1.247776149 0.905572765 0.147230975 0.287255367 0.269314325 20.47430586 0.070749419 0.144637964 9509.879695 -3.978175023 -0.342203384 HGLTSGS(ph)ASPPPPALPLYPDPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGLTSGSASPPPPALPLYPDPVR 23 0 Q92610;H0YM74 Q92610 ZNF592 Zinc finger protein 592 1 HGLT(0.003)S(0.066)GS(0.543)AS(0.388)PPPPALPLYPDPVR 87.052 0.0042472 183470000 70626 72507 76411 80356 82252 73586 89664 70888 89578 TRUE FALSE 66205.64473 77875.49372 78223.505 82418.071 75792.25971 94829.08363 76219.7156 79738.52284 74626.8531 0.887155789 1.043531792 1.048195144 1.104402337 1.015616451 1.270709935 1.021344361 1.068496386 1 16.18740723 5.692687306 0.965534965 1.083565645 6.86E-11 0.364016271 0.076617411 10.80080476 2.004670083 0.021080982 18.85550559 492818.8447 -5.692687306 -1.083565645 HGLTSGSAS(ph)PPPPALPLYPDPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGLTSGSASPPPPALPLYPDPVR 23 0 Q92610;H0YM74 Q92610 ZNF592 Zinc finger protein 592 1 HGLTS(0.001)GS(0.094)AS(0.905)PPPPALPLYPDPVR 192.18 6.40E-18 208070000 118700 138740 136510 137000 142650 125440 125270 114890 150310 TRUE FALSE 111270.7789 149012.454 139748.0817 140515.6519 131446.8444 161652.4917 106486.9264 129234.2694 125222.29 0.888586041 1.189983461 1.116000048 1.12212971 1.049708039 1.290924257 0.850383158 1.03203886 1 16.93413186 1.715599595 16.82219809 0.956329896 1.117757201 0.282426394 0.111177367 0.205550469 140.9015123 0.045940219 0.025401662 51.9516798 -1.715599595 0.161427305 HGLYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HGLYEK 6 0 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4;A0A2R8Y8A0 E7ETK0 RPS24 40S ribosomal protein S24 0 ; 103.28 0.034817 3275700000 9174000 8806700 8845000 8752100 10220100 6740300 10579900 8527400 10682600 FALSE TRUE 8599815.716 9458757.231 9054807.577 8976693.703 9417454.572 8686115.19 8993542.214 9592064.661 8899605.048 0.966314311 1.062828876 1.01743926 1.008662031 1.058187922 0.976011311 1.010555206 1.077807904 1 23.08530988 -2.917067009 1.784413046 0.000142856 1.023096652 0.035860224 0.035966489 688877.1714 42664.6119 2833733.791 0.008303104 0.001210411 2.917067009 1.022953796 HGNQYIQVNEPWKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HGNQYIQVNEPWKR 14 1 P56192 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ; 151.78 4.44E-06 348000000 638290 556330 588730 631020 657810 417700 785830 556030 967590 FALSE TRUE 598340.5683 597521.2521 602694.9536 647213.0415 606148.2561 538283.2092 668002.0868 625451.5695 806092.9781 0.742272398 0.741255994 0.747674239 0.802901227 0.751958239 0.667768141 0.828691112 0.775904997 1 19.62058673 0.340689045 0.866886699 1.001997666 0.74804967 0.783784552 0.040566412 1.063862462 1.036967273 0.041046282 0.012255928 2.191235446 -0.340689045 -0.253947996 HGNRNS(ph)NSYGIPEPAHAYAQPQTTTPLPAVSGSPGAAITPLPSTQNGPVFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGNRNSNSYGIPEPAHAYAQPQTTTPLPAVSGSPGAAITPLPSTQNGPVFAK 52 1 P46109 P46109 CRKL Crk-like protein 1 HGNRNS(0.302)NS(0.302)Y(0.262)GIPEPAHAY(0.079)AQPQT(0.018)T(0.018)T(0.018)PLPAVSGSPGAAITPLPSTQNGPVFAK 211.29 3.55E-42 795750000 225810 225070 207120 197740 316810 157540 266420 227150 352370 TRUE FALSE 211676.9552 241734.417 212032.9842 202814.3432 291929.0206 203019.2406 226472.7943 255510.1775 293557.1706 0.721075744 0.823466231 0.722288554 0.690885332 0.994453721 0.691583313 0.771477644 0.870393242 1 18.16328197 0.971057526 3.050509833 0.999307657 0.774019442 0.410052677 0.088410953 0.238352881 5.484189884 0.07678663 0.020167882 9.355295844 -0.971057526 -0.225288215 HGNRNSNS(ph)YGIPEPAHAYAQPQTTTPLPAVSGSPGAAITPLPSTQNGPVFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGNRNSNSYGIPEPAHAYAQPQTTTPLPAVSGSPGAAITPLPSTQNGPVFAK 52 1 P46109 P46109 CRKL Crk-like protein 1 HGNRNS(0.054)NS(0.278)Y(0.252)GIPEPAHAY(0.252)AQPQT(0.054)T(0.054)T(0.054)PLPAVSGSPGAAITPLPSTQNGPVFAK 116 1.39E-10 487780000 42054 39871 37541 39982 52057 27228 48791 38447 59490 TRUE FALSE 39421.91521 42823.09033 38431.49025 41008.00581 47968.65321 35088.28159 41475.2425 43247.19258 49560.73468 0.795426369 0.864052775 0.775442303 0.827429336 0.967876153 0.707985501 0.836856894 0.872609998 1 15.59690995 0.863738541 2.684202959 0.999738072 0.823910965 0.41219728 0.065898224 0.498697474 7.003634922 0.05755463 0.015292021 7.306990478 -0.863738541 -0.175827107 HGPPLGESVAYHSESPNSQTDVGRPLS(ph)GSGISAFVQAHPSNGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGPPLGESVAYHSESPNSQTDVGRPLSGSGISAFVQAHPSNGQR 44 1 O95835;O95835-2;H0YG09 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 HGPPLGESVAYHSESPNS(0.008)QT(0.002)DVGRPLS(0.736)GS(0.21)GIS(0.045)AFVQAHPSNGQR 187.24 1.83E-28 118570000 14644 26279 23961 20346 26402 21334 24394 20003 19720 TRUE FALSE 13727.45818 28224.7245 24529.36624 20868.11281 24328.49342 27492.77947 20736.34616 22500.41858 16428.6046 0.835582724 1.71802324 1.493088843 1.270230388 1.480861826 1.673470154 1.262209826 1.369587931 1 14.00392233 0.712657266 1.207666705 1.002512261 1.446004245 0.174277596 0.249593388 1.387393643 3.404822582 0.217544506 0.066577403 5.16008987 -0.712657266 0.443491984 HGQALGELAEQLEQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HGQALGELAEQLEQAR 16 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ; 228.84 3.74E-15 573400000 662660 762880 656620 732250 789800 530020 838090 685450 742250 FALSE TRUE 621185.2935 819364.429 672195.3365 751040.7747 727772.2939 683028.1698 712426.1849 771029.9414 618363.6799 1.004563033 1.325052644 1.08705501 1.214561591 1.176932471 1.104573558 1.152115184 1.246887498 1 19.23809606 -1.765272896 2.794314371 0.962613033 1.169449675 0.25049558 0.088685374 24359412.93 14739176.29 6153982.726 0.019063103 0.017168293 1.765272896 0.206836641 HGRPGIGATHS(ph)SR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HGRPGIGATHSSR 13 1 K7EM56;A0A0B4J2B4;S4R417;K7ELC2;P62841;K7EQJ5 K7EM56 RPS15 40S ribosomal protein S15 1 HGRPGIGAT(0.031)HS(0.945)S(0.025)R;HGRPGIGAT(0.028)HS(0.972)SR 92.575 0.0036294 34729000 14047.1 29217.4 24345.1 25188.3 34088 21840.1 28945.1 23381.6 45117 TRUE FALSE 13167.91709 31380.6867 24922.57727 25834.67442 31410.86598 28144.98233 24605.05097 26300.84423 37586.68123 0.350334657 0.834888468 0.663069376 0.687335875 0.835691393 0.748802007 0.654621535 0.699738401 1 15.19793392 -5 0.214894952 2.439537745 0.659619214 0.378635813 0.131759625 171.2516218 1.711518352 106.9562294 0.246513782 1.00E-05 5 -1.779918531 HGS(ph)DPAFAPGPR ddPTM_SK-BR-3_Pertuzumab_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 165.07 5.83E-05 3713830000 3957890 3384730 3376950 3224250 3633880 2631220 4140520 3122700 4190860 TRUE FALSE 3710172.73 3635338.931 3457052.849 3306989.714 3348489.723 3390810.5 3519687.465 3512575.969 3491378.392 1.062667037 1.041233153 0.990168484 0.947187426 0.959073852 0.971195362 1.00810828 1.006071406 1 21.73536529 4.08283514 1.831453833 0.981750508 1.058414978 0.678700527 0.019904466 0.239039962 1.509747136 0.005987211 0.020052868 12101.38671 -4.08283514 0.07666447 HGS(ph)FVNKPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HGSFVNKPTR 10 1 P29353-2;P29353-7;P29353;P29353-6;Q5T181;Q5T182 P29353-2 SHC1 SHC-transforming protein 1 1 HGS(1)FVNKPTR;HGS(1)FVNKPTR 78.469 0.018112 437250000 691260 611680 483250 598170 601000 261351 702720 416490 514610 TRUE FALSE 647995.2705 656969.4237 494712.9182 613520.0549 553799.8843 336798.791 597353.6597 468489.6933 428718.2665 1.511471102 1.53240362 1.153934779 1.431056484 1.291757146 0.785594684 1.393347815 1.092768211 1 18.70967036 8 0.203588588 1.023187806 3.679974375 0.445197099 0.17816766 48.55927799 0.593402568 0.296825073 41.41692657 100000000 -8 2.656786569 WTLGFCDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WTLGFCDER 9 0 M0R1L2;O95336;M0R0U3;M0R261 M0R1L2 PGLS 6-phosphogluconolactonase 0 ; 105.57 0.0071582 119115000 71858 112734 67188 66211 105467 63451 97718 92791 209130 FALSE TRUE 67360.53605 121080.9427 68781.73109 67910.08635 97184.04725 81768.27366 83066.09307 104376.1606 174224.852 0.386629894 0.69496941 0.39478714 0.389784153 0.557808178 0.469326119 0.476775225 0.599088818 1 17.4105909 0.804102146 2.854390005 0.999906448 0.492386402 0.753158215 0.092840363 0.461686202 5.863159048 0.086178245 0.022688907 6.369453132 -0.804102146 -0.507520046 HGS(ph)GADS(ph)DYENTQSGDPLLGLEGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGSGADSDYENTQSGDPLLGLEGKR 25 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 2 HGS(1)GADS(0.997)DY(0.003)ENTQSGDPLLGLEGKR 138.34 1.07E-05 53411000 71133 72074 55042 75745 86106 35173 75294 48169 125530 TRUE FALSE 66680.91251 77410.43395 56347.62223 77688.74494 79343.58209 45326.87411 64004.3637 54183.00568 104578.232 0.637617516 0.740215554 0.538808327 0.742876825 0.758700741 0.433425515 0.612023769 0.518109788 1 16.67422306 -1.069185562 5.050964481 1.000007476 0.624005028 0.556307867 0.105882538 8.55E-06 1.58E-06 0.098315185 0.023172651 0.085273569 1.069185562 -0.376002448 HGS(ph)GADSDYENTQSGDPLLGLEGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGSGADSDYENTQSGDPLLGLEGKR 25 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 HGS(0.991)GADS(0.009)DYENTQSGDPLLGLEGKR 178.69 1.35E-17 83074000 107120 101410 96230 109930 137910 66505 140400 87611 223510 TRUE FALSE 100415.5504 108918.5019 98512.62104 112750.9899 127079.1049 85703.91388 119348.3234 98549.42621 186204.7371 0.539274951 0.584939479 0.529055397 0.605521598 0.682469774 0.460267098 0.640952133 0.529253056 1 17.50653025 -1.741734085 2.708787176 1.085217101 0.573276594 0.821348829 0.062804581 14917267.89 11880754.44 8531004.251 0.014839789 0.018124495 1.741734085 -0.511940507 HGS(ph)GPPSSGGGLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HGSGPPSSGGGLYR 14 0 Q9HC52 Q9HC52 CBX8 Chromobox protein homolog 8 1 HGS(1)GPPSSGGGLYR;HGS(1)GPPSSGGGLYR;HGS(0.98)GPPS(0.014)S(0.005)GGGLYR;HGS(0.694)GPPS(0.247)S(0.058)GGGLYR 178.01 1.46E-07 704240000 340318 317566 327561 335211 344842 250195 360767 261968 333262 TRUE FALSE 319018.1039 341078.9171 335330.9016 343813.0818 317759.5003 322422.2349 306673.3375 294675.2815 277638.4192 1.149041637 1.228500429 1.207797186 1.238348362 1.14450839 1.16130266 1.104578172 1.061363489 1 18.08284769 1.486238061 0.817906075 1.001150429 1.20932641 0.856879076 0.028072304 0.176105107 0.244401406 0.023906498 0.009726277 30.6364233 -1.486238061 0.208175982 HGS(ph)PTAPICLGSPEFTDQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HGSPTAPICLGSPEFTDQGR 20 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 HGS(0.891)PT(0.109)APICLGSPEFTDQGR;HGS(0.979)PT(0.021)APICLGSPEFTDQGR;HGS(0.995)PT(0.005)APICLGSPEFTDQGR 225.34 3.33E-25 528550000 458497 397566 417645 434349 542128 357043 523770 385268 532906 TRUE FALSE 429800.4912 427002.2003 427551.7366 445495.1307 499551.4537 460115.518 445235.5509 433369.5579 443960.5459 0.968105151 0.961802134 0.963039938 1.003456579 1.125215874 1.036388306 1.002871888 0.976144304 1 18.76007195 3.09826855 4.716546323 1.030076376 0.964063428 0.35252755 0.039129185 0.225990812 8.59975433 0.011700792 0.014119341 1253.916306 -3.09826855 -0.066012948 HGS(ph)VSADEAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HGSVSADEAAR 11 0 A0A1B0GU90;A0A1B0GW73;H3BNF1;A0A1B0GTV3;A0A0S2Z5D0;H3BUV4;A0A1B0GUD2;H3BUT1;A0A1B0GTU6;Q9NWW5;Q9NWW5-2 A0A1B0GU90 CLN6 Ceroid-lipofuscinosis neuronal protein 6 1 HGS(0.999)VS(0.001)ADEAAR;HGS(0.997)VS(0.003)ADEAAR 147.33 3.71E-05 240160000 408950 349990 302020 347610 372640 245620 420280 354620 390220 TRUE FALSE 383354.5495 375903.6238 309184.057 356530.2611 343374.3576 316526.5067 357262.9157 398895.0876 325089.7611 1.179226772 1.156307177 0.951072885 1.096713289 1.056244763 0.9736588 1.098966988 1.227030609 1 18.31047859 -0.455240459 6.225239146 0.999998833 1.080574104 0.088901663 0.085835431 0 0 0.08074712 0.019032279 0.350557725 0.455240459 0.080575271 HGSAS(ph)QVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGSASQVQK 9 0 H0Y465;P21359-2;P21359-6;P21359;J3QSG6 H0Y465 NF1 Neurofibromin;Neurofibromin truncated 1 HGS(0.174)AS(0.826)QVQK 92.866 0.0063035 187530000 416150 326870 357900 387050 411860 304700 447370 320740 361070 TRUE FALSE 390103.9143 351071.7949 366389.557 396982.3583 379514.177 392661.9436 380291.0217 360785.095 300805.0844 1.296866092 1.16710725 1.218029801 1.319732873 1.261661443 1.305370035 1.264243995 1.199398261 1 18.19846943 -0.383784452 8.192714308 1.000000001 1.248686166 0.731097392 0.048323717 0 0 0.049470462 0.0116603 0.413252556 0.383784452 0.248686166 HGSGADS(ph)DYENTQSGDPLLGLEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGSGADSDYENTQSGDPLLGLEGK 24 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 HGS(0.478)GADS(0.522)DYENTQSGDPLLGLEGK 302.23 1.75E-62 486130000 858620 561730 664980 676310 653980 464280 849640 576800 682910 TRUE FALSE 804880.5069 603321.0737 680753.6396 693665.2596 602619.0488 598310.099 722244.3697 648814.7497 568927.9092 1.414731979 1.060452588 1.196555185 1.219249835 1.059218644 1.051644838 1.269483107 1.140416456 1 19.11788633 -4.999999999 0.021449652 1.79E-06 1.953432817 0.261271042 0.106976926 5276.864545 8.563493361 536.7747092 281.1982183 1.00E-05 4.999999999 1.95343103 HGSGADSDYENT(ph)QSGDPLLGLEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGSGADSDYENTQSGDPLLGLEGK 24 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 HGS(0.194)GADS(0.233)DY(0.233)ENT(0.339)QSGDPLLGLEGK 87.802 0.040824 184830000 233870 155230 222240 187490 224930 133960 226530 163310 232560 TRUE FALSE 219232.4942 166723.3907 227511.6377 192301.3108 207264.9051 172632.0773 192563.9295 183699.613 193744.2336 1.131556228 0.860533434 1.174288563 0.992552435 1.069786188 0.891030789 0.993907927 0.948155254 1 17.56379385 2.255228391 24.98621857 0.959254772 1.035598589 0.191149275 0.088034775 440.9250248 660977.6937 0.028903545 0.024118772 179.9817172 -2.255228391 0.076343817 HGSLGFLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HGSLGFLPR 9 0 P39023;H7C422;H7C3M2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ; 105.52 0.0030845 971510000 349680 1010510 590070 570980 1046970 606220 451110 819530 874300 FALSE TRUE 327794.153 1085329.212 604066.7391 585632.3135 964745.1995 781225.8728 383470.2434 921850.1245 728373.6818 0.450035691 1.490071977 0.829336307 0.804027284 1.324519575 1.072561918 0.526474601 1.265627998 1 19.47431927 HGSYEDAVHSGALND ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HGSYEDAVHSGALND 15 0 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;; 277.31 1.42E-33 1724300000 776560 1688830 1455770 1531240 1440880 1424830 1795200 1524880 1321240 FALSE TRUE 727956.4958 1813872.73 1490301.552 1570534.211 1327719.097 1836155.291 1526026.426 1715264.625 1100716.508 0.66134785 1.647901813 1.353937676 1.426828978 1.206231656 1.6681455 1.386393694 1.558316434 1 20.07001152 4.748564502 24.92764503 1.432416089 0.661347411 0.572193351 0.201192174 866.6666085 2159511.686 0.041612909 0.56597388 56048.56557 -4.748564502 -0.771068678 HGT(ph)PDPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGTPDPSPR 9 0 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 HGT(1)PDPS(1)PR 71.548 0.087429 54607000 72731 51743 52378 53648 56211 42247 72038 49298 63661 TRUE FALSE 68178.89654 55574.10556 53620.43089 55024.69851 51796.4148 54443.02308 61236.57067 55452.96382 53035.56783 1.285531565 1.047864817 1.011027751 1.037505598 0.976635434 1.02653795 1.15463213 1.045580656 1 15.69467259 4.738415849 6.546790592 1.042911963 1.290232428 0.731126887 0.047183478 0.06933166 18.4876988 0.012281817 0.076171106 54753.99964 -4.738415849 0.247320465 HGTDLWIDNMSSAVPNHS(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HGTDLWIDNMSSAVPNHSPEK 21 0 Q8N6H7;E9PIY6;H0YF45;E9PJT7;E9PK28;E9PN48 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 HGTDLWIDNMSSAVPNHS(1)PEK;HGTDLWIDNMSSAVPNHS(1)PEK 196.8 1.58E-21 212810000 531600 360440 467950 462590 403980 363600 581370 338360 340400 TRUE FALSE 498328.1049 387127.3526 479049.995 474460.8426 372253.0404 468565.4174 494198.9657 380604.9908 283585.0409 1.757243976 1.365119089 1.68926398 1.673081348 1.312668112 1.652292434 1.742683479 1.342119421 1 18.11342191 0.973810331 5.339613763 1.000277214 1.586844677 0.630624857 0.149162866 0.110066616 12.37085151 0.13757831 0.034709847 9.414783353 -0.973810331 0.586567463 HGTDLWIDNMSSAVPNHS(ph)PEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 HGTDLWIDNMSSAVPNHSPEKK 22 1 Q8N6H7;E9PIY6;H0YF45;E9PJT7;E9PK28;E9PN48 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK 260.97 1.31E-37 7569850000 7753440 4944590 6299160 6518500 6250030 3978246 7367750 4433077 6677010 TRUE FALSE 7268166.031 5310692.588 6448579.05 6685775.746 5759177.855 5126701.039 6263024.286 4986556.422 5562573.896 1.306619232 0.954718569 1.159279709 1.201921246 1.035344062 0.921641876 1.125921993 0.896447672 1 22.40732117 2.496830929 22.5205254 1.004040415 1.122343868 0.339486715 0.106973324 313.0215494 357663.0539 0.033291287 0.030905741 313.9286333 -2.496830929 0.118303453 HGVESTLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HGVESTLER 9 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;; 173.75 5.52E-05 2356530000 865824 1057840 847995 872092 952490 769450 908202 849149 1069455 FALSE TRUE 811633.6214 1136163.574 868109.8419 894471.3572 877685.2776 991577.724 772025.5414 955167.1219 890956.0516 0.910969312 1.275218427 0.974357647 1.003945543 0.985105018 1.112936741 0.866513606 1.072069851 1 19.76499474 3.73183201 24.54032758 0.994981725 1.120814599 0.094749434 0.107942396 236.0460885 1229648.329 0.025104587 0.043427242 5393.019738 -3.73183201 0.125832874 HGVIVAADSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HGVIVAADSR 10 0 P28074;H0YJM8;P28074-2 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;;; 123.63 0.00045709 2908600000 1469970 2324950 1364320 1284530 2211560 875884 1427520 2038980 1829400 FALSE TRUE 1377967.202 2497091.717 1396682.315 1317493.215 2037872.999 1128737.492 1213476.628 2293551.141 1524061.322 0.904141574 1.638445699 0.916421337 0.864462076 1.337133204 0.740611599 0.796212469 1.504894264 1 20.53948952 3.777259263 7.024046273 0.991758642 1.312757842 0.098832288 0.294255343 0.356216902 40.70686506 0.07007194 0.126207699 5987.68939 -3.777259263 0.320999201 HGVYNPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HGVYNPNK 8 0 P40926;G3XAL0 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 ;;; 141.78 0.00062799 1728590000 2281210 5198440 1498380 1640410 6899110 1325110 1815220 5399640 6801870 FALSE TRUE 2138433.138 5583337.907 1533922.281 1682505.698 6357281.73 1707647.746 1543044.613 6073796.94 5666593.955 0.377375396 0.985307568 0.270695641 0.29691658 1.121887642 0.301353469 0.272305485 1.071860272 1 22.4340504 1.222340766 24.97114214 1.035930745 0.528900866 0.335853175 0.302505864 323.614494 498204.2314 0.278255096 0.070425276 16.68555917 -1.222340766 -0.507029879 HGWQIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGWQIER 7 0 O15541 O15541 RNF113A RING finger protein 113A 0 93.374 0.014982 84460000 73324 252520 235670 256060 260520 249820 180190 201170 169730 FALSE TRUE 68734.78173 271216.8435 241260.2037 262630.9331 240059.8101 321938.9785 153172.1823 226286.5173 141400.9665 0.486098387 1.918069234 1.706213258 1.857348925 1.697723969 2.276780608 1.083247067 1.600318038 1 17.10943246 1.136252393 1.348994379 1.062629242 1.678662606 0.100606879 0.494552462 0.75849725 2.760146795 0.420146664 0.129158319 13.68523921 -1.136252393 0.616033364 HGYIGEFEIIDDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 HGYIGEFEIIDDHR 14 0 P62244;I3L3P7;I3L246;H3BN98 P62244 RPS15A 40S ribosomal protein S15a 0 ;;;;;;;; 213.18 8.07E-10 21886510000 6669898 7330207 7248683 7277645 7408373 6121663 8022453 6435702 6446952 FALSE TRUE 6252440.99 7872943.153 7420625.184 7464401.692 6826549.269 7888887.731 6819560.649 7239213.561 5370914.062 1.164129777 1.46584791 1.381631711 1.389782373 1.271021876 1.4688166 1.269720679 1.347855035 1 22.35673621 -0.246804432 0.628671351 0.970995784 1.36962999 0.564888878 0.094021916 4.657786062 1.717269581 0.410158847 0.032880662 0.56649433 0.246804432 0.398634206 HHEDNLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HHEDNLLR 8 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;; 110.87 0.0033424 869460000 375776 597410 443540 498600 518340 495430 540960 474340 448170 FALSE TRUE 352256.8509 641642.858 454060.9783 511394.9201 477631.6673 638452.5984 459848.07 533562.3932 373367.5317 0.943458713 1.718528805 1.216123363 1.369682355 1.279253354 1.709984249 1.231623082 1.429054076 1 18.51023695 -1.084724363 4.407812191 0.999979785 1.383056951 0.191874735 0.230105839 13743136.76 3384498.098 4684.017879 0.047179396 0.082276467 1.084724363 0.383077167 HHEEEIVHHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HHEEEIVHHK 10 0 Q9UII2 Q9UII2 ATPIF1 "ATPase inhibitor, mitochondrial" 0 ; 162.36 3.93E-06 277850000 282480 216339 246200 220494 287000 196358 230633 235780 305700 FALSE TRUE 264800.081 232356.9647 252039.9803 226152.2493 264460.1777 253043.367 196051.7227 265217.652 254676.6951 1.03974995 0.912360531 0.989646815 0.887997425 1.038415304 0.993586661 0.769806294 1.041389562 1 17.95830742 HHEEEIVHHKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HHEEEIVHHKK 11 1 Q9UII2 Q9UII2 ATPIF1 "ATPase inhibitor, mitochondrial" 0 ;; 165.66 8.68E-06 525010000 743310 592730 601670 601010 844250 486960 721140 565790 1424350 FALSE TRUE 696787.5539 636616.3459 615941.8965 616432.9341 777946.0105 627537.4469 613011.7517 636430.127 1186616.783 0.587205207 0.536497001 0.51907398 0.519487793 0.65560004 0.528845922 0.516604653 0.536340069 1 20.17842266 -1.380314682 5.197686869 1.000273485 0.545154036 0.915783564 0.042868271 0.00013085 1.56E-05 0.039977303 0.009417181 0.041656744 1.380314682 -0.45511945 HHFETLT(ph)ESPCRELFPAALGDVEASEAEDHFFNPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HHFETLTESPCRELFPAALGDVEASEAEDHFFNPR 35 1 O43379-4 O43379-4 WDR62 WD repeat-containing protein 62 1 HHFET(0.1)LT(0.522)ES(0.378)PCRELFPAALGDVEASEAEDHFFNPR 181.18 2.01E-20 68841000 29010 49460 32921 40037 80833 23047 39751 42314 152690 TRUE FALSE 27194.31588 53122.06986 33701.90167 41064.4172 74484.70224 29700.29476 33790.70658 47596.99604 127205.0526 0.2137833 0.417609747 0.264941533 0.322820646 0.5855483 0.233483609 0.265639657 0.374175358 1 16.95679645 0.942655497 20.25974215 1.000000001 0.331058886 0.791243752 0.107625616 765.0379698 270288.097 0.097492547 0.024373137 8.76305419 -0.942655497 -0.668941115 HHFETLTES(ph)PCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HHFETLTESPCR 12 0 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 HHFETLTES(1)PCR;HHFETLTES(1)PCR 205.28 6.67E-08 726280000 523290 573910 533640 493640 612110 474660 619750 512480 697370 TRUE FALSE 490538.213 616402.8936 546298.1928 506307.6381 564037.3497 611686.6365 526824.241 576464.2561 580974.4418 0.844336993 1.060981085 0.940313641 0.871480054 0.970847096 1.052863246 0.906794177 0.99223686 1 19.14811517 2.492465301 24.88502505 0.979550641 0.949877336 0.10958536 0.067468316 2562.603054 4156040.719 0.022061905 0.020228951 310.7887584 -2.492465301 -0.029673305 HHGDVMDLQFFDQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HHGDVMDLQFFDQER 15 0 Q8NFH3;B4E301;F5H0E3;B4DVD1;Q8NFH3-2 Q8NFH3 NUP43 Nucleoporin Nup43 0 122.27 6.36E-05 60717000 52888 53425 54853 60793 50874 48823 60032 41512 64277 FALSE TRUE 49577.83449 57380.64259 56154.13906 62353.0513 46878.56126 62917.40752 51030.75891 46694.86458 53548.75345 0.925844792 1.071558886 1.048654459 1.164416486 0.875437022 1.174955596 0.952977532 0.872006565 1 15.70856537 1.559478337 8.718121073 0.929136423 1.046753488 0.199554567 0.096137613 0.153819252 20.08695712 0.045405242 0.021194502 36.26421967 -1.559478337 0.117617065 HHGKDS(ph)DKEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HHGKDSDKEER 11 2 Q92766;Q92766-2;Q92766-5;Q92766-3;A0A087X055;Q92766-4 Q92766 RREB1 Ras-responsive element-binding protein 1 1 HHGKDS(1)DKEER;HHGKDS(1)DKEER;HHGKDS(1)DKEER;HHGKDS(1)DKEER 188.59 1.46E-06 130381000 217930 97017 128352 108944 82911 74535 172406 71434 112039 TRUE FALSE 204290.1503 104200.2396 131396.5701 111739.6875 76399.50451 96052.04453 146555.3208 80352.69215 93338.9671 2.188690926 1.116363753 1.40773542 1.197138676 0.818516713 1.029066932 1.570140804 0.860869738 1 16.51019188 4.740578817 24.7907718 1.174706976 2.188691317 0.66725935 0.233732083 102.2131815 1255444.253 0.054667418 0.358763006 55027.37765 -4.740578817 1.013984341 HHGPQTLYLPVTLSSIPVFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HHGPQTLYLPVTLSSIPVFQR 21 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 148.91 4.95E-08 337490000 309250 551340 349980 291980 517910 236950 407650 457790 281710 FALSE TRUE 289894.5945 592161.7873 358281.6909 299472.7011 477235.4377 305353.6184 346526.6669 514946.0892 234690.7811 1.235219352 2.523157427 1.526611694 1.276030953 2.033464781 1.301089106 1.476524409 2.194147068 1 17.84040165 -2.626671827 0.16325592 1.97E-13 1.94347157 0.137852388 0.448309226 90.15081422 1.731478082 36.58753407 1.939683211 0.002362263 2.626671827 1.94347157 HHGT(ph)PTSTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HHGTPTSTKK 10 1 H0Y9P1;Q9NSY1 H0Y9P1 BMP2K BMP-2-inducible protein kinase 1 HHGT(1)PTSTKK;HHGT(0.999)PTSTKK 169.23 3.58E-06 197580000 252511 214662 228226 257294 285080 157598 328180 230378 420340 TRUE FALSE 236706.7873 230555.7978 233639.6285 263896.5996 262690.9668 203093.9842 278972.4557 259141.2004 350182.5385 0.675952571 0.658387476 0.667193828 0.753597255 0.750154385 0.579966052 0.796648676 0.740017482 1 18.41774762 -5 0.200255666 2.400132319 0.649040124 0.740630629 0.056967475 66.7619333 0.661060601 37.23503402 0.126587482 1.00E-05 5 -1.751092195 GFGSDKEAILDIITSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GFGSDKEAILDIITSR 16 1 E5RK69;P08133;P08133-2;E7EMC6;E5RFF0;E5RJF5;E5RK63;E5RIU8;E5RJR0;E5RI05 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ; 208.2 1.41E-11 775080000 1638500 1555400 1566740 1341630 2467320 935470 2153500 2008830 4573600 FALSE TRUE 1535949.21 1670563.434 1603903.813 1376058.497 2273546.64 1205525.003 1830602.667 2259636.847 3810236.613 0.403111241 0.438440864 0.420945987 0.361147781 0.596694345 0.316391113 0.480443304 0.593043707 1 21.86144916 0.805827989 1.775240449 0.999418076 0.426971057 0.860420874 0.072557477 0.211380618 1.18631754 0.060370805 0.017068603 6.394815066 -0.805827989 -0.572447019 HHHHDSDSNSPCCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HHHHDSDSNSPCCK 14 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 0 100.19 0.0006548 14867000 7756.8 28880 20966 29107 26662 20032 30391 21100 25157 FALSE TRUE 7271.315734 31018.30525 21463.32342 29853.9349 24568.07407 25814.91321 25834.15169 23734.38145 20958.13418 0.346944803 1.480012724 1.024104686 1.424455757 1.17224529 1.231737185 1.232655134 1.132466337 1 14.35522266 4.748985436 24.91024746 1.22503869 0.34694429 0.762167519 0.151751094 616.142688 1472250.994 0.031835768 0.453050526 56102.91619 -4.748985436 -0.8780944 HHIEVLHYLLQS(ph)WPDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HHIEVLHYLLQSWPDPR 17 0 M0QXZ8;Q6ZW31-2;Q6ZW31 M0QXZ8 SYDE1 Rho GTPase-activating protein SYDE1 1 HHIEVLHY(0.433)LLQS(0.567)WPDPR 53.995 0.084143 684630000 178220 682520 515920 582030 693070 523330 446120 532930 608350 TRUE FALSE 167065.5283 733054.491 528157.866 596965.8752 638639.0779 674406.8754 379228.4476 599467.4836 506812.4549 0.329639745 1.446401887 1.042116982 1.177883198 1.260109281 1.330683311 0.748261894 1.182819163 1 18.95109245 1.742435493 25 0.958100027 1.140926787 0.018296299 0.317827564 1.93191798 12526.50649 0.132992979 0.073751433 55.26313176 -1.742435493 0.182826761 HHISIAEIYETELVDIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HHISIAEIYETELVDIEK 18 0 P54920;M0R0Y2;M0R2M1;M0R058;M0R0I4;M0R027 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;;;; 207.5 4.25E-16 618675000 464077 770870 778596 822690 843562 678787 1079053 735017 874677 FALSE TRUE 435031.249 827946.0169 797064.6648 843801.6182 777312.0433 874741.7877 917259.0201 826785.4904 728687.7581 0.597006391 1.136215077 1.093835674 1.157974192 1.066728561 1.200434312 1.258781982 1.134622451 1 19.47494123 4.738738244 6.957852935 1.143789579 0.588683609 0.846283892 0.071357347 0.040223931 14.60841726 0.017140813 0.104944202 54794.66094 -4.738738244 -0.55510597 HHLGDDVVLFTTDGAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HHLGDDVVLFTTDGAHK 17 0 P16278-3;P16278;C9J4G9;C9J539 P16278-3 GLB1 Beta-galactosidase 0 ; 68.944 0.012446 143045000 232475 260290 247310 245970 263540 197478 304680 227088 322690 FALSE TRUE 217924.8047 279562.1424 253176.31 252282.0066 242842.6315 254486.6928 258996.0625 255440.4367 268830.9543 0.810638809 1.039917978 0.941767702 0.938441063 0.903328384 0.946642076 0.963416074 0.950189822 1 18.03633974 0.536040045 1.004974135 0.99986432 0.94495646 0.095972592 0.056901446 4.330288835 6.448696954 0.051531553 0.016336603 3.435896276 -0.536040045 -0.05490786 HHNQSTAINLNNPESQSMHLETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HHNQSTAINLNNPESQSMHLETR 23 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 105.51 0.00053307 299410000 223300 219070 198420 164930 187150 148690 269820 232570 298140 FALSE TRUE 209324.0516 235290.1707 203126.6161 169162.383 172451.9939 191614.3892 229362.9959 261606.8764 248378.5079 0.842762336 0.947304872 0.817810759 0.68106691 0.694311256 0.77146123 0.923441395 1.05325891 1 17.92218082 1.516288103 3.487004993 1.022003453 0.80578113 0.61749997 0.076576012 0.171651577 4.464123879 0.060856987 0.023416183 32.83130175 -1.516288103 -0.216222323 HHPEDVEPALRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HHPEDVEPALRK 12 1 P14550;Q5T621;V9GYP9;V9GYG2 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ; 71.555 0.018006 577290000 961190 1054120 1025960 1078510 1246600 811730 1159640 994530 1512620 FALSE TRUE 901030.8337 1132168.142 1050296.256 1106186.393 1148697.065 1046063.274 985762.7476 1118699.26 1260153.95 0.715016474 0.898436371 0.833466622 0.877818454 0.911552961 0.830107523 0.782255809 0.887748088 1 20.26516856 -3.151802968 1.097860674 3.863054607 0.844296745 0.41396274 0.059013232 72919.87946 1320.295089 517756.3363 0.01636787 0.000705013 3.151802968 -3.018757862 HHPLHDFILELYQTGSTEPVEVPPELCHGIQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HHPLHDFILELYQTGSTEPVEVPPELCHGIQGK 33 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 118.61 4.81E-07 145160000 222110 208400 205240 181810 254130 165840 252880 212780 243960 FALSE TRUE 208208.5316 223830.1528 210108.3897 186475.5524 234171.6549 213715.3158 214962.9916 239346.0514 203241.5 1.024439062 1.101301422 1.033786848 0.917507263 1.152184249 1.051533844 1.057672728 1.177643599 1 17.63283549 HHQEEDAGPTQPS(ph)PAKPQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HHQEEDAGPTQPSPAKPQLK 20 1 Q9C086;B8ZZ93;B8ZZH7;F8WCL7;J3KQ70;H7C171;C9JKY0 Q9C086 INO80B;INO80B-WBP1 INO80 complex subunit B 1 HHQEEDAGPT(0.001)QPS(0.999)PAKPQLK 124.31 1.64E-05 203760000 178460 96956 123600 106480 102670 69907 150180 101930 128680 TRUE FALSE 167290.5072 104134.7231 126531.8504 109212.4571 94606.71235 90088.01605 127661.9032 114656.1849 107202.4767 1.560509723 0.971383557 1.180307156 1.018749384 0.882504913 0.840353869 1.19084845 1.069529254 1 16.70997871 4.742561506 24.94975878 1.031871306 1.560509933 0.697195227 0.111833731 239.8934447 1495929.25 0.027315231 0.210268567 55279.16901 -4.742561506 0.528638627 HHTAAFEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HHTAAFEER 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 137.95 0.0001502 205590000 92547 168280 112420 123110 144190 59767 95517 142050 92141 FALSE TRUE 86754.64847 180739.6263 115086.6555 126269.211 132865.899 77020.76266 81195.11259 159785.2552 76762.07185 1.130175963 2.354543356 1.499264581 1.644942717 1.730879533 1.003370034 1.057750405 2.081565171 1 16.22810603 2.260674641 23.66330358 1.255294266 1.740263306 0.154471512 0.430398945 181.0599807 193743.7877 0.14110791 0.11794424 182.2529814 -2.260674641 0.48496904 HHVLHDQNVDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HHVLHDQNVDKR 12 1 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;E9PFG7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 ; 206.69 3.55E-08 216580000 105647 82276 73489 71853 106272 74207 86967 89148 170269 FALSE TRUE 99034.74286 88367.80065 75232.19378 73696.86963 97925.8258 95629.35625 73927.10571 100278.324 141850.0039 0.698165246 0.622966501 0.530364411 0.519540836 0.690347713 0.674158291 0.521163931 0.70693212 1 17.11400666 0.925311372 5.922255609 0.999983482 0.601444695 0.767609072 0.067699754 0.289721304 22.30304711 0.064232166 0.016157207 8.419986045 -0.925311372 -0.398538787 HHYDS(ph)DEKSETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HHYDSDEKSETR 12 1 Q9BQ39 Q9BQ39 DDX50 ATP-dependent RNA helicase DDX50 1 HHYDS(1)DEKSETR;HHYDS(1)DEKSETR;HHYDS(0.976)DEKS(0.024)ETR 211.7 1.74E-08 4448324000 3644290 2791971 3041409 3277189 3068659 2707594 3799525 2372382 2474299 TRUE FALSE 3416200.394 2998691.438 3113552.658 3361287.218 2827658.901 3489232.434 3229821.499 2668579.115 2061322.512 1.657285735 1.454741517 1.510463617 1.630645956 1.371769281 1.692715435 1.56686859 1.294595629 1 20.97513881 0.989753744 3.227403789 1.001860597 1.544482181 0.783921251 0.095863199 0.097588318 2.538132255 0.08568614 0.022379929 9.766832599 -0.989753744 0.542621584 HHYEQQQEDLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HHYEQQQEDLAR 12 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y7I0;A0A2R8Y5M9;A0A2R8YE38;K7EMY3;Q12873-3;Q12873;Q12873-2;A0A5F9ZHX5 Q14839-2;Q12873-3 CHD4;CHD5;CHD3 Chromodomain-helicase-DNA-binding protein 4;Chromodomain-helicase-DNA-binding protein 3 0 ; 156.69 3.79E-05 361210000 94450 110640 110608 108312 121617 82269 127015 95008 118402 FALSE TRUE 88538.5431 118831.9007 113231.674 111091.4693 112065.6914 106018.7248 107970.2799 106869.9579 98639.94129 0.897593226 1.204703685 1.147929252 1.126232111 1.136108659 1.07480523 1.094589864 1.08343493 1 16.58988432 0.778806527 0.733563477 1.000392737 1.121257464 0.086758687 0.081304574 1.734245161 1.898987316 0.075273155 0.027596948 6.009059812 -0.778806527 0.120864728 HHYPGCINLSFAYVEGESLLMALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HHYPGCINLSFAYVEGESLLMALK 24 0 H0YGN5;Q9Y697-2;Q9Y697-3;Q9Y697 H0YGN5 NFS1 "Cysteine desulfurase, mitochondrial" 0 71.174 0.017464 12152000 12498 15432 9987.9 11060 19709 11803 12453 12454 9295.1 FALSE TRUE 11715.77249 16574.60134 10224.8177 11343.81832 18161.13464 15210.33449 10585.78826 14008.90931 7743.687761 1.512944846 2.140401556 1.320406765 1.464911638 2.345282403 1.964223631 1.367021577 1.809074661 1 12.91880507 0.155504654 0.838904586 0.990131918 1.7533826 0.317195915 0.338644329 4.900532883 3.836604446 0.467361294 0.10903615 1.430555312 -0.155504654 0.763250682 HIADLAGNSEVILPVPAFNVINGGSHAGNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HIADLAGNSEVILPVPAFNVINGGSHAGNK 30 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90;A0A2R8YEM5 P06733 ENO1 Alpha-enolase;Enolase 0 ;;; 273 2.89E-71 13007304000 12016046 12297975 11490638 10749507 14258090 7858785 13791180 12026827 15000370 FALSE TRUE 11263983.13 13208529.87 11763201.36 11025357.55 13138317.13 10127488.65 11723320.59 13528402.83 12496711.34 0.901355791 1.056960468 0.941303759 0.88226072 1.05134197 0.810412306 0.938112458 1.082557039 1 23.57504515 1.251075977 24.98409128 1.041278519 0.946763268 0.232587209 0.075576755 300.6094457 600106.1803 0.049402741 0.017764633 17.82690612 -1.251075977 -0.09451525 HIADLAGNSEVILPVPAFNVINGGSHAGNKLAMQEFMILPVGAANFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HIADLAGNSEVILPVPAFNVINGGSHAGNKLAMQEFMILPVGAANFR 47 1 P06733;A0A2R8Y6G6;P06733-2;K7EM90 P06733 ENO1 Alpha-enolase;Enolase 0 77.804 0.00018401 89165000 44430 57788 122510 123060 96745 225440 102340 28838 31328 FALSE TRUE 41649.20561 62066.68365 125415.9951 126217.9279 89147.03795 290520.8683 86995.06708 32438.48778 26099.15441 1.595806705 2.378110902 4.805366222 4.836092616 3.415705986 11.13142839 3.333252323 1.242894205 1 14.67171545 4.170569059 1.797971559 4.684709813 1.625415216 0.08888726 2.79984165 0.808500359 4.774156368 0.727431567 2.860545486 14810.47744 -4.170569059 -3.059294598 HIAEDADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 179.68 0.00024309 7783190000 2834774 3488990 2903850 3201440 3855200 2524920 2989720 2978770 3125370 FALSE TRUE 2657350.556 3747318.45 2972730.693 3283594.37 3552428.143 3253823.415 2541439.241 3350675.992 2603725.556 1.020595488 1.439214068 1.141721978 1.261113854 1.364363512 1.24967987 0.976078003 1.28687756 1 21.31214596 1.769484528 25 1.087785484 1.261475147 0.21855601 0.139245081 33.63973619 27209.87325 0.057909802 0.032122125 58.81451606 -1.769484528 0.173689663 HIAEEADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 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 ;;;;;;;;; 168.27 0.00030783 9367692000 2221664 2562732 2393165 2395924 2487120 1987519 2523722 2187045 2363325 FALSE TRUE 2082614.016 2752479.344 2449932.004 2457407.466 2291791.628 2561283.471 2145313.315 2460102.383 1968870.79 1.057770793 1.397998974 1.244333562 1.24813039 1.16401322 1.300889568 1.089616102 1.249499152 1 20.908937 0.374366223 0.368973402 0.967815234 1.272968336 0.292987176 0.100889164 3.077777221 0.763227186 0.279383952 0.079166352 2.367915626 -0.374366223 0.305153102 HIAEEADRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HIAEEADRK 9 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;P06753-7;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;P67936;P67936-2 TPM3;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-4 chain 0 ;;; 132.01 0.00020582 2970540000 2362850 1972500 2051900 2098600 2306110 1489330 2569320 1794490 2406590 FALSE TRUE 2214963.436 2118545.952 2100572.037 2152453.629 2124997.423 1919275.394 2184074.318 2018536.027 2004914.582 1.104766984 1.056676415 1.047711487 1.073588695 1.059894243 0.957285368 1.089360284 1.006794028 1 20.93510934 8 0.132627689 0.992990208 1.304958016 0.337243475 0.036298693 104.7570386 0.936017204 0.167382765 6.138365547 100000000 -8 0.311967808 HIANYISGIQTIGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HIANYISGIQTIGHR 15 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 146.27 2.26E-06 548460000 114910 148270 131460 140550 163160 120070 145290 130870 141640 FALSE TRUE 107717.9882 159248.0651 134578.2933 144156.751 150346.0718 154732.2598 123505.1133 147209.4076 117999.369 0.912869189 1.349567091 1.14050011 1.221673914 1.274126066 1.31129735 1.0466591 1.247544024 1 16.84841962 -1.090429444 6.032566534 0.999999361 1.196175163 0.169051743 0.129899333 1.00E-06 1.51E-07 0.112719395 0.026568129 0.081202716 1.090429444 0.196175803 HIDCAAIYGNEPEIGEALKEDVGPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HIDCAAIYGNEPEIGEALKEDVGPGK 26 1 P14550;Q5T621;V9GYP9;V9GYG2 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ; 255.94 7.74E-53 541700000 672190 407533 480260 490930 543810 355729 656430 459219 696170 FALSE TRUE 630118.8278 437707.1674 491651.994 503528.0949 501101.3562 458422.1875 558004.4155 516553.503 579974.7296 1.086459109 0.754700412 0.847712786 0.868189715 0.8640055 0.79041752 0.962118498 0.890648293 1 19.14563052 1.673004242 8.671401572 0.9442397 0.853010713 0.137062086 0.091192785 0.195648762 24.39757067 0.040595369 0.02148426 47.09819265 -1.673004242 -0.091228987 HIDFSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 HIDFSLR 7 0 P46781 P46781 RPS9 40S ribosomal protein S9 0 ;;;;;; 157.21 0.0014914 3804950000 715460 1482110 734809 830201 1700648 538470 664547 1334743 1209596 FALSE TRUE 670680.6357 1591846.967 752239.0165 851505.3632 1567085.966 693917.5477 564904.3467 1501388.602 1007706.613 0.665551488 1.579673037 0.746486136 0.844993326 1.555101401 0.688610691 0.560584141 1.489906469 1 19.94264424 HIDIHPENTHILDGNAVDLQAECDAFEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HIDIHPENTHILDGNAVDLQAECDAFEEK 29 0 D6RAY7;D6R9P4;D6RFF8;P46926;D6R917;D6RB13 D6RAY7 GNPDA1 Glucosamine-6-phosphate isomerase;Glucosamine-6-phosphate isomerase 1 0 168.26 1.24E-12 212290000 142420 98568 108960 103600 123970 96053 167610 97607 160900 FALSE TRUE 133506.1864 105866.0773 111544.5827 106258.5514 114233.8963 123781.9418 142478.4365 109793.4488 134044.7505 0.995982207 0.789781598 0.832144356 0.792709531 0.852207161 0.923437444 1.062916943 0.819080556 1 17.0323552 2.146682709 3.791027064 0.972566317 0.837999154 0.251233191 0.083242009 0.235316824 6.493478443 0.030755356 0.021942539 140.1789199 -2.146682709 -0.134567163 HIDLVEGDEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HIDLVEGDEGR 11 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;; 150.06 3.41E-05 5064870000 3619650 4020630 4112860 3587140 3778310 3019900 3880320 3578660 4403930 FALSE TRUE 3393102.568 4318321.629 4210418.981 3679192.085 3481576.774 3891696.106 3298502.039 4025463.579 3668885.633 0.924831927 1.177011785 1.147601589 1.002809151 0.948946662 1.060729741 0.899047386 1.097189714 1 21.8069105 3.184813624 7.408060797 0.991013456 1.112338899 0.13157943 0.086366233 0.256696824 29.51645626 0.023382634 0.028162345 1530.430542 -3.184813624 0.121325443 HIDMVEGDEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HIDMVEGDEGR 11 0 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 ;;;; 153.34 3.25E-05 1474640000 1366860 1855225 1743180 1989496 2086917 1328089 2042322 1581992 1808971 FALSE TRUE 1281310.673 1992587.789 1784529.053 2040549.836 1923018.957 1711486.735 1736094.776 1779507.184 1507042.054 0.850215606 1.322184596 1.184126912 1.354009884 1.276022094 1.135659573 1.151988275 1.180794643 1 20.52328824 0.604857665 0.814915595 1.000793617 1.210373272 0.127741665 0.139439412 2.272664364 2.582060513 0.127438431 0.043108832 4.025850702 -0.604857665 0.209579656 HIDSSPYSPAYLS(ph)PPPESSWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HIDSSPYSPAYLSPPPESSWR 21 0 Q53ET0;H0YDQ8 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 HIDSSPYSPAYLS(1)PPPESSWR;HIDSSPYSPAYLS(1)PPPESSWR 282.86 2.63E-45 488120000 189238 266590 235340 305930 322050 181347 207340 186026 210780 TRUE FALSE 177393.9314 286328.601 240922.3759 313780.6817 296757.4921 233698.935 176251.2919 209251.7556 175599.4563 1.010219138 1.630577947 1.371999555 1.786911465 1.689968171 1.330863659 1.003712059 1.191642389 1 17.42192885 1.947738728 4.422058112 1.078803069 1.512843181 0.453572247 0.215794216 0.187511011 7.485352678 0.092952488 0.05559774 88.66224582 -1.947738728 0.434040112 HIEALLGS(ph)PCGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HIEALLGSPCGK 12 0 P49589-3;E9PLP0 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 1 HIEALLGS(1)PCGK 103.88 0.0014163 84930000 42283 71359 72049 63963 66462 60548 69611 64343 60928 TRUE FALSE 39636.58251 76642.49461 73758.0363 65604.39887 61242.34261 78027.22469 59173.47679 72376.36519 50758.72319 0.780882182 1.509937402 1.453110553 1.292475357 1.206538281 1.537218034 1.165779458 1.425890185 1 15.63136816 -1.035586377 4.707367295 0.999990604 1.325664654 0.138762689 0.221771337 1.98E-05 4.05E-06 0.194019516 0.04572952 0.092132663 1.035586377 0.32567405 HIEIFTDLSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HIEIFTDLSSR 11 0 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;; 202.65 3.93E-08 1546740000 1461820 1736230 1600420 1657880 1790400 1342800 1716530 1561960 1671920 FALSE TRUE 1370327.296 1864782.276 1638382.718 1700424.008 1649789.206 1730444.561 1459152.262 1756974.144 1392865.751 0.983818645 1.33880977 1.176267502 1.220809691 1.184456725 1.242362776 1.047590021 1.261409539 1 20.40962478 -0.419645818 0.386536905 0.951252513 1.208064196 0.195446429 0.104795839 10.44247417 1.602036891 0.789852219 0.068415352 0.380499581 0.419645818 0.256811684 HIELGVT(ph)GGGSPENGDGALLAITPPAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HIELGVTGGGSPENGDGALLAITPPAVK 28 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 HIELGVT(0.5)GGGS(0.5)PENGDGALLAITPPAVK 103.15 0.0039714 67844000 91082 76457 86070 82164 103540 75642 113760 88142 105420 TRUE FALSE 85381.34021 82117.95583 88111.62105 84272.46734 95408.38606 97478.61745 96702.7441 99146.72272 87824.72096 0.972178895 0.935020971 1.003266735 0.959552919 1.086350005 1.109922313 1.101087974 1.128915887 1 16.42233947 2.719613517 6.768179799 1.09461411 0.96793227 0.702230902 0.037834701 0.080508206 17.26066514 0.010909686 0.010581877 524.3406371 -2.719613517 -0.12668184 HIEPELAGRDS(ph)PIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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;HIEPELAGRDS(1)PIR 180.31 2.98E-07 522020000 543340 539410 576580 540830 547780 555110 678350 556920 506730 TRUE FALSE 509333.3193 579348.4777 590256.7499 554708.6134 504759.5684 715361.2455 576637.715 626452.6879 422153.4894 1.206512162 1.372364536 1.398204124 1.313997461 1.195677831 1.694552487 1.365943263 1.483945303 1 18.68740811 HIEPELAGRDS(ph)PIRAEMPGNLQHYGR ddPTM_SK-BR-3_Pertuzumab_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 217.4 1.77E-34 1172390000 159467 187093 176682 199783 234610 142653 215575 184016 249040 TRUE FALSE 149486.2451 200945.5604 180872.9805 204909.77 216184.677 183834.6053 183251.5301 206990.8027 207473.6151 0.720507256 0.968535494 0.871787867 0.987642549 1.04198636 0.886062573 0.883252215 0.997672897 1 17.66256835 4.742811773 24.53035776 0.942061995 0.720507141 0.606844923 0.058448152 243.2623092 1403622.241 0.013837836 0.107260093 55311.03342 -4.742811773 -0.221554854 HIEWESVLTNTAGCLR ddPTM_SK-BR-3_Pertuzumab_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 ; 174.62 3.81E-09 537280000 365260 509020 441670 416180 539920 398030 454920 471550 483540 FALSE TRUE 342399.0286 546708.3704 452146.621 426859.8834 497516.8611 512934.7995 386708.9693 530424.0555 402834.0502 0.849975389 1.35715531 1.122414108 1.059642012 1.235041727 1.273315399 0.959970909 1.316730935 1 18.61982611 -1.293839212 3.720647184 0.999643597 1.154611937 0.075464378 0.159377398 66.05933453 35669389.26 21147.325 0.033671387 0.050834761 1.293839212 0.15496834 HIHITQATETTTTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HIHITQATETTTTR 14 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 112.15 0.00035277 75480000 23825 32901 33279 26595 35920 28167 32217 27533 34559 FALSE TRUE 22333.83578 35337.02427 34068.3936 27277.47273 33098.98809 36298.35565 27386.35994 30970.55566 28790.87964 0.775726065 1.227368692 1.183305061 0.947434502 1.149634485 1.260758827 0.951216506 1.07570717 1 14.81332425 1.655468294 15.18739576 1.01041319 1.113751569 0.050557304 0.145475448 0.328048591 91.8949324 0.06410389 0.035332384 45.23434376 -1.655468294 0.103338379 HIIEDPCTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HIIEDPCTLR 10 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ; 97.813 0.0058027 248150000 454700 481090 451160 451890 471390 408020 560160 414770 508880 FALSE TRUE 426241.1387 516710.4042 461861.7283 463486.2624 434368.9309 525808.7503 476169.2083 466554.9475 423944.6405 1.005416976 1.218815748 1.089438771 1.09327072 1.024588801 1.240276914 1.123187234 1.10050913 1 18.69351636 0.829055269 3.578981111 1.000031577 1.12377785 0.178540248 0.073458048 1.555720582 30.27483298 0.064884519 0.016713106 6.746138749 -0.829055269 0.123746273 HIISATSLSTS(ph)PTELGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HIISATSLSTSPTELGSR 18 0 Q5JSZ5;A0A1W2PQP5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 HIISATSLST(0.266)S(0.717)PT(0.017)ELGSR;HIISATSLS(0.001)T(0.122)S(0.876)PT(0.001)ELGSR;HIISATSLS(0.002)T(0.174)S(0.823)PT(0.001)ELGSR 223.07 3.45E-19 1346800000 740405 712730 798599 808322 800371 619043 803300 656958 902357 TRUE FALSE 694064.3727 765501.2708 817542.1454 829064.911 737513.0902 797750.6648 682852.6225 738980.6524 751747.7873 0.923267597 1.018295343 1.087521851 1.102849819 0.981064531 1.061194563 0.908353352 0.983016731 1 19.51988919 1.748876158 25 0.95672137 1.035536554 0.220519205 0.056435424 3.297748565 8008.081861 0.025303046 0.014031937 56.08880119 -1.748876158 0.078815184 HIKEEPLS(ph)EEEPCTSTAIAS(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HIKEEPLSEEEPCTSTAIASPEK 23 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 2 HIKEEPLS(0.997)EEEPCT(0.004)S(0.004)T(0.011)AIAS(0.985)PEK;HIKEEPLS(1)EEEPCTSTAIAS(1)PEK 163.48 8.77E-12 1334820000 2284100 1280560 1542860 1566340 1681590 1171000 2321700 1335810 2196400 TRUE FALSE 2141142.258 1375373.995 1579457.368 1606534.936 1549524.705 1509048.69 1973582.639 1502588.819 1829806.651 1.170146724 0.751649905 0.863182658 0.877980707 0.846824283 0.824703905 1.078574415 0.821173548 1 20.80325978 1.762318007 25 0.972941789 0.86818324 0.061226314 0.125677554 25.84067728 27212.14256 0.052735609 0.029245946 57.85195059 -1.762318007 -0.104758548 HIKEEPLS(ph)EEEPCTSTAIAS(ph)PEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HIKEEPLSEEEPCTSTAIASPEKK 24 2 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 2 HIKEEPLS(1)EEEPCTST(0.001)AIAS(0.999)PEKK;HIKEEPLS(0.91)EEEPCT(0.038)S(0.043)T(0.046)AIAS(0.963)PEKK;HIKEEPLS(1)EEEPCT(0.038)S(0.027)T(0.02)AIAS(0.915)PEKK 142.72 1.38E-07 2812690000 1579200 543480 837460 810060 897470 568330 1253850 665130 1295820 TRUE FALSE 1480360.691 583719.8247 857324.9467 830847.511 826986.3264 732397.6449 1065846.833 748172.9446 1079539.271 1.371289337 0.540711988 0.794158184 0.769631577 0.76605488 0.678435389 0.987316406 0.693048382 1 20.04198429 -1.932742262 8.185635416 1.056076331 0.800782764 0.046900943 0.225266569 0.12425045 0.001020911 0.117557471 0.045717071 0.011675023 1.932742262 -0.255293567 HIKEEPLS(ph)EEEPCTSTAIASPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HIKEEPLSEEEPCTSTAIASPEK 23 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 1 HIKEEPLS(1)EEEPCTSTAIASPEK;HIKEEPLS(1)EEEPCTSTAIASPEK;HIKEEPLS(1)EEEPCTSTAIASPEK;HIKEEPLS(1)EEEPCTSTAIASPEK;HIKEEPLS(0.91)EEEPCT(0.083)S(0.006)T(0.002)AIASPEK;HIKEEPLS(0.99)EEEPCT(0.01)STAIASPEK 298.16 5.58E-62 4670660000 6564900 4411960 4860240 5198910 5405650 3372130 6557070 4333090 6636560 TRUE FALSE 6154014.628 4738626.109 4975527.188 5332322.832 4981112.054 4345609.189 5573898.226 4874085.825 5528875.262 1.11306809 0.857068732 0.899916701 0.964449835 0.900926828 0.785984307 1.008143241 0.881569143 1 22.39855459 -1.864937914 5.429299235 1.015045745 0.918584671 0.057202657 0.089035361 0.016604812 0.00041307 0.088279676 0.018171628 0.013647782 1.864937914 -0.096461074 HILAILQDCPSLRPPIDHLCELLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HILAILQDCPSLRPPIDHLCELLPR 25 1 E7EMD0;P16435;H0Y4R2 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 ; 127.92 7.52E-05 211533000 116605 126411 91829 83403 139755 93364 110767 132857 82569 FALSE TRUE 109306.9012 135770.602 94007.22724 85543.26218 128779.206 120316.6712 94158.51666 149444.4889 68787.70048 1.589047176 1.973762766 1.366628432 1.243583687 1.872125469 1.749101515 1.368827799 2.17254666 1 16.06986301 -1.275512909 3.593605092 0.998455988 1.644152084 0.337747339 0.291955993 5143960.356 3678924.579 58458.81155 0.063861475 0.053025783 1.275512909 0.645696096 HILGFDTGDAVLNEAAQILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HILGFDTGDAVLNEAAQILR 20 0 Q9Y224 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ;;; 312.09 2.65E-66 1562242000 1316184 1550717 1471941 1437665 1601925 1356845 1721366 1417794 1752418 FALSE TRUE 1233806.393 1665533.7 1506856.136 1474557.918 1476116.272 1748544.125 1463263.149 1594808.702 1459928.115 0.845114482 1.140832678 1.032144063 1.010020906 1.011088325 1.197691932 1.002284382 1.092388513 1 20.4774659 HILLAVANDEELNQLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 285.75 2.44E-36 371800000 587030 458149 500189 410563 586890 368851 645969 488609 798283 FALSE TRUE 550288.8402 492070.8287 512053.7193 421098.7417 540798.0268 475332.2959 549111.9453 549612.9092 665044.4102 0.827446757 0.739906721 0.769954174 0.633188905 0.81317581 0.714737676 0.825677108 0.826430387 1 19.34309116 0.806300311 0.971246291 0.999065748 0.74814171 0.65888226 0.055620557 0.441797692 0.805961832 0.047214445 0.015560201 6.401773594 -0.806300311 -0.250924038 HILRPGTALVLLEAQAATGFIIDPVENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HILRPGTALVLLEAQAATGFIIDPVENR 28 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 198.99 2.95E-25 671889000 365834 409105 369734 381641 443380 333951 395515 328554 274362 FALSE TRUE 342937.103 439395.5599 378504.2651 391434.5542 408558.7233 430357.2325 336211.1975 369574.6901 228569.2098 1.50036439 1.922374236 1.655972235 1.712542799 1.787461766 1.882831169 1.470938268 1.616904965 1 17.80227155 0.567003751 0.815341927 0.997189977 1.750211899 0.719543282 0.138913523 0.684565635 0.751894838 0.127830453 0.042752127 3.689807856 -0.567003751 0.753021922 HINMDGTINVDDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HINMDGTINVDDFK 14 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 176.32 2.24E-06 142740000 144340 124340 142340 138710 144630 114310 175100 123410 159790 FALSE TRUE 135306.0171 133546.263 145716.372 142269.5334 133271.3432 147309.4413 148845.3805 138818.0102 133120.0167 1.016421275 1.00320197 1.094624051 1.068731337 1.001136767 1.106591217 1.118129221 1.042803431 1 17.02236799 4.069795142 4.083601135 1.070195578 1.010376224 0.198238976 0.040533791 0.290520907 8.754768089 0.010090235 0.02319772 11743.43484 -4.069795142 -0.059819354 HIPESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HIPESK 6 0 O95202 O95202 LETM1 "LETM1 and EF-hand domain-containing protein 1, mitochondrial" 0 ; 119.7 0.020787 1803490000 3754560 3267050 3720670 3354170 3673370 2909920 4069790 3078210 3715460 FALSE TRUE 3519568.792 3508945.781 3808926.049 3440243.681 3384878.338 3749966.665 3459562.772 3462531.294 3095325.723 1.137059265 1.133627313 1.230541271 1.111431878 1.093545119 1.211493394 1.117673253 1.118632288 1 21.5616598 0.579266464 0.968939859 0.999559827 1.156566681 0.543144524 0.042533592 1.041753858 1.531944117 0.040293501 0.012967356 3.795477877 -0.579266464 0.157006854 HIPGAAFFDIDQCSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HIPGAAFFDIDQCSDR 16 0 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 ;;; 250.31 8.44E-21 658460000 441628 459647 460644 401848 546588 385491 515485 481947 575050 FALSE TRUE 413987.2918 493679.7421 471570.6932 412160.1 503661.1833 496775.9938 438192.8098 542119.1438 479070.44 0.864147017 1.030495102 0.984345211 0.860332981 1.05133012 1.036958143 0.914673028 1.131606333 1 18.86987827 HISDLYEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HISDLYEDLR 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;E9PIA2;Q15149-4;Q15149-5;Q15149-8;E9PKG0 Q15149-3;Q15149-4;Q15149-5;Q15149-8;E9PKG0 PLEC Plectin 0 ;;;;; 223.31 4.50E-09 1836122000 780195 2289330 1760985 1907898 1898057 1716268 2056195 2063752 1257113 FALSE TRUE 731363.9876 2458834.375 1802756.396 1956857.893 1748991.26 2211726.71 1747887.649 2321415.98 1047292.719 0.698337699 2.347800506 1.721349116 1.868491833 1.670011858 2.11185151 1.668958083 2.216587529 1 19.9982333 -0.996116729 7.398452074 0.999999969 1.833230262 0.224951496 0.452737675 2.03E-07 2.74E-08 0.377592648 0.088999437 0.100898166 0.996116729 0.833230293 HISEGCVFIYCQVGEKPYWKDPNNDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HISEGCVFIYCQVGEKPYWKDPNNDFR 27 2 Q9BRA2;I3L2R6 Q9BRA2 TXNDC17 Thioredoxin domain-containing protein 17 0 71.86 0.011827 311700000 52997 96244 80893 88889 92836 77568 130860 72444 106540 FALSE TRUE 49680.01237 103370.0059 82811.82016 91170.04223 85545.03504 99960.62239 111238.7578 81488.79287 88757.78573 0.559725685 1.164630292 0.933009082 1.027177971 0.963803168 1.126218073 1.253284508 0.91810304 1 16.43758606 2.240934954 24.71336605 1.113509812 0.966597013 0.107067474 0.176488659 103.3748832 1075997.575 0.058341413 0.046664933 174.1546016 -2.240934954 -0.1469128 HISEGCVFIYCQVGEKPYWKDPNNDFRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HISEGCVFIYCQVGEKPYWKDPNNDFRK 28 3 Q9BRA2;I3L2R6 Q9BRA2 TXNDC17 Thioredoxin domain-containing protein 17 0 158.94 6.40E-12 600670000 454190 655870 579910 644910 825530 558150 1115300 582800 1292500 FALSE TRUE 425763.0587 704431.2972 593665.7391 661459.4824 760696.2038 719278.8442 948071.1189 655563.8629 1076773.4 0.395406367 0.654205701 0.551337671 0.614297755 0.706458948 0.667994626 0.880474127 0.60882249 1 20.03828325 1.477588512 0.082152596 1.499371694 3.50E-22 0.680969012 0.094296664 7.844349959 0.652819589 5.732383266 5.579597125 30.03229435 -1.477588512 -1.499371694 HISESCPFPSPGGQLAEVHSVS(ph)PEQGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HISESCPFPSPGGQLAEVHSVSPEQGAK 28 0 Q5T1V6;Q5T1V6-2;Q5T1V5 Q5T1V6 DDX59 Probable ATP-dependent RNA helicase DDX59 1 HISESCPFPSPGGQLAEVHS(0.486)VS(0.514)PEQGAK;HISESCPFPSPGGQLAEVHS(0.178)VS(0.822)PEQGAK 184.43 1.83E-17 287380000 207387 403830 402810 406690 454610 346230 517970 425850 507780 TRUE FALSE 194407.0179 433729.9934 412364.8434 417126.3539 418906.7644 446180.9804 440305.2071 479018.3099 423028.2376 0.459560381 1.02529797 0.974792713 0.986048488 0.990257215 1.054730963 1.040841173 1.132355402 1 18.69039444 4.738763769 24.97050416 1.022013272 0.459560212 0.938577937 0.045494067 3.702120119 454742.4132 0.010917014 0.06349935 54797.88152 -4.738763769 -0.56245306 HISFGGNLITFS(ph)PLQPGEF ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HISFGGNLITFSPLQPGEF 19 0 Q15398-1;Q15398 Q15398-1 DLGAP5 Disks large-associated protein 5 1 HISFGGNLIT(0.002)FS(0.998)PLQPGEF 116.6 0.00012075 54845000 59249 148050 124230 134350 140770 122110 155400 121980 125600 TRUE FALSE 55540.71085 159011.776 127176.7943 137797.6485 129714.492 157361.1747 132099.2127 137209.4715 104636.5486 0.530796472 1.519658075 1.215414652 1.316916988 1.239667151 1.50388346 1.262457664 1.311295846 1 16.67502733 4.747781035 24.91891557 1.316529268 0.530796042 0.725620155 0.147436227 553.173904 1494963.628 0.030783056 0.387057173 55947.54514 -4.747781035 -0.785733226 HITESVNSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HITESVNSIR 10 0 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 0 137.46 9.06E-05 444630000 48949 65674 60407 64589 74323 65657 62268 55540 73114 FALSE TRUE 45885.36947 70536.57129 61839.88257 66246.46309 68485.97138 84611.11005 52931.49147 62474.29126 60910.80107 0.753320736 1.158030597 1.015253149 1.087597962 1.124364976 1.389098626 0.869000088 1.025668521 1 15.89441046 1.623035805 24.99999999 0.960487106 1.0918941 0.116505278 0.159327862 1.669698518 2745.253546 0.068638462 0.037876486 41.97935916 -1.623035805 0.131406994 HITIFSPEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HITIFSPEGR 10 0 G3V5Z7;P60900;G3V3I1;G3V295;G3V3U4;G3V4S5;G3V2S7 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ; 197.21 3.19E-07 418380000 300690 690140 323280 300140 740410 188286 339220 636910 631110 FALSE TRUE 281870.3496 741238.6837 330948.3543 307842.1005 682261.1853 242641.1116 288357.1102 716429.6155 525773.6639 0.536105874 1.409805653 0.629450231 0.585503082 1.297632864 0.461493468 0.548443427 1.362619821 1 19.00408235 5.008811296 19.82069824 0.874589121 0.030174884 0.09119186 0.35590377 3136.75361 55655.41258 0.079925605 73005.40091 102049.5974 -5.008811296 -0.844414238 HITLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HITLDK 6 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 0 ;;;;; 144.29 0.011291 2799080000 6278270 7103330 6274370 6166400 7886590 4364880 7322930 6847230 8084460 FALSE TRUE 5885324.288 7629267.944 6423201.019 6324640.264 7267209.034 5624949.998 6224924.629 7702121.738 6735111.398 0.873827312 1.132760469 0.953688906 0.939055034 1.079003539 0.835168072 0.924249691 1.143577483 1 22.68327038 3.727570349 24.82063313 0.96944858 1.028219788 0 0.105023106 58.99377451 3260176.555 0.02561484 0.042840638 5340.357723 -3.727570349 0.058771208 HIYLLPSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HIYLLPSGR 9 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ; 87.913 0.013139 458820000 269260 603530 244290 237890 637400 164551 318480 541850 504930 FALSE TRUE 252407.4972 648215.9892 250084.6742 243994.6601 587341.1751 212054.2024 270726.8806 609501.1653 420653.921 0.600036003 1.540972179 0.594514069 0.580036576 1.39625746 0.504106088 0.643585777 1.448937321 1 18.68227427 5.011326784 20.9657802 0.929809505 0.030280789 0.073620262 0.389219369 6350.768283 165472.5234 0.086699641 177138.3418 102642.3967 -5.011326784 -0.899528716 HIYYITGETK ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 185.29 1.47E-06 15062050000 21825780 18103260 19285750 18948370 20675830 15136900 23884660 17864800 20736810 FALSE TRUE 20459743.39 19443644.21 19743217.1 19434617.25 19052033.71 19506677.3 20303376.97 20095259.61 17275702.45 1.184307466 1.125490802 1.142831509 1.124968279 1.10282252 1.129139458 1.175256232 1.163209407 1 24.04224104 -2.207035583 2.471444849 0.539011744 1.141907904 0.76516803 0.024970235 2202863.448 676322.388 5673317.382 0.006226271 0.006208182 2.207035583 0.60289616 HKDAAIYLVTSLASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HKDAAIYLVTSLASK 15 1 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 152.89 1.65E-06 275990000 485420 488040 470840 493520 601910 363750 706970 544450 603190 FALSE TRUE 455038.4287 524174.9894 482008.5471 506184.5587 554638.4166 468758.72 600966.4117 612425.781 502513.6922 0.905524438 1.043105884 0.959194853 1.007305008 1.103727968 0.932827756 1.195920471 1.218724565 1 18.93880338 1.720299761 9.308296326 1.153475922 0.999034779 0.420489272 0.079876727 0.088190303 21.46725987 0.034209479 0.018389879 52.5169821 -1.720299761 -0.154441142 HKDSNYQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HKDSNYQR 8 1 Q6PGP7 Q6PGP7 TTC37 Tetratricopeptide repeat protein 37 0 ; 123.16 0.00081697 15208800 22175.9 51583 35163 37941 49609 32226 31375 40208 43902 FALSE TRUE 20787.95 55402.25899 35997.08297 38914.63029 45712.90925 41529.12305 26670.61002 45228.05731 36574.47258 0.5683732 1.514779437 0.984213317 1.063983362 1.249858331 1.135467448 0.729213797 1.236601764 1 15.15854944 HKEEDKNSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HKEEDKNSER 10 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ;;;; 203.83 1.19E-07 458593000 566613 287131 405535 369837 372271 291989 468147 315077 550080 FALSE TRUE 531149.7038 308390.478 415154.4817 379327.6436 343034.3373 376281.4843 397952.7034 354415.057 458268.0943 1.159037058 0.672947739 0.905920545 0.82774177 0.748545102 0.821094658 0.868384049 0.773379298 1 18.80583232 -1.578838154 5.588757254 1.000732298 0.834629014 0.115844514 0.128666614 0.001022226 7.70E-05 0.108474581 0.025457244 0.02637314 1.578838154 -0.166103285 HKELAPYDENWFYTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HKELAPYDENWFYTR 15 1 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ;; 241.93 4.00E-18 2623340000 4011570 5074050 4333890 4269930 5580790 2703430 4780660 3892600 7363990 FALSE TRUE 3760492.995 5449737.942 4436691.917 4379503.633 5142497.265 3483866.354 4063844.414 4378599.679 6134892.496 0.612968034 0.888318409 0.723189839 0.713868032 0.838237552 0.567877327 0.662414935 0.713720686 1 22.54860663 -0.933635153 4.577169216 1.000003318 0.723785225 0.469893454 0.09470688 10733706.93 4690106.985 369.2261344 0.022448562 0.116510441 0.933635153 -0.276218093 HKETGNHY(ph)AMKILDKQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HKETGNHYAMKILDKQK 17 3 P17612-2;P17612;Q15136;K7ERP6;K7EMV1 P17612-2 PRKACA;KIN27 cAMP-dependent protein kinase catalytic subunit alpha 1 HKET(0.003)GNHY(0.997)AMKILDKQK 53.777 0.069494 105240000 610560 162650 212620 186110 198140 131590 201210 141670 205120 TRUE FALSE 572346.1395 174692.7752 217663.4468 190885.8977 182578.8837 169577.8968 171040.4284 159357.8114 170884.1469 3.349322626 1.022287781 1.273748623 1.117048604 1.06843664 0.992355932 1.000914547 0.932548831 1 17.38265904 4.739235074 24.99916317 1.066592606 3.349323329 0.983313159 0.094076091 7.132758813 264326.8429 0.024621952 0.147605365 54857.38152 -4.739235074 2.282730723 HKHEIESGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HKHEIESGR 9 1 O00178;F5H716 O00178 GTPBP1 GTP-binding protein 1 0 ; 114.5 0.00097861 96693000 107213 106233 116088 117697 114172 93870 121572 91489 124909 FALSE TRUE 100502.7297 114098.6019 118841.6622 120717.3043 105205.3917 120968.7451 103343.4072 102911.603 104060.881 0.965807024 1.09646008 1.142039747 1.160064216 1.010998472 1.162480502 0.99310525 0.988955716 1 16.6670683 1.632969968 7.839388888 0.992177611 1.09591479 0.340073817 0.062295986 0.119150708 15.47996844 0.029719836 0.015067098 42.95067251 -1.632969968 0.10373718 HKLDVTSVEDYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HKLDVTSVEDYK 12 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;; 162.6 3.74E-05 2944050000 6478200 4487960 5158820 5040230 5515870 3706410 6609210 4764160 6733190 FALSE TRUE 6072741.026 4820253.228 5281189.647 5169570.835 5082675.82 4776390.398 5618220.317 5358975.863 5609377.091 1.082605239 0.859320589 0.941493068 0.921594457 0.90610343 0.851501035 1.001576508 0.955360243 1 22.41940914 1.638575723 12.90120668 0.983723735 0.920143233 0.15054281 0.064002842 0.187412057 63.37149384 0.027383745 0.014907001 43.50866151 -1.638575723 -0.063580503 HKMS(ph)PPPSGFGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.991)PPPS(0.009)GFGER;HKMS(0.999)PPPS(0.001)GFGER 142.39 5.08E-05 1544000000 1385475 1098438 1199092 1205869 1332703 977811 1442574 1154034 1490697 TRUE FALSE 1298760.593 1179767.492 1227535.028 1236813.64 1228037.882 1260089.162 1226273.421 1298117.685 1241890.04 1.045793549 0.949977417 0.988440996 0.995912359 0.988845906 1.014654375 0.987425119 1.045275864 1 20.24410601 2.121449733 0.995851782 1.013945206 0.985443164 0.04877199 0.027714363 1.070929218 1.982904144 0.019742068 0.010204153 132.2664607 -2.121449733 -0.028502042 HKPGGGDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HKPGGGDVK 9 1 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 0 91.855 0.0062914 207470000 714640 515080 568280 602120 631080 420630 664240 518050 688210 FALSE TRUE 669911.9581 553217.0591 581759.87 617571.4186 581517.5225 542059.0526 564643.3785 582729.6829 573343.305 1.168430768 0.964896693 1.0146798 1.077140717 1.014257108 0.945435393 0.984825974 1.016371305 1 19.12903973 2.470344304 24.5962241 0.983398311 1.035278563 0.22288098 0.055443587 251.9360981 914364.2691 0.018518172 0.015532647 295.3549841 -2.470344304 0.051880252 HKS(ph)DNETNLQQQVVWGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HKSDNETNLQQQVVWGNR 18 1 A0A0U1RR27;Q7Z401;Q7Z401-2 A0A0U1RR27 DENND4A C-myc promoter-binding protein 1 HKS(0.998)DNET(0.002)NLQQQVVWGNR 155.76 1.00E-08 240940000 57938 49336 49748 57808 57565 39079 60618 47115 59470 TRUE FALSE 54311.764 52988.88877 50928.04605 59291.45115 53044.07711 50360.47291 51528.89365 52997.41146 49544.07281 1.096231313 1.069530335 1.027934184 1.196741563 1.070644259 1.01647826 1.040061721 1.069702357 1 15.59642485 2.421233695 7.661378055 1.035570696 1.086434219 0.303488838 0.045694719 0.373908272 43.91633939 0.01599899 0.013381818 263.7750382 -2.421233695 0.050863523 HKSDFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HKSDFGK 7 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 ; 136.8 0.0017696 3226200000 4648400 11776700 10260900 11151500 11739300 8101100 14238600 10794400 10476500 FALSE TRUE 4357464.942 12648659.12 10504293.39 11437666.37 10817342.73 10439756.06 12103654.11 12142104.6 8727904.469 0.499256718 1.449220619 1.203529831 1.310471077 1.239397472 1.196135464 1.386776649 1.391182115 1 23.05720388 4.745670205 24.99671187 1.28971129 0.499256348 0.780924632 0.128339847 346.6689791 1218828.873 0.027277948 0.277076432 55676.27933 -4.745670205 -0.790454942 HKSDNET(ph)NLQQQVVWGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HKSDNETNLQQQVVWGNR 18 1 A0A0U1RR27;Q7Z401;Q7Z401-2 A0A0U1RR27 DENND4A C-myc promoter-binding protein 1 HKS(0.32)DNET(0.68)NLQQQVVWGNR 136.96 8.34E-06 175140000 110250 86805 104300 107440 121790 70859 118240 91683 123270 TRUE FALSE 103349.6493 93232.13252 106774.0453 110197.0923 112225.1047 91314.843 100511.0097 103129.8244 102695.4406 1.006370377 0.907850747 1.039715537 1.073047563 1.092795396 0.889181082 0.978729037 1.004229825 1 16.64801261 3.968526245 23.61180223 1.006893978 0.953037159 0.118944366 0.060021351 331.5214501 910747.981 0.015817436 0.029165513 9300.927206 -3.968526245 -0.053856819 HKSDSPES(ph)DAEREK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HKSDSPESDAEREK 14 2 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 HKSDS(0.001)PES(0.999)DAEREK 109.89 0.0003868 280940000 121590 161970 165930 180640 201950 128790 238270 171640 271930 TRUE FALSE 113979.8989 173962.4273 169865.938 185275.5282 186089.6616 165969.5823 202543.6255 193069.6318 226543.1263 0.503126715 0.767899826 0.749817224 0.817837783 0.821431507 0.732618045 0.89406211 0.852242286 1 17.78942619 6.569923417 0.142033253 1.023354003 2.69E-18 0.717797411 0.068160222 28.16905939 0.387428342 0.291071002 5.524565949 3714697.189 -6.569923417 -1.023354003 HKSEEHNDKEHSSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HKSEEHNDKEHSSDK 15 2 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 0 70.98 0.014502 7877400 6175.6 17684 14686 18083 18976 12201 19453 17092 19528 FALSE TRUE 5789.08022 18993.34176 15034.35886 18547.04039 17485.70151 15723.23063 16536.20324 19225.97382 16268.65064 0.355842678 1.167481076 0.92413066 1.140047863 1.074809576 0.96647417 1.0164459 1.181780483 1 13.98980698 4.744451639 24.99681888 1.050780791 0.355842376 0.868866552 0.085784833 212.0358254 899686.2063 0.018954172 0.17169145 55520.27888 -4.744451639 -0.694938414 HKSETDTSLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HKSETDTSLIR 11 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;;;;; 227.2 2.51E-12 2172379000 1376940 2776740 2472190 2795580 2977540 2092820 3131260 2751000 2610980 FALSE TRUE 1290759.783 2982332.719 2530831.514 2867319.316 2743696.019 2696983.16 2661756.632 3094468.406 2175190.57 0.593400781 1.371067326 1.163498752 1.318192233 1.261358916 1.239883621 1.223688935 1.422619447 1 21.05271037 4.744604183 24.99733455 1.256828166 0.593400491 0.760807573 0.115652667 286.0269467 1183028.696 0.023571289 0.216523982 55539.78357 -4.744604183 -0.663427675 HLAAVEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HLAAVEER 8 0 Q92922;F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 Q92922;F8VXC8 SMARCC1;SMARCC2 SWI/SNF complex subunit SMARCC1;SWI/SNF complex subunit SMARCC2 0 ;;; 126.41 0.0012203 1196070000 869340 1138780 1041760 1028840 1186920 940580 1118210 1007050 1187120 FALSE TRUE 814929.5612 1223096.456 1066471.039 1055241.776 1093704.091 1212110.177 950544.7915 1132782.409 988982.0029 0.824008484 1.236722663 1.078352322 1.066997957 1.10588877 1.225613988 0.961134569 1.14540245 1 19.91558474 0.138424437 0.708624341 0.99796481 1.095355372 0.022679471 0.12166186 11.8638141 7.115916708 0.192999306 0.039741803 1.375385487 -0.138424437 0.097390562 HLAEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLAEIK 6 0 H0YC42;P55327-8;H0YC44;P55327-2;P55327-4;P55327-3;E5RFR7 H0YC42;P55327-2 TPD52 0 102.98 0.035077 318980000 709420 821290 604420 576110 844000 411930 795820 781660 1045000 FALSE TRUE 665018.6686 882099.1662 618757.1278 590893.958 777715.6445 530847.5039 676494.179 879251.9716 870582.749 0.763877609 1.0132284 0.710739018 0.678733824 0.893327654 0.609761111 0.777059021 1.009957954 1 19.73162191 1.237869258 24.99757029 1.004979097 0.78638667 0.415314023 0.111577121 19.10642243 690587.1472 0.089143286 0.027307867 17.29295686 -1.237869258 -0.218592427 HLAETAEEKDTELLDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLAETAEEKDTELLDLR 17 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6;H7BZD9 Q8NEY1-5 NAV1 Neuron navigator 1 0 253.02 3.19E-27 42470000 59963 59503 58154 52773 61747 43635 72386 48787 82685 FALSE TRUE 56210.02287 63908.66403 59533.44034 54127.24452 56897.6397 56231.71614 61532.3913 54878.16434 68884.33933 0.816005835 0.927767685 0.864252179 0.785769959 0.825988029 0.816320759 0.893271125 0.796671128 1 16.07188841 -1.950624246 7.239499398 1.065574046 0.850656017 0.546428075 0.044795505 0.031764562 0.000216645 0.029059398 0.010419826 0.011204068 1.950624246 -0.214918029 HLAEYTHVEAECPFLTFDDLLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HLAEYTHVEAECPFLTFDDLLNR 23 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;; 184.7 1.89E-17 513160000 341194 297152 332475 327282 322513 293467 377947 316965 223982 FALSE TRUE 319839.2766 319153.4433 340361.464 335680.6102 297184.1299 378186.1589 321277.356 356538.778 186597.9572 1.714055616 1.710380156 1.824036389 1.798951153 1.592644069 2.026743296 1.72176245 1.910732482 1 17.50957367 -0.985058539 4.989767017 0.999994509 1.784368966 0.811986229 0.119068384 7.87E-06 1.60E-06 0.101260551 0.023867135 0.103500265 0.985058539 0.784374456 HLAFLAESCATLSQEQHSQELLAELLTHLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLAFLAESCATLSQEQHSQELLAELLTHLER 31 0 Q969Z0;Q969Z0-2;C9J7P5;C9IZN7 Q969Z0 TBRG4 Protein TBRG4 0 136.67 4.41E-07 68845000 13779 4355.8 7901.5 15080 7502 9097.7 9242.4 6436.6 7855.1 FALSE TRUE 12916.59699 4678.307964 8088.927311 15466.97833 6912.823182 11724.0583 7856.587922 7240.223679 6544.033064 1.973797635 0.714896749 1.236076779 2.363523867 1.056355173 1.791564649 1.200572773 1.106385559 1 12.67596432 1.512963632 7.822964899 1.085571126 1.416231754 0.128988546 0.472669598 0.308482646 39.07033141 0.257798376 0.118865196 32.58094165 -1.512963632 0.330660628 HLAGEVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLAGEVAK 8 0 Q13200;Q13200-3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 96.253 0.0090721 433390000 968820 948360 885500 891810 1077590 654130 1109240 897340 1218000 FALSE TRUE 908183.2856 1018577.561 906504.4782 914695.3544 992960.4282 842966.7121 942919.7597 1009374.874 1014707.931 0.895019402 1.00381354 0.893364928 0.90143708 0.978567721 0.830748126 0.929252379 0.994744244 1 19.9526331 1.244905282 6.414242547 0.998420864 0.921949406 0.320914148 0.047396252 0.168068999 29.45881211 0.035800589 0.011219224 17.5754026 -1.244905282 -0.076471459 HLAGYEQQDAHEFLIAALDVLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLAGYEQQDAHEFLIAALDVLHR 23 0 Q9UPT9-2;Q9UPT9 Q9UPT9-2 USP22 Ubiquitin carboxyl-terminal hydrolase 22 0 163.91 5.18E-12 40994000 11376 15753 12362 12167 15502 9949.9 12579 12958 10774 FALSE TRUE 10663.99647 16919.36851 12655.23248 12479.22582 14284.53545 12822.27461 10692.89573 14575.83482 8975.749797 1.188089765 1.885008929 1.409935968 1.390326836 1.591458739 1.428546349 1.191309469 1.623912782 1 13.13181675 -3.152719161 0.157151393 0.033672536 1.648338218 0.287268789 0.212494791 72.3601983 1.13613513 24.05511306 0.972522925 0.000703527 3.152719161 1.614665681 HLAPPPLLS(ph)PLLPSIKPTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLAPPPLLSPLLPSIKPTVR 20 1 Q14676;Q14676-3;Q14676-2;H0Y6Z8 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 HLAPPPLLS(1)PLLPSIKPTVR 121.25 1.97E-05 197860000 778160 673180 814850 685470 809350 563000 852770 660580 881500 TRUE FALSE 729456.3547 723022.9476 834178.6268 703060.3207 745786.9158 725528.9605 724905.0552 743054.8671 734371.9553 0.993306388 0.984545968 1.13590752 0.957362704 1.01554384 0.987958425 0.987108849 1.011823589 1 19.48615144 HLAQVGDSMDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLAQVGDSMDR 11 0 P55957;P55957-2 P55957 BID BH3-interacting domain death agonist;BH3-interacting domain death agonist p15;BH3-interacting domain death agonist p13;BH3-interacting domain death agonist p11 0 ; 156.14 3.12E-05 315779000 246724 292085 279739 282134 327749 241789 287968 263527 420750 FALSE TRUE 231281.9853 313711.2773 286374.5412 289374.0361 302008.9156 311589.5592 244789.8718 296428.926 350524.1069 0.659817629 0.894977752 0.816989575 0.825546747 0.861592426 0.888924765 0.698353885 0.845673437 1 18.41915414 -2.530364158 1.887339237 2.843851819 0.816053901 0.37289237 0.07662626 2609248.027 148083.6749 20577843.92 0.018458578 0.002948736 2.530364158 -2.027797918 HLCEEENLLQVVWHSMQDEFIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLCEEENLLQVVWHSMQDEFIR 22 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 0 190.88 9.38E-18 53520000 30646 39954 41064 47486 56190 44121 45714 40147 44656 FALSE TRUE 28727.92156 42912.23573 42038.05747 48704.57115 51777.06406 56858.01646 38859.61009 45159.44132 37202.62511 0.772201464 1.153473326 1.129975569 1.309170281 1.391758348 1.528333452 1.044539464 1.213877816 1 15.1831168 5.224718154 1.082411457 1.245396945 1.83E-13 0.444178635 0.157880587 4.146476916 1.932955434 0.045169068 7.613921083 167771.4871 -5.224718154 -1.245396945 HLCEPGADGAETFADGVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HLCEPGADGAETFADGVPR 19 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;A0A2R8Y5M9;A0A2R8YE38;K7EMY3 Q14839-2 CHD4;CHD5 Chromodomain-helicase-DNA-binding protein 4 0 ;;; 302.96 4.38E-50 1606100000 891150 963830 929830 965150 982280 901360 1149520 862570 904310 FALSE TRUE 835374.5122 1035192.976 951886.0067 989917.383 905135.6911 1161568 977160.1476 970263.7633 753374.8189 1.108843156 1.374074299 1.263495916 1.313977264 1.201441392 1.541819517 1.297043813 1.287889824 1 19.52300829 0.678772812 3.266242365 1.000010166 1.311436914 0.410630072 0.111874965 3.961793927 39.28275209 0.096736117 0.025087594 4.772795344 -0.678772812 0.311426748 HLCICSVDPPGCTDIDDALHCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLCICSVDPPGCTDIDDALHCR 22 0 Q9Y2L1;G3V1J5;Q9Y2L1-2;F2Z2C0 Q9Y2L1 DIS3 Exosome complex exonuclease RRP44 0 ; 144.88 5.61E-08 451660000 110509 112302 124371 104267 122064 114913 160077 112566 161228 FALSE TRUE 103592.439 120616.9569 127321.1389 106942.6677 112477.5858 148086.5176 136074.9399 126620.1129 134318.0052 0.771247598 0.897995445 0.947908202 0.796190113 0.837397679 1.102506826 1.013080411 0.942689051 1 17.03529318 2.251532674 24.99789482 1.018484528 0.867550808 0.620128621 0.063101041 165.3458206 318630.5016 0.022447306 0.01867324 178.4566245 -2.251532674 -0.15093372 HLDAHTAAHS(ph)QSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLDAHTAAHSQSPR 14 0 H7C3X3;H0Y6N5;E9PHI4;O94901-9 H7C3X3 SUN1 1 HLDAHT(0.328)AAHS(0.361)QS(0.311)PR;HLDAHT(0.005)AAHS(0.497)QS(0.497)PR 81.317 0.023135 144434000 157995 174875 144162 145975 166891 124739 185644 169485 147169 TRUE FALSE 148106.375 187822.927 147581.5907 149720.9656 153784.0541 160749.1243 157808.4056 190645.5753 122605.5432 1.207990856 1.531928509 1.20371059 1.221159841 1.254299358 1.311108129 1.287122928 1.554950702 1 16.90366468 3.890903343 7.928348497 1.275593654 1.389562358 0.068977568 0.155354696 0.578740209 46.84540387 0.035777715 0.064825277 7778.634101 -3.890903343 0.113968704 HLDGEEDGSS(ph)DQSQASGTTGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLDGEEDGSSDQSQASGTTGGR 22 0 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 1 HLDGEEDGS(0.006)S(0.994)DQSQASGTTGGR;HLDGEEDGS(0.145)S(0.855)DQSQASGTTGGR 227.49 2.84E-26 455520000 165578 173550 149845 155764 146824 140048 172161 124365 112548 TRUE FALSE 155214.7685 186399.8226 153399.3942 159761.1679 135293.0353 180477.5841 146347.0563 139892.244 93763.01171 1.655394443 1.987988858 1.636033137 1.70388264 1.442925444 1.924827081 1.560818639 1.491976862 1 16.51673129 -2.342514343 0.202710363 1.61E-11 1.861032615 0.680164189 0.154199083 21.76537026 0.570919211 10.20505035 0.372194008 0.004544495 2.342514343 1.861032615 HLDHVAALFPGDVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HLDHVAALFPGDVDR 15 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;; 107.61 0.0006616 1335880000 986710 1152310 1027670 1065240 1226090 906380 1213120 1056940 1258480 FALSE TRUE 924953.5824 1237628.231 1052046.818 1092575.862 1129797.837 1168037.192 1031223.918 1188901.286 1048431.558 0.882226003 1.180456866 1.003448255 1.042105089 1.077607621 1.114080536 0.983587255 1.133980827 1 19.99980125 -1.08831029 4.046493181 0.999989482 1.057055399 0.033749105 0.084248196 7.77E-06 1.75E-06 0.071446303 0.016836611 0.081599916 1.08831029 0.057065918 HLDLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HLDLEK 6 0 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZHJ1;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZGZ8 P55263-3 ADK Adenosine kinase 0 ;;;; 132.72 0.014776 2992550000 5941260 5071050 5088810 5004140 5704120 3561860 5975380 4683800 5364760 FALSE TRUE 5569407.142 5446515.818 5209518.976 5132554.704 5256141.425 4590111.16 5079427.242 5268582.74 4469346.898 1.246134451 1.218637967 1.165610792 1.148390318 1.176042394 1.027020561 1.136503242 1.178826093 1 22.0916326 7.999999999 0.072514219 0.866754669 1.835708838 0.63419213 0.046502787 144.7347597 0.772053661 1.734404668 14.23282584 99999999.88 -7.999999999 0.968954169 HLDRS(ph)PESDRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 HLDRSPESDRPR 12 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 HLDRS(1)PESDRPR;HLDRS(1)PESDRPR;HLDRS(1)PESDRPR;HLDRS(1)PESDRPR;HLDRS(0.995)PES(0.005)DRPR;HLDRS(0.999)PES(0.001)DRPR;HLDRS(1)PESDRPR 154.99 3.18E-05 37083280000 3962000 4423410 4235150 4180350 4746340 3426380 4521540 3701240 5351020 TRUE FALSE 3714025.492 4750923.879 4335609.758 4287624.858 4373581.602 4415520.283 3843577.053 4163347.961 4457900.193 0.833133388 1.065731325 0.972567705 0.961803691 0.981085581 0.990493302 0.862194506 0.93392579 1 22.08793289 1.770203779 25 0.917692172 0.979701236 0.02457891 0.066241148 48.75459423 38538.73103 0.028096709 0.015585099 58.91200171 -1.770203779 0.062009064 HLDVDLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLDVDLDR 8 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 0 ; 112.84 0.0029633 163771000 93301 109406 96970 103288 125128 87226 108725 109306 129642 FALSE TRUE 87461.45696 117506.5341 99270.17419 105938.5449 115300.9516 112406.7302 92422.6956 122953.0947 108003.9127 0.809798967 1.087984048 0.919134981 0.980876917 1.067562728 1.040765352 0.855734698 1.138413338 1 16.72072405 4.757164069 24.00257196 0.998638633 0.809798681 0.362928671 0.082397725 2728.518941 3520295.024 0.01856581 0.598697801 57169.45718 -4.757164069 -0.188839952 HLDVDLDRQS(ph)LSS(ph)IDKNPSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLDVDLDRQSLSSIDKNPSER 21 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 2 HLDVDLDRQS(0.993)LS(0.256)S(0.751)IDKNPS(0.001)ER;HLDVDLDRQS(0.978)LS(0.28)S(0.742)IDKNPSER 78.978 0.0043537 2395200000 440710 345410 388060 422060 422390 374370 597440 408370 422190 TRUE FALSE 413126.7478 370984.5158 397264.9665 432890.7741 389217.1932 482444.5416 507859.4184 459355.8934 351723.7615 1.174577305 1.054761027 1.129480035 1.230769204 1.106599087 1.371657517 1.443915578 1.306013251 1 18.42408328 2.241110844 24.99942785 1.332884069 1.130547816 0.186251642 0.126344542 65.89704063 645984.3612 0.041244444 0.033038191 174.2251488 -2.241110844 -0.202336252 HLDVDLDRQS(ph)LSSIDKNPSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HLDVDLDRQSLSSIDKNPSER 21 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 HLDVDLDRQS(0.96)LS(0.024)S(0.016)IDKNPSER;HLDVDLDRQS(0.996)LS(0.003)S(0.001)IDKNPSER;HLDVDLDRQS(0.999)LS(0.001)SIDKNPSER;HLDVDLDRQS(0.992)LS(0.007)S(0.001)IDKNPSER 237.98 3.69E-30 3756380000 2726530 2282110 2597910 2740410 2923090 2163210 3655780 2780940 3163710 TRUE FALSE 2555881.354 2451079.799 2659533.652 2810733.56 2693522.303 2787693.61 3107629.728 3128146.481 2635666.363 0.969728715 0.929965884 1.009055505 1.066422367 1.021951162 1.057680763 1.179067947 1.186852223 1 21.32973633 2.924773475 0.786794333 1.129332417 0.947197537 0.488002128 0.059118323 0.456895685 0.624740061 0.034969163 0.041675414 840.9563907 -2.924773475 -0.18213488 HLDYLIQCTNEMNVNIPQLADSLFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLDYLIQCTNEMNVNIPQLADSLFER 26 0 Q13492-3;Q13492-2;Q13492-5;Q13492;E9PK13;E9PKP6;E9PLJ8 Q13492-3 PICALM Phosphatidylinositol-binding clathrin assembly protein 0 113.9 0.0015021 57052000 34725 39827 34033 35310 40270 28966 37814 33651 31928 FALSE TRUE 32551.62424 42775.83252 34840.27883 36216.11438 37107.35664 37328.01398 32144.14175 37852.40142 26599.01054 1.223790794 1.608173825 1.309833641 1.361558706 1.395065301 1.403360998 1.208471334 1.423075545 1 14.69908496 -3.815150379 0.192113169 1.77E-17 1.452611363 0.492362689 0.114358963 61.88250556 0.91583173 24.28529785 0.288926434 0.000153056 3.815150379 1.452611363 HLEAADKGHS(ph)PAQKPK ddPTM_SK-BR-3_Pertuzumab_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 210.38 4.67E-12 746620000 1782570 752370 1107120 1021730 1238770 784480 1597360 1007180 2248910 TRUE FALSE 1671002.126 808076.2576 1133381.409 1047949.322 1141482.001 1010946.641 1357850.697 1132928.64 1873552.392 0.891889724 0.431306998 0.604937131 0.559338146 0.609260785 0.539588135 0.724746584 0.604695468 1 20.83734489 -0.066614615 0.590089136 1.029110144 0.585275764 0.472433126 0.123237132 3.754106132 1.437681856 0.366140948 0.04607554 0.857798703 0.066614615 -0.44383438 HLECTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLECTK 6 0 B4DXZ6;P51114;P51114-3;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 ; 95.793 0.042942 381030000 1186610 1147400 1131740 1186110 1303290 905860 1384120 1117460 1248490 FALSE TRUE 1112342.198 1232354.69 1158585.407 1216547.591 1200934.861 1167367.077 1176584.056 1256977.341 1040108.953 1.069447768 1.184832306 1.113907734 1.169634764 1.154624096 1.122350762 1.131212314 1.208505452 1 19.98830323 -1.810495874 2.826624325 0.95795918 1.144321708 0.57482073 0.03900605 1502032.464 1411108.564 385109.2416 0.007981845 0.015470492 1.810495874 0.186362528 HLEDEL ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLEDEL 6 0 O95881 O95881 TXNDC12 Thioredoxin domain-containing protein 12 0 ; 126.07 0.041062 345020000 781770 966700 876760 908050 873830 680980 978580 695470 704750 FALSE TRUE 732840.4112 1038275.474 897557.1612 931352.1003 805202.9167 877567.8712 831851.0137 782300.9604 587122.6721 1.248189596 1.768413184 1.528738718 1.586298987 1.371438977 1.494692528 1.41682659 1.332431871 1 19.16330244 0.594720548 0.461772635 0.965131301 1.575375082 0.565011187 0.135928716 1.158096232 0.497026471 0.211097589 0.075163001 3.932969224 -0.594720548 0.610243781 HLEEAFTSEHWLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLEEAFTSEHWLVR 14 0 Q8TCJ2 Q8TCJ2 STT3B Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B 0 278.46 2.05E-33 57224000 14555 21329 16927 16014 23264 13514 16155 18230 14053 FALSE TRUE 13644.02853 22908.22135 17328.51643 16424.94635 21436.93928 17415.27242 13732.70773 20506.05563 11707.46351 1.165412859 1.956719432 1.480125598 1.402946619 1.831048993 1.487535912 1.172987446 1.751537009 1 13.51514092 -1.152277569 0.259821888 0.624745911 1.638972864 0.246691882 0.267244834 21.09120687 1.22228465 5.970832646 0.385882266 0.070424283 1.152277569 1.014226953 HLEEEKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLEEEKER 8 1 Q9H6F5;Q9H6F5-2 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 0 ; 136.57 0.00047194 248880000 315610 255180 299420 264220 287670 173615 318110 263380 448850 FALSE TRUE 295856.5335 274073.7927 306522.3838 271000.3325 265077.5586 223734.8321 270412.3587 296263.5728 373934.0353 0.791199799 0.732946902 0.819723146 0.724727644 0.708888557 0.598327007 0.723155244 0.792288331 1 18.51242427 0.852718589 3.462738654 0.999907356 0.730965418 0.686920469 0.057479197 0.461839474 9.617102326 0.059141537 0.015279567 7.123912709 -0.852718589 -0.268941938 HLEEIVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HLEEIVEK 8 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;; 121.96 0.0014111 918010000 5166000 4369350 4616560 4554990 5061000 3525400 5902700 4485800 4906900 FALSE TRUE 4842669.282 4692861.22 4726066.983 4671878.755 4663529.475 4543125.75 5017644.933 5045862.004 4087906.69 1.184633028 1.147986384 1.15610931 1.14285357 1.140811136 1.111357498 1.227436268 1.234338841 1 21.96293084 HLEEIVHVEQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLEEIVHVEQGR 12 0 A0A5F9UK94;H0Y360;Q01433-2;Q01433;A0A590UK85;Q01433-5;A0A590UJY6;Q01433-3;Q01433-4;A0A590UJX5 A0A5F9UK94 AMPD2 AMP deaminase 2 0 112.44 0.00073664 230270000 149840 134920 144920 162550 165840 117810 125510 115510 127580 FALSE TRUE 140461.7819 144909.6172 148357.5708 166721.3082 152815.5954 151819.8345 106690.9407 129931.6778 106286.0738 1.321544553 1.363392324 1.395832639 1.568609153 1.437776276 1.42840759 1.003809218 1.222471328 1 16.69759305 1.75725652 9.973118495 1.087524865 1.416642467 0.77367916 0.087553265 0.069104738 28.20374619 0.039829425 0.021758575 57.18162857 -1.75725652 0.329117602 HLEFSHDQYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 HLEFSHDQYR 10 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;;;;; 204.5 1.07E-07 7754810000 811268 1080160 1330310 1404240 1300819 1748183 1334357 1039750 1218570 FALSE TRUE 760492.184 1160136.17 1361865.581 1440275.176 1198657.923 2252855.053 1134282.555 1169565.076 1015182.795 0.749118472 1.142785493 1.341497894 1.418734816 1.180731125 2.219161972 1.117318537 1.152073383 1 19.95330809 5.079501697 0.970346135 1.388143036 2.22E-10 0.236386949 0.336229744 4.728150048 2.26808318 0.096394412 8.014738535 120088.5766 -5.079501697 -1.388143036 HLEGLSEEAIMELNLPTGIPIVYELDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HLEGLSEEAIMELNLPTGIPIVYELDK 27 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;;;; 199.1 5.36E-25 2402955000 2901235 2390103 2570355 2509182 2752275 1920043 3244309 2284673 2765816 FALSE TRUE 2719651.88 2567068.713 2631325.034 2573571.858 2536122.424 2474328.245 2757854.984 2569919.453 2304183.442 1.180310487 1.114090426 1.141977234 1.116912747 1.100659946 1.073841692 1.196890375 1.115327628 1 21.13582415 -2.503476102 1.754578841 1.59E-05 1.130799955 0.559814976 0.036221965 600028.8717 39614.33487 2378689.439 0.008580311 0.003137068 2.503476102 1.130784036 HLEHPEQQDGQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLEHPEQQDGQLK 13 0 P07476 P07476 IVL Involucrin 0 91.914 0.0036508 222020000 108850 103340 121120 116540 122410 97055 128610 103600 205170 FALSE TRUE 102037.2728 110991.4011 123993.0236 119530.6137 112796.4124 125073.2029 109326.1245 116534.6881 170925.8016 0.596968228 0.649354282 0.725420168 0.699312875 0.659914485 0.731739748 0.639611594 0.681785237 1 17.38301067 -1.554504401 2.443228069 1.026423402 0.675903018 0.866277372 0.040360248 1363777.455 1186198.405 234988.6522 0.009789448 0.027893024 1.554504401 -0.350520384 HLEHSTIIYEDPQHHPLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLEHSTIIYEDPQHHPLLR 19 0 P61962;A0A087WWI6 P61962 DCAF7 DDB1- and CUL4-associated factor 7 0 152.32 1.75E-08 174360000 44895 61658 65205 53345 60352 47145 58128 49651 55153 FALSE TRUE 42085.10209 66223.22248 66751.69339 54713.92301 55612.19737 60754.99616 49412.24603 55850.03665 45947.608 0.915936736 1.441276823 1.452778421 1.190789366 1.210339336 1.322266791 1.0754041 1.215515651 1 15.48770214 1.444800922 0.681299832 1.018306767 1.314704732 0.12847013 0.162784277 0.906465737 0.942542444 0.150762112 0.068663755 27.84844322 -1.444800922 0.296397964 HLEIFHTEFQNLLDADKNEDLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLEIFHTEFQNLLDADKNEDLGR 23 1 A0A590UJ56;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;Q13616;A0A590UK34;A0A590UJ50;A0A590UJA0 A0A590UJ56 CUL1 Cullin-1 0 138.22 2.90E-06 169770000 470210 367600 424420 401640 402450 304030 526190 360260 426460 FALSE TRUE 440780.3954 394817.4865 434487.4428 411946.7624 370843.2004 391798.5255 447292.6944 405239.254 355281.071 1.240652631 1.111282077 1.222940028 1.159495386 1.043802304 1.102784689 1.258982622 1.140615944 1 18.4386013 0.966818194 23.61061771 0.999999998 1.163765666 0.370850791 0.066132972 2590.590906 1843346.008 0.062528173 0.015632043 9.264419125 -0.966818194 0.163765668 HLEIIYAINQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLEIIYAINQR 11 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 103.91 0.0026709 516980000 757130 848620 747600 698190 915470 577300 897670 753490 983990 FALSE TRUE 709742.5848 911452.7078 765333.425 716106.7374 843572.679 743957.1383 763072.7171 847564.8851 819755.7122 0.865797669 1.111858929 0.933611579 0.873561144 1.029053737 0.907535168 0.930853797 1.033923732 1 19.64483452 3.730355641 24.84592496 0.950641138 1.011303453 0.00029225 0.078375986 297.085412 2282118.719 0.018424599 0.031498902 5374.717487 -3.730355641 0.060662315 HLEINPDHPIVETLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 HLEINPDHPIVETLR 15 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;; 238.58 5.18E-18 30389330000 3956940 3861163 4005127 3809179 4045893 3393762 4293380 3585038 3498068 FALSE TRUE 3709282.189 4147047.526 4100130.504 3906928.982 3728144.884 4373485.996 3649627.527 4032637.886 2914217.852 1.272822547 1.423039641 1.406940288 1.340644104 1.279295191 1.500740925 1.252352333 1.383780517 1 21.4746773 -2.759173894 0.364301126 0.286251042 1.377692704 0.673659149 0.077618351 42.79634535 1.538216398 23.80380475 0.050925036 0.00174111 2.759173894 1.091441662 HLEINPDHSIIETLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 HLEINPDHSIIETLR 15 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;;; 280.4 6.06E-34 18971371000 2860208.8 2833936.6 2877267.4 2761015.6 2785607.3 2410455.3 3100568.1 2480570.9 2349187.9 FALSE TRUE 2681193.437 3043764.215 2945517.541 2831867.935 2566836.939 3106314.615 2635666.698 2790275.637 1957093.263 1.369987566 1.555247403 1.505047101 1.446976487 1.311555759 1.587208271 1.346725139 1.42572441 1 20.90028108 -3.127866346 0.268937 3.58E-15 1.498155519 0.718907644 0.087353718 32.45017826 0.784076947 18.27941376 0.102242424 0.000744961 3.127866346 1.498155519 HLEPEPEEEIIAEDYDDDPVDYEATR ddPTM_SK-BR-3_Pertuzumab_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 0 175.97 8.66E-13 81110000 39393 49213 50534 45885 43172 38110 52570 43848 50167 FALSE TRUE 36927.46245 52856.78173 51732.69034 47062.48678 39781.44527 49111.73834 44687.61654 49322.51932 41793.80361 0.883563095 1.264703788 1.237807662 1.12606374 0.951850318 1.175096165 1.069240238 1.18013952 1 15.35100144 3.001696098 24.93403789 1.082131882 1.17448887 0 0.12423937 119.8215678 1761415.86 0.034032845 0.040400129 1003.913046 -3.001696098 0.092356988 HLEQQEGQLEQLEEQEGQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLEQQEGQLEQLEEQEGQLK 20 0 P07476 P07476 IVL Involucrin 0 260.53 2.44E-36 131680000 176330 135930 166230 140810 161930 133460 180860 128470 263220 FALSE TRUE 165293.8201 145994.3986 170173.0541 144423.423 149212.671 171987.7355 153741.722 144509.7623 219286.8815 0.75377888 0.665768958 0.776029341 0.658604938 0.680445041 0.784304717 0.701098583 0.658998666 1 17.74245998 -1.53087182 2.982828934 1.011472967 0.711964882 0.789125092 0.047121665 13857624.99 15389060.94 1283689.641 0.010264653 0.029452908 1.53087182 -0.299508084 HLEQQEGQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLEQQEGQLK 10 0 P07476 P07476 IVL Involucrin 0 ; 145.46 3.04E-05 613850000 729200 592310 663490 644860 662970 562620 743000 643770 859930 FALSE TRUE 683560.6737 636165.2487 679228.2961 661408.1993 610903.0105 725039.2606 631594.0477 724146.1016 716402.1276 0.954157794 0.888000222 0.948110384 0.923235951 0.852737571 1.012056264 0.881619447 1.010809535 1 19.4504101 1.223019291 24.99764341 1.005404865 0.922017869 0.377587145 0.044057552 257.5466295 414242.5163 0.036142838 0.009166386 16.71164845 -1.223019291 -0.083386995 HLEQQEGQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLEQQEGQPK 10 0 P07476 P07476 IVL Involucrin 0 101.93 0.0030146 197270000 327010 241040 276190 269840 299280 255760 352320 231750 467710 FALSE TRUE 306543.0278 258886.8524 282741.3572 276764.5512 275775.756 329593.7601 299492.8868 260684.4976 389646.1795 0.786721503 0.664415221 0.725636159 0.7102971 0.707759425 0.845879614 0.768627803 0.669028753 1 18.57180515 -5 0.255573444 2.671371626 0.710506074 0.670846086 0.05717807 108.8370174 1.074326712 95.3046543 0.075695081 1.00E-05 5 -1.960865552 HLEQQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLEQQEK 7 0 P07476 P07476 IVL Involucrin 0 122.18 0.0043663 242020000 502910 419620 469670 443860 489440 371620 574640 433440 707900 FALSE TRUE 471433.7608 450689.1014 480810.7942 455250.1991 451001.3567 478900.6613 488478.0667 487555.9381 589746.9168 0.799383172 0.764207643 0.815283269 0.771941635 0.764737117 0.812044366 0.828284223 0.826720622 1 19.16973645 0.140364141 0.56752552 1.012930314 0.783210947 0.927960161 0.018225911 0.795218766 0.336532273 0.04080997 0.007817431 1.381542155 -0.140364141 -0.229719367 HLFLTSKPMVYLVNLSEKDYIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLFLTSKPMVYLVNLSEKDYIR 22 2 J3KQ32;Q9NTK5;Q9NTK5-3;Q9NTK5-2;C9JCJ9 J3KQ32 OLA1 Obg-like ATPase 1 0 114.72 0.00013147 112690000 45235 66867 42649 38051 87979 26978 51726 66409 58096 FALSE TRUE 42403.8221 71817.90226 43660.65442 39027.45308 81069.48423 34766.11065 43970.1665 74700.30983 48399.40229 0.876122846 1.483859281 0.902090777 0.806362295 1.675010029 0.718316942 0.908485734 1.543413892 1 15.56270161 3.946446701 23.1234296 1.056648731 1.219597632 0.008796629 0.33883483 503.1622692 379298.9622 0.080686971 0.145495405 8839.886742 -3.946446701 0.1629489 HLFS(ph)STENLAAGSWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLFSSTENLAAGSWK 15 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 HLFS(0.377)S(0.245)T(0.377)ENLAAGSWK;HLFS(0.333)S(0.333)T(0.333)ENLAAGSWK 239.18 5.51E-18 2093970000 3288260 2682420 2796020 2616080 2783440 1756470 3538590 2689540 2852630 TRUE FALSE 3082453.676 2881029.168 2862342.915 2683213.042 2564839.85 2263534.375 3008011.28 3025334.989 2376507.624 1.297051878 1.212295361 1.204432456 1.129057199 1.079247474 0.952462492 1.265727595 1.273017161 1 21.1804116 3.597635263 1.531583068 1.126361644 1.249628361 0.238587714 0.102222753 0.682835248 3.188429663 0.032231896 0.066089152 3959.453646 -3.597635263 0.123266717 HLFS(ph)STENLAAGSWKEPAEGGGLSSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HLFSSTENLAAGSWKEPAEGGGLSSDR 27 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 HLFS(0.333)S(0.333)T(0.333)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.385)S(0.307)T(0.307)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.494)S(0.494)T(0.013)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.387)S(0.306)T(0.306)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.333)S(0.333)T(0.333)ENLAAGSWKEPAEGGGLSSDR 208.37 1.25E-25 2292627000 321992 357600 325314 336565 407640 197211 431818 311723 674534 TRUE FALSE 301839.0955 384077.0761 333030.6017 345201.8277 375625.5987 254142.6142 367070.8997 350642.3027 561949.9177 0.537128107 0.683472075 0.592633954 0.61429287 0.668432518 0.452251359 0.653209277 0.623974293 1 19.10008203 0.375349146 1.793675268 0.999994924 0.605667022 0.775760063 0.067152728 3.046833772 8.212072473 0.058672804 0.016402645 2.373280913 -0.375349146 -0.394327902 HLFSS(ph)TENLAAGSWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLFSSTENLAAGSWK 15 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 HLFS(0.11)S(0.78)T(0.11)ENLAAGSWK 263.08 3.14E-25 517590000 825940 689960 712180 661670 738140 469220 967780 674620 767830 TRUE FALSE 774245.8897 741045.3563 729073.2459 678649.5724 680169.4619 604676.1968 822670.3734 758847.792 639674.2126 1.210375336 1.158473082 1.139757132 1.060930016 1.063306052 0.945287749 1.286077127 1.186303554 1 19.2869778 4.258896636 1.27529101 1.10765556 1.209572487 0.130515799 0.095065952 1.742387134 4.233142157 0.028673896 0.186436785 18150.83615 -4.258896636 0.101916927 HLFSS(ph)TENLAAGSWKEPAEGGGLSSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLFSSTENLAAGSWKEPAEGGGLSSDR 27 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 HLFS(0.092)S(0.575)T(0.333)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.348)S(0.582)T(0.069)ENLAAGSWKEPAEGGGLSSDR 208.53 1.22E-25 1254230000 392390 470330 380940 405090 532840 234580 572450 408480 814520 TRUE FALSE 367831.0103 505153.7226 389976.0767 415485.2952 490992.8958 302299.4379 486616.4369 459479.6272 678571.35 0.542066815 0.744437151 0.574701653 0.61229419 0.723568562 0.44549396 0.717119043 0.67712795 1 19.37214099 0.57201861 1.402051489 0.999623309 0.626218894 0.632831116 0.090047969 1.047022996 2.721251574 0.077050853 0.022636542 3.732661522 -0.57201861 -0.373404415 HLFSST(ph)ENLAAGSWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLFSSTENLAAGSWK 15 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 HLFS(0.328)S(0.26)T(0.413)ENLAAGSWK;HLFS(0.057)S(0.371)T(0.573)ENLAAGSWK 250.47 2.86E-18 2464270000 3656310 3081410 3223770 2944440 3130630 1991000 4440300 3128350 3416900 TRUE FALSE 3427468.084 3309560.803 3300239.347 3019999.315 2884762.948 2565769.379 3774518.237 3518931.384 2846597.316 1.204057934 1.162637505 1.15936291 1.060915535 1.013407457 0.901346096 1.325975478 1.236188682 1 21.44080699 -0.326637659 6.661019629 1.000000001 1.136082135 0.109096973 0.119139879 0 0 0.116269874 0.027405072 0.471370436 0.326637659 0.136082134 HLFSST(ph)ENLAAGSWKEPAEGGGLSSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLFSSTENLAAGSWKEPAEGGGLSSDR 27 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 HLFS(0.302)S(0.302)T(0.397)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.034)S(0.208)T(0.758)ENLAAGSWKEPAEGGGLSSDR 215.01 6.46E-34 1462950000 556920 694670 592710 636020 807770 372330 826350 569450 1069550 TRUE FALSE 522063.3713 746104.0896 606769.3611 652341.35 744331.0026 479815.6267 702446.489 640547.086 891035.1954 0.585906566 0.837345251 0.680971262 0.732116255 0.835355333 0.538492339 0.788348757 0.718879669 1 19.76512289 0.072548431 1.506265857 1.00019886 0.722569131 0.45904479 0.096982349 15.35283094 23.59874385 0.089371732 0.023679935 1.181812096 -0.072548431 -0.277629729 HLGGSGSVVPGS(ph)PCLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLGGSGSVVPGSPCLDR 17 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 HLGGSGSVVPGS(0.999)PCLDR 71.98 0.030801 66730000 62759 66060 75279 80174 88200 71494 92856 78833 113160 TRUE FALSE 58831.02622 70951.15114 77064.65343 82231.40057 81273.12778 92133.15719 78933.10483 88675.47358 94272.86496 0.624050476 0.752614776 0.817463789 0.872270092 0.862105207 0.977303037 0.837283399 0.940625636 1 16.52455495 6.122710459 0.304042442 0.953390234 5.15E-15 0.84259766 0.043699958 6.620440125 0.257436863 0.042365324 2.743678444 1326509.789 -6.122710459 -0.953390234 HLHPSCLGS(ph)PPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HLHPSCLGSPPLR 13 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 1 HLHPSCLGS(1)PPLR;HLHPSCLGS(1)PPLR;HLHPSCLGS(1)PPLR;HLHPSCLGS(1)PPLR;HLHPSCLGS(1)PPLR;HLHPSCLGS(1)PPLR 205.52 4.46E-08 7725460000 2327820 6004630 5036480 5906700 6367550 4889130 6165630 5105010 4613390 TRUE FALSE 2182125.901 6449219.053 5155947.684 6058275.922 5867468.308 6300542.463 5241151.02 5742381.736 3843385.405 0.567761406 1.678004773 1.341512011 1.576286342 1.526640628 1.639321015 1.363680835 1.494094693 1 21.87394622 -0.903731604 4.741361632 0.999997254 1.433099057 0.127769572 0.315787503 17635921.03 3719590.335 503.2346965 0.064696886 0.124815464 0.903731604 0.433101803 HLIATQLLSNLEDIMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLIATQLLSNLEDIMR 16 0 P48960-2;P48960-3;P48960 P48960-2 CD97 CD97 antigen;CD97 antigen subunit alpha;CD97 antigen subunit beta 0 177.88 2.88E-09 28249000 47580 47231 45113 43696 68173 40596 50404 51558 68554 FALSE TRUE 44602.05273 50728.03238 46183.10166 44817.31334 62818.96758 52315.40618 42846.38813 57995.12979 57111.89452 0.780959082 0.888221846 0.808642439 0.784728185 1.099927924 0.916015948 0.750218295 1.015464997 1 15.80150362 HLIEQDFPGMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 HLIEQDFPGMR 11 0 A0A024R571;Q9H4M9;C9JC03;C9JIJ3;C9IZH1 A0A024R571 EHD1 EH domain-containing protein 1 0 ;;;;;; 172.11 1.37E-05 1627062000 1263780 1418039 1402797 1376905 1517577 1281775 1497086 1247090 1576744 FALSE TRUE 1184682.266 1523032.083 1436072.007 1412238.713 1398392.624 1651802.635 1272611.853 1402791.932 1313575.24 0.901876215 1.159455535 1.093254473 1.075110637 1.064569871 1.257486122 0.968815347 1.067918981 1 20.32506741 1.62105353 24.99999971 1.013773115 1.099267815 0.14234421 0.091035602 1.384792215 2619.008245 0.038365806 0.021114637 41.788187 -1.62105353 0.0854947 HLIPAANTGESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLIPAANTGESK 12 0 P62258;P62258-2 P62258 YWHAE 14-3-3 protein epsilon 0 ; 160.16 6.88E-05 1294410000 2962400 2144900 2441600 2292800 2403500 1879940 2970800 2264200 2375100 FALSE TRUE 2776988.672 2303710.628 2499515.905 2351637.13 2214738.805 2422648.16 2525356.12 2546890.354 1978680.466 1.403454837 1.164266119 1.263223622 1.188487565 1.119300889 1.224375639 1.276282938 1.287166067 1 20.91610722 -1.399992035 3.659839417 0.998514409 1.233255598 0.484086345 0.077783038 5950873.24 2334876.343 69708.05445 0.016925163 0.039811447 1.399992035 0.234741189 HLLGAEHGDEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLLGAEHGDEPR 12 0 U3KQC1;A0A0A0MQU0;Q9BV38;K7EIR0 U3KQC1 WDR18 WD repeat-containing protein 18 0 ; 145.31 3.69E-05 435220000 416760 408690 437170 414870 447910 352336 479580 372370 464070 FALSE TRUE 390675.7355 438949.8328 447539.8788 425516.2666 412732.9554 454049.6835 407671.4312 418861.2142 386613.719 1.010506654 1.135370555 1.157589234 1.100623816 1.067559 1.174427241 1.054467059 1.083410116 1 18.56053331 0.896369302 1.024315964 1.001248365 1.114103553 0.282721006 0.048914284 0.734052965 1.565202968 0.043517119 0.014192567 7.877153387 -0.896369302 0.112855188 HLLIGVSSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLLIGVSSDR 10 0 P36542-2;P36542 P36542-2 ATP5C1 "ATP synthase subunit gamma, mitochondrial" 0 120.09 0.00060585 393700000 292570 289840 274040 283660 392930 286770 278260 317750 443870 FALSE TRUE 274258.566 311300.0552 280540.3582 290939.1958 362070.8628 369555.8437 236537.4962 357421.787 369785.2295 0.741669878 0.841840156 0.758657555 0.786778845 0.979138251 0.999379678 0.639661829 0.966565883 1 18.49632807 -4.999999999 0.114639315 1.54218161 0.73659703 0.228466402 0.110724295 271.7676584 2.049336967 34.6360574 1.215762976 1.00E-05 4.999999999 -0.805584579 HLLMS(ph)ISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLLMSISK 8 0 Q8TD26 Q8TD26 CHD6 Chromodomain-helicase-DNA-binding protein 6 1 HLLMS(0.5)IS(0.5)K;HLLMS(0.629)IS(0.371)K 53.17 0.089069 1077600000 240224 712420 551320 572540 529170 627970 454190 535690 303150 TRUE FALSE 225188.8087 765168.3181 564397.5708 587232.3457 487611.1228 809254.7448 386088.426 602572.0757 252552.3066 0.891652156 3.029741951 2.23477496 2.325190982 1.930733199 3.204305499 1.528746386 2.385929805 1 17.94622269 0.116246549 0.749577625 0.96937978 2.304010744 0.220237068 0.674081346 5.108200019 3.274192902 1.031388094 0.208840829 1.306912612 -0.116246549 1.334630964 HLLQAPLDDAQEILQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HLLQAPLDDAQEILQAR 17 0 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;; 269.87 1.36E-28 1184220000 1169740 1380070 1328940 1421190 1605050 1132590 1670710 1204920 2469670 FALSE TRUE 1096528.061 1482251.819 1360463.084 1457660.141 1478995.847 1459550.347 1420202.546 1355356.914 2057466.122 0.532950725 0.720425869 0.661232314 0.708473459 0.718843354 0.709392165 0.690267767 0.658750538 1 20.97243725 -5 0.322461253 4.050006074 0.668697028 0.778713866 0.054548326 144.6441513 1.274308188 301.4594228 0.043436304 1.00E-05 5 -3.381309046 HLLQAPVDDAQEILHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HLLQAPVDDAQEILHSR 17 0 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ;;; 226.74 1.14E-15 696960000 365842 445556 416969 452190 496349 379388 521250 432005 535720 FALSE TRUE 342944.6023 478545.4298 426859.7016 463793.961 457367.7517 488911.1568 443093.4015 485941.7752 446304.8711 0.768408826 1.072238868 0.956430748 1.039186419 1.024787721 1.095464532 0.992804314 1.088811274 1 18.76767003 4.744258627 24.9925264 1.029768335 0.768408714 0.782557943 0.043906733 276.4249367 1212415.709 0.009605792 0.08658173 55495.60966 -4.744258627 -0.261359621 HLLTDLPLPPELPGGDLS(ph)PPDS(ph)PEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLLTDLPLPPELPGGDLSPPDSPEPK 26 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 HLLTDLPLPPELPGGDLS(1)PPDS(1)PEPK;HLLTDLPLPPELPGGDLS(1)PPDS(1)PEPK 137.47 8.01E-06 185007000 279853 175685 214845 207078 219997 171501 273741 176657 260290 TRUE FALSE 262337.5003 188692.9002 219941.2249 212391.9721 202719.323 221010.5546 232696.0783 198713.0153 216845.9175 1.209787592 0.870170407 1.014274225 0.979460322 0.934854229 1.019205513 1.073094117 0.916378863 1 17.72631076 HLLTDLPLPPELPGGDLS(ph)PPDSPEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HLLTDLPLPPELPGGDLSPPDSPEPK 26 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 HLLTDLPLPPELPGGDLS(0.993)PPDS(0.007)PEPK;HLLTDLPLPPELPGGDLS(1)PPDSPEPK;HLLTDLPLPPELPGGDLS(1)PPDSPEPK;HLLTDLPLPPELPGGDLS(0.992)PPDS(0.008)PEPK;HLLTDLPLPPELPGGDLS(0.996)PPDS(0.004)PEPK 200.06 3.54E-25 1446030000 1910475 1368129 1581858 1477612 1520341 1135271 1856824 1315076 2153715 TRUE FALSE 1790901.78 1469426.695 1619380.419 1515530.026 1400939.551 1463005.308 1578410.479 1479266.133 1794246.053 0.998136112 0.818966101 0.902540884 0.844661201 0.780795671 0.815387224 0.879706814 0.824449986 1 20.77494632 -1.045722502 4.339251708 1.000008295 0.855729381 0.352945547 0.060314827 0.07585458 31754084.25 727.8174483 0.012851054 0.090007251 1.045722502 -0.144278914 HLLTDLPLPPELPGGDLSPPDS(ph)PEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLLTDLPLPPELPGGDLSPPDSPEPK 26 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 HLLTDLPLPPELPGGDLS(0.353)PPDS(0.647)PEPK 128.91 5.39E-05 475580000 117240 84039 91442 89362 90497 70684 111440 72747 123890 TRUE FALSE 109902.1577 90261.335 93611.04742 91655.18021 83389.73067 91089.32334 94730.60656 81829.62309 103211.9586 1.064819999 0.874524001 0.906978694 0.888028688 0.807946402 0.882546214 0.917825878 0.792830832 1 16.65525061 4.740049436 24.68799676 0.882246624 1.06482007 0.497806278 0.057108362 83.88205527 1390794.842 0.011944124 0.075341009 54960.34314 -4.740049436 0.182573446 HLLVSNVGGDGEEIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLLVSNVGGDGEEIER 16 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ; 166.77 6.56E-09 699170000 723720 753080 753420 814100 907120 646740 966360 739910 874030 FALSE TRUE 678423.6571 808838.8268 771291.4782 834991.1843 835878.4543 833443.3391 821463.2892 832289.3922 728148.7466 0.931710259 1.11081538 1.059249888 1.14673161 1.147950138 1.144605883 1.128153132 1.143021115 1 19.47387367 5.525385999 1.34302162 1.11804464 3.50E-15 0.554101803 0.048948203 6.63177028 2.193208789 0.012170497 16.84717677 335263.2877 -5.525385999 -1.11804464 HLMLPDFDLLEDIESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 HLMLPDFDLLEDIESK 16 0 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;;;;;; 238.17 6.66E-20 2845319000 3906321 3161678 3357696 3372308 3817320 2548571 4238548 3176243 4246840 FALSE TRUE 3661831.342 3395771.929 3437342.135 3458847.133 3517523.086 3284302.075 3603017.076 3572803.93 3538014.968 1.034996 0.959795806 0.971545391 0.977623657 0.994208085 0.92828948 1.01837248 1.009832904 1 21.75450872 1.613538468 25 1.010578414 0.975423007 0.230734767 0.026999789 0.612398565 2687.903026 0.011646577 0.006233606 41.07130178 -1.613538468 -0.035155408 HLMTLVMDPLQTASVQWFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLMTLVMDPLQTASVQWFER 20 0 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A1B0GTG9;A0A1B0GWF8;P30566-2;A0A096LNY6 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 0 154.75 3.79E-08 91458000 121010 153740 130390 140730 184230 138240 150910 144780 151080 FALSE TRUE 113436.2001 165123.0696 133482.9124 144341.3701 169761.3189 178147.6439 128282.4465 162856.1017 125863.772 0.901261724 1.311918966 1.060534817 1.146806327 1.348770312 1.415400485 1.019216606 1.293907684 1 16.94150356 4.753074323 23.92960016 1.198877257 0.901261344 0.299679505 0.143309916 1813.579984 2990061.626 0.032072169 0.672780958 56633.62002 -4.753074323 -0.297615913 HLNEIDLFHCIDPNDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 HLNEIDLFHCIDPNDSK 17 0 A0A087WYT3;Q15185-4;Q15185;Q15185-3 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ;;;;;;; 281.61 3.20E-36 9131020000 10402720 7829230 8448310 8141730 9044200 7039610 11764210 7659190 9730540 FALSE TRUE 9751632.325 8408914.336 8648707.903 8350660.576 8333905.015 9071831.128 10000275.92 8615456.731 8106450.012 1.202947321 1.037311563 1.066892153 1.030125463 1.028058522 1.119088024 1.233619637 1.062790336 1 22.95063884 2.065548522 7.861515124 1.137494655 1.065788928 0 0.078917499 0.432657176 45.20459605 0.027535149 0.020280583 116.2916473 -2.065548522 -0.071705727 HLNFLTSEQALADFAELIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLNFLTSEQALADFAELIK 19 0 P42785;P42785-2;E9PLY4;E9PNF7;E9PQB5;E9PL85;E9PNJ1;E9PQN3;E9PKN6;E9PIG4 P42785 PRCP Lysosomal Pro-X carboxypeptidase 0 87.49 0.0027082 59985000 129150 129850 136090 142330 182640 160630 140560 124590 129830 FALSE TRUE 121066.732 139464.2291 139318.1191 145982.4288 168296.1911 207001.2734 119484.3329 140145.3358 108160.5343 1.119324464 1.289418826 1.288067963 1.349682948 1.555985205 1.913833681 1.104694367 1.295716009 1 16.72281466 1.033145954 1.781090496 1.019473855 1.383739293 0.215519457 0.228809213 0.56966307 3.702440523 0.214672851 0.061566125 10.79309386 -1.033145954 0.364265438 HLNRPTLDDSSEEEHAIEITTQEITQLFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HLNRPTLDDSSEEEHAIEITTQEITQLFHR 30 1 H3BU86;O14662;F8W9Z6;B7ZBM8;O14662-6;O14662-2;O14662-5;B7ZBM4;B7ZBM5;Q96NX8;O14662-4 H3BU86;Q96NX8 STX16-NPEPL1;STX16 Syntaxin-16 0 ;;;; 249.46 8.89E-47 405618100 144203.3 170552.3 169726.7 167802.8 197065.4 132453.6 217536.6 174597.1 186685.7 FALSE TRUE 135177.8729 183180.1698 173752.6975 172108.9039 181588.6784 170690.8041 184919.0063 196395.9323 155526.6506 0.869162117 1.177805662 1.11718922 1.106620012 1.167572745 1.097501961 1.188985975 1.262779925 1 17.24680229 4.742657968 24.6808526 1.145748712 0.869161986 0.601288054 0.069110896 216.6803217 1305137.77 0.014676042 0.113262697 55291.44857 -4.742657968 -0.276586726 HLNSSQPSGFGPANS(ph)LEDVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HLNSSQPSGFGPANSLEDVVR 21 0 Q52LW3;F8VWZ8 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 HLNSSQPSGFGPANS(1)LEDVVR;HLNSSQPSGFGPANS(1)LEDVVR;HLNSSQPSGFGPANS(1)LEDVVR;HLNSSQPSGFGPANS(1)LEDVVR 241.69 3.32E-30 1388700000 921800 1083990 1098570 1193460 1030210 971100 1315030 1095190 1176420 TRUE FALSE 864106.1835 1164249.747 1124628.599 1224086.204 949301.4623 1251440.806 1117853.46 1231926.882 980067.902 0.881679914 1.187927638 1.147500695 1.248981016 0.968607849 1.276891941 1.140587767 1.256981154 1 19.90252218 4.74190241 24.79588503 1.161329054 0.881679796 0.40759637 0.102569441 250.4482751 1858213.122 0.020861671 0.150284126 55195.33967 -4.74190241 -0.279649257 HLNSSQPSGFGPANS(ph)LEDVVRLPDSSNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLNSSQPSGFGPANSLEDVVRLPDSSNK 28 1 Q52LW3;F8VWZ8 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 HLNSSQPSGFGPANS(1)LEDVVRLPDSSNK 165.31 4.14E-12 88916000 52761 69285 68614 68351 75474 45114 104100 70080 126060 TRUE FALSE 49458.78319 74414.93349 70241.55648 70105.00238 69546.57649 58137.67944 88491.17142 78829.64227 105019.7716 0.47094735 0.708580226 0.668841261 0.667540991 0.66222365 0.553587944 0.842614396 0.750617156 1 16.68030144 0.996093239 0.849647973 0.995715792 0.639256798 0.65216277 0.085750927 0.396853213 0.630491903 0.075703762 0.027031376 9.910446891 -0.996093239 -0.356458994 HLPDNECIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HLPDNECIEK 10 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;;;;; 178.53 2.21E-06 2577890000 7672970 6482780 7109800 6841230 7242470 5780400 9437640 6444210 8909830 FALSE TRUE 7192732.504 6962771.777 7278447.813 7016787.544 6673675.621 7449107.643 8022553.497 7248783.804 7422721.813 0.969015502 0.938034855 0.980563195 0.945311938 0.899087395 1.003554738 1.080810207 0.976566816 1 22.82351687 2.016266576 17.25463755 1.031624113 0.949990082 0.492109776 0.034161772 4.39241086 4658.356973 0.012014387 0.008856462 103.8165461 -2.016266576 -0.081634031 HLPHFKPWLHPEQSPLPSLALSELSVQHADS(ph)LENIDESAVAESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLPHFKPWLHPEQSPLPSLALSELSVQHADSLENIDESAVAESR 44 1 Q9Y365;F5H8H3;F5GY11 Q9Y365 STARD10 PCTP-like protein 1 HLPHFKPWLHPEQSPLPSLALSELSVQHADS(1)LENIDESAVAESR;HLPHFKPWLHPEQSPLPSLALS(0.002)ELS(0.106)VQHADS(0.892)LENIDESAVAESR 305.72 6.26E-98 11086400000 1092660 1485030 1129940 1113020 1541050 971660 1529600 1278860 1186520 TRUE FALSE 1024272.361 1594983.166 1156742.71 1141581.978 1420022.149 1252162.468 1300250.68 1438528.486 988482.1468 1.036207244 1.613568006 1.170221146 1.154883759 1.436568332 1.266752741 1.315401279 1.455290306 1 19.91485538 -1.410827052 5.308347665 0.999762297 1.318836953 0.24630065 0.166972392 0.000426669 4.74E-05 0.146852853 0.034588058 0.038830497 1.410827052 0.319074655 HLPNDPMFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLPNDPMFK 9 0 O75390;B4DJV2;A0A0C4DGI3;H0YIC4 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 121.6 0.0018032 0 370030 300530 338950 293020 422410 277420 321220 323580 625710 FALSE TRUE 346870.4828 322781.5539 346990.0541 300539.3893 389235.6225 357506.6505 273056.0431 363979.6753 521274.9588 0.665427098 0.619215538 0.66565648 0.576546761 0.746699253 0.685831238 0.523823442 0.698248917 1 18.99168503 0.971148658 24.04762699 1.000000002 0.637176934 0.775215429 0.060386882 937.7121233 781585.2482 0.056182079 0.01404552 9.357259169 -0.971148658 -0.362823068 HLPNLLDETQIFSYFSQFGTVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLPNLLDETQIFSYFSQFGTVTR 23 0 Q9BYG3 Q9BYG3 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 0 ; 275.2 1.01E-51 413500000 195744 240955 213530 203223 246772 171577 236293 223457 151014 FALSE TRUE 183492.7325 258795.5589 218595.0324 208438.0462 227391.5226 221108.4946 200863.0583 251356.0983 125808.7878 1.458504892 2.057054705 1.737517992 1.656784473 1.807437513 1.757496423 1.596574149 1.997921629 1 16.94087317 -1.797984157 2.768380811 0.787918823 1.768985985 0.648610444 0.175343923 22042660.15 17056785.82 31485748.64 0.039206807 0.015922668 1.797984157 0.981067162 HLPS(ph)PPLTQEVDLHSIAGPPVPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HLPSPPLTQEVDLHSIAGPPVPPR 24 0 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 HLPS(1)PPLTQEVDLHSIAGPPVPPR;HLPS(0.989)PPLT(0.011)QEVDLHSIAGPPVPPR;HLPS(1)PPLTQEVDLHSIAGPPVPPR;HLPS(1)PPLTQEVDLHSIAGPPVPPR 304.19 2.93E-62 958260000 298985 316855 335164 348355 381791 273308 346027 324769 424409 TRUE FALSE 280272.0626 340315.2739 343114.2484 357294.3791 351806.6749 352207.5828 294143.4637 365317.1246 353572.3961 0.792686493 0.962505211 0.970421481 1.010526792 0.995006055 0.996139933 0.831918631 1.033217323 1 18.43164612 4.738585349 6.820721888 0.965318263 0.789841247 0.51143492 0.05528689 0.101354979 33.24630537 0.013372737 0.082117073 54775.37371 -4.738585349 -0.175477016 HLPS(ph)PPTLDSIITEYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLPSPPTLDSIITEYLR 17 0 Q9Y4B6-3;Q9Y4B6-2;Q9Y4B6 Q9Y4B6-3 VPRBP Protein VPRBP 1 HLPS(1)PPTLDSIITEYLR;HLPS(0.993)PPT(0.007)LDSIITEYLR 310.13 2.77E-58 1688340000 166856 181088 177910 192282 176775 157269 217844 166770 196760 TRUE FALSE 156412.7808 194495.9439 182130.1092 197216.2817 162891.8046 202670.0073 185180.3146 187591.6016 163919.4849 0.954204931 1.186533401 1.111094934 1.203128974 0.993730579 1.236399732 1.129702882 1.144413074 1 17.32262783 4.748898988 24.49419786 1.135208196 0.954204797 0.310083275 0.079219035 1172.628348 2778178.2 0.016166621 0.22337918 56091.74977 -4.748898988 -0.1810034 HLPSTEPDPHVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 114.82 0.0004124 719260000 673970 841890 744310 646220 986510 634210 754310 790230 1272360 FALSE TRUE 631787.4208 904224.4116 761965.3847 662803.0992 909033.484 817296.1315 641208.2182 888891.955 1059994.896 0.596028738 0.853046005 0.71883873 0.625288953 0.857582888 0.771037799 0.604916326 0.838581354 1 20.01562589 0.992873309 23.60638546 1.000000008 0.729005072 0.491922948 0.092871637 112.3368687 372106.475 0.085185643 0.021296411 9.837240942 -0.992873309 -0.270994936 HLQDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HLQDIK 6 0 Q99733;Q99733-2;C9JZI7;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 ;; 139.92 0.011846 511870000 1392150 1359000 1327660 1309100 1544270 1052680 1551410 1375170 1696390 FALSE TRUE 1305017.817 1459621.774 1359152.722 1342693.722 1422989.263 1356571.627 1318790.473 1546863.002 1413251.55 0.923415097 1.032811019 0.961720312 0.95007412 1.00689029 0.95989396 0.933160465 1.094541875 1 20.43058685 1.2427258 24.9999991 1.047270938 0.97137612 0.415607402 0.039361778 96.24606727 577709.4272 0.026937908 0.009064006 17.48742238 -1.2427258 -0.075894817 HLQEAEQTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLQEAEQTK 9 0 Q96P70 Q96P70 IPO9 Importin-9 0 112.13 0.0020126 211200000 228760 257480 238030 282740 254150 203200 316610 267160 280310 FALSE TRUE 214442.3199 276544.0871 243676.184 289995.5871 234190.0842 261860.5413 269137.2698 300515.5141 233524.4501 0.918286371 1.184218984 1.043471824 1.241821089 1.002850383 1.121341004 1.15250146 1.286869593 1 17.83321408 1.798458145 3.759194181 1.164423893 1.093563357 0.054688861 0.112594411 0.590725677 15.22893429 0.052006892 0.027146553 62.8721258 -1.798458145 -0.070860536 HLQGGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLQGGEK 7 0 Q8N163-2;Q8N163;E5RHH8;E5RGU7;E5RFJ3;H0YC58 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 187.34 0.00058574 67509000 265510 217870 240010 243220 233080 172730 261200 215990 269150 FALSE TRUE 248892.203 234001.3215 245703.1505 249461.437 214774.837 222594.347 222035.4849 242956.827 224227.1262 1.110000414 1.043590601 1.095777994 1.112539063 0.957845024 0.99271819 0.990225797 1.08353004 1 17.7746013 2.745144314 24.99538183 1.002088829 1.083546112 0.570078832 0.036681172 396.3714319 1504846.918 0.010883487 0.011319293 556.0890122 -2.745144314 0.081457283 HLQIEIEGLIDQMIDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLQIEIEGLIDQMIDK 16 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 223.07 9.06E-15 238690000 555290 482070 503230 510030 564740 400300 608130 489110 642930 FALSE TRUE 520535.3901 517762.9644 515166.8532 523118.2333 520387.5985 515860.1117 516946.5521 550176.4602 535620.8295 0.9718356 0.966659502 0.961812582 0.976657748 0.971559674 0.963106891 0.965135267 1.027175251 1 19.03085254 1.247264938 24.99891507 1.013587628 0.96738433 0.854449624 0.007798978 50.32164456 144527.2947 0.004809751 0.001697395 17.67115505 -1.247264938 -0.046203298 HLQLAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 160.68 0.0013373 1963410000 150266 2413600 131695 135681 2190610 81656 163418 1622200 1442280 FALSE TRUE 140861.1193 2592305.455 134818.8676 139162.8042 2018568.327 105228.7616 138914.988 1824735.241 1201554.151 0.117232435 2.157460364 0.112203738 0.115819003 1.679964508 0.087577211 0.115612757 1.518645864 1 20.19647024 3.904713465 9.111946773 0.58278765 1.263452017 0.049974302 0.765204948 0.642758649 75.80202481 0.180657246 0.326600234 8029.961533 -3.904713465 0.680664366 HLQQGSES(ph)PMMIGELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLQQGSESPMMIGELR 16 0 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 HLQQGSES(1)PMMIGELR;HLQQGSES(1)PMMIGELR 216.82 9.55E-15 380230000 208130 218360 215162 224760 232990 187176 266010 226640 262040 TRUE FALSE 195103.5148 234527.6016 220265.7442 230527.7221 214691.9052 241210.6727 226124.27 254936.5029 218303.8312 0.893724649 1.074317388 1.008987076 1.055994853 0.983454592 1.10493101 1.035823645 1.167805904 1 17.73597792 2.236227032 24.99753266 1.076264735 1.016151996 0.23027349 0.064749876 102.5819071 1098836.467 0.021177129 0.016409001 172.2768937 -2.236227032 -0.060112739 HLQTGENHTSVDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLQTGENHTSVDPR 14 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 53.001 0.087951 252410000 49229 129940 115800 113440 111420 113420 149050 102090 109710 FALSE TRUE 46147.84477 139560.8928 118546.8307 116351.0625 102669.5226 146162.5128 126701.3362 114836.1612 91398.69225 0.504907058 1.526946276 1.297029835 1.273005768 1.123315007 1.5991751 1.386248896 1.25643112 1 16.4798859 4.746428374 24.97917527 1.340945406 0.504906649 0.66781517 0.176580218 532.4166184 1690318.56 0.038699063 0.423814359 55773.56101 -4.746428374 -0.836038757 HLQTYGEHYPLDHFDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLQTYGEHYPLDHFDK 16 0 F5H5P2;P12694;P12694-2 F5H5P2 BCKDHA "2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial" 0 181.72 7.86E-10 103310000 102280 75762 72215 74647 104870 53720 75297 85567 151580 FALSE TRUE 95878.47738 81371.49731 73927.9739 76562.5684 96633.93323 69228.09193 64006.91387 96250.22831 126280.3188 0.759251151 0.644371966 0.585427521 0.606290586 0.765233523 0.54820967 0.506863734 0.762195006 1 16.94627028 0.965973715 6.709835533 0.999970528 0.62199353 0.675303129 0.081767387 0.152577165 27.19246875 0.078757906 0.019764377 9.246422098 -0.965973715 -0.377976998 HLS(ph)ESSGKPLSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HLSESSGKPLSTK 13 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 HLS(0.964)ES(0.031)S(0.006)GKPLSTK;HLS(0.746)ES(0.091)S(0.163)GKPLSTK;HLS(0.897)ES(0.041)S(0.063)GKPLSTK 98.507 0.001991 1281500000 1221990 1105540 1196100 1991100 1866300 517439 919290 461160 766040 TRUE FALSE 1145507.827 1187395.332 1224472.057 2042194.997 1719728.326 666815.2394 781450.9988 518736.8411 638182.9752 1.794952031 1.860587603 1.91868493 3.200014849 2.69472611 1.04486529 1.224493647 0.812834032 1 19.2836106 2.22421664 24.99762513 1.059302847 2.224760381 0.68084145 0.431378801 165.9791805 289254.3996 0.176714353 0.131108363 167.5778601 -2.22421664 1.165457533 HLS(ph)LPAGQVVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLSLPAGQVVPK 12 0 Q8IXS8 Q8IXS8 FAM126B Protein FAM126B 1 HLS(1)LPAGQVVPK 86.378 0.0071789 123320000 207660 172120 197160 187100 216340 125640 240680 183490 365980 TRUE FALSE 194662.9313 184863.9439 201836.7283 191901.3028 199349.5291 161910.2284 204592.2684 206399.1304 304895.5737 0.638457715 0.606318884 0.661986417 0.629400094 0.653828872 0.531035024 0.671024069 0.676950236 1 18.21795568 0.550353079 1.558344628 0.999884546 0.625749886 0.902618805 0.03823574 0.565750351 1.65965751 0.033523531 0.009635471 3.551019676 -0.550353079 -0.37413466 HLS(ph)QDHTVPGRPAASELHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HLSQDHTVPGRPAASELHSR 20 1 Q8TEK3;Q8TEK3-1 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 HLS(0.999)QDHT(0.001)VPGRPAASELHSR;HLS(1)QDHTVPGRPAASELHSR;HLS(0.996)QDHT(0.004)VPGRPAASELHSR;HLS(0.999)QDHT(0.001)VPGRPAASELHSR 215.07 6.12E-25 1089630000 247759 300903 288157 325203 332663 256971 365803 293244 419716 TRUE FALSE 232252.2065 323182.1712 294992.2201 333548.2595 306536.9899 331154.3561 310954.2361 329856.1589 349662.6881 0.664217871 0.924268394 0.843647979 0.953914361 0.876664855 0.947068038 0.889297734 0.943355325 1 18.41560433 4.740384289 24.76096649 0.911428133 0.664217776 0.759990031 0.045211684 64.11393279 870430.5753 0.009525599 0.061494003 55002.73545 -4.740384289 -0.247210357 HLSDAIVEVEEALIQIHDPELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HLSDAIVEVEEALIQIHDPELR 22 0 H7C0I1;B8ZZW5;Q8NBF6-2;Q8NBF6 H7C0I1 AVL9 Late secretory pathway protein AVL9 homolog 0 ;;; 231.76 5.34E-27 207879000 35952.1 98403 79083 92903 86364 70966 93284 86974 57024 FALSE TRUE 33701.92224 105688.8605 80958.88611 95287.04826 79581.31982 91452.73216 79296.93021 97832.89535 47506.32601 0.709419672 2.224732354 1.704170642 2.005775994 1.675173108 1.925064299 1.669186756 2.059365638 1 15.53583202 -1.099831519 4.427957614 0.999936605 1.790191298 0.239003542 0.412214398 35899303.27 105344722.3 44053.75164 0.085981496 0.079463645 1.099831519 0.790254694 HLSPDGQYVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HLSPDGQYVPR 11 0 O95994;B5MC07;C9J3E2;H7C3Z9 O95994 AGR2 Anterior gradient protein 2 homolog 0 ;;; 209.85 1.48E-08 2124530000 845650 2168810 1639910 1901160 1809660 1578520 2060490 1596190 1284810 FALSE TRUE 792722.276 2329390.949 1678809.44 1949946.984 1667536.603 2034213.099 1751538.653 1795477.835 1070366.911 0.74060798 2.176254633 1.568442954 1.821755666 1.557911205 1.900482048 1.636390882 1.677441461 1 20.02967399 0.245022174 1.951335649 0.999977041 1.690691586 0.212720844 0.370441725 24.8102815 61.85266226 0.310404782 0.085512112 1.758013372 -0.245022174 0.690714545 HLSVNDLPVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLSVNDLPVGR 11 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 ; 164.9 2.22E-05 371420000 146017 270300 225849 223170 328010 236196 216626 274350 367210 FALSE TRUE 136878.0566 290313.2932 231206.2449 228896.92 302249.4177 304381.9509 184144.9424 308603.2014 305920.2787 0.447430478 0.948983488 0.755772863 0.748224083 0.988000596 0.994971475 0.601937678 1.008770006 1 18.22279622 4.746878733 24.82619649 0.854082125 0.447430255 0.477470762 0.140023044 882.9858706 2635288.794 0.031608319 0.358370609 55831.42768 -4.746878733 -0.40665187 HLT(ph)PEPDIVASTK ddPTM_SK-BR-3_Pertuzumab_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 147.1 0.00015678 211620000 612850 435210 513950 468900 490100 395800 682870 464560 587320 TRUE FALSE 574492.8125 467433.4012 526141.1367 480932.7678 451609.523 510061.0347 580479.983 522561.3386 489292.4978 1.174129616 0.955325094 1.075310043 0.982914657 0.922984769 1.042446056 1.186365999 1.067993769 1 18.90033764 1.984186608 24.30955349 1.107721964 1.015510145 0.083260981 0.082562469 721.3291707 1108880.967 0.030518628 0.020371394 96.42432504 -1.984186608 -0.092211819 HLTASEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLTASEAK 8 0 P39748;P39748-2 P39748 FEN1 Flap endonuclease 1 0 ; 121.85 0.0014156 306700000 572350 950860 465180 485280 1108180 300150 571970 940420 1293620 FALSE TRUE 536527.6352 1021262.664 476214.2893 497733.1064 1021148.013 386798.4325 486208.4084 1057833.507 1077706.465 0.497842087 0.947625997 0.441877547 0.461844781 0.947519613 0.358908891 0.451151055 0.981559953 1 20.03953285 1.223672458 24.35681319 0.990780742 0.597289857 0.402354639 0.204433257 208.7128037 341437.7327 0.189117609 0.048133762 16.73680123 -1.223672458 -0.393490885 HLTDAYFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HLTDAYFK 8 0 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ;;;; 133.86 0.00090124 6218290000 6694500 8960920 7878070 7798190 9148120 5719620 9153140 8442130 9266460 FALSE TRUE 6275503.195 9624395.841 8064941.541 7998304.758 8429663.557 7370781.444 7780711.631 9496148.514 7719827.962 0.81290713 1.246711182 1.044704828 1.036072928 1.091949665 0.954785713 1.007886661 1.230098463 1 22.88013727 HLTGEFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HLTGEFEK 8 0 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ;;;; 193.41 0.00017079 10856720000 12364700 11952900 13061600 12747900 13142300 10371700 15602000 12005000 13781400 FALSE TRUE 11590815.5 12837905.15 13371427.32 13075032.7 12110156.77 13365841.42 13262624.94 13503850.68 11481195.31 1.009547803 1.118167996 1.164637214 1.138821555 1.05478188 1.164150688 1.155160642 1.176171149 1 23.45276951 4.736163227 3.653317854 1.132524595 0.996233933 0.269570122 0.055872542 0.304236777 7.542861528 0.012008264 0.112797371 54470.73389 -4.736163227 -0.136290662 HLTGEFEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLTGEFEKK 9 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 205.09 1.01E-05 609920000 1780400 1616900 1888000 1930900 2243600 1365900 2266600 1698800 3254500 FALSE TRUE 1668967.942 1736616.958 1932784.252 1980450.163 2067396.706 1760213.156 1926744.372 1910898.92 2711302.925 0.615559378 0.640510119 0.712861788 0.730442233 0.76251041 0.649213019 0.710634121 0.704789901 1 21.37055488 -5 0.255575959 2.937819487 0.66429163 0.848869857 0.041524421 72.39810311 0.714637854 73.50605103 0.058377884 1.00E-05 5 -2.273527857 HLTSNSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HLTSNSPR 8 0 P14923 P14923 JUP Junction plakoglobin 0 ; 99.442 0.0068105 35937000 16036.1 37747 29485 29315.4 38079 21235.8 20870.2 28419.8 34149 FALSE TRUE 15032.42913 40541.82716 30184.39812 30067.68279 35088.42894 27366.23073 17740.90726 31968.07459 28449.31129 0.528393428 1.425054784 1.060988711 1.05688614 1.233366551 0.961929463 0.623597073 1.12368536 1 14.79610611 2.006458313 20.74376218 0.853644562 1.109349611 0.028880847 0.259254279 32.57024887 104609.7247 0.089871283 0.066049861 101.4981935 -2.006458313 0.255705049 HLTYENVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HLTYENVER 9 0 H3BMH2;H3BSC1;P62491-2;Q15907-2;P62491;Q15907 H3BMH2 RAB11A;RAB11B Ras-related protein Rab-11A;Ras-related protein Rab-11B 0 ;;;; 217.66 5.58E-07 4894930000 1532720 2225250 1998030 2058010 2259540 1783790 2443730 2239630 2020430 FALSE TRUE 1436789.791 2390009.825 2045424.215 2110822.021 2082084.843 2298741.216 2077315.373 2519252.736 1683207.181 0.853602461 1.419914229 1.215194564 1.254047657 1.236974787 1.365691189 1.234141226 1.496697949 1 20.68278133 4.749646337 24.6724615 1.287597329 0.853602158 0.495922665 0.134093527 1033.595469 2300324.998 0.027474096 0.415214631 56188.35748 -4.749646337 -0.433995171 HLVYESDQNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HLVYESDQNK 10 0 O43852;O43852-3;O43852-15;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;;; 216.45 7.72E-09 2835210000 3894100 3050420 3137050 2994410 3277160 2159620 3522150 3017460 2782260 FALSE TRUE 3650375.232 3276276.271 3211462.307 3071251.63 3019785.073 2783067.235 2994036.306 3394196.523 2317882.832 1.574874787 1.413477949 1.385515378 1.325024539 1.302820415 1.200693666 1.291711671 1.46435207 1 21.14437621 0.225528799 0.04334854 9.78E-16 2.393665683 0.644346042 0.09236733 92.59538715 1.431784473 44.43129751 34.13869897 1.680849381 -0.225528799 2.393665683 HLVYESDQNKDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLVYESDQNKDGK 13 1 O43852;O43852-3;O43852-15;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 69.795 0.028081 1285200000 2058500 1660500 1818100 1750100 1872000 1216500 2092600 1179600 1782100 FALSE TRUE 1929662.16 1783445.148 1861226.191 1795010.529 1724980.671 1567683.802 1778834.057 1326875.657 1484655.997 1.299736884 1.201251435 1.253641378 1.209041375 1.161872295 1.055923934 1.198145604 0.893725994 1 20.50169726 1.842676498 0.642024613 0.97295116 1.249468446 0.664658067 0.071735137 0.433955789 0.362184986 0.061267419 0.034209031 69.6107796 -1.842676498 0.276517286 HLWNHSIIEEEFVSLVTGCCYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HLWNHSIIEEEFVSLVTGCCYR 22 0 Q15021 Q15021 NCAPD2 Condensin complex subunit 1 0 181.26 2.91E-17 114420000 126110 131830 98379 116720 128050 105880 132520 134280 67778 FALSE TRUE 118217.0002 141590.8304 100712.5963 119715.2328 117993.4695 136445.8372 112649.8563 151045.1536 56465.41394 2.09361788 2.507567385 1.783615656 2.120151513 2.089659161 2.416449782 1.995024005 2.675003034 1 15.78507984 -1.364408445 3.884442695 0.995968534 2.187190548 0.678174689 0.261560543 0.008323632 0.001361953 0.230763721 0.054279792 0.043210725 1.364408445 1.191222014 HLYDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 74.743 0.079523 148370000 446510 354890 416110 400980 417880 276010 488240 348200 479430 FALSE TRUE 418563.7361 381166.4249 425980.3257 411269.8257 385061.3904 355689.6064 415032.9446 391673.5365 399410.0358 1.04795498 0.954323604 1.066523842 1.02969327 0.964075401 0.890537479 1.039114963 0.980630183 1 18.60751106 2.739726076 24.99028524 0.975370427 1.019890524 0.218233042 0.046403123 186.3406743 3995614.734 0.014441232 0.014544884 549.1943693 -2.739726076 0.044520097 HLYISSS(ph)NPDLITR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HLYISSSNPDLITR 14 0 Q16825 Q16825 PTPN21 Tyrosine-protein phosphatase non-receptor type 21 1 HLYISS(0.005)S(0.995)NPDLITR;HLYISS(0.067)S(0.933)NPDLITR;HLYISS(0.358)S(0.642)NPDLITR 242.1 1.17E-17 703090000 617390 810240 724850 715710 885910 607780 903580 737300 734570 TRUE FALSE 578748.662 870231.0127 742043.7843 734076.3303 816334.2022 783236.2195 768096.5674 829353.528 611965.5215 0.945721028 1.422026212 1.212558156 1.199538707 1.333954567 1.279869849 1.255130462 1.355229174 1 19.22309085 -1.073026995 4.726196831 0.999989018 1.264082271 0.270246215 0.127645366 1.29E-05 2.52E-06 0.107698409 0.025383704 0.084522631 1.073026995 0.264093253 HLYTLDGGDIINALCFSPNR ddPTM_SK-BR-3_Pertuzumab_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 ;; 286.6 2.92E-45 5601890000 1587920 1900660 1575360 1457270 1966140 1368470 1763890 1689730 1450740 FALSE TRUE 1488534.922 2041386.844 1612728.283 1494666.015 1811727.295 1763525.074 1499411.07 1900696.51 1208602.122 1.231617002 1.689047874 1.334374857 1.236689882 1.499027068 1.459144446 1.24061595 1.572640388 1 20.20490795 -3.097486417 0.339366707 2.33E-16 1.432490854 0.384685904 0.156618686 92.89656858 2.618574958 66.65682993 0.121044313 0.000798939 3.097486417 1.432490854 HMAAASAECQNYAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HMAAASAECQNYAK 14 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;; 211.38 3.92E-09 843148000 972393 927300 869979 865725 984290 621245 1105050 849054 892770 FALSE TRUE 911532.6579 995958.2569 890615.3127 887940.9692 906987.8338 800588.3464 939358.0113 955060.2609 743760.9195 1.225572135 1.339083879 1.197448386 1.193852683 1.219461537 1.076405503 1.262983825 1.284095784 1 19.50447942 -4.999999999 0.201847289 8.54E-13 1.26285607 0.489154871 0.070165346 123.0187384 1.219821468 50.01879189 0.162988832 1.00E-05 4.999999999 1.26285607 HMDFLSDFEMMLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HMDFLSDFEMMLQR 14 0 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 0 160.18 4.79E-06 52637000 39629 66509 58366 62435 69834 51974 45620 54598 54592 FALSE TRUE 37148.69163 71433.39556 59750.46908 64037.1878 64349.51934 66978.05007 38779.70452 61414.68049 45480.24252 0.816809444 1.57064676 1.3137676 1.408022127 1.414889538 1.472684541 0.852671454 1.350359564 1 15.47295233 1.750700852 25 1.062439859 1.364101133 0.214901923 0.233766493 4.304784038 8879.367181 0.09668115 0.053614806 56.32495476 -1.750700852 0.301661274 HMESEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HMESEK 6 0 A0A087X0W9;Q8N6M0;Q8N6M0-2 A0A087X0W9 OTUD6B OTU domain-containing protein 6B 0 ; 117.7 0.017066 83004000 152503 119075 139534 127500 134515 91681 134745 120781 158384 FALSE TRUE 142958.1095 127891.4369 142843.8124 130771.8659 123950.7345 118147.8164 114541.2382 135860.7737 131948.6872 1.083437149 0.969251302 1.082570925 0.99108122 0.939385887 0.89540729 0.868074102 1.029648544 1 17.00961747 2.869199439 3.201940029 0.927940687 1.0344021 0.351373103 0.057256748 0.237714602 4.597651227 0.017517794 0.018851183 739.9449987 -2.869199439 0.106461413 HMGIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HMGIGK 6 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ;;;; 74.849 0.060109 2996700000 8421670 8288550 8670970 8730050 9583350 6987930 10244330 8306490 9966810 FALSE TRUE 7894572.708 8902242.866 8876649.503 8954077.863 8830712.348 9005231.951 8708287.82 9343573.561 8303285.023 0.950777034 1.072135046 1.069052728 1.078377755 1.06352032 1.08453846 1.048776213 1.125286382 1 22.98525079 4.739299965 24.84861532 1.069621628 0.950776994 0.581582385 0.031132898 35.32779193 1187090.315 0.006197747 0.037546909 54865.57883 -4.739299965 -0.118844634 HMLPSGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HMLPSGFR 8 0 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ; 81.548 0.022576 661520000 778260 1534040 732080 743930 1583750 546740 834310 1424710 1114630 FALSE TRUE 729550.0958 1647621.918 749445.2833 763020.5033 1459368.664 704574.9624 709212.9609 1602588.18 928591.0522 0.785652731 1.774324568 0.807077864 0.821697023 1.571594579 0.758757002 0.763751664 1.725827721 1 19.82468385 3.89724975 9.156129375 1.030956468 1.34255799 0.036302238 0.409889287 0.737953633 78.57569113 0.097087869 0.175459713 7893.138988 -3.89724975 0.311601522 HNALIQEVISQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HNALIQEVISQSR 13 0 A0A0A0MTN0;Q13617;Q13617-2 A0A0A0MTN0 CUL2 Cullin-2 0 133.14 6.62E-06 0 295260 299470 308700 320380 335530 233980 330730 285760 360880 FALSE TRUE 276780.2037 321643.0704 316022.5098 328601.4932 309178.8273 301526.2277 281140.1068 321437.765 300646.7966 0.920615841 1.069837011 1.051142115 1.092981854 1.028378917 1.00292513 0.935117586 1.069154132 1 18.19771006 2.254226848 3.832900587 0.989109398 1.043784282 0.037960635 0.055704865 0.377390173 12.10123015 0.019916627 0.015340885 179.5671329 -2.254226848 0.054674883 HNDDEQYAWESSAGGSFTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 29 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 3100164400 1601205.3 1584878.9 1662181.2 1649517.3 1590930.9 1374959.3 1763223.4 1419644.7 1355867.1 FALSE TRUE 1500988.719 1702224.983 1701608.923 1691846.707 1465985.605 1771887.729 1498844.42 1596890.466 1129564.122 1.328821171 1.50697508 1.506429684 1.497787221 1.29783301 1.568647317 1.326922829 1.413722723 1 20.10733474 -0.366820718 0.48421009 0.924812397 1.467315976 0.693226524 0.090298214 3.705188421 0.835564094 0.562900017 0.041500598 0.429713781 0.366820718 0.542503579 HNDIVDS(ph)DS(ph)DAEDRGTLSAELTAAHFGGGGGLLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HNDIVDSDSDAEDRGTLSAELTAAHFGGGGGLLHK 35 1 P78316;E9PFK5;P78316-2 P78316 NOP14 Nucleolar protein 14 2 HNDIVDS(0.998)DS(0.989)DAEDRGT(0.006)LS(0.006)AELTAAHFGGGGGLLHK 95.252 0.00017771 93533000 36838 37202 31874 36757 34430 17196 32810 22838 44349 TRUE FALSE 34532.37534 39956.47479 32630.06633 37700.24685 31726.00668 22160.20605 27890.44509 25689.37457 36946.86539 0.934649664 1.081457774 0.883161967 1.020390944 0.858692783 0.599785822 0.754879874 0.695305929 1 15.17316435 2.482701399 5.942034514 0.736528226 0.977637694 0.446822276 0.112386841 0.115211273 16.14113229 0.034026185 0.029967144 303.8794973 -2.482701399 0.241109468 HNESVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HNESVVK 7 0 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 ; 73.208 0.049518 323700000 842800 884070 812800 870430 979810 705330 945820 826120 915680 FALSE TRUE 790050.6524 949527.4627 832079.9998 892766.7074 902859.675 908947.3209 804003.0716 929262.9005 762847.0925 1.035660567 1.24471532 1.090755943 1.170308855 1.183539511 1.191519677 1.053950496 1.218150937 1 19.54103438 -1.339716422 3.844650911 0.99957012 1.148561717 0.31500164 0.068855247 4962412.833 1742478.498 17745.99987 0.014539091 0.045738675 1.339716422 0.148991597 HNGAAEPEPEAETAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HNGAAEPEPEAETAR 15 0 Q9Y446;Q9Y446-2;E9PQ15 Q9Y446 PKP3 Plakophilin-3 0 ; 130.29 6.06E-05 446310000 548840 581120 577230 586110 592830 501660 686640 536280 598850 FALSE TRUE 514489.0841 624146.7295 590922.1682 601150.5749 546271.5232 646481.0982 583684.7065 603235.7385 498898.0663 1.031250909 1.251050609 1.184454718 1.204956715 1.094956185 1.295818008 1.169947823 1.209136253 1 18.92838555 -1.214716495 3.833017732 0.999816316 1.188881642 0.361022892 0.074547934 4788651.443 1522525.527 7292.886385 0.015215424 0.060993493 1.214716495 0.189065325 HNGPNDASDGTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HNGPNDASDGTVR 13 0 P31942;P31942-2 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;;; 281.13 4.54E-32 1105090000 1265390 1327060 1311290 1306390 1405800 1075930 1455870 1190230 1482330 FALSE TRUE 1186191.499 1425316.903 1342394.418 1339914.179 1295394.139 1386533.525 1237575.809 1338832.836 1234919.547 0.96054152 1.154177944 1.087029857 1.085021435 1.048970471 1.122772353 1.00215096 1.084145796 1 20.23598562 1.186356198 0.643642979 1.003930455 1.087891921 0.082409411 0.056856712 1.211516751 1.2147232 0.051245074 0.02255718 15.35876156 -1.186356198 0.083961466 HNGS(ph)LSPGLEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HNGSLSPGLEAR 12 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HNGS(0.639)LS(0.361)PGLEAR 231.92 2.41E-12 751180000 507980 562630 552300 673620 564230 374170 497000 342000 358910 TRUE FALSE 476186.4386 604287.7106 565400.8168 690906.2296 519917.6518 482186.8049 422479.4639 384699.4528 299005.6024 1.592566945 2.020991265 1.890937201 2.310679881 1.738822442 1.612634683 1.412948321 1.286596137 1 18.18981299 1.675799794 1.038690584 1.064574938 1.953808414 0.748668762 0.187244607 0.227281854 0.462715078 0.154798913 0.060449605 47.40234146 -1.675799794 0.889233476 HNGS(ph)SEILNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HNGSSEILNK 10 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2 Q8TDM6-4 DLG5 Disks large homolog 5 1 HNGS(0.832)S(0.168)EILNK 131.06 0.00016757 362450000 1037300 802940 997520 894980 1067700 727900 1244300 835630 1164400 TRUE FALSE 972377.2446 862390.5131 1021181.645 917946.702 983847.1489 938032.9135 1057728.767 939960.2449 970054.1177 1.002394843 0.889012785 1.052705851 0.946284012 1.014218827 0.966990291 1.090381193 0.96897712 1 19.88770571 3.971966886 24.92026318 1.009970658 0.94176187 0.194703443 0.049946868 262.5465571 1269367.32 0.011720507 0.021977018 9374.905229 -3.971966886 -0.068208788 HNGSLS(ph)PGLEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HNGSLSPGLEAR 12 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HNGS(0.02)LS(0.98)PGLEAR;HNGSLS(1)PGLEAR;HNGSLS(1)PGLEAR 170.77 4.00E-05 3075900000 1468950 1634280 1574320 1941500 1619130 1099210 1486150 991280 984590 TRUE FALSE 1377011.042 1755283.792 1611663.614 1991322.177 1491970.061 1416534.083 1263315.604 1115043.49 820255.5683 1.678758542 2.139923043 1.964831055 2.427685046 1.818908787 1.726942355 1.54014877 1.359385456 1 19.64571396 1.49713208 0.919513766 1.036169514 2.050366628 0.755546077 0.196802119 0.231301119 0.392183806 0.168070941 0.064394335 31.41463951 -1.49713208 1.014197114 HNGVGGS(ph)PPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HNGVGGSPPK 10 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 HNGVGGS(1)PPK 87.498 0.0082672 308990000 363540 201000 245770 272250 249410 170760 313070 211290 235180 TRUE FALSE 340786.6803 215882.2491 251599.7805 279236.3959 229822.3447 220055.6399 266128.0599 237670.0216 195926.9387 1.739355918 1.101850775 1.284151032 1.425206752 1.173000233 1.123151525 1.358302547 1.213054331 1 17.57995625 7.999999644 0.02708133 7.56E-08 3.030495756 0.326735783 0.170314233 2602.553256 5.412228395 201.6843498 449.4617617 99999918.09 -7.999999644 3.030495681 HNGYDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 77.923 0.036733 2368880000 1977370 2067350 1857720 2030020 2517560 1536130 2268970 2005230 2328890 FALSE TRUE 1853609.941 2220418.745 1901785.996 2082113.75 2319840.993 1979585.794 1928759.013 2255587.38 1940183.214 0.955378816 1.144437664 0.980209489 1.073153162 1.195681406 1.02030869 0.994111793 1.162564114 1 20.88776146 -1.741526012 6.183273638 0.998433377 1.06211261 0.059261619 0.081173572 0.001653104 6.91E-05 0.074114253 0.017047336 0.018133181 1.741526012 0.063679232 HNIAGTTHSGAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HNIAGTTHSGAEK 13 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 0 ; 85.837 0.0052635 97800000 142813 114288 136529 133306 137512 109169 153533 131248 131129 FALSE TRUE 133874.5893 122750.0024 139767.5324 136726.8576 126712.3622 140684.3181 130512.152 147634.6017 109242.7228 1.225478328 1.123644663 1.279421904 1.251587787 1.159915819 1.287814094 1.19469882 1.351436489 1 16.73717765 -1.012062188 4.784170155 0.999995744 1.226699034 0.554640676 0.065658493 2.73E-06 5.64E-07 0.058220028 0.013722335 0.097260794 1.012062188 0.226703289 HNIQFSSFDIFSDEEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HNIQFSSFDIFSDEEVR 17 0 O76003 O76003 GLRX3 Glutaredoxin-3 0 ;;; 275.37 1.02E-35 994570000 557023 636030 649550 672620 674420 571534 749450 607130 613930 FALSE TRUE 522159.9247 683122.323 664957.6327 689880.5679 621453.7737 736526.5877 637076.9301 682931.517 511461.1169 1.020918126 1.335629045 1.300113754 1.348842649 1.215055755 1.440044147 1.245601883 1.335255984 1 18.96426504 -1.164383708 5.158598983 0.999985776 1.290821716 0.384322353 0.11072261 1.58E-05 2.55E-06 0.093325335 0.021995917 0.068488285 1.164383708 0.290835939 HNKPEVEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HNKPEVEVR 9 1 F8WCF6;P59998;P59998-3;F8WDD7;H7C0A3;A0A0A6YYG9;P59998-2;F8WE39 F8WCF6 ARPC4-TTLL3;ARPC4 Actin-related protein 2/3 complex subunit 4 0 ;;;;; 154.24 4.58E-05 4501930000 6808860 6457880 6079550 6019120 7414410 4357510 7134690 6255160 7734090 FALSE TRUE 6382705.607 6936028.155 6223759.797 6173580.81 6832112.147 5615452.399 6064909.47 7036130.495 6443220.415 0.990607987 1.076484694 0.965939297 0.958151423 1.060356733 0.871528838 0.941285425 1.092020766 1 22.61935052 3.833645832 4.740440295 0.974974191 1.036716699 0.077351186 0.064595162 0.402349126 14.59329781 0.015971974 0.029606074 6817.824721 -3.833645832 0.061742508 HNKS(ph)PTLSCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HNKSPTLSCR 10 1 Q5T5U3;A0A087WW76;A0A452Q6Z5 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 HNKS(0.689)PT(0.311)LSCR;HNKS(0.879)PT(0.118)LS(0.003)CR;HNKS(0.999)PT(0.001)LSCR;HNKS(1)PTLSCR 115.12 0.0007665 469010000 645460 610762 565740 565888 740120 371308 617500 590247 781620 TRUE FALSE 605061.8108 655983.454 579159.62 580409.6441 681993.9607 478498.5919 524911.6076 663940.6372 651162.5725 0.929202378 1.007403499 0.889424 0.891343681 1.047348219 0.734837369 0.806114525 1.019623463 1 19.31265825 2.25033915 24.99956839 0.86174505 0.948908676 0.061278007 0.096374772 392.8861574 833888.1258 0.031912181 0.026498309 177.9668651 -2.25033915 0.087163627 HNLITEMVALNPDFKPPADYKPPATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HNLITEMVALNPDFKPPADYKPPATR 26 2 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 0 ; 169.56 4.83E-12 611660000 769250 488880 611870 579090 642910 403350 749380 535290 724070 FALSE TRUE 721104.0157 525077.1839 626383.8453 593950.4298 592418.442 519790.5972 637017.4259 602122.1348 603218.0393 1.195428466 0.870460016 1.038403702 0.984636385 0.982096694 0.861696042 1.05603179 0.998183237 1 19.20232005 HNMCGETEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HNMCGETEEEK 11 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;; 176.51 8.57E-06 1268530000 2599800 1340460 1979660 1769250 1680280 1558680 2230300 1648510 2002730 FALSE TRUE 2437083.159 1439709.053 2026618.47 1814651.95 1548317.587 2008645.613 1895887.22 1854330.102 1668461.425 1.460676958 0.862896218 1.214663066 1.087619961 0.92799124 1.203890952 1.136308692 1.111401243 1 20.6700869 4.761487523 24.18653992 1.07842104 1.460677618 0.54413357 0.112574833 3373.469951 3558723.404 0.025878882 1.397800323 57741.42841 -4.761487523 0.382256579 HNMCGETEEEKIRVDIIENQVMDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HNMCGETEEEKIRVDIIENQVMDFR 25 2 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 88.222 0.0092048 51448000 34914 30980 36277 36545 51008 24838 41394 30733 107130 FALSE TRUE 32728.79506 33273.79143 37137.50757 37482.80657 47002.03744 32008.32739 35187.35398 34570.0827 89249.31091 0.36671202 0.372818469 0.41610974 0.419978666 0.526637539 0.35863949 0.394259111 0.387342853 1 16.44555341 -1.974939588 2.551773062 1.513892514 0.404569484 0.939550469 0.047405076 8225977.552 3958045.877 24955540.93 0.01109809 0.010594011 1.974939588 -1.10932303 HNNCMASHLTPAVYAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HNNCMASHLTPAVYAR 16 0 P12532;P12532-2;F8WCN3;C9JSQ1;C9J8F6;C9J6W7;C9JT96;C9JJX8;C9J995 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ;;; 218.63 7.61E-15 1072150000 604870 731440 600470 708660 961130 517249 809750 736130 991530 FALSE TRUE 567012.2664 785596.5787 614713.432 726845.4154 885646.7268 666570.3895 688335.5049 828037.4509 826037.2375 0.686424583 0.951042572 0.744171575 0.879918462 1.072163199 0.806949565 0.833298396 1.002421457 1 19.65584729 7.999999984 0.072055465 1.123287701 0.282031709 0.263511284 0.104890266 390.8422946 2.072869808 4.096230963 33.19123203 99999996.39 -7.999999984 -0.841255992 HNQLPLVIEFTEQTAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HNQLPLVIEFTEQTAPK 17 0 P07237;H7BZ94;I3L398;I3L312;I3L4M2;I3NI03 P07237 P4HB Protein disulfide-isomerase 0 ; 122.01 5.83E-05 1263300000 1693400 1275910 1384090 1407220 1317180 1243470 2113810 1204600 1523300 FALSE TRUE 1587413.117 1370379.704 1416921.268 1443331.648 1213733.996 1602439.603 1796863.814 1354996.962 1269051.389 1.250865907 1.079845714 1.116520009 1.137331128 0.956410439 1.26270663 1.415910994 1.067724265 1 20.27531906 2.171507125 24.99999905 1.243583328 1.1067843 0.003916905 0.135584099 86.43230253 32223.78251 0.04718675 0.034849731 148.4250229 -2.171507125 -0.136799027 HNQLQDGHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HNQLQDGHER 10 0 J3KMX2;B9EGA3;Q92925-3;Q92925-2;Q92925;J3QWB6 J3KMX2 SMARCD2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 0 86.911 0.0076539 38595000 26549 31117 26268 27518 27315 21920 28854 28298 29672 FALSE TRUE 24887.34548 33420.93506 26891.08936 28224.15847 25169.79008 28247.94816 24527.61057 31831.06759 24719.55151 1.006787905 1.352004103 1.087846976 1.141774698 1.018213865 1.142737082 0.992235258 1.287687909 1 14.59336495 3.724733443 24.57671192 1.09100652 1.208815683 0.065295145 0.119537013 144.3563962 1485820.293 0.027821326 0.04547137 5305.587037 -3.724733443 0.117809164 HNS(ph)SDGFFNNGPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HNSSDGFFNNGPLR 14 0 Q9HC44 Q9HC44 GPBP1L1 Vasculin-like protein 1 1 HNS(0.823)S(0.177)DGFFNNGPLR 170.23 2.07E-06 100610000 70018 74295 65257 69576 88127 45728 70575 69588 78321 TRUE FALSE 65635.69837 79795.8791 66804.92686 71361.43795 81205.86091 58928.93127 59992.93394 78276.21498 65248.71913 1.005930833 1.222949357 1.023850395 1.093683354 1.244558698 0.903143112 0.919449987 1.199659028 1 15.99366196 2.226987125 24.99911689 0.986925227 1.118500036 0.201742466 0.108548878 297.6119078 642846.7432 0.038300346 0.028524579 168.6503027 -2.226987125 0.131574809 HNS(ph)TTSSTSSGGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.494)T(0.494)T(0.005)S(0.005)S(0.002)TSSGGYR;HNS(0.446)T(0.07)T(0.446)S(0.027)S(0.011)T(0.001)SSGGYR;HNS(0.859)T(0.139)T(0.002)SSTSSGGYR;HNS(0.85)T(0.132)T(0.013)S(0.002)S(0.003)TSSGGYR 146.26 6.59E-06 1469200000 1088800 1354900 1218600 1232060 1443870 792030 1404850 1201930 1333320 TRUE FALSE 1020653.952 1455218.206 1247505.767 1263676.745 1330474.274 1020676.203 1194205.784 1351993.606 1110780.278 0.918862147 1.310086463 1.12308959 1.137647805 1.197783486 0.91888218 1.075105318 1.217156653 1 20.08314204 2.301775067 24.99999391 1.055751084 1.159072113 0.09327624 0.121118138 117.1967256 46347.73399 0.039184356 0.032783971 200.3434125 -2.301775067 0.103321029 HNS(ph)TTSSTSSGGYRR ddPTM_SK-BR-3_Pertuzumab_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(0.734)T(0.132)T(0.132)S(0.003)STSSGGYRR;HNS(0.973)T(0.023)T(0.005)SSTSSGGYRR;HNS(0.947)T(0.052)T(0.001)SSTSSGGYRR 132.74 2.79E-05 1269560000 73204 122638 90741 94891 123263 59164.6 115654 89012 152308 TRUE FALSE 68622.29231 131718.2451 92893.41937 97326.06371 113582.4212 76244.45956 98312.75638 100125.3441 126886.8109 0.540815013 1.038076726 0.732096731 0.767030577 0.895147576 0.600885616 0.774806741 0.789091817 1 16.95318259 3.728098759 24.99439596 0.77606541 0.843001206 0 0.15866538 180.5357285 4616050.386 0.037205504 0.062562033 5346.859342 -3.728098759 0.066935796 HNS(ph)WDTVNTVLPEDPEVADLFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HNSWDTVNTVLPEDPEVADLFSR 23 0 Q8N961 Q8N961 ABTB2 Ankyrin repeat and BTB/POZ domain-containing protein 2 1 HNS(0.5)WDT(0.5)VNTVLPEDPEVADLFSR 133.1 1.56E-05 115990000 101970 93145 92237 102210 116660 72462 118360 98309 136210 TRUE FALSE 95587.87972 100041.5527 94424.9052 104832.8816 107497.9942 93380.60308 100613.0168 110583.0951 113475.671 0.842364525 0.881612347 0.832115856 0.92383575 0.947321952 0.822912984 0.886648353 0.974509285 1 16.79202349 1.20832634 3.822621065 0.996739764 0.87372754 0.592407814 0.038502577 0.14721669 4.097640412 0.034143848 0.009441947 16.15572084 -1.20832634 -0.123012223 HNS(ph)WSSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HNSWSSSSR 9 0 Q96F86;H3BPW9;H3BQ37 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 1 HNS(0.863)WS(0.128)S(0.007)S(0.001)SR;HNS(0.688)WS(0.301)S(0.01)S(0.002)SR;HNS(0.76)WS(0.234)S(0.005)S(0.001)SR 107.79 0.0028498 1307950000 894300 1513230 1353840 1371960 1573270 1390470 1391170 1371790 1357250 TRUE FALSE 838327.3594 1625271.124 1385953.724 1407166.816 1449711.72 1791876.117 1182576.973 1543061.001 1130716.207 0.741412703 1.437382001 1.225730838 1.244491596 1.282118105 1.584726659 1.045865414 1.364675762 1 20.10880545 -1.154690487 3.847952988 0.999862032 1.257969749 0.095846329 0.227050799 11302637.88 6783385.219 12533.38206 0.046762517 0.070034094 1.154690487 0.258107717 HNSPS(ph)GHLTHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HNSPSGHLTHSR 12 0 A0A087WVA8;Q8IWB9;Q8IWB9-2;J3KRZ8 A0A087WVA8 TEX2 Testis-expressed sequence 2 protein 1 HNS(0.2)PS(0.799)GHLTHSR 82.349 0.025393 69721000 36380 50857 43127 44901 49071 36377 51980 35923 48154 TRUE FALSE 34103.04074 54622.5052 44149.99281 46053.23568 45217.1616 46878.44937 44186.08156 40408.06563 40116.78631 0.850094035 1.361587261 1.10053663 1.147979186 1.127138182 1.16854947 1.101436222 1.007260784 1 15.29191842 1.352958761 2.617127936 0.997254706 1.150977688 0.11846004 0.124040315 0.444622089 5.09573196 0.097966676 0.029948931 22.54025168 -1.352958761 0.153722982 HNTPEDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HNTPEDAK 8 0 P46977;P46977-2 P46977 STT3A Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A 0 ; 96.331 0.0090166 196058000 484390 422550 415040 425820 463120 324000 552180 506100 421340 FALSE TRUE 454072.8946 453836.0417 424884.9448 436747.2621 426748.4233 417533.5403 469385.7352 569287.6991 351015.632 1.293597359 1.292922594 1.21044451 1.244238781 1.215753329 1.189501271 1.337221743 1.621830047 1 18.42117576 1.598871219 6.556261702 1.364406263 1.243103907 0.032075567 0.152362306 0.259398993 23.7437027 0.071581901 0.034099933 39.70737881 -1.598871219 -0.121302356 HNTPSLLEAALTQEAS(ph)TPDSQVWPTAPDITR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HNTPSLLEAALTQEASTPDSQVWPTAPDITR 31 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 HNT(0.021)PS(0.017)LLEAALT(0.017)QEAS(0.441)T(0.441)PDS(0.063)QVWPTAPDITR 91.532 0.00032858 56042000 19261 24302 25574 25331 29294 24832 35782 29600 29195 TRUE FALSE 18055.48839 26101.34537 26180.62736 25981.03635 26993.36741 32000.59529 30416.82128 33295.62516 24322.16589 0.742347062 1.073150536 1.076410196 1.06820406 1.109825808 1.315696777 1.25058029 1.368941619 1 14.56998409 5.664133337 0.459956449 1.2324579 2.10E-13 0.55394005 0.117928822 7.993251739 0.68387341 0.069663605 6.404044007 461459.2294 -5.664133337 -1.2324579 HNTPSLLEAALTQEAST(ph)PDSQVWPTAPDITR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HNTPSLLEAALTQEASTPDSQVWPTAPDITR 31 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 HNTPSLLEAALT(0.003)QEAS(0.034)T(0.83)PDS(0.133)QVWPTAPDITR 114.03 0.00025818 49115000 22961 32063 32453 29617 42599 32825 43174 38270 37278 TRUE FALSE 21523.912 34436.97788 33222.80049 30377.02236 39253.44638 42301.04463 36700.45951 43048.09374 31056.06097 0.693066388 1.108864962 1.069768652 0.97813507 1.263954447 1.362086604 1.181748694 1.386141461 1 14.92258724 2.736115374 24.30461057 1.254405305 1.004744774 0.432150336 0.153464627 143.7000372 1428303.248 0.044707137 0.044027577 544.6473236 -2.736115374 -0.249660531 HNTYLQECTGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HNTYLQECTGQR 12 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;X6R960 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 0 173.06 3.41E-05 88175000 35045 54047 58462 57093 58843 40326 65541 58393 56355 FALSE TRUE 32851.59601 58048.69612 59848.74625 58558.10304 54221.70814 51967.46156 55713.7355 65683.49459 46948.98643 0.699729611 1.236420646 1.274761199 1.247270868 1.154906895 1.106892087 1.186686652 1.399039672 1 15.51880639 4.740356723 24.93527019 1.210126226 0.699729433 0.689109867 0.105591458 82.09976047 1139693.896 0.02313175 0.149645246 54999.24436 -4.740356723 -0.510396793 HNVMISTEWAAPNVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HNVMISTEWAAPNVLR 16 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ;; 189.81 9.58E-10 2684540000 2368330 2840390 2304420 2392710 3114590 1782140 2905460 2579120 3381660 FALSE TRUE 2220100.453 3050695.431 2359081.931 2454110.989 2869982.665 2296614.887 2469813.246 2901128.809 2817239.1 0.78804119 1.082867064 0.837373701 0.871104973 1.018721721 0.815200558 0.876678606 1.029777277 1 21.42585058 1.233120504 24.87089283 1.0148887 0.908072847 0.217090087 0.090445194 218.7401717 999971.0609 0.07428724 0.020692787 17.1048986 -1.233120504 -0.106815852 HNWGQGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HNWGQGFR 8 0 E5RGY0;B4E1G1;Q9BUN8-2;Q9BUN8 E5RGY0 DERL1 Derlin-1 0 ;;;; 163.67 0.00033456 3102840000 1333310 1574550 1244850 1197874 1679560 964923 1527470 1567830 1825440 FALSE TRUE 1249860.507 1691131.32 1274378.43 1228613.475 1547654.133 1243480.606 1298440.054 1763577.027 1520762.271 0.821864489 1.112028719 0.837986616 0.807893185 1.017683146 0.81766929 0.853808697 1.159666478 1 20.53636321 1.244145444 24.99934647 1.079833254 0.905926299 0.343501276 0.105152147 146.6649832 656539.3161 0.073306765 0.025082453 17.5446797 -1.244145444 -0.173906956 HNYECLVYVQLPFMEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HNYECLVYVQLPFMEDLR 18 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 155.01 2.19E-08 575290000 602180 667080 618960 619100 706950 504530 787460 659690 543870 FALSE TRUE 564490.6287 716471.2973 633642.0235 634987.1541 651428.9987 650179.6206 669387.6834 742053.7487 453094.5835 1.245856052 1.581284181 1.398476271 1.401445034 1.43773292 1.434975487 1.47736854 1.637745795 1 18.78945272 -1.233775522 4.04409884 0.99964282 1.457472132 0.643240734 0.105683244 55.65302333 25500241.44 16397.5963 0.022146564 0.058374675 1.233775522 0.457829311 HNYEGTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HNYEGTLR 8 0 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 114.89 0.0025683 397900000 507790 523640 543930 530820 578620 451680 541710 502830 587750 FALSE TRUE 476008.3303 562410.8504 556832.2765 544441.7399 533177.5192 582072.6836 460485.6145 565609.4324 489650.728 0.972138512 1.148595965 1.137202999 1.111898153 1.08889355 1.188750777 0.940436904 1.15512834 1 18.9013935 1.74486454 25 1.029173059 1.11540932 0.175176782 0.07658484 1.825791063 7264.685881 0.03163546 0.017543495 55.57308926 -1.74486454 0.086236261 HNYPDLVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HNYPDLVER 9 0 Q9NZT2-2;Q9NZT2;A0A087X028;Q4VXW3 Q9NZT2-2 OGFR Opioid growth factor receptor 0 103.34 0.003438 90778000 82285 117650 95641 97610 109750 70245 89371 96774 105160 FALSE TRUE 77134.92873 126360.9284 97909.64968 100114.8379 101130.6777 90523.59117 75970.64823 108856.4469 87608.11664 0.880454137 1.44234271 1.117586514 1.142757563 1.154352834 1.033278589 0.867164495 1.242538375 1 16.41877692 2.266856728 3.538265535 1.005437959 1.186750175 0.06959483 0.163766308 0.357032595 9.410775509 0.05959214 0.045879037 184.8658653 -2.266856728 0.181312217 HPAELAMEPTPELPAEVLMVEVENVVHEDFQVTEEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HPAELAMEPTPELPAEVLMVEVENVVHEDFQVTEEVK 37 0 K7EKE6;P36776-2;P36776;P36776-3 K7EKE6 LONP1 "Lon protease homolog, mitochondrial" 0 81.91 0.0007546 214720000 15225 11787 11311 12692 15010 5037.3 10861 8937.1 14570 FALSE TRUE 14272.09443 12659.72174 11579.30226 13017.69821 13831.17515 6491.486736 9232.493879 10052.91661 12138.17287 1.175802534 1.042967659 0.9539576 1.07245945 1.139477522 0.534799331 0.760616443 0.828206742 1 13.56726365 2.255081792 24.99994072 0.752843406 1.055328644 0.563354928 0.127665879 160.6353875 243073.9939 0.041451139 0.034588293 179.9209733 -2.255081792 0.302485238 HPAKPDPSGECNPDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HPAKPDPSGECNPDLR 16 1 Q16576;E9PC52;Q16576-2;Q5JP01 Q16576 RBBP7 Histone-binding protein RBBP7 0 ;;;;; 262.36 4.21E-27 8856540000 5584560 4727670 5146620 4936360 5344360 4566630 6335920 4958240 5482210 FALSE TRUE 5235032.358 5077711.606 5268700.257 5063035.355 4924635.524 5884941.948 5385907.616 5577287.178 4567193.735 1.146225158 1.111779333 1.153596839 1.108565927 1.078262892 1.288524702 1.179259722 1.22116282 1 22.12287656 2.277205753 24.99974343 1.189947248 1.122726611 0.087095191 0.075047179 263.60727 170527.9078 0.022779999 0.019058829 189.3240355 -2.277205753 -0.067220637 HPALFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HPALFK 6 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 84.566 0.055705 975990000 2864000 2855000 2647600 2579600 3076800 2119630 3118900 2923100 2947100 FALSE TRUE 2684747.352 3066387.171 2710402.322 2645796.903 2835160.539 2731532.772 2651249.899 3288055.47 2455209.971 1.093489919 1.248930726 1.103939115 1.077625512 1.15475278 1.112545487 1.079846502 1.33921559 1 21.22741498 -2.395455011 2.105936744 3.35E-05 1.146957198 0.243844749 0.083417884 1120017.98 142037.0792 5385767.9 0.018724451 0.004022953 2.395455011 1.146923663 HPASLEFQAQITTLLVDLGTPQAEIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HPASLEFQAQITTLLVDLGTPQAEIAR 27 0 Q92797;A0A087WUE9;M0R3C7;Q92797-2 Q92797 SYMPK Symplekin 0 77.693 0.014363 25581000 29953 30054 31649 36623 34955 26641 29605 25712 25786 FALSE TRUE 28078.2952 32279.22943 32399.72923 37562.80818 32209.7753 34331.82422 25166.00509 28922.1998 21482.15002 1.307052375 1.502607021 1.508216319 1.748559067 1.499373912 1.598155873 1.171484468 1.346336367 1 14.39085077 1.709226445 6.588206775 1.195605714 1.529532005 0.59855225 0.136198171 0.091476555 9.441641603 0.063869114 0.032905072 51.19487002 -1.709226445 0.333926291 HPDADSLYVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HPDADSLYVEK 11 0 P54577 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed" 0 ;; 145.46 3.62E-05 874050000 2387300 2157000 2290650 2149300 2200190 1709820 2635000 2077560 1963380 FALSE TRUE 2237883.154 2316706.524 2344985.3 2204454.677 2027395.953 2203417.277 2239906.212 2336947.939 1635679.194 1.368167525 1.416357518 1.433646224 1.347730463 1.239482632 1.347096231 1.369404355 1.428732448 1 20.64145839 -1.982522573 2.724397649 0.665616847 1.373145326 0.812627599 0.055624276 10404698.29 9625851.102 21953026.07 0.014392799 0.01041064 1.982522573 0.70752848 HPDASVNFSEFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HPDASVNFSEFSK 13 0 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ; 222.74 1.70E-11 1506750000 2784100 2377070 2710900 2609500 2640900 2080450 2990600 2467070 2541360 FALSE TRUE 2609848.151 2553070.736 2775203.828 2676464.188 2433494.367 2681042.142 2542187.293 2775089.12 2117190.598 1.232694002 1.205876664 1.310795462 1.264158357 1.149397871 1.266320635 1.200736153 1.310741283 1 21.01371972 -1.777980686 2.906298162 0.945386651 1.24130709 0.701812733 0.049688368 13019763.41 9027787.344 4998482.087 0.011226303 0.016673214 1.777980686 0.295920438 HPDGRPTGDAFALFACEELAQAALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HPDGRPTGDAFALFACEELAQAALR 25 1 Q9H6T0-2;Q9H6T0 Q9H6T0-2 ESRP2 Epithelial splicing regulatory protein 2 0 ; 122.73 0.00010182 65157000 80192 100049 99322 92631 100786 90260 108029 89737 68777 FALSE TRUE 75172.92587 107456.7321 101677.9647 95008.06828 92870.67411 116316.5968 91831.05434 100940.862 57297.67438 1.311971676 1.875411755 1.774556574 1.65814877 1.620845438 2.030040451 1.60270125 1.761692129 1 15.80618896 -1.246777398 3.647296486 0.998720463 1.727411587 0.576292172 0.18890996 28329773.28 41026607.14 401365.3735 0.040652772 0.05665296 1.246777398 0.728691124 HPDSHQLFIGNLPHEVDKSELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HPDSHQLFIGNLPHEVDKSELK 22 1 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 131.37 4.10E-06 468000000 1034400 625570 771720 681750 925390 648400 1079700 737940 857490 FALSE TRUE 969658.7505 671887.8537 790025.5628 699244.8592 852713.6022 835582.5541 917809.0084 830073.4334 714369.3794 1.357363261 0.940532829 1.105906252 0.978828152 1.193659228 1.16967857 1.284782124 1.161966704 1 19.44631072 2.703839013 24.2586573 1.188707429 1.071511589 0.024558335 0.131056543 743.2957201 519311.1735 0.038632659 0.036425315 505.6371943 -2.703839013 -0.11719584 HPDSHQLFIGNLPHEVDKSELKDFFQSYGNVVELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HPDSHQLFIGNLPHEVDKSELKDFFQSYGNVVELR 35 2 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ; 234.8 1.02E-47 670840000 346210 443562 308599 326318 635056 235263 416300 391536 621125 FALSE TRUE 324541.3341 476403.792 315919.114 334691.8723 585181.2635 303179.6089 353879.6797 440420.1315 517455.2249 0.627187278 0.920666696 0.610524542 0.646803542 1.130882896 0.58590501 0.683884639 0.851127035 1 18.98107451 0.971787766 5.31204661 0.999866302 0.747268847 0.199327433 0.166853787 0.286143944 31.25322459 0.14860585 0.037498008 9.371039439 -0.971787766 -0.252597454 HPDVEVDGFSELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HPDVEVDGFSELR 13 0 P09874;Q5VX84;Q5VX85 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;; 263.89 3.34E-24 2588390000 2372790 2820920 2730690 2653120 2730290 2222320 2921970 2509540 2521340 FALSE TRUE 2224281.309 3029783.852 2795463.256 2721203.551 2515864.037 2863867.708 2483847.725 2822861.593 2100512.066 1.058923367 1.442402499 1.330848464 1.29549532 1.197738436 1.363414072 1.18249629 1.343892111 1 21.00230964 -3.738504394 0.293074271 8.39E-11 1.310231496 0.357034807 0.111322081 109.4333792 2.043759019 66.08685927 0.108761174 0.000182598 3.738504394 1.310231496 HPDYAILAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HPDYAILAAR 10 0 P23921 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 130.98 0.00026219 168960000 19497 50161 16913 18395 50876 11636 17100 41398 37061 FALSE TRUE 18276.71757 53874.97263 17314.18435 18867.04684 46880.40418 14995.12431 14536.01375 46566.63143 30875.27968 0.591953102 1.744922579 0.560778219 0.611072905 1.518379904 0.485667643 0.4707978 1.508217315 1 14.91416458 3.906189165 8.672061149 0.828170921 1.237744584 0.048440387 0.472152715 0.604232803 68.25133241 0.112766314 0.204066048 8057.293159 -3.906189165 0.409573663 HPEAEDPSAEHPWCAWDICEAWAEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HPEAEDPSAEHPWCAWDICEAWAEKR 26 1 P36915;A0A140T8Y2;P36915-2 P36915 GNL1 Guanine nucleotide-binding protein-like 1 0 ; 133.95 1.76E-05 193364000 67414 101732 90977 89298 97284 85521 110652 88250 148145 FALSE TRUE 63194.67808 109264.3431 93135.0174 91589.53786 89643.70706 110209.5244 94060.75984 99268.20676 123418.6424 0.512035109 0.885314738 0.754626818 0.742104564 0.726338463 0.892973073 0.762127649 0.804321007 1 16.91320081 -5 0.143101522 1.784497747 0.694976801 0.421638401 0.098026882 147.4856089 1.28185576 32.99995634 0.526420451 1.00E-05 5 -1.089520946 HPEHYVDY(ph)T(ph)Y(ph)MAT(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HPEHYVDYTYMATK 14 0 H3BLX4;Q96JM2-2;Q96JM2;Q96JM2-3 H3BLX4 ZNF462 Zinc finger protein 462 4 HPEHY(0.048)VDY(0.989)T(0.987)Y(0.99)MAT(0.987)K 49.463 0.054186 331160000 43036 167610 143910 133830 150860 176710 109980 142240 122410 TRUE FALSE 40342.45358 180020.0188 147323.6132 137264.3044 139012.0641 227723.3084 93489.52 159998.9771 101978.9802 0.395595774 1.765265925 1.444646856 1.346005854 1.363144286 2.233041632 0.916752843 1.568940744 1 16.63791229 0.022338542 1.027784857 0.997066863 1.424451719 0.047518705 0.485679004 22.09634587 20.33173116 0.668788359 0.131355619 1.052782221 -0.022338542 0.427384856 HPELADK ddPTM_SK-BR-3_Pertuzumab_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 ;;; 122.74 0.0043113 5589980000 8373600 6513520 7303900 6826800 7197900 5494640 8723600 6174780 7607400 FALSE TRUE 7849511.323 6995787.798 7477151.957 7001987.246 6632605.969 7080853.37 7415577.166 6945714.875 6337675.794 1.238547313 1.103841223 1.179794013 1.104819412 1.046536015 1.117263426 1.170078339 1.095940389 1 22.59552243 -5 0.128341705 0.580832969 1.188109298 0.470288505 0.049094735 146.9031399 1.195884391 16.06567073 0.385100545 1.00E-05 5 0.60727633 HPELTKPPPLMAAEPTAPLSHSASSDPADRLS(ph)PFLAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HPELTKPPPLMAAEPTAPLSHSASSDPADRLSPFLAAR 38 2 Q9ULP9-2;Q9ULP9 Q9ULP9-2 TBC1D24 TBC1 domain family member 24 1 HPELTKPPPLMAAEPTAPLSHSASSDPADRLS(1)PFLAAR;HPELTKPPPLMAAEPTAPLSHSASSDPADRLS(1)PFLAAR;HPELTKPPPLMAAEPTAPLSHSASSDPADRLS(1)PFLAAR;HPELTKPPPLMAAEPTAPLSHSAS(0.001)S(0.001)DPADRLS(0.999)PFLAAR;HPELTKPPPLMAAEPTAPLSHSAS(0.005)S(0.005)DPADRLS(0.99)PFLAAR 262.32 7.76E-63 3202160000 2379190 2564160 2282830 2157550 2796590 1523252 2668210 2442040 2922640 TRUE FALSE 2230280.745 2754013.074 2336979.806 2212916.386 2576957.102 1962990.124 2268136.681 2746934.07 2434832.503 0.915989392 1.131089334 0.959811323 0.908857748 1.058371407 0.806211566 0.931537047 1.128181945 1 21.2153911 5.078158163 14.35406356 0.985174192 0.00010769 0.050410874 0.099270743 620290.4597 2350004.148 0.023528126 18389763.96 119717.6445 -5.078158163 -0.985066502 HPENYDLATLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HPENYDLATLK 11 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;P78347-5 A0A494C1K3 GTF2I General transcription factor II-I 0 134.99 0.00012936 262090000 251870 248030 236650 232250 314170 172730 251810 284640 340030 FALSE TRUE 236105.9063 266394.3993 242263.4498 238209.9282 289496.3555 222594.347 214053.4282 320177.9306 283276.7963 0.833481278 0.940403177 0.855218122 0.84090872 1.021955766 0.785783904 0.755633469 1.130265291 1 18.11185291 1.230877532 24.99988468 1.065132693 0.86443774 0.522413192 0.080752701 155.9756567 507506.3169 0.072125536 0.019389677 17.01678578 -1.230877532 -0.200694954 HPEPVPEEGS(ph)EDELPPQVHKV ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HPEPVPEEGSEDELPPQVHKV 21 1 Q7Z3C6;H7C152;Q7Z3C6-2 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 HPEPVPEEGS(1)EDELPPQVHKV;HPEPVPEEGS(1)EDELPPQVHKV 222.72 1.80E-25 475830000 507680 483330 487190 483220 573060 362410 655120 506650 743180 TRUE FALSE 475905.215 519116.2561 498746.3769 495620.2433 528054.1792 467031.8838 556890.8378 569906.3678 619138.4569 0.768657172 0.838449381 0.805549019 0.800499852 0.852885446 0.754325432 0.899460907 0.920482909 1 19.23990255 1.273851829 1.587952686 0.992153557 0.809483494 0.793920634 0.033917927 0.14083417 0.650204194 0.027579603 0.008374901 18.78675746 -1.273851829 -0.182670062 HPEQIFPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HPEQIFPR 8 0 P82933 P82933 MRPS9 "28S ribosomal protein S9, mitochondrial" 0 90.601 0.013081 111260000 44194 38099 51461 45969 47915 27061 45691 34248 60811 FALSE TRUE 41427.97643 40919.8896 52681.67922 47148.64237 44151.94918 34873.0714 38840.05872 38523.93819 50661.25125 0.817744833 0.807715731 1.039881131 0.930664782 0.8715132 0.688357878 0.76666205 0.760422162 1 15.62859509 2.438469667 10.85391893 0.779082769 0.906658362 0.144256145 0.101957619 0.738990762 203.5947434 0.033832971 0.028325124 274.4540648 -2.438469667 0.127575593 HPGAHQGNLASGLHSNAIASPGS(ph)PSLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HPGAHQGNLASGLHSNAIASPGSPSLGR 28 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 HPGAHQGNLASGLHSNAIAS(0.189)PGS(0.811)PSLGR;HPGAHQGNLASGLHSNAIAS(0.004)PGS(0.993)PS(0.004)LGR;HPGAHQGNLASGLHSNAIAS(0.24)PGS(0.758)PS(0.002)LGR;HPGAHQGNLASGLHSNAIAS(0.01)PGS(0.989)PSLGR 272.04 3.22E-61 2557420000 225349 296391 327118 285041 389338 376374 380127 359971 602720 TRUE FALSE 211244.8083 318336.098 334877.3934 292355.6346 358760.964 485027.0639 323130.4853 404914.1717 502122.1383 0.420704032 0.633981404 0.666924176 0.582240081 0.714489437 0.96595435 0.643529653 0.806405735 1 18.93767881 4.283717837 0.112135884 1.167275787 3.42E-14 0.654727115 0.101921497 25.64999104 0.550730061 1.353869026 5.120595325 19218.42694 -4.283717837 -1.167275787 HPGASEAADGCS(ph)PLWGLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HPGASEAADGCSPLWGLSK 19 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 HPGASEAADGCS(1)PLWGLSK;HPGASEAADGCS(1)PLWGLSK;HPGASEAADGCS(1)PLWGLSK;HPGASEAADGCS(1)PLWGLSK;HPGASEAADGCS(1)PLWGLSK 198.1 4.87E-16 1291230000 1824420 1700210 2026210 2199840 2294810 1416450 2008460 1214150 1522540 TRUE FALSE 1710232.809 1826095.317 2074272.658 2256291.619 2114584.879 1825356.121 1707310.069 1365739.3 1268418.238 1.348319314 1.439663403 1.635322322 1.778823066 1.667103812 1.439080633 1.346015074 1.076726319 1 20.2745991 1.426081166 1.60729055 0.99941287 1.568828631 0.754403611 0.121560777 0.186941374 0.900968723 0.115814129 0.036905509 26.67357125 -1.426081166 0.569415762 HPGPPFYVPHAEIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HPGPPFYVPHAEIER 15 0 P51580 P51580 TPMT Thiopurine S-methyltransferase 0 ; 148.72 2.01E-06 261536000 129459 136536 147233 144649 129134 139916 166284 105198 132571 FALSE TRUE 121356.3923 146645.2675 150725.4363 148360.9382 118992.3365 180307.4779 141351.2579 118332.2019 110444.0437 1.09880432 1.32777887 1.364722182 1.343313169 1.077399311 1.632568601 1.279845008 1.071422215 1 16.75295609 1.215168466 4.327161981 1.01629378 1.321535458 0.348711562 0.152621039 0.199088005 7.866914233 0.123840055 0.034501508 16.41226292 -1.215168466 0.305241678 HPGSFDVVHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HPGSFDVVHVK 11 0 P62701;C9JEH7;P22090 P62701 RPS4X;RPS4Y1 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1" 0 ;;; 183.33 3.12E-06 3304440000 4244470 4820460 4895190 4961230 4967800 3850030 5547970 4679790 4708320 FALSE TRUE 3978816.199 5177371.874 5011306.218 5088543.561 4577649.027 4961471.161 4716103.403 5264072.083 3922470.975 1.014364727 1.319926115 1.277589114 1.297280106 1.167031969 1.264884098 1.202329713 1.342029582 1 21.90333134 -1.20738003 4.885543025 0.999967145 1.244897624 0.377497485 0.094455464 3.01E-05 4.89E-06 0.081527748 0.019213699 0.062032598 1.20738003 0.244930479 HPHDIIDDINSGAVECPAS ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HPHDIIDDINSGAVECPAS 19 0 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;; 232.84 1.09E-21 7092420000 2539910 2992800 3008590 2929220 3111950 2621520 3716250 2329830 3100140 FALSE TRUE 2380941.567 3214390.026 3079955.176 3004388.744 2867550 3378310.267 3159032.812 2620714.404 2582706.606 0.921878452 1.244581951 1.192530026 1.163271406 1.110288715 1.308050345 1.223148152 1.014716266 1 21.30045233 -0.072246599 7.573151849 1 1.170562163 0.113002262 0.114235321 3417838.242 451309.8539 0.10071564 0.024427131 0.846746483 0.072246599 0.170562163 HPHLSTLSLPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HPHLSTLSLPRR 12 1 O95140-2 O95140-2 MFN2 Mitofusin-2 0 74.962 0.05627 74644000 42577 267350 137830 135750 253710 193730 100210 212270 99644 FALSE TRUE 39912.18157 287144.8722 141099.3927 139233.5748 233784.64 249656.7061 85184.4408 238772.3768 83012.77268 0.480795669 3.459044469 1.699731115 1.677254841 2.816249024 3.007449312 1.02616065 2.876332992 1 16.34104571 -1.760855737 2.47601829 0.700389406 2.171540574 0.124298673 0.937267148 17941866.62 12625554.28 32732726.93 0.208585159 0.0173438 1.760855737 1.471151168 HPHTGDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HPHTGDTK 8 0 P51397;B4DQ75 P51397 DAP Death-associated protein 1 0 ;;; 124.08 0.0013201 102091000 276069 182492 228751 207851 178329 165875 225680 177207 187952 FALSE TRUE 258790.3341 196003.8976 234177.0817 213184.8086 164323.7597 213760.4197 191841.3791 199331.684 156581.597 1.652750637 1.251768416 1.495559416 1.361493385 1.049444908 1.365169495 1.225184714 1.273021146 1 17.25655514 7.999999983 0.055841368 0.514303444 2.88149082 0.514547456 0.133832433 327.8806494 1.37333034 12.54557375 64.44944417 99999996.12 -7.999999983 2.367187375 HPHTGDTKEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HPHTGDTKEEK 11 1 P51397;B4DQ75 P51397 DAP Death-associated protein 1 0 ; 80.763 0.015173 99720000 134004 97982 112498 111238 125195 55482 114632 82033 205507 FALSE TRUE 125616.9288 105236.6892 115166.5057 114092.5554 115362.6897 71498.75272 97443.99579 92275.00063 171206.5541 0.733715654 0.614676756 0.6726758 0.666402966 0.673821691 0.417616914 0.569160429 0.538968856 1 17.38537841 -1.020929962 5.266783598 1.000002729 0.608686832 0.65693144 0.088359758 2.86E-06 5.32E-07 0.086550287 0.020399956 0.095294983 1.020929962 -0.391315896 HPHVYS(ph)PVIQGNAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HPHVYSPVIQGNAR 14 0 F8VZC1 F8VZC1 ATXN2 1 HPHVY(0.444)S(0.556)PVIQGNAR;HPHVY(0.444)S(0.556)PVIQGNAR 63.283 0.073756 134008000 7600 4975.2 6891.1 4563.4 6672.8 6579.6 8478.9 7558.7 7331.2 TRUE FALSE 7124.329566 5343.568985 7054.560146 4680.50457 6148.745205 8479.023709 7207.567659 8502.420334 6107.575359 1.16647428 0.8749084 1.155050856 0.766344137 1.006740784 1.388279835 1.180102944 1.39211059 1 12.57638404 2.310162728 8.729021789 1.251513665 0.988432439 0.369689602 0.159420124 0.266488385 29.51939664 0.049489288 0.041313793 204.2503119 -2.310162728 -0.263081226 HPIGVLLNAITELQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HPIGVLLNAITELQK 15 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 148.91 3.45E-06 36604000 78846 71346 75864 81980 86021 58082 83644 68866 82169 FALSE TRUE 73911.1696 76628.53208 77663.52991 84083.74559 79265.25765 74849.33052 71102.35871 77464.07169 68454.46307 1.07971294 1.119408854 1.134528363 1.228316487 1.157926804 1.093417831 1.038681125 1.131614627 1 16.06285698 2.05631973 4.526819891 1.06187125 1.142802678 0.402273156 0.048779442 0.217736283 9.282052724 0.019170549 0.0134225 113.8465121 -2.05631973 0.080931429 HPKGEEGS(ph)DDDETENGPKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HPKGEEGSDDDETENGPKPK 20 2 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 HPKGEEGS(1)DDDETENGPKPK;HPKGEEGS(1)DDDETENGPKPK 233.22 9.08E-30 403490000 296589 109190 167256 172772 186332 95221 203360 119577 288430 TRUE FALSE 278026.0239 117274.5412 171223.3913 177205.622 171698.2363 122709.7569 172868.0559 134506.4517 240289.1697 1.15704767 0.488055876 0.712572238 0.737468202 0.714548378 0.510675355 0.71941676 0.559769098 1 17.8744121 -0.989278797 8.742853312 0.999967359 0.678255158 0.194804874 0.187152729 1.18E-09 2.69E-10 0.158107613 0.037266322 0.102499372 0.989278797 -0.321712202 HPLLSSGGPQS(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HPLLSSGGPQSPLR 14 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 HPLLSSGGPQS(1)PLR;HPLLSSGGPQS(1)PLR;HPLLSSGGPQS(1)PLR 183.88 8.74E-07 970920000 639950 906590 745650 757730 1012140 547570 760920 743460 920760 TRUE FALSE 599896.6718 973714.8669 763337.1701 777174.6346 932650.6072 705644.5699 646827.11 836282.6176 767079.2077 0.782053099 1.26937982 0.995121706 1.013160866 1.215846549 0.91991096 0.843233793 1.090216772 1 19.54901603 2.186158773 24.99950921 0.937722865 1.074243979 0.069858423 0.145248701 167.7532572 80029.35988 0.050324304 0.037167005 153.5178124 -2.186158773 0.136521114 HPLLSSGGPQSPLRGS(ph)TGSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HPLLSSGGPQSPLRGSTGSLK 21 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 HPLLSSGGPQS(0.002)PLRGS(0.908)T(0.083)GS(0.007)LK 103.75 0.00026083 291700000 114610 119960 100950 123250 131840 79008 169340 127120 222120 TRUE FALSE 107436.7647 128841.9632 103344.5817 126412.8037 121485.8182 101816.327 143949.0391 142991.2118 185046.737 0.580592592 0.696267145 0.558478271 0.683139869 0.656514242 0.550219521 0.777906389 0.772730252 1 17.49753017 1.004608956 1.069413673 0.996039018 0.625523604 0.801960374 0.059373378 0.212497611 0.511266214 0.050864927 0.016518267 10.10669025 -1.004608956 -0.370515414 HPNGTQETILLNHTFNETQIEWFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HPNGTQETILLNHTFNETQIEWFR 24 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ;; 276.19 2.80E-52 619184000 175825 187593 153029 140822 213419 155998 156040 174391 193349 FALSE TRUE 164820.4271 201482.5809 156658.9201 144435.7309 196657.9326 201032.0902 132643.2506 196164.1002 161077.8028 1.023234885 1.250840137 0.972566781 0.896683022 1.220887852 1.248043409 0.823473181 1.217822051 1 17.29739817 2.611599051 0.012138794 1.72E-07 2.139808866 0.005572256 0.154613626 6454.907569 33.70804353 2881.350778 3056.264547 408.8829971 -2.611599051 2.139808695 HPNNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HPNNLK 6 0 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 90.939 0.04846 61451000 149820 124620 129450 128840 115140 96363 131170 135110 132070 FALSE TRUE 140443.0336 133846.9945 132520.6151 132146.2525 106097.3689 124181.4338 111502.2762 151978.7809 110026.6638 1.276445443 1.216495982 1.204440911 1.201038439 0.964287793 1.128648543 1.013411408 1.381290459 1 16.74749366 2.969934034 23.54941474 1.092737071 1.222249799 0.232894206 0.115099988 460.1721087 360433.4238 0.031816208 0.033802174 933.1125581 -2.969934034 0.129512728 HPNYS(ph)PPGS(ph)PIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 HPNYSPPGSPIEK 13 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 2 HPNYS(1)PPGS(1)PIEK;HPNY(0.009)S(0.993)PPGS(0.998)PIEK;HPNY(0.031)S(0.974)PPGS(0.995)PIEK;HPNY(0.033)S(0.993)PPGS(0.974)PIEK;HPNYS(1)PPGS(1)PIEK;HPNYS(1)PPGS(1)PIEK;HPNY(0.1)S(0.934)PPGS(0.967)PIEK;HPNY(0.077)S(0.932)PPGS(0.991)PIEK 173.37 3.19E-05 5162910000 5262030 3788680 4618710 5118240 5665360 3591850 4762680 3268720 4677500 TRUE FALSE 4932688.935 4069197.809 4728267.982 5249582.704 5220425.479 4628758.786 4048560.349 3676826.887 3896795.032 1.265832279 1.044242198 1.21337354 1.34715392 1.33967156 1.187837376 1.038946189 0.943551523 1 21.89385662 1.668035422 3.098433177 0.976584914 1.219040682 0.63794472 0.085623583 0.165950189 3.705784319 0.059665754 0.026131336 46.56240696 -1.668035422 0.242455768 HPNYS(ph)PPGSPIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HPNYSPPGSPIEK 13 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 HPNYS(1)PPGSPIEK;HPNYS(1)PPGSPIEK;HPNYS(1)PPGSPIEK;HPNYS(1)PPGSPIEK 204.23 8.34E-08 8326960000 6140510 4739430 5160550 3693360 3586860 3670990 6688940 5072620 7433770 TRUE FALSE 5756186.44 5090342.329 5282960.683 3788137.87 3305162.484 4730745.219 5685995.544 5705947.773 6193025.763 0.929462699 0.821947546 0.853050009 0.611678042 0.53369106 0.763882697 0.918128837 0.921350563 1 22.56221302 1.682602577 4.0019737 0.947305076 0.757775776 0.392473033 0.114382686 0.224139358 8.401772915 0.070120546 0.032941912 48.15069688 -1.682602577 -0.189529299 HPPEQTNGVHT(ph)PPHVASALAGAVS(ph)PGALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HPPEQTNGVHTPPHVASALAGAVSPGALR 29 0 X6RKU3;Q6P3S6 X6RKU3 FBXO42 F-box only protein 42 2 HPPEQT(0.01)NGVHT(0.99)PPHVASALAGAVS(1)PGALR;HPPEQT(0.007)NGVHT(0.993)PPHVASALAGAVS(1)PGALR 115.92 0.0003752 1232960000 94190 103918 93867 95156 92087 77052 108701 89013 77693 TRUE FALSE 88294.81603 111612.1968 96093.56957 97597.86406 84854.85848 99295.66157 92402.29418 100126.469 64725.53638 1.364141898 1.724391996 1.484631491 1.507872619 1.31099506 1.53410334 1.42760183 1.546939193 1 15.9820474 -3.013665559 0.269623342 2.62E-14 1.548814805 0.627208382 0.115762519 38.34014421 0.978259786 22.01102685 0.139903336 0.000969024 3.013665559 1.548814805 HPQGEQMYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 121.8 0.0006038 1164926000 26327.8 53216.6 42468.9 56368.6 60873.9 52111 48381.3 34307.9 44706.3 FALSE TRUE 24679.98999 57156.81244 43476.28236 57815.11371 56093.10945 67154.59975 41126.97321 38591.31684 37244.52972 0.662647379 1.534636438 1.167319945 1.552311551 1.506076459 1.803072834 1.104241979 1.036160669 1 15.18474093 1.556485693 9.16364409 1.03775259 1.383543304 0.208360143 0.300068442 0.172619546 23.66664857 0.150917304 0.070367565 36.0151886 -1.556485693 0.345790714 HPSAVTACNLDLENLVTDSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HPSAVTACNLDLENLVTDSNR 21 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ; 301.57 3.71E-55 705850000 411160 632260 625780 644760 672880 534380 757890 618930 668680 FALSE TRUE 385426.2295 679073.1883 640623.7971 661305.6332 620034.7191 688646.8311 644251.4304 696204.7729 557072.9882 0.691877434 1.219002182 1.149981799 1.187107699 1.113022409 1.236187799 1.156493752 1.249755037 1 19.08750684 4.74192628 24.99143984 1.172595533 0.691877254 0.809513779 0.071856786 113.8686393 845483.8933 0.014365636 0.104112909 55198.37344 -4.74192628 -0.48071828 HPSKPDPSGECNPDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HPSKPDPSGECNPDLR 16 1 Q09028-3;Q09028;Q09028-2;Q09028-4 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 ; 180.62 1.46E-09 703840000 465550 689000 690090 711040 756230 637550 916710 726920 850040 FALSE TRUE 436412.0565 740014.2769 706459.2607 729286.4902 696838.7463 821600.3352 779257.8458 817677.5621 708162.8325 0.616259477 1.044977571 0.997594378 1.029828814 0.984009206 1.16018562 1.100393596 1.154646254 1 19.4337216 4.740020304 5.298129456 1.060006355 0.597589129 0.8336026 0.062195685 0.064400626 6.422378035 0.015540281 0.108485235 54956.65664 -4.740020304 -0.462417226 HPSSPCSVKHS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HPSSPCSVKHSPTR 14 1 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 1 HPSSPCS(0.025)VKHS(0.967)PT(0.008)R;HPSSPCS(0.021)VKHS(0.976)PT(0.004)R 135.23 2.06E-05 97791000 38862 94367 84240 85151 90913 63230 106355 85162 96858 TRUE FALSE 36429.69679 101354.0309 86238.21258 87336.11882 83773.05971 81483.47455 90408.0551 95794.66316 80691.77407 0.451467293 1.25606398 1.068736108 1.082342281 1.03818587 1.009811415 1.120412287 1.187167642 1 16.30013399 4.747008307 24.97570227 1.101257972 0.451466964 0.86856576 0.07868468 366.5219408 1083602.499 0.018682916 0.216880697 55848.08768 -4.747008307 -0.649791008 HPSVESVVQCEIDEDVIQVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HPSVESVVQCEIDEDVIQVSK 21 0 P19623;K7ESL0 P19623 SRM Spermidine synthase 0 ; 172.24 5.86E-12 198104000 81927 122137 117227 126812 117767 117339 171096 127636 102818 FALSE TRUE 76799.33531 131180.1506 120007.6798 130066.2106 108518.0549 151212.8645 145441.7432 143571.6356 85657.01157 0.896591346 1.531458408 1.401025761 1.518453752 1.266890508 1.765329676 1.697954908 1.676122397 1 16.38628372 2.246063016 24.99987825 1.610412368 1.370871162 0.086367894 0.277451853 303.4083388 1011033.642 0.087593801 0.071940929 176.2231727 -2.246063016 -0.239541206 HPTLLQDPDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HPTLLQDPDLR 11 0 O60749;O60749-2;D6RC15 O60749 SNX2 Sorting nexin-2 0 ;;; 161.99 2.57E-05 1715170000 498353 807110 687558 682700 858900 513133 729160 743960 804650 FALSE TRUE 467161.9753 866869.2642 703867.2004 700219.2378 791445.4586 661266.1671 619829.2272 836845.0437 670348.7168 0.696893965 1.293161667 1.050001563 1.044559675 1.180647384 0.986451008 0.924637001 1.248372709 1 19.35455226 HPVSCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HPVSCK 6 0 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A0D9SFP2;A0A1W2PQV5;A0A1W2PNM1;A0A1W2PQC2;A0A1W2PRT2;A0A1W2PQ78 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 ;;; 126.04 0.017664 524400000 1590340 1327720 1274630 1182740 1845230 1041630 1141520 1644040 1876330 FALSE TRUE 1490803.458 1426025.77 1304864.826 1213091.111 1700313.079 1342331.672 970359.6734 1849302.013 1563158.401 0.953712341 0.912272083 0.834761739 0.776051301 1.087742021 0.858730421 0.620768613 1.183054776 1 20.57603255 1.213146875 24.99999984 1.091527464 0.858007994 0.357342469 0.127006878 288.1386997 283440.2176 0.120765689 0.030237563 16.33604325 -1.213146875 -0.23351947 HPVTGQFLYQDSNWASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HPVTGQFLYQDSNWASK 17 0 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ; 215.45 1.22E-17 758120000 328760 326460 294200 247030 351490 226264 359380 307440 392520 FALSE TRUE 308183.4985 350631.4381 301178.5629 253369.208 323885.3932 291582.7437 305494.3053 345824.5608 327005.8762 0.942440246 1.072248126 0.92101881 0.774815459 0.99045741 0.891674324 0.934216562 1.05754846 1 18.31895704 -0.130808539 13.17392569 0.999999999 0.949204593 0.036318506 0.083908705 0 0 0.079691222 0.018783401 0.739931406 0.130808539 -0.050795406 HPWDDISYVLPEHMS(ph)M ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HPWDDISYVLPEHMSM 16 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 HPWDDISYVLPEHMS(1)M;HPWDDISYVLPEHMS(1)M 109.42 0.00062717 31454000 46609 54062 50909 47680 54981 41266 57581 45483 60496 TRUE FALSE 43691.82589 58064.80673 52116.58552 48903.54952 50663.01404 53178.8243 48947.26361 51161.65267 50398.82678 0.866921488 1.152106318 1.034083308 0.97033111 1.005241933 1.055159965 0.971198473 1.015135787 1 15.62110253 3.466007766 23.08855082 1.002983074 1.051304357 0 0.073875727 209.1074181 434423.5883 0.018910052 0.025701826 2924.204668 -3.466007766 0.048321283 HPWDDISYVLPEHMSM ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 HPWDDISYVLPEHMSM 16 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;;;;;;;;;; 198.23 4.13E-11 1065402000 488364 1084556 826963 864284 1066986 659203 890158 976151 997640 FALSE TRUE 457798.169 1164857.655 846578.9529 886462.9907 983189.2236 849504.2048 756687.0717 1098025.601 831127.439 0.550815853 1.401539162 1.018591028 1.066578901 1.182958446 1.022110648 0.910434473 1.321127843 1 19.66471018 1.242876028 24.99946533 1.160563873 1.058369744 0.042213655 0.22786679 413.2613955 2394164.909 0.151393157 0.050985101 17.49347257 -1.242876028 -0.102194129 HQAS(ph)DS(ph)ENEELPKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HQASDSENEELPKPR 15 1 Q96ST2;B8ZZB6 Q96ST2 IWS1 Protein IWS1 homolog 2 HQAS(1)DS(1)ENEELPKPR;HQAS(1)DS(1)ENEELPKPR;HQAS(1)DS(1)ENEELPKPR;HQAS(1)DS(1)ENEELPKPR 105.96 0.00072496 4968950000 4367850 2589180 3220200 2818270 2753740 2171610 3469610 2314970 2640580 TRUE FALSE 4094474.065 2780885.581 3296584.665 2890591.58 2537472.368 2798518.554 2949374.191 2603999.1 2199850.139 1.861251361 1.264125011 1.498549654 1.313994771 1.153475104 1.272140544 1.34071596 1.183716588 1 21.06897382 6.888177223 1.343054039 1.278528704 200 0.644957025 0.137521812 335.6308468 2.287997642 0.035228849 203774.909 7729959.583 -6.888177223 198.7214713 HQAS(ph)DS(ph)ENEEPPKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HQASDSENEEPPKPR 15 1 Q96ST2;B8ZZB6 Q96ST2 IWS1 Protein IWS1 homolog 2 HQAS(1)DS(1)ENEEPPKPR 104.63 0.00078442 499340000 750040 449020 535290 483790 467110 364440 561820 436650 479620 TRUE FALSE 703096.3353 482265.908 547987.3316 496204.8705 430425.0648 469647.9118 477580.3067 491166.7137 399568.3235 1.759639826 1.206967318 1.371448384 1.241852372 1.077225194 1.175388248 1.19524066 1.229243373 1 18.60808269 7.117117419 1.205747339 1.194900856 199.9999802 0.740660375 0.104330481 292.2556311 1.563755705 0.028280222 159417.784 13095359.31 -7.117117419 198.8050793 HQAS(ph)INELKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 HQASINELKR 10 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6;X6RC15 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 HQAS(1)INELKR;HQAS(1)INELKR;HQAS(1)INELKR;HQAS(1)INELKR;HQAS(1)INELKR;HQAS(1)INELKR;HQAS(1)INELKR 192.39 3.23E-07 4258170000 3721010 3040170 3093090 2658830 3521810 1810390 3426620 2641630 7953770 TRUE FALSE 3488118.626 3265267.35 3166459.555 2727060.079 3245221.249 2333020.204 2912830.142 2971443.32 6626234.404 0.526410388 0.492778726 0.477867121 0.411555027 0.489753463 0.35208839 0.439590568 0.448436192 1 22.65975781 -1.136861609 3.64481196 1.000382529 0.454327629 0.926310952 0.048325006 19875233.86 33342400.66 90862.193 0.01153854 0.072968999 1.136861609 -0.5460549 HQDDLQDVIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HQDDLQDVIGR 11 0 E5RG17;Q6P1N9;H0YBX2;G5EA19;U3KQS5;E5RID7 E5RG17 TATDN1 Putative deoxyribonuclease TATDN1 0 ;; 218.06 1.09E-11 639960000 569790 737790 610830 608250 698560 452384 657090 552131 662550 FALSE TRUE 534127.861 792416.7393 625319.1761 623858.7248 643697.9155 582979.917 558565.4546 621065.7707 551966.1248 0.967682322 1.435625673 1.132894118 1.13024821 1.166190979 1.056187854 1.011956041 1.125188201 1 19.0742202 2.789744513 0.938402584 1.040370366 1.236204354 0.149504822 0.121055094 0.685758138 1.290957061 0.064291816 0.063475818 616.2323781 -2.789744513 0.195833987 HQDRLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HQDRLSPK 8 1 Q8IVM0-2 Q8IVM0-2 CCDC50 Coiled-coil domain-containing protein 50 1 HQDRLS(1)PK;HQDRLS(1)PK 85.924 0.0099308 940410000 964110 662410 729880 797410 831500 492960 838390 628620 978940 TRUE FALSE 903768.0761 711455.5256 747193.0983 817872.8906 766197.3441 635269.5495 712681.2027 707104.5908 815548.5898 1.108171956 0.872364363 0.916184649 1.002849984 0.939487057 0.778947518 0.873867249 0.867029383 1 19.63741131 2.443758597 24.94624458 0.86575674 0.950334881 0.197867493 0.082016606 284.6918309 212871.0381 0.026579359 0.022238013 277.8168593 -2.443758597 0.084578141 HQDVFNQPTLNSFMGLGQAAWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HQDVFNQPTLNSFMGLGQAAWK 22 0 P16930;H0YLC7 P16930 FAH Fumarylacetoacetase 0 ; 154.84 2.35E-08 197518000 144415 149222 136384 135510 160265 99692 175882 163955 127038 FALSE TRUE 135376.3229 160270.5521 139619.0929 138987.416 147678.4334 128471.462 149510.1269 184425.1427 105834.5371 1.279131809 1.514350197 1.319220518 1.313251986 1.395370901 1.213889771 1.412678044 1.742579953 1 16.69145098 3.753733001 21.8913998 1.355851011 1.414515356 0.008039892 0.192234093 503.0234281 413786.0281 0.044774592 0.080658092 5671.957925 -3.753733001 0.058664345 HQDVPSQDDSKPTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HQDVPSQDDSKPTQR 15 1 Q9NRN7 Q9NRN7 AASDHPPT L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase 0 ;; 165.02 8.70E-07 764363000 1279450 1058860 1127210 1180570 1201370 860121 1407680 1003416 1401580 FALSE TRUE 1199371.508 1137259.096 1153947.954 1210865.425 1107019.246 1108423.97 1196611.452 1128694.696 1167647.243 1.027169391 0.973974891 0.988267612 1.037013046 0.948076786 0.949279824 1.024805616 0.966640141 1 20.15517306 2.72540291 24.9636842 0.980685609 0.998111244 0.166380813 0.02906648 2205.003011 4183478.075 0.009393344 0.008902397 531.3771926 -2.72540291 0.017425634 HQEGEIFDTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HQEGEIFDTEK 11 0 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ;;;;; 198.81 1.22E-07 7067450000 12623940 8982530 10995680 10415080 9689100 8458420 13301690 9047100 9694880 FALSE TRUE 11833830.13 9647605.868 11256502.72 10682348.59 8928157.17 10900228.54 11307225.07 10176650.35 8076741.897 1.46517374 1.194492283 1.393693505 1.32260616 1.105415684 1.349582379 1.399973556 1.259994498 1 22.94534201 0.968538085 21.74025051 0.999999995 1.313814518 0.481834815 0.103138606 599.1795927 414035.9516 0.093412246 0.023353062 9.301180765 -0.968538085 0.313814523 HQEGEIFDTEKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HQEGEIFDTEKEK 13 1 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ;; 204.28 4.75E-08 919400000 3434110 2007090 2405540 2359340 2685240 1507090 3083560 2074830 3673990 FALSE TRUE 3219175.185 2155697.032 2462600.545 2419884.659 2474352.082 1942162.417 2621208.804 2333877.093 3060777.334 1.051750857 0.704297241 0.804567035 0.79061114 0.808406431 0.63453241 0.856386636 0.762511231 1 21.54546666 -1.799838599 4.976212301 1.021142844 0.790487904 0.243370469 0.108348166 0.023079799 0.000928354 0.095269505 0.021590862 0.015854823 1.799838599 -0.23065494 HQEGEIFDTEKEKYEITEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HQEGEIFDTEKEKYEITEQR 20 2 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ;;; 207.67 3.87E-22 2640260000 2332700 1963430 2065220 2334160 3179380 1162080 2610890 1728480 5926880 FALSE TRUE 2186700.471 2108804.4 2114207.994 2394058.497 2929684.32 1497553.631 2219411.283 1944284.533 4937645.439 0.442863 0.427087045 0.428181412 0.484858325 0.593336309 0.303293067 0.449487779 0.393767547 1 22.23539181 -1.598397133 3.044988304 1.033596699 0.438646736 0.856136281 0.072093756 42410879.37 46767344.99 11444081.97 0.015942583 0.025211743 1.598397133 -0.594949964 HQEPVYSVAFSPDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HQEPVYSVAFSPDGR 15 0 Q9BZK7;A0A0D9SF63 Q9BZK7 TBL1XR1 F-box-like/WD repeat-containing protein TBL1XR1 0 153.74 2.60E-06 283780000 132970 157400 145100 160280 190690 112480 156270 143390 178250 FALSE TRUE 124647.6451 169054.0598 148541.8405 164393.0562 175713.9766 144951.15 132838.7642 161292.5571 148498.9235 0.839384166 1.13841943 1.000289006 1.107031973 1.18326768 0.976109097 0.894543618 1.08615304 1 17.18009295 2.046530212 24.99995487 0.970217042 1.061988023 0.072345197 0.103275987 214.2300206 115101.4569 0.035879447 0.02649872 111.3089824 -2.046530212 0.091770981 HQEVQDQDPVFQGSDSSGYQS(ph)DHKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HQEVQDQDPVFQGSDSSGYQSDHKK 25 1 Q3B726 Q3B726 TWISTNB DNA-directed RNA polymerase I subunit RPA43 1 HQEVQDQDPVFQGSDS(0.001)S(0.019)GYQS(0.979)DHKK;HQEVQDQDPVFQGSDSS(0.001)GYQS(0.999)DHKK;HQEVQDQDPVFQGSDS(0.001)S(0.004)GY(0.012)QS(0.983)DHKK 204.35 1.80E-25 1017730000 1076090 561990 787730 727160 711010 479990 1101480 592990 1075190 TRUE FALSE 1008739.448 603600.3244 806415.3276 745820.1567 655170.1427 618555.321 936323.2996 667026.1068 895733.843 1.126159803 0.673861247 0.900284536 0.832635902 0.73143395 0.690557051 1.045314193 0.744669984 1 19.77271059 -1.668543902 4.697270527 1.004491578 0.838066063 0.098367699 0.148573132 0.006494436 0.00045827 0.133684546 0.030731444 0.021451423 1.668543902 -0.166425515 HQGGWTDGGSGGGGGYQDGGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HQGGWTDGGSGGGGGYQDGGYR 22 0 Q8NCA5 Q8NCA5 FAM98A Protein FAM98A 0 ; 321.95 9.91E-68 1360710000 291980 339880 328590 311650 367820 257140 334440 299840 375580 FALSE TRUE 273705.493 365045.0688 336384.31 319647.4666 338932.9009 331372.1437 284293.8268 337275.684 312893.2717 0.874756723 1.166675994 1.075076841 1.021586258 1.083222081 1.059058068 0.908596805 1.077925653 1 18.25531111 1.952155421 23.3459861 0.984970415 1.064711625 0.045207137 0.083990054 327.0557758 159587.037 0.03225131 0.020813035 89.56852477 -1.952155421 0.079741211 HQGVMVGMGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 21 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 ;;;;;;;;;;;;;;;;;;;; 149.17 2.07E-05 45233020000 63508070 68837330 55171190 53434320 77885630 38521400 64848050 64858930 79894150 FALSE TRUE 59533213.26 73934117.54 56479876.68 54805535.12 71768806.8 49641902.84 55124686.92 72956710.18 66559300.23 0.894438689 1.110800704 0.848564761 0.823409124 1.07826865 0.745829699 0.828204124 1.096115944 1 25.98813693 3.906659521 6.480864181 0.898683909 1.012880771 0.057972565 0.125452629 0.401097909 29.40283602 0.030029677 0.054995591 8066.024214 -3.906659521 0.114196862 HQHMHDRDDLYAEQMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 17 HQHMHDRDDLYAEQMER 17 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;;;;;;;;;;;;;;;; 209.7 2.43E-12 8807960000 2506878 3318948 3084330 3319981 3499253 2453922 3258698 2822124 3578369 FALSE TRUE 2349976.981 3564686.363 3157491.764 3405177.333 3224435.785 3162329.445 2770086.487 3174472.394 2981116.097 0.788287643 1.195755632 1.059164307 1.142249152 1.081620333 1.060787082 0.929211207 1.064860371 1 21.50742113 1.933079274 9.415792515 0.991144198 1.077120657 0.030492803 0.111271394 1.031225673 139.7329837 0.042641812 0.027048594 85.71942999 -1.933079274 0.085976459 HQIVEVAGDDKYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HQIVEVAGDDKYGR 14 1 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ;; 140.84 5.91E-06 2203370000 2413860 1989440 2096750 2099860 2165230 1599090 2665540 1899140 2385570 FALSE TRUE 2262780.811 2136740.208 2146485.9 2153745.963 1995181.57 2060721.324 2265867.023 2136251.81 1987402.956 1.138561662 1.075141909 1.080045642 1.083698682 1.003913959 1.036891546 1.140114548 1.074896162 1 20.92245299 -0.655525212 0.007770185 1.23E-07 2.088689086 0.265052565 0.040733173 14035.37602 24.0745102 3364.682253 3108.696589 0.221041993 0.655525212 2.088688963 HQNS(ph)LPELEAAEAGAPGSGPVDLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HQNSLPELEAAEAGAPGSGPVDLFR 25 0 Q96BZ8 Q96BZ8 LENG1 Leukocyte receptor cluster member 1 1 HQNS(1)LPELEAAEAGAPGSGPVDLFR;HQNS(1)LPELEAAEAGAPGSGPVDLFR 187.69 8.55E-18 394830000 347090 324320 316700 337170 187870 196535 418640 225870 347180 TRUE FALSE 325366.2565 348332.9903 324212.2736 345822.353 173115.448 253271.464 355868.8185 254070.3667 289233.4151 1.124926234 1.204331768 1.120936436 1.195651453 0.598531978 0.875664604 1.230386255 0.878426743 1 18.14187471 HQNVQLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HQNVQLPR 8 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20;K7EK45;A0A087WUW5 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ;;;; 130.27 0.001055 1190730000 538030 906351 549795 537734 895506 285641 451681 771321 823060 FALSE TRUE 504355.6627 973458.1711 562836.397 551533.1648 825176.5711 368100.9197 383955.6273 867622.1247 685685.9688 0.73554905 1.419685126 0.820836976 0.804352415 1.203432196 0.53683601 0.559958413 1.265334518 1 19.38718848 3.729893458 23.37206062 0.837891774 1.124617155 0.048833452 0.288741054 96.04575526 809718.0484 0.071761901 0.12230491 5369.000673 -3.729893458 0.286725381 HQPST(ph)PDPFLKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HQPSTPDPFLKPR 13 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 HQPS(0.004)T(0.996)PDPFLKPR;HQPS(0.21)T(0.79)PDPFLKPR 101.39 0.002883 519390000 437530 388787 417250 408820 464710 323201 509480 402160 457730 TRUE FALSE 410145.7783 417573.194 427147.367 419311.0133 428213.5511 416503.882 433088.2038 452370.5613 381331.906 1.075561137 1.095038699 1.12014589 1.099595934 1.122941837 1.092234548 1.135725065 1.186290877 1 18.54068772 4.707319986 1.186563295 1.114683026 1.057997215 0.034093611 0.04662164 4.102793262 5.057829133 0.011891136 0.284054249 50970.62814 -4.707319986 -0.056685811 HQPTAIIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HQPTAIIAK 9 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 146.11 9.56E-05 2047280000 4039500 6324600 3405500 3145700 8080700 2659820 4342200 6523700 7374900 FALSE TRUE 3786674.906 6792879.965 3486280.068 3226423.988 7446074.418 3427666.855 3691127.421 7338198.305 6143981.546 0.616322637 1.105615294 0.567430101 0.52513569 1.211929815 0.557890161 0.600771241 1.194371801 1 22.55074245 1.233128695 24.99353682 1.097186002 0.751546203 0.274629205 0.240344659 191.8616738 882753.0416 0.198948303 0.05536964 17.1052212 -1.233128695 -0.345639799 HQPVPQLQAHS(ph)TPHPDDFANDDIDSYMIAMETTIGNEGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HQPVPQLQAHSTPHPDDFANDDIDSYMIAMETTIGNEGSR 40 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 1 HQPVPQLQAHS(0.499)T(0.499)PHPDDFANDDIDS(0.001)Y(0.001)MIAMETTIGNEGSR 100.72 1.99E-05 33040000 7632.5 9308.9 8024.3 7914.5 9673 8051.9 11473 8438.6 12518 TRUE FALSE 7154.795449 9998.140642 8214.640185 8117.599469 8913.321599 10376.35282 9752.73016 9492.177786 10428.66493 0.686070125 0.958717219 0.787698161 0.77839297 0.854694408 0.994983815 0.935184918 0.910200668 1 13.34826686 2.365092007 5.476970745 0.953438401 0.82540437 0.503998999 0.072298527 0.199445523 8.843304555 0.024464255 0.020305772 231.7885652 -2.365092007 -0.128034031 HQPWQS(ph)PERPLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 HQPWQSPERPLSR 13 1 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-2;V9GYS7;J3QRS2;V9GYU5;J3QL08 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 1 HQPWQS(1)PERPLSR;HQPWQS(1)PERPLSR;HQPWQS(1)PERPLSR;HQPWQS(1)PERPLSR;HQPWQS(1)PERPLSR;HQPWQS(1)PERPLSR;HQPWQS(1)PERPLSR 149.73 2.37E-05 14779380000 1925910 1730500 1984150 1744910 1885080 1675590 2196440 1702220 2024750 TRUE FALSE 1805370.731 1858628.021 2031214.975 1789687.345 1737033.421 2159305.632 1867104.213 1914745.914 1686806.145 1.070289397 1.101862254 1.204178074 1.060991715 1.029776555 1.280114872 1.106887249 1.135130981 1 20.68586275 -1.054461592 5.25293549 0.999999387 1.129554805 0.21813337 0.072814636 1.11E-06 2.00E-07 0.065775737 0.015503323 0.088214181 1.054461592 0.129555417 HQQGQGDDSSHKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HQQGQGDDSSHKK 13 1 A0A2R8Y6L5;A0A2R8Y6I6;Q13627-2;Q13627;Q13627-5;A0A2R8Y443;A0A2R8YDF3;Q13627-4;Q13627-3;E7EMI5 A0A2R8Y6L5 DYRK1A Dual specificity tyrosine-phosphorylation-regulated kinase 1A 0 130.1 5.94E-05 13912000 20507 12066 17251 17886 13364 9609.3 19394 15288 20035 FALSE TRUE 19223.50348 12959.37919 17660.20187 18344.98504 12314.44535 12383.34892 16486.04975 17196.74045 16691.02907 1.151726679 0.776427813 1.058065491 1.09909251 0.737788263 0.741916443 0.987719192 1.030298395 1 14.02678528 1.508728508 13.57846263 1.013076562 0.920308246 0.061521115 0.145602867 0.339777906 121.070126 0.076558272 0.035503227 32.26476515 -1.508728508 -0.092768316 HQQIPLHS(ph)PPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HQQIPLHSPPSK 12 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;C9JAU4 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 HQQIPLHS(1)PPSK;HQQIPLHS(0.991)PPS(0.009)K;HQQIPLHS(0.999)PPS(0.001)K 152.34 0.00011653 331472000 497180 413084 485750 509260 488840 413711 619990 391210 526660 TRUE FALSE 466062.3913 443669.1692 497272.2194 522328.4738 450448.4783 533142.6497 527028.2552 440053.4297 438757.0436 1.062233411 1.011195548 1.133365781 1.190473136 1.026646717 1.215120435 1.201184717 1.002954679 1 18.74306276 3.893310568 3.697138647 1.128740039 1.037124793 0.0873021 0.082146699 0.3681014 9.590995496 0.020136213 0.039799692 7821.869533 -3.893310568 -0.091615245 HQQQLLAS(ph)PGSSTVDNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HQQQLLASPGSSTVDNK 17 0 F2Z2X4;Q9C0E2 F2Z2X4 XPO4 Exportin-4 1 HQQQLLAS(1)PGSSTVDNK;HQQQLLAS(0.984)PGS(0.015)STVDNK 165.13 1.62E-09 1005950000 526630 431030 418570 473040 500120 334060 578770 390610 464310 TRUE FALSE 493669.1684 462943.9097 428498.6781 485179.0073 460842.5926 430497.699 491988.8115 439378.5183 386813.6614 1.276245432 1.196813753 1.10776511 1.254296463 1.191381377 1.112933027 1.271901333 1.135891935 1 18.56127922 0.984336091 23.80157287 0.999999996 1.193484382 0.544827524 0.058260469 385.7024405 586083.172 0.053425169 0.013356292 9.645751985 -0.984336091 0.193484385 HQRKY(ph)RR ddPTM_SK-BR-3_Pertuzumab_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 49.59 0.076149 248970000 176820 193690 163680 168670 201390 220060 293570 176600 217080 TRUE FALSE 165753.1518 208031.0091 167562.5669 172998.3578 185573.6418 283587.7496 249551.9039 198648.8987 180847.9456 0.916533231 1.150308943 0.926538404 0.956595648 1.02613077 1.568100476 1.379899025 1.098430497 1 17.46441768 2.369792268 10.33484355 1.312102604 1.003209671 0.370953219 0.166807165 0.287727134 25.80359878 0.054389634 0.045479494 234.3107791 -2.369792268 -0.308892933 HQS(ph)FGAAVLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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;HQS(1)FGAAVLSR 141.82 3.98E-05 3893010000 2180993 3475990 2052620 2120860 4425860 1467009 3405290 2663680 6026410 TRUE FALSE 2044488.541 3733355.916 2101309.116 2175284.858 4078270.809 1890510.683 2894698.378 2996246.311 5020563.239 0.407222944 0.743612965 0.418540513 0.433275064 0.812313403 0.376553505 0.576568453 0.596794855 1 22.25941779 0.623209083 2.239467144 0.999940277 0.546175842 0.498054138 0.144413621 2.131265777 11.67389311 0.124931154 0.033849305 4.199611174 -0.623209083 -0.453764435 HQTLEVSLSRDS(ph)PLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HQTLEVSLSRDSPLK 15 1 Q8NCF5;H3BSZ7;Q8NCF5-3;Q8NCF5-2 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 HQTLEVSLS(0.255)RDS(0.745)PLK;HQTLEVSLS(0.038)RDS(0.962)PLK 205.68 2.58E-09 1109820000 2112560 1931140 2189170 2117200 2313270 1765790 2962700 2107850 3060700 TRUE FALSE 1980338.641 2074123.615 2241098.146 2171530.936 2131595.105 2275544.908 2518470.639 2371019.712 2549849.397 0.776649257 0.813429851 0.878913927 0.851631057 0.835969021 0.892423259 0.987693878 0.92986657 1 21.28198061 2.092887197 0.479991243 1.008006302 0.802538308 0.810805263 0.031182824 0.428696164 0.217866341 0.033148689 0.028575845 123.8474864 -2.092887197 -0.205467995 HQVLFIADEIQTGLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HQVLFIADEIQTGLAR 16 0 P04181;P04181-2 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 149.09 8.69E-07 333670000 197790 204330 189650 187000 239570 188260 195160 189410 234650 FALSE TRUE 185410.677 219458.8058 194148.5876 191798.7366 220755.1386 242607.6059 165897.5698 213058.2554 195485.3991 0.948463045 1.12263528 0.993161579 0.981140983 1.129266634 1.241052309 0.8486443 1.089893447 1 17.57670133 1.716758727 25 0.970895827 1.065587694 0.143816197 0.102276959 1.618227958 1847.996829 0.044447807 0.024648547 52.09052404 -1.716758727 0.094691867 HQVLNDRDEEVELCSSVECK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HQVLNDRDEEVELCSSVECK 20 1 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ; 139.17 2.91E-07 404990000 329210 259910 312380 308520 343080 292100 493980 283470 412890 FALSE TRUE 308605.3338 279154.0068 319789.8011 316437.1455 316135.8807 376424.5282 419912.2849 318861.8535 343975.9916 0.897171144 0.811550845 0.929686399 0.919939627 0.919063796 1.094333725 1.220760446 0.926988689 1 18.39194835 2.283386138 4.395388788 1.095763219 0.886970068 0.474471204 0.083082614 0.141448572 5.857342479 0.029524759 0.023591493 192.0375418 -2.283386138 -0.208793151 HQYINEDEYEVNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HQYINEDEYEVNLK 14 0 Q93009;A0A669KBL1;Q93009-3 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7 0 ; 136.14 2.88E-05 485630000 361540 289980 270940 243992 290130 188143 346300 268310 270570 FALSE TRUE 338911.8568 311450.4209 277366.8247 250253.2478 267344.3601 242456.8299 294375.5299 301809.0941 225410.1191 1.50353435 1.381705587 1.23049855 1.110213015 1.186035309 1.075625313 1.305955257 1.338933209 1 17.78219276 4.268096645 1.289128026 1.186940636 1.520185317 0.554093991 0.10152784 0.534436327 1.324578542 0.028757156 0.188884661 18539.44142 -4.268096645 0.33324468 HQYYNQEWTLWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HQYYNQEWTLWDR 13 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 225.32 1.26E-11 1276630000 1120440 1114730 1043420 950060 1155970 945550 1211710 1115740 686435 FALSE TRUE 1050313.66 1197265.769 1068170.415 974440.148 1065184.779 1218514.935 1030025.334 1255042.595 571864.564 1.836647568 2.093617693 1.867873064 1.703970152 1.862652184 2.130775383 1.801170066 2.194650052 1 19.12531399 -1.184762981 6.045211932 0.999988983 1.934006981 0.778595092 0.156927032 2.14E-05 2.88E-06 0.139464175 0.032871634 0.06534871 1.184762981 0.934017999 HRDTHPGS(ph)PGSPGPALRPLPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HRDTHPGSPGSPGPALRPLPAR 22 2 Q8N0Y2-2;Q8N0Y2 Q8N0Y2-2 ZNF444 Zinc finger protein 444 1 HRDTHPGS(0.958)PGS(0.041)PGPALRPLPAR;HRDTHPGS(0.79)PGS(0.21)PGPALRPLPAR;HRDTHPGS(0.959)PGS(0.041)PGPALRPLPAR 96.317 0.00070413 652730000 214979 253501 222435 229935 293387 179257 282355 251051 467610 TRUE FALSE 201523.8481 272270.4778 227711.2632 235835.5214 270345.5685 231005.5859 240018.489 282395.27 389562.8701 0.517307638 0.698912804 0.584530202 0.605385008 0.693971601 0.592986662 0.616122602 0.72490294 1 18.57149665 0.845617847 2.614077052 0.999816881 0.621512589 0.84224816 0.052450471 0.208290149 2.633793435 0.045183271 0.012039937 7.008383312 -0.845617847 -0.378304292 HRDYETATLSDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HRDYETATLSDIK 13 1 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 109.84 0.0006641 335830000 610980 715930 687500 786130 675740 482810 827970 743900 842250 FALSE TRUE 572739.8524 768938.2021 703807.8247 806303.4267 622670.1062 622189.4092 703823.585 836777.5525 701673.0339 0.816248915 1.095863978 1.00304243 1.149115596 0.887407776 0.886722703 1.003064891 1.19254626 1 19.42043939 4.752241139 24.13425963 1.021423993 0.816248692 0.307801199 0.099089188 1867.172461 3293846.76 0.0229849 0.435821539 56525.07391 -4.752241139 -0.205175301 HREDIEDYISLFPLDDVQPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HREDIEDYISLFPLDDVQPSK 21 1 F5GY88;A0A0B4J1W0;O75448-2;O75448;H0YEG1;B9TX62 F5GY88 MED24 Mediator of RNA polymerase II transcription subunit 24 0 75.122 0.0075691 8620400 15508 14872 15208 13109 14286 12009 16212 14374 16686 FALSE TRUE 14537.38196 15973.13835 15568.74094 13445.39913 13164.03519 15475.80335 13781.1611 16168.62554 13900.9988 1.045779671 1.149064077 1.119972828 0.9672254 0.946984844 1.113287151 0.991379202 1.163126892 1 13.76290093 3.266827507 24.87859187 1.029153364 1.116542039 0.196015106 0.069894934 260.3228653 229116.574 0.01800904 0.024379316 1848.534274 -3.266827507 0.087388676 HREDS(ph)DVEMVEDDSRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HREDSDVEMVEDDSRK 16 2 H0Y806;E7EUC9;A0A087WX20;A0A669KB03;A0A669KBB4;A0A669KBK2;H0Y818;A0A669KAW3;P40692-2;P40692-3;P40692;H0Y4N0 H0Y806 MLH1 DNA mismatch repair protein Mlh1 1 HREDS(1)DVEMVEDDSRK;HREDS(1)DVEMVEDDSRK 168.79 3.05E-09 570870000 1471670 663830 954530 851200 1000130 594860 1159010 677710 1285920 TRUE FALSE 1379560.802 712980.6639 977171.9024 873043.2331 921583.8241 766586.4253 985227.2102 762323.5853 1071291.645 1.287754654 0.665533674 0.912143679 0.814944499 0.860254842 0.715572112 0.919662928 0.711592953 1 20.03091986 4.750638743 24.90528091 0.821009627 1.287754954 0.657934787 0.104835473 1007.40261 2077239.488 0.021900359 0.370151046 56316.90032 -4.750638743 0.466745326 HREELEQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HREELEQSK 9 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 60.518 0.057199 204062000 231410 240640 206380 204724 281750 127827 231980 241970 311980 FALSE TRUE 216926.4612 258457.236 211275.4311 209977.5644 259622.4915 164728.5798 197196.7526 272180.4871 259908.5225 0.834626195 0.994416164 0.812883814 0.807890262 0.998899494 0.633794453 0.758715992 1.047216476 1 17.98764442 3.853507486 5.664571365 0.839955518 0.92235991 0 0.13233952 0.605102532 26.31417604 0.032365272 0.059360193 7136.865071 -3.853507486 0.082404392 HREQEELRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HREQEELRR 9 2 Q8WXF1;Q8WXF1-2;A0A0U1RQF9 Q8WXF1 PSPC1 Paraspeckle component 1 0 ; 112.36 0.0011112 221431000 173131 193338 181085 175549 213511 144841 208185 188166 290660 FALSE TRUE 162295.0398 207652.9467 185380.4217 180053.8845 196742.7073 186654.2454 176969.5919 211658.9393 242146.9683 0.670233623 0.857549232 0.765569865 0.743572739 0.812492961 0.770830404 0.730835464 0.874092874 1 17.88552341 0.980947956 4.298229342 0.999690484 0.773405832 0.707254718 0.049631758 0.097758608 5.612534627 0.044840464 0.011424529 9.570793714 -0.980947956 -0.226284652 HRFS(ph)YDTFVDYDVDEEDMMNQVLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HRFSYDTFVDYDVDEEDMMNQVLQR 25 1 Q9Y508 Q9Y508 RNF114 E3 ubiquitin-protein ligase RNF114 1 HRFS(0.296)Y(0.228)DT(0.248)FVDY(0.228)DVDEEDMMNQVLQR 68.762 0.025043 19038000 13444 8595.8 11880 11837 12126 9723.8 14616 9503.4 10994 TRUE FALSE 12602.56404 9232.241976 12161.79921 12140.75746 11173.67287 12530.90321 12424.46649 10689.92041 9159.030376 1.375971421 1.007993379 1.327847896 1.325550518 1.219962421 1.368147358 1.356526398 1.167145426 1 13.16097916 0.970555819 7.41750549 1.000010668 1.268100383 0.411472381 0.108687224 0.319001608 75.38686627 0.108434633 0.027175769 9.344494635 -0.970555819 0.268089715 HRGS(ph)ADYSMEAK ddPTM_SK-BR-3_Pertuzumab_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 0.0017929 225490000 345820 248790 287190 261210 301760 249950 380240 265650 463700 TRUE FALSE 324175.7435 267210.6705 294002.2824 267913.0908 278060.9868 322106.5074 323226.542 298816.9873 386305.4744 0.839169427 0.691708216 0.761061652 0.693526519 0.719795616 0.833812951 0.8367123 0.773525117 1 18.5593826 0.463253867 0.466640223 1.015423278 0.733473614 0.655081151 0.053774545 1.229308085 0.485261609 0.097187087 0.029693406 2.905720696 -0.463253867 -0.281949664 HRGS(ph)CPGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HRGSCPGPR 9 1 Q92903;D6RGC8 Q92903 CDS1 Phosphatidate cytidylyltransferase 1 1 HRGS(1)CPGPR;HRGS(1)CPGPR 95.618 0.0047983 86238000 32501 28992 20299.9 20323 29900 25050 36168 31857 52764 TRUE FALSE 30466.82043 31138.59785 20781.42321 20844.52259 27551.77461 32281.52835 30744.94417 35834.41658 43957.34753 0.69309961 0.708382093 0.472763358 0.474198826 0.626784284 0.734382991 0.699426737 0.815208801 1 15.42381671 1.144144782 0.866293528 0.995301528 0.592225084 0.705073733 0.083333662 0.333470135 0.557506974 0.084030451 0.030468183 13.93621322 -1.144144782 -0.403076444 HRGS(ph)EEDPLLSPVETWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HRGSEEDPLLSPVETWK 17 1 Q13017-2;Q13017;H0YK04;A0A0A0MSK6 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 1 HRGS(1)EEDPLLSPVETWK 116.74 0.00015227 115830000 125460 120440 131510 173750 165450 63836 94077 63546 82835 TRUE FALSE 117607.6826 129357.5029 134629.4793 178208.7192 152456.2244 82264.41691 79971.02722 71479.85798 69009.30337 1.704229384 1.874493679 1.950888833 2.582386873 2.209212627 1.192077197 1.158844146 1.035800312 1 16.07450325 2.206447264 7.842682698 1.114356428 2.046450289 0.807253084 0.234804983 0.100200987 20.08422577 0.093660195 0.069977994 160.8597036 -2.206447264 0.932093861 HRHPLDHDCSGEGHPTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HRHPLDHDCSGEGHPTSR 18 1 A0A087X0D9;E9PFU9;Q8WV99;B8ZZ56;E7EV05;B4DEN4;Q8WV99-2 A0A087X0D9 ZFAND2B AN1-type zinc finger protein 2B 0 ;;;; 98.391 0.00041372 282937300 34624.6 53198.7 45409.62 48164.9 54193.9 37225.11 45239.5 47699.1 59746.6 FALSE TRUE 32457.50809 57137.5871 46486.75763 49400.89288 49937.7297 47971.39496 38456.25696 53654.43763 49774.50648 0.652091008 1.147928752 0.933947133 0.992493876 1.003279253 0.963774397 0.772609508 1.077950168 1 15.60311939 1.972005503 24.41126804 0.910738715 0.974766509 0 0.146023219 1980.370354 1726884.047 0.054950901 0.035568796 93.75738871 -1.972005503 0.064027794 HRHS(ph)PTGPPGFPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HRHSPTGPPGFPR 13 1 P98175-5;P98175-2;P98175 P98175-5 RBM10 RNA-binding protein 10 1 HRHS(0.818)PT(0.182)GPPGFPR;HRHS(0.946)PT(0.054)GPPGFPR;HRHS(0.998)PT(0.002)GPPGFPR;HRHS(0.717)PT(0.283)GPPGFPR;HRHS(0.965)PT(0.035)GPPGFPR;HRHS(0.991)PT(0.009)GPPGFPR 148.68 2.62E-05 14343800000 1524880 1818420 1781130 1778440 2012720 1423300 1859570 1643680 1894550 TRUE FALSE 1429440.483 1953057.709 1823379.245 1824077.781 1854649.09 1834183.605 1580744.742 1848897.066 1578337.366 0.905662195 1.237414606 1.15525317 1.155695747 1.175065059 1.162098576 1.001525261 1.171420703 1 20.58997418 1.192387205 0.776917513 1.015188494 1.147482848 0.070872362 0.099882231 1.126797082 1.554573693 0.087696506 0.034108068 15.57353505 -1.192387205 0.132294354 HRMS(ph)PGVAGSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HRMSPGVAGSPR 12 1 Q15596;E7EWM1 Q15596 NCOA2 Nuclear receptor coactivator 2 1 HRMS(1)PGVAGSPR 99.055 0.0024293 96198000 32924 27776 33369 32653 26555 20990 28832 22193 41064 TRUE FALSE 30863.34561 29832.56394 34160.52844 33490.93126 24469.47742 27049.47226 24508.90926 24963.8449 34210.15312 0.902169175 0.872038305 0.998549417 0.978976363 0.71526945 0.790685507 0.716422086 0.72972035 1 15.06213694 2.740900165 24.99336541 0.768520868 0.9370535 0.389228748 0.089512576 173.4848003 1853342.433 0.025359237 0.025740176 550.681092 -2.740900165 0.168532632 HRPELIEYDKLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HRPELIEYDKLR 12 2 O43707;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 90.926 0.0051565 93583000 260190 235500 183390 183850 271460 144850 196600 236130 199780 FALSE TRUE 243905.1724 252936.665 187740.0974 188567.9023 250140.6266 186665.8436 167121.6551 265611.3503 166435.4274 1.465464272 1.519728516 1.12800562 1.13297935 1.502928977 1.121551142 1.004123087 1.595882286 1 17.34460303 4.034601631 3.713763199 1.203670301 1.489884802 0.25993181 0.195627966 0.288299058 7.991457803 0.047100695 0.10756221 10829.33107 -4.034601631 0.286214501 HRPIGIGVQGLADAFILMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HRPIGIGVQGLADAFILMR 19 1 P23921;E9PL69 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ;; 154.49 2.12E-08 60734000 142873 233738 129250 97346 238564 89023.6 136356 195045 99521 FALSE TRUE 133930.834 251044.2047 132315.871 99844.06317 219828.1458 114723.2681 115910.6837 219396.7976 82910.30217 1.615370231 3.027901216 1.595891796 1.20424194 2.651397233 1.383703414 1.398025102 2.646194645 1 16.33926376 2.742332939 0.072311467 9.47E-12 3.808515365 0.121906074 0.650918864 78.58077655 2.283848202 47.59303985 70.15080579 552.5008348 -2.742332939 3.808515365 HRPQVAIICGSGLGGLTDKLTQAQIFDYGEIPNFPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HRPQVAIICGSGLGGLTDKLTQAQIFDYGEIPNFPR 36 2 P00491;G3V5M2;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 266.29 9.25E-63 426640000 561930 864970 343780 218200 1007800 343840 589380 779700 232420 FALSE TRUE 526759.8044 929013.2788 351934.6239 223799.3814 928651.4533 443101.0262 501007.9405 877047.2613 193627.6005 2.720478914 4.797938292 1.817585009 1.155823761 4.796069625 2.288418723 2.587482049 4.529557042 1 17.56292509 3.973420107 24.53098294 2.660835005 3.832619016 0.113611165 1.3374363 249.0028678 1650400.872 0.311638323 0.591001623 9406.327754 -3.973420107 1.171784011 HRPS(ph)PPAT(ph)PPPK ddPTM_SK-BR-3_Pertuzumab_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 113.47 0.0026626 19952700000 9770350 7585800 8388820 8214490 8619130 6490890 10119200 7620630 9951600 TRUE FALSE 9158841.234 8147460.525 8587806.772 8425287.72 7942218.298 8364704.572 8601919.902 8572082.431 8290613.67 1.104724161 0.982733106 1.035846936 1.016244159 0.957977131 1.008936721 1.037549239 1.033950293 1 22.98304746 -0.381572593 6.27059428 0.999998198 1.018642357 0.024520686 0.038539406 0 0 0.034010761 0.008016413 0.415362617 0.381572593 0.018644158 HRPS(ph)PPATPPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HRPSPPATPPPK 12 1 A9Z1X7;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 HRPS(1)PPATPPPK;HRPS(0.999)PPAT(0.001)PPPK;HRPS(1)PPATPPPK;HRPS(1)PPATPPPK 147.07 3.95E-05 1785860000 2444030 2162700 2262490 2323590 2209670 1601320 2340340 1665020 2269610 TRUE FALSE 2291062.525 2322828.558 2316157.331 2383217.253 2036131.432 2063595.089 1989427.744 1872901.412 1890797.429 1.211691157 1.228491494 1.224963233 1.260429709 1.076863867 1.091388775 1.052163343 0.990535202 1 20.85056338 2.439588298 1.36508383 1.022855107 1.232380528 0.888378928 0.033224115 0.127176266 0.478308603 0.016668014 0.011902465 275.1618988 -2.439588298 0.209525421 HRPSAGGPDS(ph)AGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HRPSAGGPDSAGR 13 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 HRPSAGGPDS(1)AGR;HRPSAGGPDS(1)AGR;HRPSAGGPDS(1)AGR;HRPSAGGPDS(1)AGR 144.08 2.45E-05 748917000 277768 347225 296094 283582 347395 227963 327433 301329 395905 TRUE FALSE 260382.9967 372933.9003 303117.4895 290859.1942 320111.998 293772.2174 278337.4614 338950.589 329825.8979 0.789455887 1.130699265 0.919022707 0.88185675 0.970548402 0.890688752 0.843892075 1.027665175 1 18.33134516 3.712847936 23.16405831 0.919199596 0.99657476 0 0.099831195 341.8627986 554807.3584 0.024226416 0.037775419 5162.355831 -3.712847936 0.077375164 HRPSAGGPDSAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HRPSAGGPDSAGR 13 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 0 141 3.61E-05 41437000 20603 26895 21908 19590 30657 20617 28759 23396 29145 FALSE TRUE 19313.49501 28886.33378 22427.66811 20092.71257 28249.32288 26568.79321 24446.85494 26317.0421 24280.51122 0.795431976 1.189692158 0.923690111 0.82752428 1.163456677 1.094243567 1.006850915 1.083875124 1 14.56751118 2.716819926 24.88676489 1.066876177 0.974953431 0.219856927 0.116019713 1618.210511 1852377.962 0.037206014 0.035106408 520.9786496 -2.716819926 -0.091922746 HRRACKDSVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HRRACKDSVGR 11 3 O15054;O15054-1 O15054 KDM6B Lysine-specific demethylase 6B 0 50.909 0.090327 536200000 676760 665610 595630 633880 794700 667500 727270 542170 854890 FALSE TRUE 634402.7997 714892.457 609758.6249 650146.434 732287.4677 860196.414 618222.6151 609861.118 712203.3362 0.890760781 1.003775777 0.856158058 0.912866313 1.028199996 1.207796103 0.86804229 0.856301967 1 19.44192967 2.753821697 23.52704597 0.992378941 0.920582452 0.120198448 0.102058172 916.7085921 1413229.221 0.031705615 0.033487235 567.3116428 -2.753821697 -0.07179649 HRS(ph)EDCGGGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HRSEDCGGGPR 11 1 Q9UGU0;Q9UGU0-2;A9JX13 Q9UGU0 TCF20 Transcription factor 20 1 HRS(1)EDCGGGPR 97.273 0.0038696 83747000 21727 26702 24616 29902 26655 17242 28698 20090 23833 TRUE FALSE 20367.14585 28679.04386 25199.90314 30669.33594 24561.62382 22219.4855 24395.00132 22598.28072 19855.11833 1.025788188 1.444415661 1.26918927 1.544656417 1.23704243 1.119080991 1.228650513 1.138158955 1 14.27722334 2.480762413 22.46396103 1.152809964 1.33873311 0.285578529 0.144067519 50.14199392 309361.9248 0.044593166 0.038191394 302.5257967 -2.480762413 0.185923147 HRS(ph)EPQHPK ddPTM_SK-BR-3_Pertuzumab_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 78.324 0.018174 322477000 441247 467837 397501 496444 570728 245973 518337 418584 528943 TRUE FALSE 413630.1379 502476.1383 406929.9114 509183.5935 525905.3251 316981.4121 440617.1789 470845.1338 440658.9962 0.938662643 1.1402834 0.923457628 1.155504819 1.19345192 0.719334939 0.999905103 1.068502261 1 18.74930313 2.276708697 24.99999954 0.944473923 1.063673005 0.194876688 0.124123328 271.2801671 177780.0039 0.04099839 0.034301103 189.1074754 -2.276708697 0.119199083 HRS(ph)IHEVDISNLEAALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HRSIHEVDISNLEAALR 17 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 HRS(0.999)IHEVDIS(0.001)NLEAALR;HRS(0.999)IHEVDIS(0.001)NLEAALR 148.44 2.19E-07 378100000 422450 594730 468240 524840 746730 302960 578300 514980 967050 TRUE FALSE 396009.6086 638764.428 479346.8739 538308.283 688084.838 390419.6339 491589.2837 579276.3866 805643.1076 0.491544711 0.792862773 0.594986625 0.668172145 0.854081455 0.484606186 0.610182448 0.719023574 1 19.61978135 0.880271082 5.117947109 0.999985351 0.651023902 0.484204796 0.115280802 0.930049111 38.88769063 0.102949597 0.026003221 7.59051219 -0.880271082 -0.348961449 HRS(ph)LTAHSLLPLAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HRSLTAHSLLPLAEK 15 1 F2Z2E2;Q86VI3 F2Z2E2 IQGAP3 Ras GTPase-activating-like protein IQGAP3 1 HRS(0.465)LT(0.465)AHS(0.07)LLPLAEK 150.7 1.89E-06 241180000 451970 569250 470440 501710 787340 291180 663780 552800 1108100 TRUE FALSE 423682.0045 611397.8623 481599.059 514584.728 725505.4924 375238.9391 564252.3512 621818.2969 923150.9514 0.458952031 0.66229457 0.521690476 0.557422085 0.785901256 0.406476252 0.611224362 0.673582469 1 19.81620705 0.788668251 2.221075775 0.999626307 0.575792018 0.623696839 0.104406768 0.504621148 4.09413865 0.088957324 0.024218587 6.147071309 -0.788668251 -0.423834289 HRS(ph)NS(ph)FSDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HRSNSFSDER 10 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 HRS(1)NS(0.962)FS(0.038)DER;HRS(1)NS(0.995)FS(0.005)DER;HRS(1)NS(0.998)FS(0.002)DER;HRS(1)NS(1)FSDER;HRS(1)NS(1)FSDER 179.55 1.19E-06 4232730000 5000320 5023210 5367020 6832780 7505410 3576982 3375092 2689437 3194882 TRUE FALSE 4687358.897 5395133.695 5494328.249 7008120.703 6915965.374 4609598.636 2869028.287 3025219.13 2661635.554 1.761082162 2.026999409 2.064267679 2.633012882 2.598389311 1.731866945 1.077919283 1.136601562 1 21.34388161 1.898198677 3.303868728 1.085278822 2.189217243 0.795516426 0.263552053 0.119218139 2.260754971 0.142825149 0.07774443 79.10404226 -1.898198677 1.103938421 HRS(ph)PTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HRSPTPK 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HRS(0.994)PT(0.006)PK;HRS(0.983)PT(0.017)PK;HRS(0.996)PT(0.004)PK;HRS(0.994)PT(0.006)PK;HRS(0.972)PT(0.028)PK 83.456 0.013485 784084000 1686770 1059925 1353650 1423070 1247610 1202150 1461650 1095291 1180970 TRUE FALSE 1581198.077 1138402.95 1385759.217 1459588.385 1149627.743 1549191.19 1242489.152 1232040.492 983858.4776 1.607139759 1.157079982 1.408494462 1.483534897 1.168488933 1.574607756 1.262873858 1.252253775 1 19.90809128 0.880692053 1.626646494 1.002248768 1.366787738 0.393609079 0.15168078 0.532950977 2.766852422 0.12904654 0.037224903 7.597873396 -0.880692053 0.36453897 S(ph)PHSTVPEHHPHPISPYEHLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPHSTVPEHHPHPISPYEHLLR 22 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.994)PHS(0.003)T(0.003)VPEHHPHPISPYEHLLR 166.29 5.84E-12 192420000 14676 24031 19657 15438 12593 17029 22923 23306 49481 TRUE FALSE 13757.45536 25810.28024 20123.27332 15834.16522 11603.99658 21944.99586 19485.90896 26215.8054 41222.30144 0.333738168 0.626124194 0.488164722 0.384116477 0.281498028 0.532357367 0.472703082 0.635961712 1 15.33113743 0.820824831 1.719668083 0.999898961 0.459968042 0.762513701 0.098533322 0.333876598 1.804709923 0.096339877 0.027414707 6.619494575 -0.820824831 -0.539930919 HRWPT(ph)GDNIHAEHQVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HRWPTGDNIHAEHQVR 16 1 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38 Q5T1Z4 PUM1 Pumilio homolog 1 1 HRWPT(1)GDNIHAEHQVR;HRWPT(1)GDNIHAEHQVR 240.13 4.16E-20 2554200000 1230020 1447930 1392590 1412720 1742140 879860 1541300 1182570 1467760 TRUE FALSE 1153035.244 1555136.244 1425622.892 1448972.787 1605319.352 1133861.299 1310196.374 1330216.468 1222781.374 0.942961079 1.271802365 1.165885352 1.184981075 1.312842497 0.927280479 1.071488658 1.087861245 1 20.22173505 2.233391453 24.99998984 1.028732374 1.187884605 0.342118659 0.105187153 134.451327 650249.4467 0.035529881 0.027034388 171.1557338 -2.233391453 0.159152231 YKSEDEANRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YKSEDEANRDR 11 2 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 52.344 0.081518 70829000 247250 282350 279650 247590 349890 211960 298720 290510 725120 FALSE TRUE 231775.0639 303255.4878 286283.4301 253943.5786 322411.0508 273149.4111 253929.7092 326780.813 604092.7875 0.383674609 0.502001504 0.473906387 0.42037181 0.533711141 0.452164662 0.420348851 0.540944735 1 19.20441064 0.825787515 4.346179721 0.999987139 0.461466581 0.939909908 0.042948474 0.354264896 8.633608471 0.038692071 0.009840589 6.695569389 -0.825787515 -0.538520558 VRGGAPDPSPGATATPGAPAQPSS(ph)PDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VRGGAPDPSPGATATPGAPAQPSSPDAR 28 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 VRGGAPDPSPGATATPGAPAQPS(0.398)S(0.602)PDAR 184.86 6.36E-18 448400000 135210 159640 116170 123710 226310 109500 162160 180710 453910 TRUE FALSE 126747.4475 171459.9117 118925.6073 126884.608 208536.5255 141110.8724 137845.6134 203272.0413 378149.4886 0.335178154 0.453418336 0.314493635 0.335540869 0.55146584 0.373161611 0.364526775 0.537544139 1 18.52859714 0.836722353 2.953695222 0.999840604 0.39046313 0.884284781 0.069267698 0.214222914 3.240272949 0.063133801 0.016567464 6.866293339 -0.836722353 -0.609377475 HS(ph)FSAGPELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HSFSAGPELLR 11 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 HS(0.999)FS(0.001)AGPELLR;HS(0.988)FS(0.012)AGPELLR;HS(1)FSAGPELLR 181.76 3.92E-06 400380000 168620 248466 196049 210617 242847 176621 215477 197578 238378 TRUE FALSE 158066.3752 266862.6812 200699.3749 216021.7888 223774.7762 227608.6155 183168.2242 222246.0482 198591.1718 0.795938579 1.343779176 1.010615794 1.087771359 1.126811299 1.146116483 0.922338201 1.119113434 1 17.59944197 1.75664084 25 1.008093714 1.108110372 0.036199691 0.14315841 17.03805961 23583.18834 0.060490311 0.03354544 57.10062207 -1.75664084 0.100016658 HS(ph)GGHFTAAVQAMDCETHSPQVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSGGHFTAAVQAMDCETHSPQVR 23 0 A0A2R8Y6L5;A0A2R8Y6I6;Q13627-2;Q13627 A0A2R8Y6L5 DYRK1A Dual specificity tyrosine-phosphorylation-regulated kinase 1A 1 HS(1)GGHFTAAVQAMDCETHSPQVR;HS(1)GGHFTAAVQAMDCETHSPQVR 227.24 1.46E-32 462520000 52027 54704 61098 48413 62211 47107 71345 46941 64763 TRUE FALSE 48770.72294 58754.34108 62547.27341 49655.35954 57325.19901 60706.02618 60647.47958 52801.68718 53953.63692 0.903937635 1.088978324 1.159278169 0.920333871 1.062489987 1.125151698 1.12406657 0.978649266 1 15.71943259 2.4770893 24.99999856 1.077749159 1.047258869 0 0.088943048 5.999354229 4683960.382 0.030791685 0.026021196 299.9779273 -2.4770893 -0.03049029 HS(ph)HSHS(ph)PMSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSHSHSPMSTR 11 0 P62995 P62995 TRA2B Transformer-2 protein homolog beta 2 HS(0.84)HS(0.162)HS(0.965)PMS(0.027)T(0.006)R;HS(0.945)HS(0.056)HS(0.997)PMS(0.001)TR 83.633 0.0087478 491810000 483150 546550 637220 625420 625880 489630 541160 482920 586620 TRUE FALSE 452910.5039 587017.1307 652335.1593 641469.336 576725.9095 630978.2325 460018.0819 543213.625 488709.3323 0.92674822 1.201158013 1.33481216 1.312578446 1.180100054 1.291111487 0.941291789 1.111527014 1 18.89861713 1.742447088 13.96303451 1.021021625 1.224616735 0.350815726 0.120444914 0.078638097 153.0403446 0.054363161 0.029937757 55.26460725 -1.742447088 0.20359511 HS(ph)LSPVPWEEDSFLQVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSLSPVPWEEDSFLQVK 17 0 P10073 P10073 ZSCAN22 Zinc finger and SCAN domain-containing protein 22 1 HS(0.857)LS(0.143)PVPWEEDSFLQVK;HS(0.553)LS(0.447)PVPWEEDSFLQVK 109.28 0.00067873 50030000 80568 77711 81631 88386 102984 64658 93678 79855 109351 TRUE FALSE 75525.3927 83464.8033 83567.32587 90654.1344 94896.05206 83323.71497 79631.85356 89825.07253 91099.61167 0.829041873 0.916192745 0.917318135 0.995109998 1.041673508 0.914644019 0.874118474 0.98600939 1 16.47515728 5.41709721 0.896916252 0.952318665 0.544466362 0.409069847 0.049584661 7.766995183 2.045184686 0.016858731 4.144549367 261274.6113 -5.41709721 -0.407852303 HS(ph)PIKEEPCGSLSETVCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSPIKEEPCGSLSETVCK 18 1 J3QQY0;Q68DK7;J3KSZ8;Q68DK7-2;Q68DK7-3;J3KTC2 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 HS(0.974)PIKEEPCGS(0.026)LSETVCK;HS(0.995)PIKEEPCGS(0.005)LSETVCK 169.06 1.16E-11 1775160000 3434200 1231670 2114490 1914790 1785900 1591240 2716630 1691420 1690010 TRUE FALSE 3219259.552 1322864.128 2164646.701 1963926.753 1645642.618 2050605.156 2309296.551 1902597.51 1407936.413 2.286509193 0.939576614 1.537460557 1.394897337 1.168833054 1.456461483 1.640199465 1.351337669 1 20.42515075 4.754782289 24.89176487 1.347257498 2.286509952 0.647441533 0.224803806 2042.565033 3134212.072 0.053154698 1.412284378 56856.78371 -4.754782289 0.939252454 HS(ph)PIKEEPCGSLSETVCKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HSPIKEEPCGSLSETVCKR 19 2 J3QQY0;Q68DK7;J3KSZ8;Q68DK7-2;Q68DK7-3;J3KTC2 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 HS(1)PIKEEPCGSLSETVCKR;HS(1)PIKEEPCGSLSETVCKR;HS(1)PIKEEPCGSLSETVCKR 187.81 9.15E-15 1176480000 1079930 559425 740560 720113 863290 621821 1191580 611688 1199120 TRUE FALSE 1012339.109 600845.4091 758126.4329 738592.3187 795490.6857 801330.6283 1012913.641 688058.5933 998979.1254 1.013373636 0.601459424 0.758901176 0.739347099 0.796303612 0.802149522 1.013948756 0.688761733 1 19.93009501 1.961628374 8.423112768 0.904128276 0.755977114 0.129247621 0.133199614 0.505312057 103.2704272 0.051267544 0.032785988 91.54368151 -1.961628374 -0.148151162 HS(ph)PQQPSNGSLR ddPTM_SK-BR-3_Pertuzumab_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 175.31 2.94E-05 284570000 265430 244010 223220 249800 267110 209720 277620 212130 216170 TRUE FALSE 248817.2101 262076.7543 228514.8838 256210.2909 246132.2581 270262.7595 235993.4583 238614.8975 180089.8305 1.381628321 1.455255711 1.26889388 1.422680505 1.366719361 1.500710833 1.310420792 1.324977078 1 17.45835719 0.5747357 1.312419573 1.000307321 1.38789847 0.778954769 0.064627925 0.712035846 1.680793467 0.05820866 0.017351885 3.75608749 -0.5747357 0.387591149 HS(ph)PS(ph)PRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSPSPRPR 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 HS(1)PS(1)PRPR;HS(1)PS(1)PRPR 77.379 0.018986 726600000 143008 142809 150457 147067 145129 128993 148129 99184 165037 TRUE FALSE 134057.3846 153382.727 154025.9111 150840.9882 133731.1538 166231.1851 125918.4316 111567.3407 137491.2585 0.975024783 1.115581664 1.120259664 1.097095116 0.972652045 1.209030937 0.915828635 0.811450429 1 17.06898037 1.607763774 7.257565444 0.892554092 1.086127383 0.493130493 0.08211333 0.083114889 9.728080289 0.038719921 0.018797025 40.5288027 -1.607763774 0.193573291 HS(ph)PTPQQSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HSPTPQQSNR 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 HS(0.991)PT(0.009)PQQSNR;HS(0.999)PT(0.001)PQQSNR;HS(0.993)PT(0.005)PQQS(0.002)NR 121.56 0.00032969 1111720000 865402 844585 740563 733645 788723 552056 815653 743073 876298 TRUE FALSE 811238.0336 907118.9522 758129.5041 752471.5728 726779.8771 711425.6053 693353.4048 835847.2998 730038.2027 1.111226824 1.242563675 1.038479221 1.030729036 0.995536774 0.974504625 0.949749482 1.144936384 1 19.47761244 3.720755958 2.537449307 1.006263776 1.180783567 0.538190907 0.060530221 0.178615451 2.283543309 0.015781556 0.029887011 5257.217664 -3.720755958 0.174519791 HS(ph)PVQMNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HSPVQMNR 8 0 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 HS(1)PVQMNR;HS(1)PVQMNR;HS(1)PVQMNR 133.89 0.00057967 879070000 638715 591554 627626 587077 668320 460478 684259 566971 615708 TRUE FALSE 598738.9683 635353.2737 642513.5851 602142.3897 615832.8431 593410.5234 581660.7153 637758.5774 512942.3572 1.16726365 1.238644586 1.252603877 1.173898746 1.200588788 1.156875651 1.133968968 1.243333814 1 18.96843718 -5 0.184065442 0.162249843 1.238495119 0.675811363 0.041619675 74.98003833 0.727448894 22.9325751 0.120236746 1.00E-05 5 1.076245276 HS(ph)QPSPEPHS(ph)PTEPPAWGSSIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSQPSPEPHSPTEPPAWGSSIVK 23 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 2 HS(0.579)QPS(0.435)PEPHS(0.493)PT(0.493)EPPAWGSSIVK 87.326 0.0030775 496080000 307170 258900 298380 311600 327340 199120 328110 230360 323300 TRUE FALSE 287944.778 278069.2254 305457.7145 319596.1835 301632.0368 256602.7116 278912.9515 259120.9531 269339.1414 1.069078844 1.032412979 1.134100721 1.186593905 1.119896779 0.952712295 1.035545558 0.962062 1 18.03906438 2.247014943 24.9999787 0.994012826 1.105108408 0.631951518 0.045667039 139.0094915 411060.2099 0.017149125 0.01412911 176.6098589 -2.247014943 0.111095582 HS(ph)S(ph)ISPVRLPLNSSLGAELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HSSISPVRLPLNSSLGAELSR 21 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 HS(0.698)S(0.751)IS(0.551)PVRLPLNSSLGAELSR;HS(0.667)S(0.708)IS(0.621)PVRLPLNS(0.003)S(0.001)LGAELSR;HS(0.728)S(0.778)IS(0.494)PVRLPLNSSLGAELSR;HS(0.735)S(0.771)IS(0.493)PVRLPLNSSLGAELSR;HS(0.664)S(0.664)IS(0.664)PVRLPLNS(0.006)S(0.001)LGAELSR;HS(0.693)S(0.741)IS(0.564)PVRLPLNS(0.002)SLGAELSR 141.48 2.06E-07 849120000 98574 105112.5 95423.8 103794 102425.5 80537.2 108009 86144.9 109698.1 TRUE FALSE 92404.4293 112895.1389 97687.2976 106457.5298 94381.41439 103786.9822 91814.05316 96900.28039 91388.77843 1.011113518 1.235328241 1.06892005 1.164886232 1.032746208 1.1356644 1.004653468 1.060308301 1 16.47972941 1.962561953 0.677167784 1.005549602 1.13509501 0.222224487 0.06830812 0.816058068 0.728554881 0.054973938 0.031132353 91.74067966 -1.962561953 0.129545408 HS(ph)S(ph)PHQS(ph)EDEEDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSSPHQSEDEEDPR 14 0 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 3 HS(1)S(1)PHQS(1)EDEEDPR;HS(1)S(1)PHQS(1)EDEEDPR 123.14 4.94E-05 221470000 435890 310470 385080 366610 306600 375490 368680 267740 216880 TRUE FALSE 408608.423 333457.5218 394214.2794 376017.8333 282520.8728 483887.8674 313399.8567 301167.9284 180681.3269 2.261486729 1.845556082 2.181820812 2.081110648 1.563641786 2.678128812 1.734544803 1.666845897 1 17.46308789 0.958593694 1.706373472 1.010621816 2.059149288 0.569170329 0.298021766 0.275427251 1.65528781 0.249202517 0.071586108 9.090623973 -0.958593694 1.048527472 HS(ph)SADNLANEMTYITETEDVFYTYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 HSSADNLANEMTYITETEDVFYTYK 25 0 J3KN34;P26045-2;P26045;P26045-3 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 HS(0.5)S(0.5)ADNLANEMTYITETEDVFYTYK;HS(0.5)S(0.5)ADNLANEMTYITETEDVFYTYK;HS(0.402)S(0.402)ADNLANEMT(0.099)Y(0.089)IT(0.004)ET(0.003)EDVFYTYK;HS(0.5)S(0.5)ADNLANEMTYITETEDVFYTYK;HS(0.5)S(0.5)ADNLANEMTYITETEDVFYTYK;HS(0.5)S(0.5)ADNLANEMTYITETEDVFYTYK;HS(0.376)S(0.376)ADNLANEMT(0.127)Y(0.111)IT(0.008)ET(0.001)EDVFYTYK 261.79 2.68E-45 677074000 332811 292834 280522 286188 304387 219498 384179 287509 301384 TRUE FALSE 311980.9536 314515.7341 287176.1143 293532.0686 280481.6729 282863.5093 326574.9255 323405.1315 251081.0634 1.24255071 1.252646177 1.143758555 1.169072907 1.117096085 1.126582409 1.300675252 1.288050668 1 17.9377937 4.1194296 4.179631562 1.178908776 1.247543215 0.122312668 0.086104317 0.531706741 16.04773455 0.021377207 0.050098388 13165.26485 -4.1194296 0.068634438 HS(ph)SIS(ph)PVRLPLNSSLGAELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSSISPVRLPLNSSLGAELSR 21 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 HS(0.569)S(0.569)IS(0.862)PVRLPLNSSLGAELSR;HS(0.512)S(0.512)IS(0.977)PVRLPLNSSLGAELSR 235.73 1.10E-29 706461000 170722 155729 170105 177741 167354 139639 181975 133069 171044 TRUE FALSE 160036.8148 167259.3372 174139.9709 182302.135 154210.6919 179950.5125 154689.5381 149682.9576 142495.6514 1.12309964 1.173785554 1.222072177 1.279352269 1.082213319 1.262849151 1.085573746 1.050438775 1 17.12055837 1.540188705 4.091378568 1.034407789 1.191482179 0.576744581 0.060002098 0.122267403 4.534247977 0.034345147 0.0143473 34.68875433 -1.540188705 0.15707439 HS(ph)SNPPLESHVGWVMDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSSNPPLESHVGWVMDSR 18 0 Q6PKG0;Q6PKG0-3;H0YC33;H0YBR8 Q6PKG0 LARP1 La-related protein 1 1 HS(0.573)S(0.427)NPPLESHVGWVMDSR 140.4 1.45E-07 617300000 554530 643520 662830 674730 748090 521940 759430 659660 752080 TRUE FALSE 519822.9572 691166.8904 678552.6406 692044.7141 689338.029 672615.605 645560.5217 742020.0031 626552.9894 0.829655218 1.103125996 1.082993222 1.104527033 1.100207071 1.07351751 1.030336672 1.184289303 1 19.257077 4.741063743 24.97203691 1.084796301 0.829655127 0.732461159 0.048474916 107.1345361 1068747.356 0.010265474 0.069457753 55088.85462 -4.741063743 -0.255141174 HS(ph)SPTEERDEPAYPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSSPTEERDEPAYPR 15 1 F5H4R1;J3KNB8;F5H538;Q9Y6R4-2;Q9Y6R4 F5H4R1 MAP3K4 Mitogen-activated protein kinase kinase kinase 4 1 HS(0.587)S(0.409)PT(0.005)EERDEPAYPR 178.51 4.29E-07 372550000 163240 295780 258570 279430 361020 258720 289680 249720 243030 TRUE FALSE 153023.0998 317679.859 264703.4025 286600.6469 332666.9455 333408.264 246245.1733 280898.0917 202466.723 0.755793829 1.56904727 1.307392141 1.415544454 1.643069738 1.646731172 1.216225411 1.38737906 1 17.62732528 0.504234244 1.316209809 1.000865917 1.398435985 0.157564257 0.259255458 3.556984636 7.66979761 0.226197587 0.067206649 3.19325973 -0.504234244 0.397570068 HS(ph)SYPAGTEDDEGMGEEPSPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSSYPAGTEDDEGMGEEPSPFR 22 0 Q92934 Q92934 BAD Bcl2-associated agonist of cell death 1 HS(0.607)S(0.393)YPAGTEDDEGMGEEPSPFR 284.65 2.11E-45 120690000 91025 106000 105050 112310 114000 73890 94617 72670 82395 TRUE FALSE 85327.90773 113848.3503 107541.8356 115192.0647 105046.8999 95220.8435 80430.05923 81743.00947 68642.74221 1.243072537 1.658563551 1.566689094 1.678139029 1.530342415 1.387194632 1.171719786 1.190847085 1 16.06681957 1.826768922 1.526873144 1.084140743 1.567328978 0.695706511 0.125561302 0.19367558 0.855724254 0.085988601 0.036030072 67.10716966 -1.826768922 0.483188234 HS(ph)YPPALGSPGALAGAGVGAAGPLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HSYPPALGSPGALAGAGVGAAGPLER 26 0 Q96IF1;H0YJL9 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 HS(0.915)Y(0.085)PPALGSPGALAGAGVGAAGPLER;HS(0.999)Y(0.001)PPALGSPGALAGAGVGAAGPLER;HS(0.991)Y(0.004)PPALGS(0.005)PGALAGAGVGAAGPLER;HS(0.991)Y(0.009)PPALGSPGALAGAGVGAAGPLER 288.48 3.36E-62 1240370000 763320 731672 685007 672345 751330 492351 816080 633823 708831 TRUE FALSE 715545.1638 785845.7562 701255.6895 689598.511 692323.5725 634484.741 693716.3801 712957.1968 590522.5269 1.211715271 1.330763384 1.187517254 1.167776807 1.172391469 1.074446295 1.174750071 1.207332768 1 19.17163257 7.999999998 0.028561385 0.225043935 2.547755192 0.5956819 0.055005123 953.5630944 2.089627954 55.33598024 128.8049382 99999999.48 -7.999999998 2.322711257 HSAS(ph)PVVFTSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HSASPVVFTSAR 12 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 HS(0.015)AS(0.985)PVVFTSAR;HS(0.029)AS(0.971)PVVFTSAR;HS(0.141)AS(0.859)PVVFTSAR 144.38 4.06E-05 945790000 717170 797620 778040 780970 825260 609870 832390 693590 785520 TRUE FALSE 672283.6099 856676.6147 796495.4762 801011.0124 760447.4085 785929.5686 707580.847 780186.2383 654411.6373 1.027309986 1.309079127 1.21711692 1.224017066 1.162032221 1.20097126 1.081247347 1.192194933 1 19.31983888 0.845955787 0.492960519 0.997221871 1.219049126 0.305251955 0.079384895 1.222874187 0.699901117 0.094198961 0.041490551 7.013838903 -0.845955787 0.221827255 HSCDALNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 224.28 4.14E-06 884510000 317893 740950 521117 551761 632500 810960 379075 462077 358264 FALSE TRUE 297996.6446 795810.709 533478.1413 565920.1214 582826.0014 1045070.987 322236.2229 519768.3306 298467.4239 0.998422678 2.666323509 1.787391516 1.896086728 1.952729024 3.501457457 1.079636158 1.741457489 1 18.18721395 1.611472611 25 1.307869947 2.149965763 0.269822099 0.665754762 0.43225154 2973.929576 0.292258167 0.154033819 40.87639726 -1.611472611 0.842095816 HSCSGS(ph)SPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSCSGSSPPR 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSCSGS(0.969)S(0.031)PPR;HSCSGS(0.673)S(0.326)PPR 128.57 0.00021013 602310000 27246.6 56529 65564 65544 55532 89238 36497 32882 25004.9 TRUE FALSE 25541.28394 60714.46598 67119.20904 67225.97001 51170.74073 114999.5619 31024.61367 36987.39008 20831.42065 1.226094195 2.914561949 3.222017843 3.22714284 2.456421076 5.520485802 1.489318189 1.775557736 1 14.34647361 1.598628023 25 1.473928901 3.100118424 0.354724905 1.062789775 0.806655553 2176.830956 0.514364649 0.243259848 39.68514974 -1.598628023 1.626189522 HSCSGSS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HSCSGSSPPR 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSCSGS(0.024)S(0.976)PPR;HS(0.005)CS(0.022)GS(0.114)S(0.859)PPR;HSCSGS(0.004)S(0.996)PPR;HSCSGS(0.027)S(0.972)PPR 177.47 2.44E-06 11893410000 633701 713460 714370 711940 712500 572169 766760 600125 716090 TRUE FALSE 594038.7856 766285.3208 731315.1937 730209.5857 656543.1241 737344.9019 651791.4563 675051.9273 596569.9529 0.995757132 1.284485276 1.225866623 1.224013349 1.10052999 1.235973918 1.09256501 1.131555359 1 19.18633179 1.014227333 0.687991828 1.001296707 1.201199183 0.261566054 0.085308601 0.829441495 0.914134019 0.0775945 0.03118986 10.3330215 -1.014227333 0.199902475 HSCSPMGDGDPEAMEES(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HSCSPMGDGDPEAMEESPR 19 0 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 HSCSPMGDGDPEAMEES(1)PR;HSCSPMGDGDPEAMEES(1)PR;HSCSPMGDGDPEAMEES(1)PR;HSCSPMGDGDPEAMEES(1)PR;HSCSPMGDGDPEAMEES(1)PR 260.48 2.66E-31 1528900000 527847 578518 582053 573156 599752 467856 623562 548436 538884 TRUE FALSE 494809.9985 621352.0747 595859.572 587864.1533 552649.8972 602918.4322 530064.667 616909.4419 448940.7791 1.102172094 1.384040176 1.327256511 1.309446993 1.23100846 1.342979877 1.180700644 1.374144365 1 18.77616562 -3.263703214 0.421146799 9.28E-11 1.294631207 0.480372474 0.090240054 147.6306587 4.034534759 131.7242886 0.04816867 0.000544875 3.263703214 1.294631207 HSDENDGGQPHKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSDENDGGQPHKR 13 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 ; 136.01 3.14E-05 138736000 122509 103881 113229 126245 138812 106727 200262 158744 184829 FALSE TRUE 114841.3804 111572.4573 115914.8454 129484.6604 127910.2655 137537.3523 170234.5722 178563.5378 153979.8459 0.745820856 0.724591304 0.75279232 0.840919535 0.830694853 0.893216587 1.105563987 1.159655258 1 17.23238201 2.030688395 1.503666406 1.109619052 0.757729563 0.871286408 0.054011824 0.120767648 0.511347305 0.034285856 0.016875603 107.3219106 -2.030688395 -0.351889489 HSDGNLCVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSDGNLCVK 9 0 P49458;Q6P2S0;Q659G3;E9PE20;P49458-2 P49458 SRP9;DKFZp564M2223 Signal recognition particle 9 kDa protein 0 ; 88.496 0.012745 1054990000 1050650 934520 923610 895530 1159750 794850 1265810 902230 1329730 FALSE TRUE 984891.692 1003712.833 945518.4654 918510.8159 1068667.913 1024310.292 1076013.542 1014875.402 1107789.473 0.889060346 0.906050164 0.85351819 0.829138423 0.964685023 0.924643461 0.971315912 0.916126599 1 20.0792523 2.723920976 24.90573351 0.952531557 0.872889245 0.65726523 0.030745197 481.1698699 818590.6709 0.00947449 0.008966442 529.5670753 -2.723920976 -0.079642312 HSDSKHDGTSNS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HSDSKHDGTSNSPSK 15 1 Q2TB10 Q2TB10 ZNF800 Zinc finger protein 800 1 HSDSKHDGT(0.001)S(0.005)NS(0.993)PS(0.001)K;HSDSKHDGTS(0.002)NS(0.997)PS(0.001)K;HSDSKHDGTS(0.002)NS(0.998)PSK;HSDSKHDGT(0.049)S(0.125)NS(0.816)PS(0.009)K 128.38 4.37E-05 258665000 259120 212575 275150 231602 305300 177521 337068 200931 481871 TRUE FALSE 242902.1417 228314.2742 281676.6879 237545.2994 281322.9695 228768.4309 286527.7826 226017.6777 401443.6171 0.605071625 0.568733103 0.701659401 0.591727678 0.700778285 0.569864412 0.713743526 0.563012259 1 18.61483785 -2.099468382 2.535028428 1.655985011 0.632961382 0.797672934 0.058993166 4153187.355 1480760.43 15694299.27 0.013008385 0.007953012 2.099468382 -1.023023629 HSDSKHDGTSNS(ph)PSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSDSKHDGTSNSPSKK 16 2 Q2TB10 Q2TB10 ZNF800 Zinc finger protein 800 1 HSDSKHDGTS(0.007)NS(0.989)PS(0.004)KK;HSDSKHDGTS(0.002)NS(0.998)PSKK 145.05 5.97E-07 67299000 132120 89504 125816 106503 144159 82596 179147 90276 270530 TRUE FALSE 123850.845 96130.96929 128800.4149 109236.0473 132837.3336 106440.1244 152285.5705 101547.1573 225376.7953 0.549527936 0.426534458 0.571489247 0.484681873 0.589401111 0.472276324 0.675693211 0.45056616 1 17.78197946 -5 0.268259062 4.195431408 0.495532559 0.788796328 0.076232646 82.70419586 0.805285371 146.2089792 0.08365874 1.00E-05 5 -3.699898849 HSEAATAQREEWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSEAATAQREEWK 13 1 Q14103-3;Q14103;H0Y8G5;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 145.81 2.52E-05 118340000 96994 162230 126300 144880 234120 94065 107920 122730 393170 FALSE TRUE 90923.31868 174241.678 129295.8956 148597.8661 215733.1596 121220.0385 91738.39788 138053.1107 327547.387 0.277588289 0.531958687 0.394739512 0.4536683 0.658631905 0.370083973 0.28007672 0.421475231 1 18.32134411 -1.369850853 3.152331799 1.00591957 0.425343899 0.722348998 0.112314938 26867336 35432576.37 1460907.469 0.0270837 0.042672604 1.369850853 -0.580575671 HSEKS(ph)PPSTENKHEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSEKSPPSTENKHEAK 16 2 H3BQL3;Q6PH81 H3BQL3 C16orf87 UPF0547 protein C16orf87 1 HS(0.146)EKS(0.854)PPSTENKHEAK;HS(0.087)EKS(0.893)PPS(0.016)T(0.004)ENKHEAK 111.57 0.00038298 186401000 381590 151587 228360 217982 238750 150209 293950 179607 361940 TRUE FALSE 357706.9631 162810.6592 233776.807 223575.7872 219999.5381 193571.8999 249874.9264 202031.3293 301529.8758 1.18630687 0.539948683 0.775302303 0.741471427 0.729611079 0.641965906 0.828690443 0.670020935 1 18.20194143 -1.21112593 4.288121719 1.000105338 0.744207316 0.150311914 0.170442353 22278106.02 6292181.045 22094.5975 0.03487984 0.061499852 1.21112593 -0.255898022 HSETFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HSETFTR 7 0 Q9UNS2-2;Q9UNS2 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 0 ;;; 135.77 0.0030453 1089050000 200272 240040 227721 232922 256768 191661 255586 212319 223940 FALSE TRUE 187737.333 257812.8114 233122.6497 238899.1729 236602.477 246990.4193 217263.252 238827.4945 186562.9673 1.006294742 1.381907755 1.249565512 1.280528372 1.268217806 1.323898429 1.164557228 1.280144168 1 17.50930311 -0.373559936 0.655377002 0.977696562 1.262432654 0.34711508 0.10240645 9.579406894 3.426503464 0.6228776 0.034592595 0.423097115 0.373559936 0.284736092 HSEVQQANLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HSEVQQANLK 10 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ;;; 157.78 8.57E-06 2138760000 3005320 3465950 2656980 2795350 3853260 1716510 3123860 3292170 4109150 FALSE TRUE 2817222.386 3722572.544 2720004.82 2867083.414 3550640.503 2212038.572 2655466.193 3703204.671 3423306.319 0.822953637 1.08742023 0.794554903 0.837518804 1.037196258 0.646170213 0.775702186 1.081762579 1 21.70695896 3.916428381 8.110854685 0.858224338 0.969731445 0.020399694 0.146726884 0.621119852 75.36100774 0.035430945 0.064302727 8249.514316 -3.916428381 0.111507107 HSGGHFTAAVQAMDCET(ph)HSPQVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSGGHFTAAVQAMDCETHSPQVR 23 0 A0A2R8Y6L5;A0A2R8Y6I6;Q13627-2;Q13627 A0A2R8Y6L5 DYRK1A Dual specificity tyrosine-phosphorylation-regulated kinase 1A 1 HSGGHFTAAVQAMDCET(0.5)HS(0.5)PQVR 119.14 0.00040111 80768000 81735 78194 83062 81282 101110 79551 123880 92983 154840 TRUE FALSE 76619.35225 83983.56512 85032.26986 83367.83373 93169.22846 102516.0823 105305.344 104592.1322 128996.2037 0.593965947 0.651054548 0.659184282 0.646281296 0.722263336 0.7947217 0.81634452 0.810815584 1 16.97696908 1.476914176 0.353892964 1.019666469 0.593101463 0.957028396 0.024544199 0.233023186 0.094448044 0.03759608 0.030459198 29.9856989 -1.476914176 -0.426565007 HSGNITFDEIVNIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 HSGNITFDEIVNIAR 15 0 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;;;;; 258.96 7.67E-25 4417532000 2788094 3031492 2962179 3037176 3224164 2550059 3392132 2622117 3200064 FALSE TRUE 2613592.173 3255946.822 3032443.285 3115115.078 2970951.165 3286219.637 2883513.298 2949494.079 2665952.645 0.980359564 1.221307073 1.137470799 1.168481024 1.114405078 1.232662419 1.081607096 1.106356516 1 21.34621972 0.922635369 1.324318677 1.002164943 1.149106817 0.251308799 0.071262986 0.616060598 2.164965249 0.059593136 0.018030973 8.368263919 -0.922635369 0.146941874 HSGPNSADSANDGFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HSGPNSADSANDGFVR 16 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ;;;; 289.1 1.76E-45 6529270000 3277470 4098450 3753800 3626670 3566550 2702170 4303460 3495930 4879800 FALSE TRUE 3072339.003 4401903.502 3842841.909 3719736.492 3286447.55 3482242.613 3658196.124 3932404.556 4065329.855 0.755741628 1.082791227 0.945271859 0.914990081 0.808408583 0.856570743 0.899852227 0.967302703 1 21.95494098 6.013877128 10.59048982 0.921970524 0.639234278 0 0.094218006 0 0 0.020734818 0 1032469.254 -6.013877128 -0.282736246 HSGSDRSS(ph)FSHYSGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSGSDRSSFSHYSGLK 16 1 Q8NC51;Q8NC51-3 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 HS(0.024)GS(0.024)DRS(0.282)S(0.665)FS(0.006)HYSGLK;HS(0.011)GS(0.011)DRS(0.13)S(0.816)FS(0.033)HYSGLK 161.8 5.01E-09 766270000 277346 632580 470730 524530 752230 279162 565550 499740 1312610 TRUE FALSE 259987.4089 679416.8814 481895.9379 537990.3278 693152.8901 359751.5376 480751.0278 562133.6391 1093526.911 0.237751267 0.621307875 0.440680456 0.491977218 0.633869074 0.328982793 0.439633468 0.514055606 1 20.06055729 0.816643394 5.705114552 0.999999243 0.470483557 0.671408587 0.118292076 3.056114418 94.93878664 0.103996834 0.026181417 6.556067163 -0.816643394 -0.529515686 HSGSRS(ph)DEDRYQNGAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSGSRSDEDRYQNGAER 17 2 Q9HCG8 Q9HCG8 CWC22 Pre-mRNA-splicing factor CWC22 homolog 1 HS(0.041)GS(0.005)RS(0.954)DEDRYQNGAER;HSGSRS(0.999)DEDRYQNGAER 190.85 1.44E-10 534930000 123976 159913 131477 142668 172951 92783 137297 141605 241770 TRUE FALSE 116216.5635 171753.1249 134595.6965 146329.1024 159368.1261 119567.9459 116710.5895 159284.696 201417.0251 0.576994737 0.852723968 0.668243891 0.726498181 0.791234634 0.59363376 0.579447489 0.790820418 1 17.61982611 0.985473181 22.85594555 1.000000007 0.69343692 0.553518486 0.090171155 211.3335189 332505.8201 0.089206638 0.02230166 9.671040023 -0.985473181 -0.306563087 HSHEGDYLESIVFIYSMPGYTCSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSHEGDYLESIVFIYSMPGYTCSIR 25 0 Q12792;Q12792-3;Q12792-4 Q12792 TWF1 Twinfilin-1 0 ; 207.22 1.95E-25 496890000 198132 189694 183160 187512 216227 199334 180190 175442 126766 FALSE TRUE 185731.2718 203739.1411 187504.6417 192323.8754 199245.4036 256878.4899 153172.1823 197346.3199 105607.9357 1.758686699 1.929202951 1.775478713 1.821111966 1.886651816 2.432378668 1.450385157 1.86866942 1 16.68835872 0.396708226 1.012868715 0.999168028 1.884046976 0.563597734 0.239732907 1.682848617 2.184943334 0.21804182 0.067150979 2.492919336 -0.396708226 0.884878948 HSHGPLQADVFVELLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSHGPLQADVFVELLSPR 18 0 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 1 HSHGPLQADVFVELLS(1)PR 105.79 0.00030131 29877000 37018 37864 44034 37656 36797 34844 38586 30148 35390 TRUE FALSE 34701.10946 40667.48996 45078.50727 38622.31671 33907.11205 44902.89715 32800.38751 33912.04416 29483.18037 1.176979858 1.379345425 1.528956738 1.309977968 1.150049337 1.523000456 1.112511849 1.150216623 1 14.84760454 1.62165598 7.15878489 1.093069353 1.360669044 0.469541002 0.128149031 0.104777662 11.65041044 0.065901054 0.032500779 41.84619556 -1.62165598 0.267599691 HSHS(ph)PASS(ph)PKPLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSHSPASSPKPLKK 14 2 Q9HDC5 Q9HDC5 JPH1 Junctophilin-1 2 HS(0.001)HS(0.999)PAS(0.201)S(0.799)PKPLKK 125.45 0.00016057 221520000 389120 174940 223100 213840 254250 162480 337630 203820 306500 TRUE FALSE 364765.6738 187892.7396 228392.0374 219327.4964 234282.2306 209385.3384 287005.5159 229267.3757 255343.1699 1.428531156 0.735844 0.894451328 0.858951882 0.917519081 0.820015426 1.123999189 0.897879414 1 17.96207794 1.744777182 25 1.016164069 0.908972264 0.004087191 0.193360649 3.721397631 15015.89537 0.081689852 0.045301501 55.5619119 -1.744777182 -0.107191806 HSHSHS(ph)PMSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSHSHSPMSTR 11 0 P62995 P62995 TRA2B Transformer-2 protein homolog beta 1 HSHS(0.004)HS(0.996)PMSTR;HSHS(0.105)HS(0.894)PMST(0.001)R 162.88 2.80E-05 142475000 35987.7 59230.9 66013.2 54011.4 62944.9 48215.6 48556.1 47972.3 52642.1 TRUE FALSE 33735.2941 63616.41747 67579.06428 55397.42397 58001.46146 62134.66101 41275.56358 53961.74726 43855.79343 0.769232328 1.450581839 1.540938129 1.263172312 1.322549586 1.416794821 0.941165587 1.230436005 1 15.42047982 1.74437493 25 1.063474603 1.340388111 0.184408855 0.220495663 1.573039693 6787.82342 0.097627584 0.05413936 55.51047328 -1.74437493 0.276913508 HSIS(ph)GPISTSKPLTALSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSISGPISTSKPLTALSDK 19 1 Q69YQ0-2;Q69YQ0;A0A494C1J1 Q69YQ0-2 SPECC1L Cytospin-A 1 HS(0.383)IS(0.515)GPIS(0.044)T(0.052)S(0.006)KPLTALSDK 57.366 0.052847 78386000 254180 173620 194760 180990 210930 118420 254780 217870 288960 TRUE FALSE 238271.3275 186475.0055 199379.7992 185634.5098 194364.4087 152605.9316 216578.1043 245071.5491 240730.7092 0.989783681 0.774620762 0.828227524 0.771129327 0.807393495 0.633927977 0.899669614 1.018031932 1 17.87706067 1.468115487 5.493015996 0.99744565 0.797908998 0.499637843 0.086000034 0.128766853 8.633782648 0.049158842 0.020246799 29.38430934 -1.468115487 -0.199536652 HSLASSEYPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSLASSEYPVR 11 0 P51570;P51570-2 P51570 GALK1 Galactokinase 0 130.01 0.00023316 161110000 79502 118080 93940 105090 91830 65689 90622 114240 111270 FALSE TRUE 74526.11174 126822.7661 96168.30116 107786.7873 84618.04222 84652.34793 77034.07239 128503.1155 92698.31817 0.803964012 1.3681237 1.037433074 1.162769611 0.912832551 0.91320263 0.831019094 1.386250776 1 16.50025554 2.745704808 24.58337807 0.976514824 1.129641199 0.014161728 0.202815557 943.8282472 3247744.283 0.058373417 0.060719518 556.8071561 -2.745704808 0.153126375 HSLDS(ph)DEEEDDDDGGSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSLDSDEEEDDDDGGSSK 18 0 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 HSLDS(1)DEEEDDDDGGSSK;HSLDS(1)DEEEDDDDGGSSK 367.96 1.01E-107 2377400000 2547900 1287510 1690520 1408990 1201830 1225280 1923340 1199760 1281470 TRUE FALSE 2388431.487 1382838.58 1730619.933 1445147.069 1107443.12 1578998.445 1634953.022 1349552.677 1067584.378 2.237229708 1.295296754 1.621061499 1.353660749 1.037335448 1.479038545 1.531450868 1.264118045 1 20.02591867 4.741641858 24.94909973 1.371701312 2.237230035 0.663717132 0.201913461 176.5514781 1429483.384 0.045641337 0.322713094 55162.23548 -4.741641858 0.865528723 HSLDS(ph)DEEEDDDDGGSSKYDILASEDVEGQEAATLPSEGGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSLDSDEEEDDDDGGSSKYDILASEDVEGQEAATLPSEGGVR 42 1 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 HS(0.08)LDS(0.25)DEEEDDDDGGS(0.204)S(0.204)KY(0.191)DILAS(0.07)EDVEGQEAATLPSEGGVR 43.055 0.041586 128080000 72164 29854 39380 35380 41857 32226 53868 28987 51863 TRUE FALSE 67647.38406 32064.42122 40314.1122 36287.9107 38569.72006 41529.12305 45790.99349 32606.09076 43206.73025 1.565667748 0.742116356 0.933051679 0.839867088 0.892678521 0.961172549 1.05981159 0.75465305 1 15.39896844 4.747080038 24.99037991 0.901684518 1.565668083 0.81460892 0.10009752 472.2084719 1385118.493 0.024054242 0.28160438 55857.31276 -4.747080038 0.663983565 HSLEEEDENEEEILTVQDLVDFSPVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSLEEEDENEEEILTVQDLVDFSPVYR 27 0 Q8TAG9-2;Q8TAG9 Q8TAG9-2 EXOC6 Exocyst complex component 6 0 100.88 0.0028834 8313000 4859.9 6958.1 6245.8 5603.9 6327.7 4139.2 9072 6155.7 6392.7 FALSE TRUE 4555.727534 7473.284964 6393.953325 5747.705561 5830.747967 5334.119846 7711.73782 6924.252695 5325.717072 0.855420495 1.403244833 1.200580737 1.079235995 1.094828713 1.001577773 1.448018683 1.300154064 1 12.37876007 1.740619792 24.99999797 1.2917337 1.14962189 0.076696898 0.180417376 0.721599992 8816.151002 0.080763786 0.044787748 55.03256961 -1.740619792 -0.14211181 HSLGLTVS(ph)PCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSLGLTVSPCR 11 0 A0A0C4DFZ6;Q9H972;G5E9D9;Q9H972-2 A0A0C4DFZ6 C14orf93 Uncharacterized protein C14orf93 1 HSLGLT(0.014)VS(0.986)PCR 67.079 0.039262 38381000 27110 43670 34042 40579 51899 45521 39992 28474 66268 TRUE FALSE 25413.23349 46903.37224 34849.49232 41620.32584 47823.06189 58662.17373 33995.57087 32029.04158 55207.44269 0.460322599 0.849584222 0.631246271 0.753889762 0.86624302 1.06257727 0.615778765 0.580158037 1 15.75257515 4.746950012 24.07502397 0.777199556 0.460322327 0.295770853 0.160200052 865.5801684 2483856.851 0.036669842 0.410303505 55840.59177 -4.746950012 -0.316877229 HSLPQEPVMPMDQSSMHSDHAQTVIPYNPS(ph)SHESLDQVGEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSLPQEPVMPMDQSSMHSDHAQTVIPYNPSSHESLDQVGEEK 42 0 P41743 P41743 PRKCI Protein kinase C iota type 1 HSLPQEPVMPMDQSSMHSDHAQTVIPYNPS(0.362)S(0.362)HES(0.276)LDQVGEEK 163.16 4.67E-20 181100000 58049 75937 90920 106530 83814 66908 122450 76104 78448 TRUE FALSE 54415.81671 81559.45449 93076.66534 109263.7402 77231.58653 86223.25344 104089.7593 85605.75193 65354.52201 0.83262512 1.247954265 1.424180951 1.671861974 1.181732865 1.319315799 1.592694064 1.30986731 1 15.99599944 4.83163612 1.706369773 1.393907118 0.542482715 0.411352481 0.191959055 1.062327147 2.550190866 0.045621607 1.586344147 67863.4791 -4.83163612 -0.851424403 HSLS(ph)LDDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSLSLDDIR 9 0 Q96NE9-3;Q96NE9-2;Q96NE9 Q96NE9-3 FRMD6 FERM domain-containing protein 6 1 HS(0.015)LS(0.985)LDDIR 84.882 0.015343 0 252750 250840 252950 239730 262490 201970 294950 238760 308550 TRUE FALSE 236930.8287 269412.4546 258950.0935 245881.8777 241875.0942 260275.4603 250724.9857 268569.7116 257051.0117 0.921726886 1.048089454 1.007387957 0.956548959 0.940961456 1.012544003 0.975389998 1.044810949 1 17.97169516 1.248292747 24.99448271 1.022405481 0.988555931 0.145308002 0.038596876 403.8437223 1037185.459 0.026522045 0.009423078 17.71302546 -1.248292747 -0.03384955 HSLSGRPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSLSGRPLK 9 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 129.85 0.00022692 1738180000 2109580 2602200 2225600 2064990 2977000 1594470 2583900 2446800 3311700 FALSE TRUE 1977545.154 2794869.596 2278392.283 2117981.139 2743198.429 2054767.605 2196468.183 2752288.366 2758955.876 0.716773027 1.013017142 0.825816862 0.767674887 0.994288619 0.744762764 0.796122983 0.997583321 1 21.39569095 1.225174556 24.47384696 0.998791905 0.848911348 0.315374487 0.097920027 261.3665002 477840.0406 0.087715654 0.022468452 16.79478915 -1.225174556 -0.149880557 HSLSGS(ph)SPGMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSLSGSSPGMK 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSLSGS(0.779)S(0.22)PGMK 177.1 3.18E-05 151500000 423190 303780 366350 356170 364300 279310 435680 324970 375020 TRUE FALSE 396703.2933 326272.1873 375039.995 365309.9252 335689.3475 359942.2628 370353.8287 365543.2198 312426.7393 1.269748211 1.044315823 1.200409401 1.169265877 1.074457802 1.152085329 1.185410153 1.170012595 1 18.25315841 -1.063230197 4.541181039 0.99999154 1.151851897 0.381349397 0.062867139 4.92E-06 1.01E-06 0.055571866 0.013097685 0.086450957 1.063230197 0.151860357 HSLSGSS(ph)PGMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 HSLSGSSPGMK 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSLSGS(0.007)S(0.993)PGMK;HSLSGS(0.03)S(0.97)PGMK;HSLSGS(0.035)S(0.965)PGMK;HSLSGS(0.044)S(0.956)PGMK;HSLSGS(0.024)S(0.976)PGMK;HSLSGS(0.037)S(0.963)PGMK;HSLSGS(0.033)S(0.967)PGMK;HSLS(0.008)GS(0.057)S(0.935)PGMK 218.4 1.90E-08 2053970000 4927010 3591600 4468880 4193860 4247960 3410280 5406360 3835880 4494590 TRUE FALSE 4618637.239 3857525.801 4574883.944 4301481.548 3914342.357 4394772.475 4595726.508 4314798.062 3744413.893 1.233474015 1.030208174 1.221789064 1.148772991 1.045381859 1.173687685 1.227355372 1.152329359 1 21.83630848 -1.284673745 9.967334394 0.999999989 1.152168391 0.324638562 0.069811665 1.67E-08 1.27E-09 0.065544226 0.015448921 0.051918992 1.284673745 0.152168403 HSMDLSYALETVLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSMDLSYALETVLNK 15 0 A2A2Q9;Q9Y312 A2A2Q9 AAR2 Protein AAR2 homolog 0 147.18 3.75E-06 39300000 118860 118460 130020 127280 142940 97537 163710 133680 150100 FALSE TRUE 111420.7648 127230.9017 133104.1358 130546.2203 131714.069 125694.3485 139163.2053 150370.2423 125047.3403 0.891028666 1.017461878 1.064429963 1.043974386 1.053313638 1.005174106 1.112884168 1.202506522 1 16.93211485 5.924957116 0.764216176 1.074967047 2.37E-14 0.488968619 0.057347009 11.91686532 1.316757744 0.019175188 16.59835722 841312.0623 -5.924957116 -1.074967047 HSMDQTGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HSMDQTGSK 9 0 Q14008;Q14008-3;Q14008-2;H0YDX5 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 ;; 105.98 0.0022838 60850100 153594 135600 140882 141541 145794 98470 158113 128936 162278 FALSE TRUE 143980.8257 145639.9651 144223.7876 145173.1817 134343.9273 126896.6905 134405.4235 145033.9434 135192.7534 1.065004019 1.077276417 1.06680117 1.073823692 0.993721364 0.938635298 0.994176242 1.072793768 1 17.0446583 2.737436392 24.17053123 0.993965194 1.071163817 0.538493593 0.032340685 45.32631069 974501.0778 0.010040585 0.00996286 546.3065308 -2.737436392 0.077198623 HSNLLQCLAQCAEVTPYLLVMEFCPLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSNLLQCLAQCAEVTPYLLVMEFCPLAK 28 0 A0A3B3ISA0 A0A3B3ISA0 0 30.749 0.095294 382720000 615820 220370 305110 283230 336300 210590 370960 251630 399310 FALSE TRUE 577276.9255 236686.4241 312347.3533 290498.1613 309888.3546 271383.9144 315337.9918 283046.5594 332662.5814 1.73532269 0.711490974 0.93893143 0.87325169 0.93153956 0.815793328 0.947921436 0.85085181 1 18.34370007 4.745389324 24.99718904 0.877864754 1.735323082 0.916483737 0.080773492 198.1493641 725327.7725 0.017884892 0.176736643 55640.28223 -4.745389324 0.857458328 HSPAPPPDPGFPAPS(ph)PPPADSPSEGFSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSPAPPPDPGFPAPSPPPADSPSEGFSLK 29 0 M0QZS0;A0A590UK10;A0A3B3IPE9;A0A087WZG4;Q6ZSZ5-2;Q6ZSZ5-1;Q6ZSZ5-6;Q6ZSZ5-5;Q6ZSZ5 M0QZS0 ARHGEF18 Rho guanine nucleotide exchange factor 18 1 HSPAPPPDPGFPAPS(0.637)PPPADS(0.121)PS(0.121)EGFS(0.121)LK 45.596 0.073947 83142000 32120 23494 32510 36124 32951 17300 21517 13738 25446 TRUE FALSE 30109.66654 25233.52021 33281.15255 37051.003 30363.16138 22294.22916 18290.7256 15453.21954 21198.89821 1.420341106 1.190322249 1.569947278 1.747779655 1.432299031 1.051669239 0.862814917 0.728963335 1 14.37170166 2.114358405 2.925039932 0.861584341 1.462462461 0.778128811 0.15161667 0.132593715 2.253790861 0.072985763 0.04790036 130.1242997 -2.114358405 0.600878121 HSPEDPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSPEDPEK 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 88.948 0.014253 223270000 407930 264700 303430 317820 292440 248370 407500 298690 242380 FALSE TRUE 382398.3895 284298.6634 310627.5029 325975.7993 269472.942 320070.387 346399.158 335982.104 201925.2122 1.893762475 1.407940397 1.538329461 1.614339268 1.334518553 1.585093727 1.715482452 1.663893777 1 17.62346153 -1.151060339 3.75407325 0.99964786 1.575391512 0.588047144 0.155585813 22978280.09 38575656.7 102244.6423 0.035988051 0.070621943 1.151060339 0.575743652 HSPTSEPTPPGDALPPVS(ph)SPHTHR ddPTM_SK-BR-3_Pertuzumab_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(0.637)S(0.359)PHT(0.003)HR;HSPTSEPTPPGDALPPVS(0.691)S(0.291)PHT(0.017)HR;HSPTSEPTPPGDALPPVS(0.482)S(0.482)PHT(0.037)HR;HSPTSEPTPPGDALPPVS(0.459)S(0.459)PHT(0.083)HR 196.02 3.38E-24 12101520000 1269557 1979620 1697450 2229240 2037870 1200091 1703728 1325024 1539289 TRUE FALSE 1190097.694 2126193.125 1737714.316 2286446.072 1877823.911 1546537.79 1448269.803 1490456.163 1282371.722 0.928044243 1.658016228 1.355078474 1.782982293 1.46433665 1.205998045 1.129368169 1.162265307 1 20.29038309 2.15535509 3.63258151 1.123062074 1.473213522 0.322627922 0.225685273 0.250322369 6.483186464 0.083976818 0.059819159 143.0062734 -2.15535509 0.350151448 HSPTSEPTPPGDALPPVSSPHT(ph)HR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSPTSEPTPPGDALPPVSSPHTHR 24 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 HSPTSEPTPPGDALPPVS(0.223)S(0.223)PHT(0.554)HR 137.64 2.28E-05 2725600000 154420 234170 193800 255950 242650 136960 202870 153980 197130 TRUE FALSE 144755.1278 251508.1905 198397.0275 262518.1103 223593.2478 176498.1286 172451.5269 173204.742 164227.7295 0.881429271 1.53145995 1.208060467 1.598500516 1.361482915 1.074715757 1.050075571 1.054661978 1 17.32533822 2.213668132 6.387543255 1.047986859 1.343945874 0.322869635 0.193064087 0.177996489 24.08284307 0.065738169 0.049656597 163.5566218 -2.213668132 0.295959015 HSQAQS(ph)KPTT(ph)PEKTDLTNGEHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSQAQSKPTTPEKTDLTNGEHAR 23 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 2 HSQAQS(0.996)KPT(0.22)T(0.784)PEKTDLTNGEHAR;HS(0.041)QAQS(0.958)KPT(0.227)T(0.772)PEKT(0.001)DLTNGEHAR 143.07 3.20E-06 446080000 401550 172133 246152 260220 272830 179098 403710 241540 346200 TRUE FALSE 376417.7023 184877.9064 251990.8417 266897.6858 251403.0323 230800.6852 343177.4334 271696.8007 288416.9835 1.305116286 0.641009084 0.873703201 0.925388244 0.871665147 0.800232644 1.189865552 0.942027746 1 18.13779659 1.750630019 25 1.058062221 0.86894326 0.1020917 0.177746858 5.321685045 11041.44705 0.075679413 0.04196821 56.31576897 -1.750630019 -0.18911896 HSQAVEELAEQLEQTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HSQAVEELAEQLEQTK 16 0 P35579 P35579 MYH9 Myosin-9 0 ;; 146.3 1.14E-06 921589000 936061 643264 748442 731610 757630 631303 987490 682374 746990 FALSE TRUE 877474.6129 690891.9359 766195.3977 750384.3512 698128.7959 813549.9278 839425.0419 767569.896 622312.5433 1.410022379 1.110200884 1.23120674 1.205799818 1.121829864 1.307301189 1.348880158 1.233415435 1 19.2472798 2.213279907 24.99962811 1.263902929 1.203054556 0 0.124067108 722.4934132 714455.1583 0.042016974 0.031043934 163.4104807 -2.213279907 -0.060848373 HSQAVEELAEQLEQTKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HSQAVEELAEQLEQTKR 17 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;; 272.76 7.87E-36 2880920000 5108140 4242250 4511130 4471230 4657360 3435200 5797770 3987940 5176900 FALSE TRUE 4788430.636 4556350.604 4618136.134 4585969.332 4291589.732 4426886.474 4928448.212 4485843.088 4312841.946 1.110272692 1.056461299 1.070787242 1.063328865 0.995072341 1.026443011 1.142737961 1.040113026 1 22.04020742 4.739506894 23.27866462 1.057794887 1.110272722 0.145820903 0.042145892 67.68718115 1664403.643 0.010041669 0.06025327 54891.7269 -4.739506894 0.052477835 HSQDLAFLSMLNDIAAVPATAMPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 237.97 1.32E-38 3563645000 2091661 2678800 2228544 2118589 3029130 2041511 2808966 2627321 2234292 FALSE TRUE 1960747.672 2877141.139 2281406.116 2172955.581 2791234.349 2630862.085 2387787.625 2955347.81 1861374.231 1.053387137 1.545708053 1.225656871 1.167393179 1.499555706 1.413397715 1.282809005 1.587723608 1 20.82793671 -0.964186429 4.624566611 0.999994311 1.350973793 0.289291723 0.17080062 8.92E-06 2.00E-06 0.147262921 0.034709641 0.108595935 0.964186429 0.350979483 HSQDLSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSQDLSSK 8 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 72.607 0.047188 0 175190 166210 156440 177110 182170 111550 191430 158050 152240 FALSE TRUE 164225.1706 178516.3613 160150.8307 181654.9424 167863.103 143752.6741 162726.8486 177782.8904 126830.1605 1.294843198 1.407522948 1.262718821 1.432269278 1.323526694 1.133426573 1.283029589 1.401739852 1 16.95253834 2.452523377 23.65245052 1.230364162 1.347929206 0.263093518 0.113211412 186.23243 179072.3551 0.035542167 0.029738389 283.4806221 -2.452523377 0.117565044 HSQELPAILDDTTLSGSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSQELPAILDDTTLSGSDR 19 0 Q15021;F5GZK7 Q15021 NCAPD2 Condensin complex subunit 1 0 ; 192.98 6.28E-15 242804000 85012 91329 86227 96147 97265 81114 97187 95496 90091 FALSE TRUE 79691.25067 98091.09419 88272.34516 98614.2948 89626.19925 104530.295 82614.71159 107418.8858 75054.23009 1.061782268 1.306936252 1.176114192 1.31390722 1.194152537 1.392730229 1.100733583 1.431216944 1 16.19564576 -1.107781584 4.506904555 0.9999769 1.242523891 0.29900191 0.118759143 2.32E-05 4.59E-06 0.096787337 0.022810823 0.07802224 1.107781584 0.242546991 HSQFIGYPITLFVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSQFIGYPITLFVEK 15 0 P07900;P07900-2;G3V2J8;Q58FG0 P07900 HSP90AA1;HSP90AA5P Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5 0 ; 172.2 1.04E-06 1339150000 1136580 1850300 887890 919960 2068620 523060 1008130 1762650 1728610 FALSE TRUE 1065443.487 1987298.137 908951.1701 943567.7311 1906158.93 674058.9308 856970.2655 1982720.733 1440093.824 0.739843105 1.379978238 0.631174966 0.655212678 1.323635237 0.468065983 0.595079467 1.376799692 1 20.45773138 5.035546003 16.07349102 0.895327221 0.160447257 0.021019275 0.343388148 27267442.66 344442084.1 0.079531491 568398634.3 108529.0503 -5.035546003 -0.734879964 HSQFLGYPITLYLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSQFLGYPITLYLEK 15 0 Q58FF8 Q58FF8 HSP90AB2P Putative heat shock protein HSP 90-beta 2 0 ; 161.14 1.67E-06 911890000 741730 1948140 547500 528410 2294510 270520 522040 1807990 1635340 FALSE TRUE 695306.4433 2092382.313 560486.9585 541969.8952 2114308.44 348614.7325 443764.9484 2033721.531 1362391.189 0.510357413 1.535816092 0.41139943 0.397807839 1.551909948 0.255884459 0.325725057 1.492758869 1 20.37770958 3.960778103 24.00516608 0.708547125 1.080993017 0.021912253 0.524933286 601.5387058 883554.7526 0.125790464 0.227754918 9136.463075 -3.960778103 0.372445892 HSQPS(ph)PEPHS(ph)PTEPPAWGSSIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSQPSPEPHSPTEPPAWGSSIVK 23 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 2 HS(0.128)QPS(0.76)PEPHS(0.616)PT(0.496)EPPAWGSSIVK;HSQPS(1)PEPHS(0.986)PT(0.014)EPPAWGSSIVK 188.8 1.07E-17 818570000 821070 694450 771490 795240 812940 516040 795980 589370 827200 TRUE FALSE 769680.6944 745867.8006 789790.1071 815647.2047 749094.9716 665012.3708 676630.1885 662954.1419 689134.9761 1.116879452 1.082324692 1.146060111 1.183581204 1.087007622 0.964995819 0.981854371 0.962009134 1 19.39442706 2.338037031 4.1901714 0.975833762 1.126906665 0.876462595 0.027588669 0.074005622 2.36710891 0.010371791 0.008456933 217.7895466 -2.338037031 0.151072903 HSQPSPEPHS(ph)PT(ph)EPPAWGSSIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSQPSPEPHSPTEPPAWGSSIVK 23 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 2 HS(0.208)QPS(0.56)PEPHS(0.616)PT(0.616)EPPAWGSSIVK 76.733 0.03317 80350000 69300 68706 71904 73169 75054 47588 72643 53454 76535 TRUE FALSE 64962.6367 73793.06373 73609.59684 75046.64041 69159.56159 61325.88307 61750.85653 60127.84957 63760.81407 1.018848922 1.157341932 1.154464508 1.177002545 1.084671873 0.961811482 0.968476602 0.943021987 1 15.96038243 2.3486615 3.572548651 0.965064022 1.136367656 0.736171326 0.044999601 0.105143592 2.601922637 0.015809746 0.01277396 223.1832 -2.3486615 0.171303634 HSQPSPEPHS(ph)PTEPPAWGSSIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HSQPSPEPHSPTEPPAWGSSIVK 23 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 HSQPSPEPHS(0.996)PT(0.004)EPPAWGSSIVK;HS(0.131)QPS(0.097)PEPHS(0.675)PT(0.097)EPPAWGSSIVK;HSQPSPEPHS(0.985)PT(0.015)EPPAWGSSIVK 250.52 1.84E-38 1099960000 812320 930570 909290 1028540 1074570 598230 969480 759040 1082100 TRUE FALSE 761478.3412 999470.3711 930858.7882 1054934.078 990177.6068 770929.2895 824115.4742 853807.8149 901490.5194 0.84468813 1.108686503 1.032577457 1.170210951 1.098378281 0.855171822 0.914169874 0.947106815 1 19.78195279 2.245176428 24.99999707 0.918739719 1.061710318 0.299472208 0.091129187 157.879236 596599.3487 0.029927296 0.024500068 175.86379 -2.245176428 0.142970599 HSQQLFPDGS(ph)PGDQWVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSQQLFPDGSPGDQWVK 17 0 H0Y9T5;Q8IU60;Q8IU60-2 H0Y9T5 DCP2 m7GpppN-mRNA hydrolase 1 HSQQLFPDGS(1)PGDQWVK 88.755 0.0019654 0 69570 65370 64162 57183 65672 55301 85399 59024 65909 TRUE FALSE 65215.73789 70210.06282 65683.95294 58650.41259 60514.38603 71265.50096 72594.21276 66393.27633 54908.36211 1.1877196 1.278677056 1.196246809 1.06815083 1.102097817 1.297898867 1.322097582 1.209165121 1 15.74473826 2.222855515 24.99552225 1.245834126 1.181436287 0 0.104959619 663.1883574 1055493.537 0.038398596 0.028455821 167.0534752 -2.222855515 -0.06439784 HSS(ph)IS(ph)PSTLTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HSSISPSTLTLK 12 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YCQ1 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 2 HS(0.001)S(0.999)IS(0.971)PS(0.025)T(0.004)LTLK;HS(0.001)S(0.999)IS(0.712)PS(0.274)T(0.014)LTLK;HS(0.036)S(0.964)IS(0.985)PS(0.014)T(0.001)LTLK;HS(0.003)S(0.997)IS(0.628)PS(0.3)T(0.072)LTLK 208 1.05E-07 756640000 3383040 2407430 2958210 2814900 2839530 2150120 3432960 2436980 3343070 TRUE FALSE 3171301.565 2585678.622 3028380.138 2887135.1 2616524.768 2770824.74 2918219.518 2741242.317 2785090.02 1.138671117 0.928400376 1.08735449 1.036639778 0.939475834 0.994877982 1.047800788 0.984256271 1 21.40929253 4.764152648 23.84440216 1.007741631 1.138671432 0.442598456 0.047738025 4314.680098 4019916.752 0.011109038 0.753380892 58096.8584 -4.764152648 0.130929801 HSS(ph)IS(ph)PVRLPLNSSLGAELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 HSSISPVRLPLNSSLGAELSR 21 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 HS(0.058)S(0.943)IS(0.999)PVRLPLNSSLGAELSR;HS(0.129)S(0.871)IS(1)PVRLPLNSSLGAELSR;HS(0.548)S(0.626)IS(0.826)PVRLPLNSSLGAELSR;HS(0.045)S(0.955)IS(1)PVRLPLNSSLGAELSR;HS(0.186)S(0.814)IS(1)PVRLPLNSSLGAELSR;HS(0.141)S(0.913)IS(0.945)PVRLPLNSSLGAELSR;HS(0.429)S(0.576)IS(0.995)PVRLPLNSSLGAELSR 278.24 9.47E-45 4176239000 1188368 1126482 1245758 1221536 1178644 1006140 1357714 991829 1236345 TRUE FALSE 1113990.168 1209887.899 1275307.968 1252882.682 1086078.055 1296596.285 1154137.39 1115661.034 1029991.032 1.081553269 1.174658673 1.238173856 1.216401544 1.054453894 1.258842304 1.120531494 1.083175483 1 19.97420035 1.111911501 1.79815145 1.002896548 1.176642165 0.420133326 0.064528216 0.289060784 1.809878021 0.056570443 0.016340254 12.93932141 -1.111911501 0.173745617 HSS(ph)ISPS(ph)TLTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSSISPSTLTLK 12 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YCQ1 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 2 HS(0.14)S(0.86)IS(0.204)PS(0.682)T(0.111)LT(0.003)LK 105.19 0.0030067 54196000 341430 256320 298520 276740 321220 227240 348410 249920 372410 TRUE FALSE 320060.5058 275298.1995 305601.0354 283841.6169 295992.6769 292840.4991 296169.155 281123.0621 310252.3651 1.031613427 0.887336344 0.985007915 0.914873338 0.954038422 0.943878378 0.954607243 0.90611094 1 18.24308268 -0.941582282 5.092813808 1.000000224 0.94501884 0.139837639 0.040855009 8.85E-08 1.84E-08 0.033754336 0.007955941 0.114397812 0.941582282 -0.054981384 HSS(ph)ISPST(ph)LTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSSISPSTLTLK 12 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YCQ1 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 2 HS(0.01)S(0.99)IS(0.001)PS(0.416)T(0.576)LT(0.008)LK 144.27 0.00065234 0 232750 157920 193780 188780 195090 147900 236320 169010 225060 TRUE FALSE 218182.593 169612.5611 198376.5531 193624.4144 179768.4184 190596.329 200886.0099 190111.2705 187496.0321 1.163665122 0.90461947 1.058030674 1.032685398 0.958785188 1.016535267 1.071414726 1.013948234 1 17.51650054 1.977223239 24.0935194 1.038285721 1.010388078 0 0.069335206 1964.148102 2077694.017 0.026094121 0.017001296 94.89061008 -1.977223239 -0.027897643 HSS(ph)NPPLESHVGWVMDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 HSSNPPLESHVGWVMDSR 18 0 Q6PKG0;Q6PKG0-3;H0YC33;H0YBR8 Q6PKG0 LARP1 La-related protein 1 1 HS(0.178)S(0.822)NPPLESHVGWVMDSR;HS(0.175)S(0.825)NPPLESHVGWVMDSR;HS(0.097)S(0.903)NPPLESHVGWVMDSR;HS(0.066)S(0.934)NPPLESHVGWVMDSR;HS(0.154)S(0.846)NPPLESHVGWVMDSR;HS(0.028)S(0.972)NPPLESHVGWVMDSR;HS(0.008)S(0.992)NPPLESHVGWVMDSR;HS(0.096)S(0.904)NPPLESHVGWVMDSR;HS(0.065)S(0.935)NPPLESHVGWVMDSR 257.34 8.21E-31 8500180000 2405380 2662130 2803830 2800600 3055650 2305297 3068850 2414360 2955960 TRUE FALSE 2254831.56 2859236.875 2870338.172 2872468.137 2815671.575 2970798.821 2608704.432 2715798.161 2462591.18 0.915633735 1.16106843 1.165576404 1.166441333 1.143377593 1.206371096 1.059333134 1.102821363 1 21.23174571 0.953686207 1.283060795 1.003470309 1.13410461 0.153906247 0.081840441 0.795481674 2.660258996 0.071286407 0.021795106 8.98847897 -0.953686207 0.130634302 HSS(ph)PHQS(ph)EDEEDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSSPHQSEDEEDPR 14 0 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 2 HS(0.486)S(0.514)PHQS(1)EDEEDPR;HS(0.385)S(0.615)PHQS(1)EDEEDPR 120.4 6.95E-05 1202140000 1208810 1243970 1360450 1449330 1496150 1158100 1438790 1088320 1388430 TRUE FALSE 1133152.74 1336074.833 1392720.516 1486522.262 1378648.414 1492424.67 1223056.797 1224199.148 1156692.063 0.979649447 1.155082563 1.204054701 1.28514953 1.191888885 1.290252365 1.05737459 1.058362192 1 20.14157341 1.601820585 7.378092348 1.03912607 1.187357192 0.39094168 0.086007495 0.122966872 14.91324907 0.044417322 0.021430478 39.97795593 -1.601820585 0.148231122 HSS(ph)PTEERDEPAYPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSSPTEERDEPAYPR 15 1 F5H4R1;J3KNB8;F5H538;Q9Y6R4-2;Q9Y6R4 F5H4R1 MAP3K4 Mitogen-activated protein kinase kinase kinase 4 1 HS(0.181)S(0.776)PT(0.043)EERDEPAYPR 111.11 0.00052598 494640000 108970 192640 196760 223630 213590 188580 195070 176870 163030 TRUE FALSE 102149.7622 206903.266 201427.2401 229368.7244 196815.503 243019.9847 165821.0644 198952.6088 135819.2398 0.752100824 1.523372288 1.483053803 1.688779327 1.449098841 1.789289831 1.220895248 1.464833768 1 17.05132834 0.37548357 1.165905153 1.000197418 1.454274638 0.170776897 0.283076644 4.734412928 7.340426082 0.249795489 0.075202817 2.37401561 -0.37548357 0.454077221 HSS(ph)YPAGTEDDEGMGEEPSPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HSSYPAGTEDDEGMGEEPSPFR 22 0 Q92934 Q92934 BAD Bcl2-associated agonist of cell death 1 HS(0.166)S(0.828)Y(0.006)PAGTEDDEGMGEEPSPFR;HS(0.024)S(0.976)YPAGTEDDEGMGEEPSPFR;HS(0.112)S(0.888)YPAGTEDDEGMGEEPSPFR 312.15 2.03E-67 1000980000 412700 423810 420955 473330 485570 310655 419960 282154 303348 TRUE FALSE 386869.8437 455189.3334 430940.2514 485476.4491 447435.2909 400336.0554 356990.8967 317381.548 252717.2591 1.530840612 1.80118024 1.705226833 1.921026094 1.770497561 1.584126295 1.412609879 1.25587603 1 17.94716467 1.408444395 1.125619809 1.022664124 1.757023885 0.862480292 0.102140877 0.143869228 0.358703464 0.088915208 0.030531693 25.61205317 -1.408444395 0.734359761 HSSADNLANEMT(ph)YITETEDVFYTYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.166)S(0.166)ADNLANEMT(0.36)Y(0.307)IT(0.001)ETEDVFYTYK 116.24 0.0048916 16175000 14532 17332 14384 15400 17947 13382 22688 12029 13639 TRUE FALSE 13622.46806 18615.27931 14725.19527 15795.19007 16537.51501 17245.16616 19286.14503 13530.84713 11362.56279 1.198890454 1.638299357 1.295939617 1.390108056 1.455438823 1.517718008 1.697341118 1.19082705 1 13.47200065 1.023888525 7.036480196 1.000244745 1.46970518 0.532244876 0.146348334 0.103117861 18.93892018 0.136897413 0.034332934 10.56546279 -1.023888525 0.469460434 HSSDINHLVTQGRES(ph)PEGSYTDDANQEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HSSDINHLVTQGRESPEGSYTDDANQEVR 29 1 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 HSSDINHLVTQGRES(1)PEGSYTDDANQEVR;HSSDINHLVTQGRES(1)PEGSYTDDANQEVR;HSSDINHLVTQGRES(1)PEGSYTDDANQEVR;HSSDINHLVT(0.002)QGRES(0.998)PEGSYTDDANQEVR 288.11 1.56E-72 3338860000 295610 1016980 773849 845273 886089 815116 782088 699388 646561 TRUE FALSE 277108.2978 1092278.257 792205.0637 866964.1362 816499.1443 1050426.757 664821.1649 786708.1313 538645.7922 0.514453657 2.027822872 1.470734711 1.609525497 1.515836856 1.950125244 1.234245537 1.460529615 1 19.03897736 0.857638076 1.23223614 1.009476716 1.559085562 0.094749228 0.417231082 1.186415685 3.480811665 0.35167314 0.107944188 7.205067869 -0.857638076 0.549608846 HSSIS(ph)PVRLPLNSSLGAELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSSISPVRLPLNSSLGAELSR 21 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 HS(0.144)S(0.144)IS(0.712)PVRLPLNSSLGAELSR;HS(0.058)S(0.045)IS(0.897)PVRLPLNSSLGAELSR 254.6 1.30E-36 505690000 117291 364900 254600 254080 368100 229020 326250 309680 552950 TRUE FALSE 109949.9657 391917.5757 260639.2322 260600.123 339190.9108 295134.3562 277331.8413 348344.2297 460659.0728 0.238679692 0.850775766 0.565796372 0.565711474 0.736316575 0.640678483 0.602032734 0.756186625 1 18.8133399 -5 0.200451392 2.680382061 0.574596003 0.415294748 0.154212034 149.0892219 1.476510031 100.1274624 0.33863136 1.00E-05 5 -2.105786058 HSSSPLS(ph)PGGPTHLTKPTTTSSSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSSSPLSPGGPTHLTKPTTTSSSER 25 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 HSSSPLS(1)PGGPTHLTKPTTTSSSER;HSSSPLS(1)PGGPTHLTKPTTTSSSER 186.43 9.32E-18 578100000 139535 353520 351420 422950 396460 326200 516890 376640 294110 TRUE FALSE 130801.7534 379694.9886 359755.8484 433803.6131 365323.6308 420368.6446 439387.1431 423664.3331 245021.141 0.533838643 1.549641746 1.468264522 1.770474218 1.490988204 1.715642344 1.79326217 1.729092973 1 17.90254671 4.742274911 4.541809545 1.60345001 0.461180821 0.6573257 0.232749708 0.109368164 5.83635985 0.050203319 0.401194183 55242.70188 -4.742274911 -1.14226919 HSSVSDSQPCEPPSVGTEYSQGAS(ph)PQPQHQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSSVSDSQPCEPPSVGTEYSQGASPQPQHQLK 32 0 A0A2R8YDI1;A0A2R8Y852;P39880-6;P39880-4;P39880-5;P39880-2;P39880;P39880-3 A0A2R8YDI1 CUX1 Homeobox protein cut-like 1 1 HSSVSDSQPCEPPSVGT(0.004)EYS(0.074)QGAS(0.921)PQPQHQLK;HSSVSDSQPCEPPSVGT(0.031)EY(0.036)S(0.154)QGAS(0.78)PQPQHQLK 169.13 5.90E-14 402900000 111549 264742 277624 232409 290961 304200 375830 332940 399830 TRUE FALSE 104567.3472 284343.7731 284209.3724 238373.0084 268110.0967 392017.6017 319477.7805 374508.2919 333095.79 0.313925755 0.853639649 0.853236159 0.715629004 0.804903889 1.176891493 0.959116837 1.124326104 1 18.34557759 5.061698884 0.391868701 1.045982104 2.26E-19 0.618843775 0.148606361 5.746227867 0.577741272 0.119692248 2.976532492 115265.3795 -5.061698884 -1.045982104 HSSVYPTQEELEAVQNMVSHTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HSSVYPTQEELEAVQNMVSHTER 23 0 Q12906;Q12906-5;Q12906-2;Q12906-3;K7EKJ9;K7ER69;K7EM82;K7EJ09;K7ERM6;K7ENK6;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;;; 258.4 6.98E-44 734990000 190346 622473 491132 545079 597137 501736 617389 543137 549283 FALSE TRUE 178432.5836 668561.5486 502781.883 559066.65 550240.2688 646579.0382 524817.251 610948.85 457604.1188 0.389927836 1.46100422 1.098726743 1.221725564 1.202437317 1.412965949 1.146880523 1.335103477 1 18.80374051 4.747672388 24.89734114 1.243103917 0.389927368 0.782617769 0.139885537 471.4286441 1288120.263 0.029637943 0.365064471 55933.55048 -4.747672388 -0.853176549 HSTDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSTDIK 6 0 F8WCI5 F8WCI5 C3orf33 0 74.335 0.080597 73439000 130280 103730 84463 96444 117820 88674 78631 119590 128240 FALSE TRUE 122126.0074 111410.2771 86466.50225 98918.91632 108566.8925 114272.7443 66841.01152 134521.0748 106835.9155 1.143117525 1.042816702 0.809339273 0.925895714 1.016202201 1.069609819 0.625641772 1.259137193 1 16.7050372 4.450492043 2.769959812 0.927252407 1.137770204 0.096402209 0.166241291 0.523353002 7.470169519 0.038884928 0.184359536 28215.77884 -4.450492043 0.210517797 HSTENDS(ph)PTNVQQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HSTENDSPTNVQQ 13 0 P49354;P49354-2;B3KVN2 P49354 FNTA Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha 1 HS(0.002)T(0.001)ENDS(0.997)PTNVQQ;HSTENDS(1)PTNVQQ;HSTENDS(1)PTNVQQ 202.01 1.02E-07 488130000 1090540 842950 888350 886550 1023070 688290 888770 715320 900450 TRUE FALSE 1022285.048 905362.8951 909422.0815 909300.3739 942722.2091 886988.1495 755507.1894 804629.2766 750159.0779 1.362757685 1.20689454 1.212305641 1.212143398 1.256696395 1.182400074 1.007129303 1.07261153 1 19.51683704 1.86244418 3.588005984 1.029260042 1.236654606 0.807257048 0.049547326 0.100855103 2.159879512 0.023599023 0.012774406 72.85245306 -1.86244418 0.207394564 HSTPS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HSTPSPTR 8 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 HST(0.002)PS(0.951)PT(0.047)R;HS(0.004)T(0.047)PS(0.947)PT(0.001)R;HST(0.033)PS(0.967)PT(0.001)R 137.05 0.00080239 1353507000 633740 827677 783489 785476 855887 556170 843445 778255 789132 TRUE FALSE 594075.3447 888959.0663 802073.7291 805632.644 788669.0875 716727.2503 716978.2524 875421.8499 657420.7712 0.903645535 1.352191937 1.220031012 1.225444463 1.199641268 1.090210839 1.090592637 1.331600534 1 19.32645751 2.352532615 6.615815909 1.129506958 1.212181198 0.005819028 0.139738106 0.588388871 31.935534 0.045271326 0.037699117 225.1814519 -2.352532615 0.08267424 HSTPSNSSNPSGPPS(ph)PNSPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 HSTPSNSSNPSGPPSPNSPHR 21 0 Q9Y5S2 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 1 HSTPSNSSNPS(0.064)GPPS(0.903)PNS(0.032)PHR;HSTPSNSSNPS(0.001)GPPS(0.961)PNS(0.039)PHR;HSTPSNSSNPS(0.001)GPPS(0.999)PNSPHR;HSTPSNSSNPSGPPS(0.987)PNS(0.013)PHR;HSTPSNSSNPSGPPS(1)PNSPHR;HSTPSNSSNPS(0.019)GPPS(0.901)PNS(0.08)PHR;HSTPSNSSNPSGPPS(0.995)PNS(0.004)PHR;HSTPSNSSNPS(0.02)GPPS(0.832)PNS(0.148)PHR 287.04 8.47E-46 2131018000 407155 857645.8 710557.5 813870.9 899914.9 716187.7 974037.8 834722.9 776441 TRUE FALSE 381671.8953 921146.7874 727412.2594 834756.2052 829239.2138 922939.4627 827989.8744 938939.8915 646847.9811 0.590048831 1.424054514 1.124549014 1.290498277 1.281969239 1.426825915 1.280037812 1.451561911 1 19.30306717 4.745114196 24.92670234 1.293324916 0.5900485 0.710346208 0.139359658 359.6932382 1368064.753 0.029414007 0.282369301 55605.04488 -4.745114196 -0.703276415 HSTS(ph)GTDEGEDGDEPDDGSNDVVDLLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSTSGTDEGEDGDEPDDGSNDVVDLLPR 28 0 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 1 HS(0.075)T(0.075)S(0.462)GT(0.388)DEGEDGDEPDDGSNDVVDLLPR;HS(0.011)T(0.072)S(0.505)GT(0.412)DEGEDGDEPDDGSNDVVDLLPR 187.92 4.81E-18 250062000 73720 90426 80317 88909 82063 80963 101361 68484 90783 TRUE FALSE 69105.99679 97121.23513 82222.15717 91190.55546 75618.10301 104335.7038 86162.85904 77034.37815 75630.73082 0.913729063 1.284150425 1.087152752 1.205734157 0.999833033 1.379541129 1.139257258 1.018559219 1 16.20668494 1.246509749 5.721254976 1.006064002 1.160735239 0.144963474 0.132388616 0.240737939 25.9224542 0.093300065 0.028954428 17.64045363 -1.246509749 0.154671238 HSTS(ph)PASSEYSWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSTSPASSEYSWK 13 0 Q96N46 Q96N46 TTC14 Tetratricopeptide repeat protein 14 1 HS(0.008)T(0.043)S(0.949)PASSEYSWK;HS(0.017)T(0.092)S(0.891)PASSEYSWK 214.73 1.95E-11 715380000 902550 839580 921570 873210 993600 742920 1154510 847660 1210760 TRUE FALSE 846061.0066 901743.3768 943430.0756 895618.0469 915566.664 957388.9437 981401.9434 953492.2169 1008676.334 0.838783441 0.893986848 0.93531497 0.887914207 0.907691232 0.949153768 0.972960215 0.94529056 1 19.94403188 7.999999998 0.119711119 1.030976327 0.485849598 0.791047604 0.02105403 46.20059999 0.380105703 0.153115127 4.202136955 99999999.47 -7.999999998 -0.545126729 HSVDELQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSVDELQK 8 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 ; 126.52 0.0021563 339610000 525960 535960 481360 512670 594500 395510 584530 442840 539420 FALSE TRUE 493041.1025 575643.0361 492778.0865 525825.9801 547810.3681 509687.3164 496885.153 498129.5488 449387.3172 1.09714067 1.280950783 1.096555394 1.170095283 1.219016085 1.13418269 1.105694651 1.108463745 1 18.77759988 0.987693026 0.624355623 0.998809714 1.18111777 0.474885484 0.05523564 0.681345603 0.628953736 0.053195509 0.02248444 9.720598968 -0.987693026 0.182308056 HSVGVVIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HSVGVVIGR 9 0 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;; 137.14 0.00017317 560680000 654731 736105 753625 708368 750495 611663 798513 641686 815240 FALSE TRUE 613752.5554 790606.9801 771501.3409 726545.9221 691554.1501 788240.1786 678783.3887 721801.9096 679171.1773 0.903678742 1.164076166 1.13594535 1.069753762 1.018232477 1.160591328 0.999429027 1.062768759 1 19.37341571 1.660890433 11.29466687 1.023706931 1.090058579 0.076824407 0.078580165 0.232577611 41.22679149 0.035396302 0.019214014 45.80263181 -1.660890433 0.066351648 HSVTAAT(ph)PPPS(ph)PTSGESGDLLSNLLQSPSSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HSVTAATPPPSPTSGESGDLLSNLLQSPSSAK 32 0 Q96QU8;Q96QU8-2 Q96QU8 XPO6 Exportin-6 2 HS(0.002)VT(0.023)AAT(0.787)PPPS(0.674)PT(0.133)S(0.131)GES(0.247)GDLLS(0.002)NLLQSPSSAK;HS(0.005)VT(0.023)AAT(0.599)PPPS(0.695)PT(0.305)S(0.294)GES(0.074)GDLLS(0.004)NLLQSPSSAK;HSVT(0.002)AAT(0.919)PPPS(0.741)PT(0.158)S(0.142)GES(0.038)GDLLSNLLQSPSSAK;HS(0.001)VT(0.005)AAT(0.244)PPPS(0.498)PT(0.429)S(0.425)GES(0.369)GDLLS(0.029)NLLQSPSSAK;HSVTAAT(1)PPPS(0.786)PT(0.121)S(0.092)GES(0.001)GDLLSNLLQSPSSAK;HSVTAAT(1)PPPS(0.988)PT(0.011)S(0.002)GESGDLLSNLLQSPSSAK 314.33 7.11E-104 1298619000 1703680 1336979 1550730 1595670 1350373 1112655 1863320 1300330 1081549 TRUE FALSE 1597049.71 1435970.316 1587514.048 1636617.594 1244320.152 1433860.436 1583932.464 1462679.063 901031.4848 1.772468262 1.593696048 1.761885211 1.816382248 1.380995196 1.59135442 1.757910229 1.62333846 1 19.78121799 0.947076513 21.73218876 0.999999999 1.667451235 0.731682205 0.12631409 1716.745935 704955.9512 0.116351839 0.02908796 8.852715604 -0.947076513 0.667451235 HSVVAGGGGGEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HSVVAGGGGGEGR 13 0 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 0 ;;; 126.19 0.00044524 949861000 442449 440719.4 445627.7 411922.3 526186.3 433946.5 546861 461342.3 489003 FALSE TRUE 414756.9069 473350.7229 456198.1995 422492.9236 484861.7505 559219.81 464864.2699 518941.9017 407385.2402 1.018095075 1.161924086 1.119820147 1.037084513 1.190179964 1.372705132 1.141092568 1.273835796 1 18.63603419 2.499107992 23.34797001 1.216554307 1.104163395 0.203402906 0.103141356 464.1492329 492885.7079 0.030054697 0.028066471 315.5789246 -2.499107992 -0.112390912 HT(ph)GEKHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HTGEKHFK 8 1 D6RGC2;D6RIY0;A0A087WTY0;Q15928;B4DXR9;Q8TF20;Q8TF20-2 D6RGC2 ZNF721;ZNF141;ZNF732 Zinc finger protein 141;Zinc finger protein 732;Zinc finger protein 721 1 HT(1)GEKHFK 73.931 0.068369 216590000 509820 516900 388640 444480 602780 376920 616370 329980 1581800 TRUE FALSE 477911.2763 555171.8138 397858.7243 455886.1093 555440.0903 485730.6852 523951.0406 371178.7294 1317787.361 0.362661906 0.421290893 0.301914206 0.345948157 0.421494474 0.368595647 0.397599079 0.281668151 1 20.32968616 -1.802272734 2.855799779 1.172660141 0.366318517 0.950517337 0.045694554 14351888.29 11774615.64 17218498.76 0.010575449 0.015766209 1.802272734 -0.806341624 HT(ph)RISELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HTRISELK 8 1 P24593;C9JXX4 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 1 HT(0.5)RIS(0.5)ELK;HT(0.5)RIS(0.5)ELK 86.011 0.026411 1007930000 259160 1100630 775240 924750 968520 867560 641210 793400 511510 TRUE FALSE 242939.6382 1182121.79 793629.0589 948480.6506 892456.346 1118010.488 545066.5132 892457.7365 426135.6765 0.57009927 2.774050274 1.862385861 2.225771516 2.094300936 2.623602176 1.27909148 2.094304199 1 18.70095331 -0.946415079 5.187488249 0.999997374 1.998148054 0.172707506 0.635812516 2.25E-05 4.57E-06 0.551375351 0.129959971 0.113131858 0.946415079 0.998150681 HTANYDTEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HTANYDTEER 10 0 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 0 64.918 0.084673 0 635650 515220 694680 592940 747080 527270 750820 594540 870760 FALSE TRUE 595865.8012 553367.4249 711158.1377 608155.8442 688407.3504 679484.2895 638241.5113 668769.6277 725424.5307 0.821402883 0.762818738 0.980333732 0.838344746 0.9489717 0.936671233 0.879817933 0.921901038 1 19.46846601 4.032322007 4.928146084 0.920161957 0.794546533 0.574318377 0.048567212 0.134772105 6.888175724 0.010879916 0.023922939 10772.63654 -4.032322007 -0.125615423 HTDEEFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HTDEEFLK 8 0 Q9H0C8;E9PC05;F8SNU7;H7C2I8 Q9H0C8 ILKAP;ILKAP3 Integrin-linked kinase-associated serine/threonine phosphatase 2C 0 101.54 0.005321 92436000 186510 169730 172360 169670 176890 123120 186410 149730 208000 FALSE TRUE 174836.672 182296.9858 176448.4606 174024.0195 162997.7729 158662.7453 158459.551 168424.1201 173283.4563 1.008963439 1.0520161 1.018264896 1.00427371 0.940642439 0.915625466 0.914452853 0.971957299 1 17.4027744 2.873917222 2.502241633 0.937438895 1.030636104 0.611326326 0.028287342 0.151611107 1.858465611 0.008834781 0.009566496 748.0269102 -2.873917222 0.093197209 HTDSWLHTSELNDGYDWGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HTDSWLHTSELNDGYDWGR 19 0 Q9H089;F8WFC6 Q9H089 LSG1 Large subunit GTPase 1 homolog 0 112.82 0.00010941 72113000 25952 56031 55797 45623 59778 44624 59784 48399 61793 FALSE TRUE 24327.71065 60179.59354 57120.53119 46793.76342 55083.27701 57506.22439 50819.94421 54441.72169 51479.3491 0.472572227 1.169004554 1.109581457 0.908981256 1.070007255 1.11707365 0.987190885 1.057544873 1 15.65170619 4.745067696 24.99864659 1.060220046 0.472571962 0.857861269 0.074116129 276.9918053 1064108.413 0.018313032 0.175543895 55599.09166 -4.745067696 -0.587648084 HTDVQFYTEVGEITTDLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HTDVQFYTEVGEITTDLGK 19 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 162.33 2.78E-11 229374000 201329 189058 205274 200159 219490 180787 271160 191964 249760 FALSE TRUE 188728.1773 203056.051 210143.1962 205295.4188 202252.1408 232977.2721 230502.0753 215931.128 208073.4425 0.907026745 0.97588644 1.009947227 0.986648831 0.972022851 1.11968769 1.107791905 1.037764 1 17.66673331 2.250508256 24.99942047 1.080361027 0.977215714 0.538275255 0.0430594 150.1612052 314199.3425 0.014343325 0.011911567 178.0361752 -2.250508256 -0.103145313 HTENTFSRPGGR ddPTM_SK-BR-3_Pertuzumab_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 ; 140.39 3.58E-05 46508000 13940.9 16337.7 14563.2 15809.1 18306 15827.5 14349.5 14885.5 24725 FALSE TRUE 13068.36395 17547.36031 14908.64598 16214.78827 16868.3206 20396.64231 12197.92569 16743.98744 20598.23777 0.634440873 0.851886482 0.723782595 0.787192985 0.818920569 0.990212975 0.592182973 0.812884463 1 14.3302333 -2.452200321 1.894244472 2.610556589 0.775928001 0.284858166 0.111319735 2714902.764 208672.7127 18724197.89 0.027431083 0.003530203 2.452200321 -1.834628588 HTGCCGDNDPIDVCEIGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 HTGCCGDNDPIDVCEIGSK 19 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;;;;;; 323.47 3.07E-62 20923010000 18574090 13869730 15562120 15237760 15889690 13722230 22496430 13427940 18288420 FALSE TRUE 17411570.86 14896659.24 15931260.84 15628786.72 14641777.84 17683615.04 19123299.17 15104447.87 15235964.55 1.14279413 0.977729975 1.045635199 1.02578256 0.961001044 1.160649526 1.25514201 0.99136801 1 23.8609775 2.225002306 24.99959418 1.138547052 1.025213942 0.070339686 0.091627479 304.4528154 561363.5817 0.031995363 0.023758589 167.8812931 -2.225002306 -0.11333311 HTGMASIDSSAPETTSDSS(ph)PTLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HTGMASIDSSAPETTSDSSPTLSR 24 0 S4R3H3;S4R393;S4R410;A7E2V4-5;A7E2V4;A7E2V4-3;A7E2V4-4;A7E2V4-2;H7BZ52;H0YCW2;S4R3B3;H7C453;S4R3U7 S4R3H3 ZSWIM8 Zinc finger SWIM domain-containing protein 8 1 HTGMASIDSSAPETT(0.002)S(0.002)DS(0.056)S(0.5)PT(0.432)LS(0.008)R 134.11 2.40E-05 144020000 76109 106210 102260 109470 99555 93517 114720 91526 119620 TRUE FALSE 71345.47355 114073.8989 104685.6555 112279.1855 91736.35189 120513.8398 97518.80101 102953.2226 99654.64923 0.715927196 1.144692192 1.050484411 1.126682863 0.92054262 1.209314776 0.978567501 1.033100045 1 16.60464949 4.74697431 24.80211145 1.062900213 0.715927001 0.616418563 0.08470322 587.3701206 1731422.16 0.0178452 0.204702336 55843.71607 -4.74697431 -0.346973212 HTGPGILSMANAGPNTNGSQFFICTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 323.61 9.62E-83 7676310000 5230410 4304610 3932010 3827490 5133590 3711730 5591350 4319060 5957450 FALSE TRUE 4903047.975 4623327.803 4025279.134 3925709.873 4730418.549 4783246.196 4752978.975 4858304.148 4963113.108 0.98789769 0.931537868 0.81103917 0.790977314 0.953115201 0.963759256 0.957660821 0.978882416 1 22.2428139 2.507107386 23.32117811 0.968363375 0.876808956 0.392691438 0.056051529 326.4241311 253870.1296 0.018964385 0.017847478 321.4455264 -2.507107386 -0.09155442 HTGPNS(ph)PDTANDGFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 HTGPNSPDTANDGFVR 16 0 P31943;G8JLB6;E9PCY7;D6RBM0;D6RIT2;D6RIU0;D6R9T0;D6RFM3;E5RGV0;D6RDU3;D6RJ04;D6RIH9;D6RAM1;E5RGH4;H0YAQ2;P55795;E7EQJ0 P31943;P55795;E7EQJ0 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 1 HTGPNS(0.972)PDT(0.028)ANDGFVR;HTGPNS(0.998)PDT(0.002)ANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HT(0.002)GPNS(0.998)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR 413.24 3.91E-140 18871750000 4661880 4784550 4838710 5039110 5131580 3411080 4790120 3911110 4990930 TRUE FALSE 4370101.252 5138803.06 4953486.486 5168422.094 4728566.407 4395803.422 4071885.975 4399420.693 4157911.54 1.051032762 1.235909665 1.191340036 1.243033202 1.137245552 1.057214272 0.979310391 1.058084245 1 21.98742763 2.257730197 2.620736364 1.011754299 1.191323011 0.639299903 0.056231949 0.14772351 2.084311998 0.021867358 0.015797047 181.0215156 -2.257730197 0.179568712 HTGPNSPDTANDGFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HTGPNSPDTANDGFVR 16 0 P31943;G8JLB6;E9PCY7;D6RBM0;D6RIT2;D6RIU0;D6R9T0;D6RFM3;E5RGV0;D6RDU3;D6RJ04;D6RIH9;D6RAM1;E5RGH4;H0YAQ2;P55795;E7EQJ0 P31943;P55795;E7EQJ0 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 ;;;;; 309.55 1.28E-57 11713190000 3236990 3731090 3678130 3624060 3871670 3221220 4229460 3421250 4049230 FALSE TRUE 3034392.574 4007343.786 3765376.981 3717059.515 3567604.656 4151133.922 3595291.737 3848400.594 3373387.354 0.899509086 1.187928739 1.116200598 1.101877468 1.057573377 1.230553591 1.065780878 1.140811947 1 21.68576656 -1.098335842 4.098175316 0.999980975 1.110634124 0.101492418 0.088678283 1.58E-05 3.48E-06 0.075113375 0.017700822 0.079737783 1.098335842 0.110653149 HTGYVIELQHVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HTGYVIELQHVVK 13 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RRC8;A0A0U1RQX9 P47897 QARS Glutamine--tRNA ligase 0 ; 194.3 6.58E-07 735470000 958640 938890 954960 956880 1085830 747650 1141490 955110 1246560 FALSE TRUE 898640.4336 1008406.393 977612.1022 981435.1608 1000553.292 963484.4179 970334.1716 1074357.586 1038501.083 0.865324503 0.971021031 0.941368399 0.945049723 0.963459074 0.927764481 0.934360289 1.03452717 1 19.98607129 HTHEGDPLESVVFIYSMPGYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HTHEGDPLESVVFIYSMPGYK 21 0 Q6IBS0;H0Y858 Q6IBS0 TWF2 Twinfilin-2 0 123.53 1.52E-05 132710000 97743 81789 94938 89375 104710 71430 104680 89947 114430 FALSE TRUE 91625.44011 87844.74266 97189.97419 91668.51381 96486.49898 92050.68143 88984.2058 101177.0809 95330.89375 0.96113061 0.92147193 1.019501343 0.961582444 1.012122043 0.965591298 0.933424646 1.061325211 1 16.5406562 4.009449167 8.539067885 0.985935286 0.942290596 0.238128932 0.036888451 0.440101242 105.3776908 0.008720465 0.018628298 10219.95931 -4.009449167 -0.04364469 HTIPEEETHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HTIPEEETHR 10 0 Q70J99;Q70J99-3;K7EQ37;Q70J99-2;K7EN81 Q70J99 UNC13D Protein unc-13 homolog D 0 ;;; 188.28 6.58E-07 1040090000 793732 962737 839820 984265 1054450 746742 986035 849209 997584 FALSE TRUE 744053.731 1034019.049 859740.927 1009522.906 971637.7504 962314.2931 838188.2057 955234.613 831080.7858 0.895284482 1.244185965 1.034485385 1.21471092 1.169125514 1.15790704 1.00855202 1.149388398 1 19.6646292 0.705843523 0.79043732 1.003174592 1.122844033 0.074732816 0.105860936 2.437448458 2.871202143 0.094592872 0.033120552 5.079763843 -0.705843523 0.119669441 HTKEDSAS(ph)VK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.05)AS(0.95)VK 89.507 0.0069437 92356000 282270 132690 182380 194360 181100 147860 298890 171620 280750 TRUE FALSE 264603.2246 142514.5057 186706.1397 199347.6067 166877.1365 190544.7817 254074.2193 193047.1348 233891.0113 1.131309934 0.609320148 0.798261287 0.852309824 0.71348247 0.814673384 1.086293218 0.825372184 1 17.83547689 1.886000652 7.536720417 0.975365796 0.788417085 0.170374624 0.147159518 0.352270455 21.0073329 0.057889472 0.036012669 76.91315956 -1.886000652 -0.18694871 HTLADNFNPVSEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HTLADNFNPVSEER 14 0 P20645;H0YGT2 P20645 M6PR Cation-dependent mannose-6-phosphate receptor 0 ; 153.23 6.45E-06 202930000 306230 330770 267430 258350 344190 228870 350160 287250 365140 FALSE TRUE 287063.6109 355260.555 273773.5659 264979.6984 317158.7058 294941.0536 297656.7587 323113.7948 304195.7751 0.943680466 1.167868143 0.899991349 0.87108277 1.042613776 0.96957643 0.978503921 1.062190278 1 18.21464059 3.966112921 24.59053172 0.972147051 1.067055464 0.152997716 0.077960936 416.503376 930392.7179 0.018526299 0.033825514 9249.386366 -3.966112921 0.094908413 HTLDQYVESDYTLLYLHHGLTSDNKPSLSWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HTLDQYVESDYTLLYLHHGLTSDNKPSLSWLR 32 1 Q07960;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ;; 362.34 4.96E-133 1840940000 1078432 1633005 964858 765976 1702915 820849 1463399 1502809 709078 FALSE TRUE 1010934.866 1753914.389 987744.8874 785632.241 1569174.925 1057814.781 1243975.905 1690438.012 590728.301 1.711336438 2.969071207 1.672079847 1.329938382 2.656339509 1.790695958 2.105834278 2.861616769 1 19.17213521 3.915190702 9.454036213 1.970105558 2.415825606 0.06505545 0.628796448 0.905985006 132.4832433 0.14630755 0.264510942 8226.037814 -3.915190702 0.445720048 HTLGDS(ph)DNES ddPTM_SK-BR-3_Pertuzumab_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;HT(0.001)LGDS(0.999)DNES;HT(0.001)LGDS(0.999)DNES 95.417 0.0078003 294086000 386050 392205 404409 400908 429743 321192 450956 376782 394522 TRUE FALSE 361887.8196 421244.2663 414001.7725 411195.978 395992.7183 413914.9163 383339.3343 423824.0621 328673.7295 1.101054898 1.281648725 1.259613213 1.251076497 1.204820108 1.25934895 1.166321795 1.289497833 1 18.32629662 -1.147760154 3.655168828 0.999823628 1.231240455 0.604400798 0.057527029 1445113.975 908630.6329 1841.447376 0.012330258 0.07116064 1.147760154 0.231416827 HTLQQHQET(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HTLQQHQETPK 11 0 Q7Z417;Q7Z417-2 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 HTLQQHQET(1)PK;HTLQQHQET(1)PK;HTLQQHQET(1)PK;HTLQQHQET(1)PK;HTLQQHQET(1)PK 174.59 2.02E-05 867151000 676091 660937 865199 748428 767054 662480 874886 827259 795302 TRUE FALSE 633775.6712 709873.4632 885721.9289 767633.9296 706812.673 853727.2215 743704.9663 930544.1072 662560.9584 0.956554507 1.071408531 1.336815757 1.158586119 1.066788896 1.288526302 1.122470253 1.40446565 1 19.33769367 4.45547879 2.767081374 1.201442174 0.962128694 0.302294159 0.122113458 0.326765088 4.645032919 0.027353063 0.131484037 28541.63117 -4.45547879 -0.239313481 HTNFVEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HTNFVEFR 8 0 M0R0N4;M0QYZ2;P53680;M0QZ21 M0R0N4 AP2S1 AP-2 complex subunit sigma 0 128.6 0.0011265 376080000 52171 96964 46323 43702 107920 24904 50087 78514 77034 FALSE TRUE 48905.71024 104143.3155 47421.80344 44823.46731 99444.39853 32093.38052 42576.91933 88316.64573 64176.52774 0.762049802 1.622763324 0.738927535 0.698440207 1.549544702 0.500079728 0.663434449 1.376151824 1 15.96975811 3.847322636 6.474280596 0.89456782 1.241609962 0.063777885 0.38289527 0.422156847 21.28217203 0.092026809 0.167537432 7035.94824 -3.847322636 0.347042143 HTNPS(ph)SSSPGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HTNPSSSSPGTR 12 0 Q8WUH2 Q8WUH2 TGFBRAP1 Transforming growth factor-beta receptor-associated protein 1 1 HTNPS(0.25)S(0.25)S(0.25)S(0.25)PGTR 84.365 0.012879 42898000 83712 81082 90698 88486 82482 78735 99150 77465 63944 TRUE FALSE 78472.61535 87085.39565 92849.39939 90756.70057 76004.19644 101464.5163 84283.37796 87136.67577 53271.33331 1.473073987 1.634751568 1.742952422 1.703668651 1.426737266 1.904673866 1.58215259 1.635714189 1 15.70107177 0.267033929 1.806666075 0.999962085 1.652399376 0.689208806 0.134413143 6.612480026 15.54333834 0.11572022 0.032256277 1.849413096 -0.267033929 0.652437291 HTNPS(ph)SSSPGTRT ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HTNPSSSSPGTRT 13 1 Q8WUH2 Q8WUH2 TGFBRAP1 Transforming growth factor-beta receptor-associated protein 1 1 HTNPS(0.308)S(0.076)S(0.308)S(0.308)PGTRT 108.97 0.0012438 85234000 109490 143580 136240 134260 151180 117060 170570 121250 154370 TRUE FALSE 102637.2163 154210.8126 139471.6771 137705.3389 139306.9326 150853.3217 144994.612 136388.3294 128604.6497 0.798083246 1.199107598 1.084499491 1.070764853 1.083218476 1.173000525 1.127444554 1.060524092 1 16.97258328 4.748591372 24.99657954 1.11116141 0.798083076 0.727896547 0.057608161 684.5032937 1705743.895 0.0128278 0.174771548 56052.03341 -4.748591372 -0.313078334 HTNPSSSS(ph)PGTRT ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HTNPSSSSPGTRT 13 1 Q8WUH2 Q8WUH2 TGFBRAP1 Transforming growth factor-beta receptor-associated protein 1 1 HTNPSS(0.003)S(0.132)S(0.852)PGT(0.012)RT 122.29 0.000145 290880000 202480 252630 254710 259480 273020 205620 296390 219060 264580 TRUE FALSE 189807.1382 271334.9881 260751.8415 266138.6961 251578.1105 264979.156 251949.071 246410.1232 220419.8887 0.861116206 1.230991403 1.182977829 1.207416888 1.141358486 1.202156292 1.143041458 1.117912384 1 17.74989488 0.794907147 2.055284499 1.0001746 1.157116864 0.127401354 0.104709409 1.264622304 9.102055904 0.089862565 0.024769675 6.236014946 -0.794907147 0.156942264 HTNYTMEHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 155.97 6.81E-06 448352000 111833 203537 112742 96112 163600 73335 108454 182125 141845 FALSE TRUE 104833.5722 218607.0913 115416.2935 98578.39664 150751.5159 94505.62401 92192.32954 204863.7072 118170.1531 0.887140867 1.849934907 0.97669581 0.834207234 1.275715669 0.79974191 0.780165948 1.733633254 1 16.85050617 3.732985719 20.89521332 1.017708784 1.430111593 0.100092388 0.363591501 43.70527096 155709.4883 0.08605537 0.149179084 5407.365413 -3.732985719 0.412402809 HTPPTIGGS(ph)LPYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HTPPTIGGSLPYR 13 0 H7C3Q7;B7Z836;E7EW77;E7EP65;A0A0C4DG21;F8WAL6;Q9NYB9-3;Q9NYB9-2;Q9NYB9-4;Q9NYB9;H0Y6B5;E9PEZ7 H7C3Q7 ABI2 Abl interactor 2 1 HTPPTIGGS(1)LPYR 108.25 0.0007927 130500000 95172 113610 107910 111360 119070 82444 128880 107780 144720 TRUE FALSE 89215.35441 122021.8026 110469.6762 114217.6861 109718.7225 106244.2444 109555.6405 121236.5703 120565.2971 0.739975404 1.012080637 0.916264289 0.94735126 0.910035683 0.881217457 0.908683038 1.005567715 1 16.87945518 -5 0.119609591 1.257444816 0.882727567 0.189471268 0.071593727 346.7261121 2.693393602 21.56253476 0.658816693 1.00E-05 5 -0.374717249 HTPS(ph)PGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPATSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPR 40 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HT(0.024)PS(0.976)PGLPAEGAPEAPRPS(0.611)S(0.389)PPPEVLEPHSLDQPPATSPR;HT(0.005)PS(0.995)PGLPAEGAPEAPRPS(0.555)S(0.445)PPPEVLEPHSLDQPPATSPR;HT(0.036)PS(0.964)PGLPAEGAPEAPRPS(0.557)S(0.443)PPPEVLEPHSLDQPPATSPR;HT(0.452)PS(0.548)PGLPAEGAPEAPRPS(0.548)S(0.452)PPPEVLEPHSLDQPPATSPR 271.65 5.97E-77 1185710000 165540 141451 143850 132968 146638 136599 188882 152863 139403 TRUE FALSE 155179.1469 151924.1792 147262.1899 136380.184 135121.643 176032.9138 160560.8976 171948.282 116135.7387 1.336187711 1.308160441 1.268017852 1.174317101 1.16348029 1.515751445 1.382527888 1.480580258 1 16.82545248 2.250080966 24.99765053 1.382198182 1.256970117 0.066249477 0.148391723 392.3498023 851346.902 0.046285769 0.038415189 177.8610969 -2.250080966 -0.125228064 HTPS(ph)PGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HT(0.124)PS(0.876)PGLPAEGAPEAPRPS(0.532)S(0.468)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR;HT(0.131)PS(0.869)PGLPAEGAPEAPRPS(0.522)S(0.478)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR;HT(0.16)PS(0.84)PGLPAEGAPEAPRPS(0.524)S(0.476)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR;HT(0.189)PS(0.811)PGLPAEGAPEAPRPS(0.513)S(0.486)PPPEVLEPHS(0.001)LDQPPATSPRPLIEVGELLDLTR;HT(0.163)PS(0.825)PGLPAEGAPEAPRPS(0.505)S(0.505)PPPEVLEPHS(0.003)LDQPPATSPRPLIEVGELLDLTR 185.66 2.98E-32 704390000 41399.7 45880.1 42627.9 36778.1 49744.9 37892.5 61222.9 48367.5 83825.6 TRUE FALSE 38808.56668 49277.11034 43639.05392 37721.88831 45838.13622 48831.44962 52043.09451 54406.28884 69834.56583 0.555721457 0.705626358 0.624891891 0.540160705 0.656381774 0.699244694 0.745234024 0.779073919 1 16.09165368 0.946532917 0.718563459 0.999700317 0.62372368 0.858546699 0.048915094 0.288753272 0.335447825 0.048662938 0.018771003 8.841641805 -0.946532917 -0.375976637 HTPS(ph)PGLPAEGAPEAPRPSS(ph)PPPEVLEPHSLDQPPATSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPR 40 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HT(0.003)PS(0.997)PGLPAEGAPEAPRPS(0.449)S(0.551)PPPEVLEPHSLDQPPATSPR 286.81 7.61E-78 446330000 112340 101400 102930 92259 104990 115350 155060 121950 109930 TRUE FALSE 105308.8399 108907.7615 105371.5482 94626.52213 96744.50891 148649.6724 131810.1925 137175.7259 91581.97283 1.149886126 1.189183397 1.150570849 1.03324398 1.056370658 1.623132456 1.439259152 1.497846374 1 16.48277602 2.252529636 24.99951255 1.435030596 1.126830501 0.390428115 0.16576552 189.8087907 339688.9406 0.051397858 0.042801883 178.8667583 -2.252529636 -0.308200095 HTPSPGLPAEGAPEAPRPS(ph)S(ph)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HT(0.04)PS(0.122)PGLPAEGAPEAPRPS(0.842)S(0.842)PPPEVLEPHS(0.085)LDQPPAT(0.033)S(0.033)PRPLIEVGELLDLT(0.003)R 47.746 0.0025848 33194000 5123.9 5770.3 5814.3 7325.9 7168.9 2490 4625.5 2609.9 3257.2 TRUE FALSE 4803.204245 6197.539016 5952.217942 7513.894997 6605.883512 3208.822578 3931.949216 2935.75176 2713.552278 1.770079864 2.283920994 2.193515117 2.769025332 2.434404366 1.182517324 1.44900441 1.081885094 1 11.40596699 2.23594796 24.99941159 1.239570549 2.29791691 0.805493648 0.270730765 29.89285407 286026.9546 0.097198046 0.075089332 172.1662262 -2.23594796 1.058346361 HTPSPGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPATSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPR 40 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HTPSPGLPAEGAPEAPRPS(0.5)S(0.5)PPPEVLEPHSLDQPPATSPR;HTPSPGLPAEGAPEAPRPS(0.5)S(0.5)PPPEVLEPHSLDQPPATSPR;HTPSPGLPAEGAPEAPRPS(0.5)S(0.5)PPPEVLEPHSLDQPPATSPR;HTPSPGLPAEGAPEAPRPS(0.354)S(0.354)PPPEVLEPHS(0.019)LDQPPAT(0.124)S(0.149)PR 245.2 3.26E-51 2369620000 374695 365873 368754 340421 363585 325050 435870 392946 304307 TRUE FALSE 351243.5088 392962.6176 377501.019 349156.7792 335030.5007 418886.6583 370515.3399 442006.1731 253516.1958 1.385487455 1.550049362 1.489060759 1.377256305 1.321534901 1.652307289 1.4615056 1.743502705 1 17.95171839 3.443667446 24.84174378 1.457849907 1.493662003 0 0.202487166 1484.347628 1102226.401 0.050377055 0.068211711 2777.585559 -3.443667446 0.035812096 HTPSPGLPAEGAPEAPRPSS(ph)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HTPSPGLPAEGAPEAPRPS(0.434)S(0.566)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR;HTPSPGLPAEGAPEAPRPS(0.436)S(0.564)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR;HTPSPGLPAEGAPEAPRPS(0.214)S(0.786)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 195.81 1.76E-41 953280000 131957 170425 147585 149952 156967 124118 204968 156547 207561 TRUE FALSE 123698.0469 183043.4443 151085.7859 153800.0222 144639.445 159948.8517 174234.9512 176092.2376 172917.7282 0.715357807 1.058557999 0.873743759 0.889440451 0.836463944 0.924999729 1.007617629 1.018358496 1 17.39972626 1.790367044 3.767849643 1.01073257 0.89918105 0.321977353 0.084457841 0.301788121 8.003391422 0.042546255 0.022056272 61.71163377 -1.790367044 -0.11155152 HTQENCETWGVNGETGTLVDMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HTQENCETWGVNGETGTLVDMK 22 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;; 229.23 2.99E-26 1163110000 1142420 791380 929180 914210 947240 774160 1175340 806760 892260 FALSE TRUE 1070917.971 849974.5986 951220.5884 937670.1764 872847.5914 997647.4246 999108.6783 907485.7619 743336.0418 1.440691573 1.143459419 1.27966429 1.261435103 1.174230149 1.34212169 1.344087495 1.220828415 1 19.50365504 0.970528319 21.47556651 0.999999996 1.272245175 0.519934076 0.084841586 421.8435193 307392.4045 0.078281679 0.01957042 9.343902949 -0.970528319 0.272245179 HTQFWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HTQFWR 6 0 P12236 P12236 SLC25A6 "ADP/ATP translocase 3;ADP/ATP translocase 3, N-terminally processed" 0 ; 92.191 0.047037 732740000 697760 828920 753660 765930 992500 551500 934750 891310 1118650 FALSE TRUE 654088.4471 890294.0993 771537.1711 785585.0605 914553.0536 710709.0971 794592.9153 1002592.016 931940.0882 0.701856756 0.95531259 0.827882802 0.842956613 0.981343184 0.762612432 0.852622315 1.075811662 1 19.82987769 1.245345198 24.99532379 1.037905852 0.855328049 0.477568645 0.082874522 116.7952332 430301.3562 0.052549703 0.018241063 17.59321452 -1.245345198 -0.182577803 HTQLEQMFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HTQLEQMFR 9 0 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ;; 117.28 0.0011768 531440000 1076330 1189210 1120140 1050910 1234860 1048980 1290680 1129340 1240980 FALSE TRUE 1008964.427 1277260.346 1146710.25 1077878.13 1137879.077 1351803.497 1097154.516 1270340.585 1033852.421 0.975926937 1.235437786 1.109162417 1.042584133 1.100620411 1.307540099 1.061229334 1.228744605 1 19.97959883 -1.031761897 4.510710115 0.99999407 1.138197939 0.146103778 0.099991239 5.31E-06 1.14E-06 0.086258967 0.020330561 0.092947584 1.031761897 0.138203869 HTQSMS(ph)SARER ddPTM_SK-BR-3_Pertuzumab_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(0.008)QS(0.008)MS(0.492)S(0.492)ARER;HT(0.007)QS(0.007)MS(0.493)S(0.493)ARER 66.989 0.037065 1641290000 414560 898550 744110 769130 861140 732160 724760 727530 788540 TRUE FALSE 388613.4296 965079.5769 761760.6406 788867.1779 793509.5381 943522.7064 616088.9663 818363.722 656927.5798 0.591562056 1.469080621 1.159580849 1.200843445 1.207910221 1.436265938 0.937833918 1.245744199 1 19.32537481 1.710847502 24.99998838 1.067491969 1.211177335 0.034938216 0.248779695 2.259998413 2028.718968 0.103915255 0.05762624 51.38631821 -1.710847502 0.143685366 HTQWGIDFLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HTQWGIDFLER 11 0 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 0 ; 188.09 3.30E-06 209140000 110184 121764 122738 116034 131345 103852 133851 121235 109995 FALSE TRUE 103287.7801 130779.5333 125649.4033 119011.6289 121029.6935 133832.3865 113781.2852 136371.4566 91636.12391 1.127151343 1.427161339 1.371177631 1.298741411 1.320764 1.460476293 1.241664098 1.488184471 1 16.48362882 -1.38684077 3.676314521 0.998070866 1.347648855 0.50322993 0.106626442 7561434.153 2853486.056 116135.5906 0.021875809 0.041035453 1.38684077 0.349577989 HTSKLS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HTSKLSR 7 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 HTS(0.002)KLS(0.998)R;HTS(0.001)KLS(0.999)R;HTSKLS(1)R;HTSKLS(1)R 86.18 0.012273 1515240000 624790 1682730 1474160 1641240 1861270 1163030 1574200 1504570 1556770 TRUE FALSE 585685.5092 1807321.08 1509127.771 1683356.997 1715093.362 1498777.881 1338163.324 1692418.876 1296935.03 0.451592019 1.393532473 1.163610926 1.297950135 1.322420416 1.155630657 1.031789021 1.304937285 1 20.30667478 4.747020719 24.92577973 1.212376458 0.45159162 0.77947844 0.126548775 486.3681234 1432940.769 0.029784461 0.345846782 55849.68385 -4.747020719 -0.760784838 HTTDLDASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 6478640000 8027530 9392020 7463650 7991740 11654400 5435640 8881900 9782600 11664500 FALSE TRUE 7525101.227 10087414.93 7640691.303 8196821.578 10739110.44 7004821.028 7550141.551 11003979.14 9717619.594 0.774377012 1.038054107 0.786271908 0.843500973 1.105117393 0.720837131 0.776953808 1.132373936 1 23.21217153 1.234005671 24.99984409 1.066187007 0.868863117 0.312634 0.124701579 149.8098748 822181.7266 0.102529631 0.028987522 17.13979689 -1.234005671 -0.197323889 HTTEAAAGALQNITAGDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HTTEAAAGALQNITAGDRR 19 1 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ;;; 188.41 1.05E-14 948820000 427158 663030 590810 602850 679020 470782 655800 552700 708200 FALSE TRUE 400422.9433 712121.4311 604824.2922 618320.1516 625692.5082 606689.1209 557468.8781 621705.8116 589996.8449 0.678686584 1.206991931 1.025131401 1.048005861 1.060501448 1.028292145 0.944867558 1.053744299 1 19.17034771 1.972344245 22.28774651 0.991703533 1.037130061 0 0.135094514 911.9341182 734921.7287 0.051149119 0.033135473 93.83054642 -1.972344245 0.045426528 HTTENKPHS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HTTENKPHSPK 11 1 A0A2R8Y6S3;C9J167;Q68D20;P54278-3;P54278 A0A2R8Y6S3 PMS2;PMS2CL Protein PMS2CL;Mismatch repair endonuclease PMS2 1 HTTENKPHS(1)PK;HTTENKPHS(1)PK;HTTENKPHS(1)PK 113.59 0.00082844 241181000 442420 270598 346744 343306 359780 281803 536400 321004 399610 TRUE FALSE 414729.7219 290633.3575 354968.9314 352115.8132 331524.3301 363154.9514 455971.7997 361082.056 332912.5094 1.245761905 0.873002213 1.066252908 1.057682734 0.995830198 1.090842011 1.369644537 1.084615464 1 18.34478356 1.989329664 23.33885517 1.201929548 1.028237887 0.063279197 0.132263905 263.5871173 576534.2299 0.047565611 0.03287927 97.57300128 -1.989329664 -0.173691661 HTTENKPHSPKT(ph)PEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HTTENKPHSPKTPEPR 16 2 A0A2R8Y6S3;C9J167;Q68D20;P54278-3;P54278 A0A2R8Y6S3 PMS2;PMS2CL Protein PMS2CL;Mismatch repair endonuclease PMS2 1 HTTENKPHS(0.001)PKT(0.999)PEPR 147.9 9.89E-07 62993000 80104 60159 74139 81460 82644 47912 111090 62150 102170 TRUE FALSE 75090.43363 64613.23496 75897.61209 83550.40151 76153.47361 61743.41661 94433.08581 69909.56431 85117.16696 0.88220081 0.759109323 0.891683955 0.981592838 0.894689947 0.725393229 1.109448178 0.821333308 1 16.37716251 4.035787348 0.179080488 1.019820925 0.678891772 0.120345562 0.107089292 22.07405346 0.935259787 0.328869216 1.777755893 10858.93787 -4.035787348 -0.340929153 HTTFEQPVFSVSKQS(ph)PPISTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HTTFEQPVFSVSKQSPPISTSK 22 1 P33981-2;P33981 P33981-2 TTK Dual specificity protein kinase TTK 1 HTTFEQPVFSVSKQS(1)PPISTSK 262.19 1.46E-37 239180000 229970 306780 303970 361650 406870 262370 469420 334740 397240 TRUE FALSE 215576.5882 329494.3104 311180.3119 370930.5513 374916.0714 338111.9598 399034.8289 376533.0259 330938.0777 0.65141065 0.995637349 0.940297696 1.12084579 1.13288889 1.021677415 1.20576886 1.137774862 1 18.33620177 5.414223048 0.61925623 1.114487793 3.38E-13 0.712614916 0.082746262 3.857912239 0.606321054 0.033779091 3.682730607 259551.2038 -5.414223048 -1.114487793 HTTSIFDDFAHYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HTTSIFDDFAHYEK 14 0 A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739 A0A024R7W5 YTHDF3 YTH domain-containing family protein 3 0 ; 168.67 2.00E-06 197268000 249547 306458 311403 305289 355048 233284 398436 323311 474860 FALSE TRUE 233928.2987 329148.4692 318789.6262 313123.2326 327163.9623 300629.3038 338694.2207 363677.09 395602.7983 0.591321143 0.832017545 0.805832587 0.791509145 0.827001133 0.759927142 0.856147181 0.919298578 1 18.59369311 -4.999999999 0.031094471 2.221553365 3.34E-14 0.653965224 0.062215447 934.2985595 2.185680891 123.680451 48.53263847 1.00E-05 4.999999999 -2.221553365 HTVDDGLDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HTVDDGLDIR 10 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;;;; 167.12 5.34E-06 2376910000 2191510 2573470 2261780 2311500 2663310 1999450 2686830 2437920 2620110 FALSE TRUE 2054347.301 2764012.396 2315430.49 2370817.003 2454144.376 2576658.757 2283964.785 2742299.679 2182796.714 0.941153744 1.2662711 1.060763228 1.086137334 1.124311925 1.180439177 1.046347912 1.256323899 1 21.05774635 -1.392147135 5.58844632 0.999950295 1.123981271 0.129189806 0.097655914 5.30E-05 5.76E-06 0.082788572 0.019505642 0.040537118 1.392147135 0.124030976 HTVDDGLDIRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HTVDDGLDIRK 11 1 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;; 155 2.06E-05 625350000 488687 493610 475736 520380 615180 381768 649190 459870 931880 FALSE TRUE 458100.953 530157.398 487020.6826 533733.8318 566866.2443 491978.2241 551849.9863 517285.7818 776343.2078 0.590075302 0.682890496 0.62732652 0.687497265 0.730174797 0.63371228 0.710832504 0.666310694 1 19.56633506 -5 0.277918848 3.402906694 0.645592713 0.880358819 0.038976373 65.86820225 0.63299353 91.165705 0.040691609 1.00E-05 5 -2.757313981 HTWMEDADSCVAHNALECAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HTWMEDADSCVAHNALECAR 20 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ;; 283.08 4.14E-45 424891000 91629 97755 85013 97177 112143 90519 130061 95826 106230 FALSE TRUE 85894.10445 104992.8819 87029.54851 99670.72634 103335.7411 116650.3658 110559.5605 107790.087 88499.52673 0.970560043 1.186366592 0.983389988 1.126228919 1.167641737 1.318090279 1.249267251 1.217973599 1 16.43338212 2.748694934 2.751619497 1.224098512 1.067993405 0.258970595 0.101649906 0.296923205 4.49823931 0.031373585 0.031523827 560.6540122 -2.748694934 -0.156105107 HVAEDLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HVAEDLGK 8 0 H0YFD6;P40939;A0A2R8Y4F5 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 ;; 118.74 0.0018279 2149350000 2017460 1841420 1669510 1659000 2370650 1573720 1681000 1786490 2943140 FALSE TRUE 1891190.78 1977760.653 1709111.566 1701572.749 2184468.712 2028027.417 1428949.656 2009537.209 2451910.921 0.771313005 0.806620108 0.697052879 0.693978209 0.89092499 0.827121165 0.5827902 0.819580023 1 21.22547514 0.983651705 24.45578465 1.000000011 0.747722384 0.461505748 0.083994095 692.6344855 1036129.548 0.081092985 0.020273246 9.630563626 -0.983651705 -0.252277627 HVAEVLEYTKDEQLESLFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HVAEVLEYTKDEQLESLFQR 20 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ;;; 294.9 8.46E-55 2431159000 1313875 1133664 1153726 1151433 1210078 892632 1409508 1035460 1309492 FALSE TRUE 1231641.909 1217601.662 1181092.926 1180980.72 1115043.355 1150320.368 1198165.361 1164739.46 1090929.326 1.128984142 1.116114155 1.082648434 1.082545581 1.022104117 1.054440779 1.098297876 1.067658035 1 20.05712621 8 0.07482909 0.945944711 1.406389124 0.634439013 0.0239379 165.1138716 0.90618555 0.906173566 7.925442264 100000000 -8 0.460444412 HVAVTNMNEHSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HVAVTNMNEHSSR 13 0 P33176;O60282;Q12840;J3KNA1;A0A0G2JMZ6 P33176;Q12840 KIF5B;KIF5C;KIF5A Kinesin-1 heavy chain;Kinesin heavy chain isoform 5C;Kinesin heavy chain isoform 5A;Kinesin-like protein 0 ;;;;; 154.72 2.68E-05 587997000 105564.9 203050 175450 185605 198491 160547 201732 189268 196146 FALSE TRUE 98957.78135 218084.0333 179611.7569 190367.9385 182902.3175 206894.3126 171484.1594 212898.5264 163407.9654 0.605587256 1.334598547 1.099161576 1.164985673 1.119298665 1.266121343 1.049423502 1.302865046 1 17.31811878 4.749047359 24.85814383 1.170090293 0.605586914 0.727297376 0.108033949 664.2802952 1574600.188 0.022902538 0.322539045 56110.9161 -4.749047359 -0.564503379 HVCQPGR ddPTM_SK-BR-3_Pertuzumab_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 76.847 0.03965 26835000 26140 28229 23774 21790 33390 18458 28345 27194 32438 FALSE TRUE 24503.94406 30319.10453 24337.93051 22349.16829 30767.68409 23786.52496 24094.93039 30589.23076 27023.88824 0.906751236 1.121937164 0.900608021 0.827015272 1.138536535 0.880203646 0.891615972 1.131932995 1 14.72194765 -0.580438347 6.295432457 1.000006864 0.971619905 0.003958398 0.115986312 0 0 0.104159226 0.024550565 0.262761452 0.580438347 -0.028386959 HVDAHATLNDGVVVQVMGLLSNNNQALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HVDAHATLNDGVVVQVMGLLSNNNQALR 28 0 Q13283;E5RH42;E5RIZ6;E5RJU8;Q13283-2;E5RIF8 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ;;;;; 206.03 1.52E-25 318059000 370371.1 410353.7 390391.1 411742.6 419391.8 360040.5 444061.8 373994 384782.4 FALSE TRUE 347190.234 440736.7149 399651.3612 422308.6122 386454.4598 463978.3476 377478.8556 420687.9742 320559.7317 1.083075008 1.374897317 1.246729772 1.31741005 1.205561465 1.447400599 1.177561678 1.3123544 1 18.29023368 -1.521885083 2.50548511 0.982402129 1.277717475 0.404883031 0.10279165 3984554.741 3666090.954 475768.2767 0.022106011 0.030068718 1.521885083 0.295315346 HVDFLEAISSALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HVDFLEAISSALR 13 0 Q7Z4Q2;Q7Z4Q2-2 Q7Z4Q2 HEATR3 HEAT repeat-containing protein 3 0 136.27 7.42E-05 23834000 70438 82039 70037 71628 93507 57007 70403 86483 71656 FALSE TRUE 66029.41132 88113.25292 71698.31071 73466.09575 86163.33741 73463.99547 59846.72374 97280.59292 59696.15068 1.106091608 1.476029056 1.20105417 1.230667219 1.443365048 1.230632036 1.002522324 1.629595741 1 15.86535029 -2.094015429 2.593839092 0.512106027 1.278261317 0.194009605 0.184383747 17374723.65 3377425.317 50603014.44 0.042816582 0.008053498 2.094015429 0.766155289 HVDNIMFENHTVADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HVDNIMFENHTVADR 15 0 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ;;;; 227.67 4.04E-13 2023480000 486408 516346 533594 525012 590946 461066 599413 515465 567834 FALSE TRUE 455964.5915 554576.7951 546251.1017 538484.6968 544535.4849 594168.2694 509536.5853 579821.9399 473058.8371 0.963864441 1.172320971 1.154721271 1.138303853 1.151094626 1.256013466 1.077110383 1.225686732 1 18.85166011 4.742227483 24.33315504 1.152963364 0.963864334 0.392422853 0.071223966 224.7201557 1491138.509 0.014412725 0.107522145 55236.66926 -4.742227483 -0.18909903 HVDNPNGDGR ddPTM_SK-BR-3_Pertuzumab_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 0 146.16 2.91E-05 88815000 89115 95866 87575 89315 90048 75908 95084 74432 85903 FALSE TRUE 83537.45122 102964.0184 89652.32036 91606.97411 82975.99332 97821.40734 80827.03692 83724.99905 71565.23435 1.167290962 1.438743537 1.25273565 1.280048545 1.159445561 1.366884469 1.129417624 1.169911617 1 16.12697129 1.002718667 0.426612249 0.982855916 1.321703483 0.480274237 0.089796781 0.922226279 0.44920239 0.115729217 0.060411308 10.06279598 -1.002718667 0.338847566 HVDSLSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HVDSLSQR 8 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 0 ;; 102.51 0.0049505 2111650000 1064920 1125510 1283190 1199770 1403810 1125920 1414800 1131870 1660090 FALSE TRUE 998268.5581 1208843.931 1313627.873 1230558.129 1293560.425 1450954.826 1202663.874 1273186.461 1383010.254 0.721808501 0.874067222 0.949832345 0.8897679 0.935322367 1.049128032 0.869598667 0.92059076 1 20.39938042 5.513474681 1.001537843 0.941020462 4.12E-08 0.656271719 0.051148526 4.700193145 1.221471778 0.01444749 6.898862898 326193.0329 -5.513474681 -0.94102042 HVDSLSQRS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HVDSLSQRSPK 11 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 1 HVDSLS(0.001)QRS(0.999)PK;HVDSLSQRS(1)PK;HVDSLS(0.004)QRS(0.996)PK;HVDSLSQRS(1)PK;HVDSLSQRS(1)PK;HVDSLSQRS(1)PK 165.36 1.31E-05 3721190000 1261670 2239980 1465850 2109770 3794260 637413 1490560 1592040 9709800 TRUE FALSE 1182704.327 2405830.45 1500620.654 2163910.27 3496274.125 821423.7856 1267064.366 1790809.699 8089171.652 0.146208336 0.297413697 0.185509805 0.267507028 0.432216582 0.101546094 0.156637097 0.22138357 1 22.94756054 -1.503409828 2.90463049 1.027959711 0.225490903 0.872682994 0.092902575 14889252.52 16548297.22 3313835.116 0.022956532 0.031375465 1.503409828 -0.802468807 HVDWVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HVDWVK 6 0 P40123;E9PDI2;F8WDB9;Q01518-2;Q01518;Q5T0R1;Q5T0R9;Q5T0R4;Q5T0R3;Q5T0R2 P40123;Q01518-2 CAP2;CAP1 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein;Adenylyl cyclase-associated protein 1 0 ; 114.67 0.025089 1419440000 3584000 2922600 3142000 2917300 3006500 2361100 3866800 3108700 2545700 FALSE TRUE 3359683.838 3138992.345 3216529.724 2992162.857 2770381.618 3042711.241 3287009.238 3496828.038 2120806.224 1.584154082 1.480093895 1.516654227 1.410861031 1.306287008 1.434695545 1.549886642 1.648820151 1 21.01618138 -2.000273787 3.469229367 0.512023174 1.486903057 0.724170841 0.095279418 0.044951058 3.55E-06 0.011531756 0.021833444 0.009993698 2.000273787 0.974879883 HVDYVADQIVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HVDYVADQIVTK 12 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 142.91 6.18E-05 196120000 468330 411560 444780 449590 479250 351530 564300 456960 565720 FALSE TRUE 439018.0613 442032.3306 455330.3916 461127.2406 441611.6382 453011.0044 479688.4537 514012.4619 471297.6773 0.93150907 0.937904751 0.966120593 0.978420355 0.937012125 0.961199315 1.01780356 1.090632283 1 18.84627905 1.645643989 3.256884231 1.047562574 0.951986024 0.707971017 0.025846644 0.097081092 2.431602777 0.01445489 0.006267737 44.22257112 -1.645643989 -0.09557655 HVEDGNVTVQHAALSALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HVEDGNVTVQHAALSALR 18 0 P52306-4;P52306;P52306-5;P52306-6;P52306-2;P52306-3;H0Y8M2 P52306-4 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 0 ; 273.46 3.01E-39 568200000 160523 179349 167579 162487 171861 132396 189118 170574 186785 FALSE TRUE 150476.152 192628.1866 171554.053 166656.6915 158363.7303 170616.5759 160761.5116 191870.5394 155609.3768 0.967012111 1.237895752 1.102466037 1.070993888 1.017700434 1.096441483 1.033109411 1.233026848 1 17.24756947 HVEEFSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HVEEFSPR 8 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ;;; 172.21 0.00028488 956910000 946936 1132692 1016121 1020409 1129308 894930 1124374 935855 1068736 FALSE TRUE 887668.9661 1216557.694 1040223.87 1046594.422 1040616.705 1153281.763 955784.5569 1052698.557 890357.0573 0.996980884 1.366370586 1.168322148 1.175477202 1.168763359 1.295302546 1.073484563 1.182333029 1 19.76402449 0.640167588 0.604965252 0.996322409 1.211568389 0.209509589 0.103270131 1.775522153 1.257151196 0.110697116 0.040283861 4.366843094 -0.640167588 0.21524598 HVENDGYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HVENDGYK 8 0 O15305;H3BRM0;H3BV55 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 ;;; 155.58 0.00040662 2681180000 2809360 2458050 2552320 2518670 2688990 1999210 3055790 2237020 2836150 FALSE TRUE 2633527.172 2640046.58 2612862.236 2583303.336 2477807.572 2576349.473 2597602.658 2516316.871 2362778.243 1.114589226 1.117348438 1.105843193 1.093332963 1.04868393 1.090389875 1.099384873 1.064982242 1 21.1720528 -5 0.124260025 0.682916127 1.13916429 0.789524906 0.016401807 70.76465484 0.564049043 5.598641404 0.150296316 1.00E-05 5 0.456248163 HVFGESDELIGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HVFGESDELIGQK 13 0 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3;U3KPS5 P60174 TPI1 Triosephosphate isomerase 0 ;;;;; 236.77 2.34E-16 9215550000 14708320 15140500 14366980 13501060 15573240 9787930 19566080 13801100 23256360 FALSE TRUE 13787752.51 16261518.37 14707771.55 13847520.06 14350180.55 12613546.5 16632327.95 15524197.71 19374723.27 0.7116361 0.839316162 0.759121632 0.714720921 0.740665059 0.651031053 0.858454994 0.801260358 1 24.20767237 0.763428235 1.182224123 0.997983696 0.754510752 0.648144178 0.057891742 0.543341381 1.356585376 0.054381194 0.016785309 5.800003228 -0.763428235 -0.243472945 HVGDLGNVTADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HVGDLGNVTADK 12 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 101.53 0.0026177 370950000 1442300 981390 1107100 986280 967920 959560 1316100 969150 940890 FALSE TRUE 1352029.018 1054053.137 1133360.935 1011589.615 891903.4676 1236569.395 1118763.023 1090150.511 783849.3806 1.724858182 1.344713873 1.445891217 1.29054081 1.137850574 1.577559957 1.427267854 1.39076529 1 19.58021694 -2.0982258 1.641748969 0.405921591 1.409808021 0.410467676 0.156981716 275676.0796 60268.76445 611014.067 0.039452705 0.007975799 2.0982258 1.00388643 HVGDLGNVTADKDGVADVS(ph)IEDSVISLSGDHCIIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGR 36 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 1 HVGDLGNVTADKDGVADVS(0.992)IEDS(0.008)VISLSGDHCIIGR;HVGDLGNVTADKDGVADVS(1)IEDSVISLSGDHCIIGR;HVGDLGNVTADKDGVADVS(1)IEDSVISLSGDHCIIGR;HVGDLGNVTADKDGVADVS(1)IEDSVISLSGDHCIIGR 237.47 7.73E-50 569731000 201728 208040 206533 208652 234336 161959 248097 193418 251066 TRUE FALSE 189102.2046 223443.4981 211432.0603 214006.3636 215932.1958 208713.9341 210897.1581 217566.6631 209161.4627 0.904096779 1.068282346 1.010855717 1.023163449 1.032370844 0.997860368 1.008298352 1.040185225 1 17.67425754 4.752500081 24.90824877 1.023095631 0.904096695 0.759270362 0.020973345 1127.870607 2015340.686 0.005005323 0.100716324 56558.78623 -4.752500081 -0.118998936 HVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGR 36 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;; 367.67 3.06E-161 909710000 552538 546146 590879 572788 604130 467042 684821 544793 747432 FALSE TRUE 517955.6329 586583.2181 604894.9289 587486.7098 556684.0667 601869.4436 582138.4486 612811.6053 622680.7706 0.831815687 0.942028798 0.971436661 0.943479769 0.894011977 0.966577855 0.934890679 0.984150522 1 19.2481332 4.738698868 4.186303106 0.951587405 0.822167854 0.635860146 0.029216278 0.136299764 5.398028673 0.006403617 0.05305062 54789.69308 -4.738698868 -0.129419551 HVGMAVAGLLADAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HVGMAVAGLLADAR 14 0 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;; 160.38 4.76E-06 1545280000 981404 1501290 991437 1008230 1497106 827960 1042747 1287535 1307089 FALSE TRUE 919979.6755 1612447.074 1014954.354 1034102.889 1379529.334 1066978.611 886396.7677 1448286.579 1088927.402 0.844849412 1.480766368 0.932067971 0.949652738 1.266869886 0.97984366 0.814009057 1.330012062 1 20.05447634 3.746680559 23.27719531 1.020718355 1.207686689 0.040037979 0.216079854 368.7938144 438889.184 0.051204027 0.092087585 5580.595679 -3.746680559 0.186968334 HVGNQQYNVTYVVK ddPTM_SK-BR-3_Pertuzumab_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 ; 170.79 3.12E-06 968080000 1244260 1246250 1195850 1213090 1485580 894820 1467330 1281140 1427550 FALSE TRUE 1166383.988 1338523.647 1224216.127 1244219.943 1368908.539 1153140.008 1247317.489 1441093.149 1189282.683 0.980745793 1.125488218 1.029373541 1.04619361 1.151037141 0.969609685 1.048798159 1.211733064 1 20.18166024 HVIECAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HVIECAK 7 0 A0A2R8YFH0;E9PHA6;A0A2R8Y6P0;A0A2R8YG02;P43246;P43246-2;A0A2R8Y713 A0A2R8YFH0 MSH2 DNA mismatch repair protein Msh2 0 83.614 0.02215 147430000 207680 235080 211290 254470 267000 212680 242930 219200 255330 FALSE TRUE 194681.6795 252485.5678 216301.8986 261000.131 246030.897 274077.2634 206504.9018 246567.6025 212713.7735 0.915228367 1.186973291 1.016868325 1.227001556 1.156628896 1.288479156 0.970811144 1.159152031 1 17.69855393 0.38424193 1.004614477 1.000575678 1.117868198 0.080458086 0.116840354 6.342656649 8.031085578 0.106215456 0.032609747 2.422378094 -0.38424193 0.11729252 HVINFDLPSDIEEYVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 HVINFDLPSDIEEYVHR 17 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8Y7T2;A0A087WVZ1;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;;;;;;; 326.37 1.19E-60 3377597000 1591580 1698223 1742260 1717391 1939245.11 1519720.2 1980809.79 1633251.9 1893768 FALSE TRUE 1491965.849 1823961.198 1783587.23 1761462.161 1786944.622 1958438.751 1683805.751 1837166.995 1577685.887 0.945667234 1.156099077 1.130508452 1.116484704 1.132636501 1.241336294 1.067262986 1.164469436 1 20.58937857 4.742973845 24.83694106 1.132629383 0.945667152 0.446084292 0.062813904 342.2881349 1926266.712 0.012952655 0.10378034 55331.6785 -4.742973845 -0.186962231 HVLEGHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HVLEGHDR 8 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1;A0A3B3IU78 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 98.033 0.0078096 99560000 75127 90302 71170 88506 82489 74005 104030 82380 90038 FALSE TRUE 70424.93518 96988.05404 72858.18601 90777.2138 76010.64668 95369.04213 88431.66727 92665.32434 75010.07613 0.938873 1.293000341 0.971311986 1.210200262 1.013339149 1.271416416 1.178930509 1.235371688 1 16.19479679 2.235431642 24.99923415 1.188585003 1.10378689 0.085823443 0.126824508 188.770129 1508173.125 0.041419855 0.031901559 171.9616654 -2.235431642 -0.084798113 HVLTGSADNSCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 HVLTGSADNSCR 12 0 Q13347;Q5TFK1 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ;;;;;; 289.75 4.33E-36 2674810000 1637444 1712228 1817625 1703059 1775883 1511503 1970690 1572732 1837975 FALSE TRUE 1534959.303 1839003.143 1860739.923 1746762.377 1636412.313 1947849.379 1675203.329 1769091.052 1531205.099 1.002451797 1.201016862 1.215212727 1.140776228 1.068708767 1.272102203 1.094042419 1.155358648 1 20.54623611 0.148700912 0.932801042 0.998554123 1.157706276 0.237219874 0.077806476 5.788967605 5.237132761 0.092044618 0.022498572 1.408318589 -0.148700912 0.159152152 HVLVILTDMSSYAEALR ddPTM_SK-BR-3_Pertuzumab_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 ;; 363.82 4.46E-90 459486000 525174 580052 600455 577473 572869 471328 604776 583127 586381 FALSE TRUE 492304.2968 622999.6536 614698.0762 592291.9348 527878.1796 607392.7422 514095.4533 655931.6896 488510.2229 1.007766621 1.275305253 1.258311592 1.212445323 1.080587785 1.24335728 1.052373992 1.34271845 1 18.89802923 2.938768509 23.41620085 1.147305699 1.214840455 0.011995288 0.120646238 330.6052122 126429.4108 0.033325052 0.035343592 868.4973731 -2.938768509 0.067534756 HVLVTLGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HVLVTLGEK 9 0 F8VPF3;H0YI43;P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;G3V1Y7;P60660-2;G8JLA2;F8VZU9;F8W180;F8VXL3 F8VPF3;P60660;P60660-2 MYL6 Myosin light polypeptide 6 0 ; 90.15 0.011625 1562990000 53192000 37943400 42427700 42316800 51286000 42856800 52474000 33599900 60587000 FALSE TRUE 49862807.67 40752768.82 43434105.08 43402720.73 47258204.44 55228862.44 44606010.84 37794921.48 50474638.29 0.987878455 0.807391003 0.860513449 0.859891664 0.936276238 1.094190356 0.883731164 0.748790338 1 25.58905533 2.736828236 23.07968059 0.935532104 0.863929832 0.060059519 0.097452443 121.5858942 1619811.42 0.029987347 0.029683511 545.542056 -2.736828236 -0.071602272 HVNGQDQIVPGLYACGEAACASVHGANR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HVNGQDQIVPGLYACGEAACASVHGANR 28 0 P31040;D6RFM5;P31040-2;A0A087X1I3;P31040-3 P31040 SDHA "Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial" 0 86.32 0.0021242 196880000 93244 118060 104700 107190 143660 113690 122660 119550 144920 FALSE TRUE 87408.02449 126801.2852 107183.5334 109940.6769 132377.5231 146510.4574 104268.2717 134476.0807 120731.9158 0.723984407 1.050271458 0.887781269 0.910618175 1.096458399 1.213518865 0.863634699 1.113840361 1 16.88144758 2.750656744 24.31669617 1.046762334 0.918451329 0.309822716 0.118647608 796.7791402 1601754.461 0.034922185 0.036758495 563.1923463 -2.750656744 -0.128311005 HVPVVYVDYPGPASLTQIYGTFNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HVPVVYVDYPGPASLTQIYGTFNR 24 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 255.37 7.79E-44 187930000 138060 174480 151070 140240 184020 119450 173890 164660 148330 FALSE TRUE 129419.071 187398.6807 154653.4517 143838.7958 169567.8115 153933.2759 147816.8088 185218.1635 123572.7648 1.047310638 1.516504718 1.251517291 1.16400079 1.372210226 1.245689341 1.196192455 1.498859104 1 16.91500128 -1.453543868 2.937203934 0.992750363 1.29378183 0.277383691 0.144924205 23259998.48 26001811.42 1385661.091 0.031622013 0.035192987 1.453543868 0.301031467 HVQLVLGQLIDENYLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HVQLVLGQLIDENYLDR 17 0 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 0 140.02 6.77E-07 72573000 60560 67347 70965 70658 68090 50946 71287 58342 64573 FALSE TRUE 56769.6577 72333.44195 72648.32331 72471.2039 62742.48606 65653.28316 60598.17615 65626.12713 53795.34914 1.055289325 1.344604006 1.350457325 1.347164858 1.166318038 1.220426751 1.12645753 1.219921948 1 15.71519383 1.229887252 0.577010636 1.011904309 1.292764201 0.347534419 0.098340894 0.728684454 0.608637792 0.096689755 0.046883977 16.97802825 -1.229887252 0.280859892 HVSDDMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 HVSDDMK 7 0 Q01518-2;Q01518;Q5T0S3 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 0 ;;;;;;; 182.13 0.00050202 4543450000 4651230 7008110 6583620 6928640 7630330 5253380 8374390 6874240 8359680 FALSE TRUE 4360117.817 7526997.756 6739786.575 7106440.633 7031074.661 6769945.525 7118727.964 7732503.996 6964395.402 0.626058339 1.080782655 0.967748984 1.020395917 1.009574307 0.972079432 1.022160224 1.110290779 1 22.73156668 4.744033981 24.99997021 1.01933527 0.626058172 0.889242357 0.043996451 177.3367557 809973.7042 0.009863079 0.086014276 55466.91114 -4.744033981 -0.393277097 HVTENRDDVFLDGTGWEGGDEWIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HVTENRDDVFLDGTGWEGGDEWIR 24 1 H7C0I1;B8ZZW5;Q8NBF6-2;Q8NBF6 H7C0I1 AVL9 Late secretory pathway protein AVL9 homolog 0 179.58 2.25E-17 45216000 39471 48655 44433 49187 48499 38681 55039 38512 37173 FALSE TRUE 37000.58057 52257.46683 45486.97174 50449.22169 44690.08418 49847.57677 46786.41291 43320.30798 30968.58615 1.194777843 1.687434698 1.468810088 1.629045041 1.443077961 1.609617453 1.510770065 1.398846811 1 14.9185179 0.794515863 2.238462376 1.000279202 1.527342417 0.575985012 0.135023587 0.493342565 4.116783795 0.111940567 0.030445523 6.230399034 -0.794515863 0.527063215 HVTLPS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HVTLPSSPR 9 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 HVTLPS(0.701)S(0.299)PR;HVTLPS(0.723)S(0.277)PR;HVTLPS(0.745)S(0.255)PR 150.06 5.55E-05 7949500000 3499700 4659500 4524000 4483400 4780400 3920900 5389400 4791900 4037600 TRUE FALSE 3280660.024 5004494.228 4631311.416 4598451.634 4404966.667 5052800.18 4581309.503 5390179.263 3363698.476 0.975313349 1.487795135 1.376850942 1.367081998 1.309560503 1.502156099 1.361985783 1.602456136 1 21.68161696 HVTLPSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HVTLPSSPR 9 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 HVTLPS(0.358)S(0.642)PR;HVTLPS(0.009)S(0.991)PR;HVTLPS(0.002)S(0.998)PR 135.1 0.00014838 4827710000 2421410 3211230 3091100 3195730 3270950 2776670 3791600 3005530 2936250 TRUE FALSE 2269858.27 3448992.81 3164422.352 3277737.842 3014062.781 3578249.554 3223084.779 3380777.036 2446170.906 0.92792301 1.409955781 1.293622757 1.339946377 1.232155437 1.462796219 1.317604085 1.382069024 1 21.22209377 -1.002555144 4.512021262 0.999991282 1.313035001 0.281292891 0.146273123 0.090097898 38617779.67 876.972278 0.030060768 0.099413384 1.002555144 0.31304372 HVTSNAS(ph)DSESSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HVTSNASDSESSYR 14 0 Q12959;Q12959-3;Q12959-5;A0A590UK48;C9JUA9;Q12959-8;A0A590UJ64 Q12959 DLG1 Disks large homolog 1 1 HVTSNAS(1)DSESSYR;HVTS(0.007)NAS(0.864)DS(0.124)ES(0.002)S(0.002)YR 123 6.79E-05 833330000 302295 436272 404418 426874 477060 335307 376040 414694 441879 TRUE FALSE 283374.8956 468574.0328 414010.9859 437828.3095 439593.632 432104.6876 319656.293 466469.4588 368126.5403 0.769775782 1.272861317 1.124643134 1.189341875 1.194137298 1.173793901 0.868332647 1.267144331 1 18.48984224 HVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILAK 37 0 E9PF18;Q16836;Q16836-3;Q16836-2;A0A0A0MSE2;A0A1W2PQV5;A0A1W2PP40 E9PF18 HADH "Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial" 0 ; 174.58 1.09E-18 374280000 248979 206385 195598 203497 305500 170282 213360 245899 285813 FALSE TRUE 233395.8488 221665.9601 200237.6769 208719.0775 281507.2623 219439.6491 181368.6487 276600.0314 238108.9639 0.980206058 0.930943365 0.840949764 0.876569593 1.182262346 0.921593398 0.761704414 1.161653165 1 17.86126241 HVVFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 HVVFGK 6 0 C9JQD4;O43447;O43447-2;H0YEL5;P62937;P23284;P45877;P62937-2 C9JQD4;P62937;P23284;P45877;P62937-2 PPIH;PPIA;PPIB;PPIC "Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase H;Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase B;Peptidyl-prolyl cis-trans isomerase C" 0 ;;;;;; 118.11 0.022145 58016185000 79394362 79771255 72092207 65542944 85093715 56717276 85068203 75823146 118463970 FALSE TRUE 74425210.61 85677601.72 73802268.19 67224886.91 78410797.88 73090632.85 72313015.69 85289832.69 98691568.1 0.754119243 0.868134972 0.74780723 0.681161402 0.794503516 0.74059653 0.732717263 0.864205872 1 26.55642349 0.969105723 3.946624442 0.999665169 0.765882283 0.725224725 0.048097207 0.119581954 5.389810775 0.048649247 0.012462323 9.313345682 -0.969105723 -0.233782887 HVVFIAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HVVFIAQR 8 0 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 91.906 0.013218 0 110280 374430 109340 91464 363210 107410 136060 298000 220090 FALSE TRUE 103377.7717 402153.1868 111933.5964 93811.12109 334684.9517 138417.5233 115659.0661 335205.956 183355.5572 0.563810409 2.193296964 0.610472888 0.511635003 1.825333014 0.754913162 0.630791168 1.828174511 1 17.48428447 3.902172889 9.819916114 0.982955581 1.482708295 0.047098301 0.606495487 0.815796784 101.8290656 0.142862907 0.257996271 7983.124259 -3.902172889 0.499752713 HWDHLTQVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HWDHLTQVK 9 0 P30084 P30084 ECHS1 "Enoyl-CoA hydratase, mitochondrial" 0 102.61 0.0020569 61895000 58396 81101 57002 52407 116460 42093 56898 89698 136030 FALSE TRUE 54741.0986 87105.80243 58354.11436 53751.85234 107313.7014 54244.56578 48366.67312 100896.9927 113325.7142 0.483042167 0.768632283 0.514923861 0.474312937 0.946949261 0.478660701 0.426793455 0.890327438 1 16.79011573 1.082915701 5.799815767 0.996883343 0.591951865 0.473944044 0.159764894 0.161187795 7.950436961 0.147784918 0.037225864 12.10363174 -1.082915701 -0.404931478 HWDQDDDFEFTGSHLTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HWDQDDDFEFTGSHLTVR 18 0 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 ;; 315.28 1.56E-61 888538000 224479 272706 310124 284716 286919 228277 316948 250300.5 285068 FALSE TRUE 210429.2601 292897.436 317480.2877 292022.2946 264385.5391 294176.8641 269424.5898 281551.0684 237488.3092 0.886061553 1.233313071 1.336824911 1.229628084 1.113257069 1.238700402 1.134475169 1.18553654 1 17.85749697 0.178620388 0.715048841 0.995080777 1.198038353 0.134295645 0.120543433 5.548558619 3.491304929 0.187850885 0.041968913 1.508760787 -0.178620388 0.202957577 HWELTAEGEEIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HWELTAEGEEIAR 13 0 K7ER00;Q9Y285;Q9Y285-2;K7ER16;K7EK06 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ; 232.6 4.74E-13 401050000 283710 317180 323590 322140 344790 278140 357730 303110 327170 FALSE TRUE 265953.0975 340664.3372 331265.7076 330406.6578 317711.5842 358434.5028 304091.7075 340953.9507 272563.2134 0.97574832 1.249854421 1.215372036 1.212220291 1.165643669 1.315050914 1.115674062 1.250916976 1 18.05623134 -1.115845335 7.343307144 0.999999937 1.195465192 0.286733912 0.092220931 8.34E-08 9.98E-09 0.07810171 0.018408744 0.076586931 1.115845335 0.195465255 HWGAGWDGGHHYPEMDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HWGAGWDGGHHYPEMDAR 18 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 0 123.36 1.19E-05 71048000 35081 54938 35418 34958 67334 21061 37653 55679 58877 FALSE TRUE 32885.34283 59005.66668 36258.13169 35855.08146 62045.85925 27140.9688 32007.2822 62630.64571 49050.04834 0.670444657 1.202968574 0.739206849 0.730989727 1.264950012 0.553332152 0.652543337 1.276872253 1 15.58196694 3.843420213 12.28941567 0.850441457 0.974200452 0 0.273802664 1.960359561 197.5862977 0.066080881 0.119164491 6973.008796 -3.843420213 0.123758994 HWLDSPWPGFFTLDGQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HWLDSPWPGFFTLDGQPR 18 0 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;E9PFG7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 158.45 4.55E-11 93198000 113420 158160 106090 95893 191510 84572 95815 161950 167060 FALSE TRUE 106321.2447 169870.331 108606.5049 98353.77673 176469.5771 108986.5635 81448.43025 182169.814 139176.6068 0.763930427 1.220537955 0.780350286 0.70668325 1.267954301 0.783081051 0.585216382 1.308911161 1 17.08655721 HWMLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HWMLDK 6 0 P62701;C9JEH7;P22090;Q8TD47 P62701 RPS4X;RPS4Y1;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1;40S ribosomal protein S4, Y isoform 2" 0 ;;; 118.03 0.016853 6885400000 11073500 13321400 10018100 9084300 14244600 6572700 11428100 12059000 13709100 FALSE TRUE 10380429.4 14307730.32 10255734.06 9317418.518 13125886.58 8470131.791 9714562.498 13564592.7 11420962.65 0.908892685 1.252760451 0.897974574 0.815817266 1.14928023 0.741630286 0.850590515 1.187692589 1 23.44518092 3.782398035 6.164265318 0.928261558 1.098822254 0.089750891 0.161808337 0.338286529 27.67993914 0.038614336 0.069762795 6058.959303 -3.782398035 0.170560695 HWPFMVVNDAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HWPFMVVNDAGR 12 0 P11142;E9PKE3;E9PNE6;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 167.2 4.99E-05 1086780000 1126200 1459700 886030 776730 1494770 658200 1225070 1558420 1272160 FALSE TRUE 1055713.152 1567777.707 907047.05 796662.2068 1377376.794 848211.655 1041382.126 1752992.168 1059828.278 0.996117177 1.479275218 0.855843413 0.751689895 1.299622612 0.80032933 0.982595151 1.654034153 1 20.0153991 3.969540303 24.43054119 1.027287153 1.259126468 0.064165086 0.287559923 465.3770181 1499744.337 0.068028851 0.125825197 9322.669828 -3.969540303 0.231839315 HWPFMVVNDAGRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HWPFMVVNDAGRPK 14 1 P11142;E9PKE3;E9PNE6;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;; 184.98 7.40E-07 12798950000 9849230 9315090 7896930 6668660 10798660 4987840 11032160 9563470 12809350 FALSE TRUE 9232784.276 10004788.96 8084248.909 6839789.106 9950576.803 6427748.437 9377990.026 10757490.28 10671386.73 0.865190674 0.9375341 0.757563109 0.640946606 0.932453959 0.602334879 0.878797691 1.008068637 1 23.34724433 1.383441231 4.547436607 0.999744341 0.798559764 0.390311584 0.109349917 0.225210139 7.139232394 0.075934802 0.026598888 24.17916122 -1.383441231 -0.201184577 HWVAPGGPYSAETPGVPS(ph)PIAALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HWVAPGGPYSAETPGVPSPIAALK 24 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 HWVAPGGPYSAETPGVPS(1)PIAALK;HWVAPGGPYSAETPGVPS(1)PIAALK 202.2 8.60E-25 1335420000 1618720 1316420 1540760 1451340 1637630 1492160 2351500 1620510 2241080 TRUE FALSE 1517407.205 1413889.107 1577307.555 1488583.842 1509017.146 1922922.369 1998914.405 1822834.241 1867029.27 0.812738841 0.757293487 0.844822082 0.797300752 0.808245039 1.029936916 1.070639029 0.97632869 1 20.83231311 2.241222365 7.858969215 1.030557367 0.802647418 0.915413543 0.032417753 0.029069359 13.25381528 0.011325375 0.008940242 174.2698931 -2.241222365 -0.227909949 HYAHTDCPGHADYVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HYAHTDCPGHADYVK 15 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ;;;; 163.27 8.95E-07 2600250000 1757713 1591973 1289385 1332740 2124910 1103359 1408551 1681385 2871080 FALSE TRUE 1647700.881 1709844.337 1319969.821 1366940.365 1958028.14 1421880.832 1197351.854 1891309.618 2391878.2 0.688873238 0.714854267 0.551854949 0.571492463 0.818615321 0.594462056 0.500590646 0.790721542 1 21.1897125 0.982876692 6.648271996 0.999941521 0.630321 0.633660396 0.090561406 0.093481388 23.22964855 0.087639298 0.02199679 9.613392896 -0.982876692 -0.369620521 HYCDSEKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 HYCDSEKPR 9 1 Q9UGI8-2;Q9UGI8;H7BYK1 Q9UGI8-2 TES Testin 0 ;;;;;; 208.25 6.22E-06 5868520000 5830790 5097570 5144550 5165210 5429470 4633900 6752540 5077680 5649740 FALSE TRUE 5465851.262 5474999.387 5266581.155 5297758.033 5003061.328 5971631.705 5740059.315 5711639.525 4706761.895 1.161276347 1.163219961 1.118939363 1.125563211 1.062951863 1.268734607 1.21953467 1.213496593 1 22.16630344 2.239645868 24.99998396 1.199178676 1.130358799 0.05492593 0.075911066 49.28013566 1135266.476 0.024365148 0.01931935 173.638437 -2.239645868 -0.068819876 HYEDFPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HYEDFPK 7 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ; 73.616 0.048409 249730000 482690 462640 475800 464350 535210 359720 602350 462020 558880 FALSE TRUE 452479.2945 496894.347 487086.2007 476266.0071 493176.7655 463565.3244 512033.2094 519704.214 465599.3175 0.971821215 1.067214509 1.046148872 1.02290959 1.059230001 0.995631452 1.099729296 1.116204845 1 18.82872942 1.696664589 10.80370739 1.080523464 1.035073637 0.179716339 0.041605439 0.171233254 33.84404931 0.017762907 0.009646712 49.73528246 -1.696664589 -0.045449827 HYEDGYPGGSDNYGS(ph)LSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HYEDGYPGGSDNYGSLSR 18 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 HYEDGYPGGSDNY(0.001)GS(0.951)LS(0.048)R 95.742 0.0011091 453640000 1268300 815730 992850 881680 1020200 687220 1257000 903640 1289700 TRUE FALSE 1188919.367 876127.498 1016400.871 904305.4015 940077.6073 885609.2579 1068524.519 1016461.443 1074440.738 1.106547178 0.815426544 0.945981323 0.841652191 0.874945982 0.824251377 0.994493676 0.946037698 1 20.03515448 1.656936926 9.498712438 0.977377406 0.893550928 0.157262986 0.084269981 0.186210635 27.50138959 0.036683956 0.019535584 45.38756937 -1.656936926 -0.083826478 HYEDGYPGGSDNYGSLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HYEDGYPGGSDNYGSLSR 18 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 0 ;;; 240.59 5.85E-24 2408560000 1288870 1556380 1502030 1441050 1579740 1270540 1710250 1427360 1787490 FALSE TRUE 1208201.927 1671615.995 1537658.861 1478029.783 1455673.593 1637324.273 1453813.89 1605569.038 1489146.371 0.811338597 1.122533034 1.032577382 0.992534925 0.97752217 1.099505263 0.976273332 1.078180808 1 20.50605414 HYELYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 80.377 0.064673 447550000 70705 134171 76816 81202 135121 80204 88218 107172 120852 FALSE TRUE 66279.70026 144105.1604 78638.1118 83285.78079 124509.1417 103357.5928 74990.52988 120552.6601 100681.0205 0.658313751 1.43130413 0.781061926 0.827224242 1.236669445 1.026584676 0.744832835 1.197372251 1 16.61943222 HYFQNTQGLIFVVDSNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HYFQNTQGLIFVVDSNDR 18 0 P61204;F5H423;F5H0C7;P84077;P84085;C9J1Z8;P18085;C9JPM4;C9JAK5 P61204;P84077;P84085;P18085 ARF3;ARF1;ARF5;ARF4 ADP-ribosylation factor 3;ADP-ribosylation factor 1;ADP-ribosylation factor 5;ADP-ribosylation factor 4 0 ;;; 310.55 3.83E-61 3957000000 3031461 3130025 3208061 3154254 2917581 3112617 3801431 3013809 2390798 FALSE TRUE 2841727.267 3361775.308 3284157.722 3235197.498 2688445.957 4011178.999 3231441.712 3390089.688 1991758.369 1.426742978 1.687842944 1.648873565 1.624292157 1.349785195 2.013888362 1.622406494 1.702058714 1 20.92561121 -0.516468445 11.76493663 1.000000002 1.646909636 0.562588035 0.175519054 0 0 0.152466118 0.035936609 0.304460919 0.516468445 0.646909634 HYFQNTQGLIFVVDSNDRER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HYFQNTQGLIFVVDSNDRER 20 1 P61204;F5H423;F5H0C7;P84077;P84085;C9J1Z8;P18085;C9JPM4;C9JAK5 P61204;P84077;P84085;P18085 ARF3;ARF1;ARF5;ARF4 ADP-ribosylation factor 3;ADP-ribosylation factor 1;ADP-ribosylation factor 5;ADP-ribosylation factor 4 0 ;;;;; 266.64 5.50E-37 5191680000 838042 1143191 1022037 1067661 1261033 859786 1043884 924138 1247354 FALSE TRUE 785590.4472 1227834.051 1046280.2 1095058.989 1161996.555 1107992.261 887363.2851 1039518.664 1039162.559 0.755984172 1.181561095 1.006849401 1.05378988 1.118204794 1.06623574 0.853921533 1.000342684 1 19.98698993 1.762621226 25 0.937681223 1.049427064 0.072276982 0.117963606 23.37189899 24301.87983 0.049367835 0.027378275 57.89235629 -1.762621226 0.11174584 HYGDQVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HYGDQVDR 8 0 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-4;Q9BQ52-2;Q9BQ52-3 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 0 ; 156.92 0.00038525 668160000 190741 180646 215394 196863 237450 203028 231560 187039 249330 FALSE TRUE 178802.8613 194021.2178 220503.2474 201914.8379 218801.6348 261638.8877 196839.7277 210391.2309 207715.2123 0.860807734 0.934073223 1.061565232 0.972075351 1.053373186 1.259603882 0.94764233 1.012883113 1 17.66424735 4.54368631 1.04960532 1.04994858 0.798964036 0.356313171 0.08469017 1.499145091 1.6800482 0.025337754 0.390492973 34969.24935 -4.54368631 -0.250984545 HYGEHVCTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HYGEHVCTAK 10 0 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 0 ; 142.83 2.03E-05 227870000 402600 403180 379400 356640 428970 285240 506500 398570 492750 FALSE TRUE 377401.9847 433031.8667 388399.5472 365791.9862 395280.4266 367584.1575 430555.0271 448332.3419 410506.8417 0.919356138 1.054871254 0.946146343 0.891074031 0.962908255 0.895439784 1.04883764 1.09214341 1 18.64704674 1.623693186 7.582395585 1.054466224 0.956612691 0.456494282 0.051244977 0.113732192 14.39256835 0.026910255 0.013414663 42.04295044 -1.623693186 -0.097853533 HYGFQLYQSDPSGNYGGWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 278.34 1.53E-39 869800000 1438550 1198460 1174300 1067370 1385580 788890 1288010 1302490 835820 FALSE TRUE 1348513.723 1287195.225 1202154.951 1094760.521 1276762.136 1016629.736 1094884.858 1465108.744 696316.2424 1.936639764 1.848578486 1.726449675 1.572217413 1.833595223 1.460011521 1.572395976 2.104085262 1 19.40938315 -2.054568545 2.464219559 1.65E-05 1.733717343 0.605713316 0.191076809 4476268.464 1574072.871 25210976.06 0.044520643 0.008819246 2.054568545 1.733700891 HYGGLTGLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HYGGLTGLNK 10 0 P18669;Q8N0Y7;P15259 P18669 PGAM1;PGAM4;PGAM2 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4;Phosphoglycerate mutase 2 0 ; 142.56 3.55E-05 2994200000 3319900 4006200 3454900 3150900 4202000 2560900 3916000 3774700 3931600 FALSE TRUE 3112113.385 4302823.216 3536851.86 3231757.428 3871991.87 3300190.257 3328832.154 4245979.604 3275390.561 0.950150319 1.313682487 1.079825991 0.986678495 1.182146617 1.007571523 1.016316098 1.296327728 1 21.64323551 3.711236639 19.66143384 1.074137166 1.169544262 0.005294227 0.129484513 65.09408469 80572.1307 0.031286015 0.048838598 5143.238208 -3.711236639 0.095407097 HYLFYDGESVSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HYLFYDGESVSGK 13 0 O75436;S4R3Q6;O75436-2;S4R2Y3 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ; 214 1.42E-09 1704020000 2200800 2140400 2205000 2140180 2344600 1517220 2694500 2038290 2744200 FALSE TRUE 2063055.857 2298877.443 2257303.641 2195100.642 2160464.574 1955216.784 2290484.74 2292774.993 2286175.292 0.902404931 1.005556071 0.9873712 0.960162876 0.945012651 0.855234851 1.001885003 1.002886787 1 21.1245046 1.587468651 25 1.001810445 0.953868977 0.27548072 0.042548929 1.550617259 1894.539714 0.023866924 0.011069654 38.67841344 -1.587468651 -0.047941467 HYLGHNDDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 49.466 0.097985 140780000 85893 172720 154050 146170 168550 202810 135540 144750 127660 FALSE TRUE 80517.11045 185508.3685 157704.1387 149920.9697 155312.7629 261357.9547 115217.0353 162822.3561 106352.7213 0.757076166 1.744274771 1.482840654 1.40965805 1.460355325 2.457463725 1.083348258 1.530965585 1 16.69849742 2.451028264 24.99683242 1.566890417 1.436644533 0.009041291 0.460543285 1258.112824 1205253.002 0.148904706 0.124585548 282.5063823 -2.451028264 -0.130245884 HYLILPSEEEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HYLILPSEEEGR 12 0 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ;; 158.4 5.95E-05 832950000 948140 1077560 1047520 1120300 964310 860960 1126810 925380 641030 FALSE TRUE 888797.6099 1157343.664 1072367.669 1149048.795 888576.9824 1109505.175 957855.3013 1040915.73 534037.9518 1.664296717 2.16715621 2.008036443 2.151623851 1.663883586 2.077577393 1.793609046 1.949141866 1 19.02658275 -1.993998008 0.356187526 3.08E-08 2.008282732 0.717898984 0.183099383 18.31428392 1.005242225 15.17699467 0.125218446 0.01013916 1.993998008 2.008282701 HYLSEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HYLSEELR 8 0 Q7L2J0;Q7L2J0-2 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 0 138.1 0.00071989 160270000 99990 134500 90719 83803 163490 63995 81687 139750 193660 FALSE TRUE 93731.80439 144458.5199 92870.89752 85953.52686 150650.1549 82469.31763 69438.79269 157198.0951 161336.8949 0.580969433 0.895384283 0.575633351 0.532758033 0.933761338 0.511162172 0.430396238 0.974346849 1 17.29971687 1.159936043 9.488650951 0.992550934 0.646165632 0.450379901 0.160539297 0.360657505 39.93644634 0.156566924 0.039197182 14.4522692 -1.159936043 -0.346385302 HYNGEAYEDDEHHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HYNGEAYEDDEHHPR 15 0 P31689 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ;;; 147.1 1.31E-06 4209113000 961165 934902 1017405 909735 1016557 812019 1141319 973205 1047295 FALSE TRUE 901007.3984 1004123.117 1041538.327 933080.3403 936720.7138 1046435.703 970188.8114 1094711.787 872494.6987 1.03267951 1.150864433 1.193747456 1.069439553 1.073611926 1.199360529 1.11197101 1.25469162 1 19.73478684 2.242990588 24.99833777 1.148405514 1.121104731 0.025561463 0.078987557 529.0604786 2985508.01 0.026193714 0.021226989 174.9808768 -2.242990588 -0.027300783 HYPVFENPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HYPVFENPK 9 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISU1;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 132.9 0.00029211 212650000 489860 504610 460980 480290 588730 296050 542210 524900 691960 FALSE TRUE 459200.537 541971.8494 471914.6633 492615.0545 542493.5206 381514.829 460910.6441 590434.9204 576467.4058 0.796576758 0.940160439 0.818631996 0.854541037 0.941065384 0.661815092 0.799543286 1.024229496 1 19.13687951 1.234087311 24.99358213 1.01211486 0.834406973 0.478290043 0.078840312 107.737112 601919.1133 0.067559048 0.019146591 17.14301918 -1.234087311 -0.177707887 HYQEEGQGTEVVQGVLLGLVVEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 HYQEEGQGTEVVQGVLLGLVVEDR 24 0 A0A087WZK9;B3KS98;O15372;E5RGU4;E5RFH0;E5RFW7 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ;;;;; 210.5 4.09E-25 841413000 480422 507592 547414 554498 553422 490705 609982 419422 474838 FALSE TRUE 450353.2446 545174.6398 560398.9186 568727.3574 509958.4685 632363.5676 518520.8619 471787.76 395584.4702 1.138450264 1.378149753 1.416635285 1.437688788 1.289126614 1.598555088 1.310771532 1.192634685 1 18.59362626 -0.425849589 6.792158861 0.999999989 1.363110222 0.405124603 0.129886397 0 0 0.114986536 0.027102586 0.375102891 0.425849589 0.363110233 HYQGEEKS(ph)D ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 HYQGEEKSD 9 1 P13984 P13984 GTF2F2 General transcription factor IIF subunit 2 1 HYQGEEKS(1)D;HYQGEEKS(1)D;HYQGEEKS(1)D;HYQGEEKS(1)D;HYQGEEKS(1)D 129.71 0.00023118 1621876000 2916960 1756270 2041520 2037120 2012830 1522260 2527370 1641520 2383790 TRUE FALSE 2734392.681 1886306.058 2089945.818 2089395.948 1854750.451 1961711.75 2148414.331 1846467.385 1985920.049 1.376889609 0.949839879 1.05238165 1.052104766 0.933950212 0.987810033 1.081823174 0.929779316 1 20.92137611 4.743825598 24.99280079 1.00565352 1.376889765 0.838120194 0.052182197 212.6056899 1009205.575 0.011874697 0.100921788 55440.30342 -4.743825598 0.371236245 HYS(ph)PEDEPSPEAQPIAAYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HYSPEDEPSPEAQPIAAYK 19 0 A0A096LP25;Q6ZSR9 A0A096LP25 AAK1 Uncharacterized protein FLJ45252 1 HYS(1)PEDEPSPEAQPIAAYK;HYS(1)PEDEPSPEAQPIAAYK;HYS(1)PEDEPSPEAQPIAAYK 262.98 1.98E-31 1475040000 1219170 1143520 1150390 1042750 1279120 979680 1480990 1144120 1982570 TRUE FALSE 1142864.326 1228187.411 1177677.794 1069508.73 1178663.075 1262497.712 1258929.298 1286965.901 1651666.259 0.691946281 0.743605074 0.713024067 0.647533195 0.713620605 0.764378218 0.762217725 0.779192463 1 20.65549077 0.346183059 0.606510588 1.010357058 0.707222622 0.91009379 0.028239921 0.666656498 0.372104722 0.044891712 0.012218075 2.219131606 -0.346183059 -0.303134436 HYSDELQSVISHLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HYSDELQSVISHLLR 15 0 O95219-2;O95219 O95219-2 SNX4 Sorting nexin-4 0 ; 248.23 1.34E-18 44439000 94345 96068 90783 92683 111032 73629 104482 95685 109283 FALSE TRUE 88440.11486 103180.9747 92936.41563 95061.40269 102311.9946 94884.49703 88815.89406 107631.4829 91042.9613 0.971410789 1.133321821 1.020797372 1.044137859 1.123777095 1.042194758 0.975538282 1.182205426 1 16.47425986 -0.714689698 8.712445269 1.000000015 1.058682238 0.073831138 0.067916818 0 0 0.059652074 0.014060129 0.192890262 0.714689698 0.058682224 HYSNWETVLILEELRGDEGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HYSNWETVLILEELRGDEGTR 21 1 Q5TFE4;Q5TFE4-2 Q5TFE4 NT5DC1 5-nucleotidase domain-containing protein 1 0 ; 258.91 9.37E-37 84167000 23959 71315 56034 58836 70465 67402 72826 58689 55825 FALSE TRUE 22459.44896 76595.2368 57363.15294 60345.83137 64930.96314 86859.86322 61906.41738 66016.45084 46507.44686 0.482921564 1.646945639 1.233418663 1.297552015 1.39614121 1.867654948 1.33110763 1.419481294 1 15.50517412 4.747116794 24.60690153 1.423352831 0.482920969 0.603124224 0.232806859 564.5050998 1623427.7 0.050799178 0.586673496 55862.04034 -4.747116794 -0.940431861 HYTEAIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HYTEAIK 7 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;; 140.98 0.0025874 946757000 1435240 1884650 1353490 1412980 2070400 1040750 1668340 1839620 1901650 FALSE TRUE 1345410.89 2024191.447 1385595.422 1449239.459 1907799.136 1341197.63 1418187.905 2069300.607 1584252.33 0.849240279 1.277695105 0.874605261 0.914778177 1.204226814 0.846580816 0.895178046 1.306168574 1 20.59537071 5.039144414 15.78239682 1.024741255 0.121408909 0.105210873 0.169697327 454840.7211 5169173.55 0.038544222 11691464.36 109432.0194 -5.039144414 -0.903332345 HYTEAIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HYTEAIKR 8 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;; 194.2 0.00010818 1546440000 1965820 2612490 2242600 2377290 3172960 1731590 2642740 2507500 2955570 FALSE TRUE 1842782.835 2805921.478 2295795.531 2438295.286 2923768.521 2231471.923 2246485.671 2820566.895 2462266.273 0.748409242 1.13956866 0.932391251 0.990264665 1.18742987 0.906267509 0.912365042 1.145516602 1 21.23155535 4.75640532 24.39913566 1.01575677 0.748408931 0.42417113 0.101195269 2861.561479 3912536.119 0.023321913 0.724043809 57069.66455 -4.75640532 -0.267347838 HYYEVSCHDQGLCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 HYYEVSCHDQGLCR 14 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;;; 220.21 2.73E-12 2258120000 399149 716350 543282 591662 762500 492768 557426 673442 634590 FALSE TRUE 374166.9766 769389.2994 556168.9056 606845.0486 702616.3258 635022.1222 473845.1462 757522.7161 528672.8294 0.707747695 1.455322189 1.052009626 1.147865021 1.329019172 1.201162774 0.896291846 1.432876202 1 19.01201566 -1.33486647 5.374706433 0.999957801 1.158562139 0.041118115 0.230379489 0.000104386 1.29E-05 0.199878708 0.047099342 0.046252321 1.33486647 0.158604338 HYYFCMMTEAEQDKWQAVLQDCIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HYYFCMMTEAEQDKWQAVLQDCIR 24 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 292.14 4.64E-62 451400000 416480 457680 388390 299810 498360 345670 536640 421450 324150 FALSE TRUE 390413.2602 491567.1034 397602.7942 307503.6322 459220.8159 445459.3175 456175.8139 474068.9602 270047.2709 1.445721925 1.820300208 1.472345167 1.13870298 1.700520114 1.649560523 1.689244303 1.755503615 1 18.04285244 3.7914038 8.38488159 1.529086639 1.656507015 0.030229297 0.264083814 1.118128133 133.5448764 0.064059593 0.115646059 6185.912885 -3.7914038 0.127420376 HYYTGTQGLIFVVDCADRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HYYTGTQGLIFVVDCADRDR 20 1 P62330 P62330 ARF6 ADP-ribosylation factor 6 0 ;; 193.85 3.53E-18 533887000 148844 182809 145441 171200 213995 176077 159997 149810 204046 FALSE TRUE 139528.1197 196344.3686 148890.9292 175593.2818 197188.6959 226907.5715 136006.9352 168514.1083 169989.4044 0.820804804 1.155038864 0.875883586 1.03296604 1.160005805 1.334833617 0.800090662 0.991321246 1 17.3750853 1.646943621 24.99999971 0.921648986 1.055727322 0.140354669 0.153644223 1.097596567 695.0117616 0.068475767 0.037971433 44.35510595 -1.646943621 0.134078336 IAALQAFADQLIAAGHYAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IAALQAFADQLIAAGHYAK 19 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 219.79 3.05E-19 202718000 611020 597540 599460 576950 750060 507570 644770 558270 749680 FALSE TRUE 572777.3489 641782.4833 613679.4743 591755.5138 691153.3132 654097.2193 548092.7243 627971.2384 624553.5649 0.917098838 1.027585974 0.982589018 0.947485607 1.106635767 1.047303636 0.877575207 1.005472186 1 19.25246578 1.759153561 25 0.948918787 1.006567143 0.087712578 0.062434523 17.52393609 21292.8053 0.027242186 0.015107572 57.43194983 -1.759153561 0.057648356 IAAPELHKGDS(ph)DS(ph)EEDEPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IAAPELHKGDSDSEEDEPTK 20 1 Q92733 Q92733 PRCC Proline-rich protein PRCC 2 IAAPELHKGDS(1)DS(1)EEDEPTK;IAAPELHKGDS(1)DS(1)EEDEPTK;IAAPELHKGDS(1)DS(1)EEDEPTK;IAAPELHKGDS(1)DS(1)EEDEPTK;IAAPELHKGDS(1)DS(1)EEDEPTK;IAAPELHKGDS(1)DS(1)EEDEPTK 208.12 7.96E-22 3049190000 3543740 1560051 2116570 2075270 2125340 1575754 2849340 1710340 2721660 TRUE FALSE 3321943.639 1675558.799 2166776.04 2128524.942 1958424.37 2030648.6 2422107.919 1923879.714 2267397.363 1.465091074 0.738978896 0.955622545 0.938752499 0.863732313 0.895585676 1.068232661 0.848496935 1 21.11260582 4.75006555 24.91560681 0.914396324 1.465091415 0.791209574 0.089020066 788.8062693 1708241.197 0.02159171 0.346496985 56242.62088 -4.75006555 0.55069509 IAAPELHKGDS(ph)DS(ph)EEDEPTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IAAPELHKGDSDSEEDEPTKK 21 2 Q92733 Q92733 PRCC Proline-rich protein PRCC 2 IAAPELHKGDS(1)DS(1)EEDEPTKK 146.15 5.98E-08 174060000 403610 125970 199300 205310 209990 140370 270470 156230 299180 TRUE FALSE 378348.7706 135296.9499 204027.4901 210578.6022 193498.2325 180892.5403 229915.5344 175735.6594 249244.9252 1.517979835 0.5428273 0.818582324 0.844866157 0.776337702 0.72576218 0.922448207 0.705072166 1 17.92720461 -0.436643803 6.345982149 0.999961911 0.823939602 0.015893559 0.257535489 29498145.09 4648318.739 0.310185816 0.05308857 0.365894766 0.436643803 -0.176022309 IAASS(ph)SFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IAASSSFR 8 0 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 1 IAAS(0.02)S(0.929)S(0.051)FR 117.01 0.0022663 2278900000 1982300 2629500 2067000 1987800 2624300 1299100 2248200 2242000 3165500 TRUE FALSE 1858231.382 2824190.916 2116030.216 2038810.313 2418198.064 1674129.081 1911103.281 2521918.635 2637157.6 0.704634179 1.070922313 0.802390504 0.773109015 0.916971388 0.634823296 0.724683 0.956301829 1 21.33055236 5.039414757 15.9105636 0.844894854 0.110301592 0.110316602 0.132620316 5481502.408 61906313.8 0.032280129 116013801.8 109500.1607 -5.039414757 -0.734593263 IAASSS(ph)FR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IAASSSFR 8 0 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 1 IAAS(0.005)S(0.17)S(0.825)FR;IAASS(0.026)S(0.974)FR;IAASS(0.015)S(0.984)FR;IAAS(0.003)S(0.297)S(0.699)FR;IAAS(0.01)S(0.069)S(0.921)FR;IAAS(0.02)S(0.149)S(0.831)FR 139.02 0.0007137 8704680000 6757930 9314550 7018380 6957460 9488660 4841820 7778750 7862870 11610470 TRUE FALSE 6334963.225 10004208.97 7184859.288 7136000.203 8743458.919 6239574.834 6612398.652 8844566.628 9672607.55 0.654938515 1.034282526 0.742804797 0.737753513 0.903940212 0.645076811 0.683621104 0.914393206 1 23.20547343 3.735175913 24.59745879 0.776966562 0.876757681 0 0.144369548 638.5447504 1949982.711 0.03403611 0.05999323 5434.704222 -3.735175913 0.099791118 IAAYLQSDQFCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IAAYLQSDQFCK 12 0 P21266 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 174.4 7.09E-05 267970000 483740 477220 398028 418970 549120 359154 572460 449920 784640 FALSE TRUE 453463.5769 512553.8653 407469.4121 429721.4795 505994.3302 462835.9294 486624.9375 506093.5024 653678.515 0.693710389 0.784106948 0.623348332 0.657389634 0.774072145 0.708048251 0.744440771 0.774223859 1 19.31822175 0.323448253 0.704265911 1.006706416 0.701893884 0.79082758 0.046839152 1.077738461 0.750765523 0.061680303 0.017104735 2.105950954 -0.323448253 -0.304812532 IACDEEFS(ph)DS(ph)EDEGEGGR ddPTM_SK-BR-3_Pertuzumab_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 221.13 9.37E-19 299340000 596270 503620 559920 532840 539690 562920 686860 467600 441680 TRUE FALSE 558950.5251 540908.5488 573201.5668 546513.5765 497304.9244 725425.8658 583871.7195 525980.8893 367960.7546 1.519049295 1.470016957 1.557779083 1.485249635 1.35151621 1.971476188 1.586777155 1.429448338 1 18.48919238 IACDEEFS(ph)DS(ph)EDEGEGGRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 199.89 2.35E-15 9689240000 1871420 2234170 2034110 2095590 2387320 1908310 2452930 1857020 2621280 TRUE FALSE 1754291.163 2399590.271 2082360.05 2149366.387 2199829.517 2459208.118 2085135.918 2088873.035 2183771.434 0.803330942 1.098828492 0.953561356 0.984245125 1.007353372 1.126128898 0.954832491 0.956543804 1 21.05839043 4.754569656 24.52703216 1.010902785 0.803330738 0.549040998 0.058913221 1868.19719 2862154.365 0.01350698 0.345998775 56828.95319 -4.754569656 -0.207572047 IACEEEFS(ph)DS(ph)EEEGEGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IACEEEFSDSEEEGEGGR 18 0 Q13547 Q13547 HDAC1 Histone deacetylase 1 2 IACEEEFS(1)DS(1)EEEGEGGR;IACEEEFS(1)DS(1)EEEGEGGR 239.58 9.33E-24 397490000 854590 830100 828740 826210 894400 753250 1028070 730970 869350 TRUE FALSE 801102.7374 891561.4677 848398.1042 847411.9474 824157.4318 970701.047 873920.4476 822233.2136 724249.8688 1.106113749 1.231013641 1.171416304 1.170054678 1.137946263 1.34028474 1.206655997 1.13528942 1 19.46612799 0.916647312 3.489300232 1.000244557 1.200226578 0.49209921 0.062478271 0.282534187 8.101622215 0.056795365 0.014679026 8.253674005 -0.916647312 0.199982021 IACEEEFS(ph)DS(ph)EEEGEGGRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IACEEEFSDSEEEGEGGRK 19 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 2 IACEEEFS(1)DS(1)EEEGEGGRK;IACEEEFS(1)DS(1)EEEGEGGRK;IACEEEFS(1)DS(1)EEEGEGGRK;IACEEEFS(1)DS(1)EEEGEGGRK;IACEEEFS(1)DS(1)EEEGEGGRK;IACEEEFS(1)DS(1)EEEGEGGRK 164.66 8.16E-11 5654620000 10813960 7179260 8164630 8150040 8914470 6778600 11622100 7267040 11047700 TRUE FALSE 10137133.55 7710819.88 8358298.879 8359183.824 8214363.485 8735471.779 9879473.999 8174345.941 9203767.499 1.101411302 0.837789512 0.908138855 0.908235005 0.892500108 0.949119128 1.073416294 0.888152155 1 23.13379311 1.992979449 21.7917017 0.999327076 0.913827606 0.070942712 0.081197608 91.78760206 284907.4863 0.02888537 0.020426389 98.39645422 -1.992979449 -0.085499469 IACKS(ph)PPPESVDTPTSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IACKSPPPESVDTPTSTK 18 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 IACKS(1)PPPESVDTPTSTK;IACKS(1)PPPESVDTPTSTK 242.71 2.86E-24 595320000 1582740 835760 1074840 969850 988740 725790 1057640 518370 744260 TRUE FALSE 1483679.129 897640.54 1100335.712 994737.993 911088.3488 935313.7908 899056.7006 583089.6356 620038.1979 2.392883428 1.447718129 1.774625686 1.604317276 1.469406807 1.508477694 1.450002119 0.940409216 1 19.24199757 7.999999996 0.114865652 0.723573596 4.712066934 0.659512415 0.234381224 66.4538303 0.528513329 1.723502255 42.2219982 99999999.03 -7.999999996 3.988493339 IACNGDASSSQIIHIS(ph)DENEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IACNGDASSSQIIHISDENEGK 22 0 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 IACNGDASSSQIIHIS(1)DENEGK;IACNGDASSSQIIHIS(1)DENEGK 286.31 2.51E-46 259060000 369200 210640 296230 245380 266660 225870 349070 245190 304230 TRUE FALSE 346092.431 226236.0048 303256.7155 251676.8662 245717.5993 291075.0023 296730.1941 275802.5112 253452.0476 1.365514441 0.892618572 1.196505289 0.992995987 0.969483583 1.148442102 1.170754772 1.08818419 1 17.95135329 IADDKYNDTFWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IADDKYNDTFWK 12 1 P14625 P14625 HSP90B1 Endoplasmin 0 ; 203.87 1.09E-07 5809200000 7971900 5652900 6501700 6607300 6359500 4713500 8812300 5619200 5115500 FALSE TRUE 7472953.009 6071446.598 6655923.394 6776854.504 5860050.523 6074210.933 7490977.424 6320769.489 4261690.003 1.753518676 1.424657024 1.561803742 1.590180069 1.375053211 1.425305672 1.757748081 1.483160316 1 22.02299422 0.96348465 24.03429281 0.999999998 1.547203057 0.644790719 0.12843832 2523.602791 1661029.668 0.118742939 0.029685735 9.193579791 -0.96348465 0.54720306 IADEGHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IADEGHPR 8 0 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 0 114.28 0.0026864 152370000 264550 324130 322100 297250 343510 269030 335200 298980 344710 FALSE TRUE 247992.2877 348128.9225 329740.3641 304877.9382 316532.1103 346694.5937 284939.8718 336308.3111 287175.6741 0.863556039 1.212250737 1.148218299 1.061642631 1.102224662 1.207256133 0.992214514 1.171089133 1 18.13157402 -1.324366963 3.936630986 0.999768187 1.105890315 0.064723958 0.106065753 0.00019615 3.37E-05 0.093349207 0.021954653 0.047384144 1.324366963 0.106122128 IADGVNEINTENMVSSIEPEKQDS(ph)PPPKPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IADGVNEINTENMVSSIEPEKQDSPPPKPPR 31 2 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 IADGVNEINTENMVSSIEPEKQDS(1)PPPKPPR;IADGVNEINTENMVSSIEPEKQDS(0.999)PPPKPPR 288.2 3.58E-73 631440000 492560 249750 318720 330640 343590 235710 412290 273660 396130 TRUE FALSE 461731.5488 268241.7499 326280.1889 339124.7822 316605.8274 303755.6506 350470.942 307827.0534 330013.3439 1.399129936 0.81282092 0.988687867 1.027609303 0.959372805 0.92043445 1.061990215 0.932771535 1 18.33216483 4.750982058 24.98531632 0.962511061 1.399130209 0.803724316 0.067738398 899.7731055 1809830.775 0.016621407 0.293203651 56361.43709 -4.750982058 0.436619147 IADGYEQAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IADGYEQAAR 10 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;; 240.46 6.54E-12 1552870000 1468340 1760870 1596030 1514740 1873850 1290560 1681120 1520900 1882410 FALSE TRUE 1376439.22 1891246.647 1633888.585 1553610.793 1726685.38 1663123.722 1429051.663 1710787.713 1568223.61 0.877705967 1.205980215 1.041872202 0.99068193 1.101045392 1.0605144 0.911255036 1.09090802 1 20.58069985 1.949385265 24.72687344 0.989616463 1.064485708 0.022556542 0.093518065 657.1368326 321030.2724 0.03614803 0.023328219 88.99902822 -1.949385265 0.074869245 IADLGNACWVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IADLGNACWVHK 12 0 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;A8MPP7;A8MPY5;E7ETV6;Q9UPE1-2;Q9UPE1-3;Q9UPE1-4;Q9UPE1;P78362;P78362-2;H7C521 H3BLV9;P78362 SRPK1;SRPK3;SRPK2 SRSF protein kinase 1;SRSF protein kinase 3;SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 0 132.79 0.00017471 240940000 460490 498270 455310 469450 573270 374110 545720 482970 575680 FALSE TRUE 431668.7529 535162.4292 466110.1682 481496.8818 528247.6867 482109.4838 463894.3522 543269.8676 479595.289 0.900068793 1.115862565 0.971882291 1.003964995 1.101444695 1.005242326 0.967262112 1.132767315 1 18.87145796 4.766794085 23.36294347 1.031590565 0.900068324 0.337307989 0.059978423 5086.331788 4208724.639 0.013485802 1.187044311 58451.28789 -4.766794085 -0.131522241 IADMGHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IADMGHLK 8 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ; 105.57 0.0043629 1322040000 2965900 5044900 2139900 2170300 5898300 1419580 2291700 4829000 4162700 FALSE TRUE 2780269.613 5418429.645 2190659.439 2225993.572 5435071.311 1829389.701 1948080.86 5431911.28 3467918.478 0.801711352 1.562444354 0.631692888 0.641881747 1.567243101 0.527518081 0.561743557 1.566331883 1 21.72563855 3.966687459 24.12122208 0.879384111 1.218997503 0.048389689 0.420864512 484.2187706 1119439.402 0.10096301 0.184744051 9261.630673 -3.966687459 0.339613391 IADPEHDHTGFLTEY(ph)VATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IADPEHDHTGFLTEYVATR 19 0 P27361;E9PQW4;P27361-3;P27361-2;E9PJF0;B3KR49 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 1 IADPEHDHTGFLTEY(1)VATR;IADPEHDHTGFLTEY(1)VATR;IADPEHDHTGFLT(0.269)EY(0.73)VATR;IADPEHDHTGFLTEY(1)VATR;IADPEHDHTGFLTEY(1)VATR 303.45 2.99E-50 4452850000 2750890 3247290 4095890 5771530 6362560 3367760 2597040 2218700 2578420 TRUE FALSE 2578716.705 3487722.73 4193046.445 5919637.231 5862870.203 4339977.641 2207637.962 2495709.579 2148065.045 1.200483529 1.623657877 1.95201093 2.755799805 2.729372752 2.020412581 1.027733293 1.161840786 1 21.03460625 1.741702396 5.645292387 1.073241669 2.042810532 0.505170776 0.458535685 0.149658046 12.12705547 0.251801768 0.130901492 55.16992529 -1.741702396 0.969568862 IADPEHDHTGFLTEYVATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IADPEHDHTGFLTEYVATR 19 0 P27361;E9PQW4;P27361-3;P27361-2;E9PJF0;B3KR49 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 ;; 229.16 5.03E-20 662980000 693210 747300 748130 707380 724290 637250 901070 686160 843440 FALSE TRUE 649823.2235 802630.8696 765875.9969 725532.5684 667407.185 821213.7301 765962.9186 771828.5864 702664.4152 0.924798822 1.142267706 1.089959845 1.032544914 0.949823516 1.168713987 1.090083548 1.098431299 1 19.42247631 2.208836551 24.99912543 1.098660791 1.052154888 0.090180167 0.075528087 568.8230657 478399.0333 0.027724555 0.020478465 161.7471179 -2.208836551 -0.046505903 IADREDEYKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IADREDEYKK 10 2 O75533;B4DGZ4;A0A494C1M2;O75533-2 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 126.71 0.00021116 1258670000 1540080 810180 984290 945150 954910 637990 1201870 852360 1198970 FALSE TRUE 1443689.142 870166.5702 1007637.824 969404.1491 879915.2205 822167.3561 1021660.751 958779.0223 998854.1614 1.445345274 0.871164784 1.008793738 0.970516204 0.880924618 0.823110508 1.022832752 0.959878889 1 19.92991453 4.743475003 24.98604074 0.941869518 1.445345482 0.854332504 0.065298612 183.4014642 932430.822 0.015157545 0.125557978 55395.5658 -4.743475003 0.503475964 IAEFTTNLTEEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IAEFTTNLTEEEEK 14 0 P35579 P35579 MYH9 Myosin-9 0 187.44 1.58E-07 0 48808 30912 33561 39090 35646 26119 44657 29193 40033 FALSE TRUE 45753.1944 33200.75664 34357.08277 40093.11558 32846.50695 33659.13129 37961.09743 32837.81031 33351.23368 1.37185913 0.995488112 1.030159277 1.202147902 0.984866325 1.009231971 1.138221686 0.984605566 1 15.02545251 4.74437382 24.93059824 1.048883321 1.371859275 0.671529471 0.072160804 373.4067508 1601350.469 0.016349404 0.147443525 55510.33135 -4.74437382 0.322975954 IAELLENVTLIHKPVSLQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IAELLENVTLIHKPVSLQPR 20 1 Q14694;Q14694-3;Q14694-2;J3KT19 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 0 119.38 3.11E-05 45486000 30982 38578 35067 38691 44185 29404 36521 31004 32059 FALSE TRUE 29042.89192 41434.35526 35898.8058 39683.87656 40714.88833 37892.45747 31045.01509 34874.91765 26708.14579 1.087417006 1.551375209 1.344114492 1.485834205 1.524437101 1.41876032 1.162380022 1.305778317 1 14.7049922 1.18350902 0.994111576 1.024638286 1.418942308 0.403156747 0.144464649 0.438813951 0.927703644 0.124303376 0.042573331 15.25840086 -1.18350902 0.394304022 IAELSGNRPLTVIMHTIFQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IAELSGNRPLTVIMHTIFQER 21 1 Q08499-10;A0A087WSZ7;A0A1B0GW84;Q08499-2;Q08499-9;Q08499-6;Q08499-11;Q08499;Q08499-3;Q08499-4;D6RHE0;Q08499-5;Q08499-8 Q08499-10 PDE4D "cAMP-specific 3,5-cyclic phosphodiesterase 4D" 0 98.132 0.00061832 31501000 33889 56072 40928 44522 52986 37026 44574 45018 36748 FALSE TRUE 31767.94798 60223.62922 41898.83149 45664.5099 48824.6933 47714.80513 37890.5425 50638.5964 30614.5214 1.0376758 1.967158932 1.368593386 1.4915964 1.594821381 1.55856773 1.237665682 1.654071143 1 14.90192851 -2.965190427 0.261379372 2.24E-05 1.5626272 0.241774809 0.253974506 74.17118895 1.891442457 41.10022156 0.317190617 0.001083452 2.965190427 1.562604808 IAELVATEFFDQGDRER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IAELVATEFFDQGDRER 17 1 O76074-2;G5E9C5;O76074;H0YA14 O76074-2 PDE5A "cGMP-specific 3,5-cyclic phosphodiesterase" 0 70.98 0.028715 9058000 3384.8 6057.9 7726.4 6741.8 8089.4 5914.5 5576.2 6270.4 8919.2 FALSE TRUE 3172.95141 6506.433219 7909.673857 6914.806002 7454.091155 7621.920136 4740.100577 7053.273243 7430.5279 0.427015611 0.875635393 1.064483434 0.930594178 1.003171141 1.025757556 0.637922452 0.949229091 1 12.85924899 4.736035828 3.833453157 0.929079924 0.378363442 0.653413297 0.117089601 0.173357365 5.051388752 0.030242789 0.268417345 54454.75746 -4.736035828 -0.550716482 IAESHLQSISNLNENQAS(ph)EEEDELGELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 550.35 0 4074270000 604949 839599 847693 860116 895768 763075 847719 822983 785028 TRUE FALSE 567086.322 901763.7836 867800.6783 882188.0327 825417.9946 983362.365 720611.4058 925734.2392 654001.7553 0.867102141 1.378840005 1.326908791 1.348907745 1.262103638 1.503608143 1.101849345 1.415491979 1 19.31893498 -1.469524705 7.712432676 0.999976692 1.287575797 0.186966335 0.179075283 6.31E-05 4.34E-06 0.152569922 0.035958167 0.033921519 1.469524705 0.287599105 IAEVDCTAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IAEVDCTAER 10 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 97.277 0.01435 206200000 175180 183440 168860 169380 193400 153260 183920 167650 191150 FALSE TRUE 164215.7965 197022.0885 172865.4389 173726.5776 178211.1441 197503.674 156342.9034 188581.4715 159245.8301 1.031209397 1.237219765 1.085525686 1.090933291 1.119094572 1.240243929 0.981770784 1.184216073 1 17.28089607 -3.055447118 0.216432503 0.757784806 1.144136865 0.145983171 0.084028021 97.30899815 2.066786059 10.83925481 0.162419133 0.000880142 3.055447118 0.386352059 IAGDYVSEEVWYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IAGDYVSEEVWYR 13 0 O95782-2;O95782;O94973-3;O94973;O94973-2;A0A0G2JQM1;A0A0G2JS82 O95782-2;O94973-3 AP2A1;AP2A2 AP-2 complex subunit alpha-1;AP-2 complex subunit alpha-2 0 ;;; 246.5 8.04E-17 510970000 427963 412310 415925 447650 418123 359206 388555 391974 256633 FALSE TRUE 401177.5598 442837.8614 425790.9374 459137.4569 385285.3062 462902.941 330294.7849 440912.8167 213799.2944 1.876421346 2.071278405 1.991545101 2.14751624 1.802088764 2.165128479 1.544882484 2.062274424 1 17.70589757 -1.603838971 0.31389846 0.220800023 2.042374186 0.725073517 0.185005574 11.47589941 0.671865402 7.08041397 0.160709336 0.024897803 1.603838971 1.821574163 IAGEASR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;; 161.89 0.0030062 35327120000 9756050 13069870 9112670 8524260 12735110 6723230 9933660 10925510 12816980 FALSE TRUE 9145436.246 14037576.77 9328826.836 8743006.943 11734945.83 8664117.358 8444199.903 12289583.97 10677743.24 0.856495239 1.314657645 0.873670272 0.818806629 1.099009928 0.811418402 0.790822528 1.150953315 1 23.34810343 3.761870722 7.998879604 0.913327666 1.111952731 0.112562467 0.163567062 0.351948546 70.8278584 0.038675469 0.069105953 5779.239886 -3.761870722 0.198625065 IAGFDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IAGFDER 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 79.454 0.075798 1017610000 1115940 1281520 1128740 1203730 1314300 934380 1414020 1127650 1274860 FALSE TRUE 1046095.307 1376405.074 1155514.246 1234619.75 1211080.18 1204120.338 1202000.828 1268439.585 1062077.63 0.984951832 1.295955244 1.087975317 1.162457164 1.140293464 1.133740419 1.131744793 1.194300255 1 20.01845779 -1.206273036 3.604124794 0.999796215 1.149410289 0.23855543 0.07826048 12222279.72 16729708.34 26640.79872 0.016775839 0.062190918 1.206273036 0.149614074 IAHFLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IAHFLDR 7 0 P60228;H0YBR5;E5RHS5;E5RIP5;E5RJ25;E5RII3 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 ; 111.65 0.0065316 825340000 821290 1448630 941170 1022460 1566760 695060 1175190 1411120 1586230 FALSE TRUE 769886.9249 1555888.072 963494.9969 1048698.055 1443712.99 895712.5386 998981.1694 1587301.438 1321477.966 0.582595355 1.177384802 0.729104096 0.793579675 1.092498723 0.67781118 0.755957493 1.20115619 1 20.33372094 1.239538685 24.99986901 1.100578122 0.849468498 0.261813104 0.186746344 35.74185973 913791.8221 0.134831181 0.042820986 17.35955888 -1.239538685 -0.251109624 IAHIMGPPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IAHIMGPPDR 10 0 A0A087WTP3;Q92945 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;;; 115.78 0.00089305 1220680000 829822 1202780 1036430 1011729 1130710 899691 1061650 990433 1203520 FALSE TRUE 777884.9223 1291835.083 1061014.609 1037691.679 1041908.598 1159417.186 902465.4384 1114090.74 1002644.737 0.775833048 1.288427531 1.058215906 1.034954497 1.039160292 1.156358921 0.90008495 1.111152035 1 19.93537908 1.748106714 25 0.996203794 1.083573351 0.01294581 0.13719926 6.124663961 16074.45405 0.058851715 0.03263623 55.98951604 -1.748106714 0.087369557 IAILTCPFEPPKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IAILTCPFEPPKPK 14 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ; 164.33 3.77E-06 207580000 689970 467660 575330 522900 590360 410620 725090 504860 734430 FALSE TRUE 646786.0093 502286.033 588977.0993 536318.4993 543995.507 529159.3281 616369.4859 567892.8823 611848.8884 1.057100898 0.820931512 0.962618566 0.876553851 0.889101079 0.86485297 1.007388422 0.928158722 1 19.22281586 1.730798465 13.47080386 0.975343272 0.904995679 0.176228065 0.066717047 0.1340366 138.0225 0.027873841 0.015327944 53.8020056 -1.730798465 -0.070347593 IAIS(ph)PLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IAISPLK 7 0 Q6MZP7-3;Q6MZP7 Q6MZP7-3 LIN54 Protein lin-54 homolog 1 IAIS(1)PLK 78.816 0.03599 76779000 226260 165240 212600 195980 170510 177210 238500 161130 236140 TRUE FALSE 212098.7905 177474.5415 217642.9724 201009.1786 157118.8324 228367.6502 202739.1391 181247.4352 196726.7085 1.078139273 0.902137503 1.106321425 1.021768626 0.798665487 1.160837041 1.030562351 0.921315853 1 17.58583331 IAIVNHDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IAIVNHDK 8 0 P61221;D6R9I9;D6RGF4 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 ; 78.516 0.030423 1422060000 1256720 3933880 2324730 2527940 3877320 2200590 2141990 3296450 2883010 FALSE TRUE 1178064.139 4225148.568 2379873.693 2592811.22 3572810.928 2835864.609 1820818.485 3708019.039 2401817.006 0.490488716 1.759146745 0.99086387 1.079520719 1.487545021 1.18071635 0.758100422 1.543839114 1 21.19569481 1.980867978 24.53043751 1.047678689 1.225854556 0 0.380435947 2086.816117 2675642.494 0.142468039 0.09353654 95.69031357 -1.980867978 0.178175867 IAIWTTECENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IAIWTTECENR 11 0 D6RBW1;P06730;P06730-3;P06730-2 D6RBW1 EIF4E Eukaryotic translation initiation factor 4E 0 ; 209.21 3.94E-08 440820000 182712 220640 215440 216322 215789 183466 248560 186406 240490 FALSE TRUE 171276.3821 236976.4152 220550.3385 221873.1888 198841.8024 236429.6559 211290.7355 209679.1994 200350.6654 0.854883021 1.182808226 1.100821593 1.107424267 0.99246889 1.180079215 1.054604611 1.046561034 1 17.61216778 1.071106478 2.25095922 1.002359603 1.085967958 0.024297632 0.095322263 0.733338958 7.535491621 0.08122456 0.02251762 11.77894728 -1.071106478 0.083608356 IAIYELLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IAIYELLFK 9 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3 P46783 RPS10 40S ribosomal protein S10 0 ; 152.59 0.00018634 235530000 759450 975360 606390 592990 1038610 409810 655410 862120 861620 FALSE TRUE 711917.3802 1047576.669 620773.8572 608207.1273 957041.7602 528115.4943 557137.355 969757.5798 717810.0557 0.991790759 1.459406511 0.864816329 0.847309288 1.333279957 0.735731535 0.77616265 1.350994698 1 19.45324261 3.889429078 5.606051923 0.9608071 1.245413042 0.139648759 0.238004257 0.303386406 14.99477719 0.057656781 0.106395744 7752.273348 -3.889429078 0.284605942 IAIYELLFKEGVMVAKKDVHMPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IAIYELLFKEGVMVAKKDVHMPK 23 3 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3 P46783 RPS10 40S ribosomal protein S10 0 132.45 1.61E-05 27427000 126790 133130 228870 287400 197060 60274 79127 32908 66745 FALSE TRUE 118854.4402 142987.0837 234298.9045 294775.1706 181583.7025 77674.12533 67262.64093 37016.63624 55604.82831 2.137484169 2.571486831 4.21364316 5.30125134 3.265610344 1.396895336 1.209654682 0.665709029 1 15.76292254 2.228439554 3.981755867 1.060808013 3.573322783 0.666089308 0.8601616 0.140957863 4.990865506 0.353404581 0.267475602 169.2152712 -2.228439554 2.512514771 IALESEGRPEEQMES(ph)DNCS(ph)GGDDDWTHLSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IALESEGRPEEQMESDNCSGGDDDWTHLSSK 31 1 Q13501;Q13501-2 Q13501 SQSTM1 Sequestosome-1 2 IALESEGRPEEQMES(1)DNCS(1)GGDDDWTHLSSK;IALES(0.001)EGRPEEQMES(0.999)DNCS(0.999)GGDDDWT(0.001)HLSSK 81.849 0.0015704 151455000 145285 103437 132045 115163 109764 113210 176585 104893 112808 TRUE FALSE 136191.8712 111095.5831 135177.1698 118118.2776 101143.5782 145891.8892 150107.7186 117989.1219 93979.61603 1.449163946 1.18212425 1.438366908 1.25684997 1.076228894 1.552378009 1.597236985 1.255475676 1 16.52006025 2.213497663 24.99998889 1.427468016 1.28756914 0 0.20064183 522.3561621 521040.2955 0.069741113 0.051528352 163.4924353 -2.213497663 -0.139898875 IALESEGRPEEQMESDNCS(ph)GGDDDWTHLSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IALESEGRPEEQMESDNCSGGDDDWTHLSSK 31 1 Q13501;Q13501-2 Q13501 SQSTM1 Sequestosome-1 1 IALESEGRPEEQMESDNCS(1)GGDDDWTHLSSK;IALESEGRPEEQMES(0.001)DNCS(0.999)GGDDDWTHLSSK;IALESEGRPEEQMES(0.025)DNCS(0.975)GGDDDWTHLSSK;IALESEGRPEEQMES(0.006)DNCS(0.994)GGDDDWTHLSSK;IALESEGRPEEQMES(0.002)DNCS(0.997)GGDDDWTHLSSK 256.56 1.16E-58 1409650000 578560 668472 749875 718260 741610 753635 1064424 704953 770295 TRUE FALSE 542348.9624 717966.3624 767662.3891 736691.7676 683366.9421 971197.1903 904823.5028 792967.9338 641727.7882 0.845138659 1.118802046 1.196243023 1.147981716 1.064886007 1.513409904 1.409980243 1.235676479 1 19.29160193 2.261374114 24.98096723 1.339918291 1.100557725 0.271774988 0.163186277 249.3288339 273016.254 0.052908806 0.044238906 182.5467538 -2.261374114 -0.239360566 IALLPLLQAETDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IALLPLLQAETDRR 14 1 U3KQP3;B4DEZ3;K7EJE1;E7ENQ6;Q9P0J0;Q9P0J0-2 U3KQP3 NDUFA13 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 0 153.81 1.01E-05 53432000 82894 93207 63553 67035 122550 84736 63828 115760 124780 FALSE TRUE 77705.81251 100108.1433 65060.50717 68755.23159 112925.4173 109197.9076 54257.58395 130212.8908 103953.4119 0.747506129 0.963009693 0.625862163 0.66140428 1.086307946 1.050450444 0.521941348 1.252608149 1 16.66557758 2.752525553 24.87279434 0.92302516 0.764442362 0.208237224 0.207593068 1660.998633 2958384.062 0.06346025 0.067004707 565.6210361 -2.752525553 -0.158582798 IALNAVDTIS(ph)Y(ph)GEFQFPPKS(ph)LNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IALNAVDTISYGEFQFPPKSLNK 23 1 Q5T0D9 Q5T0D9 TPRG1L Tumor protein p63-regulated gene 1-like protein 3 IALNAVDT(0.295)IS(0.872)Y(0.858)GEFQFPPKS(0.975)LNK 56.055 0.056851 181400000 134240 153550 170010 208920 219730 226180 230350 168290 245940 TRUE FALSE 125838.158 164919.0018 174042.7175 214281.2409 202473.2921 291474.4943 195811.156 189301.377 204891.0252 0.614171157 0.804910814 0.849440415 1.045830293 0.988199908 1.422583024 0.955684398 0.923912489 1 17.64449727 3.623303888 1.076245279 1.078300289 0.690409448 0.496751931 0.145921453 0.456213222 1.038109457 0.050823462 0.131007857 4200.528036 -3.623303888 -0.387890841 IANDNSLNHEYLPILGLAEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IANDNSLNHEYLPILGLAEFR 21 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ;; 168.75 1.04E-11 497789000 696002 1359807 834042 849460 1460159 655775 1085591 1326911 1246963 FALSE TRUE 652440.4772 1460488.525 853825.8701 871258.5817 1345484.002 845086.5969 922816.7077 1492578.759 1038836.82 0.62804905 1.405888295 0.821905668 0.838686659 1.295183206 0.813493112 0.888317289 1.436778839 1 19.98653762 1.258889918 24.99210517 1.218389807 0.982641783 0.149317689 0.254298902 410.0045987 504047.3985 0.157773383 0.057464637 18.15055538 -1.258889918 -0.235748024 IANEVIGEMNLKPEEVFLAQGTLRPDLIESASLVASGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IANEVIGEMNLKPEEVFLAQGTLRPDLIESASLVASGK 38 2 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 319.8 1.95E-110 163390000 219910 137340 168440 147340 170480 122180 208130 144250 192990 FALSE TRUE 206146.2257 147508.7965 172435.4763 151120.9938 157091.1885 157451.3826 176922.8387 162259.93 160778.7222 1.282173554 0.917464665 1.072501846 0.939931552 0.977064541 0.979304851 1.100412021 1.00921271 1 17.29471696 4.750057599 24.78723315 1.005208673 1.282173738 0.723411856 0.054831493 869.7019155 1875018.024 0.013096829 0.206032902 56241.59118 -4.750057599 0.276965066 IAQLEEELEEEQGNTELINDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IAQLEEELEEEQGNTELINDR 21 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 252.1 2.49E-36 80772000 41170 44545 47307 47187 50482 43042 56622 48801 51206 FALSE TRUE 38593.24319 47843.15815 48429.14438 48397.89831 46517.34735 55467.52667 48132.05675 54893.91227 42659.3878 0.904683475 1.121515348 1.135251744 1.134519289 1.090436355 1.300241976 1.128287564 1.286795594 1 15.38057564 5.470745272 1.173030335 1.162466025 1.45E-15 0.43243658 0.087858883 6.436207533 2.138430773 0.021870211 13.88758535 295627.8005 -5.470745272 -1.162466025 IAQLEEQLDNETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IAQLEEQLDNETK 13 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 232.42 1.83E-12 78178000 245800 187976 202141 204883 207080 149012 252280 173164 242190 FALSE TRUE 230415.8168 201893.9386 206935.88 210140.6446 190816.7721 192029.3454 214452.9561 194783.9066 201766.9244 1.141990034 1.00062951 1.025618449 1.041501947 0.945728705 0.951738477 1.062874684 0.965390671 1 17.62233017 4.739381829 24.5786996 1.003840785 1.141990086 0.580531177 0.037966024 39.95460254 1195570.683 0.008762718 0.052632665 54875.92189 -4.739381829 0.138149301 IAQNDHDLGDMSTVADPSVISHLFSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IAQNDHDLGDMSTVADPSVISHLFSHR 27 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 97.057 0.0014874 111930000 105990 131830 128300 152320 144930 114570 163420 153010 173470 FALSE TRUE 99356.2751 141590.8304 131343.3366 156228.7891 133547.7824 147644.4991 138916.6881 172113.6353 144516.7363 0.68750705 0.979753861 0.908845162 1.081042881 0.924099075 1.02164291 0.961249829 1.190959882 1 17.14087705 5.261847927 1.353891576 1.003156162 1.38E-27 0.592905238 0.082499954 3.27522729 1.996602938 0.020432147 6.378199183 182746.0197 -5.261847927 -1.003156162 IAQPGDHVSVTGIFLPILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IAQPGDHVSVTGIFLPILR 19 0 P33993;P33993-3;P33993-2;C9J8M6 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 176.42 6.74E-13 205257000 131466 299640 233340 253930 306040 234580 290540 268900 270670 FALSE TRUE 123237.7777 321825.6574 238874.935 260446.2737 282004.8529 302299.4379 246976.2242 302472.7569 225493.4284 0.546524919 1.42720637 1.059343222 1.155006048 1.25061229 1.340613073 1.095270164 1.341381694 1 17.78272586 4.750279666 24.92186571 1.211631008 0.546524503 0.701018242 0.135887789 904.7723634 1924062.26 0.029387009 0.475439418 56270.35646 -4.750279666 -0.665106505 IAQVS(ph)PGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IAQVSPGPR 9 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 IAQVS(1)PGPR;IAQVS(1)PGPR;IAQVS(1)PGPR;IAQVS(1)PGPR;IAQVS(1)PGPR 135.08 0.00024207 1642570000 2295310 2346590 2406860 2349810 2444790 1842990 2425640 1887150 2180280 TRUE FALSE 2151650.644 2520333.965 2463951.856 2410110.103 2252786.055 2375031.295 2061937.801 2122764.832 1816377.183 1.184583612 1.387560904 1.356519934 1.326877548 1.240263353 1.307565035 1.135192525 1.168680631 1 20.79263239 1.369203645 0.718244063 1.006727708 1.33507706 0.700854971 0.064172585 0.296125817 0.344019805 0.056643529 0.024251041 23.399342 -1.369203645 0.328349351 IAQVS(ph)PGPRDS(ph)PAFPDS(ph)PWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IAQVSPGPRDSPAFPDSPWR 20 1 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 3 IAQVS(1)PGPRDS(1)PAFPDS(1)PWR 89.181 0.0035591 38774000 49021 44484 51622 50852 54868 45980 61569 41489 63099 TRUE FALSE 45952.86311 47777.64165 52846.49822 52156.94841 50558.88861 59253.67958 52337.30003 46668.99298 52567.36926 0.874170874 0.908884015 1.005309928 0.992192479 0.961792255 1.127195072 0.995623345 0.887793961 1 15.68187992 4.21434705 1.467727664 1.002866824 0.868378723 0.356712092 0.05838487 0.562599689 2.005726435 0.016126015 0.083265893 16381.25045 -4.21434705 -0.134488101 IAS(ph)HDFDPTGLVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IASHDFDPTGLVQR 14 0 Q9NZN5-2 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 IAS(1)HDFDPTGLVQR;IAS(1)HDFDPTGLVQR 137.58 2.14E-05 164054000 336350 509766 400920 407880 493298 428411 411190 437231 452690 TRUE FALSE 315298.4539 547509.6051 410430.0117 418346.8913 454556.3649 552086.301 349535.8768 491820.2528 377133.1145 0.836040225 1.451767517 1.088289508 1.109281777 1.205294225 1.463903009 0.926823616 1.304102541 1 18.52471431 -1.0908978 0.5412119 0.939870936 1.187565523 0.058800837 0.20262791 70.39704217 11.51599262 6.763079559 0.080850056 0.081115192 1.0908978 0.247694587 IAS(ph)PVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IASPVSR 7 0 A0A087WU64;A6NMQ1;P09884 A0A087WU64 POLA1 DNA polymerase;DNA polymerase alpha catalytic subunit 1 IAS(0.999)PVS(0.001)R;IAS(0.991)PVS(0.009)R 149.27 0.002127 550850000 295620 261940 282810 266410 359950 277010 377680 282830 351080 TRUE FALSE 277117.6719 281334.3101 289518.3868 273246.5316 331680.979 356978.2901 321050.3902 318141.9481 292482.4799 0.947467595 0.961884316 0.989865741 0.934232135 1.13401999 1.220511704 1.09767392 1.087729932 1 18.15799068 2.734587401 24.88647532 1.121931061 0.964199972 0.631927952 0.05610678 184.1436349 1153389.43 0.016627234 0.016217705 542.7344653 -2.734587401 -0.15773109 IASEASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IASEASR 7 0 Q99880;Q96A08 Q99880 HIST1H2BL;HIST1H2BA Histone H2B type 1-L;Histone H2B type 1-A 0 ;;; 134.66 0.0073342 632549000 616872 1134890 563490 542863 1136200 416881 614300 997460 1086710 FALSE TRUE 578263.0827 1218918.436 576856.2489 556793.7836 1046967.435 537227.7772 522191.4179 1121995.077 905331.0806 0.638731062 1.346378648 0.637177118 0.615016755 1.156447025 0.593404765 0.576796079 1.239320179 1 19.78808596 3.884531429 7.818534705 0.791343341 1.035764681 0.032140891 0.292832811 0.510525085 37.70923972 0.069380521 0.125720975 7665.340105 -3.884531429 0.24442134 IASHYYITNDTVQTYNQLLKPTLSEIELFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IASHYYITNDTVQTYNQLLKPTLSEIELFR 30 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 215.71 1.08E-34 156240000 142290 133460 92977 94425 162760 75033 142100 135210 105530 FALSE TRUE 133384.3229 143341.5173 95182.45835 96848.10536 149977.4861 96693.80904 120793.4242 152091.2661 87916.36125 1.517172924 1.630430505 1.082647837 1.101593651 1.705910982 1.099838616 1.373958413 1.729954061 1 16.42384406 4.142988011 5.542620499 1.308641486 1.572400873 0.167152338 0.25369996 0.349360837 17.32718559 0.058826173 0.131816419 13899.14261 -4.142988011 0.263759387 IASLEVENQSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 267.31 1.82E-21 923403000 533249 693802 620440 609759 723260 576611 654043 598946 704270 FALSE TRUE 499873.897 745171.822 635157.1298 625406.4483 666458.0771 743069.2352 555975.324 673725.7265 586722.7872 0.851976279 1.270057748 1.082550642 1.065931752 1.135899426 1.266474136 0.947594564 1.14828628 1 19.1623195 1.715371618 24.99999376 1.034196107 1.126093712 0.075564569 0.12599386 1.95213883 2095.711677 0.052970775 0.029375003 51.92441567 -1.715371618 0.091897605 IATPFQVYSWTAPQAEHAMDCVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IATPFQVYSWTAPQAEHAMDCVR 23 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ; 213.2 1.73E-25 183287000 174590 199983 174317 155295 213380 162182 221521 184510 204122 FALSE TRUE 163662.7236 214789.9494 178451.8816 159280.1326 196621.9955 209001.3106 188305.9826 207546.4797 170052.7195 0.962423441 1.263078591 1.049391518 0.936651487 1.156241406 1.229038331 1.107338848 1.220483155 1 17.37562255 IATPQIVINYAMFLEEHKYFEESFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IATPQIVINYAMFLEEHKYFEESFK 25 1 Q9HCS7 Q9HCS7 XAB2 Pre-mRNA-splicing factor SYF1 0 145.25 1.71E-07 10462000 50762 36707 40795 40082 62029 34608 51693 42719 43215 FALSE TRUE 47584.89703 39424.82447 41762.67666 41110.57198 57157.49255 44598.76779 43942.11454 48052.56119 36002.13732 1.321724225 1.095068999 1.160005482 1.141892539 1.58761387 1.238781114 1.220541829 1.334714124 1 15.13579494 IAVDEVHCCSQWGHDFRPDYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IAVDEVHCCSQWGHDFRPDYK 21 1 P46063 P46063 RECQL ATP-dependent DNA helicase Q1 0 184.78 2.47E-17 256050000 380610 381890 404720 390080 382490 287880 514400 378060 453070 FALSE TRUE 356788.2995 410165.533 414320.1495 400090.1132 352450.7783 370986.2827 437270.4955 425261.6232 377449.6901 0.945260544 1.086676036 1.09768311 1.059982625 0.93376889 0.982876109 1.158486831 1.126671009 1 18.52592484 1.738388918 24.99999977 1.108470365 1.033290929 0.189960494 0.068720968 0.077999171 5903.175627 0.032526644 0.018037521 54.75060442 -1.738388918 -0.075179436 IAVMELFRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IAVMELFRPK 10 1 Q16531;F5GY55;Q16531-2;F5H2L3;F5GWI0;F5GZY8;F5GYG8;F5H198 Q16531 DDB1 DNA damage-binding protein 1 0 ; 170.99 3.79E-06 333610000 608680 779980 582900 534570 926290 357620 741990 787690 1065170 FALSE TRUE 570583.8053 837730.5308 596726.6633 548287.9712 853542.9199 460859.0885 630735.4878 886034.8304 887386.2457 0.642993745 0.944042726 0.672454262 0.617868458 0.961861787 0.519344413 0.710778977 0.998477083 1 19.75920267 1.2354311 24.96454513 0.999238728 0.73382622 0.410313723 0.136702942 81.72667287 651887.4503 0.107515745 0.031295166 17.19614505 -1.2354311 -0.265412508 ICANHYITPMMELKPNAGSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ICANHYITPMMELKPNAGSDR 21 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ; 174.2 1.99E-12 4036200000 2676400 2380700 2574500 2518400 2855800 2115590 3071900 2427900 3333300 FALSE TRUE 2508888.902 2556969.505 2635568.356 2583026.408 2631516.988 2726326.489 2611297.113 2731028.659 2776950.696 0.903469012 0.920783184 0.949087198 0.930166463 0.947628271 0.981769858 0.940346948 0.983463143 1 21.40507013 7.999999994 0.09456342 1.034434098 0.67500915 0.784080495 0.013970966 63.73327094 0.430152876 0.200628762 2.970736797 99999998.56 -7.999999994 -0.359424949 ICDDELILIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ICDDELILIK 10 0 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;; 154.84 3.20E-05 166057000 417101 363700 396930 383719 400018 314226 455126 357444 417927 FALSE TRUE 390995.393 390628.7264 406345.367 393565.8792 368602.1999 404937.9452 386884.0815 402071.6702 348172.2838 1.122994021 1.121940903 1.167081316 1.130376821 1.058677606 1.163039001 1.111185753 1.154806655 1 18.40944184 -1.811651774 2.498406212 0.956116124 1.129693062 0.630531011 0.03096895 4835791.45 3188832.137 1281405.473 0.007437658 0.015429371 1.811651774 0.173576938 ICDECNYGSYQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ICDECNYGSYQGR 13 0 Q7RTV0 Q7RTV0 PHF5A PHD finger-like domain-containing protein 5A 0 ; 243.91 1.21E-16 421980000 159356 158498 147473 161553 180075 145318 181455 147513 173710 FALSE TRUE 149382.1924 170233.3568 150971.1292 165698.7235 165932.6359 187268.9476 154247.5073 165930.3228 144716.6788 1.032238949 1.176321612 1.043218587 1.144987052 1.1466034 1.294038456 1.065858535 1.146587416 1 17.14287168 -1.224414562 3.807324385 0.999855033 1.130707697 0.230762248 0.075293616 8.60E-05 1.75E-05 0.067371951 0.015862069 0.059646565 1.224414562 0.130852664 ICDPGLTSFEPEALGNLVEGMDFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ICDPGLTSFEPEALGNLVEGMDFHK 25 0 Q13555-8;Q13555-9;Q13555-10;Q13555-3;Q13555-7;Q13555-4;Q13555-2;A0A2Q3DQE3;Q13555;Q8WU40;Q5SWX3;Q13555-6;Q13555-11;Q13555-5;H0Y6G2 Q13555-8 CAMK2G Calcium/calmodulin-dependent protein kinase type II subunit gamma 0 ; 170.18 8.90E-12 143712000 162443 159746 167840 156608 184291 137924 198160 171556 223171 FALSE TRUE 152275.9826 171573.7601 171821.2441 160626.8264 169817.5283 177740.4198 168447.7476 192975.1442 185922.3184 0.819030141 0.922824982 0.924156097 0.863945909 0.91337893 0.955992919 0.906011441 1.037934262 1 17.50434044 1.24416073 24.99930624 1.018967151 0.907102985 0.617165491 0.038452946 79.82159952 356342.0093 0.025573397 0.008757371 17.54529722 -1.24416073 -0.111864165 ICDQISDAVLDAHLQQDPDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ICDQISDAVLDAHLQQDPDAK 21 0 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ;;; 283.75 3.49E-45 1578260000 1523520 991220 1252700 1129740 1108950 926090 1426640 1092430 1150650 FALSE TRUE 1428165.603 1064610.96 1282414.636 1158731.041 1021857.54 1193437.149 1212728.576 1228822.29 958599.0815 1.489846621 1.110590424 1.337800818 1.208775455 1.065990527 1.244980485 1.265105089 1.281893874 1 19.87056803 -2.258887881 2.29218379 0.056001898 1.240697863 0.310408956 0.116564191 2696101.067 773469.2148 13048884.69 0.026294889 0.005509499 2.258887881 1.184695965 ICDQWDALGSLTHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ICDQWDALGSLTHSR 15 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ; 228.51 5.87E-13 1168460000 1542700 1695090 1570460 1436000 1458960 1340020 2020090 1713320 1745870 FALSE TRUE 1446145.161 1820596.227 1607712.053 1472850.191 1344379.167 1726862.021 1717196.258 1927231.773 1454473.018 0.994274313 1.251722242 1.105357083 1.012634936 0.924306708 1.187276765 1.180631223 1.325037831 1 20.4720651 2.084357452 24.62703231 1.187551577 1.085847035 0.169616738 0.116362631 42.99457605 12545.32586 0.043640082 0.032230344 121.4387958 -2.084357452 -0.101704542 ICGDIHGQYTDLLR ddPTM_SK-BR-3_Pertuzumab_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 ;; 195.78 2.58E-08 902300000 1810950 2569970 1933830 1836520 2757380 1504100 2060810 2315670 2643620 FALSE TRUE 1697605.872 2760253.253 1979701.361 1883648.212 2540826.498 1938309.253 1751810.672 2604786.497 2202382.744 0.770804202 1.25330316 0.898890698 0.855277412 1.153671634 0.880096459 0.795416091 1.182712907 1 21.07063378 3.736289773 24.20420132 0.946762675 1.055391621 0 0.169800038 620.3856302 1637754.312 0.040565654 0.071792634 5448.660812 -3.736289773 0.108628946 ICGDIHGQYYDLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 140.27 9.99E-06 648050000 1064120 2074410 1084650 1151800 2045030 864320 1089020 1759730 1610080 FALSE TRUE 997518.6287 2228001.475 1110378.41 1181357.138 1884421.593 1113835.153 925731.561 1979436.164 1341347.246 0.743669196 1.661017668 0.82780832 0.880724317 1.404872301 0.830385387 0.690150566 1.475707479 1 20.35525134 3.803589757 8.800974348 0.984224344 1.262566676 0.038677517 0.332032112 0.672045313 71.40682662 0.079165796 0.142967753 6361.94275 -3.803589757 0.278342332 ICHQIEYYFGDFNLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ICHQIEYYFGDFNLPR 16 0 P05455;E7ERC4;E9PFL9 P05455 SSB Lupus La protein 0 ; 256.26 1.24E-26 1224750000 567260 674080 552680 513270 727480 535330 716700 589460 681320 FALSE TRUE 531756.2092 723989.5846 565789.8306 526441.3772 670346.6553 689871.0806 609237.4885 663055.3786 567603.2905 0.936844832 1.275520415 0.996805057 0.927481193 1.181012631 1.215410644 1.073350875 1.168166904 1 19.11452343 ICLTDHFKPLWAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ICLTDHFKPLWAR 13 1 Q9Y3C8 Q9Y3C8 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 0 ; 205.02 4.40E-08 525310000 630060 1403350 656650 606320 1436620 374730 660410 1255690 1274450 FALSE TRUE 590625.6693 1507255.494 672226.0481 621879.1977 1323793.66 482908.4678 561387.6514 1412465.661 1061736.062 0.556282951 1.41961411 0.633138566 0.585719201 1.246819909 0.45482911 0.528745016 1.330335958 1 20.01799374 5.013160794 17.30423129 0.86524459 0.034342266 0.079692332 0.3497737 113667565.1 2746183872 0.081884387 2320486173 103076.7684 -5.013160794 -0.830902324 ICQGCPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 86.794 0.015781 119628000 156969 185426 177682 185518 225323 165794 238503 197803 237950 FALSE TRUE 147144.5905 199155.134 181896.7009 190278.706 207627.0405 213656.0364 202741.6893 222499.14 198234.6078 0.742274985 1.00464362 0.917582974 0.959866232 1.047380388 1.077793826 1.022736098 1.122403108 1 17.59684932 6.26361064 0.42355034 1.053647426 8.87E-16 0.633797017 0.062956891 12.47384067 0.631370309 0.04052434 8.699313097 1834892.561 -6.26361064 -1.053647426 ICRDPQT(ph)PVLQTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ICRDPQTPVLQTK 13 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 ICRDPQT(1)PVLQTK;ICRDPQT(1)PVLQTK;ICRDPQT(1)PVLQTK;ICRDPQT(1)PVLQTK;ICRDPQT(1)PVLQTK 181.72 1.91E-05 2502930000 2651540 2827350 2589560 2563850 3419550 1443420 3989980 2638660 6355780 TRUE FALSE 2485584.845 3036689.936 2650985.586 2629642.732 3150992.337 1860111.922 3391719.54 2968102.509 5294959.258 0.469424735 0.573505817 0.500662131 0.496631344 0.595092839 0.351298628 0.640556306 0.560552474 1 22.33618815 0.314342617 0.994030134 1.002010311 0.514970798 0.797109712 0.076319421 1.175420151 1.363857404 0.069180038 0.020612271 2.062256194 -0.314342617 -0.487039514 ICS(ph)FEEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ICSFEEAK 8 0 P16298-3;P16298;P16298-4;Q5F2G0 P16298-3 PPP3CB Serine/threonine-protein phosphatase 2B catalytic subunit beta isoform 1 ICS(1)FEEAK 85.807 0.018383 0 221440 127110 138150 150700 132750 93575 187740 98712 195930 TRUE FALSE 207580.4657 136521.3567 141426.9832 154567.2171 122324.3505 120588.5834 159590.1299 111036.4105 163228.0172 1.271720806 0.836384335 0.866438162 0.946940481 0.749407807 0.738773805 0.97771285 0.68025338 1 17.31652918 4.739712085 24.82842463 0.850253133 1.271720954 0.613173062 0.10539354 55.83009984 1203669.7 0.022328032 0.13800805 54917.66775 -4.739712085 0.421467821 ICSWNVDGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 96.665 0.015321 76713000 62007 224350 31477 45883 244250 38173 50806 175950 195560 FALSE TRUE 58126.09256 240961.1074 32223.6493 47060.43546 225067.5903 49192.92541 43188.11196 197917.7448 162919.7726 0.356777398 1.479016964 0.19778845 0.288856501 1.381462708 0.301945704 0.265088216 1.214817217 1 17.31380218 1.216562469 24.99945787 1.107409059 0.636377881 0.164495789 0.462994464 538.5862585 612052.1282 0.432931817 0.10859208 16.46502782 -1.216562469 -0.471031178 ICTEQSNS(ph)PPPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ICTEQSNSPPPIR 13 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 ICTEQSNS(1)PPPIR;ICTEQS(0.002)NS(0.998)PPPIR;ICTEQS(0.021)NS(0.979)PPPIR 221.73 1.96E-11 510536000 729850 700610 742000 707190 786610 627120 806320 699120 864110 TRUE FALSE 684169.9913 752483.8934 759600.5904 725337.6927 724832.8236 808159.3636 685419.8015 786406.671 719884.4586 0.950388612 1.04528426 1.055170147 1.007575152 1.006873832 1.122623713 0.952124738 1.09240679 1 19.45740585 4.743062418 24.25524758 1.034733861 0.95038856 0.232528146 0.048447258 433.5031672 2335541.023 0.010264565 0.080593855 55342.96442 -4.743062418 -0.084345301 ICYIFHETFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ICYIFHETFGR 11 0 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;O00429-7;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 0 ; 206.49 2.62E-08 507920000 781020 1325410 973350 866510 1354330 870130 1149060 1168200 1016650 FALSE TRUE 732137.3524 1423544.735 996438.3216 888746.1136 1247966.385 1121322.406 976769.1204 1314052.342 846964.5472 0.864425028 1.680760712 1.176481737 1.049330951 1.473457642 1.323930747 1.153258567 1.55148447 1 19.69194206 -0.993344914 7.028415024 0.999999982 1.299526335 0.116845188 0.242238482 8.53E-08 1.26E-08 0.211971386 0.04996213 0.101544192 0.993344914 0.299526353 IDAHLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDAHLNK 7 0 A0AVT1;A0AVT1-2;H0Y8S8 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 76.035 0.041852 13221600000 45939000 46771000 43283000 41898000 56562000 31787000 52409000 46678000 58175000 FALSE TRUE 43063759.99 50233973.51 44309693.2 42973173.61 52119848.68 40963390.88 44550756.99 52505851.05 48465216.68 0.888549829 1.036495387 0.914257611 0.886680728 1.075407318 0.845212168 0.919231565 1.083371842 1 25.53044637 1.24510143 24.99999058 1.041685931 0.942453634 0.261711549 0.072112874 189.0239455 722499.6119 0.04751167 0.016446688 17.58334227 -1.24510143 -0.099232296 IDASKNEEDEGHS(ph)NS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 2 IDASKNEEDEGHS(0.9)NS(0.593)S(0.506)PR;IDASKNEEDEGHS(0.976)NS(0.55)S(0.473)PR 63.559 0.024148 494300000 619010 502030 532170 586560 673940 395570 694550 487770 1025100 TRUE FALSE 580267.2691 539200.8236 544793.3237 601612.1226 621011.4709 509764.6375 590408.6754 548669.1582 854004.1876 0.679466538 0.631379601 0.637928164 0.70446039 0.727176143 0.596911168 0.691341663 0.64246659 1 19.70388362 -1.468991923 3.219248081 1.00661533 0.661018653 0.882280985 0.038570859 99998659.07 117316157.6 5854782.74 0.008893831 0.033963159 1.468991923 -0.345596677 IDASKNEEDEGHSNS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 IDASKNEEDEGHS(0.008)NS(0.619)S(0.373)PR;IDASKNEEDEGHSNS(0.862)S(0.138)PR 189.07 2.10E-14 14103950000 5666650 4901870 5035310 4922660 5843230 3414470 5979390 3980390 8585320 TRUE FALSE 5311984.492 5264809.555 5154749.931 5048983.79 5384326.286 4400172.06 5082835.979 4477350.453 7152374.629 0.742688235 0.736092533 0.720704689 0.705917133 0.75280261 0.615204361 0.710650133 0.625994958 1 22.76999087 -0.822586209 12.10641653 1 0.704408533 0.804783617 0.046216964 0 0 0.042154882 0.009936001 0.150457482 0.822586209 -0.295591467 IDASKNEEDEGHSNSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 IDASKNEEDEGHSNS(0.254)S(0.746)PR;IDASKNEEDEGHSNS(0.25)S(0.75)PR;IDASKNEEDEGHS(0.037)NS(0.022)S(0.941)PR;IDASKNEEDEGHSNS(0.374)S(0.626)PR;IDASKNEEDEGHSNS(0.047)S(0.953)PR;IDASKNEEDEGHS(0.001)NS(0.454)S(0.545)PR;IDASKNEEDEGHSNS(0.044)S(0.955)PR;IDASKNEEDEGHSNS(0.232)S(0.768)PR 246.5 1.64E-24 40576240000 41584720 34350810 36097030 36944750 43837140 25591050 44512660 31664220 66015960 TRUE FALSE 38982006.61 36894179.71 36953268.6 37892814.83 40394347.85 32978770.7 37838399.87 35617567.57 54997469.8 0.708796364 0.670834128 0.671908521 0.688991966 0.734476477 0.599641598 0.688002557 0.647621931 1 25.71286191 -1.903361751 2.480624134 1.187103483 0.675055159 0.890106219 0.035744058 3442322.309 1856195.311 3755912.885 0.007716303 0.01249218 1.903361751 -0.512048324 IDASKNEEDEGHSNSSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;;;; 234.49 5.46E-24 3501080000 5069690 4840060 4809970 4973810 5607490 3452210 6001130 4196630 8595720 FALSE TRUE 4752387.153 5198423.078 4924064.76 5101446.385 5167100.355 4448806.985 5101316.268 4720588.493 7161038.802 0.663644938 0.725931422 0.687618779 0.712389156 0.721557374 0.621251624 0.712370986 0.659204429 1 22.77173745 -1.960781873 2.564484405 1.244600391 0.691647448 0.89873127 0.032894057 3517317.891 1803961.015 5119631.695 0.007234175 0.01094506 1.960781873 -0.552952943 IDASQFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDASQFR 7 0 Q66K14-2;Q66K14;G3V133 Q66K14-2 TBC1D9B TBC1 domain family member 9B 0 ; 102.98 0.044286 0 368149 505370 413050 414320 487450 594160 331700 438160 339770 FALSE TRUE 345107.2113 542788.1206 422847.7411 424952.1526 449167.6433 765684.3466 281964.6644 492865.2405 283060.192 1.219200795 1.917571372 1.4938439 1.501278402 1.586827311 2.70502306 0.996129701 1.741202947 1 18.11074935 0.671683356 1.153729983 1.009663377 1.676842921 0.157481109 0.456528745 1.895219078 4.104566419 0.39418258 0.121850451 4.695516335 -0.671683356 0.667179544 IDDDDDERENFEITDWDLQNEFNPNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDDDDDERENFEITDWDLQNEFNPNR 26 1 Q9UBB9;F6XM96;F6UKU9;F6SQZ1;F6UQ07 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 0 ; 150.53 1.23E-07 97021000 57442 50034 55836 51995 53488 43699 67457 48642 60889 FALSE TRUE 53846.80776 53738.56942 57160.45629 53329.27973 49287.26824 56314.19191 57342.44909 54715.06077 50726.23254 1.061517977 1.059384203 1.126842137 1.051315602 0.971632739 1.110159164 1.130429882 1.078634427 1 15.63044439 IDDIFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IDDIFER 7 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;;; 157.21 0.0034697 417876000 633927 699818 689205 661893 776527 538895 730412 640922 752514 FALSE TRUE 594250.6407 751633.2529 705553.2681 678878.295 715541.7018 694465.2383 620893.5014 720942.5225 626914.552 0.947897347 1.19894051 1.125437695 1.082888079 1.141370382 1.107751026 0.99039574 1.149985305 1 19.25790929 1.921767758 10.92111009 1.046440401 1.11644266 0.076663226 0.076783255 1.276855171 174.4279359 0.029420292 0.018774715 83.51562923 -1.921767758 0.070002258 IDDIVSGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IDDIVSGHK 9 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;;; 160.36 6.54E-05 2074950000 5213500 4172550 4963480 4760500 4879180 3840570 5504060 4177520 4156650 FALSE TRUE 4887196.341 4481489.944 5081216.09 4882662.49 4495988.884 4949280.213 4678777.3 4699092.568 3462878.262 1.411310468 1.294151744 1.467338932 1.410001196 1.298338707 1.42923887 1.351123818 1.356990403 1 21.72354024 -0.289327868 0.82481513 0.985167393 1.38239603 0.82795425 0.054226447 4.392969725 2.336392206 0.265129517 0.016809494 0.513655724 0.289327868 0.397228637 IDDRDS(ph)DEEGASDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IDDRDSDEEGASDR 14 1 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 IDDRDS(0.994)DEEGAS(0.006)DR;IDDRDS(0.997)DEEGAS(0.003)DR;IDDRDS(0.998)DEEGAS(0.002)DR;IDDRDS(0.988)DEEGAS(0.012)DR 252.37 8.81E-24 1867230000 2058719 1705620 1946592 1876315 1923615 1519720 2158177 1695664 2014014 TRUE FALSE 1929867.453 1831905.879 1992766.081 1924464.419 1772542.037 1958438.493 1834578.394 1907371.383 1677862.052 1.15019435 1.09180959 1.187681716 1.146974161 1.056428945 1.167222592 1.0934024 1.13678677 1 20.67819268 -5 0.268649486 0.118803578 1.138088976 0.52334815 0.038784831 161.8813135 1.575466468 79.0005418 0.044750774 1.00E-05 5 1.019285398 IDDVVNTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IDDVVNTR 8 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;;; 165.72 0.00075059 2596040000 2270170 2442640 2441130 2380940 2552510 2049620 2676700 2194290 2440230 FALSE TRUE 2128084.112 2623495.607 2499034.756 2442038.951 2352046.161 2641312.021 2275353.684 2468251.937 2032939.849 1.046801318 1.290493474 1.229271372 1.201235223 1.156967907 1.299257341 1.119242995 1.21412935 1 20.9551361 -0.206876586 0.583297763 0.981171037 1.212913151 0.375024176 0.076557721 5.861013496 1.983107564 0.317714621 0.02903794 0.621045492 0.206876586 0.231742115 IDEDGENTQIEDTEPMS(ph)PVLNSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 285.61 1.61E-52 709140000 432372 304398 352026 360662 375962 261691 462603 324549 439752 TRUE FALSE 405310.6083 326935.9446 360376.223 369917.1975 346435.4611 337236.9435 393239.9747 365069.6571 366354.5503 1.106334309 0.892403123 0.98368158 1.009724588 0.945628929 0.92052069 1.073386353 0.99649276 1 18.48288101 1.737584246 25 1.028002187 0.967633793 0.103782302 0.060980146 0.233411022 5600.24493 0.025950302 0.014390695 54.64925504 -1.737584246 -0.060368394 IDEDGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDEDGKK 7 1 O75821;K7ENA8;K7ER90;K7EL20;K7EL60 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 81.296 0.044231 281720000 1745100 956960 1394400 1546600 1624900 1153200 2227200 1468500 2114400 FALSE TRUE 1635877.306 1027814.314 1427475.826 1586288.374 1497286.909 1486110.119 1893252.036 1651845.458 1761492.98 0.928687951 0.58349044 0.810378379 0.900536302 0.850010148 0.843665082 1.074799649 0.937753074 1 20.7483673 2.61275143 0.733559378 1.010663421 0.725945912 0.395154913 0.101550893 0.542475178 0.609113505 0.072046173 0.062826342 409.9693884 -2.61275143 -0.28471751 IDENS(ph)DKEMEVEES(ph)PEKIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDENSDKEMEVEESPEKIK 19 2 Q8N3X1-2;Q8N3X1 Q8N3X1-2 FNBP4 Formin-binding protein 4 2 IDENS(1)DKEMEVEES(1)PEKIK;IDENS(1)DKEMEVEES(1)PEKIK 82.342 0.0024637 113369000 501670 103356 217235 196023 199641 123244 276820 130130 233146 TRUE FALSE 470271.3702 111008.5858 222387.9168 201053.282 183962.0012 158822.5421 235313.4109 146377.017 194232.4264 2.421178476 0.571524476 1.144957724 1.035116977 0.947123014 0.81769324 1.211504254 0.753617816 1 17.56742455 4.74766706 24.99954556 0.948825738 2.421179239 0.861545198 0.187140452 421.085075 1155963.236 0.04279257 0.53227359 55932.86424 -4.74766706 1.472353501 IDEPLEGSEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 IDEPLEGSEDR 11 0 P61978;P61978-2;S4R359;P61978-3 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;; 232.75 2.37E-13 14077549000 3412870 3202758 3339120 3209500 3322527 2846376 3644490 2816310 3242270 FALSE TRUE 3199264.559 3439893.535 3418325.503 3291861.204 3061589.132 3668078.544 3098032.558 3167932.503 2701114.191 1.184424031 1.273509112 1.265524247 1.218704938 1.133454166 1.357987217 1.146946163 1.172824353 1 21.3651232 0.803395393 1.074004918 1.000861918 1.240738054 0.562076847 0.063546148 0.517214639 1.126826567 0.054875132 0.01747358 6.359096174 -0.803395393 0.239876136 IDESIHLQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDESIHLQLR 10 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 154.24 1.48E-05 125490000 64865 103110 82897 104810 98531 67850 95285 95126 89876 FALSE TRUE 60805.21544 110744.3717 84863.35599 107499.602 90792.77271 87437.19355 80997.89883 107002.6905 74875.11498 0.812088442 1.479054446 1.133398673 1.435718691 1.212589426 1.167773747 1.081773281 1.429082153 1 16.19219869 2.475804082 21.99083488 1.169035598 1.253322402 0 0.210054495 37.78656811 630733.8884 0.065275254 0.055168964 299.0915076 -2.475804082 0.084286804 IDFDSVSSIMASS(ph)Q ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IDFDSVSSIMASSQ 14 0 Q9UBQ5;A0A087WVB9;K7ERF1;K7EK53 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 1 IDFDSVSSIMAS(0.028)S(0.972)Q;IDFDSVSSIMAS(0.196)S(0.804)Q;IDFDSVSSIMAS(0.028)S(0.972)Q 174.59 2.64E-06 112884000 237241 271055 263666 256658 310572 252389 355066 252362 287790 TRUE FALSE 222392.5093 291124.1942 269920.282 263244.2788 286180.9279 325249.6071 301827.1496 283869.9512 239755.9898 0.927578533 1.214252017 1.125812466 1.097967475 1.193634112 1.35658595 1.258893051 1.183995242 1 17.87120733 2.5703128 5.046231582 1.235135801 1.11855853 0.127304545 0.115248842 0.359327569 14.7818954 0.035049951 0.032663721 371.8029229 -2.5703128 -0.11657727 IDFIPVS(ph)PAPS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDFIPVSPAPSPTR 14 0 Q96E09 Q96E09 FAM122A Protein FAM122A 2 IDFIPVS(1)PAPS(0.994)PT(0.006)R 159.22 7.23E-06 13247000 44240 42334 42291 39098 39464 38957 49286 40313 41100 TRUE FALSE 41471.09737 45468.45341 43294.16249 40101.32087 36364.65663 50203.25349 41896.02185 45346.16679 34240.14448 1.211183481 1.327928199 1.26442698 1.171178495 1.062047406 1.466210328 1.223593606 1.324356759 1 15.06340117 -0.96027468 4.68443243 0.999997513 1.261704631 0.362805671 0.106564361 0.009921593 30903283.6 260.9002872 0.023170292 0.109578492 0.96027468 0.261707118 IDFSSIAVPGT(ph)SSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDFSSIAVPGTSSPR 15 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 1 IDFSSIAVPGT(0.409)S(0.295)S(0.295)PR 95.755 0.044299 523710000 207250 218070 213690 257970 262500 197240 234740 178830 220820 TRUE FALSE 194278.5925 234216.1297 218758.8277 264589.9469 241884.3089 254179.9861 199542.9162 201157.3192 183963.7154 1.056070171 1.273164815 1.189141169 1.438272467 1.314847921 1.381685434 1.084686269 1.093461929 1 17.48906172 1.619869274 6.328638134 1.060703017 1.272665238 0.484154394 0.105366375 0.117318466 9.981974951 0.054788631 0.026516657 41.67439214 -1.619869274 0.211962221 IDFSSIAVPGTS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDFSSIAVPGTSSPR 15 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 1 IDFSS(0.001)IAVPGT(0.014)S(0.493)S(0.493)PR 127.83 7.94E-05 342330000 712390 749840 772260 817500 933300 626000 795010 600990 721740 TRUE FALSE 667802.7816 805358.9338 790578.3719 838478.434 860002.3828 806716.0377 675805.631 676024.9244 601276.9314 1.110640949 1.339414323 1.314832369 1.394496263 1.430293327 1.341671359 1.123950705 1.124315418 1 19.19767008 1.656986942 3.615834326 1.078422709 1.330557435 0.617432592 0.089166661 0.124299505 3.830570562 0.050827709 0.022865236 45.39279685 -1.656986942 0.252134726 IDFSSIAVPGTSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDFSSIAVPGTSSPR 15 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 1 IDFSSIAVPGTS(0.005)S(0.995)PR;IDFSSIAVPGTS(0.207)S(0.792)PR 265.73 3.25E-25 1557260000 2037220 2066260 2230490 2507400 2666100 1785910 2242700 1760470 1945410 TRUE FALSE 1909714.037 2219248.04 2283398.276 2571744.129 2456715.261 2301473.225 1906427.955 1980268.555 1620708.503 1.178320489 1.369307334 1.408888934 1.586802392 1.515827958 1.420041433 1.176292931 1.221853622 1 20.6281932 1.674506766 3.369473083 1.132585966 1.419426343 0.561315257 0.117371813 0.159735112 4.23247665 0.070193789 0.031595825 47.26141994 -1.674506766 0.286840377 IDFTPVS(ph)PAPS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDFTPVSPAPSPTR 14 0 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3;Q7Z309-5 G1UD79 SPACIA2;FAM122B Protein FAM122B 2 IDFTPVS(1)PAPS(0.998)PT(0.002)R 168.45 5.10E-06 46527000 105580 102610 109330 103290 107550 101240 135640 105880 107760 TRUE FALSE 98971.93627 110207.3512 111923.3592 105940.5963 99103.45684 130466.3445 115302.0412 119099.3511 89774.15984 1.102454609 1.2276066 1.246721322 1.18007895 1.103919625 1.453272798 1.284356673 1.326655145 1 16.45401263 2.267777508 24.99997723 1.295027638 1.190245773 0.09894575 0.121584582 364.0511623 311506.0056 0.037767881 0.03159423 185.2582291 -2.267777508 -0.104781865 IDFYFDENPYFENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IDFYFDENPYFENK 14 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;;; 321.71 7.20E-56 1893857000 3071900 2426040 2730800 2497070 2841500 2073240 3268630 2384900 3168630 FALSE TRUE 2879635.262 2605666.526 2795575.866 2561149.044 2618340.052 2671750.732 2778529.276 2682660.015 2639765.183 1.090867961 0.987082693 1.059024448 0.97021851 0.991883698 1.012116816 1.052566832 1.016249488 1 21.33197817 0.981853687 23.70958301 0.999999995 1.02228083 0.03908882 0.036435966 2572.912467 3361714.732 0.032353042 0.00808826 9.590774649 -0.981853687 0.022280835 IDGATQSS(ph)PAEPK ddPTM_SK-BR-3_Pertuzumab_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(0.009)S(0.991)PAEPK;IDGATQS(0.004)S(0.996)PAEPK;IDGATQS(0.078)S(0.922)PAEPK;IDGATQS(0.024)S(0.976)PAEPK;IDGATQS(0.008)S(0.992)PAEPK 265.36 2.71E-24 2244870000 4095030 2361234 3141150 2748320 2948510 2266374 3584300 2361781 3543160 TRUE FALSE 3838729.382 2536062.222 3215659.561 2818846.544 2716945.918 2920639.382 3046867.49 2656654.557 2951783.706 1.300477868 0.85916262 1.08939539 0.954963786 0.920442075 0.989448982 1.032212314 0.900016675 1 21.49315558 4.751650827 24.82227696 0.975398444 1.300478099 0.711336805 0.066380001 1084.504095 2056448.186 0.014969846 0.281943771 56448.2948 -4.751650827 0.325079655 IDGDKDGFVTVDELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDGDKDGFVTVDELK 15 1 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-9;O43852-13;O43852-14;O43852-11 O43852 CALU Calumenin 0 ; 202.34 5.43E-09 330500000 1124400 451279 704531 675351 604020 532871 993330 542422 482032 FALSE TRUE 1054025.811 484692.1667 721242.808 692681.65 556582.7057 686702.2073 844389.3881 610144.5807 401577.7452 2.624711712 1.20696969 1.796022854 1.724900492 1.385989917 1.710010616 2.102679738 1.519368511 1 18.61531979 -1.971602645 1.32916177 0.333948201 1.72650572 0.267029701 0.391879219 25486.87315 5823.773649 52206.36905 0.101934025 0.010675724 1.971602645 1.392557518 IDGDKDGFVTVDELKDWIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDGDKDGFVTVDELKDWIK 19 2 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-13;O43852-14;O43852-11 O43852 CALU Calumenin 0 ; 171.07 6.18E-12 997870000 3570000 1873580 2445200 2480800 2653000 1433080 3213700 1933530 3426600 FALSE TRUE 3346560.073 2012301.813 2503201.299 2544461.528 2444644.082 1846786.932 2731835.52 2174935.477 2854678.323 1.172307242 0.704913684 0.876876837 0.891330385 0.856364117 0.646933462 0.9569679 0.761884608 1 21.44489676 -1.490945934 3.237649688 1.003451579 0.846072798 0.080872597 0.144721843 34596544.61 39104321.35 1043172.941 0.030566322 0.032288961 1.490945934 -0.157378782 IDGITIHQSLAIIEYLEEMRPTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDGITIHQSLAIIEYLEEMRPTPR 24 1 A0A0C4DFM0;G3V4T6;O43708-2;O43708;G3V5G8;G3V5U6 A0A0C4DFM0 GSTZ1 Maleylacetoacetate isomerase 0 151.01 7.08E-08 70221000 20041 31274 29081 34366 34103 35721 34880 29676 29637 FALSE TRUE 18786.66958 33589.5595 29770.81505 35247.88974 31424.68794 46033.07282 29650.06781 33381.11392 24690.39324 0.760889849 1.360430317 1.205765124 1.427595316 1.272749593 1.864412299 1.200874669 1.351987941 1 14.59166219 4.739213064 24.31630112 1.349669183 0.760889605 0.397600053 0.221657265 35.12134743 1308531.574 0.047724001 0.284553731 54854.60144 -4.739213064 -0.588779578 IDGVEQLNNILVIGMTNRPDLIDEALLRPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IDGVEQLNNILVIGMTNRPDLIDEALLRPGR 31 2 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 ;; 273.68 7.15E-72 593371000 379504.4 412888 415975 435065 454376 424078 464890 366746 423482 FALSE TRUE 355751.897 443458.6571 425842.1234 446229.5045 418691.1418 546502.4343 395184.0603 412535.0454 352800.1184 1.008366717 1.256968561 1.207035092 1.264822434 1.186765877 1.549042661 1.120135849 1.16931663 1 18.42849152 0.964755411 1.931607959 1.005011389 1.240570836 0.219751082 0.136013358 0.516598829 4.082368956 0.117522257 0.033037234 9.220519929 -0.964755411 0.235559447 IDHYLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IDHYLGK 7 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;; 108.24 0.0072977 8612810000 5596700 5887000 5344400 5240300 6572700 4143070 6223800 5505200 6907200 FALSE TRUE 5246412.537 6322879.605 5471171.692 5374774.97 6056506.655 5339107.052 5290598.969 6192536.338 5754343.698 0.911730827 1.098801173 0.950789869 0.934037877 1.052510412 0.927839443 0.919409623 1.07614989 1 22.45621996 3.739664577 24.10790223 0.971501648 1.020478389 8.81E-05 0.068911216 619.3953183 1190447.821 0.016350821 0.029199825 5491.166059 -3.739664577 0.04897674 IDIIPNPQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IDIIPNPQER 10 0 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ;;;;; 132.88 0.00049334 1804080000 764913 930620 823522 832740 916300 715946 920880 796101 860281 FALSE TRUE 717038.4607 999524.0731 843056.3307 854109.5182 844337.4942 922627.9878 782802.593 895495.9623 716694.5435 1.000479866 1.394630505 1.176311915 1.191734367 1.178099515 1.287337815 1.092240202 1.249480648 1 19.45099885 -1.856849044 0.293509162 0.793484698 1.22900989 0.217419799 0.108194751 37.92919574 1.809149213 5.536497682 0.1098361 0.013904358 1.856849044 0.435525192 IDILDSALLRPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDILDSALLRPGR 13 1 P62195-2;P62195 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ; 243.88 4.77E-17 2447000000 2742710 2809030 2888410 2786030 3075060 2469560 2972690 2546030 2908610 FALSE TRUE 2571048.677 3017013.504 2956924.449 2857524.247 2833557.192 3182481.882 2526962.732 2863907.45 2423144.201 1.061038248 1.245082114 1.220284145 1.179262978 1.169372087 1.313368755 1.042844553 1.181897243 1 21.20844883 0.903220307 0.85395442 1.00459903 1.200259606 0.319409893 0.079876924 0.750298283 1.158426558 0.069384452 0.024370881 8.002400944 -0.903220307 0.195660575 IDIS(ph)PSTFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 IDISPSTFR 9 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 IDIS(0.982)PS(0.014)T(0.005)FR;IDIS(0.529)PS(0.466)T(0.005)FR;IDIS(0.997)PS(0.003)TFR;IDIS(0.987)PS(0.013)TFR;IDIS(0.893)PS(0.099)T(0.008)FR;IDIS(0.952)PS(0.047)TFR;IDIS(0.762)PS(0.237)TFR;IDIS(0.997)PS(0.003)TFR;IDIS(0.992)PS(0.008)TFR;IDIS(0.969)PS(0.027)T(0.005)FR;IDIS(0.937)PS(0.062)T(0.001)FR 184.9 4.56E-05 35880793000 5674846 5737006 5838662 5860762 6089550 5066632 6611416 5405347 5917883 TRUE FALSE 5319667.519 6161779.894 5977157.82 6011159.075 5611301.307 6529286.409 5620095.548 6080216.472 4930150.096 1.079007214 1.249815883 1.212368326 1.219264923 1.138160339 1.324358545 1.139944107 1.233272082 1 22.23320014 -1.676452699 2.713769767 0.972896242 1.204693063 0.456595366 0.068198949 10661890.12 8865357.387 1984409.673 0.014708567 0.021064313 1.676452699 0.231796821 IDIS(ph)PSTFRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDISPSTFRK 10 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 IDIS(0.996)PS(0.004)TFRK;IDIS(0.992)PS(0.008)TFRK 132.79 0.00013126 624690000 1256730 1698350 1342140 1396330 2119600 948300 2015400 1291060 5220600 TRUE FALSE 1178073.513 1824097.601 1373976.195 1432162.192 1953135.166 1222058.816 1713209.48 1452251.683 4349248.134 0.270868315 0.419405273 0.315911199 0.329289603 0.449074209 0.280981627 0.393909344 0.333908675 1 22.05233459 -1.661681442 2.672284166 1.080456936 0.35473899 0.926890082 0.057425111 5763444.371 5081167.767 3172213.39 0.012323787 0.021793077 1.661681442 -0.725717946 IDIS(ph)PSTLR ddPTM_SK-BR-3_Pertuzumab_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(0.825)PS(0.175)TLR;IDIS(0.555)PS(0.441)T(0.004)LR;IDIS(0.986)PS(0.014)TLR;IDIS(0.843)PS(0.157)TLR;IDIS(0.958)PS(0.041)TLR;IDIS(1)PSTLR;IDIS(0.942)PS(0.058)TLR 211.84 4.71E-06 39951610000 2910480 2808120 2931080 2659670 2716280 2491730 3034520 2519550 3147860 TRUE FALSE 2728318.252 3016036.127 3000606.602 2727921.635 2502954.326 3211052.001 2579521.897 2834121.364 2622461.83 1.040365286 1.150078179 1.144194576 1.040214048 0.954429268 1.224441845 0.983626098 1.080710244 1 21.32249034 3.233898117 24.97693428 1.050019165 1.12446699 0.121924187 0.078617888 190.7946703 1022084.416 0.020684597 0.025504853 1713.555272 -3.233898117 0.074447825 IDIS(ph)PSTLRK ddPTM_SK-BR-3_Pertuzumab_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(0.945)PS(0.043)T(0.012)LRK;IDIS(1)PSTLRK;IDIS(0.941)PS(0.05)T(0.009)LRK;IDIS(0.757)PS(0.237)T(0.007)LRK;IDIS(0.519)PS(0.382)T(0.099)LRK;IDIS(0.999)PS(0.001)TLRK 168.76 2.96E-06 3666923000 3753942 3981640 3841439 3711078 4650143 2892552 5045721 3473779 9679910 TRUE FALSE 3518989.471 4276444.768 3932559.747 3806310.544 4284939.527 3727584.806 4289161.978 3907487.955 8064270.486 0.436367986 0.530295304 0.487652262 0.471996884 0.531348686 0.462234595 0.531872286 0.484543265 1 22.9431126 -4.356740226 0.530331697 9.999874416 0.493650542 0.961597461 0.03189523 254.8947254 2.184923754 2695.330361 0.01238196 4.40E-05 4.356740226 -9.506223874 IDISPS(ph)TFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDISPSTFR 9 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 IDIS(0.327)PS(0.669)T(0.004)FR 175.33 5.66E-05 11247000000 1034600 986480 995620 1026300 1074600 894770 1138600 1037900 1125500 TRUE FALSE 969846.2328 1059520.006 1019236.577 1052636.596 990205.2507 1153075.574 967877.5002 1167484.1 937646.779 1.034340708 1.129977759 1.087015494 1.122636604 1.056053594 1.229754743 1.032241055 1.245121431 1 19.83868502 4.746845336 23.41924158 1.11274497 1.034340611 0.091075157 0.077944322 997.5707552 2819768.375 0.015606785 0.169396128 55827.13438 -4.746845336 -0.078404359 IDISPS(ph)TLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.16)PS(0.839)T(0.001)LR 195.8 3.22E-05 9678400000 470840 390680 421170 378830 406550 381540 451670 379550 454060 TRUE FALSE 441370.9649 419606.3537 431160.3513 388551.4192 374621.2029 491684.4042 383946.2766 426937.653 378274.4527 1.166800882 1.109264321 1.139808275 1.027168016 0.99034233 1.299808646 1.014993939 1.12864522 1 18.52907382 -5 0.201629992 0.51334632 1.125139718 0.131382188 0.088620105 295.9969932 2.934482596 58.21850652 0.190809732 1.00E-05 5 0.611793397 IDIVENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IDIVENR 7 0 P00966 P00966 ASS1 Argininosuccinate synthase 0 ;;; 134.85 0.0072917 1400460000 2337980 2691970 2579190 2727170 2681980 2344450 2849860 2363670 2229060 FALSE TRUE 2191650.005 2891286.26 2640369.605 2797153.799 2471348.109 3021254.656 2422549.95 2658779.403 1857015.486 1.180200177 1.556953231 1.421834995 1.506263045 1.330817179 1.626941013 1.304539444 1.431748643 1 20.82455442 0.053225998 0.880245309 0.993386663 1.441615254 0.505755131 0.12935299 3.890570865 2.982459461 0.187350702 0.036063805 1.13038399 -0.053225998 0.448228591 IDKEACR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDKEACR 7 1 Q14019 Q14019 COTL1 Coactosin-like protein 0 ; 76.899 0.036032 403110000 343210 439050 338570 364840 565160 259160 425770 448700 591460 FALSE TRUE 321729.0987 471557.7188 346601.0403 374202.4121 520774.6133 333975.2849 361929.7412 504721.1827 492741.505 0.652936876 0.957008318 0.703413528 0.759429454 1.056892119 0.677790041 0.734522539 1.024312297 1 18.91047147 1.230023878 24.98446121 1.012156323 0.79818858 0.345601638 0.125865278 229.269332 670976.5435 0.106427997 0.02830125 16.98337026 -1.230023878 -0.213967743 IDKTDYMVGSYGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IDKTDYMVGSYGPR 14 1 P52565;J3KTF8;J3QQX2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;; 137.19 2.07E-05 3295680000 2601270 2503770 2464400 2479220 2677610 1548976 2708610 2444570 2606280 FALSE TRUE 2438461.154 2689151.736 2522856.732 2542840.983 2467321.312 1996140.226 2302479.076 2749779.946 2171275.031 1.123054942 1.238512716 1.161924075 1.171127999 1.136346744 0.91934011 1.060427188 1.266435577 1 21.05011105 2.466494852 24.99007697 1.056564583 1.179632231 0.256276815 0.0901509 263.0836043 618688.1452 0.029854665 0.024999526 292.748617 -2.466494852 0.123067648 IDKVNEIVETNRPDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDKVNEIVETNRPDSK 16 2 Q15008;Q15008-4;Q15008-3;Q15008-2 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 146.58 6.24E-07 1740650000 2828000 1784680 2346480 2279430 2118330 1593640 2995300 1926970 2917800 FALSE TRUE 2651000.528 1916819.564 2402139.614 2337924.033 1951964.907 2053697.997 2546182.572 2167556.446 2430800.33 1.09058753 0.788554922 0.98820935 0.961791885 0.803013264 0.844864949 1.047466771 0.891704851 1 21.21299996 1.741492412 24.99999995 0.981117132 0.904851985 0.091547865 0.097146093 1.039871663 8919.359603 0.041702862 0.02312624 55.14325674 -1.741492412 -0.076265147 IDLFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IDLFER 6 0 Q9UHG3;F8W8W4 Q9UHG3 PCYOX1 Prenylcysteine oxidase 1 0 ;; 143.37 0.02654 240473000 226503 255474 231924 206257 305404 179766 258152 237405 295254 FALSE TRUE 212326.5815 274389.5608 237425.3468 211549.9038 281418.8018 231661.5259 219444.5042 267045.5368 245974.2 0.863206717 1.115521712 0.965244919 0.860049159 1.14409886 0.941812296 0.892144396 1.085664825 1 17.90814747 3.714544963 24.213544 0.973625799 1.017285695 0 0.103452224 1041.530185 2005296.21 0.025647279 0.040059663 5182.567444 -3.714544963 0.043659897 IDLGERPVVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDLGERPVVQR 11 1 Q8TC07-2;Q8TC07-3;Q8TC07;C9JA93 Q8TC07-2 TBC1D15 TBC1 domain family member 15 0 ; 140.78 3.51E-05 522770000 262246 310940 291940 375310 368000 325610 393830 303011 372410 FALSE TRUE 245832.491 333962.3211 298864.9547 384941.09 339098.7644 419608.3212 334778.8476 340842.5904 310252.3651 0.792362988 1.076421516 0.963296298 1.240735392 1.09297721 1.352474206 1.07905333 1.098597879 1 18.24308268 5.647280748 0.663191186 1.143424759 3.01E-12 0.419405267 0.114519688 8.747276243 1.186281531 0.042376306 9.948537788 443895.5061 -5.647280748 -1.143424759 IDLGVHVDGFIANVAHTFVVDVAQGTQVTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDLGVHVDGFIANVAHTFVVDVAQGTQVTGR 31 0 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 239.15 4.40E-46 390530000 220780 225970 223240 211130 232000 200460 251290 179990 222330 FALSE TRUE 206961.7739 242701.0539 228535.3582 216547.9532 213779.6558 258329.5478 213611.3974 202462.1477 185221.6867 1.117373336 1.310327415 1.233847733 1.169128503 1.154182643 1.39470465 1.153274226 1.093080143 1 17.4988935 1.199904704 2.38848188 1.011026918 1.235472567 0.467252135 0.081188549 0.219827117 2.175228056 0.069805784 0.019754726 15.84545462 -1.199904704 0.224445649 IDLPEVQIEHDPELEKES(ph)PGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDLPEVQIEHDPELEKESPGLK 22 1 Q14966;Q14966-3;Q14966-5 Q14966 ZNF638 Zinc finger protein 638 1 IDLPEVQIEHDPELEKES(1)PGLK;IDLPEVQIEHDPELEKES(1)PGLK 169.57 4.91E-12 225150000 745100 306630 431230 431390 448770 279611 574370 358010 792580 TRUE FALSE 698465.521 329333.2042 441458.9792 442460.1977 413525.4145 360330.1566 488248.5507 402708.3366 660293.2777 1.057811043 0.498768071 0.668580151 0.670096475 0.626275366 0.54571229 0.739441953 0.609893134 1 19.33274743 -1.255504751 4.791080548 1.000092496 0.658759035 0.302248294 0.151949177 0.000131685 2.05E-05 0.12905054 0.030409294 0.055525854 1.255504751 -0.34133346 IDMNLTDLLGELQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDMNLTDLLGELQR 14 0 F5H365;Q15436;Q15436-2;A0A2R8YFH5;Q15437;Q5QPE2 F5H365;A0A2R8YFH5 SEC23A;SEC23B Protein transport protein Sec23A;Protein transport protein Sec23B 0 87.18 0.01639 47509000 113310 170670 195920 206360 295380 291870 180030 202760 108720 FALSE TRUE 106218.1294 183306.5844 200567.3149 211655.547 272182.0463 376128.1309 153036.1728 228075.0323 90573.92964 1.172722988 2.023833846 2.214404473 2.336826367 3.005081566 4.152719578 1.689627174 2.518109054 1 16.46680823 4.975751352 0.860090387 2.536596392 8.60E-10 0.178709445 0.8193818 5.202287952 2.264725449 0.256419721 13.69878907 94569.55651 -4.975751352 -2.536596392 IDNSQVESGSLEDDWDFLPPKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDNSQVESGSLEDDWDFLPPKK 22 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 ; 188.8 3.78E-17 331660000 1103260 808420 853160 881700 945590 673150 1320240 772300 1069140 FALSE TRUE 1034208.926 868276.258 873397.3581 904325.9147 871327.1757 867477.4773 1122282.269 868723.355 890693.6271 1.161127569 0.97483156 0.980581124 1.015305249 0.978256888 0.973934753 1.260009317 0.975333525 1 19.76456975 IDPHAPNEMLYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IDPHAPNEMLYGR 13 0 O43813;E9PHS0 O43813 LANCL1 LanC-like protein 1 0 ;;; 119.32 0.00035834 1727360000 3516920 3732640 3900340 3703580 4081040 3375540 4286760 3648070 4853220 FALSE TRUE 3296802.255 4009008.549 3992857.907 3798620.133 3760531.581 4350003.601 3644000.134 4103539.57 4043186.229 0.815397082 0.991546845 0.987552312 0.939511543 0.930091113 1.075885046 0.901269427 1.014927173 1 21.94706122 4.741821947 24.74873233 0.976608966 0.815397013 0.52843761 0.048796903 209.1942827 1587393.071 0.010416178 0.075454786 55185.11439 -4.741821947 -0.161211953 IDPWSFVSAGPRPS(ph)PLPS(ph)PQPAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDPWSFVSAGPRPSPLPSPQPAPR 24 1 Q16584;Q16584-2;E9PID4 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 2 IDPWS(0.004)FVS(0.006)AGPRPS(0.99)PLPS(1)PQPAPR 88.191 0.0061941 19844000 34181 37431 36592 39901 44571 33992 45628 32795 39587 TRUE FALSE 32041.67222 40202.43019 37459.97952 40924.92721 41070.57345 43804.93859 38786.50499 36889.52794 32979.67396 0.971558187 1.219006296 1.135850511 1.240913639 1.245329881 1.328240499 1.176073027 1.118553446 1 15.00928952 0.957637792 2.706375312 1.000986489 1.195545864 0.298029815 0.09232364 0.349092343 6.00763187 0.083052935 0.022138886 9.070637093 -0.957637792 0.194559375 IDQLIRPINALDELCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDQLIRPINALDELCR 16 1 Q8TCU6;Q8TCU6-2 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 0 ; 180.62 2.22E-09 484570000 489760 542410 518320 512050 526940 558080 702020 487660 458380 FALSE TRUE 459106.7958 582570.6008 530614.7952 525190.0699 485556.258 719188.6363 596758.6182 548545.4245 381873.4168 1.20224864 1.525559453 1.389504406 1.375298847 1.271511021 1.88331684 1.562713172 1.436458786 1 18.54273497 IDRDS(ph)YSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDRDSYSPR 9 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 IDRDS(0.5)YS(0.5)PR 89.193 0.032285 642470000 635600 706320 672960 674040 780550 650350 848070 718460 862490 TRUE FALSE 595818.9306 758616.6677 688922.929 691337.0075 719248.7516 838095.4874 720909.7766 808161.3125 718534.8471 0.829213688 1.055782709 0.958788473 0.962148197 1.000993556 1.166395048 1.003305239 1.12473503 1 19.4546986 2.462133166 24.94415122 1.071384721 0.971232715 0.365909689 0.073906326 269.5241023 448556.5493 0.023175555 0.01939647 289.8232124 -2.462133166 -0.100152006 IDRDSYS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDRDSYSPR 9 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 IDRDS(0.269)YS(0.73)PR;IDRDS(0.131)YS(0.869)PR 96.946 0.018479 794810000 879620 977640 930810 917370 1154050 908160 1182530 956530 1119340 TRUE FALSE 824566.1544 1050025.483 952889.2528 940911.2673 1063415.568 1170331.049 1005220.605 1075954.876 932514.9228 0.884239098 1.12601467 1.021848798 1.009003979 1.140373781 1.255026617 1.077967312 1.153820545 1 19.83076729 2.73208613 24.15848819 1.136612395 1.031495001 0.285603921 0.086699708 425.1568547 1586398.688 0.025653316 0.024718458 539.6176298 -2.73208613 -0.105117394 IDRLDGAHAPELTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDRLDGAHAPELTK 14 1 O76003 O76003 GLRX3 Glutaredoxin-3 0 88.974 0.0038053 378580000 349580 289810 336680 356540 346850 261100 418400 302140 472760 FALSE TRUE 327700.4118 311267.8339 344666.2086 365689.42 319609.8001 336475.3314 355664.8042 339862.8441 393853.3019 0.832036726 0.790314141 0.875113163 0.928491442 0.81149453 0.854316391 0.903038778 0.862917341 1 18.58729884 -5 0.118158041 1.470274886 0.78285622 0.613356983 0.037574364 103.862796 0.800036914 11.68597591 0.371797906 1.00E-05 5 -0.687418666 IDRPEAISEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IDRPEAISEER 11 1 Q9Y6B6;D6RD69;Q9H029;D6R9R5 Q9Y6B6 SAR1B;DKFZp434B2017 GTP-binding protein SAR1b 0 ;;; 179.59 6.42E-06 1923770000 2011710 2179080 2222190 2233940 2316060 1976220 2602270 2123890 2302580 FALSE TRUE 1885800.662 2340421.351 2274901.396 2291266.682 2134165.99 2546722.633 2212083.772 2389062.342 1918264.523 0.983076442 1.22007227 1.18591642 1.194447718 1.112550415 1.327618064 1.153169308 1.245429039 1 20.87137025 4.743500614 24.66355691 1.191083884 0.983076338 0.334259759 0.086017697 423.0431649 2112011.48 0.017314332 0.142778572 55398.83278 -4.743500614 -0.208007546 IDRTDAISEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IDRTDAISEEK 11 1 Q9NR31;Q9NR31-2;H0Y5E8 Q9NR31 SAR1A GTP-binding protein SAR1a 0 ;;; 162.38 2.30E-05 1105260000 2268080 1945440 2101310 2088510 2148710 1676000 2686170 1826320 2217950 FALSE TRUE 2126124.921 2089482.402 2151154.066 2142104.702 1979958.984 2159833.992 2283403.746 2054340.072 1847759.816 1.150650048 1.130819267 1.164195718 1.15929824 1.071545645 1.168893258 1.2357687 1.111800383 1 20.81734581 0.9838328 24.75106944 0.999999997 1.156293046 0.596869652 0.040013202 642.3796233 983448.2802 0.040321818 0.010080454 9.634580291 -0.9838328 0.156293049 IDRVETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDRVETR 7 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 149.65 0.0018257 1232600000 967670 1101080 1107090 1110780 1215930 893360 1248950 1068570 1180470 FALSE TRUE 907105.262 1182605.109 1133350.698 1139284.495 1120435.763 1151258.53 1061681.542 1201983.317 983441.9309 0.922378062 1.20251646 1.152432759 1.158466463 1.139300377 1.170642102 1.07955692 1.222220935 1 19.90748034 -1.004394357 7.593330701 0.999999996 1.137778116 0.191325619 0.083555477 5.28E-09 5.58E-10 0.071119585 0.016763047 0.098993264 1.004394357 0.13777812 IDS(ph)LSAQLSQLQK ddPTM_SK-BR-3_Pertuzumab_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(0.98)LS(0.02)AQLSQLQK;IDS(0.976)LS(0.024)AQLSQLQK 220.49 1.35E-07 37728000 279496 187591 203122 195312 203448 138902 237866 162723 209221 TRUE FALSE 262002.8443 201480.4328 207940.1498 200324.0366 187470.0147 179000.7525 202200.2015 183039.3247 174300.6635 1.503166075 1.155936121 1.192996892 1.14930163 1.075555371 1.026965411 1.160065587 1.050135559 1 17.41121854 8 0.812811063 1.095653383 107.0280117 0.799244994 0.06331577 235.6739747 0.765464082 0.019792198 46029.57251 100000000 -8 105.9323584 IDS(ph)PGFKPASQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDSPGFKPASQQK 13 1 G3V1L9;Q07157 G3V1L9 TJP1 Tight junction protein ZO-1 1 IDS(1)PGFKPASQQK;IDS(1)PGFKPASQQK 161.26 2.57E-05 463710000 1650680 781710 1046650 971230 1358980 719460 1332110 1052650 2254190 TRUE FALSE 1547366.885 839588.6218 1071477.032 996153.4061 1252251.193 927156.4225 1132372.472 1184075.67 1877951.126 0.823965472 0.447076929 0.570556399 0.530446928 0.666817776 0.493706364 0.60298293 0.630514635 1 20.84072809 0.537792116 1.585849213 0.999960184 0.570538187 0.597981292 0.103769115 1.412691675 4.163609275 0.088252111 0.025274656 3.449785687 -0.537792116 -0.429421997 IDS(ph)PGFKPASQQVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IDSPGFKPASQQVYR 15 1 A0A087X0K9;G5E9E7;Q07157-2 A0A087X0K9 TJP1 Tight junction protein ZO-1 1 IDS(1)PGFKPASQQVYR;IDS(1)PGFKPASQQVYR;IDS(1)PGFKPASQQVYR;IDS(1)PGFKPASQQVYR 208.17 1.83E-09 1411470000 3375110 2134310 2488170 2492060 2798500 1748390 3159850 2082750 2610940 TRUE FALSE 3163867.89 2292336.533 2547190.567 2556010.479 2578717.099 2253121.81 2686059.827 2342785.922 2175157.247 1.454546744 1.053871639 1.171037437 1.175092276 1.185531346 1.035843185 1.234880757 1.077065084 1 21.05268827 5.40151589 0.019967906 2.67E-07 2.46257007 0.317558469 0.107435642 2853.530888 7.354046132 378.8951621 539.3101639 252066.9407 -5.40151589 2.462569803 IDS(ph)RPPSPEPPKQEYWGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDSRPPSPEPPKQEYWGSK 19 2 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 IDS(0.601)RPPS(0.395)PEPPKQEY(0.001)WGS(0.003)K 48.489 0.08317 84021000 590160 315720 430380 365340 392360 337520 529430 350150 417620 TRUE FALSE 553222.9391 339096.2373 440588.8168 374715.2429 361545.6283 434956.5448 450046.8865 393866.9983 347916.5241 1.590102512 0.974648267 1.266363585 1.077026289 1.039173489 1.250175012 1.293548467 1.132073273 1 18.40838167 4.753200321 24.84598228 1.149198412 1.590102848 0.617316645 0.113086201 1771.18069 3005929.254 0.026921629 0.599771799 56650.05306 -4.753200321 0.440904436 IDS(ph)TEVIYQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDSTEVIYQPR 11 0 K7EMR0;K7EQN8;K7EP59;Q15831-2;Q15831 K7EMR0 STK11 Serine/threonine-protein kinase STK11 1 IDS(0.987)T(0.013)EVIYQPR;IDS(0.957)T(0.043)EVIYQPR 171.26 1.55E-05 448560000 717360 579360 720420 670310 657810 700410 890660 575560 749030 TRUE FALSE 672461.7181 622256.4172 737508.7026 687511.2894 606148.2561 902606.9968 757113.8015 647419.933 624012.0541 1.077642193 0.997186534 1.181882141 1.101759629 0.971372672 1.44645763 1.213299962 1.037511902 1 19.25121437 IDSNIS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDSNISPK 8 0 Q9H501 Q9H501 ESF1 ESF1 homolog 1 IDSNIS(1)PK 104.94 0.0047024 671150000 2596000 1312700 1868200 1580100 1762900 1216800 2216600 1410000 1947200 TRUE FALSE 2433520.994 1409893.674 1912514.586 1620648.041 1624448.945 1568070.407 1884241.408 1586041.604 1622199.741 1.500136471 0.869124583 1.178963686 0.99904346 1.001386515 0.96663214 1.161534773 0.977710429 1 20.62952004 4.751255424 24.87217834 1.032133593 1.500136788 0.730846632 0.091409294 1016.818132 1992152.978 0.020706378 0.374316937 56396.92482 -4.751255424 0.468003195 IDSRPPS(ph)PEPPKQEYWGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDSRPPSPEPPKQEYWGSK 19 2 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 IDS(0.075)RPPS(0.925)PEPPKQEYWGSK 127.24 1.24E-05 88892000 377600 213310 285550 268780 260040 231370 359310 244290 277880 TRUE FALSE 353966.69 229103.6943 292323.3808 275677.3498 239617.5074 298162.763 305434.8012 274790.1442 231500.0328 1.529013563 0.989648647 1.262735807 1.190830716 1.03506468 1.287959917 1.319372604 1.186998295 1 17.82065287 IDTGWLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDTGWLDR 8 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 85.161 0.039408 60017000 128460 102040 111960 113480 129910 88765 122120 97126 129890 FALSE TRUE 120419.9179 109595.1478 114615.7441 116392.0889 119707.3926 114390.0145 103809.2397 109252.3949 108210.5199 1.112830047 1.012795687 1.05919225 1.07560789 1.106245426 1.057106228 0.959326689 1.009628223 1 16.72348123 1.755782592 25 0.987438412 1.064198092 0.604138896 0.030589103 4.732022724 6876.652853 0.014222961 0.007887412 56.98789196 -1.755782592 0.076759681 IDTHNIIVNQLVFPDPEKPCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDTHNIIVNQLVFPDPEKPCK 21 1 O43681 O43681 ASNA1 ATPase ASNA1 0 138.22 1.20E-06 60573000 153480 91751 121570 116420 127050 93009 172400 129720 180010 FALSE TRUE 143873.9608 98544.33951 124453.6978 119407.5343 117072.0055 119859.1884 146550.2205 145915.8275 149965.1681 0.959382519 0.657114854 0.829884028 0.796235125 0.780661316 0.799246851 0.977228395 0.972998126 1 17.19426792 1.735507097 4.156682669 0.984546968 0.787497753 0.563299324 0.07371564 0.123594119 4.767641808 0.03657848 0.018219038 54.38850193 -1.735507097 -0.197049214 IDTHPS(ph)PSHSSTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IDTHPSPSHSSTVK 14 0 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477;H0Y594;B7ZBA0 Q8NI27 THOC2 THO complex subunit 2 1 IDTHPS(0.805)PS(0.193)HS(0.002)STVK;IDTHPS(0.5)PS(0.5)HSSTVK;IDT(0.001)HPS(0.874)PS(0.125)HSSTVK 181.72 1.03E-06 1311390000 766380 1265910 1394240 1309100 1381030 1253700 2018280 1543650 1719600 TRUE FALSE 718413.6438 1359639.294 1427312.031 1342693.722 1272569.475 1615622.838 1715657.651 1736378.1 1432587.651 0.501479713 0.949079306 0.996317419 0.937250661 0.888301301 1.127765437 1.197593494 1.212057147 1 20.45019198 5.007181373 1.218437494 1.061877496 1.08E-76 0.713246972 0.107671404 1.632262999 1.351663768 0.03348176 2.546932561 101667.3194 -5.007181373 -1.061877496 IDTIEIITDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 IDTIEIITDR 10 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;; 253.98 9.92E-17 6577743000 2510356 2319561 2455028 2267602 2359521 2185309 2711550 2218486 2084924 FALSE TRUE 2353237.299 2491303.71 2513262.424 2325792.506 2174213.739 2816172.233 2304978.25 2495468.861 1736936.715 1.354820402 1.434308854 1.446951061 1.339019716 1.251751845 1.621344179 1.327036403 1.436706841 1 20.72811376 -1.169249201 4.304378862 0.999892166 1.406110458 0.622101169 0.098282994 6417929.662 1743381.166 6499.999386 0.020700977 0.067725278 1.169249201 0.406218292 IDVDAPDIDIHGPDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IDVDAPDIDIHGPDAK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 274.48 3.11E-35 1664810000 4345800 3066000 3526000 3264500 4034200 2658300 4305400 3172800 5139900 FALSE TRUE 4073804.135 3293009.83 3609638.385 3348272.597 3717370.205 3425708.056 3659845.239 3568931.064 4282017.485 0.951374942 0.769032318 0.842976097 0.781938095 0.868135223 0.800021968 0.854701143 0.833469521 1 22.02985926 -0.410784921 0.758386017 1.010655295 0.82869234 0.488529129 0.051593839 9.800885609 4.228840837 0.350711229 0.015443991 0.388342641 0.410784921 -0.181962955 IDVPQDLEDDLTATPLSHATVPQS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDVPQDLEDDLTATPLSHATVPQSPAR 27 0 E7EUC4;Q9NRH2 E7EUC4 SNRK SNF-related serine/threonine-protein kinase 1 IDVPQDLEDDLTATPLSHATVPQS(1)PAR 256.46 4.41E-53 77460000 31036 34526 34878 34803 29965 31121 37185 32165 28974 TRUE FALSE 29093.51216 37082.34096 35705.32263 35696.1039 27611.66977 40105.12749 31609.45446 36180.87105 24138.05222 1.205296595 1.536260698 1.479213082 1.478831166 1.14390629 1.661489797 1.309527967 1.498914275 1 14.55902164 -1.35889289 3.489654405 0.997528595 1.42709814 0.406565497 0.156568068 43496346.45 78027142.87 1147449.375 0.033241754 0.043763002 1.35889289 0.429569544 IDWPVGSPATIHYPALDGHLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDWPVGSPATIHYPALDGHLSR 22 0 O15498;O15498-2 O15498 YKT6 Synaptobrevin homolog YKT6 0 92.792 0.0011678 228790000 48485 59944 51674 50711 55772 44875 56548 48389 54181 FALSE TRUE 45450.4104 64382.31613 52899.73168 52012.33011 51391.89209 57829.68402 48069.15237 54430.47317 45137.84108 1.006924773 1.426349037 1.171959722 1.152299908 1.1385545 1.281179663 1.064941327 1.205872321 1 15.4620498 0.308607993 0.264707577 0.942000701 1.255666179 0.157747339 0.11707123 6.684807422 0.930637094 0.626479965 0.194718051 2.035204212 -0.308607993 0.313665478 IDYANLTGISVSSLSDSLFVLHVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IDYANLTGISVSSLSDSLFVLHVQR 25 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ;;; 302.71 2.33E-63 349177000 279509 325442 261437 228537 374750 253630 302305 329177 190119 FALSE TRUE 262015.0306 349538.0643 267638.4091 234401.6463 345318.6467 326848.8637 256977.1717 370275.4731 158386.9107 1.654271994 2.206862062 1.689776055 1.479930667 2.180222123 2.063610321 1.622464701 2.337790866 1 17.27309359 -1.018768288 5.378713498 0.999995281 1.894623076 0.492025219 0.288633812 1.49E-05 2.73E-06 0.25574988 0.060280507 0.095770491 1.018768288 0.894627795 IDYGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IDYGNR 6 0 A0A096LNH6;Q14185 A0A096LNH6 DOCK1 Dedicator of cytokinesis protein 1 0 112.66 0.062352 267260000 190240 176670 202540 230890 201450 176980 261010 166830 237810 FALSE TRUE 178333.218 189750.8306 207344.3444 236815.0283 185628.9296 228071.253 221873.9736 187659.0927 198117.9747 0.900136488 0.95776686 1.046570079 1.195323285 0.936961575 1.1511891 1.119908347 0.947208819 1 17.59600025 4.142058061 1.657683427 1.071099631 0.907923843 0.283861387 0.084080004 0.48251324 2.388368301 0.021670418 0.086960421 13869.41237 -4.142058061 -0.163175788 IDYIAGLDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IDYIAGLDSR 10 0 H3BQB1;P07741-2;P07741;H3BQF1 H3BQB1 APRT Adenine phosphoribosyltransferase 0 ;;;; 143.03 8.07E-05 458160000 764876 1143775 765725 766768 1207498 601465 836530 1006685 996555 FALSE TRUE 717003.7765 1228461.291 783888.3586 786444.565 1112665.978 775098.1815 711100.0925 1132371.838 830223.5325 0.863627383 1.479675344 0.94418952 0.947268457 1.340200481 0.933601797 0.856516426 1.363936089 1 19.6631403 3.751636347 21.68365732 1.037934699 1.214538558 0.032831928 0.224430941 184.3387498 163042.9169 0.053311624 0.095992753 5644.64127 -3.751636347 0.176603858 IEALQNHENESVYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEALQNHENESVYK 14 0 P52292 P52292 KPNA2 Importin subunit alpha-1 0 200.55 1.91E-08 280570000 188710 135230 177000 166600 172330 120220 180620 149700 135730 FALSE TRUE 176898.978 145242.5699 181198.5236 170875.2381 158795.8969 154925.5624 153537.7078 168390.3745 113075.7862 1.56442846 1.284471016 1.602452035 1.511156755 1.404331576 1.370103783 1.357830116 1.48918155 1 16.7869305 -3.10407093 0.300174989 5.63E-14 1.469042469 0.678437997 0.097183854 44.98862326 1.179117368 28.36546187 0.096744752 0.000786917 3.10407093 1.469042469 IEDFLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 IEDFLER 7 0 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 ;;;;;;; 204.1 0.00063089 11257170000 7429400 8715570 8568930 8380920 9457910 7518820 8880570 7958780 7868620 FALSE TRUE 6964407.116 9360879.871 8772189.066 8595988.596 8715123.9 9689381.276 7549010.972 8952451.202 6555296.489 1.062409172 1.42798726 1.338183419 1.311304319 1.329478219 1.478099624 1.151589556 1.365682119 1 22.6442296 -1.119465595 4.575573073 0.999970298 1.317489416 0.385218744 0.12180443 3.34E-05 6.43E-06 0.106702887 0.025147762 0.075951159 1.119465595 0.317519117 IEDGEDLKHDFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEDGEDLKHDFER 13 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 0 145.29 2.51E-05 32626000 70534 62576 68652 69996 81201 49447 80721 65126 98412 FALSE TRUE 66119.40285 67209.19215 70280.45786 71792.21586 74823.80101 63721.5462 68617.63543 73257.12446 81986.40143 0.806467923 0.81976024 0.857220913 0.875660044 0.912636726 0.777220918 0.836939227 0.893527746 1 16.32309702 -5 0.284599248 2.175277109 0.834907835 0.613395118 0.039019693 165.433538 1.573427232 115.0448645 0.043274997 1.00E-05 5 -1.340369274 IEDLEEERDFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEDLEEERDFLR 12 1 K7EMP7;Q9BWC9;K7EMI9 K7EMP7 CCDC106 Coiled-coil domain-containing protein 106 0 127.71 0.00024152 31184000 27572 27735 37401 28991 30331 28379 33420 25527 36024 FALSE TRUE 25846.31774 29788.52826 38288.16938 29734.95814 27948.92561 36571.55661 28408.98126 28714.10214 30011.36168 0.861217762 0.992575031 1.275789143 0.990790037 0.931278158 1.218590379 0.94660754 0.956774386 1 14.87322116 1.606184075 25 0.963758821 1.060826124 0.069561376 0.124251738 0.39031195 5652.266321 0.062603747 0.03132998 40.3816514 -1.606184075 0.097067303 IEDPYAISFSPWNPSVHDEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEDPYAISFSPWNPSVHDEAR 21 0 Q9H8T0;Q9H8T0-2 Q9H8T0 AKTIP AKT-interacting protein 0 75.3 0.012391 317930000 160780 183090 195270 208130 255610 185890 223520 168560 289580 FALSE TRUE 150717.0668 196646.1741 199901.8966 213470.9682 235535.4217 239553.4253 190005.2511 189605.087 241247.2272 0.624741136 0.815123043 0.828618421 0.884863924 0.97632385 0.992978979 0.787595585 0.785936855 1 17.88015284 5.485837754 0.823955115 0.89040451 3.82E-14 0.538381111 0.078548927 6.242375322 1.33793789 0.026553917 6.771633518 306081.9745 -5.485837754 -0.89040451 IEDTVFHVFDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEDTVFHVFDK 11 0 Q9Y2L1;G3V1J5;Q9Y2L1-2 Q9Y2L1 DIS3 Exosome complex exonuclease RRP44 0 122.42 0.00039113 154070000 225890 222390 225910 215930 269480 168520 257570 243130 297000 FALSE TRUE 211751.9481 238855.987 231268.6919 221471.1294 248316.1278 217168.9883 218949.7697 273485.3157 247428.7813 0.855809688 0.965352477 0.934687916 0.89509041 1.00358627 0.877703019 0.884900166 1.10530923 1 17.9166538 1.242790053 24.99998334 1.05265463 0.921690385 0.557611565 0.050181366 71.08754151 420215.0797 0.03396648 0.011409455 17.49000982 -1.242790053 -0.130964245 IEDVGS(ph)DEEDDS(ph)GKDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEDVGSDEEDDSGKDKK 17 2 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 2 IEDVGS(1)DEEDDS(1)GKDKK 129.26 1.83E-05 317800000 914530 217830 352370 384830 405390 274610 572750 279160 527730 TRUE FALSE 857291.1998 233958.3599 360728.3828 394705.3893 373552.3047 353885.4491 486871.4547 314013.7405 439648.4537 1.949947037 0.532148715 0.820492782 0.897774997 0.849661364 0.804928224 1.10741082 0.714238246 1 18.74599087 4.748318722 24.92691281 0.836149911 1.949947662 0.836999879 0.153806798 539.9547822 1379276.277 0.038741226 0.516288284 56016.85496 -4.748318722 1.11379775 IEDVGS(ph)DEEDDSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 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(0.999)DEEDDS(0.001)GK;IEDVGS(0.994)DEEDDS(0.006)GK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK 371.23 4.02E-97 77629082000 22142923 10148845 14126107 12336610 11050348 10954783 17552930 11501408 9130583 TRUE FALSE 20757036.98 10900276.04 14461184.93 12653188.3 10182498.24 14117251.02 14921031.1 12937384.11 7606629.711 2.728808653 1.432996801 1.901129078 1.663442126 1.338634669 1.855914058 1.961582418 1.70080372 1 22.85882595 -2.069242428 1.44207204 0.005701706 1.790068841 0.316281304 0.377507582 69021.08599 14343.85573 225606.1686 0.09462313 0.00852624 2.069242428 1.784367135 IEDVGS(ph)DEEDDSGKDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 15 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(0.603)DEEDDS(0.397)GKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(0.639)DEEDDS(0.361)GKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(0.999)DEEDDS(0.001)GKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK 355.43 5.54E-87 1.53297E+11 40504237 13244539 21233131 19101098 18763779 14239973 27534282 15211584 19341464 TRUE FALSE 37969149.11 14225178.45 21736790.89 19591264.51 17290147.49 18350822.04 23405772.03 17110783.75 16113248.71 2.356393164 0.882824979 1.349001141 1.215848205 1.073039199 1.138865437 1.452579331 1.061907754 1 23.94174406 4.747353715 24.99124351 1.175396629 2.356393769 0.838276137 0.166552852 452.2102526 1285218.382 0.039016804 0.470681087 55892.52316 -4.747353715 1.18099714 IEDVGS(ph)DEEDDSGKDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 32 IEDVGSDEEDDSGKDKK 17 2 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 1 IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(0.977)DEEDDS(0.023)GKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(0.995)DEEDDS(0.005)GKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(0.999)DEEDDS(0.001)GKDKK;IEDVGS(0.999)DEEDDS(0.001)GKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(0.985)DEEDDS(0.015)GKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK 251.69 4.50E-27 2.13871E+11 35635178 8977194.6 17911188 15263800 15559469 9971611 22144827 10945920.3 19003597 TRUE FALSE 33404835.82 9641875.429 18336049.84 15655494.95 14337491.07 12850253.22 18824415.77 12312542.54 15831773.89 2.109986919 0.609020536 1.158180376 0.988865496 0.905614947 0.811674883 1.189027578 0.777710863 1 23.91631958 4.748834064 24.99754609 0.944042 2.109987565 0.820769785 0.173178414 588.9429562 1432998.896 0.039266911 0.552713634 56083.36507 -4.748834064 1.165945565 IEDVGS(ph)DEEDDSGKDKKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IEDVGSDEEDDSGKDKKK 18 3 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 1 IEDVGS(1)DEEDDSGKDKKK;IEDVGS(1)DEEDDSGKDKKK;IEDVGS(1)DEEDDSGKDKKK;IEDVGS(1)DEEDDSGKDKKK 220.36 4.87E-19 2063150000 2160842 793084 1139270 1411976 2001394 695252 2029512 832247 5191420 TRUE FALSE 2025598.756 851804.7646 1166294.022 1448209.695 1844212.588 895959.9659 1725205.517 936154.87 4324938.464 0.468353197 0.196951881 0.269667195 0.334850936 0.426413602 0.207161321 0.398897124 0.216455073 1 22.04424818 -1.693389412 2.8011075 1.095988857 0.30625993 0.83677224 0.095033887 18452857.69 16707838.5 12559101.91 0.021958842 0.020258654 1.693389412 -0.789728926 IEDVGSDEEDDSGKDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IEDVGSDEEDDSGKDKK 17 2 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 0 ;;; 190.11 1.78E-10 1174500000 2200030 639660 1126980 989260 1147240 730580 1560010 889160 1707310 FALSE TRUE 2062334.049 687021.092 1153712.498 1014646.086 1057140.398 941486.586 1326100.983 1000173.583 1422348.931 1.449949449 0.483018672 0.811131834 0.713359475 0.743235626 0.661923783 0.93233169 0.703184402 1 20.439844 -0.869489869 5.534373206 1.000000121 0.782143509 0.039466913 0.255118631 3.33E-07 6.83E-08 0.216929875 0.051130834 0.135054833 0.869489869 -0.217856612 IEDVTPIPSDS(ph)TR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEDVTPIPSDSTR 13 0 P62263;A0A2R8Y811 P62263 RPS14 40S ribosomal protein S14 1 IEDVTPIPSDS(0.953)T(0.047)R 193.98 3.87E-07 0 241890 189080 190650 166380 198880 151610 197450 116300 202850 TRUE FALSE 226750.5367 203079.6799 195172.308 170649.5925 183260.767 195377.3458 167844.2055 130820.311 168993.0245 1.341774534 1.201704511 1.154913397 1.009802582 1.084427997 1.156126688 0.993201974 0.774116632 1 17.36660417 5.798840234 0.257345406 0.924977004 1.929752101 0.636215128 0.091513403 10.74038947 0.388543275 0.11684223 3.755898772 629274.6458 -5.798840234 1.004775097 IEDVTPIPSDS(ph)TRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IEDVTPIPSDSTRR 14 1 P62263;A0A2R8Y811 P62263 RPS14 40S ribosomal protein S14 1 IEDVTPIPSDS(0.702)T(0.298)RR;IEDVTPIPS(0.003)DS(0.506)T(0.491)RR 157.47 3.24E-06 288500000 731650 639860 632750 529280 629800 486920 582090 353590 657670 TRUE FALSE 685857.3325 687235.9002 647759.1288 542862.2209 580338.0485 627485.8995 494811.0084 397736.4898 547900.6283 1.251791469 1.25430756 1.182256591 0.990804158 1.059203108 1.145254937 0.903103561 0.725928151 1 19.06355473 2.847211582 0.55774661 0.88154204 1.284140185 0.620921699 0.100810174 0.595891484 0.39277645 0.081497849 0.10745253 703.4149297 -2.847211582 0.402598144 IEDVTPIPSDSTRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IEDVTPIPSDSTRR 14 1 P62263;A0A2R8Y811 P62263 RPS14 40S ribosomal protein S14 0 ;;;;; 203.74 2.34E-08 8748100000 4703160 5939110 5315760 5324260 6033020 4555740 6390530 4375230 8150510 FALSE TRUE 4408797.611 6378847.884 5441852.337 5460889.526 5559210.945 5870908.182 5432329.353 4921487.097 6790137.227 0.649294331 0.93942842 0.80143481 0.804238463 0.818718497 0.864622906 0.800032337 0.724799357 1 22.6950093 -2.150226894 2.56739071 1.448978897 0.815285256 0.383280908 0.077563393 8616939.329 1960978.853 22799444.17 0.018556824 0.00707576 2.150226894 -0.633693641 IEDYFPEFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IEDYFPEFAR 10 0 P63092-4;P63092;P63092-3;A0A590UJ58;B0AZR9;A0A590UJF0;A0A590UJY2;A0A0A0MR13;P63092-2;A0A590UJB0;Q5JWF2 P63092-4;P63092-2;Q5JWF2 GNAS Guanine nucleotide-binding protein G(s) subunit alpha isoforms short;Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas 0 ;;; 141.48 8.71E-05 150134000 230053 244593 238528 207394 273488 179698 239804 232692 264762 FALSE TRUE 215654.3934 262702.9202 244185.9968 212716.0812 252009.3557 231573.8954 203847.6164 261744.1084 220571.5118 0.977707373 1.191010199 1.107060449 0.964386015 1.142529031 1.049881254 0.92417926 1.186663256 1 17.75088694 3.441702962 24.22000591 1.037590008 1.116697084 0.030324741 0.093011658 234.1641103 160127.0615 0.024147323 0.032696194 2765.049829 -3.441702962 0.079107076 IEEACEIYAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEEACEIYAR 10 0 P54920;M0R0Y2;M0R2M1 P54920 NAPA Alpha-soluble NSF attachment protein 0 172.23 8.79E-06 348530000 121180 142500 139560 126090 142270 125470 155850 132240 151990 FALSE TRUE 113595.5601 153050.8483 142870.4291 129325.6829 131096.6881 161691.1522 132481.7393 148750.4551 126621.8871 0.897124207 1.208723482 1.128323328 1.021353305 1.03533987 1.276960531 1.046278352 1.174761003 1 16.95016728 IEEAMDGSET(ph)PQLFTVLPEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IEEAMDGSETPQLFTVLPEKR 21 1 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 1 IEEAMDGS(0.015)ET(0.984)PQLFT(0.001)VLPEKR;IEEAMDGSET(1)PQLFTVLPEKR;IEEAMDGSET(1)PQLFTVLPEKR;IEEAMDGSET(1)PQLFTVLPEKR 238.23 4.08E-30 547223000 738361 835121 643809 685164 915010 378221 1165740 811126 1736700 TRUE FALSE 692148.303 896954.2278 659080.4535 702746.4682 843148.8056 487407.2628 990948.1092 912396.8666 1446833.55 0.478388342 0.619942928 0.455533018 0.485713417 0.58275453 0.336878601 0.684908163 0.630616332 1 20.46446753 0.772795603 1.135147174 0.997363764 0.510797007 0.744783661 0.089907443 0.381929164 0.894630195 0.077580126 0.024237745 5.926463346 -0.772795603 -0.486566757 IEEDFPHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IEEDFPHIR 9 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 0 ;; 230.24 9.72E-08 231620000 514470 544880 537240 520500 562660 412540 619840 504010 646140 FALSE TRUE 482270.2411 585223.4821 549983.5865 533856.9112 518470.9533 531633.601 526900.7463 566936.758 538295.0598 0.89592173 1.087179738 1.021713977 0.991755175 0.963172416 0.987624893 0.978832588 1.053208176 1 19.03803766 4.767591556 23.83921057 1.010982606 0.895921396 0.491450919 0.036605249 6184.322725 5078193.083 0.009652977 1.013175298 58558.71738 -4.767591556 -0.11506121 IEEDNLTYQHLLPES(ph)PEPSASHALSDYETSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IEEDNLTYQHLLPESPEPSASHALSDYETSEK 32 0 Q5JTU8;B1AMJ5;A0A0A0MRG9;Q96SN8-3;Q96SN8-2;Q96SN8;Q96SN8-4 Q5JTU8 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 1 IEEDNLTYQHLLPES(0.984)PEPS(0.015)ASHALSDYETSEK;IEEDNLTYQHLLPES(0.999)PEPSASHALSDYETSEK 242.24 1.34E-46 228492000 173564 171633 188236 229870 213928 140575 198082 139209 167316 TRUE FALSE 162700.9391 184340.8859 192701.0468 235768.8534 197126.9578 181156.7205 168381.443 156589.5501 139389.8787 1.167236392 1.322484011 1.382460826 1.691434526 1.414212852 1.29964042 1.20798902 1.123392541 1 17.08876628 1.4775362 1.40632107 1.026363994 1.393692694 0.528047777 0.129525545 0.325444719 1.227824337 0.118442914 0.039386563 30.02867708 -1.4775362 0.3673287 IEEDRCS(ph)NSADITGPSFIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEEDRCSNSADITGPSFIR 19 1 Q52LW3;F8VWZ8 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 IEEDRCS(0.999)NS(0.001)ADITGPSFIR 236.02 2.14E-24 143710000 135520 142900 135290 136920 147010 145160 187360 139190 151440 TRUE FALSE 127038.0451 153480.4647 138499.1427 140433.599 135464.4276 187065.3355 159267.1074 156568.1779 126163.6857 1.006930358 1.216518556 1.097773436 1.113106345 1.073719644 1.48271933 1.262384707 1.240992422 1 16.94493719 IEEEEQEPEPPEPFEYIDD ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 IEEEEQEPEPPEPFEYIDD 19 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;;;;; 234.82 8.86E-24 807644000 4654680 4805830 4898030 4904810 4966780 4236710 5896220 4407240 5297430 FALSE TRUE 4363351.888 5161658.654 5014213.585 5030675.728 4576709.134 5459779.4 5012136.549 4957493.616 4413254.71 0.988692512 1.169580954 1.136171355 1.139901515 1.037037161 1.237132175 1.135700719 1.123319169 1 22.07341158 0.799654828 6.080452059 1.000000069 1.130757112 0.226631668 0.068252959 13.07011025 396.6316475 0.058933085 0.014814764 6.304560669 -0.799654828 0.130757043 IEEELGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IEEELGSK 8 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;; 178.83 0.00057589 3248030000 5970120 5046450 4895480 4554600 5851370 3153700 6110500 5020760 7032190 FALSE TRUE 5596460.846 5420094.409 5011603.097 4671478.747 5391827.003 4064121.994 5194287.252 5647612.938 5858472.059 0.955276528 0.925172017 0.855445421 0.797388585 0.920346969 0.693717057 0.886628322 0.96400783 1 22.48209302 1.221457181 4.070128258 0.991271737 0.859488739 0.321194121 0.073839519 0.245981525 8.234176628 0.063428994 0.017866903 16.65164645 -1.221457181 -0.131782998 IEEGERPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IEEGERPDR 9 1 Q5JR04;Q9HCE1;Q9HCE1-2 Q5JR04 MOV10 Putative helicase MOV-10 0 ; 104.52 0.0029607 586420000 395510 405210 415250 436130 422370 358390 462610 374880 324570 FALSE TRUE 370755.7351 435212.17 425099.9261 447321.8342 389198.764 461851.375 393245.9252 421684.5932 270397.1702 1.371152423 1.609529307 1.572131564 1.654314037 1.439359605 1.708048108 1.454327073 1.559500763 1 18.04472053 -0.414888323 0.81458282 0.971385334 1.560646234 0.735988202 0.102517857 6.916518396 3.293505071 0.721274374 0.029456963 0.384690691 0.414888323 0.589260901 IEEIKDFLLTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IEEIKDFLLTAR 12 1 J3KT73;J3QL01;P63173;J3KSP2 J3KT73 RPL38 60S ribosomal protein L38 0 ; 149.57 6.15E-05 615640000 1789130 2411100 1943620 2024930 2204690 1597610 2419800 1923600 2728100 FALSE TRUE 1677151.547 2589620.353 1989723.584 2076893.132 2031542.541 2058814.072 2056973.454 2163765.694 2272762.486 0.737935247 1.139415301 0.875464813 0.91381882 0.893864869 0.905864156 0.905054297 0.952042155 1 21.11601549 4.808893232 22.58847395 0.943850394 0.737925349 0.427178881 0.076369457 61403.96975 19717239.21 0.018538783 117.8521459 64401.09206 -4.808893232 -0.205925044 IEEPVSMEMDNHMSDKDESCYDNAEAAFS(ph)DDEEDLNSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IEEPVSMEMDNHMSDKDESCYDNAEAAFSDDEEDLNSK 38 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 IEEPVSMEMDNHMSDKDES(0.001)CYDNAEAAFS(0.991)DDEEDLNS(0.008)K;IEEPVSMEMDNHMSDKDESCYDNAEAAFS(1)DDEEDLNSK;IEEPVSMEMDNHMSDKDESCYDNAEAAFS(1)DDEEDLNSK 122.3 1.23E-08 189974000 101863 91868 107606 110653 118032 94762 154613 98584 144746 TRUE FALSE 95487.57666 98670.00231 110158.4651 113492.5433 108762.2428 122118.2511 131430.216 110892.4294 120586.9575 0.791856587 0.818247714 0.913518903 0.941167649 0.901940351 1.012698667 1.089920657 0.9196055 1 16.87971435 3.565161592 0.5704121 1.022410299 0.76226069 0.688549873 0.049266154 0.698952844 0.407190061 0.033543986 0.104532404 3674.189837 -3.565161592 -0.260149609 IEEVLSGVLDTELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IEEVLSGVLDTELR 14 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;P18583-8;J3QSZ5 P18583-7 SON Protein SON 0 ; 183.08 3.37E-06 11611800 32273 36590 35474 38426 36432 30131 41715 29379 38018 FALSE TRUE 30253.09054 39299.16167 36315.46003 39412.07622 33570.77768 38829.33056 35460.22301 33047.03282 31672.55019 0.955183285 1.240795624 1.146590969 1.244360684 1.059932891 1.225961608 1.119588502 1.043396652 1 14.95094541 1.222032317 2.710610143 1.004250412 1.157979202 0.243618106 0.088320332 0.305229297 3.824042844 0.071482019 0.020229122 16.67371281 -1.222032317 0.15372879 IEEVPELPLVVEDKVEGYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IEEVPELPLVVEDKVEGYK 19 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ; 159.19 3.09E-11 52403000 160467 87124 111136 115701 116332 83548 145255 88378 123144 FALSE TRUE 150423.6569 93574.75161 113772.1984 118670.0835 107195.754 107666.9513 123475.3612 99412.18784 102590.4709 1.466253694 0.912119331 1.108993822 1.156735928 1.04488997 1.049482963 1.203575344 0.969019705 1 16.64653721 4.752940348 24.67181353 1.066778238 1.466254026 0.688706308 0.08647522 1326.70298 2276224.366 0.020529232 0.44696322 56616.15198 -4.752940348 0.399475788 IEEVPELPLVVEDKVEGYKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IEEVPELPLVVEDKVEGYKK 20 2 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ; 152.32 3.70E-08 667780000 1707580 1262880 1343190 1398140 1560490 945960 1915940 1282500 2422520 FALSE TRUE 1600705.616 1356384.949 1375051.101 1434018.639 1437935.41 1219043.296 1628662.584 1442622.948 2018185.762 0.793140872 0.672081319 0.681330295 0.710548388 0.712489126 0.604029281 0.806993397 0.714811776 1 20.94462754 0.21251711 0.77719299 1.005246265 0.696557029 0.712297711 0.057540908 1.562947724 1.149605353 0.072021096 0.017797567 1.631237174 -0.21251711 -0.308689237 IEFVGQIELFNDKSNTHEFVNLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IEFVGQIELFNDKSNTHEFVNLVK 24 1 O75436;S4R3Q6;O75436-2 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ; 201.32 8.62E-25 103786000 260106 309960 286207 325960 409750 210244 357460 252899 589320 FALSE TRUE 243826.4298 332909.7609 292995.9652 334324.6854 377569.8879 270938.0298 303862.1915 284473.9968 490958.6848 0.496633296 0.67808101 0.596783343 0.680962973 0.769046153 0.55185505 0.618916012 0.579425531 1 18.9052421 -2.098786165 2.352130186 1.637243663 0.626799577 0.711454298 0.075693035 4326654.451 1329184.598 14741768.67 0.017012706 0.007965515 2.098786165 -1.010444086 IEGCIIGFDEYMNLVLDDAEEIHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEGCIIGFDEYMNLVLDDAEEIHSK 25 0 A6NHK2;P62304 A6NHK2 SNRPE Small nuclear ribonucleoprotein E 0 179.47 2.07E-17 25393000 28388 29290 25492 25947 37495 20914 35883 31669 38103 FALSE TRUE 26611.24575 31458.66208 26096.68228 26612.84395 34550.29395 26951.53229 30502.67727 35622.94436 31743.36315 0.838324712 0.991031162 0.822114599 0.838375059 1.088425753 0.849044639 0.960915109 1.122217082 1 14.95416737 1.430892782 5.471114408 1.058886922 0.909478731 0.35212419 0.086702569 0.206328406 11.49195515 0.053192663 0.020242192 26.97073499 -1.430892782 -0.149408191 IEGDMIVCAAYAHELPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 IEGDMIVCAAYAHELPK 17 0 P46777;A0A2R8Y6J3;A0A2R8Y4A2;Q5T7N0 P46777 RPL5 60S ribosomal protein L5 0 ;;;;;; 221.49 3.67E-15 2415154000 3954965 2989893 3555720 3513401 3646503 2736487 4441112 3124087 3866528 FALSE TRUE 3707430.8 3211267.789 3640063.358 3603560.818 3360121.364 3526466.374 3775208.485 3514136.139 3221179.498 1.150954426 0.996922957 1.130040521 1.118708479 1.043133848 1.094774872 1.171995689 1.090947009 1 21.61915763 3.760483818 21.56119407 1.103184413 1.063099857 0 0.059878224 180.5745557 116695.3508 0.014278062 0.025734387 5760.813525 -3.760483818 -0.040084556 IEGDNENKLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IEGDNENKLPR 11 1 B4DXZ6;P51114;P51114-3;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 ; 116.74 0.00086532 485890000 1279640 956760 1025350 1036790 1145130 737800 1339190 916990 1392900 FALSE TRUE 1199549.617 1027599.506 1049671.786 1063395.787 1055196.109 950790.8828 1138390.892 1031478.22 1160415.992 1.03372379 0.885544075 0.904565082 0.916391875 0.909325722 0.819353482 0.981019652 0.888886595 1 20.14621065 -0.882808765 6.44396861 1.000000005 0.913723757 0.16891728 0.057111797 4.04E-09 6.83E-10 0.049234757 0.011604743 0.130975853 0.882808765 -0.086276249 IEGEMQVPDVDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEGEMQVPDVDIR 13 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 184.03 2.29E-05 66179000 126910 124110 121450 119040 150200 107710 130090 113280 145080 FALSE TRUE 118966.9296 133299.2335 124330.8514 122094.7679 138403.8979 138804.1285 110584.2122 127423.2574 120865.2107 0.984294231 1.102875118 1.028673599 1.010172962 1.145109474 1.148420853 0.914938314 1.054259175 1 16.88303952 1.735114493 24.99999982 0.985414485 1.069561029 0.265496625 0.06273812 0.516815606 3700.68676 0.027551027 0.015278407 54.33935674 -1.735114493 0.084146544 IEGVYAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IEGVYAR 7 0 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ;;;; 160.77 0.0031031 2024130000 1772400 2483030 1987760 2028590 2461920 1519890 2008970 2184960 2112160 FALSE TRUE 1661468.648 2666876.125 2034910.606 2080647.054 2268570.734 1958657.57 1707743.599 2457757.066 1759626.851 0.944216467 1.515591856 1.156444393 1.182436522 1.289233983 1.113109617 0.970514628 1.396749012 1 20.74683809 2.199750857 8.887369203 1.101302667 1.248249828 0.048733054 0.180472554 0.589300497 124.4829536 0.063036427 0.046803868 158.3984242 -2.199750857 0.146947161 IEGYEDQVLITEHGDLGNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IEGYEDQVLITEHGDLGNGK 20 0 P47755;F8W9N7;C9JUG7;A0A0D9SET8;P47755-2 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 ; 344.55 3.40E-81 730400000 1921410 1285850 1545860 1386950 1385680 1296800 1930030 1359400 1438010 FALSE TRUE 1801152.378 1381055.672 1582528.529 1422541.485 1276854.282 1671165.108 1640639.919 1529124.082 1197996.841 1.503470056 1.152804101 1.320978883 1.187433419 1.065824415 1.394966206 1.369486014 1.276400763 1 20.19219267 IEGYEDQVLITEHGDLGNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IEGYEDQVLITEHGDLGNSR 20 0 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 ;;; 258.91 2.84E-36 1501920000 1411940 1341840 1530740 1471440 1347940 1317050 1776200 1370320 1309810 FALSE TRUE 1323569.196 1441191.23 1567049.876 1509199.642 1242078.23 1697260.954 1509875.299 1541407.468 1091194.249 1.212954702 1.320746724 1.436087 1.383071477 1.138274171 1.555415963 1.383690668 1.412587602 1 20.05747652 -1.542341067 6.707806239 0.999689901 1.364241176 0.480608384 0.115768118 0.000497525 3.39E-05 0.103876349 0.024463627 0.028685269 1.542341067 0.364551276 IEHLIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEHLIGK 7 0 Q9H0S4;Q9H0S4-2 Q9H0S4 DDX47 Probable ATP-dependent RNA helicase DDX47 0 80.18 0.030613 215800000 859860 787260 808220 820500 830480 601210 945640 767560 828790 FALSE TRUE 806042.8975 845549.5495 827391.3601 841555.4191 765257.4508 774769.5672 803850.0609 863391.5556 690459.5948 1.167400531 1.224618437 1.198319737 1.218833695 1.108330533 1.122107033 1.164224622 1.250459204 1 19.39719747 2.749007738 24.66194883 1.140504793 1.205351764 0.238781302 0.063078941 891.9205386 2105508.98 0.017614296 0.018474812 561.0579731 -2.749007738 0.064846971 IEHSFWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEHSFWR 7 0 Q16531;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 131.04 0.003505 375150000 218920 376650 195170 204600 424510 149960 241410 342500 412900 FALSE TRUE 205218.188 404537.5579 199799.5246 209850.3824 391170.697 193251.0176 205212.8116 385261.8789 343984.3226 0.596591689 1.17603487 0.580839043 0.610057984 1.137175945 0.561801817 0.596576059 1.119998365 1 18.39198329 -1.173406635 7.641287311 1.000000101 0.791367385 0.058623828 0.254149523 4.08E-07 4.43E-08 0.230477801 0.054324113 0.067080048 1.173406635 -0.208632716 IEIESFYEGEDFSETLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IEIESFYEGEDFSETLTR 18 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;; 294.83 6.44E-49 213507000 209698 222579 190861 216735 224702 136357 252662 202150 183585 FALSE TRUE 196573.3765 239058.9808 195388.3131 222296.787 207054.8113 175721.0523 214777.6787 227388.8725 152943.4775 1.285268125 1.563054435 1.277519749 1.453457125 1.353799552 1.148928056 1.404294464 1.486751029 1 17.22263906 -1.860631072 2.607924989 0.837824091 1.374509031 0.497457686 0.117357068 7449526.05 4977714.495 7509917.795 0.026973325 0.013783799 1.860631072 0.536684939 IEINFPAEYPFKPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEINFPAEYPFKPPK 15 1 P68036-2;P68036;P68036-3 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 155.22 2.14E-06 348490000 485440 380750 394980 373310 425700 310260 502690 365720 494020 FALSE TRUE 455057.1769 408941.1262 404349.1121 382889.7666 392267.2392 399827.0253 427316.3012 411380.947 411564.8705 1.105675459 0.993624956 0.982467507 0.930326648 0.953111568 0.971479963 1.038272049 0.999553112 1 18.65076032 -3.520526918 10.17892412 0.999998097 0.994423886 0 0.048122709 0 0 0 0.010384166 0.000301629 3.520526918 -0.005574211 IEIPIHIVPHVTIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IEIPIHIVPHVTIGK 15 0 X6RJS7;P46736-2;P46736-3;P46736;A0A087WZR3;H9KVA9;A0A0D9SF50;P46736-4 X6RJS7 BRCC3 Lys-63-specific deubiquitinase BRCC36 0 ; 202.13 3.51E-09 148666000 355979 378380 399340 403530 441200 326565 462570 385380 460800 FALSE TRUE 333698.9098 406395.6489 408812.5334 413885.263 406549.9317 420839.0142 393211.9228 433495.5413 383889.5031 0.869257709 1.058626625 1.064922406 1.078136442 1.059028518 1.096250381 1.024284122 1.129219574 1 18.55033159 4.738912215 5.671050637 1.064675738 0.862790534 0.750575071 0.035261826 0.060525702 8.150291321 0.007141697 0.047338934 54816.61514 -4.738912215 -0.201885205 IEKEIQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEKEIQQK 8 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;B4DER1;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRU9 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 118.26 0.0017511 298180000 1183200 925120 1001600 997440 1216100 777540 1269800 973610 1647100 FALSE TRUE 1109145.624 993616.8474 1025358.425 1023035.999 1120592.412 1002003.176 1079405.278 1095167.352 1372188.369 0.808304201 0.724111113 0.747243198 0.7455507 0.816646196 0.730222758 0.78663054 0.798117355 1 20.38804711 -0.294247417 0.547819838 1.028773465 0.752800783 0.847817237 0.030962953 2.306134434 0.663862845 0.162584481 0.012587153 0.507870027 0.294247417 -0.275972682 IEKEQSK ddPTM_SK-BR-3_Pertuzumab_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 95.502 0.012238 367060000 970380 903620 1136100 1167200 1608600 906920 1570900 1356900 2177000 FALSE TRUE 909645.648 970524.965 1163048.829 1197152.328 1482267.045 1168733.081 1335358.129 1526311.952 1813644.636 0.501556716 0.535124106 0.641277131 0.66008098 0.817286372 0.644411291 0.736284332 0.841571674 1 20.79046037 3.056168423 0.096953844 1.310454882 6.81E-13 0.872024186 0.053213786 10.07507218 0.327477312 1.495508385 2.852783119 1138.068554 -3.056168423 -1.310454882 IEKLELVPVPQSAHGDFYVGDAYLVLHTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEKLELVPVPQSAHGDFYVGDAYLVLHTAK 30 1 Q9Y6U3;Q9Y6U3-2;F8WBX5;C9JGB6 Q9Y6U3 SCIN Adseverin 0 142.45 3.15E-08 136620000 135460 109350 114610 106450 170510 77578 132400 132320 279070 FALSE TRUE 126981.8004 117446.3878 117328.6033 109181.6872 157118.8324 99973.50923 112547.8491 148840.4433 232491.4141 0.546178451 0.505164409 0.50465779 0.469615997 0.675804881 0.430009468 0.484094647 0.640197591 1 17.82681791 0.871653536 3.398306956 0.999819018 0.513103814 0.846661729 0.064655679 0.193343483 4.282950368 0.057425108 0.014864895 7.441380914 -0.871653536 -0.486715205 IEKLS(ph)DDEEVDITDEVDELSSQTPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEKLSDDEEVDITDEVDELSSQTPQK 26 1 A0A590UK32;A0A590UJW2;A0A590UJD8;Q5VVJ2 A0A590UK32 MYSM1 Histone H2A deubiquitinase MYSM1 1 IEKLS(1)DDEEVDITDEVDELSSQTPQK 182.6 1.12E-17 38356000 87312 46704 56173 53123 60363 37130 77931 46814 62598 TRUE FALSE 81847.29778 50162.01276 57505.45009 54486.22612 55622.33347 47848.82824 66245.97003 52658.83095 52149.9894 1.569459528 0.961879635 1.102693418 1.044798412 1.066583792 0.917523259 1.270296903 1.00975727 1 15.67037934 4.745312394 24.86846973 1.059289614 1.569459779 0.746119341 0.095583763 373.6998017 1376390.698 0.021836071 0.214946807 55630.42711 -4.745312394 0.510170165 IELGDVTPHNIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IELGDVTPHNIK 12 0 E7EQ69;Q9GZZ1;A0A087WWJ2;C9J5D1;Q9GZZ1-2;F8WCK0;C9JZU6;C9J5J3;A0A0D9SF32 E7EQ69 NAA50 N-alpha-acetyltransferase 50 0 ; 172.11 3.66E-05 208550000 490030 492160 487830 467370 565170 347800 556540 453260 696690 FALSE TRUE 459359.897 528600.0385 499401.558 479363.5055 520783.828 448204.2139 473091.9937 509850.5087 580407.9382 0.791443167 0.910738816 0.860431991 0.825907907 0.897272063 0.77222275 0.815102555 0.878434761 1 19.14670773 0.926038038 7.572233779 0.999999336 0.844976371 0.576558538 0.043094188 1.172027069 119.8116977 0.042175212 0.010567474 8.434086256 -0.926038038 -0.155022965 IELPELFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IELPELFDR 9 0 H0YHS6;Q9Y2Z4 H0YHS6 YARS2 "Tyrosine--tRNA ligase;Tyrosine--tRNA ligase, mitochondrial" 0 ;; 143.01 0.00023953 54134000 99118 109583 92345 84550 128027 97006 101558 101035 160548 FALSE TRUE 92914.38131 117696.6393 94535.46701 86719.69614 117972.2759 125010.0574 86330.32072 113649.4422 133751.5016 0.694679164 0.879964994 0.706799295 0.648364281 0.882025805 0.934644142 0.645453095 0.849705916 1 17.02919556 2.709665079 24.95517747 0.830615871 0.752761957 0.219817629 0.110237726 1681.415354 1452126.437 0.035615168 0.033583613 512.4660254 -2.709665079 -0.077853914 IENFDVSFGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IENFDVSFGDR 11 0 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 142.08 8.80E-05 125740000 146580 169670 194140 161630 196140 161230 196420 179400 221430 FALSE TRUE 137405.8195 182232.5433 198745.0925 165777.6994 180735.9556 207774.4836 166968.6445 201798.4849 184471.9025 0.744860424 0.987860703 1.077373246 0.898660973 0.979747881 1.12632049 0.905116943 1.09392532 1 17.49304157 4.736847936 4.368917044 1.008471962 0.726245285 0.556719448 0.074219937 0.145184131 6.734220221 0.016267025 0.126999679 54556.68022 -4.736847936 -0.282226677 IENHEGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 IENHEGVR 8 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;; 162.49 0.0003414 58956350000 23334780 26435015 24883728 23948604 25819826 18633484 26391277 22363213 25810869 FALSE TRUE 21874297.77 28392291.02 25473981.78 24563165.72 23792041.02 24012668.34 22434150.02 25155309.37 21502868.22 1.017273489 1.320395527 1.184678319 1.142320432 1.106458951 1.116719318 1.043309655 1.169858324 1 24.35802577 2.96430193 1.620607481 1.084296577 1.209109915 0.151976716 0.085896828 0.454641353 2.420974557 0.029068971 0.033772395 921.0897079 -2.96430193 0.124813338 IEPADAHVLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEPADAHVLQK 11 0 E7EQ69;Q9GZZ1;A0A087WWJ2;C9J5D1;Q9GZZ1-2;B0AZT5 E7EQ69 NAA50 N-alpha-acetyltransferase 50 0 117.25 0.00087982 150970000 601460 528460 598640 539150 609890 449380 699930 554550 720740 FALSE TRUE 563815.6922 567587.7283 612840.0235 552985.5018 561991.6996 579108.7109 594981.9943 623786.7882 600443.8378 0.938998215 0.945280295 1.020645038 0.920961241 0.935960475 0.964467739 0.990903656 1.038876159 1 19.19566979 1.560394107 3.066524046 1.019011112 0.958938904 0.474268607 0.028326807 0.214292009 4.54756133 0.020124775 0.007814548 36.34076849 -1.560394107 -0.060072209 IEPELDGSAQVTSHDASTNGLINFIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEPELDGSAQVTSHDASTNGLINFIK 26 0 P06744;A0A2U3TZU2;P06744-2;K7EQ48 P06744 GPI Glucose-6-phosphate isomerase 0 233.22 7.37E-45 83743000 103230 85766 93875 93968 90953 77310 124080 91183 83435 FALSE TRUE 96769.01857 92116.20388 96101.75933 96379.37797 83809.91827 99628.14198 105475.3559 102567.3983 69509.15949 1.392176503 1.325238351 1.382576916 1.386570902 1.205739199 1.433309548 1.517431036 1.475595433 1 16.08491548 -0.644119556 8.005933054 1.000000001 1.389311429 0.679679688 0.084103503 0 0 0.086681677 0.020431067 0.226924007 0.644119556 0.389311429 IEQFVYSSPHDNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IEQFVYSSPHDNK 13 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 160.78 4.33E-05 694630000 1279190 951800 1183170 1113600 1129620 828850 1290660 971630 892520 FALSE TRUE 1199127.781 1022272.262 1211235.351 1142176.861 1040904.202 1068125.54 1097137.515 1092940.144 743552.6461 1.612700577 1.37484853 1.628983983 1.536107587 1.399906526 1.436516359 1.47553441 1.469889389 1 19.50407537 -2.904397123 0.318380562 1.05E-12 1.518469254 0.795367785 0.079264 30.58969095 0.924313403 20.68119428 0.069787039 0.001246243 2.904397123 1.518469254 IEQLQNHENEDIYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IEQLQNHENEDIYK 14 0 O00629;H7C4F6 O00629 KPNA4 Importin subunit alpha-3 0 ;;; 281.07 2.66E-33 3224340000 4147610 2952557 3523810 3291570 3490950 2541470 4027150 3015060 4154440 FALSE TRUE 3888018.494 3171167.392 3607396.437 3376037.259 3216784.869 3275151.132 3423316.244 3391496.878 3461037.125 1.123368041 0.916247725 1.042287704 0.975440926 0.929428016 0.946291823 0.989101278 0.979907685 1 21.72277299 4.752474077 24.99443016 0.973309821 1.123368141 0.634417576 0.0360238 1620.558379 2911155.204 0.008394195 0.173788109 56555.39986 -4.752474077 0.15005832 IES(ph)DEEEDFENVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 342.28 4.29E-69 1633340000 3263630 1855240 2086210 2383920 2522730 1627650 2818070 2072210 2726120 TRUE FALSE 3059365.224 1992603.9 2135695.886 2445095.423 2324604.962 2097526.132 2395526.565 2330929.98 2271112.961 1.347077524 0.877368909 0.940374135 1.076606697 1.02355321 0.923567506 1.054780897 1.026338196 1 21.11496803 IES(ph)DVQEPTEPEDDLDIMLGNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IESDVQEPTEPEDDLDIMLGNK 22 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 IES(1)DVQEPTEPEDDLDIMLGNK 123.43 1.56E-05 23119000 74958 43078 46921 44937 48027 34355 70751 44416 60584 TRUE FALSE 70266.51258 46267.53994 48033.98828 46090.1595 44255.15315 44272.73079 60142.54437 49961.43537 50472.13901 1.392184163 0.916694653 0.951693136 0.91318023 0.876823412 0.877171676 1.191598881 0.989881474 1 15.62319961 -2.27803949 11.41014106 0.272516894 1.000489017 0 0.162476081 11.78500445 0.28717417 0.616594758 0.03483215 0.005271819 2.27803949 0.727972123 IES(ph)PKLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 141.08 0.0003871 28778430000 31338250 19419840 21422270 22782750 25645930 14724800 26354480 18090920 27203010 TRUE FALSE 29376844.87 20857705.16 21930416.36 23367393.94 23631802.11 18975610.72 22402870.39 20349611.19 22662651.89 1.296266872 0.92035589 0.967689768 1.031097069 1.042764202 0.837307603 0.988537021 0.897936009 1 24.43381335 4.742547809 24.9853924 0.958882615 1.296267004 0.741526474 0.062252108 192.1275106 1203902.678 0.013894223 0.106126001 55277.42568 -4.742547809 0.337384389 IES(ph)S(ph)IQSLQDLS(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IESSIQSLQDLSK 13 0 A0A087X043;O43424-2;O43424 A0A087X043 GRID2 "Glutamate receptor ionotropic, delta-2" 3 IES(0.977)S(0.513)IQS(0.513)LQDLS(0.997)K 62.203 0.037002 2052000000 2010200 1933100 2235300 2045400 1553900 2448700 3247600 2112800 1110200 TRUE FALSE 1884385.17 2076228.735 2288322.372 2097888.427 1431862.962 3155599.939 2760652.529 2376587.731 924900.4478 2.037392429 2.244813202 2.474128299 2.268231605 1.548126575 3.411826587 2.984810458 2.56956058 1 19.81893856 2.242014742 24.9999983 2.719037954 2.18832431 0.019748894 0.670979492 174.6966332 1264415.612 0.215217044 0.173327427 174.5881415 -2.242014742 -0.530713644 IESDVQEPT(ph)EPEDDLDIMLGNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IESDVQEPTEPEDDLDIMLGNK 22 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 IESDVQEPT(1)EPEDDLDIMLGNK;IESDVQEPT(1)EPEDDLDIMLGNK;IESDVQEPT(1)EPEDDLDIMLGNK 232.12 1.77E-26 340300000 935826 648652 803990 722330 830956 610385 958610 652460 837265 TRUE FALSE 877254.3212 696678.869 823061.0225 740866.2107 765696.0677 786593.2407 814875.3298 733921.0672 697520.0626 1.257676113 0.998794022 1.179981862 1.062143228 1.097740565 1.127699808 1.16824644 1.052186319 1 19.41187519 1.018131962 6.253090059 1.000098968 1.119053076 0.278607097 0.069597668 0.171150715 24.85823737 0.060208859 0.015130024 10.4263419 -1.018131962 0.118954108 IESFVETLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IESFVETLKR 10 1 P49770;G3V5E5;H0YJJ8 P49770 EIF2B2 Translation initiation factor eIF-2B subunit beta 0 ; 175.86 4.28E-06 399450000 429100 412980 371450 406530 497110 296180 487400 422910 645240 FALSE TRUE 402243.397 443557.4689 380260.9694 416962.2481 458068.9858 381682.3579 414318.8948 475711.2444 537545.2756 0.748296777 0.825153692 0.707402682 0.775678379 0.852149589 0.710046903 0.770760927 0.884969631 1 19.03602675 1.018648937 2.931424309 0.99881004 0.768923832 0.746265008 0.044658739 0.111058144 2.186486364 0.040344087 0.010686833 10.43876058 -1.018648937 -0.229886208 IESGAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IESGAFR 7 0 O94933 O94933 SLITRK3 SLIT and NTRK-like protein 3 0 81.784 0.090384 0 204400 331220 166470 185350 342550 136040 219100 276390 300830 FALSE TRUE 191606.9689 355743.8734 170418.747 190106.3948 315647.5048 175312.5396 186247.989 310897.8999 250619.5296 0.764533272 1.419457909 0.679989893 0.758545813 1.259468906 0.699516673 0.743150342 1.240517451 1 17.93513932 3.964020211 24.68198989 0.885658787 1.127644418 0.066466462 0.26016071 604.3030013 1138492.65 0.061340831 0.111470944 9204.924087 -3.964020211 0.241985631 IESLIDRDYMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IESLIDRDYMER 12 1 Q13619;A0A0A0MR50;Q13619-2;A0A669KAX4;Q13620-1;K4DI93;Q13620;Q13620-3 Q13619;A0A669KAX4 CUL4A;CUL4B Cullin-4A;Cullin-4B 0 ; 196.38 1.89E-07 466620000 358610 489530 405400 464960 551430 352140 489290 452610 628920 FALSE TRUE 336165.2402 525775.3106 415016.2794 476891.6608 508122.9122 453797.1015 415925.5068 509119.3548 523949.189 0.641598932 1.003485303 0.792092608 0.910186848 0.969794253 0.866108987 0.793827943 0.971696045 1 18.99906738 -4.451753288 0.016482679 2.029397689 2.24E-06 0.213152026 0.102050949 9374.739691 12.78785422 986.4973106 625.5096265 3.53E-05 4.451753288 -2.029395451 IESWLETHALLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IESWLETHALLEK 13 0 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 0 128.54 0.00016411 56491000 186760 186280 193100 187770 216150 151410 232430 172830 202630 FALSE TRUE 175071.025 200072.365 197680.4232 192588.4961 199174.4509 195119.6091 197579.2793 194408.2059 168809.744 1.037090756 1.185194411 1.171024957 1.140861253 1.179875321 1.155855133 1.170425798 1.151640903 1 17.36503866 -1.462255306 6.106598492 0.99991871 1.156254096 0.542700367 0.042521631 4.19E-05 3.69E-06 0.036624016 0.008627886 0.03449409 1.462255306 0.156335387 IET(ph)DEEESCDNAHGDANQPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IETDEEESCDNAHGDANQPAR 21 0 Q96T23-2;Q96T23;Q96T23-3 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 IET(1)DEEESCDNAHGDANQPAR;IET(1)DEEESCDNAHGDANQPAR 399.81 1.72E-131 1408890000 291910 252393 266140 271100 324960 249339 351010 219220 313200 TRUE FALSE 273639.8742 271080.4403 272452.9665 278056.885 299438.9524 321319.1216 298379.3091 246590.0996 260924.8967 1.048730411 1.038921329 1.044181563 1.065658695 1.147605906 1.231462102 1.143544801 0.945061597 1 17.99327508 2.929620964 4.882934151 1.116925842 1.043977692 0.032055881 0.080315219 0.411080006 18.57053932 0.024014979 0.025973672 850.3955215 -2.929620964 -0.07294815 IETELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IETELR 6 0 P63104;E7EX29;B0AZS6;E7ESK7;E9PD24;E7EVZ2 P63104;REV__P53355-4 YWHAZ 14-3-3 protein zeta/delta 0 ;;;;; 141.98 0.026948 3015560000 5626150 5996610 6027280 6111910 5879950 5155590 6924330 5208810 5242620 FALSE TRUE 5274019.314 6440605.244 6170249.928 6268751.958 5418162.446 6643925.139 5886090.999 5859141.395 4367592.853 1.20753456 1.47463499 1.412734688 1.435287621 1.240537437 1.521186924 1.347673924 1.341503568 1 22.05840694 0.552416545 1.625180194 1.00009585 1.3935001 0.592788601 0.096948952 1.391988893 4.344984248 0.082509336 0.023529394 3.567931801 -0.552416545 0.39340425 IETIEVMEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 IETIEVMEDR 10 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;;;;; 249.69 1.12E-12 2992560000 2426620 2649600 2616640 2531140 2713210 2218650 2971050 2331210 2705660 FALSE TRUE 2274742.186 2845779.141 2678707.936 2596093.338 2500125.431 2859138.238 2525568.634 2622266.7 2254067.867 1.009172004 1.262508189 1.188388325 1.151736989 1.10916156 1.268434851 1.120449243 1.163348601 1 21.10409952 0.246605675 0.988606198 0.999065005 1.174588108 0.289763484 0.075669832 4.071836364 4.382073513 0.074624472 0.021175659 1.764435043 -0.246605675 0.175523104 IETLDPALIRPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IETLDPALIRPGR 13 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ;;; 196.57 1.28E-07 1802450000 2891920 3178690 3148380 3145260 2953670 2676150 3577160 2554000 3088830 FALSE TRUE 2710919.889 3414043.515 3223061.06 3225972.697 2721700.673 3448711.061 3040798.067 2872872.522 2573284.318 1.053486344 1.326726118 1.252508725 1.253640211 1.057675848 1.340198219 1.181679788 1.116422504 1 21.29517944 1.042199494 2.115269277 1.00234364 1.228534624 0.326863228 0.096740596 0.304759328 2.83954412 0.084035808 0.023439092 11.02045419 -1.042199494 0.226190984 IETMLGDVAVAVHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IETMLGDVAVAVHPK 15 0 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 94.673 0.0043803 89680000 731020 592880 662860 655500 777640 548750 803100 555970 970770 FALSE TRUE 685266.7631 636777.4521 678583.3522 672321.2398 716567.2912 707165.2168 682682.6106 625384.0783 808742.2156 0.847324092 0.787367643 0.839060135 0.831317108 0.886026817 0.874401266 0.844128818 0.773279874 1 19.6253204 -1.99395161 3.054706477 1.157930304 0.835201902 0.696497121 0.034154601 4711987.655 6871691.76 5219205.296 0.008100419 0.010140244 1.99395161 -0.322728403 IETSIGQSTVIIDLTEDS(ph)NEQPDSLVDHNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IETSIGQSTVIIDLTEDSNEQPDSLVDHNK 30 0 Q13111;Q13111-2;Q13111-3;K7EJF1 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 IETSIGQSTVIIDLTEDS(0.991)NEQPDS(0.009)LVDHNK 99.774 0.00033442 68312000 31664 22338 29078 27388 27502 27185 35370 24993 32447 TRUE FALSE 29682.20676 23991.92876 29767.74389 28090.82245 25342.10386 35032.86819 30066.59686 28113.43107 27031.38608 1.098064549 0.887558214 1.101228912 1.039192824 0.937506637 1.296007096 1.112284689 1.040029208 1 14.72234787 2.279963254 24.99997325 1.126692579 1.008918562 0.189912582 0.099805077 195.2603571 117902.4439 0.032363452 0.027076992 190.5299501 -2.279963254 -0.117774017 IETSIGQSTVIIDLTEDSNEQPDSLVDHNKLNSEAS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IETSIGQSTVIIDLTEDSNEQPDSLVDHNKLNSEASPSR 39 1 Q13111;Q13111-2;Q13111-3;K7EJF1 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 IETSIGQSTVIIDLTEDSNEQPDSLVDHNKLNS(0.155)EAS(0.841)PS(0.004)R 264.27 4.34E-63 58310000 37806 43283 45075 44170 51227 33102 52348 31794 69733 TRUE FALSE 35439.78995 46487.71836 46144.20029 45303.47698 47203.83806 42658.01003 44498.90338 35763.55089 58094.11181 0.610040998 0.800213944 0.794300814 0.779829066 0.812540834 0.734291458 0.76597958 0.61561404 1 15.82610432 -2.433216065 2.478027097 3.918272768 0.753631459 0.549733079 0.073161994 3654874.465 1002022.128 61577977.03 0.016901062 0.003687941 2.433216065 -3.164641309 IETWHKPDLGTLENVHGLDPNTWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IETWHKPDLGTLENVHGLDPNTWK 24 1 A0A0A0MSW4;P48739;P48739-3;P48739-2;B3KYB7;B3KYB6 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 ; 180.66 2.25E-17 472840000 836970 651190 656150 679000 742050 500390 864950 660880 682500 FALSE TRUE 784585.5417 699404.7852 671714.1879 696424.2895 683772.3863 644844.4698 735258.7773 743392.3228 568586.3409 1.379888128 1.230076657 1.181375878 1.224834716 1.202583209 1.13411882 1.293134788 1.307439643 1 19.11701992 4.746984518 3.101638174 1.206595843 1.408465188 0.307686803 0.08601284 0.467427275 6.781822109 0.018753362 0.233603476 55845.02858 -4.746984518 0.201869345 IEVEKPFAIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IEVEKPFAIAK 11 1 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 138.94 0.0014129 0 442490 374690 277230 263530 328540 210930 502880 365140 612440 FALSE TRUE 414795.3408 402432.4375 283806.0265 270292.626 302737.7937 271822.0668 427477.8125 410728.5328 510219.8075 0.81297381 0.788743266 0.556242667 0.529757218 0.593347787 0.53275483 0.837830688 0.805003112 1 18.96075938 1.279784537 1.589543507 0.96971389 0.641704739 0.534091488 0.108386248 0.295618847 1.365916353 0.104093925 0.03164778 19.04515613 -1.279784537 -0.328009151 IEVIEIMTDR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;; 238.51 7.68E-12 3338239000 2343419 2569772 2555878 2419899 2633863 2178322 2758294 2187426 2580716 FALSE TRUE 2196748.588 2760040.593 2616504.633 2481997.705 2427010.024 2807168.199 2344713.421 2460530.951 2149977.828 1.021754066 1.28375305 1.21699145 1.154429443 1.128853513 1.305673093 1.090575629 1.144444803 1 21.03589035 0.89055845 1.036725455 1.002114281 1.195289779 0.279344942 0.084696115 0.730928894 1.587960283 0.073930566 0.023995974 7.77245919 -0.89055845 0.193175498 IEVLDS(ph)PASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IEVLDSPASK 10 0 Q8N5I9 Q8N5I9 C12orf45 Uncharacterized protein C12orf45 1 IEVLDS(0.974)PAS(0.026)K;IEVLDS(0.997)PAS(0.003)K 164.48 6.45E-06 277260000 1441230 927860 1145980 1045370 1101080 989380 1465080 978390 997080 TRUE FALSE 1351025.987 996559.7198 1173163.187 1072195.964 1014605.618 1274997.945 1245404.855 1100544.145 830660.9066 1.626447057 1.199719057 1.412325026 1.290774557 1.221443805 1.534919887 1.49929393 1.324901818 1 19.66390013 -1.856661917 1.766335558 0.787131129 1.381346084 0.4427958 0.136819696 240378.7188 92869.47905 214639.8213 0.035731676 0.013910351 1.856661917 0.594214955 IEVLPVDTGAGGYSGNSGS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IEVLPVDTGAGGYSGNSGSPK 21 0 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 IEVLPVDTGAGGYS(0.051)GNS(0.196)GS(0.752)PK;IEVLPVDTGAGGYSGNS(0.092)GS(0.908)PK 170.5 8.51E-12 102284000 183350 103779 147017 127302 158634 101660 154639 109833 180813 TRUE FALSE 171874.4508 111462.9051 150504.3127 130568.7848 146175.5255 131007.5917 131452.3175 123545.8918 150634.1422 1.141005938 0.739957778 0.999138113 0.866794094 0.970401022 0.869707158 0.872659515 0.820171908 1 17.20068928 IEVLQQHENEDIYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IEVLQQHENEDIYK 14 0 O00505;H0Y4S9 O00505 KPNA3 Importin subunit alpha-4 0 ;;; 207.5 9.35E-09 780870000 1012100 720524 890071 850961 914630 710100 1091720 794962 872607 FALSE TRUE 948754.4677 773872.3467 911183.9044 872798.0999 842798.6492 915094.3425 928026.721 894214.7556 726963.2544 1.305092743 1.06452746 1.253411227 1.200608276 1.159341472 1.258790368 1.276579958 1.230068714 1 19.47152292 3.755624659 24.44589196 1.214460978 1.165029585 0 0.098051302 961.0272669 824216.3723 0.022515347 0.040579654 5696.717186 -3.755624659 -0.049431393 IEVPLYSLLEQTHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IEVPLYSLLEQTHLK 15 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 227.41 7.35E-13 510620000 525280 431310 487400 465990 561200 407340 548540 444320 486960 FALSE TRUE 492403.6625 463244.6412 498961.3582 477948.0923 517125.6158 524932.4454 466291.5194 499794.3301 405683.2301 1.213763907 1.141887578 1.229928479 1.178131253 1.274702964 1.293946622 1.149398064 1.231981736 1 18.62999414 -0.737655796 6.209079685 0.999999997 1.208997758 0.653301918 0.048911711 2.07E-09 4.44E-10 0.046274393 0.010906979 0.182954967 0.737655796 0.208997761 IEWLESHQDADIEDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IEWLESHQDADIEDFK 16 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;; 314.34 9.14E-58 1468390000 3645200 2370610 2509960 2627020 2116670 1764890 3530280 2134670 2246030 FALSE TRUE 3417053.439 2546132.431 2569497.436 2694433.781 1950435.276 2274385.092 3000947.288 2401188.248 1871153.083 1.826175244 1.360729089 1.373216045 1.439985753 1.042370768 1.215499209 1.60379571 1.283266597 1 20.83549616 8 0.033368985 3.10E-07 3.425699702 0.388760762 0.191431622 1498.090767 3.823891921 118.8512062 318.5650639 100000000 -8 3.425699393 IEYDCELVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IEYDCELVPR 10 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 166.16 1.31E-05 223330000 137986 160614 151284 158307 178641 137501 168404 152028 183970 FALSE TRUE 129349.7026 172506.0277 154872.5279 162369.4256 164611.2565 177195.3066 143153.3836 171009.0305 153264.2185 0.843965433 1.12554665 1.010493704 1.059408564 1.074035793 1.156142695 0.934030036 1.115779222 1 17.2256614 4.750464749 24.73621018 1.056224055 0.843965285 0.514599937 0.065699117 1280.043346 2659811.603 0.014505259 0.235568521 56294.34225 -4.750464749 -0.21225877 IEYDDFVECLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IEYDDFVECLLR 12 0 O43920 O43920 NDUFS5 NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 0 ;;; 195.27 1.08E-06 100152000 109367 126676 110835 106092 157762 101102 106997 137462 181231 FALSE TRUE 102521.9147 136055.2228 113464.0585 108814.5003 145372.0089 130288.5061 90953.79316 154624.4333 150982.3753 0.679032334 0.901133146 0.751505322 0.720709951 0.962840918 0.862938511 0.602413315 1.024122405 1 17.20402062 1.201266797 24.99973292 1.012062117 0.790037907 0.444472383 0.106262195 184.3670036 123585.4919 0.099102499 0.024778077 15.8952293 -1.201266797 -0.22202421 IEYQFFEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 IEYQFFEDR 9 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ;;;;;;; 150.27 0.00019926 1052006000 786287 1250825 813985 816341 1186959 567182 922593 984513 812337 FALSE TRUE 737074.7002 1343437.384 833293.1086 837289.6921 1093740.028 730918.236 784258.7446 1107431.615 676752.7068 1.089134469 1.985123031 1.231311083 1.237216614 1.616159074 1.080037403 1.158855719 1.636390374 1 19.36826923 3.731858964 24.20109749 1.278864682 1.603254744 0.106741016 0.295791039 210.7874276 1076724.398 0.06938021 0.120050166 5393.354464 -3.731858964 0.324390062 IFAPNHVVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IFAPNHVVAK 10 0 Q02543;M0R3D6;M0R1A7;M0R117 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 129.38 0.00030458 3690900000 7544800 8410200 7566400 7319100 8921000 5548300 8962200 7727600 8487200 FALSE TRUE 7072584.436 9032899.959 7745878.581 7506920.497 8220380.646 7150004.141 7618401.311 8692407.871 7070631.491 1.000276205 1.277523793 1.095500252 1.061704391 1.162609119 1.011225681 1.077471131 1.229367968 1 22.75340764 3.706842442 14.29011681 1.090321828 1.167044013 0.023939015 0.09428167 4.90939875 3459.122162 0.022679771 0.03546446 5091.461239 -3.706842442 0.076722185 IFAQDGEGQR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 167.12 1.24E-05 681410000 395032 759180 417765 419964 807110 357155 511941 640590 802540 FALSE TRUE 370307.6523 815390.4771 427674.5831 430740.9872 743722.8363 460259.8506 435180.1997 720569.0716 668590.8894 0.553862845 1.219565642 0.639665586 0.644251954 1.112373573 0.688402815 0.650891609 1.077742881 1 19.35076417 1.218769833 24.99877673 1.038871687 0.808446953 0.18380457 0.217027015 515.4077786 651021.5193 0.198764565 0.04996493 16.54892674 -1.218769833 -0.230424734 IFASIAPSIYGHEDIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IFASIAPSIYGHEDIKR 17 1 P49736 P49736 MCM2 DNA replication licensing factor MCM2 0 ; 131.82 1.67E-05 338450000 767950 941860 902960 913810 1071620 637040 1143120 967910 1258920 FALSE TRUE 719885.3803 1011596.294 924378.6376 937259.9117 987459.2879 820943.1065 971719.7682 1088755.694 1048798.119 0.6863908 0.964529089 0.881369465 0.893651404 0.941515121 0.782746547 0.926507924 1.038098443 1 20.00030557 7.999999999 0.069855768 1.12067917 0.386269206 0.321108804 0.08483143 388.1784709 2.001395843 3.678732219 28.0460993 99999999.83 -7.999999999 -0.734409964 IFCCHGGLSPDLQSMEQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 324.79 1.71E-62 1614260000 1232348 1497196 1329162 1278115 1560610 1079616 1515018 1355768 1351503 FALSE TRUE 1155217.538 1608049.95 1360690.35 1310913.595 1438045.986 1391283.613 1287855.116 1525038.619 1125928.418 1.026013306 1.428199096 1.208505202 1.164295681 1.277209068 1.23567679 1.143816156 1.354472091 1 20.10268368 -1.868519929 2.279929775 0.880530031 1.2383121 0.293733444 0.111274086 6831895.498 3585123.446 4415258.089 0.025596605 0.01353568 1.868519929 0.357782068 IFCCHGGLSPDLQSMEQIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IFCCHGGLSPDLQSMEQIRR 20 1 F8W0W8;P36873;P36873-2;F8VYE8;F8VR82;F8W1A0;P62140;E7ETD8;P62136;P62136-2;P62136-3 F8W0W8;P62140;P62136 PPP1CC;PPP1CB;PPP1CA Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit;Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 ; 237.86 8.45E-30 476120000 208030 229630 213540 238420 295290 194553 259050 208145 345520 FALSE TRUE 195009.7736 246632.0441 218605.2696 244538.2608 272099.1145 250717.2928 220207.8574 234132.3614 287850.4799 0.677468989 0.85680609 0.759440352 0.849532233 0.94527935 0.870998349 0.765007783 0.813381869 1 18.13496009 -5 0.182474305 1.709507174 0.783368611 0.410788848 0.071093408 149.7697889 1.449237063 38.96283436 0.21321123 1.00E-05 5 -0.926138563 IFCSEDEQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IFCSEDEQSR 10 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ;; 229.61 3.58E-09 449950000 377525 414187 417577 441238 418436 353351 474778 343443 288859 FALSE TRUE 353896.3842 444853.8364 427482.1236 452560.9141 385573.7244 455357.6975 403589.4465 386322.6146 240646.5668 1.470606412 1.848577532 1.776389871 1.880604075 1.602240703 1.892226029 1.677104527 1.605352695 1 17.87655632 0.629606016 1.433308358 1.000278483 1.760734283 0.756239285 0.130201348 0.584245259 1.709203876 0.109401819 0.032047628 4.26192709 -0.629606016 0.760455799 IFDEVMGCFSDS(ph)PPQS(ph)PTFPEAGHTSLYDEDKVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IFDEVMGCFSDSPPQSPTFPEAGHTSLYDEDKVPR 35 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 2 IFDEVMGCFSDS(1)PPQS(0.968)PT(0.031)FPEAGHTSLYDEDKVPR;IFDEVMGCFS(0.156)DS(0.844)PPQS(0.861)PT(0.098)FPEAGHT(0.009)S(0.007)LY(0.024)DEDKVPR;IFDEVMGCFS(0.015)DS(0.984)PPQS(0.587)PT(0.402)FPEAGHT(0.006)S(0.005)LYDEDKVPR 169.82 3.55E-15 303317000 90233.3 186006 198305 179145 218794 175253 162738 145460 183803 TRUE FALSE 84585.75882 199778.0778 203008.8882 183742.164 201610.8018 225845.6961 138336.9477 163621.0012 153125.0919 0.552396461 1.304672378 1.325771536 1.199948106 1.316641181 1.474909783 0.903424422 1.068544673 1 17.22435118 1.664303027 11.11269125 0.990994823 1.227687799 0.122581176 0.248439004 0.203647742 34.38959282 0.110371138 0.059870532 46.16395696 -1.664303027 0.236692975 IFDFDDDGTLNREDLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IFDFDDDGTLNREDLSR 17 1 Q99828;Q99828-2 Q99828 CIB1 Calcium and integrin-binding protein 1 0 141.86 5.55E-07 31113000 45892 53882 46577 45363 61295 42397 45982 37863 63886 FALSE TRUE 43019.70164 57871.47934 47681.82844 46527.09138 56481.13795 54636.32564 39087.42598 42590.2789 53223.01388 0.808291348 1.087339388 0.895887417 0.874191219 1.061216452 1.026554523 0.734408353 0.800222982 1 15.69976259 1.745364302 25 0.821871459 0.96713601 0.185243562 0.108333592 1.759969505 6486.877502 0.046235516 0.025639985 55.63707653 -1.745364302 0.145264551 IFDLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 IFDLGR 6 0 P27635;X1WI28;Q96L21;A6QRI9;B8A6G2 P27635 RPL10;RPL10L 60S ribosomal protein L10;60S ribosomal protein L10-like 0 ;;;;;; 149.11 0.024845 5774242000 4676300 6381590 5322940 5222540 6493820 4349140 5752180 5515420 5963230 FALSE TRUE 4383618.73 6854089.564 5449202.65 5356559.218 5983821.572 5604666.116 4889694.01 6204032.328 4967928.389 0.882383639 1.379667545 1.096876248 1.078227945 1.204490303 1.128169667 0.984252112 1.248816779 1 22.24421295 0.55548623 0.301447838 0.980491728 1.172169723 0.015549618 0.141146933 7.86693974 1.607987343 0.481213429 0.181060553 3.593240037 -0.55548623 0.191677995 IFDLQDWTQEDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IFDLQDWTQEDER 13 0 A0A2R8YDQ9;A0A2R8Y6Y7;Q9P2R7-2;Q9P2R7;Q5T9Q5;Q5T9Q8 A0A2R8YDQ9 SUCLA2 "Succinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial" 0 ;; 121.04 0.00058456 50552000 74179 94950 85250 83017 93077 83738 90693 78207 82160 FALSE TRUE 69536.2688 101980.1968 87272.17026 85147.35677 85767.10787 107911.8012 77094.4266 87971.3161 68446.96523 1.015914564 1.489915535 1.275033451 1.243990241 1.253044713 1.576575395 1.126338127 1.285247868 1 16.06269896 0.675741226 1.124188553 1.00224247 1.313075949 0.226300158 0.160240289 1.400037106 2.915455103 0.137611714 0.042853497 4.739594926 -0.675741226 0.31083348 IFDLQDWTQEDERDKDAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IFDLQDWTQEDERDKDAAK 19 2 A0A2R8YDQ9;A0A2R8Y6Y7;Q9P2R7-2;Q9P2R7;Q5T9Q5 A0A2R8YDQ9 SUCLA2 "Succinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial" 0 ; 230.99 2.48E-20 92648000 237517 110836 133353 120926 184032 93373 155182 131708 306370 FALSE TRUE 222651.2349 119042.4128 136516.1961 124029.1659 169578.8691 120328.2693 131913.8997 148152.0337 255234.8678 0.87233863 0.46640341 0.534864994 0.48594131 0.664403224 0.471441345 0.516833381 0.580453741 1 17.9614659 0.935588275 18.15820671 1.000000001 0.552074278 0.539638392 0.122447206 495.0113399 139549.4047 0.104970681 0.026242614 8.621608045 -0.935588275 -0.447925723 IFDSEEILAGYKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IFDSEEILAGYKR 13 1 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 161.48 6.75E-05 564490000 419790 506360 440120 471120 579870 327130 553740 424480 765710 FALSE TRUE 393516.0932 543851.4213 450559.8542 483209.7368 534329.3493 421567.1205 470711.8277 477477.2624 637908.0543 0.616885287 0.852554561 0.706308458 0.757491199 0.837627532 0.660858752 0.737899176 0.748504834 1 19.28298897 -1.811986573 2.331823094 1.092485901 0.746170361 0.568368714 0.071075631 6772151.02 4033963.891 3524678.773 0.016360126 0.015417481 1.811986573 -0.34631554 IFEGTNDILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IFEGTNDILR 10 0 P49748;P49748-3;P49748-2;J3KSR4;G3V1M7;J3QRJ8 P49748 ACADVL "Very long-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 81.525 0.048271 48825000 57255 88092 53754 50897 106960 50101 48052 79083 104300 FALSE TRUE 53671.51175 94614.42334 55029.07026 52203.10319 98559.79306 64564.34538 40847.04869 88956.68663 86891.6562 0.617683148 1.088878121 0.633306726 0.600783844 1.134283743 0.743044248 0.470091727 1.023765578 1 16.40693003 2.03382519 24.99994619 0.730946321 0.827894624 0 0.240785155 732.4232899 541325.6359 0.085817689 0.063380278 108.0998745 -2.03382519 0.096948303 IFFDT(ph)DDDDDMPHSTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IFFDTDDDDDMPHSTSR 17 0 Q8NG27-3;Q8NG27 Q8NG27-3 PJA1 E3 ubiquitin-protein ligase Praja-1 1 IFFDT(1)DDDDDMPHSTSR 108.71 0.0018214 52835000 23463 26170 22282 25340 23457 18843 28024 21702 25043 TRUE FALSE 21994.49271 28107.65403 22810.53956 25990.2673 21614.78184 24282.66821 23822.06136 24411.54247 20863.16152 1.054226259 1.347238481 1.093340506 1.245749226 1.036026195 1.163901655 1.141824136 1.170078775 1 14.34867017 -4.999999992 0.130651697 0.440588271 1.236111896 0.209419551 0.091614341 188.5213346 1.552174568 27.58418162 0.620230642 1.00E-05 4.999999992 0.795523625 IFGPIWNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IFGPIWNR 8 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 186.29 0.00048449 6811100000 1167330 1654890 1436530 1276650 1839570 1180830 1553430 1586560 1653770 FALSE TRUE 1094268.899 1777419.778 1470605.17 1309411 1695097.593 1521716.452 1320507.593 1784645.508 1377745.103 0.794246263 1.290093337 1.067400034 0.950401491 1.230341947 1.104497812 0.95845566 1.295337943 1 20.39387757 -0.956101467 4.720960344 0.999998893 1.093845358 0.026467515 0.15889298 1.66E-06 3.67E-07 0.137870432 0.032495989 0.110636527 0.956101467 0.093846465 IFHELTQTDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IFHELTQTDK 10 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ;;; 182.28 1.79E-06 2058110000 5213140 4795180 4593140 4490200 5770080 3450770 5064260 4871600 6125930 FALSE TRUE 4886858.873 5150220.117 4702091.45 4605426.134 5316921.192 4446951.28 4304921.227 5479829.984 5103472.708 0.9575556 1.009159921 0.921351346 0.90241026 1.041824165 0.871357904 0.843527824 1.073745329 1 22.28304785 3.931847341 5.380068699 0.935733763 0.984432026 0.002232283 0.074339819 0.516519658 35.46354518 0.01849882 0.035004242 8547.662004 -3.931847341 0.048698262 IFHIVENDLYIDFGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IFHIVENDLYIDFGGK 16 0 H0YC42;U3KQQ8;E5RGC7;E5RK86;E5RFH3;H0YAT2;Q9Y2Q9;H7C5V3 H0YC42;E5RGC7 MRPS28 "28S ribosomal protein S28, mitochondrial" 0 180.81 2.41E-09 99771000 294200 192380 240290 223600 291530 223900 252230 254400 364420 FALSE TRUE 275786.5472 206624.0154 245989.7923 229337.9546 268634.4098 288536.2953 214410.4531 286162.4 303595.9478 0.908399961 0.680588845 0.810253872 0.75540519 0.884841882 0.95039574 0.706236215 0.942576481 1 18.21179301 -0.383664689 0.241546112 1.097001493 0.758438618 0.285753927 0.091569326 11.5946783 0.909588112 1.045890543 0.174389984 0.413366532 0.383664689 -0.338562875 IFHTVTTTDDPVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IFHTVTTTDDPVIR 14 0 O15371-2;O15371;O15371-3;B0QYA5;B0QYA4 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ; 142.38 9.42E-06 668330000 180274 200884 196830 201648 220344 176200 208559 178968 206314 FALSE TRUE 168990.9721 215757.6604 201498.9005 206822.6291 203039.0711 227066.0796 177287.5141 201312.5488 171878.8606 0.983198117 1.255289101 1.172330907 1.203304632 1.181291698 1.321082063 1.031467823 1.171246703 1 17.39103259 0.982564615 1.076565675 1.008020536 1.186637378 0.206270139 0.098222217 0.739743907 1.791966484 0.083152776 0.026877659 9.606487337 -0.982564615 0.178616842 IFILGPSHHVPLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IFILGPSHHVPLSR 14 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 ; 105.19 0.0005864 406370000 234324 383060 315720 307400 377120 270910 341190 346490 366770 FALSE TRUE 219658.0791 411422.161 323209.0275 315288.4044 347502.5164 349117.3191 290031.727 389750.0392 305553.7176 0.71888531 1.346480626 1.057781362 1.031859167 1.137287804 1.142572645 0.949200452 1.275553256 1 18.22106651 IFLGADAEEEIGT(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IFLGADAEEEIGTPR 15 0 P28749;P28749-2;H0YE05 P28749 RBL1 Retinoblastoma-like protein 1 1 IFLGADAEEEIGT(1)PR;IFLGADAEEEIGT(1)PR;IFLGADAEEEIGT(1)PR 214.53 2.75E-11 88523000 99700 118267 118757 120784 123064 112823 142488 120437 120898 TRUE FALSE 93459.95497 127023.6117 121573.9721 123883.5219 113399.0499 145393.1686 121123.2472 135473.8246 100719.3428 0.927924591 1.261164025 1.207056845 1.229987394 1.12589148 1.44354763 1.202581787 1.345062635 1 16.61998125 4.741094839 24.7747504 1.238736144 0.927924466 0.38362659 0.118261576 188.8845706 1846427.578 0.024276548 0.165038642 55092.79919 -4.741094839 -0.310811678 IFLLGLADNEAAIVQAESEETKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IFLLGLADNEAAIVQAESEETKER 24 1 Q9UHB9;Q9UHB9-4;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 143.4 2.24E-07 10483000 20974 23368 22587 24368 26965 17732 25696 25577 31214 FALSE TRUE 19661.27478 25098.19103 23122.77431 24993.32413 24847.27767 22850.94055 21843.12335 28770.34475 26004.18175 0.756081271 0.965159807 0.889194458 0.961127113 0.955510845 0.878740995 0.839985029 1.106373776 1 14.66645602 8 0.074479621 1.078579767 0.529222679 0.24804999 0.082504108 433.3706783 2.36840535 2.853518551 24.7186994 100000000 -8 -0.549357089 IFQGNVHNFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IFQGNVHNFEK 11 0 Q96DI7;Q96DI7-2;Q9NSS8 Q96DI7 SNRNP40;DKFZp434D199 U5 small nuclear ribonucleoprotein 40 kDa protein 0 133.07 0.00016936 456200000 717730 659580 657220 616750 750150 486340 754930 615640 752660 FALSE TRUE 672808.5605 708415.9895 672809.5688 632576.8492 691236.245 626738.4629 641735.2549 692504.0092 627036.1836 1.072997983 1.129784864 1.072999591 1.008836277 1.102386534 0.999525194 1.023442142 1.10440837 1 19.25818917 3.510719961 3.84542756 1.03967389 1.103444527 0.292821193 0.039756129 0.233026383 7.298611611 0.010104138 0.015509323 3241.30546 -3.510719961 0.063770637 IFQGSFGGPTLY(ph)ENPHYQSPNMHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IFQGSFGGPTLYENPHYQSPNMHR 24 0 Q8TDN6 Q8TDN6 BRIX1 Ribosome biogenesis protein BRX1 homolog 1 IFQGSFGGPT(0.001)LY(0.388)ENPHY(0.282)QS(0.33)PNMHR 91.583 0.0068786 130940000 41661 37901 40703 34859 39707 26184 46979 34853 45379 TRUE FALSE 39053.51238 40707.22948 41668.49438 35753.54096 36588.57239 33742.89574 39934.93508 39204.47377 37804.95174 1.033026378 1.076769778 1.102196735 0.945736982 0.967824867 0.892552276 1.056341385 1.037019543 1 15.20628759 3.243261616 24.9999717 0.983905994 1.076477256 0.420294464 0.048232652 108.6218108 577647.0014 0.013806397 0.018094435 1750.901103 -3.243261616 0.092571262 IFQGSFGGPTLYENPHYQS(ph)PNMHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IFQGSFGGPTLYENPHYQSPNMHR 24 0 Q8TDN6 Q8TDN6 BRIX1 Ribosome biogenesis protein BRX1 homolog 1 IFQGSFGGPT(0.006)LY(0.022)ENPHY(0.447)QS(0.525)PNMHR 78.272 0.023207 117740000 28155 33129 25615 26520 28729 20939 33133 27933 25643 TRUE FALSE 26392.82881 35581.90563 26222.5999 27200.5481 26472.74023 26983.74938 28165.01424 31420.49654 21363.01764 1.235444788 1.665584246 1.227476396 1.27325402 1.239185431 1.263105702 1.318400552 1.470789243 1 14.38282783 -4.624874861 0.153110155 1.15E-15 1.446296619 0.317424223 0.142662583 137.1438017 1.373248763 43.23769271 0.680746565 2.37E-05 4.624874861 1.446296619 IFQIHTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IFQIHTSR 8 0 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 163.32 0.0003366 342950000 86125 337400 242330 275320 269010 218330 280470 296680 245290 FALSE TRUE 80734.58999 362381.4471 248078.182 282385.1773 247883.0397 281358.3267 238416.1273 333721.1511 204349.5144 0.3950809 1.773341367 1.213989584 1.381873494 1.213034641 1.376848521 1.166707579 1.633090013 1 17.64067929 IFQVAQELSGEDMHQFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IFQVAQELSGEDMHQFHR 18 0 C4P0D6;C4P0D8;Q99598;C4P0D4;Q5VVQ1 C4P0D6 DISC1;TSNAX Translin-associated protein X 0 ; 93.754 0.0012089 90732000 80868 103376 107357 88116 108638 79815 117639 97974 115504 FALSE TRUE 75806.61623 111030.0666 109903.5587 90377.20574 100106.0097 102856.2948 100000.1241 110206.2696 96225.63622 0.787800624 1.153851208 1.142144267 0.939221701 1.040325776 1.068907402 1.039225387 1.145290111 1 16.55413368 IFSGSSHQDLSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IFSGSSHQDLSQK 13 0 B1ALA9;P60891;A0A2R8Y7H4;Q15244;B1ALA7;A0A0B4J207;P21108 B1ALA9;A0A0B4J207 PRPS1;PRPS1L1 Ribose-phosphate pyrophosphokinase 1;Ribose-phosphate pyrophosphokinase 3 0 212.59 1.27E-08 326960000 461620 727060 588690 614360 812230 480860 746080 728110 970460 FALSE TRUE 432728.0282 780892.2789 602654.0048 630125.5177 748440.7322 619676.4759 634212.2303 819016.1363 808483.9566 0.535233909 0.965872325 0.745412447 0.779391493 0.925733561 0.766467251 0.784446278 1.013027073 1 19.62485962 -4.999999997 0.074947897 1.656271894 0.60304171 0.31549551 0.121001996 408.4020786 2.18741939 44.64730328 4.833022622 1.00E-05 4.999999997 -1.053230184 IFSIVEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IFSIVEQR 8 0 B3KWE1;P12081-4;P12081;B4DDD8;P12081-3;P12081-2;B4E1C5;E7ETE2 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 ; 102 0.011746 310340000 607080 824890 824730 658930 784050 576810 719680 614820 804630 FALSE TRUE 569083.9465 885965.7139 844292.9851 675839.2594 722473.8757 743325.6833 611770.6652 691581.6304 670332.0549 0.848958277 1.321681855 1.259514563 1.008215636 1.077785063 1.108891747 0.912638238 1.031700074 1 19.3545164 3.228627909 24.96708112 1.020018633 1.198181341 0.107568647 0.135159726 248.9130266 625672.4684 0.037704992 0.045568318 1692.886763 -3.228627909 0.178162708 IFSNTDPDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IFSNTDPDKK 10 1 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ; 151.79 3.08E-05 3712900000 9944500 5919700 7120800 7018700 7567000 4963400 9650500 6140700 9721300 FALSE TRUE 9322091.496 6358000.747 7289708.739 7198811.725 6972718.344 6396253.006 8203497.116 6907379.912 8098752.228 1.151052808 0.785059299 0.900102699 0.888879116 0.860962053 0.789782528 1.01293346 0.852894337 1 22.94926822 0.347617872 0.792724188 1.0002175 0.890934865 0.048170777 0.109211733 6.121871201 5.242332393 0.113544297 0.033503455 2.22647525 -0.347617872 -0.109282635 IFTLPGDCLIYPAHDYHGFTVSTVEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IFTLPGDCLIYPAHDYHGFTVSTVEEER 28 0 M0QXB5;O95571 M0QXB5 ETHE1 "Persulfide dioxygenase ETHE1, mitochondrial" 0 55.662 0.037585 70878000 100830 61127 78532 81574 79983 54432 102160 71272 96336 FALSE TRUE 94519.23029 65652.90668 80394.81613 83667.32694 73701.45782 70145.63477 86842.05641 80170.46609 80256.89925 1.177708473 0.818034428 1.001718443 1.042493888 0.918319279 0.874013766 1.082050979 0.998923044 1 16.2923378 1.720278819 23.20653705 1.030335792 0.958343762 0.051369193 0.100036217 1.441127804 1816.305412 0.043111748 0.023902999 52.51444976 -1.720278819 -0.07199203 IFTPLLHQIELEKPKPIPYIYGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IFTPLLHQIELEKPKPIPYIYGSR 24 2 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 184.26 1.58E-17 2118700000 3421300 3285200 2872400 2483400 4748000 3271400 6712200 3864300 7108800 FALSE TRUE 3207166.94 3528439.626 2940534.684 2547128.248 4375111.233 4215800.073 5705767.923 4346766.361 5922295.355 0.541541201 0.595789202 0.496519425 0.430091391 0.738752624 0.711852385 0.963438596 0.733966494 1 22.49772501 2.284311947 1.686595791 0.887450102 0.528682285 0.741868484 0.094529878 0.17151517 0.980621629 0.044351569 0.028759971 192.4473553 -2.284311947 -0.358767817 IFTSIGEDYDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 IFTSIGEDYDER 12 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 ;;;;;;; 314.33 4.99E-46 5706490000 4294150 4651900 4577650 4304600 6044520 4269440 4639180 4843830 6592710 FALSE TRUE 4025386.817 4996331.516 4686234.02 4415063.324 5569807.782 5501958.019 3943578.027 5448592.838 5492344.11 0.732908706 0.909690183 0.853230228 0.80385774 1.014103936 1.00175042 0.718013647 0.992034135 1 22.38899059 0.738359616 0.019566756 1.841397455 1.98E-06 0.216918175 0.099503064 967.6573536 9.943080034 483.9283283 449.5841163 5.474691051 -0.738359616 -1.841395472 IFVGGIKEDTEEYNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IFVGGIKEDTEEYNLR 16 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;; 223.06 8.27E-15 1846973000 1891447 1836663 1871258 1914889 2240587 1446257 2348356 1791180 2650019 FALSE TRUE 1773064.709 1972651.44 1915645.123 1964028.294 2064620.335 1863767.918 1996241.819 2014812.766 2207713.709 0.80312257 0.893526833 0.867705407 0.889620917 0.935184814 0.844207249 0.904212267 0.912624113 1 21.07412167 -5 0.129344063 1.395391117 0.831940162 0.635596784 0.031707353 94.96574391 0.776932957 9.725065363 0.226729313 1.00E-05 5 -0.563450954 IFVGGIPHNCGETELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IFVGGIPHNCGETELR 16 0 K7EQ55;K7EK33;Q96EP5;Q96EP5-2;K7EQ02 K7EQ55 DAZAP1 DAZ-associated protein 1 0 ; 171.08 5.05E-09 1502230000 1288310 1375230 1250340 1277580 1360850 1250520 1557960 1230450 1542770 FALSE TRUE 1207676.977 1477053.46 1279998.655 1310364.866 1253974.33 1611524.824 1324358.361 1384074.391 1285271.72 0.939627752 1.149214938 0.995897315 1.019523611 0.975649204 1.25383979 1.030411189 1.076872983 1 20.29364196 IFVGGLNPEATEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IFVGGLNPEATEEK 14 0 Q99729-3;D6R9P3;D6RD18;D6RBZ0;Q99729-2 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ; 146.16 1.95E-05 58022000 150771 131552 144548 130643 156904 93613 150294 117902 160945 FALSE TRUE 141334.5122 141292.247 147976.7468 133995.5206 144581.3928 120637.5534 127758.81 132622.3242 134082.2398 1.054088241 1.053773022 1.103626752 0.999353239 1.078303831 0.89972806 0.952839169 0.98911179 1 17.03275863 2.251085917 24.9917356 0.954071355 1.060863097 0.629191326 0.036975276 125.0360492 249484.2675 0.012184708 0.010128811 178.2731414 -2.251085917 0.106791742 IFVNDDR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;; 205.95 0.00053279 5857060000 6334870 7719550 7208370 6876360 7479790 6375130 8042250 6463300 7796260 FALSE TRUE 5938381.795 8291113.514 7379355.94 7052819.039 6892357.465 8215526.539 6836389.273 7270257.232 6495013.84 0.914298559 1.276535157 1.136157077 1.085882065 1.061176717 1.264897465 1.052559616 1.119359775 1 22.63090117 0.696131225 1.05242686 1.000797778 1.136015287 0.079663032 0.105317624 2.041822631 3.883648843 0.092343346 0.029354092 4.967423924 -0.696131225 0.135217509 IFWEVFHELPLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IFWEVFHELPLEK 13 0 Q5GLZ8-6;Q5GLZ8-3;Q5GLZ8-2;Q5GLZ8 Q5GLZ8-6 HERC4 Probable E3 ubiquitin-protein ligase HERC4 0 103.88 0.0015757 23529000 66664 76267 67897 66960 81112 59383 85429 76945 68833 FALSE TRUE 62491.61924 81913.88804 69507.5489 68678.30696 74741.79071 76525.9081 72619.71453 86551.75263 57344.32762 1.089761129 1.428456683 1.212108534 1.197647785 1.303385946 1.334498306 1.266380086 1.509334161 1 15.80736316 IFYDMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IFYDMK 6 0 P60981;F6RFD5 P60981 DSTN Destrin 0 ; 133.99 0.033099 5445800000 8625000 8251000 8488100 7732200 9381400 6752100 10250400 8072800 12924400 FALSE TRUE 8085176.646 8861912.625 8689441.74 7930621.343 8644622.687 8701321.659 8713447.68 9080706.85 10767234.15 0.750905621 0.82304448 0.807026356 0.736551396 0.802863815 0.808129696 0.809255893 0.843364854 1 23.36014437 0.491712744 0.93759294 1.000919838 0.791381178 0.864397254 0.02615735 0.607670235 0.775222963 0.025379981 0.008098855 3.102506814 -0.491712744 -0.20953866 IFYPEIEEVQALDDTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IFYPEIEEVQALDDTER 17 0 P33316-2;H0YNW5;P33316;A0A0C4DGL3;H0YKC5 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 ;;;; 232.5 2.88E-16 201574000 41847.5 45832.3 50662.1 45592.2 50994.4 45177.9 46681.5 42755.9 63863.2 FALSE TRUE 39228.33967 49225.77118 51863.82894 46762.17304 46989.50553 58220.02633 39682.04244 48094.06823 53204.01935 0.7373191 0.925226548 0.974810354 0.878921811 0.883194655 1.094278723 0.745846704 0.903955544 1 15.69924762 4.739700866 24.0665557 0.919462899 0.737319025 0.298382427 0.090360626 75.86656763 1600917.902 0.020345779 0.125529973 54916.24904 -4.739700866 -0.182143874 IFYPETTDIYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IFYPETTDIYDR 12 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 166.19 0.00012234 359334000 302857 384691 318931 330810 372671 277280 328012 318132 345726 FALSE TRUE 283901.721 413173.9219 326496.1939 339299.1447 343402.9229 357326.2347 278829.6457 357851.4805 288022.0971 0.985694236 1.434521608 1.133580365 1.178031644 1.192279781 1.240620905 0.968084215 1.242444535 1 18.13581997 1.649311959 0.481633821 1.014495939 1.239504594 0.097936014 0.135459345 1.389962527 0.806169181 0.131953853 0.089947106 44.59764837 -1.649311959 0.225008655 IFYPETTDIYDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IFYPETTDIYDRK 13 1 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 157.22 7.46E-05 811680000 695890 698900 633120 683100 857990 506061 776590 643180 905740 FALSE TRUE 652335.4871 750647.2832 648137.9054 700629.5025 790606.9264 652152.5955 660147.539 723482.4388 754566.1427 0.864517304 0.994806473 0.858954396 0.928519666 1.047763584 0.864274924 0.874870342 0.958805859 1 19.52528784 3.391250874 0.005074287 1.844592507 1.59E-07 0.070035283 0.064641072 71361.48724 95.39275679 16967.53571 17710.24873 2461.789267 -3.391250874 -1.844592348 IFYVNYLSELSEHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IFYVNYLSELSEHVK 15 0 Q07960;H0YE29 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 215 2.40E-12 160298000 387740 435160 368960 402750 470570 290840 458870 452400 402610 FALSE TRUE 363472.0455 467379.6992 377711.9054 413085.2469 433613.3304 374800.7866 390066.7034 508883.1359 335411.79 1.083659121 1.393450418 1.126113979 1.231576406 1.292779035 1.117434741 1.162948695 1.517189172 1 18.35557388 IGADEEIDDFKGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IGADEEIDDFKGR 13 1 Q8WUA2 Q8WUA2 PPIL4 Peptidyl-prolyl cis-trans isomerase-like 4 0 166.48 3.06E-05 136400000 200800 161330 171390 188130 212390 130590 226880 160380 301790 FALSE TRUE 188232.2864 173275.0411 175455.4517 192957.7343 195709.7461 168289.213 192861.4503 180403.796 251419.2994 0.748678749 0.689187511 0.697859918 0.767473837 0.778419742 0.669356782 0.767090875 0.717541559 1 17.93973587 -5 0.345219316 4.070428699 0.716544058 0.837924547 0.037253685 150.9441179 1.253904174 342.2975568 0.027923857 1.00E-05 5 -3.353884641 IGAEVYHNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IGAEVYHNLK 10 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;; 167.67 5.17E-06 16288170000 14445010 20119530 11716580 11468080 23151020 7803630 13672200 19643160 21433540 FALSE TRUE 13540922.61 21609200.94 11994502.81 11762370.35 21332832.28 10056411.3 11622180.54 22095651.77 17856143.71 0.758334097 1.210182965 0.671729742 0.658729597 1.194705454 0.563190545 0.650878528 1.237425736 1 24.08991721 3.96582233 24.23384742 0.816717198 1.007086307 0.025893137 0.256980105 576.5549311 1236595.608 0.061222855 0.111707806 9243.199572 -3.96582233 0.190369109 IGALHSIVFAGFSSESLCER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IGALHSIVFAGFSSESLCER 20 0 Q9NR19;Q9NR19-2;C9J7L5 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 166.6 1.50E-11 7239300 12133 18435 15309 17087 16709 14614 16080 14994 14216 FALSE TRUE 11373.61719 19799.94658 15672.13671 17525.48135 15396.74254 18832.82456 13668.95328 16866.03391 11843.25776 0.960345322 1.671832783 1.323296092 1.47978552 1.300042847 1.590172649 1.154154841 1.424104266 1 13.53177836 0.181657487 0.605456695 0.982730151 1.406486139 0.212235018 0.207678238 4.069909556 1.976490054 0.360359885 0.075598884 1.519348799 -0.181657487 0.423755988 IGDEDVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IGDEDVGR 8 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ;;; 157.58 0.00087158 2542600000 5438500 5476190 4429610 3840890 4195240 2874980 5918140 4140420 6725270 FALSE TRUE 5098113.993 5881652.806 4534682.441 3939453.74 3865762.773 3704940.055 5030769.848 4657360.551 5602778.99 0.90992595 1.049774195 0.809363077 0.703124958 0.689972383 0.661268285 0.897906174 0.831259016 1 22.41771115 3.779168993 3.399538019 0.783519817 0.981055636 0.326296604 0.106683973 0.236093243 5.505217944 0.027389042 0.051223482 6014.077119 -3.779168993 0.197535819 IGDEYAEDS(ph)S(ph)DEEDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IGDEYAEDSSDEEDIR 16 0 Q14137;Q14137-2;A0A075B729 Q14137 BOP1 Ribosome biogenesis protein BOP1 2 IGDEYAEDS(1)S(1)DEEDIR;IGDEYAEDS(1)S(1)DEEDIR 228.9 5.38E-15 2011050000 626250 472750 526630 485190 474810 482320 618760 428650 364840 TRUE FALSE 587054.1304 507752.9019 539121.9123 497640.7968 437520.3379 621557.9542 525982.6823 482167.8961 303945.847 1.93144317 1.67053739 1.773743308 1.63726796 1.439468057 2.044962812 1.730514456 1.586361192 1 18.21345478 0.810880392 2.901873214 1.000288364 1.741123708 0.675144857 0.162137608 0.508379611 6.784083429 0.144646527 0.038014787 6.469644117 -0.810880392 0.740835344 IGDEYFTFITDCKDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IGDEYFTFITDCKDPK 16 1 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 226.25 5.58E-15 1141300000 4288700 2197500 3011600 2800300 3025600 2192500 3816700 2383400 3754700 FALSE TRUE 4020277.923 2360205.186 3083036.574 2872160.439 2787981.581 2825439.158 3244421.268 2680972.737 3128016.314 1.285248387 0.754537365 0.985620363 0.91820507 0.891293811 0.903268677 1.037213666 0.857084001 1 21.57681661 IGDKDVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IGDKDVGR 8 1 P45877 P45877 PPIC Peptidyl-prolyl cis-trans isomerase C 0 58.981 0.092581 223320000 230710 211200 229590 216650 261730 175960 287540 238330 358130 FALSE TRUE 216270.2729 226837.4678 235035.9832 222209.6058 241174.7816 226756.7955 244426.0464 268086.0251 298355.7894 0.724873727 0.760291825 0.787770815 0.744780607 0.808346243 0.760021436 0.819243518 0.89854474 1 18.18667425 1.086850863 1.328881857 1.000351246 0.765311154 0.925494634 0.022466235 0.096606266 0.346733241 0.019371016 0.005942236 12.21380165 -1.086850863 -0.235040093 IGDPLLEDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IGDPLLEDTR 10 0 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ; 130.31 0.00065137 108990000 286970 298620 277400 274950 319160 242010 314160 290760 316230 FALSE TRUE 269009.06 320730.1355 283980.059 282005.6825 294094.461 311874.3583 267054.6245 327062.026 263449.1701 1.021104222 1.21742701 1.07793112 1.070436784 1.116323354 1.183812263 1.013685579 1.241461592 1 18.00716511 -1.105631166 4.212178197 0.999983139 1.116925351 0.186919685 0.077176534 1.29E-05 2.74E-06 0.066589683 0.015692658 0.078409527 1.105631166 0.116942212 IGDQEFDHLPALLEFYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IGDQEFDHLPALLEFYK 17 0 P46109 P46109 CRKL Crk-like protein 0 ; 144.66 5.04E-07 139271000 752950 643290 650880 593440 752870 458350 764810 676730 726530 FALSE TRUE 705824.2036 690919.8609 666319.181 608668.6751 693742.6271 590668.2043 650133.8406 761221.2302 605267.4494 1.166136068 1.141511677 1.100867363 1.005619376 1.146175344 0.975879679 1.074126556 1.257660941 1 19.20721324 3.920010582 1.899519946 1.075476672 1.156056755 0.127614211 0.081160997 0.692571121 4.853132153 0.021171948 0.055296468 8317.840384 -3.920010582 0.080580084 IGDYVQQHGGVSLVEQLLQDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IGDYVQQHGGVSLVEQLLQDPK 22 0 B3KWE1;P12081-4;P12081;B4DDD8;P12081-3;P12081-2;B4E1C5;E7ETE2 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 ; 235.76 1.79E-30 764240000 816900 597290 703950 710460 767890 539050 910670 606810 880210 FALSE TRUE 765771.6872 641513.9731 720648.0264 728691.6064 707583.0169 694664.9843 774123.4877 682571.5643 733297.2646 1.044285482 0.87483481 0.98275019 0.993719248 0.964933392 0.947317026 1.055674861 0.930825188 1 19.48403863 3.681749259 8.119354288 0.986412362 0.941895155 0.00205633 0.052813364 0.530011109 86.3158468 0.012968929 0.020258951 4805.61815 -3.681749259 -0.044517208 IGEEFLTDLSQLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IGEEFLTDLSQLKK 14 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 145.69 1.36E-05 123120000 377960 236020 292350 284820 349810 199290 406710 250470 485950 FALSE TRUE 354304.1583 253495.1664 299284.6801 292128.9634 322337.3337 256821.7878 345727.6112 281741.7309 404841.8056 0.875166925 0.626158571 0.739263277 0.721587937 0.796205652 0.63437566 0.853981991 0.695930427 1 18.62699875 -2.462069922 0.32958924 1.39592307 0.720692918 0.469245061 0.083962295 41.2137749 1.622228921 11.79949771 0.064928759 0.003450882 2.462069922 -0.675230152 IGEEQSAEDAEDGPPELLFIHGGHTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IGEEQSAEDAEDGPPELLFIHGGHTAK 27 0 Q16576;E9PC52;Q16576-2;Q5JNZ6 Q16576 RBBP7 Histone-binding protein RBBP7 0 ;;;;; 298.17 5.62E-71 1265810000 1382781 905058 1083347 1058046 1052892 769430 1305282 880575 1365552 FALSE TRUE 1296235.206 972069.436 1109044.502 1085197.252 970202.1095 991551.9503 1109567.082 990516.7271 1137632.549 1.139414661 0.854466969 0.974870579 0.953908406 0.852825554 0.871592458 0.975329936 0.870682478 1 20.11760322 4.749140368 24.77737435 0.919030068 1.139414802 0.613101432 0.054974458 882.5523831 2066858.33 0.012172007 0.17405125 56122.93408 -4.749140368 0.220384734 IGEEQSPEDAEDGPPELLFIHGGHTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IGEEQSPEDAEDGPPELLFIHGGHTAK 27 0 Q09028-3;Q09028;Q09028-2;Q09028-4;H0YF10;H0YCT5;H0YDK2;H0YEU5 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 ;;;; 208.89 1.09E-25 1238140000 1189170 754270 909310 843670 927300 656012 1033610 737938 1323180 FALSE TRUE 1114741.972 810116.9356 930879.2626 865320.0005 854473.5985 845392.0149 878629.7761 830071.1837 1102332.71 1.011257275 0.734911455 0.844463068 0.784989861 0.775150361 0.766911847 0.797064052 0.753013293 1 20.0721283 -1.137223855 3.723011644 1.000116897 0.801238204 0.369860718 0.078060935 17364878.04 33812379.16 26234.18416 0.016411453 0.072908161 1.137223855 -0.198878693 IGEGT(ph)YGVVYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IGEGTYGVVYK 11 0 P06493;A0A024QZP7;A0A087WZZ9;E5RIU6;P06493-2;G3V317;K7ELV5;G3V5T9;P24941;P24941-2;E7ESI2;Q00526 P06493;G3V5T9 CDK1;CDC2;CDK2;CDK3 Cyclin-dependent kinase 1;Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 1 IGEGT(0.76)Y(0.24)GVVYK;IGEGT(0.954)Y(0.046)GVVYK;IGEGT(0.998)Y(0.002)GVVYK 194.8 3.94E-06 7254900000 8294900 5729900 6525500 6598600 7175000 5040700 8613500 6024200 7722700 TRUE FALSE 7775737.016 6154147.758 6680287.942 6767931.247 6611504.443 6495868.261 7321985.639 6776334.631 6433731.479 1.208588988 0.95654408 1.038322467 1.051944936 1.027631393 1.009657969 1.13806205 1.05325108 1 22.61722429 1.774683181 25 1.078583119 1.036240195 0 0.072603983 114.9239547 79571.95019 0.03064779 0.01700836 59.52277648 -1.774683181 -0.042342924 IGEGTY(ph)GVVYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IGEGTYGVVYK 11 0 P06493;A0A024QZP7;A0A087WZZ9;E5RIU6;P06493-2;G3V317;K7ELV5;G3V5T9;P24941;P24941-2;E7ESI2;Q00526 P06493;G3V5T9 CDK1;CDC2;CDK2;CDK3 Cyclin-dependent kinase 1;Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 1 IGEGT(0.27)Y(0.729)GVVYK;IGEGT(0.277)Y(0.723)GVVYK;IGEGT(0.326)Y(0.674)GVVYK 207.68 2.28E-07 13361700000 7120800 4581080 5709280 5150890 5322290 4298260 7050720 4600440 6193280 TRUE FALSE 6675121.839 4920267.93 5844706.818 5283070.558 4904298.812 5539097.886 5993529.992 5174815.061 5159581.558 1.293733177 0.953617629 1.132786981 1.023933918 0.950522587 1.073555641 1.161631021 1.002952469 1 22.29882264 4.753371448 24.42756325 1.049748957 1.293733414 0.562970195 0.070236163 1625.785079 2681351.217 0.016885167 0.378822066 56672.3795 -4.753371448 0.243984458 IGEHMEEHGIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IGEHMEEHGIK 11 0 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 ;;;; 132.32 0.00010693 2361540000 5457190 4521320 4927420 4645540 5351850 3570120 5695690 4512840 6251140 FALSE TRUE 5115634.219 4856083.237 5044300.729 4764752.421 4931537.289 4600755.688 4841674.161 5076278.008 5207784.35 0.98230531 0.932466268 0.968607836 0.914928903 0.946954973 0.883438211 0.929699434 0.974748121 1 22.31223828 1.061435329 4.084031616 0.999333701 0.936423554 0.391745129 0.027091805 0.192480527 6.30597006 0.025281231 0.006481322 11.5195451 -1.061435329 -0.062910147 IGEHTPSALAIMENANVLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 IGEHTPSALAIMENANVLAR 20 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BR04;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;;;; 357.72 1.97E-95 17372946000 9679244 10168980 9468803 9477557 9804779 7002281 11004466 7896681 8816787 FALSE TRUE 9073437.396 10921901.86 9693407.479 9720767.158 9034751.208 9023725.852 9354448.484 8882599.006 7345208.291 1.235286603 1.486942429 1.3196913 1.323416134 1.230019742 1.228518715 1.273544345 1.209305258 1 22.80837197 0.061277469 0.20326309 0.838640239 1.437073705 0.67672526 0.068810209 4.635393972 0.373428984 0.74518432 0.225267268 1.151535867 -0.061277469 0.598433466 IGELGAPEVWGLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_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 233.48 1.31E-17 2945063000 5554070 2978525 3763680 3436517 3891383 2736250 4914523 2862238 4573750 TRUE FALSE 5206450.673 3199058.09 3852956.267 3524703.844 3585769.476 3526160.956 4177635.9 3219594.715 3810361.577 1.366392813 0.839568116 1.011178648 0.925031332 0.941057536 0.925413739 1.096388313 0.844957795 1 21.86149648 4.748584096 24.88688938 0.954665849 1.366393052 0.747196127 0.076402863 665.7334115 1652887.15 0.01745408 0.237886769 56051.09428 -4.748584096 0.411727203 IGEWELIQESGVPLKPLFGPGYTGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IGEWELIQESGVPLKPLFGPGYTGIR 26 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 178.33 2.24E-17 395640000 769940 707550 671510 621560 726550 545630 809470 654720 729230 FALSE TRUE 721750.8298 759937.7382 687438.5343 637510.2819 669489.6938 703144.5234 688097.4883 736463.2332 607516.802 1.188034351 1.250891721 1.131554769 1.049370618 1.102010169 1.157407534 1.132639436 1.21225163 1 19.21256478 -4.999999786 0.020490519 1.23E-07 1.944718358 0.371834835 0.05869962 3507.651407 5.44012765 350.3977912 188.9257137 1.00E-05 4.999999786 1.944718235 IGEYLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IGEYLEK 7 0 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 89.296 0.067322 0 122370 101620 113950 112370 115460 84608 138890 100970 120310 FALSE TRUE 114711.0801 109144.0505 116652.9478 115253.6044 106392.2373 109032.9561 118064.7339 113576.3268 100229.4838 1.144484395 1.088941561 1.163858612 1.149897217 1.061486434 1.087833161 1.177944148 1.133162843 1 16.61294743 -1.116532689 4.744876802 0.999991842 1.126922761 0.538153791 0.036659235 3.14E-06 5.85E-07 0.03526169 0.008310726 0.076465813 1.116532689 0.126930919 IGFPWSEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IGFPWSEIR 9 0 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 ; 148.04 0.0002116 738890000 278990 818100 198043 210615 921450 145512 248970 676200 803490 FALSE TRUE 261528.5139 878672.9752 202740.6735 216019.7375 849083.034 187518.9522 211639.2598 760625.0585 669382.3283 0.390701252 1.312662343 0.302877242 0.322715029 1.268457499 0.280137291 0.31617097 1.136308842 1 19.35247094 1.217823109 24.93553199 1.068154958 0.622294302 0.199324738 0.388675605 469.2698405 564251.8945 0.363360253 0.091248213 16.5128908 -1.217823109 -0.445860655 IGGAQNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IGGAQNR 7 0 P14174 P14174 MIF Macrophage migration inhibitory factor 0 ;;;; 98.513 0.026074 910900000 711390 1030590 1097610 1220160 1353090 1268550 1102260 1026740 1081350 FALSE TRUE 666865.3698 1106895.956 1123645.828 1251471.371 1246823.77 1634759.792 936986.3459 1154930.749 900865.6992 0.740249485 1.228702521 1.247295605 1.389187503 1.384028464 1.814654274 1.040095484 1.282023225 1 19.78095252 5.079013538 1.42235594 1.324096586 2.61E-12 0.383185583 0.222501634 2.93775653 2.858766405 0.056354261 6.986175061 119953.6694 -5.079013538 -1.324096586 IGGELEEQAVMLEDFSHELESTQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IGGELEEQAVMLEDFSHELESTQSR 25 0 O43752;O43752-2 O43752 STX6 Syntaxin-6 0 ; 155.97 4.62E-08 29079000 20414.4 23965 23669 18865 25899 18658.5 29877 25299 29918 FALSE TRUE 19136.69914 25739.39354 24230.43986 19349.10784 23864.99701 24044.90605 25397.22121 28457.63584 24924.49252 0.767786912 1.032694789 0.97215379 0.776308999 0.957491792 0.964709955 1.018966432 1.141753872 1 14.60527651 1.718765591 2.151812788 1.07163881 0.925091307 0.363839164 0.089866179 0.350028117 3.380588395 0.060349351 0.025087816 52.33179018 -1.718765591 -0.146547503 IGGIGTVPVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IGGIGTVPVGR 11 0 A0A2U3TZH3;Q05639;P68104;A0A087WVQ9;Q5VTE0 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3 0 123.21 0.0008718 1367900000 811340 828100 845900 810010 863350 736450 975260 785150 977590 FALSE TRUE 760559.6777 889413.3856 865965.1475 830796.2279 795545.9736 949051.1597 829028.8169 883177.7058 814423.9135 0.933862163 1.092076707 1.063285511 1.020102939 0.976820499 1.165303651 1.017932803 1.084420154 1 19.6354204 IGGNEGIDVPIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IGGNEGIDVPIPR 13 0 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 77.305 0.061209 34433000 104570 115220 104530 110300 107520 94631 122850 83727 123320 FALSE TRUE 98025.15036 123751.0087 107009.501 113130.4847 99075.81291 121949.4335 104429.783 94180.50026 102737.0953 0.954135895 1.204540661 1.041585813 1.101164914 0.964362605 1.18700488 1.016475915 0.916713675 1 16.64859766 1.492803991 6.787615541 0.960417997 1.084243144 0.252041121 0.082952761 0.1457787 16.36141015 0.042319109 0.019022158 31.10312252 -1.492803991 0.123825147 IGGVQQDTILAEGLHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IGGVQQDTILAEGLHFR 17 0 Q99623-2;Q99623;F5GY37;J3KPX7;F5H0C5;F5H3X6;F5H2D2 Q99623-2 PHB2 Prohibitin-2 0 ;;; 218.43 4.65E-15 1027100000 568305.1 551756.1 485912.9 426151.3 719582.3 458371.7 542162.5 568405.9 745476 FALSE TRUE 532735.8982 592608.6957 497438.9835 437087.0638 663069.2088 590696.1687 460870.2663 639372.6278 621051.2396 0.857797013 0.954202581 0.80096287 0.703785833 1.067656204 0.951123081 0.742080906 1.029500606 1 19.24435278 2.738977549 24.99999956 0.925164954 0.845318965 0.224866272 0.108009264 90.83307245 5446648.682 0.034914383 0.035008391 548.2486226 -2.738977549 -0.079845989 IGGVTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IGGVTER 7 0 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 79.939 0.072735 115960000 81920 103510 105100 108830 125150 96727 95708 97874 117390 FALSE TRUE 76792.77343 111173.9881 107593.0216 111622.762 115321.2238 124650.5147 81357.47391 110093.7843 97796.85063 0.785227468 1.136784951 1.100168573 1.14137379 1.17919159 1.274586184 0.8319028 1.125739568 1 16.57750039 1.733487582 25 0.975801158 1.110903383 0.127284806 0.142597939 0.950861165 4645.233473 0.060970695 0.033811274 54.13617677 -1.733487582 0.135102225 IGHHS(ph)TSDDSSAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IGHHSTSDDSSAYR 14 0 F5H5P2;P12694;P12694-2;F5GXU9 F5H5P2 BCKDHA "2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial" 1 IGHHS(0.945)T(0.02)S(0.034)DDS(0.001)SAYR;IGHHS(0.997)T(0.003)SDDSSAYR 159.69 3.14E-06 3312600000 2143981 2004978 1802177 2022919 2557155 1704981 1962714 1824529 1971380 TRUE FALSE 2009793.056 2153428.657 1844925.489 2074830.526 2356326.361 2197181.337 1668423.257 2052325.462 1642343.942 1.223734569 1.311192255 1.123349039 1.263334965 1.434733798 1.337832643 1.015879326 1.249631949 1 20.64732486 1.742112201 24.99999719 1.098912399 1.272470244 0.435635234 0.103382463 0.655425247 4637.999225 0.047622107 0.026408733 55.22200881 -1.742112201 0.173557845 IGHHS(ph)TSDDSSAYRS(ph)VDEVNYWDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IGHHSTSDDSSAYRSVDEVNYWDK 24 1 F5H5P2;P12694;P12694-2;F5GXU9 F5H5P2 BCKDHA "2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial" 2 IGHHS(0.882)T(0.074)S(0.044)DDSSAYRS(1)VDEVNYWDK 260.65 6.69E-44 136700000 66728 86527 61205 69750 136030 36613 71016 78828 178230 TRUE FALSE 62551.61359 92933.54911 62656.8115 71539.90309 125346.7525 47182.57874 60367.81008 88669.84932 148482.2616 0.421273308 0.625889908 0.421981797 0.481807741 0.844186714 0.31776576 0.406565804 0.597174695 1 17.17993106 0.965447797 18.32736589 1.000000005 0.503477973 0.535002811 0.144843577 95.70722774 50766.62573 0.132651586 0.033163199 9.235231728 -0.965447797 -0.496522032 IGHHSTS(ph)DDSSAYRS(ph)VDEVNYWDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IGHHSTSDDSSAYRSVDEVNYWDK 24 1 F5H5P2;P12694;P12694-2;F5GXU9 F5H5P2 BCKDHA "2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial" 2 IGHHS(0.3)T(0.331)S(0.369)DDS(0.001)S(0.005)AY(0.447)RS(0.547)VDEVNYWDK 164.55 2.04E-11 123750000 71495 107620 72489 94805 157080 43482 75208 90380 203030 TRUE FALSE 67020.25557 115588.2968 74208.47331 97237.8568 144743.5704 56034.54753 63931.2586 101664.142 169142.9814 0.396234328 0.683376253 0.438732206 0.574885555 0.855746832 0.331285088 0.37797169 0.601054452 1 17.36788379 -1.652436192 2.091309347 1.088476511 0.5282408 0.462594834 0.15832963 720448.5822 465940.9071 339943.6607 0.04072574 0.022261981 1.652436192 -0.560235711 IGHPAPNFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IGHPAPNFK 9 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ;;;;; 148.38 9.01E-05 24013600000 17664060 18161240 16542700 16108240 19436420 12333030 20741420 17229100 23802320 FALSE TRUE 16558498.02 19505917.11 16935100.66 16521604.71 17909961.98 15893375.55 17631436.62 19380191.06 19829559.02 0.835041162 0.983678814 0.854033145 0.833180642 0.903195172 0.801499193 0.889149204 0.977338479 1 24.24114926 1.217990449 4.356857055 0.995564852 0.877025728 0.493513259 0.049507585 0.182384335 7.400350043 0.044271982 0.012399593 16.5192547 -1.217990449 -0.118539125 IGIIGGTGLDDPEILEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IGIIGGTGLDDPEILEGR 18 0 B4DUC8;Q13126-4;Q13126;Q13126-3;Q13126-2;J3QSB7;Q13126-7;Q13126-6;Q13126-5;F2Z2F3;F8WES2 B4DUC8 MTAP S-methyl-5-thioadenosine phosphorylase;Purine nucleoside phosphorylase 0 ; 171.29 3.17E-11 45446000 140710 164769 158613 163359 177564 136853 182645 151612 196265 FALSE TRUE 131903.2123 176968.6682 162375.3753 167551.0685 163618.8397 176360.2395 155259.0778 170541.0919 163507.1036 0.806712426 1.082330152 0.993078415 1.024732656 1.000683372 1.078609037 0.949555551 1.043019466 1 17.31899379 4.749062629 24.94169612 1.019915881 0.806712303 0.740888662 0.039909295 724.5929788 1720833.431 0.008870823 0.126650282 56112.88897 -4.749062629 -0.213203578 IGITNHDEYSLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IGITNHDEYSLVR 13 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;;;; 220.4 2.09E-11 2574670000 1214160 1515640 1394500 1441440 1726320 1231448 1494540 1436110 1846410 FALSE TRUE 1138167.893 1627859.563 1427578.199 1478429.791 1590741.791 1586947.047 1270447.602 1615411.495 1538232.243 0.73991941 1.058266442 0.92806415 0.961122612 1.034136294 1.031669343 0.825914037 1.050173992 1 20.55284191 4.751571119 24.37872709 0.975773938 0.739919195 0.54428191 0.070242933 1247.956687 2338328.243 0.016515683 0.299173775 56437.93549 -4.751571119 -0.235854744 IGKPAPDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IGKPAPDFK 9 1 P32119;A6NIW5;P32119-2 P32119 PRDX2 Peroxiredoxin-2 0 ; 91.549 0.0097381 9551100000 18100000 13956300 15430500 14834500 16544200 11447800 19406700 14259300 21665000 FALSE TRUE 16967153.31 14989638.97 15796518.75 15215178.38 15244885.27 14752594.02 16496845.5 16039604.99 18048971.54 0.940062057 0.830498233 0.875203261 0.842994203 0.844640108 0.8173648 0.914004738 0.88867141 1 24.1054133 0.772220229 1.102322006 0.998891646 0.858120661 0.56965532 0.036675848 0.541264137 1.202281833 0.031479391 0.009920686 5.918616887 -0.772220229 -0.140770986 IGKPHTVPCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IGKPHTVPCK 10 1 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 ; 119.16 0.00043854 3471500000 5275100 4999500 4583500 4171000 5524000 3271800 5548700 4711300 5937800 FALSE TRUE 4944940.907 5369668.182 4692222.784 4278034.921 5090167.323 4216315.547 4716723.947 5299516.176 4946742.82 0.999635737 1.085495725 0.948547955 0.864818544 1.028993725 0.852341773 0.953500944 1.07131427 1 22.23804747 3.832159769 4.09511079 0.950602177 1.044039236 0.184878389 0.069857449 0.291290596 8.648729919 0.016855738 0.031726348 6794.535448 -3.832159769 0.093437059 IGLDDEEKLDLFR ddPTM_SK-BR-3_Pertuzumab_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 ; 173.68 1.94E-05 173069000 544200 365790 445940 414970 449080 309390 527070 376180 496410 FALSE TRUE 510139.4934 392873.4722 456517.9074 425618.8327 413811.0683 398705.8705 448040.7466 423146.9011 413555.9641 1.233544037 0.94998865 1.103884231 1.029168649 1.000616855 0.964091695 1.083386012 1.023191388 1 18.65772305 4.75175434 24.9191841 1.025264722 1.233544178 0.666953079 0.047414373 1303.829699 2462517.18 0.010886118 0.206231437 56461.7507 -4.75175434 0.208279456 IGLIHGHQVIPWGDMASLALLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IGLIHGHQVIPWGDMASLALLQR 23 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ; 213.15 1.05E-25 300240000 260530 307750 203710 173944 356460 128603 196225 287410 137690 FALSE TRUE 244223.8924 330536.1302 208542.0974 178407.6975 328465.0695 165728.5984 166802.8829 323293.7712 114708.6495 2.129080008 2.881527519 1.818015453 1.555311638 2.863472554 1.444778569 1.4541439 2.818390528 1 16.80761465 0.761728125 0.095462189 1.13E-11 3.386492335 0.231466584 0.587795379 26.77184773 1.441755523 28.17387915 20.17144575 5.777342639 -0.761728125 3.386492335 IGNFLNYGSHTGDADGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IGNFLNYGSHTGDADGFK 18 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 129.12 2.19E-05 274140000 239400 212050 221750 208440 242300 165320 281960 187100 239060 FALSE TRUE 224416.3813 227750.4026 227010.0147 213788.9233 223270.7354 213045.2003 239682.7156 210459.8469 199159.3416 1.126818253 1.143558724 1.139841159 1.073456668 1.121065844 1.069722357 1.203472123 1.056741025 1 17.60356363 -4.620881439 0.340060816 2.48E-15 1.128588367 0.427825544 0.042725144 268.0225483 2.91894813 192.6009009 0.032296207 2.39E-05 4.620881439 1.128588367 IGNLQTDLSDGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IGNLQTDLSDGLR 13 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ; 234.24 2.74E-16 141160000 132461 176217 140228 142218 184098 113873 151920 170196 155804 FALSE TRUE 124170.5025 189264.29 143554.2744 145867.5547 169639.6857 146746.2865 129141.0064 191445.3452 129799.3059 0.956634565 1.458130217 1.105971048 1.123793026 1.306938312 1.130562953 0.994928328 1.474933506 1 16.98592314 -2.364174117 1.959407348 9.13E-05 1.193385446 0.108745364 0.174521813 2304722.442 252228.8488 10194923.66 0.039575523 0.004323405 2.364174117 1.193294176 IGNSYFKEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IGNSYFKEEK 10 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 77.744 0.029259 684220000 628700 678710 518250 691430 1036000 444470 646550 640460 1283100 FALSE TRUE 589350.7893 728962.3946 530543.1347 709173.2644 954636.739 572781.2736 549605.8298 720422.8408 1068942.321 0.551340122 0.681947361 0.496325316 0.663434547 0.893066651 0.535839271 0.514158546 0.673958573 1 20.02775258 0.967904198 22.81656567 1.000000003 0.613610831 0.515699827 0.114901188 1120.507317 796558.5037 0.109673231 0.027418308 9.287614875 -0.967904198 -0.386389172 IGPLGLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IGPLGLSPK 9 0 P30050 P30050 RPL12 60S ribosomal protein L12 1 IGPLGLS(1)PK;IGPLGLS(1)PK;IGPLGLS(1)PK;IGPLGLS(1)PK 138.76 0.00013372 564132000 1382181 816052 1050062 980299 1192027 707771 1342468 901601 1350064 TRUE FALSE 1295672.758 876473.3392 1074969.967 1005455.132 1098410.008 912092.998 1141177.386 1014167.87 1124729.597 1.151986008 0.779274718 0.955758584 0.893952764 0.976599185 0.810944249 1.014623772 0.901699282 1 20.10114677 0.641081534 0.788081179 0.998995223 0.91899098 0.011887779 0.105668428 4.095323337 4.544435891 0.094117762 0.032443209 4.376042523 -0.641081534 -0.080004243 IGQQVDREPGDVAT(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IGQQVDREPGDVATPPR 17 1 H3BT22;Q9Y5N6 H3BT22 ORC6 Origin recognition complex subunit 6 1 IGQQVDREPGDVAT(1)PPR;IGQQVDREPGDVAT(1)PPR;IGQQVDREPGDVAT(1)PPR 141.1 1.03E-06 804760000 839790 871830 943050 906080 910880 793250 1068210 862860 913260 TRUE FALSE 787229.043 936381.2003 965419.5913 929331.5468 839343.1591 1022248.398 908041.8273 970589.9704 760831.0061 1.034696321 1.230734806 1.268901482 1.221469077 1.103192631 1.343594556 1.193486885 1.275697182 1 19.53721652 -0.888032105 6.048984326 0.999999959 1.217722179 0.355671596 0.087692947 4.30E-08 7.86E-09 0.075985763 0.017910013 0.129410017 0.888032105 0.217722219 IGRPSETGIIGIIDPECR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IGRPSETGIIGIIDPECR 18 1 Q16531;F5GY55;F5H2L3;F5GWI0;F5GZY8 Q16531 DDB1 DNA damage-binding protein 1 0 ; 144.17 9.14E-08 400490000 460480 450990 402810 367240 500920 370170 632260 429750 556350 FALSE TRUE 431659.3788 484381.7689 412364.8434 376664.0001 461579.7638 477032.0698 537458.4826 483405.2335 463491.5908 0.931320842 1.04507132 0.889692179 0.812666308 0.995875164 1.029214077 1.159586265 1.04296441 1 18.82218364 2.252273438 2.929578598 1.084624604 0.934452006 0.431450843 0.07163012 0.22938107 4.066867224 0.029585858 0.021821159 178.7612728 -2.252273438 -0.150172597 IGSIS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IGSISR 6 0 A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;Q7Z4S6-3;H0YHT2;H0YI78 A0A1B0GV47 KIF21A Kinesin-like protein KIF21A 1 IGSIS(1)R;IGSIS(1)R 99.799 0.040267 515000000 427050 489270 429920 446200 389780 321220 637830 397450 624760 TRUE FALSE 400321.7028 525496.0599 440117.9054 457650.2474 359168.2511 413950.9994 542193.3128 447072.5074 520483.5199 0.769134252 1.009630545 0.845594315 0.879279036 0.69006652 0.795320089 1.041710817 0.858956125 1 18.98949296 -1.071722409 5.368528436 1.000001269 0.877815345 0.130370553 0.105145216 1.59E-06 2.76E-07 0.101649601 0.023958792 0.084776912 1.071722409 -0.122185925 IGSLGLGTGEDDDYVDDFNSTSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IGSLGLGTGEDDDYVDDFNSTSHR 24 0 O95684;O95684-2;A0A087WV25;O95684-3 O95684 FGFR1OP FGFR1 oncogene partner 0 ;;; 324.31 2.55E-74 531500000 324499 358975 343360 343223 369578 302924 384855 333297 426260 FALSE TRUE 304189.1868 385553.8825 351504.6613 352030.6833 340552.8347 390373.2412 327149.5656 374909.8641 355114.4523 0.856594782 1.085717239 0.989834852 0.991316126 0.958994579 1.099288522 0.92125106 1.055743752 1 18.43792455 IGTEPSTAPAPS(ph)PPAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IGTEPSTAPAPSPPAPK 17 0 Q6NV74 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 IGTEPSTAPAPS(1)PPAPK;IGTEPSTAPAPS(0.999)PPAPK 153.95 1.64E-07 279840000 452020 557010 553960 585710 532530 499410 586450 511560 614390 TRUE FALSE 423728.8751 598251.6 567100.1928 600740.3102 490707.2419 643581.5598 498517.2668 575429.3921 511844.3399 0.827847144 1.168815504 1.107954408 1.173677744 0.958704051 1.257377506 0.973962644 1.124227323 1 18.9653456 -0.812891306 7.588183801 1.000000003 1.085037867 0.026998146 0.125203239 0 0 0.105022211 0.024753973 0.153853965 0.812891306 0.085037864 IGTLQDRPPS(ph)PFREPPGSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IGTLQDRPPSPFREPPGSER 20 2 Q86UU1-3;Q86UU1-2;Q86UU1 Q86UU1-3 PHLDB1 Pleckstrin homology-like domain family B member 1 1 IGT(0.002)LQDRPPS(0.993)PFREPPGS(0.005)ER;IGTLQDRPPS(1)PFREPPGSER 106.38 0.00012638 274460000 346780 739150 571290 581220 689470 504940 634720 637000 504630 TRUE FALSE 325075.6588 793877.4351 584841.2686 596135.0892 635321.8074 650707.981 539549.6285 716530.8522 420403.993 0.773245888 1.888367971 1.391141089 1.418005298 1.511217348 1.547815891 1.283407478 1.70438641 1 18.68141685 -1.224546417 4.469279747 0.999839831 1.468076513 0.177586634 0.291742888 0.000410464 7.12E-05 0.249014121 0.058673277 0.059628459 1.224546417 0.468236683 IGVDHVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IGVDHVAR 8 0 Q7L5N1;E7EM64;H7C3T0 Q7L5N1 COPS6 COP9 signalosome complex subunit 6 0 155.75 0.00040391 356780000 293400 367780 325330 337580 350210 292680 360930 335080 348480 FALSE TRUE 275036.6177 395010.8139 333046.9812 346242.8743 322705.9193 377171.9647 306811.8972 376915.4756 290316.4367 0.947368399 1.360621597 1.147186101 1.192639584 1.111566134 1.299175372 1.0568189 1.298291891 1 18.14726673 -1.242471344 4.028617077 0.999847123 1.184984529 0.166208629 0.123149377 12.67845913 29070116.85 8324.879674 0.025343968 0.057217471 1.242471344 0.185137406 IGVITNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IGVITNR 7 0 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 79.307 0.076726 432800000 278740 334920 346050 306140 335010 260480 388220 310910 285280 FALSE TRUE 261294.161 359717.8253 354258.4694 313996.0707 308699.666 335676.3475 330010.0151 349727.7979 237664.925 1.099422479 1.513550328 1.490579518 1.321171269 1.298886093 1.412393299 1.388551613 1.471516244 1 17.85856948 -1.128044501 4.301224424 0.999930335 1.394739678 0.480297656 0.120811284 7.69E-05 1.56E-05 0.110737388 0.02609643 0.074465567 1.128044501 0.394809343 IHCLENVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IHCLENVDK 9 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;P11277-3;P11277;P11277-2;Q01082-3;O15020;O15020-2;A4QPE4 Q01082;Q01082-3;O15020 SPTBN1;SPTB;SPTBN2 "Spectrin beta chain, non-erythrocytic 1;Spectrin beta chain, erythrocytic;Spectrin beta chain, non-erythrocytic 2" 0 95.573 0.0061542 0 147440 205010 161430 176900 225540 138550 201000 184130 225170 FALSE TRUE 138211.9936 220189.1537 165259.1958 181439.5535 207826.9982 178547.1358 170861.916 207119.0358 187587.6723 0.736786122 1.173793304 0.880970448 0.967225358 1.107892622 0.95180634 0.910837657 1.104118587 1 17.5172055 4.765822444 24.655151 1.001775071 0.736785672 0.460644217 0.09302478 8121.62284 7344913.789 0.021426041 1.974382649 58320.66187 -4.765822444 -0.264989398 IHDENLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IHDENLR 7 0 O95232;J3KPP4;D6RDI2 O95232 LUC7L3 Luc7-like protein 3 0 ;; 194.25 0.00048478 1316410000 706470 728120 687940 669220 638210 565040 782680 628570 699560 FALSE TRUE 662253.3038 782030.7624 704258.2617 686393.3182 588087.561 728157.8753 665324.4 707048.3482 582798.9167 1.136332421 1.341853494 1.208406951 1.17775325 1.009074561 1.249415286 1.141601985 1.213194342 1 19.15263867 -5 0.089299023 0.386416252 1.355610985 0.299211756 0.086311414 236.1539516 1.468307828 27.90104932 2.001967911 1.00E-05 5 0.969194733 IHDPQLLTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IHDPQLLTER 10 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ;;;; 181.4 1.89E-06 2758740000 1999390 2760220 2045790 2094640 2733500 1568370 2267530 2239250 2629910 FALSE TRUE 1874251.749 2964589.561 2094317.105 2148392.009 2518821.936 2021132.959 1927534.927 2518825.292 2190961.031 0.855447323 1.353100087 0.95588971 0.980570616 1.149642509 0.92248695 0.879766869 1.14964404 1 21.06313239 3.733613392 24.3841853 0.993360106 1.144222731 0.053232431 0.147349911 330.7143534 1242133.714 0.035112716 0.06141773 5415.186166 -3.733613392 0.150862625 IHEAAVQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IHEAAVQELR 10 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ; 89.266 0.01163 675020000 456050 418440 536610 451630 498310 408000 443580 425960 313800 FALSE TRUE 427506.6446 449421.733 549338.6426 463219.5904 459174.7427 525782.9767 377069.297 479142.0437 261424.7528 1.635295205 1.719124636 2.101326048 1.771904097 1.756431776 2.011221092 1.442362642 1.832810545 1 17.99603622 0.061581595 0.562456102 0.94518588 1.841487607 0.639203306 0.184023545 2.324315111 0.910992136 0.470432341 0.077492804 1.152342542 -0.061581595 0.896301728 IHEDIFDIIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 IHEDIFDIIDR 11 0 P23258;K7EIS0;Q9NRH3;K7EKE5 P23258 TUBG1;TUBG2 Tubulin gamma-1 chain;Tubulin gamma chain;Tubulin gamma-2 chain 0 ;;;;;;; 206.36 2.67E-08 940286000 939155 1009290 1009797 940211 1106163 785211 1066722 939495 1037754 FALSE TRUE 880374.965 1084018.882 1033749.862 964338.406 1019289.42 1011888.669 906776.9391 1056793.019 864546.1533 1.018308811 1.253858892 1.19571391 1.115427328 1.178987861 1.170427588 1.048847347 1.222367383 1 19.72158346 -1.077039175 0.294326259 0.907231469 1.17826049 0.233826974 0.076235662 19.18971152 1.359100716 1.550259172 0.083923119 0.083745374 1.077039175 0.271029021 IHEGCEEPATHNALAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IHEGCEEPATHNALAK 16 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;; 295.37 6.74E-46 4992910000 5606690 5038960 5496940 5485050 6079890 4339550 7715420 5490850 7329870 FALSE TRUE 5255777.281 5412049.841 5627330.013 5625805.669 5602399.964 5592307.638 6558564.397 6176394.709 6106467.344 0.860690312 0.886281632 0.921536086 0.921286458 0.917453521 0.915800793 1.074035777 1.011451362 1 22.54190658 1.753685293 25 1.032546913 0.905051498 0.830062501 0.026563435 1.825378145 3021.070625 0.011708366 0.006492877 56.71334895 -1.753685293 -0.127495415 IHEKDPNSATATAPPS(ph)PLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IHEKDPNSATATAPPSPLKR 20 2 Q92766;Q92766-2;Q92766-5;Q92766-3;C9JU34;Q92766-6 Q92766 RREB1 Ras-responsive element-binding protein 1 1 IHEKDPNSAT(0.001)AT(0.007)APPS(0.992)PLKR;IHEKDPNS(0.002)AT(0.002)AT(0.015)APPS(0.982)PLKR 106.99 0.00012173 438730000 496390 283730 313750 277290 279920 155865 373220 240857 399240 TRUE FALSE 465321.836 304737.6644 321192.2982 284405.7309 257936.2123 200860.6952 317259.1258 270928.5266 332604.2648 1.399025464 0.916216948 0.965689055 0.855087445 0.775504826 0.603902946 0.953863673 0.814567206 1 18.34344714 7.703192224 0.94727687 0.838764098 199.9999997 0.677897849 0.115885496 371.8249934 1.226518379 0.033958622 159646.371 50488471.57 -7.703192224 199.1612356 IHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGR 39 0 Q99436;Q5TBG5;Q99436-2 Q99436 PSMB7 Proteasome subunit beta type-7;Proteasome subunit beta type 0 109.59 6.20E-06 16127000 862.7 2202.3 2451.9 1352.3 2849.7 1271.3 1787.4 1887.2 1341.4 FALSE TRUE 808.705147 2365.360583 2510.060226 1387.002307 2625.896057 1638.303672 1519.395963 2122.821074 1117.511674 0.72366595 2.116631654 2.24611544 1.24115241 2.349770582 1.466028239 1.359624242 1.899596329 1 10.12607419 2.052650186 24.99987743 1.447975146 1.84071717 0.055983506 0.529081235 205.9806125 97804.63321 0.18560666 0.137079583 112.8886258 -2.052650186 0.392742023 IHFPLATYAPVISAEK ddPTM_SK-BR-3_Pertuzumab_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 ; 261.27 7.96E-27 6309900000 2128020 1881290 1984480 1730790 2252600 1476740 2400640 2013040 2767300 FALSE TRUE 1994831.027 2020582.669 2031552.803 1775205.002 2075689.883 1903050.865 2040686.318 2264372.475 2305419.753 0.865278882 0.876448927 0.881207338 0.77001379 0.900352259 0.825468274 0.885169096 0.982195313 1 21.13659802 1.263516894 3.230482425 0.999697481 0.857522357 0.712010436 0.035821268 0.124049408 2.227418061 0.029191707 0.008539611 18.34496526 -1.263516894 -0.142175124 IHFVPGWDCHGLPIEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IHFVPGWDCHGLPIEIK 17 0 Q9NSE4 Q9NSE4 IARS2 "Isoleucine--tRNA ligase, mitochondrial" 0 ; 101.15 0.0006701 248630000 637280 519290 496330 421130 712550 401910 522320 574670 974480 FALSE TRUE 597393.7824 557738.7719 508103.182 431936.9088 656589.1973 517934.8925 444002.965 646418.8145 811832.9926 0.735857975 0.687011709 0.625871561 0.532051435 0.80877373 0.637982069 0.546914167 0.796246051 1 19.63082345 0.975623913 5.756011435 0.999888606 0.650008966 0.657125265 0.081178489 0.097339885 13.99280936 0.07502268 0.018886427 9.454181012 -0.975623913 -0.34987964 IHGTEEGQQILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 87.001 0.010794 445850000 325540 466970 396470 403310 486560 365570 423560 393470 402780 FALSE TRUE 305165.0325 501544.9447 405874.4556 413659.6174 448347.5403 471104.1245 360051.1101 442595.5956 335553.4159 0.909438015 1.494679896 1.209567349 1.23276831 1.336143574 1.403961641 1.073006839 1.319001907 1 18.35618292 -1.15169496 4.541044117 0.999963288 1.26127266 0.176453218 0.165494202 5.56E-05 1.04E-05 0.144892295 0.034146647 0.070518821 1.15169496 0.261309373 IHGVGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IHGVGFK 7 0 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 ; 118.06 0.0050921 3572300000 6135300 5806100 5833700 5614200 6530600 4943800 7113000 5496200 6456200 FALSE TRUE 5751302.525 6235989.685 5972078.119 5758269.877 6017713.019 6370994.804 6046471.684 6182412.669 5378618.511 1.069289914 1.159403604 1.11033681 1.070585293 1.118821312 1.184503937 1.124168162 1.149442493 1 22.35880424 -0.95769567 4.362199242 0.999996574 1.126262742 0.53504158 0.036035374 1.19E-06 2.84E-07 0.033009044 0.007780085 0.110231148 0.95769567 0.126266168 IHIPEPDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IHIPEPDLR 9 0 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 0 ; 90.629 0.011301 216690000 177915 222883 204949 213420 227010 178622 222571 180375 218964 FALSE TRUE 166779.6177 239385.4892 209810.4871 218896.7185 209181.5503 230187.2717 189198.5448 202895.2158 182417.4938 0.914274252 1.312294584 1.150166482 1.19997657 1.146718694 1.261870596 1.037173249 1.112257446 1 17.47688457 1.667489772 8.411686566 1.056526909 1.180130646 0.189704507 0.107533134 0.168460549 20.30613732 0.047372585 0.024918458 46.50394236 -1.667489772 0.123603737 IHLDDANESDHFENIQSTNWQTMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IHLDDANESDHFENIQSTNWQTMR 24 0 E1CEI4;P48506;A0A2R8YEL6;B4E2I4;A0A2R8Y648 E1CEI4 GCLC Glutamate--cysteine ligase catalytic subunit 0 177.03 2.51E-17 147050000 44871 58769 74625 59904 72874 52718 65028 54965 84853 FALSE TRUE 42062.60421 63120.31791 76395.14024 61441.23806 67150.77 67936.83079 55277.65509 61827.50124 70690.48613 0.595024967 0.892911074 1.080699036 0.869158517 0.949926556 0.961046309 0.781967392 0.874622663 1 16.10922844 4.73195961 4.133587951 0.927666961 0.569391898 0.630848837 0.080110022 0.154015692 5.841581768 0.020637548 0.162729503 53946.04498 -4.73195961 -0.358275063 IHLDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 IHLDEK 6 0 P37837 P37837 TALDO1 Transaldolase 0 ;;;;;;;;; 181.42 0.0029149 13923050000 29525030 25573600 26508360 25557800 29137150 19935400 32180920 25072060 34153080 FALSE TRUE 27677111.08 27467095.95 27137150.82 26213656.42 26848835.77 25690426.36 27355689.8 28202361.88 28452710.31 0.972740761 0.965359562 0.953763298 0.92130613 0.943630167 0.902916667 0.961444077 0.991201245 1 24.76206275 1.294428065 3.714153231 0.997580571 0.945383682 0.525362607 0.020209372 0.190313501 4.533390972 0.017225484 0.00533206 19.69826903 -1.294428065 -0.05219689 IHLGSS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IHLGSSPK 8 0 Q5JW53;Q9H410-4;Q9H410 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 IHLGS(0.005)S(0.995)PK;IHLGS(0.026)S(0.974)PK;IHLGS(0.246)S(0.754)PK;IHLGS(0.021)S(0.979)PK 132.57 0.00061625 2461950000 4060500 2671850 3293050 2998460 3379640 2511200 4241890 2813080 4219250 TRUE FALSE 3806360.553 2869676.554 3371162.701 3075405.56 3114216.707 3236142.674 3605857.974 3164299.23 3515029.918 1.08288141 0.816401744 0.959070842 0.874930124 0.885971608 0.920658643 1.02583991 0.900219715 1 21.74510554 1.917378749 9.494941447 0.977219101 0.911083902 0.081911213 0.075668812 0.833084102 91.14516284 0.02857622 0.018116074 82.67586534 -1.917378749 -0.066135199 IHMKS(ph)CFLEDATIGNSNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IHMKSCFLEDATIGNSNK 18 1 Q9H171-7;Q9H171-3;Q9H171-4;Q9H171;Q9H171-2 Q9H171-7 ZBP1 Z-DNA-binding protein 1 1 IHMKS(0.99)CFLEDAT(0.01)IGNSNK 70.414 0.031784 237620000 376290 129540 183190 185460 217930 112350 257490 146340 402570 TRUE FALSE 352738.6806 139131.2764 187535.3533 190219.2176 200814.6569 144783.6212 218881.7649 164610.8711 335378.4663 1.051763056 0.414848568 0.559175296 0.567177791 0.598770276 0.431702198 0.652641081 0.490821229 1 18.35543053 -1.130427484 4.391336376 1.000064672 0.574107615 0.329454738 0.178817361 30766323074 6092442432 20907651.56 0.036714336 0.074058091 1.130427484 -0.425957056 IHNAENIQPGEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IHNAENIQPGEQK 13 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;; 140.82 3.95E-05 1808060000 2875670 2016830 2503750 2194890 2181810 2069390 3189010 2210220 2304830 FALSE TRUE 2695686.948 2166158.192 2563140.132 2251214.593 2010459.444 2666789.299 2710847.556 2486170.832 1920138.983 1.403901994 1.12812573 1.334872191 1.172422732 1.047038501 1.388852225 1.411797573 1.294786916 1 20.87277931 IHNAENIQPGEQKYEYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IHNAENIQPGEQKYEYK 17 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 174.78 7.87E-10 370260000 604600 486560 494320 541520 661250 392440 731830 513520 1037010 FALSE TRUE 566759.1652 522585.4087 506045.5038 555416.32 609318.0924 505731.0573 622098.8855 577634.1024 863926.3317 0.656027192 0.604895799 0.585750758 0.642897779 0.70528941 0.585386784 0.720083256 0.668614998 1 19.72054877 -2.112751678 0.284184705 1.426456065 0.603363236 0.880585471 0.041521431 10.19575457 0.41511659 2.850150873 0.045245551 0.007713444 2.112751678 -0.823092829 IHPFFK ddPTM_SK-BR-3_Pertuzumab_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 873980000 2900400 3489900 2974800 3037000 3951900 2382400 3861300 3563300 4160400 FALSE TRUE 2718869.141 3748295.827 3045363.661 3114934.562 3641533.715 3070160.205 3282333.912 4008185.849 3466002.363 0.784439494 1.081446414 0.878638657 0.898711032 1.050643749 0.885792877 0.947008561 1.156429058 1 21.72484121 1.270309812 19.38014406 1.078212234 0.942463299 0.294769019 0.092763683 18.12340978 11063.25714 0.055521505 0.020259318 18.63415965 -1.270309812 -0.135748935 IHPMAYQLQLQAASNFKS(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 IHPMAYQLQLQAASNFKSPVK 21 1 P67870;Q5SRQ6 P67870 CSNK2B Casein kinase II subunit beta 1 IHPMAYQLQLQAASNFKS(1)PVK;IHPMAYQLQLQAAS(0.002)NFKS(0.998)PVK;IHPMAYQLQLQAAS(0.003)NFKS(0.997)PVK;IHPMAYQLQLQAASNFKS(1)PVK;IHPMAYQLQLQAASNFKS(1)PVK;IHPMAYQLQLQAASNFKS(1)PVK;IHPMAYQLQLQAASNFKS(1)PVK 302.77 1.81E-55 13796200000 6198646 3714996 4253118 3658532 5039892 3004961 6392538 4119758 6239264 TRUE FALSE 5810683.812 3990058.169 4354003.967 3752416.125 4644079.212 3872444.459 5434036.272 4634118.855 5197890.531 1.117892687 0.767630281 0.837648262 0.721911341 0.893454601 0.745003081 1.045431072 0.891538371 1 22.30949482 1.730348052 14.62951473 0.975631724 0.833920967 0.216507607 0.116232194 0.127322455 162.3566412 0.048757312 0.026880312 53.74623571 -1.730348052 -0.141710757 IHPQTIIAGWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IHPQTIIAGWR 11 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 178.67 7.44E-06 215160000 201196 579900 134025 119009 506040 132472 177862 451620 378400 FALSE TRUE 188603.5015 622836.3994 137204.1363 122062.9724 466297.6597 170714.5159 151193.2443 508005.7511 315242.5954 0.598280512 1.975736808 0.435233494 0.387203297 1.479170856 0.541533785 0.479609185 1.611475602 1 18.26610296 3.958333502 22.03070136 0.797181601 1.362908937 0.094476137 0.536949271 151.9741103 178207.0885 0.126025828 0.228002271 9085.17928 -3.958333502 0.565727336 IHPTSVISGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IHPTSVISGYR 11 0 P17987;E7ERF2;F5H136;F5H676 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;; 187.42 3.60E-06 2372841000 407888 701358 623269 585275 752091 507423 670216 687029 718607 FALSE TRUE 382359.0182 753287.2761 638053.235 600294.1474 693024.8066 653907.7828 569723.3328 772806.083 598666.8493 0.638684134 1.258274576 1.065790156 1.002718203 1.157613466 1.092273246 0.951653384 1.290878364 1 19.19139386 4.751237039 24.8406748 1.098511728 0.638683816 0.639717397 0.109331342 1219.115139 2388927.243 0.024860885 0.448669609 56394.53748 -4.751237039 -0.459827911 IHQESELHSYLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IHQESELHSYLSR 13 0 Q9UNE7;Q9UNE7-2;H3BTA3;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ; 230.26 2.53E-12 958500000 350030 510340 447060 416410 520480 351140 448530 440610 459630 FALSE TRUE 328122.2471 548126.1046 457664.4743 427095.7856 479603.6003 452508.4177 381277.0904 495621.1284 382914.7837 0.856906709 1.431457149 1.195212339 1.115380768 1.2525074 1.181747054 0.995723087 1.29433793 1 18.54666384 1.97686973 22.80575541 1.094342559 1.207668211 0.018277089 0.164121317 598.5028704 590103.4016 0.062399676 0.040661959 94.81340214 -1.97686973 0.113325652 IHQETFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IHQETFGK 8 0 Q15393;Q15393-2;J3QL37 Q15393 SF3B3 Splicing factor 3B subunit 3 0 124.23 0.0013137 412230000 592540 567790 549610 537940 604300 440670 692300 518280 704570 FALSE TRUE 555453.9791 609829.7624 562647.0087 551744.4511 556840.7156 567884.2753 588496.042 582988.3989 586972.7153 0.946302894 1.038940561 0.958557347 0.939983132 0.948665417 0.967479851 1.002595226 0.993212093 1 19.16293392 1.731729193 8.007330515 0.998106516 0.972347225 0.208653362 0.027862237 0.24191154 48.48169135 0.014711199 0.007819564 53.91743123 -1.731729193 -0.025759291 IHQIGPGMVQQIQSVCMECQGHGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IHQIGPGMVQQIQSVCMECQGHGER 25 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ; 308.23 1.17E-74 1125980000 145743 138876 164447 140703 153924 115457 172502 124408 165764 FALSE TRUE 136621.2058 149158.5235 168347.7605 144313.6772 141835.4299 148787.5616 146636.9265 139940.6127 138096.9175 0.989313942 1.080100311 1.219055164 1.045017367 1.027071657 1.077414067 1.061840692 1.013350733 1 17.07532159 3.072801049 25 1.044083126 1.112993526 0.152048486 0.059843461 63.76844021 21896.41004 0.017596602 0.021031962 1182.499727 -3.072801049 0.0689104 IHQPYTLTFAELVEDYEHYIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IHQPYTLTFAELVEDYEHYIK 21 0 Q9UHI6;E9PJ60 Q9UHI6 DDX20 Probable ATP-dependent RNA helicase DDX20 0 ; 247.31 1.29E-30 150268000 252060 238420 237830 225490 317910 230860 329390 251010 279720 FALSE TRUE 236284.0145 256072.8649 243471.4399 231276.4552 292942.631 297505.5343 280001.0274 282349.151 233032.9249 1.013951203 1.098869891 1.044794164 0.992462568 1.257086873 1.276667382 1.201551358 1.211627718 1 17.83017428 2.736760321 24.99884376 1.208871083 1.048956979 0.459084704 0.079954895 124.7120768 1731735.725 0.022727026 0.022459923 545.4567508 -2.736760321 -0.159914104 IHRAS(ph)DPGLPAEEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 133.98 2.30E-05 2710840000 3341960 2152310 2809360 2890300 3735680 2336580 3807320 2890790 4163650 TRUE FALSE 3132792.689 2311669.272 2875999.346 2964469.991 3442294.762 3011112.715 3236447.711 3251711.495 3468709.917 0.903157878 0.666434878 0.82912651 0.854631855 0.992384732 0.868078561 0.933040753 0.937441173 1 21.72596776 3.199036849 1.960936319 0.934587215 0.765177929 0.473868867 0.06932215 0.229925062 1.809658728 0.020262271 0.027530125 1581.382211 -3.199036849 -0.169409286 IHRAS(ph)DPGLPAEEPKEK ddPTM_SK-BR-3_Pertuzumab_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 184.2 3.38E-10 2625480000 3102380 2431960 2598500 3419080 5525300 1652310 3402770 2721560 10826500 TRUE FALSE 2908207.574 2612024.849 2660137.647 3506819.381 5091365.226 2129305.074 2892556.228 3061352.757 9019487.208 0.322436022 0.289597933 0.294932249 0.38880474 0.564484999 0.236078285 0.320700741 0.339415389 1 23.10461398 -1.697952352 2.299183475 1.133958567 0.337002757 0.846585961 0.087634516 1428809.946 990330.7493 1105692.493 0.022404799 0.02004692 1.697952352 -0.79695581 IHRAS(ph)DPGLPAVFLRPGAGIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IHRASDPGLPAVFLRPGAGIPR 22 2 H7BZB3 H7BZB3 CAD 1 IHRAS(1)DPGLPAVFLRPGAGIPR 46.656 0.084347 132670000 53930 58764 56077 65905 83986 47216 71098 51707 92672 TRUE FALSE 50554.61757 63114.9477 57407.17292 67596.23388 77390.07834 60846.49271 60437.51494 58162.73277 77204.44452 0.654814861 0.817504071 0.743573421 0.875548478 1.002404445 0.788121631 0.782824296 0.753359902 1 16.23639628 -4.999999979 0.023531869 2.046796823 3.10E-09 0.321179971 0.090491267 3385.649564 6.021429875 371.646636 182.8946713 1.00E-05 4.999999979 -2.04679682 IHS(ph)PIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IHSPIIR 7 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 1 IHS(1)PIIR;IHS(1)PIIR;IHS(1)PIIR 123.86 0.002707 468030000 194974.4 137595.9 154253.4 161744.3 178147 146486.1 208560.7 162284.2 195345.4 TRUE FALSE 182771.3003 147783.6436 157912.3635 165894.9326 164156.0532 188774.2591 177288.9592 182545.7396 162740.9908 1.123080912 0.908091089 0.970329373 1.019380132 1.008695182 1.159967493 1.089393388 1.121694902 1 17.31221815 2.380873436 6.209003509 1.100822249 0.986154166 0.270339861 0.067069222 0.203111577 11.01190547 0.022040734 0.01836044 240.3662211 -2.380873436 -0.114668083 IHTDFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 IHTDFEK 7 0 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 ;;;;;; 178.6 0.00071325 3542400000 7019390 6408690 6674090 6212580 7068970 5001110 7833060 6055830 7617590 FALSE TRUE 6580058.91 6883196.076 6832402.567 6372005.321 6513801.611 6444849.271 6658565.372 6811913.706 6346165.017 1.036855942 1.084622927 1.076619115 1.004071798 1.026415417 1.015550219 1.049226636 1.073390573 1 22.59745361 3.259269532 24.94331948 1.030853237 1.071528656 0.333802566 0.0246523 237.5029209 286063.8801 0.006614372 0.008945919 1816.642759 -3.259269532 0.040675419 IHTGERPYACPDCDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IHTGERPYACPDCDR 15 1 Q9BWE0;Q9BWE0-4 Q9BWE0 REPIN1 Replication initiator 1 0 ; 89.466 0.0038386 707000000 253530 341760 276430 257390 287010 239633 291240 266200 302190 FALSE TRUE 237662.0099 367064.266 282987.0501 263995.0632 264469.3923 308811.157 247571.2657 299435.656 251752.5368 0.944030249 1.458036017 1.124068316 1.048629208 1.050513316 1.226645661 0.983391345 1.189404722 1 17.94164679 3.60367262 4.821810683 1.08413556 1.25265052 0.076345863 0.144723517 0.305006389 11.03714323 0.035040791 0.055316299 4014.880466 -3.60367262 0.16851496 IHTVEHMISPIAVQPDPASAAAAAAAAAAAAAAVIPTVS(ph)TPPPFQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IHTVEHMISPIAVQPDPASAAAAAAAAAAAAAAVIPTVSTPPPFQGR 47 0 B7Z8Z7;A0AV96;A0AV96-2 B7Z8Z7 RBM47 RNA-binding protein 47 1 IHTVEHMISPIAVQPDPASAAAAAAAAAAAAAAVIPT(0.117)VS(0.508)T(0.374)PPPFQGR 73.238 0.00083105 39322000 26110 28984 29739 29219 28763 25982 33292 23482 24525 TRUE FALSE 24475.82171 31130.00552 30444.42312 29968.80901 26504.07 33482.58162 28300.17367 26413.77939 20431.61906 1.197938432 1.523619123 1.490064152 1.466785814 1.297208504 1.638763013 1.385116548 1.292789343 1 14.31851591 0.906915664 2.056096893 1.001652206 1.450504638 0.55458728 0.121329884 0.281908356 2.478061226 0.10399091 0.028814586 8.070782883 -0.906915664 0.448852432 IHVFYIDYGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IHVFYIDYGNR 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 185.96 4.24E-06 6220900000 3212700 4943800 3306300 3118000 5086600 2722600 3862500 4460900 4512000 FALSE TRUE 3011622.842 5309844.096 3384726.997 3198013.159 4687118.954 3508570.422 3283353.983 5017853.185 3758918.051 0.801194067 1.412599057 0.900452458 0.850780229 1.246932998 0.933399019 0.873483789 1.334919548 1 21.84188603 3.756804818 23.65675953 1.003900976 1.152355741 0.013758659 0.214947259 485.2215173 386699.7586 0.050375853 0.090792931 5712.21859 -3.756804818 0.148454765 IHVSDQELQSANASVDDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IHVSDQELQSANASVDDSR 19 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 232.2 2.90E-26 823260000 522220 728950 759640 811040 762610 675690 988640 757530 814180 FALSE TRUE 489535.1824 782922.2165 777659.0195 831852.6595 702717.6868 870750.7341 840402.6101 852109.288 678288.0982 0.721721616 1.154262058 1.146502528 1.2264002 1.036016537 1.283747623 1.239005391 1.256264543 1 19.37153865 4.742209418 4.409743205 1.180213774 0.688074584 0.697272615 0.092211573 0.108294967 5.17011665 0.020438949 0.167310383 55234.37168 -4.742209418 -0.49213919 IHVSDQELQSANASVDDSRLEELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IHVSDQELQSANASVDDSRLEELK 24 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;;; 293.88 4.12E-62 1968204000 944272 1863335 1624895 1861941 2130159 1261688 2163250 1684833 2556078 FALSE TRUE 885171.7011 2001298.262 1663438.277 1909721.558 1962864.905 1625916.844 1838890.745 1895188.109 2129452.069 0.4156805 0.939818412 0.781157886 0.896813592 0.92176994 0.763537657 0.863551132 0.88998862 1 21.02205083 4.744126541 24.94394026 0.868111475 0.415680301 0.809159329 0.070895495 234.8618174 1052511.587 0.015230903 0.13355478 55478.73385 -4.744126541 -0.452431174 IHVYGYSMAYGPAQHAISTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IHVYGYSMAYGPAQHAISTEK 21 0 Q9NRX4 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 ; 263.31 6.70E-37 940670000 598240 637400 631000 588540 725310 537020 822230 590210 871210 FALSE TRUE 560797.2263 684593.7592 645967.618 603642.9328 668347.0784 692048.9562 698944.2447 663899.0177 725799.4228 0.772661439 0.943227203 0.890008448 0.831693873 0.92084267 0.953498907 0.962999174 0.914714172 1 19.46921138 2.472447395 4.511764305 0.954491888 0.878012512 0.456698379 0.048793079 0.214582921 11.17427982 0.016284974 0.014146855 296.7887232 -2.472447395 -0.076479376 IHYFDPQYFEFEFEA ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IHYFDPQYFEFEFEA 15 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ; 128.28 0.00016977 66291000 305530 352700 315300 318850 404760 276080 355660 305450 349090 FALSE TRUE 286407.4227 378814.275 322779.0649 327032.2308 372971.7823 355779.8142 302332.0848 343586.1049 290824.6238 0.984811461 1.302552274 1.109875294 1.124499798 1.282462872 1.223348318 1.039568386 1.181420268 1 18.1497899 0.745842753 0.813222285 1.003135629 1.175069922 0.172780206 0.100680815 1.510276885 1.928559883 0.091375061 0.03193397 5.569840425 -0.745842753 0.171934292 IHYLDTTTLIEPVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IHYLDTTTLIEPVSR 15 0 P46108-2;P46108;I3L297 P46108-2 CRK Adapter molecule crk 0 62.377 0.081593 417080000 204090 234260 191760 236360 316370 199490 306940 231020 385230 FALSE TRUE 191316.3712 251604.8541 196308.6378 242425.3978 291523.5764 257079.5246 260917.1965 259863.3555 320932.6243 0.596126279 0.783980297 0.611681776 0.755377856 0.908363794 0.801038926 0.8129968 0.809713117 1 18.29191093 2.824332514 0.05526207 1.527187876 8.75E-12 0.638265504 0.072190998 53.73742887 1.112587128 12.79635431 17.61139387 667.3174999 -2.824332514 -1.527187876 IIAEGANGPTTPEADKIFLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IIAEGANGPTTPEADKIFLER 21 1 P00367;P00367-2;P00367-3;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 172.61 4.90E-12 91708000 59532 51409 50840 46429 65037 46180 57648 61709 97474 FALSE TRUE 55805.99839 55215.37585 52045.94881 47620.44674 59929.25637 59511.41633 49004.21758 69413.50449 81204.95969 0.687224014 0.679950782 0.640920813 0.586422885 0.737999952 0.732854453 0.603463357 0.854793904 1 16.30928022 1.034833315 4.115445583 0.998679504 0.666213646 0.840855078 0.049255657 0.064027144 2.48424447 0.045778246 0.011713278 10.83510975 -1.034833315 -0.332465858 IIALDGDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IIALDGDTK 9 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 121.53 0.0014219 208495000 1267470 1362410 1110590 1004970 1756520 823990 1379620 1446650 1884160 FALSE TRUE 1188141.315 1463284.254 1136933.719 1030759.232 1618570.005 1061862.537 1172758.789 1627267.437 1569681.524 0.756931452 0.932217289 0.724308531 0.656667748 1.031145478 0.67648279 0.747131677 1.036686367 1 20.58204045 1.234340596 24.99037061 1.01834332 0.792733346 0.410625055 0.114037212 108.1567386 640446.9648 0.090866687 0.025870028 17.15302009 -1.234340596 -0.225609974 IIANALSSEPACLAEIEEDKAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IIANALSSEPACLAEIEEDKAR 22 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 244.31 7.51E-31 199462000 176043 243150 210350 241780 287950 164189 342640 257550 366120 FALSE TRUE 165024.7829 261153.079 215339.6013 247984.4841 265335.5685 211587.6989 291264.3129 289705.6844 305012.2068 0.541043208 0.856205336 0.706003224 0.813031343 0.869917868 0.693702397 0.954926742 0.949816689 1 18.21850746 6.651691922 0.104587647 1.135954091 1.10E-15 0.551313062 0.094220494 68.93362567 0.685924164 1.083552497 11.15314218 4484271.738 -6.651691922 -1.135954091 IIAPPER ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;;;; 153.38 0.0040715 11444890000 5125170 5255000 5348440 5061070 5281130 4798300 5497020 4820750 4434820 FALSE TRUE 4804394.758 5644085.668 5475307.523 5190945.625 4866371.353 6183491.316 4672792.883 5422631.249 3694619.892 1.300375925 1.527649889 1.481967748 1.405001266 1.317150748 1.673647492 1.264756056 1.467710186 1 21.81699451 -0.96205674 0.4948663 0.861631626 1.452215079 0.546961882 0.121792556 12.49255029 1.956667679 2.632666982 0.053157586 0.109129775 0.96205674 0.590583453 IIAPPERK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IIAPPERK 8 1 P60709;P63267-2;Q562R1;A0A2R8YFE2;P63261;P68133;P68032;P63267;P62736;A6NL76 P60709;P63261;P68133 ACTB;ACTG2;ACTBL2;ACTG1;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Beta-actin-like protein 2;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 ;;;;; 122.52 0.0022241 22718380000 9124580 8722610 9065930 9241000 11104570 7223850 10689620 8958220 11643490 FALSE TRUE 8553488.826 9368441.12 9280978.141 9478139.705 10232461.87 9309258.226 9086810.719 10076673.49 9700116.299 0.881792399 0.965807093 0.956790399 0.977116089 1.054880328 0.959705836 0.936773379 1.038819863 1 23.20957061 6.13025953 0.845785342 0.984615137 4.15E-13 0.450659021 0.036545485 21.44856152 1.817346009 0.011784433 33.17965788 1349769.249 -6.13025953 -0.984615137 IIAPSRGS(ph)PLPVLSWANR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IIAPSRGSPLPVLSWANR 18 1 I3L413;C9J2U0;P24864-2;P24864-3;P24864;I3L1Q9 I3L413 CCNE1 G1/S-specific cyclin-E1 1 IIAPS(0.272)RGS(0.725)PLPVLS(0.003)WANR;IIAPS(0.024)RGS(0.976)PLPVLSWANR 123.29 2.08E-05 354930000 272240 322450 295700 297750 338240 272980 357950 303350 352850 TRUE FALSE 255200.9844 346324.5335 302714.1436 305390.7691 311675.9948 351784.8945 304278.7205 341223.9153 293957.0555 0.868157371 1.178146695 1.029790366 1.038895864 1.060277306 1.196722065 1.035112833 1.160795119 1 18.16524588 2.446100264 24.99937339 1.101314524 1.053397656 0.084295852 0.093054183 606.5381781 488797.5546 0.029483868 0.024668084 279.3188618 -2.446100264 -0.047916868 IIDDSEITKEDDALWPPPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IIDDSEITKEDDALWPPPDR 20 1 P61326;Q96A72;F5H6N1;F5H6P7;F5H3U9 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ;;; 220.1 7.99E-25 1201203000 1373890 1014700 1203010 1115918 1247540 950734 1384150 989365 1329150 FALSE TRUE 1287900.677 1089829.444 1231545.965 1144554.345 1149563.241 1225195.472 1176609.557 1112889.398 1107306.278 1.163093448 0.984216802 1.11219993 1.03363845 1.038161946 1.106464847 1.062587272 1.005042074 1 20.07862289 1.237535363 6.128238655 1.001343954 1.066270534 0.249886602 0.049096383 0.20472978 29.81555422 0.03590092 0.010837246 17.27966676 -1.237535363 0.064926581 IIDINYYPVPEACLSNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IIDINYYPVPEACLSNKR 18 1 P23921;E9PL69 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 145.48 1.46E-07 188050000 180720 197770 196640 197050 237370 156140 235070 181740 275410 FALSE TRUE 169409.0578 212413.0966 201304.3937 202106.6366 218727.9177 201215.0833 199823.4358 204430.6391 229442.2918 0.738351489 0.925780051 0.877363942 0.880860434 0.953302532 0.876974692 0.870909344 0.890989353 1 17.80777181 IIDKNGIHDLDNISFPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IIDKNGIHDLDNISFPK 17 1 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 160.25 1.87E-09 480200000 1258800 1348700 1266600 1202200 1755800 840560 1637400 1213500 2613400 FALSE TRUE 1180013.955 1448559.151 1296644.35 1233050.487 1617906.551 1083216.027 1391887.071 1365008.146 2177206.657 0.541985278 0.665329195 0.5955541 0.566345176 0.743111154 0.49752559 0.639299474 0.626953873 1 21.05404692 0.349260822 1.910578182 1.000004251 0.611018758 0.768097112 0.067505268 4.136428592 11.56425308 0.056511591 0.01563692 2.234914028 -0.349260822 -0.388985492 IIDKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IIDKPR 6 1 P49903;P49903-2;P49903-3;Q99611 P49903 SEPHS1;SEPHS2 "Selenide, water dikinase 1;Selenide, water dikinase 2" 0 95.62 0.039342 386290000 843000 891650 833550 895490 1057700 659210 1045700 835900 1230700 FALSE TRUE 790238.1348 957668.6938 853322.1996 918469.7895 974632.5086 849513.2256 888906.9928 940263.955 1025288.219 0.770747308 0.934048276 0.832275436 0.895816193 0.950593687 0.828560408 0.866982548 0.917072816 1 19.96759809 -5 0.243975408 1.72851159 0.863836844 0.385798749 0.052452707 189.3846258 1.885726816 68.53797315 0.073597233 1.00E-05 5 -0.864674746 IIDVVQDHYVDWEQDMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IIDVVQDHYVDWEQDMER 18 0 Q8NC56;H0Y9B7;Q8NC56-2;H0Y8H8 Q8NC56 LEMD2 LEM domain-containing protein 2 0 78.78 0.011351 19078000 22510 20110 20595 18396 20877 18608 23634 22667 14846 FALSE TRUE 21101.13928 21598.96532 21083.52313 18868.0725 19237.40463 23979.82752 20090.30111 25497.02485 12368.10669 1.706092922 1.74634371 1.704668601 1.525542508 1.555404163 1.938843844 1.624363503 2.06151398 1 13.59433705 -1.788186379 2.723515245 0.808736541 1.721985496 0.665643224 0.163068548 14689850.61 12377608.11 18771441.57 0.03603372 0.01628597 1.788186379 0.913248954 IIECTHCGCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IIECTHCGCR 10 0 P41223;C9JCD9 P41223 BUD31 Protein BUD31 homolog 0 ;; 158.79 7.88E-06 995180000 490882 705752 514509 493825 711462 454950 578138 552646 610583 FALSE TRUE 460158.5719 758006.6124 526713.3964 506497.3855 655586.6444 586286.6795 491451.5741 621645.0696 508672.7528 0.904625949 1.49016555 1.03546611 0.995723445 1.288818088 1.152581254 0.966144877 1.22209233 1 18.95637829 2.065465686 0.299797089 1.00354619 1.227706342 0.006368573 0.177068671 4.555918348 1.215683688 0.27326837 0.370686245 116.2694682 -2.065465686 0.224160152 IIEPNEVTHSGDTGVETDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IIEPNEVTHSGDTGVETDGR 20 0 Q9NQW7-4;Q9NQW7-3 Q9NQW7-4 XPNPEP1 Xaa-Pro aminopeptidase 1 0 95.622 0.0014375 0 38222 62652 52033 53520 56375 45557 62893 58035 53807 FALSE TRUE 35829.75325 67290.81927 53267.24733 54893.41381 51947.53491 58708.56634 53462.77852 65280.7975 44826.26409 0.799302685 1.501147165 1.188304411 1.224581502 1.158863804 1.309691261 1.192666389 1.456306896 1 15.45205665 4.758426824 24.53525678 1.264457054 0.799302126 0.492384292 0.144724022 2987.101737 3689067.743 0.031306562 1.228470299 57335.92514 -4.758426824 -0.465154927 IIEQLS(ph)PQAATSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IIEQLSPQAATSR 13 0 Q03468;P0DP91;D6R9X7 Q03468 ERCC6 DNA excision repair protein ERCC-6 1 IIEQLS(1)PQAATSR 159.64 4.74E-05 105880000 396820 431270 455680 426340 456760 421440 498630 402470 488850 TRUE FALSE 371983.7445 463201.6795 466488.9448 437280.6062 420887.9121 543102.8865 423865.0606 452719.2654 407257.7769 0.913386473 1.137367303 1.14543901 1.073719474 1.033468078 1.333560505 1.040778309 1.111628288 1 18.63558272 4.741751093 24.27708386 1.119070845 0.913386358 0.303458788 0.092366069 231.8897306 1764371.837 0.019718759 0.141811117 55176.11174 -4.741751093 -0.205684487 IIEVVDAIMTTAQSHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IIEVVDAIMTTAQSHQR 17 0 Q01813;Q01813-2;Q5VSR5 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ; 260.18 3.11E-27 898560000 582100 765300 610150 708120 728170 481820 736380 563520 407760 FALSE TRUE 545667.4001 821963.6083 624623.0461 726291.558 670982.4655 620913.6123 625966.6552 633876.7125 339702.2218 1.606310954 2.419659206 1.838737006 2.138024162 1.975207763 1.827817343 1.842692261 1.865977529 1 18.37391113 -1.025457903 0.322615306 0.480704551 2.076871512 0.659598564 0.213389267 7.842691624 0.64597254 3.889555819 0.184947066 0.094306602 1.025457903 1.59616696 IIFDDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IIFDDFR 7 0 P46977;P46977-2 P46977 STT3A Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A 0 ;;; 117.93 0.01191 336003000 1311470 1672410 1287420 1337030 1840400 1244520 1758560 1700420 1301840 FALSE TRUE 1229387.434 1796236.977 1317958.21 1371340.453 1695862.408 1603792.721 1494880.254 1912721.18 1084554.494 1.133541413 1.656197994 1.215206998 1.264427432 1.563648869 1.478757158 1.37833577 1.763600807 1 20.04867111 2.743796374 24.76764116 1.456500163 1.35679648 0.046041882 0.233060036 1404.186631 6642470.637 0.065837853 0.067852185 554.3657286 -2.743796374 -0.099703683 IIFEDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 IIFEDDR 7 0 P49773;D6REP8;D6RE99;D6RD60;D6RC06 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ;;;;;;;;; 175.75 0.0018083 9588910000 16851110 18942010 18166990 17575510 19342260 16914030 20788800 17345000 20482320 FALSE TRUE 15796429.11 20344496.13 18597919.58 18026527.34 17823196.92 21796835.88 17671712.43 19510561.43 17063688.47 0.925733562 1.192268375 1.089912044 1.056426187 1.044510216 1.27738126 1.035632622 1.143396486 1 24.0244262 -0.855443102 4.033124293 0.999997634 1.104122593 0.084535189 0.095379201 22895896.92 70542200.99 1003.503344 0.020351931 0.13949444 0.855443102 0.104124959 IIGEDS(ph)PSRLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IIGEDSPSRLDR 12 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 IIGEDS(0.981)PS(0.019)RLDR;IIGEDS(1)PSRLDR 166.52 3.13E-05 263710000 365650 386550 425590 390050 445530 418520 541840 421320 468490 TRUE FALSE 342764.6192 415170.5642 435685.1958 400059.3434 410539.871 539339.9299 460596.1222 473922.7294 390295.9924 0.878217112 1.063732583 1.116294311 1.025015248 1.051868015 1.381874117 1.18012004 1.214264913 1 18.57420912 2.426054942 24.9745886 1.212735198 1.043336919 0.354087133 0.109681015 103.85169 50789.27363 0.034695041 0.029027958 266.7196064 -2.426054942 -0.169398279 IIGLKDEFYNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IIGLKDEFYNR 11 1 Q5MIZ7-3;Q5MIZ7-2;Q5MIZ7;Q5MIZ7-5;Q6IN85-2;Q6IN85;G3V5Z3;Q6IN85-4 Q5MIZ7-3;Q6IN85-2 SMEK2;SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3B;Serine/threonine-protein phosphatase 4 regulatory subunit 3A 0 112.84 0.0013418 199810000 322410 420690 341080 377520 492680 276790 416680 431500 516620 FALSE TRUE 302230.9336 451838.3253 349170.5787 387207.8023 453986.9002 356694.7797 354202.7023 485373.7248 430392.7845 0.702221191 1.049827835 0.811283533 0.899661463 1.054819961 0.828765705 0.822975466 1.127745962 1 18.71529437 IIGVHQEDELLECLS(ph)PATSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IIGVHQEDELLECLSPATSR 20 0 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 1 IIGVHQEDELLECLS(1)PATSR;IIGVHQEDELLECLS(0.979)PAT(0.011)S(0.011)R 159.36 1.65E-11 83248000 146330 128564 175709 170405 119829 193972 231528 114778 127453 TRUE FALSE 137171.4665 138083.0123 179876.9005 174777.8808 110418.1137 249968.5675 196812.5258 129108.286 106180.2709 1.29187339 1.300458278 1.694070837 1.646048548 1.039911772 2.354190335 1.853569633 1.215934795 1 16.6961562 4.081417005 2.983481275 1.62508409 1.29088199 0.030902186 0.406943554 0.614871346 10.59730359 0.100832336 0.255207485 12061.93559 -4.081417005 -0.334202101 IIGVHQEDELLECLSPATSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IIGVHQEDELLECLSPATSR 20 0 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 252.55 4.43E-36 272440000 306130 395000 314681 296079 352700 250694 405980 298465 349330 FALSE TRUE 286969.8698 424246.211 322145.3819 303676.8884 325000.3647 323065.2881 345107.0679 335729.0123 291024.5662 0.986067511 1.457767695 1.106935356 1.0434751 1.116745466 1.110096279 1.185834833 1.153610558 1 18.15078141 3.724198552 24.88070608 1.11307864 1.263632799 0.114078543 0.124435909 171.9166402 1463527.295 0.029704675 0.048297523 5299.056528 -3.724198552 0.150554159 IIIEELSLVAAS(ph)PTLSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IIIEELSLVAASPTLSPR 18 0 Q16513-3;Q16513-2;Q16513;Q16513-4;B1AL79;H0Y5V5 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 IIIEELSLVAAS(0.998)PT(0.002)LSPR;IIIEELSLVAAS(0.99)PT(0.01)LSPR;IIIEELSLVAAS(0.993)PT(0.006)LSPR;IIIEELS(0.001)LVAAS(0.807)PT(0.189)LS(0.003)PR 285.5 1.24E-39 259705000 505650 567380 558039 610444 709288 607660 564130 489351 571901 TRUE FALSE 474002.2691 609389.4056 571275.9486 626109.0265 653583.3816 783081.5775 479543.9436 550447.5495 476447.0285 0.99486877 1.279028662 1.199033501 1.31412096 1.371786038 1.643585815 1.00650002 1.155317415 1 18.8619563 1.611034393 25 1.060668626 1.29205962 0.332148152 0.164365551 0.369576151 2889.630493 0.077362755 0.040621344 40.83517235 -1.611034393 0.231390995 IIILYDDDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IIILYDDDER 10 0 Q9BYV8-5;Q9BYV8-2;Q9BYV8 Q9BYV8-5 CEP41 Centrosomal protein of 41 kDa 0 ;;; 176.79 5.58E-06 169914000 251905 299421 277710 300372 339043 243089 296664 308112 333645 FALSE TRUE 236138.7157 321590.4424 284297.4123 308080.054 312415.9304 313264.8481 252181.9873 346580.4614 277957.4941 0.849549736 1.156977053 1.022808949 1.108371102 1.123970165 1.127024292 0.907268171 1.246882955 1 18.08450475 4.751356974 24.45628038 1.078039327 0.849549538 0.386231831 0.093376089 1666.414638 3184758.271 0.020628734 0.372459041 56410.1136 -4.751356974 -0.228489789 IIKNEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IIKNEVK 7 1 P50914 P50914 RPL14 60S ribosomal protein L14 0 98.392 0.022241 0 623860 610740 607740 714350 944150 560220 871430 648270 1078300 FALSE TRUE 584813.7162 655959.8251 622155.8798 732681.4304 870000.2675 721946.4196 740767.1615 729207.9365 898324.7639 0.651004781 0.730203431 0.692573449 0.81560863 0.968469648 0.803658597 0.82460953 0.811741996 1 19.77687758 7.107824872 0.107008134 1.070700054 7.28E-16 0.640967868 0.065312288 61.99985501 0.566630884 0.723553917 9.657469718 12818135.91 -7.107824872 -1.070700054 IIKPVLTQESATYIAEEYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IIKPVLTQESATYIAEEYSR 20 1 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 0 164.98 1.58E-11 270550000 179560 173770 187880 178150 187240 154950 216040 166260 193700 FALSE TRUE 168321.6601 186636.1116 192336.6023 182721.6306 172534.9257 199681.5496 183646.8076 187017.927 161370.2187 1.043077598 1.156570978 1.191896522 1.132313212 1.069186912 1.237412648 1.138046469 1.158937061 1 17.30001482 -1.50025392 3.012397994 0.99537736 1.148068388 0.383821478 0.055465447 12197850.77 14557991.59 468067.8972 0.012329052 0.031604293 1.50025392 0.152691029 IILDLISES(ph)PIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IILDLISESPIK 12 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 IILDLISES(1)PIK;IILDLISES(1)PIK 228.8 1.02E-11 344330000 1959340 1212600 1436200 1370950 1479310 1213040 1741730 1480830 1357120 TRUE FALSE 1836708.407 1302382.166 1470267.342 1406130.898 1363130.96 1563224.956 1480573.756 1665714.885 1130607.905 1.624531723 1.151930886 1.300421955 1.243694558 1.205661975 1.382641099 1.309537772 1.473291385 1 20.10866726 -2.130482267 2.653273157 0.307718594 1.311926533 0.35984854 0.137616859 7996342.821 6285667.464 34934932.56 0.030748847 0.007404875 2.130482267 1.004207939 IILDLISES(ph)PIKGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IILDLISESPIKGR 14 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 IILDLISES(1)PIKGR;IILDLISES(1)PIKGR;IILDLIS(0.025)ES(0.975)PIKGR 263.15 8.10E-25 1675089000 1570867 1298073.7 1364810.8 1369200.9 1690516 1115159.1 1781028.1 1519373.5 2126805 TRUE FALSE 1472549.239 1394184.427 1397184.757 1404336.913 1557749.693 1437087.429 1513979.471 1709070.626 1771827.506 0.83109063 0.786862391 0.788555744 0.792592342 0.879176832 0.811076374 0.854473399 0.964580706 1 20.75680673 1.260828951 1.868000925 1.003767797 0.808884744 0.864034158 0.027221842 0.109837046 0.671852105 0.02564417 0.007573618 18.23177493 -1.260828951 -0.194883053 IILHNTMESLLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IILHNTMESLLER 13 0 O15498 O15498 YKT6 Synaptobrevin homolog YKT6 0 227.63 8.79E-12 155540000 166280 288090 230500 233790 295720 202280 281020 249770 214590 FALSE TRUE 155872.8316 309420.4834 235967.5688 239789.4472 272495.3441 260674.9523 238883.6599 280954.3343 178773.5427 0.871901005 1.730795725 1.319924443 1.341302765 1.524248723 1.458129365 1.336236091 1.571565513 1 17.44777372 -1.159616035 4.232869016 0.999907069 1.416883532 0.22787018 0.22467739 0.000214047 4.25E-05 0.190063529 0.044786049 0.06924429 1.159616035 0.416976463 IILLFDAHKLDISDEFSEAIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IILLFDAHKLDISDEFSEAIK 21 1 Q9H223 Q9H223 EHD4 EH domain-containing protein 4 0 ; 209.43 1.55E-22 64860000 241821 240724 228738 239701 325415 184442 289578 217302 453166 FALSE TRUE 226685.8553 258547.4554 234163.7734 245852.1335 299858.2186 237687.4112 246158.4672 244432.633 377529.667 0.600445144 0.684840101 0.620252642 0.651212752 0.794263987 0.629586048 0.652024168 0.647452782 1 18.52623049 -1.504964543 2.842181238 1.013299007 0.660428535 0.804333155 0.052699522 6500561.934 7149259.02 674252.7085 0.012248736 0.031263346 1.504964543 -0.352870472 IILLFDAHKLDISDEFSEVIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IILLFDAHKLDISDEFSEVIK 21 1 A0A024R571;Q9H4M9;C9JC03;C9J2Z4;C9JDQ8;Q9NZN3 A0A024R571;Q9NZN3 EHD1;EHD3 EH domain-containing protein 1;EH domain-containing protein 3 0 ;;; 215.98 3.82E-25 257863600 738865 691324 755172 779913 1042691 550383 1000201 713960 1165074 FALSE TRUE 692620.7586 742510.3483 773085.0365 799926.888 960802.2549 709269.6374 850230.1455 803099.4776 970615.6227 0.713589131 0.764989076 0.796489381 0.824143842 0.989889543 0.730742037 0.875969978 0.827412478 1 19.88854056 1.360226061 0.033062972 1.73525869 1.35E-11 0.489976081 0.06942716 78.19091501 2.450608966 64.70556281 62.81503599 22.92060418 -1.360226061 -1.73525869 IINDLLQSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IINDLLQSLR 10 0 A0A087WTP3;Q92945 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ; 134.57 0.00038916 83799000 85043 156687 112836 128182 192418 94669 108414 120346 121539 FALSE TRUE 79720.31044 168288.2685 115512.5232 131471.3671 177306.2665 121998.4035 92158.32717 135371.463 101253.3557 0.787334996 1.66205127 1.140826616 1.298439604 1.751114965 1.20488257 0.910175534 1.336957793 1 16.6276102 2.001988135 24.99663697 1.068680183 1.357598874 0.130658778 0.283833023 99.99561222 1257222.006 0.097879767 0.071813036 100.4588343 -2.001988135 0.288918691 IINEPTAAAIAYGLDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IINEPTAAAIAYGLDKK 17 1 P11142;E9PKE3;P11142-2;E9PN89;E9PI65;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 ; 230.01 1.48E-15 3372300000 3623900 2897800 2532400 2452430 3614600 1760620 4078200 2953300 5471100 FALSE TRUE 3397086.568 3112356.127 2592469.724 2515363.506 3330723.897 2268882.413 3466711.77 3322026.006 4557938.065 0.745312139 0.682843005 0.568781253 0.551864345 0.730752338 0.497787021 0.760587731 0.728844043 1 22.11994989 0.798607949 1.158861189 0.997879144 0.632052639 0.637367819 0.084622814 0.44757617 1.114779443 0.073734324 0.022936553 6.289381643 -0.798607949 -0.365826506 IINEPTAAAIAYGLDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IINEPTAAAIAYGLDKR 17 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 277.98 1.32E-35 1938140000 2485000 2893300 2398300 2543100 3039400 1596230 3078300 2522100 2610200 FALSE TRUE 2329468.286 3107522.942 2455188.809 2608360.251 2800697.784 2057035.688 2616737.493 2836989.737 2174540.757 1.071246091 1.429047918 1.129060837 1.199499362 1.287949088 0.945963271 1.203351781 1.304638567 1 21.05227932 3.735687816 23.87283433 1.158698521 1.276709347 0.068207143 0.140793356 374.5165251 1043668.851 0.033071627 0.05835027 5441.113882 -3.735687816 0.118010827 IINEPTAAAIAYGLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 213.99 1.14E-12 164530000 90432 135247 93360 82116 135037 74330 112818 114960 135776 FALSE TRUE 84772.02255 145260.8286 95574.54329 84223.23558 124431.7387 95787.86435 95901.98825 129313.0091 113114.1085 0.7494381 1.284197264 0.844939191 0.744586478 1.100054984 0.846825084 0.847834011 1.143208489 1 16.78741936 3.744741909 24.13732107 0.916031112 1.057880865 0.020071602 0.177253372 596.572141 817195.8534 0.041290271 0.074202593 5555.739942 -3.744741909 0.141849753 IIPELVGS(ph)PTQSTSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 IIPELVGSPTQSTSSR 16 0 Q9NSI6-3;Q9NSI6-2;Q9NSI6;H7C409 Q9NSI6-3 BRWD1 Bromodomain and WD repeat-containing protein 1 1 IIPELVGS(0.991)PT(0.009)QSTSSR;IIPELVGS(0.96)PT(0.04)QSTSSR;IIPELVGS(0.989)PT(0.011)QSTSSR;IIPELVGS(0.572)PT(0.428)QSTSSR;IIPELVGS(0.806)PT(0.194)QSTSSR;IIPELVGS(0.978)PT(0.019)QS(0.002)TSSR;IIPELVGS(0.909)PT(0.09)QSTSSR 263.07 6.69E-27 480574000 375224 428433 432314 435872 439678 391210 452906 392894 429093 TRUE FALSE 351739.3996 460154.6251 442568.6922 447057.2134 405147.4635 504145.9762 384996.9499 441947.6808 357474.6063 0.983956324 1.287237239 1.238042324 1.25059852 1.133360122 1.410298711 1.076991045 1.236305105 1 18.44748124 -1.102042129 5.882686744 0.999998896 1.211613644 0.222831082 0.117424851 1.50E-06 2.28E-07 0.099916847 0.023550504 0.079060193 1.102042129 0.211614748 IIPGFMCQGGDFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 277.96 8.61E-33 11339754000 601044 630389 535874 550017 675686 510481.2 620937 496569 752652 FALSE TRUE 563425.7289 677063.6575 548585.1843 564131.3674 622620.3471 657848.8355 527833.2613 558566.7327 627029.5189 0.898563324 1.079795507 0.874895308 0.899688692 0.992968159 1.049151301 0.841799701 0.890814094 1 19.25817384 1.725032467 24.99999666 0.898498434 0.96699775 0.097842211 0.075586603 1.694381706 3118.01354 0.033734674 0.018707591 53.09241335 -1.725032467 0.068499316 IIPTLEEGLQLPS(ph)PTATSQLPLESDAVECLNYQHYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 IIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYK 36 0 P61978;P61978-2 P61978 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 IIPTLEEGLQLPS(0.982)PT(0.016)AT(0.001)SQLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.994)PT(0.005)AT(0.001)SQLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.872)PT(0.125)AT(0.003)SQLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.796)PT(0.094)AT(0.094)S(0.01)QLPLES(0.002)DAVECLNY(0.002)QHY(0.002)K;IIPTLEEGLQLPS(0.978)PT(0.021)ATSQLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.226)PT(0.226)AT(0.226)S(0.226)QLPLES(0.033)DAVECLNY(0.032)QHY(0.032)K;IIPTLEEGLQLPS(0.895)PT(0.092)AT(0.012)S(0.001)QLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.836)PT(0.14)AT(0.022)S(0.002)QLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.875)PT(0.122)AT(0.003)SQLPLESDAVECLNYQHYK 176.13 1.18E-18 8029024000 4444993 4532084 4852334 5009688 4487226 2620579 3638034 2775468 3838244 TRUE FALSE 4166788.823 4867644.215 4967433.654 5138245.075 4134817.371 3377097.616 3092544.576 3121991.289 3197616.28 1.303092197 1.522272777 1.553480223 1.606898585 1.29309367 1.056129729 0.967140615 0.976349573 1 21.60856539 2.363377675 2.507071562 0.984438051 1.509429163 0.892873375 0.081144422 0.078837811 1.014850926 0.031806608 0.024727764 230.8754073 -2.363377675 0.524991112 IIPVLLEHGLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IIPVLLEHGLER 12 0 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28 P18858 LIG1 DNA ligase 1;DNA ligase 0 ; 156.36 7.09E-05 133779000 206530 264370 225140 222460 267280 200123 251870 240660 283940 FALSE TRUE 193603.656 283944.2299 230480.4271 228168.7002 246288.907 257895.2614 214104.4317 270706.9308 236548.5797 0.818451991 1.200363284 0.974347119 0.964574383 1.041176858 1.090242274 0.90511823 1.144403112 1 17.85177697 3.727387204 24.99988463 1.010134469 1.051887467 0 0.113741287 56.42026873 5302660.815 0.027047395 0.045086153 5338.10613 -3.727387204 0.041752998 IIQLLDDYPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IIQLLDDYPK 10 0 F8VWS0;P05388;P05388-2;F8VU65;F8VQY6;F8VRK7;G3V210;Q8NHW5;F8VZS0;F8VS58 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 0 ; 150.85 4.85E-05 174451000 552480 453610 489690 474630 523290 354720 574310 425090 495530 FALSE TRUE 517901.263 487195.7564 501305.678 486809.8093 482192.9143 457121.9056 488197.5471 478163.4222 412822.8418 1.254536355 1.180156976 1.214336096 1.179222078 1.168038358 1.107307686 1.18258366 1.158277532 1 18.65516327 -5 0.135859516 0.378765307 1.251361498 0.815433946 0.029214004 56.61574006 0.47747674 9.522106224 0.185410176 1.00E-05 5 0.872596191 IIQQVLQGLDYLHTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IIQQVLQGLDYLHTK 15 0 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3 H3BLV9 SRPK1 SRSF protein kinase 1 0 ; 165.34 1.43E-06 65649000 200204 161245 167753 176805 182600 149634 191246 155592 139767 FALSE TRUE 187673.589 173183.7476 171732.1804 181342.1156 168259.3326 192830.9067 162570.4377 175018.0037 116438.9848 1.61177624 1.487334744 1.47486841 1.55740035 1.445042937 1.656068258 1.396185634 1.503087682 1 16.82921464 -0.407742094 0.673341782 0.956156181 1.518922647 0.824508946 0.075156171 3.915512716 1.422538713 0.501055287 0.024681647 0.391073066 0.407742094 0.562766466 IIREEYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IIREEYGR 8 1 P49770;G3V5E5;H0YJJ8 P49770 EIF2B2 Translation initiation factor eIF-2B subunit beta 0 ; 149.82 0.00045522 425810000 365390 470080 368310 418670 545380 331670 477130 435040 650390 FALSE TRUE 342520.8921 504885.2123 377046.4871 429413.781 502548.0548 427417.7448 405588.786 489355.7016 541835.7073 0.632148984 0.931804983 0.695868659 0.792516579 0.927491577 0.788832738 0.748545695 0.903144062 1 19.04749595 1.013714655 4.575068143 0.999502649 0.796190877 0.377913648 0.091345303 0.16579208 9.730190121 0.080064188 0.020338464 10.32083072 -1.013714655 -0.203311772 IIRYPDSHQLFVGNLPHDIDENELKEFFMSFGNVVELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IIRYPDSHQLFVGNLPHDIDENELKEFFMSFGNVVELR 38 2 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 159.2 3.45E-18 79640000 72193 159310 46526 47008 219460 57786 94520 127220 46324 FALSE TRUE 67674.569 171105.4782 47629.61869 48214.30486 202224.4969 74467.88012 80347.60348 143103.697 38592.22514 1.753580385 4.433677446 1.234176535 1.249326897 5.240032057 1.929608357 2.081963484 3.708096554 1 15.23602261 6.380548492 7.274840057 2.591674608 2.683582498 0 1.461803875 0 0 0.295640089 0 2401864.44 -6.380548492 0.09190789 IIS(ph)NASCTTNCLAPLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IISNASCTTNCLAPLAK 17 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 IIS(0.821)NAS(0.177)CT(0.001)T(0.001)NCLAPLAK 108.34 0.00069286 31095000 27840 32580 27947 28737 43616 21316 41544 28057 54480 TRUE FALSE 26097.5441 34992.2571 28609.91604 29474.44007 40190.5753 27469.58316 35314.86288 31559.97821 45386.93605 0.575001231 0.770976412 0.630355748 0.649403609 0.88550977 0.605231055 0.778084311 0.695353795 1 15.46998948 -5 0.228215562 2.583092447 0.66911832 0.530979411 0.09081195 120.1011772 1.202371281 87.66552368 0.142210477 1.00E-05 5 -1.913974127 IIS(ph)PGSSTPSSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IISPGSSTPSSTR 13 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 IIS(1)PGSSTPSSTR 258 6.73E-24 416800000 363450 368180 400150 411520 377750 355730 420980 331780 325600 TRUE FALSE 340702.3133 395440.4303 409641.747 422080.2999 348083.0388 458423.4762 357857.9572 373203.4633 271255.2565 1.256021054 1.457816653 1.510170723 1.556026251 1.283230575 1.690007715 1.319266442 1.37583864 1 18.04929157 0.655468979 1.281534715 1.001070355 1.458231394 0.526829488 0.130281328 0.83091585 2.102982325 0.109667874 0.032977799 4.523441505 -0.655468979 0.457161039 IIS(ph)PGSSTPSSTRS(ph)PPPGRDESYPR ddPTM_SK-BR-3_Pertuzumab_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(0.952)PGS(0.039)S(0.022)T(0.023)PS(0.065)S(0.236)T(0.21)RS(0.453)PPPGRDESYPR 79.782 0.013076 95602000 39104 42418 40138 41360 62286 25307 44781 40719 81574 TRUE FALSE 36656.55044 45558.67286 41090.09231 42421.36762 57394.30881 32612.72008 38066.50478 45802.85678 67958.77241 0.539393946 0.670386931 0.604632645 0.6242221 0.844545991 0.479889776 0.560141148 0.673980049 1 16.05237217 0.959239659 19.0302655 1.000000002 0.619342016 0.606894487 0.095977983 191.9183617 89604.26272 0.087900072 0.021975018 9.10415533 -0.959239659 -0.380657986 IISNAS(ph)CTTNCLAPLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IISNASCTTNCLAPLAK 17 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 IIS(0.208)NAS(0.781)CT(0.009)T(0.002)NCLAPLAK 155.49 1.03E-07 43699000 41715 48241 46409 43709 59455 37333 50679 36451 72480 TRUE FALSE 39104.13261 51812.81383 47509.8434 44830.64694 54785.64413 48110.43105 43080.15443 41001.98759 60382.61976 0.647605764 0.858074957 0.786813219 0.742442894 0.907308168 0.796759585 0.713452888 0.679036248 1 15.88184573 -2.124897328 2.590029514 1.470547842 0.776601899 0.461813634 0.078560866 8072110.827 1970487.988 22595590.47 0.018100649 0.007500715 2.124897328 -0.693945943 IISPGSSTPSSTRS(ph)PPPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IISPGSSTPSSTRSPPPGR 19 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 IISPGSSTPS(0.003)S(0.011)T(0.011)RS(0.975)PPPGR;IISPGS(0.001)S(0.001)T(0.001)PS(0.171)S(0.144)T(0.144)RS(0.538)PPPGR 140.47 1.06E-07 1456640000 256760 317660 288176 294103 323705 218407 283467 257226 308405 TRUE FALSE 240689.8499 341179.8769 295011.6708 301650.1809 298282.5151 281457.5554 240963.7549 289341.2323 256930.2131 0.936790761 1.327908745 1.148217126 1.17405492 1.160947603 1.095463052 0.937856829 1.12614717 1 17.97101703 2.058309208 3.638529186 1.014286265 1.174558099 0.213365561 0.105396003 0.257775315 6.926099892 0.041856251 0.027815139 114.3692329 -2.058309208 0.160271834 IISPGSSTPSSTRS(ph)PPPGRDESYPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.007)S(0.036)T(0.036)RS(0.921)PPPGRDESYPR;IISPGSSTPSST(0.001)RS(0.998)PPPGRDESYPR;IISPGSSTPS(0.116)S(0.116)T(0.116)RS(0.651)PPPGRDESYPR 237.28 9.54E-39 1339980000 266547 396640 347780 410820 534150 227181 364910 268279 743810 TRUE FALSE 249864.2991 426007.6383 356029.5058 421362.3367 492200.0137 292764.4667 310195.1332 301774.2237 619663.3058 0.403225908 0.687482435 0.574553152 0.679985942 0.79430234 0.472457323 0.500586577 0.486997085 1 19.24112501 -1.783104641 2.94379139 1.095654219 0.583869993 0.559946984 0.118184388 957173485.1 767954756.3 657330970.4 0.028064653 0.016477653 1.783104641 -0.511784226 IISSDRDLLAVVFYGTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IISSDRDLLAVVFYGTEK 18 1 P12956;B1AHC9 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;; 206.21 8.00E-16 1050009000 2700510 2579380 2655490 2588380 3175710 2107480 3117590 2659180 3270500 FALSE TRUE 2531489.9 2770359.979 2718479.477 2654802.213 2926302.547 2715875.264 2650136.322 2991184.477 2724632.422 0.929112448 1.016783019 0.997741734 0.974370778 1.07401737 0.996785931 0.972658294 1.097830464 1 21.37763018 4.740900663 23.60992731 1.011546084 0.929112383 0.307415128 0.040566926 122.5477648 1236266.31 0.008815442 0.058632875 55068.17234 -4.740900663 -0.082433701 IISSIEQKEENKGGEDKLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IISSIEQKEENKGGEDKLK 19 3 P62258;P62258-2;B4DJF2;I3L3T1;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 56.017 0.04312 423350000 617020 305200 354650 431430 505280 232730 548020 323700 878520 FALSE TRUE 578401.8196 327797.3256 363062.4655 442501.2242 465597.347 299915.3729 465849.4886 364114.6576 731889.3365 0.790285895 0.447878264 0.496061969 0.604601273 0.636158124 0.409782406 0.636502631 0.497499607 1 19.481266 -1.4620607 3.195802667 1.008546547 0.550967244 0.60005951 0.111134398 30425884.82 39176837.6 2334397.868 0.024229297 0.03450955 1.4620607 -0.457579303 IISVT(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IISVTPVK 8 0 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 IISVT(1)PVK;IIS(0.007)VT(0.993)PVK;IIS(0.005)VT(0.995)PVK 134.23 0.0098997 437230000 2161970 1725730 1912690 1874540 1820240 1597810 2570950 1946730 1907530 TRUE FALSE 2026656.157 1853504.845 1958059.91 1922643.87 1677285.693 2059071.809 2185459.915 2189783.526 1589150.92 1.275307544 1.166349163 1.2321422 1.20985606 1.055460291 1.295705639 1.375237485 1.37795819 1 20.59982471 2.045330418 24.99979963 1.303437102 1.190576643 0.040530583 0.120602598 204.2191806 112626.2959 0.040299677 0.02976327 111.0019014 -2.045330418 -0.112860459 IITDVIGNPEEERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IITDVIGNPEEERR 14 1 J3KMX2;B9EGA3;Q92925-3;Q92925-2;Q92925;J3QWB6 J3KMX2 SMARCD2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 0 ;;; 209.53 1.04E-08 645607000 563994 699522 652558 659475 747660 598077 751440 619416 839020 FALSE TRUE 528694.6223 751315.3367 668036.9839 676398.245 688941.7995 770732.1209 638768.548 696751.4511 698982.1417 0.756377868 1.074870575 0.955728257 0.967690309 0.985635767 1.102649231 0.913855319 0.996808659 1 19.41489607 4.750208434 24.99789149 0.997075837 0.756377725 0.661974129 0.05460571 1109.937064 2382040.408 0.012358281 0.202325931 56261.12781 -4.750208434 -0.240698112 IIVDELKQEVISTSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IIVDELKQEVISTSSK 16 1 P63244;J3KPE3;H0YAF8;H0Y8W2;D6RAC2;D6REE5;H0YAM7;D6RF23;H0Y9P0 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 ; 252.76 1.41E-26 702880000 2523800 2046230 2081210 2275980 2626300 1572280 2806100 1892120 3365900 FALSE TRUE 2365839.863 2197734.998 2130577.284 2334385.5 2420040.992 2026171.712 2385351.356 2128355.347 2804109.545 0.843704508 0.783755043 0.759805296 0.83248727 0.863033684 0.722572239 0.850662685 0.75901291 1 21.41911128 -1.583154654 3.489849193 1.007037168 0.799494943 0.646209176 0.046040077 98205753.77 11730198.36 5632608.985 0.009822407 0.026112313 1.583154654 -0.207542225 IIVEKPFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IIVEKPFGR 9 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 150.53 7.75E-05 17353000000 14586100 16260800 15922400 13799700 14274900 12206000 14668100 13154100 12824600 FALSE TRUE 13673182.04 17464766.55 16300086.85 14153823.66 13153806.94 15729674.05 12468754.58 14796418.34 10684091.41 1.279770222 1.634651547 1.525640901 1.324756886 1.231158218 1.472251916 1.167039302 1.384901886 1 23.34896089 1.12759285 0.266271426 0.932504095 1.569792337 0.455424327 0.135142606 1.660297898 0.425628233 0.406267576 0.275698959 13.41506711 -1.12759285 0.637288243 IIYIVHDEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IIYIVHDEVK 10 0 P25788-2;P25788;G3V4X5 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 177.78 2.29E-06 401770000 960910 1277200 641420 658420 1569200 420870 877650 1313600 1336500 FALSE TRUE 900768.3584 1371765.217 656634.7853 675316.1719 1445961.362 542368.3367 746054.5302 1477605.852 1113429.516 0.809003485 1.23201801 0.589740775 0.606519014 1.298655497 0.487115106 0.670050973 1.327076237 1 20.0865788 1.240100542 24.99993848 1.163538134 0.81829714 0.217905795 0.275727644 61.2224742 994062.5617 0.2028204 0.065086468 17.38203187 -1.240100542 -0.345240994 IIYIVHDEVKDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IIYIVHDEVKDK 12 1 P25788-2;P25788;G3V4X5 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 111.12 0.00085071 206640000 863880 658700 671990 720580 1070500 383770 814820 645610 1518300 FALSE TRUE 809811.2929 707470.8334 687929.9201 739071.3027 986427.2482 494558.169 692645.3054 726215.8297 1264885.921 0.640224766 0.55931592 0.543867165 0.584298782 0.779854714 0.390990334 0.547595078 0.574135436 1 20.27057585 -1.574357206 2.46114322 1.038611256 0.569167276 0.656700296 0.095824802 2863091.787 2471572.655 720012.6775 0.023148702 0.026646661 1.574357206 -0.46944398 IKAEYEGDGIPTVFVAVAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IKAEYEGDGIPTVFVAVAGR 20 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 197.85 1.47E-21 1362550000 3330360 3323470 3591170 3566220 4015550 2505230 4237000 3238140 4706500 FALSE TRUE 3121918.712 3569543.177 3676354.248 3657735.243 3700184.901 3228449.232 3601701.184 3642428.907 3920954.745 0.796213911 0.91037602 0.937617108 0.932868518 0.943694876 0.823383447 0.918577596 0.928964791 1 21.90277356 -5 0.227278229 1.507168957 0.892046531 0.321837163 0.048644831 217.3616332 2.176241646 50.69989873 0.08429664 1.00E-05 5 -0.615122425 IKDAFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IKDAFDR 7 1 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ; 96.711 0.011429 659700000 1023590 884030 987160 1021420 1015480 887320 1196570 1027190 863190 FALSE TRUE 959525.3291 949484.501 1010575.901 1047631.366 935728.297 1143474.88 1017155.437 1155436.933 719118.0126 1.334308573 1.320345874 1.405299108 1.456828154 1.301216602 1.590107409 1.414448559 1.606741748 1 19.45586902 3.828189028 2.201187633 1.424707954 1.327225932 0.007773109 0.169152281 0.950174833 9.055239659 0.041094026 0.090093103 6732.696353 -3.828189028 -0.097482021 IKDAFDRNPELQNLLLDDFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKDAFDRNPELQNLLLDDFFK 21 2 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 202.86 3.46E-22 317920000 1335600 1052200 1058500 1182800 1418800 773180 1459700 1015500 1676200 FALSE TRUE 1252007.18 1130105.983 1083608.12 1213152.65 1307373.171 996384.5145 1240831.536 1142287.41 1396431.391 0.896576221 0.809281423 0.775983787 0.868752062 0.936224421 0.713521997 0.888573219 0.818004678 1 20.41331326 -4.999994812 0.438089365 4.499963772 0.830192667 0.375720155 0.064711086 1155.099074 7.006688535 3910.317267 0.033070272 1.00E-05 4.999994812 -3.669771105 IKDEDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKDEDIK 7 1 G2XKQ0 G2XKQ0 Small ubiquitin-related modifier 0 80.067 0.028198 375770000 379590 204590 232770 249310 213890 196160 320050 214200 203720 FALSE TRUE 355832.1395 219738.0565 238291.4143 255707.7167 197091.9422 252788.2076 272061.4737 240943.3415 169717.8159 2.096610409 1.294725927 1.404044785 1.50666396 1.161292002 1.489461824 1.603022477 1.419670293 1 17.37277849 4.743433322 24.93881956 1.392586316 2.096610708 0.624677438 0.177871537 330.8882426 1693449.375 0.039506541 0.327314156 55390.24961 -4.743433322 0.704024392 IKDHIQNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IKDHIQNGK 9 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 117.7 0.00066657 2322300000 8542300 6558000 7935600 7309200 7619900 5879100 9476900 6560700 8577400 FALSE TRUE 8007652.691 7043561.144 8123836.179 7496766.446 7021463.791 7576300.731 8055926.824 7379817.837 7145776.528 1.120613367 0.985695693 1.13687241 1.049118513 0.982603327 1.060248764 1.127368984 1.032752397 1 22.76865937 1.000021347 24.99999419 0.999999983 1.065545217 0.146508415 0.053224306 1.111330033 1297138.834 0.049509097 0.012377274 10.00049154 -1.000021347 0.065545233 IKDIAWTEDSKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IKDIAWTEDSKR 12 2 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ; 205.62 5.60E-08 2109100000 2392110 2033440 2217640 2308010 2601160 1491040 2704750 2138110 3329730 FALSE TRUE 2242392.105 2183998.013 2270243.468 2367237.444 2396875.386 1921479.043 2299197.847 2405057.74 2773976.552 0.808367361 0.787316681 0.818407591 0.853373271 0.864057551 0.692680348 0.828845451 0.867007235 1 21.40352416 0.889427391 2.371477875 0.999439626 0.805333668 0.634708233 0.046371704 0.274988067 3.207705716 0.042211233 0.011424909 7.752243237 -0.889427391 -0.194105959 IKDMDLWEQQEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IKDMDLWEQQEEER 14 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;; 245.19 1.12E-17 2057180000 1948990 1798000 1962410 1882530 2126590 1570820 2395360 1818270 2513050 FALSE TRUE 1827006.195 1931125.791 2008959.292 1930838.907 1959576.2 2024290.234 2036198.005 2045285.012 2093605.72 0.872660109 0.922392298 0.959569069 0.922255269 0.935981489 0.966891815 0.9725795 0.976919862 1 20.99755834 8 0.163669124 1.005262936 0.557734793 0.812212085 0.015673479 29.62300475 0.311179908 0.046903657 3.218186692 100000000 -8 -0.447528143 IKDPDASKPEDWDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IKDPDASKPEDWDER 15 2 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;;;; 126.77 0.00025636 22393500000 12712150 7676980 9032560 9108010 8860810 5980620 11985900 7113750 9142690 FALSE TRUE 11916519.22 8245391.587 9246816.589 9341736.956 8164917.725 7707127.907 10188725.57 8001917.347 7616715.975 1.564521936 1.082538933 1.214016201 1.226478313 1.071973506 1.011870199 1.337679598 1.050573157 1 22.86073767 4.743933539 24.55559304 1.145675653 1.564522166 0.614714202 0.108347723 310.1562848 1417435.203 0.024116767 0.207362048 55454.0844 -4.743933539 0.418846513 IKEDEDDKTVLDLAVVLFETATLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKEDEDDKTVLDLAVVLFETATLR 24 2 P14625;H0YIV0 P14625 HSP90B1 Endoplasmin 0 173.47 2.32E-12 327180000 557800 239750 369100 352530 331560 239400 467470 261230 261210 FALSE TRUE 522888.2937 257501.3395 377855.2263 361576.5166 305520.615 308510.8937 397377.2133 293845.1405 217612.3635 2.402842767 1.183302894 1.736368376 1.66156238 1.403967174 1.417708483 1.826078293 1.350314549 1 17.731401 -2.833071013 0.221386557 9.79E-14 1.695553164 0.307872023 0.324148297 71.97537543 1.697636423 35.22400686 0.604489852 0.001468686 2.833071013 1.695553164 IKEEEPDPEEWQLS(ph)GDSTLNTNDLTHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKEEEPDPEEWQLSGDSTLNTNDLTHLR 28 1 A0A494C1G8;A0A494C0Z6;H0Y6K5;A0A494C070;H0Y7L6;Q02447-4;Q02447-3;Q02447-5;Q02447-6;Q02447-2;Q02447 A0A494C1G8 SP3 Transcription factor Sp3 1 IKEEEPDPEEWQLS(0.998)GDS(0.001)T(0.001)LNTNDLTHLR 99.269 0.00095315 41237000 32023 22559 30118 27012 24978 18950 28609 22200 45545 TRUE FALSE 30018.73759 24229.29183 30832.41318 27705.17365 23016.32864 24420.55737 24319.34604 24971.71887 37943.24527 0.791148395 0.638566671 0.812592939 0.730174065 0.606598842 0.643607504 0.640940064 0.658133449 1 15.21155546 -1.062662398 5.25788729 1.000003661 0.689536082 0.66978392 0.068356173 2.98E-06 5.31E-07 0.067234786 0.015847204 0.086564057 1.062662398 -0.310467579 IKEELIAQGLLESEDRPAEDS(ph)EDEVLAELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKEELIAQGLLESEDRPAEDSEDEVLAELR 30 2 O75528-2;O75528 O75528-2 TADA3 Transcriptional adapter 3 1 IKEELIAQGLLES(0.029)EDRPAEDS(0.971)EDEVLAELR 49.453 0.046098 22870000 23660 18372 17813 15728 17893 14487 21712 15370 17769 TRUE FALSE 22179.16283 19732.282 18235.53277 16131.60711 16487.75596 18669.16172 18456.48716 17288.97833 14803.23911 1.498264175 1.332970565 1.231860989 1.089734955 1.113793801 1.261153832 1.246787073 1.167918603 1 13.85362527 4.642398551 0.97553258 1.172290005 1.628370687 0.668001799 0.079643015 1.121686693 0.944170098 0.025031301 0.520950215 43893.33212 -4.642398551 0.456080682 IKEEPVS(ph)EEGEEDEEQEAEEEPMDTSPSGLHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IKEEPVSEEGEEDEEQEAEEEPMDTSPSGLHSK 33 1 A0A0C4DH01;Q9NVU0-3;Q9NVU0-2;Q9NVU0-5;Q9NVU0-4;Q9NVU0 A0A0C4DH01 POLR3E DNA-directed RNA polymerase III subunit RPC5 1 IKEEPVS(1)EEGEEDEEQEAEEEPMDTSPSGLHSK;IKEEPVS(1)EEGEEDEEQEAEEEPMDTSPSGLHSK;IKEEPVS(1)EEGEEDEEQEAEEEPMDTSPSGLHSK;IKEEPVS(1)EEGEEDEEQEAEEEPMDTSPSGLHSK;IKEEPVS(1)EEGEEDEEQEAEEEPMDTSPSGLHSK 359.54 3.84E-132 832250000 415870 350296 403616 403835 456506 283290 542319 387232 534631 TRUE FALSE 389841.439 376232.2803 413189.9621 414198.0898 420653.8602 365071.2242 461003.3006 435578.7676 445397.6323 0.875266079 0.844711002 0.927687828 0.929951261 0.944445659 0.819652368 1.03503761 0.977954834 1 18.76473436 2.478936086 0.334074528 1.016839431 0.842464419 0.419344109 0.051348257 1.651959443 0.41900413 0.062630524 0.103653764 301.256264 -2.478936086 -0.174375012 IKEETEIIEGEVVEIQIDRPATGTGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IKEETEIIEGEVVEIQIDRPATGTGSK 27 2 Q9Y230;Q9Y230-2;M0R0Y3;X6R2L4 Q9Y230 RUVBL2 RuvB-like 2 0 ;;; 243.75 1.44E-45 505981000 1305170 828210 1060190 1021160 1050860 756490 1299090 884480 1164130 FALSE TRUE 1223481.739 889531.5302 1085338.207 1047364.694 968329.6946 974876.3824 1104303.515 994909.275 969829.1824 1.261543539 0.917204335 1.119102443 1.079947596 0.998453864 1.005204215 1.13865775 1.02586032 1 19.88737114 4.762367119 24.11409868 1.043466467 1.261543949 0.543267165 0.064759926 3531.531751 3577067.885 0.015247193 0.875243296 57858.49317 -4.762367119 0.218077482 IKEEVLS(ph)ESEAENQQAGAAALAPEIVIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IKEEVLSESEAENQQAGAAALAPEIVIK 28 1 Q9UJX5;Q9UJX5-3 Q9UJX5 ANAPC4 Anaphase-promoting complex subunit 4 1 IKEEVLS(0.5)ES(0.5)EAENQQAGAAALAPEIVIK;IKEEVLS(0.5)ES(0.5)EAENQQAGAAALAPEIVIK 118.14 0.00011914 375257000 205529 161364 163734 184828 191072 157073 229677 155560 197138 TRUE FALSE 192665.3068 173311.5585 167617.8478 189570.9994 176065.9759 202417.4252 195239.0661 174982.0084 164234.3942 1.173111806 1.055269569 1.02060137 1.154271006 1.072040827 1.232491076 1.188783062 1.065440703 1 17.32539676 3.221890865 24.99895023 1.137809787 1.068139969 0 0.077339678 430.7334919 645952.5583 0.021413362 0.02566103 1666.828299 -3.221890865 -0.069669818 VRGGAPDPSPGATATPGAPAQPS(ph)SPDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VRGGAPDPSPGATATPGAPAQPSSPDAR 28 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 VRGGAPDPSPGATATPGAPAQPS(0.599)S(0.401)PDAR;VRGGAPDPSPGATATPGAPAQPS(0.611)S(0.389)PDAR;VRGGAPDPSPGATATPGAPAQPS(0.5)S(0.5)PDAR 193.68 1.07E-18 1461540000 582243 600125 446071 483045 873730 377951 656550 700160 1680140 TRUE FALSE 545801.45 644558.8794 456652.0148 495440.7525 805110.7703 487059.3182 558106.4226 787576.5172 1399713.78 0.389937899 0.460493344 0.326246709 0.353958616 0.575196717 0.347970653 0.398728962 0.562669689 1 20.41670042 0.838069274 2.602780821 0.999727145 0.40513493 0.874694466 0.070535453 0.198755322 2.436174749 0.063912515 0.017036512 6.887621511 -0.838069274 -0.594592215 IKELEQEREDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKELEQEREDQK 12 2 O75940 O75940 SMNDC1 Survival of motor neuron-related-splicing factor 30 0 116.51 0.00046896 129740000 206970 126400 160450 144530 152400 108470 176770 123390 188180 FALSE TRUE 194016.1172 135758.7875 164255.9498 148238.8845 140431.1188 139783.5281 150264.9796 138795.5131 156771.5423 1.237572293 0.865965758 1.047740855 0.945572661 0.895769198 0.891638406 0.958496532 0.885336146 1 17.25830417 4.74726477 24.8597267 0.938875104 1.237572458 0.740246638 0.056064931 532.6006641 1521112.208 0.01284307 0.151405263 55881.07729 -4.74726477 0.298697354 RRGNDPLT(ph)SSPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRGNDPLTSSPGR 13 2 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RRGNDPLT(0.966)S(0.014)S(0.02)PGR 67.685 0.084376 569650000 116630 162750 111540 143920 220440 70871 170770 198950 528300 TRUE FALSE 109330.3365 174800.1793 114185.7815 147613.2309 203127.5316 91330.30721 145164.6239 223789.3454 440123.3171 0.248408417 0.397161824 0.259440427 0.335390617 0.461524131 0.207510722 0.32982716 0.508469642 1 18.74754828 0.843510912 2.493173265 0.99952957 0.321253631 0.896002777 0.073066917 0.165157865 1.903518089 0.064578797 0.017318959 6.974465205 -0.843510912 -0.678275938 IKELQNAGDR ddPTM_SK-BR-3_Pertuzumab_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 0 105.25 0.0023474 293590000 403510 425320 413120 475650 502360 341910 491110 365940 505020 FALSE TRUE 378255.0294 456811.1353 422919.4015 487855.9843 462906.672 440613.8666 417472.6147 411628.4145 420728.8994 0.899046939 1.085761249 1.005206445 1.159549498 1.100249288 1.047263136 0.992260373 0.978369718 1 18.68253139 -0.719840363 5.805647445 0.999999999 1.038537985 0.016486761 0.072333193 1.98E-09 1.70E-10 0.066295013 0.015625884 0.190616125 0.719840363 0.038537986 IKENKGEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKENKGEER 9 2 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 70.1 0.030015 217830000 167760 205780 184500 194760 280170 169040 189100 220180 264630 FALSE TRUE 157260.2011 221016.1653 188876.4271 199757.8713 258166.5784 217839.1039 160746.2105 247669.9577 220461.5434 0.713322599 1.002515731 0.856731855 0.906089417 1.171027719 0.988104775 0.729134923 1.123415693 1 17.75016749 4.746677831 24.34303103 0.949658794 0.713322428 0.276574956 0.127002335 1041.656939 3123760.31 0.029690544 0.325368243 55805.60636 -4.746677831 -0.236336366 IKFPLPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IKFPLPHR 8 1 Q02543;M0R3D6;M0R1A7;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 87.616 0.0091315 1225160000 2349600 5401000 2289300 2215100 6142200 1550670 3131300 5107200 5605400 FALSE TRUE 2202542.73 5800895.66 2343603.277 2271943.216 5659816.388 1998323.256 2661790.635 5744845.162 4669822.528 0.471654483 1.242209019 0.501861316 0.486515966 1.211998177 0.427922741 0.569998243 1.230206315 1 22.15493629 1.235105514 24.99874173 1.115103254 0.723877696 0.243766191 0.300729354 138.5039242 1002040.793 0.24110238 0.069660226 17.18325813 -1.235105514 -0.391225558 IKGDVDVSAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKGDVDVSAPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 113.65 0.0012434 439870000 1061100 705510 835230 803430 956450 626050 1046900 760060 1162700 FALSE TRUE 994687.6451 757746.6945 855042.05 824047.374 881334.2751 806780.4719 889927.0639 854955.1641 968637.8587 1.026893215 0.782280692 0.882726235 0.850728027 0.909869738 0.832902064 0.918740741 0.882636536 1 19.88559787 0.218126695 0.663464543 1.004069834 0.869801322 0.215094944 0.064645698 3.755641057 2.174727536 0.095036242 0.021995363 1.65244379 -0.218126695 -0.134268512 IKGDVDVTGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKGDVDVTGPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 118.87 0.00060464 594950000 1317400 903140 1028200 1004600 1299000 729720 1373100 1018200 1419900 FALSE TRUE 1234946.286 970009.4253 1052589.39 1030379.737 1196981.78 940378.318 1167216.402 1145324.511 1182909.517 1.043990489 0.820019969 0.889830857 0.871055412 1.011896314 0.794970625 0.986733461 0.968226644 1 20.17390829 1.607205606 25 0.983121354 0.896050752 0.188327786 0.076367408 0.107245984 3518.414321 0.03461461 0.017505508 40.47674736 -1.607205606 -0.087070601 IKGEHPGLSIGDVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IKGEHPGLSIGDVAK 15 1 P09429;Q5T7C4;B2RPK0 P09429 HMGB1;HMGB1P1 High mobility group protein B1;Putative high mobility group protein B1-like 1 0 ; 166.35 8.25E-07 9541700000 31160000 23931000 27158000 27778000 30215000 19250200 34615000 25209000 38944000 FALSE TRUE 29209751.22 25702876.14 27802200.58 28490830.51 27842035.78 24807420.24 29424802.1 28356399.14 32443994.81 0.900313028 0.792222915 0.856929017 0.878154206 0.858156831 0.764622864 0.906941401 0.874010716 1 24.95144813 0.736741688 1.126496745 0.999160944 0.841793276 0.538868732 0.043381576 0.640525042 1.428446469 0.038040331 0.011883842 5.454333485 -0.736741688 -0.157367668 IKGS(ph)SPGIQDTLEAEDGAFETDEAPEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKGSSPGIQDTLEAEDGAFETDEAPEDR 28 1 Q9UNX4 Q9UNX4 WDR3 WD repeat-containing protein 3 1 IKGS(0.622)S(0.377)PGIQDTLEAEDGAFETDEAPEDR 270.81 1.25E-61 183180000 137580 112400 122250 122820 141150 106960 197810 122190 164600 TRUE FALSE 128969.1134 120722.213 125149.8277 125971.7691 130064.6484 137837.6156 168150.2269 137445.6905 137127.1966 0.940507183 0.880366666 0.912655044 0.918649052 0.948496371 1.00518073 1.22623543 1.002322616 1 17.06515521 2.096744725 3.385521919 1.103768155 0.912894186 0.513129013 0.066975168 0.143088506 3.221408706 0.026270075 0.017712465 124.9524355 -2.096744725 -0.190873969 IKGSEADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IKGSEADR 8 1 P56192 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ; 87.298 0.014066 427430000 714400 795820 776620 822420 927720 614620 1000900 802130 1166640 FALSE TRUE 669686.9792 854743.3408 795041.7931 843524.6896 854860.6134 792050.8165 850824.3369 902277.6962 971920.2472 0.689034909 0.879437735 0.81801135 0.867894966 0.879558396 0.814933961 0.875405507 0.928345406 1 19.89047841 -5 0.02865437 1.970622176 0.181498564 0.631845446 0.048849924 1113.398522 2.404130884 114.7670569 48.44289669 1.00E-05 5 -1.789123613 IKGSS(ph)PGIQDTLEAEDGAFETDEAPEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IKGSSPGIQDTLEAEDGAFETDEAPEDR 28 1 Q9UNX4 Q9UNX4 WDR3 WD repeat-containing protein 3 1 IKGS(0.206)S(0.794)PGIQDTLEAEDGAFETDEAPEDR;IKGS(0.45)S(0.55)PGIQDTLEAEDGAFETDEAPEDR 299.38 1.11E-71 227719000 269686 224990 248136 241408 256711 177735 333466 203269 263891 TRUE FALSE 252806.8347 241648.4937 254021.9031 247602.938 236549.9536 229044.2092 283465.869 228647.5821 219845.8873 1.149927514 1.099172228 1.155454424 1.126256857 1.075980799 1.041839863 1.289384453 1.040035749 1 17.74613302 2.988697908 23.8863708 1.116509064 1.131487457 0.008773791 0.080612368 2861.568933 6047812.741 0.023701864 0.026639264 974.3116785 -2.988697908 0.014978393 IKIIAPPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IKIIAPPER 9 1 P60709;P63267-2;Q562R1;A0A2R8YFE2;P63261;P68133;P68032;P63267;P62736;A6NL76 P60709;P63261;P68133 ACTB;ACTG2;ACTBL2;ACTG1;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Beta-actin-like protein 2;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 ; 121.83 0.00054982 4404200000 1577380 2013960 2085300 1974490 2225900 1963900 2661200 1686310 2922200 FALSE TRUE 1478654.602 2163075.694 2134764.301 2025158.756 2051086.793 2530846.049 2262177.765 1896849.516 2434465.942 0.607383565 0.888521649 0.876892243 0.831869825 0.842520225 1.039589836 0.92922958 0.779164532 1 21.21517389 4.73953851 5.366153294 0.898578862 0.595702206 0.585305053 0.077052894 0.10934726 11.530685 0.017722458 0.12204056 54895.72305 -4.73953851 -0.302876656 IKKPEGKPDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IKKPEGKPDQK 11 3 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;D6RBK5;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 70.54 0.022555 1983910000 4215390 2016720 2902510 2907390 3011100 1985060 4008830 2704650 5112260 FALSE TRUE 3951556.265 2166040.047 2971358.908 2981998.55 2774620.352 2558114.597 3407743.158 3042331.506 4258990.78 0.927815172 0.508580591 0.697667373 0.700165533 0.65147367 0.600638679 0.800129264 0.714331555 1 22.02208018 0.508898595 0.758687934 1.002658633 0.664696037 0.407019143 0.112165937 1.410200985 1.306249324 0.10845618 0.03573234 3.227740379 -0.508898595 -0.337962596 IKLNGLENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 117.52 0.0018812 0 284890 851670 264330 284050 966170 231490 369380 777870 913160 FALSE TRUE 267059.2434 914728.533 270600.0324 291339.2039 890290.9055 298317.4051 313994.8982 874988.7818 760747.6968 0.351048376 1.202407233 0.35570273 0.382964293 1.170284063 0.392137112 0.412745118 1.150169479 1 19.53705854 1.226765 24.96173035 1.075085045 0.632399007 0.25989615 0.324793215 354.4728523 750106.841 0.290470376 0.074996272 16.85640668 -1.226765 -0.442686038 IKLPSVTSFILDTEAVAWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKLPSVTSFILDTEAVAWDR 20 1 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28 P18858 LIG1 DNA ligase 1;DNA ligase 0 134.29 8.43E-06 74855000 117460 142410 130130 130950 182120 128570 146520 126780 153310 FALSE TRUE 110108.3883 152954.1846 133216.7451 134310.3987 167817.0298 165686.0718 124550.6862 142608.7621 127721.5706 0.862097043 1.197559534 1.043024639 1.051587434 1.313928642 1.297244241 0.975173463 1.116559728 1 16.96264267 1.629678271 24.99999954 1.034399154 1.130583214 0.102821735 0.134706275 1.991938281 2276.84152 0.060242378 0.033369233 42.62636225 -1.629678271 0.096184061 IKLYSESLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKLYSESLAR 10 1 P50395;P50395-2;Q5SX87;Q5SX91;P31150 P50395;P31150 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 128.28 0.00030435 392530000 371640 827440 414160 396280 1103800 286910 475690 682660 1268200 FALSE TRUE 348379.7158 888704.5186 423984.0708 406449.2157 1017112.001 369736.2594 404364.7006 767891.6037 1056529.227 0.329739781 0.841154694 0.401298951 0.384702292 0.962691778 0.34995365 0.382729309 0.726805832 1 20.01090125 0.976640519 6.596673858 0.999935727 0.535937436 0.342735029 0.215233162 0.203276796 43.94322825 0.19565592 0.049114085 9.476337489 -0.976640519 -0.463998291 IKNENTEGS(ph)PQEDGVELEGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 IKNENTEGSPQEDGVELEGLK 21 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 IKNENTEGS(1)PQEDGVELEGLK;IKNENTEGS(1)PQEDGVELEGLK;IKNENT(0.002)EGS(0.998)PQEDGVELEGLK;IKNENTEGS(1)PQEDGVELEGLK;IKNENTEGS(1)PQEDGVELEGLK;IKNENTEGS(1)PQEDGVELEGLK;IKNENT(0.11)EGS(0.89)PQEDGVELEGLK 359.05 5.13E-96 9587890000 6937497 3647150 4835822 4491321 4932593 3161827 6746226 4142128 7968455 TRUE FALSE 6503291.447 3917188.781 4950529.981 4606575.901 4545207.043 4074595.127 5734692.04 4659281.799 6638468.382 0.979637331 0.590074179 0.745733759 0.693921494 0.684677064 0.613785423 0.863857702 0.701860961 1 22.66241899 0.231256595 0.749412797 1.004967871 0.712507234 0.327637902 0.116084263 3.113748025 2.203357132 0.14585571 0.036478431 1.703164495 -0.231256595 -0.292460637 IKPHLMSQELPEDWDKQPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IKPHLMSQELPEDWDKQPVK 20 2 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ; 238.79 7.29E-30 1761770000 4904800 2612530 3730430 3601640 3432510 2279990 5160340 3166440 4508400 FALSE TRUE 4597817.323 2805964.44 3818917.561 3694064.18 3162934.511 2938186.1 4386594.923 3561777.004 3755918.915 1.224152445 0.747078013 1.016773165 0.983531398 0.84212002 0.782281558 1.167915235 0.94831041 1 21.84073449 1.733635151 24.99999936 1.049178787 0.919422007 0.101222382 0.144385595 0.97192904 4889.15898 0.061111602 0.033889418 54.15457492 -1.733635151 -0.12975678 IKPVTENLVLSSHTGFCQS(ph)SGDEALSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKPVTENLVLSSHTGFCQSSGDEALSK 27 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;P46100-3;A0A096LP59 P46100;P46100-3;A0A096LP59 ATRX Transcriptional regulator ATRX 1 IKPVTENLVLSSHTGFCQS(0.5)S(0.5)GDEALS(0.001)K 77.873 0.0085748 181320000 78783 45535 55380 50487 59802 41051 64256 51746 73023 TRUE FALSE 73852.11266 48906.45878 56693.63975 51782.58189 55105.39215 52901.75729 54621.40932 58206.60201 60834.98955 1.21397428 0.803919901 0.93192487 0.85119735 0.905817401 0.869594253 0.897861736 0.956794806 1 15.89261372 1.025783437 3.817852026 0.999514203 0.907672287 0.028850454 0.110531322 0.499664566 17.28244706 0.092881909 0.02389932 10.61166269 -1.025783437 -0.091841915 IKQEILPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IKQEILPEER 10 1 O75534-2;O75534;O75534-3;O75534-4 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;; 157.68 7.97E-06 1266730000 2647920 2824140 2738350 2774220 3347840 2437130 3802400 2975900 3913900 FALSE TRUE 2482191.414 3033242.264 2803304.955 2845411.182 3084914.151 3140689.868 3232265.42 3347447.666 3260644.805 0.761257838 0.930258414 0.859739445 0.872652911 0.946105551 0.963211283 0.991296389 1.026621379 1 21.63672586 2.379644664 1.018021822 1.012091452 0.862750937 0.710774165 0.042427707 0.303245978 0.619478953 0.026786903 0.017273314 239.6871016 -2.379644664 -0.149340515 IKS(ph)LEEIYLFSLPIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKSLEEIYLFSLPIK 15 1 P15880;H0YEN5;E9PQD7;E9PPT0;E9PMM9;H3BNG3;H0YE27 P15880 RPS2 40S ribosomal protein S2 1 IKS(1)LEEIYLFSLPIK 128.38 4.38E-05 114490000 1066900 618530 759600 767060 826100 547690 936800 654570 765950 TRUE FALSE 1000124.633 664326.6048 777618.0707 786744.0582 761221.4383 705799.212 796335.5368 736294.5054 638107.9968 1.567328162 1.041088042 1.218630819 1.232932454 1.192935118 1.106081127 1.247963575 1.153871303 1 19.28344109 7.998870464 0.020434688 3.97E-07 2.722648823 0.298380903 0.129386557 4958.680381 7.807925453 383.0524198 701.6643482 99740252.69 -7.998870464 2.722648426 IKSDFFELLSNHHLDSQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKSDFFELLSNHHLDSQSR 19 1 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 169.43 9.13E-12 108400000 111690 261490 219770 235650 311440 188390 282960 238010 417700 FALSE TRUE 104699.5223 280850.9917 224983.0482 241697.178 286980.7587 242775.1347 240532.7749 267726.0724 347983.1716 0.300875246 0.807082108 0.646534277 0.694565708 0.824697233 0.697663435 0.69121956 0.769364999 1 18.40865801 -4.999999966 0.044447422 2.253745334 1.27E-09 0.488263747 0.126663533 687.3079599 2.272858648 110.4212234 29.13121634 1.00E-05 4.999999966 -2.253745333 IKSDYAQLLEDMQNAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IKSDYAQLLEDMQNAFR 17 1 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 278.27 7.31E-36 540980000 854920 1045410 989790 963060 1386370 740030 1161670 918300 2158200 FALSE TRUE 801412.0833 1122813.244 1013268.286 987773.7501 1277490.093 953664.6476 987488.3679 1032951.776 1797982.477 0.445728528 0.624485087 0.563558488 0.549378964 0.710513094 0.530408199 0.54922024 0.574506031 1 20.77794753 -1.048221028 3.711887227 1.000121811 0.573224488 0.802063042 0.067333458 11473127.87 21118408.86 18052.45087 0.015169969 0.08949092 1.048221028 -0.426897323 IKSESTNHEQQS(ph)PQSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IKSESTNHEQQSPQSGK 17 1 P40818;P40818-2;A0A075B720 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 IKSESTNHEQQS(1)PQSGK;IKSESTNHEQQS(1)PQSGK;IKSESTNHEQQS(1)PQSGK;IKSESTNHEQQS(1)PQSGK 171.13 1.07E-09 507910000 690090 544430 712290 743410 789620 531440 954390 642690 1300980 TRUE FALSE 646898.4987 584740.1637 729185.8552 762487.1592 727606.4304 684858.1008 811288.0796 722931.2612 1083838.033 0.596859013 0.539508806 0.672781202 0.703506553 0.671323951 0.631882329 0.74853258 0.667010419 1 20.04771775 -5 0.141711644 2.222475129 0.527098635 0.861809335 0.045618274 46.13445093 0.39877672 15.87077357 0.263030127 1.00E-05 5 -1.695376494 IKT(ph)EDGEGIVIALSVDTPPAAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IKTEDGEGIVIALSVDTPPAAVR 23 1 Q01167 Q01167 FOXK2 Forkhead box protein K2 1 IKT(1)EDGEGIVIALSVDTPPAAVR;IKT(1)EDGEGIVIALSVDTPPAAVR;IKT(1)EDGEGIVIALSVDTPPAAVR;IKT(1)EDGEGIVIALSVDTPPAAVR 180.23 7.46E-17 191962000 569350 359521 401412 426650 480289 279241 600736 386153 437448 TRUE FALSE 533715.3998 386140.3089 410933.6822 437598.5613 442569.0393 359853.3436 510661.2138 434365.0521 364435.1028 1.464500526 1.059558495 1.127590836 1.200758538 1.214397395 0.987427778 1.401240467 1.191885877 1 18.4753024 IKTEPS(ph)SPLSDPSDIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IKTEPSSPLSDPSDIIR 17 1 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 IKTEPS(0.876)S(0.123)PLS(0.001)DPSDIIR;IKTEPS(0.77)S(0.221)PLS(0.007)DPS(0.002)DIIR;IKT(0.076)EPS(0.457)S(0.457)PLS(0.01)DPSDIIR 200.58 3.23E-11 676330000 496310 452570 458640 508090 553000 364250 554960 369100 640790 TRUE FALSE 465246.843 486078.7537 469519.1574 521128.4496 509569.6107 469403.0619 471748.9 415182.9475 533838.0093 0.871513146 0.910536053 0.879516163 0.976192104 0.95453977 0.879298689 0.883692978 0.777732084 1 19.0260425 -0.512438669 7.439597499 0.99999197 0.895225888 0.289974312 0.053028958 0 0 0.049269027 0.011612821 0.307299131 0.512438669 -0.104766083 IKTEPSS(ph)PLSDPSDIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKTEPSSPLSDPSDIIR 17 1 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 IKTEPS(0.008)S(0.992)PLSDPSDIIR 202.65 6.29E-12 1068300000 1173400 1153000 1092700 1274500 1368500 847530 1305100 962010 1635300 TRUE FALSE 1099958.989 1238369.32 1118619.36 1307205.828 1261023.53 1092198.153 1109412.371 1082119.066 1362357.866 0.807393576 0.908989738 0.82109069 0.959517217 0.925618417 0.801696955 0.814332562 0.794298689 1 20.37767429 -0.890016084 8.379340465 1 0.855904647 0.382943735 0.058157777 0 5.00E-11 0.056197263 0.013245822 0.128820184 0.890016084 -0.144095353 IKVFGPGIEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKVFGPGIEGK 11 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 158.4 0.0013293 0 1731700 1671700 1527500 1638300 1912000 1168300 2203300 1616500 2237600 FALSE TRUE 1623315.988 1795474.407 1563733.021 1680341.552 1761839.233 1505569.244 1872935.619 1818323.583 1864130.105 0.870816894 0.963170115 0.838854014 0.901407873 0.945126753 0.807652449 1.004723659 0.975427401 1 20.83007112 1.633702139 10.51653627 0.992657302 0.893912595 0.53606288 0.045992072 0.080101224 20.16527584 0.020627188 0.010946325 43.02314344 -1.633702139 -0.098744707 IKVNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKVNGK 6 1 P35268;K7ERI7;K7EMH1;K7EP65;K7EKS7;K7ELC4;K7EJT5 P35268 RPL22 60S ribosomal protein L22 0 106.84 0.028984 2829700000 2516500 2264600 2455300 2627500 2725000 2069900 3246800 2278600 3188500 FALSE TRUE 2358996.757 2432273.34 2513540.875 2694926.098 2510989.492 2667446.528 2759972.482 2563088.226 2656318.752 0.888069911 0.915655675 0.94624972 1.014534154 0.945289224 1.004189172 1.039021571 0.964902358 1 21.34099685 3.869253496 0.661074359 1.006250948 0.871741083 0.661678393 0.027189844 0.736989821 0.496973249 0.01357091 0.06466302 7400.371057 -3.869253496 -0.134509865 IKVPVDWSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKVPVDWSK 9 1 P13797;A0A0A0MSQ0;P13797-3;P13797-2;H7C4N2 P13797 PLS3 Plastin-3 0 116.77 0.0019182 0 892510 1464500 706000 662430 1695700 410850 886850 1515200 1879000 FALSE TRUE 836649.3923 1572933.104 722746.6534 679429.0753 1562526.562 529455.7254 753875.0756 1704376.055 1565382.761 0.534469532 1.00482332 0.461706026 0.43403383 0.998175399 0.338227645 0.481591528 1.08879189 1 20.57808403 1.230796466 24.99478986 1.044396236 0.619393992 0.391171891 0.226189043 204.4324775 658093.6536 0.198926204 0.053414906 17.01360972 -1.230796466 -0.425002244 IKWDEQTSNTKGDDDEES(ph)DEEAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IKWDEQTSNTKGDDDEESDEEAVK 24 2 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 IKWDEQTSNTKGDDDEES(1)DEEAVK;IKWDEQTSNTKGDDDEES(1)DEEAVK 279.32 1.91E-52 362830000 800010 216705 361370 347510 379850 239830 536410 242443 524420 TRUE FALSE 749938.8022 232750.0637 369941.8671 356427.6949 350018.1132 309065.0277 455980.3003 272712.5422 436890.9141 1.716535588 0.532741827 0.846760267 0.815827666 0.801156769 0.707419215 1.043693713 0.624211979 1 18.73691358 4.748696915 24.99712623 0.79436901 1.716536094 0.779643775 0.153717217 650.1285158 1603249.914 0.035146053 0.486083692 56065.65696 -4.748696915 0.922167085 IKWGDAGAEYVVESTGVFTTMEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 19 IKWGDAGAEYVVESTGVFTTMEK 23 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;; 255.67 1.56E-43 13556487000 20155772 17316659 18636164 19019420 20717325 13946778 23828529 15729746 23577675 FALSE TRUE 18894258.21 18598802.45 19078222.61 19507490.52 19090269.86 17972986.4 20255662.29 17693639.41 19642408.72 0.961911468 0.94686974 0.971277142 0.99313128 0.971890471 0.915009287 1.031220894 0.900787661 1 24.22746852 2.983048936 0.003673344 1.931309495 4.45E-08 0.029003251 0.038083968 76913.66461 93.74580415 24345.98305 24940.39162 961.7206384 -2.983048936 -1.931309451 IKYPENFFLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IKYPENFFLLR 11 1 F8W0W8;P36873;P36873-2;F8VYE8;F8VR82;A0A087WYY5;P62140;E7ETD8;C9JP48;C9J9S3;P62136;P62136-2;P62136-3;E9PMD7 F8W0W8;P62140;P62136 PPP1CC;PPP1CB;PPP1CA Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit;Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 ; 159.44 2.61E-05 290570000 442210 1021560 342870 299820 1191490 233910 353120 940370 581790 FALSE TRUE 414532.8655 1097197.365 351003.0383 307513.8888 1097915.182 301436.0198 300172.9342 1057777.265 484685.4905 0.855261553 2.263730578 0.724187221 0.634460686 2.265211572 0.621920866 0.619314876 2.182399278 1 18.88668937 3.957661866 22.35984293 1.09790937 1.639332946 0.050039055 0.696260652 246.4116825 283140.6294 0.166222792 0.300541023 9071.139929 -3.957661866 0.541423576 ILATPPQEDAPSVDIANIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILATPPQEDAPSVDIANIR 19 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 143.93 3.27E-07 98810000 50500 63894 43453 49120 80043 47534 64569 68233 71383 FALSE TRUE 47339.29515 68624.77824 44483.72568 50380.50236 73756.74566 61256.29415 54887.47788 76752.04025 59468.71615 0.796036945 1.153964348 0.748018934 0.84717656 1.240261274 1.030059132 0.922963895 1.290628842 1 15.85984331 2.765557292 24.98824667 1.072457697 0.90786334 0.310980569 0.151824768 1138.391124 1053698.353 0.045521138 0.048271864 582.8506598 -2.765557292 -0.164594357 ILDAVVAQEPLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ILDAVVAQEPLHR 13 0 Q15029;Q15029-3;Q15029-2;K7EP67;K7EJ74 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;; 191.06 3.88E-06 657500000 983680 1181960 1074270 1037290 1124640 875820 1258900 1050750 1234790 FALSE TRUE 922113.2247 1269473.548 1099752.192 1063908.618 1036315.311 1128655.016 1070139.632 1181938.45 1028695.572 0.896390779 1.234061449 1.069074488 1.034230774 1.007407186 1.097171065 1.040287974 1.148968152 1 19.97238467 3.498018884 22.70211441 1.055891012 1.108397088 0 0.092671889 405.6101009 440628.5398 0.022534799 0.034732567 3147.885189 -3.498018884 0.052506077 ILDDDTIITTLENLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILDDDTIITTLENLKR 16 1 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 338.69 1.10E-71 1671560000 973410 1110700 1050730 1058440 1373850 806850 1390480 1132540 1501430 FALSE TRUE 912486.0057 1192937.384 1075653.812 1085601.362 1265953.363 1039774.497 1181990.433 1273940.112 1250831.633 0.729503461 0.953715394 0.859950918 0.867903668 1.01208934 0.83126655 0.944963655 1.018474492 1 20.25445618 8 0.137643224 1.023713374 0.339707317 0.40234617 0.071223784 89.75205448 0.825828708 0.295074735 12.05039916 100000000 -8 -0.684006057 ILDEIEEHNIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ILDEIEEHNIK 11 0 Q15019-2;Q15019-3;Q15019;B5MCX3;H7C2Y0;C9J2Q4 Q15019-2 2-Sep Septin-2 0 ;;; 214.67 1.34E-11 674320000 1659480 1449460 1542070 1508210 1737360 1170780 1875690 1379060 1846970 FALSE TRUE 1555616.109 1556779.527 1578648.629 1546913.222 1600914.754 1508765.18 1594447.698 1551238.677 1538698.775 1.010994572 1.011750676 1.025963401 1.005338567 1.040434151 0.980546163 1.036231213 1.008149679 1 20.5532794 1.000497978 24.99999037 0.999999993 1.016536416 0.089401949 0.016740371 27.62510192 1386824.774 0.01366158 0.003415395 10.01147294 -1.000497978 0.016536422 ILDELDKDDSTHESLS(ph)QES(ph)ES(ph)EEDGIHVDSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILDELDKDDSTHESLSQESESEEDGIHVDSQK 32 1 Q9H6T3;Q9H6T3-2 Q9H6T3 RPAP3 RNA polymerase II-associated protein 3 3 ILDELDKDDS(0.165)T(0.172)HES(0.188)LS(0.716)QES(0.883)ES(0.876)EEDGIHVDSQK 73.422 0.012058 41392000 63572 39072 54815 47500 52132 40106 74651 42076 64945 TRUE FALSE 59593.142 41964.93153 56115.23769 48718.93042 48037.76301 51683.95113 63457.77558 47329.28122 54105.25994 1.101429733 0.775616485 1.037149396 0.900447211 0.88785754 0.955248181 1.17285779 0.874763032 1 15.72348123 1.978681 24.21303727 1.042323282 0.928722973 0.065529011 0.112744533 825.9131844 938028.9648 0.041945437 0.027399306 95.2096569 -1.978681 -0.113600309 ILDEWFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILDEWFGR 8 0 Q8IYB7;Q8IYB7-3;Q8IYB7-2;H7C440 Q8IYB7 DIS3L2 DIS3-like exonuclease 2 0 ; 124.08 0.0030712 56369000 169599 205685 201989 204065 208325 171393 213672 166750 171647 FALSE TRUE 158984.1013 220914.1314 206780.2745 209301.6534 191963.9948 220871.3768 181633.8672 187569.1046 142998.0068 1.111792429 1.544875599 1.446036061 1.463668327 1.34242427 1.544576611 1.270184608 1.311690343 1 17.12563551 0.787599228 1.001000453 1.001988393 1.427056529 0.469401695 0.129317432 0.6277366 1.190328595 0.110516346 0.035973987 6.131958803 -0.787599228 0.425068135 ILDILEYIHEHEYVHGDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ILDILEYIHEHEYVHGDIK 19 0 Q99986;H0YJ50 Q99986 VRK1 Serine/threonine-protein kinase VRK1 0 ;; 163.66 8.78E-12 186576000 617380 515040 597610 552070 580010 463740 697420 502490 658560 FALSE TRUE 578739.2879 553174.0975 611785.5914 566237.0509 534458.3542 597614.2098 592848.3455 565226.9826 548642.0815 1.054857634 1.008260424 1.115090534 1.032070032 0.974147577 1.089260613 1.080573958 1.030228999 1 19.06550576 0.994639964 22.67902029 0.999999994 1.053076702 0.139911916 0.040268332 108.2791159 458151.5967 0.038278547 0.009569637 9.877339105 -0.994639964 0.053076708 ILDQMPATPSS(ph)PMYVD ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ILDQMPATPSSPMYVD 16 0 P45985;P45985-2 P45985 MAP2K4 Dual specificity mitogen-activated protein kinase kinase 4 1 ILDQMPAT(0.001)PS(0.012)S(0.987)PMYVD;ILDQMPAT(0.007)PS(0.119)S(0.875)PMYVD;ILDQMPAT(0.004)PS(0.051)S(0.945)PMYVD 164.65 2.86E-08 143145000 339117 406280 393360 384460 393910 286375 356502 324833 328371 TRUE FALSE 317892.2723 436361.3939 402690.685 394325.8945 362973.8976 369046.8136 303047.8347 365389.1151 273563.7587 1.162040885 1.595099424 1.472017663 1.441440549 1.326834736 1.349034007 1.107777712 1.335663455 1 18.06151759 1.67621433 0.636899997 1.043442789 1.467900284 0.433294333 0.134233702 0.532209918 0.459335657 0.117968645 0.061723126 47.44760871 -1.67621433 0.424457494 ILDSVGIEADDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ILDSVGIEADDDR 13 0 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ;;; 270.93 1.04E-31 1459990000 1419740 1285260 1309570 1176290 1186490 1247890 1516620 1241570 1006930 FALSE TRUE 1330881.008 1380421.988 1340633.619 1206475.593 1093307.861 1608135.585 1289216.911 1396582.748 838866.878 1.586522299 1.645579321 1.598148233 1.438220562 1.303315091 1.917033116 1.536855185 1.664844309 1 19.67808236 -1.821614326 2.697004346 0.804957215 1.590610009 0.577105326 0.157694653 13811674.39 9101901.955 17455027.63 0.03523374 0.015079456 1.821614326 0.785652795 ILDSVGIEADDDRLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ILDSVGIEADDDRLNK 16 1 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ;;;;;; 327.97 1.67E-71 31900990000 16633660 12378660 13954070 12714740 13670990 11044349 17230070 11784060 15684810 FALSE TRUE 15592588.91 13295188.87 14285067.13 13041021.75 12597325.59 14232673.27 14646580.96 13255325.83 13066913.88 1.193287799 1.017469694 1.09322425 0.998018497 0.9640628 1.089214591 1.120890601 1.014419009 1 23.63941511 4.74586791 24.52640041 1.047195298 1.19328789 0.477473459 0.050365275 675.8881383 2268497.673 0.012355955 0.126345447 55701.63076 -4.74586791 0.146092591 ILDSVGIEADDDRLNKVISELNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILDSVGIEADDDRLNKVISELNGK 24 2 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 66.383 0.020714 154290000 105320 123980 118170 119740 178500 90064 125330 113450 148490 FALSE TRUE 98728.2092 133159.6082 120973.0482 122812.7311 164481.33 116064.0147 106537.93 127614.4822 123706.0597 0.79808709 1.076419445 0.977907214 0.992778619 1.329614171 0.938224166 0.861218361 1.031594431 1 16.91655665 4.748498985 24.09539643 1.017429549 0.798086889 0.253394384 0.122151362 1315.353393 3188941.159 0.029489525 0.385443626 56040.11077 -4.748498985 -0.21934266 ILDWHVANTDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILDWHVANTDKK 12 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ; 132.59 0.00011576 4182600000 18329700 13814100 14388100 14177600 17504800 10313700 19760800 14772700 22461000 FALSE TRUE 17182476.8 14836910.34 14729392.53 14541421.22 16130043.62 13291097.76 16797851.49 16617104.11 18712114 0.918254175 0.792904016 0.787158123 0.777112689 0.862010761 0.710293757 0.897699292 0.888039915 1 24.15746922 1.108852782 1.471873852 0.994175446 0.806031762 0.505177111 0.058869712 0.276098059 1.187981495 0.049291557 0.014792758 12.84851045 -1.108852782 -0.188143684 ILEFFGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILEFFGLK 8 0 P07237;H7BZ94;H0Y3Z3;I3L398;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ; 154.31 0.00099363 180346000 462720 599960 454740 472440 559450 345370 557070 510310 441980 FALSE TRUE 433759.1812 644381.6627 465526.6475 484563.6102 515513.0537 445072.7124 473542.5251 574023.3268 368210.6827 1.178019003 1.750035219 1.264294246 1.315995524 1.400049151 1.208744703 1.286064059 1.558953485 1 18.49017196 -4.248527006 0.152254316 4.49E-13 1.499051888 0.251454326 0.179384111 128.6139252 1.427609657 40.75917127 0.850661821 5.64E-05 4.248527006 1.499051888 ILEFVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ILEFVGR 7 0 A0A0A6YYL2;P0DMN0;P0DMM9;P0DMM9-3;P50225;H3BRY5;P50225-2;E9PKW4;P50226 A0A0A6YYL2;P50225;P50226 SULT1A4;SULT1A3;SULT1A1;SULT1A2 Sulfotransferase;Sulfotransferase 1A4;Sulfotransferase 1A3;Sulfotransferase 1A1;Sulfotransferase 1A2 0 ;; 217.6 8.09E-05 399123000 671791 890511 779861 820098 890229 683382 863379 690924 709814 FALSE TRUE 629744.8005 956445.361 798359.6712 841143.1031 820314.0054 880663.2896 733923.3342 777187.3823 591341.4578 1.064942754 1.617416382 1.35008236 1.422432153 1.387208684 1.489263568 1.241115982 1.314278531 1 19.1736319 0.739201595 0.846771022 1.001023822 1.411062408 0.380151768 0.145343761 0.875083808 1.191670839 0.126289178 0.043421371 5.485315281 -0.739201595 0.410038586 ILEGPQQSLSGS(ph)PLQPIPASPPPQIPPGLRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILEGPQQSLSGSPLQPIPASPPPQIPPGLRPR 32 1 O15446;O15446-2 O15446 CD3EAP DNA-directed RNA polymerase I subunit RPA34 1 ILEGPQQS(0.009)LS(0.02)GS(0.97)PLQPIPASPPPQIPPGLRPR 97.634 3.31E-05 229520000 271270 221720 244520 223790 241200 177540 314330 218980 299030 TRUE FALSE 254291.6949 238136.3795 250320.1299 229532.8303 222257.125 228792.9159 267199.1346 246320.135 249119.9612 1.020760013 0.955910471 1.004817634 0.921374703 0.892169073 0.91840459 1.072572159 0.988761133 1 17.9264811 1.743846163 25 1.025209247 0.955232014 0.344904752 0.04402 1.164527811 5529.519046 0.020718663 0.011489653 55.44292869 -1.743846163 -0.069977233 ILEHMPVSNQKPDTDEAEDPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILEHMPVSNQKPDTDEAEDPEK 22 1 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ; 174.01 1.87E-12 229981000 593430 272370 388320 385710 389740 252760 516700 295250 488490 FALSE TRUE 556288.2756 292536.5582 397531.1338 395607.9716 359131.3925 325727.7088 439225.6318 332112.6124 406957.8632 1.36694318 0.718837464 0.976836104 0.972110401 0.882478077 0.800396646 1.079290196 0.816085994 1 18.6345199 -0.619531698 5.895343957 1 0.935537884 3.66E-05 0.180161863 1.14E-09 1.93E-10 0.152998771 0.036062156 0.240142099 0.619531698 -0.064462116 ILELT(ph)PEPDRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ILELTPEPDRPR 12 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 ILELT(1)PEPDRPR;ILELT(1)PEPDRPR;ILELT(1)PEPDRPR;ILELT(1)PEPDRPR;ILELT(1)PEPDRPR;ILELT(1)PEPDRPR 191.06 9.46E-06 2606860000 1595660 1728100 1742650 1591470 1913380 1756860 2119940 1673690 2025040 TRUE FALSE 1495790.489 1856050.322 1783986.481 1632309.815 1763110.853 2264036.962 1802074.678 1882653.881 1687047.742 0.886631986 1.100176525 1.057460578 0.967554014 1.04508652 1.342011198 1.068182383 1.115945823 1 20.68606937 2.448463149 24.9998654 1.1441861 1.026050912 0.242779296 0.103193011 292.217017 254913.6805 0.033091223 0.027686453 280.8427064 -2.448463149 -0.118135188 ILENEKDLEEAEEYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILENEKDLEEAEEYK 15 1 E5RJD8;O75347;E5RIW3;E5RHG6 E5RJD8 TBCA Tubulin-specific chaperone A 0 158.64 1.65E-06 299130000 423720 160330 258860 207150 222000 174980 290460 180600 222190 FALSE TRUE 397200.1216 172201 265000.2814 212465.8197 204565.0155 225493.8854 246908.2195 203148.3075 185105.0536 2.145809171 0.930287946 1.431620997 1.147812097 1.105129285 1.218194107 1.33388157 1.09747575 1 17.49798476 4.74813953 24.90568064 1.187164136 2.145809709 0.811722738 0.148916907 519.3607934 1350336.415 0.033451284 0.436952146 55993.74696 -4.74813953 0.958645573 ILENEKDLEEAEEYKEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ILENEKDLEEAEEYKEAR 18 2 E5RJD8;O75347;E5RIW3;E5RHG6 E5RJD8 TBCA Tubulin-specific chaperone A 0 ;; 164.59 1.70E-11 1822180000 2365330 1286230 1703050 1579160 1944640 1093160 2171380 1366830 2758040 FALSE TRUE 2217288.218 1381463.808 1743447.15 1619683.919 1791915.819 1408737.546 1845801.727 1537481.734 2297705.306 0.96500113 0.601236287 0.758777527 0.704913687 0.779871907 0.613106277 0.803323961 0.669137913 1 21.13176235 -1.530774679 2.913999581 1.011675037 0.727191733 0.380644631 0.104811531 20768980.83 22136747.55 1911180.21 0.02197436 0.029459497 1.530774679 -0.284483304 ILENLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ILENLR 6 0 P12532;P12532-2;P17540;P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;A0A2R8Y4H0;A0A2R8Y4D6;V9GYA2;A0A2R8YEW1;A0A2R8YCK2;V9GY80;P19784;H3BSA1;H3BNI9 P12532;P68400;P19784 CKMT1A;CKMT2;CSNK2A1;CSNK2A3;CSNK2A2 "Creatine kinase U-type, mitochondrial;Creatine kinase S-type, mitochondrial;Casein kinase II subunit alpha;Casein kinase II subunit alpha 3;Casein kinase II subunit alpha" 0 ;;;;; 159.42 0.02122 2174934000 1636330 2109360 1559580 1593520 2379930 1370771 1788260 1937730 2229890 FALSE TRUE 1533915.026 2265539.209 1596573.974 1634412.421 2193019.898 1766490.335 1520127.014 2179659.856 1857706.953 0.825703442 1.219535301 0.859432631 0.879800992 1.180498299 0.950898274 0.818281383 1.173306614 1 20.82509151 3.941727204 24.82218756 0.964925747 1.049342081 0 0.15281821 853.8938293 598843.8798 0.036608493 0.066000624 8744.343386 -3.941727204 0.084416335 ILEPDDFLDDLDDEDYEEDT(ph)PKRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILEPDDFLDDLDDEDYEEDTPKRR 24 2 Q92785;J3KMZ8 Q92785 DPF2 Zinc finger protein ubi-d4 1 ILEPDDFLDDLDDEDYEEDT(1)PKRR;ILEPDDFLDDLDDEDYEEDT(1)PKRR 267.93 5.91E-43 138508000 116520 102074 102960 111050 146520 68089 130644 101908 284301 TRUE FALSE 109227.2212 109631.6652 105402.2598 113899.731 135012.9102 87745.18897 111055.145 114631.4381 236849.3264 0.46116754 0.46287514 0.445018195 0.480895313 0.57003713 0.370468391 0.468885205 0.483984649 1 17.85361004 0.537474174 2.9588594 0.999998463 0.463239583 0.924105398 0.04794573 2.734911538 17.17134779 0.04263877 0.011157656 3.447261061 -0.537474174 -0.53675888 ILEPDDFLDDLDDEDYEEDTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILEPDDFLDDLDDEDYEEDTPK 22 0 Q92785;J3KMZ8 Q92785 DPF2 Zinc finger protein ubi-d4 0 170.19 7.44E-12 19643000 65890 45796 52946 49580 60461 41017 62229 47149 69559 FALSE TRUE 61766.06252 49186.78349 54201.90412 50852.30674 55712.63695 52857.94204 52898.33916 53035.65644 57949.15353 1.065866518 0.848792096 0.935335563 0.87753321 0.961405535 0.912143471 0.912840584 0.915210201 1 15.82249997 -2.120896905 2.188108113 1.146693165 0.920250552 0.115998264 0.057929478 5637413.941 1625674.468 4100203.146 0.012385162 0.007570126 2.120896905 -0.226442613 ILEPDDFLDDLDDEDYEEDTPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILEPDDFLDDLDDEDYEEDTPKR 23 1 Q92785;J3KMZ8 Q92785 DPF2 Zinc finger protein ubi-d4 0 114.04 0.0011362 33419000 23097 19827 20390 23198 23982 16843 30053 16706 28786 FALSE TRUE 21651.4 21295.01171 20873.66043 23793.29995 22098.55046 21705.30068 25546.83165 18791.78087 23981.43064 0.902840215 0.887979205 0.870409307 0.992155152 0.921485911 0.905087816 1.065275547 0.783597157 1 14.54963011 3.252525647 24.99478619 0.952050514 0.884888732 0.113895906 0.073624524 409.244333 732466.5522 0.018750352 0.025261485 1788.651152 -3.252525647 -0.067161782 ILEQEEEEEQAGKPGEPSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILEQEEEEEQAGKPGEPSKK 20 2 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 151.82 4.03E-08 172160000 237830 99859 162770 146610 155770 111570 209440 127150 216710 FALSE TRUE 222944.6448 107252.6643 166630.9813 150372.2608 143536.4525 143778.4478 178036.4163 143024.9574 180539.701 1.234878775 0.594066921 0.922960326 0.83290412 0.795040934 0.796381333 0.986134437 0.792207789 1 17.4619566 0.232199434 0.577546562 1.005860948 0.84195914 0.029943775 0.16714859 7.932891324 3.719544217 0.289080116 0.065286412 1.706866024 -0.232199434 -0.163901808 ILEVHIDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILEVHIDK 8 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ; 90.629 0.013061 622600000 2840400 2337800 2769300 2533100 2944600 2226940 3228000 2535100 3514200 FALSE TRUE 2662624.434 2510893.144 2834989.104 2598103.635 2713342.994 2869821.427 2743991.367 2851612.815 2927657.317 0.90947271 0.857645849 0.968347315 0.887434338 0.92679665 0.980244993 0.937265216 0.974025477 1 21.48131527 3.985997794 0.157988985 1.023588954 0.790554694 0.55402446 0.029699922 12.22334863 0.446787629 0.132811059 0.62069398 9682.729371 -3.985997794 -0.23303426 ILEVHVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ILEVHVDK 8 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ;;;; 107.69 0.0039539 1452990000 6015410 5284140 5583290 5387290 5986910 4669250 7087040 5132330 7269410 FALSE TRUE 5638916.226 5675383.224 5715728.275 5525536.982 5516722.239 6017186.676 6024404.145 5773112.698 6056098.509 0.931113689 0.937135223 0.943797111 0.91239219 0.910936675 0.993574769 0.994766538 0.953272588 1 22.52995724 2.231117254 24.99999888 0.986324682 0.93005972 0.763970218 0.01605895 84.42190309 283545.3353 0.005975809 0.004500785 170.2618133 -2.231117254 -0.056264963 ILFEDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILFEDFR 7 0 A0A0A0MTR2;Q8N543;H3BR79;H3BUA6 A0A0A0MTR2 OGFOD1 Prolyl 3-hydroxylase OGFOD1 0 ; 81.297 0.064172 27822000 190399 265960 187058 195607 257540 142698 227160 217480 267990 FALSE TRUE 178482.2665 285651.9551 191495.1041 200626.6068 237313.8473 183892.5961 193099.4669 244632.8567 223260.7377 0.799434188 1.279454498 0.857719571 0.898620191 1.062944832 0.823667421 0.86490562 1.095727172 1 17.76837004 3.750036679 22.34572306 0.929618664 1.072188424 0.054422677 0.144997847 200.4884906 195499.8553 0.033725531 0.060711689 5623.888201 -3.750036679 0.14256976 ILFIFIDSDHTDNQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ILFIFIDSDHTDNQR 15 0 P07237;H7BZ94;H0Y3Z3;I3L398;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ;;;;;; 327.82 8.80E-69 3256420000 1825013.2 2341807.8 2294383.8 2359700.3 1951208.2 1852323.1 2831170.6 2028715.9 1922430.1 FALSE TRUE 1710788.882 2515197.686 2348807.667 2420254.205 1797968.179 2387058.709 2406662.852 2282005.546 1601564.097 1.068198822 1.570463331 1.46657113 1.511181606 1.12263267 1.490454683 1.502695307 1.424860579 1 20.61105011 -1.146974875 5.678592865 0.999993953 1.422458676 0.338700809 0.169373311 1.19E-05 1.79E-06 0.150556142 0.035485915 0.071289427 1.146974875 0.422464723 ILGADLDVVMSLNNLDEESNKKHPFPCPTSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILGADLDVVMSLNNLDEESNKKHPFPCPTSYR 32 2 E7EMD0;P16435;H0Y4R2 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 42.828 0.079729 105060000 95584 81396 76787 76741 96666 61283 96883 77952 98542 FALSE TRUE 89601.56806 87422.64453 78608.4239 78710.30398 89074.24229 78974.40725 82356.29357 87684.47879 82094.70359 1.09144152 1.064899935 0.95753344 0.958774446 1.085018136 0.961991502 1.003186442 1.068089352 1 16.32500153 4.296482629 3.216800175 1.002556861 1.08584895 0.338783455 0.043151478 0.263968237 5.306635878 0.010226254 0.033053373 19791.67859 -4.296482629 0.083292089 ILGADTSVDLEETGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILGADTSVDLEETGR 15 0 P25705;P25705-2;P25705-3;K7EK77;K7ERX7;K7EJP1;K7EQH4;K7ESA0 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 163.71 3.54E-06 92871000 57085 53043 53125 62762 72261 51409 48100 62286 93146 FALSE TRUE 53512.15175 56970.35891 54385.15009 64372.57918 66585.91255 66249.94374 40887.85154 70062.54421 77599.33085 0.689595531 0.73416044 0.700845606 0.829550699 0.858073283 0.85374375 0.526909847 0.902875623 1 16.24375659 1.00928161 24.92765877 1.000000076 0.737413079 0.463129801 0.096911723 129.6204943 348120.644 0.093791702 0.023447925 10.21601708 -1.00928161 -0.262586997 ILGSAS(ph)PEEEQEKPILDRPTR ddPTM_SK-BR-3_Pertuzumab_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(0.02)AS(0.98)PEEEQEKPILDRPTR;ILGS(0.036)AS(0.964)PEEEQEKPILDRPTR;ILGS(0.03)AS(0.97)PEEEQEKPILDRPTR;ILGS(0.007)AS(0.992)PEEEQEKPILDRPT(0.001)R 206.46 2.19E-22 2240550000 795544 592668 669666 629161 654093 429877 757859 496009 794703 TRUE FALSE 745752.3211 636549.7554 685550.7938 645306.3364 602723.1743 553975.5114 644225.0786 557936.8155 662061.9353 1.126408696 0.961465569 1.03547834 0.974691795 0.910372795 0.83674273 0.973058628 0.842726014 1 19.33660666 2.93897216 2.993305693 0.909940857 1.022926266 0.449449256 0.06389411 0.244569743 4.329532603 0.018547212 0.020708398 868.9047277 -2.93897216 0.112985409 ILGSASPEEEQEKPILDRPT(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILGSASPEEEQEKPILDRPTR 21 2 Q7Z422-5;Q7Z422;Q7Z422-4;Q7Z422-2;Q7Z422-3 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 ILGS(0.001)AS(0.221)PEEEQEKPILDRPT(0.778)R;ILGSAS(0.098)PEEEQEKPILDRPT(0.902)R 165.96 2.25E-11 990200000 1001020 753410 802640 742460 853960 572010 875270 669300 977670 TRUE FALSE 938367.9451 809193.2603 821678.9998 761512.7806 786893.4263 737140.0012 744031.3891 752863.5783 814490.561 1.15209186 0.993496179 1.008825687 0.934955931 0.966117306 0.905031975 0.913492955 0.924336775 1 19.63553845 8 0.533827499 0.932512099 9.160322585 0.752670645 0.035685758 56.96096364 0.545991262 0.016209626 533.923298 100000000 -8 8.227810486 ILHCLGLAEEIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILHCLGLAEEIQK 13 0 P53004 P53004 BLVRA Biliverdin reductase A 0 ; 144.92 4.15E-05 518730000 764870 727220 702650 684370 826220 539330 823360 677450 976950 FALSE TRUE 716998.152 781064.1255 719317.1898 701932.0928 761332.014 695025.8157 699904.8117 762031.1238 813890.7337 0.880951364 0.959667057 0.883800687 0.862440207 0.93542288 0.853954698 0.859949355 0.936281852 1 19.6344756 0.973280478 6.6582853 0.999987945 0.894120706 0.527409228 0.033449758 0.17456186 35.97031503 0.03355243 0.008421108 9.403304023 -0.973280478 -0.105867238 ILHDWPDDKVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILHDWPDDKVHK 12 1 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 0 145.17 4.11E-05 156360000 140560 135130 149800 152120 160130 108500 177080 125790 151520 FALSE TRUE 131762.6005 145135.1658 153353.3267 156023.6567 147554.0357 139822.1886 150528.4979 141495.1584 126230.3331 1.043826767 1.149764579 1.214869065 1.236023489 1.16892693 1.107675035 1.192490697 1.120928345 1 16.94569911 0.909880934 4.815307084 1.000016349 1.165086486 0.455272434 0.054291061 0.469947072 23.26582661 0.05076206 0.012852389 8.126077008 -0.909880934 0.165070137 ILHGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILHGFK 6 0 O14787-2;O14787;K7ESG1;Q92973-2;Q92973;Q92973-3;S4R398 O14787-2;Q92973-2 TNPO2;TNPO1 Transportin-2;Transportin-1 0 ; 88.626 0.051089 1459940000 3851600 4096600 4055400 3953900 4670600 3279100 4965700 4414800 4603300 FALSE TRUE 3610535.231 4399916.527 4151596.003 4055363.768 4303789.916 4225722.938 4221139.384 4965997.498 3834979.492 0.941474456 1.147311618 1.082560158 1.057466872 1.122245875 1.101889318 1.100694122 1.294921527 1 21.87078743 1.440841768 18.93155736 1.164242415 1.087748582 0.081755931 0.089025847 8.583097825 4480.393853 0.042752127 0.019260502 27.59572242 -1.440841768 -0.076493833 ILHLLGK ddPTM_SK-BR-3_Pertuzumab_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 0.016535 124320000 187570 234740 199050 182700 260070 142140 243400 230890 320790 FALSE TRUE 175830.3285 252120.3938 203771.56 187388.3913 239645.1513 183173.5105 206904.4296 259717.1248 267248.0766 0.657929257 0.943394606 0.762480923 0.701177699 0.896714223 0.685406282 0.774203625 0.97182037 1 18.02782004 1.217951965 7.18487712 0.98910515 0.786416012 0.488474334 0.089345145 0.151407086 31.65160806 0.074402393 0.020477295 16.51779095 -1.217951965 -0.202689138 ILHVDNHIGISIAGLTADAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILHVDNHIGISIAGLTADAR 20 0 P25786;P25786-2;F5GX11;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ; 159.06 1.51E-11 201703000 69009 75761 74584 71852 82369 66969 77823 70880 67893 FALSE TRUE 64689.84987 81370.42327 76353.1677 73695.84397 75900.071 86301.86315 66154.16362 79729.52403 56561.21969 1.143713842 1.438625682 1.349920813 1.302939441 1.341910083 1.525813333 1.169602848 1.409614652 1 15.78752561 -1.268542568 3.888805796 0.999516045 1.340823284 0.45745598 0.114603947 0.000435514 8.19E-05 0.099756477 0.023479701 0.053883703 1.268542568 0.341307239 ILHVNGFNGEGGEEDPQAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILHVNGFNGEGGEEDPQAAR 20 0 P63092-4;P63092;A0A590UJ58;B0AZR9;A0A590UJR6;A0A590UJI6;A0A590UJQ9;A0A590UKB4;A0A590UJQ2;A0A590UJ22;S4R3E3;Q5JWD1;S4R3V9;Q5JWE9;A0A590UJY8;A0A590UJB7;H0Y7E8;A0A590UJX3;Q5JWF2 P63092-4;Q5JWF2 GNAS Guanine nucleotide-binding protein G(s) subunit alpha isoforms short;Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas 0 172.3 6.55E-12 128520000 156650 120800 116960 124190 139420 72896 80865 90857 117540 FALSE TRUE 146845.5561 129744.1577 119734.3464 127376.9257 128470.5156 93939.89183 68740.04396 102200.6965 97921.81466 1.499620454 1.324977056 1.222754571 1.30080234 1.311970331 0.959335692 0.701989074 1.043696921 1 16.57934267 2.187622379 4.324684047 0.871660057 1.316458809 0.751478757 0.114883366 0.093070528 3.632478582 0.042502364 0.031375881 154.0360522 -2.187622379 0.444798752 ILIEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ILIEELR 7 0 C9JEV6;Q9UJ70;Q9UJ70-2;H7C3G9;H0YEB7;H0YE82;H7C1L7 C9JEV6 NAGK N-acetyl-D-glucosamine kinase 0 ;;; 125.62 0.0093781 152463000 548560 567700 657620 629690 587260 595770 738180 547740 617530 FALSE TRUE 514226.6088 609733.0987 673219.057 645848.9115 541138.9685 767759.1275 627496.7619 616126.5447 514460.2536 0.999545845 1.185189904 1.308592942 1.255391271 1.051857679 1.49235849 1.219718642 1.197617387 1 18.9727001 4.724301022 2.56547432 1.24034977 0.953005734 0.189010142 0.134976156 0.658846646 5.74266176 0.029771829 0.405191122 53003.06961 -4.724301022 -0.287344037 ILIPS(ph)DIESSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ILIPSDIESSK 11 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 ILIPS(1)DIESSK;ILIPS(1)DIESSK;ILIPS(1)DIESSK;ILIPS(1)DIESSK 166.7 2.11E-05 407128000 2486460 1926830 2278910 2229380 2150330 1837980 2560250 1845310 2346670 TRUE FALSE 2330836.907 2069494.498 2332966.821 2286589.665 1981451.756 2368574.989 2176364.281 2075701.016 1954995.617 1.192246615 1.058567334 1.193336088 1.169613704 1.013532582 1.211550025 1.113232307 1.06174203 1 20.89873394 1.072205235 2.545360158 1.001811943 1.134751477 0.358288727 0.061994841 0.27293978 3.608935429 0.053316875 0.014511586 11.80878554 -1.072205235 0.132939533 ILISLATGHREEGGENLDQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILISLATGHREEGGENLDQAR 21 1 E5RK69;P08133;P08133-2;E7EMC6 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 210.61 1.17E-22 137710000 75811 75466 78227 61933 93807 50921 89503 78301 152680 FALSE TRUE 71066.12484 81053.58116 80082.58138 63522.30563 86439.77662 65621.06607 76082.85606 88077.05221 127196.7216 0.55871035 0.637230112 0.629596269 0.499402066 0.679575507 0.515902181 0.598151077 0.692447502 1 16.95670196 0.818092052 2.565147654 0.999799287 0.594020144 0.848541683 0.054619065 0.255259521 2.867130364 0.048127396 0.012846308 6.577972474 -0.818092052 -0.405779144 ILIVTQT(ph)PPYVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILIVTQTPPYVK 12 0 A0A3B3ISF0;Q659C4;Q659C4-9;Q659C4-2;H0Y9K3;D6R9W6;D6RJB0;Q659C4-4 A0A3B3ISF0 LARP1B La-related protein 1B 1 ILIVT(0.087)QT(0.912)PPYVK 145.17 0.00071168 22455000 165320 143350 152350 154990 166710 127230 206790 139090 146560 TRUE FALSE 154972.9163 153963.7832 155963.8139 158967.3058 153617.2691 163959.2356 175783.7592 156455.6927 122098.1892 1.269248277 1.260983346 1.277363858 1.301962845 1.258145351 1.342847398 1.439691779 1.281392408 1 16.89768228 0.95823371 23.97858847 1 1.309434447 0.762419936 0.053500524 3422.060131 1964652.632 0.060282681 0.01507067 9.083091926 -0.95823371 0.309434447 ILKEQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ILKEQER 7 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;; 84.743 0.019445 1361890000 1256110 2227760 1213840 1194170 2769230 917730 1502420 1959510 2893860 FALSE TRUE 1177492.317 2392705.668 1242632.858 1224814.424 2551745.846 1182663.753 1277146.069 2204159.137 2410856.071 0.488412532 0.992471387 0.515432204 0.508041288 1.058439729 0.490557594 0.529747953 0.914264092 1 21.20111409 1.085273203 5.931112406 0.997354508 0.668634824 0.269798864 0.208173345 0.25662158 12.83352609 0.190076458 0.047849728 12.16951311 -1.085273203 -0.328719684 ILKLPSFELLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILKLPSFELLHK 12 1 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 ; 65.295 0.036734 130502000 101920 187244 101590 94573 176345 74142 148433 144691 270530 FALSE TRUE 95541.00913 201107.7406 103999.7628 96999.90329 162495.575 95545.59181 126176.8496 162755.9899 225376.7953 0.423916797 0.892317864 0.461448405 0.430389931 0.720995144 0.42393713 0.559848451 0.722150608 1 17.78197946 0.922351167 3.27037444 0.999451904 0.576680444 0.46797432 0.149967082 0.308694929 7.841256239 0.139156344 0.03619515 8.362789527 -0.922351167 -0.42277146 ILKS(ph)PEIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ILKSPEIQR 9 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 1 ILKS(1)PEIQR;ILKS(1)PEIQR;ILKS(1)PEIQR;ILKS(1)PEIQR;ILKS(1)PEIQR;ILKS(1)PEIQR;ILKS(1)PEIQR 149.69 5.27E-05 5015170000 7976010 5975870 6885380 6487120 6867700 5574640 8642820 5818710 8067270 TRUE FALSE 7476805.772 6418329.633 7048704.465 6653590.482 6328338.545 7183948.071 7346909.377 6545188.752 6720790.52 1.112489037 0.954996233 1.048790978 0.99000117 0.941606278 1.068914148 1.09316149 0.973871858 1 22.68019951 ILLDHEKEWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILLDHEKEWK 10 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 64.439 0.043308 407720000 99925 113610 130520 122610 136090 76249 232320 113450 319890 FALSE TRUE 93670.87262 122021.8026 133615.996 125756.3802 125402.0404 98260.8485 197485.7728 127614.4822 266498.2924 0.351487703 0.457870861 0.501376556 0.471884375 0.470554761 0.368710987 0.741039543 0.47885666 1 18.02376676 -5 0.17409275 3.085978456 0.372081757 0.764479588 0.09408938 61.0766262 0.581717954 43.74112636 0.300017968 1.00E-05 5 -2.713896699 ILLENY(ph)VRSIENER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILLENYVRSIENER 14 1 H0Y9S3;A0A494C037;E7EUS2;Q8TBZ0-2;Q8TBZ0 H0Y9S3 CCDC110 Coiled-coil domain-containing protein 110 1 ILLENY(0.999)VRS(0.001)IENER;ILLENY(0.979)VRS(0.021)IENER 72.891 0.044739 326490000 935890 266670 366220 306940 362310 280050 353900 272270 443130 TRUE FALSE 877314.3155 286414.5243 374906.9113 314816.6 333855.6341 360895.8888 300835.9804 306263.5088 369168.7403 2.376458838 0.77583634 1.015543491 0.852771553 0.904344268 0.977590596 0.814901013 0.829603039 1 18.49392087 4.741317046 24.99979005 0.89325964 2.376459369 0.970495312 0.081104366 36.82618376 333981.8901 0.01791618 0.124497218 55120.99474 -4.741317046 1.483199729 ILLSQTTGVAIPLHASSLDDVSLAST(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILLSQTTGVAIPLHASSLDDVSLASTPK 28 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 ILLSQTTGVAIPLHASSLDDVSLAS(0.264)T(0.736)PK;ILLSQTTGVAIPLHASSLDDVSLAS(0.195)T(0.805)PK 145.01 3.62E-07 216228000 76797 115386 122303 120548 146342 115123 188164 138584 147811 TRUE FALSE 71990.41286 123929.2995 125204.0849 123641.4658 134848.8896 148357.1412 159950.555 155886.5175 123140.3892 0.584620638 1.006406593 1.016758886 1.004069149 1.095082536 1.204780513 1.298928451 1.265925165 1 16.90994451 5.30650861 0.486793381 1.202396605 1.23E-12 0.683189174 0.112367365 4.596093095 0.555082512 0.066560842 3.550936464 202538.976 -5.30650861 -1.202396605 ILLVDS(ph)PGMGNADDEQQEEGTSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILLVDSPGMGNADDEQQEEGTSSK 24 0 Q9UKN8 Q9UKN8 GTF3C4 General transcription factor 3C polypeptide 4 1 ILLVDS(1)PGMGNADDEQQEEGTSSK 247.51 3.59E-38 38947000 52758 42235 49088 47758 52147 43593 68845 49118 72841 TRUE FALSE 49455.97096 45362.12335 50252.39054 48983.55113 48051.58497 56177.59143 58522.33138 55250.49042 60683.36653 0.81498397 0.747521536 0.828108152 0.807198973 0.791841121 0.925749421 0.964388344 0.910471742 1 15.8890135 2.185889259 4.217759761 0.95208661 0.795004424 0.863170541 0.030256683 0.069420279 2.553910452 0.011072929 0.008153966 153.4225719 -2.185889259 -0.157082186 ILLWDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILLWDTR 7 0 Q9BQA1;Q9BQA1-2;H0Y711 Q9BQA1 WDR77 Methylosome protein 50 0 ; 126.2 0.009247 455880000 772460 1376670 826560 787210 1440870 634400 853590 1207900 1341650 FALSE TRUE 724113.1075 1478600.079 846166.3935 807411.1413 1327709.882 817540.9814 725602.1038 1358708.974 1117719.948 0.647848425 1.322871693 0.757046875 0.722373384 1.187873479 0.731436334 0.649180598 1.215607699 1 20.09212733 3.751736053 23.49963125 0.86234262 1.035491155 0.000633909 0.252943487 502.5009576 479729.2312 0.060115025 0.10828771 5645.937328 -3.751736053 0.173148535 ILMEHIHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILMEHIHK 8 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ; 117.04 0.001247 4569900000 3572000 4848100 3530600 3286000 5312100 2487800 3944500 4273000 5379600 FALSE TRUE 3348434.896 5207058.368 3614347.499 3370324.323 4894909.094 3205987.474 3353058.844 4806493.456 4481710.006 0.747133324 1.16184634 0.806466169 0.752017493 1.092196748 0.715349157 0.748165062 1.072468645 1 22.09561787 3.744022654 23.35588327 0.859524639 0.984125502 0.007357409 0.168168334 443.8821742 613388.5169 0.039844692 0.071530779 5546.546444 -3.744022654 0.124600863 ILNDVQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ILNDVQDR 8 0 O00148;Q13838-2;Q13838;A0A0G2JJZ9;H0Y400 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ;;;; 183.47 0.00051912 1411410000 2167000 2374550 2410000 2294280 2137370 2233810 2751940 2196020 1865460 FALSE TRUE 2031371.338 2550364.153 2467166.338 2353155.109 1969509.582 2878674.684 2339312.145 2470197.931 1554102.675 1.307102401 1.641052547 1.587518237 1.514156785 1.267296952 1.852306628 1.505249417 1.58946894 1 20.56765039 -1.156845963 4.504781428 0.999914014 1.55003348 0.505416832 0.164945106 0.000129951 2.43E-05 0.143129555 0.03373062 0.069687364 1.156845963 0.550119466 ILNEIDAGVCEEMTYAEIEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILNEIDAGVCEEMTYAEIEKR 21 1 O60825;O60825-2 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 0 157.73 4.63E-09 24678000 30433 34702 39724 34706 34229 33798 42692 28946 51399 FALSE TRUE 28528.25285 37271.37219 40666.27204 35596.61472 31540.79241 43554.93394 36290.73093 32559.97182 42820.17485 0.666233918 0.870416161 0.949698879 0.831304749 0.736587193 1.01715918 0.847514777 0.760388577 1 15.38600307 -4.999999996 0.016523074 2.012193126 2.98E-10 0.185722718 0.102322819 10574.41526 13.24623766 1032.57012 627.2933181 1.00E-05 4.999999996 -2.012193126 ILNFLMHPKPSGKPLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILNFLMHPKPSGKPLPK 17 2 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;H0Y8X0 H0Y993 DEK Protein DEK 0 130.12 1.88E-05 52553000 129670 163110 124270 123190 216220 91876 196960 145580 345940 FALSE TRUE 121554.1862 175186.8341 127217.7431 126351.264 199238.9534 118399.1097 167427.6765 163755.9835 288200.3791 0.421769696 0.60786469 0.441421151 0.438414635 0.691320927 0.410822186 0.580941902 0.568201832 1 18.13671271 -0.534338948 0.556656329 1.075492371 0.506031303 0.743611126 0.089666022 4.949612608 1.232651399 0.800430736 0.034783678 0.29218711 0.534338948 -0.569461068 ILNHSVDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILNHSVDKK 9 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 99.815 0.0032988 638430000 461940 363180 454500 446710 431270 347820 576860 412810 538420 FALSE TRUE 433028 390070.2251 465280.9546 458173.3349 397399.7939 448229.9876 490365.1983 464350.2372 448554.2237 0.965386072 0.869616658 1.037290321 1.021444701 0.885957088 0.999277153 1.093212754 1.035215394 1 18.77492287 1.996367854 24.93712157 1.051436013 0.956936847 0.333669121 0.055783653 150.8876312 1035947.628 0.021180373 0.01529532 99.167155 -1.996367854 -0.094499167 ILNHVLQHAEPGNAQSVLEAIDTYCEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILNHVLQHAEPGNAQSVLEAIDTYCEQK 28 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ; 351.57 4.04E-111 3431700000 1138080 954270 950400 921860 1065510 890920 1296360 980260 1379180 FALSE TRUE 1066849.604 1024925.144 972943.9368 945516.4883 981829.1427 1148114.141 1101982.853 1102647.619 1148985.948 0.928514057 0.89202583 0.846784887 0.822913883 0.854517972 0.999241238 0.959091671 0.959670238 1 20.13192972 2.242328687 24.99994425 0.975097095 0.866982531 0.758503204 0.030940652 48.90426295 324465.944 0.011339884 0.009151338 174.7143944 -2.242328687 -0.108114564 ILPEAHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ILPEAHQR 8 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ;;; 178.65 0.0002485 454800000 968700 1408360 1048780 1093380 1540880 820840 1128170 1263900 1593560 FALSE TRUE 908070.7962 1512636.44 1073657.557 1121437.982 1419865.5 1057803.183 959011.3819 1421700.697 1327584.541 0.684002237 1.139389917 0.808730084 0.844720579 1.06951042 0.796787813 0.722373116 1.070892778 1 20.3403723 ILPKPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILPKPTR 7 1 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ; 102.41 0.0078502 3701000000 6195500 6282000 6262400 5368800 5983700 4800000 6601800 5504500 5888400 FALSE TRUE 5807734.714 6747125.816 6410947.085 5506572.497 5513764.339 6185682.079 5611921.378 6191748.942 4905587.999 1.183901851 1.37539594 1.306866187 1.122510186 1.123976237 1.260946105 1.143985467 1.26218283 1 22.22599464 -5 0.078578519 0.216217963 1.478567978 0.404585158 0.083306331 228.2737198 1.273996595 31.18137285 3.040444831 1.00E-05 5 1.262350015 ILPPGLLAYLESSDLVPEKDADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILPPGLLAYLESSDLVPEKDADR 23 1 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 124.45 5.27E-05 29174000 60948 71986 73336 70022 98040 72894 79532 63678 73737 FALSE TRUE 57133.37348 77315.91834 75075.56455 71818.88307 90340.33387 93937.31446 67606.91494 71628.33847 61429.81834 0.930059294 1.258605681 1.222135546 1.169120877 1.470626746 1.529181056 1.100555345 1.166019051 1 15.9066515 1.163448962 2.01101468 1.02267661 1.259072892 0.173609862 0.168755442 0.517022995 3.819967295 0.153345555 0.043885682 14.56964473 -1.163448962 0.236396282 ILQALHECLAALPRPQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILQALHECLAALPRPQLR 18 1 A0A0B4J2A0;Q9UHJ6 A0A0B4J2A0 TRPV1;SHPK Sedoheptulokinase 0 ; 159.69 2.55E-11 64384000 97711 117111 107690 108145 126700 84943 121559 109109 105715 FALSE TRUE 91595.44293 125782.0203 110244.4577 110920.1838 116749.4931 109464.6652 103332.3564 122731.4988 88070.48355 1.040024299 1.428197226 1.251775319 1.25944788 1.325637017 1.242921133 1.173291576 1.393559952 1 16.42637097 -1.816643401 2.74950597 0.915076796 1.271310455 0.365993254 0.109005127 83066420.57 54153325.32 46624513.33 0.023967662 0.015253047 1.816643401 0.356233659 ILQEAWTEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILQEAWTEGR 10 0 A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2 A0A087WTA5 EIF2B4 Translation initiation factor eIF-2B subunit delta 0 77.662 0.075205 59157000 53874 66366 71865 67466 71640 58946 67421 63557 69537 FALSE TRUE 50502.12251 71279.80769 73569.67174 69197.29178 66013.68338 75962.75329 57311.84696 71492.23136 57930.82547 0.871765974 1.230429691 1.269957249 1.19448137 1.139526027 1.311266544 0.989315213 1.234096541 1 15.8220436 -1.349090093 5.542315939 0.999958874 1.166607553 0.112649172 0.133379118 6.29E-05 7.38E-06 0.119757057 0.02822005 0.044762044 1.349090093 0.166648679 ILQEHEQIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILQEHEQIK 9 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 156.48 7.08E-05 394760000 373670 437570 346890 330320 487210 268780 404980 415790 530080 FALSE TRUE 350282.6617 469968.1381 355118.3946 338796.5704 448946.4919 346372.4227 344257.0087 467702.2968 441606.2236 0.79320137 1.064224445 0.804151698 0.767191567 1.01662175 0.784346787 0.779556515 1.059093536 1 18.75240098 -2.057004443 6.12825838 1.265783681 0.881097673 0.084619841 0.120128219 0.089384631 0.000831447 0.023833171 0.025820873 0.008769918 2.057004443 -0.384686009 ILQEYVEHQVDDAMMANAAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILQEYVEHQVDDAMMANAAQK 21 0 P08243-2;P08243;P08243-3 P08243-2 ASNS Asparagine synthetase [glutamine-hydrolyzing] 0 158 3.46E-10 39152000 24966 22295 22730 22419 21188 17737 24447 16495 17154 FALSE TRUE 23403.42263 23945.745 23269.16633 22994.3095 19523.97995 22857.38396 20781.3993 18554.43706 14290.88658 1.637646656 1.675595483 1.628252117 1.609019102 1.366183955 1.599437784 1.454171453 1.298340516 1 13.8028078 0.450813681 0.296177338 0.864863009 1.705542811 0.875421777 0.073730296 1.106728066 0.203362449 0.288800097 0.097899306 2.823668319 -0.450813681 0.840679802 ILQINKDDVTALHCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILQINKDDVTALHCK 15 1 O76094-2;O76094;R4GNC1;D6RDY6 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 ; 183.23 3.09E-07 967640000 2798900 2223250 2626800 2599600 2904400 2066500 3535800 2482200 3386600 FALSE TRUE 2623721.845 2387861.743 2689108.936 2666310.137 2676300.14 2663065.003 3005639.615 2792108.134 2821354.582 0.929951117 0.846352939 0.953126897 0.945046097 0.948586951 0.943895893 1.065317927 0.989633899 1 21.42795656 2.712573517 0.667012284 1.023117325 0.886524516 0.563803057 0.036846629 0.474162835 0.449487513 0.027379324 0.027756498 515.9094907 -2.712573517 -0.136592809 ILQLCMGNHELYMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILQLCMGNHELYMR 14 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 203.85 1.45E-08 1055870000 848440 1449310 683740 630370 1623400 573240 800340 1299240 966890 FALSE TRUE 795337.6549 1556618.42 699958.6357 646546.3614 1495904.712 738725.0822 680336.447 1461452.974 805509.8127 0.987371777 1.932463635 0.868963512 0.802654854 1.857090614 0.917090109 0.84460355 1.81432051 1 19.61954264 3.96088953 23.55904882 1.133240486 1.511585368 0.069717719 0.443055287 396.0370707 574817.8009 0.105167391 0.190487511 9138.80752 -3.96088953 0.378344882 ILRLS(ph)TFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILRLSTFEK 9 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 ILRLS(0.992)T(0.008)FEK;ILRLS(0.968)T(0.032)FEK 130.69 0.00021454 169032000 291641 284730 241544 210323 351343 126246 280772 196132 529380 TRUE FALSE 273387.7104 305811.7055 247273.5377 215720.2443 323749.938 162691.1708 238672.8452 220619.5119 441023.0581 0.619894369 0.693414323 0.560681654 0.489135977 0.734088461 0.368894931 0.54117997 0.500244846 1 18.75049456 -1.438395412 5.83568198 1.000228599 0.567066897 0.635341414 0.103908113 0.000298658 2.87E-05 0.097227943 0.022904969 0.0364422 1.438395412 -0.433161702 ILRPWQSSETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILRPWQSSETR 11 1 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 0 ; 181.66 5.59E-06 1252130000 814380 2283800 657020 668110 2395800 423570 757760 1989450 2335700 FALSE TRUE 763409.4095 2452894.928 672604.8247 685254.8337 2207643.532 545847.7829 644140.9227 2237837.212 1945856.581 0.39232563 1.26057334 0.34566002 0.352161018 1.134535584 0.280517993 0.331032065 1.150052493 1 20.89197395 1.222230922 24.97944027 1.075026663 0.609785573 0.254674297 0.346360069 413.3920205 632345.9299 0.324771301 0.082176276 16.68133951 -1.222230922 -0.46524109 ILS(ph)DVTHSAVFGVPASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ILSDVTHSAVFGVPASK 17 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 ILS(0.999)DVT(0.001)HSAVFGVPASK;ILS(0.999)DVT(0.001)HSAVFGVPASK;ILS(0.983)DVT(0.017)HSAVFGVPASK;ILS(0.998)DVT(0.002)HSAVFGVPASK 247.5 9.80E-21 736843000 2124683 1742382 1791746 1803516 1833959 1084453 2207620 1510196 2348418 TRUE FALSE 1991702.884 1871389.776 1834247.061 1849797.274 1689927.258 1397516.976 1876607.876 1698747.295 1956451.864 1.018017831 0.956522269 0.937537536 0.945485707 0.863771447 0.714311965 0.959189393 0.868279627 1 20.89980818 2.81678603 4.411641863 0.871529699 0.960273823 0.221415679 0.076668346 0.324097136 11.75933251 0.022608307 0.023881188 655.8220733 -2.81678603 0.088744124 ILS(ph)PDSFIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILSPDSFIK 9 0 Q8IZT6;Q8IZT6-2 Q8IZT6 ASPM Abnormal spindle-like microcephaly-associated protein 1 ILS(0.99)PDS(0.01)FIK;ILS(0.997)PDS(0.003)FIK 98.353 0.0063684 19575900 84465 62490 72004 74977 67620 55202 85775 60260 60067 TRUE FALSE 79178.48642 67116.82462 73711.96888 76901.03676 62309.39797 71137.92127 72913.83505 67783.59365 50041.42965 1.58225868 1.341225163 1.473018844 1.536747397 1.245156232 1.421580514 1.457069383 1.354549503 1 15.61083539 -3.104976382 0.317984623 8.84E-16 1.447867733 0.684541411 0.092956766 46.65882998 1.264232405 31.18578908 0.07922628 0.000785278 3.104976382 1.447867733 ILS(ph)PSMASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILSPSMASK 9 0 Q9Y6A5;A0A494BZT8;E7EMT0;C9JA91;C9JWI7;Q8IX09 Q9Y6A5 TACC3;ERIC-1s Transforming acidic coiled-coil-containing protein 3 1 ILS(0.935)PS(0.065)MASK 105.13 0.0033014 119280000 369840 411050 417700 422970 552700 279280 405930 356480 772610 TRUE FALSE 346692.3746 441484.5697 427608.0413 433824.1263 509293.1715 359903.6023 345064.565 400987.3127 643656.3997 0.538629577 0.685901002 0.664342095 0.673999554 0.79125007 0.559154857 0.536100573 0.622983494 1 19.29593122 -1.615971905 2.943207338 1.026930491 0.63644573 0.68630397 0.077739569 16505708.58 17939862.68 3438414.184 0.021375306 0.024211857 1.615971905 -0.390484761 ILSDDVPIRDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILSDDVPIRDYR 12 1 P54725-2;P54725;A0A494C0B4;K7ENJ0;K7ELW1;P54725-3 P54725-2;P54725-3 RAD23A UV excision repair protein RAD23 homolog A 0 63.944 0.06119 207720000 418100 555220 505490 516950 599030 410780 594910 481030 847050 FALSE TRUE 391931.8673 596329.0665 517480.4615 530215.8122 551984.6002 529365.5175 505708.7684 541087.6544 705671.8828 0.555402414 0.845051476 0.73331597 0.751363098 0.782211412 0.750158155 0.716634431 0.766769468 1 19.428638 -3.204251364 1.026380509 5.358916672 0.746863627 0.552244196 0.073837144 30363.76095 544.1348079 306231.737 0.019903264 0.000624811 3.204251364 -4.612053045 ILSHGGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILSHGGFR 8 0 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 155.88 0.00040195 3168400000 2461300 3382600 2666600 2527400 3316100 2276300 2850500 2941100 2724100 FALSE TRUE 2307251.627 3633051.224 2729853.011 2592257.363 3055666.883 2933430.857 2423093.988 3308302.809 2269430.112 1.016665644 1.600864995 1.202880405 1.14225036 1.346446787 1.292584796 1.067710336 1.457768094 1 21.11389863 -4.912992354 0.165417387 9.78E-10 1.345247555 0.128597019 0.181362425 216.1530447 2.071441971 71.29524187 0.660326806 1.22E-05 4.912992354 1.345247554 ILSISADIETIGEILKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILSISADIETIGEILKK 17 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 221.49 5.88E-15 288760000 131430 123800 126130 113320 140260 117080 151830 115570 179230 FALSE TRUE 123204.0309 132966.2808 129121.8632 116227.9831 129244.5454 150879.0954 129064.501 129999.1689 149315.3551 0.825126329 0.89050641 0.864759442 0.778406099 0.865581073 1.010472736 0.864375274 0.870634964 1 17.18800301 2.455005556 24.98740453 0.92366735 0.849308958 0.399542352 0.055012923 288.225137 325649.1531 0.018356364 0.015358969 285.1054741 -2.455005556 -0.074358392 ILSPSIMVS(ph)AS(ph)IDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILSPSIMVSASIDQR 15 0 Q6PKC6;E9PBK6;E9PDU5;A0A087X295;Q9NNW5 Q6PKC6 WDR6 WD repeat-containing protein 6 2 ILS(0.001)PS(0.215)IMVS(0.892)AS(0.892)IDQR 67.334 0.081739 383990000 98196 121830 132150 125370 153080 105180 122130 122270 120330 TRUE FALSE 92050.08764 130850.42 135284.6604 128587.2065 141057.7143 135543.7585 103817.7403 137535.6786 100246.1456 0.918240667 1.305291282 1.349524808 1.282714718 1.407113594 1.352109427 1.035628249 1.371979718 1 16.61318724 -1.291115735 4.208664291 0.999730502 1.25942552 0.204012031 0.156463265 0.000375552 6.33E-05 0.143798178 0.033858619 0.05115455 1.291115735 0.259695019 ILSQS(ph)TDS(ph)LNMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ILSQSTDSLNMR 12 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 2 ILS(0.002)QS(0.837)T(0.213)DS(0.947)LNMR;ILS(0.006)QS(0.617)T(0.382)DS(0.994)LNMR;ILSQS(0.846)T(0.156)DS(0.999)LNMR;ILS(0.006)QS(0.873)T(0.177)DS(0.945)LNMR 179.14 3.08E-05 503617000 1057440 1121920 1129590 1007760 1386570 983480 1204080 1139790 1802570 TRUE FALSE 991256.718 1204988.124 1156384.408 1033620.828 1277674.385 1267394.711 1023539.382 1282095.29 1501709.422 0.660085569 0.802410977 0.770045384 0.688296159 0.850813324 0.843968009 0.681582846 0.853757239 1 20.51817425 -4.999999986 0.257609362 2.479749943 0.748970613 0.552953128 0.06837385 149.1197511 1.469147975 116.5408251 0.087804312 1.00E-05 4.999999986 -1.730779331 ILSQS(ph)TDSLNMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 ILSQSTDSLNMR 12 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 ILSQS(0.96)T(0.029)DS(0.012)LNMR;ILSQS(0.948)T(0.052)DSLNMR;ILSQS(0.817)T(0.183)DSLNMR;ILSQS(0.903)T(0.097)DSLNMR;ILSQS(0.536)T(0.463)DS(0.001)LNMR;ILSQS(0.591)T(0.409)DSLNMR;ILSQS(0.922)T(0.078)DSLNMR;ILSQS(0.876)T(0.124)DSLNMR 358.07 7.43E-72 7530380000 7642810 8751250 8471290 7493610 9790520 7013570 7774950 7644990 11294290 TRUE FALSE 7164460.165 9399201.656 8672232.999 7685908.719 9021612.052 9038273.803 6609168.427 8599483.83 9409200.035 0.76143138 0.998937383 0.921675909 0.81685039 0.958807552 0.960578346 0.702415551 0.913944203 1 23.16564064 ILSQST(ph)DSLNMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILSQSTDSLNMR 12 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 ILSQS(0.366)T(0.634)DSLNMR;ILSQS(0.458)T(0.541)DSLNMR 258.79 3.35E-20 2621900000 1936690 2108010 2242990 1891710 2336410 1844950 1939770 1825240 2674400 TRUE FALSE 1815476.03 2264089.254 2296194.782 1940254.481 2152917.783 2377557.115 1648919.496 2053125.232 2228025.363 0.814836339 1.016186481 1.030596339 0.870840392 0.966289621 1.067114026 0.740081116 0.921499937 1 21.08733423 1.747625461 25 0.862844866 0.972118598 0.087953978 0.098170836 3.229103938 8925.973505 0.042019407 0.023301833 55.92750707 -1.747625461 0.109273731 ILTDILEVRQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILTDILEVRQK 11 1 B0QY16;Q6ICG6-3;Q6ICG6;Q6ICG6-2 B0QY16 KIAA0930 Uncharacterized protein KIAA0930 0 66.595 0.064601 0 166110 192900 207750 206890 247610 100160 125110 194490 117040 FALSE TRUE 155713.4716 207182.5167 212677.9281 212199.1477 228163.7094 129074.566 106350.917 218772.5046 97505.26789 1.596974963 2.124834085 2.181194234 2.176283931 2.340014179 1.32377018 1.090719704 2.243699334 1 16.57319254 2.230050234 24.99011848 1.383089272 2.10692151 0.431769644 0.380267783 156.3013486 458963.7808 0.130561788 0.097965054 169.8440095 -2.230050234 0.723832238 ILTDYGFEGHPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILTDYGFEGHPFR 13 0 O75489 O75489 NDUFS3 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial" 0 ; 211.26 2.33E-08 524260000 913030 1184700 883260 802630 1560400 821900 818060 1226880 1490600 FALSE TRUE 855885.0821 1272416.421 904211.3443 823226.8446 1437852.478 1059169.188 695399.4975 1380058.669 1241809.23 0.689224288 1.024647256 0.728140299 0.662925371 1.157869054 0.852924235 0.559988991 1.111329047 1 20.24401213 1.193158466 24.99998305 1.055665418 0.819551983 0.248050126 0.176723244 220.5171053 121419.2762 0.165091908 0.041273607 15.60121658 -1.193158466 -0.236113435 ILTEAEIDAHLVALAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ILTEAEIDAHLVALAER 17 0 G3V5Z7;P60900;P60900-2;P60900-3;H0YJC4 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ;; 182.07 7.68E-10 95747000 128563 148886 137764 124476 128928 154442 174829 134816 111192 FALSE TRUE 120516.4713 159909.6744 141031.8271 127670.2649 118802.515 199026.8982 148615.0145 151648.0744 92633.33687 1.301005398 1.726264861 1.522473786 1.378232386 1.282502811 2.148545059 1.604336187 1.637078826 1 16.49924386 4.760466489 22.28448444 1.582724869 1.301004091 0.039024169 0.301722202 3254.187802 3310195.005 0.065863881 2.591268716 57605.83669 -4.760466489 -0.281720778 ILTEAEIDAHLVALAERD ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;;;;;; 288.21 4.40E-40 1713363400 1211344.2 1508645 1374888 1304273 1649435 1141448.6 1502134 1402739.7 1599797 FALSE TRUE 1135528.329 1620346.646 1407500.993 1337742.853 1519895.029 1470966.281 1276902.952 1577874.839 1332780.546 0.851999478 1.215764029 1.056063579 1.003723274 1.140394068 1.103682287 0.958074423 1.183896962 1 20.34600782 -1.92803246 2.845088866 0.955774615 1.070863999 0.030536121 0.10802985 8398258.359 6177582.912 2387896.226 0.022925021 0.011802324 1.92803246 0.115089384 ILTFDQLALDSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILTFDQLALDSPK 13 0 J3QQ67;Q07020;G3V203;H0YHA7;Q07020-2;F8VUA6 J3QQ67 RPL18 60S ribosomal protein L18 0 190.46 1.02E-05 21985000 191930 169840 177880 203380 224630 167740 247090 179350 208510 FALSE TRUE 179917.4439 182415.1303 182099.3976 208599.0751 206988.4659 216163.815 210041.1484 201742.2423 173708.334 1.035744456 1.050123078 1.048305475 1.200858188 1.191586271 1.244406702 1.209159881 1.161384936 1 17.40630745 3.242683431 24.5551197 1.186512916 1.046392763 0.416140581 0.066370633 60.60406462 360948.3981 0.01645104 0.021488755 1748.571642 -3.242683431 -0.140120153 ILTLTYVDKLIDDVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILTLTYVDKLIDDVHR 16 1 P08240-2;P08240 P08240-2 SRPR Signal recognition particle receptor subunit alpha 0 78.069 0.013318 16942000 30111 30297 30189 31679 43410 24533 34188 28395 42260 FALSE TRUE 28226.40626 32540.2214 30905.09734 32491.93677 40000.75371 31615.27884 29061.82679 31940.17826 35206.53299 0.801737742 0.924266568 0.877822799 0.9228951 1.136174179 0.897994666 0.825466876 0.90722305 1 15.10355554 5.642519186 1.269389107 0.927429018 3.40E-10 0.189937655 0.084049423 24.45611198 5.933647571 0.023866516 50.90284543 439055.262 -5.642519186 -0.927429017 ILTTASSHEFEHTKK ddPTM_SK-BR-3_Pertuzumab_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 0 178.68 2.85E-07 328000000 695950 640980 665150 632870 744210 539650 844300 649060 940920 FALSE TRUE 652391.7318 688438.8261 680927.6721 649110.5156 685762.7486 695438.1945 717705.0531 730096.5698 783874.3734 0.832265672 0.878251477 0.868669388 0.828079776 0.874837566 0.887180673 0.915586831 0.93139487 1 19.58026294 1.192980283 0.773938455 0.998743646 0.857632883 0.889286498 0.0166228 0.191470417 0.262408336 0.01584943 0.006179469 15.59481702 -1.192980283 -0.141110763 ILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVNR 36 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 333.24 2.96E-129 145050000 43169 67568 43279 40219 85605 38978 49254 68789 65781 FALSE TRUE 40467.12935 72570.80502 44305.59832 41251.08763 78881.92861 50230.31585 41868.81995 77377.45807 54801.72614 0.738428006 1.324243051 0.808470854 0.752733363 1.439405912 0.916582732 0.764005496 1.411952935 1 15.74193372 3.932141982 24.98879892 0.986832469 1.072327928 0 0.279260143 1218.733987 677082.5043 0.067098769 0.120964643 8553.463023 -3.932141982 0.085495459 ILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVNRVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVNRVPR 39 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 93.437 0.00019408 391500000 53936 82084 72540 75670 109668 65253 84582 64071 138914 FALSE TRUE 50560.24204 88161.58477 74260.68306 77611.82031 101055.1177 84090.48181 71899.71432 72070.40539 115728.356 0.43688724 0.761797608 0.641680964 0.670637889 0.873209654 0.726619514 0.621280011 0.62275494 1 16.82038287 -2.397796904 2.273170587 3.571109454 0.679500443 0.459156156 0.11229722 5035186.914 469470.5398 66851357.4 0.025068258 0.004001318 2.397796904 -2.891609011 ILVLDDTNHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ILVLDDTNHER 11 0 K7EN66;C9K0L8;K7ERZ0;K7ERC4;P09543-2;P09543 K7EN66 CNP "2,3-cyclic-nucleotide 3-phosphodiesterase" 0 ;;;;; 220.29 9.25E-12 909792000 847558 948920 919913 854760 1110127 917834 928117 891499 1301030 FALSE TRUE 794510.8577 1019179.024 941733.7708 876694.5887 1022942.103 1182797.776 788954.4721 1002804.613 1083879.688 0.733024953 0.940306415 0.868854524 0.808848619 0.943778276 1.091262978 0.727898567 0.925199193 1 20.04777319 4.747421179 23.798415 0.900437938 0.733024782 0.235313221 0.099757347 931.5815053 2502006.532 0.022412276 0.261520941 55901.20622 -4.747421179 -0.167413156 ILVTLLHTLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ILVTLLHTLER 11 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ; 224.58 6.10E-12 463640000 155364 240695 163570 144709 258439 139773 201178 223984 270379 FALSE TRUE 145640.0446 258516.3082 167449.9576 148422.4779 238142.2434 180123.1961 171013.2265 251948.8954 225250.9982 0.64656781 1.147681077 0.743392744 0.6589204 1.05723058 0.799655484 0.759211848 1.118525101 1 17.78117397 1.233494888 24.99995238 1.059262612 0.848926662 0.249146063 0.162731605 200.5824502 989841.8531 0.133677869 0.037447609 17.11965026 -1.233494888 -0.21033595 ILYLINQGEHLGTTEATEAFFAMTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ILYLINQGEHLGTTEATEAFFAMTK 25 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 133.1 4.83E-10 0 36509 39313 40805 42718 49586 33712 45412 40889 43115 FALSE TRUE 34223.96686 42223.77543 41772.91387 43814.2162 45691.71558 43444.10713 38602.89218 45994.08166 35918.82797 0.952814131 1.175533218 1.162980983 1.219811967 1.272082586 1.209507926 1.07472583 1.280500625 1 15.13245266 4.738605227 8.142053087 1.177110944 0.951144533 0.402754769 0.084743169 0.087069044 76.06273903 0.018253153 0.108039869 54777.88085 -4.738605227 -0.225966411 IMADIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IMADIR 6 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;; 101.72 0.084216 6332940000 8895500 16164800 9027400 8340200 16402500 6879000 10058700 14510500 19029200 FALSE TRUE 8338746.534 17361658.61 9241534.191 8554223.652 15114313.81 8864855.629 8550491.315 16322167.87 15853103.59 0.526000886 1.09515834 0.582947947 0.539592995 0.953397783 0.559187391 0.539357563 1.029588167 1 23.91826197 1.220020665 24.94392268 1.014794538 0.705064247 0.33017514 0.193613682 346.3325484 465948.2172 0.183249849 0.046150606 16.59665876 -1.220020665 -0.30973029 IMAT(ph)PEQVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 IMATPEQVGK 10 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 1 IMAT(1)PEQVGK;IMAT(1)PEQVGK;IMAT(1)PEQVGK;IMAT(1)PEQVGK;IMAT(1)PEQVGK;IMAT(1)PEQVGK;IMAT(1)PEQVGK 177.83 2.55E-05 920266000 3811910 3161580 3535660 3387950 3453610 2750650 4278200 2953960 4187360 TRUE FALSE 3573329.358 3395666.673 3619527.525 3474890.533 3182377.402 3544718.002 3636723.627 3322768.408 3488462.565 1.02432785 0.973399201 1.037570981 0.996109452 0.912257862 1.01612614 1.042500402 0.95250224 1 21.73415992 1.207850774 24.99813522 0.976251208 1.00112797 0.06179076 0.038905789 727.1511346 591891.8115 0.036515941 0.009133501 16.1380395 -1.207850774 0.024876762 IMDPNIVGSEHYDVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 IMDPNIVGSEHYDVAR 16 0 P06576;H0YH81 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ;;;;;;;;;;; 202.35 3.06E-11 13565790000 6770453 8011440 7246600 6615990 9827350 7512820 6744290 7877360 12294710 FALSE TRUE 6346702.432 8604615.353 7418492.774 6785767.504 9055549.573 9681649.174 5733046.325 8860865.736 10242643.47 0.619635199 0.840077601 0.724275212 0.662501582 0.88410278 0.945229539 0.559723312 0.865095594 1 23.28808477 0.996660392 24.99514801 1.000000031 0.753780778 0.329453425 0.118293139 121.0955151 906341.5983 0.107012237 0.026753059 9.92339759 -0.996660392 -0.246219253 IMEEFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IMEEFFR 7 0 Q08499-10;A0A087WSZ7;A0A1B0GW84;Q08499-2;Q08499-9;Q08499-6;Q08499-11;Q08499;Q08499-3;Q08499-4;D6RHE0;Q08499-5;Q08499-8 Q08499-10 PDE4D "cAMP-specific 3,5-cyclic phosphodiesterase 4D" 0 81.297 0.064172 15283000 28348 32125 30623 28169 38292 22491 28704 29878 26987 FALSE TRUE 26573.74928 34503.56843 31349.39202 28891.86423 35284.70078 28983.78659 24400.10167 33608.33407 22482.69536 1.181964567 1.534672239 1.394378722 1.285071197 1.569415954 1.289159779 1.08528365 1.494853421 1 14.45652738 0.381071831 0.369058106 0.954866412 1.421503726 0.293768012 0.159176314 3.283898759 0.818769216 0.456467313 0.130424122 2.404760508 -0.381071831 0.466637314 IMEIVDAITTTAQSHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IMEIVDAITTTAQSHQR 17 0 A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 ; 272.95 1.20E-35 628040000 522800 616390 627140 588920 640410 509480 603760 543280 598210 FALSE TRUE 490078.8812 662028.157 642016.057 604032.6842 590114.7819 656558.6053 513231.793 611109.7039 498364.8864 0.983373618 1.328400485 1.288244968 1.212028979 1.184101846 1.317425491 1.029831369 1.226229457 1 18.9268429 1.067003503 0.689926667 1.008781087 1.239619552 0.18735405 0.116043464 0.929160382 1.041281482 0.105427387 0.042873494 11.6681903 -1.067003503 0.230838464 IMELHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IMELHK 6 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;Q4VXN0;Q4VXN1 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 0 ; 101.52 0.036428 432840000 565710 534020 523690 483330 698270 385000 571040 621710 1204140 FALSE TRUE 530303.2209 573559.3964 536112.1741 495733.0661 643430.6909 496143.25 485417.8533 699331.8621 1003161.255 0.52863208 0.571751943 0.534422728 0.494170866 0.641403052 0.494579757 0.483888159 0.697128063 1 19.9361221 0.930886324 3.815528587 0.999671466 0.537483135 0.912014002 0.046048491 0.080487161 2.987464575 0.04335495 0.011125997 8.528768447 -0.930886324 -0.462188331 IMEVIDAITTTAQSHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IMEVIDAITTTAQSHQR 17 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 67.994 0.037821 330300000 102070 281100 242340 238390 287490 246950 221860 261040 213300 FALSE TRUE 95681.6209 301912.9365 248088.4192 244507.491 264911.6951 318240.4561 188594.1526 293631.4186 177698.852 0.538448166 1.699014558 1.396117175 1.375965507 1.490790132 1.790897648 1.061313286 1.652410329 1 17.43907484 -1.23374362 4.228153795 0.99982481 1.402962526 0.092411576 0.361011441 0.000693603 0.000125701 0.307178997 0.072361511 0.058378964 1.23374362 0.403137716 IMEYYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IMEYYEK 7 0 P36543;C9J8H1;P36543-3;P36543-2;Q96A05 P36543 ATP6V1E1;ATP6V1E2 V-type proton ATPase subunit E 1;V-type proton ATPase subunit E 2 0 ; 116.54 0.012638 94636000 224480 222270 202210 219400 261820 146286 231400 208580 302370 FALSE TRUE 210430.1975 238727.1021 207006.5167 225030.1754 241257.7133 188516.3934 196703.7182 234621.6721 251902.4936 0.835363694 0.947696462 0.8217724 0.89332254 0.957742458 0.748370493 0.780872453 0.931398768 1 17.94250588 3.963980296 23.51788875 0.858312354 0.89770142 0 0.083222518 694.0897851 1242193.159 0.020646156 0.037561188 9204.078116 -3.963980296 0.039389066 IMGPNYT(ph)PGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IMGPNYTPGKK 11 1 P13639 P13639 EEF2 Elongation factor 2 1 IMGPNYT(1)PGKK;IMGPNYT(1)PGKK 143.46 2.18E-05 1111930000 2008560 1008380 1422870 1274650 1289280 969340 1836820 1165460 1344080 TRUE FALSE 1882847.815 1083041.504 1456621.148 1307359.677 1188025.15 1249172.722 1561405.893 1310970.246 1119744.365 1.681497915 0.967222107 1.30085151 1.167551914 1.060978904 1.115587416 1.394430677 1.170776373 1 20.09473798 4.753323755 24.54859255 1.169328948 1.68149838 0.621563485 0.130009236 1512.113775 2514333.45 0.030815258 0.693624142 56666.15622 -4.753323755 0.512169432 IMGPNYT(ph)PGKKEDLYLKPIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IMGPNYTPGKKEDLYLKPIQR 21 3 P13639 P13639 EEF2 Elongation factor 2 1 IMGPNY(0.001)T(0.999)PGKKEDLYLKPIQR 55.051 0.052612 215470000 884440 575500 703350 698340 901860 488310 961360 582620 1471800 TRUE FALSE 829084.4792 618110.6188 720033.7941 716260.5867 831031.5535 629277.1699 817212.9928 655361.3895 1226147.072 0.6761705 0.504108058 0.587232813 0.584155525 0.677758462 0.513215082 0.666488557 0.534488402 1 20.2257006 -4.889980428 0.462252286 9.999999997 0.584239282 0.790840925 0.065495644 547.9781317 3.365466713 5049.634924 0.030305207 1.29E-05 4.889980428 -9.415760715 IMGPNYTPGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IMGPNYTPGKK 11 1 P13639 P13639 EEF2 Elongation factor 2 0 107.18 0.0035796 514180000 1205800 1109500 1170600 1107400 1417800 960230 1476500 1233800 1585700 FALSE TRUE 1130331.13 1191648.534 1198367.185 1135817.759 1306451.707 1237432.813 1255112.532 1387842.646 1321036.426 0.855639639 0.902055773 0.907141666 0.859792914 0.988959639 0.93671362 0.950096839 1.050571066 1 20.33323882 2.089630228 0.663330001 1.015967324 0.883543874 0.663824829 0.035843911 0.455171921 0.389246215 0.030012824 0.018565393 122.9221727 -2.089630228 -0.13242345 IMHFPTWVDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IMHFPTWVDLK 11 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 147.37 3.53E-05 69652000 278600 259930 249750 216870 270670 196210 271380 251420 188900 FALSE TRUE 261162.9233 279175.4877 255674.1879 222435.2514 249412.67 252852.6418 230689.0884 282810.3404 157371.3697 1.659532632 1.773991599 1.624655034 1.413441669 1.58486687 1.606725813 1.465889818 1.797088893 1 17.26381357 -2.638082894 0.321307789 8.04E-24 1.649612732 0.698610347 0.124301569 32.9287314 1.154761884 23.20378185 0.110350675 0.002301003 2.638082894 1.649612732 IMIMTDQDQDGSHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IMIMTDQDQDGSHIK 15 0 Q02880;Q02880-2;E9PCY5;P11388;P11388-2;P11388-3;P11388-4 Q02880;P11388 TOP2B;TOP2A DNA topoisomerase 2-beta;DNA topoisomerase 2;DNA topoisomerase 2-alpha 0 ; 226.65 8.37E-13 633360000 526040 440450 480880 446810 492280 344100 592940 440390 509190 FALSE TRUE 493116.0954 473061.3763 492286.7007 458275.901 453618.3146 443436.084 504034.1516 495373.6609 424202.8995 1.162453383 1.11517714 1.160498199 1.080322415 1.069342796 1.045339588 1.188191199 1.167775283 1 18.69439496 -1.229892631 3.576670627 0.999785767 1.124513295 0.404278544 0.047155884 3496829.514 1206794.375 5842.685284 0.011150523 0.058898925 1.229892631 0.124727528 IMKDILEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IMKDILEK 8 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 96.847 0.0078896 5527400000 11323900 11391500 11749500 12487200 16182200 9827600 16562400 10573800 20902000 FALSE TRUE 10615157.31 12234938.51 12028203.69 12807642.69 14911315.29 12664668.58 14079021.88 11893962.21 17413321.17 0.609599812 0.702619471 0.690747249 0.735508325 0.85631656 0.727297708 0.808520198 0.683038123 1 24.05368805 -5 0.103462361 1.826876163 0.561057067 0.679563937 0.06185329 100.2296188 0.700624927 17.95476714 0.862483843 1.00E-05 5 -1.265819096 IMLFTNEDNPHGNDSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 IMLFTNEDNPHGNDSAK 17 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;;;;; 298.23 3.13E-46 2558560000 2969290 2523440 2819240 2609960 2819350 2088630 3307500 2384040 3092400 FALSE TRUE 2783447.439 2710278.123 2886113.704 2676935.992 2597929.624 2691583.575 2811571.08 2681692.642 2576258.462 1.080422434 1.052021046 1.120273352 1.039078971 1.008411874 1.044764574 1.091338902 1.040925311 1 21.29684591 3.194611157 24.9995986 1.044430189 1.082483007 0.341329345 0.029576854 180.9171195 102909.7333 0.008861477 0.010591528 1565.348917 -3.194611157 0.038052818 IMNVIGEPIDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IMNVIGEPIDER 12 0 P06576;H0YH81;F8W079 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ;;;;; 207.29 1.87E-07 712942000 817159 856466 837482 741739 1038016 815774 793655 864835 1286740 FALSE TRUE 766014.4769 919879.6338 857347.4685 760773.2785 956494.4105 1051274.711 674653.8007 972811.5535 1071974.781 0.714582554 0.85811686 0.799783244 0.709693261 0.892273239 0.980689778 0.629356037 0.907494813 1 20.03183954 1.002220153 24.9879594 1.00000005 0.802384443 0.319895799 0.099568688 60.92953167 685755.6598 0.089702283 0.022425571 10.05125179 -1.002220153 -0.197615607 IMPDSNDS(ph)PPAEREPGEVVDSLVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IMPDSNDSPPAEREPGEVVDSLVGK 25 1 Q9Y657 Q9Y657 SPIN1 Spindlin-1 1 IMPDS(0.032)NDS(0.968)PPAEREPGEVVDSLVGK;IMPDSNDS(1)PPAEREPGEVVDSLVGK;IMPDS(0.024)NDS(0.976)PPAEREPGEVVDSLVGK 235.86 1.22E-38 274222000 344882 290442 301648 280549 341824 223469 354998 280275 431399 TRUE FALSE 323296.4513 311946.6279 308803.233 287748.3623 314978.5219 287980.8726 301769.3455 315267.9507 359395.72 0.899555652 0.867975356 0.859229022 0.800644934 0.876411444 0.801291881 0.839657594 0.877216765 1 18.4552137 0.8394575 3.899164729 0.999983978 0.848842503 0.701587922 0.030703311 0.579300802 13.310536 0.028433123 0.007278512 6.909673079 -0.8394575 -0.151141475 IMQQWKNSDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IMQQWKNSDAR 11 1 P42261-3;P42261-4;P42261-2;P42261;P42261-6;P42261-5 P42261-3 GRIA1 Glutamate receptor 1 0 52.167 0.087758 178800000 50665 238930 161670 198090 201400 211320 133170 178370 118810 FALSE TRUE 47493.96809 256620.6258 165504.8887 203173.3248 185582.8564 272324.6535 113202.3948 200639.8871 98979.84346 0.479834746 2.592655402 1.672106996 2.052673733 1.874956051 2.751314247 1.14369139 2.027078243 1 16.59484714 -1.388834737 8.314525383 0.999992787 1.874751368 0.13133469 0.654888827 7.75E-05 5.70E-06 0.558405917 0.131616449 0.040847479 1.388834737 0.874758581 IMRPDDANVAGNVHGGTILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IMRPDDANVAGNVHGGTILK 20 1 O00154-6;O00154-4;O00154-7;O00154;O00154-2;O00154-3 O00154-6 ACOT7 Cytosolic acyl coenzyme A thioester hydrolase 0 129.15 2.48E-05 184990000 121080 147390 147340 108100 126820 102270 138980 107050 156290 FALSE TRUE 113501.8189 158302.909 150834.9744 110874.029 116860.0688 131793.6888 118141.2392 120415.4281 130204.1893 0.871721713 1.215805035 1.158449472 0.851539644 0.897513892 1.012207744 0.907353595 0.924819921 1 16.99041634 3.246274231 24.99951027 0.930205174 1.121588792 0.303513288 0.101145073 151.7972137 491965.5994 0.026740114 0.035544238 1763.088982 -3.246274231 0.191383619 IMRPTDVPDQGLLCDLLWSDPDKDVLGWGENDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IMRPTDVPDQGLLCDLLWSDPDKDVLGWGENDR 33 2 F8W0W8;P36873;P36873-2;F8VYE8;F8VR82 F8W0W8 PPP1CC Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-gamma catalytic subunit 0 265.39 5.12E-60 199800000 386300 285260 299200 303760 357500 233170 380720 284630 325750 FALSE TRUE 362122.1726 306380.9472 306297.1653 311554.9959 329423.3921 300482.3938 323634.5704 320166.682 271380.2206 1.334372018 1.12897302 1.128664295 1.148038701 1.213881363 1.107237636 1.192550326 1.179771618 1 18.04995605 -1.953949634 2.429873924 0.869553405 1.168820312 0.424378568 0.064588892 4859556.467 2096485.651 3575596.904 0.014177384 0.011118607 1.953949634 0.299266908 IMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDR 33 2 P62136;P62136-2;P62136-3;E9PMD7 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit;Serine/threonine-protein phosphatase 0 ; 328.81 2.64E-117 368966000 416171 322409 367428 332912 377964 274352 447551 283864 346441 FALSE TRUE 390123.6 346280.4978 376143.5657 341455.0855 348280.2321 353552.9687 380444.8824 319305.0453 288617.759 1.351696449 1.199789296 1.303258562 1.183070254 1.206717956 1.224986882 1.318161723 1.10632501 1 18.13880055 1.033836676 4.723835214 1.000857646 1.251743013 0.714759723 0.055270091 0.082631506 4.404240789 0.049345311 0.012519118 10.81027335 -1.033836676 0.250885368 IMRPTDVPDTGLLCDLLWSDPDKDVQGWGENDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IMRPTDVPDTGLLCDLLWSDPDKDVQGWGENDR 33 2 P62140 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit 0 238 4.81E-47 591210000 355280 309880 322180 298510 367470 246340 376820 294450 446460 FALSE TRUE 333043.659 332823.8376 329822.2617 306170.272 338610.3885 317454.359 320319.3392 331212.7307 371942.9418 0.895415994 0.894824986 0.886754996 0.823164624 0.910382616 0.853502845 0.861205586 0.890493389 1 18.50472179 -1.109401245 4.480600176 1.000012612 0.87663307 0.700612529 0.025274552 3.00E-06 5.96E-07 0.02305152 0.00543274 0.077731805 1.109401245 -0.123379542 IMSCS(ph)PDTQCSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IMSCSPDTQCSR 12 0 Q9C0C9;K7EQ12 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 IMS(0.03)CS(0.96)PDT(0.009)QCSR;IMS(0.001)CS(0.999)PDT(0.001)QCSR;IMS(0.014)CS(0.985)PDT(0.001)QCSR 107.53 0.0070531 902230000 675250 755610 742870 867460 1147670 960740 1295730 884070 1307180 TRUE FALSE 632987.3079 811556.1506 760491.2272 889720.4922 1057536.628 1238090.042 1101447.315 994448.0856 1089003.213 0.581253848 0.745228426 0.698336991 0.817004469 0.971105149 1.136902101 1.011427057 0.913172774 1 20.05457678 2.886560289 2.184589415 1.023229683 0.69191134 0.832844025 0.068307813 0.116696369 1.099928636 0.022777479 0.024894957 770.1233451 -2.886560289 -0.331318343 IMSS(ph)IGEGIDFSQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IMSSIGEGIDFSQER 15 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 IMS(0.002)S(0.998)IGEGIDFSQER;IMS(0.021)S(0.979)IGEGIDFSQER;IMSS(1)IGEGIDFSQER;IMS(0.004)S(0.996)IGEGIDFSQER 300.07 3.14E-44 332090000 404428 495843 427969 441261 491830 365407 519972 464988 602001 TRUE FALSE 379115.5734 532555.7316 438120.6268 452584.5043 453203.6557 470894.069 442007.0258 523042.7754 501523.144 0.755928371 1.061876681 0.873580077 0.902419977 0.90365452 0.938927893 0.881329269 1.042908551 1 18.93595675 1.234369387 24.99161458 1.021454318 0.915499401 0.287535111 0.075715036 147.8172007 881351.0082 0.058918971 0.016761188 17.15415727 -1.234369387 -0.105954918 IMT(ph)IIEPVS(ph)KK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IMTIIEPVSKK 11 1 A0A1B0GUF7;A0A1B0GVH7 A0A1B0GUF7 2 IMT(1)IIEPVS(1)KK 60.401 0.08393 81225000 85441 80966 94963 90738 87752 64264 99987 81173 93454 TRUE FALSE 80093.40033 86960.80689 97215.5672 93066.4907 80860.31189 82815.97356 84994.87758 91307.62773 77855.92366 1.028738682 1.116945286 1.248659866 1.195368141 1.038589077 1.063708061 1.091694422 1.172776886 1 16.24851919 2.74048994 24.96532551 1.079172416 1.159219521 0.202399819 0.07086112 268.0943307 3469122.236 0.022306068 0.022603033 550.1611765 -2.74048994 0.080047105 IMVGS(ph)TDDPSVFSLPDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IMVGSTDDPSVFSLPDSK 18 0 O43741 O43741 PRKAB2 5-AMP-activated protein kinase subunit beta-2 1 IMVGS(0.929)T(0.071)DDPSVFSLPDSK;IMVGS(0.915)T(0.085)DDPSVFSLPDSK;IMVGS(0.978)T(0.022)DDPSVFSLPDSK;IMVGS(0.984)T(0.016)DDPSVFSLPDSK;IMVGS(0.974)T(0.026)DDPSVFSLPDSK 336.79 4.15E-75 168820000 636972 532949 523254 528974 586540 430798 737327 561534 780440 TRUE FALSE 597105.0595 572409.0985 535665.832 542548.3684 540475.5144 555162.3892 626771.6614 631642.756 650179.5222 0.918369526 0.88038623 0.823873736 0.83445933 0.831271204 0.853860157 0.96399785 0.971489772 1 19.31047859 1.689182323 3.824845167 0.980729409 0.853580438 0.805128581 0.028234206 0.081912068 2.791910917 0.016618987 0.007790131 48.88575459 -1.689182323 -0.127148971 IMYTVFEHTFHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IMYTVFEHTFHVR 13 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 250.67 3.63E-18 418780000 213220 339350 281300 294050 355110 170779 243050 297010 266950 FALSE TRUE 199874.9408 364475.8271 287972.5688 301595.8208 327221.093 220080.1249 206606.9089 334092.3523 222394.3204 0.898741211 1.638872011 1.294873755 1.356130949 1.471355439 0.989594179 0.929011624 1.502252178 1 17.76276042 2.236905248 24.99966753 1.077135702 1.369876751 0.164836104 0.241917751 58.249115 879666.4218 0.08140225 0.063310118 172.5461397 -2.236905248 0.292741049 INEKPQVIADYESGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 INEKPQVIADYESGR 15 1 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ;;;; 207.92 2.87E-09 6962950000 7868130 7010930 7547040 7579410 8246910 5848050 9598720 7057320 8014860 FALSE TRUE 7375677.788 7530026.552 7726059.353 7773910.493 7599230.955 7536287.1 8159481.046 7938441.937 6677128.088 1.104618287 1.127734327 1.157093177 1.164259602 1.138098724 1.128671938 1.222004571 1.188900652 1 22.67079629 4.495122581 1.309781055 1.155810061 1.094897222 0.004485834 0.058595352 2.399783922 4.958885321 0.015091812 0.173750373 31269.6184 -4.495122581 -0.060912839 INETDTFGPGDDDEIQFDDIGDDDEDIDDI ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 INETDTFGPGDDDEIQFDDIGDDDEDIDDI 30 0 P47813;O14602;X6RAC9;A6NJH9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 ; 166.35 2.80E-12 48174000 147268 137529 145455 147048 143197 115078 150575 124517 140664 FALSE TRUE 138050.7588 147711.7903 148905.2613 150821.5006 131950.8852 148299.1505 127997.6766 140063.2215 117186.2697 1.178045509 1.260487177 1.27067157 1.287023651 1.125992709 1.26549937 1.092258308 1.195218706 1 16.83844402 0.949970364 0.485094653 0.995811647 1.254941553 0.579947818 0.05970475 0.697147261 0.410557314 0.067010374 0.031861707 8.911901214 -0.949970364 0.259129906 INFDDNAEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 INFDDNAEFR 10 0 E9PDQ8;Q96I99;Q96I99-2 E9PDQ8 SUCLG2 "Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial" 0 ;; 248.96 1.55E-12 499540000 653580 719100 596780 602580 858450 590790 613010 648710 1002730 FALSE TRUE 612673.5945 772342.9122 610935.9034 618043.223 791030.7998 761341.4823 521094.8414 729702.8715 835367.8851 0.733417702 0.924554231 0.731337551 0.739845563 0.946925078 0.911384668 0.623790848 0.873510802 1 19.67205216 KDYQTSPLLETQAEDHPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KDYQTSPLLETQAEDHPPR 19 1 Q9Y6U3;Q9Y6U3-3 Q9Y6U3 SCIN Adseverin 0 ;;; 322.15 2.88E-62 1494550000 1541660 1417060 1562610 1380520 2020240 1151730 1747950 1830810 4203890 FALSE TRUE 1445170.253 1521980.597 1599675.847 1415946.48 1861578.5 1484215.754 1485861.125 2059390.659 3502233.601 0.41264245 0.434574266 0.456758752 0.404298126 0.531540357 0.423791193 0.424260999 0.588022072 1 21.73984388 0.84401755 2.779057792 0.999799383 0.442202952 0.959678759 0.036031917 0.106015519 1.486511925 0.0322304 0.008520605 6.982606207 -0.84401755 -0.557596431 INFS(ph)DLDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 INFSDLDQR 9 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;E7EV93;E9PGW9;E5RGQ4;Q15154-3 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 INFS(1)DLDQR;INFS(1)DLDQR;INFS(1)DLDQR;INFS(1)DLDQR 135.02 0.000244 276908000 1056810 984220 925300 922320 854670 796140 1248270 804560 652688 TRUE FALSE 990666.1486 1057092.673 947248.553 945988.2927 787547.6658 1025972.694 1061103.502 905011.0871 543750.1563 1.821914232 1.94407792 1.742065804 1.739748084 1.448363107 1.886845791 1.951454155 1.664387728 1 19.05258438 0.967353335 21.06749097 0.999999997 1.800683655 0.749859705 0.142379492 263.777304 170221.2103 0.140451955 0.035112989 9.275841851 -0.967353335 0.800683658 INHEGEVNR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 163.88 6.27E-05 7121362000 4407440 5571490 4983330 4391750 5816130 3893760 5163290 4963160 6443750 FALSE TRUE 4131586.198 5984008.917 5101536.941 4504449.74 5359354.611 5017825.302 4389102.598 5582821.451 5368246.497 0.769634219 1.114704573 0.950317193 0.839091451 0.998343614 0.934723341 0.81760452 1.039971144 1 22.35601949 3.481710062 24.68386685 0.921793785 0.987340151 0 0.109250883 378.7396197 2037288.738 0.02749853 0.039536575 3031.866414 -3.481710062 0.065546366 INHTVILDDPFDDPPDLLIPDRS(ph)PEPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 17 INHTVILDDPFDDPPDLLIPDRSPEPTR 28 1 Q8WUA2 Q8WUA2 PPIL4 Peptidyl-prolyl cis-trans isomerase-like 4 1 INHTVILDDPFDDPPDLLIPDRS(0.991)PEPT(0.009)R;INHTVILDDPFDDPPDLLIPDRS(0.967)PEPT(0.033)R;INHTVILDDPFDDPPDLLIPDRS(0.999)PEPT(0.001)R;INHTVILDDPFDDPPDLLIPDRS(0.978)PEPT(0.022)R;INHTVILDDPFDDPPDLLIPDRS(0.977)PEPT(0.023)R;INHTVILDDPFDDPPDLLIPDRS(0.957)PEPT(0.043)R;INHTVILDDPFDDPPDLLIPDRS(0.969)PEPT(0.031)R;INHTVILDDPFDDPPDLLIPDRS(0.995)PEPT(0.005)R;INHTVILDDPFDDPPDLLIPDRS(0.971)PEPT(0.029)R;INHTVILDDPFDDPPDLLIPDRS(0.918)PEPT(0.082)R;INHTVILDDPFDDPPDLLIPDRS(0.992)PEPT(0.008)R;INHTVILDDPFDDPPDLLIPDRS(0.814)PEPT(0.186)R;INHTVILDDPFDDPPDLLIPDRS(0.885)PEPT(0.115)R;INHTVILDDPFDDPPDLLIPDRS(0.951)PEPT(0.049)R;INHTVILDDPFDDPPDLLIPDRS(0.998)PEPT(0.002)R;INHTVILDDPFDDPPDLLIPDRS(0.964)PEPT(0.036)R;INHTVILDDPFDDPPDLLIPDRS(0.948)PEPT(0.052)R 303.5 5.61E-72 18492817000 1055843.1 1149664.5 1032662.2 1029781.5 1106312.8 879236 1255699.8 960031.3 1224272.3 TRUE FALSE 989759.7651 1234786.856 1057157.435 1056207.437 1019427.455 1133057.16 1067419.272 1079893.321 1019933.344 0.970416127 1.210654464 1.036496592 1.03556516 0.999503998 1.11091295 1.046557874 1.058788133 1 19.96004344 INHTVILDDPFDDPPDLLIPDRS(ph)PEPTREQLDSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 INHTVILDDPFDDPPDLLIPDRSPEPTREQLDSGR 35 2 Q8WUA2 Q8WUA2 PPIL4 Peptidyl-prolyl cis-trans isomerase-like 4 1 INHTVILDDPFDDPPDLLIPDRS(0.97)PEPT(0.029)REQLDS(0.001)GR;INHTVILDDPFDDPPDLLIPDRS(0.984)PEPT(0.015)REQLDSGR;INHTVILDDPFDDPPDLLIPDRS(0.981)PEPT(0.015)REQLDS(0.004)GR;INHTVILDDPFDDPPDLLIPDRS(0.896)PEPT(0.083)REQLDS(0.022)GR 183.8 1.55E-20 621834000 17627.5 42084.9 20354.9 21141.6 45562.7 15287.7 29880.8 19023 134853 TRUE FALSE 16524.22624 45200.90979 20837.72784 21684.12925 41984.38933 19701.01081 25400.45144 21398.06342 112345.1631 0.147084447 0.402339616 0.185479528 0.193013465 0.373708918 0.175361451 0.226092969 0.190467153 1 16.77757849 -1.407618429 3.490041722 1.006440023 0.245530474 0.887746691 0.085250006 137325758 195748636.6 8852680.438 0.019711733 0.039118444 1.407618429 -0.760909549 INISEGNCPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 229.82 5.25E-12 2319700000 675352 666609 680660 706620 709702 568845 749428 617118 768524 FALSE TRUE 633082.9239 715965.424 696805.5766 724753.0655 653964.8677 733061.3171 637058.2287 694166.5407 640252.3795 0.988802141 1.118254999 1.088329538 1.131980276 1.021417317 1.144956802 0.995011107 1.08420767 1 19.28828118 1.712930566 14.92845178 1.029955162 1.086702923 0.193687934 0.05307414 0.215121158 110.7391393 0.021783713 0.01201468 51.63338125 -1.712930566 0.056747761 INLCIHS(ph)EEEDMNLGLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 INLCIHSEEEDMNLGLVR 18 0 P41002 P41002 CCNF Cyclin-F 1 INLCIHS(1)EEEDMNLGLVR;INLCIHS(1)EEEDMNLGLVR 214.31 6.52E-19 56830000 110556 117289 117925 125431 111379 118983 156339 100544 83190 TRUE FALSE 103636.4973 125973.1996 120722.2367 128649.7718 102631.7426 153331.4606 132897.4183 113097.1397 69305.05157 1.495367148 1.817662591 1.741896643 1.856282751 1.48086958 2.212413916 1.917571884 1.631874404 1 16.08067289 4.744663172 23.00229261 1.773130394 1.495366774 0.00567162 0.32090265 625.9076605 2359007.256 0.067002573 0.592889535 55547.3279 -4.744663172 -0.277763619 INPPPYLTCESFPHAVDHILQHLL ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 INPPPYLTCESFPHAVDHILQHLL 24 0 Q9H0R4;Q9H0R4-2 Q9H0R4 HDHD2 Haloacid dehalogenase-like hydrolase domain-containing protein 2 0 109.08 0.0012801 18898000 33940 34035 29139 31579 31309 25297 35383 27916 28843 FALSE TRUE 31815.75598 36554.98681 29830.19084 32389.3706 28850.11743 32599.83324 30077.64763 31401.37405 24028.91697 1.324061173 1.521291487 1.241428853 1.34793302 1.200641605 1.356691743 1.251727145 1.306816037 1 14.552484 -4.83033473 0.116412918 1.06E-13 1.495749783 0.628657917 0.080807311 91.66442959 0.726479663 21.93638287 0.801504592 1.48E-05 4.83033473 1.495749783 INPPSSGGTSS(ph)SPIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 INPPSSGGTS(0.006)S(0.497)S(0.497)PIK;INPPSS(0.003)GGT(0.003)S(0.019)S(0.69)S(0.285)PIK;INPPSSGGT(0.01)S(0.039)S(0.638)S(0.314)PIK 154.47 2.59E-06 796178000 778840 537830 652050 576210 675410 501990 787460 600850 750130 TRUE FALSE 730093.7947 577651.4928 667516.9339 590996.5241 622366.0231 646906.3639 669387.6834 675867.4451 624928.457 1.168283804 0.924348198 1.068149364 0.945702692 0.995899636 1.035168677 1.071142906 1.081511712 1 19.25333151 2.007388081 5.272765349 1.057756383 1.010641926 0.024567645 0.070019954 0.41742725 36.22475553 0.025861698 0.017508285 101.7157207 -2.007388081 -0.047114457 INPPSSGGTSSS(ph)PIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 INPPSSGGTSSSPIK 15 0 A0A0C4DG88;P14859-4;P14859-5;P14859-3;P14859;P14859-2;P14859-6;A0A0A0MT46 A0A0C4DG88 POU2F1 "POU domain protein;POU domain, class 2, transcription factor 1" 1 INPPSSGGTSS(0.064)S(0.935)PIK;INPPSSGGTS(0.012)S(0.262)S(0.726)PIK;INPPSSGGT(0.006)S(0.022)S(0.075)S(0.896)PIK 291.17 6.79E-44 1173420000 1242510 838790 964070 922480 1010710 733670 1219860 849480 1111210 TRUE FALSE 1164743.517 900894.8844 986938.1957 946152.3986 931332.9136 945468.6189 1036953.318 955539.4479 925741.8723 1.258173095 0.973159918 1.066105169 1.022047751 1.006039525 1.021309122 1.120132241 1.03218778 1 19.82025045 4.748702417 24.96555902 1.036116513 1.25817322 0.75930336 0.04022596 764.9033881 1882885.78 0.009964728 0.139147232 56066.36713 -4.748702417 0.222056707 INPYMS(ph)SPCHIEMILTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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;INPYMS(0.5)S(0.5)PCHIEMILTEK;INPYMS(0.54)S(0.46)PCHIEMILTEK;INPYMS(0.5)S(0.5)PCHIEMILTEK;INPY(0.154)MS(0.423)S(0.423)PCHIEMILTEK 255.2 9.56E-31 838240000 1616670 1551020 1575320 1643870 1835970 1498550 2234600 1471170 1781670 TRUE FALSE 1515485.511 1665859.135 1612687.334 1686054.487 1691780.322 1931157.058 1899542.475 1654848.813 1484297.767 1.021011784 1.122321391 1.086498525 1.135927389 1.139784994 1.301057713 1.279758359 1.114903525 1 20.50134911 2.685115027 2.381145263 1.208722518 1.091639467 0.095332372 0.091157555 0.399547334 4.468753885 0.030365613 0.02919433 484.3006223 -2.685115027 -0.117083051 INPYMSS(ph)PCHIEMILTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 INPYMSSPCHIEMILTEK 18 0 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 1 INPYMS(0.122)S(0.878)PCHIEMILTEK 260.56 6.17E-31 240200000 655970 634000 680250 703760 757200 607340 916990 608990 742910 TRUE FALSE 614914.0086 680942.0197 696385.8512 721819.6731 697732.5664 782669.1987 779495.8624 685023.7421 618913.5216 0.993537848 1.100221591 1.125174725 1.166269031 1.127350659 1.264585716 1.259458446 1.106816572 1 19.23937832 5.212283386 0.636597631 1.180430032 0.763493307 0.239715439 0.078575003 6.453843777 1.282169476 0.031790289 2.239364242 163035.9528 -5.212283386 -0.416936725 INPYMSSPCHIEMILTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 INPYMSSPCHIEMILTEK 18 0 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 0 ; 247.46 2.20E-24 962670000 394910 590700 583700 608540 666570 525450 813890 557480 778700 FALSE TRUE 370193.288 634436.0426 597545.6396 624156.1667 614220.281 677138.885 691854.7503 627082.6052 648729.9394 0.570643138 0.977966337 0.921100759 0.962120181 0.946804277 1.043791636 1.066475752 0.966631208 1 19.3072585 4.739106851 6.226581412 0.986312289 0.56075794 0.901637643 0.043083028 0.043330148 8.995123673 0.012197438 0.077812905 54841.18763 -4.739106851 -0.42555435 INS(ph)SPNVNTTASGVEDLNIIQVTIPDDDNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 INSSPNVNTTASGVEDLNIIQVTIPDDDNER 31 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 INS(0.476)S(0.476)PNVNT(0.018)T(0.025)AS(0.005)GVEDLNIIQVTIPDDDNER;INS(0.499)S(0.499)PNVNT(0.001)T(0.001)AS(0.001)GVEDLNIIQVTIPDDDNER;INS(0.589)S(0.407)PNVNT(0.002)T(0.003)ASGVEDLNIIQVTIPDDDNER;INS(0.564)S(0.404)PNVNT(0.015)T(0.015)AS(0.002)GVEDLNIIQVTIPDDDNER 214.29 6.08E-35 365064000 332078 308432 343838 318691 362482 309496 415050 352809 439119 TRUE FALSE 311293.8308 331268.6262 351993.9997 326869.1506 334014.1259 398842.471 352817.1056 396857.9803 365827.2021 0.850931339 0.905533061 0.962186512 0.893506958 0.91303797 1.090248261 0.964436498 1.084823594 1 18.48080283 2.260808619 24.74869846 1.02676716 0.912375098 0.664305774 0.045536028 131.8488769 146668.3048 0.014773346 0.012350936 182.3092142 -2.260808619 -0.114392062 INVYYNEATGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 INVYYNEATGGK 12 0 P68371 P68371 TUBB4B Tubulin beta-4B chain 0 ; 227.81 2.81E-11 226590000 476060 478200 463890 443090 494260 372150 583800 419340 556410 FALSE TRUE 446264.2544 513606.4256 474893.6899 454460.4395 455442.8133 479583.6636 496264.6097 471695.5221 463541.5765 0.962727568 1.108005089 1.024489957 0.980409229 0.982528508 1.034607656 1.070593524 1.017590538 1 18.82233922 0.996827293 24.95109418 0.999999989 1.032249802 0 0.043802426 337.3473462 2653028.782 0.04247368 0.01061842 9.927211922 -0.996827293 0.032249813 INWAMEDKQEMVDIIETVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 INWAMEDKQEMVDIIETVYR 20 1 K7ESL1;P83876 K7ESL1 TXNL4A Thioredoxin-like protein 4A 0 113.51 0.00012558 53274000 94386 94870 88484 91021 75123 82731 97381 86077 78197 FALSE TRUE 88478.54874 101894.2735 90582.88227 93356.75296 69223.14261 106614.0967 82779.62309 96823.90293 65145.41553 1.358169996 1.564105052 1.390472093 1.433051769 1.062594229 1.636555632 1.270689924 1.486273472 1 15.99137604 -3.301951396 0.286660813 1.02E-13 1.436082546 0.373608596 0.159651515 80.65188755 1.863374016 48.46480586 0.159981245 0.00049894 3.301951396 1.436082546 INYTEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 184.89 0.0014457 18374640000 14154920 17698030 14448670 16000710 17626780 12992170 16805140 14288000 14601080 FALSE TRUE 13268988.82 19008410.56 14791399.28 16411315.31 16242443.8 16742798.57 14285365.27 16071888.25 12164065.42 1.090835043 1.562669214 1.215991427 1.349163683 1.335280865 1.376414709 1.174390697 1.321259603 1 23.53612214 -0.047757115 0.43495547 0.952469736 1.34622678 0.342093617 0.128871559 4.599644296 1.095218161 0.495156086 0.071212655 0.89586565 0.047757115 0.393757044 IPAS(ph)QTS(ph)VPFDHLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IPASQTSVPFDHLGK 15 0 P49674;H0Y5S9;H0Y682 P49674 CSNK1E Casein kinase I isoform epsilon 2 IPAS(0.846)QT(0.308)S(0.846)VPFDHLGK 53.278 0.082522 116200000 92698 103050 94895 96384 178290 71430 138300 137620 206560 TRUE FALSE 86896.19765 110679.9292 97145.95421 98857.37662 164287.8226 92050.68143 117563.1989 154802.1599 172083.8016 0.504964423 0.643174594 0.564527011 0.574472296 0.954696613 0.534917759 0.683174115 0.899574269 1 17.39275178 -1.441266187 0.125699829 1.508596426 0.409799076 0.524056082 0.125370642 35.84310177 0.782634634 6.882201715 1.329450699 0.036202104 1.441266187 -1.09879735 IPCES(ph)PPLEVVDTTASTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IPCESPPLEVVDTTASTK 18 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 IPCES(1)PPLEVVDTTASTK 164.53 3.19E-11 55252000 125350 83170 100740 86651 78323 84142 100170 59152 96767 TRUE FALSE 117504.5673 89327.99334 103129.6004 88874.61136 72171.82752 108432.4295 85150.43843 66537.25741 80615.96256 1.457584373 1.108068309 1.279270223 1.102444337 0.895254801 1.34504912 1.056247866 0.825360826 1 16.29877791 8 0.215635683 0.973288837 2.936543379 0.386655606 0.153601619 59.0228533 0.746906378 0.234288704 40.1009887 100000000 -8 1.963254542 IPDEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IPDEELR 7 0 Q99961-3;Q99961-2;Q99961;Q99962 Q99961-3 SH3GL1;SH3GL2 Endophilin-A2;Endophilin-A1 0 ; 91.906 0.045195 195570000 401470 354410 324650 325320 392380 268360 375040 328950 395040 FALSE TRUE 376342.7093 380650.8852 332350.8513 333668.262 361564.0576 345831.1755 318806.2337 370020.1316 329105.2719 1.14353291 1.156623481 1.009861827 1.013864834 1.098627365 1.050822351 0.968705946 1.124321496 1 18.32818961 4.04057482 3.403118134 1.035169937 1.149677969 0.501913614 0.046175773 0.182621532 4.188753166 0.011320318 0.026490358 10979.30424 -4.04057482 0.114508032 IPDEINDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IPDEINDR 8 0 C9J363;Q9BUL8;C9J6F3;C9J5C3;H7C5M9;C9JSA3;C9JND6 C9J363 PDCD10 Programmed cell death protein 10 0 ; 98.033 0.019883 0 204834 249720 202537 223007 213195 178140 245170 197143 244110 FALSE TRUE 192013.8056 268209.5286 207341.2733 228729.7372 196451.5247 229566.1261 208409.0345 221756.7375 203366.464 0.944176349 1.318848366 1.019545058 1.124717088 0.965997642 1.128829806 1.024795487 1.090429234 1 17.63372227 3.736199446 24.58659628 1.054188119 1.161551287 0.078974992 0.103618614 438.9255198 1188737.939 0.023370342 0.041365153 5447.527683 -3.736199446 0.107363168 IPDHDPAPNVTVLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IPDHDPAPNVTVLLR 15 0 Q9P2E9;Q9P2E9-3;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 192.4 1.36E-07 408030000 490370 545320 500380 518060 563840 402660 580150 454840 411050 FALSE TRUE 459678.617 585696.0602 512249.2499 531354.2967 519558.2808 518901.4054 493161.8933 511627.7752 342443.0995 1.342350357 1.710345634 1.49586676 1.551657188 1.517210543 1.515292339 1.440127992 1.494051934 1 18.38550476 -1.603691335 0.337599487 0.587902082 1.561859014 0.748458151 0.092342132 11.19949543 0.715859345 3.912288162 0.071227121 0.024906268 1.603691335 0.973956932 IPDPEAVKPDDWDEDAPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IPDPEAVKPDDWDEDAPAK 19 1 P27824;P27824-2;P27824-3;D6RGY2 P27824 CANX Calnexin 0 ; 155.93 1.92E-08 380460000 1371380 611590 713920 673470 792900 530770 1125160 785180 472720 FALSE TRUE 1285547.774 656872.76 730854.5195 690752.3804 730628.8324 683994.6827 956452.7035 883211.4514 393819.9781 3.264303096 1.667951847 1.855808644 1.753980039 1.855235572 1.736820681 2.428654605 2.242678128 1 18.58717677 4.743869623 24.82146546 1.876847088 3.264303743 0.587507295 0.378070458 375.7735884 1756813.49 0.085241297 0.72849533 55445.92365 -4.743869623 1.387456654 IPDWFLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IPDWFLNR 8 0 P62269;J3JS69 P62269 RPS18 40S ribosomal protein S18 0 ; 98.997 0.016579 567360000 652680 1444140 642000 631910 1525620 550790 618630 1217230 950370 FALSE TRUE 611829.9239 1551065.628 657228.5432 648125.8804 1405803.959 709794.1317 525872.1746 1369203.845 791747.1074 0.772759279 1.959041737 0.830099077 0.818602145 1.775571955 0.896490969 0.664192101 1.729344929 1 19.59468017 3.854524863 7.808577145 1.067666464 1.441612171 0.042938224 0.467783763 0.529126207 32.33813901 0.111921493 0.202658823 7153.603465 -3.854524863 0.373945707 IPEDDGNDLTHTFFNPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IPEDDGNDLTHTFFNPDR 18 0 G5E9B7;A0A0D9SFG6;Q99418-2;Q99418;M0R2J0;Q15438-3;O43739-2;O43739;K7ENQ8;Q15438-2;Q15438 G5E9B7;K7ENQ8 CYTH2;CYTH1;CYTH3 Cytohesin-2;Cytohesin-1;Cytohesin-3 0 268.55 1.73E-31 34994000 30120 23963 30536 34071 30104 32217 36631 36725 17745 FALSE TRUE 28234.84297 25737.24545 31260.32834 34945.31954 27739.75327 41517.5249 31138.52162 41310.19709 14783.24486 1.90992189 1.740974035 2.11457827 2.363846359 1.876431969 2.808417589 2.106338757 2.794393076 1 13.85167535 3.706894971 2.522086974 2.237190599 1.827055308 0.051080244 0.510846878 0.595359104 7.511119305 0.123731212 0.231952729 5092.077101 -3.706894971 -0.410135291 IPEQSVLLLHACAHNPTGVDPRPEQWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IPEQSVLLLHACAHNPTGVDPRPEQWK 27 1 P00505;P00505-2 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 ; 125.52 4.75E-05 768590000 1117650 921130 786930 910890 1342880 814030 895520 1060280 1043510 FALSE TRUE 1047698.282 989331.4236 805596.3512 934264.9795 1237415.622 1049027.246 761245.0896 1192658.292 869341.4397 1.205163166 1.138024001 0.926674278 1.07468129 1.423394267 1.206691869 0.875657199 1.371910089 1 19.72956339 -1.155923989 4.515786365 0.999981323 1.12105388 0.045043583 0.172944483 0.359987292 51066942.74 1853.731274 0.039718269 0.069835462 1.155923989 0.121072556 IPFTVSLDNGHSFPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IPFTVSLDNGHSFPR 15 0 Q9UGT4 Q9UGT4 SUSD2 Sushi domain-containing protein 2 0 157.07 2.02E-06 225140000 105860 119390 110560 101100 152350 96521 144950 122960 189600 FALSE TRUE 99234.41157 128229.7598 113182.5354 103694.3972 140385.0456 124385.0458 123216.0931 138311.8267 157954.5351 0.628246675 0.81181436 0.71655135 0.656482557 0.888768692 0.787473723 0.780073159 0.875643276 1 17.26914983 -0.763954101 0.188534968 1.190965008 0.675805896 0.621380948 0.068340894 12.05239623 0.559602779 1.444958784 0.240107059 0.172205056 0.763954101 -0.515159111 IPGGNIYIS(ph)PLKSPYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IPGGNIYISPLKSPYK 16 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 IPGGNIYIS(1)PLKSPYK 126.61 4.28E-05 547580000 1463600 924470 1035400 1044700 1158400 977490 1749100 1123800 1232700 TRUE FALSE 1371995.889 992918.7207 1059960.177 1071508.771 1067423.937 1259675.495 1486838.693 1264108.904 1026954.406 1.3359852 0.966857647 1.03213947 1.043384949 1.039407329 1.226612873 1.447813733 1.230929918 1 19.9699407 2.14135341 4.723323003 1.289260338 1.05903265 0.129130061 0.148907793 0.225246097 8.580075275 0.053024788 0.038623094 138.4692722 -2.14135341 -0.230227688 IPGLLSPHPLLQLSYTATDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IPGLLSPHPLLQLSYTATDR 20 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 240.14 1.09E-29 14578017000 2298000 3224425 2991665 3164819 3356335 2835495 3468212 3149029 2958973 FALSE TRUE 2154172.282 3463164.782 3062628.707 3246033.614 3092741.988 3654056.376 2948185.808 3542192.203 2465101.291 0.873867654 1.404877274 1.242394671 1.316795227 1.25461051 1.482314901 1.195969439 1.436935762 1 21.2332155 4.747042805 24.58643924 1.303630401 0.87386738 0.475356154 0.137460216 654.866908 1898141.159 0.027567171 0.315936688 55852.5242 -4.747042805 -0.429763021 IPGTPGAGGRLS(ph)PENNQVLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IPGTPGAGGRLSPENNQVLTK 21 1 Q16514-2;Q16514 Q16514-2 TAF12 Transcription initiation factor TFIID subunit 12 1 IPGT(0.001)PGAGGRLS(0.999)PENNQVLTK;IPGTPGAGGRLS(1)PENNQVLTK;IPGTPGAGGRLS(1)PENNQVLTK;IPGTPGAGGRLS(1)PENNQVLTK 153.12 2.79E-08 2595150000 2336720 2340150 2308170 2367110 2779110 1658910 2721700 2263180 3756870 TRUE FALSE 2190468.866 2513417.141 2362920.882 2427854.05 2560849.911 2137810.387 2313606.352 2545743.005 3129824.127 0.699869634 0.803053794 0.754969221 0.775715808 0.818208886 0.683044893 0.739212895 0.813382127 1 21.57765016 0.86804555 3.881409036 0.99995067 0.757471874 0.778120469 0.041282884 0.323910083 8.677669501 0.038341732 0.009820053 7.379816276 -0.86804555 -0.242478797 IPIFSAAGLPHNEIAAQICR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IPIFSAAGLPHNEIAAQICR 20 0 P21281;P15313;C9JL73;C9JNS9 P21281;P15313 ATP6V1B2;ATP6V1B1 "V-type proton ATPase subunit B, brain isoform;V-type proton ATPase subunit B, kidney isoform" 0 ; 235.26 1.55E-29 570530000 319540 421320 370080 348520 454310 344600 451070 393150 454780 FALSE TRUE 299540.5618 452514.9712 378858.4724 357463.6132 418630.3252 444080.4259 383436.241 442235.6429 378874.28 0.790606746 1.19436709 0.999958277 0.94348873 1.104932024 1.172104968 1.012040831 1.167235852 1 18.53135968 2.688128631 24.92538336 1.092066724 1.020457555 0.150179086 0.113784792 892.5842929 441148.0739 0.034859203 0.032865652 487.6729096 -2.688128631 -0.071609169 IPIHNEDITYDELVLMMQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IPIHNEDITYDELVLMMQR 19 0 Q92734-2;Q92734;Q92734-4;Q92734-3;C9JTY3;C9JUE0;C9JJP5 Q92734-2 TFG Protein TFG 0 ; 194.19 3.66E-15 148251000 100572 131448 125781 125075 135108 108626 118020 115128 152229 FALSE TRUE 94277.37805 141180.5467 128764.5847 128284.6363 124497.1627 139984.5628 100323.9966 129501.9842 126820.9965 0.743389349 1.113226915 1.015325445 1.011540989 0.981676269 1.103796427 0.791067721 1.021139936 1 16.95243409 1.751700187 25 0.917517629 1.010990456 0.029791488 0.11789097 8.110693947 15455.09073 0.049227438 0.027298954 56.45471075 -1.751700187 0.093472826 IPLFNTDVDNLEGKT(ph)PPVFASEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IPLFNTDVDNLEGKTPPVFASEGK 24 1 Q96PZ0;Q96PZ0-2 Q96PZ0 PUS7 Pseudouridylate synthase 7 homolog 1 IPLFNTDVDNLEGKT(1)PPVFASEGK 187.43 3.06E-17 39628000 302420 158360 217200 192650 218100 150140 272010 185530 314970 TRUE FALSE 283492.072 170085.1392 222352.0866 197593.7252 200971.3058 193482.9807 231224.6257 208693.8289 262399.4722 1.080383545 0.648191621 0.847380083 0.753026382 0.765898285 0.737360403 0.881193181 0.795328692 1 18.00140529 0.27558157 0.848760911 1.00180762 0.793938645 0.190563062 0.115067852 4.101018874 3.642687358 0.119360319 0.033383418 1.8861732 -0.27558157 -0.207868975 IPMPDFDLHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IPMPDFDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 108.37 0.0020718 283410000 687460 884730 758840 783900 1006240 668720 784300 847430 826810 FALSE TRUE 644433.1058 950236.3298 776840.0432 804016.2011 927213.9694 861768.6082 666701.4961 953233.5009 688810.0696 0.935574455 1.379533157 1.127800068 1.167253843 1.346109777 1.251097576 0.967903237 1.383884387 1 19.39374671 -1.347763019 3.296916833 0.998626032 1.194701035 0.133117367 0.15630147 26993247.86 35087844.31 353350.9787 0.034665944 0.044899032 1.347763019 0.196075003 IPMTPTSSFVSPPPPT(ph)ASPHSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IPMTPTSSFVSPPPPTASPHSNR 23 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 IPMTPTSSFVSPPPPT(0.667)AS(0.33)PHS(0.003)NR 139.15 3.17E-06 372330000 103870 93869 122420 121170 100980 99819 135530 105200 71110 TRUE FALSE 97368.96211 100819.1584 125323.8602 124279.4273 93049.43813 128635.1249 115208.5347 118334.4516 59241.28161 1.643599859 1.70183959 2.115481921 2.097851768 1.570685772 2.171376469 1.944734002 1.997499857 1 15.85431523 -0.910502051 5.908848471 0.999999666 1.915794708 0.654121954 0.20678008 8.63E-07 1.59E-07 0.189939713 0.044769203 0.122884738 0.910502051 0.915795043 IPMTPTSSFVSPPPPTAS(ph)PHSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IPMTPTSSFVSPPPPTASPHSNR 23 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 IPMTPTSSFVSPPPPT(0.073)AS(0.838)PHS(0.089)NR;IPMTPTSSFVSPPPPT(0.215)AS(0.719)PHS(0.066)NR;IPMTPTSSFVSPPPPT(0.054)AS(0.867)PHS(0.08)NR;IPMTPTSSFVSPPPPT(0.274)AS(0.685)PHS(0.041)NR 137.9 3.68E-06 1184350000 338777 300664 334426 306762 283475 296997 355982 294192 185973 TRUE FALSE 317573.5523 322925.4754 342358.7426 314634.0323 261212.017 382735.2126 302605.8039 330922.5188 154932.9049 2.049748906 2.084292395 2.209722608 2.030776048 1.685968628 2.470328772 1.953140969 2.135908567 1 17.24128405 -1.14334923 4.736363437 0.999904974 2.084633221 0.748084262 0.196462852 0.000175819 3.18E-05 0.169641754 0.039981486 0.071887068 1.14334923 1.084728247 IPNFWVTTFVNHPQVSALLGEEDEEALHYLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IPNFWVTTFVNHPQVSALLGEEDEEALHYLTR 32 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 ;; 372.68 2.25E-148 5480090000 843954 1476482 701137 510557 1531741 506817 837346 1326619 385152 FALSE TRUE 791132.4256 1585802.264 717768.3007 523658.757 1411444.241 653126.8404 711793.7408 1492250.302 320867.643 2.465603631 4.942231783 2.236960679 1.632008613 4.398836316 2.035502347 2.218340666 4.650672434 1 18.29161879 -1.317978999 0.284028134 8.20E-50 3.28823068 0.178948819 1.227269286 33.74411115 2.018060931 33.36923197 1.445832754 0.04808626 1.317978999 3.28823068 IPNIYAIGDVVAGPMLAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IPNIYAIGDVVAGPMLAHK 19 0 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 180.14 3.43E-14 75784000 145020 139130 133980 124620 194300 132010 138690 137520 199880 FALSE TRUE 135943.4571 149431.33 137158.0689 127817.9602 179040.4618 170119.144 117894.722 154689.6747 166518.7367 0.816385349 0.89738448 0.823679494 0.767589058 1.075197094 1.021621635 0.707996736 0.928962577 1 17.34532499 IPNSYEVLFPES(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IPNSYEVLFPESPAR 15 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 IPNSYEVLFPES(1)PAR 104.21 0.0014812 28868000 23775 24990 22632 21250 24569 19770 26081 24784 34766 TRUE FALSE 22286.96519 26840.2856 23168.84173 21795.31098 22639.44985 25477.27806 22170.39617 27878.33696 28963.33 0.769489047 0.926698884 0.799937083 0.752513988 0.781659079 0.879639118 0.765464336 0.962539078 1 14.82193986 1.130168305 5.526327627 0.996460509 0.819279132 0.625034274 0.054852861 0.139411864 5.838001653 0.052326207 0.013238304 13.49485757 -1.130168305 -0.177181376 IPNYQLS(ph)PTKLPSINK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IPNYQLSPTKLPSINK 16 1 O60934;A0A0C4DG07 O60934 NBN Nibrin 1 IPNYQLS(0.851)PT(0.149)KLPSINK 177.67 7.66E-09 139210000 542940 299710 410270 381630 388280 311130 563180 368220 463490 TRUE FALSE 508958.3546 321900.8402 420001.7981 391423.2719 357786.055 400948.1802 478736.3873 414193.0776 386130.5247 1.318099249 0.833658102 1.087719751 1.013707145 0.926593554 1.038374732 1.239830463 1.072676339 1 18.55872908 1.976802762 23.72114846 1.132888261 1.011755931 0.021693565 0.137966745 734.1014939 750679.2964 0.051262275 0.033364105 94.79878304 -1.976802762 -0.12113233 IPNYQLSPT(ph)KLPSINK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IPNYQLSPTKLPSINK 16 1 O60934;A0A0C4DG07 O60934 NBN Nibrin 1 IPNYQLS(0.32)PT(0.68)KLPSINK 167.69 3.97E-08 135010000 459860 263880 339800 297070 303410 261170 467190 272720 358550 TRUE FALSE 431078.1835 283417.9498 347860.2165 304693.3191 279581.4025 336565.5393 397139.1967 306769.6923 298705.6887 1.443153578 0.948820061 1.164558392 1.020045251 0.935976157 1.126746333 1.329533423 1.026996485 1 18.18836519 1.999309752 24.99781667 1.17362857 1.081690148 0 0.168708904 74.35067189 2692715.081 0.058637727 0.042800632 99.84119081 -1.999309752 -0.091938421 IPPNATLVFEVELFEFKGEDLTEEEDGGIIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IPPNATLVFEVELFEFKGEDLTEEEDGGIIRR 32 2 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;; 230.32 7.60E-37 730953000 311934 288887 324372 361717 502848 276240 404155 305520 538286 FALSE TRUE 292410.6078 310276.4941 332066.257 370999.2706 463356.3465 355986.0036 343555.7097 343664.8445 448442.5891 0.652058067 0.691897919 0.740487779 0.827306058 1.033256782 0.793827376 0.766108568 0.766351932 1 18.77456377 6.330781518 0.325468773 0.871288933 1.70E-13 0.40792112 0.09389843 22.02277596 0.830402087 0.091311532 9.290658062 2141812.843 -6.330781518 -0.871288933 IPPYHYIHVLDQNSNVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IPPYHYIHVLDQNSNVSR 18 0 Q14764;H3BQK6;H3BP76;H3BRL2;H3BNF6;H3BUK7;H3BQE7;H3BUP3;H3BNF2;H3BPZ2 Q14764 MVP Major vault protein 0 ; 234.57 5.23E-24 349810000 236347 197253 185933 181624 214547 142918 229035 170730 226448 FALSE TRUE 221554.4632 211857.8174 190343.4186 186284.7793 197697.3441 184176.1065 194693.328 192046.0163 188652.3659 1.174405962 1.123006416 1.008963856 0.987450003 1.047945215 0.976272445 1.032021661 1.01798891 1 17.52537067 4.233321479 1.601605943 1.010734144 1.17680712 0.885145641 0.021117632 0.138028238 0.602256221 0.005368515 0.02648774 17112.81593 -4.233321479 0.166072977 IPQSHIQQICETILTSGENLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IPQSHIQQICETILTSGENLAR 22 0 O43813;E9PHS0 O43813 LANCL1 LanC-like protein 1 0 273.41 2.24E-45 761720000 156900 153230 158130 161500 159160 155450 184560 136940 199010 FALSE TRUE 147079.9091 164575.3086 161880.9183 165644.3634 146660.2156 200325.8915 156886.9414 154037.2604 165793.9453 0.88712473 0.992649691 0.976398251 0.999097784 0.884593314 1.208282311 0.946276663 0.929088575 1 17.3390318 IPRPS(ph)VSQGCS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IPRPSVSQGCSR 12 1 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4M5;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 2 IPRPS(0.812)VS(0.188)QGCS(1)R 95.662 0.070793 174560000 142220 179220 159570 166780 186110 110420 236040 160670 218940 TRUE FALSE 133318.7041 192489.6353 163355.0758 171059.8572 171493.6713 142296.4615 200647.9933 180730.0032 182397.4996 0.730923968 1.05533045 0.895599315 0.937841021 0.94021942 0.780144804 1.100058903 0.990857899 1 17.47672643 1.693598243 12.62781363 1.033240521 0.913551516 0.309498099 0.094442597 0.161545697 37.60561611 0.041127566 0.022541312 49.38536213 -1.693598243 -0.119689004 IPRPSVS(ph)QGCS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IPRPSVSQGCSR 12 1 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4M5;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 2 IPRPS(0.017)VS(0.983)QGCS(1)R 51.487 0.088419 269830000 386890 478900 397060 406290 485860 301310 578400 404360 584790 TRUE FALSE 362675.2455 514358.2543 406478.4507 416716.0892 447702.5155 388293.3056 491674.2896 454845.2361 487184.7711 0.744430588 1.055776545 0.834341455 0.855355327 0.918958354 0.797014457 1.009215227 0.933619569 1 18.89410951 1.665522915 10.70144128 0.977970448 0.887174748 0.263172464 0.085135912 0.184118028 29.56031009 0.038456588 0.020797905 46.293809 -1.665522915 -0.0907957 IPRPSVSQGCS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IPRPSVSQGCSR 12 1 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4M5;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 IPRPSVSQGCS(1)R 94.569 0.0039581 916370000 659590 548850 668110 727750 674690 730650 641270 642440 715900 TRUE FALSE 618307.4393 589487.4251 683957.8847 746425.2971 621702.569 941576.7939 545117.5168 722650.0482 596411.6651 1.036712518 0.988390167 1.146788242 1.251526992 1.042405113 1.578736381 0.913995397 1.211663169 1 19.18594895 3.828542737 2.864770071 1.169623752 1.014378801 0.109730788 0.178767329 0.539327782 8.671109956 0.043845424 0.08808401 6738.181996 -3.828542737 -0.155244951 IPS(ph)PNILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IPSPNILK 8 0 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 IPS(1)PNILK;IPS(1)PNILK;IPS(1)PNILK;IPS(1)PNILK 123.51 0.0014102 1547690000 5209280 4420110 4899920 4621940 5133960 3782290 5784160 4387520 6844450 TRUE FALSE 4883240.464 4747379.544 5016148.416 4740546.805 4730759.491 4874175.723 4916878.906 4935311.53 5702067.078 0.856398284 0.832571676 0.879707016 0.831373384 0.829656934 0.854808556 0.862297626 0.865530248 1 22.44305358 0.097838212 0.879561239 1.002126103 0.84844177 0.907051389 0.015064891 1.333728639 1.061758192 0.022399177 0.004785439 1.25267443 -0.097838212 -0.153684333 IPSIVS(ph)SPLNSPLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IPSIVSSPLNSPLDR 15 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 IPSIVS(0.694)S(0.306)PLNSPLDR;IPSIVS(0.685)S(0.315)PLNSPLDR;IPSIVS(0.575)S(0.425)PLNSPLDR 155.28 2.44E-06 141784000 122656 130616 141242 134189 138598 109675 130981 119498 127547 TRUE FALSE 114979.1799 140286.9445 144592.3269 137632.5169 127713.0722 141336.3921 111341.615 134417.5883 106258.5817 1.08206959 1.320241079 1.360759052 1.295260248 1.201908308 1.330117434 1.04783645 1.265004541 1 16.69721984 1.743978619 20.39439096 1.117478229 1.281201355 0.338859034 0.103709055 0.319981404 1211.524308 0.044575902 0.024699764 55.45984081 -1.743978619 0.163723126 IPSIVSS(ph)PLNSPLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IPSIVSSPLNSPLDR 15 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 IPSIVS(0.437)S(0.563)PLNSPLDR 150.39 3.35E-06 84505000 56790 63483 68190 61458 61078 55821 63578 54096 59418 TRUE FALSE 53235.61527 68183.34737 69807.499 63035.11633 56281.18026 71935.61652 54045.06913 60850.00468 49500.75195 1.075450638 1.377420437 1.410231083 1.273417349 1.136976269 1.453222703 1.091802993 1.22927435 1 15.59516282 1.006093876 0.682933129 1.002067789 1.31300279 0.280704354 0.12967859 0.837223897 0.908778097 0.120254927 0.048448483 10.14130575 -1.006093876 0.310935001 IPSKEEEADMS(ph)SPTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IPSKEEEADMSSPTQR 16 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 IPSKEEEADMS(0.609)S(0.389)PT(0.002)QR;IPSKEEEADMS(0.499)S(0.499)PT(0.001)QR;IPS(0.001)KEEEADMS(0.495)S(0.495)PT(0.009)QR 139.98 2.65E-06 4325700000 4831010 3945767 4346330 4633944 5076760 2525765 3375423 2622322 3928965 TRUE FALSE 4528645.708 4237915.694 4449427 4752858.848 4678051.748 3254912.353 2869309.657 2949724.674 3273195.359 1.38355497 1.294733503 1.359352715 1.452054744 1.429200287 0.994414325 0.876608128 0.90117587 1 21.64226828 2.169486031 5.012242192 0.919485518 1.371440522 0.941908839 0.054427278 0.046468451 2.199638734 0.022082118 0.016257225 147.7358963 -2.169486031 0.451955004 IPSKEEEADMSS(ph)PTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 IPSKEEEADMSSPTQR 16 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 IPSKEEEADMS(0.003)S(0.986)PT(0.01)QR;IPSKEEEADMS(0.004)S(0.995)PT(0.002)QR;IPSKEEEADMS(0.002)S(0.868)PT(0.131)QR;IPSKEEEADMS(0.047)S(0.953)PTQR;IPSKEEEADMS(0.049)S(0.949)PT(0.002)QR;IPSKEEEADMS(0.037)S(0.962)PT(0.001)QR;IPSKEEEADMS(0.029)S(0.97)PT(0.001)QR;IPSKEEEADMS(0.027)S(0.972)PT(0.001)QR;IPSKEEEADMS(0.028)S(0.971)PT(0.001)QR;IPSKEEEADMS(0.262)S(0.735)PT(0.002)QR;IPSKEEEADMS(0.017)S(0.982)PT(0.002)QR;IPSKEEEADMS(0.035)S(0.964)PT(0.001)QR;IPSKEEEADMS(0.135)S(0.864)PTQR;IPSKEEEADMS(0.008)S(0.989)PT(0.004)QR 209.71 7.00E-12 31929020000 20096560 17203990 18488520 21062580 21967360 11296750 15050190 11936790 17099810 TRUE FALSE 18838752.18 18477791.32 18927076.43 21603081.46 20242132.16 14557938.34 12793553.73 13427124.51 14245741.24 1.322412914 1.297074754 1.328612959 1.516458926 1.42092516 1.021915118 0.898061639 0.942536038 1 23.76402735 2.158809861 4.814388334 0.94257674 1.365787908 0.902548168 0.067338374 0.064570912 2.696112803 0.028258212 0.020703643 144.1484114 -2.158809861 0.423211169 IPSTENSSQEISVEERT(ph)PTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IPSTENSSQEISVEERTPTK 20 1 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 IPSTENSSQEISVEERT(0.99)PT(0.01)K;IPSTENSSQEISVEERT(0.995)PT(0.005)K;IPSTENSSQEISVEERT(0.872)PT(0.127)K 196.55 2.82E-21 1038400000 619400 469090 553260 513526 584130 419393 663480 531810 786970 TRUE FALSE 580632.8597 503821.9117 566383.5885 526703.9466 538254.7861 540464.9508 563997.3334 598207.6492 655619.623 0.88562459 0.768466797 0.863890537 0.803368185 0.820986388 0.824357496 0.860250843 0.912430971 1 19.32249951 1.032664398 1.357357563 0.999497681 0.823173332 0.75847667 0.031680109 0.184575261 0.695204246 0.026583492 0.008066142 10.78113285 -1.032664398 -0.176324349 IPTPVIHTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IPTPVIHTK 9 0 P12532;P12532-2 P12532 CKMT1A "Creatine kinase U-type, mitochondrial" 0 ; 163.94 6.26E-05 1970190000 1943290 1841450 1748720 1740600 2296060 1435070 2003810 1969610 2343690 FALSE TRUE 1821662.948 1977792.874 1790200.464 1785266.743 2115736.709 1849351.413 1703357.293 2215520.144 1952512.998 0.932983775 1.012947353 0.916869934 0.914343077 1.083596735 0.947164713 0.872392294 1.134701867 1 20.89690072 1.233839935 24.99998571 1.067350907 0.954925651 0.334979598 0.066201473 142.9570444 757032.73 0.054126508 0.015261364 17.13325723 -1.233839935 -0.112425255 IPVHPNDHVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IPVHPNDHVNK 11 0 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 ;;;;; 157.68 1.76E-05 2433680000 4385680 3639460 3868750 3530580 4620230 3291830 4081960 3727220 5931260 FALSE TRUE 4111188.117 3908929.405 3960518.577 3621180.66 4257375.773 4242127.883 3469907.993 4192571.622 4941294.389 0.832006311 0.791073977 0.801514394 0.732840502 0.861591202 0.858505393 0.702226526 0.848476389 1 22.23645758 0.981956479 24.71696356 1.000000003 0.794213895 0.620168757 0.049880848 668.6097864 915898.4108 0.045564376 0.011391094 9.593044948 -0.981956479 -0.205786108 IPYQS(ph)PVSSSESAPGTIMNGHGGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IPYQSPVSSSESAPGTIMNGHGGGR 25 0 Q5T6F2;H0YDN2 Q5T6F2 UBAP2 Ubiquitin-associated protein 2 1 IPY(0.003)QS(0.925)PVS(0.049)S(0.008)S(0.014)ESAPGTIMNGHGGGR 87.644 0.010152 158660000 27206 32560 31577 30594 36041 29518 38471 26622 38205 TRUE FALSE 25503.22502 34970.77628 32326.02135 31379.09384 33210.48524 38039.36742 32702.6307 29945.8153 31828.33869 0.80127415 1.098730808 1.015636464 0.985885382 1.04342503 1.195141468 1.02746898 0.94085386 1 14.95802424 4.746255447 24.83911752 1.045779178 0.801274021 0.535027452 0.06916541 674.0095182 2175664.634 0.015988784 0.17171493 55751.3576 -4.746255447 -0.244505157 IQAGEIGEMKDGVPEGAQLQGPVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IQAGEIGEMKDGVPEGAQLQGPVHR 25 1 P16989;P16989-3 P16989 YBX3 Y-box-binding protein 3 0 57.922 0.053878 41707000 19567 20396 22880 23625 25995 18756 24953 21127 30495 FALSE TRUE 18342.3364 21906.14106 23422.7244 24231.2575 23953.45756 24170.55272 21211.5293 23764.75246 25405.18749 0.721991774 0.862270395 0.921966209 0.953791721 0.942856949 0.951402257 0.83492906 0.935429131 1 14.63283549 5.014492294 1.244350286 0.92376151 0.511397037 0.714488119 0.042294314 1.530825899 1.305147343 0.011924594 0.950774537 103393.2755 -5.014492294 -0.412364473 IQALGLHLPDPPLES(ph)EDEDEEGATALNNHSSIPMDPEHVELVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IQALGLHLPDPPLESEDEDEEGATALNNHSSIPMDPEHVELVK 43 0 A0A2R8Y7W8;A0A2R8Y6W5;Q16626 A0A2R8Y7W8 MEA1 Male-enhanced antigen 1 1 IQALGLHLPDPPLES(0.76)EDEDEEGAT(0.159)ALNNHS(0.04)S(0.04)IPMDPEHVELVK;IQALGLHLPDPPLES(1)EDEDEEGATALNNHSSIPMDPEHVELVK;IQALGLHLPDPPLES(1)EDEDEEGATALNNHSSIPMDPEHVELVK 250.77 2.83E-56 726514000 67264 119977 118526 125399 127286 98192.2 170528 122959 130763 TRUE FALSE 63054.06631 128860.2219 121337.4927 128616.9506 117289.471 126538.6941 144958.9095 138310.7018 108937.8105 0.578807909 1.182878757 1.113823493 1.180645636 1.076664479 1.161568178 1.330657453 1.269629903 1 16.73314525 4.738967343 24.90114477 1.175915825 0.578807722 0.796451358 0.092889825 13.84293635 847212.8132 0.022344285 0.131328552 54823.57383 -4.738967343 -0.597108103 IQAQFGPLAQLS(ph)PQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IQAQFGPLAQLSPQER 16 0 P51692 P51692 STAT5B Signal transducer and activator of transcription 5B 1 IQAQFGPLAQLS(1)PQER;IQAQFGPLAQLS(1)PQER 110.26 0.00095288 94834000 54694 60895 69192 80217 69782 53789 60062 49165 62178 TRUE FALSE 51270.80017 65403.72916 70833.26691 82275.50403 64301.60321 69317.01111 51056.26069 55303.35848 51800.09011 0.989782065 1.262618058 1.367435206 1.58832743 1.241341532 1.33816391 0.985640384 1.067630546 1 15.66066699 1.736857524 7.116651871 1.022779387 1.310994796 0.442629815 0.147442352 0.117021838 17.61647804 0.071254947 0.037580587 54.55788479 -1.736857524 0.288215409 IQDFNDTFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IQDFNDTFYR 10 0 Q8TBC4;F8W8D4;Q8TBC4-2 Q8TBC4 UBA3 NEDD8-activating enzyme E1 catalytic subunit 0 ; 153.97 3.56E-05 78858000 114375 143608 136788 126622 162714 104026 138147 132445 135797 FALSE TRUE 107216.4729 154240.8857 140032.676 129871.3349 149935.0988 134056.6175 117433.1398 148981.0498 113131.6034 0.947714606 1.36337576 1.237785656 1.14796689 1.325315776 1.184961703 1.038022412 1.316882686 1 16.78764248 -0.315495448 0.38325029 0.952639054 1.22618217 0.132443965 0.133183125 11.24372895 1.821604939 0.892097699 0.092118406 0.483620333 0.315495448 0.273543116 IQDKEGIPPDQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IQDKEGIPPDQQR 13 1 M0R2S1;P62987;P0CG48;Q96C32;Q5PY61;J3QKN0;F5GXK7;F5H747;F5H388;B4DV12;F5H265;F5H2Z3;F5GYU3;F5H6Q2;M0R1M6;J3QTR3;J3QS39;P0CG47;F5GZ39;Q49A90;M0R1V7;J3QSA3;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 0 111.74 0.00087167 100210000 176860 185490 229060 223450 259400 164910 282120 128620 228880 FALSE TRUE 165790.6483 199223.8726 234493.4114 229184.1053 239027.7704 212516.8399 239818.7251 144678.4901 190678.4494 0.869477641 1.044815884 1.229784552 1.201940261 1.253564685 1.114529936 1.257712793 0.758756381 1 17.54078227 -1.454927129 8.07728952 0.999995289 1.119086931 0.004881242 0.16802774 1.32E-05 8.88E-07 0.150193778 0.035399613 0.035081073 1.454927129 0.119091643 IQDPTEDAEAEDT(ph)PR ddPTM_SK-BR-3_Pertuzumab_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 185.25 4.82E-06 462000000 310630 295950 358640 305280 333010 296480 405110 306560 365010 TRUE FALSE 291188.2228 317862.4459 367147.1102 313114.0016 306856.7379 382068.963 344367.5164 344834.6908 304087.4729 0.957580462 1.045299377 1.207373348 1.029683987 1.009106804 1.25644427 1.132462028 1.133998344 1 18.21412686 2.267238379 24.99997176 1.144863887 1.069765215 0.141896827 0.088890439 412.683331 359757.2005 0.030322332 0.025365401 185.028394 -2.267238379 -0.075098671 IQEIIEQLDVTTSEYEKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IQEIIEQLDVTTSEYEKEK 19 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;;; 209.67 1.94E-16 1128822000 1425020 993317 1052320 1017939 1619602 721597 1079361 1046190 2612882 FALSE TRUE 1335830.542 1066863.224 1077281.527 1044061.038 1492404.992 929910.3398 917520.8383 1176809.124 2176775.114 0.613674115 0.490111825 0.494897943 0.479636611 0.685603663 0.42719633 0.421504653 0.540620442 1 21.05376094 0.950448009 22.5799429 1.000000001 0.505685927 0.778774627 0.080495993 1997.547573 910247.6414 0.074778059 0.018694515 8.921708091 -0.950448009 -0.494314074 IQEQES(ph)S(ph)GEEDSDLSPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IQEQESSGEEDSDLSPEER 19 0 P41236;E7EMN6;Q6NXS1 P41236 PPP1R2;PPP1R2P3 Protein phosphatase inhibitor 2;Protein phosphatase inhibitor 2-like protein 3 2 IQEQES(1)S(1)GEEDSDLSPEER;IQEQES(1)S(1)GEEDSDLSPEER 218.88 4.77E-19 3411200000 627620 646330 613210 647950 655920 513330 719870 538970 698870 TRUE FALSE 588338.3845 694184.9457 627755.6308 664577.494 604406.6891 661520.0378 611932.1764 606261.5909 582224.0821 1.010501631 1.192298579 1.078202792 1.141446248 1.038099776 1.136194909 1.05102519 1.041285666 1 19.15121499 1.282794077 0.782526695 0.998325475 1.112529144 0.268484665 0.053157367 0.640605623 0.880081618 0.044929961 0.01776585 19.17759211 -1.282794077 0.114203669 IQEQES(ph)SGEEDSDLSPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IQEQESSGEEDSDLSPEER 19 0 P41236;E7EMN6;Q6NXS1 P41236 PPP1R2;PPP1R2P3 Protein phosphatase inhibitor 2;Protein phosphatase inhibitor 2-like protein 3 1 IQEQES(0.706)S(0.294)GEEDSDLSPEER 248.91 6.40E-25 361460000 441940 476040 472090 488480 560600 446990 508280 460040 591790 TRUE FALSE 414279.7643 511286.4969 483288.1977 501015.2238 516572.7374 576028.7567 432068.1326 517477.0067 493016.4259 0.840296068 1.037057733 0.980267943 1.016224202 1.047779973 1.1683764 0.876376749 1.049614129 1 18.91127619 4.742786321 24.53480132 1.016162394 0.840295978 0.383055966 0.072121869 358.5408862 2081615.755 0.016295707 0.126095012 55307.79206 -4.742786321 -0.175866416 IQES(ph)EVFRVTSTEFISLRIDSSDEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IQESEVFRVTSTEFISLRIDSSDEDR 26 2 A0A0D9SGJ6;J3KQV8;O43426;J3KPK1;C9JFZ1;O43426-4;O43426-2;C9J1Z6;C9JW66;O43426-5 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 IQES(0.171)EVFRVT(0.041)S(0.148)T(0.148)EFIS(0.148)LRIDS(0.171)S(0.171)DEDR 46.464 0.077133 297610000 84756 122700 109090 132480 155470 89624 161420 127700 121900 TRUE FALSE 79451.27325 131784.8357 111677.6663 135879.6611 143260.0133 115496.9939 137216.5695 143643.6261 101554.1025 0.782354147 1.297681063 1.099686409 1.338002678 1.41067677 1.137295206 1.351167173 1.414454193 1 16.631889 4.741265669 24.65631131 1.260995654 0.782353939 0.538531344 0.137760654 154.2214154 1405620.515 0.030180704 0.207770814 55114.47424 -4.741265669 -0.478641715 IQESHPELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IQESHPELR 9 0 Q9H9B4 Q9H9B4 SFXN1 Sideroflexin-1 0 ; 132.25 0.00031033 496570000 475230 440180 362890 289810 891530 468670 292430 646220 1065430 FALSE TRUE 445486.2026 472771.3852 371497.9222 297247.0152 821512.8301 603967.4208 248582.8363 726901.9895 887602.8501 0.501898121 0.532638426 0.418540704 0.334887405 0.925541001 0.680447816 0.280060881 0.818949589 1 19.75955477 -5 0.204723203 3.206910607 0.461945494 0.362147242 0.195478363 160.1786025 1.59193995 144.3294395 0.435660354 1.00E-05 5 -2.744965113 IQFKPDDGISPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IQFKPDDGISPER 13 1 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ; 127.36 0.00016223 461220000 706440 606100 621920 619980 673390 485350 743300 585180 769800 FALSE TRUE 662225.1814 650976.2746 636672.2361 635889.7364 620504.6657 625462.666 631849.0655 658241.0111 641315.4069 1.03260451 1.015064144 0.992759926 0.991539778 0.967549912 0.975280898 0.98523918 1.026392013 1 19.29067454 4.32691358 1.190649678 0.988008434 1.037328404 0.437073624 0.015761881 0.72832866 1.40158899 0.004616644 0.037332115 21228.22003 -4.32691358 0.04931997 IQFKPDDGTTPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IQFKPDDGTTPER 13 1 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 ;;;; 138.77 4.13E-05 4609100000 4656970 4009360 4309400 4379960 4628970 3472480 5232770 4011840 5791780 FALSE TRUE 4365498.561 4306217.186 4411621.003 4492357.189 4265429.369 4474928.605 4448164.717 4512727.055 4825094.502 0.904748821 0.892462766 0.914307689 0.93104025 0.884009498 0.927428179 0.921881367 0.935261901 1 22.20212577 -2.428549212 0.213968617 1.130294204 0.894729335 0.820940146 0.01339945 15.35830766 0.411072358 0.967345978 0.027652932 0.003727784 2.428549212 -0.235564868 IQFTSLYHKEEAPAS(ph)PLRPLYPQIS(ph)PLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IQFTSLYHKEEAPASPLRPLYPQISPLK 28 2 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 2 IQFT(0.116)S(0.111)LY(0.01)HKEEAPAS(0.759)PLRPLY(0.022)PQIS(0.982)PLK;IQFTSLYHKEEAPAS(1)PLRPLYPQIS(1)PLK 190.29 2.75E-18 896290000 664140 689810 758040 787850 1085030 585460 1082020 801800 1370020 TRUE FALSE 622572.6629 740884.2501 776021.0668 808067.5648 999816.1206 754472.7979 919781.146 901906.495 1141354.811 0.54546812 0.649127022 0.679912205 0.7079898 0.87599063 0.661032652 0.805867848 0.790206942 1 20.12231592 2.119820875 0.064098758 1.518721379 1.53E-18 0.768991095 0.061962825 15.44735186 0.674410129 7.127237816 8.402328899 131.7713134 -2.119820875 -1.518721379 IQFTSLYHKEEAPAS(ph)PLRPLYPQISPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IQFTSLYHKEEAPASPLRPLYPQISPLK 28 2 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 1 IQFTSLYHKEEAPAS(1)PLRPLYPQISPLK 180.36 7.80E-18 369590000 414620 439870 416860 464940 679890 333480 616820 490540 808230 TRUE FALSE 388669.6743 472438.4325 426748.1161 476871.1475 626494.1819 429750.2624 524333.5673 551784.9988 673331.1916 0.577234026 0.701643468 0.633786347 0.708226729 0.930439863 0.638244994 0.778715696 0.819485278 1 19.36095677 -4.999999998 0.066619312 2.039711305 0.324593568 0.618368257 0.082491674 219.7518506 1.059935474 35.47100525 4.885787965 1.00E-05 4.999999998 -1.715117738 IQHEELNNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IQHEELNNR 9 0 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ;; 120.76 0.00063282 1049780000 501400 745410 605430 603260 688500 507090 675050 602250 711460 FALSE TRUE 470018.269 800600.932 619791.0855 618740.6729 634427.9873 653478.6511 573832.5194 677442.2382 592712.7298 0.792995064 1.350740235 1.045685463 1.043913251 1.070380229 1.102521708 0.968146103 1.142952065 1 19.17697352 3.699925558 24.22124644 1.050355274 1.137658473 0 0.143469128 694.8959449 618893.5184 0.034635035 0.053675131 5011.013335 -3.699925558 0.087303199 IQHILCTGNLCTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IQHILCTGNLCTK 13 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ; 223.06 1.64E-11 985710000 1336060 1309940 1208680 1203380 1417670 1052120 1569180 1306080 1561380 FALSE TRUE 1252438.39 1406929.321 1237350.46 1234260.768 1306331.917 1355849.964 1333896.027 1469146.963 1300775.591 0.962839707 1.081608027 0.951240528 0.948865259 1.004271548 1.042339642 1.025462067 1.129439215 1 20.31094066 2.024154848 1.909662422 1.056702949 0.995171898 0.257385484 0.049650393 0.53257373 3.644631225 0.028523513 0.014919415 105.7194385 -2.024154848 -0.061531051 IQHPSNVLHFFNAPLEVTEENFFEICDELGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IQHPSNVLHFFNAPLEVTEENFFEICDELGVK 32 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;; 301.68 4.88E-90 1543950000 365593 601102 529402 491022 665336 502379 746568 530913 518007 FALSE TRUE 342711.1867 645608.2175 541959.6654 503622.4558 613083.1944 647407.6619 634627.0592 597198.6567 431548.2852 0.794143317 1.496027767 1.255849424 1.167012993 1.420659554 1.500197507 1.470581812 1.383851303 1 18.71916246 2.724189469 23.7588099 1.402923422 1.244151783 0.082981052 0.223383546 921.869731 1524058.411 0.06665643 0.063152014 529.8945697 -2.724189469 -0.15877164 IQHSITAQDHQPTPDSCIISMVVGQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IQHSITAQDHQPTPDSCIISMVVGQLK 27 0 P61970;H3BRV9 P61970 NUTF2 Nuclear transport factor 2 0 ; 115.95 0.00040497 221234000 283720 304380 270910 234750 295950 198603 343340 267140 278400 FALSE TRUE 265962.4717 326916.6119 277336.1131 240774.0824 272707.2808 255936.462 291859.3544 300493.017 231933.2415 1.146719935 1.409528922 1.195758363 1.038118042 1.175800757 1.103491938 1.258376559 1.295601334 1 17.82335008 3.648401278 4.640410978 1.160287648 1.298642033 0.183788577 0.109390266 0.288040644 11.27917411 0.027745945 0.044488121 4450.422861 -3.648401278 0.138354386 IQIISTDSAVAS(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IQIISTDSAVASPQR 15 0 P49116;P49116-2;C9J2Y1;C9JMI6;C9JKS0 P49116 NR2C2 Nuclear receptor subfamily 2 group C member 2 1 IQIISTDSAVAS(1)PQR;IQIISTDSAVAS(1)PQR;IQIISTDSAVAS(1)PQR;IQIISTDSAVAS(1)PQR 236.82 1.07E-17 334741000 356757 381471 384072 351238 437730 362189 478070 419355 442487 TRUE FALSE 334428.2162 409715.5098 393182.3692 360251.3617 403352.4515 466747.0847 406387.8417 471712.3949 368633.0611 0.907211673 1.111445372 1.066595514 0.977262757 1.094184147 1.266156332 1.102418325 1.279625852 1 18.49182594 2.471755682 24.92497412 1.168379141 1.03965577 0.330381949 0.095424431 163.6391121 760152.0154 0.029599496 0.024841215 296.3163952 -2.471755682 -0.128723371 IQLVEEELDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 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 ;;;;;;;;;;;; 237.51 8.27E-12 6455658000 2049295.6 2228077 2139857.3 2058100 2161672 1953457.8 2389666.4 1945786.6 1689964.4 FALSE TRUE 1921033.846 2393046.139 2190615.726 2110914.33 1991903.001 2517389.355 2031358.108 2188722.34 1407898.424 1.364469065 1.699729255 1.555947282 1.499337093 1.414805903 1.788047569 1.442830018 1.554602451 1 20.42511182 -0.167875758 0.990746644 0.991487089 1.559063703 0.634884695 0.128063293 7.307458819 5.467172724 0.35786599 0.035489764 0.679397966 0.167875758 0.567576614 IQLVEEELDRAQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 261.39 1.52E-24 7422150000 2281410 3529770 2963970 3209890 4148950 2271420 3156630 2682510 4743360 FALSE TRUE 2138620.621 3791117.844 3034276.768 3292261.212 3823108.203 2927142.081 2683322.636 3017427.278 3951662.573 0.54119515 0.959372865 0.767848143 0.833133182 0.967468283 0.740736849 0.679036377 0.763584244 1 21.91402833 -1.48313908 8.580312733 1.000007606 0.793002388 0.227652183 0.124879031 1.73E-05 1.04E-06 0.115121582 0.027133421 0.032874634 1.48313908 -0.207005217 IQNS(ph)DDEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IQNSDDEER 9 0 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 IQNS(1)DDEER;IQNS(1)DDEER 192.99 3.58E-05 1295630000 1504060 1175610 1436220 1269280 1091960 1453390 1528460 1118780 777790 TRUE FALSE 1409923.569 1262653.388 1470287.817 1301851.874 1006201.866 1872960.099 1299281.613 1258462.146 647971.8243 2.175902588 1.948623907 2.269061341 2.009118028 1.552848177 2.890496205 2.005151403 1.94215566 1 19.30557156 3.053089857 24.97564989 2.004125886 2.115183746 0.019590442 0.478019216 641.1804653 301632.9377 0.126943817 0.151726862 1130.029698 -3.053089857 0.11105786 IQNS(ph)PQKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IQNSPQKK 8 1 X6R7X0;Q96MN5 X6R7X0 TCEANC2 Transcription elongation factor A N-terminal and central domain-containing protein 2 1 IQNS(1)PQKK 72.652 0.02793 177770000 463630 220010 286150 272830 327200 199960 378860 264730 372810 TRUE FALSE 434612.2259 236299.7693 292937.6131 279831.2797 301503.0319 257685.2059 322053.4602 297782.1232 310585.6026 1.399331528 0.7608201 0.94317834 0.900979561 0.970756627 0.829675309 1.036923339 0.958776327 1 18.24463143 -1.129580534 6.977536962 1.000000042 0.950607673 0 0.170762442 9.82E-08 1.23E-08 0.146018471 0.034416855 0.074202659 1.129580534 -0.049392369 IQNTGDY(ph)YDLYGGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IQNTGDYYDLYGGEK 15 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 1 IQNT(0.001)GDY(0.499)Y(0.499)DLY(0.001)GGEK 122.45 0.0011898 0 50969 46969 42651 47633 53734 44636 50119 41753 59303 TRUE FALSE 47778.94127 50446.63363 43662.70186 48855.34342 49513.94839 57521.6886 42604.12123 46965.95396 49404.94619 0.967088216 1.021084679 0.883771874 0.988875552 1.002206301 1.164290077 0.862345261 0.950632631 1 15.59236786 -2.44103945 2.147927751 1.214358208 0.975800933 0.003470756 0.081987707 8475767.024 1582532.397 8732753.19 0.019041519 0.003622101 2.44103945 -0.238557275 IQNTGDYY(ph)DLYGGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IQNTGDYYDLYGGEK 15 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 1 IQNTGDY(0.227)Y(0.773)DLYGGEK 229.75 4.34E-12 66298000 153330 134190 127870 136320 155410 113930 173900 137410 194300 TRUE FALSE 143733.349 144125.5672 130903.1368 139818.202 143204.7255 146819.7415 147825.3094 154565.941 161870.0748 0.887955042 0.890378085 0.808692632 0.863768069 0.884689315 0.907022139 0.913234331 0.954876565 1 17.30447677 1.387712153 0.806834314 0.998599044 0.859439267 0.786464536 0.023534931 0.260947876 0.366054881 0.023349015 0.009308095 24.41811604 -1.387712153 -0.139159777 IQPAGNTS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IQPAGNTSPR 10 0 P49674;H0Y5S9;H0Y682 P49674 CSNK1E Casein kinase I isoform epsilon 1 IQPAGNT(0.001)S(0.999)PR;IQPAGNT(0.002)S(0.998)PR;IQPAGNT(0.006)S(0.994)PR;IQPAGNT(0.487)S(0.513)PR 160.11 7.84E-06 5396540000 4949200 5969040 5363730 5550240 5859080 4544130 6457810 5123250 4737840 TRUE FALSE 4639438.407 6410993.932 5490960.209 5692668.555 5398931.491 5855946.563 5489521.342 5762899.04 3947063.896 1.175415075 1.624243767 1.391150575 1.442253965 1.367834834 1.483620918 1.390786034 1.460047061 1 21.91234844 -1.604505484 2.506452709 0.955906167 1.432353482 0.572566868 0.112507148 5360906.339 4596988.329 1549340.772 0.026263827 0.024859622 1.604505484 0.476447315 IQPFDDDEDEDIWEDSDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IQPFDDDEDEDIWEDSDTR 19 0 O75170-6;O75170-2;O75170-4;O75170-3;O75170-5;O75170;T1ECW5;A0A0A0MSJ8 O75170-6 PPP6R2 Serine/threonine-protein phosphatase 6 regulatory subunit 2 0 ; 215 9.69E-19 46027000 80359 67842 68161 70675 72038 54905 87324 62803 79595 FALSE TRUE 75329.47363 72865.09227 69777.81111 72488.64015 66380.42607 70755.18219 74230.57688 70644.0928 66310.0803 1.136018435 1.098853929 1.052295681 1.093176781 1.001060861 1.067035085 1.119446343 1.065359784 1 16.01694058 1.339548732 0.00885063 1.44E-07 2.121466012 0.359801426 0.035949518 1954.908864 16.12111762 1939.449304 1922.355365 21.85489538 -1.339548732 2.121465868 IQPGSQQADFLDALIVSMDVIQHETIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IQPGSQQADFLDALIVSMDVIQHETIGK 28 0 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 96.748 0.0015066 33388000 18759 21304 24928 25120 26073 14952 21245 22773 27501 FALSE TRUE 17584.90768 22881.37033 25519.30393 25764.62173 24025.33175 19268.39967 18059.50948 25616.25918 22910.90544 0.767534383 0.998710871 1.113849647 1.124557115 1.04864174 0.841014325 0.788249488 1.118081485 1 14.48374685 2.250300923 24.99570241 0.902369053 1.028278195 0.035291328 0.1327988 387.3378949 824661.4509 0.045573231 0.037838552 177.9512009 -2.250300923 0.125909143 IQPQPPDEDGDHS(ph)DKEDEQPQVVVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IQPQPPDEDGDHSDKEDEQPQVVVLK 26 1 Q96AT1 Q96AT1 KIAA1143 Uncharacterized protein KIAA1143 1 IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK 298.9 9.85E-71 3328530000 4007120 1749518 2406610 2274370 2389600 1717836 3172100 1986457 2904100 TRUE FALSE 3756321.512 1879054.133 2463695.926 2332734.185 2201930.455 2213747.366 2696473.053 2234470.529 2419386.949 1.552592285 0.7766654 1.018314134 0.964184 0.910119176 0.915003434 1.114527403 0.923568894 1 21.2062101 4.749350003 24.99641665 0.956133747 1.552592625 0.824555199 0.08693704 670.3754187 1553068.744 0.021242833 0.314884982 56150.03138 -4.749350003 0.596458878 IQQFDDGGS(ph)DEEDIWEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 210.88 2.34E-16 148330000 505390 349720 403830 416280 428680 334730 517870 356050 446350 TRUE FALSE 473758.542 375613.6327 413409.0383 426962.4496 395013.202 431361.1171 440220.2012 400503.6263 371851.3015 1.274053742 1.010117838 1.111759019 1.14820749 1.062288072 1.160036594 1.183860859 1.077053179 1 18.5043663 0.990653896 23.37684148 0.999999993 1.123642867 0.270171517 0.070687993 248.4565354 621453.0534 0.065450628 0.016362657 9.787097078 -0.990653896 0.123642875 IQQYISHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IQQYISHR 8 0 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ;;; 162.97 0.00033863 1713110000 1238410 1936010 1324700 1182670 1828000 1080280 1567770 1609400 1768260 FALSE TRUE 1160900.129 2079354.195 1356122.51 1213019.314 1684436.254 1392139.299 1332697.443 1810337.133 1473125.983 0.788052171 1.411525029 0.9205747 0.823432163 1.143443449 0.945023926 0.904673096 1.228908562 1 20.49044939 3.737105442 24.77151615 0.982471612 1.150840653 0.032037251 0.189473508 611.9184289 1518204.726 0.044104459 0.078321293 5458.903815 -3.737105442 0.168369041 IQRPNTTQEGEEMETDMDVADVAMES(ph)SPGSSISMEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IQRPNTTQEGEEMETDMDVADVAMESSPGSSISMEHR 37 1 A0A087X1S3 A0A087X1S3 HUWE1 1 IQRPNTTQEGEEMETDMDVADVAMES(0.458)S(0.458)PGS(0.072)S(0.011)IS(0.002)MEHR 76.363 0.0010291 72255000 9440.4 14905 13330 16156 18010 12933 13941 12114 13091 TRUE FALSE 8849.542216 16008.58171 13646.19389 16570.59031 16595.56725 16666.54715 11850.67647 13626.45957 10906.02753 0.811435896 1.467865514 1.251252471 1.51939744 1.521687636 1.528195955 1.086617143 1.249442983 1 13.41283808 1.667196688 8.577365357 1.127062177 1.364819514 0.201593357 0.220675497 0.18525463 22.87540284 0.100571545 0.053043213 46.47256974 -1.667196688 0.237757337 IQRPPEDSIQPYEK ddPTM_SK-BR-3_Pertuzumab_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 ;; 190.44 5.51E-07 2355090000 1478560 1343120 1435510 1372210 1594400 1079740 1731570 1321940 1769260 FALSE TRUE 1386019.569 1442566.002 1469560.975 1407423.232 1469182.256 1391443.41 1471937.154 1486987.119 1473959.076 0.940337891 0.97870153 0.997016131 0.954859097 0.99675919 0.944017668 0.998628237 1.008838809 1 20.49126504 1.573432713 8.447889156 1.003939023 0.97341664 0.385169369 0.019647325 0.127989789 17.82430713 0.009886403 0.004646381 37.4483522 -1.573432713 -0.030522383 IQSQNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IQSQNDR 7 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRU9 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 121.31 0.010353 100180000 106950 144130 115300 122720 133610 107820 130810 141670 136430 FALSE TRUE 100256.1904 154801.5352 118034.9704 125869.203 123116.8096 138945.8837 111196.2549 159357.8114 113658.9516 0.882079141 1.361982782 1.038501313 1.107428858 1.083212609 1.222480779 0.978332576 1.402070044 1 16.79435179 3.766390679 24.87228305 1.114087267 1.169489448 0 0.16749715 1327.551256 840829.9833 0.038113711 0.06870901 5839.701908 -3.766390679 0.055402181 IQSSLSSAS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IQSSLSSASPSK 12 0 Q5W0B1 Q5W0B1 RNF219 RING finger protein 219 1 IQSSLSS(0.001)AS(0.997)PS(0.001)K;IQSSLS(0.001)S(0.004)AS(0.994)PS(0.001)K;IQSSLSSAS(0.998)PS(0.002)K;IQSSLSS(0.001)AS(0.999)PSK 319.82 1.23E-46 680850000 1649930 1164260 1286300 1234120 1375500 946890 1666240 1141160 1200600 TRUE FALSE 1546663.827 1250463.022 1316811.643 1265789.609 1267473.779 1220241.772 1416402.781 1283636.338 1000212.104 1.546335843 1.25019785 1.316532402 1.265521187 1.267204999 1.219983008 1.41610242 1.283364132 1 19.93187454 -2.228026079 1.841214282 0.174692495 1.3138577 0.523615848 0.095925296 1446662.72 233153.1998 4960703.912 0.021545458 0.005915261 2.228026079 1.139165205 IQST(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IQSTPVK 7 0 P62820;E7END7;P62820-2;P62820-3 P62820 RAB1A Ras-related protein Rab-1A 1 IQS(0.035)T(0.965)PVK;IQS(0.035)T(0.965)PVK;IQS(0.474)T(0.526)PVK 153.7 0.019322 1347840000 8780300 5552400 6837500 6547500 6459900 5441000 8557000 6492200 6901700 TRUE FALSE 8230756.696 5963505.473 6999688.729 6715519.935 5952565.512 7011728.373 7273957.289 7302765.461 5749761.683 1.431495277 1.037174374 1.217387627 1.167964918 1.035271693 1.219481564 1.265088484 1.270098808 1 22.45507073 IQTYLQSTKPIIDLYEEMGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IQTYLQSTKPIIDLYEEMGK 20 1 P30085;P30085-3;A0A494BXC7;P30085-2 P30085 CMPK1 UMP-CMP kinase 0 ; 275.5 1.49E-44 325180000 752340 540030 654810 617260 680460 468930 872400 589050 916330 FALSE TRUE 705252.3824 580014.3831 670342.4024 633099.9366 627019.4164 604302.4786 741591.719 662594.1892 763388.6033 0.923844526 0.759789157 0.878114239 0.829328515 0.821363345 0.791605319 0.971447197 0.867964476 1 19.54205812 1.732519417 10.18557095 0.938428184 0.829887574 0.475979896 0.055263163 0.07590539 32.39514015 0.023382156 0.012676255 54.01562645 -1.732519417 -0.108540609 IQVLQQQADDAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 376.2 5.01E-97 1582550000 1361630 1558130 1448500 1466090 1527260 1331340 1717200 1335840 1339620 FALSE TRUE 1276408.009 1673495.566 1482859.104 1503712.351 1407315.16 1715676.246 1459721.802 1502622.565 1116028.768 1.143705293 1.499509345 1.328692545 1.347377769 1.261002584 1.537304678 1.30796073 1.346401283 1 20.08994279 0.377187444 1.720857144 1.000008547 1.363457974 0.483828503 0.111501517 4.737400775 12.18420402 0.094837687 0.026695395 2.383347917 -0.377187444 0.363449427 IQVLQQQADDAEERAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IQVLQQQADDAEERAER 17 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;Q5VU61;P06753-3;P06753-4 P06753-2;P06753-3 TPM3 Tropomyosin alpha-3 chain 0 ;;; 270.42 1.27E-35 852760000 165425 319332 227650 279364 438830 162368 223463 208746 742780 FALSE TRUE 155071.3445 342975.6735 233049.9655 286532.9532 404366.062 209241.0058 189956.7977 234808.3976 618805.2195 0.250597991 0.554254655 0.376612799 0.463042237 0.653462591 0.338137106 0.30697349 0.379454455 1 19.23912584 -1.407221971 3.376706607 1.005738905 0.420870904 0.706468497 0.118393417 130739110 182630199.9 7302221.219 0.027976151 0.039154171 1.407221971 -0.584868001 IQVTPPGFQLVFLPFADDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IQVTPPGFQLVFLPFADDKR 20 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 152.81 9.64E-08 896150000 1419130 1199190 1223370 1087530 1318940 984770 1433640 1248830 1118790 FALSE TRUE 1330309.187 1287979.275 1252388.914 1115437.861 1215355.773 1269057.113 1218678.991 1404749.175 932056.7213 1.427283508 1.381867912 1.343683153 1.196748905 1.303950441 1.361566398 1.307515909 1.507149879 1 19.83005823 -1.534289498 3.050861936 0.98686553 1.346605284 0.650396385 0.081352266 12690863.1 15156605.17 1384822.034 0.019172927 0.029222038 1.534289498 0.359739755 IQYQLVDISQDNALRDEMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 IQYQLVDISQDNALRDEMR 19 1 Q5T123;Q9H299 Q5T123 SH3BGRL3 SH3 domain-binding glutamic acid-rich-like protein 3 0 ;;;;;;;;;;; 317.01 8.87E-62 8807230000 3381585 4090405 3903804 3949748 4350909 3622837 4378487 3670060 5875000 FALSE TRUE 3169937.631 4393262.842 3996404.074 4051105.221 4009206.158 4668691.23 3721973.522 4128275.07 4894424.546 0.647662989 0.897605592 0.816521746 0.827697962 0.819137392 0.953879498 0.760451711 0.843464851 1 22.22270782 -5 0.235688178 1.939613376 0.810019773 0.354662793 0.07868871 196.2644447 1.961696145 88.42497546 0.117909734 1.00E-05 5 -1.129593603 IRDEMVATEQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IRDEMVATEQER 12 1 P16615-5;P16615-2;P16615-3;P16615;H7C5W9;P16615-4 P16615-5 ATP2A2 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 0 101.61 0.0023484 332250000 83714 116290 97915 90693 108550 90660 90288 99677 116970 FALSE TRUE 78474.49017 124900.2326 100237.59 93020.33592 100024.9209 116832.0703 76750.15259 112121.8929 97446.95134 0.805304723 1.281725399 1.028637517 0.9545741 1.026455107 1.198929968 0.787609582 1.150594157 1 16.57232943 3.548454526 7.295893381 1.005510277 1.100161975 0 0.159482923 0.696226095 60.99554963 0.039324425 0.060971538 3535.529991 -3.548454526 0.094651698 IRDGDFVVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IRDGDFVVLK 10 1 Q9UJA5;Q9UJA5-2;Q9UJA5-3 Q9UJA5 TRMT6 tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 0 88.596 0.01227 0 178590 175480 142520 148310 213990 95393 153990 161580 223590 FALSE TRUE 167412.3707 188472.7218 145900.6417 152115.8857 197184.0886 122931.4105 130900.6291 181753.6187 186271.3846 0.898755174 1.011817903 0.783269218 0.816635824 1.058584973 0.659958645 0.702741483 0.975746324 1 17.50704654 2.232102544 24.9999999 0.793012357 0.904958475 0.039821318 0.133231405 303.5236495 1174966.903 0.047166814 0.035660963 170.648527 -2.232102544 0.111946118 IRDIDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IRDIDLK 7 1 Q13243;Q13243-3;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ;;; 139.88 0.0024279 2422300000 4084340 3424390 3828630 3847740 4248390 3279750 5048020 3683420 5186840 FALSE TRUE 3828708.45 3677935.399 3919446.912 3946479.523 3914738.587 4226560.583 4291116.265 4143303.095 4321122.896 0.886044795 0.851152695 0.90704361 0.913299533 0.905954003 0.978116264 0.993055826 0.958848706 1 22.04297483 2.548449152 0.769446411 0.995223674 0.869624144 0.845540268 0.019206843 0.223652022 0.271751919 0.013762151 0.011039839 353.5486243 -2.548449152 -0.12559953 IRDPNQGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IRDPNQGGK 9 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JHW9;F8WCF2;B1AN92;B1AN91;A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-4;O43432-2 Q04637-9;A0A0A0MSA7 EIF4G1;EIF4G3 Eukaryotic translation initiation factor 4 gamma 1;Eukaryotic translation initiation factor 4 gamma 3 0 ;;;;; 146.88 8.55E-05 4101950000 4522180 4623080 4775340 4893060 5008070 4015760 5681270 4613010 5149800 FALSE TRUE 4239144.826 4965377.654 4888613.32 5018624.204 4614756.384 5175044.722 4829416.306 5188954.453 4290265.111 0.988084586 1.157359167 1.139466488 1.169770183 1.075634317 1.206229589 1.125668503 1.20947175 1 22.03263537 4.741896097 24.70409482 1.142730529 0.988084518 0.352975476 0.062010156 256.0096326 1896020.633 0.012324685 0.08903526 55194.53731 -4.741896097 -0.154646011 IRDQAWDDVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IRDQAWDDVVR 11 1 O00566 O00566 MPHOSPH10 U3 small nucleolar ribonucleoprotein protein MPP10 0 ; 165.09 3.31E-05 217800000 175465 224740 206270 215990 236260 180837 222180 191826 217430 FALSE TRUE 164482.9589 241379.9834 211162.8218 221532.6691 217705.0926 233041.7063 188866.1716 215775.8984 181139.5283 0.90804564 1.332563829 1.165746779 1.222994622 1.20186408 1.286531484 1.042655755 1.191213758 1 17.46674188 0.863273897 0.861671378 1.005219043 1.19734015 0.13494345 0.121860919 1.226082971 1.880938225 0.104960248 0.036510185 7.299177034 -0.863273897 0.192121107 LILGLMMPPAHYDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LILGLMMPPAHYDAK 15 0 E5RK69;P08133;P08133-2;E7EMC6 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ; 194.85 3.46E-08 344190000 845070 764910 789940 607580 1146360 527320 1062340 975270 1958110 FALSE TRUE 792178.5772 821544.7323 808677.7498 623171.5314 1056329.51 679548.7237 903051.9793 1097034.606 1631288.791 0.485615166 0.503616979 0.495729361 0.382011778 0.647542922 0.416571687 0.553581919 0.672495644 1 20.63758078 0.860718552 1.57846489 0.999420422 0.49148611 0.844032402 0.069350618 0.184352772 0.882726578 0.057303028 0.016609978 7.256355511 -0.860718552 -0.507934312 IRDTPEDIVLEAPASGLAFHPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IRDTPEDIVLEAPASGLAFHPAR 23 1 Q9H6Y2;D6RGJ8 Q9H6Y2 WDR55 WD repeat-containing protein 55 0 ;; 206.46 8.22E-25 284747000 270582 313805 291003 293757 344462 233138 318591 273956 371315 FALSE TRUE 253646.7556 337039.4487 297905.7286 301295.3019 317409.344 300441.1559 270821.2372 308160.0097 309340.1277 0.819960726 1.089543252 0.96303616 0.973993591 1.026085256 0.971232404 0.87548046 0.996185047 1 18.23883447 1.989507054 24.38974713 0.938378855 0.989454438 0 0.076099057 888.8236918 2065976.216 0.027394377 0.018970471 97.61286381 -1.989507054 0.051075582 IRDTS(ph)QEPCGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IRDTSQEPCGR 11 1 Q12955;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 IRDT(0.194)S(0.806)QEPCGR;IRDT(0.088)S(0.912)QEPCGR 157.09 1.86E-05 1125940000 223130 216190 254130 265630 274040 205005 252130 218140 291580 TRUE FALSE 209164.6916 232196.9325 260158.0836 272446.5155 252518.0038 264186.6155 214325.4472 245375.2592 242913.4143 0.861066863 0.955883532 1.070991013 1.121578717 1.039539148 1.087575243 0.88231211 1.01013466 1 17.89008264 1.743366979 24.99999892 0.954459499 1.025063767 0.102245774 0.080001021 1.837142528 9596.118321 0.037291169 0.020679862 55.38178881 -1.743366979 0.070604268 IRDVTK ddPTM_SK-BR-3_Pertuzumab_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 ; 99.375 0.035449 457240000 735250 777020 832170 867940 960270 780170 1122620 929420 1238810 FALSE TRUE 689232.015 834551.3693 851909.4654 890212.8098 884854.2677 1005392.414 954293.5529 1045460.133 1032044.608 0.667831613 0.808638854 0.825457988 0.862572027 0.857379866 0.974175347 0.924663087 1.012998978 1 19.9770739 6.689688705 0.199426447 1.035226035 1.24E-14 0.875305961 0.036627379 9.7352201 0.184167406 0.065113568 2.834822733 4894278.795 -6.689688705 -1.035226035 IREDCCPGKPLNVFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IREDCCPGKPLNVFR 15 2 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 76.391 0.01631 180950000 289660 178540 188360 185330 237740 142570 250340 201970 262920 FALSE TRUE 271530.6977 191759.2874 192827.9882 190085.8816 219068.8594 183727.6446 212803.841 227186.3991 219036.9535 1.239657023 0.875465461 0.88034455 0.867825627 1.000145665 0.83879748 0.971543101 1.037205802 1 17.74081476 1.474281067 8.587285152 1.014206065 0.930576288 0.037265331 0.114999481 0.260332338 64.96127365 0.058855099 0.026766793 29.80444693 -1.474281067 -0.083629777 IREDLPNLESSEETEQINK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IREDLPNLESSEETEQINK 19 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;;;; 332.26 2.38E-75 2029534000 2000210 1699740 1834670 1825070 1934160 1489720 2326010 1687200 1991840 FALSE TRUE 1875020.427 1825590.518 1878189.239 1871904.386 1782258.876 1919777.98 1977246.394 1897850.634 1659389.036 1.129946255 1.100158238 1.131855881 1.128068431 1.074045228 1.156918564 1.191550836 1.143704455 1 20.66222073 IREEFPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IREEFPDR 8 1 P04350;M0QYM7;M0R042;K7ES63;K7ESM5;Q9BUF5 P04350;K7ESM5 TUBB4A;TUBB6 Tubulin beta-4A chain;Tubulin beta-6 chain 0 112.75 0.0051062 0 62777 102450 82560 84266 100600 80401 78948 83385 95656 FALSE TRUE 58847.89963 110035.5046 84518.36219 86428.40822 92699.2818 103611.4635 67110.48032 93795.8008 79690.39564 0.738456613 1.380787531 1.060584045 1.08455238 1.163242836 1.300175042 0.842140132 1.177002574 1 16.28211824 1.738411424 24.99999973 0.997069736 1.144436521 0.06843162 0.186277755 0.091664947 7230.338487 0.077989565 0.043249211 54.75344182 -1.738411424 0.147366785 IREESGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IREESGAR 8 1 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ;;;;; 154.75 0.00038302 9831330000 2237040 2999780 2463580 2504540 3282900 2081200 2856700 2572560 3388560 FALSE TRUE 2097027.66 3221886.832 2522017.281 2568810.737 3025074.277 2682008.655 2428364.355 2893749.779 2822987.445 0.742839882 1.141303989 0.893385936 0.9099618 1.07158616 0.950060426 0.860210824 1.025066471 1 21.42879128 -0.331205969 7.588205409 0.99998812 0.956791166 0.015953839 0.112173388 0 0 0.099203481 0.023382485 0.466438114 0.331205969 -0.043196953 IREESNTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IREESNTK 8 1 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7BZC3 Q00341 HDLBP Vigilin 0 95.608 0.0097062 0 143480 138610 132920 128980 148220 97049 147020 112950 143420 FALSE TRUE 134499.8429 148872.8286 136072.9252 132289.8452 136579.3991 125065.4708 124975.7159 127052.0561 119482.2755 1.125688663 1.245982536 1.138854484 1.107192214 1.143093388 1.046728231 1.045977032 1.063354842 1 16.86643709 2.573399022 0.575871548 1.014205996 1.200882871 0.702739414 0.037447368 0.411909549 0.283185451 0.030104888 0.029929947 374.4544727 -2.573399022 0.186676875 IREEYPDR ddPTM_SK-BR-3_Pertuzumab_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 1.37742E+11 34123450 42527590 36242470 34770470 45823250 28161390 37974530 39459140 47317060 FALSE TRUE 31987724.18 45676377.01 37102158.5 35662739.13 42224476.79 36291126.13 32280601.76 44385700.49 39419537.01 0.811468795 1.15872434 0.941212437 0.904697057 1.071156081 0.920638061 0.818898552 1.125982288 1 25.2324075 3.718101616 24.2720208 0.95199269 1.021920891 0 0.120569261 669.1275558 1800641.476 0.029936388 0.047156978 5225.184334 -3.718101616 0.069928201 IREHLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IREHLEK 7 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 160.88 0.0012129 9559200000 7520650 6667150 7082040 7014240 8110890 6165910 11078640 7065460 14262720 FALSE TRUE 7049945.941 7160792.723 7250029.333 7194237.273 7473893.417 7945908.122 9417500.781 7947598.234 11882179.89 0.593320923 0.602649749 0.61015987 0.60546443 0.629000191 0.668724779 0.79257349 0.668867018 1 23.5022962 0.233808687 0.325449139 1.076835279 0.573406032 0.896268312 0.040394025 1.138414305 0.207405954 0.16948068 0.042683001 1.71320245 -0.233808687 -0.503429247 IRELESQISELQEDLESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 IRELESQISELQEDLESER 19 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;;; 276.08 1.69E-39 1006566000 413097 419336 438048 445356 450649 369414 511731 417779 437470 FALSE TRUE 387241.9962 450384.0738 448438.7054 456784.5889 415256.8454 476057.8249 435001.6872 469939.6278 364453.4308 1.062528058 1.235779487 1.230441718 1.253341443 1.139396176 1.306224018 1.19357276 1.289436696 1 18.47537496 -1.070292661 4.611290525 0.999990447 1.218523062 0.470259094 0.071173015 7.16E-06 1.44E-06 0.059793049 0.01409263 0.085056467 1.070292661 0.218532615 IRELETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IRELETR 7 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 131.22 0.0088177 0 133610 155740 137470 158250 164350 121790 175200 144880 173080 FALSE TRUE 125247.5886 167271.1516 140730.8533 162310.9629 151442.614 156948.7959 148930.3865 162968.5869 144191.8299 0.86861779 1.160059844 0.975997416 1.125659915 1.050285679 1.088472184 1.032862865 1.130220673 1 17.1376299 4.756154831 24.42234144 1.068517606 0.868617562 0.540885268 0.058413274 1934.643223 2685397.81 0.012305343 0.361720881 57036.75781 -4.756154831 -0.199900044 IREYFGEFGEIEAIELPMDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IREYFGEFGEIEAIELPMDPK 21 1 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 86.546 0.0024951 32027000 90691 81809 80537 82710 112520 53920 104050 76278 148630 FALSE TRUE 85014.8122 87866.22348 82447.37567 84832.47863 103683.1331 69485.82868 88448.66845 85801.47621 123822.6928 0.68658507 0.70961325 0.665850288 0.685112532 0.837351625 0.561172004 0.714317113 0.692938219 1 16.91791621 0.179129804 2.456360408 1.000001217 0.692419945 0.676283154 0.066499263 43.06525089 126.9193045 0.056922996 0.015199612 1.51053156 -0.179129804 -0.307581272 IREYFGGFGEVESIELPMDNK ddPTM_SK-BR-3_Pertuzumab_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 ;; 275.76 8.00E-45 561661000 1809520 1466600 1503260 1573466 1818160 1227204 2060010 1572770 2261850 FALSE TRUE 1696265.373 1575188.59 1538918.037 1613843.801 1675369.048 1581477.873 1751130.625 1769133.797 1884332.623 0.90019424 0.835939776 0.816691288 0.856453782 0.88910473 0.839277447 0.929310783 0.93886492 1 20.84562222 1.34174518 0.939240627 0.998800016 0.845515013 0.759168908 0.027436293 0.221688103 0.409293547 0.024610314 0.008935036 21.9657067 -1.34174518 -0.153285003 IRGPEESQPPQLYAADEEEAPGTRDPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IRGPEESQPPQLYAADEEEAPGTRDPTR 28 2 Q5RKV6 Q5RKV6 EXOSC6 Exosome complex component MTR3 0 124.08 2.34E-05 108930000 74154 64891 70382 75062 78281 62686 85330 64440 87535 FALSE TRUE 69512.83351 69695.59716 72051.49428 76988.218 72133.12603 80782.43058 72535.55866 72485.47585 72924.843 0.953211973 0.955718165 0.988023989 1.055720038 0.989143385 1.107749119 0.994661842 0.993975069 1 16.15412275 3.551546413 2.7528913 1.025503076 0.958708953 0.374989805 0.036351701 0.256691364 3.835162094 0.009555001 0.01564152 3560.790419 -3.551546413 -0.066794123 IRIDS(ph)LSAQLSQLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IRIDSLSAQLSQLQK 15 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 IRIDS(0.803)LS(0.197)AQLSQLQK 196.76 5.31E-09 125200000 159490 181400 162800 179020 197630 142770 211230 171010 278080 TRUE FALSE 149507.8056 194831.0447 166661.6929 183613.9563 182108.937 183985.3813 179558.0225 192360.9749 231666.6515 0.645357476 0.84099737 0.719403038 0.79257828 0.786081794 0.794181554 0.775070651 0.830335198 1 17.82169086 -5 0.202645833 2.051132916 0.739319397 0.699828996 0.049641718 76.51171215 0.75917907 32.49015776 0.10364429 1.00E-05 5 -1.31181352 IRIDSLSAQLSQLQK ddPTM_SK-BR-3_Pertuzumab_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 ; 173.58 8.77E-07 749660000 954590 1250430 824520 914130 1697870 658780 1285350 1243090 2511630 FALSE TRUE 894843.9159 1343013.138 844078.0038 937588.1234 1564526.139 848959.0916 1092623.7 1398292.523 2092422.727 0.427659241 0.641845991 0.403397455 0.448087335 0.747710354 0.4057302 0.522181147 0.668264832 1 20.99674291 0.882547622 2.604260266 0.999467289 0.515912572 0.667105318 0.109037153 0.259888471 3.627553374 0.095832748 0.025583598 7.630405564 -0.882547622 -0.483554718 IRIEDPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IRIEDPPR 8 1 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ;;;;; 118.18 0.0017663 1330540000 1622190 1930810 1771350 1856630 2133830 1587440 2198180 1890180 2495090 FALSE TRUE 1520660.024 2073769.181 1813367.258 1904274.269 1966247.599 2045708.158 1868583.316 2126173.134 2078643.36 0.731563698 0.997655115 0.872380175 0.916113993 0.945928309 0.984155434 0.898943682 1.022865766 1 20.98721082 4.747474134 24.86468331 0.944476848 0.73156358 0.666763514 0.049111804 655.0533569 1827260.926 0.010787808 0.130363389 55908.02283 -4.747474134 -0.212913268 IRLDETDDPDDYGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IRLDETDDPDDYGDR 15 1 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;;; 166.04 1.27E-06 4017800000 2202390 2166670 2296100 2172640 2157670 2107470 2611140 2081210 1947880 FALSE TRUE 2064546.341 2327092.501 2350564.576 2228393.621 1988215.302 2715862.377 2219623.798 2341053.65 1622766.244 1.2722389 1.434028166 1.448492403 1.373206787 1.225201294 1.673600487 1.367802544 1.442631468 1 20.63002377 -0.942507347 6.236020663 0.999999895 1.413541195 0.528520903 0.119849687 1.58E-07 2.66E-08 0.103960833 0.024503797 0.114154399 0.942507347 0.4135413 IRLDETDDPDDYGDRESGCSFVLALMQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IRLDETDDPDDYGDRESGCSFVLALMQK 28 2 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 114.21 0.0002407 216570000 203130 252950 232580 237900 317680 182680 302220 269790 402750 FALSE TRUE 190416.4559 271678.6812 238096.9074 244004.9168 292730.6943 235416.7504 256904.9167 303473.8754 335528.4231 0.567512147 0.809703925 0.709617699 0.727225773 0.872446786 0.70162983 0.76567259 0.904465477 1 18.35607546 -5 0.110022702 1.828687787 0.608854708 0.593113805 0.077366053 123.2325168 0.902048699 22.72651859 0.907825334 1.00E-05 5 -1.219833079 IRLESEEEGVPSTAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IRLESEEEGVPSTAIR 16 1 P06493;A0A024QZP7;A0A087WZZ9;E5RIU6;P06493-2 P06493 CDK1;CDC2 Cyclin-dependent kinase 1 0 ; 204.13 2.37E-11 577100000 299989 322430 339000 346010 432550 300337 369310 321430 535130 FALSE TRUE 281213.224 346303.0527 347041.2401 354889.2024 398579.2678 387039.4163 313935.394 361561.2431 445813.3459 0.630786912 0.776789335 0.778445157 0.796048852 0.894049654 0.868164715 0.704185725 0.811014848 1 18.76608028 -5 0.133188658 1.67177469 0.701376579 0.531903891 0.069193238 131.8567402 1.098696326 24.08027499 0.504761723 1.00E-05 5 -0.970398111 IRPVS(ph)LPVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IRPVSLPVDR 10 1 Q52LW3 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 IRPVS(1)LPVDR;IRPVS(1)LPVDR;IRPVS(1)LPVDR 126.56 0.00022968 559670000 379410 538775 440291 449730 681620 312541 539210 515320 926190 TRUE FALSE 355663.4054 578666.4616 450734.9104 461270.8332 628088.3147 402766.513 458360.4663 579658.8364 771602.9056 0.460940988 0.74995371 0.584153983 0.597808575 0.8140046 0.521986776 0.594036729 0.751239831 1 19.55749905 0.922680889 3.704224728 0.99970854 0.627637348 0.590062128 0.101544285 0.224940482 7.529598433 0.088927032 0.022870183 8.369141084 -0.922680889 -0.372071191 IRS(ph)SVEKENQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IRSSVEKENQK 11 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 IRS(0.808)S(0.192)VEKENQK 137.21 6.55E-05 776510000 664330 398780 438400 482080 521160 285600 602240 387490 740760 TRUE FALSE 622750.7712 428306.0861 448799.055 494450.989 480230.1959 368048.0837 511939.7029 435868.9795 617122.3705 1.009120396 0.694037531 0.727244833 0.801220329 0.778176613 0.596394008 0.829559464 0.706292626 1 19.23519707 -1.094576295 4.464562144 1.000022079 0.756607531 0.309968159 0.107763834 0.59563552 57007368.63 2624.167936 0.022423636 0.080431044 1.094576295 -0.243414549 IRSS(ph)VEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 IRSSVEK 7 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 IRS(0.36)S(0.64)VEK;IRS(0.021)S(0.979)VEK;IRS(0.01)S(0.99)VEK;IRS(0.003)S(0.997)VEK;IRS(0.037)S(0.963)VEK;IRS(0.149)S(0.851)VEK;IRS(0.144)S(0.856)VEK 126.29 0.0024019 8044790000 7883160 5185300 6129180 5744720 5321270 4985270 7793230 5081670 4795260 TRUE FALSE 7389767.087 5569225.007 6274567.044 5892139.241 4903358.919 6424436.52 6624707.51 5716127.686 3994900.127 1.849800208 1.394083664 1.570644282 1.47491528 1.227404632 1.608159482 1.658291146 1.430856218 1 21.92972801 0.970449484 21.96600973 0.999999995 1.527506594 0.51614928 0.16328987 548.4412868 407678.4882 0.147763708 0.036940927 9.342206952 -0.970449484 0.527506599 IRSS(ph)VEKENQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IRSSVEKENQK 11 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 IRS(0.237)S(0.763)VEKENQK;IRS(0.114)S(0.886)VEKENQK;IRS(0.119)S(0.881)VEKENQK 187.75 2.72E-06 6029380000 3747850 2395060 2727820 2879600 3338210 1826820 3665160 2369580 4598980 TRUE FALSE 3513278.759 2572392.734 2792525.179 2953495.411 3076040.452 2354193.278 3115603.284 2665427.279 3831380.527 0.916974634 0.671401004 0.728856129 0.770869766 0.802854332 0.614450395 0.813180331 0.695683256 1 21.86943289 -1.195611904 4.416017155 1.000071881 0.743664763 0.460464134 0.084031851 5.23E-05 9.53E-06 0.071543506 0.016858248 0.063736483 1.195611904 -0.256407118 IRTPS(ph)GEFLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IRTPSGEFLER 11 1 Q9UNN5;B3KT28;B1ANM7;Q9UNN5-2 Q9UNN5 FAF1 FAS-associated factor 1 1 IRT(0.006)PS(0.994)GEFLER;IRT(0.006)PS(0.994)GEFLER 185.14 2.78E-06 881380000 600300 747980 650600 761090 805710 473780 745400 603110 599750 TRUE FALSE 562728.2946 803361.2175 666032.5392 780620.8579 742432.7867 610552.5948 633634.19 678409.6111 499647.8505 1.126249806 1.607854846 1.333003912 1.562342072 1.4859121 1.221965819 1.268161545 1.357775502 1 18.93055212 0.763173348 0.534737536 0.995221595 1.438415889 0.383973097 0.148500421 1.163326887 0.727456588 0.169193762 0.068632431 5.796600205 -0.763173348 0.443194294 IRVDIIENQVMDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IRVDIIENQVMDFR 14 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 147.7 7.26E-06 201593000 230476 336504 308430 357791 493421 257577 365696 289573 836890 FALSE TRUE 216050.9186 361419.1063 315746.1053 366972.5228 454669.705 331935.2985 310863.2798 325726.8265 697207.6525 0.309880303 0.518380865 0.452872403 0.526346091 0.652129539 0.476092449 0.445869001 0.467187681 1 19.41122888 -1.50344365 2.73556493 1.02255114 0.485203373 0.787895664 0.084587926 7342673.591 7600811.426 1239225.344 0.019918957 0.031373022 1.50344365 -0.537347767 IRVDVADQAQDKDRDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IRVDVADQAQDKDRDDR 17 3 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;;; 223.29 1.35E-15 7693890000 4714610 4022190 4092090 4371360 5259480 3026050 5492230 3867980 7408440 FALSE TRUE 4419530.976 4319997.133 4189156.307 4483536.498 4846421.657 3899621.511 4668721.099 4350905.817 6171923.504 0.716070277 0.699943402 0.678744042 0.726440711 0.785236832 0.631832444 0.756445069 0.704951352 1 22.55728875 -4.999999943 0.384492131 5.212988477 0.703884875 0.826149275 0.041412764 227.0178048 1.672626761 798.6965196 0.024733814 1.00E-05 4.999999943 -4.509103602 IRYESLTDPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IRYESLTDPSK 11 1 P08238;Q58FF7;Q58FF6;P07900;P07900-2;G3V2J8;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AB3P;HSP90AB4P;HSP90AA1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 4;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-beta 2 0 ;;;; 163.51 2.18E-05 4371280000 7459190 5773730 6316980 6047380 6548400 4621300 7329120 6359820 6116050 FALSE TRUE 6992332.613 6201222.977 6466821.749 6202566.009 6034115.079 5955394.289 6230186.496 7153857.527 5095241.744 1.372325979 1.217061582 1.269188406 1.217325167 1.184264728 1.168814865 1.222746007 1.404027107 1 22.28071917 -1.293552318 4.255289246 0.999757955 1.245491353 0.518499166 0.077121173 18.93772491 20281366.53 7985.210101 0.016739867 0.050868354 1.293552318 0.245733398 IRYESLTDPSKLDSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IRYESLTDPSKLDSGK 16 2 P08238;Q58FF7;P07900;P07900-2;G3V2J8;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AB3P;HSP90AA1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-beta 2 0 ; 186.97 7.96E-10 2277500000 4679700 3430570 3887800 4099600 4934400 2806740 5258400 3690300 6663400 FALSE TRUE 4386805.931 3684572.972 3980020.452 4204802.677 4546872.128 3617000.274 4469951.737 4151042.078 5551235.493 0.790239567 0.663739266 0.716961198 0.757453486 0.819073904 0.651566715 0.805217459 0.747769048 1 22.40437747 -5 0.237743225 2.496924428 0.709514781 0.677641327 0.055399445 89.9799461 0.898688531 64.92822706 0.082044819 1.00E-05 5 -1.787409646 IS(ph)APNVDFNLEGPK ddPTM_SK-BR-3_Pertuzumab_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 293.17 1.63E-43 5275570000 6613210 3650990 4598470 4000310 5404980 3308720 5148790 3936030 7407420 TRUE FALSE 6199300.991 3921313.098 4707547.88 4102964.727 4980494.673 4263893.751 4376776.739 4427452.01 6171073.748 1.004574122 0.63543449 0.762840969 0.664870474 0.807071002 0.690948435 0.709240712 0.717452455 1 22.55709011 -1.664266413 5.092437418 1.005174106 0.734821952 0.36050185 0.103506997 0.005342911 0.000352247 0.088064567 0.020434822 0.021663748 1.664266413 -0.270352154 IS(ph)ASSATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.998)AS(0.002)SATR;IS(1)ASSATR 208.59 5.67E-05 2786860000 2531320 2683770 2646390 2620870 3139250 2123880 2686890 2544240 3338690 TRUE FALSE 2372889.2 2882479.123 2709163.621 2688125.961 2892705.968 2737009.678 2284015.788 2861893.965 2781441.07 0.853115036 1.036325793 0.974014388 0.966450805 1.040002608 0.984025765 0.821162746 1.028924896 1 21.40740111 1.92157127 25 0.923267283 0.984638615 0 0.075244519 220.9506 70428.44654 0.028241597 0.018227077 83.47785293 -1.92157127 0.061371332 IS(ph)DAELEAELEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 281.48 4.63E-28 877122000 1954049 1124893 1385522 1393549 1418824 1031765 1675364 1141771 1371419 TRUE FALSE 1831748.561 1208181.248 1418387.236 1429309.827 1307395.286 1329618.806 1424158.722 1284323.623 1142520.309 1.603252517 1.05747026 1.241454725 1.251014809 1.144308137 1.16375945 1.246506263 1.12411448 1 20.12378838 8 0.023631409 5.20E-08 2.80743826 0.345183421 0.131997519 3188.912389 5.797246346 241.6317172 486.4529919 100000000 -8 2.807438208 IS(ph)DAELEAELEKLSLSEGGLVPSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ISDAELEAELEKLSLSEGGLVPSSK 25 1 Q8WUX9 Q8WUX9 CHMP7 Charged multivesicular body protein 7 1 IS(1)DAELEAELEKLSLSEGGLVPSSK;IS(0.998)DAELEAELEKLS(0.002)LSEGGLVPSSK;IS(1)DAELEAELEKLSLSEGGLVPSSK;IS(1)DAELEAELEKLSLSEGGLVPSSK 181.9 1.40E-17 206134000 574681 401616 417081 500867 647532 278739 599921 377305 1091591 TRUE FALSE 538712.742 431352.0665 426974.3583 513720.0952 596677.4487 359206.4244 509968.4154 424412.3598 909397.4102 0.592384293 0.474327353 0.469513497 0.564901647 0.656123981 0.394993894 0.560776191 0.466696249 1 19.79455137 -1.231934517 3.958000968 1.000440392 0.516281411 0.799339851 0.07513546 24949754.06 36722859.53 126470.1365 0.016765877 0.058622655 1.231934517 -0.484158981 IS(ph)DS(ph)ESEDPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISDSESEDPPR 11 0 Q96ST2;Q96ST2-3;B8ZZB6 Q96ST2 IWS1 Protein IWS1 homolog 2 IS(1)DS(1)ESEDPPR;IS(1)DS(1)ESEDPPR 154.86 4.65E-05 790770000 1600180 1214910 1377310 1264560 1283730 1140760 1481620 1260760 1156170 TRUE FALSE 1500027.59 1304863.201 1409980.444 1297010.75 1182911.024 1470078.893 1259464.836 1418168.661 963197.7579 1.55734124 1.354719931 1.463853536 1.346567452 1.228108158 1.526248251 1.307586968 1.472354612 1 19.87747251 -1.613308186 2.975997832 0.97181746 1.39886323 0.611776177 0.101728985 14661527.13 16880365.9 3252919.154 0.022292768 0.024360815 1.613308186 0.42704577 IS(ph)EDETER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISEDETER 8 0 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5;G3V3T3 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 IS(1)EDETER;IS(1)EDETER 178.84 0.0002596 1268550000 1901250 1080670 1475300 1316960 1123840 1501650 1829620 1180710 757070 TRUE FALSE 1782254.156 1160683.931 1510294.813 1350755.423 1035578.14 1935151.978 1555285.466 1328124.243 630710.1261 2.825789665 1.84028111 2.394594204 2.141642202 1.641924074 3.068211366 2.465927535 2.105760138 1 19.26661757 0.882100808 6.227623488 1.000008673 2.309212846 0.499969822 0.4174143 1.752826052 92.27435392 0.382952382 0.096223168 7.622559243 -0.882100808 1.309204173 IS(ph)EDETERNGDDGTHDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISEDETERNGDDGTHDK 17 1 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5;G3V3T3 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 IS(0.997)EDET(0.003)ERNGDDGTHDK 155.49 5.96E-08 339490000 261480 137700 176970 190000 186770 139580 246860 171370 193980 TRUE FALSE 245114.4336 147895.4513 181167.812 194875.7217 172101.8376 179874.4801 209845.6347 192765.9217 161603.4848 1.516764529 0.915174889 1.12106377 1.205888115 1.064963653 1.113060651 1.298521718 1.192832704 1 17.30209878 IS(ph)FVEEDVHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISFVEEDVHPK 11 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 IS(1)FVEEDVHPK 196.33 3.92E-08 64159000 165580 106480 128830 141210 147630 95069 178660 110380 145230 TRUE FALSE 155216.6434 114363.89 131885.9084 144833.6877 136035.7353 122513.877 151871.5916 124161.186 120990.1748 1.282886347 0.945232869 1.090054698 1.197069828 1.124353573 1.012593603 1.255239046 1.026208832 1 16.88453037 3.472579094 24.87951666 1.12145253 1.065851687 0 0.115926467 388.1544152 2126099.298 0.029385276 0.040307882 2968.787371 -3.472579094 -0.055600843 IS(ph)IPDVDLDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISIPDVDLDLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 IS(1)IPDVDLDLK 121.08 0.00043967 7321900 46431 25369 32646 27592 37277 29328 40066 32340 49737 TRUE FALSE 43524.96659 27247.34716 33420.37854 28300.05743 34349.41479 37794.5175 34058.47525 36377.72019 41435.57339 1.050425107 0.657583447 0.806562473 0.682989401 0.828983696 0.912127296 0.821962205 0.877934519 1 15.33858227 2.478470825 15.66681861 0.880512742 0.774854403 0.129163784 0.114429876 0.767651142 8872.414267 0.035504327 0.030500438 300.9336998 -2.478470825 -0.105658339 IS(ph)MPDVDLHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISMPDVDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 IS(1)MPDVDLHLK 178.67 4.79E-06 44158000 159850 110000 120280 100100 141790 73687 122620 110310 167470 TRUE FALSE 149845.2738 118144.5145 123133.0984 102668.7355 130654.3854 94959.24069 104234.2693 124082.4463 139518.1751 1.074019738 0.846803754 0.882559554 0.735880722 0.936468566 0.680622726 0.747101725 0.889364029 1 17.09009355 7.892793509 1.000718556 0.815659923 199.9992952 0.328639917 0.099535983 1373.07019 2.356994469 0.027222802 626423.9738 78125625.76 -7.892793509 199.1836352 IS(ph)MSEVDLNVAAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 ISMSEVDLNVAAPK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 IS(1)MSEVDLNVAAPK;IS(1)MSEVDLNVAAPK;IS(0.86)MS(0.14)EVDLNVAAPK;IS(0.998)MS(0.002)EVDLNVAAPK;IS(0.813)MS(0.187)EVDLNVAAPK;IS(0.999)MS(0.001)EVDLNVAAPK;IS(1)MSEVDLNVAAPK;IS(0.699)MS(0.301)EVDLNVAAPK;IS(0.984)MS(0.016)EVDLNVAAPK 365.28 6.13E-97 2618965000 3418920 2442860 2735630 2585360 3142580 1850976 2988190 2083942 3598190 TRUE FALSE 3204935.9 2623731.896 2800520.435 2651704.715 2895774.443 2385322.723 2540138.65 2344126.746 2997628.844 1.069157013 0.875269099 0.934245226 0.884600747 0.966021677 0.795736513 0.847382642 0.781993658 1 21.51539033 2.243387453 24.99855576 0.842261663 0.931864775 0.222448724 0.078995726 161.3403249 835597.3932 0.024821941 0.020146229 175.1408501 -2.243387453 0.089603112 IS(ph)PGATLPESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ISPGATLPESR 11 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 IS(1)PGATLPESR;IS(1)PGATLPESR;IS(1)PGATLPESR;IS(1)PGATLPESR;IS(1)PGATLPESR;IS(1)PGATLPESR 244.94 6.90E-16 3119200000 3150560 3136730 3076130 3073970 3294450 2349770 3410350 2718990 3687530 TRUE FALSE 2953372.074 3368976.753 3149097.256 3152853.274 3035717.186 3028110.454 2898999.678 3058461.887 3072057.421 0.961366169 1.096651622 1.025077603 1.026300242 0.988170718 0.985694614 0.943667152 0.995574453 1 21.55077375 2.771344582 1.632755544 0.972962538 1.042921612 0.235341997 0.036448109 0.348229218 1.857311171 0.013411725 0.013397746 590.6695494 -2.771344582 0.069959074 IS(ph)PPIKEEETKGDSVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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;IS(1)PPIKEEETKGDSVEK 119.06 7.22E-05 2132460000 3445480 987310 1597390 1680860 1670980 1048430 2234940 1169850 2338220 TRUE FALSE 3229833.557 1060411.46 1635280.845 1723993.713 1539747.971 1351094.721 1899831.495 1315908.348 1947955.977 1.658062911 0.544371368 0.839485525 0.885027041 0.7904429 0.693596127 0.975294882 0.675532899 1 20.89352964 4.748853875 24.99856931 0.793310379 1.658063389 0.791431581 0.138313829 639.1112542 1552137.637 0.03151878 0.443974592 56085.92343 -4.748853875 0.864753009 IS(ph)QEHLADHFDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISQEHLADHFDSR 13 0 P19174-2;P19174;V9GY71;V9GYH5 P19174-2 PLCG1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1" 1 IS(1)QEHLADHFDSR 148.24 1.02E-06 0 129720 104940 126820 129630 134210 109840 177860 124040 107380 TRUE FALSE 121601.0568 112709.8668 129828.2303 132956.5253 123669.688 141549.0249 151191.5442 139526.667 89457.5843 1.35931523 1.259925222 1.451282541 1.486252131 1.382439387 1.582303233 1.690091962 1.559696343 1 16.44891618 3.610368466 1.268901483 1.511988996 1.30050226 0.024261738 0.189515895 0.82997473 2.653754597 0.058067942 0.133561573 4077.260556 -3.610368466 -0.211486736 IS(ph)RESSVDCLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISRESSVDCLK 11 1 H3BRD5;B2RTY4-5;B2RTY4-2;B2RTY4;B2RTY4-4;H3BMM1 H3BRD5 MYO9A Unconventional myosin-IXa 1 IS(0.999)RES(0.001)SVDCLK;IS(0.983)RES(0.016)SVDCLK 59.185 0.061524 1024520000 131874 782380 513860 567750 580440 620620 377990 433370 378770 TRUE FALSE 123620.2417 840308.2293 526049.0019 582319.4262 534854.5838 799782.9191 321313.9086 487477.1985 315550.8401 0.391760141 2.662988408 1.667081608 1.84540604 1.694987038 2.53456121 1.018263518 1.544845193 1 18.26751294 1.656039141 10.74577503 1.214413771 1.880041728 0.166127673 0.626643105 0.172757369 30.37749145 0.269156555 0.145286932 45.29383989 -1.656039141 0.665627957 IS(ph)SKSPGHMVILDQTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISSKSPGHMVILDQTK 16 1 Q9NWH9;Q9NWH9-3 Q9NWH9 SLTM SAFB-like transcription modulator 1 IS(0.333)S(0.333)KS(0.333)PGHMVILDQTK;IS(0.333)S(0.333)KS(0.333)PGHMVILDQTK 200.99 2.06E-11 720420000 797800 1001430 867310 876660 1482450 461870 1167820 992940 2942830 TRUE FALSE 747867.1221 1075576.919 887883.0028 899156.5798 1366024.357 595204.3712 992716.2325 1116910.745 2451652.662 0.305046116 0.43871505 0.362156931 0.366755289 0.55718511 0.242776793 0.40491716 0.455574626 1 21.22532317 0.643207996 2.398159278 0.999950238 0.385722509 0.846820067 0.081890555 0.882989326 5.522404814 0.069998682 0.018790875 4.397521744 -0.643207996 -0.614227729 IS(ph)SPMHPSAGGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISSPMHPSAGGQR 13 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 1 IS(0.5)S(0.5)PMHPSAGGQR;IS(0.5)S(0.5)PMHPSAGGQR 62.861 0.0473 547030000 201291 297960 275860 305450 333860 222784 314260 295400 303170 TRUE FALSE 188692.5556 320021.2684 282403.5295 313288.3641 307639.9823 287098.1242 267139.6304 332281.3403 252568.9684 0.747093187 1.267064875 1.118124413 1.240407189 1.218043468 1.13671179 1.057689835 1.315606356 1 17.94631787 4.746766068 24.95481199 1.169329109 0.747092972 0.655613479 0.09614572 598.1430433 1819059.292 0.020945256 0.236798542 55816.94567 -4.746766068 -0.422236137 IS(ph)WYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISWYLR 6 0 M0QYT0;M0R076;Q13011;M0R248;M0QZW4 M0QYT0;Q13011 ECH1 "Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial" 1 IS(1)WYLR 84.568 0.05843 8648100 22420 27353 21910 25139 30591 24689 26800 21682 19189 TRUE FALSE 21016.77222 29378.24458 22429.71555 25784.1093 28188.50626 31816.31351 22781.5888 24389.04543 15986.23193 1.314679551 1.837721653 1.403064564 1.612894734 1.763298967 1.990232197 1.425075583 1.525628149 1 13.96454231 0.723304043 1.475234053 1.002721103 1.63959301 0.474829366 0.205120363 0.799694567 2.820229667 0.182568376 0.053328637 5.288153384 -0.723304043 0.636871907 IS(ph)YTPPES(ph)PVPSYASSTPLHVPVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISYTPPESPVPSYASSTPLHVPVPR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 2 IS(0.457)Y(0.084)T(0.459)PPES(0.985)PVPS(0.004)Y(0.001)AS(0.003)S(0.003)T(0.004)PLHVPVPR 64.984 0.024996 99216000 42165 49849 52431 49267 61936 50797 57748 49647 56543 TRUE FALSE 39525.96792 53539.87183 53674.68808 50531.27463 57071.7964 65461.26928 49089.22351 55845.53724 47105.60802 0.839092617 1.13659231 1.13945431 1.072723116 1.211571165 1.389670403 1.042109965 1.185539038 1 15.52361121 4.74141985 4.491533172 1.154197366 0.817264578 0.450248277 0.10694036 0.17778867 9.108180475 0.023859285 0.190617065 55134.0442 -4.74141985 -0.336932788 ISAEDGLKHEYFR ddPTM_SK-BR-3_Pertuzumab_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 0 128.95 9.57E-05 87299000 95352 134270 126060 118750 165180 95887 135000 136590 260970 FALSE TRUE 89384.08853 144211.4905 129050.2027 121797.326 152207.4291 123568.0203 114758.0033 153643.5622 217412.4211 0.411126872 0.663308425 0.593573275 0.560213282 0.70008617 0.568357685 0.527835543 0.70669174 1 17.73007484 0.913140604 4.384604049 0.999898937 0.586680216 0.74961357 0.07764985 0.204948787 8.9828367 0.06877437 0.017490299 8.187298116 -0.913140604 -0.413218721 ISAPELLLHS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISAPELLLHSPAR 13 0 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 ISAPELLLHS(1)PAR 130.39 9.18E-05 130040000 113320 152690 154920 140100 151340 171720 170800 161610 163140 TRUE FALSE 106227.5035 163995.3265 158594.7756 143695.2032 139454.3669 221292.7764 145190.1256 181787.3642 135910.8801 0.78159676 1.206638691 1.166902719 1.057275202 1.026072135 1.628219729 1.068274487 1.337548283 1 17.05230143 ISASELRGILATLAPQAGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISASELRGILATLAPQAGSR 20 1 Q86US8 Q86US8 SMG6 Telomerase-binding protein EST1A 0 31.111 0.095179 192020000 388510 27016 57793 45235 55920 28659 53230 28125 63397 FALSE TRUE 364193.8526 29016.29275 59163.87725 46395.80668 51528.26877 36932.38806 45248.65566 31636.46816 52815.63114 6.895569451 0.549388356 1.12019635 0.8784484 0.975625353 0.699270032 0.856728485 0.598998203 1 15.68867735 4.740225777 24.99994571 0.839415546 6.89557146 0.991299908 0.178437541 11.32181098 169966.1642 0.039649776 0.253850119 54982.66379 -4.740225777 6.056155914 ISATEDTPEAEGEVPELYHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISATEDTPEAEGEVPELYHQR 21 0 A0A1B0GUA3;Q96EK5;A0A1B0GUH6 A0A1B0GUA3 KIAA1279 KIF1-binding protein 0 ; 181.54 4.99E-17 284240000 201448 257460 238550 258560 273340 191115 296210 261410 295790 FALSE TRUE 188839.7293 276522.6063 244208.5187 265195.0873 251872.979 246286.798 251796.0604 294047.6139 246420.7381 0.766330507 1.122156392 0.991022592 1.076188187 1.022125739 0.999456458 1.021813595 1.193274625 1 17.91076415 4.747884348 24.91339283 1.048456645 0.766330352 0.66589531 0.063791196 716.1724349 1913600.445 0.013930222 0.179195517 55960.85582 -4.747884348 -0.282126293 ISDDKYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ISDDKYGR 8 1 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 ;;;;; 189.7 0.00017356 4766960000 7079890 6161350 6726250 6655640 6536180 5151790 7601250 5684370 7322310 FALSE TRUE 6636772.323 6617542.765 6885799.826 6826434.99 6022854.788 6639028.141 6461513.129 6394076.107 6100169.157 1.087965293 1.084812994 1.128788342 1.119056671 0.987325865 1.088335089 1.059235074 1.048180131 1 22.54041782 2.773344856 24.99944774 1.046101022 1.105704113 0.525955028 0.031627426 520.673593 374207.127 0.009133885 0.009687461 593.3963294 -2.773344856 0.059603091 ISDEDWDIIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ISDEDWDIIHR 11 0 P51659-3;P51659;P51659-2;A0A2R8YD50;E7ER27;A0A2R8YDT8;A0A2R8YF45 P51659-3 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 ;;;;; 223.78 6.69E-12 1040272000 1482250 1700075 1670591 1688388 1961339 1291797 1851153 1693775 1552825 FALSE TRUE 1389478.618 1825950.322 1710218.207 1731714.895 1807303.347 1664717.823 1573589.793 1905246.537 1293648.476 1.074077421 1.41147333 1.322011535 1.338628636 1.397059078 1.286839396 1.216396743 1.472769901 1 20.30301422 -1.529161988 3.281948273 0.990935031 1.318476705 0.444123159 0.110655017 22253660.5 21880721.85 1720220.263 0.02409492 0.029569094 1.529161988 0.327541674 ISDYFEYQGGNGS(ph)SPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISDYFEYQGGNGSSPVR 17 0 B3KRP1;Q9UKI8;Q9UKI8-4;Q9UKI8-5;Q9UKI8-2;C9JWT6 B3KRP1 TLK1 Serine/threonine-protein kinase tousled-like 1 1 ISDYFEYQGGNGS(0.5)S(0.5)PVR;ISDYFEYQGGNGS(0.5)S(0.5)PVR 141.22 6.63E-07 130902000 91647 90180 91287 88309 111737 93002 124104 94757 126997 TRUE FALSE 85910.97786 96857.02103 93452.37075 90575.15845 102961.6267 119850.1676 105495.7573 106587.62 105800.3803 0.812010105 0.915469498 0.883289554 0.856094829 0.973168778 1.132795245 0.997120776 1.007440803 1 16.69098529 2.549386011 4.534265438 1.035900767 0.87877599 0.739356751 0.046725836 0.109657257 4.259052039 0.014746753 0.013588946 354.3121221 -2.549386011 -0.157124776 ISDYFEYQGGNGSS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ISDYFEYQGGNGSSPVR 17 0 B3KRP1;Q9UKI8;Q9UKI8-4;Q9UKI8-5;Q9UKI8-2;C9JWT6 B3KRP1 TLK1 Serine/threonine-protein kinase tousled-like 1 1 ISDYFEYQGGNGS(0.001)S(0.999)PVR;ISDYFEYQGGNGS(0.18)S(0.82)PVR;ISDYFEYQGGNGS(0.064)S(0.936)PVR 336.33 3.44E-72 1001460000 1030960 986770 1049750 929570 1136150 1116150 1429970 1167820 1395380 TRUE FALSE 966434.0539 1059831.478 1074650.566 953424.34 1046921.362 1438364.386 1215559.274 1313624.898 1162482.064 0.831353949 0.911697058 0.924444858 0.820162624 0.900591411 1.237321788 1.04565852 1.130017347 1 20.14877703 2.327249044 8.579400615 1.104773841 0.885024696 0.728261471 0.068430551 0.129119768 11.13588653 0.021485167 0.01794173 212.4462373 -2.327249044 -0.219749145 ISEGLPT(ph)PTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISEGLPTPTK 10 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 ISEGLPT(0.994)PT(0.006)K;ISEGLPT(0.997)PT(0.003)K 126.12 0.0090755 283270000 1793890 1133980 1483740 1247680 1338750 1185610 1752160 1375030 1251960 TRUE FALSE 1681613.627 1217941.059 1518935.013 1279697.581 1233609.975 1527876.36 1489439.874 1546705.522 1042999.788 1.612285684 1.167728961 1.456313828 1.226939445 1.182751895 1.464886549 1.428034685 1.482939441 1 19.99230743 ISEGLPT(ph)PTKMT(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ISEGLPTPTKMTPR 14 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 2 ISEGLPT(0.995)PT(0.005)KMT(1)PR;ISEGLPT(1)PTKMT(1)PR;ISEGLPT(1)PTKMT(1)PR 178.72 9.60E-06 853280000 2528250 1819280 2076340 1884950 2250520 1216930 3347030 2076510 3186390 TRUE FALSE 2370011.346 1953981.384 2125591.765 1933321.008 2073773.237 1568237.936 2845173.924 2335766.844 2654560.924 0.89280729 0.736084588 0.800731958 0.728301615 0.781211393 0.590771122 1.071805849 0.87990704 1 21.34004182 1.708002225 10.88329227 0.979560017 0.758168006 0.602675104 0.087498776 0.07068913 17.85969449 0.036876876 0.020050025 51.05076156 -1.708002225 -0.221392011 ISEGLPTPTKMT(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ISEGLPTPTKMTPR 14 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 ISEGLPT(0.001)PT(0.024)KMT(0.975)PR;ISEGLPT(0.001)PT(0.009)KMT(0.99)PR;ISEGLPT(0.004)PT(0.064)KMT(0.932)PR;ISEGLPTPT(0.009)KMT(0.991)PR 132.4 8.18E-05 1443340000 2109850 2166310 1993870 2129770 2423880 1544540 3121150 2050180 2892970 TRUE FALSE 1977798.255 2326705.846 2041165.538 2184423.504 2233518.242 1990423.624 2653162.533 2306149.486 2410114.618 0.820624148 0.965392197 0.846916376 0.906356689 0.92672698 0.825862641 1.100844961 0.956862993 1 21.20067033 1.741896003 25 1.023741743 0.890216935 0.561276243 0.056848453 0.387855561 2923.100372 0.023379511 0.012965106 55.19452539 -1.741896003 -0.133524808 ISELGSQLSDEAVEDGLFHEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISELGSQLSDEAVEDGLFHEFK 22 0 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 0 89.946 0.0024527 34120000 23832 23425 21326 28100 30341 15097 28157 22272 50700 FALSE TRUE 22340.39766 25159.41137 21831.86279 28821.09357 27958.14025 19455.25882 23935.11925 25052.70823 42237.84247 0.528919006 0.595660429 0.516879213 0.682352409 0.6619216 0.460612041 0.56667476 0.593134184 1 15.36624852 0.68277069 3.955386299 0.999998901 0.571013483 0.807612397 0.065133598 3.401408024 42.02885796 0.060616455 0.015495031 4.81693394 -0.68277069 -0.428985418 ISEQFTAMFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISEQFTAMFR 10 0 Q13509;A0A0B4J269;Q13509-2;Q5JP53;P07437;Q5ST81;P68371;Q13885;Q9BVA1;P04350 Q13509;Q5JP53;P68371;Q13885;Q9BVA1;P04350 TUBB3;TUBB;TUBB4B;TUBB2A;TUBB2B;TUBB4A Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-2B chain;Tubulin beta-4A chain 0 ; 205.59 3.86E-07 1200780000 167321 249829 135482 156630 292011 115388.1 148423 224846 227241 FALSE TRUE 156848.6773 268326.5991 138695.697 160649.391 269077.634 148698.7713 126168.349 252918.518 189313.0091 0.828515051 1.417370103 0.73262634 0.848591398 1.421337262 0.785465151 0.666453667 1.335980656 1 17.53041403 ISESVLRDS(ph)PPPHEDYEDEVFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISESVLRDSPPPHEDYEDEVFVR 23 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 ISES(0.004)VLRDS(0.996)PPPHEDYEDEVFVR;ISES(0.001)VLRDS(0.999)PPPHEDYEDEVFVR 204.88 9.94E-25 536340000 1094410 663450 830580 691940 754820 712810 1009910 814780 867830 TRUE FALSE 1025912.832 712572.5283 850281.7498 709696.3519 695539.482 918586.6755 858483.371 916507.0766 722983.5666 1.418998825 0.985599896 1.176073412 0.981621692 0.962040514 1.270549869 1.187417544 1.267673456 1 19.46360333 2.216843819 24.99912962 1.198624355 1.09271105 0.051627544 0.150488014 532.2574106 612700.1832 0.051336348 0.037948848 164.7569785 -2.216843819 -0.105913305 ISEVFDCWFESGSMPYAQVHYPFENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISEVFDCWFESGSMPYAQVHYPFENK 26 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 75.23 0.024672 28321000 42183 41221 42458 38364 46697 34185 54526 45003 39186 FALSE TRUE 39542.84133 44273.04573 43465.12381 39348.48519 43029.60599 44053.65455 46350.33249 50621.72361 32645.60345 1.211276164 1.356171768 1.331423506 1.205322648 1.318082726 1.349451378 1.419803208 1.550644444 1 14.99460109 2.229957326 3.636972187 1.372283587 1.296017553 0 0.146566472 0.706317349 20.08244227 0.05124624 0.038470452 169.8076791 -2.229957326 -0.076266034 ISEVFDCWFESGSMPYAQVHYPFENKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISEVFDCWFESGSMPYAQVHYPFENKR 27 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 241.48 2.15E-45 427380000 584550 635950 581640 575550 741580 484810 820070 628110 785610 FALSE TRUE 547964.059 683036.3997 595436.7755 590319.5874 683339.2982 624766.7768 697108.1167 706530.9161 654486.6158 0.837242574 1.043621647 0.909776856 0.901958227 1.04408445 0.954590608 1.065122036 1.079519274 1 19.32000416 2.19935918 1.337313151 1.049527683 0.944504493 0.35120093 0.064507418 0.513035573 1.770836257 0.038177051 0.021336404 158.2556341 -2.19935918 -0.10502319 ISGETIFVTAPHEATAGIIGVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISGETIFVTAPHEATAGIIGVNR 23 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 282.2 5.01E-52 646710000 366260 411280 396780 435420 413890 307090 497860 396120 377240 FALSE TRUE 343336.4404 441731.5991 406191.809 446593.6144 381384.749 395741.8978 423210.5149 445576.454 314276.2069 1.092467176 1.405552152 1.292467581 1.421022669 1.213533639 1.259216858 1.346619647 1.417786152 1 18.26167353 -0.98967863 6.02080216 0.99999974 1.314721876 0.466903219 0.102416352 3.18E-07 5.34E-08 0.088147763 0.02077661 0.102405049 0.98967863 0.314722136 ISGLIYEETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ISGLIYEETR 10 0 P62805 P62805 HIST1H4A Histone H4 0 ;;; 204.86 4.17E-07 473627000 471181 700820 397568 432325 899710 382111 514595 638800 752000 FALSE TRUE 441690.6223 752709.442 406998.5007 443419.1914 829050.4059 492420.2426 437436.257 718555.5862 626486.3419 0.705028335 1.201477816 0.649652632 0.707787484 1.323333568 0.786003157 0.6982375 1.146961295 1 19.25692353 3.978260399 24.99079876 0.873816585 0.980820171 0 0.243516162 216.1962551 4742737.738 0.058088894 0.115416694 9511.749377 -3.978260399 0.107003586 ISGWTQALPDMVVSHLFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ISGWTQALPDMVVSHLFGK 19 0 Q92597;Q92597-3;Q92597-2 Q92597 NDRG1 Protein NDRG1 0 ;;; 179.41 3.59E-14 558570000 1134706 2182820 1463682 1429137 2144200 667072 1241434 2019510 714307 FALSE TRUE 1063686.777 2344438.264 1498401.228 1465811.075 1975803.181 859644.8574 1055292.497 2271650.269 595084.5471 1.787454879 3.939672565 2.5179636 2.463198015 3.320205828 1.444576005 1.773348849 3.817357181 1 19.18273513 2.24487838 24.98578571 2.018679003 2.90552686 0.153585737 0.912876662 244.0512022 965187.1556 0.299095238 0.24452935 175.7431394 -2.24487838 0.886847857 ISGWTQALPDMVVSHLFGKEEMQSNVEVVHTYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISGWTQALPDMVVSHLFGKEEMQSNVEVVHTYR 33 1 Q92597;Q92597-3;Q92597-2 Q92597 NDRG1 Protein NDRG1 0 ; 180.33 8.28E-20 231559000 141428 297817 146999 195004 400626 89797 212380 217902 170010 FALSE TRUE 132576.2739 319867.6806 150485.8857 200008.1328 369162.45 115719.9362 180535.5906 245107.5444 141634.2327 0.936046826 2.258406562 1.062496565 1.412145418 2.606449324 0.817033665 1.274660703 1.730567107 1 17.11181048 0.497913072 0.404599005 0.959574136 1.608593398 0.057293936 0.571575886 6.298568313 2.00261377 1.224306406 0.395329733 3.147118329 -0.497913072 0.649019262 ISHEGS(ph)PVKPVAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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;ISHEGS(1)PVKPVAIR 139.88 6.10E-06 238000000 531050 386200 450630 437290 461990 369900 554380 403990 469110 TRUE FALSE 497812.5285 414794.6498 461319.1564 448511.6017 425707.169 476684.1252 471255.8656 454429.0408 390812.5104 1.27378862 1.06136482 1.180410412 1.147638803 1.089287466 1.219725859 1.205836182 1.162780179 1 18.57611713 -1.188968513 5.457716164 0.999993934 1.161914673 0.422918222 0.061208785 4.31E-06 6.40E-07 0.056484705 0.013313074 0.064718954 1.188968513 0.161920739 ISHLNDLSIPVDEEDPSEDIFTVLTAEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ISHLNDLSIPVDEEDPSEDIFTVLTAEEK 29 0 Q96PZ0;Q96PZ0-2;E7EUH7 Q96PZ0 PUS7 Pseudouridylate synthase 7 homolog 0 ;;; 173.11 1.52E-12 182423000 195070 144447 182305 155626 176439 123262 214464 142195 213189 FALSE TRUE 182860.9169 155142.0062 186629.3607 159619.6266 162582.1927 158845.7384 182307.1142 159948.3588 177606.3786 1.029585302 0.873515959 1.050803254 0.89872688 0.915407396 0.894369558 1.026467155 0.900577783 1 17.43832387 -1.154093565 4.140740699 1.000015162 0.951754834 0.056802393 0.06465007 8.23E-06 1.68E-06 0.056906474 0.013408771 0.070130419 1.154093565 -0.048260328 ISHQSQDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISHQSQDKK 9 1 Q9NRX4;Q9NRX4-2 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 ; 135.86 0.00013568 735310000 1328970 1890670 1951930 1943220 2255720 1506320 2458490 2099860 2967570 FALSE TRUE 1245792.14 2030657.174 1998230.701 1993086.315 2078564.85 1941170.131 2089862.248 2362032.143 2472263.396 0.503907529 0.821375739 0.808259632 0.806178791 0.840753802 0.785179336 0.84532346 0.95541282 1 21.23740103 6.935526268 0.173364716 0.980674529 2.44E-35 0.655837116 0.076551721 31.02191991 0.469522217 0.195094469 7.392938911 8620377.17 -6.935526268 -0.980674529 ISHSLYSGIEGLDES(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISHSLYSGIEGLDESPSR 18 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3;B1AP52 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 ISHSLYSGIEGLDES(1)PSR;ISHSLYSGIEGLDES(0.984)PS(0.016)R 340.02 1.57E-75 407450000 324230 351220 355190 315530 378100 325370 374010 308460 311740 TRUE FALSE 303937.0231 377224.6942 363615.2745 323627.034 348405.5512 419299.0371 317930.6726 346971.91 259708.5801 1.170300276 1.452492228 1.400089571 1.246116066 1.341524993 1.614498208 1.224182399 1.336004802 1 17.98653415 0.552106868 1.242115376 1.00072592 1.371237214 0.426595106 0.126172687 1.481280987 3.120286686 0.110931034 0.033457925 3.565388573 -0.552106868 0.370511295 ISIEMNGTLEDQLSHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISIEMNGTLEDQLSHLK 17 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 133.52 2.27E-05 0 164570 126200 133920 124050 122600 89243 156150 127110 152770 FALSE TRUE 154269.8575 135543.9793 137096.6456 127233.333 112971.4905 115006.0054 132736.7571 142979.9633 127271.7001 1.212130092 1.064997004 1.077196624 0.999698542 0.887640304 0.903625907 1.042940081 1.123423064 1 16.95755213 5.60219125 0.682015228 0.994269076 1.73461819 0.46096732 0.070667564 8.531082106 1.256191166 0.028619752 6.405346886 400120.9123 -5.60219125 0.740349114 ISIPDVGLHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISIPDVGLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 108.7 0.0020282 267670000 180050 184130 189130 184640 241030 136680 222830 191140 271700 FALSE TRUE 168780.9919 197763.1768 193616.2529 189378.175 222100.4761 176137.2972 189418.7102 215004.2498 226351.5148 0.745658769 0.873699374 0.855378649 0.836655214 0.981219305 0.778158244 0.836834294 0.949868836 1 17.78820544 -5 0.155385517 1.533761099 0.813361949 0.393917473 0.064563857 151.0478626 1.370545687 24.77795008 0.282387595 1.00E-05 5 -0.72039915 ISKEEAMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ISKEEAMR 8 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ;; 83.883 0.016275 1092770000 1083700 1766790 927750 908460 1950290 562820 1055190 1568420 2203500 FALSE TRUE 1015873.151 1897604.97 949756.6681 931772.6216 1797122.09 725296.9974 896974.0554 1764240.69 1835721.615 0.553391725 1.033710643 0.517375108 0.50757839 0.978973106 0.395101845 0.488622048 0.96106113 1 20.80791586 1.161497562 8.064888757 0.989203475 0.653081336 0.313179487 0.20944097 0.363697897 32.89301963 0.20002456 0.050195717 14.50432633 -1.161497562 -0.336122139 ISKPGAVST(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISKPGAVSTPVK 12 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 ISKPGAVS(0.043)T(0.957)PVK 92.8 0.012175 563630000 930990 519840 714180 636050 784200 673230 948950 719090 864580 TRUE FALSE 872720.9978 558329.4945 731120.6869 652372.1198 722612.0953 867580.572 806663.7571 808869.9694 720276.0126 1.211648011 0.775160473 1.015056276 0.905725178 1.003243316 1.204511266 1.119937001 1.12300001 1 19.45819033 2.416878609 6.094522459 1.123797412 0.949970701 0.212808038 0.118869542 0.21975556 16.17891415 0.037818618 0.031622545 261.1431326 -2.416878609 -0.173826711 ISLGMPVGPNAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISLGMPVGPNAHK 13 0 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 77.22 0.026541 143070000 224520 236740 230210 219240 266860 183410 275880 228130 302030 FALSE TRUE 210467.694 254268.4759 235670.6899 224866.0696 245901.8921 236357.4896 234514.3551 256612.5327 251619.2418 0.836453097 1.010528742 0.936616326 0.893675968 0.977277772 0.939345846 0.932020753 1.01984463 1 17.94088273 1.239264622 24.99999624 1.009922341 0.94053732 0.312692005 0.046624272 22.78908082 809530.3538 0.032994496 0.01040925 17.34860752 -1.239264622 -0.069385021 ISLPGQMAGT(ph)PITPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISLPGQMAGTPITPLK 16 0 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 1 ISLPGQMAGT(1)PITPLK;ISLPGQMAGT(0.999)PIT(0.001)PLK 171.98 5.29E-08 115760000 455470 386630 395750 361220 493040 328900 469830 457250 430100 TRUE FALSE 426962.9457 415256.4875 405137.3769 370489.5167 454318.6272 423848.0908 399383.3532 514338.669 358313.5314 1.191590348 1.158919357 1.130678418 1.033981372 1.267936004 1.182897249 1.11461979 1.435443052 1 18.450863 2.720660101 24.92228835 1.197976857 1.134127863 0.084236046 0.116243466 2232.012491 3107550.773 0.034122098 0.032223766 525.6057417 -2.720660101 -0.063848994 ISLS(ph)PFSTTDSAYEWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISLSPFSTTDSAYEWK 16 0 Q9UPY3-2;Q9UPY3;H0YJZ6;Q9UPY3-3 Q9UPY3-2 DICER1 Endoribonuclease Dicer 1 IS(0.001)LS(0.994)PFS(0.004)T(0.001)TDSAYEWK 172.91 2.77E-12 0 80083 67266 82537 94316 93726 59532 80971 61362 70279 TRUE FALSE 75070.74798 72246.44463 84494.81662 96736.30824 86365.13803 76717.92198 68830.15025 69023.18077 58548.98088 1.2821871 1.233948799 1.443147521 1.652228729 1.475092081 1.310320365 1.175599459 1.178896366 1 15.83735644 1.664813498 1.774194166 1.083687087 1.405401584 0.573689244 0.119176985 0.284204774 1.825564431 0.101015384 0.038054585 46.21825002 -1.664813498 0.321714498 ISLSKS(ph)PTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISLSKSPTK 9 1 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 ISLS(0.356)KS(0.601)PT(0.043)K 148.18 0.00023839 310460000 430620 317390 285440 269560 477340 166490 333790 391580 642800 TRUE FALSE 403668.2629 340889.8858 292210.7716 276477.366 439851.6419 214552.9603 283741.2883 440469.625 535512.5274 0.753797983 0.636567528 0.545665613 0.516285524 0.821365737 0.40064975 0.529849955 0.82251974 1 19.0305608 1.038015178 4.140006741 0.99759051 0.591516849 0.558321658 0.120217584 0.12449954 4.794869971 0.108965893 0.027872539 10.91478481 -1.038015178 -0.406073661 ISLSKS(ph)PTKTDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISLSKSPTKTDPK 13 2 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 IS(0.033)LS(0.226)KS(0.719)PT(0.018)KT(0.005)DPK;IS(0.006)LS(0.04)KS(0.933)PT(0.019)KT(0.001)DPK 104.21 0.00080874 12164800000 29211000 12036200 18597100 16815200 19395200 10872200 23957000 13900500 32890000 TRUE FALSE 27382735.65 12927372.77 19038231.99 17246706.5 17871979.23 14010827.64 20364870.26 15636008.02 27400446.52 0.999353628 0.471794237 0.694814662 0.629431586 0.652251386 0.511335742 0.743231328 0.570647928 1 24.70769607 -1.304620979 3.692258992 1.000958496 0.645143697 0.34711392 0.145813685 10330865.68 11090351.14 67310.1349 0.029612474 0.049588277 1.304620979 -0.355814799 ISMFCHVEPEQVICVHDVSSIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISMFCHVEPEQVICVHDVSSIYR 23 0 P17812;B4E1E0;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6;A0A3B3ITB8 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ; 241.65 1.53E-37 615520000 444220 509040 545810 492180 564390 458000 586800 479210 503830 FALSE TRUE 416417.0632 546729.8513 558756.871 504810.1721 520065.086 590217.165 498814.7876 539040.4234 419737.5181 0.992089211 1.30255178 1.331205448 1.202680605 1.239024542 1.406157752 1.188396953 1.284232169 1 18.6791279 -0.486160844 7.942076883 1.00000001 1.25728394 0.319370779 0.109945328 0 0 0.096462225 0.022736364 0.3264669 0.486160844 0.25728393 ISMPDFDLHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISMPDFDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 179.19 7.21E-06 3277000000 7425800 6901900 7202800 6754100 8521000 5374200 8471800 7045100 9096400 FALSE TRUE 6961032.433 7412923.857 7373653.817 6927421.641 7851795.032 6925644.297 7201532.238 7924696.243 7578152.075 0.918565946 0.978196767 0.973014759 0.914130724 1.036109457 0.913896188 0.95030189 1.045729376 1 22.85341466 1.246880865 24.99898779 1.022864693 0.95790059 0.349508096 0.03838364 173.3085052 520733.7159 0.023960864 0.008421844 17.65553432 -1.246880865 -0.064964103 ISMPDFDLHLKGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISMPDFDLHLKGPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 210.56 3.04E-09 158425000 453840 594820 505200 590190 953330 446590 880650 545840 2322400 FALSE TRUE 425434.9645 638861.0917 517183.5826 605335.2746 878459.3073 575513.2832 748604.7081 613989.3255 1934776.437 0.219888436 0.330198921 0.267309221 0.312870915 0.454036596 0.297457253 0.386920522 0.31734381 1 20.88373544 -5 0.299808388 6.614494394 0.289072345 0.926914083 0.05997382 61.04380741 0.564962658 215.3226846 0.054975379 1.00E-05 5 -6.325422049 ISMPDLDLHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISMPDLDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 136.5 9.79E-05 972970000 1469600 1407690 1318950 1325600 1715750 1090490 1681650 1489600 1972110 FALSE TRUE 1377620.359 1511916.832 1350236.117 1359617.14 1581001.916 1405296.76 1429502.194 1675579.839 1642952.101 0.838503057 0.920244012 0.821835351 0.827545209 0.962293371 0.855348589 0.870081479 1.019859215 1 20.64785899 1.240673139 24.98090776 1.00992966 0.871617957 0.644913084 0.042905692 30.86153443 364980.917 0.030294701 0.0098284 17.40496439 -1.240673139 -0.138311702 ISMPDLDLHLKS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ISMPDLDLHLKSPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ISMPDLDLHLKS(1)PK;ISMPDLDLHLKS(1)PK;ISMPDLDLHLKS(1)PK 232.84 1.05E-14 2166050000 6670230 3564700 5218600 6683850 7268680 2690600 4844060 2832290 5222020 TRUE FALSE 6252752.211 3828634.097 5342387.656 6855368.907 6697827.193 3467332.542 4117738.173 3185907.641 4350431.126 1.437271854 0.880058547 1.228013386 1.575790699 1.539577802 0.797008949 0.946512668 0.732319981 1 22.05272695 2.219465187 24.99995398 0.870879244 1.267370187 0.53464337 0.209945597 243.0403124 318189.1421 0.08588018 0.063526444 165.7544463 -2.219465187 0.396490943 ISMPDVDLHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ISMPDVDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;; 184.24 4.99E-06 3768413000 4569330 3868551 4117727 3896305 4716240 3155547 4693400 3907965 4889110 FALSE TRUE 4283343.792 4154982.541 4215401.429 3996290.783 4345845.535 4066502.193 3989668.241 4395883.033 4073085.956 1.051621262 1.020106766 1.034940454 0.981145703 1.06696632 0.998383593 0.979519776 1.079251231 1 21.95769083 8 0.651908868 1.015541914 3.981700284 0.063721808 0.033584166 588.3865668 3.740761471 0.012202132 2520.186918 99999999.99 -8 2.96615837 ISMPDVDLHLKGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISMPDVDLHLKGPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 60.55 0.055309 911170000 433430 1063900 761480 824330 993620 772110 744150 856960 896060 FALSE TRUE 406302.39 1142672.263 779542.6652 845483.7034 915585.0933 995005.6228 632571.6158 963953.3424 746501.7972 0.544275167 1.530702628 1.044260936 1.132594331 1.226500856 1.332891128 0.847381236 1.291294068 1 19.50978621 1.7459615 24.99999998 1.035361173 1.173757364 0.009666476 0.273316149 5.142288156 17419.70835 0.114297089 0.063383151 55.71363575 -1.7459615 0.138396191 ISMPDVDLHMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISMPDVDLHMK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 98.353 0.0055837 354130000 910200 937110 902760 854900 1232640 665180 1045310 983010 1477910 FALSE TRUE 853232.2068 1006494.599 924173.8935 876838.1813 1135833.427 857206.6677 888575.4697 1105740.962 1231237.273 0.692987635 0.817465992 0.750605845 0.712160199 0.922513841 0.696215657 0.72169312 0.898073009 1 20.23167738 1.037566516 4.230567587 0.998765712 0.763333277 0.588732692 0.068748035 0.118620383 4.797187867 0.06119353 0.015628491 10.90351477 -1.037566516 -0.235432435 ISMPDVDLHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISMPDVDLHVK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 99.671 0.0046011 418110000 1182100 1025110 1093500 1018300 1291240 812110 1155130 1018670 1437360 FALSE TRUE 1108114.471 1101010.211 1119438.336 1044431.302 1189831.219 1046552.973 981928.9802 1145853.192 1197455.33 0.925391071 0.919458274 0.934847679 0.872208988 0.993633072 0.873980805 0.820013035 0.956906836 1 20.19154041 ISMQDVDLSLGS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 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;ISMQDVDLSLGS(1)PK;ISMQDVDLS(0.001)LGS(0.999)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLS(0.001)LGS(0.999)PK 311.09 1.05E-55 2539170000 6017934 3903234 4942988 6505782 6864334 2914884 4174982 2770811 4346837 TRUE FALSE 5641282.253 4192233.507 5060238.01 6672731.38 6325236.897 3756363.692 3548982.208 3116752.853 3621321.823 1.557796443 1.157652844 1.397345571 1.842623138 1.746665225 1.037290767 0.980023975 0.860667183 1 21.78808496 2.121070392 6.736261921 0.961201718 1.481311836 0.681932102 0.191987611 0.159444393 8.781637864 0.082427031 0.060698491 132.1509811 -2.121070392 0.520110119 ISNDNPEEHVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ISNDNPEEHVLK 12 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 ;;; 142.57 6.15E-05 759910000 1894480 1740770 1904110 1853740 2020730 1391330 2226510 1724930 2385250 FALSE TRUE 1775907.879 1869658.422 1949276.388 1901310.107 1862030.017 1792984.385 1892665.495 1940291.308 1987136.366 0.893702068 0.940880784 0.980947469 0.956809074 0.937041891 0.902295593 0.952458788 0.976425846 1 20.92225945 -5 0.230627958 1.304426439 0.938330632 0.348040702 0.02677275 222.0425253 2.222214026 31.45748085 0.047897305 1.00E-05 5 -0.366095807 ISNLS(ph)PEEEQGLWK ddPTM_SK-BR-3_Pertuzumab_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 333.98 1.66E-68 1334725000 2228623 1545208 1851033 1778630 2059685 1378316 2179066 1662374 2559558 TRUE FALSE 2089137.465 1659616.808 1894940.377 1824272.657 1897925.648 1776213.454 1852335.283 1869925.053 2132351.234 0.979734216 0.778303678 0.888662405 0.855521655 0.890062396 0.832983528 0.868682069 0.876931072 1 21.02401366 0.577113309 2.041264645 0.999987448 0.861873384 0.37915753 0.050877935 2.708071069 11.97238257 0.043148426 0.011845255 3.776707134 -0.577113309 -0.138114064 ISNYGWDQSDKFVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISNYGWDQSDKFVK 14 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 222.45 3.55E-12 2537200000 4428900 3233200 4126900 3961000 4056000 2888300 4814900 3467300 3996600 FALSE TRUE 4151703.055 3472589.492 4224792.017 4062645.966 3737458.121 3722105.322 4092950.444 3900200.037 3329541.641 1.246929308 1.042963226 1.268880967 1.220181756 1.122514305 1.11790322 1.229283453 1.171392479 1 21.66689215 -1.123510853 4.536857669 0.999981561 1.17467884 0.396957326 0.06867861 1.22E-05 2.35E-06 0.063253909 0.014907516 0.075246993 1.123510853 0.174697279 ISPDTVLHLILPESPGSHEESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ISPDTVLHLILPESPGSHEESR 22 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 ;; 247.52 2.67E-31 132807300 104439 163951 142693 165047 176656 135195 179194 153846 137794 FALSE TRUE 97902.34942 176090.1026 146077.7453 169282.3854 162782.1504 174223.6018 152325.5233 173054.0118 114795.2912 0.852842903 1.53394883 1.272506422 1.474645725 1.418021146 1.517689445 1.326931807 1.50750096 1 16.80870394 -1.407610049 3.319899709 0.995920541 1.378282168 0.241953955 0.200316668 27947301.36 38513910.45 1083782.38 0.041926473 0.039119199 1.407610049 0.382361627 ISPFEHQTYCQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 168.98 4.51E-05 1033680000 731920 1261210 875220 866200 1257070 647240 966290 1195920 1228030 FALSE TRUE 686110.4337 1354591.301 895980.6317 888428.1585 1158344.793 834087.6809 821403.7851 1345233.245 1023063.86 0.670642822 1.324053516 0.875781725 0.868399514 1.132231172 0.815284083 0.802886132 1.314906427 1 19.96446477 4.99559938 15.83495255 0.997267863 0.392566796 0.239634534 0.190954903 1917961.743 63304114.68 0.044578324 19629565.4 98991.83627 -4.99559938 -0.604701068 ISQHEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISQHEAK 7 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 73.248 0.049407 210770000 289900 353920 335970 348050 385430 242950 389410 368800 391660 FALSE TRUE 271755.6765 380124.6051 343939.3671 356981.5522 355159.8825 313085.721 331021.5856 414845.4918 326289.4158 0.832866968 1.164992141 1.054092932 1.09406415 1.088481162 0.959533794 1.014502983 1.271403459 1 18.31579266 4.752153433 24.43387276 1.076222892 0.832866747 0.437173674 0.088298342 1649.767858 2965481.816 0.02001039 0.389871192 56513.65986 -4.752153433 -0.243356146 ISQMPVILTPLHFDRDPLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISQMPVILTPLHFDRDPLQK 20 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ; 237.15 8.22E-30 668880000 1576160 1401580 1482260 1334180 1589710 1103500 1880410 1322900 1665530 FALSE TRUE 1477510.959 1505354.442 1517419.907 1368417.318 1464860.589 1422062.536 1598459.977 1488066.977 1387542.283 1.064840313 1.084907076 1.093602642 0.986216661 1.055723207 1.024878703 1.15200812 1.072448022 1 20.40410031 -0.801796541 7.777868627 1 1.072185598 0.180806333 0.043392003 0 0 0.042184938 0.009943085 0.157835053 0.801796541 0.072185598 ISQRDPS(ph)PESNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ISQRDPSPESNK 12 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 ISQRDPS(1)PESNK;ISQRDPS(0.997)PES(0.003)NK;ISQRDPS(0.998)PES(0.002)NK;ISQRDPS(0.998)PES(0.002)NK 174.4 1.85E-05 1924650000 3155220 2564620 2752260 2799690 3166010 1860500 3352350 2428990 4273670 TRUE FALSE 2957740.412 2754507.133 2817544.907 2871534.785 2917364.346 2397596.147 2849696.239 2732254.748 3560366.868 0.830740348 0.773658231 0.791363646 0.80652778 0.819399925 0.673412667 0.800393989 0.767408205 1 21.76359448 -0.975523781 5.20839695 1.00000101 0.781133658 0.712592084 0.043325239 4.64E-07 9.13E-08 0.038330844 0.009034625 0.105797698 0.975523781 -0.218867352 ISQRDPS(ph)PESNKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISQRDPSPESNKK 13 2 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 IS(0.009)QRDPS(0.99)PESNKK;IS(0.001)QRDPS(0.999)PES(0.001)NKK 67.646 0.027437 327720000 1124060 714150 862970 856380 937950 583750 1226310 718100 1429410 TRUE FALSE 1053707.091 767026.4091 883440.0559 878356.1606 864287.1905 752269.1486 1042436.2 807756.3657 1190832.237 0.884849317 0.644109544 0.74186777 0.737598575 0.725784173 0.631717152 0.875384599 0.678312478 1 20.18353875 -1.108791149 0.475527405 1.102388938 0.727368111 0.464174456 0.086045258 17.23288978 2.317409125 2.436588837 0.039625908 0.07784108 1.108791149 -0.375020826 ISREPEPAAGPQAEESATVSAPAPMS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISREPEPAAGPQAEESATVSAPAPMSPTR 29 1 Q9BWG6-2;Q9BWG6 Q9BWG6-2 SCNM1 Sodium channel modifier 1 1 ISREPEPAAGPQAEESATVS(0.011)APAPMS(0.926)PT(0.062)R 126.82 3.02E-05 210900000 98641 120210 116080 119440 136740 94254 140130 118570 170180 TRUE FALSE 92467.23589 129110.4735 118833.4724 122505.0326 126000.992 121463.5997 119118.8074 133373.7255 141775.8586 0.652207201 0.910666137 0.838178471 0.864075406 0.888733761 0.856729777 0.840191049 0.940736504 1 17.11325237 -5 0.021836408 2.127933844 4.38E-12 0.496007042 0.064063847 2702.967626 4.464728247 301.1615969 155.9462262 1.00E-05 5 -2.127933844 ISRPGDSDDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 ISRPGDSDDSR 11 1 A0A3B3ITJ4;M0R1W6;B4DVF8;M0QYL7;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;;;;;; 160.15 2.54E-05 21238776000 7279720 7600970 7430950 7047130 7010300 6349390 8270590 6609390 7518170 FALSE TRUE 6824095.32 8163753.728 7607215.643 7227971.287 6459739.316 8182355.819 7030491.81 7434586.891 6263338.858 1.089529958 1.303418818 1.214562363 1.154012492 1.03135715 1.306388814 1.122483067 1.187000585 1 22.5785005 -4.999999999 0.188262156 0.192930957 1.223394281 0.266308991 0.087610501 162.5987517 1.587613449 49.07913778 0.229912088 1.00E-05 4.999999999 1.030463324 ISS(ph)LLEEQFQQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISSLLEEQFQQGK 13 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 1 IS(0.044)S(0.956)LLEEQFQQGK;IS(0.012)S(0.988)LLEEQFQQGK 163.27 4.09E-05 81918000 220144 174404 199921 193249 212744 160310 246911 183431 256450 TRUE FALSE 206365.58 187317.0536 204663.2205 198208.0965 196035.9444 206588.8946 209888.9878 206332.7641 213646.8383 0.965919186 0.876760242 0.957951085 0.927737092 0.91757007 0.966964437 0.982410924 0.965765587 1 17.70486844 2.129620462 4.325628721 0.9794481 0.925929367 0.489887293 0.025308966 0.174559351 5.782286229 0.009393323 0.006765774 134.7784513 -2.129620462 -0.053518733 ISS(ph)PTETER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISSPTETER 9 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 1 IS(0.004)S(0.907)PT(0.09)ETER;IS(0.028)S(0.971)PT(0.002)ETER 150.06 9.03E-05 1395000000 1946730 1914900 1877480 1934690 1903940 1566620 2058790 1585090 1994730 TRUE FALSE 1824887.644 2056681.188 1922014.712 1984337.421 1754412.233 2018877.762 1750093.552 1782991.976 1661796.677 1.098141349 1.237625046 1.156588372 1.194091581 1.055732183 1.214876519 1.053133381 1.072930281 1 20.66431245 1.441375223 0.613132299 0.997821955 1.181150427 0.466533995 0.057283194 0.527604404 0.464676461 0.049810631 0.024701712 27.62963978 -1.441375223 0.183328471 ISSDLDGHPVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ISSDLDGHPVPK 12 0 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 ;;;;;; 115.92 0.00089758 9035870000 15964460 18157060 15585020 14319100 23712500 12927960 19963860 20805760 25252830 FALSE TRUE 14965272.95 19501427.61 15954704.03 14686552.35 21850215.9 16660052.18 16970464.53 23403404.94 21037969.53 0.71134588 0.926963393 0.758376611 0.698097425 1.038608591 0.791903998 0.80665886 1.112436488 1 24.32649213 1.24435988 24.9942181 1.056218277 0.824576062 0.473493609 0.103924589 104.5914841 450793.497 0.06767418 0.023225735 17.55334463 -1.24435988 -0.231642215 ISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMR 34 0 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 ;;;;; 342.34 3.02E-118 2530387000 539598 1120915 630128 584022 1285638 519773 684232 1061804 597205 FALSE TRUE 505825.5244 1203908.713 645074.9337 599008.9933 1184669.177 669823.0273 581637.7637 1194372.567 497527.6274 1.016678264 2.419782634 1.296561031 1.203971318 2.381112349 1.346303181 1.169056212 2.400615566 1 18.92441711 -1.831100832 2.684786135 0.771440745 1.649401433 0.121917839 0.551669566 30569000.24 19644613.56 44917493.78 0.12227869 0.01475364 1.831100832 0.877960688 ISSIQSIVPALEIANAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISSIQSIVPALEIANAHR 18 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 189.9 3.04E-14 1551350000 807530 834130 711490 692370 1034010 748110 709190 828060 986500 FALSE TRUE 756988.1388 895889.8531 728366.8788 710137.3864 952803.0256 964077.2124 602853.5433 931445.1138 821846.777 0.921081837 1.090093529 0.886256294 0.864075161 1.159343873 1.173061986 0.733535204 1.133356168 1 19.64850992 ISSLLEEQFQQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ISSLLEEQFQQGK 13 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 202.65 2.14E-07 93126000 80088 74116 80211 84405 86638 65578 94209 77048 94176 FALSE TRUE 75075.43504 79603.62576 82113.6428 86570.9752 79833.80096 84509.30403 80083.23504 86667.6124 78457.4172 0.956894042 1.014609308 1.046601401 1.103413524 1.017543067 1.077135943 1.020722296 1.104645239 1 16.25962222 4.761770657 1.229282893 1.053213883 0.910157607 0.437897624 0.0349987 1.353288232 1.680351779 0.008746376 0.24987139 57779.08454 -4.761770657 -0.143056276 ISSLPVSRPIS(ph)PSPSAILER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ISSLPVSRPISPSPSAILER 20 1 Q5T5P2;Q5T5P2-3;Q5T5P2-7;Q5T5P2-9;Q5T5P2-2;Q5T5P2-10;Q5T5P2-8;Q5T5P2-6;Q5T5P1;Q5T5P2-4;Q5T5P0 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 ISSLPVSRPIS(0.869)PS(0.113)PS(0.018)AILER;ISSLPVSRPIS(0.976)PS(0.024)PSAILER;ISSLPVS(0.001)RPIS(0.835)PS(0.165)PSAILER;ISSLPVS(0.003)RPIS(0.896)PS(0.074)PS(0.028)AILER;ISSLPVSRPIS(0.907)PS(0.066)PS(0.027)AILER;ISSLPVSRPIS(0.957)PS(0.029)PS(0.015)AILER 256.89 2.03E-36 3855846000 1768264 1921010 1894340 1914825 2089297 1623434 2027737 1600543 2214737 TRUE FALSE 1657591.513 2063243.579 1939274.639 1963962.651 1925212.041 2092093.042 1723696.661 1800374.317 1845083.087 0.898383127 1.118238845 1.051050033 1.064430467 1.043428372 1.133874705 0.934210862 0.975768695 1 20.81525435 1.691199203 10.05450982 0.967170064 1.059291067 0.255220508 0.064607002 0.131518207 21.74965958 0.027765247 0.014985384 49.11330978 -1.691199203 0.092121003 ISSPTETER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ISSPTETER 9 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;; 232.97 9.02E-10 6459200000 1743980 1835340 1793280 1838420 1901210 1534760 1899980 1560690 2088850 FALSE TRUE 1634827.405 1971230.483 1835817.448 1885596.97 1751896.636 1977820.297 1615095.638 1755545.582 1740207.441 0.939443981 1.132756037 1.05494173 1.08354724 1.006717127 1.136542835 0.928105236 1.008813973 1 20.73082786 1.723706811 14.8309942 0.976767762 1.065965605 0.272701388 0.060853655 0.135454434 113.4412843 0.025267006 0.013934339 52.93059924 -1.723706811 0.089197844 ISTAS(ph)GDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ISTASGDGR 9 0 P63092-4;P63092;P63092-3;A0A590UJ58;B0AZR9;A0A590UJF0;A0A590UJY2;A0A0A0MR13;P63092-2;Q5JWF2 P63092-4;P63092-2;Q5JWF2 GNAS Guanine nucleotide-binding protein G(s) subunit alpha isoforms short;Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas 1 IST(0.007)AS(0.993)GDGR;IS(0.001)T(0.129)AS(0.87)GDGR;IS(0.006)T(0.113)AS(0.88)GDGR;IST(0.015)AS(0.985)GDGR;IST(0.004)AS(0.996)GDGR 144.55 0.00010415 1605770000 2721790 2867770 2486780 2523560 2956440 1913750 2630380 2333520 2123890 TRUE FALSE 2551438.022 3080102.675 2545767.596 2588318.822 2724253.128 2466218.558 2235978.938 2624865.109 1769399.038 1.441979999 1.740762037 1.43877528 1.462823685 1.539648813 1.393817056 1.263693994 1.483478318 1 20.75482801 -2.889139301 0.116067316 2.05E-05 1.798168189 0.68092783 0.107406052 43.75736518 0.559482377 12.19406662 1.245428123 0.001290805 2.889139301 1.798147674 ISVIVETVYTHVLHPYPTQITQSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISVIVETVYTHVLHPYPTQITQSEK 25 0 P04843 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ; 255.2 4.26E-45 420010000 361010 334880 337380 333430 451510 294764 491120 402770 321390 FALSE TRUE 338415.0285 359674.8636 345382.8129 341986.3783 416050.2259 379857.5817 417481.1153 453056.7211 267747.9327 1.263931434 1.343333859 1.289955106 1.277269911 1.553887724 1.418713406 1.55923189 1.692101659 1 18.03051591 2.748014657 24.09144564 1.48321966 1.301296534 0.127275597 0.181333036 616.7096215 1571541.893 0.048959158 0.051277228 559.7764927 -2.748014657 -0.181923127 ISVSS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISVSSPGR 8 0 O75864;O75864-2 O75864 PPP1R37 Protein phosphatase 1 regulatory subunit 37 1 ISVS(0.041)S(0.959)PGR;ISVS(0.003)S(0.997)PGR 142.92 0.00063962 915730000 2773850 3310200 2919760 2961660 3343700 2279700 3352700 2747680 2735380 TRUE FALSE 2600239.68 3555290.652 2989018.086 3037661.21 3081099.29 2937812.382 2849993.76 3090733.896 2278827.407 1.141042833 1.560140378 1.311647419 1.3329931 1.352054693 1.28917722 1.250640462 1.356282572 1 21.11986023 -3.417642496 0.20892016 0.215286484 1.399266756 0.456017207 0.107542882 54.29882051 0.979776639 18.48279779 0.224434947 0.000382259 3.417642496 1.183980272 ISVYYNEATGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISVYYNEATGGK 12 0 Q5JP53;P07437 Q5JP53 TUBB Tubulin beta chain 0 ; 265.82 2.72E-21 1084360000 509190 412644 482810 465260 561390 401107 527250 467510 694500 FALSE TRUE 477320.7068 443196.5911 494262.4812 477199.3593 517300.6939 516900.0795 448193.7572 525879.6526 578583.4634 0.824981592 0.766002866 0.854263062 0.82477186 0.894081367 0.893388962 0.774639764 0.908908889 1 19.14216556 -5 0.152289028 1.597764956 0.784348954 0.60152872 0.043576986 94.67817949 0.850565201 17.09429108 0.212006468 1.00E-05 5 -0.813416002 ISYT(ph)PPES(ph)PVPSYASSTPLHVPVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ISYTPPESPVPSYASSTPLHVPVPR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 2 IS(0.412)Y(0.127)T(0.462)PPES(0.997)PVPS(0.003)YASSTPLHVPVPR;IS(0.018)Y(0.032)T(0.95)PPES(0.987)PVPS(0.002)YAS(0.003)S(0.003)T(0.004)PLHVPVPR;IS(0.111)Y(0.216)T(0.674)PPES(0.993)PVPS(0.004)Y(0.001)ASSTPLHVPVPR;IS(0.15)Y(0.118)T(0.734)PPES(0.997)PVPS(0.001)YASSTPLHVPVPR 99.34 0.012398 848649000 198152 233504 217287 222846 240388 192103 234375 199321 244122 TRUE FALSE 185750.02 250792.8791 222441.1503 228564.6056 221508.8962 247560.0176 199232.6446 224206.6656 203376.4611 0.913330968 1.233146047 1.093740883 1.123849852 1.089157 1.2172501 0.979624896 1.102421905 1 17.63379319 1.704472646 13.01440168 1.031396272 1.123251647 0.150229352 0.091734173 0.200424865 62.86076761 0.03848137 0.021124834 50.63754551 -1.704472646 0.091855374 ISYT(ph)PPESPVPSYASSTPLHVPVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ISYTPPESPVPSYASSTPLHVPVPR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 1 IS(0.009)Y(0.004)T(0.983)PPES(0.004)PVPSYASSTPLHVPVPR;IS(0.026)Y(0.013)T(0.961)PPESPVPSYASSTPLHVPVPR 148.15 8.10E-07 275230000 198813 228520 208309 231534 217449 185035 246490 190895 195506 TRUE FALSE 186369.6492 245439.8586 213250.1879 237475.5544 200371.4327 238451.6007 209531.1128 214728.661 162874.7856 1.144251079 1.506923602 1.309289139 1.458025277 1.23021763 1.464017895 1.286455187 1.3183665 1 17.31340375 0.183955961 0.818947771 0.994218159 1.364714035 0.474189283 0.111917282 2.686778688 2.082808257 0.132955974 0.032195173 1.527411164 -0.183955961 0.370495875 IT(ph)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ITPEPAVSNTEEPSTTSTASNYPDVLTRPSLHR 33 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 IT(1)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR;IT(1)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR 136.66 2.99E-08 1378700000 191124 185322 223756 210283 207579 219722 286487 189707 159993 TRUE FALSE 179161.89 199043.4337 229063.598 215679.2178 191276.5827 283152.1745 243530.934 213392.3365 133289.1347 1.34415975 1.493320773 1.718546665 1.618130527 1.435050074 2.124345508 1.827087665 1.60097323 1 17.02419966 ITADGAHFELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ITADGAHFELR 11 0 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 182.35 5.83E-06 193170000 158700 184310 161860 177030 209280 136910 168970 171520 160300 FALSE TRUE 148767.2503 197956.5042 165699.3956 181572.8895 192843.993 176433.6945 143634.5171 192934.6496 133544.8944 1.113986805 1.482321769 1.240776717 1.359639321 1.444038679 1.321156419 1.075552291 1.444717527 1 17.0269653 -0.599094146 0.377846713 0.903458901 1.337579703 0.300960886 0.139945451 10.99303022 1.454897857 1.449424296 0.09714916 0.251713121 0.599094146 0.434120802 ITADLLSNGIDVYPQKEFDEDSEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ITADLLSNGIDVYPQKEFDEDSEDR 25 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 ; 212.01 9.55E-26 425040000 673250 494311 585030 530805 553419 490699 670560 506128 515029 FALSE TRUE 631112.4843 530910.3008 598907.1879 544426.355 509955.7041 632355.8355 570015.7532 569319.1949 429067.3327 1.470893811 1.237358942 1.395834971 1.268859952 1.188521393 1.473791611 1.328499538 1.326876114 1 18.71084454 0.573228543 4.054802674 1.000000095 1.332624656 0.566238646 0.092475789 23.9397126 226.5290034 0.080785747 0.020618192 3.743075121 -0.573228543 0.332624561 ITADLLSNGIDVYPQKEFDEDSEDRLVNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ITADLLSNGIDVYPQKEFDEDSEDRLVNEK 30 2 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 76.162 0.0023136 201610000 60701 43321 50994 42009 56838 37718 67643 41481 82881 FALSE TRUE 56901.83276 46528.53192 52203.60176 43087.02206 52374.17275 48606.5743 57500.56012 46659.99416 69047.62567 0.82409543 0.673861432 0.756052091 0.62401888 0.758522429 0.703957215 0.832766653 0.675765368 1 16.07530419 -2.546851007 0.363744283 1.441026782 0.720615712 0.607985397 0.067032156 41.24857263 1.681365989 14.37933624 0.044050521 0.002838893 2.546851007 -0.72041107 ITAEEMYDIFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ITAEEMYDIFGK 12 0 Q9Y3B4 Q9Y3B4 SF3B6 Splicing factor 3B subunit 6 0 179.67 0.0002877 0 71589 67541 70415 71401 94745 65204 83539 66109 97481 FALSE TRUE 67108.37228 72541.80592 72085.27705 73233.27054 87304.10988 84027.3363 71013.10249 74362.85417 81210.79135 0.826347966 0.893253282 0.887631753 0.901767725 1.075030897 1.034681905 0.874429387 0.915677005 1 16.30938383 2.9801757 24.40157869 0.970717632 0.879132595 0.429863629 0.058867918 654.497784 805617.2939 0.018894525 0.020309907 955.3790193 -2.9801757 -0.091585037 ITAHSS(ph)PPLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ITAHSSPPLTK 11 0 A0A1W2PNZ9;Q15652-3;Q15652;Q15652-2 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 ITAHS(0.045)S(0.955)PPLTK 96.464 0.0045042 295040000 418210 359010 423790 401060 444280 357570 523650 420370 523000 TRUE FALSE 392034.9826 385591.4739 433842.4989 411351.8786 409388.0409 460794.6543 445133.5438 472854.1198 435707.9213 0.899765562 0.884976965 0.99571864 0.944100069 0.939592835 1.05757695 1.021632892 1.085254816 1 18.73300182 3.124210748 0.540009319 1.048523756 0.883442617 0.645450047 0.038618256 0.655060687 0.393529233 0.029686907 0.054038665 1331.100198 -3.124210748 -0.165081139 ITDDSRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ITDDSRR 7 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ; 98.458 0.018035 735840000 1155590 1275090 1137960 1171380 1529040 1852020 2308400 1076120 1421830 FALSE TRUE 1083263.685 1369498.99 1164952.949 1201439.594 1408955.366 2386668.109 1962276.85 1210475.951 1184517.388 0.914519024 1.15616622 0.983483198 1.014286161 1.189476306 2.014886513 1.656604513 1.021914886 1 20.17586795 2.462796244 24.98759379 1.527096036 1.041403673 0.257986591 0.302050496 239.6080767 417953.7461 0.098393468 0.082353248 290.2660508 -2.462796244 -0.485692363 ITDFENRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ITDFENRR 8 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 123.16 0.0021802 640230000 1021910 1332530 1065330 1028520 1310710 762540 1217410 1080740 1420420 FALSE TRUE 957950.4773 1431191.908 1090600.131 1054913.564 1207772.124 982672.9192 1034870.672 1215672.768 1183342.726 0.809529189 1.20944835 0.921626598 0.891469176 1.020644398 0.830421228 0.874531655 1.027320946 1 20.17443654 3.722263813 23.91492457 0.924696778 1.046299348 0.032103327 0.115760224 187.4520372 922902.03 0.027800988 0.044674662 5275.502255 -3.722263813 0.12160257 ITDKEAAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 ITDKEAAER 9 1 Q9NQG5;A2A2M0 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ;;;;;; 98.04 0.0057304 3775170000 5861730 5740310 5731340 5924700 6512910 4221960 6978370 5149130 7701530 FALSE TRUE 5494854.783 6165328.525 5867290.091 6076737.832 6001412.32 5440771.314 5932028.203 5792010.215 6416094.889 0.856417319 0.960916045 0.914464358 0.947108473 0.935368386 0.847987975 0.924554313 0.902731383 1 22.61326405 -0.882162612 4.392121266 1.000001005 0.915573071 0.368388265 0.036142112 913.8182075 19791048.98 52.98778707 0.007913225 0.131170867 0.882162612 -0.084427934 ITDLYTDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ITDLYTDLR 9 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 101.64 0.0089423 26045000 67180 88929 71450 76722 95716 57665 80601 75835 87120 FALSE TRUE 62975.32372 95513.39569 73144.82774 78690.81641 88198.85146 74311.94939 68515.62831 85303.16668 72579.10918 0.867678378 1.31599019 1.00779451 1.084207526 1.215209892 1.023875193 0.944013079 1.175312947 1 16.14726673 2.061002658 24.9978729 1.021151084 1.115303934 0.039406134 0.130921254 150.4049742 61632.32907 0.045379823 0.033515216 115.0807432 -2.061002658 0.09415285 ITDSAGHILYSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ITDSAGHILYSK 12 0 P49755;G3V2K7 P49755 TMED10 Transmembrane emp24 domain-containing protein 10 0 103.88 0.0021983 331060000 420770 847100 477620 523550 983690 387840 721850 795950 576280 FALSE TRUE 394434.7568 909820.1654 488949.3719 536985.1794 906434.9554 499803.1119 613615.2938 895326.1096 480095.1451 0.821576225 1.895083037 1.01844265 1.118497416 1.888031913 1.041050127 1.27811185 1.864893071 1 18.87296082 -1.270549963 4.949289528 0.999909496 1.368917224 0.078572965 0.393444856 0.000351102 5.17E-05 0.340412376 0.080216374 0.053635216 1.270549963 0.369007729 ITEAEKNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 ITEAEKNER 9 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;; 205.59 1.34E-05 12587300000 10502400 9073000 9708000 9718100 13286800 7525790 11416900 9152200 16370200 FALSE TRUE 9845073.531 9744774.36 9938278.344 9967482.899 12243308.32 9698363.402 9705041.834 10294872.32 13637907.86 0.72189031 0.71453587 0.728724555 0.73086598 0.897740947 0.711132785 0.711622481 0.754871819 1 23.70111901 -1.901237059 1.818142151 1.170490408 0.742174731 0.672667684 0.055520995 249631.1869 92068.25932 181755.7052 0.014449362 0.012553445 1.901237059 -0.428315677 ITEFCHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 ITEFCHR 7 0 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 ;;;;;;;; 186.43 0.00059898 8114610000 6290990 8276440 6046100 6010200 7063370 4822905 7561130 6814390 6385430 FALSE TRUE 5897248.166 8889236.229 6189516.347 6164431.907 6508641.412 6215199.38 6427408.751 7665181.592 5319660.482 1.108576043 1.671015709 1.163517177 1.158801756 1.22350692 1.168345123 1.208236648 1.440915566 1 22.34290274 3.735242653 22.79192253 1.201745673 1.42615919 0.175667243 0.171157571 128.2945902 360037.8849 0.039244448 0.069015495 5435.539464 -3.735242653 0.224413516 ITELKEEIEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ITELKEEIEVK 11 1 Q9NQP4;E9PQY2 Q9NQP4 PFDN4 Prefoldin subunit 4 0 139.89 3.54E-05 191020000 897350 498160 679960 646770 735680 497540 916610 637520 986680 FALSE TRUE 841186.4653 535044.2847 696088.9723 663367.2132 677902.6604 641171.7211 779172.8399 717115.7754 821996.7338 1.023345265 0.650908042 0.846826932 0.807019281 0.824702377 0.780017359 0.947902598 0.872407086 1 19.64877314 1.36922644 0.875257573 0.989612855 0.800129908 0.214728993 0.097291788 0.633574396 1.027263558 0.082385137 0.031204477 23.40057021 -1.36922644 -0.189482946 ITES(ph)EEVVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ITESEEVVSR 10 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 ITES(1)EEVVSR 148.18 2.68E-05 67345000 107980 120530 105640 121280 133340 96769 132770 107270 185540 TRUE FALSE 101221.7245 129454.1666 108145.8307 124392.2501 122868.0143 124704.6394 112862.3711 120662.8956 154572.1754 0.654850877 0.837499804 0.699646171 0.804751889 0.794890891 0.806772882 0.730159686 0.780624943 1 17.23792112 0.94674139 21.58847353 1 0.765087668 0.647980541 0.05487092 1843.158286 747129.2757 0.046812668 0.011703167 8.84588705 -0.94674139 -0.234912332 ITESEEVVSR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 253.64 1.01E-16 1821400000 1149560 1254893 1175244 1179576 1185685 1027005 1283397 1039816 1335440 FALSE TRUE 1077611.092 1347806.583 1203121.343 1209845.917 1092566.083 1323484.671 1090963.534 1169639.317 1112546.437 0.968598753 1.211460968 1.081412248 1.087456557 0.982040881 1.189599488 0.980600448 1.0513173 1 20.08543412 1.845564808 0.535387764 0.99962569 1.111891468 0.06885388 0.08222182 1.500111523 0.94912576 0.074086854 0.049528398 70.07527453 -1.845564808 0.112265777 ITFDAFPGEPDKELNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ITFDAFPGEPDKELNPK 17 1 Q12904;Q12904-2 Q12904 AIMP1 Aminoacyl tRNA synthase complex-interacting multifunctional protein 1;Endothelial monocyte-activating polypeptide 2 0 ; 201.96 1.00E-11 568000000 1277630 780260 967730 936900 1071250 708500 1281790 868950 1491040 FALSE TRUE 1197665.419 838031.2623 990685.0126 960942.4402 987118.3462 913032.4485 1089597.489 977440.3203 1242175.792 0.964167413 0.674647878 0.797540106 0.773596174 0.7946688 0.735026761 0.877168511 0.786877612 1 20.24443793 0.125349721 0.587433118 1.011699426 0.77798376 0.372020707 0.078863108 3.176807247 1.404244028 0.15969979 0.029944401 1.334595701 -0.125349721 -0.233715667 ITFHGEGDQEPGLEPGDIIIVLDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ITFHGEGDQEPGLEPGDIIIVLDQK 25 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ; 225.26 7.56E-34 495190000 307651 244631 281675 253716 288684 235786 345594 263778 352039 FALSE TRUE 288395.6731 262743.7338 288356.464 260226.7821 266011.9231 303853.5905 293775.388 296711.2639 293281.4166 0.983341108 0.895875834 0.983207417 0.887293798 0.907019361 1.036047882 1.001684291 1.011694731 1 18.16192613 2.238262217 24.99999995 1.012179675 0.93157982 0.592916424 0.033353851 5.388633902 451396.1407 0.011356919 0.008916973 173.0861097 -2.238262217 -0.080599856 ITFITS(ph)FGGSDEEAAAAAAAAAASGVTTGKPPAPPQPGGPAPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ITFITSFGGSDEEAAAAAAAAAASGVTTGKPPAPPQPGGPAPGR 44 1 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 IT(0.246)FIT(0.204)S(0.303)FGGS(0.247)DEEAAAAAAAAAASGVTTGKPPAPPQPGGPAPGR 174.73 4.27E-21 66580000 65511 62652 64687 61473 76833 58971 74611 60532 86039 TRUE FALSE 61410.78345 67290.81927 66221.40619 63050.50125 70798.84611 75994.97039 63423.7732 68089.55345 71678.53507 0.85675277 0.938786196 0.923866624 0.879628765 0.987727303 1.060219357 0.884836348 0.949929479 1 16.12925353 2.731153326 24.93097351 0.96947541 0.910281196 0.362243404 0.049269243 805.0382485 2709539.174 0.015880115 0.015247317 538.4598499 -2.731153326 -0.059194214 ITFITSFGGS(ph)DEEAAAAAAAAAASGVTTGKPPAPPQPGGPAPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ITFITSFGGSDEEAAAAAAAAAASGVTTGKPPAPPQPGGPAPGR 44 1 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 IT(0.163)FIT(0.142)S(0.123)FGGS(0.571)DEEAAAAAAAAAASGVTTGKPPAPPQPGGPAPGR 141.03 7.08E-14 79334000 50429 43561 50431 52071 54417 48213 64364 46623 69778 TRUE FALSE 47272.73891 46786.30177 51627.24714 53407.23002 50143.30833 62131.31043 54713.21573 52443.98418 58131.60102 0.813202081 0.80483422 0.888109844 0.918729728 0.862582613 1.068804391 0.941195748 0.902159639 1 15.82703502 3.416614427 0.728911246 0.969922254 0.793486364 0.566794946 0.05264399 0.567204921 0.620753652 0.026950796 0.062402863 2609.843268 -3.416614427 -0.17643589 ITGMLLEIDNSELLHMLESPESLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ITGMLLEIDNSELLHMLESPESLR 24 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YB75;H0YAS6;H0YAS7;B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0Y6X6;H0YER0 P11940-2;B1ANR0 PABPC1;PABPC4 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 4 0 ; 217.94 9.17E-33 274880000 126490 161061 157359 168463 198633 168801 168504 159487 158193 FALSE TRUE 118573.2167 172986.124 161091.6298 172786.0458 183033.1654 217531.1084 143238.3895 179399.303 131789.5663 0.899716267 1.312593469 1.222339782 1.311075304 1.388828953 1.650594311 1.086872 1.361255735 1 17.00787663 4.739766267 23.42986494 1.29958415 0.899715965 0.330029752 0.17519553 47.81576806 928934.7098 0.038082448 0.234779883 54924.51958 -4.739766267 -0.399868185 ITITNDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ITITNDK 7 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931;P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13;P54652;P17066 A0A0G2JIW1;Q53FA3;P11142;P54652;P17066 HSPA1B;HSPA1A;HSPA1L;HSPA8;HSPA2;HSPA6 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like;Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2;Heat shock 70 kDa protein 6 0 ; 98.523 0.026056 218830000 939240 519590 488740 446600 598580 364770 610320 550450 748720 FALSE TRUE 880454.645 558060.9842 500333.1436 458060.5121 551569.9414 470073.1775 518808.1819 619174.8942 623753.7951 1.411541945 0.894681505 0.802132424 0.734361082 0.884275087 0.753619747 0.831751544 0.992659121 1 19.25061716 4.744718839 3.627769865 0.840120968 1.479672072 0.790499703 0.088827757 0.112900426 2.702278327 0.019391101 0.197626401 55554.44824 -4.744718839 0.639551104 ITITNDKGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ITITNDKGR 9 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931;P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13;P54652;P17066 A0A0G2JIW1;Q53FA3;P11142;P54652;P17066 HSPA1B;HSPA1A;HSPA1L;HSPA8;HSPA2;HSPA6 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like;Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2;Heat shock 70 kDa protein 6 0 154.84 6.82E-05 602520000 461060 650770 489780 592230 990170 510880 814380 842010 1419200 FALSE TRUE 432203.0776 698953.6879 501397.8129 607427.6244 912406.0424 658362.7626 692271.2793 947136.802 1182326.352 0.365553112 0.591168155 0.424077339 0.513756311 0.771704057 0.55683675 0.58551624 0.801078992 1 20.17319688 -1.891768218 0.138755671 1.6597136 0.321234067 0.728847001 0.098270218 24.46593483 0.507557677 5.954196125 0.747229437 0.012830151 1.891768218 -1.338479533 ITKFENAFLSHVVSQHQALLGTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ITKFENAFLSHVVSQHQALLGTIR 24 1 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ; 212.82 9.73E-26 155010000 133542 268469 173721 136211 354080 131670 166765 248364 349420 FALSE TRUE 125183.8446 288346.7241 177841.7442 139706.4049 326271.9851 169680.9915 141760.1364 279372.7921 291099.5447 0.430037927 0.99054337 0.610931028 0.479926566 1.120826161 0.582896795 0.486981649 0.959715662 1 18.15115306 1.108799482 8.052404021 0.998150482 0.691485114 0.245669278 0.222892167 0.343001542 21.88023345 0.202867203 0.050811747 12.84693366 -1.108799482 -0.306665368 ITKPGS(ph)IDSNNQLFAPGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ITKPGSIDSNNQLFAPGGR 19 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 ITKPGS(1)IDSNNQLFAPGGR;ITKPGS(1)IDSNNQLFAPGGR;ITKPGS(1)IDSNNQLFAPGGR;ITKPGS(1)IDSNNQLFAPGGR 270.74 1.58E-39 2821590000 1934290 1190840 1559410 1307920 1040170 1110540 1664790 1036510 1949760 TRUE FALSE 1813226.242 1279011.033 1596399.942 1341483.442 958479.244 1431134.87 1415170.195 1165920.555 1624332.46 1.116290098 0.787407174 0.982803694 0.825867533 0.59007578 0.881060316 0.871231863 0.717784434 1 20.63141552 4.744714323 24.42563778 0.835515623 1.116290272 0.35804193 0.119539729 572.9621336 2274144.972 0.027121676 0.248059589 55553.87064 -4.744714323 0.280774649 ITKPGSIDSNNQLFAPGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ITKPGSIDSNNQLFAPGGR 19 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 278.08 1.43E-39 937860000 805180 811490 843320 855330 883220 744510 1055960 808950 1079920 FALSE TRUE 754785.2211 871573.564 863323.9486 877279.2159 813855.4639 959437.9509 897628.6011 909949.1882 899674.3755 0.838953783 0.968765575 0.959596019 0.975107483 0.904611142 1.066428007 0.997726095 1.011420591 1 19.77904341 6.441627939 0.563949323 0.998133547 7.98E-97 0.533718509 0.042131326 19.01552209 0.983898327 0.018656823 18.84625563 2764572.217 -6.441627939 -0.998133547 ITKPGSIDSNNQLFAPGGRLS(ph)WGK ddPTM_SK-BR-3_Pertuzumab_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 242.63 9.64E-38 11386100000 3185720 2554560 2914430 2514780 2841220 1583990 3335960 2541780 5133280 TRUE FALSE 2986331.472 2743702.28 2983561.656 2579313.512 2618082.042 2041262.199 2835763.768 2859126.828 4276502.406 0.698311655 0.641576228 0.697663972 0.603136224 0.6122017 0.477320484 0.663103513 0.668566636 1 22.02799992 0.615729426 2.204513879 0.999933542 0.629242126 0.778037292 0.062056504 1.276916878 6.743789321 0.059993079 0.016289982 4.127902457 -0.615729426 -0.370691416 ITLDNAYMEK ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 154.84 3.20E-05 940062000 1626300 1655944 1524423 1573019 1888431 1089212 1670575 1579769 1860110 FALSE TRUE 1524512.786 1778551.817 1560583.033 1613385.331 1740121.247 1403649.823 1420087.788 1777006.637 1549645.624 0.983781558 1.147715187 1.007058007 1.041131795 1.122915601 0.90578762 0.916395184 1.146718069 1 20.5635069 2.242700242 24.99923157 0.975041745 1.064238986 0.133775969 0.080979749 156.0856825 942605.7657 0.027311865 0.022084671 174.863933 -2.242700242 0.089197242 ITLPVDFVTADKFDENAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ITLPVDFVTADKFDENAK 18 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;; 263.15 6.42E-31 4427071000 6103765 4395977 3993763 3969642 4497513 2463846 6529032 3812501 5908490 FALSE TRUE 5721741.244 4721459.711 4088496.944 4071509.734 4144296.471 3175118.343 5550064.264 4288500.142 4922324.849 1.162406265 0.959193035 0.830602829 0.827151775 0.84193884 0.645044454 1.127529051 0.871234686 1 22.23090844 -0.91911463 7.46480178 1 0.906115842 0.035491752 0.150169153 2.06E-09 2.76E-10 0.138109632 0.032552752 0.120471792 0.91911463 -0.093884158 ITLQDVVSHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ITLQDVVSHSK 11 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 141.38 3.82E-05 318720000 749220 618880 661960 662490 726990 544670 747040 590950 820780 FALSE TRUE 702327.6576 664702.5191 677662.0038 679490.615 669895.1379 701907.387 635028.2872 664731.4083 683786.5156 1.027115396 0.97209071 0.99104324 0.993717483 0.979684628 1.026500773 0.928693785 0.972132958 1 19.38318645 1.737820903 24.99999973 0.960876029 0.993587297 0.236918165 0.024860519 0.135767781 4166.147008 0.010319197 0.005722518 54.67904271 -1.737820903 0.032711268 ITNDFYPEEDGKTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 ITNDFYPEEDGKTK 14 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;; 149.44 6.83E-06 565610000 968550 627543 778600 739570 852040 509424 969890 631000 1223230 FALSE TRUE 907930.1844 674006.9367 797068.7597 758548.6183 785124.2154 656486.439 824463.9985 709781.739 1019065.011 0.890944321 0.661397388 0.78215693 0.744357436 0.770435848 0.64420467 0.809039649 0.696502904 1 19.95881466 -1.065475052 4.440983639 1.00001753 0.745318883 0.541704103 0.072192515 8361414.999 2006059.993 1463.035755 0.014574571 0.086005247 1.065475052 -0.254698647 ITNQVHGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ITNQVHGLK 9 0 P51665 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ; 78.556 0.029436 514720000 1461860 1997400 1699690 1666940 2023990 1381190 1887980 1883100 2196000 FALSE TRUE 1370364.792 2145289.574 1740007.449 1709716.503 1865033.99 1779917.131 1604894.926 2118209.18 1829473.413 0.74904876 1.172626811 0.951097423 0.934540229 1.019437602 0.97291227 0.877244192 1.157824522 1 20.80299702 1.233047085 24.99746607 1.078912204 0.972847097 0.158568018 0.113383822 295.5788373 1340038.54 0.092336088 0.02567445 17.10200721 -1.233047085 -0.106065106 ITPAHDQNDYEVGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ITPAHDQNDYEVGQR 15 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ;;; 255.91 9.72E-25 4306610000 1314980 1421100 1464320 1363070 1390510 1205050 1468330 1298270 1701780 FALSE TRUE 1232677.749 1526319.723 1499054.362 1398048.684 1281304.954 1552928.373 1248167.548 1460361.867 1417741.924 0.869465541 1.076585023 1.057353483 0.986109432 0.903764593 1.095353355 0.880391224 1.030061849 1 20.43516351 3.052185846 9.462017943 0.973151044 1.025005942 0 0.081793802 0.905148884 155.5891943 0.021905736 0.026185237 1127.679917 -3.052185846 0.051854898 ITPFNLQEEMEEGHFDADGNYFLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ITPFNLQEEMEEGHFDADGNYFLNR 25 0 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 0 ; 279.44 3.39E-53 278380000 56561 69992 63747 62642 71535 56691 72904 57662 79526 FALSE TRUE 53020.94797 75174.28051 65259.10894 64249.49977 65916.92966 73056.7714 61972.72201 64861.22763 66252.59684 0.800284827 1.134661645 0.985004544 0.969765758 0.994933524 1.102700496 0.935400648 0.978999024 1 16.01568938 1.630331812 25 0.967891511 1.011569933 0.003210932 0.090085288 2.776615597 3081.192045 0.038415841 0.021282377 42.69055607 -1.630331812 0.043678422 ITPHTS(ph)PAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ITPHTSPAPR 10 0 A0A0C4DFZ9;Q58A45-2;Q58A45-4;Q58A45-3;Q58A45 A0A0C4DFZ9 PAN3 PAB-dependent poly(A)-specific ribonuclease subunit PAN3 1 ITPHT(0.108)S(0.892)PAPR;ITPHT(0.019)S(0.981)PAPR 121.04 0.00033852 496970000 537420 552150 565900 590840 567760 532940 628450 553300 505230 TRUE FALSE 503783.8415 593031.7605 579323.4152 606001.9547 523170.4198 686791.1264 534219.7567 622380.723 420903.8491 1.196909562 1.408948295 1.376379466 1.439763395 1.242968961 1.631705502 1.269220412 1.47867672 1 18.68313118 -0.901425541 6.214020207 0.999999943 1.383140052 0.47517184 0.125670392 8.45E-08 1.48E-08 0.10309854 0.024300555 0.125479985 0.901425541 0.383140109 ITPLEIEVLEETVQTMDTS ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ITPLEIEVLEETVQTMDTS 19 0 Q99436 Q99436 PSMB7 Proteasome subunit beta type-7 0 ; 119.69 0.00019464 14263700 31849 37419 41102 34818 40139 29526 40652 32431 36929 FALSE TRUE 29855.62794 40189.54169 42076.95885 35711.48883 36986.64485 38049.67689 34556.60999 36480.08174 30765.31133 0.970431523 1.306326507 1.36767538 1.160771248 1.202219099 1.236772041 1.123232904 1.1857537 1 14.90901697 0.848695875 0.609523541 1.000092336 1.243469648 0.204698024 0.108957269 1.281194282 1.062277339 0.114544768 0.046535206 7.058231112 -0.848695875 0.243377312 ITPPAAKPGS(ph)PQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ITPPAAKPGSPQAK 14 1 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 ITPPAAKPGS(1)PQAK;ITPPAAKPGS(1)PQAK;ITPPAAKPGS(1)PQAK;ITPPAAKPGS(1)PQAK 141.6 5.83E-06 3773330000 5975610 3726950 4527270 4538260 4505060 2897480 5508180 3544140 5211940 TRUE FALSE 5601607.237 4002897.256 4634658.982 4654719.435 4151250.76 3733935.439 4682279.544 3986633.681 4342033.544 1.29008843 0.921894595 1.067393638 1.072013698 0.956061421 0.859950851 1.078360979 0.918148983 1 22.04993944 4.746824615 24.56168245 0.990627836 1.290088621 0.63045509 0.073447149 541.636945 1609768.909 0.016644468 0.187683976 55824.47086 -4.746824615 0.299460785 ITPSYVAFTPEGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ITPSYVAFTPEGER 14 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 199.82 4.68E-08 634700000 324032 434114 349622 375625 398582 291280 405971 345697 333931 FALSE TRUE 303751.4155 466256.2523 357915.1989 385264.1734 367278.9775 375367.8075 345099.4174 388858.0314 278195.7588 1.091862136 1.676000577 1.28655879 1.384867171 1.320217746 1.349293782 1.240491296 1.397785621 1 18.0857409 -3.920448341 0.188148913 2.53E-15 1.439425527 0.313701439 0.150688662 87.64345447 1.234992896 33.54374212 0.396980074 0.000120102 3.920448341 1.439425527 ITS(ph)PLMEPSSIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 ITSPLMEPSSIEK 13 0 P28066 P28066 PSMA5 Proteasome subunit alpha type-5 1 IT(0.008)S(0.992)PLMEPSSIEK;IT(0.001)S(0.999)PLMEPSSIEK;IT(0.13)S(0.87)PLMEPSSIEK;IT(0.061)S(0.939)PLMEPSSIEK;IT(0.031)S(0.969)PLMEPSSIEK 242.8 6.25E-17 598473000 2218400 1876780 1968620 1943370 1856460 1214113 1929390 1442752 2518410 TRUE FALSE 2079554.304 2015738.744 2015316.596 1993240.164 1710661.12 1564607.714 1640095.881 1622882.763 2098071.101 0.991174371 0.960758071 0.960556863 0.950034612 0.815349451 0.745736268 0.781716063 0.773511804 1 21.00063214 2.741637738 4.043128975 0.799615021 0.965791419 0.488174402 0.070540191 0.14404763 5.636573742 0.020130317 0.020184732 551.6171225 -2.741637738 0.166176398 ITSDEPLTKDDIPVFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ITSDEPLTKDDIPVFLR 17 1 A0A1W2PQD2;Q9UBB4-2;Q9UBB4;B1AHE4 A0A1W2PQD2 ATXN10 Ataxin-10 0 75.911 0.019174 77085000 179910 177320 170730 177820 202830 137660 205390 162400 211250 FALSE TRUE 168649.7542 190448.9573 174779.7962 182383.1622 186900.55 177400.2073 174593.6762 182675.9975 175991.0103 0.958286187 1.082151622 0.99311775 1.036320901 1.061989187 1.00800721 0.992060197 1.037984822 1 17.42514221 2.051489856 24.99988494 1.006857711 1.030321789 0.043685315 0.035797742 239.0406676 116060.4028 0.012309343 0.009091052 112.587417 -2.051489856 0.023464078 ITSEIPQTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ITSEIPQTER 10 0 F8VZQ9;H0YHG0;P82979 F8VZQ9 SARNP SAP domain-containing ribonucleoprotein 0 ;;; 135.87 0.0003085 631460000 399825 498015 480837 502819 499156 405320 507755 411999 474753 FALSE TRUE 374800.667 534888.5488 492242.6807 515722.1868 459954.3013 522329.3042 431621.8515 463437.9821 395513.6573 0.947630151 1.35238958 1.244565571 1.303930161 1.162928998 1.320635317 1.091294431 1.171736989 1 18.59336799 1.070840565 0.951723474 1.006952953 1.240260915 0.213575792 0.119555939 0.682780013 1.345082847 0.101207973 0.034690143 11.77173738 -1.070840565 0.233307963 ITVGNDHFCVS(ph)TPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ITVGNDHFCVSTPER 15 0 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 ITVGNDHFCVS(0.8)T(0.2)PER 68.639 0.033515 88300000 49712 45609 53743 41572 55696 44936 67177 58228 75831 TRUE FALSE 46600.61466 48985.93782 55017.80934 42638.8079 51321.86083 57908.29372 57104.43249 65497.89398 63174.31621 0.737651271 0.775409071 0.870888878 0.67493897 0.812384904 0.916642984 0.90391849 1.036780418 1 15.94705052 1.821865032 1.242237067 1.010685357 0.78143339 0.744980512 0.05701753 0.239746937 0.689033528 0.045269397 0.018591956 66.3536828 -1.821865032 -0.229251967 ITVGNDHFCVST(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ITVGNDHFCVSTPER 15 0 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 ITVGNDHFCVS(0.036)T(0.964)PER 89.011 0.024152 67521000 71813 66847 72233 69360 86694 101110 115790 82420 111110 TRUE FALSE 67318.35252 71796.42143 73946.40087 71139.89503 79885.40295 130298.8156 98428.36444 92710.31843 92565.0232 0.727254747 0.775632296 0.798858989 0.768539699 0.863019315 1.407646335 1.063342946 1.001569656 1 16.49817954 2.456926532 24.5341307 1.128157869 0.778294486 0.680065808 0.114452314 101.2288021 122979.7721 0.036712971 0.030719798 286.3693487 -2.456926532 -0.349863383 ITVGNDHFCVST(ph)PERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ITVGNDHFCVSTPERR 16 1 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 ITVGNDHFCVS(0.441)T(0.559)PERR 64.723 0.045235 147490000 70819 74853 79498 67656 86739 63948 78899 64197 99958 TRUE FALSE 66386.56521 80395.194 81383.7301 69392.1675 79926.86883 82408.74949 67068.82741 72212.13677 83274.36405 0.797202908 0.965425493 0.977296327 0.833295676 0.959801612 0.98960527 0.805395852 0.86715927 1 16.34558481 1.743042108 25 0.872056984 0.930352224 0.001810207 0.078738597 1.847840951 10354.26416 0.033849158 0.018771068 55.34037631 -1.743042108 0.05829524 ITVNGDS(ph)SAEAEELANEI ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 ITVNGDSSAEAEELANEI 18 0 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 1 ITVNGDS(0.5)S(0.5)AEAEELANEI;ITVNGDS(0.5)S(0.5)AEAEELANEI;ITVNGDS(0.5)S(0.5)AEAEELANEI;ITVNGDS(0.5)S(0.5)AEAEELANEI 265.38 5.09E-31 329985000 704660 702850 739280 762590 692350 615231 904460 618558 555533 TRUE FALSE 660556.5885 754889.7453 756816.0707 782159.3505 637975.6238 792838.2023 768844.6196 695786.3279 462810.9534 1.427270862 1.631097405 1.635259635 1.690019099 1.378479958 1.713092995 1.661249834 1.503392093 1 18.82006348 0.854927695 4.806630835 1.000016862 1.603621401 0.741086363 0.108722888 0.659972708 21.43852716 0.09603586 0.02431324 7.160241911 -0.854927695 0.603604539 ITVQAS(ph)PGLDR ddPTM_SK-BR-3_Pertuzumab_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 137.58 7.92E-05 407250000 276930 372610 339140 347790 398520 314650 433030 322670 383840 TRUE FALSE 259597.4456 400198.4321 347184.561 356714.8802 367221.8468 405484.3471 368101.1716 362956.0598 319774.6243 0.811813777 1.251501532 1.085716422 1.11551966 1.148377072 1.268031658 1.151126899 1.135037092 1 18.28669593 4.74866046 24.85377084 1.154995435 0.811813573 0.647994528 0.076687847 757.7182238 1864558.449 0.01670883 0.228051738 56060.95092 -4.74866046 -0.343181862 ITWSIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ITWSIIR 7 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 79.116 0.077928 24744000 73879 94083 68605 70031 110260 58817 90508 91724 94582 FALSE TRUE 69255.04527 101049.0032 70232.343 71828.11402 101600.6244 75796.51309 76937.16564 103175.9433 78795.65318 0.878919616 1.282418498 0.891322556 0.911574575 1.289419153 0.961937747 0.976413832 1.309411613 1 16.26582842 IVAHAVEVPAVQS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IVAHAVEVPAVQSPR 15 0 Q96FF9;B5MBX0;H0YCL8 Q96FF9 CDCA5 Sororin 1 IVAHAVEVPAVQS(1)PR;IVAHAVEVPAVQS(1)PR;IVAHAVEVPAVQS(1)PR;IVAHAVEVPAVQS(1)PR 131.31 3.50E-05 2167050000 1267000 1284430 1353800 1403530 1595290 1230890 1395180 1121660 1352130 TRUE FALSE 1187700.732 1379530.534 1385912.775 1439546.956 1470002.358 1586227.961 1185985.711 1261701.72 1126450.768 1.054374293 1.224670064 1.230335861 1.277949287 1.304985891 1.408164481 1.052851793 1.120068232 1 20.10335283 1.622528674 11.20239369 1.064223815 1.247514279 0.493751246 0.091680184 0.081053117 31.52956031 0.043602048 0.022884331 41.93036802 -1.622528674 0.183290464 IVDAVIQEHQPSVLLELGAYCGYSAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IVDAVIQEHQPSVLLELGAYCGYSAVR 27 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ;; 240.86 3.51E-45 1120724000 713448 699401 722928 694909 782963 795160 812790 674666 881135 FALSE TRUE 668794.5632 751185.3778 740076.1936 712741.5414 721472.2443 1024709.784 690919.6851 758899.5352 734067.8762 0.911080004 1.023318691 1.008184962 0.970947735 0.982841325 1.395933288 0.941220434 1.03382747 1 19.48555394 IVDDLKDEAEQYRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IVDDLKDEAEQYRK 14 2 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;;; 177.84 1.15E-06 445207000 1857200 1253480 1460700 1508650 1622340 973070 1998500 1341330 2103920 FALSE TRUE 1740961.167 1346288.963 1495348.494 1547364.513 1494927.961 1253979.513 1698843.478 1508798.003 1752762.16 0.993267202 0.768095634 0.85313828 0.882814878 0.852898354 0.715430502 0.969237879 0.860811602 1 20.74119881 0.956295366 1.102343923 0.994607464 0.843283373 0.208808284 0.08204177 0.755524465 1.895953883 0.070286996 0.022479486 9.042642587 -0.956295366 -0.15132409 IVDNVRPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IVDNVRPDR 9 1 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ;;;; 97.277 0.0062014 3697140000 2057109 2456010 2386310 2296500 2433760 2166730 2617860 2100180 2808240 FALSE TRUE 1928358.22 2637855.536 2442914.4 2355432.078 2242622.307 2792229.777 2225336.196 2362392.096 2339526.602 0.824251461 1.127516795 1.04419176 1.006798587 0.958579528 1.193502042 0.951190807 1.009773556 1 21.1577852 1.608320561 24.99999999 0.985363428 1.038917898 0.022090049 0.098500531 0.175521867 7392.010504 0.044599386 0.022815767 40.58079591 -1.608320561 0.05355447 IVDQIRPDR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;; 175.93 4.88E-05 14150790000 9909510 10285740 10964270 10211230 10779750 10017230 11794430 9395420 11706540 FALSE TRUE 9289291.458 11047306.89 11224347.66 10473267.45 9933151.918 12909041.68 10025964.72 10568458.87 9752642.847 0.952489659 1.132750073 1.15090318 1.073890187 1.018508734 1.323645486 1.028025416 1.083650764 1 23.21736179 1.027086991 1.923648554 1.005142534 1.111277376 0.077128311 0.099294886 0.733009196 5.632481443 0.085363923 0.024143904 10.64356192 -1.027086991 0.106134843 IVDS(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IVDSPEK 7 0 E9PQC4;Q9BZD4 E9PQC4 NUF2 Kinetochore protein Nuf2 1 IVDS(1)PEK 68.626 0.07671 0 284250 208020 243580 238770 221280 189510 313790 223870 206470 TRUE FALSE 266459.2999 223422.0172 249357.8326 244897.2424 203901.5614 244218.4606 266740.1026 251820.6623 172008.8232 1.549102511 1.298898586 1.449680476 1.423748142 1.185413386 1.419801939 1.550735001 1.463998519 1 17.39212304 -2.133828788 2.369676931 0.141774428 1.413488192 0.592885153 0.108721426 1958615.617 476663.7817 9077556.594 0.026983316 0.007348035 2.133828788 1.271713763 IVDS(ph)PEKLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IVDSPEKLK 9 1 E9PQC4;Q9BZD4 E9PQC4 NUF2 Kinetochore protein Nuf2 1 IVDS(1)PEKLK;IVDS(1)PEKLK;IVDS(1)PEKLK;IVDS(1)PEKLK 129.34 0.001312 775000000 2810250 1762610 2058930 2128280 2477790 1364730 2992760 1872670 3197730 TRUE FALSE 2634361.469 1893115.478 2107768.792 2182895.268 2283194.368 1758705.396 2544023.421 2106476.972 2664008.205 0.98887138 0.710626745 0.791202065 0.819402607 0.857052303 0.660172665 0.954960806 0.790717149 1 21.3451671 0.452709814 0.68381803 1.002476759 0.799856979 0.218102273 0.100197752 2.401277796 1.786742923 0.107895827 0.034032885 2.836023427 -0.452709814 -0.202619781 IVEDEPNKICEADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IVEDEPNKICEADR 14 1 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 ;;;; 204.43 1.25E-08 3746920000 3080160 2619540 2861900 3140460 3206480 2422190 3882670 2753870 3493410 FALSE TRUE 2887378.284 2813493.467 2929785.619 3221049.52 2954655.995 3121436.932 3300499.678 3097696.732 2910337.303 0.992111217 0.966724189 1.006682496 1.106761583 1.015228026 1.07253442 1.134060879 1.064377221 1 21.47275494 3.390666803 4.924927947 1.074246947 0.982532146 0.454792578 0.039643618 0.155875695 6.52579553 0.010860954 0.014968486 2458.480697 -3.390666803 -0.091714801 IVEGQGQSSEVIT(ph)PPEEISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IVEGQGQSSEVITPPEEISR 20 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 IVEGQGQSSEVIT(1)PPEEISR 177.61 7.25E-16 28454000 65074 92322 91554 93720 101640 76234 95005 85491 99785 TRUE FALSE 61001.1345 99157.61694 93725.70411 96125.01387 93657.6044 98241.51824 80759.88223 96164.73954 83130.23886 0.733801988 1.192798412 1.127456211 1.156318269 1.126637018 1.181778371 0.971486229 1.156796141 1 16.34308574 -0.204770811 8.44611536 1.000000002 1.09406445 0.02504992 0.138340712 0 0 0.120338832 0.028364135 0.624064084 0.204770811 0.094064448 IVEIDAHIGCAMSGLIADAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IVEIDAHIGCAMSGLIADAK 20 0 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ; 169.19 1.11E-11 33163800 88251 81212 81009 78111 99270 57262 101047 78108 116822 FALSE TRUE 82727.52744 87225.02098 82930.57174 80115.4605 91473.73464 73792.60983 85895.94042 87859.95574 97323.6535 0.850024886 0.896236607 0.852111165 0.823185912 0.939892116 0.758218657 0.882580312 0.902760558 1 16.57050286 0.889804233 2.254899207 0.999460144 0.858404695 0.482889087 0.047023809 0.362471811 3.80105398 0.040040225 0.010921208 7.75897286 -0.889804233 -0.14105545 IVELFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IVELFR 6 0 P40763;P40763-2;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 ; 158.08 0.022184 313470000 702650 954270 798030 795120 1004200 624280 858130 890560 1024840 FALSE TRUE 658672.3908 1024925.144 816959.6485 815524.1253 925334.1827 804499.5017 729461.373 1001748.376 853787.5833 0.771471035 1.200445127 0.956865226 0.955183867 1.083799063 0.94227126 0.854382738 1.173299303 1 19.70351766 3.713353519 24.15149332 0.980221195 1.035215924 0 0.134869763 1079.180016 1893110.406 0.033344911 0.051984815 5168.36907 -3.713353519 0.054994729 IVENLGILTGPQLFSLNKEELKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IVENLGILTGPQLFSLNKEELKK 23 2 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 229.45 3.00E-33 106150000 790280 530950 640380 669010 791760 455140 865160 563930 1069300 FALSE TRUE 740817.7855 570262.0905 655570.116 686177.9292 729578.3634 586531.5294 735437.2898 634337.9019 890826.9221 0.831606867 0.640149143 0.735911881 0.770270759 0.818990025 0.658412442 0.825566978 0.712077606 1 19.76478563 -5 0.267497584 2.746126518 0.723192072 0.561978451 0.06820132 139.6585497 1.361121173 134.4571099 0.078459357 1.00E-05 5 -2.022934446 IVEPEVVGES(ph)DS(ph)EVEGDAWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IVEPEVVGESDSEVEGDAWR 20 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 IVEPEVVGES(1)DS(1)EVEGDAWR;IVEPEVVGES(1)DS(1)EVEGDAWR;IVEPEVVGES(1)DS(1)EVEGDAWR;IVEPEVVGES(1)DS(1)EVEGDAWR;IVEPEVVGES(1)DS(1)EVEGDAWR;IVEPEVVGES(1)DS(1)EVEGDAWR 245.48 8.47E-30 781766000 1512341 1505601 1561775 1526403 1559589 1412111 1735088 1392577 1520836 TRUE FALSE 1417686.276 1617077.265 1598821.041 1565573.085 1437105.171 1819764.522 1474927.662 1566443.304 1266998.647 1.118932747 1.27630544 1.261896408 1.235654899 1.134259437 1.436279768 1.164111474 1.236341734 1 20.27298355 0.35648708 1.42503012 1.00000409 1.242981666 0.397631782 0.089545656 4.059339447 8.038150752 0.076067637 0.022107553 2.27241203 -0.35648708 0.242977576 IVEPEVVGES(ph)DSEVEGDAWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IVEPEVVGESDSEVEGDAWR 20 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 IVEPEVVGES(0.677)DS(0.323)EVEGDAWR;IVEPEVVGES(0.997)DS(0.003)EVEGDAWR;IVEPEVVGES(0.976)DS(0.024)EVEGDAWR;IVEPEVVGES(0.998)DS(0.002)EVEGDAWR;IVEPEVVGES(1)DSEVEGDAWR 303.13 5.30E-55 681640000 454851 457106 481049 411233 444574 416824 443988 388277 405604 TRUE FALSE 426382.6878 490950.6039 492459.7094 421785.935 409658.9514 537154.3222 377416.1212 436754.2382 337906.0721 1.261837898 1.452920336 1.457386387 1.248234257 1.212345634 1.589655726 1.116926129 1.292531488 1 18.36626275 0.705940548 0.480072373 0.980898702 1.397172623 0.389987145 0.134507749 1.392490137 0.693904633 0.183004504 0.072463518 5.080898834 -0.705940548 0.416273921 IVEYS(ph)PPSAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IVEYSPPSAPR 11 0 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 1 IVEY(0.042)S(0.894)PPS(0.064)APR;IVEYS(1)PPSAPR;IVEYS(0.998)PPS(0.002)APR 166.7 2.11E-05 762560000 743170 866760 880040 847850 909470 748790 924650 758410 827750 TRUE FALSE 696656.3163 930935.8123 900914.9644 869607.2664 838043.8948 964953.5174 786007.3165 853099.158 689593.1775 1.010242472 1.349978281 1.306444138 1.261043895 1.215272892 1.399308388 1.13981307 1.237104986 1 19.39538598 0.581859891 0.934789538 1.0004463 1.267476541 0.308501146 0.109808278 1.451491777 2.01962533 0.096846994 0.031474694 3.818210709 -0.581859891 0.267030241 IVFLDTQPILSPSILDHLINNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IVFLDTQPILSPSILDHLINNDR 23 0 Q9H0W8-2;Q9H0W8 Q9H0W8-2 SMG9 Protein SMG9 0 83.602 0.0076885 64637000 60840 76927 92668 98170 107290 78107 98050 92944 75223 FALSE TRUE 57032.133 82622.75512 94866.12872 100689.2084 98863.87619 100655.2229 83348.31275 104548.263 62667.79534 0.910070838 1.318424474 1.513793938 1.606713749 1.577586632 1.606171438 1.330002313 1.668293298 1 15.93543662 4.865780461 1.484149381 1.490977793 0.54339194 0.453877733 0.192827669 1.259689746 2.041293623 0.045104975 1.913696422 73414.26597 -4.865780461 -0.947585853 IVFSGNLFQHQEDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IVFSGNLFQHQEDSK 15 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 162.29 1.60E-06 260720000 132660 145150 135530 134730 178560 124980 162630 117870 235970 FALSE TRUE 124357.0474 155897.057 138744.8356 138187.3999 164536.6179 161059.6971 138245.1413 132586.329 196585.0826 0.632586388 0.793025875 0.705774995 0.7029394 0.836974076 0.819287481 0.703233122 0.674447558 1 17.58479432 -2.216530768 2.4526942 1.884429785 0.739670467 0.621830636 0.065149781 9884448.63 2362092.849 48360908.56 0.015025456 0.006073922 2.216530768 -1.144759318 IVFSGNLFQHQEDSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IVFSGNLFQHQEDSKK 16 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 212.69 2.51E-12 184990000 400760 319170 385540 342650 389720 253770 435640 342160 494540 FALSE TRUE 375677.147 342801.6789 394685.1909 351442.9791 359112.9633 327029.2794 370319.8263 384879.4292 411998.0791 0.911841987 0.832046789 0.957978231 0.853020917 0.87163747 0.793764088 0.89883872 0.934177727 1 18.65227809 1.0363957 2.398423601 0.998325426 0.873904274 0.474789272 0.044111819 0.241220875 2.971942508 0.040589646 0.011093373 10.87415954 -1.0363957 -0.124421152 IVGAPMHDLLLWNNATVTTCHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IVGAPMHDLLLWNNATVTTCHSK 23 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ; 268.13 1.28E-44 528690000 564432 602288 602826 522250 650990 459680 742800 596272 790786 FALSE TRUE 529105.2087 646882.0302 617125.3174 535651.8192 599863.8714 592382.1537 631424.0358 670717.8718 658798.7079 0.803136379 0.981911504 0.936743363 0.813073573 0.910541967 0.899185361 0.958447593 1.01809227 1 19.3294782 1.51172663 2.803205195 1.00835318 0.904285996 0.446852752 0.0537684 0.262555926 4.294276761 0.040576938 0.01448307 32.48827329 -1.51172663 -0.104067184 IVGCICEEDNTSVVWFWLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IVGCICEEDNTSVVWFWLHK 20 0 P10606 P10606 COX5B "Cytochrome c oxidase subunit 5B, mitochondrial" 0 ; 233.52 1.71E-29 61941000 74667 108899 71207 56278 134232 59756 71273 121372 115452 FALSE TRUE 69993.72575 116961.9953 72896.06367 57722.18876 123689.9602 77006.58714 60586.27532 136525.5614 96182.31535 0.727719285 1.216044705 0.757894665 0.600133076 1.285994829 0.800631456 0.62991076 1.419445569 1 16.55348404 1.234844222 24.99999762 1.2097227 0.875273305 0.255644056 0.247164184 142.9769272 961727.9931 0.198677654 0.057134008 17.17292299 -1.234844222 -0.334449395 IVGCSVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 100.02 0.0064024 369850000 137580 714170 154250 121850 888700 133330 200550 717290 744320 FALSE TRUE 128969.1134 767047.8899 157908.8828 124976.8773 818905.0868 171820.2066 170479.3893 806845.2355 620088.1835 0.207985117 1.236998076 0.254655526 0.201546942 1.320626822 0.277089955 0.274927654 1.301178214 1 19.24211387 1.229959905 24.99988739 1.150589335 0.567082844 0.26577987 0.420528593 291.2229083 846472.2458 0.363432565 0.096579201 16.98086873 -1.229959905 -0.583506491 IVGCTHITAQTAVLIETLCALGAQCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IVGCTHITAQTAVLIETLCALGAQCR 26 0 O43865-2;O43865 O43865-2 AHCYL1 Putative adenosylhomocysteinase 2 0 ;;; 189.51 8.53E-18 251901700 94884.6 130304.1 124916.7 116612.4 161646.6 133670.9 148143.5 133272.9 117537.6 FALSE TRUE 88945.94226 139951.9511 127879.7831 119604.8716 148951.5281 172259.5189 125930.7575 149912.3149 97919.81524 0.908354882 1.429250564 1.305964302 1.221457284 1.521158182 1.759189582 1.286059999 1.530970157 1 16.57931322 4.740846854 24.19559435 1.39809101 0.908354619 0.344562016 0.204091404 141.6057286 1498478.126 0.044375448 0.29605362 55061.34989 -4.740846854 -0.489736392 IVGELEQMVSEDVPLDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 IVGELEQMVSEDVPLDHR 18 0 Q00341;A0A024R4E5;Q00341-2 Q00341 HDLBP Vigilin 0 ;;;;;;;;;;;;; 219.68 7.20E-19 1304112800 814694 917988 902390 901620 957344 833713 1044041 815702 959156 FALSE TRUE 763703.7568 985956.7867 923795.1169 924757.0956 882158.064 1074392.409 887496.7445 917544.1903 799066.6672 0.955744731 1.233885516 1.15609267 1.157296548 1.103985562 1.344559163 1.110666708 1.148269885 1 19.60795635 0.641727133 1.877132738 1.0002127 1.165416309 0.180026266 0.098605943 2.568638123 11.52863159 0.08379593 0.023342114 4.382552556 -0.641727133 0.165203609 IVHKGDECILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IVHKGDECILK 11 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 62.258 0.049337 154570000 386350 344370 368380 333990 404800 290230 424170 355960 369270 FALSE TRUE 362169.0432 369867.5131 377118.1476 342560.7488 373008.6409 374014.6895 360569.6463 400402.3896 307636.4514 1.177263102 1.202287672 1.225856513 1.113524575 1.212498191 1.215768443 1.172064119 1.301544039 1 18.23086693 -1.240861047 4.23156223 0.999876895 1.20074134 0.644175223 0.047303699 4.91E-05 8.81E-06 0.040923944 0.009639968 0.057430018 1.240861047 0.200864445 IVHSLDYYNTCEYPNEDEMPNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IVHSLDYYNTCEYPNEDEMPNR 22 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 214.35 1.15E-25 134530000 38399 37709 30852 35366 44950 31292 41965 26661 37584 FALSE TRUE 35995.67513 40501.0136 31583.82401 36273.55143 41419.80832 40325.49242 35672.73783 29989.68454 31310.9876 1.149618006 1.293508021 1.008713759 1.158492728 1.322852184 1.287902283 1.139304141 0.957800658 1 14.93438139 1.342522703 4.326536592 0.979524612 1.195179268 0.502051118 0.090785161 0.191959817 5.567703029 0.071252036 0.023992154 22.0050674 -1.342522703 0.215654656 IVIFTQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IVIFTQGR 8 0 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZHJ1 P55263-3 ADK Adenosine kinase 0 ; 122.18 0.0032608 197696000 515550 486970 446700 382570 589330 354700 465920 431800 534430 FALSE TRUE 483282.6458 523025.7655 457295.9349 392387.3939 543046.399 457096.1319 396059.6214 485711.1805 445230.1805 1.085466949 1.174731158 1.027100037 0.881313557 1.219698086 1.026651274 0.889561487 1.090921509 1 18.76419187 3.772249499 3.784197381 1.009795396 1.13051774 0.17778436 0.097811776 0.334225779 9.955619267 0.025242281 0.046331108 5919.015801 -3.772249499 0.120722343 IVILPDYLEIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IVILPDYLEIAR 12 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 104.79 0.0048843 30029000 109880 126980 112600 113600 121530 90896 132920 108220 114440 FALSE TRUE 103002.8069 136381.7313 115270.9252 116515.1683 111985.524 117136.1996 112989.88 121731.5052 95339.22469 1.080382259 1.430489201 1.209060862 1.222111557 1.174600742 1.228625469 1.185135293 1.276824996 1 16.54078227 -4.884861842 0.196106719 1.90E-11 1.279011492 0.34367604 0.091810292 131.4235613 1.350366199 51.49203397 0.216758017 1.30E-05 4.884861842 1.279011492 IVKPNGEKPDEFESGISQALLELEMNSDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IVKPNGEKPDEFESGISQALLELEMNSDLK 30 2 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 139.57 3.25E-08 799580000 135890 67033 90720 83698 93082 64948 123090 80426 133740 FALSE TRUE 127384.8875 71996.19307 92871.92124 85845.83238 85771.71519 83697.43326 104633.7972 90467.36314 111417.93 1.143306894 0.646181392 0.833545563 0.770484897 0.76981968 0.751202551 0.939110942 0.811964135 1 16.76562189 0.835894348 0.846929817 0.995320778 0.801823367 0.104229441 0.134669326 1.43425264 2.097913055 0.116888412 0.040796569 6.85321486 -0.835894348 -0.19349741 IVLDNSVFSEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 188.96 8.53E-06 2096160000 1535468 2518550 2161010 2457040 2593960 2017338 2636260 2306098 2392320 FALSE TRUE 1439365.799 2705026.063 2212270.178 2520091.806 2390240.845 2599710.732 2240977.287 2594019.412 1993026.337 0.722201093 1.357245518 1.110005491 1.264454844 1.199302187 1.304403601 1.124409269 1.301547984 1 20.92652934 4.749072054 24.89759978 1.213529405 0.7222008 0.668583875 0.107346767 767.885022 1818790.323 0.022080089 0.317056087 56114.10677 -4.749072054 -0.491328605 IVLDSDAAEYGGHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IVLDSDAAEYGGHQR 15 0 Q04446;E9PGM4 Q04446 GBE1 "1,4-alpha-glucan-branching enzyme" 0 ; 175.29 2.63E-11 368250000 295610 380580 357140 390480 408130 334560 427900 359890 423810 FALSE TRUE 277108.2978 408758.5392 365611.5295 400500.3779 376077.1161 431142.0409 363740.3674 404823.0587 353073.3731 0.784846207 1.157715564 1.035511475 1.134326201 1.065152868 1.22111174 1.030211835 1.146569211 1 18.4296085 4.745006569 24.95225214 1.100012898 0.784846062 0.678115877 0.067978633 375.4568491 1453352.277 0.013973 0.132092648 55591.26657 -4.745006569 -0.315166836 IVLHPDTEHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IVLHPDTEHSK 11 0 Q9NW13;Q9NW13-2;H7C5G8 Q9NW13 RBM28 RNA-binding protein 28 0 101.95 0.0016964 210940000 317720 719880 533060 607610 655650 719710 475230 499840 451070 FALSE TRUE 297834.4723 773180.6642 545704.4349 623202.3013 604157.8938 927478.5935 403973.6733 562246.1243 375783.503 0.792569312 2.057516251 1.452177732 1.658407824 1.607728623 2.468119505 1.075017051 1.496196932 1 18.51954221 1.612365979 25 1.214185541 1.694584801 0.207820333 0.441732753 0.604013375 3337.350254 0.191049154 0.101412589 40.96056881 -1.612365979 0.48039926 IVLLDSSLEYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IVLLDSSLEYK 11 0 P49368;P49368-2;B4DUR8;Q5SZX6 P49368 CCT3 T-complex protein 1 subunit gamma 0 125.82 0.00074539 31475000 279240 262800 275320 260430 312780 232740 317230 254440 344630 FALSE TRUE 261762.8669 282257.9854 281850.7204 267113.0747 288215.5205 299928.2598 269664.3065 286207.3941 287109.0266 0.911719391 0.983103836 0.981685333 0.930354151 1.003853915 1.044649356 0.939240085 0.996859616 1 18.13123916 2.710532504 24.8172803 0.992715732 0.961941971 0.285252583 0.033514113 1220.136378 1080359.47 0.010780906 0.010165871 513.4906078 -2.710532504 -0.030773761 IVLQNGAHEVFNHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IVLQNGAHEVFNHR 14 0 A6NP24;Q08257;C9JH92;Q08257-2;Q08257-3 A6NP24 CRYZ Quinone oxidoreductase 0 89.992 0.0034287 671210000 153140 164440 142950 148860 210200 140200 172980 178980 212550 FALSE TRUE 143555.2408 176615.3087 146340.8415 152679.9996 193691.7399 180673.464 147043.2549 201326.047 177074.0319 0.810707472 0.997409427 0.82643875 0.862238229 1.093846104 1.020327273 0.830405528 1.13695975 1 17.43399313 2.77176747 24.81368722 0.991728965 0.886773664 0.338116123 0.094692517 885.7523664 661873.2528 0.028552642 0.030282692 591.2449854 -2.77176747 -0.104955301 IVNGWQVEEADDWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IVNGWQVEEADDWLR 15 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;;; 381.34 3.51E-98 829569000 430307 486526 454660 437503 491960 403478 532963 455496 463172 FALSE TRUE 403374.853 522548.8913 465444.7499 448730.0677 453323.4461 519955.5487 453050.1459 512365.6783 385865.601 1.045376556 1.354225124 1.206235406 1.162918038 1.174822127 1.34750428 1.174113849 1.327834554 1 18.55773891 -1.380572427 3.216626435 0.99764231 1.232076461 0.343540324 0.09681524 16094910.89 18490732.07 343061.8165 0.020775388 0.041632029 1.380572427 0.234434151 IVNHPTMLQDPDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IVNHPTMLQDPDVR 14 0 Q13596-2;Q13596;H0YK42;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 0 ; 117.2 0.00031704 450420000 249080 363780 276140 283400 396700 232560 334150 354540 438700 FALSE TRUE 233490.5274 390714.6497 282690.1712 290672.5238 365544.7822 299696.2967 284047.3096 398805.0994 365478.1359 0.638863189 1.06905068 0.77348039 0.795321239 1.000182354 0.820011561 0.777193713 1.091187298 1 18.47942558 1.232759865 24.99956235 1.045593721 0.854412938 0.323654425 0.122531428 182.9086475 788243.4241 0.099220597 0.027444419 17.09070056 -1.232759865 -0.191180783 IVNHWAS(ph)PELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IVNHWASPELR 11 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 IVNHWAS(1)PELR;IVNHWAS(1)PELR;IVNHWAS(1)PELR;IVNHWAS(1)PELR 212.11 7.39E-09 764414000 697223 948460 772430 779880 876220 600969 877030 767360 737700 TRUE FALSE 653585.057 1018684.965 790752.4044 799893.0411 807405.2157 774458.9944 745527.4934 863166.5852 614573.1043 1.063478132 1.657548887 1.286669395 1.301542543 1.313765946 1.260157643 1.213081875 1.40449782 1 19.22922511 -4.427687602 0.149711801 1.42E-09 1.443468596 0.24338817 0.156087231 127.7221408 1.333050969 38.63061822 0.758661309 3.74E-05 4.427687602 1.443468595 IVPEGEWGQFMDALREPLPATLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IVPEGEWGQFMDALREPLPATLR 23 1 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ; 184.29 3.09E-17 196569000 46251 57022 59356 62587 76881 74510 48384 43540 56201 FALSE TRUE 43356.23247 61243.96821 60763.95235 64193.08838 70843.07638 96019.82743 41129.26838 48976.06484 46820.69003 0.926005842 1.308053516 1.297801299 1.371041058 1.513072027 2.050799067 0.878442166 1.046034666 1 15.51485858 1.609701511 25 0.971651044 1.393984958 0.352224072 0.278251596 0.209362848 2786.438084 0.133600036 0.069294131 40.71003826 -1.609701511 0.422333915 IVQIPFCGEIDCEDWIKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IVQIPFCGEIDCEDWIKK 18 1 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 123.53 5.42E-05 98395000 187440 136840 155270 147020 215460 146430 301930 152270 310110 FALSE TRUE 175708.465 146971.776 158953.0777 150792.7821 198538.6407 188701.9639 256658.3995 171281.2447 258350.6376 0.680116243 0.568884897 0.615261024 0.583674898 0.768485197 0.730410289 0.99344984 0.662979764 1 17.97897092 2.349190581 1.500509619 0.879886941 0.603736922 0.544462271 0.10338694 0.26075219 1.180472433 0.048532536 0.032435128 223.4552594 -2.349190581 -0.276150019 IVSGIITPIHEQWEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IVSGIITPIHEQWEK 15 0 Q5QPM7;Q5QPM9;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 0 ; 247.38 2.91E-18 794950000 1003990 931420 974870 966820 1153050 848750 1139210 926900 1060430 FALSE TRUE 941152.0581 1000383.306 997994.3768 991630.238 1062494.104 1093770.347 968396.0364 1042625.505 883437.3824 1.065329673 1.132376019 1.129671889 1.122468052 1.202681849 1.238084745 1.096168281 1.180191744 1 19.75276836 -1.031263553 4.369114253 0.999992225 1.144715505 0.452535647 0.050408268 3.98E-06 8.82E-07 0.046652909 0.010995552 0.0930543 1.031263553 0.14472328 IVSGS(ph)PISTPSPSPLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IVSGSPISTPSPSPLPR 17 0 Q9ULM3 Q9ULM3 YEATS2 YEATS domain-containing protein 2 1 IVSGS(0.997)PIS(0.002)TPSPSPLPR;IVSGS(0.998)PIS(0.001)T(0.001)PSPSPLPR;IVSGS(0.997)PIS(0.001)T(0.001)PSPSPLPR 268.18 6.85E-28 237299000 284112 296483 321440 230622 288935 285032 341587 276254 322595 TRUE FALSE 266329.9371 318434.9098 329064.7086 236540.151 266243.2106 367316.1113 290369.2005 310744.92 268751.8105 0.990988439 1.184866101 1.224418574 0.88014347 0.990665738 1.366748416 1.080436258 1.156252378 1 18.03591495 IVSRPEELREDDVGTGAGLLEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IVSRPEELREDDVGTGAGLLEIK 23 2 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;; 234.37 2.57E-37 2827400000 2315460 1852070 2156660 2034030 2229180 1605060 2614810 1919020 2603260 FALSE TRUE 2170539.492 1989199.19 2207816.994 2086226.653 2054109.195 2068414.766 2222743.515 2158613.871 2168759.088 1.000820932 0.917206157 1.018009333 0.961944858 0.947135717 0.953731918 1.02489185 0.99532211 1 21.04843837 1.744538593 18.53304037 1.007509457 0.965818246 0.3064018 0.028537417 0.250529679 774.6247597 0.01267937 0.007020171 55.53139617 -1.744538593 -0.041691211 IVTDRETGSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IVTDRETGSSK 11 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;; 158.4 2.73E-05 2381130000 1087519 1614880 1335370 1539620 2199690 966964 1794390 1343910 4187590 FALSE TRUE 1019453.127 1734447.395 1367045.607 1579129.256 2026935.221 1246110.809 1525337.878 1511700.122 3488654.176 0.2922196 0.49716805 0.39185472 0.452647117 0.581007781 0.357189548 0.437228169 0.433318995 1 21.73423916 -1.817619365 2.134032171 1.230613851 0.434929934 0.842736248 0.077315645 862124.7418 452496.6206 1020772.293 0.018071201 0.015218808 1.817619365 -0.795683918 IVYGHLDDPASQEIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IVYGHLDDPASQEIER 16 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ; 220.52 1.14E-14 717850000 593680 636580 562970 541690 807180 598590 523560 615040 862890 FALSE TRUE 556522.6285 683713.0456 576323.9143 555590.6825 743787.3388 771393.2157 445057.0385 691829.0979 718868.0845 0.774165164 0.951096676 0.801710253 0.772868756 1.034664572 1.073066439 0.619108078 0.96238672 1 19.45536753 IWDDGDDFCIFSESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IWDDGDDFCIFSESR 15 0 Q6P158-2;Q6P158 Q6P158-2 DHX57 Putative ATP-dependent RNA helicase DHX57 0 ; 149.23 7.90E-06 48175000 54279 65178 65160 62307 71977 51365 67753 54879 63301 FALSE TRUE 50881.77428 70003.84694 66705.62597 63905.90311 66324.21676 66193.24166 57594.06664 61730.76395 52735.65416 0.964845797 1.327448157 1.264905632 1.211815879 1.257673159 1.255189543 1.092127661 1.170569796 1 15.68649107 1.114987839 0.914883683 1.009058214 1.234398273 0.251014349 0.103015376 0.622864833 1.146376708 0.089809468 0.03154827 13.03130288 -1.114987839 0.225340059 IWDILGDRPSLVHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IWDILGDRPSLVHSR 15 1 Q13610;B4DJV5 Q13610 PWP1 Periodic tryptophan protein 1 homolog 0 ; 126.77 4.94E-05 109976000 124945 250190 175124 181564 267710 151227 191772 214230 238950 FALSE TRUE 117124.9155 268714.3279 179278.024 186223.2396 246685.1365 194883.7799 163017.5689 240977.0871 199067.7013 0.588367247 1.349864022 0.900588206 0.935476918 1.239202215 0.97898242 0.818905166 1.210528305 1 17.60289964 -0.412447051 7.537959823 1.000000014 1.014097662 0 0.221520328 0 0 0.194405205 0.045821746 0.386859217 0.412447051 0.014097648 IWDLEGK ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 158.08 0.0033356 2616776000 7152190 6386770 7040840 6614090 7089690 5373360 8231540 5862760 7237260 FALSE TRUE 6704547.195 6859653.096 7207852.05 6783818.747 6532894.346 6924561.803 6997296.995 6594738.492 6029314.552 1.11199161 1.137716906 1.195467907 1.125139299 1.083521898 1.148482426 1.160546018 1.093779141 1 22.52356257 0.930469105 3.949082146 1.00008471 1.14221503 0.682126554 0.029663051 0.182247286 7.288916195 0.029793394 0.007626703 8.520578946 -0.930469105 0.14213032 IWDPTPSHT(ph)PAGAATPGRGDT(ph)PGHATPGHGGATSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 IWDPT(0.002)PS(0.021)HT(0.563)PAGAAT(0.414)PGRGDT(0.973)PGHAT(0.027)PGHGGATSSAR 105.85 1.48E-05 878870000 212750 349970 320050 334380 306620 285300 409380 261490 269260 TRUE FALSE 199434.3573 375882.1429 327641.7371 342960.7569 282539.302 367661.4785 347997.2695 294137.6021 224318.7665 0.889066753 1.675660707 1.460607787 1.528899085 1.259543757 1.639013464 1.551351565 1.311248304 1 17.7751908 0.939151851 4.800219667 1.000163026 1.467555455 0.250503698 0.226486852 0.357645854 23.00650517 0.194332348 0.049215821 8.692643141 -0.939151851 0.467392429 IWDPTPSHTPAGAAT(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IWDPTPSHTPAGAATPGR 18 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 IWDPTPSHT(0.223)PAGAAT(0.776)PGR;IWDPTPSHT(0.03)PAGAAT(0.97)PGR 112.54 0.0010037 430880000 567270 473300 508800 478620 456370 536780 662950 475120 372160 TRUE FALSE 531765.5833 508343.6245 520868.9763 490902.1995 420528.5411 691739.6721 563546.802 534439.7779 310044.0918 1.715128904 1.639584943 1.679983558 1.583330283 1.356350765 2.231100964 1.817634385 1.723754111 1 18.24211387 IWDPTPSHTPAGAAT(ph)PGRGDT(ph)PGHAT(ph)PGHGGATSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 3 IWDPTPSHT(0.003)PAGAAT(0.997)PGRGDT(0.999)PGHAT(0.993)PGHGGAT(0.003)S(0.003)S(0.002)AR;IWDPT(0.001)PS(0.002)HT(0.094)PAGAAT(0.903)PGRGDT(1)PGHAT(0.999)PGHGGATSSAR 103.37 1.07E-05 313380000 261754 302795 309259 292936 268881 251587 329625 242804 278426 TRUE FALSE 245371.2844 325214.2569 316594.7695 300453.2337 247764.1709 324216.0827 280200.7913 273118.6139 231954.9019 1.057840478 1.402058134 1.364897948 1.295308835 1.06815665 1.397754822 1.207996852 1.17746429 1 17.82348481 0.586456256 0.599096734 0.990772061 1.298307325 0.28299729 0.12338902 1.707879251 1.139724084 0.143893822 0.050376767 3.85883542 -0.586456256 0.307535263 IWDPTPSHTPAGAAT(ph)PGRGDT(ph)PGHATPGHGGATSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 IWDPTPS(0.001)HT(0.104)PAGAAT(0.895)PGRGDT(0.951)PGHAT(0.047)PGHGGAT(0.001)S(0.001)S(0.001)AR 82.472 0.00081019 426340000 124990 194270 178280 167220 158560 160460 199690 129750 164860 TRUE FALSE 117167.099 208653.9529 182508.8858 171511.1483 146107.3372 206782.1971 169748.3383 145949.5731 137343.801 0.853093465 1.519209105 1.328846912 1.248772403 1.063807294 1.505580854 1.235937386 1.062658614 1 17.06743227 1.232463026 3.752756424 1.012006611 1.291338563 0.162469813 0.19610721 0.310801032 8.33016246 0.160330626 0.045801933 17.07902311 -1.232463026 0.279331953 IWDPTPSHTPAGAAT(ph)PGRGDTPGHATPGHGGATSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 IWDPTPSHT(0.002)PAGAAT(0.998)PGRGDTPGHATPGHGGATSSAR;IWDPTPSHT(0.001)PAGAAT(0.999)PGRGDT(0.001)PGHATPGHGGATSSAR;IWDPTPSHTPAGAAT(0.807)PGRGDT(0.192)PGHAT(0.002)PGHGGATSSAR;IWDPTPSHTPAGAAT(1)PGRGDTPGHATPGHGGATSSAR;IWDPT(0.002)PS(0.004)HT(0.029)PAGAAT(0.842)PGRGDT(0.109)PGHAT(0.015)PGHGGATSSAR 165.22 5.54E-18 6549260000 822162 1417081 1393652 1430374 1497765 1229261 1671842 1335458 1498594 TRUE FALSE 770704.348 1522003.152 1426710.084 1467079.818 1380136.579 1584128.695 1421164.813 1502192.871 1248468.98 0.617319581 1.219095689 1.142767747 1.17510314 1.105463252 1.268857073 1.13832609 1.20322803 1 20.25172855 4.741916674 24.96001948 1.166314267 0.617319373 0.844556046 0.072603832 99.75159378 741848.9642 0.014635688 0.106200899 55197.15248 -4.741916674 -0.548994894 IWDPTPSHTPAGAATPGRGDT(ph)PGHAT(ph)PGHGGATSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 IWDPTPSHTPAGAAT(0.212)PGRGDT(0.772)PGHAT(0.806)PGHGGAT(0.072)S(0.071)S(0.067)AR 61.483 0.011999 485140000 68537 90137 81392 78308 91893 84320 79298 67411 90860 TRUE FALSE 64247.39151 96810.83727 83322.65668 80317.51586 84676.09446 108661.8152 67408.00107 75827.41174 75694.87902 0.848768006 1.278961517 1.100770062 1.061069347 1.118650238 1.435523996 0.890522608 1.001750881 1 16.20790808 1.618274876 25 0.9596018 1.149161253 0.22885957 0.152136229 0.962522738 2305.915274 0.065232326 0.03567884 41.52167612 -1.618274876 0.189559453 IWDPTPSHTPAGAATPGRGDT(ph)PGHATPGHGGATSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 IWDPTPSHTPAGAAT(0.001)PGRGDT(0.836)PGHAT(0.159)PGHGGAT(0.001)S(0.001)S(0.001)AR 119.06 1.25E-06 358210000 116700 188150 174530 175020 188890 165310 182240 149760 196230 TRUE FALSE 109395.9553 202080.8218 178669.934 179511.3095 174055.3413 213032.3134 154914.8038 168457.8657 163477.9453 0.669178678 1.236135072 1.092929898 1.098076619 1.064702282 1.303125709 0.94761898 1.030462338 1 17.31873649 1.613860227 25 0.991777666 1.099758776 0.043290298 0.16671732 1.290350917 5360.799617 0.072091172 0.038664656 41.10174179 -1.613860227 0.107981109 IWDPVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IWDPVHR 7 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8;A0A494C1S4;A0A494C159 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ;;; 95.352 0.013529 579750000 777607 948552 947391 951251 1034728 797667 1046362 928180 1066210 FALSE TRUE 728937.9659 1018783.777 969863.5619 975661.7111 953464.6368 1027940.514 889469.732 1044065.316 888252.663 0.82064259 1.146952685 1.091878023 1.098405613 1.073416018 1.157261393 1.001370183 1.175414789 1 19.76061058 4.745371054 24.70315083 1.094552199 0.820642441 0.678126445 0.058980942 365.0615332 1324128.692 0.012459647 0.122535253 55637.94152 -4.745371054 -0.273909759 IWDYQNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IWDYQNK 7 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 81.119 0.065295 202490000 874560 591960 695990 675590 708970 437130 862240 596260 695900 FALSE TRUE 819822.8507 635789.3343 712499.2115 692926.7832 653290.356 563322.3348 732955.1166 670704.3735 579749.7943 1.4140977 1.096661595 1.228977084 1.195216954 1.126848793 0.97166457 1.264261107 1.156885919 1 19.14507088 IWEDLDDDDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IWEDLDDDDPK 11 0 O75717;C9JYB3 O75717 WDHD1 WD repeat and HMG-box DNA-binding protein 1 0 ; 147.12 0.00093858 25639000 155742 89851 113601 100466 104652 79871 134880 87382 101567 FALSE TRUE 145994.3862 96503.66153 116295.6694 103044.1276 96433.05407 102928.4611 114655.9962 98291.83505 84614.81155 1.725399886 1.140505542 1.374412674 1.217802483 1.139671085 1.216435506 1.355034586 1.161638645 1 16.3686226 4.744866064 24.86705727 1.229131291 1.725400125 0.683825354 0.110635498 387.2955708 1527348.404 0.024275066 0.22886535 55573.28435 -4.744866064 0.496268834 IWEQIQPDLHTNDECVATYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IWEQIQPDLHTNDECVATYK 20 0 Q12904;Q12904-2 Q12904 AIMP1 Aminoacyl tRNA synthase complex-interacting multifunctional protein 1;Endothelial monocyte-activating polypeptide 2 0 ;;; 257.22 3.26E-36 1135870000 1113140 990170 1036380 1048890 1107260 884246 1365260 1040620 1500150 FALSE TRUE 1043470.554 1063483.217 1060963.423 1075806.293 1020300.266 1139513.466 1160551.937 1170543.698 1249765.274 0.834933228 0.850946365 0.848930151 0.860806678 0.816393516 0.911781988 0.928615926 0.936610836 1 20.25322573 1.572018249 0.909831383 0.991143032 0.843234377 0.876628296 0.019836074 0.16231953 0.264032262 0.01693369 0.006688754 37.3265842 -1.572018249 -0.147908655 IWGEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 IWGEDLR 7 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;;;;;; 139.92 0.0061873 3015847000 6449080 7777670 7543400 7396700 7922800 6283600 8432980 6571960 7371340 FALSE TRUE 6045443.595 8353536.779 7722333.01 7586511.845 7300575.247 8097573.314 7168532.937 7392483.673 6141015.733 0.98443708 1.360285846 1.257500932 1.23538388 1.188822104 1.31860488 1.167320399 1.203788427 1 22.55004587 0.471588154 0.914534027 0.999143472 1.241461599 0.28982888 0.101752314 1.975398982 2.375567273 0.09210977 0.029349025 2.962021143 -0.471588154 0.242318127 IWGLDFGDCHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IWGLDFGDCHK 11 0 Q9UNX4 Q9UNX4 WDR3 WD repeat-containing protein 3 0 ; 169.52 1.68E-05 438680000 975700 935150 976740 985670 1081530 726550 1248030 922210 1130740 FALSE TRUE 914632.6787 1004389.479 999908.7341 1010963.961 996590.9965 936293.1904 1060899.488 1037349.949 942012.1891 0.970935078 1.066217073 1.061460505 1.073196263 1.057938536 0.993928955 1.12620569 1.101206503 1 19.8453862 4.739209246 23.77355636 1.064553493 0.970935027 0.32315887 0.040041929 30.36737333 1112516.181 0.008941446 0.053284115 54854.11918 -4.739209246 -0.093618466 IWGLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IWGLGR 6 0 P41743 P41743 PRKCI Protein kinase C iota type 0 ; 141.66 0.027043 157071000 230800 269490 252550 240700 268040 230060 279010 249450 286840 FALSE TRUE 216354.64 289443.32 258540.6053 246876.7695 246989.2196 296474.5873 237175.0407 280594.3816 238964.5509 0.905383828 1.21123957 1.081920328 1.033110428 1.033581 1.240663463 0.992511399 1.174209231 1 17.86643709 -1.05823146 4.255227679 0.999994304 1.091841738 0.057687144 0.10261218 7.77E-06 1.72E-06 0.087831277 0.020699996 0.087451757 1.05823146 0.091847433 IWHHTFYNELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 181.62 3.55E-06 8908288000 264245.3 4360444 161244.1 141865.5 4479509 257823.9 172044 2736283 2700584 FALSE TRUE 247706.6584 4683295.811 165068.8862 145506.0089 4127706.433 332253.4745 146247.5994 3077913.956 2249839.084 0.110099722 2.081613678 0.073369197 0.064673963 1.834667404 0.147678773 0.065003582 1.368059599 1 21.10139039 3.95231027 22.46353204 0.574806262 1.216780383 0.042996583 0.769125054 233.428732 211343.3388 0.182805762 0.329874498 8960.046631 -3.95231027 0.641974121 IWHVIGDHFNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IWHVIGDHFNK 11 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 0 79.07 0.01628 86962000 822890 503760 582800 567980 652970 562110 740320 461470 717120 FALSE TRUE 771386.7838 541058.9146 596624.2912 582555.3284 601688.3702 724382.0319 629315.8888 519085.5453 597428.0392 1.291179411 0.905647005 0.998654653 0.975105436 1.00713112 1.212500894 1.053375214 0.868867062 1 19.18840542 2.060482878 0.005111906 2.17E-05 2.049939476 0.037621467 0.126103541 45037.35661 163.8039808 32642.26917 33031.98849 114.9430928 -2.060482878 2.04991782 IWLS(ph)TETLANED ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IWLSTETLANED 12 0 Q9NXD2 Q9NXD2 MTMR10 Myotubularin-related protein 10 1 IWLS(0.498)T(0.498)ET(0.004)LANED;IWLS(0.868)T(0.132)ET(0.001)LANED;IWLS(0.493)T(0.493)ET(0.013)LANED 232.42 1.17E-12 94821100 180250 209369 206929 214837 208225 192003 259543 208443 267122 TRUE FALSE 168968.4743 224870.8986 211837.4536 220350.0811 191871.8484 247431.1492 220626.9366 234467.5674 222537.6125 0.75928052 1.010484907 0.951917526 0.99017006 0.862199636 1.111862154 0.991414144 1.053608712 1 17.76368967 2.239131675 24.99998886 1.036080098 0.936342519 0.368802903 0.078054271 19.08106946 835390.3185 0.025979204 0.020522779 173.4329753 -2.239131675 -0.099737578 IWSEPFYQETYLPYMIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IWSEPFYQETYLPYMIR 17 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 187.11 1.13E-09 18883000 16683 18716 15058 16300 22355 13162 19487 17803 17119 FALSE TRUE 15638.84081 20101.75211 15415.18287 16718.2856 20599.32848 16961.65573 16565.10526 20025.74374 14261.72831 1.096560001 1.409489206 1.080877614 1.172248218 1.444378131 1.189312779 1.161507561 1.404159672 1 13.7998612 -1.835819867 2.644233003 0.911605366 1.240307345 0.25321946 0.131925068 20720810.24 14664862.61 11642777.07 0.0289382 0.014594195 1.835819867 0.32870198 IWSLAETATSPDNPRRS(ph)PPGAGGSPPGAAVAPSALQLSPAAAAAAAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IWSLAETATSPDNPRRSPPGAGGSPPGAAVAPSALQLSPAAAAAAAHR 48 2 P78415 P78415 IRX3 Iroquois-class homeodomain protein IRX-3 1 IWS(0.015)LAET(0.009)AT(0.009)S(0.009)PDNPRRS(0.911)PPGAGGS(0.046)PPGAAVAPSALQLSPAAAAAAAHR;IWS(0.01)LAET(0.006)AT(0.006)S(0.031)PDNPRRS(0.935)PPGAGGS(0.012)PPGAAVAPSALQLSPAAAAAAAHR 168.15 1.05E-21 393900000 158532 220054 192167 218868 258950 149495 236600 195185 237630 TRUE FALSE 148609.7651 236347.0271 196725.292 224484.5234 238613.1116 192651.7797 201124.0265 219554.2769 197968.0179 0.750675623 1.193864694 0.993722593 1.133943381 1.205311414 0.973145974 1.015942013 1.109039123 1 17.59490785 4.752006918 24.52897548 1.075959808 0.750675343 0.606562007 0.082862283 1232.911892 2249047.838 0.019220673 0.371733283 56494.59738 -4.752006918 -0.325284465 IWSTVPTDEEDEMEESTNRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IWSTVPTDEEDEMEESTNRPR 21 1 Q9GZL7 Q9GZL7 WDR12 Ribosome biogenesis protein WDR12 0 196.31 8.86E-22 109640000 148680 179460 146520 150330 184960 142040 197780 163460 123070 FALSE TRUE 139374.3842 192747.4051 149995.5236 154187.7223 170433.9877 183044.6422 168124.7251 183868.3408 102528.8219 1.35936785 1.879933871 1.462959593 1.503847595 1.662303189 1.785299379 1.639780131 1.793333205 1 16.64567 -1.055292059 6.669019066 0.999999677 1.645352917 0.607315948 0.160522864 7.03E-07 1.00E-07 0.142159219 0.033507232 0.088045658 1.055292059 0.64535324 IWYEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 IWYEHR 6 0 O75874;P48735;P48735-2;H0YL11 O75874;P48735 IDH1;IDH2 "Isocitrate dehydrogenase [NADP] cytoplasmic;Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;;;;;; 150.82 0.010463 3427830000 1858861 2440389 1984248 1877632 2835790 1546618 1868152 2176090 2818540 FALSE TRUE 1742518.208 2621077.941 2031315.3 1925815.216 2613078.492 1993101.509 1588039.951 2447779.627 2348107.466 0.742094744 1.11625127 0.865086172 0.820156336 1.112844506 0.848811879 0.676306333 1.04244787 1 21.16306701 2.049905795 24.99998933 0.843351864 0.94563022 0 0.153771821 254.9735394 127726.1842 0.053901089 0.039808584 112.1775097 -2.049905795 0.102278356 IY(ph)T(ph)EMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IYTEMR 6 0 C9J466;C9JB88;C9J6S4;F8WDG5;A0A3B3IRY8;P54762-6;P54762 C9J466 EPHB1 Ephrin type-B receptor 1 2 IY(1)T(1)EMR;IY(1)T(1)EMR 62.717 0.059197 973840000 24599 33868 27052 47861 44479 43420 44134 31614 32665 TRUE FALSE 23059.3925 36375.62196 27693.68621 49089.19429 40985.79876 55954.64914 37516.51642 35561.07749 27213.00048 0.847366777 1.336700155 1.017663827 1.803887606 1.506110978 2.056173452 1.378624766 1.306767974 1 14.73200841 3.250967158 24.99998548 1.554164896 1.117901388 0.303717455 0.306759273 253.3797613 510573.6207 0.078227028 0.105181404 1782.243988 -3.250967158 -0.436263507 IYAS(ph)EEDD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IYASEEDD 8 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 IY(0.014)AS(0.986)EEDD 61.679 0.088576 50636000 111270 128080 135380 132010 142100 112840 143490 119800 131480 TRUE FALSE 104305.8093 137563.1765 138591.2775 135397.6001 130940.0392 145415.0762 121975.0066 134757.2937 109535.1386 0.952258888 1.255881704 1.265267742 1.236111095 1.195415835 1.327565547 1.113569656 1.230265424 1 16.74103423 -0.057511325 0.892100328 0.996250499 1.211911469 0.250674713 0.103709481 9.346393861 6.647836078 0.212998642 0.030128356 0.875968875 0.057511325 0.21566097 IYDALDVSLIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IYDALDVSLIER 12 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;; 218.11 8.16E-11 94507000 160224 204865 188357 182977 220832 164877 223381 173344 217415 FALSE TRUE 150195.8658 220033.4178 192824.917 187672.4996 203488.7455 212474.3133 189887.0928 194986.38 181127.0319 0.829229432 1.214801653 1.064583872 1.036137442 1.123458731 1.173067935 1.048364183 1.076517281 1 17.46664235 0.719098097 1.635045157 1.00042319 1.087894089 0.023729704 0.103394582 2.990879333 12.50316631 0.088490402 0.025318599 5.237187193 -0.719098097 0.087470899 IYDDDFFQNLDGVANALDNVDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 IYDDDFFQNLDGVANALDNVDAR 23 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;;; 337.87 7.91E-87 277025200 213041.4 250743.8 238154.7 236016.5 250937.3 204072.8 271316.6 213289.8 249728.7 FALSE TRUE 199707.5191 269309.1319 243803.8419 242073.083 231229.6967 262985.3045 230635.1946 239919.501 208047.3667 0.959913707 1.294460661 1.171866993 1.163547931 1.111428135 1.264064567 1.108570603 1.153196529 1 17.6665525 0.44497951 0.929651034 0.999410367 1.174157524 0.196765982 0.091938011 2.663524679 3.197797689 0.083111152 0.026211001 2.78598972 -0.44497951 0.174747157 IYEDGDDDMKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 IYEDGDDDMKR 11 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;;;;;; 203.83 5.66E-08 8361260000 12114900 8801050 10112620 9707360 10416990 7397160 12397600 8935210 11177980 FALSE TRUE 11356650.03 9452688.899 10352496.12 9956467.292 9598881.626 9532600.009 10538694.97 10050790.64 9312302.925 1.219531852 1.015075323 1.111700962 1.069173476 1.030774203 1.023656563 1.131695893 1.079302372 1 23.15070656 4.750423407 24.61759435 1.065119476 1.219531968 0.581158817 0.042770162 1127.066196 2338827.758 0.009853181 0.160640477 56288.98358 -4.750423407 0.154412492 IYEFPETDDEEENKLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IYEFPETDDEEENKLVK 17 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4 E7EPK1 7-Sep Septin-7 0 ; 214.22 5.48E-15 583490000 902280 438120 591590 610820 615340 426570 794910 473260 880260 FALSE TRUE 845807.9054 470558.8607 605622.7942 626494.6753 567013.6786 549713.8342 675720.6251 532347.5528 733338.9193 1.153365631 0.641666286 0.825842974 0.854304413 0.773194581 0.749604064 0.921430197 0.725922952 1 19.48412058 -1.334003032 3.220205366 1.001312804 0.816500046 0.122468142 0.137891548 92356537.33 135708535.5 1174247.428 0.029603208 0.046344368 1.334003032 -0.184812758 IYGADDIELLPEAQHK ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 207.5 1.73E-11 2852440000 4638900 4089820 4467560 4264980 4819660 3257830 5255370 4182750 5714870 FALSE TRUE 4348559.53 4392634.528 4573532.633 4374426.607 4441143.345 4198312.635 4467376.057 4704975.545 4761021.278 0.91336696 0.922624427 0.960620078 0.918800054 0.932813169 0.881809257 0.938323061 0.988228212 1 22.18283965 1.245710973 3.957929512 0.997936159 0.925421655 0.694578344 0.01954011 0.124502513 3.839142715 0.017102453 0.005008556 17.60803824 -1.245710973 -0.072514504 IYHLPDAES(ph)DEDEDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IYHLPDAESDEDEDFK 16 0 Q15019-2;Q15019-3;Q15019;B5MCX3;H7C2Y0 Q15019-2 2-Sep Septin-2 1 IYHLPDAES(1)DEDEDFK;IYHLPDAES(1)DEDEDFK 237.31 6.02E-20 229870000 350018 185271 237015 226521 224949 201504 292944 209575 193992 TRUE FALSE 328110.9982 198988.6576 242637.1077 232333.9124 207282.4129 259674.9337 249019.7668 235740.9001 161613.482 2.030220463 1.231262734 1.501341997 1.437589918 1.282581196 1.606765293 1.540835354 1.458671005 1 17.30218803 -1.962155477 1.88464995 0.588736093 1.484667587 0.348377694 0.217028831 932834.9835 317030.9615 1676190.887 0.051856973 0.010910497 1.962155477 0.895931494 IYHLPDAES(ph)DEDEDFKEQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 IYHLPDAESDEDEDFKEQTR 20 1 Q15019-2;Q15019-3;Q15019;B5MCX3;H7C2Y0 Q15019-2 2-Sep Septin-2 1 IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR 309.49 1.89E-66 36028894000 10516437 6538896 7618810 7861530 8603254 6274872 9161364 6932973 8810252 TRUE FALSE 9858231.981 7023042.664 7799531.771 8063270.169 7927589.135 8086325.682 7787702.518 7798569.94 7339764.025 1.343126557 0.956848563 1.062640671 1.098573488 1.08008774 1.101714668 1.061029005 1.062509628 1 22.80730225 2.722609925 0.01094171 1.94E-05 2.151471206 0.146762391 0.093566493 5688.665001 24.62241199 2348.45481 2490.484696 527.9708254 -2.722609925 2.151451782 IYHPNIDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IYHPNIDEK 9 0 P68036-2;P68036;P68036-3;A0A1B0GUS4 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ;;; 137.95 0.0001502 5314730000 5945780 4913220 5358420 5161270 5544280 3817610 6552100 4902970 7283720 FALSE TRUE 5573644.243 5276999.921 5485524.253 5293716.926 5108854.613 4919692.033 5569673.432 5515116.597 6068020.077 0.918527654 0.869641144 0.90400562 0.87239608 0.841931066 0.810757376 0.91787327 0.908882391 1 22.53279443 0.875295649 1.560220725 0.99878951 0.874154488 0.599238681 0.032299902 0.379819141 1.800930125 0.030270784 0.008801996 7.504048784 -0.875295649 -0.124635021 IYHPNVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 IYHPNVDK 8 0 P61088;F8VSD4;F8VV71;F8VQQ8;Q5JXB2 P61088 UBE2N;UBE2NL Ubiquitin-conjugating enzyme E2 N;Putative ubiquitin-conjugating enzyme E2 N-like 0 ;;;; 105.57 0.0043629 3133930000 6121380 6760630 5557720 5310970 7569100 4126910 6500400 6660900 7970900 FALSE TRUE 5738253.753 7261194.08 5689551.743 5447258.482 6974653.418 5318281.922 5525725.367 7492528.027 6640505.296 0.864129083 1.093470113 0.856795001 0.820307829 1.050319683 0.800885126 0.832124232 1.128306912 1 22.66286159 1.235420732 24.99999413 1.064153467 0.91015719 0.302874229 0.101406265 112.4593739 895334.1204 0.084008 0.024454974 17.19573452 -1.235420732 -0.153996278 IYITLTGVHQVPTENVQVHFTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IYITLTGVHQVPTENVQVHFTER 23 0 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 312.56 1.86E-73 2004900000 572990 656210 613280 704280 695750 580280 729660 686850 498820 FALSE TRUE 537127.5787 704796.4712 627827.2912 722353.0171 641108.6015 747797.4159 620254.2568 772604.7344 415563.7195 1.292527604 1.69600097 1.510784656 1.738248512 1.542744401 1.799477146 1.492561135 1.859172729 1 18.66471018 -0.870084659 5.874329547 0.999999858 1.61462555 0.574185027 0.166824815 2.63E-07 5.03E-08 0.136718048 0.032224746 0.134869995 0.870084659 0.614625692 IYKPLLFMDLLDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IYKPLLFMDLLDER 14 1 A0A0J9YWM9;H3BSH7;Q969X6;A0A0J9YXV4;Q969X6-2 A0A0J9YWM9 CIRH1A Cirhin 0 134.24 3.64E-05 74894000 127850 170530 146920 146140 193000 96610 156150 168310 169430 FALSE TRUE 119848.0967 183156.2186 150405.0118 149890.1998 177842.5585 124499.7387 132736.7571 189323.874 141151.0384 0.849076975 1.297590302 1.065560788 1.061913546 1.259945095 0.882032042 0.940388102 1.341285733 1 17.10688022 2.239689775 24.99939609 1.020221731 1.125164842 0.023418526 0.170174749 78.99334653 1748938.172 0.057122022 0.045289068 173.6559925 -2.239689775 0.104943111 IYKTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 88.643 0.046576 325720000 391210 565630 551520 508100 669060 467710 711360 490920 1076900 FALSE TRUE 366724.8644 607509.8337 564602.3148 521138.7062 616514.7265 602730.2844 604698.1719 552212.4426 897158.433 0.408762657 0.677148886 0.629322864 0.580877008 0.687186013 0.671821456 0.674014923 0.615512737 1 19.77500325 -5 0.198072896 2.653498869 0.56829865 0.730461183 0.075288345 72.6194338 0.71755061 47.51461834 0.171215145 1.00E-05 5 -2.085200219 IYKVPSTEAEALASSLMGLFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IYKVPSTEAEALASSLMGLFEK 22 1 P50395;Q5SX87;V9GYF8;Q5SX90;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 0 105.16 0.00056862 0 75447 77264 75008 79127 106610 63819 102560 72570 118760 FALSE TRUE 70724.90695 82984.70695 76787.22518 81157.53278 98237.28064 82242.50929 87182.08012 81630.52425 98938.18878 0.714839313 0.838753043 0.776113108 0.820285208 0.992915697 0.831251414 0.88117724 0.825065885 1 16.59423987 7.999999748 0.044122519 1.329555048 0.016630757 0.501936781 0.062019424 530.4996487 1.775639411 13.59061197 49.83760158 99999941.87 -7.999999748 -1.312924291 IYNDDKNTYIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IYNDDKNTYIR 11 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 160.52 2.50E-05 588610000 1077240 874560 974040 1006310 1067320 719550 1287460 984900 1221100 FALSE TRUE 1009817.471 939313.3324 997144.6888 1032133.618 983496.9926 927272.4041 1094417.325 1107866.933 1017290.521 0.992653967 0.923348161 0.980196579 1.014590814 0.966780848 0.911511888 1.075815907 1.089036917 1 19.95630032 1.681708777 7.987357306 1.061217591 0.963983506 0.554051892 0.037846895 0.081509606 9.430208262 0.017699714 0.009285645 48.05170226 -1.681708777 -0.097234085 IYNISGNGS(ph)PLADSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 IYNISGNGSPLADSK 15 0 Q53HL2 Q53HL2 CDCA8 Borealin 1 IYNISGNGS(1)PLADSK;IYNISGNGS(1)PLADSK;IYNISGNGS(1)PLADSK;IYNISGNGS(1)PLADSK 364.41 2.30E-97 1187190000 1201340 840810 1037750 931660 924960 817000 1272250 818390 1208890 TRUE FALSE 1126150.274 903064.4473 1062365.92 955567.9729 852317.3727 1052854.637 1081487.923 920567.793 1007118.449 1.118190492 0.896681466 1.054856974 0.948813889 0.846293078 1.045412918 1.073843821 0.914061095 1 19.94180194 IYNYYKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IYNYYKK 7 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 107.66 0.01191 274320000 667170 1333700 809850 874470 1792400 630970 1169600 1216800 2170800 FALSE TRUE 625413.0206 1432448.536 829060.0244 896910.3807 1651632.134 813120.7961 994229.338 1368720.159 1808479.456 0.345822574 0.792073435 0.458429329 0.495947232 0.913271162 0.449615722 0.549759819 0.756834784 1 20.78634578 0.96566456 3.574105749 0.999164025 0.584519959 0.408507958 0.167265454 0.222511096 7.659356334 0.145657022 0.037611547 9.239842328 -0.96566456 -0.414644066 IYPSREEYEAHQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IYPSREEYEAHQDR 14 1 Q06587;Q06587-2 Q06587 RING1 E3 ubiquitin-protein ligase RING1 0 ;; 104.95 0.00061754 433280000 193995 382830 305551 366260 399150 368222 291319 284176 386477 FALSE TRUE 181853.1992 411175.1315 312798.814 375658.8517 367802.3691 474521.7138 247638.4204 319655.9991 321971.492 0.564811494 1.277054465 0.9715109 1.166745693 1.142344519 1.473800401 0.769131512 0.992808392 1 18.29657343 1.634922673 25 0.910713436 1.110264862 0.108668029 0.239381521 1.478891076 1361.573953 0.100694188 0.055818917 43.14422511 -1.634922673 0.199551426 IYPTFLHLHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IYPTFLHLHGK 11 0 Q08945;E9PMD4 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 229.53 1.43E-12 765160000 995480 1488010 943860 882390 1693600 672460 1120150 1431570 1542130 FALSE TRUE 933174.6838 1598183.809 966248.8049 905033.6213 1560591.488 866588.2855 952193.9065 1610304.666 1284738.54 0.726353771 1.243975921 0.752097625 0.704449655 1.214715242 0.674525017 0.741157735 1.253410414 1 20.29304335 1.236651056 24.99989302 1.126705194 0.881335456 0.203400026 0.213226387 87.40023275 1144087.553 0.167485894 0.050023593 17.24451786 -1.236651056 -0.245369738 IYQY(ph)IQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 IY(0.001)QY(0.999)IQSR;IYQY(1)IQSR;IYQY(1)IQSR;IYQY(1)IQSR;IYQY(1)IQSR;IYQY(1)IQSR;IYQY(1)IQSR 238.31 1.17E-07 8214510000 3142350 3447260 3381810 3210770 3696340 2851040 3524860 2880340 3992690 TRUE FALSE 2945675.923 3702498.717 3462028.13 3293163.794 3406044.367 3674088.965 2996339.966 3239956.789 3326284.245 0.885575527 1.113103525 1.040809466 0.990042808 1.023978745 1.104562537 0.90080695 0.97404688 1 21.66548003 1.731826371 24.99998824 0.95279249 1.036537729 0.172566212 0.067494721 0.877057136 3234.201991 0.028950858 0.016054695 53.92949722 -1.731826371 0.083745239 IYSAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IYSAER 6 0 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881;E9PKD3 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 ; 102.81 0.08195 418450000 423660 605190 457490 457010 661890 389640 515930 577080 742850 FALSE TRUE 397143.8769 649998.8973 468341.8788 468737.6503 609907.8293 502122.7427 438571.0862 649129.7083 618863.536 0.641730937 1.050310544 0.756777305 0.757416818 0.985528786 0.811362624 0.708671719 1.048906052 1 19.23926179 1.2193359 24.99549695 1.024453257 0.830614271 0.328420592 0.122559826 343.4080111 446478.7064 0.111360903 0.028014423 16.57051093 -1.2193359 -0.193838985 IYSFTDNAPS(ph)PSIGGSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IYSFTDNAPSPSIGGSSR 18 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 IYSFTDNAPS(0.977)PS(0.022)IGGS(0.001)S(0.001)R 94.01 0.0021431 79721000 103970 90785 111370 81054 92264 126420 135380 114170 86573 TRUE FALSE 97462.70329 97506.81586 114011.749 83133.98286 85017.95762 162915.4017 115081.0258 128424.3758 72123.40702 1.351332491 1.351944118 1.580787066 1.152663002 1.178784546 2.258842288 1.595612722 1.780619928 1 16.13817993 IYSHDGTDSPPDADEVVIVLNNFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IYSHDGTDSPPDADEVVIVLNNFK 24 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ; 188.19 1.71E-17 116470000 242212 269420 235285 239220 270200 175075 313800 243170 217422 FALSE TRUE 227052.3833 289368.1371 240866.0713 245358.7902 248979.5819 225616.3104 266748.6032 273530.3098 181132.8636 1.253512912 1.597546306 1.329775649 1.354579094 1.374568794 1.245584627 1.472668172 1.510108681 1 17.4666888 -1.459648668 4.269201887 0.998016268 1.402116495 0.553629505 0.110388099 0.001985021 0.000251243 0.101793348 0.023884349 0.034701746 1.459648668 0.404100227 IYVASVHQDLSDDDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 230.38 2.31E-15 535290000 710160 596880 689340 641700 668720 548660 889100 645880 821010 FALSE TRUE 665712.3533 641073.6163 705691.4703 658167.1084 616201.4287 707049.2352 755787.709 726519.5398 683978.1271 0.973294798 0.937272101 1.031745669 0.962263386 0.900908091 1.033730769 1.104988126 1.062197037 1 19.38359066 2.01329878 21.61782887 1.067885182 0.967516875 0.527531288 0.041573468 31.76668944 51637.30438 0.015092493 0.011134115 103.1095235 -2.01329878 -0.100368307 IYVDDGLISLQVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IYVDDGLISLQVK 13 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 178.81 3.32E-05 112790000 357380 374970 366030 352670 455060 312260 406790 365270 386330 FALSE TRUE 335012.2237 402733.169 374712.4045 361720.1093 419321.4232 402404.3929 345795.616 410874.7636 321849.0272 1.040898668 1.251310816 1.164248989 1.123881319 1.302851299 1.250289294 1.074403173 1.276607132 1 18.29602458 -0.83815274 5.708450325 0.999999958 1.185786833 0.310072771 0.086987513 4.34E-08 9.00E-09 0.076601674 0.018055183 0.1451601 0.83815274 0.185786875 IYVEIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 IYVEIER 7 0 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ;; 116.3 0.012765 324155000 386939 412649 438383 460921 482780 373340 492870 401294 433647 FALSE TRUE 362721.1787 443201.9613 448781.6518 472749.0132 444864.4062 481117.1973 418968.7191 451396.4393 361268.5142 1.00402101 1.226793767 1.242238485 1.308580722 1.231395454 1.331744058 1.159715565 1.24947628 1 18.462712 -1.162276225 3.35037264 0.999660637 1.225163166 0.369504546 0.089709043 8043363.504 13352666.05 30824.03297 0.019622991 0.068821443 1.162276225 0.225502529 IYVVDVGSEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IYVVDVGSEPR 11 0 Q13228;Q13228-4;Q13228-2;A6PVX1;F2Z2W8;F8WCR4 Q13228 SELENBP1 Selenium-binding protein 1 0 155.42 7.34E-05 189770000 272190 343010 273870 287280 325490 231340 320510 289150 361280 FALSE TRUE 255154.1138 368406.8173 280366.3257 294652.0912 299927.3284 298124.1025 272452.501 325251.014 300980.034 0.847744318 1.224024107 0.931511376 0.978975539 0.996502407 0.990511226 0.905217856 1.080639834 1 18.19930826 3.740809398 24.75260158 0.975937082 1.06726328 0.020695804 0.101063042 680.4567781 1230477.885 0.023186713 0.041507552 5505.660125 -3.740809398 0.091326198 KAAALEAMKDYTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAAALEAMKDYTK 13 2 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 109.55 0.00063461 543530000 508070 682670 639640 755800 975340 641590 735780 600960 1075160 FALSE TRUE 476270.8056 733215.5971 654812.5629 775195.1076 898740.7307 826806.6177 625456.6196 675991.1789 895708.8502 0.531725019 0.818586974 0.731055144 0.865454335 1.003384895 0.923075191 0.698281165 0.754699676 1 19.77267034 5.191395283 1.3811731 0.837760485 1.12E-30 0.456205775 0.106720037 4.099717394 2.99501362 0.029516014 6.48990246 155380.0593 -5.191395283 -0.837760485 KAAALEFLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAAALEFLNR 10 1 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 134.2 0.00028378 536420000 567900 1020600 409020 527300 1276300 334570 537410 1009500 961420 FALSE TRUE 532356.1527 1096166.286 418722.1476 540831.4107 1176064.546 431154.9277 456830.3596 1135538.297 800952.791 0.664653596 1.368577897 0.522780059 0.675235066 1.468331916 0.538302547 0.570358659 1.417734366 1 19.61135769 3.976627688 24.99996197 0.836557297 1.05174392 0.00643054 0.379786605 72.00539887 3647549.966 0.090327062 0.176523076 9476.057524 -3.976627688 0.215186623 KAAALEFLNRFEEAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAAALEFLNRFEEAKR 16 3 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 187.56 5.78E-10 571620000 372220 616080 415770 499700 874860 267760 542350 481370 1566490 FALSE TRUE 348923.4146 661695.2042 425632.2607 512523.148 806152.0246 345057.9653 461029.6524 541470.1041 1305032.699 0.267367565 0.507033429 0.326146817 0.392728204 0.617725537 0.264405609 0.353270575 0.414909224 1 20.31565452 0.927158103 19.80874771 1 0.393844749 0.762941913 0.106414167 1589.893178 432360.0015 0.094757778 0.023689445 8.455866208 -0.927158103 -0.606155251 KAAAPAPEEEMDECEQALAAEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAAAPAPEEEMDECEQALAAEPK 23 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 199.89 4.06E-24 318580000 553050 374580 484160 480500 502650 409950 693350 424190 716840 FALSE TRUE 518435.5877 402314.293 495644.5038 492830.4435 463173.8966 528295.91 589388.6042 477151.0553 597194.773 0.868118093 0.6736735 0.829954524 0.825242393 0.775582637 0.884629159 0.986928605 0.798987327 1 19.18784201 2.169512118 0.599949353 0.966209443 0.757642084 0.383305956 0.07542214 0.683649893 0.491683532 0.064277026 0.045649021 147.7447706 -2.169512118 -0.208567358 KAAEAHVDAHYYEQNEQPTGTCAACITGDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAAEAHVDAHYYEQNEQPTGTCAACITGDNR 31 1 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZHJ1;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZGZ8 P55263-3 ADK Adenosine kinase 0 84.097 0.0003028 590930000 65470 66995 59189 61275 65018 38993 56458 48437 83827 FALSE TRUE 61372.34957 71955.37951 60592.99103 62847.42024 59911.74855 50249.6461 47992.64703 54484.46607 69835.73216 0.87881014 1.030351903 0.867650258 0.899932145 0.857895331 0.719540621 0.687221936 0.780180352 1 16.09167777 2.620244941 1.946235184 0.761400067 0.935792708 0.217256918 0.096262325 0.322173737 2.428559132 0.034825318 0.031538728 417.1045632 -2.620244941 0.174392641 KAAEVLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAAEVLNK 8 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 80.688 0.039766 672150000 874620 710140 807110 806270 969830 617770 1004250 759470 1054570 FALSE TRUE 819879.0954 762719.5045 826255.0303 826960.2532 893663.4639 796110.1703 853672.0355 854291.5013 878555.4542 0.933212686 0.868151806 0.94046998 0.941272687 1.017196421 0.906158133 0.971676895 0.97238199 1 19.74477383 3.49751443 1.93120085 0.965894187 0.89759208 0.410421909 0.03342648 0.288805122 2.156335721 0.009167415 0.015664402 3144.23089 -3.49751443 -0.068302107 KAAGGAT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KAAGGATPK 9 1 P16403 P16403 HIST1H1C Histone H1.2 1 KAAGGAT(1)PK;KAAGGAT(1)PK;KAAGGAT(1)PK 71.548 0.031571 537240000 832490 426180 597820 518200 596390 299594 712320 432340 659790 TRUE FALSE 780385.9369 457734.8106 612000.5727 531497.8893 549551.9351 386081.9243 605514.2289 486318.6007 549666.7866 1.419743663 0.832749625 1.113402861 0.966945616 0.999791053 0.702392674 1.101602359 0.884751658 1 19.06819778 4.748309101 24.89026197 0.958380793 1.419743927 0.591808772 0.12238326 872.0185145 2226427.91 0.026645289 0.352911239 56015.61401 -4.748309101 0.461363134 KAALEEVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KAALEEVER 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;; 139.86 0.00017715 2474390000 3221770 3163020 3035060 3394870 3960790 2408030 3840550 3319380 4131690 FALSE TRUE 3020125.167 3397213.292 3107053.056 3481988.112 3649725.53 3103189.17 3264695.181 3733811.9 3442084.247 0.877411751 0.986964016 0.902666185 1.011592937 1.060324289 0.901543642 0.948464636 1.084753199 1 21.71485098 8 0.336024506 0.993975865 0.030511403 0.221799261 0.060469483 111.2731374 1.583390963 0.05201165 66.9757529 100000000 -8 -0.963464462 KAALLAQYADVT(ph)DEEDEADEKDDSGATTMNIGSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAALLAQYADVTDEEDEADEKDDSGATTMNIGSDK 35 2 Q96MW1 Q96MW1 CCDC43 Coiled-coil domain-containing protein 43 1 KAALLAQYADVT(1)DEEDEADEKDDSGATTMNIGSDK 305.38 9.77E-91 262830000 233280 119120 149160 142610 152950 116230 202300 126450 227390 TRUE FALSE 218679.4212 127939.7687 152698.1456 146269.614 140937.924 149783.7142 171966.9931 142237.5609 189437.14 1.154364034 0.675367928 0.806062347 0.77212744 0.743982537 0.790677658 0.90777866 0.750843055 1 17.53135968 -1.409690221 9.035654669 1.000000873 0.811652081 0.141857388 0.131476845 2.07E-06 1.35E-07 0.114017674 0.026874099 0.038932275 1.409690221 -0.188348792 KAALS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAALSSPR 8 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 KAALS(0.5)S(0.5)PR;KAALS(0.5)S(0.5)PR 57.598 0.067536 420180000 333670 499450 323730 299140 603980 223270 406010 541450 680570 TRUE FALSE 312786.1903 536429.7977 331409.0285 306816.4388 556545.8471 287724.4245 345132.5697 609051.2244 566978.4703 0.551672077 0.946120225 0.584517836 0.541143015 0.981599613 0.507469753 0.608722531 1.074205206 1 19.11293443 1.234565152 24.99963754 1.037102798 0.686021253 0.453925618 0.164981282 96.95340866 606596.1033 0.132565603 0.03790885 17.16189149 -1.234565152 -0.351081545 KAAS(ph)LTEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAASLTEDR 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 KAAS(0.748)LT(0.252)EDR;KAAS(0.748)LT(0.252)EDR 110.38 0.0014066 213350000 1269110 839090 1138520 858160 807380 865770 1152750 922360 1025620 TRUE FALSE 1189678.671 901217.0967 1165526.232 880181.8385 743971.6316 1115703.744 979905.8391 1037518.676 854437.3962 1.392353232 1.054749126 1.364086166 1.030130285 0.870715204 1.305775882 1.146843342 1.214271146 1 19.70461527 4.752168773 23.91397452 1.143767293 1.392353536 0.237485503 0.147509524 1997.671765 3510447.875 0.033790532 0.637468824 56515.65601 -4.752168773 0.248586243 KAAS(ph)LTEDRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KAASLTEDRDR 11 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 KAAS(0.801)LT(0.199)EDRDR;KAAS(0.989)LT(0.011)EDRDR;KAAS(0.829)LT(0.171)EDRDR 142.97 1.95E-05 7389650000 8628950 6636100 7437510 5852780 6574210 4514990 7950090 6519770 11240370 TRUE FALSE 8088879.423 7127443.749 7613931.249 6002972.244 6057898.066 5818394.318 6758047.81 7333777.636 9364279.631 0.863801567 0.761131024 0.813082431 0.641050084 0.646915545 0.621339232 0.721683683 0.783165169 1 23.15873659 0.828020607 3.269350174 0.999925016 0.726550061 0.561744231 0.07623364 0.731617653 12.48194244 0.077711174 0.020175685 6.730085899 -0.828020607 -0.273374955 KAAS(ph)PS(ph)PQSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KAAS(1)PS(1)PQSVR;KAAS(0.76)PS(0.892)PQS(0.348)VR;KAAS(1)PS(0.996)PQS(0.004)VR;KAAS(1)PS(0.99)PQS(0.01)VR 138.01 0.00010744 5537490000 9016800 6583120 7491700 7434400 7259300 5875810 8471300 5948810 7182600 TRUE FALSE 8452454.583 7070541.055 7669406.662 7625179.29 6689183.861 7572060.961 7201107.209 6691532.023 5983777.659 1.412561607 1.181618278 1.281699806 1.274308593 1.117886433 1.265431537 1.203438299 1.118278854 1 22.51262514 -5 0.093764678 0.215844167 1.417166971 0.627451567 0.069022876 136.2269634 0.881373869 20.9313873 1.322772473 1.00E-05 5 1.201322804 KAAS(ph)PSPQS(ph)VR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KAAS(0.993)PS(0.008)PQS(0.999)VR 176.94 5.48E-06 405780000 1025600 738730 876760 832270 838640 655390 904270 666530 808620 TRUE FALSE 961409.5267 793426.3378 897557.1612 853627.4572 772776.5973 844590.4536 768683.1083 749747.7377 673656.0981 1.42715182 1.177791369 1.33236701 1.267156134 1.147138131 1.253741272 1.141061605 1.112953241 1 19.36165276 1.357871977 0.300799241 0.963789027 1.335164031 0.670894793 0.069070319 0.946328816 0.311881729 0.135204802 0.108008236 22.79669963 -1.357871977 0.371375004 KAAS(ph)PSPQSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KAAS(0.801)PS(0.199)PQSVR;KAAS(0.5)PS(0.5)PQSVR;KAAS(0.731)PS(0.269)PQSVR;KAAS(0.988)PS(0.012)PQS(0.001)VR;KAAS(0.943)PS(0.054)PQS(0.003)VR 147.52 2.21E-05 9136660000 4424630 3860351 3948930 3858414 4290640 2963184 4443400 3526875 5468410 TRUE FALSE 4147700.306 4146175.405 4042600.484 3957427.436 3953670.442 3818607.118 3777153.421 3967213.107 4555697.044 0.910442522 0.910107798 0.887372546 0.868676604 0.867851923 0.838204797 0.829105488 0.870824611 1 22.11924038 3.533057705 1.552156615 0.863916611 0.909774277 0.00371254 0.04769479 0.73643446 3.562538486 0.013492745 0.025771268 3412.38249 -3.533057705 0.045857666 KAASLT(ph)EDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAASLTEDR 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 KAAS(0.139)LT(0.861)EDR;KAAS(0.296)LT(0.704)EDR 114.02 0.00099983 2125300000 3836100 2285000 3006100 2319900 2334800 2521200 3481300 2641900 3112200 TRUE FALSE 3596005.349 2454183.778 3077406.112 2379432.562 2151434.226 3249029.512 2959311.384 2971747.031 2592753.714 1.38694444 0.946554917 1.186925736 0.917724097 0.829787347 1.25311922 1.141377743 1.146174052 1 21.30605374 -0.809078396 7.987151858 1.000000007 1.091858313 0.032813206 0.165877493 0 0 0.149183527 0.035162895 0.155210681 0.809078396 0.091858306 KAASLT(ph)EDRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KAASLTEDRDR 11 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 KAAS(0.098)LT(0.902)EDRDR;KAAS(0.073)LT(0.927)EDRDR;KAAS(0.11)LT(0.89)EDRDR;KAAS(0.082)LT(0.918)EDRDR;KAAS(0.072)LT(0.928)EDRDR;KAAS(0.164)LT(0.836)EDRDR 151.9 5.34E-05 47175500000 18906300 15173530 15897100 12707760 14184800 10417710 16888200 13941860 24692300 TRUE FALSE 17722988.43 16296993.95 16274186.72 13033862.64 13070783.03 13425133.76 14355971.19 15682531.91 20570995.61 0.861552293 0.792231657 0.791122949 0.63360388 0.635398659 0.652624404 0.697874399 0.762361346 1 24.29410828 0.869434432 6.269216038 0.999999101 0.726336027 0.572440019 0.074489196 2.340607457 112.1741061 0.078512221 0.019724872 7.40345485 -0.869434432 -0.273663074 KAASLTEDRDR ddPTM_SK-BR-3_Pertuzumab_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 0 ;;;; 119.39 0.00033359 1174430000 1808380 3483930 2700540 3065340 3735960 2574360 3005670 3132600 3432690 FALSE TRUE 1695196.724 3741883.802 2764598.084 3144001.814 3442552.772 3317535.941 2554997.687 3523712.006 2859751.863 0.592777557 1.308464504 0.966726561 1.099396719 1.203794223 1.160078251 0.89343335 1.23217404 1 21.44745854 4.754013363 24.62902484 1.099594212 0.5927771 0.617531699 0.127277197 1611.87581 2569000.551 0.029208718 0.69465654 56756.20683 -4.754013363 -0.506817112 KAASPS(ph)PQS(ph)VR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KAAS(0.104)PS(0.898)PQS(0.998)VR 211.75 5.52E-09 615860000 1029100 734600 836960 829850 847260 689330 956460 666170 787450 TRUE FALSE 964690.468 788990.5484 856813.0864 851145.3559 780719.6173 888328.3807 813047.7023 749342.7909 656019.5079 1.470521008 1.202693729 1.30607867 1.297439094 1.190085977 1.354118849 1.23936513 1.142256872 1 19.32337919 1.039844543 1.910872706 1.001606944 1.288425897 0.615638214 0.078601379 0.207460678 1.557858402 0.066106173 0.018742101 10.96085779 -1.039844543 0.286818953 KAAVLS(ph)DS(ph)EDEEKASAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAAVLSDSEDEEKASAK 17 2 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 KAAVLS(1)DS(1)EDEEKASAK 122.3 3.08E-05 85295000 266600 129970 167980 153420 192800 115880 214360 153070 286550 TRUE FALSE 249913.9819 139593.114 171964.5649 157357.0169 177658.2657 149332.6748 182218.708 172181.1264 238722.9538 1.046878727 0.584749442 0.720352032 0.659161653 0.744202696 0.625548036 0.763306189 0.721259199 1 17.86497777 0.128962006 1.210408953 1.000716544 0.712635771 0.297479889 0.125606425 8.26461764 10.34687253 0.120354449 0.032016981 1.345742616 -0.128962006 -0.288080773 KADGYNQPDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KADGYNQPDSK 11 1 O60506-2;O60506;O43390;O43390-3;B4DT28;O43390-2;O43390-4 O60506-2;O43390;O43390-2 SYNCRIP;HNRNPR Heterogeneous nuclear ribonucleoprotein Q;Heterogeneous nuclear ribonucleoprotein R 0 ;;;; 176.25 1.42E-05 3225520000 5578940 3972250 4596470 4384320 4885530 3595430 5619990 4067060 6227840 FALSE TRUE 5229764.104 4266359.523 4705500.439 4496829.074 4501840.181 4633372.274 4777324.673 4574841.394 5188373.271 1.007977613 0.822292326 0.906931748 0.866712713 0.867678547 0.893029864 0.920775053 0.881748701 1 22.30685085 -0.403060046 0.585092102 1.012987081 0.886825657 0.297323313 0.048566552 9.820114405 2.894774992 0.318329456 0.018031239 0.39531196 0.403060046 -0.126161424 KADIDLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KADIDLTK 8 1 P62269 P62269 RPS18 40S ribosomal protein S18 0 ;; 80.763 0.039455 2973690000 8071430 7046840 7874900 8856640 10429730 6926520 12008100 9402210 12401440 FALSE TRUE 7566253.604 7568595.366 8061696.347 9083916.377 9610621.077 8926093.881 10207596.88 10576096.62 10331559.55 0.732343802 0.732570463 0.780298106 0.879239609 0.930219783 0.863963842 0.988001553 1.02366894 1 23.30055471 2.899114958 0.542656543 1.015271067 0.698939492 0.903169354 0.033281369 0.267615247 0.165979206 0.027146654 0.038568186 792.711133 -2.899114958 -0.316331575 KADKVEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KADKVEQR 8 2 Q99832-3;Q99832;Q99832-4 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;;;; 95.523 0.0053937 6270320000 6256810 5747310 6027750 6179770 7583640 4697630 7878200 6439190 8995450 FALSE TRUE 5865207.431 6172846.812 6170731.077 6338353.361 6988051.505 6053759.521 6696937.048 7243137.046 7494051.282 0.782648425 0.823699569 0.823417247 0.845784626 0.932479809 0.80780866 0.893633736 0.966518212 1 22.83731442 1.396375003 0.217442086 1.048340709 0.75870161 0.721815733 0.038050367 1.333960458 0.301749825 0.158682416 0.140110077 24.91007314 -1.396375003 -0.289639099 KADLVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KADLVNR 7 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 96.492 0.020351 862860000 831090 1027620 827700 948870 1232190 736630 1138390 1062750 1240000 FALSE TRUE 779073.5604 1103706.054 847333.4349 973219.6106 1135418.768 949283.1228 967698.9878 1195436.677 1033035.989 0.754159166 1.06841007 0.820236123 0.94209652 1.099108627 0.91892551 0.936752444 1.157207192 1 19.97845909 8 0.220196798 1.027777248 0.167546748 0.223343749 0.108208901 96.44959394 1.235254791 0.159673084 29.51187075 99999999.99 -8 -0.8602305 KADRDQS(ph)PFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KADRDQSPFSK 11 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 KADRDQS(1)PFSK;KADRDQS(1)PFSK 74.789 0.0208 298330000 365050 421530 338320 440300 571000 194615 358300 300450 994400 TRUE FALSE 342202.1721 452740.5198 346345.1102 451598.8434 526155.9633 250797.1912 304576.2413 337961.8439 828428.2159 0.413074018 0.546505432 0.41807498 0.545127308 0.635125595 0.302738591 0.367655562 0.407955496 1 19.66001717 -1.544549869 4.450348051 1.005128798 0.454333663 0.756589997 0.097232246 0.00508798 0.000520706 0.096809967 0.022668893 0.028539748 1.544549869 -0.550795134 KADS(ph)DSEDKGEESKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KADSDSEDKGEESKPK 16 3 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 1 KADS(0.707)DS(0.293)EDKGEESKPK;KADS(0.611)DS(0.389)EDKGEESKPK;KADS(0.926)DS(0.074)EDKGEESKPK;KADS(0.792)DS(0.208)EDKGEESKPK 188.44 8.41E-10 6575300000 8571950 1381054 3021770 2958940 3053350 1706020 4280330 1918980 4238310 TRUE FALSE 8035446.951 1483308.675 3093447.811 3034871.41 2813552.208 2198520.279 3638534.253 2158568.877 3530908.68 2.275744767 0.420092619 0.876105301 0.85951569 0.796835167 0.622649997 1.030480984 0.611335232 1 21.75160808 4.746881092 24.99275754 0.773119834 2.275745515 0.865659384 0.185528038 353.2077164 1060929.454 0.042228272 0.48384361 55831.73087 -4.746881092 1.502625681 KADYQAVDDEIEANLEEFDISEDDIDDGFRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 KADYQAVDDEIEANLEEFDISEDDIDDGFRR 31 2 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;;;;; 416.89 4.36E-176 1325760000 298632 334920 353536 334845 399026 264919.8 408722 324135 614184 FALSE TRUE 279941.1562 359717.8253 361922.0409 343437.6896 367688.1076 341397.8456 347437.9305 364603.9683 511672.7226 0.547109791 0.70302326 0.707331122 0.671205781 0.718600174 0.667219163 0.679023749 0.712572612 1 18.9648618 -5 0.324249947 4.108674708 0.668061739 0.831794248 0.046367666 128.9340035 1.131029097 275.5036405 0.037952696 1.00E-05 5 -3.440612969 KAEAAASALADADADLEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KAEAAASALADADADLEER 19 1 O43633;M0R1T5 O43633 CHMP2A Charged multivesicular body protein 2a 0 ;; 222.72 3.80E-19 761390000 1057140 1045820 1072930 1086070 1219330 837800 1246480 981670 1235850 FALSE TRUE 990975.4944 1123253.601 1098380.406 1113940.395 1123568.74 1079659.259 1059581.896 1104233.66 1029578.651 0.962505869 1.090983773 1.066825157 1.081938125 1.091289858 1.048641848 1.029141285 1.072510254 1 19.97362261 -1.953277774 9.601663748 0.97899916 1.058999424 0.16707722 0.038217845 0.01780592 8.66E-05 0.038350011 0.008087966 0.011135821 1.953277774 0.080000264 KAEAGAGS(ph)ATEFQFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KAEAGAGSATEFQFR 15 1 P46783;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 1 KAEAGAGS(0.971)AT(0.029)EFQFR;KAEAGAGS(0.983)AT(0.017)EFQFR;KAEAGAGS(0.951)AT(0.049)EFQFR 176.7 4.80E-07 1614750000 366682 333628 349800 365050 455327 248275 388872 312668 459542 TRUE FALSE 343732.0282 358330.1643 358097.4212 374417.801 419567.4541 319947.9621 330564.2537 351705.2881 382841.4714 0.897844288 0.935975308 0.935367372 0.977996975 1.095930001 0.835719184 0.863449439 0.918670819 1 18.54638759 -0.384748398 7.434862897 1.00000096 0.930083821 0.082384662 0.070220068 0 0 0.069025713 0.016269517 0.41233633 0.384748398 -0.069917139 KAEAGAGSATEFQFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KAEAGAGSATEFQFR 15 1 P46783;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 0 ;; 199.08 1.22E-08 1605660000 1581990 1748770 1618170 1767830 1877510 1365880 1982040 1662990 2314380 FALSE TRUE 1482976.07 1878250.75 1656553.757 1813195.511 1730057.938 1760187.383 1684851.502 1870617.962 1928095.027 0.76914055 0.974148434 0.859166034 0.940407753 0.89728873 0.912915265 0.873842564 0.970189714 1 20.87874473 -4.999999992 0.144239802 1.350409472 0.867702854 0.316766666 0.055557886 183.6807185 1.603480947 18.38774991 0.284297162 1.00E-05 4.999999992 -0.482706617 KAEDS(ph)DS(ph)EPEPEDNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KAEDSDSEPEPEDNVR 16 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 2 KAEDS(1)DS(1)EPEPEDNVR;KAEDS(1)DS(1)EPEPEDNVR;KAEDS(1)DS(1)EPEPEDNVR;KAEDS(1)DS(1)EPEPEDNVR;KAEDS(1)DS(1)EPEPEDNVR;KAEDS(1)DS(1)EPEPEDNVR 233.65 7.84E-20 5295500000 6533210 3752890 4671130 4449410 4737350 3537310 5727050 3790100 6345120 TRUE FALSE 6124308.048 4030757.88 4781931.409 4563589.393 4365297.641 4558473.974 4868332.02 4263302.328 5286078.481 1.158573046 0.762523276 0.904627396 0.863322293 0.825810221 0.862354577 0.920972331 0.80651514 1 22.33376641 -0.520610872 6.726513356 1.000000014 0.877795612 0.090841543 0.106947101 0 0 0.090059191 0.021227155 0.301570689 0.520610872 -0.122204403 KAEDS(ph)DSEPEPEDNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAEDSDSEPEPEDNVR 16 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 1 KAEDS(0.95)DS(0.05)EPEPEDNVR 158.52 5.79E-09 242100000 391860 263270 330890 312180 317880 249460 400410 271250 398910 TRUE FALSE 367334.1821 282762.7847 338738.8671 320191.0673 292914.9871 321475.0524 340372.2377 305116.1596 332329.3439 1.10533177 0.850851091 1.01928666 0.963475158 0.881399709 0.967338751 1.024201576 0.918113808 1 18.34225416 -1.304315097 4.806689483 1.0000169 0.962688771 0.01845378 0.073377954 1.20E-05 1.74E-06 0.064240176 0.0151347 0.049623216 1.304315097 -0.037328129 KAEEDAALQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAEEDAALQAK 11 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 0 ; 120.59 0.00069219 466370000 1577880 1035620 1198190 1161360 1293170 875070 1558360 1122050 1687950 FALSE TRUE 1479123.307 1112298.382 1226611.633 1191162.464 1191609.645 1127688.503 1324698.385 1262140.412 1406220.24 1.051843278 0.790984478 0.87227562 0.847066789 0.847384791 0.801928795 0.942027676 0.897541065 1 20.42339113 1.027068266 1.207531141 0.99526844 0.861052779 0.195619541 0.074681852 0.640724082 1.934688496 0.063194065 0.019779391 10.64310303 -1.027068266 -0.134215661 KAEEVQAWAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAEEVQAWAQR 11 1 Q9BYN8 Q9BYN8 MRPS26 "28S ribosomal protein S26, mitochondrial" 0 104.24 0.0033991 0 182400 196410 175020 149650 271650 144970 173790 213400 342520 FALSE TRUE 170983.9096 210952.4008 179171.5571 153490.2724 250315.7048 186820.4856 147731.8029 240043.4598 285351.1992 0.599205155 0.739272873 0.627898385 0.537899517 0.87721974 0.654703699 0.517719229 0.841221135 1 18.1223791 1.012013289 6.199394528 0.999760131 0.654926357 0.574908951 0.101658361 0.089126251 14.153374 0.09415809 0.023665005 10.28047755 -1.012013289 -0.344833774 KAEGAPNQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KAEGAPNQGR 10 1 Q9P2E9;A0A087WVV2;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;;;; 165.63 9.29E-06 2196260000 1194950 1162610 1055420 1080940 1303070 863225 1412470 1101790 1141950 FALSE TRUE 1120160.213 1248690.854 1080455.061 1108678.75 1200732.139 1112424.044 1200683.236 1239350.907 951351.1677 1.17744136 1.312544617 1.135705823 1.165372775 1.262133457 1.16930959 1.262082054 1.302727057 1 19.85961845 -1.075779435 4.484319191 0.999983981 1.223427147 0.571020621 0.060856409 9.25E-06 1.91E-06 0.055950318 0.013186671 0.083988643 1.075779435 0.223443166 KAEGAQNQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KAEGAQNQGK 10 1 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;;;; 150.09 3.56E-05 4424740000 4571960 3017970 4000040 3777200 3894370 2575740 4362350 3430920 3460290 FALSE TRUE 4285809.185 3241423.639 4094922.838 3874129.347 3588521.889 3319314.324 3708256.116 3859277.914 2882745.245 1.486711041 1.124422508 1.420494178 1.343902779 1.244827963 1.15144213 1.286362755 1.338750943 1 21.45901192 2.612381268 5.075315621 1.22038427 1.319653739 0.212699517 0.128489703 0.485774243 18.09007012 0.039550542 0.037086283 409.6201084 -2.612381268 0.099269469 KAEGAQNQGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAEGAQNQGQK 11 1 Q9P2E9 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 149.49 5.51E-05 43868000 77182 56687 66989 63240 65864 42537 70799 64086 61001 FALSE TRUE 72351.31639 60884.16446 68578.01071 64862.84547 60691.30712 54816.74137 60183.34722 72087.27817 50819.53902 1.423690923 1.198046374 1.34944181 1.276336754 1.19425143 1.078654833 1.184256063 1.418495318 1 15.63309567 2.763519542 3.874529129 1.177023975 1.301151661 0.246505128 0.119069977 0.358271828 12.08166553 0.035727174 0.03646755 580.1222759 -2.763519542 0.124127686 KAEGEPQEES(ph)PLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 227.91 8.80E-12 18990890000 38875880 15120150 22643930 20544210 19513130 17600260 30636660 18652300 24237990 TRUE FALSE 36442708.07 16239661.64 23181054.71 21071409.21 17980647.48 22681169.35 26042977.25 20981080.71 20192512.89 1.804763393 0.804241737 1.148002472 1.043525852 0.890461112 1.123246496 1.289734339 1.039052486 1 24.26731712 4.750731368 24.99432916 1.0561905 1.804763853 0.760763163 0.134174269 1035.615508 2126741.573 0.03410261 0.580119169 56328.91272 -4.750731368 0.748573352 KAEGEPQEES(ph)PLKSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KAEGEPQEESPLKSK 15 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 KAEGEPQEES(1)PLKSK;KAEGEPQEES(1)PLKSK;KAEGEPQEES(0.996)PLKS(0.004)K;KAEGEPQEES(0.999)PLKS(0.001)K;KAEGEPQEES(1)PLKSK;KAEGEPQEES(0.996)PLKS(0.004)K;KAEGEPQEES(0.998)PLKS(0.002)K;KAEGEPQEES(1)PLKSK 239.56 4.32E-18 19872470000 5740980 2346880 3398300 3347300 3854220 2213942 4602480 2802260 6897490 TRUE FALSE 5381662.31 2520645.437 3478909.281 3433197.385 3551525.108 2853071.115 3912380.851 3152128.33 5746254.36 0.936551356 0.438658869 0.605422082 0.597467005 0.618059154 0.496509715 0.680857582 0.548553568 1 22.45419042 -1.375241126 2.91411462 1.006054477 0.598914317 0.447473062 0.133262131 16357080.99 19760149.68 837616.5618 0.031000368 0.042146244 1.375241126 -0.407140159 KAEGS(ph)PNQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KAEGSPNQGK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGS(1)PNQGK;KAEGS(1)PNQGK;KAEGS(1)PNQGK;KAEGS(1)PNQGK;KAEGS(1)PNQGK 135.91 8.06E-05 965590000 3044229 1472422 2343235 2146006 2132357 1469573 2598648 1918414 2012226 TRUE FALSE 2853696.141 1581441.657 2398817.641 2201076.147 1964890.283 1893814.869 2209004.857 2157932.211 1676372.481 1.702304335 0.943371282 1.43095742 1.312999451 1.17210841 1.129710067 1.317729134 1.287262965 1 20.67691131 2.744914143 23.46713137 1.206073316 1.293993534 0.11036349 0.204744818 827.5996441 3056787.135 0.059414863 0.061555428 555.7943698 -2.744914143 0.087920218 KAEGS(ph)PNQGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAEGSPNQGKK 11 2 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGS(1)PNQGKK 66.215 0.033038 115840000 396810 168400 257120 249600 246970 150710 311290 217990 282250 TRUE FALSE 371974.3704 180868.5112 263219.0078 256005.1586 227573.9724 194217.5304 264614.9544 245206.5314 235140.6516 1.581922853 0.769192864 1.119410897 1.088732028 0.967820625 0.825963223 1.125347542 1.04280791 1 17.84316445 4.752789243 24.72673041 0.99480324 1.581923322 0.713771433 0.117311575 1206.047925 2095847.538 0.027456502 0.582131328 56596.45679 -4.752789243 0.587120082 KAEGS(ph)PSEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KAEGSPSEGK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGS(0.795)PS(0.205)EGK;KAEGS(0.996)PS(0.004)EGK;KAEGS(0.986)PS(0.014)EGK 175.88 2.82E-06 607610000 4405420 2137760 2974010 2779110 3031170 1814220 3328800 2556510 3185470 TRUE FALSE 4129692.626 2296041.975 3044554.922 2850426.668 2793114.135 2337955.863 2829677.343 2875695.901 2653794.478 1.556146363 0.865192084 1.147245933 1.074094732 1.052498284 0.88098603 1.066275993 1.083616657 1 21.33962522 4.749199311 24.99882298 1.023400387 1.556146664 0.783960006 0.088240808 697.0500992 1637897.741 0.020255823 0.29427461 56130.55174 -4.749199311 0.532746276 KAEGS(ph)PSEGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KAEGSPSEGKK 11 2 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGS(0.547)PS(0.453)EGKK;KAEGS(0.944)PS(0.056)EGKK;KAEGS(0.994)PS(0.006)EGKK 85.163 0.0080466 2105100000 8647700 3170950 4830830 4357320 4610450 3038770 6197100 3663910 5402600 TRUE FALSE 8106455.894 3405730.437 4945419.569 4469136.208 4248363.855 3916013.569 5267902.386 4121357.229 4500871.158 1.80108597 0.756682499 1.098769415 0.992949154 0.943898127 0.870056803 1.170418393 0.915679895 1 22.10177284 4.748139041 24.86952914 0.977147487 1.801086442 0.839271617 0.114442874 469.9178184 1220072.987 0.026592418 0.346797459 55993.68383 -4.748139041 0.823938955 KAEGSPS(ph)EGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAEGSPSEGK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGS(0.462)PS(0.538)EGK 114.31 0.00084067 544610000 2220200 1077100 1541100 1374800 1448300 936280 1730100 1358400 1617100 TRUE FALSE 2081241.645 1156849.605 1577655.62 1410079.696 1334556.36 1206568.837 1470687.566 1527999.23 1347195.563 1.544869729 0.858709482 1.17106652 1.046677805 0.990618138 0.89561521 1.091665981 1.13420744 1 20.36152786 4.75036445 24.73923059 1.026652471 1.544870091 0.740929698 0.096859422 819.9692287 1718507.099 0.02232711 0.368712829 56281.34278 -4.75036445 0.51821762 KAEGT(ph)PNQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KAEGTPNQGK 10 1 Q9P2E9;A0A087WVV2;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGT(1)PNQGK;KAEGT(1)PNQGK;KAEGT(1)PNQGK;KAEGT(1)PNQGK;KAEGT(1)PNQGK 139.78 7.83E-05 2231148000 8737070 4260780 6384260 5684430 6115840 4170290 7514640 5387310 7192380 TRUE FALSE 8190232.385 4576252.585 6535697.662 5830302.098 5635526.597 5374185.024 6387889.494 6059927.512 5991925.313 1.36687825 0.763736586 1.090750856 0.973026497 0.940520167 0.896904541 1.066082963 1.011348973 1 22.51458821 1.643044384 24.99999666 1.029047563 0.983396805 0 0.155916376 3.441808794 2429.033287 0.065299931 0.036209019 43.95865383 -1.643044384 -0.045650758 KAELLDNEKPAAVVAPITTGYTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAELLDNEKPAAVVAPITTGYTVK 24 2 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 143.48 1.37E-07 1574410000 3513000 1970760 2423990 2447800 2628730 1807850 3196400 2345940 2594150 FALSE TRUE 3293127.601 2116677.121 2481488.187 2510614.692 2422280.15 2329746.947 2717129.494 2638835.773 2161169.606 1.523771013 0.979412775 1.148215383 1.161692578 1.120819089 1.078002828 1.25724954 1.221022064 1 21.04338087 1.74420242 25 1.185965467 1.142350859 0 0.155612224 6.439506488 28639.59989 0.065523578 0.036336657 55.48842781 -1.74420242 -0.043614609 KAEPSEVDMNS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 KAEPSEVDMNSPK 13 1 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 KAEPSEVDMNS(1)PK;KAEPSEVDMNS(1)PK;KAEPSEVDMNS(1)PK;KAEPSEVDMNS(1)PK;KAEPSEVDMNS(1)PK;KAEPSEVDMNS(1)PK;KAEPSEVDMNS(1)PK;KAEPSEVDMNS(1)PK;KAEPS(0.001)EVDMNS(0.999)PK 154.49 1.93E-05 7885050000 20111970 8562310 13445760 12187660 12750950 9320000 16046990 9494600 14568410 TRUE FALSE 18853197.7 9196272.341 13764699.78 12500415.99 11749541.82 12010532.7 13640892.82 10680021.71 12136848.26 1.553384973 0.75771503 1.134124732 1.029955696 0.968088385 0.989592392 1.123923817 0.879966651 1 23.53289049 4.754486417 24.89664906 0.995886668 1.553385415 0.726427532 0.10937015 1596.386432 2495571.655 0.025268849 0.653665656 56818.06208 -4.754486417 0.557498747 KAEPSEVDMNSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAEPSEVDMNSPK 13 1 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 113.35 0.0013294 139650000 206660 146380 171310 167860 162550 129870 189450 143330 194050 FALSE TRUE 193725.5195 157218.1275 175373.5541 172167.5718 149783.9787 167361.3607 161043.7313 161225.066 161661.8014 1.198338246 0.97251253 1.084817518 1.064986103 0.926526721 1.035256067 0.996176771 0.997298463 1 17.3026193 4.746513517 24.80748244 1.01373644 1.198338347 0.633628197 0.044986825 604.9172086 1886869.619 0.010399582 0.115319531 55784.49638 -4.746513517 0.184601906 KAEQGS(ph)EEEGEGEEEEEEGGESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 KAEQGSEEEGEGEEEEEEGGESK 23 1 Q5STZ8;Q8NE71 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 KAEQGS(1)EEEGEGEEEEEEGGESK;KAEQGS(1)EEEGEGEEEEEEGGESK;KAEQGS(1)EEEGEGEEEEEEGGESK;KAEQGS(1)EEEGEGEEEEEEGGESK;KAEQGS(1)EEEGEGEEEEEEGGESK;KAEQGS(1)EEEGEGEEEEEEGGESK;KAEQGS(1)EEEGEGEEEEEEGGESK 273.79 6.84E-52 9012920000 10403650 3874355 5921333 5435322 5426266 4258371 7498370 4609547 6321490 TRUE FALSE 9752504.118 4161216.275 6061789.815 5574801.564 5000108.957 5487693.579 6374059.03 5185059.09 5266392.481 1.851837696 0.790145492 1.151032673 1.058561736 0.949437205 1.042021384 1.210327383 0.984556147 1 22.32838361 4.749303552 24.99770385 1.034955429 1.85183816 0.840217241 0.11345275 636.0168426 1479917.069 0.027531854 0.408861938 56144.02606 -4.749303552 0.816882731 KAEQGS(ph)EEEGEGEEEEEEGGESKADDPYAHLSK ddPTM_SK-BR-3_Pertuzumab_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 210.64 7.04E-28 996530000 735240 473410 575180 654780 816320 355060 791360 524080 1556890 TRUE FALSE 689222.6408 508461.769 588823.5412 671582.7633 752209.5201 457560.0581 672702.9146 589512.5416 1297035.001 0.531383224 0.392018541 0.453976601 0.517783069 0.579945429 0.352773871 0.518646693 0.454507813 1 20.30678598 -4.140679964 0.573095608 10 0.466045358 0.855259971 0.067759738 675.1946301 6.611526702 7727.400096 0.026395712 7.23E-05 4.140679964 -9.533954642 KAERS(ph)PNQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 116.54 0.00056191 2342370000 2139410 1939400 1761520 1984640 2652370 920140 1807570 1592490 3644620 TRUE FALSE 2005508.147 2082995.194 1803304.086 2035569.222 2444063.559 1185769.481 1536541.659 1791315.882 3036309.377 0.660508498 0.686028641 0.593913157 0.670409029 0.804945497 0.390529862 0.506055697 0.589964875 1 21.53388737 -1.548922132 7.967730426 1.000099925 0.607588326 0.54794041 0.110438806 0.000201902 1.14E-05 0.110132904 0.025952053 0.028253865 1.548922132 -0.3925116 KAESGWFHVEEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAESGWFHVEEDR 13 1 O43719;Q5H919;Q5H918 O43719 HTATSF1 HIV Tat-specific factor 1 0 129.95 9.59E-05 150670000 312720 230490 272770 258090 211640 247840 355280 240210 263500 FALSE TRUE 293147.4134 247555.7194 279240.2332 264713.0263 195018.6481 319387.3847 302009.0623 270200.7473 219520.1477 1.335400948 1.127712978 1.272048311 1.205871211 0.888386101 1.454934264 1.375769219 1.230869923 1 17.74399383 KAEVEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KAEVEGK 7 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;; 97.431 0.019245 5057200000 8048500 5277620 6554800 6197700 6592100 4912950 7696400 6011580 7933200 FALSE TRUE 7544758.752 5668380.476 6710282.951 6356743.475 6074383.057 6331238.91 6542396.27 6762138.996 6609097.67 1.141571683 0.857663294 1.015309999 0.961817148 0.919094158 0.95795814 0.989907639 1.023156161 1 22.65602189 1.531838507 3.765086829 1.010865617 0.964019661 0.023220988 0.072898735 0.53382202 16.63410541 0.042796058 0.017230388 34.02816318 -1.531838507 -0.046845956 KAFEEAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAFEEAEK 8 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 121.73 0.0022779 1207470000 2261000 1761430 1654630 1643330 2332500 1017510 1992950 1960730 3127500 FALSE TRUE 2119488.046 1891848.11 1693878.605 1685500.63 2149314.859 1311248.619 1694125.649 2205531.457 2605500.046 0.8134669 0.726097899 0.650116513 0.646901017 0.824914535 0.503261791 0.65021133 0.846490661 1 21.31312885 1.019543125 3.821279871 0.998369072 0.681327138 0.563339999 0.091509052 0.130651825 4.669271193 0.083664559 0.021519798 10.46027554 -1.019543125 -0.317041933 KAGEIWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAGEIWK 7 1 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 80.165 0.049147 1317290000 3499900 1911540 2102200 1859940 2220190 1418830 2329400 1761870 2837700 FALSE TRUE 3280847.506 2053072.411 2152065.177 1907669.209 2045825.233 1828423.188 1980128.095 1981843.348 2364069.538 1.387796532 0.868448401 0.910322282 0.806942934 0.86538285 0.773421915 0.837592999 0.83831855 1 21.17284104 4.739183914 5.868436818 0.854815334 1.403531506 0.878861868 0.061246318 0.040141181 6.307647694 0.01344241 0.087985295 54850.91973 -4.739183914 0.548716173 KAGEQQETASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 KAGEQQETASR 11 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;;;;; 210.31 2.11E-08 1364735000 1103542.8 1086292 1079618 1083225 1143742 851607.8 1239950 973822 1316663 FALSE TRUE 1034474.026 1166722.19 1105227.049 1111022.387 1053917.117 1097453.147 1054031.009 1095405.82 1096903.439 0.943085771 1.063650772 1.007588279 1.012871642 0.960811206 1.000501145 0.960915037 0.998634685 1 20.0650051 2.863014243 6.677077374 0.981492603 1.016854161 0.069010212 0.032609223 0.364608977 18.35042082 0.009218256 0.009800726 729.4814339 -2.863014243 0.035361559 KAGGTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAGGTPR 7 1 P16403 P16403 HIST1H1C Histone H1.2 0 73.616 0.077621 120140000 83553 83738 99061 92193 87306 71225 83079 76528 93107 FALSE TRUE 78323.56688 89938.04865 101410.7737 94558.82846 80449.33894 91786.50126 70622.07522 86082.68926 77566.84021 1.009755801 1.159490942 1.307398541 1.21906253 1.037161482 1.183321391 0.910467347 1.109787237 1 16.24315241 2.213847295 1.512242921 1.009041797 1.187456074 0.246283722 0.10257425 0.445270413 1.993540136 0.057965778 0.033863866 163.6241091 -2.213847295 0.178414277 KAGNFYVPAEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAGNFYVPAEPK 12 1 P18124;A8MUD9;C9JZ88;C9JIJ5 P18124 RPL7 60S ribosomal protein L7 0 ; 114.82 0.0016304 2070200000 6572000 5779100 6070600 5979200 6986500 4473900 7785600 5670300 7986900 FALSE TRUE 6160670.251 6206990.577 6214597.499 6132636.395 6437808.472 5765442.302 6618221.558 6378249.437 6653834.793 0.925882659 0.932844107 0.933987346 0.921669471 0.967533561 0.866484138 0.994647713 0.958582477 1 22.66575462 1.617312483 25 0.982461156 0.928425649 0.519723625 0.026864835 0.538151297 1420.409981 0.010956904 0.005974489 41.4297663 -1.617312483 -0.054035507 KAGTQIENIDEDFRDGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KAGTQIENIDEDFRDGLK 18 2 O43707;F5GXS2;O43707-3;K7EP19 O43707 ACTN4 Alpha-actinin-4 0 ;; 222.79 3.09E-19 891520000 1340490 985650 1051180 1037430 1197530 782730 1330930 1014960 1261470 FALSE TRUE 1256591.124 1058628.552 1076114.486 1064052.21 1103480.824 1008691.444 1131369.402 1141679.99 1050922.508 1.195702932 1.007332647 1.0239713 1.012493502 1.050011601 0.959815245 1.076548836 1.086359824 1 20.00322486 4.742717824 24.95546201 1.027346414 1.195703 0.671642058 0.037055528 238.5558422 1431981.474 0.0083708 0.064172253 55299.06954 -4.742717824 0.168356586 KAGTQIENIEEDFRDGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KAGTQIENIEEDFRDGLK 18 2 P12814-3;P12814;P12814-2;P12814-4;G3V2N5;G3V5M4;G3V380 P12814-3 ACTN1 Alpha-actinin-1 0 ;;; 217.42 4.74E-19 437604000 765282 575866 647007 629650 750723 452066 752164 614925 1060796 FALSE TRUE 717384.3657 618503.7178 662354.3116 645807.885 691764.2439 582570.1155 639383.9909 691699.7399 883742.2946 0.811757421 0.699868866 0.749488075 0.73076494 0.782766931 0.659208141 0.723495973 0.782693942 1 19.75326621 0.816189968 3.348200817 0.999956167 0.731942607 0.794291836 0.041753097 0.416530546 6.97954159 0.036469951 0.009446249 6.549225854 -0.816189968 -0.26801356 KAHEILPNLVCCSAK ddPTM_SK-BR-3_Pertuzumab_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 1210910000 1584400 1546200 1358310 1349630 1801760 909670 1730910 1518280 2117200 FALSE TRUE 1485235.232 1660682.257 1390529.755 1384263.791 1660257.038 1172276.962 1471376.114 1707840.6 1763825.642 0.842053317 0.941522913 0.788360097 0.784807612 0.941281835 0.664621793 0.834195897 0.96825931 1 20.75027652 1.21082602 5.393799553 0.990781259 0.829539373 0.403909442 0.079092404 0.183651462 13.87228959 0.06804019 0.018626916 16.24897687 -1.21082602 -0.161241886 KAHS(ph)NMLTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAHSNMLTVK 10 1 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 KAHS(1)NMLTVK 73.885 0.01869 230400000 160280 208860 207370 231940 217600 159860 244800 188120 247720 TRUE FALSE 150248.3609 224324.2117 212288.9143 237891.9731 200510.5738 206008.9869 208094.5126 211607.1961 206373.9317 0.728039436 1.086979397 1.028661482 1.152722978 0.97158867 0.998231633 1.008337201 1.025358166 1 17.65490122 4.74440385 24.93650609 1.035825999 0.728039298 0.775912787 0.051662788 291.5629512 1244233.325 0.011991978 0.108858667 55514.16993 -4.74440385 -0.307786701 KAIVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KAIVER 6 1 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ;;; 91.906 0.075939 2164300000 5281110 5450930 5686390 5473320 6097900 4482600 6369300 5309200 6324500 FALSE TRUE 4950574.752 5854522.529 5821273.856 5613774.658 5618995.532 5776653.851 5414282.595 5972065.307 5268900.092 0.9395841 1.111147 1.104836637 1.065454755 1.06644564 1.096368075 1.027592571 1.133455788 1 22.32907039 -0.237992772 7.629604122 1 1.073001071 0.128658363 0.054397044 0 0 0.047483686 0.011192012 0.578105669 0.237992772 0.073001071 KAKDDATLSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAKDDATLSGK 11 2 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 103.88 0.0015044 323800000 459480 363580 413210 451770 490790 300010 569660 357820 739180 FALSE TRUE 430721.967 390499.8415 423011.5363 463363.183 452245.3332 386618.0167 484244.7715 402494.6147 615806.0827 0.699444158 0.634127938 0.686923283 0.752449831 0.73439569 0.62782429 0.786359188 0.653606104 1 19.23211659 -5 0.270933645 3.098742179 0.674335321 0.765864875 0.052227979 94.23917515 0.914480527 110.6885143 0.059118689 1.00E-05 5 -2.424406857 KAKS(ph)S(ph)S(ph)GGSSLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAKSSSGGSSLAK 13 2 O94762-4;O94762;J3KS37 O94762-4 RECQL5 ATP-dependent DNA helicase Q5 3 KAKS(1)S(1)S(1)GGSSLAK 63.134 0.047122 832530000 1328800 1238900 1186500 1242900 1344100 1023500 1603400 1185000 1684800 TRUE FALSE 1245632.78 1330629.445 1214644.34 1274794.918 1238539.808 1318967.835 1362985.055 1332949.859 1403595.996 0.887458203 0.948014563 0.865380312 0.908234935 0.882404774 0.939706182 0.971066503 0.949667755 1 20.42069631 2.003696265 3.463535907 0.968917896 0.901114722 0.658840079 0.024689058 0.154021469 3.796246998 0.010912142 0.006685741 100.8547287 -2.003696265 -0.067803174 KALAAAGYDVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KALAAAGYDVEK 12 1 P10412;P22492;Q02539;P16402;P16403 P10412;P16402;P16403 HIST1H1E;HIST1H1T;HIST1H1A;HIST1H1D;HIST1H1C Histone H1.4;Histone H1t;Histone H1.1;Histone H1.3;Histone H1.2 0 136.51 0.00042334 0 501130 425170 394700 408530 558510 317280 541390 390560 661460 FALSE TRUE 469765.1678 456650.0292 404062.4704 419013.5714 514646.8775 408873.5854 460213.5955 439322.2757 551058.0528 0.852478546 0.828678624 0.733248463 0.760380089 0.933924974 0.74197915 0.835145396 0.797234109 1 19.07184479 -4.999990208 0.457997227 5.633996766 0.804077675 0.500801431 0.059227725 1169.694408 6.552561496 5508.223771 0.028948663 1.00E-05 4.999990208 -4.829919091 KALDSNSLENDDLSAPGREPGHFNPESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KALDSNSLENDDLSAPGREPGHFNPESR 28 2 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ; 196.8 3.38E-25 366970000 100566 112461 106996 115644 138911 89160 142724 107553 193376 FALSE TRUE 94271.75358 120787.7295 109533.9956 118611.6208 128001.4904 114899.0446 121323.8612 120981.2288 161100.2963 0.585174303 0.74976727 0.67991182 0.736259483 0.794545344 0.713214359 0.753095208 0.750968381 1 17.29759962 -5 0.176869047 2.11963362 0.662091365 0.78841636 0.048023092 57.49308039 0.550674843 22.5812582 0.143702427 1.00E-05 5 -1.457542255 KALEEAGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KALEEAGFK 9 1 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ; 127.42 0.00071485 923250000 993430 942700 965290 1093260 1356420 873500 1346290 1151370 1887850 FALSE TRUE 931252.9896 1012498.489 988187.1346 1121314.902 1249892.245 1125665.27 1144426.313 1295121.079 1572755.639 0.592115499 0.643773555 0.628315747 0.712961934 0.794714839 0.715728014 0.727656786 0.823472539 1 20.5848631 -5 0.079968043 2.077042054 0.372028345 0.902658589 0.036412353 73.66785049 0.417393499 13.80731386 1.293658042 1.00E-05 5 -1.705013709 KALERPYTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KALERPYTSK 10 2 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ; 150.06 1.25E-05 1910580000 2915570 3064000 3227700 3280700 3846800 2535060 4223700 3337000 4869500 FALSE TRUE 2733089.678 3290861.748 3304262.568 3364888.316 3544687.845 3266890.669 3590395.396 3753631.796 4056748.992 0.673714268 0.811206647 0.814509987 0.829454404 0.873775492 0.805297709 0.885042531 0.925280761 1 21.95189261 7.999999994 0.0661334 1.207595199 0.014454402 0.818875621 0.036475516 117.5156461 0.576214149 1.920576338 13.1985246 99999998.57 -7.999999994 -1.193140797 KALVVPEPEPDS(ph)DSNQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KALVVPEPEPDSDSNQER 18 1 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 1 KALVVPEPEPDS(0.664)DS(0.336)NQER 105.16 0.00029753 442720000 135530 160320 153590 157650 213150 138940 187390 175080 284410 TRUE FALSE 127047.4192 172190.2596 157233.2273 161695.5659 196410.0588 179049.7225 159292.6091 196939.1234 236940.1336 0.536200505 0.726724751 0.663598964 0.682432155 0.828943817 0.755674945 0.672290535 0.831176721 1 17.85416306 -4.999999999 0.114905546 1.955723743 0.551609641 0.715351757 0.066390779 91.61714466 0.692004536 20.40438862 0.710904793 1.00E-05 4.999999999 -1.404114102 KALVVPEPEPDSDS(ph)NQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KALVVPEPEPDSDSNQER 18 1 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 1 KALVVPEPEPDS(0.018)DS(0.982)NQER;KALVVPEPEPDS(0.089)DS(0.911)NQER;KALVVPEPEPDS(0.059)DS(0.941)NQER;KALVVPEPEPDS(0.011)DS(0.989)NQER 132.36 9.17E-06 1891080000 1303831 1500210 1448795 1411197 1845880 1415410 1823040 1614530 2748580 TRUE FALSE 1222226.545 1611287.109 1483161.102 1447410.704 1700912.031 1824015.89 1549692.076 1816107.625 2289824.241 0.533764349 0.703672832 0.647718316 0.63210559 0.742813357 0.796574626 0.676773373 0.79312097 1 21.12680544 -5 0.119434718 2.051987215 0.530403254 0.801011102 0.055568368 66.98774744 0.519842716 16.88794751 0.51851211 1.00E-05 5 -1.521583961 KAMEAVAAQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAMEAVAAQGK 11 1 P18669;P15259 P18669 PGAM1;PGAM2 Phosphoglycerate mutase 1;Phosphoglycerate mutase 2 0 111.79 0.0025856 304730000 1138200 1143000 1030300 1021200 1288200 684280 1277300 1036200 1417900 FALSE TRUE 1066962.094 1227628.909 1054739.203 1047405.721 1187029.968 881820.5276 1085780.723 1165571.851 1181243.33 0.903253434 1.039268437 0.892905954 0.886697681 1.004898769 0.746518948 0.919184638 0.986733065 1 20.17187475 3.807701856 5.695629488 0.908552853 0.978119076 0.05022519 0.081800706 0.428212014 23.0308386 0.019461458 0.03547975 6422.46662 -3.807701856 0.069566223 KANLQIDQINTDLNLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KANLQIDQINTDLNLER 17 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 302.14 2.95E-46 1169550000 1181440 1603150 1392490 1574810 1896890 1013510 1681390 1321950 2539310 FALSE TRUE 1107495.779 1721848.894 1425520.52 1615222.291 1747915.911 1306093.884 1429281.179 1486998.367 2115482.756 0.523519171 0.81392717 0.673851165 0.763524205 0.826249189 0.617397556 0.675628849 0.702912072 1 21.0125555 -1.213456356 3.703256688 1.000356724 0.707202916 0.523206576 0.089855787 22473550.36 40751407.6 94629.01152 0.019884234 0.061170727 1.213456356 -0.293153808 KANNSQEPS(ph)PQLASSVASTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KANNSQEPSPQLASSVASTR 20 1 Q96HC4;Q96HC4-4;Q96HC4-7;H0Y8Y3 Q96HC4 PDLIM5 PDZ and LIM domain protein 5 1 KANNSQEPS(1)PQLASSVASTR;KANNSQEPS(1)PQLASSVASTR 176.71 3.80E-14 405980000 361160 327500 352420 370940 375630 279841 408840 296470 379290 TRUE FALSE 338555.6403 351748.4408 360779.5688 380458.9484 346129.535 360626.5539 347538.2375 333484.9321 315984.0487 1.071432693 1.113184169 1.141765131 1.204044793 1.095401924 1.141280882 1.099860069 1.055385338 1 18.26949221 1.110874029 1.586591856 1.000602453 1.129913716 0.60435378 0.034591906 0.238066514 1.176396766 0.031182598 0.009214408 12.90844798 -1.110874029 0.129311263 KAPAEGVLTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAPAEGVLTLR 11 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 100.22 0.006718 395110000 560330 704780 601140 616290 740680 499050 720450 661040 717000 FALSE TRUE 525259.9455 756962.6445 615399.3247 632105.0448 682509.9806 643117.6336 612425.2108 743572.2991 597328.068 0.879349178 1.267247741 1.030253487 1.058220898 1.142604905 1.076657315 1.025274457 1.24483067 1 19.18816399 -1.548411697 4.186009313 0.998768283 1.095689376 0.059598395 0.111398069 0.001150644 0.000124132 0.096920204 0.02255711 0.028287092 1.548411697 0.096921093 KAPAGPSLEETSVSS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAPAGPSLEETSVSSPK 17 1 K7EIX2;Q6AI08;A0A087WXZ7 K7EIX2 HEATR6 HEAT repeat-containing protein 6 1 KAPAGPSLEETSVS(0.031)S(0.969)PK 108.17 0.000643 0 68346 40345 54661 50213 60165 42011 76366 50923 79744 TRUE FALSE 64068.34586 43332.18578 55957.58473 51501.55059 55439.88359 54138.89371 64915.62725 57280.84865 66434.21123 0.964387846 0.652257097 0.842300732 0.775226342 0.834508043 0.814924911 0.977141537 0.862219143 1 16.01963875 1.82491236 5.306732313 0.940312956 0.796502374 0.342116863 0.084435033 0.217505723 9.376479558 0.036278536 0.020923959 66.82090609 -1.82491236 -0.143810582 KAPAGQEEPGT(ph)PPS(ph)SPLSAEQLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAPAGQEEPGTPPSSPLSAEQLDR 24 1 P13051;Q68DM5;F5GYA2;P13051-2 P13051 UNG;DKFZp781L1143 Uracil-DNA glycosylase 2 KAPAGQEEPGT(0.999)PPS(0.524)S(0.474)PLS(0.003)AEQLDR 79.021 0.016742 357030000 101240 85657 92638 87920 97380 78372 129080 92643 115600 TRUE FALSE 94903.56912 91999.13341 94835.41711 90176.17605 89732.16761 100996.7241 109725.6523 104209.6825 96305.6132 0.98544172 0.95528319 0.984734056 0.936354311 0.9317439 1.04871067 1.139348462 1.082072779 1 16.55533227 2.084084004 4.898979113 1.090469855 0.961297407 0.657245622 0.038652769 0.101379701 4.289389685 0.013825813 0.009954422 121.3623575 -2.084084004 -0.129172448 KAPAGQEEPGT(ph)PPSS(ph)PLSAEQLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAPAGQEEPGTPPSSPLSAEQLDR 24 1 P13051;Q68DM5;F5GYA2;P13051-2 P13051 UNG;DKFZp781L1143 Uracil-DNA glycosylase 2 KAPAGQEEPGT(0.996)PPS(0.361)S(0.636)PLS(0.006)AEQLDR 99.885 0.0039742 386300000 281290 225690 259220 216170 261000 232920 346510 267300 319980 TRUE FALSE 263684.561 242400.3224 265368.8208 221717.2882 240502.1128 300160.2229 294554.0423 300672.9934 266573.2709 0.989163543 0.909319684 0.99548173 0.831731131 0.902198904 1.125995198 1.104964655 1.127918761 1 18.0241726 2.238443102 24.99999988 1.100146096 0.928628186 0.663751831 0.057817977 1.732085669 368328.6636 0.019726454 0.015508503 173.1582158 -2.238443102 -0.17151791 KAPAGQEEPGT(ph)PPSSPLSAEQLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KAPAGQEEPGTPPSSPLSAEQLDR 24 1 P13051;Q68DM5;F5GYA2;P13051-2 P13051 UNG;DKFZp781L1143 Uracil-DNA glycosylase 1 KAPAGQEEPGT(0.985)PPS(0.014)S(0.001)PLSAEQLDR;KAPAGQEEPGT(1)PPSSPLSAEQLDR;KAPAGQEEPGT(0.998)PPS(0.002)SPLSAEQLDR 158.77 1.33E-11 2304200000 2192250 1829120 2180260 1924550 2228660 1880200 2628640 2175680 2776030 TRUE FALSE 2055040.986 1964549.948 2231976.797 1973937.211 2053630.034 2422983.218 2234499.835 2447318.437 2312692.659 0.888592342 0.849464342 0.965098751 0.853523361 0.887982251 1.047689241 0.966189704 1.058211703 1 21.14114212 2.248229958 24.99985259 1.011113631 0.892327061 0.719091447 0.039957154 110.1527196 284797.175 0.013422455 0.011097342 177.1046477 -2.248229958 -0.118786569 KAPAPFRPASER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAPAPFRPASER 12 2 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ; 137.84 4.79E-05 1241280000 561710 723760 622730 681090 816800 480280 738210 667630 761580 FALSE TRUE 526553.5738 777347.9435 637501.4497 698567.9225 752651.8228 618929.0393 627522.2637 750985.0751 634467.378 0.829914338 1.225197655 1.004782077 1.101030481 1.186273477 0.975509633 0.989053631 1.183646474 1 19.27518646 -0.036144753 7.662874083 1.000000003 1.066649027 0.024518835 0.119497295 7089060.731 925117.685 0.104407288 0.025322487 0.920142831 0.036144753 0.066649023 KAPDFVFYAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAPDFVFYAPR 11 1 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 ; 159.99 4.49E-05 2277400000 2351000 4054500 2320400 2154800 4826900 1627230 2417600 3696800 3917400 FALSE TRUE 2203855.107 4354699.399 2375440.984 2210095.816 4447814.745 2096984.885 2055103.324 4158353.618 3263560.633 0.675291608 1.334339971 0.727867888 0.677203847 1.362871797 0.642545098 0.629712009 1.274176915 1 21.63801541 KAPEPEEEIEEVEES(ph)EDEGEDPALDSLSQAIAFQQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAPEPEEEIEEVEESEDEGEDPALDSLSQAIAFQQAK 37 1 G3V1V1;Q8TBF4 G3V1V1 ZCRB1 Zinc finger CCHC-type and RNA-binding motif-containing protein 1 1 KAPEPEEEIEEVEES(0.927)EDEGEDPALDS(0.036)LS(0.036)QAIAFQQAK 46.557 0.034331 22364000 25375 15928 22525 18771 17330 13586 25969 14793 22746 TRUE FALSE 23786.82405 17107.32569 23059.30364 19252.69564 15968.97171 17508.05765 22075.18953 16639.93861 18949.54566 1.255271471 0.902782895 1.216878972 1.015997744 0.842710005 0.923930208 1.164945584 0.878118078 1 14.20987564 4.756377236 24.0109215 1.013213538 1.255271821 0.304436924 0.121185469 3065.133476 4130671.419 0.028504194 0.860263619 57065.97422 -4.756377236 0.242058282 KAPGFGGFGSSAVSGGSTAAMITETIIETDKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAPGFGGFGSSAVSGGSTAAMITETIIETDKPK 33 2 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 252 1.91E-59 176660000 205470 103480 142210 132180 162910 101910 176750 122210 197350 FALSE TRUE 192609.9995 111141.7669 145583.2884 135571.9626 150115.7057 131329.7626 150247.9784 137468.1875 164411.0101 1.171515213 0.675999538 0.885483815 0.82459175 0.913051417 0.798789342 0.913855941 0.836125193 1 17.32694739 -1.519545484 0.55859703 1.076403028 0.858174907 0.066788827 0.126266398 117.7580071 14.93778413 12.85204525 0.047770215 0.030231139 1.519545484 -0.21822812 KAPKPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAPKPER 7 2 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 0 52.786 0.080773 136140000 163530 144370 147670 160130 175340 124230 179240 149930 203700 FALSE TRUE 153294.9492 155059.305 151172.8021 164239.2069 161569.5037 160093.1843 152364.626 168649.0905 169701.154 0.903322962 0.913719803 0.890817761 0.967814319 0.952082528 0.943383003 0.897840836 0.993800493 1 17.37263685 -4.999999984 0.064316124 1.281783212 0.816553916 0.481258492 0.028056236 317.613462 1.483934115 13.52643727 1.992118672 1.00E-05 4.999999984 -0.465229296 KAPKS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAPKSPAK 8 2 P10412 P10412 HIST1H1E Histone H1.4 1 KAPKS(1)PAK;KAPKS(1)PAK 56.783 0.060225 5858100000 8390800 9985700 3548300 3253300 15165100 1600080 4543500 8875200 14842900 TRUE FALSE 7865634.806 10725051.62 3632467.352 3336785.186 13974094.22 2061997.121 3862244.355 9983288.257 12365524.1 0.636093929 0.867334982 0.293757654 0.269845836 1.130085074 0.166753718 0.312339722 0.807348575 1 23.55982005 1.028421003 6.339427186 0.999429781 0.520699804 0.234141781 0.295941652 0.208632749 25.72809598 0.275477247 0.069208467 10.67630575 -1.028421003 -0.478729977 KAPPDGWELIEPTLDELDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAPPDGWELIEPTLDELDQK 20 1 P41223;C9JCD9;P41223-2;F8WCN7 P41223 BUD31 Protein BUD31 homolog 0 128.01 3.29E-05 31895000 122820 95728 108160 107450 114780 85539 139570 90940 121430 FALSE TRUE 115132.9154 102815.8007 110725.6063 110207.3489 105765.6418 110232.7207 118642.7742 102294.0592 101162.5485 1.13809821 1.016342532 1.094531602 1.089408586 1.04550195 1.089659388 1.172793449 1.011185075 1 16.62631576 3.727716387 24.78170379 1.085023976 1.064597597 0 0.057550682 123.1025039 5125911.404 0.014282587 0.023957412 5342.153801 -3.727716387 -0.020426379 KAPPQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAPPQGR 7 1 I3L0N3;P46459;P46459-2;K7EQD6;I3L2G1 I3L0N3 NSF Vesicle-fusing ATPase 0 94.407 0.022806 223780000 84631 91337 90457 87634 91122 74826 98132 82709 82770 FALSE TRUE 79334.09678 98099.68652 92602.68276 89882.8368 83965.64569 96427.0515 83418.01761 93035.40071 68955.15229 1.150517317 1.422659269 1.342940733 1.303497039 1.217684871 1.398402415 1.20974307 1.349216087 1 16.07337073 -3.549753324 0.315008944 1.57E-14 1.326093695 0.519733261 0.088240831 81.29324934 1.717401137 53.12973355 0.074833674 0.000281998 3.549753324 1.326093695 KAPPRPGPVPEAAQPFLFTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAPPRPGPVPEAAQPFLFTPR 21 2 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43;A0A2R8Y4C3;A0A2R8Y454 Q7Z406 MYH14 Myosin-14 0 ; 157.85 9.67E-10 367060000 646780 749580 624220 647820 799390 514320 791990 697400 834740 FALSE TRUE 606299.1943 805079.6831 639026.7932 664444.158 736609.134 662795.8347 673238.452 784471.9252 695416.5014 0.871850457 1.157694247 0.918912324 0.955462168 1.059234477 0.9530919 0.96810825 1.128060556 1 19.40751778 1.260066469 24.99445812 1.064030399 0.993105561 0.129452812 0.084005727 449.5462411 522472.4688 0.05258219 0.019162878 18.19979386 -1.260066469 -0.070924838 KAPSDLYQIILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAPSDLYQIILK 12 1 P07384;E9PL37 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 134.77 0.00022378 508880000 1538210 1671540 1519940 1553120 1933330 1179710 1911350 1688560 2127260 FALSE TRUE 1441936.182 1795302.561 1555993.695 1592975.689 1781494.06 1520273.126 1624760.812 1899380.433 1772206.563 0.81363889 1.013032339 0.87799793 0.898865697 1.00524064 0.857841945 0.916801035 1.071760184 1 20.75711534 1.248999767 24.99573052 1.035880089 0.918419268 0.397845169 0.063009467 177.5011868 425019.3602 0.039012768 0.013912892 17.74188527 -1.248999767 -0.117460821 KAPT(ph)PQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KAPTPQEK 8 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 KAPT(1)PQEK;KAPT(1)PQEK;KAPT(1)PQEK;KAPT(1)PQEK;KAPT(1)PQEK;KAPT(1)PQEK 119.45 0.0032732 3580040000 12006280 5484160 7828260 6987350 6978430 5376730 9853220 6551500 8809510 TRUE FALSE 11254828.37 5890212.913 8013950.024 7166657.231 6430372.257 6928904.667 8375821.134 7369469.197 7339145.869 1.533533815 0.802574716 1.09194587 0.976497451 0.876174472 0.944102323 1.141252849 1.004131724 1 22.80718074 4.750766637 24.7329125 0.985675967 1.533534207 0.765701888 0.096247681 850.3080542 1722932.406 0.023449331 0.40091777 56333.48729 -4.750766637 0.54785824 KAPTTDEDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAPTTDEDKK 10 2 Q99613-2;Q99613;B5ME19 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 96.229 0.003871 186640000 761180 378620 525570 468570 512790 360860 733280 497490 723960 FALSE TRUE 713539.1025 406653.4188 538036.7686 480594.2995 472517.5419 465034.4239 623331.4714 559602.7216 603126.399 1.18306727 0.674242446 0.89207962 0.796838441 0.783446957 0.771039743 1.03350056 0.927836557 1 19.20210086 1.73202769 10.54788302 0.983654071 0.830081313 0.174760415 0.135572973 0.130210384 61.6786472 0.057851022 0.031433763 53.95450216 -1.73202769 -0.153572757 KAQCPIVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KAQCPIVER 9 1 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;;;; 187.5 6.49E-05 7286570000 8151730 8781330 8803000 8628760 9834800 7543210 10812900 8281550 10225700 FALSE TRUE 7641527.771 9431508.81 9011811.317 8850188.59 9062414.48 9720812.273 9191606.027 9315519.747 8518964.609 0.897001939 1.107119144 1.057852888 1.038880779 1.063792948 1.141079077 1.078958119 1.09350375 1 23.02224667 4.744293373 24.85259927 1.07773661 0.897001854 0.672266159 0.038395953 326.8615515 1416962.28 0.008466552 0.076132355 55500.04983 -4.744293373 -0.180734756 KAQLVVIAHDVDPIELVVFLPALCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAQLVVIAHDVDPIELVVFLPALCR 25 1 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 142.42 2.26E-07 172240000 243350 342120 287300 301530 449720 231370 393840 276820 501670 FALSE TRUE 228119.1579 367450.9208 294114.8917 309267.7703 414400.8053 298162.763 334787.3482 311381.5864 417938.0361 0.545820524 0.87919952 0.703728463 0.739984743 0.991536471 0.713413801 0.801045417 0.745042469 1 18.67292954 -5 0.18788336 1.923201253 0.733492873 0.307965417 0.114412306 177.5844497 1.732992603 61.71842485 0.292073248 1.00E-05 5 -1.189708379 KAQPQDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KAQPQDSR 8 1 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ;;; 107.47 0.0064102 437403000 1205030 1370540 1071640 1065970 1411640 802880 1162160 1313430 1388580 FALSE TRUE 1129609.323 1472016.208 1097059.807 1093324.595 1300775.489 1034658.422 987904.897 1477414.627 1156817.027 0.976480547 1.272471076 0.948343412 0.945114542 1.124443588 0.8944011 0.853985439 1.27713769 1 20.14172926 3.822660752 5.630440763 0.987827335 1.139260776 0.096112678 0.140208601 0.344285469 16.32836869 0.033788547 0.061777363 6647.536833 -3.822660752 0.151433441 KAQVS(ph)PQS ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KAQVSPQS 8 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KAQVS(0.942)PQS(0.058);KAQVS(0.982)PQS(0.018);KAQVS(0.985)PQS(0.015) 78.116 0.033324 13065400000 15442200 13076400 14066400 13104300 14323100 11065500 15624100 11781400 14262200 TRUE FALSE 14475700.27 14044590.26 14400061.65 13440578.52 13198221.5 14259930.22 13281411.25 13252333.72 11881746.68 1.218314163 1.182030777 1.211948212 1.131195512 1.110798088 1.200154371 1.117799563 1.11535232 1 23.5022436 -4.99999996 0.100667569 0.441438471 1.282009563 0.784700015 0.030245752 79.40614171 0.54347245 9.178399365 0.477064656 1.00E-05 4.99999996 0.840571091 KAQVSPQS(ph) ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAQVSPQS 8 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KAQVS(0.237)PQS(0.763) 62.466 0.08417 3866200000 5030900 4197400 4382000 4357600 4513800 3538800 4938700 3779900 4464700 TRUE FALSE 4716024.949 4508179.863 4485943.109 4469423.393 4159304.356 4560394.112 4198187.784 4251828.836 3719512.727 1.267914723 1.212035069 1.206056664 1.201615298 1.118239044 1.226072996 1.128692948 1.143114474 1 21.8266822 -5 0.096512983 0.36506338 1.332609879 0.818922287 0.031947911 71.67011306 0.474545143 9.131132324 0.533784624 1.00E-05 5 0.967546499 KAS(ph)FLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KASFLR 6 1 P46777;A0A2R8Y4A2 P46777 RPL5 60S ribosomal protein L5 1 KAS(1)FLR 81.548 0.037724 88342000 274770 252960 254180 222180 322210 163220 293910 219480 434340 TRUE FALSE 257572.6362 271689.4216 260209.2696 227881.5149 296904.9263 210338.9643 249840.924 246882.5611 361845.8481 0.711829741 0.750842999 0.719116361 0.629775127 0.820528764 0.581294398 0.690462321 0.682286566 1 18.46501569 -1.523854698 6.90998052 1.000153566 0.700463561 0.685797907 0.06416942 0.000139377 9.60E-06 0.057043301 0.013438426 0.029932659 1.523854698 -0.299690005 KAS(ph)GS(ph)ENEGDYNPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KASGSENEGDYNPGR 15 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 KAS(1)GS(1)ENEGDYNPGR 159.26 6.21E-06 469280000 923140 642330 690100 822300 810760 454470 741310 475750 628350 TRUE FALSE 865362.3153 689888.7815 706469.4979 843401.6102 747086.18 585668.1113 630157.4475 535148.4348 523474.3257 1.653113195 1.317903759 1.349578123 1.611161367 1.427168714 1.11880962 1.203798193 1.022301207 1 18.99775925 2.242578313 6.4108297 1.113276513 1.441423195 0.718345465 0.118625887 0.093089604 16.23394734 0.043218786 0.034032611 174.8148465 -2.242578313 0.328146682 KAS(ph)GS(ph)ENEGDYNPGRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KASGSENEGDYNPGRK 16 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 KAS(1)GS(1)ENEGDYNPGRK;KAS(1)GS(1)ENEGDYNPGRK 81.884 0.0061865 294420000 298870 190411 207210 255950 241790 119216 242340 138927 254960 TRUE FALSE 280164.2602 204509.2286 212125.1191 262518.1103 222800.7887 153631.7239 206003.3668 156272.3418 212405.5289 1.319006439 0.962824412 0.998679837 1.235928799 1.048940627 0.723294373 0.969858778 0.735726337 1 17.69646179 2.380361826 7.707741797 0.86312967 1.085747461 0.463085816 0.1356661 0.237227522 16.58932996 0.044776885 0.037385525 240.0832303 -2.380361826 0.222617791 KAS(ph)GSENEGDYNPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KASGSENEGDYNPGR 15 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KAS(0.812)GS(0.188)ENEGDYNPGR 60.134 0.039128 0 122500 171230 149040 143130 196830 130800 158250 143980 137450 TRUE FALSE 114832.9437 183908.0474 152575.2992 146802.9581 181371.7658 168559.8366 134521.8816 161956.2199 114508.707 1.002831546 1.606061688 1.33243404 1.282024415 1.583912442 1.472026372 1.17477426 1.41435725 1 16.80509778 -1.091671356 3.592607603 0.99980961 1.373101813 0.275151436 0.181531251 24469088.91 40309111.89 58314.57662 0.040888314 0.08097084 1.091671356 0.373292204 KAS(ph)GSENEGDYNPGRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KASGSENEGDYNPGRK 16 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KAS(0.977)GS(0.023)ENEGDYNPGRK;KAS(0.707)GS(0.293)ENEGDYNPGRK 179.41 1.37E-09 205790000 380920 295260 298310 348740 390970 193002 398900 265510 592290 TRUE FALSE 357078.8972 317121.3576 305386.0541 357689.2588 360264.7933 248718.5443 339088.6482 298659.508 493432.9727 0.723662416 0.642683759 0.618900785 0.724899386 0.73011901 0.504057406 0.687203059 0.605268647 1 18.9124946 -1.855708136 3.698968231 1.10221165 0.650673589 0.710715006 0.069213099 0.039158464 0.00152752 0.044980981 0.014407329 0.013940934 1.855708136 -0.451538062 KAS(ph)LTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KASLTSK 7 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 KAS(0.979)LT(0.001)S(0.02)K;KAS(0.949)LT(0.007)S(0.044)K 110.53 0.0041541 1815340000 4133300 2244300 3060600 2543600 2872800 2230900 3854100 2804600 5642400 TRUE FALSE 3874604.131 2410470.307 3133198.877 2608873.082 2647181.876 2874924.614 3276213.485 3154760.484 4700646.989 0.824270391 0.512795433 0.666546304 0.555002979 0.563152664 0.611601897 0.696970756 0.671133249 1 22.16442791 0.392747959 0.854725508 1.002724937 0.612001325 0.636299165 0.086612937 1.233969958 1.237562614 0.082096145 0.025351316 2.470290107 -0.392747959 -0.390723613 KAS(ph)PEAASTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(1)PEAASTPR 121.79 0.00024766 169330000 128070 87019 100460 94960 89676 81439 115660 102580 96393 TRUE FALSE 120054.3273 93461.9773 102842.9586 97396.83437 82633.2087 104949.1172 98317.85673 115387.3388 80304.38558 1.49499092 1.16384649 1.280664286 1.21284577 1.028999949 1.306891479 1.224314912 1.436874686 1 16.29319116 4.745555292 24.33196327 1.217528492 1.49499111 0.333197303 0.12732113 648.5409819 2255956.181 0.027092569 0.265833497 55661.54953 -4.745555292 0.277462618 KAS(ph)PEPEGEAAGK ddPTM_SK-BR-3_Pertuzumab_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 229.22 3.75E-12 6314440000 10748650 5462840 7342530 6876330 7228250 5174610 9379000 6086260 9335550 TRUE FALSE 10075911.18 5867314.358 7516698.279 7052788.269 6660572.402 6668435.904 7972706.02 6846142.959 7777386.395 1.295539487 0.754406951 0.96648127 0.906832696 0.856402404 0.857413476 1.025113787 0.880262676 1 22.89085399 -0.953992519 7.208468531 1.000000001 0.927837852 0.005865348 0.144916037 4.60E-09 6.38E-10 0.123503187 0.02910998 0.111175088 0.953992519 -0.072162149 KAS(ph)PEPPDSAEGALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KASPEPPDSAEGALK 15 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK 209.01 1.59E-09 11804450000 9817720 5447330 7105850 6537880 7292190 4926860 8588380 6056980 10064450 TRUE FALSE 9203246.43 5850655.981 7274404.118 6705653.069 6719490.813 6349164.501 7300632.15 6813207.286 8384628.276 1.097633208 0.697783585 0.867588148 0.799755558 0.801405929 0.757238639 0.870716257 0.812583106 1 22.99931539 -1.443465992 8.688305549 1.000002547 0.825667738 0.180462688 0.105525188 4.52E-06 2.90E-07 0.088721105 0.02091146 0.036019195 1.443465992 -0.174334809 KAS(ph)SPNLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KASSPNLHR 9 1 A0A087X030;P51956-2;P51956 A0A087X030 NEK3 Serine/threonine-protein kinase Nek3 1 KAS(0.5)S(0.5)PNLHR 78.096 0.014454 90814000 132520 214120 212620 208690 252210 251360 194660 206020 185470 TRUE FALSE 124225.8098 229973.6676 217663.4468 214045.3387 232402.444 323923.5515 165472.5401 231742.0505 154513.8588 0.803978431 1.488369195 1.408698537 1.385282462 1.50408802 2.096404517 1.070923614 1.499814012 1 17.23737672 0.121547588 1.279255532 0.999425617 1.425126248 0.126798149 0.330288049 17.90126027 23.82156043 0.32186089 0.086279021 1.322962663 -0.121547588 0.425700631 KAS(ph)SPSPLTIGTPESQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KASSPSPLTIGTPESQR 17 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 KAS(0.486)S(0.486)PS(0.028)PLTIGTPESQR 84.946 0.0031592 271880000 293330 136110 149140 164460 199920 125530 181420 171680 251500 TRUE FALSE 274970.9989 146187.726 152677.6712 168680.322 184219.0896 161768.4732 154217.7552 193114.6259 209523.0252 1.312366498 0.697716759 0.728691613 0.805068187 0.879230764 0.772079694 0.736042041 0.921686892 1 17.67674927 1.023944013 6.169236465 0.999793876 0.813487395 0.050760375 0.176894712 0.293898483 36.53820908 0.15492353 0.038942958 10.56681279 -1.023944013 -0.186306481 KAS(ph)VHSSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KASVHSSGR 9 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 1 KAS(0.378)VHS(0.311)S(0.311)GR;KAS(0.766)VHS(0.22)S(0.014)GR;KAS(0.898)VHS(0.062)S(0.04)GR;KAS(0.659)VHS(0.197)S(0.144)GR 122.52 0.0003574 1209770000 356421 801020 599080 675000 980500 324303 860510 563690 1150950 TRUE FALSE 334113.2458 860328.3543 613290.4605 692321.6428 903495.4851 417924.0115 731484.5141 634067.9373 958849.0096 0.348452408 0.897251127 0.63961109 0.722034059 0.942270864 0.435860086 0.762877686 0.661280276 1 19.87094413 -1.3599286 3.341059526 1.002169397 0.696244131 0.231191094 0.182338764 54446546.72 80551293.2 1186047.893 0.03983936 0.04365876 1.3599286 -0.305925266 KASDSELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 84.507 0.024765 1551350000 3400420 4188850 3539540 3845950 4698530 2804910 4503480 3986970 4763080 FALSE TRUE 3187593.782 4498996.812 3623499.56 3944643.588 4329526.407 3614641.983 3828224.982 4484751.981 3968091.177 0.803306587 1.133793709 0.91315935 0.994090965 1.091085414 0.910927149 0.964752273 1.130203864 1 21.92001375 4.76393974 24.35211423 1.008369156 0.803306218 0.407860732 0.080383244 6072.070534 5826217.753 0.018132171 1.285277935 58068.38397 -4.76393974 -0.205062938 KASDVHEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 KASDVHEVR 9 1 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;; 134.68 0.00015723 41449060000 77485700 83808700 83535000 82283800 89946500 68675700 96133800 76917600 85547600 FALSE TRUE 72636008.35 90013983.35 85516489.65 84395341.61 82882464.72 88501259.73 81719429.15 86520931.68 71269152.9 1.019178781 1.263014638 1.199908883 1.184177701 1.162950047 1.241789135 1.146631128 1.214002526 1 26.08677444 -1.582381921 2.661751758 0.985483613 1.187781067 0.409440095 0.066800885 10068648.88 9402826.684 1027403.968 0.015200741 0.026158816 1.582381921 0.202297454 KASFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KASFLR 6 1 P46777;A0A2R8Y4A2 P46777 RPL5 60S ribosomal protein L5 0 ; 114.19 0.040888 1692030000 2083690 3083400 1935060 1970430 3310800 1347210 2399100 2954900 3385800 FALSE TRUE 1953275.562 3311698.144 1980960.537 2020994.57 3050783.123 1736127.657 2039377.227 3323825.77 2820688.107 0.692481936 1.174074559 0.702296908 0.716489911 1.081574073 0.615497918 0.723006993 1.178374086 1 21.42761572 1.236209532 24.99997065 1.089187088 0.829725079 0.275730838 0.183512366 88.8332179 944493.4176 0.147326473 0.043562295 17.22699519 -1.236209532 -0.259462009 KASGPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KASGPPK 7 1 P52943;H0YFA4;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 74.127 0.075399 1416500000 565260 451340 471790 452420 446260 413890 492080 408080 557950 FALSE TRUE 529881.3856 484757.6832 482981.0816 464029.8631 411212.5397 533373.3241 418297.1722 459029.6863 464824.5405 1.139960005 1.042883155 1.039061064 0.998290371 0.884661854 1.147472385 0.899903374 0.987533244 1 18.82632671 8 0.459209976 0.97946519 4.734311106 0.300905987 0.071607259 105.868347 1.245791525 0.037732307 374.8918706 100000000 -8 3.754845915 KASGPPVSELITK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KASGPPVSELITK 13 1 P10412;P16402;P16403 P10412;P16402;P16403 HIST1H1E;HIST1H1D;HIST1H1C Histone H1.4;Histone H1.3;Histone H1.2 0 130.06 0.00023489 172500000 1092900 969850 970350 988010 1203300 766550 1302900 884620 1411000 FALSE TRUE 1024497.34 1041658.703 993367.1602 1013364.009 1108797.672 987840.5411 1107542.241 995066.7543 1175494.985 0.871545479 0.886144745 0.845062866 0.862074294 0.943260232 0.840361341 0.94219223 0.84650872 1 20.16483695 -5 0.215490091 1.591878668 0.864766675 0.498495036 0.03739014 115.2139625 1.151707933 29.50771017 0.066947452 1.00E-05 5 -0.727111993 KASGS(ph)ENEGDYNPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KASGSENEGDYNPGR 15 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KAS(0.033)GS(0.967)ENEGDYNPGR;KAS(0.1)GS(0.9)ENEGDYNPGR 211.13 9.40E-10 944730000 534810 447420 423640 471150 523880 346430 508230 370150 507820 TRUE FALSE 501337.1968 480547.4423 433688.9409 483240.5067 482736.578 446438.7172 432025.6297 416364.0423 423061.5614 1.185021856 1.135880652 1.025120173 1.142246308 1.141055161 1.055257102 1.021188567 0.984168926 1 18.69050809 1.868310161 2.172500824 0.997104081 1.113892838 0.639874573 0.042112227 0.228597799 2.005895489 0.027063999 0.012877618 73.8431409 -1.868310161 0.116788757 KASS(ph)PNLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KASSPNLHR 9 1 A0A087X030;P51956-2;P51956 A0A087X030 NEK3 Serine/threonine-protein kinase Nek3 1 KAS(0.111)S(0.889)PNLHR;KAS(0.117)S(0.883)PNLHR 151.1 3.93E-05 223680000 571220 566810 579750 582980 644040 490140 714730 572130 661150 TRUE FALSE 535468.3599 608777.2022 593501.9438 597940.2538 593459.6963 631635.4612 607562.8717 643561.6899 550799.7938 0.972165142 1.105260403 1.077527534 1.085585471 1.077450832 1.146760526 1.103055736 1.168413092 1 19.07116849 4.740205946 24.78335777 1.099296491 0.972165094 0.42583068 0.044818827 110.8137604 1669010.509 0.009433148 0.059847514 54980.15322 -4.740205946 -0.127131397 KASSPS(ph)PLTIGTPESQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KASSPSPLTIGTPESQR 17 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 KAS(0.004)S(0.011)PS(0.985)PLTIGTPESQR;KAS(0.01)S(0.004)PS(0.985)PLTIGTPESQR 150.64 1.71E-07 954890000 389140 380950 397350 419050 443960 298270 500360 380960 501250 TRUE FALSE 364784.422 409155.9344 406775.3296 429803.5324 409093.1724 384375.707 425335.6631 428523.6946 417588.1368 0.873550731 0.979807371 0.974106527 1.029252257 0.979657075 0.92046606 1.018553033 1.026187424 1 18.6717212 4.763523309 3.266175413 0.989235352 0.85371484 0.577189762 0.031646672 0.287571613 4.701274423 0.00751426 0.101514687 58012.73078 -4.763523309 -0.135520512 KASTAPGAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KASTAPGAEER 11 1 F5GYV5;F8WCT1;Q66PJ3-2;A0A0C4DH18;Q66PJ3-5 F5GYV5 ARL6IP4 ADP-ribosylation factor-like protein 6-interacting protein 4 0 70.412 0.083118 89815000 86740 70899 71684 70960 85712 62232 94550 73953 82298 FALSE TRUE 81311.09824 76148.43573 73384.37833 72780.95373 78980.52527 80197.36815 80373.10526 83186.19484 68561.93213 1.185951091 1.110651835 1.070337081 1.06153592 1.151958861 1.169706945 1.172270132 1.213300038 1 16.06512015 2.610809301 8.282620203 1.156394033 1.101644553 0.035583141 0.064899163 0.549337477 34.40350473 0.019141781 0.018027151 408.1401325 -2.610809301 -0.05474948 KASVHS(ph)SGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KASVHSSGR 9 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 1 KAS(0.323)VHS(0.644)S(0.034)GR 116.24 0.00082458 541610000 81120 184250 151830 145220 200810 69615 202210 123560 276000 TRUE FALSE 76042.844 197892.0617 155431.4793 148946.5911 185039.1926 89711.72039 171890.4877 138986.738 229933.817 0.330716225 0.860647922 0.675983556 0.647780274 0.804749797 0.390163229 0.74756506 0.604464101 1 17.81085914 -1.587805183 2.639663604 1.027873044 0.658410899 0.311837499 0.167642488 18707803.01 17508026.01 3634438.084 0.037055138 0.025834188 1.587805183 -0.369462145 KASVHSS(ph)GR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KASVHSSGR 9 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 1 KAS(0.303)VHS(0.208)S(0.488)GR 112.02 0.0012433 236390000 92467 208520 160860 183110 271860 79499 221150 154170 311870 TRUE FALSE 86679.65553 223959.0378 164675.6752 187808.9126 250509.2122 102449.0707 187990.6106 173418.4639 259816.8822 0.333618258 0.861988012 0.633814376 0.722851075 0.964176038 0.394312601 0.723550406 0.667464186 1 17.98713565 -1.8989572 2.37042525 1.184334535 0.680002885 0.234940443 0.189002401 21047294.78 10498210.3 21626823.5 0.041742041 0.012619519 1.8989572 -0.50433165 KASVVDPSTESSPAPQEGSEQPASPAS(ph)PLSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KASVVDPSTESSPAPQEGSEQPASPASPLSSR 32 1 Q66K14-2;Q66K14 Q66K14-2 TBC1D9B TBC1 domain family member 9B 1 KASVVDPSTESSPAPQEGSEQPASPAS(0.98)PLS(0.01)S(0.01)R 185.31 7.20E-20 396260000 197860 233830 215130 257850 248170 171160 282240 195800 200190 TRUE FALSE 185476.2958 251143.0165 220232.9852 264466.8675 228679.7293 220571.1134 239920.7322 220246.061 166776.9957 1.112121579 1.505861257 1.320523758 1.585751478 1.371170696 1.322551186 1.438572095 1.320602161 1 17.34756078 0.870133417 5.017027222 1.000009143 1.391736735 0.469411147 0.125325506 0.970708898 36.75623026 0.105727534 0.026723364 7.4153801 -0.870133417 0.391727593 KAT(ph)KSPAKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KATKSPAKPK 10 3 P16401 P16401 HIST1H1B Histone H1.5 1 KAT(0.62)KS(0.38)PAKPK 89.629 0.011707 595800000 2443300 1071000 1625100 1560400 2152500 859500 2207500 843710 3292900 TRUE FALSE 2290378.214 1150297.954 1663648.139 1600442.506 1983451.333 1107623.697 1876505.868 949049.0507 2743293.717 0.834900835 0.419312722 0.606441858 0.583401805 0.723018217 0.403756875 0.684033888 0.345952402 1 21.38747767 -1.173593544 4.445058231 1.000066688 0.5694961 0.434325984 0.152272526 19137780.23 5052803.822 17008.06407 0.030633235 0.067051185 1.173593544 -0.430570588 KATDAEADVASLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KATDAEADVASLNR 14 1 P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;H0YKX5;H0YKP3 P09493-3 TPM1 Tropomyosin alpha-1 chain 0 ;; 210.08 9.21E-09 772970000 921480 1043150 997340 1023910 1299460 768770 1164480 906920 1291200 FALSE TRUE 863806.2117 1120385.911 1020997.376 1050185.264 1197405.653 990701.4191 989877.0345 1020150.958 1075690.379 0.803024949 1.041550556 0.949155441 0.976289539 1.113150845 0.920991243 0.920224866 0.948368581 1 20.03683145 -0.233653773 6.87522248 1 0.965607652 0.019180961 0.080761403 9769268.89 1420938.072 0.072232447 0.017518942 0.583910422 0.233653773 -0.034392348 KATDAEADVASLNRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KATDAEADVASLNRR 15 2 P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;H0YKX5;H0YKP3 P09493-3 TPM1 Tropomyosin alpha-1 chain 0 70.281 0.026522 37369000 35560 47975 48810 53762 66221 39683 67389 47947 92200 FALSE TRUE 33334.36308 51527.11892 49967.79625 55141.62394 61020.26978 51138.8379 57284.64506 53933.28849 76811.22437 0.43397776 0.670827986 0.650527272 0.717884976 0.794418658 0.665772982 0.745784819 0.70215374 1 16.22902953 -4.999999942 0.047210572 2.288864074 5.25E-09 0.728548853 0.072825127 333.0342987 1.166504397 56.32889479 13.69540442 1.00E-05 4.999999942 -2.288864069 KATGAAT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KATGAATPK 9 1 P10412 P10412 HIST1H1E Histone H1.4 1 KAT(0.002)GAAT(0.998)PK;KAT(0.001)GAAT(0.999)PK;KATGAAT(1)PK;KAT(0.001)GAAT(0.999)PK;KATGAAT(1)PK 98.974 0.0033116 2416859000 7876260 4344870 5492390 4604700 5721420 2379112 7200690 3840793 7429000 TRUE FALSE 7383298.946 4666568.696 5622672.084 4722864.398 5272082.752 3065923.013 6121013.382 4320324.461 6189051.907 1.192961225 0.754003806 0.90848682 0.76309982 0.851840125 0.495378462 0.989006632 0.698059174 1 22.56128699 4.74347167 24.52721009 0.807165197 1.192961434 0.402101205 0.147722143 374.927421 1872412.821 0.030871686 0.254542158 55395.14075 -4.74347167 0.385796238 KATLELTHNWGTEDDETQSYHNGNSDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KATLELTHNWGTEDDETQSYHNGNSDPR 28 1 Q04760 Q04760 GLO1 Lactoylglutathione lyase 0 ; 212.38 2.36E-26 744180000 213180 421780 353330 352090 398810 320480 449010 352960 904390 FALSE TRUE 199837.4443 453009.0301 361711.1545 361125.2255 367489.0713 412997.3734 381685.1189 397027.833 753441.4664 0.265232872 0.601253117 0.48007864 0.47930097 0.48774734 0.548147921 0.506588947 0.526952458 1 19.52313591 -5 0.307223898 5.377129174 0.474254161 0.793008194 0.083350489 121.2776577 1.105669625 342.949821 0.072558764 1.00E-05 5 -4.902875013 KATQAS(ph)QEY ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KATQASQEY 9 1 P16104 P16104 H2AFX Histone H2AX 1 KAT(0.007)QAS(0.993)QEY;KATQAS(1)QEY;KAT(0.002)QAS(0.998)QEY;KATQAS(0.999)QEY 112.45 0.0020764 1613000000 3419100 3133270 3138260 2974470 3628280 2345480 3856830 3036420 4407500 TRUE FALSE 3205104.634 3365260.571 3212701.009 3050799.936 3343329.525 3022582 3278534.147 3415523.721 3671859.776 0.872883179 0.916500296 0.874951987 0.830859598 0.91052756 0.823174681 0.892881086 0.93018904 1 21.80807953 0.987052253 2.288911548 0.999208006 0.876026259 0.661595634 0.029493244 0.184085421 2.134124328 0.026742911 0.007325518 9.706267427 -0.987052253 -0.123181747 KAVAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAVAVR 6 1 P62277;J3KMX5 P62277 RPS13 40S ribosomal protein S13 0 ; 110.54 0.04589 2312700000 5169300 5655000 5424700 5479600 5873000 4628500 6113500 5602500 6203000 FALSE TRUE 4845762.74 6073702.084 5553376.446 5620215.813 5411758.271 5964672.813 5196837.43 6301984.458 5167679.227 0.937705792 1.175324903 1.074636447 1.087570564 1.047231849 1.154226598 1.005642417 1.21949993 1 22.30108509 KAVIFCLSADKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAVIFCLSADKK 12 2 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ; 147.18 3.68E-05 1246570000 1980890 1462530 1581000 1448990 2127830 1352900 2183100 1785600 2955010 FALSE TRUE 1856909.631 1570817.243 1618502.067 1486173.537 1960718.815 1743460.268 1855764.422 2008536.091 2461799.741 0.754289474 0.638076776 0.65744668 0.60369392 0.796457479 0.708205561 0.753824282 0.815881185 1 21.23128198 0.787870304 0.553715652 1.008911387 0.66236604 0.777193791 0.05294301 0.497478326 0.336012405 0.058054285 0.023697021 6.135787413 -0.787870304 -0.346545348 KAVLFCLSEDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAVLFCLSEDKK 12 2 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 201.95 8.01E-08 4210800000 7405800 4366600 5501400 5282800 6707800 4467600 8975100 5452900 10078500 FALSE TRUE 6942284.198 4689907.607 5631895.806 5418365.592 6180996.446 5757323.595 7629367.076 6133706.568 8396333.24 0.826823329 0.558566159 0.670756584 0.64532522 0.736154256 0.685694985 0.90865463 0.73052205 1 23.001328 1.323601247 0.559616987 0.989066129 0.644943346 0.519426934 0.090133791 0.513832363 0.404292371 0.083767981 0.043099075 21.06692977 -1.323601247 -0.344122783 KAVS(ph)PLLLTTTNSSEGLSMGNYIGLINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAVSPLLLTTTNSSEGLSMGNYIGLINR 28 1 P19525-2;P19525;C9JZT2 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 1 KAVS(1)PLLLTTTNSSEGLSMGNYIGLINR 210.21 7.86E-26 60604000 92872 95697 93513 95486 114300 76680 115170 91990 143090 TRUE FALSE 87059.3073 102782.5055 95731.17252 97936.33242 105323.3391 98816.2712 97901.32769 103475.154 119207.3546 0.730318256 0.862216143 0.803064315 0.821562837 0.883530546 0.828944418 0.821269191 0.868026594 1 16.86311372 -5 0.201287339 1.787476845 0.801066974 0.699752965 0.03769636 79.19510281 0.784897815 25.0562306 0.082873988 1.00E-05 5 -0.986409871 KAVS(ph)PSSSEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAVSPSSSEKR 11 2 Q76FK4-2;Q76FK4-4;Q76FK4;F8WE42;F5H101 Q76FK4-2 NOL8 Nucleolar protein 8 1 KAVS(0.419)PS(0.419)S(0.064)S(0.099)EKR 84.753 0.0082058 91108000 122930 81445 94757 96658 87945 60346 126550 68121 116040 TRUE FALSE 115236.0307 87475.27254 97004.68079 99138.40792 81038.15445 77766.91056 107575.0023 76626.0568 96672.17435 1.192028953 0.904865057 1.003439526 1.025511308 0.838277974 0.804439448 1.11278145 0.792638185 1 16.56081307 4.744313283 24.4992528 0.944656163 1.192029096 0.373822163 0.103811764 523.8944461 2231055.381 0.023027588 0.20254422 55502.59419 -4.744313283 0.247372932 KAVVLPGGTATS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KAVVLPGGTATSPK 14 1 Q8N1G0;F8WCX2;Q8N1G0-2;H0Y5I5 Q8N1G0 ZNF687 Zinc finger protein 687 1 KAVVLPGGTAT(0.019)S(0.981)PK;KAVVLPGGTAT(0.08)S(0.92)PK 161.1 2.85E-06 1485720000 4242300 2201160 2926700 2754200 3251300 2163640 4125100 2735900 4294300 TRUE FALSE 3976782.016 2364136.177 2996122.706 2824877.435 2995956.013 2788247.744 3506579.551 3077483.137 3577553.588 1.111592578 0.660824812 0.837478079 0.789611494 0.837431485 0.779372741 0.980161293 0.860219997 1 21.77054195 1.741692941 11.52158465 0.938902299 0.814270505 0.145138497 0.118552137 0.128811914 109.2484546 0.050555939 0.02763359 55.16872423 -1.741692941 -0.124631793 KAVVVCPKDEDYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAVVVCPKDEDYK 13 2 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 116.96 0.00030598 129530000 212270 177880 168830 195340 277500 113700 172300 151240 411120 FALSE TRUE 198984.3996 191050.4203 172834.7273 200352.7551 255706.2694 146523.3442 146465.2146 170122.6469 342501.4161 0.580973947 0.55780914 0.504624855 0.584969129 0.746584561 0.427803616 0.427633895 0.496706405 1 18.38575043 -1.047961674 5.019841411 1.000005483 0.533637847 0.712455067 0.091560283 8.19E-06 1.55E-06 0.091327633 0.021525772 0.089544378 1.047961674 -0.466367636 KAYS(ph)FCGTVEYMAPEVVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 244.67 9.64E-25 1422890000 937850 1105650 911460 983100 1262140 663140 1338270 890010 1668230 TRUE FALSE 879151.6426 1187513.476 933080.2616 1008328.01 1163016.616 854577.7528 1137608.837 1001129.708 1389791.636 0.632578021 0.854454327 0.671381405 0.725524593 0.836828044 0.614896313 0.818546326 0.720345181 1 20.40643717 -1.926516533 0.570742388 1.235862677 0.740206764 0.50393559 0.082546907 81.38213126 7.789087539 25.55523835 0.030286794 0.011843593 1.926516533 -0.495655913 KAYWQVHLDQVEVASGLTLCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KAYWQVHLDQVEVASGLTLCK 21 1 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GU92;A0A1B0GU03;C9JH19;H7C469 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 116.21 8.78E-05 93488000 126330 137790 118160 119700 180910 88449 155850 134170 233760 FALSE TRUE 118423.2308 147992.115 120962.811 122771.7047 166702.0584 113982.7905 132481.7393 150921.4198 194743.9459 0.608097111 0.759931788 0.621137723 0.630426297 0.856006371 0.585295681 0.680286818 0.774973616 1 17.57121895 0.878027571 2.824230234 0.999696039 0.680031663 0.620064699 0.079948856 0.298409732 4.834001785 0.06941603 0.018333028 7.551401665 -0.878027571 -0.319664376 KCEAEEAEPPAATQPQTSETQTSHLPESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KCEAEEAEPPAATQPQTSETQTSHLPESER 30 1 S4R3H4;Q9UKV3;E7EQT4;A0A087WYN3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ; 171.15 9.79E-13 587700000 378999 329496 341395 334181 381427 267942 421285 309672 433240 FALSE TRUE 355278.1291 353892.2267 349493.0506 342756.6502 351471.262 345292.5057 358117.2253 348335.2309 360929.4452 0.984342325 0.980502509 0.968314044 0.949650007 0.973794925 0.956675911 0.992208394 0.96510616 1 18.46135732 0.126786748 0.747704039 1.000593998 0.971099196 0.324736919 0.012727353 4.625886529 2.980490259 0.020786515 0.004296695 1.339019027 -0.126786748 -0.029494802 KCEPIVMTVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KCEPIVMTVPR 11 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ; 155.02 5.09E-05 1090440000 1823090 1975780 1759860 1779820 2065900 1467390 2069200 1769340 2038800 FALSE TRUE 1708986.051 2122068.807 1801604.71 1825493.194 1903652.547 1891001.672 1758942.67 1990245.994 1698511.109 1.006167132 1.24936999 1.060696454 1.074760821 1.120777213 1.113328999 1.035579138 1.171759186 1 20.69583922 -4.999999996 0.153332769 0.614507814 1.140282956 0.128278586 0.071444771 223.0773785 2.010935473 26.2601935 0.316528105 1.00E-05 4.999999996 0.525775142 KCGHTNNLRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KCGHTNNLRPK 11 2 M0R2S1;P62987 M0R2S1 UBA52 Ubiquitin-60S ribosomal protein L40;Ubiquitin;60S ribosomal protein L40 0 180.97 3.86E-06 273340000 511830 443860 456420 457430 551260 325100 562010 431760 614980 FALSE TRUE 479795.4739 476723.8562 467246.4979 469168.4282 507966.2633 418951.0924 477741.8179 485666.1864 512335.8651 0.936486213 0.930490892 0.911992561 0.915743871 0.991471216 0.817727434 0.932477795 0.947944931 1 18.96673036 0.948457615 2.724786079 0.999475801 0.917933322 0.270396443 0.042383532 0.382605249 6.656302939 0.036686033 0.009764602 8.880912992 -0.948457615 -0.081542479 KCGVCQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KCGVCQK 7 1 P21291;E9PS42;E9PP21 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 102.71 0.033418 0 209680 241230 186120 170660 281220 211500 250430 249460 289260 FALSE TRUE 196556.5031 259090.9202 190534.8543 175039.4245 259134.1156 272556.6166 212880.3464 280605.6301 240980.6373 0.815652682 1.07515244 0.79066458 0.726363024 1.075331688 1.131031188 0.883391914 1.164432268 1 17.87855771 2.70677799 24.97359921 1.037088223 0.878941579 0.401868813 0.117888693 835.8159462 656752.0579 0.038373146 0.036181394 509.0705692 -2.70677799 -0.158146644 KCLEELQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KCLEELQK 8 1 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 ; 130.66 0.0016652 601400000 1258370 1264600 1080730 1047320 1587650 711250 1324840 1459270 1352710 FALSE TRUE 1179610.868 1358232.3 1106365.426 1074196.004 1462962.373 916576.3288 1126192.541 1641463.072 1126933.962 1.04674356 1.205245689 0.981748233 0.953202264 1.298179328 0.813336326 0.99934209 1.456574322 1 20.10397155 -0.13405718 0.003490773 2.10E-05 2.123255572 0 0.187835034 463773.759 459.9551108 141773.5185 137989.1601 0.734417167 0.13405718 2.123234589 KCLELFSELAEDKENYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KCLELFSELAEDKENYK 17 2 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 283.76 2.21E-36 2791000000 536170 245390 369530 318030 282770 286160 472830 301390 277060 FALSE TRUE 502612.0768 263558.9309 378295.4261 326191.1882 260562.3848 368769.7466 401933.531 339019.2049 230816.8961 2.177535896 1.141852851 1.638941657 1.413203252 1.1288705 1.597672236 1.741352292 1.468779845 1 17.81638931 4.753648819 24.39065897 1.437779753 2.177536645 0.498956708 0.243675983 1795.221666 2901976.208 0.056513168 1.288055882 56708.586 -4.753648819 0.739756892 KCLELFTELAEDKENYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KCLELFTELAEDKENYK 17 2 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 237.21 1.85E-20 3940700000 1156480 547170 751480 733110 643370 614510 1121610 635450 669460 FALSE TRUE 1084097.981 587683.0361 769305.4605 751922.8438 592842.3154 791909.0613 953434.993 714787.3313 557722.8011 1.943793546 1.053718863 1.379368853 1.348201727 1.062969479 1.419897232 1.709514101 1.281617552 1 19.08918873 2.023293892 24.97704482 1.448085692 1.312270384 0 0.303763768 792.9526245 850245.7125 0.104173591 0.076932908 105.5100654 -2.023293892 -0.135815307 KCLELFTELAEDKENYKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KCLELFTELAEDKENYKK 18 3 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 240.07 2.68E-24 1088400000 2140500 1148900 1443700 1459400 1679100 999120 2011400 1188700 2196000 FALSE TRUE 2006529.926 1233965.751 1477945.246 1496850.675 1547230.259 1287549.725 1709809.243 1337111.812 1829473.413 1.096780041 0.674492312 0.807852814 0.818186623 0.845724375 0.703781599 0.934590921 0.730872502 1 20.80299702 -1.425824216 3.188856233 1.002729044 0.814998323 0.160935692 0.121973081 90142195.03 123261754.5 2251684.039 0.02610349 0.037512481 1.425824216 -0.187730721 KCS(ph)LPAEEDSVLEK ddPTM_SK-BR-3_Pertuzumab_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(0.999)LPAEEDS(0.001)VLEK;KCS(0.855)LPAEEDS(0.145)VLEK;KCS(1)LPAEEDSVLEK 233.1 2.16E-17 2689680000 3740780 2097098 2619830 2428039 2860594 2173260 3940810 2605202 4806710 TRUE FALSE 3506651.257 2252369.318 2681973.605 2490346.591 2635934.486 2800644.882 3349922.125 2930467.204 4004439.048 0.875691006 0.562468124 0.669750138 0.621896491 0.658253117 0.699385069 0.836552157 0.731804672 1 21.93316873 0.937803402 0.647373947 0.996215252 0.654070172 0.520390546 0.090629602 0.594661459 0.573339675 0.084735958 0.034519997 8.665695061 -0.937803402 -0.342145081 KCSEVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KCSEVAR 7 1 Q9NVI7-3;Q9NVI7-2;Q9NVI7;Q5SV16;Q5T9A4-3;Q5T9A4 Q9NVI7-3 ATAD3A;ATAD3B ATPase family AAA domain-containing protein 3A;ATPase family AAA domain-containing protein 3B 0 84.743 0.034187 39876000 85741 102360 69383 70073 125030 70559 78010 119430 150160 FALSE TRUE 80374.62386 109938.8409 71028.79753 71871.19181 115210.6481 90928.23787 66313.12471 134341.0984 125097.3259 0.642496738 0.878826466 0.567788296 0.574522207 0.920968113 0.726859964 0.530092264 1.073892646 1 16.93269143 1.224867885 24.99999961 1.036946641 0.695169533 0.553976071 0.128778886 201.3468694 367605.5857 0.11900693 0.030393201 16.78293394 -1.224867885 -0.341777108 KCSTPEEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KCSTPEEIK 9 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;;; 107.03 0.0045543 1578480000 3411770 2656660 2733320 2541400 3491430 1971760 3189790 2917220 4807880 FALSE TRUE 3198233.406 2853361.871 2798155.641 2606616.627 3217227.172 2540975.103 2711510.602 3281441.339 4005413.768 0.798477658 0.712376308 0.698593405 0.650773373 0.803219682 0.634385172 0.676961423 0.819251525 1 21.93351985 0.95029984 3.685521113 0.999611036 0.706248549 0.73941944 0.055102553 0.11706951 4.278284633 0.048971838 0.012606721 8.91866476 -0.95029984 -0.293362486 KCSTPEEIKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KCSTPEEIKK 10 2 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ; 140.24 2.23E-05 2677300000 7684100 4387300 6089700 5655300 6328400 4707400 7870800 5464900 10476900 FALSE TRUE 7203165.898 4712140.257 6234150.56 5800424.572 5831392.992 6066349.962 6690646.609 6147204.795 8728237.707 0.825271508 0.539873044 0.714250777 0.664558502 0.668106574 0.69502575 0.766551833 0.704289342 1 23.05725896 -0.399380181 0.389768252 1.080556656 0.656760747 0.623997464 0.073611134 4.295630556 0.676306426 0.534360269 0.047332783 0.398675749 0.399380181 -0.423795909 KCYEMASHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KCYEMASHLR 10 1 P07737;K7EJ44;CON__P02584 P07737 PFN1 Profilin-1 0 87.184 0.0084708 271520000 303720 643710 271690 261190 750640 210060 274560 583590 406040 FALSE TRUE 284710.7074 691370.9582 278134.6151 267892.5776 691687.7623 270700.912 233392.2769 656452.4961 338269.3009 0.841668773 2.043847776 0.822228368 0.791950605 2.04478432 0.800252672 0.689959971 1.940620962 1 18.36781273 3.950283908 21.46364131 1.117380655 1.516678721 0.037301487 0.553915779 166.1743689 132900.8111 0.132680278 0.239386696 8918.337601 -3.950283908 0.399298066 KDAENHEAQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KDAENHEAQLK 11 1 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 ;; 165.58 1.39E-05 1201290000 2609370 1929750 2092090 2007540 2234400 1556610 2618410 1927970 2623430 FALSE TRUE 2446054.19 2072630.698 2141715.363 2059056.875 2058919.237 2005978.038 2225803.729 2168681.298 2185562.585 1.119187438 0.94832823 0.979937787 0.942117553 0.942054577 0.917831432 1.018412259 0.992275999 1 21.05957326 -0.338402122 6.411290107 1 0.977005106 0.000984263 0.056700712 0 0 0.050075609 0.011802934 0.458773029 0.338402122 -0.022994894 KDCEVVMMIGLPGAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDCEVVMMIGLPGAGK 16 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 138.08 1.37E-05 906130000 3349300 2679200 3068500 2977100 3223800 2461600 4099500 2736000 4283200 FALSE TRUE 3139673.292 2877570.756 3141286.269 3053497.426 2970615.752 3172223.959 3484818.033 3077595.623 3568306.249 0.879877755 0.806424829 0.880329784 0.855727399 0.832500224 0.888999917 0.976602844 0.862480798 1 21.76680801 1.474313358 0.50647382 0.994289015 0.838039712 0.535169304 0.040614802 0.586402508 0.38423808 0.040839659 0.024445778 29.80666306 -1.474313358 -0.156249303 KDDDS(ph)DDESQSSHTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 KDDDSDDESQSSHTGK 16 1 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 KDDDS(0.887)DDES(0.113)QSSHTGK;KDDDS(0.974)DDES(0.026)QSSHTGK;KDDDS(1)DDESQSSHTGK;KDDDS(1)DDESQSSHTGK;KDDDS(0.998)DDES(0.002)QSSHTGK;KDDDS(0.988)DDES(0.012)QSSHTGK;KDDDS(1)DDESQSSHTGK;KDDDS(1)DDESQSSHTGK;KDDDS(1)DDESQSSHTGK;KDDDS(1)DDESQSSHTGK;KDDDS(0.999)DDESQSSHTGK 304.43 1.47E-46 9721681000 8785120 4784430 6258322 6331908 5963246 3942568 9065180 5070811 6950980 TRUE FALSE 8235275.021 5138674.175 6406772.353 6494395.479 5494916.714 5080723.379 7705940.416 5703912.916 5790816.533 1.422126737 0.88738335 1.106367697 1.121499091 0.948901883 0.877375988 1.330717416 0.984992856 1 22.46533536 KDDDS(ph)DDESQSSHTGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KDDDSDDESQSSHTGKK 17 2 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 KDDDS(1)DDESQSSHTGKK;KDDDS(1)DDESQSSHTGKK;KDDDS(1)DDESQSSHTGKK;KDDDS(0.999)DDES(0.001)QSSHTGKK 204.82 4.40E-12 430390000 768050 339994 506858 507988 455974 259584 679392 385594 671672 TRUE FALSE 719979.1215 365167.5095 518880.9111 521023.8321 420163.6414 334521.6868 577523.4768 433736.2597 559565.604 1.286675086 0.652591058 0.927292363 0.931121978 0.750874676 0.597823891 1.032092524 0.775130309 1 19.09394776 -1.564845169 2.908696232 1.007885864 0.854428325 0.036716026 0.1980989 38219793.1 41243859.07 2344807.047 0.042249102 0.027236722 1.564845169 -0.153457539 KDDEDSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDDEDSFR 8 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 109.29 0.0058472 802550000 1483220 1181190 1331770 1264080 1367290 1012360 1558680 1200310 1683570 FALSE TRUE 1390387.908 1268646.537 1363360.213 1296518.433 1259908.559 1304611.898 1324970.404 1350171.346 1402571.291 0.991313538 0.904514833 0.972043434 0.924386833 0.898284862 0.930157281 0.944672412 0.962640084 1 20.41964267 0.96520182 1.852067147 0.999655359 0.935451799 0.342881039 0.027846388 0.406495438 2.925318982 0.024412647 0.006913071 9.230002539 -0.96520182 -0.06420356 KDDEENYLDLFSHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KDDEENYLDLFSHK 14 1 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ;;; 240.2 1.41E-17 4395920000 12467640 7608760 9741850 8913680 9621180 6812870 12424360 7948030 12642670 FALSE TRUE 11687312.67 8172120.507 9972931.282 9142420.12 8865571.333 8779634.971 10561442.56 8940359.041 10532526.7 1.109639975 0.775893642 0.946869784 0.868017749 0.841732623 0.833573483 1.002745387 0.848833266 1 23.32834824 0.006093978 0.669391293 1.004095053 0.893521624 0.072544495 0.097237555 10.80263904 5.327150231 0.218599059 0.03289386 1.014130813 -0.006093978 -0.11057343 KDDEVQVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 169.93 9.31E-05 5317560000 9756100 8092800 8577700 8363200 9425400 7972800 10709000 7435000 10500700 FALSE TRUE 9145483.116 8691999.333 8781167.095 8577813.871 8685167.104 10274417.93 9103284.867 8363276.116 8748065.333 1.04542922 0.99359104 1.003783895 0.980538387 0.992810041 1.174478875 1.040605496 0.956014364 1 23.06053256 KDDPTLLSSGR ddPTM_SK-BR-3_Pertuzumab_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 ;; 196.11 9.88E-08 3326310000 3245910 3671220 2850320 2813930 3914470 2229750 4301650 3301660 6236200 FALSE TRUE 3042754.287 3943040.949 2917930.936 2886140.208 3607043.316 2873442.628 3656657.517 3713879.519 5195337.933 0.585670139 0.75895755 0.561644108 0.55552502 0.694284638 0.553080986 0.703834392 0.714848498 1 22.30878616 0.660112422 1.200090763 0.99957699 0.629451044 0.746144576 0.06824571 0.561777597 1.282309862 0.062098622 0.018985386 4.572065273 -0.660112422 -0.370125946 KDDRVEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDDRVEER 8 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 96.89 0.0048485 201581000 258298 250343 245628 289930 305970 218876 346180 269410 373720 FALSE TRUE 242131.5893 268878.6562 251454.4122 297370.0947 281940.3504 282061.948 294273.5228 303046.4315 311343.7177 0.777698651 0.863607136 0.80764248 0.95511834 0.905559786 0.905950344 0.945172509 0.973350077 1 18.24814864 3.769005016 0.245463352 1.013639401 0.695360522 0.757692428 0.03488747 2.933132249 0.229375653 0.054909329 0.281011437 5874.961373 -3.769005016 -0.31827888 KDDRVEERDPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDDRVEERDPPR 12 3 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 119.69 0.00021484 562230000 177907 211208 181653 196987 250471 137624 225746 194985 431260 FALSE TRUE 166772.1184 226846.0601 185961.8949 202042.0199 230800.018 177353.8147 191897.483 219329.3065 359279.92 0.464184356 0.631390867 0.517596127 0.562352663 0.642396096 0.493636869 0.534116917 0.610469148 1 18.45474878 0.784049652 3.868854127 0.999988812 0.554568803 0.866322937 0.055160049 0.69195413 12.06899389 0.048741406 0.012480244 6.082045325 -0.784049652 -0.445420008 KDDS(ph)DDDGGGWITPSNIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KDDSDDDGGGWITPSNIK 18 1 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 1 KDDS(1)DDDGGGWITPSNIK;KDDS(1)DDDGGGWITPSNIK;KDDS(1)DDDGGGWITPSNIK;KDDS(1)DDDGGGWITPSNIK;KDDS(1)DDDGGGWITPSNIK;KDDS(1)DDDGGGWITPSNIK 243.27 2.71E-24 6091180000 10177700 4124910 6167820 5633070 5461300 4220930 8130810 4671540 5893890 TRUE FALSE 9540695.925 4430322.628 6314123.603 5777624.113 5032391.528 5439443.97 6911670.523 5254792.052 4910161.683 1.943051276 0.902276323 1.285929876 1.176666775 1.024893242 1.10779325 1.407625852 1.070187173 1 22.2273391 4.749587861 24.90998203 1.146199245 1.943051757 0.756266759 0.145921389 812.4153194 1835168.095 0.034740686 0.528590297 56180.79254 -4.749587861 0.796852513 KDDS(ph)HS(ph)AEDS(ph)EDEKEDHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDDSHSAEDSEDEKEDHK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 KDDS(1)HS(1)AEDS(1)EDEKEDHK;KDDS(1)HS(1)AEDS(1)EDEKEDHK 80.786 0.0059327 1103450000 2196700 399100 803560 722710 770780 468520 902250 435860 576100 TRUE FALSE 2059212.468 428649.7793 822620.8227 741255.9621 710246.048 603774.1182 766965.9886 490278.0804 479945.1883 4.290515914 0.89312236 1.713989103 1.544459618 1.479848252 1.258006399 1.59802829 1.021529317 1 18.87251013 4.744193921 24.99989111 1.363574991 4.290517166 0.917592399 0.280009944 155.7429813 691147.3842 0.062006058 0.549270252 55487.34195 -4.744193921 2.926942175 KDDS(ph)HS(ph)AEDS(ph)EDEKEDHKNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KDDSHSAEDSEDEKEDHKNVR 21 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 KDDS(1)HS(1)AEDS(1)EDEKEDHKNVR;KDDS(1)HS(1)AEDS(1)EDEKEDHKNVR;KDDS(1)HS(1)AEDS(1)EDEKEDHKNVR 131.2 8.93E-06 1140010000 1679080 376461 639290 688720 873900 392627 806820 367433 990590 TRUE FALSE 1573989.38 404334.5641 654454.2607 706393.7212 805267.4191 505972.0411 685844.8311 413307.8189 825254.1295 1.907278405 0.489951579 0.793033609 0.855971144 0.975781145 0.613110584 0.831071068 0.500824902 1 19.65447893 4.746384975 24.89731405 0.746097995 1.907279001 0.806241384 0.177066123 368.7108131 1173218.6 0.039355214 0.42744129 55767.98787 -4.746384975 1.161181006 KDDSHS(ph)AEDS(ph)EDEKEDHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KDDSHSAEDSEDEKEDHK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 KDDS(0.117)HS(0.883)AEDS(1)EDEKEDHK;KDDS(0.103)HS(0.897)AEDS(1)EDEKEDHK;KDDS(0.139)HS(0.861)AEDS(1)EDEKEDHK;KDDS(0.126)HS(0.874)AEDS(1)EDEKEDHK;KDDS(0.17)HS(0.83)AEDS(1)EDEKEDHK 173.36 1.50E-11 6207720000 5213560 1006270 1930864 1915470 1765773 1357091 2493180 1301745 1470269 TRUE FALSE 4887252.586 1080775.278 1976665.006 1964624.203 1627096.311 1748861.141 2119350.805 1464270.729 1224871.606 3.990012148 0.882358014 1.613773229 1.603942972 1.328381117 1.427791397 1.730263641 1.195448341 1 20.2241991 4.745478145 24.9965945 1.392693583 3.990013345 0.902804153 0.27210718 234.9206552 848868.0078 0.063133576 0.629797357 55651.66279 -4.745478145 2.597319762 KDDSHS(ph)AEDS(ph)EDEKEDHKNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KDDSHSAEDSEDEKEDHKNVR 21 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 KDDS(0.006)HS(0.994)AEDS(1)EDEKEDHKNVR;KDDSHS(1)AEDS(1)EDEKEDHKNVR;KDDS(0.067)HS(0.933)AEDS(1)EDEKEDHKNVR;KDDS(0.001)HS(0.999)AEDS(1)EDEKEDHKNVR;KDDS(0.147)HS(0.853)AEDS(1)EDEKEDHKNVR;KDDS(0.251)HS(0.749)AEDS(1)EDEKEDHKNVR;KDDS(0.129)HS(0.871)AEDS(1)EDEKEDHKNVR;KDDS(0.189)HS(0.811)AEDS(1)EDEKEDHKNVR 204.99 2.80E-22 19023300000 8404900 2056406 3262618 3930578 4247769 2392841 4670031 2576263 4915739 TRUE FALSE 7878852.312 2208664.44 3340008.84 4031443.286 3914166.357 3083615.352 3969803.206 2897915.107 4095270.404 1.923890619 0.539320783 0.81557712 0.984414431 0.955777268 0.752969901 0.969362903 0.70762485 1 21.96552728 4.747987779 24.99650757 0.829222603 1.923891197 0.843226483 0.146717669 497.7539145 1319787.707 0.035729096 0.459451233 55974.18498 -4.747987779 1.094668594 KDDSHSAEDS(ph)EDEKEDHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDDSHSAEDSEDEKEDHK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KDDSHSAEDS(1)EDEKEDHK;KDDSHSAEDS(1)EDEKEDHK 233.26 4.63E-24 1184430000 1759570 385058 685425 657527 629946 474130 859584 461989 616187 TRUE FALSE 1649441.655 413568.095 701683.6047 674400.256 580472.5822 611003.6341 730697.3592 519669.3436 513341.409 3.21314748 0.805639459 1.366894609 1.313746065 1.130772956 1.190248095 1.423414021 1.012326951 1 18.96955912 4.74509935 24.99993785 1.183221034 3.213148391 0.922291764 0.187559918 193.4106895 739459.6038 0.043802245 0.421487059 55603.14411 -4.74509935 2.029927358 KDDSHSAEDS(ph)EDEKEDHKNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDDSHSAEDSEDEKEDHKNVR 21 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KDDSHSAEDS(1)EDEKEDHKNVR;KDDSHSAEDS(1)EDEKEDHKNVR 212.76 3.15E-23 955700000 1135280 314876 490990 617970 633210 400181 727830 423410 899130 TRUE FALSE 1064224.851 338189.7467 502636.5147 633828.1564 583480.2408 515706.7583 618698.6483 476273.6705 749059.3944 1.420748287 0.451485889 0.671023578 0.846165419 0.778950568 0.688472452 0.825967411 0.63582898 1 19.51472059 -1.931685686 2.377894403 1.171030416 0.751283314 0.045287607 0.253228969 23722714.6 11021458.31 22516596.29 0.055930552 0.011703461 1.931685686 -0.419747102 KDDTDDEIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KDDTDDEIAK 10 1 P27824;P27824-2;H0Y9Q7;D6RDP7;D6RAU8;D6RB85;D6RAQ8 P27824 CANX Calnexin 0 ;;;; 158.4 1.28E-05 2034330000 7334890 3249420 3826150 3511840 4260410 2757170 5846240 4071190 3144350 FALSE TRUE 6875812.328 3490010.438 3916908.085 3601959.76 3925814.584 3553120.22 4969650.586 4579487.033 2619537.672 2.624819029 1.332300152 1.495266942 1.375036442 1.49866697 1.356392106 1.897147974 1.748204304 1 21.32088078 4.743689877 24.97268739 1.497370796 2.624819504 0.69107559 0.243176237 318.405222 1550160.987 0.056327858 0.475644551 55422.98046 -4.743689877 1.127448708 KDDVS(ph)PVMQFSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KDDVSPVMQFSSK 13 1 Q8IZE3;Q8IZE3-2 Q8IZE3 SCYL3 Protein-associating with the carboxyl-terminal domain of ezrin 1 KDDVS(1)PVMQFSSK;KDDVS(1)PVMQFSSK;KDDVS(1)PVMQFSSK;KDDVS(0.999)PVMQFSSK 194.21 7.42E-07 1506330000 2243900 1588060 1759900 1827990 1860760 1120975 2131530 1559820 2507810 TRUE FALSE 2103458.304 1705641.615 1801645.659 1874899.318 1714623.416 1444582.285 1811926.865 1754566.961 2089240.31 1.006805342 0.816393216 0.862344868 0.89740721 0.820692291 0.691439026 0.867265894 0.839810984 1 20.99454701 4.743401054 24.44283328 0.839097183 1.006805437 0.284306179 0.076942518 436.8326547 2205777.479 0.016649327 0.136537425 55386.13431 -4.743401054 0.167708254 KDDYEYCMSEYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDDYEYCMSEYLR 13 1 P53611;Q5T4U8 P53611 RABGGTB Geranylgeranyl transferase type-2 subunit beta 0 ; 193.96 2.29E-06 305270000 205941 193512 171108 185548 227700 137869 192317 185172 240300 FALSE TRUE 193051.5204 207839.8298 175166.7626 190309.4758 209817.3605 177669.5422 163480.8512 208291.1318 200192.3776 0.964330025 1.038200517 0.874992168 0.950632977 1.048078668 0.887494041 0.81661876 1.040454858 1 17.61102752 2.172325367 25 0.908499652 0.969045803 0.002714579 0.078105253 121.9852379 46040.58922 0.02846143 0.021020164 148.70493 -2.172325367 0.060546151 KDEDLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KDEDLFR 7 1 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 ;;;; 126.41 0.0063409 1676068000 2725250 2778350 2451230 2430400 3038200 1883880 2836520 2603960 3684010 FALSE TRUE 2554681.467 2984061.925 2509374.333 2492768.179 2799592.028 2427725.574 2411210.159 2929070.138 3069124.931 0.832381061 0.97228428 0.817618829 0.812208116 0.912179234 0.791015559 0.785634411 0.954366539 1 21.54939594 1.062476641 6.043307733 0.999406901 0.851265658 0.483470545 0.057126043 0.164845074 10.6473434 0.057900217 0.014564473 11.54719876 -1.062476641 -0.148141243 KDEEGQKEEDKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDEEGQKEEDKPR 13 3 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 0 134.21 4.30E-05 213870000 648530 207050 344940 353750 370520 228340 479710 256360 508360 FALSE TRUE 607939.665 222380.1974 353122.1397 362827.8239 341420.8538 294258.0512 407781.9389 288367.1103 423511.4319 1.435474037 0.525086646 0.833796004 0.856713176 0.806166795 0.69480545 0.962859343 0.680895694 1 18.69204139 -1.924397764 7.767368516 1.04615874 0.821563219 0.025941177 0.240884145 0.126907607 0.001235231 0.153724835 0.048350874 0.011901515 1.924397764 -0.22459552 KDEEKEDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDEEKEDPK 9 2 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W543;F8W118;F8VUX1;H0YHC3;H0YH88;F8W020;P55209-3;F8VXI6 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 100.88 0.0024533 376580000 2581200 606420 1340700 1147200 1056500 901730 1806300 946820 1181000 FALSE TRUE 2419647.3 651319.9678 1372502.037 1176639.094 973526.7517 1162044.813 1535462.084 1065032.561 983883.4704 2.459282397 0.661988932 1.394984344 1.195913062 0.989473633 1.181079719 1.560613762 1.082478356 1 19.90812793 4.752884894 24.7768466 1.163737272 2.459283406 0.746623664 0.242178655 1222.285368 2114158.361 0.059070646 1.265217013 56608.92323 -4.752884894 1.295546134 KDEESGGGSNPFQHLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDEESGGGSNPFQHLEK 17 1 Q9Y678;D6RG17 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ; 129.2 2.23E-05 251920000 714740 575240 604380 609960 656850 528370 802410 610060 743820 FALSE TRUE 670005.6992 617831.3681 618716.179 625612.6063 605263.6506 680901.8416 682096.0697 686227.3339 619671.6367 1.081226991 0.997030252 0.998458123 1.009587287 0.976748999 1.098810727 1.100737922 1.107404782 1 19.24114441 2.229482449 24.99945168 1.087293619 1.008418515 0.366527982 0.040650727 156.4306715 430774.8905 0.013633427 0.010214424 169.6221051 -2.229482449 -0.078875103 KDEKTDTLEDLFPTTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDEKTDTLEDLFPTTK 16 2 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 62.165 0.044518 192700000 213350 130540 156560 147800 233960 99042 225760 153210 407930 FALSE TRUE 199996.8043 140205.3174 160273.6771 151592.7982 215585.7253 127633.8176 191909.3839 172338.6058 339843.8477 0.588496175 0.412558057 0.471609765 0.446066037 0.63436701 0.375566068 0.564698714 0.507111154 1 18.37451248 -3.457023107 0.358718531 2.753879764 0.473523968 0.793747313 0.079981075 53.62849573 1.24019241 70.58931042 0.052191482 0.000349122 3.457023107 -2.280355796 KDELS(ph)DWS(ph)LAGEDDRDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDELSDWSLAGEDDRDSR 18 2 B4DXZ6;P51114;P51114-3;H7C4S4;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 2 KDELS(1)DWS(1)LAGEDDRDSR;KDELS(1)DWS(0.999)LAGEDDRDS(0.001)R 85.013 0.018259 261750000 624960 442300 465480 447450 515610 329620 690680 474060 520680 TRUE FALSE 585844.8692 475048.3522 476521.4054 458932.3245 475116.0705 424775.9431 587118.946 533247.4345 433775.1443 1.350572703 1.095148854 1.098544745 1.057995901 1.095304968 0.979253765 1.353509886 1.229317635 1 18.72658786 1.738482437 25 1.226839713 1.106338788 0.06318165 0.127346115 0.068790101 6088.226106 0.053479291 0.029657105 54.7623955 -1.738482437 -0.120500925 KDELS(ph)DWSLAGEDDRDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDELSDWSLAGEDDRDSR 18 2 B4DXZ6;P51114;P51114-3;H7C4S4;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 1 KDELS(1)DWSLAGEDDRDSR;KDELS(1)DWSLAGEDDRDSR 188.39 1.99E-14 329800000 568910 393395 433010 415470 450650 367945 631330 423010 406900 TRUE FALSE 533302.9386 422522.3751 443281.2017 426131.6636 415257.7668 474164.7484 536667.9275 475823.7297 338985.7613 1.57323109 1.24643104 1.307669089 1.257078356 1.225000617 1.398774823 1.583157727 1.403668779 1 18.37086515 2.068571961 10.15076022 1.417973117 1.30696027 0 0.178251947 0.998223881 140.9455498 0.060604701 0.044742643 117.1040624 -2.068571961 -0.111012846 KDELSDWS(ph)LAGEDDRDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDELSDWSLAGEDDRDSR 18 2 B4DXZ6;P51114;P51114-3;H7C4S4;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 1 KDELS(0.012)DWS(0.545)LAGEDDRDS(0.444)R 122.13 2.89E-05 137360000 276080 181840 228470 206450 201170 174950 311290 199020 197300 TRUE FALSE 258800.6456 195303.6228 233889.4163 211747.8565 185370.9197 225455.2249 264614.9544 223868.0851 164369.3554 1.574506665 1.188199725 1.422950256 1.288244126 1.127770558 1.371637824 1.6098801 1.361981889 1 17.32658183 2.005691779 24.98701627 1.416478596 1.309421526 0 0.195825217 431.9478214 1896247.444 0.066923803 0.049285681 101.3192063 -2.005691779 -0.10705707 KDELYLNLVLEYVPETVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDELYLNLVLEYVPETVYR 19 1 P49840;A8MT37;M0QYV0 P49840 GSK3A Glycogen synthase kinase-3 alpha 0 65.521 0.042814 0 124990 97538 106110 114770 125420 92322 124780 106600 87693 FALSE TRUE 117167.099 104759.815 108626.9793 117715.1925 115570.0191 118973.8627 106070.3974 119909.2447 73056.47178 1.603788086 1.43395667 1.486890575 1.611290412 1.58192719 1.628519141 1.451895976 1.641322688 1 16.15672446 -1.174334595 4.33542996 0.999858519 1.537418061 0.840427802 0.075652758 0.00010319 1.97E-05 0.073062187 0.017216426 0.066936871 1.174334595 0.537559542 KDENEIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDENEIEK 8 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 ; 92.538 0.018771 541950000 464980 295530 344510 376750 455650 265380 472560 351600 572870 FALSE TRUE 435877.7318 317411.3487 352681.9399 386418.0428 419865.087 341990.8979 401704.015 395498.034 477254.2961 0.913302898 0.665078033 0.738981174 0.809669072 0.879751299 0.71658003 0.84169806 0.82869455 1 18.86439866 -0.167063417 0.343164892 1.057675415 0.751496499 0.401890103 0.0758488 5.288093483 0.795296569 0.465586196 0.067013899 0.680669958 0.167063417 -0.306178916 KDEPDAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KDEPDAFK 8 1 P13674;P13674-2 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ;; 107.24 0.0064785 1462270000 2997860 1923350 2197580 2341120 2402730 1251910 2750520 1934210 1589990 FALSE TRUE 2810229.294 2065756.835 2249707.635 2401197.103 2214029.278 1613316.094 2338105.061 2175700.376 1324610.397 2.12155159 1.559520323 1.69839195 1.812757251 1.671456968 1.217955179 1.76512661 1.642520986 1 20.33713666 -2.631151545 0.184970208 6.41E-16 1.838423247 0.547846327 0.208807123 39.88688586 0.861779966 17.25929088 0.641784229 0.002338021 2.631151545 1.838423247 KDEPDAFKELGTGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDEPDAFKELGTGNR 15 2 P13674;P13674-2 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 112.34 0.00043398 78319000 195440 198190 182160 198370 253290 120600 233540 170590 275880 FALSE TRUE 183207.7593 212864.1938 186480.9212 203460.51 233397.6251 155415.2622 198522.8451 191888.537 229833.8457 0.797131331 0.926165566 0.811372758 0.885250427 1.015505895 0.67620703 0.863766798 0.834901128 1 17.81023174 -1.736720421 2.598195833 1.030335395 0.853277822 0.220547625 0.087789565 18501691.31 14333642.71 3624286.325 0.020751537 0.018334944 1.736720421 -0.177057573 KDEQEHEFYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KDEQEHEFYK 10 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;; 123.67 0.00029594 1770180000 3553500 2439490 2647730 2478360 2994500 1860700 3424300 2580380 3729500 FALSE TRUE 3331092.778 2620112.378 2710535.406 2541958.913 2759324.049 2397853.884 2910858.005 2902546.123 3107022.357 1.072117415 0.843287263 0.872390055 0.818133448 0.888092757 0.771753019 0.936864197 0.934189005 1 21.56710119 1.22280808 2.077697703 0.989595599 0.871745919 0.179155744 0.079485179 0.439657214 3.297049932 0.066693329 0.019265617 16.70352303 -1.22280808 -0.11784968 KDEQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDEQER 6 1 P13639;O00268;A0A0G2JRY5 P13639;O00268 EEF2;TAF4 Elongation factor 2;Transcription initiation factor TFIID subunit 4 0 ; 101.28 0.058844 298600000 577280 510630 779630 757340 701770 526060 801280 527750 618640 FALSE TRUE 541149.0753 548437.5765 798123.1918 776774.6266 646655.815 677924.9821 681135.5027 593640.7492 515384.9874 1.049989985 1.064131843 1.54859612 1.507173561 1.254704407 1.315375881 1.321605245 1.151839428 1 18.97529099 1.011744628 3.168641447 1.00106142 1.304443404 0.272099907 0.158663 0.309960677 7.381509742 0.157908984 0.041390586 10.27411987 -1.011744628 0.303381984 KDETNVK ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 112.41 0.010198 5729410000 7657390 4425490 5799000 5318610 6024580 3875910 6113540 5595370 7174180 FALSE TRUE 7178127.629 4753157.884 5936555.018 5455094.537 5551433.789 4994822.297 5196871.432 6293964.261 5976763.011 1.201005898 0.795272939 0.993272614 0.912717223 0.928836191 0.835706935 0.869512715 1.053072416 1 22.51093291 1.231456792 24.98551945 1.026536248 0.917937283 0.094492209 0.111310854 331.3244046 1165280.879 0.088137208 0.023886655 17.03949786 -1.231456792 -0.108598965 KDGADFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KDGADFAK 8 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78;P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5 H3BPS8;P04075;P09972 ALDOA;ALDOC Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase C 0 ;;; 111.06 0.0053021 11157100000 13803400 12073600 11243000 10742900 12931300 8028400 14685700 11082100 11353600 FALSE TRUE 12939469.83 12967541.91 11509689.27 11018581 11915727.86 10346068.75 12483715.62 12465724.58 9458610.813 1.368009541 1.370977426 1.216847748 1.16492593 1.259775679 1.093825399 1.319825487 1.317923406 1 23.17319688 -5 0.104151316 0.285276396 1.411532366 0.474564053 0.087540025 173.1235805 1.216310809 27.78799819 1.309176643 1.00E-05 5 1.12625597 KDGLVSLLTTSEGADEPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDGLVSLLTTSEGADEPQR 19 1 P51570;P51570-2;K7ERJ9 P51570 GALK1 Galactokinase 0 ; 269.01 8.74E-32 606140000 713040 610510 617540 656460 664220 515560 742700 565540 728580 FALSE TRUE 668412.0992 655712.7956 632188.3404 673305.875 612054.8405 664393.8026 631339.0299 636148.9139 606975.2912 1.101217972 1.080295698 1.04153884 1.109280534 1.008368626 1.094597774 1.040139589 1.048063938 1 19.21127826 1.857836196 0.009107944 3.34E-08 2.103334256 0.421965803 0.028727768 1316.00275 10.41404093 1194.125742 1209.290247 72.08355483 -1.857836196 2.103334223 KDGNASGTTLLEALDCILPPTRPTDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDGNASGTTLLEALDCILPPTRPTDK 26 2 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ; 167.27 5.97E-12 319450000 605070 370030 459130 448140 459160 393380 574790 434320 423070 FALSE TRUE 567199.7488 397427.4062 470020.7804 459640.0311 423099.4258 506942.42 488605.5756 488545.8081 352456.8839 1.60927414 1.127591556 1.333555399 1.304102862 1.20042889 1.438310452 1.386284672 1.386115098 1 18.42708726 -1.338635168 3.322380846 0.997908306 1.329670533 0.404562731 0.131055575 25494872.21 36443205.47 523858.5837 0.029716076 0.045852691 1.338635168 0.331762227 KDGNASGTTLLEALDCILPPTRPTDKPLR ddPTM_SK-BR-3_Pertuzumab_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 ; 198.4 4.82E-25 416280000 1216510 886730 1008090 989640 1080490 870160 1278620 982290 936010 FALSE TRUE 1140370.811 952384.4118 1032002.371 1015035.838 995632.6739 1121361.066 1086902.801 1104931.069 779783.8841 1.462419055 1.221344056 1.323446652 1.301688658 1.276805913 1.438040833 1.393851326 1.416970896 1 19.57271481 KDGS(ph)SPPLLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDGSSPPLLEK 11 1 H7BYY2;Q6W2J9-4;Q6W2J9-2;Q6W2J9;Q6W2J9-3 H7BYY2 BCOR BCL-6 corepressor 1 KDGS(0.607)S(0.393)PPLLEK;KDGS(0.57)S(0.43)PPLLEK 86.497 0.0088363 462700000 1964840 1178580 1476950 1418260 1443330 1011510 1897590 1187280 1468030 TRUE FALSE 1841864.172 1265843.29 1511983.951 1454654.953 1329976.684 1303516.517 1613063.996 1335514.522 1223006.309 1.50601363 1.035025968 1.23628467 1.189409197 1.087465105 1.065829756 1.318933503 1.091993158 1 20.22200042 7.999999915 0.01841313 2.44E-08 2.644485222 0.247309183 0.132752636 7192.746776 10.21170356 556.7052298 960.7363445 99999980.49 -7.999999915 2.644485198 KDGSS(ph)PPLLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDGSSPPLLEK 11 1 H7BYY2;Q6W2J9-4;Q6W2J9-2;Q6W2J9;Q6W2J9-3 H7BYY2 BCOR BCL-6 corepressor 1 KDGS(0.201)S(0.799)PPLLEK 101.42 0.0020189 233920000 931730 551970 716460 640340 720150 557700 1015600 602840 806830 TRUE FALSE 873414.6825 592838.4331 733454.7695 656772.2085 663592.3239 718698.9365 863320.2084 678105.901 672164.8607 1.299405449 0.881983674 1.091182852 0.977099886 0.987246378 1.069230153 1.284387594 1.008838665 1 19.3584556 1.990265041 24.48848116 1.14120775 1.027659601 0 0.133854676 676.7338914 1702337.06 0.047493841 0.033079729 97.78337914 -1.990265041 -0.11354815 KDIDHETVVEEQIIGENS(ph)PPDYSEYMTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KDIDHETVVEEQIIGENSPPDYSEYMTGK 29 1 P25490;A0A494C032;H0YJV7;H0YJU4 P25490 YY1 Transcriptional repressor protein YY1 1 KDIDHETVVEEQIIGENS(0.996)PPDY(0.001)S(0.002)EYMTGK;KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK;KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK;KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK;KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK;KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK 352.87 2.14E-120 1885750000 1726580 1270886 1467635 1376211 1587310 1072536 1827160 1325514 1915140 TRUE FALSE 1618516.44 1364983.722 1502447.995 1411526.904 1462649.076 1382159.732 1553194.321 1491007.341 1595490.762 1.014431721 0.855525933 0.94168392 0.884697635 0.916739295 0.866291279 0.973490012 0.934513302 1 20.60556882 1.652409929 8.965088369 0.965424107 0.909029627 0.236294219 0.046859422 0.152050428 21.51160185 0.020265337 0.01068295 44.91691591 -1.652409929 -0.05639448 KDIHFMPCSGLTGANLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDIHFMPCSGLTGANLK 17 1 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 174.87 8.44E-10 481560000 475970 424470 408640 441180 503550 340190 539750 414440 645030 FALSE TRUE 446179.8873 455898.2005 418333.1338 452501.4257 464003.2142 438397.3305 458819.4983 466183.7463 537370.3259 0.83030243 0.848387375 0.778482014 0.84206627 0.86347011 0.81581976 0.85382366 0.867527892 1 19.03555713 0.126282874 0.581028902 1.010267107 0.823552355 0.843966337 0.022601125 1.262351004 0.548667083 0.051320384 0.009618032 1.33746638 -0.126282874 -0.186714752 KDISENKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDISENKR 8 2 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 120.12 0.00087915 428200000 951360 910040 782120 697590 1260300 594110 1083800 1120300 1461500 FALSE TRUE 891816.0758 977420.3085 800672.2557 715491.3404 1161321.122 765619.9124 921294.2515 1260171.921 1217566.208 0.732457972 0.802765633 0.657600589 0.587640603 0.953805316 0.628811729 0.756668709 1.034992522 1 20.21556879 1.263507998 6.252300613 1.019503226 0.728938564 0.580526438 0.101209634 0.099074548 12.56479865 0.068698399 0.022911229 18.3445895 -1.263507998 -0.290564661 KDKS(ph)PVREPIDNLTPEER ddPTM_SK-BR-3_Pertuzumab_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 200.54 1.45E-15 45510250000 14421480 7878770 10789510 10195530 10902920 7492023 13341430 8994150 15267750 TRUE FALSE 13518865.31 8462122.329 11045442.27 10457164.56 10046648.64 9654848.417 11341006.43 10117089.43 12719463.89 1.062848672 0.665289229 0.86838898 0.822138783 0.789864159 0.759060956 0.891626135 0.795402189 1 23.60053453 -1.113281096 3.777022316 1.000077956 0.82068199 0.201829841 0.103004165 27521313.49 50084122.27 27266.90484 0.021999304 0.077040467 1.113281096 -0.179395966 KDLGSTEDGDGT(ph)DDFLTDKEDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDLGSTEDGDGTDDFLTDKEDEK 23 2 Q15527 Q15527 SURF2 Surfeit locus protein 2 1 KDLGSTEDGDGT(1)DDFLTDKEDEK 147.17 5.72E-06 99072000 227300 70600 120390 97864 96462 66505 155960 85961 132350 TRUE FALSE 213073.6987 75827.29746 123245.7077 100375.3559 88886.26363 85703.91388 132575.2459 96693.42007 110259.93 1.932467205 0.687714 1.117774224 0.910352074 0.806152005 0.777289754 1.202388265 0.876958838 1 16.75054906 4.747322153 24.95697601 0.933913161 1.932467725 0.807821729 0.154746417 483.8060128 1378076.828 0.036202026 0.434344267 55888.46126 -4.747322153 0.998554564 KDLYANTVLSGGTTMYPGIADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KDLYANTVLSGGTTMYPGIADR 22 1 P60709;A0A2R8Y793;P63261 P60709;P63261 ACTB;ACTG1 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 ;;;; 281.28 1.78E-45 21627190000 16951330 16528260 16405140 16214180 18610970 13255470 18851830 15401780 18330080 FALSE TRUE 15890376.51 17752029.57 16794277.67 16630263.31 17149339.49 17082109 16025173.1 17324726.14 15270671.23 1.040581404 1.162491766 1.099773377 1.089032896 1.123024602 1.118622014 1.04940856 1.134509798 1 23.86426014 -4.895845149 0.246703762 0.408262013 1.114524612 0.397025576 0.037887904 155.9266473 1.626403822 46.31041564 0.052095696 1.27E-05 4.895845149 0.706262599 KDNDFIYHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KDNDFIYHDR 10 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;;;;;; 153.54 1.04E-05 8531180000 16477460 16120250 16217170 16456020 17669590 13007470 20213430 15811170 17146310 FALSE TRUE 15446165.19 17313810.08 16601848.93 16878309.33 16281891.68 16762515.43 17182613.82 17785229.38 14284480.09 1.081324983 1.212071421 1.162229834 1.181583735 1.139830891 1.173477461 1.202886889 1.245073623 1 23.76794519 -1.340421527 5.193649211 0.999933205 1.177977453 0.609346344 0.043922757 3.08E-05 3.91E-06 0.038504828 0.009072276 0.045664475 1.340421527 0.178044249 KDPEDTGAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDPEDTGAEK 10 1 O75363;G3XAF7;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 ; 84.352 0.028185 618330000 1737660 956030 1199670 1238680 1350610 965800 1594180 1165410 1391840 FALSE TRUE 1628902.962 1026815.456 1228126.739 1270466.626 1244538.539 1244610.782 1355147.509 1310914.004 1159532.912 1.404792348 0.885542312 1.059156429 1.095671035 1.073310232 1.073372535 1.168701202 1.13055351 1 20.14511234 1.95565187 20.95788763 1.119131537 1.067994401 0 0.135143513 310.9322237 146935.5095 0.052114887 0.033628422 90.29254 -1.95565187 -0.051137136 KDPEDTGAEKS(ph)PTTSADLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KDPEDTGAEKSPTTSADLK 19 2 O75363;G3XAF7;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 KDPEDT(0.004)GAEKS(0.864)PT(0.108)T(0.02)S(0.004)ADLK;KDPEDTGAEKS(0.851)PT(0.112)T(0.015)S(0.021)ADLK;KDPEDT(0.034)GAEKS(0.852)PT(0.102)T(0.008)S(0.004)ADLK 153.94 2.13E-08 2593790000 1299030 475269 740150 841800 803160 408125 787170 442506 877040 TRUE FALSE 1217726.031 510458.4113 757706.7075 863402.0132 740083.0534 525944.0621 669141.1662 497753.8482 730656.3581 1.666619359 0.698629945 1.037021986 1.181680011 1.012901681 0.719824109 0.915808312 0.681242068 1 19.47883351 2.372089823 6.529663087 0.82963071 1.057361298 0.224322518 0.25527816 0.396802611 21.81243434 0.08422552 0.070179598 235.5536416 -2.372089823 0.227730587 KDPEDTGAEKS(ph)PTTSADLKSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDPEDTGAEKSPTTSADLKSDK 22 3 O75363;G3XAF7;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 KDPEDT(0.04)GAEKS(0.83)PT(0.045)T(0.045)S(0.038)ADLKS(0.003)DK 52.329 0.084087 98301000 236800 68208 118680 163220 199270 66492 144620 71012 327700 TRUE FALSE 221979.1107 73258.19129 121495.1456 167408.5015 183620.138 85687.16099 122935.5736 79878.00452 273004.753 0.813096139 0.268340351 0.445029415 0.613207278 0.672589528 0.31386692 0.450305616 0.292588329 1 18.05856654 -1.299582812 5.324691098 1.000100307 0.461931702 0.455273704 0.176092243 0.000195087 2.57E-05 0.158630222 0.037382591 0.050166891 1.299582812 -0.538168605 KDPEDTGAEKSPT(ph)TSADLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDPEDTGAEKSPTTSADLK 19 2 O75363;G3XAF7;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 KDPEDTGAEKS(0.294)PT(0.696)T(0.009)S(0.002)ADLK 175.48 1.18E-10 1274800000 1805900 642420 944880 1052400 937790 505920 1084100 510370 921580 TRUE FALSE 1692871.943 689985.4452 967292.9998 1079406.366 864139.7563 651970.8911 921549.2693 574090.818 767762.3444 2.204942656 0.898696648 1.259885962 1.405912095 1.125530267 0.849183209 1.200305376 0.747745474 1 19.55030028 4.744352883 24.96618952 1.083670844 2.204943149 0.763395446 0.199803702 301.6593221 1300192.962 0.045484377 0.406470256 55507.65536 -4.744352883 1.121272306 KDPELWGSVLLESNPYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDPELWGSVLLESNPYR 17 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 211.09 4.46E-12 1355660000 411250 423400 413930 374470 435160 304920 470200 414980 407000 FALSE TRUE 385510.5966 454748.9765 423748.6151 384079.5342 400984.289 392945.454 399697.8751 466791.1665 339069.0707 1.136967745 1.341169148 1.249741282 1.132747182 1.182603557 1.15889501 1.178809599 1.376684596 1 18.37121966 -1.782915325 2.670212788 0.941178496 1.223508414 0.410030097 0.082709753 11235828.26 8310681.003 4306261.624 0.019884442 0.016484838 1.782915325 0.282329918 KDPELWGSVLLESNPYRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDPELWGSVLLESNPYRR 18 2 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 169.19 1.06E-11 999760000 166285 194514 180492 184311 221345 177495 248900 196028 261369 FALSE TRUE 155877.5187 208916.019 184773.3555 189040.7323 203961.4566 228734.9251 211579.7557 220502.5273 217744.8254 0.715872436 0.959453427 0.848577481 0.868175544 0.936699443 1.050472381 0.971686722 1.012664833 1 17.73227891 2.523520914 3.408387041 1.004160896 0.867178236 0.584646541 0.062703995 0.186874907 4.395990817 0.020521033 0.018313711 333.826581 -2.523520914 -0.13698266 KDPLEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDPLEGR 7 1 Q14165;F5GX14 Q14165 MLEC Malectin 0 74.127 0.090494 0 96921 101450 88044 91096 146960 80047 133470 122860 139730 FALSE TRUE 90854.88762 108961.4636 90132.44526 93433.67759 135418.3544 103155.2694 113457.4126 138199.3414 116408.1603 0.780485555 0.936029427 0.774279441 0.802638555 1.16330637 0.886151531 0.974651711 1.187196336 1 16.82883267 2.761778166 24.96056782 1.0222097 0.83395696 0.54680865 0.097875184 658.6786424 708126.7678 0.02858351 0.03030072 577.800836 -2.761778166 -0.18825274 KDPNAEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDPNAEGR 8 1 H0YER2;H0YE76;H0YCB3;A0A5F9ZH79;A0A5F9ZHP1;Q8N9N2-2;Q8N9N2 H0YER2 ASCC1 Activating signal cointegrator 1 complex subunit 1 0 77.677 0.052261 96365000 95949 99826 89355 87322 109590 66088 115620 93650 119490 FALSE TRUE 89943.72336 107217.2209 91474.5428 89562.83036 100983.2435 85166.53275 98283.85436 105342.4086 99546.34707 0.903536152 1.077058316 0.918914109 0.899709864 1.014434446 0.855546539 0.987317539 1.058224754 1 16.60308076 1.473351429 24.99999882 1.026998793 0.955373809 0.218734396 0.064186953 0.968774092 6425.889335 0.033527698 0.01552136 29.74071664 -1.473351429 -0.071624984 KDPSGASNPSADS(ph)PLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 KDPSGASNPSADSPLHR 17 1 P55317-2;P55317 P55317-2 FOXA1 Hepatocyte nuclear factor 3-alpha 1 KDPSGASNPS(0.011)ADS(0.989)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPS(0.008)ADS(0.992)PLHR 233.28 1.96E-20 9757320000 5427810 4578920 5105970 4685920 5256780 5104730 7482070 5278600 5429920 TRUE FALSE 5088093.061 4917948.001 5227086.02 4806168.64 4843933.704 6578382.683 6360203.064 5937644.83 4523631.273 1.12478068 1.087168185 1.15550665 1.06245809 1.070806485 1.454226104 1.405995025 1.312583734 1 22.10904991 2.250963762 24.9999938 1.340036805 1.104211006 0.345739794 0.12470963 180.6674534 364156.054 0.038889701 0.032321695 178.2230051 -2.250963762 -0.235825799 KDQGELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KDQGELER 8 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;; 145.46 0.00091235 2973050000 3881350 3869460 3944950 3957300 3838180 3314390 4532670 3526550 3852910 FALSE TRUE 3638423.232 4155958.845 4038526.077 4058851.018 3536744.825 4271200.588 3853038.213 3966847.53 3209834.43 1.133523648 1.294758012 1.258172708 1.264504792 1.101846498 1.330660718 1.200385346 1.235841791 1 21.61406745 -3.390158088 0.446895333 2.20E-08 1.239270377 0.507719881 0.069729112 190.0562429 4.727698948 180.6444502 0.033790322 0.000407232 3.390158088 1.239270355 KDREDS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDREDSPER 9 2 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 1 KDREDS(1)PER;KDREDS(1)PER 97.716 0.005121 503570000 606161 399433 509695 447324 419760 364421 546420 434869 533585 TRUE FALSE 568222.465 429007.4349 521785.2061 458803.0912 386793.7428 469623.4268 464489.3937 489163.3519 444526.2164 1.278265362 0.965089165 1.17380075 1.032117059 0.87012583 1.056458336 1.044908886 1.10041508 1 18.76190898 4.749554237 24.5826871 1.037633192 1.278265538 0.484558465 0.080040639 1192.549646 2666579.704 0.018810294 0.278680607 56176.44304 -4.749554237 0.240632346 KDRHDT(ph)PDPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDRHDTPDPSPR 12 2 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 KDRHDT(1)PDPS(1)PR 128.06 0.00028544 227970000 370320 429810 400640 430280 494540 233040 458800 355710 739280 TRUE FALSE 347142.3322 461633.5796 410143.37 441321.7133 455700.8233 300314.8649 390007.1993 400121.1765 615889.3921 0.563643954 0.749539748 0.665936734 0.716560017 0.73990692 0.487611686 0.633242274 0.649664017 1 19.23231175 -1.530198069 2.845315951 1.015816555 0.656548211 0.654666355 0.079615026 18753460.05 19750902.82 2281198.528 0.018926388 0.029498636 1.530198069 -0.359268344 KDRNNTEVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDRNNTEVER 10 2 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 52.79 0.083144 69345000 438120 229900 283300 232980 260760 195610 310290 248520 225810 FALSE TRUE 410698.8513 246922.0352 290020.0098 238958.6612 240280.9615 252079.4315 263764.8951 279548.2691 188120.8522 2.183164952 1.312571319 1.541668594 1.270240159 1.277269152 1.339986655 1.402103446 1.486003629 1 17.52130025 4.740518434 24.95925315 1.358894848 2.183165238 0.764863724 0.148046988 77.41814805 986892.2427 0.031486894 0.20665691 55019.72741 -4.740518434 0.82427039 KDS(ph)DDEKSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KDSDDEKSDR 10 2 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 KDS(1)DDEKSDR;KDS(0.998)DDEKS(0.002)DR;KDS(0.998)DDEKS(0.002)DR;KDS(1)DDEKSDR;KDS(1)DDEKSDR 184.02 8.37E-07 1892230000 6578390 1851110 3336770 3207920 2892780 2079560 4065880 2465880 3238610 TRUE FALSE 6166660.313 1988168.11 3415919.76 3290240.658 2665592.728 2679895.213 3456239.04 2773750.546 2698065.069 2.285586209 0.736886643 1.266062779 1.219481582 0.987964582 0.993265598 1.281006555 1.028051761 1 21.36349371 4.748718867 24.9970311 1.079705326 2.285586871 0.848084266 0.162351707 542.295229 1334432.939 0.038260259 0.529143332 56068.49088 -4.748718867 1.205881545 KDS(ph)DTESSDLFTNLNLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KDSDTESSDLFTNLNLGR 18 1 Q9Y3S2 Q9Y3S2 ZNF330 Zinc finger protein 330 1 KDS(0.996)DT(0.004)ESSDLFTNLNLGR;KDS(0.979)DT(0.021)ESSDLFTNLNLGR;KDS(0.964)DT(0.036)ESSDLFTNLNLGR 323.51 4.33E-62 509310000 995655 425222 623981 527609 461787 421538 743326 451213 444903 TRUE FALSE 933338.7308 456705.8793 638782.124 541148.3402 425520.1118 543229.1775 631871.167 507547.9363 370645.8151 2.518141829 1.232189494 1.723430018 1.460014704 1.148050496 1.46562879 1.704784301 1.369361033 1 18.4996817 4.745406951 24.99363984 1.441573958 2.518142324 0.698642228 0.230901964 460.1140573 1679677.394 0.051828697 0.514610804 55642.54049 -4.745406951 1.076568366 KDS(ph)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR 375.03 1.52E-176 779408000 155140.5 96692.6 106158.5 103130.6 122699.6 75943.5 126809.2 103631.1 138518.4 TRUE FALSE 145430.533 103851.8207 108676.6298 105777.1058 113063.2684 97867.15561 107795.3377 116569.671 115398.7842 1.2602432 0.899938604 0.941748481 0.916622359 0.979761348 0.848077875 0.934111555 1.010146439 1 16.8162685 4.742076899 24.99562376 0.932944763 1.260243323 0.808495685 0.048631705 128.9100161 916321.6535 0.010458726 0.076656638 55217.52025 -4.742076899 0.327298561 KDS(ph)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHRGDEQGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDSLDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHRGDEQGKR 48 3 Q96TC7;H0YLG5;H0YMB1;Q96TC7-2 Q96TC7 RMDN3 Regulator of microtubule dynamics protein 3 1 KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHRGDEQGKR 164.58 1.28E-21 82174000 56787 33672 32772 36066 55562 25219 57205 31104 138200 TRUE FALSE 53232.80304 36165.10992 33549.36732 36991.51462 51198.38465 32499.3159 48627.64132 34987.40287 115133.5272 0.462357094 0.314114496 0.291395288 0.32129229 0.444687016 0.282274996 0.422358652 0.303885443 1 16.81294849 -4.028555644 0.56150247 9.999968071 0.346396972 0.901967062 0.066690823 407.5780926 4.697343763 4546.462392 0.025916817 9.36E-05 4.028555644 -9.653571099 KDS(ph)LTQAQEQGNLLN ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KDSLTQAQEQGNLLN 15 1 Q5JTD0-4;Q5JTD0-2;Q5JTD0 Q5JTD0-4 TJAP1 Tight junction-associated protein 1 1 KDS(0.998)LT(0.002)QAQEQGNLLN;KDS(0.997)LT(0.003)QAQEQGNLLN;KDS(1)LTQAQEQGNLLN;KDS(1)LTQAQEQGNLLN;KDS(0.999)LT(0.001)QAQEQGNLLN 246.03 4.06E-18 1366983000 3960180 2637930 3023080 2841700 3232740 2209750 3879240 2805720 4377260 TRUE FALSE 3712319.403 2833245.082 3094788.885 2914622.833 2978853.641 2847668.953 3297583.975 3156020.318 3646667.028 1.018003392 0.776940988 0.848662316 0.799256639 0.816870204 0.780896345 0.904273395 0.865453384 1 21.79814704 0.758532842 1.112481036 0.9985598 0.834394468 0.299535572 0.071038203 0.923227297 2.057773486 0.06055486 0.019013718 5.734992334 -0.758532842 -0.164165332 KDS(ph)PHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDSPHSR 7 1 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8W6A0;F8VWU8;F8VPY7;Q8NEY8-6;F8WF16;B7Z8L1;Q8NEY8-3;Q8NEY8-5 F8W0Q9;Q8NEY8-6 PPHLN1 Periphilin-1 1 KDS(0.853)PHS(0.147)R;KDS(0.64)PHS(0.36)R 83.862 0.013456 198096000 249380 145204 218627 189695 179076 152606 218990 164692 232013 TRUE FALSE 233771.751 155955.0552 223812.9357 194562.8949 165012.0933 196660.8748 186154.4825 185254.1587 193288.5314 1.209444498 0.806851054 1.157921445 1.006593063 0.853708661 1.017447199 0.963091194 0.958433267 1 17.56039651 2.98465028 24.92954751 0.958612072 1.026472592 0.119834638 0.113132416 1837.414165 2984159.543 0.032088701 0.035072424 965.273269 -2.98465028 0.06786052 KDS(ph)QNSSQHSVSSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KDSQNSSQHSVSSHR 15 1 A0A087WT53;Q96QZ7-7;Q96QZ7-6;Q96QZ7-2;Q96QZ7;A0A087WXD2;H7C5T8;H7C4U7;H7C535;Q96QZ7-4;Q96QZ7-3;Q96QZ7-5 A0A087WT53 MAGI1 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1" 1 KDS(0.991)QNS(0.008)S(0.002)QHSVSSHR;KDS(0.956)QNS(0.043)S(0.001)QHSVSSHR;KDS(0.946)QNS(0.027)S(0.027)QHSVSSHR;KDS(0.411)QNS(0.294)S(0.294)QHSVSSHR;KDS(0.333)QNS(0.333)S(0.333)QHSVSSHR 210.43 8.87E-10 453857700 162758.8 277121.6 270883.6 295467.7 346968.9 225274.6 313725.5 268630.8 388704.9 TRUE FALSE 152572.0172 297639.9716 277309.0869 303049.9014 319719.3622 290307.72 266685.2738 302169.9467 323827.5411 0.471152073 0.919131123 0.856348061 0.93583733 0.987313683 0.896488665 0.823541052 0.933119974 1 18.30486616 4.739645755 24.99565743 0.905570087 0.471151935 0.86884509 0.05445903 32.13270867 740067.6442 0.012840634 0.079089158 54909.28079 -4.739645755 -0.434418152 KDS(ph)SSVVEWTQAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KDSSSVVEWTQAPK 14 1 Q8TC07-2;Q8TC07-3;Q8TC07;F8WCB5 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 KDS(0.8)S(0.153)S(0.046)VVEWTQAPK;KDS(0.913)S(0.031)S(0.056)VVEWTQAPK;KDS(0.756)S(0.109)S(0.135)VVEWTQAPK 208.17 5.16E-09 1745590000 1566780 875950 1180630 952690 1130510 765390 1663880 1237670 2753630 TRUE FALSE 1468718.037 940806.2494 1208635.101 977137.6383 1041724.305 986345.6679 1414396.641 1392195.824 2294031.364 0.640234506 0.410110456 0.526860757 0.425947811 0.454102032 0.429961719 0.616555058 0.606877415 1 21.12945369 0.683769462 0.983292605 0.999206953 0.476844188 0.822844933 0.073511798 0.3774272 0.631738843 0.063418647 0.020566376 4.828024462 -0.683769462 -0.522362765 KDSEDNPQTLLFSATCPHWVFNVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDSEDNPQTLLFSATCPHWVFNVAK 25 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 131.57 5.16E-05 91587000 100620 98373 86700 87333 109700 78340 110900 93950 123560 FALSE TRUE 94322.37381 105656.6393 88756.56494 89574.11263 101084.6045 100955.4863 94271.57455 105679.8643 102937.0378 0.916311328 1.026420048 0.862241297 0.870183508 0.982004211 0.980749868 0.91581783 1.026645672 1 16.65140265 KDSETGENIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KDSETGENIR 10 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;;;;;; 178.67 3.51E-06 12792380000 8105380 6401060 6277240 5895430 8597500 5828360 6906020 6981090 11312240 FALSE TRUE 7598078.734 6875001.143 6426139.097 6046716.715 7922287.031 7510912.916 5870526.413 7852694.454 9424154.064 0.806234563 0.729508569 0.681879674 0.641619043 0.840636409 0.79698537 0.622923434 0.833251918 1 23.16793169 0.979055334 9.005246271 0.999997687 0.725272271 0.601560015 0.070223767 0.233274741 98.10008757 0.065505774 0.016392378 9.529175689 -0.979055334 -0.274725416 KDSGS(ph)PNPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDSGSPNPAR 10 1 H0YBT0;A0A087WUS5;P01106;P01106-2;H0YBG3;A0A0B4J1R1;A0A494C1T8 H0YBT0 MYC Myc proto-oncogene protein 1 KDS(0.282)GS(0.718)PNPAR 55.196 0.080961 260250000 156170 133970 138190 144850 192620 126980 177460 148250 247130 TRUE FALSE 146395.5985 143889.2782 141467.9321 148567.0962 177492.4022 163637.0647 150851.5205 166759.3388 205882.4065 0.711064151 0.698890598 0.687129777 0.721611423 0.862105729 0.794808393 0.732707195 0.809973721 1 17.65146103 -4.999999999 0.131868797 1.884988404 0.636148016 0.782922497 0.044434769 67.52279268 0.559177667 15.68183175 0.340931277 1.00E-05 4.999999999 -1.248840388 KDSLSVNEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDSLSVNEFK 10 1 Q99584 Q99584 S100A13 Protein S100-A13 0 ; 145.01 5.00E-05 1960720000 5107800 4372800 4396100 4071000 5950600 3245200 5767900 4575500 6672600 FALSE TRUE 4788111.916 4696566.662 4500377.568 4175468.752 5483263.88 4182036.559 4903056.942 5146761.247 5558899.953 0.861341624 0.844873392 0.809580602 0.7511322 0.986393698 0.752313694 0.882019281 0.925859665 1 22.40636799 1.11747629 1.961382477 0.997321405 0.834519543 0.406493455 0.065981825 0.278844219 2.054990144 0.055099543 0.015705468 13.10618487 -1.11747629 -0.162801862 KDSNELS(ph)DS(ph)AGEEDSADLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDSNELSDSAGEEDSADLKR 20 2 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 2 KDS(0.105)NELS(0.895)DS(1)AGEEDSADLKR 132.53 6.09E-05 260870000 1237500 643800 760620 833850 806150 508480 1150400 694150 1267500 TRUE FALSE 1160047.084 691467.6219 778662.2656 855248.0027 742838.2309 655269.9215 977908.1998 780816.1555 1055946.062 1.098585549 0.654832332 0.737407235 0.809935312 0.703481227 0.620552456 0.926096735 0.739447008 1 20.01010471 0.339204707 0.866159972 1.000939525 0.763644751 0.165583793 0.140995059 3.894102971 3.785510395 0.140139975 0.041791322 2.183758997 -0.339204707 -0.237294773 KDSSS(ph)VVEWTQAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDSSSVVEWTQAPK 14 1 Q8TC07-2;Q8TC07-3;Q8TC07;F8WCB5 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 KDS(0.184)S(0.305)S(0.511)VVEWTQAPK 114.99 0.00027299 223890000 309360 189730 232760 224280 230650 131130 301620 242930 500650 TRUE FALSE 289997.7098 203777.8066 238281.1771 230035.4045 212535.6794 168985.1023 256394.8811 273260.3453 417088.2807 0.695290957 0.488572362 0.571296745 0.551526895 0.50957001 0.405154281 0.61472569 0.655161888 1 18.66999325 0.777984094 1.641384167 0.998972007 0.536244979 0.781783495 0.075185915 0.320142818 1.484107074 0.065592399 0.018794515 5.997691098 -0.777984094 -0.462727027 KDT(ph)PRKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDTPRKEK 8 3 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 1 KDT(1)PRKEK 62.408 0.082109 748120000 1550100 520700 929820 890980 933500 413430 1117700 611920 2058500 TRUE FALSE 1453082.008 559253.1698 951875.7695 913844.0552 860186.6756 532780.5295 950111.2612 688319.559 1714923.052 0.847316156 0.326109775 0.555054507 0.532877586 0.50158908 0.31067314 0.554025593 0.401370521 1 20.70971241 -1.221809212 5.08236693 1.000056635 0.489335619 0.51464951 0.150923342 8.42E-05 1.29E-05 0.127096471 0.029953617 0.060005463 1.221809212 -0.510721016 KDTEVLFCFEQFDELTLLHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KDTEVLFCFEQFDELTLLHLR 21 1 Q12931-2;Q12931;I3L0K7 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ;; 232.79 2.30E-27 148370000 368642 297891 252603 243241 420887 265121 307498 317514 289574 FALSE TRUE 345569.3553 319947.1596 258594.8624 249482.9759 387832.2328 341657.1288 261391.5296 357156.3218 241242.2287 1.432457979 1.326248565 1.071930333 1.034159638 1.607646534 1.416240974 1.083523109 1.480488403 1 17.88012294 -1.258217919 4.418104294 0.999852905 1.278544408 0.187652123 0.192775518 0.000271198 4.55E-05 0.181223122 0.042692251 0.055180049 1.258217919 0.278691503 KDTFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KDTFFK 6 1 Q96KP4;Q96KP4-2;J3QKT2;J3QRH4;J3QRA8;J3KRJ8 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 91.065 0.077472 1943600000 1360300 1066600 1100000 1105800 1295100 848760 1539700 1009000 1393800 FALSE TRUE 1275161.251 1145572.174 1126092.519 1134176.7 1193388.07 1093783.234 1308836.279 1134975.871 1161165.776 1.0981733 0.986570736 0.96979479 0.976756914 1.027749952 0.941969921 1.12717435 0.977445163 1 20.14714252 1.757863103 25 1.047556419 0.995255635 0.057738115 0.056832503 14.68319698 19035.27356 0.023800676 0.013199203 57.26155042 -1.757863103 -0.052300784 KDVGRPQPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KDVGRPQPGR 10 2 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ;;;;;;; 187.16 7.09E-07 11766432000 4801259 5281385 4604524 4516724 4815535 3167439 5948839 4741164 6980645 FALSE TRUE 4500756.77 5672424.241 4713745.484 4632630.785 4437342.306 4081827.22 5056865.818 5333108.762 5815530.253 0.773920275 0.97539244 0.810544401 0.796596455 0.763015944 0.701883929 0.869545097 0.917046001 1 22.47147931 1.10737793 2.388698704 0.995243816 0.821238797 0.446114421 0.071300537 0.294147227 3.240363825 0.072432905 0.020021201 12.80495128 -1.10737793 -0.174005019 KDVHMPK ddPTM_SK-BR-3_Pertuzumab_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 ; 81.278 0.013189 867780000 2879900 2561500 2591600 2395000 3020700 1624860 2995100 2542900 3230500 FALSE TRUE 2699652.2 2751156.125 2653073.976 2456459.755 2783466.407 2093930.705 2546012.56 2860386.663 2691308.68 1.003100172 1.022237302 0.985793267 0.91273802 1.034242719 0.778034389 0.946012837 1.062823705 1 21.35987644 3.443756897 4.734100918 0.943962576 1.009209389 0.072213765 0.077588826 0.393184125 20.82861248 0.020600103 0.029238718 2778.157715 -3.443756897 0.065246813 KDWDDDQND ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KDWDDDQND 9 1 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;; 109.02 0.0516 11528300000 13765500 10522700 11610400 10946800 11784900 8705700 14432600 9787400 13516400 FALSE TRUE 12903941.93 11301811.66 11885804.17 11227713.42 10859361.49 11218894.26 12268565.62 11009378.43 11260425.52 1.145955089 1.003675362 1.055537746 0.99709495 0.964382871 0.996311751 1.089529485 0.977705364 1 23.42475801 4.742466509 24.68110252 1.017836637 1.145955148 0.560633293 0.037180175 273.0767475 1725471.861 0.008959718 0.068325301 55267.07869 -4.742466509 0.128118511 KDWYDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDWYDVK 7 1 P61247;E9PFI5;D6RG13;H0Y8L7;H0Y9Y4;D6RI02 P61247 RPS3A 40S ribosomal protein S3a 0 ; 90.629 0.027255 3931400000 7323400 5844800 6384300 5947500 6815200 4810600 7695200 5478200 7855900 FALSE TRUE 6865041.467 6277555.074 6535738.611 6100122.919 6279961.683 6199342.126 6541376.199 6162165.329 6544699.539 1.048946774 0.959181554 0.998630811 0.932070736 0.959549273 0.947230975 0.999492209 0.941550531 1 22.64189553 4.742815122 24.56558004 0.968781494 1.048946815 0.516524474 0.024809828 272.1679636 1571429.282 0.005459519 0.042805094 55311.46002 -4.742815122 0.080165321 KDYEEIGPSICR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KDYEEIGPSICR 12 1 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ; 185.95 1.99E-05 1872800000 1524500 1224920 1294650 1244670 1483910 942450 1532350 1165070 1736410 FALSE TRUE 1429084.266 1315614.351 1325359.709 1276610.339 1367369.694 1214520.016 1302588.343 1310531.554 1446591.953 0.987897287 0.909457811 0.916194582 0.88249512 0.945235242 0.839573325 0.900453193 0.905944175 1 20.4642266 4.741410479 4.739556235 0.905706687 0.992811136 0.233259576 0.041505721 0.229031219 14.43848622 0.008654527 0.066228836 55132.85457 -4.741410479 0.087104449 RFEELGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RFEELGVK 8 1 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 93.111 0.01812 789500000 450620 556770 353330 399890 602410 263780 475200 512550 1186000 FALSE TRUE 422416.4986 597993.8301 361711.1545 410151.8544 555099.1486 339929.0039 403948.1715 576542.9958 988048.9381 0.427525887 0.605226935 0.366086274 0.415112894 0.561813415 0.344040655 0.408834174 0.583516639 1 19.91422297 0.870433438 3.753660587 0.999872549 0.451214179 0.822330252 0.080699746 0.263024916 6.794701562 0.076742789 0.019702815 7.420504587 -0.870433438 -0.54865837 KEAEDSLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEAEDSLRR 9 2 O43776;K7EIU7;O43776-2;K7EJ19;K7EPK2;K7EMQ6 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 78.342 0.016898 284550000 367050 347940 353990 337800 381810 256670 396610 361060 513590 FALSE TRUE 344076.9957 373701.8396 362386.81 346468.5199 351824.1827 330766.4623 337142.0124 406139.1358 427868.5111 0.804165268 0.873403464 0.846958354 0.809754658 0.822271735 0.773056333 0.787957056 0.949214829 1 18.70680798 1.107192062 4.66413511 0.997124 0.821806218 0.839872859 0.028956898 0.089365931 2.998205783 0.032974266 0.008402377 12.79947223 -1.107192062 -0.175317782 KEAESCDCLQGFQLTHSLGGGTGSGMGTLLLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEAESCDCLQGFQLTHSLGGGTGSGMGTLLLSK 33 1 Q3ZCM7;A0A075B736;Q5SQY0 Q3ZCM7 TUBB8 Tubulin beta-8 chain 0 ; 313.68 2.01E-104 2218930000 1823190 1562240 1663540 1506770 2006230 1322250 2407980 1631140 2736900 FALSE TRUE 1709079.792 1677909.875 1702999.954 1545436.269 1848668.789 1703962.11 2046925.754 1834791.42 2280093.709 0.749565593 0.735895138 0.746899107 0.677795067 0.81078632 0.747321087 0.897737556 0.804700005 1 21.12066169 1.09492808 0.549281611 0.999254671 0.727538106 0.758345104 0.045403955 0.376144492 0.287091759 0.043830537 0.020928854 12.44308536 -1.09492808 -0.271716565 KEAESSPFVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KEAESSPFVER 11 1 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;;; 186.16 6.65E-06 7752380000 5197020 5964850 5522220 6052210 6074830 4261960 6859260 5338930 5321610 FALSE TRUE 4871747.795 6406493.7 5653209.666 6207519.955 5597737.356 5492318.665 5830777.641 6005507.163 4433398.912 1.098874225 1.445052392 1.275141213 1.400171759 1.262628847 1.238850546 1.315193547 1.354605638 1 22.07998175 -1.551198893 3.000569145 0.986074275 1.309477656 0.490830859 0.095096987 17011023.37 17036904.97 1881240.928 0.020815346 0.028106134 1.551198893 0.323403382 KEAPPMEKPEVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEAPPMEKPEVVK 13 2 K7EM56;A0A0B4J2B4;S4R417;K7ELC2;P62841;K7EQJ5;S4R456;K7EJ78 K7EM56 RPS15 40S ribosomal protein S15 0 ; 151.9 2.31E-05 498030000 1592870 978730 1289070 1271420 1318570 913170 1650880 1143450 1726620 FALSE TRUE 1493175.11 1051196.188 1319647.349 1304046.79 1215014.831 1176787.355 1403345.87 1286212.25 1438435.968 1.038054626 0.730791089 0.917418209 0.906572707 0.844677732 0.818102009 0.975605381 0.894174144 1 20.45606957 1.281205454 1.076367322 0.988292625 0.865470576 0.128101562 0.084373673 0.737310264 1.750130014 0.072283823 0.02443375 19.10756976 -1.281205454 -0.122822049 KECSEAMEVETSVISIDS(ph)PQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KECSEAMEVETSVISIDSPQK 21 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 KECSEAMEVETSVISIDS(1)PQK;KECSEAMEVETSVIS(0.001)IDS(0.998)PQK;KECSEAMEVETSVISIDS(1)PQK 216.14 3.86E-25 417020000 877250 511460 643410 609120 671090 506170 918240 602500 804590 TRUE FALSE 822344.4884 549329.0306 658671.989 624751.0504 618385.2984 652293.062 780558.4365 677723.4513 670298.7311 1.226832829 0.819528674 0.982654387 0.932048684 0.922551796 0.973137844 1.164493382 1.011076733 1 19.35444468 1.925010336 9.646344072 1.075150547 0.953553314 0.082091195 0.111878431 0.745071926 92.21390309 0.042670008 0.027082753 84.14151661 -1.925010336 -0.121597233 KEDEVEEWQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEDEVEEWQHR 11 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 218.01 7.09E-12 1883750000 2919700 2001430 2458900 2177530 2612500 1961500 2785600 2165570 2606400 FALSE TRUE 2736961.189 2149617.96 2517226.269 2233409.106 2407324.788 2527753.208 2367925.14 2435946.182 2171375.002 1.260473749 0.989980062 1.159277539 1.028569042 1.108663767 1.164125591 1.090518744 1.121844996 1 21.05017747 -1.704495127 3.337412226 0.989024341 1.106329204 0.18280119 0.074523982 0.00583807 0.000516921 0.069217003 0.01489053 0.01974717 1.704495127 0.117304863 KEDGTFYEFGEDIPEAPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KEDGTFYEFGEDIPEAPER 19 1 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;;; 229.68 1.20E-19 4542720000 4812850 4339030 4787450 4522560 5020170 3553440 5600030 4239950 5821990 FALSE TRUE 4511622.31 4660296.296 4901010.575 4638616.546 4625906.099 4579260.443 4760357.49 4769317.091 4850262.258 0.930181106 0.960833878 1.010463005 0.956364069 0.953743499 0.944126358 0.981463937 0.983311177 1 22.20963133 1.231999494 2.094290394 0.997327878 0.965258401 0.269923178 0.021361188 0.50505529 3.823624403 0.020947299 0.006061232 17.06080402 -1.231999494 -0.032069477 KEDIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEDIQK 6 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 91.065 0.077472 429200000 623170 474780 529840 513130 548920 350030 648960 501230 648750 FALSE TRUE 584166.9021 509933.2052 542408.055 526297.7845 505810.0374 451077.9787 551654.4726 563809.6688 540469.4339 1.080850952 0.943500545 1.003586921 0.973778999 0.935871681 0.834604051 1.020695044 1.043185116 1 19.0438535 1.56976402 16.5842513 1.024432956 0.961561801 0.169954387 0.061646118 0.304087483 121.8216984 0.031775269 0.014733878 37.13334051 -1.56976402 -0.062871154 KEDLEAEEEYSSLCELLGSPEQRPGMQDPLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEDLEAEEEYSSLCELLGSPEQRPGMQDPLSPK 33 2 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4;A8MXE8;Q7Z5J4-4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 KEDLEAEEEYSSLCELLGSPEQRPGMQDPLS(1)PK;KEDLEAEEEYSSLCELLGSPEQRPGMQDPLS(1)PK 232.78 2.05E-38 109904000 239628 109562 146218 147567 140117 97534 204200 108855 199112 TRUE FALSE 224630.1112 117674.0845 149686.36 151353.8191 129112.776 125690.4825 173582.1057 122445.7864 165878.9209 1.35418117 0.709397456 0.902383252 0.912435518 0.778355534 0.757724259 1.0464386 0.73816363 1 17.33977104 4.749129762 24.92168329 0.856003334 1.354181462 0.660827692 0.112251592 884.454259 2085470.702 0.025290906 0.363921905 56121.56357 -4.749129762 0.498178128 KEDLELIMTEMEISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KEDLELIMTEMEISR 15 1 Q9NX55 Q9NX55 HYPK Huntingtin-interacting protein K 0 ;; 134.21 5.86E-05 106381000 255583 231592 251179 252486 264411 192776 300240 231337 290526 FALSE TRUE 239586.5163 248739.3127 257137.0845 258965.2182 243645.2266 248427.3017 255221.7993 260219.9337 242035.3337 0.989882397 1.027698348 1.062394819 1.069947987 1.006651479 1.026409235 1.054481572 1.075132005 1 17.88485815 4.678682415 2.360886973 1.044418104 0.980936848 0.294990457 0.0252712 0.582557873 4.361211708 0.005988153 0.071891697 47718.02005 -4.678682415 -0.063481255 KEDLVFIFWAPESAPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KEDLVFIFWAPESAPLK 17 1 G3V1A4;E9PQB7;P23528;E9PP50;E9PK25;Q9Y281;Q9Y281-3 G3V1A4;P23528;Q9Y281 CFL1;CFL2 Cofilin-1;Cofilin-2 0 ;; 183.56 1.10E-09 9452036000 20619980 16748850 17012770 16378510 20817680 13194590 21968660 18092510 23864670 FALSE TRUE 19329412.26 17988952.28 17416320.94 16798810.3 19182743.39 17003653.94 18674663.38 20351399.7 19881502.41 0.972230965 0.904808496 0.876006279 0.844946722 0.964853812 0.85524995 0.939298399 1.023634899 1 24.24492345 1.395925715 3.982613094 1.010464439 0.900084056 0.532760702 0.041460031 0.157349787 4.072680475 0.028385072 0.009789917 24.88431642 -1.395925715 -0.110380383 KEDLYLKPIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEDLYLKPIQR 11 2 P13639 P13639 EEF2 Elongation factor 2 0 ; 177.93 4.37E-06 11788900000 11630100 10825900 11139900 10579600 12583400 8344100 14553300 11040700 14053100 FALSE TRUE 10902192.8 11627460.9 11404143.69 10851090.45 11595150.52 10752906.21 12371167.77 12419155.7 11707546.82 0.931210694 0.993159462 0.974084824 0.926845787 0.990399671 0.918459382 1.056683177 1.060782065 1 23.48093547 1.684026558 8.076296701 1.043484959 0.962495184 0.61489819 0.030684556 0.076616477 9.08322824 0.013892381 0.007304456 48.30883425 -1.684026558 -0.080989775 KEDMEYALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEDMEYALR 9 1 Q13242;H0YIB4 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 81.525 0.033731 277040000 128020 152810 113580 148830 171420 103580 149770 157300 168430 FALSE TRUE 120007.4567 164124.2114 116274.1712 152649.2298 157957.3647 133481.8645 127313.3789 176939.2513 140317.9449 0.855253808 1.169659458 0.828647906 1.087881025 1.125710363 0.951281496 0.907320721 1.260988047 1 17.09834 1.25032713 24.99996852 1.130494099 0.992927544 0.173667089 0.127777515 331.1407592 703574.3245 0.080461055 0.028862861 17.79619395 -1.25032713 -0.137566555 KEDMMFHKIY(ph)IQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEDMMFHKIYIQK 13 2 O43306-2;O43306 O43306-2 ADCY6 Adenylate cyclase type 6 1 KEDMMFHKIY(1)IQK;KEDMMFHKIY(1)IQK 74.326 0.012537 320872000 69597 468550 279869 353460 457060 325420 270390 325140 410580 TRUE FALSE 65241.048 503241.9295 286507.6248 362530.382 421164.3513 419363.4712 229847.5297 365734.4447 342051.5456 0.190734551 1.471245887 0.837615349 1.059870615 1.231289134 1.226024196 0.671967523 1.069237808 1 18.38385422 4.756991984 24.44626194 1.057858937 0.190733535 0.615049711 0.21861866 2195.166978 2911474.166 0.052646462 1.755140592 57146.80883 -4.756991984 -0.867125401 KEDMTYAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEDMTYAVR 9 1 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ; 76.332 0.057293 991430000 926950 1328690 1082610 1114190 1418890 841230 1276000 1355850 1280730 FALSE TRUE 868933.8542 1427067.59 1108290.02 1142782.002 1307456.103 1084079.445 1084675.646 1525130.857 1066967.889 0.814395506 1.337498161 1.038728561 1.071055665 1.22539405 1.016037554 1.016596335 1.42940652 1 20.02508533 KEDQDRS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KEDQDRSPR 9 2 O60318 O60318 MCM3AP Germinal-center associated nuclear protein 1 KEDQDRS(1)PR;KEDQDRS(1)PR;KEDQDRS(1)PR;KEDQDRS(1)PR 131.36 0.00026411 680167000 1365090 985020 1192170 1047460 1143450 1000790 1451910 1253890 1229840 TRUE FALSE 1279651.454 1057951.906 1220448.835 1074339.597 1053648.049 1289701.827 1234209.574 1410440.927 1024571.759 1.248962254 1.032579608 1.191179461 1.048574282 1.028378969 1.258771594 1.204610183 1.376615073 1 19.9665896 2.224159329 24.98392075 1.225778716 1.107676139 0.152895157 0.114318965 350.2996747 607709.6409 0.038072714 0.028244356 167.5557474 -2.224159329 -0.118102577 KEDQYMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEDQYMK 7 1 P53004 P53004 BLVRA Biliverdin reductase A 0 114.89 0.0093038 140920000 384900 377660 360710 354670 420610 240010 378770 384840 499970 FALSE TRUE 360809.7961 405622.3394 369266.2115 363771.4327 387576.9873 309296.9908 321976.9548 432888.1211 416521.7771 0.866244734 0.97383225 0.886547191 0.873355135 0.93050834 0.742570996 0.773013495 1.039292889 1 18.6680324 KEDS(ph)LRGT(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEDSLRGTPAR 11 2 O60318 O60318 MCM3AP Germinal-center associated nuclear protein 2 KEDS(1)LRGT(1)PAR 66.262 0.069736 180840000 72473 125770 102240 121430 121170 107920 110290 99147 96176 TRUE FALSE 67937.0443 135082.1417 104665.1811 124546.0994 111653.797 139074.7521 93753.03838 111525.7212 80123.60428 0.847902998 1.685921931 1.306296466 1.554424573 1.3935194 1.73575257 1.170105105 1.391920923 1 16.2899397 0.713671699 1.123179101 1.004417002 1.42915191 0.172655311 0.256465225 1.43075624 3.099373085 0.214722788 0.067039906 5.172157002 -0.713671699 0.424734908 KEECPAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KEECPAVR 8 1 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 ;;;;;;; 177.36 0.00040932 9542340000 13829770 12442910 12340550 11892620 10929930 9168770 15494520 10909900 10508690 FALSE TRUE 12964189.38 13364196 12633273.67 12197804.76 10071537.39 11815645.06 13171260.57 12272025.03 8754721.75 1.48082255 1.526512936 1.443024009 1.393282975 1.150412049 1.349631135 1.504475065 1.401760716 1 23.0616299 -3.552617776 0.227938961 5.40E-21 1.472327206 0.5998138 0.104707179 58.80046368 1.066254275 28.08706035 0.206340328 0.000280145 3.552617776 1.472327206 KEEEESQPAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEEEESQPAKK 11 2 O75400-3;O75400;O75400-2;F5H578 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 101.39 0.0018668 119800000 480900 247810 351660 328770 348830 225200 458250 292430 510330 FALSE TRUE 450801.3274 266158.1102 360001.5413 337206.7948 321434.2989 290211.5842 389539.6667 328940.5292 425152.6261 1.06032822 0.626029557 0.846758362 0.793142919 0.756044486 0.682605649 0.916234883 0.773699864 1 18.69762132 0.282170477 0.79309652 1.00234715 0.787107217 0.182591629 0.121661008 4.020212109 3.245031681 0.134385233 0.036975746 1.915007491 -0.282170477 -0.215239933 KEEELQAALAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KEEELQAALAR 11 1 P35579;P35749;P35749-2;P35749-4;P35749-3;Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 P35579;P35749;Q7Z406 MYH9;MYH11;MYH14 Myosin-9;Myosin-11;Myosin-14 0 ;;;;; 213.63 2.99E-09 3522640000 5813550 5250510 4908520 4897990 5179990 3557170 6003560 5164930 5242170 FALSE TRUE 5449690.283 5639263.224 5024952.412 5023680.716 4773174.48 4584067.233 5103381.912 5809782.88 4367217.961 1.247863132 1.291271302 1.150607196 1.150316004 1.092955406 1.04965387 1.168565883 1.330316676 1 22.0582831 3.833496632 2.363334599 1.135310658 1.269935331 0.295038893 0.086848522 0.363832564 4.001249345 0.022746227 0.048751479 6815.482891 -3.833496632 0.134624673 KEEENADS(ph)DDEGELQDLLSQDWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEEENADSDDEGELQDLLSQDWR 23 1 Q96NB3;J3QQQ3 Q96NB3 ZNF830 Zinc finger protein 830 1 KEEENADS(1)DDEGELQDLLSQDWR;KEEENADS(1)DDEGELQDLLSQDWR 211.87 2.50E-25 216549000 238721 180905 191285 201446 201841 145050 226073 158573 238690 TRUE FALSE 223779.8787 194299.3944 195822.3705 206615.4454 185989.222 186923.5803 192175.4524 178371.1881 198851.097 1.125364064 0.977109995 0.984768872 1.039046043 0.935319065 0.940017848 0.966428927 0.897008821 1 17.601329 7.481969136 1.184382188 0.964430554 140.3622338 0.613395595 0.039044574 953.4515173 2.02828353 0.010737171 360499.7164 30336755.8 -7.481969136 139.3978032 KEEESAGGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEEESAGGTK 10 1 P61081 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ; 124.12 0.00071195 421890000 1210580 693760 931000 897240 907210 641110 996800 751100 1155900 FALSE TRUE 1134811.959 745126.7123 953083.7597 920264.6974 835961.3861 826188.0494 847339.0938 844876.4884 962972.8226 1.178446507 0.773777509 0.989730694 0.955649709 0.868104859 0.857955728 0.87992005 0.877362755 1 19.87713556 2.741718875 24.35805936 0.885375772 0.943518771 0.081929756 0.105708546 565.4396424 4360958.095 0.030496653 0.031140273 551.7201874 -2.741718875 0.058142999 KEEEVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEEEVER 7 1 D6RCC6;E7EUJ7;Q8TC20-2;Q8TC20-4;Q8TC20;Q8TC20-3;Q8TC20-5 D6RCC6 CAGE1 Cancer-associated gene 1 protein 0 87.251 0.031233 1344000000 1844800 1498100 1633100 1636100 1956200 1474500 2303600 1681500 2555200 FALSE TRUE 1729337.261 1609020.883 1671837.903 1678085.096 1802567.943 1900164.213 1958196.566 1891438.976 2128720.613 0.812383387 0.755862875 0.785372159 0.788306876 0.846784652 0.892632035 0.919893646 0.888533218 1 21.02155518 1.972496439 0.577377763 0.98297051 0.76535579 0.880287575 0.025472792 0.230172378 0.158458795 0.022827276 0.015037069 93.86343413 -1.972496439 -0.21761472 KEEGEAFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEEGEAFAR 9 1 P61019;P61019-2;H7C125 P61019 RAB2A Ras-related protein Rab-2A 0 92.445 0.016149 13290000000 1473100 1823000 1758200 1882900 2011600 1636100 2458800 1950200 2316800 FALSE TRUE 1380901.301 1957976.817 1799905.334 1931218.402 1853617.05 2108415.51 2090125.766 2193686.763 1930111.113 0.715451712 1.014437357 0.93253975 1.000573692 0.960368052 1.09238038 1.082904374 1.136559832 1 20.88025247 6.075488135 0.449001971 1.066464935 4.15E-23 0.621552624 0.071297179 10.99760528 0.674295888 0.043447106 8.052808821 1189838.822 -6.075488135 -1.066464935 KEELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KEELLK 6 1 P42766;F2Z388 P42766 RPL35 60S ribosomal protein L35 0 ;;;; 102.71 0.056608 5883670000 10645200 8608390 9275600 9685100 10791300 7593220 12927400 8965370 12486100 FALSE TRUE 9978935.934 9245764.153 9495621.612 9933636.063 9943794.828 9785259.348 10989056.38 10084716.18 10402089.25 0.959320354 0.888837226 0.912857157 0.954965472 0.95594208 0.940701345 1.056427812 0.969489488 1 23.31036999 2.340857265 1.091519216 1.011863071 0.915027641 0.478614409 0.032904582 0.342817264 0.801016772 0.0204903 0.01274983 219.2084365 -2.340857265 -0.096835429 KEELMFFLWAPELAPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEELMFFLWAPELAPLK 17 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 147.56 6.33E-07 262700000 563690 523100 468840 435390 710360 347500 553390 583920 724050 FALSE TRUE 528409.6491 561830.8683 479961.1062 446562.8445 654571.1911 447817.6088 470414.3069 656823.6974 603201.3775 0.876008691 0.931415095 0.795689672 0.740321328 1.085161963 0.742401502 0.779862786 1.088896216 1 19.2022802 1.234307684 24.99886926 1.04444818 0.848211782 0.374523847 0.104380972 115.7463815 680316.2887 0.083798056 0.023831961 17.15172024 -1.234307684 -0.196236398 KEELTLEGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KEELTLEGIR 10 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3KTB5;J3KTN0 P60842;J3KTN0 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;;;; 140.78 6.20E-05 7084100000 9110410 9440280 8945370 8972440 10755280 7076620 9988380 8893240 10472310 FALSE TRUE 8540205.701 10139248.15 9157558.401 9202688.001 9910603.694 9119525.315 8490715.147 10003580.59 8724413.807 0.978885904 1.16216956 1.049647415 1.05482021 1.13596213 1.045288029 0.973213254 1.146619224 1 23.05662677 2.016305645 24.80996213 1.030038542 1.083999049 0.051600824 0.06634379 424.3258703 645633.2601 0.022816341 0.016845503 103.8258858 -2.016305645 0.053960506 KEENLADWYSQVITK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEENLADWYSQVITK 15 1 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 200.94 1.07E-08 794750000 2363200 1924490 2136630 2050750 2449800 1673580 2687700 1990300 2842500 FALSE TRUE 2215291.53 2066981.242 2187311.873 2103375.717 2257402.59 2156715.378 2284704.336 2238793.336 2368068.387 0.93548461 0.872855384 0.923669217 0.888224229 0.953267483 0.910748773 0.964796603 0.945409072 1 21.17527931 1.424178185 0.460777266 1.000873692 0.897583899 0.595319983 0.023493046 0.534022028 0.309327614 0.02317222 0.014794325 26.55694936 -1.424178185 -0.103289793 KEEPEPETEAVSS(ph)SQEIPTMPQPIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEEPEPETEAVSSSQEIPTMPQPIEK 26 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 KEEPEPETEAVS(0.009)S(0.495)S(0.495)QEIPTMPQPIEK 140.52 1.93E-07 150000000 231610 150610 176740 160020 199380 131590 234830 147350 270370 TRUE FALSE 217113.9435 161761.3211 180932.3563 164126.3841 183721.4991 169577.8968 199619.4216 165746.9719 225243.5003 0.963907696 0.718161993 0.803274483 0.728662021 0.815657272 0.752864773 0.886238321 0.735856847 1 17.78112595 -4.999954087 0.435910079 5.196018066 0.793339897 0.390705615 0.077197848 1062.554704 6.500627407 4288.434248 0.038222145 1.00E-05 4.999954087 -4.402678169 KEEPEPETEAVSSS(ph)QEIPTMPQPIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEEPEPETEAVSSSQEIPTMPQPIEK 26 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 KEEPEPETEAVS(0.012)S(0.103)S(0.885)QEIPTMPQPIEK 205.42 2.08E-25 147030000 192740 116440 143870 146610 157380 115930 190140 129750 227180 TRUE FALSE 180676.7475 125061.3388 147282.6643 150372.2608 145020.0096 149397.109 161630.2722 145949.5731 189262.1904 0.954637306 0.660783533 0.778193806 0.794518232 0.766238673 0.789365846 0.854001911 0.771150185 1 17.5300267 -0.664918266 0.38724453 1.069636771 0.76760653 0.393403728 0.075970622 9.115251744 1.201454903 0.851125749 0.049247752 0.216312559 0.664918266 -0.302030241 KEEPSNNVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KEEPSNNVK 9 1 Q14974;Q14974-2;J3KTM9;J3QRG4 Q14974 KPNB1 Importin subunit beta-1 0 ;; 131.82 0.000517 409913000 633106 558608 594887 613256 753414 465105 838680 675550 1016160 FALSE TRUE 593481.0256 599967.9176 608998.0006 628993.1872 694243.9036 599373.2632 712927.7199 759893.9046 846556.3314 0.701053201 0.708715883 0.719382725 0.743002165 0.820079985 0.708013443 0.842150361 0.897629462 1 19.69124655 1.188983779 0.603526408 1.007917648 0.711406711 0.875177311 0.034864837 0.231287091 0.208276888 0.032937643 0.01521469 15.45196724 -1.188983779 -0.296510936 KEEPSQNDIS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KEEPSQNDISPK 12 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 KEEPSQNDIS(1)PK;KEEPSQNDIS(1)PK;KEEPSQNDIS(1)PK;KEEPSQNDIS(1)PK;KEEPSQNDIS(1)PK 164.01 3.58E-05 1707180000 2763070 1178100 1813780 1590850 1542380 1289950 2268680 1238180 1861660 TRUE FALSE 2590134.381 1265327.75 1856803.718 1631673.904 1421247.696 1662337.624 1928512.495 1392769.499 1550936.919 1.670044957 0.815847333 1.19721421 1.052056911 0.916380079 1.071828005 1.243449989 0.898018147 1 20.56470858 4.751902077 24.85267595 1.043897806 1.6700454 0.702499472 0.131508083 1222.341952 2276953.981 0.030874302 0.598419045 56480.96099 -4.751902077 0.626147594 KEEQEVQATLESEEVDLNAGLHGNWTLENAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KEEQEVQATLESEEVDLNAGLHGNWTLENAK 31 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;; 243.24 3.31E-46 346879000 255816 169541 197854 190855 210663 154664 269732 188734 274168 FALSE TRUE 239804.9332 182093.992 202547.1903 195752.6624 194118.3778 199312.986 229288.1907 212297.8554 228407.5896 1.049899146 0.797232668 0.886779597 0.857032215 0.849877091 0.872619804 1.003855393 0.929469357 1 17.80125106 1.760073705 11.75103631 0.974553544 0.873037736 0.278337736 0.067945766 0.249445817 129.9100497 0.028762524 0.015817887 57.55376047 -1.760073705 -0.101515808 KEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK 41 1 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ;;; 450.08 1.86E-258 3949030900 2298782.7 1966853.8 2436318.1 2105599 2464773 1764678.5 2816988.2 2015113.3 2146405 FALSE TRUE 2154905.994 2112481.702 2494108.716 2159632.235 2271199.671 2274112.536 2394606.971 2266704.631 1788156.139 1.205099458 1.181374297 1.394793587 1.207742539 1.270134985 1.271763962 1.339148701 1.2676212 1 20.77004129 -0.676209136 7.12152665 1.000000006 1.274303752 0.632473837 0.063811064 0 0 0.060877335 0.014348925 0.210761298 0.676209136 0.274303746 KEES(ph)DEEETASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEESDEEETASK 12 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 KEES(1)DEEETASK;KEES(1)DEEETASK 198.98 1.08E-07 509830000 985370 344180 518250 536410 569660 424110 626920 442710 589600 TRUE FALSE 923697.4506 369663.4453 530543.1347 550175.1887 524921.2015 546543.6721 532919.166 497983.318 491191.951 1.880522367 0.752584493 1.080113657 1.120081849 1.068668166 1.112688575 1.084950934 1.013826299 1 18.90592739 4.750358559 24.90278521 1.029835652 1.880522906 0.86554106 0.105460506 656.1364344 1384928.658 0.026921143 0.443731744 56280.57935 -4.750358559 0.850687254 KEES(ph)EES(ph)DDDMGFGLFD ddPTM_SK-BR-3_Pertuzumab_2h_R1 36 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 228.15 7.41E-16 97022271000 52537935 30654165 38350743 36982693 38125236 27635396 50361822 31389449 46299626 TRUE FALSE 49249679.43 32923831.27 39260440.73 37931731.51 35131033.75 35613286.2 42810534.33 35308490.8 38571919.31 1.276827296 0.853569951 1.017850328 0.98340275 0.910792991 0.923295673 1.109888621 0.915393671 1 25.2010476 -0.148316651 6.905003572 0.999999996 0.99003293 0 0.121271117 0 0 0.104592948 0.024652794 0.710695146 0.148316651 -0.009967065 KEES(ph)EESDDDMGFGLFD ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KEESEESDDDMGFGLFD 17 1 P05387;H0YDD8;P05386-2;P05386 P05387;P05386 RPLP2;RPLP1 60S acidic ribosomal protein P2;60S acidic ribosomal protein P1 1 KEES(0.716)EES(0.284)DDDMGFGLFD;KEES(0.999)EES(0.001)DDDMGFGLFD;KEES(0.633)EES(0.367)DDDMGFGLFD;KEES(0.944)EES(0.056)DDDMGFGLFD;KEES(0.988)EES(0.012)DDDMGFGLFD 238.05 3.27E-20 3369578000 3126420 1765820 2385200 2308250 2369930 1920963 2713570 1901250 2913910 TRUE FALSE 2930742.953 1896563.15 2441778.07 2367483.603 2183805.258 2475513.834 2306695.37 2138625.248 2427559.596 1.207279507 0.781263271 1.005857106 0.975252515 0.899588731 1.019754093 0.950211634 0.880977444 1 21.21107528 KEES(ph)SPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEESSPSR 8 1 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 1 KEES(0.815)S(0.184)PS(0.001)R 75.474 0.023456 152860000 327120 205320 266630 250180 240320 243790 324310 258360 223390 TRUE FALSE 306646.1431 220522.1064 272954.5895 256600.0424 221446.2366 314168.2154 275682.7262 290616.8147 186104.7658 1.647707095 1.184935299 1.46667168 1.378793505 1.189900944 1.688125578 1.481330825 1.561576424 1 17.50575548 2.249176195 24.99852059 1.481463486 1.360801872 0 0.219827564 573.9201623 1351518.769 0.067772163 0.056147826 177.4909423 -2.249176195 -0.120661614 KEESEES(ph)DDDMGFGLFD ddPTM_SK-BR-3_Pertuzumab_2h_R1 18 KEESEESDDDMGFGLFD 17 1 P05387;H0YDD8;P05386-2;P05386 P05387;P05386 RPLP2;RPLP1 60S acidic ribosomal protein P2;60S acidic ribosomal protein P1 1 KEES(0.02)EES(0.98)DDDMGFGLFD;KEESEES(1)DDDMGFGLFD;KEESEES(1)DDDMGFGLFD;KEES(0.109)EES(0.891)DDDMGFGLFD;KEES(0.001)EES(0.999)DDDMGFGLFD;KEES(0.202)EES(0.798)DDDMGFGLFD;KEES(0.058)EES(0.942)DDDMGFGLFD;KEES(0.002)EES(0.998)DDDMGFGLFD;KEES(0.157)EES(0.843)DDDMGFGLFD;KEES(0.002)EES(0.998)DDDMGFGLFD;KEES(0.002)EES(0.998)DDDMGFGLFD;KEES(0.162)EES(0.838)DDDMGFGLFD;KEES(0.084)EES(0.916)DDDMGFGLFD;KEES(0.011)EES(0.989)DDDMGFGLFD;KEES(0.287)EES(0.713)DDDMGFGLFD;KEES(0.071)EES(0.929)DDDMGFGLFD;KEES(0.003)EES(0.997)DDDMGFGLFD;KEESEES(1)DDDMGFGLFD 254.58 3.46E-26 8367679000 15688600 10636394 12455468 12821919 13308279 9289737 14939971 10210498 13507768 TRUE FALSE 14706678.53 11423923.68 12750917.58 13150951.15 12263100.45 11971533.27 12699861.04 11485301.15 11253234.26 1.306884598 1.015168032 1.133089145 1.168637464 1.089740084 1.06383045 1.12855209 1.02062224 1 23.42383637 2.847041668 0.016458925 3.00E-06 2.213424734 0.339969055 0.073794495 1393.1906 8.319566767 531.5939714 586.1588739 703.1397789 -2.847041668 2.213421735 KEESEESDDDMGFGLFD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEESEESDDDMGFGLFD 17 1 P05387;H0YDD8;P05386-2;P05386 P05387;P05386 RPLP2;RPLP1 60S acidic ribosomal protein P2;60S acidic ribosomal protein P1 0 101.53 0.021815 30637000 120600 97039 103290 99226 125670 84955 114770 107790 179130 FALSE TRUE 113051.8613 104223.8685 105740.0876 101772.3071 115800.3851 109480.1294 97561.30397 121247.8188 149232.0458 0.757557539 0.698401392 0.708561536 0.681973544 0.775975324 0.733623457 0.653755723 0.812478433 1 17.18719784 0.945392224 4.918405176 0.999914416 0.712718815 0.868659625 0.035238986 0.088838718 6.363082496 0.032681979 0.008268842 8.81844933 -0.945392224 -0.287195602 KEESEKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KEESEKPR 8 2 P83916;J3KS05;K7ELA4 P83916 CBX1 Chromobox protein homolog 1 0 ;; 99.802 0.0036867 368459000 515910 357654 406924 404361 432954 294994 486950 387026 560052 FALSE TRUE 483620.114 384135.0743 416576.4294 414737.5878 398951.5393 380153.979 413936.3681 435347.048 466575.7031 1.036530858 0.823307068 0.892837811 0.888896668 0.855062826 0.814774487 0.887179434 0.933068407 1 18.83175166 1.00202745 2.667885019 0.999150191 0.876023259 0.262902132 0.060793386 0.301056432 4.912947912 0.051987782 0.013932858 10.04679289 -1.00202745 -0.123126932 KEESS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEESSPSR 8 1 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 1 KEES(0.084)S(0.887)PS(0.029)R;KEES(0.09)S(0.82)PS(0.09)R 88.596 0.0069133 40421000 495780 311760 438370 379160 368170 358710 459570 374600 350970 TRUE FALSE 464750.0148 334843.0348 448768.3434 388889.8875 339255.4133 462263.7538 390661.7449 421369.6346 292390.8396 1.589482131 1.145189894 1.534823539 1.330034443 1.160280581 1.58097892 1.336094337 1.441117769 1 18.15753859 -1.214268126 4.784413733 0.999934261 1.377668455 0.37804338 0.156427083 9.74E-05 1.60E-05 0.134489284 0.031693928 0.061056496 1.214268126 0.377734195 KEESSPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEESSPSR 8 1 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 0 ; 99.136 0.011268 183338000 264850 244110 237090 241450 280720 195999 263250 259830 270120 FALSE TRUE 248273.5113 262184.1584 242713.8868 247646.0158 258673.3836 252580.7295 223778.1064 292270.3475 225035.227 1.103265096 1.165080516 1.078559522 1.100476664 1.149479515 1.122405292 0.994413672 1.29877598 1 17.77979133 -1.221281609 4.090337532 0.99992406 1.116330199 0.200269756 0.077108247 4.83E-05 9.20E-06 0.067566916 0.015915294 0.060078405 1.221281609 0.116406139 KEETPGT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 KEETPGTPK 9 1 Q99442 Q99442 SEC62 Translocation protein SEC62 1 KEET(0.035)PGT(0.965)PK;KEET(0.007)PGT(0.993)PK;KEET(0.003)PGT(0.997)PK;KEET(0.003)PGT(0.997)PK;KEET(0.002)PGT(0.998)PK;KEET(0.004)PGT(0.996)PK;KEET(0.019)PGT(0.981)PK 100.73 0.0026159 7966640000 35026620 14901280 18489710 16454560 20416120 16444690 29930130 19799340 18194650 TRUE FALSE 32834366.38 16004586.28 18928294.65 16876811.87 18812720.29 21192005.05 25442384.86 22271331.18 15157845.37 2.16616317 1.055861561 1.248745728 1.113404409 1.241121005 1.398088219 1.678496134 1.469293995 1 23.85356136 2.007448797 13.47710572 1.478058639 1.297580838 0 0.352947763 2.177106362 3917.413557 0.123518253 0.089964861 101.7299421 -2.007448797 -0.180477801 KEETQPPVALKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEETQPPVALKK 12 2 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ; 100.55 0.0017826 250400000 663350 483330 573030 556810 681000 436860 770720 498140 1064970 FALSE TRUE 621832.1076 519116.2561 586622.5422 571098.6873 627517.007 562974.3902 655157.691 560333.8755 887219.627 0.700877312 0.585104567 0.661192025 0.64369483 0.707284857 0.6345378 0.738439132 0.631561632 1 19.75893176 -5 0.262688419 3.238450369 0.633411228 0.844763893 0.045186508 65.75348219 0.644424084 79.48263444 0.052509963 1.00E-05 5 -2.60503914 KEEVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEEVSR 6 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ; 105.95 0.052177 360470000 846540 655370 772590 794130 787900 624350 859090 691660 907120 FALSE TRUE 793556.5725 703894.2767 790916.1996 814508.7203 726021.5122 804589.7095 730277.4299 778015.2735 755715.8118 1.050072739 0.931427219 1.046578869 1.077797642 0.960707055 1.064672324 0.966338693 1.029507735 1 19.52748428 3.932404552 15.72361069 1.018706853 0.983118268 0.058854784 0.047269049 9.710712706 3413.560359 0.011055354 0.019936341 8558.635911 -3.932404552 -0.035588585 KEEWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KEEWDR 6 1 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 0 ;;; 101.99 0.057602 2125450000 3394870 3049420 3357860 3263290 3521480 2537120 4085620 3112700 3992870 FALSE TRUE 3182391.147 3275202.23 3437510.025 3347031.546 3244917.166 3269545.357 3473019.21 3501327.447 3326434.202 0.956697458 0.984598531 1.033391859 1.006192019 0.975494168 0.98289795 1.044066709 1.052576794 1 21.66554507 1.725678178 8.409053378 1.035700577 0.994379935 0.391699911 0.024279219 0.118724509 24.88198639 0.011949502 0.006369318 53.17141015 -1.725678178 -0.041320642 KEFSPFGTITSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEFSPFGTITSAK 13 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;H0YAP2;H0YB86 P11940-2 PABPC1 Polyadenylate-binding protein 1;Polyadenylate-binding protein 0 ; 203.27 1.40E-07 1501940000 3810400 3142200 3744700 3420000 3647400 2873700 4498100 3312600 4735600 FALSE TRUE 3571913.866 3374851.757 3833526.052 3507762.99 3360947.917 3703290.539 3823651.663 3726185.402 3945197.767 0.905382715 0.855432847 0.971694267 0.889122218 0.851908603 0.938683118 0.969191379 0.944486341 1 21.91166619 2.007662731 24.38086355 0.964336364 0.899238208 0.493285627 0.0353372 126.2646834 401739.5127 0.013303511 0.009805143 101.7800666 -2.007662731 -0.065098157 KEGDLIAAQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KEGDLIAAQAR 11 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;; 128.57 0.00042197 1755580000 4178230 4932950 3703580 3746010 5509780 2878110 4531470 4614030 6086500 FALSE TRUE 3916722.043 5298190.751 3791430.667 3842138.959 5077064.104 3708973.635 3852018.142 5190101.802 5070623.83 0.77243396 1.044879472 0.747724697 0.757725102 1.001270115 0.731462984 0.759673419 1.023562776 1 22.27373182 -1.328064768 5.233272729 1.000045257 0.851371759 0.118890112 0.123870355 6.17E-05 7.92E-06 0.113107586 0.026651606 0.046982404 1.328064768 -0.148673498 KEGGLGPLNIPLLADVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEGGLGPLNIPLLADVTR 18 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ; 220.28 1.10E-18 1593340000 2970300 3236400 3137600 3165500 3682400 2448670 3689900 3127500 3889300 FALSE TRUE 2784394.225 3476026.423 3212025.354 3246732.089 3393199.158 3155561.278 3136633.75 3517975.259 3240150.704 0.859340963 1.072797762 0.99131974 1.002031197 1.04723498 0.973893367 0.968051809 1.085744331 1 21.62762949 4.752580493 24.8551111 1.01391206 0.859340849 0.608015805 0.039843572 1644.073796 2914638.6 0.0092449 0.195561009 56569.25934 -4.752580493 -0.154571211 KEGVFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEGVFAK 7 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 103.56 0.013385 2348300000 4174600 3435700 3602100 3386600 3836100 2609100 4195100 3466900 4251500 FALSE TRUE 3913319.238 3690082.803 3687543.513 3473505.89 3534828.18 3362304.815 3566083.7 3899750.097 3541897.184 1.104865284 1.041837922 1.041120993 0.980690774 0.998004176 0.949294867 1.00682869 1.101034246 1 21.7560909 5.01991629 0.780373253 1.004530405 1.197733202 0.353833944 0.039816616 4.170087698 1.434990553 0.01387151 0.774335832 104692.6733 -5.01991629 0.193202797 KEIEDAAQFATADPEPPLEELGYHIYSSDPPFEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEIEDAAQFATADPEPPLEELGYHIYSSDPPFEVR 35 1 P08559-3;P08559;P08559-2;P08559-4;Q5JPU3 P08559-3 PDHA1 "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial" 0 108.11 1.14E-05 24478000 59763 52064 51547 41958 69243 46440 51653 52568 107990 FALSE TRUE 56022.54051 55918.87273 52769.71918 43034.71331 63804.93409 59846.47411 43908.11217 59131.23052 89965.77136 0.6227095 0.621557198 0.58655329 0.478345405 0.709213439 0.665213816 0.488053529 0.657263642 1 16.45708859 0.969155384 23.83002252 1.000000002 0.594177848 0.762252106 0.070380426 1019.688829 787795.2166 0.064739776 0.016184944 9.314410708 -0.969155384 -0.405822153 KEKPELSEPSHLNGPS(ph)SDPEAAFLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEKPELSEPSHLNGPSSDPEAAFLSR 26 2 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 KEKPELSEPSHLNGPS(0.722)S(0.278)DPEAAFLSR 221.31 1.32E-34 291860000 263220 250810 270700 237560 311940 199970 326730 238600 532780 TRUE FALSE 246745.5301 269380.2334 277121.1318 243656.1918 287441.4907 257698.0928 277739.8697 268389.7352 443855.5761 0.555914003 0.606909652 0.624349781 0.54895377 0.647601396 0.580589964 0.625743788 0.604678075 1 18.7597308 -5 0.428853888 8.795720233 0.596862287 0.946043865 0.030107912 194.1204456 1.220275942 1429.279765 0.015090609 1.00E-05 5 -8.198857946 KEKPELSEPSHLNGPSS(ph)DPEAAFLSR ddPTM_SK-BR-3_Pertuzumab_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(0.25)S(0.75)DPEAAFLSR;KEKPELSEPSHLNGPS(0.058)S(0.942)DPEAAFLSR;KEKPELSEPSHLNGPS(0.006)S(0.994)DPEAAFLSR;KEKPELSEPSHLNGPS(0.212)S(0.788)DPEAAFLSR 226.1 8.52E-35 3452550000 1656020 1579850 1669260 1683960 2006180 1222880 2077190 1495480 3346340 TRUE FALSE 1552372.664 1696823.738 1708855.635 1727173.265 1848622.715 1575905.604 1765734.643 1682193.97 2787814.236 0.556842219 0.60865739 0.61297328 0.619543886 0.663108284 0.565283577 0.633376005 0.603409635 1 21.410703 -4.60371095 0.522568766 10 0.60756547 0.942728718 0.030372116 396.2931074 2.63668898 4150.330853 0.012331311 2.49E-05 4.60371095 -9.39243453 KEKT(ph)PELPEPSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEKTPELPEPSVK 13 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KEKT(1)PELPEPSVK;KEKT(1)PELPEPSVK 141 0.0018889 970840000 1924180 759540 1098260 1049080 1164130 771710 1439420 878420 1715730 TRUE FALSE 1803749.009 815777.1319 1124311.246 1076001.169 1072703.926 994490.1493 1223592.334 988092.6706 1429363.579 1.261924562 0.570727521 0.786581708 0.752783396 0.750476605 0.695757303 0.856039955 0.69128155 1 20.4469415 -1.922523111 7.928390304 1.05499046 0.773767815 0.099690846 0.182673881 0.096179966 0.000939878 0.095806829 0.036437265 0.011952999 1.922523111 -0.281222646 KELIINEILVMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KELIINEILVMK 12 1 Q13177;H7C1X3 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 0 140.08 9.52E-05 94871000 215790 201680 228650 222840 257830 165020 255670 215230 265280 FALSE TRUE 202284.0891 216612.597 234073.686 228558.4517 237581.0718 212658.5951 217334.657 242101.9393 221003.0542 0.915299971 0.980133952 1.059142313 1.034186846 1.075012618 0.962242788 0.983401147 1.095468749 1 17.75370678 4.594804427 2.108830473 1.025377643 0.902436288 0.452573714 0.040865234 0.491490777 3.089600431 0.010426809 0.102356565 39337.28901 -4.594804427 -0.122941355 KELNQLEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KELNQLEDK 9 1 P35555 P35555 FBN1 Fibrillin-1 0 74.267 0.066662 880740000 990500 688500 941200 969180 950560 491090 657610 678100 697120 FALSE TRUE 928506.3731 739477.2564 963525.7085 994050.7996 875906.852 632859.7108 559007.4855 762762.2777 580766.1684 1.598761125 1.273278811 1.659059637 1.711619674 1.508191936 1.089697963 0.96253452 1.313372437 1 19.14759789 2.242904924 5.850479732 1.072409381 1.536464583 0.705863195 0.146943396 0.089572585 10.76269849 0.054289984 0.042632651 174.9463651 -2.242904924 0.464055203 KELNSNHDGADET(ph)SEKEQQEAIEHIDEVQNEIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 34 2 Q01105-2 Q01105-2 SET Protein SET 1 KELNS(0.001)NHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;KELNS(0.002)NHDGADET(0.499)S(0.499)EKEQQEAIEHIDEVQNEIDR 112.14 9.14E-06 358140000 283040 158282 221715 189887 191563 181318 283820 206587 235860 TRUE FALSE 265325.0316 170001.364 226974.1845 194759.8219 176518.4147 233661.5631 241263.8259 232379.8417 196493.4423 1.350299677 0.865175764 1.155123458 0.99117721 0.898342523 1.189157055 1.227846706 1.182634082 1 17.58412164 2.184607798 24.99994159 1.175936729 1.037837125 0.082024982 0.147838075 156.1888366 72371.53945 0.050333655 0.037173897 152.9705393 -2.184607798 -0.138099604 KELNYFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KELNYFAK 8 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 133.13 0.0014951 821340000 2790000 4987200 2503300 2679400 5309700 1734500 3264000 4487900 5072900 FALSE TRUE 2615378.88 5356457.477 2562679.458 2748157.94 4892697.58 2235221.993 2774593.501 5048224.194 4226200.218 0.618848787 1.267440538 0.606379094 0.650266859 1.157706055 0.528896379 0.656522019 1.194506633 1 22.01092969 5.019722429 17.14356428 0.851891494 0.111238028 0.077198021 0.268524513 213711301.5 4306506546 0.061596968 4183057776 104645.9511 -5.019722429 -0.740653466 KELQAAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KELQAAGK 8 1 P06744;A0A2U3TZU2;P06744-2 P06744 GPI Glucose-6-phosphate isomerase 0 ; 99.815 0.010496 2070200000 3163500 3945400 2500000 2557800 4227000 1600070 3318500 3528200 4171900 FALSE TRUE 2965502.182 4237521.521 2559301.181 2623437.478 3895028.471 2061984.234 2820921.732 3968703.537 3475582.938 0.85323879 1.219226126 0.736366021 0.754819414 1.120683505 0.593277235 0.811639884 1.141881407 1 21.72882354 3.9682084 24.0368861 0.856595797 1.051802121 0.091579052 0.19302403 333.0025523 898073.0324 0.045395797 0.083502195 9294.122655 -3.9682084 0.195206324 KELQAEATVSGS(ph)PEAPGTNVVSEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KELQAEATVSGSPEAPGTNVVSEPR 25 1 Q9BZV1-2;Q9BZV1;K7EJ02 Q9BZV1-2 UBXN6 UBX domain-containing protein 6 1 KELQAEATVS(0.086)GS(0.914)PEAPGTNVVSEPR;KELQAEATVS(0.001)GS(0.999)PEAPGTNVVSEPR 233.16 1.44E-38 301380000 223048 242956 232840 257544 279803 177226 259675 207420 253922 TRUE FALSE 209087.8238 260944.715 238363.0748 264153.0151 257828.4011 228388.2692 220739.1445 233316.8436 211540.7778 0.988404345 1.233543328 1.126794925 1.248709671 1.218811823 1.079641814 1.043482712 1.102940275 1 17.69057627 2.107263765 5.851042266 1.055640522 1.171416055 0.324126942 0.076829843 0.224806731 10.83448673 0.02689232 0.019708649 128.0158562 -2.107263765 0.115775532 KELS(ph)PAGSISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KELSPAGSISK 11 1 A0A494C0Q6;A0A494C0K5;A0A494C0W0;O95453-2;O95453-3;O95453;O95453-4 A0A494C0Q6 PARN Poly(A)-specific ribonuclease PARN 1 KELS(1)PAGSISK;KELS(1)PAGSISK 149.97 2.09E-05 732550000 2492900 1591610 1929860 1823930 2059020 1392320 2490550 1757930 2561800 TRUE FALSE 2336873.839 1709454.46 1975637.191 1870735.132 1897312.875 1794260.182 2117115.149 1977411.43 2134219.03 1.094955019 0.800974238 0.925695612 0.876543178 0.888996325 0.840710422 0.991985883 0.926526941 1 21.02527681 1.694812584 9.500525117 0.968645484 0.893506721 0.130038249 0.079314658 0.196988753 31.57885801 0.034121749 0.018326265 49.52364301 -1.694812584 -0.075138763 KELSDIAHR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;; 162.36 4.14E-05 10427830000 14955600 17524400 16360100 16654400 18064800 12366400 19299500 15172500 16097700 FALSE TRUE 14019555.69 18821924.81 16748169.3 17081780.1 16646063.48 15936378.93 16405719.14 17066820.02 13410889.87 1.045385938 1.403480678 1.24884847 1.273724582 1.24123482 1.188316292 1.22331324 1.272609065 1 23.67690163 -4.033640496 0.281648013 5.89E-13 1.268434789 0.381553191 0.090708907 117.1848001 1.862880284 67.71219972 0.095476523 9.25E-05 4.033640496 1.268434789 KEMQPTHPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 118.4 0.00039594 2092603000 3033678 3310750 3113100 3110630 3579100 2425620 3718180 3067690 3713690 FALSE TRUE 2843805.509 3555881.375 3186944.202 3190454.032 3298011.923 3125857.117 3160673.427 3450697.849 3093851.148 0.91917981 1.149338221 1.030089701 1.031224154 1.065989204 1.010345026 1.021598414 1.115340617 1 21.56097236 3.689327639 24.87545521 1.038095701 1.062403501 0 0.064481139 1168.533336 769116.6185 0.015665155 0.024269065 4890.211461 -3.689327639 0.0243078 KENPLQFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KENPLQFK 8 1 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-3;A0A2R8Y5P0;E9PNV3;E9PQ82 P15311;A0A2R8Y5S7 EZR;RDX Ezrin;Radixin 0 ; 156.35 0.00063239 3966600000 3508700 3766000 2741400 2542000 4610800 2009370 3182300 3407600 4677100 FALSE TRUE 3289096.73 4044838.559 2806427.303 2607232.024 4248686.367 2589442.5 2705143.658 3833046.361 3896461.795 0.844123952 1.038079871 0.720250178 0.669128086 1.090396003 0.664562528 0.694256431 0.983724867 1 21.89373324 3.975305665 24.61173357 0.805656366 0.945482059 0.057113565 0.159043644 134.8991308 1828719.263 0.037553282 0.072428189 9447.255578 -3.975305665 0.139825692 KENQWCEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KENQWCEEK 9 1 E5RJR5;P63208 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ;;;; 175.49 8.64E-05 3177010000 3656190 2732530 3129860 2963490 3605280 2468450 4300480 2885490 4605500 FALSE TRUE 3427355.594 2934849.364 3204101.757 3039538.171 3322135.852 3181051.443 3655662.948 3245749.778 3836812.297 0.89328206 0.764918671 0.835094737 0.792204032 0.86585832 0.829087064 0.952786497 0.845949587 1 21.87147676 1.251719999 0.512895853 0.996446027 0.808082902 0.522509496 0.048638914 0.573091046 0.396398294 0.04738159 0.025460392 17.85336149 -1.251719999 -0.188363124 KENSETTLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KENSETTLTR 10 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 0 178.49 3.54E-06 328540000 168200 151750 169940 180230 189500 145300 206000 162910 225080 FALSE TRUE 157672.6622 162985.7279 173971.0571 184855.0069 174617.4344 187245.7513 175112.2124 183249.6721 187512.6939 0.840863938 0.86919837 0.927782826 0.985826629 0.931229938 0.998576402 0.933868576 0.977265423 1 17.51662874 3.94684717 1.115405998 0.967161808 0.8380596 0.789284392 0.024492633 0.26070813 0.558643053 0.007131799 0.028909297 8848.041894 -3.94684717 -0.129102208 KEPAITSQNS(ph)PEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KEPAITSQNSPEAR 14 1 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;E5RIS7 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 1 KEPAIT(0.001)S(0.014)QNS(0.985)PEAR;KEPAITSQNS(1)PEAR;KEPAITSQNS(1)PEAR;KEPAITSQNS(1)PEAR 247.28 5.05E-18 2528000000 1697250 1373730 1570280 1429000 1510160 1356750 1911760 1392880 1699300 TRUE FALSE 1591022.152 1475442.399 1607527.783 1465670.559 1391558.125 1748421.7 1625109.336 1566784.134 1415675.852 1.123860487 1.042217677 1.135519675 1.035315081 0.982963807 1.235043811 1.147938869 1.106739323 1 20.43305954 2.242929786 24.99999912 1.139752499 1.069461712 0.118402291 0.071864926 181.7220689 1039802.514 0.023685585 0.019182719 174.9563807 -2.242929786 -0.070290787 KEPAVLELEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEPAVLELEGK 11 1 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 0 ; 131.26 0.0018824 0 2134350 1663860 1727080 1699310 1972430 1241690 2110540 1608590 2067070 FALSE TRUE 2000764.843 1787053.926 1768047.153 1742917.172 1817523.304 1600145.746 1794084.12 1809426.002 1722062.663 1.161842067 1.037740359 1.026703146 1.012110191 1.055433895 0.929202973 1.041822785 1.0507318 1 20.71570621 KEPEKPIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KEPEKPIDR 9 2 O00422;O00422-2;U3KQ12 O00422 SAP18 Histone deacetylase complex subunit SAP18 0 ;; 121.6 0.00034266 1324120000 3127150 2184900 2608340 2450930 2666280 1889310 3156940 2319370 3517200 FALSE TRUE 2931427.264 2346672.269 2670211.057 2513825.013 2456881.124 2434723.127 2683586.155 2608948.45 2930156.598 1.000433651 0.800869234 0.911286127 0.857914903 0.838481167 0.830919115 0.915850763 0.890378505 1 21.48254634 0.655518753 1.151861767 0.999448555 0.869842383 0.309770327 0.055656418 1.232424143 2.612962529 0.047363633 0.014634189 4.523959967 -0.655518753 -0.129606172 KEPFFHGHDNYDQLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KEPFFHGHDNYDQLVR 16 1 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2 P68400 CSNK2A1 Casein kinase II subunit alpha 0 ;; 183.7 7.90E-10 794060000 836210 747410 766350 736300 850760 609770 882170 789900 749480 FALSE TRUE 783873.1088 802749.0141 784528.1839 755194.7046 783944.7414 785800.7002 749896.7982 888520.7538 624386.9462 1.255428406 1.285659508 1.256477556 1.209497907 1.255543131 1.258515581 1.201012934 1.423029035 1 19.25208085 -1.245085787 4.077648917 0.999783898 1.261590281 0.65735585 0.060676886 4110014.206 1254976.333 7953.160981 0.012674816 0.056874058 1.245085787 0.261806383 KEPGPPGGSS(ph)SFLHKPFPGGPLQVCPQACPSASER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEPGPPGGSSSFLHKPFPGGPLQVCPQACPSASER 35 2 Q8TDM6-4;Q8TDM6;Q8TDM6-3 Q8TDM6-4 DLG5 Disks large homolog 5 1 KEPGPPGGS(0.309)S(0.346)S(0.346)FLHKPFPGGPLQVCPQACPSASER 67.087 0.0026305 159520000 138730 141030 160570 135710 160010 107610 185050 178750 221930 TRUE FALSE 130047.1369 151472.0079 164378.7962 139192.5484 147443.46 138675.2601 157303.4704 201067.331 184888.4493 0.70338162 0.819261606 0.889070122 0.752846102 0.797472533 0.750048262 0.850802043 1.087506179 1 17.49629557 1.341372838 4.648996912 1.042017486 0.801064696 0.783944796 0.054793813 0.09630751 3.149679696 0.040492379 0.013847937 21.94688246 -1.341372838 -0.24095279 KEQEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEQEEER 7 1 Q9UNN5;B3KT28;B1ANM7;Q9UNN5-2 Q9UNN5 FAF1 FAS-associated factor 1 0 112.41 0.010198 189430000 529190 400850 532930 485260 453590 330740 493230 379870 416000 FALSE TRUE 496068.9425 430529.3511 545571.3513 497712.5931 417966.8711 426219.2689 419274.7404 427297.6057 346566.9125 1.431379986 1.242269055 1.574216498 1.436122651 1.206020702 1.229832547 1.209794488 1.23294403 1 18.4027744 2.729056461 12.75919233 1.194705036 1.416750673 0.576610116 0.103703918 0.778111176 1040.854577 0.032124397 0.031180203 535.8663193 -2.729056461 0.222045637 KEQQLQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEQQLQER 8 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ; 137.95 0.0011642 219713000 225220 271820 197961 211070 320500 172867 252050 260880 332380 FALSE TRUE 211123.8822 291945.8356 202656.7284 216486.4135 295329.2228 222770.8966 214257.4424 293451.4423 276903.6307 0.762445338 1.054322888 0.731867357 0.781811394 1.066541533 0.804506954 0.773761766 1.059760183 1 18.07902444 1.226769003 24.99675928 1.029880204 0.859378074 0.278330275 0.117718297 338.4576641 717465.7695 0.104966806 0.027108245 16.85656202 -1.226769003 -0.17050213 KEQSEVSVS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KEQSEVSVSPR 11 1 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 KEQS(0.001)EVSVS(0.999)PR;KEQSEVSVS(1)PR;KEQSEVS(0.001)VS(0.999)PR 147.66 2.25E-05 1554890000 2402183 2161022 2306237 2332527 2466884 1928070 2704931 2161389 2669201 TRUE FALSE 2251834.654 2321026.317 2360942.031 2392383.592 2273144.882 2484672.509 2299351.708 2431243.174 2223694.109 1.012654863 1.043770502 1.061720684 1.075860021 1.022238118 1.117362545 1.034023384 1.093335259 1 21.08452691 4.853093421 1.338841764 1.060352192 0.982586604 0.146744258 0.033964508 2.838862321 3.72288627 0.007982751 0.321781968 71300.63888 -4.853093421 -0.077765588 KEQT(ph)PEHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KEQTPEHGK 9 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 KEQT(1)PEHGK;KEQT(1)PEHGK;KEQT(1)PEHGK;KEQT(1)PEHGK 92.925 0.0070187 793650000 3346010 1516860 2435310 2065110 2122560 1680200 2780440 1814900 2939420 TRUE FALSE 3136589.207 1629169.893 2493076.703 2118104.219 1955862.7 2165246.464 2363538.834 2041494.26 2448811.813 1.280861678 0.665289952 1.018076069 0.864951814 0.798698654 0.884202883 0.965177815 0.833667271 1 21.22365048 -0.962555478 6.713938557 1.000000009 0.899604883 0.020739595 0.161439137 2.23E-08 3.63E-09 0.136137156 0.032087832 0.109004524 0.962555478 -0.100395126 KEREEEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KEREEEFK 8 2 E9PK91;Q9NYF8-3;H0YF63;Q9NYF8;Q9NYF8-2;H0YF14;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 ;; 87.258 0.0086906 443967000 406515 315454 336299 327128 364274 240038 407273 311776 580950 FALSE TRUE 381071.9518 338810.5424 344276.1711 335522.6583 335665.3895 309333.0739 346206.1946 350701.9199 483985.6919 0.78736202 0.700042477 0.711335432 0.693249127 0.693544035 0.639136816 0.715323201 0.724612165 1 18.88460487 0.534660913 2.234222838 0.999988704 0.70244007 0.867534294 0.035911786 1.537661573 6.992381126 0.032209485 0.008721263 3.425002661 -0.534660913 -0.297548634 KES(ph)APQVLLPEEEK ddPTM_SK-BR-3_Pertuzumab_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 143.95 5.51E-06 812810000 4736240 2110560 3047020 2576320 3168660 2408470 4370250 2968880 5549250 TRUE FALSE 4439807.193 2266828.058 3119296.753 2642432.733 2919806.225 3103756.191 3714971.584 3339551.203 4623044.325 0.960364401 0.490332322 0.674727849 0.571578498 0.631576515 0.671366306 0.803576891 0.722370578 1 22.14041176 0.860129605 0.720166313 0.996629073 0.637616198 0.372391569 0.126628585 0.788904477 0.881369893 0.11375004 0.042927698 7.246521836 -0.860129605 -0.359012875 KES(ph)DIRPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KESDIRPSK 9 2 A0A2R8YFA9;O94851-5;O94851-3;O94851;O94851-4;O94851-6;O94851-2 A0A2R8YFA9;O94851-4 MICAL2 Protein-methionine sulfoxide oxidase MICAL2 1 KES(1)DIRPSK 79.466 0.021155 253780000 510300 276560 329780 301550 377180 235330 475460 333200 456220 TRUE FALSE 478361.2339 297036.7902 337602.5373 309288.2835 347557.8043 303265.9507 404169.187 374800.7535 380073.9347 1.258600473 0.781523706 0.888254906 0.813758207 0.914447881 0.797913045 1.063396224 0.986125907 1 18.53592056 1.703757149 10.08429795 1.017128066 0.888589899 0.109590448 0.135950488 0.194893961 39.37491113 0.05883584 0.031797866 50.5541892 -1.703757149 -0.128538166 KES(ph)SPNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KESSPNSR 8 1 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 1 KES(0.5)S(0.5)PNSR 57.836 0.066614 230530000 45367 41641 57070 52631 47148 44630 52170 46796 61478 TRUE FALSE 42527.56045 44724.14297 58423.72735 53981.60056 43445.18627 57513.95649 44347.59282 52638.58361 51216.92464 0.830341938 0.873229763 1.140711352 1.053979733 0.848258395 1.122948262 0.865877698 1.027757601 1 15.64433301 4.293602808 4.263151859 1.003232932 0.842399146 0.327337307 0.094004344 0.249873424 8.822122984 0.022144625 0.064750247 19660.87344 -4.293602808 -0.160833785 KESPELLELIEDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KESPELLELIEDLK 14 1 Q9NQZ2 Q9NQZ2 UTP3 Something about silencing protein 10 0 134.15 6.48E-05 28251000 177110 118150 140240 138310 139290 111300 157960 108950 127480 FALSE TRUE 166025.0013 126897.9489 143566.559 141859.2688 128350.7253 143430.5032 134275.3644 122552.6473 106202.7644 1.563283236 1.194864838 1.35181565 1.335739889 1.208544108 1.350534555 1.264330219 1.153949692 1 16.69646179 -4.893839695 0.125504319 3.20E-12 1.438127867 0.57701549 0.096790019 110.1101 0.90632519 27.64915137 0.761757592 1.28E-05 4.893839695 1.438127867 KESS(ph)PNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KESSPNSR 8 1 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 1 KES(0.267)S(0.726)PNS(0.007)R 71.896 0.029129 181130000 46715 38757 48097 48296 43991 37327 57879 42585 49916 TRUE FALSE 43791.19154 41626.60861 49237.88355 49535.35712 40536.12431 48102.69895 49200.58127 47901.83099 41584.69713 1.05306025 1.001007858 1.184038527 1.191191966 0.974784647 1.156740394 1.183141508 1.151910061 1 15.3437651 4.033647943 5.169570759 1.130777349 1.029120463 0.192639097 0.076878594 0.278867545 15.60825813 0.018284684 0.04010626 10805.57652 -4.033647943 -0.101656886 KESYSIYVYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KESYSIYVYK 10 1 Q16778;P33778;P23527;P06899;Q6DRA6;Q6DN03 Q16778 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST2H2BD;HIST2H2BC Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C 0 ; 153.34 2.63E-05 11750800000 15986200 15324600 14826200 12966400 16493500 9859100 19959600 15328700 18588000 FALSE TRUE 14985652.28 16459249.33 15177884.47 13299139.78 15198167.04 12705262.12 16966843.28 17242521.94 15485542.72 0.967718894 1.06287843 0.98013255 0.858810054 0.981442325 0.820459596 1.095657 1.113459325 1 23.88441861 1.612182365 25 1.078425631 0.960698702 0.374248831 0.07380366 0.445755443 2566.891411 0.035843128 0.018999437 40.94325484 -1.612182365 -0.117726929 KESYSVYVYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 92.925 0.014648 192230000 978510 1438720 1706010 884230 1100840 670690 1152780 954210 1470870 FALSE TRUE 917266.8058 1545244.326 1746477.363 906920.8388 1014384.467 864307.3153 979931.3409 1073345.219 1225372.295 0.748561731 1.261040691 1.425262649 0.740118609 0.827817367 0.705342628 0.799700911 0.87593397 1 20.22478871 3.225057433 24.99956426 0.805991946 1.209874484 0.373285179 0.188366142 178.1092457 329747.7883 0.053122536 0.063822833 1679.026044 -3.225057433 0.403882538 KET(ph)ES(ph)EAEDNLDDLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KETESEAEDNLDDLEK 16 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KET(1)ES(1)EAEDNLDDLEK;KET(1)ES(1)EAEDNLDDLEK;KET(1)ES(1)EAEDNLDDLEK;KET(1)ES(1)EAEDNLDDLEK;KET(1)ES(1)EAEDNLDDLEK 262.15 6.23E-27 3177983000 11119680 4178230 6283770 6077980 6456170 4302110 8363370 4784660 8234540 TRUE FALSE 10423719.08 4487590.497 6432823.992 6233951.257 5949128.451 5544059.318 7109360.31 5382035.333 6860142.077 1.519461108 0.654154163 0.937710024 0.90872043 0.86720193 0.808155175 1.036328436 0.784537007 1 22.70980702 4.750892827 24.86547834 0.873259888 1.519461538 0.773524846 0.109656085 857.2399619 1728422.41 0.025430417 0.441306036 56349.85811 -4.750892827 0.64620165 KET(ph)PPPLVPPAAR ddPTM_SK-BR-3_Pertuzumab_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 84.859 0.0055969 5830600000 3511120 2272320 2682380 2574260 2661070 1968660 3373450 2285510 3330240 TRUE FALSE 3291365.267 2440564.937 2746007.32 2640319.87 2452080.296 2536980.183 2867632.49 2570860.955 2774401.43 1.186333467 0.879672606 0.989765681 0.951671896 0.883823181 0.914424335 1.033604027 0.926636256 1 21.40374512 -1.374854675 5.298797984 1.000017621 0.963812524 0.005170833 0.089756754 1.66E-05 1.96E-06 0.077356118 0.018224138 0.042183764 1.374854675 -0.036205097 KET(ph)QSPEQVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KETQSPEQVK 10 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 KET(0.5)QS(0.5)PEQVK 138.55 3.62E-05 5911300000 5900300 2929900 4066500 3477200 3427900 3066300 5041500 3138900 4728600 TRUE FALSE 5531010.755 3146832.845 4162959.3 3566430.839 3158686.561 3951491.033 4285573.878 3530798.575 3939366.112 1.404035725 0.798817057 1.056758672 0.905331147 0.801826099 1.003077886 1.087884131 0.896285969 1 21.90953207 4.750852265 24.80247204 0.951451102 1.404036037 0.6870103 0.097514121 1085.532076 2190376.054 0.023470227 0.405930658 56344.59551 -4.750852265 0.452584935 KET(ph)SFGSSENITMTSLSK ddPTM_SK-BR-3_Pertuzumab_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(0.331)S(0.331)FGS(0.331)S(0.006)ENITMTSLSK 129.32 2.95E-05 0 188290 167070 182370 160640 176950 120600 223550 156060 207860 TRUE FALSE 176505.265 179440.0366 186695.9025 164762.2944 163053.0608 155415.2622 190030.7528 175544.4345 173166.8232 1.019278761 1.036226417 1.078127433 0.95146571 0.941595265 0.897488672 1.097385454 1.013730178 1 17.40180303 3.24206119 24.99983864 0.98801308 1.047559423 0.216749691 0.054073005 151.0408688 1078667.147 0.016168472 0.021049173 1746.068146 -3.24206119 0.059546344 KETEGDVTSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KETEGDVTSVK 11 1 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 124.07 0.00057216 299360000 504720 375980 384470 381880 428630 294480 522240 371250 487620 FALSE TRUE 473130.4762 403817.9504 393589.81 391679.6873 394967.1288 379491.5955 443934.9602 417601.3797 406233.0719 1.164677396 0.994054838 0.968876828 0.964174791 0.972267292 0.934172084 1.092808516 1.027984693 1 18.63194817 -0.740275022 7.340555639 1 1.008765717 0 0.068664435 0 0 0.063720314 0.015019022 0.181854888 0.740275022 0.008765717 KETES(ph)EAEDNLDDLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KETESEAEDNLDDLEK 16 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KET(0.004)ES(0.996)EAEDNLDDLEK;KET(0.029)ES(0.971)EAEDNLDDLEK;KET(0.068)ES(0.932)EAEDNLDDLEK;KET(0.001)ES(0.999)EAEDNLDDLEK;KET(0.179)ES(0.821)EAEDNLDDLEK 257.96 6.67E-27 11159750000 13552280 5201463 7587780 7589480 7617000 5441824 10280570 5923772 9392800 TRUE FALSE 12704066.99 5586584.733 7767765.725 7784238.906 7018791.545 7012790.248 8739093.969 6663367.974 7825081 1.623506132 0.713933151 0.99267544 0.994780617 0.896960881 0.89619395 1.11680556 0.851539808 1 22.89967426 4.750212104 24.96669433 0.935959036 1.623506548 0.804510676 0.106982711 793.7103566 1700722.745 0.025924661 0.420959609 56261.60324 -4.750212104 0.687547512 KETKPEPMEEDLPENKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KETKPEPMEEDLPENKK 17 3 P31948;P31948-2;P31948-3;F5H783 P31948 STIP1 Stress-induced-phosphoprotein 1 0 88.264 0.0028468 174390000 197560 78409 113820 103810 118890 78139 143450 93121 168650 FALSE TRUE 185195.0723 84214.48394 116519.8641 106473.9403 109552.859 100696.4608 121941.0042 104747.3618 140501.2255 1.318102896 0.599386117 0.829315643 0.75781503 0.77972885 0.716694538 0.867899933 0.745526322 1 17.10022319 -0.601235333 6.865499162 0.999999972 0.803106904 0.063856575 0.190025897 0 1.74E-10 0.160123869 0.037741558 0.250475163 0.601235333 -0.196893068 KETQFHGSEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KETQFHGSEGR 11 1 O95163 O95163 IKBKAP Elongator complex protein 1 0 72.958 0.029129 97795000 45106 85018 83221 86991 93422 73538 97980 95538 91477 FALSE TRUE 42282.89598 91312.82118 85195.04142 89223.33634 86085.01297 94767.22681 83288.8086 107466.1296 76208.89774 0.554828862 1.198191076 1.117914626 1.170773217 1.129592679 1.24351919 1.092901368 1.410152001 1 16.21767183 4.740230665 24.97016194 1.168739908 0.554828654 0.765647422 0.107022121 60.28237381 901250.0823 0.021775433 0.139159058 54983.2827 -4.740230665 -0.613911255 KETQS(ph)PEQVK ddPTM_SK-BR-3_Pertuzumab_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(0.426)QS(0.574)PEQVK;KET(0.013)QS(0.987)PEQVK;KETQS(1)PEQVK;KET(0.002)QS(0.998)PEQVK;KET(0.001)QS(0.999)PEQVK;KETQS(1)PEQVK;KET(0.002)QS(0.998)PEQVK;KET(0.056)QS(0.944)PEQVK;KET(0.001)QS(0.999)PEQVK 219.89 6.46E-09 27758630000 15919290 7896130 10694310 9541080 9355650 7730520 13378620 8424210 12420350 TRUE FALSE 14922930.06 8480767.681 10947984.08 9785920.266 8620894.988 9962195.629 11372620.13 9475991.162 10347313.35 1.442203358 0.819610598 1.058050889 0.945745039 0.833152984 0.962780897 1.099089179 0.915792423 1 23.30275289 4.749191248 24.82713021 0.961377419 1.442203657 0.754661522 0.087347128 726.2779107 1696137.139 0.020999426 0.30364238 56129.50956 -4.749191248 0.480826239 KETQS(ph)PEQVKSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KETQSPEQVKSEK 13 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 KET(0.004)QS(0.996)PEQVKSEK;KET(0.004)QS(0.996)PEQVKSEK;KETQS(0.616)PEQVKS(0.384)EK;KET(0.044)QS(0.956)PEQVKSEK;KET(0.001)QS(0.999)PEQVKSEK;KETQS(1)PEQVKSEK 175.33 1.45E-05 3354610000 4607970 2691170 3092890 3652610 4589560 1999340 3994740 2633890 9284930 TRUE FALSE 4319565.383 2890427.027 3166254.811 3746342.156 4229114.471 2576517.001 3395765.822 2962736.964 7735215.2 0.558428598 0.373671185 0.409329893 0.484322939 0.546735205 0.333089246 0.439000821 0.383019333 1 22.88301 -1.372106829 3.177473689 1.005740499 0.432221915 0.852393178 0.073031428 19779229.64 26363208.51 1049731.383 0.016229241 0.042451513 1.372106829 -0.573518585 KETTSGTSTEPVKNS(ph)SPAPPQPAPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KETTSGTSTEPVKNSSPAPPQPAPGK 26 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 KETTSGTSTEPVKNS(0.5)S(0.5)PAPPQPAPGK 93.767 0.0044906 329500000 488140 264790 342130 320580 362780 256540 486040 288730 561000 TRUE FALSE 457588.1888 284395.3271 350245.4852 328806.6255 334288.7222 330598.9334 413162.8142 324778.5761 467365.4758 0.979079997 0.60850735 0.749403846 0.703532123 0.715261908 0.70736704 0.884025106 0.694913495 1 18.83419164 -0.144311997 0.499170358 1.030384572 0.72935152 0.315380912 0.107422451 5.578913261 1.545838742 0.434485664 0.048828645 0.717278813 0.144311997 -0.301033052 KETTSGTSTEPVKNSS(ph)PAPPQPAPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KETTSGTSTEPVKNSSPAPPQPAPGK 26 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 KETTSGTSTEPVKNS(0.125)S(0.874)PAPPQPAPGK;KETTSGTSTEPVKNS(0.082)S(0.918)PAPPQPAPGK;KETTSGTSTEPVKNS(0.225)S(0.775)PAPPQPAPGK 214.29 2.33E-34 1276290000 1660290 1044150 1253720 1288520 1443930 995900 1905790 1186370 2257900 TRUE FALSE 1556375.413 1121459.952 1283458.83 1321585.605 1330529.562 1283400.163 1620034.482 1334490.906 1881041.903 0.827400713 0.59619084 0.682312727 0.702581693 0.707336482 0.682281538 0.861243165 0.709442413 1 20.84310056 0.479521953 0.439257042 1.022861273 0.670869448 0.578117231 0.074801953 1.385821817 0.499658446 0.141182605 0.044132254 3.016629355 -0.479521953 -0.351991825 KEVEETDEMDQVELVDFDPNQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEVEETDEMDQVELVDFDPNQER 23 1 P31689 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 148.29 1.73E-07 47971000 69152 59031 61034 61811 66572 52586 75411 57858 88774 FALSE TRUE 64823.89976 63401.71666 62481.7553 63397.17491 61343.70366 67766.72454 64103.82063 65081.69866 73957.0459 0.876507424 0.857277571 0.84483844 0.85721616 0.829450432 0.916298423 0.866770973 0.879993216 1 16.17439998 -0.532229809 0.417786798 1.035323838 0.85377465 0.795088783 0.021721948 3.563415064 0.57262628 0.195086836 0.012594283 0.293609559 0.532229809 -0.181549188 KEVEGDDVPESIMLEMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEVEGDDVPESIMLEMK 17 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 175.39 1.98E-09 85842000 329120 219070 233070 237260 261810 148650 327730 223950 363580 FALSE TRUE 308520.9667 235290.1707 238598.5305 243348.4933 241248.4987 191562.8419 278589.929 251910.6505 302896.1492 1.018570119 0.776801459 0.787723882 0.803405702 0.79647265 0.632437363 0.919753948 0.831673335 1 18.20846371 0.818405018 1.347964309 0.99715125 0.803033624 0.239937949 0.099383123 0.881270096 2.964873719 0.085983874 0.025738402 6.582714468 -0.818405018 -0.194117627 KEVEVVEIIQATIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEVEVVEIIQATIIR 15 1 Q14764;H3BQK6;I3L155 Q14764 MVP Major vault protein 0 ; 206.8 5.96E-09 321420000 1265000 1275650 1223430 1408590 1389380 1047610 1550640 1187200 1027280 FALSE TRUE 1185825.908 1370100.453 1252450.337 1444736.804 1280263.699 1350038 1318135.927 1335424.533 855820.3315 1.385601468 1.600920664 1.463450086 1.688130967 1.495949152 1.577478299 1.540201698 1.560402907 1 19.70694843 -1.534777594 5.987060458 0.999110619 1.542508883 0.813450155 0.08110634 0.000828471 6.44E-05 0.067570234 0.015902793 0.029189214 1.534777594 0.543398264 KEVLAS(ph)PDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEVLASPDR 9 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 KEVLAS(1)PDR;KEVLAS(1)PDR 67.079 0.037923 563420000 2169200 1809490 1884220 1845700 1828030 1315240 1981650 1716690 1201880 TRUE FALSE 2033433.644 1943466.522 1928914.588 1893063.787 1684463.898 1694928.437 1684519.979 1931022.525 1001278.464 2.030837293 1.940985044 1.92645169 1.890646664 1.682313122 1.692764299 1.682369132 1.928556936 1 19.93341182 -2.109549275 0.207270617 1.26E-14 2.029604201 0.855108512 0.111555696 12.26348267 0.359905692 6.290506168 0.266520648 0.007770531 2.109549275 2.029604201 KEVLAS(ph)PDRLWGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KEVLASPDRLWGSR 14 2 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 KEVLAS(0.991)PDRLWGS(0.009)R;KEVLAS(1)PDRLWGSR;KEVLAS(1)PDRLWGSR;KEVLAS(1)PDRLWGSR 221.37 3.38E-12 5045143000 1044102 1053271 1036618 1053865 1166080 821252 1214900 824314 1112912 TRUE FALSE 978753.5196 1131256.281 1061207.068 1080908.96 1074500.781 1058334.12 1032737.024 927231.4174 927159.7975 1.055647066 1.22013086 1.14457839 1.165828116 1.158916493 1.141479736 1.113871661 1.000077247 1 19.82245849 1.34531128 2.31149093 0.992150493 1.157015154 0.680178333 0.040852601 0.148325893 1.341845791 0.033014991 0.009957328 22.14681509 -1.34531128 0.164864661 KEVQDEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KEVQDEEK 8 1 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ;;;;; 125.97 0.001987 3266940000 5422760 3718050 4129830 4205160 4417760 3135980 5389030 3704100 5753480 FALSE TRUE 5083359.132 3993338.291 4227791.518 4313071.525 4070806.95 4041286.518 4580994.981 4166565.039 4793187.019 1.06053845 0.833127995 0.882041844 0.899833766 0.849290239 0.843131407 0.95573049 0.869268197 1 22.1925538 -0.200828174 0.777094163 1.004242175 0.890257379 0.165178021 0.067735164 13.48813857 7.052873941 0.241873794 0.020917299 0.629755293 0.200828174 -0.113984796 KEVS(ph)PEVVR ddPTM_SK-BR-3_Pertuzumab_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 142.97 6.31E-05 3277320000 8824800 7017100 7616500 7665200 7870900 5970300 9200800 6787400 9558800 TRUE FALSE 8272471.521 7536653.385 7797166.977 7861902.009 7252751.264 7693828.69 7821225.456 7634821.831 7963374.528 1.038814826 0.946414533 0.979128503 0.987257598 0.910763551 0.966151807 0.982149644 0.958742026 1 22.92494848 -1.033354432 4.442502619 1.000001569 0.969097765 0.069011544 0.032479985 4.53E-07 9.86E-08 0.02822874 0.00665324 0.092607374 1.033354432 -0.030903804 KEVTEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEVTEEEK 8 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 0 ; 114.5 0.0042411 485990000 682940 381370 476870 470700 460390 378610 601070 419860 433190 FALSE TRUE 640196.0045 409607.0316 488181.5816 482778.9589 424232.8265 487908.5608 510945.1336 472280.4452 360887.7905 1.77394753 1.134998308 1.352724017 1.33775365 1.175525573 1.351967491 1.415800554 1.308662852 1 18.46119081 -2.101921366 1.883763587 0.47710113 1.336056742 0.29212847 0.171783578 1710814.245 414522.1671 3829419.418 0.041976107 0.007908218 2.101921366 0.858955612 KEVVEEAENGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 KEVVEEAENGR 11 1 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;; 240.65 1.73E-15 15420990000 20211760 18193830 17979790 18792850 19701030 14455370 22913450 16547250 18280320 FALSE TRUE 18946742.02 19540920.1 18406279.11 19275106.35 18153790.57 18628400.66 19477790.89 18613210.59 15229216.5 1.244104844 1.283120514 1.208616288 1.265666317 1.192037068 1.223201513 1.278975244 1.222204083 1 23.86033839 0.954761247 22.57208156 1 1.243368345 0.871328271 0.029050024 1051.733147 524767.9108 0.026865264 0.006716316 9.010756367 -0.954761247 0.243368345 KEWDLKPIADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KEWDLKPIADR 11 2 P30038-2;P30038;P30038-3;Q5TF55 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 ; 100.19 0.0023714 949240000 1461510 1640810 1134030 1189430 2225430 849880 1354470 1682360 2593700 FALSE TRUE 1370036.698 1762297.28 1160929.727 1219952.788 2050653.705 1095226.559 1151379.798 1892406.349 2160794.714 0.63404297 0.8155783 0.537269792 0.564585233 0.949027546 0.506862846 0.532850155 0.875791827 1 21.04313059 1.054942298 5.292138265 0.998273058 0.649511393 0.444369149 0.138160767 0.154849123 8.501918162 0.128900157 0.032553322 11.34860024 -1.054942298 -0.348761665 KEWSGLLEELAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEWSGLLEELAR 12 1 Q01813;Q01813-2;Q5VSR5;V9GYV7 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 153.32 0.00011312 234000000 801860 1125300 822880 849330 1096100 474100 935240 983230 863240 FALSE TRUE 751673.014 1208618.383 842399.1022 871125.2457 1010016.727 610964.9736 795009.4443 1105988.43 719159.6673 1.045210192 1.680598117 1.171365888 1.211309929 1.404440173 0.849554002 1.10547001 1.537889957 1 19.45595259 3.725448306 23.51030131 1.172840209 1.413596937 0.07701217 0.243654316 60.74303748 853670.294 0.059431172 0.097745557 5314.327391 -3.725448306 0.240756729 KEYEEDGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KEYEEDGAR 9 1 P61163 P61163 ACTR1A Alpha-centractin 0 ;; 130.01 0.0020899 0 998820 866650 922190 941970 1040250 710930 1136300 926860 1292370 FALSE TRUE 936305.6391 930817.6677 944064.7823 966142.545 958552.9612 916163.95 965922.3639 1042580.511 1076665.098 0.869634988 0.864537793 0.876841633 0.897347324 0.890298165 0.850927509 0.897142822 0.968342443 1 20.03813813 1.205788954 2.683270724 0.998543059 0.875180343 0.923700583 0.012981783 0.063329214 0.785779569 0.011886127 0.003339208 16.06160546 -1.205788954 -0.123362717 KEYEQELSDDLHVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KEYEQELSDDLHVER 15 1 Q7Z7F7;Q7Z7F7-2;X6R631 Q7Z7F7 MRPL55 "39S ribosomal protein L55, mitochondrial" 0 203.99 3.33E-09 77481000 123620 102510 118340 96272 148480 104690 114840 119590 219240 FALSE TRUE 115882.8449 110099.9471 121147.0807 98742.50251 136818.9797 134912.3035 97620.80812 134521.0748 182647.4277 0.63446196 0.602800425 0.663283804 0.540618085 0.749087909 0.738648801 0.534476775 0.736506812 1 17.47870191 -4.99999998 0.320734122 4.415953693 0.62675448 0.690308419 0.074665461 179.6336139 1.589060221 416.4757099 0.062670752 1.00E-05 4.99999998 -3.789199213 KFAETQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFAETQPK 8 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 130.66 0.0016652 4716300000 8513400 6808700 7453200 7040100 8164000 5080800 8797300 6806300 9503900 FALSE TRUE 7980561.491 7312823.232 7629993.424 7220760.885 7522832.372 6547544.48 7478226.535 7656081.538 7917637.692 1.007947294 0.923611753 0.963670443 0.911984252 0.95013597 0.826956819 0.94450224 0.96696538 1 22.91663862 1.071551217 3.071976063 0.998312029 0.930212355 0.195230686 0.045661842 0.350667696 6.712321396 0.040733164 0.010788926 11.79101567 -1.071551217 -0.068099674 KFAYLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFAYLGR 7 1 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 151.51 0.0030086 627660000 784630 2653200 683030 766810 3136600 449970 884670 2642920 2674000 FALSE TRUE 735521.4089 2849645.689 699231.7942 786487.6428 2890264.088 579869.0343 752021.9464 2972894.38 2227692.125 0.33017193 1.279191885 0.313881701 0.353050421 1.297425284 0.260300348 0.33757894 1.334517614 1 21.08711843 1.231135213 24.99997337 1.167258959 0.620041147 0.263537513 0.395463253 264.1254401 889224.7844 0.340876332 0.091944435 17.02688541 -1.231135213 -0.547217812 KFDDRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KFDDRPK 7 2 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 0 64.265 0.041875 289020000 646550 659650 630490 619780 778700 491630 771650 665760 862290 FALSE TRUE 606083.5896 708491.1724 645445.5205 635684.6041 717544.0431 633555.6001 655948.2461 748881.6015 718368.2284 0.843694871 0.986250706 0.898488401 0.884900778 0.998852698 0.881937111 0.913108654 1.04247595 1 19.45436402 1.243402433 24.9989517 1.021237994 0.920382464 0.456683314 0.047782554 95.34981358 492324.061 0.03119885 0.010580918 17.51468912 -1.243402433 -0.100855531 KFDEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KFDEGR 6 1 P07237;H7BZ94;I3L398;I3L312;I3L3U6;H0Y4J5;Q13087-2;Q13087 P07237 P4HB;PDIA2 Protein disulfide-isomerase;Protein disulfide-isomerase A2 0 ;;;;; 138.37 0.019777 12088190000 33450300 31613500 30524200 30930500 28749700 22974900 38466300 27372400 29861600 FALSE TRUE 31356705.43 33954196.43 31248248.44 31724229 26491814.53 29607380.66 32698635.42 30789904.39 24877506.05 1.260444089 1.364855318 1.256084448 1.275217417 1.064890286 1.190126559 1.314385588 1.237660412 1 24.56833853 -5 0.154646739 0.107140592 1.328116248 0.503684475 0.077712137 117.9276481 1.067545633 32.58873851 0.37896774 1.00E-05 5 1.220975657 KFDEVLVNHFCEEFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFDEVLVNHFCEEFGK 16 1 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 243.09 3.61E-20 767760000 2533200 1790130 2088790 2052520 2247900 1651860 2698000 1898030 2646400 FALSE TRUE 2374651.534 1922673.088 2138337.085 2105191.138 2071359.002 2128725.166 2293459.947 2135003.224 2204698.744 1.077086627 0.872079731 0.969899897 0.954865668 0.939520199 0.965540155 1.040260015 0.968387735 1 21.0721501 1.944199568 8.136893471 1.006458243 0.951075744 0.088369256 0.052973414 0.536535526 72.34000302 0.020582385 0.01298608 87.94265394 -1.944199568 -0.0553825 KFDGVEGPRT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFDGVEGPRTPK 12 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YAN4 Q6PKG0 LARP1 La-related protein 1 1 KFDGVEGPRT(1)PK;KFDGVEGPRT(1)PK 84.874 0.01928 579800000 787890 603500 718430 980600 1091550 461410 793120 515760 947120 TRUE FALSE 738577.3713 648183.7679 735471.4989 1005763.856 1005824.066 594611.5766 674199.019 580153.7713 789039.5534 0.936046068 0.821484506 0.932109798 1.27466849 1.274744798 0.753589062 0.854455288 0.735265766 1 19.5897381 KFDLGQDVIDFTGHALALYR ddPTM_SK-BR-3_Pertuzumab_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 ;; 250.79 4.95E-31 3489366000 5593826 8168436 5928422 5233791 9345968 4671049 7543300 7130035 7759548 FALSE TRUE 5243718.416 8773235.501 6069046.969 5368098.938 8611973.373 6019505.018 6412252.194 8020235.565 6464429.31 0.81116494 1.357155455 0.93883724 0.830405699 1.332209382 0.931173462 0.991928581 1.240671864 1 22.62409158 1.380885712 0.004860344 0.000131915 2.102180101 0 0.197671114 57017.18529 265.9709572 57618.82671 57389.4218 24.03730157 -1.380885712 2.102048186 KFDLNSPWEAFPVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KFDLNSPWEAFPVYR 15 1 O75489 O75489 NDUFS3 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial" 0 77.562 0.016968 0 148550 165400 150830 144830 214030 116390 145070 166450 256150 FALSE TRUE 139252.5207 177646.3881 154407.7588 148546.583 197220.9472 149989.9036 123318.1003 187231.6489 213396.9102 0.652551719 0.832469355 0.723570733 0.696104657 0.924197764 0.702868207 0.577881377 0.877386878 1 17.70317976 1.002643326 24.4349761 1.000000017 0.735110174 0.485925273 0.093964446 40.4705053 374103.937 0.090865073 0.022716268 10.06105044 -1.002643326 -0.264889843 KFDQLLAEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFDQLLAEEK 10 1 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4;P35749;P35749-2;P35749-4;P35749-3;Q7Z406;Q7Z406-6;Q7Z406-2;A0A0C4DFM8;A1L2Z2 P35579;P35580;P35749;Q7Z406 MYH9;MYH10;MYH11;MYH14 Myosin-9;Myosin-10;Myosin-11;Myosin-14 0 ; 151.26 3.23E-05 1873930000 7191000 8653000 5082800 5234600 10383900 2674700 5942000 8442200 10599200 FALSE TRUE 6740928.146 9293677.123 5203366.416 5368928.698 9568390.381 3446842.47 5051052.263 9496227.254 8830125.047 0.76340121 1.052496661 0.589274375 0.608024085 1.083607574 0.390350358 0.572024998 1.075435195 1 23.07400244 3.975382662 24.51185493 0.716911753 0.915134491 0.037626627 0.245134325 133.877238 1887556.073 0.058120472 0.112163057 9448.930665 -3.975382662 0.198222738 KFDSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 120.65 0.032061 2044680000 3724480 3856870 3337860 3643410 4378940 2659300 4274260 4239360 5581700 FALSE TRUE 3491371.445 4142436.668 3417035.615 3736906.069 4035035.716 3426996.74 3633374.393 4768653.428 4650078.211 0.75081994 0.890831612 0.734834009 0.803622197 0.867735021 0.736976151 0.781357695 1.025499618 1 22.14882355 1.237990493 24.99999944 1.012749917 0.797637011 0.753784131 0.051683575 6.995512406 306622.5769 0.038826339 0.011935026 17.29778494 -1.237990493 -0.215112906 KFDVNTSAVQVLIEHIGNLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KFDVNTSAVQVLIEHIGNLDR 21 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 306.51 4.81E-56 2248978000 2923454 3471073 3369210 3569080 4051520 3011241 4406160 3583880 3629300 FALSE TRUE 2740480.233 3728074.857 3449129.252 3660668.635 3733329.962 3880537.393 3745497.213 4031335.307 3023546.384 0.906379425 1.233013946 1.14075619 1.210720184 1.234752006 1.283439015 1.238776171 1.333313532 1 21.52781028 4.740366487 24.71155522 1.217064144 0.906379302 0.529975059 0.08940433 97.76622608 1337707.145 0.019041646 0.1227416 55000.48096 -4.740366487 -0.310684841 KFEEDLLLLEDQNSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KFEEDLLLLEDQNSK 15 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 121.82 0.00018073 61145000 220210 164790 185180 181880 213470 123260 224250 170040 239480 FALSE TRUE 206427.4492 176991.2231 189572.557 186547.3487 196704.9273 158843.161 190625.7943 191269.8683 199509.2409 1.03467613 0.887132958 0.950194368 0.935031119 0.985943941 0.796169442 0.955473508 0.9587018 1 17.60609605 1.042244754 2.633765704 0.998016247 0.927822433 0.094880041 0.062358471 0.513145605 7.667392033 0.053272866 0.014365423 11.02160277 -1.042244754 -0.070193814 KFEEETVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KFEEETVK 8 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 125.97 0.001987 159440000 558680 439790 419270 416920 563380 304840 558220 451170 726870 FALSE TRUE 523713.2161 472352.5092 429215.2824 427618.873 519134.4074 392842.3593 474520.0933 507499.5676 605550.7012 0.864854446 0.78003792 0.708801561 0.706165268 0.85729305 0.648735702 0.783617445 0.838079399 1 19.20788823 0.896922173 2.24890838 0.999309079 0.756464722 0.560778219 0.066123189 0.293028319 3.09106867 0.057857555 0.015793529 7.887187634 -0.896922173 -0.242844357 KFEEFQTDMAAHEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFEEFQTDMAAHEER 15 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 142.01 3.03E-06 173030000 315579 274049 272357 280467 278354 214930 332280 267829 270600 FALSE TRUE 295827.4737 294339.8731 278817.4367 287664.258 256493.1997 276976.8019 282457.6987 301268.0402 225435.1119 1.312251101 1.305652304 1.236796852 1.276040168 1.137769523 1.228632042 1.252944568 1.336384726 1 17.78235271 -1.868818553 2.674495501 0.88513251 1.257663347 0.687146515 0.055269592 8029252.085 3820677.43 5808534.152 0.013111325 0.013526376 1.868818553 0.372530837 KFELLPTPPLS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KFELLPTPPLSPSR 14 1 H0YBT0;A0A087WUS5;P01106;P01106-2;H0YBG3;A0A0B4J1R1;P04198 H0YBT0 MYC;MYCN Myc proto-oncogene protein;N-myc proto-oncogene protein 1 KFELLPTPPLS(0.964)PS(0.036)R 81.157 0.0087529 300940000 242680 275380 243510 270140 539610 267160 333490 376790 386510 TRUE FALSE 227491.092 295769.4217 249286.1722 277072.2497 497231.2073 344284.755 283486.2705 423833.0609 321998.984 0.706496304 0.918541475 0.774183102 0.86047554 1.544201168 1.069210687 0.880394922 1.316255895 1 18.29669661 2.96648419 24.99272348 1.131983435 0.821019367 0.45783073 0.186594139 627.9596363 468269.3371 0.055833782 0.059257061 925.7296845 -2.96648419 -0.310964068 KFELLPTPPLS(ph)PSRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFELLPTPPLSPSRR 15 2 H0YBT0;A0A087WUS5;P01106;P01106-2;H0YBG3;A0A0B4J1R1 H0YBT0 MYC Myc proto-oncogene protein 1 KFELLPTPPLS(0.998)PS(0.002)RR;KFELLPT(0.001)PPLS(0.997)PS(0.002)RR 150.65 1.64E-06 575510000 1345210 1325820 1368200 1430140 2589930 1555840 1756500 1687880 2170620 TRUE FALSE 1261015.707 1423985.092 1400654.35 1466839.814 2386527.345 2004985.751 1493129.132 1898615.533 1808329.499 0.697337354 0.787458863 0.774557043 0.811157377 1.319741422 1.108750232 0.82569528 1.049927867 1 20.78622615 2.970913798 24.53878237 1.038530379 0.767204004 0.582949693 0.123048963 446.8603198 376997.0846 0.038953524 0.041390686 935.2200273 -2.970913798 -0.271326375 KFEQGFITDPVVLSPSHTVGDVLEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFEQGFITDPVVLSPSHTVGDVLEAK 26 1 P20839-3;P20839-7;P20839-5;P20839-6;P20839;C9K0R9 P20839-3 IMPDH1 Inosine-5-monophosphate dehydrogenase 1 0 ; 255.7 8.50E-53 462320000 1045550 1070640 1076600 1024390 1243420 887290 1465460 1117190 1611410 FALSE TRUE 980110.8919 1149911.3 1102137.46 1050677.582 1145766.809 1143436.219 1245727.878 1256673.631 1342455.261 0.730088309 0.856573275 0.820986362 0.782653703 0.853486028 0.851749963 0.927947406 0.936100939 1 20.35644258 1.590555202 0.865722191 0.995803848 0.809130395 0.799778238 0.034810526 0.238309264 0.352730101 0.030093034 0.012273481 38.95428181 -1.590555202 -0.186673453 KFESEILEAISQNSVVIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KFESEILEAISQNSVVIIR 19 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;; 318.13 1.37E-61 556054000 1590504 1540721 1673185 1652846 1751865 1397070 2052791 1632229 1958343 FALSE TRUE 1490957.194 1654797.586 1712873.738 1695260.827 1614280.59 1800381.429 1744994.047 1836016.384 1631482.902 0.91386627 1.014290486 1.049887643 1.039091997 0.989456027 1.103524546 1.069575442 1.125366611 1 20.63775244 6.22429896 0.669424937 1.062491993 3.28E-12 0.530337866 0.041300302 14.93157519 1.047697989 0.015068353 18.79129488 1676096.27 -6.22429896 -1.062491993 KFGDPVVQSDMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFGDPVVQSDMK 12 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 128.35 0.00040641 2428200000 4130000 3623900 2858800 2577400 4672600 1814830 4126800 3955800 5602900 FALSE TRUE 3871510.672 3892217.327 2926612.086 2643540.448 4305632.844 2338741.96 3508024.651 4449690.338 4667739.794 0.8294187 0.83385482 0.626986982 0.566342719 0.922423493 0.501043773 0.751546746 0.953285859 1 22.15429271 1.235282527 4.435687695 0.989729562 0.712109551 0.417714517 0.127587413 0.178186274 7.800760943 0.102241311 0.029717421 17.19026323 -1.235282527 -0.277620011 KFGEEIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KFGEEIAR 8 1 Q8WUM4;Q8WUM4-2;F8WDK9 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;; 118.18 0.0031054 1233840000 2477540 2471340 2397370 2374140 2593170 1973220 2734260 2236560 2663840 FALSE TRUE 2322475.194 2654320.585 2454236.749 2435064.452 2389512.889 2542856.581 2324283.097 2515799.439 2219227.895 1.046523973 1.196055886 1.105896674 1.0972575 1.076731639 1.145829406 1.047338627 1.133637264 1 21.0816264 -4.999999995 0.151684044 0.591712979 1.145419656 0.310241038 0.04664489 136.2476593 1.221554232 16.66149159 0.210083989 1.00E-05 4.999999995 0.553706677 KFGFEIIETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KFGFEIIETK 10 1 E7EQ69;Q9GZZ1;A0A087WWJ2;C9J5D1;Q9GZZ1-2;B0AZT5 E7EQ69 NAA50 N-alpha-acetyltransferase 50 0 86.028 0.022188 149880000 268130 220430 240930 233650 273450 186560 273710 202280 307930 FALSE TRUE 251348.2219 236750.8666 246644.9734 239645.8546 251974.34 240416.8435 232669.7265 227535.1033 256534.4937 0.979783336 0.92288122 0.961449549 0.934166206 0.982224014 0.937171606 0.906972482 0.886957149 1 17.9687933 1.998764995 24.99058767 0.921248123 0.952002797 0.074512888 0.034192356 79.69591477 1612688.484 0.011538746 0.008403572 99.71603363 -1.998764995 0.030754674 KFGGPGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFGGPGAR 8 1 P62249;M0R210 P62249 RPS16 40S ribosomal protein S16 0 ; 103.56 0.0076141 5498100000 6540700 7329000 6947500 6599800 7505800 5608000 7902000 5939400 8028500 FALSE TRUE 6131329.262 7871646.786 7112297.981 6769162.041 6916324.745 7226938.562 6717168.459 6680947.164 6688491.484 0.916698373 1.176894193 1.06336354 1.012061099 1.034063475 1.080503515 1.00428751 0.998872045 1 22.67324943 1.988192258 0.665123428 0.994336701 1.073578784 0.013700174 0.06696233 1.434470362 1.239219603 0.057964311 0.03377276 97.31779443 -1.988192258 0.079242083 KFGLHGS(ph)SGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFGLHGSSGK 10 1 Q9NV70-2 Q9NV70-2 EXOC1 Exocyst complex component 1 1 KFGLHGS(0.794)S(0.206)GK;KFGLHGS(0.962)S(0.038)GK 89.992 0.0053521 1347980000 1583120 1147190 1419630 1404030 1571620 1136480 2024670 1402760 2263600 TRUE FALSE 1484035.345 1232129.141 1453304.294 1440059.787 1448191.305 1464563.327 1721089.53 1577897.674 1885790.537 0.786956619 0.653375397 0.770660509 0.76363719 0.767949185 0.776630966 0.912662089 0.836730084 1 20.84673801 1.461778807 0.464429878 1.002700106 0.708196416 0.763498853 0.045546567 0.378833997 0.220252217 0.047031974 0.030373731 28.958683 -1.461778807 -0.29450369 KFGQGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KFGQGSR 7 1 A0A2R8Y851;P62273;P62273-2;A0A2R8Y6P7 A0A2R8Y851 RPS29 40S ribosomal protein S29 0 ;;; 127.56 0.0061612 7091820000 4294820 5776940 3892360 3664150 5982980 2813960 4752360 5316740 6524190 FALSE TRUE 4026014.883 6204670.649 3984688.617 3758178.292 5513100.885 3626304.571 4039787.737 5980546.693 5435260.541 0.7407216 1.141559011 0.733118235 0.691444001 1.014321364 0.667181369 0.743255582 1.100323829 1 22.37391776 1.232251518 24.99687071 1.050162001 0.832507998 0.283514813 0.151694919 230.4119664 912857.0507 0.133539241 0.03662877 17.0707074 -1.232251518 -0.217654003 KFGYVDFESAEDLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KFGYVDFESAEDLEK 15 1 P19338 P19338 NCL Nucleolin 0 ;;;;; 265.77 4.92E-25 6024090000 18039300 12677710 14945840 14685760 15642870 10660040 18972130 12466040 20635520 FALSE TRUE 16910252.41 13616380.84 15300362.38 15062621.46 14414342.09 13737420.5 16127435.24 14022452.54 17191318.4 0.983650702 0.792049831 0.890005177 0.876176051 0.838466356 0.799090574 0.938115091 0.815670573 1 24.03517685 -1.391182017 4.025916064 1.000481341 0.864011225 0.323001178 0.060563234 0.000232824 3.52E-05 0.05217893 0.012255559 0.040627302 1.391182017 -0.136470116 KFHTVSGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFHTVSGSK 9 1 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ; 137.98 9.71E-05 2805300000 3374900 3353300 3511900 3398400 4221100 2458770 3978900 3742300 5171600 FALSE TRUE 3163671.033 3601581.821 3595203.926 3485608.697 3889591.833 3168576.984 3382300.883 4209534.393 4308426.55 0.734298472 0.835939009 0.834458679 0.809021265 0.902787082 0.73543716 0.785043181 0.977046804 1 22.03872966 1.224579026 12.91266172 0.988660024 0.809831933 0.70260344 0.049493993 0.491595967 445.5163778 0.04224913 0.011431611 16.77177494 -1.224579026 -0.178828091 KFIEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 4955300000 11108600 11941500 11577400 11640200 13994000 10468100 13803600 12161200 13170800 FALSE TRUE 10413332.56 12825661.09 11852021.4 11938907.24 12894967.69 13490070.53 11733878.33 13679552.59 10972508.39 0.949038468 1.168890524 1.080156056 1.08807456 1.17520691 1.229442717 1.069388868 1.246711518 1 23.38739004 4.745552541 24.2855175 1.133317071 0.949038339 0.365136697 0.07590338 568.7906886 1975541.351 0.01603338 0.158636714 55661.19698 -4.745552541 -0.184278733 KFLDAGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFLDAGHK 8 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 90.629 0.0084784 2213200000 10093900 10924700 10051400 10412000 13489700 6829000 12502100 10841400 13563100 FALSE TRUE 9462140.817 11733576.16 10289823.95 10679189.55 12430273.38 8800421.44 10627526.17 12194972.65 11299330.99 0.837407173 1.038431051 0.910657805 0.945116977 1.100089323 0.778844469 0.940544726 1.079265017 1 23.42973402 1.253243429 24.69057559 1.039632485 0.941400958 0.178800827 0.091855754 304.6864314 512365.7514 0.057222981 0.020691888 17.91609797 -1.253243429 -0.098231528 KFLDGIYVSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFLDGIYVSEK 11 1 A0A2R8Y5Y7;P32969;D6RAN4;H0Y9R4;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 201.04 7.18E-08 2347500000 10142500 10460700 9569600 9242700 11876600 6952600 11256800 9723500 12928100 FALSE TRUE 9507699.03 11235221.11 9796595.431 9479883.33 10943859.74 8959702.754 9568947.343 10937500.38 10770316.59 0.882768761 1.043165353 0.909592151 0.880186135 1.016113097 0.831888522 0.888455531 1.015522644 1 23.36055732 KFLDGNELTLADCNLLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFLDGNELTLADCNLLPK 18 1 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ; 175.39 5.58E-12 487520000 1901630 1592740 1679490 1609390 1933920 1326480 2255900 1541920 2146580 FALSE TRUE 1782610.373 1710668.127 1719328.296 1650689.672 1782037.724 1709413.242 1917648.738 1734432.106 1788301.931 0.99681734 0.956587977 0.961430655 0.923048644 0.99649712 0.955886259 1.072329401 0.96987655 1 20.77015891 1.772575783 25 1.021303377 0.963246346 0.324186015 0.032749032 30.89870538 22720.11857 0.013532954 0.007508939 59.23464404 -1.772575783 -0.058057031 KFLETVELQISLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFLETVELQISLK 13 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ; 136.33 0.00011806 191639000 872520 939820 881290 876710 1035490 664100 1056130 878360 1006400 FALSE TRUE 817910.5307 1009405.251 902194.615 899207.8629 954166.7924 855814.8892 897773.1111 988025.1795 838425.3384 0.975531742 1.203929801 1.076058384 1.072496049 1.138046226 1.020740727 1.070784803 1.178429532 1 19.67732279 3.704912975 23.80149965 1.080318552 1.116229676 0 0.074993548 777.3859873 833154.9394 0.018145343 0.028136079 5068.89126 -3.704912975 0.035911124 KFLPLFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFLPLFDR 8 1 P61604;B8ZZL8;S4R3N1 P61604;S4R3N1 HSPE1;HSPE1-MOB4 "10 kDa heat shock protein, mitochondrial" 0 ; 171.36 0.00046474 1858470000 1686370 4770900 1456960 1274280 6904900 936890 1509220 5187400 5899400 FALSE TRUE 1580823.112 5124142.4 1491519.779 1306980.182 6362617.007 1207354.934 1282926.472 5835058.309 4914752.028 0.321648601 1.042604463 0.303478135 0.265930036 1.294595733 0.24565938 0.26103585 1.187253858 1 22.2286872 1.225606052 24.99967021 1.093627322 0.548864774 0.291124584 0.362721013 340.143176 656387.4484 0.325468106 0.083435404 16.81148403 -1.225606052 -0.544762548 KFMQDPMEIFVDDETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KFMQDPMEIFVDDETK 16 1 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;H0YCC6 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 109.35 0.0015698 37541000 96489 66123 83604 82215 96904 66629 101020 73388 97211 FALSE TRUE 90449.92573 71018.81572 85587.12636 84324.77609 89293.55073 85863.71067 85872.98882 82550.65335 80985.85609 1.116860772 0.876928629 1.056815727 1.041228434 1.102582044 1.060230944 1.060345509 1.019321859 1 16.30538235 3.724288625 24.76541493 1.054099782 0.975891331 0.077908417 0.063598103 151.7914198 1327114.912 0.01494765 0.024339295 5300.155669 -3.724288625 -0.078208451 KFMTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFMTNR 6 1 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4 E7ETK0 RPS24 40S ribosomal protein S24 0 ; 119.57 0.033516 2236700000 2002680 3489700 1825250 1766170 3883500 1453560 2294870 3126800 3679300 FALSE TRUE 1877335.834 3748081.019 1868545.792 1811492.912 3578505.575 1873179.175 1950775.548 3517187.863 3065201.061 0.612467436 1.222784719 0.609599747 0.590986652 1.167461939 0.611111356 0.636426619 1.147457473 1 21.54755028 -1.230593571 7.647683414 1.000000234 0.821061761 0.042838514 0.259752065 9.66E-07 9.73E-08 0.234933736 0.05537434 0.05880394 1.230593571 -0.178938473 KFNHDGEEEEEDDDYGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KFNHDGEEEEEDDDYGSR 18 1 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;Q6PJT7-9;Q6PJT7-2;H0YJA2;Q6PJT7-3;Q6PJT7-11;G3V5I6 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 0 222.7 3.60E-19 281740000 312550 244990 287880 309830 295310 253010 326590 252430 357080 FALSE TRUE 292988.0534 263129.3145 294708.6495 317780.7623 272117.5438 326049.8797 277620.8614 283946.4412 297481.0412 0.984896558 0.884524652 0.990680443 1.068238706 0.914739113 1.09603583 0.933238839 0.954502647 1 18.1824382 3.743561206 5.432913418 0.993707865 0.929768239 0.142418916 0.060169506 0.271496325 25.29491658 0.014273942 0.024902597 5540.65624 -3.743561206 -0.063939626 KFPSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KFPSLR 6 1 Q14137;Q14137-2 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 97.602 0.065557 245060000 518700 587530 607640 537200 611630 393170 644930 554010 642280 FALSE TRUE 486235.4929 631031.3325 622053.5077 550985.4615 563595.047 506671.7964 548228.7337 623179.368 535079.3187 0.908716663 1.179322972 1.162544479 1.029726701 1.053292526 0.946909699 1.024574702 1.164648579 1 19.02939324 3.216891507 24.32419212 1.031479527 1.115343578 0.01603484 0.091542063 307.8876005 345611.3206 0.0255083 0.030517981 1647.750709 -3.216891507 0.083864051 KFQEQECPPS(ph)PEPTRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFQEQECPPSPEPTRK 16 2 P62070-2;P62070-3;P62070;P62070-4 P62070-2 RRAS2 Ras-related protein R-Ras2 1 KFQEQECPPS(1)PEPTRK;KFQEQECPPS(1)PEPTRK 155.86 1.14E-07 319750000 518140 440410 383340 378130 638270 314560 502740 475380 575770 TRUE FALSE 485710.5423 473018.4146 392433.0058 387833.456 588142.8489 405368.3655 427358.8042 534732.2394 479670.2674 1.012592556 0.986132447 0.818130771 0.808541789 1.22613989 0.845097962 0.890942869 1.114791297 1 18.87168349 KFQGIKHECQANGPEDLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KFQGIKHECQANGPEDLNR 19 2 P60981;P60981-2 P60981 DSTN Destrin 0 160.97 1.83E-11 446070000 218290 316270 304020 333670 447370 219430 372540 243920 1133100 FALSE TRUE 204627.6186 339686.9599 311231.498 342232.5371 412235.3648 282775.8789 316681.0855 274373.9489 943978.2899 0.21677153 0.359846157 0.329701966 0.362542805 0.436700048 0.299557608 0.335474967 0.290657054 1 19.84839415 -1.846057814 2.563068226 1.268187111 0.334712982 0.932583115 0.05668651 6365140.776 4042674.032 10458588.22 0.013491485 0.014254178 1.846057814 -0.933474129 KFS(ph)APGQLCISMTSNLGGSAPISAASATSLGHFTK ddPTM_SK-BR-3_Pertuzumab_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 219.61 7.23E-37 240100000 82943 102580 97144 79315 107290 76859 150810 123550 144630 TRUE FALSE 77751.74569 110175.1299 99448.30155 81350.35718 98863.87619 99046.9456 128197.4406 138975.4895 120490.3187 0.645294548 0.914389896 0.825363421 0.675160943 0.820513028 0.822032398 1.063964657 1.153416233 1 16.87855771 1.730837191 3.781916962 1.088113278 0.798670055 0.716763864 0.085283342 0.108261751 3.408953407 0.045663677 0.022275569 53.80680333 -1.730837191 -0.289443223 KFS(ph)GSGLAMGLGSASASAWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KFSGSGLAMGLGSASASAWR 20 1 Q92796-2 Q92796-2 DLG3 Disks large homolog 3 1 KFS(0.994)GS(0.006)GLAMGLGSASASAWR;KFS(0.887)GS(0.113)GLAMGLGSASASAWR;KFS(0.934)GS(0.066)GLAMGLGSASASAWR 260.07 1.56E-36 840497000 1286300 1237988 1097332 1042555 1367698 710369 1165416 1018239 1575138 TRUE FALSE 1205792.779 1329649.92 1123361.233 1069308.726 1260284.516 915440.9984 990672.69 1145368.381 1312237.292 0.918883183 1.01326942 0.856065622 0.814874515 0.960409008 0.69761849 0.754949349 0.872836329 1 20.3235972 3.729306943 2.666890827 0.827242507 0.968119556 0.184750252 0.09217615 0.332769867 4.719069741 0.024396779 0.045935299 5361.754722 -3.729306943 0.140877049 KFS(ph)HS(ph)TLRHFGLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KFSHSTLRHFGLGK 14 2 Q7Z449 Q7Z449 CYP2U1 Cytochrome P450 2U1 2 KFS(0.667)HS(0.667)T(0.667)LRHFGLGK 61.375 0.045848 90476000 100460 541370 398320 379310 484460 500540 367570 526270 248050 TRUE FALSE 94172.38793 581453.5981 407768.3385 389043.7368 446412.4658 645037.7724 312456.2909 591975.968 206648.8525 0.455712126 2.813727688 1.973242694 1.882631972 2.160246526 3.12141957 1.51201561 2.86464677 1 17.65682183 4.75127658 24.68969851 2.20694184 0.455710813 0.408936287 0.644518634 1588.430363 3084078.774 0.134316933 2.410908538 56399.67216 -4.75127658 -1.751231028 KFS(ph)PSQVPVQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KFSPSQVPVQTR 12 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 KFS(0.96)PS(0.04)QVPVQTR;KFS(0.976)PS(0.024)QVPVQTR;KFS(0.987)PS(0.013)QVPVQTR 183.31 9.65E-06 2445400000 1568577 1538615 1445428 1457633 1635630 1121488 1544636 1308002 1929550 TRUE FALSE 1470402.566 1652535.656 1479714.235 1495038.331 1507174.218 1445243.38 1313032.171 1471308.929 1607495.64 0.914716363 1.028018748 0.920509019 0.93004192 0.937591481 0.899065194 0.816818497 0.915280199 1 20.61638339 3.115536631 1.048574304 0.889945345 0.975562324 0.065838364 0.054736906 0.652375521 1.545834367 0.023040744 0.032331956 1304.778018 -3.115536631 0.085616979 KFSAPR ddPTM_SK-BR-3_Pertuzumab_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 83.377 0.091487 265250000 156080 823270 125250 110390 782190 94633 147550 738540 669600 FALSE TRUE 146311.2314 884225.7674 128220.9891 113222.7943 720759.9526 121952.0109 125426.2473 830748.3447 557839.4342 0.26228198 1.585090105 0.22985286 0.202966638 1.292056295 0.218614898 0.22484292 1.489224845 1 19.0894904 -1.357893647 6.513041048 1.000021289 0.67624092 0.028836231 0.565093194 0.000164724 1.62E-05 0.51594109 0.121600497 0.04386381 1.357893647 -0.323780369 KFSGFSAKPNNSGEAPSS(ph)PTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KFSGFSAKPNNSGEAPSSPTPK 22 2 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 KFSGFSAKPNNSGEAPS(0.005)S(0.99)PT(0.005)PK;KFSGFSAKPNNSGEAPS(0.002)S(0.998)PTPK 176.44 1.80E-13 5389500000 5742200 3069890 4226900 3831330 4355460 2916520 5731800 3512390 6396300 TRUE FALSE 5382805.952 3297187.85 4327164.064 3929648.414 4013399.741 3758471.978 4872369.801 3950919.623 5328716.208 1.010150614 0.618758388 0.812046259 0.737447494 0.753164474 0.705324103 0.91436091 0.741439301 1 22.34535657 0.209791116 0.57991321 1.010593534 0.761830886 0.243344863 0.111464228 3.615684402 1.675787251 0.198139363 0.043137989 1.621030237 -0.209791116 -0.248762648 KFVIKPIDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KFVIKPIDK 9 2 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 82.261 0.01066 91193000 178220 145190 159450 151510 184180 120960 206360 164780 202110 FALSE TRUE 167065.5283 155940.0187 163232.2293 155398.0031 169715.2457 155879.1884 175418.2338 185353.1457 168376.5353 0.992213838 0.926138659 0.969447607 0.922919591 1.007950695 0.925777384 1.041821139 1.100825275 1 17.36133158 1.635649818 5.429523962 1.056695296 0.956021187 0.566904965 0.037008309 0.085861801 5.44338626 0.017417634 0.008338878 43.21652249 -1.635649818 -0.100674109 KFVVQLFAEEWGQYVDLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KFVVQLFAEEWGQYVDLPK 19 1 Q96CN7;D6RGE2 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 110.33 0.00038149 42499000 105450 97362 91616 87952 128470 71245 98293 102620 112670 FALSE TRUE 98850.07273 104570.7838 93789.17478 90208.99722 118380.4844 91812.27493 83554.87716 115432.3329 93864.64912 1.053112899 1.114059284 0.999195924 0.961054008 1.261182836 0.978134748 0.890163421 1.229774297 1 16.5182943 7.999999937 0.222249994 1.019608544 1.354596081 0 0.118257636 277.2056054 3.568693504 0.174764919 33.4354474 99999985.48 -7.999999937 0.334987537 KFYGPEGPYGVFAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KFYGPEGPYGVFAGR 15 1 O00264 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 0 154.46 3.97E-06 248310000 170410 253890 173750 194720 301230 136400 233290 222410 355470 FALSE TRUE 159744.3423 272688.2798 177871.4321 199716.8449 277572.6109 175776.4657 198310.3303 250178.3781 296139.7606 0.539422136 0.920809415 0.600633403 0.674400643 0.937302746 0.593559154 0.669651147 0.84479834 1 18.17591868 0.985904961 4.227092358 0.999443064 0.715776692 0.353457674 0.13101502 0.199013594 10.76196603 0.116066957 0.029604465 9.680659858 -0.985904961 -0.283666371 KFYPLEIDYGQDEEAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KFYPLEIDYGQDEEAVK 17 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 160.45 4.95E-09 63814000 93744 72583 81943 76660 90087 66017 103840 69057 111040 FALSE TRUE 87876.73038 77957.12084 83886.72666 78627.22539 83011.93041 85075.0362 88270.156 77678.91846 92506.70665 0.949949831 0.842718584 0.906817783 0.849962432 0.897361212 0.919663442 0.954202773 0.839711209 1 16.49727034 2.292749529 3.5259598 0.928224755 0.882550507 0.135418987 0.048895875 0.402424361 10.23167904 0.016589213 0.012994891 196.2228271 -2.292749529 -0.045674247 KFYPLEIDYGQDEEAVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KFYPLEIDYGQDEEAVKK 18 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 256.25 7.77E-31 312060000 476490 270710 352670 329680 400200 243540 485720 279350 539440 FALSE TRUE 446667.3415 290753.6501 361035.4989 338140.1469 368769.9063 313846.0445 412890.7952 314227.4624 449403.9791 0.993910518 0.646976136 0.803365159 0.752419121 0.820575526 0.698360627 0.918751979 0.699209346 1 18.77765337 -4.999974293 0.345530087 3.413320744 0.777859215 0.263264279 0.105638641 509.3017253 4.22724465 908.650044 0.073557897 1.00E-05 4.999974293 -2.635461529 KGAAEEEQQDS(ph)GSEPRGDEDDIPLGPQSNVSLLDQHQHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGAAEEEQQDSGSEPRGDEDDIPLGPQSNVSLLDQHQHLK 40 2 Q9UJV9;D6RGI7;A0A499FJW5 Q9UJV9 DDX41 Probable ATP-dependent RNA helicase DDX41 1 KGAAEEEQQDS(0.832)GS(0.168)EPRGDEDDIPLGPQSNVSLLDQHQHLK 103.95 5.94E-06 89373000 43908 35048 43402 43283 40537 29782 56716 41675 58396 TRUE FALSE 41159.87666 37642.99039 44431.51594 44393.71506 37353.38754 38379.57993 48211.96233 46878.21549 48649.33035 0.846052276 0.773761738 0.913301696 0.912524689 0.767808874 0.788902533 0.991009783 0.96359426 1 15.57013233 1.688147231 6.771702931 0.982785309 0.836692172 0.657490121 0.05126252 0.0862812 8.242600995 0.026765073 0.013724942 48.76937966 -1.688147231 -0.146093137 KGAAPT(ph)PPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KGAAPTPPGK 10 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 KGAAPT(1)PPGK;KGAAPT(1)PPGK;KGAAPT(1)PPGK;KGAAPT(1)PPGK 61.11 0.054921 2523090000 6907200 4460840 5683220 5267220 6144800 4384460 7397800 5536900 7424300 TRUE FALSE 6474890.682 4791125.235 5818028.662 5402385.783 5662212.195 5650182.426 6288568.568 6228194.153 6185136.367 1.046846876 0.774619176 0.940646789 0.873446511 0.915454706 0.913509758 1.016722703 1.006961493 1 22.56037397 1.812105472 3.52790631 1.009962657 0.895286837 0.301915669 0.067293853 0.237199312 5.258092038 0.03266169 0.016985565 64.87919795 -1.812105472 -0.11467582 KGADSLEDFLYHEGYACTSIHGDR ddPTM_SK-BR-3_Pertuzumab_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 ;; 239.02 6.98E-38 1610420000 788650 1133920 1160750 1190680 1410440 1055100 1402530 1142490 1400630 FALSE TRUE 739289.8043 1217876.617 1188283.538 1221234.865 1299669.732 1359690.242 1192233.647 1285132.391 1166855.805 0.633574261 1.043725036 1.018363652 1.046603068 1.113822056 1.165259869 1.02174891 1.101363499 1 20.15419486 4.741429775 4.675157148 1.064448354 0.606804225 0.880448725 0.049890971 0.061439295 3.671286308 0.011937183 0.092331916 55135.30417 -4.741429775 -0.457644129 KGAEPSGGAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KGAEPSGGAAR 11 1 O00762;K4DI81;A0A0A0MSE8;A0A087WVK1;O00762-3;O00762-4 O00762 UBE2C Ubiquitin-conjugating enzyme E2 C 0 ;;; 139.46 6.26E-05 335613000 428884 432619 428286 398497 471639 343474 481903 389544 457801 FALSE TRUE 402040.916 464650.5609 438445.1462 408723.1077 434598.3754 442629.368 409646.1189 438179.4259 381391.0556 1.054143536 1.218304819 1.149594726 1.071664114 1.139508568 1.160565675 1.074084232 1.148898013 1 18.54091148 -5 0.187484712 0.42063652 1.159603385 0.353912086 0.050934083 132.4464521 1.291757679 28.50973197 0.136368501 1.00E-05 5 0.738966864 KGAGDGS(ph)DEEVDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 15 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 204.07 1.50E-08 32203070000 40011180 14665100 21648690 20482680 18198480 15911380 29657830 16945070 17589050 TRUE FALSE 37506951.67 15750919.26 22162207.15 21008300.25 16769244.79 20504737.11 25210913.72 19060699.29 14653323.93 2.559620729 1.074904189 1.51243549 1.43368838 1.144398696 1.399323267 1.720491122 1.300776492 1 23.80472462 4.747209241 24.92931012 1.365396103 2.559621359 0.760065376 0.217164424 550.7271659 1587412.81 0.05100745 0.604639461 55873.93281 -4.747209241 1.194225256 KGAGDGS(ph)DEEVDGKADGAEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KGAGDGSDEEVDGKADGAEAK 21 2 P35579;P35579-2 P35579 MYH9 Myosin-9 1 KGAGDGS(1)DEEVDGKADGAEAK;KGAGDGS(1)DEEVDGKADGAEAK;KGAGDGS(1)DEEVDGKADGAEAK 120.57 1.67E-05 1952590000 2105080 634890 994580 981980 910720 639320 1314380 706500 960830 TRUE FALSE 1973326.8 681897.9162 1018171.907 1007179.269 839195.7249 823881.3055 1117300.921 794708.0802 800461.2658 2.465237089 0.851881216 1.271981482 1.258248603 1.048390173 1.02925818 1.395821346 0.992812662 1 19.61047207 4.745890798 24.99861112 1.129557857 2.465237716 0.87358977 0.162268367 295.667596 1008310.774 0.037721875 0.390250149 55704.56633 -4.745890798 1.335679859 KGAGDGS(ph)DEEVDGKADGAEAKPAE ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 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 240.52 8.35E-37 65575890000 18443140 5990870 9350850 9972590 10632640 6068380 13519120 6996750 14329520 TRUE FALSE 17288816.79 6434440.248 9572656.578 10228503.54 9797595.344 7820222.794 11492053.46 7870309.639 11937830.54 1.448237746 0.538995777 0.80187573 0.856814269 0.820718246 0.655079059 0.962658451 0.659274699 1 23.50903734 -1.293457204 3.47391727 1.000644676 0.814454825 0.027229675 0.247430369 46273781.59 56677573.1 298174.3872 0.054396066 0.050879495 1.293457204 -0.186189852 KGASLS(ph)NGQGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGASLSNGQGSR 12 1 O43639 O43639 NCK2 Cytoplasmic protein NCK2 1 KGAS(0.072)LS(0.927)NGQGS(0.001)R 56.215 0.054892 0 58421 53767 52725 49731 66737 41819 57871 54927 91975 TRUE FALSE 54764.53389 57747.96462 53975.6619 51007.18165 61495.74522 53891.46643 49193.7808 61784.75686 76623.77832 0.714719831 0.753655926 0.704424437 0.665683457 0.802567383 0.70332562 0.642017163 0.80633921 1 16.22550455 0.948193206 6.128956397 0.999977393 0.713467075 0.814607633 0.043655333 0.154216238 17.07547178 0.041839646 0.010516847 8.875507712 -0.948193206 -0.286510319 HRSNS(ph)FSDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 HRSNSFSDER 10 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 HRS(0.002)NS(0.989)FS(0.009)DER;HRS(0.003)NS(0.986)FS(0.012)DER;HRS(0.303)NS(0.654)FS(0.043)DER 122.97 0.0002874 1917826000 966398 2177860 1227757 1332901 2223790 1076266 2795610 2672260 6177990 TRUE FALSE 905912.8742 2339111.02 1256879.976 1367105.496 2049142.504 1386966.522 2376434.234 3005897.543 5146843.558 0.176013291 0.454474863 0.244204037 0.265620177 0.398135766 0.269479052 0.461726533 0.584027377 1 22.2952565 0.880941768 1.113348082 0.999134396 0.310376074 0.883396563 0.080729562 0.188962223 0.465475718 0.069880553 0.022132095 7.602243358 -0.880941768 -0.688758322 KGAVAEDGDELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGAVAEDGDELR 12 1 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;G3V5D9;G3V2D9 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 152.99 9.71E-05 1101410000 2357800 2199200 2286000 2368200 2326800 2126770 2859700 2226700 2102520 FALSE TRUE 2210229.507 2362031.056 2340225 2428972.021 2144062.514 2740733.974 2430914.533 2504708.397 1751595.829 1.261837617 1.34850233 1.336053078 1.386719459 1.224062354 1.564706839 1.387828455 1.429957959 1 20.74023849 -0.588243942 12.30907303 0.999999959 1.36944677 0.610065851 0.092312571 0 0 0.083560562 0.019695413 0.258081015 0.588243942 0.36944681 KGAVAEDGDELRTEPEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGAVAEDGDELRTEPEAK 18 2 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;G3V5D9 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 213.5 4.22E-17 1089300000 1558920 1170510 1362380 1442030 1661010 876150 1749980 1189860 2287300 FALSE TRUE 1461349.98 1257175.778 1394696.297 1479034.931 1530560.975 1129080.282 1487586.745 1338416.64 1905534.853 0.766897534 0.659749559 0.731918545 0.776178367 0.803218567 0.592526702 0.780666248 0.70238371 1 20.86176457 -1.306905518 3.091477797 1.001987806 0.723207627 0.647892581 0.063273567 12167944.52 16100070.69 223790.3467 0.014443846 0.049328111 1.306905518 -0.278780179 KGAVECCPNCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGAVECCPNCR 11 1 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ; 187.85 5.46E-06 418180000 517830 556960 557710 525290 686200 529720 734920 551950 945980 FALSE TRUE 485419.9447 598197.8979 570939.1446 538769.8307 632308.62 682641.5647 624725.5687 620862.1725 788089.8267 0.615944945 0.759047862 0.724459478 0.683640129 0.802330646 0.866197661 0.792708582 0.787806353 1 19.58800055 -4.99999998 0.073609905 1.855638265 0.468790154 0.76935373 0.04966723 137.7483112 0.726208879 19.52390432 2.196594106 1.00E-05 4.99999998 -1.386848112 KGCVITISGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGCVITISGR 10 1 O00154-6;O00154-4;O00154-7;O00154;O00154-5;K7EKP8 O00154-6 ACOT7 Cytosolic acyl coenzyme A thioester hydrolase 0 ; 176.42 4.01E-06 1723700000 1678570 1596790 1731380 1539490 1650640 1446850 1801500 1475840 1336870 FALSE TRUE 1573511.3 1715017.993 1772449.151 1578995.92 1521005.393 1864532.107 1531381.799 1660101.873 1113737.76 1.412820285 1.539875951 1.591442092 1.417744801 1.365676416 1.6741213 1.374993157 1.490568006 1 20.08697815 -2.811679839 0.356935892 6.56E-13 1.513438881 0.700974251 0.098818565 41.71823903 1.433250763 31.75048564 0.069294165 0.001542837 2.811679839 1.513438881 KGDECELLGHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGDECELLGHSK 12 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ; 162.93 3.98E-05 2114760000 4768100 3207700 3488800 3341900 4973500 3004900 3883000 4020800 7881200 FALSE TRUE 4469673.132 3445201.446 3571555.984 3427658.812 4582901.372 3872365.85 3300780.198 4522805.731 6565776.806 0.680753133 0.524721072 0.543965488 0.522049243 0.697998349 0.589780305 0.502725008 0.688845488 1 22.64653428 0.912506215 4.767537876 0.999940175 0.571034929 0.801977773 0.065466801 0.201057153 10.03615445 0.060504334 0.015325622 8.175347369 -0.912506215 -0.428905246 KGDEVDGVDEVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KGDEVDGVDEVAK 13 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;; 119.54 0.00054566 1092300000 3090840 1713900 2253900 2097060 2228240 1520940 2937500 1955360 3327740 FALSE TRUE 2897389.842 1840798.939 2307363.572 2150874.11 2053243.019 1960010.688 2497049.145 2199491 2772318.696 1.045114274 0.663992542 0.832286553 0.775839413 0.740623011 0.70699328 0.900707826 0.793375958 1 21.40266168 0.510387406 0.908172113 0.999670473 0.787344713 0.225442514 0.107835378 2.129002559 2.6330599 0.095765628 0.030876162 3.238824425 -0.510387406 -0.212325759 KGDEYIINGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGDEYIINGQK 11 1 B7Z9I1;Q5T4U5;P11310;P11310-2 B7Z9I1 ACADM "Medium-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 117.23 0.0014146 345250000 609850 455410 476630 436810 733610 444080 525490 550280 1237700 FALSE TRUE 571680.5771 489129.0303 487935.8887 448019.2841 675995.2298 572278.687 446697.6529 618983.6693 1031119.874 0.554426882 0.474366795 0.473209664 0.434497768 0.65559325 0.555006941 0.433216025 0.600302336 1 19.97578063 -4.999999999 0.348866475 6.625814844 0.494499406 0.820911679 0.070377713 168.3885971 1.384619884 708.0231342 0.052754645 1.00E-05 4.999999999 -6.131315439 KGDGGGAGGGGGGGGSGGGGS(ph)GGGGGGGSSRPPAPQENTTSEAGLPQGEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGDGGGAGGGGGGGGSGGGGSGGGGGGGSSRPPAPQENTTSEAGLPQGEAR 51 2 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 KGDGGGAGGGGGGGGS(0.464)GGGGS(0.531)GGGGGGGS(0.002)S(0.002)RPPAPQENTTSEAGLPQGEAR 61.903 0.00058572 148460000 10464 8061.1 9492.7 10635 10771 7582.1 12320 7717.6 12883 TRUE FALSE 9809.076919 8657.952232 9717.871327 10907.91211 9925.089108 9770.929185 10472.73037 8681.159349 10732.74407 0.913939329 0.806685799 0.905441447 1.016320899 0.924748512 0.910384997 0.975773791 0.808848072 1 13.38973136 3.590769023 4.189032231 0.939510941 0.854163917 0.209088272 0.062402383 0.272228126 8.237481361 0.015358928 0.024416533 3897.346535 -3.590769023 -0.085347024 KGDIFLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGDIFLVR 8 1 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 124.74 0.0020712 4561500000 6658400 7485100 7321000 7112100 8489300 5761000 10011400 8218100 11792100 FALSE TRUE 6241662.63 8039304.592 7494657.577 7294608.527 7822584.622 7424107.178 8510283.511 9244147.875 9823922.33 0.635353418 0.818339592 0.7628987 0.74253524 0.79627916 0.75571721 0.866281636 0.940983404 1 23.22786772 1.37197657 1.472821112 0.998255174 0.759149874 0.782258571 0.048396145 0.164918001 0.667781341 0.040405718 0.012787954 23.54922235 -1.37197657 -0.2391053 KGDIIQLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGDIIQLQR 9 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 136.96 0.00028562 1396050000 1032230 1943630 928490 881790 2266370 687420 1167120 2029460 2419250 FALSE TRUE 967624.5669 2087538.388 950514.2213 904418.2243 2088378.442 885866.9947 992121.191 2282842.548 2015461.546 0.480100734 1.035761953 0.471611192 0.448740005 1.036178758 0.439535548 0.492255083 1.132664899 1 20.94267883 1.231405922 24.9999103 1.066332687 0.644289806 0.383325471 0.229899038 193.6676953 676683.9366 0.197698326 0.053526329 17.0375021 -1.231405922 -0.42204288 KGDIVDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KGDIVDIK 8 1 P46778;M0R181;G3V1B3 P46778 RPL21 60S ribosomal protein L21 0 ;;; 96.89 0.013822 7010690000 10669200 8134040 9335400 8916100 9156000 6695640 11126600 7416400 10349900 FALSE TRUE 10001433.82 8736292.785 9556840.096 9144902.221 8436924.694 8628562.573 9458269.624 8342353.866 8622434.827 1.159931506 1.01320485 1.108369073 1.060593951 0.97848518 1.000710675 1.096937213 0.967517184 1 23.03966389 2.985687322 22.89666994 1.020671934 1.079364508 0.35423463 0.050504928 315.6361562 504940.7476 0.014627926 0.016112983 967.580979 -2.985687322 0.058692574 KGDRS(ph)PEPGQTWTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 KGDRSPEPGQTWTR 14 2 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 KGDRS(0.982)PEPGQT(0.018)WTR;KGDRS(0.997)PEPGQT(0.003)WTR;KGDRS(1)PEPGQTWTR;KGDRS(0.998)PEPGQT(0.002)WTR;KGDRS(0.999)PEPGQT(0.001)WTR;KGDRS(0.99)PEPGQT(0.002)WT(0.008)R;KGDRS(1)PEPGQTWTR;KGDRS(0.993)PEPGQT(0.007)WTR;KGDRS(0.991)PEPGQT(0.002)WT(0.006)R;KGDRS(0.999)PEPGQT(0.001)WTR 184.2 1.04E-06 71536570000 24180460 19720890 20778220 22385840 24746200 12202020 18091180 13400870 23864130 TRUE FALSE 22667048.17 21181045.22 21271089.19 22960298.55 22802733.27 15724545.09 15378575.51 15073998.12 19881052.53 1.140133206 1.065388524 1.069917659 1.154883451 1.146958051 0.790931218 0.773529243 0.758209259 1 24.2448908 2.23542816 24.99988236 0.806949797 1.104211137 0.782186638 0.074076687 32.40147548 258589.4775 0.024928713 0.019195527 171.9602863 -2.23542816 0.29726134 KGDSNANSDVCAAALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGDSNANSDVCAAALR 16 1 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 0 ; 232.74 2.19E-16 650410000 160189 162355 170731 158567 193481 120120 179781 164850 240740 FALSE TRUE 150163.0564 174375.9331 174780.8199 162636.0977 178285.7827 154796.694 152824.5081 185431.8854 200558.9388 0.748722831 0.86944982 0.871468612 0.810914231 0.888944586 0.771826451 0.761993003 0.924575521 1 17.61366674 1.023135936 5.656446481 0.999715514 0.825221128 0.623213353 0.048444587 0.101856826 9.922047006 0.048706844 0.012269929 10.54716976 -1.023135936 -0.174494386 KGDSSAEELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KGDSSAEELK 10 1 P26373;P26373-2 P26373 RPL13 60S ribosomal protein L13 0 ;;; 160.52 1.18E-05 10289820000 13893790 9106480 10988780 10590090 11354320 8334850 14661340 9802680 13838960 FALSE TRUE 13024202.49 9780733.254 11249439.05 10861849.64 10462597.51 10740985.89 12463008.18 11026566.18 11529148.17 1.129676043 0.8483483 0.97573896 0.942120743 0.90749094 0.931637423 1.080999913 0.956407708 1 23.45878259 1.765172418 25 1.019952276 0.943342668 0.088964951 0.077731912 28.70386119 26982.47725 0.032450026 0.017996104 58.23343621 -1.765172418 -0.076609609 KGDSVGLR ddPTM_SK-BR-3_Pertuzumab_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 79.148 0.046157 94366000 256250 283680 225220 245380 305740 199210 269770 268690 316840 FALSE TRUE 240211.7699 304683.9624 230562.3248 251676.8662 281728.4137 256718.6931 229320.4929 302236.538 263957.3571 0.910040063 1.154292366 0.873483229 0.953475474 1.067325483 0.972576388 0.868778561 1.145020322 1 18.00994535 3.97151969 24.9730649 0.970748619 1.045147183 0.025607342 0.100487764 538.0235241 2398646.281 0.023615203 0.044116109 9365.25679 -3.97151969 0.074398564 KGDVEGSQS(ph)QDEGEGSGESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KGDVEGSQSQDEGEGSGESER 21 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 1 KGDVEGSQS(1)QDEGEGSGESER;KGDVEGSQS(1)QDEGEGSGESER;KGDVEGS(0.001)QS(0.999)QDEGEGSGESER;KGDVEGSQS(1)QDEGEGSGESER;KGDVEGS(0.011)QS(0.989)QDEGEGSGESER;KGDVEGSQS(1)QDEGEGSGESER 279.48 3.87E-45 5106160000 3735860 3069010 3081130 3372140 3600220 2448260 4184550 3032930 4056500 TRUE FALSE 3502039.191 3296242.694 3154215.859 3458674.821 3317473.244 3155032.918 3557115.575 3411597.987 3379443.944 1.036276751 0.975380195 0.933353508 1.023444945 0.981662457 0.933595281 1.05257422 1.009514596 1 21.68835445 1.725904975 20.00014611 1.023233612 0.976248097 0.216979581 0.035133372 0.372858727 574.0109542 0.015695905 0.008695925 53.19918451 -1.725904975 -0.046985515 KGDVEGSQSQDEGEGSGESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGDVEGSQSQDEGEGSGESER 21 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 184.29 6.43E-17 242560000 123100 100750 114650 113650 134000 97822 140260 108960 171790 FALSE TRUE 115395.3907 108209.6348 117369.5521 116566.4514 123476.1805 126061.6234 119229.3151 122563.8959 143117.1392 0.806300289 0.756091377 0.820094314 0.814482822 0.862763057 0.880828279 0.833089005 0.856388666 1 17.12683693 -4.999999999 0.099792112 1.579586511 0.699349106 0.857007194 0.024173658 64.37989937 0.437642958 7.722360152 0.411434585 1.00E-05 4.999999999 -0.880237404 KGDVLHMHYTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGDVLHMHYTGK 12 1 A0A494C1N0;P26885 A0A494C1N0 FKBP2 Peptidyl-prolyl cis-trans isomerase FKBP2 0 ; 144.27 2.56E-05 1579950000 1157710 1245200 1290270 1327550 1504230 950320 1642980 1331650 1367890 FALSE TRUE 1085250.998 1337395.904 1320875.814 1361617.181 1386093.844 1224661.957 1396630.402 1497909.434 1139580.322 0.952325147 1.173586344 1.1590897 1.194840903 1.216319567 1.074660498 1.225565565 1.31443954 1 20.12007118 4.738681645 7.22907182 1.176260488 0.949432964 0.390344274 0.085087927 0.098165922 43.71038739 0.017934835 0.108671291 54787.52041 -4.738681645 -0.226827523 KGDVVHCWYTGTLQDGTVFDTNIQTS(ph)AK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGDVVHCWYTGTLQDGTVFDTNIQTSAK 28 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 1 KGDVVHCWYTGTLQDGTVFDTNIQT(0.109)S(0.891)AK;KGDVVHCWYTGTLQDGTVFDTNIQT(0.026)S(0.974)AK 269.27 5.23E-55 586870000 703950 408980 548920 498000 569310 416120 724450 469170 612550 TRUE FALSE 659891.0261 439261.3047 561940.6416 510779.5231 524598.6891 536247.0889 615825.448 527746.9073 510311.4478 1.293114291 0.860771019 1.10117193 1.000917235 1.027997101 1.050823161 1.206763929 1.034166311 1 18.96101848 1.976896955 23.60150651 1.109661283 1.03406169 0 0.12015316 971.5409764 992500.0482 0.044815337 0.029150074 94.81934583 -1.976896955 -0.075599593 KGDVVHCWYTGTLQDGTVFDTNIQTSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGDVVHCWYTGTLQDGTVFDTNIQTSAK 28 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 318.02 4.00E-83 317110000 192430 149380 153960 161480 193730 127750 211220 174270 233250 FALSE TRUE 180386.1498 160440.2506 157612.0039 165623.8502 178515.2273 164629.3512 179549.5219 196027.9931 194319.0681 0.928298759 0.825653664 0.811099011 0.852329376 0.918670664 0.84721151 0.923993325 1.008794428 1 17.56806795 1.457441519 2.173870388 1.008891843 0.853990105 0.695579019 0.037701389 0.161128267 1.439686262 0.03253027 0.010498215 28.67091272 -1.457441519 -0.154901739 KGDVVIVLTGWRPGSGFTNTMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGDVVIVLTGWRPGSGFTNTMR 22 2 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 135.68 3.18E-06 799370000 1131750 1912530 1406680 1277100 2018470 1298050 1459000 1630290 1377390 FALSE TRUE 1060915.788 2054135.711 1440047.114 1309872.548 1859947.508 1672775.963 1240236.495 1833835.295 1147494.711 0.92454961 1.790104732 1.254948803 1.141506393 1.62087676 1.45776355 1.080821099 1.598120913 1 20.13005607 -3.18866531 0.350585801 4.64E-09 1.387156091 0.131645379 0.270776722 200.4473154 5.436696208 147.9056054 0.193933002 0.000647642 3.18866531 1.387156086 KGDYIEAESSYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGDYIEAESSYSR 13 1 Q99614 Q99614 TTC1 Tetratricopeptide repeat protein 1 0 ; 155.06 7.18E-05 570800000 475170 498160 464420 473590 539340 359080 603800 445110 578380 FALSE TRUE 445429.9579 535044.2847 475436.2617 485743.1212 496982.412 462740.5668 513265.7954 500682.9633 481844.6415 0.924426505 1.110408291 0.986700319 1.00809074 1.031416289 0.960352211 1.065210135 1.039096257 1 18.87820854 1.662537918 23.53448735 1.039312732 1.014999013 0.044522502 0.051236833 1.045344597 425.651837 0.022293584 0.012360796 45.97671293 -1.662537918 -0.024313718 KGDYQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGDYQK 6 1 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 91.041 0.077516 784860000 1169800 813440 1100200 959870 1008700 671550 976600 840650 980370 FALSE TRUE 1096584.306 873667.944 1126297.264 984501.8893 929480.7709 865415.5833 830167.8963 945607.003 816739.9136 1.342635872 1.069701541 1.379015822 1.205404405 1.138037649 1.059597516 1.016440953 1.157782285 1 19.63951721 2.55451686 2.374012598 1.055375603 1.24210044 0.495301802 0.091024545 0.25716887 2.880397818 0.032799423 0.028992254 358.5228664 -2.55451686 0.186724836 KGEDEYANVDAIVVSVGVDEEIVYAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KGEDEYANVDAIVVSVGVDEEIVYAK 26 1 Q9Y5B9;G3V5A4;G3V401 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;; 203.99 6.35E-25 71640000 291339 203886 230528 235229 257521 167128 301471 214964 263410 FALSE TRUE 273104.612 218981.9316 235996.233 241265.3744 237296.3394 215375.1405 256268.2223 241802.7286 219445.1693 1.244523235 0.99788905 1.07542232 1.099433517 1.081346836 0.981453095 1.1678007 1.101882212 1 17.74350099 -0.470424101 6.098356002 1.000003008 1.084490243 0.121996101 0.075487675 0 0 0.066879287 0.015763599 0.338513426 0.470424101 0.084487235 KGEDFVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KGEDFVK 7 1 P40926;G3XAL0;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 ;; 82.75 0.037908 10325900000 18551900 12394700 12908600 12329800 17816800 11198100 14422900 14839000 25277600 FALSE TRUE 17390769.7 13312416.48 13214798.09 12646203.54 16417540.4 14430809.68 12260320.04 16691681.81 21058605.26 0.825827232 0.632160408 0.627524849 0.60052427 0.779611954 0.685269015 0.582200003 0.792629978 1 24.32790655 0.961187283 5.312267335 0.999894613 0.664997069 0.64406771 0.076746263 0.125027862 12.46821485 0.069746763 0.017598543 9.145075242 -0.961187283 -0.334897544 KGEDVLGSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGEDVLGSVR 10 1 P56192;P56192-2;F5H2V6 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 126.76 0.00059955 147810000 431010 524350 409290 425780 573020 273450 443600 505790 572760 FALSE TRUE 404033.8535 563173.4196 418998.5521 436706.2356 528017.3207 352390.5759 377086.2982 568938.9949 477162.6558 0.846742402 1.1802546 0.878104242 0.915214614 1.106577211 0.738512479 0.790267833 1.19233764 1 18.86412161 3.747262589 20.20469228 0.921856718 1.034878949 0.009644118 0.157341305 103.1106814 103428.0041 0.038422646 0.069007615 5588.079661 -3.747262589 0.11302223 KGEFETGFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGEFETGFEK 10 1 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ; 138 0.00012237 2793600000 4444900 3120800 3853300 3524100 3947800 2933100 4740100 3381800 5377200 FALSE TRUE 4166701.643 3351867.279 3944702.096 3614534.372 3637755.713 3779838.355 4029366.01 3804025.174 4479710.582 0.930127419 0.748232998 0.880570747 0.806867834 0.812051503 0.843768428 0.899470164 0.84916762 1 22.0949741 0.367589581 0.535759053 1.008169146 0.826752356 0.473629749 0.050953787 1.789937713 0.827504768 0.080727943 0.02199594 2.33125393 -0.367589581 -0.18141679 KGEIFELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGEIFELK 8 1 P63010;P63010-2;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1;K7ERB2;K7EN71;A0A087WXS3;K7EKZ5;K7EJX1;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ; 111.06 0.0053021 1481450000 4593700 3400000 3902400 3934000 4408500 2927200 5195400 3765500 5528600 FALSE TRUE 4306188.517 3651739.538 3994966.771 4034953.1 4062274.193 3772235.121 4416398.002 4235630.964 4605840.944 0.934940778 0.792849684 0.867369677 0.876051333 0.881983169 0.819011157 0.958868979 0.919621632 1 22.13503316 1.378222745 1.068807312 0.992579276 0.854204472 0.486224743 0.044574207 0.33823464 0.774296487 0.037768319 0.013100076 23.89036277 -1.378222745 -0.138374804 KGENYVYINEATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KGENYVYINEATR 13 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 159.13 7.39E-05 2040020000 2112100 2107970 2165170 2184700 2296140 1572280 2521070 2000610 1889880 FALSE TRUE 1979907.431 2264046.292 2216528.855 2240763.101 2115810.427 2026171.712 2143058.958 2250390.562 1574446.819 1.257525759 1.437994771 1.407814369 1.423206598 1.343843692 1.286910226 1.361150426 1.42932142 1 20.5864136 -1.958940793 2.706942796 0.710113441 1.374472803 0.78492564 0.060543372 11268244.16 5013402.142 20493772.35 0.014448792 0.010991557 1.958940793 0.664359362 KGEQCVHTASGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KGEQCVHTASGPR 13 1 Q04721 Q04721 NOTCH2 Neurogenic locus notch homolog protein 2;Notch 2 extracellular truncation;Notch 2 intracellular domain 0 ;; 106.17 0.00090541 193804000 189709 199319 183726 193898 216407 126588 214488 184743 203968 FALSE TRUE 177835.4523 214076.7862 188084.0675 198873.7509 199411.2672 163131.9006 182327.5156 207808.5702 169924.4231 1.046556163 1.259835298 1.106868948 1.170365903 1.17352917 0.960026214 1.072991818 1.22294704 1 17.3745337 2.325126733 24.99999997 1.066416485 1.160998511 0.19932307 0.085839645 32.44726008 9364.714731 0.027780219 0.023242591 211.4105875 -2.325126733 0.094582026 KGEQGGPPPKAS(ph)PSTAGETPSGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGEQGGPPPKASPSTAGETPSGVK 24 2 A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2;A0A087WW69;F8W8L6 A0A087WTA5 EIF2B4 Translation initiation factor eIF-2B subunit delta 1 KGEQGGPPPKAS(0.945)PS(0.042)T(0.012)AGET(0.001)PSGVK 54.683 0.055417 246070000 194530 97704 139480 110320 128610 86948 171860 101690 191030 TRUE FALSE 182354.7145 104938.1058 142788.5315 113150.998 118509.4894 112048.4761 146091.1885 114386.2203 159145.8589 1.145833865 0.659383201 0.897218014 0.71098927 0.744659586 0.704061525 0.917970405 0.718750844 1 17.27999009 -0.216113599 8.779852547 0.999999997 0.804808887 0.140437251 0.14482469 0 0 0.122118702 0.028783654 0.607975951 0.216113599 -0.19519111 KGEQPTGQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGEQPTGQQR 10 1 Q92733;H0YE12;H0Y679 Q92733 PRCC Proline-rich protein PRCC 0 76.655 0.056675 34015000 40414 44198 47572 49243 59766 41333 57942 50273 73113 FALSE TRUE 37884.55988 47470.46591 48700.43031 50506.65875 55072.21944 53265.16611 49254.13501 56549.69471 60909.96797 0.621976355 0.779354636 0.79954779 0.82920186 0.904157748 0.874490135 0.808638334 0.928414455 1 15.89439073 7.210934448 0.175659895 0.976928124 1.38E-27 0.792535988 0.04621371 22.46734466 0.316585897 0.115437215 5.514650904 16253034.17 -7.210934448 -0.976928124 KGES(ph)PSLESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGESPSLESR 10 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 KGES(0.677)PS(0.323)LESR 91.307 0.0042236 0 433780 285620 369080 337240 340610 267230 434180 314730 333130 TRUE FALSE 406630.4841 306767.602 377834.7519 345894.1493 313859.8646 344374.9629 369078.7397 354024.7333 277528.4509 1.465184859 1.105355509 1.361427092 1.246337621 1.130910591 1.240863637 1.32987713 1.275634019 1 18.08227615 -1.894123786 2.318654948 0.851185222 1.261954329 0.39445324 0.104553268 7940491.816 3972521.07 6453611.745 0.023202024 0.01276075 1.894123786 0.410769108 KGESGQSWPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KGESGQSWPR 10 1 A0A087WYT3;Q15185-4;Q15185;Q15185-3;B4DDC6 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ;;; 140.39 6.31E-05 13363900000 6629910 6633900 6415590 6620980 7256900 4907980 7827100 6189580 7104900 FALSE TRUE 6214955.768 7125080.859 6567770.824 6790885.556 6686972.347 6324834.152 6653499.018 6962362.688 5919046.291 1.049992763 1.20375488 1.109599503 1.147293875 1.12973814 1.068556291 1.12408295 1.176264274 1 22.49693331 -2.127203673 2.519474953 0.729349286 1.129388473 0.432264094 0.04530442 2068100.53 1106100.206 3214279.263 0.010279773 0.007460988 2.127203673 0.400039187 KGESQTDIEITR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KGESQTDIEITR 12 1 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;;; 190.81 9.88E-06 8299040000 8116040 6714870 7294610 7429170 7065620 6123550 9021890 6618360 6496660 FALSE TRUE 7608071.544 7212045.962 7467641.594 7619815.08 6510714.707 7891319.477 7669141.35 7444676.815 5412325.476 1.405693648 1.33252259 1.379747324 1.407863425 1.202942198 1.458027517 1.416977117 1.375504272 1 22.36781717 -1.127315858 4.678069784 0.999971761 1.372637047 0.745633432 0.068358125 2.06E-05 3.84E-06 0.062002495 0.014612921 0.074590607 1.127315858 0.372665287 KGESQTDIEITREEDFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGESQTDIEITREEDFTR 18 2 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 134.06 6.38E-06 110090000 83659 91820 93792 96411 129810 50044 85231 89587 187710 FALSE TRUE 78422.93253 98618.44834 96016.79053 98885.06948 119615.2462 64490.8904 72451.4028 100772.1342 156379.9883 0.501489566 0.630633429 0.61399666 0.632338386 0.764901235 0.412398614 0.463303544 0.644405561 1 17.25469638 -1.296770461 3.094165682 1.002756733 0.580510766 0.625244251 0.101459163 16749427.5 22225343.29 434483.2049 0.025512447 0.05049281 1.296770461 -0.422245967 KGESVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KGESVKR 7 2 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ;; 81.548 0.015131 4908160000 3587250 3210960 3302838 3266280 4288570 2552632 4091570 3532240 5514250 FALSE TRUE 3362730.426 3448702.819 3381182.877 3350098.275 3951763.011 3289535.42 3478077.063 3973247.939 4593886.052 0.73200127 0.750715795 0.736018012 0.729251496 0.860222253 0.716068136 0.757109999 0.864899106 1 22.13128364 0.983971236 2.608070587 0.999281883 0.752547478 0.803131595 0.039837979 0.109576185 1.722349701 0.035398025 0.009503501 9.637651896 -0.983971236 -0.246734405 KGETLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KGETLR 6 1 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;;; 100.74 0.059833 2242910000 4392360 4204560 4481320 4283920 4374250 3833920 5080200 3622190 4709690 FALSE TRUE 4117450.028 4515869.997 4587619.027 4393852.64 4030714.05 4940710.466 4318471.172 4074428.395 3923612.313 1.049402872 1.150947045 1.169233518 1.119848825 1.027296717 1.259224936 1.100636563 1.038438069 1 21.90375107 1.227114856 3.374410397 1.007573584 1.135224141 0.33040522 0.063820879 0.238764819 4.876001205 0.052831708 0.014946426 16.86999122 -1.227114856 0.127650557 KGFLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGFLFR 6 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 120.96 0.031844 671830000 1039340 1772460 947910 895320 1695600 616090 1028360 1538470 1764400 FALSE TRUE 974289.5647 1903694.783 970394.8728 918295.427 1562434.416 793945.1816 874166.9648 1730551.366 1469910.242 0.662822489 1.295109544 0.660172877 0.624728913 1.062945459 0.540131744 0.594707718 1.177317714 1 20.48729663 3.834149209 6.591452922 0.768377466 1.015804353 0.047096152 0.263545305 0.407565542 21.93635513 0.062430852 0.113504831 6825.73163 -3.834149209 0.247426887 KGFNGCDS(ph)PEPDGEDSLEQSPLLEDKYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KGFNGCDSPEPDGEDSLEQSPLLEDKYR 28 2 Q14814-4;Q14814;Q05BX2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 KGFNGCDS(1)PEPDGEDSLEQSPLLEDKYR;KGFNGCDS(1)PEPDGEDSLEQSPLLEDKYR;KGFNGCDS(1)PEPDGEDSLEQSPLLEDKYR 190.73 2.44E-18 456920000 614565 397060 446529 465069 532316 346613 688670 364289 615840 TRUE FALSE 576100.4737 426458.7355 457120.8787 477003.4579 490510.0486 446674.5463 585410.3268 409771.2835 513052.3255 1.122888339 0.831218795 0.890982958 0.92973647 0.956062421 0.870621814 1.14103435 0.798692966 1 18.96874645 KGFSEGLWEIENNPTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGFSEGLWEIENNPTVK 17 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 154.49 2.18E-07 515010000 802690 663850 674300 687140 869280 494030 889000 653460 1210800 FALSE TRUE 752451.0657 713002.1447 690294.7144 704773.1757 801010.2553 636648.4411 755702.7031 735045.9194 1008709.658 0.745954061 0.70684576 0.684334396 0.698687844 0.794093968 0.631151329 0.749177622 0.728699199 1 19.94407955 0.100003356 1.085806523 1.001493875 0.710101133 0.81047586 0.043007236 2.484472357 2.634615685 0.04685158 0.011390416 1.258935139 -0.100003356 -0.291392741 KGGDGIKPPPIIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGGDGIKPPPIIGR 14 2 J3KQ32;Q9NTK5;Q9NTK5-3;C9JTK6 J3KQ32 OLA1 Obg-like ATPase 1 0 127.05 4.60E-05 561280000 1229700 1144400 1239400 1300400 1456200 1036400 1661000 1156300 1808200 FALSE TRUE 1152735.272 1229132.567 1268799.153 1333770.466 1341835.926 1335591.855 1411948.47 1300666.6 1506399.739 0.765225353 0.815940507 0.842272553 0.885402746 0.890756877 0.886611848 0.937299997 0.863427261 1 20.52267322 8 0.113255247 1.039353855 0.223536505 0.841456816 0.025435203 34.39652128 0.270387006 0.186659531 4.400792798 100000000 -8 -0.81581735 KGGEFDEFVNDDT(ph)DDDLPISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 KGGEFDEFVNDDTDDDLPISK 21 1 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK;KGGEFDEFVNDDT(1)DDDLPISK 255.95 1.15E-36 7151400000 5132758 3154360 3808307 3729773 3837883 2754136 5189876 3354751 5227239 TRUE FALSE 4811507.839 3387912.097 3898641.84 3825485.29 3536471.15 3549210.354 4411702.274 3773599.047 4354779.042 1.104879902 0.777975659 0.895255948 0.878456806 0.812089687 0.815015026 1.01307144 0.866542025 1 22.05416809 1.74003612 25 0.956602168 0.867740541 0.120483773 0.096738324 0.401745255 6838.638139 0.04051143 0.022465676 54.95865806 -1.74003612 -0.088861627 KGGEFDEFVNDDT(ph)DDDLPISKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGGEFDEFVNDDTDDDLPISKK 22 2 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 KGGEFDEFVNDDT(1)DDDLPISKK;KGGEFDEFVNDDT(1)DDDLPISKK 214.3 7.23E-24 167487000 459940 293040 348140 382790 445360 236110 541830 300910 823990 TRUE FALSE 431153.1764 314736.9865 356398.0452 392613.0395 410383.2221 304271.1241 460587.6216 338479.2759 686460.7458 0.628081327 0.45849233 0.519181974 0.571938078 0.597824748 0.44324621 0.670959883 0.493078851 1 19.3888177 -5 0.31948467 5.317897289 0.523886937 0.78032537 0.074786302 133.3044802 1.182687716 388.9368272 0.060395251 1.00E-05 5 -4.794010352 KGGHERPPS(ph)PGLR ddPTM_SK-BR-3_Pertuzumab_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 115.15 0.00035833 989970000 346210 349370 316260 340490 391480 265420 394430 307700 392490 TRUE FALSE 324541.3341 375237.7183 323761.8365 349227.5498 360734.74 342042.4453 335288.8832 346117.0223 326980.8834 0.992539168 1.147583046 0.990155244 1.068036597 1.103228838 1.046062515 1.025408213 1.058523724 1 18.31884677 0.611531786 0.507525582 0.997750606 1.063604065 0.104594637 0.047542901 3.363433705 1.721023587 0.064987717 0.023415269 4.088196726 -0.611531786 0.065853459 KGGHS(ph)SPASSDKNSNSNHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGGHSSPASSDKNSNSNHR 19 2 Q13029-5;Q13029-3;Q13029-2;Q13029 Q13029-5 PRDM2 PR domain zinc finger protein 2 1 KGGHS(0.5)S(0.5)PASSDKNSNSNHR 68.552 0.011481 15670000 8318 8765.4 9867.1 11358 9592.4 5733.9 16626 6827.2 9502 TRUE FALSE 7797.391228 9414.399336 10101.15227 11649.46551 8839.051598 7389.183848 14133.08565 7679.590949 7916.054815 0.985009757 1.1892792 1.276033644 1.47162517 1.116598079 0.933442734 1.785369856 0.970128571 1 12.95056589 4.838558796 1.56549598 1.271383202 0.825765225 0.049373487 0.259760459 3.275078668 6.321062358 0.065019954 2.400051663 68953.89388 -4.838558796 -0.445617977 KGGPDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGGPDDR 7 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ; 82.452 0.039204 987760000 4166800 3215300 4240000 3999400 4046000 3156800 4040700 3477800 3789200 FALSE TRUE 3906007.426 3453364.158 4340574.802 4102031.375 3728243.481 4068116.914 3434834.547 3912010.986 3156758.041 1.237347739 1.093959091 1.375010294 1.299444342 1.181035554 1.288700895 1.088089268 1.239249551 1 21.59001225 0.608206373 0.655765183 0.999407908 1.241382479 0.398059364 0.087871823 1.454275477 1.151824143 0.096901363 0.034198718 4.057012752 -0.608206373 0.241974571 KGHAVGDIPGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KGHAVGDIPGVR 12 1 D6RD47;P62266 D6RD47 RPS23 40S ribosomal protein S23 0 ;;; 112.5 0.00082263 3105910000 3121590 3859340 3519440 3824380 4205730 2900280 3918150 3416250 4366640 FALSE TRUE 2926215.254 4145089.549 3602922.779 3922520.065 3875428.931 3737543.754 3330659.782 3842776.333 3637819.574 0.804387132 1.139443412 0.990407222 1.078261301 1.065316421 1.027413174 0.915564863 1.056340551 1 21.79464256 1.962037447 24.57835542 0.978812326 1.033082902 0 0.093675207 1257.808789 814349.1054 0.034934524 0.022556014 91.62994954 -1.962037447 0.054270576 KGHYAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGHYAER 7 1 P16104 P16104 H2AFX Histone H2AX 0 89.298 0.028822 26407000 24858 66842 18768 18871 65085 11542 18984 52974 59670 FALSE TRUE 23302.18215 71791.05123 19213.18582 19355.26181 59973.48664 14873.98803 16137.52544 59587.92051 49710.69152 0.468755944 1.444177279 0.386500071 0.389358128 1.20645046 0.299211047 0.324628866 1.198694259 1 15.60126855 3.928962752 10.07175502 0.627305496 1.01204293 0.049313879 0.421184516 0.901305714 184.6068313 0.099847827 0.180626259 8491.07647 -3.928962752 0.384737434 KGIIRPGTAFELLEAQAATGYVIDPIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGIIRPGTAFELLEAQAATGYVIDPIK 27 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 ; 143.9 1.01E-07 97590000 400670 369454 389180 384960 476780 331425 498270 379210 362589 FALSE TRUE 375592.7799 396808.7586 398411.5334 394838.7253 439335.622 427102.0173 423559.0392 426555.2032 302070.5535 1.243394219 1.313629396 1.318935357 1.30710763 1.454413934 1.41391477 1.402185795 1.412104551 1 18.20452603 -1.174237751 5.112903666 0.999978539 1.357850262 0.757456702 0.063702254 1.64E-05 2.66E-06 0.065091632 0.015341326 0.066951799 1.174237751 0.357871723 KGISLNPEQWSQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGISLNPEQWSQLK 14 1 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 163.8 6.77E-06 92176000 337830 347590 283370 297840 375600 223890 368320 301210 423560 FALSE TRUE 316685.8233 373325.9253 290091.6702 305483.0786 346101.8911 288523.4084 313093.8353 338816.7315 352865.0997 0.89746995 1.057984838 0.822103604 0.865721997 0.980833444 0.817659238 0.887290456 0.960187709 1 18.42875722 3.976245058 24.99989015 0.894814555 0.983049185 0.135705346 0.072891737 57.14107166 1630454.867 0.016548663 0.032208538 9467.712425 -3.976245058 0.08823463 KGLIAAICAGPTALLAHEIGFGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGLIAAICAGPTALLAHEIGFGSK 24 1 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ; 257.48 4.34E-44 523340000 815510 911450 839100 820430 1142050 563620 971260 896460 1206380 FALSE TRUE 764468.6848 978934.7064 859003.8483 841483.6228 1052358 726327.9444 825628.5797 1008385.004 1005027.384 0.760644632 0.974037844 0.854706908 0.837274323 1.047093856 0.72269468 0.82149859 1.003340824 1 19.93880338 1.226752564 24.76154912 1.001670577 0.866898278 0.2814152 0.093764941 299.8591693 628784.0727 0.082434947 0.021293454 16.85592397 -1.226752564 -0.134772299 KGLTPSQIGVILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGLTPSQIGVILR 13 1 P62277;J3KMX5 P62277 RPS13 40S ribosomal protein S13 0 ; 240.42 4.57E-09 0 1779800 2230400 2005560 2123400 2616300 1699500 2468600 1892730 2892200 FALSE TRUE 1668405.495 2395541.137 2053132.83 2177890.039 2410826.352 2190118.061 2098456.347 2129041.507 2409473.136 0.692435815 0.994217823 0.852108621 0.903886417 1.000561623 0.908961394 0.870919172 0.883612884 1 21.20028629 4.750784374 24.70305679 0.918610392 0.692435651 0.638902356 0.055064028 1085.93268 2194520.011 0.01257482 0.21493907 56335.78802 -4.750784374 -0.226174741 KGLVGPELHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 140.31 2.51E-05 1041380000 1296330 1631760 1445780 1574080 1766960 1328240 2011500 1470820 1667630 FALSE TRUE 1215195.019 1752577.208 1480074.584 1614473.558 1628190.089 1711681.326 1709894.249 1654455.115 1389291.78 0.874686684 1.261489655 1.065344664 1.162083863 1.171956901 1.232053159 1.230766837 1.190862236 1 20.4059182 3.047941896 5.680358323 1.187102036 1.108497794 0.08755948 0.115057066 0.453197495 33.58376531 0.03095517 0.036876402 1116.713834 -3.047941896 -0.078604242 KGNAEGS(ph)S(ph)DEEGKLVIDEPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KGNAEGSSDEEGKLVIDEPAK 21 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 2 KGNAEGS(1)S(1)DEEGKLVIDEPAK;KGNAEGS(1)S(1)DEEGKLVIDEPAK;KGNAEGS(1)S(1)DEEGKLVIDEPAK;KGNAEGS(1)S(1)DEEGKLVIDEPAK 142.94 6.97E-07 805320000 5924690 1169900 2466050 2120140 1977580 1532950 3202260 1675950 2104720 TRUE FALSE 5553874.229 1256520.613 2524545.871 2174546.382 1822268.844 1975487.78 2722110.841 1885196.047 1753428.635 3.167436711 0.716607787 1.439776801 1.24016817 1.039260343 1.126642819 1.552450318 1.075148432 1 20.74174728 4.746850477 24.99553034 1.181565541 3.167437696 0.880292949 0.233668048 349.8918923 1054968.1 0.055444196 0.63254161 55827.79524 -4.746850477 1.985872155 KGNAEGS(ph)S(ph)DEEGKLVIDEPAKEK ddPTM_SK-BR-3_Pertuzumab_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 96.793 0.0016794 1162740000 1302690 278720 516110 541140 589290 339450 749900 345060 796470 TRUE FALSE 1221156.958 299356.7188 528352.3729 555026.5685 543009.5405 437443.7045 637459.4567 388141.5006 663534.0116 1.840383367 0.451155048 0.796270219 0.836470413 0.818359769 0.659263424 0.960703514 0.584960972 1 19.33981089 4.748598745 24.84896892 0.754651617 1.840384011 0.807814374 0.165039549 535.7987611 1326318.486 0.037710118 0.513919213 56052.985 -4.748598745 1.085732395 KGNEAVASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGNEAVASR 9 1 Q8NBJ4-2;Q8NBJ4 Q8NBJ4-2 GOLM1 Golgi membrane protein 1 0 87.184 0.021859 44651000 63114 75603 59842 56376 79560 46417 72233 79262 82158 FALSE TRUE 59163.8074 81200.72478 61261.4805 57822.7036 73311.67853 59816.83438 61402.33223 89158.03518 68445.29904 0.864395484 1.186359413 0.895042923 0.84480168 1.071098813 0.873936344 0.897100796 1.302617366 1 16.06266384 1.255952645 24.99979637 1.151308833 0.959839665 0.301291782 0.127947914 265.8494685 382142.3466 0.08210244 0.029831547 18.02821153 -1.255952645 -0.191469168 KGNEQHAFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGNEQHAFTR 10 1 Q13045-3;Q13045;Q13045-2;K7EQZ7 Q13045-3 FLII Protein flightless-1 homolog 0 ; 90.685 0.0069214 105297000 200878 251294 205923 199178 273870 152589 244113 232972 288660 FALSE TRUE 188305.4046 269900.0692 210807.5908 204289.2447 252361.3549 196638.9672 207510.5219 262059.067 240480.7812 0.783037229 1.122335298 0.876608891 0.849503414 1.049403423 0.817690987 0.862898569 1.089729773 1 17.87556208 1.234546071 24.99992238 1.044864905 0.921908035 0.213997974 0.106131343 182.397852 1135774.555 0.086803757 0.024832326 17.16113749 -1.234546071 -0.122956869 KGNS(ph)PNSEPPTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KGNSPNSEPPTPK 13 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 KGNS(0.998)PNS(0.002)EPPTPK;KGNS(0.999)PNS(0.001)EPPTPK;KGNS(0.962)PNS(0.038)EPPTPK;KGNS(0.961)PNS(0.039)EPPTPK 129.32 9.50E-05 1836260000 2245380 1307080 1690050 1478640 1658400 1239810 2130940 1466390 2822320 TRUE FALSE 2104845.674 1403857.563 1730138.784 1516584.406 1528155.954 1597723.02 1811425.33 1649472.019 2351256.559 0.895200341 0.597066942 0.735835814 0.645010175 0.649931607 0.679518794 0.770407348 0.701527876 1 21.16500054 -0.046523715 0.731960284 1.011084067 0.692603466 0.54457522 0.082746667 3.776361202 2.042960638 0.193041383 0.026090298 0.898413532 0.046523715 -0.318480602 KGNYAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 ;;;;;; 133.6 0.0052206 20216090000 13762660 28248630 10355940 9784080 27824540 6251980 12072570 22502000 26392340 FALSE TRUE 12901279.68 30340187.96 10601587.79 10035156.06 25639312.87 8056825.134 10262400.2 25311424.23 21987287.95 0.586760846 1.379896785 0.482168961 0.456407178 1.166097107 0.366431056 0.46674243 1.151184461 1 24.39016633 3.924547929 8.53764593 0.678681957 1.0259082 0.068797279 0.351615879 0.516437762 78.27266674 0.08304584 0.150704961 8405.197622 -3.924547929 0.347226243 KGNYSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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 ;;;;;;;; 137.9 0.0045498 23633910000 16838450 29347840 12425820 11715760 28873700 7870940 14364080 24128520 26559200 FALSE TRUE 15784561.47 31520784.61 12720566.32 12016406.24 26606076.07 10143152.6 12210319.55 27141018.84 22126297.94 0.713384657 1.424584659 0.574907124 0.543082547 1.20246397 0.458420683 0.551846476 1.226640756 1 24.39925875 3.921059657 7.433639755 0.751092846 1.104097534 0.097521069 0.324371155 0.366864341 42.07206482 0.076855624 0.140138475 8337.95711 -3.921059657 0.353004689 KGPEADSEWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KGPEADSEWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 128.67 0.00051845 3130120000 5196900 4981200 5268600 5051800 5811900 4117610 6215700 5048200 7058500 FALSE TRUE 4871635.306 5350013.231 5393573.68 5181437.741 5355456.818 5306297.163 5283713.489 5678478.882 5880390.75 0.828454352 0.909805735 0.917213483 0.881138339 0.910731454 0.902371524 0.898531018 0.965663529 1 22.48748059 -5 0.12315503 1.338776859 0.854714817 0.669542927 0.026315183 100.397802 0.79550089 8.340589654 0.230887495 1.00E-05 5 -0.484062043 KGPEFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KGPEFTR 7 1 Q9NQG5;E9PIQ9 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ;;; 99.802 0.016452 1253340000 1142290 1265190 1185870 1154910 1372640 899700 1421160 1199870 1514590 FALSE TRUE 1070796.108 1358865.984 1213999.396 1184546.946 1264838.391 1159428.785 1208070.251 1349676.411 1261795.144 0.848629124 1.076930744 0.962120834 0.938779128 1.002411839 0.918872441 0.957421858 1.069647808 1 20.26704627 1.251622656 24.99674034 1.034823911 0.968383902 0.202661617 0.06073088 343.3356277 657046.4245 0.038974907 0.014046706 17.8493603 -1.251622656 -0.066440009 KGPGAGSALDDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGPGAGSALDDGR 13 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 93.237 0.0091493 240160000 508790 479570 543760 513500 558260 457200 654120 527020 626250 FALSE TRUE 476945.7421 515077.8618 556658.244 526677.2794 514416.5115 589186.218 556040.7786 592819.6071 521724.8293 0.914171064 0.98725963 1.066957547 1.009492456 0.985992007 1.129304539 1.065774039 1.136268726 1 18.99292957 6.678891096 0.467134481 1.072322195 8.25E-13 0.479245176 0.049431597 22.35296158 0.868213535 0.027297989 19.42477746 4774095.43 -6.678891096 -1.072322195 KGPGQPS(ph)SPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KGPGQPSSPQR 11 1 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.875)S(0.125)PQR;KGPGQPS(0.5)S(0.5)PQR;KGPGQPS(0.734)S(0.266)PQR;KGPGQPS(0.5)S(0.5)PQR;KGPGQPS(0.689)S(0.311)PQR;KGPGQPS(0.576)S(0.424)PQR 120.21 0.00029583 7799300000 8106130 6450530 6907550 6353850 6607650 5362400 8071190 6081100 6657050 TRUE FALSE 7598781.793 6928133.953 7071400.348 6516900.548 6088711.823 6910437.829 6860989.989 6840338.721 5545945.349 1.370150861 1.249225068 1.275057705 1.175074787 1.09786726 1.246034246 1.237118211 1.233394542 1 22.40300197 -5 0.12155067 0.284503656 1.342327809 0.602435902 0.063711296 116.0662533 0.911568451 20.7552917 0.600781002 1.00E-05 5 1.057824153 KGPGQPS(ph)SPQRLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGPGQPSSPQRLDR 14 2 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.908)S(0.092)PQRLDR 127.22 6.37E-05 3217900000 857590 794580 776210 800230 872020 602790 985670 701400 1295100 TRUE FALSE 803914.9727 853411.53 794622.0678 820765.2566 803535.0668 776805.6875 837877.934 788971.334 1078939.443 0.745097399 0.790972594 0.736484399 0.76071485 0.744745288 0.719971535 0.776575497 0.731247095 1 20.04118246 -1.648701827 2.815521173 1.025271331 0.753518142 0.931680241 0.021201848 3655113.925 3531587.264 670838.1622 0.004837002 0.02245423 1.648701827 -0.271753189 KGPGQPSS(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGPGQPSSPQR 11 1 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.218)S(0.782)PQR;KGPGQPS(0.01)S(0.99)PQR 115.63 0.00067246 3659990000 2525670 1920510 2000510 1864020 2032320 1604960 2373180 1832020 2007960 TRUE FALSE 2367592.823 2062706.559 2047963.042 1911853.909 1872709.785 2068285.898 2017343.691 2060751.73 1672818.504 1.41533156 1.233072538 1.22425896 1.142893807 1.119493705 1.236407831 1.205954911 1.231903954 1 20.67384949 8 0.022071824 1.70E-10 2.794232695 0.569553247 0.069213212 2173.606841 3.693415884 167.9561127 322.9268242 99999999.96 -8 2.794232695 KGPGQPSS(ph)PQRLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGPGQPSSPQRLDR 14 2 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.026)S(0.974)PQRLDR 149.52 5.88E-06 2001200000 1638900 1524200 1640700 1496900 1925300 1278100 1951400 1486400 2573200 TRUE FALSE 1536324.175 1637053.354 1679618.179 1535312.988 1774094.704 1647066.722 1658805.686 1671980.312 2143716.296 0.716663943 0.763652054 0.783507678 0.716192246 0.827579054 0.768323087 0.773799074 0.779944769 1 21.03168256 -5 0.293526401 2.854031091 0.754855872 0.858612222 0.030150325 84.25024509 0.789046423 95.77510611 0.02868775 1.00E-05 5 -2.099175218 KGPGRPTGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGPGRPTGSK 10 2 P26583 P26583 HMGB2 High mobility group protein B2 0 82.489 0.010045 1470000000 1641100 1318300 1344000 1509400 1705400 1144700 1820600 1281400 1726400 FALSE TRUE 1538386.48 1415908.304 1375880.315 1548133.759 1571464.763 1475156.307 1547617.932 1441385.611 1438252.687 1.069621836 0.984464216 0.956633231 1.076399004 1.092620773 1.025658649 1.076040355 1.002178285 1 20.45588573 3.231672672 24.99995912 1.051813675 0.992772638 0.154688291 0.04212402 183.8618818 667331.9301 0.011503483 0.014034543 1704.796998 -3.231672672 -0.059041036 KGPPTQELDRDS(ph)EEEEEEDDEDGEDEEEVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGPPTQELDRDSEEEEEEDDEDGEDEEEVPK 31 2 Q14687;Q14687-2;Q14687-3;H0Y613;H7C3B5 Q14687 GSE1 Genetic suppressor element 1 1 KGPPTQELDRDS(1)EEEEEEDDEDGEDEEEVPK 295.03 1.34E-81 174470000 181650 81427 111910 122590 105610 72373 151010 86681 123930 TRUE FALSE 170280.8508 87455.9398 114564.558 125735.8669 97315.81661 93265.91022 128367.4524 97503.31366 103245.2824 1.649284566 0.847069598 1.109634798 1.217836438 0.942569136 0.903343069 1.243325113 0.944385171 1 16.65571634 4.749827018 24.8010154 1.037390193 1.649284965 0.691732349 0.130562423 900.1601749 1981503.582 0.030447412 0.472532638 56211.73855 -4.749827018 0.611894771 KGPQVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KGPQVR 6 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;; 120.76 0.031984 14806530000 16132570 14427550 15776760 15197790 14401740 13357400 17804360 13761080 14713300 FALSE TRUE 15122861.24 15495780.81 16150992.2 15587791.02 13270685.43 17213464.54 15134761.51 15479181.13 12257555.18 1.233758365 1.264182016 1.317635692 1.271688424 1.082653534 1.404314669 1.234729217 1.262827775 1 23.54716792 0.214606298 2.071160005 0.999994524 1.264642863 0.508739924 0.079811198 21.89952942 56.13850213 0.069524417 0.018984279 1.639103201 -0.214606298 0.264648339 KGPSGYGFNLHSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGPSGYGFNLHSDK 14 1 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ; 130.72 3.92E-05 2955800000 6595700 9026600 5503300 5095800 11083700 3627600 6503600 9102600 11938800 FALSE TRUE 6182886.911 9694938.856 5633840.875 5226566.855 10213230.91 4674829.231 5528445.556 10239079.65 9946137.152 0.621637005 0.974744135 0.566435068 0.525487109 1.026854019 0.470014555 0.55583846 1.029452891 1 23.24570489 1.225878957 24.97683109 1.014726794 0.685552794 0.364687153 0.184911326 286.6417874 564530.5597 0.168640267 0.043301702 16.82205146 -1.225878957 -0.329174 KGPSS(ph)TGASGQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGPSSTGASGQAK 13 1 Q9NWH9;H7BXE3 Q9NWH9 SLTM SAFB-like transcription modulator 1 KGPS(0.004)S(0.624)T(0.371)GASGQAK 145.69 2.57E-05 256580000 434070 282310 348200 316770 384040 244840 495150 319660 681610 TRUE FALSE 406902.3335 303212.5261 356459.4684 324898.8545 353879.0475 315521.3334 420906.8542 359570.2547 567844.8876 0.716573033 0.533970689 0.627740913 0.572161274 0.623196678 0.555647044 0.741235615 0.633219146 1 19.11513737 0.024051646 0.555928502 1.029261378 0.597031368 0.775148816 0.0637263 1.664172999 0.621722267 0.165019239 0.025229144 1.056943193 -0.024051646 -0.432230011 KGPST(ph)PYTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGPSTPYTK 9 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 KGPS(0.145)T(0.85)PY(0.004)TK;KGPS(0.102)T(0.893)PY(0.005)TK 71.268 0.029336 1593940000 3288800 2754200 3141100 2588000 3697500 2047460 4104800 2842100 5123700 TRUE FALSE 3082959.879 2958123.834 3215608.375 2654412.461 3407113.265 2638528.464 3489323.347 3196942.441 4268521.37 0.72225476 0.693009025 0.753330743 0.621857602 0.798195199 0.618136407 0.817454815 0.748957816 1 22.02530497 0.381492055 0.729182694 1.004666387 0.707389114 0.675113768 0.062193311 1.111046528 0.860902072 0.063785983 0.019062958 2.407088482 -0.381492055 -0.297277273 KGQAVDYEGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KGQAVDYEGSR 11 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;;; 188.26 5.17E-06 5003040000 2622050 2870960 2556720 2732700 2779340 1972300 3139430 2364890 2442490 FALSE TRUE 2457940.571 3083528.866 2617366.606 2802825.708 2561061.848 2541670.992 2668701.617 2660151.722 2034822.64 1.207938482 1.515379672 1.286287342 1.37742998 1.258616745 1.249087239 1.311515591 1.307313802 1 20.95647162 -4.187347118 0.188398176 7.27E-11 1.394639005 0.57439695 0.084691475 62.70113389 0.807731671 23.85158376 0.223469146 6.50E-05 4.187347118 1.394639005 KGQGGAGAGDDEEED ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KGQGGAGAGDDEEED 15 1 P46781 P46781 RPS9 40S ribosomal protein S9 0 ;;;; 128.85 0.001425 3459600000 5360550 3847870 4401480 4419770 4461480 3520600 5290460 3644570 4823240 FALSE TRUE 5025042.744 4132770.299 4505885.184 4533188.781 4111093.358 4536940.068 4497204.637 4099602.587 4018210.085 1.250567451 1.02851026 1.121366252 1.128161217 1.023115584 1.129094789 1.119205951 1.02025591 1 21.93812156 1.267098039 0.013143971 1.44E-05 2.142156288 0.317688232 0.062672754 995.2234083 11.48362073 942.7090337 926.3356648 18.49686126 -1.267098039 2.14214189 KGQGTAATGNQAT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGQGTAATGNQATPK 15 1 Q5T1M5;Q5T1M5-2;Q5T1M5-3 Q5T1M5 FKBP15 FK506-binding protein 15 1 KGQGTAATGNQAT(1)PK 73.783 0.021533 24454000 73507 37941 50592 52768 54331 37946 67653 44760 72990 TRUE FALSE 68906.32808 40750.19112 51792.06613 54122.11622 50064.06242 48900.3942 57509.06071 50348.38453 60807.49747 1.133188027 0.670150768 0.851738162 0.890056629 0.823320553 0.804183633 0.945756084 0.827996327 1 15.8919616 0.260866651 0.554736852 1.007351602 0.840168463 0.069677951 0.120019677 5.470767768 2.457711897 0.212948018 0.049903494 1.823335766 -0.260866651 -0.167183139 KGQSEEIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KGQSEEIQK 9 1 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 0 ;;;;; 143.5 0.00016321 2245070000 3478620 2879050 3012080 3224960 3718810 2337750 3750980 3091150 4167100 FALSE TRUE 3260899.384 3092217.858 3083527.96 3307717.933 3426749.664 3012620.475 3188555.371 3477086.882 3471584.09 0.939311651 0.890722442 0.888219291 0.952797872 0.987085312 0.867794182 0.918472746 1.001585096 1 21.72716269 1.243167824 8.566967856 1.001121522 0.915230998 0.476935666 0.03454968 0.08716546 63.77436164 0.026769765 0.008545249 17.50523009 -1.243167824 -0.085890524 KGQTHTLEDFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGQTHTLEDFQR 12 1 Q99714;Q99714-2;Q5H928 Q99714 HSD17B10 3-hydroxyacyl-CoA dehydrogenase type-2 0 ; 135.6 8.10E-05 488960000 313940 296160 288770 267570 386640 241980 244690 306190 598910 FALSE TRUE 294291.0558 318087.9946 295619.7608 274436.2992 356274.854 311835.6978 208001.0061 344418.4955 498948.0519 0.589823038 0.637517259 0.592486051 0.550029804 0.714051999 0.624986302 0.416879083 0.690289288 1 18.92853009 0.98033329 24.52337958 1.000000006 0.58827584 0.747927735 0.074871553 583.338719 727394.6636 0.074065815 0.018516454 9.557257557 -0.98033329 -0.411724165 KGS(ph)DDAPYSPTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGSDDAPYSPTAR 13 1 O75151;E7ET14;A0A087WW48 O75151 PHF2 Lysine-specific demethylase PHF2 1 KGS(1)DDAPYSPTAR 51.971 0.090722 0 363210 314440 297630 302060 296720 190060 298890 220270 389910 TRUE FALSE 340477.3344 337721.4648 304689.9242 309811.371 273416.8081 244927.2366 254074.2193 247771.1944 324831.5021 1.048165995 1.039681997 0.937993767 0.953760239 0.84171888 0.754013189 0.78217235 0.762768367 1 18.30933203 3.058805911 1.16170864 0.800376967 1.028834793 0.562852133 0.074143302 0.281156444 0.804994491 0.028252493 0.036670178 1145.001118 -3.058805911 0.228457827 KGS(ph)FSALVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KGSFSALVGR 10 1 Q13619;A0A087WWN2 Q13619 CUL4A Cullin-4A 1 KGS(0.979)FS(0.021)ALVGR;KGS(0.868)FS(0.132)ALVGR;KGS(1)FSALVGR 138.21 4.33E-05 842220000 1365870 1064580 1162900 999033 1129200 882428 1749120 1238330 2109940 TRUE FALSE 1280382.635 1143402.611 1190484.537 1024669.878 1040517.187 1137170.639 1486855.694 1392938.226 1757777.383 0.728410006 0.650482036 0.677266956 0.582934954 0.591950492 0.646936665 0.845872582 0.792442911 1 20.74532094 1.299472429 1.140710762 0.976459873 0.644515577 0.78816499 0.058740809 0.193344076 0.504932294 0.053892491 0.017912384 19.92839988 -1.299472429 -0.331944296 KGS(ph)GS(ph)EQEGEDEEGGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGSGSEQEGEDEEGGER 17 1 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 2 KGS(1)GS(1)EQEGEDEEGGER;KGS(1)GS(1)EQEGEDEEGGER 222.06 1.22E-14 770170000 2431200 1177570 1510260 1534870 1486910 1053170 1943760 1192570 1887790 TRUE FALSE 2279035.532 1264758.508 1546084.08 1574257.363 1370134.087 1357203.082 1652311.233 1341464.99 1572705.653 1.449117657 0.804192765 0.983072756 1.00098665 0.871195499 0.86297336 1.05061696 0.852966343 1 20.58481725 4.74722916 24.84230406 0.930258864 1.449117945 0.808739548 0.07959918 427.3039895 1224538.256 0.018194713 0.213372535 55876.49557 -4.74722916 0.518859081 KGS(ph)ITEYTAAEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 KGSITEYTAAEEK 13 1 J3KN59;Q12982;Q12982-2 J3KN59 BNIP2 BCL2/adenovirus E1B 19 kDa protein-interacting protein 2 1 KGS(0.995)IT(0.005)EYTAAEEK;KGS(0.982)IT(0.018)EYTAAEEK;KGS(0.989)IT(0.011)EYTAAEEK;KGS(0.83)IT(0.17)EYTAAEEK;KGS(0.998)IT(0.002)EYTAAEEK;KGS(0.996)IT(0.004)EYTAAEEK;KGS(0.9)IT(0.1)EYTAAEEK 288.21 1.24E-33 4258120000 10127710 4241861 6047730 5884020 5506520 4448692 8168400 4907410 5889050 TRUE FALSE 9493834.71 4555932.802 6191185.012 6035013.915 5074060.131 5732957.162 6943624.252 5520110.941 4906129.51 1.935096636 0.928620574 1.261928573 1.23009674 1.034228738 1.16852952 1.415295751 1.125145785 1 22.22615389 4.749743425 24.97904234 1.167350679 1.935097086 0.754732954 0.140973311 883.1455641 1972644.948 0.034211316 0.529402408 56200.91994 -4.749743425 0.767746407 KGS(ph)ITEYTAAEEKEDGRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KGSITEYTAAEEKEDGRR 18 3 J3KN59;Q12982;Q12982-2 J3KN59 BNIP2 BCL2/adenovirus E1B 19 kDa protein-interacting protein 2 1 KGS(0.995)IT(0.004)EYTAAEEKEDGRR;KGS(0.973)IT(0.027)EYTAAEEKEDGRR;KGS(0.999)IT(0.001)EYTAAEEKEDGRR 196.1 1.10E-14 1738580000 1474880 911470 1005760 1155260 1277850 665990 1424850 869920 2074990 TRUE FALSE 1382569.894 978956.1872 1029617.102 1184905.927 1177492.816 858250.5016 1211206.97 978531.4269 1728660.764 0.799792488 0.566309022 0.595615475 0.685447343 0.681158987 0.496482896 0.700662036 0.566063306 1 20.72122335 -1.605394107 2.915257347 1.026257404 0.628426497 0.636339251 0.086184425 16041448.02 16170970.59 3215032.398 0.019731068 0.024808808 1.605394107 -0.397830907 KGS(ph)KVGDFGDAINWPTPGEIAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGSKVGDFGDAINWPTPGEIAHK 23 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;H0YAX9 Q6PKG0 LARP1 La-related protein 1 1 KGS(1)KVGDFGDAINWPTPGEIAHK 107.2 0.00071477 185320000 80775 48449 60381 62478 91360 22398 62584 49933 264660 TRUE FALSE 75719.43694 52036.21437 61813.26583 64081.29126 84184.95413 28863.939 53200.1102 56167.24497 220486.5362 0.343419776 0.236006312 0.28034939 0.290635847 0.381814489 0.130910211 0.241285074 0.254742289 1 17.75033104 -1.290501716 4.071564571 1.000950828 0.2638496 0.921610791 0.066897189 15517320.92 9837463.862 123069.7482 0.014801035 0.051226925 1.290501716 -0.737101228 KGS(ph)LAALYDLAVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGSLAALYDLAVLK 14 1 Q6P4R8-3;Q6P4R8;E9PQ59;Q6P4R8-2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 KGS(1)LAALYDLAVLK 133.09 2.85E-05 56112000 389720 285860 254930 200740 325290 170750 374350 317410 754450 TRUE FALSE 365328.1209 307025.3718 260977.06 205891.3283 299743.0356 220042.7531 318219.6928 357039.3372 628527.4211 0.581244523 0.488483655 0.415219848 0.32757732 0.476897309 0.350092527 0.506294049 0.568056898 1 19.26161616 0.697673806 1.530014317 0.999509805 0.440536501 0.850465194 0.07248736 0.373436441 1.348095376 0.066203666 0.019175842 4.985099216 -0.697673806 -0.558973304 KGS(ph)LSSVTPSPTPENEDLHAATVNPDPSLKEFEGATLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGSLSSVTPSPTPENEDLHAATVNPDPSLKEFEGATLR 38 2 H0YAJ5;G5E9Y1;Q92870-2 H0YAJ5 APBB2 Amyloid beta A4 precursor protein-binding family B member 2 1 KGS(0.238)LS(0.238)S(0.238)VT(0.238)PS(0.041)PT(0.008)PENEDLHAATVNPDPSLKEFEGATLR 50.935 0.023252 40496000 36340 22385 25240 24965 27917 20967 37637 23742 42161 TRUE FALSE 34065.54427 24042.40869 25838.70472 25605.64417 25724.51143 27019.83253 31993.68125 26706.24096 35124.05673 0.969863605 0.684499768 0.735641242 0.729005888 0.7323901 0.76926856 0.910876597 0.760340446 1 15.10017186 0.793362229 0.629756211 0.997356891 0.751656899 0.333150239 0.090205618 1.051183124 0.891642666 0.089973403 0.035219904 6.213870945 -0.793362229 -0.245699993 KGS(ph)PTPGFSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KGSPTPGFSTR 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 KGS(0.716)PT(0.284)PGFSTR;KGS(0.878)PT(0.121)PGFS(0.001)TR;KGS(0.608)PT(0.392)PGFSTR;KGS(0.521)PT(0.479)PGFSTR;KGS(0.992)PT(0.008)PGFSTR 171.46 8.89E-06 13907400000 6166290 4323620 4706680 4764630 5032430 3742910 6413530 4311070 6000700 TRUE FALSE 5780352.916 4643745.324 4818324.672 4886898.472 4637203.248 4823427.356 5451880.717 4849316.579 4999144.404 1.156268443 0.928908019 0.963829864 0.977546972 0.92759938 0.964850576 1.09056276 0.970029307 1 22.25324977 1.793247552 25 1.030001711 0.974629585 0.024286976 0.071243082 324.6833584 148467.2825 0.029417754 0.016991894 62.1223037 -1.793247552 -0.055372125 KGS(ph)QITQQSTNQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGSQITQQSTNQSR 14 1 P50750;P50750-2 P50750 CDK9 Cyclin-dependent kinase 9 1 KGS(1)QITQQSTNQSR 148.06 4.82E-06 76701000 80359 46785 56476 49746 48822 36262 62927 46149 58168 TRUE FALSE 75329.47363 50249.01008 57815.63739 51022.56658 44987.71706 46730.25074 53491.68054 51910.80424 48459.38502 1.554486785 1.036930412 1.193074105 1.052893398 0.928359224 0.964317866 1.103845633 1.071222926 1 15.56448848 4.739869785 24.92017559 1.055657561 1.554486954 0.823467851 0.074125719 48.03920363 914329.2481 0.018867499 0.117544356 54937.61294 -4.739869785 0.498829393 KGS(ph)SGNASEVSVACLTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KGSSGNASEVSVACLTER 18 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1;C9J8U1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 KGS(0.841)S(0.153)GNAS(0.006)EVSVACLTER;KGS(0.964)S(0.035)GNAS(0.001)EVSVACLTER;KGS(0.994)S(0.006)GNASEVSVACLTER;KGS(0.953)S(0.047)GNASEVSVACLTER 245.37 2.03E-24 6265920000 2582930 1718490 1989080 1982850 2004700 1604071 2471350 1741050 2459320 TRUE FALSE 2421269.022 1845728.788 2036261.917 2033733.288 1847258.949 2067140.258 2100794.01 1958423.925 2048843.604 1.181773473 0.900863679 0.993859128 0.992624954 0.901610521 1.008930234 1.025355965 0.955867945 1 20.96637843 KGS(ph)SSQAPASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGSSSQAPASK 11 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 KGS(0.968)S(0.03)S(0.002)QAPASK;KGS(0.771)S(0.217)S(0.012)QAPASK 124.16 0.00021735 305810000 970640 639400 843340 1134610 1066530 400740 677230 400440 759220 TRUE FALSE 909889.375 686741.8413 863344.4231 1163726.013 982769.036 516427.1325 575685.6486 450435.8155 632501.2773 1.438557372 1.085755659 1.364968663 1.83987931 1.553781899 0.816483936 0.910173101 0.712150049 1 19.27070887 2.232072133 24.98224696 0.857149601 1.410949148 0.685221171 0.199695877 105.3983633 405805.5875 0.081558619 0.061661393 170.6365782 -2.232072133 0.553799547 KGS(ph)VSHDTVQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.833)VS(0.167)HDTVQPR;KGS(0.909)VS(0.091)HDTVQPR;KGS(0.791)VS(0.209)HDTVQPR;KGS(0.889)VS(0.111)HDTVQPR 164.8 3.45E-05 1538570000 976670 838710 951840 1084460 1191010 656860 1067270 856520 1655660 TRUE FALSE 915541.9681 900808.9611 974418.0943 1112289.08 1097472.879 846484.8188 907242.7715 963458.4074 1379319.65 0.663763449 0.653082091 0.706448352 0.806404142 0.795662469 0.613697353 0.657746572 0.698502633 1 20.3955254 -0.947803169 3.57356088 1.000052198 0.695319209 0.705955388 0.060915419 6229816.602 11408423.04 4176.078334 0.015411282 0.112770844 0.947803169 -0.304732989 KGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSR 37 1 P06576;H0YH81;H0YI37 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ; 129.51 8.57E-09 185645000 383120 383760 352850 342770 535900 357540 345890 428170 627060 FALSE TRUE 359141.2031 412173.9897 361219.7686 351566.0585 493812.5757 460755.9938 294027.0056 481627.967 522399.635 0.687483641 0.789001297 0.691462521 0.672982971 0.945277413 0.881999073 0.562839225 0.921953108 1 18.99479436 -4.999999903 0.239426274 2.395851355 0.731217569 0.297743567 0.11831325 223.0663251 2.226323887 151.3862512 0.183059846 1.00E-05 4.999999903 -1.664633786 KGSLESPATDVFGSTEEGEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGSLESPATDVFGSTEEGEKR 21 2 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 56.882 0.047738 139270000 33563 27039 33454 35848 32482 26518 37792 29021 36068 FALSE TRUE 31462.35174 29040.99569 34247.54468 36767.92037 29930.99475 34173.31612 32125.44044 32644.33573 30048.01779 1.047069126 0.966486239 1.13976053 1.223638798 0.996105465 1.137290198 1.069136762 1.086405631 1 14.8749822 3.978183346 7.619191883 1.098236837 1.007237851 0.208940644 0.069356299 0.155625916 71.59995861 0.01609613 0.031973744 9510.061957 -3.978183346 -0.090998987 KGSMSNGHGS(ph)PGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGSMSNGHGSPGEK 14 1 Q15742;Q15742-2;Q15742-3 Q15742 NAB2 NGFI-A-binding protein 2 1 KGS(0.017)MS(0.015)NGHGS(0.968)PGEK 59.372 0.06212 46870000 30964 25275 34118 34386 32506 24853 39934 24430 32096 TRUE FALSE 29026.01851 27146.3873 34927.29507 35268.40298 29953.10988 32027.65765 33946.26743 27480.13928 26738.97025 1.085532399 1.015236826 1.306231868 1.318988826 1.120204316 1.197789494 1.26954281 1.027718682 1 14.70665629 -3.004063401 9.338129548 1.022439875 1.168365167 0 0.121817125 0 0 0 0.026045514 0.000990687 3.004063401 0.145925291 KGSPT(ph)PGFSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGSPTPGFSTR 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 KGS(0.209)PT(0.791)PGFSTR 90.966 0.0065005 5403800000 1432200 1070400 1111100 1102800 1201300 898320 1510300 1008600 1357400 TRUE FALSE 1342561.159 1149653.53 1137455.817 1131099.715 1106954.744 1157650.401 1283844.536 1134525.93 1130841.171 1.187223452 1.016635722 1.005849315 1.00022863 0.978877293 1.023707335 1.13530049 1.003258423 1 20.10896488 -0.41258231 7.671439107 0.999996609 1.040933757 0.040060823 0.066123756 0 0 0.062229435 0.014667618 0.386738751 0.41258231 0.040937148 KGSS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGSSPSR 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KGS(0.066)S(0.819)PS(0.114)R 68.456 0.066101 57179000 182130 136710 222530 180940 194470 144820 265330 139370 215100 TRUE FALSE 170730.8084 146832.1506 227808.5167 185583.2267 179197.1107 186627.183 225546.2297 156770.6513 179198.4204 0.952747284 0.819383063 1.271264089 1.035629814 0.999992691 1.041455514 1.258639609 0.874843935 1 17.45119839 4.103094531 5.755446002 1.088963906 0.888480991 0.261744981 0.123792324 0.236598803 10.40068797 0.029025124 0.06425398 12679.27819 -4.103094531 -0.200482916 KGSSS(ph)QAPASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGSSSQAPASK 11 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 KGS(0.208)S(0.344)S(0.448)QAPASK 75.961 0.022453 200130000 121680 67345 106710 146040 136760 50334 60303 52434 80793 TRUE FALSE 114064.266 72331.29387 109241.2116 149787.6336 126019.4213 64864.6087 51261.12498 58980.50032 67308.12636 1.694658167 1.074629436 1.62300182 2.22540192 1.872276471 0.963696543 0.761588945 0.876276068 1 16.03849308 2.155589464 6.249625907 0.858858681 1.625428885 0.644940757 0.291254612 0.158953962 9.552740695 0.124298255 0.091626018 143.0834701 -2.155589464 0.766570203 KGT(ph)TPPRS(ph)PEASPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGTTPPRSPEASPK 14 2 Q9HDC5 Q9HDC5 JPH1 Junctophilin-1 2 KGT(0.554)T(0.447)PPRS(0.999)PEASPK 120.31 0.00025843 647300000 910110 455240 540950 525960 641640 459690 897400 587880 897650 TRUE FALSE 853147.8397 488946.4433 553781.5895 539457.024 591248.1827 592395.0406 762843.2011 661278.1121 747826.416 1.140836726 0.653823445 0.740521567 0.721366633 0.790622222 0.79215581 1.020080576 0.884266854 1 19.51234391 1.766594589 12.37683474 0.964306297 0.777400194 0.223998467 0.134593703 0.477624272 210.1910172 0.058159393 0.032171754 58.42444412 -1.766594589 -0.186906103 KGTENGVNGTLTSNVADS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 259.7 1.62E-36 1837330000 1636170 1373440 1480170 1329270 1509170 1465970 2120490 1679100 1736650 TRUE FALSE 1533765.04 1475130.927 1515280.331 1363381.319 1390645.876 1889171.741 1802542.21 1888739.331 1446791.896 1.060114481 1.019587496 1.047338139 0.94234791 0.961192746 1.305766051 1.24588907 1.305467176 1 20.46442599 2.241278418 24.99999493 1.238498055 1.010675764 0.549519706 0.092454706 44.48476031 409201.6322 0.029482643 0.023635351 174.2923871 -2.241278418 -0.227822291 KGTVEGFEPADNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KGTVEGFEPADNK 13 1 P37108;H0YLA2 P37108 SRP14 Signal recognition particle 14 kDa protein 0 ;;; 163.8 6.11E-05 1555460000 2657830 2236840 2262690 2252200 2895490 1644630 3161060 2224940 4366640 FALSE TRUE 2491481.165 2402457.961 2316362.075 2309995.265 2668089.895 2119407.983 2687088.399 2502728.657 3637819.574 0.684883105 0.660411522 0.636744629 0.634994457 0.733431068 0.582603931 0.738653565 0.687974927 1 21.79464256 -0.183208483 0.621118624 1.025486154 0.655338724 0.845872367 0.044602225 2.026275465 0.76908345 0.16262609 0.015391379 0.655830359 0.183208483 -0.37014743 KGVAINFVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGVAINFVK 9 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 89.047 0.018709 0 608070 662350 570090 530770 800170 409680 668900 701200 871640 FALSE TRUE 570011.9841 711391.0832 583612.804 544390.4568 737327.8759 527947.9654 568604.6548 788746.3635 726157.653 0.784970016 0.979664788 0.80369986 0.749686317 1.015382642 0.727043175 0.783031966 1.086191628 1 19.46992327 1.236006677 24.99998956 1.043095887 0.840959742 0.448836787 0.095779595 63.42628026 620803.0328 0.075645617 0.022277329 17.21895047 -1.236006677 -0.202136145 KGVAINFVTEEDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGVAINFVTEEDKR 14 2 Q14240;Q14240-2 Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ; 201.24 1.02E-08 1597130000 2251930 1788400 1833900 1880730 2547320 1290610 2390350 1954000 3322800 FALSE TRUE 2110985.721 1920814.997 1877400.974 1928992.716 2347263.763 1663188.156 2031939.208 2197961.201 2768203.214 0.762583365 0.693885112 0.678202006 0.696839273 0.847937663 0.600818664 0.734028195 0.794002836 1 21.40051842 0.851125231 2.22308062 0.999543422 0.709029703 0.668675485 0.062893587 0.301619199 2.84751257 0.054696273 0.014923998 7.097824077 -0.851125231 -0.290513719 KGVAINMVTEEDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KGVAINMVTEEDKR 14 2 P60842 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;;; 153.24 3.63E-06 9696160000 4512280 2871140 3470590 3621900 3968450 2627700 4788470 2932900 4679870 FALSE TRUE 4229864.449 3083722.193 3552914.034 3714844.086 3656783.945 3386274.333 4070483.377 3299079.021 3898769.464 1.084922945 0.79094756 0.911291131 0.952824762 0.937932847 0.868549517 1.044043105 0.846184688 1 21.89458742 2.356954798 0.856428481 0.961466489 0.902301956 0 0.09128357 1.953526319 2.800460999 0.063794653 0.041369311 227.4860649 -2.356954798 -0.059164534 KGVEGLIDIENPNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KGVEGLIDIENPNR 14 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ;;;;; 220.25 7.55E-12 2033980000 2746220 2920160 2719310 3007790 3113030 2293920 3394540 2490640 3492070 FALSE TRUE 2574338.992 3136371.685 2783813.317 3084974.984 2868545.181 2956137.465 2885560.24 2801601.887 2909220.957 0.88488947 1.078079572 0.956893051 1.060412746 0.986018327 1.016126829 0.991866992 0.963007598 1 21.47220144 4.76216583 24.57031408 1.006892423 0.884889294 0.500071767 0.038227569 4557.112821 4743333.589 0.008312711 0.500704563 57831.68281 -4.76216583 -0.122003129 KGVITVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGVITVK 7 1 P10809;E7EXB4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 103.74 0.032652 0 2400200 2102320 2106650 1905940 2942200 1977880 2380700 2255640 3546700 FALSE TRUE 2249975.766 2257977.96 2156620.733 1954849.647 2711131.48 2548861.848 2023736.136 2537261.619 2954732.857 0.76148196 0.764190223 0.729886875 0.661599455 0.917555532 0.862636986 0.684913403 0.858711004 1 21.49459627 -5 0.208596929 2.104000558 0.737137085 0.468213853 0.077284024 131.2112331 1.307421094 60.40573361 0.164506661 1.00E-05 5 -1.366863473 KGVNLPGAAVDLPAVSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGVNLPGAAVDLPAVSEK 18 1 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 199.41 2.61E-15 2443450000 5963300 4498000 5252400 5095600 5514000 3955700 6781600 4858500 5489000 FALSE TRUE 5590067.698 4831036.6 5376989.408 5226361.723 5080952.682 5097646.375 5764762.037 5465094.42 4572850.44 1.222447087 1.056460661 1.175850704 1.142911143 1.111112806 1.114763415 1.260649591 1.195117682 1 22.1246623 KGVNLPGAAVDLPAVSEKDIQDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KGVNLPGAAVDLPAVSEKDIQDLK 24 2 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 168.65 5.74E-12 1199760000 1606670 1402570 1387770 1602080 2182730 843610 1869650 1240080 4042200 FALSE TRUE 1506111.393 1506417.742 1420688.56 1643192.085 2011307.191 1087146.512 1589313.339 1394906.718 3367530.706 0.447245036 0.447336008 0.421878428 0.487951626 0.597264692 0.322831952 0.471952145 0.41422242 1 21.68325967 -1.528187185 2.768394455 1.027172291 0.449695408 0.864678017 0.068210152 8035916.851 8276482.931 1637284.673 0.015883904 0.029635538 1.528187185 -0.577476883 KGWESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGWESR 6 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 0 94.662 0.070915 531280000 1603200 1692000 1705100 1777900 2308900 1532700 2272900 1883800 2561900 FALSE TRUE 1502858.574 1817277.441 1745545.777 1823523.924 2127568.308 1975165.609 1932099.746 2118996.577 2134302.339 0.704145119 0.851462048 0.817853096 0.854388758 0.996844856 0.925438525 0.905260567 0.992828681 1 21.02533313 7.21112257 0.206405341 1.008588593 8.05E-20 0.762050806 0.045387446 18.72919573 0.30608529 0.078631198 5.774408557 16260075.94 -7.21112257 -1.008588593 KGWEVVESDLYAMNFNPIISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGWEVVESDLYAMNFNPIISR 21 1 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 141.69 2.46E-07 370530000 292680 359270 278570 302410 379570 252770 336390 318060 350770 FALSE TRUE 274361.6812 385870.7246 285177.812 310170.3526 349760.1033 325740.5956 285951.4424 357770.4911 292224.2209 0.938873856 1.320461129 0.975886978 1.061412198 1.196889506 1.114694034 0.978534365 1.224301292 1 18.15671623 -5 0.208101715 0.524840442 1.117783702 0.040933211 0.122311289 453.7804183 4.52023383 90.32808743 0.249251113 1.00E-05 5 0.592943259 KGWS(ph)MSEQSEESVGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.988)MS(0.011)EQSEESVGGR;KGWS(0.999)MS(0.001)EQSEESVGGR;KGWS(0.5)MS(0.5)EQSEESVGGR;KGWS(0.914)MS(0.082)EQS(0.004)EESVGGR;KGWS(0.998)MS(0.002)EQSEESVGGR 256.4 7.51E-27 1822370000 1478409 1175383 1121941 1203868 1092427 803381 1595630 1102625 2329790 TRUE FALSE 1385878.02 1262409.58 1148553.97 1234761.291 1006632.19 1035304.053 1356380.095 1240290.158 1940932.998 0.714026719 0.650413786 0.591753539 0.636168942 0.518633148 0.533405354 0.698828912 0.639017503 1 20.88831889 0.30523627 1.136681086 1.000652858 0.614163535 0.787661123 0.061746131 1.62434951 2.249629353 0.060394481 0.017931796 2.019464719 -0.30523627 -0.386489324 KGYEVIYLTEPVDEYCIQALPEFDGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGYEVIYLTEPVDEYCIQALPEFDGKR 27 2 P14625 P14625 HSP90B1 Endoplasmin 0 173.96 1.34E-12 208570000 237750 216060 227010 228100 265870 173870 327490 211950 259870 FALSE TRUE 222869.6519 232057.3072 232394.7844 233953.4322 244989.6427 224063.4465 278385.9148 238412.4241 216496.0182 1.029439958 1.071877946 1.07343676 1.08063619 1.131612695 1.034954122 1.285870831 1.101232374 1 17.72398097 2.534766903 1.347554821 1.146151948 1.063554735 0.011266565 0.078232838 0.750182606 2.764177405 0.036640559 0.028701032 342.583864 -2.534766903 -0.082597213 KHDSGAADLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KHDSGAADLER 11 1 Q9NX55;Q9NX55-3;J3QT56 Q9NX55;J3QT56 HYPK Huntingtin-interacting protein K 0 ; 89.629 0.0078482 427446000 858634 719630 814986 847751 860872 576974 862056 740711 919025 FALSE TRUE 804893.6306 772912.154 834317.8528 869505.7259 793262.5857 743537.0274 732798.7057 833190.3989 765633.7904 1.05127757 1.009506325 1.089708766 1.135667909 1.036086176 0.971139253 0.957113851 1.08823619 1 19.54629498 2.464044768 9.991365006 0.995874284 1.066389481 0.309201977 0.04651106 0.289536686 202.7691042 0.016222506 0.013753401 291.1017176 -2.464044768 0.070515197 KHEADELS(ph)GDASVEDDAFIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KHEADELSGDASVEDDAFIK 20 1 Q9NWH9;H7BXE3;H0YL55;H0YKU6;H0YNF3;H0YMR6;H0YLE6 Q9NWH9 SLTM SAFB-like transcription modulator 1 KHEADELS(0.5)GDAS(0.5)VEDDAFIK 48.848 0.071499 34741000 67091 35010 46862 40834 35147 28930 52816 39653 36299 TRUE FALSE 62891.89407 37602.17683 47973.58877 41881.86957 32386.6964 37281.62136 44896.73112 44603.76434 30240.4624 2.079726601 1.243439215 1.586403942 1.384961282 1.070972261 1.232838998 1.48465756 1.474969653 1 14.88419258 4.743366401 24.87204707 1.344048669 2.079726924 0.623329869 0.186413872 321.2726821 1662667.146 0.042703225 0.350825529 55381.71508 -4.743366401 0.735678254 KHEAFESDLAAHQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KHEAFESDLAAHQDR 15 1 O43707;O43707-2;F6THM6;A0A494C060;P12814-3;P12814;P12814-2;P12814-4;H9KV75;P35609-2;P35609;A0A494C1A0;H7C5W8 O43707;P12814-3 ACTN4;ACTN2;ACTN1 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2 0 ;;;;; 186.85 1.48E-07 7906360000 3549810 2744320 2884240 2248420 2003450 2222800 3842980 2904010 2797100 FALSE TRUE 3327633.729 2947512.308 2952655.535 2306118.264 1846107.119 2864486.276 3266760.825 3266582.041 2330245.94 1.42801825 1.264893228 1.267100388 0.989645867 0.792237028 1.229263498 1.401895298 1.401818574 1 21.1520508 4.601681583 1.193577635 1.1726312 1.490343312 0.169711934 0.190531924 2.745168272 3.941353564 0.060128587 1.019212983 39965.16251 -4.601681583 0.317712112 KHEAFESDLAAHQDRVEQIAAIAQELNELDYYDSHNVNTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KHEAFESDLAAHQDRVEQIAAIAQELNELDYYDSHNVNTR 40 2 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 61.394 0.0035079 220130000 77860 90901 76199 80638 80396 50604 81622 75807 101370 FALSE TRUE 72986.88158 97631.40462 78006.47626 82707.3076 74082.02246 65212.55331 69383.53884 85271.67082 84450.69212 0.864254392 1.156075837 0.923692563 0.979356184 0.877222206 0.772196789 0.821586385 1.009721397 1 16.36582163 3.183897761 1.520358078 0.872478508 1.025843148 0.092466068 0.10458669 0.485823289 2.323868002 0.034417236 0.048188319 1527.206492 -3.183897761 0.153364641 KHEDFDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KHEDFDK 7 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 116.73 0.0034996 717050000 1354450 824720 979710 996060 1125540 676520 1255120 927830 1408210 FALSE TRUE 1269677.392 885783.1269 1002949.184 1021620.586 1037144.629 871820.3416 1066926.408 1043671.618 1173170.654 1.082261467 0.755033485 0.854904767 0.8708201 0.884052653 0.743131734 0.909438371 0.889616199 1 20.16198146 0.846942223 1.594885988 0.998795594 0.853365481 0.140849203 0.09310955 0.932376053 4.491782441 0.0792872 0.022918459 7.029787924 -0.846942223 -0.145430113 KHEDSAIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KHEDSAIPR 9 1 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 0 ; 66.595 0.041081 181629000 178155 179579 210618 205102 240161 168085 217906 197241 286880 FALSE TRUE 167004.5966 192875.216 215613.9584 210365.2646 221299.7238 216608.4109 185233.0182 221866.973 238997.8747 0.698770216 0.807016448 0.902158476 0.880197219 0.925948501 0.906319402 0.775040441 0.92832195 1 17.86663826 4.707725245 1.367252331 0.88690322 0.626290714 0.568528573 0.057175552 0.970848604 1.686307598 0.01539406 0.344942633 51018.21329 -4.707725245 -0.260612506 KHEEEEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KHEEEEAK 8 1 P25789;H0YN18;P25789-2 P25789 PSMA4 Proteasome subunit alpha type-4 0 ; 122.13 0.00091102 427540000 1621910 855040 1020870 924190 917860 760600 1233640 941880 891530 FALSE TRUE 1520397.548 918348.0513 1045085.518 947906.28 845774.9781 980172.8727 1048667.135 1059475.791 742727.8835 2.047045199 1.236452908 1.407090728 1.276249756 1.138741384 1.319693113 1.411912974 1.426465621 1 19.50247422 4.74164183 24.8689365 1.30200913 2.047045495 0.763439104 0.1340606 126.8903065 1024097.419 0.029418645 0.208915513 55162.23191 -4.74164183 0.745036365 KHEEEEAKAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KHEEEEAKAER 11 2 P25789;H0YN18;P25789-2 P25789 PSMA4 Proteasome subunit alpha type-4 0 ; 225.23 3.38E-12 1282340000 1055150 758790 802410 846570 1100900 487160 949730 791380 1722200 FALSE TRUE 989110.045 814971.6011 821443.5441 868294.4194 1014439.755 627795.1836 807326.8034 890185.535 1434753.694 0.689393621 0.568021957 0.572532796 0.605187094 0.707048017 0.437563037 0.562693657 0.620444846 1 20.45237166 0.798884937 5.01489901 0.999998324 0.583490853 0.748245419 0.073821394 1.966146655 48.77845025 0.066704745 0.016858846 6.293394221 -0.798884937 -0.41650747 KHEENEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KHEENEAK 8 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 66.692 0.039615 36625000 129750 72079 99525 96047 93569 70843 106540 85607 122510 FALSE TRUE 121629.1791 77415.80416 101885.78 98511.72863 86220.46818 91294.22406 90565.31607 96295.22239 102062.2896 1.191715174 0.758515261 0.99827057 0.965211824 0.844782814 0.89449516 0.887353365 0.943494633 1 16.63909039 4.758450466 24.52139038 0.904656883 1.191715523 0.58930574 0.073313683 2538.851294 3129981.619 0.016500311 0.649716395 57339.04637 -4.758450466 0.28705864 KHFTILDAPGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KHFTILDAPGHK 12 1 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1;H3BSV8 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 194.24 7.23E-07 290780000 142390 161730 166410 164730 205130 154130 188600 154000 245830 FALSE TRUE 133478.0641 173704.6575 170357.3238 168957.2507 189019.9173 198624.8289 160321.1809 173227.239 204799.3849 0.651750317 0.84816982 0.831825368 0.824989053 0.922951587 0.96985071 0.782820617 0.845838668 1 17.64385186 5.376883792 1.277862125 0.871712767 6.97E-19 0.517332101 0.068263519 5.300609748 2.345118821 0.017867003 9.027381745 238168.2095 -5.376883792 -0.871712767 KHGGPKDEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KHGGPKDEER 10 2 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;;;;; 176.42 1.50E-06 10579050000 10149610 8146190 8272100 7773980 10012520 5527980 9390650 7574240 12702040 FALSE TRUE 9514364.028 8749342.384 8468318.118 7973473.488 9226177.068 7123818.087 7982609.211 8519900.537 10581987.47 0.899109365 0.826814661 0.80025781 0.753494891 0.871875638 0.67320228 0.754358218 0.80513236 1 23.33510728 5.23379381 0.958382652 0.788180401 1.083185176 0.060292379 0.086876453 8.900003232 3.362316409 0.023810836 3.405274265 171314.3765 -5.23379381 0.295004775 KHGLAHDEMKS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KHGLAHDEMKSPR 13 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 KHGLAHDEMKS(1)PR;KHGLAHDEMKS(1)PR;KHGLAHDEMKS(1)PR;KHGLAHDEMKS(1)PR;KHGLAHDEMKS(1)PR;KHGLAHDEMKS(1)PR 203.99 5.34E-08 2760013000 5227240 3734320 4183280 4468580 4580850 3200770 5102810 3232960 4835200 TRUE FALSE 4900076.379 4010812.938 4282509.377 4583251.328 4221088.519 4124780.339 4337691.013 3636602.173 4028173.883 1.216451057 0.99569012 1.063139155 1.137798779 1.047891338 1.023982692 1.076838076 0.902791756 1 21.94169453 1.251061535 24.99937951 0.95139588 1.068711975 0.388499425 0.065986567 201.5183243 403002.0225 0.040923622 0.014715333 17.82631331 -1.251061535 0.117316095 KHGLEVIYMIEPIDEYCVQQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KHGLEVIYMIEPIDEYCVQQLK 22 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 199.29 1.16E-22 2898200000 2681710 2294840 2193750 2336640 2881250 1909120 3049970 2095720 2852730 FALSE TRUE 2513866.558 2464752.341 2245786.786 2396602.138 2654968.247 2460251.952 2592655.313 2357375.255 2376590.934 1.05776157 1.037095744 0.944961438 1.00842013 1.117133037 1.035202111 1.090913576 0.991914604 1 21.18046217 2.956192083 24.98235271 1.055556526 1.004627958 0.096858997 0.047176198 676.9990251 386072.4735 0.013730159 0.014563908 904.0492355 -2.956192083 -0.050928568 KHLEINPDHPIVETLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KHLEINPDHPIVETLR 16 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;; 238.83 3.39E-20 7891620000 2668042 3149789 2985774 2964627 3682141 2319694 3580468 2661523 4260030 FALSE TRUE 2501054.014 3383002.655 3056597.969 3040704.348 3392960.499 2989352.001 3043610.063 2993820.005 3549003.472 0.704720081 0.953226076 0.861255277 0.856776944 0.956031891 0.842307432 0.857595685 0.843566378 1 21.75898256 -2.604079692 2.056800922 3.286903492 0.869170624 0.279213242 0.069427523 2399302.586 143979.2546 25633884.11 0.015186381 0.002488401 2.604079692 -2.417732868 KHLEINPDHSIIETLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KHLEINPDHSIIETLR 16 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 263.45 2.46E-27 5269220000 2133870 2482710 2176940 2346130 3012550 1831560 2686950 2207800 3285390 FALSE TRUE 2000314.886 2666532.432 2228578.045 2406335.668 2775956.475 2360301.639 2284066.792 2483448.69 2737037.185 0.730832192 0.974240484 0.814230094 0.879175366 1.014219496 0.862356439 0.834503384 0.907349269 1 21.3841836 -3.372162771 1.247364206 7.163705701 0.880256195 0.190752687 0.079312598 1167051.479 9043.344208 20484578.26 0.021766536 0.00042446 3.372162771 -6.283449506 KHLFSS(ph)TENLAAGSWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KHLFSSTENLAAGSWK 16 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 KHLFS(0.026)S(0.968)T(0.006)ENLAAGSWK;KHLFS(0.003)S(0.99)T(0.006)ENLAAGSWK 190.91 4.78E-10 297830000 556300 488870 524770 476020 509840 320366 704720 509120 721020 TRUE FALSE 521482.176 525066.4435 537217.7922 488235.4791 469799.223 412850.4635 599053.7783 572684.7527 600677.104 0.868157239 0.874124284 0.894353703 0.812808539 0.782116082 0.687308474 0.997297507 0.953398671 1 19.19623015 1.615444743 19.49712909 0.981546062 0.833577651 0.618261874 0.05999833 0.128669192 319.7418927 0.030663036 0.016409127 41.2519747 -1.615444743 -0.147968411 KHNGVGGS(ph)PPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KHNGVGGSPPK 11 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 KHNGVGGS(1)PPK;KHNGVGGS(1)PPK 68.283 0.035318 186645000 146604 90445 107918 103914 102886 78527 147078 95884 111948 TRUE FALSE 137428.3173 97141.64191 110477.8659 106580.6092 94805.74858 101196.4701 125025.0193 107855.3285 93263.15559 1.473554229 1.04158648 1.184582113 1.14279437 1.016540219 1.085063758 1.340561753 1.156462354 1 16.50901962 -1.206788015 0.014153104 2.63E-06 2.18601728 0.14938293 0.136676402 8790.76892 22.18394332 1871.524815 1563.285472 0.062117216 1.206788015 2.186014651 KHNMCGETEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 KHNMCGETEEEK 12 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;;;;;;;;;;; 206.51 4.26E-08 6603197000 14507176 7812255 11098140 10507635 11224673 8901380 13730417 9639515 15969530 FALSE TRUE 13599197.75 8390682.489 11361393.12 10777278.7 10343132.46 11471063.9 11671668.44 10843029.67 13304112.28 1.02218002 0.630683379 0.85397604 0.810071238 0.777438753 0.862219415 0.877297801 0.815013392 1 23.66536891 0.159732394 0.387845093 1.027720747 0.791658197 0.193000764 0.098970315 4.894767004 1.123853761 0.328752057 0.068719581 1.444549386 -0.159732394 -0.23606255 KHPDADSLYVEEVDVGEIAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KHPDADSLYVEEVDVGEIAPR 21 1 Q12904;Q12904-2;A0A5F9ZHC5 Q12904 AIMP1 Aminoacyl tRNA synthase complex-interacting multifunctional protein 1;Endothelial monocyte-activating polypeptide 2 0 ;; 181.26 3.31E-17 1184650000 1527420 1560300 1533600 1552140 1802150 1288590 1929540 1574740 2109980 FALSE TRUE 1431821.509 1675826.235 1569977.716 1591970.54 1660616.409 1660585.014 1640223.39 1771349.755 1757810.707 0.814548178 0.953359898 0.89314379 0.905655276 0.944707187 0.944689327 0.933105814 1.007702222 1 20.74534829 8 0.100766935 1.04897562 0.532462105 0.586342899 0.035308705 98.3074018 0.700621308 0.405020645 7.026277954 99999999.9 -8 -0.516513515 KHPDASVNFSEFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KHPDASVNFSEFSK 14 1 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ;;; 257.54 3.82E-24 5195700000 4157610 3777890 3906600 3879630 4224100 3018150 4958860 3414280 4642930 FALSE TRUE 3897392.612 4057608.906 3999266.397 3979187.874 3892356.225 3889440.909 4215324.979 3840560.374 3867994.989 1.007600223 1.049021242 1.033937843 1.028746905 1.006298156 1.005544454 1.089795874 0.992907278 1 21.88315449 KHPEVDVLINFASLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KHPEVDVLINFASLR 15 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 200.77 4.38E-09 1172540000 2623500 3468800 2471800 2258900 4027900 1813460 2821700 3439400 3058800 FALSE TRUE 2459299.818 3725633.561 2530432.263 2316867.198 3711564.982 2336976.463 2398612.28 3868816.661 2548266.519 0.965087364 1.462026649 0.993001416 0.909193438 1.456505806 0.917084789 0.94127214 1.518215081 1 21.28108474 3.843122928 7.753067417 1.088718308 1.245367994 0.025682989 0.246246944 0.662496846 40.91879445 0.058430171 0.10579496 6968.237234 -3.843122928 0.156649686 KHPS(ph)SPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KHPSSPAR 8 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 KHPS(0.869)S(0.131)PAR;KHPS(0.713)S(0.287)PAR;KHPS(0.5)S(0.5)PAR;KHPS(0.5)S(0.5)PAR;KHPS(0.664)S(0.336)PAR 139.86 0.00040356 1282580000 591227 2870550 445012 482902 2957770 320152 545966 2509830 2845840 TRUE FALSE 554223.1574 3083088.509 455567.8948 495294.0829 2725478.675 412574.6852 464103.4668 2823187.8 2370850.919 0.233765503 1.30041433 0.19215375 0.208909839 1.14957826 0.174019666 0.195753965 1.190790942 1 21.17697352 1.223569192 24.9942829 1.095395936 0.523582448 0.266183409 0.413126685 395.3542924 659131.3716 0.383616071 0.09746044 16.73282202 -1.223569192 -0.571813487 KHPSS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KHPSSPAR 8 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 KHPS(0.169)S(0.831)PAR;KHPS(0.221)S(0.779)PAR 101.39 0.0033236 544720000 119076 621860 89377 88411 607730 57294 108238 543460 602640 TRUE FALSE 111623.2457 667903.1614 91497.06465 90679.77594 560001.3373 73833.84771 92008.71673 611312.1773 502055.4908 0.222332487 1.330337331 0.182244924 0.180617039 1.115417215 0.147063122 0.183264038 1.217618746 1 18.9374873 1.225039808 24.99639019 1.108809787 0.512909372 0.274906846 0.421845845 378.1467463 699072.4959 0.391514025 0.100072599 16.78957907 -1.225039808 -0.595900415 KHRS(ph)PT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KHRSPTPK 8 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 KHRS(1)PT(1)PK 73.781 0.08067 171920000 353770 225160 250040 283260 290940 191470 319320 219630 320790 TRUE FALSE 331628.1672 241831.0807 255971.0669 290528.9312 268090.746 246744.2807 271440.9304 247051.289 267248.0766 1.240900108 0.904893624 0.957803215 1.087113273 1.003153135 0.923278041 1.015688995 0.924426818 1 18.02782004 2.454287495 24.1203593 0.96984212 1.012524393 0.095486883 0.094009429 576.3501578 608820.5474 0.031625285 0.026462013 284.6344713 -2.454287495 0.042682273 KHS(ph)PDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KHSPDLR 7 1 Q8IWI9-3;Q8IWI9;H3BP52;H3BTF4 Q8IWI9-3 MGA MAX gene-associated protein 1 KHS(1)PDLR;KHS(1)PDLR;KHS(1)PDLR 90.108 0.010646 479030000 1254120 985350 1128550 1010750 1225170 960940 1486180 1138720 1456550 TRUE FALSE 1175626.868 1058306.339 1155319.739 1036687.556 1128950.09 1238347.778 1263341.106 1280891.699 1213442.395 0.968836158 0.872152105 0.952101017 0.854336028 0.930369744 1.02052457 1.041121615 1.055585089 1 20.21067419 2.248147417 3.813246362 1.035378097 0.910279113 0.716174468 0.035757802 0.10205317 3.246453523 0.012338811 0.009451916 177.0709907 -2.248147417 -0.125098983 KHS(ph)PS(ph)PPPPTPTESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(1)PS(1)PPPPTPTESR;KHS(1)PS(0.999)PPPPT(0.001)PTESR;KHS(0.999)PS(0.999)PPPPT(0.002)PTESR 123.19 0.00036488 6541860000 3392320 2218670 2713550 2682930 2873150 2258980 3429420 2276610 3721390 TRUE FALSE 3180000.747 2382942.635 2777916.687 2751778.526 2647504.389 2911110.855 2915210.308 2560849.77 3100265.968 1.02571869 0.768625228 0.896025282 0.88759434 0.853960407 0.938987456 0.940309747 0.826009703 1 21.56396056 2.236723229 24.97657719 0.92401349 0.871696258 0.045431056 0.075552955 110.9949761 1508778.223 0.025319046 0.019661228 172.4738385 -2.236723229 -0.052317231 KHS(ph)PSPPPPTPTESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KHSPSPPPPTPTESR 15 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 1 KHS(0.868)PS(0.132)PPPPTPTESR;KHS(0.935)PS(0.065)PPPPTPTESR;KHS(0.964)PS(0.036)PPPPTPTESR;KHS(0.939)PS(0.061)PPPPTPTESR 104.84 0.00083446 279631000 148048 126884 141670 132774 148133 127407 168497 120057 183751 TRUE FALSE 138781.94 136278.6234 145030.4793 136181.2056 136499.2317 164187.3326 143232.4391 135046.3807 153081.771 0.906586977 0.89023417 0.947405288 0.889597793 0.891675284 1.072546597 0.935659668 0.882184599 1 17.22394297 KHS(ph)QTDLVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KHSQTDLVSR 10 1 E9PN66;E9PNB3;E9PKN9;E9PS55;E9PMY0;E9PMW4;E9PQ46;E9PIN5;E9PIK4;U3KQ32;E9PKZ4;E9PPM1;O14683 E9PN66 TP53I11 Tumor protein p53-inducible protein 11 1 KHS(1)QTDLVSR;KHS(0.92)QT(0.08)DLVSR;KHS(1)QTDLVSR 223.03 2.84E-09 2703080000 2317110 1564150 1134190 1581930 2100390 1083360 2395560 1577110 1229700 TRUE FALSE 2172086.221 1679961.293 1161093.522 1622525.002 1935433.842 1396108.445 2036368.017 1774015.655 1024455.126 2.120235593 1.639858351 1.133376654 1.583793141 1.889232425 1.362781453 1.987757166 1.731667508 1 19.96642536 2.989459455 24.75131941 1.67004532 1.536494418 0 0.366681016 2045.985358 4804405.174 0.103688504 0.116782049 976.0216578 -2.989459455 -0.133550902 KHSVSTSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KHSVSTSDR 9 1 F8WAJ0;Q9H8H2-4;Q9H8H2-2;Q9H8H2;Q9H8H2-3 F8WAJ0 DDX31 Probable ATP-dependent RNA helicase DDX31 0 91.584 0.0069162 24161000 12151 19407 18119 15909 17993 14555 16874 14932 17323 FALSE TRUE 11390.4906 20843.91447 18548.79124 16317.25187 16579.90236 18756.79222 14343.90035 16796.29307 14431.67939 0.789269931 1.444316625 1.285282935 1.130655098 1.148854677 1.29969574 0.993917614 1.163848823 1 13.81695157 1.644303068 0.942198853 1.023549947 1.229061473 0.027161161 0.181245181 1.04260234 1.773686577 0.153509262 0.061335929 44.08624074 -1.644303068 0.205511526 KHT(ph)GERPYSCPHCPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KHTGERPYSCPHCPAR 16 2 O15156;O15156-2 O15156 ZBTB7B Zinc finger and BTB domain-containing protein 7B 1 KHT(1)GERPYSCPHCPAR;KHT(1)GERPYSCPHCPAR 121.82 9.72E-05 146067000 125345 79859 93468 93817 101454 69903 138436 85141 165420 TRUE FALSE 117499.8802 85771.84345 95685.1051 96224.50305 93486.21209 90082.86132 117678.807 95771.04127 137810.3333 0.852620245 0.622390509 0.694324604 0.698238664 0.678368667 0.653672763 0.8539186 0.694948187 1 17.07232454 0.242163746 0.558225413 1.015291882 0.690295589 0.552349591 0.078322929 1.895848596 0.847594567 0.14196057 0.032327699 1.746480519 -0.242163746 -0.324996294 KIALESEGRPEEQMES(ph)DNCS(ph)GGDDDWTHLSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KIALESEGRPEEQMESDNCSGGDDDWTHLSSK 32 2 Q13501;Q13501-2 Q13501 SQSTM1 Sequestosome-1 2 KIALES(0.033)EGRPEEQMES(0.967)DNCS(0.997)GGDDDWT(0.002)HLSSK 56.933 0.022878 62228000 29845 33530 29119 36593 35132 26987 48469 26429 41852 TRUE FALSE 27977.05472 36012.59609 29809.71643 37532.03833 32372.87444 34777.7088 41201.52341 29728.71883 34866.63083 0.802402012 1.032867106 0.854964065 1.076445801 0.928477277 0.997449653 1.181689267 0.852640996 1 15.08955934 3.012615476 1.201020312 1.029738082 0.921003245 0.095494059 0.109160896 0.873970916 2.655695667 0.043204107 0.053303375 1029.474221 -3.012615476 -0.108734837 KIALESEGRPEEQMESDNCS(ph)GGDDDWTHLSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KIALESEGRPEEQMESDNCSGGDDDWTHLSSK 32 2 Q13501;Q13501-2 Q13501 SQSTM1 Sequestosome-1 1 KIALES(0.002)EGRPEEQMES(0.182)DNCS(0.816)GGDDDWTHLSSK 74.196 0.0012949 217390000 32210 31973 43013 45798 45488 41651 52023 37751 65219 TRUE FALSE 30194.0336 34340.31419 44033.28867 46973.25422 41915.55597 53674.96755 44222.63411 42464.29545 54333.52757 0.555716423 0.632028063 0.810425729 0.864535331 0.771449193 0.987879307 0.813910602 0.781548656 1 15.7295551 4.231206711 0.866817563 0.869736599 0.48862709 0.698366453 0.075209772 0.651807971 0.621048797 0.024758496 0.204654538 17029.68876 -4.231206711 -0.381109509 KICTLPSPPS(ph)PLASLAPVADSSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KICTLPSPPSPLASLAPVADSSTR 24 1 Q9UER7-3;Q9UER7;Q9UER7-2 Q9UER7-3 DAXX Death domain-associated protein 6 1 KICTLPSPPS(1)PLASLAPVADSSTR 223.53 4.64E-33 490710000 421120 437060 411550 435440 541960 379680 561480 444320 605860 TRUE FALSE 394762.8509 469420.3772 421312.1603 446614.1276 499396.6478 489287.4524 477291.2865 499794.3301 504738.052 0.782114305 0.930027715 0.834714479 0.884843387 0.989417473 0.969388875 0.945621763 0.990205371 1 18.94517533 2.828958454 4.623443444 0.972243883 0.864048742 0.696255319 0.039669227 0.136525112 5.036717615 0.011535103 0.012234539 674.4635035 -2.828958454 -0.108195141 KIDFLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KIDFLTK 7 1 Q99471;H3BPF6;Q99471-3;H3BMQ1 Q99471 PFDN5 Prefoldin subunit 5 0 85.731 0.033024 294950000 462130 396490 410750 402080 473550 287050 443520 422410 562180 FALSE TRUE 433206.1082 425846.5321 420493.184 412398.0535 436359.2932 369916.6751 377018.2934 475148.8183 468348.5262 0.924965243 0.909251355 0.897821089 0.880536674 0.931697804 0.789832047 0.804995153 1.014519726 1 18.837223 1.219955874 24.99836221 1.007260048 0.87634346 0.572900992 0.046750178 225.3406392 302772.1954 0.049175036 0.012382482 16.59418295 -1.219955874 -0.130916588 KIDKYTEVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KIDKYTEVLK 10 2 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 99.671 0.0025514 439880000 566460 681900 614370 659560 1081000 416690 822180 735750 1852400 FALSE TRUE 531006.2798 732388.5855 628943.1465 676485.4262 996102.6205 536981.6386 698901.7417 827610.0071 1543222.473 0.344089261 0.47458393 0.407551832 0.438358978 0.645469229 0.347961262 0.452884632 0.536286907 1 20.55751463 -5 0.315589316 6.052986252 0.428030484 0.810977203 0.083592403 123.1817826 1.102706524 414.6687387 0.071026757 1.00E-05 5 -5.624955768 RLSS(ph)LRAST(ph)SK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLSSLRASTSK 11 2 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 RLS(0.423)S(0.577)LRAS(0.199)T(0.692)S(0.109)K;RLS(0.445)S(0.555)LRAS(0.024)T(0.972)S(0.004)K 98.062 0.0064021 2994000000 5479700 5120400 4501800 4519100 6758600 3051200 9785700 6117600 13955700 TRUE FALSE 5136735.359 5499519.744 4608584.822 4635067.757 6227806.819 3932031.908 8318425.131 6881395.826 11626403.51 0.441816367 0.473019858 0.396389547 0.398667374 0.535660646 0.338198472 0.715477071 0.591876569 1 23.47090155 0.884866749 0.734666198 0.998286327 0.426371029 0.810344106 0.084700238 0.308804104 0.362210992 0.074180344 0.027889503 7.671260823 -0.884866749 -0.571915298 KIDYFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KIDYFER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 86.744 0.031831 1450910000 2214890 3299620 2090270 2184120 3713400 1496670 2445970 3121360 4041130 FALSE TRUE 2076263.989 3543927.298 2139852.191 2240168.217 3421764.543 1928734.333 2079219.506 3511068.667 3366639.296 0.61671709 1.052660231 0.635604828 0.66540191 1.016373969 0.572896043 0.617594973 1.042900162 1 21.68287773 1.223014439 24.95972624 1.021450386 0.752001711 0.328223898 0.166900573 335.4584084 538570.485 0.155200151 0.039357463 16.71146176 -1.223014439 -0.269448675 KIEDNNTLVFIVDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KIEDNNTLVFIVDVK 15 1 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3;K7EMA7 P62750 RPL23A 60S ribosomal protein L23a 0 164.62 2.36E-06 32007000 186850 128360 155220 160900 177810 121360 214170 152380 226660 FALSE TRUE 175155.392 137863.908 158901.8917 165028.9664 163845.5199 156394.6619 182057.1968 171404.9784 188828.9817 0.927587442 0.730099303 0.841512199 0.873959945 0.867692652 0.828234419 0.964138 0.907726011 1 17.52672068 1.668218798 0.550465601 0.998475325 0.8107019 0.443331289 0.056320098 0.59814357 0.415840457 0.052240836 0.031287411 46.58207151 -1.668218798 -0.187773425 KIEEAMDGSET(ph)PQLFTVLPEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KIEEAMDGSETPQLFTVLPEKR 22 2 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 1 KIEEAMDGS(0.007)ET(0.993)PQLFTVLPEKR 173.92 1.53E-10 222900000 261150 272490 219130 216050 318200 130290 343590 239900 588220 TRUE FALSE 244805.0877 292665.4431 224327.8671 221594.2088 293209.8556 167902.6079 292071.8692 269852.0431 490042.282 0.499559113 0.59722488 0.457772473 0.452194059 0.59833583 0.342628818 0.596013609 0.550670938 1 18.90254671 0.38048229 1.267149705 1.000259519 0.505207161 0.794381135 0.078610938 1.319511333 2.306509599 0.068390919 0.02032398 2.401498334 -0.38048229 -0.495052358 KIEEIKDFLLTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KIEEIKDFLLTAR 13 2 J3KT73;J3QL01;P63173;J3KSP2 J3KT73 RPL38 60S ribosomal protein L38 0 ; 209.56 2.08E-08 2629600000 12090200 10239400 10964400 10075100 12188700 8002100 13284300 9798800 14418600 FALSE TRUE 11333495.96 10997535.83 11224480.75 10333644.12 11231448.67 10312176.37 11292442.54 11022201.75 12012042.51 0.943511143 0.915542533 0.934435649 0.860273689 0.935015728 0.858486503 0.940093454 0.917595966 1 23.51797815 0.445403388 1.348922668 0.999954121 0.912241241 0.448858869 0.030406719 2.42829209 5.014752325 0.026126192 0.007704353 2.78871022 -0.445403388 -0.087712879 KIEFPLPDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KIEFPLPDEK 10 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 118.87 0.0012318 872930000 2398100 1760030 2061420 2053110 1974300 1590650 2671000 1724460 2584600 FALSE TRUE 2248007.202 1890344.453 2110317.856 2105796.279 1819246.442 2049844.833 2270508.346 1939762.627 2153213.563 1.044024262 0.877917771 0.980078285 0.977978364 0.844898283 0.951993276 1.054474292 0.900868665 1 21.03805999 1.980017928 24.74660568 0.994183716 0.938481211 0.062597095 0.066023442 1308.73957 1620794.3 0.024751901 0.016216803 95.50320092 -1.980017928 -0.055702505 KIEFPLPDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KIEFPLPDRR 10 2 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ; 137.16 5.55E-05 599290000 1166330 1677770 1235530 1199820 1844680 1016500 1319770 1440950 1810080 FALSE TRUE 1093331.487 1801993.837 1264837.355 1230609.412 1699806.274 1309947.049 1121882.741 1620855.779 1507965.954 0.725037249 1.194983104 0.838770498 0.816072411 1.127217938 0.868684764 0.743970868 1.074862317 1 20.52417243 3.747518368 24.14695134 0.904422342 1.000567489 0 0.163528735 839.388648 993694.118 0.039194078 0.070532704 5591.371746 -3.747518368 0.096145146 KIEFSLPDLEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KIEFSLPDLEGR 12 1 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ; 136.33 0.00017946 724240000 2345200 2382700 2493200 2302200 2581000 2320300 2998400 2103900 2597300 FALSE TRUE 2198418.118 2559117.587 2552339.881 2361278.35 2378298.671 2990132.943 2548817.756 2366576.546 2163793.851 1.016001648 1.182699353 1.179567028 1.091267705 1.099133668 1.381893632 1.177939273 1.093716273 1 21.04513163 0.990365492 3.752100113 1.000761937 1.171290699 0.229568994 0.094510695 0.272319624 10.39906257 0.086908892 0.022364107 9.780599877 -0.990365492 0.170528761 KIEFVVVGPEAPLAAGIVGNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KIEFVVVGPEAPLAAGIVGNLR 22 1 P22102;P22102-2;F8WD69;C9JBJ1;C9JTV6;C9JZG2;C9JKQ7 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 139.02 9.67E-07 104570000 153900 176550 152560 183440 201760 132070 187650 164670 209420 FALSE TRUE 144267.6737 189621.9457 156178.7952 188147.381 185914.5835 170196.465 159513.6246 185229.412 174466.4491 0.826907835 1.086867685 0.895179538 1.078415833 1.065617971 0.975525472 0.914293983 1.061690732 1 17.4125901 4.758614205 24.12098243 0.999561897 0.826907571 0.414402364 0.067336536 3187.728279 3834183.688 0.01574389 0.603558233 57360.66868 -4.758614205 -0.172654326 KIEIGDGAELTAEFLYDEVHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KIEIGDGAELTAEFLYDEVHPK 22 1 Q6IBS0 Q6IBS0 TWF2 Twinfilin-2 0 ;; 202.43 9.14E-23 163154000 275778 195623 228233 218032 266509 172845.1 292645 214519 344727 FALSE TRUE 258517.5473 210107.1305 233646.7945 223627.0702 245578.4582 222742.6745 248765.599 241302.1694 287189.8367 0.90016259 0.731596678 0.813562197 0.778673343 0.855108457 0.775593862 0.866206137 0.840218345 1 18.13164517 0.261149183 0.516940167 1.013366786 0.795361761 0.582320244 0.048408271 1.695446699 0.677827195 0.091355544 0.021182918 1.824522331 -0.261149183 -0.218005025 KIEISQHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KIEISQHAK 9 1 Q6P4E4;E9PEL3;P61513;G5E9R3;M0R0A1;C9J4Z3;M0R2L6 Q6P4E4 RPL37A 60S ribosomal protein L37a 0 ; 97.456 0.0043354 2324400000 2649600 4162900 3287600 3430600 4786700 2410800 4001800 4160800 5165700 FALSE TRUE 2483766.266 4471125.447 3365583.425 3518635.004 4410771.891 3106758.824 3401767.241 4680285.039 4303511.298 0.577148773 1.03894823 0.782055208 0.817619558 1.024923971 0.721912552 0.790463183 1.087550308 1 22.03708283 1.237831994 24.99904686 1.043775219 0.838541614 0.309438768 0.136056484 23.82273588 817085.5969 0.098975381 0.030319096 17.29147314 -1.237831994 -0.205233604 KIEMVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KIEMVR 6 1 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;; 123.96 0.029765 4181970000 5495130 6467190 5200710 4818740 6484530 4087380 5883760 6024490 7641500 FALSE TRUE 5151199.622 6946027.477 5324073.297 4942397.027 5975261.171 5267340.253 5001544.81 6776660.838 6366084.284 0.809162963 1.091098887 0.83631838 0.776363744 0.938608555 0.827406616 0.785654821 1.064494364 1 22.60197483 1.224057257 24.92810067 1.032247288 0.878458063 0.345522214 0.093768929 339.9649338 584308.0833 0.092242558 0.023484346 16.75163715 -1.224057257 -0.153789225 KIENISHLTELQEFWMNDNLLESWSDLDELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KIENISHLTELQEFWMNDNLLESWSDLDELK 31 1 Q15435;H7C003;C9J177;Q15435-2;H7C3Q5 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 0 350.5 1.15E-120 43078000 67926 47510 49500 52985 61193 33914 57340 48007 44508 FALSE TRUE 63674.63291 51027.68983 50674.16338 54344.6848 56387.14862 43704.42125 48742.39932 54000.77963 37079.32727 1.717254265 1.376176258 1.36664193 1.465632977 1.520716603 1.178673522 1.314543788 1.456358127 1 15.17832745 -3.985367269 0.103850544 5.11E-12 1.676726288 0.568364186 0.126952171 109.2205946 0.958101384 25.64305978 1.964757269 0.000103427 3.985367269 1.676726288 KIEPELDGSAQVTSHDASTNGLINFIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KIEPELDGSAQVTSHDASTNGLINFIK 27 1 P06744;A0A2U3TZU2;P06744-2;K7EQ48 P06744 GPI Glucose-6-phosphate isomerase 0 ;;; 375 3.03E-127 4078330000 2518987 2513045 2305971 2614012 3162078 1502658 3268499 2588725 3828518 FALSE TRUE 2361328.1 2699113.467 2360669.721 2681091.973 2913741.149 1936450.971 2778417.918 2911933.015 3189513.613 0.740341126 0.846246103 0.740134706 0.840595871 0.913537769 0.607130493 0.871110224 0.912970869 1 21.60490501 1.207593179 2.4854327 0.987280469 0.789748482 0.42853852 0.083806345 0.245611245 2.610219012 0.070321017 0.019885105 16.12847032 -1.207593179 -0.197531987 KIESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KIESER 6 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;; 113.7 0.041559 578600000 1151890 1218950 1161190 1216490 1388760 930700 1380670 1217740 1301820 FALSE TRUE 1079795.261 1309202.326 1188733.975 1247707.193 1279692.392 1199377.981 1173651.351 1369777.52 1084537.832 0.995627104 1.207152289 1.096074236 1.150450594 1.179942602 1.10588856 1.082167276 1.263005752 1 20.04864895 -0.75098826 5.972967318 0.999999995 1.134590251 0.250744787 0.073356338 3.72E-09 7.78E-10 0.062358778 0.014698104 0.177423744 0.75098826 0.134590256 KIESFGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KIESFGSK 8 1 P30405 P30405 PPIF "Peptidyl-prolyl cis-trans isomerase F, mitochondrial" 0 ; 115.78 0.0038446 1343240000 2032410 1626970 1448250 1208330 2027300 1244510 1607870 1855000 3689000 FALSE TRUE 1905205.086 1747432.552 1482603.174 1239337.793 1868084.036 1603779.834 1366784.82 2086600.833 3073282.068 0.619925228 0.568588406 0.482416889 0.403261974 0.607846593 0.521845961 0.44473133 0.67894869 1 21.55134875 0.93153224 4.265331884 0.999793352 0.518482851 0.835269734 0.067623749 0.117376232 5.578477077 0.063631702 0.016209581 8.541462537 -0.93153224 -0.481310501 KIFDIDEAEEGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KIFDIDEAEEGVK 13 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;; 129.93 0.00023725 387941000 559340 367119 447400 429870 469190 308853 585750 386456 600430 FALSE TRUE 524331.9079 394300.8727 458012.5393 440901.192 432341.71 398013.8473 497922.2253 434705.8823 500214.3541 1.048214438 0.78826381 0.915632539 0.88142451 0.864312882 0.795686577 0.995417707 0.8690392 1 18.93218693 0.814140785 0.869869642 0.99659632 0.880098232 0.119003219 0.080915968 1.466676116 2.215537784 0.070155099 0.024140092 6.518396665 -0.814140785 -0.116498088 KIFVGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KIFVGTK 7 1 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ; 103.56 0.032784 0 6401200 5722800 6314800 5800800 6561000 5135900 7194600 5662100 6816200 FALSE TRUE 6000560.318 6146522.067 6464590.038 5949658.349 6045725.526 6618550.956 6115836.521 6369025.649 5678532.186 1.056709749 1.082413882 1.138426239 1.047745818 1.064663425 1.165539041 1.077010101 1.121597173 1 22.43708663 -1.151672396 4.790518466 0.999991661 1.096613325 0.381926327 0.037579992 3.10E-06 5.49E-07 0.033682827 0.007938433 0.070522484 1.151672396 0.096621664 KIGDEYFTFITDCKDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KIGDEYFTFITDCKDPK 17 2 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 208.34 2.96E-12 2556600000 4099000 2181210 2663000 2854400 3056500 2074920 3941800 2495920 4143000 FALSE TRUE 3842450.907 2342709.058 2726167.618 2927648.736 2816454.819 2673915.72 3350763.684 2807541.106 3451506.535 1.113267748 0.678749709 0.789848604 0.848223437 0.816007384 0.774709737 0.970811919 0.813424827 1 21.71879479 0.997036978 0.680269431 0.993353759 0.812565629 0.08281863 0.12149465 1.351840523 1.453362611 0.11160066 0.04495879 9.932006103 -0.997036978 -0.180788129 KIGELVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KIGELVR 7 1 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 117.04 0.0085324 554570000 849150 1010300 893280 956060 1077300 748080 1157700 1022700 1265600 FALSE TRUE 796003.2173 1085103.663 914469.0234 980594.1182 992693.2036 964038.5519 984113.6326 1150386.346 1054363.184 0.754961127 1.029155494 0.867318811 0.930034483 0.941509737 0.914332525 0.93337253 1.091072188 1 20.00794047 1.322849163 6.410331204 1.044414828 0.919227688 0.375412561 0.071999291 0.200982711 11.81406904 0.044219816 0.015811495 21.03047895 -1.322849163 -0.125187141 KIHPQTIIAGWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KIHPQTIIAGWR 12 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 160.56 4.28E-05 885620000 1596570 2833400 1663770 1631280 3473900 1123060 2027600 2562100 3680900 FALSE TRUE 1496643.534 3043187.884 1703235.41 1673141.407 3201073.907 1447269.191 1723580.203 2881983.825 3066534.01 0.488057047 0.992386803 0.555426877 0.545613191 1.043873603 0.471956021 0.562061336 0.939817988 1 21.54817752 1.12900679 6.140205872 0.993131058 0.680677763 0.285989661 0.199562934 0.276501534 13.1265269 0.18149132 0.045715996 13.45881397 -1.12900679 -0.312453295 KIHSQEEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KIHSQEEALR 10 1 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ; 186.87 8.39E-07 558450000 274470 521510 253240 285530 578250 165325 277790 476350 585640 FALSE TRUE 257291.4126 560123.143 259246.9724 292857.1832 532836.5775 213051.6437 236137.9684 535823.3461 487892.9006 0.527352237 1.148045283 0.531360411 0.600248913 1.092117915 0.436677073 0.4839955 1.098239686 1 18.89620497 1.219426714 24.99552357 1.049120227 0.705343261 0.268874982 0.245984961 404.9727972 529021.1636 0.232632383 0.058531124 16.57397632 -1.219426714 -0.343776966 KIIPTLEEGLQLPS(ph)PTATSQLPLESDAVECLNYQHYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYK 37 1 P61978;P61978-2 P61978 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 KIIPTLEEGLQLPS(0.999)PT(0.001)ATSQLPLESDAVECLNYQHYK;KIIPTLEEGLQLPS(0.803)PT(0.118)AT(0.019)S(0.019)QLPLES(0.003)DAVECLNY(0.019)QHY(0.019)K 286.56 2.46E-77 1437005000 853863 1038313 966974 1145939 1220910 546254 918569 641981 1255998 TRUE FALSE 800421.239 1115190.775 989911.0799 1175345.735 1125024.654 703948.6621 780838.106 722133.741 1046363.82 0.764955003 1.06577727 0.946048651 1.123266796 1.075175414 0.672757074 0.746239588 0.690136382 1 19.99695313 2.239665505 24.99999848 0.752098318 1.003837009 0.397615242 0.131325427 23.97258451 542437.7615 0.042646722 0.033825093 173.6462882 -2.239665505 0.251738692 KILDSVGIEADDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KILDSVGIEADDDR 14 1 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ; 217.37 9.27E-12 1220800000 1870140 1551250 1637770 1571020 1467630 1541440 2126060 1545650 1327720 FALSE TRUE 1753091.276 1666106.164 1676618.678 1611335.033 1352368.26 1986428.705 1807277.04 1738627.805 1106114.955 1.584908755 1.506268546 1.515772543 1.456751874 1.222629035 1.795860997 1.633896217 1.571832835 1 20.0770699 -1.231588896 4.079416973 0.999605766 1.538549962 0.577725216 0.143996383 100.8042342 38882137.37 27171.2009 0.033476178 0.058669327 1.231588896 0.538944196 KILDSVGIEADDDRLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KILDSVGIEADDDRLNK 17 2 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ; 288.21 3.44E-37 4174300000 8636000 5986000 6746100 6128800 6623300 5137500 8811900 5564000 8545700 FALSE TRUE 8095488.176 6429209.668 6906120.678 6286075.384 6103132.735 6620612.85 7490637.401 6258677.648 7119367.463 1.137107786 0.903059113 0.970046948 0.882954197 0.857257722 0.929943971 1.052149287 0.879105859 1 22.76331764 -0.072805682 7.36732788 0.999999995 0.950547054 0.030419746 0.085999545 10490018.72 1423855.857 0.077354063 0.018761116 0.845657136 0.072805682 -0.049452941 KILGVGGEDDDGEVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KILGVGGEDDDGEVHR 16 1 E9PN66;E9PNB3;E9PKN9;E9PS55;E9PMY0;E9PMW4;E9PQ46;E9PIN5;E9PIK4;U3KQ32;E9PKZ4;E9PPM1;O14683 E9PN66 TP53I11 Tumor protein p53-inducible protein 11 0 ; 112.8 0.00046148 115777000 162059 217404 173072 187432 229316 176398 206020 187897 207169 FALSE TRUE 151916.0165 233500.8184 177177.3496 192241.8224 211306.4464 227321.239 175129.2136 211356.3541 172591.1555 0.880207424 1.352913002 1.02657259 1.113856743 1.224317931 1.317108274 1.014705609 1.224607098 1 17.39699901 -0.469866827 7.403205191 1.000002872 1.151442446 0.087814755 0.144518365 0 0 0.124630598 0.029375714 0.338948076 0.469866827 0.151439573 KINS(ph)SPNVNTTASGVEDLNIIQVTIPDDDNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KINSSPNVNTTASGVEDLNIIQVTIPDDDNER 32 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 KINS(0.491)S(0.491)PNVNT(0.009)T(0.009)ASGVEDLNIIQVTIPDDDNER 185.8 5.26E-20 60166000 120840 104190 110530 105480 123260 96295 155920 116450 202920 TRUE FALSE 113276.8401 111904.336 113151.8238 108186.7954 113579.6568 124093.8033 132541.2435 130989.0388 169051.3411 0.670073596 0.661954737 0.66933408 0.639964136 0.671864867 0.734059857 0.78402953 0.774847676 1 17.36710194 0.815987076 0.547907538 1.007167634 0.653460838 0.961347181 0.020836414 0.206138719 0.139166433 0.025151923 0.010480071 6.546166935 -0.815987076 -0.353706796 KIPDPDS(ph)DDVSEVDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KIPDPDSDDVSEVDAR 16 1 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8YGP5;A0A2R8Y7R0;A0A2R8Y583 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 1 KIPDPDS(1)DDVSEVDAR;KIPDPDS(1)DDVSEVDAR;KIPDPDS(1)DDVSEVDAR 158.52 5.79E-09 2571470000 1927990 1416710 1740330 1623120 1560060 1339920 1978470 1403130 1707160 TRUE FALSE 1807320.547 1521604.682 1781611.449 1664772.007 1437539.181 1726733.152 1681816.791 1578313.869 1422223.967 1.270770701 1.06987698 1.252694013 1.170541381 1.010768496 1.214107758 1.18252598 1.109750578 1 20.43971724 -4.933494159 0.26008779 6.49E-11 1.173739169 0.309771667 0.078386299 239.5829619 2.433014059 127.7992888 0.097746718 1.17E-05 4.933494159 1.173739169 KIPDPDSDDVSEVDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KIPDPDSDDVSEVDAR 16 1 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8YGP5;A0A2R8Y7R0;A0A2R8Y583 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 0 ;;; 127.78 0.00010318 1406580000 999770 895950 990010 978390 922370 764800 1164540 858780 997020 FALSE TRUE 937196.1803 962287.0702 1013493.505 1003497.144 849930.7809 985585.3445 989928.0381 966000.5734 830610.921 1.128321524 1.158529278 1.2201784 1.20814345 1.023259819 1.186578842 1.191807154 1.163000087 1 19.66381332 0.913052895 20.11181943 1 1.165893161 0.448482293 0.055419142 8810.267798 2037916.94 0.051717352 0.012929338 8.185644798 -0.913052895 0.165893161 KIPEPS(ph)PVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.999)PVT(0.001)R 139.3 2.57E-05 8169370000 5069240 5002620 5104510 5033670 5015660 4350280 6142640 4655080 5403730 TRUE FALSE 4751965.317 5373019.19 5225591.388 5162842.494 4621750.296 5606135.215 5221608.157 5236276.985 4501812.554 1.055567121 1.193523525 1.160774982 1.146836398 1.0266421 1.245306229 1.159890177 1.163148604 1 22.10207456 -1.063384503 4.705566094 0.999994064 1.151642395 0.334642605 0.062972124 3.58E-06 7.13E-07 0.055705209 0.01312933 0.086420246 1.063384503 0.151648331 KIPIPET(ph)PPQT(ph)PPQVLDSPHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KIPIPETPPQTPPQVLDSPHQR 22 1 G3V160;Q969H4-2;Q969H4 G3V160 CNKSR1 Connector enhancer of kinase suppressor of ras 1 2 KIPIPET(0.992)PPQT(0.568)PPQVLDS(0.44)PHQR;KIPIPET(1)PPQT(0.936)PPQVLDS(0.064)PHQR 97.804 0.0010191 280350000 252920 258471 289065 281298 261821 206489 276869 232667 287785 TRUE FALSE 237090.1887 277608.4618 295921.7583 288516.5829 241258.6348 266099.0222 235355.0638 261715.9871 239751.8243 0.988898372 1.157899267 1.234283656 1.20339682 1.006284876 1.109893628 0.981661201 1.091612078 1 17.87118227 2.736114238 24.88645693 1.038186042 1.162776841 0.329593259 0.075046623 205.7081099 2092608.996 0.023147077 0.022755024 544.6458985 -2.736114238 0.124590799 KIPIPETPPQTPPQVLDS(ph)PHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KIPIPETPPQTPPQVLDSPHQR 22 1 G3V160;Q969H4-2;Q969H4 G3V160 CNKSR1 Connector enhancer of kinase suppressor of ras 1 1 KIPIPETPPQTPPQVLDS(1)PHQR;KIPIPETPPQTPPQVLDS(1)PHQR;KIPIPETPPQTPPQVLDS(1)PHQR 183.47 2.00E-17 336595000 266368 257462 247810 249239 311628 228576 300850 253135 304517 TRUE FALSE 249696.5024 276524.7544 253688.1702 255634.8947 287153.9939 294562.1806 255740.3355 284739.462 253691.1454 0.984253912 1.090005542 0.999988272 1.007661873 1.131903888 1.161105485 1.008077499 1.122386284 1 17.95271364 2.755724787 24.95071701 1.085126195 1.028650568 0.231510493 0.057280829 1318.041353 1915969.663 0.016732158 0.017705148 569.8030732 -2.755724787 -0.056475626 KIPNPDFFEDLEPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KIPNPDFFEDLEPFR 15 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 ; 201.3 1.04E-08 1037300000 1371580 1677410 1263370 1326370 1929470 1058750 1780840 1736150 1455700 FALSE TRUE 1285735.256 1801607.182 1293337.733 1360406.9 1777937.209 1364393.938 1513819.575 1952912.149 1212734.266 1.060195372 1.485574567 1.066464245 1.121768336 1.466056711 1.12505598 1.248269812 1.610338064 1 20.20983203 1.443282357 24.99994835 1.346547228 1.234251428 0.015659742 0.208060284 92.75021962 68532.38505 0.101086642 0.046496733 27.75123767 -1.443282357 -0.1122958 KIPSVEDSLGEGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KIPSVEDSLGEGSR 14 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ; 144.33 1.42E-05 740230000 395820 461120 469910 470610 503720 343680 488640 384660 444960 FALSE TRUE 371046.3328 495261.8046 481056.4871 482686.6493 464159.8631 442894.8368 415372.9683 432685.6477 370693.3014 1.000952354 1.336041959 1.297721014 1.302118618 1.252139872 1.194774319 1.120530009 1.167233522 1 18.49986652 1.320688251 0.812399717 1.015664005 1.26371297 0.334020482 0.096714675 0.537389724 0.77877266 0.085295716 0.033279377 20.9260978 -1.320688251 0.248048966 KIPVPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KIPVPPR 7 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 93.262 0.041363 0 141650 138520 148350 134090 144690 140840 137790 117550 118930 FALSE TRUE 132784.3794 148776.1649 151868.9321 137530.9764 133326.6311 181498.2217 117129.6687 132226.3763 99079.81468 1.340175895 1.501578958 1.532793865 1.388082697 1.345648773 1.831838526 1.182174887 1.334544041 1 16.59630355 1.066552699 1.359492739 1.01772045 1.479414186 0.442550402 0.163305916 0.351488665 1.321589442 0.138284502 0.042083851 11.6560848 -1.066552699 0.461693736 KIPVVFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KIPVVFR 7 1 P10768;X6RA14;U3KQT1;H7BZT7 P10768 ESD S-formylglutathione hydrolase 0 100.74 0.034889 0 406210 631630 436830 408060 706010 325200 460600 596580 673820 FALSE TRUE 380786.0412 678396.5424 447191.8139 418531.5104 650562.8225 419079.9608 391537.306 671064.3262 561355.089 0.678333641 1.208498071 0.796629126 0.745573557 1.158914981 0.746550569 0.697485983 1.195436435 1 19.09855412 3.75107967 24.28263815 0.87653081 0.987668446 0 0.214379208 975.7839031 988980.4369 0.05109881 0.092048844 5637.410635 -3.75107967 0.111137636 KIQALQQQADEAEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KIQALQQQADEAEDR 15 1 P67936;A0A2R8Y5V9;A0A2R8YGX3;A0A590UJB9;A0A590UK79 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;;;;; 276.59 2.42E-33 5953540000 4276950 4369410 4283950 4415790 4919840 3576300 5114780 4075780 5452560 FALSE TRUE 4009263.334 4692925.663 4385567.317 4529106.647 4533455.612 4608719.754 4347866.222 4584650.105 4542492.511 0.882613086 1.033116874 0.965453945 0.99705319 0.998010586 1.014579494 0.957154296 1.009280718 1 22.11505271 4.751387682 24.82735789 0.994010636 0.882613009 0.722903816 0.022162421 1013.11535 1960891.475 0.005037949 0.090753358 56414.10238 -4.751387682 -0.111397628 KIQEESLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KIQEESLR 8 1 Q99613-2;Q99613;B5ME19 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 ; 171.56 0.00046283 285330000 182238 499720 164066 190448 542600 110206 193516 484860 484760 FALSE TRUE 170832.0489 536719.7888 167957.723 195335.2181 499986.3847 142020.6832 164500.0723 545395.8383 403850.4243 0.423008219 1.329006376 0.415890916 0.483682092 1.238048432 0.351666544 0.407329205 1.3504897 1 18.62346153 1.230850368 24.99537862 1.175244921 0.68877535 0.258595334 0.357931447 279.6938053 906684.9612 0.313336326 0.084196707 17.01572146 -1.230850368 -0.486469571 KIQNDAGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 133.23 0.0004536 451100000 685190 1066580 669770 653280 1095360 519680 785190 904270 1124560 FALSE TRUE 642305.181 1145550.693 685657.2607 670044.2708 1009334.844 669703.1797 667458.0488 1017170.1 936863.6711 0.685590872 1.222750682 0.731864498 0.715199331 1.077355089 0.714835253 0.712438821 1.085718372 1 19.8374796 5.037325725 14.18131295 0.888218894 0.000147596 0.114822934 0.186942674 16481412.4 197456269.6 0.043843944 357268907.9 108974.7107 -5.037325725 -0.888071299 KIQVLQQQADDAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KIQVLQQQADDAEER 15 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;Q5VU61;P06753-3;P06753-4 P06753-2;P06753-3 TPM3 Tropomyosin alpha-3 chain 0 ;;;;;;; 290.39 1.09E-43 16694310000 8513980 9039890 8832010 8902900 9649360 7710060 10302240 7820940 8552310 FALSE TRUE 7981105.19 9709212.862 9041509.448 9131363.487 8891538.189 9935829.16 8757514.753 8797401.575 7124874.211 1.120174891 1.3627206 1.269006186 1.281617502 1.247957217 1.394526958 1.229146578 1.234744827 1 22.76443311 0.649902194 1.50633472 1.000361975 1.28546774 0.566075394 0.074018515 0.84533036 2.759370472 0.062492616 0.018130109 4.465830071 -0.649902194 0.285105764 KIS(ph)ADTIGDEGFFDLLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KISADTIGDEGFFDLLSR 18 1 H0Y4A4;A0A2R8Y6E3;P81274 H0Y4A4 GPSM2 G-protein-signaling modulator 2 1 KIS(0.999)ADT(0.001)IGDEGFFDLLSR;KIS(0.998)ADT(0.002)IGDEGFFDLLSR 214.17 8.64E-19 94459000 139869 104828 121986 104574 125647 110689 175471 140706 250190 TRUE FALSE 131114.849 112589.5742 124879.5655 107257.5459 115779.1915 142643.1174 149160.7525 158273.4538 208431.6727 0.629054343 0.540174978 0.599139103 0.514593317 0.555477917 0.684363924 0.715633812 0.759354141 1 17.669215 1.058689258 0.716894024 0.997632075 0.562051823 0.915713354 0.041043597 0.176229052 0.21078941 0.038557758 0.015283994 11.44693609 -1.058689258 -0.435580252 SEIDLLNIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEIDLLNIRR 10 1 E5RK69;H0YC77;P08133;P08133-2;E7EMC6;E5RFF0 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 146.11 4.69E-05 46539000 94914 104000 103670 97846 154380 61720 123810 131100 275590 FALSE TRUE 88973.50217 111700.2682 106129.1014 100356.894 142255.6175 79537.56206 105245.8399 147468.1236 229592.2486 0.387528336 0.486515851 0.462250368 0.437109243 0.619601134 0.346429649 0.45840328 0.642304453 1 17.80871441 0.905184562 2.74940889 0.999298896 0.459553127 0.856442657 0.07090917 0.127360729 2.108427862 0.062052016 0.01646091 8.038676699 -0.905184562 -0.539745769 KIS(ph)ENSYSLDDLEIGPGQLSSSTFDSEKNESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KISENSYSLDDLEIGPGQLSSSTFDSEKNESR 32 2 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KIS(0.996)ENS(0.004)YSLDDLEIGPGQLSSSTFDSEKNESR;KIS(0.564)ENS(0.187)YS(0.249)LDDLEIGPGQLSSSTFDSEKNESR;KIS(0.758)ENS(0.222)YS(0.02)LDDLEIGPGQLSSSTFDSEKNESR 177.57 1.08E-19 2813410000 416786 308606 353359 442162 547716 291361 411449 311955 683028 TRUE FALSE 390700.1082 331455.5093 361740.8423 453508.6255 504700.5947 375472.1908 349756.0422 350903.2684 569026.2143 0.686611791 0.582496027 0.635719117 0.796990743 0.88695491 0.659850428 0.614657169 0.616673291 1 19.11813559 -1.614301311 2.675400548 1.030178381 0.675135278 0.530758391 0.092671896 25443619.56 23435068.54 5359415.086 0.026066264 0.024305171 1.614301311 -0.355043103 RRVEHHDHAVVSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RRVEHHDHAVVSGR 14 2 O95831-3;O95831;E9PMA0;O95831-5;O95831-2 O95831-3 AIFM1 "Apoptosis-inducing factor 1, mitochondrial" 0 ;;;; 134.24 2.39E-05 363844000 82385 160783 109866.5 126583 225407 91231 120471 164920 388880 FALSE TRUE 77228.66991 172687.5406 112472.5853 129831.3341 207704.4435 117567.9087 102407.4919 185510.625 323973.4157 0.238379651 0.533029972 0.347166094 0.400746875 0.641115701 0.362893691 0.316098442 0.57261064 1 18.30551591 0.915357233 5.041408985 0.999933708 0.414029043 0.735611085 0.112351245 0.261204492 14.53956493 0.101604813 0.025679521 8.229192709 -0.915357233 -0.585904664 KIS(ph)LEDIQAFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KISLEDIQAFEK 12 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 1 KIS(1)LEDIQAFEK;KIS(1)LEDIQAFEK;KIS(1)LEDIQAFEK 163.56 3.65E-05 467808000 1369210 805144 965004 878670 758130 685156 1148537 612191 1144694 TRUE FALSE 1283513.59 864757.6995 987894.3506 901218.1598 698589.5279 882949.4146 976324.5393 688624.3939 953637.1764 1.345913962 0.906799484 1.03592265 0.945032537 0.732552741 0.925875623 1.023790351 0.722103134 1 19.86308095 4.740013114 24.71580233 0.924219731 1.345914124 0.609901438 0.108761328 74.03351293 1259613.434 0.024728157 0.155430762 54955.74682 -4.740013114 0.421694394 KIS(ph)PPSYAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KISPPSYAR 9 1 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 KIS(0.916)PPS(0.084)YAR;KIS(0.97)PPS(0.03)YAR;KIS(0.782)PPS(0.216)Y(0.002)AR 111.79 0.0012662 2173370000 768280 648220 696630 666580 735620 497710 758120 594980 858820 TRUE FALSE 720194.7262 696214.8833 713154.3926 683685.5713 677847.3725 641390.7974 644446.944 669264.5627 715477.3938 1.006593265 0.973077402 0.996753215 0.955565581 0.947405716 0.89645152 0.900722999 0.935409796 1 19.44854666 2.855693717 1.967975114 0.922291912 0.988566024 0.375363784 0.03065575 0.26379402 2.023587308 0.009961387 0.010670435 717.2882498 -2.855693717 0.066274112 KIS(ph)PVKFSNTDSVLPPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KISPVKFSNTDSVLPPKR 18 3 G3V2F4;E7EPD8;Q9NUW8;G3V3Q0;G3V5F9;G3V5B8;G3V554;G3V4W8;G3V5H9;G3V2U6;Q9BRS7 G3V2F4 TDP1 Tyrosyl-DNA phosphodiesterase 1 1 KIS(0.999)PVKFS(0.001)NTDSVLPPKR;KIS(0.997)PVKFS(0.003)NTDSVLPPKR 140.2 7.12E-07 1842460000 1248680 875450 1011870 1012740 1217400 639470 1527540 949140 1874320 TRUE FALSE 1170527.348 940269.2289 1035872.034 1038728.623 1121790.315 824074.6081 1298499.558 1067642.218 1561483.883 0.749624995 0.602163902 0.663389514 0.66521892 0.718412996 0.527750953 0.831580506 0.683735663 1 20.57448625 0.327686593 0.623290486 1.010973264 0.653544363 0.614934997 0.080093434 1.405092848 0.80741721 0.107519547 0.02876619 2.126603836 -0.327686593 -0.357428901 KISELDAFLKEPALNEANLSNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KISELDAFLKEPALNEANLSNLK 23 2 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ; 257.66 7.21E-44 392840000 1144460 936230 992020 1082520 1241130 709250 1339800 905500 1607830 FALSE TRUE 1072830.292 1005549.443 1015551.183 1110299.296 1143656.656 913998.9613 1138909.428 1018553.668 1339472.786 0.800934743 0.750705392 0.758172315 0.828907692 0.853811043 0.682357246 0.850266941 0.760413858 1 20.35323384 -5 0.34414334 3.404554371 0.776233494 0.619189259 0.052456107 254.9488902 2.124184336 451.1736796 0.03780451 1.00E-05 5 -2.628320877 KISENS(ph)YSLDDLEIGPGQLSSSTFDSEKNESRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KISENSYSLDDLEIGPGQLSSSTFDSEKNESRR 33 3 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KIS(0.384)ENS(0.504)YS(0.112)LDDLEIGPGQLSSSTFDSEKNESRR 125.36 5.80E-07 64137000 33671 33285 31667 47647 69105 24340 47650 35698 123490 TRUE FALSE 31563.59221 35749.45603 32418.15619 48869.70269 63677.77206 31366.56287 40505.32486 40154.97388 102878.7212 0.306803893 0.347491256 0.315110412 0.475022455 0.618959599 0.304888732 0.393719171 0.390313696 1 16.65058509 -5 0.354342519 8.261211507 0.36919544 0.800696719 0.094995497 200.2722075 1.621137223 1106.785466 0.071993359 1.00E-05 5 -7.892016067 KISLEDIQAFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KISLEDIQAFEK 12 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 99.481 0.0060484 245270000 495600 441280 494590 432260 559040 330520 596710 463370 630080 FALSE TRUE 464581.2807 473952.8304 506321.9084 443352.5234 515135.2535 425935.7585 507238.8751 521222.7645 524915.5775 0.885059047 0.902912488 0.964577791 0.844616815 0.981367815 0.811436689 0.966324675 0.992964939 1 19.00172589 1.53034421 8.035473969 0.990815419 0.906443992 0.41147666 0.049895421 0.116183013 13.42768996 0.024352688 0.011283907 33.91128209 -1.53034421 -0.084371427 KISPPS(ph)YAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KISPPSYAR 9 1 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 KIS(0.18)PPS(0.82)YAR 120.57 0.00039383 608790000 269180 278020 269510 276700 286440 195300 301550 261790 338010 TRUE FALSE 252332.5043 298604.8901 275902.9045 283800.5905 263944.1578 251679.9396 256335.377 294475.0578 281593.9474 0.896086392 1.060409476 0.979789896 1.007836259 0.937321843 0.893768996 0.910301444 1.045743563 1 18.1032568 2.735578671 24.56397422 0.943211923 0.9973869 0.00905198 0.059584208 371.5183825 3060396.213 0.017843673 0.01752389 543.9746624 -2.735578671 0.054174977 KISSDLDGHPVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KISSDLDGHPVPK 13 1 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 ;;; 125.61 0.00012863 5572310000 14267300 14321000 14286400 13298400 20101600 11296890 18019000 17694200 22962300 FALSE TRUE 13374335.16 15381341.74 14625280.15 13639659.46 18522901.42 14558118.75 15317218.23 19903359.82 19129743.79 0.699138227 0.804053724 0.764530896 0.713007953 0.968277549 0.761020059 0.800701693 1.040440481 1 24.18931422 1.244086575 21.58218554 1.020220591 0.789431474 0.634743636 0.07345833 13.13241836 51301.52825 0.048455024 0.016415726 17.54230167 -1.244086575 -0.230789117 KISSIQSIVPALEIANAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KISSIQSIVPALEIANAHR 19 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 221.41 1.74E-19 1106900000 1169970 1499820 1138890 1071340 2123230 1032030 1198100 1482780 2266070 FALSE TRUE 1096743.666 1610868.233 1165905.009 1098832.398 1956480.08 1329960.307 1018456.028 1667908.347 1887848.278 0.580949051 0.853282678 0.617584062 0.58205546 1.036354512 0.704484742 0.539479809 0.88349703 1 20.84831139 1.018457532 9.705634887 0.99999016 0.707594282 0.327007647 0.148130899 0.251582265 121.4692497 0.136314334 0.034100837 10.43416096 -1.018457532 -0.292395878 KITIGQAPTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KITIGQAPTEK 11 1 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 107.14 0.0026574 0 682850 446360 554900 590610 631650 422240 701700 550960 927770 FALSE TRUE 640111.6374 479408.9588 568062.49 605766.0525 582042.757 544133.8335 596486.5993 619748.5688 772919.1934 0.828174074 0.620257542 0.734957153 0.783737883 0.753044771 0.703998346 0.771732161 0.801828411 1 19.55995807 -0.260773352 0.412675227 1.055402498 0.712421746 0.67403295 0.055574221 3.390050621 0.639557327 0.331752616 0.034706605 0.548563173 0.260773352 -0.342980752 KIVDQIRPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KIVDQIRPDR 10 2 P17844;P17844-2;J3KTA4;J3QSF1;J3KRZ1;A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 P17844;A0A1X7SBZ2 DDX5;DDX17 Probable ATP-dependent RNA helicase DDX5;Probable ATP-dependent RNA helicase DDX17 0 ; 160.52 4.14E-06 7921900000 8695400 9491000 9325800 8995000 10492800 8461200 10730300 8597200 12810400 FALSE TRUE 8151170.436 10193723.52 9547012.38 9225826.928 9668737.814 10903811.08 9121391.13 9670579.345 10672261.48 0.76377162 0.955160585 0.8945632 0.864467849 0.905968977 1.021696395 0.854682126 0.90614153 1 23.34736258 -1.667933112 0.013593773 1.946477978 1.13E-06 0.27298968 0.063131458 5748.104372 11.9851352 947.7308576 774.6045124 0.021481613 1.667933112 -1.946476848 KIVEPEVVGES(ph)DS(ph)EVEGDAWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KIVEPEVVGESDSEVEGDAWR 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 KIVEPEVVGES(1)DS(1)EVEGDAWR;KIVEPEVVGES(1)DS(1)EVEGDAWR;KIVEPEVVGES(1)DS(1)EVEGDAWR;KIVEPEVVGES(1)DS(1)EVEGDAWR 172.05 2.14E-11 1155240000 784710 842090 807260 831440 1025660 599300 922280 720690 1458710 TRUE FALSE 735596.4018 904439.2198 826408.5884 852776.158 945108.8009 772308.1812 783992.676 810669.7329 1215241.877 0.605308635 0.744246258 0.680036299 0.701733683 0.777712502 0.635518077 0.645133031 0.667085087 1 20.21281206 -1.074722616 5.54923526 1.000002305 0.685797896 0.794818868 0.050730259 1.40E-06 2.34E-07 0.047646268 0.011230251 0.084193271 1.074722616 -0.314204409 KIVEPEVVGES(ph)DSEVEGDAWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KIVEPEVVGESDSEVEGDAWR 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 KIVEPEVVGES(0.997)DS(0.003)EVEGDAWR;KIVEPEVVGES(0.831)DS(0.169)EVEGDAWR 210.11 1.36E-22 245910000 305260 328590 306730 351680 455650 238090 356690 317330 613500 TRUE FALSE 286154.3215 352919.1455 314005.7804 360704.7042 419865.087 306822.7179 303207.6458 356949.349 511102.8866 0.55987616 0.690505091 0.614369022 0.705737951 0.821488389 0.600314978 0.593241897 0.698390399 1 18.96325421 0.960215031 21.24181792 1.000000002 0.655306357 0.679693134 0.073829835 580.7344063 310064.3284 0.069622222 0.017405555 9.12462512 -0.960215031 -0.344693645 KIVLATNIAETSITINDIVHVVDSGLHKEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KIVLATNIAETSITINDIVHVVDSGLHKEER 31 2 H7BXY3;Q7L2E3-3;Q7L2E3;Q7L2E3-2 H7BXY3 DHX30 Putative ATP-dependent RNA helicase DHX30 0 102.03 5.86E-05 29789000 37171 43691 52905 60970 75847 95049 73772 35637 121250 FALSE TRUE 34844.53346 46925.9271 54159.93158 62534.59342 69890.28257 122488.1033 62710.57347 40086.3579 101012.5917 0.344952376 0.464555223 0.536170102 0.61907721 0.691896737 1.212602323 0.620819369 0.396845158 1 16.62417562 3.141038602 1.545780714 0.783536438 0.439362409 0.340878406 0.217664341 0.459460604 2.26667084 0.074804093 0.100708145 1383.689363 -3.141038602 -0.344174029 KIVSWLEYESSFSNEEAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KIVSWLEYESSFSNEEAQK 19 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 215.75 6.40E-19 14685000 34885 29919 34251 34366 32846 26349 31347 28207 37408 FALSE TRUE 32701.61012 32134.23389 35063.44989 35247.88974 30266.40765 33955.52856 26646.80836 31728.70604 31164.36314 1.049327078 1.031121148 1.125113635 1.131031929 0.971186465 1.089562729 0.855041005 1.018108597 1 14.92760961 1.760134248 25 0.944680604 1.067805948 0.394986655 0.062596407 9.021849575 10463.3469 0.027021755 0.014985466 57.56178435 -1.760134248 0.123125344 KIWCFGPDGTGPNILTDITK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KIWCFGPDGTGPNILTDITK 20 1 P13639 P13639 EEF2 Elongation factor 2 0 208.44 9.10E-22 410250000 881700 866770 828260 886730 1158800 608040 1052800 827030 1547300 FALSE TRUE 826515.9709 930946.5527 847906.7183 909484.993 1067792.522 783571.2773 894942.4137 930286.516 1289045.634 0.641184415 0.72219829 0.657778667 0.705549105 0.828358977 0.607869308 0.694267441 0.721686255 1 20.29787191 0.693697784 3.214194889 0.999992662 0.694084074 0.729052849 0.058219931 1.754259323 17.86014254 0.051432375 0.01335893 4.939668267 -0.693697784 -0.305908588 KIYEDGDDDMKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KIYEDGDDDMKR 12 2 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;; 144.27 3.54E-05 2637450000 4321130 3125030 3446910 3626850 4461160 2511700 4737430 3124070 6072200 FALSE TRUE 4050678.187 3356410.473 3528672.333 3719921.111 4110798.489 3236787.016 4027096.352 3514117.016 5058710.592 0.800733332 0.663491301 0.697543824 0.735349659 0.812617843 0.639844276 0.796071702 0.694666546 1 22.27033827 -5 0.343125286 4.038620094 0.715378481 0.661529167 0.060041528 225.1518371 1.881167068 501.7812035 0.043123723 1.00E-05 5 -3.323241613 KKAENAEGQTPAIGPDGEPLDET(ph)SQMSDLPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKAENAEGQTPAIGPDGEPLDETSQMSDLPVK 32 2 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8YGP5;A0A2R8Y7R0 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 1 KKAENAEGQTPAIGPDGEPLDET(0.543)S(0.453)QMS(0.004)DLPVK 119.77 2.27E-05 67382000 38107 20688 28210 29431 29669 18722 40693 30220 59639 TRUE FALSE 35721.95089 22219.76105 28879.15452 30186.24929 27338.91642 24126.73747 34591.46243 33993.03352 49684.86562 0.718970464 0.44721387 0.581246506 0.60755421 0.550246359 0.485595305 0.696217289 0.684172798 1 15.60051884 0.776064504 0.980490516 0.998753143 0.554948933 0.735556023 0.079389113 0.390545288 0.707209411 0.069384864 0.022723285 5.971239681 -0.776064504 -0.44380421 KKAENAEGQTPAIGPDGEPLDETSQMS(ph)DLPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKAENAEGQTPAIGPDGEPLDETSQMSDLPVK 32 2 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8YGP5;A0A2R8Y7R0 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 1 KKAENAEGQTPAIGPDGEPLDET(0.046)S(0.246)QMS(0.708)DLPVK 81.205 0.0003734 67969000 80273 44217 53344 48409 55695 42996 93892 62333 109110 TRUE FALSE 75248.85622 47490.87269 54609.34487 49651.2569 51320.93936 55408.24722 79813.76625 70115.41226 90898.83612 0.8278308 0.522458534 0.600770562 0.546225442 0.564594021 0.609559479 0.878050475 0.771356546 1 16.4719742 1.748783791 4.765041918 0.870138121 0.594646649 0.616661445 0.099964872 0.110211 5.702803733 0.046513299 0.023983307 56.07687339 -1.748783791 -0.275491473 KKAEPSEVDMNS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 KKAEPSEVDMNSPK 14 2 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 KKAEPSEVDMNS(1)PK;KKAEPSEVDMNS(1)PK;KKAEPSEVDMNS(1)PK;KKAEPSEVDMNS(1)PK;KKAEPSEVDMNS(1)PK;KKAEPSEVDMNS(1)PK;KKAEPSEVDMNS(1)PK 191.21 3.27E-07 5125000000 12043080 4412093 7372230 6875330 7042290 4967362 9726180 5225952 9512720 TRUE FALSE 11289325.12 4738768.956 7547102.777 7051762.608 6489216.951 6401358.771 8267829.602 5878423.611 7924985.577 1.424523112 0.597953007 0.952317541 0.889813936 0.818830127 0.807743902 1.043261154 0.741758272 1 22.91797688 KKDASDDLDDLNFFNQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKDASDDLDDLNFFNQK 17 2 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 179.17 5.24E-10 395450000 851660 559550 693850 632710 833860 484980 933660 568600 1309500 FALSE TRUE 798356.1209 600979.6642 710308.4497 648946.4098 768371.9992 624985.853 793666.3507 639590.9616 1090935.99 0.731808399 0.550884442 0.651100024 0.594852875 0.704323632 0.572889572 0.727509549 0.586277259 1 20.05713502 -5 0.364291691 5.612647207 0.626908679 0.741897467 0.066228255 224.8349643 1.766780643 814.5050459 0.04142963 1.00E-05 5 -4.985738528 KKDEEFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKDEEFQR 8 2 V9GY93;Q9HC07-2;Q9HC07 V9GY93 TMEM165 Transmembrane protein 165 0 ; 117.01 0.0012152 277659000 137324 164771 111832 131034 206370 84920 169897 182200 252510 FALSE TRUE 128729.136 176970.8163 114484.7079 134396.5543 190162.5327 109435.0254 144422.5221 204948.0711 210364.4497 0.61193389 0.84125819 0.544220794 0.638874841 0.903967058 0.520216346 0.686534832 0.974252405 1 17.68253139 1.23304332 6.681011239 0.99176145 0.679227819 0.540233563 0.118594053 0.101335311 21.07101295 0.090978453 0.027019642 17.10185894 -1.23304332 -0.31253363 KKDELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KKDELER 7 2 M0R0F0;M0R0R2;P46782;M0QZN2 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;;;;;; 118.5 0.0028086 14627940000 20137700 14289630 16365470 16060260 17603880 12696120 21955200 15196980 22119900 FALSE TRUE 18877317.3 15347649.07 16753666.68 16472393.46 16221342.28 16361283.74 18663221.58 17094356.41 18427945.79 1.024385329 0.832846441 0.909144561 0.893881155 0.88025776 0.88785174 1.012767337 0.927632228 1 24.13539192 1.750129706 25 0.978431464 0.895585073 0.30093198 0.052948459 3.297890599 7138.972781 0.022059851 0.012233355 56.25092989 -1.750129706 -0.082846391 KKDELS(ph)DYAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 125.52 0.00017038 373430000 957790 460550 597500 639650 640640 402550 789560 539490 769070 TRUE FALSE 897843.6336 494649.6012 611672.9822 656064.5019 590326.7186 518759.6501 671172.8079 606846.5141 640707.2486 1.401332099 0.772036843 0.954684036 1.02396922 0.921367317 0.80966721 1.04754989 0.947151004 1 19.28930579 4.750662582 24.99453227 0.92988572 1.401332388 0.740054331 0.086901582 1000.457047 2066234.631 0.020702282 0.353415433 56319.99167 -4.750662582 0.471446668 KKDQEDDEQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKDQEDDEQQR 11 2 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 ; 119.01 0.00036163 50805000 81222 56122 61436 65815 70104 51576 79910 58858 93960 FALSE TRUE 76138.46001 60277.33127 62893.29093 67503.92432 64598.31463 66465.15393 67928.23735 66206.55086 78277.469 0.972674014 0.770047014 0.803466077 0.862367233 0.825247871 0.84909687 0.867787861 0.845793198 1 16.25630949 -0.354256343 0.490924629 1.026034623 0.830422153 0.413253451 0.05405749 6.312326345 1.467218284 0.342517081 0.025557131 0.442327211 0.354256343 -0.19561247 KKDQVTAQEIFQDNHEDGPTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKDQVTAQEIFQDNHEDGPTAK 22 2 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 274.97 1.21E-45 911470000 588114 424817 482261 509477 595822 362652 717148 503832 847620 FALSE TRUE 551304.9946 456270.8927 493700.4587 522551.0424 549028.5436 467343.7452 609618.3151 566736.5343 706146.7462 0.780722984 0.646141748 0.699147113 0.74000347 0.777499219 0.661822415 0.86330259 0.802576146 1 19.4296085 0.900321359 0.537648587 1.006987046 0.69456956 0.711959743 0.055317439 0.50646005 0.347203901 0.058427165 0.025744862 7.949162213 -0.900321359 -0.312417486 KKDTEVLFCFEQFDELTLLHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKDTEVLFCFEQFDELTLLHLR 22 2 Q12931-2;Q12931;I3L0K7 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ; 218.57 7.02E-26 85815000 162945 169884 123416 124919 315670 123927 161883 176427 306700 FALSE TRUE 152746.5633 182462.3881 126343.4858 128124.633 290878.5516 159702.7131 137610.147 198454.2993 255509.7886 0.597811004 0.714111147 0.494476108 0.501447063 1.138424297 0.625035596 0.53857094 0.776699399 1 17.96301904 KKEEEDDDMKELENWAGS(ph)M ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKEEEDDDMKELENWAGSM 19 3 Q9H444 Q9H444 CHMP4B Charged multivesicular body protein 4b 1 KKEEEDDDMKELENWAGS(1)M 96.54 0.0069632 132090000 449100 110720 221310 241000 319950 182380 293660 188240 273270 TRUE FALSE 420991.6327 118917.824 226559.5777 247184.468 294822.4176 235030.1453 249628.4092 211742.1784 227659.4716 1.849216418 0.522349556 0.995168688 1.085764042 1.295014943 1.032375871 1.096499115 0.930082886 1 17.79651796 4.760006089 24.45060445 0.987428279 1.849217603 0.657447704 0.19379284 2896.825095 3302682.841 0.050544807 2.330793309 57544.8005 -4.760006089 0.861789324 KKEEEQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKEEEQER 8 2 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 0 50.473 0.087372 20700000 47589 32836 41252 35951 37343 22384 39823 33655 46789 FALSE TRUE 44610.48944 35267.21161 42230.51692 36873.56352 34410.23141 28845.89743 33851.91085 37856.90083 38979.61363 1.144456943 0.90476042 1.08340009 0.945970473 0.882775077 0.740025227 0.868451678 0.971197436 1 15.25043217 2.943130829 3.51520059 0.871294952 1.020033376 0.333931559 0.092603135 0.25450406 6.270970197 0.027412504 0.030426073 877.2650524 -2.943130829 0.148738423 KKEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 66.073 0.057577 69967000 167690 87831 145330 115710 113680 97333 167980 98367 127360 FALSE TRUE 157194.5822 94334.09863 148777.2962 118679.3145 104752.0314 125431.457 142792.9584 110648.3365 106102.7932 1.481531046 0.889082142 1.402199619 1.118531482 0.987269309 1.182169227 1.345798297 1.042840939 1 16.69510311 KKEEKEDEISLEDLIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKEEKEDEISLEDLIER 17 3 Q8WU90;Q8WU90-2 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 0 149.57 1.40E-07 47865000 208760 88964 113330 124570 130590 87724 158510 95805 170360 FALSE TRUE 195694.0842 95550.98713 116018.2411 127766.6771 120333.9882 113048.4947 134742.897 107766.4651 141925.8154 1.3788477 0.673245997 0.817456928 0.900235639 0.847865399 0.79653229 0.949389627 0.759315455 1 17.11477751 -1.605389272 8.43806147 1.000062957 0.865476373 0.017203993 0.190727181 0.000200674 9.38E-06 0.164052661 0.038649553 0.024809084 1.605389272 -0.134586584 KKEEMNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKEEMNR 7 2 Q99543;Q99543-2;H7C3L7 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 0 ; 74.486 0.025901 272620000 353400 366940 343700 342900 454010 285920 439540 416190 541390 FALSE TRUE 331281.3248 394108.6194 351852.7263 351699.3945 418353.886 368460.4625 373635.0575 468152.2376 451028.5115 0.734501958 0.873799792 0.780111938 0.779771978 0.927555299 0.816933859 0.828406737 1.037965951 1 18.78285911 1.242788213 24.9912014 1.018983028 0.82375992 0.70355091 0.053617407 49.7657297 294201.7099 0.035579505 0.011967274 17.48993571 -1.242788213 -0.195223108 KKEEPSQNDIS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KKEEPSQNDISPK 13 2 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 KKEEPSQNDIS(1)PK;KKEEPSQNDIS(1)PK;KKEEPSQNDIS(1)PK;KKEEPSQNDIS(1)PK;KKEEPSQNDIS(1)PK;KKEEPSQNDIS(1)PK;KKEEPS(0.002)QNDIS(0.998)PK;KKEEPSQNDIS(1)PK 188.27 3.26E-06 25878990000 21016340 6971930 12331560 10406370 10797150 8095670 16082230 8041990 14091070 TRUE FALSE 19700964.79 7488138.951 12624070.43 10673415.07 9949185.393 10432758.51 13670848.91 9046050.154 11739179.39 1.678223336 0.637875843 1.075379293 0.909213048 0.847519666 0.88871276 1.16454894 0.770586244 1 23.48482823 4.752507963 24.74517912 0.923075626 1.678223924 0.723592022 0.148734216 1160.327956 2058595.745 0.034673737 0.716747583 56559.81281 -4.752507963 0.755148298 KKEEPSQNDISPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKEEPSQNDISPK 13 2 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 119.62 0.00018824 284010000 1249630 717520 940580 891810 916140 691300 1189970 756340 1336320 FALSE TRUE 1171417.889 770645.9274 962891.0018 914695.3544 844190.0599 890867.0877 1011545.046 850770.7139 1113279.559 1.052222579 0.692230376 0.864913933 0.821622338 0.758291171 0.80021867 0.908617281 0.764202223 1 20.08638449 -1.639257986 2.580258324 1.02048132 0.825282591 0.219871566 0.098081727 13161008.17 11246969.17 1793321.694 0.022085373 0.022947851 1.639257986 -0.195198729 KKEIQNGNLHES(ph)DSESVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKEIQNGNLHESDSESVPR 19 2 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 1 KKEIQNGNLHES(0.998)DS(0.002)ESVPR 133.41 6.13E-06 304630000 198500 176310 157280 156930 274760 127690 240440 179450 312650 TRUE FALSE 186076.2393 189364.1759 161010.7559 160957.0895 253181.4579 164552.0301 204388.2541 201854.7275 260466.6952 0.714395517 0.727018768 0.618162548 0.617956508 0.972030062 0.631758429 0.784700147 0.774973274 1 17.99073939 -0.805319805 0.276202436 1.151340609 0.673401963 0.438888207 0.100900809 11.24057241 0.843157918 1.511313471 0.129565604 0.156559777 0.805319805 -0.477938646 KKELDEEESIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKELDEEESIR 11 2 A0A1B0GUA3;Q96EK5 A0A1B0GUA3 KIAA1279 KIF1-binding protein 0 ; 101.53 0.0018071 305310000 325400 188287 225835 246312 267887 169395 318760 225794 410560 FALSE TRUE 305033.7949 202227.9654 231191.9128 252632.7829 246848.2356 218296.5866 270964.8972 253984.8779 342034.8837 0.891820716 0.591249533 0.675930801 0.738617009 0.721704854 0.638229014 0.792214216 0.7425701 1 18.38378395 0.321892935 0.678353794 1.00758518 0.692539673 0.515954314 0.083088389 1.718427627 1.126330279 0.105766675 0.028889365 2.098422504 -0.321892935 -0.315045507 KKEPAITSQNS(ph)PEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 KKEPAITSQNSPEAR 15 2 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;E5RIS7 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 1 KKEPAITSQNS(1)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITS(0.002)QNS(0.998)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITSQNS(1)PEAR 270.08 8.28E-27 76406660000 28947090 22284300 25013502 23887517 27700360 19489503 30866890 23224487 35691450 TRUE FALSE 27135343.31 23934252.76 25606834.08 24500511.13 25524885.46 25115806.13 26238686.4 26124115.33 29734316.42 0.91259348 0.804937044 0.861187919 0.823980978 0.858431891 0.844674072 0.882437855 0.878584695 1 24.82562557 0.396579176 0.677274703 1.003395499 0.844274694 0.712293084 0.028827355 0.966327199 0.674075172 0.032239594 0.009615725 2.49217868 -0.396579176 -0.159120806 KKEPELFQTVAEGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKEPELFQTVAEGLR 15 2 A0A024R571;Q9H4M9;C9JC03;C9JIJ3;C9IZH1 A0A024R571 EHD1 EH domain-containing protein 1 0 ; 239.58 4.65E-18 1052480000 1553950 1315530 1415750 1389040 1593520 1156960 1934300 1388570 2216700 FALSE TRUE 1456691.043 1412933.21 1449332.259 1424685.118 1468371.367 1490955.57 1644269.672 1561936.021 1846718.45 0.788799746 0.765104832 0.784814956 0.771468503 0.795124653 0.807354023 0.890373772 0.845790013 1 20.8165325 0.993253833 0.524818748 1.003206656 0.768401816 0.913882961 0.020945635 0.242974264 0.166676729 0.022390045 0.0104907 9.845864004 -0.993253833 -0.23480484 KKEPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKEPPR 6 2 R4GMQ1;O60341;O60341-2;O75494-2;O75494 R4GMQ1;O75494-2 KDM1A;SRSF10 Lysine-specific histone demethylase 1A;Serine/arginine-rich splicing factor 10 0 ; 67.889 0.054886 650020000 1503300 1460330 1635630 1638770 1834380 1403220 2107210 1712920 1840600 FALSE TRUE 1409211.136 1568454.353 1674427.916 1680823.613 1690315.194 1808306.835 1791253.423 1926781.833 1533391.969 0.919015597 1.022865897 1.091976448 1.096147395 1.10233732 1.179285447 1.168164082 1.256548796 1 20.5482951 5.034331291 0.515691546 1.158838248 0.696211167 0.530428507 0.066114763 3.975005717 0.647644852 0.033789319 1.184560112 108225.9212 -5.034331291 -0.462627081 KKEPPRAS(ph)PPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KKEPPRASPPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGR 47 3 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 1 KKEPPRAS(0.995)PPGGLAEPPGS(0.005)AGPQAGPTVVPGSATPMETGIAETPEGR;KKEPPRAS(0.903)PPGGLAEPPGS(0.087)AGPQAGPT(0.01)VVPGSATPMETGIAETPEGR;KKEPPRAS(0.896)PPGGLAEPPGS(0.026)AGPQAGPT(0.075)VVPGS(0.002)ATPMETGIAETPEGR 106.74 9.70E-08 1302590000 359723 311189 310614 315371 341621 236998 394222 301280 396179 TRUE FALSE 337208.5796 334229.7574 317981.9108 323463.9538 314791.4647 305415.4753 335112.0709 338895.4712 330054.1655 1.021676485 1.012651232 0.963423414 0.980032939 0.953756982 0.925349555 1.015324471 1.026787439 1 18.33234328 1.600657612 25 1.015800418 0.977619708 0.287861909 0.027983586 0.865258384 2991.159585 0.015201425 0.007264655 39.87104438 -1.600657612 -0.038180709 KKEPVGDDESVPENVLSFDDLTADALANLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKEPVGDDESVPENVLSFDDLTADALANLK 30 2 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 258.02 1.90E-58 114770000 600760 359590 467290 432160 527090 335150 611340 389940 632960 FALSE TRUE 563159.504 386214.4178 478374.3395 443249.9572 485694.4776 431902.3643 519675.2424 438624.8674 527314.8869 1.067975735 0.732417057 0.907189141 0.84057926 0.921071052 0.819059683 0.985512177 0.831808239 1 19.0083052 0.029837842 0.399459311 1.018568581 0.864964954 0.083554477 0.095110444 8.236471372 1.806201814 0.35509211 0.060512566 1.071119293 -0.029837842 -0.153603626 KKEQSEVSVS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKEQSEVSVSPR 12 2 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 KKEQSEVS(0.001)VS(0.999)PR 112.8 0.00064431 457200000 914110 733030 846790 801330 942010 674490 1033100 828930 1133700 TRUE FALSE 856897.4868 787304.3039 866876.2587 821893.4844 868028.3345 869204.3136 878196.2458 932423.7352 944478.146 0.907270846 0.833586576 0.917836228 0.870209107 0.919056029 0.920301139 0.929821669 0.987236962 1 19.84915789 1.613416774 0.571468404 1.005157175 0.872882377 0.74111993 0.024652428 0.348011554 0.260248169 0.022219986 0.012534736 41.05979476 -1.613416774 -0.132274799 KKFS(ph)FK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKFSFK 6 2 P49006 P49006 MARCKSL1 MARCKS-related protein 1 KKFS(1)FK;KKFS(1)FK 78.934 0.053928 3081800000 12116100 5546100 6918800 6068800 6745700 4039800 8476800 4862300 7547700 TRUE FALSE 11357774.93 5956739.015 7082917.203 6224535.682 6215919.933 5206024.679 7205782.535 5469368.858 6287940.11 1.80627912 0.947327568 1.126428859 0.989916503 0.9885463 0.827938019 1.145968697 0.869818854 1 22.58415605 4.740899583 24.97816439 1.001384334 1.806279404 0.872235149 0.09840634 66.38368639 708876.8598 0.021551977 0.144238226 55068.03545 -4.740899583 0.804895069 KKGDDS(ph)DEEDLCISNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKGDDSDEEDLCISNK 16 2 H3BRG5;Q9Y3M8-5;Q9Y3M8-3;Q9Y3M8-4;Q9Y3M8-2;Q9Y3M8 H3BRG5;Q9Y3M8-3 STARD13 StAR-related lipid transfer protein 13 1 KKGDDS(1)DEEDLCISNK;KKGDDS(1)DEEDLCISNK 187.19 7.20E-10 399660000 1219630 394380 658730 622550 710820 487120 1015580 541550 1426430 TRUE FALSE 1143295.535 423580.3056 674355.3867 638525.687 654995.0645 627743.6363 863303.2072 609163.7096 1188349.618 0.962086846 0.35644418 0.567472212 0.537321406 0.551180439 0.528248275 0.726472407 0.512613208 1 20.18052792 -0.899394159 0.475810039 1.131736702 0.557402814 0.366818413 0.162122024 15.07782179 2.322974853 2.985629027 0.075334306 0.126068284 0.899394159 -0.574333887 KKGDGGGAGGGGGGGGSGGGGS(ph)GGGGGGGSSRPPAPQENTTSEAGLPQGEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKGDGGGAGGGGGGGGSGGGGSGGGGGGGSSRPPAPQENTTSEAGLPQGEAR 52 3 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 KKGDGGGAGGGGGGGGS(0.012)GGGGS(0.988)GGGGGGGSSRPPAPQENTTSEAGLPQGEAR 174.99 4.63E-25 123270000 51877 38528 43627 45145 55829 35531 63875 46759 71124 TRUE FALSE 48630.11117 41380.65321 44661.85304 46303.49713 51444.41554 45788.2229 54297.53674 52596.96408 59252.94492 0.820720577 0.698372938 0.753749085 0.781454782 0.868217025 0.772758602 0.916368576 0.887668354 1 15.85459924 1.621127204 0.495704832 1.000522712 0.735187425 0.729994017 0.045796621 0.382564292 0.232895519 0.043925255 0.028681107 41.7952766 -1.621127204 -0.265335287 KKGDGGGAGGGGGGGGSGGGGSGGGGGGGSSRPPAPQENTTSEAGLPQGEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKGDGGGAGGGGGGGGSGGGGSGGGGGGGSSRPPAPQENTTSEAGLPQGEAR 52 3 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 0 167.34 1.52E-24 141660000 51562 41354 45545 46122 56478 37967 62136 49430 75230 FALSE TRUE 48334.82646 44415.89319 46625.34891 47305.5686 52042.4457 48927.45656 52819.28364 55601.44431 62673.627 0.771214764 0.70868554 0.743938897 0.754792261 0.83037233 0.780670577 0.842767304 0.887158554 1 15.93557087 1.148817852 0.440419105 1.011553031 0.724368963 0.913236522 0.024739214 0.261850903 0.141255976 0.029683329 0.016842774 14.08697851 -1.148817852 -0.287184068 KKHPDASVNFSEFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKHPDASVNFSEFSK 15 2 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 112.72 0.00044519 367090000 601040 533620 580660 566410 635230 418630 702200 493390 860290 FALSE TRUE 563421.9793 573129.78 594433.5294 580945.0395 585341.5982 539481.6851 596911.6289 554990.8276 716702.0413 0.7861314 0.7996765 0.829401195 0.810580975 0.816715405 0.752727987 0.832858837 0.774367583 1 19.45101394 -2.1324725 2.579125875 1.431143327 0.803698561 0.865145723 0.024745013 3728681.754 868409.9482 9464218.596 0.005545492 0.007371018 2.1324725 -0.627444767 KKKDPNAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKKDPNAPK 9 3 O15347;E7ES08;E7EQU1;E9PES6 O15347 HMGB3 High mobility group protein B3 0 ; 58.978 0.046126 809300000 1251290 725110 929530 953810 1036340 816730 1330710 736300 1450780 FALSE TRUE 1172973.993 778797.8989 951578.8906 978286.3794 954950.0368 1052506.692 1131182.389 828228.6758 1208635.446 0.97049445 0.644361293 0.787316717 0.809413941 0.790105933 0.870822295 0.935916941 0.685259297 1 20.20494773 2.272379739 4.095480807 0.875938029 0.776300087 0.074731075 0.111399774 0.394127806 14.37068299 0.038564977 0.030351967 187.2318545 -2.272379739 -0.099637942 KKKEPIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKKEPIEK 8 3 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 82.029 0.0093449 825930000 1976300 1132000 1541300 1583100 1656500 1192500 2222100 1201400 2588300 FALSE TRUE 1852606.911 1215814.458 1577860.364 1623725.026 1526405.172 1536755.391 1888916.734 1351397.435 2156296.009 0.859161684 0.563843949 0.731745715 0.753015829 0.707882946 0.712682946 0.876000663 0.626721669 1 21.04012381 -5 0.191957498 2.212456509 0.673751485 0.406848506 0.097053745 121.4229597 1.19147954 56.18214262 0.238383492 1.00E-05 5 -1.538705023 KKLEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 121.05 0.0025174 1510520000 4117740 3526730 3610560 3455570 4528520 2548810 4382990 3766420 5702540 FALSE TRUE 3860018.004 3787852.759 3696204.188 3544245.776 4172868.306 3284610.071 3725801.339 4236665.828 4750749.234 0.81250721 0.797316922 0.778025529 0.74603933 0.878360044 0.691387802 0.784255526 0.891788983 1 22.17972363 1.020873874 3.078471772 0.998642673 0.782078896 0.698317522 0.047242075 0.113741793 2.483602552 0.04085113 0.010754018 10.4923767 -1.020873874 -0.216563776 KKNDIYGED ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KKNDIYGED 9 2 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;; 114.51 0.0064599 13506100000 8673190 6752410 7540600 7494790 7785830 5560300 9917290 6913050 10248090 FALSE TRUE 8130350.52 7252365.462 7719466.593 7687119 7174362.318 7165468.346 8430284.432 7776159.51 8537617.574 0.952297342 0.849460098 0.904171044 0.900382212 0.840323692 0.839281952 0.987428209 0.910811411 1 23.02540211 1.721758058 10.06806853 0.9608225 0.879235877 0.486152946 0.041059718 0.084862313 25.94220225 0.017948876 0.009712358 52.69362271 -1.721758058 -0.081586623 KKNLQYYDISAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKNLQYYDISAK 12 2 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 136.27 6.35E-05 416330000 453610 608210 589520 684690 939280 466050 847120 492060 1778540 FALSE TRUE 425219.3598 653242.5012 603503.6928 702260.3046 865512.7377 600591.0693 720102.2203 553494.7742 1481690.184 0.286982639 0.44087658 0.407307613 0.473958937 0.584138808 0.40534187 0.486000534 0.373556348 1 20.49881239 -5 0.386516903 9.253715973 0.426048076 0.838204595 0.07820067 233.4247419 1.708261881 1618.860608 0.047710706 1.00E-05 5 -8.827667897 KKPALSDGSNPDGDLLQEHWLVEDMFIFENVGFTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKPALSDGSNPDGDLLQEHWLVEDMFIFENVGFTK 35 2 P47224 P47224 RABIF Guanine nucleotide exchange factor MSS4 0 76.476 0.0017187 201190000 519150 305630 380280 360810 478200 354480 476880 385810 597950 FALSE TRUE 486657.3282 328259.1632 389300.4212 370068.9954 440644.101 456812.6215 405376.2711 433979.2278 498148.2821 0.976932664 0.658958738 0.781495059 0.742889233 0.884564128 0.917021373 0.813766273 0.871184833 1 18.92621572 2.731882421 24.01942339 0.881642096 0.766788248 0.224477783 0.092231979 395.6758986 1423120.294 0.027328662 0.02633698 539.3645771 -2.731882421 -0.114853849 KKPAPGPHSS(ph)PPEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKPAPGPHSSPPEEK 15 2 O75182-2;O75182;M0QYC5 O75182-2 SIN3B Paired amphipathic helix protein Sin3b 1 KKPAPGPHS(0.05)S(0.95)PPEEK 103.5 0.00076579 316780000 664760 360910 469700 452570 500340 349110 627060 413450 604550 TRUE FALSE 623153.8582 387632.1519 480841.5058 464183.7124 461045.3147 449892.3897 533038.1743 465070.1426 503646.6995 1.237283713 0.769650933 0.954719859 0.921645497 0.915414149 0.893269806 1.058357327 0.92340552 1 18.94205253 1.752542045 25 0.997945482 0.926389222 0.008018213 0.121323614 12.26747045 21966.04809 0.051031267 0.028299483 56.56425161 -1.752542045 -0.071556261 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGS(ph)PTEFLEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGSPTEFLEEK 44 3 P27816-6;P27816;P27816-2;P27816-5;H7C456 P27816-6 MAP4 Microtubule-associated protein 4 1 KKPCSETSQIEDT(0.004)PS(0.014)S(0.014)KPT(0.013)LLANGGHGVEGS(0.048)DT(0.048)T(0.048)GS(0.798)PT(0.012)EFLEEK;KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDT(0.002)T(0.021)GS(0.961)PT(0.016)EFLEEK;KKPCSETSQIEDTPSSKPTLLANGGHGVEGS(0.002)DT(0.016)T(0.122)GS(0.849)PT(0.012)EFLEEK;KKPCSETSQIEDTPSSKPTLLANGGHGVEGS(0.001)DT(0.013)T(0.09)GS(0.769)PT(0.126)EFLEEK;KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDT(0.003)T(0.046)GS(0.861)PT(0.091)EFLEEK 152.86 2.55E-14 2687080000 2995140 1478110 1939620 2056190 2115790 1505130 2658190 1678510 2386610 TRUE FALSE 2807679.534 1587550.802 1985628.702 2108955.317 1949624.388 1939636.597 2259619.087 1888075.668 1988269.373 1.412122307 0.798458611 0.998671875 1.06069899 0.980563506 0.975540147 1.136475328 0.94960758 1 20.9230818 KKPEDS(ph)PSDDDVLIVYELTPTAEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKPEDSPSDDDVLIVYELTPTAEQK 25 2 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 KKPEDS(0.496)PS(0.496)DDDVLIVY(0.008)ELTPTAEQK 65.779 0.02405 59643000 107770 36824 62301 61863 61236 45250 82024 53402 107380 TRUE FALSE 101024.8681 39550.48728 63778.80914 63450.50931 56426.77157 58312.94043 69725.26267 60069.35725 89457.5843 1.129304674 0.442114412 0.712950273 0.709280379 0.630765653 0.651850158 0.779422597 0.671484232 1 16.44891618 -0.382414709 0.652604163 1.027532184 0.68392923 0.189522148 0.173693709 13.72877028 4.848214699 1.088550771 0.059175587 0.414557991 0.382414709 -0.343602955 KKPFVYTQGQAVLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKPFVYTQGQAVLNR 15 2 Q9H4A4;A6NKB8;C9JMZ3;A0A087WU27;A0A087WUS4 Q9H4A4 RNPEP Aminopeptidase B 0 ; 247.64 1.53E-18 1930040000 1725020 2029330 1586430 1584300 2480300 1119750 2080470 2082810 2821600 FALSE TRUE 1617054.077 2179583.705 1624060.869 1624955.82 2285507.243 1443003.647 1768522.838 2342853.413 2350656.732 0.687915873 0.927223305 0.690896653 0.691277377 0.972284559 0.613872552 0.752352657 0.996680367 1 21.16463245 1.235942106 24.90940797 0.998340346 0.767960256 0.441619062 0.110217683 60.74556335 577800.697 0.084474671 0.024842614 17.21639056 -1.235942106 -0.23038009 KKPLKQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKPLKQPK 8 3 Q9Y2S6 Q9Y2S6 TMA7 Translation machinery-associated protein 7 0 ; 83.265 0.0080097 886270000 2448320 2302920 1928950 2131740 3234670 1516330 3185700 2652360 3739200 FALSE TRUE 2295084.022 2473430.593 1974705.605 2186444.057 2980632.066 1954069.855 2708033.86 2983512.985 3115103.364 0.73676015 0.794012366 0.633913349 0.701884914 0.956832477 0.62728893 0.869323917 0.957757299 1 21.5708486 1.452201229 3.242861453 0.977197051 0.741784364 0.53078149 0.092662503 0.18044247 3.551986342 0.065839201 0.022911046 28.32704215 -1.452201229 -0.235412687 KKPNATRPVT(ph)PPR ddPTM_SK-BR-3_Pertuzumab_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 110.97 0.0010454 1958100000 1824500 1518300 1748300 1715100 1904300 1308300 2348300 1649800 2540700 TRUE FALSE 1710307.802 1630716.512 1789770.502 1759112.37 1754743.96 1685984.972 1996194.216 1855781.162 2116640.756 0.808029325 0.77042668 0.845571218 0.831086883 0.829023042 0.796538083 0.943095426 0.876757738 1 21.013345 1.191000736 0.463041816 1.006614482 0.795009572 0.753544334 0.034461408 0.453663757 0.266674811 0.039165822 0.022053592 15.5238964 -1.191000736 -0.21160491 KKPS(ph)SEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KKPSSEER 8 2 O75475 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 KKPS(0.5)S(0.5)EER;KKPS(0.616)S(0.384)EER;KKPS(0.636)S(0.364)EER 101.95 0.0039836 660230000 1192760 605540 857610 777270 741991 697080 1068260 675808 911420 TRUE FALSE 1118107.281 650374.8117 877952.9142 797216.0641 683718.0199 898315.6799 908084.3302 760184.1164 759298.114 1.472553744 0.856547382 1.156269057 1.049938159 0.90046058 1.183086937 1.195952306 1.00116687 1 19.5343069 KKPSSEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKPSSEER 8 2 O75475 O75475 PSIP1 PC4 and SFRS1-interacting protein 0 76.827 0.01957 422610000 909900 845120 922770 933700 1209000 805740 1181700 1084200 1284700 FALSE TRUE 852950.9832 907693.5641 944658.5402 957660.3228 1114050.017 1038344.058 1004515.055 1219564.757 1070275.271 0.796945428 0.84809356 0.882631381 0.894779455 1.040900456 0.970165421 0.938557662 1.139486999 1 20.02955047 3.249370149 0.561362541 1.02931974 0.791724437 0.67704543 0.056334443 0.657881455 0.421556648 0.040237056 0.083084306 1775.702266 -3.249370149 -0.237595303 KKQDPPVTHDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKQDPPVTHDLR 12 2 P25685;P25685-2;M0R080;M0QZD0;M0QYT3;M0QXK0;M0R128;A0A1B0GX60;M0R1D6 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 205.72 5.92E-08 3626800000 2329100 2472200 2426800 2455300 2679200 1879740 2864100 2232000 3464000 FALSE TRUE 2183325.789 2655244.26 2484364.842 2518307.155 2468786.439 2422390.423 2434654.794 2510670.113 2885836.022 0.756566129 0.920095335 0.860882193 0.872643884 0.855483964 0.839406815 0.843656665 0.869997496 1 21.4605579 0.942388749 17.65709638 1.000000001 0.857515095 0.565083473 0.040649299 263.6803515 80815.92243 0.036191875 0.009047939 8.757673472 -0.942388749 -0.142484905 KKQPAS(ph)PDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKQPASPDGR 10 2 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 KKQPAS(1)PDGR 83.769 0.012111 78120000 205200 133710 170170 157120 153620 146370 210330 140160 172270 TRUE FALSE 192356.8983 143610.0275 174206.5128 161151.9652 141555.3049 188624.6429 178792.9691 157659.2845 143517.0241 1.340307183 1.000648031 1.213838664 1.122876998 0.986331104 1.31430152 1.245796241 1.098540647 1 17.13086236 2.227948395 24.99989778 1.196253982 1.125379214 0 0.130541962 618.4216731 1456845.695 0.044574827 0.033255907 169.0240075 -2.227948395 -0.070874769 KKQPAS(ph)PDGRT(ph)SPINEDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKQPASPDGRTSPINEDIR 19 3 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 2 KKQPAS(1)PDGRT(0.625)S(0.375)PINEDIR;KKQPAS(1)PDGRT(0.6)S(0.4)PINEDIR 97.542 0.0020829 1130350000 911950 923440 906620 997290 1260930 603380 1151520 826620 2296780 TRUE FALSE 854872.6774 991812.4584 928125.4545 1022882.15 1161901.644 777566.0109 978860.2662 929825.3266 1913432.58 0.446774392 0.518341994 0.48505783 0.534579666 0.60723417 0.406372306 0.511572906 0.485946218 1 20.86773164 -1.7455721 2.614490093 1.107913906 0.500781733 0.898345188 0.052911353 5739335.383 4364992.74 4004398.422 0.012415463 0.017965028 1.7455721 -0.607132173 KKS(ph)EPDDELLFDFLNSSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKSEPDDELLFDFLNSSQK 19 2 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 1 KKS(1)EPDDELLFDFLNSSQK 173.47 3.31E-12 155150000 861020 312310 506770 470420 470040 375100 663380 401150 463400 TRUE FALSE 807130.2952 335433.7574 518790.8237 482491.7736 433124.9545 483385.2808 563912.3275 451234.4605 386055.5463 2.090710269 0.868874338 1.343824298 1.249798839 1.121923927 1.252113291 1.460702567 1.168832995 1 18.55844891 4.752625085 24.9998622 1.207914165 2.090710867 0.741729508 0.167723142 1363.341216 2423323.821 0.040562377 0.85811848 56575.06808 -4.752625085 0.882796702 KKS(ph)EPDDELLFDFLNSSQKEPTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKSEPDDELLFDFLNSSQKEPTGR 24 3 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 1 KKS(1)EPDDELLFDFLNSSQKEPTGR 157.96 6.64E-09 154170000 384130 186680 233080 255850 292310 141410 327080 204170 359390 TRUE FALSE 360087.989 200501.9814 238608.7677 262415.5442 269353.1517 182232.7714 278037.3905 229661.0739 299405.4873 1.202676652 0.669667023 0.796941866 0.87645536 0.899626637 0.608648736 0.928631579 0.767056997 1 18.19174114 -1.123222851 4.62213351 1.000015604 0.823877091 0.072632405 0.162283393 2.31E-05 4.38E-06 0.138973165 0.032753389 0.075296909 1.123222851 -0.176138513 KKS(ph)IPLSIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKSIPLSIK 9 2 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 KKS(0.997)IPLS(0.003)IK 109.84 0.0012435 277690000 366850 295030 229610 202230 443490 117940 479490 308890 1461300 TRUE FALSE 343889.5133 316874.3282 235056.4576 207419.5642 408660.0844 151987.3634 407594.9259 347455.5965 1217399.59 0.282478749 0.260287855 0.193080776 0.170379197 0.335682785 0.124845913 0.334807839 0.285408012 1 20.21537135 -0.153118518 0.802907691 1.025192011 0.230835265 0.929112161 0.065478881 1.692186341 0.962132639 0.191560079 0.019298384 0.702880479 0.153118518 -0.794356747 KKS(ph)PIINESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KKSPIINESR 10 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 KKS(1)PIINESR;KKS(1)PIINESR;KKS(1)PIINESR;KKS(0.986)PIINES(0.014)R;KKS(1)PIINESR 153 8.89E-06 9731160000 11855720 7752670 9111010 8998510 10281630 7029370 12243920 8501260 13135280 TRUE FALSE 11113691.65 8326685.753 9327127.46 9229427.001 9474152.254 9058635.007 10408057.86 9562661.025 10942916.91 1.015605961 0.76092013 0.852343807 0.843415615 0.86577942 0.827808077 0.951122808 0.873867644 1 23.38349401 1.034071579 0.698541992 0.996275416 0.845505361 0.226353073 0.069713194 0.856922222 0.974766357 0.062272409 0.024927049 10.81612206 -1.034071579 -0.150770055 KKS(ph)PNELVDDLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KKSPNELVDDLFK 13 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 KKS(1)PNELVDDLFK;KKS(1)PNELVDDLFK;KKS(1)PNELVDDLFK 190.24 2.39E-06 7383027000 3538600 1432825 2108047 2198172 2105608 1548178 2872910 1707246 3483470 TRUE FALSE 3317125.343 1538912.854 2158050.87 2254580.815 1940242.041 1995111.856 2442143.816 1920399.421 2902056.353 1.14302582 0.530283587 0.743628175 0.776890777 0.668574902 0.687482121 0.841521845 0.661737467 1 21.4686441 -1.454495916 3.14178986 1.00505974 0.737823968 0.176313497 0.160794415 140850411.4 172114114.8 6257629.271 0.034648968 0.035115923 1.454495916 -0.267235772 KKS(ph)SSDPGIPGGPQAIPATNSPDHSDHTLSVSSDSGHSTASAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKSSSDPGIPGGPQAIPATNSPDHSDHTLSVSSDSGHSTASAR 43 2 Q68CZ2;E9PCX8;C9JHU5 Q68CZ2 TNS3 Tensin-3 1 KKS(0.615)S(0.193)S(0.193)DPGIPGGPQAIPATNSPDHSDHTLSVSSDSGHSTASAR 109.38 2.27E-06 252830000 37801 118930 141690 165030 204060 81758 145570 122780 147070 TRUE FALSE 35435.10289 127735.7009 145050.9537 169264.9492 188033.9507 105360.2074 123743.1299 138109.3533 122523.0669 0.289211687 1.042544104 1.183866495 1.38149455 1.534682044 0.859921401 1.009957823 1.127211037 1 16.90269386 4.763665427 2.898551194 1.150380958 0.109305432 0.665734184 0.191532648 0.297515882 3.393176163 0.048823561 0.747082719 58031.71793 -4.763665427 -1.041075527 KKSEAPSGESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 97.463 0.003514 26431000 127050 135990 128320 121820 162720 94844 158850 137830 219960 FALSE TRUE 119098.1673 146058.8411 131363.811 124946.1074 149940.6276 122223.9231 135031.9172 155038.3789 183247.255 0.649931522 0.797058821 0.71686646 0.681844361 0.818242148 0.666989108 0.73688371 0.846061126 1 17.48343206 0.971085024 2.632620094 0.999151304 0.729188821 0.743987793 0.052915578 0.133829592 2.16016265 0.045662543 0.012230652 9.355888209 -0.971085024 -0.269962483 KKT(ph)GGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKTGGSK 7 2 O60231;A0A140T947;A2AB15 O60231 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 1 KKT(1)GGSK 91.065 0.031992 0 167640 897130 619500 664950 748420 705650 457370 603530 435800 TRUE FALSE 157147.7116 963554.4387 634194.8325 682013.7428 689642.1122 909359.6997 388791.6145 678882.049 363062.1646 0.432839681 2.653965443 1.74679406 1.878504039 1.899515233 2.504694205 1.070867891 1.869878261 1 18.46985707 1.057676293 0.995439848 1.052516839 1.906793012 0.091754831 0.646778297 0.988584048 2.106871826 0.549073972 0.184374119 11.42026794 -1.057676293 0.854276173 KKTDELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KKTDELR 7 2 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;H0Y8X0;A0A494C198;D6RDA2;D6R9L5 H0Y993 DEK Protein DEK 0 ;; 124.08 0.0023517 1028370000 2671800 2460120 2373740 2376950 3210920 1651569 3278470 2703710 4560290 FALSE TRUE 2504576.807 2642269.845 2430046.234 2437946.561 2958747.295 2128350.159 2786893.859 3041274.145 3799148.138 0.659246946 0.69549008 0.639629239 0.641708739 0.778792294 0.560217733 0.733557565 0.800514756 1 21.85724454 0.949198656 1.714821064 0.998310074 0.666896844 0.784063127 0.056028841 0.16695058 1.011800401 0.04678572 0.013418356 8.896079521 -0.949198656 -0.33141323 KKTEFLDLDNSPLSPPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKTEFLDLDNSPLSPPSPR 19 2 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 KKTEFLDLDNSPLSPPS(1)PR 154.13 2.03E-08 93948000 192540 155040 189660 165710 217420 141540 209080 183180 275130 TRUE FALSE 180489.2651 166519.3229 194158.8248 169962.3991 200344.7102 182400.3003 177730.395 206050.4262 229209.0256 0.78744397 0.726495488 0.847081934 0.741517044 0.874069901 0.795781492 0.775407489 0.898962969 1 17.80630433 -5 0.170297141 1.809307946 0.750030574 0.663628999 0.047486583 77.14622196 0.728686148 20.94833347 0.159210595 1.00E-05 5 -1.059277373 KKVEAQLQELQVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKVEAQLQELQVK 13 2 P35579 P35579 MYH9 Myosin-9 0 68.034 0.028981 1239900000 1181500 1011800 1019600 1017300 1026200 780620 1198700 875070 1192200 FALSE TRUE 1107552.024 1086714.725 1043785.393 1043405.64 945606.3915 1005972.322 1018966.063 984324.4158 993214.1181 1.11511909 1.094139426 1.050916791 1.050534443 0.952067006 1.012845371 1.025927889 0.991049561 1 19.92174524 3.579761025 1.054616592 1.002264856 1.108915713 0.768875717 0.023202208 0.271778305 0.601819226 0.008520712 0.020970258 3799.802511 -3.579761025 0.106650857 KKVENTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKVENTR 7 2 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 85.161 0.011819 3937200000 3197560 3445520 2970740 3028640 3999100 2205410 3241180 3726300 3643700 FALSE TRUE 2997430.427 3700629.886 3041207.356 3106360.03 3685026.818 2842076.065 2755195.149 4191536.758 3035542.931 0.987444584 1.219099835 1.001866034 1.023329302 1.213959711 0.936266141 0.907644929 1.380819462 1 21.53352315 3.863572224 8.446825816 1.050195214 1.118409944 0 0.149926917 1.010261474 68.79417196 0.036210874 0.065481487 7304.192733 -3.863572224 0.06821473 KKWNLDELPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKWNLDELPK 10 2 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4;X6RLV5 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ; 132.76 0.00012091 1452240000 3961900 2898500 3206800 3003100 3973100 2443600 4662100 3107300 5959600 FALSE TRUE 3713931.751 3113107.956 3282866.81 3080164.63 3661068.753 3149027.651 3963061.386 3495253.245 4964904.26 0.748036932 0.627022757 0.661214525 0.620387518 0.737389597 0.634257477 0.798215067 0.703992074 1 22.24333447 0.127700778 0.473375177 1.032331318 0.656414413 0.761500153 0.055193036 1.463375844 0.455705811 0.142844204 0.026740203 1.341840135 -0.127700778 -0.375916905 KKWPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKWPER 6 2 A0A494C039;Q9Y4L1;A0A087X054 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 83.614 0.031939 834540000 2438500 2350000 2400600 2582000 3111900 1958100 3312600 2646400 2977800 FALSE TRUE 2285878.638 2523996.445 2457543.366 2648258.491 2867503.927 2523371.683 2815906.383 2976808.865 2480785.943 0.921433244 1.01741807 0.990630962 1.067507859 1.155885269 1.017166229 1.135086399 1.199945878 1 21.24236583 3.142480965 3.394087114 1.105544555 0.986180611 0.442263971 0.063758736 0.213072162 4.835772817 0.017629928 0.021926428 1388.292461 -3.142480965 -0.119363944 MSYLTAMGADYLS(ph)CDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MSYLTAMGADYLSCDSR 17 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 MSYLTAMGADYLS(1)CDSR;MSYLTAMGADYLS(1)CDSR;MSYLTAMGADYLS(0.949)CDS(0.051)R;MSYLTAMGADYLS(1)CDSR 279.19 3.10E-36 381779000 268884 341936 260376 257035 418868 168806 278633 360065 812010 TRUE FALSE 252055.0304 367253.2972 266552.2417 263630.9533 385971.7969 217537.5519 236854.5684 405019.9079 676480.2852 0.372597747 0.542888396 0.3940281 0.389709736 0.570558825 0.321572641 0.350127821 0.598716499 1 19.36768836 0.916110793 4.264823194 0.999808121 0.426311291 0.842341197 0.07944636 0.149819124 6.392717609 0.075829638 0.019314404 8.243483888 -0.916110793 -0.573496831 KKYDVDTLDMVFLDHWKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKYDVDTLDMVFLDHWKDR 19 3 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 179.95 2.08E-14 72102000 113270 164270 155470 178500 344540 89805 186510 139430 1179000 FALSE TRUE 106180.6329 176432.7217 159157.8218 183080.6122 317481.2182 115730.2456 158544.557 156838.1424 982217.2834 0.108102998 0.179626977 0.162039321 0.186395226 0.32322911 0.117825503 0.161414953 0.159677645 1 19.90568268 -1.683937833 2.790656473 1.108192719 0.175273167 0.952095274 0.058172243 14142463.96 12845019.54 10845257.46 0.013642134 0.020704377 1.683937833 -0.932919552 KKYELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KKYELR 6 2 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 94.262 0.025131 3162900000 4337900 4174900 4053200 4021000 5241400 3461000 5145300 4881800 8994800 FALSE TRUE 4066398.582 4484013.94 4149343.818 4124185.668 4829761.587 4460134.515 4373810.032 5491303.476 7493509.771 0.542656073 0.598386347 0.553725016 0.550367691 0.644525961 0.595199666 0.583679766 0.732807942 1 22.83721017 0.88966526 2.086230513 0.999881524 0.579744271 0.952868925 0.02982902 0.085169651 0.75615562 0.02734104 0.007550302 7.75649041 -0.88966526 -0.420137252 KKYPDRVPVIVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KKYPDRVPVIVEK 13 3 F5GZY7;H6UMI1;Q9H0R8;O95166;Q9H0R8-2 F5GZY7 GABARAPL1;GABARAP Gamma-aminobutyric acid receptor-associated protein-like 1;Gamma-aminobutyric acid receptor-associated protein 0 99.927 0.0011548 268180000 650540 506790 566840 553240 697730 454700 885340 584870 892970 FALSE TRUE 609823.8626 544313.2589 580285.7125 567437.075 642933.1003 585964.5086 752591.4861 657892.307 743927.5382 0.819735567 0.731675104 0.780029886 0.762758529 0.864241566 0.787663419 1.011646226 0.884349985 1 19.50480258 1.97882168 1.166816927 0.976693794 0.768049228 0.672526619 0.054394058 0.237830434 0.59802303 0.036866444 0.016894979 95.2405029 -1.97882168 -0.208644567 KLAEPAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLAEPAER 8 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 0 81.338 0.037071 112740000 95762 72454 73004 73439 89855 68716 108840 81273 133630 FALSE TRUE 89768.42736 77818.56955 74735.68935 75323.56907 82798.15076 88553.19369 92520.45242 91420.11295 111326.2897 0.806354255 0.699013411 0.671321119 0.67660181 0.743743019 0.795438291 0.831074607 0.821190693 1 16.7644348 1.144568921 0.630772785 0.995466845 0.702170032 0.794925931 0.043735468 0.305774659 0.296286988 0.043507978 0.019190467 13.94983018 -1.144568921 -0.293296813 KLAEVTEEEWLSIPEVGDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLAEVTEEEWLSIPEVGDAR 20 1 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 83.213 0.0047522 25844000 39638 47821 39294 43802 53833 26672 49503 42629 71628 FALSE TRUE 37157.12834 51361.7166 40226.07224 44926.03348 49605.17333 34371.77342 42080.48471 47951.32449 59672.82407 0.622680909 0.860722069 0.674110416 0.752872588 0.831285834 0.5760038 0.705186747 0.803570557 1 15.86478643 0.899986041 3.817393647 0.999854928 0.725067555 0.519521287 0.085785927 0.364934509 11.48798149 0.07811348 0.02003643 7.943027037 -0.899986041 -0.274787372 KLALDIEIATYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KLALDIEIATYR 12 1 K7EPI4 K7EPI4 GFAP 0 ;; 180.84 3.03E-05 803443000 1074953 1202199 1176329 1169852 1313874 1044894 1403662 1175586 1326067 FALSE TRUE 1007673.611 1291211.065 1204232.079 1199872.383 1210687.636 1346537.935 1193195.914 1322360.5 1104737.851 0.912138214 1.168794084 1.090061392 1.086115029 1.095904911 1.218875532 1.080071542 1.196990307 1 20.07527263 4.746690126 24.60352016 1.121433025 0.912138084 0.502738082 0.063933122 615.1839096 1861768.126 0.013261304 0.147215622 55807.18625 -4.746690126 -0.20929494 KLAPEYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLAPEYEK 8 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 122.26 0.0022418 667630000 1440740 1412930 1232890 1340130 1431270 897390 1643550 1233650 1342300 FALSE TRUE 1350566.655 1517544.807 1262134.733 1374520.005 1318863.828 1156451.925 1397114.935 1387673.918 1118261.458 1.207737819 1.357057239 1.128657993 1.229157988 1.179387716 1.034151644 1.249363398 1.240920813 1 20.09282611 -5 0.087102922 0.403835421 1.371615418 0.372443072 0.083236528 240.1313546 1.462561161 27.65871694 2.112812735 1.00E-05 5 0.967779998 KLAT(ph)PPAAQESSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLATPPAAQESSR 13 1 H0Y760;Q9Y4B4 H0Y760 RAD54L2 Helicase ARIP4 1 KLAT(0.999)PPAAQES(0.001)S(0.001)R 52.298 0.089984 193730000 533050 416570 511110 482850 584820 421210 602720 469730 651710 TRUE FALSE 499687.352 447413.2762 523233.7706 495240.7485 538890.5963 542806.4892 512347.7314 528376.8245 542935.3908 0.920344042 0.82406357 0.963712772 0.912154111 0.992550137 0.999762584 0.943662432 0.973185453 1 19.050421 3.664900475 1.587618523 0.971251106 0.867923901 0.560186193 0.03542326 0.255223392 1.268882839 0.009995998 0.021595726 4622.750726 -3.664900475 -0.103327206 KLAVNMVPFPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLAVNMVPFPR 11 1 Q13509;A0A0B4J269;Q13509-2;Q5JP53;P07437;Q5ST81;A6NNZ2;CON__ENSEMBL:ENSBTAP00000025008;Q9H4B7;P68371;Q13885;Q3ZCM7;A0A075B736;Q5SQY0;Q9BVA1;P04350;K7ESM5;Q9BUF5 Q13509;Q5JP53;P68371;Q13885;Q3ZCM7;Q9BVA1;P04350;K7ESM5 TUBB3;TUBB;TUBB1;TUBB4B;TUBB2A;TUBB8;TUBB2B;TUBB4A;TUBB6 Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-8 chain-like protein LOC260334;Tubulin beta-1 chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-8 chain;Tubulin beta-2B chain;Tubulin beta-4A chain;Tubulin beta-6 chain 0 ; 173.64 1.91E-05 2280300000 1823210 6638700 1394720 1325630 7526900 728440 1916530 6154100 6604800 FALSE TRUE 1709098.541 7130236.256 1427803.417 1359647.91 6935767.636 938728.8028 1629164.119 6922452.932 5502416.211 0.310608735 1.295837316 0.259486626 0.247100157 1.260494912 0.170603016 0.296081586 1.258075119 1 22.39163384 1.228936515 24.99808438 1.129037816 0.574819707 0.252031609 0.41379642 331.2707511 860427.5811 0.367874352 0.096698994 16.94090142 -1.228936515 -0.554218109 KLCLNICVGESGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLCLNICVGESGDR 14 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ; 211.75 5.45E-09 983480000 1045990 1069030 1145980 1103560 1233400 857500 1349790 1008650 1267330 FALSE TRUE 980523.353 1148182.094 1173163.187 1131879.218 1136533.739 1105046.33 1147401.52 1134582.173 1055804.436 0.928697891 1.087495046 1.111155766 1.072053857 1.076462364 1.046639219 1.08675573 1.074613948 1 20.0099112 4.741089278 24.98496663 1.076745577 0.928697839 0.676109453 0.030226421 122.3745172 1209076.625 0.00658173 0.044930234 55092.09372 -4.741089278 -0.148047738 KLCQPQSTGSLLGDPAASS(ph)PPGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KLCQPQSTGSLLGDPAASSPPGER 24 1 U3KQ90;P55199 U3KQ90 ELL RNA polymerase II elongation factor ELL 1 KLCQPQSTGSLLGDPAAS(0.094)S(0.906)PPGER;KLCQPQSTGSLLGDPAAS(0.04)S(0.96)PPGER;KLCQPQSTGSLLGDPAAS(0.226)S(0.774)PPGER 183.81 1.68E-17 1518010000 962580 1043850 960390 985640 1154750 922230 1305650 980460 1557610 TRUE FALSE 902333.8361 1121137.74 983170.9043 1010933.191 1064060.593 1188462.83 1109879.904 1102872.589 1297634.828 0.695368078 0.863985549 0.757663776 0.779058306 0.820000026 0.915868474 0.855309891 0.849909824 1 20.30745302 -4.999999984 0.081760524 1.637523082 0.634909309 0.658506891 0.049285498 152.3291632 0.879603217 17.13122017 1.524651166 1.00E-05 4.999999984 -1.002613773 KLDALCNIHENIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLDALCNIHENIR 13 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 142.55 2.62E-05 1132300000 1040530 1412030 1129790 1217090 1617830 975790 1438340 1357840 1976390 FALSE TRUE 975405.0847 1516578.17 1156589.152 1248322.59 1490772.158 1257484.732 1222674.27 1527369.313 1646517.741 0.592404844 0.921082192 0.702445606 0.75815921 0.905409107 0.763723767 0.742581898 0.92763611 1 20.65098663 1.087800684 4.318376503 0.997574105 0.780085459 0.431364651 0.0939188 0.178909624 5.692374552 0.081230987 0.020775268 12.240543 -1.087800684 -0.217488646 KLDDDSDS(ph)PSFFEEKPEEPVVLALDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLDDDSDSPSFFEEKPEEPVVLALDPK 27 2 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 KLDDDS(0.116)DS(0.868)PS(0.016)FFEEKPEEPVVLALDPK 78.228 0.0072394 34819000 61487 25967 34540 38985 43175 28908 56629 31038 63321 TRUE FALSE 57638.63843 27889.6237 35359.30511 39985.4211 39784.20966 37253.27032 48138.00717 34913.16262 52752.31603 1.092627637 0.528690033 0.670289151 0.757984182 0.754169914 0.706192128 0.912528791 0.661831845 1 15.68694681 0.094982969 0.410338479 1.0349555 0.708950917 0.134606897 0.157809297 5.979412993 1.436225221 0.542745597 0.100716233 1.244465808 -0.094982969 -0.326004583 KLDEAVAEAHLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KLDEAVAEAHLGK 13 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;;; 120.3 0.00018207 6168610000 16974480 13208460 14991330 14567470 16159330 10985080 19340950 13861020 21622480 FALSE TRUE 15912077.6 14186428.12 15346931.43 14941295.94 14890241.41 14156294.27 16440954.1 15591598.86 18013548.4 0.883339431 0.787542121 0.851966036 0.829447681 0.826613451 0.785869278 0.91269936 0.865548448 1 24.10257906 0.813985095 0.854879423 0.998728941 0.826664453 0.666225232 0.036442396 0.454271835 0.665538215 0.031816015 0.011025325 6.516060313 -0.813985095 -0.172064488 KLDELYGTWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLDELYGTWR 10 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ; 164.9 9.65E-06 6275000000 8540300 14234100 9403500 9201800 16334600 5401300 7740300 12972700 13604300 FALSE TRUE 8005777.868 15288007.57 9626555.461 9437933.767 15051746.41 6960567.627 6579713.872 14592370.15 11333654.44 0.706372151 1.348903626 0.849377887 0.832735268 1.328057643 0.614150331 0.58054654 1.287525592 1 23.43410979 2.219578661 24.99654292 0.800365014 1.028360102 0.032321289 0.284160101 495.0886852 651957.506 0.100709718 0.074496368 165.7977608 -2.219578661 0.227995087 KLDEMTDRDWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLDEMTDRDWR 11 2 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ; 122.34 0.00022089 212012000 593310 654770 627590 642530 793320 451410 757450 570190 1036320 FALSE TRUE 556175.7862 703249.8521 642476.7312 659018.4076 731015.8473 581724.739 643877.4043 641379.4766 863351.4971 0.644205504 0.814557981 0.744165885 0.763325725 0.846718688 0.673798263 0.745788252 0.742894961 1 19.71958852 -1.42147138 5.816811199 1.000106781 0.752437495 0.646694665 0.058659504 7.35E-05 7.31E-06 0.051411895 0.0121127 0.03789035 1.42147138 -0.247669286 KLDEQYQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLDEQYQK 8 1 P61758;P61758-2 P61758 VBP1 Prefoldin subunit 3 0 130.66 0.0016652 155500000 475550 442730 416040 439720 537060 380020 457920 424760 626460 FALSE TRUE 445786.1744 475510.1899 425908.6653 451003.9596 494881.474 489725.6049 389259.1471 477792.221 521899.7789 0.854160497 0.91111399 0.816073665 0.864158173 0.948230856 0.938351815 0.745850378 0.915486537 1 18.99341327 0.990986023 24.97467901 1.000000014 0.865159127 0.33880178 0.058817857 432.1961391 1197472.918 0.056439849 0.014109962 9.794584632 -0.990986023 -0.134840887 KLDGFPLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLDGFPLLR 9 1 P09661;H0YKK0 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 0 ; 130.98 0.00055464 449120000 1005070 1308270 1040260 1118920 1599050 913060 1371160 1294500 1613260 FALSE TRUE 942164.4628 1405135.672 1064935.458 1147633.382 1473467.063 1176645.6 1165567.287 1456121.175 1343996.484 0.701017059 1.045490586 0.792364765 0.853896119 1.096332528 0.875482647 0.867239834 1.083426327 1 20.35809793 7.999999999 0.115228975 1.040296127 0.439314305 0.190640561 0.117372269 221.9257522 1.769594917 0.862854377 21.32077666 99999999.83 -7.999999999 -0.600981822 KLDKENLS(ph)DER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLDKENLSDER 11 2 Q9BZI7-2;Q9BZI7 Q9BZI7-2 UPF3B Regulator of nonsense transcripts 3B 1 KLDKENLS(1)DER 59.68 0.051371 208160000 473730 302380 370680 380260 413060 250440 446540 306580 558820 TRUE FALSE 444080.0849 324768.5298 379472.7046 390018.1154 380619.9338 322737.9624 379585.4725 344857.1879 465549.3319 0.953884056 0.697602827 0.815107398 0.837758941 0.817571647 0.693241168 0.815349624 0.740753266 1 18.82857453 -1.193768479 5.797206252 1.000004482 0.788486218 0.412918114 0.075770401 3.88E-06 5.40E-07 0.064933231 0.015304585 0.064007597 1.193768479 -0.211518263 KLDLEAWFPGSGAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLDLEAWFPGSGAFR 15 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 118.55 0.00045307 274620000 512330 626610 552630 504180 669300 366120 554600 594060 589050 FALSE TRUE 480264.1798 673004.8564 565738.6446 517118.1124 616735.8778 471812.9005 471442.8787 668229.6987 490733.7496 0.978665478 1.37142566 1.152842341 1.053765128 1.256762712 0.961443758 0.960689741 1.361695011 1 18.90458097 3.474462936 4.717318794 1.086144609 1.220009761 0.020118034 0.158472795 0.380347155 22.18899146 0.041371403 0.060592007 2981.693073 -3.474462936 0.133865152 KLDNTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLDNTK 6 1 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 85.272 0.088032 822170000 2072100 1560200 1750200 1644600 1861500 1408800 1870700 1685700 2118600 FALSE TRUE 1942410.96 1675718.831 1791715.571 1686803.22 1715305.299 1815497.69 1590205.902 1896163.356 1764991.973 1.100521129 0.949420086 1.015140917 0.955700222 0.971848782 1.028615267 0.900970614 1.074318402 1 20.75123019 4.748143875 24.56586594 0.981035419 1.100521211 0.351318085 0.047870854 1028.31425 2635924.825 0.010099726 0.130829222 55994.30714 -4.748143875 0.119485793 KLDPAQS(ph)ASRENLLEEQGSIALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLDPAQSASRENLLEEQGSIALR 23 2 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 KLDPAQS(0.89)AS(0.11)RENLLEEQGSIALR 162.91 8.38E-12 193450000 31372 28317 30302 29915 29991 23245 33852 27595 50443 TRUE FALSE 29408.48252 30413.62014 31020.77775 30682.66955 27635.62784 29955.45415 28776.20687 31040.29649 42023.73743 0.69980645 0.72372478 0.738172748 0.7301271 0.657619468 0.712822228 0.684760772 0.738637218 1 15.35891685 0.863007556 6.984805247 0.999999843 0.709790196 0.939175654 0.023264669 1.24744069 63.62226255 0.023297619 0.005842937 7.294702018 -0.863007556 -0.290209647 KLDPAQSAS(ph)RENLLEEQGSIALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLDPAQSASRENLLEEQGSIALR 23 2 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 KLDPAQS(0.396)AS(0.604)RENLLEEQGSIALR 148.34 5.60E-08 227100000 29599 26976 19525 27799 24808 26117 36215 20986 36036 TRUE FALSE 27746.45143 28973.33111 19988.14222 28512.3694 22859.67975 33656.55393 30784.89695 23606.1483 30021.3588 0.924223704 0.965090598 0.665797386 0.949736139 0.761447205 1.121086962 1.025433164 0.786311787 1 14.87370166 2.248435882 24.99852276 0.994473022 0.847331154 0.219574798 0.120622659 274.0966885 693856.0138 0.040933051 0.033859986 177.1886429 -2.248435882 -0.147141868 KLDPELHLDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLDPELHLDIK 11 1 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 133.77 0.00010047 1146900000 5716000 4099200 4838100 4655800 5605800 3473400 6138900 4624500 6879000 FALSE TRUE 5358245.763 4402709.033 4952862.017 4775275.71 5165543.081 4476114.194 5218428.936 5201879.005 5730850.46 0.934982652 0.768247063 0.864245552 0.833257776 0.901357158 0.781055835 0.910585431 0.907697564 1 22.45031782 1.045072578 1.192458271 0.998081407 0.841458934 0.450410723 0.051985253 0.374852555 1.106625182 0.043672584 0.013746322 11.09360193 -1.045072578 -0.156622472 KLDPGSEETQTLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KLDPGSEETQTLVR 14 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;;; 176.29 3.61E-06 7293760000 3624910 3879270 2712470 2625120 3276770 1583287 3947130 3009400 4677950 FALSE TRUE 3398033.354 4166495.187 2776811.069 2692485.024 3019425.702 2040356.254 3355294.5 3385130.215 3897169.924 0.871923324 1.069107909 0.712519886 0.690882121 0.774773941 0.523548189 0.860956685 0.868612424 1 21.89399541 3.91614921 4.673075347 0.758517122 0.973554018 0.257626584 0.134507415 0.219306076 9.633869106 0.032000709 0.061204071 8244.213114 -3.91614921 0.215036896 KLDTNSDGQLDFSEFLNLIGGLAMACHDSFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLDTNSDGQLDFSEFLNLIGGLAMACHDSFLK 32 1 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 97.469 2.30E-05 63555000 24742 85996 60786 48246 93291 64229 52517 66440 36401 FALSE TRUE 23193.44239 92363.23332 62227.87263 49484.07404 85964.30118 82770.86963 44642.56339 74735.18025 30325.43794 0.764818052 3.045734525 2.052002439 1.631767829 2.834725795 2.729420422 1.472116033 2.464438614 1 14.88824086 -0.522036899 0.67592443 0.88035507 2.204110625 0.190500255 0.702111062 20.68298264 6.960663066 6.772594188 0.237499319 0.300582091 0.522036899 1.323755554 KLDVEEPDS(ph)ANSSFYSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLDVEEPDSANSSFYSTR 18 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 KLDVEEPDS(0.97)ANS(0.021)S(0.01)FYSTR 110.85 0.000145 0 225360 168140 209160 212240 195010 177150 239750 207030 243420 TRUE FALSE 211255.1199 180589.2605 214121.374 217686.4377 179694.7012 228290.3292 203801.7132 232878.1512 202791.6294 1.04173491 0.890516344 1.055868896 1.073448832 0.88610512 1.125738423 1.004980895 1.148361754 1 17.62963858 3.306797249 0.611991697 1.055956998 0.958539837 0.087512754 0.082634199 1.985968818 1.533227289 0.05123294 0.109163002 2026.736313 -3.306797249 -0.097417161 KLDVEEPDSANSSFYSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KLDVEEPDSANSSFYSTR 18 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;; 298.81 3.07E-49 1791080000 1961890 1737780 1868380 1737180 1948160 1460000 2199620 1668480 2333100 FALSE TRUE 1839098.807 1866447.039 1912698.856 1781758.98 1795159.372 1881478.299 1869807.401 1876793.401 1943690.538 0.946189103 0.960259364 0.984055239 0.916688611 0.923582915 0.967992724 0.96198822 0.965582414 1 20.89036711 0.757671951 1.083600806 0.999696246 0.953222607 0.381568333 0.019703409 1.086605717 2.309654979 0.019988792 0.006325982 5.723635263 -0.757671951 -0.046473639 KLDVSIEMPEELDISQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLDVSIEMPEELDISQLR 18 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 157.14 1.04E-08 357630000 652520 626000 672710 679340 703210 543290 743470 625260 733360 FALSE TRUE 611679.938 672349.6914 688666.9989 696773.0145 647982.7232 700129.0034 631993.5755 703325.0874 610957.4783 1.001182504 1.100485247 1.12719301 1.140460735 1.060602 1.145953734 1.034431361 1.151185004 1 19.22071245 -0.46985647 6.583777023 1.000000003 1.096488534 0.262810858 0.05005883 0 0 0.04344148 0.010239255 0.33895616 0.46985647 0.096488531 KLDYGQHVVAGT(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KLDYGQHVVAGTPGR 15 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 1 KLDYGQHVVAGT(1)PGR;KLDYGQHVVAGT(1)PGR;KLDYGQHVVAGT(1)PGR 107.45 0.00088137 670000000 754360 765780 772230 750970 862060 590900 940420 810110 990360 TRUE FALSE 707145.9542 822479.148 790547.6603 770241.1616 794357.285 761483.2375 799412.7514 911254.0168 825062.518 0.857081662 0.99686888 0.958166979 0.933554906 0.962784356 0.922940045 0.96891173 1.104466628 1 19.65414392 1.383609696 6.360348981 1.050912408 0.948422056 0.519301233 0.043922233 0.162618734 8.657963359 0.026973596 0.009817095 24.18854226 -1.383609696 -0.102490352 KLDYGQHVVAGTPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLDYGQHVVAGTPGR 15 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 156.17 1.41E-06 1678400000 1350100 1337200 1431500 1365200 1643000 1209100 1577400 1352200 1644200 FALSE TRUE 1265599.651 1436207.679 1465455.856 1400233.343 1513965.408 1558147.542 1340883.514 1521025.147 1369772.398 0.923948864 1.048500964 1.069853545 1.022237961 1.10526786 1.137522952 0.978909719 1.110421811 1 20.38550476 4.741905895 3.931419987 1.05980796 0.91076368 0.423083832 0.049780872 0.233781051 7.381496996 0.011034664 0.100491078 55195.78255 -4.741905895 -0.14904428 KLEAAEDIAYQLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KLEAAEDIAYQLSR 14 1 P35232 P35232 PHB Prohibitin 0 ;;;; 218.78 8.43E-12 2419088000 4506264 4294328 4051073 3873275 5853837 3349853 4328340 4718248 6816504 FALSE TRUE 4224224.98 4612284.513 4147166.365 3972669.794 5394100.255 4316901.181 3679345.599 5307331.649 5678785.446 0.743860641 0.812195593 0.730291081 0.699563284 0.949868648 0.760180363 0.647910655 0.934589218 1 22.43715097 1.069053539 6.370912722 0.999096228 0.763642145 0.542597062 0.079017708 0.136874947 8.949751696 0.074479436 0.018713476 11.7233988 -1.069053539 -0.235454084 KLEAAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KLEAAEER 8 1 P16949;P16949-2;A2A2D0;E5RIR6;E7EVN3;Q9H169-3;Q9H169;Q9H169-4;Q9H169-2;E5RGX5;Q93045;Q93045-2 P16949;E5RGX5 STMN1;STMN4;STMN2 Stathmin;Stathmin-4;Stathmin-2 0 ;;;;;;; 152.28 0.00073707 13494640000 19006550 21470780 18007030 17652310 25533920 13088390 20576580 21170290 26406250 FALSE TRUE 17816963.96 23060498.89 18434165.26 18105298.16 23528588.92 16866795.72 17491312.85 23813447.31 21998876.28 0.809903367 1.048258038 0.837959404 0.823010136 1.069535944 0.766711695 0.795100287 1.082484714 1 24.3909265 1.22711044 24.99798993 1.041242423 0.885792278 0.293896129 0.104324651 332.1178673 725055.6597 0.094869661 0.024553437 16.86981968 -1.22711044 -0.155450146 KLEAELLQIEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 170.52 6.56E-05 539875000 1144096 1206423 1171450 1165346 1344140 975748 1417215 1098483 1557109 FALSE TRUE 1072489.074 1295747.814 1199237.347 1195250.751 1238576.666 1257430.608 1204716.768 1235631.021 1297217.449 0.826761215 0.998867087 0.924469023 0.921395833 0.954794948 0.969329089 0.928693003 0.952524206 1 20.3069889 -2.615526729 0.008304246 1.98691749 4.68E-08 0.264621983 0.042212573 20901.19083 20.65886871 2675.182381 2280.770805 0.002423669 2.615526729 -1.986917444 KLEDGPK ddPTM_SK-BR-3_Pertuzumab_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 55172600000 65429700 38958000 50520000 44964100 48206900 35990100 61857000 39852000 64182900 FALSE TRUE 61334571.87 41842490.86 51718358.26 46117954.93 44420924.53 46379857.62 52582117.1 44827609.93 53470359.35 1.147076111 0.782536182 0.967234163 0.862495698 0.83075792 0.867393789 0.983388138 0.83836373 1 25.67223604 -0.14370734 7.904851253 1.000000014 0.90388549 0.06670874 0.103755353 0 0 0.088261098 0.02080334 0.718278158 0.14370734 -0.096114524 KLEDNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KLEDNPK 7 1 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ;;; 104.37 0.013096 5361140000 6856440 4645460 5436020 5449720 5913230 3774010 6689860 4788970 6508900 FALSE TRUE 6427307.659 4989414.692 5564964.961 5589569.042 5448828.769 4863505.421 5686777.599 5386883.446 5422522.541 1.185298468 0.920127976 1.026268664 1.03080605 1.00485129 0.89690829 1.048732865 0.99342758 1 22.37053271 4.751847105 24.86115647 0.99074359 1.185298604 0.624974876 0.047508282 1368.806471 2561207.328 0.010808761 0.208285698 56473.81213 -4.751847105 0.194555015 KLEDQLQGGQLEEVILQAEHELNLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLEDQLQGGQLEEVILQAEHELNLAR 26 1 A0A087X1G1;H7BYD0;Q16718-2;Q16718;A0A087WXR5 A0A087X1G1 NDUFA5 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 0 63.697 0.02783 6111000 4764 4772.5 4943.7 4869.2 7134.2 5157.1 4378.9 3909.8 6731 FALSE TRUE 4465.829744 5125.860866 5060.966899 4994.151916 6573.90871 6645.871051 3722.324597 4397.947137 5607.552616 0.796395513 0.914099468 0.902526868 0.890611691 1.172331168 1.185164279 0.663805559 0.784289946 1 12.45315554 -2.560851973 2.208601831 2.503788852 0.913271006 0.027514802 0.161312912 14884217.33 2260278.404 109917732.4 0.042584265 0.002748831 2.560851973 -1.590517846 KLEDSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KLEDSTR 7 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;; 146.81 0.0035178 676740000 1509150 1667520 1382540 1542020 1921380 1053120 1836790 1653970 1610800 FALSE TRUE 1414694.995 1790984.916 1415334.502 1581590.844 1770482.565 1357138.648 1561380.391 1860471.795 1341947.074 1.054210723 1.334616656 1.054687274 1.178579152 1.319338594 1.011320546 1.163518608 1.386397297 1 20.35589634 -1.025093057 4.203759437 0.999986462 1.183322595 0.176218537 0.127299255 7444356.861 1815831.431 993.8454621 0.027019952 0.094385861 1.025093057 0.183336133 KLEDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLEDVK 6 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 0 ; 91.626 0.076449 2788700000 3177400 2055440 2428100 2256310 2212400 1599710 2911100 1980220 2723800 FALSE TRUE 2978532.206 2207626.916 2485695.679 2314210.735 2038647.028 2061520.308 2474607.58 2227454.826 2269180.184 1.312602775 0.972874227 1.095415735 1.019844414 0.898406853 0.908486828 1.090529345 0.981612144 1 21.11373974 4.742144226 24.65280158 1.004141443 1.312602918 0.700582055 0.064869462 174.9370548 1203384.138 0.015836255 0.116763814 55226.08111 -4.742144226 0.308461475 KLEDVKNS(ph)PTFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLEDVKNSPTFK 12 2 H0YC42;P55327-2;P55327-3 H0YC42;P55327-2 1 KLEDVKNS(0.967)PT(0.033)FK 140.22 3.10E-05 313660000 1866100 941990 1300900 1784800 1584300 612320 1123900 603160 947910 TRUE FALSE 1749304.132 1011735.92 1331757.962 1830600.99 1459875.469 789086.8438 955381.6288 678465.8537 789697.6973 2.215156684 1.281168634 1.686414899 2.318103492 1.848651039 0.999226472 1.209806781 0.859146299 1 19.59094096 2.23804578 24.99977655 1.052047673 1.784969981 0.661966345 0.298974956 10.21738736 496101.2702 0.113646201 0.089082162 172.9998712 -2.23804578 0.732922308 KLEEEGEQFVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLEEEGEQFVK 11 1 H0YF61;P22307-6;P22307-2;P22307-4;P22307-7;P22307-8;P22307 H0YF61 SCP2 Non-specific lipid-transfer protein 0 ; 173.19 2.00E-05 1306920000 2351250 1648190 1865360 1715580 1861660 1348500 2278590 1702750 2268100 FALSE TRUE 2204089.46 1770223.703 1909607.22 1759604.687 1715452.733 1737790.059 1936936.583 1915342.086 1889539.458 1.166469137 0.936854584 1.010620452 0.931234688 0.907868172 0.919689743 1.025083956 1.013655512 1 20.84960321 1.616335636 25 1.014527799 0.973015635 0.041240071 0.074014287 1.965530364 5785.112587 0.032852694 0.017846751 41.33668411 -1.616335636 -0.041512163 KLEEEQIILEDQNCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KLEEEQIILEDQNCK 15 1 P35579 P35579 MYH9 Myosin-9 0 ;;;; 233.14 2.04E-17 2758920000 7208630 4851550 5479230 5393560 5983840 4380370 8313110 4752060 7284040 FALSE TRUE 6757454.716 5210763.81 5609199.923 5531967.881 5513893.344 5644911.71 7066636.331 5345365.152 6068286.667 1.113568802 0.858687813 0.924346563 0.911619405 0.908640881 0.93023155 1.164519199 0.880868925 1 22.53285781 1.938777193 24.99817443 1.036900953 0.927090758 0.092209195 0.095472164 327.5368352 133737.2 0.03565905 0.023017318 86.85147386 -1.938777193 -0.109810195 KLEEIIHQITNVEALIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLEEIIHQITNVEALIAR 18 1 Q15042-4;Q15042;Q15042-3 Q15042-4 RAB3GAP1 Rab3 GTPase-activating protein catalytic subunit 0 ; 241.32 3.54E-24 164997000 313550 315970 336920 353970 362130 281840 413920 328670 394770 FALSE TRUE 293925.4652 339364.7476 344911.9015 363053.4695 333689.7706 363202.6327 351856.5386 369705.173 328880.3367 0.893715532 1.031879105 1.04874589 1.103907498 1.014623659 1.104361046 1.06986189 1.124132798 1 18.32720323 5.710953861 0.996033202 1.071162021 1.78E-12 0.64862843 0.03945533 6.221093129 1.144273782 0.010357536 11.25652956 513989.0432 -5.710953861 -1.071162021 KLEELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLEELK 6 1 Q15172;Q15172-2;Q9Y2C4-3;Q9Y2C4-4;Q9Y2C4;Q9Y2S6 Q15172;Q9Y2S6 PPP2R5A;EXOG;TMA7 "Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform;Nuclease EXOG, mitochondrial;Translation machinery-associated protein 7" 0 88.942 0.081342 545990000 1264100 921820 1168800 927660 1039700 740160 1243000 875500 1208300 FALSE TRUE 1184982.237 990072.512 1196524.488 951465.3261 958046.1559 953832.1765 1056623.689 984808.1022 1006626.924 1.177181147 0.98355457 1.188647412 0.945201547 0.951739053 0.947552816 1.049667622 0.978324818 1 19.94109766 3.221358134 24.99824192 0.982486124 1.098293447 0.506253115 0.063197588 215.4065354 313022.9938 0.01772364 0.021231439 1664.784922 -3.221358134 0.115807324 KLEEQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KLEEQAR 7 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ;; 90.709 0.037908 657060000 1997170 2799340 2010100 2100890 3473270 1619980 2762860 3144110 4248780 FALSE TRUE 1872170.695 3006606.046 2057780.521 2154802.394 3200493.385 2087641.928 2348594.792 3536659.055 3539631.17 0.528916886 0.849412242 0.581354503 0.608764668 0.904188383 0.589790808 0.663513988 0.999160332 1 21.75516761 1.236339379 24.90856586 0.99958038 0.683219826 0.565828269 0.117989736 39.51313454 443039.4208 0.088347805 0.02621231 17.23214653 -1.236339379 -0.316360555 KLEESASFESLSPSSRPAS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLEESASFESLSPSSRPASPTR 22 2 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 KLEESASFESLSPS(0.007)S(0.007)RPAS(0.986)PT(0.001)R 210.79 2.12E-23 62017000 99097 78003 109090 99169 123020 103600 84467 87014 130870 TRUE FALSE 92894.69566 83778.42328 111677.6663 101713.8444 113358.5054 133507.6382 71801.9575 97877.88944 109026.9515 0.852034239 0.768419387 1.024312473 0.93292386 1.039729203 1.224537936 0.658570716 0.897740311 1 16.73432529 4.013297059 5.588981848 0.954054632 0.813183888 0.170306191 0.142221444 0.368738245 30.79120931 0.036468862 0.078325196 10310.91149 -4.013297059 -0.140870744 KLEEVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KLEEVER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 119.21 0.007749 1795640000 3882150 3685580 3919070 3907580 4465350 3466680 4903600 3964070 5067100 FALSE TRUE 3639173.161 3958464.178 4012032.191 4007855.118 4114659.423 4467454.239 4168350.703 4458992.865 4221368.275 0.86208379 0.937720644 0.950410372 0.949420865 0.974721738 1.058295308 0.987440666 1.056290893 1 22.00927927 4.058367682 0.413507948 1.029856603 0.830372844 0.721141493 0.030347963 1.656962834 0.337639942 0.024304904 0.155754999 11438.46326 -4.058367682 -0.199483759 KLEEVLS(ph)TEGAEENGNSDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLEEVLSTEGAEENGNSDKK 20 2 O15355 O15355 PPM1G Protein phosphatase 1G 1 KLEEVLS(0.864)T(0.136)EGAEENGNSDKK 105.46 0.00013345 115340000 95843 37207 60781 49470 61189 42604 66561 34930 84081 TRUE FALSE 89844.35771 39961.84499 62222.75402 50739.48395 56383.46276 54903.08318 56580.79597 39291.08739 70047.33792 1.282623443 0.570497697 0.888295771 0.724359918 0.804933698 0.783799711 0.807750839 0.560921922 1 16.0960426 4.752201424 24.82442949 0.76329211 1.282623822 0.602575267 0.13141403 1354.423568 2464821.071 0.027619942 0.554369817 56519.90509 -4.752201424 0.519331712 KLEEVVNKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLEEVVNKK 9 2 Q8WU90 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 0 70.942 0.028676 259170000 140080 142410 142200 141870 183870 101210 165700 123560 218210 FALSE TRUE 131312.6428 152954.1846 145573.0512 145510.6244 169429.5919 130427.684 140854.8233 138986.738 181789.3413 0.722334114 0.841381477 0.800778803 0.800435401 0.932010594 0.717466068 0.774824433 0.764548334 1 17.47190809 -1.781392966 2.449097976 1.058829607 0.798153461 0.526561022 0.06122007 11112834.28 7411355.865 3906368.831 0.014041992 0.016542724 1.781392966 -0.260676146 KLEEVVQILGDKFPCTLVAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLEEVVQILGDKFPCTLVAQK 21 2 Q9BY32 Q9BY32 ITPA Inosine triphosphate pyrophosphatase 0 ; 256.52 1.06E-36 426060000 982830 664000 741280 750860 796380 562100 1066130 715470 1016540 FALSE TRUE 921316.4247 713163.2509 758863.5117 770128.3388 733835.5272 724369.1451 906273.704 804798.0044 846872.9069 1.087904002 0.842113669 0.89607721 0.909378884 0.866523797 0.855345754 1.070141336 0.950317336 1 19.69178595 1.744096743 25 1.009432919 0.89855774 0.269247821 0.074029867 1.175607639 5328.633245 0.031181154 0.017291382 55.47492744 -1.744096743 -0.11087518 KLEGDSTDLSDQIAELQAQIAELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLEGDSTDLSDQIAELQAQIAELK 24 1 P35579 P35579 MYH9 Myosin-9 0 ; 211.64 4.53E-25 276160000 705320 425730 500780 451860 435190 304360 633800 463070 474180 FALSE TRUE 661175.2802 457251.4922 512658.7381 463455.4926 401011.9329 392223.7911 538767.5739 520885.3088 395036.2947 1.67370768 1.157492358 1.297750979 1.173197245 1.015126808 0.992880392 1.363843224 1.318575827 1 18.59162568 4.740444446 24.86804988 1.183885018 1.673707859 0.58221432 0.134609986 120.250225 1587269.7 0.032063333 0.208804963 55010.35483 -4.740444446 0.48982284 KLEHLITELVHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLEHLITELVHQR 13 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 205.61 2.79E-08 652290000 919360 1072200 972510 1077160 1240760 840810 1300500 1156580 1111820 FALSE TRUE 861818.8987 1151586.804 995578.3965 1104801.749 1143315.715 1083538.198 1105502.098 1300981.559 926250.0594 0.930438697 1.243278521 1.074848402 1.192768344 1.234348871 1.169811744 1.193524456 1.404568395 1 19.8210422 4.746224176 24.31106776 1.188711601 0.930438512 0.371539029 0.105739824 658.4076155 2088589.468 0.022624324 0.238100197 55747.34333 -4.746224176 -0.258273089 KLEKEEEEGISQES(ph)S(ph)EEEQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KLEKEEEEGISQESSEEEQ 19 2 P17096;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 2 KLEKEEEEGIS(0.004)QES(0.996)S(0.999)EEEQ;KLEKEEEEGIS(0.162)QES(0.9)S(0.938)EEEQ;KLEKEEEEGIS(0.003)QES(0.998)S(0.999)EEEQ;KLEKEEEEGIS(0.005)QES(0.996)S(0.999)EEEQ 146.25 5.77E-07 2934650000 3625700 3075990 2454380 3264960 5470850 1378860 2902230 2795840 12806600 TRUE FALSE 3398773.909 3303739.5 2512599.053 3348744.401 5041191.509 1776914.498 2467067.554 3144906.778 10669095.73 0.31856251 0.309655062 0.235502532 0.313873311 0.472504103 0.166547807 0.231234925 0.294767885 1 23.34693457 -1.447016591 2.906721012 1.017644493 0.285491763 0.886013019 0.079675108 12202387.17 13986698.19 1755341.721 0.020359785 0.035725919 1.447016591 -0.73215273 KLELAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLELAER 7 1 Q5JWM4;Q9H6P5 Q5JWM4 TASP1 Threonine aspartase 1;Threonine aspartase subunit alpha;Threonine aspartase subunit beta 0 75.38 0.069955 123660000 133200 387450 114150 118800 447960 66389 117740 364710 380180 FALSE TRUE 124863.2498 416137.2011 116857.6919 121848.6091 412779.0286 85554.42656 100085.98 410244.8463 316725.5019 0.394231753 1.313873365 0.36895574 0.384713603 1.30327058 0.270121686 0.316002278 1.295269386 1 18.27287351 1.225319847 24.9721032 1.14763489 0.645911371 0.235983128 0.391608663 405.4269107 764612.6108 0.35958997 0.092046064 16.80040871 -1.225319847 -0.501723519 KLELSDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KLELSDNR 8 1 P39687;H0YN26 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;;; 137.95 0.0011642 3085540000 7804200 15288000 6580600 6262600 16269400 3828590 7368700 13720300 16129500 FALSE TRUE 7315749.053 16419939.43 6736694.94 6423308.919 14991666.95 4933841.781 6263831.843 15433309.66 13437382.25 0.544432607 1.221959688 0.501339831 0.478017876 1.115668712 0.367172838 0.46614971 1.148535434 1 23.67974878 1.22413629 24.88813025 1.074268006 0.690556014 0.255200379 0.285073955 388.0899911 669600.8439 0.267916057 0.068233356 16.75468587 -1.22413629 -0.383711992 KLELSENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLELSENR 8 1 Q92688;Q92688-2 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 0 ; 125.97 0.001987 1532030000 1256650 4280900 790640 781910 4592100 487820 835910 3695100 4216300 FALSE TRUE 1177998.52 4597862.29 809394.3542 801975.1344 4231454.99 628645.7149 710573.0557 4156441.369 3512572.292 0.335366342 1.308973 0.230427814 0.228315624 1.204659901 0.178970186 0.202294215 1.18330415 1 21.74409649 1.220351526 24.97255168 1.091652592 0.55281547 0.242744519 0.412663376 428.1032228 587099.1595 0.388916296 0.097997489 16.60930752 -1.220351526 -0.538837122 KLENCNYAVELGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLENCNYAVELGK 13 1 P13797;A0A0A0MSQ0;P13797-3;P13797-2;P13796 P13797;P13796 PLS3;LCP1 Plastin-3;Plastin-2 0 ; 166.09 5.49E-05 591480000 1349030 1055700 1111030 1074340 1313150 801070 1366000 1204160 1510940 FALSE TRUE 1264596.62 1133865.126 1137384.156 1101909.383 1210020.496 1032325.905 1161180.981 1354502.027 1258754.353 1.004641309 0.90078348 0.903579125 0.875396681 0.961284061 0.820117048 0.922484183 1.076065416 1 20.26356534 1.300434587 7.113448351 1.037355897 0.906593797 0.501679777 0.051799362 0.139545752 12.89146209 0.031794458 0.011398776 19.97259922 -1.300434587 -0.1307621 KLENEVEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLENEVEQR 9 1 P12270 P12270 TPR Nucleoprotein TPR 0 ; 132.25 0.0004976 502760000 1138870 1083380 1117170 1062770 1151950 864250 1234500 965200 1262280 FALSE TRUE 1067590.16 1163594.582 1143669.8 1090042.477 1061480.494 1113744.945 1049398.186 1085707.345 1051597.313 1.015208147 1.106502049 1.08755489 1.036558827 1.009398256 1.059098317 0.997908774 1.0324364 1 20.00415093 3.12544121 4.311612419 1.021270891 1.080080498 0.359690526 0.029236497 0.179664271 5.902423519 0.00805194 0.009806219 1334.876876 -3.12544121 0.058809607 KLEPGGFGEKPVRPGGGDT(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLEPGGFGEKPVRPGGGDTSPR 22 3 Q5JSZ5;A0A494C0D3;H0Y412;A0A494C065 Q5JSZ5 PRRC2B Protein PRRC2B 1 KLEPGGFGEKPVRPGGGDT(0.819)S(0.181)PR;KLEPGGFGEKPVRPGGGDT(0.556)S(0.444)PR 76.611 0.011008 1569210000 1815210 1269080 1439750 1549700 1663620 1164620 1701120 1413520 1893120 TRUE FALSE 1701599.246 1363044.004 1473901.55 1589467.926 1532965.996 1500826.888 1446052.848 1590001.084 1577146.042 1.078910387 0.86424717 0.934537139 1.007812773 0.971987346 0.95160933 0.916879484 1.008150825 1 20.58888483 1.219397943 24.880725 1.004075493 0.948651161 0.059625583 0.057141919 530.1891555 688375.7769 0.051949317 0.013069019 16.57287835 -1.219397943 -0.055424333 KLERPPET(ph)PTVDPTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLERPPETPTVDPTVK 16 2 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 KLERPPET(0.995)PT(0.005)VDPTVK 136.49 0.00081789 233070000 244560 190680 203670 210640 219520 110740 257030 215870 337170 TRUE FALSE 229253.4262 204798.1456 208501.1486 216045.379 202279.7847 142708.8403 218490.7376 242821.8447 280894.1488 0.816155933 0.729093669 0.742276582 0.769134494 0.720128153 0.508052022 0.777840117 0.864460316 1 18.09966705 1.073267146 2.541018191 0.994631711 0.717459573 0.568696903 0.081192624 0.183329023 2.411363277 0.074602757 0.020313655 11.837695 -1.073267146 -0.277172138 KLES(ph)TESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.919)T(0.081)ESR;KLES(0.831)T(0.163)ES(0.006)R;KLES(0.84)T(0.159)ESR;KLES(0.855)T(0.145)ESR;KLES(0.496)T(0.496)ES(0.008)R 157.68 0.0002285 3025970000 5171150 5094240 4188590 4863940 4708420 2301915 3559080 2800480 3742610 TRUE FALSE 4847496.952 5471422.83 4287945.333 4988756.935 4338639.686 2966440.492 3025428.995 3150126.093 3117944.213 1.554709328 1.754817424 1.375247612 1.600014816 1.391506515 0.951409098 0.970328136 1.010321506 1 21.57216368 2.36085361 3.269684334 0.975100034 1.566165208 0.898401062 0.093773659 0.071743033 1.524979917 0.035897177 0.028927803 229.5374805 -2.36085361 0.591065174 KLEST(ph)ESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLESTESR 8 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 KLES(0.03)T(0.959)ES(0.011)R 129.89 0.00062783 600230000 347260 377170 321960 333400 382020 180400 283870 197760 296900 TRUE FALSE 325525.6165 405096.0592 329597.0432 341955.6084 352017.6902 232478.5515 241306.3288 222450.7713 247345.472 1.316076716 1.637774308 1.332537202 1.382501995 1.42318227 0.939894107 0.975584178 0.899352511 1 17.91616796 2.24214436 13.04832035 0.953772833 1.435025311 0.865400793 0.090936677 0.085813636 301.6436131 0.032284519 0.025733687 174.6402565 -2.24214436 0.481252477 KLESTESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 KLESTESR 8 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;;;; 175.73 0.00042398 22761510000 26840450 26235790 25967040 25211270 28523600 21829320 31016840 24564790 33223920 FALSE TRUE 25160554.15 28178315.19 26582990.45 25858233.87 26283471.51 28131090.31 26366152.79 27631758.11 27678633.12 0.909024446 1.018052989 0.960415579 0.934230883 0.949594274 1.016346804 0.952581462 0.998306455 1 24.72226936 2.277565215 24.99999446 0.985095266 0.96289051 0.215740061 0.032282159 384.0793798 246174.1596 0.011095998 0.009283461 189.4808022 -2.277565215 -0.022204755 KLEVEANNAFDQYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KLEVEANNAFDQYR 14 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;;; 268.61 5.10E-25 5782300000 4031835 4284560 4137500 3946560 4755470 3373330 4651610 4252340 4695340 FALSE TRUE 3779489.644 4601793.28 4235643.454 4047835.411 4381994.569 4347155.61 3954144.264 4783254.01 3911657.421 0.966211822 1.176430547 1.082825769 1.034813373 1.120239862 1.111333417 1.010861596 1.222820277 1 21.8993486 -1.081783577 4.277353861 0.999989157 1.091766286 0.124879497 0.075402521 6.95E-06 1.49E-06 0.065087314 0.015339415 0.082835486 1.081783577 0.091777129 KLFADAEEEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KLFADAEEEQR 11 1 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 ;;; 129.71 0.00038385 1014420000 1332540 1403100 1387100 1409210 1484250 1212020 1705850 1269830 1739860 FALSE TRUE 1249138.7 1506986.984 1420002.667 1445372.714 1367682.992 1561910.498 1450073.629 1428371.071 1449466.126 0.861792268 1.039684168 0.979672889 0.997175918 0.943577064 1.077576406 1.000419122 0.985446327 1 20.46709019 2.26822479 24.99999517 1.016440264 0.978225203 0.169690464 0.051769553 439.3673399 370282.6576 0.016772287 0.014030745 185.4491258 -2.26822479 -0.038215062 KLFADAEEEQRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLFADAEEEQRR 12 2 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 60.161 0.052815 111410000 49733 121810 91864 94896 124420 97769 60751 91669 92468 FALSE TRUE 46620.30031 130828.9391 94043.05746 97331.19202 114648.5551 125993.3232 51641.95153 103114.0764 77034.49343 0.605187342 1.698316343 1.220791535 1.26347546 1.488275576 1.635544255 0.67037439 1.338544227 1 16.23321696 1.741840631 25 0.984996921 1.355534627 0.156130313 0.337866632 0.825992816 6330.579372 0.140958684 0.078168827 55.18748864 -1.741840631 0.370537707 KLFAPQQILQCS(ph)PAN ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLFAPQQILQCSPAN 15 1 P04183;K7ERV3 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 1 KLFAPQQILQCS(1)PAN;KLFAPQQILQCS(1)PAN 248.81 2.04E-18 2489000000 2700070 2629540 2656940 2418420 3305100 2593340 3330500 2938880 5572200 TRUE FALSE 2531077.438 2824233.878 2719963.871 2480480.752 3045530.778 3341995.159 2831122.444 3305805.637 4642163.822 0.545236561 0.608387378 0.585925869 0.534337186 0.656058445 0.719921848 0.609871291 0.712126018 1 22.14636601 -4.999989135 0.182974058 2.632934667 0.538314758 0.890521487 0.044314246 40.2009987 0.389329857 23.7399772 0.128176377 1.00E-05 4.999989135 -2.094619908 KLFIGGLSFETTDDSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLFIGGLSFETTDDSLR 17 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 238.7 4.72E-20 801550000 517110 621500 570390 573590 710260 507030 646740 580880 751270 FALSE TRUE 484745.0082 667516.5067 583919.9202 588309.2905 654479.0447 653401.3301 549767.341 653404.1467 625878.1836 0.774503763 1.066527839 0.932960975 0.939974113 1.045697169 1.043975245 0.87839352 1.043979745 1 19.25552236 4.752723868 24.44993852 0.986296539 0.774503565 0.558681839 0.060956254 1439.927816 2485680.596 0.014120095 0.290644383 56587.93783 -4.752723868 -0.211792974 KLFIGGLSFETTDESLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 255.24 7.42E-27 1998573000 2195559 2560372 2338223 2388929 3098513 2012324 2867032 2396066 3339280 FALSE TRUE 2058142.881 2749944.607 2393686.754 2450232.963 2855168.288 2593249.271 2437147.168 2695220.114 2781932.595 0.739824856 0.988501523 0.860440241 0.880766474 1.026325473 0.932175451 0.876062623 0.968830129 1 21.40765603 4.749421504 24.83659218 0.930974741 0.739824737 0.547993878 0.056873526 1192.709497 2727420.844 0.01294836 0.19480466 56159.27649 -4.749421504 -0.191150004 KLFIGGLSFETTEESLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KLFIGGLSFETTEESLR 17 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;; 278.34 1.28E-35 2322930000 1645790 1966980 1782190 1760490 2427810 1409410 1985610 1926740 2899650 FALSE TRUE 1542782.942 2112617.246 1824464.388 1805667.154 2237139.596 1816283.787 1687886.214 2167297.73 2415679.683 0.638653772 0.874543616 0.755259235 0.747477891 0.926091159 0.751872775 0.698721037 0.897179268 1 21.20399774 1.011546614 5.823199177 0.999785424 0.779127958 0.477069898 0.081161468 0.113257132 14.50987752 0.073293192 0.01844787 10.26943649 -1.011546614 -0.220657466 KLFVGGIKEDTEEHHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLFVGGIKEDTEEHHLR 17 2 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 136.34 3.42E-06 732040000 245350 361580 256000 339260 593020 173170 352580 268450 928920 FALSE TRUE 229993.9815 388351.7594 262072.4409 347965.986 546446.6013 223161.3678 299713.9022 301966.5734 773877.2509 0.297196979 0.501826044 0.338648591 0.449639766 0.706115344 0.288367913 0.387288684 0.390199574 1 19.56174522 -2.011316553 2.898960879 1.624438714 0.42099448 0.696347717 0.120383222 47658264.05 19053000.44 198361297.6 0.027136918 0.009742792 2.011316553 -1.203444234 KLFVGGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLFVGGLK 8 1 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ; 131.06 0.0030715 0 6313600 7445600 5740900 5456300 8934100 4451800 7581500 7949800 9436200 FALSE TRUE 5918443.046 7996879.971 5877076.859 5596317.895 8232451.824 5736962.391 6444724.458 8942350.03 7861237.26 0.752864066 1.017254626 0.74760202 0.711887672 1.047220883 0.729778558 0.81981045 1.137524506 1 22.90632496 1.246153416 24.95655569 1.068762273 0.83929113 0.401981278 0.11964902 146.5868217 481823.695 0.077837589 0.027220667 17.62598581 -1.246153416 -0.229471143 KLGAGEGGEASVS(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KLGAGEGGEASVSPEK 16 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 KLGAGEGGEAS(0.061)VS(0.939)PEK;KLGAGEGGEAS(0.003)VS(0.997)PEK;KLGAGEGGEAS(0.06)VS(0.94)PEK;KLGAGEGGEAS(0.001)VS(0.999)PEK 195.15 5.98E-11 5557870000 8951270 4429350 6074760 5394440 5669920 4335330 7908140 5315160 5883230 TRUE FALSE 8391025.989 4757303.683 6218856.176 5532870.463 5224627.355 5586869.393 6722387.823 5978769.426 4901280.906 1.712006749 0.970624572 1.268822639 1.128862142 1.065971826 1.139879452 1.371557344 1.219838149 1 22.2247274 4.751481324 24.79775854 1.164056824 1.71200714 0.679942933 0.121526626 1211.815424 2325701.392 0.029398387 0.540722792 56426.2676 -4.751481324 0.547950315 KLGAGEGGEASVS(ph)PEKTSTTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KLGAGEGGEASVSPEKTSTTSK 22 2 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 KLGAGEGGEAS(0.018)VS(0.982)PEKTSTTSK;KLGAGEGGEAS(0.205)VS(0.792)PEKT(0.003)STTSK;KLGAGEGGEAS(0.029)VS(0.971)PEKTSTTSK;KLGAGEGGEAS(0.02)VS(0.98)PEKTSTTSK;KLGAGEGGEAS(0.002)VS(0.998)PEKTSTTSK 231.68 5.12E-27 4474910000 3451610 2026150 2366820 2606600 3509550 1475160 3292160 2151510 5705960 TRUE FALSE 3235579.891 2176168.254 2422962.088 2673489.769 3233924.1 1901014.745 2798531.171 2420130.76 4753598.414 0.680659073 0.457793878 0.509711144 0.562413889 0.680310749 0.399910674 0.588718467 0.509115527 1 22.1805886 -1.553469226 2.829790213 1.025150452 0.538411167 0.717937927 0.088719517 14308545.35 14644950.48 2724094.461 0.019393895 0.027959588 1.553469226 -0.486739284 KLGCEVLGVSVDSQFTHLAWINTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KLGCEVLGVSVDSQFTHLAWINTPR 25 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ;;; 359.82 1.22E-103 1980915000 1335790 1895720 1410570 1248670 2067750 1292200 1846850 1734630 1457990 FALSE TRUE 1252185.288 2036081.081 1444029.387 1280712.986 1905357.256 1665237.163 1569931.988 1951202.374 1214642.05 1.030908891 1.676280746 1.188851799 1.054395397 1.568657413 1.370969466 1.292505877 1.60640114 1 20.21209979 -1.050220869 4.492661477 0.999981525 1.357585598 0.196345109 0.220996391 0.510448385 60354682.06 2552.071914 0.047183609 0.089079779 1.050220869 0.357604073 KLGEMWNNTAADDKQPYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLGEMWNNTAADDKQPYEK 19 2 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 180.86 1.57E-13 389100000 412710 263460 316490 299640 403020 223790 404600 266380 558810 FALSE TRUE 386879.2178 282966.8525 323997.2923 307329.2697 371368.4349 288394.5401 343933.9861 299638.1294 465541.0009 0.83103146 0.607823697 0.695958662 0.660155108 0.797713701 0.619482579 0.738783449 0.643634242 1 18.82854871 -1.204768371 4.316288012 1.000111259 0.692476308 0.623240284 0.073297926 6.98E-05 1.29E-05 0.06179674 0.014560271 0.062406759 1.204768371 -0.307634952 KLGEMWSEQSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLGEMWSEQSAK 12 1 P26583 P26583 HMGB2 High mobility group protein B2 0 183.89 2.41E-05 517410000 690520 585360 596120 562420 751830 431290 715440 521860 876430 FALSE TRUE 647301.5858 628700.6635 610260.2479 576852.6494 692784.3045 555796.4216 608166.4138 587015.3698 730148.171 0.886534558 0.861059013 0.835803296 0.790048749 0.948827008 0.761210455 0.832935612 0.803967459 1 19.47782974 -1.126994545 5.177023509 1.000004858 0.839299329 0.481082664 0.052202081 2.62E-06 4.42E-07 0.045244718 0.01066396 0.074645813 1.126994545 -0.160705529 KLGEWVGLCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLGEWVGLCK 10 1 P25398 P25398 RPS12 40S ribosomal protein S12 0 106.01 0.0039663 795790000 2237200 2419600 2302100 2356100 3215500 1908500 3174600 2726800 4205100 FALSE TRUE 2097177.646 2598749.702 2356706.899 2416561.515 2962967.601 2459452.968 2698598.202 3067246.982 3503241.644 0.598639163 0.74181286 0.672721764 0.689807259 0.845778825 0.70205062 0.770314605 0.875545365 1 21.74025907 -1.267469666 0.150068338 1.32390492 0.58774376 0.75999496 0.056646636 15.01794788 0.426845068 2.182090588 0.356078346 0.054016984 1.267469666 -0.736161159 KLGGSLADSYLDEGFLLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLGGSLADSYLDEGFLLDK 19 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 149.34 1.39E-07 333860000 602620 434860 532670 518640 586060 403340 662510 502890 563390 FALSE TRUE 564903.0899 467057.4869 545305.1839 531949.1805 540033.2117 519777.7103 563172.7759 565676.9235 469356.5694 1.203569156 0.995101629 1.161814321 1.133358336 1.150581982 1.10742609 1.19988259 1.205217867 1 18.84032483 3.733176804 24.14077738 1.146908827 1.082648776 0.017668369 0.07605026 321.705595 1282476.23 0.017531449 0.030601118 5409.745128 -3.733176804 -0.064260051 KLGGSLADSYLDEGFLLDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLGGSLADSYLDEGFLLDKK 20 2 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 179.58 3.25E-17 437990000 430660 304370 374950 367430 407450 240960 470070 300750 605820 FALSE TRUE 403705.7594 326905.8715 383843.9911 376858.8759 375450.5206 310521.2403 399587.3674 338299.2995 504704.7283 0.799885035 0.647717077 0.760531791 0.746691788 0.743901334 0.615253282 0.791725033 0.67029152 1 18.94508008 -1.836013412 2.696593205 1.100886743 0.720708966 0.674790028 0.060646168 15670151.72 9920375.625 10192678.13 0.013497732 0.014587692 1.836013412 -0.380177777 KLGPGRPLPTFPTSECTS(ph)DVEPDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLGPGRPLPTFPTSECTSDVEPDTR 25 2 Q8TDD1-2;Q8TDD1;H0YHZ9 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 KLGPGRPLPTFPTSECT(0.043)S(0.957)DVEPDTR;KLGPGRPLPTFPTS(0.001)ECT(0.199)S(0.796)DVEPDT(0.004)R 196.45 4.49E-25 770430000 748266 921437 817790 869682 1036357 680968 1117660 735031 1305030 TRUE FALSE 701433.3668 989661.1542 837188.365 891999.5125 954965.7017 877552.407 950077.2588 826801.2384 1087212.062 0.64516702 0.910274259 0.770032263 0.820446667 0.878361945 0.807158454 0.873865635 0.760478353 1 20.05220194 -5 0.234090831 1.974555158 0.800798758 0.389047123 0.074976604 172.2347866 1.722365643 79.87254217 0.111056251 1.00E-05 5 -1.173756401 KLGQSESQGPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLGQSESQGPPR 12 1 F5H169;F5H5V4;F5GX23;J3KN29;O00233-2;O00233 F5H169 PSMD9 26S proteasome non-ATPase regulatory subunit 9 0 98 0.0073846 68277000 66634 68842 67369 64691 74279 51111 76943 57413 84264 FALSE TRUE 62463.49689 73939.13331 68967.02449 66351.08058 68445.42697 65865.91598 65406.11145 64581.13943 70199.79403 0.889796014 1.053267098 0.982439129 0.945174861 0.975008943 0.938263664 0.931713723 0.91996195 1 16.09917918 3.322979586 4.151619909 0.947259555 0.994480898 0 0.046020576 0.355742684 11.47179621 0.012165638 0.016615325 2103.679556 -3.322979586 0.047221343 KLGSSLDWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLGSSLDWDR 10 1 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 116.24 0.0017907 253440000 493210 931160 424040 454600 1079100 300540 448530 882860 1120300 FALSE TRUE 462340.8665 1000104.055 434098.429 466265.8056 994351.8389 387301.0191 381277.0904 993087.0144 933314.6926 0.495375108 1.071561461 0.465114749 0.499580484 1.065398249 0.414973666 0.408519327 1.064043052 1 19.83200408 1.21794717 24.99749164 1.032022093 0.645994244 0.312530598 0.246230116 358.0167499 434148.0382 0.232899781 0.058491574 16.51760857 -1.21794717 -0.386027849 KLHELTVMQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLHELTVMQDR 11 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 131.13 0.00013615 117730000 386290 395900 400330 367610 430410 299110 444730 355710 466900 FALSE TRUE 362112.7984 425212.8479 409826.0166 377043.495 396607.3348 385458.2014 378046.8652 400121.1765 388971.3737 0.930949738 1.0931726 1.053614853 0.969334816 1.019631165 0.990968044 0.971914364 1.028664842 1 18.56930446 3.250005686 24.8425117 0.994427673 1.044282801 0.034580267 0.0451031 299.4567054 649991.3789 0.011775571 0.015809496 1778.302692 -3.250005686 0.049855128 KLITS(ph)EEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KLITSEEER 9 1 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 KLIT(0.191)S(0.809)EEER;KLIT(0.097)S(0.903)EEER;KLIT(0.086)S(0.914)EEER;KLIT(0.136)S(0.864)EEER 124.45 0.00070905 176870000 1130440 1156810 1050840 1146850 1357890 895710 1235780 1116000 1451090 TRUE FALSE 1059687.778 1242461.416 1075766.421 1176280.113 1251246.797 1154286.936 1050486.261 1255335.057 1208893.705 0.876576472 1.027767298 0.889876767 0.973021952 1.035034587 0.95482914 0.868964953 1.038416407 1 20.20525597 4.777454719 22.99595483 0.961812079 0.876575822 0.189666055 0.058696838 15426.80006 9120488.465 0.013672534 3.569201534 59903.8477 -4.777454719 -0.085236258 KLITS(ph)EEERS(ph)PAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLITSEEERSPAKR 14 3 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 KLIT(0.122)S(0.878)EEERS(1)PAKR;KLIT(0.11)S(0.89)EEERS(1)PAKR 88.036 0.0096262 359910000 503820 305080 366810 365040 450940 251780 493510 333980 761700 TRUE FALSE 472286.8055 327668.4406 375510.9064 374407.5444 415524.9914 324464.7987 419512.757 375678.1382 634567.3492 0.744265847 0.516365112 0.591758947 0.590020184 0.654816218 0.511316567 0.661100445 0.592022484 1 19.27541377 -1.204959158 0.614049845 1.131787991 0.594354513 0.757294228 0.069469862 17.32299712 3.13308768 3.986043129 0.024292388 0.06237935 1.204959158 -0.537433477 KLKDVLLQVDDERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLKDVLLQVDDERR 14 3 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 111.43 0.00028556 1148680000 400460 771300 612480 699040 964940 532640 902840 577230 1716100 FALSE TRUE 375395.9234 828407.8545 627008.3148 716978.5499 889157.5048 686404.5213 767467.5236 649298.4361 1429671.824 0.262574891 0.57943917 0.438568002 0.501498692 0.621931194 0.480113345 0.536813771 0.454159077 1 20.44725259 -5 0.318485028 5.715239998 0.47374712 0.742499261 0.095616539 152.1356445 1.352901146 483.2345841 0.076949605 1.00E-05 5 -5.241492878 KLKDYAFVHFEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLKDYAFVHFEDR 13 2 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 90.334 0.0042271 87504000 101220 156380 133260 124580 209400 114100 207060 128980 400940 FALSE TRUE 94884.82088 167958.5379 136420.9901 127776.9337 192954.5687 147038.8177 176013.2753 145083.4369 334020.5238 0.284068834 0.502838975 0.408420981 0.382542163 0.577672792 0.440208931 0.526953473 0.434354857 1 18.34957723 -5 0.261303072 4.56598308 0.40901681 0.840235206 0.076896439 69.02950909 0.677544826 132.1736423 0.090503564 1.00E-05 5 -4.15696627 KLLDIVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLLDIVAR 8 1 Q12931-2;Q12931 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 136.57 0.0012594 226250000 194240 245340 159100 158970 326390 122150 158300 249640 320360 FALSE TRUE 182082.8651 263505.2289 162873.9271 163049.4393 300756.646 157412.7221 134564.3846 280808.1035 266889.8464 0.682239761 0.987318298 0.61026648 0.6109241 1.126894298 0.589804087 0.50419447 1.052149819 1 18.02588489 1.208365758 24.99904361 1.026075638 0.734577931 0.293965876 0.190516445 312.9277579 259073.0698 0.181475503 0.045392024 16.15718725 -1.208365758 -0.291497707 KLLEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLLEDR 6 1 P35579;Q9Y6N9-5;Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 P35579;Q7Z406 MYH9;MYH14 Myosin-9;Myosin-14 0 102.72 0.056601 835100000 2408700 2732600 2436500 2422700 2828200 1942100 3074000 2524700 3073200 FALSE TRUE 2257943.767 2934924.547 2494294.931 2484870.584 2606084.58 2502752.743 2613082.238 2839914.353 2560263.066 0.881918658 1.146337103 0.974233845 0.970552837 1.01789719 0.977537338 1.020630369 1.109227559 1 21.28786062 1.453185065 21.37555899 1.058052434 1.009114091 0.086127652 0.07053419 9.886654993 8833.453607 0.036024212 0.016648787 28.39128602 -1.453185065 -0.048938343 KLLEGEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KLLEGEEER 9 1 P20700;E9PBF6;P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8;Q03252 P20700;P02545;P02545-2;Q03252 LMNB1;LMNA;LMNB2 Lamin-B1;Prelamin-A/C;Lamin-A/C;Lamin-B2 0 ;;;;;;; 188.28 6.34E-05 14255340000 23080500 22510200 21839000 21521800 24234700 18277800 26490300 20156100 27574800 FALSE TRUE 21635932.7 24176878.63 22357031.39 22074085.82 22331404.42 23554304.14 22518325.44 22672633.45 22972387.74 0.941823416 1.052432116 0.973213218 0.96089645 0.972097662 1.025331124 0.980234432 0.98695154 1 24.45339748 KLLELDPEHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLLELDPEHQR 11 1 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 138.75 3.31E-05 321860000 1336570 1762080 1383340 1597890 1824050 988310 1733800 1401750 1127630 FALSE TRUE 1252916.47 1892546.237 1416153.478 1638894.563 1680796.471 1273619.053 1473832.786 1576761.573 939421.2682 1.33371099 2.014587385 1.507474363 1.744578942 1.789182902 1.355748583 1.56887313 1.678439297 1 19.84141273 -2.580769832 0.252652284 6.21E-17 1.722984584 0.46567572 0.206231248 36.73908061 1.079262086 20.44719665 0.28237106 0.00262561 2.580769832 1.722984584 KLLEPVDHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLLEPVDHGK 10 1 A0A0C4DG89;Q7L014;D6RJA6 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 99.522 0.0030105 166580000 269160 256920 256250 245490 290380 195260 319760 270690 417390 FALSE TRUE 252313.7561 275942.6241 262328.371 251789.689 267574.7261 251628.3922 271814.9565 304486.2424 347724.9126 0.725613112 0.793565874 0.754413508 0.724105981 0.769501167 0.723642118 0.781695377 0.875652653 1 18.40758691 1.019144662 2.039990234 0.999025273 0.753748743 0.930212879 0.022611012 0.074726273 0.656049515 0.020912024 0.005852735 10.45068271 -1.019144662 -0.24527653 KLLEQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLLEQER 7 1 Q63HQ0;Q96BQ5 Q63HQ0 AP1AR;CCDC127 AP-1 complex-associated regulatory protein;Coiled-coil domain-containing protein 127 0 74.301 0.074644 431430000 368810 726990 383650 501390 1154400 353270 585180 839620 1251000 FALSE TRUE 345726.8404 780817.096 392750.3592 514256.5163 1063738.081 455253.3141 497437.6915 944448.4052 1042200.018 0.331727916 0.749200808 0.376847392 0.493433609 1.020665959 0.436819522 0.4772958 0.906206475 1 19.99120075 1.14803061 5.238492145 0.987095834 0.560507373 0.407110757 0.200576198 0.199932225 8.403999859 0.178617855 0.045498619 14.06146628 -1.14803061 -0.426588461 KLLLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLLLNR 6 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-4 Q04637-9;A0A0A0MSA7 EIF4G1;EIF4G3 Eukaryotic translation initiation factor 4 gamma 1;Eukaryotic translation initiation factor 4 gamma 3 0 99.511 0.062077 316090000 159110 400810 164440 174040 426470 130440 211220 353810 465090 FALSE TRUE 149151.5891 430486.3894 168340.5945 178506.161 392976.7665 168095.9105 179549.5219 397983.9573 387463.4744 0.384943611 1.111037344 0.434468293 0.460704487 1.014229192 0.433836791 0.463397284 1.027152193 1 18.56370079 1.222808827 24.86938436 1.013576607 0.636411029 0.298396761 0.252596519 343.3660161 542100.2723 0.231108837 0.058584115 16.70355176 -1.222808827 -0.377165578 KLLVLDVDYTLFDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLLVLDVDYTLFDHR 15 1 Q8WVY7 Q8WVY7 UBLCP1 Ubiquitin-like domain-containing CTD phosphatase 1 0 96.993 0.0022627 66249000 74722 94834 84698 88949 105770 75172 95331 77327 96158 FALSE TRUE 70045.2834 101855.608 86707.07656 91231.58193 97463.25086 96872.93608 81037.00156 86981.44617 80108.6086 0.874378979 1.271468945 1.082369025 1.138848665 1.216638918 1.209269987 1.011589178 1.085793995 1 16.28966966 1.695124918 8.74189121 1.037627542 1.145868991 0.147779911 0.109090278 0.193571959 27.74300385 0.047961541 0.025533306 49.55927196 -1.695124918 0.108241448 KLLYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLLYEK 6 1 H7C4X7;P05408-2;P05408 REV__J3KTF2 SCG5 Neuroendocrine protein 7B2;N-terminal peptide;C-terminal peptide 0 ; 105.12 0.053316 2607100000 1633660 1777780 1647500 1610340 1913270 1153330 2002610 1708340 1996530 FALSE TRUE 1531412.137 1909408.681 1686579.478 1651664.051 1763009.492 1486277.648 1702337.222 1921630.01 1663296.245 0.920709189 1.147966688 1.013998248 0.993006541 1.059949181 0.893573621 1.023472053 1.155314344 1 20.66561372 5.038298175 12.981266 1.033904505 0.565109779 0.186107503 0.075607813 810038.9495 9375522.531 0.0176999 8316045.498 109218.9948 -5.038298175 -0.468794726 KLMHQAALLGQALQDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLMHQAALLGQALQDSR 17 1 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881;E9PKD3;A0A0B4J225;E9PIZ5 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 196.87 1.01E-11 330270000 252660 373750 276820 299840 522400 216170 296700 320640 687550 FALSE TRUE 236846.4616 401422.8389 283386.3011 307534.402 481372.8113 278574.7698 252212.5894 360672.6098 572793.4633 0.413493653 0.700816026 0.4947443 0.536902779 0.840395085 0.486344184 0.4403203 0.629673055 1 19.1276555 -1.778759682 2.880840263 1.099729557 0.567287889 0.527302007 0.128590806 29418620.31 21710799.83 20551608.11 0.029631875 0.016643334 1.778759682 -0.532441668 KLNCQVIGASVDSHFCHLAWVNTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KLNCQVIGASVDSHFCHLAWVNTPK 25 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;; 233.26 1.52E-38 1836710000 1806080 2073950 1754160 1708130 2461560 1504450 2393200 2175250 2377620 FALSE TRUE 1693040.677 2227507.416 1795769.504 1751963.508 2268239.007 1938760.292 2034361.877 2446834.751 1980779.862 0.854734395 1.124560815 0.906597214 0.884481684 1.145124226 0.978786351 1.027050969 1.235288584 1 20.91763712 1.977175354 1.120324315 1.094187821 0.978400482 0.186093346 0.109903266 0.959122843 2.219853555 0.080799402 0.037054514 94.88014816 -1.977175354 -0.115787339 KLNIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLNIAR 6 1 A0A5F9ZHD4;A0A5F9ZI66;A0A5F9ZHJ0;A0A5F9ZHL1;P24752;A0A5F9ZHJ7 A0A5F9ZHD4 ACAT1 "Acetyl-CoA acetyltransferase, mitochondrial" 0 ; 136.58 0.021019 1250770000 2100500 3074300 1833410 1797100 4256000 1506680 1851300 3321700 4986400 FALSE TRUE 1969033.454 3301924.371 1876899.351 1843216.628 3921750.928 1941634.057 1573714.752 3736421.557 4154137.627 0.473993313 0.794851945 0.451814437 0.443706202 0.944058979 0.467397624 0.378830673 0.89944578 1 21.98611758 1.091993406 6.149013964 0.996425864 0.571620127 0.457721088 0.175617261 0.174055678 8.722692072 0.164140578 0.041285778 12.35928669 -1.091993406 -0.424805737 KLNQGTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLNQGTER 8 1 E7EMD0;P16435;H0Y4R2 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 ; 118.18 0.0031054 191347000 214185 276060 170985 175244 360770 172772 233677 309850 377320 FALSE TRUE 200779.5432 296499.7696 175040.8449 179741.0577 332436.5795 222648.4717 198639.3032 348535.4546 314342.8544 0.638727874 0.943236869 0.556846903 0.571799407 1.057560478 0.70829818 0.631919258 1.108774861 1 18.26197944 1.233440836 24.99998113 1.054387586 0.733284502 0.413685751 0.160623383 131.7120077 643116.1229 0.132706368 0.037151223 17.11751967 -1.233440836 -0.321103084 KLNSSSSSSSNSSNEREDFDSTSSSSS(ph)TPPLQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLNSSSSSSSNSSNEREDFDSTSSSSSTPPLQPR 34 2 A0A669KAX4;Q13620-1;K4DI93;Q13620;A0A669KAU9 A0A669KAX4 CUL4B Cullin-4B 1 KLNSSSSSSSNSSNEREDFDST(0.001)S(0.001)S(0.019)S(0.003)S(0.099)S(0.512)T(0.365)PPLQPR 186.71 2.50E-20 106530000 69457 76054 72583 63511 88837 65631 93974 76585 109970 TRUE FALSE 65109.81035 81685.11729 74304.70304 65140.79978 81860.10037 84577.60427 79883.47111 86146.80583 91615.29657 0.71068711 0.89161003 0.811051274 0.711025366 0.893520006 0.923182126 0.871944687 0.940310287 1 16.48330088 2.50531474 20.87656724 0.916529209 0.804282388 0.561787136 0.062087605 84.6031351 62646.3437 0.019531544 0.018344767 320.1214238 -2.50531474 -0.112246821 KLNTTTMSNATANSSIRPIFGGTVYHS(ph)PVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLNTTTMSNATANSSIRPIFGGTVYHSPVSR 31 2 O43663-2;O43663-4;O43663;O43663-3;G3V3N7 O43663-2 PRC1 Protein regulator of cytokinesis 1 1 KLNTTTMSNATANSSIRPIFGGT(0.001)VY(0.001)HS(0.998)PVS(0.001)R;KLNTTTMSNATANSSIRPIFGGTVYHS(0.999)PVS(0.001)R 350.62 9.15E-121 693840000 185428 212600 210440 200585 251510 185675 263570 200804 342140 TRUE FALSE 173822.3925 228341.1252 215431.7362 205732.3507 231757.4191 239276.3583 224050.1254 225874.8214 285034.6237 0.609829045 0.801099608 0.755809008 0.721780211 0.813085148 0.839464186 0.786045297 0.792446961 1 18.12077765 -5 0.121298803 1.748157202 0.660372395 0.708205766 0.052649859 87.21094674 0.683980244 15.99886184 0.466359587 1.00E-05 5 -1.087784807 KLNVTEQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KLNVTEQEK 9 1 P06733;K7EM90;A0A2R8YEM5;A0A2R8Y879;A0A2R8Y6I8 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;;; 195.27 5.04E-05 19046150000 28867910 23942690 22296090 20290820 30021600 14771310 31481000 26094100 33927200 FALSE TRUE 27061119.04 25715431.68 22824963.78 20811516.79 27663824.64 19035547.4 26760716.31 29352005.83 28264531.14 0.957423242 0.909812781 0.807547936 0.736312118 0.978746985 0.673478265 0.946794984 1.038474888 1 24.75248943 1.504861027 7.595360347 1.010893564 0.845984881 0.385211463 0.093258614 0.113548428 14.7654278 0.047234005 0.021677847 31.97871635 -1.504861027 -0.164908683 KLNVTEQEKIDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLNVTEQEKIDK 12 2 P06733;K7EM90;A0A2R8YEM5;A0A2R8Y879 P06733 ENO1 Alpha-enolase;Enolase 0 ; 220.19 1.70E-11 5544400000 5451600 3455000 3873500 3672800 5130900 2365500 5232800 3563400 8805700 FALSE TRUE 5110394.087 3710811.795 3965381.249 3767050.266 4727939.811 3048381.449 4448190.219 4008298.334 7335971.783 0.696621285 0.505837796 0.540539327 0.51350392 0.644487186 0.415538873 0.606353235 0.546389552 1 22.80655666 -0.272264321 1.275633807 1.002810132 0.549969075 0.757934365 0.078241437 16.29844303 15.34638454 0.313004761 0.01944443 0.534239111 0.272264321 -0.452841058 KLPDIFQSYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLPDIFQSYDR 11 1 Q658Y4;E7ER68;P0C866 Q658Y4 FAM91A1;LINC00869 Protein FAM91A1;Putative uncharacterized protein encoded by LINC00869 0 109.22 0.0031393 157820000 252800 347340 237180 230820 394410 188650 237600 335470 337660 FALSE TRUE 236977.6993 373057.415 242806.0216 236743.232 363434.6296 243110.1925 201974.0858 377354.168 281302.3646 0.842430527 1.326179449 0.863149593 0.841597021 1.29197147 0.864230888 0.717996402 1.341453949 1 18.10176215 3.858974695 7.795273725 0.961289113 1.115048375 0.014947151 0.227760477 0.631890788 38.8342866 0.055112368 0.099805264 7227.276906 -3.858974695 0.153759261 KLPEEHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLPEEHAR 8 1 P41743;E9PBE1;Q05513-2;Q05513-3;Q05513 P41743;Q05513 PRKCI;PRKCZ Protein kinase C iota type;Protein kinase C zeta type 0 123.35 0.00087711 87677000 152450 182150 174020 179840 212970 135260 182190 184480 226370 FALSE TRUE 142908.4266 195636.5755 178147.8366 184454.9989 196244.1953 174307.3662 154872.3009 207512.7341 188587.3846 0.757783597 1.03737891 0.944643445 0.978087687 1.040600864 0.924279037 0.821223017 1.10035321 1 17.52487365 7.9998936 0.007422117 1.822799608 0.000151116 0.075050626 0.099137455 119499.1667 68.590859 7540.669564 9397.924679 99975503.45 -7.9998936 -1.822648492 KLPEYNPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLPEYNPR 8 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 101.65 0.0084132 425960000 487800 551700 374250 385370 543260 270920 394940 414850 558150 FALSE TRUE 457269.4687 592548.442 383127.3867 395259.2466 500594.551 349130.206 335722.4134 466644.9357 464991.1592 0.983393898 1.274321953 0.823945529 0.850036046 1.07656789 0.750831922 0.721997412 1.003556576 1 18.82684376 3.875089123 4.468171427 0.867618166 1.136186482 0.347462421 0.133211509 0.193978567 6.554817356 0.033351252 0.062970049 7500.48114 -3.875089123 0.268568317 KLPFPDETHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLPFPDETHER 11 1 E9PLG8;E9PLV6;E9PPZ9;O43292-2;O43292 E9PLG8 GPAA1 Glycosylphosphatidylinositol anchor attachment 1 protein 0 122.39 0.00025429 45354000 115810 126640 100120 100270 132660 94895 139240 125800 101570 FALSE TRUE 108561.6588 136016.5574 102494.8937 102843.098 122241.4187 122289.646 118362.2546 141506.4069 84617.31083 1.282972216 1.607431813 1.211275715 1.215390763 1.444638426 1.445208372 1.398794803 1.672310376 1 16.36866522 -1.001855018 4.25398012 0.999978077 1.405972744 0.422347266 0.150541629 7826772.461 3686567.18 1570.884053 0.033526106 0.099573777 1.001855018 0.405994667 KLPGDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLPGDDR 7 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 0 ; 77.282 0.061682 206349000 1080100 1075210 1059100 1049520 1215200 827770 1234520 1027290 1160770 FALSE TRUE 1012498.469 1154819.667 1084222.352 1076452.46 1119763.094 1066733.761 1049415.187 1155549.418 967029.9881 1.047018688 1.194192198 1.121187932 1.113153132 1.157940403 1.103103083 1.085194047 1.194946829 1 19.8832011 -1.724764274 2.579850523 0.974902289 1.128752295 0.429367021 0.046009883 6327389.666 4923021.197 1021460.66 0.010284596 0.018846718 1.724764274 0.153850006 KLPIDVTEGEVISLGLPFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLPIDVTEGEVISLGLPFGK 20 1 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;K7ES59;K7EKJ7;K7ELW5 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 166.06 2.53E-11 293720000 1502100 1380600 1426300 1395200 1676200 1112300 1845800 1381200 2052200 FALSE TRUE 1408086.242 1482821.061 1460132.51 1431003.194 1544558.013 1433402.953 1569039.426 1553645.86 1709674.562 0.82359899 0.867311881 0.854041197 0.837003267 0.903422235 0.838406902 0.917741575 0.908737777 1 20.7052903 0.817625164 0.527908567 1.004872962 0.848386972 0.801778953 0.023320053 0.464600361 0.29430535 0.024953018 0.010539169 6.570904631 -0.817625164 -0.15648599 KLPIQEFHLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLPIQEFHLSR 11 1 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 ; 179.35 4.64E-06 1494070000 419860 1143150 785730 785980 1176620 683430 999810 1101300 1185560 FALSE TRUE 393581.7121 1227790.015 804367.8866 806149.5775 1084213.011 880725.1464 849897.7723 1238799.729 987682.377 0.398490164 1.243102078 0.814399351 0.816203262 1.097734491 0.89170888 0.860497051 1.254249097 1 19.91368764 4.756046961 24.47868902 0.978406716 0.398489531 0.57286432 0.161756218 2078.566299 2909668.687 0.036641099 1.094202731 57022.59291 -4.756046961 -0.579917185 KLPKNEPQNATGAPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLPKNEPQNATGAPGR 16 2 P51148;P51148-2 P51148 RAB5C Ras-related protein Rab-5C 0 78.234 0.012207 186370000 262870 268070 344960 343800 377100 413740 426070 244020 326040 FALSE TRUE 246417.4359 287918.1817 353142.6141 352622.4901 347484.0871 533180.0215 362184.7589 274486.4342 271621.8177 0.907207816 1.059996521 1.300126098 1.298211215 1.279293726 1.962949906 1.333415563 1.010546342 1 18.05123984 4.21370018 1.025890777 1.376381649 0.857099977 0.198756596 0.265757961 1.263483918 1.843780967 0.083743213 0.597394311 16356.86918 -4.21370018 -0.519281673 KLPS(ph)DSGDLEALEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KLPSDSGDLEALEGK 15 1 O60524-4;O60524-3;O60524;G3V5V3;O60524-5;O60524-2 O60524-4 NEMF Nuclear export mediator factor NEMF 1 KLPS(0.84)DS(0.16)GDLEALEGK;KLPS(0.963)DS(0.037)GDLEALEGK;KLPS(0.98)DS(0.02)GDLEALEGK;KLPS(0.947)DS(0.053)GDLEALEGK 178.32 4.39E-07 655580000 1991920 1040510 1563400 1874090 1471310 760420 1175090 688830 883190 TRUE FALSE 1867249.283 1117550.443 1600484.586 1922182.322 1355759.248 979940.9096 998896.1635 774831.9418 735779.8834 2.537782461 1.518865177 2.175221996 2.612442071 1.842615269 1.331839769 1.357601894 1.053075735 1 19.48891471 2.279649028 3.075587022 1.212994536 2.100273289 0.696989755 0.316368586 0.166258758 3.238474663 0.12715944 0.096658656 190.3921455 -2.279649028 0.887278753 KLPVDSVFNKFEDEDSDDVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLPVDSVFNKFEDEDSDDVPR 21 2 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 112.45 0.00012623 530590000 630470 453340 518090 525120 539630 361040 635940 480100 742500 FALSE TRUE 591010.0081 486905.7653 530379.3395 538595.4682 497249.6366 465266.387 540586.7008 540041.5418 618571.9533 0.955442621 0.787144911 0.857425457 0.870707871 0.803867091 0.752162112 0.87392695 0.873045632 1 19.2385819 0.783944259 1.738912763 0.99945859 0.834948231 0.43851693 0.055377839 0.652079796 3.394046712 0.048351565 0.013709242 6.080569529 -0.783944259 -0.164510358 KLPVESIQIVLEELRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLPVESIQIVLEELRK 16 2 K7ENE3;Q9BRG1;K7EKV4 K7ENE3 VPS25 Vacuolar protein-sorting-associated protein 25 0 103.01 0.00082818 26396000 77449 71669 81505 84416 92664 65330 97222 69265 99480 FALSE TRUE 72601.60534 76975.44733 83438.33709 86582.25748 85386.54323 84189.71046 82644.46366 77912.88772 82876.14533 0.876025363 0.928801008 1.006783517 1.044718684 1.030290959 1.015849737 0.997204483 0.94011235 1 16.33866928 4.331408548 1.560720688 1.007358832 0.871136308 0.717701364 0.027662469 0.297333545 1.136894124 0.007798168 0.049060769 21449.07403 -4.331408548 -0.136222524 KLQELSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLQELSSK 8 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 168.83 0.00048835 8303800000 13196500 12256300 11386200 11649800 15597200 9004400 15941200 13698300 17786000 FALSE TRUE 12370554.62 13163769.2 11656286.04 11948753.59 14372258.83 11603824.11 13550965.05 15408562.91 14817401.7 0.834866657 0.888399294 0.786661945 0.806400058 0.969958102 0.783121383 0.914530451 1.039896415 1 23.82078915 1.422255149 3.883906645 1.017252319 0.846501138 0.627191267 0.055243848 0.135426597 3.556499989 0.037590248 0.013243871 26.43961635 -1.422255149 -0.170751182 KLQIQCVVEDDKVGTDLLEEEITKFEEHVQSVDIAAFNK ddPTM_SK-BR-3_Pertuzumab_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 79.422 0.00086855 336660000 1392200 512490 728350 745130 773820 531450 1035700 545460 730950 FALSE TRUE 1305064.687 550435.2928 745626.806 764251.2973 713047.2986 684870.9876 880406.4 613561.8817 608949.7229 2.143140292 0.903909259 1.224447237 1.25503185 1.170946093 1.124675752 1.445778472 1.007573957 1 19.21596359 4.748061074 24.99357321 1.164873113 2.143140813 0.806967138 0.153574662 580.5731591 1527326.535 0.036645614 0.476681856 55983.63247 -4.748061074 0.9782677 KLS(ph)ASSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLSASSPR 8 1 A0A0A0MRY2;B0QZE2;B7Z2J6;E7ENI9;J3QKD2;Q15326-5;Q15326-2;Q15326;Q15326-4;Q15326-6;Q15326-3 A0A0A0MRY2 ZMYND11 Zinc finger MYND domain-containing protein 11 1 KLS(0.995)AS(0.005)SPR;KLS(0.998)AS(0.002)SPR 130.94 0.00062866 1218510000 730320 803860 659070 651140 894570 491480 698570 674440 718730 TRUE FALSE 684610.5749 863378.6308 674703.4516 667849.3548 824314.0807 633362.2975 593825.9137 758645.3186 598769.3198 1.143362815 1.441921959 1.126817005 1.115370031 1.376680557 1.057773464 0.991744056 1.267007666 1 19.19164078 2.659209153 0.386830714 1.02409347 1.326880498 0.189905486 0.135801575 1.987464542 0.614503232 0.140538293 0.227483667 456.2565925 -2.659209153 0.302787028 KLS(ph)CSLEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLSCSLEDLR 10 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 KLS(0.784)CS(0.216)LEDLR 113.24 0.0016042 134390000 271780 282660 260630 279820 289660 214610 356910 236180 240910 TRUE FALSE 254769.7749 303588.4405 266812.2667 287000.6549 266911.272 276564.4231 303394.6589 265667.5929 200700.5647 1.269402382 1.512643679 1.329404664 1.429994257 1.329897963 1.377995242 1.511678153 1.323701273 1 17.61468515 0.973933708 23.20791002 0.999999998 1.404087536 0.715865318 0.077412214 493.9333576 439770.4801 0.068410793 0.017102698 9.417458345 -0.973933708 0.404087539 KLS(ph)DASDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KLSDASDER 9 1 Q658Y4;E7ER68 Q658Y4 FAM91A1 Protein FAM91A1 1 KLS(0.999)DAS(0.001)DER;KLS(1)DASDER;KLS(0.944)DAS(0.056)DER;KLS(0.993)DAS(0.007)DER;KLS(1)DASDER;KLS(1)DASDER 122.78 0.00035289 7301970000 27478840 19231750 23856540 23948710 19623300 15806800 21559790 14215060 14678750 TRUE FALSE 25758988.46 20655688.78 24422428.39 24563274.44 18082165.17 20369966.56 18327099.64 15989841.53 12228771.8 2.106424822 1.689105752 1.997128477 2.008646073 1.478657503 1.665741 1.498686863 1.307559074 1 23.54377618 1.460961663 0.55156647 0.992384182 1.933530705 0.804716583 0.150953348 0.32727165 0.243852147 0.146099503 0.080243638 28.90424718 -1.460961663 0.941146524 KLS(ph)DGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLSDGHK 7 1 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 KLS(1)DGHK 80.706 0.019627 0 525250 315260 381100 405300 415200 257050 423390 328200 382000 TRUE FALSE 492375.5401 338602.1784 390139.872 415700.6842 382591.8668 331256.1621 359906.6001 369176.4925 318241.7322 1.547174648 1.063977927 1.225923041 1.306241898 1.202205205 1.040894794 1.130922075 1.160050537 1 18.27976351 2.390386369 5.78544373 1.096786338 1.240308945 0.332240203 0.128054001 0.308634111 16.25427601 0.042670717 0.035540408 245.6893711 -2.390386369 0.143522607 KLS(ph)FLSWGTNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLSFLSWGTNK 11 1 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 KLS(0.997)FLS(0.003)WGTNK 86.548 0.008813 247730000 190500 278230 159690 141540 356960 91616 160060 232780 211060 TRUE FALSE 178576.9451 298830.4387 163477.9222 145172.156 328925.8015 118064.0519 136060.4889 261843.0954 175832.7225 1.015607007 1.699515508 0.929735489 0.825626504 1.870674564 0.671456656 0.773806417 1.489160218 1 17.42384406 3.85911159 5.818402027 1.051827322 1.391910575 0.07416423 0.392893243 0.43578146 19.60733181 0.096135466 0.176119961 7229.555407 -3.85911159 0.340083252 KLS(ph)FTESLTSGASLLTLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLSFTESLTSGASLLTLNK 19 1 P19838;P19838-2;P19838-3 P19838 NFKB1 Nuclear factor NF-kappa-B p105 subunit;Nuclear factor NF-kappa-B p50 subunit 1 KLS(0.45)FT(0.307)ES(0.244)LTSGASLLTLNK;KLS(0.388)FT(0.388)ES(0.223)LTSGASLLTLNK 281.4 6.68E-40 520440000 1952870 1493220 1684830 1615740 1976780 1250816 2316130 1670090 2444530 TRUE FALSE 1830643.353 1603779.562 1724794.963 1657202.624 1821531.673 1611906.274 1968847.808 1878604.413 2036522.151 0.898906674 0.78750902 0.8469316 0.813741517 0.894432536 0.791499505 0.966769651 0.922457147 1 20.95767608 1.687442451 6.897699441 0.958229085 0.835197338 0.661850514 0.041648642 0.071005436 6.943166386 0.018678926 0.009603526 48.69030004 -1.687442451 -0.123031747 KLS(ph)GDQITLPTTVDYSSVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KLSGDQITLPTTVDYSSVPK 20 1 O00559-2;E9PND3;E9PN10;O00559;E9PJ38 O00559-2 EBAG9 Receptor-binding cancer antigen expressed on SiSo cells 1 KLS(0.994)GDQIT(0.006)LPTTVDYSSVPK;KLS(1)GDQITLPTTVDYSSVPK;KLS(1)GDQITLPTTVDYSSVPK;KLS(1)GDQITLPTTVDYSSVPK 288.57 3.36E-46 6070610000 3574120 2267120 2674310 2740760 3034470 2047820 3946130 2720450 4255980 TRUE FALSE 3350422.209 2434979.924 2737745.896 2811092.542 2796154.967 2638992.39 3354444.441 3060104.171 3545629.443 0.944944265 0.686755332 0.77214665 0.792833145 0.78862019 0.744294471 0.946078685 0.86306373 1 21.75761034 1.721253448 7.235922544 0.926988355 0.774929682 0.468157672 0.073113587 0.098730456 13.62748822 0.033089836 0.017335401 52.63243319 -1.721253448 -0.152058673 KLS(ph)GDQPAAR ddPTM_SK-BR-3_Pertuzumab_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 173.25 2.12E-06 52890000000 29758900 24195970 24948770 25327290 26877410 18156160 28499980 21493010 25899630 TRUE FALSE 27896343.57 25987464.79 25540566.61 25977231.14 24766566.64 23397548.65 24226672.58 24176459.61 21576814.43 1.292885178 1.204416197 1.183704234 1.203941908 1.147832397 1.084383829 1.122810443 1.120483271 1 24.36297855 8 0.079925094 0.858188633 1.946803235 0.886018754 0.026591035 60.60375094 0.352879417 0.725330553 7.289355337 100000000 -8 1.088614602 KLS(ph)HDAESEREDPAPAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLSHDAESEREDPAPAKK 18 3 Q92766;Q92766-2;Q92766-5;Q92766-3;C9JU34;Q92766-6 Q92766 RREB1 Ras-responsive element-binding protein 1 1 KLS(1)HDAESEREDPAPAKK 99.93 0.0006743 137130000 412650 220800 257110 246090 239590 160150 326490 171740 430580 TRUE FALSE 386822.9731 237148.2617 263208.7706 252405.086 220773.5679 206382.7052 277535.8555 193182.117 358713.4163 1.078362156 0.661107868 0.733757809 0.703639938 0.615459467 0.575341473 0.773698007 0.538541655 1 18.45247218 -1.407993944 3.116302493 1.004221391 0.703907744 0.271798533 0.148887745 34967704.54 44821798.56 1320097.764 0.03203404 0.039084635 1.407993944 -0.300313647 KLS(ph)LPTDLKPDLDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLSLPTDLKPDLDVK 15 2 H0Y332;Q5T5C0-2;Q5T5C0;Q5JRH0 H0Y332 STXBP5 Syntaxin-binding protein 5 1 KLS(0.966)LPT(0.034)DLKPDLDVK 105.38 0.0010394 108150000 421880 172950 244600 234780 269190 168300 350540 222080 434390 TRUE FALSE 395475.2839 185755.398 250402.0275 240804.8523 248048.9033 216885.4779 297979.7813 249807.1769 361887.5027 1.092812769 0.513295973 0.691933337 0.665413562 0.685430973 0.599317402 0.823404453 0.690289593 1 18.46518176 0.22605772 0.767927818 1.005126879 0.68782556 0.220148371 0.156425669 3.955814816 2.891818529 0.193000188 0.048441443 1.682897712 -0.22605772 -0.317301319 KLS(ph)LQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 99.973 0.0062079 298090000 753070 666650 690970 707510 766310 586030 914420 744750 1079700 TRUE FALSE 705936.693 716009.4596 707360.1347 725665.9044 706127.1037 755207.3476 777311.2101 837733.6769 899491.0949 0.784817879 0.796016174 0.786400375 0.806751627 0.785029566 0.839594024 0.864167766 0.931341824 1 19.77874947 1.280831993 0.960525507 1.000521918 0.790268839 0.980934119 0.009912042 0.052167531 0.10180774 0.007979959 0.002827451 19.09114574 -1.280831993 -0.210253079 KLS(ph)LQERPAGSYLEAQAGPYATGPASHISPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLSLQERPAGSYLEAQAGPYATGPASHISPR 31 2 J3KPJ3;Q8N5S9;Q8N5S9-2 J3KPJ3 CAMKK1 Calcium/calmodulin-dependent protein kinase kinase 1 1 KLS(0.866)LQERPAGS(0.134)YLEAQAGPYATGPASHISPR 252.15 1.32E-58 147940000 161910 349660 296290 296970 287110 257510 451480 341960 462270 TRUE FALSE 151776.3421 375549.1902 303318.1387 304590.753 264561.5387 331848.9567 383784.7653 384654.4587 385114.1506 0.394107414 0.975163311 0.7876058 0.790910312 0.686969145 0.861689855 0.996548075 0.998806349 1 18.55492661 1.884311416 3.213540641 0.998248494 0.771795641 0.399024086 0.146393337 0.290765402 5.196289573 0.071815062 0.038455495 76.61457837 -1.884311416 -0.226452853 KLS(ph)MGSDDAAYTQALLVHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLSMGSDDAAYTQALLVHQK 20 1 A0A1B0GV57;Q9NYJ8 A0A1B0GV57 TAB2 TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 1 KLS(1)MGSDDAAYTQALLVHQK;KLS(1)MGSDDAAYTQALLVHQK 299.97 4.01E-55 1244180000 1361740 962920 1157310 1020940 1247100 912610 1595050 1248580 2191250 TRUE FALSE 1276511.124 1034215.599 1184761.94 1047139.049 1149157.797 1176065.692 1355887.06 1404467.961 1825516.219 0.699260358 0.566533229 0.649001048 0.573612569 0.629497445 0.644237328 0.742741722 0.769353867 1 20.79987306 0.938535947 0.807544773 0.999071573 0.612850557 0.896784393 0.04021702 0.186663962 0.265443069 0.034560387 0.012531706 8.680324215 -0.938535947 -0.386221016 KLS(ph)PIIEDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLSPIIEDSR 10 1 O60566-3;O60566 O60566-3 BUB1B Mitotic checkpoint serine/threonine-protein kinase BUB1 beta 1 KLS(1)PIIEDSR;KLS(1)PIIEDSR 94.09 0.0051091 466900000 1010530 898710 1026740 963080 1170630 737320 1168270 981340 1574760 TRUE FALSE 947282.7311 965251.4235 1051094.758 987794.2633 1078693.442 950172.3146 993098.7592 1103862.459 1311922.383 0.722056993 0.735753453 0.801186695 0.752936512 0.822223522 0.72425955 0.756979812 0.841408359 1 20.32325094 0.904539385 2.813675662 0.999735473 0.761125076 0.853964879 0.03171978 0.135545561 2.3546404 0.029161156 0.007712526 8.026743495 -0.904539385 -0.238610398 KLS(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLSPLR 6 1 Q8IZD2-6;Q8IZD2-5;Q8IZD2-7;Q8IZD2;Q8IZD2-8;Q8IZD2-4;Q8IZD2-3 Q8IZD2-6 KMT2E Histone-lysine N-methyltransferase 2E 1 KLS(1)PLR 79.474 0.054103 0 56997 65926 53624 51779 65776 36147 67632 61520 84596 TRUE FALSE 53429.65951 70807.22964 54895.9866 53107.7368 60610.21829 46582.0521 57491.20946 69200.90742 70476.38109 0.758121497 1.00469446 0.778927433 0.753553687 0.860007528 0.660959762 0.815751441 0.981902112 1 16.10485222 1.23082825 7.450776666 0.992861371 0.814709407 0.432177427 0.08826684 0.141144069 46.09085219 0.075250195 0.022106959 17.01485492 -1.23082825 -0.178151964 KLS(ph)PPPLPPR ddPTM_SK-BR-3_Pertuzumab_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 77.26 0.020539 624018000 627810 637570 662320 634090 731550 474622 655160 569940 737370 TRUE FALSE 588516.4928 684776.3462 678030.5432 650361.8229 674097.0139 611637.6666 556924.8402 641098.2636 614298.1834 0.958030658 1.114729564 1.103748247 1.058707059 1.097344957 0.995669014 0.90660343 1.043627152 1 19.22857959 2.129843436 5.02853479 0.968206506 1.077569045 0.317406578 0.055518365 0.178943922 7.205658328 0.020136325 0.014689013 134.8476665 -2.129843436 0.109362538 KLS(ph)PTEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KLSPTEPK 8 1 O14828;O14828-2 O14828 SCAMP3 Secretory carrier-associated membrane protein 3 1 KLS(0.906)PT(0.094)EPK;KLS(0.859)PT(0.141)EPK;KLS(0.944)PT(0.056)EPK 142.07 0.00038184 2773000000 4958200 2832320 3375880 3205780 3337570 2220770 4234080 2773630 5063900 TRUE FALSE 4647875.113 3042027.92 3455957.468 3288045.742 3075450.715 2861870.248 3599219.011 3119923.811 4218702.376 1.101730982 0.721081425 0.819199166 0.779397419 0.729003955 0.678376902 0.853157841 0.739545844 1 22.00836788 -1.547622547 2.939128443 1.009665786 0.792893992 0.212927866 0.117891339 22206574.82 23655259.32 1694817.533 0.025759992 0.028338539 1.547622547 -0.216771794 KLS(ph)PTKEAFGEQPLQLTTKPDLLAWDPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLSPTKEAFGEQPLQLTTKPDLLAWDPAR 29 3 O00257 O00257 CBX4 E3 SUMO-protein ligase CBX4 1 KLS(0.901)PT(0.099)KEAFGEQPLQLTTKPDLLAWDPAR 275.59 2.09E-70 636780000 1058500 692810 875700 912680 1149600 565450 1186500 732970 1369300 TRUE FALSE 992250.3745 744106.3733 896472.0175 936100.914 1059315.053 728686.2357 1008595.34 824482.918 1140754.984 0.869819013 0.652292897 0.785858515 0.820597698 0.928608744 0.638775413 0.884147213 0.722751975 1 20.12155753 -5 0.250262233 2.319969108 0.76163578 0.301970455 0.097163051 208.1795117 2.064096739 140.6868744 0.128260921 1.00E-05 5 -1.558333327 KLS(ph)SAMSAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLSSAMSAAK 10 1 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 1 KLS(0.5)S(0.5)AMSAAK;KLS(0.802)S(0.198)AMSAAK 138.73 3.49E-05 1263470000 2157270 2558100 1469680 1569650 3365000 1001740 2000070 2741300 4362800 TRUE FALSE 2022250.322 2747504.386 1504541.504 1609929.876 3100726.474 1290926.076 1700178.071 3083557.339 3634620.495 0.55638555 0.75592607 0.413947345 0.442943047 0.85310873 0.355174929 0.467773203 0.848384953 1 21.7933733 1.081369845 4.478617297 0.994881336 0.550324699 0.520654265 0.152927126 0.148881237 5.120933285 0.141462474 0.036066516 12.06062586 -1.081369845 -0.444556638 KLS(ph)SIGIQVDCIQPVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLSSIGIQVDCIQPVPK 17 1 Q9Y2H0-3;Q9Y2H0 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 KLS(0.916)S(0.084)IGIQVDCIQPVPK 181.65 4.85E-10 633860000 2727000 1667600 1957600 1664800 2241500 1559000 2741200 2277100 3318100 TRUE FALSE 2556321.938 1791070.839 2004035.196 1707521.586 2065461.632 2009057.992 2330182.508 2561400.948 2764287.674 0.92476697 0.647932144 0.724973459 0.617707629 0.747194893 0.726790489 0.842959483 0.926604337 1 21.39847633 1.39338981 1.450549378 0.994969459 0.713521732 0.583435606 0.08146531 0.23504771 0.928251903 0.067112223 0.021457602 24.73943686 -1.39338981 -0.281447727 KLS(ph)SSDAPAQDTGSSAAAVETDASR ddPTM_SK-BR-3_Pertuzumab_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(0.649)S(0.176)S(0.176)DAPAQDTGSSAAAVETDASR;KLS(0.675)S(0.163)S(0.163)DAPAQDTGSSAAAVETDASR;KLS(0.626)S(0.187)S(0.187)DAPAQDTGSSAAAVETDASR;KLS(0.717)S(0.217)S(0.066)DAPAQDTGSSAAAVETDASR 233.17 1.44E-38 3469270000 1211680 944720 1154600 1432880 1578960 798980 1007160 754991 1153210 TRUE FALSE 1135843.112 1014668.052 1181987.657 1469650.127 1454954.851 1029632.556 856145.708 849253.2883 960731.801 1.182268673 1.056140799 1.230299295 1.529719455 1.514423536 1.07171695 0.891139137 0.883965002 1 19.87377422 2.006138417 24.28996648 0.930061265 1.271405695 0.586050685 0.145407097 93.48537835 369922.7297 0.062144014 0.045760868 101.4234589 -2.006138417 0.34134443 KLSAS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_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(0.069)AS(0.466)S(0.466)PR 53.683 0.082711 231190000 455030 562050 473630 473860 674320 342020 521650 518180 749790 TRUE FALSE 426550.4846 603664.7668 484864.7273 486020.0498 621361.6273 440755.6218 443433.4253 582875.9137 624645.2052 0.68286842 0.966412232 0.776224204 0.77807377 0.994743291 0.705609549 0.709896469 0.933131174 1 19.25267745 1.035331763 7.436646834 0.999887743 0.811667593 0.308253288 0.104382969 0.212491148 33.79746521 0.097666847 0.024477692 10.84755255 -1.035331763 -0.18822015 KLSASS(ph)PR ddPTM_SK-BR-3_Pertuzumab_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(0.006)AS(0.381)S(0.613)PR 65.347 0.039511 185890000 318350 347150 311840 301280 397430 230410 338560 328090 466650 TRUE FALSE 298425.0418 372853.3472 319236.9921 309011.3549 366217.451 296925.6266 287796.071 369052.7587 388763.1003 0.767626973 0.959075969 0.821160732 0.794857729 0.942006715 0.763770086 0.74028649 0.949299865 1 18.56853177 1.048602237 7.413132671 0.999835635 0.834604606 0.4242181 0.072425614 0.190755996 22.71802788 0.071416218 0.01789965 11.18413078 -1.048602237 -0.16523103 KLSCS(ph)LEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KLSCSLEDLR 10 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 KLS(0.327)CS(0.673)LEDLR;KLS(0.01)CS(0.99)LEDLR;KLSCS(1)LEDLR;KLS(0.01)CS(0.99)LEDLR 142.35 2.20E-05 3410370000 10409460 10168420 9916550 10712540 11333410 8080610 13896900 9543890 8789310 TRUE FALSE 9757950.48 10921300.4 10151775.25 10987441.91 10443329.7 10413350.93 11813188.86 10735465.68 7322317.38 1.332631457 1.491508744 1.386415628 1.50054161 1.426232865 1.422138701 1.613312869 1.466129521 1 22.80386888 -0.687712609 6.075144085 0.999999995 1.462327 0.783740238 0.074999614 4.29E-09 1.06E-09 0.071966303 0.01696262 0.205251997 0.687712609 0.462327005 KLSEEEILENPDLFLTSEATDYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLSEEEILENPDLFLTSEATDYGR 24 1 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 113.24 0.0023453 27497000 30738 28331 28716 30080 35883 24899 36038 24000 40181 FALSE TRUE 28814.16345 30428.65672 29397.15708 30851.90373 33064.89393 32086.9371 30634.43646 26996.45283 33474.53152 0.860778692 0.909009188 0.878194727 0.92165304 0.987762709 0.958547757 0.91515654 0.806477391 1 15.03077624 3.138415179 5.567389158 0.931688272 0.887837169 0.156526588 0.053523043 0.429104914 19.9632542 0.015043316 0.018164312 1375.356167 -3.138415179 -0.043851103 KLSELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLSELLR 7 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 153.04 0.0028434 5715800000 6148400 12314000 5583000 5611000 13155000 4167200 6603800 11742600 9917100 FALSE TRUE 5763582.619 13225741.37 5715431.396 5754987.759 12121859.36 5370202.991 5613621.497 13208689.46 8261871.943 0.697612195 1.600816554 0.69178407 0.696571891 1.467204944 0.649998333 0.679461209 1.598752625 1 22.97803727 3.953724043 24.15438497 0.929529616 1.205300378 0.023043622 0.395469454 635.5263838 656093.6283 0.093758256 0.169175802 8989.262099 -3.953724043 0.275770762 KLSEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KLSEQR 6 1 P16152 P16152 CBR1 Carbonyl reductase [NADPH] 1 0 ;; 116.54 0.037659 1848110000 4587400 5190900 4420100 4298300 5992700 3527800 5076600 5128600 6976000 FALSE TRUE 4300282.823 5575239.637 4524946.859 4408601.655 5522057.515 4546218.591 4315410.959 5768916.999 5811660.533 0.739940469 0.959319562 0.77859793 0.758578659 0.950168628 0.782258111 0.742543535 0.992645212 1 22.47051901 1.219596444 24.4044268 0.996323012 0.823247602 0.473126575 0.078853316 192.2986032 247454.4638 0.073248307 0.018445946 16.58045499 -1.219596444 -0.173075409 KLSFT(ph)ESLTSGASLLTLNK ddPTM_SK-BR-3_Pertuzumab_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(0.239)FT(0.456)ES(0.304)LTSGASLLTLNK 226.24 9.07E-20 253730000 219150 164710 175130 173760 196340 135150 254630 186250 249660 TRUE FALSE 205433.7927 176905.2998 179284.1663 178218.9758 180920.2484 174165.611 216450.5954 209503.7225 207990.1331 0.987709319 0.850546596 0.861983997 0.856862646 0.869850149 0.837374391 1.040677229 1.007277217 1 17.66615556 1.724962502 7.885103819 1.016248113 0.871483422 0.697511729 0.042825077 0.05714008 10.07394198 0.019305381 0.010222212 53.08386085 -1.724962502 -0.144764692 KLSFTES(ph)LTSGASLLTLNK ddPTM_SK-BR-3_Pertuzumab_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(0.015)FT(0.023)ES(0.961)LTSGASLLTLNK 261.54 2.26E-31 394210000 1211600 938450 1076600 991080 1193600 788580 1441800 1070600 1446200 TRUE FALSE 1135768.119 1007933.814 1102137.46 1016512.791 1099859.471 1016230.244 1225615.475 1204266.767 1204819.877 0.942687069 0.836584649 0.914773637 0.843705196 0.912882906 0.843470683 1.017260338 0.999540919 1 20.20038605 1.701203849 7.026718825 1.005573639 0.88062534 0.731147112 0.035128248 0.056829515 6.202662874 0.015317086 0.007936909 50.25784347 -1.701203849 -0.124948299 KLSGDQPAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLSGDQPAAR 10 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 0 105.25 0.0063661 0 123650 108960 112810 116930 116020 79149 120660 80314 135600 FALSE TRUE 115910.9672 117027.5118 115485.9065 119930.6218 106908.2572 101998.0314 102568.1532 90341.37969 112967.484 1.026056022 1.035939791 1.02229334 1.061638425 0.94636309 0.902897257 0.907944034 0.799711355 1 16.78554805 2.528817617 3.137381428 0.897161648 1.033892783 0.625669767 0.048840216 0.147700141 2.903948512 0.015569341 0.013860469 337.9228952 -2.528817617 0.136731136 KLSPT(ph)EPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLSPTEPK 8 1 O14828;O14828-2 O14828 SCAMP3 Secretory carrier-associated membrane protein 3 1 KLS(0.396)PT(0.604)EPK 123.51 0.00078781 1095100000 2241000 1255200 1471200 1323700 1398000 973620 1777100 1110300 2136000 TRUE FALSE 2100739.81 1348136.314 1506097.559 1357668.383 1288206.719 1254688.289 1510640.353 1248923.399 1779487.801 1.180530605 0.757597952 0.846365768 0.762954589 0.72391995 0.705083951 0.848918634 0.701844316 1 20.76303061 4.741173468 24.96798157 0.787092517 1.180530748 0.648374638 0.089505675 132.4516833 1265614.406 0.018500376 0.127444318 55102.77465 -4.741173468 0.39343823 KLSSERPS(ph)SDGEGVVENGITTCNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLSSERPSSDGEGVVENGITTCNGK 25 2 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 KLS(0.034)S(0.034)ERPS(0.466)S(0.466)DGEGVVENGITTCNGK 177.79 1.58E-17 231650000 167270 137460 154310 153330 170970 120100 204840 128830 180870 TRUE FALSE 156800.8693 147637.6814 157970.3061 157264.7074 157542.7059 154770.9203 174126.1436 144914.7091 150681.6285 1.040610397 0.979798817 1.048371375 1.043688663 1.045533602 1.027138622 1.155589738 0.961727787 1 17.20114401 3.734357129 3.783645667 1.052920438 1.007220666 0.01187841 0.051995113 0.451186875 14.24429943 0.013329957 0.023635923 5424.467723 -3.734357129 -0.045699772 KLSSWDQAET(ph)PGHT(ph)PSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLSSWDQAETPGHTPSLR 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 KLS(0.001)S(0.001)WDQAET(0.998)PGHT(0.995)PS(0.005)LR;KLSSWDQAET(1)PGHT(0.999)PS(0.001)LR 141.36 5.32E-08 837420000 557120 747690 607940 695500 811060 417300 901630 658310 1033070 TRUE FALSE 522250.8537 803049.7456 622360.6239 713347.7075 747362.6193 537767.7357 766438.9518 740501.4526 860643.9431 0.60681407 0.933080111 0.723133682 0.828853457 0.868376087 0.624843456 0.890541272 0.860403955 1 19.71505698 1.015268852 1.556603197 0.995019227 0.787363078 0.316191822 0.105653032 0.479916959 2.37467557 0.089243265 0.026217154 10.35783175 -1.015268852 -0.207656149 KLSSWDQAET(ph)PGHTPSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLSSWDQAETPGHTPSLR 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 KLS(0.001)SWDQAET(0.999)PGHTPSLR 113.42 0.00018856 243050000 367120 357460 364280 372140 421760 260520 465720 322340 503370 TRUE FALSE 344142.6145 383926.7103 372920.8936 381689.7424 388636.6709 335727.8948 395889.6095 362584.8586 419354.2951 0.820648837 0.915518727 0.889274053 0.910184412 0.926750186 0.800582941 0.944045677 0.864626553 1 18.67781011 -1.419480851 3.054321249 1.00185697 0.889644325 0.384515496 0.045638757 39025621 49024750.46 632586.8862 0.009628933 0.038064414 1.419480851 -0.112212646 KLSSWDQAETPGHT(ph)PSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLSSWDQAETPGHTPSLR 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 KLSSWDQAETPGHT(1)PSLR;KLSSWDQAET(0.003)PGHT(0.994)PS(0.003)LR 142.41 8.61E-08 454703000 325580 437110 410110 450520 494520 349010 498050 397320 517460 TRUE FALSE 305202.529 469474.0792 419838.0029 462081.1059 455682.394 449763.5213 423372.0262 446926.2766 431092.5831 0.707974437 1.08903307 0.973892893 1.071883684 1.057040673 1.043310739 0.982090722 1.036729218 1 18.71763822 4.745050385 24.95364141 1.029729563 0.707974289 0.881314234 0.037333726 231.9978012 892024.4462 0.008570779 0.082561441 55596.87545 -4.745050385 -0.321755274 KLSVEEFFMDLHNFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLSVEEFFMDLHNFR 15 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 179.81 4.25E-07 294550000 383640 732620 537550 538180 967230 426580 554210 642980 1007640 FALSE TRUE 359628.6572 786863.9471 550300.9398 551990.6099 891267.6574 549726.7211 471111.3555 723257.4684 839458.3744 0.428405586 0.937347188 0.655542856 0.657555665 1.061717513 0.654858821 0.561208715 0.861576334 1 19.67909926 KLSVPT(ph)S(ph)DEEDEVPAPKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KLSVPTSDEEDEVPAPKPR 19 2 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 2 KLS(0.001)VPT(0.999)S(1)DEEDEVPAPKPR;KLS(0.001)VPT(0.999)S(1)DEEDEVPAPKPR;KLS(0.001)VPT(0.999)S(1)DEEDEVPAPKPR;KLS(0.029)VPT(0.971)S(1)DEEDEVPAPKPR;KLS(0.002)VPT(0.998)S(1)DEEDEVPAPKPR;KLS(0.001)VPT(0.999)S(1)DEEDEVPAPKPR 162.11 5.34E-11 1770520000 1111363 784856 835363 829436 1004099 662761 1184500 806897 1314123 TRUE FALSE 1041804.774 842967.5549 855178.2048 850720.732 925241.1149 854089.3417 1006895.221 907639.8666 1094787.382 0.95160466 0.769982893 0.781136337 0.777064795 0.845133156 0.780141748 0.919717598 0.829055835 1 20.06221928 0.744077471 0.656102415 0.999656971 0.805869775 0.409233124 0.062489447 0.952301589 0.838544359 0.060993115 0.023040985 5.547246577 -0.744077471 -0.193787196 KLSVPTS(ph)DEEDEVPAPKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KLSVPTSDEEDEVPAPKPR 19 2 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 KLSVPT(0.064)S(0.936)DEEDEVPAPKPR;KLSVPT(0.14)S(0.859)DEEDEVPAPKPR;KLSVPT(0.165)S(0.835)DEEDEVPAPKPR;KLSVPT(0.036)S(0.964)DEEDEVPAPKPR;KLSVPT(0.197)S(0.803)DEEDEVPAPKPR;KLSVPT(0.248)S(0.752)DEEDEVPAPKPR 187.79 9.18E-15 11921430000 5014560 3467620 4168230 3955770 4124150 3124794 4810470 3327558 4824400 TRUE FALSE 4700707.641 3724366.193 4267102.384 4057281.755 3800255.895 4026871.301 4089184.682 3743010.941 4019176.473 1.169569854 0.926649083 1.061685749 1.009480868 0.945530986 1.001914528 1.017418546 0.93128803 1 21.93846849 4.751947897 24.94646137 0.991814377 1.169569973 0.647384518 0.042256905 1431.634427 2667724.403 0.009554721 0.188677981 56486.92028 -4.751947897 0.177755596 KLT(ph)ATPTPLGGMTGFHMQTEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLTATPTPLGGMTGFHMQTEDR 22 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 KLT(0.537)AT(0.414)PT(0.049)PLGGMTGFHMQTEDR 65.899 0.017128 197840000 129430 133150 150780 156550 147040 110730 175940 113730 191510 TRUE FALSE 121329.2073 143008.5645 154356.5728 160567.338 135492.0715 142695.9534 149559.4303 127929.4409 159545.7438 0.760466588 0.896348352 0.96747534 1.006403143 0.849236516 0.89438897 0.937407835 0.801835497 1 17.2836106 4.733532949 3.132843464 0.92227762 0.736956078 0.389442258 0.063255512 0.352068683 5.389887798 0.014348441 0.159992001 54141.83232 -4.733532949 -0.185321543 KLT(ph)SDEEGEPSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLTSDEEGEPSGK 13 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 KLT(0.537)S(0.463)DEEGEPSGK 179.74 7.91E-06 498510000 1290500 661500 880730 785930 868720 637340 1181300 717250 1135800 TRUE FALSE 1209729.909 710478.1483 901621.3315 806098.2944 800494.2354 821329.7116 1004175.032 806800.2414 946227.6425 1.27847661 0.7508533 0.952858795 0.851907362 0.845984834 0.868004352 1.061240432 0.852649199 1 19.85182778 1.767113019 25 0.976749363 0.902049338 0.005971725 0.14796247 67.22959112 58899.29749 0.06178151 0.034264995 58.49422868 -1.767113019 -0.074700025 KLTATEGPGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLTATEGPGSPR 12 1 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 KLTATEGPGS(1)PR;KLTATEGPGS(1)PR 107.03 0.0011384 757980000 843920 841060 843120 820170 912500 639510 916190 785450 847480 TRUE FALSE 791100.5536 903332.9575 863119.2046 841216.9507 840835.9308 824126.1554 778815.815 883515.1615 706030.1131 1.120491235 1.279453866 1.222496305 1.191474606 1.190934941 1.167267713 1.103091498 1.25138453 1 19.42937019 -5 0.165548541 0.239600785 1.245141874 0.507999759 0.056353777 96.52483351 0.901338289 23.97862565 0.207265836 1.00E-05 5 1.005541089 KLTDIINNDHENVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLTDIINNDHENVK 14 1 Q8N335;C9K0P5;C9JFA7;C9JM46 Q8N335 GPD1L Glycerol-3-phosphate dehydrogenase 1-like protein;Glycerol-3-phosphate dehydrogenase [NAD(+)] 0 130.72 3.92E-05 355550000 313970 260280 261440 313750 361660 197090 372630 268700 376270 FALSE TRUE 294319.1782 279551.402 267641.4803 321801.3562 333256.6825 253986.6835 316757.5908 302247.7865 313468.1062 0.938912675 0.891801738 0.853807692 1.026584044 1.063127878 0.81024729 1.010493842 0.964205865 1 18.25795914 3.245981347 24.99962726 0.974032282 0.888327635 0.242905487 0.069432718 228.2733691 769023.1258 0.018546362 0.024619857 1761.90037 -3.245981347 -0.085704647 KLTGIKHELQANCYEEVKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLTGIKHELQANCYEEVKDR 20 3 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 188.32 1.56E-17 3328200000 2100750 2184190 2140800 2399500 3554600 1491350 2924800 1960910 6964900 FALSE TRUE 1969267.807 2345909.7 2191580.787 2461075.232 3275436.055 1921878.535 2486253.393 2205733.93 5802413.195 0.339387724 0.404298974 0.377701607 0.424146842 0.564495486 0.331220558 0.428486099 0.380140789 1 22.4682216 -1.948476253 2.458513427 1.442950888 0.407009007 0.893223253 0.064516717 6943792.67 3259108.422 17583254.37 0.014322419 0.01125962 1.948476253 -1.035941881 KLTS(ph)DEEGEPSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KLTSDEEGEPSGK 13 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 KLT(0.295)S(0.705)DEEGEPSGK;KLT(0.376)S(0.624)DEEGEPSGK;KLT(0.173)S(0.827)DEEGEPSGK;KLT(0.168)S(0.832)DEEGEPSGK 178.43 8.95E-06 3974940000 6889000 3669160 4456030 4387550 4672710 3509780 6123340 3967330 5771960 TRUE FALSE 6457829.787 3940828.424 4561729.136 4500141.961 4305734.205 4522996.509 5205202.013 4462659.884 4808582.588 1.342979905 0.819540551 0.948663988 0.935856228 0.895426901 0.940609094 1.082481567 0.928061399 1 22.19718027 1.808967539 24.99997087 1.012564286 0.953274062 0 0.143671568 577.559072 205118.1696 0.054923422 0.035081339 64.41211198 -1.808967539 -0.059290224 KLTS(ph)DEEGEPSGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KLTSDEEGEPSGKR 14 2 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 KLT(0.022)S(0.978)DEEGEPSGKR;KLT(0.088)S(0.912)DEEGEPSGKR;KLT(0.041)S(0.959)DEEGEPSGKR 131.45 2.93E-05 2022610000 1572480 903682 1106808 1199807 1289144 815829 1556900 998508 2116340 TRUE FALSE 1474061.284 970591.5556 1133062.008 1230596.079 1187899.83 1051345.588 1323457.299 1123173.922 1763109.182 0.836057857 0.550499972 0.642649939 0.697969299 0.673752847 0.596302032 0.750638311 0.637041616 1 20.74969039 -2.36298406 0.399483319 1.485364178 0.65222888 0.608552679 0.081127786 41.06972346 2.026557441 17.57969377 0.047119045 0.004335268 2.36298406 -0.833135298 KLTSDLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLTSDLGR 8 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 102.07 0.013123 0 830720 1417200 856700 988970 1731700 723840 1174700 1437800 1649700 FALSE TRUE 778726.7181 1522130.963 877021.3286 1014348.645 1595699.267 932800.8574 998564.6404 1617312.495 1374354.413 0.566612739 1.107524339 0.638133309 0.738054635 1.161053694 0.678719295 0.726569967 1.176779789 1 20.39032266 1.238499748 25 1.088389946 0.81543809 0.266850387 0.19616291 2.17601713 890039.4812 0.142684018 0.044340796 17.31808025 -1.238499748 -0.272951856 KLVEALCAAGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLVEALCAAGHR 12 1 P23919-2;P23919;G5E9E9;H7C3A4 P23919-2 DTYMK Thymidylate kinase 0 124.86 0.00020485 212740000 426320 569780 395960 375270 648940 305110 479010 479620 633540 FALSE TRUE 399637.3922 611967.1041 405352.3582 384900.0635 597974.8701 393190.304 407186.8974 539501.6128 527798.0812 0.757178562 1.159472014 0.768006502 0.729256277 1.132961432 0.744963496 0.771482338 1.022174259 1 19.00962658 3.924107141 13.19756725 0.862357057 0.984123924 0.021274791 0.16620681 3.371696269 837.1747616 0.039248749 0.070791042 8396.671077 -3.924107141 0.121766867 KLVEESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLVEESR 7 1 Q15404 Q15404 RSU1 Ras suppressor protein 1 0 ; 122.52 0.006948 257560000 467680 506800 462740 479960 572190 351940 509950 510200 654740 FALSE TRUE 438408.7436 544323.9993 473716.4113 492276.5862 527252.5055 453539.3647 433487.7316 573899.5931 545459.6642 0.803741821 0.997917967 0.868471937 0.902498605 0.966620522 0.831481032 0.79472005 1.05213938 1 19.05711299 1.220266491 24.99994807 1.026069817 0.887623314 0.453523438 0.065972962 278.3002053 380302.6978 0.064149871 0.016161063 16.60605573 -1.220266491 -0.138446503 KLVIIEGDLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KLVIIEGDLER 11 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;P06753-7;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;;; 170.66 2.48E-05 6850480000 10924480 13261540 11400760 12115420 14048890 9722380 13231000 11565190 12318080 FALSE TRUE 10240736.3 14243438.22 11671191.41 12426322.19 12945546.85 12529073.28 11247134.38 13009129.43 10262112.87 0.997916942 1.387963512 1.137308813 1.210893151 1.261489424 1.220905815 1.095986228 1.26768528 1 23.29082446 -2.225158789 0.325072006 0.74236085 1.218594957 0.230298041 0.107236751 56.03216771 2.469978303 10.59730834 0.087652951 0.005954444 2.225158789 0.476234107 KLVIIESDLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KLVIIESDLER 11 1 H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;H0YL42;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 ;;; 160.69 4.36E-05 1145060000 2842470 3484960 3025960 3154660 4022120 2328690 3315380 3145900 3437940 FALSE TRUE 2664564.877 3742990.064 3097737.2 3235613.916 3706238.92 3000945 2818269.547 3538672.54 2864125.604 0.930324031 1.306852625 1.081564718 1.129703918 1.294021084 1.04777004 0.983989509 1.235515836 1 21.44966333 KLVILEGELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KLVILEGELER 11 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;; 141.37 6.12E-05 2388310000 2578130 3000780 2824370 2803850 3435400 2392420 3400440 2713160 3727320 FALSE TRUE 2416769.445 3222960.874 2891365.39 2875801.538 3165597.542 3083072.816 2890575.59 3051903.998 3105206.213 0.778295958 1.037921688 0.931134743 0.926122564 1.019448412 0.992872165 0.930880396 0.982834565 1 21.56625765 4.750504554 24.99906949 0.973381512 0.77829584 0.725816539 0.038427319 1015.62193 2125693.079 0.008967607 0.149096061 56299.50209 -4.750504554 -0.195085672 KLVIPSELGYGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KLVIPSELGYGER 13 1 A0A494C1N0;P26885 A0A494C1N0 FKBP2 Peptidyl-prolyl cis-trans isomerase FKBP2 0 184.02 1.58E-05 881010000 839170 946970 954530 989410 1095800 727180 1172400 909850 1088400 FALSE TRUE 786647.8477 1017084.644 977171.9024 1014799.936 1009740.288 937105.0612 996609.504 1023446.775 906739.0087 0.867557081 1.121695035 1.077677141 1.119175337 1.113595289 1.033489298 1.099113962 1.128711532 1 19.79032783 4.743399693 24.99070304 1.090811288 0.86755699 0.733116698 0.041483341 232.7043195 1201728.341 0.008702632 0.071471704 55385.96071 -4.743399693 -0.223254299 KLVWVPSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLVWVPSDK 9 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ; 127.42 0.0022987 0 17502300 15418100 15518100 15096400 17864500 11486700 20512400 14133900 18362100 FALSE TRUE 16406862.29 16559672.17 15886196.66 15483799.18 16461494.23 14802723.82 17436756.05 15898548.53 15297346.89 1.072529923 1.08251923 1.038493588 1.012188538 1.076101258 0.967666088 1.139854916 1.03930104 1 23.86677812 4.004760311 4.172236909 1.046618002 1.077030369 0.089228448 0.046345582 0.584378217 23.1201229 0.01125325 0.024484362 10110.21312 -4.004760311 0.030412367 KLWGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KLWGDR 6 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;; 105.12 0.053316 19212330000 8328200 9427620 9355010 9085560 10274620 8424030 11488610 8550830 10935950 FALSE TRUE 7806952.828 10125650.79 9576915.255 9318710.851 9467692.791 10855910.71 9765999.586 9618419.948 9110669.296 0.856902229 1.111405811 1.051175819 1.022834937 1.039187406 1.191560176 1.071929983 1.055731433 1 23.11912561 2.437524756 24.9988504 1.091501096 1.033835929 0.106741998 0.080132586 345.0169292 217821.1026 0.025920882 0.021686992 273.8575739 -2.437524756 -0.057665167 KLYEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KLYEGK 6 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 105.12 0.053316 1239400000 1309770 1135690 1231410 1229580 1481380 970400 1428440 1228660 1558130 FALSE TRUE 1227793.834 1219777.669 1260619.627 1261133.104 1365038.39 1250538.727 1214258.683 1382060.906 1298068.037 0.945862465 0.939687007 0.971150657 0.971546227 1.051592329 0.963384577 0.935435315 1.06470606 1 20.30793457 3.559686755 1.708217549 0.99087763 0.943715048 0.25069631 0.038541889 0.59366583 3.456572713 0.011753874 0.022125447 3628.162709 -3.559686755 -0.047162582 KLYGDADYLEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KLYGDADYLEER 12 1 P17812;B4E1E0;P17812-2;A0A3B3IRI2 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ;;;;; 178.67 3.48E-05 3400430000 4072640 4196720 4244400 3995230 4964130 3432660 4503250 3918940 6149000 FALSE TRUE 3817740.732 4507449.515 4345079.172 4097754.366 4574267.254 4423613.217 3828029.469 4408228.286 5122692.176 0.745260617 0.879898569 0.848202278 0.799922038 0.89294205 0.863532897 0.74726908 0.860529607 1 22.28847077 0.972357626 24.05422046 1.000000002 0.83036032 0.538607945 0.050400473 1516.663905 1319793.09 0.04728689 0.011821723 9.38334374 -0.972357626 -0.169639682 KMALIQMGSVEEAVQALIDLHNHDLGENHHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KMALIQMGSVEEAVQALIDLHNHDLGENHHLR 32 1 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 230.45 3.85E-37 84979000 90047 151080 83794 95520 136230 59596 92830 78792 191260 FALSE TRUE 84411.11901 162266.1204 85781.63325 97971.20491 125531.0453 76800.39774 78911.00329 88629.35464 159337.4704 0.529763142 1.018380171 0.538364473 0.614866074 0.787831293 0.481998349 0.495244484 0.556236737 1 17.28172605 3.803579825 6.787612076 0.607431627 0.802572693 0.0535053 0.195386918 0.386471406 28.37745428 0.045414716 0.082317978 6361.797262 -3.803579825 0.195141066 KMAVDALEYDESAEDANPAGALEEILENPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KMAVDALEYDESAEDANPAGALEEILENPER 31 1 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 66.201 0.0096003 3953100 5065.8 4717 6157.4 5200.3 6128 4255.7 6244.4 5523.7 9494.8 FALSE TRUE 4748.740621 5066.251588 6303.456436 5333.748502 5646.731599 5484.251504 5308.11019 6213.346104 7910.056541 0.600342184 0.640482348 0.796891451 0.674299668 0.713867413 0.693326461 0.671058438 0.785499582 1 12.94947229 -5 0.249571328 2.841591397 0.670023421 0.778100801 0.052889929 90.88558137 0.901599281 85.26042247 0.079138985 1.00E-05 5 -2.171567976 KMDADGFLPITLIASFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KMDADGFLPITLIASFHR 18 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 0 84.499 0.0024717 28026000 58802 128480 85377 77687 153950 63751 96403 120400 117670 FALSE TRUE 55121.68778 137992.7929 87402.18276 79680.57994 141859.388 82154.87879 81948.26511 135432.205 98030.11682 0.562293401 1.40765713 0.891585011 0.812817352 1.447100061 0.838057542 0.835949887 1.38153671 1 16.58093742 4.771163866 23.55559962 1.057089949 0.562291385 0.290386738 0.251101871 9182.888894 6634309.321 0.057038746 8.0465574 59042.38143 -4.771163866 -0.494798564 KMDGAPDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KMDGAPDGR 9 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 49.715 0.085806 0 44929 58154 38079 40386 73876 32536 47083 56670 81307 FALSE TRUE 42116.97409 62459.78267 38982.25186 41422.37313 68074.07696 41928.61502 40023.34125 63745.37425 67736.33644 0.621778152 0.922101577 0.575499856 0.611523671 1.004986106 0.618997383 0.590869589 0.941080926 1 16.04764234 1.111228959 6.141789587 0.996050409 0.711899189 0.364889193 0.145529307 0.219747555 10.21473728 0.134452682 0.033835705 12.91900182 -1.111228959 -0.28415122 KMEDSVGCLETAEEVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KMEDSVGCLETAEEVKR 17 2 P35579 P35579 MYH9 Myosin-9 0 ; 233.65 2.30E-20 1372540000 1347380 1019060 1112720 1130060 1281100 801130 1535790 982360 1675830 FALSE TRUE 1263049.891 1094512.263 1139114.244 1159059.253 1180487.574 1032403.226 1305512.547 1105009.808 1396123.147 0.904683726 0.783965415 0.81591244 0.830198436 0.845546882 0.739478626 0.935098419 0.791484484 1 20.41299477 -0.697028257 0.459363604 1.044822066 0.820349238 0.446296233 0.057800785 9.65487201 1.609762251 0.687819415 0.02809073 0.20089621 0.697028257 -0.224472829 KMEEEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KMEEEQR 7 1 Q9BQ61;K7EN60;K7ELS0;K7ERU7 Q9BQ61 C19orf43 Uncharacterized protein C19orf43 0 ; 96.711 0.013151 243726000 429340 401623 424080 396142 483820 326100 500580 421710 546410 FALSE TRUE 402468.3758 431359.5848 434139.3779 406307.6744 445822.7288 420239.7762 425522.6762 474361.4218 455210.6411 0.884136572 0.947604353 0.953710961 0.892570686 0.979376773 0.923176522 0.934781918 1.042070152 1 18.79617476 1.247261737 24.9652859 1.021035079 0.934653253 0.614946624 0.029572286 100.9914318 289770.6765 0.018329014 0.006467577 17.67102482 -1.247261737 -0.086381826 KMEES(ph)DEEAVQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KMEESDEEAVQAK 13 1 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 KMEES(1)DEEAVQAK;KMEES(1)DEEAVQAK;KMEES(1)DEEAVQAK;KMEES(1)DEEAVQAK 187.75 2.87E-06 2654520000 5089940 2772930 3434470 3439230 3728850 2493270 4789910 3149690 5362220 TRUE FALSE 4771369.741 2978240.622 3515937.25 3527486.464 3436001.162 3213036.574 4071707.463 3542935.73 4467230.841 1.068082199 0.666686081 0.78705072 0.789636039 0.769156841 0.7192457 0.911461173 0.793094393 1 22.09094938 0.554602101 0.782860258 0.999971639 0.786483421 0.192178369 0.111923681 2.002902075 2.035179144 0.104467101 0.035035396 3.585932419 -0.554602101 -0.213488218 KMEIYRPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KMEIYRPHK 9 2 Q92769;Q92769-3;H3BM24;E5RFI6;E5RJ04;E5RGV4;E5RHE7;E5RH52;E5RG37;E5RFP9;E5RK19;Q13547;Q5TEE2 Q92769;Q13547 HDAC2;HDAC1 Histone deacetylase 2;Histone deacetylase 1 0 ; 132.78 0.00017745 1311110000 2318700 2190600 2229900 2243700 2582600 1862800 2702900 2367300 2815400 FALSE TRUE 2173576.706 2352794.303 2282794.281 2301277.141 2379773.014 2400560.12 2297625.237 2662862.616 2345491.552 0.926704129 1.003113527 0.973269027 0.981149192 1.014615897 1.023478476 0.979592203 1.13531111 1 21.16145887 2.264973387 0.785729605 1.042775155 0.972829516 0.324445681 0.043996694 0.863555828 1.02479689 0.032585495 0.020278189 184.0659203 -2.264973387 -0.069945639 KMENCLGESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KMENCLGESR 10 1 Q9UHB6;Q9UHB6-4;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;; 115.33 0.0019845 1052270000 1297820 1416470 1216040 1237430 1801050 1020880 1513910 1390020 2353380 FALSE TRUE 1216591.763 1521346.913 1244885.043 1269184.549 1659602.798 1315591.483 1286913.25 1563567.057 1960585.675 0.620524662 0.775965535 0.634955697 0.6473497 0.846483181 0.671019635 0.656392254 0.79749999 1 20.90285326 0.928126799 4.061400291 0.999841738 0.69676792 0.665506804 0.069286973 0.186363707 7.817693047 0.062219075 0.015896789 8.474748117 -0.928126799 -0.303073818 KMGS(ph)CDGEGLLTSPDQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KMGSCDGEGLLTSPDQPR 18 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 KMGS(1)CDGEGLLTSPDQPR;KMGS(1)CDGEGLLTSPDQPR;KMGS(1)CDGEGLLTSPDQPR 202.2 8.08E-16 1302830000 1480510 974800 1188230 969650 1157170 909510 1236450 902980 1278620 TRUE FALSE 1387847.522 1046975.206 1216415.377 994532.8606 1066290.536 1172070.772 1051055.801 1015719.041 1065210.062 1.30288623 0.982881446 1.141948823 0.933649518 1.00101433 1.100318908 0.986712235 0.953538722 1 20.02270653 4.74342678 24.92849522 1.021874237 1.30288635 0.66924568 0.063853342 306.025083 1567658.932 0.014725006 0.121264179 55389.41517 -4.74342678 0.281012114 KMGSCDGEGLLTS(ph)PDQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KMGSCDGEGLLTSPDQPR 18 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 KMGSCDGEGLLT(0.096)S(0.904)PDQPR;KMGSCDGEGLLT(0.056)S(0.944)PDQPR;KMGSCDGEGLLT(0.073)S(0.927)PDQPR;KMGSCDGEGLLT(0.151)S(0.849)PDQPR;KMGSCDGEGLLT(0.1)S(0.9)PDQPR 183.86 3.75E-14 2328620000 1775940 1686740 1846550 1962060 2394400 1293980 1814280 1583700 2211900 TRUE FALSE 1664787.086 1811627.985 1890351.038 2012409.781 2206353.483 1667531.02 1542245.557 1781428.431 1842719.601 0.903440266 0.983127321 1.025848446 1.092086816 1.197335439 0.904929334 0.836939899 0.966738743 1 20.81340513 2.091476812 24.99999336 0.904951546 1.034451422 0.281558876 0.086411845 20.41023364 5569.747011 0.032530821 0.024025607 123.4459403 -2.091476812 0.129499876 KMIDQVFGVLES(ph)PELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KMIDQVFGVLESPELSR 17 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 KMIDQVFGVLES(1)PELSR 90.884 0.0022616 44057000 61536 68911 64942 78581 80272 55970 69037 60024 85490 TRUE FALSE 57684.5716 74013.24214 66482.45491 80597.5215 73967.76092 72127.6304 58685.54276 67518.12853 71221.16671 0.809935785 1.039202888 0.933464839 1.131651238 1.038564297 1.012727448 0.823990191 0.948006494 1 16.12001845 -0.847557258 6.386282345 0.999999999 0.968886525 0.010720845 0.097846091 2.08E-09 3.26E-10 0.093164278 0.02195903 0.142050492 0.847557258 -0.031113473 KMKDTDSEEEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KMKDTDSEEEIR 12 2 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 70.26 0.026863 350230000 610890 507990 565970 531300 626480 349150 737860 548680 1085500 FALSE TRUE 572655.4854 545602.1082 579395.0757 544934.0575 577278.7879 449943.937 627224.743 617183.9058 904323.0374 0.633242173 0.603326561 0.640694809 0.602587831 0.638354619 0.497547799 0.693584833 0.68248168 1 19.78647869 0.616549029 1.292523369 0.999544286 0.610859086 0.867908642 0.047137429 0.41775929 1.018559786 0.040516422 0.012139722 4.135700006 -0.616549029 -0.3886852 KMKDTDSEEEIREAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KMKDTDSEEEIREAFR 16 3 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 176.81 1.34E-09 177190000 225190 280060 261180 313980 447440 155000 375580 247710 1091100 FALSE TRUE 211095.7599 300795.9338 267375.3129 322037.2584 412299.8673 199745.9838 319265.2657 278637.1388 908988.3612 0.232231532 0.330912855 0.294146025 0.354280948 0.453581019 0.21974537 0.351231412 0.306535431 1 19.7939023 -1.742543687 2.610821181 1.144661779 0.319964689 0.914406049 0.065588251 10759414.45 8207120.216 10060771.98 0.014715367 0.018090739 1.742543687 -0.824697089 KMLGEDS(ph)DEEEEMDTSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KMLGEDSDEEEEMDTSER 18 1 A0A087X0M4;A0A087WWF4;Q9BWU0;H7C256 A0A087X0M4 SLC4A1AP Kanadaptin 1 KMLGEDS(1)DEEEEMDTSER;KMLGEDS(1)DEEEEMDTSER;KMLGEDS(1)DEEEEMDTSER;KMLGEDS(1)DEEEEMDTSER 156.92 4.96E-09 1100760000 1565410 1111678 1263870 1218936 1388060 920463 1506280 1117750 1778130 TRUE FALSE 1467433.782 1193987.796 1293849.593 1250215.961 1279047.367 1186185.726 1280427.298 1257303.548 1481348.616 0.990606645 0.806014049 0.873426808 0.843971465 0.863434409 0.800747179 0.864365946 0.848756015 1 20.49847977 -1.397975999 5.089362186 1.000125114 0.855048101 0.407146109 0.052053668 6.41E-05 7.58E-06 0.043721685 0.010296435 0.039996685 1.397975999 -0.145077013 KMMDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KMMDKR 6 2 Q5T5C7 Q5T5C7 SARS 0 ;; 67.035 0.048168 71579800 46615.3 172255 77487.2 82667.9 175796 72473.7 78377.8 129321 171745 FALSE TRUE 43697.73158 185008.9394 79325.23298 84789.29827 161989.6913 93395.68068 66625.77651 145467.0115 143079.65 0.305408432 1.293048588 0.554413105 0.592602081 1.132164436 0.652753069 0.465655154 1.016685542 1 17.12645897 3.78941254 24.99930771 0.735030713 0.885961517 0 0.323566337 437.1513833 175438.1225 0.076737195 0.138339918 6157.615125 -3.78941254 0.150930805 KMPFTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KMPFTEK 7 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 101.54 0.014404 1675100000 1785360 1811800 1830920 1846300 2367200 1412360 2467500 2007950 2858200 FALSE TRUE 1673617.505 1945947.557 1874350.287 1893679.184 2181289.661 1820085.404 2097521.282 2258646.978 2381147.955 0.702861618 0.817230846 0.787162462 0.795279932 0.916066411 0.764373083 0.880886581 0.948553815 1 21.18322584 KMPKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KMPKPR 6 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ; 94.95 0.024691 1016480000 1088650 1164970 1190970 1187480 1154690 791740 1230000 989710 1435990 FALSE TRUE 1020513.34 1251225.591 1219220.371 1217952.747 1064005.305 1020302.485 1045572.919 1113277.472 1196313.992 0.853048068 1.045900657 1.019147464 1.018087856 0.889403043 0.852871814 0.873995394 0.930589694 1 20.19016467 2.734373166 24.83498217 0.894715331 1.000205363 0.208482125 0.065829886 327.6668 1943323.501 0.019575415 0.019052663 542.4668034 -2.734373166 0.105490031 KMPLDLS(ph)PLATPIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KMPLDLSPLATPIIR 15 1 B8ZZU6;E9PBF9;P15336-5;P15336;E9PEK8;H7C2N6;P15336-3;P15336-7;P15336-4;C9JCI8 B8ZZU6 ATF2 Cyclic AMP-dependent transcription factor ATF-2 1 KMPLDLS(1)PLATPIIR;KMPLDLS(0.999)PLAT(0.001)PIIR 161.08 1.02E-06 119300000 568420 577220 570550 531750 888900 493790 736830 716140 1130050 TRUE FALSE 532843.6069 619957.9694 584083.7154 545395.6053 819089.3797 636339.157 626349.1819 805551.6554 941437.3546 0.565989446 0.658522807 0.620416975 0.579322249 0.8700413 0.675922996 0.665311589 0.855661454 1 19.84450557 -5 0.113419694 2.122211275 0.488565475 0.677987168 0.080571979 94.26190177 0.705392166 24.07376431 0.874340579 1.00E-05 5 -1.6336458 KMQQNIQELEEQLEEEESAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KMQQNIQELEEQLEEEESAR 20 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 254.32 6.39E-36 578680000 518560 611180 570980 612320 673770 463430 683710 513540 764890 FALSE TRUE 486104.2553 656432.4031 584523.9152 628033.1679 620854.8221 597214.7178 581194.0328 577656.5994 637224.9176 0.762845648 1.030142396 0.917296074 0.985575345 0.974310334 0.937211809 0.912070474 0.906519164 1 19.28144316 7.998819472 0.005899091 1.816491307 8.64E-06 0.080307854 0.070515179 163442.8423 74.61214764 10522.48643 12534.07619 99728542.61 -7.998819472 -1.816482668 KMS(ph)DDEDDDEEEYGKEEHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KMSDDEDDDEEEYGKEEHEK 20 2 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 1 KMS(1)DDEDDDEEEYGKEEHEK;KMS(1)DDEDDDEEEYGKEEHEK;KMS(1)DDEDDDEEEYGKEEHEK;KMS(1)DDEDDDEEEYGKEEHEK 188.8 1.26E-17 2176760000 2814170 673543 1203026 1111258 1049574 763513 1539850 836527 1207847 TRUE FALSE 2638036.123 723412.8245 1231562.345 1139774.762 967144.6918 983926.8085 1308963.788 940969.2374 1006249.533 2.621652023 0.718919911 1.223913458 1.132695941 0.961138028 0.977815916 1.300834182 0.935125142 1 19.94055668 4.745970717 24.99457324 1.049222091 2.621652769 0.904101963 0.162683026 260.1319215 877414.5426 0.0383675 0.401920293 55714.81809 -4.745970717 1.572430678 KMS(ph)GGSTMSSGGGNTNNSNSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 KMSGGSTMSSGGGNTNNSNSK 21 1 Q86U70-2;Q86U70;A0A6E1WJ75;Q86U70-3 Q86U70-2 LDB1 LIM domain-binding protein 1 1 KMS(0.678)GGS(0.138)T(0.138)MS(0.036)S(0.01)GGGNTNNSNSK;KMS(0.991)GGS(0.007)T(0.001)MSSGGGNTNNSNSK;KMS(0.94)GGS(0.049)T(0.01)MSSGGGNTNNSNSK;KMS(0.693)GGS(0.152)T(0.152)MS(0.003)SGGGNTNNSNSK;KMS(0.487)GGS(0.234)T(0.234)MS(0.037)S(0.006)GGGNTNNSNSK;KMS(0.989)GGS(0.009)T(0.002)MSSGGGNTNNSNSK;KMS(0.918)GGS(0.066)T(0.016)MSSGGGNTNNSNSK;KMS(0.979)GGS(0.014)T(0.006)MSSGGGNTNNSNSK;KMS(1)GGSTMSSGGGNTNNSNSK 244.74 1.53E-30 1742836000 1781098 1224921 1445479 1495389 1556028 1093265 1833694 1364421 1964501 TRUE FALSE 1669622.256 1315615.425 1479766.444 1533763.213 1433823.838 1408872.858 1558748.608 1534771.965 1636613.092 1.020169192 0.803864659 0.904163881 0.937156877 0.876092123 0.860846626 0.952423401 0.937773242 1 20.64228187 1.224817531 1.298971044 0.99456734 0.89079549 0.202110641 0.057461115 0.526016494 1.746099075 0.049726275 0.015649537 16.78098815 -1.224817531 -0.10377185 KMS(ph)QPGS(ph)PSPK ddPTM_SK-BR-3_Pertuzumab_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(1)QPGS(0.696)PS(0.304)PK;KMS(0.987)QPGS(0.642)PS(0.371)PK 147.75 2.31E-05 117746000 648030 299170 439610 356790 293840 264010 517980 328470 440090 TRUE FALSE 607470.9591 321320.8581 450037.7568 365945.8354 270762.9917 340225.4012 440313.7077 369480.2026 366636.1359 1.65687694 0.876402587 1.227477907 0.998117206 0.738506015 0.927964725 1.200955565 1.007757191 1 18.48398946 4.746171811 24.95365815 1.01463946 1.656877256 0.676994574 0.142758622 585.4366857 1919335.101 0.034846489 0.370739968 55740.62202 -4.746171811 0.642237796 KMS(ph)QPGSPS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(1)QPGS(0.048)PS(0.952)PK 102.5 0.0019111 148870000 698820 321320 475610 413000 354160 292530 570210 374850 511870 TRUE FALSE 655082.1036 345110.8671 486891.6938 423598.2792 326345.7022 376978.6622 484712.3041 421650.8476 426435.5902 1.536180654 0.809291896 1.141770774 0.993346449 0.765287208 0.884022513 1.136660061 0.988779683 1 18.70196832 4.74920831 24.69208054 0.974343808 1.536181031 0.682361377 0.122343259 808.8142606 1875602.928 0.02941067 0.423743552 56131.71476 -4.74920831 0.561837223 KNDKEAAGEGPALYEDPPDQK ddPTM_SK-BR-3_Pertuzumab_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 61.511 0.02719 164690000 145760 101490 108200 134100 188780 78664 166010 101790 370720 FALSE TRUE 136637.1418 109004.4252 110766.5551 137541.233 173953.9803 101373.0198 141118.3417 114498.7056 308844.4371 0.442414126 0.352942816 0.358648374 0.445341462 0.563241423 0.328233271 0.456923696 0.370732614 1 18.23652082 -2.092464302 2.424522381 1.989905111 0.409262467 0.878245236 0.068447719 4672622.527 1362761.238 25537475.04 0.016028542 0.008082314 2.092464302 -1.580642644 KNELEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KNELEQK 7 1 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 90.71 0.02716 285550000 392020 265420 307110 306850 347140 234410 362210 259000 348030 FALSE TRUE 367484.168 285071.973 314394.7942 314724.2905 319877.0247 302080.3617 307899.9731 291336.7201 289941.5446 1.267442265 0.983204988 1.08433855 1.085474974 1.103246605 1.041866429 1.0619381 1.00481192 1 18.14540254 KNGFVVLK ddPTM_SK-BR-3_Pertuzumab_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 ; 129.47 0.003537 0 1613340 1887470 1625430 1571560 2113060 1384980 2057530 1766650 2328200 FALSE TRUE 1512363.929 2027220.243 1663985.967 1611888.89 1947108.791 1784801.243 1749022.478 1987220.141 1939608.379 0.779726436 1.045169873 0.857897906 0.831038321 1.003866972 0.920186395 0.901740009 1.024547101 1 20.88733396 1.23802832 24.99986499 1.012273591 0.91549612 0.239404794 0.077474932 21.15130071 992947.4326 0.05641904 0.017390049 17.29929163 -1.23802832 -0.096777471 KNGSTAVAESVAS(ph)PQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KNGSTAVAESVASPQK 16 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 KNGSTAVAES(0.002)VAS(0.998)PQK;KNGSTAVAESVAS(1)PQK;KNGSTAVAESVAS(1)PQK;KNGSTAVAESVAS(1)PQK;KNGSTAVAESVAS(1)PQK;KNGSTAVAESVAS(1)PQK 191.79 3.91E-10 5644470000 6578920 4183370 4977060 4613170 5331460 3948290 7104090 4618460 6178450 TRUE FALSE 6167157.141 4493111.068 5095118.214 4731551.752 4912748.638 5088097.228 6038897.656 5195084.897 5147226.781 1.198151433 0.872918808 0.98987638 0.919242915 0.954445733 0.988512347 1.17323326 1.009297845 1 22.29536392 1.966669028 20.12260744 1.080287533 0.968937137 0.086993089 0.097183225 84.92226568 51267.83553 0.036297439 0.023459941 92.61237626 -1.966669028 -0.111350396 KNHLEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KNHLEGK 7 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 114.6 0.0038093 1031280000 4105970 3507680 3765230 3587950 4179100 2762170 4562800 3645820 4531600 FALSE TRUE 3848984.667 3767392.277 3854543.034 3680022.871 3850890.344 3559563.639 3878650.499 4101008.652 3775246.685 1.019531964 0.997919498 1.021004283 0.974776797 1.020036746 0.942869152 1.027389949 1.086288922 1 21.84813949 1.498316336 8.987595609 1.04764856 0.998392443 0.289356261 0.031326354 0.108758026 22.02398792 0.015039519 0.006951631 31.50041938 -1.498316336 -0.049256116 KNIIEATHMYDNAAEACSTTEEVFNS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KNIIEATHMYDNAAEACSTTEEVFNSPR 28 1 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 KNIIEATHMYDNAAEACSTTEEVFNS(1)PR 228.49 4.28E-35 268670000 141010 135900 140680 153390 196400 160140 211410 146140 264980 TRUE FALSE 132184.4358 145962.1774 144016.996 157326.2471 180975.5362 206369.8183 179711.0331 164385.9007 220753.1262 0.598788511 0.661200953 0.652389384 0.712679588 0.819809619 0.934844375 0.814081487 0.744659446 1 17.75207434 2.842192827 2.23310421 0.858214658 0.644478109 0.695237425 0.069684302 0.174059175 1.708294535 0.022367331 0.023769035 695.3329767 -2.842192827 -0.213736549 KNILEESLCELVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KNILEESLCELVAK 14 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 119.31 0.0003123 36520000 172720 163110 157350 178280 182710 125300 219150 165310 180050 FALSE TRUE 161909.7635 175186.8341 161082.4163 182854.9666 168360.6936 161472.0759 186290.492 185949.3174 149998.4918 1.079409276 1.16792397 1.073893573 1.219045368 1.122415909 1.07649133 1.2419491 1.23967458 1 17.19458847 3.251845488 24.997867 1.160943397 1.115374268 0.046280885 0.079184222 650.6076843 1224228.89 0.020573884 0.027704352 1785.852099 -3.251845488 -0.045569129 KNLQYYDISAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KNLQYYDISAK 11 1 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 134.98 0.00020787 839990000 1774180 1598820 1595410 1620650 1739700 1295950 2010100 1669480 2119120 FALSE TRUE 1663137.241 1717198.296 1633253.879 1662238.623 1603070.98 1670069.727 1708704.166 1877918.253 1765425.182 0.94206045 0.972682566 0.925133444 0.94155144 0.90803677 0.945987258 0.967871187 1.063720101 1 20.75158425 1.427408235 3.969190369 1.030977167 0.941187336 0.734489452 0.022574257 0.105322897 2.926666662 0.015477237 0.005513057 26.75520202 -1.427408235 -0.089789831 KNLTQDEMQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KNLTQDEMQR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 94.191 0.013263 131000000 160830 178980 171330 164740 185950 134250 193350 165950 208210 FALSE TRUE 150763.9374 192231.8654 175394.0285 168967.5073 171346.2371 173005.7956 164358.9625 186669.2228 173458.4059 0.869164781 1.108230324 1.011159001 0.974109651 0.987823197 0.99739067 0.947541064 1.076161295 1 17.40423023 3.468417296 21.42095529 0.991129467 1.024196094 0 0.067202278 108.7605668 267663.6041 0.017144107 0.023392577 2940.473674 -3.468417296 0.033066627 KNNIDTHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KNNIDTHAR 9 1 O43847;O43847-2;F5H7V1;G3V1R5 O43847 NRD1 Nardilysin 0 64.297 0.045723 76245000 74920 105130 85220 88354 120020 76796 102280 99016 107860 FALSE TRUE 70230.89094 112913.9346 87241.45864 90621.31322 110594.1133 98965.75852 86944.06352 111378.3656 89857.4692 0.781581003 1.256589303 0.970887111 1.008500618 1.230772626 1.101363742 0.967577479 1.239500362 1 16.45535081 4.759933642 24.54653717 1.090049296 0.781580603 0.435736898 0.112526695 4259.454747 4891807.387 0.025312133 1.167030388 57535.20197 -4.759933642 -0.308468693 KNPDSQYGELIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KNPDSQYGELIEK 13 1 P30085;P30085-3;Q5T0D2 P30085 CMPK1 UMP-CMP kinase 0 ;; 236.4 1.65E-16 2171050000 3850110 2801040 3467500 3222800 3529580 2656200 4393120 3036280 5043350 FALSE TRUE 3609138.488 3008431.916 3549750.737 3305502.504 3252381.024 3423001.82 3734412.44 3415366.242 4201582.304 0.858995071 0.716023559 0.844860455 0.786728015 0.774084806 0.814693507 0.888810969 0.812876196 1 22.00250131 0.090224993 0.372510933 1.035081437 0.781134753 0.628142004 0.04628781 2.488315824 0.508695062 0.180739179 0.03496724 1.230906296 -0.090224993 -0.253946685 KNPEVPVNFAEFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KNPEVPVNFAEFSK 14 1 O15347;E7ES08;E7EQU1;E9PES6 O15347 HMGB3 High mobility group protein B3 0 ; 155.92 9.16E-06 1305320000 1514300 1424670 1363980 1488300 1617040 1088140 1804730 1248140 1776990 FALSE TRUE 1419522.666 1530154.049 1396334.25 1526492.298 1490044.201 1402268.354 1534127.491 1403973.026 1480398.889 0.9588785 1.033609293 0.943214873 1.031135803 1.006515347 0.947223322 1.036293327 0.948374818 1 20.49755453 KNPLPPSVGVVDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KNPLPPSVGVVDKK 14 2 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 92.575 0.0027583 1139200000 2394800 1451400 1827200 1757500 1872400 1427000 2450400 1500000 2341200 FALSE TRUE 2244913.743 1558863.166 1870542.047 1802600.425 1725349.257 1838951.735 2082985.268 1687278.302 1950438.595 1.150978938 0.799237243 0.959036625 0.924202602 0.884595527 0.942840107 1.067957368 0.865076351 1 20.89536715 1.982969027 23.80476523 0.990271235 0.924192187 0 0.100902341 976.1522891 1364398.693 0.037143558 0.024644468 96.15437005 -1.982969027 -0.066079048 GPS(ph)WDPFRDWYPHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 136.49 1.37E-05 3377229000 2100514 3053036 2133701 2127251 3599935 1483191 2521700 2997178 6366680 TRUE FALSE 1969046.578 3279085.962 2184313.395 2181839.862 3317210.627 1911364.164 2143594.495 3371382.271 5304039.978 0.371235245 0.618224217 0.411820688 0.41135434 0.625412071 0.36036006 0.404143729 0.635625351 1 22.33866022 0.919608253 3.983543374 0.999727535 0.466232094 0.772094074 0.093643823 0.163858324 6.279192182 0.086369952 0.022093295 8.310138325 -0.919608253 -0.533495441 KNQKPSQVNGAPGS(ph)PTEPAGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KNQKPSQVNGAPGSPTEPAGQK 22 2 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 KNQKPS(0.003)QVNGAPGS(0.889)PT(0.108)EPAGQK;KNQKPSQVNGAPGS(0.966)PT(0.034)EPAGQK 147.25 4.15E-08 1257150000 1046000 631870 797380 865400 849870 590740 1165270 756150 1073690 TRUE FALSE 980532.7272 678654.3123 816294.2302 887607.6291 783124.6384 761277.0481 990548.5813 850556.992 894484.2027 1.096199043 0.758710227 0.912586525 0.992312247 0.875504158 0.851079366 1.107396395 0.950891016 1 19.77069648 1.748170131 25 1.02615363 0.897725969 0.195247401 0.096322907 2.988854782 7792.492686 0.041785024 0.02317181 55.99769246 -1.748170131 -0.128427661 KNQTALDALHAQTVSQTAASS(ph)PQDAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KNQTALDALHAQTVSQTAASSPQDAYR 27 1 Q8TEK3;Q8TEK3-1 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 KNQTALDALHAQTVSQTAAS(0.208)S(0.792)PQDAYR 196.06 3.03E-25 114060000 127840 128150 139250 146050 159600 114370 132910 127700 157060 TRUE FALSE 119838.7226 137638.3593 142553.0758 149797.8903 147065.6598 147386.7624 112981.3794 143643.6261 130845.6714 0.915878388 1.051913739 1.089474908 1.144844065 1.123962744 1.1264168 0.863470516 1.097809539 1 16.99750667 1.762903965 25 0.974229868 1.07886337 0.189606127 0.084495502 19.273641 19807.57985 0.037070745 0.020558872 57.93005823 -1.762903965 0.104633502 KNREELDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KNREELDK 8 2 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;; 164.68 0.00018485 16032290000 21675890 12704430 15876690 14566240 15732520 13080770 19906210 13949220 20455990 FALSE TRUE 20319234.74 13645079.22 16253292.58 14940034.38 14496951.34 16856975.95 16921458.61 15690810.82 17041753.12 1.192320684 0.800685183 0.953733602 0.876672387 0.850672536 0.989157385 0.992941189 0.920727505 1 24.02257042 2.189673407 24.9938175 0.977529374 0.916462498 0.019604027 0.105886194 308.1566131 157544.4274 0.036281662 0.026795835 154.7652335 -2.189673407 -0.061066877 KNREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 KNREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR 39 3 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;; 271.48 6.65E-77 2747099000 766911 750934 748717 749072 921240 567573 947378 694064 1518014 FALSE TRUE 718911.4095 806533.9347 766476.9208 768294.4557 848889.5265 731422.1113 805327.4639 780719.4182 1264647.657 0.568467751 0.637753868 0.606079422 0.607516609 0.671245878 0.57836039 0.63679987 0.61734145 1 20.27030406 -4.667815289 0.513078549 9.999826612 0.614950665 0.944571675 0.029285266 363.9276557 2.332280803 3741.422325 0.011728129 2.15E-05 4.667815289 -9.384875946 KNS(ph)FGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KNSFGYR 7 1 Q92615;H0Y4V9 Q92615 LARP4B La-related protein 4B 1 KNS(1)FGYR;KNS(1)FGYR;KNS(1)FGYR;KNS(1)FGYR 120.09 0.0028391 5664630000 8522000 6584800 6856300 6503200 7053200 5610330 8975000 6656000 10521200 TRUE FALSE 7988623.232 7072345.443 7018934.674 6670083.122 6499270.123 7229941.195 7629282.07 7487016.252 8765143.75 0.911408125 0.806871586 0.800778045 0.760978178 0.74149042 0.824851412 0.870411517 0.854180657 1 23.06334632 0.825485847 0.953386989 0.997830246 0.803897872 0.608573971 0.046923324 0.517298064 0.926155555 0.044055859 0.014647164 6.690920143 -0.825485847 -0.193932373 KNS(ph)IHELLLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KNSIHELLLER 11 1 F5H527;Q76I76;A0A3B3IS79 F5H527 SSH2 Protein phosphatase Slingshot homolog 2 1 KNS(1)IHELLLER;KNS(1)IHELLLER 162.59 1.53E-05 376820000 363420 298590 307820 277160 349220 258700 428050 358760 515490 TRUE FALSE 340674.1909 320697.9143 315121.6358 284272.3948 321793.6699 333382.4904 363867.8763 403551.9757 429451.3888 0.793277656 0.746761852 0.733777196 0.661943126 0.749313376 0.77629855 0.847285364 0.939691863 1 18.71213531 1.404848342 1.331403339 0.998252258 0.734448866 0.898413062 0.032039694 0.115615152 0.390817338 0.029112321 0.009517806 25.40085538 -1.404848342 -0.263803392 KNS(ph)LISSLEEEVSILNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KNSLISSLEEEVSILNR 17 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 KNS(0.998)LIS(0.001)S(0.001)LEEEVSILNR;KNS(1)LISSLEEEVSILNR;KNS(0.996)LIS(0.004)S(0.001)LEEEVSILNR;KNS(1)LISSLEEEVSILNR;KNS(1)LISSLEEEVSILNR;KNS(0.991)LIS(0.009)SLEEEVSILNR 223.07 1.93E-15 2161943800 363535 251259 302323 276271 292776 245304 379558 254811 533099 TRUE FALSE 340781.9933 269862.4778 309494.2443 283360.5816 269782.554 316119.2826 322646.8015 286624.7143 444121.3329 0.767317325 0.607632324 0.696868674 0.638025153 0.607452365 0.711785855 0.726483458 0.645374795 1 18.76059435 -2.859732369 0.397180983 1.736819298 0.664198868 0.785718572 0.053042861 44.71885142 1.591130369 27.8888092 0.031292124 0.001381235 2.859732369 -1.07262043 KNS(ph)STDQGS(ph)DEEGSLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KNSSTDQGSDEEGSLQK 17 1 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 2 KNS(0.605)S(0.183)T(0.213)DQGS(0.999)DEEGSLQK 68.42 0.044888 0 168300 87440 105630 121890 126740 83216 150470 96138 128530 TRUE FALSE 157766.4034 93914.14858 108135.5935 125017.9038 116786.3516 107239.1083 127908.4204 108141.0409 107077.5127 1.473385023 0.877066961 1.009881447 1.167545833 1.090671129 1.001509146 1.194540452 1.009932321 1 16.70829601 KNS(ph)TGSGHSAQELPTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KNSTGSGHSAQELPTIR 17 1 O94763-3;O94763;O94763-2;O94763-4;I3L280 O94763-3 URI1 Unconventional prefoldin RPB5 interactor 1 1 KNS(0.943)T(0.052)GS(0.005)GHSAQELPTIR;KNS(0.94)T(0.056)GS(0.004)GHSAQELPTIR;KNS(0.941)T(0.041)GS(0.018)GHSAQELPTIR;KNS(0.949)T(0.032)GS(0.019)GHSAQELPTIR 249.51 2.23E-21 4024240000 1163180 1145980 1211350 1348990 1627170 913930 1315950 1093380 1730170 TRUE FALSE 1090378.64 1230829.552 1240083.794 1383607.367 1499378.632 1177766.755 1118635.514 1229890.9 1441393.45 0.756475368 0.853916432 0.860336776 0.959909571 1.04022856 0.817102891 0.776079227 0.853265221 1 20.45903276 -3.496036903 0.012429467 1.90730916 2.63E-06 0.159541516 0.085484817 18368.07729 22.47461559 1990.03277 1490.495619 0.000319127 3.496036903 -1.907306531 KNS(ph)WEPKPITVPQFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KNSWEPKPITVPQFK 15 2 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 KNS(1)WEPKPITVPQFK 112.36 0.00040162 772060000 1633900 794750 1030900 1074900 1152100 832340 1650800 1125300 2362500 TRUE FALSE 1531637.116 853594.1169 1055353.435 1102483.754 1061618.713 1072623.046 1403277.865 1265796.182 1968183.488 0.778198336 0.433696412 0.536206833 0.560152933 0.539390113 0.544981224 0.712981221 0.643129154 1 20.90843329 0.606105721 0.654030287 1.006192371 0.539312037 0.6540181 0.094617797 0.759169848 0.597561062 0.09737625 0.034333684 4.037436653 -0.606105721 -0.466880335 KNSAS(ph)AERDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KNSASAERDR 10 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 KNS(0.006)AS(0.994)AERDR;KNS(0.001)AS(0.999)AERDR 87.863 0.0099123 352200000 671460 655870 639300 708880 882430 470170 805140 672530 1200190 TRUE FALSE 629434.5172 704431.2972 654464.4979 727071.0609 813127.5074 605900.4464 684416.7316 756496.8509 999870.5355 0.629516017 0.704522508 0.654549239 0.727165203 0.813232792 0.605978899 0.684505351 0.756594803 1 19.93138178 0.822272787 2.978829151 0.999898627 0.688306828 0.748065018 0.05659666 0.397642452 5.765101534 0.051475772 0.013491546 6.641601083 -0.822272787 -0.311591798 KNTFTAWS(ph)DEES(ph)DYEIDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KNTFTAWSDEESDYEIDDR 19 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 2 KNTFTAWS(1)DEES(0.978)DY(0.022)EIDDR;KNTFTAWS(1)DEES(0.999)DY(0.001)EIDDR 113.91 0.00058747 512750000 806990 488130 660690 601740 564900 578280 816480 516730 495110 TRUE FALSE 756481.9364 524271.6531 676361.8788 617181.6671 520535.0327 745220.0484 694056.4038 581244.878 412472.9425 1.834015904 1.271044956 1.63977272 1.496296129 1.261985888 1.806712566 1.682671352 1.409170925 1 18.65393996 0.941553389 7.768157464 1.000003702 1.552934291 0.463651351 0.192963231 0.933669306 123.6608302 0.177773295 0.044532244 8.740844402 -0.941553389 0.552930589 KNTFTAWS(ph)DEES(ph)DYEIDDRDVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KNTFTAWSDEESDYEIDDRDVNK 23 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 2 KNTFTAWS(1)DEES(1)DYEIDDRDVNK;KNT(0.005)FT(0.024)AWS(0.971)DEES(1)DYEIDDRDVNK;KNTFTAWS(1)DEES(1)DYEIDDRDVNK;KNT(0.001)FT(0.001)AWS(0.998)DEES(0.998)DY(0.002)EIDDRDVNK;KNTFTAWS(1)DEES(1)DYEIDDRDVNK 258.02 6.68E-44 1948250000 2584730 1434284 1823994 1883610 2108990 1272395 2426090 1594286 2788560 TRUE FALSE 2422956.363 1540479.88 1867259.999 1931946.622 1943358.433 1639714.781 2062320.327 1793336.117 2323131.321 1.042970038 0.66310495 0.803768595 0.831613178 0.836525432 0.705820961 0.887732996 0.771947802 1 21.14763928 -1.565561666 2.663284058 1.013580966 0.804924305 0.226025272 0.10341769 16556994.58 15993415.92 1596951.401 0.023060551 0.027191824 1.565561666 -0.208656661 KNTFTAWS(ph)DEESDYEIDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KNTFTAWSDEESDYEIDDR 19 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 KNTFTAWS(1)DEESDYEIDDR;KNTFTAWS(0.998)DEES(0.002)DYEIDDR 215.08 2.54E-19 373880000 754250 445700 625440 544850 506580 566370 726030 503370 463980 TRUE FALSE 707042.8389 478700.0918 640275.7322 558831.7734 466795.2502 729871.8248 617168.5416 566216.8526 386538.7406 1.829164233 1.238427204 1.656433534 1.445732898 1.207628631 1.888224253 1.596653781 1.464838561 1 18.56025349 KNTFTAWS(ph)DEESDYEIDDRDVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KNTFTAWSDEESDYEIDDRDVNK 23 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 KNTFT(0.004)AWS(0.996)DEESDYEIDDRDVNK;KNTFT(0.003)AWS(0.94)DEES(0.058)DYEIDDRDVNK 224.14 1.07E-32 423560000 206231 116658 163246 150557 182703 114838 191046 124327 231070 TRUE FALSE 193323.3698 125295.4797 167118.2722 154420.5475 168354.2434 147989.8664 162400.4259 139849.4996 192502.9242 1.00426199 0.650875722 0.868133681 0.802172477 0.874554213 0.768766848 0.843625761 0.726479871 1 17.55452084 -1.128985625 4.231286167 1.000039468 0.808682813 0.264827657 0.094658299 27670823797 5696115955 11091190.75 0.019476519 0.074304373 1.128985625 -0.191356655 KNTLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KNTLAR 6 1 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ; 107.66 0.049833 4314900000 6457300 8952500 6030800 6548900 9553200 3825700 7059400 8484400 9843600 FALSE TRUE 6053149.12 9615352.415 6173853.424 6716955.861 8802930.208 4930117.485 6000908.506 9543696.016 8200639.568 0.738131346 1.172512502 0.752850235 0.819077074 1.07344435 0.601186949 0.731761036 1.163774598 1 22.967305 3.884860108 8.63364542 0.848344596 0.983046532 0.005518531 0.198244713 0.720327361 60.59950387 0.047581427 0.086042156 7671.143513 -3.884860108 0.134701936 KNVFIIGATNRPDIIDPAILRPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KNVFIIGATNRPDIIDPAILRPGR 24 3 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 206.33 3.83E-25 1532320000 2801680 3238300 2629300 2412450 3623500 2119280 3237800 2963900 3289000 FALSE TRUE 2626327.85 3478067.101 2691668.238 2474357.551 3338924.926 2731081.732 2752321.948 3333949.439 2740044.652 0.958498194 1.269346869 0.982344662 0.903035485 1.218565881 0.996728915 1.004480692 1.21675004 1 21.38576797 3.837284814 8.242497131 1.042172626 1.134314887 0.042937121 0.124254155 0.602613293 40.99545775 0.029213051 0.052831167 6875.191739 -3.837284814 0.092142261 KPAFNLSAFGTLS(ph)PSLGNSSILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPAFNLSAFGTLSPSLGNSSILK 23 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 KPAFNLSAFGTLS(0.972)PS(0.028)LGNSSILK;KPAFNLSAFGTLS(0.998)PS(0.001)LGNSSILK 157.26 5.24E-09 911700000 1236750 1084310 1085620 1017760 1309760 949700 1380240 1126870 1307700 TRUE FALSE 1159344.025 1164593.441 1111371.419 1043877.445 1206896.733 1223862.973 1173285.826 1267562.2 1089436.422 1.064168594 1.068987063 1.020134261 0.958181151 1.1078175 1.12339091 1.076965853 1.163502683 1 20.05515057 2.63234182 23.92421615 1.099586169 1.033370123 0.29183364 0.05076604 26.40052417 5930.861499 0.01520173 0.014332329 428.8859504 -2.63234182 -0.066216046 KPALPVS(ph)PAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KPALPVSPAAR 11 1 A0A087X0M4;A0A087WWF4;Q9BWU0 A0A087X0M4 SLC4A1AP Kanadaptin 1 KPALPVS(1)PAAR;KPALPVS(1)PAAR;KPALPVS(1)PAAR;KPALPVS(1)PAAR;KPALPVS(1)PAAR;KPALPVS(1)PAAR 130.21 0.00014015 3665270000 8644850 7379960 8295790 7941000 8419980 7633180 9764420 7902270 7989090 TRUE FALSE 8103784.27 7926379.917 8492570.056 8144779.504 7758708.735 9836755.152 8300335.869 8888885.805 6655659.268 1.217577996 1.190923333 1.275992312 1.223737451 1.16573106 1.477953536 1.247109495 1.335537991 1 22.66615015 3.691408744 0.938669114 1.272318382 1.201142498 0 0.122479917 2.530950271 4.192596142 0.042915816 0.132195551 4913.701199 -3.691408744 -0.071175884 KPANDITSQLEINFGDLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPANDITSQLEINFGDLGR 19 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ; 274.27 3.39E-39 4166200000 2313100 2068190 2233310 1981970 2108470 1858990 2482800 2124380 1616460 FALSE TRUE 2168327.2 2221320.94 2286285.168 2032830.706 1942879.271 2395650.235 2110527.189 2389613.519 1346662.383 1.610149082 1.649500994 1.697741911 1.509532553 1.442736721 1.778953853 1.567228145 1.774471129 1 20.36095677 -1.053249183 4.548988501 0.999968925 1.629762286 0.775156831 0.106426065 6580301.431 1523569.03 2038.676566 0.023119463 0.088460791 1.053249183 0.629793361 KPAPPRPKPPS(ph)GK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPAPPRPKPPSGK 13 3 Q9UBC2;Q9UBC2-2 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 KPAPPRPKPPS(1)GK 56.339 0.087708 320620000 494070 200480 282750 233530 274180 212920 372240 236300 262560 TRUE FALSE 463147.0406 215323.7478 289456.9635 239522.7752 252647.0088 274386.5475 316426.0677 265802.5752 218737.0398 2.117369061 0.984395455 1.323310235 1.095026135 1.155026186 1.254412823 1.446604873 1.215169481 1 17.73883801 4.7473397 24.99311126 1.209080614 2.117369524 0.808897291 0.142082435 519.5164436 1478976.128 0.034340161 0.414010058 55890.71938 -4.7473397 0.90828891 KPASFMTSICDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KPASFMTSICDER 13 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;; 194.23 1.92E-06 4890370000 5044820 6224150 4802550 5073960 6898320 3966280 5692930 5867190 7185420 FALSE TRUE 4729073.721 6684992.542 4916468.754 5204166.404 6356553.774 5111280.649 4839327.997 6599721.587 5986126.982 0.79000558 1.116747533 0.821310468 0.869371201 1.061880878 0.853854364 0.808423879 1.102502771 1 22.51319145 1.224584283 24.99607326 1.051251409 0.912613278 0.235573228 0.109925145 419.7742604 750726.6248 0.100012108 0.025514841 16.77197797 -1.224584283 -0.138638131 KPAT(ph)PAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KPATPAEDDEDDDIDLFGSDNEEEDKEAAQLR 32 2 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;H0YE72;P29692-3;E9PL71 P29692;P29692-3 EEF1D Elongation factor 1-delta 2 KPAT(1)PAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPAT(1)PAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPAT(1)PAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPAT(1)PAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPAT(1)PAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPAT(1)PAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR 270.23 3.71E-61 14140396000 2004040 853632 1049303 1104826 1097774 736262 1517519 964826 1492929 TRUE FALSE 1878610.714 916835.8015 1074192.963 1133177.706 1011559.258 948808.8872 1289981.114 1085286.65 1243749.505 1.510441376 0.737154707 0.863673077 0.911098015 0.8133143 0.76286172 1.037171157 0.872592628 1 20.24626452 4.745755129 24.99707576 0.868251711 1.510441675 0.819440604 0.09373641 359.2522921 1248178.901 0.022388296 0.230790619 55687.1676 -4.745755129 0.642189964 KPAT(ph)PAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLREER ddPTM_SK-BR-3_Pertuzumab_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 63.533 0.019869 39544000 44758 39898 37470 47628 70323 25083 42549 33921 121740 TRUE FALSE 41956.67668 42852.08943 38358.80609 48850.21511 64800.11525 32324.05491 36169.17246 38156.11152 101420.8075 0.413689042 0.422517731 0.378214363 0.481658708 0.638923282 0.318712261 0.356624773 0.376215813 1 16.62999414 -1.508439452 3.005596289 1.019352474 0.418113235 0.808773137 0.088092614 33822909.25 38253800.63 5375709.979 0.021201505 0.031014197 1.508439452 -0.601239239 KPATPAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLR ddPTM_SK-BR-3_Pertuzumab_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 421.64 7.20E-208 3.23154E+11 10112260 5527160 8100432 6306884 6240881 4540572 8452596 5325943 7242145 TRUE FALSE 9479351.697 5936396.677 8292578.072 6468729.321 5750747.381 5851361.426 7185207.7 5990898.707 6033384.213 1.571150015 0.983924853 1.374448863 1.072156039 0.953154511 0.969830732 1.19090836 0.992958263 1 22.52453603 4.746677243 24.83703295 1.092960844 1.571150274 0.587946627 0.131021626 730.0454176 2233897.326 0.031528508 0.351257038 55805.53073 -4.746677243 0.47818943 KPATPAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLREER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KPATPAEDDEDDDIDLFGSDNEEEDKEAAQLREER 35 3 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;H0YE72;P29692-3;E9PL71 P29692;P29692-3 EEF1D Elongation factor 1-delta 1 KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER 327.32 8.49E-117 10233990000 1867008 2023395 1511792 2468384 3898310 943626 1714171 1475853 7907186 TRUE FALSE 1750155.302 2173209.271 1547652.42 2531726.912 3592152.458 1216035.508 1457146.972 1660116.496 6587425.574 0.265681226 0.329902668 0.234940403 0.384327213 0.545304447 0.184599506 0.22120128 0.252012941 1 22.65128333 -1.956444009 2.734034002 1.533998084 0.297443677 0.819057823 0.103044474 11071596.47 6469887.433 37559878.88 0.025177874 0.01105493 1.956444009 -1.236554407 KPCNSQPSELSSETSGIARPEEGRPVVSGTGNDITT(ph)PPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPCNSQPSELSSETSGIARPEEGRPVVSGTGNDITTPPNK 40 3 P27816-6;P27816 P27816-6 MAP4 Microtubule-associated protein 4 1 KPCNSQPSELS(0.007)S(0.008)ET(0.008)S(0.008)GIARPEEGRPVVS(0.265)GT(0.265)GNDIT(0.144)T(0.296)PPNK;KPCNSQPSELSSETSGIARPEEGRPVVS(0.004)GT(0.004)GNDIT(0.216)T(0.776)PPNK 69.344 0.001648 1872170000 987690 650642 839910 726482 778000 686792 989950 683760 597850 TRUE FALSE 925872.246 698816.2107 859833.0618 745124.7581 716899.0183 885057.7013 841516.1877 769128.9411 498064.9727 1.858938686 1.403062349 1.726347181 1.49603927 1.439368471 1.77699246 1.689571108 1.544234153 1 18.92597443 0.947318426 16.75262139 0.999999997 1.615537097 0.639466668 0.146641177 95.45456917 30355.25831 0.131548688 0.032887538 8.857648168 -0.947318426 0.615537099 KPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGS(ph)PTEFLEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGSPTEFLEEK 43 2 P27816-6;P27816;P27816-2;P27816-5;H7C456 P27816-6 MAP4 Microtubule-associated protein 4 1 KPCSETSQIEDTPSSKPTLLANGGHGVEGS(0.003)DT(0.039)T(0.149)GS(0.582)PT(0.228)EFLEEK 118.7 2.97E-07 40402000 78006 47463 56369 56591 54942 46807 72830 47749 58716 TRUE FALSE 73123.7437 50977.20991 57706.0993 58043.22087 50627.07695 60319.42105 61909.81762 53710.56776 48915.92028 1.494886395 1.042139443 1.179699758 1.186591615 1.03498159 1.233124527 1.265637389 1.098018139 1 15.57801646 4.749393814 24.76126768 1.146450266 1.494886623 0.618908006 0.089152947 987.4947657 2257051.668 0.020880552 0.306356093 56155.696 -4.749393814 0.348436357 KPDCDDWESGLNAMECALHLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPDCDDWESGLNAMECALHLEK 22 1 G3V192;P02794;G3V1D1;E9PPQ4 G3V192 FTH1 "Ferritin;Ferritin heavy chain;Ferritin heavy chain, N-terminally processed" 0 109.05 0.00026114 60809000 147030 127580 137780 148160 167700 99261 155460 140890 178760 FALSE TRUE 137827.6548 137026.1559 141048.2067 151962.0364 154529.5185 127916.0393 132150.2162 158480.4266 148923.8012 0.925491115 0.920109176 0.947116616 1.020401274 1.037641514 0.85893617 0.887368004 1.064171243 1 17.18421482 -2.310642175 0.006759217 1.979015523 1.29E-06 0.068507428 0.064755848 61212.40206 53.04828172 8244.860367 7309.515655 0.004890551 2.310642175 -1.979014236 KPDHVPISSEDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPDHVPISSEDER 13 1 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 136.83 4.40E-05 645830000 876250 888990 977710 916670 915530 771780 1038590 835030 1104600 FALSE TRUE 821407.0767 954811.7446 1000901.743 940193.3041 843627.9669 994580.3572 882863.0713 939285.3336 920235.124 0.892605656 1.037573681 1.087658705 1.021688131 0.916752626 1.080789389 0.959388583 1.020701459 1 19.811643 2.97508416 24.92871608 0.994549626 1.028181226 0 0.064503331 2249.185339 2250351.753 0.018689774 0.019924278 944.2438386 -2.97508416 0.033631599 KPDIYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPDIYER 7 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31;A0A3B3IRR8 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 78.934 0.0545 274720000 506190 541490 495890 513280 606360 407560 609790 482790 567290 FALSE TRUE 474508.4715 581582.483 507652.745 526451.6338 558738.9315 525215.9558 518357.6505 543067.3943 472605.6342 1.004026269 1.230587282 1.074157201 1.113934316 1.182251948 1.111319709 1.096808021 1.149092086 1 18.8502773 -1.484539131 3.143965179 0.99702021 1.125165273 0.275299158 0.060867462 8576309.271 11467975.14 225169.1661 0.013182709 0.032768825 1.484539131 0.128145063 KPEDRPNTSEILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPEDRPNTSEILR 13 2 P19525-2;P19525 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 0 ; 106.42 0.00077341 671750000 278180 297960 299590 269200 290370 202684 321010 289170 323130 FALSE TRUE 260769.2104 320021.2684 306696.4163 276108.1278 267565.5115 261195.5805 272877.5306 325273.511 269197.5155 0.968691 1.188797259 1.139298837 1.025671159 0.993937522 0.970274856 1.013670316 1.208307998 1 18.03830557 3.233746029 24.38905903 1.028141399 1.123953631 0.081551807 0.085979687 129.4430121 655714.1774 0.023537 0.029017606 1712.955296 -3.233746029 0.095812233 KPEDWDEEMDGEWEPPVIQNPEYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KPEDWDEEMDGEWEPPVIQNPEYK 24 1 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;;;;; 281.28 4.68E-52 4071150000 4054450 2460580 2882420 2841200 2877040 2000110 4002380 2427250 2997860 FALSE TRUE 3800689.212 2642763.903 2950792.364 2914110.002 2651088.884 2577509.288 3402260.275 2730297.506 2497497.799 1.521798823 1.058164658 1.181499485 1.16681184 1.061497986 1.03203666 1.362267577 1.093213178 1 21.25205198 4.746030622 24.7407873 1.138509872 1.521799035 0.590753071 0.104177272 595.0428159 1970736.864 0.024345008 0.256258551 55722.50377 -4.746030622 0.383289163 KPEDWDERPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPEDWDERPK 10 2 P27824;P27824-2;P27824-3;D6RGY2 P27824 CANX Calnexin 0 ; 122.51 0.00027369 1147860000 3732700 1920920 2328990 2252100 2937800 1806950 3409800 2554300 2091180 FALSE TRUE 3499076.97 2063146.916 2384234.743 2309892.699 2707077.039 2328587.132 2898532.145 2873209.978 1742148.548 2.008483704 1.184254303 1.368559957 1.325887337 1.553872683 1.336618013 1.663768654 1.649233632 1 20.73243621 2.732083597 24.11850501 1.487490408 1.406666596 0 0.287069359 1803.846453 6716977.252 0.08449531 0.081523558 539.6144828 -2.732083597 -0.080823812 KPEEES(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KPEEESPR 8 1 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33 P49321 NASP Nuclear autoantigenic sperm protein 1 KPEEES(1)PR;KPEEES(1)PR;KPEEES(1)PR;KPEEES(1)PR;KPEEES(1)PR;KPEEES(1)PR;KPEEES(1)PR;KPEEES(1)PR 115 0.0015602 12445980000 25548680 15817730 19153560 17383020 15799760 18646200 25353760 18543120 13272660 TRUE FALSE 23949633.72 16988891.19 19607891.49 17829097.72 14558910.58 24029055.24 21552199.06 20858269.35 11057367.3 2.165943581 1.53643184 1.773287524 1.612417969 1.316670613 2.17312626 1.949125725 1.886368498 1 23.39850459 4.753748643 23.26337216 1.711664826 2.165944458 0.170116575 0.334447623 1998.984013 3061688.494 0.074627667 1.593841187 56721.62219 -4.753748643 0.454279633 KPEEES(ph)PRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPEEESPRK 9 2 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33 P49321 NASP Nuclear autoantigenic sperm protein 1 KPEEES(1)PRK;KPEEES(1)PRK 94.122 0.0046627 302470000 259060 132364 158208 157354 146493 127702 199512 145268 156446 TRUE FALSE 242845.897 142164.3683 161960.7685 161391.97 134988.0307 164567.4943 169597.0278 163405.0296 130334.1519 1.86325605 1.090768353 1.242657938 1.238293783 1.035707286 1.262658267 1.301247795 1.253739156 1 16.99185564 4.74398727 24.96960421 1.194289296 1.863256337 0.809751796 0.104103497 241.6395862 1111819.689 0.023649357 0.204746172 55460.94558 -4.74398727 0.66896704 KPEEES(ph)PRKDDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 KPEEESPRKDDAK 13 3 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33 P49321 NASP Nuclear autoantigenic sperm protein 1 KPEEES(1)PRKDDAK;KPEEES(1)PRKDDAK;KPEEES(1)PRKDDAK;KPEEES(1)PRKDDAK;KPEEES(1)PRKDDAK;KPEEES(1)PRKDDAK;KPEEES(1)PRKDDAK;KPEEES(1)PRKDDAK;KPEEES(1)PRKDDAK 146.58 8.35E-05 26472780000 21968030 6549802 11104820 9579831 10999903 7176397 14379970 8731355 14041740 TRUE FALSE 20593090.22 7034756.155 11368231.57 9825665.682 10136014.99 9248106.315 12223827 9821483.892 11698082.88 1.760381631 0.601359746 0.97180296 0.839938115 0.866468044 0.790565976 1.044942759 0.839580638 1 23.47976878 4.749231809 24.98936815 0.867256328 1.760382136 0.836221047 0.123925908 598.484682 1401480.199 0.028815486 0.423735394 56134.75213 -4.749231809 0.893125808 KPEENPASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KPEENPASK 9 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;; 122.51 0.0026959 829250000 2234090 1476510 1783050 1729830 1899920 1341800 2190710 1594630 2255300 FALSE TRUE 2094262.295 1585832.337 1825344.788 1774220.366 1750707.947 1729155.878 1862233.373 1793723.066 1878875.86 1.114635799 0.844032525 0.971508989 0.944298878 0.931784789 0.920314063 0.991142317 0.954678861 1 20.84143832 1.709126678 9.705717337 0.979242572 0.942425279 0.014555943 0.068290486 0.335430978 70.370166 0.029603565 0.015954359 51.18311084 -1.709126678 -0.036817293 KPEKPLFSS(ph)ASPQDSSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPEKPLFSSASPQDSSPR 18 2 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A1B0GWJ4;Q5VW27;O00712-5;Q5VW26;A0A2R8Y7V8;Q5VW30;A0A1B0GWI9;Q5VW31;A0A1B0GVN4;A0A1B0GWB8;O00712-6 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 KPEKPLFS(0.068)S(0.465)AS(0.465)PQDS(0.002)SPR 113.54 0.00019226 354950000 149310 134900 137390 146660 164840 119400 183810 141140 171460 TRUE FALSE 139964.9536 144888.1364 140648.9557 150423.5439 151894.1313 153868.8417 156249.3969 158761.6397 142842.2183 0.979857043 1.014322923 0.984645557 1.053074824 1.063370011 1.077194428 1.093860056 1.111447593 1 17.12406292 3.07237511 2.898320415 1.076724839 0.996093946 0.555728996 0.030634674 0.164678782 2.806377862 0.008637339 0.010461089 1181.340546 -3.07237511 -0.080630893 KPEKPLFSSAS(ph)PQDSSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPEKPLFSSASPQDSSPR 18 2 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A1B0GWJ4;Q5VW27;O00712-5;Q5VW26;A0A2R8Y7V8;Q5VW30;A0A1B0GWI9;Q5VW31;A0A1B0GVN4;A0A1B0GWB8;O00712-6 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 KPEKPLFSSAS(1)PQDSSPR 173.89 3.75E-12 450690000 455890 344490 372280 372730 439730 317740 472580 371580 432290 TRUE FALSE 427356.6587 369996.398 381110.6574 382294.8828 405195.3796 409466.3799 401721.0162 417972.5809 360138.0063 1.186646928 1.027373928 1.05823504 1.061523294 1.125111409 1.136970752 1.115464098 1.160590034 1 18.45819033 2.738258613 24.5526349 1.117140292 1.069898025 0.003550019 0.059361501 42.67505564 3469293.011 0.016917702 0.016858647 547.3417963 -2.738258613 -0.047242267 KPEKPLFSSASPQDS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPEKPLFSSASPQDSSPR 18 2 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A1B0GWJ4;Q5VW27;O00712-5;Q5VW26;A0A2R8Y7V8;Q5VW30;A0A1B0GWI9;Q5VW31;A0A1B0GVN4;A0A1B0GWB8;O00712-6 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 KPEKPLFS(0.008)S(0.031)AS(0.319)PQDS(0.386)S(0.256)PR 148.28 3.68E-08 382900000 352200 299480 337880 294260 349970 295180 462610 343470 409460 TRUE FALSE 330156.4307 321653.8108 345894.6732 301811.2098 322484.7679 380393.6742 393245.9252 386352.9856 341118.4808 0.967864391 0.942938682 1.014001564 0.884769448 0.94537466 1.115136516 1.152813311 1.132606432 1 18.37991339 2.23592811 24.92440737 1.117233627 0.955474372 0.666619373 0.051733977 34.42925677 325968.0886 0.017652722 0.013633367 172.1583571 -2.23592811 -0.161759254 KPENEVAQNGGAETSHTEPVS(ph)PIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPENEVAQNGGAETSHTEPVSPIPK 25 1 O95104-2;O95104-3;O95104 O95104-2 SCAF4 "Splicing factor, arginine/serine-rich 15" 1 KPENEVAQNGGAETSHTEPVS(1)PIPK;KPENEVAQNGGAETSHTEPVS(1)PIPK 119.75 0.0001948 171398000 274710 138337 200039 183309 183862 143496 208333 160276 170205 TRUE FALSE 257516.3915 148579.6154 204784.0195 188013.0193 169422.2202 184920.9657 177095.4007 180286.8114 141796.6859 1.816095981 1.0478356 1.444208785 1.325933805 1.194824964 1.304127558 1.248938927 1.271445875 1 17.11346429 8 0.029812433 2.50E-11 3.151044418 0.327395856 0.184537303 1965.151445 4.491690312 151.6917822 366.3121735 99999999.91 -8 3.151044418 KPESPYGNLCDAPDS(ph)PRPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPESPYGNLCDAPDSPRPVK 20 2 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 KPES(0.22)PYGNLCDAPDS(0.78)PRPVK;KPES(0.002)PYGNLCDAPDS(0.998)PRPVK 101.43 0.0001954 352820000 349310 245710 313850 325790 327490 234270 335620 246700 377380 TRUE FALSE 327447.3106 263902.6241 321294.6702 334150.323 301770.2564 301899.9459 285296.8967 277501.0381 314392.84 1.041522799 0.839404053 1.021952886 1.062843298 0.959850919 0.960263427 0.907453544 0.882656991 1 18.26220884 -0.376319912 7.474957664 1.000007501 0.953989938 0.026551406 0.070385981 0 0 0.066682734 0.015717271 0.420416825 0.376319912 -0.046017563 KPFKLS(ph)GLSFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPFKLSGLSFK 11 2 P49006 P49006 MARCKSL1 MARCKS-related protein 1 KPFKLS(0.992)GLS(0.008)FK 61.732 0.044586 134700000 748920 350850 407230 354660 395230 282780 421720 219050 480050 TRUE FALSE 702046.4341 376827.2991 416889.6879 363761.176 364190.2301 364413.9955 358487.0011 246398.8747 399926.5538 1.755438411 0.942241258 1.042415624 0.909569951 0.910642783 0.9112023 0.896382092 0.616110314 1 18.60937555 4.740191206 5.248896634 0.913300661 1.792017378 0.851099409 0.111981688 0.057870556 5.544689274 0.026117413 0.183744187 54978.28723 -4.740191206 0.878716717 KPGDLSDELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KPGDLSDELR 10 1 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ;;; 129.82 0.00046984 2055890000 5934600 5847500 5654600 5637400 6227000 4382450 6819000 5652900 6771000 FALSE TRUE 5563163.98 6280454.984 5788729.782 5782065.228 5737956.539 5647592.172 5796554.254 6358677.009 5640876.358 0.98622335 1.113382848 1.026211073 1.025029599 1.017210124 1.001190562 1.027598176 1.127249847 1 22.42748788 3.723146681 24.7492497 1.030249581 1.062159234 0.008055503 0.046879571 389.8978898 2427871.05 0.011420631 0.018459516 5286.237621 -3.723146681 0.031909652 KPGGEREER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KPGGEREER 9 2 E9PKP7;P17480-2;P17480;E9PLT2 E9PKP7 UBTF Nucleolar transcription factor 1 0 ;; 95.523 0.0044924 130451000 153581 225677 166627 160294 239526 104573 174121 167215 322040 FALSE TRUE 143968.6394 242386.3599 170579.4711 164407.4154 220714.5942 134761.5275 148013.1725 188092.1608 268289.4435 0.536616862 0.903450977 0.635803887 0.612798675 0.82267342 0.502299031 0.551692122 0.701079246 1 18.03343076 0.959255245 22.30412122 1.000000003 0.664205877 0.426599269 0.125145108 2129.358329 1165636.46 0.122928793 0.030732198 9.104482075 -0.959255245 -0.335794126 KPGGFDISLFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPGGFDISLFYR 12 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 173.06 5.47E-05 578020000 429490 873280 389880 368870 970080 250840 448350 866430 675570 FALSE TRUE 402608.9876 937938.5598 399128.1377 378335.8287 893893.8299 323253.436 381124.0798 974605.6927 562813.0027 0.715351255 1.666518996 0.709166519 0.672222971 1.5882608 0.574353177 0.677177105 1.731668757 1 19.10229613 5.019711806 16.27466862 1.042096953 0.031475162 0.056927059 0.442854307 17772029.62 348677880.8 0.10104852 444640310.9 104643.3914 -5.019711806 -1.010621791 KPGINVASDWSIHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPGINVASDWSIHLR 15 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 206.63 2.47E-09 1225510000 1068350 1851660 1459270 1468200 1828270 1078400 1714850 1736190 1409700 FALSE TRUE 1001483.881 1988758.833 1493884.574 1505876.498 1684685.049 1389716.574 1457724.162 1952957.143 1174411.963 0.852753473 1.693408187 1.272027722 1.282238725 1.434492412 1.183329715 1.241237494 1.662923408 1 20.16350714 3.648000356 24.99999803 1.300906373 1.378032657 0 0.265286741 308.1969605 97375.53355 0.064101317 0.099305366 4446.316324 -3.648000356 0.077126285 KPGMFFNPEESELDLTYGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KPGMFFNPEESELDLTYGNR 20 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;; 289.14 3.27E-54 9403050000 5734770 6473760 6108130 5808320 7135200 5123960 7087730 6479610 7762900 FALSE TRUE 5375840.983 6953083.926 6253017.728 5957371.325 6574830.174 6603164.071 6024990.686 7288603.572 6467221.84 0.831244252 1.075126863 0.966878496 0.921163905 1.016639036 1.02102019 0.93161961 1.12700689 1 22.62471467 1.245741646 24.99998547 1.063503453 0.977620495 0.22405253 0.072895428 229.065189 797486.0696 0.046319529 0.01614659 17.60928189 -1.245741646 -0.085882958 KPGMTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPGMTR 6 1 P40926;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial" 0 89.369 0.080564 3611300000 3210100 3072500 2960300 2797600 4048500 2814800 2663300 3360200 4784800 FALSE TRUE 3009185.571 3299991.097 3030519.714 2869391.152 3730547.141 3627387.066 2263962.89 3779728.367 3986185.969 0.754903458 0.827856784 0.760255477 0.719833739 0.935868815 0.909989422 0.56795215 0.948206731 1 21.92657759 1.020274163 24.99462694 1.000000269 0.781855558 0.386088051 0.101679691 190.4503287 234792.3756 0.095503004 0.023875751 10.47789791 -1.020274163 -0.218144711 KPGPPLS(ph)PEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KPGPPLSPEIR 11 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPGPPLS(1)PEIR;KPGPPLS(1)PEIR;KPGPPLS(1)PEIR;KPGPPLS(1)PEIR;KPGPPLS(1)PEIR;KPGPPLS(1)PEIR 139.6 2.39E-05 6113180000 6200120 5483950 5935540 5927350 6322620 5594930 6990470 5867420 6328400 TRUE FALSE 5812065.557 5889987.364 6076333.812 6079455.836 5826066.929 7210095.465 5942313.92 6599980.303 5272149.157 1.102409166 1.117189061 1.152534504 1.153126677 1.10506489 1.367581844 1.127114151 1.251857659 1 22.32995976 KPGPPLS(ph)PEIRS(ph)PAGS(ph)PELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KPGPPLSPEIRSPAGSPELR 20 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 3 KPGPPLS(1)PEIRS(1)PAGS(1)PELR;KPGPPLS(1)PEIRS(1)PAGS(1)PELR;KPGPPLS(1)PEIRS(1)PAGS(1)PELR 66.501 0.017336 1027850000 793070 872500 845460 953850 1034920 681880 884480 763950 1046950 TRUE FALSE 743433.1644 937100.8078 865514.7105 978327.4059 953641.5579 878727.6866 751860.4351 859330.8392 872207.2814 0.852358356 1.074401496 0.992326857 1.121668469 1.093365738 1.007475752 0.86202036 0.985236947 1 19.73431151 1.981273397 23.30073107 0.934002999 1.034377408 0.148819596 0.08148789 421.658234 524650.4302 0.030820944 0.020304951 95.7796834 -1.981273397 0.100374409 KPGPSGPSES(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KPGPSGPSESPK 12 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPGPSGPS(0.208)ES(0.792)PK;KPGPSGPS(0.001)ES(0.999)PK;KPGPSGPSES(1)PK;KPGPSGPS(0.003)ES(0.997)PK 153.48 4.33E-05 2965910000 5428130 2476180 3456850 3204770 3392560 2370854 4526240 3106780 4065090 TRUE FALSE 5088393.033 2659518.944 3538848.114 3287009.824 3126122.023 3055281.062 3847572.332 3494668.322 3386600.218 1.502507738 0.785306435 1.04495597 0.970592811 0.923085638 0.902167621 1.136116484 1.031910499 1 21.69140626 -0.27544185 7.204311824 1.000000001 1.012998275 0 0.191533603 0 0 0.164964881 0.038882595 0.530344598 0.27544185 0.012998274 KPGS(ph)HASSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPGSHASSSAR 11 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 KPGS(0.696)HAS(0.222)S(0.063)S(0.019)AR 53.377 0.084765 58269000 13320 21693 19626 19213 22435 15193 22454 17349 21470 TRUE FALSE 12486.32498 23299.17229 20091.53799 19706.03811 20673.0456 19578.97246 19087.23115 19515.06084 17886.5183 0.69808583 1.302610821 1.123278307 1.101725768 1.155789252 1.094621778 1.06712949 1.091048605 1 14.12658497 0.826979669 0.861778581 1.001849366 1.113212391 0 0.153384898 2.886697033 4.327740357 0.134488676 0.046538363 6.713974209 -0.826979669 0.111363025 KPHLQGKPGRPLS(ph)PANVPALPGETVTSPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPHLQGKPGRPLSPANVPALPGETVTSPVR 30 3 Q8IY33;Q8IY33-5;Q8IY33-3 Q8IY33 MICALL2 MICAL-like protein 2 1 KPHLQGKPGRPLS(1)PANVPALPGETVTSPVR 61.499 0.01734 833110000 544720 509360 549360 513000 509810 412330 619320 558950 703430 TRUE FALSE 510626.9476 547073.5444 562391.0786 526164.4485 469771.5791 531362.9774 526458.7155 628736.1379 586022.9887 0.871342861 0.933535979 0.95967409 0.897856328 0.801626537 0.906727189 0.89835847 1.072886474 1 19.16059773 1.247015617 24.99931657 1.036443244 0.902940796 0.626994261 0.044888943 115.9563039 342860.9396 0.032625602 0.011487187 17.66101329 -1.247015617 -0.133502448 KPIDSLRDS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 KPIDSLRDSR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 KPIDSLRDS(1)R;KPIDSLRDS(1)R;KPIDSLRDS(1)R;KPIDSLRDS(1)R;KPIDSLRDS(1)R;KPIDSLRDS(1)R;KPIDSLRDS(1)R 143.94 2.61E-05 11958120000 10417980 9204670 9408050 8654370 7791320 9063320 12203510 8284380 6412270 TRUE FALSE 9765937.228 9886193.344 9631213.389 8876455.786 7179421.156 11679753.35 10373706.97 9318703.079 5342020.712 1.828135411 1.850646764 1.802915771 1.66162886 1.343952325 2.186392375 1.941906916 1.744415378 1 22.34895414 3.435989367 8.744211352 1.732259905 1.833182726 0.022777482 0.323632997 1.483707346 290.7401311 0.08506747 0.115755715 2728.910969 -3.435989367 0.100922821 KPIETGS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KPIETGSPK 9 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 KPIET(0.012)GS(0.988)PK;KPIET(0.152)GS(0.848)PK;KPIET(0.001)GS(0.999)PK;KPIET(0.001)GS(0.999)PK;KPIET(0.06)GS(0.94)PK 104.3 0.0020107 20642400000 25991900 12864310 16489240 15564880 16385920 12095960 22464400 13967140 23577300 TRUE FALSE 24365113.38 13816796.9 16880372.56 15964301.17 15099035.94 15587867.29 19096071.77 15710968.17 19642096.31 1.240453818 0.703427815 0.859397708 0.81275954 0.768707968 0.793594891 0.97220131 0.799862088 1 24.22744557 -1.346877596 6.742943393 1.000005762 0.853945975 0.062919445 0.149661557 1.16E-05 1.12E-06 0.129422607 0.030503998 0.044990664 1.346877596 -0.146059786 KPIFQANLELAQLELISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPIFQANLELAQLELISR 18 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 0 191.95 3.19E-14 56097000 159870 179960 160570 167420 193000 140020 189650 172010 168250 FALSE TRUE 149864.0221 193284.4256 164378.7962 171716.2806 177842.5585 180441.501 161213.7431 193485.8271 140167.9881 1.069174382 1.37894842 1.172727086 1.225074876 1.26878156 1.287323186 1.150146659 1.380385278 1 17.09679737 -1.0198463 11.51435648 1.000008267 1.243136631 0.381441241 0.09665855 0 0 0.081932642 0.019311709 0.095533062 1.0198463 0.243128364 KPIGWDTDISWLTGEELHVEVLENVPLTTHNFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPIGWDTDISWLTGEELHVEVLENVPLTTHNFVR 34 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y467 P15056 BRAF Serine/threonine-protein kinase B-raf 0 64.686 0.0023545 14820000 21388 22998 16417 15535 25096 12703 19708 18591 16743 FALSE TRUE 20049.36326 24700.79585 16806.41899 15933.6544 23125.06139 16370.14988 16752.96836 20912.12727 13948.48514 1.43738643 1.770858671 1.20489206 1.142321496 1.657890528 1.173614893 1.201060058 1.49924003 1 13.76782083 8 0.093099517 0.852357333 2.917612805 0.287243637 0.207060421 171.7055111 1.143366027 3.17600208 45.27797747 100000000 -8 2.065255472 KPIKS(ph)PSKDASSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPIKSPSKDASSGK 14 3 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 KPIKS(0.98)PS(0.02)KDASSGK 98.062 0.015069 2108500000 729900 251690 428030 441860 445840 289830 554420 366970 625960 TRUE FALSE 684216.8619 270325.3895 438183.0737 453198.8757 410825.5248 373499.216 471289.868 412787.0123 521483.2321 1.31205918 0.518377913 0.840263017 0.869057426 0.787801984 0.716224785 0.903748844 0.791563346 1 18.99226134 -0.10239743 0.762991941 1.006583205 0.808766667 0.034096308 0.200243497 17.61408916 9.68686074 0.531605201 0.062071121 0.789955396 0.10239743 -0.197816538 KPITDDDVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KPITDDDVDR 10 1 P53618 P53618 COPB1 Coatomer subunit beta 0 ;;;;; 137.59 0.00013987 5364100000 8280620 8310900 8195100 8799800 8524600 6814340 10445200 8145220 9003100 FALSE TRUE 7762350.776 8926247.683 8389491.642 9025617.766 7855112.303 8781529.336 8879039.228 9162168.647 7500424.448 1.034921534 1.190099006 1.118535584 1.203347601 1.047289038 1.170804319 1.183804902 1.221553355 1 22.83854081 KPLAAPGDGEGLGQTAQPS(ph)PPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPLAAPGDGEGLGQTAQPSPPAR 23 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 KPLAAPGDGEGLGQTAQPS(1)PPAR;KPLAAPGDGEGLGQTAQPS(1)PPAR 202.05 1.32E-24 596810000 482770 517690 561600 618750 615570 423180 527910 398220 474560 TRUE FALSE 452554.2875 556020.3063 574921.4172 634628.1725 567225.6153 545345.1962 448754.7964 447938.6436 395352.8702 1.144684462 1.406389957 1.454198162 1.605219591 1.434732509 1.379388484 1.135074082 1.133009717 1 18.59278137 1.703620152 2.383265514 1.0712711 1.424711346 0.624194522 0.115939106 0.17039661 2.082630313 0.075502049 0.031868261 50.53824452 -1.703620152 0.353440246 KPLFHGDSEIDQLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPLFHGDSEIDQLFR 15 1 P06493;A0A024QZP7;A0A087WZZ9;P06493-2 P06493 CDK1;CDC2 Cyclin-dependent kinase 1 0 ; 258.23 5.29E-25 4837500000 4372600 5175700 5150300 4940800 5755900 4423400 6408000 5309700 6021300 FALSE TRUE 4098926.771 5558914.213 5272467.548 5067589.293 5303854.832 5700363.772 5447179.889 5972627.733 5016306.131 0.817120539 1.108168853 1.051065746 1.010223292 1.057322798 1.136366805 1.08589463 1.190642592 1 22.25819396 2.438185859 4.797474758 1.108343119 1.02488456 0.215237676 0.088722662 0.343865433 18.54338011 0.028991554 0.024498746 274.2747699 -2.438185859 -0.083458558 KPLHYAADCGQLEILEFLLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KPLHYAADCGQLEILEFLLLK 21 1 P58546 P58546 MTPN Myotrophin 0 ;; 139.11 3.43E-07 2448385000 4001120 3411080 2871200 2616167 4162010 2787202 4135660 3798940 3155360 FALSE TRUE 3750697.041 3663639.912 2939306.22 2683302.274 3835142.523 3591821.971 3515556.177 4273246.021 2628710.032 1.426820378 1.393702565 1.118155363 1.020767693 1.458944683 1.366381962 1.337369331 1.625605704 1 21.32592358 KPLPDHVSIVEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KPLPDHVSIVEPK 13 1 P23396;P23396-2;E9PPU1;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 0 ;; 129.95 9.59E-05 4088380000 4733600 6628700 7010400 6795600 7334800 5765300 8575300 6391200 7458200 FALSE TRUE 4437332.426 7119495.845 7176689.999 6969986.601 6758754.395 7429648.518 7289513.374 7189155.389 6213378.238 0.714157783 1.145833325 1.155038326 1.121770852 1.087774498 1.19575024 1.173196463 1.157044544 1 22.56694645 4.738937856 24.76332458 1.14124025 0.714157636 0.846380153 0.055417858 8.709351342 571474.6461 0.011742984 0.068932605 54819.85165 -4.738937856 -0.427082614 KPLS(ph)PVRDNIQLTPEAEEDIFNKPECGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPLSPVRDNIQLTPEAEEDIFNKPECGR 28 3 Q9UQ84;H0YAZ2 Q9UQ84 EXO1 Exonuclease 1 1 KPLS(1)PVRDNIQLTPEAEEDIFNKPECGR 141.46 6.93E-07 93524000 154060 76884 98748 81175 98004 64463 118480 79842 115540 TRUE FALSE 144417.6596 82576.57136 101090.3492 83258.08793 90307.16117 83072.42163 100715.0239 89810.44945 96255.62758 1.500355493 0.857888244 1.050227937 0.864968522 0.938201365 0.863039634 1.046328682 0.933041025 1 16.55458327 4.744313156 24.94269282 0.948267573 1.500355739 0.858233326 0.071018226 207.6170585 900189.0752 0.015697563 0.140220306 55502.57803 -4.744313156 0.552088167 KPLSLAGDEETECQS(ph)SPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPLSLAGDEETECQSSPK 18 1 Q86TN4;Q86TN4-4;F5H1K3;Q86TN4-2 Q86TN4 TRPT1 tRNA 2-phosphotransferase 1 1 KPLSLAGDEETECQS(0.63)S(0.37)PK 113.42 8.27E-05 0 259700 140920 161780 173200 185670 135170 265690 140390 168200 TRUE FALSE 243445.8406 151353.8634 165617.498 177644.6052 171088.2272 174191.3847 225852.251 157918.0005 140126.3334 1.737331126 1.08012434 1.18191559 1.267746047 1.220956997 1.243102424 1.611775928 1.126968763 1 17.09636858 KPLSLAGDEETECQSS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPLSLAGDEETECQSSPK 18 1 Q86TN4;Q86TN4-4;F5H1K3;Q86TN4-2 Q86TN4 TRPT1 tRNA 2-phosphotransferase 1 1 KPLSLAGDEETECQS(0.002)S(0.998)PK;KPLSLAGDEETECQS(0.008)S(0.992)PK 211.92 1.52E-16 902860000 1414390 748050 910830 924590 974760 722630 1439950 782930 926730 TRUE FALSE 1325865.855 803436.4003 932435.3177 948316.5447 898206.2816 931241.5501 1224042.865 880680.5339 772052.7761 1.717325416 1.040649584 1.207735205 1.228305336 1.163400106 1.206188979 1.585439368 1.140699912 1 19.55833995 KPLSTHSTEYNLDSVPS(ph)PAEEFADFATFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPLSTHSTEYNLDSVPSPAEEFADFATFSK 30 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9 Q6ULP2-7 AFTPH Aftiphilin 1 KPLSTHSTEYNLDS(0.004)VPS(0.996)PAEEFADFATFSK;KPLSTHSTEYNLDSVPS(1)PAEEFADFATFSK 211.33 2.17E-26 339260000 604650 822190 829530 867410 956980 670250 935520 848520 984290 TRUE FALSE 566806.0358 883065.8031 849206.8433 889669.2091 881822.6511 863740.2944 795247.4609 954459.5898 820005.6402 0.691222118 1.076902109 1.035610978 1.084954987 1.07538608 1.053334577 0.969807306 1.163967103 1 19.64527431 4.7408494 24.99781705 1.053099645 0.691221993 0.8297705 0.052103207 77.73884991 849001.0164 0.011437649 0.076668682 55061.67259 -4.7408494 -0.361877652 KPLTSSSAAPQRPISTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPLTSSSAAPQRPISTQR 18 2 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ; 216.35 5.07E-19 1389480000 717770 752220 717860 701160 745210 617850 835540 685330 863390 FALSE TRUE 672846.057 807915.1515 734887.9782 719152.9527 686684.2126 796213.265 710258.5338 770894.9591 719284.6313 0.935437833 1.123220372 1.021692868 0.999816931 0.954676609 1.106951588 0.987451285 1.071752302 1 19.45620325 KPLVIIAEDVDGEALSTLVLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KPLVIIAEDVDGEALSTLVLNR 22 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;; 221.14 1.54E-25 1983510000 729440 728030 720580 652880 996100 682540 729070 773690 1020540 FALSE TRUE 683785.6525 781934.0987 737672.4979 669634.0061 917870.3241 879578.2179 619752.7219 870286.8996 850205.2811 0.804259474 0.919700355 0.867640456 0.787614499 1.079586712 1.034548053 0.728944804 1.023619729 1 19.69745169 2.774020739 24.99916938 0.943015803 0.861092618 0.246937124 0.102581761 1314.477472 926696.2236 0.032148217 0.034097219 594.3205384 -2.774020739 -0.081923185 KPLVLCGDLNVAHEEIDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KPLVLCGDLNVAHEEIDLR 19 1 P27695;G3V3M6;G3V5Q1;H7C4A8 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ;;; 199.16 4.59E-16 2944340000 3372701 3838118 3787505 3846658 4112385 3183098 4438406 3612981 4174014 FALSE TRUE 3161609.665 4122296.25 3877346.407 3945369.757 3789414.871 4102006.719 3772908.224 4064069.631 3477344.098 0.909202419 1.185472629 1.115030983 1.134592852 1.089744001 1.179637851 1.084997089 1.168728063 1 21.7295544 4.748326377 24.82570816 1.12638044 0.90920229 0.588244135 0.05512072 749.7596049 1905933.949 0.011235643 0.147820586 56017.84233 -4.748326377 -0.21717815 KPMS(ph)PITAQMSQLELQQAALEGLALPHDLAVQAANFYQPGFGKPQVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPMSPITAQMSQLELQQAALEGLALPHDLAVQAANFYQPGFGKPQVDR 48 2 B1AKL4;Q9NRA8;B0QYZ7;H7C0J7 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 KPMS(0.883)PIT(0.116)AQMSQLELQQAALEGLALPHDLAVQAANFYQPGFGKPQVDR 181.28 2.81E-29 129940000 114120 91084 83250 72096 121320 67352 98830 107330 76340 TRUE FALSE 106977.4329 97827.95413 85224.72931 73946.10542 111792.0166 86795.42903 84011.35899 120730.3868 63598.36082 1.682078461 1.538215024 1.340046004 1.16270458 1.757781413 1.364743177 1.320967363 1.898325447 1 15.95670196 -1.311527253 3.436956374 0.998035741 1.474982962 0.325343298 0.225506851 24665417.06 37204783.63 517854.47 0.049339625 0.048805947 1.311527253 0.476947221 KPMVLGHEASGTVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPMVLGHEASGTVEK 15 1 Q00796;A0A6I8PIS1;H0YKB3;Q00796-2 Q00796 SORD Sorbitol dehydrogenase 0 ; 187.37 2.23E-07 424760000 925720 799270 895670 928960 1035700 733900 1090160 908560 1148530 FALSE TRUE 867780.8377 858448.7824 916915.7154 952798.6863 954360.2998 945765.0161 926700.6285 1021995.716 956832.9232 0.906930371 0.897177304 0.958281946 0.99578376 0.997415825 0.988432769 0.968508301 1.068102582 1 19.86790751 3.63180876 1.454660134 0.999442341 0.900140247 0.72204308 0.025717921 0.214193438 0.897735517 0.007697857 0.016808177 4283.598521 -3.63180876 -0.099302094 KPNEGADGQWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KPNEGADGQWK 11 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;;; 174.9 1.68E-05 5504320000 11852160 8435900 10042000 9273800 9892810 7579250 12389680 8608530 11358230 FALSE TRUE 11110354.46 9060502.814 10280200.98 9511781.409 9115868.608 9767256.436 10531962.5 9683323.92 9462468.036 1.174149748 0.957520044 1.086418569 1.00521147 0.963371139 1.032210244 1.113024896 1.023340199 1 23.17378509 0.996699231 24.89069843 0.999999975 1.042656896 0.05087702 0.065999088 360.7168045 2720145.908 0.059214905 0.014803726 9.92428507 -0.996699231 0.042656921 KPNEGADGQWKK ddPTM_SK-BR-3_Pertuzumab_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 ; 161.21 3.41E-05 1365500000 2097460 1805850 1921800 1950080 2398970 1338910 2642640 1802710 4445000 FALSE TRUE 1966183.723 1939557.013 1967386.004 2000122.354 2210564.573 1725431.582 2246400.665 2027782.312 3703100.784 0.530956039 0.523765656 0.531280707 0.540120961 0.596949611 0.465942377 0.606626931 0.547590365 1 21.82030238 -5 0.350763933 6.321523953 0.528005064 0.935649625 0.037749212 87.75714525 0.717726993 351.2125447 0.02496473 1.00E-05 5 -5.793518889 KPNFEVGSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPNFEVGSSR 10 1 Q6FI81-3;Q6FI81;H3BV90;H3BT65;H3BPG7;H3BUG4 Q6FI81-3 CIAPIN1 Anamorsin 0 102.05 0.0048084 622110000 560250 634710 601310 604750 635000 511330 707470 568890 700990 FALSE TRUE 525184.9526 681704.5888 615573.3572 620268.9088 585129.6615 658942.6703 601391.4413 639917.1688 583990.2404 0.899304331 1.167321886 1.054081583 1.062122046 1.001951096 1.128345347 1.029797075 1.095766889 1 19.15558473 -1.31609344 3.363595239 0.999681459 1.064204584 0.039358642 0.073106979 4933183.061 1939895.709 11300.98169 0.015151037 0.048295488 1.31609344 0.064523125 KPNIFYSGPAS(ph)PARPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KPNIFYSGPASPARPR 16 2 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 KPNIFYSGPAS(1)PARPR;KPNIFYS(0.002)GPAS(0.998)PARPR;KPNIFYSGPAS(1)PARPR;KPNIFYSGPAS(1)PARPR 229.51 1.62E-15 24036965600 4210953 3890714 4287793 3979466 4292143 3783408 4968481 3878725 4564254 TRUE FALSE 3947396.968 4178786.513 4389501.475 4081585.835 3955055.402 4875616.471 4223503.399 4362992.354 3802450.521 1.03811922 1.098971963 1.154387533 1.073409322 1.040133298 1.282230089 1.110731981 1.147415944 1 21.85849804 4.689544268 2.27556567 1.125698543 1.021596112 0.080378278 0.075928729 1.154716724 7.700136313 0.017480151 0.230825125 48926.51344 -4.689544268 -0.104102431 KPPAPPS(ph)PVQS(ph)QSPSTNWSPAVPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVK 25 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KPPAPPS(0.994)PVQS(0.595)QS(0.386)PS(0.012)T(0.011)NWS(0.002)PAVPVK 89.149 0.051202 102240000 94284 74875 80426 86558 83732 67544 103710 79914 83300 TRUE FALSE 88382.93274 80418.82291 82333.7427 88779.22482 77156.02648 87042.85631 88159.6483 89891.43881 69396.69186 1.273589999 1.158827903 1.186421723 1.279300532 1.111811304 1.25427962 1.270372491 1.295327434 1 16.08257927 -1.012205671 4.484393822 0.999991764 1.221500122 0.589024633 0.059775187 4.87E-06 1.07E-06 0.057256042 0.013494877 0.097228666 1.012205671 0.221508358 KPPAPPS(ph)PVQSQS(ph)PSTNWS(ph)PAVPVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPPAPPSPVQSQSPSTNWSPAVPVKK 26 2 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 3 KPPAPPS(0.999)PVQS(0.004)QS(0.996)PS(0.002)T(0.001)NWS(1)PAVPVKK;KPPAPPS(1)PVQS(0.002)QS(0.989)PS(0.007)T(0.002)NWS(1)PAVPVKK 191.71 3.98E-18 2485100000 2416900 1497710 1783900 1651280 2173270 1416620 2618900 1944220 3153200 TRUE FALSE 2265630.543 1608602.007 1826214.95 1693654.64 2002590.141 1825575.197 2226220.258 2186960.147 2626910.55 0.86246962 0.612355075 0.695194951 0.644732513 0.762336632 0.694951413 0.847467097 0.832521742 1 21.32493564 1.211882654 0.809244772 0.99471524 0.687641486 0.615326876 0.072547065 0.327027876 0.482600839 0.061709503 0.023532118 16.28855857 -1.211882654 -0.307073754 KPPAPPS(ph)PVQSQSPSTNWS(ph)PAVPVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPPAPPSPVQSQSPSTNWSPAVPVKK 26 2 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KPPAPPS(1)PVQSQSPS(0.003)T(0.001)NWS(0.996)PAVPVKK;KPPAPPS(1)PVQS(0.001)QS(0.002)PS(0.006)T(0.003)NWS(0.99)PAVPVKK 179.62 1.22E-17 1462530000 1757950 1195830 1417360 1408040 1528810 1047210 1915040 1276190 1993150 TRUE FALSE 1647923.048 1284370.497 1450980.449 1444172.69 1408743.43 1349522.527 1627897.53 1435525.131 1660480.389 0.992437525 0.773493325 0.873831729 0.869731856 0.848395102 0.812730181 0.980377451 0.86452399 1 20.66316925 1.10381471 0.763226005 0.993502277 0.85334046 0.22707635 0.067691432 0.772518826 1.035976388 0.059272724 0.022859452 12.70032136 -1.10381471 -0.140161817 KPPAPPS(ph)PVQSQSPSTNWSPAVPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVK 25 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KPPAPPS(1)PVQSQSPSTNWSPAVPVK 225.23 4.65E-34 500790000 963980 746370 859570 902100 779350 575830 909020 649000 750460 TRUE FALSE 903646.2126 801632.0114 879959.4063 925249.4133 718142.9947 742062.7732 772720.8899 730029.0786 625203.3778 1.445363612 1.282193986 1.407477051 1.479917489 1.148655014 1.18691421 1.23595124 1.167666562 1 19.25396605 2.726112519 24.95013541 1.171545016 1.384103863 0.70802396 0.080426647 457.7813722 917545.2742 0.024760076 0.023492404 532.2461382 -2.726112519 0.212558847 KPPAPPS(ph)PVQSQSPSTNWSPAVPVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVKK 26 2 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KPPAPPS(1)PVQSQSPSTNWSPAVPVKK 249.13 5.16E-46 1142800000 1878400 1473600 1615000 1851500 1739300 1085100 1866100 1215300 1868700 TRUE FALSE 1760834.297 1582706.877 1653308.563 1899012.625 1602702.394 1398350.755 1586295.629 1367032.88 1556801.898 1.131058678 1.016639869 1.061990331 1.219816489 1.029483839 0.898220099 1.018945077 0.878103298 1 20.57015394 2.47321015 22.65852011 0.956873785 1.088685342 0.547114308 0.06687618 30.72692875 178003.4097 0.022441859 0.01888251 297.3104336 -2.47321015 0.131811557 KPPLS(ph)PAQTNPVVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KPPLSPAQTNPVVQR 15 1 Q8IY33;Q8IY33-4;Q8IY33-2 Q8IY33 MICALL2 MICAL-like protein 2 1 KPPLS(0.999)PAQT(0.001)NPVVQR;KPPLS(1)PAQTNPVVQR;KPPLS(1)PAQTNPVVQR 105.5 0.00080238 829310000 425000 442990 474020 522400 544010 366134 437490 374177 473670 TRUE FALSE 398400.0086 475789.4405 485263.9782 535805.6684 501285.649 471830.9421 371892.436 420893.8221 394611.417 1.009600816 1.205716358 1.229726149 1.357805794 1.270327283 1.195684975 0.942426955 1.066603256 1 18.59007317 1.808571941 6.29974962 1.002463395 1.221989281 0.53793822 0.09088392 0.164971655 11.06769724 0.040514161 0.023763179 64.35346574 -1.808571941 0.219525886 KPPPGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPPPGER 7 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 73.931 0.091946 0 62957 54360 62252 61691 72381 52153 73639 59153 70936 FALSE TRUE 59016.63375 58384.87096 63728.64684 63274.0955 66696.48823 67208.72447 62597.51558 66538.38226 59096.32334 0.998651531 0.98796114 1.078385985 1.070694282 1.128606391 1.137274211 1.059245517 1.125930997 1 15.85078076 3.858474631 1.708837561 1.093149924 0.990258545 0.471483961 0.040396122 0.284848947 1.60992129 0.010547475 0.027230154 7218.959924 -3.858474631 -0.10289138 KPPPNLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPPPNLFK 8 1 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ; 107.9 0.010536 0 2148200 2239200 2170000 2027460 2635500 1571550 2864400 2530400 3630200 FALSE TRUE 2013747.997 2404992.698 2221473.425 2079488.056 2428518.461 2025230.973 2434909.812 2846326.01 3024296.168 0.665856743 0.795223935 0.734542287 0.687594052 0.803002856 0.669653652 0.805116191 0.941153198 1 21.528168 1.257869131 2.540026038 0.995597748 0.736202963 0.816370427 0.047551505 0.103327614 1.112926099 0.038857287 0.011219401 18.10794352 -1.257869131 -0.259394785 KPPQHLS(ph)PDTTGPPPPPLETLEAEFGSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPPQHLSPDTTGPPPPPLETLEAEFGSLK 29 1 A0A3B3ISF0;A0A3B3IT29;A0A3B3ISF8 A0A3B3ISF0 1 KPPQHLS(0.417)PDT(0.194)T(0.194)GPPPPPLET(0.194)LEAEFGSLK 49.618 0.04322 64662000 132460 99659 109450 108690 115470 83555 125800 97248 122250 TRUE FALSE 124169.565 107037.8561 112046.2057 111479.1694 106401.452 107675.9721 106937.4579 109389.6269 101845.6852 1.219193182 1.050980764 1.100156628 1.094589026 1.044732055 1.057246282 1.049994976 1.074072275 1 16.63602534 4.741440948 24.85422022 1.063762509 1.219193243 0.758563731 0.028292703 120.7303837 1041716.698 0.006291891 0.044440095 55136.72263 -4.741440948 0.155430734 KPQSSSTEPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KPQSSSTEPAR 11 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WT54 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 0 ;; 139.89 6.23E-05 230254000 351556 387395 378686 379305 458340 340554 447570 399061 523310 FALSE TRUE 329552.7375 416078.1289 387668.6107 389038.6085 422343.8253 438866.4114 380461.0335 448884.6443 435966.1803 0.755913537 0.954381665 0.889217165 0.892359605 0.968753643 1.006652422 0.872684742 1.029631803 1 18.7338567 4.741265511 24.56787885 0.940301817 0.755913452 0.555503012 0.05419516 150.1643958 1363807.547 0.011914289 0.082109978 55114.45419 -4.741265511 -0.184388365 KPRPPPALGPEETSASAGLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPRPPPALGPEETSASAGLPK 21 2 Q01105 Q01105 SET Protein SET 0 62.739 0.021735 449510000 787360 606800 709450 680490 696720 502400 773940 646440 758680 FALSE TRUE 738080.5431 651728.1034 726278.489 697952.5255 642002.4216 647434.7242 657894.8819 727149.457 632051.4067 1.167753976 1.031131481 1.149081358 1.104265441 1.015743996 1.024338713 1.040888249 1.15045936 1 19.26968238 2.762218479 21.96026286 1.046278879 1.105407558 0.273078191 0.053490221 246.6425068 228942.8858 0.015424441 0.016344471 578.3869413 -2.762218479 0.059128679 KPRPPS(ph)LK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPRPPSLK 8 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 KPRPPS(1)LK;KPRPPS(1)LK 82.489 0.015861 1107930000 2319600 1494810 1633900 1676200 1884370 1087860 1744320 1248290 1508680 TRUE FALSE 2174420.377 1605487.288 1672656.88 1719214.13 1736379.181 1401907.522 1482775.409 1404141.754 1256871.562 1.730025918 1.277367821 1.330809711 1.367851881 1.381508847 1.115394417 1.17973503 1.11717203 1 20.2614058 8 0.13575324 0.921034712 3.054197918 0.703436782 0.109691493 47.53391979 0.432630401 0.499076128 19.57794358 100000000 -8 2.133163207 KPRPS(ph)EGDEDCLPASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KPRPSEGDEDCLPASK 16 2 P78346;P78346-2;Q5VU10 P78346 RPP30 Ribonuclease P protein subunit p30 1 KPRPS(1)EGDEDCLPASK;KPRPS(1)EGDEDCLPASK;KPRPS(1)EGDEDCLPASK 155.16 2.25E-07 872530000 1145830 772080 930140 1120000 999750 557050 828660 434810 616630 TRUE FALSE 1074114.546 829245.6065 952203.36 1148741.096 921233.6678 717861.292 704410.1259 489096.9856 513710.4694 2.090894793 1.614227577 1.853579821 2.236164463 1.793293543 1.397404442 1.371220109 0.952086856 1 18.97059595 1.806842926 1.320911536 0.996868694 1.885216715 0.804283144 0.187682659 0.199113277 0.65180603 0.152089541 0.061839468 64.09777076 -1.806842926 0.888348021 KPS(ph)DEEFASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KPSDEEFASR 10 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E9PDQ5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 1 KPS(1)DEEFASR;KPS(1)DEEFASR;KPS(1)DEEFASR;KPS(1)DEEFASR 130.72 0.0001649 2968600000 4123490 3089220 3646840 4000210 3713220 2111910 2875170 2256390 3193790 TRUE FALSE 3865408.122 3317949.063 3733344.767 4102862.161 3421598.68 2721584.133 2444064.95 2538105.258 2660725.816 1.452764542 1.247009009 1.403130208 1.542008626 1.285964401 1.022872825 0.918570766 0.953914621 1 21.34338842 2.258813371 3.185420901 0.953234681 1.384952518 0.878972208 0.077164049 0.082205112 1.734879404 0.03137688 0.023627649 181.473565 -2.258813371 0.431717837 KPS(ph)EDEVLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPSEDEVLNK 10 1 Q8NDI1-3;Q8NDI1-2;Q8NDI1 Q8NDI1-3 EHBP1 EH domain-binding protein 1 1 KPS(1)EDEVLNK;KPS(1)EDEVLNK 112.5 0.00098767 453120000 2286100 1330550 1790800 2107480 1868220 808440 1277890 685150 1064340 TRUE FALSE 2143017.082 1429065.306 1833278.622 2161561.505 1721497.537 1041823.504 1086282.258 770692.4857 886694.7781 2.416859933 1.611676692 2.067541917 2.437774032 1.941477022 1.174951663 1.225091525 0.869174495 1 19.75807805 2.241250523 4.082243238 1.089091248 2.050256602 0.809866557 0.2477997 0.099218085 3.75978949 0.096084822 0.073690421 174.2811926 -2.241250523 0.961165353 KPS(ph)FSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KPSFSK 6 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 KPS(0.988)FS(0.012)K;KPS(0.995)FS(0.005)K;KPS(0.993)FS(0.007)K 87.476 0.036531 892140000 2024400 1617510 1680470 1700900 1852690 1087980 2236000 1574860 2335070 TRUE FALSE 1897696.418 1737272.123 1720331.542 1744547.974 1707187.201 1402062.164 1900732.558 1771484.738 1945331.732 0.975513012 0.89304672 0.884338395 0.89678688 0.877581532 0.720731658 0.977073744 0.910633754 1 20.89158476 1.604128695 25 0.957897299 0.876724994 0.281551846 0.065993995 0.499159528 3316.600667 0.031945294 0.015672526 40.19098917 -1.604128695 -0.081172305 KPS(ph)GSPDLWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPSGSPDLWK 10 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPS(0.78)GS(0.22)PDLWK 97.551 0.0036636 1027700000 4888700 2613500 3269400 3397600 3221100 2308700 4510200 3002300 3511600 TRUE FALSE 4582724.994 2807006.259 3346951.712 3484788.168 2968127.799 2975184.211 3833937.381 3377143.764 2925491.274 1.566480486 0.959499105 1.144064842 1.191180503 1.014574142 1.016986185 1.31052771 1.154385178 1 21.48024748 4.750555747 24.74753442 1.109776441 1.566480806 0.653807711 0.10666719 1103.645384 2276917.6 0.026073979 0.432376824 56306.1388 -4.750555747 0.456704366 KPS(ph)LIGLDPEQGHLNPMSYTQHCITTMAAPSWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KPSLIGLDPEQGHLNPMSYTQHCITTMAAPSWK 33 1 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 1 KPS(1)LIGLDPEQGHLNPMSYTQHCITTMAAPSWK;KPS(1)LIGLDPEQGHLNPMSYTQHCITTMAAPSWK;KPS(0.995)LIGLDPEQGHLNPMS(0.001)YT(0.001)QHCIT(0.001)T(0.001)MAAPSWK;KPS(1)LIGLDPEQGHLNPMSYTQHCITTMAAPSWK 230.71 3.16E-37 6028170000 4992040 4932350 4784990 4382540 6110170 3414270 7379020 4724860 6145610 TRUE FALSE 4679597.127 5297546.326 4898492.222 4495003.396 5630301.895 4399914.323 6272604.454 5314769.172 5119867.989 0.91400738 1.034703695 0.956761431 0.877952987 1.099696693 0.859380424 1.225149646 1.038067619 1 22.28767518 1.741218331 25 1.105711131 0.968443488 0.302180445 0.09117561 0.458279824 4337.237874 0.037080133 0.020562813 55.10846716 -1.741218331 -0.137267642 KPS(ph)LVASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPSLVASK 8 1 P56211;H3BMD8;P56211-2;H3BQ52 P56211 ARPP19 cAMP-regulated phosphoprotein 19 1 KPS(0.973)LVAS(0.027)K;KPS(0.999)LVAS(0.001)K 115.29 0.0026407 639830000 1402230 875750 946990 755390 840240 575690 1159550 892640 1362640 TRUE FALSE 1314466.927 940591.4412 969453.05 774774.5863 774250.9398 741882.3575 985686.2422 1004088.069 1135206.581 1.15790989 0.828564119 0.853988222 0.68249656 0.682035281 0.653521896 0.868287992 0.884498104 1 20.11452343 1.010526545 2.147653923 0.996510494 0.806932557 0.14347353 0.142715626 0.591702473 5.857781527 0.13187754 0.036571659 10.245344 -1.010526545 -0.189577938 KPS(ph)PAAS(ph)PATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPSPAASPATK 11 1 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 2 KPS(1)PAAS(0.959)PAT(0.041)K 95.631 0.0011971 0 64019 36834 44562 54343 49965 34294 61691 50744 71887 TRUE FALSE 60012.16507 39561.22769 45619.03168 55737.53338 46040.95045 44194.12108 52441.00726 57079.5001 59888.59529 1.002063327 0.660580324 0.761731536 0.930686938 0.768776596 0.737938849 0.875642633 0.953094656 1 15.86999367 1.35678239 2.376045695 0.989939999 0.790772854 0.314050832 0.098021015 0.303701919 2.910877083 0.082692585 0.025132279 22.73957744 -1.35678239 -0.199167144 KPS(ph)PAASPATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KPSPAASPATK 11 1 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 KPS(1)PAASPATK;KPS(1)PAASPATK;KPS(1)PAASPATK;KPS(1)PAASPATK 153.23 2.00E-05 1452610000 2874260 2119560 2448910 2246390 2593480 1771710 2908380 2250050 3308500 TRUE FALSE 2694365.197 2276494.428 2506999.302 2304036.171 2389798.542 2283173.916 2472295.419 2530973.695 2756289.976 0.977533286 0.825927042 0.909555716 0.835919366 0.867034515 0.828350404 0.89696492 0.918253782 1 21.39429624 0.925525763 1.799538189 0.99924375 0.87110389 0.429224577 0.04510312 0.36073555 2.403154785 0.037729592 0.010708996 8.424143632 -0.925525763 -0.12813986 KPS(ph)PAQAAETPALELPLPSVPAPAPL ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KPSPAQAAETPALELPLPSVPAPAPL 26 1 A0A5H1ZRP4;Q8WX92;Q8WX92-2 A0A5H1ZRP4 NELFB Negative elongation factor B 1 KPS(0.646)PAQAAET(0.354)PALELPLPSVPAPAPL;KPS(0.822)PAQAAET(0.178)PALELPLPSVPAPAPL;KPS(0.909)PAQAAET(0.091)PALELPLPSVPAPAPL 110.18 0.00138 194821000 327661 315017 301617 321522 323683 258589 393787 289472 345707 TRUE FALSE 307153.2829 338341.1865 308771.4977 329772.7989 298262.2429 333239.4465 334742.2951 325613.2164 288006.2683 1.066481242 1.174770217 1.072099921 1.145019519 1.035610248 1.157056228 1.162274339 1.130576839 1 18.13574069 5.083607504 15.70303196 1.118367269 3.40E-05 0.033444244 0.058181304 4398131.67 12220683.48 0.012506964 167083427.6 121229.274 -5.083607504 -1.118333296 KPS(ph)PEPEGEVGPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KPSPEPEGEVGPPK 14 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK 152.04 4.15E-06 6235510000 8106530 4371580 5404410 5625710 5668280 3726890 6954640 4547950 4887690 TRUE FALSE 7599156.758 4695256.332 5532605.157 5770075.243 5223116.154 4802782.642 5911856.296 5115771.569 4071902.963 1.866242105 1.153086499 1.358727162 1.417046353 1.282721175 1.179493393 1.451865712 1.25635891 1 21.95727175 -4.925760649 0.075482239 1.84E-27 1.694080116 0.356531614 0.185505781 381.3650046 2.083770507 67.54095081 7.38551824 1.19E-05 4.925760649 1.694080116 KPS(ph)PQPS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_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(0.983)PQPS(0.639)S(0.378)PR;KPS(1)PQPS(0.549)S(0.451)PR 107.99 0.0077344 2673510000 5376180 4620150 4611110 4670750 4964050 3813170 5937960 4231760 5453360 TRUE FALSE 5039694.491 4962230.713 4720487.707 4790609.353 4574193.537 4913970.277 5047618.023 4760104.551 4543158.986 1.109293007 1.092242365 1.039032031 1.054466588 1.006831051 1.081619704 1.111037065 1.04775214 1 22.11526436 4.296789625 2.615072016 1.056808466 1.106805518 0.285277205 0.032849496 0.446591244 5.834994503 0.008702172 0.031784563 19805.67395 -4.296789625 0.049997052 KPS(ph)PQPSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPSPQPSSPR 10 1 O75909;G3V5E1;O75909-1;O75909-4 O75909 CCNK Cyclin-K 2 KPS(0.695)PQPS(0.309)S(0.996)PR 124.12 0.00029676 301860000 564010 522460 503320 522800 535220 415990 643370 476220 592360 TRUE FALSE 528709.6209 561143.482 515258.9881 536215.9331 493185.9802 536079.56 546902.6413 535677.1153 493491.2892 1.07136566 1.13708893 1.044109591 1.086576288 0.999381328 1.086299944 1.1082316 1.085484439 1 18.91266509 3.96891698 22.43256504 1.066105165 1.106631497 0.16388796 0.040075196 143.0042761 391016.5161 0.009787176 0.018095615 9309.299013 -3.96891698 0.040526333 KPS(ph)PS(ph)ESPEPWKPFPAVSPEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPSPSESPEPWKPFPAVSPEPR 22 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 KPS(0.92)PS(0.581)ES(0.499)PEPWKPFPAVSPEPR 87.339 0.0015282 212690000 128010 74176 93403 93304 101650 69063 118820 88141 124970 TRUE FALSE 119998.0826 79668.06822 95618.56327 95698.3386 93666.81904 89000.36696 101004.0441 99145.59787 104111.6997 1.152589795 0.765217247 0.918422844 0.919189091 0.899676207 0.854854615 0.970150755 0.952300252 1 16.66777268 1.630724631 7.647376561 0.971833109 0.900142768 0.046823651 0.097681491 0.26697082 33.28899566 0.045749878 0.02303938 42.72918713 -1.630724631 -0.07169034 KPS(ph)VPDSASPADDSFVDPGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPSVPDSASPADDSFVDPGER 21 1 P16333-2;P16333;C9JAB9;C9K098;C9JVV5;H7C5C7;C9J869 P16333-2 NCK1 Cytoplasmic protein NCK1 1 KPS(1)VPDSASPADDSFVDPGER;KPS(0.996)VPDS(0.004)ASPADDSFVDPGER 180.65 3.25E-17 332920000 377810 322240 331000 354070 403220 261730 378760 312120 457060 TRUE FALSE 354163.5465 346098.9849 338851.4763 363156.0356 371552.7277 337287.2022 321968.4542 351088.8691 380773.7333 0.930115487 0.908936081 0.889902445 0.953731846 0.975783504 0.885794299 0.84556372 0.922040672 1 18.53857444 4.745396143 20.90496703 0.911910392 0.930115562 0 0.046270146 548.337657 1676470.867 0.011016077 0.097640551 55641.15588 -4.745396143 0.01820517 KPS(ph)VSEEVQATPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPSVSEEVQATPNK 14 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 KPS(1)VSEEVQATPNK;KPS(0.974)VS(0.026)EEVQATPNK 184.22 3.78E-08 0 105900 78765 88844 109948 137731 70948 105925 77092 140712 TRUE FALSE 99271.90804 84596.84255 90951.42164 112769.4518 126914.1628 91429.53586 90042.52961 86717.1059 117226.2582 0.846840201 0.721654379 0.775862192 0.96198116 1.082642787 0.779940751 0.768108878 0.739741311 1 16.83893624 3.388299458 11.38993895 0.871332845 0.766508167 0.152923286 0.112651921 0.872696898 106.1615538 0.032628518 0.044187321 2445.115947 -3.388299458 -0.104824678 KPSDGS(ph)PDTKPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KPSDGSPDTKPSR 13 2 Q92733 Q92733 PRCC Proline-rich protein PRCC 1 KPSDGS(0.939)PDT(0.06)KPSR;KPSDGS(1)PDTKPSR;KPS(0.001)DGS(0.999)PDTKPSR;KPSDGS(1)PDTKPSR;KPS(0.001)DGS(0.999)PDTKPSR;KPS(0.001)DGS(0.999)PDT(0.001)KPSR 169.09 1.52E-05 3051612000 5675970 3032687 4141870 3786870 4130580 3167060 5790850 3931650 5558310 TRUE FALSE 5320721.17 3257230.301 4240117.112 3884047.495 3806180.909 4081338.809 4922565.802 4422525.157 4630592.153 1.149036882 0.703415501 0.915674923 0.838779872 0.821964186 0.881385938 1.063053199 0.955066871 1 22.14276526 1.832988596 6.479559319 1.008803137 0.862421468 0.182221134 0.114751396 0.304879279 17.0207741 0.046200338 0.02781738 68.07514825 -1.832988596 -0.146381669 KPSDSVHITNDDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPSDSVHITNDDER 14 1 A6NHR9;A6NHR9-2 A6NHR9 SMCHD1 Structural maintenance of chromosomes flexible hinge domain-containing protein 1 0 106.19 0.00062077 122720000 177060 240250 204480 245190 231920 182370 268880 220720 209080 FALSE TRUE 165978.1307 258038.36 209330.3622 251481.9905 213705.9387 235017.2585 228563.9402 248277.3779 174183.1973 0.952894041 1.481419356 1.201782752 1.443778702 1.226903295 1.349253327 1.312204298 1.425380758 1 17.41024593 -1.090866575 4.685647763 0.99998289 1.311264685 0.273282501 0.152210283 2.31E-05 4.48E-06 0.125158991 0.029498637 0.081121024 1.090866575 0.311281795 KPSETQELVQQVLSLATQDSDNPDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPSETQELVQQVLSLATQDSDNPDLR 26 1 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1 P63010 AP2B1 AP-2 complex subunit beta 0 175.9 1.52E-12 178390000 100640 82016 99734 93130 101870 70898 104160 88696 63463 FALSE TRUE 94341.12205 88088.54998 102099.7376 95519.87347 93869.54112 91365.10167 88542.17497 99769.89084 52870.61531 1.784377229 1.666115468 1.931124444 1.806672249 1.775457701 1.728088488 1.674695376 1.887057494 1 15.6901785 -1.716000875 2.659526263 0.863794694 1.77537462 0.897342573 0.083067262 7710798.736 6282757.415 6990936.958 0.020062376 0.019230879 1.716000875 0.911579926 KPSGS(ph)PDLWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPSGSPDLWK 10 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPS(0.298)GS(0.702)PDLWK 108.71 0.0014731 1225500000 3713400 2174700 2759300 2641500 2485300 2016800 3771900 2387000 2873300 TRUE FALSE 3480984.923 2335717.051 2824751.899 2709285.362 2290114.563 2599017.42 3206338.612 2685022.204 2393727.668 1.454210924 0.975765574 1.180064022 1.131826898 0.956714748 1.085761532 1.339475102 1.121690759 1 21.1908276 KPSGS(ph)PDLWKLS(ph)PDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPSGSPDLWKLSPDQR 16 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 KPS(0.439)GS(0.561)PDLWKLS(1)PDQR 75.646 0.015508 231890000 1000900 498810 710980 677130 795410 475820 866380 666680 879540 TRUE FALSE 938255.4557 535742.4114 727844.7813 694506.3022 732941.7071 613181.5097 736474.3621 749916.4655 732739.092 1.280476865 0.731150306 0.993320528 0.947822096 1.000276517 0.836834716 1.005097681 1.023442688 1 19.48294006 1.581629071 13.98174912 1.011387738 0.940495741 0.002161563 0.140185018 0.42960851 192.3854617 0.068187592 0.031844914 38.16181929 -1.581629071 -0.070891997 KPSKYPLCSADAAVST(ph)TPPGS(ph)PPPPPPLPEPPVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPSKYPLCSADAAVSTTPPGSPPPPPPLPEPPVLK 35 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 2 KPS(0.006)KY(0.003)PLCS(0.01)ADAAVS(0.336)T(0.373)T(0.273)PPGS(1)PPPPPPLPEPPVLK 116.73 1.04E-05 197020000 96139 63936 78499 79699 91085 65298 96211 79552 143540 TRUE FALSE 90121.8316 68669.88797 80361.03335 81744.21127 83931.55152 84148.47258 81785.05373 89484.24232 119582.2467 0.753638889 0.574248184 0.672014748 0.683581497 0.701873011 0.703687001 0.68392304 0.748307084 1 16.8676437 -1.901448025 0.285064294 1.334705987 0.6427873 0.824092463 0.045712487 10.85530083 0.49055086 2.47092147 0.050801367 0.012547349 1.901448025 -0.691918687 KPSKYPLCSADAAVSTT(ph)PPGS(ph)PPPPPPLPEPPVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPSKYPLCSADAAVSTTPPGSPPPPPPLPEPPVLK 35 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 2 KPSKYPLCSADAAVS(0.337)T(0.087)T(0.576)PPGS(1)PPPPPPLPEPPVLK 143.39 2.29E-10 333410000 939440 645090 812490 785540 873440 629930 1058400 798400 1476700 TRUE FALSE 880642.1273 692853.1348 831762.6465 805698.2863 804843.5457 811780.5649 899702.7457 898081.9975 1230229.23 0.715835802 0.563190272 0.676103791 0.654917203 0.654222421 0.659861223 0.731329352 0.730011916 1 20.23049573 0.113702024 0.459850873 1.038995947 0.631458753 0.876933972 0.039886693 1.046331245 0.307354975 0.112655395 0.020726754 1.299277817 -0.113702024 -0.407537194 KPSPQPSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KPSPQPSSPR 10 1 O75909;G3V5E1;O75909-1;O75909-4 O75909 CCNK Cyclin-K 1 KPSPQPS(0.093)S(0.906)PR;KPSPQPS(0.001)S(0.999)PR;KPS(0.002)PQPS(0.124)S(0.874)PR 117.95 0.00094267 204051000 588450 616290 593160 596150 620030 501210 716740 547160 618890 TRUE FALSE 551619.9649 661920.7528 607230.0353 611448.2183 571335.3449 645901.1905 609271.4909 615474.1304 515593.2608 1.069874273 1.283804121 1.177730745 1.185911967 1.108112515 1.252733966 1.181690176 1.193720278 1 18.97587388 -0.756101206 5.705697357 0.999999985 1.190908044 0.455647151 0.061687275 1.04E-08 2.39E-09 0.053859732 0.01269486 0.175347183 0.756101206 0.190908059 KPSPSES(ph)PEPWKPFPAVS(ph)PEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KPSPSESPEPWKPFPAVSPEPR 22 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 KPS(0.092)PS(0.109)ES(0.799)PEPWKPFPAVS(1)PEPR;KPS(0.138)PS(0.171)ES(0.691)PEPWKPFPAVS(1)PEPR;KPS(0.084)PS(0.112)ES(0.804)PEPWKPFPAVS(1)PEPR 105.9 0.0002703 543793000 735520 472166 598210 580490 624790 470114 746020 516130 595710 TRUE FALSE 689485.1161 507125.6619 612399.8237 595386.3562 575721.5137 605828.2801 634161.2267 580569.9666 496282.1526 1.389300648 1.021849485 1.23397511 1.199693265 1.160068946 1.220733563 1.277823962 1.169838495 1 18.92080105 0.966771924 22.1728995 0.999999996 1.200972638 0.339162351 0.092263557 1250.012366 834128.1919 0.084005022 0.021001256 9.263432122 -0.966771924 0.200972643 KPSPSES(ph)PEPWKPFPAVSPEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPSPSESPEPWKPFPAVSPEPR 22 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPSPSES(1)PEPWKPFPAVSPEPR;KPS(0.001)PSES(0.999)PEPWKPFPAVSPEPR 236.05 9.17E-31 2267900000 957490 681790 747760 754930 843270 605970 978160 683390 974110 TRUE FALSE 897562.4101 732270.441 765497.2203 774302.7819 777042.9758 780903.7019 831493.9888 768712.7458 811524.748 1.106019764 0.902339014 0.943282657 0.954133295 0.957509894 0.962267268 1.024607063 0.947244983 1 19.63027557 1.952059931 18.78938567 0.993373451 0.958359529 0 0.056110034 65.65788719 25731.22057 0.021572045 0.013913042 89.54883308 -1.952059931 -0.035013922 KPSQTAS(ph)YER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KPSQTASYER 10 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 KPSQT(0.02)AS(0.98)YER;KPSQT(0.021)AS(0.979)YER;KPS(0.001)QT(0.004)AS(0.995)YER;KPSQT(0.133)AS(0.867)YER;KPS(0.001)QT(0.043)AS(0.956)YER 136.6 6.94E-05 1816596000 1779780 2218770 1514534 1362237 2122970 1148662 2200448 2165140 3024600 TRUE FALSE 1668386.747 2383050.039 1550459.462 1397194.308 1956240.5 1480262.072 1870511.25 2435462.495 2519774.72 0.662117424 0.945739324 0.615316698 0.554491755 0.776355316 0.587458101 0.742332731 0.966539777 1 21.26486333 1.242598656 4.298753931 0.995856386 0.705865399 0.5385664 0.110428086 0.164053544 6.484938097 0.095599585 0.028126842 17.48230354 -1.242598656 -0.289990986 KPSVS(ph)EEVQATPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPSVSEEVQATPNK 14 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 KPS(0.208)VS(0.792)EEVQATPNK 136.04 1.80E-05 453020000 643350 443450 446590 601850 717930 440080 655670 475170 772100 TRUE FALSE 603083.8719 476283.4994 457183.3257 617294.4899 661546.6738 567123.9519 557358.3704 534496.0205 643231.522 0.937584449 0.740454227 0.710760138 0.959676988 1.028473654 0.881679353 0.86649729 0.830954333 1 19.29497858 3.233633168 24.99979145 0.919049133 0.772091381 0.335401521 0.084489776 121.4505818 616188.8048 0.024448177 0.030100248 1712.510203 -3.233633168 -0.146957752 KPTDGASSSNCVTDISHLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KPTDGASSSNCVTDISHLVR 20 1 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 ;;; 238.96 7.77E-30 3237460000 2654780 2686610 2590770 2524430 2898020 2233260 2992130 2563800 2954640 FALSE TRUE 2488622.059 2885529.4 2652224.288 2589211.148 2670421.199 2877965.908 2543487.884 2883896.074 2461491.496 1.011022001 1.172268685 1.077486675 1.051887098 1.084879311 1.169195958 1.033311668 1.171605134 1 21.23110132 -1.933379912 2.676575446 0.934819691 1.098279866 0.212888509 0.058194172 36225451.6 19663121.83 14747203.76 0.012517452 0.011657894 1.933379912 0.163460176 KPTETQELVQQVLSLATQDSDNPDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPTETQELVQQVLSLATQDSDNPDLR 26 1 Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 Q10567-4 AP1B1 AP-1 complex subunit beta-1 0 ; 225.3 2.93E-34 487570000 682970 559560 669900 649390 644640 500900 715340 634780 415960 FALSE TRUE 640224.1268 600990.4046 685790.3443 666054.4468 594012.5748 645501.6986 608081.4079 714033.6803 346533.5888 1.847509585 1.734291925 1.979001074 1.922048737 1.714155839 1.862739196 1.754754597 2.060503522 1 18.40263567 -1.211319067 3.729126958 0.999034081 1.849502564 0.859365546 0.109190355 1651478.634 807664.9753 12369.41539 0.023674644 0.061472508 1.211319067 0.850468482 KPTSAKPSSTTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPTSAKPSSTTPR 13 2 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;B5MEG9;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 0 79.614 0.011266 305010000 214430 222800 242870 251690 262170 228500 287410 239880 245740 FALSE TRUE 201009.2091 239296.3438 248630.9911 258148.7915 241580.2257 294464.2406 244315.5387 269829.546 204724.4065 0.981852689 1.16887062 1.214466782 1.260957577 1.180026505 1.438344581 1.193387456 1.318013571 1 17.64332358 5.660140387 0.872437173 1.247879556 9.83E-14 0.316825421 0.111385784 9.827430146 1.759288098 0.030949854 17.15508104 457235.9686 -5.660140387 -1.247879556 KPTTEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPTTEEK 7 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 96.668 0.020143 967260000 1162100 698230 863090 828260 865200 590720 1025500 717620 841990 FALSE TRUE 1089366.235 749927.6757 883562.9024 849514.5538 797250.682 761251.2745 871735.7953 807216.4367 701456.4295 1.553006273 1.069100865 1.259611952 1.211072446 1.136564794 1.085243848 1.242751165 1.150772026 1 19.41999397 4.746871122 24.87212917 1.160728523 1.553006483 0.710336931 0.081411445 526.1764388 1574731.395 0.017745356 0.201014231 55830.44921 -4.746871122 0.39227796 KPVADCVISIPSFFTDAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPVADCVISIPSFFTDAER 19 1 O95757;E9PDE8 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 109.03 0.00042232 188070000 488790 507230 494690 502900 527240 434380 547400 487840 386190 FALSE TRUE 458197.5064 544785.837 506424.2804 515805.2654 485832.6972 559778.4544 465322.4518 548747.8979 321732.3941 1.424157203 1.69328873 1.574054368 1.603212094 1.510052162 1.739888381 1.446302767 1.705603501 1 18.29550168 -1.255446359 4.058431403 0.999439031 1.589737796 0.751175564 0.106176333 125.0130313 24797275.45 23847.47245 0.021459997 0.05553332 1.255446359 0.590298765 KPVGEVHSQFSTGHANS(ph)PCTIIIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPVGEVHSQFSTGHANSPCTIIIGK 25 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 KPVGEVHSQFSTGHANS(0.997)PCT(0.003)IIIGK 112.06 0.0011374 253930000 262730 270770 355510 313990 340400 265320 411150 306950 460340 TRUE FALSE 246286.1983 290818.0925 363942.8651 322047.515 313666.3571 341913.5769 349501.8744 345273.3832 383506.2801 0.642195998 0.758313769 0.948988019 0.839745088 0.817891058 0.891546227 0.911332858 0.900306986 1 18.54889068 4.471678414 1.785969752 0.893263813 0.621398988 0.741821341 0.051550564 0.264596065 1.254325666 0.012890589 0.101852992 29626.36806 -4.471678414 -0.271864825 KPVTDCVISVPSFFTDAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPVTDCVISVPSFFTDAER 19 1 Q92598-2;Q92598;Q92598-4 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 97.488 0.0017771 473580000 720250 661940 727470 675300 781210 670820 831050 749960 638900 FALSE TRUE 675170.8382 710950.7263 744725.9319 692629.3413 719856.9178 864474.8441 706441.7676 843594.1569 532263.4625 1.268489922 1.335712061 1.399167864 1.301290414 1.352444736 1.624148387 1.327240769 1.584918403 1 19.02178101 -1.274501194 5.589422352 0.99996528 1.394248253 0.53415686 0.117072494 4.62E-05 6.00E-06 0.103396991 0.024368763 0.053149454 1.274501194 0.394282972 KPVTVSPT(ph)TPTS(ph)PTEGEAS ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 2 KPVTVS(0.017)PT(0.453)T(0.52)PT(0.129)S(0.879)PT(0.001)EGEAS;KPVTVS(0.006)PT(0.486)T(0.486)PT(0.104)S(0.915)PT(0.002)EGEAS 170.47 2.69E-11 831630000 1081930 1163000 1135400 1369990 1296160 672460 884900 745240 1216270 TRUE FALSE 1014213.933 1249109.73 1162332.224 1405146.263 1194364.822 866588.2855 752217.46 838284.8545 1013266.68 1.000934851 1.232755162 1.147113832 1.386748712 1.178727028 0.855242063 0.742368692 0.827309208 1 19.95058249 2.231204421 5.190828133 0.821973279 1.200155989 0.675408455 0.113815582 0.087533645 6.762902237 0.039359294 0.030317808 170.2959898 -2.231204421 0.37818271 KPVTVSPTT(ph)PTS(ph)PTEGEAS ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 2 KPVTVSPT(0.082)T(0.918)PT(0.095)S(0.863)PT(0.041)EGEAS(0.001);KPVTVS(0.001)PT(0.205)T(0.793)PT(0.245)S(0.756)PT(0.001)EGEAS 179.14 8.07E-14 714370000 972290 985970 969550 1153450 1122340 589970 759220 671060 1027940 TRUE FALSE 911436.1045 1058972.245 992548.1839 1183049.48 1034195.944 760284.7616 645382.0093 754843.3182 856370.1733 1.064301552 1.236582354 1.159017695 1.381469739 1.207650588 0.887799208 0.753625044 0.881445129 1 19.70787502 2.217424536 5.160933586 0.84538178 1.215616986 0.729161906 0.098900604 0.080919827 5.787353381 0.034836972 0.026431944 164.9774307 -2.217424536 0.370235206 KPVTVSPTT(ph)PTSPTEGEAS ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 KPVTVSPT(0.091)T(0.446)PT(0.015)S(0.446)PT(0.002)EGEAS 183.17 5.35E-14 1790600000 481810 489060 510420 548660 579880 366910 466140 395120 602980 TRUE FALSE 451654.3722 525270.5113 522527.4034 562739.5445 534338.5639 472830.9607 396246.6344 444451.6018 502338.7426 0.899103202 1.04565001 1.040189337 1.120239187 1.063701679 0.941259195 0.788803651 0.88476473 1 18.93830102 2.045542701 4.743007455 0.866597697 1.039124435 0.421296745 0.075448859 0.145419205 7.310730869 0.028313189 0.019817561 111.0561724 -2.045542701 0.172526738 KPVTVSPTTPT(ph)SPTEGEAS ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 KPVTVSPT(0.009)T(0.107)PT(0.505)S(0.3)PT(0.039)EGEAS(0.039) 166.48 3.84E-11 1873500000 508060 528640 501770 565550 584050 353880 444040 397080 553280 TRUE FALSE 476261.4315 567781.0556 513672.2214 580062.9705 538181.0689 456039.4112 377460.3243 446656.3121 460933.9937 1.033252999 1.231805559 1.114416008 1.258451272 1.16758815 0.989381164 0.818903204 0.969024455 1 18.81420064 2.134984628 3.864333021 0.908314931 1.169208395 0.65934661 0.077562301 0.11116077 3.127816722 0.028362458 0.020171853 136.4534838 -2.134984628 0.260893464 KPVTVSPTTPTS(ph)PTEGEAS ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 KPVTVSPTTPT(0.045)S(0.915)PT(0.04)EGEAS;KPVTVSPT(0.036)T(0.228)PT(0.343)S(0.392)PT(0.001)EGEAS;KPVTVSPTTPT(0.017)S(0.978)PT(0.005)EGEAS;KPVTVSPTTPT(0.002)S(0.993)PT(0.004)EGEAS;KPVTVSPTTPT(0.171)S(0.825)PT(0.004)EGEAS 237.99 3.27E-24 3414100000 3575680 3635400 3697740 4092340 4271560 2594220 3059010 2740030 3950110 TRUE FALSE 3351884.572 3904568.799 3785452.139 4197356.373 3936088.908 3343129.2 2600339.849 3082128.777 3290811.122 1.018558783 1.186506504 1.150309756 1.275477752 1.196084723 1.015898232 0.790182041 0.93658635 1 21.65001179 2.041424432 4.213112833 0.887862489 1.169838781 0.671343088 0.082039148 0.103979143 4.030023508 0.031942609 0.021684881 110.0080413 -2.041424432 0.281976293 KPVVDCVVSVPCFYTDAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPVVDCVVSVPCFYTDAER 19 1 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 139.38 2.98E-07 1630350000 2172700 2126500 2117300 1969210 2256700 1904110 2503700 2061100 2158600 FALSE TRUE 2036714.585 2283948.273 2167523.356 2019743.262 2079467.885 2453795.646 2128293.428 2318432.872 1798315.715 1.132567863 1.270048554 1.205307465 1.123130519 1.156341941 1.364496582 1.183492648 1.289224608 1 20.77821489 -1.049287805 4.77487548 0.999993676 1.219023543 0.448186302 0.07508792 4.65E-06 9.25E-07 0.066857951 0.015758115 0.089271369 1.049287805 0.219029867 KPWTSLS(ph)SESVSCPQGS(ph)LSPATSLMQVSERPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KPWTSLSSESVSCPQGSLSPATSLMQVSERPR 32 2 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 2 KPWT(0.037)S(0.042)LS(0.918)S(0.003)ESVS(0.01)CPQGS(0.612)LS(0.376)PAT(0.002)SLMQVSERPR;KPWT(0.113)S(0.125)LS(0.589)S(0.169)ES(0.003)VS(0.001)CPQGS(0.598)LS(0.395)PAT(0.004)S(0.001)LMQVS(0.001)ERPR 109.59 2.18E-06 253661000 67283 71883 72377 79770 84563 72933 103027 83781 96571 TRUE FALSE 63071.87713 77205.29211 74093.81662 81817.03325 77921.76309 93987.57313 87579.05781 94241.24227 80452.67623 0.78396245 0.959636096 0.920961491 1.016958504 0.968541592 1.168234266 1.088578552 1.171387289 1 16.29585279 2.980022568 0.822524787 1.115668497 0.879446335 0.612481581 0.072080966 0.38677604 0.579142881 0.037843767 0.047571832 955.0422133 -2.980022568 -0.236222161 KPWTSLS(ph)SESVSCPQGSLS(ph)PATSLMQVSERPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KPWTSLSSESVSCPQGSLSPATSLMQVSERPR 32 2 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 2 KPWT(0.021)S(0.017)LS(0.941)S(0.021)ESVSCPQGS(0.033)LS(0.935)PAT(0.025)S(0.007)LMQVSERPR 155.81 4.50E-11 177080000 132810 134640 121130 123020 137700 112020 151450 125210 162690 TRUE FALSE 124497.6592 144608.8857 124003.2608 126176.9015 126885.5975 144358.3555 128741.4785 140842.7441 135535.988 0.918557949 1.066940876 0.914910222 0.930947591 0.936176431 1.065092435 0.949869333 1.039153853 1 17.04831645 2.276237249 24.99991796 1.004969335 0.96268638 0.228254959 0.052337688 341.1179025 226343.5926 0.018014662 0.015071776 188.9023012 -2.276237249 -0.042282955 KQAEILQESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQAEILQESR 10 1 E5RJD8;O75347;E5RIW3;O75347-2 E5RJD8 TBCA Tubulin-specific chaperone A 0 98.105 0.0089855 325750000 843820 674100 687900 662350 817280 498580 847320 655470 874890 FALSE TRUE 791006.8125 724011.0654 704217.3128 679347.0224 753094.1255 642511.9522 720272.2321 737306.8724 728865.207 1.085258021 0.993340138 0.966183193 0.932061259 1.033241974 0.881523697 0.988210475 1.011581929 1 19.47529251 4.877237467 1.78859594 0.969640692 1.155742131 0.399880548 0.042569408 1.24604221 3.02871049 0.009867401 0.438084776 75376.76014 -4.877237467 0.186101439 KQALYLMFDTSQESPVKS(ph)SPVR ddPTM_SK-BR-3_Pertuzumab_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 KQALYLMFDTSQESPVKS(0.633)S(0.367)PVR 229.6 1.40E-26 1049900000 1304700 1097100 1074900 1023600 1426600 776810 1288800 1055400 1585800 TRUE FALSE 1223041.156 1178330.426 1100397.136 1049867.309 1314560.591 1001062.437 1095556.405 1187169.013 1321119.735 0.925761022 0.891917965 0.832927634 0.794679907 0.995035163 0.757737857 0.829263522 0.898608189 1 20.3333298 0.931138973 5.62389077 0.999985325 0.857315326 0.299721356 0.066730234 0.564595577 43.57239921 0.059504323 0.014987487 8.533731465 -0.931138973 -0.14267 KQALYLMFDTSQESPVKSS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_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 KQALYLMFDTSQESPVKS(0.051)S(0.949)PVR 220.66 5.21E-26 962800000 1369200 1155700 1137500 1152300 1632500 751250 1258800 1103900 1756400 TRUE FALSE 1283504.216 1241269.231 1164482.037 1181869.969 1504290.035 968123.6795 1070054.626 1241724.345 1463245.493 0.877162596 0.848298687 0.795821373 0.8077045 1.028050346 0.661627652 0.731288517 0.848609718 1 20.4807404 KQAVGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQAVGSPR 8 1 A0A0D9SFM0;Q149N8-4;Q149N8;K4DI94;Q149N8-2 A0A0D9SFM0 SHPRH E3 ubiquitin-protein ligase SHPRH 1 KQAVGS(1)PR;KQAVGS(1)PR 78.496 0.018666 277190000 588360 633700 558270 521430 690070 369850 649360 672440 852190 TRUE FALSE 551535.5979 680619.8074 571512.428 534810.7766 635874.6858 476619.691 551994.4964 756395.6142 709953.9836 0.776861051 0.958681581 0.804999255 0.753303438 0.895656198 0.67133885 0.777507429 1.065414987 1 19.43736599 1.238058417 24.99976024 1.03270758 0.813384833 0.585728219 0.079230776 10.04363586 499736.0862 0.064367708 0.019815881 17.30049054 -1.238058417 -0.219322747 KQDADSLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KQDADSLQR 9 1 P14324-2;P14324;A0A087WVN4;A0A087X1D8 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 ;;; 161.51 0.00010339 2993320000 2774690 3356500 3002210 3439860 3594570 2613000 3484830 3191250 3568280 FALSE TRUE 2601027.106 3605018.752 3073423.839 3528132.631 3312266.972 3367330.681 2962312.093 3589684.587 2972711.016 0.874968031 1.212704071 1.033879117 1.186840097 1.114224341 1.132747402 0.996501872 1.207545761 1 21.50334779 -0.976759113 7.430078234 0.999999998 1.097483941 0.07463989 0.104697363 3.94E-09 4.42E-10 0.08822776 0.020795482 0.105497189 0.976759113 0.097483943 KQDAETPPPPDPPAPETLLAPPPLPS(ph)TPDPPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQDAETPPPPDPPAPETLLAPPPLPSTPDPPRR 33 2 Q86WR7;Q86WR7-2 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 KQDAETPPPPDPPAPET(0.005)LLAPPPLPS(0.498)T(0.498)PDPPRR;KQDAETPPPPDPPAPETLLAPPPLPS(0.5)T(0.5)PDPPRR 123.21 6.31E-08 1461960000 250948 242932 272533 248024 320115 210882 325698 291015 344926 TRUE FALSE 235241.6126 260918.9381 278997.6115 254388.7157 294974.4592 271760.21 276862.6085 327348.8634 287355.6223 0.818642805 0.908000115 0.970914051 0.885274886 1.026513617 0.945727833 0.963484223 1.139176818 1 18.13247775 7.718326574 0.242857186 1.03139723 1.65E-15 0.526055398 0.059265127 36.7902722 0.559390561 0.074444154 14.94532999 52278916 -7.718326574 -1.03139723 KQDDS(ph)PPRPIIGPALPPGFIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQDDSPPRPIIGPALPPGFIK 21 2 A0A0A0MRI1;Q8IXQ4;Q8IXQ4-4 A0A0A0MRI1 GPALPP1 GPALPP motifs-containing protein 1 1 KQDDS(1)PPRPIIGPALPPGFIK;KQDDS(1)PPRPIIGPALPPGFIK 103.73 0.00022497 989190000 2426440 1662600 1861160 1929460 2275720 1423070 2517700 1762830 2652500 TRUE FALSE 2274573.452 1785700.634 1905307.594 1978973.21 2096994.131 1833887.207 2140194.258 1982923.206 2209780.614 1.029320937 0.808089555 0.862215725 0.895551892 0.948960326 0.829895599 0.968509835 0.897339398 1 21.07547172 0.815035078 0.54902164 1.001321443 0.879855418 0.131227584 0.066966561 1.738197 1.17693662 0.07279755 0.030294012 6.531833082 -0.815035078 -0.121466025 KQDEDKDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQDEDKDKR 9 3 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 0 74.162 0.018343 126190000 332790 127840 192690 194660 206070 120930 226510 158840 253440 FALSE TRUE 311961.2679 137305.4066 197260.6978 199655.3052 189886.0934 155840.5279 192546.9283 178671.5236 211139.2267 1.477514495 0.650307424 0.934268354 0.94560972 0.899340669 0.738093675 0.911942945 0.846226097 1 17.68783511 4.75053101 24.99875343 0.856256908 1.477514871 0.775389156 0.103369524 849.2800921 1773588.569 0.02353772 0.396855884 56302.93186 -4.75053101 0.621257962 KQDPPVTHDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQDPPVTHDLR 11 1 P25685;P25685-2;M0R080;M0QZD0;M0QYT3;M0QXK0;M0R128;A0A1B0GX60;M0R1D6 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 89.629 0.0078482 425900000 146810 122780 127450 134110 116690 85346 140110 98403 136700 FALSE TRUE 137621.4242 131870.759 130473.1742 137551.4896 107525.6381 109984.0047 119101.8062 110688.8312 113883.8869 1.208436311 1.157940448 1.145668433 1.207822225 0.944169022 0.965755628 1.045817889 0.97194462 1 16.79720411 2.740511258 24.99976178 0.991457756 1.170579387 0.893921793 0.033176402 56.53760362 724599.0079 0.010497374 0.010645178 550.1881826 -2.740511258 0.179121631 KQEAEWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KQEAEWK 7 1 P09496-2;F8WF69;P09496-4;P09496-3;P09496;P09496-5;C9J8P9 P09496-2 CLTA Clathrin light chain A 0 ;; 121.05 0.0071768 1353350000 2658370 2494970 2202740 2208660 3317740 1602420 2874430 2792080 3885910 FALSE TRUE 2491987.367 2679700.175 2254990.033 2265337.955 3057178.084 2065012.641 2443435.906 3140677.334 3237326.517 0.769767076 0.827750973 0.696559343 0.699755784 0.944352714 0.637875923 0.754769682 0.970145371 1 21.62637145 1.221906397 6.623106305 0.989489641 0.75908505 0.558134101 0.08273366 0.110577055 19.06171794 0.066110756 0.018609759 16.66887912 -1.221906397 -0.230404591 KQEELNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQEELNR 7 1 O14828;O14828-2 O14828 SCAMP3 Secretory carrier-associated membrane protein 3 0 95.741 0.021235 147170000 87514 102920 88838 97603 116870 86749 115180 102650 140150 FALSE TRUE 82036.65496 110540.3039 90945.27931 100107.6582 107691.5016 111792.028 97909.82828 115466.0785 116758.0596 0.702620917 0.946746668 0.778920784 0.857393987 0.922347477 0.957467334 0.838570191 0.988934544 1 16.83316261 8 0.071502052 1.14034138 0.263809602 0.436578788 0.071574276 253.0344246 1.332615729 2.78767176 22.24512047 99999999.98 -8 -0.876531777 KQEELQQLEQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KQEELQQLEQQR 12 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 178.22 3.57E-05 2215940000 2039400 2054430 2014760 2010470 2106580 1637850 2478820 1885350 1920130 FALSE TRUE 1911757.594 2206542.135 2062551.059 2062062.064 1941137.704 2110670.707 2107143.953 2120740.098 1599647.898 1.195111497 1.379392388 1.289378157 1.289072468 1.213478107 1.319459557 1.31725485 1.325754311 1 20.60932296 -1.456889228 5.834770821 0.999797278 1.29910813 0.740332882 0.053998202 0.000133149 1.24E-05 0.048887488 0.011515173 0.034922938 1.456889228 0.299310852 KQEESVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQEESVQK 8 1 Q9NVI7-3;Q9NVI7-2;Q9NVI7;Q5T9A4-3;Q5T9A4;J3QSF3;H0Y2W2;Q5T9A4-2;Q5T2N8 Q9NVI7-3 ATAD3A;ATAD3B;ATAD3C ATPase family AAA domain-containing protein 3A;ATPase family AAA domain-containing protein 3B;ATPase family AAA domain-containing protein 3C 0 100.48 0.0097432 93459000 161380 111600 115160 102740 159680 105420 122760 147010 213150 FALSE TRUE 151279.5139 119862.9801 117891.6496 105376.4823 147139.3769 135853.0426 104353.2776 165364.5221 177573.888 0.85192432 0.675003411 0.663901945 0.593423298 0.828609311 0.765050786 0.587661164 0.931243461 1 17.43805993 1.106607661 5.712362831 0.996222854 0.699523926 0.594675351 0.088435245 0.124565711 5.361007242 0.080475264 0.020295016 12.7822604 -1.106607661 -0.296698928 KQEFLEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQEFLEQK 8 1 Q9BY43;Q9BY43-2;H0YI89;E9PQI5;E9PQ80;E9PSI1 Q9BY43 CHMP4A Charged multivesicular body protein 4a 0 95.81 0.015051 201110000 376320 339210 324000 333260 390980 206200 397070 300820 373070 FALSE TRUE 352766.803 364325.4613 331685.433 341812.0158 360274.0079 265726.5926 337533.0397 338378.0392 310802.2069 1.135020264 1.172210021 1.06719137 1.099773452 1.159174549 0.854970096 1.08600593 1.088724699 1 18.24563722 KQEGPATQVDSAVGTLPATS(ph)PQSTSVQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQEGPATQVDSAVGTLPATSPQSTSVQAK 29 1 Q13428-6 Q13428-6 TCOF1 Treacle protein 1 KQEGPATQVDSAVGTLPAT(0.019)S(0.973)PQS(0.006)T(0.001)SVQAK;KQEGPATQVDSAVGTLPAT(0.012)S(0.987)PQS(0.001)TSVQAK 211.87 3.53E-26 1932590000 2124260 1481680 1726720 1560060 1839200 1318390 2118500 1534160 2132720 TRUE FALSE 1991306.359 1591385.129 1767678.614 1600093.781 1694756.651 1698987.791 1800850.592 1725703.253 1776755.254 1.120754451 0.895669297 0.994891452 0.900570733 0.953849241 0.956230627 1.013561428 0.971266723 1 20.76081353 1.752856061 25 0.995295006 0.961230722 0.019701874 0.062867979 13.77708383 24126.38179 0.026202918 0.014531045 56.605165 -1.752856061 -0.034064285 KQEKT(ph)PKT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQEKTPKTPK 10 3 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 2 KQEKT(1)PKT(1)PK 88.075 0.021245 860280000 3203400 771070 1368600 1541200 2075100 558850 1617900 844560 4344700 TRUE FALSE 3002904.912 828160.8251 1401063.838 1580749.801 1912130.017 720180.9228 1375310.915 950005.1751 3619541.502 0.829636823 0.228802688 0.387083236 0.43672653 0.528279622 0.198970207 0.379968268 0.262465612 1 21.78737553 -1.264151126 3.606784549 1.001357334 0.383801079 0.511263562 0.181162719 197005555.3 319321605.9 2975331.514 0.039033392 0.054431321 1.264151126 -0.617556254 KQELEEICHDLEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KQELEEICHDLEAR 14 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;; 253.79 2.00E-24 12954467000 12761250 12131300 12620750 12417120 13173080 10386960 16369600 11403221 14123140 FALSE TRUE 11962546.14 13029514.07 12920120.15 12735764.32 12138519.43 13385506.73 13915130.45 12826938.24 11765896.7 1.016713511 1.107396607 1.098099064 1.082430405 1.031669727 1.13765292 1.18266638 1.090179404 1 23.48810794 2.208001221 24.99857942 1.125499199 1.077629299 0.005360297 0.055341881 376.7232294 308169.7025 0.01935587 0.014296752 161.4363097 -2.208001221 -0.0478699 KQELEEILHDLESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQELEEILHDLESR 14 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ; 176.23 1.47E-06 66755000 304140 297940 303830 307400 353580 249310 360570 319380 459480 FALSE TRUE 285104.4203 319999.7876 311036.9911 315288.4044 325811.2531 321281.7498 306505.8759 359255.296 382789.8196 0.744806695 0.835967341 0.812552934 0.823659325 0.851149211 0.839316338 0.80071585 0.938518418 1 18.54619294 1.093510745 3.761565524 0.998331205 0.818844939 0.828818343 0.029655399 0.074699343 1.910459024 0.025974735 0.006733299 12.40254311 -1.093510745 -0.179486266 KQELELVVSELEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KQELELVVSELEAR 14 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 ;; 199.58 3.28E-08 248991000 549760 594428 545567 573943 652720 457354 699460 585328 673458 FALSE TRUE 515351.5029 638440.0676 558508.1069 588671.3491 601458.0041 589384.6753 594582.4665 658407.4893 561053.5091 0.918542518 1.137930799 0.995463174 1.049224966 1.072015404 1.050496371 1.059760712 1.173519956 1 19.09777885 2.105675331 1.29701969 1.082245137 1.040886444 0.075283767 0.068986824 1.413269609 4.483495335 0.042944484 0.021924581 127.5484928 -2.105675331 -0.041358693 KQELLEALTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQELLEALTK 10 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 136.27 0.0072033 0 3044800 3172500 2569100 2541000 3735500 1667100 3041200 3067100 4528900 FALSE TRUE 2854231.403 3407395.201 2630040.265 2606206.362 3442128.898 2148364.707 2585200.293 3450034.187 3772997.332 0.756489112 0.903100347 0.697069209 0.690752241 0.91230621 0.569405308 0.685184766 0.914401438 1 21.84727965 1.070073994 4.878244243 0.997761856 0.748523061 0.440218896 0.101777882 0.17397039 7.264456143 0.097507448 0.024721774 11.75097748 -1.070073994 -0.249238795 KQEVPHDGPMCDLLWSDPEDTTGWGVSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KQEVPHDGPMCDLLWSDPEDTTGWGVSPR 29 1 P60510;H3BTA2;H3BV22 P60510 PPP4C Serine/threonine-protein phosphatase 4 catalytic subunit;Serine/threonine-protein phosphatase 0 ;; 279.01 1.83E-71 151633000 156140 162110 159457 164556 185773 123467 177079 143446 201821 FALSE TRUE 146367.4761 174112.7931 163239.3953 168778.7856 171183.138 159109.9186 150527.6479 161355.5489 168135.7713 0.870531446 1.035548781 0.97087844 1.003824375 1.01812444 0.94631807 0.895274377 0.959674123 1 17.35926717 2.078811913 7.697405823 0.935280621 0.987104768 0.035427205 0.051455264 0.37443404 31.48183425 0.017690542 0.013035228 119.8979928 -2.078811913 0.051824147 KQEVQAWDGEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KQEVQAWDGEVR 12 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;; 167.89 7.70E-05 2418660000 4257700 4078900 4342600 4247800 4773100 3550250 5158300 4022500 5374000 FALSE TRUE 3991218.157 4380906 4445608.523 4356805.74 4398239.98 4575149.542 4384860.802 4524717.98 4477044.683 0.891484995 0.978526307 0.992978368 0.973143234 0.982398053 1.021912861 0.979409658 1.010648385 1 22.09411529 4.806967424 2.392543539 0.992338463 0.856122946 0.826716741 0.014646915 0.282019095 1.677466924 0.003385202 0.085013862 64116.14814 -4.806967424 -0.136215518 KQFS(ph)LENVQEGEILHDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQFSLENVQEGEILHDAK 18 1 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 KQFS(1)LENVQEGEILHDAK 146.65 3.87E-08 240800000 266860 224850 219470 220300 252750 164390 290570 199850 284940 TRUE FALSE 250157.709 241498.128 224675.932 225953.271 232900.0345 211846.7244 247001.726 224801.7124 237381.6732 1.053820649 1.017341081 0.946475476 0.951856426 0.981120536 0.892430833 1.040525676 0.947005341 1 17.85684903 4.39222778 2.081870245 0.96723345 1.054289029 0.379674578 0.038557019 0.406582238 3.034855391 0.009366472 0.050789607 24673.33074 -4.39222778 0.087055579 KQGGLGPMNIPLVSDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQGGLGPMNIPLVSDPK 17 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ; 173.34 2.39E-09 1716070000 4456900 3161900 3740000 3592070 3797800 2819700 4607700 3581700 4518300 FALSE TRUE 4177950.585 3396010.366 3828714.566 3684248.598 3499536.108 3633701.616 3916818.161 4028883.129 3764166.541 1.109927135 0.902194504 1.017148026 0.978768755 0.929697469 0.965340289 1.040553896 1.070325419 1 21.84389903 1.693137354 5.83795599 1.04190404 0.976038644 0.147451203 0.057668123 0.207022304 15.97390416 0.027057355 0.013588735 49.33298049 -1.693137354 -0.065865397 KQGGLGPMNIPLVSDPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KQGGLGPMNIPLVSDPKR 18 2 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;;; 216.96 4.88E-19 9510910000 4321750 4030520 4223600 4245790 5090960 3262630 5542240 3872740 7654140 FALSE TRUE 4051259.382 4328943.895 4323785.787 4354744.16 4691136.538 4204498.317 4711232.564 4356260.114 6376614.586 0.635330759 0.678878084 0.678069174 0.68292416 0.735678231 0.659362152 0.73882975 0.683161896 1 22.60435925 -5 0.270133809 3.149028703 0.66564531 0.922814055 0.028695056 47.11697179 0.457689154 56.45420417 0.030779416 1.00E-05 5 -2.483383394 KQGGS(ph)PDEPDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KQGGSPDEPDSK 12 1 Q9ULX6;Q9ULX6-2;V9GZ50 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 1 KQGGS(1)PDEPDSK;KQGGS(1)PDEPDSK;KQGGS(0.945)PDEPDS(0.055)K 130.61 0.00022602 1272390000 3530420 1705530 2222650 2107400 2462090 1570910 2865890 1907700 3949240 TRUE FALSE 3309457.314 1831809.216 2275372.308 2161479.452 2268727.383 2024406.215 2436176.4 2145880.544 3290086.331 1.005887682 0.556766307 0.691584378 0.656967397 0.689564697 0.615304892 0.740459719 0.652226212 1 21.64969401 -1.58281688 4.243242048 1.005331818 0.685888184 0.375418491 0.11974403 0.005353081 0.000526299 0.102757839 0.023881068 0.02613263 1.58281688 -0.319443634 KQGGSPDEPDS(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQGGSPDEPDSK 12 1 Q9ULX6;Q9ULX6-2;V9GZ50 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 1 KQGGS(0.007)PDEPDS(0.993)K 173.72 6.32E-05 0 187310 96993 121690 118260 147310 92684 159470 118610 233910 TRUE FALSE 175586.6015 104174.4626 124576.5443 121294.7518 135740.8668 119440.3662 135558.9539 133418.7196 194868.9099 0.901049847 0.534587394 0.639283836 0.62244281 0.696575287 0.612926743 0.695641773 0.684658829 1 17.57214441 0.009743846 0.809241708 1.008222029 0.648409403 0.527975983 0.095662783 3.752772391 2.461105441 0.175238883 0.028693245 1.022689615 -0.009743846 -0.359812626 KQIS(ph)VR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KQISVR 6 1 P11216;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 1 KQIS(1)VR;KQIS(1)VR;KQIS(1)VR;KQIS(1)VR;KQIS(1)VR;KQIS(1)VR 119.29 0.012947 33000500000 40495200 43756900 35794000 38968200 40145400 24080100 61615900 36754700 64821000 TRUE FALSE 37960677.72 46996706.41 36643050.58 39968189.99 36992542.22 31031633.96 52377167.81 41343605.2 54001956.34 0.702950046 0.870277849 0.678550428 0.740124853 0.685022261 0.57463907 0.969912414 0.765594582 1 25.68650834 1.694821233 10.58035109 0.899071024 0.724225245 0.497817293 0.09499194 0.108435745 20.18836066 0.043347514 0.023501557 49.52462929 -1.694821233 -0.174845779 KQIT(ph)MEELVR ddPTM_SK-BR-3_Pertuzumab_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 205.3 9.35E-08 14333829000 22160150 22550920 17771830 22703310 16788580 12616670 28831760 18550340 24720350 TRUE FALSE 20773185.77 24220613.58 18193386.2 23285915.37 15470072.65 16258897.81 24508705.25 20866390.78 20594363.89 1.00868305 1.176079714 0.883415788 1.130693597 0.751179922 0.789482885 1.190068573 1.013208803 1 24.29574623 -0.276571443 6.711327379 0.999636233 1.001338688 0 0.150720182 0 0 0.141645551 0.033386177 0.528966973 0.276571443 0.001702455 KQLELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQLELR 6 1 Q15233;Q15233-2;H7C367 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 106.42 0.051536 1872810000 4257100 4856300 4434000 4309400 5566600 3483900 5153600 4792400 6281200 FALSE TRUE 3990655.71 5215865.505 4539176.574 4419986.5 5129421.691 4489645.374 4380865.524 5390741.689 5232827.142 0.762619441 0.996758609 0.867442484 0.844665107 0.980239085 0.857977008 0.837189039 1.030177673 1 22.31915917 1.228701433 24.99605458 1.01508893 0.887529026 0.403443144 0.068501617 233.4164518 591761.5481 0.058871237 0.015438023 16.93173385 -1.228701433 -0.127559903 KQLLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQLLEK 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 82.305 0.095553 664890000 736430 890110 839320 840870 1036500 669300 1130400 970190 1123000 FALSE TRUE 690338.1609 956014.6706 859229.0668 862448.1478 955097.471 862516.0448 960907.0141 1091320.357 935564.0451 0.73788445 1.02185914 0.918407533 0.921848325 1.020878769 0.921920898 1.027088438 1.166483858 1 19.83547689 1.564283387 4.010493898 1.087523506 0.938525992 0.365786264 0.087725125 0.181870094 6.587195349 0.048252213 0.02053421 36.66767613 -1.564283387 -0.148997514 KQLQDEMLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 137.46 0.00026308 1999100000 3820670 5050400 3721600 3885330 5772600 2842398 4669030 4948520 6962850 FALSE TRUE 3581541.085 5424336.871 3809878.109 3985034.146 5319243.282 3662952.16 3968952.297 5566353.615 5800705.353 0.617431996 0.935116773 0.656795661 0.686991306 0.916999392 0.631466682 0.68421891 0.959599441 1 22.46779691 1.185789539 6.963448741 0.986730363 0.741999006 0.462208696 0.110531713 0.209009442 21.2545576 0.099092455 0.025295075 15.3387348 -1.185789539 -0.244731357 KQMVIDVLHPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQMVIDVLHPGK 12 1 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4 E7ETK0 RPS24 40S ribosomal protein S24 0 ; 129.37 0.00015285 4619000000 10624900 10282200 10487100 10069500 11741300 8339600 13097200 10103700 13099000 FALSE TRUE 9959906.475 11043504.79 10735858.96 10327900.42 10819185.66 10747107.14 11133396.45 11365169.19 10912692.28 0.912690125 1.011987189 0.983795629 0.94641177 0.991431389 0.984826371 1.020224539 1.041463362 1 23.37950374 1.802296069 2.583523559 1.024379395 0.97636992 0.38685678 0.028659901 0.29492873 3.761091141 0.016129005 0.007654404 63.43019824 -1.802296069 -0.048009475 KQNGAIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQNGAIGR 8 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 127.56 0.0018775 203960000 213290 235610 222880 250610 295710 179960 244540 236290 412150 FALSE TRUE 199940.5596 253054.8096 228166.8189 257041.0769 272486.1294 231911.5306 207873.4972 265791.3266 343359.5024 0.582306761 0.736996669 0.6645129 0.748606271 0.793588433 0.675418997 0.605410643 0.774090493 1 18.38936036 0.976679238 18.45390578 1.000000003 0.690234766 0.709374431 0.063246077 31.16444221 24661.47259 0.059835435 0.014959006 9.477182368 -0.976679238 -0.309765237 KQNLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 124.37 0.029477 848390000 1016690 1167090 1065370 1042140 1311490 828700 1188490 1129870 1412360 FALSE TRUE 953057.1877 1253502.558 1090641.08 1068883.077 1208490.866 1067932.237 1010286.958 1270936.757 1176627.992 0.809990239 1.06533464 0.926920902 0.908429074 1.02707982 0.907620968 0.858629036 1.080151726 1 20.16622683 1.223432108 24.99929582 1.040075874 0.939802009 0.260020295 0.076167933 410.3593667 678084.8196 0.069338072 0.017606633 16.72754121 -1.223432108 -0.100273865 KQNS(ph)PVAPTAQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQNSPVAPTAQPK 13 1 Q6P1N0-2;Q6P1N0 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 KQNS(1)PVAPTAQPK 78.441 0.014223 359990000 125390 73523 98666 91662 104120 71604 118730 77952 112970 TRUE FALSE 117542.0637 78966.71942 101006.4041 94014.2021 95942.8352 92274.91241 100927.5387 87684.47879 94114.57719 1.248925164 0.839048761 1.07322805 0.99893348 1.019425875 0.980452924 1.072390078 0.931677976 1 16.52213058 1.394662603 0.003791156 9.87E-08 2.009978643 0.024265985 0.10459451 64160.90642 235.9706046 62638.37682 62453.30799 24.81204743 -1.394662603 2.009978544 KQPAS(ph)PDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQPASPDGR 9 1 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 KQPAS(1)PDGR;KQPAS(1)PDGR 84.479 0.0094719 252450000 888900 610730 797270 669310 553870 736840 900990 672350 503140 TRUE FALSE 833265.3357 655949.0847 816181.6209 686485.6277 510371.2844 949553.7464 765894.9139 756294.3775 419162.6836 1.98792824 1.564903343 1.947171475 1.637754635 1.217597139 2.265358496 1.827202048 1.804297966 1 18.67715076 -1.068704534 4.708623777 0.99996924 1.780951642 0.439512534 0.277359182 1.95366752 81174058.53 5600.382779 0.060549021 0.085368071 1.068704534 0.780982403 KQPDVSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQPDVSSR 8 1 Q96T58 Q96T58 SPEN Msx2-interacting protein 0 ; 87.913 0.024031 71367000 95764 101227 96183 91779 101993 68830 104477 91731 115763 FALSE TRUE 89770.30218 108721.9524 98464.50618 94134.20452 93982.8812 88700.10364 88811.64377 103183.8173 96441.40744 0.930827376 1.127336849 1.020977491 0.976076636 0.974507566 0.919730497 0.920887056 1.069911981 1 16.55736508 3.321639238 2.781219558 0.964243206 1.052081297 0.075728623 0.063976341 0.337170189 5.247282186 0.017850876 0.025084116 2097.197051 -3.321639238 0.087838091 KQPPKEPSEVPT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQPPKEPSEVPTPK 14 2 P17096-2 P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KQPPKEPSEVPT(1)PK 116.6 0.016765 1146200000 4263900 1757600 2364200 2092900 2763500 1360500 3399100 2011900 4466900 TRUE FALSE 3997030.11 1887734.533 2420279.94 2146607.357 2546465.857 1753254.264 2889436.511 2263090.144 3721345.533 1.074081962 0.507272038 0.650377644 0.576836345 0.684286325 0.471134499 0.776449401 0.608137601 1 21.82739292 -1.428444938 2.897037958 1.007674833 0.650767344 0.270672331 0.168739402 16785432.08 19211947.05 1058574.107 0.035559278 0.037286796 1.428444938 -0.35690749 KQPPKEPSEVPTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQPPKEPSEVPTPK 14 2 P17096-2 P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 0 ; 122.33 6.15E-05 1061690000 1923330 1315550 1426110 1426910 1639220 1010980 1861770 1294960 2138140 FALSE TRUE 1802952.209 1412954.691 1459938.003 1463526.926 1510482.273 1302833.514 1582614.872 1456638.607 1781270.621 1.012171978 0.793228538 0.819604829 0.82161964 0.847980231 0.731406839 0.888475257 0.817752558 1 20.76447529 -1.908888804 9.480104136 1.022721058 0.8339755 0.314213539 0.072818918 0.028181352 0.000270845 0.056820409 0.014672725 0.012334206 1.908888804 -0.188745559 KQPPVS(ph)PGTALVGSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KQPPVSPGTALVGSQK 16 1 P17096;P17096-3 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KQPPVS(0.981)PGT(0.019)ALVGSQK;KQPPVS(0.998)PGT(0.002)ALVGSQK;KQPPVS(0.749)PGT(0.251)ALVGSQK 211.64 4.03E-12 4866500000 3813920 2338570 3148680 2655140 2900300 2460030 3771070 2717990 3863740 TRUE FALSE 3575213.555 2511720.156 3223368.177 2723275.388 2672522.137 3170200.726 3205633.062 3057337.035 3218856.833 1.110709093 0.780314343 1.001401536 0.846038059 0.830270582 0.984884041 0.99589178 0.949820757 1 21.61811698 2.182552841 24.7068117 0.98385471 0.904426593 0.114959406 0.092995658 141.7037099 62508.67794 0.031832558 0.023509915 152.2484364 -2.182552841 -0.079428117 KQPPVSPGTALVGSQKEPS(ph)EVPTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQPPVSPGTALVGSQKEPSEVPTPK 25 2 P17096;P17096-3 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KQPPVSPGTALVGSQKEPS(0.934)EVPT(0.065)PK 152.49 6.45E-08 927770000 837000 384050 517950 496320 609340 332130 737040 402940 953460 TRUE FALSE 784613.6641 412485.4616 530236.0186 509056.4115 561484.8944 428010.5393 626527.6943 453247.946 794321.3664 0.987778621 0.51929292 0.66753337 0.640869594 0.706873714 0.538838004 0.788758456 0.570610291 1 19.59936329 -1.408001618 3.423331311 1.003139276 0.665278895 0.352065963 0.136563233 56665675.05 84887921 1768134.428 0.028853281 0.039083944 1.408001618 -0.337860381 KQPSNNLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQPSNNLDR 9 1 P17252 P17252 PRKCA Protein kinase C alpha type 0 83 0.027037 37839000 91560 99673 75921 72955 128270 68230 93030 107880 147250 FALSE TRUE 85829.42304 107052.8926 77721.88197 74827.14881 118196.1916 87926.89338 79081.01515 121349.0555 122673.0237 0.699660124 0.872668574 0.633569465 0.609972319 0.963505977 0.716758181 0.644648781 0.98920734 1 16.9044585 1.224810563 24.89536017 0.994604025 0.736145416 0.496209133 0.108990218 210.9001375 381836.6481 0.098898817 0.025256947 16.78071893 -1.224810563 -0.258458609 KQQDTPGS(ph)PDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KQQDTPGSPDHR 12 1 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;H0Y954 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 KQQDT(0.02)PGS(0.98)PDHR;KQQDT(0.005)PGS(0.995)PDHR;KQQDT(0.018)PGS(0.982)PDHR;KQQDT(0.017)PGS(0.983)PDHR;KQQDT(0.199)PGS(0.801)PDHR;KQQDT(0.008)PGS(0.992)PDHR;KQQDT(0.163)PGS(0.837)PDHR;KQQDT(0.001)PGS(0.999)PDHR 132.81 0.00010679 3874608000 8044985 7386062 8245741 9210450 10066190 5394901 7317916 5953352 6503394 TRUE FALSE 7541463.75 7932933.716 8441333.87 9446805.74 9275632.042 6952321.34 6220662.432 6696641.102 5417935.528 1.391944166 1.464198619 1.558035127 1.743617231 1.712023333 1.283204886 1.148161029 1.236013435 1 22.3693118 2.067489705 4.969723599 1.159619226 1.563477742 0.751214982 0.118514037 0.110203374 5.253440211 0.0483351 0.034623903 116.8126039 -2.067489705 0.403858516 KQQDTPGSPDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KQQDTPGSPDHR 12 1 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;H0Y954 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 ;;; 95.273 0.0039855 282632000 197230 303658 281456 267814 360000 218366 307464 301433 327190 FALSE TRUE 184885.7264 326141.1543 288132.2692 274686.5606 331727.0522 281404.7193 261362.6276 339067.5736 272579.8753 0.678280912 1.196497555 1.057056281 1.00772869 1.216990256 1.032375259 0.958847851 1.243920056 1 18.05631953 4.748469798 24.79306205 1.084553331 0.678280664 0.630633032 0.098770563 806.8644704 2018752.594 0.02239756 0.299976831 56036.34466 -4.748469798 -0.406272667 KQQLAEEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQQLAEEEAR 10 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 93.623 0.010773 0 149450 168900 148090 166170 155350 118110 186420 164620 151500 FALSE TRUE 140096.1913 181405.5317 151602.7647 170434.2035 143149.4377 152206.4396 158468.0516 185173.1694 126213.6713 1.109992205 1.437289082 1.201159615 1.350362459 1.134183296 1.205942574 1.255553777 1.467140346 1 16.94550866 2.761941191 24.73442398 1.229792097 1.289541997 0.032486801 0.143406965 2591.249306 2741289.255 0.04003125 0.04243389 578.0177707 -2.761941191 0.059749901 KQQMAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQQMAR 6 1 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ; 142.53 0.018463 790890000 1180490 2947100 1277700 1208370 2885300 930620 1192290 2614800 2416300 FALSE TRUE 1106605.238 3165306.35 1308007.647 1239378.82 2658700.177 1199274.887 1013517.183 2941263.536 2013003.92 0.549728308 1.572429303 0.649778987 0.615686243 1.320762543 0.595763811 0.503484953 1.461131549 1 20.94091855 3.805207599 9.075254366 0.828192699 1.128949935 0.017273494 0.400206616 0.788827089 85.29132959 0.095067337 0.171649901 6385.68658 -3.805207599 0.300757236 KQQMGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQQMGK 6 1 P31946-2;P31946;Q4VY19;A0A0J9YWE8;A0A0J9YWZ2 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ; 103.71 0.05524 666000000 908090 730310 978460 897680 961840 675560 948700 898100 932350 FALSE TRUE 851254.2679 784382.9123 1001669.533 920715.9886 886300.9663 870583.2052 806451.2423 1010229.762 776734.7618 1.09593945 1.009846541 1.289590195 1.185367302 1.141059999 1.120824312 1.038258209 1.300610983 1 19.56706251 -0.116101791 7.764178842 0.999999995 1.140169735 0.191759749 0.094170141 0 0 0.088959628 0.020967985 0.765417185 0.116101791 0.140169741 KQQNVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 KQQNVDR 7 1 Q13268;C9JZP6;Q13268-2 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;;;;;;;;; 199.07 0.00061772 27319230000 25730930 24572430 21617350 19536980 30550080 19453460 19011740 26508700 29199780 FALSE TRUE 24120477.02 26391798.28 22130123.75 20038331.98 28150799.95 25069358.1 16161106.08 29818369.55 24326148.08 0.991545268 1.084914808 0.909725768 0.823736332 1.1572239 1.030551899 0.664351217 1.225774399 1 24.53600456 3.965107839 7.200923332 0.94731326 1.039189342 0.008384558 0.160701193 0.437922244 129.4873793 0.039538278 0.075969483 9228.005374 -3.965107839 0.091876083 KQS(ph)AGPNS(ph)PTGGGGGGGSGGTR ddPTM_SK-BR-3_Pertuzumab_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(0.798)PT(0.202)GGGGGGGSGGTR 64.397 0.086151 260900000 200970 165260 207800 193500 219400 162370 246820 210860 396330 TRUE FALSE 188391.6464 177496.0224 212729.1141 198465.5376 202169.209 209243.5831 209811.6324 237186.3352 330179.9626 0.57057262 0.537573573 0.644282325 0.601082925 0.612300054 0.633725867 0.63544629 0.718354722 1 18.33289305 -5 0.19071012 2.711285124 0.541504724 0.961307373 0.025331523 23.96637589 0.234794918 15.50004747 0.068000603 1.00E-05 5 -2.169780399 KQS(ph)FDDNDS(ph)EELEDKDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KQSFDDNDSEELEDKDSK 18 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 2 KQS(1)FDDNDS(1)EELEDKDSK;KQS(1)FDDNDS(1)EELEDKDSK;KQS(1)FDDNDS(1)EELEDKDSK;KQS(1)FDDNDS(1)EELEDKDSK;KQS(1)FDDNDS(1)EELEDKDSK 177.6 4.99E-14 1640830000 6245430 1456681 2730426 2636472 2363307 1692213 3965640 1812933 5183120 TRUE FALSE 5854539.685 1564535.177 2795192.994 2704128.335 2177702.401 2180727.422 3371029.097 2039281.676 4318023.788 1.355837756 0.362326669 0.647331541 0.626242112 0.504328486 0.505029043 0.78068794 0.472271987 1 22.04193976 -1.015065048 4.641967046 1.000007802 0.628638202 0.126673708 0.274549702 2.11051E+11 44777778080 23452874.67 0.058242349 0.09659062 1.015065048 -0.3713696 KQS(ph)LGELIGTLNAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 23 KQSLGELIGTLNAAK 15 1 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 1 KQS(0.999)LGELIGT(0.001)LNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(0.999)LGELIGT(0.001)LNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(0.999)LGELIGT(0.001)LNAAK;KQS(1)LGELIGTLNAAK;KQS(0.998)LGELIGT(0.002)LNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK 292.88 6.15E-44 1.44237E+11 6840795 5626660.3 5805812.4 5002498.9 6019989 3827975.6 7526990 5023088 8916804 TRUE FALSE 6412641.852 6043264.083 5943529.012 5130871.491 5547203.347 4933050.014 6398387.727 5650231.594 7428531.808 0.863244854 0.813520658 0.800094711 0.690697923 0.746742895 0.664067967 0.861326019 0.760612156 1 22.82464567 -0.072754784 1.089472836 1.001719275 0.776617753 0.540508279 0.06500051 9.490620539 8.66807356 0.126605294 0.019007443 0.84575625 0.072754784 -0.225101522 KQS(ph)LPATSIPTPASFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQSLPATSIPTPASFK 16 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 KQS(1)LPATSIPTPASFK;KQS(1)LPATSIPTPASFK 175.85 2.07E-09 1983880000 4967200 3661400 4137800 3519500 4225800 3708700 6972900 4775000 9563100 TRUE FALSE 4656311.819 3932493.866 4235950.57 3609816.328 3893922.714 4779341.484 5927378.378 5371169.261 7966956.83 0.584453 0.493600499 0.531689911 0.453098517 0.488759108 0.599895492 0.743995293 0.674180791 1 22.92559733 1.086787196 0.709422035 0.991475975 0.502500594 0.875341224 0.056836199 0.218433118 0.257633148 0.054481193 0.02187889 12.21201127 -1.086787196 -0.488975381 KQS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQSPPR 6 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 KQS(1)PPR;KQS(1)PPR 81.548 0.037724 1053600000 444510 380380 410650 389640 420710 326120 458380 373490 438830 TRUE FALSE 416688.9126 408543.731 420390.8119 399638.8221 387669.1337 420265.5499 389650.1744 420121.0487 365586.438 1.139782194 1.117502425 1.149908115 1.093144549 1.060403487 1.149565482 1.065822289 1.149170223 1 18.47985303 -5 0.19480397 0.499854705 1.13453006 0.523774812 0.034092707 103.7548634 1.021602487 20.20055473 0.0794298 1.00E-05 5 0.634675355 KQS(ph)SEGIPVAQPSVMDDIEVWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KQSSEGIPVAQPSVMDDIEVWLR 23 1 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-4;Q6ZVM7-3 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 1 KQS(0.79)S(0.21)EGIPVAQPSVMDDIEVWLR;KQS(0.815)S(0.185)EGIPVAQPSVMDDIEVWLR;KQS(0.747)S(0.253)EGIPVAQPSVMDDIEVWLR;KQS(0.89)S(0.11)EGIPVAQPSVMDDIEVWLR;KQS(0.804)S(0.196)EGIPVAQPSVMDDIEVWLR;KQS(0.5)S(0.5)EGIPVAQPSVMDDIEVWLR 152.15 3.99E-08 965629000 931352 766768 817569 840824 881689 669265 996874 731245 1545359 TRUE FALSE 873060.3408 823540.3005 836962.1228 862400.9674 812444.7025 862470.9409 847401.9982 822542.5479 1287428.599 0.678142727 0.639678426 0.650103721 0.669863142 0.631060008 0.669917494 0.658212812 0.63890343 1 20.29606099 -1.693723091 2.707455303 1.051327367 0.65356453 0.980729442 0.01522046 1930025.169 1673265.362 678091.7849 0.00335533 0.020243095 1.693723091 -0.397762836 KQS(ph)SSEISLAVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KQSSSEISLAVER 13 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 KQS(0.929)S(0.049)S(0.023)EISLAVER;KQS(0.937)S(0.052)S(0.011)EISLAVER;KQS(0.873)S(0.112)S(0.015)EISLAVER;KQS(0.955)S(0.043)S(0.002)EISLAVER 206.61 3.71E-08 1092480000 818994 735949 706888 618731 805520 553823 810850 784553 1473320 TRUE FALSE 767734.6275 790439.4297 723655.7172 634608.685 742257.7085 713702.7095 689270.5701 882506.1691 1227413.374 0.625489867 0.643987956 0.589577833 0.517029306 0.604733274 0.581468904 0.561563516 0.718996703 1 20.22718978 0.900783697 3.292315676 0.999761049 0.591436647 0.933003651 0.034917933 0.101312613 2.413117238 0.035649063 0.009261063 7.957629164 -0.900783697 -0.408324403 KQS(ph)VFSAPSLSAGASAAEPLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KQSVFSAPSLSAGASAAEPLDR 22 1 Q14573 Q14573 ITPR3 "Inositol 1,4,5-trisphosphate receptor type 3" 1 KQS(1)VFSAPSLSAGASAAEPLDR;KQS(0.995)VFS(0.005)APSLSAGASAAEPLDR;KQS(1)VFSAPSLSAGASAAEPLDR 294.19 1.09E-55 1321400000 566781 526361 397137 363991 650620 291050 745990 594320 773340 TRUE FALSE 531307.1889 565333.3161 406557.2772 373331.6253 599522.9297 375071.4102 634135.7249 668522.1603 644264.558 0.824672384 0.877486289 0.631040885 0.579469444 0.930553951 0.582169864 0.984278457 1.037651617 1 19.29729371 1.612425309 6.859986391 1.015725584 0.743190909 0.536576874 0.118330002 0.094724739 9.668840623 0.059862017 0.029049159 40.96616489 -1.612425309 -0.272534675 KQSAGPNS(ph)PTGGGGGGGSGGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.981)PT(0.019)GGGGGGGSGGTR;KQSAGPNS(0.933)PT(0.067)GGGGGGGSGGTR 185.44 2.17E-17 734630000 531800 562540 611130 705930 757640 433710 572280 457000 719320 TRUE FALSE 498515.5873 604191.0469 625626.2922 724045.3589 698138.0106 558915.0363 486471.9268 514057.456 599260.845 0.831884131 1.008227138 1.043996612 1.208230714 1.164998542 0.932674045 0.811786605 0.857819196 1 19.19282459 2.028347765 9.750870262 0.86972788 1.051576681 0.319551364 0.109584123 0.3606661 118.8592663 0.041479208 0.030467464 106.745055 -2.028347765 0.181848801 KQSDS(ph)VKGK ddPTM_SK-BR-3_Pertuzumab_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 KQSDS(1)VKGK;KQS(0.002)DS(0.998)VKGK 107.85 0.0014126 973890000 1484220 673020 774970 674780 867330 323425 809200 406620 1783040 TRUE FALSE 1391325.32 722851.1011 793352.6544 692095.9972 799213.4004 416792.5471 687867.9722 457387.4021 1485439.105 0.936642448 0.486624526 0.534086286 0.465920141 0.538031749 0.280585415 0.463073828 0.307913936 1 20.50245803 -1.27083348 3.898507693 1.000728381 0.491202278 0.438292517 0.176966542 74802271.84 169323443.2 694121.2482 0.039242299 0.053600214 1.27083348 -0.509526103 KQSEPFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQSEPFFK 8 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 143.03 0.00097476 2726100000 5820600 5443000 5563200 5852700 7088700 4518300 7734500 6272200 9119200 FALSE TRUE 5456299.036 5846005.383 5695161.731 6002890.191 6531982.096 5822659.862 6574783.529 7055297.977 7597146.608 0.718203731 0.769500141 0.749644837 0.790150632 0.859794135 0.766427208 0.865428018 0.92867735 1 22.85702623 1.301588383 0.434943785 1.014199201 0.739276258 0.858798221 0.032895044 0.342156304 0.184469548 0.038167009 0.023929767 20.02573122 -1.301588383 -0.274922943 KQSFDDNDS(ph)EELEDKDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KQSFDDNDSEELEDKDSK 18 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 KQS(0.001)FDDNDS(0.999)EELEDKDSK;KQSFDDNDS(1)EELEDKDSK;KQS(0.024)FDDNDS(0.976)EELEDKDSK;KQS(0.006)FDDNDS(0.994)EELEDKDSK;KQSFDDNDS(1)EELEDKDSK 198.39 9.07E-16 10002100000 7967000 2096591 3630890 3439050 3647240 2300928 4657200 2639291 4600370 TRUE FALSE 7468359.692 2251824.779 3717016.425 3527301.845 3360800.483 2965168.561 3958896.095 2968812.291 3832538.527 1.948671785 0.587554375 0.96985755 0.920356526 0.87691238 0.773682649 1.03296968 0.774633385 1 21.86986886 4.747687277 24.99958044 0.865670532 1.948672345 0.870946937 0.130853402 403.432989 1105053.005 0.030101341 0.374761992 55935.46812 -4.747687277 1.083001813 KQSS(ph)EGIPVAQPSVMDDIEVWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQSSEGIPVAQPSVMDDIEVWLR 23 1 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-4;Q6ZVM7-3 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 1 KQS(0.42)S(0.58)EGIPVAQPSVMDDIEVWLR 108.01 0.00079123 18260000 21264 18817 16167 21188 21609 15536 24626 19300 38752 TRUE FALSE 19933.1242 20210.23026 16550.48887 21731.71995 19911.91631 20020.99099 20933.55992 21709.64748 32284.04085 0.617429655 0.626013031 0.512652333 0.67314126 0.616772739 0.620151334 0.648418208 0.672457565 1 14.97853355 -0.641855153 0.431871508 1.10568491 0.59165746 0.903560797 0.039274755 2.846427575 0.448194976 0.455082605 0.022907611 0.228110275 0.641855153 -0.514027451 KQSS(ph)SEISLAVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQSSSEISLAVER 13 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 KQS(0.165)S(0.417)S(0.417)EISLAVER 235.4 6.73E-17 543460000 458010 392230 409500 342500 427360 317240 470560 477770 904000 TRUE FALSE 429343.9717 421271.1173 419213.5334 351289.1299 393796.8695 408822.038 400003.8965 537420.6362 753116.5599 0.570089671 0.559370408 0.556638316 0.466447225 0.52288967 0.542840325 0.531131458 0.713595564 1 19.52251364 0.925567422 2.495925353 0.99951036 0.536270075 0.962729361 0.029397041 0.063981429 0.886474171 0.0293379 0.007895907 8.424951743 -0.925567422 -0.463240285 KQTDFEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQTDFEHR 8 1 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ; 174.41 0.00017665 437900000 1073520 1491810 1119850 1165870 1545860 752250 1248440 1237550 1019490 FALSE TRUE 1006330.299 1602265.165 1146413.371 1195788.198 1424454.391 969412.3632 1061248.012 1392060.842 849330.5328 1.184851198 1.886503667 1.349784715 1.407918533 1.677149633 1.141384097 1.249511198 1.639009535 1 19.69596659 -3.359202078 0.123813165 1.57E-11 1.703596302 0.215603784 0.241390751 115.4660821 1.38220634 32.28925519 2.201268607 0.000437319 3.359202078 1.703596302 KQTIDNSQGAYQEAFDISKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQTIDNSQGAYQEAFDISKK 20 2 P27348 P27348 YWHAQ 14-3-3 protein theta 0 237.5 7.51E-30 670310000 587270 381830 437460 450200 469980 330240 634680 420440 684230 FALSE TRUE 550513.819 410101.0905 447836.7578 461752.8942 433069.6666 425574.927 539515.6261 472932.8595 570027.5927 0.965766966 0.71944077 0.785640491 0.810053584 0.759734568 0.746586538 0.946472825 0.829666608 1 19.12067223 1.194416178 0.944470482 0.986633502 0.78776838 0.335013934 0.079905667 0.499736687 0.965185909 0.0688341 0.024158075 15.646463 -1.194416178 -0.198865123 KQVEELFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQVEELFER 9 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 185.96 6.77E-05 416730000 400470 518500 425540 423110 563160 308940 418000 474930 635300 FALSE TRUE 375405.2976 556890.2795 435634.0098 433967.7189 518931.6853 398125.9628 355324.7805 534226.0559 529264.3258 0.709296431 1.052196894 0.823093469 0.819945154 0.980477353 0.752225199 0.671356 1.009374768 1 19.01362889 2.224455204 24.99729153 0.810955057 0.890947478 0 0.139325784 668.0101662 1183824.298 0.049048606 0.036402125 167.6699382 -2.224455204 0.079992421 KQVEIAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KQVEIAQR 8 1 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ;;;; 143.37 0.00096602 3247430000 3175980 5021330 2813410 3013580 5830790 2058850 3356950 4807810 5128360 FALSE TRUE 2977201.081 5393114.498 2880145.414 3090913.565 5372863.274 2653206.572 2853606.512 5408075.662 4272403.586 0.696844533 1.262313915 0.674127656 0.723460109 1.257573908 0.621010286 0.667915953 1.26581573 1 22.0266165 3.960436201 24.5456273 0.851942799 1.013501272 0.003539418 0.2698249 933.302751 1372997.511 0.064511112 0.116719238 9129.273142 -3.960436201 0.161558472 KQVENER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KQVENER 7 1 Q9H307 Q9H307 PNN Pinin 0 ; 131.06 0.0056162 496740000 743550 701490 651910 674670 771040 579190 725470 669680 711020 FALSE TRUE 697012.5328 753429.0495 667373.6131 691983.1744 710485.6286 746392.7506 616692.5084 753291.0221 592346.1686 1.176697968 1.271940445 1.126661483 1.168207395 1.199443275 1.260061751 1.04110154 1.271707427 1 19.17608101 -4.999999996 0.201472107 0.161200094 1.213371386 0.381585514 0.072801252 142.6474153 1.41399758 48.20083689 0.158642479 1.00E-05 4.999999996 1.052171292 KQVENERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KQVENERR 8 2 Q9H307 Q9H307 PNN Pinin 0 ;; 99.802 0.0036867 170386000 180532 260119 175042 197059 328524 133607 207120 225866 443050 FALSE TRUE 169232.8244 279378.4814 179194.0789 202115.8676 302723.0502 172177.172 176064.2788 254065.8673 369102.0928 0.458498686 0.756913837 0.485486488 0.547587975 0.820160753 0.46647574 0.477006991 0.688334941 1 18.49366039 0.947935917 8.789403293 0.999999127 0.579691868 0.542247867 0.123463901 1.084647594 183.0563299 0.1137225 0.028461908 8.870251157 -0.947935917 -0.420307259 KQVEVFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQVEVFR 7 1 A0A087X1Z3;Q9UL46;H0YLG1;H0YLD2 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 130.22 0.0057473 1997500000 1878400 2142200 1782200 2123900 2260500 1137900 2209900 1982000 2169700 FALSE TRUE 1760834.297 2300810.717 1824474.626 2178402.87 2082969.448 1466393.258 1878546.011 2229457.063 1807563.053 0.974148201 1.272879921 1.009356007 1.2051601 1.152363368 0.811254277 1.039269976 1.233404865 1 20.78561454 KQVFELLAALCIYSPEGHVLTLDALDHYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQVFELLAALCIYSPEGHVLTLDALDHYK 29 1 Q27J81-2;Q27J81;Q27J81-3 Q27J81-2 INF2 Inverted formin-2 0 111.2 0.00013199 38845000 41225 62223 29607 27660 68501 30854 41800 61587 21264 FALSE TRUE 38644.80084 66830.05566 30309.29202 28369.80243 63121.20778 39761.04893 35532.47805 69276.27252 17714.90103 2.181485563 3.772533392 1.71094899 1.601465477 3.563170219 2.244497379 2.005796024 3.910621482 1 14.11267578 -1.844968419 2.726011563 0.402337326 2.582440958 0.264735925 0.847972429 48499626.06 46815817.42 191992425 0.197138558 0.014289979 1.844968419 2.180103633 KQVNYNDGSQEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQVNYNDGSQEDR 13 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y7I0;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 124.51 0.00021626 0 87473 67399 84689 89006 83701 68008 96899 85929 88951 FALSE TRUE 81998.22107 72389.29209 86697.86307 91290.04465 77127.46109 87640.80558 82369.89452 96657.4248 74104.50345 1.106521429 0.976854155 1.169940544 1.231909538 1.04079317 1.182665041 1.11153696 1.304339417 1 16.1772736 3.869282087 4.58953785 1.151537655 1.038128149 0.187568336 0.092176394 0.290424953 10.04512104 0.02116746 0.039738441 7400.858269 -3.869282087 -0.113409507 KQVS(ph)AR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQVSAR 6 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 KQVS(1)AR 60.973 0.077281 100020000 345690 276060 320040 375300 200210 172470 396240 215050 206040 TRUE FALSE 324053.88 296499.7696 327631.4999 384930.8334 184486.3142 222259.2892 336827.4905 241899.4659 171650.5929 1.887869272 1.727344861 1.908711729 2.24252551 1.074778194 1.294835546 1.962285622 1.409255056 1 17.38911532 2.740988176 24.99695333 1.44841282 1.900417982 0.482828988 0.293840427 246.5141039 2538404.505 0.093128582 0.094603312 550.7927002 -2.740988176 0.452005162 KQYQDS(ph)PNQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KQYQDSPNQK 10 1 H0Y9T5;Q8IU60 H0Y9T5 DCP2 m7GpppN-mRNA hydrolase 1 KQYQDS(1)PNQK 77.185 0.020678 174370000 169320 109430 136790 130660 140170 101760 192570 126690 176610 TRUE FALSE 158722.5634 117532.3111 140034.7234 134012.9568 129161.6136 131136.4601 163695.9162 142507.5254 147132.6501 1.078771866 0.798818692 0.951758317 0.910830851 0.87785827 0.891280487 1.112573696 0.968564933 1 17.1667579 1.756576314 25 1.035792655 0.906475866 0.287464134 0.078945358 7.104254308 9868.601058 0.032848227 0.018216007 57.09213896 -1.756576314 -0.129316789 KRAPS(ph)PLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRAPSPLPK 9 2 Q9BSL1 Q9BSL1 UBAC1 Ubiquitin-associated domain-containing protein 1 1 KRAPS(1)PLPK 77.597 0.025321 295620000 686060 553800 566410 573900 685790 408480 818300 647400 1081400 TRUE FALSE 643120.7293 594803.9282 579845.5127 588627.2456 631930.8197 526401.5449 695603.5117 728229.3151 900907.3539 0.713858896 0.660227631 0.643623909 0.653371563 0.701438186 0.58430153 0.772114368 0.80832875 1 19.78101923 1.026798927 1.317032479 0.996394916 0.659394534 0.869575448 0.041908411 0.13194459 0.469225059 0.035123916 0.010733122 10.63650447 -1.026798927 -0.337000382 SRHSS(ph)IS(ph)PVRLPLNSSLGAELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRHSSISPVRLPLNSSLGAELSR 23 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 S(0.28)RHS(0.33)S(0.39)IS(0.999)PVRLPLNSSLGAELSR 117.21 0.00021524 47437000 15295 22701 14256 21818 31498 8474.2 25917 36257 91221 TRUE FALSE 14337.71325 24381.80566 14594.15905 22377.88682 29024.27414 10920.56397 22030.98645 40783.76626 75995.62579 0.18866498 0.320831698 0.192039461 0.294462827 0.381920325 0.143699902 0.289898086 0.536659391 1 16.21362876 0.920547933 2.286298426 0.998662976 0.256620767 0.921546069 0.069560974 0.090090556 1.017667575 0.061648016 0.016807917 8.328138377 -0.920547933 -0.742042209 KRDAEDDGEEEDD ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KRDAEDDGEEEDD 13 2 Q9BTT0;Q5TB19;Q9BTT0-3;Q9BTT0-2;Q5TB25;H0YCE2 Q9BTT0 ANP32E Acidic leucine-rich nuclear phosphoprotein 32 family member E 0 ;; 138.02 0.00021432 1602390000 1924340 1273780 1459740 1511160 1701270 1113880 1791500 1383710 2468250 FALSE TRUE 1803898.994 1368091.997 1494365.722 1549938.924 1567659.117 1435439.074 1522881.206 1556469.239 2056283.129 0.877261973 0.665322774 0.7267315 0.753757545 0.762375129 0.698074625 0.740598989 0.756933331 1 20.97160749 0.562241234 2.319112599 0.999992823 0.73517323 0.669075794 0.05540158 2.357299861 11.83467886 0.048250065 0.013000351 3.649566101 -0.562241234 -0.264819593 KRDFTNEAPPAPLPDASASPLS(ph)PHRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRDFTNEAPPAPLPDASASPLSPHRR 26 3 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 KRDFTNEAPPAPLPDAS(0.008)AS(0.236)PLS(0.757)PHRR;KRDFTNEAPPAPLPDAS(0.008)AS(0.224)PLS(0.768)PHRR 133.72 3.23E-05 414670000 553870 810070 685900 834870 1181260 516860 898900 666520 1995520 TRUE FALSE 519204.2654 870048.4257 702169.8719 856294.1776 1088488.605 666069.0915 764118.29 749736.4892 1662454.82 0.312311805 0.523351621 0.422369296 0.515078165 0.654747781 0.400653951 0.459632515 0.450981573 1 20.6648837 -1.086879971 4.419363557 1.000046554 0.471511973 0.778982463 0.089134043 19173969.58 9431136.083 8538.201292 0.019237747 0.081869102 1.086879971 -0.528534581 KRDNS(ph)MQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRDNSMQSR 9 2 Q9H7E2-2;Q9H7E2;Q9H7E2-3 Q9H7E2-2 TDRD3 Tudor domain-containing protein 3 1 KRDNS(0.808)MQS(0.192)R 66.498 0.050057 12528000 18198 18785 17420 20385 30572 16519 24357 22980 46850 TRUE FALSE 17059.01966 20175.86095 17833.21063 20908.11361 28170.99844 21287.76714 20704.89397 25849.10359 39030.43234 0.437069708 0.516926402 0.45690528 0.535687472 0.721770084 0.545414587 0.530480774 0.662280739 1 15.25231182 -5 0.173528801 2.849356358 0.434484516 0.828466136 0.068274587 53.73187878 0.51115542 34.09483519 0.237444307 1.00E-05 5 -2.414871841 KRDS(ph)DAGSSTPTTSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KRDSDAGSSTPTTSTR 16 2 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3;K7EP28 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 1 KRDS(0.997)DAGS(0.003)STPTTSTR;KRDS(1)DAGSSTPTTSTR;KRDS(1)DAGSSTPTTSTR;KRDS(1)DAGSSTPTTSTR;KRDS(0.979)DAGS(0.018)S(0.003)TPTTSTR;KRDS(0.996)DAGS(0.004)STPTTSTR 189.19 8.33E-10 1244088000 981397 794957 826502 784623 801634 646841 977504 732982 1167454 TRUE FALSE 919973.1136 853816.4434 846107.0177 804757.7545 738676.8993 833573.4961 830936.3499 824496.4162 972598.3854 0.945892084 0.877871541 0.869944913 0.827430691 0.7594881 0.857058277 0.854346833 0.847725463 1 19.89148467 -1.488088358 6.311097779 1.000085385 0.854752676 0.496652162 0.04588436 5.49E-05 4.45E-06 0.044214556 0.010415364 0.032502116 1.488088358 -0.145332708 KRDS(ph)QGTYSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 KRDSQGTYSSR 11 2 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 KRDS(0.995)QGTYS(0.004)SR;KRDS(0.997)QGT(0.001)YS(0.002)SR;KRDS(0.985)QGT(0.009)YS(0.005)S(0.001)R;KRDS(0.995)QGT(0.005)YSSR;KRDS(1)QGTYSSR;KRDS(0.999)QGT(0.001)YSSR;KRDS(0.672)QGT(0.212)YS(0.043)S(0.074)R;KRDS(1)QGTYSSR;KRDS(1)QGTYSSR 171.26 1.16E-05 10851690000 2955810 2656932 2527306 2541010 2973990 2088517 3068870 2409651 3093770 TRUE FALSE 2770811.128 2853654.01 2587254.892 2606216.619 2740424.822 2691437.954 2608721.433 2710501.232 2577399.8 1.07504126 1.107183297 1.003823656 1.011180577 1.06325174 1.044245426 1.012152415 1.051641748 1 21.29748491 4.003379205 5.065915482 1.028052085 1.089958555 0.588452969 0.022368899 0.121526237 8.399879397 0.005367533 0.01143681 10078.11258 -4.003379205 0.06190647 KRDS(ph)SLR ddPTM_SK-BR-3_Pertuzumab_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(0.812)S(0.188)LR;KRDS(0.677)S(0.323)LR;KRDS(0.651)S(0.349)LR;KRDS(0.63)S(0.37)LR;KRDS(0.5)S(0.5)LR 96.331 0.010089 535088000 908391 785515 807561 803049 957970 662977 1079820 835643 1171110 TRUE FALSE 851536.4288 843675.3479 826716.7283 823656.5969 882734.9005 854367.6974 917911.0156 939974.868 975644.1753 0.872794048 0.864736724 0.847354752 0.844218228 0.904771353 0.875695995 0.940825599 0.96344025 1 19.89599556 1.53229299 0.948292186 0.999803442 0.858314228 0.909076198 0.01561994 0.128251608 0.227410007 0.013285292 0.005075676 34.06379183 -1.53229299 -0.141489214 KREAEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KREAEDR 7 2 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;H0Y8L4;H0Y9I0;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 0 ; 83.843 0.087333 235686000 409340 379320 335680 311580 490840 301040 304210 408980 473860 FALSE TRUE 383720.1401 407405.2475 343642.4881 319575.6703 452291.4064 387945.361 258596.5346 460042.0533 394769.7047 0.9720101 1.032007377 0.8704885 0.809524304 1.145709513 0.982713102 0.655056686 1.165342851 1 18.59065175 KREDDDDDDDDDDDYDNL ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KREDDDDDDDDDDDYDNL 18 2 Q16594 Q16594 TAF9 Transcription initiation factor TFIID subunit 9 0 202.97 4.90E-15 303410000 296920 175360 195520 202220 218110 152000 268020 188950 292530 FALSE TRUE 278336.3072 188343.8369 200157.8267 207409.3076 200980.5204 195879.9325 227832.8892 212540.8234 243704.8532 1.14210408 0.772835807 0.821312436 0.851067613 0.824688215 0.80375885 0.934872187 0.872123885 1 17.89477546 0.779962575 1.016218769 0.997831711 0.854045717 0.09116354 0.105219864 1.557516581 3.014158187 0.091683832 0.029671431 6.025076638 -0.779962575 -0.143785995 KREDS(ph)APPSSVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KREDSAPPSSVAR 13 2 Q9BZE4-2;Q9BZE4;Q9BZE4-3 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 1 KREDS(0.968)APPS(0.013)S(0.019)VAR;KREDS(0.995)APPS(0.005)SVAR;KREDS(1)APPSSVAR;KREDS(0.999)APPSSVAR 161.26 3.34E-05 514722000 616436 472522 524436 500323 591578 380672 587855 392828 623962 TRUE FALSE 577854.3711 507508.0205 536875.8696 513162.1352 545117.8502 490565.8267 499711.6001 441873.4405 519818.7113 1.111645962 0.976317338 1.032813667 0.987194428 1.048669158 0.943724833 0.961318993 0.850052972 1 18.98764904 2.221644125 20.58555511 0.938603202 1.022023077 0.433467812 0.051976181 29.88161919 36360.59195 0.017549468 0.013026448 166.5881577 -2.221644125 0.083419875 KREDSAPPSSVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KREDSAPPSSVAR 13 2 Q9BZE4-2;Q9BZE4;Q9BZE4-3 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 178.67 8.10E-06 102240000 282560 274240 298900 280970 303090 233420 327030 250710 355020 FALSE TRUE 264875.074 294545.0149 305990.0492 288180.1659 279286.534 300804.5647 277994.8875 282011.6954 295764.8685 0.895559623 0.995875597 1.034571992 0.974355634 0.944285694 1.017039536 0.939918554 0.953499639 1 18.17409117 3.015682937 24.96749925 0.967911354 0.990232497 0 0.042102407 749.6671242 1193473.678 0.011854151 0.014164046 1036.77123 -3.015682937 0.022321143 KREEGS(ph)DIEDEDMEELLNDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 KREEGSDIEDEDMEELLNDTR 21 2 F5H5U2;Q8NHQ9;Q8NHQ9-2 F5H5U2 DDX55 ATP-dependent RNA helicase DDX55 1 KREEGS(1)DIEDEDMEELLNDTR;KREEGS(1)DIEDEDMEELLNDTR;KREEGS(1)DIEDEDMEELLNDTR;KREEGS(1)DIEDEDMEELLNDTR;KREEGS(1)DIEDEDMEELLNDTR;KREEGS(1)DIEDEDMEELLNDTR;KREEGS(1)DIEDEDMEELLNDTR 278.24 5.62E-45 1728973000 2264853 1610824 1787518 1767227 1934086 1351491 2272178 1625410 2351719 TRUE FALSE 2123099.894 1730091.085 1829918.771 1812577.037 1782190.687 1741644.512 1931486.003 1828346.016 1959201.906 1.083655486 0.883059107 0.934012347 0.925160919 0.909651364 0.888956113 0.985853473 0.933209595 1 20.90183465 0.833800798 1.070664002 0.998099426 0.932298286 0.062533902 0.058303645 1.604956163 3.56157259 0.05005408 0.015992266 6.820257914 -0.833800798 -0.06580114 KREELSNVLAAMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KREELSNVLAAMR 13 2 Q9Y3U8 Q9Y3U8 RPL36 60S ribosomal protein L36 0 ; 184.98 5.09E-06 1361220000 1599140 4635400 1179570 1131550 5518900 689660 1442140 4170000 4650000 FALSE TRUE 1499052.682 4978609.839 1207549.957 1160587.489 5085467.856 888753.6463 1225904.495 4690633.679 3873884.96 0.386963655 1.28517235 0.311715492 0.299592657 1.31275655 0.229421796 0.316453511 1.210834531 1 21.88534968 1.224210352 24.99469764 1.105417583 0.614001665 0.220458956 0.399884326 435.7738085 758991.1145 0.366679298 0.093384375 16.75754337 -1.224210352 -0.491415918 KREHS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KREHSPSK 8 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 KREHS(0.999)PS(0.001)K;KREHS(0.998)PS(0.002)K;KREHS(0.999)PS(0.001)K;KREHS(1)PSK;KREHS(0.994)PS(0.006)K;KREHS(0.999)PS(0.001)K 129.89 0.00055903 619510000 1127466 594514 746825 717674 768732 466785 860737 740165 702230 TRUE FALSE 1056899.916 638532.4352 764540.0417 736090.7299 708358.8896 601538.2519 731677.4775 832576.2296 585023.2764 1.80659464 1.091465008 1.306854056 1.258224689 1.21082172 1.028229604 1.250680968 1.423150605 1 19.1581345 4.745167175 24.95400445 1.204407802 1.80659492 0.689367254 0.128668247 412.9898815 1559885.891 0.028207729 0.271162096 55611.82853 -4.745167175 0.602187117 KREHS(ph)PSKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KREHSPSKEK 10 3 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 KREHS(0.994)PS(0.006)KEK;KREHS(1)PSKEK 115.34 0.00088177 1032410000 1075460 568710 664960 885290 1133420 393100 920970 678200 1622900 TRUE FALSE 1008148.878 610817.8801 680733.1652 908008.0402 1044405.765 506581.5886 782879.0984 762874.7629 1352027.506 0.745657077 0.451779182 0.503490619 0.671589917 0.772473756 0.374682901 0.579040807 0.564245002 1 20.36669307 0.237508021 3.432137919 1.000000004 0.564052334 0.519660971 0.124874459 295.202679 1323.132783 0.115136002 0.02972112 1.727857893 -0.237508021 -0.435947671 KREPEDEGEDDD ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KREPEDEGEDDD 12 2 P39687 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;;;;;;; 231.83 9.97E-12 15823249000 13333735 9702326 10564142 10501222 11507758 7885733 12832364 9229167 12728275 FALSE TRUE 12499200.33 10420696.31 10814728.44 10770701.14 10603985.11 10162216.1 10908270.15 10381448.82 10603843.67 1.178742417 0.98272821 1.019887577 1.015735564 1.000013338 0.958352124 1.028709068 0.979026958 1 23.33808397 4.741952139 24.9896991 1.000103746 1.178742484 0.880248721 0.020932104 99.70097072 734591.8106 0.004614605 0.033870344 55201.66019 -4.741952139 0.178638738 KRES(ph)ES(ph)ESDETPPAAPQLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KRESESESDETPPAAPQLIK 20 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 2 KRES(0.5)ES(0.5)ES(0.5)DET(0.5)PPAAPQLIK;KRES(0.995)ES(0.825)ES(0.09)DET(0.09)PPAAPQLIK;KRES(0.906)ES(0.932)ES(0.158)DET(0.004)PPAAPQLIK;KRES(0.65)ES(0.65)ES(0.65)DET(0.051)PPAAPQLIK 190.93 8.10E-17 1694200000 2583050 1274425 1760053 1649274 1633590 1150278 2138210 1364458 2027010 TRUE FALSE 2421381.511 1368784.753 1801802.288 1691597.163 1505294.431 1482344.585 1817605.261 1534813.585 1688688.936 1.433882499 0.810560621 1.066982942 1.00172218 0.891398291 0.877807957 1.076341073 0.908878807 1 20.68747217 4.749853132 24.99917336 0.959524435 1.433882776 0.759512297 0.084778372 831.7137842 1841198.942 0.019525006 0.303833886 56215.11875 -4.749853132 0.47435834 KRES(ph)ESESDET(ph)PPAAPQLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRESESESDETPPAAPQLIK 20 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 2 KRES(0.869)ES(0.144)ES(0.09)DET(0.897)PPAAPQLIK 165.48 1.83E-11 343730000 776360 422080 552150 518260 551960 369320 708520 443290 723040 TRUE FALSE 727769.0134 453331.2424 565247.2587 531559.429 508611.2881 475936.6886 602284.0036 498635.7323 602359.953 1.208196212 0.752591935 0.938387846 0.882461436 0.84436438 0.790120071 0.999873914 0.827803591 1 19.20026633 -0.914863761 5.027980476 1.000000368 0.894889672 0.045005848 0.128887502 0.000297355 75822391.69 69.77304332 0.026482424 0.121656758 0.914863761 -0.105110696 KRES(ph)IEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRESIEGK 8 2 Q7LBC6;H0Y9V5 Q7LBC6 KDM3B Lysine-specific demethylase 3B 1 KRES(1)IEGK 63.415 0.038327 21343000 102460 107340 106220 100990 120810 92312 114250 88882 114030 TRUE FALSE 96047.2115 115287.5653 108739.5886 103581.5744 111322.0699 118960.9758 97119.27315 99979.11335 94997.65634 1.011048222 1.213583258 1.144655487 1.090359261 1.171840172 1.252251692 1.022333359 1.052437683 1 16.5356043 1.62762876 9.479253974 1.027331059 1.153064534 0.428828237 0.066248715 0.091117614 19.77727409 0.030553952 0.01584021 42.42567494 -1.62762876 0.125733475 KRESES(ph)ES(ph)DETPPAAPQLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRESESESDETPPAAPQLIK 20 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 2 KRES(0.362)ES(0.651)ES(0.984)DET(0.004)PPAAPQLIK;KRES(0.101)ES(0.911)ES(0.985)DET(0.004)PPAAPQLIK 219.22 4.60E-24 1265900000 1843420 959590 1314260 1181040 1272370 875630 1667480 981080 1544790 TRUE FALSE 1728043.633 1030639.042 1345434.868 1211347.486 1172443.193 1128410.166 1417456.854 1103569.998 1286954.569 1.342738644 0.800835606 1.045440841 0.941251164 0.911021431 0.876806527 1.101403956 0.857505015 1 20.2955297 4.752333767 24.92538728 0.948875873 1.342738917 0.663862438 0.089537665 1404.230573 2541202.126 0.020307736 0.412225434 56537.13113 -4.752333767 0.393863043 KRET(ph)DDEGEDD ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 KRETDDEGEDD 11 2 Q92688 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 1 KRET(1)DDEGEDD;KRET(1)DDEGEDD;KRET(1)DDEGEDD;KRET(1)DDEGEDD;KRET(1)DDEGEDD;KRET(1)DDEGEDD;KRET(1)DDEGEDD;KRET(1)DDEGEDD;KRET(1)DDEGEDD;KRET(1)DDEGEDD 283.82 2.31E-27 1.81441E+11 24041338 14737329 18076715 16639935 17012698 13290557 21096579 14945256 20365043 TRUE FALSE 22536633.57 15828496.17 18505503.22 17066943.9 15676589.33 17127325.05 17933342.83 16811204.11 16965985.76 1.328342125 0.932954701 1.090741409 1.005950621 0.924001089 1.009509574 1.05701744 0.990876943 1 24.01614192 4.746826059 24.90867829 1.007589665 1.328342292 0.809719363 0.049730435 438.6714951 1321945.941 0.011709285 0.134953724 55824.65639 -4.746826059 0.320752627 KRETDDEGEDD ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRETDDEGEDD 11 2 Q92688 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 0 ; 138.76 0.00020176 495730000 945390 655280 762370 720860 793650 663370 830310 657790 899490 FALSE TRUE 886219.7275 703797.613 780453.7764 739358.488 731319.9304 854874.1501 705812.7237 739916.5295 749359.3081 1.182636578 0.939199134 1.041494738 0.986654173 0.975926932 1.140806741 0.941888245 0.987398864 1 19.51529811 4.751421761 24.56008596 1.002102965 1.182636725 0.496508739 0.057268996 1383.300258 2641538.663 0.012588963 0.229829706 56418.52936 -4.751421761 0.18053376 KREVS(ph)PPGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KREVSPPGAR 10 2 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 KREVS(1)PPGAR 60.657 0.076129 81108000 72505 72130 75725 78977 89566 62185 103070 69786 126700 TRUE FALSE 67967.04148 77470.58025 77521.23276 81003.68353 82531.84765 80136.80001 87615.61035 78498.93572 105552.9515 0.643914173 0.73394992 0.734429797 0.76742225 0.781899952 0.759209467 0.830063102 0.743692475 1 16.68760739 -5 0.122389812 1.812820098 0.635482931 0.844527683 0.036105513 51.80242008 0.408743048 10.39197642 0.293862707 1.00E-05 5 -1.177337166 KRFPQHTIMAGNVVTGEMVEELILSGADIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRFPQHTIMAGNVVTGEMVEELILSGADIIK 31 2 A0A087WWM4;Q9P2T1;Q9P2T1-3;F8WAN9;H0YNJ6;Q9P2T1-2;H0YNH0;H0YLB8 A0A087WWM4 GMPR2 GMP reductase;GMP reductase 2 0 76.164 0.0017589 72102000 36963 45370 36473 44016 45957 33229 42945 38147 45825 FALSE TRUE 34649.55181 48729.24201 37338.15678 45145.52508 42347.7226 42821.67287 36505.79593 42909.73692 38176.51146 0.907614407 1.276419456 0.97804004 1.182547157 1.109261192 1.121675901 0.956237082 1.123982661 1 15.22039766 1.764433788 25 1.023587309 1.106994725 0.076599862 0.108621182 34.14897169 33018.1811 0.045105169 0.025015033 58.13447944 -1.764433788 0.083407416 KRGEEGTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KRGEEGTER 9 2 A0A669KBI7;Q9UMN6;Q9UMN6-2 A0A669KBI7 KMT2B Histone-lysine N-methyltransferase 2B 0 ;; 64.841 0.038386 28896600 45751.7 49232.2 47897.3 52652.9 53601 47931 56734 38565.6 51106 FALSE TRUE 42888.18277 52877.40331 49033.44657 54004.06256 49391.39368 61767.90161 48227.26339 43380.60005 42576.07844 1.007330509 1.241951003 1.151666578 1.268413262 1.160073813 1.450765403 1.132731458 1.018896095 1 15.37775545 1.357825831 4.346119776 1.010878227 1.214903643 0.358177561 0.110956859 0.218836046 6.304645551 0.075697024 0.025797771 22.79427751 -1.357825831 0.204025417 KRGS(ph)VR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRGSVR 6 2 A0A0A0MSW4;P48739;P48739-3 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 1 KRGS(1)VR 67.993 0.076638 816250000 637990 459010 636480 567180 515980 417130 543310 416130 717300 TRUE FALSE 598059.3447 492995.578 651577.6062 581734.799 475457.0122 537548.6595 461845.7093 468084.7465 597577.9961 1.000805499 0.82498951 1.090364121 0.97348765 0.795640093 0.899545604 0.772862643 0.783303183 1 19.1887675 2.747982189 24.01554316 0.835307199 0.96750008 0.295942764 0.091880026 446.7384707 1138733.194 0.02693069 0.028194092 559.734646 -2.747982189 0.132192881 KRHNS(ph)ISEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRHNSISEAK 10 2 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 KRHNS(0.994)IS(0.006)EAK 121.28 0.00027092 46592000 60312 51118 39237 49866 71720 25559 93462 68067 284810 TRUE FALSE 56537.17958 54902.82991 40167.72017 51145.64598 66087.4005 32937.46838 79448.24076 76565.31478 237273.3711 0.238278654 0.231390609 0.169288783 0.215555778 0.278528518 0.13881654 0.33483842 0.322688191 1 17.85619067 0.108759042 0.758027936 1.019678597 0.209641153 0.962928333 0.047382771 0.61307158 0.397070879 0.073519619 0.014739987 1.284573746 -0.108759042 -0.810037444 KRHS(ph)FTSLTMANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRHSFTSLTMANK 13 2 Q7Z6J0;H0YA90;Q7Z6J0-3 Q7Z6J0 SH3RF1 E3 ubiquitin-protein ligase SH3RF1 1 KRHS(0.333)FT(0.333)S(0.333)LT(0.001)MANK 115.14 0.00035896 604000000 571870 527480 509120 541270 724870 423200 692470 566670 937610 TRUE FALSE 536077.6775 566535.168 521196.5668 555159.9046 667941.6342 545370.9699 588640.5521 637419.9969 781116.8338 0.686296408 0.725288643 0.667245339 0.710725823 0.855111048 0.698193851 0.753588358 0.816036692 1 19.57517883 -5 0.165796875 2.060563416 0.662405673 0.771155528 0.048031836 60.10692943 0.561625018 20.80236934 0.178603615 1.00E-05 5 -1.398157742 KRKPS(ph)PEPEGEVGPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRKPSPEPEGEVGPPK 16 3 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 KRKPS(1)PEPEGEVGPPK 127.5 0.00036408 231720000 370840 253110 246750 321510 417070 210260 491280 297510 688250 TRUE FALSE 347629.7864 271850.5278 252603.0265 329760.4909 384315.0046 270958.6487 417617.1248 334654.7784 573376.6287 0.606285239 0.474122094 0.440553406 0.575120217 0.670266253 0.472566608 0.728346961 0.58365612 1 19.12912357 -0.490322949 0.289152894 1.188204439 0.477435981 0.729824218 0.084403939 4.375102386 0.41683442 0.877296457 0.102022555 0.323353117 0.490322949 -0.710768458 KRKS(ph)ELEFETLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRKSELEFETLK 12 3 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 KRKS(1)ELEFETLK;KRKS(1)ELEFETLK 147.92 0.00033689 1970920000 1733400 905540 1252240 1237130 1379470 878150 1593400 1128400 1927120 TRUE FALSE 1624909.588 972587.1238 1281943.724 1268876.85 1271131.991 1131657.649 1354484.462 1269283.224 1605471.222 1.012107577 0.605795426 0.798484399 0.790345434 0.791750094 0.704875699 0.843667855 0.790598552 1 20.61456537 0.174006882 0.699582267 1.006713321 0.766519664 0.266654575 0.103634394 3.781276107 2.29146938 0.156332427 0.034263739 1.492818064 -0.174006882 -0.240193657 KRLS(ph)QSDEDVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRLSQSDEDVIR 12 2 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y917;Q9H7D7-3;Q9H7D7-4 A0A499FIZ0 WDR26 WD repeat-containing protein 26 1 KRLS(0.997)QS(0.003)DEDVIR;KRLS(0.98)QS(0.02)DEDVIR 121.62 0.00029379 970760000 751620 728620 707400 749490 955800 639000 877380 649900 1263250 TRUE FALSE 704577.4459 782567.7829 724179.8621 768723.1823 880735.3235 823468.9267 745825.0142 731041.4456 1052405.414 0.669492418 0.743599161 0.688118716 0.730443964 0.836878366 0.782463598 0.708686029 0.694638621 1 20.00525914 -1.461607703 3.306033255 1.004427654 0.732523585 0.748717411 0.048829794 12961214.56 17630175.49 532700.0182 0.011777208 0.034545565 1.461607703 -0.27190407 KRLS(ph)VER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRLSVER 7 2 P11388;P11388-2;P11388-3;P11388-4;J3KTB7 P11388 TOP2A DNA topoisomerase 2-alpha 1 KRLS(1)VER 97.565 0.0093747 544250000 885370 1186700 817720 872190 1318900 449780 994770 1153700 2083800 TRUE FALSE 829956.2721 1274564.503 837116.7046 894571.872 1215318.914 579624.1844 845613.4735 1297741.985 1736000.318 0.478085323 0.734196008 0.482209995 0.515306283 0.700068371 0.333884838 0.487104446 0.747547089 1 20.72733578 0.984209246 3.907281211 0.998881327 0.541564242 0.643180214 0.114136779 0.125286 5.421875205 0.108577509 0.027844454 9.642935147 -0.984209246 -0.457317085 KRNDS(ph)EEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRNDSEEEER 10 2 Q9Y5B6-2;Q9Y5B6;Q9Y5B6-3;Q9Y5B6-4 Q9Y5B6-2 PAXBP1 PAX3- and PAX7-binding protein 1 1 KRNDS(1)EEEER;KRNDS(1)EEEER 143.46 2.67E-05 528788000 819480 503620 687920 663220 577560 617630 811170 601800 482840 TRUE FALSE 768190.2096 540908.5488 704237.7873 680239.348 532200.7674 795929.7546 689542.589 676936.0547 402250.8847 1.909729074 1.344704435 1.750742668 1.691082292 1.323056798 1.978689879 1.714210248 1.682870269 1 18.61773607 KRNDS(ph)EEEERER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 157.58 0.00040971 718610000 494157 347238 431776 436141 378739 339060 537821 364563 368051 TRUE FALSE 463228.5955 372947.8628 442017.9306 447333.1164 348994.3667 436941.1178 457179.7339 410079.4931 306620.9104 1.510753441 1.216315816 1.441577908 1.458912622 1.138194933 1.425020613 1.491025949 1.337415288 1 18.22609656 0.958717313 22.53689438 0.999999997 1.377020695 0.502451168 0.11875435 2005.800435 1095001.405 0.109073735 0.027268434 9.093211928 -0.958717313 0.377020697 KRNEDEDS(ph)PNKLYTLVTYVPVTTFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRNEDEDSPNKLYTLVTYVPVTTFK 25 3 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 1 KRNEDEDS(0.8)PNKLY(0.073)T(0.124)LVT(0.003)YVPVTTFK;KRNEDEDS(1)PNKLYTLVTYVPVTTFK 194.23 1.17E-17 540920000 1535320 813450 1051950 984620 1216910 676070 1470160 963240 1452850 TRUE FALSE 1439227.062 873678.6844 1076902.751 1009887.016 1121338.797 871240.4339 1249723.156 1083502.634 1210359.949 1.189090124 0.721833769 0.889737595 0.834369162 0.926450679 0.719819286 1.032521902 0.895190423 1 20.20700472 1.667348738 13.39881743 0.972335225 0.863180432 0.092065327 0.134438847 0.243221069 49.4326239 0.056348035 0.030933812 46.48884305 -1.667348738 -0.109154793 KRNEDEDSPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KRNEDEDSPNK 11 2 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 0 ;;;; 217.22 6.47E-12 9217000000 11480621 6796212 8446123 7985129 8551037 6340603 10783093 7067116 9695707 FALSE TRUE 10762069.43 7299410.608 8646469.026 8190040.929 7879473.047 8171032.155 9166268.31 7949460.989 8077430.865 1.332362926 0.903679738 1.070447915 1.013941322 0.975492478 1.011588003 1.134799971 0.984157107 1 22.94546507 4.752014761 24.91641367 1.018965841 1.332363141 0.734354279 0.060461014 1237.714622 2292144.578 0.014862676 0.292271149 56495.61764 -4.752014761 0.3133973 KRNEDEDSPNKLYTLVTYVPVTTFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRNEDEDSPNKLYTLVTYVPVTTFK 25 3 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 0 193.4 1.54E-18 192360000 361140 325080 328480 328780 492110 228130 504720 306300 911190 FALSE TRUE 338536.8921 349149.2614 336271.7007 337217.0514 453461.6657 293987.4276 429041.9216 344542.2292 759106.5025 0.445967583 0.459947663 0.44298356 0.444228906 0.597362378 0.387280871 0.565193316 0.453878643 1 19.53394278 -5 0.321640552 6.032692721 0.453067583 0.878482382 0.06144846 93.11263838 0.821921648 319.1127805 0.046937919 1.00E-05 5 -5.579625138 KRNS(ph)TQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRNSTQLK 8 2 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;H0YBA1 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 KRNS(0.929)T(0.071)QLK 68.536 0.029352 80776000 108990 107060 119270 112160 116080 112180 156960 108250 149350 TRUE FALSE 102168.5105 114986.8338 122099.1407 115038.2155 106963.545 144564.5449 133425.3051 121765.2508 124422.5202 0.821141625 0.92416416 0.981326697 0.924577121 0.859679943 1.161884076 1.072356555 0.97864318 1 16.92488811 2.248301106 24.99991962 1.064320355 0.916987194 0.565188054 0.064790413 147.537375 378669.2751 0.02223302 0.018384031 177.1336638 -2.248301106 -0.147333161 KRPAS(ph)PSHNGSSGGGYGASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KRPASPSHNGSSGGGYGASK 20 2 K7ELX9;K7EQ79;K7ENM4;K7ENP7;Q6PI98;Q6PI98-3;Q6PI98-4 K7ELX9 INO80C INO80 complex subunit C 1 KRPAS(0.888)PS(0.111)HNGS(0.001)SGGGYGASK;KRPAS(0.985)PS(0.015)HNGSSGGGYGASK;KRPAS(0.993)PS(0.007)HNGSSGGGYGASK 268.31 2.60E-37 1626730000 1691880 1595430 1693690 1793320 1996190 1438140 2349600 1662980 2371880 TRUE FALSE 1585988.251 1713557.297 1733865.127 1839339.627 1839417.29 1853307.672 1997299.293 1870606.714 1975997.905 0.802626484 0.867185786 0.877463039 0.930840879 0.930880182 0.937909735 1.010780066 0.94666432 1 20.91414999 3.965103778 0.334111597 1.005475529 0.736779589 0.86864338 0.022347679 1.268229032 0.168185588 0.022791004 0.132932528 9227.919093 -3.965103778 -0.26869594 KRPASPS(ph)HNGSSGGGYGASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRPASPSHNGSSGGGYGASK 20 2 K7ELX9;K7EQ79;K7ENM4;K7ENP7;Q6PI98;Q6PI98-3;Q6PI98-4 K7ELX9 INO80C INO80 complex subunit C 1 KRPAS(0.12)PS(0.877)HNGS(0.003)SGGGYGASK 249.44 1.07E-30 183760000 245680 235030 270720 258960 308930 231330 350580 276030 381570 TRUE FALSE 230303.3274 252431.8657 277141.6062 265605.352 284667.884 298111.2157 298013.7836 310492.9531 317883.502 0.724489714 0.794101815 0.871833878 0.835543054 0.895510092 0.937800212 0.93749371 0.976750763 1 18.27813862 7.301775061 0.178259847 1.028722238 1.05E-10 0.947240628 0.019359578 9.234843762 0.128244029 0.046046843 2.44454283 20034340.97 -7.301775061 -1.028722238 KRPES(ph)GSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRPESGSIR 9 2 B7ZM87;O75044;A0A075B7E9 B7ZM87 SRGAP2 SLIT-ROBO Rho GTPase-activating protein 2 1 KRPES(0.5)GS(0.5)IR 63.408 0.060059 82781000 216120 226260 175530 186650 227970 120960 207410 141540 164540 TRUE FALSE 202593.435 243012.5258 179693.6545 191439.755 210066.1558 155879.1884 176310.796 159211.5806 137077.211 1.477951247 1.772814927 1.310893716 1.396583382 1.532465931 1.137163407 1.286215226 1.161473737 1 17.06462922 2.673840272 0.264253641 0.957058864 1.787532798 0.667466015 0.127348883 1.652736809 0.256335196 0.207418048 0.462715325 471.8894543 -2.673840272 0.830473933 KRPESGS(ph)IR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRPESGSIR 9 2 B7ZM87;O75044;A0A075B7E9 B7ZM87 SRGAP2 SLIT-ROBO Rho GTPase-activating protein 2 1 KRPES(0.1)GS(0.9)IR;KRPES(0.282)GS(0.718)IR 84.507 0.012164 109033000 239684 242630 212136 197069 241728 127063 259520 168191 183813 TRUE FALSE 224682.6063 260594.5777 217167.9661 202126.1242 222743.658 163744.0254 220607.3853 189190.0166 153133.4228 1.467234273 1.701748533 1.418161771 1.319934737 1.45457245 1.06928992 1.440622048 1.235458681 1 17.22442967 7.999999995 0.067727661 0.531831522 3.327170844 0.600770419 0.129212368 161.4229709 0.809030716 6.024703105 43.28932194 99999998.87 -7.999999995 2.795339322 KRPIYEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRPIYEDK 8 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 88.177 0.0083241 946650000 1286710 1430120 1439450 1421410 1699740 1184780 1676340 1509060 1870080 FALSE TRUE 1206177.118 1536007.573 1473594.434 1457885.787 1566249.277 1526806.753 1424988.379 1697469.463 1557951.567 0.77420707 0.985914842 0.945853815 0.93577093 1.005326038 0.980009126 0.914655121 1.089552139 1 20.57121895 4.740852451 24.87174195 0.972893697 0.774206996 0.641258675 0.048438929 120.3290947 1305761.708 0.010438894 0.069881566 55062.05949 -4.740852451 -0.198686701 KRPPS(ph)DIHDSDGSSSSSHQSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRPPSDIHDSDGSSSSSHQSLK 22 2 O43665 O43665 RGS10 Regulator of G-protein signaling 10 1 KRPPS(0.984)DIHDS(0.016)DGSSSSSHQSLK 223.57 3.61E-26 149790000 36077 173710 130240 178070 231690 143790 181250 146310 223720 TRUE FALSE 33819.00497 186571.6691 133329.3543 182639.5777 213494.002 185299.8388 154073.2451 164577.1256 186379.6867 0.181452204 1.001030061 0.715364194 0.97993285 1.145478919 0.994206193 0.826663291 0.883020722 1 17.50788511 4.742100071 24.9797173 0.925547674 0.18145192 0.806638574 0.116926386 156.9911129 1107917.605 0.028941977 0.213427848 55220.46652 -4.742100071 -0.744095754 KRPQS(ph)PS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRPQSPSPR 9 2 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 2 KRPQS(1)PS(1)PR;KRPQS(1)PS(1)PR 84.718 0.017177 277924000 725915 584224 677638 634383 723838 519974 731481 563914 751910 TRUE FALSE 680481.2759 627480.5528 693711.8934 650662.3418 666990.6833 670082.0527 621802.2148 634319.9042 626411.3635 1.086316941 1.001706849 1.107438233 1.038714142 1.064780625 1.069715672 0.992641978 1.012625155 1 19.25675086 1.732455029 8.03864592 1.002675804 1.059106792 0.49699068 0.028200183 0.097008447 19.83412452 0.012953965 0.006889908 54.00761867 -1.732455029 0.056430988 KRPQS(ph)PSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KRPQSPSPR 9 2 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 KRPQS(0.973)PS(0.027)PR;KRPQS(0.986)PS(0.014)PR;KRPQS(0.996)PS(0.004)PR;KRPQS(0.996)PS(0.004)PR;KRPQS(0.993)PS(0.007)PR;KRPQS(0.99)PS(0.01)PR;KRPQS(0.998)PS(0.002)PR;KRPQS(0.798)PS(0.202)PR 109.39 0.0015124 4937270000 4331778 4057621 3894705 3839464 4107649 2850401 4389240 3531990 4251163 TRUE FALSE 4060659.747 4358051.481 3987089.242 3937991.146 3785050.817 3673265.496 3731114.21 3972966.726 3541616.432 1.146555486 1.230526107 1.125782342 1.111919154 1.06873539 1.037172028 1.053506014 1.121794752 1 21.75597654 3.287345558 1.245600906 1.055993003 1.192852958 0.674090351 0.036885344 0.226990031 0.738247933 0.012446551 0.020178851 1937.963342 -3.287345558 0.136859955 KRPYEENR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 164.96 0.00018396 1959240000 1241375 2075997 1617159 1580430 2135981 1105647 1684912 1898556 2327634 FALSE TRUE 1163679.555 2229705.978 1655518.775 1620986.509 1968229.668 1424829.34 1432275.088 2135594.896 1939136.848 0.600101821 1.149844571 0.853740042 0.835931982 1.015002974 0.734775032 0.738614755 1.101312111 1 20.88698319 2.250375442 24.99945712 0.852716409 0.918661332 0 0.178166013 953.1191605 2016741.53 0.058509311 0.048588739 177.9817373 -2.250375442 0.065944923 KRQDCSSS(ph)DTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRQDCSSSDTEK 12 2 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;P46100-3;A0A096LP59 P46100;P46100-3;A0A096LP59 ATRX Transcriptional regulator ATRX 1 KRQDCS(0.031)S(0.169)S(0.799)DTEK 79.771 0.011551 17283000 47185 23264 26553 28530 28119 24472 40373 20963 33659 TRUE FALSE 44231.77508 24986.49077 27182.8497 29262.1281 25910.64717 31536.66913 34319.44345 23580.2767 28041.09545 1.577391124 0.891066856 0.969393287 1.043544399 0.924024071 1.124658956 1.2238981 0.840918527 1 14.77525509 4.746318497 24.68871608 1.013444949 1.577391451 0.722756307 0.11176576 481.7929745 1533217.195 0.028555717 0.306290131 55759.452 -4.746318497 0.563946502 KRQEEIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 KRQEEIER 8 2 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6;H0YFJ7 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ;;;;;; 196.79 8.39E-05 1278062000 1023398 1108825 1010380 1036631 1285955 794968 1216893 1112485 1657928 FALSE TRUE 959345.346 1190923.557 1034346.691 1063232.706 1184961.282 1024462.356 1034431.192 1251381.201 1381209.106 0.69456923 0.862232627 0.748870454 0.769784026 0.85791592 0.741714163 0.748931633 0.906004164 1 20.39750032 1.041713984 3.993891145 0.998749505 0.780746722 0.689504308 0.051619049 0.101400498 3.546697022 0.046254862 0.011866301 11.00814101 -1.041713984 -0.218002783 KRQS(ph)PEPSPVTLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.999)PEPS(0.001)PVTLGR;KRQS(0.991)PEPS(0.009)PVTLGR;KRQS(0.961)PEPS(0.013)PVT(0.025)LGR 167.99 2.80E-06 1699270000 1078570 1049680 1080340 1029110 1142810 787930 1270620 884820 1332040 TRUE FALSE 1011064.229 1127399.399 1105966.175 1055518.705 1053058.312 1015392.6 1080102.327 995291.7247 1109713.919 0.911103494 1.015936973 0.996622784 0.951162896 0.948945755 0.915003933 0.973316013 0.896890368 1 20.08175637 3.163839001 5.833727085 0.945517091 0.986495861 0.06936659 0.039039596 0.310119924 18.07350163 0.010380433 0.012558806 1458.273557 -3.163839001 0.040978769 KRQS(ph)VSGLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KRQSVSGLHR 10 2 Q8N1G4;J3KRP5 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 KRQS(0.99)VS(0.01)GLHR;KRQS(0.999)VS(0.001)GLHR;KRQS(0.999)VS(0.001)GLHR;KRQS(1)VSGLHR;KRQS(1)VSGLHR;KRQS(1)VSGLHR 125.82 0.00020819 1870826000 761787 873346 786017 774358 976592 516099 1126079 711943 1690718 TRUE FALSE 714108.1115 938009.4466 804661.6944 794229.3373 899894.4037 665088.4031 957233.908 800830.6507 1408526.243 0.506989568 0.66595099 0.571279164 0.563872587 0.638890761 0.472187442 0.679599626 0.568559269 1 20.42575501 -1.196370527 0.683616038 1.115940572 0.589157138 0.799086544 0.065530609 21.24582637 4.500864276 4.842705819 0.021123906 0.063625246 1.196370527 -0.526783433 KRS(ph)EASPHENTNHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRSEASPHENTNHK 14 2 Q9NP74-3;Q9NP74-2;Q9NP74;S4R313 Q9NP74-3 PALMD Palmdelphin 1 KRS(0.926)EAS(0.074)PHENTNHK 91.518 0.002528 26733000 17209 12745 18199 13641 17765 8775.4 16265 15494 28570 TRUE FALSE 16131.91941 13688.65306 18630.68887 13991.05115 16369.80856 11308.71552 13826.21425 17428.46001 23801.48243 0.677769524 0.575117668 0.782753298 0.587822678 0.687764244 0.47512652 0.580897189 0.732242626 1 14.53876381 0.909229657 4.366097485 0.999893871 0.626932108 0.678803393 0.081692496 0.278339032 11.75852577 0.07938697 0.020193259 8.113900117 -0.909229657 -0.372961763 KRS(ph)EGFSMDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KRSEGFSMDR 10 2 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;K7ERA4 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 1 KRS(1)EGFSMDR;KRS(0.706)EGFS(0.294)MDR;KRS(0.893)EGFS(0.107)MDR 171.76 2.05E-06 1076600000 1221807 1241040 1206060 1659450 2280590 1154293 1453250 1354070 2012080 TRUE FALSE 1145336.281 1332927.893 1234668.313 1702034.296 2101481.661 1487518.651 1235348.654 1523128.62 1676250.849 0.683272603 0.795184022 0.736565361 1.015381616 1.253679699 0.887408141 0.736971232 0.90865196 1 20.67680663 3.248604091 24.70006075 0.946977179 0.750267712 0.392670642 0.132233135 229.2607683 563820.2437 0.040828602 0.054632167 1772.572842 -3.248604091 -0.196709468 KRS(ph)FVPEEEKHEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRSFVPEEEKHEER 14 3 A0A0U1RRH6;O94880;O94880-2;B4DG57 A0A0U1RRH6 PHF14 PHD finger protein 14 1 KRS(1)FVPEEEKHEER;KRS(1)FVPEEEKHEER 104.89 0.00073596 608550000 342850 290120 288740 398980 485910 285380 318310 289510 482700 TRUE FALSE 321391.6305 311600.7867 295589.0492 409218.5023 447748.5887 367764.5732 270582.3705 325655.9608 402134.2516 0.799214763 0.774867561 0.735050665 1.017616631 1.113430619 0.91453183 0.672865764 0.809819008 1 18.6173177 3.267003772 24.99417599 0.897826629 0.765864448 0.244061377 0.12112838 380.4860667 334346.3088 0.037907994 0.051318079 1849.284681 -3.267003772 -0.131962181 KRS(ph)GEAAV ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRSGEAAV 8 2 A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 1 KRS(1)GEAAV;KRS(1)GEAAV 88.441 0.011508 1482290000 2099300 1693880 1855340 1793290 2125800 1407780 2202800 1768770 3660700 TRUE FALSE 1967908.56 1819296.638 1899349.541 1839308.857 1958848.243 1814183.233 1872510.59 1989604.828 3049705.521 0.645278223 0.596548298 0.622797686 0.603110315 0.642307341 0.59487161 0.61399718 0.652392441 1 21.54023851 0.614039562 2.459105601 0.999991595 0.614855027 0.979889795 0.01711436 0.385622939 2.323085098 0.014481845 0.003873431 4.111871763 -0.614039562 -0.385136568 KRS(ph)GNSDSIER ddPTM_SK-BR-3_Pertuzumab_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(0.895)GNS(0.105)DSIER;KRS(0.971)GNS(0.029)DSIER;KRS(0.687)GNS(0.313)DSIER;KRS(0.664)GNS(0.334)DS(0.002)IER 144.18 2.90E-05 1267760000 992630 1084820 929510 1093810 1207420 635500 1070360 882570 1486870 TRUE FALSE 930503.0602 1165141.202 951558.4161 1121879.016 1112594.104 818958.5335 909869.4547 992760.8073 1238701.791 0.751192149 0.940614771 0.76819007 0.905689347 0.898193666 0.661142608 0.734534705 0.801452629 1 20.24039748 2.271781062 24.9999894 0.768449566 0.855624719 0.025162469 0.104063407 341.1418989 256724.5142 0.032586693 0.027262322 186.9739322 -2.271781062 0.087175153 KRS(ph)HPSGSGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRSHPSGSGAK 11 2 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 1 KRS(0.986)HPS(0.014)GSGAK 128.74 0.0001354 95310000 103910 112930 133630 133090 146510 91581 169320 114700 190020 TRUE FALSE 97406.45858 121291.4547 136799.7667 136505.3147 135003.6956 118018.948 143932.0379 129020.5475 158304.4344 0.615310992 0.766191138 0.864156252 0.862296216 0.852810574 0.745518901 0.909210398 0.815015372 1 17.27234214 5.029102608 1.096450376 0.856870517 0.354470081 0.603316489 0.064795672 1.902578046 1.237059483 0.016677289 1.284222764 106930.7487 -5.029102608 -0.502400436 KRS(ph)PGGSGGASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRSPGGSGGASR 12 2 E7ER77;Q7Z2K6 E7ER77 ERMP1 Endoplasmic reticulum metallopeptidase 1 1 KRS(1)PGGSGGASR;KRS(1)PGGSGGASR 111.7 0.0007063 1527882000 328664.1 336583 247357 269487.5 436295 189338.4 322030 328178.2 592618 TRUE FALSE 308093.6007 361503.9555 253224.4249 276403.0055 402030.1506 243997.3224 273744.5911 369151.9707 493706.2273 0.624042363 0.732224824 0.512905065 0.559853188 0.814310471 0.494215606 0.554468581 0.747715848 1 18.91329332 0.940031701 4.309504025 0.999764593 0.612166388 0.616356301 0.097453626 0.183060626 9.40079034 0.090477537 0.023036627 8.710271681 -0.940031701 -0.387598205 KRS(ph)PPLGGAPSPSSLSLPPSTGFPLQASGVPSPYLSSLASSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRSPPLGGAPSPSSLSLPPSTGFPLQASGVPSPYLSSLASSR 42 2 I3NI13;I3L270;Q8NBZ0 I3NI13 INO80E INO80 complex subunit E 1 KRS(0.808)PPLGGAPS(0.061)PS(0.061)S(0.061)LS(0.01)LPPSTGFPLQASGVPSPYLSSLASSR 133.17 1.90E-09 64223000 141250 139450 97575 71992 156730 72401 125650 124470 71253 TRUE FALSE 132409.4146 149775.0231 99889.52508 73839.4366 144421.058 93301.99337 106809.949 140010.3535 59360.41399 2.230601267 2.523146539 1.682763282 1.243917143 2.432952338 1.571788118 1.79934643 2.358648535 1 15.85721353 -1.612178302 0.113147337 2.27E-31 2.568777855 0.316001479 0.42620685 73.40591602 1.346672573 30.45416014 6.276422883 0.024424276 1.612178302 2.568777855 KRS(ph)PS(ph)PSPTPEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KRSPSPSPTPEAK 13 2 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 KRS(0.953)PS(0.735)PS(0.312)PTPEAK;KRS(0.985)PS(0.823)PS(0.191)PT(0.001)PEAK;KRS(0.993)PS(0.911)PS(0.096)PTPEAK;KRS(0.993)PS(0.888)PS(0.118)PTPEAK;KRS(0.848)PS(0.943)PS(0.208)PTPEAK;KRS(0.857)PS(0.965)PS(0.178)PTPEAK 170.16 1.46E-05 10073190000 11591640 6622130 7750180 7612040 8190510 5593670 10106720 6702060 10446080 TRUE FALSE 10866139.94 7112439.396 7934017.929 7807377.834 7547260.384 7208471.723 8591311.162 7538826.944 8702561.764 1.248613941 0.817281117 0.911687632 0.897135584 0.867245828 0.828316066 0.987216339 0.866276753 1 23.05300872 4.746104874 24.99222944 0.893235277 1.248614112 0.774565471 0.059602955 406.642764 1347073.098 0.013253519 0.140257277 55732.03152 -4.746104874 0.355378835 KRS(ph)PSPS(ph)PTPEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRSPSPSPTPEAK 13 2 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 KRS(0.89)PS(0.373)PS(0.737)PTPEAK 132.47 6.35E-05 1789200000 1344900 776600 921090 921490 1042300 720680 1233900 863070 1309800 TRUE FALSE 1260725.11 834100.2721 942938.6898 945136.9935 960441.9624 928728.6167 1048888.15 970826.1894 1091185.918 1.155371499 0.764397944 0.864141182 0.866155783 0.880181779 0.851118587 0.961236882 0.889698238 1 20.0574655 0.931604194 0.827374886 0.996241366 0.877458624 0.040014419 0.10365361 1.58564136 2.346548518 0.090907041 0.032542195 8.542877792 -0.931604194 -0.118782742 KRS(ph)S(ph)SEDAESLAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRSSSEDAESLAPR 14 2 Q4G0J3;Q4G0J3-3;H0YA82 Q4G0J3 LARP7 La-related protein 7 2 KRS(0.964)S(0.645)S(0.385)EDAES(0.006)LAPR 84.208 0.040454 384190000 866530 699740 681890 770210 759460 332600 549650 376250 749270 TRUE FALSE 812295.4341 751549.4777 698064.7528 789974.8926 699815.0751 428616.2207 467235.0852 423225.6407 624211.9965 1.301313398 1.203997171 1.11831358 1.265555447 1.121117632 0.686651687 0.748519874 0.678015871 1 19.25167656 2.316545947 4.98103794 0.754121914 1.200245514 0.809948629 0.102239144 0.07495703 3.32824931 0.032845245 0.026934358 207.2745337 -2.316545947 0.4461236 KRS(ph)SITEPEGPNGPNIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRSSITEPEGPNGPNIQK 18 2 Q13625-2;Q13625;Q13625-3 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 KRS(0.333)S(0.333)IT(0.333)EPEGPNGPNIQK 139.6 6.95E-08 205800000 117730 108870 91590 94849 126230 55826 141140 86479 209700 TRUE FALSE 110361.4895 116930.8481 93762.55805 97282.98592 116316.405 71942.05994 119977.3673 97276.09351 174699.7153 0.631721061 0.669324778 0.536706988 0.556858297 0.665807639 0.411804105 0.686763382 0.556818844 1 17.41451773 -1.452027125 5.215732094 1.000565277 0.592299754 0.713939839 0.081648234 0.000479426 5.04E-05 0.070620276 0.016623085 0.035316111 1.452027125 -0.408265523 KRS(ph)SSEDAESLAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRSSSEDAESLAPR 14 2 Q4G0J3;Q4G0J3-3;H0YA82 Q4G0J3 LARP7 La-related protein 7 1 KRS(0.954)S(0.04)S(0.006)EDAESLAPR;KRS(0.968)S(0.028)S(0.004)EDAESLAPR 184.83 9.83E-07 1719710000 407140 459350 375560 467460 551770 224388 371010 319220 698100 TRUE FALSE 381657.8342 493360.752 384468.4606 479455.815 508436.2099 289165.173 315380.4948 359075.3197 581582.6001 0.656240118 0.848307277 0.661072839 0.824398486 0.874228716 0.497203962 0.542279798 0.617410699 1 19.14962458 2.241055154 24.99999088 0.612498924 0.770240044 0.067726777 0.153897395 98.87000335 990876.0117 0.049362694 0.039522591 174.2028093 -2.241055154 0.15774112 KRS(ph)VSHGSNHTQKPDEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRSVSHGSNHTQKPDEQR 18 3 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 KRS(0.6)VS(0.4)HGSNHTQKPDEQR;KRS(0.761)VS(0.238)HGSNHTQKPDEQR 158.78 1.82E-11 306030000 51377 115446 95195 110775 181072 65604 147773 136356 439460 TRUE FALSE 48161.40528 123993.742 97453.07035 113617.674 166851.3355 84542.80981 125615.8105 153380.3468 366111.287 0.13154854 0.338677736 0.266184283 0.310336442 0.455739393 0.230921069 0.343108271 0.4189446 1 18.48192273 -5 0.260938759 5.500107204 0.255874351 0.8888707 0.078246984 57.18929604 0.561546111 137.8746406 0.09530084 1.00E-05 5 -5.244232854 KRSPPLGGAPS(ph)PSSLSLPPSTGFPLQASGVPSPYLSSLASSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRSPPLGGAPSPSSLSLPPSTGFPLQASGVPSPYLSSLASSR 42 2 I3NI13;I3L270;Q8NBZ0 I3NI13 INO80E INO80 complex subunit E 1 KRS(0.316)PPLGGAPS(0.48)PS(0.089)S(0.089)LS(0.02)LPPS(0.005)T(0.001)GFPLQASGVPSPYLSSLASSR 117.19 8.11E-07 85502000 55960 69314 42509 31893 68991 35555 61040 55744 30265 TRUE FALSE 52457.56349 74446.08068 43517.33355 32711.42837 63572.72516 45819.15131 51887.61867 62703.76111 25213.57598 2.080528503 2.952618888 1.725948496 1.297373621 2.521368853 1.817241289 2.057923823 2.48690472 1 14.62191313 3.894611349 5.21918525 1.903256159 2.546566536 0.223083173 0.511263521 0.276353217 12.75045406 0.11959204 0.222636988 7845.332392 -3.894611349 0.643310377 KRSS(ph)ISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.071)S(0.929)ISK;KRS(0.069)S(0.931)ISK;KRS(0.021)S(0.977)IS(0.001)K 99.815 0.0080734 1529969000 2687706 2072221 2458270 2260091 3131043 1739510 3522833 3319992 5211950 TRUE FALSE 2519487.279 2225650.399 2516581.325 2318088.761 2885143.513 2241678.298 2994616.896 3734500.309 4342041.875 0.580254026 0.512581514 0.579584766 0.53387066 0.664466994 0.516272842 0.689679414 0.860079294 1 22.04994221 1.218884389 1.683958104 0.998178759 0.560850352 0.919859939 0.045023877 0.077600679 0.402415738 0.037664424 0.011189518 16.55329251 -1.218884389 -0.437328407 KRT(ph)EEPDRDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KRTEEPDRDER 11 3 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 1 KRT(1)EEPDRDER;KRT(1)EEPDRDER;KRT(1)EEPDRDER;KRT(1)EEPDRDER;KRT(1)EEPDRDER;KRT(1)EEPDRDER 192.54 7.14E-07 2610988000 1195006 936481 1043220 1053832 1174664 820016 1230121 994894 1320082 TRUE FALSE 1120212.708 1005819.028 1067965.671 1080875.113 1082410.628 1056741.307 1045675.776 1119108.706 1099751.786 1.018605036 0.91458731 0.97109701 0.982835515 0.984231753 0.96089074 0.950828895 1.017601171 1 20.06874651 1.235349261 24.99983049 1.008800603 0.963779013 0.256257651 0.027063064 100.1885512 779883.6151 0.02158801 0.006262165 17.19290489 -1.235349261 -0.04502159 KRT(ph)PS(ph)AGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRTPSAGK 8 2 P46013;P46013-2 P46013 MKI67 Antigen KI-67 2 KRT(1)PS(1)AGK 61.344 0.095531 34223000 367360 148130 249940 220220 221420 169280 300810 190680 347470 TRUE FALSE 344367.5934 159097.6993 255868.6948 225871.218 204030.5664 218148.388 255706.3331 214486.8177 289475.0123 1.189628047 0.549607713 0.883905982 0.78027881 0.704829632 0.753600065 0.883345098 0.740951062 1 18.14307929 -1.560684457 2.786336806 1.012260582 0.793968099 0.107737498 0.164961044 24980072.81 25407577.2 2286275.269 0.035732953 0.027498914 1.560684457 -0.218292482 KRT(ph)SESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRTSESR 7 2 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;H7C1M2 P18583-7 SON Protein SON 1 KRT(0.491)S(0.491)ES(0.018)R;KRT(0.613)S(0.387)ESR 82.749 0.038017 659720000 1027070 793900 1154400 983480 863270 767060 1114920 882650 968330 TRUE FALSE 962787.5221 852681.1821 1181782.913 1008717.762 795472.2565 988497.7698 947748.0964 992850.7955 806709.4673 1.193474926 1.056986705 1.464942412 1.250410219 0.986070312 1.225345443 1.174831999 1.23074147 1 19.62168966 KRT(ph)SFDDRLEDDDFDLIEENLGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KRTSFDDRLEDDDFDLIEENLGVK 24 3 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 1 KRT(0.5)S(0.5)FDDRLEDDDFDLIEENLGVK;KRT(0.5)S(0.5)FDDRLEDDDFDLIEENLGVK;KRT(0.5)S(0.5)FDDRLEDDDFDLIEENLGVK;KRT(0.5)S(0.5)FDDRLEDDDFDLIEENLGVK;KRT(0.5)S(0.5)FDDRLEDDDFDLIEENLGVK 187.48 1.93E-17 352169000 692910 496424 527286 541241 554547 306130 568914 399075 1011717 TRUE FALSE 649542 533179.7495 539793.4729 555130.1604 510995.1156 394504.7614 483610.6272 448900.3922 842854.8968 0.770645104 0.632587829 0.640434641 0.658630759 0.606267007 0.468057744 0.573776849 0.532595105 1 19.68492476 -1.381095572 4.755527998 1.000447341 0.607485529 0.702420523 0.079679283 0.000379704 4.94E-05 0.077516115 0.018250369 0.041581909 1.381095572 -0.392961812 KRTEEPDRDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KRTEEPDRDER 11 3 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 ;;;;; 186.58 1.74E-06 1141700000 1050750 1143470 1010699 1153840 1508210 805416 1275520 1144840 2552010 FALSE TRUE 984985.4331 1228133.709 1034673.258 1183449.488 1389761.27 1037926.524 1084267.617 1287775.794 2126063.044 0.463290793 0.577656298 0.486661607 0.556638944 0.653678297 0.488191791 0.50998846 0.605709129 1 21.01975295 0.803479555 3.762540193 0.99997876 0.535219397 0.876783869 0.054512712 0.487585686 8.970251205 0.049536366 0.012709314 6.360328619 -0.803479555 -0.464759362 KRVDIIPGFEFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRVDIIPGFEFDR 13 2 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 89.541 0.0041634 55189000 113640 149480 100680 113150 158100 79270 146990 150760 255060 FALSE TRUE 106527.4753 160547.6547 103068.1771 116053.6206 145683.4637 102153.9622 124950.2141 169582.7179 212488.8382 0.501332099 0.755558062 0.485052194 0.546163373 0.685605253 0.48074978 0.588031894 0.798078239 1 17.69702753 1.027426521 2.929323718 0.997646948 0.583199509 0.723936684 0.087465307 0.119595172 2.308514639 0.079244786 0.021011047 10.65188629 -1.027426521 -0.414447439 KRVEDAYILTCNVSLEYEKTEVNSGFFYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KRVEDAYILTCNVSLEYEKTEVNSGFFYK 29 3 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 63.901 0.0059856 31350000 53618 58275 53134 58490 82828 44926 69654 52614 92476 FALSE TRUE 50262.14509 62589.74164 54394.36357 59990.95242 76323.02299 57895.40689 59210.02934 59182.97372 77041.15818 0.652406406 0.812419531 0.706042911 0.778687053 0.990678551 0.751486715 0.768550613 0.768199429 1 16.23334177 -5 0.194334856 1.941324972 0.741375941 0.408416653 0.085741283 146.5400094 1.442098567 53.76524995 0.21407546 1.00E-05 5 -1.199949031 KRVPDHHPC ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRVPDHHPC 9 2 P78371;P78371-2 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 67.993 0.03337 183163000 269710 383460 180966 195686 429200 154911 270270 412550 545290 FALSE TRUE 252829.3325 411851.7774 185258.599 200707.6341 395492.3633 199631.2909 229745.5226 464057.7756 454277.5763 0.556552526 0.906608204 0.407809253 0.441817172 0.87059627 0.439447821 0.505738197 1.021529126 1 18.79321457 1.231859432 24.99978379 1.010764894 0.59559853 0.509200337 0.171748727 141.5807658 528164.7079 0.149101097 0.040659073 17.05530272 -1.231859432 -0.415166364 KRVS(ph)SGSSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRVSSGSSER 10 2 K7EMM8;Q49A26-4;Q49A26-2;Q49A26-3;Q49A26;K7EPU6 K7EMM8 GLYR1 Putative oxidoreductase GLYR1 1 KRVS(0.933)S(0.025)GS(0.034)S(0.007)ER;KRVS(0.939)S(0.022)GS(0.031)S(0.008)ER 67.115 0.050356 104726000 126414 132527 125628 117300 140284 93636 143856 115145 176342 TRUE FALSE 118501.9734 142339.437 128607.9555 120310.1166 129266.6605 120667.1931 122286.1283 129521.1067 146909.381 0.806633127 0.968892769 0.875423711 0.818941008 0.879907462 0.821371599 0.832391556 0.881639456 1 17.164567 0.960461785 22.08036691 1.000000001 0.865798745 0.467485519 0.04679281 1663.881997 929207.9063 0.047995596 0.011998899 9.129810962 -0.960461785 -0.134201256 KS(ph)EAGHASSPDSEVTSLCQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSEAGHASSPDSEVTSLCQK 20 1 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 KS(0.322)EAGHAS(0.322)S(0.322)PDS(0.03)EVT(0.003)SLCQK 77.514 0.0046698 219910000 17287 45093 32053 38215 36885 30922 29393 37362 34696 TRUE FALSE 16205.03753 48431.73264 32813.3123 39195.6616 33988.20089 39848.67942 24985.79252 42026.72794 28905.01346 0.560630686 1.675547832 1.135211798 1.35601603 1.175858331 1.378607884 0.86441034 1.453959813 1 14.81903212 1.767007515 25 1.094114467 1.261914416 0.009585612 0.316216067 62.98631817 55386.58466 0.131286873 0.072816225 58.48002031 -1.767007515 0.167799948 KS(ph)HSSPSLHQDEAPTTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSHSSPSLHQDEAPTTAK 18 1 Q8NDX1-2;Q8NDX1 Q8NDX1-2 PSD4 PH and SEC7 domain-containing protein 4 1 KS(0.492)HS(0.492)S(0.015)PS(0.001)LHQDEAPTTAK 145.13 4.38E-08 39230000 32783 51616 46413 48227 62161 35620 61151 44488 104920 TRUE FALSE 30731.17055 55437.70235 47513.93828 49464.58647 57279.12581 45902.91576 51981.97525 50042.42473 87408.17419 0.351582342 0.634239336 0.543586898 0.56590344 0.655306284 0.52515587 0.594703822 0.572514244 1 16.41548058 -5 0.300704397 4.633787439 0.542079437 0.758440872 0.079666544 124.7591102 1.152620848 285.8421296 0.071339007 1.00E-05 5 -4.091708001 KS(ph)LDSDES(ph)EDEEDDYQQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSLDSDESEDEEDDYQQKR 19 2 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 KS(0.685)LDS(0.315)DES(1)EDEEDDYQQKR 136.53 2.78E-05 1200300000 1437600 749930 903620 1038000 1268300 574390 1334900 824340 1965300 TRUE FALSE 1347623.182 805455.5975 925054.2931 1064636.837 1168692.834 740207.0686 1134744.138 927260.6636 1637278.734 0.823087208 0.491947755 0.564994997 0.650247765 0.713802 0.45209594 0.693067169 0.566342581 1 20.64286852 -1.519682554 2.566604483 1.023025899 0.605901271 0.540345165 0.109674524 5117507.005 4861960.947 821247.3793 0.025924219 0.0302216 1.519682554 -0.417124628 KS(ph)LPEEDVAEIQHAEEFLIKPESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSLPEEDVAEIQHAEEFLIKPESK 24 2 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 KS(1)LPEEDVAEIQHAEEFLIKPESK;KS(1)LPEEDVAEIQHAEEFLIKPESK 163.49 7.93E-12 95692000 147474 58221 97207 89658 87837 60236 117521 74153 149570 TRUE FALSE 138243.8656 62531.74342 99512.79594 91958.77607 80938.63634 77625.15535 99899.81706 83411.16528 124605.8007 1.109449679 0.501836536 0.798620894 0.737997553 0.649557531 0.622965824 0.801726858 0.669400339 1 16.92701171 -1.090229005 4.649544102 1.000011825 0.71950997 0.205729246 0.159694061 2.39E-05 4.68E-06 0.135171939 0.031858457 0.081240202 1.090229005 -0.280501855 KS(ph)LSDSESDDS(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 KS(0.898)LS(0.102)DS(0.268)ES(0.268)DDS(0.464)K 240.53 2.19E-16 248930000 1731000 618920 979640 884400 872190 564660 1209200 651530 1015700 TRUE FALSE 1622659.8 664745.4808 1002877.523 907095.2013 803691.7156 727668.1755 1027891.686 732874.9547 846173.1083 1.9176452 0.785590412 1.185191911 1.071997198 0.949795861 0.859951904 1.21475343 0.86610523 1 19.69059331 4.747264327 24.91963723 1.008103496 1.917645684 0.814368863 0.138739125 443.0865085 1268574.661 0.031340831 0.371024749 55881.02029 -4.747264327 0.909542189 KS(ph)MKS(ph)S(ph)TYEELDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSMKSSTYEELDR 13 2 Q4W5G0 Q4W5G0 TIGD2 Tigger transposable element-derived protein 2 3 KS(0.765)MKS(0.781)S(0.585)T(0.543)Y(0.325)EELDR 51.695 0.071368 29039000 1938.2 1668.5 2434.5 2390.1 1581.8 1383.6 965.73 875.73 2810.8 TRUE FALSE 1816.891522 1792.037476 2492.24749 2451.434012 1457.571809 1783.022859 820.9277519 985.0668182 2341.659322 0.775899169 0.765285308 1.064308316 1.046879019 0.622452547 0.761435638 0.350575229 0.420670423 1 11.19331548 2.449345572 2.278325263 0.551445628 0.909970249 0.262990516 0.209186039 0.310460816 3.279197674 0.0791591 0.064564897 281.4139174 -2.449345572 0.358524622 KS(ph)PEIHR ddPTM_SK-BR-3_Pertuzumab_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 88.056 0.011569 1631970000 1791960 1363280 1612300 1460790 1510120 1227590 1742580 1374750 1399240 TRUE FALSE 1679804.422 1464218.67 1650544.517 1498276.345 1391521.267 1581975.305 1481296.306 1546390.564 1165697.805 1.441029069 1.256087696 1.415928306 1.285304252 1.193723846 1.357105846 1.270737837 1.326579288 1 20.1527624 -3.876280173 0.249015773 7.05E-15 1.348382958 0.66497202 0.071925792 57.00732299 0.943123429 29.0715447 0.098264572 0.00013296 3.876280173 1.348382958 KS(ph)PEIHRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KSPEIHRR 8 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 KS(1)PEIHRR;KS(1)PEIHRR;KS(1)PEIHRR;KS(1)PEIHRR;KS(1)PEIHRR 93.258 0.0058421 366085000 590351 437479 488632 465928 502520 381472 583746 453586 731992 TRUE FALSE 553401.9847 469870.4004 500222.5818 477884.5013 463054.1063 491596.7737 496218.7065 510217.2106 609817.8064 0.907487415 0.770509479 0.82028202 0.783651275 0.759331888 0.806137126 0.813716329 0.836671552 1 19.21801875 0.559762216 1.454173062 0.999981389 0.802775628 0.685602069 0.040292167 0.972125146 2.619361102 0.034528612 0.010063623 3.628793178 -0.559762216 -0.197205761 KS(ph)PEKNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KSPEKNER 8 2 P19525-2;P19525 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 1 KS(1)PEKNER;KS(1)PEKNER;KS(1)PEKNER 108.72 0.0029589 419200000 1020070 406190 611940 593540 632070 391135 691380 543910 659870 TRUE FALSE 956225.6396 436264.7302 626455.5058 608771.2413 582429.7718 504049.325 587713.9875 611818.3608 549733.4341 1.739435116 0.793593228 1.139562317 1.107393518 1.059476713 0.916897707 1.069089037 1.112936421 1 19.0683727 4.750177609 24.9754778 1.024048814 1.739435546 0.824446392 0.103625397 709.1933045 1524672.734 0.024299437 0.390248786 56257.13469 -4.750177609 0.715386732 KS(ph)PGSTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSPGSTSR 8 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 KS(0.914)PGS(0.065)T(0.02)S(0.001)R;KS(0.977)PGS(0.009)T(0.012)S(0.001)R 80.24 0.015902 247330000 177145 107673 170730 150136 141669 109078 150534 116736 155873 TRUE FALSE 166057.8107 115645.221 174779.7962 153988.7439 130542.8882 140567.0479 127962.8242 131310.7466 129856.7893 1.278776501 0.890559682 1.345942689 1.18583514 1.005283504 1.082477463 0.98541497 1.011196621 1 16.98656192 2.734452048 24.63424465 1.018909511 1.156269398 0.297468155 0.119361837 427.6433048 2564062.377 0.037799717 0.036838384 542.5653418 -2.734452048 0.137359887 KS(ph)PGVEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSPGVEIK 8 1 Q9Y597-3;Q9Y597-2;Q9Y597 Q9Y597-3 KCTD3 BTB/POZ domain-containing protein KCTD3 1 KS(1)PGVEIK 62.338 0.049166 232750000 860450 544860 627670 673580 799580 370080 824700 512890 843600 TRUE FALSE 806595.9704 585202.0013 642558.6288 690865.2032 736784.2122 476916.0883 701043.8911 576925.4455 702797.7101 1.14769294 0.832674883 0.914286742 0.98302142 1.048358868 0.678596531 0.997504518 0.8208983 1 19.42274997 KS(ph)PLSSILFSALDSDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSPLSSILFSALDSDTR 17 1 A0A1W2PRB5;A0A0J9YVS1;A0A0G2JNB1;A0A0G2JNT7;Q7Z3B3;A0A0G2JQF5;A0A3B3IT55;A0A0G2JQF4;A0A1W2PPV8;A0A1W2PRR3;I3L233 A0A1W2PRB5 KANSL1 KAT8 regulatory NSL complex subunit 1 1 KS(1)PLSSILFSALDSDTR 181.69 4.83E-10 77892000 68480 64223 60400 63430 69507 53069 72154 54382 57641 TRUE FALSE 64193.95904 68978.13774 61832.71652 65057.72119 64048.2006 68389.1588 61335.17754 61171.71241 48020.34472 1.336807543 1.436435705 1.287635832 1.354794964 1.333772195 1.424170509 1.277274828 1.273870747 1 15.55135814 0.621586465 1.011194713 0.999754753 1.36059581 0.846608697 0.047217992 0.43192174 0.711401434 0.042637308 0.013627679 4.183949796 -0.621586465 0.360841057 KS(ph)PPKADEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KSPPKADEK 9 2 Q13427;E9PG73;C9JM79;Q13427-2 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 KS(1)PPKADEK;KS(1)PPKADEK;KS(1)PPKADEK 73.624 0.022643 1980210000 9791200 2895170 4855000 4374500 4306300 3105740 6369500 3352350 5109200 TRUE FALSE 9178386.27 3109531.399 4970162.893 4486757.076 3968100.569 4002316.721 5414452.607 3770898.277 4256441.513 2.156352023 0.730547193 1.167680298 1.054109885 0.932257745 0.940296421 1.272060849 0.885927427 1 22.02121638 4.747409039 24.92279686 1.014404091 2.156352634 0.855590591 0.149438099 408.2245583 1149794.83 0.035157059 0.425206541 55899.64364 -4.747409039 1.141948543 KS(ph)PPKADEKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSPPKADEKER 11 3 Q13427;E9PG73;C9JM79;Q13427-2 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 KS(1)PPKADEKER 64.52 0.048495 176750000 471350 194120 298650 298400 323340 186240 363300 250260 430180 TRUE FALSE 441849.0449 208492.8468 305734.119 306057.4492 297946.1807 240004.4646 308826.5377 281505.5119 358380.1789 1.232905922 0.581764447 0.853099968 0.854002166 0.831369027 0.669692351 0.861728845 0.785494088 1 18.45113132 -1.108466042 4.372902933 1.000024001 0.809972098 0.072033806 0.169366329 3.48E-05 7.10E-06 0.144055137 0.033949835 0.077899372 1.108466042 -0.190051903 KS(ph)PPPAKDEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KSPPPAKDEAR 11 2 Q8IXJ6-5;Q8IXJ6-2;Q8IXJ6-3;Q8IXJ6 Q8IXJ6-5 SIRT2 NAD-dependent protein deacetylase sirtuin-2 1 KS(1)PPPAKDEAR;KS(1)PPPAKDEAR;KS(1)PPPAKDEAR 103.21 0.0014424 360300000 875220 513778 626880 634990 648130 449829 802860 531626 783970 TRUE FALSE 820441.5425 551818.6577 641749.8896 651284.9184 597228.4842 579687.3299 682478.5964 598000.6764 653120.3424 1.256187397 0.844895836 0.98259057 0.997189762 0.914423339 0.887565878 1.044950757 0.915605651 1 19.31698932 4.750823844 24.87444212 0.948663753 1.256187599 0.723514256 0.059794449 981.9562968 1991738.375 0.013961402 0.239491806 56340.90833 -4.750823844 0.307523846 KS(ph)PRPAGPQLFLPDPDPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KSPRPAGPQLFLPDPDPQR 19 2 Q9BUH6 Q9BUH6 C9orf142 Protein PAXX 1 KS(1)PRPAGPQLFLPDPDPQR;KS(1)PRPAGPQLFLPDPDPQR;KS(1)PRPAGPQLFLPDPDPQR;KS(1)PRPAGPQLFLPDPDPQR 112.86 0.00014831 3828470000 5533250 5509400 5571990 6207590 6370000 3508590 6287400 4491890 5597600 TRUE FALSE 5186933.76 5917321.709 5704160.234 6366887.269 5869725.895 4521462.976 5344662.739 5052712.354 4663324.398 1.112282423 1.2689063 1.223196104 1.365310822 1.258699888 0.969579336 1.146105714 1.083500079 1 22.15292736 2.257370863 24.98401441 1.067686387 1.251218443 0.607867041 0.077517381 160.8911141 213697.2542 0.025312348 0.021144133 180.8718009 -2.257370863 0.183532055 KS(ph)PSLTEASEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSPSLTEASEK 11 1 Q6PJP8 Q6PJP8 DCLRE1A DNA cross-link repair 1A protein 1 KS(0.784)PS(0.108)LT(0.108)EASEK 93.258 0.0057479 2834400000 852520 1091600 1042500 1083400 1235300 826240 1590100 1126800 1436100 TRUE FALSE 799162.295 1172423.2 1067228.592 1111201.878 1138284.521 1064762.075 1351679.267 1267483.46 1196405.632 0.667969352 0.979954597 0.892029061 0.928783556 0.951420229 0.889967454 1.129783436 1.059409473 1 20.19027518 1.751843495 18.97890011 1.070787316 0.90102011 0.459087127 0.089863061 0.624386992 898.2809039 0.037880721 0.020979378 56.47334279 -1.751843495 -0.169767207 KS(ph)PSSDSWTCADTSTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSPSSDSWTCADTSTER 17 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;H0YIQ0 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 KS(0.934)PS(0.057)S(0.009)DSWTCADTSTER;KS(0.791)PS(0.172)S(0.037)DSWTCADTSTER 229.1 7.46E-16 881800000 672400 565120 661600 638250 584840 428240 637520 449530 465060 TRUE FALSE 630315.6843 606962.0728 677293.4644 654628.5756 538909.0255 551865.9361 541929.7944 505654.81 387438.4816 1.626879399 1.566602446 1.74813163 1.689632307 1.390953793 1.424396291 1.398750563 1.305122836 1 18.56360773 1.28791272 0.495688644 0.99588902 1.670477881 0.859455622 0.081017352 0.318160779 0.208467532 0.09301597 0.052232381 19.40495856 -1.28791272 0.674588861 KS(ph)PTMEQAVQTASAHLPAPAAVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSPTMEQAVQTASAHLPAPAAVGR 24 1 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 KS(0.997)PT(0.003)MEQAVQTASAHLPAPAAVGR 97.542 0.002752 268900000 99384 88114 96161 106950 105450 78136 122080 95529 93888 TRUE FALSE 93163.73285 94638.05224 98441.98433 109694.5181 97168.38236 100692.5948 103775.2373 107456.0059 78217.48626 1.191085744 1.209934719 1.258567477 1.402429601 1.242284648 1.287341227 1.326752396 1.373810526 1 16.25520355 3.783496066 2.628268175 1.292074406 1.204541362 0.041081108 0.1099006 0.595594053 8.15107589 0.026363749 0.052206894 6074.297599 -3.783496066 -0.087533044 KS(ph)SMCSLAQPATTTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSSMCSLAQPATTTAR 16 1 H3BPV0 H3BPV0 MTSS1L 1 KS(0.496)S(0.496)MCS(0.008)LAQPATTTAR 88.57 0.0037272 154420000 91898 80996 77065 76088 96447 57254 116790 93925 116580 TRUE FALSE 86146.26822 86993.02812 78893.01819 78040.5469 88872.44167 73782.30036 99278.42373 105651.743 97122.04486 0.886989852 0.895708366 0.812308043 0.803530723 0.915059416 0.759686438 1.022202774 1.087824532 1 16.56751118 1.623674911 6.103209122 1.047071565 0.84899409 0.757166618 0.051036896 0.058571 4.619881133 0.025000545 0.012078495 42.04118138 -1.623674911 -0.198077475 KS(ph)SPEMEDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSSPEMEDAR 10 1 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 KS(0.622)S(0.378)PEMEDAR;KS(0.5)S(0.5)PEMEDAR 70.438 0.023167 456280000 742500 577110 627630 611120 686140 499360 702360 565400 876360 TRUE FALSE 696028.2504 619839.8249 642517.68 626802.3738 632253.3322 643517.1256 597047.6384 635991.4346 730089.8545 0.953346011 0.84899115 0.880052881 0.858527714 0.865993861 0.881421816 0.817772819 0.871113919 1 19.47771451 0.935962223 22.87582191 1 0.866695625 0.572685491 0.034444259 10096.27435 3606632.95 0.030499846 0.007624962 8.629034847 -0.935962223 -0.133304375 KS(ph)SPPASSPQPEAPTSSWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KSSPPASSPQPEAPTSSWR 19 1 P43250-2 P43250-2 GRK6 G protein-coupled receptor kinase 6 1 KS(0.489)S(0.489)PPAS(0.016)S(0.005)PQPEAPTSSWR;KS(0.5)S(0.5)PPASSPQPEAPTSSWR;KS(0.607)S(0.392)PPAS(0.002)SPQPEAPTSSWR;KS(0.649)S(0.35)PPASSPQPEAPTSSWR 150.94 4.32E-08 1202520000 851468 789265 808431 852310 869990 583473 932708 727743 1047240 TRUE FALSE 798176.1378 847703.0018 827607.3651 874181.7176 801664.4948 751912.1832 792857.0942 818603.3155 872448.8786 0.914868662 0.971636302 0.948602704 1.001986178 0.918867013 0.861840965 0.908771979 0.938282271 1 19.73471107 2.512684256 23.97037415 0.913140257 0.959642604 0.107246757 0.04067602 488.8462138 329494.1083 0.011952139 0.011263396 325.5998951 -2.512684256 0.046502348 KS(ph)SPSKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSSPSKDR 8 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 KS(0.59)S(0.403)PS(0.007)KDR;KS(0.469)S(0.265)PS(0.265)KDR 91.701 0.0064181 311010000 1068070 479830 854110 774500 654860 533990 868150 633010 847030 TRUE FALSE 1001221.405 515357.1125 874369.8925 794374.9812 603429.9372 688144.2444 737978.967 712042.6919 705655.221 1.418853536 0.730324239 1.239089383 1.125726782 0.855134234 0.975184798 1.045806713 1.00905183 1 19.42860394 2.787871478 24.99228597 0.985156607 1.080567927 0.126709585 0.178185674 1136.992021 576260.8259 0.05201563 0.055170823 613.5803994 -2.787871478 0.09541132 KS(ph)SPSSPAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSSPSSPAVR 10 1 B3KNS5;Q8WVR3-2;Q8WVR3-3;Q8WVR3 B3KNS5 C7orf43 Uncharacterized protein C7orf43 1 KS(0.747)S(0.163)PS(0.09)SPAVR;KS(0.787)S(0.193)PS(0.013)S(0.006)PAVR 86.114 0.014595 52547000 179393 157158 158283 163809 181363 128069 212015 154994 188904 TRUE FALSE 168165.1124 168794.1418 162037.5475 168012.6163 167119.4816 165040.4413 180225.319 174345.3421 157374.702 1.068565088 1.072562106 1.029628939 1.067596088 1.061920877 1.048710111 1.145198794 1.107835884 1 17.26384412 1.782643984 25 1.100123548 1.057039977 0.04383482 0.038651946 111.7650601 63404.30766 0.015884921 0.008851069 60.62391563 -1.782643984 -0.043083571 KS(ph)SPSVKPAVDPAAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KSSPSVKPAVDPAAAK 16 2 Q6FI81-3;Q6FI81;H3BV90;H3BT65;H3BPG7 Q6FI81-3 CIAPIN1 Anamorsin 1 KS(0.612)S(0.388)PSVKPAVDPAAAK;KS(0.629)S(0.371)PSVKPAVDPAAAK;KS(0.482)S(0.482)PS(0.035)VKPAVDPAAAK 171.68 2.53E-09 5036500000 9500160 4468060 6566830 5657510 6280410 4802450 9533250 5286040 8051710 TRUE FALSE 8905561.944 4798879.811 6722598.309 5802691.285 5787171.933 6188839.354 8103827.665 5946013.73 6707827.585 1.327637276 0.715414902 1.002202013 0.865062677 0.862749058 0.922629462 1.208115081 0.886429124 1 22.67741418 1.913282915 25 1.057322895 0.921766182 0.024704912 0.175026763 158.4420527 45674.30796 0.065192074 0.042074076 81.89981398 -1.913282915 -0.135556713 KS(ph)SSLESLQTAVAEVTLNGDIPFHRPR ddPTM_SK-BR-3_Pertuzumab_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(0.313)S(0.313)S(0.313)LES(0.057)LQT(0.003)AVAEVTLNGDIPFHRPR 69.981 0.010167 15505000 11777 12147 10849 12201 11156 7852 14357 8195.4 9978.5 TRUE FALSE 11039.89859 13046.37652 11106.3434 12514.09832 10279.85276 10118.74493 12204.30113 9218.61373 8313.023886 1.328024404 1.569389995 1.336017261 1.505360563 1.236596081 1.21721591 1.468094078 1.108936274 1 13.02115764 0.359637137 0.258853625 0.878007592 1.493574082 0.539813319 0.120063292 3.474039251 0.485019206 0.645403725 0.214241761 2.288954381 -0.359637137 0.61556649 KS(ph)SSLESLQTAVAEVTLNGDIPFHRPRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSSSLESLQTAVAEVTLNGDIPFHRPRPR 29 3 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 KS(0.322)S(0.322)S(0.322)LES(0.034)LQTAVAEVTLNGDIPFHRPRPR 145.36 4.41E-08 214950000 133900 147240 142640 138800 184560 117840 177020 130990 218340 TRUE FALSE 125519.438 158141.8028 146023.4882 142361.843 170065.4021 151858.495 150477.4944 147344.3898 181897.6435 0.690055328 0.869399954 0.802778339 0.782648089 0.934951101 0.834856858 0.827264672 0.810040125 1 17.47276733 -5 0.197415824 1.764681409 0.796026959 0.485595146 0.060347584 125.0922732 1.235204105 37.84965374 0.138800383 1.00E-05 5 -0.96865445 KS(ph)STPEEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KSSTPEEVK 9 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 1 KS(0.379)S(0.379)T(0.241)PEEVK;KS(0.567)S(0.285)T(0.148)PEEVK;KS(0.333)S(0.333)T(0.333)PEEVK 120.96 0.00038423 1567250000 2164239 1162937 1516808 1385002 1546223 1062793 1907738 1305058 1949797 TRUE FALSE 2028783.144 1249042.066 1552787.402 1420543.496 1424788.883 1369604.086 1621690.397 1467997.364 1624363.285 1.248971313 0.768942562 0.955936038 0.874523273 0.877136843 0.843163656 0.998354502 0.9037371 1 20.63144289 0.781520993 1.054390695 0.997354659 0.914539638 0.003791762 0.129241083 3.177362111 6.573950107 0.109614581 0.035051506 6.046735788 -0.781520993 -0.08281502 KS(ph)STSDWPTDNQDGWDGKQENEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSSTSDWPTDNQDGWDGKQENEER 24 2 A0A3B3IS53;A0A3F2YNX6;Q92794;A0A3B3ISZ3;A5PLL3 A0A3B3IS53 KAT6A;MYST3 Histone acetyltransferase KAT6A;Histone acetyltransferase 1 KS(0.489)S(0.489)T(0.011)S(0.011)DWPTDNQDGWDGKQENEER 127.63 4.35E-05 87407000 118840 74688 90350 115600 139680 74582 108870 82973 135560 TRUE FALSE 111402.0165 80217.97723 92493.14467 118566.4917 128710.0962 96112.61266 92545.9542 93332.3617 112934.1602 0.986433301 0.710307466 0.819000597 1.0498727 1.139691445 0.851049961 0.81946821 0.826431626 1 16.78512241 5.068778013 20.68796259 0.881573128 3.764161379 0.019661628 0.1291215 1725.817913 530759.1783 0.032137178 5122.655747 117159.6358 -5.068778013 2.882588251 KS(ph)STTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSSTTLR 7 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 KS(0.683)S(0.317)TTLR;KS(0.5)S(0.209)T(0.209)T(0.082)LR 98.033 0.0070807 318650000 364106 326255 357883 358437 347175 281836 370830 318534 362670 TRUE FALSE 341317.2554 350411.2597 366372.1538 367635.1003 319909.2759 363197.478 315227.4841 358303.6711 302138.0341 1.129673252 1.159772091 1.212598589 1.21677862 1.058818288 1.20209122 1.043322748 1.185893965 1 18.20484828 0.414642115 0.368060926 0.980798489 1.179814557 0.375624222 0.060564038 2.709582642 0.689767414 0.161936686 0.048274042 2.598017756 -0.414642115 0.199016067 KS(ph)STVATLQGTPDHGDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KSSTVATLQGTPDHGDPR 18 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 KS(0.572)S(0.323)T(0.104)VAT(0.001)LQGTPDHGDPR;KS(0.612)S(0.315)T(0.073)VATLQGTPDHGDPR;KS(0.627)S(0.354)T(0.019)VATLQGTPDHGDPR;KS(0.488)S(0.488)T(0.025)VATLQGTPDHGDPR;KS(0.574)S(0.319)T(0.107)VATLQGTPDHGDPR 219.23 4.56E-19 11323130000 8210290 8025290 7705750 6985480 9388700 5564090 11629000 10446100 18488200 TRUE FALSE 7696422.605 8619490.822 7888534.029 7164739.243 8651349.374 7170352.458 9885339.408 11750318.58 15402399.98 0.499689828 0.559619983 0.512162652 0.465170314 0.561688398 0.465534752 0.641805136 0.762888809 1 23.87665183 1.066604768 1.422322693 0.996814407 0.515541211 0.947806657 0.037685592 0.076014932 0.311242578 0.032412661 0.009757751 11.65748239 -1.066604768 -0.481273196 KS(ph)SVNGSSATSSG ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSSVNGSSATSSG 13 1 R4GMX3;P35226 R4GMX3 COMMD3-BMI1;BMI1 Polycomb complex protein BMI-1 1 KS(0.5)S(0.5)VNGS(0.001)SATSSG;KS(0.646)S(0.354)VNGSSATSSG 95.854 0.0047724 662930000 862780 788610 809200 1026160 1208810 707610 854100 673100 1098060 TRUE FALSE 808780.1399 846999.5049 828394.6061 1052493.003 1113874.939 911885.5199 726035.6341 757138.0167 914786.6923 0.88411883 0.925898367 0.905560403 1.150533793 1.217633518 0.996828581 0.793666589 0.82766619 1 19.80307585 1.755961268 25 0.855287398 1.004010229 0.233646488 0.116821427 10.16982431 14627.00645 0.058013155 0.032171639 57.01134251 -1.755961268 0.148722831 KS(ph)SWPSQAAPSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSSWPSQAAPSLR 13 1 P0DO92 P0DO92 1 KS(0.5)S(0.5)WPS(0.001)QAAPSLR 41.644 0.086325 146090000 101370 124280 110060 101580 127790 63259 77506 111960 58832 TRUE FALSE 95025.43265 133481.8205 112670.6752 104186.7148 117753.8889 81520.84638 65884.69483 125938.4525 49012.55913 1.938797613 2.723420749 2.298812328 2.125714646 2.402524801 1.663264433 1.344241068 2.56951391 1 15.58086386 2.234335056 23.29710711 1.637377675 2.348192105 0.351856725 0.437799359 44.36484181 244593.3426 0.146518542 0.112248888 171.5280128 -2.234335056 0.710814431 KS(ph)T(ph)SHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSTSHGK 7 1 Q8WWL7 Q8WWL7 CCNB3 G2/mitotic-specific cyclin-B3 2 KS(0.647)T(0.705)S(0.647)HGK 59.757 0.087951 128630000 140010 240140 261230 239600 234620 242380 230470 230490 224890 TRUE FALSE 131247.024 257920.2155 267426.499 245748.5416 216193.8916 312351.1713 195913.1631 259267.1839 187354.4062 0.700528089 1.376643447 1.427383025 1.311677407 1.153930116 1.66716747 1.045682176 1.383832861 1 17.51541038 -1.20342651 3.38637985 0.999458612 1.283143815 0.083088001 0.258306245 211537083.2 323353869.7 1274077.426 0.055753664 0.062599878 1.20342651 0.283685203 KS(ph)TAALEEDAQILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.746)T(0.254)AALEEDAQILK;KS(0.5)T(0.5)AALEEDAQILK;KS(0.942)T(0.058)AALEEDAQILK 217.82 3.44E-12 389193000 1022035 755398 826366 782531 1124750 382049 1030856 712936 1649600 TRUE FALSE 958067.6537 811328.4539 845967.7918 802612.0703 1036416.672 492340.3443 876288.7128 801947.629 1374271.103 0.697146037 0.590370017 0.615575624 0.584027466 0.754157364 0.358255619 0.637638899 0.58354398 1 20.3902352 -1.247383406 6.053329873 1.000011162 0.598601318 0.598751794 0.102194659 1.36E-05 1.69E-06 0.087242138 0.020562598 0.056573962 1.247383406 -0.401409844 KS(ph)VKEDSVPTGAEENVVCESPVEIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSVKEDSVPTGAEENVVCESPVEIIK 26 2 O75363 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 KS(0.819)VKEDS(0.152)VPT(0.029)GAEENVVCESPVEIIK 82.157 0.0083446 49552000 95762 33975 49722 38265 49869 28745 52133 22984 99316 TRUE FALSE 89768.42736 36490.54435 50901.42932 39246.94468 45952.4899 37043.21486 44316.14063 25853.60299 82739.51799 1.084952264 0.441029211 0.615200941 0.474343405 0.55538745 0.447708855 0.535610331 0.312469828 1 16.33628893 -1.20275269 4.864238123 1.000060297 0.544697702 0.313703785 0.2044168 0.000116916 1.92E-05 0.173118744 0.040799096 0.062697079 1.20275269 -0.455362595 KS(ph)YSTSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSYSTSLK 8 1 A0A0B4J2B6 A0A0B4J2B6 IGHV2OR16-5 1 KS(0.836)Y(0.034)S(0.043)T(0.043)S(0.043)LK 64.836 0.040321 277880000 192810 773700 544650 617840 859200 554400 440290 615450 640160 TRUE FALSE 180742.3663 830985.553 557569.3552 633694.8204 791721.8978 714446.2801 374272.602 692290.2873 533313.1604 0.338904756 1.558156848 1.045482086 1.188222732 1.48453471 1.339637446 0.701787673 1.298093388 1 19.0246234 1.761865263 25 0.972225899 1.205711462 0.029170288 0.361682401 31.92686281 34275.1236 0.151951263 0.084268168 57.79167241 -1.761865263 0.233485562 KSADTLWGIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSADTLWGIQK 11 1 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 122.35 0.0006296 1789030000 3400400 6411800 2911500 2871700 7194200 1962040 3044600 5136000 5333600 FALSE TRUE 3187575.034 6886536.343 2980562.155 2945392.684 6629196.552 2528449.097 2588090.495 5777240.906 4443387.704 0.71737495 1.549839177 0.670785975 0.662870962 1.491923954 0.569036345 0.582458851 1.300188345 1 22.0832286 3.897547879 7.588855363 0.85866276 1.181636176 0.056865682 0.365292072 0.480339335 39.80816757 0.088028786 0.159768072 7898.559232 -3.897547879 0.322973416 KSAEPSANTTLVS(ph)ETEEEGSVPAFGAAAK ddPTM_SK-BR-3_Pertuzumab_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(0.999)ET(0.001)EEEGSVPAFGAAAK;KSAEPSANT(0.001)T(0.002)LVS(0.996)ET(0.001)EEEGSVPAFGAAAK;KSAEPSANTTLVS(0.852)ET(0.147)EEEGSVPAFGAAAK;KSAEPSANTTLVS(0.998)ET(0.001)EEEGSVPAFGAAAK 315.86 2.01E-92 5180460000 3722510 2264740 2800160 2532140 2930980 2043080 3497560 2866150 2819130 TRUE FALSE 3489524.744 2432423.706 2866581.118 2597118.999 2700792.654 2632884.029 2973133.348 3223995.137 2348598.991 1.485789936 1.03569137 1.220549412 1.10581628 1.149959046 1.12104452 1.265917834 1.372731211 1 21.16336897 1.71178978 10.6205781 1.238699574 1.168533783 0 0.150273392 0.373388265 98.87515351 0.063323411 0.034377358 51.49793084 -1.71178978 -0.070165791 KSATVKPGAVGAGEFVS(ph)PCES(ph)GDNTGEPSALEEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSATVKPGAVGAGEFVSPCESGDNTGEPSALEEQR 35 2 Q12888;Q12888-2;A6NNK5 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 KSATVKPGAVGAGEFVS(1)PCES(0.997)GDNT(0.003)GEPSALEEQR 124.88 2.56E-08 85915000 138080 96143 112450 108870 139470 94108 167030 120930 210420 TRUE FALSE 129437.8193 103261.5278 115117.3671 111663.7885 128516.5888 121275.4519 141985.4021 136028.3767 175299.5426 0.738380816 0.589057599 0.656689489 0.636988476 0.733125637 0.691818416 0.809958771 0.775976792 1 17.41946271 0.973286937 0.488829535 1.009040282 0.634423104 0.828868335 0.047047448 0.367165759 0.221414748 0.051879381 0.024940446 9.403443883 -0.973286937 -0.374617178 KSATVKPGAVGAGEFVS(ph)PCESGDNTGEPSALEEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSATVKPGAVGAGEFVSPCESGDNTGEPSALEEQR 35 2 Q12888;Q12888-2;A6NNK5 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 KSATVKPGAVGAGEFVS(1)PCESGDNTGEPSALEEQR;KSATVKPGAVGAGEFVS(1)PCESGDNTGEPSALEEQR 291.05 2.69E-90 300260000 151206 114060 136237 149786 167675 103577 180831 139797 226790 TRUE FALSE 141742.2864 122505.1211 139468.606 153629.7623 154506.4819 133477.9985 153717.0703 157250.9632 188937.2839 0.75020813 0.6483904 0.738174081 0.813125706 0.817765973 0.706467224 0.813587806 0.832291859 1 17.5275479 -5 0.108151818 1.829491948 0.602104191 0.755059439 0.046380171 79.55686063 0.57501677 14.48991817 0.610015412 1.00E-05 5 -1.227387757 KSCHTAVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSCHTAVGR 9 1 P02787;H7C5E8 P02787 TF Serotransferrin 0 74.684 0.026222 148320000 63136 158090 109610 138680 202220 132450 127430 140600 191080 FALSE TRUE 59184.43046 169795.1481 112210.001 142238.7636 186338.4569 170686.1649 108323.0545 158154.2195 159187.5136 0.371790658 1.066636097 0.704891976 0.893529652 1.170559504 1.072233374 0.680474568 0.99350895 1 17.28036765 4.748083194 24.42809231 0.922561062 0.371790251 0.565644714 0.15724065 758.4657709 1945621.907 0.037633869 0.47702409 55986.48391 -4.748083194 -0.550770811 KSCTLYVGNLSFYTTEEQIYELFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSCTLYVGNLSFYTTEEQIYELFSK 25 1 P52298-2;P52298 P52298-2 NCBP2 Nuclear cap-binding protein subunit 2 0 133.95 8.84E-05 37808000 28650 28652 19017 21414 33166 17099 25400 26387 25183 FALSE TRUE 26856.84764 30773.42389 19468.09222 21963.51949 30561.27615 22035.20372 21591.5058 29681.47503 20979.79461 1.280129198 1.466812448 0.927944843 1.046889157 1.456700445 1.050305979 1.029157158 1.414764805 1 14.35671293 4.054251336 6.121766324 1.127236135 1.368829492 0.239182007 0.178492944 0.290435438 17.99851086 0.042132937 0.092272379 11330.55899 -4.054251336 0.241593357 KSCVEEPEPEPEAAEGDGDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSCVEEPEPEPEAAEGDGDKK 21 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 134.29 4.77E-06 147370000 376290 114890 171080 174710 183360 116820 251520 137730 222950 FALSE TRUE 352738.6806 123396.5751 175138.0984 179193.3544 168959.6452 150544.0376 213806.911 154925.8937 185738.2047 1.89911753 0.664357531 0.942929855 0.964763037 0.909665545 0.810517351 1.151119724 0.834108922 1 17.50291107 4.747433127 24.90074773 0.910526306 1.899118067 0.856054808 0.127507583 412.5533588 1157807.027 0.031042318 0.374765151 55902.74417 -4.747433127 0.98859176 KSDGACDS(ph)PS(ph)SDKENSSQIAQDHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSDGACDSPSSDKENSSQIAQDHQK 25 2 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 2 KSDGACDS(0.999)PS(0.621)S(0.379)DKENSSQIAQDHQK 112.8 0.0011946 320730000 405070 122420 191480 167210 169320 122010 320830 119210 232380 TRUE FALSE 379717.3918 131484.1042 196021.996 171500.8917 156022.2902 157232.3063 272724.5199 134093.6309 193594.2768 1.961408148 0.679173508 1.012540243 0.885877902 0.805924084 0.812174352 1.408742678 0.692652867 1 17.56267678 4.747343265 24.91353773 0.932916024 1.961408698 0.713133409 0.208774497 633.2413541 1796260.426 0.050175003 0.599343424 55891.17822 -4.747343265 1.028492674 KSDGACDS(ph)PSS(ph)DKENSSQIAQDHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSDGACDSPSSDKENSSQIAQDHQK 25 2 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 2 KS(0.001)DGACDS(0.999)PS(0.162)S(0.833)DKENS(0.003)S(0.003)QIAQDHQK 97.257 0.0045847 240880000 663500 184780 317940 263290 248950 176640 469990 199880 384170 TRUE FALSE 621972.7194 198461.3035 325481.6869 270046.4671 229398.4712 227633.1005 399519.3627 224835.458 320049.5452 1.94336386 0.620095565 1.016972815 0.843764571 0.716759248 0.711243318 1.248304735 0.702502039 1 18.28793573 4.746873729 24.92363339 0.871123148 1.943364416 0.764885854 0.189071889 499.0558729 1496189.861 0.044152204 0.506649054 55830.78438 -4.746873729 1.072241268 KSDGACDS(ph)PSSDKENSSQIAQDHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSDGACDSPSSDKENSSQIAQDHQK 25 2 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 KS(0.009)DGACDS(0.955)PS(0.018)S(0.018)DKENSSQIAQDHQK 81.532 0.011305 140970000 152440 46274 80429 64733 74802 54334 116490 58970 115850 TRUE FALSE 142899.0525 49700.17511 82336.81386 66394.15837 68927.35266 70019.34376 99023.40594 66332.53431 96513.88658 1.480606134 0.514953618 0.853108467 0.687923373 0.714170314 0.725484656 1.02600164 0.687284873 1 16.55844891 -0.280352743 7.21719791 1 0.811891951 0.029430666 0.264743831 0 226795249.1 0.227532636 0.055184767 0.524381374 0.280352743 -0.188108049 KSDGACDSPSSDKENSSQIAQDHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSDGACDSPSSDKENSSQIAQDHQK 25 2 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 0 67.413 0.02616 48605000 54249 28835 36976 33211 29138 23626 46902 26182 42156 FALSE TRUE 50853.65193 30969.9734 37853.08818 34063.25049 26849.61902 30446.44266 39869.48052 29450.88033 35119.89126 1.448001406 0.881835686 1.077824755 0.969913324 0.764513159 0.866928728 1.135239293 0.838581194 1 15.10000076 4.743776243 24.9523011 0.955134463 1.448001617 0.667371081 0.111950442 343.8097866 1644782.393 0.02639556 0.22389504 55434.00323 -4.743776243 0.492867154 KSDGIYIINLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSDGIYIINLK 11 1 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 158.01 0.0022258 0 7870600 6780100 6808900 6445100 7805100 5593500 8023400 6993000 6280700 FALSE TRUE 7377993.195 7282105.659 6970410.323 6610492.178 7192118.93 7208252.647 6820365.656 7866091.443 5232410.595 1.410056237 1.391730547 1.332160425 1.263374129 1.374532598 1.377616018 1.303484413 1.503339866 1 22.31904433 -1.878297306 2.801831532 0.835278433 1.361211039 0.762128111 0.064732654 11131412.97 5900825.883 12089256.38 0.014362627 0.013234352 1.878297306 0.525932606 KSDGIYIINLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSDGIYIINLKR 12 2 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 110.29 0.00084674 364090000 457250 651540 540980 588470 920550 436830 798540 580940 1272850 FALSE TRUE 428631.5387 699780.6995 553812.3011 603571.1365 848253.7163 562935.7297 678806.3403 653471.6378 1060403.112 0.404215655 0.659919508 0.52226582 0.569190273 0.799935144 0.530869556 0.640139898 0.616248321 1 20.01618138 -5 0.214182346 2.97556835 0.541976489 0.646803829 0.097550696 90.85186393 0.907747507 77.22583559 0.181378716 1.00E-05 5 -2.433591861 KSDIDEIVLVGGSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KSDIDEIVLVGGSTR 15 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;; 234.77 1.86E-17 2756160000 6172790 5953890 5490110 5628760 6225890 3737510 7824880 5154970 5623780 FALSE TRUE 5786446.093 6394722.211 5620338.002 5773203.511 5736933.713 4816468.464 6651611.887 5798579.352 4685134.787 1.235065021 1.364896103 1.199610739 1.23223851 1.224497047 1.028031995 1.4197269 1.237654756 1 22.15965912 -1.79433001 2.307522347 0.915577621 1.251855134 0.351441517 0.102957542 7961443.92 4818701.359 3764451.779 0.026179862 0.016057206 1.79433001 0.336277514 KSDIYVCMISFAHNVAAQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSDIYVCMISFAHNVAAQGK 20 1 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 192.6 6.74E-18 338220000 284450 361030 357180 322490 428910 251960 400750 362170 504510 FALSE TRUE 266646.7823 387761.0369 365652.4783 330765.6394 395225.1387 324696.7618 340661.2579 407387.7217 420304.0217 0.634414063 0.922572749 0.8699714 0.786967581 0.940331565 0.772528325 0.810511535 0.96926915 1 18.68107374 -4.999999994 0.173588371 1.632463901 0.807692733 0.298428679 0.091842058 197.8438163 1.882340764 42.89582513 0.298255913 1.00E-05 4.999999994 -0.824771168 KSDLFQEDLYPPTAGPDPALTAEEWLGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KSDLFQEDLYPPTAGPDPALTAEEWLGGR 29 1 P31146 P31146 CORO1A Coronin-1A 0 ;; 147.41 8.30E-08 384900000 567580 561500 563970 567600 600150 477730 702190 523190 591580 FALSE TRUE 532056.181 603074.0442 577347.6347 582165.5769 553016.6399 615642.8957 596903.1283 588511.4232 492841.4762 1.079568597 1.223667393 1.171467221 1.181243067 1.122098416 1.249170221 1.211146296 1.194119106 1 18.91076415 -1.590052235 6.459493162 0.99958224 1.185772426 0.564290353 0.049134279 0.000270844 1.72E-05 0.043589179 0.010251412 0.025700866 1.590052235 0.186190186 KSDPVVSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KSDPVVSYR 9 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;; 101.48 0.0063391 1312150000 454165 641870 580743 671310 776670 555171 801070 670910 788640 FALSE TRUE 425739.6234 689394.7227 594518.4982 688536.9511 715673.4711 715439.8553 680956.9903 754674.5904 657010.8892 0.647994775 1.049289645 0.904883782 1.047984078 1.089287077 1.088931503 1.036447038 1.148648527 1 19.32555776 4.739629447 24.82763964 1.037395053 0.64799464 0.791276632 0.06406443 40.00109655 929043.3689 0.016027655 0.098473283 54907.21888 -4.739629447 -0.389400413 KSDSDMWINQSSSLDSSTSS(ph)QEHLNHSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSDSDMWINQSSSLDSSTSSQEHLNHSSK 29 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 KSDSDMWINQSSSLDS(0.001)S(0.002)T(0.009)S(0.042)S(0.926)QEHLNHS(0.016)S(0.004)K 144.18 2.55E-08 258290000 68340 115210 103940 107290 130570 94367 161090 127940 134650 TRUE FALSE 64062.72139 123740.2683 106405.5059 110043.243 120315.5589 121609.221 136936.05 143913.5906 112176.0451 0.571090925 1.103089952 0.948558186 0.980987009 1.072560178 1.084092605 1.22072453 1.28292623 1 16.7754051 4.739846557 24.90224957 1.084181418 0.57109075 0.713661407 0.102613287 63.22298231 1224173.067 0.026520251 0.164338247 54934.67473 -4.739846557 -0.513090668 KSDVEAIFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSDVEAIFSK 10 1 B4DY08;G3V4W0;G3V5X6;G3V3K6;G3V251;B4DSU6;G3V4M8;G3V2H6;P07910;G3V2Q1;G3V576;G3V555;G3V575;P07910-2;G3V4C1;B2R5W2;P07910-4;A0A0G2JNQ3;O60812;B2RXH8;A0A0G2JPF8;P0DMR1;B7ZW38 B4DY08;P07910;P07910-2 HNRNPC;HNRNPCL1;HNRNPCL2;HNRNPCL4;HNRNPCL3 Heterogeneous nuclear ribonucleoproteins C1/C2;Heterogeneous nuclear ribonucleoprotein C-like 1;Heterogeneous nuclear ribonucleoprotein C-like 2;Heterogeneous nuclear ribonucleoprotein C-like 4;Heterogeneous nuclear ribonucleoprotein C-like 3 0 ; 127.56 0.00056584 4000900000 14838800 12860300 13464900 12459800 18000000 9819100 16744400 14060500 22266300 FALSE TRUE 13910066 13812489.99 13784293.79 12779539.56 16586352.61 12653714.77 14233732.67 15815984.38 18549910.68 0.749872397 0.74461221 0.743092192 0.688927283 0.894147303 0.682144242 0.767320819 0.852617818 1 24.1449089 0.953278587 2.332994565 0.99925972 0.749953693 0.66301938 0.057101601 0.180133239 2.185130952 0.04828336 0.013151326 8.98004653 -0.953278587 -0.249306027 KSDVETIFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSDVETIFSK 10 1 Q9UKM9;Q9UKM9-2;Q5QPM1;Q5QPL9;Q5QPM2 Q9UKM9 RALY RNA-binding protein Raly 0 ; 134.99 0.00025021 1100070000 1938210 1487130 1672330 1608180 2036370 1204480 2117100 1705980 2381100 FALSE TRUE 1816900.896 1597238.653 1711998.457 1649448.621 1876441.715 1552193.823 1799660.509 1918975.358 1983679.028 0.91592484 0.805190069 0.863042072 0.831509835 0.945940189 0.782482348 0.907233723 0.967381987 1 20.91974718 1.317510697 2.771066625 0.992733938 0.853970763 0.533693038 0.048328096 0.181315707 2.29285305 0.037442756 0.011245655 20.77354891 -1.317510697 -0.138763175 KSDYIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSDYIK 6 1 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ; 95.541 0.069313 4041300000 6054400 6336000 5559000 5818800 7112100 3975800 7574600 6214000 4719100 FALSE TRUE 5675465.911 6805124.033 5690862.105 5968120.259 6553544.355 5123548.918 6438859.049 6989831.579 3931451.723 1.443605648 1.730944321 1.447521808 1.518044905 1.666952774 1.303220611 1.637781538 1.777926341 1 21.90663071 -1.347088734 3.704332026 0.997853404 1.565213185 0.602331956 0.144466611 7774914.527 5835276.023 124051.9569 0.030901033 0.044968797 1.347088734 0.567359781 KSEAPAEVTHFS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSEAPAEVTHFSPK 14 1 Q6PID6 Q6PID6 TTC33 Tetratricopeptide repeat protein 33 1 KSEAPAEVTHFS(1)PK;KSEAPAEVTHFS(1)PK 118.52 0.00011305 350170000 864730 521090 606750 640910 736110 476680 779310 582940 1018160 TRUE FALSE 810608.0929 559672.0458 621142.3965 657356.8357 678298.8899 614289.7777 662459.7003 655721.3422 848222.5184 0.955655002 0.659817481 0.732287086 0.77498159 0.79967093 0.724208288 0.78099754 0.773053448 1 19.69408326 -0.436593588 0.729486241 1.017589892 0.756788455 0.446057143 0.076837082 10.73016683 4.29526553 0.593486333 0.024889629 0.365937074 0.436593588 -0.260801437 KSEAPSGESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 153.34 2.63E-05 783380000 1380410 1372590 1421390 1401670 1576970 1229710 1706650 1405080 1634960 FALSE TRUE 1294012.602 1474217.992 1455106.042 1437639.225 1453121.137 1584707.314 1450753.676 1580507.331 1362074.614 0.950030629 1.082332772 1.068301272 1.055477586 1.066844006 1.163451178 1.065105877 1.160367659 1 20.3773743 4.739007137 6.265267226 1.085052994 0.946898762 0.42724114 0.048232655 0.110734289 23.69749492 0.010222079 0.064963097 54828.59747 -4.739007137 -0.138154232 KSEEEIDFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KSEEEIDFLR 10 1 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ;;; 161.99 1.11E-05 2063140000 3606520 3630940 3676570 3782950 4347310 2901180 4831680 3789720 5133380 FALSE TRUE 3380794.351 3899778.576 3763779.977 3880026.902 4005889.809 3738703.569 4107214.439 4262874.884 4276585.715 0.790535856 0.911890661 0.880089919 0.9072721 0.936702799 0.874226268 0.960395678 0.996793977 1 22.02802803 8 0.11112738 1.051293406 0.396519318 0.680338805 0.035172602 64.84212849 0.50176135 0.291093257 6.521196028 99999999.99 -8 -0.654774088 KSEESYNVNDYSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSEESYNVNDYSLR 14 1 Q96DR7;Q96DR7-4 Q96DR7 ARHGEF26 Rho guanine nucleotide exchange factor 26 0 25.178 0.097263 84836000 15854 23021 22791 20318 27233 17833 18458 19725 17445 FALSE TRUE 14861.72644 24725.49879 23331.61328 20839.39428 25094.23003 22981.09761 15690.39426 22187.70967 14533.3168 1.022597019 1.701297724 1.605388061 1.433904907 1.726669168 1.581269983 1.079615512 1.526679008 1 13.82707637 1.750943167 24.99994586 1.222880726 1.549769884 0.262158936 0.238553456 4.251832109 8598.182967 0.10004711 0.055481165 56.35639019 -1.750943167 0.326889158 KSEGLITSENEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSEGLITSENEK 12 1 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 0 83.692 0.017037 0 211530 169180 193140 189540 198920 130560 196260 158800 219800 FALSE TRUE 198290.7149 181706.2632 197721.372 194403.9173 183297.6256 168250.5525 166832.635 178626.5296 183113.96 1.082881474 0.992312455 1.079772247 1.061655361 1.001003012 0.918829741 0.91108638 0.975493783 1 17.48238226 2.450183705 3.905420708 0.940017849 1.047396987 0.632954197 0.036198964 0.127717577 4.310047627 0.012441102 0.010603428 281.9575351 -2.450183705 0.107379138 KSEIEYYAMLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSEIEYYAMLAK 12 1 E5RI99;P62888 E5RI99 RPL30 60S ribosomal protein L30 0 ; 184.98 2.19E-05 4344300000 13004700 13133500 12336300 12202100 14523300 8534300 14660100 12798800 13184400 FALSE TRUE 12190759.04 14105918.01 12628922.86 12515226.54 13382698.6 10998013.87 12461954.1 14396758.35 10983838.47 1.109881494 1.284243031 1.149773178 1.139421941 1.218399073 1.001290569 1.134571866 1.310721967 1 23.38887898 3.651347486 4.319077128 1.135783621 1.211846198 0.05771648 0.099786273 0.479511354 16.81449441 0.024875516 0.040288972 4480.716699 -3.651347486 0.076062576 KSES(ph)DKDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSESDKDVK 9 2 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 KS(0.01)ES(0.99)DKDVK 89.46 0.0063094 256450000 780880 215250 354720 322490 306730 208730 420970 246130 427230 TRUE FALSE 732006.1147 231187.334 363134.1259 330765.6394 282640.6631 268986.9626 357849.4566 276859.8723 355922.553 2.05664437 0.64954393 1.020261635 0.929319136 0.794107203 0.755745766 1.005413828 0.777865493 1 18.44120383 4.745035463 24.99997 0.868447739 2.056644902 0.901749527 0.123455286 205.8453687 794766.6878 0.027693905 0.264301561 55594.96528 -4.745035463 1.188197163 KSESEVEEAAAIIAQRPDNPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSESEVEEAAAIIAQRPDNPR 21 2 Q16643;Q16643-3;Q16643-2;D6R9W4;D6R9Q9 Q16643 DBN1 Drebrin 0 ; 171.07 4.15E-12 272170000 394640 353800 358040 365050 385360 289860 451810 326810 349660 FALSE TRUE 369940.1869 379995.7201 366532.8779 374417.801 355095.3801 373537.8765 384065.2849 367612.9479 291299.4871 1.269965116 1.304484687 1.258268188 1.285336287 1.219004481 1.2823156 1.318455067 1.261975953 1 18.15214364 0.949158111 23.32608784 1 1.279049256 0.913617736 0.026603517 2095.801918 961548.2026 0.025564373 0.006391093 8.895249035 -0.949158111 0.279049257 KSGVS(ph)SDNEDDDDEEDGNYLHPSLFASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSGVSSDNEDDDDEEDGNYLHPSLFASK 28 1 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 KS(0.025)GVS(0.487)S(0.487)DNEDDDDEEDGNYLHPSLFASK 181.38 6.56E-18 92185000 77040 100300 109350 104340 114350 76458 139850 110950 156780 TRUE FALSE 72218.20392 107726.3164 111943.8336 107017.541 105369.4123 98530.18341 118880.7908 124802.3517 130612.4052 0.552919945 0.824778598 0.857068925 0.819352043 0.806733573 0.754370791 0.910179938 0.955516833 1 16.9949324 7.659065627 0.122674879 1.043447615 8.59E-20 0.609785547 0.076500049 70.41737808 0.640182959 0.507957841 12.45659705 45610583.37 -7.659065627 -1.043447615 KSHS(ph)PVKRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSHSPVKRPR 10 3 P78549-3;P78549-2;P78549;H3BUV2;H3BRL9;A0A494C106;H3BPD5 P78549-3 NTHL1 Endonuclease III-like protein 1 1 KS(0.001)HS(0.999)PVKRPR;KSHS(1)PVKRPR 85.42 0.01017 2474300000 2578400 1795860 1991360 1941020 2461700 1204980 2273600 1870850 2480300 TRUE FALSE 2417022.547 1928827.343 2038596 1990829.859 2268368.012 1552838.165 1932694.787 2104429.741 2066321.907 1.169722171 0.933459272 0.986582 0.963465495 1.097780556 0.75149867 0.935330928 1.018442351 1 20.97863359 2.278782248 24.99990838 0.916419489 1.008027984 0.195138565 0.098408357 257.9628922 160336.8074 0.032018056 0.026787915 190.0125332 -2.278782248 0.091608496 KSKS(ph)PPKVPIVIQDDSLPAGPPPQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSKSPPKVPIVIQDDSLPAGPPPQIR 26 3 Q7Z422-5;Q7Z422;Q7Z422-4 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 KS(0.208)KS(0.792)PPKVPIVIQDDSLPAGPPPQIR;KS(0.116)KS(0.884)PPKVPIVIQDDSLPAGPPPQIR 263.91 3.17E-52 1019130000 1274400 652900 839320 821350 988270 576440 1150070 630850 1510620 TRUE FALSE 1194637.579 701241.3953 859229.0668 842427.2315 910655.2607 742848.8703 977627.6802 709613.0112 1258487.763 0.949264358 0.557209546 0.682747256 0.669396443 0.723610739 0.590271032 0.776827323 0.56386167 1 20.26325976 -1.633264335 2.782446333 1.03050682 0.679997709 0.414222541 0.115718979 29078762.71 27510957.02 6396289.736 0.025994914 0.023266747 1.633264335 -0.350509111 KSLDS(ph)DES(ph)EDEEDDYQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KSLDSDESEDEEDDYQQK 18 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 KS(0.003)LDS(0.997)DES(1)EDEEDDYQQK;KS(0.002)LDS(0.998)DES(1)EDEEDDYQQK;KS(0.003)LDS(0.997)DES(1)EDEEDDYQQK;KS(0.202)LDS(0.798)DES(1)EDEEDDYQQK;KS(0.011)LDS(0.989)DES(1)EDEEDDYQQK;KS(0.002)LDS(0.998)DES(1)EDEEDDYQQK;KS(0.022)LDS(0.978)DES(1)EDEEDDYQQK;KS(0.005)LDS(0.995)DES(1)EDEEDDYQQK 283.08 6.96E-39 13058590000 25049000 8935910 13541750 13751290 13750010 9471860 19521800 10652660 16171980 TRUE FALSE 23481227.8 9597534.074 13862966.7 14104171.38 12670139.68 12206232.22 16594687.32 11982668.05 13472772.06 1.742865365 0.712365208 1.028961719 1.046864841 0.940425595 0.905992632 1.231720335 0.889398855 1 23.68354338 4.751179287 24.75046027 0.976599514 1.742865919 0.771860001 0.132090418 901.8861979 1768937.361 0.032650699 0.581103535 56387.03867 -4.751179287 0.766266406 KSLDS(ph)DES(ph)EDEEDDYQQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KSLDSDESEDEEDDYQQKR 19 2 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 KSLDS(1)DES(1)EDEEDDYQQKR;KS(0.003)LDS(0.997)DES(1)EDEEDDYQQKR;KSLDS(1)DES(1)EDEEDDYQQKR 197.54 3.85E-15 3107070000 8634640 4234070 5116930 5927780 6875760 3299560 7881210 4436960 10862200 TRUE FALSE 8094213.296 4547564.948 5238305.996 6079896.871 6335765.545 4252089.408 6699495.726 4990924.223 9049228.648 0.894464447 0.502536197 0.57886768 0.671869074 0.700144266 0.469884183 0.740338872 0.551530348 1 23.10936339 -1.458115594 2.813711577 1.011198521 0.62502232 0.449378465 0.124871895 21054797.67 23122960.72 1851212.308 0.027602257 0.034824461 1.458115594 -0.386176201 KSLESINSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KSLESINSR 9 1 E5RI99;P62888;E5RJH3;A0A0C4DH44 E5RI99 RPL30 60S ribosomal protein L30 0 ;;;; 183.33 0.00010248 1891720000 1803590 2196100 2090180 2036370 2350130 1624870 2085980 1969500 2091390 FALSE TRUE 1690706.521 2358701.529 2139760.057 2088626.702 2165560.27 2093943.591 1773206.664 2215396.41 1742323.498 0.970374631 1.353767846 1.228107214 1.198759418 1.242915149 1.201811026 1.017725277 1.271518414 1 20.73258108 1.920192898 8.426341072 1.100568952 1.223787752 0.122965685 0.119410069 0.558164257 54.5002089 0.046132041 0.029036501 83.21332933 -1.920192898 0.123218801 KSLPAPVAQRPDS(ph)PGGGLQAPGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSLPAPVAQRPDSPGGGLQAPGQK 24 2 Q5JVS0;Q5JVS0-2 Q5JVS0 HABP4 Intracellular hyaluronan-binding protein 4 1 KSLPAPVAQRPDS(1)PGGGLQAPGQK 274.99 2.76E-52 962220000 668370 520470 593150 556820 687410 482370 740590 615390 1074700 TRUE FALSE 626537.9148 559006.1403 607219.7981 571108.9439 633423.5915 621622.3884 629545.4048 692222.7961 895325.6272 0.69978776 0.624360706 0.678211122 0.637878473 0.707478455 0.694297549 0.703146862 0.773151996 1 19.77205296 0.347395464 0.589467549 1.014445439 0.65708495 0.945554667 0.024621399 0.429423124 0.228933264 0.034993582 0.009465767 2.225335333 -0.347395464 -0.357360489 KSLS(ph)DS(ph)ESDDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 KS(0.001)LS(0.996)DS(0.749)ES(0.253)DDS(0.001)K 139.6 3.94E-05 48863000 525860 180580 282230 284740 287900 188370 392740 227770 350370 TRUE FALSE 492947.3613 193950.3311 288924.6289 292046.9105 265289.4953 242749.3611 333852.283 256207.5859 291890.9835 1.688806401 0.664461535 0.989837457 1.000534196 0.908864988 0.831643918 1.143756751 0.877750942 1 18.15507012 4.751142689 24.99887569 0.928389466 1.688806876 0.783556849 0.125810717 978.0300871 1943178.8 0.030559686 0.549146599 56382.28718 -4.751142689 0.76041741 KSLS(ph)DSESDDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 KSLS(0.565)DS(0.435)ESDDSK;KSLS(0.776)DS(0.187)ES(0.037)DDSK;KS(0.003)LS(0.861)DS(0.105)ES(0.031)DDSK;KSLS(0.868)DS(0.077)ES(0.044)DDS(0.01)K;KS(0.002)LS(0.833)DS(0.105)ES(0.061)DDSK;KSLS(0.879)DS(0.076)ES(0.045)DDSK 220.27 1.25E-07 7112023000 12353410 5528197 7765798 7141928 7725537 5475822 10292150 6039083 9404384 TRUE FALSE 11580232.12 5937510.458 7950006.396 7325201.964 7118804.487 7056602.919 8748937.655 6793075.806 7834731.556 1.478063675 0.757844786 1.014713311 0.934965278 0.908621366 0.900682157 1.116686334 0.867046402 1 22.90145241 4.751096793 24.92611068 0.942583358 1.478064023 0.760726962 0.095226403 981.5421216 1951597.427 0.02268488 0.403687795 56376.32907 -4.751096793 0.535480665 KSLS(ph)PGVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSLSPGVSR 9 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 KSLS(0.993)PGVS(0.007)R 104.81 0.0017357 0 582230 650400 632410 589830 774630 523440 743090 744930 1085600 TRUE FALSE 545789.2636 698556.2927 647411.0638 604966.0364 713793.6845 674548.6307 631670.553 837936.1503 904406.3468 0.603477923 0.772392073 0.715840912 0.668909543 0.789240021 0.745846856 0.698436665 0.926504058 1 19.78661159 1.136887155 4.03370432 0.995660319 0.720646373 0.793677873 0.053391041 0.085683814 2.35144521 0.046103734 0.011981598 13.70525609 -1.136887155 -0.275013946 KSLSDS(ph)ESDDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 KSLS(0.339)DS(0.661)ESDDSK;KS(0.001)LS(0.254)DS(0.745)ESDDSK;KSLS(0.207)DS(0.793)ESDDSK;KSLS(0.083)DS(0.901)ES(0.016)DDSK 234.36 3.12E-16 8953900000 14657910 6461953 8891668 8431439 8932212 6280671 12229830 7027595 10727450 TRUE FALSE 13740497.58 6940402.724 9102582.564 8647803.999 8230712.1 8093798.76 10396080.53 7905005.705 8936969.293 1.537489626 0.776594671 1.018531257 0.96764392 0.920973524 0.905653639 1.163266896 0.884528686 1 23.09135424 4.750084465 24.99618985 0.961047826 1.537489967 0.769581882 0.100172252 883.8323264 1917070.501 0.024292999 0.388936247 56245.07038 -4.750084465 0.576442141 KSMS(ph)EDGGLQESNPCADDFVSASTADVSHTNLGTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSMSEDGGLQESNPCADDFVSASTADVSHTNLGTIR 36 1 H7C0I1;B8ZZW5;Q8NBF6-2;Q8NBF6;A0A1W2PRP5 H7C0I1 AVL9 Late secretory pathway protein AVL9 homolog 1 KS(0.425)MS(0.574)EDGGLQESNPCADDFVSASTADVSHTNLGTIR 121.01 7.25E-07 146020000 36228 32928 39990 47273 39756 20198 24887 13948 22989 TRUE FALSE 33960.55415 35366.02338 40938.58168 48486.10521 36633.72413 26028.83471 21155.42539 15689.4385 19151.98739 1.77321306 1.846598093 2.137563108 2.531648765 1.912789696 1.359067035 1.104607316 0.819206811 1 14.22520649 2.07811464 2.138608608 0.978115041 2.060340449 0.845830347 0.211765177 0.127091031 1.117713085 0.119064556 0.067980583 119.7056474 -2.07811464 1.082225408 KSNLDEEVNVIPPHT(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KSNLDEEVNVIPPHTPVR 18 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR 124.86 2.36E-05 1554670000 1136220 1141880 1116230 1087890 1165910 829560 1699550 1155350 1476720 TRUE FALSE 1065106.018 1226425.983 1142707.503 1115807.099 1074344.132 1069040.505 1444718.255 1299597.991 1230245.892 0.865766775 0.996895004 0.928844803 0.906978927 0.873275935 0.868964905 1.174332924 1.056372551 1 20.23051527 1.746026578 25 1.088819494 0.918448041 0.654385415 0.057650519 0.960676382 3225.881025 0.025958252 0.014395242 55.72198484 -1.746026578 -0.170371454 KSNS(ph)PGTASSGSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KSNSPGTASSGSSR 14 1 Q96GY0;H0YAP0 Q96GY0 ZC2HC1A Zinc finger C2HC domain-containing protein 1A 1 KS(0.062)NS(0.937)PGTASSGSSR;KS(0.025)NS(0.972)PGT(0.002)ASSGSSR;KS(0.034)NS(0.966)PGTASSGSSR 116.09 0.00023377 257218000 244920 242132 235251 229589 296653 185501 273704 189534 346616 TRUE FALSE 229590.8944 260059.7052 240831.2648 235480.6424 273355.07 239052.1273 232664.6261 213197.7371 288763.5504 0.795082669 0.900597409 0.834008532 0.815479108 0.946639802 0.827847306 0.805727128 0.738312494 1 18.13952912 -0.137321648 7.84201779 0.999999999 0.839253024 0.455391437 0.057039795 7220185.598 920705.1205 0.053129032 0.012885683 0.728917458 0.137321648 -0.160746975 KSPS(ph)SDSWTCADTSTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSPSSDSWTCADTSTER 17 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;H0YIQ0 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 KS(0.318)PS(0.587)S(0.095)DSWTCADTSTER;KS(0.008)PS(0.885)S(0.107)DSWTCADTSTER 196.1 9.99E-12 994940000 520100 430790 437140 497480 449330 336440 503510 342720 355110 TRUE FALSE 487547.8694 462686.1398 447509.1672 510246.179 414041.4343 433564.7664 428013.3499 385509.3464 295839.8469 1.648012851 1.563975052 1.512673739 1.724737842 1.399545865 1.465538773 1.446773835 1.303101494 1 18.17445686 0.702506854 0.466650748 0.966400571 1.598265796 0.849834098 0.077336762 0.549266004 0.259966083 0.10975551 0.043512427 5.04088575 -0.702506854 0.631865225 KSPSDLWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSPSDLWK 8 1 Q02880;Q02880-2;P11388;P11388-2;P11388-3;P11388-4 Q02880;P11388 TOP2B;TOP2A DNA topoisomerase 2-beta;DNA topoisomerase 2-alpha 0 ; 105.4 0.0070485 821560000 1245590 1907060 1060690 1085010 2321500 717090 1600900 1917720 2589300 FALSE TRUE 1167630.745 2048260.707 1085850.068 1112853.194 2139178.754 924102.242 1360859.907 2157151.563 2157129.102 0.541289227 0.949530885 0.503377413 0.515895498 0.991678594 0.428394499 0.630866231 1.000010412 1 21.04068109 1.235500529 24.89821064 1.00000545 0.660571459 0.379548301 0.184928634 81.05006284 659398.528 0.144088728 0.042011908 17.19889437 -1.235500529 -0.339433991 KSPSGPVKS(ph)PPLSPVGTTPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSPSGPVKSPPLSPVGTTPVK 21 2 C9J4K0;Q9BVC5-2;Q9BVC5 C9J4K0 C2orf49 Ashwin 1 KS(0.186)PS(0.186)GPVKS(0.572)PPLS(0.056)PVGTTPVK 109.26 0.00015651 800240000 412780 217790 278390 293760 323920 191110 361690 250870 476780 TRUE FALSE 386944.8366 233915.3982 284993.5423 301298.3789 298480.6298 246280.3546 307457.9423 282191.6717 397202.3379 0.974175627 0.588907405 0.717502177 0.758551373 0.751457384 0.620037525 0.774058743 0.710448164 1 18.59951459 -0.609010989 1.045571033 1.009802654 0.720844685 0.379603767 0.10387517 51.31258517 29.76271974 2.144875891 0.028119411 0.246030535 0.609010989 -0.28895797 KSRVS(ph)VS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSRVSVSPGR 10 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KS(0.108)RVS(0.892)VS(1)PGR;KS(0.008)RVS(0.993)VS(1)PGR 84.759 0.072317 2170890000 3425000 3567980 3540020 3819040 4242800 2545300 4071100 3150430 5327810 TRUE FALSE 3210635.364 3832156.952 3623990.946 3917043.032 3909587.603 3280086.791 3460676.349 3543768.12 4438564.092 0.723350006 0.863377631 0.816478228 0.882502303 0.880822609 0.73899728 0.779683762 0.798404179 1 22.0816616 -1.135978793 3.676376667 1.000112377 0.814206828 0.542126196 0.054648234 14379006.5 26521220.45 21545.25764 0.013074578 0.073117479 1.135978793 -0.185905548 KSS(ph)DSKPGVSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSSDSKPGVSSK 12 2 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 KS(0.014)S(0.979)DS(0.007)KPGVSSK 134.76 7.30E-05 373680000 577240 284710 424950 388220 431610 332260 526840 385260 924530 TRUE FALSE 541111.5788 305790.2246 435030.0147 398182.3825 397713.0916 428178.0682 447845.2329 433360.5591 770219.9703 0.702541611 0.397016744 0.564812692 0.516972291 0.516362996 0.555916601 0.581451079 0.562645187 1 19.554911 -1.172695241 0.445560306 1.2053095 0.519762123 0.775923975 0.075759393 8.5656826 1.009649989 2.214030651 0.037609931 0.067190018 1.172695241 -0.685547377 KSS(ph)GTGTEPVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KSSGTGTEPVAK 12 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9;A0A0U1RR74 Q6ULP2-7 AFTPH Aftiphilin 1 KS(0.491)S(0.509)GTGTEPVAK;KS(0.168)S(0.824)GT(0.009)GTEPVAK;KS(0.017)S(0.81)GT(0.017)GT(0.156)EPVAK;KS(0.003)S(0.974)GT(0.003)GT(0.02)EPVAK 186.72 6.98E-06 1638926000 2202950 1375170 1570660 1631070 1766730 1354270 2237900 1629260 3065660 TRUE FALSE 2065071.292 1476989.018 1607916.797 1672926.018 1627978.152 1745225.764 1902347.671 1832676.697 2553981.541 0.808569388 0.578308415 0.629572599 0.655026667 0.637427533 0.683335308 0.744855685 0.717576329 1 21.28431667 0.376539639 0.583191859 1.013255069 0.642597739 0.724135835 0.062498569 1.03148851 0.553476497 0.089426227 0.025084928 2.379795498 -0.376539639 -0.37065733 KSS(ph)HVGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSSHVGDR 8 1 Q01804-5;Q01804-3;Q01804 Q01804-5 OTUD4 OTU domain-containing protein 4 1 KS(0.201)S(0.799)HVGDR 65.842 0.038727 13884000 34524 28415 30745 30172 33604 25128 30982 31763 42797 TRUE FALSE 32363.20447 30518.87617 31474.28592 30946.2646 30964.87739 32382.04568 26336.53672 35728.68047 35653.90422 0.907704364 0.855975715 0.882772493 0.867962858 0.868484899 0.908232812 0.738671887 1.002097281 1 15.12177244 1.194868327 24.94786198 1.001049597 0.859764514 0.602519712 0.047140471 102.9432872 58777.22216 0.044345775 0.011086704 15.66276121 -1.194868327 -0.141285083 KSS(ph)LGNDETDKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KSSLGNDETDKEK 13 2 H7C1N2;J3KR05;O75128-2;O75128-3;O75128;O75128-7;A0A0J9YWK3;A0A3B3IU00;O75128-5;O75128-4 H7C1N2;O75128-3 COBL Protein cordon-bleu 1 KS(0.285)S(0.715)LGNDETDKEK;KS(0.017)S(0.982)LGNDETDKEK;KS(0.142)S(0.858)LGNDETDKEK 161.19 3.35E-05 905300000 1718740 561284 899540 809910 843240 564942 1219160 684490 1333920 TRUE FALSE 1611167.131 602842.0514 920877.5136 830693.6618 777015.3319 728031.5843 1036358.276 769950.0832 1111280.135 1.449829869 0.542475324 0.828663705 0.747510583 0.699207434 0.655128767 0.932580583 0.692849678 1 20.08379111 -0.331469428 13.050765 0.999999975 0.792194924 0.040979905 0.248368382 0 0 0.21048829 0.049612566 0.466155241 0.331469428 -0.207805051 KSS(ph)LLSEEQQETSTLVETIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSSLLSEEQQETSTLVETIR 20 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 KS(0.242)S(0.757)LLS(0.001)EEQQETSTLVETIR 199.37 8.96E-22 42091000 45726 40908 37153 36002 37391 28903 50069 38465 51443 TRUE FALSE 42864.09128 43936.87088 38034.2867 36925.87227 34454.46169 37246.8269 42561.61827 43267.43992 42856.83097 1.000169409 1.025201115 0.887473148 0.861609957 0.80394329 0.869098952 0.993111654 1.009580945 1 15.38723755 1.621713439 6.345993204 1.003510928 0.913503852 0.314418708 0.064476275 0.196150916 16.75921095 0.038886937 0.018859857 41.85173235 -1.621713439 -0.090007076 KSS(ph)LVTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.005)S(0.962)LVT(0.031)S(0.002)K;KS(0.143)S(0.857)LVTSK;KS(0.107)S(0.886)LVT(0.006)S(0.001)K;KS(0.049)S(0.921)LVT(0.028)S(0.003)K;KS(0.006)S(0.992)LVT(0.002)SK;KS(0.004)S(0.986)LVT(0.01)SK 155.99 0.00042386 16459640000 28004450 18637610 21108990 18612180 19869690 15588790 30029220 22027160 35815970 TRUE FALSE 26251701.46 20017558.04 21609705.21 19089800.05 18309204.7 20089020.61 25526617.24 24777299.41 29838053.23 0.879806107 0.670873461 0.724233081 0.639780347 0.613619279 0.673268476 0.855505453 0.830392627 1 24.83065007 1.269682621 1.334007498 0.979326349 0.695507406 0.587235783 0.079671901 0.262875245 0.903211154 0.070275873 0.02215076 18.60726835 -1.269682621 -0.283818943 KSS(ph)PSKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSSPSKDR 8 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 KS(0.178)S(0.519)PS(0.303)KDR 77.288 0.026463 159450000 688940 305920 567630 499300 468740 337920 578620 404100 554800 TRUE FALSE 645820.4752 328570.6351 581094.4517 512112.8833 431927.0512 435472.0183 491861.3026 454552.7745 462200.2959 1.397274041 0.710883654 1.257235136 1.107989086 0.934501893 0.942171656 1.064173492 0.983454097 1 18.81815866 2.748587685 24.42827548 0.991477478 1.073583448 0.099976818 0.177118114 1806.6691 4401463.31 0.052083302 0.054603235 560.5155756 -2.748587685 0.08210597 KSS(ph)PSTGSLDSGNESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSSPSTGSLDSGNESK 16 1 Q15057;A0A0U1RQT1;A0A087X1H5 Q15057 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 1 KS(0.174)S(0.507)PS(0.308)T(0.011)GSLDSGNESK;KS(0.209)S(0.695)PS(0.086)T(0.011)GSLDSGNESK 225.39 4.24E-15 881360000 1165450 633700 833730 768490 925040 621630 1177860 800700 1415000 TRUE FALSE 1092506.565 680619.8074 853506.4693 788210.7545 852391.0898 801084.4897 1001250.828 900669.1576 1178827.359 0.926774016 0.577370217 0.724030082 0.668639686 0.723083905 0.679560483 0.849361716 0.764038221 1 20.16892102 0.820405728 0.68989779 0.999174897 0.695788153 0.429422949 0.095431853 0.770194005 0.779305014 0.087069428 0.033148164 6.613109722 -0.820405728 -0.303386744 KSS(ph)TPEEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSSTPEEVK 9 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 1 KS(0.089)S(0.456)T(0.456)PEEVK 154.36 8.04E-05 130920000 506980 273270 347640 336810 359610 240000 443000 297810 408670 TRUE FALSE 475249.0268 293503.1951 355886.185 345453.1148 331367.6812 309284.1039 376576.2626 334992.2341 340460.3369 1.3959013 0.862077497 1.045308796 1.014664786 0.973293054 0.908429178 1.106079686 0.98393909 1 18.37712721 4.749983544 24.78656714 0.989919368 1.395901569 0.785690538 0.067141289 717.6976473 1557296.53 0.015880355 0.250013105 56232.00172 -4.749983544 0.405982201 KSS(ph)TTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KSSTTLR 7 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 KS(0.094)S(0.901)T(0.003)T(0.002)LR;KS(0.071)S(0.914)T(0.008)T(0.008)LR;KS(0.023)S(0.969)T(0.004)T(0.004)LR 101.38 0.0055746 1986610000 1656360 1307930 1413230 1435500 1391640 1063250 1533790 1247680 1404160 TRUE FALSE 1552691.384 1404770.498 1446752.483 1472337.36 1282346.208 1370193.015 1303812.429 1403455.594 1169796.625 1.327317374 1.200867286 1.236755563 1.258626781 1.096212949 1.171308743 1.114563336 1.199743241 1 20.1578263 4.543223128 0.025976961 3.73E-10 2.511369971 0.690439008 0.051021943 460.6068568 1.981744475 79.73156788 113.870512 34931.97395 -4.543223128 2.511369971 KSS(ph)VNGSSATSSG ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSSVNGSSATSSG 13 1 R4GMX3;P35226 R4GMX3 COMMD3-BMI1;BMI1 Polycomb complex protein BMI-1 1 KS(0.261)S(0.731)VNGS(0.008)SATSSG 83.511 0.010772 54848000 145830 133520 146190 184680 218930 122130 159240 127540 190720 TRUE FALSE 136702.7606 143405.9597 149657.6958 189419.2015 201736.1209 157386.9484 135363.4403 143463.6498 158887.5999 0.860374005 0.902562313 0.941909223 1.192158492 1.269678194 0.990555263 0.851944648 0.9029254 1 17.27764701 -1.340860685 2.882306683 1.000224957 0.98186857 0 0.138600586 45338310.77 56308541.91 88048.18131 0.037043096 0.045618323 1.340860685 -0.018356387 KSS(ph)WLMLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSSWLMLK 8 1 Q6H8Q1-7;Q6H8Q1-2;Q6H8Q1;D6RAL0;Q6H8Q1-3 Q6H8Q1-7 ABLIM2 Actin-binding LIM protein 2 1 KS(0.095)S(0.905)WLMLK 49.813 0.068307 48291000 32823 120080 70841 85325 105000 112300 79073 95260 73278 TRUE FALSE 30768.66702 128970.8481 72521.38197 87514.58395 96753.72355 144719.187 67216.73773 107153.4207 61047.42841 0.5040125 2.112633595 1.187951464 1.433550704 1.584894337 2.370602509 1.101057645 1.755248722 1 15.8976429 2.737722213 7.306889345 1.597133002 1.422864457 0.031537916 0.537622954 0.641445981 271.7657671 0.157458611 0.157202736 546.6661881 -2.737722213 -0.174268545 KSSEAS(ph)PTAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSSEASPTAQR 11 1 J3KNN7;Q7Z569 J3KNN7 BRAP BRCA1-associated protein 1 KSS(0.001)EAS(0.989)PT(0.01)AQR 115.1 0.00071571 100750000 254550 256640 240050 249240 268530 195310 307400 205100 301690 TRUE FALSE 238618.1699 275641.8926 245744.0994 255635.9204 247440.737 251692.8264 261308.2238 230707.1865 251335.99 0.949399129 1.096706813 0.977751333 1.017108295 0.98450181 1.001419758 1.039676903 0.9179234 1 17.93925775 3.743830358 24.36982564 0.996849097 1.034671199 0.051114277 0.047307111 669.2839924 976127.1512 0.010955212 0.019675067 5544.091103 -3.743830358 0.037822102 KSSGEIVYCGQVFEKS(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSSGEIVYCGQVFEKSPLR 19 2 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 1 KSSGEIVYCGQVFEKS(1)PLR;KSSGEIVYCGQVFEKS(1)PLR 183.63 1.39E-14 682830000 869880 666960 796160 785860 891620 552110 915150 701580 788510 TRUE FALSE 815435.7636 716342.4124 815045.2912 806026.4981 821595.7618 711495.1942 777931.7533 789173.8074 656902.587 1.241334377 1.090484992 1.240739962 1.227010692 1.250711716 1.083106093 1.184242182 1.201355913 1 19.32531992 -0.877712511 5.087248757 0.999999641 1.183711657 0.497505246 0.059685017 2.31E-07 5.08E-08 0.05490712 0.012941707 0.13252185 0.877712511 0.183712016 KSSPS(ph)KDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSSPSKDR 8 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 KS(0.004)S(0.321)PS(0.676)KDR 101.39 0.0042734 595270000 712290 300000 575190 494180 445370 339830 623020 400390 579490 TRUE FALSE 667709.0404 322212.3121 588833.7784 506861.4954 410392.4367 437933.4043 529603.9348 450379.5729 482769.3754 1.383080772 0.667424921 1.219699941 1.049903994 0.850079681 0.907127558 1.097012283 0.932908332 1 18.88097464 4.774244211 24.0315904 0.975577232 1.383082305 0.4381817 0.148202864 11634.74725 7835321.777 0.034279012 7.220086199 59462.64334 -4.774244211 0.407505073 KSSS(ph)LESLQTAVAEVTLNGDIPFHRPR ddPTM_SK-BR-3_Pertuzumab_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(0.185)S(0.185)S(0.627)LES(0.004)LQTAVAEVTLNGDIPFHRPR 109.54 0.00079633 98599000 137150 90506 101230 120360 109320 68370 95784 82581 89134 TRUE FALSE 128566.0263 97207.15841 103631.2234 123448.6414 100734.4482 88107.30911 81422.07842 92891.41963 74256.95957 1.73136669 1.309064618 1.395575903 1.66245214 1.356565752 1.186519211 1.096490873 1.250945638 1 16.18023863 2.299346164 3.13598136 1.131606975 1.470041475 0.630969784 0.138420818 0.179983136 3.611916608 0.05231045 0.04044597 199.2260682 -2.299346164 0.3384345 KSSSISEEKGDS(ph)DDEKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSSSISEEKGDSDDEKPR 18 3 S4R3H4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 KSSSISEEKGDS(1)DDEKPR 185.45 3.79E-14 423670000 828270 237180 397920 397160 469760 246520 525360 294540 533030 TRUE FALSE 776430.0592 254741.054 407358.8503 407351.798 432866.9445 317686.3221 446587.1452 331313.9674 444063.8495 1.748464911 0.573658618 0.917342969 0.917327088 0.974785372 0.715406855 1.005682281 0.746095337 1 18.7604076 4.749653917 24.99804169 0.850872653 1.748465429 0.800230956 0.140067765 703.5389438 1585350.042 0.031992108 0.489737028 56189.33815 -4.749653917 0.897592776 KSST(ph)PEEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KSSTPEEVK 9 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 1 KS(0.001)S(0.449)T(0.55)PEEVK;KS(0.01)S(0.086)T(0.905)PEEVK;KS(0.023)S(0.306)T(0.671)PEEVK 188.29 7.65E-05 1703610000 7488800 3853840 5006730 4778030 5283400 3412500 6729470 4341600 6471050 TRUE FALSE 7020089.376 4139182.324 5125492 4900642.339 4868463.076 4397633.353 5720448.447 4883658.317 5390989.95 1.30218929 0.767796335 0.95075154 0.909043123 0.90307404 0.815737628 1.061112801 0.905892677 1 22.36211879 1.720986047 24.99999991 0.990069407 0.919748335 0.008704103 0.146725013 3.093739313 4383.424918 0.061425289 0.034063425 52.60003669 -1.720986047 -0.070321072 KSST(ph)VATLQGTPDHGDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSSTVATLQGTPDHGDPR 18 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 KS(0.278)S(0.278)T(0.444)VATLQGTPDHGDPR 183.42 3.72E-14 677680000 683550 670130 639590 612230 803080 478850 1032400 896820 1555900 TRUE FALSE 640767.8257 719747.1225 654761.3768 627940.8583 740009.3363 617086.2215 877601.2043 1008789.951 1296210.239 0.494339426 0.555270357 0.505135168 0.48444368 0.570902246 0.476069547 0.677051591 0.778261058 1 20.3058683 1.131724036 1.279668858 0.995729312 0.516124306 0.948916322 0.037458942 0.075879751 0.251734102 0.031208476 0.009723248 13.54328558 -1.131724036 -0.479605007 KSSTPEEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KSSTPEEVK 9 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;; 178.46 8.17E-05 6545100000 13347300 10516800 10022800 9979100 12911500 7095800 12887600 10971300 16630700 FALSE TRUE 12511916.32 11295474.81 10260545.55 10235180.6 11897482.87 9144242.269 10955224.02 12341090.96 13854928.73 0.90306609 0.815267623 0.740570071 0.738739318 0.858718446 0.659999228 0.790709518 0.890736517 1 23.72389595 1.026157069 2.978672843 0.998275638 0.779927061 0.525797224 0.066985361 0.169444589 3.400758916 0.059956991 0.015859311 10.62079605 -1.026157069 -0.218348576 KSSTPEEVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSSTPEEVKK 10 2 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 102.62 0.0016439 2105800000 7485500 4610600 5787700 5719700 6474900 4020300 7240100 5059500 9537600 FALSE TRUE 7016995.917 4951973.621 5924986.977 5866477.185 5966387.472 5180895.346 6154514.219 5691189.712 7945712.945 0.883117219 0.62322584 0.745683492 0.738319799 0.750893911 0.652036561 0.774570421 0.716259164 1 22.92174524 -1.014369826 0.758603525 1.049145613 0.725056912 0.578966391 0.070348727 32.53150642 9.130736208 3.809239652 0.021484053 0.096745366 1.014369826 -0.3240887 KSVAAEGALLPQTPPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSVAAEGALLPQTPPSPR 18 1 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 KSVAAEGALLPQT(0.076)PPS(0.924)PR 95.153 0.0011216 163700000 178210 147860 192630 179100 188660 150190 202750 174310 248500 TRUE FALSE 167056.1542 158807.7082 197199.2746 183696.0092 173843.4046 193547.4149 172349.5197 196072.9872 207023.7446 0.806941998 0.767099004 0.952544236 0.887318552 0.839726887 0.934904425 0.83251088 0.947103858 1 17.65943672 7.999999986 0.045644494 1.25447815 0.213775816 0.515731923 0.051314683 538.2536247 1.861237797 10.66684864 40.87865911 99999996.77 -7.999999986 -1.040702334 KSVKEDSVPTGAEENVVCES(ph)PVEIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KSVKEDSVPTGAEENVVCESPVEIIK 26 2 O75363 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 KSVKEDSVPTGAEENVVCES(1)PVEIIK 86.211 0.0067626 92925000 97163 82360 93213 114970 171980 77528 149050 83402 305550 TRUE FALSE 91081.74127 88458.0201 95424.05638 117920.3248 158473.3845 99909.07504 126701.3362 93814.92329 254551.7311 0.357812304 0.347505082 0.374870978 0.463246996 0.62255866 0.39249026 0.497742976 0.36854954 1 17.95759935 -5 0.249342507 4.451526298 0.373378963 0.817678528 0.084649458 73.30096392 0.72728037 128.972029 0.120426722 1.00E-05 5 -4.078147335 KSVS(ph)NGALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSVSNGALR 9 1 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 KSVS(1)NGALR;KS(0.223)VS(0.777)NGALR 131.32 0.00020603 750400000 926480 1117170 1022190 1018950 1212210 756228 1216440 1050090 1650040 TRUE FALSE 868493.2706 1199886.429 1046436.83 1045097.982 1117007.916 974538.7473 1034046.115 1181196.048 1374637.664 0.631797959 0.872874693 0.761245568 0.760271604 0.812583523 0.708942271 0.752231764 0.859278106 1 20.39061996 0.952350024 3.410107649 0.999603677 0.768155705 0.608214289 0.062850877 0.174441389 5.257151183 0.056244247 0.014581582 8.96086685 -0.952350024 -0.231447972 KSYESSEDCSEAAGS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSYESSEDCSEAAGSPAR 18 1 Q6P6C2-3;Q6P6C2;K7ER58 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 KSYESSEDCSEAAGS(1)PAR;KSYESSEDCSEAAGS(1)PAR 237.19 4.69E-24 892040000 559360 494860 530960 485940 625290 541340 772620 515910 798180 TRUE FALSE 524350.6561 531499.9493 543554.6219 498410.0431 576182.2457 697616.0701 656772.8037 580322.4992 664958.6016 0.788546317 0.799297803 0.817426259 0.749535448 0.866493409 1.049112033 0.987689763 0.872719742 1 19.342905 2.43854588 5.401501818 0.979299791 0.796067674 0.784336114 0.046602261 0.080176275 5.848446463 0.015548811 0.013117142 274.5022322 -2.43854588 -0.183232117 KSYS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KSYSPR 6 1 P35251-2;P35251;A0A1W2PP02 P35251-2 RFC1 Replication factor C subunit 1 1 KS(0.019)Y(0.055)S(0.926)PR;KS(0.148)Y(0.012)S(0.84)PR 64.711 0.064901 359930000 1613030 1468520 1507340 1417490 1619890 1225580 1791720 1388890 1575370 TRUE FALSE 1512073.332 1577250.749 1543094.817 1453865.193 1492670.374 1579385.05 1523068.22 1562295.974 1312430.57 1.152116818 1.201778429 1.175753485 1.107765414 1.13733283 1.20340465 1.160494318 1.190383712 1 20.32380967 -1.135450726 4.406141477 0.99997384 1.168642381 0.757076521 0.029543649 7.60E-06 1.49E-06 0.028644909 0.006750623 0.073206438 1.135450726 0.168668542 KT(ph)GSYGALAEITASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTGSYGALAEITASK 15 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4;A0A3B3ISH4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 KT(0.5)GS(0.5)YGALAEITASK 181.85 3.35E-07 152310000 224650 346290 157050 128770 382990 32725 442980 246720 964110 TRUE FALSE 210589.5575 371929.6719 160775.3002 132074.4562 352911.5103 42172.17625 376559.2614 277523.5351 803193.8126 0.262190214 0.463063418 0.200169993 0.164436596 0.439385245 0.052505604 0.468827393 0.345524991 1 19.61538863 0.278965479 1.005455497 1.003076517 0.28925394 0.733898245 0.133610889 1.634463928 1.859817506 0.127313189 0.037160861 1.900927175 -0.278965479 -0.713822577 KT(ph)MEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTMEVK 6 1 Q68D51-2;Q68D51 Q68D51-2 DENND2C DENN domain-containing protein 2C 1 KT(1)MEVK 58.661 0.067537 414670000 405970 344920 350470 372700 445930 339510 392870 288050 485290 TRUE FALSE 380561.0624 370458.2357 358783.3139 382264.113 410908.4566 437521.0255 333962.7907 324013.6766 404291.9639 0.941302564 0.916313627 0.887436175 0.945514992 1.01636563 1.082190755 0.826043603 0.801434868 1 18.625038 1.620513761 25 0.860306131 0.951747675 0.216933348 0.075193172 1.167383758 2302.011229 0.035079769 0.019287936 41.73628223 -1.620513761 0.091441544 KT(ph)PESFLGPNAALVDLDSLVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTPESFLGPNAALVDLDSLVSR 22 1 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 KT(0.956)PES(0.044)FLGPNAALVDLDSLVSR 59.636 0.035973 80085000 96783 81712 80937 67783 88385 84601 115050 77928 113440 TRUE FALSE 90725.52479 87762.0415 82856.86386 69522.42654 81443.59863 109023.9353 97799.32057 87657.48234 94506.13115 0.959996179 0.928638602 0.876735328 0.735639325 0.86178111 1.153617591 1.034846304 0.927532228 1 16.52812031 2.265124012 24.99473968 1.036565231 0.874551427 0.488791489 0.079316596 183.8916727 173031.683 0.027916047 0.023350045 184.1297707 -2.265124012 -0.162013804 KT(ph)PESFLGPNAALVDLDSLVSRPGPTPPGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTPESFLGPNAALVDLDSLVSRPGPTPPGAK 31 2 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 KT(0.986)PES(0.014)FLGPNAALVDLDSLVSRPGPTPPGAK 288.28 2.95E-71 119920000 237350 120440 164300 135330 153350 127870 277060 161400 262650 TRUE FALSE 222494.6872 129357.5029 168197.2736 138802.7969 141306.5096 164783.9932 235517.4251 181551.1453 218812.0182 1.016830287 0.591180978 0.768683891 0.634347227 0.645789526 0.753084746 1.076345929 0.829712859 1 17.73933245 1.862637475 6.2064996 0.969435305 0.712272047 0.412181552 0.130508021 0.194795904 8.88197418 0.05200483 0.03145472 72.88488533 -1.862637475 -0.257163258 KT(ph)PPEDCEGPFRPAEILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTPPEDCEGPFRPAEILK 18 2 P49790-3;P49790 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 KT(1)PPEDCEGPFRPAEILK 144.27 4.74E-06 137400000 262610 111630 182370 151360 169710 118500 213850 147800 174380 TRUE FALSE 246173.7089 119895.2014 186695.9025 155244.1539 156381.6612 152709.0263 181785.1778 166253.1553 145274.8515 1.694537674 0.825299081 1.285121965 1.068623731 1.076453767 1.051173171 1.251318972 1.144404236 1 17.14842545 4.756148921 24.97661702 1.101861284 1.694538166 0.68620621 0.128631235 2232.812624 3170697.403 0.029675056 0.926332836 57035.98171 -4.756148921 0.592676882 SSFATCVLVSEEDKHAIIVEPEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSFATCVLVSEEDKHAIIVEPEKR 24 2 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 91.238 0.0055528 28039000 31656 33021 19507 10475 43224 20068 28581 36382 80028 FALSE TRUE 29674.70747 35465.9092 19969.71525 10743.80623 39829.3614 25861.30582 24295.54438 40924.37279 66670.8098 0.445092951 0.531955579 0.299527114 0.161147079 0.597403294 0.387895481 0.364410519 0.613827444 1 16.02476763 0.923090856 3.033541264 0.999416508 0.398576375 0.722594016 0.119249432 0.174388312 3.746965027 0.110715093 0.029035607 8.377045139 -0.923090856 -0.600840134 KT(ph)SLDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTSLDLR 7 1 Q5T457;A0A0A0MRN9;Q9GZV1-2;Q9GZV1 Q5T457 ANKRD2 Ankyrin repeat domain-containing protein 2 1 KT(0.663)S(0.337)LDLR;KT(0.5)S(0.5)LDLR 100.48 0.0057225 1239470000 2975600 2217280 2907400 2309100 2697900 2715900 3292900 2751500 5841500 TRUE FALSE 2789362.508 2381449.718 2976364.901 2368355.415 2486017.817 3499936.241 2799160.215 3095030.832 4866515.912 0.573174435 0.489354142 0.611600774 0.486663448 0.510841403 0.719187259 0.575187725 0.63598494 1 22.21445784 -2.758290865 0.249496489 1.745754291 0.516990186 0.82888107 0.062503736 18.67382976 0.502541491 7.490139751 0.08877709 0.001744653 2.758290865 -1.228764105 KT(ph)SLDVSNSAEPGFLAPGAR ddPTM_SK-BR-3_Pertuzumab_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(0.657)S(0.343)LDVSNSAEPGFLAPGAR;KT(0.687)S(0.313)LDVSNSAEPGFLAPGAR 250.97 3.50E-31 1304820000 1148090 919060 1061690 894200 1023260 807650 1376790 1218600 2032900 TRUE FALSE 1076233.096 987108.1587 1086873.788 917146.6859 942897.2872 1040805.444 1170353.121 1370744.892 1693595.857 0.635472207 0.582847528 0.641755106 0.541538102 0.556742793 0.614553608 0.691046282 0.809369536 1 20.69165821 1.077744205 1.325587436 0.997858892 0.594059644 0.947515412 0.031536797 0.087969423 0.314880184 0.029970748 0.00919044 11.96035872 -1.077744205 -0.403799249 KT(ph)SLFEEDEEDDLFAIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KTSLFEEDEEDDLFAIAK 18 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 1 KT(0.5)S(0.5)LFEEDEEDDLFAIAK;KT(0.5)S(0.5)LFEEDEEDDLFAIAK;KT(0.5)S(0.5)LFEEDEEDDLFAIAK 82.36 0.003175 116708000 123701 84445 99647 111602 117642 74102 108109 89641 174935 TRUE FALSE 115958.7752 90697.39566 102010.6739 114465.8963 108402.8719 95494.04445 91899.05908 100832.8762 145737.2184 0.795670293 0.622335164 0.699963091 0.785426657 0.743824214 0.655248162 0.630580576 0.691881438 1 17.15300983 -1.562570867 7.585277322 1.000147847 0.692507169 0.706887059 0.059733975 0.00014976 8.64E-06 0.057995706 0.013663241 0.027379728 1.562570867 -0.307640678 KT(ph)SPAPGGPAGEGPLQSLTCLIGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTSPAPGGPAGEGPLQSLTCLIGEK 25 1 A0A5F9ZHP4;C9J1X3;A0A5F9ZI29;A0A5F9ZGX5;A0A5F9ZHJ2;A0A499FJ16;Q07912;Q07912-3;A0A5F9ZHI7;A0A5F9ZHQ1;A0A5F9ZHB0;A0A5F9ZHL4;Q07912-2 A0A5F9ZHP4 TNK2 Activated CDC42 kinase 1 1 KT(0.5)S(0.5)PAPGGPAGEGPLQSLTCLIGEK 111.67 0.001477 32669000 69133 62732 64545 56328 80609 51169 103800 52570 83280 TRUE FALSE 64806.08894 67376.74255 66076.03788 57773.47184 74278.2943 65940.65964 88236.15363 59133.48022 69380.02999 0.934074098 0.971125878 0.952378341 0.83271039 1.070600493 0.950427085 1.271780275 0.852312693 1 16.08223284 2.705283184 24.67486618 1.057802966 0.935632135 0.150204016 0.113128562 805.675129 597398.8269 0.034443655 0.032475872 507.3214018 -2.705283184 -0.12217083 KT(ph)SPASLDFPESQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KTSPASLDFPESQK 14 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KT(0.5)S(0.5)PASLDFPESQK;KT(0.5)S(0.5)PASLDFPESQK;KT(0.5)S(0.5)PASLDFPESQK;KT(0.5)S(0.5)PASLDFPESQK 194.37 8.85E-08 4635630000 4182200 2315920 3011350 2855880 3232250 2422260 4236720 2710330 3958170 TRUE FALSE 3920443.567 2487393.127 3082780.644 2929166.716 2978402.123 3121527.14 3601463.168 3048720.667 3297525.856 1.188904572 0.754321038 0.934876868 0.888292266 0.903223281 0.94662704 1.09217132 0.924547919 1 21.65295254 1.972381499 9.544632169 1.01680407 0.908896338 0.050671643 0.114457205 0.770471383 257.1291435 0.043278724 0.028194185 93.83859554 -1.972381499 -0.107907732 KTAFVVEHDFIMATYLADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTAFVVEHDFIMATYLADR 19 1 P61221 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 172.84 4.92E-12 25293000 58474 83068 65247 68677 92013 58195 80135 64400 81520 FALSE TRUE 54814.21672 89218.44115 66794.68965 70439.36809 84786.67014 74994.95178 68119.50069 72440.48176 67913.78536 0.807114733 1.313701492 0.983521818 1.037188072 1.248445653 1.104266997 1.003029066 1.066653572 1 16.05141683 1.757562391 13.21129266 1.026405552 1.102311559 0.025588915 0.139205062 0.818416805 560.7782519 0.059889152 0.032991013 57.22191543 -1.757562391 0.075906007 KTAPTLS(ph)PEHWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTAPTLSPEHWK 12 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KTAPT(0.062)LS(0.938)PEHWK;KTAPT(0.062)LS(0.938)PEHWK 130.29 0.00010298 1326360000 2515400 1951060 2179200 2165200 2437400 1539160 2685300 1991520 2827100 TRUE FALSE 2357965.604 2095518.512 2230891.653 2220762.698 2245976.436 1983490.506 2282664.194 2240165.656 2355238.746 1.001157784 0.889726579 0.947204039 0.942903432 0.953608818 0.842161122 0.969185904 0.951141645 1 21.16744188 1.022479985 1.825434796 0.997643741 0.928873221 0.181295061 0.043192892 0.51322333 3.533238028 0.036716163 0.010473762 10.53125152 -1.022479985 -0.06877052 KTDFSWEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTDFSWEEER 10 1 Q92552;Q92552-2;G5EA06;D6RH20;D6RJC7 Q92552 MRPS27 "28S ribosomal protein S27, mitochondrial" 0 87.641 0.020424 315070000 291060 262990 256510 240440 340290 243370 238860 269720 345870 FALSE TRUE 272843.0742 282462.0532 262594.5383 246610.0975 313564.9961 313626.9682 203045.1605 303395.1357 288142.0626 0.946904703 0.980287469 0.911337054 0.855862887 1.088230553 1.088445628 0.704670324 1.052935948 1 18.13642075 KTDVEERPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTDVEERPR 9 2 A0A0C4DGA6;Q14527-2;Q14527 A0A0C4DGA6 HLTF Helicase-like transcription factor 0 79.659 0.014801 124040000 285800 321990 291560 286110 368370 231380 314720 320110 360560 FALSE TRUE 267912.2882 345830.4746 298475.9409 293452.067 339439.7061 298175.6499 267530.6577 360076.4381 300380.2067 0.891910593 1.151309131 0.993660482 0.976935432 1.130033533 0.992660779 0.890640101 1.19873557 1 18.19643023 KTDVKEEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTDVKEEDK 9 2 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 0 79.693 0.014747 40369000 298900 109870 171340 168060 177610 123830 227380 157400 169270 FALSE TRUE 280192.3826 118004.8891 175404.2657 172372.7041 163661.227 159577.7108 193286.4799 177051.7365 141017.7435 1.986929982 0.836808803 1.243845359 1.222347627 1.160571876 1.131614411 1.370653615 1.255528078 1 17.10551717 4.75326631 24.85459478 1.164007009 1.986930607 0.759220358 0.14752583 1318.550873 2228486.892 0.036498608 0.826994577 56658.66138 -4.75326631 0.822923598 KTEAAATTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTEAAATTR 9 1 E7EVA0;P27816-4;B5MEG9;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 0 ; 125.22 0.0008142 381470000 351190 442330 356600 364720 468520 291200 421160 429640 478620 FALSE TRUE 329209.6448 475080.5734 365058.7204 374079.3327 431724.3291 375264.7128 358010.9679 483281.4998 398735.23 0.825634707 1.191468769 0.915541675 0.938164738 1.082734348 0.941137588 0.897866406 1.212036117 1 18.60507155 1.244349123 24.99979954 1.106018055 0.983690042 0.19052699 0.11369361 223.8486916 966804.3119 0.076241165 0.026196645 17.55290987 -1.244349123 -0.122328014 KTEELEEESFPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTEELEEESFPER 13 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ; 167.61 5.07E-05 762570000 948420 794410 829550 822300 845480 671720 1031680 731990 1073120 FALSE TRUE 889060.0852 853228.943 849227.3177 843401.6102 779079.4113 865634.6595 876989.1616 823380.5628 894009.3394 0.994463979 0.954384821 0.949908776 0.943392393 0.871444376 0.968261316 0.980961969 0.92099772 1 19.76993038 KTEFLDLDNSPLSPPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTEFLDLDNSPLSPPSPR 18 1 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 KTEFLDLDNSPLSPPS(1)PR;KTEFLDLDNSPLSPPS(1)PR 248.07 1.15E-24 300090000 698650 621280 679250 639410 706930 655360 831510 684250 719660 TRUE FALSE 654922.7436 667280.2176 695362.1308 655818.3431 651410.5694 844551.7931 706832.7949 769680.1187 599544.0968 1.092367929 1.112979381 1.159818159 1.09386173 1.086509855 1.408656674 1.17895047 1.28377566 1 19.19350634 KTEGT(ph)PNQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTEGTPNQGK 10 1 Q9P2E9;A0A087WVV2;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KT(0.02)EGT(0.98)PNQGK 97.273 0.0036163 108720000 354300 193710 278180 242540 270090 184780 317650 232740 305580 TRUE FALSE 332124.9954 208052.49 284778.561 248763.987 248878.2209 238122.9863 270021.3314 261798.1013 254576.7239 1.304616504 0.817248674 1.118635501 0.977167053 0.977615774 0.935368256 1.060667791 1.028366212 1 17.95774099 -1.570040671 3.048034888 0.999352933 1.013228181 0 0.127164075 1598719998 225517504.1 7405142.257 0.026008621 0.026912828 1.570040671 0.013875248 KTEITDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTEITDK 7 1 Q9Y265;H7C4G5;Q9Y265-2;E7ETR0;H7C4I3 Q9Y265 RUVBL1 RuvB-like 1 0 ; 87.328 0.031143 575010000 804380 617860 671650 664210 774400 477430 837430 640900 835410 FALSE TRUE 754035.2917 663606.9973 687581.8552 681254.7531 713581.7478 615256.2906 711865.1458 720917.7758 695974.674 1.083423463 0.953493025 0.987940913 0.978849919 1.02529844 0.884021091 1.022831968 1.035839094 1 19.40867528 1.580176247 25 1.022027457 0.981228335 0.085842061 0.050916088 1.683507801 1513.263512 0.024565243 0.011376482 38.03437175 -1.580176247 -0.040799122 KTEPATGFIDGDLIESFLDISRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTEPATGFIDGDLIESFLDISRPK 24 2 Q16531;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 241.84 7.49E-38 345670000 167220 147310 146480 135880 188080 111340 177980 151560 217810 FALSE TRUE 156753.9987 158216.9857 149954.5748 139366.9108 173308.9555 143482.0505 151293.5513 170482.5996 181456.1039 0.863867323 0.871929807 0.82639587 0.768047521 0.955101271 0.790725952 0.833774935 0.939525295 1 17.46926106 1.074657569 3.665501852 0.998355387 0.843358158 0.535479978 0.050221864 0.145867058 3.776408537 0.043647817 0.011317414 11.87565489 -1.074657569 -0.154997229 KTERDELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTERDELLK 9 2 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 98.048 0.0035309 147418000 154596 168697 153707 178617 266130 101763 200675 138526 393020 FALSE TRUE 144920.1123 181187.5014 157353.0026 183200.6146 245229.2233 131140.3261 170585.6467 155821.276 327422.423 0.442609003 0.553375361 0.480581022 0.559523728 0.748968935 0.400523351 0.520995615 0.475902886 1 18.3207936 -1.002218675 5.384270984 1.00000202 0.523918766 0.719738669 0.093578795 2.10E-06 3.89E-07 0.083907113 0.019777012 0.099490434 1.002218675 -0.476083254 KTES(ph)PIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTESPIK 7 1 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 KT(0.115)ES(0.885)PIK;KT(0.007)ES(0.993)PIK 56.783 0.073213 608150000 3112900 1721360 2099100 1628570 2157900 1226740 2494400 2376500 3097800 TRUE FALSE 2918069.146 1848811.285 2148891.643 1670361.863 1988427.239 1580879.924 2120387.877 2673211.256 2580757.167 1.130702719 0.71638328 0.832659372 0.64723713 0.770482114 0.612564384 0.821614642 1.035824405 1 21.29936297 1.30086766 5.010490148 1.018876697 0.772776815 0.310811938 0.140514832 0.202306592 9.225217705 0.095156904 0.032078288 19.99252558 -1.30086766 -0.246099882 KTES(ph)PIKLSPATPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTESPIKLSPATPSR 15 2 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 KTES(1)PIKLSPATPSR;KT(0.01)ES(0.99)PIKLSPATPSR 175.59 4.42E-07 1144620000 2284580 1290280 1648360 1563550 1881740 1168850 2180050 1578060 3461960 TRUE FALSE 2141592.216 1385813.674 1687459.878 1603673.34 1733955.731 1506278.02 1853171.741 1775084.265 2884136.511 0.742541904 0.480495174 0.58508322 0.556032398 0.601204459 0.522263081 0.642539538 0.615464718 1 21.45970802 0.038279613 0.782203192 1.010767713 0.570474018 0.766869871 0.070444652 2.005574643 1.282202184 0.12249615 0.021211256 1.092143268 -0.038279613 -0.440293695 KTESASVQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTESASVQGR 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 149.49 3.73E-05 726360000 647380 589360 547970 580470 656250 480650 698150 536360 569140 FALSE TRUE 606861.6414 632996.8276 560968.1072 595365.8429 604710.7722 619405.8523 593468.8888 603325.7267 474146.8572 1.279902275 1.335022721 1.183110462 1.255657048 1.275365982 1.306358658 1.251656274 1.27244485 1 18.85497445 -1.279125758 2.949621617 0.998000648 1.268129339 0.824294504 0.03915912 3442226.093 4289055.919 61130.47768 0.00947087 0.052586497 1.279125758 0.270128691 KTETLLYAMLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTETLLYAMLPK 12 1 O75343 O75343 GUCY1B2 Guanylate cyclase soluble subunit beta-2 0 42.556 0.087924 1390800000 7543900 2972700 3379300 2632600 4335100 1847900 3531200 3675900 4810300 FALSE TRUE 7071740.765 3192801.801 3459458.592 2700156.973 3994638.733 2381358.732 3001729.342 4134844.207 4007429.854 1.764657404 0.796720571 0.863261172 0.673787707 0.996808148 0.594235911 0.749041019 1.031794531 1 21.93424584 4.739257244 24.9777214 0.815727165 1.764657701 0.800017292 0.145183744 22.02386498 789513.3862 0.031046659 0.185929348 54860.18205 -4.739257244 0.948930536 KTFEINPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTFEINPR 8 1 P14625;H0YIV0;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ; 156.92 0.00061773 1491710000 2979700 3603900 3469900 3493200 3817400 2389200 4230100 3011400 3212300 FALSE TRUE 2793205.896 3870736.506 3552207.667 3582841.426 3517596.803 3078923.255 3595835.775 3387379.919 2676146.378 1.043741822 1.44638445 1.327359257 1.338806224 1.314426158 1.150506295 1.343661843 1.265767802 1 21.3517256 -1.558999599 0.386626282 0.788267573 1.314277432 0.355384402 0.11370493 26.9490124 2.085575891 5.579112923 0.070958885 0.027605804 1.558999599 0.526009859 KTGQIWPNDGEGAFHGDADGSFGT(ph)PPGYGCAADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTGQIWPNDGEGAFHGDADGSFGTPPGYGCAADR 34 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 KTGQIWPNDGEGAFHGDADGS(0.054)FGT(0.946)PPGYGCAADR 129.55 4.02E-08 155840000 131180 147000 122020 148660 195600 152250 188160 145950 228420 TRUE FALSE 122969.678 157884.033 124914.372 152474.8673 180238.365 196202.1034 159947.1548 164172.1788 190295.2264 0.646204744 0.82967942 0.656424096 0.801254294 0.947151268 1.031040595 0.84052111 0.862723579 1 17.53787985 2.908991181 3.962573585 0.926469148 0.728129913 0.652893869 0.075198777 0.154041001 4.393971591 0.02286664 0.024813309 810.9445896 -2.908991181 -0.198339236 KTGS(ph)YGALAEITASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTGSYGALAEITASK 15 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4;A0A3B3ISH4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 KT(0.001)GS(0.999)YGALAEITASK;KT(0.251)GS(0.749)YGALAEITASK 211.12 8.06E-12 160510000 387090 604540 264565 221814 608320 81045 759890 435870 1537210 TRUE FALSE 362862.7279 649300.7706 270840.6067 227506.1228 560545.001 104441.3758 645951.549 490289.329 1280639.72 0.283344896 0.507012831 0.211488526 0.177650372 0.437707024 0.081554066 0.504397559 0.382847198 1 20.28843323 0.397292069 1.013820247 1.001572326 0.309979703 0.715068095 0.135978259 1.233389072 1.604576598 0.12498018 0.038493321 2.496272942 -0.397292069 -0.691592622 KTHETLSHAGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTHETLSHAGQK 12 1 Q16890-5;E9PPQ1;J3KNE7;Q16890;E9PNK6;E9PNQ9;Q16890-4;Q16890-3;Q16890-2 Q16890-5 TPD52L1 Tumor protein D53 0 130.56 8.71E-05 85513000 98927 208140 156030 163430 242250 125670 172010 204490 246360 FALSE TRUE 92735.33566 223550.9022 159731.1053 167623.8905 223224.6622 161948.8889 146218.6974 230021.0266 205240.9245 0.451836474 1.089212119 0.778261478 0.816717674 1.087622572 0.789067236 0.712424668 1.120736653 1 17.6469589 4.754661324 24.51501256 0.898951132 0.45183603 0.492192269 0.14884399 2198.771344 3347786.92 0.034160936 0.882354363 56840.94946 -4.754661324 -0.447115103 KTKFENLCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTKFENLCK 9 2 P07900;P07900-2;Q58FG0 P07900 HSP90AA1;HSP90AA5P Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5 0 ; 78.653 0.016403 652240000 642470 721370 623620 622230 928150 475400 751650 680360 984970 FALSE TRUE 602258.9495 774780.9854 638412.5609 638197.4752 855256.843 612640.2625 638947.0605 765304.4437 820572.1439 0.73395003 0.94419606 0.778009058 0.777746942 1.042268921 0.74660134 0.778660433 0.93264736 1 19.64627065 1.034110544 5.378644968 0.999532007 0.834181966 0.275482162 0.095813274 0.20230907 14.7198842 0.085667037 0.021616641 10.81709251 -1.034110544 -0.165350041 KTKPPRPDS(ph)PATTPNISVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTKPPRPDSPATTPNISVK 19 3 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 KTKPPRPDS(1)PATTPNISVK 112.85 0.0010421 1042100000 400630 267200 343370 357210 481870 265420 511230 387860 608960 TRUE FALSE 375555.2834 286983.766 351514.8986 366376.6134 444025.874 342042.4453 434575.8075 436285.1748 507320.642 0.740272034 0.565685175 0.69288507 0.72217959 0.875237152 0.674213539 0.856609749 0.859979151 1 18.95253834 1.700000813 0.312556612 1.024655587 0.597443858 0.662527744 0.072258904 0.777896521 0.259006801 0.114151743 0.116634253 50.11881713 -1.700000813 -0.42721173 KTLDSVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTLDSVAK 8 1 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 129.85 0.0017205 910710000 2253800 2118700 2022200 2009800 2445800 1480500 2531500 2161100 3272400 FALSE TRUE 2112738.681 2275570.753 2070167.539 2061374.871 2253716.734 1907896.316 2151925.076 2430918.092 2726215.299 0.774971324 0.834699575 0.759355851 0.756130622 0.826683327 0.699833324 0.789345242 0.89168236 1 21.37846807 1.030292052 2.808645919 0.99846226 0.778269806 0.798123778 0.037506505 0.101181345 1.773008213 0.034418438 0.009182023 10.72240116 -1.030292052 -0.220192454 KTLEEEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KTLEEEAK 8 1 P35579 P35579 MYH9 Myosin-9 0 ;; 161.63 0.00055542 1089500000 2060510 1385830 1564680 1544970 1647990 995910 2009410 1370390 1973210 FALSE TRUE 1931546.357 1488438.295 1601794.948 1584616.546 1518563.513 1283413.05 1708117.625 1541486.208 1643868.504 1.175000527 0.905448515 0.974405766 0.96395578 0.923774322 0.780727319 1.0390841 0.937718683 1 20.64866347 4.743826078 24.57562221 0.940176149 1.175000653 0.537527582 0.068316108 342.8201666 1599989.43 0.015221131 0.129982641 55440.36468 -4.743826078 0.234824504 KTLPLTTAPEAGEVTPSDSGGQEDS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 KTLPLTTAPEAGEVTPSDSGGQEDS(1)PAK;KTLPLTTAPEAGEVTPSDSGGQEDS(1)PAK 202.58 2.30E-25 922820000 1167260 778680 1044080 1136450 1073700 510540 864610 575680 660890 TRUE FALSE 1094203.28 836334.2774 1068846.071 1165613.231 989375.9331 657924.6101 734969.7571 647554.9152 550583.1895 1.98735323 1.518997117 1.941298047 2.117051979 1.796959936 1.194959495 1.334893203 1.176125475 1 19.07060104 2.257192419 6.325556458 1.216437731 1.847240554 0.796053801 0.174318866 0.07937267 11.43501855 0.064080754 0.051509213 180.7974993 -2.257192419 0.630802824 KTNHRLS(ph)LPMPASGTSLSAAIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTNHRLSLPMPASGTSLSAAIHR 23 2 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 1 KT(0.305)NHRLS(0.695)LPMPASGTSLSAAIHR;KT(0.293)NHRLS(0.707)LPMPASGTSLSAAIHR 254.27 7.73E-44 1878120000 654370 1072740 814670 972890 1307050 607230 1173840 891180 1271020 TRUE FALSE 613414.1498 1152166.786 833994.3571 997856.0045 1204399.565 782527.4434 997833.5894 1002445.785 1058878.551 0.579305482 1.088100977 0.787620409 0.94237059 1.137429372 0.739015294 0.942349421 0.946705157 1 20.0141057 4.754601898 24.58646907 0.936295094 0.579305142 0.481784755 0.119612231 2200.488114 3372616.946 0.026386017 0.678992184 56833.17233 -4.754601898 -0.356989951 KTPCGEGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KTPCGEGSK 9 1 P60866;P60866-2;G3XAN0 P60866 RPS20 40S ribosomal protein S20 0 ;;;;; 99.752 0.0082166 5700050000 6334720 5144610 5420500 5011340 5938100 3760810 6015430 5254690 6967790 FALSE TRUE 5938241.183 5525522.277 5549076.82 5139939.469 5471745.579 4846494.795 5113472.116 5910749.613 5804820.835 1.022984404 0.951885068 0.955942824 0.885460484 0.942620924 0.834908593 0.880900938 1.018248415 1 22.46882011 5.249263704 0.749341114 0.915527319 1.174293956 0.169503329 0.056343222 7.558292693 1.88064735 0.019365417 1.957640399 177526.7099 -5.249263704 0.258766636 KTPEKLDNTPAS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KTPEKLDNTPASPPR 15 2 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911;H0Y8P9 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 KTPEKLDNT(0.033)PAS(0.967)PPR;KTPEKLDNTPAS(1)PPR;KTPEKLDNT(0.108)PAS(0.892)PPR 141.83 2.45E-06 560170000 2263540 1294840 1451230 930230 1065390 1582860 3714100 2779920 2445450 TRUE FALSE 2121869.072 1390711.301 1485653.861 954101.2767 981718.567 2039805.986 3157205.185 3126999.131 2037288.597 1.041516197 0.682628521 0.729230931 0.468319156 0.481875061 1.001235657 1.549709349 1.534882754 1 20.95821893 1.970156893 4.373684819 1.402035903 0.679471302 0.672099277 0.216474508 0.109458108 4.764666672 0.091891696 0.056431904 93.35915084 -1.970156893 -0.722564601 KTPEKLDNTPAS(ph)PPRS(ph)PAEPNDIPIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KTPEKLDNTPASPPRSPAEPNDIPIAK 27 3 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911;H0Y8P9 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 2 KT(0.003)PEKLDNT(0.015)PAS(0.985)PPRS(0.997)PAEPNDIPIAK;KT(0.002)PEKLDNT(0.041)PAS(0.961)PPRS(0.997)PAEPNDIPIAK;KTPEKLDNT(0.009)PAS(0.991)PPRS(1)PAEPNDIPIAK 251.01 2.78E-46 2198150000 1407120 869250 1089590 1201960 1526120 655020 1145220 758370 1325340 TRUE FALSE 1319050.871 933610.1745 1115435.589 1232804.329 1406264.691 844113.6406 973504.8927 853054.1639 1104132.192 1.194649409 0.845560143 1.010237359 1.116536894 1.273637977 0.764504148 0.881692337 0.772601478 1 20.07448148 2.20605308 24.99993895 0.845919747 1.045718257 0.415128005 0.132283385 222.845374 171378.0609 0.050188471 0.037069334 160.7137668 -2.20605308 0.19979851 KTPEKLDNTPAS(ph)PPRSPAEPNDIPIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTPEKLDNTPASPPRSPAEPNDIPIAK 27 3 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911;H0Y8P9 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 KT(0.039)PEKLDNT(0.171)PAS(0.78)PPRS(0.01)PAEPNDIPIAK 58.498 0.043894 482230000 311990 182730 192410 121270 165670 181170 535630 401060 583160 TRUE FALSE 292463.1028 196259.5193 196974.0561 124381.9935 152658.9465 233470.838 455317.254 451133.2238 485826.8286 0.601990433 0.403970114 0.405440878 0.256021253 0.314225023 0.480563905 0.937200721 0.928588537 1 18.89008264 1.767468484 3.486483197 0.961396746 0.392213335 0.891931262 0.089804111 0.065593666 1.586758676 0.048647971 0.024240794 58.54212517 -1.767468484 -0.569183411 KTPSKPPAQLS(ph)PSVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTPSKPPAQLSPSVPK 16 2 F5H8D7;P18887;M0QYS5 F5H8D7 XRCC1 DNA repair protein XRCC1 1 KTPSKPPAQLS(0.851)PS(0.149)VPK 93.322 0.0023331 1656800000 1380900 750540 983010 891630 1073600 800950 1339200 884050 1519500 TRUE FALSE 1294471.934 806110.7625 1006327.461 914510.7353 989283.7867 1032171.263 1138399.393 994425.5885 1265885.634 1.022582056 0.636795885 0.794959224 0.722427612 0.78149539 0.815374814 0.89929087 0.785557212 1 20.27171564 0.793586086 0.547314162 1.000374004 0.766005427 0.224458164 0.103969416 1.424037678 0.946053498 0.112790442 0.046371561 6.217074704 -0.793586086 -0.234368577 KTQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYR 37 2 P11388;P11388-2;P11388-3;P11388-4;J3KTB7 P11388 TOP2A DNA topoisomerase 2-alpha 0 62.383 0.0082568 22005000 7461.9 11376 5464.9 4389.3 16617 2647.4 7920.8 8688.6 2777.3 FALSE TRUE 6994.872999 12218.29088 5594.530009 4501.936869 15311.96785 3411.661403 6733.149573 9773.390836 2313.750688 3.023174897 5.280729225 2.417948501 1.945731186 6.617812338 1.474515565 2.910058378 4.224046647 1 11.1760177 -0.826527107 0.287879237 4.70E-17 3.832522014 0.183791202 1.569900265 21.41246034 1.680807803 23.56227113 1.827360631 0.149098369 0.826527107 3.832522014 KTQMAEVLPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 KTQMAEVLPSPR 12 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 KTQMAEVLPS(1)PR;KTQMAEVLPS(1)PR;KTQMAEVLPS(1)PR;KTQMAEVLPS(1)PR;KTQMAEVLPS(1)PR;KTQMAEVLPS(1)PR;KTQMAEVLPS(1)PR 117.67 0.00043425 2990730000 3995210 3903840 4234550 4144260 4560380 3294250 5212390 3887090 5403920 TRUE FALSE 3745156.938 4192884.376 4334995.526 4250608.728 4202226.15 4245246.497 4430840.509 4372401.743 4501970.841 0.831892758 0.931344188 0.962910618 0.944166206 0.933419229 0.942975121 0.984200179 0.971219472 1 22.10212528 5.765179504 1.053552332 0.961309507 2.20E-10 0.807006241 0.020018312 5.637261891 0.96864729 0.005768688 10.06272728 582343.8647 -5.765179504 -0.961309506 KTQQLHPVLQKPSVFGNDS(ph)DDDDETSVSESLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTQQLHPVLQKPSVFGNDSDDDDETSVSESLQR 33 2 Q9H0G5 Q9H0G5 NSRP1 Nuclear speckle splicing regulatory protein 1 1 KTQQLHPVLQKPSVFGNDS(1)DDDDETSVSESLQR;KTQQLHPVLQKPS(0.001)VFGNDS(0.999)DDDDETSVSESLQR 375.96 9.04E-149 2894850000 1177390 1084660 1128540 1236540 1510370 774020 1552640 1036590 2449570 TRUE FALSE 1103699.262 1164969.355 1155309.502 1268271.71 1391751.633 997467.0088 1319836.046 1166010.543 2040720.942 0.540837916 0.570861665 0.566128116 0.621482185 0.681990175 0.488781679 0.646749891 0.571371871 1 20.96064748 -5 0.376824562 6.708866047 0.576463302 0.851561877 0.054308371 192.1869599 1.451976172 895.5627211 0.033465631 1.00E-05 5 -6.132402746 KTQYEEHIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTQYEEHIYR 10 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 0 97.456 0.0039249 35469000 62655 82317 53927 55098 95229 43202 62708 70471 77528 FALSE TRUE 58733.53539 88411.83633 55206.17391 56511.90796 87750.09848 55673.71607 53305.51755 79269.45948 64588.07595 0.909355706 1.368856945 0.854742506 0.874958839 1.358611434 0.861981337 0.825315149 1.227307956 1 15.97898022 3.961045455 23.87743269 0.984468682 1.164411811 0.066805096 0.204178747 455.7654548 676951.7001 0.049226883 0.089165026 9142.089203 -3.961045455 0.179943129 DRVVVVSHDENLCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRVVVVSHDENLCR 14 1 Q7L5L3-1;Q7L5L3 Q7L5L3-1 GDPD3 Glycerophosphodiester phosphodiesterase domain-containing protein 3 0 ; 217.48 3.45E-12 539950000 134227 229740 164029 154489 254070 160254 190502 250580 535230 FALSE TRUE 125825.9717 246750.1886 167919.8453 158453.4493 234116.3671 206516.7283 161937.9936 281865.4646 445896.6553 0.282186399 0.55337977 0.376589157 0.355359134 0.525046251 0.46314931 0.363173825 0.632131821 1 18.76634985 0.933464322 3.626280167 0.999571684 0.42804017 0.838116363 0.082054343 0.106208084 3.545723762 0.072962769 0.018801139 8.579546302 -0.933464322 -0.571531514 KTS(ph)LDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTSLDLR 7 1 Q5T457;A0A0A0MRN9;Q9GZV1-2;Q9GZV1 Q5T457 ANKRD2 Ankyrin repeat domain-containing protein 2 1 KT(0.211)S(0.789)LDLR 88.155 0.011524 392680000 1400400 1056300 1356000 1057700 1305300 1248700 1473700 1272400 2667500 TRUE FALSE 1312751.464 1134509.551 1388164.96 1084842.373 1202787.003 1609179.419 1252732.366 1431261.941 2222277.017 0.590723593 0.51051671 0.624658829 0.488167031 0.541240806 0.724112884 0.563715665 0.644051993 1 21.08360724 -4.671344377 0.243525004 3.0588769 0.539409012 0.820015909 0.062312202 55.4900887 0.641305869 56.37115841 0.088320999 2.13E-05 4.671344377 -2.519467887 KTS(ph)LDVSNSAEPGFLAPGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KTSLDVSNSAEPGFLAPGAR 20 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6 Q8NEY1-5 NAV1 Neuron navigator 1 1 KT(0.325)S(0.674)LDVS(0.001)NSAEPGFLAPGAR;KT(0.186)S(0.813)LDVS(0.001)NSAEPGFLAPGAR;KT(0.019)S(0.981)LDVSNSAEPGFLAPGAR;KT(0.22)S(0.78)LDVSNSAEPGFLAPGAR 241.62 5.79E-30 1542180000 1848630 1407843 1542710 1363654 1738050 1378152 2163730 1818940 3321750 TRUE FALSE 1732927.548 1512081.161 1579303.81 1398647.67 1601550.564 1776002.11 1839298.774 2046038.663 2767328.466 0.626209563 0.546404657 0.570696189 0.505414405 0.578735262 0.641774958 0.664647799 0.73935519 1 21.40006246 0.83258688 0.738003046 1.002143252 0.558582207 0.943348613 0.033121074 0.179812967 0.206229165 0.031170022 0.011552651 6.801220881 -0.83258688 -0.443561045 KTS(ph)PGPTHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTSPGPTHR 9 1 Q14678;Q14678-2;Q5W0W3 Q14678 KANK1 KN motif and ankyrin repeat domain-containing protein 1 1 KT(0.18)S(0.812)PGPT(0.008)HR 63.662 0.045691 122650000 68315 50223 58436 64342 62222 43710 69882 53851 76387 TRUE FALSE 64039.2861 53941.56318 59822.12952 65993.12465 57335.33511 56328.36743 59403.84285 60574.41589 63637.51622 1.006313412 0.847637783 0.940045009 1.037016033 0.900967519 0.885144028 0.933472052 0.951866438 1 15.95758991 0.910613864 2.653504551 0.999798381 0.927569788 0.105005406 0.055033424 0.757906559 11.7517335 0.050861381 0.013559871 8.139802431 -0.910613864 -0.072228592 KTS(ph)QSEEEEAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KTSQSEEEEAPR 12 1 Q7RTP6;A0A5F9ZHV5;Q7RTP6-2;Q7RTP6-4;Q7RTP6-3;J3KSK6;Q7RTP6-5 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 KT(0.029)S(0.907)QS(0.064)EEEEAPR;KT(0.293)S(0.706)QS(0.001)EEEEAPR;KT(0.15)S(0.85)QSEEEEAPR 145.69 3.76E-05 402410000 513447 467817 482654 504784 530254 364217 479848 391842 505356 TRUE FALSE 481311.2688 502454.6574 494102.7808 517737.612 488609.9898 469360.5353 407899.2471 440764.3363 421008.8189 1.143233223 1.193453996 1.173616225 1.229754791 1.160569489 1.114847277 0.968861527 1.046924236 1 18.68349093 1.981174234 2.875697712 1.004057587 1.183344012 0.876210214 0.029865356 0.076686088 1.201326771 0.013714783 0.007786992 95.75781639 -1.981174234 0.179286425 KTSATVGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTSATVGPK 9 1 P16104 P16104 H2AFX Histone H2AX 0 83.081 0.026667 751120000 640430 565070 587810 647560 627450 395630 718340 547040 705930 FALSE TRUE 600346.6295 606908.3708 601753.1308 664177.4859 578172.608 509841.9585 610631.5857 615339.1482 588105.7225 1.020814127 1.031971544 1.023205706 1.12935049 0.983109985 0.866922288 1.038302404 1.046307024 1 19.165716 KTSFDQDS(ph)DVDIFPSDFPTEPPSLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 KTSFDQDSDVDIFPSDFPTEPPSLPR 26 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KT(0.13)S(0.09)FDQDS(0.78)DVDIFPSDFPTEPPSLPR;KT(0.002)S(0.01)FDQDS(0.987)DVDIFPSDFPTEPPSLPR;KT(0.147)S(0.147)FDQDS(0.707)DVDIFPSDFPTEPPSLPR;KT(0.033)S(0.026)FDQDS(0.942)DVDIFPSDFPTEPPSLPR;KT(0.062)S(0.062)FDQDS(0.876)DVDIFPSDFPTEPPSLPR;KT(0.086)S(0.086)FDQDS(0.828)DVDIFPSDFPTEPPSLPR;KT(0.088)S(0.059)FDQDS(0.854)DVDIFPSDFPTEPPSLPR 207.7 1.54E-25 4594184000 1868308 1516747 1629971 1582869 1725373 1134158 2103929 1410565 1814625 TRUE FALSE 1751373.937 1629048.526 1668634.682 1623488.098 1589869.164 1461571.003 1788464.378 1586677.145 1511752.365 1.158505836 1.077589534 1.103775143 1.0739114 1.051673013 0.966805832 1.18304057 1.049561544 1 20.5277904 7.999999506 0.804766539 1.069321639 22.62351655 0.197885234 0.058189838 972.3386302 3.28001768 0.018570861 38229.19754 99999886.32 -7.999999506 21.55419491 KTSS(ph)DDES(ph)EEDEDDLLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KTSSDDESEEDEDDLLQR 18 1 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 2 KT(0.283)S(0.33)S(0.387)DDES(1)EEDEDDLLQR;KT(0.033)S(0.163)S(0.804)DDES(1)EEDEDDLLQR;KT(0.047)S(0.25)S(0.703)DDES(1)EEDEDDLLQR 259.83 3.60E-30 961160000 2562230 1344210 1672790 1590870 1799930 1213740 2256830 1430120 2076540 TRUE FALSE 2401864.598 1443736.707 1712469.369 1631694.418 1658570.758 1564127.035 1918439.293 1608673.63 1729952.059 1.388399514 0.834553015 0.989894119 0.943202101 0.958737989 0.904144728 1.108955178 0.929894919 1 20.72230063 -0.700560192 8.290313125 1 0.991034201 0 0.153083477 0 0 0.131230352 0.030931291 0.199269031 0.700560192 -0.008965799 KTSTS(ph)PPPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTSTSPPPEK 10 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KT(0.165)S(0.122)T(0.069)S(0.644)PPPEK;KT(0.018)S(0.018)T(0.101)S(0.862)PPPEK 74.769 0.025113 954820000 2379300 1252860 1685260 1585470 1414250 1559920 2316600 1369490 1423820 TRUE FALSE 2230383.86 1345623.058 1725235.163 1626155.844 1303180.51 2010243.581 1969247.336 1540473.841 1186175.244 1.880315638 1.134421802 1.454452175 1.370923776 1.098640792 1.694727311 1.660165601 1.298689927 1 20.17788574 2.22033681 24.99991219 1.497037442 1.361536619 0 0.288796098 818.4200931 1122723.974 0.098725716 0.073057869 166.0874473 -2.22033681 -0.135500823 KTTHFVEGGDAGNREDQINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KTTHFVEGGDAGNREDQINR 20 2 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ;;; 178.32 3.74E-17 3303290000 1172540 1436510 1272640 1391780 1499730 1034910 1493160 1182160 1805370 FALSE TRUE 1099152.814 1542870.695 1302827.622 1427495.431 1381947.255 1333671.717 1269274.52 1329755.278 1504042.084 0.730799242 1.025816173 0.866217532 0.949106043 0.918822199 0.886725 0.843908913 0.884121058 1 20.5204135 2.228723027 20.82820599 0.885528475 0.913522295 0 0.084570151 125.7144052 266147.5456 0.028433984 0.021358925 169.3257574 -2.228723027 0.02799382 KTTPGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTTPGFR 7 1 Q15274 Q15274 QPRT Nicotinate-nucleotide pyrophosphorylase [carboxylating] 0 ; 110.12 0.011024 1225710000 997200 1089330 1054710 991140 1325420 815500 1142020 1186270 1657000 FALSE TRUE 934787.0321 1169985.127 1079728.219 1016574.33 1221326.86 1050921.611 970784.703 1334378.421 1380435.995 0.677167964 0.847547536 0.782164637 0.736415403 0.88473994 0.761296876 0.703244994 0.966635487 1 20.39669257 1.16181014 6.752262747 0.992210194 0.77787714 0.671553275 0.061813898 0.135399824 9.409558589 0.056660257 0.014293997 14.51476938 -1.16181014 -0.214333054 KTTPS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTTPSPGR 8 1 Q14686 Q14686 NCOA6 Nuclear receptor coactivator 6 1 KTT(0.022)PS(0.977)PGR;KT(0.01)T(0.041)PS(0.949)PGR 67.726 0.03574 181245000 392150 386920 332180 352460 420490 255690 399490 363520 444150 TRUE FALSE 367606.0315 415567.9594 340059.4665 361504.7203 387466.4116 329503.5522 339590.1832 408906.2722 370018.4957 0.993480152 1.123100505 0.919033698 0.976990946 1.047154172 0.890505626 0.917765428 1.105096845 1 18.49723786 3.973029929 23.85813911 0.970144922 1.061738709 0.166315291 0.070870403 133.0009716 775595.4882 0.016963102 0.032127604 9397.880724 -3.973029929 0.091593787 KTTTT(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KTTTTPGR 8 1 P17096;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KT(0.02)T(0.02)T(0.124)T(0.837)PGR 67.726 0.034193 622140000 743280 710160 571720 455690 781460 190140 850710 584050 1551900 TRUE FALSE 696759.4316 762740.9853 585281.4684 467383.7769 720087.2839 245030.3313 723153.9331 656969.9282 1292877.864 0.538921309 0.589955947 0.452696643 0.36150652 0.556964663 0.189523186 0.559336619 0.508145391 1 20.30215456 0.501468237 1.765678202 0.999864722 0.46619762 0.669662665 0.117618919 1.987225449 6.37303613 0.106089273 0.029784585 3.172986592 -0.501468237 -0.533667102 KTTTTPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KTTTTPGR 8 1 P17096;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 0 ;;;;; 128.6 0.0018062 3770060000 3508260 3515370 3476640 3406510 3788240 2934850 3552770 3021690 4009290 FALSE TRUE 3288684.269 3775651.653 3559107.543 3493926.814 3490726.911 3782093.552 3020065.121 3398954.648 3340113.598 0.984602521 1.13039618 1.065564819 1.046050295 1.045092273 1.132324827 0.904180362 1.017616482 1 21.67146574 1.740244531 25 0.968774482 1.072735579 0.420426707 0.051320039 0.210476191 3142.623025 0.021520423 0.011934157 54.98503822 -1.740244531 0.103961096 KTVEDEDQDS(ph)EEEKDNDSYIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KTVEDEDQDSEEEKDNDSYIK 21 2 Q9Y5T5-4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5 Q9Y5T5-4 USP16 Ubiquitin carboxyl-terminal hydrolase 16 1 KTVEDEDQDS(1)EEEKDNDSYIK;KTVEDEDQDS(1)EEEKDNDSYIK;KTVEDEDQDS(1)EEEKDNDSYIK;KTVEDEDQDS(1)EEEKDNDSYIK 210.79 9.62E-23 1275240000 4055320 1134420 1883430 1830760 1797630 1211690 2572680 1331670 2219190 TRUE FALSE 3801504.76 1218413.637 1928105.849 1877740.401 1656451.391 1561485.233 2186930.518 1497931.931 1848792.852 2.056209139 0.659031992 1.042899883 1.01565754 0.895963758 0.844597182 1.182896458 0.810221615 1 20.81815216 4.747500255 24.9134097 0.939303738 2.056209742 0.858258432 0.143622097 406.3716993 1132470.818 0.03383259 0.412757526 55911.38556 -4.747500255 1.116906004 KTVGVEPAADGK ddPTM_SK-BR-3_Pertuzumab_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 ; 113.35 0.001885 478850000 828920 646560 738150 747860 787300 566400 944220 682650 1003540 FALSE TRUE 777039.3769 694431.9751 755659.2666 767051.3537 725468.6338 729910.4853 802642.9767 767880.3552 836042.6909 0.929425477 0.830617841 0.903852488 0.917478691 0.867741135 0.873054084 0.960050229 0.918470269 1 19.67321709 1.134935502 0.678719958 0.998917212 0.879519344 0.513132905 0.033372258 0.50977704 0.559261251 0.031046902 0.012984767 13.64380495 -1.134935502 -0.119397868 KTVT(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KTVTPAK 7 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 KT(0.053)VT(0.947)PAK;KT(0.047)VT(0.953)PAK;KTVT(1)PAK 79.201 0.019493 2239130000 7229100 3730920 5632500 4932080 4798680 3956980 5906100 4524600 6963100 TRUE FALSE 6776643.535 4007161.199 5766105.56 5058645.523 4421811.03 5099295.89 5020535.135 5089506.27 5800913.627 1.168202799 0.690781049 0.993999554 0.872042897 0.762261139 0.879050477 0.865473175 0.877362877 1 22.46784871 -2.026183745 7.243637324 1.193520693 0.874956289 0.060873606 0.12776128 0.078415628 0.000283451 0.024294214 0.025405833 0.009414912 2.026183745 -0.318564404 KTYDLLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTYDLLFK 8 1 P61026 P61026 RAB10 Ras-related protein Rab-10 0 ; 88.681 0.023158 229350000 1080270 1130340 918880 994320 1488470 753660 1342500 1463580 1394890 FALSE TRUE 1012657.829 1214031.55 940676.2675 1019835.935 1371571.57 971229.4074 1141204.588 1646311.185 1162073.848 0.871422957 1.044711188 0.809480628 0.877599936 1.180279182 0.835772537 0.982041365 1.416701002 1 20.14827032 1.403678492 9.846821952 1.207446546 0.93938373 0.366758304 0.14606085 0.346590771 43.15583389 0.085602038 0.031753731 25.33252569 -1.403678492 -0.268062817 KTYVTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTYVTPR 7 1 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 ; 138.1 0.0045197 4801000000 3124700 3802500 3768300 3588900 4033000 2758600 3775300 3621700 3717600 FALSE TRUE 2929130.605 4084041.056 3857685.856 3680997.25 3716264.448 3554963.038 3209228.813 4073877.217 3097108.543 0.94576298 1.318662552 1.245576576 1.18852704 1.199914177 1.147832886 1.036201595 1.315380834 1 21.56249051 2.158026296 3.890355694 1.115253303 1.208465911 0.020974056 0.125946676 0.511651637 15.00696412 0.046671551 0.033612225 143.88857 -2.158026296 0.093212608 KVAT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVATPK 6 1 P07305-2;P07305 P07305-2 H1F0 "Histone H1.0;Histone H1.0, N-terminally processed" 1 KVAT(1)PK 54.066 0.096586 164130000 598570 311430 408980 346470 448590 196440 462980 302550 516420 TRUE FALSE 561106.5722 334488.6012 418681.1987 355361.0068 413359.5509 253149.0391 393560.4471 340324.0335 430226.1658 1.304213032 0.777471544 0.973165354 0.825986504 0.960795934 0.588409212 0.914775712 0.791035182 1 18.71473574 4.744246861 24.90508982 0.850755674 1.304213238 0.57738483 0.121033382 399.2926151 1748801.233 0.025705539 0.228701705 55494.10623 -4.744246861 0.453457564 KVCGDSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVCGDSDK 8 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ; 100.57 0.0096386 462890000 1116640 574140 872860 816400 731480 568000 888750 705410 618960 FALSE TRUE 1046751.496 616649.923 893564.6514 837350.2062 674032.5114 731972.3793 755490.1883 793481.9913 515651.5774 2.029958875 1.195865484 1.73288455 1.623868214 1.307147192 1.419509629 1.465117574 1.538794849 1 18.97603705 -3.21076844 0.187951893 5.75E-12 1.631242844 0.393589671 0.222606311 69.57477109 1.247320242 28.35458936 0.616018945 0.000615505 3.21076844 1.631242844 KVCGEEGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVCGEEGVR 9 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 103.22 0.005544 116030000 127550 139080 125870 125420 156790 112020 150360 110560 189420 FALSE TRUE 119566.8732 149377.6279 128855.6958 128638.4895 144476.3459 144358.3555 127814.9139 124363.6594 157804.5783 0.757689507 0.946598822 0.816552328 0.815175903 0.915539634 0.914791935 0.809956943 0.78808651 1 17.26777954 2.755645555 24.63957805 0.871233638 0.849861294 0.070422057 0.0754805 3918.192362 5650733.863 0.022149991 0.023422143 569.699128 -2.755645555 -0.021372344 KVDAETVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVDAETVGR 9 1 P11172-2;P11172-3;P11172;P11172-4;E9PFD2 P11172-2 UMPS Uridine 5-monophosphate synthase;Orotate phosphoribosyltransferase;Orotidine 5-phosphate decarboxylase 0 136.48 0.00030736 240760000 453350 409450 502520 431630 514060 397590 504080 423090 551010 FALSE TRUE 424975.6328 439766.104 514440.0117 442706.3565 473687.8012 512367.7787 428497.8836 475913.7178 459042.8713 0.925786368 0.958006608 1.120679666 0.964411789 1.031903186 1.116165419 0.933459401 1.036752224 1 18.80826937 4.349712823 4.068671846 1.028318461 0.933015127 0.288228252 0.058007847 0.274219581 7.779056537 0.013730612 0.042384733 22372.41277 -4.349712823 -0.095303334 KVDAVFVGTGDLFAAMLLAWTHKHPNNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVDAVFVGTGDLFAAMLLAWTHKHPNNLK 29 2 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 162.07 1.98E-12 44955000 110250 119460 117580 124970 144460 73520 156410 99576 101260 FALSE TRUE 103349.6493 128304.9427 120369.0531 128176.9418 133114.6943 94744.0305 132957.7725 112008.2828 84359.05184 1.225116298 1.520938653 1.426865885 1.519421319 1.577953894 1.123104497 1.576093728 1.32775654 1 16.36425526 0.979085432 23.13038325 0.999999994 1.435350587 0.446365844 0.147687962 490.6017426 542580.5542 0.125328106 0.031332026 9.529836121 -0.979085432 0.435350592 KVDEAIALFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVDEAIALFQK 11 1 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 109 0.0021817 0 1212300 1126900 1090600 1014200 1323500 765110 1257400 1109200 1574000 FALSE TRUE 1136424.307 1210336.849 1116469.547 1040226.089 1219557.649 985984.8365 1068864.543 1247686.062 1311289.232 0.866646564 0.923012879 0.851428899 0.793285008 0.930044737 0.751920181 0.81512493 0.951495697 1 20.32255451 -1.969912465 6.510935939 1.090919941 0.857256232 0.326502159 0.062882928 0.045851824 0.000211885 0.033638633 0.013785148 0.010717353 1.969912465 -0.233663708 KVDEGAGDSAAVASGGAQTLALAGS(ph)PAPSGHPK ddPTM_SK-BR-3_Pertuzumab_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(0.973)PAPS(0.027)GHPK 300.47 3.48E-90 3755030000 2225895 1574922 2088910 1810609 1993796 1691815 2768343 2053220 2989248 TRUE FALSE 2086580.205 1691530.864 2138459.932 1857072.292 1837211.305 2180214.526 2353255.667 2309569.037 2490323.198 0.837875263 0.6792415 0.858707791 0.745715373 0.737740108 0.875474528 0.944959943 0.927417389 1 21.24790156 2.003456695 2.857714503 0.950249117 0.769971437 0.712632153 0.053848718 0.142433608 2.236840187 0.025191105 0.014620562 100.7991095 -2.003456695 -0.18027768 KVDIIADAAYSIFQKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVDIIADAAYSIFQKPK 17 2 Q6YN16-2;Q6YN16 Q6YN16-2 HSDL2 Hydroxysteroid dehydrogenase-like protein 2 0 148.24 2.08E-07 104480000 363930 270440 273900 297100 391850 254750 349990 292420 461440 FALSE TRUE 341152.2709 290463.659 280397.0373 304724.089 361075.6816 328292.1895 297512.2486 328929.2807 384422.683 0.887440534 0.755584079 0.729397743 0.792679783 0.939267368 0.853987561 0.773919599 0.855644829 1 18.55233394 2.977817275 24.12002831 0.860809291 0.772805765 0.242856131 0.07338992 679.9561196 739340.2553 0.021684588 0.02319444 950.2049208 -2.977817275 -0.088003526 KVDLTLLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVDLTLLSPK 10 1 E7EVA0;P27816-4;B5MEG9 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 KVDLTLLS(1)PK 87.519 0.0078528 428310000 1136100 689620 896060 817660 1014500 511650 815100 719420 1494600 TRUE FALSE 1064993.529 740680.1823 917314.9664 838642.5399 934825.2623 659355.0491 692883.322 809241.1706 1245141.605 0.855319206 0.594856183 0.736715377 0.673531859 0.750778272 0.52954222 0.556469497 0.649918987 1 20.24787839 -1.076734312 5.06153896 1.000007284 0.656830741 0.531996592 0.097209771 7.76E-06 1.42E-06 0.091447932 0.021554027 0.083804181 1.076734312 -0.343176543 KVDQYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVDQYK 6 1 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 85.265 0.088045 683490000 2405300 2293100 2379700 2455200 2879900 1869900 3254600 2527700 3243600 FALSE TRUE 2254756.567 2462883.51 2436147.608 2518204.589 2653724.271 2409709.775 2766602.944 2843288.909 2702222.206 0.834408274 0.911428936 0.901534893 0.931901375 0.982052573 0.891751156 1.023825109 1.052203961 1 21.36571488 2.541347021 0.505558029 1.030613821 0.868416168 0.64989681 0.039590646 0.619464038 0.329023991 0.034702094 0.038190447 347.8139693 -2.541347021 -0.162197653 KVDSSVLGSLSSVPLTGFSFS(ph)PGNSSLFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVDSSVLGSLSSVPLTGFSFSPGNSSLFGK 30 1 Q9UKX7-2;Q9UKX7 Q9UKX7-2 NUP50 Nuclear pore complex protein Nup50 1 KVDSSVLGSLSSVPLTGFS(0.011)FS(0.989)PGNSSLFGK;KVDSSVLGSLSSVPLTGFS(0.002)FS(0.997)PGNSSLFGK 285.41 3.99E-72 666710000 1338070 1056730 1156780 947580 1413320 1022080 1639510 1252960 1636480 TRUE FALSE 1254322.587 1134971.389 1184219.368 971896.507 1302323.548 1317137.904 1393680.696 1409394.814 1363340.916 0.9200359 0.832492721 0.868615732 0.712878559 0.955244234 0.966110449 1.022253994 1.033780178 1 20.37871494 2.525361005 7.667907365 1.001983431 0.838362335 0.697506988 0.053843746 0.153915038 21.98823451 0.016707664 0.015596036 335.2439932 -2.525361005 -0.163621097 KVDT(ph)TPNQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVDTTPNQGK 10 1 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KVDT(0.675)T(0.325)PNQGK 160.69 1.41E-05 86747000 269890 159640 195490 178500 208520 142610 276880 181330 216170 TRUE FALSE 252998.0667 171459.9117 200127.1151 183080.6122 192143.6803 183779.1919 235364.4144 203969.4497 180089.8305 1.404843716 0.952079922 1.111262721 1.016607166 1.066932429 1.020486229 1.306927847 1.132598377 1 17.45835719 KVDTT(ph)PNQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KVDTTPNQGK 10 1 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KVDT(0.03)T(0.97)PNQGK;KVDT(0.097)T(0.903)PNQGK;KVDT(0.091)T(0.909)PNQGK;KVDT(0.062)T(0.938)PNQGK 164.81 3.54E-06 3593780000 11795950 6618010 8499960 7247670 8526800 6311700 11736210 7667670 8774510 TRUE FALSE 11057662.55 7108014.346 8701583.065 7433657.482 7857139.523 8133785.328 9976474.264 8624995.478 7309987.595 1.512678702 0.972370234 1.19036906 1.016917934 1.074849912 1.112694819 1.364773077 1.179891944 1 22.80143753 KVDVDEYDENKFVDEEDGGDGQAGPDEGEVDSCLR ddPTM_SK-BR-3_Pertuzumab_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 605820000 680050 407044 496940 481230 525940 407867 697850 436490 679030 FALSE TRUE 637486.8844 437181.9613 508727.6515 493579.1765 484634.7939 525611.5817 593213.871 490986.7373 565695.5063 1.126908164 0.772822051 0.899295904 0.872517407 0.856706105 0.929142226 1.048645189 0.867934661 1 19.10966619 1.994699759 13.71237251 0.980425291 0.885806487 0.063928636 0.09988447 1.184874889 3047.044269 0.035487692 0.024977651 98.78699146 -1.994699759 -0.094618805 KVDWLTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVDWLTEK 8 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3QL52;Q14240;Q14240-2;E7EQG2;P38919;I3L3H2;J3KTN0 P60842;Q14240;P38919;J3KTN0 EIF4A1;EIF4A2;EIF4A3 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed;Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ; 135.55 0.0013293 4158500000 14191000 15140700 12277600 12074300 17543100 9229300 14680100 15422700 17950000 FALSE TRUE 13302810.64 16261733.18 12568830.47 12384146.98 16165335.69 11893649.08 12478955.29 17348258.04 14954029.04 0.889580367 1.087448282 0.840497931 0.828147849 1.081002026 0.795347465 0.834487833 1.160105949 1 23.8340309 1.238937175 24.99999927 1.080052979 0.912727397 0.305055205 0.107737754 12.55386437 833966.3286 0.081906404 0.025691101 17.33553206 -1.238937175 -0.167325582 KVEAPETNIDKT(ph)PK ddPTM_SK-BR-3_Pertuzumab_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 123.55 0.0048719 369250000 1781270 677910 963330 860210 1038630 560280 1560570 739270 1729890 TRUE FALSE 1669783.49 728103.1618 986180.6425 882284.4449 957060.1894 722023.7406 1326577.016 831569.4868 1441160.183 1.158638373 0.505220148 0.684296343 0.612204289 0.664090085 0.501001727 0.920492414 0.57701392 1 20.45879927 -1.312863119 4.801727675 1.000156592 0.687956927 0.17459619 0.200717766 0.000299715 4.29E-05 0.173111465 0.040782423 0.048656054 1.312863119 -0.312199665 KVEDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVEDAK 6 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 94.662 0.070915 176230000 432260 228730 337150 291740 299660 209850 330960 257560 353530 FALSE TRUE 405205.6182 245665.4072 345147.3572 299226.5423 276125.9124 270430.2884 281335.6205 289716.933 294523.5591 1.375800358 0.834111227 1.171883697 1.015968105 0.93753421 0.918195778 0.955222806 0.983679994 1 18.16802352 2.999090811 24.89986567 0.955137559 1.073708674 0.214619154 0.134497644 59.53015303 1630442.044 0.036284057 0.04285437 997.9087054 -2.999090811 0.118571115 KVEDLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVEDLAR 7 1 Q9NVP1;H7C452 Q9NVP1 DDX18 ATP-dependent RNA helicase DDX18 0 81.594 0.042935 163630000 245890 494130 207290 228650 637130 141320 274530 526020 600900 FALSE TRUE 230500.1838 530715.8993 212207.0167 234517.5461 587092.3799 182116.7899 233366.7751 591694.7549 500605.908 0.460442396 1.060147095 0.423900344 0.468467396 1.172763586 0.36379273 0.46616864 1.181957195 1 18.93331579 1.231788627 24.99212242 1.090978803 0.643292554 0.321680512 0.277345699 207.8874935 767177.1512 0.234985297 0.064006712 17.05252233 -1.231788627 -0.447686249 KVEEAEPEEFVVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KVEEAEPEEFVVEK 14 1 Q13185;S4R2Y4;C9JMM0;B8ZZ43 Q13185 CBX3 Chromobox protein homolog 3 0 ;;;;;;; 214.22 1.12E-11 9346870000 20592000 13070960 16244240 15175210 16184370 11562220 20585830 14138905 21923170 FALSE TRUE 19303183.48 14038747.48 16629561.04 15564631.58 14913314.86 14900045.22 17499175.9 15904178.41 18264051.3 1.056894944 0.768654624 0.910507793 0.852200387 0.816539256 0.815812712 0.958121263 0.870791379 1 24.12250348 0.791123417 0.941424045 0.997214924 0.865075128 0.152969825 0.082468797 1.323143215 2.257747724 0.071134342 0.023673908 6.181920519 -0.791123417 -0.132139796 KVEEDEAGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVEEDEAGGR 10 1 Q92890;Q92890-1 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 0 69.03 0.093321 327700000 157240 131620 148860 160880 192830 134460 205020 163720 231750 FALSE TRUE 147398.6291 141365.2818 152391.0295 165008.4532 177685.9096 173276.4192 174279.1543 184160.8024 193069.4278 0.763448832 0.732199206 0.789306889 0.854658632 0.920321315 0.89748243 0.90267608 0.953857918 1 17.55876021 3.01074894 0.412447583 0.985153522 0.692869017 0.922104995 0.023782022 0.414451846 0.133498472 0.024984975 0.050533387 1025.059181 -3.01074894 -0.292284505 KVEEDLKADEPSS(ph)EES(ph)DLEIDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KVEEDLKADEPSSEESDLEIDK 22 2 P50502;Q3KNR6;F6VDH7 P50502 ST13 Hsc70-interacting protein 2 KVEEDLKADEPS(0.009)S(0.991)EES(1)DLEIDK;KVEEDLKADEPS(0.041)S(0.959)EES(1)DLEIDK;KVEEDLKADEPS(0.08)S(0.92)EES(1)DLEIDK 239.15 7.54E-31 417693000 2766410 587850 1177220 1051970 882430 948500 1770040 833860 758890 TRUE FALSE 2593265.336 631375.0257 1205144.214 1078965.331 813127.5074 1222316.552 1504638.934 937969.2566 632226.3564 4.101798842 0.99865344 1.906191038 1.706612387 1.286133517 1.93335273 2.379905423 1.483597207 1 19.27008165 4.748362486 24.91126048 1.665933995 4.10180022 0.765512779 0.435491199 668.8237645 1699766.539 0.105523961 1.408392531 56022.50003 -4.748362486 2.435866225 KVEEEEDESALKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVEEEEDESALKR 13 2 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 105.58 0.00081074 232770000 552250 320270 438560 390250 405320 298360 513720 352580 451570 FALSE TRUE 517685.6583 343983.124 448962.8503 400264.4757 373487.8022 384491.6885 436692.4551 396600.3891 376200.0497 1.376091414 0.91436225 1.193415181 1.063967099 0.992790411 1.022040504 1.160798505 1.05422737 1 18.52114051 4.756475016 24.71335101 1.061929077 1.376091721 0.612176018 0.081041603 2367.823124 3266408.061 0.018781485 0.596795339 57078.82397 -4.756475016 0.314162644 KVEEEGS(ph)PGDPDHEASTQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KVEEEGSPGDPDHEASTQGR 20 1 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 1 KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(1)PGDPDHEASTQGR 210.79 2.05E-22 5655157000 5006919 4080020 4529649 4529402 4912068 3824427 5625590 4031270 5769550 TRUE FALSE 4693544.877 4382108.926 4637094.413 4645634.124 4526293.994 4928476.991 4782085.005 4534582.933 4806574.832 0.976484304 0.911690565 0.964739877 0.96651655 0.941688032 1.025361544 0.994904932 0.943412532 1 22.19657776 2.262503577 24.9981534 0.992212878 0.949052983 0.341660452 0.02646155 230.2657761 240413.0323 0.008888223 0.007432792 183.0221181 -2.262503577 -0.043159895 KVEEEQEADEEDVS(ph)EEEAESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KVEEEQEADEEDVSEEEAESK 21 1 Q9H3N1 Q9H3N1 TMX1 Thioredoxin-related transmembrane protein 1 1 KVEEEQEADEEDVS(1)EEEAESK;KVEEEQEADEEDVS(1)EEEAESK;KVEEEQEADEEDVS(1)EEEAESK;KVEEEQEADEEDVS(1)EEEAESK;KVEEEQEADEEDVS(1)EEEAESK 328.37 3.13E-80 3176020000 5693910 2391390 2891670 2768020 3499370 2267650 4490850 3126710 3760940 TRUE FALSE 5337538.337 2568451.004 2960261.778 2839052.079 3224543.596 2922283.743 3817488.734 3517086.626 3133214.817 1.703534117 0.819749412 0.944800134 0.906114724 1.029148585 0.932679026 1.218393553 1.122516914 1 21.57921226 -0.074840855 7.832037285 0.999999991 1.047353438 0 0.249717204 0 0 0.222464144 0.052435302 0.841703522 0.074840855 0.047353446 KVEEVLEEEEEEYVVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVEEVLEEEEEEYVVEK 17 1 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 0 ; 104.61 0.0013501 137873000 169316 118135 137939 136255 151002 89485 173189 129407 182308 FALSE TRUE 158718.8138 126881.8383 141210.9782 139751.534 139142.912 115317.8668 147220.9173 145563.7488 151879.617 1.045030379 0.835410576 0.929755954 0.920146737 0.916139471 0.759271514 0.969326366 0.9584153 1 17.21256874 1.590848406 24.99999996 0.972934387 0.895632217 0.188008488 0.072787529 1.441655452 2111.896292 0.03550803 0.016503786 38.98058978 -1.590848406 -0.07730217 KVEEVVYDLSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVEEVVYDLSIR 12 1 E9PGT1;Q15631 E9PGT1 TSN Translin 0 ; 185.87 2.00E-05 412380000 1010160 1054960 1007190 964490 1116600 766690 1162670 998140 1292790 FALSE TRUE 946935.8888 1133070.336 1031081.022 989240.4463 1028906.74 988020.9568 988338.4272 1122759.976 1077014.997 0.879222565 1.052046944 0.957350664 0.918502016 0.95533186 0.91736973 0.917664498 1.042473855 1 20.03860691 1.232232412 24.99983021 1.021236946 0.951470089 0.315736987 0.04676118 232.8483406 919833.6354 0.042747179 0.011742733 17.06995643 -1.232232412 -0.069766857 KVEGAPTQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KVEGAPTQGR 10 1 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;; 151.26 3.23E-05 680057000 832580 728860 733720 768430 804790 546823 871880 678810 741060 FALSE TRUE 780470.304 782825.5528 751124.1849 788149.2147 741585.0398 704681.9232 741149.6881 763560.9227 617372.2986 1.264180958 1.267995915 1.216647049 1.276619013 1.201195845 1.141421351 1.200490676 1.236791681 1 19.23578123 -5 0.159371325 0.160842635 1.287232866 0.808388033 0.035643635 54.99143885 0.504975706 14.56888896 0.148948434 1.00E-05 5 1.126390232 KVEGAQNQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KVEGAQNQGK 10 1 Q9P2E9 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;;;; 171.92 6.21E-06 2260470000 3523790 2712870 2857620 2894990 3238400 2027386 3613970 2705130 3031210 FALSE TRUE 3303242.274 2913733.718 2925404.096 2969280.345 2984069.127 2612659.426 3072088.749 3042871.435 2525281.469 1.308068948 1.153825327 1.158446744 1.17582154 1.18167783 1.034601275 1.216533201 1.204963278 1 21.26801277 -5 0.229450112 0.106327923 1.191299524 0.417606345 0.066929 167.1875249 1.673528063 69.6985466 0.109456367 1.00E-05 5 1.084971601 KVEGNFNPFAS(ph)PQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVEGNFNPFASPQK 14 1 Q5TH58;Q9H6K1-2;Q9H6K1 Q5TH58 C6orf106 Uncharacterized protein C6orf106 1 KVEGNFNPFAS(1)PQK 178.71 1.20E-06 471450000 1114600 688960 877340 728450 888570 620420 1068700 769840 1185300 TRUE FALSE 1044839.176 739971.3153 898150.9191 747143.2603 818785.2965 799525.1823 908458.3563 865956.2186 987465.7727 1.058101662 0.749364014 0.909551444 0.756626995 0.829178407 0.809673818 0.919989717 0.876948085 1 19.91337122 0.863078003 1.058904327 0.997329227 0.845158297 0.183571266 0.089552129 0.986366703 2.189968131 0.075351124 0.024221048 7.295885381 -0.863078003 -0.15217093 KVELS(ph)ES(ph)EEDKGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KVELSESEEDKGGK 14 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KVELS(1)ES(1)EEDKGGK;KVELS(1)ES(1)EEDKGGK;KVELS(1)ES(1)EEDKGGK;KVELS(1)ES(1)EEDKGGK;KVELS(1)ES(1)EEDKGGK;KVELS(1)ES(1)EEDKGGK 139.98 4.95E-05 2931590000 26778200 6968070 12266600 11881660 13170170 8097780 16951100 8920380 17246100 TRUE FALSE 25102200.26 7483993.153 12557569.54 12186563.51 12135837.97 10435477.63 14409439.92 10034109.08 14367614.5 1.747137652 0.520893232 0.874019104 0.848196721 0.844666175 0.726319434 1.00291109 0.698383791 1 23.77631721 4.749582867 24.9852726 0.808812713 1.747138197 0.808405979 0.142677804 680.8048461 1543221.065 0.032988075 0.500986699 56180.14641 -4.749582867 0.938325483 KVELS(ph)ESEEDKGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KVELSESEEDKGGK 14 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KVELS(0.975)ES(0.025)EEDKGGK;KVELS(0.522)ES(0.478)EEDKGGK;KVELS(0.999)ES(0.001)EEDKGGK;KVELS(0.99)ES(0.01)EEDKGGK 144.66 4.59E-06 4765230000 7338780 2491112 3918461 3751295 3605925 2574991 5121950 2786974 4384480 TRUE FALSE 6879458.86 2675556.524 4011408.745 3847559.581 3322730.196 3318349.1 4353961.147 3134933.839 3652681.963 1.883399357 0.732490962 1.098209148 1.053351926 0.90966863 0.908469211 1.191990212 0.858255351 1 21.80052471 4.748379389 24.88215931 0.980076929 1.883399877 0.831074652 0.129465996 509.3559073 1290752.048 0.030357911 0.404167576 56024.68056 -4.748379389 0.903322948 KVELSES(ph)EEDKGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVELSESEEDKGGK 14 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KVELS(0.015)ES(0.985)EEDKGGK;KVELS(0.397)ES(0.603)EEDKGGK 208.13 4.42E-09 695420000 3094900 940130 1511110 1457640 1498750 974720 1965950 1102120 1759300 TRUE FALSE 2901195.734 1009738.203 1546954.243 1495045.51 1381044.221 1256105.841 1671174.048 1239722.108 1465661.464 1.979444642 0.688930035 1.055464908 1.020048317 0.942266856 0.857023174 1.140218317 0.845844786 1 20.48312048 4.74755785 24.99949424 0.949765873 1.979445173 0.870029536 0.125786403 404.4702978 1123827.455 0.029372582 0.360316036 55918.80084 -4.74755785 1.0296793 KVELSSSSQHGPSYDVYNPFYMYQHIS(ph)PDLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVELSSSSQHGPSYDVYNPFYMYQHISPDLSR 32 1 Q8N9U0;Q8N9U0-2 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 KVELSSSSQHGPSYDVYNPFYMYQHIS(0.996)PDLS(0.004)R 188.65 2.98E-20 199190000 65763 142300 95810 109220 161020 93671 151430 133390 124090 TRUE FALSE 61647.01122 152836.0401 98082.65844 112022.7701 148374.1387 120712.2971 128724.4773 150044.0351 103378.5773 0.596322882 1.478411137 0.948771602 1.083616867 1.435250344 1.16767226 1.245175554 1.451403559 1 16.65757773 2.799975239 24.69850127 1.264608751 1.089050673 0.158580818 0.248974115 456.4345275 183558.3704 0.069958745 0.074202444 630.9213719 -2.799975239 -0.175558077 KVENTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KVENTR 6 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;; 101.64 0.05819 743601000 1087220 884120 965590 908610 1002280 691800 899430 1007450 756930 FALSE TRUE 1019172.841 949581.1647 988494.2508 931926.4709 923564.9718 891511.4296 764568.8214 1133232.35 630593.493 1.616212112 1.505853097 1.567561768 1.477856148 1.464596419 1.413765666 1.212459104 1.797088557 1 19.26635076 -3.375345602 0.194150595 9.19E-16 1.585441987 0.478408796 0.157174473 56.65383833 0.984013855 23.60771481 0.395802747 0.000421361 3.375345602 1.585441987 KVEQNSRPVS(ph)CSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 KVEQNSRPVSCSGR 14 2 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 1 KVEQNS(0.002)RPVS(0.966)CS(0.032)GR;KVEQNSRPVS(0.999)CS(0.001)GR;KVEQNSRPVS(0.893)CS(0.107)GR;KVEQNSRPVS(0.997)CS(0.003)GR;KVEQNSRPVS(0.969)CS(0.031)GR;KVEQNSRPVS(0.981)CS(0.019)GR;KVEQNSRPVS(0.998)CS(0.002)GR 185.59 9.14E-07 10181470000 3695190 4033970 3551020 3704660 4956710 2835070 4409420 3652330 5509480 TRUE FALSE 3463914.654 4332649.336 3635251.871 3799727.848 4567429.991 3653508.685 3748268.406 4108331.44 4589912.195 0.754679939 0.943950375 0.792009023 0.827843254 0.995101823 0.795986618 0.816631832 0.895078438 1 22.13003512 0.940219547 6.286939675 0.999992312 0.851054045 0.311344209 0.072198921 0.613900669 62.31632338 0.064063291 0.016094623 8.714039956 -0.940219547 -0.148938268 KVEQNSRPVSCSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KVEQNSRPVSCSGR 14 2 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 0 ;;; 142.32 5.30E-06 398592000 266637 281848 269579 267707 323478 231141 315763 258778 431668 FALSE TRUE 249948.6661 302716.3192 275973.5412 274576.8148 298073.3427 297867.6544 268417.2696 291087.0029 359619.8221 0.695035843 0.841767613 0.767403586 0.763519689 0.828856822 0.828284861 0.746391753 0.809429806 1 18.45611302 KVESLWPIFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVESLWPIFR 10 1 P41223;P41223-2 P41223 BUD31 Protein BUD31 homolog 0 ; 142.08 5.83E-05 550960000 1369090 1467260 1410930 1442780 1729780 1162630 1631000 1482490 1545350 FALSE TRUE 1283401.101 1575897.457 1444397.926 1479804.177 1593930.056 1498262.407 1386446.691 1667582.14 1287421.102 0.996877478 1.224073036 1.121931219 1.149432905 1.238079797 1.163770273 1.076917793 1.295288805 1 20.29605259 -1.0998866 7.93317059 0.999999989 1.157294147 0.259378169 0.084047876 1.46E-08 1.75E-09 0.071716875 0.016903828 0.079453567 1.0998866 0.157294158 KVEVDGS(ph)LSDSHVSPPAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVEVDGSLSDSHVSPPAKR 19 2 Q9ULI0-2;Q9ULI0;C9JG15 Q9ULI0-2 ATAD2B ATPase family AAA domain-containing protein 2B 1 KVEVDGS(0.49)LS(0.49)DS(0.02)HVSPPAKR 52.061 0.068077 66133000 38030 53757 54830 50294 59697 41366 67277 52951 79395 TRUE FALSE 35649.77019 57737.22421 56130.59349 51584.62919 55008.63843 53307.69268 57189.43842 59562.04891 66143.46159 0.538976481 0.87290902 0.848618928 0.779890075 0.83165648 0.805940472 0.864627237 0.90049791 1 16.01331093 8 0.066570896 1.183729253 0.031297496 0.525142276 0.081199375 274.2352397 1.352844164 4.298664028 29.90499615 100000000 -8 -1.152431757 KVEVDGSLS(ph)DSHVSPPAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVEVDGSLSDSHVSPPAKR 19 2 Q9ULI0-2;Q9ULI0;C9JG15 Q9ULI0-2 ATAD2B ATPase family AAA domain-containing protein 2B 1 KVEVDGS(0.031)LS(0.95)DS(0.018)HVS(0.001)PPAKR 68.569 0.012603 66161000 47355 84355 71110 72774 95283 57468 108850 71181 119700 TRUE FALSE 44391.13508 90600.73197 72796.76278 74641.50405 87799.85753 74058.07868 92528.95301 80068.10454 99721.29671 0.445152004 0.908539449 0.730002168 0.748501138 0.880452425 0.742650578 0.92787555 0.802918807 1 16.60561402 7.396010911 0.113096066 1.048341326 3.21E-16 0.418259022 0.116881341 100.9957084 0.908787581 0.93666342 16.341526 24889198.46 -7.396010911 -1.048341326 KVEWTSDTVDNEHMGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVEWTSDTVDNEHMGR 16 1 O60927 O60927 PPP1R11 Protein phosphatase 1 regulatory subunit 11 0 186.83 9.34E-10 101310000 130090 146500 132740 144090 156260 122520 142640 118270 168560 FALSE TRUE 121947.8991 157347.0124 135888.6555 147787.5933 143987.9699 157889.5351 121252.4562 133036.2698 140426.2471 0.868412435 1.120495746 0.967687012 1.052421441 1.025363655 1.124359145 0.863460064 0.947374673 1 17.09945309 1.729056125 24.99999932 0.928968475 1.031482805 0.214692881 0.079835014 0.97973207 2563.843998 0.032943169 0.018268669 53.58659046 -1.729056125 0.10251433 KVFASLPQVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVFASLPQVER 11 1 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ; 116.51 0.00157 877960000 1291750 1423300 1252990 1207560 1656150 991670 1412670 1337400 1758610 FALSE TRUE 1210901.673 1528682.613 1282711.515 1238548.034 1526082.66 1277949.031 1200853.248 1504377.334 1465086.63 0.826505169 1.04340766 0.875519228 0.84537529 1.041633053 0.872268577 0.819646582 1.026818007 1 20.48255454 KVFIEDVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KVFIEDVSR 9 1 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ;;; 164.64 9.96E-05 2428630000 3557330 9528670 2716940 2941780 10503680 1578200 2617690 8229730 7445530 FALSE TRUE 3334683.065 10234182.64 2781387.1 3017271.055 9678763.343 2033800.72 2225191.686 9257229.906 6202822.943 0.537607327 1.649923387 0.448406657 0.486435141 1.5603804 0.327883085 0.358738546 1.492422078 1 22.56449351 3.957941542 23.07533234 0.748423285 1.15770998 0.036081596 0.515348508 343.4390805 413196.4185 0.123508287 0.22326487 9076.983413 -3.957941542 0.409286694 KVFSDVMEDLYNYINPHNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVFSDVMEDLYNYINPHNGK 20 1 P23921 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 195.93 1.17E-21 139440000 427070 407460 408090 432310 465680 268710 467380 376230 562080 FALSE TRUE 400340.451 437628.7624 417770.0875 443403.8065 429107.3713 346282.2149 397300.7079 423203.1437 468265.2168 0.854943815 0.934574567 0.892165535 0.946907416 0.916376779 0.739500186 0.848452316 0.903768054 1 18.83696635 KVFVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVFVGR 6 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;H0YBN4;Q13148;A0A087WYY0;A0A087X260;G3V162;B1AKP7;K7EN94;A0A0A0N0M3;A0A087WXQ5;Q13148-4;A0A087WV68;A0A087WXV3;K7EJM5;A0A087WX67;A0A087WW61;A0A087WZC9;A0A087WZM1;B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0YCC8 P11940-2;Q13148;B1ANR0 PABPC1;TARDBP;TDP43;PABPC4 Polyadenylate-binding protein 1;Polyadenylate-binding protein;TAR DNA-binding protein 43;Polyadenylate-binding protein 4 0 ; 119.7 0.033331 4128100000 4632200 5321500 5332200 5273000 6135000 4587300 5625600 5136100 6237200 FALSE TRUE 4342278.871 5715509.397 5458682.302 5408314.107 5653181.847 5911579.041 4782093.506 5777353.391 5196171.026 0.835668966 1.099946358 1.050520138 1.040826809 1.087951459 1.137679844 0.920311029 1.111848198 1 22.30901749 4.746083891 24.68912064 1.053964125 0.835668842 0.555166853 0.061992942 583.6737234 1915385.853 0.014177509 0.147060979 55729.33892 -4.746083891 -0.218295283 KVGDDIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 KVGDDIAK 8 1 P30050 P30050 RPL12 60S ribosomal protein L12 0 ;;;;;; 102.06 0.0080774 10600700000 15801730 10779020 13022970 12561670 12925480 9788240 16962860 11552540 16684500 FALSE TRUE 14812727.93 11577109.86 13331881 12884023.72 11910364.94 12613945.99 14419436.62 12994900.05 13899749.16 1.065683111 0.832900631 0.959145438 0.926924908 0.85687625 0.907494505 1.037388261 0.934901767 1 23.72855551 1.756505537 25 0.992670667 0.915654312 0.168696815 0.066905729 10.10527171 14092.77894 0.028053098 0.015557105 57.0828354 -1.756505537 -0.077016354 KVGGGGTAGGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVGGGGTAGGDR 12 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 ; 81.494 0.028053 200737000 177687 163861 169160 167030 178591 150205 202411 170260 164358 FALSE TRUE 166565.8879 175993.4389 173172.5551 171316.2726 164565.1833 193566.7451 172061.3496 191517.3358 136925.588 1.21647013 1.285321769 1.264720186 1.251163315 1.201858511 1.413663786 1.256604789 1.398696464 1 17.06303255 -1.507077152 7.53102111 0.99994487 1.284184783 0.625832615 0.069499691 5.74E-05 3.76E-06 0.060054618 0.014152276 0.031111636 1.507077152 0.284239913 KVGTLWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVGTLWR 7 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C0V6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 116.73 0.0086442 1147210000 832780 1530060 831320 749010 1469170 634050 976130 1431420 1912230 FALSE TRUE 780657.7864 1643347.234 851039.303 768230.8647 1353787.315 817089.9421 829768.3684 1610135.938 1593066.46 0.490034663 1.031562258 0.534214563 0.482234034 0.849799647 0.512903864 0.520862368 1.010714856 1 20.60337502 1.225705554 24.97499166 1.005357838 0.651401494 0.426402991 0.179057164 265.6046055 516004.611 0.167536636 0.042972012 16.81533615 -1.225705554 -0.353956343 KVGWIFTDLVSEDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVGWIFTDLVSEDTR 15 1 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 130.87 9.15E-05 76213000 105030 121650 124800 134740 158280 114790 142280 109340 167890 FALSE TRUE 98456.35978 130657.0926 127760.3149 138197.6565 145849.3273 147928.0095 120946.4349 122991.3397 139868.0744 0.703923038 0.934145216 0.913434431 0.98805719 1.042763532 1.057625267 0.864717952 0.879338192 1 17.09370717 5.313778176 1.403944368 0.959607023 8.33E-18 0.606516334 0.064610945 4.16510155 2.370508056 0.018226865 8.397704171 205957.7677 -5.313778176 -0.959607023 KVGYTPDWIFLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVGYTPDWIFLLR 13 1 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 146.96 6.82E-05 92837000 78680 281970 104410 97915 289080 50435 85480 222900 141800 FALSE TRUE 73755.55925 302847.3522 106886.6545 100427.6647 266376.8229 64994.76576 72663.06756 250729.5557 118132.6639 0.624345179 2.563620781 0.904801864 0.850126132 2.25489559 0.550184543 0.615097172 2.122440545 1 16.8500484 3.741541099 23.37744497 1.129256912 1.733015647 0.038902408 0.739160026 395.5500547 641256.9163 0.176709321 0.316346084 5514.943903 -3.741541099 0.603758736 KVICIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVICIPK 7 1 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 92.925 0.04214 0 444240 586860 362040 391130 673940 277240 457910 596440 850890 FALSE TRUE 416435.8114 630311.725 370627.7598 401167.058 621011.4709 357274.6874 389250.6465 670906.8469 708870.962 0.587463493 0.889176957 0.52284235 0.565923954 0.876057145 0.504005251 0.549113544 0.946444251 1 19.43516351 1.175448704 6.959183476 0.984114448 0.648424067 0.503938895 0.136595217 0.199413041 17.33161991 0.127616455 0.032324679 14.97782336 -1.175448704 -0.335690381 KVIDDTNITR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVIDDTNITR 10 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 149.38 3.76E-05 355600000 398160 440980 726710 662160 639920 848950 679770 333000 522900 FALSE TRUE 373239.8763 473630.618 743947.9044 679152.1466 589663.2645 1094028.083 577844.7992 374575.783 435624.6119 0.856792445 1.087244855 1.707772894 1.559030707 1.353604109 2.511400994 1.326474178 0.859859091 1 18.73272594 4.299540321 2.277152436 1.537678629 0.877439987 0.175519917 0.448395395 0.497942444 4.799598106 0.110513853 0.451120095 19931.51547 -4.299540321 -0.660238642 KVIEINPYLLGTMAGGAADCSFWER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVIEINPYLLGTMAGGAADCSFWER 25 1 P28074;H0YJM8;P28074-2 P28074 PSMB5 Proteasome subunit beta type-5 0 120.6 4.76E-07 0 49435 61937 44479 42529 74935 32786 55489 45937 62009 FALSE TRUE 46340.95159 66522.87993 45534.06288 43620.36614 69049.90737 42250.78596 47168.93958 51672.33557 51659.29731 0.897049592 1.287723283 0.881430164 0.844385588 1.336640469 0.817873803 0.913077453 1.000252389 1 15.6567404 KVIIWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVIIWR 6 1 P55735;P55735-4;P55735-3;P55735-2;A8MXL6 P55735 SEC13 Protein SEC13 homolog 0 ; 136.58 0.021019 347670000 463050 653900 669680 770990 801590 658080 902930 750560 743830 FALSE TRUE 434068.5271 702315.4364 685565.1258 790774.9087 738636.3549 848057.013 767544.0289 844269.0682 619679.9677 0.700472098 1.133351848 1.106321265 1.276102101 1.191964229 1.368540307 1.238613589 1.362427563 1 19.24116381 5.188063936 0.950363119 1.243456828 8.63E-31 0.655334528 0.114956715 2.443326417 0.971445919 0.031989938 3.82158034 154192.7436 -5.188063936 -1.243456828 KVIQYLAYVASSHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVIQYLAYVASSHK 14 1 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 ; 142.85 6.03E-06 317421000 491370 876690 622480 638610 1035420 523500 939510 919650 1142290 FALSE TRUE 460616.0288 941601.0398 637245.5196 654997.8138 954102.2899 674625.9517 798639.1975 1034470.327 951634.4195 0.484026239 0.989456687 0.669632693 0.688287225 1.002593297 0.708912937 0.839228995 1.087045935 1 19.86004793 1.345214765 4.553943278 1.041672279 0.780765344 0.360188204 0.153266195 0.227309 7.139777972 0.102672432 0.035044162 22.14189386 -1.345214765 -0.260906935 KVIS(ph)PPPFAPSPTLPPTFHPEEFLDEDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVISPPPFAPSPTLPPTFHPEEFLDEDLK 29 1 Q5TC82-2;Q5TC82 Q5TC82-2 RC3H1 Roquin-1 1 KVIS(1)PPPFAPSPTLPPTFHPEEFLDEDLK 161.01 3.10E-12 103950000 179460 95222 138650 120510 126010 107770 172310 108300 132680 TRUE FALSE 168227.9189 102272.336 141938.8435 123602.4906 116113.6829 138881.4495 146473.7151 121821.4934 110534.8509 1.521944596 0.925249685 1.284109422 1.118221897 1.05047125 1.256449422 1.325136045 1.102109357 1 16.75414179 KVLVTVEEDDTIMEELVDNHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KVLVTVEEDDTIMEELVDNHGK 22 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;; 273.87 1.41E-45 159872000 277850 216033 241137 236826 240629 184446 317968 229160 251529 FALSE TRUE 260459.8645 232028.3081 246856.8835 242903.3561 221730.969 237692.566 270291.6503 257771.1304 209547.185 1.242965228 1.1072843 1.178049152 1.159182149 1.058143392 1.134315243 1.289884425 1.230134065 1 17.67691561 KVMDDLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KVMDDLDR 8 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;; 129.85 0.0017205 735420000 982980 1118190 1042000 1095370 1243210 782750 1151920 1081580 1203710 FALSE TRUE 921457.0365 1200981.951 1066716.732 1123479.049 1145573.301 1008717.218 979200.2899 1216617.644 1002803.025 0.918881389 1.197624979 1.063735056 1.120338712 1.142371207 1.005897662 0.976463239 1.213216967 1 19.93560682 2.233699914 24.99896215 1.037917183 1.101512402 0.025643618 0.09603951 291.8119399 1500792.914 0.03255991 0.024805208 171.2773419 -2.233699914 0.063595219 KVMDS(ph)DEDDDY ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KVMDSDEDDDY 11 1 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 KVMDS(0.999)DEDDDY(0.001);KVMDS(0.978)DEDDDY(0.022);KVMDS(1)DEDDDY;KVMDS(1)DEDDDY;KVMDS(1)DEDDDY;KVMDS(1)DEDDDY;KVMDS(0.994)DEDDDY(0.006);KVMDS(1)DEDDDY 115.37 0.0081097 13891410000 31565920 23546310 25957220 25110340 26343490 19260880 31574520 22023310 25217770 TRUE FALSE 29590265.41 25289703.29 26572937.52 25754713.84 24274578.56 24821183.38 26840213.85 24772968.73 21008761.27 1.408472638 1.203769369 1.264850277 1.225903493 1.155450254 1.181468201 1.277572414 1.179173223 1 24.32448776 -5 0.141199879 0.206126721 1.317690079 0.634688364 0.062453381 96.2345138 0.830123288 21.60933403 0.363212155 1.00E-05 5 1.111563358 KVMDSDEDDDY(ph) ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVMDSDEDDDY 11 1 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 KVMDS(0.115)DEDDDY(0.885) 125.48 0.0003436 13271000000 4633000 3179700 3668500 3644000 3739400 2776900 4424900 3011900 3574800 TRUE FALSE 4343028.8 3415128.296 3755518.552 3737511.209 3445722.608 3578545.951 3761427.324 3387942.345 2978142.786 1.458301066 1.14673088 1.26102703 1.254980529 1.157003829 1.201603217 1.263011076 1.137602388 1 21.50598149 -5 0.136343831 0.217322872 1.317955075 0.521921282 0.081584968 123.8735293 1.046933568 26.39196399 0.507073514 1.00E-05 5 1.100632203 KVNAEGS(ph)VDSVFSQVCTHLDALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVNAEGSVDSVFSQVCTHLDALK 23 1 P00568;Q5T9B7 P00568 AK1 Adenylate kinase isoenzyme 1 1 KVNAEGS(1)VDSVFSQVCTHLDALK 194.25 1.73E-18 49576000 191680 178030 191470 168200 209790 157730 197620 151290 225550 TRUE FALSE 179683.091 191211.5264 196011.7588 172516.2968 193313.9397 203264.0905 167988.7156 170178.8895 187904.2479 0.956248158 1.017600872 1.043147034 0.918107487 1.028789619 1.081742924 0.894012336 0.905668134 1 17.51963816 1.69007706 10.27292402 0.925713486 1.010150243 0.302257269 0.052665133 0.122416468 20.53319699 0.023617821 0.012769261 48.98657326 -1.69007706 0.084436757 KVNAEGSVDSVFSQVCTHLDALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVNAEGSVDSVFSQVCTHLDALK 23 1 P00568;Q5T9B7 P00568 AK1 Adenylate kinase isoenzyme 1 0 261.82 5.59E-44 571620000 428070 333680 372360 360190 442880 318390 482810 339390 590040 FALSE TRUE 401277.8628 358386.0144 381192.555 369433.0852 408097.9913 410304.0244 410417.1227 381763.5886 491558.5122 0.816337939 0.729081087 0.775477477 0.751554649 0.830212439 0.834700273 0.834930354 0.776639157 1 18.90700363 -5 0.169183343 1.829873906 0.73862164 0.773205924 0.03537616 56.98497912 0.536865448 15.80435224 0.123792406 1.00E-05 5 -1.091252265 KVNEEKDGPIS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVNEEKDGPISPK 13 2 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 KVNEEKDGPIS(1)PK 58.159 0.056928 374570000 677120 294020 427600 374210 502540 236310 568940 331740 811580 TRUE FALSE 634740.2679 315789.5467 437742.8739 383812.8621 463072.5355 304528.8608 483632.7288 373158.4692 676122.055 0.938795389 0.46705997 0.647431733 0.567668011 0.684894883 0.450405158 0.715303879 0.55190992 1 19.36692418 -1.585183631 3.787752218 1.01034024 0.614730896 0.408584313 0.139879349 0.010680418 0.001169668 0.11842645 0.027407008 0.025990604 1.585183631 -0.395609344 KVNELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 KVNELR 6 1 P50502;Q3KNR6;Q8IZP2;F8WAQ7 P50502 ST13;ST13P4 Hsc70-interacting protein;Putative protein FAM10A4 0 ;;;;;;; 100.07 0.061064 4706780000 13079890 13161540 13235470 13498830 14490400 11012700 15567190 12665820 14723580 FALSE TRUE 12261243.03 14136034.12 13549421.6 13845232.83 13352382.44 14191887.71 13233034.38 14247175.51 12266119.38 0.999602454 1.152445503 1.104621696 1.128737819 1.088558005 1.156998988 1.078828109 1.161506347 1 23.54817556 -0.790325877 7.690079282 1.000002742 1.112082305 0.335401927 0.047997049 0 0 0.039636845 0.009342494 0.162059361 0.790325877 0.112079563 KVNLGVGAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVNLGVGAYR 10 1 P17174 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 90.827 0.016941 279910000 293280 439050 304340 296280 512780 277200 332090 409550 488270 FALSE TRUE 274924.1283 471557.7188 311559.0885 303883.0464 472508.3273 357223.14 282296.1875 460683.219 406774.5827 0.675863586 1.159260531 0.765925655 0.747055149 1.161597473 0.878184516 0.693986791 1.132527052 1 18.63387001 1.209821258 24.99969559 1.066263628 0.88400268 0.177351776 0.174408905 456.155467 396788.0121 0.159639004 0.039937918 16.21142748 -1.209821258 -0.182260948 KVNVTVDYIRPAS(ph)PATETVPAFSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KVNVTVDYIRPASPATETVPAFSER 25 2 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 1 KVNVTVDYIRPAS(0.998)PAT(0.002)ETVPAFSER;KVNVTVDYIRPAS(0.995)PAT(0.005)ETVPAFSER;KVNVTVDYIRPAS(0.987)PAT(0.013)ETVPAFSER;KVNVTVDYIRPAS(0.991)PAT(0.009)ETVPAFSER;KVNVTVDYIRPAS(0.978)PAT(0.022)ETVPAFSER 198.21 4.04E-25 4564960000 2557750 2680010 2698900 2838420 3089270 2432070 3034860 2608280 3528810 TRUE FALSE 2397664.993 2878440.729 2762919.183 2911258.663 2846651.196 3134169.128 2579810.917 2933929.5 2939828.814 0.815579799 0.979118483 0.939823152 0.990281696 0.968305087 1.066105997 0.877537803 0.997993314 1 21.48730072 4.740594865 24.64948924 0.970199805 0.815579736 0.5229537 0.048136302 121.1955187 1468429.192 0.010574672 0.069402233 55029.41105 -4.740594865 -0.154620069 KVNVTVDYIRPASPATETVPAFSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVNVTVDYIRPASPATETVPAFSER 25 2 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 291.64 4.19E-63 3271000000 935020 1170790 1073000 1072600 1216080 917520 1344600 978830 1461540 FALSE TRUE 876498.7673 1257476.51 1098452.067 1100124.732 1120573.982 1182393.129 1142989.713 1101039.08 1217599.532 0.719858003 1.032750487 0.902145605 0.903519345 0.920314071 0.971085401 0.938723844 0.904270289 1 20.21560828 4.752957552 24.98736731 0.944636353 0.719857847 0.725482967 0.043818836 1391.019221 2414216.182 0.010091047 0.223080947 56618.39471 -4.752957552 -0.224778506 KVPCS(ph)PDFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVPCSPDFQR 10 1 Q68DQ2 Q68DQ2 CRYBG3 Very large A-kinase anchor protein 1 KVPCS(1)PDFQR 61.167 0.057178 239460000 405150 354800 343210 400510 450850 329950 437480 341100 417080 TRUE FALSE 379792.3847 381069.7612 351351.1033 410787.7647 415442.0596 425201.2087 371883.9354 383687.0859 347466.6536 1.093032614 1.096708871 1.011179345 1.182236512 1.195631452 1.22371803 1.070272303 1.104241463 1 18.406515 3.233781505 24.99897092 1.137963112 1.065374843 0.148340232 0.068375299 187.1445975 978931.2654 0.01901985 0.023459397 1713.095226 -3.233781505 -0.072588268 KVPGVTAIELDEDTGTFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVPGVTAIELDEDTGTFR 18 1 B4DXZ6;P51114;P51114-3;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 284.88 2.23E-39 362340000 529530 532340 617920 577890 638470 490640 714210 555150 641320 FALSE TRUE 496387.6625 571755.0075 632577.3542 592719.6358 588327.1417 632279.8031 607120.8409 624461.6995 534279.5489 0.929078539 1.070142042 1.183981973 1.109381104 1.101159763 1.183425052 1.136335542 1.168792069 1 19.02723527 4.705701266 2.035126471 1.134863163 0.878668045 0.568714591 0.053721896 0.414791366 1.997017112 0.011909606 0.192473433 50781.00205 -4.705701266 -0.256195118 KVPLDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KVPLDER 7 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ;;; 100.15 0.016044 1486540000 4485450 6126010 4487490 4586470 6550640 3177970 4897930 5527310 6768060 FALSE TRUE 4204713.691 6579586.155 4593935.382 4704166.585 6036179.158 4095398.349 4163530.867 6217406.821 5638427.063 0.745724587 1.166918731 0.814754777 0.834304768 1.070543095 0.726337027 0.738420631 1.102684623 1 22.42686132 3.746398537 23.70374864 0.873136147 0.987735969 0 0.164332634 571.4387175 702645.1885 0.039426061 0.070904209 5576.972932 -3.746398537 0.114599822 KVPS(ph)DKER ddPTM_SK-BR-3_Pertuzumab_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 67.061 0.047308 340050000 399380 216670 254500 245580 330520 197661 352790 277420 513240 TRUE FALSE 374383.5187 232712.4722 260536.8602 251881.9986 304562.2925 254722.5219 299892.4146 312056.4977 427576.9283 0.875593359 0.544258721 0.609333299 0.589091651 0.712298237 0.595734954 0.701376512 0.729825388 1 18.70582448 0.599116403 0.965082293 1.00080722 0.634313593 0.559964162 0.093068033 0.858666046 1.280375246 0.081672227 0.026382056 3.972980218 -0.599116403 -0.366493627 KVPS(ph)PEAFLGKPWSSWIDAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVPSPEAFLGKPWSSWIDAAK 21 2 Q9ULK2;C9IZF2;Q9ULK2-2 Q9ULK2 ATXN7L1 Ataxin-7-like protein 1 1 KVPS(1)PEAFLGKPWSSWIDAAK;KVPS(1)PEAFLGKPWSSWIDAAK 205 2.60E-22 142872000 421030 245110 287150 290260 305680 210900 417570 247160 350240 TRUE FALSE 394678.4839 263258.1994 293961.3336 297708.563 281673.1259 271783.4063 354959.255 278018.4701 291782.6814 1.352645339 0.902240661 1.007466695 1.02030923 0.965352448 0.93145832 1.216519272 0.952827182 1 18.15453473 KVPVQEIDDDFFPS(ph)S(ph)GEEAEAASVGEGGGGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVPVQEIDDDFFPSSGEEAEAASVGEGGGGGR 32 1 Q03468;P0DP91 Q03468 ERCC6 DNA excision repair protein ERCC-6 2 KVPVQEIDDDFFPS(0.999)S(0.999)GEEAEAAS(0.001)VGEGGGGGR 65.048 0.016753 41579000 67780 63577 61033 62253 58691 50752 78643 54856 73435 TRUE FALSE 63537.77079 68284.30723 62480.73158 63850.51737 54081.64561 65403.27851 66851.21224 61704.89235 61178.22409 1.038568408 1.116153799 1.021290378 1.043680465 0.884001561 1.06906141 1.092728879 1.008608754 1 15.90073061 3.792535765 4.43896914 1.023793154 1.080467941 0.147718862 0.058299153 0.417438966 16.18606818 0.015497473 0.028458842 6202.057162 -3.792535765 0.056674787 KVPYVDEEGNLVKPLKPNGIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVPYVDEEGNLVKPLKPNGIK 21 3 Q3KQV9;Q3KQV9-2 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 152.04 2.47E-08 123530000 258490 195680 242950 237660 269850 181930 335540 231820 216570 FALSE TRUE 242311.5723 210168.3508 248712.8887 243758.758 248657.0695 234450.2376 285228.892 260763.2373 180423.0679 1.343018801 1.164864079 1.37849828 1.351039869 1.3781889 1.299447129 1.580889269 1.44528768 1 17.46102428 3.767656974 4.139928672 1.382570529 1.246433734 0.022742072 0.154043491 0.415827693 15.46524384 0.037350953 0.067757196 5856.753883 -3.767656974 -0.136136795 KVQIPVSRPDPEPVS(ph)DNEEDS(ph)YDEEIHDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVQIPVSRPDPEPVSDNEEDSYDEEIHDPR 30 2 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 2 KVQIPVSRPDPEPVS(1)DNEEDS(0.759)Y(0.241)DEEIHDPR;KVQIPVSRPDPEPVS(1)DNEEDS(0.987)Y(0.013)DEEIHDPR 168.25 1.23E-12 798170000 576280 580450 574060 617180 709890 475930 681280 557500 763810 TRUE FALSE 540211.6635 623427.122 587676.9743 633017.8837 654138.103 613323.2649 579128.3887 627105.1022 636325.1766 0.848955351 0.979730403 0.923548204 0.994802511 1.027993433 0.963851954 0.910113901 0.985510436 1 19.27940468 4.742817133 24.82907758 0.965606371 0.8489553 0.538261898 0.035550472 342.7748804 1999388.613 0.008736044 0.067659849 55311.7161 -4.742817133 -0.116651071 KVQIPVSRPDPEPVS(ph)DNEEDSY(ph)DEEIHDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KVQIPVSRPDPEPVSDNEEDSYDEEIHDPR 30 2 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 2 KVQIPVS(0.001)RPDPEPVS(0.999)DNEEDS(0.487)Y(0.513)DEEIHDPR;KVQIPVSRPDPEPVS(1)DNEEDS(0.465)Y(0.535)DEEIHDPR;KVQIPVS(0.001)RPDPEPVS(0.999)DNEEDS(0.193)Y(0.807)DEEIHDPR 166.89 6.28E-12 806750000 815410 745273 759310 830230 984260 704798 887710 788190 1036620 TRUE FALSE 764374.9436 800453.7884 777321.1918 851535.1074 906960.1899 908261.7412 754606.1266 886597.2565 863601.4252 0.885101531 0.926878726 0.90009253 0.986027909 1.050206917 1.051714037 0.873789812 1.026627829 1 19.7200061 3.232764404 22.41806028 0.989879688 0.908359964 0.424461791 0.050946218 42.97115639 166200.5758 0.015227924 0.018724188 1709.087917 -3.232764404 -0.081519724 KVQSGNINAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVQSGNINAAK 11 1 P49368;P49368-2;Q5SZX6;E9PRC8;Q5SZW8;E9PM09;Q5SZX9 P49368 CCT3 T-complex protein 1 subunit gamma 0 176.32 1.41E-05 522230000 1310600 1160800 1289300 1400400 1717200 1066600 1781500 1423700 1961900 FALSE TRUE 1228571.885 1246746.84 1319882.805 1436336.635 1582338.039 1374510.105 1514380.614 1601452.079 1634446.216 0.75167471 0.762794657 0.80754129 0.878791006 0.968118757 0.840963803 0.9265405 0.979813263 1 20.64037047 3.786752105 0.281760113 1.005197554 0.616298635 0.8114189 0.038644484 2.01679985 0.202836258 0.051417663 0.263158213 6120.009619 -3.786752105 -0.388898919 KVQVAALQAS(ph)PPLDQDDR ddPTM_SK-BR-3_Pertuzumab_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 260.18 6.09E-31 9715150000 10489960 10007580 11221380 11048280 12493310 9260860 11771760 9520800 13785500 TRUE FALSE 9833412.129 10748551.64 11487556.43 11331797.57 11512135.83 11934319.94 10006693.87 10709492.84 11484610.99 0.856225094 0.935909074 1.000256468 0.986694071 1.002396671 1.039157526 0.871313262 0.932508105 1 23.45319865 4.698066174 2.161008212 0.970888356 0.831596341 0.404453425 0.045973462 0.6869803 3.932542737 0.012270386 0.179162606 49896.05087 -4.698066174 -0.139292015 KVQVAALQASPPLDQDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 103.99 0.00083333 342090000 488470 446820 460730 424260 521840 395570 506320 464360 645600 FALSE TRUE 457897.5346 479903.0177 471658.7332 435147.2299 480856.7914 509764.6375 430402.0164 522336.3682 537845.1893 0.851355639 0.892269797 0.876941437 0.809056655 0.894043121 0.947790642 0.800234017 0.971164898 1 19.03683145 1.084833401 6.755721934 0.999385693 0.87047422 0.576902562 0.042378549 0.133808147 8.068721814 0.037944449 0.009524262 12.15719551 -1.084833401 -0.128911473 KVS(ph)IVSKPVLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVSIVSKPVLYR 12 2 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 KVS(1)IVSKPVLYR;KVS(0.988)IVS(0.012)KPVLYR 114.29 0.00074726 1982860000 2018720 1963520 1816050 1871860 2492200 1091770 2869300 2152780 4584400 TRUE FALSE 1892371.919 2108901.064 1859127.564 1919895.097 2296472.665 1406946.276 2439075.102 2421559.322 3819234.024 0.495484672 0.552179063 0.486780216 0.502691138 0.601291424 0.368384411 0.638629392 0.63404319 1 21.86485189 0.721849905 1.182772169 0.998885424 0.511080135 0.835840163 0.067552428 0.318323327 0.761154275 0.056443541 0.017378835 5.270476788 -0.721849905 -0.487805289 KVS(ph)LVLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVSLVLEK 8 1 Q9P2M7;Q9P2M7-2;H0Y4A8 Q9P2M7 CGN Cingulin 1 KVS(1)LVLEK 110.31 0.0036558 136050000 106350 68923 84707 81579 87427 76467 108140 81868 224880 TRUE FALSE 99693.74334 74026.13063 86716.29004 83672.45525 80560.83608 98541.78156 91925.41092 92089.40001 187346.0752 0.532136813 0.395130405 0.462866863 0.446619739 0.430010802 0.525987969 0.490671666 0.491546993 1 17.51534623 -3.982483648 0.326774312 3.480227975 0.441831676 0.944326781 0.040380009 31.67475341 0.523605543 53.34672568 0.031694227 0.000104116 3.982483648 -3.038396299 KVS(ph)PIKINLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVSPIKINLK 10 2 H0Y6F5;Q9H4I2;Q9H4I2-2 H0Y6F5 ZHX3 Zinc fingers and homeoboxes protein 3 1 KVS(1)PIKINLK;KVS(1)PIKINLK 106.17 0.0012792 931850000 1896620 1178790 1382390 1321330 1854670 1009480 1987690 1454600 2877600 TRUE FALSE 1777913.94 1266068.838 1415180.944 1355237.565 1709011.7 1300900.488 1689654.337 1636210.012 2397309.97 0.741628726 0.528120624 0.590320385 0.565315951 0.712887245 0.542650097 0.704812627 0.68251917 1 21.19298503 0.241370992 0.599573454 1.017902426 0.595737923 0.722570827 0.072545668 1.289316588 0.647317602 0.116663901 0.027037771 1.743295429 -0.241370992 -0.422164503 KVS(ph)SAEGAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVSSAEGAAK 10 1 P05114;A6NL93;F2Z2W6;F2Z2Y5;H7BXJ5;A0A494C035 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 KVS(0.979)S(0.021)AEGAAK;KVS(0.866)S(0.134)AEGAAK 130.72 0.0001649 418650000 1011580 577700 642880 734890 794450 459250 805660 550390 899640 TRUE FALSE 948267.0135 620473.5091 658129.4172 753748.5216 732057.1017 591828.0197 684858.7624 619107.4031 749484.2721 1.265226035 0.827867284 0.87810971 1.005689578 0.976747784 0.789647017 0.913773361 0.826044556 1 19.51553868 2.278869269 24.99986677 0.876260482 0.953842836 0.114171404 0.128460898 404.0365876 250586.2703 0.042557723 0.035605923 190.0506105 -2.278869269 0.077582354 KVS(ph)TSGQIR ddPTM_SK-BR-3_Pertuzumab_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(0.944)T(0.05)S(0.006)GQIR 82.278 0.01158 245650000 162110 152860 149440 164980 233940 126770 199230 154950 258240 TRUE FALSE 151963.8245 164177.9135 152984.7874 169213.6661 215567.2961 163366.4411 169357.3111 174295.8486 215138.0757 0.706354856 0.763128112 0.711100473 0.786535185 1.001995093 0.759356244 0.787202872 0.810158072 1 17.71490335 -5 0.093190574 1.660132907 0.623337659 0.467529063 0.076599827 191.1008863 1.230287155 25.18671889 1.617847681 1.00E-05 5 -1.036795248 KVSVS(ph)ESNVLLDEEVLTDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVSVSESNVLLDEEVLTDPK 20 1 H0Y465;P21359-2;P21359-6;P21359;J3QSG6 H0Y465 NF1 Neurofibromin;Neurofibromin truncated 1 KVS(0.223)VS(0.388)ES(0.388)NVLLDEEVLTDPK;KVS(0.316)VS(0.623)ES(0.06)NVLLDEEVLTDPK 151.66 4.49E-08 184293000 370750 212741 263035 322730 328290 184701 318000 213198 233255 TRUE FALSE 347545.4193 228492.565 269274.3144 331011.7982 302507.4277 238021.1803 270318.8522 239816.2396 194323.2336 1.788491334 1.175837602 1.385703137 1.703408244 1.556722899 1.224872476 1.391078396 1.234109968 1 17.56809888 0.971012461 0.916370078 1.002546583 1.44969942 0.416228592 0.18612706 0.718750406 1.295910816 0.176137272 0.060531154 9.35432514 -0.971012461 0.447152837 KVT(ph)SPLQS(ph)PTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.568)S(0.432)PLQS(0.999)PT(0.001)K;KVT(0.546)S(0.454)PLQS(0.999)PT(0.001)K 92.265 0.0087635 937370000 1025440 588080 754460 766040 911250 492490 835260 737450 1177070 TRUE FALSE 961259.5409 631622.0551 772356.1475 785697.8833 839684.1008 634663.8681 710020.5172 829522.2558 980609.4128 0.980267503 0.64411176 0.787628731 0.801234287 0.856288028 0.647213722 0.724060475 0.845925243 1 19.90331908 0.944200767 4.433338083 0.999847042 0.761008328 0.329223924 0.098623367 0.271232339 15.26510161 0.087054074 0.022131463 8.794289686 -0.944200767 -0.238838714 KVTAEADSSS(ph)PTGILATSESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KVTAEADSSSPTGILATSESK 21 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-7 A0MZ66 KIAA1598 Shootin-1 1 KVTAEADS(0.002)S(0.016)S(0.975)PT(0.007)GILATSESK;KVTAEADS(0.045)S(0.232)S(0.697)PT(0.026)GILATSESK;KVTAEADS(0.001)S(0.006)S(0.99)PT(0.002)GILATSESK;KVTAEADS(0.006)S(0.039)S(0.877)PT(0.078)GILATSESK;KVTAEADS(0.006)S(0.025)S(0.925)PT(0.044)GILATSESK 237.97 4.34E-30 2007310000 3792190 2641690 3228110 3222890 3176430 2322760 3746140 2565970 3434820 TRUE FALSE 3554843.597 2837283.476 3304682.294 3305594.814 2926966.001 2993303.105 3184441.084 2886337.003 2861526.352 1.24228931 0.991527991 1.154866979 1.155185872 1.022868791 1.046051211 1.112847024 1.008670425 1 21.44835346 2.732065427 24.93539343 1.051250374 1.115044187 0.299317886 0.069690689 897.1882422 3444344.953 0.021585582 0.020799543 539.5919071 -2.732065427 0.063793813 KVTEELLTDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVTEELLTDNR 11 1 Q9UHB9;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ; 145 5.84E-05 599540000 738180 796890 791750 816100 947690 684330 961860 798680 937590 FALSE TRUE 691978.6315 855892.5648 810530.6839 837042.5077 873262.2502 881884.9618 817638.0225 898396.9561 781100.1719 0.885902547 1.095752626 1.037678281 1.071619925 1.117990088 1.129029276 1.04677742 1.150168683 1 19.57514805 4.741221959 24.84949863 1.080931957 0.885902471 0.648353227 0.045183753 133.8050957 1249290.373 0.00971236 0.066923219 55108.92748 -4.741221959 -0.195029487 KVTFFEPGS(ph)GDENGTSNKEDEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KVTFFEPGSGDENGTSNKEDEFR 23 2 O95793-2;O95793-3;O95793;Q5JW30 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 1 KVTFFEPGS(1)GDENGTSNKEDEFR;KVTFFEPGS(1)GDENGTSNKEDEFR;KVTFFEPGS(1)GDENGTSNKEDEFR 208.88 4.90E-25 524030000 670200 477180 497490 528540 549610 376409 672100 420814 637640 TRUE FALSE 628253.3783 512510.9037 509290.6977 542103.2312 506445.8476 485072.1678 571324.8445 473353.5542 531213.7647 1.182675262 0.964792213 0.958730236 1.020499218 0.953374858 0.913139305 1.075508359 0.891079233 1 19.018933 4.74037784 24.90473328 0.975573507 1.182675336 0.615712848 0.052208953 99.47771095 1363211.439 0.011394185 0.074012867 55001.91879 -4.74037784 0.207101829 KVTFFEPGSGDENGTSNKEDEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVTFFEPGSGDENGTSNKEDEFR 23 2 O95793-2;O95793-3;O95793;Q5JW30 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 100.64 0.0012835 81635000 109180 94651 93340 95199 111910 71168 125710 96715 154060 FALSE TRUE 102346.6187 101659.0585 95554.06888 97641.96751 103121.04 91713.04628 106860.9525 108790.0806 128346.3907 0.797424985 0.792067918 0.74450141 0.760769095 0.803458823 0.714574409 0.832598034 0.847628671 1 16.9696832 0.868869783 1.270590134 0.998868705 0.770252935 0.850828282 0.030018779 0.201247247 0.631326814 0.025952776 0.007907231 7.393835476 -0.868869783 -0.22861577 KVTHAVVTVPAYFNDAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVTHAVVTVPAYFNDAQR 18 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 182.34 4.47E-14 760640000 1433200 1863640 1336550 1340980 1790370 945890 1809740 1503150 1251790 FALSE TRUE 1343498.57 2001625.845 1368253.597 1375391.817 1649761.562 1218953.088 1538386.288 1690821.586 1042858.162 1.288285041 1.919365372 1.312022715 1.318867577 1.581961596 1.168857983 1.475163492 1.621334183 1 19.99211152 -3.627412763 0.164551395 2.61E-17 1.607495548 0.268981318 0.22018789 99.43217124 1.402272552 35.50976464 0.878560202 0.000235824 3.627412763 1.607495548 KVTNINDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVTNINDR 8 1 Q8TF74;A8MWR2;J3QKM5 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 0 75.294 0.062152 114100000 130970 151700 120370 135790 171530 106020 146980 144920 211940 FALSE TRUE 122772.8215 162932.0258 123225.2332 139274.6013 158058.7257 136626.2529 124941.7135 163013.581 176565.8448 0.695337321 0.922783373 0.697899604 0.788796958 0.895182904 0.773797747 0.707621078 0.92324527 1 17.42984677 1.047045692 5.61326711 0.999332508 0.788424106 0.495349364 0.076875002 0.135106587 9.169615834 0.070681323 0.017813008 11.14411773 -1.047045692 -0.210908402 KVTS(ph)PLQS(ph)PTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVTSPLQSPTK 11 1 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3;A0A1B0GUN0;A0A1B0GUM1 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 2 KVT(0.171)S(0.829)PLQS(0.999)PT(0.001)K 116 0.0036675 621310000 1686300 945540 1138300 1134700 1442100 766100 1332000 1084100 1851600 TRUE FALSE 1580757.493 1015548.765 1165301.014 1163818.323 1328843.283 987260.6334 1132278.966 1219452.271 1542555.998 1.024765062 0.658354553 0.755435145 0.754473954 0.861455457 0.640016074 0.734027787 0.790540034 1 20.55689143 0.856680562 5.500281347 0.999997579 0.756593735 0.281252752 0.108869182 2.43197657 92.72504123 0.093856158 0.023652102 7.189199939 -0.856680562 -0.243403843 KVTSVVFHPSQDLVFSASPDATIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVTSVVFHPSQDLVFSASPDATIR 24 1 Q9UMS4 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ; 220.52 6.50E-33 505890000 231634 356520 346690 359710 400060 302310 383660 339730 435430 FALSE TRUE 217136.4414 382917.1118 354913.6505 368940.7676 368640.9014 389581.9894 326133.7447 382146.0383 362753.92 0.598577795 1.055583663 0.97838681 1.017055219 1.016228581 1.073956663 0.899049539 1.053458053 1 18.46863168 4.742766529 24.99877238 1.006450768 0.598577634 0.874440382 0.049163066 137.4106718 816700.7045 0.011155785 0.086809898 55305.27153 -4.742766529 -0.407873133 KVVAEVYDQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 145.6 5.80E-05 1266380000 1207430 1328060 1155030 1109320 1212460 835180 1332660 1211780 1549060 FALSE TRUE 1131859.112 1426390.944 1182427.857 1137787.029 1117238.282 1076282.908 1132840.005 1363073.4 1290511.879 0.877062141 1.105290829 0.91624717 0.881655604 0.865732661 0.833996901 0.877822222 1.056226931 1 20.29951199 3.694331865 5.221957373 0.902696641 1.008903966 0.080295326 0.086218006 0.252780565 18.14905019 0.021315151 0.034728557 4946.885574 -3.694331865 0.106207325 KVVDPFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVVDPFSK 8 1 P61247;E9PFI5;H0Y8L7;H0Y9Y4;D6RI02 P61247 RPS3A 40S ribosomal protein S3a 0 ; 81.338 0.037071 537190000 3099400 2511100 2976700 2800900 2975900 2434200 3548900 2599700 3301300 FALSE TRUE 2905414.087 2697024.457 3047308.73 2872775.836 2742184.818 3136914.024 3016775.391 2924278.268 2750291.703 1.056402157 0.980632147 1.107994736 1.044534961 0.997052355 1.140575024 1.096892882 1.063261131 1 21.39115321 2.247045498 24.99982464 1.086764777 1.039557494 0.109435635 0.048705164 310.5564191 915023.8801 0.016222286 0.01336801 176.6222847 -2.247045498 -0.047207283 KVVDYSQFQES(ph)DDADEDYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 63 KVVDYSQFQESDDADEDYGR 20 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYS(0.003)QFQES(0.997)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYS(0.002)QFQES(0.998)DDADEDYGR;KVVDY(0.001)S(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(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDY(0.001)S(0.001)QFQES(0.998)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;KVVDYS(0.003)QFQES(0.997)DDADEDYGR;KVVDYSQFQES(0.998)DDADEDY(0.001)GR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDY(0.002)S(0.002)QFQES(0.996)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYS(0.001)QFQES(0.999)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYS(0.003)QFQES(0.996)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;KVVDYS(0.005)QFQES(0.995)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR 308.16 2.07E-66 2.357E+11 27263787.1 25181310.1 26586479.6 27292056.9 27859961.9 22551564.4 31989644.5 23762914.8 30289597.4 TRUE FALSE 25557395.33 27045760.5 27217123.45 27992417.29 25671952.87 29061834.95 27193094.28 26729767.02 25234067.92 1.012813131 1.071795502 1.078586439 1.109310531 1.017352928 1.151690447 1.077634188 1.059273008 1 24.58886946 4.747237104 3.60479368 1.077658861 1.004793912 0.137341776 0.04280499 0.476695419 11.11949817 0.009041991 0.094929261 55877.51757 -4.747237104 -0.072864949 KVVDYSQFQES(ph)DDADEDYGRDSGPPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KVVDYSQFQESDDADEDYGRDSGPPTK 27 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK 286.3 7.47E-62 26547690000 5288990 5537810 4767460 5644640 6923820 3364820 6817850 4811020 12230600 TRUE FALSE 4957961.557 5947835.214 4880546.403 5789491.019 6380051.107 4336188.911 5795576.686 5411686.437 10189233.85 0.486588259 0.583737237 0.478990518 0.568196893 0.626156118 0.425565747 0.568794158 0.531118092 1 23.28054224 -0.365958227 1.552701713 1.001351138 0.53437111 0.864111115 0.058118226 42.07493997 46.18339691 0.440614776 0.014310784 0.430568024 0.365958227 -0.466980028 KVVDYSQFQES(ph)DDADEDYGRDSGPPTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KVVDYSQFQESDDADEDYGRDSGPPTKK 28 3 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KVVDYSQFQES(1)DDADEDYGRDSGPPTKK;KVVDYS(0.001)QFQES(0.999)DDADEDYGRDSGPPTKK;KVVDYS(0.002)QFQES(0.998)DDADEDYGRDSGPPTKK 224.54 9.55E-34 1971280000 887291 253871 313877 407431 583913 191048 483975 235492 945600 TRUE FALSE 831757.0402 272667.873 321322.3107 417886.3692 538054.8284 246200.4562 411407.4418 264893.6946 787773.2512 1.055833057 0.346124818 0.4078868 0.530465294 0.683007233 0.312527058 0.522240938 0.336256269 1 19.58742091 -1.141678765 5.26367829 1.000015313 0.49535902 0.306511112 0.221098654 3.55E-05 5.79E-06 0.191306591 0.045090029 0.072164106 1.141678765 -0.504656293 KVVDYSQFQESDDADEDYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVVDYSQFQESDDADEDYGR 20 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 223.44 1.04E-24 358090000 272330 252540 254480 258930 260820 198470 300500 220380 281820 FALSE TRUE 255285.3514 271238.3244 260516.3858 265574.5822 240336.2493 255765.0671 255442.8147 247894.9281 234782.4214 1.087327364 1.155275266 1.109607714 1.131151901 1.023655212 1.089370599 1.087998042 1.05584961 1 17.84096487 1.097015618 0.221983219 0.971368026 1.151909517 0.553679352 0.031079085 2.07246317 0.409015298 0.14538372 0.100375254 12.50303992 -1.097015618 0.18054149 KVVEAVNS(ph)DS(ph)DSEFGIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVVEAVNSDSDSEFGIPK 18 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 KVVEAVNS(1)DS(0.992)DS(0.008)EFGIPK;KVVEAVNS(0.999)DS(0.887)DS(0.114)EFGIPK 148.89 2.31E-07 577380000 1358140 886090 1064220 1057200 1053740 757180 1371880 863170 1187330 TRUE FALSE 1273136.442 951697.0256 1089463.801 1084329.542 970983.511 975765.5742 1166179.33 970938.6746 989156.9526 1.287092446 0.962129441 1.101406403 1.096215862 0.981627343 0.986461827 1.17896288 0.981582015 1 19.91583993 4.751634438 24.55108508 1.047017017 1.287092646 0.553417099 0.070260966 1375.678107 2583300.675 0.016287964 0.304199009 56446.16467 -4.751634438 0.240075628 KVVGCSCVVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVVGCSCVVVK 11 1 P25398 P25398 RPS12 40S ribosomal protein S12 0 93.958 0.014209 242410000 907260 874460 714230 688540 1009900 564040 960910 862000 1154600 FALSE TRUE 850476.2161 939205.9283 731171.8729 706209.1021 930586.5277 726869.1916 816830.4662 969622.5975 961889.801 0.884172194 0.976417389 0.760140998 0.734189199 0.967456487 0.755667843 0.849193395 1.008039171 1 19.8755121 1.240091099 22.86556226 1.004019808 0.846885124 0.385660666 0.082522413 13.69408445 204684.7518 0.061278391 0.019612034 17.38165394 -1.240091099 -0.157134684 KVVGDVAYDEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 1427140000 4348590 3164440 3605370 3447830 4088720 2499030 4424930 3489220 5405670 FALSE TRUE 4076419.514 3398738.43 3690891.079 3536307.155 3767608.424 3220459.393 3761452.826 3924856.798 4503428.755 0.905181304 0.754700166 0.819573547 0.785247718 0.836608866 0.715112766 0.835241997 0.871526344 1 22.10259241 0.919786628 1.948786774 0.999011755 0.799260815 0.595320669 0.050632016 0.251592601 1.988872088 0.042252141 0.011822592 8.313552209 -0.919786628 -0.199750941 KVVGSMPTAGSAGS(ph)VPENLNLFPEPGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVVGSMPTAGSAGSVPENLNLFPEPGSK 28 1 A0A087WV97;Q8WU79-3;Q8WU79-2;Q8WU79 A0A087WV97 SMAP2 Stromal membrane-associated protein 2 1 KVVGSMPT(0.002)AGS(0.001)AGS(0.996)VPENLNLFPEPGSK 87.803 1.07E-06 0 168060 150080 168980 155100 176390 128770 222100 153920 192220 TRUE FALSE 157541.4246 161192.0794 172988.2854 159080.1286 162537.0409 165943.8086 188798.1669 173137.2508 160137.2402 0.983790057 1.006587095 1.080250198 0.993398715 1.0149859 1.03625995 1.178977274 1.081180434 1 17.28894932 1.966749963 21.44522556 1.106859028 1.022591329 0.256169824 0.050854426 113.4399948 73164.17337 0.019456593 0.012573298 92.6296371 -1.966749963 -0.084267699 KVVNPLFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVVNPLFEK 9 1 P62424;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 146.11 0.0026308 0 1046700 2228400 820470 850870 2829800 522320 828750 2194700 2187900 FALSE TRUE 981188.9154 2393393.055 839931.9359 872704.7647 2607558.923 673105.3048 704486.6312 2468713.126 1822725.356 0.538308699 1.313084852 0.460811023 0.478791148 1.43058246 0.369285094 0.3865018 1.354407628 1 20.79766576 3.964851761 24.57368201 0.722087566 0.969276688 0.001224029 0.427851535 918.6443009 1839891.616 0.102960813 0.187396613 9222.565768 -3.964851761 0.247189122 KVVVS(ph)PTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KVVVSPTK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 KVVVS(0.976)PT(0.024)K;KVVVS(0.5)PT(0.5)K;KVVVS(0.5)PT(0.5)K 107.03 0.0043243 18561030000 21506300 13646240 16395250 14112910 16136030 12333530 20740830 13580380 17311940 TRUE FALSE 20160259.07 14656621.81 16784153.07 14475071.16 14868771.29 15894019.89 17630935.09 15275920.34 14422465.37 1.397837232 1.016235534 1.163750624 1.003647489 1.030945189 1.102032106 1.222463333 1.059175386 1 23.78181446 4.747191016 24.6231913 1.090066796 1.397837425 0.651694996 0.073471348 615.9764333 1757380.262 0.017729844 0.206163608 55871.58804 -4.747191016 0.307770629 KVVVSPT(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KVVVSPTK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 KVVVS(0.181)PT(0.819)K;KVVVS(0.256)PT(0.744)K;KVVVS(0.193)PT(0.807)K;KVVVS(0.218)PT(0.782)K 90.913 0.0075356 10476900000 35733800 21725900 26376500 24969900 27715300 19752000 34527400 23204000 30118500 TRUE FALSE 33497285.24 23334508.24 27002163.04 25610669.91 25538652.14 25454081.75 29350336.91 26101070.48 25091527.78 1.335003813 0.929975586 1.076146629 1.020689937 1.017819734 1.014449259 1.169730961 1.040234405 1 24.58069698 -0.509516752 7.583513856 0.999960924 1.064306349 0.03572339 0.110405816 0 0 0.096520419 0.022750081 0.309373598 0.509516752 0.064345425 KVVVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVVVVR 6 1 P40429;M0QYS1 P40429 RPL13A 60S ribosomal protein L13a 0 ; 106.84 0.050958 3487300000 3536200 3536500 3689300 3492600 3669000 3092200 4121500 3274400 3803900 FALSE TRUE 3314875.554 3798346.14 3776811.938 3582226.029 3380851.54 3984867.942 3503519.337 3683216.048 3169004.516 1.046030556 1.198592845 1.191797588 1.130394738 1.066849707 1.257451014 1.105558329 1.162262796 1 21.59559828 -0.980474283 0.746286728 0.973345528 1.15371222 0.331320737 0.063534983 47.90120591 13.45725564 3.034926683 0.020179738 0.104598563 0.980474283 0.180366692 KVVYENAYGQFIGPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KVVYENAYGQFIGPHR 16 1 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881;E9PKD3 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 ; 204.82 1.57E-11 669660000 1032970 1235480 1099520 1049580 1403270 869600 1302990 1134350 1639230 FALSE TRUE 968318.2516 1326956.225 1125601.134 1076514 1293062.835 1120639.403 1107618.746 1275976.095 1365631.923 0.709062402 0.971679266 0.824234638 0.788290008 0.946860433 0.820601353 0.811066823 0.934348467 1 20.38113726 1.02757675 4.780249367 0.999521606 0.849981745 0.344719076 0.075267457 0.183636056 10.69572121 0.066667232 0.016901906 10.65557157 -1.02757675 -0.14953986 KVYDDAHNMLNT(ph)LISQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVYDDAHNMLNTLISQK 17 1 Q99707-2;Q99707;B1ANE3 Q99707-2 MTR Methionine synthase 1 KVY(0.009)DDAHNMLNT(0.981)LIS(0.01)QK 63.631 0.03974 153170000 71803 287750 220140 247680 294620 266180 206350 251890 200300 TRUE FALSE 67308.9784 309055.3094 225361.8248 254035.8881 271481.7336 343021.8449 175409.7332 283339.021 166868.636 0.403365066 1.852087467 1.350534349 1.522370496 1.626918875 2.055640012 1.051184557 1.697976491 1 17.34835329 -1.120025326 4.122882077 0.999892104 1.476355782 0.081369844 0.459293846 28139180.57 7644326.065 28227.97735 0.094752516 0.075853334 1.120025326 0.476463678 KVYEDSGIPLPAES(ph)PK ddPTM_SK-BR-3_Pertuzumab_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 116.94 0.00023798 271730000 616060 385890 437230 469020 493680 360150 630740 415830 449670 TRUE FALSE 577501.9043 414461.6971 447601.3021 481055.8472 454908.3642 464119.4585 536166.3925 467747.2909 374617.172 1.541578837 1.106360648 1.194823237 1.284126525 1.214328649 1.238916668 1.431238161 1.248600774 1 18.51505751 1.950239186 24.9844472 1.289665559 1.236023677 0 0.156451535 1747.293389 877297.9703 0.059386639 0.038334009 89.1741926 -1.950239186 -0.053641882 KVYENYPTYDLTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KVYENYPTYDLTER 14 1 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;A0A494C198 H0Y993 DEK Protein DEK 0 243.04 2.62E-17 478200000 645240 773720 605270 658960 797640 581040 769310 627220 1020600 FALSE TRUE 604855.5802 831007.0339 619627.2902 675870.0292 734996.5719 748776.8156 653959.1074 705529.7977 850255.2667 0.711381163 0.977361819 0.728754428 0.794902491 0.864442245 0.88064943 0.769132675 0.82978586 1 19.69753651 -1.109591888 5.181101186 1.00000427 0.82474249 0.346978392 0.077507797 3.54E-06 6.08E-07 0.069408388 0.016359315 0.077697691 1.109591888 -0.17526178 KWDGS(ph)EEDEDNSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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;KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK 276.14 3.37E-32 6697577000 10062080 4363819 5977915 5913773 6411782 4120322 8070407 4675453 8327150 TRUE FALSE 9432312.374 4686920.699 6119713.967 6065530.427 5908226.506 5309792.074 6860324.392 5259193.599 6937294.87 1.359652797 0.67561215 0.882147016 0.874336545 0.851661435 0.765398066 0.988904828 0.758104376 1 22.72594178 -1.10484217 6.976675923 1.000000071 0.874641286 0.021044595 0.186786972 1.81E-07 2.33E-08 0.158162387 0.037279211 0.078552105 1.10484217 -0.125358786 KWDGS(ph)EEDEDNSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KWDGSEEDEDNSKK 14 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 KWDGS(0.98)EEDEDNS(0.02)KK;KWDGS(1)EEDEDNSKK;KWDGS(1)EEDEDNSKK 174.02 2.05E-06 1903310000 2204430 647162 1131830 1049450 1050810 723632 1494170 769737 1541250 TRUE FALSE 2066458.661 695078.5479 1158677.542 1076380.664 968283.6214 932532.8112 1270133.08 865840.3589 1284005.418 1.60938469 0.541336149 0.902393032 0.83829916 0.754111788 0.726268595 0.989196044 0.674327652 1 20.29221986 4.750118255 24.9794351 0.800660373 1.609385173 0.764469797 0.140616966 823.2156142 1779176.02 0.03167002 0.512269709 56249.44675 -4.750118255 0.808724801 KWDSNVIETFDIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KWDSNVIETFDIAR 14 1 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;F5GWK5;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 ; 206.95 1.62E-08 670400000 1417480 1697350 1405750 1389110 1713220 1050550 1711870 1633980 1534830 FALSE TRUE 1328762.457 1823023.56 1439095.054 1424756.914 1578670.612 1353826.731 1455190.986 1837986 1278656.958 1.039186037 1.425733109 1.125473916 1.114260479 1.234631855 1.058788069 1.138062071 1.437434794 1 20.28619783 3.734414004 24.50423719 1.158007045 1.264730126 0.031420721 0.148669629 536.8599191 1803875.075 0.03470253 0.060933614 5425.178157 -3.734414004 0.106723081 KWDTCAPEVILHAVGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KWDTCAPEVILHAVGGK 17 1 O95861-3;O95861-4;O95861;A6NF51;O95861-2 O95861-3 BPNT1 "3(2),5-bisphosphate nucleotidase 1" 0 ; 143.46 3.56E-07 756150000 1049570 947760 942190 849430 1196270 649840 1244590 1044140 1919720 FALSE TRUE 983879.2872 1017933.137 964539.1917 871227.8119 1102319.78 837438.2587 1057975.284 1174503.177 1599306.33 0.615191267 0.636484154 0.603098464 0.544753557 0.689248682 0.523625926 0.661521351 0.734382873 1 20.60901487 0.84424734 1.651645517 0.999214842 0.60691778 0.875065643 0.047002785 0.171335589 0.88257164 0.039308323 0.011283618 6.986301755 -0.84424734 -0.392297062 KWENPGLGAESHTDS(ph)LRNSSTEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KWENPGLGAESHTDSLRNSSTEIR 24 2 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KWENPGLGAESHT(0.002)DS(0.978)LRNS(0.019)STEIR;KWENPGLGAES(0.031)HT(0.031)DS(0.358)LRNS(0.358)S(0.102)T(0.121)EIR 178.7 2.06E-17 778310000 209862 169490 185437 186496 218482 135047 227944 186240 310830 TRUE FALSE 196727.112 182039.216 189835.6532 191281.8031 201323.305 174032.8766 193765.9133 209492.474 258950.465 0.759709437 0.702988566 0.733096398 0.738681057 0.777458751 0.672070145 0.748274051 0.809005977 1 17.98231662 0.837734786 2.047563474 0.999672015 0.728727332 0.894733002 0.028911442 0.161176493 1.260257067 0.025380226 0.0070122 6.882318808 -0.837734786 -0.270944683 KWENPGLGAESHTDSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KWENPGLGAESHTDSLR 17 1 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 259.95 2.07E-27 480160000 806880 909400 920040 886680 1119780 705850 1020140 970450 1640320 FALSE TRUE 756378.8211 976732.9222 941863.7833 909433.7099 1031836.996 909617.4365 867179.4775 1091612.819 1366539.995 0.55349922 0.714748874 0.689232504 0.665500983 0.755072665 0.665635429 0.634580386 0.798815126 1 20.38209625 0.947966005 3.837718967 0.999693925 0.676230441 0.803076287 0.052871905 0.103362164 4.158882937 0.047288969 0.012133918 8.870865709 -0.947966005 -0.323463485 KWENPGLGAESHTDSLRNS(ph)STEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KWENPGLGAESHTDSLRNSSTEIR 24 2 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KWENPGLGAESHT(0.002)DS(0.115)LRNS(0.878)S(0.005)TEIR;KWENPGLGAESHTDSLRNS(0.995)S(0.005)TEIR 274.78 2.80E-52 691330000 456320 402420 421100 414580 532530 365630 525440 458880 801930 TRUE FALSE 427759.7458 432215.5955 431088.6909 425218.8247 490707.2419 471181.4455 446655.1499 516172.1781 668082.7023 0.64027963 0.646949238 0.645262464 0.636476327 0.734500744 0.705274128 0.668562662 0.772617187 1 19.34966718 -2.511665534 0.234460901 1.497511515 0.622870701 0.929970876 0.029041695 10.0210644 0.283071593 2.593105695 0.050492324 0.003078467 2.511665534 -0.874640814 KWQIFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KWQIFK 6 1 B4DZG7;F8VYN9;P40616-2;P40616;F8W1Z8 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ; 121.87 0.03121 953600000 1286030 1393000 1210970 1273120 1448570 903680 1507770 1383750 1416980 FALSE TRUE 1205539.678 1496139.169 1239694.78 1305790.415 1334805.155 1164557.746 1281693.886 1556514.234 1180476.884 1.021231076 1.267402344 1.050164385 1.106155006 1.130733836 0.986514655 1.085742468 1.318546983 1 20.17093836 3.800845316 10.62736326 1.094808869 1.161149388 0.026924591 0.108083684 1.476612137 206.1664492 0.025468857 0.045942308 6321.866435 -3.800845316 0.066340519 KWQTMIEAHVDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KWQTMIEAHVDVK 13 1 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;D6RB09;D6RAS7;D6RED7 P61247 RPS3A 40S ribosomal protein S3a 0 ; 123.38 0.00014544 887810000 3888100 3179500 3595200 3472900 3863500 2752590 4176300 3087000 3629700 FALSE TRUE 3644750.761 3414913.488 3680479.842 3562020.494 3560076.295 3547218.048 3550102.586 3472418.745 3023879.621 1.205322704 1.129315289 1.217138346 1.177963722 1.177320773 1.173068539 1.174022458 1.148332335 1 21.52796928 0.481992266 1.328901978 0.999908397 1.178638277 0.858152992 0.022747133 0.787928364 1.672341027 0.020404152 0.006044655 3.033837157 -0.481992266 0.178729881 KWQVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KWQVSR 6 1 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ; 135.35 0.021868 808530000 675380 849100 661400 595440 944120 560500 813320 880590 1279970 FALSE TRUE 633109.1714 911968.2475 677088.7203 610719.9985 869972.6236 722307.251 691370.2165 990533.5999 1066334.738 0.593724605 0.855236367 0.634968267 0.572728222 0.815853214 0.677373835 0.648361337 0.928914312 1 20.02422896 1.141429985 4.784571127 0.992808419 0.695270467 0.627131206 0.089778108 0.132642755 4.747452452 0.08168838 0.020910034 13.84936894 -1.141429985 -0.297537952 KWS(ph)DSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KWSDSSK 7 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 KWS(0.971)DS(0.029)SK 90.05 0.010672 98949000 461430 228500 362550 372750 261550 202440 307940 194890 216450 TRUE FALSE 432549.92 245418.3778 371149.8572 382315.3961 241008.918 260881.1417 261767.2558 219222.4455 180323.0967 2.3987494 1.360992476 2.058249132 2.120168759 1.33653937 1.446742799 1.451656835 1.21572028 1 17.46022467 2.723149378 24.07277599 1.341735156 1.892900219 0.569805393 0.293181703 434.3515212 678467.4723 0.091118256 0.086224008 528.6270445 -2.723149378 0.551165063 KWS(ph)LNTYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KWSLNTYK 8 1 P53367;P53367-2 P53367 ARFIP1 Arfaptin-1 1 KWS(1)LNTYK;KWS(1)LNTYK 151.13 0.00029286 1564310000 3797500 2465230 2747900 2727600 2785000 1578840 3176700 2167010 3105400 TRUE FALSE 3559821.254 2647758.194 2813081.486 2797594.834 2566277.334 2034625.478 2700383.326 2437565.969 2587088.678 1.375995065 1.023450884 1.087354102 1.081367971 0.99195569 0.786453706 1.043792333 0.942204258 1 21.30289808 8 0.782773245 0.979385216 82.74035436 0.639987221 0.088275927 301.7909635 1.121605005 0.029354591 43682.05839 100000000 -8 81.76096914 KY(ph)DPELSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KYDPELSSR 9 1 H3BRD5;B2RTY4-5;B2RTY4-2;B2RTY4;B2RTY4-4;H3BV44 H3BRD5 MYO9A Unconventional myosin-IXa 1 KY(1)DPELSSR;KY(1)DPELSSR 74.92 0.036027 150770000 799130 683920 825250 731420 657290 657390 899550 718240 578760 TRUE FALSE 749113.8798 734558.1484 844825.3197 750189.4755 605669.0948 847167.8212 764670.8285 807913.845 482161.2171 1.553658514 1.523469998 1.752163571 1.555889294 1.256154733 1.757021907 1.585923549 1.675609353 1 18.87915609 -1.131204159 5.134856212 0.999979616 1.589415534 0.626156163 0.141356341 3.12E-05 5.27E-06 0.129269184 0.030467987 0.073925767 1.131204159 0.589435917 KY(ph)SLVRDVVS(ph)SLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KYSLVRDVVSSLRR 14 3 A8MV53;A0A0A6YYI3;A0A0B4J1V8;Q9NQ55-2;Q9NQ55;Q9NQ55-3;C9J3W3;C9JHF7 A8MV53 PPAN;PPAN-P2RY11 Suppressor of SWI4 1 homolog 2 KY(1)S(0.072)LVRDVVS(0.464)S(0.464)LRR 59.261 0.088132 760500000 135660 635230 412180 469160 589390 469350 414870 464380 432370 TRUE FALSE 127169.2828 682263.0902 421957.1042 481199.4399 543101.6869 604843.7257 352664.095 522358.8652 360204.6538 0.353047306 1.894098488 1.171437126 1.335905671 1.507758662 1.679166883 0.979065904 1.45017245 1 18.4584573 -1.002025244 7.712661659 0.999999993 1.336628994 0.039244606 0.420694545 4.29E-08 5.57E-09 0.360306106 0.084924962 0.099534756 1.002025244 0.336629001 KYAEAVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KYAEAVTR 8 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 114.4 0.0042704 2241600000 2904100 3556500 2408470 2492490 3686200 1614260 3269600 2961000 4417600 FALSE TRUE 2722337.565 3819826.961 2465600.046 2556451.513 3396700.721 2080270.657 2779353.833 3330687.368 3680274.021 0.739710562 1.037919171 0.669950126 0.694636187 0.922947776 0.56524885 0.75520296 0.9050107 1 21.81138176 1.045684794 4.062834633 0.998108423 0.778157413 0.265409043 0.131108635 0.26756316 9.465756118 0.124319952 0.031856319 11.10925138 -1.045684794 -0.21995101 KYDAFLASESLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KYDAFLASESLIK 13 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ; 230.36 6.78E-12 2101710000 6912200 6746800 6241400 6254600 7915600 4631900 7692300 6371600 8839800 FALSE TRUE 6479577.741 7246340.092 6389448.955 6415103.625 7293940.706 5969054.337 6538911.027 7167108.286 7364380.273 0.879853769 0.983971471 0.867615294 0.87109891 0.990435099 0.810530434 0.887910562 0.973212683 1 22.81213269 -0.998455634 5.706901616 1.000000179 0.906826417 0.197220235 0.05823432 1.24E-07 2.17E-08 0.052462827 0.012365583 0.100356236 0.998455634 -0.093173762 KYDEVLHMVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KYDEVLHMVR 10 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 78.653 0.019058 268020000 133570 261900 119600 111850 303710 73848 127230 260470 245700 FALSE TRUE 125210.0921 281291.3485 122436.9685 114720.2604 279857.8417 95166.71878 108153.0426 292990.2529 204691.0827 0.61170272 1.374223756 0.598154872 0.560455584 1.367220487 0.464928504 0.528372029 1.431377708 1 17.64308873 7.312228793 7.2202833 0.859801116 0.847324346 0 0.387850134 0 0 0.080663126 0 20522430.48 -7.312228793 -0.01247677 KYDVDTLDMVFLDHWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KYDVDTLDMVFLDHWK 16 1 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ; 241.79 4.16E-20 2821800000 4064500 3457400 3707200 3395600 4528400 2926000 4653700 4043900 5273500 FALSE TRUE 3810110.2 3713389.493 3795136.535 3482736.845 4172757.731 3770688.7 3955920.888 4548789.817 4393318.782 0.867251021 0.845235613 0.86384274 0.792734836 0.949796256 0.858277964 0.90044021 1.035388061 1 22.06687976 1.359203006 3.472728045 1.018440089 0.862431248 0.719804782 0.039223439 0.115752197 2.262312505 0.028896944 0.009353311 22.86667431 -1.359203006 -0.156008841 KYDYDSSSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KYDYDSSSVR 10 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ;;; 154.66 2.26E-05 2232800000 3700670 4351800 3353570 3416860 4700640 2544150 3492040 3917460 4257890 FALSE TRUE 3469051.671 4674011.8 3433118.264 3504542.412 4331470.696 3278604.804 2968441.021 4406563.504 3547220.652 0.977963316 1.317654654 0.967833298 0.987968541 1.221088599 0.924274277 0.83683574 1.242258077 1 21.75825764 3.801556841 6.125656373 1.008953428 1.166131403 0.093820792 0.147927607 0.361127674 23.11312532 0.036481501 0.066271868 6332.232338 -3.801556841 0.157177975 KYEAAYGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KYEAAYGK 8 1 H0YFD6;P40939;A0A2R8Y4F5 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 105.4 0.0070485 331530000 750360 700010 533370 506860 1003700 453610 539180 792990 1302200 FALSE TRUE 703396.307 751839.4688 546021.7883 519866.8857 924873.4507 584559.8433 458334.9645 891996.5471 1084854.407 0.648378531 0.693032598 0.503313426 0.47920429 0.852532325 0.538837137 0.422485231 0.822226965 1 20.04907001 1.021149584 6.048218562 0.999549427 0.587618198 0.566504939 0.12189841 0.098705227 12.16972039 0.116271581 0.029239672 10.49903985 -1.021149584 -0.411931229 KYEDICPSTHNMDVPNIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 247.4 1.45E-24 9477530000 5688200 5941700 6528120 6370480 6857740 5411380 8275080 6230650 7963460 FALSE TRUE 5332185.716 6381629.65 6682970.089 6533957.302 6319160.763 6973557.56 7034308.576 7008560.368 6634307.08 0.803729109 0.961913516 1.007335055 0.984874113 0.952497478 1.051135782 1.060292882 1.056411813 1 22.66151436 5.742726111 0.795951259 1.024356635 4.45E-20 0.789284483 0.03431566 5.169041393 0.755492997 0.012437873 6.804926535 553001.247 -5.742726111 -1.024356635 KYEDICPSTHNMDVPNIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 172.66 4.76E-12 2642600000 1707510 2451150 2328370 2415170 2900040 1740710 3073820 2182360 4294700 FALSE TRUE 1600639.997 2632635.696 2383600.036 2477147.351 2672282.557 2243224.719 2612929.227 2454832.45 3577886.825 0.447370215 0.735807426 0.666203307 0.692349275 0.746888509 0.626969166 0.730299575 0.686112381 1 21.77067632 -5 0.204146424 2.492393208 0.62719039 0.64726618 0.080375852 89.32906919 0.887414142 54.48218712 0.166997068 1.00E-05 5 -1.865202818 KYEDNQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KYEDNQR 7 1 P07942;G3XAI2 P07942 LAMB1 Laminin subunit beta-1 0 ; 94.114 0.039834 0 286010 307240 292700 301460 327110 242650 345360 280660 306890 FALSE TRUE 268109.1446 329988.3693 299642.9822 309195.974 301420.1001 312699.1159 293576.4742 315701.0188 255668.0764 1.048661015 1.290690547 1.171999987 1.209364807 1.178950866 1.223066721 1.148271925 1.234808128 1 17.96391251 -1.760049642 2.67857239 0.955743039 1.194419699 0.46375601 0.06329863 12998695.85 9880070.161 3789059.898 0.01360716 0.017376022 1.760049642 0.238676661 KYEEIDNAPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KYEEIDNAPEER 12 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ;;;;; 190.27 1.10E-05 5641960000 7025890 5957820 5926970 5701280 8681110 5565480 6072850 6799050 11541160 FALSE TRUE 6586152.086 6398943.192 6067560.527 5847584.497 7999330.639 7172143.728 5162282.52 7647926.359 9614865.837 0.684996775 0.665525999 0.631060342 0.608181601 0.831975274 0.745943194 0.53690635 0.795427257 1 23.1968353 0.990628809 21.8121608 1.000000004 0.667655585 0.643423735 0.078462228 46.266783 107691.1154 0.074547054 0.018636763 9.786531743 -0.990628809 -0.332344419 KYEEVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 KYEEVAR 7 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;P06753-7;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;H0YL42;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2 TPM3;TPM1;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain 0 ;;;;;; 157.86 0.0023209 46190310000 40646300 44307200 40658900 40671100 46927100 31885350 46358600 39548100 42794900 FALSE TRUE 38102320.64 47587751.19 41623348.31 41714789.28 43241634.86 41090132.93 39407558.3 44485767.34 35652154.72 1.068724203 1.334779105 1.167484788 1.170049597 1.212875777 1.152528739 1.105334547 1.247772195 1 25.08748594 -5 0.170203818 0.254606686 1.234135003 0.325320557 0.076534498 134.0201585 1.265618791 33.6279251 0.256223212 1.00E-05 5 0.979528317 KYEFGESDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KYEFGESDLR 10 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 110.08 0.0031008 2446810000 7621200 8820700 8316100 8925800 10329500 6903100 10896900 9100400 10634300 FALSE TRUE 7144202.696 9473793.806 8513361.819 9154851.139 9518262.737 8895912.908 9263011.007 10236604.97 8859366.63 0.806401066 1.069353398 0.960944746 1.03335278 1.074372823 1.004125157 1.045561313 1.155455621 1 23.07877213 4.74341434 24.72218436 1.037613389 0.806400955 0.666710942 0.052431025 265.9824941 1354714.852 0.011859049 0.09758882 55387.8287 -4.74341434 -0.231212434 KYEGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KYEGGR 6 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 124.37 0.029477 4573210000 3577220 3233860 3306810 3546100 3244080 2428840 3388010 3083360 2446700 FALSE TRUE 3353328.186 3473298.359 3385249.095 3637098.93 2989303.043 3130006.679 2880009.353 3468324.283 2038329.964 1.645135108 1.7039922 1.660795433 1.784352384 1.466545209 1.53557409 1.412925976 1.70155193 1 20.95895618 -2.701264467 0.198533775 1.74E-20 1.748490735 0.75865058 0.110000965 21.98452216 0.494795393 9.762551975 0.274917833 0.001989461 2.701264467 1.748490735 KYELGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KYELGR 6 1 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;;;; 123.96 0.029765 3024860000 4947540 4889020 4615660 4508270 4900280 3738180 5232090 4657090 3906670 FALSE TRUE 4637882.303 5251008.128 4725145.635 4623959.841 4515431.776 4817331.882 4447586.677 5238537.938 3254621.539 1.425014321 1.613400534 1.45182645 1.42073657 1.387390737 1.480151171 1.366544965 1.609569001 1 21.63405836 -2.062346501 2.669367151 0.31115266 1.469563852 0.758171836 0.083300805 16993708.75 14698597.01 70505568.14 0.020261227 0.008662704 2.062346501 1.158411192 KYELGRPAANTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KYELGRPAANTK 12 2 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 148.72 3.75E-05 6219400000 6868800 6645900 6167100 6622600 8103500 5214800 8784300 6826000 10470700 FALSE TRUE 6438894.069 7137969.351 6313386.524 6792547.128 7467083.798 6720228.105 7467175.764 7678241.126 8723072.527 0.738145195 0.81828614 0.723757197 0.778687453 0.856015329 0.770396908 0.856025872 0.880222089 1 23.05640495 0.924046623 0.556963175 1.005712914 0.766551444 0.799668367 0.036104815 0.413500044 0.304928407 0.037735575 0.016553862 8.395501112 -0.924046623 -0.23916147 KYEMFAQTLQQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KYEMFAQTLQQSR 13 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 213.99 2.38E-09 366780000 205770 1249800 125430 149490 1306700 81154 158520 986320 1132200 FALSE TRUE 192891.223 1342336.492 128405.2588 153326.1665 1204077.053 104581.8424 134751.3976 1109464.223 943228.5057 0.204501053 1.423129692 0.136133777 0.162554636 1.276548626 0.110876465 0.14286188 1.176241193 1 19.84724779 1.218146619 24.98148514 1.088121251 0.527103704 0.205770861 0.481983645 475.6578537 582067.5376 0.452173382 0.113584237 16.52519598 -1.218146619 -0.561017547 KYES(ph)DEDSLGS(ph)SGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KYESDEDSLGSSGR 14 1 O00418 O00418 EEF2K Eukaryotic elongation factor 2 kinase 2 KYES(1)DEDS(0.03)LGS(0.85)S(0.12)GR 200.67 1.26E-08 228540000 1351800 1015000 1138200 1185600 1249800 825330 1448200 1017100 949060 TRUE FALSE 1267193.251 1090151.656 1165198.641 1216024.503 1151645.749 1063589.373 1231055.854 1144087.174 790655.7548 1.602711728 1.37879431 1.473711706 1.537994881 1.456570375 1.345199053 1.557006127 1.447010493 1 19.59269017 0.94324365 22.85021498 1 1.469569768 0.788173856 0.077422573 3838.255113 1545290.94 0.068574453 0.017143613 8.774929779 -0.94324365 0.469569768 KYESVLQLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KYESVLQLGR 10 1 A0A087X1E4;P53365;P53365-2;P53365-3;E9PRV8 A0A087X1E4 ARFIP2 Arfaptin-2 0 143.97 5.30E-05 519230000 472380 611530 525670 497860 679360 415500 579830 596010 621200 FALSE TRUE 442814.579 656808.3175 538139.1406 510635.9305 626005.806 535448.1049 492889.8744 670423.1605 517517.7069 0.855651069 1.269151391 1.039846818 0.986702336 1.209631666 1.034646927 0.952411614 1.295459366 1 18.9812487 3.711345608 23.98684218 1.06482422 1.110705627 0 0.14483554 1306.870688 1987093.834 0.035503645 0.055232923 5144.528862 -3.711345608 0.045881407 KYFLHDDRDDGVDYWAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KYFLHDDRDDGVDYWAK 17 2 Q9NYF8;Q9NYF8-2;H0YF14;Q9NYF8-4 Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 68.257 0.02238 244780000 580120 624900 582180 626230 775310 427300 749930 587660 1272100 FALSE TRUE 543811.3247 671168.2462 595989.5845 642300.122 714420.2801 550654.5734 637484.9585 661030.6446 1059778.292 0.513136879 0.633310053 0.56237195 0.606070276 0.674122395 0.519594124 0.601526719 0.623744277 1 20.01533105 0.553760759 2.265484668 0.999987205 0.590129257 0.876954143 0.048244945 1.306769495 6.271920124 0.041461546 0.011206534 3.578992257 -0.553760759 -0.409857948 KYGGSVGSQPPPVAPEPGPVPS(ph)SPSQEPPTKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KYGGSVGSQPPPVAPEPGPVPSSPSQEPPTKR 32 2 A0A087WTZ5;Q04323;E9PJ81;E9PRQ7;Q04323-2;E9PS08 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 1 KYGGSVGSQPPPVAPEPGPVPS(0.487)S(0.487)PS(0.025)QEPPTKR;KYGGSVGSQPPPVAPEPGPVPS(0.55)S(0.42)PS(0.022)QEPPT(0.008)KR 124.17 7.67E-08 351150000 225779 197165 222277 241712 285250 159526 250263 167461 289154 TRUE FALSE 211647.8954 211763.3018 227549.5154 247914.7391 262847.6156 205578.5665 212738.3865 188368.8745 240892.3294 0.878599563 0.879078642 0.944610881 1.029151654 1.091141492 0.85340437 0.883126445 0.781962941 1 17.87802893 -0.810715647 7.018281596 1 0.919514232 0.078940602 0.088210677 6.43E-10 9.16E-11 0.086258251 0.020331265 0.154626652 0.810715647 -0.080485769 KYHNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KYHNPK 6 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 81.672 0.039767 2286600000 6287300 5821400 6284100 5700300 6648900 3833900 6039200 6104900 6510700 FALSE TRUE 5893789.116 6252422.513 6433161.82 5846579.349 6126722.214 4940684.692 5133678.025 6867110.204 5424022.109 1.086608608 1.152728065 1.186050073 1.077904778 1.129553326 0.910889482 0.946470704 1.26605498 1 22.37093163 2.361661011 10.5778726 1.013784214 1.136671694 0.176133194 0.098662541 0.444969081 39.26513463 0.032973724 0.027573454 229.9646126 -2.361661011 0.12288748 KYHNVGLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KYHNVGLSK 9 1 Q14103-3;Q14103;H0Y8G5;H0YA96;Q14103-2;Q14103-4 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ; 129.38 0.00025371 2354800000 5413200 5710100 5004300 4779500 6309900 3927800 6120800 5778000 7473200 FALSE TRUE 5074397.475 6132881.745 5123004.359 4902150.062 5814345.907 5061692.097 5203042.863 6499396.019 6225874.641 0.815049735 0.985063481 0.822856973 0.787383355 0.933900254 0.813008997 0.835712757 1.043933004 1 22.5698451 1.237530637 24.99974345 1.02196657 0.862407939 0.557678382 0.061200272 21.00848472 509797.0964 0.048113953 0.014644061 17.27947874 -1.237530637 -0.159558631 KYHPDTNKDDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KYHPDTNKDDPK 12 2 Q96EY1-2;Q96EY1;I3L1T6 Q96EY1-2 DNAJA3 "DnaJ homolog subfamily A member 3, mitochondrial" 0 101.39 0.0016209 132800000 321550 163900 204450 218760 225090 149350 243340 162040 304070 FALSE TRUE 301424.7595 176035.3265 209299.6505 224373.752 207412.3394 192464.9205 206853.4261 182271.0507 253318.7526 1.189903062 0.694916285 0.826230385 0.885736842 0.818780044 0.759773678 0.81657368 0.719532403 1 17.95059435 4.748704676 24.7248453 0.803493097 1.189903311 0.648512723 0.086313704 698.1848291 1701696.244 0.018434523 0.253183127 56066.65886 -4.748704676 0.386410214 KYIEIDS(ph)DEEPRGELLSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KYIEIDSDEEPRGELLSLR 19 2 E7EW05;Q9NVU7-2;Q9NVU7 E7EW05 SDAD1 Protein SDA1 homolog 1 KYIEIDS(1)DEEPRGELLSLR;KYIEIDS(1)DEEPRGELLSLR;KYIEIDS(1)DEEPRGELLSLR 194.77 1.25E-15 612080000 417110 499230 437330 431530 574000 320028 538150 356250 774850 TRUE FALSE 391003.8297 536193.5086 447703.6741 442603.7904 528920.3554 412414.8884 457459.4034 400728.5967 645522.5293 0.605716783 0.830634849 0.693552361 0.685651965 0.81936777 0.638885352 0.708665279 0.620781737 1 19.30010792 -1.8712712 4.486972476 1.07627874 0.711592802 0.604536144 0.075671925 0.041453136 0.001189268 0.052599879 0.015879943 0.013450202 1.8712712 -0.364685938 KYKPLDLRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KYKPLDLRPK 10 3 P42766 P42766 RPL35 60S ribosomal protein L35 0 76.143 0.016157 567150000 2117800 1820100 2048000 1817100 2361100 1425400 2480400 2004000 2703200 FALSE TRUE 1985250.678 1954862.098 2096579.527 1863729.862 2175668.73 1836889.841 2108487.047 2254203.811 2252018.457 0.88154281 0.868048879 0.93097795 0.827581966 0.966097202 0.815663759 0.936265438 1.000970398 1 21.10278722 1.416259109 3.965572425 0.998307852 0.886282847 0.552542226 0.043898698 0.152478947 4.104143033 0.027876134 0.009802906 26.07708896 -1.416259109 -0.112025005 KYNRFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KYNRFEK 7 2 P62280;M0QZC5;M0R1H5 P62280 RPS11 40S ribosomal protein S11 0 ; 82.671 0.013418 2423720000 1944840 2318820 1948770 1998130 2806570 1536670 2527930 2085220 3131100 FALSE TRUE 1823115.936 2490507.846 1994995.745 2049405.399 2586153.313 1980281.683 2148890.365 2345564.307 2608499.182 0.698913746 0.954766581 0.764805969 0.785664574 0.991433438 0.759165154 0.82380335 0.899200706 1 21.31478855 0.955519095 3.437353957 0.999659208 0.833067816 0.288606681 0.088450125 0.32075021 9.9032093 0.076554282 0.019833739 9.026493944 -0.955519095 -0.166591393 KYPDYESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KYPDYESK 8 1 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;; 114.51 0.0042358 1008880000 2943670 2515680 2462890 2659730 2772620 1760520 3366560 2373110 2838210 FALSE TRUE 2759430.949 2701943.565 2521310.914 2727983.175 2554869.609 2268753.544 2861775.582 2669398.007 2364494.415 1.167027899 1.142715139 1.066321366 1.153727899 1.080514123 0.959508946 1.210311838 1.128950862 1 21.1731003 -2.503851731 1.882404777 3.46E-05 1.112600815 0.214570646 0.068299881 2080073.584 136781.8412 8861139.859 0.015951705 0.003134356 2.503851731 1.112566184 KYPNVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KYPNVFK 7 1 O43865-2;O43865 O43865-2 AHCYL1 Putative adenosylhomocysteinase 2 0 ; 102.72 0.013689 627620000 627850 957630 804870 811510 1312370 705850 1149500 1193290 1571810 FALSE TRUE 588553.9892 1028533.922 823961.8965 832334.7205 1209301.754 909617.4365 977143.1464 1342274.883 1309464.757 0.449461497 0.785461324 0.629235642 0.635629723 0.923508439 0.694648277 0.74621569 1.025056136 1 20.3205458 4.128229282 0.087347365 1.307073807 5.95E-12 0.548930214 0.12023246 50.69438794 0.877516711 3.760963196 10.25226943 13434.74048 -4.128229282 -1.307073807 KYPS(ph)PQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 KYPSPQK 7 1 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 KYPS(1)PQK;KYPS(1)PQK;KYPS(1)PQK;KYPS(1)PQK;KYPS(1)PQK;KYPS(1)PQK 85.958 0.012513 4990180000 12495400 7389040 8599100 8329650 9592490 6087270 11268040 7940860 12641080 TRUE FALSE 11713335.22 7936132.21 8803074.713 8543402.921 8839134.53 7844566.03 9578502.009 8932293.851 10531202.08 1.112250541 0.753582748 0.835904073 0.811246698 0.839328166 0.744887997 0.909535486 0.848174195 1 23.32816679 0.503798985 1.158090704 0.999694373 0.839070092 0.14271484 0.103434212 3.059150629 5.460687976 0.088591501 0.027080505 3.190060981 -0.503798985 -0.16062428 KYS(ph)AAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KYSAAK 6 1 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 1 KYS(1)AAK;KYS(1)AAK;KYS(1)AAK 61.353 0.075976 1083330000 2175050 1581310 1539980 1192730 1904950 483030 2359120 1280230 5109800 TRUE FALSE 2038917.503 1698391.838 1576509.053 1223337.471 1755342.911 622472.9197 2005391.857 1440069.534 4256941.369 0.478963022 0.398969986 0.370338446 0.287374752 0.412348388 0.146225392 0.471087498 0.338287378 1 22.02138579 -0.745655808 1.238934003 1.017763691 0.363777978 0.814096944 0.0956559 68.083253 44.58311056 5.732770421 0.02486092 0.179615657 0.745655808 -0.653985713 KYS(ph)CDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KYSCDR 6 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q03001-3;Q03001-9;Q6P0N6;Q15149-4;Q15149-5;Q15149-8;F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A494C1D7;E7ETB9 Q15149-3;Q15149-4;Q15149-5;Q15149-8;F6QMI7 PLEC;DST Plectin;Dystonin 1 KYS(1)CDR;KYS(1)CDR 66.27 0.062385 524280000 885320 1081870 1017110 968980 1083320 1023280 1186060 990260 1153180 TRUE FALSE 829909.4015 1161972.78 1041236.33 993845.6673 998240.4171 1318684.324 1008221.314 1113896.141 960706.8082 0.863852941 1.20949781 1.083823203 1.034494248 1.039068745 1.372618902 1.049457863 1.159454822 1 19.87373669 KYS(ph)S(ph)CS(ph)TIFLDDSTVSQPNLRT(ph)T(ph)VK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KYSSCSTIFLDDSTVSQPNLRTTVK 25 2 Q8N7R7-3;Q8N7R7;H7BZD2 Q8N7R7-3 CCNYL1 Cyclin-Y-like protein 1 5 KY(0.191)S(0.619)S(0.628)CS(0.36)T(0.362)IFLDDS(0.366)T(0.35)VS(0.349)QPNLRT(0.891)T(0.885)VK 46.31 0.057861 492270000 173140 268920 279560 316780 272450 232150 395400 271910 327870 TRUE FALSE 162303.4765 288831.1166 286191.2952 324909.1111 251052.876 299167.9364 336113.4407 305858.562 273146.3789 0.594199627 1.057422463 1.047757969 1.189505468 0.919114788 1.09526598 1.230524974 1.119760633 1 18.05931477 4.747765139 3.836942607 1.093122428 0.539951842 0.751862485 0.088195151 0.134162009 3.853795963 0.021425317 0.211726877 55945.49739 -4.747765139 -0.553170586 KYSCDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KYSCDR 6 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q03001-3;Q03001-9;Q6P0N6;Q15149-4;Q15149-5;Q15149-8;F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A494C1D7;E7ETB9 Q15149-3;Q15149-4;Q15149-5;Q15149-8;F6QMI7 PLEC;DST Plectin;Dystonin 0 91.626 0.076449 200480000 350570 468760 343360 394330 495720 294490 458300 449920 418330 FALSE TRUE 328628.4495 503467.4781 351504.6613 404449.1754 456788.1508 379504.4824 389582.1696 506093.5024 348508.0205 0.942958067 1.444636704 1.008598485 1.160516119 1.310696236 1.088940455 1.117857113 1.452171751 1 18.41083233 -1.164879576 4.218997566 0.999943081 1.189947116 0.111285932 0.169432159 8.11E-05 1.60E-05 0.146624827 0.034549461 0.068410131 1.164879576 0.190004035 KYTELPHGAIS(ph)EDQAVGPADIPCDSTGQTST ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KYTELPHGAISEDQAVGPADIPCDSTGQTST 31 1 Q9H773;H3BPN2;H3BSA6 Q9H773 DCTPP1 dCTP pyrophosphatase 1 1 KYTELPHGAIS(1)EDQAVGPADIPCDSTGQTST 187.33 1.11E-18 130130000 139730 101690 122240 94095 119310 97138 122950 88588 174090 TRUE FALSE 130984.5487 109219.2334 125139.5905 96509.637 109939.8739 125180.1637 104514.7889 99648.40681 145033.2543 0.90313459 0.753063385 0.862833776 0.665431093 0.758032179 0.863113527 0.720626379 0.687072818 1 17.1460242 4.747078292 23.45347901 0.780730796 0.903134742 0.111447249 0.099200074 908.3148152 2500912.587 0.020902118 0.230849871 55857.08811 -4.747078292 0.122403945 KYTELPHGAISEDQAVGPADIPCDSTGQT(ph)ST ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KYTELPHGAISEDQAVGPADIPCDSTGQTST 31 1 Q9H773;H3BPN2;H3BSA6 Q9H773 DCTPP1 dCTP pyrophosphatase 1 1 KYTELPHGAISEDQAVGPADIPCDS(0.006)T(0.023)GQT(0.324)S(0.324)T(0.324);KYTELPHGAISEDQAVGPADIPCDS(0.014)T(0.065)GQT(0.307)S(0.307)T(0.307) 157.47 4.79E-10 601910000 602430 589710 586460 578880 647550 549420 730830 551950 577630 TRUE FALSE 564724.9817 633372.742 600371.1081 593735.0408 596694.0351 708028.6349 621248.8262 620862.1725 481219.8214 1.173528098 1.31618174 1.247602616 1.233812521 1.239961466 1.471320597 1.290987608 1.290184122 1 18.87633654 -0.14531104 7.69302335 1 1.288619814 0.565650455 0.077779801 0 0 0.071818329 0.016927743 0.715630694 0.14531104 0.288619814 KYTGEDFDEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 KYTGEDFDEDLR 12 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;; 146.96 0.00010451 1744680000 4970210 5810500 5681490 6191210 7267080 4745330 7444610 6249890 7517510 FALSE TRUE 4659133.428 6240715.466 5816257.626 6350086.93 6696352.851 6115229.737 6328359.843 7030202.524 6262789.016 0.743939069 0.996475444 0.928700873 1.013939143 1.069228555 0.976438727 1.010469908 1.122535424 1 22.57837385 5.366621897 1.259929408 1.013732369 3.97E-38 0.707571272 0.053837428 3.461102742 1.538928921 0.014564781 6.695682762 232606.5271 -5.366621897 -1.013732369 KYTLENKEEGS(ph)LSDTEADAVSGQLPDPTTNPSAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 KYTLENKEEGSLSDTEADAVSGQLPDPTTNPSAGK 35 2 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 KY(0.019)T(0.021)LENKEEGS(0.319)LS(0.319)DT(0.319)EADAVS(0.002)GQLPDPTTNPSAGK;KYT(0.004)LENKEEGS(0.457)LS(0.457)DT(0.082)EADAVSGQLPDPTTNPSAGK;KYT(0.014)LENKEEGS(0.47)LS(0.47)DT(0.046)EADAVSGQLPDPTTNPSAGK 161.5 8.10E-15 3180340000 2723550 1408290 1764210 1794380 1878090 1180576 2395500 1462100 3243400 TRUE FALSE 2553087.867 1512561.257 1806057.894 1840426.829 1730592.387 1521389.126 2036317.014 1644646.403 2702055.587 0.944868743 0.559781695 0.668401458 0.681121009 0.640472533 0.563048789 0.753617736 0.608664904 1 21.36562592 -1.228539673 4.008694449 1.000262306 0.666519198 0.450914129 0.111258432 520706.2926 52343242.76 26350.62547 0.022976665 0.059082699 1.228539673 -0.333743108 KYTLENKEEGSLS(ph)DTEADAVSGQLPDPTTNPSAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KYTLENKEEGSLSDTEADAVSGQLPDPTTNPSAGK 35 2 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 KYT(0.006)LENKEEGS(0.114)LS(0.849)DT(0.031)EADAVSGQLPDPTTNPSAGK 214.37 1.12E-36 1657700000 1059900 539920 709320 720130 795150 500900 980360 606180 1297900 TRUE FALSE 993562.751 579896.2386 726145.4054 738609.755 732702.1265 645501.6986 833364.1192 681862.9074 1081272.105 0.91888318 0.536309256 0.671565836 0.683093323 0.677629732 0.596983586 0.770725625 0.630611762 1 20.0442982 -2.13942427 0.495367048 1.387921342 0.669027233 0.464970325 0.104271548 71.37801058 5.006290802 31.00716649 0.045022341 0.00725397 2.13942427 -0.718894109 KYVATLGVEVHPLVFHTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KYVATLGVEVHPLVFHTNR 19 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 249.28 2.14E-25 1519500000 1562230 1879130 1616170 1393650 2272350 1151240 1906660 1702690 2191470 FALSE TRUE 1464452.813 2018262.74 1654506.316 1429413.418 2093888.797 1483584.299 1620774.034 1915274.595 1825699.5 0.80213245 1.105473678 0.906231456 0.782940138 1.146896736 0.81261144 0.887755095 1.049063438 1 20.80001789 KYVIS(ph)DEEEEDDD ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 174.95 2.02E-05 4389800000 9353280 7558620 8368790 8033910 8804150 6828550 9642070 7342510 10075050 TRUE FALSE 8767874.901 8118268.09 8567301.651 8240073.732 8112707.573 8799841.533 8196331.116 8259238.536 8393459.068 1.044608049 0.967213639 1.020711673 0.981725611 0.966551157 1.048416566 0.976514099 0.984008913 1 23.00083406 4.759745721 24.06327424 0.993946299 1.044608134 0.290515733 0.025247993 4094.886989 4651090.258 0.005497702 0.236065134 57510.31161 -4.759745721 0.050661835 LAAAEETAVS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LAAAEETAVSPR 12 0 Q9BUH6 Q9BUH6 C9orf142 Protein PAXX 1 LAAAEETAVS(1)PR;LAAAEETAVS(1)PR;LAAAEETAVS(1)PR;LAAAEETAVS(1)PR;LAAAEETAVS(1)PR;LAAAEETAVS(1)PR 234.04 5.44E-16 11000440000 3800040 3771020 3895780 3605040 3804810 3154900 4170610 3422500 2937170 TRUE FALSE 3562202.28 4050230.245 3988189.741 3697551.43 3505995.57 4065668.414 3545265.749 3849806.659 2446937.352 1.455779927 1.655224332 1.629869983 1.511093623 1.432809699 1.661533513 1.448858405 1.573316397 1 21.22254573 -2.70085244 0.335085509 2.73E-19 1.586186448 0.792701948 0.087145766 26.90026383 0.941942332 19.40100764 0.069084029 0.00199135 2.70085244 1.586186448 LAAAILGGVDQIHIKPGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LAAAILGGVDQIHIKPGAK 19 1 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ; 244.08 1.03E-24 704630000 1671870 1337270 1570580 1480270 1639330 1193890 2022820 1503070 2085000 FALSE TRUE 1567230.641 1436282.862 1607834.899 1518256.234 1510583.635 1538546.662 1719516.92 1690731.598 1737000.03 0.902262875 0.826875554 0.925638959 0.874068053 0.869650897 0.885749358 0.989934882 0.973363022 1 20.72816635 1.752781932 4.755797028 0.986732693 0.87844028 0.793002086 0.025762862 0.078278072 3.983226466 0.012772258 0.006618379 56.59550401 -1.752781932 -0.108292412 LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK 37 2 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ; 392.13 1.14E-179 1991920000 2040400 805450 1100580 1078670 1105200 623680 1400880 872280 1781080 FALSE TRUE 1912695.006 865086.3561 1126686.277 1106350.498 1018402.05 803726.2914 1190831.049 981186.0781 1483806.242 1.289046341 0.58301841 0.7593217 0.745616555 0.686344363 0.541665258 0.802551584 0.66126294 1 20.50087128 -1.45306495 3.07229039 1.005499429 0.735676098 0.111234269 0.205551939 40780689.56 51240299.32 1946970.282 0.043800558 0.035231818 1.45306495 -0.26982333 LAADFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAADFQR 7 0 O94874;O94874-3 O94874 UFL1 E3 UFM1-protein ligase 1 0 76.847 0.092244 94788000 128450 165640 117630 119520 175320 81127 141880 136370 200460 FALSE TRUE 120410.5438 177904.1579 120420.2391 122587.0855 161551.0744 104547.0479 120606.4111 153396.0947 167001.931 0.721012883 1.065282041 0.721070939 0.734045917 0.967360518 0.626022988 0.722185728 0.918528868 1 17.34950526 5.046477882 16.21385372 0.827485344 0.117397638 0.057057584 0.143717549 13046338.49 118360019 0.033524814 286362379.1 111295.5709 -5.046477882 -0.710087706 LAAELEDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LAAELEDRR 9 1 Q9NQG5;A2A2M0;A0A087X2D2 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ;;; 167.12 9.66E-05 1192540000 1389360 1853740 1567690 1553640 1881180 1219000 1684810 1541820 1824960 FALSE TRUE 1302402.438 1990992.838 1604876.347 1593509.033 1733439.711 1570905.511 1432188.382 1734319.621 1520362.386 0.856639476 1.309551497 1.055588037 1.048111323 1.140149037 1.03324413 0.942004613 1.140727787 1 20.53598381 2.121305062 5.969537699 1.013285547 1.107596614 0.017116375 0.121399389 0.449613359 21.78598481 0.043479267 0.031926422 132.222408 -2.121305062 0.094311066 LAAFADALEFADEEKES(ph)PVEFTGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LAAFADALEFADEEKESPVEFTGHK 25 1 Q5SY16 Q5SY16 NOL9 Polynucleotide 5-hydroxyl-kinase NOL9 1 LAAFADALEFADEEKES(0.994)PVEFT(0.006)GHK;LAAFADALEFADEEKES(0.995)PVEFT(0.005)GHK;LAAFADALEFADEEKES(1)PVEFTGHK 250.25 1.04E-39 242292000 355042 213333 240187 255667 265502 153827 316178 236873 369560 TRUE FALSE 332820.555 229128.3973 245884.3491 262227.8481 244650.5439 198234.3577 268770.0442 266447.1155 307878.0486 1.081014241 0.744218038 0.798642028 0.851726355 0.79463458 0.643872984 0.872975665 0.865430701 1 18.23199948 0.906626368 1.926454852 0.998178672 0.80846371 0.183554693 0.111080766 0.637592518 4.859045568 0.096092646 0.026918699 8.065408483 -0.906626368 -0.189714962 LAAGRPFNT(ph)YPR ddPTM_SK-BR-3_Pertuzumab_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 146 9.55E-05 1404230000 435291 780130 431747 424285 710830 233534 777590 467043 1373640 TRUE FALSE 408046.9133 837891.6369 441988.2427 435172.8714 655004.2792 300951.4747 660997.5983 525354.3466 1144370.61 0.356568851 0.732185561 0.386228237 0.380272674 0.572370763 0.262984275 0.577607982 0.459077105 1 20.12612292 -0.701318667 1.309153841 1.010346096 0.480978505 0.606250056 0.134766642 138.7133629 99.93724601 7.415871523 0.035816555 0.19892132 0.701318667 -0.529367591 LAALKDEPQTVPDVPS(ph)FGESPPLSPIDMDTQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAALKDEPQTVPDVPSFGESPPLSPIDMDTQER 33 1 P17535;U3KPR5 P17535 JUND Transcription factor jun-D 1 LAALKDEPQT(0.003)VPDVPS(0.497)FGES(0.497)PPLS(0.003)PIDMDTQER 55.541 0.061106 46994000 18921 19103 17875 21086 21019 14236 21500 21627 25585 TRUE FALSE 17736.76838 20517.406 18299.00344 21627.10246 19368.25253 18345.7021 18276.2746 24327.17856 21314.69821 0.832137908 0.962594253 0.858515718 1.014656752 0.908680589 0.860706631 0.857449372 1.141333474 1 14.37956101 1.244072135 24.99999956 1.070666755 0.901503897 0.553527836 0.063978784 85.88927446 389603.6195 0.042187488 0.014433919 17.54171839 -1.244072135 -0.169162858 LAAPSVSHVS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 179.14 1.36E-05 900330000 557460 802420 755190 678140 829090 749980 958400 776970 809450 TRUE FALSE 522569.5737 861832.0117 773103.4634 695542.2205 763976.6158 966487.0511 814696.8173 873976.4148 674347.5658 0.774926166 1.278023464 1.146446584 1.031429868 1.132912247 1.433217973 1.208125985 1.296032579 1 19.36313284 2.450205904 24.99651429 1.257199046 1.106511463 0.170596234 0.165880632 380.9682428 353806.3253 0.053042741 0.044379614 281.9719473 -2.450205904 -0.150687583 LAAQENRPVTDHLDEQAVQGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LAAQENRPVTDHLDEQAVQGLK 22 1 Q9BTW9-4;Q9BTW9;J3KR97;I3L439;I3L500;I3L4D2;I3L163;I3L143;I3L131;I3L3H4;I3L1S3;Q9BTW9-3;Q9BTW9-5;I3L0V3 Q9BTW9-4 TBCD Tubulin-specific chaperone D 0 ; 116.48 9.74E-05 205790000 226294 188229 210399 227668 210262 158348 248196 199153 198784 FALSE TRUE 212130.6625 202165.671 215389.7636 233510.3463 193748.8707 204060.497 210981.3139 224017.6904 165605.6662 1.280938433 1.220765422 1.300618322 1.410038386 1.169941072 1.232207217 1.273998159 1.352717546 1 17.33739251 -1.439804587 3.529795489 0.997103002 1.27503085 0.630425286 0.067309735 5253977.932 2144643.002 115710.2343 0.014950449 0.036324146 1.439804587 0.277927847 LAAQLGAPTS(ph)PIPDSAIVNTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAAQLGAPTSPIPDSAIVNTR 21 0 Q9H8Y5;B8ZZS4 Q9H8Y5 ANKZF1 Ankyrin repeat and zinc finger domain-containing protein 1 1 LAAQLGAPT(0.102)S(0.898)PIPDSAIVNTR 142.26 1.55E-07 118250000 70057 82846 88659 95103 104080 67734 91654 65622 92360 TRUE FALSE 65672.25743 88980.00404 90762.03335 97543.50399 95905.97664 87287.70623 77911.33357 73815.05115 76944.51933 0.853501432 1.1564177 1.179577625 1.267712175 1.246430252 1.134423959 1.012565083 0.959328251 1 16.23153095 1.703014511 3.460205879 0.981966442 1.156442199 0.277719093 0.112450162 0.244230431 6.643848367 0.063180393 0.029436164 50.46781605 -1.703014511 0.174475757 LAASGEGGLQELSGHFENQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAASGEGGLQELSGHFENQK 20 0 Q16643;Q16643-3;Q16643-2;D6RFI1 Q16643 DBN1 Drebrin 0 237.24 1.36E-29 73096000 103860 101770 112920 107690 105050 89868 120050 87978 92729 FALSE TRUE 97359.588 109305.1567 115598.5157 110453.5077 96799.79675 115811.4327 102049.617 98962.24696 77251.93085 1.260286791 1.414918119 1.496383514 1.429783133 1.253040483 1.499139652 1.320997623 1.281032666 1 16.23728337 0.747778495 1.154791816 1.000163422 1.404725138 0.668174916 0.084921068 0.48311568 1.138403508 0.076445766 0.023729067 5.594721788 -0.747778495 0.404561716 LAASTEPQGPRPVLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LAASTEPQGPRPVLGR 16 1 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;F5GWK5;F5H3G8;F5H5A8;F5GY07 Q9Y365 STARD10 PCTP-like protein 0 ;;; 160.65 7.94E-09 2150080000 1213890 1288380 1147740 1248540 1273130 977020 1410230 1093790 1502290 FALSE TRUE 1137914.792 1383772.996 1174964.935 1280579.65 1173143.505 1259069.813 1198779.103 1230352.089 1251548.094 0.909205805 1.105649078 0.938809256 1.023196517 0.937353915 1.006009933 0.957837025 0.983064171 1 20.2552823 3.771866172 23.97509755 0.977037318 1.021690227 0.033719918 0.054406223 296.7221519 158986.4545 0.012153407 0.021909697 5913.793724 -3.771866172 0.044652909 LACDVDQVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LACDVDQVTR 10 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 105.98 0.0081486 0 55912 70956 64810 70040 71875 59001 85681 60701 59549 FALSE TRUE 52412.56773 76209.65607 66347.32381 71837.34498 66230.22743 76033.6309 72833.92947 68279.65347 49609.8872 1.056494394 1.536178782 1.337381066 1.448044917 1.335020722 1.532630594 1.468133342 1.376331561 1 15.59834006 0.948138927 20.5800121 0.999999998 1.408559055 0.431017882 0.137926103 1287.918993 511086.445 0.117377959 0.02934449 8.874398505 -0.948138927 0.408559056 LADALQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LADALQELR 9 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;; 204.91 3.68E-05 1522840000 1182840 2089200 1143180 1190750 2140480 813760 1160170 1792390 2044640 FALSE TRUE 1108808.156 2243886.542 1170296.769 1221306.661 1972375.335 1048679.302 986213.279 2016173.837 1703376.375 0.650947243 1.317316933 0.687045322 0.716991664 1.157921035 0.615647438 0.578975553 1.183633791 1 20.69996581 3.834989776 7.586956359 0.810573112 1.026425163 0.022655775 0.266054208 0.521966144 32.82734323 0.063815313 0.115578816 6838.955465 -3.834989776 0.215852051 LADDVDLEQVANETHGHVGADLAALCSEAALQAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LADDVDLEQVANETHGHVGADLAALCSEAALQAIR 35 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 302.55 9.25E-91 3697110000 1381420 1447020 1536520 1517920 1581180 1332220 1711650 1331460 1756940 FALSE TRUE 1294959.388 1554158.866 1572966.98 1556872.397 1457000.501 1716810.287 1455003.973 1497695.712 1463695.364 0.884719198 1.061804871 1.074654617 1.063658761 0.995426055 1.172928691 0.994062022 1.023229115 1 20.48118389 4.740348933 24.85507495 1.053191146 0.884719136 0.479871398 0.053272474 115.7955098 1609253.3 0.011388116 0.073590524 54998.25785 -4.740348933 -0.16847201 LADELHMPSLPEMMFGDNVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LADELHMPSLPEMMFGDNVLR 21 0 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 ; 177.61 6.40E-17 233580000 351250 424570 394290 433590 402420 316230 444430 346990 408120 FALSE TRUE 329265.8895 456005.6046 403642.745 444716.6535 370815.5565 407520.4674 377791.8474 390312.4653 340002.1354 0.968423004 1.341184531 1.187177088 1.307981942 1.09062714 1.198582082 1.111145514 1.147970629 1 18.37518428 1.007349267 0.578554163 1.001471349 1.215354694 0.192160323 0.106246105 1.140042513 0.928723787 0.101537468 0.045246131 10.17066306 -1.007349267 0.213883345 LADFGVLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LADFGVLHR 9 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 120.12 0.0007167 190040000 430690 466200 389350 357050 437440 378390 540680 505030 650200 FALSE TRUE 403733.8817 500717.9331 398585.5659 366212.5075 403085.2269 487625.0504 459610.0534 568084.1072 541677.4195 0.745340062 0.924383988 0.735835668 0.676071208 0.74414257 0.900212992 0.848494024 1.04874984 1 19.04707443 1.484206776 1.559343514 1.025397918 0.784867332 0.614969202 0.076115339 0.268204094 1.245569188 0.068638951 0.022579601 30.49346496 -1.484206776 -0.240530586 LADHFGGK ddPTM_SK-BR-3_Pertuzumab_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 ;;; 124.98 0.0012814 1974560000 7318460 6760780 7096990 6717920 7562030 5589290 8198700 6487660 9225500 FALSE TRUE 6860410.652 7261355.186 7265333.954 6890313.201 6968138.668 7202827.288 6969381.048 7297658.632 7685704.451 0.892619629 0.9447872 0.945304884 0.8965103 0.906636303 0.937172036 0.906797951 0.949510702 1 22.87374607 0.944821265 4.954552373 0.999979411 0.922916211 0.645078835 0.019231283 0.195056301 14.1112267 0.018898449 0.004780078 8.806863505 -0.944821265 -0.0770632 LADILS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LADILSPR 8 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 LADILS(1)PR;LADILS(1)PR;LADILS(1)PR;LADILS(1)PR;LADILS(1)PR;LADILS(1)PR;LADILS(1)PR 123.79 0.0013977 263296000 712059 894447 819895 870620 965788 735266 1170917 932599 780272 TRUE FALSE 667492.4983 960672.7866 839343.2966 892961.5832 889938.9063 947525.3582 995348.8661 1049036.038 650039.5625 1.026849036 1.477868182 1.291218789 1.37370344 1.369053451 1.4576426 1.53121275 1.613803372 1 19.310168 2.61048286 1.808047088 1.452547919 1.317450651 0.02993487 0.197438996 0.876247393 5.72807877 0.072103562 0.064168266 407.8334662 -2.61048286 -0.135097268 LADLIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LADLIER 7 0 P05091;F8VP50;Q5SYQ7;Q5SYQ9;Q5SYQ8;P00352 P05091 ALDH2;ALDH1A1 "Aldehyde dehydrogenase, mitochondrial;Retinal dehydrogenase 1" 0 ;;;;; 148.21 0.0048845 604277000 945107 1076780 909103 873319 1337880 893970 905152 1041540 1580700 FALSE TRUE 885954.4399 1156505.912 930667.3525 895729.8441 1232808.302 1152044.627 769432.8606 1171578.562 1316870.958 0.672772404 0.878222657 0.70672631 0.680195609 0.936164849 0.874834865 0.584288731 0.889668463 1 20.32868255 1.00202647 24.99130539 1.000000041 0.765690172 0.353931251 0.108507036 53.27331616 656978.703 0.100802578 0.025200644 10.04677023 -1.00202647 -0.234309869 LADQCTGLQGFLVFHSFGGGTGSGFTSLLMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 LADQCTGLQGFLVFHSFGGGTGSGFTSLLMER 32 0 P68363;F8VQQ4;Q9BQE3;F5H5D3 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 ;;;;;;;;; 365.58 6.68E-148 2815767000 573088 847612.9 420682 304907 927608.1 412690.9 561323.5 964818.3 185451.5 FALSE TRUE 537219.4451 910371.0411 430660.7757 312731.4298 854757.5016 531828.0634 477158.2522 1085277.989 154498.4466 3.477183473 5.892428443 2.787476413 2.024172001 5.53246664 3.442287448 3.08843398 7.024523628 1 17.23723281 3.968676511 24.08437569 3.616666459 4.792652045 0.063216883 1.782748259 496.9439641 1417291.182 0.41199243 0.759345571 9304.14587 -3.968676511 1.175985586 LADS(ph)PPPQVWQLISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LADSPPPQVWQLISK 15 0 Q5HY81;P11441 Q5HY81 UBL4A Ubiquitin-like protein 4A 1 LADS(1)PPPQVWQLISK;LADS(1)PPPQVWQLISK 146.86 4.00E-06 125395000 247850 207331 223640 205462 254870 217490 327610 255350 396150 TRUE FALSE 232337.5109 222682.003 228944.8464 210734.5028 234853.5383 280275.8323 278487.9219 287231.0096 330030.0058 0.703989052 0.674732597 0.693709185 0.638531343 0.711612684 0.849243485 0.843826067 0.870317864 1 18.33223767 1.686926092 0.751416822 0.979987653 0.671506101 0.899719026 0.035685874 0.176805696 0.198894853 0.032486761 0.014983413 48.63244364 -1.686926092 -0.308481553 LADSGDGAGPS(ph)PEEKDFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LADSGDGAGPSPEEKDFLK 19 1 Q92917 Q92917 GPKOW G patch domain and KOW motifs-containing protein 1 LADSGDGAGPS(1)PEEKDFLK;LADSGDGAGPS(1)PEEKDFLK 225.34 1.06E-19 382000000 1135490 545850 767530 723090 779180 503440 928210 622590 1307410 TRUE FALSE 1064421.708 586265.302 785736.1741 741645.7136 717986.3459 648774.9553 789033.5276 700321.732 1089194.825 0.977255569 0.538255681 0.721391762 0.680911896 0.659190009 0.595646381 0.724419093 0.642971961 1 20.0548306 -1.564815545 4.685660186 1.002933528 0.67899135 0.405121339 0.116079048 0.003112176 0.000289046 0.098330305 0.022989946 0.027238579 1.564815545 -0.323942178 LADVDKDGLLDDEEFALANHLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LADVDKDGLLDDEEFALANHLIK 23 1 A0A024R571;Q9H4M9 A0A024R571 EHD1 EH domain-containing protein 1 0 131.59 1.81E-05 503750000 471050 309460 352220 357940 401830 253490 508360 341690 567110 FALSE TRUE 441567.8213 332372.7404 360574.8247 367125.3464 370271.8927 326668.4479 432136.1374 384350.7487 472455.6773 0.934622744 0.703500363 0.763192913 0.777057752 0.783717734 0.691426654 0.914659635 0.81351705 1 18.84981947 0.933675045 0.873871043 0.995426408 0.768306954 0.408939214 0.077319699 0.585856916 0.956221711 0.066849665 0.023340684 8.583710169 -0.933675045 -0.227119454 LAEAFAEELHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAEAFAEELHER 12 0 Q99707-2;Q99707;B1ANE3 Q99707-2 MTR Methionine synthase 0 112.51 0.0012664 57090000 28583 40309 32682 30681 40533 26697 37360 37360 50964 FALSE TRUE 26794.04105 43293.5203 33457.23247 31468.3264 37349.70168 34403.99051 31758.21483 42024.47824 42457.77916 0.631074955 1.019684052 0.788011835 0.741167509 0.879690422 0.810310647 0.747995196 0.989794546 1 15.37374129 1.221553227 24.09455713 0.994897714 0.819850268 0.376934601 0.100918783 204.8207995 290159.421 0.091482346 0.023140597 16.65532941 -1.221553227 -0.175047446 LAEAFHIS(ph)EDSDPFNIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAEAFHISEDSDPFNIR 17 0 Q12986;Q12986-2 Q12986 NFX1 Transcriptional repressor NF-X1 1 LAEAFHIS(0.974)EDS(0.026)DPFNIR 67.995 0.02436 11745000 26663 16739 19973 18217 19493 17707 21164 12853 22720 TRUE FALSE 24994.21042 17978.37298 20446.76899 18684.47906 17962.09841 22818.72345 17990.65468 14457.72534 18927.88522 1.320496724 0.94983527 1.080245825 0.98714034 0.948975451 1.20556117 0.950484138 0.763832048 1 14.20822561 4.743848942 24.49075537 0.997626428 1.320496907 0.468506343 0.111410922 388.4113933 1798696.119 0.024978028 0.211606288 55443.2835 -4.743848942 0.322870479 LAEAHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAEAHAK 7 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 68.422 0.062495 46925000 300460 345240 312450 320810 396040 261160 344950 331530 369430 FALSE TRUE 281654.7449 370801.9288 319861.4615 329042.5277 364936.6159 336552.6524 293227.9499 372922.2503 307769.7464 0.915147601 1.204803049 1.039288186 1.069119144 1.185745578 1.093520908 0.952751053 1.21169236 1 18.2314919 -1.093575987 4.481606138 0.999992718 1.084041696 0.065638534 0.099610095 6.62E-06 1.34E-06 0.088116347 0.020767423 0.080616514 1.093575987 0.084048978 LAEAHQQECCQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LAEAHQQECCQK 12 0 Q9Y5X3;A0A087WUY5 Q9Y5X3 SNX5 Sorting nexin-5 0 ;;; 225.97 1.64E-11 1242500000 1828440 1546710 1660560 1628780 1867160 1375250 1954770 1585550 2243920 FALSE TRUE 1714001.204 1661230.018 1699949.267 1670577.252 1720520.785 1772262.35 1661670.386 1783509.408 1869395.256 0.916874695 0.88864568 0.909357859 0.893645818 0.920362229 0.948040466 0.888881247 0.954056881 1 20.83414021 -0.403391709 0.32912592 1.030561979 0.898128079 0.687667252 0.019483676 4.225495457 0.513004649 0.16212404 0.017678763 0.395010183 0.403391709 -0.1324339 LAEDEAFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 173.73 0.00012845 211120000 215070 230680 198380 225220 208870 179830 246910 208300 182390 FALSE TRUE 201609.1526 247759.7872 203085.6673 230999.5265 192466.1927 231744.0017 209888.1377 234306.7135 151947.9307 1.326830525 1.630557166 1.336547766 1.520254507 1.26665886 1.525154049 1.381316196 1.542019772 1 17.2132175 -1.57592742 3.156946685 0.979640369 1.444924062 0.595342054 0.114268058 2455075.131 1842003.038 327257.7381 0.023462548 0.026550492 1.57592742 0.465283693 LAEDEAFQRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAEDEAFQRR 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 0 164.33 9.92E-06 222590000 191520 281820 229690 233430 284760 179210 282650 233420 289470 FALSE TRUE 179533.1051 302686.246 235138.3553 239420.209 262396.0983 230945.0178 240269.2565 262563.0008 241155.587 0.744470022 1.255149217 0.975048342 0.992803907 1.08807804 0.957659827 0.996324653 1.088770134 1 17.87960471 3.712966769 24.82799992 1.011701468 1.059930341 0 0.13097626 1680.437177 2947612.824 0.031692507 0.049348422 5163.768557 -3.712966769 0.048228873 LAEDEGDS(ph)EPEAVGQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LAEDEGDSEPEAVGQSR 17 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 LAEDEGDS(1)EPEAVGQSR;LAEDEGDS(1)EPEAVGQSR;LAEDEGDS(1)EPEAVGQSR;LAEDEGDS(1)EPEAVGQSR;LAEDEGDS(1)EPEAVGQSR 440.08 2.39E-182 7611530000 3337190 2877790 3035060 2554140 2655700 2268240 3540950 2309530 2934800 TRUE FALSE 3128321.235 3090864.566 3107053.056 2619683.557 2447132.035 2923044.066 3010017.42 2597879.904 2444962.92 1.279496392 1.264176458 1.270797618 1.071461467 1.000887177 1.195537176 1.23110964 1.062543682 1 21.22138116 8 0.11962142 0.974315645 2.004977926 0.461354382 0.081699464 97.12616088 0.798595806 0.609339817 16.68819995 100000000 -8 1.030662281 LAEEEDLFDSAHPEEGDLDLASESTAHAQSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LAEEEDLFDSAHPEEGDLDLASESTAHAQSSK 32 0 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 ; 255.21 2.21E-59 264220000 307820 311160 329630 341870 368650 278830 437410 324710 453500 FALSE TRUE 288554.0957 334198.6102 337448.9793 350642.963 339697.7161 359323.6946 371824.4312 365250.7583 377807.9203 0.763758725 0.884572801 0.893176032 0.928098497 0.899128096 0.951075071 0.984162616 0.966763105 1 18.52729342 7.674438271 0.227818751 1.00173753 3.49E-17 0.864005356 0.024752472 15.08649938 0.224306408 0.035748178 5.454860101 47253966.73 -7.674438271 -1.00173753 LAEGAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAEGAER 7 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 79.597 0.074894 475050000 705900 733010 716790 650730 760770 620980 708260 677850 815310 FALSE TRUE 661718.9791 787282.8231 733792.5973 667428.8335 701022.193 800246.8452 602062.9882 762481.0646 679229.4939 0.974220032 1.15908221 1.080330881 0.982626402 1.032084442 1.178168575 0.886391115 1.122567662 1 19.37353958 3.407408705 8.848462294 1.028317258 1.0931681 0.018453517 0.089987734 0.652272862 75.69019314 0.023146165 0.031386424 2555.104722 -3.407408705 0.064850843 LAEIGAPIQGNREELVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAEIGAPIQGNREELVER 18 1 Q13435;E9PPJ0;H0YCG1;E9PJ04;E9PJT3 Q13435 SF3B2 Splicing factor 3B subunit 2 0 75.97 0.0063561 0 89398 94725 95947 108920 121290 72606 122030 75587 147150 FALSE TRUE 83802.73876 101738.5376 98222.90815 111715.0716 111764.3727 93566.17354 103732.7344 85024.20334 122589.7144 0.683603345 0.829910879 0.801232866 0.911292372 0.911694535 0.763246525 0.846178123 0.693567187 1 16.90347841 -2.552988503 2.301570246 4.488437411 0.813858633 0.378126499 0.077835221 5599910.123 475549.2873 102503865.7 0.018732806 0.002799055 2.552988503 -3.674578778 LAELEEFINGPNNAHIQQVGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LAELEEFINGPNNAHIQQVGDR 22 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;;; 355.31 3.26E-96 3159717000 2539459 3083681 2956376 3138515 3332981 2537715 3463230 2885167 3049048 FALSE TRUE 2380518.794 3311999.95 3026502.635 3219054.608 3071222.117 3270312.124 2943950.813 3245386.451 2540142.191 0.937159661 1.303863997 1.191469771 1.267273391 1.209074881 1.287452386 1.158970873 1.277639678 1 21.27647783 -1.103006833 7.92890271 0.999999984 1.213601924 0.265423437 0.105671291 2.74E-08 2.99E-09 0.088279484 0.020807672 0.078884771 1.103006833 0.21360194 LAELSDYRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LAELSDYRR 9 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ; 124.95 0.00082607 498490000 266150 476800 263390 271020 530150 201482 282650 417170 564750 FALSE TRUE 249492.1466 512102.7681 269637.7352 277974.832 488514.1575 259646.5826 240269.2565 469254.5928 470489.5766 0.530281985 1.088446575 0.573100338 0.590820383 1.038310266 0.551864686 0.510679234 0.997375109 1 18.84380324 1.205232949 23.69347621 0.99868953 0.714315593 0.266904528 0.205985238 180.8270897 128547.3291 0.194832277 0.048726122 16.04105578 -1.205232949 -0.284373937 LAENFCVCHLATGDMLR ddPTM_SK-BR-3_Pertuzumab_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 ; 193.22 1.43E-10 1066600000 547510 661810 559940 587090 745810 446070 573090 606600 590070 FALSE TRUE 513242.3264 710811.101 573222.0412 602155.7233 687237.0911 574843.1677 487160.4748 682335.3453 491583.505 1.044059292 1.445962067 1.16607257 1.224930693 1.398006817 1.169370334 0.991002485 1.388035478 1 18.90707698 0.574172819 0.339002957 0.974058105 1.280354089 0.129698118 0.15413593 4.326232895 1.084105417 0.421024437 0.155018148 3.751222451 -0.574172819 0.306295983 LAEQAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 210.67 0.00028393 26989130000 7899260 9341910 8268770 8313330 9204990 7090830 9275470 8240340 9879890 FALSE TRUE 7404859.417 10033594.74 8464909.129 8526664.122 8482067.217 9137837.511 7884699.383 9269164.588 8230872.532 0.899644526 1.219019575 1.028433996 1.035936845 1.030518597 1.110190624 0.957942108 1.12614605 1 22.97261394 3.714465563 24.48877628 1.038234662 1.094619225 0 0.090961719 791.5642515 1531680.482 0.021735504 0.033941359 5181.620027 -3.714465563 0.056384563 LAEQAERYDEMVESMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LAEQAERYDEMVESMK 16 1 P62258;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 ; 223.97 7.50E-15 625470000 586830 632730 572100 646240 802860 432430 780120 552480 956680 FALSE TRUE 550101.3578 679577.9876 585670.4822 662823.6125 739806.6142 557265.5211 663148.2483 621458.3442 797003.9276 0.690211602 0.852665795 0.734840146 0.831644098 0.92823459 0.69920047 0.832051418 0.779743139 1 19.60422731 -2.155290724 2.176032233 1.441742211 0.797141648 0.440973381 0.072944499 4993386.417 1166272.309 10868140.52 0.016279905 0.006993737 2.155290724 -0.644600563 LAEQAERYDEMVESMKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LAEQAERYDEMVESMKK 17 2 P62258;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 ; 202.5 5.92E-12 546200000 683110 638960 665220 684980 800230 402240 902700 578860 1144170 FALSE TRUE 640355.3645 686269.2632 680999.3325 702557.7465 737383.1638 518360.1582 767348.5153 651131.9452 953200.6354 0.671794941 0.719963078 0.714434409 0.737051278 0.773586521 0.543810127 0.805023084 0.68310062 1 19.86242039 -1.107612606 0.809953223 1.054963239 0.709654426 0.635612496 0.069814881 46.45260083 13.36988156 6.26801463 0.020416922 0.078052603 1.107612606 -0.345308813 LAETYLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LAETYLHR 8 0 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ; 170.66 0.00029388 738110000 350470 499550 353390 418910 551360 293240 382490 433770 429840 FALSE TRUE 328534.7083 536537.2018 361772.5777 429659.9398 508058.4097 377893.6276 325139.1754 487927.1393 358096.9271 0.917446321 1.498301608 1.010264401 1.199842577 1.418773441 1.055283078 0.907964159 1.362556063 1 18.44999061 2.093028879 24.99984061 1.055243289 1.222231045 0.080225289 0.203402545 32.05841295 8598.647808 0.070786747 0.052279476 123.8878965 -2.093028879 0.166987756 LAFPSPFGHLSEGFSHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAFPSPFGHLSEGFSHSR 18 0 Q13501;Q13501-2;E7EMC7;C9JRJ8;E9PFW8 Q13501 SQSTM1 Sequestosome-1 0 208.49 3.62E-16 134900000 65302 262120 196070 221380 245530 195270 211800 202790 202180 FALSE TRUE 61214.86439 281527.6375 200720.873 227060.9856 226247.0642 251641.2791 180042.5563 228108.7779 168434.8519 0.36343348 1.671433402 1.191682545 1.348064151 1.343231889 1.493997687 1.068915098 1.354284908 1 17.36183116 -1.456924707 0.87671408 0.909860162 1.269817282 0.029569802 0.349351173 786.0245579 191.7600957 164.5962179 0.098593772 0.034920085 1.456924707 0.359957119 LAFVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LAFVIR 6 0 P18124;A8MUD9;C9JZ88;C9JIJ5 P18124 RPL7 60S ribosomal protein L7 0 ; 128.66 0.038452 610700000 550290 866010 618760 632090 850260 528060 726230 744330 848270 FALSE TRUE 515848.3312 930130.2815 633437.2794 648310.4995 783484.0094 680502.3497 617338.5535 837261.239 706688.257 0.729951752 1.316181884 0.896346123 0.91739249 1.108669914 0.962945603 0.873565603 1.184767443 1 19.43071441 3.749916119 24.42480829 0.980209841 1.077337493 0 0.169676536 938.0269565 1005092.269 0.039475756 0.071098954 5622.327231 -3.749916119 0.097127652 LAGESESNLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LAGESESNLRK 11 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 122.51 0.00062416 938270000 674880 664490 665920 625110 828750 506290 829600 658560 1121270 FALSE TRUE 632640.4655 713689.531 681715.9369 641151.3809 763663.318 652447.7041 705209.1816 740782.6657 934122.7933 0.677256213 0.764021107 0.729792637 0.686367344 0.817519199 0.698460319 0.754942698 0.793024933 1 19.83325268 0.645282751 1.452387041 0.999984467 0.73390756 0.810878365 0.040555978 0.491388227 1.502856014 0.03408434 0.009961662 4.418580295 -0.645282751 -0.266076907 LAGFLDLTEQEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAGFLDLTEQEFR 13 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 146.16 9.81E-05 18424000 6357.1 19448 13578 17084 16518 11670 12200 13043 10145 FALSE TRUE 5959.220459 20887.95016 13900.07657 17522.40436 15220.74291 15038.93955 10370.72326 14671.44726 8451.733961 0.705088504 2.471439618 1.644641991 2.073231889 1.800901801 1.779391025 1.227052733 1.735909735 1 13.04503164 1.231048693 0.729439786 1.054719619 1.852166153 0.140737444 0.476298961 0.908628454 1.119990404 0.412051028 0.168274334 17.02349365 -1.231048693 0.797446534 LAGGDWFTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LAGGDWFTSR 10 0 P30153;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ;;; 181.53 4.37E-06 1224695000 559047 637349 565230 549701 684330 396845 604800 558945 658670 FALSE TRUE 524057.2462 684538.9831 578637.5225 563807.2583 630585.4823 511407.7093 514115.8547 628730.5136 548733.7218 0.955030145 1.247488455 1.054496014 1.027469674 1.149164808 0.931977914 0.936913177 1.145784355 1 19.06574671 2.241627136 24.99945427 0.989449873 1.101562291 0.138699878 0.09623582 112.8980118 920395.9945 0.032881805 0.02641537 174.4323918 -2.241627136 0.112112418 LAGLEQAILS(ph)PGQNSGNYFAPIPLEDHAENKVDILEMLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAGLEQAILSPGQNSGNYFAPIPLEDHAENKVDILEMLQK 40 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 LAGLEQAILS(0.998)PGQNS(0.002)GNYFAPIPLEDHAENKVDILEMLQK 191.5 9.51E-25 80188000 199190 131340 168220 196310 231370 107970 149930 133610 171480 TRUE FALSE 186723.0535 141064.5503 172210.2578 201347.647 213199.1335 139139.1863 127449.3884 150291.5026 142858.8802 1.307045479 0.987439843 1.205457145 1.409416388 1.492375785 0.973962459 0.892134869 1.052027724 1 17.12423119 2.092563262 13.88088628 0.96031964 1.236033211 0.51601919 0.140706258 0.746052367 108.4771815 0.0582084 0.042989819 123.7551446 -2.092563262 0.275713571 LAGLVEELEADEWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LAGLVEELEADEWR 14 0 A0A087WUN5;Q96DE5 A0A087WUN5 ANAPC16 Anaphase-promoting complex subunit 16 0 ;; 160.36 1.11E-05 27401200 21168.5 21898.4 27287 19961.9 23160.9 18675.4 22928.4 23629.3 26273.7 FALSE TRUE 19843.60137 23519.78032 27934.26053 20474.15615 21341.93634 24066.68481 19490.49928 26579.47012 21888.44974 0.906578657 1.074529289 1.276210095 0.935386306 0.975031882 1.099515274 0.890446766 1.214314876 1 14.41788216 3.186391939 24.99999297 1.008841326 1.11057333 0.043342085 0.125354684 198.0273497 94896.66571 0.034990882 0.041822145 1536.002557 -3.186391939 0.101732004 LAGS(ph)PPGSGQWKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAGSPPGSGQWKPK 14 1 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 1 LAGS(1)PPGSGQWKPK 176.81 1.31E-06 1752600000 6381100 4062100 5402100 5396100 5031200 3861300 6844400 3827300 4603600 TRUE FALSE 5981718.342 4362862.111 5530240.363 5534573.062 4636069.847 4975994.627 5818145.76 4305146.83 3835229.42 1.559676798 1.137575262 1.441958162 1.443087872 1.208811609 1.297443799 1.517026786 1.122526545 1 21.87088145 1.0478081 6.15189307 1.000795673 1.356394045 0.500864881 0.131388567 0.134753866 11.02535337 0.119255688 0.029982379 11.16369852 -1.0478081 0.355598372 LAHEVGWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LAHEVGWK 8 0 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ;;;; 119.41 0.0017002 11486660000 9670570 9522360 10092690 9484460 9953900 7973000 11801170 8983410 10593320 FALSE TRUE 9065306.286 10227405.44 10332093.37 9727847.301 9172160.846 10274675.67 10031694.12 10105008.51 8825226.457 1.027203815 1.15888306 1.170745411 1.102277358 1.03931167 1.164239322 1.136706708 1.145014076 1 23.07320187 -1.758217588 2.48418903 0.968300566 1.126437347 0.340339835 0.050461599 6814408.76 4757797.917 1319847.245 0.012484001 0.017449477 1.758217588 0.158136781 LAHGGQVNLDMEDHRDEDFVKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAHGGQVNLDMEDHRDEDFVKPK 23 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 229.1 2.09E-33 275780000 477860 376440 436080 438740 505900 402140 466010 399580 628420 FALSE TRUE 447951.5956 404312.0093 446424.0235 449998.8112 466168.6547 518231.2898 396136.1267 449468.4426 523532.6423 0.855632599 0.772276601 0.852714783 0.859542987 0.890429015 0.989873884 0.756659843 0.85852993 1 18.99791997 -5 0.193312263 1.64215179 0.821045007 0.337652193 0.063520381 162.4082431 1.596322754 40.48410347 0.165662051 1.00E-05 5 -0.821106783 LAHHLVALYYQSEEQAEEELLDMAVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LAHHLVALYYQSEEQAEEELLDMAVLK 27 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ;; 252.6 5.06E-53 792612000 543378 488741 509715 485383 580200 473646 574305 524819 432979 FALSE TRUE 509368.9409 524927.8922 521805.6805 497838.7495 534633.4324 610379.9112 488193.2968 590343.8074 360712.0077 1.412120833 1.455254832 1.446599141 1.380155744 1.48216145 1.692153014 1.353415707 1.636607029 1 18.46048792 -1.646916437 7.066311174 0.998483624 1.474029199 0.668265451 0.106652631 0.002285356 0.000114193 0.092627236 0.021776106 0.02254673 1.646916437 0.475545574 LAHYIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAHYIDR 7 0 Q03252 Q03252 LMNB2 Lamin-B2 0 79.116 0.033497 300450000 196000 229940 194540 202390 233200 160120 248070 207020 298660 FALSE TRUE 183732.7099 246964.9969 199154.5807 207583.67 214885.4127 206344.0447 210874.2065 232866.9027 248811.7166 0.738440747 0.992577843 0.800422839 0.834300221 0.863646679 0.829318038 0.847525227 0.935916145 1 17.9246949 1.049397112 3.296133264 0.999030601 0.853407628 0.408633969 0.063763755 0.217707672 5.057150066 0.056999579 0.014918272 11.20461948 -1.049397112 -0.145622973 LAHYNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LAHYNK 6 0 Q16778;P33778;P23527;P06899;Q6DRA6;Q6DN03;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;Q99880 Q16778;P58876;Q99880 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST2H2BD;HIST2H2BC;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;HIST1H2BL Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type 1-L 0 ;;;;; 116.12 0.023846 25671490000 12492510 16936380 11085200 9597290 16135960 7310080 12011120 15351320 12126890 FALSE TRUE 11710626.1 18190367.2 11348146.18 9843572.71 14868706.79 9420381.427 10210164.06 17267966.09 10102833.72 1.159142715 1.80052129 1.12326368 0.974337793 1.471736268 0.932449419 1.010623786 1.709220064 1 23.26825667 3.770940803 5.747892428 1.155087436 1.511851995 0.158203439 0.287472794 0.265521144 21.70827455 0.068155102 0.122452221 5901.206371 -3.770940803 0.356764558 LAHYNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 72.234 0.083633 501370000 151150 373100 176880 176140 389320 148790 184520 298750 295660 FALSE TRUE 141689.7913 400724.7122 181075.6771 180660.0506 358744.3776 191743.2576 156852.939 336049.5951 246312.436 0.575244164 1.626895981 0.735146305 0.733458909 1.456460679 0.778455448 0.63680479 1.364322487 1 17.91012994 3.762983806 23.107317 0.925521571 1.177638525 0.010443146 0.368603596 335.388382 216096.8691 0.087687292 0.158068099 5794.07091 -3.762983806 0.252116954 LAIQGPEDS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LAIQGPEDSPSR 12 0 Q15773 Q15773 MLF2 Myeloid leukemia factor 2 1 LAIQGPEDS(0.844)PS(0.156)R;LAIQGPEDS(0.996)PS(0.004)R;LAIQGPEDS(1)PSR;LAIQGPEDS(0.876)PS(0.124)R;LAIQGPEDS(0.993)PS(0.007)R;LAIQGPEDS(0.786)PS(0.214)R 278.45 6.48E-28 7964010000 2760600 2971510 2867990 2632550 2837450 2545350 3012370 2507350 2945360 TRUE FALSE 2587818.974 3191523.692 2936020.077 2700105.69 2614608.123 3280151.225 2560693.084 2820398.167 2453760.388 1.054633935 1.300666401 1.196539031 1.100395011 1.065551525 1.336785466 1.043579111 1.149418737 1 21.22656294 0.255713159 0.32114294 0.961852567 1.204690965 0.180048718 0.100608231 5.665550229 1.026469489 0.408629081 0.106457916 1.801827283 -0.255713159 0.242838398 LAIQGPEDSPS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAIQGPEDSPSR 12 0 Q15773 Q15773 MLF2 Myeloid leukemia factor 2 1 LAIQGPEDS(0.01)PS(0.99)R 250.53 3.32E-17 1421300000 640570 653180 659860 545270 624010 568800 706980 556550 662720 TRUE FALSE 600477.8672 701542.1268 675512.1908 559262.5513 575002.7717 733003.3263 600974.9123 626036.4926 552107.7507 1.087609921 1.270661616 1.223515138 1.012959066 1.041468393 1.32764542 1.088510189 1.133902742 1 19.07459033 -4.999999953 0.142436797 0.425630357 1.219923434 0.1595119 0.101139562 221.9137613 1.923713301 35.99147256 0.584723537 1.00E-05 4.999999953 0.794293077 LAIRES(ph)IESEIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAIRESIESEIRR 13 2 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 1 LAIRES(0.999)IES(0.001)EIRR 65.231 0.030864 138780000 13144 15117 15821 16010 15298 15846 15944 15953 20013 TRUE FALSE 12321.3405 16236.27841 16196.28159 16420.8437 14096.55679 20420.48296 13553.34522 17944.76717 16672.70101 0.739012863 0.973824121 0.971425181 0.984894031 0.84548729 1.224785531 0.812906392 1.076296345 1 14.02520022 4.738670048 6.803216296 0.977608597 0.735032328 0.316568463 0.113534764 0.128560829 41.58107267 0.023323668 0.143523623 54786.05738 -4.738670048 -0.242576269 LALDMEIHAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 171.92 1.40E-05 2044060000 2784808 3915640 3097633 3323538 3986550 2474730 3460694 3418990 4237020 FALSE TRUE 2610511.838 4205558.06 3171110.318 3408825.612 3673462.444 3189144.377 2941795.062 3845858.428 3529833.99 0.739556547 1.191432252 0.898373784 0.965718394 1.040689861 0.903482823 0.8334089 1.089529547 1 21.7511689 2.221805994 24.97416245 0.929609107 0.988293149 0 0.131209086 866.9016422 1292180.765 0.045890814 0.033984837 166.6502593 -2.221805994 0.058684041 LALEAEVSELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LALEAEVSELR 11 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 120.12 0.0011509 13813000 17915 20274 17273 19319 21419 16005 23272 16095 21653 FALSE TRUE 16793.73213 21775.10806 17682.72372 19814.75825 19736.83814 20625.38368 19782.57965 18104.49618 18038.97442 0.930969341 1.207114526 0.980251056 1.098441507 1.094121965 1.143378953 1.09665767 1.003632233 1 14.1388297 -0.632191358 7.329838168 0.999996189 1.079863183 0.054253603 0.080939476 0 0 0.069672588 0.016421987 0.233243013 0.632191358 0.079866993 LALLEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LALLEEAR 8 0 Q5TZA2-2;Q5TZA2;B1AKD8 Q5TZA2-2 CROCC Rootletin 0 ; 94.302 0.024324 76082000 38994 143387 33367.1 35668 168272 29790 36389 129675 123507 FALSE TRUE 36553.43515 154003.5227 34158.58337 36583.30127 155056.5959 38389.8894 30932.80727 145865.2092 102892.8838 0.355257174 1.496736382 0.331981981 0.355547438 1.506971038 0.373105389 0.300631162 1.417641374 1 16.65078368 3.958918636 24.31202666 0.68849036 0.995884584 0.001862454 0.521506123 846.466219 1130570.375 0.124620684 0.225278531 9097.428188 -3.958918636 0.307394224 LALLHEGTGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LALLHEGTGPR 11 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 141.88 3.79E-05 355050000 122540 162650 156110 127370 165480 133810 170130 133600 189070 FALSE TRUE 114870.4401 174692.7752 159813.0029 130638.5298 152483.8683 172438.7748 144620.5859 150280.2541 157512.9956 0.729275954 1.109068967 1.014602016 0.829382549 0.968071668 1.094759033 0.918150184 0.954081621 1 17.26511134 LALLIHNDS(ph)LTSLIYGEQSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LALLIHNDSLTSLIYGEQSEK 21 0 G3V4J5;Q9P1W3 G3V4J5 TMEM63C Calcium permeable stress-gated cation channel 1 1 LALLIHNDS(0.958)LT(0.042)SLIYGEQSEK;LALLIHNDS(0.802)LT(0.169)S(0.029)LIYGEQSEK 172.66 3.42E-12 141191000 373480 310480 351490 336520 329890 315050 445980 319100 350270 TRUE FALSE 350104.5535 333468.2623 359827.5088 345155.6729 303981.7701 405999.8206 379109.4393 358940.3374 291807.6742 1.199778431 1.142767281 1.233098169 1.18281904 1.041719588 1.391326742 1.2991757 1.230057909 1 18.1546583 2.238453156 25 1.264663095 1.168680148 0.049672233 0.110848284 5.210328044 1211519.309 0.036224103 0.028462412 173.1622243 -2.238453156 -0.095982947 LALLNVATQGVHLWDLQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LALLNVATQGVHLWDLQDR 19 0 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y9R3 A0A499FIZ0 WDR26 WD repeat-containing protein 26 0 ; 192.18 8.03E-15 217965000 138931 139097 147205 142129 186666 122288 148241 123182 132839 FALSE TRUE 130235.5567 149395.8866 150696.7721 145776.2708 172006.0053 157590.5604 126013.6383 138561.5439 110667.3127 1.17682045 1.34995495 1.361709871 1.317247769 1.554262059 1.424002775 1.138670807 1.252054834 1 16.75586964 1.215451618 1.287340637 1.029461459 1.361441004 0.490909372 0.111143722 0.336413642 1.102442113 0.10066938 0.031708559 16.4229669 -1.215451618 0.331979544 LALPGHAESYNPPPEYLLS(ph)EEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LALPGHAESYNPPPEYLLSEEER 23 0 Q14137;Q14137-2 Q14137 BOP1 Ribosome biogenesis protein BOP1 1 LALPGHAESYNPPPEYLLS(1)EEER 138.4 2.44E-06 56214000 35285 32718 35705 32935 39785 30037 38063 28403 36672 TRUE FALSE 33076.57484 35140.47476 36551.93946 33780.16786 36660.44658 38708.19429 32355.80651 31949.17707 30551.20629 1.082660191 1.150215623 1.196415589 1.10569015 1.199967237 1.266993975 1.059068051 1.045758284 1 14.89894172 1.578740189 6.887800173 1.033080346 1.167583053 0.592507285 0.052076978 0.087081343 8.424409479 0.027287712 0.012824 37.90881324 -1.578740189 0.134502707 LALPGHAESYNPPPEYLLSEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LALPGHAESYNPPPEYLLSEEER 23 0 Q14137;Q14137-2 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 ;;; 209.71 7.90E-25 1326420000 484293 502540 493946 518181 487088 416917 578221 443774 544261 FALSE TRUE 453981.9656 539748.5845 505662.6324 531478.4017 448834.0733 537274.1698 491522.129 499180.1608 453420.323 1.00123868 1.190393454 1.115218279 1.172153904 0.989885214 1.184936234 1.084031977 1.100921453 1 18.79048953 -0.545496102 0.441924051 0.972536166 1.121048835 0.168666022 0.069665412 13.6766314 2.373994505 0.613538112 0.035693857 0.284776336 0.545496102 0.148512669 LALQLHPDRNPDDPQAQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LALQLHPDRNPDDPQAQEK 19 1 Q9UBS4 Q9UBS4 DNAJB11 DnaJ homolog subfamily B member 11 0 ;;; 160.67 1.86E-11 1126790000 1254464 1075426 1121818 1094015 1236304 813054 1354183 1061340 1290853 FALSE TRUE 1175949.338 1155051.66 1148428.053 1122089.277 1139209.671 1047769.491 1151135.831 1193850.635 1075401.295 1.09349816 1.074065714 1.067906518 1.043414474 1.059334479 0.974305588 1.070424442 1.110144316 1 20.03644368 3.589152441 1.291090358 1.043491587 1.083954058 0.175930747 0.037035594 0.859057764 2.857612052 0.01182383 0.026265186 3882.866339 -3.589152441 0.040462471 LALQTSDWIRVDPWESEQAQWMETVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LALQTSDWIRVDPWESEQAQWMETVK 26 1 D6REC8;D6R975;D6RGH7;D6RHV4;A0A2R8YE08;A0A2R8Y594;A0A2R8YGL3;A0A2R8YEU0;A0A2R8YFG2;Q96T66-2;Q96T66 D6REC8 NMNAT3 Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 0 33.665 0.085966 70196000 24750 23310 33904 34789 30470 43947 42428 21728 12914 FALSE TRUE 23200.94168 25035.89665 34708.21889 35681.74464 28077.00911 56633.78548 36066.31528 24440.78863 10758.56997 2.15650795 2.327065467 3.226099656 3.316588053 2.609734303 5.264062568 3.35233357 2.271750678 1 13.39319871 4.064487557 1.813052073 3.250795965 2.160192678 0.045223169 1.080569742 0.774305445 4.803521581 0.277295528 0.909951244 11600.78979 -4.064487557 -1.090603288 LALS(ph)PLSLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LALSPLSLGK 10 0 P49454 P49454 CENPF Centromere protein F 1 LALS(1)PLSLGK;LALS(0.991)PLS(0.009)LGK;LALS(0.934)PLS(0.066)LGK 170.04 4.67E-06 366669000 1837317 1547972 1746526 1630047 1701791 1337544 1988106 1530689 1777026 TRUE FALSE 1722322.609 1662585.458 1787954.421 1671876.766 1568139.2 1723671.24 1690007.962 1721798.891 1480428.881 1.163394359 1.123043112 1.207727332 1.129319204 1.05924656 1.164305332 1.141566464 1.163040598 1 20.49758375 -1.542965219 2.802347185 0.992395972 1.145449449 0.584649242 0.038113562 10690324.34 11339794.05 616401.972 0.009301632 0.028644074 1.542965219 0.153053477 LALSEEDKEVIIDSTNIIFHCAATVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LALSEEDKEVIIDSTNIIFHCAATVR 26 1 E9PNW8;Q8WVX9 E9PNW8 FAR1 Fatty acyl-CoA reductase 1 0 ; 219.55 1.93E-34 201828000 322334 251015 267284 237314 347276 214138 373049 326663 324065 FALSE TRUE 302159.6903 269600.4118 273624.1027 243403.879 320002.3438 275956.1644 317113.7657 367447.5946 269976.458 1.119207551 0.998607115 1.013510973 0.901574459 1.185297215 1.022148992 1.174597845 1.36103569 1 18.04247408 2.005783995 1.479150242 1.192873696 1.018143185 0.220695183 0.115038424 0.493687535 2.015640836 0.070180973 0.033699909 101.3407222 -2.005783995 -0.174730511 LALVTGGEIASTFDHPELVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LALVTGGEIASTFDHPELVK 20 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 337.95 4.00E-80 522940000 771260 662720 762130 741980 798280 676650 862710 627660 773430 FALSE TRUE 722988.2133 711788.4784 780208.0835 761020.463 735586.3089 871987.8705 733354.6445 706024.7327 644339.5365 1.12206092 1.104679192 1.21086483 1.181086089 1.141612872 1.353304929 1.138149381 1.095733992 1 19.2974616 1.040346073 2.532232325 1.003082753 1.180854832 0.425973731 0.068929161 0.250787872 3.455691716 0.063567025 0.017238401 10.97352287 -1.040346073 0.177772079 LAMDLPGHADEVYAVDWSPDGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAMDLPGHADEVYAVDWSPDGQR 23 0 A0A0A0MRH0;Q9NVX2;K7EN33;Q9NVX2-2 A0A0A0MRH0 NLE1 Notchless protein homolog 1 0 127.05 4.77E-05 78986000 31118 44183 43868 51816 43617 29747 43719 33690 43651 FALSE TRUE 29170.37993 47454.35529 44908.56968 53145.68628 40191.49676 38334.476 37163.74182 37896.27066 36365.3661 0.802147292 1.304932698 1.234926923 1.461436855 1.105213588 1.054147946 1.021954288 1.042097873 1 15.15027748 2.488458785 23.21857393 1.037245003 1.229828033 0.184373068 0.164705268 297.4268823 609115.8041 0.051549511 0.046010422 307.9348093 -2.488458785 0.19258303 LAMQEFMILPVGAANFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LAMQEFMILPVGAANFR 17 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90 P06733 ENO1 Alpha-enolase;Enolase 0 ; 262.07 5.89E-27 894900000 819750 1184140 813660 769550 1244620 576380 953780 1109350 919790 FALSE TRUE 768443.3108 1271814.958 832960.3994 789297.9558 1146872.566 742771.5493 810769.5435 1247854.789 766271.1069 1.002834772 1.659745417 1.087030937 1.030050525 1.496692953 0.96933258 1.058071401 1.62847689 1 19.54749538 3.744576793 22.36250808 1.170572593 1.376765324 0.0444574 0.267687088 259.0717558 331892.7339 0.062680334 0.112507873 5553.628093 -3.744576793 0.206192731 LANVQLLDTDGGFVHSDGAISCHDMFDFLHLTGGGYAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LANVQLLDTDGGFVHSDGAISCHDMFDFLHLTGGGYAK 38 0 P68402;J3KNE3 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 191.02 3.53E-24 63455000 13399 24294 21765 19831 36089 21332 30028 26824 20699 FALSE TRUE 12560.38051 26092.75304 22281.27608 20339.89703 33254.71552 27490.2021 25525.58017 30173.03545 17244.20318 0.728382772 1.513131849 1.292102386 1.179520841 1.928457649 1.594170622 1.480241209 1.749749474 1 14.07382385 2.784819239 24.99471407 1.574984702 1.253061937 0.250526848 0.306466406 618.0419241 333942.7175 0.085133607 0.090297624 609.2832507 -2.784819239 -0.321922766 LAPEYEAAATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LAPEYEAAATR 11 0 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 103.7 0.0062791 233550000 231710 267670 230070 255170 274930 195071 282120 212320 245740 FALSE TRUE 217207.6847 287488.5653 235527.369 261718.0942 253338.1068 251384.831 239818.7251 238828.6194 204724.4065 1.060976014 1.40427109 1.150460627 1.278392248 1.237459232 1.227918231 1.171422251 1.166585966 1 17.64332358 0.693038935 0.674213617 0.997069302 1.246261257 0.376593771 0.088315573 1.088654039 0.967229449 0.08390827 0.030758525 4.932180191 -0.693038935 0.249191955 LAPGGHVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 LAPGGHVGR 9 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;;;;;;;; 172.15 5.64E-05 13787750000 12284870 14740280 14241950 14470040 14872210 12343830 15642150 12818560 14358230 FALSE TRUE 11515981.92 15831665.67 14579775.78 14841365.72 13704206.62 15907293.34 13296754.82 14418985.43 11961748.66 0.962733982 1.323524355 1.218866589 1.24073546 1.145669167 1.329846814 1.111606271 1.205424545 1 23.51192497 0.349474781 0.833614118 0.998300189 1.214425281 0.223703479 0.107356587 3.03945791 2.815947162 0.105902265 0.03162873 2.23601535 -0.349474781 0.216125092 LAPPS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_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 4677070000 1353820 1970230 1895580 1921380 2046100 1902150 1925400 1497850 1615460 TRUE FALSE 1269086.823 2116107.879 1940544.053 1970685.864 1885407.56 2451269.826 1636704.145 1684859.87 1345829.29 0.942977562 1.572344944 1.44189465 1.464291109 1.400926235 1.821382433 1.216130572 1.251912024 1 20.36006399 1.560608331 9.363299685 1.164023922 1.459622954 0.265438749 0.223365135 0.14522565 21.20322498 0.109147575 0.050939266 36.35869872 -1.560608331 0.295599032 LAPS(ph)EDELTCFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 225.09 1.58E-08 0 43501 38686 42423 42171 44709 37829 53865 36184 52528 TRUE FALSE 40778.35006 41550.35169 43429.29359 43253.17926 41197.73549 48749.6182 45788.44331 40701.65205 43760.73746 0.931847872 0.949489294 0.992425999 0.988401516 0.941431472 1.11400358 1.04633619 0.930095204 1 15.41734943 2.286370096 24.99996708 1.031725676 0.964769782 0.273545889 0.048880573 139.1111999 72741.71959 0.016423454 0.013740817 193.36154 -2.286370096 -0.066955894 LAPVPS(ph)PEPQKPAPVS(ph)PESVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LAPVPSPEPQKPAPVSPESVK 21 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 LAPVPS(1)PEPQKPAPVS(0.862)PES(0.138)VK;LAPVPS(1)PEPQKPAPVS(0.979)PES(0.021)VK;LAPVPS(1)PEPQKPAPVS(0.997)PES(0.003)VK 156.52 8.11E-09 1818880000 3714980 1952800 2672540 2402050 2492220 1937610 3313490 2168690 3532010 TRUE FALSE 3482466.033 2097387.344 2735933.911 2463690.67 2296491.094 2496966.553 2816662.935 2439455.72 2942494.713 1.183508 0.712792222 0.929800791 0.837279557 0.780457169 0.848588288 0.957236362 0.829043366 1 21.48860839 -1.011131624 5.311851954 1.000000707 0.873544621 0.069276372 0.126785603 9.38E-07 1.75E-07 0.108481641 0.025569225 0.097469419 1.011131624 -0.126456085 LAPVPS(ph)PEPQKPAPVSPESVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LAPVPSPEPQKPAPVSPESVK 21 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 LAPVPS(1)PEPQKPAPVSPESVK;LAPVPS(1)PEPQKPAPVSPESVK;LAPVPS(1)PEPQKPAPVSPESVK 203.72 3.44E-22 1379320000 2503650 1706270 1931480 1988360 2157360 1374200 2640120 1755970 2766330 TRUE FALSE 2346951.016 1832604.006 1977295.618 2039384.684 1987929.648 1770909.232 2244258.516 1975206.72 2304611.652 1.018371583 0.795189942 0.857973453 0.884914681 0.862587693 0.768419803 0.973812015 0.857067054 1 21.13609223 0.669863955 0.833214322 0.998576823 0.86159273 0.187044456 0.074988848 1.600448908 1.999779095 0.066930604 0.022849467 4.675886442 -0.669863955 -0.136984093 LAPVPSPEPQKPAPVS(ph)PESVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAPVPSPEPQKPAPVSPESVK 21 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 LAPVPSPEPQKPAPVS(0.982)PES(0.018)VK 187.26 1.78E-17 341180000 353950 200130 246630 255510 294360 207110 350900 245380 435690 TRUE FALSE 331796.9013 214947.8334 252480.1801 262066.8192 271242.153 266899.2949 298285.8026 276016.2331 362970.5243 0.914115277 0.592190878 0.695594169 0.722005787 0.747284242 0.735319474 0.821790704 0.760437046 1 18.46949287 0.43334733 0.461120009 1.019976756 0.69857183 0.46317267 0.083622476 1.734606535 0.655449731 0.155484108 0.04574898 2.712359995 -0.43334733 -0.321404926 LAQANGWGVMVSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LAQANGWGVMVSHR 14 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;; 171.76 2.25E-06 14435230000 4297260 8332270 4172010 3359220 8778060 3407020 4622270 7066020 5895580 FALSE TRUE 4028302.167 8949199.941 4270972.047 3445423.272 8088666.577 4390571.366 3929203.525 7948228.151 4911569.611 0.820165952 1.822065175 0.869573759 0.701491284 1.646859806 0.893924288 0.799989379 1.618266416 1 22.22775272 3.830030425 7.439410653 1.049718567 1.384006062 0.053341098 0.398991583 0.49438688 31.4715624 0.094402126 0.171027508 6761.303405 -3.830030425 0.334287495 LAQDDLHIMDSLELPTGDPQYLTELAHYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAQDDLHIMDSLELPTGDPQYLTELAHYR 29 0 K7ES61;X6RAY8;Q9BYD3-2;Q9BYD3;K7EJ73;K7ELQ0 K7ES61 MRPL4 "39S ribosomal protein L4, mitochondrial" 0 187.38 3.45E-18 25325000 20327 22308 22327 18679 25610 22233 19001 20685 24268 FALSE TRUE 19054.76935 23959.70753 22856.60698 19158.33476 23598.69391 28651.30618 16151.97645 23267.56778 20217.51402 0.942488247 1.18509662 1.130534989 0.947610806 1.16724014 1.417152779 0.798910115 1.150861958 1 14.30331799 1.709304822 25 0.975563672 1.132031578 0.167685421 0.155571623 1.284018215 1091.440688 0.066503001 0.036879235 51.20410999 -1.709304822 0.156467906 LAQGHTTVDELAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LAQGHTTVDELAR 13 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;;; 179.39 1.38E-05 3118582000 1280737 1952541 1741493 1926128 1880606 1567423 2041043 1626934 1721761 FALSE TRUE 1200577.957 2097109.167 1782802.036 1975555.705 1732910.791 2019912.575 1735007.55 1830060.291 1434387.966 0.836996674 1.462023676 1.24290086 1.377281288 1.208118606 1.408205188 1.209580386 1.275847493 1 20.45200386 -1.040086363 6.621115647 0.999999879 1.27498041 0.166047985 0.171531261 2.66E-07 3.85E-08 0.143677595 0.033865119 0.09118295 1.040086363 0.274980531 LAQGLTHLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LAQGLTHLGK 10 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 113.69 0.0014551 1047710000 3084600 2862300 3002000 2789600 3227400 2418000 3560900 2786500 3627800 FALSE TRUE 2891540.392 3074227.67 3073208.858 2861185.859 2973933.023 3116037.347 3026976.103 3134400.659 3022296.744 0.956736098 1.017182604 1.016845505 0.946692566 0.983997693 1.031016347 1.001548279 1.037092293 1 21.52721389 2.24894071 24.99704906 1.016310689 0.991506375 0.27575298 0.025181718 368.2353425 886774.8931 0.009066035 0.007511757 177.3947284 -2.24894071 -0.024804314 LAQMCGLHIVVHADELEELINYYQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LAQMCGLHIVVHADELEELINYYQDR 26 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 235.57 3.71E-45 500883000 455520 419995 457245 480469 503160 470546 468455 491567 227202 FALSE TRUE 427009.8163 451091.8668 468091.0673 492798.648 463643.8432 606384.9915 398214.5217 552940.222 189280.5184 2.255962842 2.383192262 2.473001824 2.603536022 2.44950641 3.203631291 2.103832581 2.921273814 1 17.5301664 4.620709528 1.520810013 2.474218836 2.204958167 0 0.583110664 5.39125326 13.92413479 0.134863194 2.036990077 41755.09997 -4.620709528 -0.269260669 LAQMISDHNDADFEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 1520610000 2518340 2215160 2498480 2368740 2365500 1867300 3065800 2305850 2784100 FALSE TRUE 2360721.595 2379172.751 2557745.125 2429525.879 2179723.172 2406359.197 2606111.751 2593740.448 2319415.724 1.01780874 1.025763828 1.102754068 1.047473229 0.939772525 1.037485075 1.123607003 1.118273202 1 21.14533 1.761478287 24.99961642 1.09297955 1.034075807 0.164299159 0.052023114 19.13316351 20887.27894 0.023892083 0.013249889 57.74020043 -1.761478287 -0.058903743 LAQTLSTQLFQMVHTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAQTLSTQLFQMVHTQR 17 0 P53367;P53367-2 P53367 ARFIP1 Arfaptin-1 0 239.58 2.74E-20 57668000 73390 91223 93973 81028 94667 67997 94756 86874 86796 FALSE TRUE 68796.6509 97977.24584 96202.08394 83107.31566 87232.23569 87626.63006 80548.21747 97720.41013 72309.18688 0.951423379 1.354976457 1.330426853 1.149332737 1.206378324 1.211832602 1.113941685 1.351424547 1 16.14189133 3.218629343 24.90134041 1.177623229 1.259733115 0 0.14052819 616.1072649 769738.2865 0.037894289 0.04534899 1654.357418 -3.218629343 0.082109886 LAS(ph)LSSHVTELEEDLDTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LASLSSHVTELEEDLDTAR 19 0 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 1 LAS(0.992)LS(0.004)S(0.005)HVTELEEDLDTAR;LAS(0.669)LS(0.162)S(0.162)HVT(0.008)ELEEDLDTAR;LAS(0.72)LS(0.14)S(0.14)HVTELEEDLDTAR 200.29 4.21E-16 25841700 23699.8 28995.6 33358.4 39602 35460.1 22285.9 35179.2 24254.9 29675.7 TRUE FALSE 22216.47182 31142.46439 34149.677 40618.25437 32675.20679 28719.47755 29904.40555 27283.17766 24722.63396 0.898628838 1.25967421 1.381312244 1.642958207 1.321671746 1.161667385 1.209596259 1.103570829 1 14.59354484 1.410786091 1.204548347 1.017693784 1.311776888 0.214348206 0.183462292 0.641481655 1.806651503 0.167204479 0.056239139 25.75052519 -1.410786091 0.294083104 LAS(ph)PELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LASPELER 8 0 P05412;P17535 P05412;P17535 JUN;JUND Transcription factor AP-1;Transcription factor jun-D 1 LAS(1)PELER;LAS(1)PELER;LAS(1)PELER;LAS(1)PELER;LAS(1)PELER 164.97 0.000343 4473750000 4830810 5650690 5409600 5962540 5674540 2877940 4181410 3409860 5064070 TRUE FALSE 4528458.225 6069072.967 5537918.267 6115548.871 5228884.518 3708754.559 3554446.389 3835588.527 4218844.002 1.073388403 1.43856302 1.312662489 1.449579285 1.239411677 0.879092604 0.842516667 0.909156282 1 22.00841631 2.308785128 4.08575125 0.88627486 1.33776737 0.759068993 0.110617262 0.087094581 2.849162623 0.037040972 0.029791437 203.603448 -2.308785128 0.45149251 LAS(ph)PMKPVPGT(ph)PPSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LASPMKPVPGTPPSSK 16 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 2 LAS(1)PMKPVPGT(0.997)PPS(0.002)S(0.002)K;LAS(1)PMKPVPGT(0.91)PPS(0.042)S(0.048)K;LAS(1)PMKPVPGT(0.98)PPS(0.017)S(0.003)K 116.94 0.00046863 530670000 2000020 937790 1392610 1214550 1258780 1023930 1819680 1196530 1507170 TRUE FALSE 1874842.318 1007224.947 1425643.367 1245717.409 1159920.496 1319521.969 1546835.877 1345919.404 1255613.59 1.493168227 0.802177481 1.135415687 0.99211845 0.923787784 1.050898126 1.231936233 1.07192166 1 20.25996112 1.971479494 23.75569872 1.130646819 1.034149443 0 0.188410653 1201.981048 1001168.06 0.070268436 0.045483771 93.64390042 -1.971479494 -0.096497376 LAS(ph)PMKPVPGTPPSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LASPMKPVPGTPPSSK 16 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 LAS(1)PMKPVPGTPPSSK 87.156 0.0039761 640880000 1110400 609390 803360 672170 708820 563520 938630 666010 733450 TRUE FALSE 1040902.046 654509.8697 822416.0786 689419.0202 653152.1364 726199.076 797891.1453 749162.8146 611032.4567 1.703513512 1.071154016 1.345944998 1.128285433 1.068931984 1.188478726 1.305808123 1.22606059 1 19.22088949 4.746698872 24.90768555 1.189076189 1.703513779 0.701246088 0.109233686 561.735679 1719189.597 0.024918099 0.279522373 55808.31005 -4.746698872 0.51443759 LAS(ph)PSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LASPSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR 38 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LAS(0.965)PS(0.026)GS(0.007)T(0.001)SSGLEVVAPEGTSAPGGGPGTLDDSATICR;LAS(0.935)PS(0.024)GS(0.036)T(0.005)SSGLEVVAPEGTSAPGGGPGTLDDSATICR;LAS(0.387)PS(0.387)GS(0.095)T(0.095)S(0.018)S(0.018)GLEVVAPEGTSAPGGGPGTLDDSATICR 222.52 1.38E-39 1182790000 539816 494762 534305 556856 553130 530685 665556 461467 726912 TRUE FALSE 506029.8802 531394.6933 546978.9669 571145.8677 509689.401 683885.1445 565762.0565 519082.1708 605585.6912 0.83560409 0.877488853 0.90322307 0.943129727 0.841647034 1.129295415 0.934239472 0.857157258 1 19.20797159 3.609006233 0.677636083 0.966237839 0.838475611 0.215163095 0.078156748 1.575569517 1.334302116 0.040628606 0.127882424 4064.491626 -3.609006233 -0.127762228 LAS(ph)YLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LASYLDR 7 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 LAS(1)YLDR;LAS(1)YLDR 130.75 0.0037061 103077000 301450 290340 274010 264750 318560 196770 357160 220610 476430 TRUE FALSE 282582.7826 311837.0757 280509.6466 271543.9332 293541.5826 253574.3047 303607.1737 248153.6441 396910.7551 0.711955468 0.785660433 0.706732289 0.68414355 0.739565705 0.638869825 0.76492554 0.625212698 1 18.59845513 -1.580177609 3.597559102 1.008798215 0.71507507 0.767167086 0.050536821 0.003329974 0.000388596 0.04569015 0.010502672 0.026291925 1.580177609 -0.293723145 LASDDRPS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_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;LAS(0.066)DDRPS(0.934)PPR;LAS(0.001)DDRPS(0.999)PPR;LASDDRPS(1)PPR;LASDDRPS(1)PPR;LAS(0.002)DDRPS(0.998)PPR 121.45 0.0010822 10278730000 4079440 4152680 4263710 4023840 4356240 3533620 4744190 3656370 4422890 TRUE FALSE 3824115.132 4460148.748 4364847.215 4127098.547 4014118.483 4553718.73 4032842.752 4112875.843 3684681.086 1.037841551 1.210457199 1.184592944 1.120069404 1.089407303 1.235851523 1.094488955 1.116209449 1 21.81310833 0.755436717 1.0945166 1.000519792 1.154315195 0.336408183 0.059811321 0.877180949 1.893871082 0.053231761 0.016792614 5.694252445 -0.755436717 0.153795402 LASDLLEWIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LASDLLEWIR 10 0 O43707;O43707-2;K7EJH8;P12814-3;P12814;P12814-2;P12814-4;H9KV75;G3V2W4 O43707;P12814-3 ACTN4;ACTN1 Alpha-actinin-4;Alpha-actinin-1 0 ; 171.46 9.34E-06 512220000 1026020 1027770 845620 836780 957170 652150 883360 941280 893880 FALSE TRUE 961803.2397 1103867.16 865678.5057 858253.1915 881997.7292 840415.1182 750908.3687 1058800.88 744685.6533 1.291556022 1.482326342 1.162475068 1.152503996 1.184389313 1.128550167 1.008356164 1.421809156 1 19.50627204 3.791203234 3.205446389 1.141248488 1.390365505 0.385585475 0.123361785 0.214426395 4.374190625 0.030188836 0.057522539 6183.056765 -3.791203234 0.249117017 LASDLLEWIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LASDLLEWIRR 11 1 O43707;O43707-2;K7EJH8;P12814-3;P12814;P12814-2;P12814-4;H9KV75;G3V2W4 O43707;P12814-3 ACTN4;ACTN1 Alpha-actinin-4;Alpha-actinin-1 0 ; 172.8 2.07E-05 133190000 288812 405450 310650 332800 402730 269950 404180 372450 500830 FALSE TRUE 270735.7725 435469.9399 318018.7647 341340.2114 371101.2103 347880.1827 343576.9612 418951.2024 417238.2375 0.648875746 1.043696145 0.762199473 0.81809427 0.889422821 0.8337687 0.823455116 1.004105484 1 18.67051185 1.233974627 24.90895928 1.002052861 0.845924261 0.331812134 0.099039478 137.1728813 745011.4875 0.077395757 0.021891132 17.13857175 -1.233974627 -0.1561286 LASDS(ph)DAESDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LASDSDAESDSR 12 0 A0A0A0MRB5;Q8WXG6-6;Q8WXG6-8;Q8WXG6-5;Q8WXG6-4;Q8WXG6-7;Q8WXG6-3;Q8WXG6-2;Q8WXG6 A0A0A0MRB5 MADD MAP kinase-activating death domain protein 1 LAS(0.002)DS(0.998)DAESDSR;LASDS(1)DAESDSR 371.27 1.55E-86 1292240000 733190 745330 727430 720340 786950 691590 894480 755810 913930 TRUE FALSE 687300.9467 800515.0087 744684.9831 738825.1439 725146.1214 891240.806 760361.0279 850174.5422 761389.1788 0.902693348 1.051387426 0.978060897 0.97036465 0.952398775 1.170545669 0.998649638 1.1166097 1 19.53827454 2.28435424 24.99997359 1.067094616 0.982882921 0.38504682 0.061979228 141.2514487 77112.38801 0.019494325 0.016310068 192.4660971 -2.28435424 -0.084211695 LASLEELKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LASLEELKR 9 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 116.12 0.0021905 296740000 454120 651250 516370 461380 735060 341250 612950 620280 707570 FALSE TRUE 425697.4398 699469.2276 528618.5402 473219.7919 677331.3527 439763.3353 521043.8378 697723.3234 589471.9959 0.722167368 1.186602981 0.896766163 0.802785875 1.14904755 0.746029223 0.883916185 1.183641171 1 19.16906375 1.248402598 24.98802676 1.091820607 0.931525151 0.172690452 0.15900063 332.5885274 844431.169 0.103338368 0.036711993 17.7175064 -1.248402598 -0.160295457 LASLGDTAS(ph)PLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LASLGDTASPLVK 13 0 Q6P4F7-3;Q6P4F7 Q6P4F7-3 ARHGAP11A Rho GTPase-activating protein 11A 1 LASLGDT(0.002)AS(0.998)PLVK 184.22 1.02E-05 44110000 148290 111520 140740 130490 133810 103290 169340 119150 193950 TRUE FALSE 139008.7936 119777.0568 144078.4193 133838.5943 123301.1024 133108.1462 143949.0391 134026.1398 161578.492 0.860317434 0.74129332 0.891693055 0.828319367 0.763103435 0.823798666 0.890892329 0.829480076 1 17.30187565 -0.567184974 0.369393021 1.055585786 0.811009698 0.568560566 0.047422714 6.598976151 0.861120854 0.485642012 0.03545042 0.270903756 0.567184974 -0.244576089 LASLSSHVTELEEDLDTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LASLSSHVTELEEDLDTAR 19 0 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 0 ;; 277.44 1.66E-39 336902000 58766.2 98045 99191 95250 95362.7 84973.7 104946 88041.1 105954 FALSE TRUE 55088.12844 105304.3538 101543.8574 97694.27626 87873.29822 109504.2278 89210.32157 99033.22514 88269.59291 0.624089526 1.192985606 1.150383207 1.106771574 0.995510405 1.240565682 1.010657449 1.121940431 1 16.42962892 4.744448874 24.9769178 1.11127465 0.624089312 0.768767578 0.082302702 287.2734049 1218526.71 0.018278986 0.165075986 55519.92537 -4.744448874 -0.487185338 LASQEAELQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LASQEAELQLR 11 0 A0A087WYC6;A0A0C4DFR0;Q96DT5 A0A087WYC6 DNAH11 "Dynein heavy chain 11, axonemal" 0 62.633 0.079739 296360000 127350 198830 195240 184760 181800 177450 177300 163860 125740 FALSE TRUE 119379.3908 213551.5801 199871.185 189501.2544 167522.1613 228676.9343 150715.511 184318.2817 104753.1817 1.139625441 2.038616648 1.908020184 1.80902624 1.599208336 2.183007052 1.438767859 1.75954829 1 16.67663454 0.334918396 0.794327359 0.99111056 1.806273796 0.358830129 0.300684934 2.331315283 1.979331776 0.315910093 0.092140032 2.162312189 -0.334918396 0.815163237 LASS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LASSPK 6 0 Q9P2E9;Q9P2E9-3;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 LAS(0.004)S(0.996)PK;LAS(0.002)S(0.998)PK;LAS(0.012)S(0.988)PK;LAS(0.004)S(0.996)PK;LAS(0.026)S(0.974)PK;LAS(0.017)S(0.983)PK 118.06 0.023277 3863490000 23077700 11928500 17112600 15109700 15020900 10560300 17997400 13522500 12021300 TRUE FALSE 21633307.95 12811698.55 17518518.95 15497440.48 13841219.11 13608887.18 15298856.95 15210813.89 10014867.37 2.160119266 1.27926792 1.749251219 1.547443407 1.38206714 1.358868438 1.527614534 1.518823298 1 23.25563998 -2.212289555 0.084626388 4.64E-15 2.109508465 0.456424846 0.224400411 116.6504607 1.311975225 31.60148145 7.549555171 0.006133529 2.212289555 2.109508465 LASTLVHLGEYQAAVDGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LASTLVHLGEYQAAVDGAR 19 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 276.4 1.81E-39 1738520000 1573110 2102900 1924550 2093000 2281000 1861060 2456600 2039290 2117500 FALSE TRUE 1474651.853 2258600.904 1970201.235 2146709.923 2101859.461 2398317.81 2088255.636 2293899.846 1764075.57 0.835934627 1.28033115 1.116846278 1.216903606 1.191479263 1.359532352 1.183767675 1.300341031 1 20.75048093 4.744761099 24.96817413 1.213703113 0.835934456 0.575134365 0.099812125 451.7168665 1818927.867 0.020831577 0.193944455 55559.85447 -4.744761099 -0.377768657 LASYLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 LASYLDR 7 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;; 206.65 0.0004959 24109170000 8359500 16974780 8125090 7723740 17591100 6137210 8056660 14980440 16616010 FALSE TRUE 7836293.817 18231610.37 8317820.972 7921944.245 16209565.97 7908922.898 6848638.627 16850780.91 13842690.59 0.566096148 1.317056844 0.60088181 0.57228356 1.170983767 0.571342894 0.494747649 1.217305321 1 23.72262105 5.010412017 19.08471067 0.833079786 0.144218412 0.079173206 0.303463327 98371862.53 2741970674 0.070956729 1796002077 102426.4255 -5.010412017 -0.688861374 LAT(ph)QSNEITIPVTFESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 LAT(0.779)QS(0.221)NEITIPVTFESR 264.66 1.94E-26 48078000 35066 36194 31691 30958 42015 27898 32036 30768 60590 TRUE FALSE 32871.28165 38873.84142 32442.72549 31752.43469 38715.31138 35951.69971 27232.49921 34609.45253 50477.13757 0.651211286 0.770127691 0.642721181 0.629045865 0.766987061 0.712237291 0.539501654 0.6856461 1 15.62334248 -2.158258772 2.296967842 1.754236331 0.673447885 0.695904633 0.067578519 3384703.609 816199.4147 13281804.3 0.01686605 0.006946103 2.158258772 -1.080788446 LATELYHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LATELYHQK 9 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 105.52 0.0030845 266280000 343330 484010 383100 389960 463240 251280 399600 449620 407450 FALSE TRUE 321841.5882 519846.604 392187.3129 399967.0338 426858.999 323820.4568 339683.6897 505756.0467 339443.9628 0.948143504 1.531465164 1.155381612 1.178300626 1.257524204 0.95397324 1.000706234 1.489954461 1 18.3728139 3.15675557 1.364568961 1.111159167 1.286920007 0.002880207 0.209034762 0.928639877 3.608084534 0.072690156 0.101327563 1434.681738 -3.15675557 0.17576084 LATKSS(ph)PVKVGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LATKSSPVKVGEK 13 2 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 1 LAT(0.004)KS(0.125)S(0.872)PVKVGEK;LAT(0.047)KS(0.167)S(0.786)PVKVGEK 74.786 0.017304 772640000 2495400 1543090 1953130 2088500 2998000 1224140 2857800 1676990 6878200 TRUE FALSE 2339217.368 1657341.989 1999459.166 2142094.446 2762549.173 1577529.346 2429299.421 1886365.893 5730183.985 0.408227271 0.289230153 0.348934549 0.373826469 0.482104795 0.275301692 0.423947892 0.329198137 1 22.45015003 -4.366786595 0.484021454 10 0.355866158 0.908950111 0.062921882 255.1920912 2.466608654 2439.799427 0.028338399 4.30E-05 4.366786595 -9.644133842 LATNTS(ph)APDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.029)S(0.971)APDLK;LATNT(0.015)S(0.985)APDLK;LATNT(0.026)S(0.974)APDLK;LATNT(0.002)S(0.998)APDLK 255.34 1.93E-20 1774070000 4243140 3358680 3561380 2856650 5211700 1949720 4879000 3659760 8725400 TRUE FALSE 3977569.442 3607360.162 3645857.615 2929956.475 4802394.105 2512572.513 4147439.244 4116689.092 7269074.372 0.547190638 0.496261281 0.501557341 0.403071468 0.660661022 0.345652333 0.570559473 0.566329203 1 22.79334024 0.503476426 1.381729887 0.999955159 0.497458215 0.769169069 0.085015997 0.91708862 2.117788185 0.069404151 0.02040962 3.187692538 -0.503476426 -0.502496944 LATQS(ph)NEITIPVTFESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 LAT(0.012)QS(0.988)NEITIPVTFESR;LATQS(1)NEITIPVTFESR;LAT(0.087)QS(0.913)NEITIPVTFESR 247.4 1.00E-20 226769000 177133 174872 184105 180715 233006 143472 171912 194260 328636 TRUE FALSE 166046.5617 187819.7048 188472.0575 185352.4528 214706.6487 184890.0373 146135.3916 218513.7886 273784.5285 0.606486285 0.68601285 0.688395574 0.677001194 0.78421761 0.675312218 0.53376059 0.798123217 1 18.0626814 0.991397535 21.84665076 1.000000003 0.667161572 0.74559635 0.063376243 35.11061586 89167.6948 0.06298584 0.01574646 9.803869797 -0.991397535 -0.332838431 LATQSNEITIPVTFESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;; 340.92 3.66E-72 619499000 668373 756626 737813 717574 909469 620915 793057 753869 1095108 FALSE TRUE 626540.727 812647.3763 755314.2728 735988.1637 838042.9734 800163.0808 674145.4652 847991.2041 912327.4001 0.686749874 0.890740951 0.827898266 0.806714962 0.918577008 0.877056943 0.73892932 0.929481241 1 19.79919212 -5 0.246725639 1.981595414 0.819456354 0.364892162 0.073802321 209.951522 2.086930347 103.7299547 0.103683261 1.00E-05 5 -1.16213906 LAVEEFVHATS(ph)EGEAPGGCEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAVEEFVHATSEGEAPGGCEGR 22 0 Q5C9Z4 Q5C9Z4 NOM1 Nucleolar MIF4G domain-containing protein 1 1 LAVEEFVHAT(0.196)S(0.804)EGEAPGGCEGR 93.176 0.0012631 23814000 19912 23959 21335 22500 22078 17775 27024 15123 17189 TRUE FALSE 18665.74346 25732.94929 21841.07628 23077.38809 20344.08294 22906.35395 22972.00208 17011.13984 14320.04485 1.303469623 1.796988037 1.525210046 1.6115444 1.420671733 1.599600712 1.604185064 1.187925039 1 13.80574839 1.108889678 3.603803093 1.00661767 1.575533507 0.685352238 0.131127857 0.107354026 2.498712817 0.114495956 0.029912972 12.84960206 -1.108889678 0.568915837 LAVNNIAGIEEVNMIKDDGTVIHFNNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LAVNNIAGIEEVNMIKDDGTVIHFNNPK 28 1 Q96K17;E9PL10 Q96K17 BTF3L4 Transcription factor BTF3 homolog 4;Transcription factor BTF3 0 ; 164.66 4.35E-12 236723000 688889 518663 581181 560019 612848 448791 751477 501258 677519 FALSE TRUE 645772.6672 557065.3482 594966.8878 574390.0356 564717.3902 578349.6762 638800.0002 563841.1647 564436.702 1.144101128 0.986940336 1.054089654 1.017634101 1.000497289 1.024649308 1.131747808 0.9989449 1 19.10645228 LAVYIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LAVYIDR 7 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;; 125.08 0.0095001 3600680000 2989780 3604860 3332260 3228680 3939370 2918250 3779450 3241220 4183880 FALSE TRUE 2802655.007 3871767.585 3411302.781 3311533.395 3629987.771 3760701.401 3212756.559 3645893.452 3485563.399 0.804075177 1.110801079 0.978694802 0.950071198 1.041435015 1.07893645 0.921732355 1.045998318 1 21.73296044 4.756256861 24.74994989 1.013380468 0.804074979 0.575230259 0.057182866 2503.859169 3501829.35 0.013423542 0.412823559 57050.15923 -4.756256861 -0.209305489 LAWEQQEPGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAWEQQEPGER 11 0 Q14137;Q14137-2 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 91.549 0.024796 80247000 68173 69578 68411 70168 81589 62166 84841 76319 85905 FALSE TRUE 63906.17362 74729.62752 70033.74123 71968.62967 75181.32905 80112.31502 72119.87968 85847.59515 71566.90053 0.892957123 1.044192594 0.978577257 1.005613337 1.050504193 1.119404563 1.007726744 1.199543288 1 16.12700488 2.706462221 2.81520104 1.076422771 0.988869947 0.338528582 0.066784632 0.342074864 5.419924562 0.020756301 0.020296683 508.7005661 -2.706462221 -0.087552824 LAWVGDVFTATPAEPRPLT(ph)SPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAWVGDVFTATPAEPRPLTSPLR 23 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 LAWVGDVFTATPAEPRPLT(0.576)S(0.424)PLR 97.346 0.0053787 12786000 12514 12776 10419 13772 19578 9974.1 14266 10179 19472 TRUE FALSE 11730.77108 13721.94833 10666.1436 14125.41284 18040.42285 12853.46075 12126.94574 11449.87056 16221.99741 0.723139746 0.84588525 0.657511115 0.870756694 1.112096273 0.792347603 0.74756181 0.70582372 1 13.98566385 4.748906328 22.27597279 0.820603826 0.723139493 0.051147637 0.135897246 1192.738223 2567904.051 0.032261572 0.405603702 56092.69775 -4.748906328 -0.097464333 LAWVGDVFTATPAEPRPLTS(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LAWVGDVFTATPAEPRPLTSPLR 23 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 LAWVGDVFTATPAEPRPLT(0.046)S(0.954)PLR;LAWVGDVFTATPAEPRPLT(0.009)S(0.991)PLR 249.24 3.79E-38 1919380000 989010 1229820 1178510 1407600 1588150 949210 1133140 940820 2053680 TRUE FALSE 927109.6295 1320877.152 1206464.814 1443721.399 1463423.105 1223231.518 963236.1766 1058283.448 1710907.541 0.541881783 0.772033042 0.705160732 0.843833676 0.85534903 0.714960621 0.562997213 0.618550929 1 20.70633037 4.745210227 23.72624846 0.736980021 0.541881597 0.21166497 0.125445847 665.3723273 2373958.531 0.02944491 0.277176964 55617.34167 -4.745210227 -0.195098425 LAYIAHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LAYIAHPK 8 0 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 0 67.757 0.058268 387240000 291990 1554800 167850 122290 1633900 85717 203240 1409500 1436800 FALSE TRUE 273714.8671 1669919.01 171831.4813 125428.1684 1505580.085 110462.1064 172766.0488 1585479.178 1196988.798 0.228669531 1.395099948 0.143553124 0.104786418 1.257806328 0.092283325 0.144333889 1.324556404 1 20.19097822 1.227049869 24.93786618 1.162278509 0.513533595 0.255492077 0.481044911 357.6048609 774720.2672 0.43902943 0.113578587 16.86746698 -1.227049869 -0.648744914 LCAAAASILGKPADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LCAAAASILGKPADR 15 1 P30046;J3KQ18;B5MC82;P30046-2;A6NHG4 P30046 DDT;DDTL D-dopachrome decarboxylase;D-dopachrome decarboxylase-like protein 0 ; 192.32 1.27E-07 1241800000 3604800 3945000 3688200 3708000 4208400 2886100 4975100 3793300 4610300 FALSE TRUE 3379182.003 4237091.905 3775685.846 3803153.558 3877889.24 3719270.218 4229129.942 4266901.855 3840811.146 0.879809466 1.10317632 0.983043868 0.990195407 1.009653714 0.968355401 1.10110333 1.110937688 1 21.8729796 1.721777538 9.652900783 1.078527941 1.00238581 0.257942833 0.062065966 0.140846922 38.76057863 0.027497019 0.014829725 52.69598637 -1.721777538 -0.076142131 LCAGIMITAS(ph)HNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LCAGIMITASHNPK 14 0 Q96G03-2;Q96G03 Q96G03-2;Q96G03 PGM2 Phosphoglucomutase-2 1 LCAGIMITAS(1)HNPK;LCAGIMITAS(1)HNPK;LCAGIMITAS(1)HNPK;LCAGIMIT(0.001)AS(0.999)HNPK;LCAGIMIT(0.001)AS(0.999)HNPK 181.72 1.43E-06 5020480000 7600260 6088530 6094360 5918740 7096020 4586630 8719250 5802110 8541350 TRUE FALSE 7124573.293 6539331.096 6238921.097 6070624.889 6538727.213 5910715.623 7411879.408 6526516.206 7115743.506 1.001240881 0.918994774 0.87677712 0.853125873 0.918909908 0.830653272 1.041617001 0.917193853 1 22.76258308 1.733925918 25 0.985429355 0.898401943 0.359219967 0.054317351 0.528206227 2822.179819 0.023267377 0.012902918 54.19084436 -1.733925918 -0.087027412 LCCTLSSLSSAAETGRDPLDS(ph)EEEATSGAQDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LCCTLSSLSSAAETGRDPLDSEEEATSGAQDER 33 1 O43822-2;O43822 O43822-2 C21orf2 Protein C21orf2 1 LCCTLSSLSSAAET(0.001)GRDPLDS(0.998)EEEATSGAQDER 79.867 0.00081261 50817000 82905 103080 109700 101800 112220 95018 136820 92267 125730 TRUE FALSE 77716.12404 110712.1505 112302.1358 104412.3603 103406.6939 122448.1541 116305.1112 103786.7381 104744.8508 0.741956511 1.056969862 1.072149466 0.996825711 0.987224605 1.169013591 1.110365907 0.99085289 1 16.6765198 4.738551085 8.631703694 1.058753358 0.740202591 0.719895402 0.059641948 0.044988835 56.15021921 0.014238202 0.08355235 54771.05233 -4.738551085 -0.318550767 LCDDGPQLPTS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LCDDGPQLPTSPR 13 0 O60504-2;O60504;H0YAZ3;H0YB51 O60504-2 SORBS3 Vinexin 1 LCDDGPQLPT(0.001)S(0.999)PR;LCDDGPQLPT(0.017)S(0.983)PR;LCDDGPQLPTS(1)PR 212.03 1.80E-08 635770000 1440880 1687320 1581930 1857390 1787820 1202120 1765780 1284360 1073840 TRUE FALSE 1350697.893 1812250.928 1619454.127 1905053.772 1647411.829 1549152.529 1501017.682 1444715.173 894609.1667 1.509818972 2.025745986 1.810236455 2.129481614 1.841487758 1.731652868 1.677847419 1.614912106 1 19.77089802 0.66961496 0.718511866 0.993715852 1.887254404 0.717399126 0.164085262 0.575513213 0.559585702 0.154400158 0.055099754 4.673206374 -0.66961496 0.893538552 LCDEQLSSQSHYDFGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LCDEQLSSQSHYDFGLR 17 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 276.67 9.21E-36 1025970000 523500 813040 745140 798630 832150 649350 844480 773280 736210 FALSE TRUE 490735.0695 873238.3276 762815.0727 819124.1979 766796.2957 836806.8037 717858.0638 869825.7102 613331.7949 0.800113533 1.423761714 1.243723347 1.335531933 1.250214488 1.364362341 1.170423692 1.41819765 1 19.22630822 -0.925356423 4.146075118 0.999991169 1.266105289 0.157273886 0.179356534 16104508.67 42991756.89 2393.593803 0.037475176 0.118752723 0.925356423 0.26611412 LCDFGSASHVADNDITPY(ph)LVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 LCDFGSASHVADNDITPYLVSR 22 0 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 LCDFGSASHVADNDIT(0.01)PY(0.988)LVS(0.002)R;LCDFGSASHVADNDIT(0.002)PY(0.993)LVS(0.004)R;LCDFGSASHVADNDIT(0.001)PY(0.999)LVSR;LCDFGSASHVADNDIT(0.003)PY(0.997)LVSR;LCDFGSASHVADNDITPY(1)LVSR;LCDFGSASHVADNDIT(0.001)PY(0.999)LVSR;LCDFGSASHVADNDIT(0.012)PY(0.987)LVS(0.001)R;LCDFGSASHVADNDIT(0.021)PY(0.979)LVSR;LCDFGSASHVADNDITPY(0.998)LVS(0.002)R;LCDFGSASHVADNDITPY(1)LVSR 324.35 2.68E-67 38199840000 5626257 7348681 7162804 7065697 7508334 6385789 8149563 6772929 7454775 TRUE FALSE 5274119.618 7892784.988 7332709.093 7247014.747 6918659.735 8229262.62 6927611.685 7618544.095 6210524.893 0.849222845 1.27087245 1.180690718 1.166892472 1.114021738 1.325051064 1.115463154 1.226715008 1 22.56628377 4.747607332 24.54883117 1.186473105 0.849222618 0.55948421 0.090324842 614.0280053 1666157.705 0.018727787 0.228427302 55925.17251 -4.747607332 -0.337250487 LCDSYEIRPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LCDSYEIRPGK 11 1 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;; 191.53 1.63E-06 5233280000 7604850 6864060 7215230 6962780 7783300 6171320 9152180 6743820 9460180 FALSE TRUE 7128876.014 7372282.144 7386378.663 7141456.723 7172031.014 7952879.901 7779895.574 7585800.772 7881214.843 0.904540246 0.935424588 0.93721321 0.906136537 0.910015925 1.009093149 0.987144207 0.962516683 1 22.9099866 2.242247681 24.99999999 0.989190661 0.92291097 0.823989338 0.01624444 40.36957521 273726.3632 0.005861011 0.004727911 174.6818093 -2.242247681 -0.066279691 LCEIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LCEIER 6 0 H0Y993;A0A494C028;P35659;P35659-2;H0Y8X0;A0A494C198;D6RDA2;D6R9L5 H0Y993 DEK Protein DEK 0 120.9 0.046264 390620000 819120 755200 802210 753280 793990 694840 1030800 731930 840890 FALSE TRUE 767852.7414 811115.7938 821238.8 772610.4401 731633.2282 895429.0282 876241.1095 823313.0717 700540.0266 1.096086893 1.157843611 1.1722939 1.102878366 1.044384618 1.278198239 1.250808057 1.175254861 1 19.41810796 2.233633694 24.99999557 1.205635892 1.127897869 0.060609797 0.082996054 212.6924438 1079223.923 0.028429235 0.021646798 171.251228 -2.233633694 -0.077738023 LCHDNNEDHQLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LCHDNNEDHQLDR 13 0 Q96PM5-2;Q96PM5;D6RAF6;H0YAI4;Q96PM5-5;Q96PM5-3;Q96PM5-4;Q96PM5-6 Q96PM5-2 RCHY1 RING finger and CHY zinc finger domain-containing protein 1 0 157.86 2.77E-05 243270000 167350 264420 225720 185600 318370 107140 294030 174560 596030 FALSE TRUE 156875.8622 283997.9319 231074.185 190362.8102 293366.5044 138069.5787 249942.9311 196354.2003 496548.7425 0.315932453 0.571943714 0.465360528 0.38337185 0.590811091 0.27805846 0.503360314 0.395437917 1 18.92157582 -1.496354844 3.283840727 1.012151308 0.452067031 0.749760814 0.101743437 53080280.72 63092716.68 5767074.846 0.021486948 0.031889312 1.496354844 -0.560084277 LCLNICVGESGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LCLNICVGESGDR 13 0 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 143 9.45E-05 92095000 57228 60346 59109 60969 67652 53299 58453 47659 61036 FALSE TRUE 53646.20163 64814.08063 60511.09339 62533.56776 62338.88482 68685.55606 49688.5153 53609.33106 50848.69729 1.055016244 1.274645843 1.190022491 1.22979685 1.225968179 1.350783004 0.977183644 1.05429114 1 15.63392319 1.678048423 8.265898067 1.01309655 1.223799592 0.62893474 0.07601029 0.071099211 8.462952012 0.033716528 0.017754537 47.64841112 -1.678048423 0.210703041 LCLTLHNNEGSYLAHTQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LCLTLHNNEGSYLAHTQGK 19 0 Q15428;K7EMT0 Q15428 SF3A2 Splicing factor 3A subunit 2 0 ; 243.29 1.09E-24 461880000 419540 444900 454420 461380 538230 399290 558090 423800 508340 FALSE TRUE 393281.7403 477840.8589 465199.057 473219.7919 495959.5869 514558.5411 474409.5856 476712.3629 423494.77 0.928657845 1.128327651 1.09847651 1.117415906 1.17111148 1.21502927 1.12022537 1.125662928 1 18.69198463 4.738618016 8.746478289 1.129251458 0.927619782 0.548684841 0.054769793 0.05916211 79.94687642 0.011971838 0.070247777 54779.494 -4.738618016 -0.201631676 LCPNNREIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LCPNNREIQR 10 1 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 0 63.283 0.072587 3544300000 504200 1841700 1407100 1374100 1555200 1586800 1126600 1313500 1005200 FALSE TRUE 472643.022 1978061.384 1440477.076 1409361.732 1433060.865 2044883.4 957676.7888 1477493.366 837425.6262 0.564399998 2.362074102 1.720125384 1.682969434 1.71126942 2.441868671 1.14359623 1.764327864 1 19.67560154 -0.968785113 6.319664443 0.999999778 1.731514561 0.126038042 0.538927493 1.52E-06 2.48E-07 0.468777247 0.110491824 0.107452095 0.968785113 0.731514784 LCQSFQTFSICYAETGLLGAHFVCDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LCQSFQTFSICYAETGLLGAHFVCDR 26 0 P31930 P31930 UQCRC1 "Cytochrome b-c1 complex subunit 1, mitochondrial" 0 56.468 0.0869 13786000 6261.8 7416.1 4521.7 4768.2 6344 6225.5 5192.7 6490.5 4250 FALSE TRUE 5869.885116 7965.19576 4628.956859 4890.560085 5845.76783 8022.700787 4414.102842 7300.853212 3540.647544 1.657856379 2.24964379 1.307375784 1.381261485 1.651044832 2.265885177 1.246693659 2.062010726 1 11.78979752 -1.988712617 2.791739726 0.336661988 1.713451178 0.278669559 0.367313784 187242953.7 162954763.3 801338023.3 0.083695213 0.010263308 1.988712617 1.376789191 LCS(ph)SSSSDTSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LCSSSSSDTSSR 12 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 LCS(0.891)S(0.103)S(0.003)S(0.003)SDTSSR;LCS(0.445)S(0.445)S(0.097)S(0.01)S(0.003)DTSSR;LCS(0.453)S(0.453)S(0.083)S(0.008)S(0.004)DTSSR 181.44 7.68E-05 734540000 547120 560310 573760 655250 787760 501510 625790 490540 636260 TRUE FALSE 512876.7358 601795.9354 587369.8581 672064.8243 725892.5073 646287.7957 531958.599 551784.9988 530064.0956 0.967574941 1.135326728 1.108111006 1.267893506 1.369442891 1.219263483 1.003574103 1.040977881 1 19.0158073 1.703034236 6.990796045 1.017655414 1.175631516 0.348786448 0.104748966 0.162283245 17.80404807 0.055209508 0.028605839 50.47010821 -1.703034236 0.157976102 LCSAHGVLVPGGFGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LCSAHGVLVPGGFGVR 16 0 P17812;B4E1E0;P17812-2;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6 P17812 CTPS1 CTP synthase 1;CTP synthase 0 83.729 0.0062474 0 260810 416570 339070 327000 402700 302610 371310 344400 395110 FALSE TRUE 244486.3677 447413.2762 347112.9005 335391.3736 371073.5664 389968.5945 315635.5126 387399.0981 329163.5885 0.742750341 1.359242917 1.054530065 1.01892003 1.127322643 1.184725796 0.958901664 1.176919658 1 18.32844523 -0.498471347 0.392472311 0.974849742 1.104120079 0 0.163229573 36.28504731 5.417239664 1.402055252 0.10466956 0.317342803 0.498471347 0.129270337 LCSS(ph)SSSDTSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LCSSSSSDTSSR 12 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 LCS(0.002)S(0.748)S(0.247)S(0.002)SDTSSR;LCS(0.051)S(0.91)S(0.034)S(0.004)S(0.001)DTSSR 281.54 4.58E-28 1289960000 1296590 1292990 1253040 1543200 1832420 974230 1341050 998030 1394830 TRUE FALSE 1215438.746 1388724.325 1282762.701 1582801.125 1688509.125 1255474.386 1139972.002 1122636.242 1162023.862 1.045967115 1.195091056 1.103903924 1.362107248 1.45307612 1.080420486 0.981022886 0.966104294 1 20.14820826 2.008068609 24.99914388 0.992880757 1.219709397 0.497722362 0.115397284 172.8877999 535659.53 0.045415511 0.033483421 101.8752316 -2.008068609 0.22682864 LCSSS(ph)SSDTSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LCSSSSSDTSSR 12 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 LCS(0.023)S(0.288)S(0.53)S(0.023)S(0.136)DTSSR 196.7 0.00011892 0 189400 184600 160370 207530 267060 138230 197950 150030 203590 TRUE FALSE 177545.7921 198267.9761 164174.0521 212855.5711 246086.1849 178134.757 168269.2352 168761.5758 169609.5138 1.046791469 1.168967304 0.967953085 1.254974243 1.450898475 1.050263945 0.992097857 0.995000646 1 17.37185757 2.014029324 24.99974082 1.001411251 1.159818802 0.307136799 0.126307863 337.6446666 601668.0625 0.049984621 0.03689977 103.2831141 -2.014029324 0.158407551 LCTSYSHSSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LCTSYSHSSTR 11 0 B4DQA8;E9PCW1;K7EJC8;G5E9T8;O95249;F6RU00 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 0 ; 80.014 0.025568 111668000 1472600 1056200 1306560 1288140 1498030 1017500 1730020 1228760 2177380 FALSE TRUE 1380432.595 1134402.147 1337552.22 1321195.853 1380380.767 1311235.732 1470619.562 1382173.391 1813961.212 0.761004472 0.62537288 0.737365392 0.728348459 0.760975901 0.722857647 0.810722717 0.761964138 1 20.79071218 -4.999991002 0.148348338 1.991839204 0.642887841 0.815559618 0.040660505 48.14695942 0.426732144 13.9486427 0.192687315 1.00E-05 4.999991002 -1.348951363 LCWFLDEAAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LCWFLDEAAAR 11 0 M0R1L2;O95336 M0R1L2 PGLS 6-phosphogluconolactonase 0 99.815 0.010454 50448000 228200 171530 179830 157900 211060 156850 230790 150630 217620 FALSE TRUE 213917.3693 184230.2597 184095.6525 161951.9813 194484.199 202130.0488 196185.182 169436.4871 181297.8161 1.179922483 1.016174732 1.015432268 0.893292511 1.072733269 1.114906142 1.082115528 0.934575444 1 17.46800202 4.740320461 24.20109204 1.023823813 1.179922566 0.370030067 0.066488298 120.8578114 1661794.696 0.016021821 0.103584568 54994.65233 -4.740320461 0.156098752 LCYSSDHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LCYSSDHEK 9 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;; 173.39 5.55E-05 5341786000 1955960 4413400 1795100 2010600 5433620 1267310 2210460 4330130 6527540 FALSE TRUE 1833539.955 4740172.728 1837680.62 2062195.4 5006885.403 1633161.824 1879022.044 4870756.262 5438051.404 0.337168559 0.87166751 0.337929983 0.379215871 0.920713144 0.300321145 0.345532233 0.895680438 1 22.37465836 1.119209343 5.772386925 0.991098784 0.512756636 0.412886688 0.223413833 0.201480495 8.704546462 0.20637236 0.052060533 13.15858964 -1.119209343 -0.478342148 LCYVALDFEQEMATAAS(ph)SSSLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LCYVALDFEQEMATAASSSSLEK 23 0 P60709;A0A2R8Y793;A0A2R8YEA7;P63261;I3L4N8;Q6S8J3 P60709;P63261;Q6S8J3 ACTB;ACTG1;POTEE "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;POTE ankyrin domain family member E" 1 LCYVALDFEQEMAT(0.021)AAS(0.491)S(0.398)S(0.075)S(0.015)LEK 59.814 0.041555 33255000 16257 13452 15902 16893 17324 12344 16685 13509 15494 TRUE FALSE 15239.50339 14448.00008 16279.20295 17326.50298 15963.44292 15907.51241 14183.23915 15195.62839 12907.9513 1.180629135 1.119310085 1.261176353 1.342312391 1.236713909 1.232380882 1.098798625 1.177230068 1 13.65597242 0.996443257 0.942007322 1.007777158 1.222288627 0.521873228 0.065796267 0.533130286 1.017919415 0.066203355 0.02255952 9.918437413 -0.996443257 0.214511469 LCYVALDFEQEMATAASS(ph)SSLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LCYVALDFEQEMATAASSSSLEK 23 0 P60709;A0A2R8Y793;A0A2R8YEA7;P63261;I3L4N8;Q6S8J3 P60709;P63261;Q6S8J3 ACTB;ACTG1;POTEE "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;POTE ankyrin domain family member E" 1 LCYVALDFEQEMATAAS(0.004)S(0.827)S(0.165)S(0.004)LEK;LCYVALDFEQEMATAASS(0.898)S(0.099)S(0.003)LEK;LCYVALDFEQEMATAAS(0.016)S(0.899)S(0.084)S(0.002)LEK 195.3 3.20E-19 60711000 150653 126433 125709 128660 139227 98476 152553 103112 124784 TRUE FALSE 141223.8977 135794.2309 128690.8768 131961.6334 128292.673 126904.4226 129679.0939 115985.7602 103956.7443 1.358487116 1.306257058 1.237927157 1.269389825 1.234096681 1.220742564 1.247433197 1.115711741 1 16.66562383 -5 0.095021729 0.129827443 1.455122265 0.900150499 0.031528036 59.20262366 0.387155148 10.17017865 0.62019175 1.00E-05 5 1.325294822 LCYVALDFEQEMATAASSSSLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 238.79 3.40E-37 185174000 319470 260780 306090 301610 330840 271640 315480 253695 302130 FALSE TRUE 299474.943 280088.4225 313350.5993 309349.8232 304857.1609 350058.0583 268176.7028 285369.3792 251702.5512 1.189797011 1.112775462 1.244924209 1.229029351 1.211180258 1.390760867 1.065450873 1.133756404 1 17.94136031 1.607638289 25 1.074685637 1.218037584 0.50276663 0.07583296 0.040450588 2285.209057 0.036935805 0.018763157 40.51709402 -1.607638289 0.143351947 LDAENAIVHMGGQWLGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDAENAIVHMGGQWLGGR 18 0 E7ETJ9;Q01085;Q01085-2 E7ETJ9 TIAL1 Nucleolysin TIAR 0 ; 138.08 2.77E-06 312610000 556310 613180 550810 500160 685000 490400 610440 594700 455060 FALSE TRUE 521491.5501 658580.4852 563875.4733 512994.9524 631202.8632 631970.519 518910.189 668949.6041 379107.5462 1.375576813 1.737186431 1.48737602 1.353164709 1.664970454 1.666995356 1.368767766 1.764537823 1 18.53224765 -1.252479177 4.802695711 0.999858166 1.551943363 0.559067904 0.154151382 0.000213569 3.32E-05 0.136162492 0.032085643 0.055914034 1.252479177 0.552085197 LDAFIEALHQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDAFIEALHQEK 12 0 O60313-10;O60313-9;O60313-2;E5KLJ9;O60313-13;O60313;O60313-11;A0A2R8YDM2;A0A2R8Y3X5;A0A2R8YFD1 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 ; 213.06 1.31E-08 219362000 996480 807770 798870 750190 1140490 588320 934690 880090 1091410 FALSE TRUE 934112.0956 867578.1313 817819.5737 769441.1455 1050920.516 758158.4334 794541.9117 989971.1738 909246.6202 1.027347339 0.954172512 0.899447472 0.846240314 1.155814597 0.833831456 0.873846429 1.088781802 1 19.79431213 1.233467317 24.99986874 1.044390911 0.934266626 0.159503183 0.097058817 224.3023118 1100900.087 0.078044138 0.021849086 17.11856345 -1.233467317 -0.110124285 LDALVAEEHLTVDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LDALVAEEHLTVDAR 15 0 A6NFX8;Q9UKK9 A6NFX8 NUDT5 ADP-sugar pyrophosphatase 0 ;;; 247.64 2.73E-18 527206000 661235 956114 758990 729335 1119882 564671 1064790 943879 1090030 FALSE TRUE 619849.4817 1026905.675 776993.6012 748050.9709 1031930.985 727682.351 905134.6245 1061724.371 908096.9511 0.682580732 1.130832643 0.855628466 0.823756725 1.136366534 0.80132672 0.996737874 1.16917513 1 19.79248681 1.464459116 7.969646303 1.084770103 0.92932699 0.196087123 0.145919889 0.209743921 41.03263851 0.074877484 0.033205132 29.1379582 -1.464459116 -0.155443113 LDAMFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LDAMFR 6 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;K7EIV0;Q96L46;K7EMQ1 A0A0C4DGQ5 CAPNS1;CAPNS2 Calpain small subunit 1;Calpain small subunit 2 0 ;; 166.66 0.016052 904552000 931928 1387750 974131 891646 1391850 838358 1120202 1229340 1439040 FALSE TRUE 873600.29 1490500.454 997237.8473 914527.1459 1282539.715 1080378.345 952238.1095 1382825.805 1198854.927 0.728695583 1.243270074 0.83182529 0.762833872 1.069803932 0.901175213 0.794289691 1.153455496 1 20.19322566 3.751953611 24.52752804 0.911933662 1.027181064 0 0.173013645 827.5182447 817353.6401 0.040441917 0.072863315 5648.766339 -3.751953611 0.115247402 LDAQSLNLSQEDFDRYMSGQT(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDAQSLNLSQEDFDRYMSGQTSPR 24 1 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3;Q3HKR1;A0A0A0MSJ3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 LDAQSLNLSQEDFDRYMS(0.028)GQT(0.486)S(0.486)PR;LDAQSLNLSQEDFDRYMS(0.002)GQT(0.563)S(0.435)PR 114.31 0.0020516 341880000 121936 143703 135663 152281 181166 101848 162178 121278 206035 TRUE FALSE 114304.2434 154342.9196 138880.9904 156188.7883 166937.9531 131249.8642 137860.9145 136419.8253 171646.4275 0.665928473 0.899190982 0.809110871 0.909944883 0.97256876 0.764652467 0.80316798 0.794772296 1 17.3890803 4.746628126 24.48411613 0.856569165 0.665928347 0.387354062 0.078927118 841.1468357 2552720.481 0.01791098 0.197031841 55799.21975 -4.746628126 -0.190640818 LDAQSLNLSQEDFDRYMSGQTS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LDAQSLNLSQEDFDRYMSGQTSPR 24 1 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3;Q3HKR1;A0A0A0MSJ3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 LDAQSLNLSQEDFDRYMSGQT(0.294)S(0.706)PR;LDAQSLNLSQEDFDRYMS(0.001)GQT(0.216)S(0.784)PR;LDAQSLNLSQEDFDRYMS(0.002)GQT(0.289)S(0.709)PR;LDAQSLNLSQEDFDRYMS(0.004)GQT(0.27)S(0.726)PR;LDAQSLNLSQEDFDRYMS(0.003)GQT(0.379)S(0.618)PR;LDAQSLNLSQEDFDRY(0.001)MS(0.248)GQT(0.226)S(0.526)PR 135.32 1.74E-05 2026830000 741838 977551 955195 973145 1121370 748812 1047167 783003 1421999 TRUE FALSE 695407.6838 1049929.893 977852.6765 998117.5482 1033302.124 964981.8685 890154.0298 880762.6482 1184658.18 0.587011254 0.886272438 0.825430232 0.842536324 0.872236516 0.814565656 0.751401581 0.743474078 1 20.17603942 4.746560189 24.73249734 0.831520922 0.587011114 0.544254296 0.072769015 678.6351843 2098098.577 0.016365206 0.178689893 55790.49166 -4.746560189 -0.244509808 LDDGHLNNSLSS(ph)PVQADVYFPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDDGHLNNSLSSPVQADVYFPR 22 0 Q3ZCW2;F8WF17;B9A055;U3KQ88 Q3ZCW2 LGALSL Galectin-related protein;Galectin 1 LDDGHLNNS(0.004)LS(0.214)S(0.782)PVQADVYFPR;LDDGHLNNS(0.05)LS(0.362)S(0.588)PVQADVYFPR 137.12 2.24E-06 376021000 45289 44382 42443 41864 48267 39116 46105 40397 51579 TRUE FALSE 42454.44233 47668.08946 43449.768 42938.30112 44476.30452 50408.1542 39191.98327 45440.65437 42970.13169 0.987998888 1.109330774 1.011162086 0.99925924 1.035051622 1.173097503 0.91207501 1.057493952 1 15.39104658 1.707439805 25 0.986307488 1.051686359 0.172764851 0.064595019 1.213123792 968.8485023 0.027445242 0.015219747 50.98469255 -1.707439805 0.065378871 LDDHALTGASDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDDHALTGASDSR 13 0 Q12788;J3KNP2 Q12788 TBL3 Transducin beta-like protein 3 0 199.96 1.14E-07 191370000 195760 256370 251630 253830 277570 205350 285850 237720 268830 FALSE TRUE 183507.731 275351.9016 257598.7824 260343.7075 255770.7719 264631.2114 242989.4462 267399.8653 223960.5363 0.819375297 1.229466164 1.150197203 1.162453492 1.142035004 1.181597507 1.08496546 1.193959747 1 17.77288501 -0.421963971 6.909615076 1.000000821 1.133901059 0.088967435 0.114252547 0 0 0.097263462 0.022925218 0.378473982 0.421963971 0.133900238 LDDIEEFENIRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDDIEEFENIRK 12 1 Q8NHZ8 Q8NHZ8 CDC26 Anaphase-promoting complex subunit CDC26 0 120.14 0.00070896 93728000 131450 109090 110320 117220 125790 92324 143090 107140 145720 FALSE TRUE 123222.7791 117167.1371 112936.8425 120228.0637 115910.9608 118976.44 121634.9829 120516.6648 121398.3906 1.015028111 0.96514572 0.930299339 0.990359617 0.954798167 0.980049566 1.001948891 0.992736924 1 16.88938977 1.957886691 3.969466511 0.997624411 0.965612717 0.213265355 0.022306722 0.289815224 9.291463117 0.010351135 0.006156203 90.75837079 -1.957886691 -0.032011694 LDDIHPFYADLMNILYDKDHYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDDIHPFYADLMNILYDKDHYK 22 1 Q9BZE4-2;Q9BZE4;Q5T3R7 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 ; 236.93 1.07E-30 436770000 980024 655379 773740 702662 779616 510265 972452 660558 774751 FALSE TRUE 918686.0472 703903.9431 792093.4782 720693.4965 718388.1042 657570.222 826641.8504 743030.1204 645440.053 1.42334837 1.090579892 1.227214634 1.11659246 1.113020645 1.018793642 1.280741483 1.151199274 1 19.29992358 LDDLVNWAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDDLVNWAR 9 0 F5H5N1;A0A087WXF6;A0A087WTI3;F5GXJ1;O75251-2;O75251 F5H5N1 NDUFS7 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial" 0 ; 157.91 0.00015683 240470000 446160 478420 427600 418760 583480 393770 442490 473160 680720 FALSE TRUE 418235.642 513842.7146 437742.8739 429506.0906 537655.8344 507445.0067 376142.7324 532235.0676 567103.4344 0.737494462 0.906082883 0.771892476 0.75736817 0.94807367 0.894801505 0.663270066 0.938514979 1 19.11325237 1.012277622 24.63078011 1.000000079 0.815153212 0.378799357 0.086016715 151.7917628 304515.9771 0.080080461 0.020020115 10.28673665 -1.012277622 -0.184846866 LDDLVRPYVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDDLVRPYVHK 11 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 132.56 0.00010807 382350000 845310 762010 818950 845600 792910 676410 1016000 703630 613300 FALSE TRUE 792403.556 818430.0133 838375.8807 867299.5276 730638.047 871678.5864 863660.2321 791479.7544 510936.2679 1.550885317 1.601824072 1.64086195 1.697471059 1.429998403 1.706041714 1.690348261 1.549077261 1 18.96278382 0.897178446 8.534422612 1.000000111 1.621864053 0.847004681 0.081721935 2.206718233 183.3015189 0.073916931 0.018502773 7.891843167 -0.897178446 0.621863942 LDDPSCPRPECYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LDDPSCPRPECYR 13 1 P41091;H7BZU1 P41091 EIF2S3 Eukaryotic translation initiation factor 2 subunit 3 0 ;;;; 128.31 0.00015209 5062180000 6410040 6411310 6283800 5879720 6557050 5336860 7017960 5915090 5686930 FALSE TRUE 6008847.039 6886010.063 6432854.703 6030603.57 6042085.743 6877524.845 5965682.05 6653602.007 4737744.644 1.268292719 1.453436304 1.357788397 1.27288489 1.275308442 1.451645321 1.259181847 1.404381727 1 22.17576901 -3.032864976 0.437705271 1.28E-16 1.354585773 0.663783627 0.075992879 95.5264391 3.140991783 89.03564974 0.039687211 0.000927118 3.032864976 1.354585773 LDDSFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDDSFVR 7 0 Q99615;A0A6I8PUD4;A0A6I8PU73;A0A6I8PS32;A0A6I8PIK4;A0A6I8PR89;A0A6I8PLE7;A0A6I8PU89;A0A6I8PRZ0;K7EIH8;K7EK03;Q99615-2;K7ESP1;K7ER44;K7EPP7;A0A6I8PUC2;K7ELJ8;K7EJV7;K7EN19;K7EJL5;K7EJE9 Q99615 DNAJC7 DnaJ homolog subfamily C member 7 0 111.65 0.015195 39691000 80530 107670 96719 95364 118200 86229 100670 95264 105620 FALSE TRUE 75489.77105 115641.9988 99013.22035 97811.20169 108917.0488 111121.9125 85575.46807 107157.9201 87991.33967 0.857922738 1.314242961 1.125260971 1.111600324 1.237815553 1.262873289 0.972544212 1.217823487 1 16.42507392 0.488543069 0.69539867 1.000526948 1.15757681 0.059369126 0.139603945 4.062966824 3.206216702 0.146696184 0.047705903 3.079945766 -0.488543069 0.157049862 LDDTVHVVIATPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDDTVHVVIATPGR 14 0 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ; 173.59 2.67E-06 413280000 721450 816220 768470 799790 860970 692040 869480 704990 824140 FALSE TRUE 676295.7323 876653.7781 786698.4713 820313.9654 793352.8892 891820.7137 739109.5459 793009.5534 686585.7099 0.985012829 1.276830795 1.145812475 1.19477285 1.155504517 1.29892117 1.076500043 1.155004455 1 19.3890803 0.77055703 1.111636016 1.002054466 1.179861217 0.233431157 0.089972927 1.030597264 2.320309412 0.075573968 0.023754062 5.895993965 -0.77055703 0.177806752 LDEEEEDNEGGEWER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDEEEEDNEGGEWER 15 0 Q99613-2;Q99613 Q99613-2 EIF3C Eukaryotic translation initiation factor 3 subunit C 0 328.53 1.96E-68 125240000 118500 121400 115810 109440 116760 99232 155740 106770 124990 FALSE TRUE 111083.2965 130388.5823 118557.0679 112248.4157 107590.1406 127878.6675 132388.2328 120100.4695 104128.3615 1.066791937 1.252190857 1.138566536 1.077981196 1.033245304 1.228086812 1.271394564 1.153388642 1 16.66800354 LDEIYVAGLVAHSDLDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LDEIYVAGLVAHSDLDER 18 0 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;;;; 264.22 5.99E-31 763187000 1074106 996276 1115026 1009354 1002495 989788 1210931 979080 892467 FALSE TRUE 1006879.623 1070041.312 1141474.943 1035255.732 923763.0866 1275523.728 1029363.138 1101320.293 743508.4921 1.354227468 1.439178332 1.535254749 1.392392613 1.242437842 1.715546952 1.384467224 1.481247766 1 19.50398969 -1.166904831 4.707948051 0.999956174 1.450746584 0.556279546 0.124200386 6.33E-05 1.12E-05 0.108360216 0.025537702 0.068091855 1.166904831 0.45079041 LDELEELLTNNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LDELEELLTNNR 12 0 O75306;O75306-2 O75306 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" 0 ;;; 160.18 0.00014575 94953000 110344 105310 98390 93113 138020 99495 96143 109186 137926 FALSE TRUE 103437.766 113107.262 100723.8573 95502.43722 127180.4659 128217.5913 81727.2497 122818.1124 114905.2596 0.900200447 0.984352347 0.876581783 0.831140694 1.106828934 1.115854851 0.711257692 1.068864149 1 16.81008531 LDELYGTWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LDELYGTWR 9 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;;;;; 133.05 0.00066955 951900000 889209 1132248 913904 898118 1132044 698804 833211 1026514 824967 FALSE TRUE 833554.996 1216080.82 935582.2345 921165.2284 1043137.831 900537.3707 708278.7457 1154676.533 687274.6782 1.212841128 1.769424742 1.361293038 1.340315972 1.517788831 1.310301979 1.030561387 1.680080133 1 19.39052728 -0.368893752 0.13956823 0.626276466 1.680647256 0.196790483 0.223074508 27.84448677 1.086992278 6.285680801 1.993106092 0.4276675 0.368893752 1.05437079 LDETDDPDDYGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LDETDDPDDYGDR 13 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;; 196.76 3.24E-07 1279510000 2337940 2239620 2420390 2315570 2178630 2252930 2815610 2263160 1621600 FALSE TRUE 2191612.509 2405443.795 2477802.794 2374991.446 2007529.188 2903314.318 2393435.419 2545720.508 1350944.484 1.622281696 1.780564504 1.834126289 1.758022979 1.486019012 2.14909965 1.77167563 1.884400534 1 20.36553696 -0.829573403 5.926595953 0.999999908 1.794431217 0.676429613 0.17070087 1.86E-07 3.71E-08 0.149625994 0.035267181 0.1480562 0.829573403 0.794431309 LDETDDPDDYGDRESGCSFVLALMQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDETDDPDDYGDRESGCSFVLALMQK 26 1 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 160.69 1.64E-11 260170000 671340 641910 638090 679900 731180 484910 799010 597410 814080 FALSE TRUE 629322.0278 689437.6843 653225.7961 697347.3851 673756.0722 624895.6451 679205.8681 671997.9536 678204.7888 0.927923303 1.01656269 0.963168953 1.028225392 0.993440452 0.921396686 1.001476072 0.99084814 1 19.37136145 -0.555884574 0.003523765 1.529636613 0.451536374 0.039501826 0.034561636 218754.7322 178.9628153 27845.14712 26911.27584 0.278045216 0.555884574 -1.078100238 LDFIESDS(ph)PCSSEALSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LDFIESDSPCSSEALSK 17 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-4 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 LDFIESDS(1)PCSSEALSK;LDFIESDS(0.986)PCS(0.012)S(0.002)EALSK;LDFIES(0.002)DS(0.919)PCS(0.073)S(0.006)EALSK 362.73 1.05E-88 215899000 407465 303246 341959 356223 398664 296673 463245 340700 478960 TRUE FALSE 381962.493 325698.6494 350070.429 365364.2853 367354.5376 382317.679 393785.7128 383237.145 399018.4818 0.957255141 0.816249533 0.877328858 0.91565755 0.92064542 0.95814529 0.986885898 0.960449609 1 18.60609605 2.547070319 1.041874723 0.984660026 0.867659901 0.548315367 0.036501619 0.318558491 0.705266333 0.02060954 0.015710075 352.4279299 -2.547070319 -0.117000125 LDFIESDSPCS(ph)SEALSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDFIESDSPCSSEALSK 17 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-4 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 LDFIESDS(0.403)PCS(0.517)S(0.08)EALSK 113.59 0.00042478 31450000 68680 49679 57644 55755 61608 46053 72609 56098 74328 TRUE FALSE 64381.4414 53357.28485 59011.3429 57185.76769 56769.55619 59347.75349 61721.95452 63101.95879 61922.17662 1.039715412 0.861682967 0.952992064 0.923510297 0.916788771 0.958424861 0.996766553 1.01905266 1 15.91816856 1.82528875 2.370022256 1.009067627 0.929746768 0.305790229 0.044451744 0.286241297 3.035251747 0.024597808 0.011597444 66.87884273 -1.82528875 -0.079320859 LDFLPEMMVDHCSLNSS(ph)PVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LDFLPEMMVDHCSLNSSPVSK 21 0 Q92879-4;G5EA30;F5H0D8;E9PKU1;F5H3J7 Q92879-4 CELF1 CUGBP Elav-like family member 1 1 LDFLPEMMVDHCSLNS(0.167)S(0.833)PVSK;LDFLPEMMVDHCSLNS(0.002)S(0.998)PVSK;LDFLPEMMVDHCSLNS(0.017)S(0.982)PVSK 260.14 8.97E-37 345190000 420344 601322 705227 714178 867430 606255 900930 711248 828913 TRUE FALSE 394035.4194 645844.5066 721955.3175 732505.0166 799305.5468 781270.9768 765843.9103 800048.8784 690562.0653 0.570601021 0.935244693 1.045460435 1.06073741 1.157470975 1.13135519 1.109015321 1.15854739 1 19.39741156 5.074616528 0.948766468 1.108098815 7.73E-14 0.908693735 0.052361783 0.912305024 0.422604891 0.015072068 1.204256053 118745.3271 -5.074616528 -1.108098815 LDFLRPYTVPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDFLRPYTVPNK 12 1 Q99436 Q99436 PSMB7 Proteasome subunit beta type-7 0 117.03 0.00070933 273360000 495980 512140 459990 442030 553810 377150 594600 498550 558450 FALSE TRUE 464937.4971 550059.3785 470901.18 453373.2382 510315.9966 486027.0825 505445.25 560795.0649 465241.0873 0.999347456 1.182310405 1.012165935 0.974490969 1.096885057 1.044677901 1.086415761 1.205385939 1 18.82761899 1.489370668 7.240394384 1.116548592 1.061549184 0.060791123 0.075653998 0.295569908 39.73083797 0.039893733 0.018046638 30.85820557 -1.489370668 -0.054999408 LDFLRPYTVPNKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDFLRPYTVPNKK 13 2 Q99436 Q99436 PSMB7 Proteasome subunit beta type-7 0 130.07 8.23E-05 645870000 1292900 1030800 1123300 1019000 1288200 856340 1528700 1188400 1484800 FALSE TRUE 1211979.697 1107121.505 1149945.206 1045149.265 1187029.968 1103551.456 1299485.627 1336774.356 1236977.288 0.979791391 0.895021692 0.929641326 0.844921952 0.959621474 0.892135585 1.050533134 1.080678173 1 20.23838758 1.699765511 5.936052646 1.049531285 0.914745825 0.668586051 0.041926871 0.071459933 5.813002918 0.019166639 0.009685165 50.09167004 -1.699765511 -0.13478546 LDFNLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDFNLIR 7 0 P31939-2;P31939;C9JLK0 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 103.75 0.043522 0 56262 103320 59625 61362 117240 41819 52191 89406 84334 FALSE TRUE 52740.66185 110969.9203 61039.33316 62936.65281 108032.4433 53891.46643 44365.44407 100568.5359 70258.11058 0.750670085 1.57946064 0.868787001 0.895791992 1.537650848 0.767049754 0.631463666 1.431415321 1 16.10037716 LDGEEQRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDGEEQRPR 9 1 P51687 P51687 SUOX "Sulfite oxidase, mitochondrial" 0 64.04 0.083761 0 206860 185130 171860 200020 189560 142800 194150 145070 162310 FALSE TRUE 193913.0019 198837.2178 175936.6004 205152.8518 174672.7222 184024.0418 165039.0099 163182.3088 135219.4124 1.434061858 1.470478345 1.301119397 1.517184908 1.291772528 1.360929163 1.220527489 1.206796464 1 17.04494276 1.169233193 0.521598865 0.990599195 1.431973893 0.813514532 0.064665974 0.339257276 0.240354747 0.064578585 0.033027178 14.7649912 -1.169233193 0.441374699 LDGLVET(ph)PTGYIESLPR ddPTM_SK-BR-3_Pertuzumab_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(0.969)PT(0.029)GYIES(0.001)LPR;LDGLVET(0.985)PT(0.015)GYIESLPR;LDGLVET(0.91)PT(0.09)GYIESLPR;LDGLVET(0.977)PT(0.023)GYIESLPR;LDGLVET(0.907)PT(0.093)GYIESLPR;LDGLVET(0.909)PT(0.091)GYIESLPR;LDGLVET(0.941)PT(0.059)GYIESLPR 333.65 4.77E-71 1387268000 729520 722498 740853 703769 779198 604819 885834 683507 867685 TRUE FALSE 683860.6454 775992.5037 758426.383 721828.904 718002.9322 779420.4269 753011.4154 768844.3535 722862.768 0.946044914 1.073499062 1.049198294 0.998569764 0.993276959 1.078241212 1.04170729 1.063610394 1 19.46336226 2.23433015 24.99999365 1.049576101 1.024928584 0.103303167 0.04000794 296.0221916 1749335.505 0.014465196 0.011070852 171.526075 -2.23433015 -0.024647517 LDGLVETPTGYIES(ph)LPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDGLVETPTGYIESLPR 17 0 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W118;F8VUX1;H0YHC3;F8W020;P55209-3;F8VXI6;F8VRJ2 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 1 LDGLVETPT(0.001)GYIES(0.999)LPR;LDGLVETPTGYIES(1)LPR 218.12 4.98E-15 55817000 131850 142773 129633 135226 153023 118298 164780 126514 189924 TRUE FALSE 123597.7439 153344.0615 132707.956 138696.1281 141005.1908 152448.7122 140072.7687 142309.5514 158224.4574 0.781154481 0.969155237 0.838732255 0.876578314 0.891171903 0.963496508 0.885278869 0.899415638 1 17.2716131 2.458146128 23.93663155 0.924636706 0.879413671 0.234107426 0.056515766 295.6319169 372928.2092 0.01815933 0.015195836 287.1746683 -2.458146128 -0.045223035 LDGLVETPTGYIESLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDGLVETPTGYIESLPR 17 0 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W118;F8VUX1;H0YHC3;F8W020;P55209-3;F8VXI6;F8VRJ2 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 ; 237.32 9.70E-19 36290000 79200 79181 82119 79934 82767 65275 77960 68857 85800 FALSE TRUE 74243.01338 85043.64363 84066.90146 81985.24177 76266.81369 84118.83285 66270.62175 77453.94802 71479.42571 1.038662701 1.189763947 1.176099285 1.146976783 1.066975748 1.176825807 0.927128626 1.083583804 1 16.12524042 1.748528703 24.99999961 1.0011184 1.142209964 0.495486826 0.060817905 1.808539187 4545.197218 0.02622764 0.014544625 56.04394563 -1.748528703 0.141091565 LDGQTPHDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDGQTPHDER 10 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 ; 140.78 3.87E-05 2093650000 1342900 1356380 1371240 1367090 1634640 1188710 1523270 1385830 1658110 FALSE TRUE 1258850.286 1456807.787 1403766.46 1402171.844 1506261.968 1531871.28 1294869.805 1558853.926 1381360.729 0.911311766 1.054617925 1.016220044 1.015065663 1.090418988 1.10895818 0.937387156 1.128491561 1 20.39765868 4.74293807 24.50834624 1.038934247 0.911311699 0.349355475 0.056503543 392.6930887 2198490.673 0.012433852 0.098447163 55327.12075 -4.74293807 -0.127622548 LDHFNFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDHFNFER 8 0 Q9UHL4;R4GNE8;R4GMV4 Q9UHL4 DPP7 Dipeptidyl peptidase 2 0 ; 138.4 0.00070713 298360000 200226 257130 194700 219784 284390 156984 230947 210655 231555 FALSE TRUE 187694.2121 276168.1727 199318.3759 225424.0295 262055.1566 202302.7324 196318.6414 236955.7405 192906.9746 0.972977843 1.431613208 1.033235716 1.168563397 1.358453509 1.048706159 1.017685554 1.228342008 1 17.55754578 2.142806159 20.45938378 1.068038631 1.202818132 0.138663889 0.146275831 7.248476614 1537.372891 0.051116952 0.0377524 138.9332384 -2.142806159 0.134779501 LDHKFDLMYAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LDHKFDLMYAK 11 1 P68363;P68363-2;P68366-2;P68366;Q9BQE3;F5H5D3;A6NHL2-2;A6NHL2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA4A;TUBA1C;TUBAL3 Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain;Tubulin alpha chain-like 3 0 ;; 166.04 1.26E-05 5180730000 9374010 20986300 7122830 7453060 26357500 3637140 8566450 18721800 27675600 FALSE TRUE 8787307.447 22540147.49 7291786.891 7644318.138 24287488.27 4687123.274 7281990.35 21059257.94 23056363.57 0.38112287 0.97761069 0.316259191 0.331549167 1.053396309 0.203289789 0.315834296 0.913381587 1 24.45866165 1.119425105 6.435496231 0.992395924 0.525379911 0.296728898 0.285624931 0.270432667 13.25885423 0.266217938 0.066931824 13.16512857 -1.119425105 -0.467016013 LDHKFDLMYAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDHKFDLMYAKR 12 2 P68363;P68363-2;P68366-2;P68366;Q9BQE3;F5H5D3;A6NHL2-2;A6NHL2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA4A;TUBA1C;TUBAL3 Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain;Tubulin alpha chain-like 3 0 ; 147.73 3.85E-05 762910000 1038550 1794990 2093050 2696200 1992920 1127400 1254870 878960 1726600 FALSE TRUE 973549.0094 1927892.927 2142698.134 2765389.057 1836404.102 1452862.078 1066713.893 988700.0908 1438419.306 0.676818648 1.34028577 1.489619978 1.922519425 1.276682046 1.010040725 0.741587581 0.687351794 1 20.45605286 2.135661674 2.865597255 0.795367079 1.39240459 0.381490326 0.310905738 0.252231109 4.139629415 0.135624627 0.090186295 136.6663746 -2.135661674 0.597037511 LDHLAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 761270000 4581000 2978100 3083500 2609500 2649400 2037690 3809600 3105700 3703900 FALSE TRUE 4294283.387 3198601.623 3156642.076 2676464.188 2441326.811 2625938.024 3238385.847 3493453.481 3085695.162 1.391674538 1.036590284 1.022992198 0.867378029 0.791175629 0.851003708 1.049483399 1.132144719 1 21.55716411 6.215558514 1.028531873 0.952554943 9.238407203 0.631821334 0.102401631 23.02347218 1.588990463 0.031784231 395.0391947 1642700.973 -6.215558514 8.28585226 LDIDPETITWQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 250.76 5.76E-17 881588000 1293830 1401900 1403550 1327800 1496150 1144202 1483900 1231170 1556610 FALSE TRUE 1212851.49 1505698.135 1436842.869 1361873.596 1378648.414 1474514.543 1261402.971 1384884.285 1296801.735 0.935263624 1.161085842 1.107989626 1.050178728 1.063114258 1.137039305 0.972703025 1.067922912 1 20.3065265 1.735247734 24.99999978 1.014936126 1.087866747 0.151919331 0.065250814 0.593598155 4418.858681 0.028295756 0.015691366 54.35603058 -1.735247734 0.072930621 LDIDS(ph)PPITAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LDIDSPPITAR 11 0 P14618;B4DNK4;H3BUW1;H3BTJ2;H3BT25;H3BN34;H3BQZ3;P14618-2;H3BTN5;H3BQ34;H3BU13 P14618;P14618-2;H3BU13 PKM Pyruvate kinase PKM;Pyruvate kinase 1 LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(0.998)PPIT(0.002)AR;LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(1)PPITAR 264.84 7.05E-21 5005440000 3573790 3663830 3721870 3513630 3955950 3009260 4056680 3234980 3827790 TRUE FALSE 3350112.863 3935103.785 3810154.514 3603795.694 3645265.645 3877984.511 3448418.494 3638874.374 3188907.121 1.050552034 1.233997616 1.194815142 1.130103687 1.143108127 1.216085751 1.081379408 1.141103907 1 21.60463065 0.615240933 0.593272442 0.996275827 1.174710541 0.395391977 0.056932243 1.283454444 0.861813514 0.06479615 0.023209284 4.123262011 -0.615240933 0.178434714 LDIDSPPITAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LDIDSPPITAR 11 0 P14618;B4DNK4;H3BUW1;H3BTJ2;H3BT25;H3BN34;H3BQZ3;P14618-2;H3BTN5;H3BQ34;H3BU13 P14618;P14618-2;H3BU13 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;; 244.61 1.60E-15 2097036000 1150063 1365956 1274502 1262788 1390015 1130483 1469110 1081756 1309515 FALSE TRUE 1078082.61 1467092.804 1304733.789 1295193.278 1280848.829 1456835.09 1248830.594 1216815.618 1090948.487 0.988206705 1.344786506 1.195962784 1.187217631 1.174069028 1.335383942 1.144720039 1.115374037 1 20.05715155 1.075238197 1.864681934 1.004562264 1.217319507 0.284249388 0.099402209 0.351473574 2.438452325 0.084556159 0.024165192 11.89154264 -1.075238197 0.212757242 LDIFEFLNHVEDGLKDHYDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDIFEFLNHVEDGLKDHYDIK 21 1 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 271.05 7.67E-45 22236000 107490 40966 62715 65911 49218 56589 69037 57574 20227 FALSE TRUE 100762.3928 43999.16527 64202.62942 67602.38785 45352.61682 72925.32565 58685.54276 64762.24064 16850.98303 5.979615112 2.611074095 3.810022793 4.011777101 2.691392944 4.327660026 3.482618353 3.843232203 1 14.04054514 LDINLLDNVVNCLYHGEGAQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDINLLDNVVNCLYHGEGAQQR 22 0 O14980;C9JKM9;C9J673;C9IYM2;F8WF71;C9IZS4;C9JQ02;C9JV99;C9JF49 O14980 XPO1 Exportin-1 0 ; 356.44 2.83E-96 1682960000 713640 911360 819280 842930 856060 732060 1026620 764500 796560 FALSE TRUE 668974.5463 978838.0427 838713.7085 864561.0109 788828.5008 943393.838 872687.8617 859949.5079 663608.99 1.008085418 1.475022276 1.263867309 1.302816906 1.188694717 1.421610997 1.31506335 1.295867779 1 19.33997391 -1.385314231 2.097794437 0.984409424 1.303926419 0.319505248 0.127243683 212963.0868 174736.9761 19910.07317 0.02962034 0.041179946 1.385314231 0.319516995 LDIPTGT(ph)TPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDIPTGTTPQR 11 0 P52732 P52732 KIF11 Kinesin-like protein KIF11 1 LDIPT(0.26)GT(0.466)T(0.273)PQR 127.78 0.0031255 68038000 100870 93173 106410 101030 100770 95232 116050 99277 84500 TRUE FALSE 94556.72676 100071.6259 108934.0955 103622.6008 92855.93069 122723.9324 98649.37986 111671.952 70396.40411 1.343203931 1.421544568 1.54743835 1.47198713 1.319043662 1.743326722 1.401341178 1.586330345 1 16.10321412 -1.561288856 6.813858341 0.999506935 1.481082507 0.594062987 0.124501448 0.000825412 5.31E-05 0.106698378 0.025124809 0.027460671 1.561288856 0.481575571 LDKDNLSYIEHIFEISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDKDNLSYIEHIFEISR 17 1 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 194.27 5.03E-11 366100000 1409700 1270000 1427000 1278400 1495500 1149200 1649600 1437700 1430400 FALSE TRUE 1321469.393 1364032.121 1460849.114 1311205.908 1378049.463 1480955.384 1402257.794 1617200.01 1191656.999 1.108934361 1.144651626 1.225897313 1.100321577 1.156414525 1.242769845 1.176729373 1.357101927 1 20.18453761 2.285342557 17.01541999 1.20664232 1.155480533 0.048023289 0.092990347 14.31949535 5206.23145 0.028746069 0.02404824 192.9045881 -2.285342557 -0.051161788 LDKENALDR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 164.65 5.66E-05 5918420000 9495100 10393600 9252700 9488200 11580700 6721800 10371700 9103900 10338000 FALSE TRUE 8900818.64 11163152.96 9472178.413 9731683.275 10671198.54 8662274.541 8816559.871 10240541.96 8612521.014 1.033474244 1.29615393 1.099814839 1.129945954 1.239033091 1.005776883 1.023690956 1.189029546 1 23.03800417 2.23112469 24.99884476 1.05125771 1.168778113 0.255410069 0.088297641 207.1916753 696551.9886 0.03057592 0.023027023 170.2647284 -2.23112469 0.117520403 LDKSQIHDIVLVGGSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDKSQIHDIVLVGGSTR 17 1 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 163.79 1.61E-09 2351100000 3066900 4672100 4319400 4501400 5899400 3189900 5185800 3782800 9628900 FALSE TRUE 2874948.204 5018027.145 4421858.208 4616913.545 5436084.921 4110772.346 4408237.433 4255090.907 8021774.385 0.358393052 0.62555077 0.551231934 0.575547669 0.677666145 0.512451753 0.549533959 0.530442606 1 22.93548996 -1.499528011 4.244091706 1.003325863 0.557459114 0.745322395 0.08293092 0.002347888 0.000276868 0.07223912 0.016917989 0.031657163 1.499528011 -0.445866749 LDLAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 LDLAGR 6 0 P60709;A0A2R8Y793;P63267-2;A0A2R8YEA7;Q562R1;Q9BYX7;P63261;I3L3I0;I3L1U9;I3L4N8;P68133;P68032;P63267;P62736;Q6S8J3;A5A3E0;P0CG38;P0CG39 P60709;P63261;P68133;Q6S8J3 ACTB;ACTG2;ACTBL2;POTEKP;ACTG1;ACTA1;ACTC1;ACTA2;POTEE;POTEF;POTEI;POTEJ "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Beta-actin-like protein 2;Putative beta-actin-like protein 3;Putative beta-actin-like protein 3, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I;POTE ankyrin domain family member J" 0 ;;;;;;;;; 159.65 0.021057 37197740000 19838000 25166700 21182500 19181500 24190800 16232380 21367200 21053700 21257800 FALSE TRUE 18596374.99 27030068.65 21684958.9 19673729.76 22290952.15 20918404.6 18163386.72 23682300.79 17709735.85 1.050065069 1.526282994 1.224465406 1.110899108 1.258683491 1.181181062 1.025615903 1.337247545 1 24.07803936 3.52909257 4.286289568 1.152109815 1.336385449 0.105591631 0.151090257 0.292122024 11.09889541 0.037722382 0.058358139 3381.369022 -3.52909257 0.184275634 LDLFEISQPTEDLEFHGVMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDLFEISQPTEDLEFHGVMR 20 0 P55196-5;P55196;J3KN01;P55196-3;Q5TIG5;P55196-6;P55196-2;E9PFY5;F8W9I4;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 0 ; 158.58 2.68E-11 57762000 44330 49495 42010 41599 53557 42182 48727 46336 35161 FALSE TRUE 41555.46443 53159.6613 43006.49704 42666.50077 49350.84926 54359.25863 41420.83871 52121.1516 29292.40195 1.418643118 1.814793522 1.468179261 1.456572282 1.684766218 1.85574603 1.414047191 1.779340311 1 14.83823888 -0.953082883 4.658432719 0.999991894 1.610701602 0.565633465 0.168408481 1.29E-05 2.90E-06 0.148422026 0.034982943 0.11140819 0.953082883 0.610709708 LDLHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDLHLK 6 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 76.592 0.07465 524580000 1996760 1946750 1916420 2032450 1983680 1374330 2357240 2080790 1301350 FALSE TRUE 1871786.356 2090889.396 1961878.387 2084606.108 1827889.775 1771076.761 2003793.746 2340581.212 1084146.278 1.726507201 1.928604505 1.809606718 1.922808896 1.686017664 1.633614206 1.848268805 2.15891643 1 20.04812799 -1.108990823 4.561954122 0.999928118 1.834377412 0.760817891 0.147867609 0.000101976 1.99E-05 0.135053975 0.031829803 0.077805299 1.108990823 0.834449294 LDLIHESILHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDLIHESILHK 11 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77;H0YEC5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 170.52 9.03E-06 75721000 78169 242670 224480 251690 278740 211360 331110 267010 254210 FALSE TRUE 73276.54183 260637.5393 229804.7716 258148.7915 256848.8848 272376.2009 281463.1294 300346.7863 211780.7087 0.346001967 1.230695378 1.085107199 1.218943845 1.212805861 1.286123757 1.329031011 1.418197097 1 17.69221165 4.738680865 24.23410103 1.227733479 0.346001647 0.847934427 0.116647934 2.318672891 466443.0667 0.027533584 0.159277004 54787.42192 -4.738680865 -0.881731831 LDLITVEAFKPILSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDLITVEAFKPILSTR 16 1 O95456;O95456-2 O95456 PSMG1 Proteasome assembly chaperone 1 0 180.64 2.22E-09 50506000 141430 113540 119780 125980 137100 94659 128500 110230 81375 FALSE TRUE 132578.1488 121946.6197 122621.2382 129212.8601 126332.719 121985.5166 109232.6179 123992.4581 67792.9868 1.955632212 1.798808778 1.808759932 1.905991551 1.8635072 1.799382538 1.611267228 1.828986507 1 16.04884841 -2.197111724 0.302586172 5.30E-11 1.876638331 0.913768009 0.080256395 10.45091781 0.43531354 7.195901292 0.081583381 0.006351675 2.197111724 1.876638331 LDLLEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LDLLEDR 7 0 Q14697;F5H6X6;Q14697-2;E9PKU7;E9PNH1 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;;; 204.1 0.00063089 2056428000 2784000 3420190 3162610 3073640 3483870 2413270 3271790 2978500 2795590 FALSE TRUE 2609754.41 3673424.426 3237628.603 3152514.806 3210260.903 3109941.873 2781215.463 3350372.281 2328987.969 1.12055298 1.577262088 1.390143979 1.353598579 1.378393082 1.335318995 1.194173392 1.438552851 1 21.15127176 -1.013721644 0.278518024 0.782374 1.419724511 0.384670217 0.129952243 13.36595127 0.909131007 2.446150277 0.160852936 0.096889866 1.013721644 0.637350511 LDLRDDKDTIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 87.083 0.0060452 329540000 3250000 2052820 2097060 2119390 3366200 1549160 3347500 2449910 5460600 FALSE TRUE 3046588.301 2204812.929 2146803.254 2173777.136 3101832.231 1996377.343 2845573.452 2755786.656 4549190.583 0.669698982 0.484660488 0.471908841 0.477838221 0.681842665 0.438842319 0.625512033 0.605775161 1 22.11717845 0.104056926 0.644149144 1.020891234 0.521464312 0.732774414 0.084853699 1.701771142 0.855794747 0.162872471 0.030046918 1.270740659 -0.104056926 -0.499426922 LDLRDPAALFETHGAEEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDLRDPAALFETHGAEEIR 19 1 A0A087WVI0;E9PBL8;Q8WTW3;J3KRP4 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 0 ; 94.632 0.00094053 49827000 83320 157554 144733 158377 155780 105222 127256 135851 115530 FALSE TRUE 78105.14993 169219.4621 148166.1351 162441.222 143545.6672 135597.8833 108175.1442 152812.2964 96247.29665 0.81150487 1.758173663 1.539431654 1.687748411 1.491425445 1.408848747 1.123929169 1.587704816 1 16.5544584 1.999345581 4.290466966 1.252185636 1.517644679 0.085201989 0.294397164 0.381843017 16.87568003 0.117311502 0.075230388 99.84942795 -1.999345581 0.265459043 LDLVHTAALMLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDLVHTAALMLDK 13 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 148.62 4.34E-05 26485000 119990 110240 112420 101300 104330 81069 129360 114350 80350 FALSE TRUE 112480.0401 118402.2843 115086.6555 103899.5295 96136.34265 104472.3043 109963.6689 128626.8492 66939.06592 1.680334772 1.768806939 1.719274894 1.552150871 1.436176937 1.56070753 1.642742805 1.921551301 1 16.0305608 3.255267567 6.236840723 1.555324339 1.73333153 0.13792944 0.22816879 0.326709391 45.69135345 0.058281398 0.076378036 1799.979535 -3.255267567 0.178007191 LDNARQS(ph)AER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 126.83 0.00097898 894870000 748010 1147890 698240 832580 1280850 487430 746190 891420 1564350 TRUE FALSE 701193.3893 1232880.97 714802.5825 853945.4124 1180257.208 628143.1282 634305.7368 1002715.749 1303249.879 0.538034494 0.946005052 0.548476999 0.65524304 0.905626179 0.481982111 0.486710758 0.769396388 1 20.3136823 0.986280246 23.6027994 1.000000018 0.659991096 0.323477325 0.160272408 448.5647238 771691.8972 0.155315281 0.03882882 9.689028791 -0.986280246 -0.340008921 LDNLHSCFCALQALIDSCAGPGSLATEPHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDNLHSCFCALQALIDSCAGPGSLATEPHVR 31 0 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;C9JBE1;E7EMB6 E5RIA4 DNPEP Aspartyl aminopeptidase 0 243.21 2.96E-46 85149000 108050 102340 102870 90569 107710 94480 137580 98413 90970 FALSE TRUE 101287.3434 109917.3601 105310.125 92893.15387 99250.89108 121754.8422 116951.1562 110700.0797 75786.51931 1.336482323 1.450355038 1.38956276 1.225721338 1.309611419 1.606550127 1.543165688 1.460682991 1 16.20965363 -0.679136076 8.917602605 1 1.424700572 0.579059552 0.111011263 0 0 0.115020691 0.027110637 0.209345642 0.679136076 0.424700572 LDNLVAILDINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDNLVAILDINR 12 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 216.06 9.30E-11 184648000 239960 619840 279330 300110 878340 319810 295620 601050 381040 FALSE TRUE 224941.3319 665733.5985 285955.8395 307811.3307 809358.7195 412133.9553 251294.5254 676092.4156 317441.9624 0.708606166 2.097182091 0.900812978 0.969661756 2.549627382 1.298297025 0.791623525 2.129814252 1 18.27613332 -1.244308152 4.12036106 0.999684187 1.410462617 0.042636505 0.634992594 0.001700454 0.00031187 0.567365735 0.133627784 0.056975986 1.244308152 0.41077843 LDNS(ph)PNMNITQPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDNSPNMNITQPSK 14 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 LDNS(1)PNMNITQPSK 228.99 5.68E-12 74038000 94031 63667 72707 69887 79395 65284 113570 78517 91564 TRUE FALSE 88145.76756 68380.97093 74431.64437 71680.41874 73159.63696 84130.431 96541.23283 88320.02029 76281.37687 1.155534564 0.896430737 0.975751192 0.939684385 0.959075989 1.102896073 1.265593737 1.157818906 1 16.21904326 2.1073641 4.180338962 1.173550447 0.970115436 0.353029216 0.094440954 0.167410802 5.300532344 0.034272821 0.024362624 128.0454351 -2.1073641 -0.203435011 LDNTPAS(ph)PPRS(ph)PAEPNDIPIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LDNTPASPPRSPAEPNDIPIAK 22 1 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911;H0Y8P9 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 2 LDNTPAS(1)PPRS(1)PAEPNDIPIAK;LDNT(0.001)PAS(0.999)PPRS(1)PAEPNDIPIAK;LDNT(0.165)PAS(0.869)PPRS(0.967)PAEPNDIPIAK;LDNT(0.107)PAS(0.895)PPRS(0.998)PAEPNDIPIAK 248.92 1.72E-31 2094790000 3511460 2637260 3178110 2993900 3330610 2117300 2704300 2178520 1843440 TRUE FALSE 3291683.987 2832525.474 3253496.27 3070728.543 3069037.326 2728530.139 2298815.32 2450513.018 1535757.955 2.143361183 1.844382746 2.11849547 1.99948731 1.998386084 1.776666779 1.496860435 1.595637522 1 20.55051943 1.249802043 0.666011324 1.01832324 2.038354885 0.896171632 0.11104915 0.194478747 0.20517635 0.105489321 0.04612451 17.77469034 -1.249802043 1.020031645 LDNTPAS(ph)PPRSPAEPNDIPIAK ddPTM_SK-BR-3_Pertuzumab_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 1 LDNT(0.216)PAS(0.752)PPRS(0.032)PAEPNDIPIAK;LDNT(0.019)PAS(0.967)PPRS(0.014)PAEPNDIPIAK;LDNT(0.001)PAS(0.999)PPRSPAEPNDIPIAK;LDNT(0.023)PAS(0.959)PPRS(0.018)PAEPNDIPIAK;LDNT(0.008)PAS(0.992)PPRSPAEPNDIPIAK;LDNTPAS(1)PPRSPAEPNDIPIAK 204.35 7.14E-23 2895910000 3691540 2441370 2591590 1556045 1922930 2613520 6022780 4999030 4021450 TRUE FALSE 3460493.101 2622131.575 2653063.739 1595975.749 1771910.835 3368000.797 5119720.052 5623169.9 3350244.015 1.032907778 0.782668833 0.791901643 0.476375972 0.528890083 1.005300146 1.52816333 1.678435921 1 21.67583475 1.92180312 3.827042289 1.444826107 0.729789183 0.645929845 0.22819191 0.133080139 3.475267584 0.104944434 0.059914763 83.52242981 -1.92180312 -0.715036924 LDNVPHT(ph)PSSYIETLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDNVPHTPSSYIETLPK 17 0 Q99733;Q99733-2;E9PNJ7;C9J6D1;A8MXH2;E9PS34;E9PNW0;E9PJJ2;E9PP22;E9PKI2 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 LDNVPHT(0.761)PS(0.238)S(0.001)YIETLPK;LDNVPHT(0.982)PS(0.018)SYIETLPK 155.76 3.25E-07 807840000 620200 470500 598620 542710 555730 420660 774900 523300 840610 TRUE FALSE 581382.7891 505336.3096 612819.5491 556636.8574 512085.2075 542097.7132 658710.9388 588635.1569 700306.7605 0.830183031 0.721592791 0.875073016 0.794847185 0.73122985 0.774086077 0.940603427 0.840539018 1 19.41762749 1.259261215 0.96519397 0.985235261 0.788727297 0.534618162 0.059725119 0.38086528 0.753544328 0.054294333 0.019108364 18.16607968 -1.259261215 -0.196507964 LDPELHLDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDPELHLDIK 10 0 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 128.17 0.00033681 151531000 371720 303668 344960 324130 360110 242282 406000 316840 393480 FALSE TRUE 348454.7087 326151.8947 353142.6141 332447.7246 331828.4132 312224.8803 345124.0691 356398.1715 327805.646 1.062991785 0.994955086 1.077292653 1.014161069 1.012271806 0.952469502 1.052831375 1.087224018 1 18.32248118 -1.707188978 5.100281073 0.999048825 1.029626407 0.054472596 0.040738901 0.000431712 2.48E-05 0.038647672 0.008826848 0.019625061 1.707188978 0.030577582 LDPFADGGKT(ph)PDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDPFADGGKTPDPK 14 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 LDPFADGGKT(1)PDPK 101.67 0.0020949 330470000 919640 394820 529910 484310 587720 277780 951940 530230 861610 TRUE FALSE 862081.374 424052.8836 542479.7154 496738.2145 541562.8419 357970.5766 809205.4344 596430.3827 717801.7248 1.201002093 0.590766042 0.755751479 0.692027056 0.754474144 0.498703979 1.127338381 0.83091244 1 19.45322586 1.716618344 14.23495601 0.982978345 0.729413578 0.243938749 0.194895471 0.161170705 88.59703455 0.0815202 0.044902795 52.07368891 -1.716618344 -0.253564767 LDPHLVLDQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LDPHLVLDQLR 11 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ;;; 104.87 0.0025425 476208000 666574 5363500 334604 394655 5065170 331842.7 438381 3987970 3095580 FALSE TRUE 624854.3232 5760619.121 342540.9649 404782.5154 4667371.98 427640.3005 372649.8388 4485876.833 2578907.7 0.242294179 2.233743814 0.13282405 0.1569589 1.809825137 0.165822259 0.144499099 1.739448385 1 21.29832871 3.9553963 22.38771415 0.655035554 1.355642425 0.053431849 0.793015296 216.907393 223524.9686 0.187562478 0.338752903 9023.9421 -3.9553963 0.700606871 LDPHNHVLYSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LDPHNHVLYSNR 12 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;; 70.889 0.02664 1912760000 1946570 5869400 1780420 1721850 6090100 1097880 1867410 4798330 4527400 FALSE TRUE 1824737.658 6303976.483 1822652.403 1766035.586 5611808.112 1414820.133 1587409.207 5397412.063 3771747.692 0.483791019 1.671367493 0.483238157 0.468227392 1.487853529 0.375109962 0.420868344 1.431010901 1 21.84680174 3.899520638 8.744799292 0.753731033 1.150930757 0.035033042 0.492510515 0.644869618 66.76072115 0.117191574 0.211965497 7934.519614 -3.899520638 0.397199724 LDPITGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 138.37 0.0064966 808800000 199784 323103 274787 273008 291048 297620 268581 260841 287776 FALSE TRUE 187279.8761 347025.8823 281305.0774 280013.8475 268190.2641 383538.0625 228309.7724 293407.573 239744.3265 0.781164997 1.447483189 1.173354471 1.167968609 1.11865114 1.599779516 0.952305215 1.223835314 1 17.87113715 1.623682131 25 1.066036463 1.234522365 0.093402936 0.223134103 1.784057087 2813.386221 0.093395735 0.051571849 42.0418803 -1.623682131 0.168485901 LDPPPS(ph)PHANR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 75.669 0.018878 216770000 2796870 2539950 2979030 2752220 2756050 2543490 3360510 2457930 2213120 TRUE FALSE 2621818.899 2728010.541 3049693.998 2822846.625 2539600.95 3277754.273 2856632.723 2764807.971 1843735.975 1.422014288 1.479610193 1.654083904 1.531047104 1.377421163 1.777778553 1.549371907 1.499568273 1 20.81420064 0.715516739 3.387265197 1.000016023 1.551477606 0.691632184 0.112741089 1.793929314 20.77514955 0.102266973 0.026442298 5.194176929 -0.715516739 0.551461583 LDQETAQWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDQETAQWLR 10 0 Q96G03;E9PD70;E7ENQ8 Q96G03 PGM2 Phosphoglucomutase-2 0 125.97 0.00091895 141050000 303700 172150 160270 151960 185040 129050 182150 150130 189050 FALSE TRUE 284691.9591 184896.1651 164071.6801 155859.5509 170507.7048 166304.64 154838.2985 168874.061 157496.3337 1.807610072 1.173971233 1.041749203 0.989607486 1.082613803 1.055927057 0.983123193 1.07224122 1 17.26495872 5.036800394 1.547489382 1.033179192 2.701793336 0.974712595 0.038878805 0.347315302 0.433079916 0.010244015 1.096417665 108842.9726 -5.036800394 1.668614144 LDQEVAEVDKNIELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDQEVAEVDKNIELLK 16 1 F5H442;Q99816;Q99816-2 F5H442 TSG101 Tumor susceptibility gene 101 protein 0 185.33 1.53E-09 19990000 94173 60083 71417 67785 77757 48240 96098 58053 110560 FALSE TRUE 88278.88003 64531.60784 73111.04497 69524.47786 71650.27888 62166.10489 81688.99703 65301.04484 92106.82176 0.958440193 0.700617029 0.793763628 0.754824415 0.77790415 0.67493486 0.886894103 0.708970775 1 16.49102039 -1.448416179 5.559091402 1.000190411 0.778182098 0.387466186 0.086001462 0.000177596 1.76E-05 0.072865622 0.017159964 0.035610971 1.448416179 -0.222008312 LDQPMTEIVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDQPMTEIVSR 11 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 102.52 0.0066466 47462000 43314 49820 48783 48352 54546 38736 57974 37836 60855 FALSE TRUE 40603.05406 53508.72464 49940.1558 49592.79418 50262.17719 49918.45437 49281.3369 42559.90789 50697.90736 0.800882249 1.055442471 0.985053593 0.978201996 0.991405362 0.984625539 0.972058601 0.839480564 1 15.62963858 -0.640452121 5.203020087 0.999999992 0.967211986 0.000248775 0.076823506 9007899.741 1731282.659 0.327749581 0.016403282 0.228848399 0.640452121 -0.032788006 LDQPVS(ph)APPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LDQPVSAPPSPR 12 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 LDQPVS(1)APPS(1)PR;LDQPVS(1)APPS(1)PR;LDQPVS(1)APPS(1)PR;LDQPVS(1)APPS(1)PR;LDQPVS(1)APPS(1)PR;LDQPVS(1)APPS(1)PR;LDQPVS(1)APPS(1)PR;LDQPVS(1)APPS(1)PR 161.19 9.65E-05 15510890000 11378310 12932430 12409660 14246750 13504240 8518520 11357180 8815140 10794020 TRUE FALSE 10666161.89 13889960.57 12704023 14612345.72 12443671.46 10977678.44 9654276.294 9915729.634 8992428.33 1.186126983 1.544628443 1.41274665 1.624961044 1.383794344 1.220769078 1.073600583 1.102675414 1 23.10027933 2.089974329 2.129608526 1.065324468 1.457717964 0.688711437 0.114959206 0.165359461 1.44859968 0.055694355 0.032127942 123.0196051 -2.089974329 0.392393495 LDQPVSAPPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LDQPVSAPPSPR 12 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 LDQPVSAPPS(1)PR;LDQPVSAPPS(1)PR;LDQPVSAPPS(1)PR;LDQPVSAPPS(1)PR;LDQPVS(0.001)APPS(0.999)PR;LDQPVSAPPS(1)PR 247.21 1.36E-16 15656500000 4923530 5049880 5271920 5566450 5561960 3967980 4237570 3414860 3926270 TRUE FALSE 4615375.046 5423778.37 5396972.432 5709294.531 5125146.097 5113471.411 3602185.718 3841212.788 3270950.172 1.411019674 1.658166002 1.649970849 1.745454449 1.566867677 1.563298473 1.101265849 1.174341578 1 21.64127835 1.76608044 3.457671516 1.091829401 1.622793453 0.863028761 0.095171224 0.070980496 1.694148071 0.049134509 0.024403852 58.35531804 -1.76608044 0.530964052 LDRAS(ph)PDLWPEQLPGVAEFAASFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDRASPDLWPEQLPGVAEFAASFK 24 1 Q52LA3 Q52LA3 LIN52 Protein lin-52 homolog 1 LDRAS(1)PDLWPEQLPGVAEFAASFK;LDRAS(1)PDLWPEQLPGVAEFAASFK 231.94 4.65E-34 1328870000 500320 405240 462470 454810 531150 429720 640980 522660 694010 TRUE FALSE 469005.8643 435244.3913 473440.0068 466481.1946 489435.6216 553773.1881 544870.9996 587915.2515 578175.2475 0.811182883 0.752789735 0.818852085 0.806816267 0.846517771 0.957794701 0.942397659 1.01684611 1 19.14114732 2.241995561 0.986659881 1.003317836 0.783333713 0.926942482 0.02452301 0.120847966 0.224589165 0.016382547 0.009345574 174.580431 -2.241995561 -0.219984123 LDRDEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDRDEER 7 1 P40818;A0A075B720;H0YM17;H0YLH2;H0YM47;H0YNL5;H0YKV1 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 0 72.879 0.060528 0 110520 150010 143530 149390 163190 137500 152130 138930 135530 FALSE TRUE 103602.7505 161116.8965 146934.5994 153223.6003 150373.7157 177194.0179 129319.5188 156275.7163 112909.1674 0.917576073 1.426960274 1.301352253 1.357051901 1.331811394 1.569350141 1.145341178 1.384083506 1 16.7848031 -0.705583236 7.549486531 1.000007431 1.316437755 0.230071899 0.173600422 0 0 0.147952549 0.03487275 0.196977565 0.705583236 0.316430324 LDRDPASGTALQEISFWLNLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDRDPASGTALQEISFWLNLER 22 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 164.05 1.31E-11 115700000 217900 277240 250220 265380 325320 241980 302680 284600 227670 FALSE TRUE 204262.028 297767.1381 256155.3366 272190.1001 299770.6795 311835.6978 257295.9439 320132.9365 189670.4062 1.076931463 1.569918808 1.35052875 1.435068894 1.580482087 1.644092529 1.356542378 1.687838092 1 17.53313507 -1.148679513 4.821956794 0.999963493 1.464961039 0.402478334 0.177148201 6.13E-05 1.08E-05 0.151263267 0.035650301 0.071010159 1.148679513 0.464997546 LDRETEELHHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDRETEELHHDR 12 1 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ; 129.29 0.00014233 1823680000 1643340 1948460 1864570 1855610 2043910 1476360 2074290 1618550 2085000 FALSE TRUE 1540486.283 2092726.006 1908798.481 1903228.094 1883389.553 1902561.165 1763269.471 1820629.53 1737000.03 0.886866008 1.204793304 1.098905266 1.095698365 1.084277214 1.095314411 1.015123454 1.04814594 1 20.72816635 1.753350695 6.512553473 1.024199066 1.095839917 0.071082691 0.079546235 0.287409982 34.13801351 0.036243156 0.019336558 56.66967149 -1.753350695 0.071640851 LDRLDLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LDRLDLAR 8 1 O14579;M0QXB4;O14579-3;O14579-2 O14579 COPE Coatomer subunit epsilon 0 ;; 123.21 0.001238 455090000 409880 904900 370479 435020 1024260 316188 455400 810200 820890 FALSE TRUE 384226.3425 971899.7375 379266.9368 446183.3497 943818.7513 407466.3427 387116.9977 911355.2535 683878.1558 0.561834501 1.421159207 0.554582616 0.652431059 1.380097819 0.595817163 0.566061358 1.332628109 1 19.38337978 3.958783802 24.76526669 0.826025556 1.044751446 0.00411969 0.364111477 1039.30151 1403609.049 0.086950872 0.157126294 9094.604185 -3.958783802 0.218725889 LDRPAGGPS(ph)AESPRPSSAYNGDLNGLLVPDPLCSGDSTSANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDRPAGGPSAESPRPSSAYNGDLNGLLVPDPLCSGDSTSANK 42 2 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 LDRPAGGPS(0.49)AES(0.49)PRPS(0.008)S(0.008)AY(0.003)NGDLNGLLVPDPLCSGDSTSANK 94.434 6.55E-05 48254000 41447 36484 37886 42686 47225 31725 52711 43482 47777 TRUE FALSE 38852.90626 39185.31332 38784.67381 43781.39503 43516.139 40883.49249 44807.47489 48910.82342 39802.71005 0.976137208 0.984488576 0.974422942 1.099960153 1.093295882 1.027153489 1.125739299 1.228831488 1 15.28057904 3.237540769 24.96989881 1.098787072 0.979104112 0.457865776 0.060202868 21.88511837 535840.4293 0.016168123 0.020398504 1727.988188 -3.237540769 -0.11968296 LDRPAGGPSAES(ph)PRPSSAYNGDLNGLLVPDPLCSGDSTSANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDRPAGGPSAESPRPSSAYNGDLNGLLVPDPLCSGDSTSANK 42 2 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 LDRPAGGPS(0.03)AES(0.967)PRPS(0.001)S(0.001)AYNGDLNGLLVPDPLCSGDSTSANK 334.48 1.56E-133 577800000 324440 258210 293170 261470 326360 268780 406240 325400 357780 TRUE FALSE 304133.8795 277328.1371 300124.1308 268179.7629 300729.0021 346372.4227 345328.0833 366026.9063 298064.2067 1.020363642 0.930430863 1.006911008 0.899738234 1.00894034 1.162073188 1.158569448 1.228013623 1 18.18526361 2.321790993 4.252741331 1.152094084 0.964993584 0.602130148 0.066388118 0.120366765 4.071319288 0.021225329 0.0172301 209.7929999 -2.321790993 -0.187100499 LDS(ph)ELTARKELEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDSELTARKELEQK 14 2 Q8IUG5-2;Q8IUG5;Q8IUG5-3 Q8IUG5-2 MYO18B Unconventional myosin-XVIIIb 1 LDS(0.5)ELT(0.5)ARKELEQK 77.562 0.012692 386350000 212420 870960 620910 673360 947280 495020 626560 610970 1308000 TRUE FALSE 199125.0114 935446.7846 635638.2784 690639.5576 872884.4499 637924.238 532613.1447 687250.9494 1089686.35 0.182736079 0.858455082 0.583322236 0.633796649 0.801041924 0.58542005 0.488776559 0.63068694 1 20.05548151 -1.504705817 2.666942427 1.018367503 0.615359676 0.322227219 0.182348068 13209749.77 13327310.36 1769381.528 0.040948043 0.031281976 1.504705817 -0.403007826 LDS(ph)PPPS(ph)PITEASEAAEAAEAGNLAVSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDSPPPSPITEASEAAEAAEAGNLAVSSR 29 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 LDS(0.992)PPPS(0.91)PIT(0.096)EAS(0.002)EAAEAAEAGNLAVSSR;LDS(0.99)PPPS(0.92)PIT(0.088)EAS(0.002)EAAEAAEAGNLAVSSR 165.8 2.42E-12 221540000 123340 108928 111704 132085 121648 78613 113128 72298 97476 TRUE FALSE 115620.3696 116993.1425 114353.6716 135474.5247 112094.2568 101307.2969 96165.50663 81324.56445 81206.62588 1.423779997 1.440684688 1.408181542 1.668269347 1.380358506 1.247525012 1.184207638 1.001452327 1 16.30930983 1.787133545 1.275689606 1.001216906 1.466351834 0.843649667 0.081660914 0.16553536 0.505039732 0.065428443 0.026248169 61.25387174 -1.787133545 0.465134928 LDS(ph)PPPSPITEASEAAEAAEAGNLAVSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LDSPPPSPITEASEAAEAAEAGNLAVSSR 29 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 LDS(0.685)PPPS(0.144)PIT(0.169)EAS(0.003)EAAEAAEAGNLAVSSR;LDS(1)PPPSPITEASEAAEAAEAGNLAVSSR;LDS(0.807)PPPS(0.083)PIT(0.098)EAS(0.011)EAAEAAEAGNLAVSSR;LDS(0.999)PPPSPITEASEAAEAAEAGNLAVSSR;LDS(0.816)PPPS(0.148)PIT(0.029)EAS(0.007)EAAEAAEAGNLAVSSR 279.72 1.68E-71 367093000 325251 259177 242180 195853 192997 244290 471304 311209 362680 TRUE FALSE 304894.1205 278366.7348 247924.624 200878.9196 177839.7941 314812.5573 400636.3406 350064.1287 302146.365 1.009094121 0.921297646 0.820544785 0.664839769 0.58858823 1.041920717 1.325967766 1.15859123 1 18.20488806 2.01653978 10.5709314 1.194371743 0.813774297 0.582471659 0.141038945 0.230208432 142.3319933 0.054122396 0.039543425 103.8818752 -2.01653978 -0.380597446 LDS(ph)SEMDHS(ph)ENEDYTMSSPLPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDSSEMDHSENEDYTMSSPLPGK 23 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 LDS(0.835)S(0.216)EMDHS(0.949)ENEDYTMSSPLPGK;LDS(0.794)S(0.382)EMDHS(0.824)ENEDYTMSSPLPGK 106.1 0.00069289 257070000 325870 234813 269558 278812 275174 153118 276900 202864 266717 TRUE FALSE 305474.3784 252198.7988 275952.0431 285966.7879 253562.944 197320.6809 235381.4156 228192.017 222200.2096 1.374770883 1.135007025 1.241907213 1.286978029 1.141146286 0.88803103 1.059321303 1.026965804 1 17.76150065 2.450438413 6.259887238 1.00146083 1.234201858 0.737591069 0.074087852 0.090813904 11.64104119 0.024257904 0.020554727 282.1229478 -2.450438413 0.232741028 LDS(ph)SEMDHSENEDYTMSSPLPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDSSEMDHSENEDYTMSSPLPGK 23 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 LDS(0.343)S(0.343)EMDHS(0.313)ENEDYT(0.001)MSSPLPGK 88.917 0.0032074 131150000 103220 80200 92839 91437 86034 81991 138120 100220 113860 TRUE FALSE 96759.64445 86138.09145 95041.18492 93783.42822 79277.23668 105660.4707 117410.1882 112732.6876 94856.03044 1.020068455 0.908092939 1.001951953 0.988692314 0.835763802 1.113903567 1.237772524 1.188460945 1 16.53345187 2.067340562 6.96072532 1.170370598 0.954341544 0.558829249 0.08023564 0.126022941 10.61447597 0.027308567 0.020058403 116.7724957 -2.067340562 -0.216029054 LDS(ph)SPSVSSTLAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.709)S(0.291)PSVSSTLAAK 253.84 3.22E-24 729920000 748710 533010 610480 527970 618970 509310 787190 581840 564410 TRUE FALSE 701849.5776 572474.615 624960.8739 541518.6041 570358.593 656339.529 669158.1674 654484.0048 470206.3248 1.49264172 1.217496628 1.329120518 1.151661676 1.212996429 1.395854319 1.42311605 1.391908127 1 18.84293442 2.232489131 24.9888397 1.349168047 1.272875638 0 0.15062786 444.9883539 1831448.905 0.05015349 0.037992665 170.8004973 -2.232489131 -0.076292409 LDS(ph)SPSVSSTLAAKDDPDGKQEAKPQQAAGMLSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDSSPSVSSTLAAKDDPDGKQEAKPQQAAGMLSPK 35 3 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 LDS(0.19)S(0.175)PS(0.162)VS(0.162)S(0.162)T(0.149)LAAKDDPDGKQEAKPQQAAGMLSPK 71.878 0.0029779 164960000 237980 111700 153650 158850 223660 107400 262730 132780 458450 TRUE FALSE 223085.2566 119970.3842 157294.6506 162926.3599 206094.6458 138404.6365 223336.0756 149357.8753 381931.7333 0.584097202 0.314114732 0.4118397 0.42658503 0.539611213 0.362380563 0.584753913 0.391059088 1 18.54295527 -5 0.287416633 5.288409257 0.409540563 0.763105866 0.095002395 103.8992728 0.983570892 266.620587 0.093324855 1.00E-05 5 -4.878868694 LDS(ph)SPVSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDSSPVSSPR 10 0 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 2 LDS(0.5)S(0.5)PVS(0.281)S(0.719)PR 95.401 0.010888 57715000 203410 190980 211360 188150 183300 189680 257110 184130 192660 TRUE FALSE 190678.9312 205120.3579 216373.559 192978.2475 168904.3574 244437.5368 218558.7424 207119.0358 160503.8014 1.188002587 1.277978192 1.348089934 1.202328206 1.052338673 1.522939237 1.361704461 1.290430719 1 17.29224794 2.238525129 25 1.335068101 1.240306635 0.0187722 0.150116503 2.436979136 1713461.467 0.050669409 0.039865735 173.1909241 -2.238525129 -0.094761465 LDSEDKDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LDSEDKDK 8 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;; 114.84 0.0023517 19458030000 38635070 13657490 22265310 19560420 18917330 14291620 26299690 16161010 20045720 FALSE TRUE 36216969.93 14668704.77 22793453.67 20062373.49 17431639.21 18417378.69 22356295.64 18178747.67 16699959.83 2.168686051 0.878367668 1.364880748 1.20134262 1.043813242 1.1028397 1.338703558 1.088550383 1 23.9933413 4.748131707 24.98814835 1.151560166 2.168686596 0.828501989 0.148535311 521.0996342 1360456.043 0.034167373 0.444311184 55992.73831 -4.748131707 1.01712643 LDSEDKDKEGKPLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDSEDKDKEGKPLLK 15 3 P13639 P13639 EEF2 Elongation factor 2 0 90.754 0.0025812 1517800000 4046700 1665300 2469600 2451400 3147200 1425400 3725800 1877000 6833200 FALSE TRUE 3793424.271 1788600.545 2528180.078 2514307.074 2900031.607 1836889.841 3167150.879 2111347.582 5692694.776 0.666367058 0.314192244 0.444109544 0.44167256 0.50943037 0.322674922 0.556353538 0.370887192 1 22.44068032 -1.664987741 2.927382208 1.058137161 0.443832411 0.719569297 0.107132952 39200258.89 38254964.52 17077477.73 0.022581396 0.021627796 1.664987741 -0.61430475 LDSGDLLQQAQEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDSGDLLQQAQEIR 14 0 Q6XQN6-3;Q6XQN6;Q6XQN6-2;C9J8U2;G5E977 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 0 118.37 0.0019686 0 37655 37151 42144 47951 47570 36775 46221 35808 40011 FALSE TRUE 35298.24077 39901.6987 43143.67558 49181.50384 43834.04409 47391.34551 39290.59014 40278.70762 33332.90562 1.058960811 1.197066321 1.294326876 1.475464048 1.315038196 1.421758608 1.178732829 1.208376734 1 15.02465946 0.88423499 1.482222702 1.003337452 1.286269658 0.364091085 0.117085147 0.614185944 2.642652 0.111262245 0.032717494 7.660109711 -0.88423499 0.282932206 LDSHPCLEVTAAALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LDSHPCLEVTAAALR 15 0 Q9H4A4;A6NKB8;A0A087WU27;A0A087WUS4 Q9H4A4 RNPEP Aminopeptidase B 0 ;;; 206.63 3.80E-09 1612100000 2733390 3560930 2998640 3111650 3894850 2577030 3694290 3488080 3666690 FALSE TRUE 2562311.999 3824584.962 3069769.157 3191500.207 3588964.192 3320976.726 3140365.511 3923574.466 3054695.751 0.838810869 1.252034662 1.004934503 1.044784969 1.174900705 1.08717103 1.028045267 1.284440346 1 21.54259726 LDSLHPDLIYNVSWNHNGSLFCSACK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDSLHPDLIYNVSWNHNGSLFCSACK 26 0 Q9BR76;A0A087WW53;F5H390 Q9BR76 CORO1B Coronin-1B;Coronin 0 ; 262.74 3.92E-53 323931000 276290 400430 354761 332922 386944 309285 502151 362240 289779 FALSE TRUE 258997.5021 430078.2538 363176.0985 341465.3422 356554.9791 398570.5587 426858.1193 407466.4614 241413.0129 1.072839857 1.781504024 1.504376645 1.41444464 1.476950123 1.650990367 1.768165329 1.687839676 1 17.88114392 4.753428079 24.57977887 1.579918939 1.072839402 0.269637561 0.229193817 2508.992132 4147926.944 0.049627002 1.118906153 56679.76993 -4.753428079 -0.507079537 LDSQEPGRQT(ph)PDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LDSQEPGRQTPDR 13 1 Q8TB03-2;Q8TB03 Q8TB03-2 CXorf38 Uncharacterized protein CXorf38 1 LDS(0.001)QEPGRQT(0.999)PDR;LDSQEPGRQT(1)PDR;LDSQEPGRQT(1)PDR 102.58 0.0027135 1014960000 920820 993590 1001410 937270 1119240 934550 1371280 1064030 1212920 TRUE FALSE 863187.5199 1067156.437 1025163.918 961321.935 1031339.405 1204339.414 1165669.294 1196876.488 1010475.816 0.854238673 1.056093001 1.014535827 0.951355707 1.020647292 1.191853773 1.153584555 1.184468216 1 19.94660336 2.342192628 5.491866391 1.147283691 0.990905164 0.504126418 0.074812835 0.160830564 7.275984631 0.024239028 0.02007136 219.8834931 -2.342192628 -0.156378528 LDSQNAQGYEWIFIAWSPDHSHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LDSQNAQGYEWIFIAWSPDHSHVR 24 0 Q12792;Q12792-3;F8VS81;F8W1Q9 Q12792 TWF1 Twinfilin-1 0 ;; 204.65 6.14E-25 510934000 91671.3 123670 106940 119377 125546 96769 105581 115825 99817 FALSE TRUE 85933.75697 132826.6555 109476.6673 122440.4159 115686.1236 124704.6394 89750.10922 130286.0062 83156.89786 1.03339301 1.597301714 1.316507351 1.472402399 1.391178923 1.499630729 1.079286404 1.566749236 1 16.34354832 -2.482953018 0.353243635 0.422953549 1.390913994 0.251644463 0.191316881 76.32455213 3.152045723 34.03886377 0.132854975 0.003288872 2.482953018 0.967960445 LDSQPQETS(ph)PELPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LDSQPQETSPELPR 14 0 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 LDSQPQET(0.037)S(0.963)PELPR;LDSQPQET(0.02)S(0.98)PELPR;LDSQPQET(0.194)S(0.806)PELPR;LDSQPQET(0.093)S(0.907)PELPR;LDSQPQET(0.002)S(0.998)PELPR;LDSQPQET(0.071)S(0.929)PELPR;LDSQPQETS(1)PELPR;LDSQPQET(0.004)S(0.996)PELPR 309.91 1.13E-55 14420810000 6236810 6512200 6597910 6360030 6597340 5584200 7160540 5495470 9960270 TRUE FALSE 5846459.195 6994370.064 6754415.541 6523239.137 6079211.529 7196267.888 6086883.502 6181591.527 8297836.591 0.704576323 0.842914896 0.813997175 0.786137334 0.732626084 0.867246277 0.733550659 0.74496424 1 22.98430382 -1.524546543 6.540616977 1.000166074 0.786174574 0.637584396 0.052238201 0.000119264 8.67E-06 0.047684067 0.01123059 0.029885014 1.524546543 -0.2139915 LDSS(ph)PSVSSTLAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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(0.063)S(0.937)PS(0.001)VSSTLAAK;LDS(0.05)S(0.942)PS(0.008)VSSTLAAK;LDS(0.015)S(0.985)PSVSSTLAAK;LDS(0.007)S(0.993)PSVSSTLAAK;LDS(0.022)S(0.978)PSVSSTLAAK;LDS(0.252)S(0.748)PSVSSTLAAK;LDS(0.009)S(0.991)PSVSSTLAAK 383.98 7.95E-114 10070730000 10533610 7255910 8313980 7518240 8388200 7231330 10971430 8199990 8046520 TRUE FALSE 9874330.153 7793145.126 8511191.532 7711170.767 7729424.608 9318897.58 9326365.925 9223776.802 6703503.829 1.473010295 1.162548023 1.269663112 1.150319439 1.153042469 1.390153242 1.391267338 1.375963531 1 22.67648394 2.231890894 24.99471688 1.331814084 1.230577402 0 0.147712311 358.1313136 1342080.675 0.049034103 0.037050597 170.5653831 -2.231890894 -0.101236682 LDSS(ph)PSVSSTLAAKDDPDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LDSSPSVSSTLAAKDDPDGK 20 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 LDS(0.091)S(0.88)PS(0.002)VS(0.012)S(0.012)T(0.002)LAAKDDPDGK;LDS(0.125)S(0.844)PS(0.024)VS(0.005)S(0.001)TLAAKDDPDGK;LDS(0.211)S(0.749)PS(0.024)VS(0.007)S(0.007)T(0.001)LAAKDDPDGK 169.56 6.42E-12 695170000 2672730 1399650 1808640 1751270 2221870 1331690 2720400 1753130 3137860 TRUE FALSE 2505448.6 1503281.542 1851541.795 1796210.553 2047373.293 1716127.285 2312501.275 1972012.14 2614130.895 0.958425076 0.575059782 0.708281976 0.687115766 0.783194635 0.656481008 0.884615717 0.754366258 1 21.31789995 0.8203349 0.601455691 1.00098559 0.701615772 0.32361815 0.110631751 1.028967701 0.819490652 0.109210618 0.044053723 6.61203129 -0.8203349 -0.299369818 LDSSDIYNELKETYPNYLPLYVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDSSDIYNELKETYPNYLPLYVAR 24 1 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8;A0A494C0A3;A0A494C1S6 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 154.6 5.25E-08 48864000 32268 44074 38585 42010 51406 25856 43096 43455 57645 FALSE TRUE 30248.40348 47337.28482 39500.25442 43088.04772 47368.78012 33320.20746 36634.15488 48880.45241 48023.6771 0.629864377 0.985707211 0.822516242 0.897225084 0.98636304 0.693828742 0.762835274 1.017840685 1 15.55145825 1.224199726 24.95608257 1.008920538 0.838383577 0.303310459 0.114289758 348.3120762 605272.2815 0.103700414 0.026408741 16.75713335 -1.224199726 -0.17053696 LDSSEMDHS(ph)ENEDYTMSSPLPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LDSSEMDHSENEDYTMSSPLPGK 23 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 LDS(0.001)SEMDHS(0.999)ENEDYTMSSPLPGK;LDS(0.009)S(0.009)EMDHS(0.982)ENEDYTMSSPLPGK;LDS(0.03)S(0.025)EMDHS(0.944)ENEDYTMSSPLPGK 214.78 1.81E-32 684770000 782600 581430 713870 614010 701640 631450 1024770 787940 860520 TRUE FALSE 733618.463 624479.6822 730803.3335 629766.5361 646536.0247 813739.3643 871115.252 886316.0435 716893.6528 1.023329555 0.871091102 1.019402711 0.878465772 0.901857649 1.135090764 1.215124794 1.236328485 1 19.45139959 2.168727804 5.280169205 1.173448289 0.937932929 0.61209425 0.081355942 0.112878549 5.816656379 0.028088229 0.02070079 147.4781916 -2.168727804 -0.23551536 LDT(ph)PDINIVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDTPDINIVLK 11 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 LDT(1)PDINIVLK;LDT(1)PDINIVLK 162.72 0.00027714 40042000 264270 143273 176272 164208 188968 143878 287690 182035 276240 TRUE FALSE 247729.8124 153881.082 180453.2551 168421.8553 174127.2155 185413.2429 244553.5553 204762.4705 230133.7594 1.076460112 0.668659315 0.784123353 0.731843323 0.75663482 0.805675983 1.062658325 0.889754163 1 17.81211311 1.833561444 6.486812299 0.98514199 0.780030017 0.342864018 0.114863231 0.219170643 12.19888043 0.046469667 0.02799373 68.16500077 -1.833561444 -0.205111973 LDTDDLDEIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDTDDLDEIEK 11 0 Q9NUU7;I3L0H8;F6QDS0;H3BQK0;Q9UMR2;Q9UMR2-2;Q9UMR2-4;I3L352;Q9UMR2-3;Q9NUU7-2 Q9NUU7 DDX19A;DDX19B ATP-dependent RNA helicase DDX19A;ATP-dependent RNA helicase DDX19B 0 203.94 8.12E-08 45645000 168040 124720 146970 143810 162240 109650 184760 134910 198810 FALSE TRUE 157522.6764 133954.3986 150456.1978 147500.4081 149498.3248 141304.175 157056.9532 151753.8105 165627.3266 0.95106695 0.808769913 0.908402018 0.890555991 0.902618716 0.853145298 0.948255076 0.916236551 1 17.3375812 0.88248738 0.55806154 1.002595546 0.87516697 0.410919603 0.04060555 0.892297557 0.646463563 0.041863869 0.017969988 7.629347212 -0.88248738 -0.127428576 LDTGPQSLS(ph)GK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDTGPQSLSGK 11 0 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 LDTGPQS(0.001)LS(0.999)GK;LDTGPQSLS(1)GK 173.59 1.26E-05 315710000 627030 388680 515220 440090 384960 347050 663930 422720 602140 TRUE FALSE 587785.3116 417458.2716 527441.2617 451383.4545 354726.7945 447237.7011 564379.8601 475497.5225 501638.944 1.171729824 0.832188722 1.051436034 0.899817408 0.707135677 0.891552991 1.125071861 0.947887974 1 18.93628983 1.759232216 25 1.03522471 0.919977157 0.110833387 0.129882211 18.65483574 22580.57903 0.057488929 0.031881331 57.44235221 -1.759232216 -0.115247553 LDTHPAMVTVLEMGAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDTHPAMVTVLEMGAAR 17 0 Q12931-2;Q12931;I3L0K7 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ; 149.73 3.14E-07 414330000 919980 1072810 954630 905380 1110650 791100 990700 1013740 1085360 FALSE TRUE 862400.094 1152241.969 977274.2744 928613.5836 1023424.029 1019477.728 842153.7322 1140307.671 904206.4043 0.953764638 1.274312992 1.080808839 1.026992929 1.1318478 1.127483418 0.931373333 1.261114349 1 19.78629261 3.64366281 6.599219606 1.070933499 1.14883919 0 0.117062112 0.550141679 35.74857463 0.02858578 0.044647393 4402.129453 -3.64366281 0.077905692 LDTIPDIPPPRPPKPHPAHDRSPVETCS(ph)IPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDTIPDIPPPRPPKPHPAHDRSPVETCSIPR 31 3 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 LDTIPDIPPPRPPKPHPAHDRS(0.246)PVET(0.353)CS(0.401)IPR 51.568 0.029749 357720000 197210 172990 216100 206040 223470 131580 185350 153610 247660 TRUE FALSE 184866.9781 185798.3596 221225.994 211327.3352 205919.5676 169565.01 157558.4882 172788.5466 206323.9461 0.896003502 0.900517672 1.072226459 1.024250162 0.99804008 0.821838731 0.763646156 0.837462398 1 17.65455175 2.236408184 25 0.827776875 0.982527109 0.341189477 0.080375475 50.15533607 582530.574 0.028702238 0.022239953 172.3487681 -2.236408184 0.154750235 LDVFARPAS(ph)PSLQLLPWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDVFARPASPSLQLLPWR 18 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 LDVFARPAS(0.953)PS(0.047)LQLLPWR;LDVFARPAS(0.5)PS(0.5)LQLLPWR 218.25 4.83E-19 1511520000 1194280 1832710 1336520 1208900 1860790 1116060 1968480 1394400 2303100 TRUE FALSE 1119532.147 1968405.755 1368222.886 1239922.421 1714651.059 1438248.404 1673324.698 1568493.909 1918697.731 0.583485417 1.025907168 0.713099757 0.646231243 0.893653561 0.749596135 0.872114805 0.817478378 1 20.87169602 0.434076917 0.727182439 1.002478796 0.792247737 0.229166708 0.125801848 3.119141437 2.522199599 0.13608678 0.042597045 2.716920415 -0.434076917 -0.210231058 LDVGNFSWGSECCTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LDVGNFSWGSECCTR 15 0 P62241 P62241 RPS8 40S ribosomal protein S8 0 ;;;;; 354.47 3.93E-82 2204320000 385091 358026 377128 389860 390477 384076 438248 348613 408095 FALSE TRUE 360988.8417 384534.6176 386073.6543 399864.4676 359810.5115 494952.5062 372536.7809 392138.1004 339981.3081 1.061790261 1.13104635 1.135573177 1.176136623 1.058324393 1.455822701 1.095756655 1.153410764 1 18.3750959 5.093876937 0.714128932 1.171654886 0.949648628 0.040603189 0.120258601 12.92724576 3.503470287 0.041957168 2.591032151 124130.0519 -5.093876937 -0.222006258 LDVTILS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LDVTILSPSR 10 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 1 LDVTILS(0.698)PS(0.302)R;LDVTILS(0.978)PS(0.022)R;LDVTILS(0.547)PS(0.453)R;LDVT(0.001)ILS(0.992)PS(0.007)R 148.92 2.54E-05 748790000 652730 681730 721910 705770 832780 621656 801990 661370 1028020 TRUE FALSE 611876.7945 732205.9985 739034.0461 723881.2531 767376.8181 801117.9955 681739.0448 743943.5004 856436.8207 0.714444755 0.854944557 0.86291718 0.845224348 0.896011007 0.935408166 0.796017906 0.868649598 1 19.7079873 -3.984268306 0.019698104 2.017172101 3.73E-06 0.51394034 0.053026854 2819.889169 4.981691207 326.8161553 197.8497844 0.000103689 3.984268306 -2.017168373 LDVTILS(ph)PSRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDVTILSPSRK 11 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 1 LDVTILS(0.5)PS(0.5)RK 92.039 0.0023254 0 143700 118670 132110 132080 150040 106290 152340 115640 220170 TRUE FALSE 134706.0735 127456.4503 135243.7116 135469.3964 138256.4636 136974.1975 129498.0313 130077.9086 183422.2046 0.734404397 0.694880157 0.737335547 0.738565959 0.753760778 0.746769988 0.706010657 0.709172092 1 17.48480877 -2.206527476 2.518073421 1.907342318 0.726023727 0.953577551 0.018884664 1723822.609 448789.664 8916568.975 0.004729919 0.006215449 2.206527476 -1.181318591 LDVTILSPS(ph)RK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDVTILSPSRK 11 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 1 LDVTILS(0.345)PS(0.654)RK 95.428 0.0014848 0 93414 93285 93679 95158 104840 76551 98004 80445 155820 TRUE FALSE 87567.38449 100191.9185 95901.11012 97599.91538 96606.2893 98650.031 83309.21002 90488.73533 129812.6354 0.674567497 0.771819463 0.738765605 0.751852199 0.74419789 0.759941671 0.641765032 0.697071861 1 16.98607129 -1.235735863 4.295642832 1.000143151 0.72533539 0.820529736 0.040767471 6570492.145 1890151.964 8827.173758 0.010110124 0.058111775 1.235735863 -0.274807762 LDVTILSPSRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDVTILSPSRK 11 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ; 119.39 0.00095101 404720000 790430 874460 721330 820700 1065280 632630 903130 795830 1270210 FALSE TRUE 740958.3973 939205.9283 738440.2882 841760.5514 981617.2059 815260.0111 767714.0407 895191.1273 1058203.745 0.700203907 0.887547349 0.697824301 0.795461701 0.927625904 0.770418754 0.725487926 0.845953467 1 20.013186 0.979619955 21.00805618 1.000000004 0.788476825 0.452066346 0.074184385 160.8766008 165835.5786 0.067918884 0.016979721 9.541572501 -0.979619955 -0.211523179 LDWELEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDWELEQR 8 0 Q13769;F8WCP5;C9JXG5;H7C072 Q13769 THOC5 THO complex subunit 5 homolog 0 ; 84.476 0.040538 143767000 123599 212418 178961 196436 212190 164242 178018 190462 197486 FALSE TRUE 115863.1592 228145.6497 183206.0394 201476.8803 195525.4533 211655.9992 151325.8535 214241.6 164524.3108 0.704231239 1.386698711 1.113549958 1.224602488 1.188428946 1.286472486 0.919778073 1.302188102 1 17.32794125 -0.831440295 6.914736813 0.999999999 1.153355038 0.043582462 0.199577892 5.12E-09 3.70E-10 0.171686094 0.0404668 0.14742112 0.831440295 0.153355039 LDYDEDASAMLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDYDEDASAMLK 12 0 P50502;Q8NFI4;H7C3I1 P50502 ST13;ST13P5 Hsc70-interacting protein;Putative protein FAM10A5 0 ; 155.11 0.00063813 41951000 400874 341429 363039 359661 376090 289251 436574 327135 453903 FALSE TRUE 375784.0119 366708.7584 371650.4565 368890.5102 346553.4085 372753.0681 371113.7817 367978.5249 378143.657 0.993759924 0.969760438 0.982828747 0.975530075 0.916459663 0.985744601 0.981409511 0.973118332 1 18.52857489 0.621368478 1.025581531 0.999729581 0.971415653 0.146575 0.021001979 2.508759405 4.227987309 0.019384745 0.006170739 4.181850261 -0.621368478 -0.028313928 LDYFLLSHSLLPALCDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LDYFLLSHSLLPALCDSK 18 0 P27695 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 237.59 7.44E-24 742780000 3669100 4137300 3359600 3182200 4884900 2346700 4005600 4103100 3248000 FALSE TRUE 3439457.581 4443629.997 3439291.299 3263860.639 4501259.659 3024154.195 3404997.466 4615381.067 2705887.817 1.271101322 1.64220777 1.27103987 1.206206931 1.663505645 1.117619945 1.258366088 1.705680863 1 21.3676706 -1.906620882 2.798922177 0.789424895 1.384416276 0.257692037 0.208721042 47456706.51 18504121.91 65204207.73 0.04690883 0.012398785 1.906620882 0.594991381 LDYGQHVVAGTPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LDYGQHVVAGTPGR 14 0 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ;;; 164.65 4.09E-06 2029310000 3288800 3261450 3469680 3315690 3547380 2929740 3883370 3235200 3374870 FALSE TRUE 3082959.879 3502931.152 3551982.448 3400776.219 3268783.084 3775508.378 3301094.72 3639121.842 2811582.395 1.096521263 1.245893116 1.263339269 1.209559508 1.162613299 1.342841094 1.17410563 1.294332277 1 21.4229509 -1.776787433 2.66847441 0.942091075 1.228250335 0.50175873 0.069906392 11562143.9 8038237.647 4352278.733 0.015640059 0.016719087 1.776787433 0.286159261 LDYVPS(ph)SAS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LDYVPSSASR 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 2 LDYVPS(0.99)S(0.012)AS(0.998)R 104.17 0.0039717 174510000 445980 697700 512200 458350 747170 296900 757270 576590 1248300 TRUE FALSE 418066.9079 749358.434 524349.6259 470112.037 688490.2821 382610.2102 643724.3937 648578.5307 1039950.666 0.402006481 0.720571137 0.504206251 0.452052249 0.662041292 0.367911885 0.618995126 0.623662787 1 19.98808366 0.656234692 1.623931836 0.999563437 0.543362195 0.635583193 0.110796441 0.844494252 3.135032367 0.096832635 0.027687337 4.531423907 -0.656234692 -0.456201241 LDYVPSSAS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LDYVPSSASR 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 LDYVPSSAS(1)R;LDYVPSSAS(1)R;LDYVPSSAS(1)R;LDYVPSSAS(1)R;LDYVPSSAS(1)R;LDYVPSSAS(1)R;LDYVPSSAS(1)R;LDYVPSSAS(1)R 207.34 1.40E-07 13179880000 7185810 7240810 7742520 6893400 8016460 6445570 7916750 6489320 8018060 TRUE FALSE 6736062.979 7776927.106 7926176.231 7070296.314 7386879.568 8306301.424 6729706.833 7299525.887 6679793.987 1.008423762 1.16424655 1.186589923 1.058460235 1.105854399 1.243496647 1.007472213 1.092777098 1 22.67137218 1.640163474 13.19386525 1.03781696 1.134983457 0.286366578 0.069466266 0.142604039 47.89192565 0.030891268 0.016857977 43.66801732 -1.640163474 0.097166497 LDYWEDDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 151.44 0.0016674 80301000 530580 661200 580210 629230 671130 469380 705600 576720 615570 FALSE TRUE 497371.9449 710155.936 593972.8552 645377.1071 618422.157 604882.3863 599801.8305 648724.7615 512827.3903 0.969862286 1.384785504 1.158231535 1.258468481 1.205907034 1.179504835 1.169597884 1.26499632 1 18.96811379 -1.908654124 2.443192381 0.874390802 1.210020563 0.256965368 0.10480275 8025940.337 4360086.585 5786361.614 0.02320571 0.012340873 1.908654124 0.335629761 LDYWEDDLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LDYWEDDLRR 10 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6;Q5T321;A0A0D9SF28;F5GXV7;Q8NFP9 A0A494C1L5;Q5T321 LRBA;NBEA Lipopolysaccharide-responsive and beige-like anchor protein;Neurobeachin 0 ;; 155.26 2.09E-05 256248000 284129 357566 313563 335154 352106 267055 358701 307141 371331 FALSE TRUE 266345.8731 384040.5587 321000.8624 343754.6191 324453.0151 344149.4432 304917.1151 345488.23 309353.4572 0.860975906 1.241429665 1.0376508 1.111203418 1.048810051 1.112479706 0.98565931 1.116807399 1 18.23889663 1.754389868 25 1.034213925 1.085957939 0.006824028 0.100106879 17.59805359 27827.14424 0.042036964 0.0233123 56.80543212 -1.754389868 0.051744014 LEAAEER ddPTM_SK-BR-3_Pertuzumab_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 94.407 0.033089 176840000 221790 228200 232930 233880 255190 183460 244640 221070 258710 FALSE TRUE 207908.5598 245096.1654 238455.2096 239881.7568 235148.4068 236421.9238 207958.5031 248671.0761 215529.6297 0.964640268 1.137180841 1.106368577 1.112987375 1.091025894 1.096934673 0.964871992 1.153767473 1 17.71752669 1.874416065 17.87095008 1.034425657 1.09471921 0.080194626 0.066230609 3.82728558 531.6033115 0.024789142 0.015979046 74.88866086 -1.874416065 0.060293554 LEAALGEAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 113.63 0.0023454 546830000 721980 675340 682750 737920 945690 535520 920450 697050 1298270 FALSE TRUE 676792.5606 725342.8763 698945.1524 756856.2765 871419.3221 690115.9306 782437.0675 784078.2269 1081580.35 0.625744135 0.670632447 0.646225824 0.699768886 0.805690786 0.638062563 0.723420195 0.724937567 1 20.04470942 -5 0.20583088 2.469919165 0.640954083 0.819490094 0.046828601 56.26109498 0.559598791 34.0281748 0.099734285 1.00E-05 5 -1.828965082 LEAEEGRNS(ph)LS(ph)PVQATQKPLVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LEAEEGRNSLSPVQATQKPLVSK 23 2 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 2 LEAEEGRNS(1)LS(0.999)PVQAT(0.001)QKPLVSK;LEAEEGRNS(1)LS(0.868)PVQAT(0.13)QKPLVS(0.002)K;LEAEEGRNS(1)LS(0.999)PVQAT(0.001)QKPLVSK;LEAEEGRNS(1)LS(0.996)PVQAT(0.004)QKPLVSK 166.28 6.52E-12 1645160000 2431390 1556101 2014674 1853782 2023914 1558028 2643090 1803381 2480760 TRUE FALSE 2279213.64 1671316.337 2062463.019 1901353.185 1864963.959 2007805.391 2246783.192 2028537.088 2066705.13 1.102824785 0.808686403 0.997947404 0.919992483 0.902385121 0.971500657 1.087132925 0.981531936 1 20.97890113 1.977430132 8.954472389 1.031881162 0.933678929 0.15046191 0.07897629 0.402512487 148.0441667 0.029451859 0.019380689 94.93582562 -1.977430132 -0.098202232 LEAEIATYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LEAEIATYR 9 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;; 208.72 2.23E-05 2405090000 4037400 3697750 3805610 3466810 4032880 3323180 4553330 3600130 4812470 FALSE TRUE 3784706.341 3971535.258 3895880.866 3555774.214 3716153.873 4282528.119 3870600.438 4049614.155 4009237.667 0.943996504 0.990596115 0.971726096 0.886895342 0.926897875 1.068165191 0.965420551 1.010070864 1 21.93489651 2.268756502 24.99982912 1.005614669 0.951554444 0.435874065 0.037053341 241.7386033 200139.8062 0.013246855 0.011081748 185.6763121 -2.268756502 -0.054060225 LEAEIATYRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEAEIATYRR 10 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 195.27 5.97E-07 754000000 321535 565890 414590 455340 676480 341790 571450 444370 1126760 FALSE TRUE 301410.6983 607789.0844 424424.2706 467024.7953 623351.9896 440459.2245 485766.3776 499850.5727 938696.4769 0.32109495 0.647482013 0.452142179 0.49752482 0.664061286 0.469224329 0.51749036 0.532494353 1 19.84029922 0.59932777 3.940723986 0.999999876 0.520404425 0.714235689 0.096794498 10.85716285 106.1898685 0.082389618 0.02106395 3.974914306 -0.59932777 -0.479595451 ERASS(ph)PPDRIDIFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 ERASSPPDRIDIFGR 15 2 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 ERAS(0.007)S(0.993)PPDRIDIFGR 151.96 1.52E-06 32484000 4762.6 6895.2 4512.4 6086.9 6748.4 4393.6 6849.7 7635.7 15209 TRUE FALSE 4464.517367 7405.727782 4619.436259 6243.100159 6218.407886 5661.960996 5822.651074 8589.033953 12670.51965 0.352354717 0.58448493 0.364581437 0.49272645 0.490777652 0.446860993 0.459543195 0.67787543 1 13.62918807 0.942435777 2.49238973 0.999233895 0.45988157 0.87734411 0.065869931 0.09838424 1.382721438 0.057088119 0.015383388 8.758621869 -0.942435777 -0.539352326 LEAPDADELPKGEFDPGQDTYQHPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEAPDADELPKGEFDPGQDTYQHPPK 26 1 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ; 144.76 1.43E-07 603330000 1088580 603160 686370 678180 974630 595590 800480 732130 1291410 FALSE TRUE 1020447.721 647818.594 702651.0205 695583.247 898086.4913 767527.1644 680455.4553 823538.0421 1075865.328 0.948490201 0.602137254 0.653103137 0.646533752 0.834757351 0.713404498 0.632472706 0.765465733 1 20.03706607 0.955667423 12.31014064 0.999999993 0.698713657 0.400513039 0.105214053 6.430784406 1786.392641 0.094373527 0.023596922 9.029577356 -0.955667423 -0.301286336 LEAPLEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LEAPLEELR 9 0 Q16401-2;Q16401;F2Z3J2 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ;; 146.58 0.0002197 114173000 170178 264353 177592 194884 285857 126018 193782 237553 272003 FALSE TRUE 159526.8628 283925.9712 181804.5661 199885.0534 263406.9443 162397.3509 164726.1881 267212.015 226603.9421 0.703989795 1.252961306 0.802300986 0.882089921 1.16241113 0.716657219 0.726934344 1.179202853 1 17.78981343 2.224797199 24.99991944 0.860289198 0.975415321 0 0.206555889 688.4295403 1250457.477 0.073093838 0.054261779 167.8020257 -2.224797199 0.115126123 LEAQHQALVTLWHQLHVDMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEAQHQALVTLWHQLHVDMK 20 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 287.39 6.83E-46 256919000 567007 499145 541165 548668 584179 423174 674891 521247 375561 FALSE TRUE 531519.044 536102.2152 554001.6894 562747.7498 538299.9378 545337.4641 573697.3599 586325.8354 312877.4429 1.69880909 1.713457545 1.770666764 1.798620395 1.720481773 1.74297469 1.833616878 1.873979249 1 18.25523812 -1.220116759 6.840593082 0.99999645 1.767438847 0.950910268 0.054914665 3.05E-06 3.48E-07 0.054565294 0.012861104 0.060239761 1.220116759 0.767442396 LEAS(ph)YSDSPPGEEDLLVHVAEGSK ddPTM_SK-BR-3_Pertuzumab_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(0.991)YS(0.009)DSPPGEEDLLVHVAEGSK;LEAS(0.932)Y(0.001)S(0.062)DS(0.005)PPGEEDLLVHVAEGSK;LEAS(0.999)YS(0.001)DSPPGEEDLLVHVAEGSK 194.19 1.93E-18 107417000 183541 135909 143199 152213 170162 103411 198339 139027 219015 TRUE FALSE 172053.4964 145971.8438 146595.7479 156119.0433 156798.1629 133264.077 168599.9082 156384.827 182459.9816 0.942965657 0.800021147 0.80344055 0.855634435 0.859356455 0.730374276 0.924037736 0.857091104 1 17.47722055 0.763579461 1.02700177 0.998413084 0.830146684 0.387062969 0.060694424 0.791509298 1.538605262 0.05264454 0.016954268 5.802023202 -0.763579461 -0.1682664 LEASYSDS(ph)PPGEEDLLVHVAEGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEASYSDSPPGEEDLLVHVAEGSK 24 0 Q7Z3C6;C9JS65;C9JFV2;F2Z3I6;C9JX27;C9IYZ9;C9JKV7;C9JDK4;C9JXG2;Q7Z3C6-3 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 LEASYS(0.001)DS(0.999)PPGEEDLLVHVAEGSK;LEAS(0.011)YS(0.195)DS(0.794)PPGEEDLLVHVAEGSK 254.96 5.15E-44 212526000 248624 221652 218848 248314 275036 219169 323841 237217 364335 TRUE FALSE 233063.0676 238063.3447 224039.1779 254686.1576 253435.782 282439.5324 275284.0484 266834.0646 303525.1348 0.76785426 0.784328273 0.738123971 0.839094126 0.834974613 0.930530951 0.90695635 0.879116864 1 18.21145646 2.601800727 1.162930683 0.928186484 0.76360301 0.786892316 0.036703217 0.195657592 0.541857929 0.017801329 0.014515107 399.7612801 -2.601800727 -0.164583474 LEAVSHTSDMHR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;;;;; 225.15 1.06E-11 7719940000 2537694 6584360 4006616 4188512 5828670 3372381 4813950 5491420 5361760 FALSE TRUE 2378864.262 7071872.865 4101654.824 4295996.309 5370909.77 4345932.649 4092142.888 6177035.875 4466847.618 0.532559977 1.583190982 0.918243731 0.961751257 1.202393775 0.972930581 0.91611428 1.382862458 1 22.09082561 3.737370323 24.5695933 1.037565951 1.168259572 0 0.291167201 1113.160774 2668504.873 0.0678639 0.12058453 5462.234272 -3.737370323 0.130693621 LECVEPNCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LECVEPNCR 9 0 H0Y5B4;H7BZ11;J3KQN4;P83881;Q969Q0 H0Y5B4;Q969Q0 RPL36A;RPL36A-HNRNPH2;RPL36AL 60S ribosomal protein L36a;60S ribosomal protein L36a-like 0 ;;; 178.94 0.0001172 2139720000 1654110 1846550 1805510 1801500 1759060 1767420 2275260 1580180 2045740 FALSE TRUE 1550582.208 1983270.483 1848337.55 1847729.54 1620910.523 2277645.462 1934105.885 1777468.951 1704292.778 0.909809763 1.163691186 1.084518795 1.084162043 0.951075158 1.336416778 1.134843679 1.042936386 1 20.70074176 LEDAADVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEDAADVYR 9 0 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 161.86 0.00014938 349020000 586480 732750 611330 647440 751360 520940 669660 622460 706640 FALSE TRUE 549773.2637 787003.5724 625831.0363 664054.4065 692351.2164 671326.9212 569250.6998 700175.5012 588697.2189 0.933881197 1.336856277 1.063077956 1.128006699 1.17607353 1.140360273 0.966966858 1.189364377 1 19.16716629 1.901615468 10.9546232 1.04946503 1.148230727 0.077830681 0.114884261 1.087002086 116.0211519 0.043977471 0.028060539 79.72884416 -1.901615468 0.098765698 LEDAGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEDAGVR 7 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 ; 124.34 0.0096679 417520000 798730 919740 920080 914800 1039840 767920 1004140 909930 1000780 FALSE TRUE 748738.9151 987838.5066 941904.7321 938275.3168 958175.1609 989606.0379 853578.529 1023536.764 833743.3527 0.898044839 1.184823247 1.129729825 1.125376669 1.149244738 1.186943242 1.023790506 1.227640089 1 19.66924383 -0.919218122 7.122716378 0.999999998 1.120415312 0.128070268 0.094162384 2.99E-09 4.19E-10 0.080197519 0.018902736 0.120443087 0.919218122 0.120415314 LEDEHLVFFCQMGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LEDEHLVFFCQMGK 14 0 Q8NFU3;Q8NFU3-4;R4GNF9;Q8NFU3-2;Q8NFU3-3 Q8NFU3 TSTD1 Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1 0 ;; 269.7 1.14E-25 1726434000 4086190 3971800 3880570 3801090 4517310 2886610 4711510 3956780 4668170 FALSE TRUE 3830442.662 4265876.205 3972618.953 3898632.405 4162538.695 3719927.447 4005062.815 4450792.693 3889022.269 0.984937189 1.096901974 1.021495553 1.002471093 1.070330383 0.956519965 1.029837974 1.144450297 1 21.89097607 -1.033670178 3.930046215 0.999994608 1.037727839 0.046269778 0.054675339 3242357.816 852889.038 164.9748526 0.011778624 0.09254007 1.033670178 0.037733232 LEDFFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 LEDFFAR 7 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;;;; 198.39 0.00093189 1450156000 3182991 3596215 3542008 3382412 3739856 3083314 3970560 3436365 3987529 FALSE TRUE 2983773.275 3862482.5 3626026.102 3469210.418 3446142.796 3973416.698 3375211.389 3865402.735 3321984.649 0.898189965 1.162703296 1.091524039 1.044318618 1.03737469 1.196097248 1.016022572 1.163582359 1 21.66361398 LEDFRDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 117.04 0.0019666 2472710000 6581410 7774040 6916200 6764030 7501790 5477220 7728350 6915450 8430300 FALSE TRUE 6169491.296 8349638.01 7080255.53 6937606.461 6912629.674 7058404.499 6569555.664 7778859.155 7023228.468 0.878440923 1.188860372 1.008119779 0.98780874 0.984252428 1.005008527 0.935403952 1.107590219 1 22.74370294 3.603664196 5.856949932 0.995308387 1.068178298 0 0.086318429 0.423202934 19.14102354 0.021005252 0.032839157 4014.802597 -3.603664196 0.072869911 LEDFRDYRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEDFRDYRR 9 2 O43707;O43707-2;K7EJH8;F6THM6;P12814-3;P12814;P12814-2;P12814-4;H9KV75;P35609-2;P35609;A0A494C1A0;Q08043;A0A087WSZ2 O43707;P12814-3 ACTN4;ACTN2;ACTN1;ACTN3 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2;Alpha-actinin-3 0 55.567 0.071792 561770000 706750 907580 783570 788920 970390 666820 898620 800190 1192000 FALSE TRUE 662515.7791 974778.1675 802156.6504 809165.0228 894179.4838 859320.1091 763880.2734 900095.4829 993047.4994 0.667154169 0.981602761 0.807772691 0.81483013 0.900439792 0.865336361 0.769228334 0.90639721 1 19.9215032 0.992947358 23.08258178 1.000000007 0.842057676 0.306652166 0.082485924 123.5409091 404341.0879 0.072802935 0.018200734 9.838918376 -0.992947358 -0.157942331 LEDLASLVYLNESSVLHTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEDLASLVYLNESSVLHTLR 20 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;H0YEV9 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 250.04 1.48E-30 166311000 283460 307710 312350 313410 323670 328770 348140 290720 217720 FALSE TRUE 265718.7446 330493.1686 319759.0895 321452.6312 298250.2638 423680.5619 295939.639 327017.032 181381.1255 1.464974616 1.822092391 1.762912699 1.772249623 1.644329106 2.335858049 1.631590047 1.802927571 1 17.46866481 0.103818737 1.82861275 0.999895507 1.792336359 0.543356146 0.224299791 22.54669171 44.47380545 0.197103766 0.053992756 1.270043911 -0.103818737 0.792440851 LEDLCELQLLYQGMQEEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEDLCELQLLYQGMQEEQK 19 0 H0Y876;H7C4R2;Q96JN2-2;Q96JN2;Q96JN2-4 H0Y876 CCDC136 Coiled-coil domain-containing protein 136 0 66.022 0.016059 844400000 388270 565460 474240 486050 748800 433870 542850 588410 1132600 FALSE TRUE 363968.8738 607327.2468 485489.1968 498522.8659 689992.2685 559121.2257 461454.6821 661874.2838 943561.7431 0.385739329 0.643653954 0.514528276 0.528341542 0.731263506 0.592564535 0.489056159 0.701463671 1 19.8477574 -5 0.253843807 3.678139534 0.533939375 0.683588773 0.094919677 108.9957236 1.077545481 151.5972529 0.125930501 1.00E-05 5 -3.144200159 LEDLDTCMMT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 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;LEDLDTCMMT(1)PK;LEDLDTCMMT(1)PK;LEDLDT(0.001)CMMT(0.999)PK;LEDLDT(0.052)CMMT(0.948)PK;LEDLDTCMMT(1)PK 270.16 4.31E-22 2626977000 5569870 3605101 4374088 4115903 4833691 3343577 6613930 4250069 6362110 TRUE FALSE 5221261.779 3872026.429 4477843.433 4221524.039 4454072.407 4308813.401 5622232.597 4780699.47 5300232.74 0.985100473 0.730538944 0.84483902 0.796478994 0.840354118 0.812947961 1.060752022 0.901979159 1 22.33762428 1.752293058 25 0.988585556 0.822836272 0.480850169 0.073990172 3.071350453 5599.423522 0.030566723 0.016950927 56.53183174 -1.752293058 -0.165749284 LEDLITVITQTESHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEDLITVITQTESHR 15 0 A0A2R8YE46;A0A2R8Y6X9;Q9HBG4 A0A2R8YE46 ATP6V0A4 V-type proton ATPase 116 kDa subunit a isoform 4 0 ; 183.41 5.07E-07 105057000 113648 125998 126575 129011 148934 112027 158500 123601 134318 FALSE TRUE 106534.9745 135327.023 129577.4188 132321.6407 137237.3244 144367.3763 134734.3964 139032.8569 111899.4581 0.95205979 1.209362631 1.157980753 1.18250475 1.226434218 1.290152596 1.204066568 1.242480163 1 16.77184352 4.739941651 24.85272934 1.199586676 0.952059702 0.482037968 0.076547846 83.20858836 1497234.479 0.016027707 0.099973975 54946.70457 -4.739941651 -0.247526973 LEDLLQDAQDEKEQLNEYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LEDLLQDAQDEKEQLNEYK 19 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;;; 278.74 1.34E-39 749971000 1779339 966322 1259789 1218694 1274643 832446 1732678 1036766 1431091 FALSE TRUE 1667973.348 1037869.486 1289671.79 1249967.751 1174537.68 1072759.647 1472879.019 1166208.517 1192232.667 1.399033422 0.87052596 1.081728278 1.048426021 0.98515811 0.899790516 1.235395624 0.97817192 1 20.18523438 LEDLLR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 176.25 0.0091956 496526000 1011690 1158640 1003060 965870 1082060 864150 1120820 1118190 840690 FALSE TRUE 948370.1288 1244426.911 1026853.057 990655.8594 997079.3724 1113616.077 952763.4462 1257798.483 700373.4079 1.354092143 1.776804912 1.466150835 1.414468123 1.423639677 1.590031923 1.360364964 1.795896973 1 19.41776478 -1.157149788 4.334138626 0.999883303 1.524924555 0.520934316 0.157510461 10556243.03 2818364.299 11655.77171 0.034324728 0.069638629 1.157149788 0.525041253 LEDLVCDVVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LEDLVCDVVDR 11 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;;;; 185.61 1.02E-05 362121000 572829 486365 531051 524623 504299 610021 662230 503242 253622 FALSE TRUE 536976.6554 522375.9707 543647.7805 538085.7144 464693.3908 786124.1598 562934.7593 566072.8715 211290.8497 2.541409891 2.472307586 2.572983076 2.546658859 2.199306744 3.720578344 2.664264733 2.67911683 1 17.68887077 LEDNDSAAS(ph)DPDAETTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEDNDSAASDPDAETTAR 18 0 Q9BYV8-5;Q9BYV8-2;Q9BYV8;F8WF85;C9J6R3;C9J9X8;C9JCX6;C9JXA0 Q9BYV8-5 CEP41 Centrosomal protein of 41 kDa 1 LEDNDS(0.009)AAS(0.991)DPDAETTAR;LEDNDS(0.02)AAS(0.98)DPDAETTAR 219.22 7.81E-19 366740000 616560 605030 595160 597120 726960 542280 680690 653070 895780 TRUE FALSE 577970.6102 649827.0507 609277.4763 612443.1101 669867.494 698827.4328 578626.8537 734607.2271 746268.531 0.774480748 0.870768395 0.816431956 0.820673906 0.897622593 0.936428918 0.775360115 0.98437385 1 19.50933533 -4.999998867 0.114152049 1.511185136 0.768688644 0.474036107 0.058372408 147.405309 1.108177979 17.23315986 0.613202031 1.00E-05 4.999998867 -0.742496492 LEDQLSEGRNS(ph)PEKAENKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEDQLSEGRNSPEKAENKR 19 3 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 LEDQLSEGRNS(1)PEKAENKR;LEDQLS(0.01)EGRNS(0.99)PEKAENKR 117.4 7.10E-05 235280000 517520 270800 332230 350140 390400 275740 447540 319230 510370 TRUE FALSE 485129.347 290850.3138 340110.6525 359125.1852 359739.5588 355341.6617 380435.5318 359086.5682 425185.9499 1.140981604 0.684054386 0.799910375 0.844630885 0.846075838 0.83573237 0.894750948 0.844540061 1 18.6977344 0.339996088 0.576951342 1.006208915 0.828398899 0.081113197 0.116556282 4.302188767 2.200120661 0.177061347 0.04714663 2.187741919 -0.339996088 -0.177810017 LEDS(ph)EVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEDSEVR 7 0 Q8N163-2;Q8N163;H0YB24;G3V119;A0A087X2B6 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 1 LEDS(1)EVR 118.18 0.0053129 108900000 176950 142440 179950 160780 160960 179800 241770 165370 136580 TRUE FALSE 165875.0154 152986.4058 184218.499 164905.887 148318.8509 231705.3412 205518.833 186016.8085 113783.9157 1.457807234 1.34453455 1.619020561 1.449289964 1.303513331 2.036362871 1.806220429 1.634825164 1 16.79593711 2.267489684 24.99908851 1.711854707 1.448293311 0.05564068 0.276455343 332.8561125 287636.9179 0.086330559 0.07221809 185.1354916 -2.267489684 -0.263561397 LEDSENHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEDSENHR 8 0 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E9PDQ5;E7EUY6;F6SJA5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 0 143.45 0.0012591 0 85094 85769 85131 86875 97404 77931 98556 88388 116300 FALSE TRUE 79768.11844 92119.426 87150.34752 89104.35958 89754.28275 100428.4146 83778.44275 99423.43637 96888.77867 0.823295737 0.950774974 0.899488555 0.919656134 0.926364064 1.036532981 0.864686746 1.026160488 1 16.56404197 8 0.132950154 1.01398906 0.546719089 0.351907477 0.054976769 104.1985503 0.932824762 0.248342337 9.171354149 100000000 -8 -0.467269972 LEDTAGDTGHSSLEAPRS(ph)PDTLAPVASER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEDTAGDTGHSSLEAPRSPDTLAPVASER 29 1 O43310;O43310-2 O43310 CTIF CBP80/20-dependent translation initiation factor 1 LEDTAGDTGHSSLEAPRS(1)PDTLAPVASER;LEDTAGDTGHSSLEAPRS(1)PDTLAPVASER 275.85 2.23E-71 313020000 108486 228150 211810 262280 214520 153399 178025 148609 124923 TRUE FALSE 101696.0549 245042.4634 216834.2332 269010.5488 197672.4645 197682.8011 151331.804 167163.1608 104072.5443 0.977165069 2.354535148 2.08349123 2.584836863 1.899371885 1.899471205 1.454099206 1.606217682 1 16.66722999 1.43012418 0.997447915 1.09051151 2.076389661 0.325588901 0.431520318 0.484920149 0.969129952 0.366124259 0.132455851 26.92304516 -1.43012418 0.985878151 LEDTHFVQCPSVPSHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEDTHFVQCPSVPSHK 16 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3;Q9H1B7 Q7Z5L9;Q9H1B7 IRF2BP2;IRF2BPL Interferon regulatory factor 2-binding protein 2;Interferon regulatory factor 2-binding protein-like 0 180.64 1.41E-09 221950000 415810 374900 372600 430240 424780 378730 588490 381450 450110 FALSE TRUE 389785.1943 402657.9861 381438.248 441280.6868 391419.4923 488063.2028 500251.3878 429074.8722 374983.7332 1.039472275 1.073801209 1.017212786 1.176799546 1.043830592 1.301558333 1.33406157 1.144249295 1 18.51646849 2.246830847 24.99254482 1.237538624 1.068326834 0.22443305 0.102406773 173.2808065 523652.8923 0.033187349 0.027333125 176.5350102 -2.246830847 -0.16921179 LEDVEDELIREEVILS(ph)PVPSVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LEDVEDELIREEVILSPVPSVLK 23 1 Q4G0A6 Q4G0A6 FAM188B Protein FAM188B 1 LEDVEDELIREEVILS(0.999)PVPS(0.001)VLK;LEDVEDELIREEVILS(1)PVPSVLK;LEDVEDELIREEVILS(1)PVPSVLK;LEDVEDELIREEVILS(1)PVPSVLK 151.65 4.28E-08 78605000 157440 149533 163905 222189 240402 112462 168522 128914 212654 TRUE FALSE 147586.1114 160604.5789 167792.904 227890.7459 221521.7967 144927.9537 143253.6906 145009.1967 177160.6736 0.833063616 0.906547574 0.947122748 1.28635064 1.25040051 0.818059397 0.808608861 0.81851798 1 17.43469886 LEDVKNS(ph)PTFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LEDVKNSPTFK 11 1 H0YC42;P55327-2;P55327-3 H0YC42;P55327-2 1 LEDVKNS(0.935)PT(0.065)FK;LEDVKNS(0.685)PT(0.315)FK;LEDVKNS(1)PTFK;LEDVKNS(0.997)PT(0.003)FK 214.45 8.20E-12 4226970000 8310380 4372100 6192550 8232590 7037050 2998610 5046030 2842590 3815420 TRUE FALSE 7790248.15 4695814.833 6339440.21 8443852.197 6484388.479 3864260.029 4289424.647 3197493.619 3178601.753 2.450841205 1.477320909 1.9944116 2.656467482 2.040012868 1.215710658 1.349469037 1.005943452 1 21.59996084 2.235211328 7.609541571 1.190417294 2.043266864 0.685893174 0.326703495 0.0884007 33.93037638 0.124793243 0.097258143 171.8744528 -2.235211328 0.852849571 LEEAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEEAEK 6 0 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;H0YL80;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5;H0YKP3;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;P67936-2;A0A2R8YHD2;Q8ND24;E9PN76;Q8ND24-2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2;Q8ND24 TPM3;TPM1;TPM4;RNF214 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain;RING finger protein 214 0 ; 138.62 0.028444 847170000 1875980 1497480 1627740 1574400 1666520 1189860 1978920 1420420 1724090 FALSE TRUE 1758565.761 1608354.977 1666350.761 1614801.769 1535638.242 1533353.266 1682199.317 1597762.564 1436328.241 1.224348105 1.119768401 1.160146208 1.124256784 1.069141578 1.067550733 1.171180284 1.112393754 1 20.45395405 -5 0.099322262 0.616156499 1.216487716 0.542083197 0.042093713 165.6794295 1.12211304 13.48774988 0.728212457 1.00E-05 5 0.600331217 LEEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEEALR 6 0 A0A1B0GUG6;A0A1B0GTG4;Q86WH2;Q8WWW0-2;Q8WWW0;Q155Q3-2;Q155Q3 A0A1B0GUG6 RASSF3;RASSF5;DIXDC1 Ras association domain-containing protein 3;Ras association domain-containing protein 5;Dixin 0 ; 119.22 0.049314 166981000 450050 447940 454210 447570 369240 321905 500110 377750 476420 FALSE TRUE 421882.1739 481105.9437 464984.0757 459055.4039 340241.3798 414833.7478 425123.1483 424912.919 396902.4242 1.062936753 1.212151689 1.171532466 1.156595112 0.857241879 1.045178166 1.071102423 1.070572748 1 18.59842485 2.952456847 24.99982773 1.019582244 1.165469505 0.489091318 0.071005728 319.5406978 168025.4137 0.020980998 0.022254212 896.3071214 -2.952456847 0.145887261 LEECVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LEECVR 6 0 P24534 P24534 EEF1B2 Elongation factor 1-beta 0 ;;;; 178.98 0.0078552 2966040000 2571190 2867020 2784050 2784240 2838050 2505740 3158300 2432680 2774090 FALSE TRUE 2410263.808 3079297.144 2850088.981 2855688.312 2615161.001 3229106.461 2684742.235 2736405.453 2311076.458 1.042918247 1.332408166 1.23323007 1.235652894 1.131577016 1.397230477 1.161684732 1.184039344 1 21.14013356 0.775852911 1.551884208 1.001003932 1.236765973 0.317980152 0.098930211 0.804441182 3.352454147 0.083653888 0.024232902 5.96833114 -0.775852911 0.235762041 LEEEDEDEEDGESGCTFLVGLIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LEEEDEDEEDGESGCTFLVGLIQK 24 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;;; 221.41 9.29E-33 243363000 259704 223617.6 233612.4 240139.9 264985 201675.7 340695 245485 368423 FALSE TRUE 243449.5902 240174.4798 239153.7964 246302.2964 244174.147 259896.2007 289610.9476 276134.3426 306930.8212 0.79317414 0.782503624 0.779178173 0.802468437 0.795534792 0.846758236 0.943570758 0.899663128 1 18.227554 1.781432244 1.011237522 0.977108855 0.781790349 0.909611134 0.022798406 0.125574555 0.238572278 0.017914982 0.007429241 60.45500263 -1.781432244 -0.195318506 LEEEPS(ph)ASSPQYACDFNLFLEDSADNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEEEPSASSPQYACDFNLFLEDSADNR 27 0 Q2NKX8;B5MDQ0 Q2NKX8 ERCC6L DNA excision repair protein ERCC-6-like 1 LEEEPS(0.372)AS(0.261)S(0.352)PQY(0.016)ACDFNLFLEDSADNR 99.838 0.0021021 23060000 24753 24031 24974 29474 23715 17725 21100 16037 15962 TRUE FALSE 23203.75392 25810.28024 25566.39507 30230.35274 21852.51956 22841.91976 17936.25088 18039.25475 13297.83908 1.744926659 1.940937929 1.922597718 2.273328212 1.643313581 1.717716662 1.34880944 1.35655535 1 13.6989042 1.664016045 0.967848469 1.065187417 1.952199375 0.795360854 0.162363173 0.208702122 0.371738152 0.134842694 0.053718682 46.13346182 -1.664016045 0.887011958 LEEEPSASS(ph)PQYACDFNLFLEDSADNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LEEEPSASSPQYACDFNLFLEDSADNR 27 0 Q2NKX8;B5MDQ0 Q2NKX8 ERCC6L DNA excision repair protein ERCC-6-like 1 LEEEPSAS(0.025)S(0.969)PQY(0.005)ACDFNLFLEDSADNR;LEEEPS(0.003)AS(0.112)S(0.882)PQY(0.003)ACDFNLFLEDSADNR;LEEEPS(0.027)AS(0.104)S(0.741)PQY(0.127)ACDFNLFLEDSADNR 200.12 3.22E-25 119826000 109998 111990 121298 136294 123858 95761 106262 75459.3 79960.1 TRUE FALSE 103113.4215 120281.8561 124175.2458 139791.5348 114130.6923 123405.6462 90328.99959 84880.55971 66614.24275 1.547918542 1.805647729 1.864094535 2.098523214 1.713307659 1.852541454 1.356001297 1.274210382 1 16.02354305 1.482933906 1.507746704 1.054416695 1.836122502 0.791055855 0.149613065 0.153562883 0.6661293 0.12482596 0.04119157 30.40422277 -1.482933906 0.781705807 LEEEVDDVFLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEEEVDDVFLIR 12 0 H0Y8R1;F5H5I6;H0YAK1;Q12849 H0Y8R1 GRSF1 G-rich sequence factor 1 0 145.89 0.00014953 4064200 12528 13047 12750 9621.4 12978 16634 15148 12597 13558 FALSE TRUE 11743.89484 14013.01346 13052.43602 9868.301413 11958.76023 21435.96577 12876.69803 14169.76318 11295.08221 1.039735225 1.240629611 1.155585747 0.873681238 1.05875814 1.897814055 1.140026941 1.254507308 1 13.46340715 LEEGVAS(ph)DEEAEEAQPGSGPSPEPEGSPPAHPQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEEGVASDEEAEEAQPGSGPSPEPEGSPPAHPQ 33 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;A1L2Z2 Q7Z406 MYH14 Myosin-14 1 LEEGVAS(1)DEEAEEAQPGSGPSPEPEGSPPAHPQ;LEEGVAS(1)DEEAEEAQPGSGPSPEPEGSPPAHPQ 174.73 4.42E-15 329470000 43980 50428 47932 51999 58025 37538 57111 52937 63221 TRUE FALSE 41227.37031 54161.74159 49068.96968 53333.38237 53467.95056 48374.61122 48547.73574 59546.30098 52669.00668 0.782763392 1.028341809 0.931647904 1.012614168 1.015169147 0.918464468 0.921751497 1.130575736 1 15.68466663 4.746555859 24.72055683 0.983446479 0.782763276 0.516112107 0.06368825 714.2569834 2208357.809 0.014257534 0.155688911 55789.93552 -4.746555859 -0.200683203 LEEHQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEEHQAR 7 0 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 149.4 0.0020189 157090000 327180 332190 315860 301290 383290 259520 341400 333790 464310 FALSE TRUE 306702.3878 356785.6932 323352.3484 309021.6115 353187.9495 334439.211 290210.2394 375464.4163 386813.6614 0.792894405 0.922370973 0.835938284 0.798890118 0.913069999 0.864600309 0.750258505 0.970659658 1 18.56127922 1.08856842 7.425031076 0.999385148 0.845324411 0.570422424 0.052670155 0.156537817 10.38796754 0.05042905 0.01264063 12.2622007 -1.08856842 -0.154060737 LEEIEADKAPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEEIEADKAPAR 12 1 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 110.38 0.0013645 233650000 407640 351410 342950 347060 385150 344670 418170 310670 461470 FALSE TRUE 382126.5401 377428.762 351084.936 355966.1472 354901.8726 444170.6338 355469.2906 349457.8334 384447.6758 0.993962414 0.981742863 0.913219036 0.925915722 0.923147401 1.155347429 0.924623331 0.908986724 1 18.55242773 LEELHVIDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LEELHVIDVK 10 0 Q16531;F5GY55;F5H2L3;F5GWI0 Q16531 DDB1 DNA damage-binding protein 1 0 ;;; 164.97 6.00E-06 851870000 4066020 3197460 3419240 2876570 3832570 2317009 4403750 3073110 4375110 FALSE TRUE 3811535.066 3434203.265 3500345.987 2950387.656 3531575.412 2985891.885 3743448.57 3456794.548 3644875.877 1.045724243 0.942200333 0.960347103 0.809461764 0.968915138 0.819202625 1.027044184 0.948398427 1 21.79743825 -0.177058538 7.685444284 0.999999999 0.940175418 0.057979703 0.075800762 0 0 0.066616701 0.015701707 0.66518349 0.177058538 -0.059824581 LEELKESILADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEELKESILADK 12 1 O75832;B1AJY5;B1AJY7;O75832-2;B1AJY6 O75832 PSMD10 26S proteasome non-ATPase regulatory subunit 10 0 160.31 6.24E-05 56951000 323090 239910 258520 265790 337720 176030 344490 258440 374240 FALSE TRUE 302868.3736 257673.186 264652.2165 272610.6214 311196.8335 226847.0034 292836.9226 290706.8029 311776.9263 0.971426517 0.826466503 0.848851195 0.874377154 0.998139398 0.727593944 0.939251426 0.932419234 1 18.25015464 1.210869968 2.205370774 0.989233294 0.870250884 0.197808634 0.07651889 0.401660814 3.387168938 0.064064683 0.018331765 16.25062125 -1.210869968 -0.118982411 LEELTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEELTNR 7 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 163.34 0.0028812 502810000 364470 400710 388680 411320 459030 354170 446200 341920 495930 FALSE TRUE 341658.4733 430378.9853 397899.6731 421875.1676 422979.6354 456413.1295 379296.4523 384609.4647 413156.0792 0.826947709 1.041686198 0.963073505 1.021103619 1.023776865 1.104699053 0.918046403 0.93090598 1 18.65632737 4.747400797 24.59508173 0.999397437 0.826947598 0.501566283 0.054335531 807.0555861 2245322.519 0.01276696 0.151755744 55898.5828 -4.747400797 -0.172449839 LEEPPELNRQS(ph)PNPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LEEPPELNRQSPNPR 15 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR 199.15 4.58E-09 21914690000 4761720 5286370 4834800 4998480 5718910 4067270 5880080 4673970 5367450 TRUE FALSE 4463692.445 5677778.335 4949483.739 5126749.459 5269769.878 5241424.822 4998416.592 5257525.443 4471587.92 0.998234302 1.269745432 1.106873851 1.146516529 1.178500786 1.172161862 1.11781691 1.175762512 1 22.09235581 -1.636850493 2.442616341 0.980170616 1.152902693 0.302699611 0.068729533 3645571.53 2973779.87 455894.4024 0.015865386 0.023075414 1.636850493 0.172732077 LEEPTPAPSTSYS(ph)PQADSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEEPTPAPSTSYSPQADSLR 20 0 G3V1L9;Q07157 G3V1L9 TJP1 Tight junction protein ZO-1 1 LEEPTPAPSTSYS(1)PQADSLR 242.9 8.64E-30 115500000 53271 59024 55771 59701 69840 44880 56435 54593 85137 TRUE FALSE 49936.8632 63394.19837 57093.91446 61233.02873 64355.04812 57836.12743 47973.09567 61409.05622 70927.08469 0.704059153 0.893793938 0.804966321 0.863323637 0.907340946 0.815430772 0.676372022 0.865805446 1 16.11404903 -2.498247283 1.857547897 2.550433005 0.81595268 0.368905485 0.075472027 1837531.393 121458.3047 11972082.43 0.018674696 0.003175066 2.498247283 -1.734480325 LEEQAAQHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEEQAAQHK 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 ; 129.85 0.00037767 341880000 419560 443520 420350 424120 482290 312550 505320 421250 440290 FALSE TRUE 393300.4885 476358.6823 430320.9005 435003.6372 444412.8889 402778.1112 429551.9572 473843.9898 366802.7546 1.072239735 1.29867804 1.173167036 1.185933398 1.211585473 1.098078207 1.171070696 1.291822332 1 18.48464495 -1.805032022 2.828264205 0.946193922 1.191543692 0.406119347 0.071252913 8837584.387 7740697.949 3261327.058 0.016594321 0.015666356 1.805032022 0.24534977 LEEQLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LEEQLGR 7 0 Q9BR76;A9Z1Z3-3;A9Z1Z3 Q9BR76 CORO1B;FER1L4 Coronin-1B;Fer-1-like protein 4 0 ;;;; 204.1 0.00063089 1215460000 1427080 1732820 1556180 1694120 1660360 1346920 1841400 1432690 1764390 FALSE TRUE 1337761.61 1861119.796 1593093.324 1737593.987 1529962.023 1735753.939 1565299.165 1611564.5 1469901.911 0.910102641 1.266152375 1.083809275 1.182115606 1.040859946 1.180863788 1.064900422 1.096375539 1 20.48728845 0.706997094 0.724681445 0.999338261 1.127074135 0.081067518 0.09656791 2.14056975 2.175710919 0.087287944 0.03147658 5.093274627 -0.706997094 0.127735874 LEEQRPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 11527000000 8264500 8467200 8701700 8340100 8197500 7487200 9212400 7000300 8185000 FALSE TRUE 7747239.698 9094120.298 8908108.433 8554121.086 7553701.417 9648633.095 7831086.144 7874302.865 6818870.623 1.136147043 1.333669577 1.306390593 1.254477693 1.107764296 1.414989905 1.14844328 1.154781092 1 22.70110138 1.056128278 1.375117298 1.004230208 1.26670413 0.419907982 0.093386749 0.361300331 1.390795374 0.080656947 0.024451222 11.37963357 -1.056128278 0.262473922 LEETDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LEETDRR 7 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RQT0;C9J165;A0A0U1RR66;A0A0U1RQL2;A0A0U1RQJ6;A0A0U1RRJ7 P47897 QARS Glutamine--tRNA ligase 0 ;;; 184.89 0.00099642 2550080000 3175661 3522550 3419044 3556138 3674517 2969006 4019860 3261930 3605760 FALSE TRUE 2976902.047 3783363.267 3500145.338 3647394.522 3385935.257 3826109.834 3417119.312 3669189.141 3003935.362 0.9910007 1.259468934 1.165186636 1.214205395 1.127166483 1.273699122 1.13754755 1.22146075 1 21.51842234 -1.070905938 6.846226831 0.999999921 1.181637857 0.309581697 0.080762831 8.37E-08 1.13E-08 0.066853506 0.015757516 0.084936442 1.070905938 0.181637936 LEEVMQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LEEVMQELR 9 0 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;;;; 179.36 0.00011608 351745000 554552 707146 535379 521556 600748 451335 606676 609666 496414 FALSE TRUE 519843.5802 759503.8256 548078.4427 534940.01 553567.6754 581628.0877 515710.5659 685784.1421 413559.2964 1.256998899 1.836505266 1.325271726 1.293502563 1.338544872 1.406395873 1.247005134 1.658248643 1 18.65773467 -4.081354793 0.124012758 5.27E-14 1.628699079 0.255268487 0.198372582 140.5225966 1.399026789 38.24940998 1.732984466 8.29E-05 4.081354793 1.628699079 LEEWLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LEEWLGR 7 0 P56192;P56192-2 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;; 139.92 0.0061873 257080000 241798 272366 270315 276789 269413 250319 312448 245167 279880 FALSE TRUE 226664.2948 292532.262 276726.9995 283891.8743 248254.3897 322582.0317 265599.323 275776.6396 233166.2199 0.972114635 1.254608245 1.186822858 1.217551472 1.06470993 1.383485274 1.139098636 1.182746968 1 17.83099927 -0.415161925 7.355092627 0.999997591 1.187026202 0.195493844 0.109320603 0 0 0.092030964 0.021691906 0.384448415 0.415161925 0.187028611 LEFLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEFLHK 6 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 118.06 0.022193 903390000 1857420 1712010 1803400 1682930 1903170 1363440 2216110 1750510 1844380 FALSE TRUE 1741167.398 1838769.002 1846177.5 1726116.833 1753702.705 1757042.994 1883824.879 1969065.027 1536541.063 1.133173359 1.196693695 1.201515237 1.123378265 1.141331493 1.143505395 1.226016619 1.281491966 1 20.55125489 LEGDHTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEGDHTIR 8 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 0 111.95 0.0056896 0 128450 176770 182840 192910 182940 163020 179140 168570 126110 FALSE TRUE 120410.5438 189858.2347 187177.0511 197860.3972 168572.6303 210081.2276 152279.6201 189616.3356 105061.4263 1.146096603 1.807116479 1.781596326 1.883282991 1.604514961 1.999603803 1.449434159 1.804814024 1 16.68087355 -0.76004049 6.19707825 0.999999985 1.702952931 0.4375471 0.243123643 4.36E-08 8.55E-09 0.209171537 0.049302203 0.173763882 0.76004049 0.702952945 LEGDSDDLLEDS(ph)DSEEHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LEGDSDDLLEDSDSEEHSR 19 0 Q9NR09;A0A3B3IUB9 Q9NR09 BIRC6 Baculoviral IAP repeat-containing protein 6 1 LEGDSDDLLEDS(1)DSEEHSR;LEGDSDDLLEDS(1)DSEEHSR;LEGDSDDLLEDS(1)DSEEHSR;LEGDSDDLLEDS(0.999)DS(0.001)EEHSR;LEGDSDDLLEDS(1)DSEEHSR;LEGDSDDLLEDS(0.998)DS(0.002)EEHSR 400.14 5.97E-128 3232420000 2102300 2211910 2224770 2369430 2301760 1872150 2833170 2116710 1814000 TRUE FALSE 1970720.796 2375682.118 2277542.595 2430233.585 2120989.054 2412609.313 2408362.46 2380985.903 1511231.681 1.304049419 1.572017148 1.507077057 1.608114504 1.403483715 1.596452313 1.59364212 1.575526726 1 20.52729342 -0.984943864 4.992008162 0.999995453 1.530798712 0.735488404 0.097822994 4.45E-06 9.05E-07 0.085182369 0.020077505 0.103527598 0.984943864 0.530803259 LEGELHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEGELHK 7 0 Q6P9F0-2;Q6P9F0 Q6P9F0-2 CCDC62 Coiled-coil domain-containing protein 62 0 70.912 0.055741 142110000 332740 326110 319530 356410 377020 244260 364070 316720 437400 FALSE TRUE 311914.3974 350255.5237 327109.4025 365556.084 347410.37 314773.8968 309481.0834 356263.1892 364395.1143 0.855978538 0.961197091 0.897677794 1.003186019 0.95338921 0.863825788 0.849300858 0.97768377 1 18.47514409 3.564233881 0.004379012 1.835707002 1.16E-07 0.082525599 0.056630063 110995.2545 117.664521 24165.29973 25162.91063 3666.349656 -3.564233881 -1.835706887 LEGELQAPDLELSLPAIHVEGLDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEGELQAPDLELSLPAIHVEGLDIK 25 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 194.77 1.18E-18 210830000 469200 389000 409380 425080 498940 324930 504860 379590 581790 FALSE TRUE 439833.6095 417801.9648 419090.6869 435988.2725 459755.265 418732.0162 429160.9299 426982.6471 484685.4905 0.907461886 0.862006338 0.864665221 0.899528212 0.948564118 0.863925214 0.885442082 0.880947863 1 18.88668937 -1.805096254 2.409056347 1.038853306 0.885422855 0.638503508 0.02610425 5779622.797 3661061.77 1309727.903 0.006814175 0.015664039 1.805096254 -0.153430451 LEGENTQDKNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEGENTQDKNK 11 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 141.13 3.49E-05 807940000 1141970 780710 913230 911660 1082370 647890 1205730 839430 1592110 FALSE TRUE 1070496.136 838514.5807 934892.2469 935054.739 997365.0263 834925.3254 1024941.98 944234.6833 1326376.556 0.807083126 0.63218441 0.704846782 0.70496929 0.751947116 0.62947835 0.772738311 0.71189036 1 20.33905898 -0.729716071 0.533327094 1.063307533 0.698317984 0.716957663 0.056098931 6.637794822 1.355364346 0.772411213 0.022580505 0.186330491 0.729716071 -0.364989549 LEGFHTQISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LEGFHTQISK 10 0 Q06323;Q06323-3;Q06323-2;H0YKK6;H0YLU2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;; 165.63 5.79E-06 5131220000 6589710 7173760 6637450 6558850 8034180 5061220 7994530 6702730 7512730 FALSE TRUE 6177271.814 7704912.655 6794893.448 6727161.195 7403207.911 6522312.052 6795824.444 7539580.595 6258806.829 0.986972754 1.231051359 1.085653166 1.074831254 1.182846525 1.042101511 1.085801916 1.204635452 1 22.57745622 -1.706709834 2.674452655 0.981001614 1.115753617 0.176486819 0.075411416 23767700.96 17276475.29 3004291.089 0.016962976 0.019646725 1.706709834 0.134752003 LEGGRQDS(ph)EDEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEGGRQDSEDEEER 14 1 A0A3B3ISZ4;Q9BYE7-3;Q9BYE7 A0A3B3ISZ4 PCGF6 Polycomb group RING finger protein 6 1 LEGGRQDS(1)EDEEER;LEGGRQDS(1)EDEEER 155.49 3.53E-06 1460950000 667200 761650 712940 716600 779450 602010 814110 618800 846440 TRUE FALSE 625441.143 818043.3585 729851.2735 734989.1692 718235.1412 775800.5142 692041.7633 696058.5421 705163.6958 0.886944615 1.160075828 1.035009712 1.042295815 1.018536753 1.10017081 0.981391651 0.987087887 1 19.42759868 1.646870212 8.806493627 0.988127228 1.052724174 0.090143445 0.069180052 0.202967652 29.38701723 0.031390884 0.016443149 44.34760919 -1.646870212 0.064596946 LEGPVS(ph)PDVEPGKEETEESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEGPVSPDVEPGKEETEESK 20 1 O14686;O14686-3;A0A3B3ISC8 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 LEGPVS(1)PDVEPGKEETEESK 196.28 1.07E-21 275530000 1376200 586770 857530 830840 802970 590240 1080900 667520 1060500 TRUE FALSE 1290066.099 630215.0613 877871.0166 852160.761 739907.9752 760632.7063 918829.0796 750861.3414 883495.6989 1.460183791 0.713319897 0.993633605 0.964533005 0.837477733 0.860935381 1.039992703 0.849875492 1 19.75286359 4.751382667 25 0.908242344 1.460184139 0.761845446 0.097116762 1040.262185 2028232.035 0.022634444 0.420470818 56413.45087 -4.751382667 0.551941795 LEGVDGGQS(ph)PR ddPTM_SK-BR-3_Pertuzumab_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 234.83 1.74E-15 3123010000 4060670 4301640 4316670 4271100 4485230 3373270 4740270 3547360 3480270 TRUE FALSE 3806519.913 4620137.901 4419063.451 4380703.657 4132978.128 4347078.289 4029510.52 3990255.705 2899390.454 1.312869023 1.593485933 1.524135339 1.510905043 1.425464488 1.49930765 1.389778502 1.376239513 1 21.4673182 0.333809786 0.590600119 0.979421617 1.508063531 0.786626798 0.076026985 0.941197747 0.497711502 0.112459881 0.029867458 2.156799559 -0.333809786 0.528641914 LEGVLAEVAQHYQDTLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEGVLAEVAQHYQDTLIR 18 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 233.63 9.55E-24 608480000 1046760 935470 829240 798460 879060 556240 945620 749770 1282940 FALSE TRUE 981245.1601 1004733.172 848909.9644 818949.8354 810022.1736 716817.4582 803833.0597 843380.4349 1068809.026 0.918073422 0.940049296 0.794257855 0.766226534 0.757873628 0.670669353 0.752082964 0.789084312 1 20.02757267 3.840110414 1.997904865 0.766108472 0.930831361 0.290277735 0.085039082 0.314534076 2.459666954 0.021335165 0.049466859 6920.068827 -3.840110414 0.16472289 LEHDVNIQFPDKDDGNQPQDQITITGYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEHDVNIQFPDKDDGNQPQDQITITGYEK 29 1 Q00341;A0A024R4E5;Q00341-2 Q00341 HDLBP Vigilin 0 276.9 2.05E-71 359570000 653420 388940 503500 461050 487210 391210 654490 411060 659570 FALSE TRUE 612523.6086 417737.5223 515443.2578 472881.3236 448946.4919 504145.9762 556355.3005 462381.7459 549483.506 1.114726105 0.760236691 0.938050464 0.86059239 0.817033609 0.917490645 1.012505916 0.841484304 1 19.06771665 1.998797202 24.90723699 0.95578929 0.88174566 0.039456657 0.102787078 94.45143536 1955899.462 0.035240471 0.025682482 99.72342873 -1.998797202 -0.074043629 LEHEISHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LEHEISHLK 9 0 P12270 P12270 TPR Nucleoprotein TPR 0 ;; 147.75 5.30E-05 268362000 333883 309851 314219 308100 332451 254555 364963 316578 325655 FALSE TRUE 312985.859 332792.6904 321672.4231 316006.3676 306341.6395 328040.8961 310240.1863 356103.4602 271301.0767 1.153647685 1.226654514 1.185665855 1.164781104 1.129157478 1.209139677 1.143527295 1.312576657 1 18.04953525 -1.19725927 4.26654205 0.999929217 1.188302173 0.567247812 0.052295379 3.14E-05 5.91E-06 0.045152287 0.010638502 0.063495176 1.19725927 0.188372956 LEHEVDLCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LEHEVDLCR 9 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;A0A087X1S3 Q7Z6Z7-2;A0A087X1S3 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ;; 125.56 0.00049806 144380000 294736 420600 368154 394378 473280 316458 437610 417050 491786 FALSE TRUE 276288.9999 451741.6616 376886.7867 404498.4072 436110.4979 407814.2873 371994.4431 469119.6105 409703.7395 0.674362895 1.102605659 0.919900773 0.987294887 1.064453301 0.995388248 0.907959599 1.145021549 1 18.64422154 4.749313849 24.80635021 1.004338683 0.674362686 0.67243305 0.07443861 846.5490814 1952839.968 0.016670418 0.244156023 56145.35717 -4.749313849 -0.329975997 LEHEVFDAGEVFGIMQVEEVEEEEDEAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 LEHEVFDAGEVFGIMQVEEVEEEEDEAAR 29 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ;;;;;;;; 280.47 2.40E-71 540409800 222576 245028 260147 254287 272302 228856.8 294738 242449 269388 FALSE TRUE 208645.3655 263170.1281 266317.8097 260812.4349 250916.4993 294924.043 250544.7731 272719.2913 224425.4025 0.929686939 1.172639662 1.186665176 1.162134197 1.118039654 1.314129505 1.116383307 1.215189049 1 17.77587646 4.738842196 24.99999653 1.170680675 0.929686905 0.44666358 0.080098634 18.06871988 1603478.721 0.016208805 0.094600079 54807.77804 -4.738842196 -0.24099377 LEHEYIQNFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LEHEYIQNFK 10 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ;;; 173.32 3.45E-06 3719530000 8077750 7475060 7844400 7531120 8625500 6010720 9339200 7274880 10143100 FALSE TRUE 7572178.047 8028521.22 8030472.872 7724381.289 7948088.024 7745917.288 7938873.661 8183164.782 8450151.083 0.896099723 0.950103867 0.950334828 0.914111619 0.940585316 0.916660213 0.939494878 0.968404553 1 23.01054571 1.049736456 2.415928244 0.999525258 0.93268226 0.659182238 0.01711006 0.170912659 2.099871232 0.015788574 0.004317423 11.21337783 -1.049736456 -0.066842999 LEHGDGGILDLDDILCDVADDKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LEHGDGGILDLDDILCDVADDKDR 24 1 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 0 ;;; 263.71 2.07E-44 97946000 319957 195661 235701 222378 272457 219979 359352 211652 310848 FALSE TRUE 299931.4625 210147.944 241291.939 228084.596 251059.3263 283483.3662 305470.5037 238077.2181 258965.4606 1.158190987 0.811490241 0.931753364 0.88075296 0.969470313 1.094676354 1.179580099 0.919339658 1 17.98240017 2.3742188 4.236024437 1.07637419 0.921183326 0.125927519 0.111389009 0.26230694 8.519347181 0.037526147 0.030938767 236.711196 -2.3742188 -0.155190864 LEHGQATAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LEHGQATAK 9 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 145.25 9.76E-05 909850000 1338330 1489780 1407080 1384120 1570110 981010 1644110 1402100 1531670 FALSE TRUE 1254566.314 1600084.861 1440456.602 1419638.863 1446799.894 1264211.662 1397590.969 1577155.271 1276024.382 0.983183654 1.25396104 1.128862914 1.112548383 1.133834051 0.990742559 1.095269799 1.235991485 1 20.28322447 2.999969003 1.804632638 1.08785764 1.151928252 0 0.094332019 0.912628311 6.007978412 0.030923133 0.036719078 999.9286298 -2.999969003 0.064070611 LEHLSS(ph)LPTQMDYKGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEHLSSLPTQMDYKGQK 17 1 A0A5F9YFS9 A0A5F9YFS9 1 LEHLS(0.009)S(0.969)LPT(0.021)QMDY(0.001)KGQK 67.43 0.049173 187810000 471050 199600 277010 339430 313070 157770 219370 139840 232900 TRUE FALSE 441567.8213 214378.5917 283580.808 348140.3485 288482.7451 203315.6378 186477.505 157299.3318 194027.4854 2.275800361 1.104887749 1.461549674 1.794283669 1.486813811 1.047870292 0.961088088 0.810706439 1 17.56590151 2.19927256 3.429337765 0.936510759 1.544700556 0.544688759 0.301500811 0.208258245 5.077294457 0.118233504 0.086009694 158.2240732 -2.19927256 0.608189797 LEHQGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LEHQGIR 7 0 O75436;S4R3Q6;O75436-2 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ;;; 129.68 0.0036367 752370000 601778 772810 636940 633295 769110 491852 676558 701589 667189 FALSE TRUE 564113.7892 830029.6565 652048.5176 649546.4219 708707.203 633841.6878 575114.4088 789183.931 555830.8457 1.014901914 1.493313412 1.173106032 1.16860449 1.275041154 1.140349969 1.034693222 1.41982752 1 19.08428637 3.716192352 22.14679668 1.168298818 1.301758845 0.022381968 0.16351009 172.8903084 350354.7961 0.039467413 0.061992161 5202.263573 -3.716192352 0.133460028 LEHSSSVQEDSES(ph)PSPEDIPDYLLQYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEHSSSVQEDSESPSPEDIPDYLLQYR 27 0 Q9HB65-2;Q9HB65 Q9HB65-2 ELL3 RNA polymerase II elongation factor ELL3 1 LEHSSSVQEDS(0.001)ES(0.97)PS(0.029)PEDIPDYLLQYR 211.19 6.84E-26 50009000 13535 23238 16823 16425 29786 13040 25491 23001 28393 TRUE FALSE 12687.86851 24958.5657 17222.0495 16846.49331 27446.72771 16804.43631 21668.8612 25872.72548 23654.02487 0.53639364 1.055150903 0.728081145 0.712204092 1.160340697 0.710426086 0.916075015 1.093798016 1 14.52979807 1.421728566 5.247015766 1.040947074 0.8415476 0.208447742 0.180082754 0.326274897 15.68936107 0.110609243 0.041199696 26.40757765 -1.421728566 -0.199399473 LEIEPEWAYGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEIEPEWAYGK 11 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ; 202.05 9.62E-08 65368000 233520 208373 227270 214720 224430 186718 264860 204385 226100 FALSE TRUE 218904.4 223801.1537 232660.9517 220230.0787 206804.1731 240620.4555 225146.7018 229902.9172 188362.4493 1.162144583 1.188141026 1.235176929 1.169182496 1.097905521 1.277433248 1.195284424 1.220534761 1 17.52315186 -1.231647646 3.759188025 0.999746828 1.196633661 0.619236119 0.04755076 5061960.231 11220953.06 15060.19824 0.010787761 0.058661391 1.231647646 0.196886833 LEIFHPFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEIFHPFFK 9 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 0 113.22 0.0018358 35796000 175980 202000 187770 185080 264730 158630 226140 220630 319430 FALSE TRUE 164965.7259 216956.2902 192223.9931 189829.4661 243939.1737 204423.9059 192232.4064 248176.1412 266115.0694 0.619903737 0.815272471 0.722334115 0.713336026 0.91666802 0.768178617 0.72236573 0.932589581 1 18.02169068 -5 0.122301153 1.788269557 0.658568892 0.528514557 0.080737219 128.5134613 1.013531233 24.71704796 0.700671018 1.00E-05 5 -1.129700665 LEILSGDHEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LEILSGDHEQR 11 0 Q4G0J3;Q4G0J3-3;H0YA82;Q4G0J3-2 Q4G0J3 LARP7 La-related protein 7 0 ;;; 234.3 1.71E-15 642150000 672240 871420 812310 867510 860260 672410 900960 775840 875250 FALSE TRUE 630165.6984 935940.8435 831578.3768 889771.7753 792698.6497 866523.8513 765869.4121 872705.3318 729165.1207 0.864229076 1.283578735 1.140452763 1.220261022 1.087131882 1.188378087 1.050337421 1.196855564 1 19.47588603 1.740671923 24.99999999 1.091123561 1.151214901 0.014255972 0.120829653 1.098153247 13085.68479 0.050537242 0.028025353 55.03917596 -1.740671923 0.060091339 LEIS(ph)PDSS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEISPDSSPER 11 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 2 LEIS(1)PDS(0.004)S(0.996)PER 208.27 2.94E-08 123650000 410610 453180 446920 402090 464360 369500 411320 390930 426470 TRUE FALSE 384910.6531 486733.9187 457521.1535 412408.3101 427891.0387 476168.6517 349646.3845 439738.471 355289.4019 1.083372178 1.369964643 1.287742193 1.160767273 1.204345068 1.34022757 0.984117124 1.237690932 1 18.43863513 1.458427715 0.59162245 1.012351467 1.272366913 0.235217361 0.11569059 0.816994213 0.677319332 0.106375868 0.054757819 28.73609262 -1.458427715 0.260015446 LEKHELIEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LEKHELIEFR 10 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 166.14 3.39E-06 1454080000 1480290 1800400 1603340 1777980 2073540 1181440 2009900 1666640 2206870 FALSE TRUE 1387641.291 1933703.489 1641371.982 1823605.977 1910692.533 1522502.549 1708534.154 1874723.673 1838529.14 0.754756213 1.051766571 0.892763648 0.991883097 1.039250611 0.828109012 0.92929403 1.019686679 1 20.81012061 LEKPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LEKPAK 6 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;; 84.244 0.051138 39284550000 15909280 11753040 12228070 12314160 12539350 10106350 16685370 11385970 13333700 FALSE TRUE 14913546.56 12623247.31 12518125.59 12630162.19 11554560.03 13023889.18 14183553.67 12807533.42 11108219.33 1.342568608 1.136388015 1.126924597 1.137010516 1.040181121 1.17245517 1.276852144 1.152978082 1 23.40512423 4.739998221 24.4665616 1.144409511 1.342568695 0.432063515 0.074939611 100.476085 1709765.785 0.018083445 0.114687505 54953.86227 -4.739998221 0.198159184 LEKPAKYDDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEKPAKYDDIK 11 2 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 134.21 8.19E-05 17421700000 53186000 32197000 40705000 40947000 43469000 27277000 54490000 31927000 58668000 FALSE TRUE 49857183.2 34580899.38 41670541.82 41997769.34 40055120.09 35151427.09 46319730.36 35913156.23 48875931.79 1.020076372 0.707524094 0.852577952 0.859273016 0.819526475 0.719197073 0.947700201 0.734782027 1 25.54262087 -1.506697793 2.722291914 1.007821216 0.827475648 0.219287732 0.098859107 17127762.57 17741509.07 998713.23 0.022886163 0.031138824 1.506697793 -0.180345568 LEKPAKYDDIKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEKPAKYDDIKK 12 3 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 103.76 0.0027039 3760400000 6599300 3462300 5175800 5533400 5610100 3351400 6286400 3811800 8140400 FALSE TRUE 6186261.593 3718652.295 5298572.42 5675396.412 5169505.376 4318894.775 5343812.68 4287711.621 6781714.651 0.91219727 0.548335117 0.781302767 0.836867474 0.762271143 0.636844072 0.787973684 0.63224595 1 22.69321865 -1.089755083 4.450515486 1.000022269 0.727982362 0.370363154 0.107058461 19658106.13 58515718.96 7235.932453 0.023758981 0.081328904 1.089755083 -0.272039907 LEKPETQSS(ph)PITVQSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEKPETQSSPITVQSSK 17 1 Q96CB8;A0A087WXN4;E9PGI3 Q96CB8 INTS12 Integrator complex subunit 12 1 LEKPET(0.011)QS(0.353)S(0.607)PIT(0.029)VQSSK;LEKPETQS(0.048)S(0.945)PIT(0.007)VQSSK 192.63 1.06E-10 641650000 631040 376750 449110 432780 533820 411830 683230 484240 734620 TRUE FALSE 591544.3328 404644.962 459763.1013 443885.8675 491895.9305 530718.6355 580786.0043 544698.4299 612007.1762 0.966564374 0.661176826 0.751238089 0.7252952 0.803742096 0.867177145 0.948985611 0.890019678 1 19.22318904 2.138787439 1.747093234 0.944241138 0.752629659 0.443958986 0.082714582 0.284523371 1.683225831 0.043194395 0.024483779 137.6535574 -2.138787439 -0.191611479 LELASLGLGAPTPPSGLSQGPTSWLRPPPT(ph)SPGPQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LELASLGLGAPTPPSGLSQGPTSWLRPPPTSPGPQAR 37 1 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 LELASLGLGAPTPPS(0.002)GLS(0.066)QGPT(0.066)S(0.066)WLRPPPT(0.4)S(0.4)PGPQAR 115.84 1.00E-05 73491000 52858 68455 50271 60441 90249 43002 52292 42423 51438 TRUE FALSE 49549.71213 73523.47943 51463.45186 61992.01839 83161.20759 55415.97932 44451.30006 47719.60493 42852.6655 1.156280748 1.715727098 1.200939341 1.446631561 1.940630918 1.293174618 1.03730537 1.113573785 1 15.38709732 1.998975652 24.99995412 1.082138514 1.492127725 0.441337066 0.2262129 35.11249989 856960.1071 0.081843459 0.059675548 99.76441312 -1.998975652 0.409989211 LELMDIIAENVLSEDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LELMDIIAENVLSEDRR 17 1 A0A2R8YF87;Q96AX1;H3BMM5;F5H6Y0 A0A2R8YF87 VPS33A Vacuolar protein sorting-associated protein 33A 0 83.54 0.0088268 29632000 49856 50161 46219 48608 64593 38307 50485 46015 49822 FALSE TRUE 46735.60196 53874.97263 47315.33651 49855.36357 59520.12634 49365.60904 42915.24293 51760.07404 41506.38634 1.125985808 1.297992367 1.139953166 1.20114922 1.433999237 1.189349722 1.033943128 1.247038796 1 15.34104571 1.989960726 24.95298465 1.100985662 1.238982248 0.282114423 0.106220126 604.7334238 1503087.974 0.038900552 0.027038967 97.71488515 -1.989960726 0.137996586 LELQGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LELQGPR 7 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;; 162.31 0.0029707 614146000 747620 1442020 682777 725527 1455040 643678 780018 1160400 1351500 FALSE TRUE 700827.7987 1548788.661 698972.7929 744145.2511 1340767.028 829497.3894 663061.5422 1305278.494 1125925.919 0.622445746 1.375568885 0.620798208 0.660918484 1.190812828 0.73672466 0.588903347 1.159293407 1 20.10268048 3.952865108 23.70294513 0.818586049 1.04597453 0.030850839 0.278685185 432.3628386 422502.3134 0.066005098 0.119089303 8971.500961 -3.952865108 0.227388482 LELQGPRGS(ph)PNAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LELQGPRGSPNAR 13 1 P19338;H7BY16 P19338 NCL Nucleolin 1 LELQGPRGS(1)PNAR;LELQGPRGS(1)PNAR;LELQGPRGS(1)PNAR;LELQGPRGS(1)PNAR 131.45 7.89E-05 586480000 91363 287120 154194 184747 413381 95441 163072 141837 2293290 TRUE FALSE 85644.75292 308378.6635 157851.5545 189487.9208 380915.7238 122993.2673 138620.8675 159545.6617 1910525.084 0.044827861 0.161410424 0.082622079 0.099181069 0.199377505 0.064376683 0.072556424 0.083508802 1 20.86553777 -1.147766891 4.44884092 1.000144584 0.103672075 0.973786368 0.046353747 108548828 216919035.5 222199.4823 0.010637766 0.071159536 1.147766891 -0.896472509 LELSSSAS(ph)PQEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LELSSSASPQEER 13 0 A0A075B6T1;Q9C0C7-6;Q9C0C7-4;Q9C0C7-2;Q9C0C7-3;Q9C0C7;Q9C0C7-5 A0A075B6T1 AMBRA1 Activating molecule in BECN1-regulated autophagy protein 1 1 LELSSSAS(0.999)PQEER;LELSSS(0.001)AS(0.999)PQEER 267.88 7.36E-17 0 198536 181650 197470 182626 208120 170532 233960 178145 211600 TRUE FALSE 186109.9862 195099.555 202154.0817 187312.4923 191775.0947 219761.82 198879.87 200386.7954 176282.593 1.05574795 1.106743165 1.146761448 1.062569418 1.087884467 1.246645039 1.128187795 1.136736146 1 17.4275305 4.718174146 2.228440434 1.126454867 1.039371933 0.059025826 0.063710321 1.365751552 8.188246029 0.014845946 0.231161881 52260.57051 -4.718174146 -0.087082934 LELVHHGPMAVAFEVYDDFLHYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LELVHHGPMAVAFEVYDDFLHYK 23 0 P53634 P53634 CTSC Dipeptidyl peptidase 1;Dipeptidyl peptidase 1 exclusion domain chain;Dipeptidyl peptidase 1 heavy chain;Dipeptidyl peptidase 1 light chain 0 ; 85.35 0.0024798 97883000 207130 226155 177054 149782 252348 162873 222322 230993 121272 FALSE TRUE 194166.103 242899.7515 181253.8045 153625.6597 232529.606 209891.7911 188986.88 259832.9845 101030.9198 1.921848316 2.404212019 1.794042902 1.520580631 2.301568733 2.077500547 1.870584574 2.571816481 1 16.62443736 -1.787619606 2.820045113 0.737054494 2.044335806 0.536734433 0.308612333 29315650.44 16336282.45 52137746.56 0.070110576 0.016307237 1.787619606 1.307281312 LELVHHGPMAVAFEVYDDFLHYKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LELVHHGPMAVAFEVYDDFLHYKK 24 1 P53634 P53634 CTSC Dipeptidyl peptidase 1;Dipeptidyl peptidase 1 exclusion domain chain;Dipeptidyl peptidase 1 heavy chain;Dipeptidyl peptidase 1 light chain 0 ; 130.87 1.81E-05 95024000 325440 367190 294320 273620 459020 183270 368090 320140 443140 FALSE TRUE 305071.2913 394377.1297 301301.4094 280641.5524 422970.4208 236177.0739 312898.3217 360110.1837 369177.0712 0.826354926 1.068260086 0.816143344 0.760181426 1.145711513 0.63973928 0.847556216 0.975440275 1 18.49395343 3.879518155 7.028727027 0.867170665 0.961281831 0.019553403 0.150102316 0.614528248 37.82570323 0.035300358 0.064165263 7577.364088 -3.879518155 0.094111165 LENEGS(ph)DEDIETDVLYSPQMALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LENEGSDEDIETDVLYSPQMALK 23 0 O60502;O60502-3 O60502 MGEA5 Protein O-GlcNAcase 1 LENEGS(0.989)DEDIET(0.011)DVLYSPQMALK 99.185 0.001767 16062000 41225 38782 40823 44725 38335 30026 60170 33985 33543 TRUE FALSE 38644.80084 41653.45963 41791.34084 45872.71922 35324.32374 38694.01877 51148.06709 38228.10206 27944.4566 1.382914736 1.490580412 1.495514528 1.641567767 1.264090558 1.384676013 1.830347529 1.368003057 1 14.7702745 0.983360355 24.77960465 0.999999984 1.510408934 0.508876015 0.153808914 760.3296609 1132277.748 0.1463643 0.036591075 9.62410506 -0.983360355 0.51040895 LENGELEHIRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LENGELEHIRPK 12 1 M0R1K3;Q15102;M0R389;M0QZT2;M0QXS6;M0R323 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ;;;;; 241.15 1.85E-16 3125067000 4307590 3783230 4091260 3796340 4260630 3315220 4886260 3812080 5520080 FALSE TRUE 4037985.631 4063344.286 4188306.619 3893760.512 3926017.306 4272270.196 4153610.675 4288026.579 4598742.987 0.878062906 0.883577164 0.910750314 0.846701049 0.853715313 0.929008255 0.903205656 0.932434492 1 22.13280814 0.906423878 0.836197504 0.999636811 0.881724402 0.740328838 0.02253281 0.394723709 0.588123204 0.021809853 0.007737843 8.061648869 -0.906423878 -0.11791241 LENGGFPYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LENGGFPYEK 10 0 Q9BRT3;J3KTI2 Q9BRT3 MIEN1 Migration and invasion enhancer 1 0 79.659 0.049325 0 44687 32567 42019 40782 50749 30406 52529 41574 67832 FALSE TRUE 41890.12044 34978.29457 43015.71052 41828.53516 46763.37825 39183.7186 44652.76411 46764.60542 56510.40099 0.7412816 0.618970914 0.761199881 0.740191795 0.827518075 0.693389498 0.790168948 0.827539791 1 15.78622881 -5 0.120139763 1.890597928 0.60784427 0.749115404 0.050045819 70.11662437 0.546325946 15.00256196 0.451663697 1.00E-05 5 -1.282753658 LENGGFPYEKDLIEAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LENGGFPYEKDLIEAIR 17 1 Q9BRT3 Q9BRT3 MIEN1 Migration and invasion enhancer 1 0 109.89 0.00053337 838280000 65123 65572 67433 78988 81519 45123 71536 54938 102580 FALSE TRUE 61047.06768 70427.01911 69032.5426 81014.96581 75116.82657 58149.27759 60809.84091 61797.13023 85458.73531 0.714345555 0.824105562 0.80778802 0.948000992 0.878983597 0.680436908 0.711569633 0.723122452 1 16.38294035 2.247833208 24.99995638 0.747466389 0.834697858 0.029163087 0.10555001 370.9707488 1000179.154 0.033969425 0.02805937 176.9429274 -2.247833208 0.087231469 LENLGIPEEELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LENLGIPEEELLR 13 0 Q01658 Q01658 DR1 Protein Dr1 0 ; 141.38 9.26E-05 32427000 52871 54319 51754 55640 58080 45369 65280 50512 63255 FALSE TRUE 49561.89849 58340.83528 52981.62932 57067.8166 53518.63108 58466.2938 55491.87003 56818.53439 52697.33186 0.940501098 1.107092773 1.005394912 1.082935598 1.015585215 1.109473511 1.053029975 1.078205146 1 15.6854423 3.228425911 24.99667407 1.060457211 1.035073889 0.077793149 0.051594763 634.3862992 1564677.497 0.013452469 0.016254618 1692.099556 -3.228425911 -0.025383322 LENNDNKPVTNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LENNDNKPVTNSR 13 1 A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739 A0A024R7W5 YTHDF3 YTH domain-containing family protein 3 0 ;; 169.3 2.62E-05 1543910000 908460 732002 786897 798898 888823 590871 977329 755261 1194520 FALSE TRUE 851601.1102 786200.1897 805562.5684 819399.0752 819018.4269 761445.8657 830787.5895 849556.9984 995146.8951 0.855754175 0.790034309 0.809491114 0.823395098 0.823012593 0.765159264 0.834839151 0.853700094 1 19.92454997 0.722730053 1.605469533 0.999785866 0.809624704 0.853020926 0.024129828 0.316562456 1.290735804 0.020889964 0.00599869 5.28116885 -0.722730053 -0.190161162 LENNENKPVTNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LENNENKPVTNSR 13 1 Q9Y5A9;Q9Y5A9-2 Q9Y5A9 YTHDF2 YTH domain-containing family protein 2 0 ;; 169.4 2.61E-05 487140000 568905 454216 530769 499786 537533 425689 672907 471777 743780 FALSE TRUE 533298.2516 487846.6253 543359.0913 512611.3549 495317.3265 548578.5038 572010.8423 530679.397 619638.313 0.86066055 0.787308685 0.876897183 0.827275112 0.799365236 0.885320504 0.923136659 0.856434126 1 19.24106682 0.730543946 0.398336785 1.012164112 0.821260639 0.650234876 0.036301511 1.066961844 0.392832751 0.066754237 0.027975161 5.377048402 -0.730543946 -0.190903473 LENSPGHGKS(ph)PDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LENSPGHGKSPDHR 14 1 Q8IY63-2;Q8IY63 Q8IY63-2 AMOTL1 Angiomotin-like protein 1 1 LENSPGHGKS(1)PDHR 60.062 0.057933 42758000 56034 47760 58287 57245 58667 44838 70690 50038 78922 TRUE FALSE 52526.93196 51296.20009 59669.59517 58714.00362 54059.53047 57782.00272 60090.69075 56285.35445 65749.40834 0.798895888 0.780177364 0.907530526 0.892996684 0.822205581 0.878821638 0.91393508 0.856058722 1 16.00469029 -5 0.021299824 2.127299897 5.24E-09 0.658272023 0.03717702 1774.901174 2.860450891 196.1985806 103.2452337 1.00E-05 5 -2.127299891 LENVSQLSLDKS(ph)PTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LENVSQLSLDKSPTEK 16 1 Q86W56-3;Q86W56-2;Q86W56 Q86W56-3 PARG Poly(ADP-ribose) glycohydrolase 1 LENVSQLSLDKS(0.991)PT(0.009)EK 223.89 5.03E-15 294060000 814230 380430 562950 620060 522050 295320 681040 384210 534610 TRUE FALSE 763268.7977 408597.433 576303.4398 635971.7894 481050.2988 380574.0899 578924.3745 432179.4643 445380.1373 1.713746828 0.917412787 1.293958557 1.427930292 1.080089251 0.854492731 1.299843271 0.970360885 1 18.76467769 2.576462505 10.22111741 1.061688526 1.260502129 0.268587041 0.227080653 0.882421588 85.793377 0.070631314 0.066558209 377.1051859 -2.576462505 0.198813603 LEPAS(ph)PPEDTSAEVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEPASPPEDTSAEVSR 16 0 E9PFE2;Q9UHL9-2;Q9UHL9;Q9UHL9-3 E9PFE2 GTF2IRD1 General transcription factor II-I repeat domain-containing protein 1 1 LEPAS(1)PPEDTSAEVSR 188 1.31E-09 288690000 369930 351720 403560 387550 328830 290520 432210 324920 277760 TRUE FALSE 346776.7416 377761.7148 413132.6338 397495.1891 303005.0182 374388.4078 367404.1229 365486.9772 231400.0616 1.498602633 1.632504815 1.78536095 1.71778342 1.309442254 1.617927001 1.587744275 1.579459291 1 17.82002972 -2.599692814 0.322252297 6.43E-11 1.645728527 0.678266323 0.127512705 33.17742548 1.190303003 23.22221843 0.115253229 0.002513664 2.599692814 1.645728527 LEPGS(ph)DVEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEPGSDVEVK 10 0 Q9ULI0-2;Q9ULI0;H7BYF1 Q9ULI0-2 ATAD2B ATPase family AAA domain-containing protein 2B 1 LEPGS(1)DVEVK;LEPGS(1)DVEVK 177.1 2.48E-06 247140000 1201210 655820 888050 778010 646350 794030 1222420 748340 481660 TRUE FALSE 1126028.41 704377.5952 909114.9654 797975.0538 595588.2783 1023253.571 1039129.469 841771.8963 401267.8344 2.806176608 1.75538016 2.265606379 1.988634487 1.484266186 2.550051321 2.589615664 2.097780645 1 18.61420599 4.755402438 23.17075941 2.066870629 2.806178237 0.204224872 0.486251595 2073.557085 2852641.998 0.109505427 2.768092937 56938.03014 -4.755402438 0.739307608 LEPKPQPPVAEATPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEPKPQPPVAEATPR 15 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;K7EJ51;K7ER14;K7EJL9 Q9UHD8 9-Sep Septin-9 0 ; 120.63 0.00010946 352490000 223780 199120 220860 196517 211090 165103 256830 200793 273520 FALSE TRUE 209774.0093 213863.052 226098.9035 201559.9589 194511.8429 212765.5559 218320.7258 225862.448 227867.745 0.92059545 0.938540257 0.99223742 0.884548004 0.853617272 0.933723884 0.958102806 0.991199733 1 17.7978372 1.444566121 2.355347357 0.997185212 0.927171575 0.421631897 0.036042995 0.355034808 3.663175734 0.033720181 0.01087175 27.83339103 -1.444566121 -0.070013637 LEPNS(ph)PMHGGTLLEDVVGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEPNSPMHGGTLLEDVVGGR 20 0 Q5VY60;Q7Z4H7-3;Q7Z4H7 Q5VY60 HAUS6 HAUS augmin-like complex subunit 6 1 LEPNS(1)PMHGGTLLEDVVGGR 225.88 3.09E-25 43100000 27013 29495 33147 34876 39044 30477 30853 24847 30849 TRUE FALSE 25322.30455 31678.84049 33933.26249 35770.9772 35977.64174 39275.21515 26226.87908 27949.20264 25700.10261 0.985299745 1.232634786 1.320355137 1.39186126 1.39990265 1.528212387 1.020497057 1.087513271 1 14.6494865 1.630048849 9.918107371 1.039569539 1.30790907 0.455515334 0.140854802 0.096823577 22.72877419 0.069159891 0.036228265 42.6627503 -1.630048849 0.268339532 LEPQELS(ph)PLSATVFPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LEPQELSPLSATVFPK 16 0 Q3T8J9-3;Q3T8J9;A0A087WUE6;Q3T8J9-2;Q9H869-7;Q9H869-5;Q9H869-6;Q9H869-4;Q9H869-3;Q9H869-2;Q9H869;Q9H869-8;Q9H869-9 Q3T8J9-3 GON4L;YY1AP1 GON-4-like protein;YY1-associated protein 1 1 LEPQELS(0.939)PLS(0.057)AT(0.004)VFPK;LEPQELS(1)PLSATVFPK;LEPQELS(1)PLSATVFPK 223.06 9.52E-15 184005000 327202 261331 309311 294755 345135 240010 373835 288870 394563 TRUE FALSE 306723.0109 280680.2192 316648.003 302318.9123 318029.4893 309296.9908 317781.9123 324936.0554 328707.8863 0.933117286 0.85388952 0.963311244 0.919719072 0.967514022 0.940947886 0.96676084 0.98852528 1 18.32644654 3.115758068 0.309403226 1.002387357 0.864955119 0.57063765 0.026964785 1.840931891 0.303476668 0.031820275 0.08991727 1305.443463 -3.115758068 -0.137432238 LEPQIASASEYAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LEPQIASASEYAHR 14 0 O60664-4;O60664;O60664-3;K7ER39;K7EL96 O60664-4 PLIN3 Perilipin-3 0 ;;;; 254.45 2.96E-24 2393330000 1730400 2268390 2154010 2102990 2372480 1872670 2351510 1959970 2516090 FALSE TRUE 1622097.353 2436343.956 2205104.134 2156956.284 2186154.991 2413279.429 1998922.906 2204676.569 2096138.324 0.773850339 1.162301136 1.051984074 1.029014287 1.042944049 1.151297794 0.953621659 1.051780096 1 20.99930249 1.666090906 24.99999981 1.001897695 1.051976903 0.005246335 0.10792068 1.148100488 466.4324196 0.045645419 0.025312452 46.35439385 -1.666090906 0.050079207 LEPTAPALS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LEPTAPALSPR 11 0 Q96IF1 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 LEPT(0.001)APALS(0.999)PR;LEPT(0.004)APALS(0.996)PR;LEPTAPALS(1)PR 111.63 0.00088108 162462000 594265 589360 538068 540701 608930 438799 556009 515908 567410 TRUE FALSE 557071.0144 632996.8276 550831.2271 554576.3031 561107.0941 565473.148 472640.6122 580320.2495 472705.6054 1.178473469 1.339093128 1.165273313 1.173195953 1.187011721 1.196248027 0.999862508 1.227656797 1 18.85058245 2.249734931 0.25016792 0.983579536 1.323456131 0.41600909 0.076590064 2.127998177 0.397564247 0.155718583 0.26012669 177.7194381 -2.249734931 0.339876594 LEPTNVQTVTCS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LEPTNVQTVTCSPR 14 0 J3KTI7;J3QR52;J3QLN7;Q99741 J3KTI7 CDC6 Cell division control protein 6 homolog 1 LEPTNVQTVTCS(1)PR;LEPTNVQTVTCS(1)PR;LEPTNVQTVTCS(1)PR;LEPTNVQTVTCS(1)PR 285.9 1.10E-33 1604040000 1278680 1290900 1485130 1339780 1525310 1438960 1888490 1291180 1331580 TRUE FALSE 1198649.701 1386479.579 1520357.985 1374161.023 1405518.305 1854364.392 1605328.456 1452386.665 1109330.696 1.080516122 1.249834323 1.370518269 1.238729829 1.266996677 1.671606492 1.447114429 1.3092459 1 20.08125807 5.84438209 0.67552291 1.377773764 2.25E-08 0.136408937 0.172428191 18.22416383 2.022427365 0.06301518 27.12378837 698846.9753 -5.84438209 -1.377773742 LEPVS(ph)PPS(ph)PPHTDPELELVPPR ddPTM_SK-BR-3_Pertuzumab_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(0.998)PPS(0.879)PPHT(0.122)DPELELVPPR;LEPVS(1)PPS(1)PPHTDPELELVPPR;LEPVS(1)PPS(0.997)PPHT(0.003)DPELELVPPR;LEPVS(1)PPS(1)PPHTDPELELVPPR;LEPVS(1)PPS(1)PPHTDPELELVPPR 130.78 6.92E-06 1637559000 793931 851100 858816 820516 918270 743495 951290 749762 938310 TRUE FALSE 744240.2759 914116.3296 879187.5211 841571.8297 846152.7783 958129.9369 808652.8958 843371.4361 781699.9993 0.952079156 1.169395331 1.124712194 1.076591826 1.082452065 1.225700317 1.034479847 1.078893996 1 19.57625551 1.109607511 1.612110961 1.006730367 1.110889401 0.127903133 0.073669449 0.589417613 3.003201236 0.062976868 0.018548584 12.87085834 -1.109607511 0.104159034 LEPVSPPS(ph)PPHTDPELELVPPR ddPTM_SK-BR-3_Pertuzumab_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(0.993)PPHT(0.001)DPELELVPPR 75.226 0.0078742 38954000 17246 20545 17136 14368 14997 17798 18043 15952 21723 TRUE FALSE 16166.60364 22066.17318 17542.47401 14736.7072 13819.19611 22935.99367 15337.61965 17943.64231 18097.29096 0.893316225 1.219308084 0.969342541 0.814304596 0.763605787 1.267371659 0.847509148 0.991509854 1 14.14348613 3.670766248 5.328001817 0.943412782 1.084082228 0.06671213 0.157602231 0.376759991 22.56575721 0.039429145 0.062943105 4685.61119 -3.670766248 0.140669446 LEPVYSPPGS(ph)PPPGDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEPVYSPPGSPPPGDPR 17 0 E9PJN1;O75676-2;O75676;A0A0A6YYC0 E9PJN1 RPS6KA4 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-4 1 LEPVYS(0.148)PPGS(0.851)PPPGDPR 78.932 0.015331 261960000 42029 65461 49267 70912 73882 44228 59412 41266 62496 TRUE FALSE 39398.47991 70307.80055 50435.63651 72731.72197 68079.60575 56995.90562 50503.72215 46418.15094 52065.01386 0.756716977 1.350384747 0.968704947 1.396940413 1.307588353 1.094706433 0.970012652 0.891542084 1 15.66802663 1.800849695 3.265009892 0.944643326 1.169321781 0.188511413 0.189067122 0.350821282 6.914271186 0.095082321 0.048055245 63.21930176 -1.800849695 0.224678455 LEQDEYALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LEQDEYALR 9 0 P55084-2;P55084;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ;;; 171.56 0.00013226 951340000 1617140 1693850 1481680 1392860 2125470 1238630 1293440 1646740 2363790 FALSE TRUE 1515926.094 1819264.416 1516826.149 1428603.146 1958544.16 1596202.374 1099500.68 1852339.114 1969258.178 0.769795505 0.923832353 0.770252558 0.725452438 0.994559363 0.810560236 0.558332418 0.940627864 1 20.90922084 1.990355466 24.90748978 0.759046028 0.840187639 0 0.143431724 1297.733143 3351461.608 0.052155483 0.03632657 97.80374078 -1.990355466 0.081141611 LEQEHTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEQEHTNR 8 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 111.46 0.0032301 221890000 177140 259160 187150 213530 276740 173920 200040 218450 272270 FALSE TRUE 166053.1236 278348.4761 191589.2864 219009.5413 255005.9567 224127.8806 170045.8591 245723.9634 226826.3781 0.732071486 1.227143326 0.844651702 0.965538238 1.124234134 0.988103247 0.749674092 1.083312997 1 17.7912289 1.964423049 24.94118575 0.904608443 0.998924109 0 0.159496098 1602.987987 1123771.006 0.06069101 0.039193287 92.1346624 -1.964423049 0.094315666 LEQEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEQEKR 6 1 A0A087WUT6;O60841;CON__ENSEMBL:ENSBTAP00000034412 A0A087WUT6;REV__Q1RMZ1 EIF5B Eukaryotic translation initiation factor 5B 0 88.942 0.081342 454460000 364660 336700 313740 348510 359750 203800 380060 338510 495890 FALSE TRUE 341836.5815 361629.6183 321182.061 357453.3566 331496.6862 262633.7516 323073.5313 380773.7187 413122.7554 0.82744554 0.875356328 0.777449455 0.865247319 0.802416913 0.635728117 0.782027925 0.921696309 1 18.656211 1.07469187 3.923128384 0.997300881 0.79571302 0.541339623 0.065484913 0.161322105 4.662785561 0.065461128 0.016858492 11.8765929 -1.07469187 -0.201587861 LEQENDDLAHELVTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 174.59 3.82E-09 898410000 1326220 1185490 1250840 1250960 1370520 1001750 1619950 1168780 1737060 FALSE TRUE 1243214.258 1273264.913 1280510.515 1283061.751 1262884.888 1290938.963 1377053.536 1314704.756 1447133.464 0.859087491 0.879853134 0.884859999 0.886622957 0.872680315 0.892066278 0.95157328 0.908488946 1 20.46476655 1.000431552 0.467600004 1.003692267 0.870519745 0.835574669 0.017038866 0.420100019 0.237884154 0.021143609 0.010566407 10.00994179 -1.000431552 -0.133172522 LEQGEEPWIMGGEFPCQHS(ph)PEAWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LEQGEEPWIMGGEFPCQHSPEAWR 24 0 I3L0D1;Q9NYW8 I3L0D1 RBAK-RBAKDN;RBAK RB-associated KRAB zinc finger protein 1 LEQGEEPWIMGGEFPCQHS(1)PEAWR;LEQGEEPWIMGGEFPCQHS(1)PEAWR;LEQGEEPWIMGGEFPCQHS(1)PEAWR 217.57 7.98E-33 141174000 151462 133460 129369 115462 140171 121384 146490 97727 118012 TRUE FALSE 141982.2638 143341.5173 132437.6938 118424.9504 129162.5351 156425.5903 124525.1844 109928.4311 98315.03481 1.444156167 1.457981656 1.347074677 1.204545679 1.313761779 1.591064791 1.266593504 1.118124316 1 16.58512444 1.241510213 2.622141048 1.016987584 1.386566664 0.641537234 0.102922415 0.16975689 1.963884904 0.093122318 0.026649664 17.43854368 -1.241510213 0.36957908 LEQHLTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEQHLTGR 8 0 Q7Z2Z2-2;Q7Z2Z2 Q7Z2Z2-2 EFTUD1 Elongation factor Tu GTP-binding domain-containing protein 1 0 62.201 0.081135 35840000 55044 86480 70629 74345 87928 60816 80489 67589 85282 FALSE TRUE 51598.8943 92883.06918 72304.35323 76252.81857 81022.48956 78372.59193 68420.42167 76027.63543 71047.88326 0.726255195 1.307330562 1.017684833 1.073259541 1.14039273 1.103095382 0.96301844 1.070090085 1 16.11650405 1.753372115 25 1.009538784 1.088182905 0.003761817 0.146469522 15.01236093 25372.19292 0.061758235 0.034247715 56.67246652 -1.753372115 0.078644121 LEQMPSKEDAIEHFMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEQMPSKEDAIEHFMK 16 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 165.9 4.13E-09 293130000 1221000 874430 1020700 978200 1005500 749710 1305100 952450 969830 FALSE TRUE 1144579.79 939173.707 1044911.486 1003302.268 926532.086 966139.1065 1109412.371 1071365.479 807959.1077 1.41663084 1.162402525 1.293272736 1.241773573 1.146756163 1.195777233 1.373104604 1.326014484 1 19.62392275 4.754401971 23.9101361 1.236378953 1.416631089 0.242846377 0.105946899 2555.881071 3857598.773 0.02363102 0.568452855 56807.01527 -4.754401971 0.180252136 LEQQLVHVERPILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEQQLVHVERPILR 14 1 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;C9JBE1;E7EMB6;E7EPX3;B9ZVU2;F8WAN0;C9JRG3;C9J1E2 E5RIA4 DNPEP Aspartyl aminopeptidase 0 151.07 4.23E-06 445760000 95420 97672 108400 93437 91126 71829 110670 75666 89528 FALSE TRUE 89447.83253 104903.7365 110971.2992 95834.75161 83969.33154 92564.86625 94076.06091 85113.06666 74585.19843 1.199270558 1.406495373 1.487846135 1.284903086 1.125817633 1.241062144 1.261323465 1.141152245 1 16.18660173 3.002734651 6.232788621 1.18611591 1.391322976 0.450323456 0.102990387 0.126834478 21.61256855 0.029457356 0.033859806 1006.316634 -3.002734651 0.205207065 LEQTSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEQTSVR 7 0 O15234 O15234 CASC3 Protein CASC3 0 ; 103.29 0.019566 2368100000 1415450 1948760 1416310 1450110 1766460 1172130 1557290 1612740 1602910 FALSE TRUE 1326859.511 2093048.218 1449905.542 1487322.278 1627729.357 1510504.903 1323788.822 1814094.139 1335373.966 0.993623917 1.567387317 1.085767417 1.113787086 1.218931475 1.131147485 0.99132442 1.358491468 1 20.34881239 3.733215633 24.48963496 1.123311493 1.323015356 0.107503256 0.172194067 285.9016785 1148853.883 0.039920259 0.069687462 5410.228819 -3.733215633 0.199703863 LEQTSVRDPS(ph)PEADAPVLGSPEKEEAASEPPAAAPDAAPPPPDRPIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEQTSVRDPSPEADAPVLGSPEKEEAASEPPAAAPDAAPPPPDRPIEK 48 3 O15234 O15234 CASC3 Protein CASC3 1 LEQT(0.165)S(0.165)VRDPS(0.651)PEADAPVLGS(0.009)PEKEEAAS(0.009)EPPAAAPDAAPPPPDRPIEK 47.873 0.011575 162780000 20617 15316 14753 15588 18261 12752 21111 16468 19783 TRUE FALSE 19326.61877 16450.01258 15102.94813 15988.01447 16826.85472 16433.29539 17945.60153 18524.06605 16481.0895 1.172654197 0.998114389 0.916380445 0.970082377 1.020979513 0.997100064 1.088860147 1.123958829 1 14.008524 1.747806364 6.726273431 1.079134201 0.998380389 0.103099135 0.072115716 0.227772193 30.00118923 0.034673739 0.018400422 55.95080812 -1.747806364 -0.080753812 LES(ph)EDDSLGWGAPDWSTEAGFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LESEDDSLGWGAPDWSTEAGFSR 23 0 F5H4R1;J3KNB8;F5H538;Q9Y6R4-2;Q9Y6R4;F5H1X6 F5H4R1 MAP3K4 Mitogen-activated protein kinase kinase kinase 4 1 LES(0.874)EDDS(0.126)LGWGAPDWSTEAGFSR 120.75 4.65E-05 10062000 17247 18067 18302 20069 16246 13210 24550 15210 15876 TRUE FALSE 16167.54106 19404.69948 18736.13208 20584.00452 14970.10469 17023.51255 20868.95541 17109.00198 13226.19304 1.222388106 1.467141711 1.41659297 1.556306071 1.131852881 1.28710601 1.577850509 1.293569656 1 13.69111024 2.758974872 24.96015574 1.319245652 1.424360567 0.11970991 0.171818899 2166.101578 2648451.787 0.050958351 0.053985859 574.0832453 -2.758974872 0.105114914 LES(ph)IDNHSSTGGQSDQGYGSKDELIKDDAEIHVPEEQAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LESIDNHSSTGGQSDQGYGSKDELIKDDAEIHVPEEQAAR 40 2 Q5VZ89-7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 LES(0.94)IDNHS(0.045)S(0.008)T(0.007)GGQSDQGYGSKDELIKDDAEIHVPEEQAAR 142.41 1.73E-13 193100000 44563 42970 43966 50304 41238 27397 70549 41913 62408 TRUE FALSE 41773.88138 46151.54351 45008.89428 51594.8858 37999.33383 35306.06915 59970.83239 47145.93031 51991.70163 0.803472094 0.887671341 0.86569381 0.992367708 0.730873055 0.679071237 1.153469314 0.906797216 1 15.66599375 1.732218014 24.99999998 1.025078378 0.840798529 0.432742823 0.103562254 0.611171003 2392.029998 0.04606744 0.025546737 53.97815231 -1.732218014 -0.18427985 LES(ph)VEEYNELMVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LESVEEYNELMVR 13 0 O15018 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 LES(1)VEEYNELMVR;LES(1)VEEYNELMVR 154.6 4.85E-05 53607000 38830 35220 32503 39406 35116 26741 47006 34930 38965 TRUE FALSE 36399.69961 37827.72545 33273.98651 40417.22467 32358.13101 34460.6926 39957.88668 39291.08739 32461.48978 1.121319442 1.165310825 1.025029558 1.245082248 0.996815957 1.061586909 1.230932005 1.210390763 1 14.98644159 1.749227175 25 1.170115787 1.102244168 0.029789416 0.092936223 6.24478238 14664.39943 0.03910201 0.021684219 56.13415307 -1.749227175 -0.067871619 LESALTELEQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LESALTELEQLR 12 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ; 129.7 0.00053399 14193700 21853.8 22214.5 21437.2 20268 22829.5 18537.6 22069.2 17568.6 29580 FALSE TRUE 20486.00967 23859.28469 21945.70051 20788.11119 21036.56316 23889.10419 18760.12834 19762.07838 24642.90691 0.831314656 0.968200902 0.890548367 0.843573823 0.853655912 0.969410966 0.761279033 0.801937793 1 14.58888483 3.453383202 4.783433747 0.859319927 0.915041449 0 0.078133704 0.447529273 25.65691861 0.020386919 0.029154969 2840.424184 -3.453383202 0.055721522 LESALTELEQLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LESALTELEQLRK 13 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 177.36 2.49E-05 91269000 376410 363970 349030 335210 429210 289600 426350 345390 481090 FALSE TRUE 352851.17 390918.7175 357309.1564 343812.0561 395501.5779 373202.8187 362422.7755 388512.7018 400792.971 0.88038263 0.975363207 0.891505546 0.857829555 0.98679769 0.931161087 0.9042643 0.969360068 1 18.61249768 1.052464542 4.404225299 0.999570112 0.921435824 0.336969018 0.03977053 0.208019908 8.230964122 0.035901472 0.009149729 11.28403805 -1.052464542 -0.078134288 LESDYEILER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LESDYEILER 10 0 A0A0A0MSX9;P41252;J3KR24;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;; 269.23 6.54E-18 1138320000 1205030 1326640 1345010 1352900 1335270 1142890 1420130 1169750 1238150 FALSE TRUE 1129609.323 1424865.806 1376914.272 1387617.704 1230403.28 1472823.79 1207194.69 1315795.862 1031494.766 1.095118812 1.38136019 1.334872767 1.345249389 1.192835214 1.427853866 1.170335255 1.275620493 1 19.97630507 0.363121676 0.708650818 0.994551285 1.306973258 0.41236042 0.102797083 1.900203403 1.384277328 0.115282406 0.033558287 2.30739356 -0.363121676 0.312421972 LESENDEYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LESENDEYER 10 0 O94906 O94906 PRPF6 Pre-mRNA-processing factor 6 0 106.4 0.0056337 114360000 327970 361570 360670 370130 389520 326490 433750 374850 393420 FALSE TRUE 307442.9431 388341.019 369225.2627 379628.1624 358928.6704 420742.3629 368713.2142 421650.8476 327755.6604 0.938024816 1.18484916 1.126525968 1.15826577 1.095110516 1.283707388 1.124963681 1.286479224 1 18.32226117 4.74212658 24.49400866 1.162362588 0.938024703 0.398929683 0.084471774 235.3617031 1616565.763 0.017178958 0.126059001 55223.83713 -4.74212658 -0.224337886 LESESTS(ph)PSLEMK ddPTM_SK-BR-3_Pertuzumab_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(0.016)S(0.984)PSLEMK;LESEST(0.047)S(0.947)PS(0.007)LEMK;LESEST(0.05)S(0.755)PS(0.195)LEMK;LESEST(0.209)S(0.788)PS(0.003)LEMK;LESEST(0.002)S(0.612)PS(0.386)LEMK;LESES(0.001)T(0.011)S(0.494)PS(0.494)LEMK 333.71 6.27E-62 1089650000 5343970 3818280 4445090 4205980 4735320 3525290 5184020 3864060 6072540 TRUE FALSE 5009500.457 4100989.424 4550529.634 4313912.568 4363427.069 4542983.995 4406724.327 4346496.397 5058993.844 0.990216753 0.810633409 0.899493017 0.85272145 0.862508871 0.898001487 0.871067343 0.859162223 1 22.27041905 -1.825639421 2.300941771 1.04958369 0.875047048 0.390389754 0.046501488 6749155.899 3892279.968 1851111.622 0.010532158 0.014940343 1.825639421 -0.174536642 LESLSETPGPSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LESLSETPGPSSPR 14 0 A0A2R8YF49;H0Y895;Q12774-2;C9J591;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 LESLSETPGPS(0.001)S(0.999)PR;LESLSETPGPS(0.001)S(0.999)PR;LESLSETPGPSS(1)PR;LESLSETPGPSS(1)PR;LESLSETPGPSS(1)PR;LESLSETPGPSS(1)PR 393.84 3.42E-114 4407240000 5854520 6207280 6333900 6101170 6850090 5881790 7003100 5888290 6275060 TRUE FALSE 5488096.044 6666873.47 6484143.099 6257736.351 6312111.563 7579767.29 5953050.169 6623455.968 5227711.948 1.049808425 1.275294725 1.240340547 1.197031591 1.207432932 1.449920609 1.138748697 1.266989466 1 22.31774822 -0.458444763 7.321904147 0.999999999 1.234717333 0.326921074 0.102522639 0 0 0.088166156 0.020780962 0.347980764 0.458444763 0.234717333 LESTESR ddPTM_SK-BR-3_Pertuzumab_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 0 113.1 0.014436 102430000 227060 246260 232450 246950 269150 218490 290410 216740 292240 FALSE TRUE 212848.7199 264493.3466 237963.8238 253287.1551 248012.0447 281564.5161 246865.7165 243800.4661 243463.2561 0.874253977 1.08637891 0.977411654 1.040350643 1.018683676 1.156496963 1.013975252 1.001385055 1 17.89334453 4.749062152 24.64816445 1.038757563 0.874253865 0.496340293 0.051437338 1026.951939 2410301.545 0.011554953 0.163035522 56112.82734 -4.749062152 -0.164503698 LESTS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LESTSPK 7 0 Q03111 Q03111 MLLT1 Protein ENL 1 LES(0.019)T(0.168)S(0.813)PK;LES(0.043)T(0.228)S(0.73)PK;LES(0.007)T(0.021)S(0.972)PK;LES(0.02)T(0.176)S(0.803)PK 104.2 0.0086064 1949260000 13394300 7455500 9555700 8759600 10042200 7046900 12314700 8497200 12422000 TRUE FALSE 12555974.67 8007512.977 9782365.717 8984386.166 9253526.12 9081225.633 10468225.06 9558094.125 10348687.95 1.213291456 0.773770841 0.945275939 0.86816669 0.894173847 0.877524347 1.011550943 0.923604439 1 23.30294453 1.740552187 25 0.97616135 0.90908033 0.02137062 0.115295772 0.878658369 11098.96772 0.048182341 0.026719438 55.02400367 -1.740552187 -0.067081019 LETELDEEKNTVELLTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LETELDEEKNTVELLTDR 18 1 Q9P2M7 Q9P2M7 CGN Cingulin 0 76.713 0.013477 23728000 33575 30541 32178 31666 40128 27582 39171 28573 89712 FALSE TRUE 31473.60068 32802.28742 32941.27736 32478.60317 36976.50875 35544.47564 33297.6722 32140.40195 74738.48764 0.421116371 0.438894182 0.440753866 0.434563291 0.49474521 0.475584625 0.445522424 0.430038163 1 16.18956375 -1.859214837 2.59044958 1.23821912 0.448308055 0.984334177 0.021898664 3866749.037 2415896.746 5680916.131 0.00535259 0.013828821 1.859214837 -0.789911065 LETHMTPEMFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LETHMTPEMFR 11 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;; 176.95 8.20E-06 718040000 341968 1090020 423339 483392 1099890 313182 431633 942570 964000 FALSE TRUE 320564.8333 1170726.215 433380.801 495796.6571 1013509.076 403592.5593 366913.6387 1060251.939 803102.1723 0.39915822 1.45775501 0.539633456 0.617351906 1.261992697 0.502541984 0.456870435 1.320195581 1 19.61522402 3.851262247 13.73740177 0.764291551 1.003335356 0 0.397059372 1.86328578 203.8887846 0.094422116 0.170243969 7100.063729 -3.851262247 0.239043805 LETLGSASTST(ph)PGRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LETLGSASTSTPGRR 15 1 Q96FF9;B5MBX0 Q96FF9 CDCA5 Sororin 1 LETLGSAST(0.001)S(0.03)T(0.969)PGRR 103.27 0.0008707 289430000 122830 140560 117670 137600 157200 109900 154450 112640 195610 TRUE FALSE 115142.2896 150967.2087 120461.188 141131.049 144854.1461 141626.3459 131291.6563 126703.352 162961.4273 0.706561617 0.926398419 0.739200619 0.866039598 0.888886091 0.869078949 0.805660938 0.777505168 1 17.314171 -1.516290707 3.096346759 1.005465506 0.827985771 0.396980787 0.068478674 41147800.76 58710993.39 1961121.686 0.014990746 0.030458555 1.516290707 -0.177479735 LETLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LETLLR 6 0 A0A1W2PR85;O95816-2;O95816;Q9UL42;O15056-3;O15056-2;O15056 A0A1W2PR85 BAG2;PNMA2;SYNJ2 BAG family molecular chaperone regulator 2;Paraneoplastic antigen Ma2;Synaptojanin-2 0 110.56 0.066533 142580000 302510 325990 328490 300170 351510 279650 353210 312310 322790 FALSE TRUE 283576.4391 350126.6388 336281.9379 307872.8704 323903.8225 360380.4153 300249.4395 351302.591 268914.2637 1.054523606 1.302000995 1.250517296 1.144873709 1.204487326 1.340131276 1.116524782 1.306373958 1 18.03678675 -1.349906434 3.367749888 0.998570649 1.221297878 0.356164798 0.090455877 2996598.415 3603804.992 25531.79854 0.019071922 0.044677984 1.349906434 0.22272723 LEVQAEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEVQAEEER 9 0 Q9H307 Q9H307 PNN Pinin 0 146.27 0.00022141 152780000 139340 175020 156360 155770 177260 132940 172580 157500 197360 FALSE TRUE 130618.9581 187978.6629 160068.933 159767.3219 163338.7146 171317.6199 146703.2312 177164.2217 164419.341 0.794425749 1.14328802 0.973540777 0.971706376 0.99342762 1.041955398 0.892250451 1.077514486 1 17.32702049 LEVS(ph)PEAQPTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEVSPEAQPTAR 12 0 Q6WKZ4 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 LEVS(1)PEAQPTAR;LEVS(1)PEAQPTAR 145.81 0.00030313 191130000 319760 302740 316300 325930 364320 277270 390020 311880 443110 TRUE FALSE 299746.7924 325155.1846 323802.7854 334293.9156 335707.7768 357313.3479 331540.1218 350818.9045 369152.0784 0.811987281 0.880816345 0.877152817 0.905572351 0.909402375 0.967929937 0.89811257 0.95033707 1 18.49385576 8 0.108282678 1.037891042 0.422917613 0.801560896 0.023368467 47.29249094 0.358130642 0.207728466 4.343058178 100000000 -8 -0.61497343 LEVTEIVKPS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LEVTEIVKPSPK 12 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 LEVTEIVKPS(1)PK;LEVTEIVKPS(1)PK;LEVTEIVKPS(1)PK 125.89 0.00017997 1686510000 4875400 2147770 3090120 2817420 3289650 2211910 4476980 2871750 4957300 TRUE FALSE 4570257.417 2306793.126 3163419.106 2889719.767 3031294.159 2850452.51 3805698.411 3230294.309 4129894.605 1.106628099 0.558559805 0.76598059 0.699707872 0.733988261 0.690199819 0.921500129 0.782173546 1 21.97767353 1.102782424 0.866286167 0.987881119 0.734461763 0.154209842 0.148494849 0.827078608 1.383269817 0.126976041 0.045702088 12.67016947 -1.102782424 -0.253419356 LEYDDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEYDDLR 7 0 P15924 P15924 DSP Desmoplakin 0 ; 102.72 0.019862 179177000 808000 997810 925170 946510 1023800 840640 1080600 916950 690880 FALSE TRUE 757428.7223 1071688.891 947115.4693 970799.049 943394.8778 1083319.121 918574.0618 1031433.226 575567.6647 1.315968163 1.861968551 1.645532797 1.686681008 1.639068585 1.88217509 1.595944522 1.792027748 1 19.13462602 -0.770787689 13.96029151 1.000007543 1.692207694 0.637728451 0.160113169 0 0 0.133574794 0.031483881 0.16951663 0.770787689 0.692200151 LEYDDLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LEYDDLRR 8 1 P15924 P15924 DSP Desmoplakin 0 ; 122.13 0.0022503 736430000 655850 873710 732470 799510 974420 615360 846520 688130 838840 FALSE TRUE 614801.5192 938400.3975 749844.5343 820026.7802 897892.9838 793004.4425 719592.1847 774044.5453 698832.1849 0.879755587 1.34281222 1.072996566 1.173424461 1.284847784 1.134756612 1.029706703 1.107625782 1 19.41458653 1.87963572 4.949393144 1.052538629 1.170353494 0.116366674 0.126194367 0.40539611 14.15114098 0.052984399 0.030987051 75.79415573 -1.87963572 0.117814865 LFAGSLAPLLQPGAAGGEIPAVQASSGS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFAGSLAPLLQPGAAGGEIPAVQASSGSPK 30 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 LFAGSLAPLLQPGAAGGEIPAVQAS(0.012)S(0.018)GS(0.97)PK;LFAGSLAPLLQPGAAGGEIPAVQASS(0.003)GS(0.997)PK 203.64 1.10E-25 829240000 2008530 1283260 1618680 1601850 1680300 1054830 1844280 1203230 1255180 TRUE FALSE 1882819.693 1378273.906 1657075.854 1642956.183 1548336.016 1359342.297 1567747.335 1353455.914 1045682.349 1.800565625 1.318061749 1.584683776 1.571180946 1.480694417 1.299957199 1.499257721 1.294327972 1 19.99601323 -3.22713506 0.169276218 6.68E-09 1.619829448 0.631160957 0.131390292 44.1306144 0.721710417 15.9637125 0.485976863 0.000592741 3.22713506 1.619829442 LFDANKDR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 127.56 0.0010679 4743830000 9299500 13868400 8508600 9204600 15451800 5570910 10485300 11618900 14429200 FALSE TRUE 8717460.895 14895230.77 8710428.01 9440805.619 14238277.96 7179141.281 8913126.606 13069545.24 12020873.3 0.725193642 1.239113864 0.724608586 0.7853677 1.184462859 0.597222939 0.741470805 1.087237583 1 23.51903837 3.948378862 21.26805627 0.849532729 1.014236946 0.027106759 0.216152891 139.2791272 103059.9942 0.051496244 0.092890748 8879.302704 -3.948378862 0.164704217 LFDDEAS(ph)VDEPR ddPTM_SK-BR-3_Pertuzumab_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 189.3 8.50E-06 635030000 1069830 1144260 1126780 1091530 1219380 897020 1236900 1032960 1203450 TRUE FALSE 1002871.25 1228982.201 1153507.754 1119540.508 1123614.814 1155975.112 1051438.328 1161927.33 1002586.42 1.000284095 1.225811737 1.150531994 1.116652375 1.12071617 1.152992987 1.048725882 1.15892985 1 19.93529517 -0.026780608 0.365989252 0.974164438 1.147877968 0.219675646 0.064054725 5.986938728 1.095624706 0.297405852 0.049339705 0.940198149 0.026780608 0.173713531 LFDDS(ph)DER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFDDSDER 8 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 LFDDS(1)DER;LFDDS(1)DER 108.7 0.003945 165429000 600640 446600 555440 483680 390690 543020 608420 439760 235300 TRUE FALSE 563047.0146 479666.7287 568615.2991 496092.0477 360006.7834 699781.0588 517193.0693 494665.004 196026.9099 2.872294497 2.446943274 2.900700212 2.530734418 1.836517157 3.569821404 2.638377912 2.523454582 1 17.58069219 3.0328253 23.22455126 2.501121974 2.702092774 0.039402188 0.665835979 457.9858829 324028.3994 0.17642335 0.210863658 1078.51279 -3.0328253 0.2009708 LFDEEEDS(ph)SEKLFDDSDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFDEEEDSSEKLFDDSDER 19 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 LFDEEEDS(0.5)S(0.5)EKLFDDSDER 188.69 9.46E-15 24411000 99809 51430 63679 68463 59879 53478 81217 49451 39915 TRUE FALSE 93562.13285 55237.93071 65189.49595 70219.87649 55176.34488 68916.23046 69039.26483 55625.06621 33252.92864 2.813650908 1.661144837 1.960413672 2.111689988 1.659292794 2.072486042 2.076185998 1.672786984 1 15.02119379 -1.958253915 0.316745935 8.74E-12 2.05161045 0.515676123 0.321442187 28.21787386 1.39120742 21.19639364 0.283797641 0.011008955 1.958253915 2.05161045 LFDFPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFDFPGR 7 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 135.87 0.0070624 478500000 1697070 2031070 1950490 2012140 2190400 1766400 2124600 1846950 1996510 FALSE TRUE 1590853.418 2181452.536 1996756.544 2063774.919 2018374.82 2276331.005 1806035.954 2077545.773 1663279.583 0.956455808 1.311536893 1.20049363 1.24078654 1.213491009 1.3685799 1.085828247 1.249065878 1 20.66559926 -0.870333375 5.604182422 0.999999901 1.212125647 0.234286755 0.114504645 1.25E-07 2.52E-08 0.097729888 0.023035145 0.134792778 0.870333375 0.212125746 LFDHPES(ph)PTPNPTEPLFLAQAEVYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LFDHPESPTPNPTEPLFLAQAEVYK 25 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 LFDHPES(0.498)PT(0.498)PNPT(0.004)EPLFLAQAEVYK;LFDHPES(0.495)PT(0.495)PNPT(0.011)EPLFLAQAEVYK;LFDHPES(0.5)PT(0.5)PNPTEPLFLAQAEVYK;LFDHPES(0.5)PT(0.5)PNPTEPLFLAQAEVYK;LFDHPES(0.5)PT(0.5)PNPTEPLFLAQAEVYK 276.27 2.90E-53 3864286000 1179786 1079348 1247673 1217730 1231589 980404 1506587 1069207 1221536 TRUE FALSE 1105945.3 1159264.049 1277268.393 1248979.013 1134864.968 1263430.719 1280688.266 1202699.848 1017653.75 1.086759912 1.139153714 1.255110977 1.227312348 1.115177896 1.241513353 1.258471524 1.18183601 1 19.95681535 4.440943946 2.611249986 1.201316487 1.088882218 0.102262635 0.079478998 0.480674397 5.986284644 0.017962311 0.087803933 27602.21574 -4.440943946 -0.112434269 LFDHPESPT(ph)PNPTEPLFLAQAEVYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LFDHPESPTPNPTEPLFLAQAEVYK 25 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 LFDHPES(0.418)PT(0.582)PNPTEPLFLAQAEVYK;LFDHPES(0.394)PT(0.606)PNPTEPLFLAQAEVYK;LFDHPES(0.299)PT(0.701)PNPTEPLFLAQAEVYK 273.33 2.04E-52 3077872000 1869495 1693571 1914483 1858706 1958836 1515457 2233946 1712695 1912804 TRUE FALSE 1752486.645 1818964.759 1959895.441 1906403.543 1804996.922 1952944.835 1898986.536 1926528.741 1593544.655 1.099741158 1.141458291 1.22989678 1.196328911 1.132693029 1.225535054 1.191674504 1.208958114 1 20.60380802 -0.96036028 4.468577008 0.999995893 1.181650931 0.637181241 0.042211914 1.67E-06 3.89E-07 0.03957949 0.009328764 0.109556896 0.96036028 0.181655038 LFDHPESPTPNPTEPLFLAQAEVYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LFDHPESPTPNPTEPLFLAQAEVYK 25 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 338.62 3.42E-88 4475920000 3055180 2888450 3104340 3134520 3436590 2689590 4190290 3047900 3658640 FALSE TRUE 2863961.737 3102313.843 3177976.411 3214957.09 3166694.084 3466030.971 3561994.915 3428437.024 3047989.348 0.939623276 1.017823059 1.042646823 1.054779634 1.038945259 1.137153243 1.168637586 1.124819228 1 21.53942643 3.545791411 0.64179479 1.120674212 0.95871395 0.44034036 0.051451138 0.877312472 0.680404873 0.029785185 0.086900333 3513.916288 -3.545791411 -0.161960262 LFDHPESPTPNPTEPLFLAQAEVYKELR ddPTM_SK-BR-3_Pertuzumab_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 0 119.45 7.17E-05 60713000 61573 99871 99603 145130 108280 49296 66707 41484 81576 FALSE TRUE 57719.25584 107265.5528 101965.6302 148854.2815 99776.12558 63526.95495 56704.90463 46663.36872 67960.4386 0.8493067 1.578352862 1.500367453 2.19030784 1.468150113 0.934763758 0.834381087 0.686625479 1 16.05240754 2.23136308 4.205233521 0.839217219 1.559760227 0.498685601 0.326177566 0.161494892 6.607660055 0.119773148 0.091284212 170.3582147 -2.23136308 0.720543009 LFDQAFGLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LFDQAFGLPR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;; 219.54 1.46E-08 2735900000 1740709 2785336 1461222 1322071 2933833 635706 1727391 2600322 2156282 FALSE TRUE 1631761.131 2991565.176 1495882.876 1355997.58 2703421.591 819224.0024 1468384.756 2924977.926 1796384.604 0.908358448 1.665325548 0.832718602 0.754848142 1.504923603 0.456040427 0.817411123 1.62825818 1 20.77666483 3.849328524 5.85984489 0.961412971 1.325795461 0.077615525 0.389750914 0.396589058 17.91854969 0.093249026 0.170603316 7068.520539 -3.849328524 0.36438249 LFDSTIADEGTWTLEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFDSTIADEGTWTLEDR 17 0 Q8WVJ2 Q8WVJ2 NUDCD2 NudC domain-containing protein 2 0 258.78 8.24E-27 22919000 15525 19749 17132 18056 18583 14208 17965 14646 20600 FALSE TRUE 14553.31796 21211.23651 17538.37913 18519.34753 17123.56614 18309.61895 15271.31503 16474.58534 17161.72692 0.848010112 1.235961661 1.021947221 1.079107459 0.997776402 1.066886744 0.889847222 0.959960814 1 14.06690711 1.752820236 24.99998572 0.941759705 1.061526194 0.138655123 0.099108996 6.375195058 11192.30864 0.042828485 0.023750821 56.60049581 -1.752820236 0.11976649 LFDSTTLEHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFDSTTLEHQK 11 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ; 208.56 1.92E-08 442930000 710470 908340 642510 611580 1056480 430380 724740 895340 1162890 FALSE TRUE 666002.9509 975594.4387 657750.6406 627274.1782 973508.3224 554623.7194 616071.9652 1007125.17 968796.1464 0.68745417 1.007017258 0.678936062 0.647477986 1.00486395 0.572487537 0.635914963 1.039563559 1 19.8858336 1.22436951 24.89592079 1.01978207 0.75703942 0.368365657 0.147710338 292.1328231 512482.5922 0.138270143 0.035246586 16.76368571 -1.22436951 -0.26274265 LFDTPHT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFDTPHTPK 9 0 P30291 P30291 WEE1 Wee1-like protein kinase 1 LFDTPHT(1)PK;LFDTPHT(1)PK 124.42 0.0019503 883890000 2499220 2022790 2312270 2095540 2606100 1724090 2809170 2096890 2695060 TRUE FALSE 2342798.281 2172559.476 2367118.136 2149315.104 2401427.419 2221806.795 2387961.038 2358691.332 2245237.075 1.043452519 0.967630323 1.054284272 0.957277576 1.06956519 0.989564451 1.063567435 1.050531081 1 21.09843636 2.71488847 24.99071663 1.036830535 1.007426533 0.12213901 0.038234472 1549.994616 1636326.399 0.011094054 0.010463011 518.6668239 -2.71488847 -0.029404002 LFDVCGS(ph)QDFESDLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LFDVCGSQDFESDLDR 16 0 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7;E7EN38 Q92878-2 RAD50 DNA repair protein RAD50 1 LFDVCGS(1)QDFESDLDR;LFDVCGS(0.994)QDFES(0.006)DLDR;LFDVCGS(0.988)QDFES(0.012)DLDR 289.95 1.76E-45 144485000 117694 112947 108541 102439 107611 120947 168339 102848 78252 TRUE FALSE 110327.7426 121309.7134 111115.6438 105067.7582 99159.66614 155862.4355 143098.1297 115688.7992 65191.23567 1.692370784 1.860828563 1.704456782 1.61168533 1.521058239 2.390849535 2.195051655 1.774606632 1 15.9923904 2.277225558 24.99920295 1.983186484 1.703579212 0 0.378278327 331.8161481 214537.7986 0.11951906 0.09999504 189.3326695 -2.277225558 -0.279607272 LFDVCGSQDFESDLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFDVCGSQDFESDLDR 16 0 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7;E7EN38 Q92878-2 RAD50 DNA repair protein RAD50 0 93.011 0.010648 29016000 22287 22633 20145 22935 21650 19924 21684 19131 19830 FALSE TRUE 20892.09645 24308.77087 20622.84891 23523.55093 19949.69633 25675.73536 18432.6855 21519.54746 16520.24489 1.264636002 1.471453421 1.248337966 1.423922653 1.207590835 1.554198229 1.115763454 1.302616735 1 14.01194745 0.726964891 0.699154959 0.998553307 1.35708233 0.409035765 0.126680018 0.969447559 0.940785011 0.113643913 0.041750136 5.332917817 -0.726964891 0.358529023 LFEAEAQDLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LFEAEAQDLFR 11 0 Q9H223 Q9H223 EHD4 EH domain-containing protein 4 0 ;;;; 161.17 6.19E-05 185526000 214454 298165 256661 235839 317216 195877 246860 279569 373804 FALSE TRUE 201031.707 320241.4468 262749.1201 241891.028 292303.1349 252423.5101 209845.6347 314473.8051 311413.6975 0.645545487 1.028347338 0.843730132 0.776751408 0.938632877 0.81057292 0.673848441 1.009826503 1 18.24847288 LFEAVEEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFEAVEEGR 9 0 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 0 110.81 0.005181 112080000 76061 84082 86063 80819 85195 74415 89525 70030 70440 FALSE TRUE 71300.47778 90307.51877 88104.455 82892.95237 78504.12836 95897.40247 76101.55736 78773.39966 58683.10894 1.215008528 1.538901404 1.501359703 1.412552161 1.337763622 1.634156816 1.296822182 1.342352187 1 15.84065768 0.740182024 1.128583904 1.001606766 1.450756022 0.543968441 0.120205186 0.608603344 1.366451507 0.104194858 0.032540205 5.497712483 -0.740182024 0.449149257 LFECDRDQMYYNLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFECDRDQMYYNLLK 15 1 P42704 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ; 215.48 1.06E-11 283740000 208392 236301 186062 190341 298740 153963 172850 227216 302780 FALSE TRUE 195349.1167 253796.9719 190475.4785 195225.4723 275278.1655 198409.6187 146932.7472 255584.4178 252244.062 0.774444858 1.006156379 0.755123736 0.77395468 1.091316732 0.786577956 0.582502304 1.013242555 1 17.94446078 LFEDDDS(ph)NEKLFDEEEDS(ph)SEKLFDDSDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFEDDDSNEKLFDEEEDSSEKLFDDSDER 29 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 2 LFEDDDS(1)NEKLFDEEEDS(0.529)S(0.471)EKLFDDSDER 101.24 0.00036059 27106000 66890 25989 32119 31946 36422 24742 47755 27301 32755 TRUE FALSE 62703.4743 27913.2526 32880.87785 32765.78844 33561.56304 31884.61375 40594.58109 30709.58995 27287.97889 2.297842378 1.022913889 1.204958344 1.200740757 1.229902851 1.168449077 1.487636048 1.125388951 1 14.73597792 4.744313372 24.97119323 1.20244352 2.297842857 0.872031851 0.134331843 221.7485469 962523.9507 0.032851826 0.292016673 55502.60561 -4.744313372 1.095399337 LFEEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFEEIR 6 0 F8VRQ3;G3V1Z2;Q8N4U5-2;Q8N4U5 F8VRQ3 TCP11L2 T-complex protein 11-like protein 2 0 105.27 0.077053 95175000 155050 204060 178670 193600 216750 163310 233360 191030 207760 FALSE TRUE 145345.6973 219168.8147 182908.1368 198568.1038 199727.3293 210454.9459 198369.8344 214880.516 173083.5138 0.839743163 1.266260488 1.056762327 1.147238691 1.153936183 1.215915608 1.146093178 1.241484595 1 17.40110879 3.056712862 8.145123839 1.163166281 1.100039612 0.080603488 0.121643753 0.793277408 101.213505 0.032133054 0.038421586 1139.496149 -3.056712862 -0.063126669 LFEGNALLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LFEGNALLR 9 0 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 ;;; 99.136 0.012892 635312000 915889 1392500 998807 1055069 1561924 789179 1073465 1256207 1286844 FALSE TRUE 858565.1424 1495602.149 1022499.174 1082143.857 1439256.79 1017002.166 912508.8888 1413047.209 1072061.423 0.800854432 1.395071324 0.953769207 1.009404716 1.342513366 0.948641695 0.851172208 1.318065531 1 20.03195614 LFEHYYQELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFEHYYQELK 10 0 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ; 123.79 0.00045266 553780000 1613560 1625560 1426560 1423480 1925430 977320 1513390 1607320 2102230 FALSE TRUE 1512570.16 1745918.154 1460398.677 1460008.907 1774214.495 1259456.419 1286471.219 1807997.44 1751354.232 0.863657467 0.996896072 0.833868243 0.83364569 1.013052906 0.719132883 0.734557976 1.032342519 1 20.74003948 3.862845088 5.32826587 0.856475291 0.936077904 0 0.115366529 0.553583462 22.70841961 0.028794307 0.053116559 7291.973598 -3.862845088 0.079602613 LFELEEQDLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFELEEQDLFR 11 0 Q9NZN4;Q9NZN4-2 Q9NZN4 EHD2 EH domain-containing protein 2 0 ; 123.63 0.00085159 41641000 41850 56967 52730 51487 60311 39535 52397 48510 59005 FALSE TRUE 39230.6832 61184.89595 53980.7805 52808.24359 55574.41734 50948.1127 44540.55628 54566.58028 49156.68431 0.798074235 1.244691273 1.098137135 1.074284084 1.13055667 1.036443231 0.906093584 1.110054127 1 15.58509999 2.014188815 8.344313526 0.989025878 1.096285118 0.023317309 0.12214057 0.302221779 131.8744751 0.043466264 0.031323814 103.3210508 -2.014188815 0.10725924 LFENLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LFENLR 6 0 Q92769;Q92769-3;Q13547;Q96G03 Q92769;Q13547;Q96G03 HDAC2;HDAC1;PGM2 Histone deacetylase 2;Histone deacetylase 1;Phosphoglucomutase-2 0 ;;;;;; 144.29 0.026267 1392680000 1565705 2112877 1606275 1678634 2202588 1308522 1945383 1909215 2279086 FALSE TRUE 1467710.319 2269316.612 1644376.602 1721710.59 2029605.623 1686271.059 1653690.879 2147584.695 1898691.823 0.773011344 1.195200076 0.866057662 0.906787805 1.068949473 0.888122569 0.870963291 1.131086503 1 20.85657433 1.233325268 24.99996603 1.065543227 0.953294248 0.149870177 0.121923092 290.6085353 1387646.369 0.100259089 0.02802463 17.11296523 -1.233325268 -0.112248978 LFFAGEHTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFFAGEHTIR 10 0 R4GMQ1;O60341;O60341-2;R4GMP9 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 196.27 3.36E-07 132500000 168670 202500 173930 176340 227320 156080 206590 224360 206550 FALSE TRUE 158113.2458 217493.3107 178055.7017 180865.1829 209467.2042 201137.7623 175613.7474 252371.8399 172075.4706 0.918859877 1.263941397 1.034753536 1.051080565 1.217298453 1.168892705 1.020562354 1.466634605 1 17.39268193 2.744467931 24.7367086 1.16249496 1.094555055 0.095802757 0.151702025 1510.595004 6325576.009 0.043474943 0.044955993 555.2236164 -2.744467931 -0.067939904 LFGGLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFGGLLR 7 0 C9JP16;O75718 C9JP16 CRTAP Cartilage-associated protein 0 82.141 0.058848 68531000 149520 243650 153420 136460 274150 115330 152460 235900 239230 FALSE TRUE 140161.8101 261690.0995 157059.1949 139961.7946 252619.3649 148623.8988 129600.0384 265352.6343 199300.9675 0.703267083 1.313039785 0.788050338 0.702263498 1.267527037 0.745725927 0.650273002 1.331416689 1 17.60458919 3.757503523 22.09074778 0.8911474 1.051360009 0 0.271306836 276.4231193 200979.9982 0.064818734 0.116814438 5721.415965 -3.757503523 0.160212609 LFGPYVWGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFGPYVWGR 9 0 Q9H4A4;C9JMZ3;H7C2T3 Q9H4A4 RNPEP Aminopeptidase B 0 ; 164.78 0.00014425 358750000 234750 352010 235800 207250 382030 184117 270630 341720 220160 FALSE TRUE 220057.4165 378073.1867 241393.2874 212568.3859 352026.9048 237268.589 230051.5439 384384.4942 183413.8737 1.199786102 2.061311825 1.316112475 1.158954781 1.919303582 1.293624 1.254275586 2.095722022 1 17.48474325 -1.566151026 2.871170829 0.969749696 1.53288687 0.178830726 0.361782267 69555379.02 70273631.65 16041630.56 0.083671628 0.027154948 1.566151026 0.563137174 LFHEVVQAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFHEVVQAFR 10 0 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 0 74.841 0.040783 129390000 29073 76525 42235 40700 61944 45120 27471 48253 27134 FALSE TRUE 27253.37283 82190.99062 43236.83414 41744.4309 57079.16811 58145.41154 23351.97858 54277.49327 22605.16011 1.20562618 3.635939327 1.912697541 1.846677073 2.52505038 2.572218523 1.033037522 2.401110765 1 14.46436452 1.197793395 0.38292916 0.949338112 2.55721702 0.163322005 0.749058222 1.700457888 0.750809492 1.053100988 0.668392849 15.76860938 -1.197793395 1.607878908 LFHTAPNVPHYAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFHTAPNVPHYAK 13 0 P53582;H0Y955 P53582 METAP1 Methionine aminopeptidase 1 0 164.11 2.17E-05 450750000 475760 604550 417840 411830 628480 356270 514420 581400 782330 FALSE TRUE 445983.0309 649311.511 427751.3621 422398.255 579121.716 459119.3654 437287.4966 653989.0698 651754.069 0.684281161 0.996252332 0.656307927 0.648094542 0.88855865 0.704436516 0.670939419 1.003429209 1 19.31396816 1.22545554 24.8694144 1.00171491 0.759500301 0.466071424 0.11170714 231.4483317 439203.9399 0.104536901 0.02678393 16.80565874 -1.22545554 -0.242214609 LFIGGLNTETNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFIGGLNTETNEK 13 0 P38159;P38159-2;H3BT71;H0Y6E7;H3BR27;P38159-3;H3BNC1;Q96E39;A0A1B0GUK8 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 116.77 0.00036515 87552000 169370 104630 122910 115710 132290 96848 138560 100570 144540 FALSE TRUE 158769.434 112376.9141 125825.4832 118679.3145 121900.477 124806.4454 117784.2143 113126.3859 120415.3402 1.318515014 0.933244168 1.044929018 0.985583018 1.012333452 1.036466327 0.978149579 0.939468224 1 16.87765967 4.745119443 24.99807239 0.993817253 1.31851516 0.890082855 0.036130372 228.1775849 869644.7314 0.008217125 0.079433119 55605.71674 -4.745119443 0.324697907 LFIGGLS(ph)FETTDDSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFIGGLSFETTDDSLR 16 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 LFIGGLS(0.999)FETT(0.001)DDSLR;LFIGGLS(0.852)FET(0.074)T(0.074)DDSLR 150.59 7.61E-07 17997800 26312 24419 20379.9 20719.4 19268.5 17481.1 21188.9 15771.1 20716.6 TRUE FALSE 24665.17889 26227.00817 20863.32085 21251.09488 17755.22974 22527.60979 18011.82115 17740.15655 17258.86563 1.429130942 1.51962526 1.20884659 1.231314696 1.02875995 1.305277547 1.043627174 1.027886591 1 14.07505002 4.165104214 0.362130798 1.012747621 1.7461737 0.744909544 0.090692972 1.906753142 0.27305019 0.081859769 0.592085466 14625.28081 -4.165104214 0.733426079 LFIGGLS(ph)FETTDESLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.999)FETTDESLR;LFIGGLS(0.978)FET(0.009)T(0.009)DES(0.003)LR;LFIGGLS(0.998)FET(0.002)TDESLR;LFIGGLS(0.999)FETTDESLR 125.5 8.05E-05 51601300 49910.7 47210 49028.4 47917.9 47751.3 33668.6 40294.3 38640.4 40036.8 TRUE FALSE 46786.87838 50705.47752 50191.3768 49147.55444 44001.10552 43388.17826 34252.54379 43464.739 33354.39943 1.402719856 1.520203583 1.504790302 1.473495409 1.319199454 1.30082325 1.026927313 1.303118621 1 15.02558944 2.262033987 1.321044264 1.107129552 1.492488692 0.740106805 0.092059717 0.190775313 0.651379826 0.050230272 0.029748389 182.8243285 -2.262033987 0.38535914 LFIGGLS(ph)FETTEESLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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;LFIGGLS(0.999)FET(0.001)T(0.001)EESLR;LFIGGLS(1)FETTEESLR 244.36 4.96E-20 139407000 121116.5 112200 101667 101523.1 79644.8 89381.3 92127.7 61033.2 104195.5 TRUE FALSE 113536.0345 120507.4047 104078.5893 104128.3546 73389.81868 115184.2303 78314.00666 68653.32937 86804.59792 1.307949546 1.388260618 1.198998575 1.199571879 0.845460038 1.326936972 0.90218731 0.790895079 1 16.40548384 3.069207639 0.573148448 0.921334197 1.39675786 0.522742552 0.146840945 0.722546275 0.503719782 0.10496709 0.172535953 1172.755934 -3.069207639 0.475423662 LFIGGLSFETTDDSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFIGGLSFETTDDSLR 16 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 163.99 1.75E-08 45534000 60165 70279 52994 57952 51205 57098 69590 52599 59709 FALSE TRUE 56399.38005 75482.53029 54251.04271 59439.14643 47183.56585 73581.26569 59155.62554 59166.10093 49743.18217 1.13381126 1.517444743 1.090622681 1.194920466 0.948543374 1.479223131 1.189220773 1.189431362 1 15.60221118 -5 0.149818361 0.202589564 1.304700343 0.13527056 0.169269124 257.7109507 2.295930619 61.75828182 0.819475517 1.00E-05 5 1.102110779 LFIGGLSFETTDDSLREHFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFIGGLSFETTDDSLREHFEK 21 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 286 1.20E-45 284420000 439510 662100 547790 647240 1006190 370530 631980 547720 1391140 FALSE TRUE 412001.8536 711122.5729 560783.8375 663849.2742 927167.8962 477495.9959 537220.466 616104.0477 1158949.747 0.355495874 0.613592241 0.483872436 0.572802467 0.800006988 0.412007507 0.463540777 0.53160549 1 20.14438658 -0.7968785 4.252595952 1.000003498 0.531689945 0.597580237 0.121422736 47875597.45 114201098 2812.454173 0.027681993 0.159632568 0.7968785 -0.468313552 LFIGGLSFETTDESLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LFIGGLSFETTDESLR 16 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;F8W646 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ;; 269.81 1.02E-27 409574000 149240 141578 163610 162975 168879 126820 155745 134559 152913.4 FALSE TRUE 139899.3348 152060.5824 167490.9065 167157.2144 155615.9246 163430.8752 132392.4831 151358.9874 127391.1657 1.0981871 1.193650922 1.314776465 1.312157036 1.221559782 1.282905878 1.039259531 1.188143515 1 16.95890571 1.741734736 10.81414622 1.087000506 1.243403906 0.480912652 0.078556829 0.076604404 49.91589654 0.035680952 0.019439813 55.17403375 -1.741734736 0.1564034 LFIGGLSFETTEESLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LFIGGLSFETTEESLR 16 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;; 339.5 1.40E-71 658600000 211147 218441 203496.6 206121.4 246486.6 181941.3 229082.1 182972.2 228695.5 FALSE TRUE 197931.6862 234614.5989 208323.6355 211410.8241 227128.5367 234464.7997 194733.3658 205816.6819 190524.7436 1.038876539 1.231412752 1.093420369 1.109623979 1.192120941 1.230626507 1.022089636 1.080262217 1 17.53961885 1.661515456 8.530303033 1.038693147 1.152228618 0.423899781 0.063035075 0.110843583 13.81931931 0.028940213 0.01521595 45.86859697 -1.661515456 0.113535471 LFIHESIHDEVVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFIHESIHDEVVNR 14 0 P49419;P49419-2;A0A1B0GW77;A0A1B0GW82;A0A1B0GTG2;A0A1B0GUA1;A0A1B0GV49;A0A1B0GTJ4;A0A1B0GUY0 P49419 ALDH7A1 Alpha-aminoadipic semialdehyde dehydrogenase 0 138.42 8.97E-06 36010000 20701 23118 21309 22515 30017 20105 27984 21337 28461 FALSE TRUE 19405.36136 24829.68077 21814.45954 23092.77302 27659.5859 25908.98712 23788.05899 24000.97142 23710.67523 0.818422975 1.047194166 0.920026921 0.973939915 1.166545686 1.092714015 1.003263667 1.012243269 1 14.53324913 4.742772295 24.23633323 1.02323435 0.818422848 0.490293656 0.066733983 263.8005366 1517964.854 0.016710097 0.127935484 55306.00587 -4.742772295 -0.204811501 LFIVDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFIVDAR 7 0 Q9UNZ2;Q9UNZ2-5;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ; 121.29 0.010358 260043000 934680 1079760 1093430 996960 1037290 959780 1123500 1010930 969970 FALSE TRUE 876180.0473 1159706.554 1119366.676 1022543.681 955825.4276 1236852.905 955041.6051 1137146.836 808075.7408 1.084279608 1.43514586 1.385224948 1.265405741 1.182841384 1.530615068 1.181871398 1.407228034 1 19.624131 -1.495268117 2.809819346 0.987755715 1.321605467 0.334798453 0.135899537 18598492.61 20025704.34 1762819.802 0.029251766 0.031969208 1.495268117 0.333849752 LFKDDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFKDDIR 7 1 Q9UBT2;Q9UBT2-2;K7EPL2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 69.198 0.055076 431540000 1227100 1404400 1421700 1389700 1640700 1132800 1659500 1387400 2120400 FALSE TRUE 1150298.001 1508383.237 1455423.395 1425362.055 1511846.04 1459820.971 1410673.381 1560619.944 1766491.542 0.651176626 0.853886476 0.823906235 0.806888695 0.855846747 0.826395675 0.798573527 0.883457354 1 20.75245541 -5 0.147665125 1.646654646 0.757380969 0.600793997 0.054288618 102.8356023 0.909215956 19.52715256 0.274843308 1.00E-05 5 -0.889273678 LFLEFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LFLEFER 7 0 O43663-2;O43663-4;O43663;O43663-3;H0YL53 O43663-2 PRC1 Protein regulator of cytokinesis 1 0 ;; 105.12 0.018609 41019000 159142 243260 144409 163287 271332 113463 154223 215355 206387 FALSE TRUE 149181.5863 261271.2235 147834.4497 167477.2209 250022.6792 146217.9262 131098.6929 242242.5458 171939.6764 0.867639101 1.519551676 0.859804164 0.974046389 1.454130219 0.850402474 0.762469115 1.408881015 1 17.39154297 LFNHLSAVSESIQALGWVAMAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFNHLSAVSESIQALGWVAMAPK 23 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 87.772 0.0063651 54853000 45045 68212 55041 45178 78635 37141 62645 78761 40597 FALSE TRUE 42225.71386 73262.48745 56346.59851 46337.34397 72459.3243 47863.00377 53251.96382 88594.48422 33821.09843 1.248502143 2.166177057 1.666019175 1.370072118 2.142429656 1.415181824 1.574519051 2.619503456 1 15.0456359 -1.166083805 4.353099402 0.999838951 1.768760396 0.247408269 0.424821104 68.99846794 110450715.5 38209.07812 0.08911562 0.068220704 1.166083805 0.768921445 LFNPNDDGKEEPPTTLLWVQYYLAQHYDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFNPNDDGKEEPPTTLLWVQYYLAQHYDK 29 1 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 161.49 3.84E-12 69597000 174940 108720 118450 118780 140520 99523 163760 125950 99092 FALSE TRUE 163990.8177 116769.7419 121259.6899 121828.0959 129484.126 128253.6745 139205.7083 141675.1348 82552.90504 1.986493602 1.414483741 1.468872475 1.475757829 1.568498722 1.553593716 1.686260565 1.716173824 1 16.33303136 -1.958706017 2.873905211 0.559318541 1.579188072 0.566333366 0.165627295 13278818.57 11064602.77 38332691.52 0.039442661 0.0109975 1.958706017 1.019869532 LFNVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LFNVDR 6 0 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;;;;; 178.24 0.0081811 2504216000 2982033 3681637 3287153 3140337 3865990 2699983 3568900 3305420 3346914 FALSE TRUE 2795392.878 3954229.234 3365125.821 3220923.364 3562370.74 3479424.262 3033776.577 3718108.963 2788292.432 1.002546521 1.418154419 1.206876934 1.155159813 1.277617333 1.247869206 1.088041033 1.333471669 1 21.41095045 -4.318052616 0.266957215 1.90E-09 1.243184235 0.211063297 0.120903254 191.2681714 2.621330698 104.4412486 0.142174015 4.81E-05 4.318052616 1.243184234 LFNVPTT(ph)T(ph)DT(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFNVPTTTDTK 11 0 Q8WW62 Q8WW62 TMED6 Transmembrane emp24 domain-containing protein 6 3 LFNVPT(0.621)T(0.69)T(0.69)DT(1)K 44.543 0.065373 0 508020 251710 315940 313220 306340 222540 405660 266730 335660 TRUE FALSE 476223.935 270346.8703 323434.246 321257.7555 282281.2921 286783.6854 344835.049 300031.8276 279636.1776 1.703012604 0.966780739 1.156625186 1.148841893 1.009459129 1.025560025 1.233156067 1.072936379 1 18.09319149 4.745565581 24.9936128 1.088913131 1.70301289 0.8478026 0.083257372 315.3795582 1125241.631 0.019648523 0.198228766 55662.86823 -4.745565581 0.614099759 LFNYHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFNYHK 6 0 P04181 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ; 99.511 0.038715 1196550000 1552980 1666010 1366410 1199820 2177200 1215070 1338830 1732050 2500300 FALSE TRUE 1455781.754 1789363.114 1398821.89 1230609.412 2006211.494 1565840.984 1138084.871 1948300.255 2082983.777 0.698892507 0.85903843 0.671547184 0.590791645 0.96314312 0.751729803 0.546372412 0.93534106 1 20.99022017 1.059046824 8.578574146 0.999835008 0.729516134 0.418673816 0.119703857 0.229772489 29.14062085 0.113075258 0.028304871 11.45636454 -1.059046824 -0.270318873 LFPADT(ph)SPSTATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LFPADTSPSTATK 13 0 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 LFPADT(0.725)S(0.275)PSTATK;LFPADT(0.606)S(0.386)PS(0.007)T(0.002)ATK;LFPADT(0.596)S(0.403)PS(0.001)TATK 167.71 0.00035155 557590000 1340510 1000120 1160510 1039040 1313880 998010 1479790 1156100 1672660 TRUE FALSE 1256609.872 1074169.925 1188037.845 1065703.525 1210693.165 1286119.286 1257909.227 1300441.63 1393482.24 0.90177674 0.770852971 0.852567626 0.764777257 0.868825687 0.922953482 0.902709192 0.933231578 1 20.41026318 1.722899543 0.723274166 0.987604922 0.81625419 0.619880206 0.044142085 0.379630988 0.396492195 0.037356137 0.017965014 52.83230303 -1.722899543 -0.171350733 LFPADTS(ph)PSTATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFPADTSPSTATK 13 0 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 LFPADT(0.124)S(0.863)PS(0.011)T(0.001)ATK 139.48 4.08E-05 142010000 432880 339030 392160 371040 412250 326450 507900 373440 521790 TRUE FALSE 405786.8135 364132.134 401462.2204 380561.5146 379873.5479 420690.8155 431745.1101 420064.806 434699.8781 0.933487295 0.837663299 0.923538838 0.875458066 0.873875442 0.967773024 0.99320274 0.966332928 1 18.72966017 2.169583396 4.950938461 0.984157353 0.885939403 0.734121027 0.027898341 0.095961855 4.448311162 0.009891137 0.007279582 147.769021 -2.169583396 -0.09821795 LFPDIPIGYSGHETGIAISVAAVALGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFPDIPIGYSGHETGIAISVAAVALGAK 28 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 0 199.46 4.76E-25 56492000 47777 59592 53849 53651 67781 53065 72362 59599 54420 FALSE TRUE 44786.72285 64004.25369 55126.32371 55027.77549 62457.75368 68384.00406 61511.98988 67040.06634 45336.95043 0.987863595 1.411745895 1.215924829 1.213751145 1.377634646 1.508350328 1.356773874 1.478707008 1 15.46839973 2.729736244 22.27137083 1.378825469 1.242826032 0.103481663 0.171871474 283.7430257 716120.127 0.049373019 0.047330626 536.7057454 -2.729736244 -0.135999436 LFPDT(ph)PLALDANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LFPDTPLALDANK 13 0 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 LFPDT(1)PLALDANK;LFPDT(1)PLALDANK;LFPDT(1)PLALDANK 200.55 1.22E-06 637791000 1372790 1074190 1200410 1016610 1220340 890050 1475820 1096650 1862300 TRUE FALSE 1286869.524 1153724.145 1228884.292 1042697.934 1124499.419 1146992.986 1254534.492 1233569.167 1551470.099 0.829451709 0.743632859 0.792077329 0.672070918 0.724796063 0.739294291 0.808610164 0.795096965 1 20.56520446 0.53084649 1.002558349 1.00009082 0.752499 0.754868872 0.043323098 0.766862923 1.131411082 0.040607221 0.012871417 3.395052467 -0.53084649 -0.24759182 LFPDT(ph)PLALDANKK ddPTM_SK-BR-3_Pertuzumab_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 107.75 0.00050738 868500000 1907800 1184600 1394400 1282000 1510300 912630 1756600 1385200 3005600 TRUE FALSE 1788394.204 1272309.017 1427475.826 1314898.29 1391687.13 1176091.466 1493214.137 1558145.269 2503945.943 0.714230356 0.508121599 0.570090513 0.525130462 0.555797594 0.46969523 0.596344399 0.622275922 1 21.25577199 0.590470989 1.605742626 0.999845309 0.552406451 0.817391949 0.064419212 0.660766429 2.158397459 0.054594907 0.015617128 3.894672902 -0.590470989 -0.447438858 LFPEFDDS(ph)DYDEVPEEGPGAPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFPEFDDSDYDEVPEEGPGAPAR 23 0 Q96P48-3;Q96P48 Q96P48-3 ARAP1 "Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1" 1 LFPEFDDS(0.594)DY(0.406)DEVPEEGPGAPAR 63.361 0.02485 18711000 12470 12939 13163 12717 14471 13034 11656 10445 11393 TRUE FALSE 11689.52496 13897.01702 13475.23258 13043.33975 13334.50603 16796.70421 9908.291009 11749.08124 9491.434698 1.231586723 1.464164003 1.419725574 1.374222145 1.404898886 1.769669681 1.04391921 1.237861463 1 13.21241046 1.629666333 13.0108163 1.1057784 1.438064048 0.560129103 0.145940003 0.076281969 35.16634746 0.063183243 0.034139416 42.62519055 -1.629666333 0.332285648 LFPLIQAMHPTLAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFPLIQAMHPTLAGK 15 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;Q9H361;H0YB75;H0YAS6 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 147.35 3.72E-06 157280000 125320 168110 144360 145680 169960 107110 190470 163260 188460 FALSE TRUE 117476.4449 180557.0393 147784.2874 149418.3954 156612.0272 138030.9182 161910.7917 183643.3704 157004.8085 0.748234694 1.150009615 0.941272365 0.951680378 0.997498285 0.879150897 1.031247344 1.169667172 1 17.26044922 1.487352231 7.226228364 1.090216455 0.969545613 0.209048473 0.108572808 0.19096038 25.91241059 0.056307336 0.025417749 30.71512101 -1.487352231 -0.120670842 LFQECCPHSTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LFQECCPHSTDR 12 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;; 245.5 1.80E-16 38526950000 10468800 15610340 13567920 13593190 16538960 12621790 16296900 12570080 17185150 FALSE TRUE 9813576.495 16766145.82 13889757.47 13942014.27 15240056.8 16265495.88 13853331.14 14139482.16 14316837.44 0.685457004 1.17107887 0.970169391 0.973819415 1.064484867 1.136109559 0.967625091 0.987612118 1 23.7712095 4.752745513 24.85611194 1.036085151 0.685456745 0.702875004 0.07117678 1330.981995 2332228.773 0.016720534 0.358156994 56590.75822 -4.752745513 -0.350628406 LFQEDPEAFLLYHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFQEDPEAFLLYHR 14 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 0 ; 178.67 1.96E-06 128983000 136920 191639 152286 151107 188967 114248 147764 166979 174826 FALSE TRUE 128350.4216 205828.151 155898.2958 154984.6614 174126.2941 147229.5429 125608.16 187826.6957 145646.4112 0.881246716 1.413204413 1.070388859 1.064115897 1.195541261 1.010869693 0.862418504 1.289607442 1 17.15211063 2.889452235 1.048252125 1.023443618 1.183279483 0 0.173155413 1.083148919 2.537332265 0.080885591 0.088484034 775.2686731 -2.889452235 0.159835865 LFQLGPPS(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFQLGPPSPVK 11 0 Q9NZH5-2;Q9NZH5;O95997 Q9NZH5-2 PTTG2;PTTG1 Securin-2;Securin 1 LFQLGPPS(1)PVK;LFQLGPPS(1)PVK 172.1 1.44E-05 802600000 1693080 1163800 1295080 1107060 1258710 1034960 1613590 1240160 1198860 TRUE FALSE 1587113.145 1249968.963 1325799.909 1135469.034 1159855.994 1333736.151 1371647.159 1394996.706 998762.5211 1.589079598 1.25151769 1.327442591 1.136875894 1.16129307 1.335388666 1.373346647 1.396725124 1 19.92978216 4.740580241 24.41574959 1.269639724 1.589079746 0.421284125 0.123364476 133.5163535 1613947.038 0.027736458 0.181733319 55027.5581 -4.740580241 0.319440023 LFQQIYSDGSDEVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFQQIYSDGSDEVKR 15 1 Q9Y2Z0;Q9Y2Z0-2 Q9Y2Z0 SUGT1 Suppressor of G2 allele of SKP1 homolog 0 161.82 2.61E-06 93281000 58112 46330 54361 46634 58198 47071 66156 52310 75445 FALSE TRUE 54474.87365 49760.32141 55650.46859 47830.70739 53627.36384 60659.63357 56236.52196 58841.01865 62852.74211 0.866706397 0.791696905 0.885410353 0.760996351 0.853222342 0.965107194 0.894734582 0.936172658 1 15.93968807 2.355567865 5.39189161 0.935776011 0.828289925 0.636015339 0.043953605 0.137784719 5.969750708 0.014200858 0.011769942 226.7607396 -2.355567865 -0.107486086 LFRPPS(ph)PAPAAPGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LFRPPSPAPAAPGAR 15 1 Q86U90 Q86U90 YRDC "YrdC domain-containing protein, mitochondrial" 1 LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR 141.6 2.87E-06 7323500000 4339860 4988290 5104180 5039920 5367950 4510300 5128210 4367790 5321450 TRUE FALSE 4068235.909 5357628.182 5225253.56 5169252.88 4946372.86 5812350.391 4359282.518 4913118.196 4433265.617 0.917661214 1.208506019 1.178646626 1.1660147 1.115740244 1.311076505 0.983311828 1.108239077 1 22.07993837 1.647436237 13.66023107 1.034726652 1.158756661 0.225298609 0.102965105 0.167292606 48.78627073 0.043704357 0.023958927 44.40544609 -1.647436237 0.124030009 LFS(ph)ADPFDLEAQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFSADPFDLEAQAK 14 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2;H0YII4;H0YI90 Q5TDH0 DDI2 Protein DDI1 homolog 2 1 LFS(1)ADPFDLEAQAK 106.17 0.0010039 12246000 49165 40104 42270 72016 71986 19972 27379 19793 25729 TRUE FALSE 46087.85041 43073.34189 43272.66436 73864.05248 66332.50994 25737.59218 23273.77312 22264.19962 21434.66368 2.150155052 2.009517972 2.018817043 3.446009397 3.094637309 1.200746257 1.085800714 1.038700674 1 14.38765816 2.157233759 7.671149321 1.079848864 2.438631845 0.711797127 0.460052779 0.159003223 12.92472176 0.193934707 0.143180683 143.6262294 -2.157233759 1.358782981 LFSDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFSDLR 6 0 Q9UL54-2;Q9UL54-4;Q9UL54 Q9UL54-2 TAOK2 Serine/threonine-protein kinase TAO2 0 100.78 0.086717 26777000 122440 282380 126000 130160 284070 89559 129830 274410 199180 FALSE TRUE 114776.699 303287.709 128988.7795 133500.126 261760.2881 115413.2294 110363.1968 308670.6926 165935.5712 0.691694361 1.827743785 0.777342546 0.804529884 1.577481465 0.695530371 0.665096675 1.860183987 1 17.34026366 3.85402047 8.560203985 1.00919285 1.334827143 0.019457782 0.473324875 0.665633369 44.74183313 0.112403012 0.20319993 7145.300041 -3.85402047 0.325634293 LFSLELVDESGEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFSLELVDESGEIR 14 0 P27694 P27694 RPA1 "Replication protein A 70 kDa DNA-binding subunit;Replication protein A 70 kDa DNA-binding subunit, N-terminally processed" 0 169.58 7.70E-06 13662000 31768 32347 33036 35009 31755 31419 34151 30104 30734 FALSE TRUE 29779.69759 34742.00554 33819.62952 35907.39021 29261.09039 40489.15526 29030.37459 33862.55067 25604.29685 1.16307422 1.356881844 1.320857578 1.402397044 1.142819526 1.581342206 1.133808703 1.322533904 1 14.64409832 0.304498579 0.878341474 0.997853762 1.317983676 0.325821202 0.135861032 2.897665693 2.782386028 0.129828032 0.03773087 2.016037375 -0.304498579 0.320129914 LFSLS(ph)NPSLSTTNLSGPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFSLSNPSLSTTNLSGPSR 19 0 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 LFSLS(0.996)NPS(0.004)LSTTNLSGPSR;LFSLS(1)NPSLSTTNLSGPSR 372.22 4.99E-108 300120000 253830 334540 292810 275130 357100 205002 291080 230100 224020 TRUE FALSE 237943.2334 359309.6897 299755.5915 282190.3016 329054.8065 264182.7495 247435.2563 258828.4915 186629.6148 1.274948961 1.925255486 1.606152335 1.512033886 1.763143576 1.415545704 1.325809179 1.386856485 1 17.50981841 1.297424503 0.611994612 1.01180478 1.676106415 0.506740853 0.181801652 0.497992271 0.453726449 0.166835144 0.07897433 19.83464826 -1.297424503 0.664301635 LFSQDHLVIYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFSQDHLVIYK 11 0 Q9BW91-2;Q9BW91;H7C386 Q9BW91-2 NUDT9 "ADP-ribose pyrophosphatase, mitochondrial" 0 87.618 0.01359 278730000 629040 671740 638220 620060 817330 571350 799000 668580 1012900 FALSE TRUE 589669.5093 721476.3285 653358.8798 635971.7894 753140.1988 736289.4699 679197.3676 752053.6847 843840.4464 0.698792659 0.854991405 0.774268267 0.753663553 0.892514932 0.872545839 0.804888377 0.89122735 1 19.68661071 -4.999999999 0.109587549 1.61411445 0.707214897 0.636680862 0.051295789 112.919621 0.82415436 15.41549485 0.623344909 1.00E-05 4.999999999 -0.906899553 LFVGEPVWTAYNRPADHFEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFVGEPVWTAYNRPADHFEAR 21 1 Q9BV57;Q9BV57-2;A0A0G2JQN5;H7C382 Q9BV57 ADI1 "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase" 0 ; 161.08 1.22E-11 283410000 347920 349100 338290 323900 379880 374450 485970 306500 423640 FALSE TRUE 326144.3083 374947.7272 346314.3986 332211.8224 350045.7572 482547.6363 413103.31 344767.1997 352931.7472 0.924100229 1.062380277 0.981250345 0.941291978 0.99182281 1.367254831 1.17049065 0.976866497 1 18.42902968 2.403615601 24.99999869 1.157049118 0.989542204 0.285453537 0.112290402 44.57931138 15160.59294 0.036859478 0.030838854 253.2885749 -2.403615601 -0.167506914 LFVGGIKEDTEEHHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LFVGGIKEDTEEHHLR 16 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;; 206.63 1.26E-11 3474720000 2971739 3633270 3319100 3791950 4978000 2323328 3747650 3083350 6666650 FALSE TRUE 2785743.161 3902281.091 3397830.619 3889257.857 4587047.96 2994035.078 3185724.674 3468313.035 5553943.047 0.501579353 0.702614531 0.611787084 0.700269669 0.825908354 0.539082784 0.573596929 0.624477602 1 22.40508095 -1.268193138 4.584662721 1.000160038 0.637498563 0.606754557 0.092347347 0.000145833 2.33E-05 0.086319929 0.020336883 0.053927075 1.268193138 -0.362661474 LFVGNLPADITEDEFKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LFVGNLPADITEDEFKR 17 1 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;; 260.24 4.96E-27 1895320000 690404 592901 647921 602956 679312 497052 687068 566813 867580 FALSE TRUE 647192.846 636800.007 663289.9921 618428.8718 625961.5757 640542.8434 584048.5318 637580.8508 722775.2932 0.895427462 0.881048388 0.917698762 0.855630896 0.866052813 0.886226811 0.808063775 0.882128729 1 19.46318767 3.229232888 24.94412292 0.868630071 0.897219039 0 0.04975265 507.4043448 1356895.295 0.012942295 0.015668816 1695.246623 -3.229232888 0.028588968 LFVGNLPPDITEEEMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFVGNLPPDITEEEMR 16 0 Q15233;C9JYS8;C9IZL7;C9J4X2 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 139.46 4.17E-06 21445000 34854 42761 36993 34080 43978 38541 45222 38503 49647 FALSE TRUE 32672.55036 45927.06893 37870.49143 34954.5505 40524.14528 49667.16104 38441.38092 43310.18431 41360.59497 0.789943916 1.11040639 0.915617666 0.845117207 0.979776652 1.200832848 0.929420405 1.047136395 1 15.33596932 2.467980762 24.99649231 1.039796609 0.944311062 0.226770397 0.106370853 379.3089829 1037287.884 0.035636248 0.029854413 293.7519529 -2.467980762 -0.095485546 LFVGNLPTDITEEDFKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LFVGNLPTDITEEDFKR 17 1 Q8WXF1;Q8WXF1-2;X6RDA4 Q8WXF1 PSPC1 Paraspeckle component 1 0 180.14 1.41E-09 354210000 612740 538860 546430 538590 623280 462490 716320 497940 886670 FALSE TRUE 574389.6972 578757.7551 559391.5776 552411.1312 574330.103 596003.3551 608914.466 560108.9051 738679.0489 0.777590346 0.783503683 0.757286373 0.747836468 0.777509669 0.806850223 0.82432887 0.758257468 1 19.49458813 -5 0.27656575 2.57919518 0.765692359 0.899561037 0.023165049 65.69286908 0.632555628 59.3956052 0.02744777 1.00E-05 5 -1.813502821 LFVLLPEQS(ph)PVSYSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFVLLPEQSPVSYSK 15 0 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 LFVLLPEQS(1)PVSYSK;LFVLLPEQS(1)PVSYSK 202.63 6.10E-09 318100000 1629520 1481460 1594650 1557520 1673890 1383980 1911990 1453450 1533180 TRUE FALSE 1527531.252 1591148.84 1632475.851 1597488.6 1542429.432 1783512.559 1625304.85 1634916.432 1277282.353 1.195922928 1.245729917 1.27808534 1.250693393 1.207586895 1.396333829 1.272471075 1.279996101 1 20.28464605 -1.268655277 6.166928214 0.999991688 1.269051748 0.703683437 0.054181274 5.88E-06 6.97E-07 0.049822834 0.011742992 0.053869721 1.268655277 0.26906006 LFVPALDKPETDLLSHLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFVPALDKPETDLLSHLDR 19 1 V9GYV5;V9GY92;Q9UNI6 V9GYV5 DUSP12 Dual specificity protein phosphatase 12 0 ; 207.56 1.87E-16 253610000 523440 480200 530810 493190 554000 424440 643140 455820 597330 FALSE TRUE 490678.8248 515754.5076 543401.0639 505846.0904 510491.0747 546968.9378 546707.1276 512730.1304 497631.7641 0.986027943 1.03641798 1.091974233 1.016506837 1.025841017 1.09914394 1.098617828 1.030340439 1 18.92471905 2.257846571 24.97964904 1.07003024 1.039635796 0.029795375 0.040129082 523.5316723 678089.2442 0.013723206 0.011465339 181.0700291 -2.257846571 -0.030394444 LFVT(ph)PPEGSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LFVTPPEGSSR 11 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 LFVT(0.995)PPEGS(0.004)S(0.001)R;LFVT(0.549)PPEGS(0.424)S(0.027)R;LFVT(1)PPEGSSR;LFVT(1)PPEGSSR 129.34 0.0024513 373303000 1193500 1224830 1366900 1239700 1304150 1267760 1497770 1142440 1632750 TRUE FALSE 1118800.965 1315517.688 1399323.513 1271512.801 1201727.32 1633741.732 1273193.293 1285076.149 1360233.477 0.822506565 0.967126387 1.02873774 0.934775406 0.88347136 1.201074491 0.93601085 0.944746744 1 20.37542287 LFYSTFATDDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LFYSTFATDDRK 12 1 P30084 P30084 ECHS1 "Enoyl-CoA hydratase, mitochondrial" 0 ; 237.67 6.60E-16 685580000 481240 489970 461720 425180 689160 460600 505400 513780 1061620 FALSE TRUE 451120.0474 526247.8886 472672.2164 436090.8386 635036.1535 593567.7428 429619.9619 577926.564 884428.7637 0.510069398 0.595014443 0.534437861 0.493076273 0.718018431 0.671131206 0.485759825 0.653446143 1 19.75438642 -5 0.304898243 4.634923299 0.555998255 0.753880506 0.075992438 138.5198281 1.268986987 322.4844635 0.072366284 1.00E-05 5 -4.078925044 LGADES(ph)EEEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGADESEEEGR 11 0 O43847;O43847-2;F5H7V1 O43847 NRD1 Nardilysin 1 LGADES(1)EEEGR;LGADES(1)EEEGR 194.98 2.90E-07 693340000 768320 658390 734640 685500 650020 677180 925970 658690 597610 TRUE FALSE 720232.2227 707137.8807 752066.0077 703091.0905 598970.0513 872670.8729 787129.3948 740928.8965 497865.0303 1.446641517 1.420340529 1.51058211 1.412212242 1.203077169 1.752826208 1.581009605 1.48821237 1 18.92539516 2.244446243 24.99973617 1.521077251 1.417433731 0 0.206939427 437.7594508 1859429.457 0.065736237 0.053662367 175.5683563 -2.244446243 -0.10364352 LGADES(ph)EEEGRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGADESEEEGRR 12 1 O43847;O43847-2;F5H7V1 O43847 NRD1 Nardilysin 1 LGADES(1)EEEGRR 98.253 0.0027336 151660000 308350 297130 313930 322770 324190 278690 347070 276730 318170 TRUE FALSE 289050.9239 319129.8144 321376.5678 331052.8246 298729.4251 359143.2788 295030.0755 311280.3497 265065.3715 1.090489196 1.20396645 1.212442674 1.248947845 1.127002835 1.354923417 1.113046468 1.174353134 1 18.01598868 0.677418825 1.300805466 1.000938866 1.202095 0.393299421 0.075122222 1.005720729 2.684980881 0.062912307 0.018867955 4.757938505 -0.677418825 0.201156135 LGAGEGGEASVS(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LGAGEGGEASVSPEK 15 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 LGAGEGGEAS(0.001)VS(0.999)PEK;LGAGEGGEASVS(1)PEK;LGAGEGGEASVS(1)PEK;LGAGEGGEASVS(1)PEK;LGAGEGGEASVS(1)PEK;LGAGEGGEASVS(1)PEK 355.38 1.60E-82 6652850000 10630340 5571940 7353140 6476340 6210950 5481690 8989230 6131520 5698610 TRUE FALSE 9965005.995 5984492.235 7527559.953 6642533.849 5723167.041 7064164.915 7641378.413 6897053.769 4747475.177 2.099011711 1.260563144 1.585592272 1.399171897 1.205518055 1.487983539 1.609566797 1.452783535 1 22.17872903 4.746694911 24.72200679 1.415941854 2.099012107 0.589909873 0.186942896 630.3431681 1915708.068 0.041280998 0.46192101 55807.80109 -4.746694911 0.683070253 LGAGEGGEASVS(ph)PEKTSTTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LGAGEGGEASVSPEKTSTTSK 21 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 LGAGEGGEAS(0.003)VS(0.997)PEKTSTTSK;LGAGEGGEAS(0.001)VS(0.997)PEKT(0.001)STTSK;LGAGEGGEASVS(1)PEKTSTTSK;LGAGEGGEAS(0.002)VS(0.998)PEKTSTTSK;LGAGEGGEASVS(0.999)PEKTSTTSK 283.37 2.27E-45 15805900000 6624430 3670100 4467970 4576350 5313660 2928410 6065460 3856400 7319600 TRUE FALSE 6209818.751 3941838.023 4573952.358 4693786.889 4896346.578 3773794.428 5156000.582 4337880.029 6097911.474 1.018351739 0.646424278 0.750085071 0.769736804 0.802954684 0.618866713 0.845535493 0.711371434 1 22.53988378 -1.162990163 3.457772922 1.000306871 0.758176027 0.290294587 0.111362037 45373375.84 75109475.85 156105.4762 0.023640603 0.0687084 1.162990163 -0.242130844 LGAGGGS(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LGAGGGSPEK 10 0 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 LGAGGGS(1)PEK;LGAGGGS(1)PEK;LGAGGGS(1)PEK;LGAGGGS(1)PEK 145.31 3.22E-05 1443450000 5327130 2809460 3750730 3594910 3117810 3122310 4846560 3127290 2856950 TRUE FALSE 4993714.442 3017475.342 3839699.087 3687161.477 2872949.779 4023670.211 4119863.321 3517739.041 2380106.588 2.098105382 1.267790004 1.613246695 1.549158132 1.207067697 1.690542025 1.730957488 1.477975422 1 21.18259475 -1.942571939 1.655252645 0.549923735 1.560197776 0.347223968 0.248415286 183522.4113 56197.75132 318155.5931 0.062007401 0.011413742 1.942571939 1.010274041 LGAGGGS(ph)PEKS(ph)PSAQELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LGAGGGSPEKSPSAQELK 18 1 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 2 LGAGGGS(1)PEKS(0.86)PS(0.141)AQELK;LGAGGGS(1)PEKS(0.969)PS(0.031)AQELK;LGAGGGS(0.999)PEKS(0.501)PS(0.501)AQELK;LGAGGGS(1)PEKS(0.939)PS(0.061)AQELK 177.5 5.32E-14 1556770000 4356330 1800140 2564990 2452690 2570040 1860550 3434720 2068730 3812220 TRUE FALSE 4083675.082 1933424.239 2625832.774 2515630.178 2368199.425 2397660.581 2919715.622 2327015.494 3175935.854 1.285817872 0.608773076 0.826790242 0.792090991 0.745669791 0.754946161 0.919324494 0.732702297 1 21.59875034 -1.746464613 6.780198274 1.003568328 0.8131535 0.068619476 0.179968941 0.008689982 0.000324949 0.155989697 0.036189887 0.017928146 1.746464613 -0.190414828 LGAGGGS(ph)PEKSPSAQELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LGAGGGSPEKSPSAQELK 18 1 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 LGAGGGS(0.999)PEKS(0.001)PSAQELK;LGAGGGS(0.822)PEKS(0.171)PS(0.007)AQELK;LGAGGGS(0.94)PEKS(0.06)PSAQELK;LGAGGGS(0.998)PEKS(0.002)PSAQELK;LGAGGGS(0.511)PEKS(0.366)PS(0.123)AQELK;LGAGGGS(0.993)PEKS(0.005)PS(0.002)AQELK 310.4 1.02E-60 13347490000 12265800 5925193 8349930 8098260 8404000 5868552 11193630 6650340 10117380 TRUE FALSE 11498105.47 6363900.455 8547994.283 8306075.062 7743983.74 7562707.694 9515249.098 7480649.588 8428723.917 1.364157325 0.755025377 1.014150465 0.985448704 0.91876111 0.897254171 1.128907435 0.88751864 1 23.0068828 LGAGGGSPEKS(ph)PSAQELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGAGGGSPEKSPSAQELK 18 1 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 LGAGGGSPEKS(0.999)PS(0.001)AQELK 120.33 2.91E-05 564450000 593130 376580 420240 403310 433830 289270 501100 353000 599640 TRUE FALSE 556007.0521 404462.375 430208.2913 413659.6174 399758.7418 372777.5531 425964.707 397072.827 499556.2102 1.113001982 0.809643373 0.861180949 0.828054199 0.800227749 0.746217434 0.852686241 0.794851148 1 18.93028749 4.740850855 24.825729 0.828256954 1.113002091 0.626474518 0.066795733 107.4019366 1164133.955 0.013691697 0.091511758 55061.85706 -4.740850855 0.284745137 LGAPENSGIST(ph)LER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LGAPENSGISTLER 14 0 A0A1B0GV68;M0QYB0;Q9Y4F1-3;C9JME2;Q9Y4F1;Q9Y4F1-2 A0A1B0GV68;C9JME2 FARP1 "FERM, RhoGEF and pleckstrin domain-containing protein 1" 1 LGAPENSGIS(0.066)T(0.934)LER;LGAPENSGIS(0.087)T(0.913)LER;LGAPENSGIS(0.083)T(0.917)LER 170.48 3.54E-05 431241000 443130 508830 423910 427170 660370 345980 494360 475590 702340 TRUE FALSE 415395.2843 546504.3026 433965.3454 438131.9054 608507.204 445858.8095 420235.3074 534968.4584 585114.9167 0.70993795 0.934011913 0.741675409 0.748796335 1.039978962 0.762002124 0.718209869 0.914296394 1 19.15836047 1.008585348 8.696458011 0.999989434 0.812608905 0.281405613 0.104113169 0.149915641 97.08357549 0.095023007 0.023783529 10.19965185 -1.008585348 -0.187380529 LGAPQTHLGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGAPQTHLGLK 11 0 Q96C19;H0Y4Y4;Q9BUP0;A0A087X1Z2;Q9BUP0-2;Q8WYH2;C9JTV4 Q96C19;Q9BUP0 EFHD2;EFHD1;PP1187 EF-hand domain-containing protein D2;EF-hand domain-containing protein D1 0 76.655 0.021352 0 213870 239700 199380 200610 256360 139380 220430 245520 266890 FALSE TRUE 200484.2585 257447.6374 204109.3878 205757.9922 236226.5197 179616.7434 187378.5679 276173.7125 222344.3348 0.901683682 1.157878107 0.917987804 0.92540245 1.062435523 0.807831436 0.842740464 1.242099164 1 17.76243612 LGASNS(ph)PGQPNSVK ddPTM_SK-BR-3_Pertuzumab_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 367.13 5.47E-97 20416380000 18554250 14200840 15426040 14431070 16146580 13433980 20996920 15702980 20270210 TRUE FALSE 17392972.61 15252284.97 15791952.95 14801395.69 14878492.74 17312151.94 17848626.77 17663531.62 16886981 1.029963415 0.903197852 0.935155488 0.876497444 0.881062917 1.02517744 1.056945985 1.045985166 1 24.0094081 2.158460744 6.49245847 1.040149765 0.921514777 0.583219525 0.044695766 0.133282482 8.683420302 0.015931969 0.011752512 144.0325812 -2.158460744 -0.118634987 LGASNS(ph)PGQPNSVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGASNSPGQPNSVKR 15 1 P49756 P49756 RBM25 RNA-binding protein 25 1 LGASNS(1)PGQPNSVKR;LGAS(0.001)NS(0.999)PGQPNSVKR 154.52 1.51E-06 2561020000 2315900 2155080 2243990 2151550 2757960 1906940 3093530 2374750 4056150 TRUE FALSE 2170951.953 2314644.366 2297218.502 2206762.416 2541360.947 2457442.621 2629683.895 2671242.765 3379152.361 0.642454592 0.684977805 0.67982093 0.653052061 0.752070542 0.727236407 0.778208146 0.790506754 1 21.68822997 0.299746925 0.327311029 1.061546504 0.648543497 0.955594992 0.021693633 0.651995254 0.125740015 0.080473957 0.021874853 1.99409996 -0.299746925 -0.413003008 LGCEVLGVSVDSQFTHLAWINTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LGCEVLGVSVDSQFTHLAWINTPR 24 0 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ;;; 382.31 2.30E-120 814783000 746423 1018319 875388 871965 1068837 795193 1083206 951633 800247 FALSE TRUE 699705.7168 1093716.398 896152.6167 894341.0981 984894.8535 1024752.31 920789.3163 1070446.475 666680.6059 1.049536631 1.640540296 1.344200819 1.341483598 1.477311391 1.537096326 1.381155096 1.60563614 1 19.34663623 -0.988089949 4.625639747 0.999990926 1.435067541 0.383873527 0.167352743 1.37E-05 2.99E-06 0.141322357 0.033309304 0.10278034 0.988089949 0.435076615 LGCHPQTGFADIQGHPFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGCHPQTGFADIQGHPFFR 19 0 P41743 P41743 PRKCI Protein kinase C iota type 0 163.45 1.48E-11 256310000 428720 495990 481270 510620 536820 406370 615030 490960 593110 FALSE TRUE 401887.1805 532713.6157 492685.9517 523723.3737 494660.3226 523682.4221 522811.9612 552257.4367 494116.1094 0.813345635 1.078114244 0.997105624 1.05991965 1.001101387 1.059836772 1.058075119 1.117667338 1 18.91449057 4.743414093 24.99388173 1.045852053 0.813345539 0.785109148 0.038329576 217.9580153 1122378.393 0.008445128 0.069450364 55387.79718 -4.743414093 -0.232506514 LGDAS(ph)DTEAADGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGDASDTEAADGER 14 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 LGDAS(0.911)DT(0.089)EAADGER;LGDAS(0.988)DT(0.012)EAADGER 294.48 1.49E-43 531910000 908350 754250 808710 821920 827460 668740 893260 671100 677110 TRUE FALSE 851497.995 810095.4548 827892.9831 843011.8587 762474.6294 861794.3819 759323.9556 754888.3123 564095.9667 1.509491372 1.436095102 1.467645635 1.494447591 1.351675379 1.527744272 1.346090028 1.33822675 1 19.1055811 0.501496499 0.724934298 0.993025104 1.46488302 0.880233178 0.052904669 0.467681406 0.399602377 0.050633301 0.016631458 3.173193085 -0.501496499 0.471857917 LGDAVEQGVINNTVLGYFIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGDAVEQGVINNTVLGYFIGR 21 0 P41250 P41250 GARS Glycine--tRNA ligase 0 91.441 0.0046874 24400000 19220 15346 17228 25632 19425 18498 22636 15638 16576 FALSE TRUE 18017.05451 16482.23381 17636.6563 26289.76051 17899.43886 23838.07231 19241.94194 17590.43872 13809.35851 1.304698874 1.193555355 1.277152467 1.903764066 1.296181777 1.726225898 1.393398681 1.273805637 1 13.75335868 0.927798497 2.821470578 1.001319134 1.423645918 0.296457961 0.217973971 0.465306915 8.557596449 0.209119963 0.055343578 8.468344104 -0.927798497 0.422326784 LGDDEDREPSLRPDDDRVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGDDEDREPSLRPDDDRVPR 20 3 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 102.33 0.00013212 166420000 274230 229360 260110 240460 260890 226950 274540 223880 207880 FALSE TRUE 257066.4338 246342.053 266279.932 246630.6107 240400.7518 292466.7808 233375.2757 251831.9108 173183.485 1.484358822 1.42243386 1.537559612 1.424100056 1.388127463 1.688768307 1.3475608 1.454133521 1 17.40194183 0.217302107 1.068692328 0.998205014 1.476331697 0.716269517 0.092928917 2.188355809 2.545440769 0.088375342 0.024869824 1.649309297 -0.217302107 0.478126683 LGDDIDLIVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LGDDIDLIVR 10 0 O15371-2;O15371;O15371-3 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ;;;; 166.16 1.31E-05 196383000 474425 466781 504241 474514 475895 402608 536254 438202 431951 FALSE TRUE 444731.5861 501341.9509 516201.8346 486690.8326 438520.1264 518834.3938 455847.691 492912.4843 359855.5876 1.235861277 1.393175397 1.434469416 1.352461513 1.218600298 1.441785015 1.266751738 1.369750815 1 18.45705853 -3.282545481 0.343881361 3.28E-08 1.362919335 0.638095535 0.079281206 65.12877078 1.655986239 46.87936834 0.059225403 0.00052174 3.282545481 1.362919303 LGDLNYLIYVFPDRPKDEVYSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGDLNYLIYVFPDRPKDEVYSK 22 2 P51692 P51692 STAT5B Signal transducer and activator of transcription 5B 0 87.509 0.0015882 33988000 152540 107260 127270 113410 154380 102890 153900 114930 151480 FALSE TRUE 142992.7937 115201.642 130288.9045 116320.2926 142255.6175 132592.6727 130824.1237 129279.2635 126197.0094 1.133091777 0.912871411 1.03242466 0.92173573 1.127250307 1.050679991 1.0366658 1.024424145 1 16.9453182 2.743930965 24.9928092 1.049152511 0.99090328 0.100992187 0.068394038 810.680549 3772792.22 0.019151888 0.019776083 554.5375566 -2.743930965 -0.058249232 LGDLWTLDIDTLTWNKPSLSGVAPLPR ddPTM_SK-BR-3_Pertuzumab_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 0 186.62 9.74E-18 81105000 70272 77383 58669 49864 86585 46546 71987 70333 56863 FALSE TRUE 65873.80096 83112.51784 60060.65639 51143.59466 79784.96337 59983.07459 61193.21764 79114.22987 47372.19795 1.390558256 1.754457708 1.267846099 1.079612027 1.684214937 1.266208392 1.29175382 1.670056136 1 15.53175299 -3.736293756 0.20570139 1.34E-32 1.490177513 0.233561802 0.223187325 119.1767108 1.892737304 51.77280172 0.497067119 0.00018353 3.736293756 1.490177513 LGDNGEAFFVQETDNDQEVIPMHLAT(ph)SPILSEGASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGDNGEAFFVQETDNDQEVIPMHLATSPILSEGASR 36 0 A0A0A0MS66;Q14693-6;Q14693;Q14693-2;Q14693-4;Q14693-3;Q14693-5;Q14693-7 A0A0A0MS66 LPIN1 Phosphatidate phosphatase LPIN1 1 LGDNGEAFFVQETDNDQEVIPMHLAT(0.569)S(0.424)PILS(0.006)EGAS(0.001)R 132.17 1.99E-08 18896000 5926.9 7130.4 5790.3 7239.8 8504.4 5917.6 8820.6 7484.1 5993.6 TRUE FALSE 5555.945909 7658.342235 5927.64865 7425.585525 7836.498729 7625.915056 7498.032916 8418.50636 4993.22944 1.112695897 1.53374531 1.187137247 1.487130847 1.569424923 1.52725108 1.501639972 1.685984284 1 12.28575748 4.748201052 23.82214363 1.447275754 1.112695545 0.204952396 0.1994567 1028.321786 2540944.939 0.043506131 0.541949351 56001.67959 -4.748201052 -0.334580209 LGDS(ph)SGPALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGDSSGPALK 10 0 Q9UHD8 Q9UHD8 9-Sep Septin-9 1 LGDS(0.5)S(0.5)GPALK 114.76 0.0013765 285960000 652240 557100 502230 538990 526120 501160 689950 465930 542300 TRUE FALSE 611417.4627 598348.2637 514143.1328 552821.3959 484800.6575 645836.7563 586498.4027 524102.3861 451786.6266 1.353332362 1.324404549 1.138022027 1.22363382 1.073074387 1.429517206 1.298175661 1.16006618 1 18.78528204 0.955237857 4.406177868 1.000239801 1.258487654 0.406234731 0.102405186 0.238550396 14.07679662 0.097399272 0.024772282 9.020650504 -0.955237857 0.258247853 LGDS(ph)SGPALKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGDSSGPALKR 11 1 Q9UHD8 Q9UHD8 9-Sep Septin-9 1 LGDS(0.933)S(0.067)GPALKR;LGDS(0.98)S(0.02)GPALKR 82.925 0.010784 580780000 900960 636520 714720 703950 621490 400840 1022370 624500 1013070 TRUE FALSE 844570.5219 683648.6031 731673.4959 722014.5488 572680.6824 516556.0009 869075.1097 702470.1997 843982.0723 1.00069723 0.810027399 0.86693014 0.855485647 0.678546027 0.612046177 1.029731719 0.832328343 1 19.68685283 1.660181635 14.83040113 0.947784016 0.809259475 0.269955855 0.115905645 0.194321475 48.25606437 0.052765253 0.029068814 45.72793978 -1.660181635 -0.138524541 LGDSHDLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LGDSHDLQR 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 125.57 0.00049789 1035500000 2310910 2569440 2316680 2292240 2962450 1785700 2487440 2352750 3091560 FALSE TRUE 2166274.268 2759684.011 2371632.744 2351062.759 2729791.127 2301202.602 2114471.464 2646496.017 2575558.664 0.84108908 1.071489479 0.920822646 0.912836035 1.05988311 0.893477067 0.82097585 1.027542511 1 21.29645397 LGDSS(ph)LSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGDSSLSR 8 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 LGDS(0.103)S(0.897)LSR;LGDS(0.039)S(0.961)LSR 154.05 0.00045228 269180000 972670 930920 954990 1012830 1183340 784720 1358170 1083850 1259940 TRUE FALSE 911792.321 999846.2854 977642.8138 1038820.933 1090405.25 1011255.925 1154525.017 1219171.058 1049647.874 0.868664952 0.952554004 0.931400746 0.989685168 1.03882957 0.963423973 1.099916501 1.161504813 1 20.001474 2.68473303 0.740214476 1.086605163 0.912916146 0.577892972 0.054452842 0.462764399 0.538007043 0.036709227 0.034274844 483.8748284 -2.68473303 -0.173689017 LGDVGMAELCPGLLHPSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LGDVGMAELCPGLLHPSSR 19 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 ;;; 280.25 1.26E-39 1775180000 913728 1892026 1860945 1909110 2090641 1608704 2089782 1976301 1985947 FALSE TRUE 856539.3955 2032113.574 1905087.494 1958100.995 1926450.489 2073110.73 1776438.59 2223046.53 1654479.616 0.517709247 1.228249387 1.151472327 1.183514729 1.164384542 1.253028874 1.073714401 1.343653019 1 20.65794609 4.741269778 24.99328497 1.176961659 0.51770901 0.829210815 0.093706952 85.33295907 787193.9571 0.018926957 0.130834493 55114.99571 -4.741269778 -0.659252649 LGDVYVNDAFGTAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 LGDVYVNDAFGTAHR 15 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ;;;;;;;;;;; 254.2 1.09E-24 41073365000 18143482.4 24265590 18364765 18508848 21388702 12153491 24098114 18195889 22167793 FALSE TRUE 17007914.22 26062239.53 18800385.9 18983816.38 19708919.62 15662006.56 20484825.52 20467685.8 18467845.14 0.920947414 1.411222551 1.018006473 1.027938898 1.067201911 0.848068978 1.109215795 1.10828771 1 24.1385122 3.726840675 24.99141788 1.026017034 1.205157615 0.139275331 0.137854653 16.91364425 1506689.168 0.032657608 0.054293933 5331.392721 -3.726840675 0.179140582 LGEESIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGEESIR 7 0 Q02487-2;J3QRL9;Q14574-2;Q08554-2 Q02487-2 DSC2;DSC3 Desmocollin-2 0 113.1 0.014436 121750000 111270 136610 144640 135850 202060 116380 129000 147140 194430 FALSE TRUE 104305.8093 146724.7465 148070.9291 139336.141 186191.0227 149977.0167 109657.6476 165510.7529 161978.3769 0.643948972 0.905829218 0.914140096 0.860214454 1.149480728 0.92590764 0.676989421 1.021807701 1 17.30544171 4.738737389 6.085202356 0.912422755 0.637041999 0.345065407 0.122097753 0.165065295 30.77580831 0.029367628 0.188032181 54794.55309 -4.738737389 -0.275380756 LGEGT(ph)YAT(ph)VYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGEGTYATVYK 11 0 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;H0YBX5;Q00537;Q00537-2;F5H6Z0 E5RJM2;Q00537 CDK16;CDK17 Cyclin-dependent kinase 16;Cyclin-dependent kinase 17 2 LGEGT(0.999)Y(0.004)AT(0.973)VY(0.023)K 69.815 0.083159 814160000 67650 223680 196900 225930 228760 210540 108350 133320 80356 TRUE FALSE 63415.90726 240241.4999 201570.561 231727.7463 210794.1124 271319.4802 92103.92337 149965.2955 66944.06448 0.947296937 3.588690077 3.011029619 3.461512953 3.148809592 4.052928102 1.37583405 2.240158207 1 16.03066853 1.672371245 8.26930329 1.613130158 3.114050609 0.393477828 0.868152877 0.113794011 13.4138337 0.385590513 0.202686951 47.02959564 -1.672371245 1.50092045 LGELTDLHGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGELTDLHGLR 11 0 Q70J99;Q70J99-3;K7EQ37;Q70J99-2;K7EN81 Q70J99 UNC13D Protein unc-13 homolog D 0 192.5 1.37E-06 100590000 167940 160140 150760 162660 192670 135210 202990 188220 154460 FALSE TRUE 157428.9352 171996.9322 154336.0984 166834.131 177538.4754 174242.932 172553.534 211719.6813 128679.6282 1.223417704 1.336629074 1.199382533 1.296507718 1.379693724 1.354083273 1.340954559 1.645324006 1 16.97342415 2.899923382 4.49523137 1.36300465 1.261718973 0.056875873 0.157560897 0.556805111 18.80941782 0.043331863 0.046629162 794.1881129 -2.899923382 -0.101285677 LGEMWNNTAADDKQPYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGEMWNNTAADDKQPYEK 18 1 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 111.65 0.00027243 912720000 152080 85227 119900 104740 92333 74403 125180 86719 112570 FALSE TRUE 142561.5843 91537.29576 122744.0846 107427.8057 85081.53863 95881.93827 106410.4211 97546.05804 93781.33977 1.520148727 0.97607153 1.308832705 1.14551366 0.907233132 1.022398896 1.134665184 1.040143575 1 16.51701327 4.747644371 24.59579474 1.085477215 1.520149012 0.614177954 0.112047833 709.8598653 1922012.999 0.027018537 0.330603183 55929.94226 -4.747644371 0.434671797 LGETYKDHENIVIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGETYKDHENIVIAK 15 1 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ; 185.12 2.62E-07 2645600000 13044500 9502400 10621300 11690500 12252300 6733900 13891200 9029400 14486000 FALSE TRUE 12228068.03 10205967.58 10873242.25 11990498.02 11290053.78 8677867.614 11808343.52 10156740.47 12068193.02 1.013247635 0.845691444 0.900983456 0.993562003 0.935521479 0.719069342 0.978468235 0.841612365 1 23.52470634 LGEVALLQGNHQIVEMCYQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGEVALLQGNHQIVEMCYQR 20 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 214.66 1.25E-24 182120000 113760 127950 116840 128040 139090 97571 138850 103820 122700 FALSE TRUE 106639.9647 137423.5511 119611.5 131325.7232 128166.4325 125738.1638 118030.7315 116782.1555 102220.5773 1.043233833 1.344382459 1.170131329 1.284728834 1.253822232 1.230067048 1.154667041 1.142452514 1 16.64132612 0.983550743 1.037278486 1.002666215 1.233733309 0.422069797 0.079812248 0.473175448 1.071171288 0.066958517 0.02193347 9.628325044 -0.983550743 0.231067094 LGEVVNTHGPVEPDKDNIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGEVVNTHGPVEPDKDNIR 19 1 P30419;P30419-2;K7EN82 P30419 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 0 142.78 9.12E-08 615870000 185930 114410 139800 138210 153040 124220 183690 138480 192510 FALSE TRUE 174292.9732 122881.0354 143116.122 141756.7026 141020.8557 160080.2975 156147.3898 155769.5328 160378.8373 1.086757929 0.766192332 0.892362885 0.883886583 0.879298404 0.998138533 0.973615923 0.971259896 1 17.29112426 2.243133122 24.9171491 0.983010873 0.88113847 0.193857422 0.079143142 136.4235807 743422.0107 0.026090504 0.021155675 175.0383144 -2.243133122 -0.101872403 LGEWVGLCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGEWVGLCK 9 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 ; 128.69 0.00095471 716260000 1038210 957770 988260 949820 1125920 775410 1215910 928200 1256200 FALSE TRUE 973230.2894 1028684.287 1011701.994 974193.9892 1037494.785 999258.2793 1033595.583 1044087.813 1046532.105 0.929957414 0.982945753 0.966718545 0.930878264 0.991364508 0.954828117 0.987638677 0.997664389 1 19.99718514 1.580757836 3.552343589 0.997759199 0.963117531 0.423632076 0.019535677 0.197161393 5.737895547 0.011468507 0.004779224 38.08533988 -1.580757836 -0.034641668 LGEYEDVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGEYEDVSR 9 0 K7EP07;Q99426-2;Q99426;A0A494C0X0;K7EK42;K7EL99 K7EP07 TBCB Tubulin-folding cofactor B 0 160.26 0.00015221 405390000 542690 531040 550930 538570 580450 484910 617240 466190 516470 FALSE TRUE 508724.0016 570358.7541 563998.3198 552390.618 534863.7984 624895.6451 524690.5922 524394.8477 430267.8205 1.182342665 1.325590079 1.310807578 1.283829726 1.243095051 1.452341113 1.219451159 1.218763809 1 18.71487542 0.827341546 1.604468255 1.001425098 1.29991601 0.618096789 0.071510273 0.375865423 1.789877518 0.061003235 0.017595388 6.719570989 -0.827341546 0.298490912 LGFEEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGFEEFK 7 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;U3KQE2;K7EIV0;A0A075B7C0;U3KPR7;Q96L46 A0A0C4DGQ5 CAPNS1;CAPNS2 Calpain small subunit 1;Calpain small subunit 2 0 ; 105.95 0.018175 504530000 1065190 1144300 992150 971840 1324610 723180 1225140 1152430 1467170 FALSE TRUE 998521.6593 1229025.163 1015684.267 996779.0597 1220580.474 931950.3262 1041441.631 1296313.422 1222289.849 0.816927066 1.005510406 0.830968422 0.815501381 0.998601498 0.762462625 0.852041463 1.060561391 1 20.22115501 1.240258126 24.99680774 1.03028074 0.874729182 0.417721087 0.078996816 42.08587747 619820.646 0.057053834 0.018381997 17.38834011 -1.240258126 -0.155551558 LGFHLPLEVAYQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 120.57 0.00025912 256860000 237540 301200 213700 209580 332160 192010 258890 262260 279330 FALSE TRUE 222672.7954 323501.1614 218769.0649 214958.1776 306073.4935 247440.17 220071.8479 295003.7383 232708.0185 0.956876333 1.390159065 0.940101103 0.923724842 1.315268359 1.063307451 0.945699462 1.267699069 1 17.8281614 7.999999986 0.141182839 1.017105287 1.499364908 0 0.173887689 309.0121585 2.900424267 0.685544566 30.1568661 99999996.67 -7.999999986 0.482259621 LGFSLT(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGFSLTPSK 9 0 P38432 P38432 COIL Coilin 1 LGFS(0.001)LT(0.997)PS(0.002)K;LGFS(0.003)LT(0.996)PS(0.002)K 124.12 0.0060193 579730000 1461720 1252420 1229020 1137880 1399520 896940 1715180 1203110 1437340 TRUE FALSE 1370233.554 1345150.48 1258172.935 1167079.927 1289607.345 1155872.017 1458004.682 1353320.932 1197438.668 1.144303746 1.123356474 1.050720148 0.974646934 1.076971521 0.965287031 1.217602805 1.130179747 1 20.19152033 -0.162474766 7.284047755 1 1.086527531 0.109955483 0.076282165 4979504.346 683617.6803 0.073468916 0.017818829 0.68789988 0.162474766 0.086527531 LGFTQSQIDEIDHDYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGFTQSQIDEIDHDYER 17 0 Q13546-2;Q13546 Q13546-2 RIPK1 Receptor-interacting serine/threonine-protein kinase 1 0 148.26 3.69E-07 60171000 22757 27486 28486 24496 27971 28352 25021 24395 21616 FALSE TRUE 21332.67999 29521.09204 29161.70137 25124.60883 25774.27049 36536.76214 21269.33333 27440.76945 18008.14996 1.184612525 1.639318426 1.619361314 1.395179899 1.431255879 2.028901483 1.181094859 1.523797254 1 14.13636235 0.603250539 1.043927014 1.003080348 1.540135468 0.285129636 0.244636341 1.532739306 2.607732395 0.212838121 0.067307888 4.010980389 -0.603250539 0.53705512 LGFVDVQNCIS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LGFVDVQNCISR 12 0 Q14573 Q14573 ITPR3 "Inositol 1,4,5-trisphosphate receptor type 3" 1 LGFVDVQNCIS(1)R;LGFVDVQNCIS(1)R;LGFVDVQNCIS(1)R 175.15 2.99E-05 610888000 1536530 1618260 1276610 1269110 1820420 1594950 2105420 1648930 1817420 TRUE FALSE 1440361.33 1738077.654 1306891.792 1301677.511 1677451.556 2055386.173 1789731.817 1854802.54 1514080.861 0.951310704 1.147942424 0.863158518 0.859714659 1.107900905 1.357514137 1.182058279 1.225035325 1 20.53001083 2.481625648 24.6615061 1.212071334 0.973364851 0.469544623 0.117010078 135.0818937 739579.3365 0.038410019 0.032916691 303.1277169 -2.481625648 -0.238706483 LGGAVPFAPPEVS(ph)PEQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LGGAVPFAPPEVSPEQAK 18 0 A0A096LNZ0;A0A096LP25;Q6ZSR9 A0A096LNZ0;A0A096LP25 AAK1 Uncharacterized protein FLJ45252 1 LGGAVPFAPPEVS(1)PEQAK;LGGAVPFAPPEVS(1)PEQAK;LGGAVPFAPPEVS(1)PEQAK;LGGAVPFAPPEVS(1)PEQAK 296.79 2.46E-49 624460000 2298560 1629560 1998640 1822040 1925670 1574520 2458210 1666700 2324180 TRUE FALSE 2154697.233 1750214.318 2046048.685 1868796.631 1774435.646 2029058.364 2089624.231 1874791.164 1936259.343 1.112814376 0.903915234 1.056701775 0.965158225 0.916424575 1.047926958 1.079206791 0.96825416 1 20.88484077 LGGLDTRPHYITR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGGLDTRPHYITR 13 1 Q8N1B4-2;Q8N1B4 Q8N1B4-2 VPS52 Vacuolar protein sorting-associated protein 52 homolog 0 77.078 0.016179 121930000 137700 189600 138380 155620 224680 114450 177100 180460 324300 FALSE TRUE 129081.6028 203638.1813 141662.4389 159613.4727 207034.5391 147489.8571 150545.4991 202990.8282 270172.2349 0.477775234 0.753734673 0.524341219 0.590784144 0.766305757 0.54591049 0.557220468 0.751338598 1 18.04351989 0.942608446 4.041671881 0.999696523 0.610111932 0.653962898 0.092788198 0.15900807 7.123145029 0.082965652 0.021208223 8.762104862 -0.942608446 -0.389584592 LGGLRPES(ph)PESLTSVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LGGLRPESPESLTSVSR 17 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 LGGLRPES(0.525)PES(0.174)LT(0.057)S(0.008)VS(0.236)R;LGGLRPES(0.61)PES(0.093)LT(0.255)S(0.036)VS(0.006)R;LGGLRPES(0.993)PES(0.005)LTSVS(0.001)R;LGGLRPES(0.982)PES(0.016)LT(0.002)SVSR;LGGLRPES(0.997)PES(0.003)LTSVSR;LGGLRPES(0.996)PES(0.003)LT(0.001)SVSR 229.08 3.22E-15 10829460000 4455430 4321730 4567120 4006640 4210640 3735180 5140930 3864780 4869660 TRUE FALSE 4176572.589 4641715.386 4675454.243 4109457.166 3879953.319 4813465.83 4370095.273 4347306.29 4056882.287 1.029503026 1.144158262 1.152474712 1.012959429 0.956387946 1.186493837 1.077205342 1.071587979 1 21.95194001 -4.999999996 0.19074392 0.614786999 1.106182624 0.0845978 0.070327976 297.9278119 2.918881558 43.64768879 0.191314256 1.00E-05 4.999999996 0.491395625 LGGLRPESPES(ph)LTSVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGGLRPESPESLTSVSR 17 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 LGGLRPES(0.344)PES(0.644)LT(0.011)SVSR;LGGLRPES(0.068)PES(0.805)LT(0.1)S(0.013)VS(0.013)R 185.3 1.54E-09 758570000 1120200 1083240 1207970 1052440 1081010 1014300 1393520 1106740 1312160 TRUE FALSE 1050088.682 1163444.217 1236623.619 1079447.392 996111.8352 1307111.944 1184574.613 1244918.925 1093152.019 0.960606268 1.064302308 1.131245789 0.987463201 0.911229013 1.195727512 1.083632095 1.138834218 1 20.06006261 2.219963902 24.99949334 1.111537481 1.033574821 0.236462572 0.077427691 417.8780184 561748.6778 0.029005606 0.021460076 165.9448971 -2.219963902 -0.077962661 LGGPEGPGS(ph)PLLAT ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGGPEGPGSPLLAT 14 0 Q9C086 Q9C086 INO80B INO80 complex subunit B 1 LGGPEGPGS(1)PLLAT;LGGPEGPGS(1)PLLAT 187.85 7.03E-08 0 398680 424490 423500 410280 451990 373390 499380 390760 504820 TRUE FALSE 373727.3305 455919.6813 433545.62 420808.4794 416492.5286 481181.6315 424502.605 439547.2462 420562.2807 0.888637302 1.084071735 1.030871383 1.000585404 0.990323069 1.14413882 1.009369181 1.045141864 1 18.68195994 LGGS(ph)AVISLEGKPL ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGGSAVISLEGKPL 14 1 G3V1A4;P23528;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 1 LGGS(0.999)AVIS(0.001)LEGKPL;LGGS(1)AVISLEGKPL 134.88 9.51E-05 119062000 540650 512320 499160 523030 597420 373320 621380 475190 724110 TRUE FALSE 506811.6816 550252.7059 511000.3109 536451.8353 550501.0431 481091.4237 528209.8376 534518.5175 603251.3631 0.840133504 0.912144986 0.847076927 0.889267506 0.91255665 0.79749745 0.87560488 0.886062677 1 19.20239974 0.721266581 2.851907825 0.999981276 0.869396738 0.589609024 0.034388619 1.38237748 13.27681878 0.030617648 0.008052109 5.263402486 -0.721266581 -0.130584537 LGGS(ph)LIVAFEGCPV ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGGSLIVAFEGCPV 14 0 P60981;P60981-2 P60981 DSTN Destrin 1 LGGS(1)LIVAFEGCPV 75.294 0.032155 6277200 18934 23124 19253 23182 23358 16765 25715 16097 22576 TRUE FALSE 17748.95474 24836.12502 19709.69025 23776.88937 21523.5569 21604.78334 21859.27448 18106.74588 18807.91975 0.943695793 1.320514195 1.047946318 1.264195598 1.144387959 1.148706695 1.162237757 0.962719223 1 14.19905267 1.241516401 24.94490234 0.981359554 1.15860735 0.302561984 0.103711071 72.44009888 611392.6645 0.067023828 0.022063228 17.43879214 -1.241516401 0.177247796 LGGSLADSYLDEGFLLDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGGSLADSYLDEGFLLDKK 19 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 219.79 4.89E-19 881140000 1259660 845990 1056150 981140 1164040 746022 1282560 919560 1462910 FALSE TRUE 1180820.129 908627.9799 1081202.377 1006317.713 1072620.994 961386.4407 1090252.035 1034369.09 1218740.87 0.968885313 0.745546491 0.887147057 0.825702771 0.88010587 0.788835809 0.894572473 0.848719457 1 20.21695998 -0.233108398 0.633231537 1.011835409 0.843105768 0.34398357 0.061659964 6.956353857 2.619770048 0.25529609 0.021140838 0.584644141 0.233108398 -0.168729641 LGGSPTSLGTWGSWIGPDHDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGGSPTSLGTWGSWIGPDHDK 21 0 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 326.18 2.72E-68 1732870000 2367830 1819310 1991480 1902690 1994910 1656880 2608400 1940070 1533890 FALSE TRUE 2219631.747 1954013.605 2038718.846 1951516.247 1838237.816 2135194.359 2217294.635 2182292.01 1277873.85 1.736972509 1.52911307 1.595399144 1.527158762 1.438512742 1.670896043 1.735143603 1.707752303 1 20.28531399 -1.701696779 2.836148727 0.912896557 1.611284883 0.793919951 0.098843198 15259660.01 13942071.96 9515402.279 0.024905452 0.019874821 1.701696779 0.698388326 LGGSPTSLGTWGSWIGPDHDKFSAMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LGGSPTSLGTWGSWIGPDHDKFSAMK 26 1 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;; 339.67 1.33E-95 1369640000 1295680 1359140 1232250 1254860 1591960 817121 1675070 1245010 1696630 FALSE TRUE 1214585.702 1459772.14 1261479.552 1287061.832 1466933.883 1053010.568 1423908.804 1400452.239 1413451.492 0.859304835 1.032771303 0.892481673 0.910580829 1.037838151 0.744992363 1.007398423 0.990803184 1 20.43079094 1.586118109 24.99999976 0.999352135 0.925372483 0.183055066 0.083350704 1.70880862 1957.834033 0.041081665 0.019044624 38.55832051 -1.586118109 -0.073979652 LGGSVLGQIPFLQNCEDEDS(ph)DEDDELDSVQHKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGGSVLGQIPFLQNCEDEDSDEDDELDSVQHKK 33 1 F5GYK2;Q9NRL3;Q9NRL3-3;R4GN16;Q9NRL3-2 F5GYK2 STRN4 Striatin-4 1 LGGSVLGQIPFLQNCEDEDS(1)DEDDELDSVQHKK;LGGSVLGQIPFLQNCEDEDS(1)DEDDELDSVQHKK 304.95 1.33E-90 510500000 897480 583900 659910 688750 849030 601480 1190760 627000 1219180 TRUE FALSE 841308.3288 627132.5635 675563.3768 706424.4911 782350.6086 775117.5118 1012216.592 705282.3302 1015690.982 0.828311311 0.617444257 0.665126883 0.695511237 0.770264404 0.763143048 0.996579285 0.694386721 1 19.95403011 2.217894913 1.621761724 0.894910267 0.682185774 0.377895439 0.102533939 0.327858076 1.700743218 0.051743316 0.030987117 165.1562119 -2.217894913 -0.212724493 LGHAEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LGHAEQK 7 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;;; 120.65 0.0045151 892470000 3171980 2506060 2974160 2793440 2831210 2524290 3424020 2706590 2876700 FALSE TRUE 2973451.434 2691611.29 3044708.48 2865124.4 2608858.187 3253011.545 2910619.988 3044513.719 2396560.186 1.240716362 1.123114415 1.270449412 1.195515313 1.088584465 1.357366931 1.214499016 1.270368146 1 21.19253374 -1.062594234 4.662342351 0.999990746 1.217192538 0.453819774 0.075817073 6.75E-06 1.36E-06 0.067985175 0.016023577 0.086577645 1.062594234 0.217201792 LGHDPYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LGHDPYR 7 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-6 P18583-7 SON Protein SON 0 ;;;;; 107.43 0.0074794 2227026000 814926 1090665 969482 932106 1052133 859206 1031409 901079 1024023 FALSE TRUE 763921.2363 1171418.971 992478.5709 956025.418 969502.7183 1107244.824 876758.7956 1013580.697 853106.9459 0.895457762 1.373120893 1.163369465 1.12063959 1.136437492 1.297896858 1.027724367 1.188105081 1 19.70236708 0.539444671 0.552311078 0.994842744 1.185222267 0.075490945 0.133757263 3.331151313 1.863281069 0.171529743 0.057529045 3.462937641 -0.539444671 0.190379523 LGHDPYRLT(ph)PDPYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGHDPYRLTPDPYR 14 1 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-6 P18583-7 SON Protein SON 1 LGHDPYRLT(1)PDPYR;LGHDPY(0.001)RLT(0.999)PDPYR 98.227 0.0039015 202217000 111237 115660 110557 89112 108390 113098 131505 97430 109710 TRUE FALSE 104274.8747 124223.5867 113179.4642 91398.76479 99877.48662 145747.5566 111787.0461 109594.35 91398.69225 1.140879286 1.359139652 1.238305073 1.000000794 1.09276713 1.594635033 1.22307052 1.199080066 1 16.4798859 -2.365674253 1.123148919 0.364965792 1.246640794 0.163693833 0.160667812 22230.3196 2203.777295 35331.9698 0.046300149 0.004308497 2.365674253 0.881675002 LGHEEQQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGHEEQQKR 9 1 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 ; 137.95 9.75E-05 594890000 491010 576330 520580 530760 598940 390480 628340 568160 811250 FALSE TRUE 460278.5606 619002.0729 532928.4034 544380.2002 551901.6684 503205.2371 534126.2502 639096.0267 675847.1341 0.68103945 0.915890653 0.78853394 0.805478299 0.816607248 0.744554814 0.790306303 0.94562216 1 19.36633744 1.136535591 4.120291322 0.99572533 0.801919261 0.618209315 0.059400325 0.140716035 3.989703975 0.053849968 0.013960316 13.69416608 -1.136535591 -0.193806068 LGHPDTLNQGEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGHPDTLNQGEFK 13 0 P06702 P06702 S100A9 Protein S100-A9 0 ; 215.34 2.93E-11 1917430000 2830300 2287600 2518500 2064630 2162200 1396310 3141400 2178340 4293300 FALSE TRUE 2653156.575 2456976.284 2578240.009 2117611.901 1992389.534 1799402.03 2670376.233 2450310.544 3576720.494 0.74178471 0.686935501 0.720839108 0.592054063 0.557043676 0.503087125 0.746599081 0.685071855 1 21.77020595 0.533306043 1.405883059 0.99959436 0.650747792 0.655894629 0.079454633 1.352823887 3.339452309 0.078849858 0.023124971 3.414334319 -0.533306043 -0.348846568 LGHPEALSAGTGS(ph)PQPPSFTYAQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LGHPEALSAGTGSPQPPSFTYAQQR 25 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 LGHPEALSAGT(0.011)GS(0.989)PQPPSFTYAQQR;LGHPEALSAGT(0.004)GS(0.996)PQPPSFTYAQQR;LGHPEALSAGT(0.003)GS(0.997)PQPPSFTYAQQR;LGHPEALSAGTGS(1)PQPPSFTYAQQR;LGHPEALSAGT(0.002)GS(0.998)PQPPSFTYAQQR;LGHPEALSAGT(0.001)GS(0.999)PQPPSFTYAQQR 332.07 4.40E-88 11975230000 1076558 1142600 1219234 1234095 1291182 1155392 1389350 1146884 1569090 TRUE FALSE 1009178.156 1227199.293 1248154.806 1265763.967 1189777.774 1488934.914 1181029.866 1290074.992 1307198.742 0.772015856 0.938800852 0.954831707 0.96830262 0.910173592 1.139027193 0.903481489 0.986900423 1 20.31804707 5.557411497 1.047535397 0.978851208 2.32E-12 0.500525073 0.064706336 6.935049292 1.748990825 0.017215923 11.42838704 360920.4554 -5.557411497 -0.978851208 LGHPEPNHVTEASELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LGHPEPNHVTEASELLR 17 0 Q70J99;Q70J99-3;K7EQ37;Q70J99-2;K7EN81;K7EIH3 Q70J99 UNC13D Protein unc-13 homolog D 0 ;; 171.56 9.89E-10 773030000 431004 556296 408791 458280 526558 431961 549344 516416 542940 FALSE TRUE 404028.229 597484.7347 418487.7156 470040.2407 485204.2587 556661.1284 466974.9671 580891.6744 452319.8065 0.893235766 1.320934273 0.925203163 1.039176781 1.072701774 1.230680418 1.032399997 1.284249918 1 18.78698365 2.426987568 24.99987202 1.133857155 1.069296416 0.077592466 0.13991785 373.9842531 186490.2868 0.045486903 0.038057078 267.2929894 -2.426987568 -0.064560738 LGIAVIHGEAQDAESDLVDGRHS(ph)PPMVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 20 LGIAVIHGEAQDAESDLVDGRHSPPMVR 28 1 O60256;O60256-2;O60256-3;O60256-4;E7EPA1;I3L0S1;C9K0K7 O60256 PRPSAP2 Phosphoribosyl pyrophosphate synthase-associated protein 2 1 LGIAVIHGEAQDAES(0.028)DLVDGRHS(0.972)PPMVR;LGIAVIHGEAQDAES(0.009)DLVDGRHS(0.991)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.049)DLVDGRHS(0.951)PPMVR;LGIAVIHGEAQDAES(0.195)DLVDGRHS(0.805)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.001)DLVDGRHS(0.999)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.002)DLVDGRHS(0.998)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR 231.56 1.38E-35 12330576000 3345892 3636214 3517652 3596107 3741973 3028019 4068882 3350488 3895051 TRUE FALSE 3136478.592 3905443.068 3601092.367 3688389.194 3448093.535 3902158.93 3458790.918 3768803.802 3244941.825 0.966574676 1.203547946 1.109755601 1.136658034 1.062605655 1.202535867 1.065902289 1.161439559 1 21.62976118 -1.395617812 3.556071008 0.999150237 1.120410909 0.19555889 0.071254906 5004422.799 1991904.818 32624.58201 0.014446989 0.040214455 1.395617812 0.121260673 LGIDDLVHFDFMDPPAPETLMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 LGIDDLVHFDFMDPPAPETLMR 22 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ;;;;;;;; 139.11 3.49E-07 935719000 1404746 1433133 1416494 1422457 1634620 1211095 1643891 1415871 1715868 FALSE TRUE 1316825.455 1539243.658 1450093.907 1458959.655 1506243.539 1560718.466 1397404.806 1592645.611 1429478.546 0.921192878 1.076786821 1.014421595 1.020623681 1.053701396 1.091809647 0.977562629 1.114144466 1 20.44705754 4.749309541 24.72842674 1.041174566 0.921192798 0.450521026 0.042417969 1217.126308 2799995.731 0.009037877 0.132605744 56144.80028 -4.749309541 -0.119981768 LGIHEDSQNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 LGIHEDSQNR 10 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;;;; 231.38 7.12E-10 82280610000 20229950 25453800 21526360 22216440 25421210 18436673 22958200 21362820 21697370 FALSE TRUE 18963793.54 27338425.84 22036975.42 22786551.46 23424730.71 23759041.2 19515831.04 24030015.1 18075938.78 1.049118044 1.512420803 1.219133108 1.260601275 1.29590673 1.314401509 1.079657952 1.329392371 1 24.10756724 0.077000731 0.327174927 0.938309333 1.31844929 0.236618633 0.133581093 5.672666687 0.933164342 0.625615837 0.129327724 1.193990114 -0.077000731 0.380139957 LGIHEDSQNRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LGIHEDSQNRK 11 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;; 156.58 2.01E-05 12610320000 11080440 11166450 10960050 10493590 12014110 8334720 13253120 9893710 12501170 FALSE TRUE 10386935.04 11993225.58 11220027.56 10762873.29 11070570.26 10740818.36 11265937.69 11128961.47 10414643.97 0.997339426 1.151573267 1.077331841 1.033436507 1.062981154 1.031318823 1.08174007 1.068587799 1 23.31211018 3.452813869 7.151491083 1.05235711 1.09450826 0.037106417 0.044071555 0.286493627 56.550789 0.011169558 0.015476381 2836.703008 -3.452813869 0.04215115 LGIHEDSTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 LGIHEDSTNR 10 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;; 236.32 3.86E-12 84723179800 18715588.9 23620182 21231927 20383154 23450685 17728373 22583458 20605192 21058334 FALSE TRUE 17544213.6 25369044.85 21735558.33 20906220.24 21608962.8 22846266.49 19197278.13 23177795.58 17543562.01 1.000037141 1.446060089 1.238947844 1.191674771 1.231731776 1.302259283 1.094263418 1.321156762 1 24.06443836 -3.394786772 0.239231064 0.419212103 1.271194111 0.211345601 0.12536893 94.52229048 1.883561753 27.20820817 0.190340093 0.000402915 3.394786772 0.851982008 LGIHEDSTNRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 LGIHEDSTNRR 11 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;; 199.03 3.35E-08 22946090000 9753020 12180120 11490430 11249750 12536800 9364500 12324280 10303040 11803160 FALSE TRUE 9142595.888 13081948.76 11762988.43 11538437.63 11552210.3 12067879.13 10476368.63 11589397.22 9833136.345 0.92977414 1.330394322 1.196260075 1.173423944 1.174824582 1.227266531 1.065414763 1.178606379 1 23.22922022 0.760030702 0.617042034 1.000018071 1.195058037 0.143750582 0.10692912 1.653819597 1.323907782 0.107437352 0.041717706 5.754806187 -0.760030702 0.195039966 LGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGTDNDSENWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGTDNDSENWK 51 0 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 ; 197.75 5.78E-40 146835000 35684.2 109280 73322 68573 115856 68417 101782 115506 56057.8 FALSE TRUE 33450.78962 117371.2049 75061.23247 70332.69927 106757.1371 88167.87724 86520.734 129927.1784 46701.39103 0.716269663 2.513227172 1.60725903 1.506008659 2.285951976 1.887906876 1.852637193 2.782083691 1 15.5111779 2.746446517 24.28254673 1.99384403 1.743875155 0.057130204 0.619018664 1574.401372 4847950.881 0.174768823 0.182197912 557.75891 -2.746446517 -0.249968875 LGIYDADGDGDFDVDDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LGIYDADGDGDFDVDDAK 18 0 Q12797;Q12797-10;E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2;E5RHK2;G3XAN5;E5RG29;Q12797-4;Q12797-3;Q12797-9;Q12797-5;Q12797-8 Q12797 ASPH Aspartyl/asparaginyl beta-hydroxylase 0 ;; 276.71 9.59E-39 310694000 1079543 726562 764024 747279 966576 606098 1055513 768947 822977 FALSE TRUE 1011976.331 780357.4065 782147.0101 766455.4443 890665.0199 781068.6534 897248.6246 864951.7256 685616.8221 1.476008607 1.138182993 1.140793202 1.117906416 1.29907113 1.139220375 1.308673585 1.261567245 1 19.38704298 -2.129600686 2.409662282 0.550714026 1.218852537 0.296501773 0.111349735 5438301.906 1626813.925 13364431.28 0.025623017 0.007419922 2.129600686 0.668138511 LGLALNFSVFHYEIANSPEEAISLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGLALNFSVFHYEIANSPEEAISLAK 26 0 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 67.614 0.034216 8253900 8897.4 7761.9 8694.1 7545.5 15893 8442.7 12303 9670.6 12231 FALSE TRUE 8340.527616 8336.599152 8900.328158 7739.130305 14644.82789 10879.97043 10458.27937 10877.9957 10189.56708 0.818536013 0.818150475 0.873474612 0.759515124 1.437237497 1.067755906 1.026371315 1.067562106 1 13.31480514 2.794623772 24.9999993 1.109131519 0.826883434 0.596671593 0.123246763 204.2225015 91067.61343 0.035679707 0.037844054 623.1947299 -2.794623772 -0.282248085 LGLALNYSVFYYEIQNAPEQACHLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LGLALNYSVFYYEIQNAPEQACHLAK 26 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;; 261.74 7.68E-53 934139000 981784 878153 849476 701055 999308 704696 1132155 972105 859049 FALSE TRUE 920335.892 943172.3618 869625.9719 719045.2582 920826.3807 908130.2954 962398.8682 1093474.449 715668.1722 1.285981308 1.317890607 1.215124559 1.004718787 1.286666665 1.268926481 1.34475572 1.527907055 1 19.44893129 2.199438738 2.762754628 1.322314672 1.222318919 0.03056213 0.153131353 0.712533734 11.10562296 0.061548382 0.042855202 158.2846273 -2.199438738 -0.099995752 LGLAVIHGEAQCTELDMDDGRHS(ph)PPMVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 15 LGLAVIHGEAQCTELDMDDGRHSPPMVK 28 1 C9J168;B4DP31;Q14558;Q14558-2;C9JUN4 C9J168 PRPSAP1 Phosphoribosyl pyrophosphate synthase-associated protein 1 1 LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK 279.62 6.45E-62 5080350000 2777266 2504849 2647059 2657727 2807178 2170973 3418778 2507016 2879788 TRUE FALSE 2603441.879 2690310.626 2709848.49 2725928.774 2586713.563 2797697.662 2906163.977 2820022.466 2399132.779 1.085159563 1.121367959 1.129511678 1.136214218 1.078186913 1.166128731 1.211339365 1.175434095 1 21.19408157 2.207377285 24.8905341 1.162151419 1.115462449 0 0.059512287 373.4973932 298123.3113 0.019948495 0.014734672 161.2045461 -2.207377285 -0.04668897 LGLDPTQEDCVATHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGLDPTQEDCVATHR 15 0 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 ; 171.46 1.08E-06 480780000 886220 496740 564690 553890 583370 400070 714720 445090 574310 FALSE TRUE 830753.0721 533519.1465 578084.7135 568103.7551 537554.4734 515563.7144 607554.3711 500660.4663 478453.9508 1.736328169 1.115089855 1.2082348 1.187373945 1.123523951 1.077561829 1.269828309 1.046413067 1 18.86802055 4.740525984 24.95298823 1.148258016 1.736328374 0.84653335 0.080945319 59.49350485 755293.4466 0.017263065 0.113421845 55020.6839 -4.740525984 0.588070358 LGLDYEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LGLDYEER 8 0 Q99623-2;Q99623;F5GY37;J3KPX7;F5H3X6;F5GWA7 Q99623-2 PHB2 Prohibitin-2 0 ;;;;; 129.55 0.0025258 3760600000 7001970 7613820 7420410 6789010 10296800 7002860 7198330 7756980 11514300 FALSE TRUE 6563729.197 8177555.155 7596425.629 6963227.49 9488130.863 9024472 6119007.243 8725456.028 9592488.945 0.684257155 0.852495656 0.791913931 0.725904145 0.989120855 0.940785239 0.637895678 0.909613353 1 23.19347377 -5 0.287509423 2.42789712 0.801068573 0.2276645 0.110909345 390.5264706 3.696369845 334.3096749 0.116740833 1.00E-05 5 -1.626828547 LGLGIDEDDPTADDTSAAVTEEMPPLEGDDDTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 LGLGIDEDDPTADDTSAAVTEEMPPLEGDDDTSR 34 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;;;; 313.77 1.50E-104 4370920000 2192764 2342143 2314624 2340227 2362578 2010699 2663790 2112001 2216261 FALSE TRUE 2055522.815 2515557.705 2369527.974 2400281.187 2177030.654 2591155.16 2264379.419 2375688.974 1846352.722 1.113288264 1.362446988 1.283356071 1.300012267 1.17909792 1.403391199 1.226406738 1.28669292 1 20.81624676 -0.391654013 1.095798087 0.995160267 1.280325395 0.500242781 0.08394322 24.5411288 17.60337152 0.618944349 0.021908563 0.405831718 0.391654013 0.285165128 LGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASR 34 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;; 164.35 2.71E-14 1373205000 769800 804977 832513 826807 837420 712622 981922 795509 845241 FALSE TRUE 721619.5921 864578.3347 852260.6015 848024.2674 771652.4112 918344.4029 834691.9118 894830.0498 704164.8166 1.024787912 1.227806778 1.210314093 1.204297982 1.095840623 1.304161158 1.185364409 1.270767906 1 19.42555362 -1.13997859 4.905087851 0.999988068 1.197338238 0.353800301 0.08039275 9.24E-06 1.62E-06 0.068568396 0.016160749 0.072447167 1.13997859 0.19735017 LGLGTLSSS(ph)LSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGLGTLSSSLSR 12 0 O95248;O95248-5;O95248-4 O95248 SBF1 Myotubularin-related protein 5 1 LGLGT(0.009)LS(0.202)S(0.202)S(0.586)LS(0.001)R 80.31 0.021699 40030000 66826 82715 73529 76476 90437 60961 81454 74995 98225 TRUE FALSE 62643.47995 88839.30466 75273.1426 78438.50363 83334.44283 78559.45108 69240.72888 84358.29083 81830.61294 0.765526222 1.085648775 0.919865316 0.958547184 1.018377351 0.960025206 0.846147015 1.030889148 1 16.32035304 1.974725213 24.89381796 0.932209493 0.966557785 0 0.095023947 3215.03244 3166566.872 0.035711462 0.023164721 94.34637388 -1.974725213 0.034348291 LGLHVTPSNVDQVST(ph)PPAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGLHVTPSNVDQVSTPPAAK 20 0 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 1 LGLHVTPSNVDQVS(0.124)T(0.876)PPAAK 122.04 0.00011478 155860000 126220 112160 131620 129540 128220 93575 158520 121840 144130 TRUE FALSE 118320.1155 120464.4431 134742.0886 132864.2157 118150.1184 120588.5834 134751.3976 137051.9922 120073.7719 0.985395175 1.003253593 1.122160872 1.106521546 0.983979403 1.00428746 1.1222384 1.141398243 1 16.87356153 1.718839604 11.44660821 1.098285901 1.041689051 0.136570604 0.059772019 0.198747417 75.8377888 0.028210467 0.015393532 52.34070929 -1.718839604 -0.056596849 LGLLDTQTSQVLTAVDKDNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGLLDTQTSQVLTAVDKDNK 20 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 201.38 1.15E-21 102490000 245100 167460 195710 202140 221940 153190 292600 186000 229440 FALSE TRUE 229759.6285 179858.9126 200352.3336 207327.2546 204509.7277 197413.4662 248727.3464 209222.5094 191144.9818 1.202017581 0.940955452 1.048169467 1.084659679 1.069919418 1.032794397 1.30124968 1.094574953 1 17.5443078 LGLPLLTDCAQPSRPHGS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LGLPLLTDCAQPSRPHGSPSR 21 1 U3KQ90;P55199 U3KQ90 ELL RNA polymerase II elongation factor ELL 1 LGLPLLTDCAQPS(0.025)RPHGS(0.94)PS(0.035)R;LGLPLLTDCAQPS(0.063)RPHGS(0.936)PS(0.001)R;LGLPLLTDCAQPS(0.001)RPHGS(0.992)PS(0.006)R;LGLPLLTDCAQPSRPHGS(0.659)PS(0.34)R 199.92 4.68E-22 1324930000 778948 769806 839715 687190 909411 819988 982154 808684 1020188 TRUE FALSE 730195.0351 826803.2372 859633.4363 704824.4588 837989.5284 1056705.224 834889.1256 909649.9775 849912.0321 0.859141896 0.972810369 1.01143813 0.82929107 0.985972073 1.243311289 0.982324163 1.07028721 1 19.696954 2.465966862 24.9958863 1.074657346 0.939302636 0.41003733 0.086549262 231.3068836 518332.1039 0.028273801 0.023673761 292.3929264 -2.465966862 -0.135354711 LGLPLLTDCAQPSRPHGSPS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGLPLLTDCAQPSRPHGSPSR 21 1 U3KQ90;P55199 U3KQ90 ELL RNA polymerase II elongation factor ELL 1 LGLPLLTDCAQPSRPHGS(0.374)PS(0.626)R 197.54 5.48E-22 159300000 91125 89888 94908 84776 99890 96897 111750 92162 100620 TRUE FALSE 85421.64891 96543.40105 97159.26258 86951.49569 92045.04234 124869.5909 94994.12494 103668.6286 83825.87197 1.019036807 1.151713651 1.159060566 1.037287101 1.09805052 1.489630683 1.133231575 1.23671399 1 16.35510796 LGLVLDQAEAEGVCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGLVLDQAEAEGVCR 15 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ; 223.21 3.02E-12 116061000 119064 138405 118731 120180 140629 119024 160567 119959 121458 FALSE TRUE 111611.9968 148652.6502 121547.3554 123264.0223 129584.5656 153384.2966 136491.469 134936.1452 101185.8752 1.103039299 1.469104754 1.201228484 1.218193963 1.280658643 1.51586668 1.348918204 1.333547247 1 16.62664839 -1.246241344 6.718472637 0.999997228 1.321322769 0.382289022 0.122455083 4.79E-06 5.37E-07 0.11160454 0.026305215 0.05672293 1.246241344 0.321325541 LGMIVDKIDADKDGFVTEGELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGMIVDKIDADKDGFVTEGELK 22 2 O43852-2;O43852-4;O43852-8;O43852-7 O43852-2 CALU Calumenin 0 ; 217.84 6.91E-26 184845000 623040 312790 429710 412040 507620 281290 576860 347240 895200 FALSE TRUE 584045.0386 335949.2971 439902.9241 422613.644 467753.5728 362493.8566 490365.1983 390593.6784 745785.3368 0.783127543 0.4504638 0.589851935 0.566669286 0.62719599 0.486056562 0.657515205 0.523734725 1 19.50840091 -1.515228598 3.170616532 1.012280469 0.576153624 0.657927995 0.093692158 58516452.39 70404465.16 6224199.919 0.01989755 0.030533135 1.515228598 -0.436126844 LGMLS(ph)PEGTCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 LGMLSPEGTCK 11 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 LGMLS(0.998)PEGT(0.002)CK;LGMLS(1)PEGTCK;LGMLS(0.994)PEGT(0.006)CK;LGMLS(1)PEGTCK;LGMLS(0.993)PEGT(0.007)CK;LGMLS(1)PEGTCK;LGMLS(0.999)PEGT(0.001)CK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(0.996)PEGT(0.004)CK;LGMLS(1)PEGTCK;LGMLS(0.999)PEGT(0.001)CK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK 241.78 1.02E-15 8162810000 19973280 15865960 19068990 18243240 19708480 15966920 25414920 17082610 24844550 TRUE FALSE 18723188.06 17040692.19 19521315.45 18711392.42 18160655.48 20576310.6 21604188.69 19215411.46 20697834.1 0.904596489 0.82330799 0.943157402 0.904026592 0.877418158 0.994128685 1.043789827 0.928377886 1 24.30297647 2.227219981 12.5967612 1.000413787 0.889130335 0.599352322 0.040770455 0.380156358 417.4596487 0.01474328 0.01118728 168.7407524 -2.227219981 -0.111283452 LGNDFHTNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LGNDFHTNK 9 0 H3BNC9;P08708;H0YN88;A0A075B716;H0YN73;A0A0J9YYC4 H3BNC9 RPS17 40S ribosomal protein S17 0 ;;; 107.83 0.0027098 1540990000 5536000 5222100 4913300 4596560 5821600 4002950 5663600 4731880 4982560 FALSE TRUE 5189511.642 5608749.718 5029845.796 4714515.512 5364395.019 5158536.683 4814395.758 5322665.634 4150938.547 1.250201992 1.351200374 1.211736994 1.135770973 1.292333037 1.242739834 1.15983306 1.282280037 1 21.98500614 -5 0.168121466 0.077326458 1.300096831 0.585528291 0.063156705 91.46652983 0.859551892 28.19177016 0.227263918 1.00E-05 5 1.222770373 LGNDFHTNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LGNDFHTNKR 10 1 H3BNC9;P08708;H0YN88;A0A075B716;H0YN73;A0A0J9YYC4 H3BNC9 RPS17 40S ribosomal protein S17 0 ;;; 189.58 6.46E-07 4528410000 8248700 9455980 7833730 7421390 10453130 5905610 8725080 8387740 10664420 FALSE TRUE 7732428.591 10156110.6 8019549.775 7611835.432 9632183.336 7610463.737 7416835.254 9434967.803 8884459.407 0.870331917 1.143132084 0.902649155 0.856758423 1.084160881 0.856604031 0.834809966 1.061963072 1 23.08285256 3.737874627 22.57660244 0.927064881 1.025219681 0.037539356 0.108066129 208.1584507 437016.4201 0.025878516 0.045926257 5468.58072 -3.737874627 0.0981548 LGNSGAS(ph)PSSAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LGNSGASPSSAGK 13 0 Q8IWI9-3;Q8IWI9 Q8IWI9-3 MGA MAX gene-associated protein 1 LGNSGAS(0.999)PS(0.001)SAGK;LGNSGAS(1)PSSAGK;LGNSGAS(0.999)PSSAGK;LGNSGAS(1)PSSAGK 218.57 2.51E-11 608233000 1101360 807580 924710 844420 998410 720000 1196830 865300 1119780 TRUE FALSE 1032427.844 867374.0635 946644.5579 866089.2468 919998.906 927852.3118 1017376.452 973334.6098 932881.4839 1.106708474 0.929779483 1.014753293 0.928402227 0.986190552 0.994608991 1.090574172 1.043363628 1 19.83133428 1.881070406 7.057033983 1.052893077 0.985052196 0.152091251 0.054021086 0.329895437 17.80019412 0.02104777 0.012995716 76.04495485 -1.881070406 -0.067840881 LGPGGLDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LGPGGLDDR 9 0 Q9Y446;Q9Y446-2;E9PQ15;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 0 ;;; 155.38 0.0001709 458270000 1165820 1231340 1235760 1178130 1317330 1040520 1415410 1127840 1339450 FALSE TRUE 1092853.407 1322509.695 1265072.811 1208362.81 1213872.216 1340901.233 1203182.411 1268653.307 1115887.142 0.979358365 1.185164382 1.133692435 1.082871883 1.087809125 1.201645921 1.078229478 1.136901089 1 20.08975969 -1.2846938 2.94071021 0.999064502 1.118953114 0.227347229 0.062519617 8087473.9 10405819.66 67377.49774 0.013581037 0.051916595 1.2846938 0.119888612 LGPGGLDDRYS(ph)LVSEQLEPAATSTYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LGPGGLDDRYSLVSEQLEPAATSTYR 26 1 Q9Y446;Q9Y446-2;E9PQ15;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 1 LGPGGLDDRYS(1)LVSEQLEPAATSTYR;LGPGGLDDRYS(1)LVSEQLEPAATSTYR;LGPGGLDDRYS(0.999)LVS(0.001)EQLEPAATSTYR;LGPGGLDDRYS(1)LVSEQLEPAATSTYR 334.57 2.59E-95 884750000 585710 710290 521720 510494 750340 315643 865170 617360 880450 TRUE FALSE 549051.4566 762880.6107 534095.4448 523594.1403 691411.3231 406764.0101 735445.7903 694438.755 733497.2071 0.74853926 1.040059326 0.728149255 0.713832494 0.94262298 0.554554273 1.002656565 0.946750374 1 19.48443195 1.60568169 25 0.981047429 0.810766743 0.316563096 0.132374507 0.29032015 3269.210769 0.063982319 0.031858391 40.33496551 -1.60568169 -0.170280686 LGPGRPLPTFPTSECT(ph)SDVEPDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGPGRPLPTFPTSECTSDVEPDTR 24 1 Q8TDD1-2;Q8TDD1;H0YHZ9 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 LGPGRPLPTFPT(0.001)S(0.007)ECT(0.496)S(0.496)DVEPDTR 96.158 0.010666 461370000 243000 240670 244840 232020 263150 260970 356090 215470 241790 TRUE FALSE 227791.0638 258489.4572 250647.7204 237974.026 242483.2605 336307.8025 302697.6103 242371.9038 201433.687 1.130848902 1.283248403 1.244318784 1.181401332 1.203787034 1.669570803 1.50271593 1.203234213 1 17.61994545 LGPGRPLPTFPTSECTS(ph)DVEPDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LGPGRPLPTFPTSECTSDVEPDTR 24 1 Q8TDD1-2;Q8TDD1;H0YHZ9 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 LGPGRPLPTFPT(0.001)S(0.005)ECT(0.059)S(0.935)DVEPDTR;LGPGRPLPTFPT(0.001)S(0.004)ECT(0.206)S(0.789)DVEPDTR;LGPGRPLPTFPTS(0.001)ECT(0.187)S(0.813)DVEPDTR;LGPGRPLPTFPT(0.006)S(0.019)ECT(0.192)S(0.783)DVEPDTR;LGPGRPLPTFPT(0.001)S(0.014)ECT(0.18)S(0.806)DVEPDTR 184.75 1.53E-17 2035620000 1121348 1091711 1200417 1144243 1208396 1146498 1652240 1038070 1137625 TRUE FALSE 1051164.83 1172542.418 1228891.458 1173606.213 1113493.453 1477473.361 1404501.951 1167675.325 947748.0382 1.109118445 1.237187914 1.296643632 1.238310358 1.174883416 1.55893054 1.481936015 1.232052484 1 19.85414404 2.281300431 24.99999866 1.378791265 1.227647057 0.039376776 0.159827196 230.0078342 134538.5556 0.051222185 0.042855274 191.1174893 -2.281300431 -0.151144208 LGPLFSLLNENHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGPLFSLLNENHR 13 0 Q16401-2;Q16401;F2Z3J2 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ; 211.38 2.24E-08 191455000 342570 745440 371770 352400 778280 242270 455610 664810 737800 FALSE TRUE 321129.1552 800633.1532 380588.56 361443.1806 717157.0282 312209.4161 387295.5102 747812.9919 614656.4136 0.522453111 1.302570242 0.619189114 0.588041014 1.166760831 0.507941362 0.63010082 1.216635791 1 19.22942066 1.233048032 24.99306307 1.10831795 0.788697268 0.21186464 0.273723668 243.4153692 1103543.325 0.230757255 0.06415557 17.10204451 -1.233048032 -0.319620682 LGPQNFIDET(ph)SDIENLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGPQNFIDETSDIENLLK 18 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 1 LGPQNFIDET(0.5)S(0.5)DIENLLK 95.018 0.020748 27660000 102500 60993 76215 70371 61420 70898 126540 65536 52096 TRUE FALSE 96084.70797 65508.98518 78022.85579 72176.839 56596.32096 91365.10167 107566.5017 73718.31386 43400.84105 2.21389046 1.509394371 1.797726816 1.663028579 1.304037424 2.105145879 2.478442794 1.698545744 1 15.40543538 2.191896694 24.99941666 2.006791922 1.684026339 0 0.44842779 268.5547404 143871.9905 0.153763283 0.11356204 155.5595557 -2.191896694 -0.322765583 LGPSDYFGEIALLMNRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGPSDYFGEIALLMNRPR 18 1 P10644 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 0 ; 242.93 4.20E-24 210620000 209840 223040 214539 184206 233780 182280 240170 198388 234320 FALSE TRUE 196706.489 239554.1137 219627.9664 188933.0378 215419.8618 234901.2769 204158.7381 223157.1785 195210.4782 1.007663578 1.22715807 1.125082877 0.967842708 1.103526121 1.203323095 1.045839035 1.143161886 1 17.57467097 -5 0.255193656 0.304124179 1.121333023 0.10976634 0.081787474 376.5176181 3.71786753 137.1217259 0.109985828 1.00E-05 5 0.817208844 LGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQAR 34 0 Q9NR31;Q5SQT8;Q9NR31-2 Q9NR31 SAR1A GTP-binding protein SAR1a 0 ; 226.1 5.87E-37 442092000 234866 298802 304313 291177 287407 272349 310605 281215 266360 FALSE TRUE 220166.1563 320925.611 311531.4481 298649.0948 264835.2136 350971.7351 264032.6638 316325.3118 221902.7952 0.992173875 1.446244112 1.403909526 1.345855488 1.193473986 1.5816463 1.189857313 1.425512966 1 17.75956832 -1.622314844 2.73447519 0.968652691 1.338136774 0.268947449 0.165196439 28301933.77 25896722.64 6293253.347 0.036639514 0.023860809 1.622314844 0.369484083 LGQHVPTLHPTSEELTIAGMTFTTFDLGGHVQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGQHVPTLHPTSEELTIAGMTFTTFDLGGHVQAR 34 0 Q9Y6B6;D6RD69;D6RDB2;D6RAA2 Q9Y6B6 SAR1B GTP-binding protein SAR1b 0 ; 144.55 8.34E-11 80555000 37644 42799 38894 41831 46671 37727 45692 43809 37237 FALSE TRUE 35287.92924 45967.88249 39816.58405 42904.45428 43005.64792 48618.17245 38840.90878 49278.65009 31021.90414 1.137516546 1.48178791 1.283499036 1.38303742 1.386299427 1.567220769 1.252047863 1.588511455 1 14.92099962 -0.987947142 4.939660902 0.999996171 1.382941938 0.431895159 0.138746409 5.03E-06 1.03E-06 0.115365779 0.027191703 0.102814142 0.987947142 0.382945767 LGQSDPAPLQHQMDIYQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LGQSDPAPLQHQMDIYQK 18 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ;;;;; 234.11 9.29E-24 3864990000 4195650 4755730 3768510 3205640 6557460 3020810 4219940 5688460 5824330 FALSE TRUE 3933051.756 5107849.198 3857900.837 3287902.15 6042463.543 3892868.808 3587199.173 6398676.753 4852211.696 0.810568871 1.052684738 0.795080899 0.677608966 1.24530089 0.802287503 0.739291564 1.318713435 1 22.21021106 1.240930477 24.99998009 1.159356713 0.879595178 0.300629481 0.180387631 71.6977747 756419.2389 0.126003263 0.041067588 17.41528065 -1.240930477 -0.279761535 LGS(ph)LVDEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGSLVDEFK 9 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 1 LGS(1)LVDEFK 127.42 0.00046765 6771500 63459 33034 37681 42788 41446 25687 51079 27348 50406 TRUE FALSE 59487.21447 35479.87173 38574.81111 43886.01252 38190.99835 33102.41991 43420.17814 30762.458 41992.91296 1.416601285 0.844901419 0.918602888 1.045081406 0.909462946 0.788285869 1.033988239 0.732563088 1 15.35785825 4.743159854 24.98625248 0.911359197 1.41660149 0.712487959 0.101305102 240.6212537 1307175.975 0.021739417 0.174745173 55355.38229 -4.743159854 0.505242293 LGS(ph)PDYGNSALLSLPGYRPTTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGSPDYGNSALLSLPGYRPTTR 22 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 LGS(1)PDYGNSALLSLPGYRPTTR;LGS(0.999)PDYGNS(0.001)ALLSLPGYRPTTR 241.71 6.77E-31 968150000 876580 548660 647560 613500 607770 516720 791320 541540 898780 TRUE FALSE 821716.4225 589283.3573 662920.429 629243.4487 560038.1958 665888.6758 672668.9123 609152.4611 748767.8117 1.097424876 0.787004126 0.88534846 0.840371927 0.747946409 0.889312635 0.898367827 0.813539861 1 19.51415889 -1.040943811 7.821326179 1.000000004 0.862867027 0.155747323 0.093916987 6.36E-09 7.69E-10 0.080752843 0.019033627 0.091003101 1.040943811 -0.137132977 LGS(ph)PGAPQQEDAMDDKELIEYFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGSPGAPQQEDAMDDKELIEYFK 23 1 H0YGG4 H0YGG4 EIF2B1 1 LGS(1)PGAPQQEDAMDDKELIEYFK;LGS(1)PGAPQQEDAMDDKELIEYFK 242.9 1.40E-37 368910000 575950 202773 279520 299430 311520 173084 389960 217839 303100 TRUE FALSE 539902.3176 217786.5239 286150.3464 307113.8807 287054.4758 223050.541 331489.1182 245036.6787 252510.6519 2.138136802 0.862484502 1.133220893 1.216241289 1.136801452 0.883331215 1.312772811 0.970401355 1 17.94598472 4.74571526 24.93726797 1.077363638 2.138137314 0.848593491 0.142441078 303.0763224 1056335.475 0.032629495 0.334151724 55682.05562 -4.74571526 1.060773676 LGS(ph)PHRRPLSVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGSPHRRPLSVDK 13 2 M0QXN6;M0QX46;Q6UUV9;Q6UUV9-2;Q6UUV9-3 M0QXN6 CRTC1 CREB-regulated transcription coactivator 1 1 LGS(0.999)PHRRPLS(0.001)VDK 49.559 0.090962 133770000 79043 78490 80969 91097 102100 55952 99664 95622 129780 TRUE FALSE 74095.83973 84301.48127 82889.62292 93434.70325 94081.47785 72104.4341 84720.30844 107560.6172 108118.8796 0.685318235 0.779711014 0.766652626 0.864184901 0.87016697 0.666899568 0.78358478 0.994836587 1 16.72225894 -5 0.120727878 1.73740211 0.683770335 0.473796566 0.081891839 146.2818355 1.143588375 25.85269045 0.765669645 1.00E-05 5 -1.053631775 LGS(ph)PKPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LGSPKPER 8 1 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 LGS(1)PKPER;LGS(1)PKPER;LGS(1)PKPER;LGS(1)PKPER;LGS(1)PKPER;LGS(1)PKPER 98.353 0.0045919 10457700000 17786830 7909480 10396340 9851630 9849970 6510830 12631300 7651140 12555850 TRUE FALSE 16673584.06 8495106.129 10642946.09 10104439.5 9076393.089 8390400.927 10737353.83 8606401.671 10460197.52 1.594002793 0.812136302 1.017470853 0.96598936 0.867707619 0.802126433 1.026496279 0.82277621 1 23.31840676 4.744075365 24.96706326 0.918350633 1.594003085 0.85978125 0.086245857 198.2035804 897304.8533 0.019079493 0.167234952 55472.1968 -4.744075365 0.675652452 LGS(ph)PLAVDEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LGSPLAVDEALR 12 0 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 LGS(1)PLAVDEALR;LGS(1)PLAVDEALR;LGS(1)PLAVDEALR;LGS(1)PLAVDEALR 226.59 1.57E-11 175921000 430734 298578 325278 343641 383996 235371 339891 259707 298915 TRUE FALSE 403775.1278 320685.0258 332993.7478 352459.4098 353838.5031 303318.7868 288927.4999 292131.9906 249024.1554 1.621429564 1.287766744 1.337194567 1.415362334 1.420900324 1.218029577 1.160238851 1.173107043 1 17.92592617 1.62209582 0.798353369 1.019552693 1.398443945 0.691207945 0.095289371 0.357785905 0.455165054 0.085598252 0.037009392 41.88859757 -1.62209582 0.378891252 LGS(ph)PLAVDEALRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LGSPLAVDEALRR 13 1 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 LGS(1)PLAVDEALRR;LGS(1)PLAVDEALRR;LGS(1)PLAVDEALRR;LGS(1)PLAVDEALRR 197.7 8.07E-08 350978000 474505 365073 369764 412970 484294 255089 401059 309651 494437 TRUE FALSE 444806.5791 392103.3848 378534.9767 423567.5094 446259.5028 328729.0533 340923.9262 348311.609 411912.2705 1.079857559 0.95190994 0.918969897 1.02829544 1.083384824 0.798055986 0.827661496 0.845596584 1 18.65197758 2.228469927 24.99515583 0.84872313 0.992190365 0.461290474 0.074680471 181.0187301 448389.331 0.027139072 0.020274581 169.2271056 -2.228469927 0.143467235 LGS(ph)PSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LGSPSGK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LGS(0.859)PS(0.141)GK;LGS(0.724)PS(0.276)GK;LGS(0.99)PS(0.01)GK;LGS(0.99)PS(0.01)GK;LGS(0.985)PS(0.015)GK;LGS(0.985)PS(0.015)GK;LGS(0.907)PS(0.093)GK;LGS(0.993)PS(0.007)GK 158.37 0.001493 14183360000 46261100 23605600 30814400 28769000 29905100 17984320 29747100 20789430 29686000 TRUE FALSE 43365700.33 25353383.19 31545332.12 29507261.25 27556474.08 23176101.23 25286798.51 23385036.1 24731214.82 1.753480395 1.02515721 1.275526995 1.193118149 1.114238596 0.937119402 1.022464877 0.945567626 1 24.55982977 4.741342059 24.97718866 1.078990346 1.75348064 0.803052668 0.107059622 123.6827843 1110603.832 0.027668879 0.191847097 55124.16944 -4.741342059 0.674490294 LGS(ph)PVDNLEDMDRDDLTDDSVFTR ddPTM_SK-BR-3_Pertuzumab_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 267.1 1.02E-44 926383000 247183 179133 195098 178781 190642 164052 211685 160912 249580 TRUE FALSE 231712.2573 192396.1937 199725.8167 183368.8231 175669.7463 211411.1492 179944.7994 181002.2174 207923.4857 1.114411181 0.925322087 0.960573627 0.881905296 0.844876882 1.016773784 0.865437586 0.870523197 1 17.6656932 LGS(ph)SSNLQFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LGSSSNLQFK 10 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 LGS(0.815)S(0.168)S(0.018)NLQFK;LGS(0.809)S(0.172)S(0.019)NLQFK;LGS(0.827)S(0.135)S(0.038)NLQFK;LGS(0.723)S(0.256)S(0.021)NLQFK 193.94 5.43E-07 1027600000 1830720 1197250 1269220 1259060 1488700 767877 1726760 1145740 1734590 TRUE FALSE 1716138.503 1285895.636 1299326.498 1291369.611 1371783.507 989550.6245 1467848.368 1288788.161 1445075.723 1.187576869 0.889846542 0.89914077 0.893634562 0.949281401 0.684774236 1.01575879 0.891848185 1 20.46271366 4.739655288 24.6273212 0.898807146 1.187576983 0.497898661 0.08971003 58.55030863 1317020.156 0.01895776 0.116791975 54910.48603 -4.739655288 0.288769837 LGS(ph)VDSFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LGSVDSFER 9 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 LGS(0.998)VDS(0.002)FER;LGS(0.999)VDS(0.001)FER;LGS(0.996)VDS(0.004)FER 181.44 4.98E-05 525990000 1963170 1263170 1413690 1652340 1952710 1056320 1516410 1096410 1707410 TRUE FALSE 1840298.694 1356696.421 1447223.394 1694741.842 1799352.033 1361262.436 1289038.398 1233299.202 1422432.241 1.293768969 0.953786326 1.017428706 1.191439419 1.264982599 0.956996331 0.906221303 0.867035467 1 20.4399285 2.023795056 24.38364786 0.918401473 1.103803477 0.457638513 0.110129492 182.9909805 187516.3677 0.0432948 0.031973532 105.6318913 -2.023795056 0.185402004 LGSDPQKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGSDPQKK 8 1 Q96KP4;J3QKT2;J3QRH4;A0A087WYZ1;J3KSV5;J3QRD0;J3QKQ0;J3QLU1;J3QR27;A0A087WVS2;J3QL02;J3KRD5 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 69.954 0.084315 643820000 1799000 1241200 1415200 1397900 1735700 976160 1835900 1390300 1939700 FALSE TRUE 1686403.801 1333099.739 1448769.212 1433772.481 1599385.123 1257961.545 1560623.839 1563882.015 1615951.539 1.043598004 0.824962697 0.896542487 0.887262053 0.989748198 0.778464895 0.965761535 0.967777794 1 20.6239525 1.564966571 10.85490907 0.977364975 0.894644588 0.176003875 0.074728285 0.171626869 32.92962513 0.036127699 0.016843285 36.72540305 -1.564966571 -0.082720387 LGSGPDGAEEIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGSGPDGAEEIKR 13 1 E9PGT3;Q15418-4;Q15418;Q15418-2;Q15418-3 E9PGT3 RPS6KA1 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1 0 119.25 0.00058243 261700000 233610 212600 217290 233810 245540 163780 278280 197920 245910 FALSE TRUE 218988.7671 228341.1252 222444.2214 239809.9604 226256.2789 211060.6273 236554.4974 222630.7477 204866.0324 1.068936439 1.114587531 1.085803336 1.170569653 1.104410898 1.030237296 1.154678961 1.086713815 1 17.64432127 -1.468345225 8.557789486 0.999997065 1.104333897 0.389503623 0.040033429 2.04E-06 1.27E-07 0.035170896 0.008289626 0.03401377 1.468345225 0.104336832 LGSLVENNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGSLVENNER 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 ; 123.75 0.0010558 244470000 295210 276730 286710 288330 330490 228480 325760 275030 363500 FALSE TRUE 276733.3331 297219.3771 293510.8966 295729.0359 304534.6485 294438.4669 276915.3122 309368.1009 302829.5017 0.91382554 0.981474313 0.969228212 0.976552926 1.005630716 0.972291224 0.91442647 1.021591685 1 18.20814623 4.742964619 24.07837191 0.974144311 0.9138255 0.323758738 0.02899141 351.5267532 1921808.504 0.00680963 0.052910803 55330.50308 -4.742964619 -0.060318811 LGSQHS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LGSQHSPGR 9 0 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 1 LGSQHS(1)PGR;LGS(0.001)QHS(0.999)PGR;LGS(0.002)QHS(0.998)PGR;LGSQHS(1)PGR;LGSQHS(1)PGR 124.6 0.00033825 6734618000 3912980 5513520 4971590 5069250 6005450 4270800 5339680 4930680 5857170 TRUE FALSE 3668073.567 5921746.758 5089518.463 5199335.537 5533806.182 5503710.629 4539044.555 5546286.252 4879570.488 0.751720582 1.213579509 1.043025913 1.065531393 1.134076492 1.127908828 0.930213953 1.136634109 1 22.21832273 -1.061062112 5.88509985 0.999999818 1.060969295 0.008793675 0.129920962 2.78E-07 4.42E-08 0.112586392 0.026536788 0.086883616 1.061062112 0.060969476 KIS(ph)GTTALQEALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KISGTTALQEALK 13 1 J3KP58;P30622-2;P30622-1;P30622;F5H0N7;Q9UDT6;Q9UDT6-2 J3KP58;Q9UDT6 CLIP1;CLIP2 CAP-Gly domain-containing linker protein 1;CAP-Gly domain-containing linker protein 2 1 KIS(0.969)GT(0.02)T(0.011)ALQEALK 183.36 6.38E-06 626730000 972790 836650 629590 475470 1070400 490310 885760 1138300 2393800 TRUE FALSE 911904.8104 898596.4365 644524.1721 487671.3652 986335.1018 631854.5375 752948.511 1280419.261 1994259.315 0.457264912 0.45059157 0.323189751 0.244537589 0.494587185 0.316836699 0.377557976 0.642052541 1 20.92742159 0.963134254 2.638928353 0.998648555 0.376733785 0.878063156 0.075018997 0.090454522 1.468275978 0.069073036 0.018484468 9.186165263 -0.963134254 -0.62191477 LGSS(ph)SNLQFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGSSSNLQFK 10 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 LGS(0.052)S(0.884)S(0.064)NLQFK 189.24 1.08E-06 231020000 602100 369350 434970 390820 452620 256080 555410 380750 557080 TRUE FALSE 564415.6358 396697.0583 445287.6938 400849.1029 417073.051 330006.1389 472131.4267 428287.4756 464099.7491 1.216151564 0.854766802 0.959465491 0.86371325 0.898671141 0.711067264 1.01730593 0.922834965 1 18.82407539 4.743756428 24.87827256 0.90128396 1.216151705 0.565209673 0.086165293 369.5810649 1769547.005 0.018903609 0.160574493 55431.47416 -4.743756428 0.314867745 LGSSGLGS(ph)ASSIQAAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGSSGLGSASSIQAAVR 17 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 LGSSGLGS(0.998)AS(0.001)S(0.002)IQAAVR 234.3 4.14E-20 101570000 102880 105980 107260 121300 139020 65104 109550 105120 128920 TRUE FALSE 96440.92445 113826.8695 109804.2579 124412.7634 128101.93 83898.46792 93123.99451 118244.4634 107402.4191 0.897939965 1.059816626 1.022362985 1.158379526 1.192728534 0.781159946 0.867056769 1.100947859 1 16.71266696 2.239582651 24.99999145 0.914693988 1.063572772 0.2298071 0.113961233 35.28294162 863083.0559 0.039996629 0.031696046 173.6131634 -2.239582651 0.148878784 LGSSGLGSASS(ph)IQAAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGSSGLGSASSIQAAVR 17 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 LGSSGLGS(0.19)AS(0.037)S(0.773)IQAAVR 294.04 4.73E-46 91798000 81194 101900 97443 101800 103880 62332 98116 95026 105410 TRUE FALSE 76112.21248 109444.782 99754.39398 104412.3603 95721.68383 80326.23652 83404.41666 106890.2053 87816.39003 0.866719897 1.246291062 1.135942777 1.188984884 1.09002071 0.914706657 0.949759113 1.217201086 1 16.42220261 2.465667304 22.467529 1.005092319 1.136976162 0.079680777 0.126465438 102.9302456 201897.7198 0.041024667 0.034367774 292.1913155 -2.465667304 0.131883843 LGSSLDWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LGSSLDWDR 9 0 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 ;;; 194.22 7.60E-05 657823000 960000 1862410 945390 971400 1999650 583374 929230 1672030 1997560 FALSE TRUE 899915.3136 2000304.774 967815.0972 996327.7686 1842605.555 751784.6035 789900.588 1880786.626 1664154.331 0.540764337 1.201994753 0.581565711 0.598699141 1.107232377 0.451751733 0.47465585 1.130175604 1 20.6663578 5.012233487 18.3640915 0.780552104 0.138535727 0.072597997 0.284619857 92271113.25 2378814311 0.066531746 1542425974 102856.9132 -5.012233487 -0.642016377 LGSVDS(ph)FER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGSVDSFER 9 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 LGSVDS(1)FER 144.7 0.00010378 88857000 167500 164550 148540 114480 107300 120460 260980 238590 222570 TRUE FALSE 157016.474 176733.4532 152063.4389 117417.7506 98873.09083 155234.8465 221848.4718 268378.4867 185421.6291 0.846807758 0.953143676 0.820095475 0.633247325 0.533233859 0.837199237 1.196454118 1.447395797 1 17.50045002 1.724421794 3.989107383 1.251413673 0.780102695 0.640930066 0.156776539 0.12267721 4.402481156 0.087664768 0.042863666 53.01781123 -1.724421794 -0.471310978 LGTGFSDEELEEHHQSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LGTGFSDEELEEHHQSLK 18 0 P18858;P18858-3;F5GZ28 P18858 LIG1 DNA ligase 1;DNA ligase 0 ;; 276.14 2.49E-39 515303000 461515 894620 899030 893610 929770 772600 1078520 902350 1020950 FALSE TRUE 432629.6 960858.5957 920355.4162 916541.5455 856749.6147 995637.0779 916805.9385 1015010.384 850546.8494 0.50864876 1.129695085 1.082074922 1.077590901 1.007292679 1.17058464 1.077901751 1.193362111 1 19.69803118 4.740569649 24.99930712 1.095783423 0.50864856 0.898729548 0.061563476 46.81827213 582539.5675 0.012953857 0.084982869 55026.21606 -4.740569649 -0.587134863 LGTLS(ph)PAFSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGTLSPAFSTR 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 1 LGT(0.004)LS(0.996)PAFSTR 111.96 0.0016679 77830000 65800 66616 77699 75305 83248 50638 75137 73650 74480 TRUE FALSE 61681.69546 71548.31795 79542.05697 77237.45379 76710.03789 65256.36856 63870.90439 82845.36462 62048.80684 0.994083506 1.153097402 1.281927261 1.24478548 1.236285463 1.051694172 1.029365553 1.335164507 1 15.92111585 2.239573662 24.99927938 1.096280975 1.194563492 0.089769492 0.118606775 54.725357 1350514.219 0.041163418 0.032609896 173.6095703 -2.239573662 0.098282516 LGVADIIDCVVLTS(ph)SPEATETSQQLQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LGVADIIDCVVLTSSPEATETSQQLQLR 28 0 Q8NCF5;H3BSZ7;Q8NCF5-3;Q8NCF5-2 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 LGVADIIDCVVLT(0.063)S(0.495)S(0.427)PEAT(0.014)ETSQQLQLR;LGVADIIDCVVLT(0.009)S(0.536)S(0.453)PEAT(0.002)ETSQQLQLR;LGVADIIDCVVLT(0.088)S(0.583)S(0.329)PEATETSQQLQLR 174.28 9.54E-13 419510000 342585 333190 332055 340865 363492 336764 463891 329181 430596 TRUE FALSE 321143.2164 357859.7343 339931.5014 349612.173 334944.8046 433982.2999 394334.8511 370279.9725 358726.7458 0.895230757 0.997583086 0.947605679 0.974591878 0.933704577 1.209785177 1.099262477 1.032206204 1 18.45252579 2.263939545 24.99965661 1.098343644 0.957104785 0.548210917 0.060439337 149.3114517 147079.5636 0.01929704 0.0161395 183.6282711 -2.263939545 -0.14123886 LGVADIIDCVVLTSS(ph)PEATETSQQLQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGVADIIDCVVLTSSPEATETSQQLQLR 28 0 Q8NCF5;H3BSZ7;Q8NCF5-3;Q8NCF5-2 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 LGVADIIDCVVLT(0.001)S(0.043)S(0.954)PEAT(0.002)ETSQQLQLR 143.29 7.18E-08 44030000 60559 60524 61804 53936 72871 66242 82624 63321 75282 TRUE FALSE 56768.72029 65005.25994 63270.02007 55320.08907 67148.00561 85364.99005 70235.29824 71226.76624 62716.94786 0.905157573 1.036486343 1.008818545 0.88205965 1.07065168 1.361115184 1.119877491 1.135686105 1 15.93656773 2.475207849 24.99612043 1.172628418 0.979309605 0.454824603 0.099203081 51.31081297 670287.1718 0.031376646 0.026419969 298.6811735 -2.475207849 -0.193318813 LGVDLDAQTWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGVDLDAQTWR 11 0 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 147.74 8.18E-05 85179000 150770 194260 158550 168450 198610 142010 177800 169780 191450 FALSE TRUE 141333.5748 208643.2125 162310.8809 172772.7122 183011.9718 183005.9817 151140.5406 190977.4067 159495.7582 0.886127484 1.308142705 1.017650141 1.083243305 1.147440997 1.14740344 0.947614798 1.197382356 1 17.28315853 0.128119685 0.319583588 0.980050387 1.116935368 0.014859314 0.123926409 14.28273392 2.345709542 0.570549665 0.127765049 1.343135059 -0.128119685 0.136884982 LGVEPSDDDCVSVQHVCTIVSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGVEPSDDDCVSVQHVCTIVSFR 23 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 287.81 8.88E-53 335470000 156667 176430 164755 148781 188972 153557 174817 167001 177109 FALSE TRUE 146861.4921 189493.0608 168663.0664 152598.9723 174130.9014 197886.4131 148604.8138 187851.4425 147548.3637 0.99534477 1.284277616 1.143103604 1.034230191 1.180161521 1.341163047 1.007160025 1.273151648 1 17.1708284 -1.781459392 2.732516274 0.959258564 1.16116548 0.145891367 0.119308406 41604827.34 26108099.85 11197953.72 0.026059546 0.016540194 1.781459392 0.201906916 LGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLK 35 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;; 263.19 1.38E-60 6313720000 776167 2333470 980945 622552 2295710 759899 1609010 2061570 618904 FALSE TRUE 727588.093 2506242.547 1004213.479 638527.7383 2115414.197 979269.5054 1367753.888 2318961.553 515604.9241 1.41113488 4.86078086 1.947641366 1.238405043 4.102781215 1.899263292 2.652716884 4.497555093 1 18.97590652 -1.703993627 2.682410984 0.700632465 2.863277108 0.166766964 1.280548057 26895113.17 22240096.83 54265136.89 0.284253278 0.019769987 1.703993627 2.162644644 LGVIEDHSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 LGVIEDHSNR 10 0 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ;;;;;;;;; 236.92 3.70E-12 28602920000 14448760 17849540 15512830 16299560 15996850 12807280 17590960 13387420 11568450 FALSE TRUE 13544437.9 19171138.51 15880801.65 16717834.3 14740521.93 16504533.83 14953358.85 15058868.86 9637600.96 1.405374425 1.989202354 1.647796139 1.734646866 1.529480416 1.712514753 1.551564432 1.562512177 1 23.20024264 -0.817111371 0.315000234 0.680674193 1.756872229 0.638533111 0.153051196 6.706217303 0.599649513 2.152209554 0.143117559 0.152366197 0.817111371 1.076198035 LGVQVVITDPEKLDQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LGVQVVITDPEKLDQIR 17 1 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 169.28 1.82E-09 1254390000 2903600 2166020 2470610 2436600 2721790 1942620 2962800 2198440 2738210 FALSE TRUE 2721868.859 2326394.375 2529214.036 2499127.281 2508031.593 2503422.858 2518555.645 2472920.073 2281185.061 1.193181958 1.019818345 1.108728125 1.095539035 1.099442406 1.097422081 1.104055821 1.084050617 1 21.12135206 0.868055516 6.739749842 1.000000108 1.094886584 0.36125602 0.041634162 4.440963914 226.7958622 0.036238092 0.009092972 7.379985626 -0.868055516 0.094886476 LGVS(ph)VS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGVSVSPSR 9 0 E7ERS3;Q86VM9;H3BP01 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 2 LGVS(1)VS(0.995)PS(0.005)R 109.39 0.0037493 0 332390 364020 352090 328470 464540 244420 453450 370430 608690 TRUE FALSE 311586.3032 390972.4196 360441.7411 336899.0963 428056.9023 314980.0862 385459.3821 416679.0009 507095.7067 0.614452655 0.771003214 0.710796278 0.664369845 0.844134345 0.621145243 0.760131425 0.821696961 1 18.95189853 0.916792466 1.848155499 0.999003558 0.715577532 0.648400281 0.0686175 0.250788277 1.760640953 0.057285984 0.016173914 8.256433091 -0.916792466 -0.283426026 LGVSVS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 LGVSVSPSR 9 0 E7ERS3;Q86VM9;H3BP01 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 LGVS(0.002)VS(0.986)PS(0.012)R;LGVS(0.006)VS(0.829)PS(0.165)R;LGVS(0.002)VS(0.995)PS(0.002)R;LGVSVS(0.982)PS(0.018)R;LGVSVS(1)PSR;LGVS(0.003)VS(0.993)PS(0.004)R;LGVS(0.003)VS(0.993)PS(0.005)R;LGVS(0.009)VS(0.987)PS(0.004)R;LGVSVS(1)PSR 172.6 5.88E-05 19241750000 10848470 11908930 11849330 10583650 12649670 10642390 12466410 11218340 13464830 TRUE FALSE 10169483.63 12790679.57 12130401.7 10855244.38 11656215.94 13714675.23 10597187.55 12618974.44 11217462.89 0.906576089 1.140247104 1.081385499 0.967709409 1.039113395 1.222618284 0.94470449 1.124940155 1 23.41924308 -1.121668318 3.880112867 0.999976668 1.05970257 0.025946063 0.096213869 1.75E-05 3.96E-06 0.083951729 0.019779883 0.075566913 1.121668318 0.059725903 LGYEEHIPGQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LGYEEHIPGQTR 12 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 72.29 0.04229 746490000 731430 947370 879040 890980 917930 837970 1077000 845810 949620 FALSE TRUE 685651.1019 1017514.261 899891.2439 913844.0552 845839.4806 1079878.336 915513.8484 951411.2404 791122.2872 0.866681565 1.286165587 1.137486907 1.155123639 1.069164014 1.364995467 1.157234303 1.202609578 1 19.59354119 4.750316848 24.54387129 1.184352851 0.866681318 0.462922908 0.102399832 1137.974384 2375728.701 0.021761973 0.349317489 56275.17426 -4.750316848 -0.317671534 LGYFSVDPDSHQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LGYFSVDPDSHQGK 14 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RR79 P47897 QARS Glutamine--tRNA ligase 0 ;;; 208.68 7.71E-09 2354470000 3943020 4006390 4229950 4360520 4753870 3444460 5621820 4060010 5442440 FALSE TRUE 3696233.417 4303027.284 4330286.412 4472418.326 4380520.226 4438819.686 4778880.281 4566911.186 4534061.604 0.815214644 0.949044733 0.95505681 0.986404402 0.966136019 0.978994128 1.053995446 1.007245067 1 22.11237256 6.470941645 0.475186005 1.010527397 5.82E-16 0.803750534 0.027345352 9.954912116 0.46484463 0.016012256 8.023745197 2957615.035 -6.470941645 -1.010527397 LHAEFAAERDWEQFHQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHAEFAAERDWEQFHQPR 18 1 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 ; 191.21 1.53E-14 329520000 42463 110068 79188 88288 93412 70347 88763 69450 138563 FALSE TRUE 39805.31663 118217.5492 81066.37676 90553.61955 86075.79833 90655.03691 75453.81219 78120.98538 115435.9401 0.344826027 1.02409656 0.702262888 0.784449102 0.745658572 0.785327661 0.653642289 0.676747513 1 16.81673294 -1.390980876 3.287419922 1.002554607 0.740897641 0.208274431 0.16805725 51483274.29 66613637.54 1244433.49 0.037585967 0.040646123 1.390980876 -0.261656966 LHAGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHAGEK 6 0 Q0VGE8;Q96JF6 Q0VGE8 ZNF816;ZNF594 Zinc finger protein 816;Zinc finger protein 594 0 74.849 0.079243 70434000 77417 72351 84035 83187 99363 66355 83394 84396 114410 FALSE TRUE 72571.60816 77707.94332 86028.34988 85321.71926 91559.43079 85510.61132 70889.84389 94933.02638 95314.23188 0.761393202 0.81528164 0.902576123 0.895162428 0.960606081 0.897144211 0.743748782 0.99600054 1 16.54040403 7.99988123 0.026521421 1.50130928 2.59E-07 0.354665714 0.071805814 2580.631388 5.257416554 99.94962301 219.0979222 99972655.91 -7.99988123 -1.501309021 LHCESESFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHCESESFK 9 0 C9JLU1;P52434;P52434-2;P52434-4 C9JLU1 POLR2H "DNA-directed RNA polymerases I, II, and III subunit RPABC3" 0 ; 166.07 6.10E-05 889130000 870500 1250120 709950 731060 1494400 433570 796520 1283790 1348390 FALSE TRUE 816016.9589 1342680.186 726790.3493 749820.2373 1377035.852 558734.6206 677089.2205 1444074.007 1123334.998 0.726423516 1.195262489 0.646993417 0.667494771 1.225846123 0.497389133 0.602749155 1.285523918 1 20.0993568 3.965964562 23.72084958 0.80330028 0.985181053 0.008098139 0.286267636 517.6717047 1100655.829 0.068694309 0.125498744 9246.227236 -3.965964562 0.181880774 LHCTPGDGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHCTPGDGQR 10 0 F6T1Q0;Q6L8Q7-2;Q6L8Q7 F6T1Q0 PDE12 "2,5-phosphodiesterase 12" 0 65.5 0.068781 81654000 52956 58615 57183 48715 66730 52829 65976 63662 62673 FALSE TRUE 49641.57849 62954.91559 58539.40776 49965.10937 61489.29498 68079.87469 56083.51129 71610.34084 52212.47142 0.950760942 1.205744794 1.121176726 0.956957371 1.177674477 1.303900636 1.074140139 1.371517932 1 15.67210683 2.508842459 24.91861572 1.191722022 1.090965786 0.176496741 0.127887111 1260.130279 989894.7964 0.038128569 0.035915699 322.7323195 -2.508842459 -0.100756236 LHDAFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHDAFFK 7 0 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ; 97.602 0.011877 760560000 3398000 3466800 3299600 3212400 3687100 2476000 3850800 3309700 4161700 FALSE TRUE 3185325.246 3723485.479 3377868.07 3294835.623 3397530.039 3190781.005 3273408.289 3722923.331 3467085.384 0.918732853 1.073952634 0.974267344 0.950318569 0.979938381 0.920306439 0.944138354 1.073790495 1 21.72529194 5.044141905 17.31452559 0.985683215 0.529646691 0.157762863 0.050742744 17294340.7 163795917.6 0.012391178 261794829.3 110698.5431 -5.044141905 -0.456036524 LHDALDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHDALDAK 8 0 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 60.91 0.089305 259730000 292710 221570 220500 235230 344280 182450 259930 255810 410970 FALSE TRUE 274389.8036 237975.2733 225730.3641 241266.4 317241.6376 235120.3532 220955.9096 287748.4416 342376.452 0.801427207 0.695069044 0.659304584 0.704681641 0.926587199 0.686730503 0.64535954 0.840444604 1 18.38522395 0.97762476 5.33430788 0.999850169 0.720914106 0.527039238 0.081975813 0.124135312 14.17607275 0.078471887 0.019798778 9.497838051 -0.97762476 -0.278936062 LHDEKEETAGSYDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LHDEKEETAGSYDSR 15 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610;A0A2R8YEF8 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ;; 246.27 2.21E-18 2551680000 1992320 1560710 1867890 1823240 1970620 1389210 2271920 1673120 2421410 FALSE TRUE 1867624.248 1676266.592 1912197.233 1870027.425 1815855.454 1790252.375 1931266.687 1882012.715 2017261.028 0.925821806 0.83096167 0.9479176 0.927013113 0.900158893 0.887466892 0.957370742 0.932954481 1 20.94396635 -4.999999952 0.078421304 1.322162993 0.811732965 0.452876347 0.033179394 216.5672901 1.206574544 11.94020309 1.169543166 1.00E-05 4.999999952 -0.510430028 LHDETLTYLNQGQSYEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHDETLTYLNQGQSYEIR 18 0 F8VX55;Q12800-2;Q12800-3;Q12800-4;Q12800;C9JWL3;Q9NZI7-4;Q9NZI7 F8VX55 TFCP2;UBP1 Alpha-globin transcription factor CP2;Upstream-binding protein 1 0 307.21 1.14E-50 134030000 81900 90011 89316 86708 93798 87799 97205 76666 99149 FALSE TRUE 76774.0252 96675.5081 91434.6177 88933.07408 86431.48344 113145.146 82630.01266 86237.91886 82600.39137 0.929463213 1.170400121 1.106951386 1.076666498 1.04638104 1.369789466 1.000358609 1.044037654 1 16.333861 -0.246656777 7.665349065 0.999994412 1.10396741 0.051494241 0.117342414 0 0 0.102352713 0.024124766 0.566686965 0.246656777 0.103972998 LHDFGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LHDFGYR 7 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;;;; 173.38 0.00086556 1940020000 1090302 1575561 1213546 1316831 1631630 927972 1355841 1292741 1569097 FALSE TRUE 1022061.944 1692217.176 1242331.884 1350623.113 1503488.361 1195862.452 1152545.229 1454142.56 1307204.574 0.781868396 1.294531254 0.950372963 1.0332148 1.150155371 0.914824256 0.881686962 1.112406266 1 20.31805351 2.222965803 24.97296212 0.956312994 1.063561641 0.02730183 0.144334944 515.4909704 825483.1904 0.050310145 0.037283707 167.0959037 -2.222965803 0.107248647 LHDFLAHSSEESEETS(ph)SPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHDFLAHSSEESEETSSPPR 20 0 P46100;P46100-4;A0A096LNL9;P46100-6;A0A096LNW1;A0A087WWG0 P46100 ATRX Transcriptional regulator ATRX 1 LHDFLAHSSEESEET(0.002)S(0.975)S(0.023)PPR;LHDFLAHSSEESEET(0.013)S(0.545)S(0.442)PPR 205.68 1.40E-21 203425000 80728 160601 154816 155491 163414 119416 186070 138303 159356 TRUE FALSE 75675.37858 172492.0651 158488.3086 159481.1623 150580.1236 153889.4606 158170.5309 155570.434 132758.4541 0.570023047 1.299292511 1.193809537 1.201288184 1.134241315 1.15916882 1.191415883 1.171830713 1 17.01844421 4.745112111 24.96072416 1.184881678 0.570022764 0.861175784 0.075320503 236.8162519 902228.8166 0.016567358 0.159445662 55604.77798 -4.745112111 -0.614858914 LHDINAQLVEDQGFLDTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHDINAQLVEDQGFLDTLK 19 0 Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 Q10567-4 AP1B1 AP-1 complex subunit beta-1 0 122.64 3.28E-05 59719000 284660 200350 255880 234650 230510 205670 301090 201900 198560 FALSE TRUE 266843.6387 215184.1225 261949.5944 240671.5163 212406.6744 265043.5902 255944.3497 227107.6594 165419.0533 1.613137263 1.300842426 1.583551527 1.454920165 1.28405205 1.602255514 1.547248305 1.372923221 1 17.33576589 0.898525775 5.449670374 1.000018669 1.476748202 0.633875024 0.115147255 0.576197583 30.25669824 0.1047375 0.026402488 7.916364366 -0.898525775 0.476729533 LHDINAQMVEDQGFLDSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHDINAQMVEDQGFLDSLR 19 0 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1 P63010 AP2B1 AP-2 complex subunit beta 0 177.61 3.98E-14 78943000 77432 89130 97357 98543 108580 81319 105760 89263 88436 FALSE TRUE 72585.66934 95729.27794 99666.35402 101071.7802 100052.5648 104794.4752 89902.26983 100407.682 73675.46028 0.985208224 1.299337358 1.352775451 1.371851358 1.358017506 1.422379647 1.220247142 1.362837526 1 16.16889655 -1.2668074 4.884888319 0.999920004 1.305232146 0.362923716 0.123017256 9.86E-05 1.48E-05 0.109599831 0.025826181 0.054099419 1.2668074 0.305312141 LHDMLGPHMLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHDMLGPHMLR 11 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 ; 124.67 0.00019912 459360000 50981 100319 41138 42317 88133 32987 45900 75586 58262 FALSE TRUE 47790.19021 107746.7231 42113.81279 43402.92586 81211.38969 42509.8114 39017.72111 85023.07849 48537.69581 0.984599483 2.219856574 0.867651669 0.894210678 1.673161207 0.875810248 0.803864305 1.751691692 1 15.566818 3.861441074 6.069277607 1.097547558 1.667360794 0.16163469 0.443611109 0.285041022 13.49009125 0.10467472 0.191327549 7268.437731 -3.861441074 0.569813236 LHDTFGFVDEDVFFQLSAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LHDTFGFVDEDVFFQLSAVK 20 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H2E6;F5H3E1 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ;; 119.38 5.18E-05 51984000 77076 84229 85110 86102 97188 70910 110113 79684 107288 FALSE TRUE 72251.95074 90465.4028 87128.84939 88311.52309 89555.24652 91380.56587 93602.57789 89632.72281 89380.93969 0.808359713 1.012133047 0.974803461 0.988035295 1.001950157 1.022371953 1.047231974 1.002816967 1 16.44767959 4.739459766 24.91938113 1.00700966 0.808359648 0.91166057 0.019349598 23.53562581 652171.4539 0.005467025 0.0332487 54885.77057 -4.739459766 -0.198650013 LHDVEHVLIDVGTGYYVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHDVEHVLIDVGTGYYVEK 19 0 Q99471;H3BPF6;Q99471-3 Q99471 PFDN5 Prefoldin subunit 5 0 92.977 0.0010584 169920000 137490 150490 128550 143940 136590 112910 159940 112970 168400 FALSE TRUE 128884.7463 161632.4362 131599.2667 147633.7441 125862.7724 145505.2841 135958.4818 127074.5532 140292.9521 0.918682973 1.152106601 0.938031916 1.052324738 0.897142519 1.037153199 0.969104148 0.905780022 1 17.09808301 3.790353824 8.769029919 0.974135187 1.050349955 0.104301552 0.074820827 0.544773064 70.39446812 0.016938561 0.030568053 6170.975532 -3.790353824 0.076214768 LHDVNSDGFLDEQELEALFTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHDVNSDGFLDEQELEALFTK 21 0 P80303-2;P80303;E9PKG6;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 107.78 0.00033511 41562000 28013 31724 28755 30773 38725 20272 43810 31861 34869 FALSE TRUE 26259.71633 34072.87797 29437.08218 31562.68728 35683.69471 26124.19731 37241.09721 35838.91598 29049.13864 0.903975731 1.172939356 1.013354735 1.086527476 1.228390802 0.899310566 1.282003493 1.233734206 1 14.82620777 2.690579283 0.81432151 1.155697497 1.051766377 0.069545364 0.131984825 1.651174136 2.321338497 0.081952646 0.074435788 490.4325457 -2.690579283 -0.10393112 LHEDLCEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHEDLCEKR 9 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 136.33 0.00012718 347930000 227680 203150 255370 273080 283210 197030 284060 201380 429730 FALSE TRUE 213429.9152 218191.4374 261427.497 280087.6951 260967.829 253909.3625 241467.8401 226522.7363 358005.2868 0.596164144 0.609464288 0.730233621 0.78235631 0.728949651 0.709233556 0.674481213 0.632735729 1 18.44962137 -2.5745928 2.231287526 7.025345329 0.685314125 0.745459236 0.058208351 2757418.172 157134.9403 84628359.91 0.014911818 0.002663221 2.5745928 -6.340031205 LHEEGIIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LHEEGIIYR 9 0 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 ;;;; 207.29 1.19E-05 2066538000 1412938 1365619 1414748 1384978 1496370 1211456 1434937 1289811 1589628 FALSE TRUE 1324504.733 1466730.852 1448306.491 1420518.88 1378851.136 1561183.681 1219781.518 1450846.743 1324308.817 1.000147938 1.107544428 1.093631992 1.072649265 1.041185499 1.178866787 0.921070299 1.095550164 1 20.33680815 1.732973301 25 1.002084495 1.084595224 0.256733348 0.061425109 0.681616957 3025.730496 0.024981625 0.013853545 54.07210798 -1.732973301 0.082510729 LHELNQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHELNQK 7 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 104.11 0.0082248 139815000 203070 198271 211672 193964 235328 159030 226180 204078 269600 FALSE TRUE 190360.2112 212951.1911 216692.9598 198941.4446 216846.2881 204939.3794 192266.4088 229557.5875 224602.0183 0.847544526 0.948126792 0.964786343 0.885750921 0.965469009 0.912455644 0.856031527 1.022063779 1 17.77701137 1.217012466 24.9992665 1.011032019 0.918224508 0.493707324 0.041485005 254.1223273 294814.4417 0.04014355 0.010071875 16.48209699 -1.217012466 -0.092807511 LHEVFHDQLHTFLVMELLNGGELFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHEVFHDQLHTFLVMELLNGGELFER 26 0 O75582-3;O75582;O75582-2 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 0 ; 139.36 1.16E-07 45903300 45959.2 54682 40932.9 41109.8 61172 35225.1 51983.6 54753 22608.3 FALSE TRUE 43082.69571 58730.71218 41903.84772 42164.74707 56367.79788 45394.01454 44189.14177 61589.03258 18834.82867 2.287395147 3.118197314 2.224806418 2.238658381 2.992742798 2.410110297 2.346139831 3.269954489 1 14.20111529 -0.933934445 7.773955418 0.999999995 2.594581706 0.631942458 0.3862017 5.11E-08 7.23E-09 0.342692259 0.080773341 0.116430176 0.933934445 1.594581711 LHFFMPGFAPLT(ph)SR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHFFMPGFAPLTSR 14 0 Q5JP53;P07437;Q5ST81;A6NNZ2;P68371;Q13885;Q3ZCM7;A0A075B736;Q5SQY0;Q9BVA1;P04350;K7ESM5;Q9BUF5 Q5JP53;P68371;Q13885;Q3ZCM7;Q9BVA1;P04350;K7ESM5 TUBB;TUBB4B;TUBB2A;TUBB8;TUBB2B;TUBB4A;TUBB6 Tubulin beta chain;Tubulin beta-8 chain-like protein LOC260334;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-8 chain;Tubulin beta-2B chain;Tubulin beta-4A chain;Tubulin beta-6 chain 1 LHFFMPGFAPLT(0.5)S(0.5)R 90.453 0.021142 77021000 29785 50943 37530 35172 46515 14684 26288 40667 47460 TRUE FALSE 27920.81002 54714.87273 38420.22932 36074.57307 42861.89953 18923.03243 22346.35845 45744.36447 39538.6194 0.706165527 1.383833668 0.971713983 0.912388283 1.084051497 0.478596186 0.565178015 1.156954015 1 15.27097488 2.268327152 24.99902321 0.732459021 1.052431507 0.107885324 0.258426515 268.642392 225614.7687 0.086261081 0.072161931 185.4928407 -2.268327152 0.319972486 LHFFMPGFAPLTS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHFFMPGFAPLTSR 14 0 Q5JP53;P07437;Q5ST81;A6NNZ2;P68371;Q13885;Q3ZCM7;A0A075B736;Q5SQY0;Q9BVA1;P04350;K7ESM5;Q9BUF5 Q5JP53;P68371;Q13885;Q3ZCM7;Q9BVA1;P04350;K7ESM5 TUBB;TUBB4B;TUBB2A;TUBB8;TUBB2B;TUBB4A;TUBB6 Tubulin beta chain;Tubulin beta-8 chain-like protein LOC260334;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-8 chain;Tubulin beta-2B chain;Tubulin beta-4A chain;Tubulin beta-6 chain 1 LHFFMPGFAPLT(0.305)S(0.695)R 138.66 9.10E-06 69749000 93606 157150 106500 103520 130850 43236 67369 125410 121110 TRUE FALSE 87747.36755 168785.5495 109026.2303 106176.4985 120573.5688 55717.53132 57267.64387 141067.7146 100895.9586 0.869681688 1.672867297 1.080580747 1.052336485 1.195028726 0.552227583 0.567591058 1.398150298 1 16.62250886 2.983711081 1.262982844 0.833442358 1.316953618 0.103145388 0.322890001 0.566852196 1.887730882 0.128195925 0.153176374 963.1880392 -2.983711081 0.48351126 LHFFMPGFAPLTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 158.11 5.12E-06 1102720000 262260 2153170 275180 258990 1782310 85253 211272 1589200 1474420 FALSE TRUE 245845.6147 2312592.947 281707.3995 265636.1219 1642334.562 109864.1571 179593.725 1787615.118 1228329.777 0.200146263 1.882713414 0.229341831 0.216257985 1.337046934 0.089441907 0.146209697 1.455321813 1 20.22826651 3.85437825 7.192494781 0.55797077 1.144430982 0.04782 0.637610871 0.428268804 24.02208851 0.150555985 0.273174566 7151.188897 -3.85437825 0.586460212 LHGELQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LHGELQDR 8 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;;; 168.27 0.00030783 7110050000 1589710 2446880 2104720 2042310 2355580 1994520 2089550 1983050 2096320 FALSE TRUE 1490212.889 2628049.541 2154644.952 2094719.132 2170582.249 2570305.546 1776241.376 2230638.158 1746430.649 0.853290618 1.504811853 1.233742063 1.199428751 1.242867703 1.471747846 1.017069516 1.277255503 1 20.73597792 0.803945384 0.811671324 1.005259786 1.266714319 0.089115513 0.193349468 1.674949729 2.225585949 0.170906956 0.060414476 6.367154432 -0.803945384 0.261454532 LHGGFDS(ph)DCS(ph)EDGEALNGEPELDLTSK ddPTM_SK-BR-3_Pertuzumab_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 163.75 5.87E-12 889439000 207409 152495 170024 161405 168685 164207 281034 132457 198534 TRUE FALSE 194427.6409 163785.8885 174057.0496 165546.9256 155437.1605 211610.8952 238895.5607 148994.548 165397.3928 1.175518172 0.990256773 1.05235667 1.000904082 0.939779992 1.279408893 1.444373195 0.90082767 1 17.33557697 2.23291899 24.99988616 1.22317621 1.0275087 0.064156657 0.162659339 187.4527417 830655.7553 0.056731131 0.043060685 170.9696373 -2.23291899 -0.195667509 LHGGFDSDCS(ph)EDGEALNGEPELDLTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHGGFDSDCSEDGEALNGEPELDLTSK 27 0 O00178;F8WAZ4 O00178 GTPBP1 GTP-binding protein 1 1 LHGGFDS(0.124)DCS(0.876)EDGEALNGEPELDLTSK 180.6 1.16E-17 36421000 38125 27392 32396 33329 37068 36172 46860 29372 42910 TRUE FALSE 35738.82431 29420.13218 33164.44842 34184.27857 34156.82881 46614.2692 39833.77803 33039.15886 35748.04379 0.999742098 0.822985793 0.927727643 0.956255922 0.955488054 1.303966994 1.114292526 0.924222848 1 15.12557668 2.4543527 24.89742045 1.107788636 0.914200894 0.331146342 0.10616137 202.9719666 221948.5722 0.03536692 0.029591728 284.6772094 -2.4543527 -0.193587742 LHGLDEEAEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHGLDEEAEQK 11 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 136.67 9.44E-05 362030000 424480 326150 395010 371230 400840 307490 456660 338610 424260 FALSE TRUE 397912.5545 350298.4854 404379.8237 380756.3903 369359.6433 396257.3713 388188.0724 380886.2039 353448.2652 1.125801408 0.991088428 1.144099048 1.077262015 1.045017559 1.12111845 1.098288238 1.077629292 1 18.43113954 3.973725688 24.95550039 1.087557658 1.05116896 0.012715415 0.050879651 350.7670316 2577977.355 0.011480711 0.021751212 9412.948623 -3.973725688 -0.036388698 LHHCPGNHS(ph)WDSTISGSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHHCPGNHSWDSTISGSQR 19 0 O43353-2;O43353 O43353-2 RIPK2 Receptor-interacting serine/threonine-protein kinase 2 1 LHHCPGNHS(1)WDSTISGSQR;LHHCPGNHS(1)WDSTISGSQR 174.85 6.17E-12 341540000 112259 108153 113426 111880 106235 94928 125020 89081 120567 TRUE FALSE 105232.9096 116160.7607 116116.5183 114751.0302 97891.73163 122332.1726 106274.4116 100202.9589 100443.5888 1.047681697 1.156477601 1.156037132 1.142442555 0.974594126 1.217919173 1.058050722 0.997604328 1 16.61602596 1.485749184 5.764349117 1.006325491 1.121897551 0.346942494 0.066131803 0.153257722 11.81244232 0.036499115 0.015716844 30.60195586 -1.485749184 0.11557206 LHHS(ph)QSPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHHSQSPAR 9 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 LHHS(0.582)QS(0.418)PAR 100.93 0.0027866 118200000 18504 102810 23458 17538 93143 23380 17941 82549 67204 TRUE FALSE 17345.86767 110422.1594 24014.43484 17988.05477 85827.9245 30129.42646 15250.91361 92855.42436 55987.21825 0.309818352 1.972274438 0.428927094 0.321288596 1.532991408 0.538148302 0.272399917 1.658511126 1 15.77280988 3.843231788 8.181098768 0.754468507 1.249744539 0.028871879 0.620244098 0.551993404 36.09714819 0.146639817 0.265246601 6969.984107 -3.843231788 0.495276031 LHHSQS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHHSQSPAR 9 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 LHHS(0.055)QS(0.945)PAR;LHHS(0.135)QS(0.865)PAR 147.91 5.88E-05 229228000 46472 177875 65151 56229 170346 52744 50011 144267 124616 TRUE FALSE 43563.40047 191045.0501 66696.41249 57671.93134 156967.7123 67970.33657 42512.31483 162279.0525 103816.7845 0.419618086 1.840213516 0.642443443 0.555516447 1.511968541 0.65471433 0.409493658 1.56312925 1 16.66368018 3.748564012 23.31863096 0.849426472 1.234369715 0.014504492 0.512353157 431.9133352 469692.08 0.121620695 0.218897248 5604.850233 -3.748564012 0.384943243 LHIACFPVQLDTLSDGASVDESHGIS(ph)PPLQGEISQTQENSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHIACFPVQLDTLSDGASVDESHGISPPLQGEISQTQENSK 41 0 E9PG22;Q8IW35;Q8IW35-2 E9PG22 CEP97 Centrosomal protein of 97 kDa 1 LHIACFPVQLDTLSDGASVDES(0.16)HGIS(0.84)PPLQGEISQTQENSK 448.71 9.07E-258 119150000 33404 31202 31538 29064 34735 28686 41394 32512 44780 TRUE FALSE 31313.30327 33512.22855 32286.09625 29809.83145 32007.05321 36967.18252 35187.35398 36571.19477 37305.92871 0.839365333 0.898308384 0.865441429 0.799064183 0.857961571 0.990919776 0.943210776 0.98030517 1 15.1871173 2.24473151 24.97729551 0.971199576 0.857760725 0.823069956 0.029004711 65.8935364 266711.1469 0.010600615 0.008660333 175.6837164 -2.24473151 -0.113438851 LHIIEVGTPPTGNQPFPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHIIEVGTPPTGNQPFPK 18 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 160.81 3.97E-11 202650000 289460 296110 285500 314230 333610 231840 365590 282040 358830 FALSE TRUE 271343.2153 318034.2925 292272.1948 322293.6738 307409.6163 298768.4444 310773.1735 317253.3148 298938.9549 0.90768771 1.063877047 0.977698591 1.078125378 1.028335757 0.999429614 1.039587409 1.061264548 1 18.18949138 4.748700803 24.63614452 1.029717029 0.907687627 0.597246895 0.031817539 812.1131961 1973024.988 0.006957822 0.097194939 56066.15886 -4.748700803 -0.122029401 LHIVDTVCAHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHIVDTVCAHFR 12 0 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 201.46 8.57E-08 87330000 55208 112420 64715 64486 104900 42303 58308 86543 62990 FALSE TRUE 51752.62983 120743.6938 66250.07036 66140.81993 96661.57715 54515.18937 49565.2567 97348.08405 52476.56207 0.986204656 2.300907091 1.262469715 1.260387825 1.841995232 1.03884834 0.944521797 1.855077395 1 15.67938559 3.727129293 24.99999497 1.293533098 1.750730798 0.07396987 0.444501636 0.636268786 1961292.352 0.107879104 0.179799411 5334.93697 -3.727129293 0.4571977 LHKTEDGGWEWS(ph)DDEFDEESEEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LHKTEDGGWEWSDDEFDEESEEGK 24 1 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 LHKTEDGGWEWS(1)DDEFDEESEEGK;LHKTEDGGWEWS(1)DDEFDEESEEGK;LHKT(0.001)EDGGWEWS(0.999)DDEFDEESEEGK;LHKT(0.002)EDGGWEWS(0.998)DDEFDEESEEGK;LHKT(0.015)EDGGWEWS(0.985)DDEFDEESEEGK;LHKTEDGGWEWS(1)DDEFDEESEEGK;LHKT(0.001)EDGGWEWS(0.999)DDEFDEESEEGK;LHKTEDGGWEWS(1)DDEFDEESEEGK 234.52 1.41E-37 4030180000 3342920 889166 1354918 1311547 1352666 884364 1884121 939866 1711558 TRUE FALSE 3133692.604 955000.7758 1387057.295 1345203.516 1246433.069 1139665.53 1601614.547 1057210.339 1425887.913 2.197713142 0.669758659 0.972767412 0.943414629 0.874145196 0.799267264 1.123240146 0.741440004 1 20.44342915 4.744662697 24.95642539 0.89572001 2.197713729 0.907131077 0.131436672 184.1094209 752953.5305 0.030155007 0.277951839 55547.26717 -4.744662697 1.301993718 LHKTEDGGWEWS(ph)DDEFDEESEEGKAAISQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHKTEDGGWEWSDDEFDEESEEGKAAISQLR 31 2 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 LHKTEDGGWEWS(1)DDEFDEESEEGKAAISQLR 164.11 8.27E-13 81340000 27041 8910.6 12323 16781 20880 7181.1 19075 9450.8 39409 TRUE FALSE 25348.55208 9570.350095 12615.30738 17211.62887 19240.16903 9254.166995 16214.88083 10630.75318 32831.38331 0.772082974 0.291500057 0.384245381 0.524243182 0.586029801 0.281869543 0.493883571 0.323798516 1 15.00278792 -1.418895764 2.909926436 1.011443438 0.437999486 0.557102266 0.151237773 17112290.33 20061632.42 1619966.321 0.034540187 0.03811573 1.418895764 -0.573443952 LHLDEDYPCSLVGNWNTWYGEQDQAVHLWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHLDEDYPCSLVGNWNTWYGEQDQAVHLWR 30 0 Q9BPW8;H7C2U6 Q9BPW8 NIPSNAP1 Protein NipSnap homolog 1 0 123.53 9.34E-06 156690000 37779 26707 25150 23156 34939 26253 24234 33720 29524 FALSE TRUE 35414.47983 28684.41407 25746.56988 23750.22216 32195.03188 33831.81492 20600.33668 37930.01623 24596.25367 1.439832273 1.166210694 1.046767944 0.965603237 1.308940472 1.375486502 0.837539609 1.542105425 1 14.58615097 3.091146482 0.014361459 2.97E-05 2.338938729 0.027477976 0.224549923 6952.603355 31.03098354 2397.990777 2653.919264 1233.520815 -3.091146482 2.338909018 LHLGFIEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHLGFIEIR 9 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ; 155.58 7.30E-05 871860000 622480 1491050 684770 693700 1732520 451860 674610 1307670 1529850 FALSE TRUE 583520.088 1601448.893 701013.0678 711501.5164 1596454.868 582304.6467 573458.4933 1470935.478 1274508.152 0.457839432 1.256523068 0.550026351 0.55825576 1.252604674 0.456885777 0.44994494 1.154120102 1 20.28150917 3.91432039 20.1502317 0.726421601 0.912859917 0 0.344524103 53.18225953 17062.41016 0.082685747 0.149064519 8209.56961 -3.91432039 0.186438316 LHLIYLINDVLHHCQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHLIYLINDVLHHCQR 16 0 Q8IWX8 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 145.43 4.24E-07 38161000 11689 18375 17300 13544 20506 11678 15852 17142 14260 FALSE TRUE 10957.40636 19735.50412 17710.36417 13891.56197 18895.54148 15049.24902 13475.13976 19282.21643 11879.91388 0.922347289 1.661249764 1.490782202 1.169331875 1.590545325 1.266780987 1.134279247 1.623093958 1 13.53623676 -3.478471946 0.265581659 2.18E-16 1.410991844 0.13675813 0.246048986 141.6616254 2.888930956 77.90463544 0.302370077 0.000332298 3.478471946 1.410991844 LHLSGIDANPNALFPPVEFPAPR ddPTM_SK-BR-3_Pertuzumab_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 ;; 199.31 2.63E-24 6208235000 892898 2770301 2354366 2443513 2773833 2662418 2979660 2658835 2271529 FALSE TRUE 837013.108 2975416.969 2410212.673 2506217.68 2555987.345 3431014.856 2532887.645 2990796.403 1892396.135 0.442303328 1.572301334 1.273630097 1.324362079 1.350661892 1.813053193 1.338455304 1.580428298 1 20.85178269 4.743810414 24.90201126 1.425438582 0.442302893 0.660579018 0.216859796 296.237394 1405133.235 0.045978342 0.392609764 55438.36503 -4.743810414 -0.983135689 LHNAIEGGTQLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LHNAIEGGTQLSR 13 0 O60832;O60832-2;C9IYT0;H7C0M1;H7BZF2 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ;;; 162.37 4.06E-05 1066820000 592620 670390 637520 577970 708810 524610 728290 639070 750720 FALSE TRUE 555528.9721 720026.3731 652642.2755 592801.6887 653142.9218 676056.3907 619089.6756 718859.2963 625419.9822 0.888249477 1.151268577 1.043526421 0.947845777 1.044326917 1.080963848 0.989878311 1.149402508 1 19.25446579 LHNQVNGTEWSWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHNQVNGTEWSWK 13 0 O14980 O14980 XPO1 Exportin-1 0 ; 264.28 3.14E-24 2204300000 2277300 2120440 2194720 2397200 2407900 1746560 3055200 2202690 2444800 FALSE TRUE 2134767.858 2277439.584 2246779.795 2458716.21 2218793.247 2250763.519 2597101.123 2477700.695 2036747.086 1.048126138 1.118174956 1.103121644 1.207177969 1.089380838 1.105077569 1.275122052 1.216498952 1 20.95783541 4.36225024 0.590413565 1.169140228 1.0235569 0.076682437 0.079256531 4.779930342 1.712191552 0.040101223 0.447365248 23027.68288 -4.36225024 -0.145583327 LHNTIVEINNHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHNTIVEINNHK 12 0 Q9NTJ3;E9PD53;Q9NTJ3-2 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 0 ; 174.05 1.82E-05 234010000 435470 551460 487900 533400 600400 438610 612480 557090 586140 FALSE TRUE 408214.71 592290.6722 499473.2184 547087.947 553247.0059 565229.5868 520644.31 626643.9128 488309.4474 0.83597545 1.212941251 1.022862083 1.120371416 1.13298444 1.157523349 1.066217975 1.283292626 1 18.89743616 4.750240896 24.6024378 1.121712763 0.835975236 0.537972554 0.084002032 1047.75527 2206859.165 0.017693332 0.281184762 56265.33332 -4.750240896 -0.285737527 LHPESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LHPESK 6 0 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;; 118.06 0.022193 2354060000 4200300 3849300 4012200 3772600 3947300 3121860 4452900 3587400 4002300 FALSE TRUE 3937410.721 4134306.177 4107371.279 3869411.303 3637294.981 4023090.303 3785228.984 4035294.787 3334290.274 1.180884205 1.23993589 1.231857739 1.160490235 1.090875323 1.206580703 1.135242787 1.210240997 1 21.66894828 -5 0.149910016 0.337331752 1.244897392 0.610245199 0.045424197 86.44527677 0.77037939 17.07222609 0.225964985 1.00E-05 5 0.90756564 LHPPS(ph)PVPQGVCPAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LHPPSPVPQGVCPAHR 16 0 Q96F44-3;Q96F44;Q96F44-2 Q96F44-3 TRIM11 E3 ubiquitin-protein ligase TRIM11 1 LHPPS(1)PVPQGVCPAHR;LHPPS(1)PVPQGVCPAHR;LHPPS(1)PVPQGVCPAHR 114.55 0.00096062 506230000 181931 173476 174217 177444 157859 170527 189042 150254 109353 TRUE FALSE 170544.2635 186320.3435 178349.5095 181997.5135 145461.3909 219755.3766 160696.9071 169013.5426 91101.27785 1.872029323 2.045200111 1.957705904 1.997749293 1.596699787 2.412209596 1.763936916 1.855226915 1 16.47518367 0.488441445 1.356836364 1.000223346 1.967747167 0.67256037 0.207173219 1.233541655 2.719688003 0.172898845 0.051010924 3.079225148 -0.488441445 0.967523821 LHPPS(ph)PVPQGVCPAHREPLAAFCGDELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LHPPSPVPQGVCPAHREPLAAFCGDELR 28 1 Q96F44-3;Q96F44;Q96F44-2 Q96F44-3 TRIM11 E3 ubiquitin-protein ligase TRIM11 1 LHPPS(1)PVPQGVCPAHREPLAAFCGDELR;LHPPS(1)PVPQGVCPAHREPLAAFCGDELR;LHPPS(1)PVPQGVCPAHREPLAAFCGDELR;LHPPS(1)PVPQGVCPAHREPLAAFCGDELR 148.66 4.28E-08 549047000 115073 136503 127299 133126 133949 125039 150824 92444 128884 TRUE FALSE 107870.7863 146609.8242 130318.5924 136542.2385 123429.1859 161135.7295 128209.3414 103985.8369 107372.4278 1.004641402 1.365432702 1.213706303 1.271669472 1.149542657 1.500717948 1.194062051 0.968459399 1 16.71226404 1.31370873 4.836209326 0.983718388 1.262980991 0.409491957 0.129488445 0.167075203 6.520052829 0.08589325 0.029051932 20.59248364 -1.31370873 0.279262603 LHPTDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LHPTDK 6 0 G8JLM4 G8JLM4 USHBP1 0 ;; 110.24 0.028873 2281950000 2999480 2691640 2951180 2757830 3152930 2301200 3288780 2775490 3007930 FALSE TRUE 2811747.901 2890931.826 3021183.383 2828600.587 2905311.596 2965519.083 2795657.971 3122016.036 2505887.051 1.122056918 1.153656078 1.205634301 1.128782155 1.159394473 1.18342089 1.115636066 1.245872608 1 21.25688996 -1.069128232 4.460347425 0.999988503 1.163156381 0.626658022 0.039847403 4.09E-06 8.53E-07 0.034606926 0.008156356 0.085284826 1.069128232 0.163167878 LHPVILASIVDSYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHPVILASIVDSYER 15 0 O00303;E9PQV8;A0A1W2PP79 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 ; 237.48 9.72E-18 585770000 865380 1069300 1007270 937720 1119690 832370 1059740 962960 983900 FALSE TRUE 811217.4105 1148472.085 1031162.92 961783.4828 1031754.064 1072661.707 900841.8251 1083187.676 819680.7338 0.989674854 1.401121238 1.258005559 1.173363534 1.258726748 1.308633548 1.099015492 1.321475095 1 19.64470256 -3.893163849 0.316674477 0.008469093 1.249769868 0.238787699 0.119540571 186.9170216 3.25372819 121.5671914 0.101017942 0.00012789 3.893163849 1.241300775 LHQEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LHQEGK 6 0 O43488;H7C5H7;H7C4Q7 O43488 AKR7A2 Aflatoxin B1 aldehyde reductase member 2 0 ;;;; 80.555 0.064204 1715450000 2751980 2092910 2464720 2478180 2486150 1853790 2670080 2236000 2741290 FALSE TRUE 2579738.484 2247871.234 2523184.322 2541774.294 2290897.808 2388949.079 2269726.292 2515169.522 2283750.99 1.129605853 0.984289112 1.104842136 1.112982241 1.003129421 1.04606373 0.99385892 1.101332647 1 21.12297392 2.722143155 24.92130224 1.027049838 1.070141769 0.20753156 0.04970028 1524.380813 2313972.635 0.015413573 0.014565578 527.4036795 -2.722143155 0.043091931 LHQLAMQQSHFPMTHGNTGFSGIESS(ph)SPEVK ddPTM_SK-BR-3_Pertuzumab_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(0.191)S(0.716)S(0.093)PEVK 264.82 8.71E-59 1195100000 557390 407880 525980 556360 777900 573760 961480 645470 848900 TRUE FALSE 522503.9549 438079.8596 538456.494 570637.1395 716806.8719 739395.1978 817314.9999 726058.3504 707213.1059 0.738821086 0.619445335 0.761377991 0.806881454 1.013565594 1.045505508 1.155684182 1.026647193 1 19.43178549 2.857226642 1.443139176 1.083816943 0.682085488 0.89940018 0.053654421 0.098047889 0.415193193 0.02020645 0.021505801 719.8245291 -2.857226642 -0.401731455 LHQLAMQQSHFPMTHGNTGFSGIESSS(ph)PEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.01)S(0.208)S(0.781)PEVK;LHQLAMQQSHFPMTHGNTGFSGIES(0.002)S(0.038)S(0.961)PEVK;LHQLAMQQSHFPMTHGNTGFSGIES(0.071)S(0.175)S(0.754)PEVK;LHQLAMQQSHFPMTHGNTGFSGIES(0.001)S(0.033)S(0.966)PEVK;LHQLAMQQS(0.001)HFPMT(0.001)HGNT(0.003)GFS(0.012)GIES(0.045)S(0.181)S(0.757)PEVK;LHQLAMQQSHFPMTHGNTGFSGIES(0.008)S(0.195)S(0.797)PEVK 220.96 1.01E-34 8291080000 1096074 987164 951983 1158970 1589143 1292416 2111666 1301962 1438518 TRUE FALSE 1027472.685 1060254.65 974564.4863 1188711.132 1464338.119 1665515.519 1795041.287 1464514.822 1198420.053 0.857356052 0.884710371 0.81320776 0.991898567 1.221890535 1.389759388 1.497839829 1.222037981 1 20.19270224 2.765489348 2.279267564 1.338441297 0.854800642 0.662077156 0.134401642 0.146556922 1.501447183 0.04398983 0.044514806 582.7594814 -2.765489348 -0.483640655 LHQLDAEKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHQLDAEKER 10 1 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8;A0A494C0A3;A0A494C1S6 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 81.017 0.013383 127510000 65981 102080 53886 71391 137060 42294 64982 81611 188610 FALSE TRUE 61851.36699 109638.1094 55164.20137 73223.01392 126295.8605 54503.59121 55238.55236 91800.313 157129.7725 0.393632384 0.697755159 0.35107415 0.466003436 0.803767857 0.346869917 0.351547332 0.584232457 1 17.26159704 0.971438411 22.43581658 1.000000005 0.489165143 0.523328101 0.15289915 658.1241664 516973.899 0.143017432 0.035755659 9.36350424 -0.971438411 -0.510834863 LHQLS(ph)GSDQLESTAHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.94)GS(0.06)DQLESTAHSR;LHQLS(0.796)GS(0.204)DQLESTAHSR;LHQLS(0.997)GS(0.003)DQLESTAHSR;LHQLS(0.988)GS(0.012)DQLESTAHSR 269.16 2.28E-28 840021000 419592 485338 487373 459562 532114 448422 521250 425634 480041 TRUE FALSE 393330.4857 521272.9305 498933.7177 471355.139 490323.9129 577874.1519 443093.4015 478775.3418 399919.0559 0.983525241 1.303446092 1.247586756 1.178626354 1.226057888 1.444977786 1.10795771 1.197180616 1 18.6093485 0.792922184 1.411299159 1.002463868 1.233759392 0.22873523 0.120021692 0.956626841 3.414627753 0.103477242 0.030608989 6.207577975 -0.792922184 0.231295523 LHS(ph)PQTHWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LHSPQTHWK 9 0 Q9H8Y5;B8ZZS4 Q9H8Y5 ANKZF1 Ankyrin repeat and zinc finger domain-containing protein 1 1 LHS(1)PQTHWK;LHS(1)PQTHWK;LHS(1)PQTHWK 138.45 0.00022778 522720000 602530 495960 498290 533680 586170 394554 551580 483370 606910 TRUE FALSE 564818.7228 532681.3944 510109.6741 547375.1323 540134.5727 508455.3348 468875.6996 543719.8085 505612.8002 1.117097357 1.053536212 1.008893908 1.082597458 1.068277094 1.005621959 0.927341435 1.075367966 1 18.94767346 2.130691315 5.155946159 0.986897675 1.057136088 0.305423901 0.045123632 0.232091753 9.645866026 0.016803526 0.012277118 135.1111888 -2.130691315 0.070238413 LHS(ph)SNPNLSTLDFGEEK ddPTM_SK-BR-3_Pertuzumab_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(0.583)S(0.417)NPNLSTLDFGEEK 195.09 2.43E-11 879840000 587310 440130 508980 475710 664590 411960 692790 553990 813300 TRUE FALSE 550551.3155 472717.6832 521053.246 487917.524 612395.7822 530886.1644 588912.571 623156.871 677554.9759 0.812555933 0.697681664 0.76901988 0.720115033 0.903831872 0.783532235 0.869173118 0.919714109 1 19.36997848 1.500706492 0.498256636 1.004468972 0.735181497 0.703627144 0.051228962 0.414009337 0.263158571 0.049073317 0.030189328 31.67426105 -1.500706492 -0.269287475 LHSELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHSELK 6 0 D6RBP0;A0A494C0G8;Q96NL6-2;Q96NL6 D6RBP0 SCLT1 Sodium channel and clathrin linker 1 0 91.584 0.047726 88614000 204240 235110 184450 193770 265840 174070 233000 236530 298390 FALSE TRUE 191456.983 252517.789 188825.2411 198742.4663 244961.9987 224321.1832 198063.8131 266061.2912 248586.7813 0.770181672 1.015813422 0.759594859 0.799489278 0.985418442 0.902385807 0.796759232 1.070295411 1 17.92339006 1.231162353 24.99996591 1.035147784 0.867149319 0.399327961 0.088383195 189.6381746 640792.0615 0.075089421 0.020262681 17.0279495 -1.231162353 -0.167998465 LHSFESHKDEIFQVQWSPHNETILASSGTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHSFESHKDEIFQVQWSPHNETILASSGTDR 31 1 Q09028-3;Q09028;Q09028-2;Q09028-4;H0YF10;H0YCT5;H0YDK2;H0YEU5 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 ; 109.44 3.80E-05 815580000 432960 382030 506260 478190 488170 424720 545710 424090 648030 FALSE TRUE 405861.8065 410315.8987 518268.7263 490461.165 449831.0974 547329.7692 463885.8516 477038.57 539869.6066 0.751777469 0.76002778 0.959988708 0.908480787 0.833221748 1.013818453 0.859255357 0.883618126 1 19.04225147 4.113838688 3.146286898 0.914821765 0.752740522 0.587144191 0.057750218 0.165158432 3.128389871 0.013464078 0.034433393 12996.86741 -4.113838688 -0.162081243 LHSFLGDDVFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHSFLGDDVFLR 12 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ; 206.36 9.10E-08 518670000 413700 585060 479700 527170 592130 357300 520700 488760 328080 FALSE TRUE 387807.2555 628378.4512 491078.7105 540698.0747 545626.4983 460446.7097 442625.8689 549782.7619 273321.3285 1.418869349 2.299046527 1.79670834 1.978250573 1.996282183 1.684635122 1.619434061 2.011488693 1 18.06023852 -2.082165248 0.287085179 4.05E-11 1.958634245 0.514488853 0.252076427 25.2201324 1.053012006 16.85555024 0.268665566 0.008276272 2.082165248 1.958634245 LHSLVKPSVDYVCQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHSLVKPSVDYVCQLK 16 1 O43813 O43813 LANCL1 LanC-like protein 1 0 ; 138.73 3.03E-06 967620000 2706400 1924220 2385200 2078250 2448700 1915040 3185000 2211700 3425000 FALSE TRUE 2537011.255 2066691.251 2441778.07 2131581.413 2256388.98 2467880.96 2707438.818 2487835.614 2853345.374 0.889135707 0.724304625 0.855759731 0.747046408 0.790787193 0.864907902 0.948864741 0.871901326 1 21.44422295 2.006466123 2.99903883 0.932978398 0.795913249 0.556566778 0.056260867 0.180157925 3.158960862 0.02452414 0.014482394 101.5000188 -2.006466123 -0.137065149 LHSS(ph)NPNLSTLDFGEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LHSSNPNLSTLDFGEEK 17 0 Q9H4L5-5;Q9H4L5;Q9H4L5-7;Q9H4L5-3;Q9H4L5-6;Q9H4L5-2;Q9H4L5-8;Q9H4L5-4 Q9H4L5-5;Q9H4L5-6 OSBPL3 Oxysterol-binding protein-related protein 3 1 LHS(0.02)S(0.98)NPNLSTLDFGEEK;LHS(0.002)S(0.523)NPNLS(0.111)T(0.364)LDFGEEK;LHS(0.001)S(0.757)NPNLS(0.175)T(0.067)LDFGEEK;LHS(0.135)S(0.865)NPNLSTLDFGEEK 325.67 2.16E-59 2260840000 2153011 1613782 1857674 1666010 2359115 1477166 2622854 1991622 2937479 TRUE FALSE 2018257.885 1733268.098 1901738.905 1708762.637 2173839.624 1903599.844 2229581.392 2240280.391 2447194.778 0.824723027 0.708267325 0.777109743 0.69825363 0.888298571 0.777870181 0.911076393 0.915448337 1 21.2226975 1.609034891 0.706183585 0.997522326 0.748596258 0.695089045 0.053278095 0.306303485 0.318632949 0.043683608 0.020463451 40.64759843 -1.609034891 -0.248926068 LHSS(ph)SLELGPRPLEQENER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LHSSSLELGPRPLEQENER 19 1 Q86X02 Q86X02 CDR2L Cerebellar degeneration-related protein 2-like 1 LHS(0.027)S(0.956)S(0.016)LELGPRPLEQENER;LHS(0.118)S(0.858)S(0.024)LELGPRPLEQENER;LHS(0.002)S(0.992)S(0.006)LELGPRPLEQENER;LHS(0.005)S(0.995)SLELGPRPLEQENER 242.53 1.24E-24 860990000 188672 255660 194216 211901 242663 139378 278852 228509 368096 TRUE FALSE 176863.3563 274589.3324 198822.8952 217338.7384 223605.2268 179614.166 237040.7313 257038.8517 306658.3996 0.576743884 0.895424136 0.648353006 0.708732383 0.729167136 0.585714157 0.772979744 0.838192764 1 18.22627294 1.005183184 2.015226362 0.997164927 0.711121906 0.540744248 0.090760134 0.258876241 2.230671203 0.081477219 0.022818899 10.12006225 -1.005183184 -0.286043021 LHSYS(ph)SPSTK ddPTM_SK-BR-3_Pertuzumab_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(0.563)S(0.437)PSTK;LHSYS(0.643)S(0.357)PSTK;LHSYS(0.673)S(0.326)PSTK 105.17 0.0016648 4225470000 3266500 2393480 2830350 2510240 2989610 2469450 3807330 2936820 4648500 TRUE FALSE 3062055.596 2570695.75 2897487.239 2574657.008 2754818.09 3182340.127 3236456.212 3303488.442 3872635.32 0.790690407 0.663810438 0.748195221 0.664833323 0.711354895 0.82175053 0.835724499 0.853033702 1 21.88488422 1.312745967 0.711645341 0.992872999 0.706358452 0.804315657 0.044395325 0.241374326 0.280615818 0.039564247 0.016783825 20.54688392 -1.312745967 -0.286514548 LHTDDELNWLDHGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LHTDDELNWLDHGR 14 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;;;; 278.82 1.97E-33 1891078000 682873 754609 738793 708386 778951 694888 853170 682935 892708 FALSE TRUE 640133.1979 810481.0355 756317.5188 726564.3841 717775.3306 895490.885 725245.0789 768200.9381 743709.2677 0.86073043 1.089782084 1.016953199 0.976946793 0.965128931 1.204087301 0.97517284 1.032931781 1 19.50437922 LHTFESHKDEIFQVHWSPHNETILASSGTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHTFESHKDEIFQVHWSPHNETILASSGTDR 31 1 Q16576;E9PC52;Q16576-2;Q5JP02 Q16576 RBBP7 Histone-binding protein RBBP7 0 41.434 0.051203 226560000 92416 137860 149020 127100 155800 132310 173360 164670 136990 FALSE TRUE 86631.84753 148067.2978 152554.8248 130361.6012 143564.0965 170505.7491 147366.2774 185229.412 114125.484 0.759092925 1.297407841 1.336728831 1.142265484 1.257949508 1.494019943 1.2912653 1.623032871 1 16.80026145 4.738989738 5.308240291 1.319125781 0.736018577 0.503119868 0.170260633 0.116888819 11.77997342 0.036161012 0.248863954 54826.40097 -4.738989738 -0.583107203 LHTVQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 99.919 0.010175 368610000 1210720 1068140 1162070 1192290 1331810 876560 1390830 1183290 1555050 FALSE TRUE 1134943.196 1147226.197 1189634.849 1222886.18 1227215.015 1129608.642 1182287.953 1331026.361 1295502.109 0.876064337 0.885545604 0.918280905 0.943947657 0.947289091 0.871946587 0.912609825 1.027421223 1 20.30507993 -4.999987854 0.026204251 1.640703638 0.468826299 0.488460603 0.036594028 1731.34814 3.423884532 112.9739115 51.31570803 1.00E-05 4.999987854 -1.171877339 LHVAILER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHVAILER 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 105.57 0.0043629 492600000 292130 552580 305710 371170 579760 232060 373430 495480 427170 FALSE TRUE 273846.1048 593493.5982 312961.5856 380694.8506 534227.9882 299051.9548 317437.6383 557341.7687 355872.5674 0.769506081 1.667713818 0.879420372 1.069750482 1.501177773 0.840334384 0.891998056 1.566127372 1 18.4410012 2.211691289 24.99977687 1.038967473 1.198812153 0.016662423 0.325702139 732.7325583 681745.0549 0.115399799 0.085251107 162.8138285 -2.211691289 0.159844679 LHVAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHVAVK 6 0 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6;Q96SI9;Q96SI9-2 Q12906;Q12906-7;Q96SI9 ILF3;STRBP Interleukin enhancer-binding factor 3;Spermatid perinuclear RNA-binding protein 0 ; 87.758 0.052076 894720000 3297300 3481900 3450200 3160100 4129900 2638900 4085600 3617800 4832900 FALSE TRUE 3090927.879 3739703.499 3532040.373 3241193.516 3805554.313 3400707.591 3473002.209 4069490.294 4026257.768 0.767692497 0.928828633 0.877251427 0.805013912 0.945183973 0.844632358 0.862588142 1.010737645 1 21.94100811 1.238175375 24.99988997 1.005368892 0.869463793 0.563700352 0.052229289 7.195881196 466673.7761 0.037338965 0.011522843 17.30515027 -1.238175375 -0.135905099 LHVENEDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHVENEDKK 9 1 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 ; 201.1 1.43E-05 1216060000 3815090 2039050 2596350 2643360 2627680 1958900 3342020 2201910 3342660 FALSE TRUE 3576310.327 2190023.384 2657936.648 2711193.093 2421312.612 2524402.63 2840915.127 2476823.311 2784748.452 1.284248969 0.786434905 0.954462026 0.973586354 0.869490604 0.906510112 1.020169389 0.889424432 1 21.40911558 -0.242080978 7.92702016 1 0.945248243 0 0.132077607 0 0 0.113197412 0.026680886 0.572689238 0.242080978 -0.054751757 LHVGNIS(ph)PTCTNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LHVGNISPTCTNK 13 0 Q9BWF3;E9PB51;D6R9K7;J3QRR5;Q9BWF3-3;Q9BWF3-4;Q9BWF3-2 Q9BWF3 RBM4 RNA-binding protein 4 1 LHVGNIS(0.999)PT(0.001)CTNK;LHVGNIS(1)PTCTNK;LHVGNIS(0.997)PT(0.003)CTNK;LHVGNIS(1)PTCTNK;LHVGNIS(1)PTCTNK 244.05 5.37E-17 2719213000 3324270 2671637 2958911 3087900 3267350 2352542 3551790 2610937 3759030 TRUE FALSE 3116209.875 2869447.783 3029097.766 3167140.742 3010745.511 3031682.685 3019232.063 2936918.232 3131623.609 0.995078037 0.916281182 0.967261122 1.011341444 0.961400822 0.968086547 0.964110774 0.93782606 1 21.57847939 3.642901781 6.050723502 0.971942559 0.947670978 0.046830395 0.027748806 0.410592105 23.36666693 0.006902531 0.010820605 4394.422213 -3.642901781 -0.024271581 LHYCVSCAIHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHYCVSCAIHSK 12 0 P62854;Q5JNZ5 P62854 RPS26;RPS26P11 40S ribosomal protein S26;Putative 40S ribosomal protein S26-like 1 0 ; 221.55 1.56E-11 2093140000 1432530 1985150 1281020 1278070 2249400 1231720 1915210 2003710 2106910 FALSE TRUE 1342870.504 2132132.572 1311406.399 1310867.44 2072741.198 1587297.569 1628042.04 2253877.604 1755253.11 0.76505804 1.214715165 0.747132361 0.746825305 1.180878807 0.904312637 0.927525513 1.284075551 1 20.74324765 1.265220902 24.95402538 1.142037814 0.938135798 0.202807792 0.176403679 297.6765112 278625.973 0.110284556 0.040247387 18.41708541 -1.265220902 -0.203902016 LHYTPPLQS(ph)PIIDNDPLLGQS(ph)PWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHYTPPLQSPIIDNDPLLGQSPWR 24 0 C9J5J4;H7C4T7;H0Y322;Q5TKA1-3;Q5TKA1;Q5TKA1-2 C9J5J4 LIN9 Protein lin-9 homolog 2 LHY(0.012)T(0.051)PPLQS(0.937)PIIDNDPLLGQS(1)PWR 59.996 0.0037095 0 12572 15940 16979 16610 21064 14925 18597 14834 19701 TRUE FALSE 11785.14096 17120.21419 17381.7499 17036.24072 19409.71841 19233.60521 15808.5525 16686.05755 16412.77583 0.718046788 1.043102908 1.059037794 1.03798656 1.182598155 1.171867904 0.963185793 1.016650549 1 14.00253164 4.740644205 4.562524405 1.062335978 0.695394583 0.707707853 0.069019829 0.111251204 6.057901503 0.01681093 0.131431486 55035.66334 -4.740644205 -0.366941394 LHYTPPLQS(ph)PIIDNDPLLGQSPWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LHYTPPLQSPIIDNDPLLGQSPWR 24 0 C9J5J4;H7C4T7;H0Y322;Q5TKA1-3;Q5TKA1;Q5TKA1-2 C9J5J4 LIN9 Protein lin-9 homolog 1 LHYT(0.003)PPLQS(0.997)PIIDNDPLLGQSPWR 147.23 1.17E-07 75724000 35178 39816 38883 41134 42417 41407 47814 36154 45262 TRUE FALSE 32976.27177 42764.01807 39805.32312 42189.56808 39085.73992 53360.52871 40644.73458 40667.90648 37707.4798 0.87452866 1.134099078 1.055634673 1.1188647 1.036551372 1.415117876 1.077895813 1.07851033 1 15.20256311 4.740268776 24.24444479 1.122292832 0.874528533 0.303365539 0.113791279 116.4206044 1652173.29 0.025204553 0.159961945 54988.10789 -4.740268776 -0.247764299 LHYTPPLQSPIIDNDPLLGQS(ph)PWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LHYTPPLQSPIIDNDPLLGQSPWR 24 0 C9J5J4;H7C4T7;H0Y322;Q5TKA1-3;Q5TKA1;Q5TKA1-2 C9J5J4 LIN9 Protein lin-9 homolog 1 LHYTPPLQSPIIDNDPLLGQS(1)PWR;LHYTPPLQSPIIDNDPLLGQS(1)PWR 200.03 1.02E-24 258629000 76605.7 100027 94703 97774 115223 78300 96033 81709.2 101051 TRUE FALSE 71811.08598 107433.1032 96949.39988 100283.0464 106173.8504 100903.9389 81633.74318 91910.77348 84184.93529 0.853015872 1.276155915 1.151624095 1.191223181 1.261197743 1.198598521 0.969695384 1.091772218 1 16.36127447 1.749928279 15.12974099 1.023600809 1.174277649 0.207259668 0.120484118 0.274180887 358.7382935 0.051113453 0.028214345 56.22484651 -1.749928279 0.15067684 LIALLEVLSQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIALLEVLSQKR 12 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;O75369-5;O75369-4;Q14315-2;Q14315 O75369-8;Q14315-2 FLNB;FLNC Filamin-B;Filamin-C 0 161.99 0.00036888 0 83866 98150 93341 102690 115740 69865 116250 84266 144820 FALSE TRUE 78616.97677 105417.1281 95555.0926 105325.1993 106650.2473 90033.89134 98819.39171 94786.79559 120648.6064 0.651619435 0.873753384 0.792011573 0.872991428 0.883974133 0.746248912 0.819067825 0.785643518 1 16.88045173 -2.572535958 2.114696438 4.070161845 0.811034273 0.436758879 0.069740733 2045034.727 153960.8176 30081185.24 0.015435998 0.002675864 2.572535958 -3.259127572 LIALSIDSVEDHLAWSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LIALSIDSVEDHLAWSK 17 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;; 324.38 5.44E-59 3253065900 5486563 6333339 6186324 6040020 7140611 5458178 7958173 6054023 8363194 FALSE TRUE 5143168.816 6802266.009 6333066.527 6195017.139 6579816.216 7033865.382 6764918.839 6809881.098 6967322.893 0.738184364 0.976309856 0.908966991 0.889153156 0.944382271 1.009550654 0.970949523 0.977402828 1 22.73217299 2.500332942 3.840869313 0.985945694 0.900129547 0.406198696 0.060884207 0.269454411 8.702091113 0.020093523 0.017783774 316.4702881 -2.500332942 -0.085816148 LIAQACVSIFPDSGHFNVDNIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LIAQACVSIFPDSGHFNVDNIR 22 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 235.76 1.79E-30 1117000000 440750 636760 558850 500660 660270 486020 635910 568290 387230 FALSE TRUE 413164.2443 683906.3729 572106.1859 513507.7832 608415.0576 626326.0841 540561.199 639242.2575 322598.8114 1.280737032 2.119990368 1.773429305 1.591784486 1.885980469 1.941501524 1.675645352 1.981539407 1 18.2993816 -1.045642806 4.612679126 0.999973661 1.805867041 0.521259639 0.234272368 6.87E-05 1.42E-05 0.202576765 0.047745916 0.09002377 1.045642806 0.805893379 LICCDILDVLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LICCDILDVLDK 12 0 P62258;P62258-2;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 114.86 0.00045967 0 186690 144820 173810 194230 253030 207500 172310 144520 152950 FALSE TRUE 175005.4062 155542.6235 177932.8553 199214.2706 233158.0445 267401.8815 146473.7151 162563.6401 127421.6569 1.373435336 1.220692206 1.396409838 1.563425523 1.829814885 2.09855913 1.149519781 1.27579286 1 16.95925098 1.60022002 25 1.159414614 1.533560684 0.386137741 0.255881913 0.893820181 2913.427358 0.147707557 0.070409115 39.83089089 -1.60022002 0.37414607 LIDDMVAQAMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIDDMVAQAMK 11 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 80.688 0.055193 40600000 120370 155650 157080 163230 194220 118980 209860 169400 196390 FALSE TRUE 112836.2566 167174.488 160806.0118 167418.7581 178966.7446 153327.5945 178393.4412 190549.9629 163611.2403 0.689660786 1.021778746 0.982854305 1.023271738 1.093853603 0.937145848 1.090349544 1.164650806 1 17.31991234 4.741020315 4.921289199 1.035859864 0.671173846 0.746453399 0.064056662 0.087800572 6.434679694 0.014784488 0.10958325 55083.34615 -4.741020315 -0.364686018 LIDHLHNCPSFHLSSIEVLILDEADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LIDHLHNCPSFHLSSIEVLILDEADR 26 0 B7Z6D5;Q96GQ7 B7Z6D5 DDX27 Probable ATP-dependent RNA helicase DDX27 0 ;; 148.95 5.67E-08 257958000 108809 362496 291188 324063 324965 320232 351252 333313 168925 FALSE TRUE 101998.8389 389335.581 298095.1169 332379.0052 299443.5597 412677.7799 298585.0235 374927.8618 140730.3262 0.724782225 2.766536478 2.118200994 2.36181507 2.127782745 2.932401217 2.121682167 2.664158266 1 17.10257373 4.74828917 24.59789395 2.334053287 0.724781139 0.444719181 0.534243149 839.7976296 2123308.724 0.107092766 1.390913538 56013.04336 -4.74828917 -1.609272148 LIDLES(ph)PTPESQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LIDLESPTPESQK 13 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 LIDLES(0.59)PT(0.41)PESQK;LIDLES(0.995)PT(0.005)PESQK;LIDLES(0.919)PT(0.081)PESQK;LIDLES(0.638)PT(0.362)PESQK;LIDLES(0.895)PT(0.105)PESQK;LIDLES(0.989)PT(0.011)PESQK 348.58 7.31E-76 1667760000 4052450 3362160 3656680 3720160 4161470 2777470 3957020 2950430 3749080 TRUE FALSE 3798814.388 3611097.825 3743418.176 3815625.604 3834644.933 3579280.501 3363701.586 3318797.68 3123334.328 1.216268894 1.156167559 1.198532652 1.221651352 1.227740783 1.145980585 1.076958543 1.06258163 1 21.57465558 1.679085584 1.630812583 1.025971191 1.197865329 0.895319922 0.024884429 0.115065178 0.609430923 0.020592985 0.007754801 47.76233864 -1.679085584 0.171894138 LIDLHSPSEIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LIDLHSPSEIVK 12 0 P60866;P60866-2;G3XAN0 P60866 RPS20 40S ribosomal protein S20 0 ;;; 192.3 4.26E-06 3947840000 6568600 7590580 6486280 6128940 8604050 4542890 7215070 7062870 8879490 FALSE TRUE 6157483.051 8152594.441 6640137.625 6286218.977 7928322.62 5854348.595 6133237.235 7944684.867 7397445.755 0.832379615 1.102082355 0.897625727 0.849782369 1.071764888 0.791401355 0.829102022 1.073976766 1 22.81859578 3.729570147 24.64530651 0.912398604 0.990503046 0 0.116595106 244.02572 2455795.338 0.02832553 0.0481801 5365.005199 -3.729570147 0.078104443 LIDLHTNVATAVLEHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIDLHTNVATAVLEHIK 17 0 Q8WVM8;Q8WVM8-2;Q8WVM8-3 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 175.51 7.06E-10 59324000 59971 72578 56778 59278 73554 48289 63736 64572 77313 FALSE TRUE 56217.52216 77951.75064 58124.80097 60799.17384 67777.36554 62229.25039 54179.3785 72633.95634 64408.96084 0.872821443 1.21026251 0.902433454 0.943955205 1.052297144 0.966158273 0.841177653 1.127699553 1 15.9749738 3.818705047 8.476455405 0.963531652 1.063782619 0.038200331 0.112146813 0.549441816 45.83284911 0.02642438 0.047756651 6587.263668 -3.818705047 0.100250967 LIDVLENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LIDVLENR 8 0 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ; 101.72 0.012083 51033000 78013 95480 87538 91341 105770 71330 92650 84837 98103 FALSE TRUE 73130.30559 102549.4385 89614.4427 93684.9647 97463.25086 91921.81305 78757.99262 95429.0862 81728.97553 0.894790435 1.25475008 1.096483128 1.146288254 1.192517711 1.124715102 0.963648352 1.167628562 1 16.31856003 1.923597242 11.34605043 1.040701262 1.136312045 0.083973365 0.105887593 1.477340659 215.8361573 0.039784209 0.025425086 83.86818452 -1.923597242 0.095610783 LIDWGLAEFYHPAQEYNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIDWGLAEFYHPAQEYNVR 19 0 P19784;H3BSA1 P19784 CSNK2A2 Casein kinase II subunit alpha 0 160.67 3.10E-11 100650000 99450 104360 109970 100540 113150 87315 112120 97969 114840 FALSE TRUE 93225.60202 112086.923 112578.5403 103120.0266 104263.6554 112521.4231 95308.64687 110200.6453 95672.46211 0.974424615 1.171569337 1.176707883 1.077844391 1.089797975 1.176110874 0.996197284 1.151853343 1 16.54581611 0.699589844 0.500777871 0.998699678 1.124691718 0.1018778 0.074631388 2.478071823 1.322630224 0.097647364 0.038198562 5.007141258 -0.699589844 0.12599204 LIDWGLAEFYHPGQEYNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LIDWGLAEFYHPGQEYNVR 19 0 P68400;E7EU96;A0A2R8YD58;Q8NEV1;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2;A0A2R8Y4H0;A0A2R8Y4D6 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 ; 197.38 7.90E-16 923170000 650280 780640 687590 696140 857660 611280 754830 705220 807790 FALSE TRUE 609580.1356 838439.3979 703899.9595 714004.131 790302.8432 787746.6127 641650.249 793268.2694 672964.6305 0.905813037 1.245889249 1.045968729 1.060983146 1.174360148 1.170561686 0.953468013 1.178766659 1 19.36017116 -0.24493784 0.463103614 0.985477553 1.103249473 0.045216888 0.107347413 17.23655872 3.944758573 0.558692706 0.054342938 0.568934356 0.24493784 0.11777192 LIEDFLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LIEDFLAR 8 0 A6NKE1;A0A087WWM0;O43617;O43617-2 A6NKE1 TRAPPC3 Trafficking protein particle complex subunit 3 0 ;;;;; 180.7 0.00055295 196600000 493927 647182 591066 587296 653352 506434 629010 570063 647112 FALSE TRUE 463012.9908 695100.0287 605086.3646 602367.0096 602040.3694 652633.2745 534695.7899 641236.6204 539104.8267 0.858855213 1.289359683 1.122390924 1.11734672 1.116740826 1.210586962 0.991821559 1.189447003 1 19.0402063 -0.009622484 0.479290192 0.986938397 1.134276146 0.04483137 0.12059069 10.3846519 2.976027817 0.396636067 0.058401707 0.978087066 0.009622484 0.147337749 LIEDKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LIEDKPR 7 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;;;; 147.52 0.0019572 5627630000 7257610 6677480 7436490 7310370 8230120 6370640 9150750 7181650 10260650 FALSE TRUE 6803369.145 7171887.567 7612887.055 7497966.471 7583759.574 8209740.349 7778679.989 8078294.811 8548081.229 0.795894302 0.839005547 0.890596012 0.877151991 0.887188525 0.960419085 0.909991351 0.945041887 1 23.02716919 8 0.127167171 1.030586651 0.284386813 0.892753385 0.019253633 25.12848239 0.21710759 0.10311181 3.352893898 100000000 -8 -0.746199839 LIEDTEDWRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 206.36 2.43E-08 3893390000 3431110 4034620 3807230 3796410 4115490 3301130 4180450 3475150 3723030 FALSE TRUE 3216362.95 4333347.463 3897539.294 3893832.308 3792276.016 4254112.642 3553630.332 3909030.127 3101632.241 1.036990429 1.397118396 1.256609098 1.255413926 1.222671072 1.371572227 1.145729105 1.260313868 1 21.56459621 0.114725223 0.655329147 0.989591174 1.268404691 0.337693144 0.103602264 3.603927833 1.878106484 0.188094337 0.035683253 1.302342528 -0.114725223 0.278813517 LIEECISQIVLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LIEECISQIVLHK 13 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 143.86 4.10E-05 159010000 1062700 1116880 1181050 1061730 1372150 1051640 1383210 1132900 1240850 FALSE TRUE 996187.504 1199574.957 1209065.064 1088975.789 1264386.874 1355231.396 1175810.502 1274345.059 1033744.119 0.963669332 1.160417685 1.16959801 1.053428764 1.223113971 1.310993089 1.137428964 1.232747094 1 19.97944769 4.739965328 4.797471935 1.170693997 0.95192992 0.325713844 0.088367172 0.195872602 12.98793019 0.019254861 0.143580196 54949.70025 -4.739965328 -0.218764077 LIEEVMIGEDKLIHFSGVALGEACTIVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIEEVMIGEDKLIHFSGVALGEACTIVLR 29 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 119.85 3.45E-05 115440000 105720 177590 175030 180000 220600 165660 119930 133890 116170 FALSE TRUE 99103.17392 190738.9484 179181.7943 184619.1047 203274.9659 213483.3527 101947.6099 150606.4612 96780.47651 1.023999648 1.970841178 1.851425005 1.9076069 2.100371616 2.205851432 1.053390245 1.556165734 1 16.56242842 1.711327189 9.321747175 1.236439366 1.870922759 0.426601954 0.347665886 0.101054977 20.50407146 0.154426704 0.082940853 51.44310677 -1.711327189 0.634483393 LIEGLSHEVIVSAACGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LIEGLSHEVIVSAACGR 17 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 214.53 5.91E-15 954200000 639780 734820 713560 769330 842410 687520 780520 694580 856830 FALSE TRUE 599737.3118 789226.8374 730485.9802 789072.3103 776250.5167 885995.863 663488.272 781299.842 713819.5377 0.840180578 1.105639165 1.023348258 1.105422685 1.087460451 1.241204277 0.92949021 1.094534123 1 19.44519986 4.743848148 24.66648895 1.071206934 0.84018046 0.448041021 0.081314371 432.9536735 2019665.266 0.017983614 0.153065776 55443.18202 -4.743848148 -0.231026473 LIEGVHPGSLVEKLPDS(ph)PALAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIEGVHPGSLVEKLPDSPALAK 22 1 G0XQ39;Q13586;H0YDB2;E9PNJ4 G0XQ39 STIM1 Stromal interaction molecule 1 1 LIEGVHPGSLVEKLPDS(1)PALAK 136.01 3.12E-06 352090000 128890 97192 103710 101790 146760 93973 171830 133740 206890 TRUE FALSE 120823.005 104388.1968 106170.0502 104402.1037 135234.0616 121101.4796 146065.6867 150437.7334 172358.7224 0.700997334 0.60564499 0.615983042 0.605725676 0.784608169 0.702613003 0.847451667 0.87281764 1 17.39505478 1.601654373 0.680598963 0.995647981 0.620724054 0.863720768 0.0480566 0.199591508 0.196106466 0.041641252 0.020022981 39.96265858 -1.601654373 -0.374923927 LIESAEELIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LIESAEELIR 10 0 Q13217;X6R9L0 Q13217 DNAJC3 DnaJ homolog subfamily C member 3 0 ;; 94.309 0.019057 46810400 123193 105284 100847 105318 102751 84148 115217 91163 98816 FALSE TRUE 115482.57 113079.3369 103239.1385 108020.6382 94681.35094 108440.1616 97941.28047 102544.9012 82322.97122 1.402798858 1.373606118 1.254074494 1.312156699 1.150120671 1.317252766 1.189719941 1.245641401 1 16.32900743 -3.625644256 0.051395946 3.88E-10 1.869010331 0.772356566 0.055812641 175.2026232 0.855860016 27.96572356 8.300161646 0.000236786 3.625644256 1.86901033 LIEVDDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LIEVDDER 8 0 P62753;A2A3R7 P62753 RPS6 40S ribosomal protein S6 0 ;;;;; 180.93 0.00055023 10436450000 10783930 13089510 13334700 12680300 13111700 12316450 14215600 11545670 13260800 FALSE TRUE 10108983.07 14058670.94 13651005.38 13005697.97 12081959.97 15872009.17 12084102.75 12987172.31 11047486.81 0.915048214 1.272567343 1.23566614 1.177253993 1.093638778 1.436707682 1.093832738 1.175577082 1 23.39721487 0.69849676 1.538378701 1.000985845 1.196930669 0.128853128 0.135510283 1.863007211 6.795873495 0.115885124 0.033530198 4.99455454 -0.69849676 0.195944824 LIEVDDERK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LIEVDDERK 9 1 P62753;A2A3R7 P62753 RPS6 40S ribosomal protein S6 0 ;;; 187.64 6.46E-05 1815580000 2416870 1856220 2169330 2094870 2249640 1726560 2699860 1843320 2681820 FALSE TRUE 2265602.421 1993656.46 2220787.532 2148627.911 2072962.349 2224989.844 2295041.057 2073462.56 2234206.917 1.014052192 0.892332955 0.99399367 0.961696025 0.92782917 0.995874566 1.027228517 0.928053057 1 21.09133137 2.213070151 24.38395781 0.99424839 0.954108543 0.102002278 0.041168625 283.548012 271237.1317 0.014435562 0.010665807 163.3315753 -2.213070151 -0.040139847 LIFPYVELDLHSYDLGIENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIFPYVELDLHSYDLGIENR 20 0 O75874;C9J4N6;C9JLU6;C9JJE5 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 324.19 4.17E-67 669370000 414910 532000 434580 500410 570660 428020 611000 520150 588710 FALSE TRUE 388941.5237 571389.8335 444888.4428 513251.3678 525842.6655 551582.4257 519386.2222 585091.8725 490450.4978 0.793029114 1.165030592 0.907101624 1.046489646 1.072162569 1.12464444 1.058998257 1.192968251 1 18.903748 2.8983738 3.36266743 1.093480506 0.992000703 0.229346196 0.104647256 0.426656 9.072270826 0.030485353 0.033179517 791.3594622 -2.8983738 -0.101479802 LIFYDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIFYDLR 7 0 Q15046;Q15046-2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 86.866 0.045975 132430000 511870 954310 508650 511200 1023700 418440 593390 859350 816810 FALSE TRUE 479832.9704 1024968.105 520715.4182 524318.2575 943302.7314 539236.8352 504416.6783 966641.7392 680479.1342 0.705139873 1.506244724 0.765218788 0.77051335 1.386233147 0.792436988 0.741266929 1.42053105 1 19.3761914 3.939321616 23.32132697 0.954575583 1.159516308 0.014103633 0.311574688 337.2569323 208077.7052 0.073812967 0.13307471 8696.041741 -3.939321616 0.204940725 LIGDAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIGDAAK 7 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;Q53FA3;P34931;P11142;E9PKE3;E9PNE6;P11142-2;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25;E9PI65;P11021;P54652 A0A0G2JIW1;Q53FA3;P11142;P11021;P54652 HSPA1B;HSPA1A;HSPA1L;HSPA8;HSPA5;HSPA2 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like;Heat shock cognate 71 kDa protein;78 kDa glucose-regulated protein;Heat shock-related 70 kDa protein 2 0 105.39 0.018466 132830000 203690 342400 163490 159380 366880 102080 203530 336240 407630 FALSE TRUE 190941.4065 367751.6523 167368.06 163469.9606 338066.7247 131548.8389 173012.566 378220.3042 339593.9196 0.562263914 1.082915892 0.492847635 0.481368927 0.995502879 0.387371008 0.509468975 1.113742863 1 18.3734511 1.23032981 24.99953747 1.056871679 0.658894998 0.361768565 0.22706966 232.2776132 705472.299 0.203543312 0.054317232 16.99533814 -1.23032981 -0.397976681 LIGEYGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LIGEYGLR 8 0 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 ;;; 164.52 0.00076689 754090000 825430 1472070 893250 872630 1566870 657581 791390 1338850 1079560 FALSE TRUE 773767.8097 1581063.594 914438.3118 895023.1632 1443814.351 847413.9598 672728.4164 1506008.37 899374.4618 0.860339984 1.757959184 1.016749253 0.995161861 1.605353957 0.942225953 0.747995907 1.674506486 1 19.77856239 3.738583651 23.95045288 1.10883942 1.377492027 0.02345046 0.360543529 534.6367257 1117101.075 0.086973461 0.15492596 5477.515953 -3.738583651 0.268652607 LIGQHLNGLGLNQTVDLLMQESGCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIGQHLNGLGLNQTVDLLMQESGCR 25 0 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y917;Q9H7D7-3;Q9H7D7-4 A0A499FIZ0 WDR26 WD repeat-containing protein 26 0 192.58 4.92E-18 41771000 30228 35715 33448 32212 39712 30369 38132 32299 34580 FALSE TRUE 28336.08344 38359.37576 34241.40236 33038.61445 36593.17971 39136.0373 32414.4606 36331.60125 28808.3746 0.983605768 1.331535579 1.188591957 1.146840629 1.270227155 1.358495154 1.12517492 1.26114721 1 14.81420064 -0.401902522 7.986853258 1.000000011 1.21736071 0.262069953 0.108835894 0 0 0.093982009 0.022151772 0.39636699 0.401902522 0.217360698 LIHEDGIIRPYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LIHEDGIIRPYDR 13 1 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2;A0A3B3IU50 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 0 ;;; 153.81 2.54E-05 521480000 28953.8 36128.5 35541.4 38061.5 41259 35081.1 38958.4 38142.9 43964.7 FALSE TRUE 27141.63334 38803.49173 36384.45879 39038.22253 38018.68457 45208.44408 33116.94959 42905.12503 36626.70755 0.741033938 1.05943161 0.993386008 1.065840343 1.038004427 1.234302702 0.904174899 1.171416376 1 15.1606084 4.739586112 24.66071491 1.050424311 0.741033821 0.539000929 0.091959081 53.26957387 1280793.323 0.019444577 0.11904881 54901.74043 -4.739586112 -0.30939049 LIHEQEQQS(ph)SS ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LIHEQEQQSSS 11 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 1 LIHEQEQQS(0.755)S(0.194)S(0.051);LIHEQEQQS(0.758)S(0.232)S(0.01) 109.95 0.0011326 0 269160 259540 249860 240774 310730 229093 305680 272060 338150 TRUE FALSE 252313.7561 278756.6117 255786.7972 246952.6685 286326.5192 295228.4301 259846.1218 306027.2899 281710.5805 0.895648845 0.989514172 0.907977247 0.876618365 1.016385394 1.047984884 0.922386803 1.086318055 1 18.10385422 2.718475834 24.8917107 1.005398325 0.927875006 0.46382348 0.05084122 836.483944 1036680.156 0.015978768 0.01508358 522.9688654 -2.718475834 -0.077523319 LIHEQEQQSS(ph)S ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LIHEQEQQSSS 11 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 1 LIHEQEQQS(0.162)S(0.825)S(0.014);LIHEQEQQS(0.044)S(0.478)S(0.478);LIHEQEQQS(0.074)S(0.463)S(0.463);LIHEQEQQS(0.158)S(0.823)S(0.019);LIHEQEQQS(0.093)S(0.453)S(0.453);LIHEQEQQS(0.033)S(0.484)S(0.484) 145.31 3.81E-05 2614790000 1695530 2135700 2065770 1975310 2342880 1636210 1758800 1759780 2186720 TRUE FALSE 1589409.804 2293829.45 2114771.04 2025999.799 2158879.656 2108557.265 1495084.268 1979492.407 1821742.305 0.872466868 1.259140463 1.160850815 1.112122056 1.185063139 1.157439919 0.820689218 1.086592984 1 20.79688747 1.764218499 24.99999923 0.953162874 1.146092768 0.258743053 0.119357893 16.0953164 15693.03846 0.050208794 0.027845112 58.10566806 -1.764218499 0.192929893 LIHEQEQQSSS ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LIHEQEQQSSS 11 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ; 136.96 0.00020556 528170000 395480 413120 461440 405170 496090 406540 477840 447510 635440 FALSE TRUE 370727.6128 443707.8347 472385.5747 415567.3482 457129.0925 523901.4984 406192.328 503382.6086 529380.9589 0.700304018 0.83816357 0.892335787 0.785006225 0.863516311 0.989649306 0.767296823 0.950889147 1 19.01394678 7.999999792 0.036687195 1.405326253 1.77E-09 0.449617938 0.072384577 993.7043955 2.782125007 30.68208707 90.62173649 99999952.08 -7.999999792 -1.405326251 LIHFSGVALGEACTIVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIHFSGVALGEACTIVLR 18 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 188.04 3.99E-14 83194000 86440 189300 144670 138890 173230 183850 159330 184350 90284 FALSE TRUE 81029.8747 203315.969 148101.6407 142454.1525 159625.2146 236924.5104 135439.9456 207366.5033 75215.01714 1.077309795 2.703129996 1.969043501 1.893958919 2.12225192 3.149962859 1.800703514 2.75698273 1 16.19873311 2.464039151 24.97401966 2.279493687 2.048152709 0.006896198 0.687477005 1064.758033 2032633.39 0.213648505 0.178842737 291.0979529 -2.464039151 -0.231340978 LIHGEDS(ph)DS(ph)EGEEEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LIHGEDSDSEGEEEGR 16 0 Q9C0C9 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 2 LIHGEDS(1)DS(1)EGEEEGR;LIHGEDS(1)DS(1)EGEEEGR 223.32 1.29E-14 741700000 867490 874580 921240 925040 899910 844070 1001680 845020 704150 TRUE FALSE 813195.3494 939334.8132 943092.2478 948778.0925 829234.6987 1087739.307 851487.3831 950522.6071 586622.816 1.386232051 1.601258573 1.60766377 1.617356275 1.413573895 1.854239687 1.451507442 1.620330102 1 19.16207366 -1.321544308 2.925332961 0.994044491 1.575675304 0.641574394 0.133579154 10275730.91 12694968.44 530974.8133 0.030052677 0.047693115 1.321544308 0.581630812 LIHLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LIHLNK 6 0 O43813;E9PHS0 O43813 LANCL1 LanC-like protein 1 0 ; 132.11 0.015041 2350100000 5205100 5142500 5121100 4753800 5727200 4348000 6046300 5220100 7791600 FALSE TRUE 4879322.082 5523256.051 5242574.91 4875790.556 5277408.814 5603197.016 5139713.446 5871840.976 6491131.624 0.751690516 0.850892629 0.807651919 0.751146462 0.813018302 0.863208041 0.791805458 0.904594347 1 22.63003858 1.005547414 3.109177231 0.999694664 0.809513329 0.762207488 0.036399281 0.106142903 2.453016945 0.032894408 0.008638225 10.12855321 -1.005547414 -0.190181336 LIHPDEDISLEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LIHPDEDISLEER 13 0 J3QRS9;O43670-2;O43670;O43670-4;X6R4W8;O43670-3;J3KS31 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 ;;;;; 240.65 7.42E-17 2700890000 3697020 4563470 4017190 3906800 4613010 3771080 4471220 3995800 4840990 FALSE TRUE 3465630.118 4901354.067 4112479.644 4007055.102 4250722.803 4859729.578 3800802.07 4494684.426 4032997.495 0.859318688 1.215312946 1.019707959 0.993567466 1.053985976 1.204991965 0.942426092 1.114477366 1 21.94342108 -2.407634697 0.477462746 0.906108203 1.060028831 0.012324708 0.109781126 519.4277576 28.85454645 51.16610988 0.049842199 0.003911698 2.407634697 0.153920628 LIHPDEDISLEERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIHPDEDISLEERR 14 1 J3QRS9;O43670-2;O43670;O43670-4;X6R4W8;O43670-3;J3KS31 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 137.84 1.23E-05 58343000 25957 44991 36107 36078 48626 31041 40871 32936 89906 FALSE TRUE 24332.3977 48322.18045 36963.47509 37003.82256 44807.11011 40002.03279 34742.77298 37048.1321 74900.10779 0.324864655 0.645155019 0.49350363 0.494042314 0.598224908 0.534071765 0.463854779 0.494633896 1 16.19268017 -1.42838761 3.342496258 1.005929178 0.517056685 0.769590624 0.084749556 23906144.4 30132596.96 1325386.97 0.018659995 0.037291718 1.42838761 -0.488872493 LIHTLDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LIHTLDDR 8 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;;;;;; 168.72 0.00030521 3071642000 1936334 2452477 1942027 1961687 2549468 1614874 2066696 2210710 2681166 FALSE TRUE 1815142.311 2634060.949 1988092.798 2012027.21 2349243.067 2081061.909 1756814.121 2486722.01 2233662.074 0.812630672 1.179256692 0.890059791 0.900775114 1.051745067 0.931681624 0.786517415 1.113293743 1 21.09097951 3.742932866 24.26203747 0.936098247 1.025889379 0 0.126323162 722.78838 1109069.284 0.030124856 0.054054575 5532.645784 -3.742932866 0.089791132 LIICVFLEKDEDIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LIICVFLEKDEDIYR 15 1 Q9BQ69 Q9BQ69 MACROD1 O-acetyl-ADP-ribose deacetylase MACROD1 0 ; 154.6 2.23E-06 96402000 192037 164955 172535 171368 193677 144900 195927 171787 167641 FALSE TRUE 180017.747 177168.4398 176627.6117 175765.593 178466.3897 186730.2777 166549.5652 193234.9851 139660.6341 1.288965557 1.268563908 1.264691463 1.258519225 1.277857507 1.337028712 1.192530496 1.383603808 1 17.0915659 -1.927137396 2.668280486 0.82358264 1.276063727 0.756407048 0.050467218 2813461.177 1752013.985 3093369.95 0.010535746 0.011826673 1.927137396 0.452481087 LIILDEIHLLHDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LIILDEIHLLHDDR 14 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;;; 203.85 8.36E-09 240398000 208344 212976 231341 215096 199794.3 227411.7 253727 219208 115212.5 FALSE TRUE 195304.1209 228744.9646 236828.5178 220615.7275 184103.2616 293061.7661 215682.9918 246576.6013 95982.78945 2.034782715 2.383187298 2.467406075 2.298492561 1.918086176 3.05327411 2.247100684 2.568966819 1 16.55048812 3.027675775 24.33715892 2.288826069 2.34414999 0 0.5349502 2377.535325 2090703.06 0.138026927 0.164969202 1065.800146 -3.027675775 0.055323921 LIILDEIHLLHDDRGPVLEALVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LIILDEIHLLHDDRGPVLEALVAR 24 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;; 295.87 3.79E-62 283205600 164143.2 227462.1 196476.9 198274.6 225408.6 165992.5 219679.1 195304.4 189058.3 FALSE TRUE 153869.7701 244303.6306 201137.4249 203362.6619 207705.9178 213911.8401 186740.2584 219688.5843 157503.2484 0.976930773 1.551102171 1.277036677 1.291164875 1.318740534 1.358142402 1.185627981 1.394819386 1 17.26502206 -3.334357338 0.371930654 5.73E-09 1.319916164 0.260429046 0.149091179 167.2674829 4.226455111 130.6911703 0.094490566 0.000463066 3.334357338 1.319916159 LIKDDFLQQNGYTPYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LIKDDFLQQNGYTPYDR 17 1 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 259.56 3.01E-27 2181100000 2131800 1961650 1955500 1719350 2127360 1478520 2327700 1870400 2440900 FALSE TRUE 1998374.443 2106892.607 2001885.383 1763471.432 1960285.727 1905344.722 1978682.994 2103923.557 2033498.021 0.982727508 1.036092775 0.98445406 0.867210793 0.96399687 0.936978892 0.973043973 1.034632705 1 20.95553216 -0.161477091 6.558662707 1.000000002 0.974120532 0.030758515 0.047837671 6403230.361 976301.1799 0.047441454 0.011506243 0.689481962 0.161477091 -0.025879469 LIKDDIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 116.52 0.0020575 2475150000 5332290 5109770 5366530 5544990 5686000 4421230 6537890 4703700 5977360 FALSE TRUE 4998551.487 5488102.688 5493826.626 5687283.831 5239444.496 5697567.328 5557594.089 5290967.299 4979700.001 1.003785667 1.102095043 1.103244498 1.142093666 1.052160671 1.14415875 1.116049981 1.062507239 1 22.2476274 0.951678844 4.487749117 1.000070703 1.099465902 0.34203929 0.041524277 0.243391224 14.7743856 0.036323534 0.009229143 8.947028977 -0.951678844 0.099395199 LILADALCYAHTFNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LILADALCYAHTFNPK 16 0 P28838-2;P28838 P28838-2 LAP3 Cytosol aminopeptidase 0 ; 184 1.89E-09 140423000 288890 272819 233887 243043 285470 205382 268841 264357 328710 FALSE TRUE 270808.8906 293018.8026 239434.9101 249279.8949 263050.3377 264672.4493 228530.7878 297362.5534 273846.1775 0.988908785 1.070012389 0.874340888 0.910291672 0.960576993 0.966500434 0.834522468 1.085874399 1 18.06300622 3.995121352 9.266354609 0.933911555 1.027567642 0.164742423 0.071890917 0.354763965 165.4151739 0.016406242 0.034301242 9888.293578 -3.995121352 0.093656087 LILDVFCGSQMHFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LILDVFCGSQMHFVR 15 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;; 242.79 6.07E-18 560906000 371177 1506785 431197 408829 1555459 241667 403437 1461332 869900 FALSE TRUE 347945.6941 1618348.929 441425.1965 419320.2443 1433299.525 311432.3398 342945.3672 1643782.517 724708.0702 0.480118421 2.233104605 0.609107604 0.578605733 1.97776123 0.429734886 0.47321864 2.268199548 1 19.46704043 3.863832495 8.871367943 0.97731852 1.472744989 0.016627659 0.751286445 0.725870238 52.18703534 0.178554909 0.322660609 7308.571422 -3.863832495 0.495426469 DYNHWLATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DYNHWLATK 9 0 P31327;P31327-3;Q5R211 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 ; 159.83 6.58E-05 890170000 3555500 3370500 2950900 2552000 5285700 2245000 2655700 4193300 8331500 FALSE TRUE 3332967.602 3620055.327 3020896.742 2617488.641 4870582.443 2893095.055 2257502.439 4716842.736 6940918.826 0.480191122 0.521552754 0.435230092 0.377109819 0.701720127 0.416817302 0.325245475 0.679570364 1 22.72669523 0.968687649 5.382946684 0.999794445 0.464689263 0.748926091 0.100115379 0.091182325 10.10929019 0.094429356 0.023817061 9.304384494 -0.968687649 -0.535105182 LILIESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LILIESR 7 0 P62277 P62277 RPS13 40S ribosomal protein S13 0 ;;; 154.92 0.0038296 657243000 777926 1488090 804762 830120 1469230 616836 831230 1257050 1154560 FALSE TRUE 729237.0003 1598269.732 823851.3347 851422.2846 1353842.602 794906.5397 706594.7783 1413995.46 961856.4773 0.758155731 1.661650953 0.856522105 0.885186413 1.407530785 0.826429471 0.734615605 1.470069073 1 19.87546211 3.755394667 19.07060262 0.996537366 1.269836637 0.040486284 0.322841388 49.09187533 33108.71075 0.076678824 0.138081016 5693.701136 -3.755394667 0.27329927 LILPHVDIQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LILPHVDIQLK 11 0 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 189.57 0.00094561 0 1283070 1429970 1053610 997070 1897550 826290 1033600 1401850 2020960 FALSE TRUE 1202764.939 1535846.467 1078602.127 1022656.504 1748524.077 1064826.509 878621.2755 1576874.058 1683648.72 0.71437998 0.912213129 0.640633711 0.607404913 1.038532597 0.632451708 0.521855459 0.93658139 1 20.68315973 1.046845074 11.12017543 0.999988473 0.726257462 0.317115856 0.15065606 0.587989393 136.3902637 0.144645037 0.036171855 11.13897102 -1.046845074 -0.273731011 LILS(ph)QNHSDEEEEEEENEEENLAMAVGMGERPEVLHLTEPTTNISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LILSQNHSDEEEEEEENEEENLAMAVGMGERPEVLHLTEPTTNISR 46 1 Q8TD26 Q8TD26 CHD6 Chromodomain-helicase-DNA-binding protein 6 1 LILS(0.57)QNHS(0.43)DEEEEEEENEEENLAMAVGMGERPEVLHLTEPTTNISR 78.342 0.00016042 41494000 6055.7 6938.3 5968.9 7455.5 6327.5 5352.3 7666.6 4582 7932.9 TRUE FALSE 5676.684547 7452.018951 6110.485127 7646.820752 5830.563674 6897.422123 6517.064503 5154.072786 6608.847742 0.858952236 1.127582181 0.924591603 1.157058091 0.882236042 1.043664855 0.986112066 0.779874645 1 12.69018304 1.429565284 14.06830894 0.887549404 1.006997721 0.141597094 0.108993357 1.954141372 575.3158298 0.057134477 0.023215589 26.88842003 -1.429565284 0.119448317 LIMGIGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LIMGIGHR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;; 128.86 0.0011154 2364490000 1967770 4157710 2133490 1984600 4302720 1682230 2546880 3680650 4163560 FALSE TRUE 1844610.788 4465551.174 2184097.39 2035528.196 3964801.728 2167862.492 2164998.988 4140187.255 3468634.938 0.531797327 1.287408809 0.629670585 0.586838405 1.143043819 0.624990099 0.624164557 1.19360709 1 21.72593658 -1.349494392 7.578499642 1.00000201 0.828988306 0.035725468 0.281263365 8.90E-06 7.64E-07 0.253773023 0.059814172 0.044720393 1.349494392 -0.171013704 LIMVQHWPETVCEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIMVQHWPETVCEK 14 0 D6RHI9;O00584;H0YAE9;A0A087WZM2;A0A087WWI1;O00584-2;J3QQ64 D6RHI9 RNASET2 Ribonuclease T2 0 114.74 0.00045984 184710000 280770 294250 259640 261990 324050 216740 328150 262880 354270 FALSE TRUE 263197.1069 316036.5762 265798.7834 268713.1069 298600.4202 279309.3195 278946.9539 295701.1467 295140.0483 0.891770224 1.070802075 0.900585281 0.910459656 1.011724508 0.946361977 0.945134201 1.001901126 1 18.17104017 1.22649552 24.17569343 1.000950631 0.959503259 0.110603306 0.053706842 427.8736121 857319.7353 0.047472961 0.012258473 16.84595048 -1.22649552 -0.041447372 LINQVLELQHTLEDLSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LINQVLELQHTLEDLSAR 18 0 A0A0C4DGB0;Q9UIL1-3;Q9UIL1-2;Q9UIL1 A0A0C4DGB0 SCOC Short coiled-coil protein 0 ; 251.75 1.82E-30 394510000 442070 480000 474800 477570 513880 421320 503260 405890 462650 FALSE TRUE 414401.6278 515539.6994 486062.4802 489825.2547 473521.9377 542948.2444 427800.835 456566.26 385430.7262 1.075165003 1.337567725 1.261089081 1.270851599 1.228552644 1.408679193 1.109929245 1.184561139 1 18.55611206 1.067124964 1.253201274 1.009134696 1.267059247 0.402373367 0.094794538 0.387189259 1.251438898 0.07943507 0.02470182 11.67145405 -1.067124964 0.257924551 LINYHQEQAVNCLLGNVFYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LINYHQEQAVNCLLGNVFYER 21 0 P35573-2;P35573-3;P35573 P35573-2 AGL "Glycogen debranching enzyme;4-alpha-glucanotransferase;Amylo-alpha-1,6-glucosidase" 0 ; 250.81 4.11E-31 309730000 209016 270790 225769 231537 308530 230296 276130 268050 291480 FALSE TRUE 195934.0617 290839.5734 231124.3473 237478.6314 284299.2984 296778.7167 234726.87 301516.6326 242830.105 0.806877144 1.197708058 0.951794455 0.977962067 1.170774515 1.222166077 0.966630023 1.241677314 1 17.88958777 2.745914802 24.74257596 1.114087109 1.013974039 0.202956154 0.128124821 1014.440334 3413005.361 0.037189519 0.038735941 557.0764536 -2.745914802 -0.10011307 LIPDSIGKDIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LIPDSIGKDIEK 12 1 P61247;D6RG13;D6RAT0;H0Y9Y4;D6RB09;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ; 155.98 5.74E-05 1172470000 3173800 3014000 2980100 3061100 4229600 2108040 4040800 2709900 7475100 FALSE TRUE 2975157.523 3237159.696 3050789.379 3139653.008 3897424.277 2716596.927 3434919.553 3048236.98 6227457.519 0.477748345 0.519820438 0.489893246 0.504162895 0.625845181 0.436228897 0.551576553 0.489483384 1 22.57021184 -1.591229641 2.800630001 1.034858679 0.513241961 0.903680373 0.050083458 6611549.819 6659547.665 1705284.603 0.010987911 0.025631284 1.591229641 -0.521616718 LIPGPLS(ph)PVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 196.67 6.26E-08 2371505000 2555087 3051424 3062965 3382276 3177850 2107232 2180680 1726111 2462203 TRUE FALSE 2395168.666 3277354.608 3135619.976 3469070.928 2928274.48 2715555.67 1853707.278 1941619.758 2051245.413 1.16766558 1.597738909 1.528642042 1.691202285 1.427559307 1.323857035 0.903698439 0.946556539 1 20.96806868 1.927027152 2.443754493 0.935799995 1.51518941 0.750312448 0.139244068 0.126688963 1.379698011 0.072944301 0.037688435 84.53316939 -1.927027152 0.579389415 LIQHAQIPPEDSEIITNMAHLGVPIVTDSTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIQHAQIPPEDSEIITNMAHLGVPIVTDSTLR 32 0 A0A1B0GWF2;A0A1B0GVQ5;A0A2R8Y5D4;A0A0D9SG72;A0A1B0GTP9;P61764;P61764-2 A0A1B0GWF2 STXBP1 Syntaxin-binding protein 1 0 143.09 3.26E-10 58606000 54181 54911 49148 56760 62203 47172 60762 67499 48922 FALSE TRUE 50789.90793 58976.66757 50313.81377 58216.55769 57317.82729 60789.79063 51651.30219 75926.39873 40756.60215 1.246176208 1.447045741 1.234494809 1.42839576 1.406344599 1.491532351 1.267311293 1.862922686 1 15.31474616 3.182268529 24.99585752 1.417338413 1.328090079 0.041469536 0.218731993 306.9328299 136288.3879 0.055986377 0.066916556 1521.487991 -3.182268529 -0.089248334 LIQNLDANHDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LIQNLDANHDGR 12 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;;;;;; 257.19 3.41E-21 23616100000 13131560 16655840 12794250 11452240 19261100 10942850 13866420 16271280 19760700 FALSE TRUE 12309679.1 17889055.72 13097735.65 11746123.87 17748410.9 14101873.15 11787279.05 18302785.13 16462511.51 0.747740045 1.086654106 0.79560981 0.713507405 1.078110766 0.856605211 0.716007338 1.111785715 1 23.97268111 1.218892937 24.99949521 1.055892963 0.868126001 0.269818472 0.135411862 399.0858911 507262.989 0.12530179 0.031505251 16.55361831 -1.218892937 -0.187766962 LIQSHPESAEDLQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LIQSHPESAEDLQEK 15 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 203.52 5.37E-09 505180000 807980 604010 746440 692700 813120 536190 898230 675230 1048000 FALSE TRUE 757409.9741 648731.5289 764145.9093 710475.8547 749260.8352 690979.3487 763548.7503 759533.9519 873082.0297 0.867512958 0.743036172 0.875228081 0.813756131 0.858179197 0.791425462 0.874544114 0.869945694 1 19.73575768 -0.703745641 0.307211866 1.077260245 0.807577869 0.634026028 0.040574124 6.375243523 0.586429647 0.501458481 0.040547275 0.197812786 0.703745641 -0.269682376 LIRPEYAWIVQPVSGAVYDRPGAS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LIRPEYAWIVQPVSGAVYDRPGASPK 26 2 Q12769;G3V198 Q12769 NUP160 Nuclear pore complex protein Nup160 1 LIRPEYAWIVQPVSGAVYDRPGAS(1)PK;LIRPEYAWIVQPVSGAVYDRPGAS(1)PK 205.58 1.74E-25 4431200000 3512540 2326420 2246730 2310890 2771190 1935370 3451050 2507920 2135090 TRUE FALSE 3292696.391 2498670.557 2300023.497 2370191.35 2553551.916 2494079.901 2933597.09 2821039.333 1778729.686 1.851150525 1.404750018 1.293070844 1.332519139 1.435604261 1.402169155 1.649265267 1.585985411 1 20.76241585 4.739125008 23.83783774 1.411568966 1.851150729 0.401799497 0.175535015 26.11192644 1102319.716 0.040189881 0.238946702 54843.48048 -4.739125008 0.439581764 LIRPEYAWIVQPVSGAVYDRPGAS(ph)PKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LIRPEYAWIVQPVSGAVYDRPGASPKR 27 3 Q12769;G3V198 Q12769 NUP160 Nuclear pore complex protein Nup160 1 LIRPEYAWIVQPVSGAVYDRPGAS(1)PKR;LIRPEYAWIVQPVSGAVYDRPGAS(1)PKR 137.35 5.93E-05 2946200000 2025760 1901370 1662830 1770030 2117220 1271270 2261750 1739310 2251460 TRUE FALSE 1898971.298 2042149.413 1702273.113 1815451.966 1950942.082 1638265.012 1922621.585 1956466.682 1875676.781 1.012419259 1.088753368 0.907551413 0.967891688 1.04012701 0.873426077 1.025028195 1.0430724 1 20.83897981 -0.599690414 7.396265041 1 0.992901399 0 0.064577709 0 0 0.0595283 0.014030955 0.251367766 0.599690414 -0.007098601 LIS(ph)WYDNEFGYSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LISWYDNEFGYSNR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 LIS(1)WYDNEFGYSNR;LIS(1)WYDNEFGYSNR;LIS(1)WYDNEFGYSNR 155.28 6.18E-06 55565000 39592 49855 43216 39496 59631 37374 55450 36405.5 84231 TRUE FALSE 37114.00739 53546.31607 44241.10393 40509.53423 54947.8218 48163.26708 47135.78727 40950.80681 70172.30195 0.528898246 0.763069111 0.630463911 0.577286666 0.78304146 0.686357234 0.671714992 0.583575081 1 16.09861407 -2.029850219 2.644527894 1.402348686 0.664526962 0.646207642 0.080280057 10055121.89 3677378.75 24541232.85 0.017415814 0.009335762 2.029850219 -0.737821724 LISGGHDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LISGGHDNR 9 0 Q15061;C9JEE7 Q15061 WDR43 WD repeat-containing protein 43 0 ;;;;; 179.1 5.02E-05 1005246000 774579 1136034 1135747 1150721 1106199 990698 1166350 961630 1124126 FALSE TRUE 726099.4831 1220147.139 1162687.455 1180250.449 1019322.593 1276696.43 991466.6454 1081691.622 936502.1085 0.775331392 1.302877087 1.24152145 1.260275272 1.088435983 1.363260604 1.058691311 1.155033836 1 19.83692272 0.954789057 1.24507043 1.005442504 1.190968111 0.058303351 0.165950783 1.134729957 3.581670935 0.141458785 0.043604713 9.011333382 -0.954789057 0.185525607 LISGVSRPDEVLECIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LISGVSRPDEVLECIER 17 1 Q9H974-2;Q9H974-3;Q9H974;Q9H974-4 Q9H974-2 QTRTD1 Queuine tRNA-ribosyltransferase subunit QTRTD1 0 101.67 0.00093977 54313000 22555 28850 25052 27413 34664 20870 32553 24860 35053 FALSE TRUE 21143.32281 30986.08402 25646.24527 28116.46399 31941.62927 26894.8302 27671.97986 27963.82572 29202.42785 0.724026198 1.061079037 0.878223051 0.962812549 1.093800469 0.920979254 0.947591755 0.957585646 1 14.8338007 4.751797284 24.89119395 0.97147364 0.724026027 0.61325588 0.063149145 1459.769858 2745006.763 0.01441473 0.276984944 56467.33398 -4.751797284 -0.247447612 LISKPVASDSTYFAWCPDGEHILTATCAPR ddPTM_SK-BR-3_Pertuzumab_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" 0 109.62 0.00014445 102370000 65583 64623 67134 52645 75011 65101 74321 75256 77330 FALSE TRUE 61478.2771 69407.75416 68726.45018 53995.95983 69119.93864 83894.60187 63177.25601 84651.87726 64423.12343 0.954288985 1.077373317 1.06679786 0.838145637 1.072905736 1.302243626 0.980661176 1.31399834 1 15.97529099 2.476176231 24.9982188 1.141789598 1.00766911 0.269235691 0.125348641 48.73664888 1289130.791 0.039880295 0.033620818 299.3479108 -2.476176231 -0.134120488 LISQDIHSNTYNYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LISQDIHSNTYNYK 14 0 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 0 85.837 0.0088422 0 211870 256490 215640 259320 382420 157220 243740 235860 685040 FALSE TRUE 198609.4349 275480.7865 220755.0826 265974.5902 352386.2758 202606.8617 207193.4498 265307.6402 570702.3985 0.348008762 0.482704799 0.386812958 0.466047788 0.617460653 0.35501316 0.363049902 0.46487914 1 19.1223791 0.945474867 21.98343007 1 0.431011154 0.83077099 0.080208422 1708.259035 688736.7765 0.075294771 0.018823693 8.820127583 -0.945474867 -0.568988847 LISSDGHEFIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LISSDGHEFIVK 12 0 E5RHG8;Q15369-2;Q15369;R4GMY8 E5RHG8 TCEB1 Transcription elongation factor B polypeptide 1 0 ;;; 167.18 4.99E-05 2019220000 5978840 6897200 6764330 6862870 7621960 5628550 8477850 6851790 7582250 FALSE TRUE 5604635.077 7407875.865 6924783.102 7038982.863 7023362.007 7253421.013 7206675.097 7707251.064 6316723.492 0.887269339 1.172740246 1.096261869 1.114340824 1.111867888 1.148288511 1.140888169 1.220134311 1 22.59074499 4.744620805 24.90078299 1.130843926 0.887269226 0.6334277 0.056844596 369.1695821 1516840.902 0.011835318 0.10803572 55541.90926 -4.744620805 -0.243574701 LISWYDNEFGYSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 26 LISWYDNEFGYSNR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;;;;;;;;; 476.56 1.35E-222 71389758000 7650892 9515814 8703358 8878057 9839981 7806229.8 9828491 8355355 8481859 FALSE TRUE 7172036.327 10220374.77 8909805.762 9105882.973 9067188.585 10059761.62 8354800.018 9398539.464 7066181.938 1.014980422 1.446378661 1.26090806 1.288656739 1.283180742 1.423648826 1.182364124 1.330073234 1 22.75249947 -1.040269214 4.449955793 0.999989625 1.290990378 0.339243527 0.121208632 1.65E-05 3.56E-06 0.103223539 0.024328718 0.091144567 1.040269214 0.291000754 LITLEEEMTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LITLEEEMTK 10 0 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 182.39 4.15E-06 16624000 60439 60621 57934 60364 53717 39244 63918 46179 54894 FALSE TRUE 56656.23088 65109.44192 59308.22184 61913.04244 49498.2835 50573.10573 54334.08929 51944.5498 45731.83677 1.238879408 1.423722433 1.296869446 1.353828029 1.082359402 1.105862115 1.188102056 1.13585094 1 15.48091124 2.742248683 24.97615548 1.120309544 1.338981874 0.734936558 0.066796561 155.6891567 1054353.531 0.01942527 0.019903766 552.3936574 -2.742248683 0.21867233 LITS(ph)EEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LITSEEER 8 0 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LIT(0.048)S(0.952)EEER;LIT(0.156)S(0.844)EEER 155.5 0.00042801 233940000 825970 1040190 981970 972390 1104780 967140 1089870 896790 1005240 TRUE FALSE 774274.0121 1117206.75 1005262.792 997343.1737 1018015.035 1246337.618 926454.1114 1008756.206 837458.9499 0.9245516 1.334043597 1.200372618 1.190915894 1.215599923 1.488237266 1.106268088 1.204544062 1 19.67565895 0.713249561 1.534819318 1.001377621 1.229134606 0.162167567 0.144409065 1.600546284 5.952136863 0.123592783 0.035795363 5.167132053 -0.713249561 0.227756985 LITSEEERS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LITSEEERSPAK 12 1 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LITSEEERS(1)PAK;LITSEEERS(1)PAK 166.62 3.11E-05 481290000 1634690 1466640 1426960 1351320 1580310 1254540 1838390 1532000 1511440 TRUE FALSE 1532377.671 1575231.552 1460808.165 1385997.159 1456198.827 1616705.332 1562740.486 1723273.572 1259170.9 1.216973543 1.251006954 1.160134947 1.100722038 1.156474334 1.283944326 1.241086882 1.368577985 1 20.26404267 2.246600283 24.95740836 1.244679784 1.181367417 0.030732506 0.100258114 428.3579484 1329745.64 0.032014876 0.026353313 176.4413137 -2.246600283 -0.063312367 LITSEEERS(ph)PAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LITSEEERSPAKR 13 2 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LITSEEERS(1)PAKR;LITSEEERS(1)PAKR;LITSEEERS(1)PAKR;LITSEEERS(1)PAKR 265.37 1.34E-24 2169230000 1687850 1143590 1338290 1357210 1413460 1122520 1826760 1365680 1754890 TRUE FALSE 1582210.481 1228262.594 1370034.871 1392038.306 1302452.553 1446573.301 1552854.297 1536188.154 1461987.522 1.082232548 0.840132063 0.937104353 0.952154711 0.890878023 0.989456667 1.062152907 1.05075326 1 20.47949957 2.012748847 4.618483053 1.041343173 0.927144404 0.318612164 0.063220654 0.179675346 9.849606275 0.024508646 0.016333597 102.979042 -2.012748847 -0.114198769 LIVAYVDDLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIVAYVDDLDR 11 0 O14776;O14776-2 O14776 TCERG1 Transcription elongation regulator 1 0 102.07 0.0067891 8522500 38228 64677 44360 52423 65121 36727 47356 59151 42397 FALSE TRUE 35835.37772 69465.75238 45412.24015 53768.26293 60006.65935 47329.48869 40255.40743 66536.13256 35320.6668 1.014572514 1.966716901 1.285712991 1.522289011 1.698910716 1.339994201 1.139712556 1.883773399 1 15.10822496 -3.050882983 0.28369644 5.41E-10 1.522465657 0.161772601 0.312038485 114.3121719 2.967985825 69.02525658 0.331815421 0.000889441 3.050882983 1.522465656 LIVAYVDDLDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LIVAYVDDLDRR 12 1 O14776;O14776-2 O14776 TCERG1 Transcription elongation regulator 1 0 ;;; 196.16 3.36E-07 571208000 403918 647971 484103 477483 802505 451438 513813 544435 830534 FALSE TRUE 378637.4934 695947.4471 495586.1518 489736.0222 739479.4944 581760.8221 436771.5107 612408.9082 691912.5099 0.547233195 1.005831571 0.716255516 0.707800502 1.068747109 0.840801133 0.631252513 0.885095875 1 19.4002301 -2.57987363 1.489710374 2.422944239 0.805310133 0.132038208 0.160406133 1050380.549 60519.75314 5011992.28 0.041312404 0.002631033 2.57987363 -1.617634106 LIVDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LIVDGR 6 0 Q99832-3;Q99832;F8WAM2;F8WBP8;A0A0D9SG95 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 105.42 0.076756 885760000 1641400 1978660 1837740 1911560 2146700 1655650 2112200 1869560 1982060 FALSE TRUE 1538667.704 2125162.045 1881332.061 1960613.866 1978106.841 2133609.278 1795495.219 2102978.681 1651241.381 0.931824821 1.287008713 1.139344061 1.187357517 1.19795135 1.292124399 1.087360842 1.273574358 1 20.6551196 -1.173465267 4.691196734 0.999976018 1.180849835 0.203077898 0.108043594 2.34E-05 4.12E-06 0.09036613 0.021296678 0.067070992 1.173465267 0.180873817 LIVENLSS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.154)S(0.846)R 72.272 0.049531 143590000 242470 316000 292390 317230 359570 315310 320050 307570 336200 TRUE FALSE 227294.2355 339396.9688 299325.6289 325370.6589 331330.8226 406334.8784 272061.4737 345970.7915 280086.0481 0.811515736 1.21175964 1.068691679 1.161681066 1.182960826 1.450750158 0.971349611 1.235230366 1 18.09551059 4.743912059 24.5116658 1.1595884 0.811515541 0.398912883 0.134550233 436.222847 1997985.741 0.029153229 0.250176996 55451.34177 -4.743912059 -0.348072858 LIVENLSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LIVENLSSR 9 0 Q08170;A0A0D9SEM4;Q13243;Q13243-3;B4DJK0;B4DUA4;Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q08170;Q13243;Q13247 SRSF4;SRSF5;SRSF6 Serine/arginine-rich splicing factor 4;Serine/arginine-rich splicing factor 5;Serine/arginine-rich splicing factor 6 0 ;; 135.71 0.00049586 76435000 261386 279355 330376 352545 307167 249062 347330 271883 485710 FALSE TRUE 245026.3168 300038.7349 338212.6747 361591.9016 283043.3429 320962.1562 295251.091 305828.191 404641.8632 0.605538722 0.741492075 0.835832141 0.893609719 0.699491003 0.793200569 0.72966027 0.755799681 1 18.62628606 -2.395495361 2.153844304 2.678153754 0.763969367 0.49208469 0.077339195 2616413.281 276464.8947 21388202.42 0.018171393 0.00402258 2.395495361 -1.914184386 LIVLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIVLDR 6 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 106.76 0.074087 37634000 60975 99231 66120 77511 96135 54330 75978 85784 83980 FALSE TRUE 57158.68359 106578.1665 67688.39762 79500.06349 88584.94489 70014.18903 64585.80425 96494.32123 69963.19547 0.816982175 1.523346179 0.967485793 1.136312642 1.266164936 1.000728863 0.923139714 1.379215466 1 16.09430856 2.224470465 24.98940033 1.051247561 1.169985637 0.007980018 0.218586035 700.086741 1241620.776 0.076552744 0.056809161 167.6758301 -2.224470465 0.118738076 LIVMLRDPVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIVMLRDPVER 11 1 Q7LFX5-2;Q7LFX5 Q7LFX5-2 CHST15 Carbohydrate sulfotransferase 15 0 54.776 0.077826 115700000 46523 165280 119220 128230 137080 137490 101400 120160 92145 FALSE TRUE 43611.20848 177517.5032 122047.9547 131520.5989 126314.2898 177181.131 86196.01135 135162.2405 76765.40422 0.568110191 2.31246751 1.589882265 1.713279572 1.645458537 2.308085691 1.122849703 1.76071815 1 16.22816866 -1.22998322 4.343796206 0.999693629 1.677710975 0.122859612 0.511672909 0.001351761 0.000239622 0.441127784 0.103928839 0.058886641 1.22998322 0.678017346 LIYEDRVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIYEDRVDR 9 1 Q12955 Q12955 ANK3 Ankyrin-3 0 65.305 0.061045 2392300000 1760100 2390800 2527000 2349500 2316600 2118900 2648900 2474700 1939300 FALSE TRUE 1649938.483 2567817.32 2586941.633 2409792.148 2134663.581 2730592.033 2251722.036 2783671.742 1615618.302 1.021242753 1.589371275 1.601208423 1.491560318 1.321267269 1.690121998 1.393721545 1.722976114 1 20.62365496 -1.247711366 5.790242644 0.999978094 1.497179517 0.348774938 0.204322264 5.11E-05 6.64E-06 0.174893416 0.041220961 0.056531256 1.247711366 0.497201424 LIYGTVTEDNEEEDDDTLEELGGLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIYGTVTEDNEEEDDDTLEELGGLFR 26 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 0 94.542 0.0081601 3214800 3800.3 3523.2 4990.5 3757.5 3022.7 3437.8 4361.3 3187.6 3561.1 FALSE TRUE 3562.446007 3784.061394 5108.877017 3853.923811 2785.309335 4430.237052 3707.363553 3585.578877 2966.729404 1.200799103 1.275499339 1.722056959 1.29904797 0.938848461 1.493306752 1.249646681 1.208596534 1 11.53465763 3.007488459 24.98542388 1.213658408 1.430423941 0.188066377 0.200685883 285.7576765 953427.6379 0.057106139 0.068129126 1017.392329 -3.007488459 0.216765533 LIYKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LIYKPR 6 1 B7Z6D5;Q96GQ7;A0A087X059 B7Z6D5 DDX27 Probable ATP-dependent RNA helicase DDX27 0 67.29 0.090437 142930000 477490 517740 484490 579980 649110 487520 720130 613000 754900 FALSE TRUE 447604.7532 556074.0083 495982.3316 594863.2687 598131.519 628259.1098 612153.1919 689534.3994 628902.3132 0.711723814 0.884197747 0.78864765 0.945875466 0.95107222 0.99897726 0.97336769 1.096409387 1 19.26247642 2.958615641 0.71270755 1.031494653 0.784496096 0.745902045 0.05562848 0.352374819 0.396343603 0.034113026 0.043844156 909.1083386 -2.958615641 -0.246998557 LKAEAELLQQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKAEAELLQQQK 12 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 124.07 0.00021311 0 898710 822650 828730 859210 961340 613700 1035940 822520 1129660 FALSE TRUE 842461.3453 883559.862 848387.867 881258.7832 885840.2343 790865.2274 880610.4142 925213.4326 941112.4481 0.895176073 0.938846217 0.90147343 0.936401155 0.941269278 0.840351468 0.935712216 0.983106147 1 19.84400759 1.272200381 3.706518806 0.995748458 0.912196256 0.562583756 0.029628334 0.157826635 3.910412062 0.023392875 0.007046801 18.71545463 -1.272200381 -0.083552202 LKAEATEAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LKAEATEAAR 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;; 174.24 2.89E-06 1933210000 2721930 3346450 2701550 2843210 3585510 2114720 3247210 3066610 3431480 FALSE TRUE 2551569.26 3594224.64 2765632.042 2916171.582 3303918.508 2725205.334 2760321.006 3449483.009 2858743.82 0.892549113 1.257274127 0.967429128 1.020088461 1.155723883 0.953287705 0.965571307 1.206642927 1 21.44694991 3.764214733 24.25144333 1.031765445 1.104379946 0.00023445 0.120195091 606.3333995 396411.596 0.028241088 0.050909961 5810.516423 -3.764214733 0.072614501 LKAEGSEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 LKAEGSEIR 9 1 P07237;H7BZ94;I3L3U6;I3L0S0;I3NI03;I3L514 P07237 P4HB Protein disulfide-isomerase 0 ;;;;;;;; 133.89 0.00024095 9620180000 17801280 23842080 16873010 18844300 24525750 11969330 21096470 19790460 24185990 FALSE TRUE 16687129.66 25607372.41 17273245.77 19327876.64 22599596.53 15424681.27 17933250.17 22261342.5 20149192.02 0.828178601 1.270888301 0.857267415 0.959238297 1.121613041 0.765523563 0.89002329 1.104825567 1 24.26421865 3.846128974 8.05951591 0.944407642 1.078300584 0.049535805 0.150064037 0.48606401 30.97149603 0.035559814 0.064340724 7016.636434 -3.846128974 0.133892942 LKAEQEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LKAEQEAR 8 1 Q8N5G2;Q8N5G2-2;Q8N5G2-3 Q8N5G2 TMEM57 Macoilin 0 ;;; 96.331 0.0082232 546886000 556600 614181 453948 478764 618933 357968 547341 592956 657161 FALSE TRUE 521763.3996 659655.6003 464715.8609 491049.8948 570324.4988 461307.5505 465272.2983 666987.8619 547476.5837 0.953033271 1.204901945 0.848832397 0.896933146 1.041733137 0.842606906 0.849848765 1.218294776 1 19.06243773 3.970728486 24.26998098 0.939201612 1.088196853 0.12099152 0.129640148 263.4476583 1000180.736 0.030491893 0.056729223 9348.210551 -3.970728486 0.148995241 LKATVT(ph)PS(ph)PVKGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKATVTPSPVKGK 13 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 LKAT(0.011)VT(0.992)PS(0.998)PVKGK;LKAT(0.049)VT(0.958)PS(0.993)PVKGK 125.52 0.0003765 5843700000 13824700 6110900 9044900 8634600 9154200 6182900 12844000 6786800 15042600 TRUE FALSE 12959436.7 6563357.394 9259449.299 8856178.454 8435266.058 7967802.859 10918161.44 7634146.92 12531892.88 1.03411646 0.523732325 0.738870767 0.706691203 0.673103907 0.635802024 0.871230032 0.60917748 1 23.57910101 -4.999993203 0.422921074 6.4094938 0.708544878 0.257503593 0.143526895 1219.214003 7.838407215 6132.665284 0.074695931 1.00E-05 4.999993203 -5.700948921 LKATVT(ph)PSPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKATVTPSPVK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 LKAT(0.003)VT(0.885)PS(0.113)PVK 107.46 0.0035479 5306000000 2675600 3247900 1630800 1455800 3841200 1291000 2686300 3240900 4081900 TRUE FALSE 2508138.972 3488377.895 1669483.346 1493158.293 3539527.647 1663690.742 2283514.253 3645533.499 3400604.52 0.737556795 1.025811109 0.490937225 0.439086134 1.04085248 0.489233821 0.671502446 1.072025129 1 21.6973598 1.239159211 24.99707608 1.036012695 0.701757108 0.315038087 0.206396247 18.81095575 785841.9387 0.154386604 0.048647077 17.34439719 -1.239159211 -0.334255588 LKATVTPS(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKATVTPSPVK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 LKATVT(0.011)PS(0.989)PVK 129.74 0.00062779 605590000 1388600 1771600 811990 754250 2361700 643740 1425100 2050300 2408700 TRUE FALSE 1301690.005 1902771.107 831250.7862 773605.3319 2176221.609 829577.2878 1211419.485 2306284.468 2006672.409 0.64868087 0.948222091 0.414243392 0.385516504 1.084492715 0.413409425 0.60369569 1.149307908 1 20.93637368 1.241410315 24.97927847 1.074654069 0.64305764 0.38080298 0.229041355 70.2035662 615422.3315 0.161200771 0.053004908 17.43453284 -1.241410315 -0.431596429 LKATVTPS(ph)PVKGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKATVTPSPVKGK 13 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 LKAT(0.008)VT(0.206)PS(0.786)PVKGK;LKATVT(0.032)PS(0.967)PVKGK 163.18 3.09E-05 22822200000 13002700 8836500 10782700 9715700 11530500 8348100 16176000 8406200 18066400 TRUE FALSE 12188884.22 9490763.654 11038470.74 9965021.311 10624941.04 10758060.95 13750558.97 9455732.574 15051001.13 0.809838769 0.630573579 0.733404419 0.66208362 0.705929191 0.714773779 0.913597631 0.628246088 1 23.84335612 -0.816618193 0.291949786 1.13807786 0.684955534 0.467713627 0.088643364 10.04032954 0.807853748 1.313378683 0.100516639 0.15253932 0.816618193 -0.453122327 LKAWNDIKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKAWNDIKK 9 2 P36578;H3BM89;H3BTP7 P36578 RPL4 60S ribosomal protein L4 0 72.434 0.026301 163350000 468320 563550 346210 427310 795720 295020 573450 550230 953640 FALSE TRUE 439008.6872 605275.8284 354422.2647 438275.498 733227.361 380187.4848 487466.4961 618927.4267 794471.3233 0.552579652 0.761859882 0.446110834 0.551656788 0.922912306 0.478541482 0.613573432 0.77904313 1 19.59963562 0.969402631 3.021306699 0.998830295 0.616464013 0.446645706 0.138126043 0.229766197 5.164997822 0.123692118 0.032522697 9.319714976 -0.969402631 -0.382366282 LKCGSGPVHISGQHLVAVEEDAES(ph)EDEEEEDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LKCGSGPVHISGQHLVAVEEDAESEDEEEEDVK 33 1 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 1 LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK 310.14 2.39E-104 1037140000 166390 331871 330381 395074 465746 347191 800077 310248 1000430 TRUE FALSE 155975.9469 356443.0742 338217.7933 405212.2677 429168.1879 447419.4055 680112.8814 348983.1457 833451.77 0.187144539 0.427670907 0.405803678 0.486185623 0.514928642 0.536826991 0.816019482 0.418720265 1 19.66873919 0.993767217 0.133934851 1.368047674 1.52E-17 0.722791222 0.119117855 4.053897634 0.395493386 2.071187064 1.510065007 9.857509794 -0.993767217 -1.368047674 LKDALVR ddPTM_SK-BR-3_Pertuzumab_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 62.2 0.079245 128130000 281690 275080 287230 281780 344350 270950 343800 281490 369190 FALSE TRUE 264059.5257 295447.2094 294043.2312 289010.9519 317306.14 349168.8665 292250.3817 316634.6461 307569.8039 0.858535273 0.960585876 0.956021129 0.939659707 1.031655696 1.135250802 0.950192047 1.029472471 1 18.23055435 2.740266668 22.35266973 1.028781639 0.938568152 0.46390285 0.053275976 34.54049869 452549.4637 0.016125176 0.016295453 549.8784097 -2.740266668 -0.090213487 LKDDEVAQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LKDDEVAQLK 10 1 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 ;;; 160.67 6.66E-06 3939900000 11811180 6651840 8559110 8100000 8521400 6321740 10744470 7575030 9466660 FALSE TRUE 11071939.33 7144349.155 8762136.131 8307859.713 7852163.618 8146723.713 9133436.47 8520789.17 7886613.289 1.403890228 0.905883032 1.111013791 1.053412841 0.99563188 1.032981258 1.158093612 1.080411687 1 22.91097447 4.753430429 24.85176624 1.04855419 1.403890501 0.730918421 0.068875462 1446.01598 2416667.795 0.01695504 0.390112792 56680.07663 -4.753430429 0.355336311 LKDDEVAQLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKDDEVAQLKK 11 2 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 ; 158.2 1.69E-05 9874100000 21728600 12540900 16421600 15981300 19767900 11000500 22261200 15523100 30179000 FALSE TRUE 20368645.71 13469441.28 16811128.11 16391407.21 18215408.87 14176165.77 18923339.72 17461193.21 25141929.94 0.810146467 0.535736171 0.668649071 0.651955011 0.724503207 0.563845568 0.752660586 0.694504887 1 24.58359206 0.017752622 0.591084803 1.022468957 0.645617296 0.609958542 0.081480163 2.486044894 1.019103577 0.20157574 0.030475663 1.041723885 -0.017752622 -0.376851661 LKDEEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKDEEIR 7 1 A0A0A0MTN0;Q13617;Q13617-2;Q5T2B5 A0A0A0MTN0 CUL2 Cullin-2 0 ; 80.165 0.027954 331110000 1074080 1021030 1091610 1112280 1141100 868390 1249430 940890 1361730 FALSE TRUE 1006855.25 1096628.124 1117503.505 1140822.988 1051482.609 1119080.096 1062089.571 1058362.188 1134448.466 0.887528416 0.966661912 0.985063261 1.005619049 0.926866791 0.986453003 0.936216675 0.93293104 1 20.11355964 3.856924174 0.003361347 1.911604605 9.39E-09 0.102564616 0.035563704 159285.4735 113.7889808 31782.24865 32934.22576 7193.233763 -3.856924174 -1.911604596 LKDENGALIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKDENGALIR 10 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;E1CKY7;O60237-4;O60237;O60237-6 O14974 PPP1R12A;sm-M20;PPP1R12B Protein phosphatase 1 regulatory subunit 12A;Protein phosphatase 1 regulatory subunit 12B 0 ; 115.39 0.0011213 276880000 309870 330560 334560 313180 371640 263130 362470 324390 395390 FALSE TRUE 290475.7898 355035.0063 342495.9212 321216.729 342452.8935 339091.3594 308120.9885 364890.8056 329396.8547 0.881841419 1.077833626 1.039766823 0.975166352 1.039636198 1.029431079 0.935409626 1.107754371 1 18.32946725 LKDIALGMQTEIEEQDDILDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKDIALGMQTEIEEQDDILDR 21 1 O95721;C9JAF7 O95721 SNAP29 Synaptosomal-associated protein 29;Synaptosomal-associated protein 0 230.49 8.23E-26 47810000 48416 43424 51054 48027 54452 40288 57338 49126 58093 FALSE TRUE 45385.72899 46639.15814 52265.02499 49259.45413 50175.55957 51918.49158 48740.6992 55259.48924 48396.903 0.93778168 0.963680633 1.07992499 1.017822445 1.036751454 1.072764751 1.007103682 1.141798045 1 15.56262711 4.216307628 2.654573569 1.04832501 0.942530034 0.503764032 0.041558466 0.212962401 2.935771963 0.009508707 0.030187962 16455.36909 -4.216307628 -0.105794975 LKDISTLEPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKDISTLEPLK 11 1 Q92688;Q92688-2 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 0 97.463 0.0031175 0 681540 757840 642620 703380 909230 506090 943850 788950 820450 FALSE TRUE 638883.628 813951.2621 657863.2499 721429.9216 837822.7435 652189.9673 802328.4548 887452.1442 683511.5947 0.934707813 1.190837534 0.962475626 1.055475763 1.225762299 0.954175426 1.173832984 1.298371748 1 19.38260629 1.60493278 15.07168045 1.177429108 1.065627247 0.131864498 0.119135327 0.117500357 216.2902539 0.054173751 0.027000784 40.26547066 -1.60493278 -0.111801862 LKDLDLDAFAEELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LKDLDLDAFAEELER 15 1 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;; 214.28 2.28E-12 309735000 713957 662190 721231 687297 791131 560081 833117 661938 969853 FALSE TRUE 669271.7058 711219.2366 738338.9399 704934.2046 728998.7625 721767.2925 708198.8401 744582.4164 807978.2688 0.828328845 0.880245502 0.913810394 0.872466788 0.902250457 0.893300378 0.876507287 0.921537676 1 19.62395697 -5 0.20105994 1.517831088 0.868964497 0.752400605 0.021958547 75.53493253 0.748471944 15.69614226 0.052230707 1.00E-05 5 -0.648866592 LKDLFDYS(ph)PPLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 LKDLFDYSPPLHK 13 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 LKDLFDYS(1)PPLHK;LKDLFDY(0.034)S(0.966)PPLHK;LKDLFDY(0.003)S(0.997)PPLHK;LKDLFDY(0.003)S(0.997)PPLHK;LKDLFDYS(1)PPLHK;LKDLFDYS(1)PPLHK;LKDLFDY(0.013)S(0.987)PPLHK;LKDLFDY(0.005)S(0.995)PPLHK;LKDLFDYS(1)PPLHK;LKDLFDYS(1)PPLHK 147.17 2.58E-05 34127850800 1705697.5 1499860.3 1930685.8 1389602.6 1544865.8 1144621 1905331.8 1285151.4 2419366.6 TRUE FALSE 1598940.938 1610911.517 1976482.579 1425262.155 1423538.272 1475054.501 1619644.985 1445605.381 2015558.685 0.793299124 0.799238211 0.980612767 0.707130071 0.706274783 0.731834063 0.803571237 0.717223166 1 20.94274836 4.46906867 24.332156 0.806236713 0.794783829 0.001796994 0.106057746 3929.616711 11874076.05 0.025734311 0.071622053 29448.87236 -4.46906867 -0.011452885 LKDLFDYSPPLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKDLFDYSPPLHK 13 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 89.541 0.0044477 117210000 499540 423950 483900 473200 524350 378960 565360 441300 841640 FALSE TRUE 468274.6831 455339.6991 495378.3365 485343.1131 483169.6661 488359.6001 480589.5165 496397.2764 701164.8468 0.667852482 0.649404632 0.706507662 0.692195445 0.689095679 0.696497553 0.685415874 0.707960872 1 19.41939414 -5 0.34014349 4.406998099 0.674481421 0.97917436 0.014421618 52.83973411 0.445065659 130.7134858 0.01209979 1.00E-05 5 -3.732516677 LKDLFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKDLFGK 7 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;Q9H361;H0YBN4;H0YAP2 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ; 103.56 0.0076133 1087020000 3570200 3110800 3243400 3205300 3787900 2560900 4366700 3241500 4472300 FALSE TRUE 3346747.555 3341126.869 3320334.98 3287553.425 3490413.614 3300190.257 3711953.873 3646208.41 3725844.238 0.898252139 0.896743572 0.891163121 0.882364698 0.936811469 0.885756367 0.996271888 0.978626099 1 21.82913593 1.718434379 6.36393505 0.990185918 0.898306764 0.882773243 0.015957487 0.040046298 4.083713545 0.007478619 0.003854108 52.29189479 -1.718434379 -0.091879154 LKDLGHPVEEEDELES(ph)GDQEDEDDESEDPGKDLDHI ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LKDLGHPVEEEDELESGDQEDEDDESEDPGKDLDHI 36 2 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 1 LKDLGHPVEEEDELES(0.985)GDQEDEDDES(0.015)EDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI 245.35 2.96E-50 2112490000 375779 244787 285255 295407 295158 196922 377417 235201 317393 TRUE FALSE 352259.6632 262911.2842 292021.3833 302987.6437 271977.4813 253770.1846 320826.8246 264566.3626 264418.0579 1.332207286 0.994301548 1.10439274 1.14586593 1.028588908 0.959730915 1.213331749 1.000560872 1 18.01246118 4.74849702 24.74395442 1.067337644 1.332207452 0.542935211 0.079065723 961.9757458 2395487.087 0.017864996 0.238897879 56039.85725 -4.74849702 0.264869808 LKDLGHPVEEEDELESGDQEDEDDESEDPGKDLDHI ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKDLGHPVEEEDELESGDQEDEDDESEDPGKDLDHI 36 2 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 171.88 3.31E-18 103680000 108140 66001 80519 83703 93134 67477 113400 71042 131030 FALSE TRUE 101371.7104 70887.78271 82428.9487 85850.96069 85819.63132 86956.5145 96396.72275 79911.75008 109160.2465 0.928650435 0.649391926 0.755118748 0.786467267 0.786180263 0.796595073 0.883075349 0.732059084 1 16.73608803 -1.109117195 0.262595307 1.146573696 0.742249212 0.372601466 0.079916543 15.03137864 0.902043437 1.701442274 0.112935002 0.077782662 1.109117195 -0.404324485 LKDLPFIVSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKDLPFIVSHR 11 1 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ; 163.99 1.40E-05 414360000 1028580 1280920 1053300 1011110 1460840 867330 1332590 1277120 1124890 FALSE TRUE 964203.0139 1375760.65 1078284.773 1037056.794 1346111.519 1117714.091 1132780.501 1436571.243 937138.5919 1.02887985 1.46804396 1.150613989 1.106620518 1.436406024 1.192688147 1.208765182 1.532933608 1 19.8379029 -1.364396211 4.825607998 0.99977191 1.266244428 0.20399219 0.164893118 0.000360812 4.75E-05 0.14236648 0.033527597 0.043211942 1.364396211 0.266472518 LKDLSR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 124.59 0.016679 19357530000 11130220 17100850 11811910 11820570 20231610 9361790 15788710 17372110 19640030 FALSE TRUE 10433599.4 18367014.73 12092094.08 12123905.84 18642700.96 12064386.8 13421339.51 19541056.17 16361982.11 0.637673316 1.122542159 0.739036016 0.740980265 1.139391354 0.737342622 0.820275894 1.19429639 1 23.96384419 1.246797811 24.99703257 1.097148214 0.862914322 0.26646314 0.170377137 216.6713334 657536.8604 0.108959259 0.03830503 17.6521582 -1.246797811 -0.234233893 LKDPANFQYPAESVLAYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKDPANFQYPAESVLAYK 18 1 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ; 167.22 2.16E-11 1481060000 3404600 3073600 3127100 3112700 3525300 2411900 4025300 2997100 3692300 FALSE TRUE 3191512.163 3301172.542 3201276.289 3192577.152 3248437.158 3108176.376 3421743.634 3371294.532 3076031.277 1.037542169 1.073192125 1.04071643 1.037888391 1.056048156 1.010450186 1.11238909 1.095988379 1 21.55263874 1.735144705 25 1.079895921 1.046275514 0.093762988 0.033298505 0.642664607 4641.927195 0.013784222 0.007644027 54.343137 -1.735144705 -0.033620407 LKDQNIFVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKDQNIFVSR 10 1 Q9NW13;Q9NW13-2 Q9NW13 RBM28 RNA-binding protein 28 0 114.72 0.001202 294300000 365160 360990 371050 406910 444880 387840 381270 345990 431360 FALSE TRUE 342305.2874 387718.0752 379851.4812 417351.9995 409940.9194 499803.1119 324102.103 389187.6131 359363.2293 0.952532868 1.078903025 1.057012655 1.161365341 1.14074253 1.390802039 0.90187887 1.082992308 1 18.45508327 1.627927341 24.99999993 0.994305019 1.11952985 0.222199545 0.118171301 1.365124935 1696.847429 0.052958693 0.029319062 42.45485294 -1.627927341 0.125224831 LKDSEAELQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LKDSEAELQR 10 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 ;;;;; 133.42 0.00018024 3470460000 4753320 4458960 4587940 4459850 5210630 3533020 5403200 4399310 6680490 FALSE TRUE 4455818.186 4789106.038 4696768.103 4574297.302 4801408.138 4552945.52 4593040.321 4948573.538 5565473.061 0.800618049 0.860502959 0.843911749 0.821906287 0.862713391 0.818069815 0.825274019 0.889155959 1 22.40807289 0.90842723 3.334452548 0.99988093 0.836567928 0.883255946 0.01926859 0.116628034 2.939855906 0.017707916 0.004595323 8.098922258 -0.90842723 -0.163313002 LKDSGSVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKDSGSVQR 9 1 D6R9V6;A6NJ38;A6NHM7;Q7Z5H3-4;Q7Z5H3-3;Q7Z5H3;Q7Z5H3-5;Q7Z5H3-2 D6R9V6 ARHGAP22 Rho GTPase-activating protein 22 0 51.113 0.094231 63403000 77121 275870 165630 181660 255940 192330 161680 250170 141350 FALSE TRUE 72294.13427 296295.7018 169558.8218 186321.7031 235839.5048 247852.5488 137437.585 281404.2752 117757.7718 0.613922403 2.51614562 1.439894957 1.582245488 2.002751081 2.104765952 1.16712114 2.389687498 1 16.84546275 -0.74585905 6.436312827 0.999999994 1.749379792 0.136776775 0.571588769 4.36E-08 9.03E-09 0.487307626 0.114859509 0.17953162 0.74585905 0.749379798 LKDVLLQVDDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKDVLLQVDDER 12 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 133.14 0.00015372 213418000 531240 524790 518140 517990 556150 414310 647790 480450 496760 FALSE TRUE 497990.6367 563645.9976 530430.5255 531282.5004 512472.2224 533914.5712 550659.9033 540435.2401 413847.5468 1.20331905 1.361965299 1.281705134 1.283763803 1.238311611 1.290123804 1.330586366 1.305880014 1 18.65873988 -1.131059972 4.908528915 0.99998401 1.294491766 0.803833646 0.044411623 7.32E-06 1.30E-06 0.040502635 0.009546045 0.073950315 1.131059972 0.294507756 LKDVLLQVDDERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LKDVLLQVDDERR 13 2 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 198.81 6.91E-08 2138190000 2065750 2275982 2125628 2195910 2446670 1775270 2701880 2001302 2750480 FALSE TRUE 1936458.395 2444498.075 2176048.9 2252260.768 2254518.408 2287761.63 2296758.177 2251168.96 2291407.119 0.84509574 1.066810893 0.949656166 0.982916021 0.983901284 0.998409061 1.002335272 0.982439542 1 21.12780238 2.448895738 2.640568608 0.99675714 0.976931856 0.050959351 0.054255573 1.295308019 18.42807484 0.019276569 0.016048432 281.1225852 -2.448895738 -0.019825284 LKDYAFIHFDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LKDYAFIHFDER 12 1 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;; 150.16 3.57E-05 1196849000 4749795 6201083 5171179 5011731 7403587 3833620 6146947 5870899 7802360 FALSE TRUE 4452513.81 6660217.638 5293841.808 5140340.502 6822139.142 4940323.86 5225269.363 6603893.664 6500095.711 0.684992038 1.02463378 0.814425209 0.790809971 1.049544414 0.760038633 0.803875757 1.015968681 1 22.63202953 1.227150404 24.95059214 1.007984487 0.859011324 0.257174434 0.112357936 343.8523996 751873.5997 0.096808039 0.025054615 16.8713721 -1.227150404 -0.148973163 LKDYAFVHFEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKDYAFVHFEDR 12 1 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ; 151.7 4.16E-05 2435940000 5038000 5939900 5186300 4813800 6801500 3990900 5763800 5562600 6992800 FALSE TRUE 4722680.573 6379696.376 5309321.485 4937330.258 6267337.626 5143008.043 4899571.698 6257102.855 5825656.505 0.810669247 1.095103422 0.911368784 0.847514826 1.07581654 0.882820338 0.8410334 1.074059696 1 22.47398921 3.727277387 24.99973987 0.932614851 0.982212974 0 0.10841571 27.48947994 4400623.394 0.026351163 0.043922749 5336.756493 -3.727277387 0.049598122 LKEAETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKEAETR 7 1 P06753-2;P06753-6;P06753-5;P06753-7;A0A494C034;A0A2R8Y6A3;A0A494C0I0;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YE05;K7ENT6;A0A5F9UN72;K7EPB9;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2 TPM3;TPM1;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain 0 121.96 0.0040016 936560000 2381800 2285200 2349800 2174100 2414900 1694200 2589700 1948200 2550700 FALSE TRUE 2232727.39 2454398.586 2405538.366 2229891.087 2225243.495 2183288.037 2201398.527 2191437.059 2124971.692 1.050709239 1.155026486 1.132033135 1.049374491 1.04718736 1.027443352 1.035966048 1.031278236 1 21.01901219 3.16058334 4.146582692 1.032429779 1.124689416 0.620326293 0.029501714 0.117182679 3.847031542 0.008212023 0.010139146 1447.382576 -3.16058334 0.092259637 LKECEDTHLGEEVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKECEDTHLGEEVDR 15 1 O43847;O43847-2;G3V1R5;H0Y5G9 O43847 NRD1 Nardilysin 0 57.499 0.073068 61923000 153800 131180 142370 153380 191910 129940 172580 164430 200370 FALSE TRUE 144173.9325 140892.7037 145747.0836 157315.9905 176838.1627 167451.5686 146703.2312 184959.4475 166926.9526 0.86369475 0.844038075 0.873118939 0.942424145 1.059374535 1.003142788 0.878846878 1.108026263 1 17.34885739 3.147612038 3.124304015 0.992360149 0.85663491 0.561451842 0.059194405 0.196009775 3.831531005 0.017718999 0.022229493 1404.792042 -3.147612038 -0.135725239 LKEDILENEDEQNS(ph)PPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LKEDILENEDEQNSPPK 17 1 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 LKEDILENEDEQNS(1)PPK;LKEDILENEDEQNS(1)PPK;LKEDILENEDEQNS(1)PPK;LKEDILENEDEQNS(1)PPK;LKEDILENEDEQNS(1)PPK;LKEDILENEDEQNS(1)PPK;LKEDILENEDEQNS(1)PPK 288.92 4.94E-38 3482300000 9930180 4295380 6133570 5765860 5848630 4249400 9009620 5235110 7820120 TRUE FALSE 9308667.76 4613414.405 6279061.177 5913821.729 5389302.192 5476132.797 7658711.122 5888725.007 6514891.452 1.428829295 0.708133733 0.96380135 0.907739104 0.82722824 0.840556261 1.175570027 0.903886895 1 22.63530971 1.756093596 25 1.042196157 0.914601134 0.017046699 0.200372536 17.43237703 24883.06725 0.084024511 0.046596893 57.02871635 -1.756093596 -0.127595023 LKEDILENEDEQNS(ph)PPKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LKEDILENEDEQNSPPKK 18 2 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 LKEDILENEDEQNS(1)PPKK;LKEDILENEDEQNS(1)PPKK;LKEDILENEDEQNS(1)PPKK;LKEDILENEDEQNS(1)PPKK;LKEDILENEDEQNS(1)PPKK 205.02 5.26E-16 4392990000 6074890 2315840 3608290 3380610 3376010 2343170 5260890 2799350 4728770 TRUE FALSE 5694673.479 2487307.203 3693880.343 3467362.176 3110871.793 3019605.141 4472068.384 3148855.01 3939507.738 1.445529203 0.631375128 0.937650232 0.880151127 0.789660029 0.766493009 1.135184567 0.799301644 1 21.90958394 -0.194040365 6.222180401 0.999999987 0.903350639 0.004498882 0.227515978 3767461.702 691987.3983 0.197394487 0.047875195 0.639675379 0.194040365 -0.096649347 LKEDVLEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKEDVLEQR 9 1 O43818 O43818 RRP9 U3 small nucleolar RNA-interacting protein 2 0 ; 108.67 0.0023477 336430000 549220 471850 539160 535280 582390 378980 611960 464560 753740 FALSE TRUE 514845.3006 506786.265 551949.1298 549016.191 536651.4386 488385.3738 520202.2792 522561.3386 627935.9247 0.819901013 0.807066844 0.878989572 0.874318811 0.854627706 0.777763072 0.828432104 0.832188951 1 19.26025783 -1.07974096 3.632038312 1.000073022 0.834575135 0.74887573 0.030179803 5913123403 9937809736 5301898.186 0.007601109 0.083226003 1.07974096 -0.165497887 LKEEEEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LKEEEEDK 8 1 P27797 P27797 CALR Calreticulin 0 ;;; 124.92 0.001171 1073740000 2634180 1090720 1505410 1425190 1261770 1071370 2132640 1157910 1226170 FALSE TRUE 2469311.376 1171478.044 1541119.036 1461762.788 1162675.674 1380657.127 1812870.43 1302477.612 1021514.306 2.417304743 1.146805323 1.508661237 1.430976326 1.138188342 1.351578846 1.774689224 1.275045885 1 19.96227798 4.746283333 24.95059707 1.374431936 2.417305258 0.702308848 0.221019053 544.1470087 1757991.265 0.051698911 0.554965354 55754.93748 -4.746283333 1.042873322 LKEEEEDKKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKEEEEDKKR 10 3 P27797 P27797 CALR Calreticulin 0 158.05 3.55E-06 1240100000 1715600 624720 976970 935860 861170 624980 1296900 661000 1070500 FALSE TRUE 1608223.658 670974.9188 1000144.19 959875.752 793537.182 805401.5803 1102441.885 743527.305 891826.6343 1.803291802 0.75236026 1.121455843 1.076303079 0.889788611 0.903092091 1.236161651 0.833712828 1 19.76640376 4.749128337 24.98502445 0.991730739 1.803292261 0.766678886 0.143105591 740.4254575 1750537.2 0.033222936 0.480075765 56121.37943 -4.749128337 0.811561521 LKEEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKEEEER 7 1 A0A087WUT6;O60841;Q9H2L5-3;Q9H2L5;Q9H2L5-2 A0A087WUT6 EIF5B;RASSF4 Eukaryotic translation initiation factor 5B;Ras association domain-containing protein 4 0 120.15 0.0042142 523630000 1221700 895830 1031600 981740 1131200 748780 1195500 942870 1359600 FALSE TRUE 1145235.978 962158.1853 1056070.039 1006933.11 1042360.115 964940.6306 1016245.873 1060589.395 1132673.977 1.011090571 0.849457306 0.932368944 0.888987592 0.92026491 0.851913834 0.897209519 0.936358932 1 20.11130123 0.932361898 3.392035422 0.999848218 0.901250854 0.286559359 0.045577278 0.33071216 9.414527659 0.038361325 0.009944575 8.557795377 -0.932361898 -0.098597364 LKEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKEEEK 6 1 Q7Z6E9;A0A2R8Y880;H3BSK8;Q93034;I3L121;I3L3S9;J3KNW5;Q96AJ1-2;Q96AJ1 Q7Z6E9;Q93034 RBBP6;CUL5;CLUAP1 E3 ubiquitin-protein ligase RBBP6;Cullin-5;Clusterin-associated protein 1 0 65.038 0.095851 374460000 862150 552740 739820 677320 743920 571620 869100 621020 911640 FALSE TRUE 808189.5705 593665.4447 757368.8798 694701.1779 685495.524 736637.4145 738786.5233 698555.714 759481.3946 1.064133468 0.781672137 0.997218477 0.914704669 0.902583696 0.969921607 0.972751312 0.919779891 1 19.5346551 1.40443368 0.400398259 0.997780348 0.912383821 0.02295293 0.074648461 2.661441652 1.273816784 0.089542692 0.063511456 25.37661438 -1.40443368 -0.085396527 LKEEHGIELS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKEEHGIELSSPR 13 1 O14647;O14647-2 O14647 CHD2 Chromodomain-helicase-DNA-binding protein 2 1 LKEEHGIELS(0.855)S(0.145)PR 54.805 0.081478 133680000 267420 212640 240710 221250 211670 193030 289690 213520 233360 TRUE FALSE 250682.6596 228384.0869 246419.7549 226927.6496 195046.292 248754.6274 246253.6739 240178.442 194410.7084 1.289448825 1.174750551 1.267521511 1.167259002 1.003269283 1.27953151 1.266667232 1.23541776 1 17.56874816 3.222273254 24.68603609 1.179348584 1.232461245 0.111790235 0.101065571 658.1908259 997589.434 0.028931663 0.034677572 1668.296559 -3.222273254 0.053112661 LKEEISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LKEEISK 7 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;; 110.87 0.006116 3624070000 6092740 3528920 4132860 3477260 5050190 3346280 4157010 4366120 6306100 FALSE TRUE 5711406.279 3790204.909 4230893.391 3566492.379 4653568.449 4312296.714 3533704.942 4911239.693 5253571.171 1.087147408 0.721453043 0.805336647 0.678870099 0.885791454 0.820831502 0.672629118 0.934838329 1 22.32486701 1.043180719 7.824777072 0.999885738 0.794017012 0.231274506 0.119477878 0.22948852 33.96562141 0.103293023 0.025874457 11.04538147 -1.043180719 -0.205868726 LKEELIDAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKEELIDAIR 10 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 160.15 6.81E-06 139410000 834210 751710 846660 755990 852610 605360 938650 747900 1048100 FALSE TRUE 781998.2852 807367.3906 866743.175 775389.9833 785649.4499 780117.6048 797908.1465 841276.9613 873165.339 0.895590159 0.924644342 0.992644962 0.888021946 0.899771687 0.893436294 0.913811063 0.963479565 1 19.73589534 1.029157063 3.721441881 0.999559097 0.921228753 0.469212152 0.030168919 0.205998162 6.624612799 0.031969341 0.008246264 10.69441574 -1.029157063 -0.078330344 LKEENEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKEENEK 7 1 Q5M775-4;Q5M775;J3KSG2;Q5M775-5;Q5M775-3;Q5M775-2;I3L414;I3L3F1;A0A494BZY0;A0A494C199;A0A494C0J4;A0A494C1N2;Q9BXL6-3;Q9BXL6-2;Q9BXL6 Q5M775-4;I3L3F1 SPECC1;CARD14 Cytospin-B;Caspase recruitment domain-containing protein 14 0 ; 94.85 0.012675 976150000 1252020 671360 805550 726110 958600 574030 993040 688130 1231780 FALSE TRUE 1173658.303 721068.1929 824658.0264 744743.2119 883315.4228 739743.1424 844142.8709 774044.5453 1026187.96 1.143706951 0.702666783 0.80361304 0.725737624 0.86077352 0.720865154 0.822600638 0.754291197 1 19.96886357 -1.186318706 3.855841271 1.00014396 0.801275407 0.161101889 0.127088141 12689568.37 7808361.595 14197.12345 0.025897025 0.065115037 1.186318706 -0.198868552 LKEFLEDYDDDRDDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKEFLEDYDDDRDDPK 16 2 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 92.307 0.0027086 457900000 1051620 617670 791080 759680 848030 618370 991420 683500 1037170 FALSE TRUE 985800.9814 663402.9295 809844.7912 779174.6749 781429.1446 796883.3806 842765.7749 768836.4796 864059.6266 1.140894622 0.767774479 0.937255678 0.901760308 0.904369468 0.922255081 0.975356039 0.88979563 1 19.72077135 1.954685281 6.859912779 0.951692826 0.90825868 0 0.095148721 0.861939052 105.3717218 0.037327213 0.023478335 90.09180343 -1.954685281 -0.043434146 LKEHEDYCGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKEHEDYCGAR 11 1 O14545;F8VNX8;F8VVF3;O14545-2 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 0 ; 131.17 0.00012549 355160000 336070 271850 302780 288700 283930 261470 361690 260070 422920 FALSE TRUE 315035.9786 291978.0569 309962.0846 296108.5308 261631.2831 336952.1444 307457.9423 292540.312 352331.9198 0.894145437 0.828701688 0.879744545 0.840424935 0.742570481 0.956348617 0.872637206 0.830297499 1 18.42657566 -1.086875152 4.003041597 1.000031005 0.857196147 0.407655206 0.054669824 5702720.397 3098109.931 1454.417986 0.011929875 0.081870011 1.086875152 -0.142834858 LKELIFEETAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKELIFEETAR 11 1 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 ; 160.69 2.48E-05 632920000 1611300 1760260 1693270 1669430 1964190 1342950 2096420 1594760 2411840 FALSE TRUE 1510451.609 1890591.482 1733435.164 1712270.4 1809930.441 1730637.864 1782081.283 1793869.296 2009288.323 0.751734628 0.940925929 0.862711013 0.85217755 0.900781844 0.861318828 0.886921634 0.892788395 1 20.93825317 -5 0.234063798 1.691861256 0.861615414 0.455800023 0.047000638 156.947209 1.569500462 51.47414354 0.071621268 1.00E-05 5 -0.830245843 LKELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKELLR 6 1 E5RHX8;Q9NPA8-2;Q9NPA8;J3KNT2;E5RI00;E5RHT9;E5RJ84 E5RHX8 ENY2 Transcription and mRNA export factor ENY2 0 107.66 0.028344 182060000 429470 523900 480450 484850 595740 401910 595790 489190 609070 FALSE TRUE 402590.2393 562690.1011 491846.5009 497292.0718 548952.9835 517934.8925 506456.8205 550266.4483 507412.2823 0.793418396 1.10894064 0.969323207 0.980055251 1.081867749 1.020737792 0.998116991 1.084456304 1 18.95279892 4.751126837 24.96734283 1.027784319 0.793418247 0.712563571 0.047282394 1081.608524 2148967.636 0.010689116 0.19013019 56380.22918 -4.751126837 -0.234366072 LKETAENSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKETAENSLK 10 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 147.71 2.41E-05 1218390000 1307440 1050120 1080970 1121180 1385270 927680 1380800 1189740 1315210 FALSE TRUE 1225609.664 1127871.977 1106611.119 1149951.377 1276476.482 1195486.156 1173761.859 1338281.658 1095692.954 1.118570362 1.02936865 1.00996462 1.049519733 1.164994698 1.091077707 1.071250713 1.221402084 1 20.06341214 2.920958713 10.18145432 1.108867836 1.04008404 0.160192384 0.063753241 0.808110178 100.8825588 0.017800387 0.018893897 833.6019325 -2.920958713 -0.068783795 LKEVFSMAGVVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKEVFSMAGVVVR 13 1 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 119.31 0.00032716 111352000 311830 320540 293320 301550 409120 252820 358250 300380 418050 FALSE TRUE 292313.1169 344273.1151 300277.6889 309288.2835 376989.3655 325805.0298 304533.7383 337883.1042 348274.7543 0.83931756 0.988510108 0.862186206 0.888058292 1.082448156 0.935482764 0.874406584 0.970162494 1 18.40986637 LKEVLEYNAIGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKEVLEYNAIGGK 13 1 P14324-2;P14324;A0A087WVN4;A0A087X1D8 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 135.37 7.73E-05 246960000 588400 518850 538880 598670 591110 392450 691190 556270 732550 FALSE TRUE 551573.0943 557266.1939 551662.4881 614032.8857 544686.605 505743.9441 587552.4762 625721.534 610282.6725 0.903799369 0.913127996 0.903945848 1.006145043 0.892515271 0.828704413 0.962754642 1.025297886 1 19.2191181 1.485829413 6.264705419 1.007644823 0.910353794 0.506067615 0.042993211 0.114815222 10.8858406 0.024378193 0.010706549 30.60760956 -1.485829413 -0.097291028 LKEVVLQVEEERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKEVVLQVEEERR 13 2 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;A1L2Z2 Q7Z406 MYH14 Myosin-14 0 118.2 0.00025097 61650000 135880 147730 123390 145200 171060 101890 164570 145740 186470 FALSE TRUE 127375.5134 158668.0829 126316.8691 148926.0778 157625.6376 131303.989 139894.2563 163935.9598 155346.9524 0.819942145 1.021378794 0.813127436 0.958667522 1.014668362 0.845230543 0.900527845 1.055289192 1 17.24513441 1.243184926 24.99949633 1.027644617 0.913003745 0.302654377 0.073845993 127.6490182 690113.6688 0.049415601 0.016699259 17.50591948 -1.243184926 -0.114640872 LKFNFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKFNFK 6 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 106.29 0.029414 783490000 488954 641384 611386 661864 849920 445883 893420 791594 922730 FALSE TRUE 458351.2419 688872.7387 625888.3646 678848.5508 783170.7116 574602.1838 759459.9651 890426.2534 768720.4019 0.596252214 0.896129122 0.814195074 0.883089026 1.018797875 0.747478774 0.987953439 1.15832265 1 19.55209943 6.495561716 0.230091249 1.038851273 1.12E-11 0.492765617 0.111797531 23.97121714 0.569580019 0.160540597 8.147011035 3130125.252 -6.495561716 -1.038851273 LKFS(ph)DDEEEEEVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LKFSDDEEEEEVVK 14 1 Q5JSZ5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 LKFS(1)DDEEEEEVVK;LKFS(1)DDEEEEEVVK;LKFS(1)DDEEEEEVVK;LKFS(1)DDEEEEEVVK 230.06 6.37E-13 713019000 2358750 927400 1315650 1274580 1327070 947980 1707150 1152390 1511870 TRUE FALSE 2211120.048 996065.661 1346857.839 1307287.881 1222847.275 1221646.437 1451178.706 1296268.428 1259529.13 1.755513227 0.790823838 1.06933441 1.037917941 0.970876533 0.969923131 1.152159701 1.029169074 1 20.26445306 4.748806119 24.99748334 1.005715978 1.755513639 0.869265426 0.091764405 532.9034683 1300178.518 0.022971392 0.32230907 56079.75647 -4.748806119 0.749797662 LKFS(ph)DEEDGRDS(ph)DEEGAEGHR ddPTM_SK-BR-3_Pertuzumab_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 165.32 7.97E-12 4022970000 3404980 1906540 2364230 2214180 2280900 1942270 2913420 2132950 2576200 TRUE FALSE 3191868.38 2047702.205 2420310.652 2270999.607 2101767.315 2502971.819 2476579.718 2399253.503 2146215.577 1.487207722 0.954099032 1.127710878 1.058141424 0.979289936 1.166225726 1.153928685 1.117899585 1 21.03336356 4.749436008 24.82361669 1.077494358 1.487207981 0.758744422 0.073876915 759.7073535 1734032.746 0.017932059 0.268226071 56161.15205 -4.749436008 0.409713623 LKGDDLQAIKK ddPTM_SK-BR-3_Pertuzumab_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 ; 131.69 0.00011139 5377500000 4061400 2715690 3197530 3006270 3792200 2092230 4088700 3163700 5393400 FALSE TRUE 3807204.224 2916762.513 3273376.922 3083415.978 3494375.909 2696222.836 3475637.393 3558694.909 4493206.697 0.847324524 0.649149418 0.728516879 0.686239513 0.777702016 0.600066504 0.773531606 0.792016737 1 22.099314 0.81391154 1.570888558 0.999047471 0.710766643 0.615849786 0.068838872 0.385259049 1.730582935 0.057092806 0.016526195 6.514956799 -0.81391154 -0.288280829 LKGDNEKHS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKGDNEKHSPR 11 2 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 LKGDNEKHS(1)PR;LKGDNEKHS(1)PR 92.063 0.0053614 198806000 574690 363780 429560 405190 453550 330460 544160 417350 680560 TRUE FALSE 538721.1788 390714.6497 439749.3661 415587.8614 417930.0125 425858.4374 462568.2597 469457.0662 566970.1394 0.950175576 0.689127385 0.775612921 0.732997794 0.737128789 0.751112639 0.815860003 0.828010214 1 19.11291323 0.742939672 1.087242456 0.999324644 0.761321443 0.494416131 0.06974711 0.654179334 1.379196025 0.059338507 0.018740668 5.532732487 -0.742939672 -0.238003201 LKGEIDASVPELEGDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKGEIDASVPELEGDLR 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 155.11 1.03E-07 414330000 750430 664580 677920 661820 794600 539750 777130 634080 780770 FALSE TRUE 703461.9259 713786.1947 694000.5825 678803.4217 732195.3213 695567.0629 660606.571 713246.2838 650454.443 1.081492998 1.097365392 1.066947255 1.043583342 1.125667338 1.069355541 1.015607746 1.09653534 1 19.31108849 -5 0.127193374 0.749629775 1.105496725 0.375674949 0.030174909 149.9748537 1.213836744 9.510379984 0.23534158 1.00E-05 5 0.355866951 LKGEMMDLQHGSLFL ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKGEMMDLQHGSLFL 15 1 F5GZQ4 F5GZQ4 LDHA 0 84.874 0.0074422 194510000 185560 551500 540430 742520 788400 669660 708330 411710 719650 FALSE TRUE 173946.1308 592333.6338 553249.2548 761574.3203 726482.2443 862979.971 602122.4923 463112.8998 599535.7659 0.290134702 0.987987152 0.92279608 1.270273374 1.211741293 1.43941366 1.004314549 0.772452498 1 19.1934863 4.808471628 2.011288149 1.096715333 1.96E-29 0.63101499 0.189039716 0.647806068 2.451276442 0.049055786 1.388258016 64338.60323 -4.808471628 -1.096715333 LKGEMMDLQHGSLFLQTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LKGEMMDLQHGSLFLQTPK 19 1 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50;C9J7H8;F5H793 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 ;; 211.89 6.49E-17 699635000 787078 1445630 1370140 1455670 1743270 1099888 1901280 1635430 1809510 FALSE TRUE 737816.193 1552665.949 1402640.368 1493024.957 1606360.606 1417407.81 1616200.715 1839617.036 1507491.091 0.489433203 1.029966916 0.93044687 0.990403834 1.065585472 0.94024291 1.072112946 1.22031702 1 20.52371805 4.739088564 24.87483322 1.021915844 0.489433031 0.811666006 0.081897624 17.1021139 805560.7921 0.019038977 0.113037107 54838.87849 -4.739088564 -0.532482813 LKGEMMDLQHGSLFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 237.59 5.50E-20 4067040000 2761960 9016070 6390940 7572070 9428760 4880650 7984510 7699340 7751540 FALSE TRUE 2589093.854 9683629.204 6542536.115 7766382.136 8688263.223 6289614.424 6787306.85 8660619.547 6457757.897 0.400927674 1.499534259 1.01312812 1.202643744 1.345399342 0.973962562 1.051031482 1.341118649 1 22.62260192 4.754264593 24.69220161 1.175160964 0.400926993 0.661132266 0.174903592 1566.440767 2462949.744 0.040138284 0.995412474 56789.04861 -4.754264593 -0.774233971 LKGPDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKGPDVK 7 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 69.825 0.053526 488870000 345830 450610 246220 218530 554630 210690 298140 361000 600110 FALSE TRUE 324185.1176 483973.6333 252060.4547 224137.8498 511071.5971 271512.7827 253436.6748 406071.6447 499947.7641 0.648437979 0.9680484 0.504173581 0.448322537 1.02224999 0.543082302 0.506926309 0.812228144 1 18.93141784 -1.628661249 8.045331576 1.000333611 0.675821818 0.203185283 0.197801788 0.001141604 5.27E-05 0.184720553 0.043495956 0.023514663 1.628661249 -0.324511793 LKGSGNLEAIHIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKGSGNLEAIHIIK 14 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 131.53 3.35E-05 1334490000 5577800 5073700 5650600 5597500 6521700 4591500 7223300 5356100 7577200 FALSE TRUE 5228695.455 5449362.027 5784634.9 5741141.327 6009511.989 5916991.513 6140233.223 6024820.875 6312516.369 0.828306043 0.863263033 0.91637543 0.909485376 0.951999431 0.93734276 0.972707691 0.954424594 1 22.58978379 8 0.193894637 1.003766756 0.17911684 0.955277117 0.010717566 8.616445209 0.102019738 0.018126811 2.141167588 99999999.99 -8 -0.824649916 LKGTS(ph)PSSSSRPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKGTSPSSSSRPQR 14 2 H3BVG0;Q8N1F7;Q8N1F7-2 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 LKGT(0.008)S(0.334)PS(0.025)S(0.097)S(0.202)S(0.334)RPQR;LKGT(0.435)S(0.528)PS(0.037)SSSRPQR 120.9 9.27E-05 628910000 1183660 815760 1009000 937070 896340 661100 1153470 846350 1034990 TRUE FALSE 1109576.833 876159.7192 1032933.956 961116.8027 825945.0721 851948.8379 980517.8818 952018.6605 862243.4827 1.286848617 1.016139567 1.197960874 1.114669837 0.957902366 0.988060629 1.137170534 1.104118129 1 19.71773579 4.748837949 24.47160224 1.075641678 1.286848776 0.452941377 0.075921778 1127.221064 2683979.919 0.018297105 0.254056591 56083.86683 -4.748837949 0.211207098 LKGVIDLIFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKGVIDLIFEK 11 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 114.82 0.00081704 0 145770 166820 137420 155640 213380 101500 152630 176250 156910 FALSE TRUE 136646.5159 179171.5264 140679.6673 159633.9859 196621.9955 130801.4023 129744.5484 198255.2005 130720.7073 1.045331828 1.370643795 1.076185022 1.221183615 1.504138094 1.000617308 0.992532485 1.516631944 1 16.99612817 -1.022426235 4.785921689 0.99999579 1.200829378 0.10322916 0.195552449 8.26E-06 1.69E-06 0.178013329 0.041957265 0.094967229 1.022426235 0.200833587 LKLEDFFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKLEDFFAR 9 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 162.36 5.82E-05 9203000000 7212600 7755300 6654800 6261400 8928100 4785800 7998100 7436500 10367600 FALSE TRUE 6761176.241 8329510.481 6812654.999 6422078.125 8226923.04 6167382.769 6798859.156 8364963.395 8637180.583 0.78279899 0.96437841 0.788759125 0.743538712 0.952500988 0.71405046 0.787161863 0.968483096 1 23.04212902 1.167855912 6.084653825 0.992560798 0.825369788 0.415840578 0.081311148 0.218873573 13.70249476 0.075393444 0.019166394 14.71824108 -1.167855912 -0.16719101 LKLEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKLEDR 6 1 Q9C0C9 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 0 70.912 0.081731 86258000 240240 239250 243380 229270 246650 181110 285590 204080 275650 FALSE TRUE 225203.8072 256964.3189 249153.0885 235153.4564 227279.1039 233393.5169 242768.4308 229559.8372 229642.2342 0.980672427 1.118976741 1.08496196 1.023999166 0.989709514 1.016335334 1.057159331 0.999641194 1 17.80902847 3.209256919 7.469520451 1.018814841 1.077210986 0.201630599 0.039709794 0.215327584 41.72960078 0.011086232 0.013512084 1619.037542 -3.209256919 0.058396145 LKLGEIVTTIPTIGFNVETVEYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKLGEIVTTIPTIGFNVETVEYK 23 1 P61204;F5H423;F5H0C7;P84077;P84085;C9J1Z8;P18085;C9JPM4 P61204;P84077;P84085;P18085 ARF3;ARF1;ARF5;ARF4 ADP-ribosylation factor 3;ADP-ribosylation factor 1;ADP-ribosylation factor 5;ADP-ribosylation factor 4 0 ; 175.86 9.40E-13 386630000 952480 690670 819860 855950 968630 644810 1104170 748560 1037400 FALSE TRUE 892865.977 741807.9254 839307.4664 877915.1261 892557.7071 830956.1794 938609.9591 842019.3638 864251.2381 1.033109283 0.8583244 0.971138286 1.015810088 1.032752593 0.961475255 1.086038316 0.974276144 1 19.72109124 3.435815767 3.088537064 1.018294863 0.928375203 0.190479057 0.053961073 0.254163464 4.918760243 0.014169842 0.021045981 2727.820364 -3.435815767 -0.08991966 LKLS(ph)PS(ph)PSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LKLSPSPSSR 10 1 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 2 LKLS(1)PS(0.997)PS(0.003)SR;LKLS(0.939)PS(0.668)PS(0.387)S(0.006)R;LKLS(1)PS(0.974)PS(0.025)S(0.001)R 98.105 0.0073231 900480000 2161760 1357850 1630080 1537710 1642870 1152580 2137630 1389580 1705440 TRUE FALSE 2026459.3 1458386.627 1668746.267 1577170.242 1513845.617 1485311.135 1817112.226 1563072.122 1420791.046 1.426289464 1.02646102 1.174519133 1.11006488 1.065494902 1.045411385 1.27894403 1.100142154 1 20.43826296 4.748837535 24.83981189 1.115312614 1.426289653 0.610721271 0.081033556 966.4004894 2335786.235 0.018968175 0.263486851 56083.81337 -4.748837535 0.310977038 LKLS(ph)PSPS(ph)SR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LKLSPSPSSR 10 1 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 2 LKLS(0.858)PS(0.275)PS(0.644)S(0.223)R;LKLS(0.977)PS(0.097)PS(0.864)S(0.063)R;LKLS(0.996)PS(0.016)PS(0.917)S(0.071)R 153 0.00020364 1578550000 2608410 1610920 1959470 1798130 1857150 1367170 2404220 1607050 1987760 TRUE FALSE 2445154.274 1730194.193 2005949.554 1844273.06 1711296.93 1761849.785 2043729.531 1807693.73 1655990.015 1.47655134 1.044809557 1.211329498 1.113698177 1.033398097 1.063925368 1.234143632 1.091609076 1 20.65926254 4.745478542 24.95137251 1.115608564 1.47655151 0.706906323 0.07571896 457.279205 1649258.67 0.01745325 0.174431077 55651.71364 -4.745478542 0.360942946 LKLS(ph)PSPSS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKLSPSPSSR 10 1 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 2 LKLS(0.991)PS(0.034)PS(0.15)S(0.825)R 126.56 0.0045344 793610000 1379600 892560 1045100 961440 968130 729040 1279200 795170 1021300 TRUE FALSE 1293253.299 958646.0711 1069890.266 986112.1781 892096.975 939502.013 1087395.836 894448.7249 850838.4321 1.51997518 1.126707533 1.257454089 1.158988758 1.048491631 1.104207306 1.278028583 1.051255669 1 19.69852568 4.740934987 24.93425603 1.151765903 1.519975313 0.641244555 0.090587554 137.1218837 1439882.62 0.020475639 0.137374693 55072.5248 -4.740934987 0.368209411 LKLS(ph)PSPSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LKLSPSPSSR 10 1 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 1 LKLS(0.939)PS(0.06)PS(0.001)SR;LKLS(0.862)PS(0.136)PS(0.002)SR;LKLS(0.499)PS(0.499)PS(0.002)SR;LKLS(0.77)PS(0.229)PS(0.001)SR;LKLS(0.977)PS(0.023)PSSR;LKLS(0.881)PS(0.119)PSSR 175.88 1.61E-06 11835870000 17430900 13382210 14499790 13528580 14319510 10158260 18574610 12588720 13420930 TRUE FALSE 16339931.08 14373042.75 14843731.87 13875746.27 13194913.45 13090784.76 15789519.67 14160449.4 11180890.08 1.461415949 1.285500765 1.327598408 1.241023404 1.180130862 1.170817767 1.412188078 1.266486774 1 23.41453171 -3.888120373 0.273385328 2.72E-31 1.316850033 0.522273129 0.089610948 95.92705878 1.628894423 54.18296952 0.10912042 0.000129384 3.888120373 1.316850033 LKLSPS(ph)PSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKLSPSPSSR 10 1 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 1 LKLS(0.416)PS(0.584)PSSR 157.56 5.42E-06 1219000000 2483000 1888600 2200500 2100200 2000400 1428800 2565600 2011400 1778500 TRUE FALSE 2327593.462 2028433.909 2252696.899 2154094.688 1843296.653 1841271.365 2180912.098 2262527.718 1481656.86 1.570939618 1.369030822 1.520390422 1.453841807 1.244077966 1.242711058 1.471941416 1.527025439 1 20.49877994 -1.844422596 2.757917125 0.843725735 1.419721647 0.586237465 0.112130521 76875265.97 47517410.35 78949044.09 0.026719555 0.01430795 1.844422596 0.575995912 LKNEITR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKNEITR 7 1 Q86VP6 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 121.05 0.004082 1430160000 1959700 2198870 2019000 2093830 2503600 1711380 2455270 2313420 2362250 FALSE TRUE 1837045.875 2361676.623 2066891.633 2147561.223 2306977.355 2205427.624 2087125.057 2602255.579 1967975.214 0.933470026 1.200054048 1.050263041 1.091254202 1.172259355 1.120658232 1.060544382 1.322300993 1 20.90828062 2.954702333 21.66941339 1.131157618 1.087097925 0.078663389 0.104478257 350.7407884 167785.482 0.029143696 0.030914983 900.9534085 -2.954702333 -0.044059693 LKNGFPHPEPDCNPSEAAS(ph)EES(ph)NSEIEQEIPVEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKNGFPHPEPDCNPSEAASEESNSEIEQEIPVEQK 35 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 2 LKNGFPHPEPDCNPS(0.004)EAAS(0.876)EES(0.62)NS(0.499)EIEQEIPVEQK 164.28 1.69E-14 464290000 352830 216660 254900 247700 262030 253930 441260 199980 411980 TRUE FALSE 330747.0001 232701.7318 260946.3484 254056.4014 241451.2208 327235.4688 375097.1595 224947.9432 343217.8765 0.96366484 0.678000034 0.760293581 0.740219023 0.703492555 0.953433638 1.092883515 0.655408586 1 18.38876517 2.229851564 24.96755074 0.951007398 0.754186815 0.237388045 0.134330205 203.6257759 583759.8647 0.0461284 0.034592469 169.7663314 -2.229851564 -0.196820582 LKNGFPHPEPDCNPSEAASEES(ph)NS(ph)EIEQEIPVEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LKNGFPHPEPDCNPSEAASEESNSEIEQEIPVEQK 35 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 2 LKNGFPHPEPDCNPS(0.023)EAAS(0.59)EES(0.697)NS(0.69)EIEQEIPVEQK;LKNGFPHPEPDCNPS(0.006)EAAS(0.608)EES(0.732)NS(0.654)EIEQEIPVEQK;LKNGFPHPEPDCNPS(0.182)EAAS(0.593)EES(0.632)NS(0.593)EIEQEIPVEQK 124.33 6.58E-08 680060000 434310 259518 334670 316178 299468 282745 521558 243717 507043 TRUE FALSE 407127.3124 278732.9827 342608.5304 324291.6628 275948.9913 364368.8915 443355.2198 274145.6039 422414.2477 0.963810559 0.659856963 0.811072383 0.767710049 0.653266297 0.862586652 1.049574493 0.648997058 1 18.68829897 2.011278515 23.48800042 0.917794243 0.760979101 0.160930579 0.134122136 140.7718894 293161.1779 0.045503091 0.03356845 102.6309892 -2.011278515 -0.156815142 LKNGFPHPEPDCNPSEAASEES(ph)NSEIEQEIPVEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKNGFPHPEPDCNPSEAASEESNSEIEQEIPVEQK 35 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 LKNGFPHPEPDCNPSEAAS(0.021)EES(0.489)NS(0.489)EIEQEIPVEQK 166.28 6.44E-15 576780000 325010 212090 296670 269450 306700 261610 458450 228080 453050 TRUE FALSE 304668.2043 227793.3643 303707.1525 276364.5432 282613.0192 337132.5601 389709.6785 256556.2901 377433.0282 0.807211297 0.603533203 0.804665013 0.732221408 0.748776599 0.89322485 1.032526699 0.679739903 1 18.52586115 2.234304919 4.250366404 0.920317681 0.727624721 0.353892433 0.107828554 0.190249689 8.026900406 0.037951965 0.029024513 171.5161105 -2.234304919 -0.192692959 LKNGFPHPEPDCNPSEAASEESNS(ph)EIEQEIPVEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKNGFPHPEPDCNPSEAASEESNSEIEQEIPVEQK 35 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 LKNGFPHPEPDCNPSEAAS(0.001)EES(0.027)NS(0.971)EIEQEIPVEQK 193.6 2.85E-21 185670000 110450 73793 89745 70959 94206 80261 134760 65868 122460 TRUE FALSE 103537.1317 79256.7105 91873.79378 72779.92807 86807.44077 103431.0478 114553.9891 74091.76479 102020.6349 1.014864608 0.776869411 0.900541286 0.713384387 0.850881205 1.013824781 1.122851168 0.72624293 1 16.63850146 2.249347606 16.18254312 0.993056676 0.841598374 0.152264727 0.125930317 4.020644783 6030.779942 0.041153328 0.033736447 177.5610098 -2.249347606 -0.151458302 LKNWEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKNWEIR 7 1 P49756 P49756 RBM25 RNA-binding protein 25 0 71.501 0.04938 335400000 419920 539840 436320 429450 595880 330090 548890 492510 704420 FALSE TRUE 393637.9568 579810.3153 446669.7164 440470.4141 549081.9885 425381.6244 466589.0401 554000.9576 586847.7513 0.670766746 0.988008072 0.761133898 0.750570166 0.935646404 0.724858575 0.795076814 0.944028424 1 19.16262674 1.110925203 4.29557293 0.996582813 0.815602015 0.353110454 0.095013589 0.22934049 6.875467053 0.084582643 0.021702842 12.90996911 -1.110925203 -0.180980799 LKPAFIKPYGTVTAANSSFLTDGASAMLIMAEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKPAFIKPYGTVTAANSSFLTDGASAMLIMAEEK 34 2 P55084-2;P55084;B5MD38;F5GZQ3 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 194.98 1.47E-21 139120000 210230 136490 135790 114370 239110 111860 153870 185280 218530 FALSE TRUE 197072.0796 146595.8616 139011.0029 117304.9278 220331.2651 144152.1661 130798.622 208412.6159 182055.9312 1.082480962 0.80522431 0.763562066 0.644334557 1.210239423 0.791801537 0.718452956 1.144772458 1 17.47402222 LKPEGLHQLLAGFEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKPEGLHQLLAGFEDK 16 1 Q9BY32;Q9BY32-3;Q9BY32-2 Q9BY32 ITPA Inosine triphosphate pyrophosphatase 0 ; 217.88 8.32E-15 785700000 3203900 2146600 2591000 2407040 2758120 1838110 3372100 2322960 2913510 FALSE TRUE 3003373.618 2305536.498 2652459.744 2468808.722 2541508.381 2368742.518 2866484.91 2612986.669 2427226.359 1.237368574 0.949864642 1.092794553 1.017131638 1.04708338 0.975905073 1.180971399 1.076531927 1 21.21087723 1.744181724 25 1.103189541 1.044331588 0.009945505 0.089053212 2.65758238 11863.21474 0.036671247 0.020335983 55.48578368 -1.744181724 -0.058857953 LKPEYDIMCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKPEYDIMCK 10 1 J3KQ32;Q9NTK5;Q9NTK5-3;Q9NTK5-2;C9JCJ9 J3KQ32 OLA1 Obg-like ATPase 1 0 143.17 3.14E-05 322550000 881370 832720 746350 701360 1000500 564370 971800 804330 1044100 FALSE TRUE 826206.625 894375.4552 764053.7745 719358.085 921924.7658 727294.4572 826087.6117 904752.371 869832.9649 0.949845152 1.028215176 0.878391375 0.827007154 1.059887131 0.836131173 0.949708329 1.040144956 1 19.73037886 1.318974865 6.234837275 1.019276896 0.93285615 0.194059795 0.074511147 0.317062016 18.52403195 0.04905115 0.017456975 20.84370245 -1.318974865 -0.086420746 LKPEYLEELPTMMQHFSQFLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKPEYLEELPTMMQHFSQFLGK 22 1 A0A0A0MR85;Q03013-3;Q03013-2;Q03013;A6NNT0 A0A0A0MR85 GSTM4 Glutathione S-transferase Mu 4 0 81.356 0.0032992 25195000 57168 82012 77434 82473 96372 106630 88691 75551 99301 FALSE TRUE 53589.95693 88084.25381 79270.77105 84589.39681 88803.33187 137412.35 75392.60792 84983.70866 82727.02159 0.647792655 1.064757949 0.95822102 1.022512296 1.073450127 1.661033449 0.911341983 1.027278718 1 16.33607102 2.86663108 2.668016829 1.155301215 0.940347801 0.183821178 0.226667128 0.520546146 7.213616081 0.071979297 0.077560593 735.5819767 -2.86663108 -0.214953414 LKPGGVGAPSSS(ph)SPSPSPSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKPGGVGAPSSSSPSPSPSAR 21 1 Q92797 Q92797 SYMPK Symplekin 1 LKPGGVGAPS(0.003)S(0.012)S(0.491)S(0.491)PS(0.002)PSPSAR 132.35 7.08E-06 362620000 258530 215160 215950 230130 251030 199270 305380 252570 222950 TRUE FALSE 242349.0688 231090.6703 221072.436 236035.5254 231315.1164 256796.0141 259591.104 284103.9205 185738.2047 1.304788475 1.244174136 1.190236744 1.27079685 1.245382536 1.382569701 1.397618247 1.529593338 1 17.50291107 2.244468754 24.04043249 1.365333885 1.242734774 0.039023788 0.13711011 148.3916856 603813.0317 0.042566456 0.034696132 175.5774569 -2.244468754 -0.12259911 LKPGGVGAPSSSS(ph)PSPSPSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LKPGGVGAPSSSSPSPSPSAR 21 1 Q92797 Q92797 SYMPK Symplekin 1 LKPGGVGAPSSS(0.004)S(0.761)PS(0.216)PS(0.018)PS(0.001)AR;LKPGGVGAPSSS(0.008)S(0.991)PS(0.001)PSPSAR;LKPGGVGAPSS(0.002)S(0.033)S(0.932)PS(0.033)PSPSAR 198.93 5.02E-22 1582540000 1065860 941680 977190 1017170 1050990 885370 1350760 1125070 932270 TRUE FALSE 999149.7252 1011402.967 1000369.408 1043272.304 968449.4849 1140961.946 1148226.078 1265537.466 776668.1143 1.286456476 1.302233153 1.28802688 1.343266558 1.246928343 1.469046978 1.47839992 1.629444344 1 19.56693871 2.233644108 24.99999999 1.440085519 1.2961264 0.056398648 0.162165162 208.0525255 1057916.626 0.051995031 0.039610971 171.2553343 -2.233644108 -0.143959118 LKPGYLEATVDWFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKPGYLEATVDWFR 14 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 235.22 2.85E-17 4752800000 6100000 9685200 6209400 5402900 10137000 3844100 6967600 8925500 8617100 FALSE TRUE 5718211.889 10402302.29 6356689.9 5541547.561 9340880.911 4953829.266 5922873.064 10039868.32 7178850.341 0.796535882 1.449020636 0.885474637 0.771926882 1.301166686 0.690058858 0.825044789 1.398534284 1 22.77532139 3.739491147 23.43680366 0.95336202 1.168743426 0.0308677 0.271157313 391.4945151 741740.5792 0.064136508 0.114417128 5488.973666 -3.739491147 0.215381405 LKPKPIDVQVITHHMQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LKPKPIDVQVITHHMQR 17 2 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ;; 124.29 1.63E-05 1252660000 3299210 3002880 2930640 2680070 3479960 2107550 3562040 2866190 3127570 FALSE TRUE 3092718.335 3225216.36 3000156.165 2748845.134 3206657.979 2715965.472 3027945.17 3224040.131 2605558.362 1.186969511 1.237821577 1.151444623 1.054992732 1.230698965 1.042373685 1.162109901 1.237370146 1 21.31316114 -5 0.172782832 0.403920954 1.197484698 0.319374751 0.070780561 156.654153 1.48788406 32.48032178 0.230806356 1.00E-05 5 0.793563744 LKPLEVELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKPLEVELR 9 1 P49755 P49755 TMED10 Transmembrane emp24 domain-containing protein 10 0 83.397 0.014772 321540000 360550 740500 350620 424430 900800 291280 453400 765130 490010 FALSE TRUE 337983.8191 795327.3905 358936.872 435321.5924 830054.8017 375367.8075 385416.8792 860658.1648 408224.1654 0.827936824 1.948261416 0.879264145 1.066378792 2.03333088 0.919513932 0.944130485 2.108297935 1 18.63900206 -1.451381487 4.313624202 0.998626012 1.319534075 0.041054755 0.508537053 0.006167124 0.000784352 0.451899298 0.106077659 0.035368652 1.451381487 0.320908063 LKPNLGNGADLPNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKPNLGNGADLPNYR 15 1 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 ; 226.93 7.29E-13 2547400000 3986300 3855300 3903500 3832300 4362800 3494700 4970300 3961900 4622800 FALSE TRUE 3736804.599 4140750.423 3996092.863 3930643.306 4020163.287 4503563.158 4225049.657 4456551.936 3851224.816 0.970289915 1.07517754 1.037616097 1.020621619 1.043866167 1.169384644 1.097066481 1.15717782 1 21.87688591 2.363631983 8.545205193 1.114008639 1.03573878 0.341014828 0.051954241 0.257663312 18.3183562 0.015937891 0.01331455 231.0106398 -2.363631983 -0.078269859 LKPPVHYNGPSK ddPTM_SK-BR-3_Pertuzumab_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 ; 113.24 0.0007133 658390000 1230100 1261920 1049380 1046030 1398850 826330 1395820 1246120 1665010 FALSE TRUE 1153110.237 1355353.87 1074271.789 1072872.901 1288989.964 1064878.057 1186529.749 1401700.825 1387109.075 0.831304659 0.977106916 0.774468143 0.773459651 0.929263594 0.767695977 0.855397583 1.010519541 1 20.40364981 1.247320695 8.561628825 1.005755384 0.847316734 0.495775558 0.067517873 0.100762545 62.49411168 0.049366007 0.016163342 17.67342395 -1.247320695 -0.15843865 LKPQYLEELPGQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKPQYLEELPGQLK 14 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 200 1.81E-08 2149280000 4685900 3483100 4503000 4128400 4806000 3547900 5014900 4247400 6238600 FALSE TRUE 4392617.884 3740992.348 4609813.286 4234341.733 4428556.146 4572121.135 4262962.301 4777697.24 5197337.357 0.845166973 0.719790172 0.886956718 0.814713659 0.852081718 0.879704514 0.820220434 0.919258634 1 22.30934128 -5 0.098233619 1.562776163 0.710571433 0.613063241 0.045333197 118.5229087 0.795815127 13.54247186 0.754023896 1.00E-05 5 -0.852204729 LKPVELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKPVELR 7 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 98.997 0.0098974 1886260000 5548700 5978900 5537100 5862100 5860500 4337300 7172500 5561900 5726800 FALSE TRUE 5201416.772 6421583.977 5668442.627 6012531.411 5400239.97 5589408.1 6097050.211 6256315.458 4770960.083 1.090224332 1.345973109 1.188113614 1.260235111 1.131897957 1.171547865 1.277950372 1.311332593 1 22.18584819 3.72427511 24.54929706 1.206444745 1.245569549 0 0.106953474 466.2126859 4021369.172 0.025639417 0.041872741 5299.990729 -3.72427511 0.039124805 LKPVPVAQENQGVFFSGDSYLVLHNGPEEVSHLHLWIGQQSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKPVPVAQENQGVFFSGDSYLVLHNGPEEVSHLHLWIGQQSSR 43 1 P40121-2;P40121;E7ENU9;B8ZZL6 P40121-2 CAPG Macrophage-capping protein 0 113.98 7.24E-07 71407000 9803.1 13880 7693.1 5841.9 17819 7983.6 8123.8 13647 6683.7 FALSE TRUE 9189.54147 14907.68964 7875.583965 5991.813044 16419.56762 10288.33572 6905.711608 15350.85799 5568.147292 1.650376865 2.677315965 1.41439936 1.076087382 2.948838592 1.847712565 1.240217122 2.756905877 1 12.44298166 -1.195507495 3.623450482 0.998907163 1.916881797 0.171475831 0.653362552 299813535.6 527720085.9 3878770.349 0.148117769 0.063751808 1.195507495 0.917974634 LKQEYFVVAATLQDIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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" 0 216.96 4.67E-15 382150000 1210100 1882500 1259200 1185600 2123400 848760 1575700 1762600 1482200 FALSE TRUE 1134362.001 2021882.259 1289068.819 1216024.503 1956636.729 1093783.234 1339438.413 1982664.49 1234811.245 0.918652147 1.637401884 1.043939974 0.984785738 1.58456342 0.885789823 1.084731305 1.605641752 1 20.2358591 3.754403675 23.74198274 1.160700698 1.332757834 0.014396785 0.296961439 630.1283347 548350.3846 0.069589959 0.125401881 5680.723806 -3.754403675 0.172057137 LKQFEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKQFEER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 105.57 0.0072026 316470000 651960 716920 661330 674340 846500 513200 752480 690470 1060520 FALSE TRUE 611154.9874 770001.5028 677017.0599 691644.7061 780019.3046 661352.5089 639652.6097 776676.6994 883512.3608 0.691733375 0.871523181 0.766279104 0.782835348 0.88286179 0.748549243 0.723988297 0.879078476 1 19.75289079 0.979614366 5.745143447 0.999918933 0.787630058 0.594438558 0.05906445 0.1077052 15.88923229 0.054625332 0.013752376 9.541449724 -0.979614366 -0.212288875 LKQNLEEQLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKQNLEEQLDR 11 1 Q8WZA0-2;Q8WZA0 Q8WZA0-2 LZIC Protein LZIC 0 106.17 0.0021586 69463000 155940 164460 176600 171880 211030 133950 214940 176250 222560 FALSE TRUE 146179.9938 176636.7895 180789.0354 176290.7318 194456.5551 172619.1905 182711.7424 198255.2005 185413.2982 0.788400806 0.952665161 0.975059703 0.950798748 1.048773507 0.930996817 0.985429547 1.069260956 1 17.5003852 5.533361049 1.117984418 0.990492357 9.86E-15 0.705268416 0.041384758 4.506268479 1.263685337 0.010934366 8.059788573 341476.679 -5.533361049 -0.990492357 LKQSAEEQAQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKQSAEEQAQAR 12 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 186.16 1.11E-05 518150000 594590 818680 754810 869270 1029820 595540 1018320 779830 1274620 FALSE TRUE 557375.6733 879295.919 772714.4496 891576.9399 948942.0913 767462.7302 865632.3696 877193.4921 1061877.688 0.524896304 0.828057628 0.727686869 0.83962301 0.893645382 0.722741177 0.81519028 0.826077713 1 20.01818617 1.972338586 0.041086128 1.634354133 1.78E-13 0.513888965 0.086604498 66.44025474 2.134429052 40.28027775 43.56553241 93.82932362 -1.972338586 -1.634354133 LKQVEDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LKQVEDEK 8 1 P35579 P35579 MYH9 Myosin-9 0 ;; 136.33 0.00072577 1465960000 3173790 1964680 2391490 2354840 2469120 1823220 3385150 2226160 2761190 FALSE TRUE 2975148.149 2110146.951 2448217.272 2415269.181 2275205.275 2349554.016 2877578.184 2504100.976 2300329.551 1.293357357 0.917323759 1.064289798 1.049966593 0.989077967 1.021398875 1.250941711 1.088583579 1 21.13340913 LKS(ph)DERPVHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LKSDERPVHIK 11 2 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 1 LKS(1)DERPVHIK;LKS(1)DERPVHIK;LKS(1)DERPVHIK;LKS(1)DERPVHIK 129.38 0.00012848 2654320000 7661300 4261410 5415100 7455600 8217400 3351200 4767190 3159110 6767300 TRUE FALSE 7181792.909 4576929.23 5543548.729 7646923.318 7572038.551 4318637.038 4052394.116 3553531.838 5637793.912 1.27386581 0.811829822 0.983283323 1.356368012 1.343085375 0.766015414 0.71879075 0.630305381 1 22.42669931 2.144067438 9.909123598 0.749998601 1.092840735 0.465543388 0.19255866 0.33947286 32.76523981 0.076983722 0.056851361 139.3373153 -2.144067438 0.342842134 LKS(ph)EDELRPEVDEHTQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 190.19 1.63E-10 1478700000 1209100 502220 755460 980340 833320 482680 693600 328960 475580 TRUE FALSE 1133424.589 539404.8914 773379.868 1005497.184 767874.4087 622021.8803 589601.1191 370031.3801 396202.6256 2.860719531 1.361436943 1.951980673 2.537835741 1.938085108 1.569959006 1.488130267 0.933944795 1 18.59587892 1.653518538 1.366925831 0.959511157 2.013934044 0.556576844 0.409868645 0.343185015 1.233604351 0.339238466 0.124609605 45.03172028 -1.653518538 1.054422887 LKS(ph)EDGVEGDLGETQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LKSEDGVEGDLGETQSR 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LKS(1)EDGVEGDLGETQSR;LKS(1)EDGVEGDLGETQSR;LKS(1)EDGVEGDLGETQSR;LKS(1)EDGVEGDLGETQSR 321.95 7.18E-59 3966550000 4581570 3165740 3867470 6640740 5823960 1734460 2287900 1124540 1320190 TRUE FALSE 4294817.712 3400134.684 3959208.215 6811152.631 5366569.674 2235170.445 1944850.635 1264941.294 1099841.76 3.904941481 3.091476253 3.599798042 6.192847805 4.879401627 2.032265482 1.768300409 1.15011208 1 20.06886454 2.12575842 5.098721724 1.513665141 4.142751561 0.728168289 0.864542224 0.137654504 5.606482079 0.372867081 0.272027274 133.5852231 -2.12575842 2.62908642 LKS(ph)IEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKSIEER 7 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 LKS(1)IEER 104.82 0.004884 354820000 833640 703820 676850 1049800 1386300 698110 778650 693430 1352800 TRUE FALSE 781463.9605 755931.5651 692905.2016 1076739.645 1277425.59 899643.0241 661898.6611 780006.2619 1127008.941 0.693396416 0.670741409 0.614817839 0.955395833 1.133465356 0.79825722 0.587305599 0.692102994 1 20.10406753 3.256298803 24.99340419 0.831758934 0.655623314 0.258076972 0.155749797 410.5623499 578485.6212 0.047783225 0.064561111 1804.258679 -3.256298803 -0.17613562 LKS(ph)IS(ph)REPS(ph)PALGPNLDGSGLLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKSISREPSPALGPNLDGSGLLPR 24 2 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 3 LKS(1)IS(1)REPS(1)PALGPNLDGSGLLPR 153.63 5.47E-08 33889000 70414 59773 59467 60401 67120 48424 75960 64273 73218 TRUE FALSE 66006.91343 64198.65511 60877.58532 61950.99192 61848.66595 62403.2227 64570.50318 72297.62553 60997.44279 1.082125912 1.052481091 0.998035041 1.015632608 1.013955063 1.023046538 1.058577216 1.185256664 1 15.89646114 1.485620013 5.934620895 1.101887366 1.029338424 0.200508793 0.04966306 0.170850395 14.15271097 0.026032828 0.011288674 30.59285536 -1.485620013 -0.072548942 LKS(ph)ISREPS(ph)PALGPNLDGSGLLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKSISREPSPALGPNLDGSGLLPR 24 2 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 2 LKS(0.968)IS(0.065)REPS(0.968)PALGPNLDGSGLLPR 169.39 4.97E-12 46245000 19422 20370 19156 25029 27939 13104 24355 17673 29658 TRUE FALSE 18206.41169 21878.21599 19610.38937 25671.28651 25744.78364 16886.91207 20703.19385 19879.51295 24707.8882 0.736866362 0.885474947 0.793689416 1.038991528 1.04196617 0.68346238 0.837918388 0.80458163 1 14.59268409 -2.61101202 2.077803666 3.735494069 0.852980357 0.138515252 0.115313689 5856662.985 232055.7246 76048369.15 0.028625318 0.002448995 2.61101202 -2.882513712 LKS(ph)PSMAVPSPGWVASPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKSPSMAVPSPGWVASPK 18 1 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 LKS(0.956)PS(0.044)MAVPSPGWVASPK 134.66 6.10E-06 369420000 595520 438870 548470 520450 528990 309640 542070 371550 565300 TRUE FALSE 558247.4662 471364.3914 561479.9674 533805.6281 487445.2592 399028.0414 460791.6358 417938.8354 470947.778 1.185370209 1.000884628 1.19223403 1.133470956 1.035030383 0.847287237 0.978434674 0.887441994 1 18.84520757 2.463483603 4.972124024 0.929217847 1.115333316 0.661902755 0.066943564 0.11025873 7.638666477 0.021906639 0.01886587 290.7258191 -2.463483603 0.18611547 LKS(ph)PSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LKSPSQK 7 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 LKS(0.633)PS(0.367)QK;LKS(0.859)PS(0.141)QK;LKS(0.977)PS(0.023)QK;LKS(0.883)PS(0.117)QK 106.18 0.0046998 1271550000 3286840 1962560 2522410 2391530 2426820 1895540 3095000 2272530 2946530 TRUE FALSE 3081122.552 2107869.984 2582242.756 2452900.709 2236227.347 2442751.626 2630933.483 2556260.373 2454735.108 1.255175168 0.858695497 1.051943547 0.99925271 0.910985197 0.995118218 1.071778977 1.041358949 1 21.22713592 1.760537429 24.99999259 1.044464277 0.994448663 0 0.105111253 37.8559789 43098.28218 0.044179746 0.024499855 57.61524716 -1.760537429 -0.050015614 LKS(ph)VEDEMDSPGEEPFYTGQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKSVEDEMDSPGEEPFYTGQGR 22 1 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;A0A590UJA3;S4R3W2;A0A590UK73;B1AKN7 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 1 LKS(1)VEDEMDSPGEEPFYTGQGR 184.66 2.32E-17 67422000 106030 62630 85447 108700 135380 52397 71905 52830 117370 TRUE FALSE 99393.77157 67267.19037 87473.84319 111489.426 124747.8009 67523.16331 61123.51278 59425.94179 97780.18876 1.016502145 0.687942938 0.894596792 1.140204651 1.275798324 0.690560779 0.625111421 0.607750328 1 16.57725457 5.17428932 8.097242061 0.848386966 5.350646467 0.038470905 0.223947542 35478.27918 39744.36201 0.056945357 2797803.732 149378.9218 -5.17428932 4.502259501 LKSDEDEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKSDEDEER 9 1 Q96AY3;H0Y827;Q96AY3-2 Q96AY3 FKBP10 Peptidyl-prolyl cis-trans isomerase FKBP10 0 ; 147.91 8.32E-05 830940000 1534010 1212990 1296630 1311340 1290330 919730 1634130 1183830 1282700 FALSE TRUE 1437999.052 1302801.042 1327386.676 1344991.204 1188992.687 1185241.12 1389107.377 1331633.781 1068609.083 1.345673619 1.219155875 1.24216301 1.258637256 1.112654483 1.109143782 1.299920989 1.246137434 1 20.02730275 -4.306007514 0.272939786 2.51E-32 1.243722519 0.497660482 0.072693862 129.2581507 1.784657045 72.6875459 0.087752782 4.94E-05 4.306007514 1.243722519 LKSDGIPMYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKSDGIPMYK 10 1 Q9UGI8-2;Q9UGI8 Q9UGI8-2 TES Testin 0 109.6 0.0018215 413790000 1703500 1633000 1597400 1691700 2152800 1123300 1987200 1804800 2504000 FALSE TRUE 1596880.976 1753909.019 1635291.082 1735111.886 1983727.772 1447578.475 1689237.808 2030133.253 2086066.224 0.765498697 0.840773413 0.783911395 0.83176261 0.950941897 0.693927383 0.809771899 0.973187347 1 20.99235353 1.218797945 6.080264777 0.99135186 0.810436085 0.561362972 0.064653514 0.117219683 14.26397004 0.052672266 0.014696508 16.54999799 -1.218797945 -0.180915775 LKSEDEPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LKSEDEPTR 9 1 O14787-2;O14787;A0A075B780;K7ENW1;K7ESC1;E7EW37;Q92973-2;Q92973 O14787-2;Q92973-2 TNPO2;TNPO1 Transportin-2;Transportin-1 0 ;; 117.02 0.0011117 1223980000 1978010 2036870 2005370 2036070 2206230 1515750 2467310 1973890 2552510 FALSE TRUE 1854209.885 2187681.974 2052938.323 2088319.003 2032961.595 1953322.419 2097359.771 2220334.512 2126479.591 0.871962229 1.028781082 0.965416424 0.982054571 0.956022152 0.918570969 0.98630609 1.04413629 1 21.02003558 1.448783356 7.152532048 1.02045337 0.96415041 0.28895442 0.042325669 0.231177568 29.2373261 0.024224844 0.010086632 28.10498488 -1.448783356 -0.05630296 LKSEDGVEGDLGETQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LKSEDGVEGDLGETQSR 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 218.79 4.14E-15 1146650000 822940 702450 770900 691950 921810 583964 900030 709930 1317700 FALSE TRUE 771433.6544 754460.1289 789186.112 709706.6085 849414.761 752544.9269 765078.857 798566.3232 1097767.357 0.702729635 0.687267775 0.718901056 0.646500011 0.77376573 0.685523141 0.696940797 0.727445864 1 20.06614092 0.663810875 3.010433588 0.999996498 0.701651553 0.896098472 0.031697091 1.03204955 8.939800956 0.026626118 0.006958771 4.611167249 -0.663810875 -0.298344945 LKT(ph)PSTPVACSTPAQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKTPSTPVACSTPAQLK 17 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 LKT(0.695)PS(0.184)T(0.121)PVACSTPAQLK;LKT(0.497)PS(0.078)T(0.425)PVACSTPAQLK 222.51 5.40E-15 1432670000 1828400 1371080 1595630 1588000 1949080 1133650 2308780 1496760 1994580 TRUE FALSE 1713963.708 1472596.19 1633479.097 1628750.768 1796007.119 1460916.352 1962599.873 1683633.781 1661671.713 1.03146951 0.886213672 0.983033583 0.980188058 1.08084353 0.879184703 1.181099647 1.013216851 1 20.66420395 2.783836588 0.928136641 1.054958611 0.945970461 0.086385251 0.08343935 0.847602188 1.561301755 0.044222068 0.043422295 607.9062212 -2.783836588 -0.10898815 LKTDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKTDLK 6 1 Q8IZT6;Q8IZT6-2;Q5VYL4 Q8IZT6 ASPM Abnormal spindle-like microcephaly-associated protein 0 82.671 0.053469 429170000 1187100 892720 953200 933740 1128600 756380 1234600 917100 1360600 FALSE TRUE 1112801.53 958817.9177 975810.3541 957701.3492 1039964.309 974734.6272 1049483.191 1031601.954 1133507.07 0.981733206 0.845886138 0.860877166 0.844901081 0.91747492 0.859928141 0.925872647 0.910097503 1 20.11236196 0.781114535 0.769305611 0.999818834 0.876027767 0.387462354 0.042560292 0.845138323 1.006658696 0.038395972 0.013814818 6.041079274 -0.781114535 -0.123791068 LKTEEGEIDYS(ph)AEEGENRR ddPTM_SK-BR-3_Pertuzumab_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 152.88 2.68E-08 293752000 561980 460190 455690 463230 558850 316060 610860 407140 785630 TRUE FALSE 526806.675 494262.9464 466499.182 475117.266 514960.1753 407301.3912 519267.2139 457972.3252 654503.2776 0.804895396 0.755172607 0.712753011 0.725920377 0.786795411 0.622306114 0.793376033 0.699725029 1 19.32004089 -1.073059966 4.372393322 1.000021624 0.737117329 0.703007192 0.05359478 6336353.224 1555049.44 1407.29456 0.01099434 0.084516214 1.073059966 -0.262904295 LKTEGSDLCDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LKTEGSDLCDR 11 1 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ;; 115.8 0.00097944 1844920000 2042710 2051640 1717050 1821830 2456600 1583890 2509190 2044180 2721960 FALSE TRUE 1914860.427 2203545.56 1757779.237 1868581.242 2263668.545 2041133.331 2132960.254 2299400.373 2267647.291 0.844426042 0.971732054 0.775155485 0.824017584 0.99824543 0.900110585 0.940604944 1.014002654 1 21.11276483 1.839529798 0.888159376 1.003889366 0.868709845 0.407462145 0.063239489 0.623751262 0.916423251 0.055279799 0.024788406 69.10823441 -1.839529798 -0.13517952 LKTEKEPDATPPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LKTEKEPDATPPSPR 15 2 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;A0A090HNM7 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 1 LKTEKEPDAT(0.005)PPS(0.995)PR;LKTEKEPDAT(0.006)PPS(0.994)PR;LKTEKEPDATPPS(1)PR;LKTEKEPDAT(0.023)PPS(0.977)PR;LKTEKEPDATPPS(1)PR 130.09 3.23E-05 3620070000 5634170 4236390 4791990 4845300 5289750 3360220 6201460 3947100 8503680 TRUE FALSE 5281537.357 4550056.724 4905658.266 4969638.601 4874314.373 4330260.965 5271608.645 4439904.124 7084360.872 0.745520655 0.642267779 0.692463068 0.701494276 0.68803869 0.61124229 0.744119158 0.626719079 1 22.75620627 -1.7492313 2.671525018 1.068136387 0.681291161 0.833155912 0.044794685 4813019.278 3916237.644 2171172.12 0.00946848 0.017814297 1.7492313 -0.386845227 LKTNILQYASTRPPTLS(ph)PIPHIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKTNILQYASTRPPTLSPIPHIPR 24 2 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 LKTNILQYAS(0.001)T(0.001)RPPT(0.046)LS(0.953)PIPHIPR;LKTNILQYASTRPPT(0.013)LS(0.987)PIPHIPR 175.46 8.44E-13 386140000 273780 318420 296490 289860 428410 325780 403060 299710 395710 TRUE FALSE 256644.5985 341996.1481 303522.8828 297298.2983 394764.4067 419827.3974 342624.8948 337129.4532 329663.4446 0.778504874 1.037409982 0.920705306 0.901823673 1.197477043 1.273503035 1.03931722 1.022647366 1 18.33063439 2.74813487 24.95635991 1.117076756 0.932759848 0.466692287 0.102984587 622.3267128 1622163.728 0.030983496 0.032481374 559.9314615 -2.74813487 -0.184316908 LKTPSTPVACS(ph)TPAQLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKTPSTPVACSTPAQLKR 18 2 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 LKTPSTPVACS(0.924)T(0.076)PAQLKR 96.79 0.00079697 263510000 203780 185860 194330 174310 222190 113090 277870 166850 298040 TRUE FALSE 191025.7736 199621.2678 198939.5994 178783.0897 204740.0937 145737.2471 236205.9731 187681.5898 248295.1986 0.769349446 0.803967491 0.801222096 0.720042477 0.824583378 0.586951532 0.951311078 0.755880866 1 17.92169684 0.464740536 0.837561434 1.000094972 0.773991204 0.370549847 0.090908653 1.862576748 1.93955197 0.084038627 0.026944168 2.915684554 -0.464740536 -0.226103768 LKTS(ph)LGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKTSLGK 7 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 LKT(0.027)S(0.973)LGK;LKT(0.025)S(0.975)LGK 77.192 0.023446 531860000 745090 501250 654100 595650 636060 469670 890310 574640 967800 TRUE FALSE 698456.1469 538363.0716 669615.5609 610935.3874 586106.4133 605256.1045 756816.2807 646385.0689 806267.9278 0.866282935 0.667722296 0.830512461 0.757732469 0.726937527 0.750688554 0.938665988 0.801700088 1 19.62089981 1.161664623 0.739769742 0.990471611 0.757771206 0.471937523 0.072434973 0.500636082 0.636517415 0.064708375 0.02575813 14.50990681 -1.161664623 -0.232700405 KRAQEEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KRAQEEAER 9 2 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 145.89 5.41E-05 25409000 30067 44567 17787.4 19851.4 60196 12751.4 37381 81477 187370 FALSE TRUE 28185.16014 47866.78705 18209.32553 20360.82053 55468.44898 16432.52218 31776.06608 91649.5828 156096.7365 0.180562136 0.306648224 0.116654108 0.130437195 0.355346628 0.105271401 0.203566498 0.587133241 1 17.25208085 1.005072942 2.73680924 0.997164666 0.198421933 0.915499671 0.080508078 0.063348389 1.092023419 0.073142205 0.019536014 10.11749367 -1.005072942 -0.798742733 LKVFDGIPPPYDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKVFDGIPPPYDKK 14 2 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 63.037 0.040648 231020000 686720 648160 621360 632240 873940 474620 850980 668590 1208160 FALSE TRUE 643739.421 696150.4408 636098.9526 648464.3488 805304.2777 611635.0892 723383.4491 752064.9332 1006510.291 0.639575598 0.691647614 0.631984549 0.644269964 0.800095424 0.607678923 0.718704474 0.747200441 1 19.94093049 -0.351969629 0.461776931 1.059212715 0.660010408 0.78998738 0.05267937 2.907830403 0.615113346 0.328768373 0.026174495 0.444662362 0.351969629 -0.399202307 LKVPEWVDTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKVPEWVDTVK 11 1 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ; 161.25 2.42E-05 5088900000 6417400 4910900 5659500 4915600 5710700 4352600 7028900 4736300 6447200 FALSE TRUE 6015746.389 5274508.146 5793746.013 5041742.618 5262204.658 5609124.961 5974981.698 5327637.481 5371120.669 1.120016987 0.982012595 1.07868476 0.938676103 0.979721921 1.04431185 1.112427381 0.991904261 1 22.3567917 2.015456807 24.74108353 1.055044269 1.018422455 0 0.060960131 569.1390891 910993.8053 0.021587846 0.015939214 103.6231539 -2.015456807 -0.036621815 LKVPPAINQFTQALDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKVPPAINQFTQALDR 16 1 P62424;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 ; 263.71 5.31E-27 2806200000 1555660 1806030 1545170 1734370 1920820 1367760 1979940 1532840 1857350 FALSE TRUE 1458294.018 1939750.34 1581822.162 1778876.87 1769966.545 1762610.108 1683066.378 1724218.448 1547346.286 0.942448391 1.253598085 1.022280647 1.149630749 1.143872294 1.139118066 1.087711518 1.114306774 1 20.56136467 0.092039603 1.013639228 0.999177903 1.115959821 0.133816993 0.082361956 10.66803362 10.26046502 0.096074698 0.022119967 1.236060142 -0.092039603 0.116781918 LKVTEGGEPYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKVTEGGEPYR 11 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 163.99 2.13E-05 569760000 780570 920320 818630 924970 1114220 660120 1118860 842970 1158140 FALSE TRUE 731715.5171 988461.4504 838048.2902 948706.2962 1026713.656 850685.9278 951097.33 948216.6601 964838.9521 0.758380987 1.024483359 0.868588782 0.983279431 1.064129566 0.881686965 0.9857576 0.982771952 1 19.87992863 4.748699099 24.51414753 0.96650469 0.758380836 0.562863674 0.059359868 823.6348184 1991439.159 0.013282372 0.180523499 56065.93887 -4.748699099 -0.208123854 LKVTELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LKVTELR 7 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 101.33 0.0083363 591240000 2020100 2570700 2412900 2301800 2762000 2003500 2642400 2464300 3205700 FALSE TRUE 1893665.547 2761037.303 2470135.127 2360868.085 2545083.661 2581877.926 2246196.651 2771973.28 2670647.96 0.709065955 1.033845473 0.924919781 0.884005724 0.952983583 0.966760863 0.841068042 1.03794035 1 21.34875838 7.999918912 0.013175883 1.719707787 6.50E-06 0.160560913 0.090615077 20307.74702 20.66706819 1107.862068 1637.420837 99981330.5 -7.999918912 -1.719701285 LKYALTGDEVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKYALTGDEVKK 12 2 P62701;C9JEH7;P22090;Q8TD47 P62701 RPS4X;RPS4Y1;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1;40S ribosomal protein S4, Y isoform 2" 0 119.87 0.00026503 481030000 972840 726400 839800 834030 1039100 634370 1204800 726690 1611800 FALSE TRUE 911951.681 780183.4118 859720.4526 855432.6218 957493.2775 817502.3209 1024151.425 817418.8461 1342780.167 0.679151884 0.581020952 0.640254059 0.637060811 0.713067783 0.608813223 0.762709675 0.608751057 1 20.3567917 -5 0.232586744 2.909820805 0.613936533 0.795062484 0.054894171 63.24882677 0.632742786 56.85973085 0.082238069 1.00E-05 5 -2.295884272 LLAAGQLADALSQFHAAVDGDPDNYIAYYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLAAGQLADALSQFHAAVDGDPDNYIAYYR 30 0 Q13217;X6R9L0 Q13217 DNAJC3 DnaJ homolog subfamily C member 3 0 ; 259.67 2.92E-58 240740000 107998 131253 115883 111867 151679 114126 129407 123366 79445 FALSE TRUE 101238.598 140971.1087 118631.7995 114737.6966 139766.7432 147072.3235 110003.6217 138768.5167 66185.11627 1.529627863 2.129951818 1.792424131 1.733587596 2.111754894 2.222135909 1.662059809 2.096672553 1 16.0142192 -1.439710766 4.435259606 0.997005439 1.914874096 0.608778686 0.229169876 0.006140701 0.000775731 0.200793675 0.047217926 0.036331994 1.439710766 0.917868656 LLAAVEAFYS(ph)PPSHDRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLAAVEAFYSPPSHDRPR 18 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 1 LLAAVEAFY(0.006)S(0.853)PPS(0.141)HDRPR;LLAAVEAFY(0.009)S(0.81)PPS(0.181)HDRPR;LLAAVEAFY(0.04)S(0.857)PPS(0.103)HDRPR 111.83 0.0001771 116598000 246969 286571 275196 267863 310226 263081 305580 264498 335170 TRUE FALSE 231511.6511 307789.015 281723.7791 274736.8181 285862.1014 339028.2139 259761.1159 297521.1575 279227.9617 0.829113423 1.102285792 1.008938279 0.983915853 1.023758866 1.214162836 0.930283322 1.065513481 1 18.09108389 2.470599677 24.99548688 1.050036867 1.005705331 0.083973803 0.097193495 600.5045385 2301551.731 0.031677968 0.02656175 295.528709 -2.470599677 -0.044331536 LLAAVEAFYSPPSHDRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLAAVEAFYSPPSHDRPR 18 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ; 153.95 1.77E-08 242190000 145740 175704 151271 160280 178496 137383 175053 144424 158254 FALSE TRUE 136618.3936 188713.307 154859.2196 164393.0562 164477.6442 177043.2419 148805.4278 162455.6543 131840.385 1.036240857 1.431377092 1.174596232 1.246909709 1.247551303 1.342860473 1.12867865 1.232214653 1 17.00843284 0.445612266 0.710467125 0.996487554 1.256998592 0.295672241 0.108997966 2.044795237 1.609028941 0.114130243 0.035957731 2.790051796 -0.445612266 0.260511038 LLACIASRPGQCGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLACIASRPGQCGR 14 1 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 222.81 3.42E-12 5119100000 932910 1152590 1032460 1015050 1260020 993600 1332680 1024500 1688280 FALSE TRUE 874520.8284 1237928.963 1056950.439 1041097.901 1161063.112 1280436.19 1132857.006 1152411.08 1406495.161 0.62177308 0.880151597 0.751478191 0.74020724 0.825500964 0.91037369 0.805446785 0.819349481 1 20.42367316 -5 0.110470839 1.641671622 0.687109725 0.513045355 0.071585058 146.8756655 1.078322911 21.29079276 0.839852589 1.00E-05 5 -0.954561897 LLAEGHPDPDAELQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLAEGHPDPDAELQR 15 0 P49756 P49756 RBM25 RNA-binding protein 25 0 111.74 0.0019025 0 390860 487140 443400 448200 487960 367070 472920 415430 519650 FALSE TRUE 366396.7703 523208.3525 453917.6574 459701.5708 449637.5899 473037.1501 402010.0364 467297.35 432917.0579 0.846344037 1.208564881 1.048509522 1.061869849 1.038622946 1.092673854 0.928607522 1.079415425 1 18.72373112 1.762641114 25 0.996334084 1.067748966 0.026501275 0.09558382 30.21426721 31390.55133 0.040708068 0.022575473 57.89500742 -1.762641114 0.071414881 LLAETHYQLGLAYGYNSQYDEAVAQFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLAETHYQLGLAYGYNSQYDEAVAQFSK 28 0 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 ;; 186.3 9.08E-18 94547200 65297.8 67662.9 55977 50084 68192.9 51526 70487.4 59918.9 59966.2 FALSE TRUE 61210.92726 72672.73152 57304.80087 51369.24023 62837.30471 66400.71975 59918.46874 67399.90656 49957.45382 1.225261149 1.454692462 1.147072088 1.028259775 1.2578164 1.329145396 1.199389964 1.349146151 1 15.60841233 3.911403669 5.936930237 1.2011502 1.349048329 0.197175138 0.125307076 0.298148046 19.90864686 0.030325887 0.056010446 8154.61889 -3.911403669 0.147898129 LLAHVTLELQHYHQLLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLAHVTLELQHYHQLLEK 18 0 P56192;H0YIP0 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;; 188.96 1.22E-14 174654000 207114.8 284251.8 267314 252942.4 310590.9 209460.1 300735.9 281544 316464 FALSE TRUE 194151.8544 305298.099 273654.8143 259433.3302 286198.3436 269927.8306 255643.3437 316695.3882 263644.114 0.736416419 1.15799323 1.037970506 0.984028531 1.085548011 1.023834086 0.969653143 1.201223056 1 18.00823226 4.750557973 24.57239103 1.054120887 0.736416173 0.648769644 0.074215244 932.2751581 1909395.153 0.016916413 0.278982142 56306.42743 -4.750557973 -0.317704714 LLALLSLGEVGHHIDLSGQLELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLALLSLGEVGHHIDLSGQLELK 23 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 133.16 1.39E-05 48035000 115670 124020 127330 112770 139570 103480 147940 132410 113330 FALSE TRUE 108430.4212 133202.5698 130350.3277 115663.8691 128608.7352 133352.9961 125757.7704 148941.68 94414.49086 1.14845105 1.410827603 1.380617811 1.225064797 1.362171569 1.412420858 1.331975307 1.577529875 1 16.52672068 LLANQQVFHISCFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLANQQVFHISCFR 14 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 125.53 9.07E-05 245510000 56328 108960 84511 85364 113450 77476 91112 97540 113490 FALSE TRUE 52802.53103 117027.5118 86515.64083 87554.58476 104540.0946 99842.06348 77450.60144 109718.0837 94547.78583 0.558474538 1.237760469 0.915046715 0.926035274 1.105685276 1.055995787 0.819168855 1.160451117 1 16.52875605 4.757398249 24.39232008 1.016021404 0.558473973 0.586785461 0.123363397 2305.705693 2985525.971 0.028869458 1.000273756 57200.29238 -4.757398249 -0.457547431 LLAS(ph)PSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLASPSSR 8 0 C9J470;E9PHA2;Q15003;C9JZP1 C9J470 NCAPH Condensin complex subunit 2 1 LLAS(0.924)PS(0.076)SR 148.73 0.00054192 461990000 450310 511320 521450 504260 523520 490700 553000 468940 623350 TRUE FALSE 422125.9009 549178.6648 533819.0402 517200.1653 482404.851 632357.1242 470082.7838 527488.1913 519308.858 0.812860968 1.057518385 1.027941334 0.995939425 0.928936304 1.217689848 0.905208483 1.015750421 1 18.98623331 4.745183218 24.47127167 1.019418974 0.81286084 0.373904522 0.083671669 582.05553 2150684.296 0.017969689 0.17162814 55613.88289 -4.745183218 -0.206558134 LLASPS(ph)SR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLASPSSR 8 0 C9J470;E9PHA2;Q15003;C9JZP1 C9J470 NCAPH Condensin complex subunit 2 1 LLAS(0.107)PS(0.877)S(0.016)R;LLAS(0.271)PS(0.656)S(0.073)R;LLAS(0.323)PS(0.676)S(0.002)R 128.87 0.0011696 937570000 1027260 1248300 1227560 1207100 1323400 1060860 1320870 1180370 1442240 TRUE FALSE 962965.6303 1340725.431 1256678.303 1238076.23 1219465.502 1367113.06 1122817.806 1327741.793 1201520.827 0.801455629 1.115857005 1.045906384 1.030424277 1.014934968 1.137818862 0.934497165 1.105051001 1 20.19643023 4.748561235 24.83553381 1.047389194 0.801455482 0.624337601 0.0601146 834.1740373 2071542.263 0.013350573 0.182463216 56048.14395 -4.748561235 -0.245933712 LLASS(ph)PALPSSGAQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLASSPALPSSGAQAR 16 0 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 1 LLAS(0.002)S(0.998)PALPSSGAQAR;LLAS(0.001)S(0.999)PALPSSGAQAR;LLAS(0.127)S(0.873)PALPSSGAQAR 195.23 8.95E-11 424140000 646381 689784 718160 677161 789563 611802 754446 653795 1017449 TRUE FALSE 605925.167 740856.3251 735195.0943 694538.0977 727553.9069 788419.3056 641323.8262 735422.7449 847630.1889 0.714846138 0.874032491 0.867353598 0.819388109 0.858338833 0.930145382 0.756608052 0.867622171 1 19.69307545 -2.136891678 1.752610101 1.277337615 0.840378416 0.409787964 0.061643723 662912.1678 137674.051 729909.6942 0.015280333 0.007296395 2.136891678 -0.4369592 LLASSDPLAQIAEDKPYAELWMGTHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLASSDPLAQIAEDKPYAELWMGTHPR 27 1 H3BPB8;P34949-2;P34949;H3BPU7;H3BUG1;H3BU66;H3BPM5;H3BQX0;H3BT46;H3BMZ9;H3BPP3;H3BP57;H3BT48;H3BUZ9 H3BPB8 MPI Mannose-6-phosphate isomerase 0 ; 252.24 5.37E-53 169655000 860050 893060 853480 876090 1023600 701770 1055620 874680 1125660 FALSE TRUE 806221.0057 959183.0916 873724.9486 898571.9526 943210.585 904359.6067 897339.5809 983885.7234 937780.074 0.859712238 1.022823067 0.931694939 0.958190494 1.005790815 0.964362148 0.956876357 1.049164672 1 19.8388901 4.751889665 24.5053363 0.979710407 0.859712134 0.551122976 0.035433832 1330.176022 2445460.202 0.007891485 0.149890533 56479.34678 -4.751889665 -0.119998273 LLDDAMAADKSDEWFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLDDAMAADKSDEWFAK 17 1 Q9HC38-2;F6TLX2;Q9HC38;I3L1I0 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ; 184.41 6.68E-10 305350000 884330 596610 673500 621420 666460 497270 944010 556270 963140 FALSE TRUE 828981.3639 640783.6252 689475.738 637366.6893 614118.92 640823.7765 802464.4643 625721.534 802385.7119 1.03314572 0.798598001 0.859282173 0.79433953 0.765366221 0.79864804 1.000098148 0.779826366 1 19.61393639 -0.808232485 5.220474274 1.000000088 0.853318786 0.199205911 0.092205125 8.98E-08 2.03E-08 0.084307998 0.019871574 0.155513292 0.808232485 -0.146681302 LLDDLFR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;; 197.62 0.00097263 366936800 796709 1229670 884239 895423 1332534 701480 928203 1125515 1261262 FALSE TRUE 746844.4059 1320716.046 905213.5666 918401.0701 1227882.155 903985.8884 789027.5772 1266038.025 1050749.224 0.710773217 1.256927929 0.861493443 0.874044015 1.168577741 0.860325059 0.75091902 1.204890754 1 20.00298696 LLDEEEATDNDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LLDEEEATDNDLR 13 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;;;; 332.56 4.10E-62 3136410000 2160210 2468140 2295540 2397840 2490730 2110400 2703670 2094670 2548070 FALSE TRUE 2025006.312 2650883.654 2349991.293 2459372.634 2295118.113 2719638.221 2298279.783 2356194.16 2122780.656 0.95394044 1.248778882 1.107034439 1.158561827 1.081184769 1.281167799 1.082674169 1.109956487 1 21.01752388 0.862078465 1.64548241 1.001425146 1.145088787 0.157878643 0.0911705 0.847275542 4.421445873 0.07607291 0.021872861 7.279113055 -0.862078465 0.143663641 LLDESES(ph)AASSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLDESESAASSR 12 0 Q8N108-17;Q8N108;Q8N108-13;Q8N108-12;Q8N108-19;Q8N108-16;Q8N108-14;Q8N108-18;Q8N108-15 Q8N108-17 MIER1 Mesoderm induction early response protein 1 1 LLDES(0.039)ES(0.961)AASSR 129.17 0.00025069 86254000 159030 132130 150730 145400 124050 127640 144820 110560 126910 TRUE FALSE 149076.5962 141913.0427 154305.3868 149131.2102 114307.6134 164487.5959 123105.5854 124363.6594 105727.9011 1.410002417 1.3422478 1.459457581 1.41051897 1.081148989 1.555763372 1.164362331 1.176261498 1 16.68999662 1.146979594 0.733627297 0.993873407 1.388513726 0.483795654 0.128397141 0.517405385 0.648736165 0.111636288 0.044520963 14.02747792 -1.146979594 0.394640319 LLDEVFFSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLDEVFFSEK 10 0 P25789;H0YN18;H0YMZ1;H0YL69;H0YLC2;H0YMI6;H0YMA1;H0YKT8;H0YLS6 P25789 PSMA4 Proteasome subunit alpha type-4;Proteasome subunit alpha type;Proteasome subunit beta type 0 ;;; 190.24 2.15E-06 207382000 1063034 1114833 938031 857985 1311560 707574 1148781 1141639 1075670 FALSE TRUE 996500.5995 1197376.395 960281.5383 880002.3477 1208555.368 911839.1273 976531.9538 1284175.142 896133.7279 1.111999882 1.336158163 1.071582855 0.981998914 1.348632833 1.017525732 1.089716773 1.433017308 1 19.77335451 3.957939685 18.65963822 1.131574173 1.23556236 0.051874846 0.156848191 47.24458592 45960.49641 0.036760136 0.066659433 9076.944596 -3.957939685 0.103988187 LLDFGS(ph)LSNLQVTQPTVGMNFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLDFGSLSNLQVTQPTVGMNFK 22 0 H3BNC9;P08708 H3BNC9 RPS17 40S ribosomal protein S17 1 LLDFGS(0.96)LS(0.04)NLQVTQPTVGMNFK;LLDFGS(0.957)LS(0.043)NLQVTQPTVGMNFK 272.3 1.55E-45 583920000 1004820 1072160 937090 979920 1157540 620290 1382690 1005070 1517170 TRUE FALSE 941930.1099 1151543.842 959318.2173 1005066.406 1066631.478 799357.6534 1175368.471 1130555.202 1263944.526 0.745230578 0.911071506 0.758987596 0.795182372 0.843891054 0.632430963 0.929920932 0.89446584 1 20.26950171 1.60316194 25 0.93417267 0.795425613 0.490020744 0.076058881 0.411030518 2173.68511 0.03674841 0.017878752 40.10162205 -1.60316194 -0.138747057 LLDFGSLS(ph)NLQVTQPTVGMNFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLDFGSLSNLQVTQPTVGMNFK 22 0 H3BNC9;P08708 H3BNC9 RPS17 40S ribosomal protein S17 1 LLDFGS(0.369)LS(0.631)NLQVTQPTVGMNFK 192.58 3.42E-17 116400000 159910 178760 152880 145600 174040 102650 212770 152000 223800 TRUE FALSE 149901.5185 191995.5764 156506.3858 149336.3425 160371.6004 132283.3886 180867.1138 170977.5346 186446.3342 0.803992844 1.029763214 0.839417876 0.800961538 0.860148853 0.709498469 0.970075998 0.917033501 1 17.50840091 1.605057805 25 0.957677878 0.859983116 0.3055362 0.083073396 0.436847447 3848.227222 0.043694253 0.021623696 40.27706397 -1.605057805 -0.097694761 LLDGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLDGKR 6 1 Q68DA7-5;A0A5F9ZHS8;H0YM30;Q68DA7;H0YLM7 Q68DA7-5 FMN1 Formin-1 0 98.415 0.064075 993850000 1472500 1663200 1641100 1569600 1962400 1292200 1892000 1544500 2749400 FALSE TRUE 1380338.853 1786345.059 1680027.667 1609878.593 1808281.02 1665237.163 1608312.164 1737334.225 2290507.378 0.602634537 0.77989055 0.733474025 0.702848028 0.78946745 0.727016721 0.702164149 0.75849318 1 21.12723578 0.864649591 6.622667747 0.99999968 0.727864849 0.744015046 0.051103343 1.887027276 92.29708593 0.044357976 0.01113347 7.322334946 -0.864649591 -0.272134831 LLDGPSTEKDLDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLDGPSTEKDLDEK 14 1 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;E5RIS7 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 0 73.296 0.023846 0 214880 140060 140220 156890 163520 109680 206830 152460 279150 FALSE TRUE 201431.0444 150430.1881 143546.0846 160916.063 150677.7988 141342.8355 175817.7616 171494.9666 232558.0616 0.866153781 0.646850026 0.617248371 0.691939303 0.647914752 0.607774396 0.756016628 0.737428603 1 17.82723143 0.63602518 1.105839326 0.999413713 0.670720744 0.619676888 0.075508684 0.726483651 1.408048524 0.067166341 0.020959013 4.325389084 -0.63602518 -0.328692969 LLDHMAPPPVADQAS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLDHMAPPPVADQASPR 17 0 A0A0C4DFS6;Q9C004 A0A0C4DFS6 SPRY4 Protein sprouty homolog 4 1 LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR 72.644 0.018006 114407000 105370 124184 118555 122983 119386 108943 122415 96086 90153 TRUE FALSE 98775.07979 133378.7126 121367.1806 126138.952 110009.9051 140393.0756 104060.0072 108082.5486 75105.88189 1.315144398 1.775875727 1.615947746 1.679481671 1.464730889 1.869268718 1.385510756 1.43906903 1 16.19663828 0.874043962 1.137832015 1.00488169 1.630808452 0.562846034 0.16494619 0.409238271 1.045165516 0.137292923 0.043167162 7.482452387 -0.874043962 0.625926762 LLDIACWIHHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLDIACWIHHK 11 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;A0A1B0GU92;A0A1B0GU03;C9JH19;F8WD96;F8W787;A0A1B0GV01 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ; 140.07 2.24E-05 2495400000 4375400 6694500 4347400 4097400 7671200 3461000 5314900 6286200 8545900 FALSE TRUE 4101551.524 7190167.746 4450522.381 4202546.221 7068734.896 4460134.515 4517980.086 7071045.908 7119534.081 0.576098306 1.009921108 0.625114274 0.590283883 0.992864816 0.626464382 0.634589291 0.993189418 1 22.7633514 1.223536873 24.57460463 0.996595154 0.735807619 0.342484228 0.157189962 262.4430429 429267.7015 0.141829942 0.036063242 16.73157686 -1.223536873 -0.260787535 LLDIDETEY(ph)HADGGKVPIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLDIDETEYHADGGKVPIK 19 1 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2;J3QLU9 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 LLDIDETEY(1)HADGGKVPIK 211.16 1.70E-16 111940000 188450 124750 103510 122620 212000 59439 91508 90011 100720 TRUE FALSE 176655.2509 133986.6198 105965.3061 125766.6368 195350.3752 76598.07439 77787.22492 101249.0715 83909.18132 2.105314914 1.596805233 1.262857108 1.498842377 2.328116805 0.912868809 0.927040685 1.206650689 1 16.35654106 2.189182029 24.99999461 0.993835582 1.656985864 0.570917982 0.314771827 90.9181476 46030.53883 0.118129346 0.087244447 154.5902247 -2.189182029 0.663150281 LLDIDETEYHADGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLDIDETEYHADGGK 15 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2;J3QLU9 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 0 160.78 1.69E-06 95590000 275660 235550 215500 193810 265970 191450 279260 263280 165720 FALSE TRUE 258406.9327 252990.3671 220611.7618 198783.4927 245081.7891 246718.5071 237387.5555 296151.0876 138060.2614 1.871696678 1.832463335 1.597938172 1.439831351 1.775179813 1.787034912 1.719448834 2.145085664 1 17.0749386 -1.894847975 2.866597411 0.625574348 1.749761845 0.636268057 0.182589444 77723315.48 84524452.51 199778163.8 0.042278917 0.012739489 1.894847975 1.124187498 LLDIDETEYHADGGKVPIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLDIDETEYHADGGKVPIK 19 1 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2;J3QLU9 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 0 108.49 0.00016456 54046000 80119 84005 79936 79266 101280 64869 97538 85860 104900 FALSE TRUE 75104.49481 90224.81761 81832.11967 81300.09976 93325.87734 83595.62724 82913.0824 96579.81 87391.51232 0.859402622 1.032420829 0.936385211 0.930297435 1.067905508 0.956564602 0.948754406 1.105139474 1 16.41520555 4.751379059 23.95482819 0.988568692 0.859402473 0.346797557 0.058371283 1369.361599 2558949.965 0.012875484 0.226071807 56412.98217 -4.751379059 -0.129166219 LLDLSDSTSVAS(ph)FPSADETDGNLPESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLDLSDSTSVASFPSADETDGNLPESR 27 0 Q13464 Q13464 ROCK1 Rho-associated protein kinase 1 1 LLDLSDSTS(0.01)VAS(0.989)FPSADETDGNLPESR;LLDLS(0.001)DS(0.007)T(0.006)S(0.033)VAS(0.952)FPSADETDGNLPESR;LLDLSDSTSVAS(1)FPSADETDGNLPESR;LLDLSDSTS(0.002)VAS(0.998)FPSADETDGNLPESR 243.24 1.76E-45 263461000 251177 277582 289344 261791 303505 253724 283424 257848 333505 TRUE FALSE 235456.2799 298134.4601 296207.3763 268509.0003 279668.9416 326969.9999 240927.2024 290040.8904 277840.861 0.847450152 1.073040369 1.066104443 0.966412929 1.006579596 1.176824743 0.867141001 1.043910134 1 18.08389926 1.706432671 25 0.962207205 1.030786099 0.057827587 0.09418852 1.640187734 1268.403642 0.039924565 0.022140167 50.86659547 -1.706432671 0.068578894 LLDPEDISVDHPDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLDPEDISVDHPDEK 15 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 239.75 8.16E-18 325020000 552370 455490 545810 542450 597490 416300 638490 458060 612240 FALSE TRUE 517798.1477 489214.9535 558756.871 556370.1854 550565.5456 536479.0519 542754.352 515249.7993 510053.1888 1.01518461 0.959144976 1.095487457 1.09080817 1.07942771 1.051810015 1.064113241 1.01018837 1 18.96028817 3.987965521 6.829481828 1.0610209 0.988207218 0.408666302 0.033980206 0.117890004 28.07493211 0.007902212 0.016175724 9726.699988 -3.987965521 -0.072813683 LLDSSTVTHLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLDSSTVTHLFK 12 0 G3V5Z7;P60900;G3V3I1;G3V295;P60900-2;G3V3U4 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ; 229.29 8.53E-12 1964500000 4743600 6495600 5021700 4742200 7545200 3606800 5500700 6271100 5716900 FALSE TRUE 4446706.544 6976540.983 5140817.095 4863892.881 6952630.428 4648024.608 4675921.101 7054060.639 4762712.457 0.933650012 1.464825148 1.079388508 1.021244285 1.459804784 0.975919636 0.981776906 1.481101516 1 22.18335202 LLDSVEQDFHLEIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LLDSVEQDFHLEIAK 15 0 Q6IBS0;H0Y858;H7C5I2;Q9NR96-4 Q6IBS0 TWF2 Twinfilin-2 0 ;;;; 208.39 2.92E-09 279342000 776795 717165 726255 702717 862076 588658 857648 733045 1049612 FALSE TRUE 728176.7876 770264.6428 743482.1116 720749.9079 794372.0284 758594.0085 729051.6444 824567.2819 874424.9764 0.832749301 0.880881338 0.850252602 0.824255857 0.908450753 0.867534699 0.833749794 0.942982307 1 19.73797508 1.050608242 4.131431665 0.999199576 0.858763576 0.792653546 0.025238263 0.076440479 2.713698604 0.022833317 0.005844832 11.23590975 -1.050608242 -0.140436001 LLDTVDDMLANDIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LLDTVDDMLANDIAR 15 0 A0A024R571;Q9H4M9;C9J2Z4 A0A024R571 EHD1 EH domain-containing protein 1 0 ;;;; 198.49 1.84E-08 87786500 112428.7 142098.3 134156.9 135700 139054.1 116518.1 147002 131824.6 172921 FALSE TRUE 105391.9884 152619.406 137339.165 139182.2917 128133.3519 150154.984 124960.4148 148283.1915 144059.368 0.731587191 1.059420211 0.953351156 0.966145372 0.889448244 1.042313222 0.867423039 1.02932002 1 17.13630395 3.844510121 0.008502671 1.885451634 6.52E-05 0.09092833 0.094137459 24976.05357 45.39533712 4809.805643 5260.472902 6990.530277 -3.844510121 -1.885386443 LLDVTCSSLSVTQEEAEELLQALHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLDVTCSSLSVTQEEAEELLQALHR 25 0 Q9P000;E9PJ95 Q9P000 COMMD9 COMM domain-containing protein 9 0 298.23 4.41E-63 102070000 92740 94010 105280 107820 117870 121170 108120 91462 85485 FALSE TRUE 86935.56895 100970.5982 107777.2913 110586.8437 108612.9657 156149.812 91908.40974 102881.232 71217.00125 1.220713698 1.417787838 1.513364638 1.552815224 1.525098835 2.192591786 1.290540294 1.444616176 1 16.11993407 0.801054949 1.799823898 1.003752593 1.540582351 0.294362995 0.258449955 0.897319753 5.12666469 0.23449783 0.066123199 6.324918721 -0.801054949 0.536829758 LLDVVHPAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLDVVHPAAK 10 0 Q99832-3;Q99832;F8WAM2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 117.7 0.00092313 2343000000 8374400 8302500 8464200 7890300 9513500 6468800 9951900 8087500 10328300 FALSE TRUE 7850261.253 8917225.739 8664974.821 8092778.456 8766348.086 8336237.548 8459704.984 9097242.178 8604440.007 0.912350048 1.036351666 1.0070353 0.940535171 1.018816806 0.96882976 0.983179031 1.057273009 1 23.03664987 1.261877857 24.96788109 1.028636527 0.988088099 0.188659281 0.038966137 352.8503371 377830.2654 0.024441446 0.008912678 18.27586145 -1.261877857 -0.040548428 LLDWLVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLDWLVDR 8 0 J3QQY1;Q96JB5;J3KRI2;J3KRK4;J3KS63;J3QS62;Q96JB5-4;J3QL95 J3QQY1 CDK5RAP3 CDK5 regulatory subunit-associated protein 3 0 102.46 0.011539 19729000 90792 119930 98637 95803 107870 74546 102680 95197 64301 FALSE TRUE 85109.49079 128809.742 100976.7162 98261.46717 99398.32533 96066.22005 87284.08723 107082.555 53568.7477 1.588790002 2.404568849 1.884993033 1.834305848 1.855528262 1.793325851 1.629384501 1.998974395 1 15.70910395 -1.899978246 0.211391961 2.32E-17 2.104941928 0.573530948 0.230931379 19.9886034 0.651065002 10.65943007 0.520708927 0.012589885 1.899978246 2.104941928 LLDYTEKPLYENLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLDYTEKPLYENLR 14 1 Q99986;H0YJ50;H0YJJ9 Q99986 VRK1 Serine/threonine-protein kinase VRK1 0 ; 136.81 2.27E-05 318380000 564120 553610 474500 461610 600160 357110 516820 476320 647280 FALSE TRUE 528812.7362 594599.8604 485755.3641 473455.6941 553025.8545 460201.8598 439327.6389 535789.6005 539244.7864 0.980654333 1.102652961 0.900806788 0.877997722 1.025556238 0.85341921 0.814709108 0.993592546 1 19.0405808 3.848720857 3.97665395 0.908468545 1.043808935 0.285324074 0.074335905 0.227704527 6.378665691 0.018843169 0.035853842 7058.637144 -3.848720857 0.135340391 LLEAHEEQNVDSYTESVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLEAHEEQNVDSYTESVK 18 0 P54920;M0R0Y2;M0R213 P54920 NAPA Alpha-soluble NSF attachment protein 0 ; 274.43 4.89E-39 480080000 856650 695090 810980 749370 761960 643430 968850 754090 752290 FALSE TRUE 803033.8057 746555.1868 830216.8286 768600.1029 702118.7352 829177.7958 823579.9369 848239.7965 626727.939 1.281311644 1.191194999 1.324684567 1.226369618 1.1202927 1.323026698 1.314094818 1.35344181 1 19.25747978 LLEAQIATGGIIDPEESHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLEAQIATGGIIDPEESHR 19 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 88.945 0.0027869 0 278500 321610 252080 296910 330760 280410 292530 212510 237020 FALSE TRUE 261069.1821 345422.339 258059.4566 304529.2133 304783.4438 361359.8149 248667.8422 239042.3413 197459.8308 1.322138184 1.749329662 1.306895968 1.54223374 1.543521245 1.830042158 1.259333816 1.210587188 1 17.59119967 1.546482174 5.736643778 1.144689828 1.544896603 0.556353699 0.168386222 0.104585245 7.159780266 0.089166704 0.040509234 35.19509763 -1.546482174 0.400206775 LLEAQIATGGIIDPEESHRLPVEVAYK ddPTM_SK-BR-3_Pertuzumab_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 0 261.6 2.59E-53 128560000 229130 211720 217450 244350 253770 183830 302160 232660 223440 FALSE TRUE 214789.1623 227395.9691 222608.0167 250620.4347 233839.9279 236898.7368 256853.9131 261708.1131 186146.4205 1.153872106 1.221597324 1.195875892 1.346361826 1.256215012 1.272647285 1.37984879 1.405926111 1 17.50607835 3.255274417 24.26233644 1.299900222 1.197898492 0.091461696 0.112983412 293.0574024 425408.6308 0.027978721 0.037772019 1800.007925 -3.255274417 -0.102001729 LLEAQIATGGIIDPVHSHR ddPTM_SK-BR-3_Pertuzumab_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 ;; 102.39 0.00022738 143073000 161762 235363 217998 230392 234641 208322 242070 213083 154814 FALSE TRUE 151637.6052 252789.5214 223169.0155 236304.2488 216213.2424 268461.1796 205773.8508 239686.8816 128974.5433 1.175717326 1.959995477 1.730333831 1.832177442 1.676402466 2.081505178 1.595460977 1.858404578 1 16.97672681 -1.541101507 5.464205025 0.99763268 1.761679718 0.473293203 0.243852975 0.00608622 0.000511137 0.204337445 0.048056453 0.02876726 1.541101507 0.764047038 LLEAQIATGGVIDPVHSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LLEAQIATGGVIDPVHSHR 19 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 Q15149-3;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 PLEC;EPPK1 Plectin;Epiplakin 0 ;;;;;; 226.57 8.51E-20 3843487000 3031770 3293454 3404611 3386639 3374357 2854303 3700312 2930730 2755678 FALSE TRUE 2842016.928 3537304.761 3485369.981 3473545.89 3109348.613 3678293.94 3145484.568 3296638.092 2295737.539 1.237953764 1.540814096 1.518191832 1.513041378 1.354400736 1.602227553 1.370141191 1.435982134 1 21.13052628 0.085837926 0.860517003 0.99262457 1.472418849 0.630746174 0.106781667 2.765152874 2.11193334 0.151419395 0.03106923 1.218534769 -0.085837926 0.479794279 LLEASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 135.82 0.031258 4670290000 1847570 3931830 1834990 1939170 3974200 1362600 2324420 3492470 3734080 FALSE TRUE 1731933.892 4222946.784 1878516.829 1988932.385 3662082.363 1755960.5 1975894.8 3928512.567 3110837.925 0.556741924 1.357494954 0.603862006 0.639355837 1.177201272 0.564465441 0.635164817 1.262847073 1 21.5688718 5.008938799 17.43231711 0.872588133 0.104590572 0.113767112 0.293329559 84042744.35 2272633105 0.06761279 1504170808 102079.5622 -5.008938799 -0.767997561 LLEDFGDGGAFPEIHVAQYPLDMGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LLEDFGDGGAFPEIHVAQYPLDMGR 25 0 Q13573;G3V3A4;G3V5R3 Q13573 SNW1 SNW domain-containing protein 1 0 ;;;;; 193.47 3.41E-18 486352000 589092 675884 616284 613316 720764 557065 691721 608925 620888 FALSE TRUE 552221.7833 725927.1546 630902.5475 629054.7269 664158.1029 717880.6223 588003.8577 684950.6267 517257.7817 1.067594926 1.403414661 1.219706247 1.216133907 1.283998282 1.387858526 1.13677141 1.324195886 1 18.98052392 -3.036113736 0.559889272 3.92E-12 1.263031108 0.366851027 0.104404352 436.471549 15.06546662 527.0622115 0.039892066 0.000920209 3.036113736 1.263031108 LLEDFLQEGEEPDEDDAYQVLSTLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLEDFLQEGEEPDEDDAYQVLSTLKR 26 1 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 0 122.39 8.47E-10 0 14654 13182 15848 15369 16355 11043 17023 13267 20664 FALSE TRUE 13736.8323 14158.009 16223.92204 15763.39456 15070.54427 14230.93483 14470.55918 14923.41415 17215.04491 0.797955066 0.822420683 0.942426937 0.915675483 0.875428694 0.826656852 0.840576325 0.866882093 1 14.07138232 -2.416931307 1.961350651 1.896360663 0.863642749 0.502051281 0.043433094 3672148.66 337724.6948 14575668 0.011447924 0.003828853 2.416931307 -1.032717914 LLEDGEDFNLGDALDSS(ph)NSMQTIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLEDGEDFNLGDALDSSNSMQTIQK 25 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 LLEDGEDFNLGDALDS(0.066)S(0.514)NS(0.355)MQT(0.066)IQK 119.83 0.0013248 23807000 13466 12886 10911 14366 13592 8689.2 16547 12884 19386 TRUE FALSE 12623.1871 13840.09285 11169.81407 14734.65588 12524.53915 11197.63098 14065.93096 14492.59576 16150.35136 0.781604487 0.856953049 0.691614307 0.912342744 0.775496388 0.693336679 0.870936529 0.897354828 1 13.97927793 1.155401977 1.814612138 0.992739789 0.788241987 0.508630816 0.068422302 0.252801146 1.554835131 0.059823335 0.017362133 14.30217134 -1.155401977 -0.204497802 LLEDGEDFNLGDALDSSNS(ph)MQTIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLEDGEDFNLGDALDSSNSMQTIQK 25 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 LLEDGEDFNLGDALDS(0.013)S(0.108)NS(0.878)MQT(0.001)IQK;LLEDGEDFNLGDALDS(0.007)S(0.35)NS(0.643)MQTIQK;LLEDGEDFNLGDALDS(0.056)S(0.356)NS(0.587)MQTIQK 276.75 2.79E-53 148645000 147417 122539 135842 142756 139234 97473 187232 123092 207494 TRUE FALSE 138190.4331 131611.9151 139064.2364 146419.3606 128299.1233 125611.8728 159158.2998 138460.3072 172861.9109 0.799426735 0.761370243 0.804481656 0.847030788 0.74220586 0.726660211 0.920725097 0.800987947 1 17.39926049 0.590770718 0.653152232 1.00244765 0.784048694 0.588933088 0.053405334 0.982379454 0.761843149 0.057795814 0.02018714 3.897361744 -0.590770718 -0.218398956 LLEDGEDFNLGDALDSSNSMQTIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLEDGEDFNLGDALDSSNSMQTIQK 25 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 251.02 7.33E-40 151593000 146104 124437 128308 126252 140570 118284 167419 122777 182183 FALSE TRUE 136959.6114 133650.445 131351.5264 129491.8401 129530.1992 152430.6706 142316.0752 138105.9787 151775.4804 0.902382988 0.88057995 0.865433112 0.853180235 0.853432972 1.004316839 0.937675011 0.909936034 1 17.21157921 2.250993598 24.99979026 0.957294975 0.870738499 0.689788143 0.030544588 128.0045005 257386.6633 0.010101357 0.008396228 178.2352492 -2.250993598 -0.086556476 LLEDS(ph)DS(ph)EDEAAPSPLQPALRPNPTAILDEAPKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLEDSDSEDEAAPSPLQPALRPNPTAILDEAPKPK 35 2 Q9BW85 Q9BW85 CCDC94 Coiled-coil domain-containing protein 94 2 LLEDS(1)DS(1)EDEAAPSPLQPALRPNPTAILDEAPKPK 169.15 4.15E-15 75516000 93888 61860 68741 67899 82261 60132 93393 60212 108860 TRUE FALSE 88011.71767 66440.17877 70371.56898 69641.40329 75800.55288 77491.13224 79389.58667 67729.60074 90690.56274 0.9704617 0.732603005 0.775952501 0.767901325 0.835815223 0.854456405 0.875389724 0.746820823 1 16.46866481 2.515975801 3.883661864 0.859588162 0.792714756 0.064528294 0.087474195 0.483171296 15.47574456 0.027689097 0.02479863 328.0770117 -2.515975801 -0.066873407 LLEDS(ph)EES(ph)SEETVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLEDSEESSEETVSR 15 0 O60231;A0A140T947;A2AB15 O60231 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 2 LLEDS(1)EES(0.993)S(0.007)EETVSR;LLEDS(1)EES(0.964)S(0.036)EETVSR;LLEDS(1)EES(0.782)S(0.218)EETVSR 308.98 6.12E-56 3494780000 2655170 2860020 2847110 2702220 2851640 2420320 3183940 2488950 3284450 TRUE FALSE 2488987.649 3071778.857 2914644.794 2771563.54 2627683.697 3119027.093 2706537.755 2799700.886 2736254.077 0.909633236 1.122621939 1.065195231 1.012904307 0.960321529 1.139889428 0.98913978 1.02318747 1 21.38377077 3.240661818 24.90432136 1.02360603 1.056471965 0 0.071024373 186.1779881 2206637.857 0.018717117 0.024198674 1740.45107 -3.240661818 0.032865936 LLEDS(ph)EESSEETVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLEDSEESSEETVSR 15 0 O60231;A0A140T947;A2AB15 O60231 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 1 LLEDS(1)EESSEETVSR 179.79 1.83E-11 0 71541 50977 63006 54259 61732 60789 61416 58139 69085 TRUE FALSE 67063.37651 54751.39012 64500.53207 55651.3778 56883.81773 78337.79747 52207.24096 65397.78213 57554.26719 1.165219883 0.951300273 1.120690701 0.966937475 0.988351003 1.361111891 0.90709592 1.136280337 1 15.81263528 LLEEALLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLEEALLR 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 129.55 0.0025258 117915000 207240 308326 220811 237306 291752 178683 243879 276266 234910 FALSE TRUE 194269.2183 331154.7779 226048.7412 243395.6737 268838.9748 230265.8814 207311.608 310758.4182 195702.0034 0.992678741 1.692137904 1.155066056 1.24370558 1.373716007 1.17661484 1.05932287 1.587916387 1 17.578299 3.736675617 24.54076991 1.223833702 1.401739407 0.026129013 0.233619271 618.441042 1588477.103 0.054304793 0.09626406 5453.503767 -3.736675617 0.177905705 LLEEEDLDELNIRDPEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLEEEDLDELNIRDPEHR 18 1 O94885;A0A087WW74 O94885 SASH1 SAM and SH3 domain-containing protein 1 0 ; 169.25 1.12E-11 32997000 48660 59382 56062 60152 65324 47306 55914 49509 72320 FALSE TRUE 45614.45746 63778.70507 57391.81711 61695.60216 60193.71654 60962.47425 47530.21478 55690.30763 60249.32479 0.757094915 1.058579582 0.952571955 1.024004873 0.999077031 1.011836638 0.788892074 0.924330817 1 15.87865745 1.764834473 25 0.882896134 0.97946283 0.062346899 0.096674577 27.27482727 25969.17802 0.040140427 0.022261589 58.18813971 -1.764834473 0.096566696 LLEEERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLEEERR 7 1 Q8NE71;Q8NE71-2;H0YGW7;Q5JSZ5;A0A494C0D3;H0Y412;A0A494C065;Q5JSZ5-5 Q8NE71;Q5JSZ5;Q5JSZ5-5 ABCF1;PRRC2B ATP-binding cassette sub-family F member 1;Protein PRRC2B 0 100.39 0.01576 221470000 223330 296220 233160 255000 308010 201900 261790 248470 375140 FALSE TRUE 209352.174 318152.437 238690.6653 261543.7317 283820.1371 260185.2524 222537.0198 279492.0264 312526.7105 0.6698697 1.018000786 0.763744849 0.836868411 0.908146816 0.832521649 0.712057601 0.894298046 1 18.25361997 2.010982817 24.75282314 0.820666111 0.854694393 0 0.116263114 1046.926781 2359529.452 0.040318289 0.02974869 102.5611347 -2.010982817 0.034028282 LLEEHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLEEHAK 7 0 P51572;P51572-2;A0A2R8Y5M6 P51572 BCAP31 B-cell receptor-associated protein 31 0 ;; 117.17 0.0052914 1025700000 2024800 1769000 1483280 1578600 2114350 1234730 2243120 1852350 1824460 FALSE TRUE 1898071.382 1899978.601 1518464.102 1619109.549 1948297.48 1591176.507 1906784.98 2083619.975 1519945.84 1.248775669 1.250030462 0.999025138 1.065241607 1.281820331 1.046863951 1.254508503 1.370851461 1 20.53558849 1.618025085 24.99999999 1.23450865 1.145380974 0.032245676 0.129867609 1.77429158 4355.053956 0.057251649 0.031290511 41.49780114 -1.618025085 -0.089127676 LLEEHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLEEHSR 7 0 P30038-2;P30038;P30038-3 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 ;;; 158.2 0.0014294 990610000 1606320 1907570 1638850 1612190 2404380 1616030 1552320 1859630 2720820 FALSE TRUE 1505783.299 2048808.468 1677724.296 1653561.525 2215549.694 2082551.627 1319564.027 2091808.899 2266697.565 0.664307106 0.903873767 0.740162394 0.729502493 0.97743507 0.918760252 0.582152665 0.922844287 1 21.11216048 1.009113651 24.99751165 1.000000126 0.792470389 0.276302184 0.120153712 200.0377584 548673.9828 0.111509457 0.027877364 10.21206688 -1.009113651 -0.207529737 LLEEIEFLEGAEGVDHPSHTLQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLEEIEFLEGAEGVDHPSHTLQHR 24 0 J3KRA9;Q96Q15-2;Q96Q15;Q96Q15-4;Q96Q15-3 J3KRA9 SMG1 Serine/threonine-protein kinase SMG1 0 42.904 0.065799 11966000 2288.7 2471.4 2290.9 2077.9 3442.2 3869.2 2414.1 2966.6 2761.3 FALSE TRUE 2145.454352 2654.385027 2345.24123 2131.222432 3171.863497 4986.175229 2052.128116 3336.98654 2300.421191 0.93263545 1.153869143 1.019483405 0.926448791 1.378818587 2.167505345 0.892066255 1.45059807 1 11.16768232 2.723414794 20.80701429 1.397133045 1.034298286 0.22236803 0.340906974 135.2255327 185767.8574 0.103979569 0.098635776 528.9502102 -2.723414794 -0.362834759 LLEELEEGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 167.97 1.18E-05 122565000 289367 200606 232620 212831 205547 180002 274664 202572 210846 FALSE TRUE 271256.036 215459.077 238137.8563 218292.6038 189404.1678 231965.6553 233480.6831 227863.5601 175654.4405 1.544259486 1.22660763 1.355717826 1.242738887 1.07827714 1.320579512 1.329204559 1.297226301 1 17.42238052 -4.258486686 0.225231735 4.97E-30 1.330011188 0.415400254 0.114409444 116.6498444 1.583451543 53.74442786 0.202100672 5.51E-05 4.258486686 1.330011188 LLEELEEGQKGVGDGTVSWGLEDDEDMTLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLEELEEGQKGVGDGTVSWGLEDDEDMTLTR 31 1 I3L0A0;Q13404;Q13404-7;Q13404-2;Q13404-1;Q13404-8;Q15819;E5RIF1;D6RG00;H0YBX6 I3L0A0 TMEM189-UBE2V1;UBE2V1;UBE2V2 Ubiquitin-conjugating enzyme E2 variant 1;Ubiquitin-conjugating enzyme E2 variant 2 0 90.616 0.00049157 22544000 17616 19837 19875 19683 24804 12749 20295 14750 37487 FALSE TRUE 16513.44601 21305.75212 20346.44439 20188.0991 22855.99389 16429.42934 17251.95316 16591.56997 31230.17752 0.528765678 0.682216811 0.651499479 0.646429214 0.731856035 0.526075439 0.552412907 0.531267232 1 14.93065315 -1.380354954 3.328735689 1.003341113 0.613920776 0.746505258 0.071976116 23203152.09 32434607.29 748633.9575 0.018399902 0.041652881 1.380354954 -0.389420338 LLEENETEAVTVPTPS(ph)PTPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LLEENETEAVTVPTPSPTPVR 21 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 LLEENETEAVTVPT(0.001)PS(0.997)PT(0.002)PVR;LLEENETEAVTVPTPS(1)PTPVR;LLEENETEAVTVPT(0.001)PS(0.993)PT(0.005)PVR;LLEENETEAVTVPTPS(0.997)PT(0.003)PVR;LLEENETEAVTVPTPS(0.996)PT(0.003)PVR;LLEENETEAVTVPTPS(0.998)PT(0.002)PVR;LLEENETEAVTVPTPS(0.996)PT(0.003)PVR;LLEENETEAVTVPT(0.002)PS(0.998)PT(0.001)PVR 354.55 1.72E-95 4947197000 4657000 5344440 5443360 5617210 5835340 4682740 6080070 4755230 5765490 TRUE FALSE 4365526.683 5740147.898 5572479.07 5761357.119 5377055.935 6034571.02 5168419.948 5348930.933 4803192.473 0.908880231 1.195069307 1.160161518 1.199484957 1.119475425 1.256366688 1.076038484 1.113619944 1 22.19556219 0.876044981 1.429891207 1.00206871 1.147630936 0.14935246 0.093664016 0.892618672 3.549851144 0.079672011 0.023602235 7.517007461 -0.876044981 0.145562226 LLEGEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LLEGEEER 8 0 P20700;E9PBF6;P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8;Q03252 P20700;P02545;P02545-2;Q03252 LMNB1;LMNA;LMNB2 Lamin-B1;Prelamin-A/C;Lamin-A/C;Lamin-B2 0 ;;;;; 161.9 0.00080229 8371600000 7071200 8040690 7573220 7301550 8086920 7098280 8831140 6924760 8550740 FALSE TRUE 6628626.214 8636031.054 7752860.355 7488920.134 7451805.924 9147438.205 7506992.541 7789331.529 7123566.254 0.93052075 1.212318486 1.088339755 1.051288058 1.046077998 1.284109374 1.053825047 1.093459547 1 22.76416824 -0.971614524 6.12279662 0.999999948 1.106663458 0.076464267 0.096445335 6.38E-08 1.06E-08 0.08395524 0.01978843 0.106754324 0.971614524 0.106663511 LLEIDPYLKPYAVDFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLEIDPYLKPYAVDFQR 17 1 Q04446 Q04446 GBE1 "1,4-alpha-glucan-branching enzyme" 0 92.551 0.0029922 61175000 167040 193730 175220 188320 236950 157860 254150 197240 247600 FALSE TRUE 156585.2646 208073.9708 179376.3011 193152.61 218340.9028 203431.6194 216042.5669 221865.8482 206273.9604 0.759113095 1.008726309 0.869602255 0.936388721 1.058499591 0.986220553 1.047357439 1.07558825 1 17.65420218 2.862157912 4.387551392 1.033112486 0.905303214 0.526097531 0.06622707 0.196628774 6.143811139 0.019114183 0.020417396 728.0444778 -2.862157912 -0.127809272 LLEIVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLEIVER 7 0 Q12792;Q12792-3;Q12792-4 Q12792 TWF1 Twinfilin-1 0 ;;; 126.67 0.0091423 154067000 345312 446664 417626 422230 437589 398672 496683 368052 386175 FALSE TRUE 323699.5383 479735.4673 427532.2859 433065.1366 403222.5251 513762.1345 422209.9951 414004.1024 321719.8977 1.006153305 1.491158833 1.328896002 1.346093728 1.253334121 1.596923716 1.312352758 1.286846432 1 18.29544564 0.773025729 2.378700139 1.000327539 1.3566232 0.307197381 0.153435691 1.045914121 9.098902046 0.130528044 0.035163476 5.929604518 -0.773025729 0.356295661 LLEKPYVR ddPTM_SK-BR-3_Pertuzumab_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 65.305 0.058929 208960000 323140 324730 357200 323300 399050 287310 425680 337460 465520 FALSE TRUE 302915.2442 348773.3471 365672.9527 331596.4253 367710.2227 370251.7329 361853.2358 379592.6238 387821.7046 0.781068312 0.899313635 0.942889344 0.855022866 0.948142454 0.954695749 0.933040187 0.978781278 1 18.56503402 5.938261631 0.762257252 0.944106839 6.82E-52 0.660753355 0.037081215 8.865161532 0.960428665 0.012123281 10.85324556 867484.3141 -5.938261631 -0.944106839 LLELDPEHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LLELDPEHQR 10 0 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ;;;;; 205.18 1.73E-07 1751270000 2468030 3338030 2697590 2986920 3171290 2006840 3040680 2510290 1764870 FALSE TRUE 2313560.408 3585181.214 2761578.109 3063569.424 2922229.676 2586182.13 2584758.262 2823705.232 1470301.796 1.573527568 2.438398175 1.878238956 2.083633056 1.987503304 1.758946454 1.757978036 1.92049363 1 20.48768088 -1.249988839 0.267881283 0.309230189 2.108807464 0.614501931 0.229918522 10.68394929 0.613655929 5.519702435 0.298013287 0.056235578 1.249988839 1.799577275 LLELFPVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLELFPVNR 9 0 E7ETZ4;Q9Y6E2;Q75MG1;B5MCH7;B5MCE7;E9PFD4 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 92.439 0.023439 41732000 75068 99334 82242 91674 109470 72345 86704 82873 104190 FALSE TRUE 70369.62788 106688.7927 84192.81908 94026.51004 100872.6678 93229.82708 73703.54012 93219.87648 86800.01591 0.81070985 1.229133331 0.969963176 1.083254525 1.162127296 1.074076152 0.84911897 1.073961514 1 16.40540769 1.79794206 24.99914026 0.958001297 1.070402548 0.071878558 0.123999084 312.9434913 131778.508 0.049033874 0.029424824 62.79745734 -1.79794206 0.112401251 LLELLGHYQESGSVIIFVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLELLGHYQESGSVIIFVDK 20 0 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ;; 103.1 0.00029021 30759300 82738 70643 80261 77695 80048 76743 88915 75893 67491 FALSE TRUE 77559.57627 75873.48122 82164.82882 79688.78524 73761.35298 98897.45828 75583.0212 85368.40811 56226.31609 1.379417712 1.349430062 1.461323354 1.41728626 1.311865299 1.758917624 1.344264153 1.518299865 1 15.77895791 -1.50523377 6.314080966 0.999670475 1.438412823 0.543134713 0.127520409 0.000531684 4.17E-05 0.110978597 0.026138863 0.031243971 1.50523377 0.438742348 LLELLGHYQESGSVIIFVDKQEHADGLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLELLGHYQESGSVIIFVDKQEHADGLLK 29 1 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 126.25 1.34E-05 26265000 55140 50682 56672 52157 73685 41185 66017 49423 98452 FALSE TRUE 51688.88583 54434.54801 58016.2866 53495.43692 67898.07733 53074.44092 56118.36372 55593.57034 82019.72518 0.630200671 0.663676303 0.707345538 0.652226483 0.827826199 0.647093621 0.684205703 0.677807323 1 16.32368329 -1.465141685 2.748701674 1.010583099 0.68737273 0.764685958 0.054686428 5230296.927 5615670.131 423737.2793 0.012914374 0.034265598 1.465141685 -0.323210369 LLEMNLMHAPQVADAILGNQMFTHYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLEMNLMHAPQVADAILGNQMFTHYDR 27 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 263.92 1.83E-53 1646740000 620559 926955 679541 631697 978748 607685 890501 863467 662645 FALSE TRUE 581719.3199 995587.7127 695660.0334 647907.4145 901881.0802 783113.7946 756978.6421 971272.7557 552045.2686 1.053752931 1.80345303 1.260150341 1.173649067 1.633708559 1.418568076 1.371225668 1.759407807 1 19.07442705 -1.372592747 3.684231365 0.997859361 1.443773068 0.239552491 0.242617408 17600699.66 6560315.87 302855.1483 0.051291329 0.042404042 1.372592747 0.445913707 LLEQALVIEEQLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLEQALVIEEQLRR 14 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y4X2;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;Q12873-3;Q12873;Q12873-2;H7C0J3;I3L229;H7C3H7 Q14839-2;Q12873-3;H7C0J3 CHD4;CHD3 Chromodomain-helicase-DNA-binding protein 4;Chromodomain-helicase-DNA-binding protein 3 0 ;;; 192.4 6.05E-07 307278000 189999.3 268481 217463.8 244670 275044 177902.6 257804.8 221570.7 307663 FALSE TRUE 178107.583 288359.6126 222622.144 250948.6464 253443.1537 229260.1926 219149.3636 249234.2896 256312.0577 0.694885697 1.125033349 0.868558998 0.979074682 0.988806988 0.894457306 0.855009965 0.972386129 1 17.96754182 2.218300864 24.87040764 0.910736696 0.951315052 0 0.115517171 1026.459307 1260049.274 0.039618691 0.029295141 165.3106615 -2.218300864 0.040578356 LLEQGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LLEQGLR 7 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;; 202.2 0.00073074 6604620000 3162330 4554020 3572470 3640350 4717620 3023940 3883780 4195580 4402230 FALSE TRUE 2964405.41 4891204.379 3657210.675 3733767.544 4347117.155 3896902.388 3301443.244 4719407.399 3667469.374 0.80829725 1.333672863 0.997202786 1.018077362 1.185317916 1.062558945 0.900196541 1.286829396 1 21.80635349 2.00222354 24.99141826 1.033783963 1.095261903 0 0.165291182 308.6673239 3469196.838 0.057888889 0.042482608 100.5133019 -2.00222354 0.06147794 LLEQWEKDDDIEEGDLPEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLEQWEKDDDIEEGDLPEHK 20 1 Q14696 Q14696 MESDC2 LDLR chaperone MESD 0 117.55 4.73E-05 69283000 130590 69246 93181 95828 96187 55808 114970 73264 92995 FALSE TRUE 122416.605 74373.04589 95391.29732 98287.10872 88632.86102 71918.86363 97731.31583 82411.17167 77473.53373 1.580108704 0.959980038 1.23127593 1.268654003 1.14404051 0.928302353 1.261480032 1.063733222 1 16.24141593 2.479524742 24.99233233 1.090671317 1.205325931 0.18846292 0.173149527 240.1051086 2496747.462 0.056174809 0.047768937 301.6648729 -2.479524742 0.114654614 LLEQYKEESK ddPTM_SK-BR-3_Pertuzumab_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 ; 113.22 0.001383 1020040000 949560 773840 860920 912480 1076240 638400 1206910 875010 1411400 FALSE TRUE 890128.7346 831135.9188 881341.429 935895.7816 991716.4517 822695.7164 1025945.05 984256.9246 1175828.222 0.757022767 0.70685148 0.749549477 0.79594601 0.843419501 0.699673389 0.872529703 0.837075439 1 20.16524588 -0.328294994 0.205344877 1.139951294 0.691968807 0.734084502 0.045879868 5.452297557 0.353555617 0.615955686 0.131962041 0.469575043 0.328294994 -0.447982486 LLEQYKEESKK ddPTM_SK-BR-3_Pertuzumab_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 94.688 0.0046782 1058600000 1007800 564930 682850 811870 1096400 694160 1207600 731430 1551000 FALSE TRUE 944723.597 606758.005 699047.5245 832703.9587 1010293.167 894552.7233 1026531.591 822750.6456 1292128.08 0.731137734 0.469580388 0.541004824 0.644443822 0.781883145 0.692309638 0.794450339 0.636740783 1 20.30131765 0.731718653 0.22912812 1.105191648 0.489983449 0.566472099 0.096196502 2.585098522 0.400250836 0.535716755 0.268193805 5.391612274 -0.731718653 -0.615208199 LLETIDQLYLEYAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLETIDQLYLEYAKR 15 1 P12814-3;P12814;P12814-2;P12814-4;H9KV75;H7C5W8;H0YJ11 P12814-3 ACTN1 Alpha-actinin-1 0 122.93 0.0012538 0 46766 45886 45622 42330 43130 40503 49193 38633 50380 FALSE TRUE 43838.99954 49283.44718 46704.17538 43416.25946 39742.74378 52195.55859 41816.96634 43456.41509 41971.25253 1.044500626 1.174219119 1.112765823 1.034428492 0.946903925 1.243602596 0.996324003 1.035385233 1 15.3571139 2.176389334 0.265413507 0.989973639 1.144595589 0.097349425 0.084520952 4.372979746 0.92908775 0.158243245 0.246380328 150.1029868 -2.176389334 0.154621949 LLETTDRPDGHQNNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLETTDRPDGHQNNLR 16 1 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;; 229.68 1.78E-15 4874330000 2675570 3507810 3290850 3345540 3419740 2960230 3496170 3278470 3238730 FALSE TRUE 2508110.85 3767531.902 3368910.516 3431392.22 3151167.415 3814800.346 2971951.765 3687794.196 2698165.04 0.929561688 1.396331153 1.248593198 1.271750308 1.16789276 1.41384989 1.101471452 1.366778585 1 21.36354717 -1.490359604 3.116229182 0.993623012 1.248265464 0.201815402 0.146635985 21947620.81 26565637.9 1205592.758 0.030809634 0.032332583 1.490359604 0.254642451 LLEVEHPAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LLEVEHPAAK 10 0 P17987;E7ERF2;F5H136;F5GZI8;F5H676;F5H726 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;;;; 135.86 0.00013302 4250870000 10206130 9352310 9904250 9587350 10644390 8194840 11885890 9269610 11784390 FALSE TRUE 9567346.542 10044764.76 10139183.49 9833377.632 9808422.547 10560557.28 10103711.14 10426941.21 9817499.179 0.974519719 1.02314903 1.032766421 1.001617362 0.999075464 1.075687106 1.029153245 1.062077116 1 23.22692414 2.262818264 24.99864731 1.043677103 1.011943076 0.314592753 0.025196396 283.5535841 292214.0537 0.008119055 0.006789565 183.1547829 -2.262818264 -0.031734026 LLEVQGSRPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLEVQGSRPGK 11 1 P62136;E9PMD7 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit;Serine/threonine-protein phosphatase 0 ; 113.24 0.0012935 2131700000 1700680 1689130 1505600 1602840 1742720 1352050 1950180 1407330 1741760 FALSE TRUE 1594237.475 1814194.943 1541313.543 1643971.588 1605853.801 1742364.886 1657768.614 1583038.248 1451049.004 1.09867928 1.250264421 1.062206403 1.132953872 1.106684748 1.200762264 1.142462184 1.090961259 1 20.46866481 0.937308129 2.786634914 1.000361779 1.14602702 0.42649427 0.052574275 0.293425112 5.320250424 0.047952874 0.012717243 8.655818252 -0.937308129 0.14566524 LLEVSDDPQVLAVAAHDVGEYVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LLEVSDDPQVLAVAAHDVGEYVR 23 0 G3V126;Q9UI12-2;Q9UI12 G3V126 ATP6V1H V-type proton ATPase subunit H 0 ;;;; 270.71 1.34E-51 502880000 337644 401597 411337 410100 434446 360717 471672 406199 474890 FALSE TRUE 316511.4648 431331.6597 421094.1079 420623.8603 400326.3636 464850.1421 400949.1624 456913.8393 395627.7911 0.800023335 1.090246109 1.064369383 1.063180772 1.011876245 1.174968373 1.013450449 1.15490835 1 18.59378425 4.740837648 24.93506804 1.072462801 0.800023237 0.684813383 0.057904725 100.7436479 1103139.461 0.011730178 0.078161753 55060.18265 -4.740837648 -0.272439564 LLFEDWTYDDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LLFEDWTYDDFR 12 0 Q9BWS9-3;Q9BWS9;Q9BWS9-2 Q9BWS9-3 CHID1 Chitinase domain-containing protein 1 0 ;;;; 276.57 1.69E-27 376361000 442461 611239 498167 539137 643971 403230 552506 506458 504246 FALSE TRUE 414768.1558 656495.7716 509983.7565 552972.1682 593396.1153 519635.9551 469662.8545 569690.3962 420084.085 0.987345559 1.562772299 1.214003993 1.316336867 1.412565095 1.236980818 1.118021061 1.356134204 1 18.6803186 0.294606357 0.419518442 0.970256599 1.327396091 0.190396808 0.1615311 4.045052945 1.170193687 0.406387195 0.100141785 1.970635747 -0.294606357 0.357139492 LLFEVFDENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLFEVFDENR 10 0 Q96PU5-7;Q96PU5;Q96PU5-2;Q96PU5-3;H0Y8H4;Q96PU5-5;Q96PU5-6;P46934-4 Q96PU5-7;Q96PU5-5;P46934-4 NEDD4L;NEDD4 E3 ubiquitin-protein ligase NEDD4-like;E3 ubiquitin-protein ligase NEDD4 0 ; 125.56 0.00094396 9421200 79440 91729 77742 83008 100137 58053.7 87620 70625 90731 FALSE TRUE 74467.9922 98520.7106 79586.07695 85138.12581 92272.64395 74812.86077 74482.19442 79442.68671 75587.40996 0.985190421 1.303401065 1.052901231 1.126353263 1.220740914 0.989752934 0.985378312 1.051004218 1 16.20585833 2.223378712 24.89577969 1.002623428 1.148228219 0.355246598 0.087110672 220.1938184 361078.6667 0.030418073 0.022550285 167.2548468 -2.223378712 0.145604792 LLFGHSTEGDILELVDGHFDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLFGHSTEGDILELVDGHFDTK 22 0 Q9UHY7;A0A0C4DGY8;D6RA00;Q9UHY7-2 Q9UHY7 ENOPH1 Enolase-phosphatase E1 0 ;; 306.13 1.22E-56 445600000 711571 779217 691225 625440 886537 523820 849211 857333 1445533 FALSE TRUE 667035.0413 836911.0375 707621.1834 641489.8493 816911.9601 675038.3305 721879.6942 964372.9123 1204264.204 0.553894269 0.694956335 0.587596294 0.532681987 0.67834945 0.560540061 0.599436313 0.800798454 1 20.19972051 1.010017011 2.943637156 0.998498975 0.606421273 0.867004619 0.05196479 0.077748033 1.570752449 0.047625691 0.012599089 10.23333075 -1.010017011 -0.392077702 LLGEGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLGEGLR 7 0 H7C3H9 H7C3H9 METTL6 0 79.454 0.075798 335480000 386380 629910 502510 482520 659320 567630 488870 529370 467880 FALSE TRUE 362197.1655 676549.1918 514429.7745 494902.2801 607539.6668 731495.5663 415568.4819 595463.0098 389787.8054 0.929216257 1.735685885 1.319768775 1.269671019 1.558642057 1.876650722 1.066140285 1.527659413 1 18.57232943 -1.35802718 4.986693174 0.999732216 1.425702975 0.166757165 0.286523919 0.000772747 9.95E-05 0.251317851 0.059199516 0.043850325 1.35802718 0.425970759 LLGGQLGLEDFIFAHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLGGQLGLEDFIFAHVK 17 0 Q8TF65 Q8TF65 GIPC2 PDZ domain-containing protein GIPC2 0 ; 157.8 1.21E-08 15812000 78790 90593 88812 92167 109936 75627 88903 88881 82520 FALSE TRUE 73858.67454 97300.59998 90918.66258 94532.16126 101302.07 97459.2872 75572.82048 99977.9885 68746.8789 1.074356767 1.415345708 1.322513313 1.37507568 1.473551551 1.41765399 1.099290931 1.454291309 1 16.0690066 -1.09808189 4.198938226 0.999947815 1.328698621 0.359157457 0.138115663 8938736.33 2337607.379 4377.415397 0.030546042 0.079784423 1.09808189 0.328750806 LLGHWEEAAHDLALACK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLGHWEEAAHDLALACK 17 0 P50502;Q8IZP2;H7C3I1 P50502 ST13;ST13P4 Hsc70-interacting protein;Putative protein FAM10A4 0 ;;; 214.53 3.42E-15 1688033000 2294272 2264848 2131178 2041273 2651493 1862900 2794443 2247419 2360150 FALSE TRUE 2150677.611 2432539.702 2181730.549 2093655.521 2443255.435 2400688.988 2375442.214 2528014.209 1966225.718 1.093810131 1.23716198 1.109603302 1.064809346 1.24261188 1.22096307 1.208122848 1.285719227 1 20.90699752 2.712195253 24.95962632 1.206889042 1.142024985 0.095331315 0.087484693 1553.621651 1470784.769 0.025771173 0.024305031 515.4603366 -2.712195253 -0.064864057 LLGIFENQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLGIFENQDR 10 0 Q9NZJ9;F8VRL4;F8VRR0;A0A0C4DGJ4 Q9NZJ9 NUDT4 Diphosphoinositol polyphosphate phosphohydrolase 2 0 ;; 113.62 0.0034053 115302000 154941 169347 159166 147845 186915 139882 164700 141117 191882 FALSE TRUE 145243.5194 181885.6281 162941.4927 151638.953 172235.4499 180263.6626 140004.764 158735.7681 159855.6546 0.90859169 1.137811662 1.019303903 0.948599243 1.077443587 1.127665224 0.875819904 0.992994389 1 17.28641025 1.73471352 25 0.948391259 1.044448141 0.183410063 0.078121174 0.606906583 3898.575249 0.033905147 0.018802151 54.28920971 -1.73471352 0.096056882 LLGLELALS(ph)SDAESAAGGPAGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLGLELALSSDAESAAGGPAGVR 23 0 O94964-2 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 LLGLELALS(0.499)S(0.499)DAES(0.002)AAGGPAGVR 96.544 0.0037567 8557100 14002 14841 13771 16255 14851 12912 17048 13327 11168 TRUE FALSE 13125.63981 15939.84308 14097.65462 16672.13082 13684.66237 16639.48479 14491.81067 14990.90529 9303.988652 1.410754065 1.71322684 1.51522698 1.791933701 1.470838248 1.78842488 1.55759118 1.611234262 1 13.18363362 0.016369006 1.592401339 0.999625522 1.615606374 0.690486486 0.127713024 13.66897935 21.17895719 0.117812505 0.02947545 1.038410345 -0.016369006 0.615980852 LLGLTPPEGGAGDRS(ph)EEEASSTEKPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLGLTPPEGGAGDRSEEEASSTEKPTK 27 2 V9GYY5;Q9UGY1 V9GYY5 NOL12 Nucleolar protein 12 1 LLGLTPPEGGAGDRS(1)EEEASSTEKPTK;LLGLTPPEGGAGDRS(1)EEEASSTEKPTK 290.39 9.18E-71 427610000 494170 311750 382530 368780 373290 301140 513960 319890 446670 TRUE FALSE 463240.7818 334832.2944 391603.7922 378243.5191 343973.3092 388074.2294 436896.4694 359828.9707 372117.8914 1.244876402 0.899801655 1.052364859 1.016461524 0.92436649 1.042879793 1.174080794 0.966975733 1 18.50540023 1.999105259 24.99775047 1.076890941 1.01057584 0 0.107403769 85.02888851 2375623.084 0.037152096 0.027120837 99.79419041 -1.999105259 -0.0663151 LLGPAPEDDGGHNDHSQPQASQDQDS(ph)HTLSPQV ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLGPAPEDDGGHNDHSQPQASQDQDSHTLSPQV 33 0 Q92610 Q92610 ZNF592 Zinc finger protein 592 1 LLGPAPEDDGGHNDHSQPQASQDQDS(0.472)HT(0.074)LS(0.454)PQV;LLGPAPEDDGGHNDHSQPQASQDQDS(0.675)HT(0.122)LS(0.203)PQV 240.3 1.19E-46 470990000 209449 219071 248158 214550 232908 241571 271721 249105 326820 TRUE FALSE 196339.961 235291.2448 254044.4249 220055.7162 214616.3452 311308.6261 230978.9586 280206.3076 272271.6307 0.721117953 0.864178336 0.933055068 0.808221245 0.788243508 1.143375185 0.84834016 1.029142503 1 18.05468714 2.273228061 24.9999955 0.982508398 0.842925883 0.485355892 0.090656094 188.785897 136139.9117 0.030064307 0.02515258 187.5979383 -2.273228061 -0.139582515 LLGPAPEDDGGHNDHSQPQASQDQDSHTLS(ph)PQV ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLGPAPEDDGGHNDHSQPQASQDQDSHTLSPQV 33 0 Q92610 Q92610 ZNF592 Zinc finger protein 592 1 LLGPAPEDDGGHNDHSQPQAS(0.085)QDQDS(0.289)HT(0.04)LS(0.585)PQV 119.59 1.45E-06 111280000 50386 54198 53058 52392 54720 51095 60437 52059 65335 TRUE FALSE 47232.4302 58210.87631 54316.56082 53736.46742 50422.51193 65845.29704 51375.03292 58558.68075 54430.16642 0.867762002 1.069459826 0.997912819 0.987255247 0.92637071 1.209720664 0.943870583 1.075849747 1 15.73211883 LLGPQWLDYDCDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLGPQWLDYDCDR 13 0 Q6P9B6 Q6P9B6 TLDC1 TLD domain-containing protein 1 0 96.334 0.0099686 39106000 145410 159130 137770 141840 163170 120910 182070 144970 181250 FALSE TRUE 136309.0477 170912.1508 141037.9695 145479.8545 150355.2864 155814.7542 154770.2938 163069.8236 150998.2041 0.902719661 1.13188201 0.934037397 0.963454204 0.995742216 1.031898062 1.024981023 1.079945451 1 17.20417187 2.213994348 6.006139217 1.035234862 0.997431883 0.113479718 0.062871574 0.491911283 55.05942534 0.022993276 0.017387938 163.6795218 -2.213994348 -0.037802978 LLGS(ph)SEDLS(ph)SDSESHLPEEPAPLSPQQAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLGSSEDLSSDSESHLPEEPAPLSPQQAFR 30 0 C9JIE2;Q86TI0-2;Q86TI0;H0Y8P0;H0YA01;H7C380;H7C0Z7 C9JIE2 TBC1D1 TBC1 domain family member 1 2 LLGS(0.706)S(0.175)EDLS(0.582)S(0.532)DS(0.003)ES(0.002)HLPEEPAPLSPQQAFR 88.744 0.00061222 48411000 17332 20313 19726 19179 19892 16249 22845 21590 20605 TRUE FALSE 16247.22106 21816.99566 20193.91004 19671.16561 18329.76256 20939.82252 19419.60433 24285.55903 17165.89239 0.946482752 1.270950275 1.176397334 1.145944829 1.067801321 1.219850506 1.131290113 1.41475657 1 14.06725724 LLGSENDT(ph)GSPDFYTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLGSENDTGSPDFYTPR 17 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 LLGSENDT(0.802)GS(0.198)PDFYTPR 282.33 5.58E-35 78904000 130570 148600 123960 128300 140950 108980 146520 119240 129250 TRUE FALSE 122397.8568 159602.4986 126900.3897 131592.3952 129880.3556 140440.7569 124550.6862 134127.3765 107677.34 1.136709513 1.48222921 1.17852456 1.222099238 1.206199517 1.304274018 1.156702851 1.245641622 1 16.71635515 -4.999999998 0.129937403 0.130456793 1.362245428 0.369683439 0.098142688 134.3622329 1.102440152 30.24374147 0.693609944 1.00E-05 4.999999998 1.231788635 LLGSENDTGS(ph)PDFYTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLGSENDTGSPDFYTPR 17 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 LLGSENDT(0.361)GS(0.639)PDFYTPR 386.84 9.27E-122 72154000 94570 101460 96488 108190 104530 85527 103410 89844 108300 TRUE FALSE 88651.03251 108972.204 98776.74092 110966.3386 96320.63545 110217.2565 87904.63051 101061.2212 90224.03036 0.982565644 1.207795789 1.094794153 1.229897824 1.067571855 1.221595356 0.974292881 1.12011424 1 16.46122411 1.729922934 20.91430635 1.035487673 1.139149955 0.246990277 0.084010658 0.367811824 868.7071411 0.033767664 0.018713643 53.69365085 -1.729922934 0.103662283 LLGWDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLGWDDR 7 0 Q8WUY1 Q8WUY1 THEM6 Protein THEM6 0 ;; 185.22 0.0014344 166115000 640670 677370 668060 612460 824850 651690 744260 751080 751940 FALSE TRUE 600571.6083 727523.1796 683906.6987 628176.7605 760069.6083 839822.3237 632665.1224 844853.9913 626436.3563 0.958711292 1.161368066 1.09174171 1.002778262 1.213322951 1.340634711 1.009943175 1.34866692 1 19.25680842 2.722506291 24.26440576 1.181861852 1.077951512 0.193804842 0.126346115 1061.434819 1604242.878 0.037547403 0.035513377 527.8448534 -2.722506291 -0.103910339 LLHDLQIGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLHDLQIGEK 10 0 P49756;P49756-2;P49756-3;E9PQU5 P49756 RBM25 RNA-binding protein 25 0 103.91 0.0044523 0 565070 499400 540270 529300 547190 403230 632920 490130 641640 FALSE TRUE 529703.2774 536376.0956 553085.4595 542882.7341 504215.9047 519635.9551 538019.5217 551323.8094 534546.1388 0.990940237 1.003423384 1.034682358 1.015595651 0.943259839 0.972106835 1.006497817 1.031386758 1 19.02795495 -2.234398215 2.180168198 0.996281098 1.001146003 0 0.027039169 49071779.23 12732959.83 940181.9274 0.006795753 0.005829104 2.234398215 0.004864905 LLHDQIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLHDQIEK 8 0 P12270 P12270 TPR Nucleoprotein TPR 0 ;; 139.74 0.00066076 539340000 1882030 1720410 1777420 1737830 1972110 1395160 2131280 1687050 2130060 FALSE TRUE 1764237.102 1847790.946 1819581.242 1782425.66 1817228.436 1797920.043 1811714.35 1897681.906 1774539.225 0.99419448 1.041279291 1.025382373 1.004444215 1.024056504 1.013175712 1.02094917 1.069394172 1 20.75901303 1.420965408 24.99996505 1.038188648 1.020273696 0.088911743 0.020802992 158.514116 70571.69332 0.011922436 0.004540843 26.3612141 -1.420965408 -0.017914952 LLHEDLDES(ph)DDDMDEK ddPTM_SK-BR-3_Pertuzumab_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 290.94 5.31E-45 484970000 666490 422740 482940 498660 495700 374340 611310 406860 333490 TRUE FALSE 624775.5806 454040.1095 494395.5649 511456.4598 456769.7216 482405.8811 519649.7406 457657.3666 277828.3646 2.248782559 1.634246777 1.779499964 1.840908003 1.644071592 1.736344962 1.870398443 1.647266532 1 18.08383437 -2.251797889 0.357849031 1.87E-11 1.822588586 0.693969875 0.17068519 27.62487883 1.317169253 22.25911837 0.1189822 0.005600182 2.251797889 1.822588586 LLHEVQELTTEVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LLHEVQELTTEVEK 14 0 Q13561;Q13561-3;Q13561-2;F8W1I6;F8VW18;F8VX93;F8VRV7;H0YHL1 Q13561 DCTN2 Dynactin subunit 2 0 ;;;; 230.36 9.43E-13 448628000 765202 632306 711907 680634 733020 571746 847677 653495 917396 FALSE TRUE 717309.3727 679122.5942 728793.7702 698100.2208 675451.5661 736799.7887 720575.7033 735085.2893 764276.681 0.938546721 0.888582121 0.953573213 0.913412954 0.88377885 0.964048501 0.942820475 0.961805204 1 19.54373549 1.215724966 0.795697467 0.998658758 0.917811785 0.537497915 0.024139777 0.440527222 0.631176963 0.021619826 0.008332797 16.4333069 -1.215724966 -0.080846974 LLHHDDPEVLADTCWAISYLTDGPNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LLHHDDPEVLADTCWAISYLTDGPNER 27 0 P52292 P52292 KPNA2 Importin subunit alpha-1 0 ;;;; 327.53 2.27E-95 1137652000 456918 519309 533116 512566 592466 513034 612461 502692 566355 FALSE TRUE 428320.318 557759.1787 545761.7633 525719.3113 545936.1103 661138.5874 520628.1589 565454.2028 471826.6917 0.907791622 1.182127227 1.156699638 1.114221218 1.157069152 1.401231848 1.103430916 1.198436232 1 18.84789751 4.739696686 24.24566989 1.173697579 0.90779149 0.386255875 0.100921328 60.51477457 1291233.696 0.021655568 0.132926527 54915.72046 -4.739696686 -0.26590609 LLHIEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LLHIEELR 8 0 Q9Y224 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ;;;;;; 194.2 0.00016665 2421104000 2275972 2716716 2545643 2434552 2827024 2283841 2795981 2383323 2991626 FALSE TRUE 2133522.975 2917864.479 2606026.854 2497026.726 2605000.939 2943148.822 2376749.606 2680886.123 2492304.294 0.856044336 1.17074969 1.045629484 1.001894806 1.045217851 1.180894656 0.953635401 1.075665652 1 21.24904879 1.663838494 24.13113901 1.010479929 1.061902929 0.029171136 0.094351053 0.92831653 378.5118086 0.040110056 0.022240906 46.11460509 -1.663838494 0.051423 LLHMDS(ph)DDEIPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LLHMDSDDEIPIR 13 0 Q1MSJ5-1;Q1MSJ5;Q1MSJ5-2 Q1MSJ5-1 CSPP1 Centrosome and spindle pole-associated protein 1 1 LLHMDS(1)DDEIPIR;LLHMDS(1)DDEIPIR;LLHMDS(1)DDEIPIR;LLHMDS(1)DDEIPIR;LLHMDS(1)DDEIPIR;LLHMDS(1)DDEIPIR 233.4 7.95E-17 431557000 499048 531576 526076 512947 558880 457403 598131 472398 521267 TRUE FALSE 467813.4765 570934.4401 538554.7712 526110.0884 514987.8192 589447.8208 508446.8093 531377.9302 434264.1702 1.077255525 1.314716892 1.240154745 1.211497804 1.185886045 1.357348502 1.170823762 1.223628304 1 18.7282134 0.318545056 1.186777708 0.999723827 1.236668481 0.446349549 0.076967624 3.05384454 4.548812929 0.067621606 0.020088668 2.082308422 -0.318545056 0.236944654 LLHQLADLVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLHQLADLVER 11 0 H0Y2X5;P47895;H0YNQ3;H0YKF9 H0Y2X5 ALDH1A3 Aldehyde dehydrogenase family 1 member A3 0 ; 182.35 0.00090158 96077000 266500 280111 221271 209302 314492 184030 264732 271787 520960 FALSE TRUE 249820.2407 300850.7099 226519.6526 214673.0437 289793.0669 237156.4735 225037.8943 305720.2052 434008.4105 0.57561152 0.693190967 0.521924569 0.494628764 0.667713021 0.546432898 0.518510445 0.704410785 1 18.72736347 0.916493912 4.306709987 0.999873869 0.577687387 0.819258738 0.063363626 0.165531816 7.209159068 0.061377428 0.015624753 8.250759187 -0.916493912 -0.422186482 LLHTLEGHAMPIR ddPTM_SK-BR-3_Pertuzumab_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" 0 169.89 1.60E-05 93155000 60215 90924 52993 60052 103790 48461 53614 88829 99867 FALSE TRUE 56446.25064 97656.10757 54250.01899 61593.03599 95638.75207 62450.904 45575.07843 99919.49619 83198.55253 0.678452316 1.173771713 0.652054841 0.740313793 1.14952423 0.750624886 0.547786915 1.200976377 1 16.34427081 3.964158532 24.6936301 0.824073351 0.955419647 0 0.240750628 1058.750579 2016895.547 0.058217129 0.105802249 9207.856287 -3.964158532 0.131346296 LLHVAVSDVNDDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLHVAVSDVNDDVR 14 0 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;; 218.11 5.51E-12 563720000 463470 516170 514120 508140 479080 486720 582840 468820 448110 FALSE TRUE 434462.24 554387.7639 526315.1692 521179.7327 441454.9893 627228.1628 495448.5528 527353.209 373317.5461 1.163787356 1.485030022 1.409832393 1.396076177 1.182518727 1.680146485 1.327150459 1.412612974 1 18.51004379 -1.01144661 3.393713989 0.999835915 1.39646505 0.398478338 0.146619294 12684612.19 21250627.41 25826.90052 0.032194725 0.097398751 1.01144661 0.396629135 LLHYAGEVTYSVTGFLDKNNDLLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLHYAGEVTYSVTGFLDKNNDLLFR 25 1 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 149.85 1.10E-07 82963000 114278 180053 130453 117518 199556 120564 143149 140115 143986 FALSE TRUE 107125.544 193384.3115 133547.4068 120533.7108 183883.6767 155368.8696 121685.1364 157608.6662 119953.8064 0.893056646 1.612156523 1.113323626 1.004834398 1.532954078 1.295239178 1.014433306 1.313911337 1 16.87211941 0.394997571 0.465375204 0.982907553 1.267772288 0.057319036 0.232701868 5.819284363 2.167413547 0.454437526 0.12714193 2.483119215 -0.394997571 0.284864735 LLIDGDGAGDDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLIDGDGAGDDRR 13 1 Q6I9Y2;H7C5E3 Q6I9Y2 THOC7 THO complex subunit 7 homolog 0 ; 218.02 3.98E-11 267650000 276660 360770 355380 344690 390350 355340 366740 326490 408420 FALSE TRUE 259344.3445 387481.7862 363809.7814 353535.329 359693.4856 457920.8895 311750.7416 367252.9952 340252.0635 0.762212407 1.138808042 1.069236077 1.039039485 1.057138293 1.345828398 0.916234683 1.079355674 1 18.37624439 4.744765737 24.5133476 1.083169218 0.762212218 0.450992917 0.110405067 478.4366712 1889996.117 0.024221962 0.224403043 55560.4477 -4.744765737 -0.320957 LLIDPNCSGHS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLIDPNCSGHSPR 13 0 Q8WYQ5-3;Q8WYQ5;Q8WYQ5-2;C9JSD5 Q8WYQ5-3 DGCR8 Microprocessor complex subunit DGCR8 1 LLIDPNCS(0.001)GHS(0.999)PR;LLIDPNCSGHS(1)PR;LLIDPNCSGHS(1)PR 165.8 2.24E-05 369019000 563500 602650 659520 602250 734470 720870 853570 688020 840230 TRUE FALSE 528231.5409 647270.8331 675164.1258 617704.7546 676787.6889 928973.4667 725585.1027 773920.8115 699990.1849 0.754627068 0.924685584 0.964533704 0.882447737 0.966853112 1.327123561 1.036564681 1.105616662 1 19.41697517 2.46115937 24.98252151 1.122304108 0.904792028 0.545419553 0.100858882 176.5746775 276361.7375 0.032132646 0.026891043 289.1740852 -2.46115937 -0.217512079 LLIHQSLAGGIIGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLIHQSLAGGIIGVK 15 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 156.17 1.18E-08 0 13007 35917 27094 28558 33901 25092 32902 31045 28959 FALSE TRUE 12192.91509 38576.33205 27736.68247 29290.84663 31238.55221 32335.65307 27968.65055 34921.03659 24125.55582 0.505394163 1.598982106 1.149680558 1.214100386 1.294832436 1.340307071 1.159295593 1.447470759 1 14.55827456 4.753468622 24.91569341 1.284666025 0.505393585 0.679446866 0.16615 1470.33072 2457314.716 0.036420471 0.842615548 56685.06147 -4.753468622 -0.77927244 LLILDEVHLLHEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLILDEVHLLHEDR 14 0 Q8N3C0;Q8N3C0-4 Q8N3C0 ASCC3 Activating signal cointegrator 1 complex subunit 3 0 157.52 3.05E-06 17692000 15674 17452 16255 18203 15348 15348 20340 16025 9970.7 FALSE TRUE 14692.99232 18744.16424 16640.57628 18670.1198 14142.62999 19778.71845 17290.20583 18025.75653 8306.525757 1.768849306 2.256558854 2.003313631 2.247644845 1.702592685 2.381106015 2.081520763 2.170071707 1 13.02002947 -1.118878638 4.692002266 0.999923199 2.092785815 0.717240417 0.212190242 0.000152718 2.87E-05 0.176200182 0.041527764 0.076053878 1.118878638 1.092862616 LLIVQDAS(ph)ER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLIVQDASER 10 0 O95772-2;C9JPX5;C9JKL2;O95772 O95772-2 STARD3NL MLN64 N-terminal domain homolog 1 LLIVQDAS(1)ER;LLIVQDAS(1)ER;LLIVQDAS(1)ER;LLIVQDAS(1)ER 174.72 4.29E-06 234044000 433250 531250 412774 385905 608740 350714 563650 550570 549480 TRUE FALSE 406133.6559 570584.3028 422565.1942 395807.9756 560932.0159 451959.4384 479135.9152 619309.8765 457768.2382 0.887203659 1.246447995 0.923098544 0.864647091 1.225362463 0.98731061 1.046677937 1.352889573 1 18.80425784 1.431688851 24.99930623 1.184225016 1.036616964 0.141379744 0.152481706 121.243552 66719.98349 0.080062637 0.034633167 27.02021813 -1.431688851 -0.147608052 LLKEEDMTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLKEEDMTK 9 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ; 152.07 7.42E-05 999380000 2337790 1408020 1846220 1645000 1980860 1321400 2334390 1709130 2446620 FALSE TRUE 2191471.897 1512271.266 1890013.21 1687213.485 1825291.246 1702866.729 1984369.891 1922518.643 2038263.316 1.075166236 0.74194107 0.92726646 0.827770127 0.895512975 0.835449824 0.973559145 0.943214072 1 20.95890901 1.681202335 6.756101934 0.968862075 0.870934068 0.177859776 0.086281352 0.187690592 17.40780571 0.039072692 0.019969735 47.99570057 -1.681202335 -0.097928007 LLKEGEEPTVYS(ph)DEEEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLKEGEEPTVYSDEEEPK 18 1 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 1 LLKEGEEPTVYS(1)DEEEPK;LLKEGEEPTVYS(1)DEEEPK 245.09 2.10E-24 201878000 507170 220700 310800 323090 429910 329750 500680 280010 261220 TRUE FALSE 475427.135 237040.8576 318172.3228 331381.0364 396146.6028 424943.472 425607.6821 314969.8649 217620.6945 2.18465958 1.089238587 1.462049938 1.522745974 1.820353546 1.952679514 1.95573166 1.447334159 1 17.73145623 2.874796598 4.633080031 1.740509543 1.460852667 0 0.393655852 0.527953206 17.63327833 0.11304123 0.120914228 749.5430779 -2.874796598 -0.279656877 LLKEGEEPTVYS(ph)DEEEPKDESAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 LLKEGEEPTVYSDEEEPKDESAR 23 2 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 1 LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPT(0.011)VY(0.001)S(0.988)DEEEPKDESAR;LLKEGEEPT(0.005)VY(0.002)S(0.993)DEEEPKDESAR;LLKEGEEPT(0.001)VYS(0.999)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPTVYS(0.92)DEEEPKDES(0.08)AR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPT(0.001)VYS(0.999)DEEEPKDESAR 238.12 1.87E-37 11438640000 7250160 3892432 3986261 4271001 6279140 3086332 6546310 4145440 7749770 TRUE FALSE 6796385.428 4180631.715 4080816.993 4380602.116 5786001.673 3977305.946 5564751.588 4663007.309 6456283.322 1.052677692 0.64752916 0.63206907 0.67850215 0.8961815 0.616036464 0.861912545 0.72224329 1 22.62227246 -0.1239175 0.565377861 1.022485346 0.731310467 0.192415522 0.141162202 7.47577728 2.562661206 0.508417248 0.056770285 0.751765688 0.1239175 -0.291174878 LLKPGEEPSEYT(ph)DEEDTKDHNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLKPGEEPSEYTDEEDTKDHNK 22 2 U3KQM0;O15173;O15173-2;U3KPU8 U3KQM0 PGRMC2 Membrane-associated progesterone receptor component 2 1 LLKPGEEPSEYT(1)DEEDTKDHNK;LLKPGEEPSEYT(1)DEEDTKDHNK 260.14 3.04E-37 791220000 1506780 444580 657170 605490 664030 566470 1026780 589490 537170 TRUE FALSE 1412473.329 477497.1658 672758.3827 621027.8985 611879.7624 730000.6931 872823.8712 663089.1241 447512.8567 3.156274302 1.067002118 1.503327497 1.38773197 1.367289795 1.631239599 1.95038837 1.481720836 1 18.77156961 0.977725836 22.8177495 0.999999968 1.631185973 0.126490914 0.566798694 1291.131065 1322644.501 0.497419787 0.124354947 9.5000488 -0.977725836 0.631186005 LLKPGEEPSEYT(ph)DEEDTKDHNKQD ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLKPGEEPSEYTDEEDTKDHNKQD 24 3 U3KQM0;O15173;O15173-2;U3KPU8 U3KQM0 PGRMC2 Membrane-associated progesterone receptor component 2 1 LLKPGEEPS(0.166)EY(0.057)T(0.774)DEEDT(0.004)KDHNKQD;LLKPGEEPSEYT(1)DEEDTKDHNKQD;LLKPGEEPSEYT(1)DEEDTKDHNKQD;LLKPGEEPSEYT(1)DEEDTKDHNKQD 228.62 3.55E-33 1404290000 666396 227626 283283 284962 364356 207698 492334 280027 444956 TRUE FALSE 624687.4639 244479.6659 290002.6065 292274.6074 335740.9495 267657.0409 418513.0873 314988.9874 370689.9691 1.685201964 0.659525982 0.78233195 0.788461064 0.905719004 0.722050941 1.129011093 0.849737014 1 18.49985355 -0.464159636 7.858848776 1.00001696 0.902539007 0 0.295473981 0 0 0.259186508 0.061090846 0.343431687 0.464159636 -0.097477953 LLLAADPGGS(ph)PAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLLAADPGGSPAQR 14 0 Q5SQI0-7;Q5SQI0-6;Q5SQI0-5;Q5SQI0-4;Q5SQI0-3;Q5SQI0-2;Q5SQI0 Q5SQI0-7 ATAT1 Alpha-tubulin N-acetyltransferase 1 1 LLLAADPGGS(1)PAQR;LLLAADPGGS(1)PAQR 163.23 4.52E-06 136785000 144566 194899 156046 171309 187709 168342 221530 186373 180104 TRUE FALSE 135517.8721 209329.5248 159747.4848 175705.079 172967.0923 216939.6026 188313.6331 209642.0793 150043.4789 0.903190683 1.395125775 1.064674626 1.17102776 1.152779805 1.445844926 1.25506043 1.397208868 1 17.19502109 2.343443076 20.75985687 1.297201261 1.164111691 0.124778981 0.167901181 6.308037557 1224.118915 0.05222975 0.043698436 220.5175079 -2.343443076 -0.13308957 LLLAEDS(ph)EEEVDFLSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 LLLAEDSEEEVDFLSER 17 0 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER 442.7 2.03E-182 2103187100 1422431.1 1633467.3 1555086.2 1559556.1 1655209.4 1373807.9 1709314 1366477.7 1343527.6 TRUE FALSE 1333403.677 1754410.919 1591973.579 1599576.95 1525215.931 1770403.939 1453018.234 1537085.449 1119284.164 1.191300404 1.567440133 1.422314038 1.429107104 1.362670874 1.581728747 1.298167419 1.373275436 1 20.09414492 0.460401406 0.925380678 0.998537304 1.436077168 0.54940847 0.114726607 1.254098797 1.518613408 0.102035952 0.032352055 2.886698365 -0.460401406 0.437539864 LLLAEDS(ph)EEEVDFLSERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLLAEDSEEEVDFLSERR 18 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 LLLAEDS(1)EEEVDFLSERR;LLLAEDS(1)EEEVDFLSERR 223.93 2.99E-19 61179000 19595.2 29378.4 22920.6 24743 28746.3 20285.9 25883.9 18695.3 38267.3 TRUE FALSE 18368.77141 31553.6073 23464.28746 25377.94727 26488.68155 26142.11002 22002.84949 21029.44936 31880.24041 0.576180454 0.989754371 0.736013504 0.796040022 0.830880859 0.820009814 0.690172006 0.659638983 1 14.96037489 1.778108939 25 0.749472362 0.809648542 0 0.13640691 198.8935903 125777.0372 0.056687585 0.031489803 59.99415477 -1.778108939 0.06017618 LLLAS(ph)PPNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLLASPPNER 10 0 Q52LW3 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 LLLAS(1)PPNER;LLLAS(1)PPNER;LLLAS(1)PPNER 111.96 0.0017665 229894000 259994 264116 278986 265583 294273 241818 296678 262072 364691 TRUE FALSE 243721.4396 283671.4235 285603.6797 272398.3094 271161.9856 311626.931 252193.8881 294792.2661 303821.7161 0.802185712 0.933677247 0.940037083 0.896572875 0.892503634 1.025690115 0.830071962 0.970280432 1 18.21286547 -2.036792283 0.011638652 1.95957085 2.14E-06 0.252656586 0.060408375 9613.590123 15.42774518 1428.45615 1178.299388 0.009187719 2.036792283 -1.959568711 LLLDTS(ph)PPGGVVLSSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLLDTSPPGGVVLSSFR 17 0 O15211;A2AB89 O15211 RGL2 Ral guanine nucleotide dissociation stimulator-like 2 1 LLLDT(0.036)S(0.964)PPGGVVLSSFR;LLLDT(0.148)S(0.852)PPGGVVLSSFR 150.59 2.95E-07 139148000 419280 549190 475990 468670 538650 422170 513600 464670 455750 TRUE FALSE 393038.0132 589852.599 487280.7076 480696.8657 496346.6018 544043.6256 436590.448 522685.0724 379682.3807 1.035175803 1.553542195 1.283390361 1.266049967 1.307267935 1.43289142 1.14988335 1.376637682 1 18.53443353 -1.911345636 0.328022259 0.684916417 1.338170849 0.274041544 0.145452628 38.23016525 2.006739062 9.353160218 0.118537106 0.012264628 1.911345636 0.653254431 LLLEAQAATGFLLDPVKGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLLEAQAATGFLLDPVKGER 20 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 152.06 6.27E-08 147297000 176367 205817 210347 213760 256540 196116 227239 198995 224843 FALSE TRUE 165328.5043 221055.9048 215336.5302 219245.4435 236392.3832 252731.5055 193166.6215 223839.9638 187315.2508 0.882621696 1.18012764 1.149594223 1.170462323 1.262002866 1.349230799 1.031238091 1.194990599 1 17.51510884 4.739524422 24.52520577 1.172246599 0.882621577 0.443634473 0.100015333 55.95022448 1423444.994 0.022153175 0.134786455 54893.94236 -4.739524422 -0.289625022 LLLEFTDTSYEEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LLLEFTDTSYEEKR 14 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;;;; 305.69 3.51E-44 5410937000 2890499 2708459 2970954 2875336 3238862 2402291 3676457 2817550 5600181 FALSE TRUE 2709587.827 2908996.123 3041426.432 2949121.99 2984494.843 3095793.414 3125206.403 3169327.32 4665474.613 0.580774316 0.623515583 0.651900757 0.63211618 0.639698014 0.663553801 0.669858195 0.679315093 1 22.15359242 -5 0.246403792 3.136242993 0.60929034 0.982464196 0.015320719 20.96316246 0.208419225 22.4796631 0.022658692 1.00E-05 5 -2.526952653 LLLEGISSTHVNHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLLEGISSTHVNHLR 15 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39 B7ZC38 SH3GLB2 Endophilin-B2 0 119.32 0.00012841 252510000 44454 101170 84083 75637 96860 79952 83300 84740 83714 FALSE TRUE 41671.70349 108660.7321 86077.48847 77577.97347 89253.00631 103032.8445 70809.93832 95319.97554 69741.59259 0.5975158 1.558047759 1.234234626 1.112363091 1.279767252 1.477351472 1.015318631 1.366759376 1 16.08973169 -0.589346778 7.362792179 1.0000032 1.234649314 0.044641167 0.269150669 0 0 0.2319069 0.054660981 0.257426483 0.589346778 0.234646114 LLLEHLECLVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 76.326 0.031419 52148000 39629 53221 46738 52156 55583 43233 55640 47009 61033 FALSE TRUE 37148.69163 57161.53822 47846.64743 53494.41126 51217.73539 55713.66527 47297.29854 52878.17713 50846.19801 0.730609034 1.124204768 0.941007377 1.052082817 1.007307083 1.095729228 0.930203248 1.039963246 1 15.63385228 4.75175896 24.89923012 1.019747553 0.730608837 0.698662648 0.060462758 1164.88755 2197568.583 0.013355215 0.257683485 56462.35136 -4.75175896 -0.289138716 LLLERPS(ph)PIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LLLERPSPIR 10 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 LLLERPS(1)PIR;LLLERPS(1)PIR;LLLERPS(1)PIR;LLLERPS(1)PIR;LLLERPS(1)PIR;LLLERPS(1)PIR;LLLERPS(1)PIR;LLLERPS(1)PIR 145.71 1.81E-05 4407821000 2829739 4029815 2755460 2600648 3752011 1972423 2818969 3572814 3819210 TRUE FALSE 2652630.687 4328186.696 2820820.812 2667385.031 3457343.191 2541829.5 2396290.768 4018887.693 3181759.178 0.83369939 1.360312473 0.886560124 0.838336556 1.086613725 0.798875515 0.753133922 1.263102412 1 21.60139321 3.734391136 22.71761421 0.918690964 1.131265845 0.073681558 0.19541714 142.0329315 443826.281 0.046515127 0.081462473 5424.892493 -3.734391136 0.21257488 LLLERPS(ph)PIRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 LLLERPSPIRDR 12 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 LLLERPS(1)PIRDR;LLLERPS(1)PIRDR;LLLERPS(1)PIRDR;LLLERPS(1)PIRDR;LLLERPS(1)PIRDR;LLLERPS(1)PIRDR;LLLERPS(1)PIRDR;LLLERPS(1)PIRDR;LLLERPS(1)PIRDR;LLLERPS(1)PIRDR 159.69 3.24E-05 15353141000 4221659 4922325 4768322 4660405 5377652 4219940 5010647 4263782 6197188 TRUE FALSE 3957432.899 5286779.065 4881428.85 4779998.882 4955312.904 5438168.173 4259346.999 4796124.568 5162837.287 0.766522879 1.024006524 0.945493452 0.925847284 0.959804198 1.053329375 0.825001208 0.9289707 1 22.2997327 -1.193107756 5.43256589 1.000002615 0.936765982 0.059269291 0.083970185 2.45E-06 3.64E-07 0.074987054 0.017673887 0.06410505 1.193107756 -0.063236633 LLLEVTYEAIVDGGINPDSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 223.77 7.97E-25 431078000 181788 220172 233200 233848 251410 235490 227870 183651 184602 FALSE TRUE 170410.2136 236473.764 238731.6141 239848.9356 231665.2727 303472.1401 193703.0089 206580.2316 153790.7336 1.108065548 1.53763337 1.552314684 1.559579891 1.506366914 1.973279748 1.259523278 1.343255388 1 17.23060905 -0.452282683 7.158418451 0.999999752 1.499015971 0.301650466 0.227898748 0 0 0.203925513 0.048065704 0.352953357 0.452282683 0.499016219 LLLFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLLFDR 6 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 100.82 0.086601 75433000 91786 120180 101680 101290 126240 91885 114520 112920 108520 FALSE TRUE 86041.2781 129078.2522 104091.8976 103889.2729 116325.6196 118410.7079 97348.78915 127018.3106 90407.31093 0.951707082 1.427741307 1.15136593 1.149124687 1.28668377 1.30974704 1.076780054 1.404956184 1 16.46415182 -1.150924816 4.340875586 0.999953584 1.225111639 0.181688129 0.146181728 5.82E-05 1.14E-05 0.125447839 0.02956225 0.070643984 1.150924816 0.225158056 LLLFDYDKVELANMNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLLFDYDKVELANMNR 16 1 Q9GZZ9-2;Q9GZZ9;E7EWE1;E7EQ61;C9JRV9;C9J5W5;C9J0F6 Q9GZZ9-2 UBA5 Ubiquitin-like modifier-activating enzyme 5 0 137.46 1.09E-05 131630000 54659 67637 60833 71021 69165 44702 66000 49999 67059 FALSE TRUE 51237.99076 72644.91386 62275.98749 72843.5191 63733.0599 57606.74172 56103.91271 56241.48521 55866.41968 0.917151861 1.300332369 1.114730241 1.303887371 1.140811605 1.031151487 1.004251087 1.006713613 1 15.76969374 2.259368067 3.649471462 1.007737663 1.178969648 0.305489321 0.10719314 0.231790165 6.592792183 0.037254115 0.028638769 181.7054975 -2.259368067 0.171231985 LLLIQAFRPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLLIQAFRPDR 11 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 194.49 4.49E-07 570750000 545540 964740 623340 627210 1058080 569850 774360 913100 728160 FALSE TRUE 511395.6252 1036170.353 638125.9192 643305.2705 974982.6649 734356.4443 658251.9068 1027102.545 606625.3919 0.843017177 1.70808932 1.051927479 1.060465452 1.607223631 1.210560016 1.085104441 1.693141366 1 19.21044636 -1.667023374 6.390148211 0.997877537 1.28485909 0.081841038 0.297207995 0.008132732 0.000423779 0.260405332 0.060983656 0.021526659 1.667023374 0.286981553 LLLPGELAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLLPGELAK 9 0 Q16778;P33778;P23527;P06899;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053;A0A2R8Y619;Q99880;Q96A08 Q16778;P58876;Q99880 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS;HIST1H2BL;HIST1H2BA Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S;Histone H2B type 1-L;Histone H2B type 1-A 0 ;; 111.95 0.004751 1823168000 3392670 3715964 3564533 3426956 4124013 2469203 4231884 3563570 4288128 FALSE TRUE 3180328.841 3991097.841 3649085.406 3514897.493 3800129.654 3182021.822 3597352.281 4008489.559 3572411.734 0.890247003 1.117199846 1.02146272 0.983900444 1.06374347 0.890720907 1.006981431 1.122068187 1 21.76846694 -2.193060218 2.235039238 0.95461565 1.016837179 0 0.079218529 54539415.58 17211477.66 12401037.99 0.017829459 0.006411207 2.193060218 0.062221529 LLLPLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLLPLFR 7 0 Q9BV86;Q9BV86-2 Q9BV86 NTMT1 "N-terminal Xaa-Pro-Lys N-methyltransferase 1;N-terminal Xaa-Pro-Lys N-methyltransferase 1, N-terminally processed" 0 110.24 0.015932 11264000 51416 73589 56064 68194 80034 53648 64284 62092 67186 FALSE TRUE 48197.96434 79037.60613 57393.86456 69943.97349 73748.45248 69135.3067 54645.21098 69844.32288 55972.22256 0.861105065 1.412086255 1.025399063 1.24961937 1.31759021 1.235171725 0.976291605 1.247839012 1 15.77242342 0.963516674 0.797180959 1.013410861 1.188985184 0.05734647 0.169751704 1.741340843 2.444852281 0.150069 0.055006086 9.194257739 -0.963516674 0.175574324 LLLPWLEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLLPWLEAR 9 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 98.997 0.013111 165244000 118614 460330 123543 121629 462790 83925 129484 372010 367530 FALSE TRUE 111190.1615 494413.3122 126473.4983 124750.2061 426444.3402 108152.7851 110069.0763 418456.2674 306186.8687 0.363144775 1.614743684 0.413059838 0.407431601 1.392758423 0.353224766 0.359483334 1.366669541 1 18.22405289 4.994042452 24.37074753 0.816594575 0.038712309 0.090512295 0.47832389 27412.84994 167860.6388 0.108207896 498468.7236 98637.58996 -4.994042452 -0.777882266 LLMHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 74.949 0.059909 9137800000 9453300 13325100 8374200 7909800 14756100 6018570 10415000 12784100 15042900 FALSE TRUE 8861634.828 14311704.27 8572839.979 8112778.859 13597215.43 7756033.456 8853367.438 14380223.03 12532142.81 0.7071125 1.141999775 0.684068168 0.647357677 1.084987271 0.618891244 0.706452805 1.147467217 1 23.57912978 1.234377023 24.99981449 1.073733681 0.811599158 0.281664077 0.18169816 153.9107414 919660.6796 0.150816142 0.042971487 17.15445889 -1.234377023 -0.262134523 LLNGNHENGDLDPTS(ph)PLENMDYIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLNGNHENGDLDPTSPLENMDYIK 24 0 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4;A8MV73;F8WE35;F5H8I0;F5H2W9;F5H2H9;F5GZ10;F5H502;F5H1K9;F5H6X8;F5H221;F5H592 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 LLNGNHENGDLDPT(0.206)S(0.794)PLENMDYIK;LLNGNHENGDLDPT(0.127)S(0.873)PLENMDYIK 201.08 9.41E-25 195642000 256309 194506 243401 219484 194532 208390 280812 200502 176490 TRUE FALSE 240267.0772 208907.4266 249174.5867 225116.331 179254.2414 268548.8101 238706.8475 225535.1161 147032.6788 1.634106643 1.420823101 1.694688478 1.531063249 1.219145586 1.826456623 1.623495195 1.533911494 1 17.16577731 0.938963186 19.7749785 0.999999999 1.567012214 0.543682123 0.161582245 1260.184376 408282.1899 0.146889638 0.036722409 8.688867727 -0.938963186 0.567012215 LLNNAFEELVAFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLNNAFEELVAFQR 14 0 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 160.38 5.30E-07 0 36060 43338 42346 43198 43663 42987 37731 41789 38798 FALSE TRUE 33803.06897 46546.79061 43350.46712 44306.53381 40233.88411 55396.64906 32073.58683 47006.44864 32322.36316 1.045810568 1.440080058 1.341191141 1.37077025 1.244769261 1.713879916 0.992303275 1.454301111 1 14.98024506 -0.932013916 5.706240634 0.99999974 1.32834022 0.198937326 0.205124945 6.07E-07 1.14E-07 0.174870895 0.041217432 0.116946192 0.932013916 0.328340479 LLNQADPCVQILIQETGEHVLVTAGEVHLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLNQADPCVQILIQETGEHVLVTAGEVHLQR 31 0 Q7Z2Z2-2;Q7Z2Z2 Q7Z2Z2-2 EFTUD1 Elongation factor Tu GTP-binding domain-containing protein 1 0 209.07 2.27E-26 39930000 11206 13285 13405 13501 15092 11910 12306 10991 12610 FALSE TRUE 10504.63646 14268.63522 13722.97293 13847.45852 13906.7352 15348.22366 10460.82954 12363.25054 10505.30954 0.99993593 1.358230824 1.306289251 1.31813903 1.323781574 1.460996804 0.995765951 1.176857331 1 13.35883105 1.698588911 9.387482597 1.067364852 1.305065277 0.437350711 0.12596996 0.099834456 16.55019772 0.055041527 0.029540389 49.95614431 -1.698588911 0.237700425 LLNTWTNRYPDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLNTWTNRYPDAK 13 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 126.48 0.00017146 191990000 302360 392580 269560 308740 430440 209400 428080 349380 588040 FALSE TRUE 283435.8273 421647.0317 275954.0905 316662.7911 396634.9787 269850.3807 363893.3781 393000.8621 489892.3251 0.578567601 0.860693279 0.563295394 0.646392635 0.809637054 0.550836106 0.742802774 0.802218859 1 18.90210516 0.934066179 1.868689527 0.998346342 0.682051276 0.5113606 0.101963132 0.327790804 2.383375541 0.089178881 0.02515796 8.591444311 -0.934066179 -0.316295065 LLPAPS(ph)FSLDDMDVDKDPGGMLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLPAPSFSLDDMDVDKDPGGMLR 23 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 LLPAPS(0.967)FS(0.033)LDDMDVDKDPGGMLR;LLPAPS(0.5)FS(0.5)LDDMDVDKDPGGMLR 109.97 0.00066728 119858000 402645 377834 260060 280742 313694 132354 475085 247087 588540 TRUE FALSE 377444.1682 405809.2225 266228.746 287946.315 289057.7386 170562.4512 403850.4147 277936.3559 490308.8719 0.769808971 0.82766037 0.542981703 0.587275351 0.589542134 0.347867357 0.823665322 0.566859732 1 18.90333134 -1.016059627 5.031743579 1.000002826 0.63990808 0.385382986 0.145761368 18437959.59 3723175.823 827.1026581 0.033166884 0.09636967 1.016059627 -0.360094746 LLPEGEETLES(ph)DDEKDEHTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 LLPEGEETLESDDEKDEHTSK 21 1 Q8N6N3 Q8N6N3 C1orf52 UPF0690 protein C1orf52 1 LLPEGEETLES(1)DDEKDEHTSK;LLPEGEETLES(1)DDEKDEHTSK;LLPEGEETLES(0.834)DDEKDEHT(0.083)S(0.083)K;LLPEGEETLES(1)DDEKDEHTSK;LLPEGEETLES(1)DDEKDEHTSK;LLPEGEETLES(1)DDEKDEHTSK;LLPEGEETLES(1)DDEKDEHTSK;LLPEGEETLES(1)DDEKDEHTSK;LLPEGEET(0.001)LES(0.999)DDEKDEHTSK 406.62 8.44E-152 4232980000 5040980 3015337 4052434 3796086 4057092 3027969 5280574 3539017 5902351 TRUE FALSE 4725474.06 3238595.689 4148559.648 3893499.994 3738464.36 3902094.495 4488800.951 3980871.063 4917210.487 0.961007073 0.658624579 0.843681526 0.791810723 0.76028154 0.793558564 0.912875494 0.809579145 1 22.22940868 0.723818933 0.56127972 1.002914519 0.783584216 0.316092943 0.082759689 1.306492716 0.864933628 0.090891949 0.035472012 5.29442661 -0.723818933 -0.219330302 LLPEKHEIENLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLPEKHEIENLR 12 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 ; 200.21 9.78E-08 198464000 261919 299380 273441 307430 336850 218141 346980 267743 327340 FALSE TRUE 245525.9573 321546.4067 279927.1496 315319.1743 310395.1598 281114.7655 294953.5702 301171.3029 272704.8393 0.900335901 1.179100479 1.026483983 1.156265415 1.13820921 1.030838933 1.081585391 1.10438562 1 18.05698078 -0.746310209 7.61728126 0.999999982 1.083696238 0.079285434 0.079903118 0 0 0.067605636 0.015934801 0.179345214 0.746310209 0.083696257 LLPGPENHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLPGPENHR 9 0 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 0 126.55 0.00047044 131510000 285160 282370 297840 288740 306160 241400 343040 257870 334940 FALSE TRUE 267312.3446 303276.9686 304904.9055 296149.5572 282115.4286 311088.2612 291604.3366 290065.6371 279036.3502 0.957983949 1.086872619 1.092706757 1.061329669 1.011034686 1.114866436 1.045040678 1.039526345 1 18.09009355 0.947291238 2.094985647 1.000546306 1.061604566 0.100838369 0.044650783 0.6616823 6.255234641 0.0393171 0.01088956 8.857093684 -0.947291238 0.06105826 LLPPVGTGRS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLPPVGTGRSPR 12 1 Q9NWZ5;Q9NWZ5-4;Q9NWZ5-3;Q9NWZ5-2 Q9NWZ5 UCKL1 Uridine-cytidine kinase-like 1 1 LLPPVGT(0.356)GRS(0.644)PR;LLPPVGT(0.06)GRS(0.94)PR 83.877 0.0076017 233162000 431740 512670 532370 523070 506490 526730 582090 453910 650470 TRUE FALSE 404718.1641 550628.6202 544998.0678 536492.8618 466712.3185 678788.4003 494811.0084 510581.6627 541902.3548 0.74684703 1.016103022 1.005712677 0.990017587 0.861247999 1.252602788 0.913099941 0.942202332 1 19.04767339 4.740804761 24.40264514 1.000153614 0.746846905 0.371836774 0.102388205 147.7979417 1606992.317 0.021946189 0.145317627 55056.01334 -4.740804761 -0.253306709 LLPPYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLPPYLR 7 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ; 101.72 0.020588 268680000 317830 417910 387920 431660 414800 310240 426750 368750 407280 FALSE TRUE 297937.5876 448852.4912 397121.6456 442737.1264 382223.2812 399801.2517 362762.7993 414789.2492 339302.3369 0.878088817 1.322868847 1.170406456 1.304845497 1.126497639 1.178303855 1.069143238 1.222476842 1 18.37221184 2.06665125 1.845320784 1.105754503 1.193107472 0.019612898 0.133329703 0.954306142 6.170121924 0.069988023 0.03766888 116.5873013 -2.06665125 0.087352969 LLPQGTVIFEDISIEHFEGTVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LLPQGTVIFEDISIEHFEGTVTK 23 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;;;; 205.43 1.55E-24 196064000 187775 181903 195340 205934 219864 173656 232487 191728 206978 FALSE TRUE 176022.4979 195371.2874 199973.557 211218.6151 202596.7683 223787.6681 197627.7327 215665.6628 172432.0347 1.020822484 1.133033591 1.159723931 1.224938368 1.174936947 1.297831163 1.146119589 1.250728516 1 17.3956683 5.395659577 0.857167968 1.191950656 0.654627012 0.275819269 0.078941185 6.910599422 1.761205106 0.022179459 4.567551675 248690.7186 -5.395659577 -0.537323644 LLPQLTYLDGYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLPQLTYLDGYDR 13 0 Q92688;Q92688-2;P39687;H0YN26 Q92688;P39687 ANP32B;ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member B;Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ; 143.97 9.56E-05 302570000 227357 317820 220930 231770 330560 246170 310730 290540 189002 FALSE TRUE 213127.1312 341351.7235 226170.5639 237717.6106 304599.151 317235.2828 264138.9212 326814.5586 157456.3452 1.353563306 2.167913418 1.436401713 1.509736621 1.934499055 2.014750707 1.677537484 2.075588368 1 17.26459237 2.729283424 24.65624942 1.795727569 1.678655027 0.002780863 0.368929459 2734.917262 7268648.845 0.108482858 0.103550874 536.1464368 -2.729283424 -0.117072541 LLPQLTYLDGYDRDDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLPQLTYLDGYDRDDK 16 1 P39687;H0YN26 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;;; 186.55 1.35E-09 1091457000 1314474 773790 975211 867863 770746 898384 1304689 851985 658478 FALSE TRUE 1232203.419 831082.2167 998343.4654 890133.8339 710214.7182 1157732.877 1109062.997 958357.2027 548573.7679 2.24619457 1.514987164 1.819889182 1.622632882 1.294656726 2.110441557 2.0217208 1.746997868 1 19.06532611 0.942876529 22.11626008 0.999999998 1.787660247 0.441800612 0.281839526 5634.953691 2181665.587 0.264694877 0.066173719 8.767515228 -0.942876529 0.787660249 LLPS(ph)PVTCTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLPSPVTCTPK 11 0 H0YCH4;Q9BU19-2;Q9BU19;Q9BU19-5 H0YCH4 ZNF692 Zinc finger protein 692 1 LLPS(0.98)PVT(0.019)CTPK;LLPS(0.991)PVT(0.009)CTPK 89.356 0.012895 275110000 729270 542700 622330 535160 738130 519850 762610 624700 1009670 TRUE FALSE 683626.2925 582882.0727 637091.9615 548893.1116 680160.2473 669922.2559 648263.7102 702695.1701 841149.5543 0.812728591 0.692958903 0.757406288 0.652551153 0.808607986 0.796436558 0.770687813 0.835398612 1 19.68200281 0.486765385 0.533786582 1.012201955 0.731016269 0.724291278 0.048498001 0.907682651 0.459194726 0.067671311 0.021399724 3.067364483 -0.486765385 -0.281185686 LLPSAPQTLPDGPLAS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LLPSAPQTLPDGPLASPAR 19 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 1 LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR 265.9 1.94E-31 4699717000 1363169 1536629 1496201 1808976 1687200 1139885 1127887 801010 676248 TRUE FALSE 1277850.686 1650402.61 1531691.594 1855397.387 1554694.118 1468951.295 958770.8151 901017.8617 563377.8401 2.268194797 2.929477329 2.718764363 3.293344634 2.759594019 2.607399849 1.701825572 1.599313636 1 19.10374329 1.592563427 1.472023817 1.166074843 2.837653616 0.845419598 0.274915055 0.129600133 0.546952645 0.217732864 0.076677222 39.13482779 -1.592563427 1.671578772 LLPYPTLAS(ph)PASD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLPYPTLASPASD 13 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 LLPYPTLAS(0.997)PAS(0.003)D 116.74 0.00058923 7176100 30383 27181 26013 24190 27537 21469 25255 24956 33700 TRUE FALSE 28481.38227 29193.50952 26630.04064 24810.75635 25374.3551 27666.75178 21468.24721 28071.81153 28075.25229 1.014465764 1.03983071 0.948523645 0.883723362 0.903797937 0.985449801 0.764668007 0.999877445 1 14.77701137 3.683817514 2.129920542 0.904913233 1.026028956 0.235329865 0.0710032 0.34348005 3.074026771 0.01912413 0.03704356 4828.558687 -3.683817514 0.121115723 LLPYPTLASPAS(ph)D ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLPYPTLASPASD 13 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 LLPYPTLAS(0.004)PAS(0.996)D;LLPYPTLAS(0.005)PAS(0.995)D;LLPYPTLAS(0.001)PAS(0.999)D;LLPYPTLASPAS(1)D 261.49 4.82E-24 167340000 228859 262854 248131 241225 242225 217587 273916 214467 241821 TRUE FALSE 214535.1237 282315.9837 254016.7845 247415.2419 223201.6256 280400.8347 232844.8387 241243.6771 201459.5129 1.06490441 1.401353451 1.260882551 1.228113969 1.107922989 1.39184708 1.155789743 1.1974797 1 17.62013041 0.175754047 0.498895203 0.978001523 1.265517925 0.289052264 0.109045062 3.541057295 1.247902243 0.255538968 0.051555891 1.498835761 -0.175754047 0.287516402 LLQAFLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLQAFLER 8 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ; 109.21 0.0085176 81232000 141563 489170 147153 146891 501160 100799 174736 427570 345340 FALSE TRUE 132702.8245 525388.6558 150643.5387 150660.4717 461800.9152 129898.035 148535.959 480953.0557 287700.523 0.461253331 1.826165105 0.523612321 0.523671178 1.60514451 0.451504341 0.516286719 1.671714221 1 18.13420832 3.940738498 20.72869313 0.845395016 1.232912833 0.020785738 0.547909617 102.2364135 58247.60689 0.129653393 0.233772913 8724.458834 -3.940738498 0.387517817 LLQDFFNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLQDFFNGK 9 0 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89;P54652;P17066 P11142;P54652;P17066 HSPA8;HSPA2;HSPA6 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2;Heat shock 70 kDa protein 6 0 ; 206.78 2.97E-05 2097320000 2360800 2632300 2129200 1865400 2886800 1540690 2898000 2635000 3335100 FALSE TRUE 2213041.742 2827198.231 2179705.629 1913269.322 2660082.373 1985462.192 2463471.804 2963985.55 2778450.264 0.796502198 1.01754502 0.784504102 0.688610247 0.957397873 0.714593389 0.886635199 1.066776537 1 21.40584898 1.342206018 5.126836656 1.031220416 0.840633314 0.405613891 0.100951911 0.210376315 7.97857297 0.070428411 0.024569569 21.9890273 -1.342206018 -0.190587101 LLQDFFNGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLQDFFNGR 9 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 280.54 4.97E-21 1618090000 1602920 2323270 1493050 1474230 2413750 1239300 2035400 2292350 2478450 FALSE TRUE 1502596.098 2495287.328 1528465.851 1512061.238 2224183.812 1597065.792 1730210.666 2578554.944 2064780.684 0.727726732 1.208499938 0.740255788 0.732310821 1.077200997 0.773479626 0.837963412 1.248827522 1 20.97755712 1.25005204 24.99807604 1.124413788 0.886414217 0.276854202 0.168816146 257.8683065 560966.3287 0.109812624 0.039333252 17.78492509 -1.25005204 -0.237999572 LLQDHPWLLSQNLVVKPDQLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLQDHPWLLSQNLVVKPDQLIK 22 1 P53396;P53396-2;P53396-3;K7ESG8 P53396 ACLY ATP-citrate synthase 0 296.69 8.68E-56 903230000 2622300 2228900 2195800 1810800 2811900 1718000 2873500 2249000 2456200 FALSE TRUE 2458174.924 2393930.075 2247885.413 1857268.194 2591064.717 2213958.711 2442645.351 2529792.601 2046244.352 1.201310548 1.169914078 1.098542024 0.907647316 1.266253815 1.081962038 1.193721243 1.23631012 1 20.964547 LLQDS(ph)SSPVDLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLQDSSSPVDLAK 13 0 Q15596;E7EWM1 Q15596 NCOA2 Nuclear receptor coactivator 2 1 LLQDS(0.468)S(0.266)S(0.266)PVDLAK 133.71 0.00010911 35867000 197810 137300 188340 157720 177290 164440 248300 175900 234650 TRUE FALSE 185429.4252 147465.8349 192807.5137 161767.3622 163366.3586 211911.1585 211069.7201 197861.5022 195485.3991 0.948558951 0.754357285 0.986301354 0.827516341 0.835695961 1.084025505 1.079721151 1.012154888 1 17.57670133 2.237871282 24.99998281 1.05493004 0.868490077 0.61035919 0.068620786 11.1427389 404086.8897 0.02358819 0.018466178 172.9303744 -2.237871282 -0.186439963 LLQDSSS(ph)PVDLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLQDSSSPVDLAK 13 0 Q15596;E7EWM1 Q15596 NCOA2 Nuclear receptor coactivator 2 1 LLQDSS(0.027)S(0.973)PVDLAK 180.27 1.37E-05 36737000 202520 149920 169870 163920 178190 161520 232750 172670 223810 TRUE FALSE 189844.6347 161020.2328 173899.3966 168126.4647 164195.6762 208148.2019 197851.2982 194228.2296 186454.6651 1.0181812 0.863589188 0.932663157 0.901701572 0.880619834 1.116347514 1.06112281 1.041691445 1 17.50846537 2.243760169 24.99967923 1.062033298 0.912760146 0.64402572 0.049772387 66.24508105 318510.4267 0.015965869 0.012981851 175.291222 -2.243760169 -0.149273151 LLQEALEAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLQEALEAEER 11 0 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;Q96JY6-4;C9JS55;B3KPU0;H0YBP7;E5RGS7;H7C1D1;A0A087WUQ1 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 0 ;;; 188.28 7.49E-06 349068000 202201 248192 223924 236837 260066 190443 256131 220153 195769 FALSE TRUE 189545.6003 266568.3939 229235.583 242914.6384 239641.4654 245420.8025 217726.5344 247639.5867 163093.8892 1.162187016 1.634447466 1.405543667 1.489415941 1.469346685 1.50478233 1.334976653 1.518386666 1 17.3153432 -2.693369516 0.491658162 7.47E-08 1.456443963 0.539124142 0.126572514 117.8780607 5.33704582 125.0886488 0.054341451 0.002025958 2.693369516 1.456443888 LLQETELVEPLT(ph)PSGAMPNQAQMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LLQETELVEPLTPSGAMPNQAQMR 24 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2;J3QLU9;P04626-6;J3KTI5;J3QRJ7 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 LLQETELVEPLT(0.955)PS(0.045)GAMPNQAQMR;LLQETELVEPLT(0.97)PS(0.03)GAMPNQAQMR;LLQETELVEPLT(0.999)PS(0.001)GAMPNQAQMR;LLQETELVEPLT(0.989)PS(0.011)GAMPNQAQMR;LLQETELVEPLT(0.958)PS(0.042)GAMPNQAQMR 167.48 4.30E-11 205308000 249858 313929 294787 440296 558277 207823 191507 148989 140614 TRUE FALSE 234219.8338 337172.6298 301779.4868 451594.7408 514432.1764 267818.1264 162792.3032 167590.6046 117144.615 1.999407602 2.878259746 2.576127694 3.855019207 4.391428291 2.286217991 1.38966954 1.430630035 1 16.83793111 1.887757435 3.587996026 1.328828563 3.075188433 0.614068897 0.668824165 0.179400793 3.888546644 0.346658428 0.190757389 77.2249143 -1.887757435 1.746359871 LLQHGINADDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLQHGINADDKR 12 1 Q96P70 Q96P70 IPO9 Importin-9 0 119.01 0.00036564 624720000 1841400 844100 1026500 933290 1043800 659330 1147900 868640 1306700 FALSE TRUE 1726150.061 906598.0423 1050849.065 957239.8015 961824.1585 849667.8677 975783.0516 977091.6161 1088603.328 1.585655689 0.832808442 0.965318622 0.87932838 0.883539608 0.780511914 0.896362363 0.897564421 1 20.05404692 4.741236278 24.99997485 0.886541633 1.585655938 0.927365746 0.060998345 56.54986869 528343.2794 0.013419501 0.09256207 55110.74452 -4.741236278 0.699114306 LLQIIDRDGEEEEEEEEPLDESSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLQIIDRDGEEEEEEEEPLDESSVK 25 1 A0A087WUB9;Q8WYA6;Q8WYA6-4;A2A2P1 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 ; 215.42 1.58E-33 77152000 75238 68881.4 71367 74591 78929 59119.3 88246 70552 93058 FALSE TRUE 70528.98788 73981.45053 73059.85894 76505.13134 72730.23472 76186.08219 75014.33154 79360.5725 77526.01862 0.909746033 0.954278987 0.942391474 0.986831682 0.938139685 0.9827163 0.967602011 1.023663719 1 16.24239296 8 0.141328688 1.018692138 0.676912523 0.595788558 0.020998966 49.02058812 0.460484201 0.076935482 3.394648725 100000000 -8 -0.341779614 LLQIIDRDGEEEEEEEEPLDESSVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLQIIDRDGEEEEEEEEPLDESSVKK 26 2 A0A087WUB9;Q8WYA6;Q8WYA6-4;A2A2P1 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 153.94 4.14E-08 139160000 60493 44400 49544 50907 57554 32519 65493 49392 90404 FALSE TRUE 56706.85111 47687.4222 50719.20708 52213.35981 53033.941 41906.7074 55672.93266 55558.69993 75314.98837 0.752929162 0.633173067 0.673427802 0.693266519 0.704161843 0.556419224 0.739201238 0.737684505 1 16.20064938 0.683882545 1.414537245 0.999425904 0.669178436 0.776029206 0.054094424 0.452836509 1.40402409 0.046353505 0.013642256 4.829281761 -0.683882545 -0.330247469 LLQIIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLQIIER 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 96.492 0.029528 73275000 188200 226800 217140 225720 229470 182220 220510 200260 216040 FALSE TRUE 176420.8979 243592.508 222290.6633 231512.3573 211448.3518 234823.9559 187446.5726 225262.9018 179981.5283 0.98021669 1.353430601 1.235074874 1.286311765 1.174833628 1.304711423 1.041476725 1.251589004 1 17.45748932 0.786585309 0.597130255 1.001833498 1.240509187 0.192733894 0.118522858 1.457752689 1.122065639 0.118644813 0.047204218 6.11765961 -0.786585309 0.238675689 LLQLVEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLQLVEDR 8 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;; 185.05 0.00049972 997400000 1163530 1439580 1382720 1268950 1405700 1225510 1453160 1270240 1633000 FALSE TRUE 1090706.734 1546168.001 1415518.771 1301513.405 1295301.992 1579294.843 1235272.148 1428832.26 1360441.75 0.801729831 1.136519076 1.040484659 0.956684404 0.952118672 1.160869138 0.907993413 1.050270811 1 20.37564376 LLQTCFS(ph)SPADDSMDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LLQTCFSSPADDSMDR 16 0 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 1 LLQT(0.003)CFS(0.82)S(0.177)PADDSMDR;LLQT(0.001)CFS(0.709)S(0.29)PADDSMDR;LLQT(0.016)CFS(0.492)S(0.492)PADDSMDR;LLQTCFS(0.657)S(0.343)PADDSMDR;LLQT(0.008)CFS(0.496)S(0.496)PADDSMDR;LLQT(0.003)CFS(0.499)S(0.499)PADDSMDR 192.85 4.91E-10 421053000 743626 806019 763320 784042 850792 628861 802418 638484 906062 TRUE FALSE 697083.7761 865697.4854 781426.3109 804161.8451 783974.2282 810402.962 682102.8702 718200.1329 754834.3988 0.923492328 1.14687074 1.035228803 1.065348699 1.038604268 1.073616893 0.903645715 0.951467148 1 19.52580064 1.748313001 21.20072345 0.945737815 1.057682198 0.353914771 0.059527134 0.725255862 1585.468001 0.025093015 0.013907476 56.01611706 -1.748313001 0.111944383 LLQTCFSS(ph)PADDSMDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLQTCFSSPADDSMDR 16 0 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 1 LLQTCFS(0.146)S(0.853)PADDSMDR;LLQTCFS(0.016)S(0.984)PADDSMDR 345 1.83E-73 153199000 208901 239404 243610 222449 250073 189136 228538 187627 248657 TRUE FALSE 195826.2593 257129.7213 249388.5442 228157.4179 230433.2753 243736.4928 194270.8485 211052.644 207154.5403 0.945314831 1.241245888 1.203876796 1.101387484 1.112373762 1.176592569 0.937806375 1.01881737 1 17.66034792 1.747852417 10.86312472 0.98537504 1.149676753 0.392316813 0.08243741 0.090737003 58.64281269 0.037730685 0.020588086 55.95674152 -1.747852417 0.164301712 LLQTCFSSPADDS(ph)MDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLQTCFSSPADDSMDR 16 0 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 1 LLQTCFSSPADDS(1)MDR;LLQTCFSSPADDS(1)MDR 176.46 3.32E-09 91711000 113038 113956 126407 123877 118886 110522 148500 100078 143541 TRUE FALSE 105963.1534 122393.4208 129405.4337 127055.8935 109549.1731 142427.9072 126233.8036 112572.9586 119583.0798 0.886104903 1.023501159 1.082138326 1.062490561 0.916092589 1.19103729 1.055615927 0.941378653 1 16.86765375 4.738763179 3.225428455 1.046172078 0.863139098 0.26288796 0.076500095 0.417566153 6.932834204 0.017221058 0.192184722 54797.80711 -4.738763179 -0.18303298 LLQTDDEEEAGLLELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLQTDDEEEAGLLELLK 17 0 P55060-3;P55060 P55060-3 CSE1L Exportin-2 0 74.816 0.023348 7359000 7925.4 5511.8 7636.5 7534.7 8212.7 5267 8056.4 6542.9 7123.7 FALSE TRUE 7429.363361 5919.899407 7817.641386 7728.053158 7567.70767 6787.497397 6848.417612 7359.795468 5934.708449 1.251849762 0.997504672 1.317274716 1.302179075 1.275160816 1.143695171 1.153960244 1.240127553 1 12.53496144 -2.524293293 0.639317841 0.567692965 1.199815503 0.321788122 0.094649882 540.8026735 33.03809072 327.0523247 0.036850816 0.002990245 2.524293293 0.632122539 LLREELQLLQEQGSYVGEVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLREELQLLQEQGSYVGEVVR 21 1 P62195-2;P62195;J3QSA9;J3KRP2;J3QQM1;J3QLH6;J3QSE0 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ; 130.83 1.30E-05 59520000 50635 67363 59093 64356 70537 55261 63554 51772 77390 FALSE TRUE 47465.84574 72350.62661 60494.71387 66007.48391 64997.30855 71213.95361 54024.66771 58235.84816 64473.10904 0.736211522 1.122182995 0.938293728 1.02379868 1.008130514 1.104552808 0.837941097 0.903257948 1 15.97640993 1.718816751 18.62330538 0.903110593 1.000494239 0.081937605 0.112342318 0.462676859 421.0827256 0.046695765 0.025854269 52.33795524 -1.718816751 0.097383646 LLRQS(ph)PPLPGREEEPGLGDSGIQSTPGSGHAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLRQSPPLPGREEEPGLGDSGIQSTPGSGHAPR 33 2 Q9C0B5;Q9C0B5-2 Q9C0B5 ZDHHC5 Palmitoyltransferase ZDHHC5 1 LLRQS(1)PPLPGREEEPGLGDSGIQSTPGSGHAPR 118.59 8.22E-07 123670000 42457 68946 50494 55982 80001 45404 69434 66707 94948 TRUE FALSE 39799.69216 74050.83358 51691.74152 57418.5929 73718.04417 58511.39773 59023.01629 75035.51579 79100.56541 0.503153068 0.93616061 0.653493957 0.725893584 0.931953442 0.739708969 0.74617692 0.948609095 1 16.27140039 -5 0.105204257 1.768767063 0.625880759 0.345871043 0.126340852 225.1742158 1.594126693 37.07082651 1.695502201 1.00E-05 5 -1.142886304 LLS(ph)AACR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLSAACR 7 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 LLS(1)AACR 69.825 0.061564 46308000 92749 92556 85067 96467 99554 75591 114650 80575 117870 TRUE FALSE 86944.00565 99408.94254 87084.82941 98942.50654 91735.43042 97412.89458 97459.29686 90634.96612 98196.73553 0.885406273 1.012344677 0.886840371 1.007594662 0.934200408 0.992017648 0.992490192 0.922993678 1 16.58338744 3.214320488 24.99993317 0.97506099 0.940320553 0.18110684 0.04436651 455.0799055 469343.2456 0.011850202 0.014170187 1638.024856 -3.214320488 -0.034740438 LLS(ph)PGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLSPGAR 7 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 1 LLS(1)PGAR;LLS(1)PGAR;LLS(1)PGAR;LLS(1)PGAR 132.38 0.0035397 604410000 908610 985690 1064090 971660 1047810 965650 1093340 928230 1563460 TRUE FALSE 851741.722 1058671.513 1089330.717 996594.4406 965519.2293 1244417.479 929403.8171 1044121.559 1302508.426 0.653924155 0.812794368 0.836332953 0.765134736 0.741276763 0.955400713 0.713549178 0.80162365 1 20.31286127 -2.361745468 2.062544243 2.159505655 0.791968794 0.413609413 0.080069968 7152824.646 708629.9595 38706387.99 0.018563157 0.00434765 2.361745468 -1.367536861 LLS(ph)PLSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LLSPLSSAR 9 0 A0A087WZ13;Q8IY67-2;E9PAU2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 LLS(1)PLSSAR;LLS(0.999)PLS(0.001)SAR;LLS(0.998)PLS(0.002)SAR;LLS(1)PLSSAR;LLS(0.842)PLS(0.158)SAR;LLS(0.998)PLS(0.002)SAR;LLS(1)PLSSAR;LLS(0.998)PLS(0.001)SAR 215.83 6.56E-07 671281000 2125987 2512530 2319460 2162123 2894110 2060571 2613110 2402660 2892810 TRUE FALSE 1992925.269 2698560.335 2374478.687 2217606.737 2666818.275 2655424.397 2221298.414 2702637.39 2409981.323 0.826946354 1.119743257 0.985268502 0.920175902 1.106572175 1.101844389 0.92170773 1.121434994 1 21.20059053 2.734322328 24.92185751 1.039539649 0.99285763 0.138587062 0.093983792 1173.212128 6898666.307 0.029121702 0.02836664 542.4033058 -2.734322328 -0.046682018 LLS(ph)PQQPALQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LLSPQQPALQR 11 0 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 LLS(1)PQQPALQR;LLS(1)PQQPALQR;LLS(1)PQQPALQR;LLS(1)PQQPALQR;LLS(1)PQQPALQR;LLS(1)PQQPALQR 195.16 2.07E-07 1888410000 1276090 1347110 1367920 1282780 1392490 1087602 1372000 1153030 1342660 TRUE FALSE 1196221.805 1446851.426 1400367.708 1315698.307 1283129.452 1401575.042 1166281.337 1296988.334 1118561.372 1.069428853 1.293493108 1.25193641 1.1762415 1.147124766 1.253015772 1.04266191 1.159514682 1 20.09321298 1.362744259 0.613500362 1.006697353 1.226738359 0.35760028 0.07682348 0.627309159 0.565596129 0.070638701 0.034093746 23.05389225 -1.362744259 0.220041006 LLS(ph)PRPSLLTPTGDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LLSPRPSLLTPTGDPR 16 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 LLS(0.999)PRPSLLTPTGDPR;LLS(0.992)PRPS(0.006)LLT(0.002)PTGDPR;LLS(1)PRPSLLTPTGDPR;LLS(1)PRPSLLTPTGDPR;LLS(0.999)PRPS(0.001)LLTPTGDPR;LLS(1)PRPSLLTPTGDPR;LLS(1)PRPSLLTPTGDPR 108.49 0.00063356 2496800000 3217496 3342740 3488160 3339370 3786140 2895880 4077200 3054268 3389530 TRUE FALSE 3016118.669 3590239.948 3570900.802 3425063.888 3488791.837 3731873.545 3465861.711 3435600.083 2823795.546 1.06810802 1.271423476 1.264574841 1.212929135 1.235497323 1.321580647 1.227377002 1.216660352 1 21.4292042 -0.771072438 7.238299693 1 1.237824646 0.536815628 0.065697572 8.59E-10 8.59E-19 0.057633184 0.013584272 0.169405522 0.771072438 0.237824647 LLS(ph)PYSPQTQETDSAVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLSPYSPQTQETDSAVQK 18 0 Q9P265 Q9P265 DIP2B Disco-interacting protein 2 homolog B 1 LLS(0.925)PY(0.004)S(0.07)PQTQETDSAVQK 160.48 1.05E-09 0 44500 38461 46828 43639 46542 43729 53005 40829 60097 TRUE FALSE 41714.82443 41308.69246 47938.78227 44758.85062 42886.77906 56352.85242 45057.39232 45926.59053 50066.42246 0.833189639 0.825077775 0.957503651 0.893989393 0.856597635 1.125561797 0.899952306 0.917313207 1 15.61155575 4.531784759 0.469750733 0.96927716 0.727690011 0.323342063 0.073380133 4.820368209 0.952680189 0.04793308 0.63584171 34023.95218 -4.531784759 -0.241587149 LLS(ph)SNEDDANILSSPTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLSSNEDDANILSSPTDR 18 0 F5GY88;A0A0B4J1W0;O75448-2;O75448;H0YEG1 F5GY88 MED24 Mediator of RNA polymerase II transcription subunit 24 1 LLS(0.985)S(0.015)NEDDANILSSPTDR;LLS(0.977)S(0.023)NEDDANILSSPTDR 245.1 3.62E-24 101522000 54927 54914 51772 55078 55341 42540 67230 49501 77802 TRUE FALSE 51489.21712 58979.8897 53000.05629 56491.39473 50994.74109 54820.60742 57149.48563 55681.30882 64816.34358 0.794386327 0.909953978 0.817695867 0.871560961 0.786757448 0.845783708 0.881714124 0.859062788 1 15.98407002 0.264228082 0.857587748 1.001519078 0.845212027 0.630484065 0.037517198 1.939753834 1.731144127 0.041118738 0.011394456 1.837503105 -0.264228082 -0.156307051 LLS(ph)VHDFDFEGDSDDSTQPQGHSLHLSSVPEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLSVHDFDFEGDSDDSTQPQGHSLHLSSVPEAR 33 0 Q9BV36-2;Q9BV36-5;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 1 LLS(0.777)VHDFDFEGDS(0.223)DDSTQPQGHSLHLSSVPEAR 209.92 2.98E-27 99499000 7378.7 20871 15543 16968 19339 13106 17690 14077 16055 TRUE FALSE 6916.880338 22416.31056 15911.6873 17403.42761 17820.19295 16889.48944 15037.54873 15834.54444 13375.31678 0.517137684 1.675946142 1.189630688 1.301160032 1.332319319 1.262735658 1.124276081 1.183863134 1 13.70728544 1.161168352 1.003513961 1.012813727 1.271772466 0.014123229 0.289588826 1.327145733 2.861198007 0.245503836 0.083439445 14.49333571 -1.161168352 0.258958739 LLS(ph)WSDNWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLSWSDNWR 9 0 Q8TCD5;J3KSY6;J3KSX6 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 1 LLS(0.992)WS(0.008)DNWR;LLS(0.943)WS(0.057)DNWR;LLS(0.998)WS(0.002)DNWR;LLS(0.972)WS(0.028)DNWR 156.58 7.40E-05 172453000 284694 322990 327696 332360 284135 262668 336065 225851 239982 TRUE FALSE 266875.5107 346904.5157 335469.1039 340888.9203 261820.1832 338495.9875 285675.1731 254048.9945 199927.4539 1.334861749 1.735151971 1.677954165 1.70506308 1.30957594 1.693094075 1.428894169 1.270705897 1 17.60911707 1.059513509 0.978772807 0.995105577 1.616024661 0.604508365 0.151782486 0.33420261 0.691273693 0.1333344 0.04509238 11.46868194 -1.059513509 0.620919083 LLS(ph)YRNNNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLSYRNNNR 9 1 A0A075B6I4 A0A075B6I4 IGLV10-54 1 LLS(0.603)Y(0.397)RNNNR 77.674 0.084005 20455000 8158.4 7972.2 7356.2 7721.1 10429 7703.4 11569 8503.7 15049 TRUE FALSE 7647.780307 8562.469983 7530.692538 7919.236498 9609.948409 9927.246526 9834.335851 9565.405664 12537.22468 0.610005843 0.68296375 0.600666633 0.631657859 0.766513216 0.791821697 0.784410913 0.762960377 1 13.6139304 0.984758134 0.293813943 1.047368588 0.591697122 0.858253033 0.044316479 0.758971955 0.204407092 0.126676665 0.073610514 9.655130189 -0.984758134 -0.455671466 LLSAEFLEQHYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLSAEFLEQHYDR 13 0 Q9Y376 Q9Y376 CAB39 Calcium-binding protein 39 0 ;;; 236.92 9.95E-17 489756000 454218 573765 512031 517348 540887 471341 530591 550836 405068 FALSE TRUE 425789.3062 616247.1576 524176.6171 530624.0255 498407.9169 607409.4951 451033.8053 619609.0871 337459.534 1.261749227 1.826136457 1.553302143 1.572407866 1.476941282 1.79994765 1.336556713 1.836098924 1 18.36435499 -1.477084673 3.039855778 0.984891028 1.589399972 0.465235398 0.1962873 30423329.47 34762341.83 3863000.809 0.042027158 0.033336141 1.477084673 0.604508944 LLSAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLSAER 6 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8;P15924;P15924-3;P15924-2;A0A075B730;P58107 Q15149-3;Q15149-4;Q15149-5;Q15149-8;P15924;A0A075B730;P58107;REV__Q15911-2 PLEC;DSP;EPPK1 Plectin;Desmoplakin;Epiplakin 0 98.807 0.091929 964560000 568240 1105300 608670 657980 1180800 481190 766940 1045000 960630 FALSE TRUE 532674.8727 1187137.562 623107.9398 674864.8808 1088064.731 620101.7415 651944.4669 1175470.55 800294.6471 0.665598445 1.483375612 0.77859816 0.843270517 1.359580168 0.774841796 0.814630548 1.468797217 1 19.61017173 3.90014305 24.99997408 0.979657868 1.132685293 0 0.307927848 201.1488862 65323.38027 0.072672971 0.131013112 7945.899178 -3.90014305 0.153027425 LLSDATVEKDESHAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLSDATVEKDESHAGK 16 1 Q14320 Q14320 FAM50A Protein FAM50A 0 ;; 209.31 7.57E-12 1313160000 2296870 1544710 1847140 1773710 2018760 1365280 2348800 1598040 2505370 FALSE TRUE 2153113.007 1659081.936 1890955.033 1819226.401 1860214.733 1759414.173 1996619.245 1797558.812 2087207.562 1.031575894 0.794881145 0.90597364 0.871607805 0.891245685 0.842951226 0.956598319 0.861226667 1 20.99314265 -0.446941144 0.507103314 1.018681407 0.882986693 0.183570597 0.06522151 12.30893026 2.821935017 0.473370865 0.028117931 0.357321259 0.446941144 -0.135694714 LLSDFLDSEVSELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLSDFLDSEVSELR 14 0 Q9BPX3 Q9BPX3 NCAPG Condensin complex subunit 3 0 ;; 219.92 1.12E-11 36774000 56565 70248 66012 66212 66561 63677 73574 61602 70736 FALSE TRUE 53024.69762 75449.23501 67577.83581 67911.11202 61333.56755 82059.51619 62542.26173 69293.1453 58929.70463 0.899795747 1.280326034 1.146753343 1.152408831 1.040792041 1.392498345 1.06130282 1.175861066 1 15.84670741 -0.240159762 7.486053764 1.000000013 1.157379396 0.095336496 0.1333536 0 0 0.112562465 0.026531228 0.575228291 0.240159762 0.157379383 LLSFS(ph)PEEFPTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLSFSPEEFPTLK 13 0 Q5JSZ5;A0A1W2PQP5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 LLSFS(1)PEEFPTLK;LLSFS(1)PEEFPTLK 213.67 4.27E-09 161555000 352840 324320 355060 355410 404750 341230 391000 323560 520100 TRUE FALSE 330756.3742 348332.9903 363482.1909 364530.4223 372962.5677 439737.5616 332373.1799 363957.1782 433291.95 0.763356841 0.803922137 0.838885169 0.841304396 0.860765052 1.014875909 0.767088287 0.839981399 1 18.72497991 -5 0.045788826 1.592221974 0.51548942 0.402766289 0.066124101 718.2648104 2.44364164 56.10421405 14.22578711 1.00E-05 5 -1.076732554 LLSGPSQES(ph)PQTLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLSGPSQESPQTLGK 15 0 Q9BWE0;Q9BWE0-4;C9JZE3;C9JYJ8;E7EVL6 Q9BWE0 REPIN1 Replication initiator 1 1 LLSGPSQES(1)PQTLGK;LLSGPSQES(1)PQTLGK;LLSGPS(0.002)QES(0.998)PQTLGK;LLSGPSQES(1)PQTLGK 336.81 4.45E-69 361292000 723200 557050 646750 588540 731480 570980 781090 601320 1101160 TRUE FALSE 677936.2029 598294.5616 662091.2154 603642.9328 674032.5114 735812.6569 663972.8058 676396.1257 917369.2822 0.739000331 0.652185083 0.721728129 0.658015201 0.73474502 0.802089923 0.723779201 0.737321533 1 19.80714307 -5 0.210004397 2.377072914 0.675227954 0.839068549 0.039032768 51.84976795 0.517056207 29.99601841 0.078696207 1.00E-05 5 -1.701844961 LLSHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLSHGK 6 0 Q02878;F8VZ45;U3KQR5;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 81.1 0.062769 1244000000 3343000 3484300 3501700 3156500 3677200 2562500 4131800 3496800 3959000 FALSE TRUE 3133767.597 3742281.197 3584761.978 3237501.134 3388407.545 3302252.151 3512274.948 3933383.177 3298217.324 0.950139815 1.134637542 1.086878646 0.98159121 1.027345142 1.001223336 1.064901006 1.192578533 1 21.65325503 -1.212259137 5.617720099 0.999997751 1.059873837 0.050570805 0.071974071 1.93E-06 2.71E-07 0.066518886 0.015678063 0.061339589 1.212259137 0.059876085 LLSLLEKDEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLSLLEKDEFK 11 1 P35270 P35270 SPR Sepiapterin reductase 0 ; 178.32 6.92E-06 461720000 2052200 1510640 1721050 1734660 2350400 1207760 2219600 1835440 3029400 FALSE TRUE 1923756.465 1622489.357 1761874.119 1779174.312 2165809.065 1556420.706 1886791.586 2064598.724 2523773.569 0.762253987 0.6428823 0.698111011 0.704965903 0.858162987 0.616703782 0.747607317 0.818060205 1 21.26715105 0.917643362 1.892857482 0.999148536 0.707635527 0.6518674 0.065781091 0.244549108 1.810180784 0.058452299 0.016435337 8.272625462 -0.917643362 -0.291513009 LLSSNEDDANILSS(ph)PTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLSSNEDDANILSSPTDR 18 0 F5GY88;A0A0B4J1W0;O75448-2;O75448;H0YEG1 F5GY88 MED24 Mediator of RNA polymerase II transcription subunit 24 1 LLSSNEDDANILS(0.035)S(0.96)PT(0.005)DR;LLSSNEDDANILS(0.003)S(0.997)PTDR 313.93 3.17E-61 358110000 448750 575370 518250 563550 508390 428400 565500 429760 406800 TRUE FALSE 420663.5385 617970.9935 530543.1347 578011.6471 468463.1001 552072.1255 480708.5248 483416.482 338902.452 1.241252567 1.823447986 1.565474465 1.705539879 1.382294809 1.629000092 1.418427403 1.426417777 1 18.37051055 0.494769497 0.539468276 0.974202698 1.613072753 0.510919568 0.164855808 1.305775265 0.676948613 0.221079452 0.070610911 3.12442063 -0.494769497 0.638870056 LLSSS(ph)LTADCSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLSSSLTADCSLR 13 0 Q147X3;Q147X3-2 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 LLSS(0.062)S(0.938)LTADCSLR;LLSS(0.012)S(0.988)LT(0.001)ADCSLR;LLS(0.009)S(0.033)S(0.937)LT(0.022)ADCSLR 223.03 1.73E-11 139132000 288196 332210 290058 354676 412210 323428 431570 325327 390240 TRUE FALSE 270158.3268 356807.1741 296938.3127 363777.5866 379836.6894 416796.4132 366860.085 365944.7921 325106.423 0.83098428 1.097508843 0.913357263 1.118949245 1.168345694 1.282030694 1.128430751 1.125615387 1 18.31055253 3.114534157 5.415229764 1.157250679 0.975374824 0.455124988 0.095522919 0.178098894 7.771001578 0.025744095 0.031030769 1301.769695 -3.114534157 -0.181875855 LLSVHDFDFEGDS(ph)DDSTQPQGHSLHLSSVPEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LLSVHDFDFEGDSDDSTQPQGHSLHLSSVPEAR 33 0 Q9BV36-2;Q9BV36-5;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 1 LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(0.999)DDS(0.001)T(0.001)QPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(0.878)DDS(0.056)T(0.056)QPQGHS(0.008)LHLS(0.002)S(0.002)VPEAR 301.24 3.00E-90 828975000 72265 230162 180463 197351 221390 196329 216119 196698 212907 TRUE FALSE 67742.06265 247203.434 184743.6676 202415.3608 204002.9224 253005.9952 183713.9623 221256.1783 177371.4463 0.381922029 1.393704788 1.041563744 1.141194736 1.150145228 1.426418967 1.035758383 1.247417118 1 17.43641425 4.747926082 24.89326142 1.183561002 0.38192158 0.752614487 0.143694529 553.0635276 1470001.77 0.031108048 0.396710909 55966.23377 -4.747926082 -0.801639422 LLSWSDNWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLSWSDNWR 9 0 Q8TCD5;J3KSY6;J3KSX6 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 0 ; 132.76 0.00068877 176045000 264320 398370 255930 254870 402040 205932 301460 334490 369270 FALSE TRUE 247776.683 427865.7293 262000.7805 261410.3957 370465.4002 265381.2254 256258.8716 376251.8128 307636.4514 0.80542043 1.390816099 0.85165714 0.849738041 1.204231158 0.862645581 0.832992548 1.223040414 1 18.23086693 3.822905816 8.162256734 0.958002066 1.136309357 0.049936314 0.198524322 0.511479658 38.86673236 0.046676213 0.084407023 6651.288965 -3.822905816 0.178307291 LLT(ph)PTHSFLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLTPTHSFLAR 11 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 LLT(0.998)PT(0.002)HSFLAR;LLT(0.983)PT(0.017)HSFLAR;LLT(0.984)PT(0.016)HSFLAR;LLT(0.999)PT(0.001)HSFLAR 187.62 1.29E-05 513014000 656581 694291 652820 586083 765963 498355 767560 695887 1084740 TRUE FALSE 615486.7672 745697.028 668305.1987 601122.882 705807.3557 642221.9984 652471.5037 782770.0238 903689.8863 0.681081836 0.825169164 0.739529355 0.66518713 0.781028278 0.710666356 0.722008195 0.866193188 1 19.78546825 1.003161768 3.315930553 0.999113426 0.739681757 0.784967675 0.046513342 0.098616026 2.666772168 0.044086083 0.011488579 10.07306806 -1.003161768 -0.259431669 LLTDDGNKWLYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLTDDGNKWLYK 12 1 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 155.42 6.22E-05 704840000 1086530 1149590 1050500 1097280 1388010 777010 1417940 1094610 2076160 FALSE TRUE 1018526.027 1234706.84 1075418.356 1125438.062 1279001.294 1001320.173 1205333.061 1231274.468 1729635.483 0.588867444 0.713853787 0.621760114 0.650679333 0.739462913 0.578919768 0.696871145 0.711869339 1 20.72203659 0.545101872 1.410027776 0.999958388 0.656770897 0.819011004 0.050628956 0.710961757 1.792523062 0.042702756 0.01252046 3.508341591 -0.545101872 -0.343187491 LLTEIHGGAGGPSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLTEIHGGAGGPSGR 15 0 K7EPJ1;Q16763 K7EPJ1 UBE2S Ubiquitin-conjugating enzyme E2 S 0 61.265 0.09072 249090000 86401 123190 109650 124050 128990 107410 134490 107090 145850 FALSE TRUE 80993.31564 132311.1158 112250.9498 127233.333 118859.6457 138417.5233 114324.473 120460.4222 121506.6928 0.666574933 1.088920394 0.923825241 1.047130245 0.978214805 1.139176124 0.940890336 0.991389194 1 16.89067626 4.746600574 24.98714219 1.01071443 0.666574764 0.738425516 0.064905338 489.2178662 1520390.664 0.014079757 0.156868533 55795.67991 -4.746600574 -0.344139666 LLTSHDCEILESEVTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLTSHDCEILESEVTGR 17 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 ;; 166.48 2.34E-09 239664000 170523 208279 199767 213374 243445 186813 252633 223643 180047 FALSE TRUE 159850.2698 223700.1939 204505.5676 218849.5381 224325.8117 240742.8804 214753.027 251565.3208 149995.9926 1.065696937 1.49137447 1.363406876 1.459035901 1.495545367 1.604995416 1.431725097 1.677146946 1 17.19456443 4.741560024 24.40974588 1.458354327 1.065696734 0.295314177 0.180018709 224.0161352 1822956.209 0.036556087 0.257244453 55151.84226 -4.741560024 -0.392657593 LLTSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLTSLR 6 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 137.44 0.029627 146360000 246850 371070 349950 380070 491550 264420 394070 339600 682010 FALSE TRUE 231400.0991 398544.4089 358250.9793 389823.2397 452945.6458 340753.7615 334982.8619 381999.8076 568178.125 0.407266822 0.701442719 0.630525822 0.686093361 0.797189518 0.599730518 0.589573669 0.672324031 1 19.11598376 -2.385399904 1.395052128 2.235299484 0.641806584 0.566213022 0.100125834 82191.51153 8234.248035 317124.7856 0.025939325 0.004117182 2.385399904 -1.593492901 LLVDADNCLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLVDADNCLHR 11 0 Q9NZB2;Q9NZB2-4;Q9NZB2-6;Q9NZB2-2;Q9NZB2-5 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 ;;; 223.07 7.21E-12 1190182000 704400 886779 767471 842374 931782 716416 906205 765411 890504 FALSE TRUE 660312.8614 952437.0399 785675.7745 863990.743 858603.6003 923233.6692 770327.973 860974.2482 741873.1295 0.890061703 1.283827385 1.05904331 1.164607139 1.157345597 1.244463012 1.038355404 1.160541087 1 19.50081296 -1.282376442 6.148306255 0.99999483 1.133552271 0.106419353 0.111077756 6.89E-06 8.03E-07 0.094071127 0.022171919 0.052194358 1.282376442 0.133557441 LLVDSQGLSGCS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLVDSQGLSGCSPR 14 0 O94885;A0A087WW74 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 LLVDSQGLSGCS(1)PR;LLVDSQGLSGCS(1)PR 152.25 7.05E-06 162097000 321080 346110 333430 338260 411460 385210 439090 344840 456910 TRUE FALSE 300984.1759 371736.3445 341339.1171 346940.3243 379145.5913 496413.8736 373252.5308 387894.0331 380648.7692 0.790713645 0.976586225 0.896729859 0.911444755 0.996051011 1.304125781 0.980569388 1.019033987 1 18.53810089 2.476553616 24.99999881 1.082178158 0.912693357 0.419961213 0.099745936 19.15678043 843628.5838 0.03223639 0.027203195 299.6081449 -2.476553616 -0.169484801 LLVDVDESTLSPEEQKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLVDVDESTLSPEEQKER 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;; 284.15 1.49E-39 493092000 900910 819890 822080 895220 923210 635300 1087650 791440 1243940 FALSE TRUE 844523.6513 880595.5087 841580.1258 918192.8608 850704.8106 818700.7968 924566.9797 890253.0262 1036318.378 0.814926831 0.849734529 0.812086463 0.88601426 0.820891368 0.790008953 0.892164994 0.859053593 1 19.98303587 0.494393822 0.842676327 1.000864256 0.832642518 0.737976571 0.030593136 0.808931543 0.874986422 0.028767203 0.009332625 3.121719106 -0.494393822 -0.168221737 LLVGNDDVHIIARS(ph)DDELLDDFFHDQSTATSQAGTLSSIPTALTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLVGNDDVHIIARSDDELLDDFFHDQSTATSQAGTLSSIPTALTR 45 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 LLVGNDDVHIIARS(0.996)DDELLDDFFHDQS(0.001)T(0.002)ATSQAGTLSSIPTALTR 97.118 1.39E-05 20852000 7744.3 9470.1 8120.2 9727.1 9559.3 5874.3 9350.4 7273.9 14105 TRUE FALSE 7259.598087 10171.27606 8312.814979 9976.713854 8808.551138 7570.115049 7948.394325 8182.062427 11750.78438 0.617796894 0.865582733 0.707426391 0.849025353 0.749613886 0.644222105 0.676413937 0.696299257 1 13.52046944 -1.058678227 5.276084166 1.000002882 0.733171563 0.535077563 0.08006407 2.69E-06 4.81E-07 0.076961247 0.018139744 0.08736184 1.058678227 -0.266831319 LLVGVDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLVGVDEK 8 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 85.212 0.039324 54547000 304710 296620 288520 269990 336140 242520 304810 291300 363360 FALSE TRUE 285638.745 318582.0534 295363.8306 276918.4005 309740.9203 312531.587 259106.5702 327669.4462 302712.8686 0.943596307 1.052423225 0.975722744 0.914788994 1.023216891 1.032435748 0.855948316 1.082443068 1 18.20759048 3.696406915 8.013525551 0.972257123 1.008269575 0 0.06839395 0.737234746 168.832512 0.017092362 0.026958743 4970.578249 -3.696406915 0.036012452 LLVHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLVHLK 6 0 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 0 84.566 0.055705 188760000 256650 299000 273180 277090 351890 212150 327520 308040 344340 FALSE TRUE 240586.7346 321138.2711 279659.9586 284200.5985 324253.9789 273394.261 278411.4165 346499.4721 286867.4295 0.838668702 1.119465781 0.974875255 0.990703612 1.130326923 0.953033468 0.970522924 1.207873172 1 18.13002465 4.755184589 24.16940442 1.034730844 0.838668458 0.364750352 0.084209613 2336.240562 3396544.69 0.018630389 0.490960805 56909.47623 -4.755184589 -0.196062387 LLVLDVDYTLFDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLVLDVDYTLFDHR 14 0 Q8WVY7 Q8WVY7 UBLCP1 Ubiquitin-like domain-containing CTD phosphatase 1 0 ; 160.84 4.69E-06 103371000 184497 242389 229204 234887 258989 216706 235654 217529 206802 FALSE TRUE 172949.6621 260335.7338 234640.8271 240914.5981 238649.0487 279265.5043 200319.8704 244687.9745 172285.4102 1.003855532 1.511072432 1.361930919 1.398345906 1.385195928 1.620946916 1.162721035 1.420247798 1 17.39444101 -1.11138326 6.865226405 0.999999714 1.370381229 0.299550817 0.171140164 6.84E-07 8.89E-08 0.147368067 0.034734959 0.077377865 1.11138326 0.370381515 LLVLEAFQVSHPCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLVLEAFQVSHPCR 14 0 A0A0C4DFM0;G3V4T6;O43708-2;O43708;G3V3B9;A0A0A0MR33;G3V267;G3V5T0;O43708-3 A0A0C4DFM0 GSTZ1 Maleylacetoacetate isomerase 0 167.89 3.58E-06 56721000 97547 129800 104390 99583 128190 82581 101510 102600 104200 FALSE TRUE 91441.7074 139410.5271 106866.1801 102138.4684 118122.4745 106420.7941 86289.51787 115409.8359 86808.34684 1.053374597 1.605957631 1.231058809 1.176597321 1.360727151 1.225928128 0.994023282 1.329478559 1 16.40554615 2.075384028 0.471105526 1.034746461 1.373171485 0.146689932 0.17144665 1.300744454 0.64543413 0.163709795 0.142761654 118.9553633 -2.075384028 0.338425025 LLVSMCQGNRDENQSINHQMAQEDAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLVSMCQGNRDENQSINHQMAQEDAQR 27 1 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;; 299.56 4.99E-71 1003900000 227139 370830 305765 289889 375200 120410 379580 296871 622090 FALSE TRUE 212922.7754 398286.639 313017.8902 297328.0425 345733.3055 155170.4123 322665.5028 333935.9978 518259.1601 0.410842281 0.768508634 0.603979465 0.57370533 0.667105055 0.299406984 0.622594886 0.644341718 1 18.98331419 0.730426532 2.55751304 0.999839578 0.581553808 0.518911757 0.130416525 1.272806176 10.8925746 0.12061953 0.032146515 5.37559489 -0.730426532 -0.418285769 LLVVDPETDEHFKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LLVVDPETDEHFKR 14 1 H3BN50;Q15599-3;H3BQS0;H3BUQ9;Q15599;Q15599-2 H3BN50;Q15599 SLC9A3R2 Na(+)/H(+) exchange regulatory cofactor NHE-RF2 0 ;;; 119.01 0.00013758 540233000 825960 739580 779730 732950 913610 613526 900240 688960 955030 FALSE TRUE 774264.638 794339.2727 798225.5638 751758.7379 841858.7559 790640.9964 765257.3694 774978.1726 795629.3233 0.973147439 0.998378578 1.003263128 0.944860522 1.058104234 0.993730338 0.961826503 0.974044256 1 19.60173692 1.895644762 8.364760834 0.97502455 0.997226425 0.059944994 0.029563056 0.693518687 50.44273278 0.011586483 0.007278598 78.64022758 -1.895644762 0.022201876 LLVVDQETDEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LLVVDQETDEELR 13 0 Q15599;Q15599-2;H3BMF5 Q15599 SLC9A3R2 Na(+)/H(+) exchange regulatory cofactor NHE-RF2 0 162.68 9.31E-05 19559000 38821 42297 39039 42195 44934 36471 38622 31808 40224 FALSE TRUE 36391.26291 45428.71389 39965.02352 43277.79514 41405.0649 46999.58564 32830.98965 35779.29882 33510.35454 1.085970692 1.355661989 1.19261715 1.291475298 1.235590177 1.402539194 0.979726717 1.067708752 1 15.03231933 1.680511234 8.116134037 1.019307541 1.2635622 0.62719119 0.088717381 0.070649922 8.295589892 0.038676516 0.020329242 47.91938485 -1.680511234 0.244254658 LLWHGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLWHGSR 7 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 134.06 0.0032115 1334230000 617320 2511000 1455030 1524940 2295800 1162660 1720620 2023100 1745960 FALSE TRUE 578683.0431 2696917.053 1489543.999 1564072.542 2115497.129 1498301.068 1462629.004 2275688.488 1454547.997 0.397843897 1.854127233 1.024059709 1.075297993 1.454401734 1.030080184 1.005555683 1.564533101 1 20.47213947 LLYDLADQLHAAVGASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LLYDLADQLHAAVGASR 17 0 H0YL12;P13804-2;P13804;H0YK49;H0YNX6 H0YL12 ETFA "Electron transfer flavoprotein subunit alpha, mitochondrial" 0 ;; 243.29 1.89E-20 285652000 401913 485700 433254 372885 613483 436019 429140 484749 630520 FALSE TRUE 376757.9828 521661.7334 443530.9895 382453.8604 565302.5199 561890.6071 364794.4409 545270.9797 525282.1387 0.717248798 0.993107694 0.844367163 0.728092262 1.076188353 1.069692963 0.694473339 1.038053533 1 19.002733 2.741585037 24.99842918 0.943108183 0.853381803 0.213190502 0.134014464 696.5788434 5757604.255 0.042330452 0.043162024 551.5501876 -2.741585037 -0.089726379 LLYNNVSNFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LLYNNVSNFGR 11 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 204.34 7.80E-08 471040000 216310 276700 210015 242580 296340 174497 269380 267700 290180 FALSE TRUE 202771.5432 297187.1559 214996.655 248805.0135 273066.6518 224871.4512 228988.9698 301122.9343 241747.0834 0.838775552 1.229330885 0.889345393 1.029195513 1.129555104 0.930193027 0.947225367 1.245611447 1 17.88313896 1.259257881 24.95374639 1.122806011 1.009742806 0.135307001 0.127835314 419.2098878 505424.6856 0.079085721 0.028809779 18.16594024 -1.259257881 -0.113063206 LMADVVEEETRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LMADVVEEETRR 12 1 Q9NPI6-2;Q9NPI6;A0A087WVE6;A0A087WT55 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 0 116.54 0.0013321 30204000 90279 78344 124760 140560 77928 102660 127760 77752 163360 FALSE TRUE 84628.59854 84144.67128 127719.3661 144167.0076 71807.84923 132296.2755 108603.5741 87459.50835 136094.1607 0.621838572 0.618282745 0.938463234 1.059318099 0.52763358 0.972093695 0.798003188 0.642639684 1 17.05424564 4.135391107 3.793583088 0.841431199 0.617913043 0.251644529 0.163042202 0.303221438 8.08227877 0.038151175 0.092902875 13658.12574 -4.135391107 -0.223518156 LMCPQEIVDYIADKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LMCPQEIVDYIADKK 15 1 O14561;H3BNK3 O14561 NDUFAB1 "Acyl carrier protein, mitochondrial;Acyl carrier protein" 0 ; 227.89 1.08E-12 329320000 1148850 609680 760880 625560 885450 692210 908890 783950 1119970 FALSE TRUE 1076945.529 654821.3416 778928.4329 641612.9287 815910.3287 892039.7899 772610.3822 881827.8832 933039.7717 1.154233251 0.701815037 0.834828757 0.687658713 0.874464684 0.956057627 0.828057287 0.945112856 1 19.83157905 2.485904435 24.57965761 0.910398616 0.815383104 0.059087484 0.134373901 767.6688807 2148325.184 0.041615129 0.036543594 306.1289733 -2.485904435 -0.095015512 LMDEVAGIVAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LMDEVAGIVAAR 12 0 O00154-6;O00154-4;O00154-7;O00154;O00154-5;K7EKP8;O00154-2;O00154-3 O00154-6 ACOT7 Cytosolic acyl coenzyme A thioester hydrolase 0 ; 123.75 0.00077991 33202000 60034 74475 76703 74606 86194 66534 71503 61145 60639 FALSE TRUE 56276.5791 79989.20649 78522.43138 76520.51627 79424.67093 85741.28571 60781.78895 68779.08785 50517.95916 1.11399154 1.58338159 1.554346864 1.514719073 1.572206642 1.697243656 1.203171901 1.361477957 1 15.62450874 1.115616557 1.203112331 1.023982071 1.515631121 0.424351163 0.173502326 0.378861099 1.130093592 0.149798844 0.047414873 13.05018167 -1.115616557 0.49164905 LMDHVGTEPSIKEDQVIQLMNAIFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LMDHVGTEPSIKEDQVIQLMNAIFSK 26 1 P04844-2;P04844;F2Z3K5;Q5JYR4;Q5JYR7 P04844-2 RPN2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 0 91.114 0.0060898 72811000 204900 167410 163230 173830 208290 123930 218510 178430 134450 FALSE TRUE 192075.6748 179805.2106 167101.8927 178290.7721 191931.7436 159706.5792 185746.454 200707.3783 112009.4264 1.714817055 1.605268559 1.491855623 1.591747925 1.713532064 1.425831595 1.658310912 1.791879351 1 16.77326063 -1.277363554 4.645833454 0.999733242 1.607247402 0.76438326 0.108543491 0.00028233 4.39E-05 0.098937469 0.023309739 0.052800307 1.277363554 0.607514159 LMDLLGEGLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LMDLLGEGLKR 11 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 131.54 0.00032246 1332850000 835170 965080 872100 823190 1098100 648980 1039730 928290 1236520 FALSE TRUE 782898.2005 1036535.527 892786.6238 844314.4491 1011859.656 836329.9907 883832.1389 1044189.05 1030136.824 0.759994384 1.006211508 0.866668003 0.81961389 0.982257533 0.811863018 0.857975483 1.013641126 1 19.97440454 1.233588267 24.9961611 1.006820647 0.882469346 0.354031507 0.074646324 150.7294526 757678.3264 0.060241822 0.016915534 17.12333161 -1.233588267 -0.124351301 LMEDLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 25 LMEDLDR 7 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;;;;;;;;;;;;;;;;;;;;; 249.47 1.87E-08 1.90372E+11 99163450 130963600 109309880 114009560 114773380 87088060 123700660 102074130 104013430 FALSE TRUE 92956986.68 140660281.2 111902762 116935238.3 105759541.7 112228969.2 105152894.4 114818309.8 86652916.58 1.072750813 1.623260783 1.2913906 1.349466849 1.220496042 1.295155127 1.213495155 1.325036875 1 26.36874497 -0.526478469 0.218132006 0.808014435 1.420761617 0.277841392 0.142342329 13.11761216 0.828365534 2.038369509 0.338556884 0.297523676 0.526478469 0.612747182 LMEDLDRNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LMEDLDRNK 9 1 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;;;; 173.32 5.06E-05 4167350000 1764325 3807750 2666659 4037370 5562180 2694451 3026290 2104107 7232560 FALSE TRUE 1653899.048 4089679.772 2729913.411 4140975.749 5125348.82 3472295.263 2572525.909 2366809.391 6025399.012 0.274487888 0.678740074 0.453067657 0.687253366 0.850623969 0.576276402 0.42694698 0.39280542 1 22.52262535 -2.105817019 2.604899825 1.844412231 0.552380218 0.423710141 0.167319618 12868269.23 4077813.678 64458832.53 0.039166352 0.007837598 2.105817019 -1.292032013 LMEEDELPSWIIKDDAEVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LMEEDELPSWIIKDDAEVER 20 1 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532;Q9HBD4;P51532-3;P51532-5;A0A2R8YF58;A0A2R8Y7Y7;A0A2R8Y526;A0A2R8YF80;A0A2R8Y6N0;A0A2R8Y440;A0A2R8YGG3;A0A2R8Y4C5;A0A2R8Y6V2;A0A2R8Y7F3;A0A2R8YG32;A0A2R8YDA1;A0A2R8Y523;A0A2R8YFK5;K7EQF0;A0A2R8Y5K3;F6VDE0;P51531-2;P51531;A0A0U1RQZ9;A0A0U1RRG6 A0A2R8Y4P4;F6VDE0 SMARCA4;SMARCA2 Transcription activator BRG1;Probable global transcription activator SNF2L2 0 ;;; 239.76 1.02E-29 221136000 349113 319304 336940 311304 343855 262947 420302 302048 432544 FALSE TRUE 327262.6405 342945.6004 344932.3759 319292.5877 316850.0153 338855.5303 357281.617 339759.3577 360349.6121 0.908180915 0.951702427 0.957215894 0.886063359 0.879285019 0.940352144 0.99148606 0.94286034 1 18.45903777 1.924762105 5.933696437 0.975237609 0.924254425 0.474269979 0.028901484 0.256559824 15.58240637 0.013726753 0.008375831 84.09343738 -1.924762105 -0.050983184 LMEEIMSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LMEEIMSEK 9 0 P17844;P17844-2;J3KTA4;J3QSF1 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 129.1 0.00092776 15462000 23119 19322 25915 21931 24415 19307 24376 18680 24605 FALSE TRUE 21672.02306 20752.62098 26529.71604 22493.78659 22497.54439 24880.61748 20721.0451 21012.23912 20498.26655 1.057261257 1.012408583 1.294241929 1.097350673 1.097533996 1.213791294 1.010868165 1.025073953 1 14.32321429 1.632944698 8.292218324 1.012504504 1.131734635 0.327860119 0.078645489 0.136563761 20.09358899 0.040129394 0.020531396 42.94817344 -1.632944698 0.11923013 LMELHGEGSSSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LMELHGEGSSSGK 13 0 P61247;D6RG13;D6RAT0;H0Y9Y4;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ;;;;; 219.43 2.25E-11 6443840000 9311780 10384700 11058700 10797300 11573100 9493340 13022900 9670200 12294600 FALSE TRUE 8728972.312 11153593.99 11321017.59 11074377 10664195.41 12233913.15 11070237.04 10877545.76 10242551.83 0.852226325 1.088946795 1.105292682 1.081212688 1.041165872 1.194420428 1.080808496 1.061995676 1 23.28807186 4.73854255 8.496979362 1.090418072 0.850796471 0.671364608 0.050137443 0.045652439 51.71174177 0.010684357 0.062803508 54769.97588 -4.73854255 -0.239621601 LMELYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LMELYER 7 0 Q9UG63;Q9UG63-2;C9JHK9;C9JZV3 Q9UG63 ABCF2 ATP-binding cassette sub-family F member 2 0 86.794 0.046098 64481000 93875 133810 112260 112460 160940 95084 119370 148210 160780 FALSE TRUE 87999.53132 143717.4316 114922.8602 115345.914 148300.4216 122533.2072 101471.5767 166714.3448 133944.7793 0.65698366 1.072960308 0.857986857 0.861145276 1.107175825 0.914803905 0.75756276 1.244649815 1 17.03127883 4.753933298 24.2799951 0.953034388 0.656983336 0.321375846 0.142413918 2445.571053 3862498.813 0.03176685 0.740176448 56745.74444 -4.753933298 -0.296051052 LMENMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LMENMR 6 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 97.071 0.096521 194140000 256770 425870 221670 217540 400480 168190 235060 325380 428680 FALSE TRUE 240699.224 457401.8579 226928.1171 223122.4447 369027.9163 216743.7227 199814.9352 366004.4092 357130.5386 0.673981074 1.280769378 0.635420645 0.624764394 1.033313806 0.606903357 0.559501117 1.024847695 1 18.44609198 3.85669883 6.254591978 0.747739635 1.010629715 0.087266279 0.233704533 0.329865706 15.99867667 0.055332846 0.100945265 7189.502348 -3.85669883 0.26289008 LMFEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LMFEELR 7 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;;;;; 164.89 0.0027471 309382000 578445 1207382 579658 587602 1252189 370418 592424 1043036 1271458 FALSE TRUE 542241.16 1296777.82 593407.7615 602680.8621 1153847.127 477351.6634 503595.521 1173261.341 1059243.446 0.511913632 1.224249085 0.560218488 0.568972944 1.089312501 0.450653403 0.475429443 1.107640878 1 20.01460277 5.010092383 17.74183685 0.772710985 0.118051901 0.083336863 0.28804343 23226408.98 618502766.1 0.067349993 368059183 102351.069 -5.010092383 -0.654659083 LMHNAS(ph)DS(ph)EVDQDDVVEWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 LMHNASDSEVDQDDVVEWK 19 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 2 LMHNAS(1)DS(1)EVDQDDVVEWK;LMHNAS(1)DS(1)EVDQDDVVEWK;LMHNAS(1)DS(1)EVDQDDVVEWK;LMHNAS(1)DS(1)EVDQDDVVEWK;LMHNAS(1)DS(1)EVDQDDVVEWK;LMHNAS(1)DS(1)EVDQDDVVEWK;LMHNAS(1)DS(1)EVDQDDVVEWK;LMHNAS(1)DS(1)EVDQDDVVEWK;LMHNAS(1)DS(1)EVDQDDVVEWK 217.32 1.92E-19 2931309000 3220805 2337140 2697910 2562610 2695387 2076491 3304047 2345381 2640179 TRUE FALSE 3019220.564 2510184.277 2761905.699 2628370.911 2483702.178 2675940.243 2808635.826 2638206.981 2199516.069 1.372674929 1.141243891 1.255687894 1.194976908 1.129203925 1.216604089 1.276933534 1.199448833 1 21.06875471 0.957504618 23.01848331 0.999999999 1.22040119 0.510497161 0.0690185 2812.233451 1523305.236 0.060936808 0.015234202 9.067856071 -0.957504618 0.220401191 LMHNAS(ph)DSEVDQDDVVEWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 LMHNASDSEVDQDDVVEWK 19 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 LMHNAS(0.999)DS(0.001)EVDQDDVVEWK;LMHNAS(0.993)DS(0.007)EVDQDDVVEWK;LMHNAS(0.792)DS(0.208)EVDQDDVVEWK;LMHNAS(0.935)DS(0.065)EVDQDDVVEWK;LMHNAS(0.998)DS(0.002)EVDQDDVVEWK;LMHNAS(0.985)DS(0.015)EVDQDDVVEWK;LMHNAS(0.956)DS(0.044)EVDQDDVVEWK;LMHNAS(0.919)DS(0.081)EVDQDDVVEWK;LMHNAS(0.83)DS(0.17)EVDQDDVVEWK 274.97 1.29E-39 4625780000 4785534 3437753 4049291 3769943 3870258 3389688 4512890 3326044 3602835 TRUE FALSE 4486015.969 3692287.809 4145342.095 3866686.12 3566303.549 4368235.899 3836224.04 3741307.915 3001498.563 1.494592076 1.230148118 1.381090814 1.288251864 1.188174331 1.455351654 1.278102907 1.246479995 1 21.51725155 -3.725392281 0.269766307 9.20E-09 1.34356705 0.553114356 0.093836211 72.85479284 1.332277044 40.32461338 0.106867159 0.000188195 3.725392281 1.343567041 LMHQAALLGQALQDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LMHQAALLGQALQDSR 16 0 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881;E9PKD3;A0A0B4J225;E9PIZ5 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 ; 271.43 3.76E-35 1338030000 1293880 1568040 1237930 1190020 1557250 1100900 1503900 1539660 1296600 FALSE TRUE 1212898.36 1684139.313 1267294.284 1220557.928 1434949.867 1418711.958 1278404.157 1731889.94 1080189.084 1.12285745 1.559115287 1.17321523 1.129948401 1.328424707 1.313392238 1.183500348 1.603321091 1 20.04285244 -1.953812059 2.711886845 0.774693965 1.300709115 0.244469654 0.166686599 29442498.13 13908411.34 41748650 0.037048281 0.011122129 1.953812059 0.52601515 LMIEMDGTENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LMIEMDGTENK 11 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879 P06733 ENO1 Alpha-enolase;Enolase 0 ;;; 213.98 1.60E-09 293010000 1265250 1139337 1107550 990560 1344540 671437 1238170 1097560 1479210 FALSE TRUE 1186060.261 1223694.697 1133821.609 1015979.447 1238945.252 865269.962 1052517.903 1234592.782 1232320.295 0.962461031 0.993000523 0.920070548 0.824444303 1.005376003 0.702146971 0.854094433 1.001844072 1 20.23294585 3.637671161 2.826719997 0.879490735 0.97558341 0.079967586 0.095074488 0.469431251 7.350450547 0.024897863 0.042984125 4341.813459 -3.637671161 0.096092675 LMIWDTR ddPTM_SK-BR-3_Pertuzumab_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 ;; 128.38 0.0087545 1254903000 2293164 5184760 2379939 2241602 5645030 1498772 2258550 4537630 4932200 FALSE TRUE 2149638.959 5568645.025 2436392.277 2299125.302 5201692.115 1931443.146 1919901.395 5104163.094 4108983.957 0.523155841 1.355236497 0.592942757 0.559536208 1.265931473 0.470053708 0.467244802 1.242195917 1 21.97035027 3.83006843 8.369500089 0.749951489 0.994120534 0.005938392 0.356298584 0.688727138 50.38025995 0.085307957 0.154228578 6761.895113 -3.83006843 0.244169045 LMKPPS(ph)PEHQSLDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LMKPPSPEHQSLDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR 43 1 Q9Y6X9;Q9Y6X9-2;H7C1V1 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 LMKPPS(0.992)PEHQS(0.007)LDT(0.001)QQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.706)PEHQS(0.269)LDT(0.025)QQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.972)PEHQS(0.023)LDT(0.004)QQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.992)PEHQS(0.008)LDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.942)PEHQS(0.048)LDT(0.01)QQEGGEEEVGPVAQQAIAVAEPSTSECLR 362.84 1.74E-155 1189570000 308250 346142 347174 364018 418488 304835 505414 358632 588030 TRUE FALSE 288957.1827 371770.7138 355409.1312 373359.3182 385621.6406 392835.9159 429631.8627 403407.9946 489883.9942 0.589848181 0.758895408 0.725496516 0.762138226 0.7871693 0.801895797 0.877007348 0.823476577 1 18.90208063 5.019355882 0.066849878 1.331333003 3.41E-11 0.860134408 0.039199721 48.00328229 0.464262532 2.647696461 7.54648572 104557.6664 -5.019355882 -1.331333003 LMLDGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LMLDGDR 7 0 P13797;A0A0A0MSQ0;P13797-3;P13797-2;U3KQI3 P13797 PLS3 Plastin-3 0 ;;; 124.59 0.019241 512240000 1138460 1760500 1448280 1505960 1652710 1416730 1491140 1588120 1506000 FALSE TRUE 1067205.821 1890849.252 1482633.886 1544605.483 1522912.823 1825716.952 1267557.4 1786400.278 1254638.871 0.850607968 1.507086458 1.181721625 1.231115598 1.213825634 1.455173273 1.010296612 1.423836228 1 20.25884073 -1.335310133 4.410964582 0.999712744 1.245579364 0.116835904 0.200207327 0.000496888 7.49E-05 0.170310367 0.040095986 0.046205095 1.335310133 0.24586662 LMLLLEVISGERLPKPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LMLLLEVISGERLPKPER 18 2 O43707 O43707 ACTN4 Alpha-actinin-4 0 90.754 0.012713 15663000 21324 21654 28548 27324 29652 20242 31318 24903 36410 FALSE TRUE 19989.3689 23257.28469 29225.17204 28025.1801 27323.25153 26085.5368 26622.15664 28012.19437 30332.93578 0.658998821 0.76673372 0.963479838 0.923919145 0.90077834 0.859974022 0.877665018 0.923491039 1 14.88859752 4.406344465 1.947098033 0.910140494 0.652483131 0.822430971 0.041543298 0.177513251 1.113049734 0.010720293 0.064531428 25488.51099 -4.406344465 -0.257657363 LMNESLMLVTALNPHIGYDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LMNESLMLVTALNPHIGYDK 20 0 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 ; 246.16 5.16E-30 432000000 750636 706241 595915 588981 941610 606471 679026 728095 971370 FALSE TRUE 703655.0327 758531.8185 610050.3852 604095.2496 867659.7489 781549.3325 577212.3551 818999.2635 809242.0717 0.869523542 0.937336114 0.753854015 0.74649511 1.072188137 0.965779412 0.713275267 1.012057198 1 19.6262118 2.77660813 24.99735431 0.91787563 0.833066515 0.209269118 0.110329578 1275.661329 838111.8704 0.035011312 0.037134508 597.8718838 -2.77660813 -0.084809115 LMQLVDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LMQLVDHR 8 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;; 161.79 0.00034549 1794583000 953767 2016796 940064 884434 2246563 704780 1082073 1845595 2095547 FALSE TRUE 894072.426 2166121.674 962362.762 907130.0738 2070127.004 908238.5449 919826.1991 2076021.598 1745786.668 0.512131546 1.240771117 0.551248775 0.519611067 1.185784633 0.520246008 0.526883505 1.189161102 1 20.73544584 -1.632002506 8.951247009 1.000114093 0.775459623 0.046692178 0.310559541 0.000660931 2.72E-05 0.281060145 0.066213235 0.023334446 1.632002506 -0.22465447 LMS(ph)DVEDVSLENVHTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LMSDVEDVSLENVHTR 16 0 Q9NSI6-3;Q9NSI6-2;Q9NSI6 Q9NSI6-3 BRWD1 Bromodomain and WD repeat-containing protein 1 1 LMS(1)DVEDVSLENVHTR 154.56 2.21E-07 14942000 29162 18823 28270 26995 23736 21345 31092 20438 16163 TRUE FALSE 27336.80248 20216.67451 28940.57775 27687.7374 21871.87031 27506.95499 26430.04324 22989.72929 13465.29088 2.030167986 1.501391591 2.149272378 2.056230173 1.624314729 2.042804365 1.9628275 1.70733254 1 13.71695778 0.852669174 3.817768931 1.000123447 1.896693813 0.667174733 0.201042502 0.510472559 12.24669516 0.1858835 0.047657371 7.123102171 -0.852669174 0.896570366 LMSELYHPDDHVL ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LMSELYHPDDHVL 13 0 P49770 P49770 EIF2B2 Translation initiation factor eIF-2B subunit beta 0 ;;;; 171.62 2.48E-05 573012000 672329 934000 812510 760031 986120 703070 860910 839750 990530 FALSE TRUE 630249.128 1003154.332 831783.1209 779534.6822 908674.113 906034.8956 731824.5378 944594.636 825204.1439 0.763749349 1.215643837 1.007972545 0.944656771 1.101150691 1.097952431 0.8868406 1.144679947 1 19.65439154 LMSNLDSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LMSNLDSNR 9 0 P26447 P26447 S100A4 Protein S100-A4 0 ;;; 154.75 0.00017436 1393170000 1522040 2508150 1515620 1521740 2684660 1510677 2035840 2153660 3498210 FALSE TRUE 1426778.233 2693856.036 1551571.222 1560790.425 2473817.633 1946784.926 1730584.692 2422549.192 2914336.152 0.489572293 0.924346368 0.532392676 0.535556073 0.848844301 0.668002874 0.593817803 0.831252493 1 21.47473586 0.998781726 4.621726372 0.999451538 0.670383095 0.404792447 0.138421769 0.161235803 10.85461729 0.125228259 0.031787264 9.971987519 -0.998781726 -0.329068443 LMYEHNLQRTACNMTYGSFGGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LMYEHNLQRTACNMTYGSFGGVK 23 1 F8WCG5;A0A5F9ZGY2;A0A5F9ZHP5;A0A5F9ZH74;A0A5F9ZH37;A0A5F9ZHE7;A0A5F9ZH14;A0A5F9ZGX9;Q3SYG4-5;Q3SYG4-6;Q3SYG4-2;Q3SYG4-4;Q3SYG4-7;Q3SYG4-3;Q3SYG4 F8WCG5 BBS9 Protein PTHB1 0 56.055 0.055276 396000000 294430 336930 325650 322760 344920 248320 413010 286550 397480 FALSE TRUE 276002.1519 361876.6478 333374.5718 331042.568 317831.3745 320005.9529 351082.9847 322326.3983 331138.0202 0.833495809 1.092827237 1.006754137 0.999711745 0.95981541 0.966382395 1.060231575 0.973389882 1 18.33707314 4.755278041 24.82573141 1.013027461 0.833495653 0.631129933 0.041581294 2084.097855 3094874.001 0.010168386 0.283765222 56921.7235 -4.755278041 -0.179531807 LNAS(ph)PAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LNASPAAR 8 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 LNAS(1)PAAR;LNAS(1)PAAR 157.25 0.00039857 1240540000 1463130 1610810 1521970 1505680 1697940 1298160 1706120 1475730 1388630 TRUE FALSE 1371555.305 1730076.048 1558071.847 1544318.298 1564590.642 1672917.718 1450303.145 1659978.139 1156858.682 1.185585868 1.495494718 1.346812598 1.334923895 1.352447508 1.446086496 1.253656274 1.434901397 1 20.14178121 -1.670352422 2.749144615 0.954988695 1.36298028 0.602384217 0.09081078 14647071.87 13195194.38 4626569.424 0.019685509 0.021362279 1.670352422 0.407991585 LNCQVIGASVDSHFCHLAWVNTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LNCQVIGASVDSHFCHLAWVNTPK 24 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;;; 275.2 3.02E-52 6962893000 5199790 5441523 5401477 5269914 6375545 4782952 6885130 5287929 6123781 FALSE TRUE 4874344.426 5844419.025 5529602.585 5405148.915 5874835.413 6163712.598 5852768.675 5948138.576 5101682.39 0.955438629 1.145586608 1.083878251 1.059483618 1.151548639 1.208172545 1.147223255 1.165917068 1 22.28254165 2.729134114 23.72908282 1.149938979 1.078975327 0.170994362 0.071678647 524.9766088 1321505.707 0.020934008 0.020011684 535.9621419 -2.729134114 -0.070963652 LNDPFQPFPGNDS(ph)PKEKDPEIFCDPFTSATTTTNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LNDPFQPFPGNDSPKEKDPEIFCDPFTSATTTTNK 35 2 P42566;B1AUU8;P42566-2 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 LNDPFQPFPGNDS(1)PKEKDPEIFCDPFTSATTTTNK 108.85 8.64E-06 246850000 515330 174780 282100 279970 272240 157260 333550 158660 298170 TRUE FALSE 483076.4152 187720.8931 288791.5452 287154.5042 250859.3686 202658.4091 283537.274 178469.0503 248403.5007 1.944724667 0.755709531 1.16259048 1.156000231 1.009886607 0.815843611 1.141438318 0.718464312 1 17.92232598 4.747072597 24.99256283 0.98594817 1.94472515 0.779327059 0.162809017 490.7211693 1440805.497 0.036221913 0.422530935 55856.35569 -4.747072597 0.95877698 LNDS(ph)PTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LNDSPTLK 8 0 Q9BYW2;C9JG86;H7C3H4;Q9BYW2-3;Q9BYW2-2;H7BZ93;H7BXT4 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 LNDS(0.997)PT(0.003)LK;LNDS(1)PTLK;LNDS(0.999)PT(0.001)LK;LNDS(0.999)PT(0.001)LK 172.1 0.00029953 1295320000 4410760 2873870 3359140 3216960 3602820 2691260 4469520 3063120 4315050 TRUE FALSE 4134698.405 3086654.325 3438820.387 3299512.64 3319869.05 3468183.073 3799356.969 3445557.275 3594840.279 1.150175831 0.858634622 0.956598936 0.917846798 0.923509473 0.964766945 1.056891732 0.95847298 1 21.77749624 1.977161441 15.94671432 1.011291164 0.944671372 0.038442928 0.078839301 15.33594679 10705.22047 0.029359842 0.019274223 94.8771085 -1.977161441 -0.066619792 LNDSHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LNDSHK 6 0 P11387 P11387 TOP1 DNA topoisomerase 1 0 ; 84.244 0.056071 238310000 738550 513610 617050 499870 626360 362320 591970 486080 649390 FALSE TRUE 692325.4738 551638.2188 631686.7174 512697.5105 577168.2122 466915.9022 503209.5941 546768.158 541002.6138 1.279708187 1.019659064 1.167622302 0.947680284 1.066849212 0.863056648 0.93014263 1.010657147 1 19.04527604 3.102185409 1.437134716 0.949606789 1.134002531 0.455121189 0.088245217 0.347389013 1.487015167 0.02981667 0.039231837 1265.276404 -3.102185409 0.184395742 LNEAQPSTIATS(ph)MRDSLIDSLT ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LNEAQPSTIATSMRDSLIDSLT 22 1 P56537;P56537-2 P56537 EIF6 Eukaryotic translation initiation factor 6 1 LNEAQPS(0.082)T(0.063)IAT(0.082)S(0.716)MRDS(0.055)LIDSLT 109.68 0.00023124 75446000 86423 91142 87199 81622 101850 74169 101540 85266 112620 TRUE FALSE 81013.9387 97890.24851 89267.40146 83716.55871 93851.11184 95580.38627 86315.01965 95911.64779 93822.99445 0.86347637 1.043350291 0.951444814 0.892281889 1.000299686 1.018730929 0.919977242 1.022261636 1 16.51765393 LNECIS(ph)PVANEMNHLPAHSHDLQR ddPTM_SK-BR-3_Pertuzumab_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 196.01 3.39E-24 605520000 134884 152064 144555 153568 165248 134631 174135 125596 179937 TRUE FALSE 126441.8512 163322.9768 147983.9129 157508.8149 152270.0887 173496.7841 148025.0733 141276.9371 149904.3523 0.843483523 1.089514576 0.987188902 1.050728765 1.015781639 1.157383235 0.98746348 0.9424472 1 17.19368274 4.749498928 24.75040431 1.032451858 0.843483398 0.481959776 0.060279533 1177.353116 2663969.029 0.013445641 0.199045173 56169.28922 -4.749498928 -0.18896846 LNEDKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LNEDKPK 7 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 59.8 0.092434 571260000 395010 203130 249720 266950 296640 167620 312700 218610 380930 FALSE TRUE 370287.0292 218169.9566 255643.4763 273800.3889 273343.091 216009.1729 265813.538 245903.9397 317350.3221 1.166808424 0.687473563 0.805556064 0.862770162 0.861329175 0.680664735 0.837602862 0.77486589 1 18.27571678 -1.589028948 2.718436038 1.014093508 0.815261252 0.114580121 0.135251127 28904904.09 27673501.95 2920858.939 0.02938308 0.025761494 1.589028948 -0.198832256 LNEHFLNTTDFLDTIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LNEHFLNTTDFLDTIK 16 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 285.31 7.93E-36 718180000 916820 711900 723280 670730 1051950 567680 777010 740150 1283380 FALSE TRUE 859437.8728 764609.8167 740436.5432 687942.0673 969334.0904 731560.0005 660504.5639 832559.3568 1069175.587 0.803832301 0.715139614 0.69253035 0.643432263 0.906618241 0.684228119 0.617769964 0.778692824 1 20.02806737 0.976736466 23.27791506 1.000000004 0.715093311 0.524471853 0.082074016 619.8131261 620197.7659 0.075811493 0.018952873 9.478431277 -0.976736466 -0.284906694 LNEQAS(ph)EEILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LNEQASEEILK 11 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 1 LNEQAS(1)EEILK 136.17 0.0012675 0 145420 92369 120450 104530 106630 92006 137170 96768 90899 TRUE FALSE 136318.4218 99208.09687 123307.1309 107212.4168 98255.70992 118566.6386 116602.6319 108849.6978 75727.36967 1.800120912 1.31006923 1.628303365 1.415768397 1.297492708 1.565703908 1.539768679 1.437389127 1 16.2085272 0.853841374 6.000935574 1.000001368 1.495314595 0.532611812 0.148064814 2.434569976 99.74389317 0.12793461 0.032169987 7.142354042 -0.853841374 0.495313227 LNEQAS(ph)EEILKVEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LNEQASEEILKVEQK 15 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 1 LNEQAS(1)EEILKVEQK 141.83 2.84E-06 92439000 96813 44419 63939 72496 70504 39754 71292 50379 72936 TRUE FALSE 90753.64715 47707.82898 65455.66327 74356.3701 64966.90024 51230.33445 60602.42644 56668.92905 60762.51042 1.493579619 0.785152369 1.077237639 1.223721166 1.069193814 0.84312406 0.997365415 0.932629818 1 15.89089386 2.361970249 9.342040109 0.945529357 1.080858431 0.181771595 0.180900199 0.624813154 48.5232093 0.060754593 0.050780362 230.1284166 -2.361970249 0.135329074 LNEQASEEILKVEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LNEQASEEILKVEQK 15 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 ; 198.07 7.40E-09 251620000 342280 246182 294306 341150 405840 222404 429720 291850 508900 FALSE TRUE 320857.3058 264409.5714 301287.0773 349904.4866 373966.9635 286608.4244 365287.4753 328288.1149 423961.3024 0.756808001 0.6236644 0.710647589 0.825321756 0.882078061 0.676024964 0.861605701 0.774335094 1 18.69357306 -5 0.067505127 1.896573521 0.419694264 0.540254079 0.074019584 226.8852781 1.107437879 31.87088131 4.278491031 1.00E-05 5 -1.476879258 LNEQYEHASIHLWDLLEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LNEQYEHASIHLWDLLEGK 19 0 Q14444-2;Q14444;G3V153 Q14444-2 CAPRIN1 Caprin-1 0 ;; 171.85 5.48E-12 349840000 181376 371197 350306 347163 401351 298098 427580 356377 406870 FALSE TRUE 170023.9999 398680.8121 358615.4237 356071.7903 369830.5114 384154.0534 363468.3485 400871.4529 338960.7685 0.501603772 1.17618571 1.057985044 1.050480833 1.091071728 1.133328954 1.072302113 1.182648525 1 18.37075878 4.743125115 24.99808586 1.098254021 0.501603531 0.916097914 0.056478963 113.9192265 623872.3312 0.012144204 0.097876411 55350.95451 -4.743125115 -0.59665049 LNFAVASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LNFAVASR 8 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 84.743 0.044492 0 134430 242150 146780 158880 244030 117280 150900 224920 174310 FALSE TRUE 126016.2663 260079.038 150261.6909 162957.1298 224864.8682 151136.8321 128273.9459 253001.7571 145216.5349 0.867781801 1.790973997 1.034742297 1.122166494 1.548479781 1.040768754 0.883328789 1.742237943 1 17.14784621 3.750432733 24.0565668 1.175203598 1.400581721 0.013605585 0.342157729 689.407645 711435.8533 0.080939629 0.145780409 5629.019242 -3.750432733 0.225378123 LNFGDDIPSALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LNFGDDIPSALR 12 0 Q9UNE7;Q9UNE7-2;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 79.201 0.05507 58345000 68243 89286 74269 71141 101610 67779 81501 84104 95522 FALSE TRUE 63971.79245 95896.82834 76030.69575 72966.5985 93629.96048 87345.697 69280.68167 94604.56954 79578.7611 0.803880226 1.205055558 0.955414418 0.916910461 1.176569718 1.097600613 0.870592614 1.188816818 1 16.28009582 LNFHPDQEDQFFSLVHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LNFHPDQEDQFFSLVHEK 18 0 Q969Z0;Q969Z0-2;H7C4R5 Q969Z0 TBRG4 Protein TBRG4 0 177.61 5.38E-14 156030000 220210 214780 222310 204410 272020 217400 220890 216800 329960 FALSE TRUE 206427.4492 230682.5347 227583.2982 209655.5067 250656.6465 280159.8508 187769.5951 243867.9572 274887.5444 0.750952356 0.83918875 0.827914188 0.762695549 0.911851598 1.019179867 0.683077859 0.887155356 1 18.06848201 2.734413146 24.96042616 0.874458803 0.807975631 0.201241594 0.095198398 854.2902557 5141295.712 0.030104107 0.029326714 542.5167432 -2.734413146 -0.066483173 LNFLY(ph)QVS(ph)LR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LNFLYQVSLR 10 0 Q9H633-2;A0A0G2JJ52;A0A0G2JHI3 Q9H633-2 2 LNFLY(1)QVS(1)LR 51.927 0.082932 141570000 109740 71001 193380 199400 69481 193760 204270 77143 82425 TRUE FALSE 102871.5693 76257.98792 197967.0649 204516.9416 64024.24253 249695.3666 173641.6098 86774.47336 68667.73501 1.498106342 1.110535944 2.882970654 2.978355723 0.932377375 3.636283715 2.528721965 1.263686262 1 16.06734476 4.069147601 4.713481249 2.328858433 1.319571013 0.119340559 0.907457329 0.342515876 12.87405577 0.209370952 0.470623556 11725.93819 -4.069147601 -1.00928742 LNFSHGTHE ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LNFSHGTHE 9 0 H3BU13 H3BU13 PKM 0 ; 140.75 0.00010835 317980000 213778 152345 286700 296300 136452 338400 365810 133797 162197 FALSE TRUE 200398.0166 163624.7823 293500.6594 303903.5596 125735.6103 436090.5865 310960.1865 150501.85 135125.2729 1.483053557 1.210911762 2.172063398 2.249050479 0.930511426 3.227305872 2.301273329 1.113794975 1 17.04393801 2.29713574 24.99999285 2.092521585 1.660673388 0.011451666 0.734659408 210.014152 89633.03944 0.242506096 0.20289506 198.2146456 -2.29713574 -0.431848197 LNFSHGTHEYHAETIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LNFSHGTHEYHAETIK 16 0 P14618;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;; 189.52 3.49E-10 8913800000 2811660 3488240 3019190 3266290 3897630 2195680 3685770 3241420 4161330 FALSE TRUE 2635683.22 3746512.919 3090806.613 3350108.531 3591525.862 2829537.172 3133123.006 3646118.422 3466777.14 0.760269009 1.080690442 0.891550419 0.966346666 1.035984062 0.816186636 0.903756682 1.051731414 1 21.72516367 1.237207317 24.99898601 1.02586573 0.933228749 0.163986861 0.094843787 70.48064974 1301722.508 0.071049326 0.021486612 17.26661943 -1.237207317 -0.092636981 LNGPGENVS(ph)EDEAQSSNQR ddPTM_SK-BR-3_Pertuzumab_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 408.64 1.22E-147 439020000 436480 426950 404050 450170 423230 387080 493260 372260 360910 TRUE FALSE 409161.4959 458561.8222 413634.2568 461722.1243 389991.223 498823.7123 419300.2422 418737.4804 300671.7894 1.360824362 1.5251242 1.375700253 1.535635003 1.297066225 1.659030643 1.394544673 1.392672991 1 18.19782999 0.62864334 1.878608385 1.000208106 1.455305461 0.648318635 0.103390613 1.020087031 4.466735676 0.08487519 0.023633084 4.252490382 -0.62864334 0.455097356 LNGTDPEDVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 141.91 8.82E-05 210540000 195140 239110 202990 206880 234880 181510 229320 194720 211720 FALSE TRUE 182926.5357 256813.9532 207805.0187 212188.891 216433.4723 233908.9904 194935.5949 219031.2206 176382.5642 1.037101011 1.456005327 1.178149436 1.203003777 1.227068408 1.326145764 1.105186308 1.241796328 1 17.42834843 -0.262353245 0.346972537 0.934560105 1.267186671 0.245131828 0.115797419 7.94870479 1.142854502 0.763324728 0.095099556 0.546571214 0.262353245 0.332626566 LNHQEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LNHQEFK 7 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 94.262 0.01433 92716000 296730 284220 268790 259290 325510 211840 319820 293520 461480 FALSE TRUE 278158.199 305263.9445 275165.8257 265943.8204 299945.7576 272994.7691 271865.9601 330166.6181 384456.0067 0.723511128 0.794015282 0.715727732 0.691740578 0.780182264 0.710080645 0.707144524 0.858789074 1 18.55245899 0.992225111 3.573829949 0.999300196 0.734641287 0.880077027 0.032638177 0.066586454 2.227234812 0.031675017 0.008186877 9.822569519 -0.992225111 -0.264658909 LNHS(ph)PPQSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LNHSPPQSSSR 11 0 A0A087X0H9;Q5T8P6-3;Q5T8P6-2;Q5T8P6 A0A087X0H9 RBM26 RNA-binding protein 26 1 LNHS(0.847)PPQS(0.081)S(0.036)S(0.036)R;LNHS(1)PPQSSSR;LNHS(0.953)PPQS(0.023)S(0.023)S(0.002)R;LNHS(1)PPQSSSR;LNHS(1)PPQSSSR;LNHS(1)PPQSSSR;LNHS(1)PPQSSSR 170 1.70E-05 3556605000 1339460 1566080 1524420 1618750 1683810 1280880 1636470 1441110 1502640 TRUE FALSE 1255625.59 1682034.193 1560579.962 1660289.866 1551570.355 1650649.263 1391096.516 1621035.756 1251839.677 1.003024279 1.343649849 1.246629254 1.326279952 1.23943216 1.318578803 1.111241752 1.294922813 1 20.25561838 -0.288656494 0.584101678 0.97546862 1.252700447 0.306178983 0.10727629 7.977914589 2.547345046 0.536324719 0.040287448 0.514450397 0.288656494 0.277231827 LNHVAAGLVS(ph)PSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LNHVAAGLVSPSLK 14 0 Q05519-2;Q05519;Q5T757;Q5T760 Q05519-2;Q5T760 SRSF11 Serine/arginine-rich splicing factor 11 1 LNHVAAGLVS(0.999)PS(0.001)LK;LNHVAAGLVS(1)PSLK 165.17 2.58E-06 2147000000 5985600 4122200 4995200 4688900 5417600 4572400 6999900 4956500 7479700 TRUE FALSE 5610971.981 4427411.977 5113688.503 4809225.112 4992123.55 5892377.653 5950329.979 5575329.936 6231289.749 0.900451144 0.710512936 0.820646882 0.771786469 0.801138087 0.945611244 0.954911458 0.894731293 1 22.57109937 2.251879924 5.622604012 0.946892867 0.789124094 0.653044961 0.053239086 0.09049697 9.007674493 0.017617458 0.013972137 178.5993705 -2.251879924 -0.157768773 LNIHQKT(ph)HTGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LNIHQKTHTGEK 12 1 Q9GZX5 Q9GZX5 ZNF350 Zinc finger protein 350 1 LNIHQKT(0.994)HT(0.006)GEK;LNIHQKT(0.998)HT(0.002)GEK;LNIHQKT(0.939)HT(0.061)GEK;LNIHQKT(0.998)HT(0.002)GEK;LNIHQKT(0.997)HT(0.003)GEK 128.85 0.00035874 2726940000 7942839 2235621 3280238 2741821 3247789 2050950 3900958 2410060 4170852 TRUE FALSE 7445710.885 2401148.705 3358046.794 2812180.769 2992720.753 2643025.971 3316045.563 2710961.296 3474709.856 2.142829529 0.691035742 0.966425092 0.809328227 0.861286518 0.760646523 0.954337398 0.780197889 1 21.72846108 4.7428982 24.99996447 0.851427841 2.14283004 0.944566031 0.098205383 84.50640141 487041.0407 0.020847272 0.164408189 55322.04168 -4.7428982 1.291402198 LNKPFLFDTKPLIVQYEVNFQNGIECGGAYVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LNKPFLFDTKPLIVQYEVNFQNGIECGGAYVK 32 2 P27824;P27824-2;P27824-3;H0Y9Q7;D6RDP7;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ; 91.113 7.19E-05 167775000 256711 236553 158895 124889 286981 137756 265668 247555 144449 FALSE TRUE 240643.9168 254067.6303 162664.0644 128093.8632 264442.6699 177523.9209 225833.5497 278462.7867 120339.5287 1.999707987 2.11125665 1.351709336 1.064437135 2.197471377 1.47519209 1.876636481 2.313976045 1 16.87675109 LNKSELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LNKSELK 7 1 P26447 P26447 S100A4 Protein S100-A4 0 ; 101.64 0.0081244 2038200000 2136710 2847200 2019150 2468600 3725600 1604230 2693000 2135100 7535300 FALSE TRUE 2002977.135 3058009.651 2067045.192 2531948.455 3433006.404 2067345.159 2289209.651 2401671.935 6277609.75 0.319066845 0.48712962 0.329272649 0.403330018 0.546865215 0.329320433 0.364662625 0.382577451 1 22.58178392 -1.466632098 3.109541574 1.013217535 0.39699205 0.873391059 0.072355291 22719429.09 27421743.19 2598807.893 0.016105571 0.034148207 1.466632098 -0.616225486 LNLKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LNLKPR 6 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 74.597 0.072876 220340000 306280 805780 244600 228770 945650 162200 343660 848120 885130 FALSE TRUE 287110.4815 865440.7896 250402.0275 234640.6255 871382.4636 209024.5069 292131.3734 954009.6489 737396.0848 0.389357209 1.173644406 0.33957602 0.318201616 1.181702048 0.283463001 0.396166157 1.293754698 1 19.49208023 1.234693077 24.99434432 1.146877506 0.603291869 0.319920063 0.340716367 126.8699476 819851.0676 0.277093826 0.079456186 17.16694742 -1.234693077 -0.543585637 LNLTS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LNLTSPK 7 0 Q8IWZ3-6;Q8IWZ3;Q8IWZ3-4;H0Y785;H0Y472;H0Y4P6;H0Y7Y3;A0A0A0MQZ8 Q8IWZ3-6;A0A0A0MQZ8 ANKHD1 Ankyrin repeat and KH domain-containing protein 1 1 LNLT(0.02)S(0.98)PK;LNLT(0.076)S(0.924)PK;LNLT(0.032)S(0.968)PK;LNLT(0.003)S(0.997)PK 110.47 0.0071281 1987690000 12632800 7669800 9833900 8957700 10000900 7089700 12102000 7990600 10291400 TRUE FALSE 11842135.6 8237679.972 10067164.75 9187569.747 9215469.656 9136381.298 10287417.45 8988243.999 8573698.855 1.381216649 0.960808178 1.17419155 1.071599307 1.074853434 1.065628902 1.199880894 1.048350794 1 23.03148631 4.754781767 24.71154978 1.087492017 1.381216912 0.640100428 0.071704696 1817.331106 2768496.096 0.016396486 0.430487947 56856.71539 -4.754781767 0.293724894 LNNDDNVDGLLVQLPLPEHIDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LNNDDNVDGLLVQLPLPEHIDER 23 0 P13995-2;P13995 P13995-2 MTHFD2 "Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial;NAD-dependent methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase" 0 ;;;;; 261.74 8.69E-44 599813000 498616 432074 444234 408516 542551 474404 452411 460284 552478 FALSE TRUE 467408.5146 464065.2085 454771.4403 418999.2122 499941.233 611356.7335 384576.1705 517751.4706 460265.8527 1.015518557 1.008254699 0.988062524 0.910341729 1.086201008 1.328268717 0.835552254 1.124896552 1 18.81210789 2.707648573 24.68985846 1.067002192 0.986415767 0.123713325 0.123447157 1470.12254 1174204.791 0.038597653 0.03639412 510.0920716 -2.707648573 -0.080586425 LNNMNKYDYVLTGYTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LNNMNKYDYVLTGYTR 16 1 O00764;F2Z2Y4 O00764 PDXK Pyridoxal kinase 0 ; 208.2 1.41E-11 1066700000 731350 904930 803520 792410 970890 692240 1018320 817670 997720 FALSE TRUE 685576.109 971931.9588 822579.8738 812744.5821 894640.2158 892078.4504 865632.3696 919757.8994 831194.0865 0.824808694 1.169320108 0.98963634 0.977803615 1.076331305 1.073249275 1.0414323 1.1065501 1 19.66482586 2.710306864 24.50985037 1.061452424 1.02008752 0.092114645 0.087996808 1920.090816 1665655.618 0.026869837 0.0253394 513.2238898 -2.710306864 -0.041364904 LNPEDIKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LNPEDIKK 8 1 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ; 99.815 0.010496 1909600000 3840000 2767800 3038000 3112100 3581700 2181350 3944800 2662600 5387200 FALSE TRUE 3599661.255 2972730.792 3110062.795 3191961.755 3300407.73 2811070.334 3353313.862 2995031.471 4488041.517 0.80205614 0.662367044 0.692966583 0.711214846 0.735378164 0.626346776 0.747166409 0.667335955 1 22.09765459 -1.733883125 2.714677286 1.056553186 0.701514605 0.778686943 0.049280948 10682570.78 8301524.389 4063864.864 0.010331011 0.01845512 1.733883125 -0.355038581 LNPNFLVDFGKEPLGPALAHELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LNPNFLVDFGKEPLGPALAHELR 23 1 Q13228;Q13228-4;Q13228-2;Q13228-3 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 255.94 8.76E-44 3812500000 1440230 1638150 1431810 1454400 1984450 980830 1794410 1563660 2415200 FALSE TRUE 1350088.575 1759440.33 1465773.209 1491722.366 1828599.302 1263979.699 1525354.879 1758886.393 2012087.517 0.670988992 0.874435289 0.728483824 0.741380459 0.908807041 0.628193201 0.758095692 0.874159985 1 20.94026163 0.995252054 3.387253215 0.99895769 0.765154487 0.4776619 0.08321717 0.182307699 5.288617886 0.073450681 0.019088657 9.891269928 -0.995252054 -0.233803203 LNQPGT(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LNQPGTPTR 9 0 P36507;G5E9C7;M0R1B6 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 LNQPGT(0.722)PT(0.278)R;LNQPGT(0.926)PT(0.074)R;LNQPGT(0.905)PT(0.095)R;LNQPGT(0.994)PT(0.006)R;LNQPGT(0.868)PT(0.132)R 134.38 0.0027999 30758500000 18047100 19870800 20251800 20800900 21534300 15837700 18327300 15183900 20552800 TRUE FALSE 16917564.23 21342054.71 20732182.26 21334686.31 19843082.94 20409786.89 15579291.51 17079643.34 17122404.9 0.988036688 1.246440253 1.210821866 1.246009917 1.158895789 1.191993006 0.909877532 0.997502596 1 24.02938201 1.759473504 10.01831282 0.966835642 1.188646006 0.605629966 0.077166154 0.09604564 37.52396458 0.03370616 0.018452144 57.47427525 -1.759473504 0.221810365 LNQS(ph)PSLAPVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LNQSPSLAPVKR 12 1 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 LNQS(0.993)PS(0.007)LAPVKR;LNQS(0.688)PS(0.312)LAPVKR;LNQS(0.886)PS(0.114)LAPVKR;LNQS(0.577)PS(0.423)LAPVKR 145.46 3.61E-05 1951970000 2168400 1877450 2056780 1842140 2241040 1667180 2508090 2140640 3316520 TRUE FALSE 2032683.715 2016458.351 2105567.793 1889412.431 2065037.758 2148467.802 2132025.188 2407903.616 2762971.386 0.735687573 0.729815141 0.762066449 0.683833514 0.747397446 0.777593214 0.771642153 0.871490609 1 21.39778919 0.97113751 1.117081081 1.000970747 0.735075235 0.934870679 0.022757459 0.120393297 0.311195286 0.020365779 0.006494379 9.357018969 -0.97113751 -0.265895511 LNQSS(ph)PDNVTDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LNQSSPDNVTDTK 13 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 LNQSS(1)PDNVTDTK;LNQS(0.065)S(0.935)PDNVTDTK;LNQS(0.01)S(0.99)PDNVTDTK;LNQS(0.003)S(0.997)PDNVTDTK 328.02 2.52E-62 843770000 3186690 2112460 2684310 2403290 2664640 2043860 3034670 2175160 2956560 TRUE FALSE 2987240.761 2268868.736 2747983.101 2464962.49 2455369.923 2633889.203 2579649.406 2446733.514 2463091.036 1.212801605 0.921146926 1.115664448 1.000759799 0.996865275 1.069343018 1.04732199 0.993358946 1 21.23203852 4.760357673 24.71044632 1.024782737 1.212801833 0.576969677 0.052123392 3843.106594 4356692.529 0.011743137 0.592312002 57591.40484 -4.760357673 0.188019096 LNRS(ph)NSELEDEILCLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LNRSNSELEDEILCLEK 17 1 Q96PC5;Q96PC5-11;Q96PC5-10;Q96PC5-9;Q96PC5-13;Q96PC5-6;G3V599;Q96PC5-14;Q96PC5-7;Q96PC5-12;Q96PC5-8;Q96PC5-5;Q86UF2;A4D2H0;A0A5F9ZHA4;G3V5K6;A0A2R8YE69;Q8IX94;P0CG41 Q96PC5 MIA2;CTAGE6;CTAGE15;CTAGE5;CTAGE4;CTAGE8 Melanoma inhibitory activity protein 2;cTAGE family member 6;cTAGE family member 15;cTAGE family member 4;cTAGE family member 8 1 LNRS(0.5)NS(0.5)ELEDEILCLEK 92.773 0.0028595 0 29039 31427 25074 27954 46501 22730 35048 28916 70152 TRUE FALSE 27221.50083 33753.88778 25668.76712 28671.34697 42848.99904 29291.78201 29792.87777 32526.22625 58443.178 0.465777217 0.577550519 0.439208955 0.490585008 0.733173665 0.501201047 0.509775115 0.556544448 1 15.83474701 -4.999999999 0.38643581 7.910410981 0.520332569 0.768752065 0.080483205 295.976332 2.166619275 1717.921972 0.050730632 1.00E-05 4.999999999 -7.390078412 LNS(ph)KWNILCEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LNSKWNILCEK 11 1 Q9Y234 Q9Y234 LIPT1 "Lipoyltransferase 1, mitochondrial" 1 LNS(1)KWNILCEK 82.287 0.050907 153680000 399340 332970 348730 333630 340260 262130 436710 281000 351080 TRUE FALSE 374346.0222 357623.4453 357002.0403 342191.5106 313537.3521 337802.6757 371229.3897 316083.4686 292482.4799 1.279892123 1.222717495 1.220592906 1.169955584 1.071986781 1.154950121 1.269236331 1.080691974 1 18.15799068 -5 0.093715545 0.399747253 1.337414048 0.568358594 0.059401479 170.0395546 1.099672027 20.38198174 1.289847653 1.00E-05 5 0.937666795 LNS(ph)SENGEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LNSSENGEDR 10 0 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 LNS(0.551)S(0.449)ENGEDR;LNS(0.5)S(0.5)ENGEDR 166.62 5.76E-06 964920000 553080 490860 540930 536280 588960 435300 579170 443970 542670 TRUE FALSE 518463.7101 527203.7851 553761.115 550041.8527 542705.4574 560964.0435 492328.8353 499400.6318 452094.8712 1.146802902 1.166135293 1.224878118 1.216651388 1.200423831 1.240810456 1.088994516 1.1046368 1 18.78626603 1.285366375 1.384782589 1.012695372 1.198519776 0.756808694 0.036467642 0.180590929 0.659261331 0.032614251 0.010219149 19.29151678 -1.285366375 0.185824404 LNS(ph)VQSSERPLFLVHPIEGSTTVFHSLASR ddPTM_SK-BR-3_Pertuzumab_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 LNS(0.998)VQS(0.001)S(0.001)ERPLFLVHPIEGSTTVFHSLASR 232.25 3.37E-36 1997400000 955480 864080 875090 910010 1113200 665470 1206600 792160 1413700 TRUE FALSE 895678.2124 928057.3823 895847.548 933362.3972 1025773.762 857580.386 1025681.532 891062.9198 1177744.337 0.760503094 0.787995623 0.760646874 0.792500009 0.870964716 0.728154964 0.870886405 0.756584338 1 20.16759496 -5 0.234653134 2.146281669 0.77054813 0.657575684 0.047213962 91.53672773 0.915225604 49.9205134 0.068395224 1.00E-05 5 -1.375733539 LNSAIIYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LNSAIIYDR 9 0 P23921 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 85.29 0.034699 58082000 167360 173920 174780 178620 175910 136120 170170 158620 158090 FALSE TRUE 156885.2363 186797.2178 178925.8641 183203.6916 162094.7382 175415.6343 144654.5883 178424.0562 131703.7577 1.191197875 1.418313502 1.358547905 1.391028584 1.230752569 1.33189544 1.098333038 1.354737779 1 17.00693698 0.735406759 0.394697025 0.979932611 1.364838869 0.457752925 0.099789593 1.382811299 0.503020211 0.174989463 0.07383685 5.437593771 -0.735406759 0.384906258 LNSGDYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LNSGDYK 7 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 127.02 0.0090623 456400000 1288780 1177050 1204240 1250200 1346940 937570 1512570 1185810 1493330 FALSE TRUE 1208117.56 1264200.007 1232805.141 1282282.249 1241156.766 1208231.239 1285774.171 1333860.989 1244083.576 0.971090354 1.016169678 0.990934344 1.030704266 0.997647417 0.97118173 1.033511088 1.07216349 1 20.24665198 1.588067981 7.139332129 1.04126719 0.999347628 0.342892367 0.024935123 0.120645729 12.99450271 0.012050679 0.005716017 38.73182679 -1.588067981 -0.041919562 LNSHMNALHLGSQANR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LNSHMNALHLGSQANR 16 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;; 294.94 6.98E-46 11269180000 2285063 3522290 3363220 3102459 3738410 3072602 3695749 3538603 3987440 FALSE TRUE 2142044.986 3783084.017 3442997.167 3182073.35 3444810.359 3959612.318 3141605.747 3980405.374 3321910.504 0.644823207 1.138827796 1.03645091 0.957904599 1.036996739 1.191968391 0.945722572 1.198227757 1 21.66358178 4.745208501 24.9697352 1.060366619 0.644823016 0.686979682 0.088747365 415.937938 1562239.54 0.019184475 0.186334569 55617.12061 -4.745208501 -0.415543602 LNSNDEDIHTANER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LNSNDEDIHTANER 14 0 A0A5F9ZHC6;A0A5F9ZHM8;P04424-3;P04424-2;P04424;F8W943 A0A5F9ZHC6 ASL Argininosuccinate lyase 0 ; 170.49 3.17E-06 553200000 279120 369220 325320 373310 333470 299300 387090 293970 320470 FALSE TRUE 261650.3774 396557.433 333036.744 382889.7666 307280.6114 385703.0513 329049.4481 330672.8016 266981.4867 0.980031914 1.485336822 1.247415123 1.434143511 1.150943517 1.444680888 1.232480395 1.238560792 1 18.02638018 0.710175917 1.373725684 1.000631936 1.307474753 0.245239473 0.15122166 1.173086656 3.589232427 0.124642472 0.036960058 5.130691672 -0.710175917 0.306842817 LNSVQS(ph)SERPLFLVHPIEGSTTVFHSLASR ddPTM_SK-BR-3_Pertuzumab_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 LNS(0.308)VQS(0.346)S(0.346)ERPLFLVHPIEGSTTVFHSLASR 54.05 0.032044 19390000 11048 9601.2 7542.9 8701 9038.5 6311.9 11338 5680.2 10029 TRUE FALSE 10356.5254 10312.08284 7721.82115 8924.282391 8328.65267 8134.043065 9637.972157 6389.385474 8355.09511 1.239546081 1.234226864 0.924205057 1.068124572 0.996835172 0.973542845 1.153544278 0.764729233 1 13.02844054 4.117309957 3.328602337 1.001762257 1.240518466 0.517763925 0.1004423 0.189977284 3.982734974 0.023622833 0.059309472 13101.16623 -4.117309957 0.238756209 LNSVQSSERPLFLVHPIEGSTTVFHSLASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LNSVQSSERPLFLVHPIEGSTTVFHSLASR 30 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 255.02 2.52E-58 13845500000 3888660 6345310 5029340 5199020 6662500 4904760 6929500 5662100 5113570 FALSE TRUE 3645275.712 6815123.355 5148638.32 5332435.655 6139254.125 6320684.59 5890485.805 6369025.649 4260082.132 0.855682027 1.599763372 1.208577243 1.251721326 1.441111682 1.483700171 1.382716488 1.495047619 1 22.02244981 2.742521882 23.93620407 1.393892741 1.287347431 0.039582183 0.227844105 638.4688027 3857989.616 0.064589381 0.066096611 552.741257 -2.742521882 -0.106545309 LNT(ph)SDFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LNTSDFQK 8 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 LNT(0.877)S(0.123)DFQK;LNT(0.984)S(0.016)DFQK;LNT(0.992)S(0.008)DFQK;LNT(0.977)S(0.023)DFQK;LNT(0.898)S(0.102)DFQK;LNT(0.845)S(0.155)DFQK;LNT(0.793)S(0.207)DFQK 193.3 0.0019156 6120059000 9773600 6650510 6741740 8395520 10862330 6048670 14797110 7557430 10453600 TRUE FALSE 9161887.822 7142920.68 6901657.256 8610963.257 10009246.42 7794822.837 12578420.73 8500991.771 8708826.627 1.052023219 0.820193235 0.792489913 0.988762738 1.149322044 0.895048572 1.444330134 0.976135148 1 23.05404692 2.956145207 3.276390088 1.130312386 0.860421748 0.22327123 0.163032468 0.259809533 5.628624427 0.049215215 0.055248755 903.9516611 -2.956145207 -0.269890638 LNTQEIFDDWAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LNTQEIFDDWAR 12 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;;; 271.21 2.42E-27 828662000 1117366 1321180 1271647 1260977 1350545 1022913 1539441 1221628 1414402 FALSE TRUE 1047432.057 1419001.542 1301811.067 1293335.805 1244478.644 1318211.377 1308616.114 1374150.945 1178329.169 0.888912949 1.204248846 1.104794061 1.09760145 1.056138366 1.118712336 1.110569226 1.16618597 1 20.16831118 LNTVAS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LNTVASPK 8 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 LNTVAS(1)PK;LNT(0.004)VAS(0.996)PK 133.85 0.0009457 109770000 1050410 654280 717180 665950 832350 543470 963910 813330 999800 TRUE FALSE 984666.7131 702723.572 734191.8483 683039.4045 766980.5885 700360.9665 819380.644 914876.0409 832926.921 1.182176597 0.843679745 0.881460101 0.820047218 0.920825788 0.840843235 0.983736536 1.098386927 1 19.6678304 1.517630236 4.796694533 1.048117895 0.899659745 0.212706778 0.104639373 0.203065743 10.25358619 0.057875455 0.024724113 32.93291974 -1.517630236 -0.14845815 LNVDFALIHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LNVDFALIHK 10 0 B1ALA9;P60891;A0A2R8Y7H4;P60891-2 B1ALA9 PRPS1 Ribose-phosphate pyrophosphokinase 1 0 ; 100.72 0.0038198 341050000 557950 672950 567460 555350 763660 457060 640710 646070 738650 FALSE TRUE 523028.9055 722775.9182 580920.4192 569601.2212 703685.2241 589005.8023 544641.4836 726733.2617 615364.5431 0.849949695 1.174549178 0.944026473 0.925632176 1.143525788 0.957165649 0.88507128 1.180980071 1 19.23108179 LNVEAVNTHR ddPTM_SK-BR-3_Pertuzumab_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 74.962 0.040422 89467000 27722 36397 33595 34340 37802 37067 35106 32379 34130 FALSE TRUE 25986.92951 39091.87175 34391.88926 35221.22254 34833.18341 47767.64117 29842.18121 36421.58942 28433.48251 0.913955211 1.374853458 1.209555996 1.238723485 1.225076225 1.679978566 1.049543657 1.280940153 1 14.79530319 0.521321987 1.335021379 1.001028672 1.263717886 0.12373152 0.200009429 3.868821044 8.713309207 0.171228923 0.050752071 3.321406162 -0.521321987 0.262689214 LNWLSVDFNNWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LNWLSVDFNNWK 12 0 A0A087WYT3;Q15185-4;Q15185;B4DDC6 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ; 261.52 5.32E-21 675180000 1213790 1337030 1031690 811120 1413490 784750 1199270 1296320 607860 FALSE TRUE 1137821.051 1436025.092 1056162.174 831934.7124 1302480.197 1011294.586 1019450.597 1458168.406 506404.2391 2.246863203 2.835728814 2.085610847 1.642827307 2.572016774 1.997010506 2.013116239 2.87945537 1 18.94992996 -1.908498908 2.684950437 0.277035736 2.272918239 0.520274594 0.387370433 2714022.076 2675479.455 12443263.21 0.091368387 0.012345284 1.908498908 1.995882503 LPADVSPINYSLCLKPDLLDFTFEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPADVSPINYSLCLKPDLLDFTFEGK 26 1 E9PLK3;P55786;P55786-2;E9PP11;E9PJY4;E9PPD4;E9PJF9;E9PPZ2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 55.588 0.084141 27454000 30492 26401 31959 24198 34541 22027 37307 31261 30776 FALSE TRUE 28583.56015 28355.75751 32717.08257 24818.96165 31828.28919 28385.83732 31713.16169 35164.00466 25639.28678 1.114834449 1.105949544 1.276052757 0.96800515 1.241387464 1.107122736 1.236897187 1.37148919 1 14.64606851 1.681582736 7.676050553 1.227698393 1.14612533 0.045730999 0.122234369 0.299832208 32.99201534 0.05409818 0.028215637 48.03775871 -1.681582736 -0.081573063 LPAELQELPGLSHQYWSAPSDKEGYSGVGLLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPAELQELPGLSHQYWSAPSDKEGYSGVGLLSR 33 1 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;H7C4A8;G3V5M0;G3V359 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 172.64 8.38E-15 231520000 484450 330140 432650 431700 485020 343000 578170 453120 477460 FALSE TRUE 454129.1393 354583.9091 442912.6623 442778.1529 446928.4857 442018.5319 491478.776 509693.0294 397768.8415 1.141691083 0.891432089 1.113492602 1.113154442 1.123588474 1.111244738 1.235588927 1.281379978 1 18.60157074 3.250032495 1.073650771 1.174966856 1.000461264 0.194946539 0.097455297 0.555718281 1.367357571 0.037122124 0.060393308 1778.412472 -3.250032495 -0.174505592 LPALGEAHVS(ph)PEVATADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPALGEAHVSPEVATADK 18 0 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 LPALGEAHVS(1)PEVATADK;LPALGEAHVS(1)PEVATADK 171.06 9.15E-12 203505000 367760 212855 274120 245740 214760 204650 292240 231910 154481 TRUE FALSE 344742.5581 228615.0057 280622.2558 252046.1044 197893.6159 263729.1328 248421.325 260864.474 128697.1231 2.678712233 1.776380079 2.18048585 1.958443968 1.537669305 2.049223218 1.930278774 2.026964299 1 16.97362028 -1.988602205 0.271942688 4.91E-19 2.107081078 0.570680706 0.283442077 23.59026463 0.971931463 15.87871065 0.340615988 0.010265918 1.988602205 2.107081078 LPASPETHLDMLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPASPETHLDMLR 13 0 P04626-5;P04626-4;P04626;J3QLU9;P04626-6;F5H1T4;J3QL83;J3KRI9;J3QLV2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 0 136.3 7.40E-05 92473000 104850 125010 111210 91307 131530 105030 111750 109400 114980 FALSE TRUE 98287.62566 134265.8705 113847.9537 93650.0922 121200.1644 135350.456 94994.12494 123058.8308 95789.0952 1.026083663 1.401682208 1.18852729 0.977669661 1.265281441 1.413004849 0.991700827 1.284685178 1 16.54757381 -4.910733603 0.22152878 1.18E-09 1.228116856 0.106813228 0.158662263 301.5344053 3.130551956 134.3296371 0.284420553 1.23E-05 4.910733603 1.228116855 LPAYLATS(ph)PIPTEDQFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPAYLATSPIPTEDQFFK 18 0 Q92539;J3KTK1 Q92539 LPIN2 Phosphatidate phosphatase LPIN2 1 LPAYLATS(1)PIPTEDQFFK 197.47 1.85E-18 0 151290 122720 132070 124090 107400 94089 141510 108750 85473 TRUE FALSE 141821.029 131806.3165 135202.7628 127274.3595 98965.23723 121250.9669 120291.8892 122327.6769 71207.00412 1.991672458 1.85103022 1.898728425 1.787385399 1.389824477 1.70279551 1.689326643 1.717916354 1 16.11973154 -2.164284794 0.161008483 4.89E-17 2.043142492 0.775695689 0.135205067 21.06653466 0.465811703 8.766160064 0.672414076 0.006850389 2.164284794 2.043142492 LPDAYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LPDAYER 7 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;; 182.95 0.0015117 8776540000 4957020 5705690 5625550 5401860 5759670 4747560 6165100 5440680 6039710 FALSE TRUE 4646768.967 6128145.224 5758990.703 5540480.873 5307328.752 6118103.502 5240700.489 6119960.874 5031643.383 0.923509202 1.217921215 1.144554624 1.101127495 1.054790323 1.215925501 1.041548474 1.216294639 1 22.26259824 -1.323939011 4.415067437 0.999872919 1.122725533 0.124092749 0.093296819 0.000103265 1.58E-05 0.079931702 0.018820626 0.047430859 1.323939011 0.122852614 LPDLS(ph)PVENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LPDLSPVENK 10 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;H7C5N8;A0A2R8YET2;A0A2R8Y7F4 E7EPN9 PRRC2C Protein PRRC2C 1 LPDLS(1)PVENK;LPDLS(1)PVENK;LPDLS(1)PVENK;LPDLS(1)PVENK;LPDLS(1)PVENK 232.39 2.47E-10 2281330000 6495290 3920680 5220610 4553400 4407050 3239580 4851790 3799590 3871860 TRUE FALSE 6088761.393 4210971.227 5344445.335 4670247.953 4060938.07 4174794.156 4124309.131 4273977.175 3225621.553 1.887624228 1.305475908 1.656873023 1.447859855 1.258962964 1.294260374 1.278609119 1.325008872 1 21.62114575 7.999999994 0.084252148 0.69116961 3.344224488 0.630943043 0.146595542 115.832514 0.706798107 3.156413986 35.63815388 99999998.58 -7.999999994 2.653054877 LPDNVTFEEGALIEPLSVGIHACR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPDNVTFEEGALIEPLSVGIHACR 24 0 Q00796;A0A6I8PIS1 Q00796 SORD Sorbitol dehydrogenase 0 ; 181.38 3.32E-17 108709000 74000 95641 89322 85648 106743 83434 99887 86418 90881 FALSE TRUE 69368.47209 102722.3592 91440.76002 87845.87268 98359.83536 107520.0414 84909.87166 97207.47753 75712.37399 0.916210501 1.356744661 1.207738646 1.160257803 1.299124967 1.420111875 1.121479452 1.283904762 1 16.20824148 -1.264736323 3.063378306 0.998726468 1.232872698 0.193077887 0.139835005 13368293.24 17705918.68 161789.8247 0.029850734 0.054358026 1.264736323 0.234146231 LPDS(ph)DDDEDEETAIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 394.62 1.23E-121 17434299000 385889 396158 343422 370122 396631 319057.2 418680 341803 352724 TRUE FALSE 361736.8963 425489.9505 351568.132 379619.9571 365481.2012 411163.8342 355902.8208 384477.857 293852.0857 1.231016943 1.447973219 1.196411899 1.291874299 1.243759085 1.399220404 1.21116316 1.308406085 1 18.16473061 -3.682337484 0.302483349 9.29E-15 1.312076535 0.559914376 0.080703645 79.99854742 1.552914101 50.04528666 0.074048917 0.000207808 3.682337484 1.312076535 LPDS(ph)PALAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LPDSPALAK 9 0 G0XQ39;Q13586;H0YDB2;E9PNJ4 G0XQ39 STIM1 Stromal interaction molecule 1 1 LPDS(1)PALAK;LPDS(1)PALAK;LPDS(1)PALAK 132.25 0.00032553 581900000 1496880 984490 1056680 984900 1151500 1039760 1624430 1256930 1231940 TRUE FALSE 1403192.953 1057382.664 1081744.949 1010174.201 1061065.835 1339921.833 1380861.802 1413860.477 1026321.255 1.367206365 1.030264801 1.054002285 0.984267057 1.033853513 1.30555791 1.345447924 1.377600308 1 19.96905096 2.234007078 24.98170708 1.293015554 1.074811373 0.212404998 0.146707285 121.0729372 664225.1658 0.049272562 0.037617061 171.398524 -2.234007078 -0.218204181 LPDSSNKIEEDRCS(ph)NSADITGPSFIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPDSSNKIEEDRCSNSADITGPSFIR 26 2 Q52LW3;F8VWZ8 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 LPDSSNKIEEDRCS(0.983)NS(0.017)ADITGPSFIR;LPDSSNKIEEDRCS(0.992)NS(0.008)ADITGPSFIR 121.9 7.30E-05 203947000 109072 158612 118093 132591 215570 77897 165777 137872 320970 TRUE FALSE 102245.3782 170355.7975 120894.2217 135993.5095 198640.0018 100384.5993 140920.2778 155085.6227 267398.0335 0.382371467 0.63708695 0.452113354 0.508580814 0.742862613 0.375412631 0.527005663 0.579980416 1 18.02862933 0.718672658 3.032014204 0.99997132 0.524075003 0.652262497 0.109678026 1.3839138 14.21837206 0.094668498 0.024733097 5.232059307 -0.718672658 -0.475896317 LPEADDIQYPSMLLLTADHDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LPEADDIQYPSMLLLTADHDDR 22 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ;;;;;;; 312.56 3.06E-67 2182267000 976145 1193540 1164253 1246393 1225353 1037210 1345537 1118842 1091485 FALSE TRUE 915049.8269 1281910.943 1191869.631 1278377.555 1129118.718 1336635.689 1143786.218 1258531.887 909309.1022 1.006313282 1.409763677 1.310742 1.405877882 1.241732559 1.469946453 1.257862937 1.384052885 1 19.79441127 -0.562201438 8.179174573 1.000000885 1.322710542 0.359483075 0.129507387 0 0 0.107628693 0.025368326 0.274030285 0.562201438 0.322709657 LPEAS(ph)QSPLVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPEASQSPLVLK 12 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 LPEAS(0.712)QS(0.288)PLVLK 113.76 0.0011867 72571000 136070 147750 145040 139400 149390 137000 143600 129460 152910 TRUE FALSE 127553.6216 158689.5637 148480.4173 142977.24 137657.512 176549.676 122068.5131 145623.366 127388.3332 1.001297516 1.245715049 1.165573123 1.122373113 1.080613182 1.385917153 0.958239346 1.143145234 1 16.95887363 1.63151682 25 1.038027973 1.1709295 0.242892356 0.110552124 1.073741623 1131.643656 0.045914957 0.025442565 42.80719984 -1.63151682 0.132901526 LPEASQS(ph)PLVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPEASQSPLVLK 12 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 LPEASQS(1)PLVLK;LPEAS(0.031)QS(0.969)PLVLK 198.48 1.92E-07 149358000 386480 337230 393890 377920 380820 286330 454960 350910 492570 TRUE FALSE 362290.9067 362198.8601 403233.2568 387618.067 350911.9334 368988.8228 386742.9716 394721.8859 410356.8849 0.882867865 0.882643556 0.982640408 0.944587702 0.855138408 0.899190038 0.94245518 0.961899021 1 18.64651963 1.177233737 1.810393892 0.997207619 0.913615787 0.423053008 0.035838453 0.363779861 2.192740281 0.035335544 0.010296164 15.03951173 -1.177233737 -0.083591832 LPEDPLLSGLLDSPALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPEDPLLSGLLDSPALK 17 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 206.53 1.60E-11 133524000 293760 254050 291510 273050 318910 239903 397740 288880 303940 FALSE TRUE 275374.086 272860.1263 298424.7549 280056.9253 293864.095 309159.1016 338102.5794 324947.3039 253210.4505 1.087530493 1.077602152 1.178564132 1.106024355 1.160552791 1.220957117 1.335263133 1.283309213 1 17.94997742 2.310911848 2.915100796 1.249955922 1.11867018 0.141874664 0.092905852 0.305624588 5.299479512 0.033344187 0.025666239 204.6029296 -2.310911848 -0.131285742 LPEEWSQWLGGSSWPGYVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPEEWSQWLGGSSWPGYVR 19 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ; 405.59 3.44E-147 203420000 43598 39581 46885 52697 39350 40688 42484 39039 69417 FALSE TRUE 40869.279 42511.61842 47997.13434 54049.29424 36259.60973 52433.96509 36113.9186 43913.10509 57830.85425 0.706703706 0.735102723 0.829957208 0.934609992 0.626994192 0.906678031 0.624474929 0.75933696 1 15.81955179 -1.750405689 2.639595185 1.051488105 0.765265598 0.337007785 0.103373886 18733215.33 14295933.35 6285063.461 0.022819511 0.01776619 1.750405689 -0.286222506 LPEHCIEYVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPEHCIEYVR 10 0 Q8TBC4;F8W8D4;Q8TBC4-2 Q8TBC4 UBA3 NEDD8-activating enzyme E1 catalytic subunit 0 ; 82.171 0.018813 451930000 285500 334710 352800 372150 378570 322270 380180 354560 401820 FALSE TRUE 267631.0646 359492.2767 361168.5826 381699.999 348838.6393 415304.1174 323175.5384 398827.5965 334753.6461 0.799486631 1.073901004 1.078908585 1.140241498 1.042075697 1.240626121 0.96541305 1.191406281 1 18.35274024 4.741505434 4.449805559 1.090614466 0.778793272 0.552998471 0.08267228 0.13979971 6.912842347 0.01708681 0.137727329 55144.91026 -4.741505434 -0.311821194 LPEHEINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPEHEINR 8 0 O43815-2;O43815 O43815-2 STRN Striatin 0 68.735 0.055739 232300000 134620 230740 175840 193380 229530 172680 170880 189650 223760 FALSE TRUE 126194.3745 247824.2297 180011.0078 198342.4582 211503.6397 222529.9128 145258.1304 213328.22 186413.0105 0.676961196 1.329436336 0.965656889 1.063994716 1.134596985 1.193746682 0.779227426 1.144384823 1 17.50814303 1.75747598 25 0.953663155 1.08373301 0.031053646 0.189679515 18.8162734 24893.20111 0.079140283 0.043887762 57.21053117 -1.75747598 0.130069855 LPESENLQEFWDNLIGGVDMVTDDDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 233.45 9.51E-45 619410000 103910 161090 133350 123070 168600 112990 165660 141740 124320 FALSE TRUE 97406.45858 173017.2712 136513.125 126228.1846 155358.8361 145608.3788 140820.8209 159436.551 103570.1889 0.940487409 1.67053158 1.318073535 1.218769474 1.500034303 1.40589083 1.35966558 1.539405815 1 16.66024928 -1.377992894 3.328832055 0.996690874 1.390310969 0.250830921 0.197472899 40668727.51 60532072.12 1320014.057 0.042317679 0.041880042 1.377992894 0.393620096 LPETNLFETEETRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LPETNLFETEETRK 14 1 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 ;;; 156 9.12E-06 698840000 837970 580120 662930 685280 671640 558720 871140 594190 931840 FALSE TRUE 785522.9535 623072.6884 678655.0127 702865.445 618892.1037 720013.3939 740520.6443 668375.9295 776309.8841 1.011867773 0.802608213 0.874206327 0.905392884 0.797223012 0.927481936 0.953898256 0.860965374 1 19.56627313 2.035805163 24.99098941 0.935046687 0.868101465 0.141634934 0.067882372 268.7738659 187595.4275 0.023098897 0.017059627 108.5938331 -2.035805163 -0.066945222 LPFPIIDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LPFPIIDDR 9 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;;;;; 182.39 0.00010791 1908602000 1150206 1336286 1186231 1165798 1286840 1017472 1241702 1176392 1150606 FALSE TRUE 1078216.66 1435226.006 1214368.959 1195714.35 1185776.777 1311199.649 1055520.312 1323267.131 958562.4254 1.124826752 1.49726921 1.266864763 1.247403736 1.237036573 1.367881334 1.101149267 1.380470479 1 19.87051286 -4.714719701 0.166416132 3.63E-10 1.360516225 0.307025347 0.12182864 124.1788677 1.267211653 41.12530591 0.430926465 1.93E-05 4.714719701 1.360516224 LPGGELNPGEDEVEGLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPGGELNPGEDEVEGLKR 18 1 O43809;H3BND3;H3BV41 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 155.49 2.96E-08 272950000 219030 164780 192210 180850 212900 147530 207510 177300 214570 FALSE TRUE 205321.3033 176980.4827 196769.312 185490.9172 196179.6928 190119.5161 176395.8019 199436.2953 178756.8808 1.148606433 0.990062491 1.100764967 1.037671481 1.097466525 1.063564743 0.986791675 1.115684579 1 17.44763925 0.574042422 0.006964679 7.11E-08 2.075527301 0.113224953 0.052879411 10870.79971 34.49541917 5219.48388 5057.712246 3.750096316 -0.574042422 2.075527229 LPHLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPHLLK 6 0 Q5XPI4;Q5XPI4-2;C9JI97 Q5XPI4 RNF123 E3 ubiquitin-protein ligase RNF123 0 84.566 0.055705 162050000 488390 476490 558080 547390 592050 460830 660370 508730 521690 FALSE TRUE 457822.5417 511769.8154 571317.9211 561436.9541 545552.7812 593864.1401 561353.6491 572246.0604 434616.5688 1.053394129 1.177520261 1.314533228 1.291798322 1.255250767 1.366409343 1.291606647 1.316668764 1 18.72938365 4.592578945 1.597230987 1.282092627 1.007252435 0.297325514 0.100108337 0.765918651 2.336897487 0.022963076 0.300400947 39136.22617 -4.592578945 -0.274840191 LPHSSS(ph)SENIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPHSSSSENIK 11 0 F5H527;Q76I76;A0A3B3IS79;K7EKN7 F5H527 SSH2 Protein phosphatase Slingshot homolog 2 1 LPHSSS(1)SENIK 228.62 2.02E-12 386880000 187110 326870 306180 305790 304500 238470 363950 289060 300370 TRUE FALSE 175399.1191 351071.7949 313442.7342 313637.0891 280585.7983 307312.4178 309379.0762 325149.7773 250236.3065 0.700933935 1.402961064 1.252586959 1.253363644 1.121283327 1.228088849 1.236347677 1.29937091 1 17.9329316 -0.774709316 8.37879304 1.00000002 1.215530628 0.071182954 0.188339893 0 0 0.162041846 0.038193629 0.167992806 0.774709316 0.215530608 LPIGDVATQYFADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPIGDVATQYFADR 14 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 206.36 2.55E-08 807580000 263850 277350 272630 266120 283880 230793 283330 272420 220956 FALSE TRUE 247336.0995 297885.2826 279096.9123 272949.0897 261585.2099 297419.1925 240847.2968 306432.2367 184077.0162 1.343655523 1.618264402 1.516196417 1.482798317 1.42106394 1.615732364 1.308405046 1.664695805 1 17.48994998 -1.751978463 2.820074966 0.900625331 1.497619204 0.641541803 0.116596584 22042897.33 18328539.46 15266292.1 0.025413957 0.017701967 1.751978463 0.596993873 LPIGDVATQYFADRDMFCAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPIGDVATQYFADRDMFCAGR 21 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 190.83 1.51E-17 1108460000 233760 370700 278210 295650 408250 263090 346940 278660 543260 FALSE TRUE 219129.3789 398147.0137 284809.2726 303236.8795 376187.6918 339039.8121 294919.5678 313451.3144 452586.3964 0.484171377 0.879714938 0.629292605 0.670008825 0.831195314 0.749116224 0.651631534 0.692577852 1 18.7878337 -1.1112252 4.275844679 1.000044606 0.709558499 0.4255683 0.109424536 4.33E-05 8.99E-06 0.095516553 0.022509907 0.077406031 1.1112252 -0.290486107 LPIVNEDDELVAIIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPIVNEDDELVAIIAR 16 0 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 148.52 2.15E-06 8514000 6139.8 4352 5284.5 6364.8 6730.9 4878.7 6113 4951 7838.6 FALSE TRUE 5755.520878 4674.226608 5409.850836 6528.131544 6202.282265 6287.101491 5196.4124 5569.143248 6530.287021 0.881358026 0.715776595 0.828424665 0.999669926 0.94977177 0.962760361 0.795740277 0.85281753 1 12.67293069 3.449557617 10.37810137 0.912298057 0.785286571 0.348202756 0.074878953 0.436966475 160.419607 0.02101374 0.028634882 2815.513521 -3.449557617 -0.127011486 LPLDINPVVHPHGHIFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPLDINPVVHPHGHIFK 17 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 104.41 0.00029599 368770000 796350 898630 845410 837460 1022840 668000 1006670 950780 1000790 FALSE TRUE 746507.875 965165.5002 865463.5244 858950.6414 942510.2723 860840.7559 855729.179 1069486.976 833751.6836 0.895359961 1.157617453 1.038035115 1.030223576 1.13044482 1.032490576 1.026359761 1.282740409 1 19.66925824 LPLLPPES(ph)PGPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LPLLPPESPGPLR 13 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;A0A669KAX5 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 LPLLPPES(1)PGPLR;LPLLPPES(1)PGPLR;LPLLPPES(1)PGPLR;LPLLPPES(1)PGPLR;LPLLPPES(1)PGPLR;LPLLPPES(1)PGPLR 173.19 2.32E-05 690045000 571611 681640 630360 650352 836601 536039 534440 570712 601594 TRUE FALSE 535834.8879 732109.3348 645312.4369 667041.1334 770897.7321 690784.7574 454305.6835 641966.6495 501184.075 1.069137897 1.460759373 1.287575701 1.330930424 1.538152888 1.378305481 0.906464723 1.280899936 1 18.93498105 1.755518201 25 1.061089258 1.358026148 0.430356362 0.15221413 5.303155776 7826.954401 0.063577914 0.035257509 56.95320919 -1.755518201 0.29693689 LPLPS(ph)PALEYTLGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPLPSPALEYTLGSR 15 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 LPLPS(1)PALEYTLGSR;LPLPS(0.957)PALEY(0.004)T(0.016)LGS(0.023)R 91.845 0.0057392 305969000 222288 254873 252022 244235 282083 197397 271049 215973 247488 TRUE FALSE 208375.3909 273744.0621 258000.0809 250502.4836 259929.339 254382.3094 230407.7187 242937.7045 206180.654 1.010644728 1.327690338 1.251330209 1.214965996 1.260687334 1.2337836 1.117504064 1.178275943 1 17.65354944 0.92568133 0.772788554 1.003451246 1.236719544 0.338492579 0.086774797 0.726799445 0.950900809 0.077595461 0.028690519 8.42716175 -0.92568133 0.233268298 LPLQLDDAVRPEAEGEEEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LPLQLDDAVRPEAEGEEEGR 20 1 P14868;P14868-2;C9J7S3;C9JLC1 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ;;;;;; 242.71 7.68E-30 5049940000 1214790 1482310 1361740 1446650 1407470 1222651 1456370 1210310 1263330 FALSE TRUE 1138758.462 1592061.775 1394041.116 1483773.488 1296932.984 1575610.496 1238000.839 1361419.868 1052472.062 1.081984505 1.512687921 1.324539783 1.409798457 1.232273075 1.497056837 1.176279052 1.2935449 1 20.00535051 0.657783877 0.754251117 0.99883228 1.358584938 0.351759424 0.134433213 1.132731598 1.184234099 0.120385292 0.042216951 4.54761695 -0.657783877 0.359752658 LPLS(ph)PPLVEDSAFEPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPLSPPLVEDSAFEPSR 17 0 O96007 O96007 MOCS2 Molybdopterin synthase catalytic subunit 1 LPLS(1)PPLVEDSAFEPSR;LPLS(0.999)PPLVEDS(0.001)AFEPSR 172.91 1.62E-09 71887000 25611 22567 28377 27929 22408 24347 26094 19348.5 20997.5 TRUE FALSE 24008.05323 24237.88416 29050.11584 28645.70542 20648.16607 31375.58366 22181.44694 21764.20282 17492.8816 1.37244702 1.385585561 1.660682128 1.637563557 1.18037534 1.793620078 1.268027044 1.24417482 1 14.09448034 1.187390504 1.719453217 1.019803995 1.500913168 0.451296354 0.179733339 0.283371048 1.548163747 0.152686131 0.044943322 15.39538323 -1.187390504 0.481109173 LPLVPES(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LPLVPESPR 9 0 C9J0I9;Q86WB0;Q86WB0-2;Q86WB0-3 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 LPLVPES(1)PR;LPLVPES(1)PR;LPLVPES(1)PR;LPLVPES(1)PR;LPLVPES(1)PR;LPLVPES(1)PR 157.38 7.20E-05 1486960000 693421 821322 805215 792713 917093 722685 910060 775501 761092 TRUE FALSE 650021.0174 882133.5355 824315.0801 813055.3576 845068.2152 931312.4277 773604.9516 872324.0069 634060.8284 1.025171385 1.391244335 1.300056782 1.282298671 1.332787293 1.468806124 1.220080025 1.375773377 1 19.27426173 -0.396937869 7.225756708 1.00000705 1.309195904 0.384213756 0.118610021 0 0 0.100880374 0.023777732 0.400924071 0.396937869 0.309188854 LPLVPES(ph)PRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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;LPLVPES(1)PRR;LPLVPES(1)PRR 125.03 0.00025714 3459284000 1959162 2485400 2074930 2132330 2731000 1535546 2171630 2261870 2652810 TRUE FALSE 1836541.548 2669421.602 2124148.319 2187049.198 2516518.276 1978833.203 1846014.242 2544269.448 2210038.873 0.830999658 1.207861832 0.96113618 0.989597615 1.138676024 0.89538389 0.83528587 1.151232894 1 21.07564032 2.217940726 24.99908621 0.941543902 1.040063927 0.015496541 0.129603212 513.1426403 622118.5819 0.045516157 0.033653827 165.1736348 -2.217940726 0.098520025 LPNFGFVVFDDSEPVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPNFGFVVFDDSEPVQK 17 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 139.3 3.02E-05 0 45623 48191 49040 51091 61113 41878 57977 45675 60823 FALSE TRUE 42767.53787 51759.11178 50203.25196 52402.08156 56313.4315 53967.49877 49283.88708 51377.62429 50671.24837 0.844019819 1.021469047 0.990764064 1.034158092 1.111348808 1.065051691 0.972620345 1.013940369 1 15.62887975 4.738966534 6.648366409 1.024252735 0.840701092 0.680591398 0.039201151 0.074642316 21.41063734 0.009884302 0.061531113 54823.47171 -4.738966534 -0.183551643 LPNGEPSPDPGGKGT(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPNGEPSPDPGGKGTPR 17 1 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 LPNGEPS(0.009)PDPGGKGT(0.991)PR 67.866 0.061583 217900000 297050 209830 261510 228130 238620 191280 292500 239440 312740 TRUE FALSE 278458.1707 225366.0315 267713.1407 233984.202 219879.7477 246499.4308 248642.3404 269334.6111 260541.6736 1.068766339 0.864990343 1.027525221 0.898068239 0.843933121 0.946103659 0.954328484 1.03374868 1 17.99115462 1.365305172 3.995925477 1.016330483 0.938112008 0.167114041 0.068014338 0.371974994 9.329312123 0.04822577 0.016219869 23.19023619 -1.365305172 -0.078218476 LPNGLGGPNGFPKPTPEEGPPELNRQS(ph)PNSSSAAASVASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPNGLGGPNGFPKPTPEEGPPELNRQSPNSSSAAASVASR 40 2 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 LPNGLGGPNGFPKPTPEEGPPELNRQS(1)PNSSSAAASVASR;LPNGLGGPNGFPKPTPEEGPPELNRQS(0.998)PNS(0.001)SSAAASVASR 275.75 1.79E-77 1306550000 559680 544230 522210 530760 606170 445600 697770 565000 799150 TRUE FALSE 524650.6279 584525.3555 534597.0678 544380.2002 558563.8534 574237.4863 593145.8663 635541.4937 665766.7023 0.788039753 0.87797325 0.802979581 0.817674117 0.838978356 0.862520586 0.890921496 0.954600901 1 19.34465719 1.334602916 1.112903373 1.000799091 0.828240338 0.871388991 0.023765145 0.14650857 0.363690666 0.020954606 0.007082264 21.60742012 -1.334602916 -0.172558753 LPNNS(ph)SRPS(ph)TPTINVLESK ddPTM_SK-BR-3_Pertuzumab_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(0.522)S(0.457)RPS(0.577)T(0.402)PT(0.042)INVLESK 100.88 0.0003219 201740000 398570 328480 310440 317640 339490 218500 405500 330190 630940 TRUE FALSE 373624.2152 352801.001 317803.7834 325791.1802 312827.8248 281577.4029 344699.0395 371414.9483 525632.038 0.710809441 0.671193869 0.604612658 0.619808453 0.595146038 0.535692999 0.655780117 0.706606374 1 19.00369369 0.750315125 1.986987276 0.99970634 0.624398347 0.863160558 0.046466301 0.339845412 2.091403048 0.045060753 0.012470061 5.62749509 -0.750315125 -0.375307992 LPNNS(ph)SRPST(ph)PTINVLESK ddPTM_SK-BR-3_Pertuzumab_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(0.531)S(0.467)RPS(0.492)T(0.496)PT(0.015)INVLESK 84.68 0.0072363 148180000 350530 307060 292430 269910 328880 192720 420570 299000 553810 TRUE FALSE 328590.953 329795.0419 299366.5777 276836.3476 303051.0914 248355.1355 357509.4329 336330.8082 461375.5333 0.712198479 0.714808259 0.648856639 0.600023902 0.656842571 0.538292817 0.774877312 0.728974087 1 18.81558197 0.7359604 1.199385772 0.998171607 0.656839544 0.750689525 0.061562206 0.437081267 1.087747118 0.056677151 0.017398653 5.444530065 -0.7359604 -0.341332063 LPNTYPNSS(ph)SPGPGGLGGSVHYATMAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.026)S(0.789)S(0.185)PGPGGLGGSVHYATMAR;LPNTYPNS(0.022)S(0.822)S(0.156)PGPGGLGGSVHYATMAR;LPNTYPNS(0.051)S(0.898)S(0.051)PGPGGLGGSVHYATMAR 250.72 1.84E-46 1071390000 359444 615550 552290 599780 635600 460040 605790 572730 472920 TRUE FALSE 336947.0417 661125.9625 565390.5796 615171.3702 585682.5399 592846.0799 514957.4134 644236.6012 393986.5968 0.85522463 1.67804176 1.435050289 1.561401772 1.486554478 1.50473667 1.307042974 1.635173903 1 18.58778703 -1.265209225 4.827184966 0.999871484 1.452822896 0.254649953 0.230528137 0.000279363 4.25E-05 0.195570062 0.046083323 0.054298868 1.265209225 0.452951412 LPNTYPNSSS(ph)PGPGGLGGSVHYATMAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LPNTYPNSSSPGPGGLGGSVHYATMAR 27 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A0U1RRC1;A0A0U1RQJ5 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 LPNTYPNS(0.007)S(0.191)S(0.803)PGPGGLGGSVHYATMAR;LPNTYPNS(0.001)S(0.13)S(0.869)PGPGGLGGSVHYATMAR;LPNTYPNS(0.002)S(0.024)S(0.974)PGPGGLGGSVHYATMAR;LPNT(0.001)Y(0.001)PNS(0.015)S(0.23)S(0.753)PGPGGLGGSVHYATMAR 242.1 2.00E-45 1083630000 384753 609908 581823 626563 627675 479614 627364 545562 494023 TRUE FALSE 360671.9965 655066.2229 595624.1163 642641.6673 578379.9374 618070.7759 533296.5924 613676.6166 411567.3698 0.876337686 1.591637897 1.447209279 1.561449509 1.405310479 1.501748732 1.295769858 1.491072086 1 18.65076908 -0.852216288 11.40355375 1.000029531 1.419082105 0.266520692 0.203529555 0 0 0.17487297 0.041217954 0.140534746 0.852216288 0.419052575 LPPEEASPYVVDHGESGPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LPPEEASPYVVDHGESGPLR 20 0 P53992;G5EA31 P53992 SEC24C Protein transport protein Sec24C 0 ;; 192.62 1.03E-17 386080000 170203 178340 175466 182293 215386 146082 195948 176212 236952 FALSE TRUE 159550.2981 191544.4792 179628.1364 186970.947 198470.4524 188253.502 166567.4165 198212.4561 197403.1804 0.808245833 0.97032114 0.909955635 0.947152658 1.005406559 0.953649792 0.843792973 1.004099608 1 17.59078571 4.745824252 24.44898183 0.943122372 0.808245746 0.442109285 0.0501839 666.7358366 2244117.194 0.011777242 0.121343488 55696.03161 -4.745824252 -0.134876626 LPPGEYILVPSTFEPNKDGDFCIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPPGEYILVPSTFEPNKDGDFCIR 24 1 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 108.07 0.0021839 80486000 54005 44229 44173 41365 47030 44916 63002 46961 54554 FALSE TRUE 50624.92345 47503.76118 45220.80442 42426.49593 43336.45351 57882.52005 53555.43498 52824.18422 45448.58497 1.113894382 1.045219806 0.994988171 0.933505322 0.953527014 1.273582447 1.178374091 1.162284464 1 15.47194776 2.248451631 24.99999534 1.173246397 1.00806969 0.424573823 0.082672729 163.2074632 412514.3897 0.027292153 0.022579387 177.1950685 -2.248451631 -0.165176708 LPPGEYVVVPSTFEPNKEGDFVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPPGEYVVVPSTFEPNKEGDFVLR 24 1 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 126.04 8.63E-05 203358000 307718 262926 272647 246944 298649 223060 318978 256027 274853 FALSE TRUE 288458.4797 282393.3146 279114.3156 253281.0011 275194.3122 287453.8009 271150.2101 287992.5345 228978.2587 1.259763618 1.233275667 1.218955534 1.106135589 1.20183599 1.255375958 1.184174479 1.25772873 1 17.8048511 -1.133497934 4.404576519 0.99996754 1.212775056 0.685111341 0.045718584 0.274978238 12897594.84 835.28141 0.010284625 0.073536349 1.133497934 0.212807515 LPPKVESLESLYFTPIPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPPKVESLESLYFTPIPAR 19 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 137.09 4.16E-06 84490000 154870 190280 160810 179820 183790 115100 209040 148110 235030 FALSE TRUE 145176.9632 204368.5292 164624.4891 184434.4856 169355.8748 148327.5015 177696.3926 166601.8595 195801.9746 0.741447901 1.043751114 0.840770321 0.941943951 0.864934458 0.757538333 0.907531157 0.850869149 1 17.57903579 2.658927358 11.13050712 0.86371554 0.908728803 0 0.096533546 2.477239435 339.3674675 0.028440101 0.026808453 455.9606437 -2.658927358 0.045013263 LPPSFPGNKDELMQHMDEVNDELIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPPSFPGNKDELMQHMDEVNDELIR 25 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 124.51 9.09E-05 317140000 331450 295190 303180 282120 297560 251690 367630 282810 322150 FALSE TRUE 310705.1362 317046.1747 310371.5728 289359.6768 274190.8379 324348.8172 312507.2944 318119.451 268381.0838 1.157701324 1.181328319 1.156458452 1.078167182 1.021647405 1.208538294 1.164416247 1.185327395 1 18.03392346 3.459553807 23.78315686 1.12310043 1.169204125 0.113271631 0.06718429 334.4414677 452771.8895 0.018351301 0.02486772 2881.069979 -3.459553807 0.046103695 LPPTFFCGVCS(ph)DTDEDNGNGEDFQSELQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPPTFFCGVCSDTDEDNGNGEDFQSELQK 29 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 LPPTFFCGVCS(0.5)DT(0.5)DEDNGNGEDFQSELQK 96.887 0.00067229 24834000 21337 19256 18609 20508 17231 18017 30096 17841 19926 TRUE FALSE 20001.55526 20681.73428 19050.41427 21034.27 15877.74677 23218.21542 25583.3842 20068.48812 16600.22187 1.204896863 1.245870955 1.147599979 1.267107763 0.956477985 1.398668981 1.541147124 1.208928909 1 14.0189149 LPPVLSHPIFDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPPVLSHPIFDNR 13 0 Q04206;Q04206-4;Q04206-2;A0A087X0W8;E9PKH5;Q2TAM5;Q04206-3;A0A087WVP0;E9PKV4;E9PQS6;E9PI38 Q04206 RELA Transcription factor p65 0 ; 105.03 0.0014851 482870000 931340 738350 750370 717770 789930 660700 784680 640020 708980 FALSE TRUE 873049.0919 793018.2023 768169.1308 736189.1934 727892.0842 851433.3644 667024.5186 719927.9059 590646.6578 1.478124155 1.342627088 1.300556129 1.246412188 1.232364688 1.44152744 1.129312271 1.218880859 1 19.1719358 -3.529247628 0.058547079 4.53E-12 1.838344159 0.663213233 0.081164914 186.1861869 1.053748266 31.67988256 8.176916323 0.000295633 3.529247628 1.838344159 LPS(ph)GSGAAS(ph)PTGSAVDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 LPS(1)GSGAAS(0.998)PT(0.002)GSAVDIR;LPS(1)GSGAAS(0.998)PT(0.002)GSAVDIR;LPS(1)GSGAAS(0.997)PT(0.003)GSAVDIR;LPS(1)GSGAAS(0.997)PT(0.003)GSAVDIR;LPS(0.998)GS(0.002)GAAS(0.967)PT(0.033)GSAVDIR 360.78 7.62E-91 2014970000 2557520 2878060 2761530 3569020 3605580 1796900 1982120 1732500 2616640 TRUE FALSE 2397449.389 3091154.557 2827034.796 3660607.096 3322412.291 2315635.86 1684919.507 1948806.439 2179905.88 1.099794909 1.418022028 1.296860943 1.679250067 1.524108138 1.062264147 0.772932227 0.893986505 1 21.05583442 2.063504575 4.505374424 0.87369102 1.401654233 0.697067381 0.157435125 0.109501335 4.459400545 0.062022443 0.043622764 115.7456224 -2.063504575 0.527963213 LPS(ph)PTPENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPSPTPENK 9 0 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 LPS(0.742)PT(0.258)PENK 80.014 0.02655 223220000 404420 257360 371850 359220 391490 257690 306750 271120 386780 TRUE FALSE 379108.0741 276415.2022 380670.4576 368438.1934 360743.9546 332080.9198 260755.6852 304969.9288 322223.9193 1.176536102 0.857835765 1.181384853 1.143422854 1.119544307 1.03059053 0.80923752 0.946453415 1 18.29770407 1.934238564 6.929095153 0.901517802 1.077048803 0.371014138 0.102906944 0.274694824 24.52120674 0.04421218 0.02748572 85.9485519 -1.934238564 0.175531001 LPS(ph)QENELLENPSVVLSTNSPAALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPSQENELLENPSVVLSTNSPAALK 25 0 Q96DR7;Q96DR7-4;Q96DR7-3 Q96DR7 ARHGEF26 Rho guanine nucleotide exchange factor 26 1 LPS(1)QENELLENPSVVLSTNSPAALK 161.16 1.36E-11 44462000 60998 53843 51829 56513 52561 41132 72741 41334 70128 TRUE FALSE 57180.24406 57829.59174 53058.40836 57963.21926 48433.07108 53006.14068 61834.16234 46494.64089 58423.18376 0.978725232 0.989839787 0.908173861 0.992127021 0.829004309 0.907279222 1.05838399 0.795825183 1 15.83425336 4.102820204 4.299744683 0.934280365 0.983995176 0.078860567 0.078040537 0.634681293 19.67693142 0.018573509 0.042910526 12671.27172 -4.102820204 0.049714811 LPS(ph)VEEAEVPKPLPPASKDEDEDIQSILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LPSVEEAEVPKPLPPASKDEDEDIQSILR 29 2 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 LPS(1)VEEAEVPKPLPPASKDEDEDIQSILR;LPS(1)VEEAEVPKPLPPASKDEDEDIQSILR;LPS(1)VEEAEVPKPLPPASKDEDEDIQSILR;LPS(1)VEEAEVPKPLPPASKDEDEDIQSILR 189.43 2.32E-18 1078450000 1018354 538252 813655 866175 679693 350703 493501 251801 488465 TRUE FALSE 954617.041 578104.7381 832955.2808 888402.5169 626312.6535 451945.2629 419505.1065 283238.9091 406937.0359 2.345859327 1.420624537 2.046889832 2.183144906 1.53908983 1.110602435 1.030884558 0.696026373 1 18.63444606 2.309449979 2.338076711 0.937173103 1.910698115 0.777212171 0.261164517 0.146095418 1.638854429 0.110046845 0.080685526 203.9153782 -2.309449979 0.973525012 LPSEGPRPAHVVVGDVLQAADVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPSEGPRPAHVVVGDVLQAADVDK 24 1 P30043;M0R192;A0A2R8YEP4;A0A2R8Y7Y9;M0QZL1 P30043 BLVRB Flavin reductase (NADPH) 0 ; 149.74 8.37E-08 1362080000 1705590 1070980 1194890 1086960 1021070 995350 1674820 1180560 1132750 FALSE TRUE 1598840.166 1150276.474 1223233.355 1114853.234 940879.281 1282691.387 1423696.289 1327955.515 943686.7072 1.694248901 1.218917746 1.296228235 1.181380669 0.997025044 1.359234349 1.508653538 1.407199555 1 19.84794846 4.742978496 24.43083352 1.271215545 1.694249137 0.416758948 0.164244086 367.6625337 2033067.37 0.040223824 0.316409241 55332.27106 -4.742978496 0.423033592 LPSETIFVGCEFLHHLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPSETIFVGCEFLHHLLR 18 0 I3L2C7;P57678 I3L2C7 GEMIN4 Gem-associated protein 4 0 ; 87.287 0.0019027 110144000 36048 56872 45291 42158 62476 36005 49133 53401 45542 FALSE TRUE 33791.82003 61082.86206 46365.32391 43239.84565 57569.38698 46399.05901 41765.96278 60068.2324 37940.74599 0.890647222 1.609954166 1.222045658 1.139667777 1.517349896 1.222934811 1.100820811 1.583211685 1 15.21146042 -1.539340638 3.07739121 0.98876147 1.294426874 0.133511142 0.227906088 59708958.59 77732914.08 5686499.068 0.049949472 0.028884135 1.539340638 0.305665404 LPSGS(ph)GAAS(ph)PTGSAVDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 LPS(0.002)GS(0.998)GAAS(0.986)PT(0.014)GSAVDIR;LPSGS(1)GAAS(0.999)PT(0.001)GSAVDIR 350.63 3.26E-90 2274180000 766320 842000 779820 722930 825120 705700 868930 771300 983230 TRUE FALSE 718357.3991 904342.5561 798317.6987 741481.6077 760318.4036 909424.1339 738642.0133 867598.5028 819122.5611 0.876984023 1.104038149 0.974601038 0.905214486 0.928210795 1.110241833 0.901747856 1.059180328 1 19.64371981 -0.392976841 7.655207066 0.999998987 0.988048077 0.000431174 0.084228846 0 0 0.074727538 0.01761345 0.404597466 0.392976841 -0.01195091 LPSGSGAAS(ph)PTGS(ph)AVDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 LPSGS(0.001)GAAS(0.991)PT(0.139)GS(0.869)AVDIR;LPSGSGAAS(0.979)PT(0.128)GS(0.893)AVDIR;LPSGSGAAS(0.999)PT(0.014)GS(0.986)AVDIR 174.72 7.52E-12 330012000 500060 535690 481070 501090 654400 355434 626900 547290 894860 TRUE FALSE 468762.1372 575353.045 492481.2076 513948.8177 603006.0637 458042.0258 532902.1649 615620.3612 745502.085 0.628787158 0.771765843 0.660603394 0.689399571 0.80885899 0.614407438 0.714823172 0.82577953 1 19.50785286 0.962076285 2.568942784 0.999026585 0.701110202 0.734867218 0.05896406 0.142788214 2.174810978 0.050921364 0.013678832 9.163814417 -0.962076285 -0.297916383 LPSGSGAAS(ph)PTGSAVDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LPSGSGAAS(0.995)PT(0.005)GSAVDIR;LPSGSGAAS(0.949)PT(0.051)GSAVDIR;LPSGSGAAS(1)PTGSAVDIR;LPSGSGAAS(0.999)PT(0.001)GSAVDIR;LPSGSGAAS(0.993)PT(0.007)GSAVDIR;LPSGSGAAS(0.872)PT(0.128)GSAVDIR;LPSGSGAAS(1)PTGSAVDIR;LPSGSGAAS(0.963)PT(0.037)GSAVDIR;LPSGSGAAS(0.973)PT(0.027)GSAVDIR;LPSGSGAAS(0.953)PT(0.047)GSAVDIR 419.91 2.60E-149 50900430000 10652060 11668510 10393540 9784780 12087700 9818020 10971640 9626880 12548610 TRUE FALSE 9985366.579 12532458.62 10640079.68 10035874.02 11138380.8 12652322.99 9326544.438 10828817.16 10454165.92 0.955156696 1.198800432 1.0177837 0.959988018 1.065449016 1.210266135 0.892136638 1.035837506 1 23.31757463 1.716300456 24.99999824 0.972688232 1.072982263 0.180913661 0.091684005 1.385497428 1549.593221 0.040527543 0.022474571 52.03558679 -1.716300456 0.100294031 LPSRPGAQGVEPQNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPSRPGAQGVEPQNLR 16 1 A0A0U1RRM1;Q8WXI9 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 0 103.63 0.0012986 123740000 44737 45437 51521 46363 45687 47314 48591 40181 62080 FALSE TRUE 41936.99103 48801.20276 52743.10245 47552.75307 42098.92731 60972.78372 41305.23065 45197.6863 51718.44695 0.810871043 0.94359374 1.019812186 0.91945439 0.814002156 1.178936865 0.798655665 0.873918089 1 15.65839133 -1.400760774 3.359983017 1.000680644 0.929623644 0.040132173 0.114656909 2552957170 6091524100 19211388.3 0.025285897 0.03974104 1.400760774 -0.071057 LPSS(ph)PASPSPK ddPTM_SK-BR-3_Pertuzumab_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(0.049)S(0.951)PASPSPK 110.31 0.0019009 180350000 387770 251500 311140 297180 355620 261870 329530 294490 506280 TRUE FALSE 363500.1679 270121.3217 318520.3877 304806.1419 327691.0397 337467.6179 280120.0357 331257.7248 421778.5973 0.861826964 0.640433923 0.755183857 0.722668585 0.776926667 0.800106075 0.664139995 0.785382964 1 18.68612636 0.973117869 23.47113467 1.000000001 0.735182312 0.603812036 0.063750797 774.0888727 675868.2916 0.056113543 0.014028386 9.399783898 -0.973117869 -0.264817689 LPSS(ph)PLGCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPSSPLGCR 9 0 C9JWC4;Q8NCD3-3;Q8NCD3-2;Q8NCD3 C9JWC4 HJURP Holliday junction recognition protein 1 LPS(0.1)S(0.9)PLGCR 62.869 0.083704 178510000 118470 159310 150920 161670 168810 144310 168280 140950 172510 TRUE FALSE 111055.1742 171105.4782 154499.8937 165818.7259 155552.3435 185969.9543 143047.9762 158547.9178 143716.9665 0.772735306 1.19057257 1.075028908 1.153786709 1.082351982 1.294001389 0.995345085 1.103195549 1 17.13287086 4.746274406 24.72814605 1.116311234 0.772735114 0.594159404 0.087992143 529.516076 1697426.347 0.018795188 0.201610455 55753.7914 -4.746274406 -0.34357612 LPSS(ph)PVYEDAASFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 LPSSPVYEDAASFK 14 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 LPSS(1)PVYEDAASFK;LPS(0.013)S(0.987)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPS(0.002)S(0.998)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPS(0.003)S(0.997)PVYEDAASFK;LPS(0.024)S(0.976)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPS(0.165)S(0.835)PVYEDAASFK;LPSS(1)PVYEDAASFK 370.65 4.23E-97 28252445000 12464780 9496790 11121080 12354440 11517990 8061478 9232370 7329384 7162924 TRUE FALSE 11684631.67 10199942.21 11384877.27 12671475.85 10613413.53 10388695.83 7848061.828 8244473.726 5967385.71 1.958082188 1.709281536 1.907850074 2.123455138 1.778570054 1.740912409 1.315159135 1.381588878 1 22.5086676 1.613691473 1.178838499 1.088217104 1.892965976 0.852174828 0.129439551 0.164562565 0.435273601 0.112983281 0.04143524 41.08577404 -1.613691473 0.804748872 LPSSPASPS(ph)PK ddPTM_SK-BR-3_Pertuzumab_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 LPSSPAS(0.078)PS(0.922)PK 168.76 1.86E-05 76065000 300560 158260 232640 187010 200350 197580 264690 187310 270190 TRUE FALSE 281748.4861 169977.7351 238158.3307 191808.9932 184615.3192 254618.1386 225002.1918 210696.0658 225093.5435 1.251695103 0.755142651 1.05804159 0.852130142 0.820171544 1.13116589 0.999594161 0.936037802 1 17.78016515 2.238739122 25 1.01892583 0.93196483 0.047720973 0.144706751 12.58622567 1763022.043 0.047720408 0.037603476 173.2762826 -2.238739122 -0.086961 LPSSPVYEDAAS(ph)FK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPSSPVYEDAASFK 14 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 LPSSPVYEDAAS(1)FK 156.17 5.92E-06 49216000 82996 60749 58329 65070 86186 63985 126980 92572 83062 TRUE FALSE 77801.42851 65246.91917 59712.59142 66739.80636 79417.29922 82456.43079 107940.5278 104129.818 69198.4156 1.124323842 0.942896143 0.862918477 0.964470151 1.14767511 1.191594202 1.559869932 1.50480061 1 16.07845139 2.282788025 1.895125679 1.404641409 0.953270994 0.463994306 0.168760661 0.224124937 1.632647126 0.075120123 0.05050182 191.7732485 -2.282788025 -0.451370414 LPSTSDDCPAIGT(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LPSTSDDCPAIGTPLR 16 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 LPSTSDDCPAIGT(1)PLR;LPSTSDDCPAIGT(1)PLR;LPSTSDDCPAIGT(1)PLR;LPSTSDDCPAIGT(1)PLR;LPSTSDDCPAIGT(1)PLR 340.31 5.77E-71 779372000 642263 569497 649499 631791 670599 715932 876531 701177 512699 TRUE FALSE 602064.9053 611663.1504 664905.423 648003.8267 617932.8596 922609.9462 745103.3139 788720.4919 427126.2247 1.409571388 1.432043071 1.556695385 1.51712489 1.446721891 2.160040505 1.744456956 1.846574727 1 18.70430295 LPSVEEAEVPKPLPPASKDEDEDIQSILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPSVEEAEVPKPLPPASKDEDEDIQSILR 29 2 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 0 94.606 0.0006966 67378000 136680 77309 101400 84909 99451 76963 118280 92390 140550 FALSE TRUE 128125.4428 83033.0388 103805.2559 87087.90869 91640.51963 99180.96871 100545.0121 103925.0949 117091.297 1.094235405 0.709130746 0.886532633 0.743760731 0.782641596 0.847039628 0.858689028 0.8875561 1 16.83727432 0.851156857 1.211795498 0.999185267 0.827660719 0.16709886 0.104419706 0.97269848 2.751167983 0.087762201 0.027050204 7.098340973 -0.851156857 -0.171524548 LPTEEEWEFAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LPTEEEWEFAAR 12 0 A8MXB9;C9J660;J3KQJ1;Q8NBJ7;A0A494C1B1;H7C3B2;C9JL30;Q8NBJ7-3;Q8NBJ7-2;F8WA42 A8MXB9 SUMF2 Sulfatase-modifying factor 2 0 ;;; 212.63 0.00019682 0 145146 165304 176289 185666 167139 137807 174061 146937 171316 FALSE TRUE 136061.571 177543.2802 180470.6583 190430.5039 154012.5771 177589.6438 147962.169 165282.4079 142722.2529 0.953331161 1.243977562 1.264488576 1.334273388 1.079106965 1.244302414 1.036714079 1.15807034 1 17.12285077 1.568724868 1.012940902 1.032598003 1.209668248 0.159306529 0.115878314 0.714360319 1.416879812 0.097062805 0.036554011 37.04459648 -1.568724868 0.177070245 LPVDSVFNKFEDEDSDDVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPVDSVFNKFEDEDSDDVPR 20 1 P49756 P49756 RBM25 RNA-binding protein 25 0 112.55 0.00013848 89553000 90948 70339 77579 85006 79188 59535 101100 72903 103080 FALSE TRUE 85255.72703 75546.97275 79419.21052 87187.39787 72968.89391 76721.78803 85940.99357 82005.10003 85875.28208 0.992785409 0.879728962 0.924820374 1.015279319 0.849707764 0.893409444 1.000765197 0.954932526 1 16.38995531 1.72139004 9.619123664 0.982590202 0.921019679 0.229172767 0.050572063 0.145395318 39.29662796 0.022871628 0.012331096 52.64898946 -1.72139004 -0.061570523 LPVWVVEDHQEVLPFIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPVWVVEDHQEVLPFIYR 18 0 Q49AR2;E5RFG1;B4DR92;E5RHP8 Q49AR2 C5orf22 UPF0489 protein C5orf22 0 173.28 8.71E-12 46199000 41647 44849 42725 37405 49275 35279 41674 45684 45307 FALSE TRUE 39040.38861 48169.66663 43738.45718 38364.87563 45405.14027 45463.47459 35425.37058 51387.74796 37744.96901 1.034320325 1.276187738 1.158789061 1.016423556 1.202945491 1.204490977 0.938545494 1.361446289 1 15.20399674 -5 0.204427987 0.348642828 1.167985923 0.077534941 0.128932099 334.7857805 3.326544508 89.86448385 0.273395135 1.00E-05 5 0.819343095 LPYDVTPEQALAHEEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LPYDVTPEQALAHEEVK 17 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 180.64 8.49E-10 171220000 88658 70878 78930 74021 82786 63669 84200 70939 71885 FALSE TRUE 83109.05404 76125.88087 80802.25687 75920.50418 76284.3215 82049.20672 71574.99167 79795.89031 59886.92911 1.387766167 1.271160201 1.349246957 1.267730794 1.273805865 1.370068694 1.195168841 1.332442513 1 15.86995353 -3.89341066 0.257458426 1.03E-12 1.328694416 0.746465822 0.056307665 46.79808307 0.777811435 24.63255016 0.068493541 0.000127817 3.89341066 1.328694416 LQAALDDEEAGGRPAMEPGNGS(ph)LDLGGDSAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 LQAALDDEEAGGRPAMEPGNGSLDLGGDSAGR 32 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(0.999)LDLGGDS(0.001)AGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR 288.09 7.77E-75 6042900000 3208960 2982850 3441670 3027760 3425130 3228310 3469620 2957850 4827260 TRUE FALSE 3008116.922 3203703.318 3523308.038 3105457.448 3156134.106 4160270.69 2949382.691 3327144.084 4021559.121 0.747997687 0.796632157 0.876104996 0.772202361 0.784803608 1.034491988 0.733392847 0.827326911 1 21.9393235 -5 0.225542752 1.901848814 0.803430501 0.314385929 0.084723569 200.0888871 2.003433732 82.457792 0.143502628 1.00E-05 5 -1.098418313 LQAALDDEEAGGRPAMEPGNGSLDLGGDSAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 LQAALDDEEAGGRPAMEPGNGSLDLGGDSAGR 32 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;;;;;;; 307.4 4.26E-91 5743040000 2729260 2853750 2917420 2905330 3008340 2687260 3262070 2580440 3136750 FALSE TRUE 2558440.488 3065044.619 2986622.58 2979885.687 2772077.111 3463028.338 2772952.887 2902613.614 2613206.161 0.979042728 1.172905783 1.14289589 1.140317871 1.060795414 1.325202883 1.061130549 1.110748037 1 21.31738952 -0.557315685 7.38767867 1.000001057 1.132451846 0.152232821 0.090177122 0 0 0.077061619 0.018163598 0.277130494 0.557315685 0.13245079 LQAEAPHIVVGTPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQAEAPHIVVGTPGR 15 0 Q14240;Q14240-2;E7EQG2 Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ; 186.85 3.65E-07 912630000 1209230 1449980 1349010 1373460 1757730 1206200 1513890 1424550 2054110 FALSE TRUE 1133546.453 1557338.028 1381009.154 1408705.309 1619684.976 1554410.359 1286896.249 1602408.203 1711265.771 0.662402341 0.910050358 0.80701033 0.823194931 0.946483593 0.908339538 0.752014252 0.936387691 1 20.70663241 -5 0.09245431 1.462327595 0.728280286 0.355558422 0.081437509 280.567109 1.794694819 25.97505585 1.703750633 1.00E-05 5 -0.734047309 LQAEEAERR ddPTM_SK-BR-3_Pertuzumab_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 ; 148.32 0.00014478 536990000 1024620 1230770 1014360 966630 1350860 697710 1166020 1038840 1416510 FALSE TRUE 960490.8632 1321897.491 1038421.098 991435.3623 1244768.905 899127.5506 991186.1258 1168541.461 1180085.33 0.813916451 1.120171108 0.879954247 0.840138706 1.054812625 0.761917404 0.839927504 0.990217767 1 20.17045975 3.729280691 24.68328752 0.893790419 0.992262194 0.017682118 0.114521423 168.5510325 1926566.341 0.027449539 0.046596967 5361.430626 -3.729280691 0.098471775 LQAFGFCEYKEPESTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQAFGFCEYKEPESTLR 17 1 P49756;P49756-2;P49756-3;E9PQU5 P49756 RBM25 RNA-binding protein 25 0 112.56 0.00041488 435190000 97285 85774 93270 88465 99001 65517 105790 85671 114560 FALSE TRUE 91196.10551 92124.79621 95482.40845 90735.16167 91225.86081 84430.69432 89927.77161 96367.21294 95439.19591 0.955541428 0.965272133 1.000452776 0.950711715 0.9558532 0.884654292 0.942251983 1.009723647 1 16.54229427 1.234306712 24.99813404 1.004861853 0.953384737 0.383166455 0.028420823 144.0394752 846395.7138 0.027096727 0.007720246 17.15168183 -1.234306712 -0.051477116 LQAKES(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LQAKESPQR 9 1 Q15061 Q15061 WDR43 WD repeat-containing protein 43 1 LQAKES(1)PQR;LQAKES(1)PQR;LQAKES(1)PQR;LQAKES(1)PQR;LQAKES(1)PQR;LQAKES(1)PQR;LQAKES(1)PQR;LQAKES(1)PQR 108.68 0.0015572 8293851000 5458810 8867330 4130980 4572070 10373430 2326271 4785470 7731490 14154750 TRUE FALSE 5117152.826 9523876.34 4228968.796 4689397.057 9558742.652 2997827.674 4067933.2 8696783.546 11792230.78 0.433942731 0.807639921 0.358623307 0.397668358 0.81059664 0.254220574 0.344967231 0.737501132 1 23.49133333 0.994849874 5.447708694 0.999556962 0.495877356 0.456476647 0.185622107 0.12822853 15.50840251 0.177000118 0.044631683 9.882114328 -0.994849874 -0.503679606 LQAKES(ph)PQRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LQAKESPQRK 10 2 Q15061 Q15061 WDR43 WD repeat-containing protein 43 1 LQAKES(1)PQRK;LQAKES(1)PQRK;LQAKES(1)PQRK 134.56 8.73E-05 1387920000 1762890 1219920 1506320 1631790 1666340 932850 2039150 1261670 3391390 TRUE FALSE 1652553.862 1310244.146 1542050.622 1673664.494 1535472.378 1202148.651 1733398.388 1419192.277 2825345.1 0.584903367 0.463746587 0.545791954 0.592375244 0.543463656 0.425487368 0.613517403 0.502307586 1 21.42999566 -4.447588882 0.523177823 9.988855395 0.52875747 0.862226524 0.05847093 547.0280431 4.327973585 5705.782841 0.024369632 3.57E-05 4.447588882 -9.460097924 LQALAEEPSQPHTRS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQALAEEPSQPHTRSPAK 18 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 LQALAEEPS(0.004)QPHT(0.414)RS(0.582)PAK 165.13 1.75E-11 473420000 178270 228160 200000 233700 379310 117920 249960 234040 657370 TRUE FALSE 167112.3989 245053.2038 204744.0944 239697.1377 349520.5227 151961.5897 212480.8185 263260.4092 547650.7002 0.305144134 0.447462596 0.373858911 0.437682518 0.638217978 0.277479038 0.387986025 0.480708614 1 19.06289649 0.779513441 3.928699675 0.999986483 0.4113738 0.782614761 0.096996355 1.03751847 18.0625545 0.087110845 0.02228196 6.018848907 -0.779513441 -0.588612683 LQALKDTANR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQALKDTANR 10 1 P29401;P29401-2;E9PFF2;F8W888;F8WAX4 P29401 TKT Transketolase 0 127.7 0.00031851 778670000 751140 1006500 947790 1007700 1369400 819150 1280000 841810 2838500 FALSE TRUE 704127.4882 1081022.307 970272.0264 1033559.288 1261852.848 1055625.307 1088075.883 946911.8316 2364736.013 0.297761562 0.457142912 0.410308813 0.437071742 0.533612564 0.446403024 0.46012573 0.40043025 1 21.17324771 -5 0.383752288 9.142852186 0.423422348 0.901061227 0.059300608 169.1814151 1.249562088 1148.091817 0.036203421 1.00E-05 5 -8.719429838 LQALVNSLCAGQS(ph)P ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LQALVNSLCAGQSP 14 0 Q6XQN6-3;Q6XQN6;Q6XQN6-2 Q6XQN6-3 NAPRT Nicotinate phosphoribosyltransferase 1 LQALVNSLCAGQS(1)P;LQALVNSLCAGQS(1)P;LQALVNSLCAGQS(1)P 222.79 3.95E-12 983959000 1148832 1353472 1416545 1636579 1276277 865359 1011452 777613 862337 TRUE FALSE 1076928.656 1453684.475 1450146.116 1678576.388 1176043.353 1115174.095 859794.1625 874699.6948 718407.3838 1.499050094 2.023482091 2.018556809 2.336524409 1.637014568 1.552286517 1.196805854 1.217553876 1 19.45444265 2.063830769 1.524549677 1.123562377 1.98043855 0.720353745 0.221495335 0.197652903 0.865796089 0.134707829 0.068472594 115.8325904 -2.063830769 0.856876173 LQAQEHGAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQAQEHGAER 10 0 Q9H5N1;B4DHR0;Q9H5N1-2 Q9H5N1 RABEP2 Rab GTPase-binding effector protein 2 0 ; 134.75 0.0044921 0 214121 250987 234999 234306 238862 192577 238953 194558 229554 FALSE TRUE 200719.5488 269570.3386 240573.2873 240318.6886 220102.742 248170.8537 203124.216 218848.9946 191239.9544 1.04956911 1.409592151 1.257965617 1.256634312 1.150924464 1.297693541 1.062143194 1.144368577 1 17.54502444 1.515777595 0.685511418 1.006574959 1.27648981 0.336059385 0.103041131 0.587390506 0.601740009 0.089358627 0.041453325 32.79273165 -1.515777595 0.269914851 LQASVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQASVR 6 0 P49327;A0A0U1RQF0;H7BZY1 P49327 FASN;SLC20A1 Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 110.63 0.066388 770160000 410890 883750 477650 442500 947280 377700 544560 804410 845030 FALSE TRUE 385173.1284 949183.7695 488980.0836 453855.2992 872884.4499 486735.8586 462908.2834 904842.3592 703989.0339 0.547129444 1.348293402 0.694584802 0.644690865 1.239911999 0.691396933 0.657550418 1.285307463 1 19.42519343 1.231159554 24.99986201 1.142653698 0.859604124 0.178980381 0.271688251 347.6575178 1174294.251 0.232634349 0.062775029 17.02783975 -1.231159554 -0.283049574 LQAVEVVITHLAPGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQAVEVVITHLAPGTK 16 0 Q9Y2V2 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 0 ; 153.74 4.22E-07 173739000 710070 679010 705390 691840 782070 586190 871120 698630 916520 FALSE TRUE 665627.9862 729284.6069 722122.1839 709593.7857 720649.3769 755413.537 740503.6431 785855.4934 763546.8911 0.871757837 0.955127466 0.945747003 0.929338845 0.943818101 0.989347931 0.969820782 1.029217069 1 19.54235723 2.004742602 0.877315796 1.010839559 0.930234633 0.637490608 0.025827076 0.408746417 0.582506536 0.020488356 0.010135769 101.0980087 -2.004742602 -0.080604926 LQAVTDDHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LQAVTDDHIR 10 0 P30043;A0A2R8YEP4 P30043 BLVRB Flavin reductase (NADPH) 0 ;;;;;;; 215.5 8.16E-09 20342990000 6720510 8809390 7115600 7413050 8262690 6044260 8198160 7479660 7905850 FALSE TRUE 6299885.276 9461646.402 7284385.392 7603281.413 7613771.657 7789139.742 6968922.016 8413512.016 6586312.561 0.956511738 1.436562009 1.105988415 1.154406406 1.15599914 1.182625281 1.058091603 1.277423739 1 22.65103955 -5 0.143898573 0.381622805 1.237660281 0.087704025 0.131171494 248.7410038 2.16859707 44.03002444 0.687165714 1.00E-05 5 0.856037477 LQAYHTQTTPLIEYYR ddPTM_SK-BR-3_Pertuzumab_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 ; 185.26 1.69E-09 869410000 427360 544620 416580 370590 615860 328630 566160 469790 452620 FALSE TRUE 400612.3005 584944.2315 426461.4743 380099.9668 567492.8399 423500.1461 481269.564 528444.3156 377074.798 1.062421309 1.551268434 1.130973156 1.008022729 1.504987453 1.123119732 1.276323866 1.401431012 1 18.5244912 -0.966924076 4.1736513 0.999987383 1.266968536 0.160599154 0.183704726 9121785.307 4371129.601 1006.254053 0.039394717 0.107913536 0.966924076 0.266981153 LQCPQVDLFYLHAPDHGTPVEETLHACQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQCPQVDLFYLHAPDHGTPVEETLHACQR 29 0 O43488;H3BLU7;H7C5H7 O43488 AKR7A2 Aflatoxin B1 aldehyde reductase member 2 0 ; 328.52 1.57E-105 671430000 232770 285480 218490 249340 277590 229140 257990 224396 259770 FALSE TRUE 218201.3412 306617.2362 223672.686 255738.4865 255789.2011 295288.9982 219306.7946 252412.3346 216412.7088 1.008264914 1.416817145 1.033546908 1.181716582 1.181950924 1.364471615 1.013372993 1.166347096 1 17.7234257 1.649279763 13.18943542 1.06788431 1.202545916 0.193647489 0.131930289 0.196158592 51.93376191 0.057261918 0.031343376 44.59434231 -1.649279763 0.134661606 LQCSLDAHEICLQDIQLDPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQCSLDAHEICLQDIQLDPER 21 0 Q06546 Q06546 GABPA GA-binding protein alpha chain 0 ; 204.21 5.42E-22 273870000 269400 339090 322020 321410 344710 303690 372990 302790 333520 FALSE TRUE 252538.7349 364196.5764 329658.4665 329657.9247 317637.8671 391360.373 317063.6122 340593.998 277853.3574 0.908892148 1.310751037 1.186447663 1.186445713 1.143185276 1.408514105 1.141118521 1.225804868 1 18.08396415 -0.969011939 4.521684263 0.999996359 1.203340904 0.16791212 0.128624705 7177404.811 1587478.792 314.4354498 0.026440726 0.107395989 0.969011939 0.203344545 LQDAEIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 LQDAEIAR 8 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;;;;; 206.16 0.00017128 32243670000 28160420 36833990 30330670 31733150 32923270 24082040 33815250 28659840 31010210 FALSE TRUE 26397909.58 39561216.95 31050127.82 32547476.35 30337609.18 31034134.01 28744967.19 32238084.11 25834405.62 1.021812151 1.531338384 1.201890544 1.259850017 1.174310322 1.201271454 1.112662223 1.24787404 1 24.62279036 1.417778812 0.312997527 0.988654592 1.333146811 0.185328178 0.133006466 1.782177276 0.621324395 0.233538255 0.192863251 26.16849899 -1.417778812 0.344492218 LQDAYYIFQEMADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQDAYYIFQEMADK 14 0 O14579;M0QXB4;O14579-2 O14579 COPE Coatomer subunit epsilon 0 173.68 6.19E-06 70615000 129330 114800 122060 114960 123750 90590 133490 133010 124590 FALSE TRUE 121235.4662 123299.9114 124955.3208 117910.0682 114031.1742 116741.8624 113474.4138 149616.5913 103795.1241 1.168026602 1.18791622 1.203865036 1.135988508 1.098617832 1.124733588 1.093253799 1.441460691 1 16.66337915 -2.327403039 2.334775036 0.000153008 1.171993661 0.243163048 0.099449264 1142111.082 751718.7815 6416733.962 0.021935386 0.004705404 2.327403039 1.171840652 LQDEFENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQDEFENR 8 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77;H0YEC5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 93.598 0.025487 352940000 352170 415020 381000 407060 445260 379800 480020 384220 470170 FALSE TRUE 330128.3083 445748.5126 390037.4999 417505.8488 410291.0757 489442.0945 408045.4573 432190.7128 391695.5896 0.842818549 1.137997273 0.995766892 1.065893668 1.047474331 1.249547116 1.041741261 1.103384169 1 18.57937336 2.453630508 24.99516167 1.106885351 1.032104411 0.135739536 0.097489278 470.2152918 500326.4332 0.030647221 0.025642415 284.204211 -2.453630508 -0.07478094 LQDGTPQAALS(ph)PLTPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQDGTPQAALSPLTPAR 17 0 A0A087WVP4;A0A087X1R1;P53814-5;P53814;P53814-6 A0A087WVP4 SMTN Smoothelin 1 LQDGTPQAALS(0.999)PLT(0.001)PAR;LQDGTPQAALS(1)PLTPAR 227.06 1.97E-15 92632000 115833 101949 117045 110592 108772 116940 115201 91410 136355 TRUE FALSE 108583.2193 109497.41 119821.3627 113429.978 100229.4859 150698.6796 97927.67952 102822.7397 113596.4696 0.955867904 0.963915608 1.054798297 0.998534359 0.882329233 1.326614112 0.862066223 0.905157881 1 16.79355847 LQDLIEEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQDLIEEIR 9 0 O75843;G3V2V9;G3V3Z2;G3V532 O75843 AP1G2 AP-1 complex subunit gamma-like 2 0 86.624 0.032598 12559000 25357 35111 31091 34520 33640 28473 39357 31258 29211 FALSE TRUE 23769.95063 37710.65497 31828.4932 35405.84164 30998.0501 36692.69288 33455.78322 35160.63011 24335.49539 0.9767605 1.549615258 1.307904059 1.454905317 1.273779292 1.507784916 1.37477305 1.444829026 1 14.57077452 -0.809699528 8.424075327 1.000002632 1.379747411 0.326291178 0.161226866 0 0 0.133639699 0.03149918 0.154988856 0.809699528 0.379744779 LQDLQGEKDALHSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQDLQGEKDALHSEK 15 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 143.14 2.93E-06 421290000 866010 722500 791670 837030 1067440 477550 1003650 719970 1788610 FALSE TRUE 811807.98 775994.6518 810448.7863 858509.6069 983607.5682 615410.9326 853161.9999 809859.8393 1490079.436 0.544808525 0.520774016 0.543896363 0.576150228 0.660104116 0.413005453 0.572561421 0.543501118 1 20.50695781 -0.025086574 2.132322905 1.000027933 0.544354128 0.84678247 0.06056891 45.89226064 93.76063455 0.056199414 0.014459429 0.943872703 0.025086574 -0.455673806 LQDLTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQDLTLR 7 0 A0A494C039;Q9Y4L1;A0A087X054;A0A1W2PS94;A0A2R8Y358;Q9BXT5 A0A494C039;A0A1W2PS94 HYOU1;TEX15 Hypoxia up-regulated protein 1;Testis-expressed sequence 15 protein 0 89.401 0.041644 44026000 66423 111000 90221 96479 102230 100270 76836 85396 70220 FALSE TRUE 62265.703 119218.5555 92361.08473 98954.81448 94201.26818 129216.3213 65315.15511 96057.87858 58499.82836 1.064374114 2.037930005 1.578826593 1.691540253 1.610282813 2.208832485 1.116501654 1.642019836 1 15.83614477 0.948855965 0.992782765 1.023469304 1.699241578 0.226079437 0.35083321 0.780399273 1.611883206 0.296633168 0.098400301 8.889062604 -0.948855965 0.675772275 LQDYEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQDYEEK 7 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 117.4 0.01219 702250000 1793950 1360850 1493020 1411670 1846770 1170000 1686510 1381200 2091600 FALSE TRUE 1681669.872 1461608.75 1528435.139 1447895.842 1701732.134 1507760.007 1433633.482 1553645.86 1742498.448 0.965091174 0.838800604 0.877151507 0.830930922 0.976604677 0.865286284 0.822745916 0.891619652 1 20.73272594 0.963959163 22.2082249 1.000000002 0.874459974 0.322396604 0.052259681 1417.128868 873231.6849 0.046678863 0.011669716 9.203630263 -0.963959163 -0.125540029 LQEAANYIES(ph)PDRETILDPNLQATL ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQEAANYIESPDRETILDPNLQATL 25 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4 Q8NEY1-5 NAV1 Neuron navigator 1 1 LQEAANY(0.154)IES(0.84)PDRET(0.006)ILDPNLQATL 80.943 0.013675 80750000 60230 58527 59375 59102 79497 62666 69754 68658 113640 TRUE FALSE 56460.31181 62860.39998 60783.40304 60618.65738 73253.6263 80756.6569 59295.03526 77230.10243 94672.74986 0.596373422 0.663975643 0.642036944 0.640296785 0.773756191 0.853008464 0.62631576 0.815758521 1 16.53066161 -5 0.114761581 2.029860275 0.523366611 0.712701316 0.068235669 88.1832861 0.665474512 21.04213902 0.736081542 1.00E-05 5 -1.506493664 LQEAANYIESPDRET(ph)ILDPNLQATL ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQEAANYIESPDRETILDPNLQATL 25 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4 Q8NEY1-5 NAV1 Neuron navigator 1 1 LQEAANY(0.315)IES(0.274)PDRET(0.412)ILDPNLQATL 65.753 0.074579 93585000 51041 47110 51053 46426 66583 49834 68304 61798 101490 TRUE FALSE 47846.43492 50598.07342 52264.00127 47617.36976 61353.83976 64220.26681 58062.4493 69513.61633 84550.66335 0.56589071 0.598434967 0.618138276 0.563181504 0.725645871 0.759547758 0.686717845 0.822153412 1 16.36752845 0.832244608 0.304947428 1.061401082 0.548051 0.896382474 0.043299828 0.670637591 0.171801942 0.119849763 0.059591395 6.795862893 -0.832244608 -0.513350083 LQEALEDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQEALEDER 9 0 Q9UH65;E7EMB1 Q9UH65 SWAP70 Switch-associated protein 70 0 ; 109.66 0.0056126 587110000 918580 1137310 1011820 975580 1201720 833850 1132480 1008310 1286460 FALSE TRUE 861087.7175 1221517.616 1035820.848 1000615.034 1107341.759 1074568.959 962675.1374 1134199.723 1071741.515 0.803447198 1.139750209 0.966483834 0.933634669 1.033217192 1.002638177 0.898234438 1.058277306 1 20.03152556 3.685763719 24.97408556 0.976686611 1.012869486 0 0.09377187 1070.856067 646645.3523 0.023013479 0.035652651 4850.245472 -3.685763719 0.036182875 LQEDGLLSNVSHVIVDEVHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LQEDGLLSNVSHVIVDEVHER 21 0 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 0 ;; 146.99 6.00E-08 62514000 71989 77437 82565 85914 75000 74842 96824 70211 66633 FALSE TRUE 67483.33699 83170.51605 84523.48079 88118.69869 69109.80254 96447.67044 82306.14007 78976.9979 55511.52183 1.215663609 1.498256818 1.522629501 1.587394757 1.244963212 1.737435171 1.482685708 1.422713615 1 15.76049962 0.75821889 3.308957016 1.000041577 1.486296012 0.481286819 0.151389156 1.529009526 19.9904855 0.130134705 0.033725008 5.730847999 -0.75821889 0.486254435 LQEDKEQMAQQLAEETQGFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 239.57 5.70E-30 773870000 1465650 1491440 1530400 1634920 1708940 1160480 2029160 1439030 1884110 FALSE TRUE 1373917.583 1601867.769 1566701.811 1676874.815 1574726.746 1495491.737 1724906.296 1618696.063 1569639.869 0.875307521 1.020532035 0.998128196 1.068318184 1.003240792 0.952761055 1.098918503 1.031253152 1 20.58200216 4.73929635 6.011463111 1.023853074 0.871275245 0.569342775 0.039967758 0.096878384 17.01054861 0.009301057 0.060339739 54865.12207 -4.73929635 -0.152577829 LQEDPNYS(ph)PQRFPNAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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;LQEDPNYS(1)PQRFPNAQR 141.7 3.72E-07 3207690000 1948280 1922470 1979310 1928400 2104270 1943840 2412310 1811820 2757930 TRUE FALSE 1826340.633 2064811.679 2026260.168 1977886.009 1939009.122 2504995.052 2050606.51 2038029.715 2297613.666 0.794885868 0.898676618 0.881897683 0.860843595 0.843923045 1.090259468 0.892494043 0.887020192 1 21.1317048 LQEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LQEEER 6 0 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ;;; 197.16 0.0005441 7715100000 8030800 8753000 9069400 8604500 8803100 8149000 9650400 7304800 8260100 FALSE TRUE 7528166.563 9401081.227 9284530.451 8825306.037 8111740.036 10501484.01 8203412.11 8216820.36 6881435.948 1.093981928 1.366151091 1.349214106 1.2824803 1.178785954 1.526059981 1.192107603 1.194056069 1 22.71427821 0.986087754 1.728562792 1.004726687 1.306632939 0.370725999 0.117806659 0.359293339 2.223644349 0.100702408 0.028918778 9.684735264 -0.986087754 0.301906253 LQEEERER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LQEEERER 8 1 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ;;; 148.94 0.00046798 2014890000 1229670 2010530 1551970 1668110 2254740 969730 1447170 1330510 3127600 FALSE TRUE 1152707.15 2159391.733 1588783.461 1710916.527 2077661.816 1249675.309 1230180.293 1496627.102 2605583.355 0.442398877 0.828755576 0.609761134 0.656634732 0.797388351 0.479614404 0.472132389 0.574392333 1 21.31317498 -1.150543741 4.369094016 1.000071244 0.618126644 0.473233015 0.129676976 19215537.41 5060165.001 13614.40028 0.031363294 0.070705998 1.150543741 -0.3819446 LQEELSENDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQEELSENDKK 11 1 O95347-2;O95347;Q5T821 O95347-2 SMC2 Structural maintenance of chromosomes protein 2 0 93.958 0.014209 99103000 119900 50551 79008 73667 87015 58730 108970 60920 116360 FALSE TRUE 112395.673 54293.84864 80882.10707 75557.41994 80181.1929 75684.3976 92630.96013 68525.9961 96938.76429 1.159450235 0.560083977 0.834362885 0.779434528 0.827132401 0.780744402 0.955561594 0.706899831 1 16.56478607 -1.027810504 0.332265555 1.096723731 0.790151359 0.069486657 0.158907819 30.70460733 2.629415292 2.969420158 0.131954563 0.093797118 1.027810504 -0.306572373 LQEENRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQEENRK 7 1 H0Y626;O95361;K7ENN8;B3KP96;O95361-2;Q309B1 H0Y626 TRIM16;TRIM16L Tripartite motif-containing protein 16;Tripartite motif-containing protein 16-like protein 0 81.548 0.043137 102370000 100950 96160 110840 111130 123470 90081 130510 110500 117850 FALSE TRUE 94631.7197 103279.7865 113469.1771 113981.7839 113773.1643 116085.9224 110941.2371 124296.1682 98180.07366 0.963858716 1.051942442 1.155725117 1.160946205 1.158821337 1.182377625 1.129977122 1.266001986 1 16.58314263 4.537937376 1.163774273 1.158233852 0.912638146 0.476910821 0.065211549 0.862855463 1.256422421 0.016586965 0.236533235 34509.39746 -4.537937376 -0.245595706 LQEGYDHSYYFIATFITDHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQEGYDHSYYFIATFITDHIR 21 0 P10768;X6RA14 P10768 ESD S-formylglutathione hydrolase 0 ; 308.37 1.06E-66 697964000 605849 701702 692183 694500 791502 572152 733058 750093 655995 FALSE TRUE 567929.9926 753656.7462 708601.9076 712322.0458 729340.6257 737322.9943 623142.7583 843743.7622 546505.1966 1.039203279 1.379047722 1.296605983 1.303413124 1.334553871 1.349160079 1.140232082 1.543889733 1 19.05987569 -1.916645673 2.733206393 0.824187417 1.297154613 0.326778635 0.134532531 19511054.19 9423991.369 21887202.36 0.028335186 0.012115862 1.916645673 0.472967195 LQEIEELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQEIEELER 9 0 P78362;P78362-2 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 0 ; 163.64 0.00014625 161001000 168358 181142 188586 176855 180423 162058 198962 155524 195234 FALSE TRUE 157820.7733 194553.9422 193059.349 181393.3987 166253.3054 208841.5138 169129.4952 174941.5138 162648.1841 0.970319922 1.196164244 1.186975127 1.11525007 1.022165149 1.284007657 1.039848653 1.075582335 1 17.31139519 1.60133617 25 1.043268031 1.140548622 0.17722492 0.089684659 0.901987979 3441.25877 0.043397802 0.020828635 39.93338908 -1.60133617 0.097280591 LQEKEDLQELNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LQEKEDLQELNDR 13 1 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;; 283.45 1.26E-32 41844000000 31922500 28907300 29491600 30563200 35338300 23110200 37883900 27421900 46526000 FALSE TRUE 29924527.71 31047626.57 30191154.68 31347503.46 32562972.47 29781739.58 32203560.89 30845584.58 38760510.03 0.77203648 0.801011817 0.77891531 0.808748477 0.840106914 0.768352624 0.830834292 0.795799244 1 25.20808422 -5 0.302715284 2.697042517 0.789562235 0.885319111 0.022751411 78.35004659 0.720963695 84.45892389 0.020030731 1.00E-05 5 -1.907480282 LQEKEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LQEKEELR 8 1 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 0 ;;;;; 132.01 0.00089427 5313170000 6773350 6970480 6244260 6414870 7465770 4172950 7978990 6073520 9327140 FALSE TRUE 6349418.114 7486581.592 6392376.796 6579486.425 6879438.54 5377612.923 6782614.523 6831812.341 7770380.078 0.817130958 0.963476885 0.822659475 0.84673933 0.885341318 0.692065622 0.872880664 0.87921212 1 22.88955374 0.801230175 2.569743628 0.999809674 0.848547897 0.344569942 0.067692435 1.04051639 11.12023861 0.063619306 0.016969714 6.327471166 -0.801230175 -0.151261777 LQELESCSGLGS(ph)TSDDTDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 LQELES(0.016)CS(0.024)GLGS(0.878)T(0.077)S(0.006)DDTDVR;LQELESCSGLGS(0.87)T(0.115)S(0.016)DDTDVR;LQELESCSGLGS(0.998)T(0.002)SDDTDVR;LQELESCSGLGS(0.957)T(0.042)S(0.001)DDTDVR 331.82 6.78E-59 403130000 389429 476948 479906 628586 599385 405801 435809 293591 329944 TRUE FALSE 365055.334 512261.7262 491289.5969 644716.581 552311.7199 522949.1611 370463.4863 330246.4826 274874.2149 1.328081407 1.863622335 1.787325149 2.345496762 2.00932532 1.902503519 1.347756415 1.201445842 1 18.06841205 1.597506177 2.637427026 1.113771482 1.888416263 0.632529277 0.252322174 0.157340038 2.493676947 0.175486656 0.067838917 39.58276949 -1.597506177 0.774644781 LQELPDAVPHGEMPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQELPDAVPHGEMPR 15 0 P33992;B1AHB1;B1AHB2 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ; 120.63 0.00012002 675850000 456140 527810 528230 499340 558220 461440 584450 469250 581800 FALSE TRUE 427591.0116 566889.6016 540759.865 512153.9098 514379.653 594650.2371 496817.1483 527836.8954 484693.8214 0.882187874 1.169582892 1.115673114 1.056654505 1.061246565 1.226857473 1.02501234 1.089010984 1 18.88671417 0.718863637 1.38695871 1.000921471 1.093740811 0.046154228 0.091744439 2.385731892 7.509317898 0.079083722 0.023408193 5.234360586 -0.718863637 0.09281934 LQELSAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQELSAEER 9 0 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 145.84 0.00022384 537320000 442750 540290 509100 494300 537860 403770 522170 466890 488470 FALSE TRUE 415039.0678 580293.6338 521176.0924 506984.5748 495618.6452 520331.8443 443875.4561 525182.2443 406941.2014 1.019899353 1.425988894 1.280715963 1.245842331 1.217912179 1.278641343 1.090760667 1.29056051 1 18.63446083 0.373971638 0.383411373 0.970617605 1.286555097 0.241888618 0.115540833 3.29063949 0.869629175 0.306257191 0.085739911 2.365765195 -0.373971638 0.315937491 LQEVFGHAIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQEVFGHAIK 10 0 P54136;P54136-2;E5RH09;E5RJM9 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 102.4 0.002952 396620000 887290 1327440 1139630 1005190 1381380 649470 999320 1096940 1557220 FALSE TRUE 831756.1028 1425725.039 1166662.562 1030984.877 1272891.987 836961.4457 849481.2432 1233895.374 1297309.922 0.64113909 1.098985689 0.89929364 0.794709776 0.981178025 0.645151503 0.654802086 0.951118428 1 20.30709174 2.250890505 24.99983589 0.765199768 0.910703016 0 0.164304123 406.5749303 824362.5781 0.054136808 0.044989742 178.1929446 -2.250890505 0.145503248 LQEVPHEGPMCDLLWSDPDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 144.56 9.59E-08 565870000 311660 328322 328357 329881 370171 302491 358468 305550 345967 FALSE TRUE 292153.7569 352631.3025 336145.7831 338346.3049 341099.2629 389815.2412 304719.0513 343698.5901 288222.8727 1.013638349 1.223467448 1.166270324 1.173905117 1.183456607 1.352478509 1.057234106 1.192475069 1 18.1368253 -0.622429405 6.309732184 1 1.174643185 0.25695263 0.090788498 5.87E-10 9.30E-11 0.078741887 0.018559641 0.238545152 0.622429405 0.174643186 LQFHDVAGDIFHQQCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LQFHDVAGDIFHQQCK 16 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;; 253.02 8.81E-27 10876528000 9213640 9579230 9126290 8701700 11187170 7343390 10871970 9924860 12986400 FALSE TRUE 8636974.719 10288486.16 9342769.909 8925000.354 10308574.8 9463307.483 9241819.029 11164000.62 10818885.94 0.798323854 0.950974639 0.86356118 0.824946339 0.952831451 0.874702583 0.854230193 1.03189928 1 23.36704861 1.235930002 24.99995985 1.015949707 0.880421718 0.589725308 0.048933331 47.94754341 455622.8551 0.037262439 0.010960741 17.21591072 -1.235930002 -0.135527989 LQGDANNLHGFEVDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LQGDANNLHGFEVDSR 16 0 C9JLU1;P52434;P52434-3;P52434-2;P52434-5 C9JLU1 POLR2H "DNA-directed RNA polymerases I, II, and III subunit RPABC3" 0 ;;; 242.42 6.00E-20 4723780000 4202460 4644900 4678640 4551630 4863540 4096360 4997300 4436970 4793280 FALSE TRUE 3939435.53 4988813.229 4789619.55 4668432.532 4481577.187 5278912.633 4248001.258 4990935.471 3993250.602 0.986523492 1.249311332 1.199428743 1.169080781 1.122287989 1.321958765 1.063795309 1.249842789 1 21.92913218 -1.076132655 4.40214353 0.999984843 1.176852861 0.231968957 0.096717322 1.26E-05 2.64E-06 0.081996418 0.019325085 0.083920361 1.076132655 0.176868019 LQGEGLSVAGIVCHVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQGEGLSVAGIVCHVGK 17 0 Q13268;C9JZP6;Q13268-2 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ; 219.68 4.25E-15 10723500000 8744700 7446100 7417500 6549900 9740200 7116800 7573100 8379100 10994100 FALSE TRUE 8197384.837 7997416.992 7593446.603 6717981.523 8975243.982 9171304.628 6437583.96 9425249.08 9159113.685 0.894997608 0.873164944 0.829059106 0.733475067 0.979924946 1.001331018 0.702861017 1.029056894 1 23.12677657 2.719138023 24.85354265 0.911037251 0.838820111 0.188379558 0.101984299 1818.387095 2326841.802 0.03281055 0.030974619 523.766868 -2.719138023 -0.072217139 LQGIDLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQGIDLDR 8 0 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7 Q92878-2 RAD50 DNA repair protein RAD50 0 74.2 0.078436 0 162490 198780 191490 195960 224680 166440 226440 183710 223090 FALSE TRUE 152320.041 213497.878 196032.2332 200988.6654 207034.5391 214488.5261 192487.4242 206646.5979 185854.8378 0.819564574 1.148734575 1.054759917 1.081428214 1.1139583 1.154064799 1.035686918 1.111870965 1 17.50381672 4.746158526 24.93008021 1.090557676 0.81956444 0.752310459 0.048299847 408.3357341 1339788.484 0.010379915 0.110760746 55738.91698 -4.746158526 -0.270993237 LQGPPT(ph)PAGK ddPTM_SK-BR-3_Pertuzumab_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 127.02 0.004105 768910000 1586270 1416090 1593730 1473410 1610760 1260880 2015420 1488640 1626170 TRUE FALSE 1486988.192 1520938.777 1631534.028 1511220.195 1484257.407 1624875.587 1713226.481 1674499.981 1354751.722 1.097609376 1.12266975 1.20430482 1.115496051 1.095593667 1.199389941 1.264605502 1.236019821 1 20.36959705 2.145682676 8.428404885 1.204952096 1.136602965 0.019184556 0.078149863 0.474881549 38.3456437 0.026909814 0.019866796 139.8565064 -2.145682676 -0.068349132 LQHFQELGEEKDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQHFQELGEEKDNR 14 1 Q13439-5;Q13439-3;Q13439-4;Q13439;H0Y6I0 Q13439-5 GOLGA4 Golgin subfamily A member 4 0 ; 148.57 4.64E-06 143000000 217734 178367 185406 209728 231273 151087 251764 163503 335110 FALSE TRUE 204106.4176 191573.4783 189803.9179 215109.9755 213109.7515 194703.3642 214014.3255 183916.7095 279177.9761 0.731097848 0.686205556 0.679867089 0.770511981 0.76334729 0.697416633 0.766587424 0.658779435 1 18.09082561 -1.791534244 2.837477279 1.07217002 0.718225291 0.836071391 0.03906962 9381048.008 6826755.225 4655211.739 0.009513977 0.016160908 1.791534244 -0.353944729 LQHLAPEELHTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LQHLAPEELHTDR 13 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 ;;;; 195.1 2.61E-07 2987250000 1046360 1139770 1065320 1101180 1157450 876400 1184080 1003650 961070 FALSE TRUE 980870.1954 1224159.757 1090589.893 1129438.143 1066548.546 1129402.453 1006538.196 1128957.912 800661.2083 1.225075207 1.528936015 1.362111568 1.410631777 1.332084701 1.410587201 1.257133712 1.410031984 1 19.61083238 -3.494389056 0.257815667 1.76E-09 1.413303663 0.625033869 0.087818448 46.73933325 0.93166961 24.84230858 0.109507165 0.00032034 3.494389056 1.413303661 LQHLAPEELHTDRES(ph)PRPGPSMLPSVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQHLAPEELHTDRESPRPGPSMLPSVPK 28 2 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 LQHLAPEELHT(0.027)DRES(0.947)PRPGPS(0.027)MLPSVPK 96.338 0.0013467 226530000 166730 129360 159150 148960 180150 121430 189510 174420 169780 TRUE FALSE 156294.6669 138937.949 162925.1132 152782.5658 166001.7457 156484.8697 161094.7348 196196.7209 141442.6212 1.105004034 0.982291956 1.15188132 1.080173462 1.173633126 1.106348768 1.138940536 1.387111744 1 17.10985739 3.356681926 0.803065732 1.168773676 1.037003441 0.144270725 0.10260872 1.171684129 1.604273318 0.047042065 0.096681152 2273.431776 -3.356681926 -0.131770235 LQHSSALTASVEEGGVPGEDPS(ph)SRPATPELAEPESAPTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQHSSALTASVEEGGVPGEDPSSRPATPELAEPESAPTLR 40 1 Q6NV74 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 LQHSSALTASVEEGGVPGEDPS(0.456)S(0.456)RPAT(0.084)PELAEPES(0.003)APT(0.001)LR 55.541 0.014476 29691000 5902.2 9114.4 7310.9 9939.7 9013.5 10106 7897.3 6886.3 14522 TRUE FALSE 5532.791838 9789.23966 7484.318 10194.76953 8305.616069 13023.43814 6713.17318 7746.069714 12098.18438 0.457324146 0.809149485 0.618631504 0.84266938 0.686517564 1.076478728 0.554890963 0.640267123 1 13.56250293 4.745179361 23.80527444 0.755621772 0.457323874 0.259109516 0.166751211 553.3138673 1989966.267 0.03594534 0.338752101 55613.38902 -4.745179361 -0.298297898 LQHYAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQHYAK 6 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 90.285 0.049203 816410000 2506900 2976500 2667100 2583000 3297500 2104400 3151900 2888100 3514500 FALSE TRUE 2349997.604 3196883.157 2730364.871 2649284.153 3038527.651 2711906.118 2679301.856 3248685.642 2927907.245 0.802620236 1.091866268 0.932531205 0.904838825 1.03778139 0.926226786 0.915091098 1.109558934 1 21.48143842 1.243291002 24.99972349 1.054779471 0.956583027 0.228409655 0.081989095 168.6219092 891191.9949 0.054831777 0.018548205 17.51019579 -1.243291002 -0.098196444 LQINS(ph)PPFDQPMSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQINSPPFDQPMSR 14 0 Q00537;Q00537-2;F5H6Z0;F8VQZ9 Q00537 CDK17 Cyclin-dependent kinase 17 1 LQINS(1)PPFDQPMSR;LQINS(1)PPFDQPMSR 96.247 0.0036159 121383000 202472 204040 207107 205954 241180 180868 242370 193096 279820 TRUE FALSE 189799.6389 219147.3339 212019.6758 211239.1283 222238.6957 233081.6555 206028.8686 217204.4607 233116.2343 0.814184561 0.940077531 0.909501976 0.906153657 0.953338562 0.999851667 0.883803177 0.931743177 1 17.83068995 LQIS(ph)TPDIKDNIVAQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQISTPDIKDNIVAQLK 17 1 O14896;O14896-2 O14896 IRF6 Interferon regulatory factor 6 1 LQIS(0.829)T(0.171)PDIKDNIVAQLK;LQIS(0.826)T(0.174)PDIKDNIVAQLK 249.2 3.32E-21 425750000 1154800 820070 848160 802020 1141340 669220 1289370 1025090 2380200 TRUE FALSE 1082523.129 880788.8361 868278.7557 822601.191 1051703.76 862412.9501 1096040.938 1153074.743 1982929.243 0.545921209 0.444185711 0.437876822 0.414841424 0.530378864 0.43491867 0.5527383 0.5815007 1 20.91920177 0.407566027 0.788724602 1.006504373 0.457577851 0.930776981 0.044647831 0.432066614 0.387993142 0.044431685 0.013760972 2.556030471 -0.407566027 -0.548926522 LQKEEEIEFLYNENTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQKEEEIEFLYNENTVR 17 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 250.04 3.24E-21 565250000 837220 750740 766840 755030 893990 626350 941860 721220 925630 FALSE TRUE 784819.8947 806325.5707 785029.8069 774405.3481 823779.6316 807167.0771 800636.8368 811265.9046 771136.3732 1.017744619 1.045632911 1.018016831 1.004239166 1.068267119 1.046724166 1.038255832 1.052039474 1 19.55662649 2.746581238 24.99046912 1.043421423 1.024880547 0.179674332 0.019914681 1097.6992 3420162.008 0.005653023 0.005919194 557.9319582 -2.746581238 -0.018540876 LQLEETDHQK ddPTM_SK-BR-3_Pertuzumab_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 2387240000 3329120 3064100 3102820 3199910 3349930 2385730 4126090 2883780 3433710 FALSE TRUE 3120756.322 3290969.152 3176420.356 3282025.108 3086840.011 3074451.522 3507421.109 3243826.281 2860601.618 1.090944052 1.150446511 1.110402908 1.147319881 1.079087696 1.074756968 1.226113097 1.133966457 1 21.44788716 LQLEETMPS(ph)PYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQLEETMPSPYGR 13 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 LQLEETMPS(1)PYGR;LQLEETMPS(1)PYGR 115.1 0.00072459 86449000 179484 174898 195228 192436 205405 165495 213870 168377 250130 TRUE FALSE 168250.4168 187847.6299 199858.9004 197374.2336 189273.3199 213270.7199 181802.179 189399.2391 208381.6871 0.807414601 0.901459397 0.959100116 0.947176483 0.90830112 1.023461912 0.872447966 0.908905392 1 17.66886897 4.767963141 1.830434798 0.939704045 0.757908694 0.492620827 0.04419948 0.793974898 2.57799849 0.010560487 0.25458772 58608.8421 -4.767963141 -0.181795351 LQLERPVS(ph)PETQADLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQLERPVSPETQADLQR 17 1 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 LQLERPVS(0.995)PET(0.005)QADLQR;LQLERPVS(0.998)PET(0.002)QADLQR 237.5 1.95E-20 651230000 434400 413180 442440 415140 432500 408560 466320 372690 468450 TRUE FALSE 407211.6794 443772.2771 452934.8857 425793.1952 398533.1946 526504.6396 396399.6451 419221.1669 390262.6687 1.043429752 1.137111778 1.160589834 1.091042596 1.021192204 1.349103263 1.015725246 1.074202583 1 18.57408594 1.597416718 24.99999999 1.033707466 1.134914051 0.227680897 0.08998199 1.166492473 2783.269894 0.043342276 0.020401834 39.57461673 -1.597416718 0.101206585 LQLKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQLKPR 6 1 Q15056;K7EJP0;Q15056-2 Q15056;Q15056-2 EIF4H;TNNI3 Eukaryotic translation initiation factor 4H 0 ; 110.17 0.026384 1761540000 2678400 5800100 2355500 2354500 5636400 1567960 3160700 5231600 5811200 FALSE TRUE 2510763.725 6229545.439 2411373.572 2414920.456 5193739.88 2020604.598 2686782.378 5884776.776 4841273.178 0.518616412 1.286757679 0.498086657 0.498819291 1.072804547 0.417370498 0.554974338 1.215543218 1 22.20695507 1.233760069 24.99801868 1.107771722 0.716467569 0.267068539 0.283858673 185.4473646 965628.0111 0.240673489 0.067778793 17.13010675 -1.233760069 -0.391304153 LQLLEDDKENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LQLLEDDKENR 11 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;;;;; 195.77 5.72E-08 4450913000 7849595 5801347 6618570 6379007 6748829 5104855 7956246 5671902 6904050 FALSE TRUE 7358302.861 6230884.768 6775565.606 6542703.119 6218803.194 6578543.768 6763280.774 6380051.45 5751719.453 1.279322283 1.083308186 1.17800697 1.137521253 1.081207671 1.143752546 1.175871116 1.109242463 1 22.45556188 -5 0.243262361 0.157507944 1.159533109 0.441160817 0.055050427 170.3703444 1.697093944 71.15952434 0.077846942 1.00E-05 5 1.002025165 LQLLSNLFHGMDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LQLLSNLFHGMDK 13 0 Q7L2H7;J3KNJ2;E9PN86 Q7L2H7 EIF3M Eukaryotic translation initiation factor 3 subunit M 0 ;;; 215.96 2.83E-11 554575000 1472250 1691150 1605530 1546570 2026080 1320990 1884300 1689530 1544630 FALSE TRUE 1380104.501 1816364.506 1643613.93 1586257.605 1866959.85 1702338.369 1601766.708 1900471.54 1286821.274 1.072491206 1.411512649 1.277266675 1.232694576 1.450830731 1.322901946 1.244746835 1.476872956 1 20.29538026 -0.543609126 8.860335965 1.000000052 1.314278778 0.405752507 0.118290549 0 0 0.10042015 0.023669256 0.286016359 0.543609126 0.314278726 LQLNGNLQLELAQVLAQERPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 369.94 2.09E-112 1241355000 1504140 1301491 1470904 1463243 1558019 1324619 2004283 1447116 1560302 FALSE TRUE 1409998.562 1397854.748 1505794.537 1500792.293 1435658.472 1707015.002 1703759.371 1627791.618 1299877.516 1.084716479 1.075374203 1.158412634 1.154564391 1.104456731 1.313212192 1.310707624 1.252265385 1 20.30994426 2.25060406 24.99415759 1.254423626 1.117658988 0.195319393 0.092754407 230.4118915 478181.117 0.029188502 0.024247682 178.075454 -2.25060406 -0.136764638 LQLNIVEMKDENATLDGGDVLFTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQLNIVEMKDENATLDGGDVLFTGR 25 1 O94760;B4DYP1;O94760-2 O94760 DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1" 0 82.486 0.018411 17027000 14594 13088 12864 14140 18161 10964 15992 13397 23776 FALSE TRUE 13680.58759 14057.04914 13169.14015 14502.85634 16734.70832 14129.12881 13594.14806 15069.64494 19807.632 0.690672544 0.709678428 0.664851818 0.732185268 0.844861633 0.713317413 0.686308594 0.760799925 1 14.2737688 -5 0.287071023 3.152719039 0.701810359 0.763165955 0.048509191 120.7474503 1.143732381 155.3966167 0.054875605 1.00E-05 5 -2.450908679 LQLPVWEYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQLPVWEYK 9 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 114.5 0.0037891 83363000 466130 402510 406800 360140 449690 324790 449460 412270 374960 FALSE TRUE 436955.7554 432312.2592 416449.4881 369381.8021 414373.1614 418551.6005 382067.6456 463742.817 312376.7537 1.398810091 1.383945041 1.333164146 1.182488126 1.326517279 1.33989356 1.223098842 1.484562508 1 18.25292757 -1.780838014 2.648260157 0.914281295 1.326259978 0.602231348 0.085112315 10986697.76 8317500.845 6102357.687 0.019586726 0.016563877 1.780838014 0.411978683 LQLQGLDLS(ph)SR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LQLQGLDLSSR 11 0 P49454 P49454 CENPF Centromere protein F 1 LQLQGLDLS(0.948)S(0.052)R;LQLQGLDLS(0.965)S(0.035)R;LQLQGLDLS(0.937)S(0.063)R;LQLQGLDLS(0.95)S(0.05)R;LQLQGLDLS(0.921)S(0.079)R;LQLQGLDLS(0.914)S(0.086)R;LQLQGLDLS(0.934)S(0.066)R 192.4 1.48E-06 445188000 753070 887786 813313 900490 886936 710045 1134712 811042 852037 TRUE FALSE 705936.693 953518.5992 832605.1684 923598.0979 817279.6243 915023.4649 964572.4697 912302.379 709826.5203 0.994520031 1.343312164 1.172969936 1.301160314 1.151379388 1.289080414 1.358884801 1.285246962 1 19.43710695 3.245899799 24.84392617 1.256339439 1.207734493 0 0.131744236 684.7925696 2318074.569 0.03396484 0.045089218 1761.569569 -3.245899799 -0.048604946 LQLS(ph)PWESSVVNR ddPTM_SK-BR-3_Pertuzumab_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(0.996)PWES(0.003)SVVNR;LQLS(0.982)PWES(0.018)SVVNR;LQLS(0.963)PWES(0.037)SVVNR;LQLS(0.982)PWES(0.018)SVVNR 246.34 3.74E-17 717320000 749700 759670 852260 764130 861210 744280 901680 698980 997730 TRUE FALSE 702777.6153 815916.7572 872476.0097 783738.8695 793574.0406 959141.5536 766481.4548 786249.1916 831202.4174 0.845495153 0.981610183 1.049655284 0.942897726 0.954730188 1.153920554 0.922135738 0.945917836 1 19.66484032 4.734039795 3.922776411 0.998019108 0.83179077 0.327921855 0.066968644 0.272498227 8.602596905 0.015180822 0.129053855 54205.05573 -4.734039795 -0.166228338 LQLWDTAGQER ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;; 256.48 3.95E-20 2900661000 2170746 2780976 2231706 2257899 2844088 1948261 2662476 2679533 2751597 FALSE TRUE 2034882.883 2986882.357 2284643.12 2315840.511 2620724.801 2510692.323 2263262.441 3014078.593 2292337.685 0.887688972 1.302985322 0.996643355 1.010252777 1.14325425 1.095254133 0.987316335 1.314849297 1 21.12838815 LQMEAPHIIVGTPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LQMEAPHIIVGTPGR 15 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;J3QR64;J3QLN6;J3KS25;J3QKZ9 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;;;;;;; 194.58 4.58E-08 10916310000 5794140 6839370 6837230 6588270 6857230 5998810 7538930 5877490 6936060 FALSE TRUE 5431495.12 7345764.071 6999412.324 6757336.162 6318690.817 7730569.064 6408537.434 6611307.564 5778386.777 0.939967387 1.271248249 1.211309072 1.16941569 1.093504305 1.337842094 1.109053042 1.144144174 1 22.46223534 0.796027788 1.538286424 1.001167718 1.182459349 0.16576898 0.107656927 1.064619473 4.487755253 0.092298081 0.026808265 6.252126959 -0.796027788 0.181291631 LQPERGS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LQPERGSPK 9 1 S4R3H4;Q9UKV3;E7EQT4;A0A087WYN3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 LQPERGS(1)PK;LQPERGS(1)PK;LQPERGS(1)PK;LQPERGS(1)PK;LQPERGS(1)PK;LQPERGS(1)PK;LQPERGS(1)PK;LQPERGS(1)PK 96.334 0.01106 16578700000 8607880 5609450 6395760 6411240 7345490 4516290 7792070 5553400 10738840 TRUE FALSE 8069128.156 6024779.515 6547470.447 6575763.273 6768604.846 5820069.607 6623721.442 6246754.215 8946458.228 0.901935487 0.673426216 0.731850558 0.735013019 0.756568094 0.650544546 0.740373595 0.698237677 1 23.09288522 -0.961472039 5.083849019 1.00000143 0.727722495 0.598550222 0.067648071 9.60E-07 1.96E-07 0.057298736 0.013505371 0.109276798 0.961472039 -0.272278935 LQPFATEADVEEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQPFATEADVEEALR 15 0 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ; 155.98 5.14E-06 34911000 35401 38604 31092 39131 39384 32491 39810 29599 41532 FALSE TRUE 33185.3146 41462.28033 31829.51692 40135.16771 36290.93951 41870.62425 33840.86008 33294.50031 34600.04089 0.959112005 1.198330385 0.919927148 1.159974574 1.048869844 1.210132219 0.978058384 0.962267658 1 15.07848612 1.602865749 25 0.977602621 1.080031797 0.209406534 0.093852506 0.707431095 3520.789653 0.044342178 0.021521402 40.07428195 -1.602865749 0.102429176 LQPFHS(ph)TELEDDAIYSVHVPAGLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LQPFHSTELEDDAIYSVHVPAGLYR 25 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QQI0 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 LQPFHS(0.95)T(0.05)ELEDDAIYSVHVPAGLYR;LQPFHS(0.99)T(0.01)ELEDDAIYSVHVPAGLYR;LQPFHS(0.964)T(0.036)ELEDDAIYSVHVPAGLYR;LQPFHS(0.938)T(0.062)ELEDDAIYSVHVPAGLYR 270.14 1.38E-46 883630000 214589 325479 305353 298152 278509 264672 369963 274754 322398 TRUE FALSE 201158.2575 349577.8038 312596.1174 305803.0851 256636.0266 341078.5098 314490.4827 309057.6417 268587.691 0.748948162 1.301540672 1.16385124 1.138559567 0.955501816 1.26989628 1.170904301 1.150676863 1 18.03503366 LQPFHSTELEDDAIY(ph)SVHVPAGLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQPFHSTELEDDAIYSVHVPAGLYR 25 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QQI0 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 LQPFHSTELEDDAIY(0.832)S(0.168)VHVPAGLYR 177.5 2.33E-17 33240000 20671 32735 28644 31020 38651 22757 34013 29997 31514 TRUE FALSE 19377.23901 35158.73346 29323.44921 31816.02572 35615.50637 29326.57647 28913.06641 33742.19148 26254.10981 0.738064979 1.339170656 1.116908911 1.211849343 1.356568805 1.117028027 1.101277728 1.2852156 1 14.68025566 -1.283365205 5.206854062 0.999968222 1.171212371 0.070554511 0.174994419 5.69E-05 7.84E-06 0.149440072 0.035216832 0.052075661 1.283365205 0.171244149 LQPQEIS(ph)PPPTANLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LQPQEISPPPTANLDR 16 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-6;B4DWJ1 E7ESA6 PTK2 Focal adhesion kinase 1 1 LQPQEIS(0.995)PPPT(0.005)ANLDR;LQPQEIS(0.997)PPPT(0.003)ANLDR;LQPQEIS(0.999)PPPT(0.001)ANLDR;LQPQEIS(0.999)PPPT(0.001)ANLDR 179.81 2.69E-09 438763000 239794 251782 280000 306748 284434 180556 213183 188609 248895 TRUE FALSE 224785.7216 270424.2013 286641.7322 314619.673 262095.701 232679.5861 181218.1882 212157.2488 207352.8166 1.084073635 1.304174237 1.38238649 1.517315647 1.264008396 1.122143359 0.873960582 1.023170325 1 17.66172812 2.106555685 2.7861773 0.957282769 1.331810975 0.65725143 0.113817188 0.150407859 2.314986208 0.051192783 0.03284864 127.8073074 -2.106555685 0.374528206 LQPS(ph)SS(ph)PENSLDPFPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQPSSSPENSLDPFPPR 17 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 2 LQPS(0.588)S(0.515)S(0.868)PENS(0.029)LDPFPPR 65.943 0.061653 9986400 30953 27615 32537 30267 29628 28806 38353 31262 36123 TRUE FALSE 29015.70698 29659.64333 33308.79301 31043.70246 27301.13639 37121.82457 32602.3237 35165.12952 30093.83794 0.964174362 0.985571976 1.106831009 1.031563423 0.90720022 1.233535738 1.083355462 1.168515946 1 14.87718049 2.238589587 25 1.127241268 1.013399798 0.369749725 0.077927074 0.859266826 741575.5327 0.026314943 0.020704797 173.2166307 -2.238589587 -0.11384147 LQPS(ph)SSPENSLDPFPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQPSSSPENSLDPFPPR 17 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 1 LQPS(0.354)S(0.354)S(0.286)PENS(0.005)LDPFPPR 61.692 0.051934 0 57157 63854 60305 60115 64151 55254 58300 49680 68769 TRUE FALSE 53579.6454 68581.8166 61735.46308 61657.65267 59112.83923 71204.93283 49558.45623 55882.65736 57291.00964 0.935219081 1.197078164 1.077576804 1.076218644 1.031799572 1.24286399 0.865030247 0.975417569 1 15.80602114 1.704004771 11.68370771 0.941597878 1.10048507 0.367554397 0.090205612 0.106635386 27.679795 0.038211816 0.020865 50.58302192 -1.704004771 0.158887192 LQPSSS(ph)PENSLDPFPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LQPSSSPENSLDPFPPR 17 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 1 LQPS(0.022)S(0.253)S(0.726)PENSLDPFPPR;LQPS(0.002)S(0.055)S(0.943)PENSLDPFPPR;LQPS(0.025)S(0.143)S(0.833)PENSLDPFPPR;LQPS(0.01)S(0.092)S(0.898)PENSLDPFPPR;LQPS(0.005)S(0.029)S(0.966)PENSLDPFPPR;LQPSSS(1)PENSLDPFPPR 327.7 6.80E-72 2088060000 1197920 1166248 1259865 1200947 1336172 1171953 1431853 1159668 1540152 TRUE FALSE 1122944.326 1252598.215 1289749.593 1231765.333 1231234.441 1510276.806 1217159.935 1304455.103 1283090.681 0.875187032 0.976235143 1.005189743 0.959998659 0.959584898 1.177061628 0.948615677 1.016650749 1 20.2911917 LQQEFEDKLEVEQQNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQQEFEDKLEVEQQNKR 17 2 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 125.12 2.70E-05 88738000 165430 112520 127510 126510 154970 103080 177910 126600 213880 FALSE TRUE 155076.0316 120851.0979 130534.5974 129756.4608 142799.2813 132837.5226 151234.0471 142406.2887 178182.0463 0.870323553 0.678245089 0.732591191 0.728224103 0.801423512 0.745515754 0.848761423 0.799217944 1 17.44299245 0.566944983 0.503596141 1.011302296 0.735700461 0.624859449 0.05584212 0.994330555 0.485065001 0.078328485 0.026980421 3.689308589 -0.566944983 -0.275601835 LQQELDDLLVDLDHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 17 LQQELDDLLVDLDHQR 16 0 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;;;;;;;;;;; 292.38 1.45E-45 15802060000 1626702.5 1948067.3 1894399.2 1871908.8 1991773.6 1646504.9 2205297.1 1730590.7 1838821 FALSE TRUE 1524890.094 2092304.23 1939335.244 1919945.149 1835347.736 2121824.136 1874633.273 1946658.758 1531909.896 0.995417615 1.365814161 1.265959081 1.253301617 1.198078125 1.385084163 1.223722934 1.270739724 1 20.54690001 -1.314829486 3.263584795 0.998500902 1.259944037 0.334723709 0.106551485 14960567.31 20479323.85 218200.3967 0.022678605 0.04843625 1.314829486 0.261443135 LQQELDDLTVDLDHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LQQELDDLTVDLDHQR 16 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ;;; 302.34 5.09E-46 164736000 160723 194200 183338 193557 214603 162945 210012 178965 232218 FALSE TRUE 150663.6343 208578.7701 187686.8639 198524.0003 197748.946 209984.5763 178522.6503 201309.1742 193459.3156 0.778787177 1.078153148 0.970161935 1.026179586 1.022173295 1.085419824 0.922791698 1.040576276 1 17.56167067 4.748228631 24.97641875 1.014312389 0.77878705 0.712028566 0.04778944 712.9463477 1841792.734 0.01079656 0.141390457 56005.23585 -4.748228631 -0.235525339 LQQGAGLESPQGQPEPGAAS(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LQQGAGLESPQGQPEPGAASPQR 23 0 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 LQQGAGLESPQGQPEPGAAS(1)PQR;LQQGAGLESPQGQPEPGAAS(1)PQR;LQQGAGLESPQGQPEPGAAS(1)PQR;LQQGAGLESPQGQPEPGAAS(1)PQR 237.92 2.34E-37 2302920000 1915290 1720790 1908580 1836190 1815180 1509390 2078240 1581220 2099660 TRUE FALSE 1795415.418 1848199.082 1953852.419 1883309.744 1672623.085 1945126.39 1766627.205 1778638.798 1749213.182 1.026413153 1.056588815 1.116989307 1.076661075 0.956214544 1.112000762 1.009955347 1.016822201 1 20.73827469 LQQHIQELEAHLEAEEGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LQQHIQELEAHLEAEEGAR 19 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 ;;; 191.79 5.13E-15 687971000 262538 361365 291471 337915 386329 307417 342823 317260 345628 FALSE TRUE 246106.2152 388120.8406 298384.8298 346586.471 355988.2787 396163.2974 291419.8738 356870.6094 287940.454 0.854712187 1.3479205 1.036272693 1.203674115 1.236326031 1.375851472 1.012083817 1.239390313 1 18.13541097 -1.585304662 2.524028533 0.984808456 1.169590554 0.093538001 0.15866207 23358482.1 20472469.78 2364717.509 0.036248496 0.025983362 1.585304662 0.184782098 LQQLFNHTMFILEQEEYQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQQLFNHTMFILEQEEYQR 19 0 P35579;P35579-2;A0A494C024;P35580;P35580-5;P35580-2;P35580-3;P35580-4;P35749;P35749-2;P35749-4;P35749-3 P35579;P35580;P35749 MYH9;MYH10;MYH11 Myosin-9;Myosin-10;Myosin-11 0 ; 284.48 6.51E-40 1243060000 614530 709470 630500 657520 671790 596530 752750 629220 451150 FALSE TRUE 576067.6643 761999.897 645455.7577 674393.0764 619030.3233 768738.5271 639882.1257 707779.5021 375850.1505 1.53270569 2.027403464 1.717322068 1.794313706 1.647013637 2.045332498 1.702492669 1.883142793 1 18.51979806 -1.197305089 4.222215451 0.999670636 1.806914276 0.707338923 0.160248935 10330222.41 2929416.63 31294.9629 0.032740042 0.063488477 1.197305089 0.80724364 LQQLGEAHQAETEVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQQLGEAHQAETEVLR 16 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 198.85 3.97E-11 670120000 265345 287300 327080 301910 295590 269981 327270 274493 269960 FALSE TRUE 248737.5301 308571.9909 334838.4921 309657.5217 272375.5538 347920.1319 278198.9017 308764.0553 224901.932 1.105982185 1.37202908 1.48881999 1.376855765 1.211085878 1.546985963 1.23697871 1.372883072 1 17.77893653 -0.315996508 0.802911013 0.984158543 1.358614141 0.391350286 0.130692607 11.23717807 5.640608214 0.689805343 0.040303599 0.483062686 0.315996508 0.374455598 LQQQAALS(ph)PTTAPAVSSVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQQQAALSPTTAPAVSSVSK 20 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR30 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LQQQAALS(0.935)PT(0.035)T(0.03)APAVSSVSK;LQQQAALS(0.798)PT(0.191)T(0.011)APAVSSVSK 244.91 6.65E-30 240110000 666560 552960 631440 604620 720010 616620 894220 686560 1180920 TRUE FALSE 624841.1994 593901.7338 646418.055 620135.5728 663463.319 794628.184 760140.0125 772278.5273 983816.823 0.63511945 0.603671049 0.657051231 0.630336419 0.674376879 0.807699325 0.772643845 0.78498203 1 19.9080302 1.145749033 0.352895808 1.02682805 0.590240875 0.922842326 0.0330079 0.341727674 0.131595407 0.056466965 0.035710005 13.98778774 -1.145749033 -0.436587174 LQQQHSEQPPLQPS(ph)PVMTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LQQQHSEQPPLQPSPVMTR 19 0 A0A0A0MSK5;J3KN66;Q5JTV8;Q5JTV8-3;Q5JTV8-2;H0YDU3 A0A0A0MSK5 TOR1AIP1 Torsin-1A-interacting protein 1 1 LQQQHSEQPPLQPS(1)PVMTR;LQQQHSEQPPLQPS(0.999)PVMT(0.001)R;LQQQHSEQPPLQPS(1)PVMTR;LQQQHSEQPPLQPS(1)PVMTR;LQQQHSEQPPLQPS(1)PVMTR;LQQQHSEQPPLQPS(1)PVMTR;LQQQHSEQPPLQPS(1)PVMTR;LQQQHSEQPPLQPS(1)PVMTR 211.5 8.14E-17 10271550000 4318520 4569680 3900220 3977380 4504510 3800590 5411270 4185940 4383330 TRUE FALSE 4048231.542 4908023.862 3992735.06 4079446.304 4150743.955 4897758.636 4599900.299 4708563.823 3651723.906 1.108580946 1.344029283 1.093383608 1.117128899 1.13665328 1.34121822 1.25965172 1.289408494 1 21.80014626 2.27038186 24.99936533 1.249326905 1.174031623 0.039981418 0.113843584 466.5259874 366509.9362 0.037080994 0.031021568 186.3725124 -2.27038186 -0.075295282 LQQQQRPEDAEDGAEGGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQQQQRPEDAEDGAEGGGK 19 1 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 165.17 2.04E-11 422830000 114560 84467 99288 93492 96060 74961 121800 87749 128510 FALSE TRUE 107389.8941 90721.02457 101643.1582 95891.163 88515.83509 96601.02381 103537.2207 98704.65581 107060.8508 1.003073423 0.84737814 0.949396138 0.895669727 0.826780606 0.902300169 0.967087595 0.921949107 1 16.7080715 1.303406418 1.247462738 0.986638067 0.901180213 0.211683765 0.052217547 0.58633878 1.784540164 0.045144243 0.014600621 20.10973828 -1.303406418 -0.085457854 LQQQQRPEDAEDGAEGGGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQQQQRPEDAEDGAEGGGKR 20 2 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 67.866 0.01225 113340000 84848 81608 82794 78713 95922 65746 102130 86336 115490 FALSE TRUE 79537.51514 87650.34123 84757.91278 80732.90884 88388.67305 84725.8029 86816.55463 97115.23965 96213.97291 0.826673224 0.910993888 0.88093143 0.839097549 0.91866774 0.880597696 0.902327926 1.009367317 1 16.55395881 1.297992661 3.714547921 1.007600371 0.881740335 0.771500699 0.028386537 0.098773267 2.336428639 0.02147398 0.006673688 19.86061358 -1.297992661 -0.125860036 LQQTEAELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQQTEAELR 9 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 79.986 0.059073 213350000 152540 221420 177750 174150 212280 136910 191840 178340 233210 FALSE TRUE 142992.7937 237814.1672 181966.3139 178618.9838 195608.3851 176433.6945 163075.373 200606.1416 194285.7444 0.735992206 1.224043318 0.936591177 0.919362274 1.006807708 0.908114463 0.839358407 1.032531451 1 17.56782052 3.707506435 22.87997538 0.935193579 1.034510132 0 0.130813327 320.5756424 373939.7786 0.031973864 0.049643853 5099.251527 -3.707506435 0.099316553 LQQTVPADAS(ph)PDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQQTVPADASPDSK 14 0 Q9NS56-2;Q9NS56 Q9NS56-2 TOPORS E3 ubiquitin-protein ligase Topors 1 LQQTVPADAS(0.999)PDS(0.001)K;LQQTVPADAS(1)PDSK 94.461 0.0043595 209372000 661400 441080 540450 511620 551890 421360 648950 472680 554760 TRUE FALSE 620004.1546 473738.0221 553269.7292 524749.0354 508546.7856 542999.7918 551645.9721 531695.1385 462166.9721 1.341515496 1.025036514 1.197120873 1.135410073 1.100352938 1.174899602 1.193607517 1.150439496 1 18.81805464 0.930475432 20.62506018 0.999999999 1.155966808 0.286803495 0.080660792 6361.052029 1887066.885 0.069802204 0.017450551 8.520703081 -0.930475432 0.155966809 LQQVLQMESHIQSTSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQQVLQMESHIQSTSDR 17 0 Q14974;Q14974-2;J3KTM9;J3QKQ5 Q14974 KPNB1 Importin subunit beta-1 0 ; 164.58 2.58E-09 714180000 435980 482090 472320 494050 530170 405520 503190 408770 490710 FALSE TRUE 408692.79 517784.4452 483523.6534 506728.1594 488532.5868 522587.0409 427741.3309 459805.8343 408807.3309 0.999719817 1.266573288 1.182766592 1.239528064 1.195019144 1.27832111 1.046315216 1.124749484 1 18.64106154 1.67637876 7.88387628 1.064744901 1.202376413 0.373906757 0.082404045 0.118633413 13.27990696 0.036406399 0.019030269 47.46557647 -1.67637876 0.137631512 LQQWYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 155.81 0.02287 6638540000 2700400 7098570 2284270 2362330 6694240 1532490 3008370 5567140 5486800 FALSE TRUE 2531386.784 7624155.509 2338453.963 2422951.387 6168501.394 1974894.985 2557292.847 6262209.684 4571017.634 0.553790641 1.667933952 0.511582792 0.530068265 1.349480988 0.432047116 0.559458101 1.36998152 1 22.12408395 3.918428806 9.681890717 0.777613613 1.177448827 0.060919451 0.428950261 0.753171605 120.0153009 0.100898942 0.182396497 8287.600457 -3.918428806 0.399835214 LQS(ph)IGTENTEENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQSIGTENTEENR 13 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 LQS(1)IGTENTEENR 311.26 1.42E-50 279070000 561270 631410 548810 670710 579780 356610 678610 455930 446150 TRUE FALSE 526141.1126 678160.2534 561828.0324 687921.5541 534246.4175 459557.5179 576858.7304 512853.8641 371684.6828 1.415557694 1.824557978 1.511571659 1.850820295 1.437364633 1.236417693 1.552011038 1.379808983 1 18.50371971 0.624378398 0.325319755 0.913251175 1.691968568 0.532555991 0.171570763 1.890589335 0.460029555 0.476984513 0.18793248 4.210933642 -0.624378398 0.778717393 LQS(ph)IGTENTEENRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQSIGTENTEENRR 14 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 LQS(1)IGTENTEENRR;LQS(1)IGTENTEENRR 225.86 1.60E-12 1178410000 379860 430580 393650 511300 442240 315620 440620 337010 333560 TRUE FALSE 356085.2407 462460.5912 402987.5639 524420.8236 407508.2543 406734.3703 374553.1215 379086.4404 277886.6811 1.281404489 1.664205673 1.450186681 1.887175094 1.466454789 1.463669898 1.347862805 1.364176357 1 18.08413716 0.998494908 0.770763815 1.008257412 1.565199359 0.527885053 0.159414828 0.506251196 0.677706039 0.140804855 0.052870597 9.96540396 -0.998494908 0.556941947 LQSECHPDTCTQMTATEQWIFLCAAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQSECHPDTCTQMTATEQWIFLCAAHK 27 0 S4R3N1;Q9Y3A3-2;Q9Y3A3-3;Q9Y3A3 S4R3N1 HSPE1-MOB4;MOB4 MOB-like protein phocein 0 ; 334.27 1.40E-95 170619000 203952 261310 274680 255460 295450 240950 305400 259310 243220 FALSE TRUE 191187.0084 280657.6643 281195.5393 262015.5361 272246.5488 310508.3535 259608.1052 291685.4243 202625.0107 0.943550886 1.385108695 1.38776323 1.2931056 1.343597949 1.53242856 1.281224387 1.439533171 1 17.62845274 -1.071043122 4.331475348 0.99997084 1.340998905 0.301462224 0.154317614 9288078.891 2296661.947 2832.023703 0.03232038 0.084909616 1.071043122 0.341028065 LQSEVAELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQSEVAELK 9 0 P53990-2;P53990;P53990-4;P53990-5;J3KR23;H3BQF7;H3BMU1;H3BUI0;P53990-3;F5GXM3 P53990-2 IST1 IST1 homolog 0 90.709 0.026165 202460000 269880 219510 227800 230530 249890 187750 282990 229800 283330 FALSE TRUE 252988.6925 235762.7488 233203.5236 236445.7901 230264.6474 241950.3771 240558.2767 258491.0359 236040.3926 1.071802541 0.998823744 0.987981426 1.001717492 0.975530691 1.025038022 1.0191403 1.095113565 1 17.84867424 1.549664337 3.259790832 1.049343734 1.004661053 0.136538275 0.034677909 0.29534634 7.019358957 0.021215469 0.008304433 35.45392622 -1.549664337 -0.044682681 LQSFDS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQSFDSPER 9 0 P78332;E9PGM9;P78332-2 P78332 RBM6 RNA-binding protein 6 1 LQSFDS(1)PER;LQSFDS(1)PER 169.33 6.14E-05 167511000 320250 326260 307830 337490 383400 275550 399080 323690 441320 TRUE FALSE 300206.1242 350416.6299 315131.873 346150.5648 353289.3106 355096.8118 339241.6589 364103.409 367660.841 0.816530048 0.953097504 0.857126563 0.941494242 0.960910903 0.965827122 0.922702722 0.990324148 1 18.488016 8 0.139802417 1.017125071 0.477763234 0.545344424 0.038618502 61.34917735 0.571423866 0.154830156 6.617359417 99999999.92 -8 -0.539361837 LQSGQFGDVGFNPYEPAVDFFSGDVMIHPVTNRPADKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQSGQFGDVGFNPYEPAVDFFSGDVMIHPVTNRPADKR 38 2 Q14137;Q14137-2;A0A075B729 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 39.375 0.084464 87960000 23636 25421 24983 24560 30120 23924 30191 25730 30362 FALSE TRUE 22156.66495 27303.19729 25575.60856 25190.25118 27754.4967 30830.47043 25664.13983 28942.44714 25294.38605 0.875951877 1.079417276 1.011117981 0.995883084 1.097259156 1.218866129 1.014618017 1.14422414 1 14.6265296 2.732126516 22.70291027 1.099430383 1.008817578 0.288680174 0.078997776 201.3339695 710409.1068 0.02335632 0.022566723 539.6678123 -2.732126516 -0.090612805 LQSIGTENTEENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQSIGTENTEENR 13 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 308.12 3.79E-50 277170000 105140 124140 96002 112260 113680 91138 120740 94520 89815 FALSE TRUE 98559.47508 133331.4548 98279.21278 115140.7817 104752.0314 117448.0611 102636.1579 106321.0301 74824.29627 1.317212189 1.78192728 1.313466583 1.53881543 1.399973492 1.569651396 1.371695599 1.4209426 1 16.19121918 -3.145508234 0.231122448 4.85E-13 1.546961608 0.53001788 0.138637868 43.80748011 0.944505511 21.29411406 0.225101681 0.000715306 3.145508234 1.546961608 LQSIGTENTEENRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LQSIGTENTEENRR 14 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;; 301.91 1.00E-43 2.31286E+11 20086290 24315150 20077230 21601490 22081520 18102640 23409060 17994390 19126750 FALSE TRUE 18829124.96 26115469.01 20553471.38 22155820.8 20347326.49 23328578.3 19899088.77 20241029.2 15934371.86 1.181667224 1.638939347 1.289882749 1.390442058 1.276945629 1.464041288 1.248815388 1.270274685 1 23.92563881 0.201927234 0.362979686 0.932139476 1.426682208 0.439333949 0.126702265 3.048370022 0.647579168 0.437608708 0.099917023 1.591941975 -0.201927234 0.494542732 LQSVEYVVFDEADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQSVEYVVFDEADR 14 0 Q8TDD1-2;Q8TDD1;F8VRX4 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 0 ; 122.45 0.0013612 0 20012.1 19777.4 19725.5 22223 15984.1 20135 25684.9 20012.7 16347.7 FALSE TRUE 18759.57838 21241.73927 20193.39818 22793.2798 14728.77326 25947.64764 21833.68769 22511.32965 13619.16326 1.377439864 1.559694885 1.482719444 1.673618222 1.081474169 1.905230677 1.60315926 1.652915764 1 13.73335045 4.745919136 22.01606998 1.531318294 1.377439451 0.002412713 0.272403452 700.7141251 2096172.707 0.056895577 0.544705764 55708.20122 -4.745919136 -0.153878843 LQTLS(ph)PSHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LQTLSPSHK 9 0 Q96GY0;H0YAP0 Q96GY0 ZC2HC1A Zinc finger C2HC domain-containing protein 1A 1 LQT(0.002)LS(0.993)PS(0.005)HK;LQT(0.029)LS(0.967)PS(0.004)HK;LQTLS(1)PSHK;LQTLS(1)PSHK 139.46 7.18E-05 1846620000 1736612 1430833 1659829 1594747 1650036 1243999 1845140 1251671 1726050 TRUE FALSE 1627920.555 1536773.364 1699200.928 1635670.908 1520448.828 1603121.317 1568478.386 1407944.88 1437961.104 1.13210333 1.068716921 1.181673776 1.137493151 1.057364364 1.114857218 1.090765516 0.979125844 1 20.45559322 1.326277317 3.637764475 0.988002306 1.115386995 0.679055622 0.035180532 0.134507821 2.908438243 0.02852487 0.009072648 21.19714237 -1.326277317 0.127384689 LQTMKEELDFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LQTMKEELDFQK 12 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 207.39 7.21E-08 3592400000 7328800 6618500 6966700 7290000 8675600 4950800 8801400 6550100 12805500 FALSE TRUE 6870103.49 7108540.627 7131953.414 7477073.742 7994253.372 6380015.59 7481711.778 7367894.404 10668179.32 0.643980878 0.66633119 0.668525828 0.700876271 0.749354986 0.598041652 0.701311025 0.690642159 1 23.34681064 -5 0.414028685 6.743167064 0.670952154 0.871109241 0.039073826 272.6120478 1.811427776 1421.494934 0.021460409 1.00E-05 5 -6.07221491 LQVEEVHQLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LQVEEVHQLSR 11 0 Q9NR28-2;Q9NR28;Q9NR28-3 Q9NR28-2 DIABLO "Diablo homolog, mitochondrial" 0 ;; 128.31 0.0011632 1026960000 538158 639353 608710 664610 754060 560447 662800 569129 525060 FALSE TRUE 504475.6514 686691.3614 623148.8887 681665.0178 694839.1693 722238.9508 563419.2931 640186.0085 437424.094 1.153287298 1.569852623 1.424587482 1.558361844 1.588479416 1.651118356 1.288039001 1.463536228 1 18.73867316 0.426047487 1.003569454 0.99978073 1.485826722 0.483316007 0.149536887 1.741384506 2.300727598 0.135470203 0.042097555 2.667150285 -0.426047487 0.486045992 LQVVDQPLPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LQVVDQPLPVR 11 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 129.39 0.00057237 276977000 602880 724846 731935 714753 769870 669575 792900 618372 760640 FALSE TRUE 565146.817 778514.352 749296.8438 733094.7721 709407.5157 862870.4329 674012.0059 695577.1054 633684.2701 0.8918429 1.228552433 1.182445074 1.156877023 1.119496805 1.361672482 1.063640109 1.097671409 1 19.27340468 1.592247046 24.99999983 1.060452263 1.169902988 0.137950583 0.118062824 1.632906914 2606.491434 0.057456966 0.02674434 39.10632868 -1.592247046 0.109450725 LQVVLEHMPVGPDAILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LQVVLEHMPVGPDAILR 17 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4;H0Y710;H0Y4L1 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 0 101.67 0.0010304 60650000 117910 151300 146000 155960 156320 129470 158700 134220 149670 FALSE TRUE 110530.2236 162502.4094 149463.1889 159962.1976 144043.2578 166845.8872 134904.4083 150977.6625 124689.1101 0.886446487 1.30326064 1.198686789 1.282888277 1.15521923 1.3380951 1.081926146 1.210832785 1 16.92797595 -1.287883734 4.180438093 0.999794141 1.195221505 0.158118105 0.129015302 0.000217834 3.71E-05 0.109930398 0.025883653 0.05153666 1.287883734 0.195427364 LRAETEQGEQQR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 217.88 3.25E-11 2435090000 689010 1033910 824360 1029660 1237140 665370 1074700 835450 1437360 FALSE TRUE 645886.094 1110461.772 843914.2085 1056082.819 1139980.015 857451.5176 913558.712 939757.7716 1197455.33 0.539382203 0.927351312 0.704756317 0.881939219 0.952002121 0.716061381 0.762916736 0.784795681 1 20.19154041 -2.419567588 2.001647036 2.437248544 0.792201737 0.239680463 0.120244485 5909865.816 463812.9073 38509615.94 0.026345116 0.003805681 2.419567588 -1.645046807 LRAPIICVLGHVDTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LRAPIICVLGHVDTGK 16 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 99.566 0.0014123 217436000 211969 205549 196097 192471 245440 160771 250220 214180 313990 FALSE TRUE 198702.2387 220768.0618 200748.5134 197410.1317 226164.1325 207182.9778 212701.8339 240920.8445 261583.0405 0.759614378 0.843969324 0.767437037 0.754674811 0.864597842 0.792035208 0.81313312 0.921010949 1 17.99690948 1.090093502 2.43136102 0.999370547 0.799409877 0.799244686 0.03489965 0.107743648 1.261678777 0.030749619 0.008451289 12.30533673 -1.090093502 -0.19996067 LRDADPILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LRDADPILR 9 1 P31327;P31327-3;P31327-2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 ; 106.4 0.0026831 622980000 466450 538940 468890 438760 766030 395310 448990 617210 1047740 FALSE TRUE 437255.7271 578843.6784 480012.2922 450019.3244 705869.0938 509429.5797 381668.1177 694270.0271 872865.4253 0.500942888 0.663153404 0.549927031 0.515565529 0.808680323 0.583629005 0.437258834 0.795391829 1 19.73539972 1.003277958 5.853864536 0.999704681 0.584351871 0.660724366 0.100692563 0.075650977 11.1163932 0.094333345 0.023739694 10.07576333 -1.003277958 -0.415352811 LRDDFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LRDDFEK 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;; 143.73 0.0021903 2648900000 3606810 2871290 3230750 3158370 3234950 2588890 3817510 2852900 3758280 FALSE TRUE 3381066.2 3083883.299 3307384.916 3239419.121 2980890.076 3336260.516 3245109.816 3209090.845 3130998.789 1.079868256 0.98495193 1.056335419 1.034628034 0.952057244 1.065557907 1.036445567 1.02494158 1 21.57819152 LRDDTELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LRDDTELR 8 1 P16930;H0YLC7;P16930-2 P16930 FAH Fumarylacetoacetase 0 129.42 0.00099537 170190000 218350 249200 251600 215760 199570 177480 252780 213550 165060 FALSE TRUE 204683.8633 267651.0273 257568.0708 221296.7669 183896.5772 228715.5949 214877.9857 240212.1876 137510.4197 1.488497117 1.946405428 1.873080392 1.609309079 1.337328311 1.663260103 1.562630572 1.746865351 1 17.06918142 -2.526009837 0.199955189 1.54E-13 1.834944858 0.537281126 0.184172394 33.40848384 0.807302393 15.46053264 0.497929883 0.002978449 2.526009837 1.834944858 LRDDTELRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LRDDTELRK 9 2 P16930;H0YLC7;P16930-2 P16930 FAH Fumarylacetoacetase 0 ; 64.73 0.038563 922740000 415600 443870 427000 434670 502140 369820 525800 396750 507780 FALSE TRUE 389588.3379 476734.5966 437128.6416 445824.3681 462703.9499 476581.0305 446961.1713 446285.1109 423028.2376 0.92095114 1.126956913 1.033332063 1.053887964 1.093789749 1.126593896 1.056575263 1.054977118 1 18.69039444 4.75173681 24.66984338 1.072683988 0.920951023 0.57650879 0.039518119 1284.845094 2405568.658 0.008712141 0.168871302 56459.47168 -4.75173681 -0.151732966 LRDEELAELEDALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LRDEELAELEDALR 14 1 Q15628-2;Q15628 Q15628-2 TRADD Tumor necrosis factor receptor type 1-associated DEATH domain protein 0 93.494 0.0041403 12089000 7675.3 9132.6 6796.6 8591.6 9081.5 8492.4 10816 7988.3 9883.1 FALSE TRUE 7194.916674 9808.787206 6957.818562 8812.075002 8368.275623 10944.01802 9194.241211 8985.656839 8233.546763 0.873853867 1.191319791 0.845057271 1.070264766 1.016363405 1.329198501 1.116680512 1.091347034 1 13.00729832 2.431096468 24.99963593 1.150846475 1.006861841 0.21720647 0.12525002 171.9545323 93400.88335 0.040142952 0.033586018 269.8338739 -2.431096468 -0.143984634 LRDENPDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LRDENPDFR 9 1 E9PNW8;Q8WVX9 E9PNW8 FAR1 Fatty acyl-CoA reductase 1 0 ; 124.67 0.00047714 621870000 888340 1056350 816780 790800 1274500 681100 1013570 1207470 1155920 FALSE TRUE 832740.3851 1134563.253 836154.4073 811093.2668 1174405.911 877722.5133 861594.588 1358225.287 962989.4845 0.864745045 1.178167853 0.868290278 0.842265964 1.219541781 0.911455969 0.8947082 1.410425876 1 19.87716052 1.259532741 24.99986728 1.205213295 0.976498542 0.267854565 0.16231035 265.4799621 316467.5774 0.099314207 0.036185665 18.17744091 -1.259532741 -0.228714754 LRDFLLDIEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LRDFLLDIEDR 11 1 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 0 110.38 0.0016437 22934000 28438 44997 30405 30534 42831 22108 27161 38888 40421 FALSE TRUE 26658.11634 48328.6247 31126.22096 31317.55413 39467.22603 28490.22071 23088.4602 43743.2524 33674.47397 0.791641656 1.435170888 0.924326865 0.930008711 1.17202205 0.846047981 0.685636848 1.299003288 1 15.03936779 3.728707575 24.53516484 0.948320458 1.165485542 0.032213721 0.228170117 106.4622465 1646569.301 0.056072177 0.094714467 5354.36009 -3.728707575 0.217165083 LRDLEDSLAR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;;;; 237.68 3.20E-12 9494188000 3555429 5479593 4259789 4517001 6178549 3154445 4908218 4428111 8505310 FALSE TRUE 3332901.046 5885307.767 4360833.207 4632914.893 5693310.685 4065082.063 4172276.277 4980970.406 7085718.815 0.470368799 0.830587259 0.615439777 0.653838377 0.803490914 0.573700731 0.588828937 0.702959084 1 22.75648278 0.961489431 21.8033243 1.000000002 0.659992851 0.517608742 0.105506668 1021.983501 578612.7127 0.09527744 0.02381936 9.151439888 -0.961489431 -0.340007151 LRDPDSHIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LRDPDSHIVK 10 1 A0A1B0GUA3;Q96EK5 A0A1B0GUA3 KIAA1279 KIF1-binding protein 0 53.08 0.087686 74214000 44573 49656 49572 47907 52475 35488 53125 54339 51369 FALSE TRUE 41783.2555 53332.58191 50747.87125 49136.37473 48353.82517 45732.8095 45159.39944 61123.34376 42795.18204 0.976354195 1.246228649 1.185831414 1.148175388 1.129889461 1.068643883 1.055244943 1.428276288 1 15.38516076 2.934993529 3.832070239 1.127387534 1.166910003 0 0.132671357 1.305277286 37.64148427 0.038686987 0.042538698 860.9809231 -2.934993529 0.039522469 LRDQELILFADLLCQYHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LRDQELILFADLLCQYHR 18 1 Q14676;Q14676-3;Q14676-2;Q14676-4;A2AB05 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 0 111.77 0.00017734 71062000 68729 102790 76131 68695 120820 66296 88348 89287 65310 FALSE TRUE 64427.37457 110400.6786 77936.86327 70457.83 111331.2846 85434.57897 75101.03758 100434.6785 54409.33908 1.184123455 2.029075898 1.432417019 1.294958387 2.04617969 1.570219018 1.380296818 1.845908813 1 15.73156668 -1.662381903 2.861950196 0.934348415 1.607811798 0.286952767 0.295831921 43688240.42 44125957.11 21161640.82 0.065947675 0.021757956 1.662381903 0.673463383 LRDTEEMLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LRDTEEMLSK 10 1 Q9H444 Q9H444 CHMP4B Charged multivesicular body protein 4b 0 ;;;; 190.36 8.30E-07 1529200000 3375090 3191780 3080950 3179470 3534120 2330520 3612530 3011760 4252370 FALSE TRUE 3163849.142 3428102.712 3154031.589 3261060.583 3256564.471 3003303.291 3070864.664 3387784.866 3542621.976 0.893081216 0.967673869 0.890309949 0.920521751 0.919252603 0.847762847 0.866833855 0.956293076 1 21.7563861 1.015101209 5.97497408 0.999900395 0.903400766 0.520603319 0.032315155 0.119905549 15.83084669 0.034022027 0.008558004 10.35383427 -1.015101209 -0.096499629 LRECLPLIIFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LRECLPLIIFLR 12 1 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ; 235.31 4.39E-16 411400000 372110 851430 327960 214410 852460 221139 378360 670890 257496 FALSE TRUE 348820.2993 914470.7631 335739.3661 219912.1236 785511.2303 284978.2394 321628.4305 754652.0933 214518.2541 1.626063482 4.262904185 1.5650853 1.025144105 3.6617454 1.328456828 1.49930565 3.517892202 1 17.71074089 3.812358978 6.267639953 1.933338307 3.089852325 0.117001499 1.125942732 0.361686637 21.49479292 0.263842123 0.47971328 6491.70802 -3.812358978 1.156514017 LREDGIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LREDGIQK 8 1 O00170;E9PMH2 O00170 AIP AH receptor-interacting protein 0 68.224 0.052041 167920000 201800 199170 195210 187720 256900 151670 270890 208130 310830 FALSE TRUE 189169.6982 213916.754 199840.4734 192537.213 236724.1103 195454.6668 230272.5593 234115.4887 258950.465 0.730524652 0.826091407 0.771732437 0.743529126 0.914167543 0.754795582 0.889253315 0.904093718 1 17.98231662 1.150656362 0.613130565 1.003878448 0.780553886 0.650431475 0.052501254 0.444956402 0.411141586 0.047365478 0.021359627 14.14673969 -1.150656362 -0.223324562 LREDLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LREDLER 7 1 P62269;J3JS69 P62269 RPS18 40S ribosomal protein S18 0 ;;;;; 200.16 0.00032884 15764950000 5868650 7025417 6796270 6401850 7298660 5192200 7182640 6099958 7274710 FALSE TRUE 5501341.672 7545586.185 6957480.734 6566132.309 6725452.685 6691103.852 6105669.812 6861551.184 6060513.905 0.907735179 1.245040652 1.148001777 1.083428305 1.109716567 1.104048923 1.007450838 1.132173161 1 22.5310087 2.196098954 1.128897411 1.044610237 1.132082866 0.002777619 0.092584582 1.044737407 2.535142403 0.060911912 0.033219551 157.0720654 -2.196098954 0.087472629 LREEIEELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LREEIEELK 9 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 65.06 0.061676 364190000 490090 1367100 1141700 1117800 1235600 1114000 1091800 1212700 888490 FALSE TRUE 459416.1417 1468321.506 1168781.663 1146484.64 1138560.96 1435593.716 928094.7258 1364108.264 740195.2791 0.620668835 1.983694773 1.579017992 1.548894829 1.538189978 1.939479697 1.253851182 1.842903222 1 19.49754641 -1.49815247 6.858150401 0.999791675 1.576088115 0.150636149 0.39274446 0.001095362 8.02E-05 0.332959848 0.078451873 0.031757589 1.49815247 0.57629644 LREEIEELKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LREEIEELKR 10 2 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;; 191.33 4.52E-07 727440000 696690 673820 684370 723490 758960 556652 913970 639614 912220 FALSE TRUE 653085.4165 723710.3339 700603.5796 742055.9783 699354.3431 717348.3959 776928.6834 719471.2159 759964.5888 0.859362957 0.95229481 0.921889769 0.976434941 0.920245961 0.943923449 1.022322217 0.946716763 1 19.53557267 8 0.188742231 1.002587723 0.501475285 0.48702292 0.032356012 46.63520811 0.542268 0.062981464 6.801435468 100000000 -8 -0.501112438 LREELSEAMSEVEGLEANEGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LREELSEAMSEVEGLEANEGSK 22 1 G5E9B7;A0A0D9SFG6;Q99418-2;Q99418;F8W8E2;A0A286YF81;M0QZ92 G5E9B7 CYTH2 Cytohesin-2 0 88.755 0.0024023 5227300 16214 14649 14415 15531 19049 11552 18654 12407 19851 FALSE TRUE 15199.19468 15733.6272 14756.93061 15929.55175 17552.96838 14886.87487 15857.00588 13956.04126 16537.73986 0.919061178 0.951377113 0.892318463 0.963224231 1.061388589 0.900175901 0.958837544 0.843890482 1 14.01347446 3.20747857 24.98496531 0.954149849 0.923359846 0.068551561 0.058256173 598.3196118 480950.9303 0.016064442 0.019202259 1612.421463 -3.20747857 -0.030790002 LREETER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LREETER 7 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7EMQ3 P50570-2 DNM2 Dynamin-2 0 ; 160.88 0.0012129 818940000 519540 583230 588610 623090 623730 558840 652170 559170 587590 FALSE TRUE 487022.9188 626412.9561 602572.1072 639079.5443 574744.7618 720168.036 554383.1629 628983.6054 489517.433 0.994904136 1.27965403 1.230951273 1.305529693 1.174104788 1.471179548 1.13250954 1.284905425 1 18.90100071 -1.138885296 3.899981778 0.999905424 1.240853022 0.26044869 0.123586249 6093691.121 3564301.968 5029.276114 0.025194689 0.072629776 1.138885296 0.240947598 LRENVFQEHQTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LRENVFQEHQTLK 13 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ; 133.54 6.37E-05 529222000 949960 995451 1084191 1067870 1341060 705780 1121820 1043510 1304340 FALSE TRUE 890503.6993 1069155.228 1109908.523 1095273.352 1235738.557 909527.2286 953613.5055 1173794.521 1086637.228 0.819504133 0.983911834 1.021415882 1.007947569 1.13721353 0.837010923 0.877582215 1.080208271 1 20.05143895 -0.135243908 11.06196674 1.000013701 0.969583312 0.008084008 0.10179768 0 0 0.095710927 0.022559282 0.73241308 0.135243908 -0.030430389 LREQGTES(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 LREQGTES(1)R;LREQGTES(1)R;LREQGTES(1)R;LREQGTES(1)R 180.24 2.96E-05 2908780000 737040 926590 606697 559085 750810 448620 1038040 809690 1166610 TRUE FALSE 690909.9821 995195.6877 621088.1393 573432.0676 691844.4112 578129.3113 882395.5387 910781.5788 971895.2544 0.710889346 1.023974223 0.639048433 0.590014269 0.711850797 0.594847345 0.90791218 0.937119072 1 19.89044131 1.580705617 6.24423243 0.953142188 0.734669767 0.446627559 0.123389793 0.150948028 12.15528756 0.073175104 0.034218543 38.08076089 -1.580705617 -0.218472421 LREQGTESR ddPTM_SK-BR-3_Pertuzumab_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" 0 ; 195.27 2.87E-05 429360000 259539 322118 275456 287760 366842 239935 360241 295587 489500 FALSE TRUE 243294.9173 345967.9519 281989.9464 295144.4088 338031.7091 309200.3395 306226.2064 332491.6876 407799.2877 0.596604567 0.848378019 0.691492003 0.723749201 0.82891687 0.758216968 0.750923838 0.815331703 1 18.63749973 -5 0.210776267 2.19368996 0.720087294 0.601706023 0.067404573 101.3483322 1.011075972 51.02534139 0.13115601 1.00E-05 5 -1.473602666 LREQLQLLEEQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LREQLQLLEEQHR 13 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 188.4 3.69E-06 883012000 800628 1240217 899469 962077 1392884 721176 1079145 1127391 1275431 FALSE TRUE 750518.1226 1332043.957 920804.8294 986765.5246 1283492.509 929367.8039 917337.2255 1268148.248 1062553.327 0.706334547 1.253625511 0.866596345 0.928673884 1.207932324 0.874655211 0.863332882 1.193491391 1 20.01910382 3.638719944 0.351074316 0.990850586 0.990791787 0 0.178676979 31772.7426 5486.908467 0.180563394 0.746603883 4352.311236 -3.638719944 -5.88E-05 LREVVETPLLHPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LREVVETPLLHPER 14 1 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 131.72 3.28E-05 59097000 58367 100980 66487 63783 115950 58949 74444 81174 119410 FALSE TRUE 54713.91366 108456.6643 68064.10304 65419.77976 106843.7547 75966.61934 63281.8133 91308.75259 99479.69958 0.550000793 1.090239162 0.684200931 0.657619394 1.074025707 0.763639412 0.636127909 0.917863172 1 16.60211453 1.006925608 24.54916625 1.000000072 0.796357847 0.154075365 0.177240931 203.9162635 722815.72 0.161325535 0.040331384 10.1607463 -1.006925608 -0.203642225 LREYEAALNSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LREYEAALNSK 11 1 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 ; 137.58 6.88E-05 643480000 707010 712250 656340 673400 708940 429580 823450 652350 891430 FALSE TRUE 662759.5061 764985.7311 671908.6947 690680.5841 653262.7121 553592.7724 699981.317 733797.3335 742644.5741 0.892431628 1.030083243 0.904751368 0.930028453 0.879643823 0.745434346 0.942552254 0.988086844 1 19.50231238 5.074968636 14.93589466 0.923413291 0.484428099 0.016907608 0.07872404 4446438.867 17629723.08 0.018998785 61151079.24 118841.6399 -5.074968636 -0.438985192 LRGDVAIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LRGDVAIK 8 1 A0A087X1E4;P53365;P53365-2;P53365-3 A0A087X1E4 ARFIP2 Arfaptin-2 0 ; 90.906 0.011733 483750000 788490 737860 759300 798230 884000 622840 970650 750100 855440 FALSE TRUE 739139.8184 792491.9221 777310.9546 818713.9332 814574.2059 802643.797 825110.0436 843751.6362 712661.5376 1.037154076 1.112017248 1.090715457 1.148811729 1.143002902 1.126262264 1.157786691 1.183944399 1 19.44285754 6.682810473 0.633366409 1.133678716 2.31E-09 0.182151964 0.050786375 46.19824436 1.830201662 0.01811646 63.57226761 4817375.202 -6.682810473 -1.133678714 LRGTQEVAPPTPLTPT(ph)SHTANTSPRPVSGMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LRGTQEVAPPTPLTPTSHTANTSPRPVSGMER 32 2 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 LRGTQEVAPPTPLT(0.001)PT(0.199)S(0.199)HT(0.199)ANT(0.199)S(0.199)PRPVS(0.006)GMER 57.882 0.038096 101280000 10887 12429 13170 10720 17951 8328.9 13052 12960 25852 TRUE FALSE 10205.6021 13349.25609 13482.39862 10995.09335 16541.20087 10733.31822 11094.97377 14578.08453 21537.13419 0.473860729 0.619825088 0.626007086 0.510517939 0.768031658 0.498363344 0.51515553 0.676881353 1 14.39453867 0.903873134 5.459146343 0.999981339 0.580877685 0.709097507 0.085733756 0.432722469 23.93776279 0.077199906 0.019459909 8.014439121 -0.903873134 -0.419103654 LKVDSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LKVDSFR 7 1 K7ESG5;K9J957;P61289;P61289-2;A0A087WTV2;K7ENH2;B7Z8D3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 87.476 0.017614 258300000 461090 788990 420180 432930 920600 301680 571480 860920 1589600 FALSE TRUE 432231.2 847407.6405 430146.868 444039.7167 848299.7895 388770.1186 485791.8794 968407.7571 1324285.491 0.326388232 0.639898003 0.324814303 0.335305129 0.640571686 0.293569718 0.366833196 0.731268117 1 20.33678274 1.025088801 3.719243823 0.997246766 0.427402244 0.706944535 0.126097664 0.102654387 3.359066531 0.115667965 0.029830816 10.59470335 -1.025088801 -0.569844522 LRGYDYGPHFQGILEASLEGDSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 259.77 3.30E-44 873694000 298678 478980 285209 358555 565327 272136.4 540064 468606 869247 FALSE TRUE 279984.2771 514444.1776 291974.2922 367756.1283 520928.4978 350697.7609 459086.4169 527112.4906 724164.0601 0.386631003 0.710397279 0.403188046 0.507835377 0.719351493 0.484279434 0.633953606 0.727890984 1 19.46595705 0.821694057 0.971012206 1.001693676 0.538843653 0.646045257 0.109834685 0.473700844 0.873806296 0.096422426 0.031828921 6.632756552 -0.821694057 -0.462850022 LRIDYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LRIDYER 7 1 P15924 P15924 DSP Desmoplakin 0 71.501 0.066711 0 27286 35825 33071 27433 41516 21163 35529 36238 40733 FALSE TRUE 25578.21797 38477.52028 33855.45974 28136.97722 38255.50083 27272.41455 30201.75629 40762.39407 33934.39915 0.753754851 1.133879521 0.997673764 0.829157961 1.127336914 0.80368049 0.890004156 1.201211605 1 15.05046085 1.247600461 24.99863017 1.100605827 0.953067021 0.19635824 0.136083342 301.1286262 832751.2002 0.089851391 0.031774366 17.68481254 -1.247600461 -0.147538806 LRIEEEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LRIEEEIR 8 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 169.09 0.00027639 1257873000 690254 1035636 725469 841466 1074711 554944 878523 918254 904889 FALSE TRUE 647052.2343 1112315.567 742677.4673 863059.4422 990307.5332 715147.324 746796.632 1032900.033 753857.1801 0.858322042 1.475499069 0.985169986 1.144858025 1.313654044 0.948650942 0.990634104 1.370153473 1 19.5239317 2.231016616 24.99859669 1.062801916 1.175426125 0.028688975 0.200965807 496.1096537 1643947.416 0.069675902 0.052466126 170.2223633 -2.231016616 0.112624209 LRLDTGS(ph)PEPETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LRLDTGSPEPETR 13 1 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 LRLDT(0.037)GS(0.963)PEPETR 81.01 0.0098301 123540000 107660 146220 123460 140590 153250 108000 145390 116190 164470 TRUE FALSE 100921.7528 157046.2809 126388.5295 144197.7774 141214.3632 139177.8468 123590.1192 130696.5773 137018.8945 0.736553547 1.146165144 0.922416795 1.052393379 1.030619636 1.015756603 0.901993259 0.953858063 1 17.06401532 -0.301097194 5.868001919 0.999999992 0.981851283 0 0.108713445 0 76567558.29 0.094478473 0.022914396 0.499922641 0.301097194 -0.018148709 LRLEGPGDEDADGAGS(ph)PSDWASPLEDPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LRLEGPGDEDADGAGSPSDWASPLEDPLR 29 1 O60347 O60347 TBC1D12 TBC1 domain family member 12 1 LRLEGPGDEDADGAGS(0.934)PS(0.065)DWAS(0.001)PLEDPLR 77.308 0.002924 14382000 12857 13572 10963 13570 19011 13411 12913 11038 16173 TRUE FALSE 12052.30332 14576.885 11223.04754 13918.22917 17517.95275 17282.53799 10976.81553 12416.1186 13473.62182 0.894511029 1.081883194 0.832964417 1.032998355 1.300166576 1.282694306 0.8146893 0.921513069 1 13.71785009 1.631681211 25 0.901094197 1.051836366 0.188245487 0.151491039 1.528786966 1600.066579 0.074326958 0.041187417 42.82340651 -1.631681211 0.150742169 LRLPLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LRLPLDK 7 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 80.684 0.04269 0 549120 402690 585020 623200 460760 473420 718400 393990 362000 FALSE TRUE 514751.5594 432505.5866 598896.9507 639192.3671 424573.7682 610088.6687 610682.5893 443180.5188 301579.8614 1.70684991 1.434132852 1.985865196 2.11947961 1.407831963 2.022975493 2.024944857 1.469529553 1 18.20218057 0.974982929 5.360906455 1.000406716 1.809658578 0.542766003 0.24327878 0.132907079 15.22823383 0.233957054 0.059018114 9.44023768 -0.974982929 0.809251862 LRLPLDKEPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LRLPLDKEPAR 11 2 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 121.04 0.00023616 364650000 216570 482400 234130 235270 499240 154590 275060 441360 422570 FALSE TRUE 203015.2703 518117.3979 239683.6742 241307.4265 460031.7042 199217.6234 233817.3065 496464.7676 352040.3371 0.576681843 1.471755772 0.680841509 0.685453913 1.306758504 0.565894309 0.664177601 1.410249665 1 18.42538122 5.007183713 19.44362698 0.941427015 0.073596247 0.117464385 0.331538542 106021285.6 3276637743 0.076523435 2360754641 101667.8672 -5.007183713 -0.867830768 LRLS(ph)PS(ph)PTSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(1)PS(0.46)PT(0.298)S(0.242)QR;LRLS(0.985)PS(0.752)PT(0.149)S(0.114)QR;LRLS(0.93)PS(0.476)PT(0.461)S(0.132)QR;LRLS(0.828)PS(0.828)PT(0.342)S(0.001)QR 108.97 0.016385 22336610000 1581650 1646955 1664502 1509842 1700505 1509112 1890923 1517604 1709239 TRUE FALSE 1482657.35 1768897.262 1703984.773 1548587.102 1566954.197 1944768.136 1607396.651 1707080.2 1423955.969 1.041224155 1.242241544 1.196655522 1.087524569 1.100423209 1.365750191 1.128824687 1.198829344 1 20.44147311 -0.580827583 7.936115048 1 1.179437379 0.248743621 0.091703074 0 0 0.081103979 0.019116391 0.262526058 0.580827583 0.179437379 LRLS(ph)PSPTSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 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(0.978)PS(0.022)PTSQR;LRLS(0.998)PS(0.002)PTSQR;LRLS(0.868)PS(0.132)PTSQR;LRLS(0.943)PS(0.057)PTSQR;LRLS(0.994)PS(0.006)PTSQR;LRLS(0.993)PS(0.007)PTSQR;LRLS(0.962)PS(0.037)PTSQR;LRLS(0.954)PS(0.046)PTSQR;LRLS(0.958)PS(0.042)PTSQR;LRLS(0.993)PS(0.007)PTSQR;LRLS(0.958)PS(0.042)PTSQR;LRLS(0.993)PS(0.007)PTSQR 150.9 2.04E-05 1.65671E+11 5412322 6102611 5577680 5577532 6419260 4649049 5632989 5447481 6348070 TRUE FALSE 5073574.427 6554454.668 5709985.204 5720660.914 5915117.214 5991153.975 4788374.594 6127610.994 5288536.107 0.959353274 1.239370316 1.079691069 1.08170972 1.118479121 1.132856778 0.905425338 1.158659196 1 22.334437 1.78301816 25 1.011687127 1.115067487 0.133867247 0.091541975 115.8387045 65162.03952 0.038415574 0.021414827 60.67617006 -1.78301816 0.10338036 LRLSPS(ph)PT(ph)SQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LRLSPSPTSQR 11 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 LRLS(0.288)PS(0.793)PT(0.852)S(0.067)QR 102.5 0.07171 106190000 167460 168310 164310 173200 191000 150760 197410 165350 202230 TRUE FALSE 156978.9775 180771.8475 168207.5108 177644.6052 175999.6305 194281.9646 167810.2032 185994.3115 168476.5065 0.931755891 1.072979558 0.998403363 1.054417668 1.044653846 1.153169475 0.996045126 1.103977731 1 17.3621879 3.136906511 6.109160092 1.060613084 1.016220866 0.169425229 0.056990826 0.429241306 22.15415633 0.015101361 0.018179529 1370.586695 -3.136906511 -0.044392218 LRLSPS(ph)PTS(ph)QR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.132)PS(0.868)PT(0.021)S(0.979)QR;LRLS(0.275)PS(0.729)PT(0.051)S(0.945)QR;LRLS(0.057)PS(0.968)PT(0.063)S(0.913)QR;LRLS(0.031)PS(0.97)PT(0.063)S(0.936)QR;LRLS(0.516)PS(0.636)PT(0.466)S(0.382)QR;LRLS(0.354)PS(0.664)PT(0.085)S(0.897)QR 207.06 2.90E-07 54453540000 12163130 13102510 12790340 11726800 13912700 11880920 14530560 12316710 13891540 TRUE FALSE 11401861.41 14072633.47 13093732.9 12027729.54 12820052.66 15310748.73 12351837.42 13854478.36 11572952.23 0.98521632 1.215993395 1.131408187 1.039296569 1.107759922 1.322976923 1.067302204 1.197142966 1 23.4642536 -1.130193806 4.879133606 0.999992011 1.140090877 0.15693655 0.096048559 7.52E-06 1.34E-06 0.083724476 0.019732923 0.07409795 1.130193806 0.140098867 LRNPSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LRNPSDR 7 1 Q9P0L0-2;Q9P0L0 Q9P0L0-2 VAPA Vesicle-associated membrane protein-associated protein A 0 ;;; 95.909 0.011965 517081000 431400 924500 586372 601795 869420 527481 605410 844770 761860 FALSE TRUE 404399.4441 992950.9419 600281.0207 617238.0785 801139.2603 679756.2018 514634.3909 950241.3941 634700.6442 0.637149888 1.564439789 0.945770303 0.972486926 1.26223168 1.070987099 0.810830106 1.497148936 1 19.27571678 3.741441602 24.87900457 1.059486134 1.193452393 0 0.291692278 1460.70121 2537687.694 0.068299228 0.122415182 5513.680569 -3.741441602 0.133966259 LRPGFMEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LRPGFMEDR 9 1 Q5BKZ1 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 0 ;; 169.76 5.31E-05 427500000 411990 614230 429920 381160 661110 288288 440160 564200 792490 FALSE TRUE 386204.2813 659708.2283 440117.9054 390941.2109 609189.0874 371512.0656 374162.0942 634641.612 660218.2993 0.584964521 0.999227421 0.666624821 0.592139314 0.922708577 0.562710949 0.566724816 0.961260257 1 19.3325836 1.130978984 7.271907832 0.995314748 0.715767645 0.373651609 0.150530093 0.266324353 15.62677034 0.146041121 0.036638597 13.52007136 -1.130978984 -0.279547103 LRPKS(ph)PPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LRPKSPPPK 9 2 Q9HCE5 Q9HCE5 METTL14 N6-adenosine-methyltransferase subunit METTL14 1 LRPKS(1)PPPK;LRPKS(1)PPPK 72.34 0.037037 3639800000 3932700 2921200 3263300 3207600 3834500 2367290 4339900 3123300 5851100 TRUE FALSE 3686559.327 3137488.688 3340707.017 3289912.446 3533353.838 3050688.193 3689172.285 3513250.88 4874513.61 0.756292755 0.643651642 0.685341612 0.674921174 0.724862852 0.625844635 0.7568288 0.720738757 1 22.21682684 0.099153061 0.709593826 1.010107144 0.681376413 0.838593324 0.041862597 1.285055722 0.747411626 0.069974256 0.013289967 1.256472711 -0.099153061 -0.328730732 LRPLFEACGEVVQIRPIFSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LRPLFEACGEVVQIRPIFSNR 21 2 A0A499FI31;Q15020-4;Q15020 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 ; 183.05 2.50E-17 336380000 306545 315500 315144 330940 317100 261943 345848 293490 340298 FALSE TRUE 287358.8956 338859.9483 322619.3645 339432.4807 292196.2451 337561.6918 293991.3031 330132.8726 283500.0654 1.013611391 1.19527291 1.137986914 1.197292425 1.030674348 1.190693524 1.037006121 1.164489582 1 18.11298954 -0.471398135 0.364101782 0.962873928 1.139369794 0.190831796 0.072279696 11.327044 1.535095549 0.591438185 0.051102987 0.337755061 0.471398135 0.176495866 LRPLWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LRPLWK 6 1 P56559;P40617;P56559-2;P36406-3;P36406-2;P36406 REV__E5RG38 ARL4C;ARL4A;TRIM23 ADP-ribosylation factor-like protein 4C;ADP-ribosylation factor-like protein 4A;E3 ubiquitin-protein ligase TRIM23 0 ; 114.67 0.022881 3908500000 3290100 5310000 3658900 3450000 5377600 2342100 4032700 4606900 5346400 FALSE TRUE 3084178.514 5703157.925 3745690.836 3538532.841 4955264.988 3018226.249 3428034.073 5182081.606 4454051.301 0.69244342 1.280442801 0.840962661 0.794452646 1.112529842 0.677636167 0.769644048 1.163453507 1 22.08668674 3.731186029 24.87458813 0.881676285 1.038120982 0 0.207726923 392.0452284 2399111.386 0.049676761 0.0855773 5385.003982 -3.731186029 0.156444696 LRPLYDIPYMFEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LRPLYDIPYMFEAR 14 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;; 204.82 1.20E-08 3317060000 1471690 2483420 1689980 1543900 2443490 1079530 1676120 2128830 2060600 FALSE TRUE 1379579.55 2667295.001 1730067.124 1583519.088 2251588.152 1391172.786 1424801.366 2394619.112 1716672.548 0.80363582 1.553758755 1.007802639 0.922435143 1.311600255 0.810389138 0.829978535 1.394918975 1 20.71118344 3.722850333 24.60062608 1.013689965 1.246828471 0.025818101 0.259987748 288.4481968 1661482.203 0.063557123 0.102445143 5282.631703 -3.722850333 0.233138506 LRPSGDDVELIGEEEDVSVYDIADHPDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LRPSGDDVELIGEEEDVSVYDIADHPDFR 29 1 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 0 ;; 282.94 1.03E-71 454443000 164808 187908 186578 189689 210151 171369 225201 179021 200586 FALSE TRUE 154492.9615 201820.9038 191003.7183 194556.7409 193646.5882 220840.4484 191434.2007 201372.1659 167106.9008 0.924515749 1.207735305 1.143003176 1.16426515 1.15881862 1.321551937 1.145579266 1.205049971 1 17.35041179 4.742698422 24.74218181 1.177995598 0.924515633 0.478431258 0.079399705 277.9326776 1661838.229 0.016487911 0.127244445 55296.59911 -4.742698422 -0.253479965 LRPTVTNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LRPTVTNDR 9 1 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 0 ;;; 172.56 5.12E-05 943620000 551118 630933 664819 617663 653433 509939 661205 638347 727117 FALSE TRUE 516624.5082 677647.9358 680588.8206 633513.2783 602115.008 657150.1111 562063.4486 718046.0281 605756.4753 0.852858416 1.118680465 1.123535362 1.045821719 0.993988562 1.084842074 0.92787031 1.185370784 1 19.2083784 3.002395453 24.96028745 1.028148214 1.06610574 0 0.100821446 326.7112007 3404237.064 0.02746832 0.032642884 1005.530974 -3.002395453 0.037957526 LRPVS(ph)PEEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LRPVSPEEIR 10 1 Q08AE8;J3KNG6;Q08AE8-4;Q08AE8-3;Q08AE8-5;Q08AE8-2;K7EMJ7 Q08AE8 SPIRE1 Protein spire homolog 1 1 LRPVS(1)PEEIR 95.428 0.004499 148510000 47297 49183 46062 52606 42749 48084 55853 40249 30078 TRUE FALSE 44336.7652 52824.56049 47154.61239 53955.95902 39391.66598 61965.07022 47478.36116 45274.17625 25057.78749 1.769380685 2.108109526 1.881834636 2.153261099 1.572032886 2.472886732 1.894754722 1.806790654 1 14.61297142 0.744521258 2.235136833 1.000653785 1.993509432 0.619531686 0.239575467 0.656300504 4.803712071 0.198539455 0.053932635 5.552917969 -0.744521258 0.992855647 LRQDLQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LRQDLQDR 8 1 P12270 P12270 TPR Nucleoprotein TPR 0 ; 148.94 0.00046798 1028570000 1082410 1180240 913700 952710 1296450 780350 1220390 1073600 1099230 FALSE TRUE 1014663.89 1267626.198 935373.3955 977158.1515 1194632.047 1005624.377 1037403.849 1207641.323 915761.4117 1.108000269 1.384231942 1.021416041 1.067044471 1.304523243 1.098129233 1.132832019 1.31872921 1 19.80461225 -2.375831366 2.000859237 4.66E-05 1.177014029 0.18177527 0.119500307 2999145.031 274821.0597 13588259.71 0.028477628 0.0042089 2.375831366 1.176967408 LRQPFFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LRQPFFQK 8 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ; 148.04 0.00048116 1197460000 439190 2443100 221020 240970 2751300 252680 331890 2211800 2313500 FALSE TRUE 411701.8819 2623989.666 226262.6988 247153.6982 2535223.996 325624.6141 282126.1756 2487948.099 1927361.904 0.213609017 1.361441077 0.117395025 0.128234193 1.315385549 0.16894835 0.14637945 1.290856737 1 20.87819606 1.225063348 24.95576832 1.14542872 0.522103037 0.241916403 0.47796574 395.4506343 731146.3704 0.436915875 0.111702596 16.79048914 -1.225063348 -0.623325683 LRRES(ph)PESEGPIYEGLIL ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LRRESPESEGPIYEGLIL 18 2 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 1 LRRES(1)PESEGPIYEGLIL;LRRES(0.965)PES(0.035)EGPIYEGLIL;LRRES(0.993)PES(0.007)EGPIYEGLIL;LRRES(0.992)PES(0.008)EGPIYEGLIL 149.84 4.67E-08 235151000 257557 318503 294417 292076 333055 266288 367855 308997 448698 TRUE FALSE 241436.9671 342085.2935 301400.7103 299571.1646 306898.2038 343161.0228 312698.5577 347575.9556 373807.4051 0.645885993 0.915137819 0.806299464 0.80140511 0.821006218 0.918015583 0.836523176 0.929826298 1 18.51193562 -4.999999997 0.054068447 1.668517279 0.530715218 0.508924327 0.067955121 442.4379301 1.761240258 40.6068167 8.068199526 1.00E-05 4.999999997 -1.137802061 LRRPEGASNESERD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LRRPEGASNESERD 14 3 O75381-2;O75381 O75381-2 PEX14 Peroxisomal membrane protein PEX14 0 103.21 0.0013804 64311000 58146 44814 58366 62765 68742 36430 49225 55877 56001 FALSE TRUE 54506.74565 48132.07519 59750.46908 64375.65616 63343.28061 46946.74961 41844.16823 62853.36645 46654.07132 1.168317022 1.031680062 1.280712859 1.379850768 1.357722463 1.006273371 0.896902822 1.347221468 1 15.50971536 2.217654427 24.99234432 1.035470415 1.22599452 0.251314861 0.150408062 334.5154856 399894.6592 0.057700812 0.042659828 165.0647835 -2.217654427 0.190524105 LRRPS(ph)PPEPWDEEDGASCSTFFGSEER ddPTM_SK-BR-3_Pertuzumab_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(1)PPEPWDEEDGASCSTFFGSEER;LRRPS(1)PPEPWDEEDGASCSTFFGSEER;LRRPS(0.97)PPEPWDEEDGAS(0.014)CS(0.006)T(0.007)FFGS(0.004)EER;LRRPS(1)PPEPWDEEDGASCSTFFGSEER 284.55 1.22E-61 1859940000 297618 402826 311662 369863 461633 271105 417187 371112 695628 TRUE FALSE 278990.6206 432651.6562 319054.7698 379354.3108 425378.2063 349368.6125 354633.6823 417446.1501 579523.1929 0.481414073 0.746564868 0.550547025 0.654597289 0.73401412 0.602855273 0.611940448 0.720326909 1 19.14450687 0.851689204 3.324405781 0.999909924 0.633260412 0.693067098 0.078079874 0.370391717 7.206953529 0.067414128 0.017480646 7.107047269 -0.851689204 -0.366649512 LRRY(ph)CVFS(ph)HEELICK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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;LRRY(1)CVFS(1)HEELICK;LRRY(1)CVFS(1)HEELICK;LRRY(1)CVFS(1)HEELICK;LRRY(1)CVFS(1)HEELICK 101.05 0.0045365 2126720000 1261940 3607570 2766180 4534760 4153480 2294980 1667550 1216520 1164580 TRUE FALSE 1182957.428 3874678.236 2831795.096 4651129.619 3827282.435 2957503.47 1417516.358 1368405.2 970204.0745 1.219287219 3.993673432 2.91876232 4.793970404 3.944822059 3.048331323 1.461049686 1.410430275 1 19.88792871 1.760485403 3.123756998 1.254345404 3.464838315 0.518010337 0.92650319 0.174723005 3.43903482 0.493885033 0.238091182 57.60834562 -1.760485403 2.210492911 LRS(ph)PFLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LRSPFLQK 8 1 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 1 LRS(1)PFLQK;LRS(1)PFLQK;LRS(1)PFLQK;LRS(1)PFLQK 126.48 0.00073725 6540640000 7032270 6371480 7151820 8077370 8551090 5137530 7262240 5506610 8132000 TRUE FALSE 6592132.774 6843231.009 7321464.548 8284648.989 7879521.885 6620651.51 6173334.531 6194122.38 6774716.665 0.973049221 1.010113241 1.08070417 1.222877561 1.163077701 0.977258805 0.911231397 0.914299843 1 22.69172918 2.060675432 6.630464141 0.934840147 1.083523887 0.473052693 0.073497609 0.192293412 16.38131235 0.030079791 0.022027776 114.9940666 -2.060675432 0.148683741 LRS(ph)PPEALVQGR ddPTM_SK-BR-3_Pertuzumab_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 172.91 2.09E-05 16149430000 2353720 2301040 2529750 2309250 2574200 2068440 2542170 2135380 3116650 TRUE FALSE 2206404.867 2471411.396 2589756.865 2368509.265 2372032.716 2665565.05 2160995.209 2401986.894 2596460.981 0.849773936 0.95183845 0.997417979 0.912206762 0.913563783 1.026614715 0.832284877 0.925100324 1 21.30811511 1.732035557 24.99999978 0.903391668 0.947224546 0.003487572 0.062857861 1.52206456 5791.571694 0.026810839 0.014867921 53.95547959 -1.732035557 0.043832878 LRS(ph)PRGS(ph)PDGSLQTGKPSAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LRSPRGSPDGSLQTGKPSAPK 21 3 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 2 LRS(1)PRGS(0.768)PDGS(0.227)LQT(0.005)GKPSAPK 136.71 6.45E-06 473600000 278210 301280 299740 352100 411450 167150 354170 293960 803600 TRUE FALSE 260797.3327 323587.0847 306849.9743 361135.4821 379136.3767 215403.4915 301065.4965 330661.5531 669473.9685 0.389555599 0.483345283 0.458344893 0.539431702 0.566319819 0.321750362 0.44970456 0.493912487 1 19.35266843 0.718200164 4.149088645 0.999998172 0.460217698 0.858788002 0.068602705 2.210237858 32.25738292 0.063829391 0.016271023 5.226370143 -0.718200164 -0.539780473 LRS(ph)PS(ph)NDSAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LRSPSNDSAHR 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 LRS(1)PS(0.998)NDS(0.002)AHR;LRS(1)PS(0.993)NDS(0.007)AHR 119.65 0.00031737 879770000 580280 629040 697020 684690 698010 676350 748040 525070 489460 TRUE FALSE 543961.3106 675614.7761 713553.6436 702260.3046 643191.1102 871601.2654 635878.3465 590626.1453 407765.964 1.334003715 1.656868978 1.749909768 1.722214129 1.577353598 2.137503721 1.55941987 1.448443954 1 18.63738183 0.93361198 2.14711788 1.004436748 1.69941993 0.539882858 0.199734631 0.268561825 2.664232447 0.175594623 0.048394139 8.582463793 -0.93361198 0.694983182 LRS(ph)PSNDSAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LRSPSNDSAHR 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 LRS(1)PSNDSAHR;LRS(1)PSNDSAHR;LRS(1)PSNDSAHR;LRS(1)PSNDSAHR 177.63 4.78E-06 3923550000 1037610 1412170 1103270 1076290 1340610 883710 1093030 1266610 1572450 TRUE FALSE 972667.8423 1516728.536 1129440.085 1103909.424 1235323.898 1138822.731 929140.2987 1424749.047 1309997.937 0.742495706 1.157809867 0.862169362 0.842680277 0.942996828 0.869331698 0.709268521 1.087596405 1 20.32113311 3.725183935 24.79655765 0.877114428 0.988869549 0 0.142449526 173.0090939 2214455.764 0.034465795 0.056483041 5311.09335 -3.725183935 0.111755122 LRS(ph)YEDMIGEEVPSDQYYWAPLAQHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 LRSYEDMIGEEVPSDQYYWAPLAQHER 27 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 LRS(1)YEDMIGEEVPSDQYYWAPLAQHER;LRS(0.999)Y(0.001)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.996)Y(0.004)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.545)Y(0.455)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.996)Y(0.004)EDMIGEEVPSDQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER 260.6 2.90E-53 2459237000 899959 904438 990845 1335088 1313093 812246 807972 637289.9 723610.8 TRUE FALSE 843632.1727 971403.5306 1014348.311 1369348.618 1209967.973 1046728.234 686824.0994 716856.9469 602835.4828 1.39944014 1.611390766 1.682628744 2.271512971 2.007127993 1.736341447 1.139322616 1.189141926 1 19.20140481 1.735005588 4.291362261 1.113305168 1.783784538 0.648882489 0.234441626 0.130337448 5.41769833 0.133422755 0.066732466 54.32573213 -1.735005588 0.670479371 LRTS(ph)TSDLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LRTSTSDLSR 10 1 Q5T5U3;A0A087WW76;A0A452Q6Z5 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 LRT(0.063)S(0.91)T(0.023)S(0.003)DLSR 80.441 0.014533 171980000 517380 350720 513960 492060 385670 382430 548300 382340 460610 TRUE FALSE 484998.1093 376687.6737 526151.3739 504687.0927 355381.0339 492831.3328 466087.5052 430075.9906 383731.2153 1.26390059 0.981644596 1.371145617 1.315209898 0.926119689 1.284313897 1.21461973 1.120774056 1 18.5497366 0.946005284 4.100098997 1.000181903 1.1906843 0.164929259 0.140051936 0.476609715 22.45340988 0.126891965 0.032407977 8.830906449 -0.946005284 0.190502396 LRVEFPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LRVEFPR 7 1 J3KTL2;Q07955;Q07955-3;Q07955-2;Q13242;S4R3G0 J3KTL2;Q13242 SRSF1;SRSF9 Serine/arginine-rich splicing factor 1;Serine/arginine-rich splicing factor 9 0 ; 153.78 0.0023269 251060000 145688 580310 135193 141903 549290 133667 169850 475520 463040 FALSE TRUE 136569.6481 623276.7562 138399.8418 145544.4712 506150.9791 172254.493 144382.5693 534889.7187 385755.6326 0.354031507 1.615729502 0.358775945 0.377297073 1.312102627 0.446537856 0.374285058 1.386602485 1 18.5573277 4.991907914 24.75758364 0.810734969 0.066100812 0.094978864 0.469289511 29935.15491 139660.6282 0.105633344 490607.7819 98153.97994 -4.991907914 -0.744634157 LS(ph)ASSSISSADLFEEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSASSSISSADLFEEPR 17 0 Q9NP61;Q9NP61-2;H0Y6A0 Q9NP61;H0Y6A0 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 1 LS(0.971)AS(0.023)S(0.005)S(0.001)ISSADLFEEPR 72.583 0.029458 26138000 29263 28451 30236 39747 37941 20758 26643 17599 23734 TRUE FALSE 27431.48107 30557.54164 30953.2122 40766.97531 34961.26691 26750.49762 22648.12949 19796.27389 19772.64207 1.38734525 1.545445547 1.565456558 2.061786946 1.768163646 1.35290456 1.145427577 1.001195178 1 14.27121804 1.867378662 2.286578893 1.032612554 1.650476724 0.709873381 0.179769429 0.178085734 1.721224401 0.113184676 0.054639893 73.68492781 -1.867378662 0.61786417 LS(ph)FSDTYQDYEEYWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSFSDTYQDYEEYWR 15 0 Q9UHI6;E9PJ60 Q9UHI6 DDX20 Probable ATP-dependent RNA helicase DDX20 1 LS(0.998)FS(0.002)DTYQDYEEYWR 100.45 0.0031257 0 12952 15238 15379 20291 18185 17339 17294 10342 13271 TRUE FALSE 12141.35744 16366.23738 15743.79714 20811.70141 16756.82345 22344.48782 14700.92525 11633.22147 11055.98437 1.098170641 1.480305763 1.42400682 1.882392442 1.515633787 2.021031062 1.329680358 1.052210376 1 13.43253986 1.387373259 4.061146836 1.032966641 1.560023629 0.441876399 0.250414216 0.207119702 5.462482793 0.179524522 0.061703823 24.3990692 -1.387373259 0.527056988 LS(ph)GPAELR ddPTM_SK-BR-3_Pertuzumab_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 97.456 0.008621 143810000 508710 411920 437420 420710 467510 402890 568740 477810 346900 TRUE FALSE 476870.7492 442418.9854 447795.809 431506.1309 430793.6504 519197.8026 483462.7169 537465.6303 289000.1489 1.650070946 1.530860752 1.549465668 1.493100029 1.4906347 1.796531263 1.672880511 1.859741707 1 18.14071071 2.294402039 24.99995899 1.647713812 1.539839781 0 0.236689959 275.9222401 123527.4837 0.071329542 0.059678542 196.9708862 -2.294402039 -0.107874031 LS(ph)IPTYGLQCTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 1 LS(0.952)IPT(0.048)YGLQCTR 62.685 0.079738 48522000 50272 49827 43294 32493 46788 38636 56819 56565 51720 TRUE FALSE 47125.56526 53516.24292 44320.95412 33326.82539 43113.45921 49789.586 48299.51843 63627.26476 43087.59788 1.093715305 1.242033568 1.028624391 0.773466775 1.000600204 1.155543322 1.120961038 1.476695567 1 15.39498505 1.65944882 2.515659788 1.242175981 1.052241018 0.171991539 0.165364005 0.431101221 6.14501092 0.110426972 0.045163957 45.65084489 -1.65944882 -0.189934963 LS(ph)LCEDSPMVTLTVDNVHLEHGVVYEYVSTAGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LSLCEDSPMVTLTVDNVHLEHGVVYEYVSTAGVR 34 0 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 1 LS(0.941)LCEDS(0.059)PMVTLTVDNVHLEHGVVYEYVSTAGVR;LS(1)LCEDSPMVTLTVDNVHLEHGVVYEYVSTAGVR;LS(0.783)LCEDS(0.217)PMVTLTVDNVHLEHGVVYEYVSTAGVR;LS(0.862)LCEDS(0.138)PMVTLTVDNVHLEHGVVYEYVSTAGVR;LS(1)LCEDSPMVTLTVDNVHLEHGVVYEYVSTAGVR 290.32 1.92E-89 398171000 98259.7 88786.2 98114.1 97983.6 95593.7 84615.6 122065.8 82850.7 77514.8 TRUE FALSE 92109.80078 95360.02263 100441.4128 100498.0251 88086.15641 109042.7501 103763.1665 93194.79227 64577.07912 1.426354398 1.476685287 1.555372497 1.556249159 1.364046773 1.688567393 1.606811084 1.443155893 1 15.97873457 0.902430545 7.227594587 1.000001283 1.530466927 0.766235079 0.090395699 1.10837252 82.05995573 0.08559601 0.021457944 7.987861838 -0.902430545 0.530465644 LS(ph)LDLSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LSLDLSHR 8 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1 Q8TDM6-4 DLG5 Disks large homolog 5 1 LS(1)LDLSHR;LS(1)LDLSHR;LS(1)LDLSHR 112.85 0.0019083 116342000 597017 524030 543348 553486 522805 450270 710356 565780 415811 TRUE FALSE 559650.7717 562829.7265 556236.4711 567689.3878 481746.0042 580255.6395 603844.7124 636418.8784 346409.4579 1.6155759 1.624752771 1.605719643 1.638781433 1.390683751 1.675057151 1.743153077 1.837186786 1 18.40211879 -1.947612495 2.918997568 0.551069256 1.638446733 0.760751008 0.113023901 428499.5931 4856863.232 1556011.677 0.026522645 0.011282037 1.947612495 1.087377477 LS(ph)LFSDLPEDTELQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSLFSDLPEDTELQR 15 0 Q9BST9 Q9BST9 RTKN Rhotekin 1 LS(1)LFSDLPEDTELQR 85.42 0.0083387 10151000 18413 21214 18044 17770 21689 14783 21713 15494 15461 TRUE FALSE 17260.5632 22784.70663 18472.0122 18226.00828 19985.63343 19050.61212 18457.33722 17428.46001 12880.45922 1.34005806 1.768935893 1.434111307 1.415012305 1.551624293 1.479032059 1.432971986 1.353093062 1 13.65289641 -0.476723405 0.316955588 0.812143017 1.568905729 0.642575977 0.114518062 4.979383359 0.546736166 1.088938329 0.113187835 0.333638834 0.476723405 0.756762712 LS(ph)LPMPASGTSLSAAIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSLPMPASGTSLSAAIHR 18 0 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 1 LS(1)LPMPASGTSLSAAIHR;LS(1)LPMPASGTSLSAAIHR 233.34 6.25E-24 505500000 433590 512830 436820 484280 519160 350500 559840 432010 333500 TRUE FALSE 406452.3759 550800.4668 447181.5767 496707.4447 478387.2678 451683.6601 475897.1893 485947.3995 277836.6955 1.462918263 1.982461193 1.609512292 1.787767609 1.721828958 1.625716356 1.712866576 1.74903966 1 18.08387763 -2.267550742 0.515662171 3.76E-11 1.729764068 0.727380134 0.135240575 55.66838879 3.673932947 63.97510419 0.055831218 0.00540069 2.267550742 1.729764068 LS(ph)PDFAEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSPDFAEELR 10 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 LS(1)PDFAEELR;LS(1)PDFAEELR 187.58 1.27E-06 53617000 87730 70846 76699 75840 79862 82953 85056 78364 59589 TRUE FALSE 82239.1359 76091.51156 78518.3365 77786.1828 73589.96067 106900.1845 72302.64242 88147.9179 49643.21094 1.656603881 1.532767726 1.58165306 1.566904745 1.482377132 2.153369664 1.456445726 1.775628857 1 15.59930881 LS(ph)PENNQVLTK ddPTM_SK-BR-3_Pertuzumab_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(1)PENNQVLTK;LS(1)PENNQVLTK 227.47 4.17E-12 1829460000 3781790 2409520 2905810 2757130 2679140 2411450 3668190 2606520 2636480 TRUE FALSE 3545094.515 2587923.368 2974737.185 2827882.624 2468731.152 3107596.468 3118178.963 2931949.76 2196434.456 1.614022447 1.178238377 1.354348261 1.287487827 1.123972147 1.414836878 1.419654912 1.334867859 1 21.06673202 4.751188873 24.57284804 1.289488028 1.614022706 0.389481061 0.134371481 1777.032442 3457781.702 0.030073258 0.533681658 56388.28331 -4.751188873 0.324534679 LS(ph)PERS(ph)SDSESNENEPHLPHGVSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSPERSSDSESNENEPHLPHGVSQR 25 1 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-2;V9GYS7 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 2 LS(0.999)PERS(0.705)S(0.296)DSESNENEPHLPHGVSQR 137.25 2.86E-05 810640000 224570 210180 238190 245420 252210 182560 314240 217130 275620 TRUE FALSE 210514.5646 225741.9459 243839.9793 251717.8927 232402.444 235262.1084 267122.6293 244239.1585 229617.2414 0.916806435 0.983122802 1.061941071 1.096249964 1.012129762 1.024583811 1.163338727 1.063679526 1 17.80887145 4.701076285 0.887795939 1.072978692 0.833366916 0.496677388 0.047463848 1.69723062 1.07980327 0.015869021 0.391949675 50243.08347 -4.701076285 -0.239611776 LS(ph)PERSS(ph)DSESNENEPHLPHGVSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSPERSSDSESNENEPHLPHGVSQR 25 1 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-2;V9GYS7 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 2 LS(0.999)PERS(0.252)S(0.748)DS(0.001)ESNENEPHLPHGVSQR 136.87 3.38E-05 839400000 177230 243210 245510 263500 272140 210160 304880 244100 339370 TRUE FALSE 166137.4907 261217.5215 251333.6131 270261.8561 250767.2222 270829.7803 259166.0744 274576.4223 282726.9546 0.587625226 0.923921534 0.888962333 0.955911178 0.886959019 0.957919915 0.916665603 0.971171718 1 18.10904991 4.738854461 6.637068639 0.929513364 0.581300145 0.90163788 0.036252717 0.030487965 8.679272455 0.007662993 0.047643263 54809.32594 -4.738854461 -0.348213219 LS(ph)PEVAPPAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LSPEVAPPAHR 11 0 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 LS(1)PEVAPPAHR;LS(1)PEVAPPAHR;LS(1)PEVAPPAHR 124.12 0.00022916 941130000 965120 792560 862170 814930 751520 829130 1037000 684940 647080 TRUE FALSE 904714.862 851241.9671 882621.0795 835842.4835 692498.6507 1068486.371 881511.477 770456.2667 539078.1677 1.67826285 1.579069638 1.637278474 1.55050331 1.284597842 1.982062037 1.63522014 1.429210665 1 19.04013496 0.903927159 3.324053747 1.000679011 1.621874892 0.578049096 0.168142664 0.27538464 6.77370914 0.151884005 0.039422769 8.015436153 -0.903927159 0.62119588 LS(ph)PGESAYQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LSPGESAYQK 10 0 A0A0G2JHC2;Q6NYC8-2;Q6NYC8 A0A0G2JHC2 PPP1R18 Phostensin 1 LS(1)PGESAYQK;LS(1)PGESAYQK;LS(1)PGESAYQK;LS(1)PGESAYQK;LS(1)PGESAYQK 301.53 1.60E-32 1081580000 2673410 2029020 2227150 2156570 2267640 1458900 2123990 1642290 2180630 TRUE FALSE 2506086.04 2179250.752 2279979.05 2211911.237 2089548.702 1880060.747 1805517.418 1847333.522 1816668.766 1.379495309 1.199586184 1.255032889 1.217564412 1.150208966 1.034894628 0.99386165 1.016879663 1 20.79286397 2.440459889 1.418641204 0.996092489 1.259450667 0.871847835 0.04581418 0.133662266 0.543775349 0.022205285 0.016027643 275.7146792 -2.440459889 0.263358178 LS(ph)PGKETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSPGKETR 8 1 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7 E9PHV5 SSFA2 Sperm-specific antigen 2 1 LS(1)PGKETR 66.056 0.078676 0 384970 286180 298020 341710 327460 248280 414680 290930 417530 TRUE FALSE 360875.4149 307369.065 305089.1751 350478.8571 301742.6125 319954.4055 352502.5837 327253.2509 347841.5457 1.037470709 0.883646789 0.877092397 1.007581933 0.867471457 0.919828035 1.013399889 0.940811283 1 18.40807073 1.755198559 25 0.984266272 0.920636304 0.134923863 0.058009506 9.477374187 14256.8081 0.025277791 0.014018011 56.91130698 -1.755198559 -0.063629968 LS(ph)PGSYPTVIQQQNATSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 343.12 4.33E-76 198357000 105337 111236 100550 120252 134373 88031 124552 97551 86238 TRUE FALSE 98744.1452 119472.0292 102935.0935 123337.8699 123819.8866 113444.1206 105876.5839 109730.4571 71844.32068 1.374418246 1.662929346 1.432751991 1.716737924 1.723447107 1.579026979 1.473694551 1.527336553 1 16.1325865 0.244446447 0.954777705 0.996381916 1.577238518 0.705408771 0.114626916 1.88788913 1.930717449 0.121082887 0.033985437 1.755684387 -0.244446447 0.580856602 LS(ph)PHKVQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 140.24 6.62E-05 11933060000 12455820 7852100 10127610 9057540 8651290 8742290 12856890 7983710 8735900 TRUE FALSE 11676232.46 8433477.654 10367841.69 9289971.811 7971852.581 11266047.2 10929118.7 8980493.768 7277821.854 1.604358103 1.158791438 1.424580307 1.276476946 1.095362423 1.547997111 1.501701872 1.233953503 1 22.79507531 0.988118764 22.43689181 0.99999999 1.360587195 0.351151405 0.162171186 173.1818546 327044.601 0.151146856 0.037786714 9.730132723 -0.988118764 0.360587205 LS(ph)PIPEEVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 175.74 2.84E-06 1159298000 3989790 2334240 2870820 2782940 2788980 2204660 3828350 2660390 2710160 TRUE FALSE 3740076.166 2507069.558 2938917.206 2854354.952 2569944.761 2841109.552 3254324.458 2992545.548 2257816.788 1.656501177 1.110395481 1.30166328 1.264210173 1.138243269 1.25834371 1.441358961 1.32541558 1 21.10649699 4.751298291 24.69768113 1.251118783 1.656501479 0.530259245 0.124763893 1522.998773 2952951.366 0.029238804 0.533568607 56402.49183 -4.751298291 0.405382696 LS(ph)PLPVVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSPLPVVSR 9 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 LS(1)PLPVVSR;LS(1)PLPVVSR 130.63 0.00037324 239420000 597830 435650 492620 427420 363080 446880 605190 460240 290730 TRUE FALSE 560412.8875 467905.9793 504305.179 438388.3208 334565.1614 575887.0015 514447.3778 517701.9771 242205.2848 2.313792979 1.931857018 2.082139452 1.809986604 1.381328907 2.377681403 2.124013843 2.137451202 1 17.88587082 4.738636366 24.998611 1.932687638 2.313793091 0.085472842 0.406591256 16.37048085 5393240.051 0.087301569 0.501659835 54781.80854 -4.738636366 0.381105453 LS(ph)PSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSPSFR 6 0 B4DF95;Q15735 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 LS(1)PSFR;LS(0.999)PS(0.001)FR 152.47 0.010756 1242290000 1545140 1534010 1819750 1732990 1876950 1335940 1450610 1231030 2584500 TRUE FALSE 1448432.446 1647589.697 1862915.329 1777461.457 1729541.918 1721604.191 1233104.497 1384726.805 2153130.253 0.67271009 0.7652067 0.865212556 0.825524352 0.803268597 0.799581998 0.572703159 0.643122636 1 21.03800417 LS(ph)PSTSGPHSHDYLPQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSPSTSGPHSHDYLPQER 18 0 Q5JR04;Q9HCE1 Q5JR04 MOV10 Putative helicase MOV-10 1 LS(0.902)PS(0.032)T(0.032)S(0.032)GPHS(0.001)HDYLPQER 53.779 0.054461 0 51132 128740 106510 95810 129430 71106 110740 112100 158110 TRUE FALSE 47931.73939 138272.0436 109036.4675 98268.64681 119265.0899 91633.14789 94135.56506 126095.9318 131720.4196 0.363889969 1.049738864 0.827787126 0.746039582 0.905441163 0.695663954 0.714661898 0.957299803 1 17.00711949 1.120175575 5.944052821 0.996231005 0.791347072 0.196251927 0.176762778 0.361437929 16.17603274 0.158062619 0.039834233 13.18789787 -1.120175575 -0.204883932 LS(ph)PSWNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSPSWNPK 8 0 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 LS(1)PSWNPK 127.76 0.0012192 66304000 360500 268540 334840 375630 318880 214740 292600 186980 239460 TRUE FALSE 337936.9485 288422.981 342782.5629 385269.3017 293836.4511 276731.952 248727.3464 210324.8646 199492.579 1.693982554 1.445783008 1.718272251 1.931246283 1.472919206 1.387179179 1.246799994 1.054299191 1 17.60597555 1.792098355 1.232362365 1.018678223 1.654082009 0.800736626 0.130301319 0.209070158 0.593001764 0.110266766 0.044436133 61.95813762 -1.792098355 0.635403785 LS(ph)PTPSMQDGLDLPSETDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSPTPSMQDGLDLPSETDLR 20 0 Q9UK58;Q9UK58-6;Q9UK58-5;Q9UK58-4 Q9UK58 CCNL1 Cyclin-L1 1 LS(0.998)PT(0.002)PSMQDGLDLPSETDLR 252.77 4.59E-36 36496000 55729 50037 52123 51018 48417 40182 58375 54562 31556 TRUE FALSE 52241.02137 53741.79154 53359.38217 52327.20825 44614.52412 51781.8911 49622.21068 61374.18581 26289.09974 1.987174224 2.044261389 2.02971508 1.99045265 1.697073105 1.969709561 1.887558386 2.334586822 1 14.68217712 -1.271492434 3.653618623 0.99789269 1.983458587 0.798665151 0.156557741 16874986.11 27891164.14 403268.9305 0.034815075 0.053518948 1.271492434 0.985565896 LS(ph)SDSFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSSDSFAR 8 0 A0A087WSV0;Q9HB09-3;Q9HB09 A0A087WSV0 BCL2L12 Bcl-2-like protein 12 1 LS(0.386)S(0.309)DS(0.305)FAR 91.658 0.012934 90154000 157420 132680 145600 140470 130510 129720 176290 124590 117340 TRUE FALSE 147567.3632 142503.7653 149053.7008 144074.698 120260.2711 167168.0582 149856.9511 140145.3358 97755.19595 1.509560303 1.457761543 1.524764994 1.473831612 1.23021871 1.710068263 1.532981952 1.433635669 1 16.57688577 0.840643086 5.342511746 1.000003869 1.494375611 0.636229258 0.11581825 1.623445435 54.09996173 0.10500917 0.026484993 6.928561654 -0.840643086 0.494371742 LS(ph)SGFDDIDLPSAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LSSGFDDIDLPSAVK 15 0 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 LS(0.982)S(0.018)GFDDIDLPSAVK;LS(0.5)S(0.5)GFDDIDLPSAVK;LS(0.983)S(0.017)GFDDIDLPSAVK;LS(0.976)S(0.024)GFDDIDLPSAVK 190.86 2.09E-07 75680000 466101 400732 449038 432996 501412 368201 524085 512072 440229 TRUE FALSE 436928.5704 430402.6142 459689.3934 444107.4104 462033.1241 474494.6515 445503.3196 576005.3164 366751.9359 1.191346323 1.173552399 1.253406863 1.210920426 1.259797369 1.293775451 1.214726566 1.570558353 1 18.48444506 3.385572124 0.834007234 1.279089768 1.180879581 0.047053406 0.137513037 1.971326154 2.889525336 0.058604834 0.12358208 2429.808933 -3.385572124 -0.098210187 LS(ph)SGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 35 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 LS(0.741)S(0.246)GPEQIT(0.013)LEASSTEGHPGAPSPQHTDQTEAFQK;LS(0.9)S(0.1)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 469.91 8.46E-257 915940000 683780 715075 727266 779707 829813 600970 929314 709801 797920 TRUE FALSE 640983.4304 768019.897 744517.093 799715.6017 764642.8343 774460.2831 789971.993 798421.2173 664741.9972 0.964258965 1.15536539 1.12000911 1.203046603 1.150285129 1.16505394 1.188388873 1.201099405 1 19.34243498 4.738580517 10.42783652 1.155679663 0.96389923 0.487549574 0.058691281 0.052182425 232.0082784 0.012131321 0.07022628 54774.76418 -4.738580517 -0.191780433 LS(ph)SLAR ddPTM_SK-BR-3_Pertuzumab_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 76.035 0.079845 46777000 108790 66095 127070 103000 69512 120800 312060 81499 206400 TRUE FALSE 101981.0281 70988.74257 130084.1604 105643.1544 64052.80792 155672.999 265269.5 91674.32955 171950.5066 0.593083615 0.412844044 0.756520949 0.614381176 0.372507236 0.905336088 1.542708453 0.533143701 1 17.39163384 2.033723265 7.077297256 1.119848725 0.566655927 0.398690929 0.266276617 0.146869166 22.96734986 0.09401113 0.068366223 108.0745075 -2.033723265 -0.553192798 LS(ph)SLRAS(ph)TSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSSLRASTSK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 LS(0.874)S(0.126)LRAS(0.937)T(0.052)S(0.011)K;LS(0.832)S(0.168)LRAS(0.983)T(0.014)S(0.003)K 110.38 0.0010773 2008190000 5499100 4203330 4357930 3955810 5540200 2949140 9841700 5246800 10329500 TRUE FALSE 5154921.147 4514548.927 4461302.158 4057322.782 5105095.04 3800508.843 8366028.451 5901874.53 8605439.719 0.599030534 0.524615717 0.518428146 0.471483494 0.593240463 0.441640284 0.972179078 0.685830675 1 23.03681748 1.742498461 10.83016586 0.86800175 0.524597892 0.760928352 0.095244985 0.038086496 25.11066607 0.038548179 0.021006346 55.2711449 -1.742498461 -0.343403858 LS(ph)SPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSSPVK 6 0 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 LS(0.556)S(0.444)PVK 90.37 0.051511 1356300000 3578200 2084700 2740300 2317000 2434800 2074900 2993400 2134900 2513100 TRUE FALSE 3354246.849 2239053.357 2805301.21 2376458.143 2243580.63 2673889.947 2544567.459 2401446.964 2093647.375 1.602106873 1.069451038 1.33991103 1.135080421 1.071613423 1.277144365 1.215375373 1.147015965 1 20.99758704 4.747827 24.8371613 1.179007613 1.602107116 0.643627301 0.102943516 714.8921821 1916117.998 0.02262705 0.280779521 55953.46684 -4.747827 0.423099504 LS(ph)SPVLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LSSPVLHR 8 0 Q16643;Q16643-3;Q16643-2;D6R9W4;D6RCR4 Q16643 DBN1 Drebrin 1 LS(0.634)S(0.366)PVLHR;LS(0.622)S(0.378)PVLHR;LS(0.845)S(0.155)PVLHR 132.01 0.00063159 4074670000 1023470 1106750 1029920 979000 967210 776970 1222350 832582 827413 TRUE FALSE 959412.8396 1188694.922 1054350.189 1004122.797 891249.2281 1001268.626 1039069.965 936531.6954 689312.425 1.39184034 1.724464667 1.529567944 1.456702014 1.292953958 1.452561407 1.507400603 1.358646183 1 19.39479849 -3.234784871 0.16819531 5.96E-18 1.639031349 0.659416649 0.108549051 39.68445578 0.643933314 14.43402531 0.445917366 0.000582392 3.234784871 1.639031349 LS(ph)STSSEETQLFHIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 1 LS(0.598)S(0.395)T(0.005)S(0.001)S(0.001)EETQLFHIPR 233.63 7.57E-20 72387000 30988 33677 27012 38414 47139 29334 38199 34945 40630 TRUE FALSE 29048.5164 36170.48012 27652.7374 39399.76827 43436.89309 37802.2496 32471.41457 39307.96017 33848.59052 0.858189837 1.068596345 0.816953881 1.164000263 1.283270364 1.116804246 0.95931364 1.161287946 1 15.04680814 3.225709868 24.9999957 1.109581384 0.933636913 0.420723379 0.109526655 245.7578156 478099.2756 0.032391282 0.038947554 1681.55032 -3.225709868 -0.175944471 LS(ph)TGSFPEDLLESDSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSTGSFPEDLLESDSSR 17 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 LS(0.333)T(0.333)GS(0.333)FPEDLLESDSSR 264.92 1.74E-27 21151000 79566 87567 77840 76660 95802 76163 90895 77903 98960 TRUE FALSE 74586.10609 94050.55179 79686.40156 78627.22539 88278.09737 98150.0217 77266.13858 87629.36104 82442.93669 0.904699773 1.14079575 0.966564326 0.953716941 1.070778176 1.190520688 0.9372075 1.062909262 1 16.33110828 LS(ph)TPQKGPSTHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSTPQKGPSTHPK 13 1 J3QQY0;Q68DK7;J3KSZ8;Q68DK7-2;Q68DK7-3;J3KTC2 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 LS(0.561)T(0.439)PQKGPSTHPK 98.573 0.0019671 399970000 732320 616560 750580 813450 915280 642940 1006700 780500 1148400 TRUE FALSE 686485.3984 662210.7439 768384.112 834324.5042 843397.6009 828546.3407 855754.6807 877947.1431 956724.6211 0.717537088 0.692164422 0.803140313 0.872063377 0.881546876 0.866023851 0.894462902 0.917659192 1 19.8677442 6.832946349 0.16534354 1.023981846 2.10E-12 0.932029139 0.023870092 9.864399718 0.146854711 0.073225621 2.310697336 6806852.639 -6.832946349 -1.023981846 LS(ph)TPQKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSTPQKK 7 1 B5MC51;P53671-3;F5GXC4;F5H2U0;Q96C90 B5MC51;Q96C90 LIMK2;PPP1R14B LIM domain kinase 2;Protein phosphatase 1 regulatory subunit 14B 1 LS(0.5)T(0.5)PQKK;LS(0.604)T(0.396)PQKK 101.46 0.005539 3007430000 1986890 978260 1247440 1136920 1207050 825990 1767470 1070360 1452030 TRUE FALSE 1862534.102 1050691.388 1277029.866 1166095.292 1112253.162 1064439.904 1502454.282 1203996.802 1209676.813 1.53969563 0.868571983 1.055678552 0.963972592 0.919463075 0.879937429 1.242029496 0.995304522 1 20.20619023 4.747190559 24.92193337 0.999631415 1.539695915 0.725560245 0.10599724 620.4083514 1791602.361 0.02615329 0.309569759 55871.52925 -4.747190559 0.5400645 LS(ph)VPTS(ph)DEEDEVPAPKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSVPTSDEEDEVPAPKPR 18 1 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 2 LS(0.99)VPT(0.02)S(0.99)DEEDEVPAPKPR 152.32 4.94E-07 233960000 511650 425600 437820 401020 480410 347020 573000 404740 503380 TRUE FALSE 479626.7398 457111.8668 448205.2972 411310.8521 442680.5365 447199.0406 487083.9695 455272.6799 419362.626 1.143704064 1.090015749 1.0687774 0.980799973 1.055603215 1.06637791 1.161486359 1.085630077 1 18.67783877 LS(ph)YSDKNLIDSMDQSAFAGFSFVNPK ddPTM_SK-BR-3_Pertuzumab_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(0.965)YS(0.035)DKNLIDSMDQSAFAGFSFVNPK;LS(0.981)YS(0.019)DKNLIDSMDQSAFAGFSFVNPK 468.4 1.73E-236 2656943000 2402792 1518664 1764015 1692876 1844099 1286096 2694106 1638968 2070919 TRUE FALSE 2252405.538 1631107.463 1805858.269 1736318.064 1699270.903 1657371.037 2290149.816 1843596.763 1725269.24 1.305538571 0.945421981 1.046710987 1.006404116 0.984930852 0.960644865 1.327415897 1.06858496 1 20.71839009 1.767634576 25 1.16593743 1.027564822 0.070533342 0.13090081 33.57736962 28888.76864 0.054471969 0.030212644 58.56451832 -1.767634576 -0.138372608 LSAEERDQLLPNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSAEERDQLLPNLR 14 1 P61457 P61457 PCBD1 Pterin-4-alpha-carbinolamine dehydratase 0 143.93 7.45E-06 0 78039 82063 88482 98360 103500 100890 88044 60363 53366 FALSE TRUE 73154.67829 88139.02991 90580.83482 100884.0841 95371.5275 130015.3052 74842.61956 67899.45343 44458.86984 1.645446197 1.982484715 2.037407499 2.26915539 2.14516311 2.924395192 1.683412552 1.527242003 1 15.44018365 1.174779044 2.176477982 1.056016508 2.133547079 0.556360464 0.338947109 0.212142137 1.798684423 0.304142479 0.086348629 14.95474611 -1.174779044 1.077530571 LSAEKVEIATLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSAEKVEIATLTR 13 1 P25789;H0YN18;P25789-2;H0YMZ1;H0YL69 P25789 PSMA4 Proteasome subunit alpha type-4;Proteasome subunit alpha type 0 ; 187.16 6.56E-06 1049360000 1233390 1543330 1396120 1478100 1979190 1161880 1766100 1491750 2329900 FALSE TRUE 1156194.322 1657599.759 1429236.626 1516030.548 1823752.401 1497295.894 1501289.701 1677998.271 1941024.638 0.595661847 0.853981823 0.736331007 0.781046525 0.939582304 0.771394585 0.773452161 0.864490969 1 20.888387 -5 0.102888114 1.6442531 0.658762045 0.48114383 0.080624311 174.6915889 1.215935756 24.22066456 1.182461338 1.00E-05 5 -0.985491055 LSAIYGGTYMLNKPIEEIIVQNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSAIYGGTYMLNKPIEEIIVQNGK 24 1 P50395;P50395-2;Q5SX87;Q5SX91 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 279.79 3.18E-52 448720000 1008070 798670 838850 851150 957390 634390 1173150 865930 1098180 FALSE TRUE 944976.6982 857804.3578 858747.9181 872991.95 882200.4513 817528.0945 997247.0485 974043.2666 914886.6635 1.032889358 0.937607238 0.938638579 0.954207756 0.964272938 0.893584011 1.0900225 1.064660034 1 19.80323351 1.714861548 9.704622064 1.056680758 0.950473378 0.55947851 0.040800986 0.067576891 16.01001044 0.017679634 0.009532921 51.86346727 -1.714861548 -0.106207381 LSAKPAPPKPEPKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSAKPAPPKPEPKPK 15 3 P05204 P05204 HMGN2 Non-histone chromosomal protein HMG-17 0 ; 105.9 0.00056023 2656100000 5109100 3162400 3968900 3963100 4292100 2652010 5622900 2875740 6504900 FALSE TRUE 4789330.551 3396547.386 4063044.182 4064799.856 3955015.779 3417602.235 4779798.345 3234782.469 5419190.167 0.883772373 0.626762908 0.749751173 0.750075146 0.729816754 0.630648147 0.8820134 0.596912522 1 22.36964584 -1.842442558 2.722616317 1.100210876 0.73082492 0.428121165 0.097625982 17245831.14 13034682.4 11306653.49 0.021410412 0.014373332 1.842442558 -0.369385956 LSAKPPAKVEAKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSAKPPAKVEAKPK 14 3 P05114;A6NEL0;F2Z2W6;F2Z2Y5;H7BXJ5;A0A494C035 P05114 HMGN1 Non-histone chromosomal protein HMG-14 0 92.38 0.0021823 410130000 1074400 832310 795290 956440 1137200 666650 1266400 669350 2068700 FALSE TRUE 1007155.222 893935.0984 814154.6544 980983.8696 1047888.899 859101.0328 1076515.077 752919.8209 1723420.606 0.584393165 0.518698161 0.472406244 0.569207462 0.608028531 0.498485993 0.624638625 0.436875258 1 20.71684341 -1.994764905 2.83760186 1.445650366 0.538835419 0.855131573 0.059619294 4124688.072 4391016.269 12029094.75 0.013628656 0.010121272 1.994764905 -0.906814948 LSALGNVTTCNDYVALVHPDLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LSALGNVTTCNDYVALVHPDLDR 23 0 P56537 P56537 EIF6 Eukaryotic translation initiation factor 6 0 ;;;; 254.25 1.63E-43 1997459000 1021432 1067202 1041162 903032 1009740 966380 1286239 1085878 841378 FALSE TRUE 957502.3944 1146218.747 1065858.854 926205.3299 930439.0935 1245358.218 1093379.403 1221452.259 700946.5763 1.366013369 1.63524409 1.520599273 1.321363655 1.327403721 1.776680649 1.55986125 1.742575397 1 19.41894497 4.777271334 21.46349152 1.520497378 1.366010823 0.005965817 0.230343169 10839.86167 6009481.984 0.049417294 9.263506578 59878.55817 -4.777271334 -0.154486555 LSASSS(ph)ISSADLFEEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSASSSISSADLFEEPR 17 0 Q9NP61;Q9NP61-2;H0Y6A0 Q9NP61;H0Y6A0 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 1 LSASS(0.014)S(0.985)ISSADLFEEPR 177.74 1.06E-09 25294000 43607 47970 37701 39761 50771 27038 48070 45416 46637 TRUE FALSE 40877.71571 51521.74871 38595.28552 40781.33458 46783.65046 34843.43167 40862.34976 51086.28757 38852.98341 1.05211266 1.326069305 0.993367359 1.049631997 1.204119899 0.89680196 1.05171717 1.314861385 1 15.24573776 3.959889212 19.10121384 1.068315045 1.202541318 0.11510407 0.132262948 37.41273636 41472.25445 0.031205131 0.056681434 9117.782167 -3.959889212 0.134226273 LSASTASELS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSASTASELSPK 12 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;H0YF21 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 LSASTASELS(1)PK 147.31 6.87E-05 159670000 606560 341930 420880 375860 420450 301930 492030 343490 576890 TRUE FALSE 568596.4923 367246.853 430863.4724 385505.2039 387429.553 389092.2896 418254.6693 386375.4826 480603.3321 1.183088952 0.764137134 0.896505379 0.802127614 0.806131641 0.809591327 0.870270015 0.803938418 1 18.87448713 4.746073072 24.91343268 0.837476948 1.183089124 0.715462825 0.067071079 413.7418017 1372050.566 0.013735081 0.145911986 55727.95054 -4.746073072 0.345612176 LSATFEGSEQVHQLEEQLEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSATFEGSEQVHQLEEQLEAR 21 0 A0A494BZV2;H0Y2S9 A0A494BZV2 MPRIP 0 103.2 0.00044366 32784000 19214 35539 31187 30518 34139 29262 29968 31744 30521 FALSE TRUE 18011.43004 38170.34454 31926.77037 31301.14355 31457.86065 37709.46437 25474.57661 35707.30828 25426.84793 0.708362676 1.501182712 1.255632254 1.231027284 1.237190734 1.483056983 1.001877098 1.40431517 1 14.63406501 -1.336728935 4.423720256 0.999711126 1.248218774 0.079443875 0.234782825 0.000591999 8.88E-05 0.201191529 0.047366591 0.046054393 1.336728935 0.248507648 LSCS(ph)LEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LSCSLEDLR 9 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 LS(0.063)CS(0.937)LEDLR;LSCS(1)LEDLR;LS(0.002)CS(0.998)LEDLR;LS(0.057)CS(0.943)LEDLR 159.12 6.95E-05 1665290000 3299230 3585980 3508220 3582440 3319730 2851090 4148840 3303740 2048880 TRUE FALSE 3092737.084 3851489.69 3591436.635 3674371.475 3059011.797 3674153.399 3526759.958 3716219.211 1706908.692 1.811893687 2.256412255 2.104059023 2.152646766 1.792135579 2.152519005 2.066167906 2.177163447 1 20.70295446 -1.084009014 4.199868105 0.999847354 2.082205208 0.82890979 0.151736137 3963754.509 2046139.343 5235.395479 0.032530008 0.082412101 1.084009014 1.082357854 LSCS(ph)LEDLRSESVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSCSLEDLRSESVDK 15 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 LSCS(0.999)LEDLRSESVDK;LS(0.047)CS(0.953)LEDLRSESVDK 146.78 2.32E-06 519070000 587790 591110 517450 637610 784200 362250 652010 511180 806680 TRUE FALSE 551001.2731 634876.3994 529724.1584 653972.1521 722612.0953 466825.6944 554247.1535 575001.9482 672039.8966 0.819893694 0.94470046 0.7882332 0.973115071 1.07525178 0.694639852 0.824723586 0.855606864 1 19.35818736 -1.62590415 8.616852855 1.000078372 0.868873058 0.125830831 0.105721075 0.000154025 6.69E-06 0.09905202 0.023332896 0.023664419 1.62590415 -0.131205313 LSDDFDS(ph)PVKGPLCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSDDFDSPVKGPLCK 15 1 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 LSDDFDS(1)PVKGPLCK 202.97 1.87E-11 0 428180 221500 306920 246980 305350 232750 423820 307700 437060 TRUE FALSE 401380.9781 237900.0905 314200.2873 253317.9249 281369.0427 299941.1466 360272.1256 346117.0223 364111.8625 1.102356225 0.653370887 0.862922414 0.695714562 0.772754397 0.823760985 0.989454513 0.950578814 1 18.47402222 1.792613729 4.18273444 0.978342838 0.796051821 0.274874753 0.120610719 0.237589435 7.697806666 0.055333763 0.029419683 62.03170659 -1.792613729 -0.182291017 LSDDNTIGKEEIQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSDDNTIGKEEIQQR 15 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 189.1 2.48E-07 605490000 494540 360230 364750 329090 406930 253190 450110 357080 713820 FALSE TRUE 463587.6242 386901.804 373402.0422 337535.0065 374971.3593 326281.8428 382620.1841 401662.224 594678.8305 0.779559655 0.650606317 0.627905389 0.5675921 0.630544321 0.548669006 0.643406431 0.675427144 1 19.18175119 0.653433406 2.363472887 0.999959961 0.63040734 0.776574923 0.06093658 1.045261301 6.576983311 0.055513419 0.014933937 4.502289383 -0.653433406 -0.369552622 LSDETLIDIMTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSDETLIDIMTR 12 0 P19367-4;P19367-2;P19367;P19367-3;B1AR62 P19367-4 HK1 Hexokinase-1 0 ; 169.58 0.00015885 36502000 147566 166544 176021 155643 162081 135099 168012 154321 181568 FALSE TRUE 138330.1075 178875.091 180196.3012 159637.0629 149351.8121 174099.8882 142820.1603 173588.3166 151263.1278 0.914499848 1.182542591 1.191277107 1.055360055 0.987364298 1.150973741 0.944183572 1.147591743 1 17.20670083 3.080100996 8.983208878 1.041023274 1.128020045 0.017464608 0.099974601 0.548489414 55.97779504 0.027108554 0.032431812 1202.544057 -3.080100996 0.086996772 LSDETLLEISKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSDETLLEISKR 12 1 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 158.42 0.00011785 78834000 61952 75232 62364 80768 85041 48951 83246 56269 84030 FALSE TRUE 58074.53491 80802.25556 63843.30353 82840.64362 78362.2229 63082.35905 70764.03512 63294.30851 70004.85015 0.829578733 1.154237962 0.911984004 1.183355774 1.119382768 0.901114122 1.010844748 0.904141761 1 16.09516726 2.231528654 24.99999462 0.958997927 1.044438155 0.126291304 0.111259703 341.0960375 1212651.488 0.038093006 0.028739329 170.4231757 -2.231528654 0.085440229 LSDFLITGGGKGS(ph)GFSLDVIDGPISQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSDFLITGGGKGSGFSLDVIDGPISQR 27 1 O43166-3;O43166-2;O43166 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 LSDFLIT(0.008)GGGKGS(0.986)GFS(0.006)LDVIDGPISQR;LSDFLIT(0.138)GGGKGS(0.804)GFS(0.058)LDVIDGPISQR 125.02 4.62E-05 502518000 230631 232509 222250 220315 283399 173937 313780 233051 291000 TRUE FALSE 216196.2174 249724.2083 227521.875 225968.6559 261141.9857 224149.7883 266731.602 262147.9304 242430.2201 0.891787407 1.03008696 0.938504593 0.932097722 1.07718413 0.924595078 1.100240729 1.081333549 1 17.88721002 1.723230586 10.55403827 1.066977701 0.973021028 0.355487598 0.059387431 0.102207704 36.80396648 0.025423393 0.013805056 52.87259006 -1.723230586 -0.093956672 LSDGFNGADLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSDGFNGADLR 11 0 A0A087X2I1;P62333;H0YJC0 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 102.52 0.0066466 48545000 113360 144060 118380 142190 151930 113990 144270 129170 157730 FALSE TRUE 106265 154726.3523 121188.0295 145838.8361 139998.0307 146897.0625 122638.0528 145297.1588 131403.844 0.808690193 1.17748726 0.92225635 1.10985213 1.065402856 1.117905367 0.933291212 1.105729896 1 17.00364795 4.760410152 24.39087908 1.047142933 0.808689846 0.467579116 0.081973304 3838.158855 4284483.584 0.018147464 0.884140941 57598.36446 -4.760410152 -0.238453088 LSDGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSDGIR 6 0 P37837 P37837 TALDO1 Transaldolase 0 113.08 0.061517 354550000 910680 1154800 993790 1020700 1135400 876060 1167300 1048000 1045700 FALSE TRUE 853682.1644 1240302.594 1017363.168 1046892.89 1046230.264 1128964.3 992274.2017 1178845.107 871165.9145 0.979930631 1.423727183 1.167817922 1.201714705 1.200954085 1.295923407 1.139018625 1.353180935 1 19.73258798 -1.108497112 4.24240437 0.999962128 1.229320507 0.241705624 0.121687373 3.84E-05 8.07E-06 0.103819647 0.024466488 0.077893799 1.108497112 0.22935838 LSDIS(ph)PIGRDPSESSFSSATLTPSSTCPSLVDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSDISPIGRDPSESSFSSATLTPSSTCPSLVDSR 34 1 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;A0A0U1RQL3 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 LSDIS(1)PIGRDPSESSFSSATLTPSSTCPSLVDSR 306.88 3.43E-91 149540000 16465 15993 21318 19282 18065 12141 17838 20708 21775 TRUE FALSE 15434.48504 17177.13836 21823.67303 19776.80876 16646.24777 15645.90961 15163.3575 23293.43938 18140.61183 0.850824944 0.94688859 1.203028499 1.090195245 0.917623282 0.862479709 0.835879057 1.28404927 1 14.14693549 2.731190625 24.40503454 0.949083952 1.040142395 0 0.152633975 1176.441369 3895667.186 0.048696025 0.046822025 538.5060975 -2.731190625 0.091058443 LSDLDSETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LSDLDSETR 9 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 ;;; 177.97 0.00011981 851160000 2351510 2399200 2454570 2359900 2525720 2130160 2676120 2204010 2544460 FALSE TRUE 2204333.187 2576839.264 2512793.56 2420459.029 2327360.139 2745102.612 2274860.65 2479185.5 2119773.188 1.03989106 1.215620274 1.185406804 1.14184812 1.09792885 1.29499827 1.07316229 1.169552249 1 21.01547848 0.141153012 0.82414333 0.997446497 1.163870334 0.286259605 0.073622853 4.57353374 3.445529709 0.097510273 0.0219142 1.384053927 -0.141153012 0.166423837 LSDPPTSPS(ph)SPSQMMPHVQTHF ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSDPPTSPSSPSQMMPHVQTHF 22 0 Q13496-2;Q13496 Q13496-2 MTM1 Myotubularin 1 LSDPPT(0.007)S(0.03)PS(0.531)S(0.427)PS(0.005)QMMPHVQTHF 101.48 0.00044915 199260000 167630 393570 311890 366130 419620 374260 279130 232470 288660 TRUE FALSE 157138.3375 422710.3323 319288.1781 375525.5157 386664.7379 482302.7864 237277.0478 261494.3912 240480.7812 0.653434078 1.757771786 1.327707672 1.561561443 1.607882077 2.005577261 0.986677799 1.087381661 1 17.87556208 1.61155206 25 1.027736713 1.505737211 0.279153698 0.348178815 0.409145028 2754.93868 0.153936866 0.081185726 40.88387574 -1.61155206 0.478000498 LSDPPTSPSS(ph)PSQMMPHVQTHF ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSDPPTSPSSPSQMMPHVQTHF 22 0 Q13496-2;Q13496 Q13496-2 MTM1 Myotubularin 1 LSDPPT(0.005)S(0.005)PS(0.169)S(0.672)PS(0.148)QMMPHVQTHF;LSDPPTSPS(0.007)S(0.992)PS(0.001)QMMPHVQTHF 206.47 5.95E-23 309665000 175777 339661 279793 372743 370343 288871 289274 224734 293125 TRUE FALSE 164775.4313 364809.8539 286429.8221 382308.2164 341257.7547 372263.3683 245900.0492 252792.5346 244200.5438 0.674754563 1.493894518 1.172928682 1.565550225 1.397448791 1.524416623 1.006959466 1.035184159 1 17.89770689 1.639359467 7.949135936 1.013532801 1.324255319 0.22323737 0.253523411 0.158083041 20.23038087 0.116726101 0.05972808 43.58724976 -1.639359467 0.310722518 LSDQFHDILIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LSDQFHDILIR 11 0 O75340-2;O75340;A0A024QZ42;H0Y9X3;A0A087WZ38 O75340-2 PDCD6 Programmed cell death protein 6 0 ;;;;; 234.63 1.67E-15 3434980000 2817670 4171480 3516180 3542560 3852430 2572600 4318920 3417490 4316880 FALSE TRUE 2641317.064 4480340.72 3599585.45 3633468.087 3549875.688 3315267.857 3671338.041 3844171.149 3596364.84 0.734440798 1.245797053 1.000895518 1.010316875 0.987073294 0.92183858 1.02084694 1.068904664 1 21.77810795 3.530799644 24.93682097 0.998337439 1.056732702 0 0.12962726 606.3443368 281680.1907 0.031741501 0.0491736 3394.686275 -3.530799644 0.058395263 LSEAACEDEDSASEGLGELFLDGLSTENPHGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSEAACEDEDSASEGLGELFLDGLSTENPHGAR 33 0 O95801 O95801 TTC4 Tetratricopeptide repeat protein 4 0 51.236 0.069255 22206000 5089.3 4813.3 6191.2 5136 6663.6 5801.2 9166.2 4474.3 7189.3 FALSE TRUE 4770.769798 5169.68174 6338.058188 5267.798455 6140.267736 7475.912265 7791.813405 5032.926204 5989.359385 0.796540914 0.863144354 1.058219716 0.879526192 1.025196075 1.248198978 1.300942706 0.840311272 1 12.54818599 2.470554589 5.463217513 1.146185499 0.922026463 0.262552838 0.144921501 0.188402633 18.65270197 0.04880019 0.042303593 295.4980295 -2.470554589 -0.224159036 LSEAVWQPEEHYSS(ph)SPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSEAVWQPEEHYSSSPEK 18 0 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 LSEAVWQPEEHYS(0.003)S(0.545)S(0.452)PEK 167.61 1.47E-11 147110000 134300 163730 179370 195570 212230 152510 239120 170660 202650 TRUE FALSE 125894.4027 175852.7396 183624.7411 200588.6573 195562.3119 196537.1612 203266.1759 191967.2767 168826.4058 0.745703269 1.041618689 1.087654151 1.188135566 1.158363296 1.164137566 1.203995162 1.137069025 1 17.36518105 5.29969959 0.958847013 1.152080624 1.51E-15 0.798415721 0.060464673 2.006232027 0.689045953 0.016895929 3.094787842 199388.263 -5.29969959 -1.152080624 LSEAVWQPEEHYSSS(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LSEAVWQPEEHYSSSPEK 18 0 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 LSEAVWQPEEHYSS(0.055)S(0.945)PEK;LSEAVWQPEEHYSS(0.101)S(0.899)PEK;LSEAVWQPEEHYSS(0.017)S(0.983)PEK 193.87 6.54E-15 561200000 496145 629020 628920 775850 830590 546540 884400 681630 774220 TRUE FALSE 465092.1701 675593.2953 643838.2794 795759.6245 765358.8118 704317.2257 751792.4304 766733.006 644997.6803 0.721075725 1.047435233 0.998202473 1.233740289 1.186607077 1.091968618 1.165573851 1.188737618 1 19.29893445 5.353691319 0.832432212 1.140102115 1.49E-15 0.695431782 0.081532375 3.221962364 0.831985064 0.025523487 4.295467601 225783.0415 -5.353691319 -1.140102115 LSEEAECPNPST(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LSEEAECPNPSTPSK 15 0 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 LSEEAECPNPS(0.001)T(0.988)PS(0.011)K;LSEEAECPNPS(0.008)T(0.989)PS(0.003)K;LSEEAECPNPS(0.017)T(0.982)PS(0.002)K;LSEEAECPNPS(0.012)T(0.987)PS(0.002)K 355.06 1.77E-81 639580000 2019270 1544520 1857630 2332310 2857400 1162390 1568350 1078930 1686400 TRUE FALSE 1892887.495 1658877.868 1901693.861 2392161.023 2632991.33 1497953.123 1333190.477 1213636.786 1404928.945 1.347319024 1.180755705 1.353587217 1.70269182 1.87410996 1.066212728 0.94893801 0.863842111 1 20.42206574 2.020729622 24.76913355 0.95083363 1.442559911 0.633969865 0.197039453 162.3193197 193949.0122 0.082396895 0.060848127 104.8889221 -2.020729622 0.491726281 LSEEFLTAHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSEEFLTAHPR 11 0 Q15813-2;Q15813;A0A2R8Y5Q8;A0A2R8YHI9;A0A2R8Y7E7;A0A2U3TZJ6;A0A2R8Y6Q1 Q15813-2 TBCE Tubulin-specific chaperone E 0 138.25 6.15E-05 67888000 53107 76310 56940 66628 80102 48703 65394 61963 83080 FALSE TRUE 49783.12767 81960.0718 58290.64369 68337.78728 73811.11204 62762.76547 55588.77679 69699.21695 69213.41128 0.719269962 1.184164605 0.842187123 0.987348926 1.066427888 0.906800637 0.803150369 1.007018953 1 16.07876399 2.040179706 24.97695514 0.899881877 0.976576223 0 0.135977215 414.2392229 257502.2196 0.047043143 0.034743608 109.6932 -2.040179706 0.076694346 LSEELSGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 101210000 115470 127440 127410 117230 141180 127730 130310 121000 122040 FALSE TRUE 108242.9388 136875.7902 130432.2254 120238.3203 130092.2923 164603.5775 110771.2252 136107.1164 101670.7356 1.064642035 1.346265367 1.282888578 1.182624671 1.279545107 1.618986786 1.089509431 1.338704944 1 16.63354496 -1.465851884 9.444828154 0.999997467 1.280871837 0.238084508 0.154551657 7.40E-06 4.19E-07 0.134424966 0.031683982 0.034209609 1.465851884 0.280874369 LSEGFSIHTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LSEGFSIHTR 10 0 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ;;;; 218.6 6.70E-09 2544300000 1709440 3272860 2617440 2650560 3279530 2266650 3029370 2875140 2804770 FALSE TRUE 1602449.202 3515185.96 2679526.913 2718577.857 3021968.943 2920995.059 2575144.092 3234107.558 2336635.767 0.685793321 1.504379077 1.146745655 1.16345812 1.293299103 1.250085743 1.102073386 1.384087158 1 21.15600144 -1.10429753 7.497122949 0.999999959 1.211950227 0.064933216 0.215699082 1.28E-07 1.53E-08 0.18289163 0.043107962 0.078650678 1.10429753 0.211950268 LSEGS(ph)QPAEEEEDQETPSR ddPTM_SK-BR-3_Pertuzumab_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 417.28 2.94E-148 299840000 235780 257600 246870 277460 281410 213810 248580 223010 307450 TRUE FALSE 221022.9507 276672.972 252725.873 284580.0933 259309.1938 275533.4761 211307.7367 250853.2894 256134.6088 0.862917166 1.080185818 0.986691623 1.111056779 1.012394205 1.075737002 0.824987055 0.979380688 1 17.96654268 1.754101896 25 0.918846553 1.027347566 0.189647419 0.081727457 6.473847298 10426.82042 0.033576645 0.018620007 56.76777814 -1.754101896 0.108501013 LSEGSQPAEEEEDQET(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSEGSQPAEEEEDQETPSR 19 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 LSEGSQPAEEEEDQET(0.993)PS(0.007)R;LSEGSQPAEEEEDQET(0.991)PS(0.009)R 383.48 9.72E-126 202751000 108963 105333 126944 115328 127668 116407 146030 119247 172326 TRUE FALSE 102143.2003 113131.9649 129955.1716 118287.5117 117641.4703 150011.8112 124134.1572 134135.2504 143563.6773 0.711483589 0.78802638 0.90520927 0.8239376 0.819437566 1.0449148 0.864662702 0.934325819 1 17.13133126 7.305500834 0.208607596 0.985539539 2.48E-13 0.612346497 0.061914798 27.24768416 0.434691974 0.102083757 8.384272882 20206953.11 -7.305500834 -0.985539539 LSEHATAPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LSEHATAPTR 10 0 P33316-2;H0YNJ9;H0YNW5;P33316;A0A0C4DGL3;H0YKC5;H0YMM5;H0YKI0 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 ;; 103.26 0.0028386 703630000 215130 469040 320990 336300 537490 285669 350576 421771 591790 FALSE TRUE 201665.3973 503768.2096 328604.0344 344930.0274 495277.7035 368137.0029 298010.3834 474430.0378 493016.4259 0.409043972 1.021808165 0.666517416 0.699631917 1.004586617 0.746703322 0.604463397 0.962300672 1 18.91127619 1.100642986 7.693606143 0.998716649 0.758259298 0.239376098 0.1788313 0.326961235 20.56313956 0.158462625 0.039706467 12.60790668 -1.100642986 -0.240457351 LSEHSGPPIVIRDS(ph)PVPCTPPALPPCAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSEHSGPPIVIRDSPVPCTPPALPPCAR 28 1 Q6ZRI6;H3BMJ2;Q6ZRI6-2 Q6ZRI6 C15orf39 Uncharacterized protein C15orf39 1 LS(0.067)EHS(0.062)GPPIVIRDS(0.869)PVPCT(0.002)PPALPPCAR 42.884 0.090797 56923000 25685 37713 33984 28197 37414 31909 38657 31717 34076 TRUE FALSE 24077.4217 40505.30976 34790.11653 28920.58276 34475.65536 41120.6103 32860.74172 35676.93727 28388.49546 0.848140111 1.426821292 1.22550054 1.018743061 1.214423477 1.448495584 1.157537277 1.256739277 1 14.79301877 -0.885242694 5.647352452 0.999999887 1.22349779 0.09901839 0.176485593 2.30E-07 4.54E-08 0.155865229 0.036737768 0.130243874 0.885242694 0.223497904 LSELEPGTGDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSELEPGTGDLR 12 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 115.7 0.0021437 81254000 154360 169510 167970 190940 174060 162440 191790 143270 158210 FALSE TRUE 144698.8831 182060.6968 171954.3277 195839.8437 160390.0297 209333.791 163032.87 161157.5749 131803.7289 1.097836035 1.381301563 1.304624149 1.485844485 1.216885372 1.588223586 1.236936704 1.222708767 1 17.00803166 0.954618644 1.854337105 1.00388064 1.345470635 0.375563959 0.136595615 0.365168308 2.630386596 0.113507618 0.032110569 9.007798103 -0.954618644 0.341589995 LSELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LSELLR 6 0 P08238;A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2;P07900;P07900-2 P08238;A0A669KBG8;Q92538-3;P07900 HSP90AB1;GBF1;HSP90AA1 Heat shock protein HSP 90-beta;Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1;Heat shock protein HSP 90-alpha 0 ;;;;;;; 150.06 0.024567 3350246000 2013259 2447880 2150155 2074483 2392734 1808402 2344932 2102496 2101796 FALSE TRUE 1887252.713 2629123.582 2201157.692 2127717.746 2204818.323 2330458.3 1993331.216 2364997.254 1750992.669 1.07781874 1.50150462 1.257091323 1.215149431 1.259181927 1.330935498 1.138400663 1.350660854 1 20.73974161 -4.477359242 0.198600191 6.34E-11 1.327226963 0.292988468 0.120327095 121.6514369 1.451830431 48.42256428 0.276134135 3.33E-05 4.477359242 1.327226963 LSELSNSQQSVQTLSLWLIHHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSELSNSQQSVQTLSLWLIHHR 22 0 Q96P16;A0A0C4DGQ6;E9PQF3;K7EQR8;Q9NQG5;E9PIQ9 Q96P16;Q9NQG5 RPRD1A;RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1A;Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ; 277.8 9.32E-46 938580000 744040 937990 862790 847110 1080120 738690 978950 923050 760400 FALSE TRUE 697471.8645 1007439.756 883255.7862 868848.2768 995291.7322 951937.8114 832165.5356 1038294.824 633484.3276 1.101008871 1.590315201 1.394281986 1.371538709 1.571138683 1.50270144 1.313632397 1.639022118 1 19.2729494 -1.11803434 4.426433177 0.999946424 1.441264453 0.432178376 0.156737173 7.46E-05 1.49E-05 0.132957323 0.031334443 0.076201875 1.11803434 0.441318029 LSEMTEAEQQQLIDDHFLFDKPVS(ph)PLLTAAGMAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSEMTEAEQQQLIDDHFLFDKPVSPLLTAAGMAR 34 1 P12532;P12532-2;F8WCN3 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 1 LSEMTEAEQQQLIDDHFLFDKPVS(0.966)PLLT(0.034)AAGMAR 91.911 0.00023501 53798000 101660 100880 102350 107860 134240 85158 126040 92653 107150 TRUE FALSE 95297.28207 108349.2602 104777.7903 110627.8702 123697.3319 109741.7322 107141.4721 104220.931 89265.97278 1.067565603 1.213780086 1.173770778 1.239306163 1.385716506 1.229379222 1.200249869 1.167532574 1 16.44582272 0.750841201 1.820888211 1.000240416 1.218596603 0.435033018 0.077100661 0.885025213 4.707114606 0.072438037 0.020345138 5.634316 -0.750841201 0.218356188 LSEMTEAEQQQLIDDHFLFDKPVSPLLTAAGMAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSEMTEAEQQQLIDDHFLFDKPVSPLLTAAGMAR 34 1 P12532;P12532-2;F8WCN3 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ; 377.66 5.49E-149 1843100000 739530 662400 660280 683710 851380 519580 758980 667050 788830 FALSE TRUE 693244.1374 711444.7852 675942.1534 701255.1561 784516.0491 669574.3113 645177.995 750332.6609 657169.177 1.05489448 1.082590009 1.028566429 1.067084673 1.193780957 1.018876622 0.98175328 1.141764841 1 19.32590529 -1.221221428 4.921177865 0.999990666 1.063471304 0.107488143 0.060962191 6.10E-06 9.65E-07 0.057645965 0.013585286 0.06008673 1.221221428 0.063480638 LSEPWEGDFQEDHNANLWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSEPWEGDFQEDHNANLWR 19 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 0 151.96 6.04E-08 37652000 65259 49174 55906 57129 66019 47768 68472 55548 86738 FALSE TRUE 61174.55568 52814.89413 57232.11672 58595.02686 60834.13405 61557.84615 58205.25926 62483.29008 72260.86745 0.846579315 0.730892058 0.792020892 0.810881864 0.841868306 0.851883576 0.805487968 0.864690562 1 16.14092695 -4.232831838 0.159607437 1.565857366 0.750027797 0.757618627 0.033877655 45.08512357 0.518687928 8.21366027 0.145516459 5.85E-05 4.232831838 -0.815829569 LSETSIKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LSETSIKDR 9 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;; 167.67 9.61E-05 579850000 1216900 1350690 1282250 1271350 1612800 980370 1454610 1255970 2865100 FALSE TRUE 1140736.401 1450696.493 1312665.576 1303974.993 1486137.194 1263386.904 1236504.734 1412780.619 2386896.301 0.477916196 0.607775249 0.549946629 0.546305674 0.622623276 0.529301128 0.518038733 0.591890238 1 21.18670446 0.936175765 16.40181084 1 0.555257187 0.919737432 0.041426277 56.25586259 14457.28393 0.037596735 0.009399364 8.633278778 -0.936175765 -0.444742813 LSEVLQAVTDHDIPQQLVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LSEVLQAVTDHDIPQQLVER 20 0 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ;;; 232.79 6.46E-27 586415000 541262 590255 573995 548183 627567 472731 591157 490254 579439 FALSE TRUE 507385.3776 633958.0944 587610.4325 562250.3039 578280.4193 609200.7656 502518.4959 551463.2911 482726.8876 1.051081658 1.313285236 1.217273054 1.164737905 1.197945327 1.261998826 1.040999598 1.14239191 1 18.88084766 1.719630797 8.356543889 1.070561405 1.214280609 0.417483289 0.076448187 0.100131737 18.72891022 0.03441964 0.018310167 52.43614993 -1.719630797 0.143719205 LSFAHPPSAEVEAIALATLHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSFAHPPSAEVEAIALATLHDR 22 0 O15067 O15067 PFAS Phosphoribosylformylglycinamidine synthase 0 ; 223.93 4.23E-26 169555000 200051 295060 278860 280530 297740 249830 315450 264040 272440 FALSE TRUE 187530.165 316906.5494 285474.6909 287728.8747 274356.7014 321951.8653 268151.201 297005.9752 226968.004 0.826240535 1.3962609 1.257775043 1.267706768 1.208790211 1.418490094 1.181449351 1.308580813 1 17.79212941 -1.1997938 4.876020508 0.999968256 1.253217902 0.157927133 0.163471425 4.92E-05 8.07E-06 0.138044477 0.032533321 0.063125699 1.1997938 0.253249646 LSFASETPLEKEPHS(ph)PADQPEQQAESTLTSAETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LSFASETPLEKEPHSPADQPEQQAESTLTSAETR 34 1 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2 H3BSS6 ZNF106 Zinc finger protein 106 1 LSFAS(0.001)ET(0.001)PLEKEPHS(0.998)PADQPEQQAESTLTSAETR;LSFASETPLEKEPHS(1)PADQPEQQAESTLTSAETR;LSFASETPLEKEPHS(1)PADQPEQQAESTLTSAETR;LS(0.001)FAS(0.008)ET(0.005)PLEKEPHS(0.987)PADQPEQQAESTLTSAETR 372.55 1.12E-148 2385240000 948810 955905 992098 961933 1175780 741374 1062056 907533 1630570 TRUE FALSE 889425.6758 1026681.201 1015631.033 986617.8293 1083438.982 955396.6386 902810.5624 1020840.493 1358417.333 0.654751419 0.755792182 0.747657593 0.7262995 0.797574468 0.703315995 0.664604713 0.751492541 1 20.37349534 0.957858408 23.09517295 1.000000001 0.725064387 0.81120592 0.041881003 1548.499031 848636.8707 0.040842895 0.010210724 9.075246028 -0.957858408 -0.274935613 LSFDKDAMVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LSFDKDAMVAR 11 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ;; 172.51 1.21E-05 5060400000 8232040 9028860 8190180 8134860 10488680 6603260 9678720 8651810 11153320 FALSE TRUE 7716811.311 9697366.189 8384454.937 8343614.28 9664941.382 8509513.967 8227485.789 9732007.523 9291758.839 0.830500602 1.043652376 0.902353912 0.897958548 1.040162745 0.915813046 0.885460539 1.047380554 1 23.14752028 1.226201531 24.99973998 1.023690313 0.938304868 0.243565357 0.067029064 384.1202312 776967.6201 0.058509474 0.015047126 16.83455074 -1.226201531 -0.085385445 LSFFFDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSFFFDFR 8 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 134.15 0.002068 313340000 377510 1411110 512260 529690 1484770 388930 663900 1423130 1255130 FALSE TRUE 353882.323 1515590.053 524411.0491 543282.7422 1368162.153 501207.7772 564354.3583 1600810.913 1045640.695 0.338435875 1.449436753 0.50152127 0.519569241 1.308443867 0.479330787 0.539721112 1.530937847 1 19.99595576 1.24107562 24.99998571 1.265468927 0.769338804 0.241854017 0.387403444 93.24653123 926981.8659 0.274418999 0.089706472 17.42110187 -1.24107562 -0.496130123 LSFQHDPETSVLVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LSFQHDPETSVLVLR 15 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;; 156.17 2.17E-06 2094640000 1636566 2362399 2091281 2142216 2371538 1754243 2599610 2065161 2207744 FALSE TRUE 1534136.255 2537313.48 2140887.173 2197188.889 2185286.972 2260664.476 2209822.614 2323000.897 1839257.264 0.8341064 1.37953158 1.163995497 1.194606612 1.188135567 1.229118145 1.20147554 1.263010315 1 20.81069186 -0.94910073 4.468931328 0.999995964 1.200628568 0.133153571 0.138477019 0.014611323 36010639.87 351.8225385 0.028301603 0.112434416 0.94910073 0.200632604 LSFS(ph)PENILIQNQDIVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LSFSPENILIQNQDIVR 17 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 LS(0.045)FS(0.955)PENILIQNQDIVR;LSFS(1)PENILIQNQDIVR;LS(0.002)FS(0.998)PENILIQNQDIVR;LSFS(1)PENILIQNQDIVR;LS(0.001)FS(0.999)PENILIQNQDIVR 303.03 1.62E-46 329563100 263319.6 298216.9 267316.5 276434.9 288188 230252 301999.1 264727.2 273516 TRUE FALSE 246838.8963 320297.1896 273657.3736 283528.6875 265554.877 296722.0146 256717.1386 297778.9737 227864.4126 1.083270939 1.405648148 1.200965831 1.24428683 1.165407419 1.302186731 1.126622344 1.306825275 1 17.7978161 -4.428586682 0.242650712 4.27E-11 1.261393659 0.33310505 0.096693182 131.0997292 1.687366531 64.57205936 0.135281961 3.73E-05 4.428586682 1.261393659 LSFSDTYQDYEEYWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSFSDTYQDYEEYWR 15 0 Q9UHI6;E9PJ60 Q9UHI6 DDX20 Probable ATP-dependent RNA helicase DDX20 0 125.53 0.00020917 23722000 14218 16105 12924 15160 14688 12161 12852 13764 15753 FALSE TRUE 13328.12076 17297.43096 13230.56338 15549.03127 13534.46373 15671.68328 10924.96191 15482.4657 13123.72253 1.015574714 1.318027786 1.008141048 1.184803414 1.031297614 1.19414924 0.832459074 1.179731258 1 13.67988938 2.519207953 0.805402099 1.001913623 1.159192826 0.075602814 0.132047392 1.100760313 1.453347155 0.087753486 0.067286979 330.5277699 -2.519207953 0.157279204 LSGAEPDDEEYQEFEEMLEHAESAQDFASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSGAEPDDEEYQEFEEMLEHAESAQDFASR 30 0 Q96GC9;K7EPE7;Q96GC9-2 Q96GC9 VMP1 Vacuole membrane protein 1 0 75.275 0.0044458 16823000 17809 18079 16518 17534 18499 15472 22777 18628 19614 FALSE TRUE 16694.36648 19417.58797 16909.81476 17983.95212 17046.16316 19938.51523 19361.8003 20953.74681 16340.29669 1.021668504 1.1883253 1.034853594 1.100589082 1.043197898 1.220205215 1.184911184 1.282335762 1 13.99614656 2.234099579 24.99798674 1.18819551 1.088001312 0.218390138 0.084833683 147.969232 829154.1296 0.02784536 0.021269934 171.4350345 -2.234099579 -0.100194198 LSGAQADLHIEDGDSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSGAQADLHIEDGDSIR 17 0 M0QXB5;O95571 M0QXB5 ETHE1 "Persulfide dioxygenase ETHE1, mitochondrial" 0 189.9 3.29E-10 157050000 123680 136510 110150 116880 148130 111250 122110 123340 152160 FALSE TRUE 115939.0896 146617.3424 112762.81 119879.3387 136496.4673 143366.069 103800.7391 138739.2705 126763.513 0.914609313 1.15662101 0.88955258 0.945692777 1.076780409 1.130972672 0.818853443 1.094473222 1 16.95178002 3.969980779 24.82881634 0.983845732 1.049174848 0.014946523 0.110556398 765.0822353 2660355.982 0.026719622 0.049434342 9332.12997 -3.969980779 0.065329116 LSGEHS(ph)ESS(ph)TPRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSGEHSESSTPRPR 14 1 Q7Z3K3-5;Q7Z3K3-7;Q7Z3K3-2;Q7Z3K3-3;Q7Z3K3-6;Q7Z3K3 Q7Z3K3-5 POGZ Pogo transposable element with ZNF domain 2 LS(0.011)GEHS(0.681)ES(0.329)S(0.547)T(0.432)PRPR 61.648 0.047408 144460000 148330 168000 171130 172100 173660 131650 173300 153450 200860 TRUE FALSE 139046.2901 180438.8948 175189.2844 176516.3774 160021.4441 169655.2178 147315.2738 172608.5703 167335.1684 0.830944812 1.078308263 1.046936434 1.054867181 0.956292964 1.013864685 0.880360508 1.031514008 1 17.35238116 2.722948707 24.05456458 0.964877484 1.022716898 0 0.079426932 1096.080454 1688816.733 0.024207743 0.022894214 528.3828428 -2.722948707 0.057839414 LSGEHS(ph)ESSTPRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.559)ES(0.279)S(0.051)T(0.112)PRPR;LSGEHS(0.907)ES(0.046)S(0.046)T(0.001)PRPR;LSGEHS(0.852)ES(0.123)S(0.025)TPRPR;LSGEHS(0.895)ES(0.102)S(0.002)TPRPR 179.85 1.10E-06 3133180000 656744 829221 723076 872680 877738 725548 985073 734666 974512 TRUE FALSE 615639.5654 890617.3856 740227.7042 895074.4462 808803.9981 935001.9293 837370.4486 826390.6673 811859.6516 0.758307873 1.097009051 0.911768066 1.10249899 0.996236229 1.151679268 1.031422669 1.017898433 1 19.63087082 4.746226613 24.75951789 1.037049154 0.758307719 0.634821796 0.06679241 527.2137147 1702740.78 0.014968093 0.160446333 55747.6562 -4.746226613 -0.278741435 LSGEHSES(ph)STPRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSGEHSESSTPRPR 14 1 Q7Z3K3-5;Q7Z3K3-7;Q7Z3K3-2;Q7Z3K3-3;Q7Z3K3-6;Q7Z3K3 Q7Z3K3-5 POGZ Pogo transposable element with ZNF domain 1 LSGEHS(0.04)ES(0.763)S(0.155)T(0.043)PRPR;LSGEHS(0.343)ES(0.479)S(0.089)T(0.089)PRPR 140.78 5.97E-06 1881830000 387971 520381 462766 468685 514286 403208 595085 455983 569892 TRUE FALSE 363688.5877 558910.5507 473743.0281 480712.2506 473896.0521 519607.6041 505857.5287 512913.4813 474773.3436 0.76602571 1.177215525 0.997829879 1.012508931 0.998152189 1.094432978 1.065471631 1.08033336 1 18.85687941 2.24446365 24.97285279 1.066543534 1.017856447 0.067214749 0.102755983 471.4230084 1994362.935 0.033816121 0.027602281 175.5753932 -2.24446365 -0.048687087 LSGFS(ph)FK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LSGFSFK 7 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 LSGFS(1)FK;LSGFS(1)FK;LSGFS(1)FK;LSGFS(1)FK;LSGFS(1)FK 154.01 0.001791 2130213000 5892471 4479257 3992810 3810666 4193941 1979032 6446300 3313111 3755316 TRUE FALSE 5523671.758 4810905.849 4087521.339 3908454.141 3864565.791 2550346.411 5479737.16 3726760.201 3128529.499 1.765580845 1.537753072 1.30653118 1.249294322 1.235265895 0.815190143 1.751537635 1.191217856 1 21.57705328 4.51157997 1.039533179 1.252627655 1.904647944 0.375845431 0.238218231 1.541409747 1.747873903 0.071996725 1.023406433 32477.30394 -4.51157997 0.652020289 LSGFS(ph)FKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSGFSFKK 8 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 LSGFS(1)FKK;LSGFS(1)FKK 129.89 0.0011349 2436000000 2932900 2213700 1855690 1706260 2247300 837040 3107600 1500840 2616300 TRUE FALSE 2749335.024 2377604.651 1899707.843 1750045.52 2070806.123 1078679.86 2641644.23 1688223.178 2179622.628 1.261381208 1.090833166 0.871576492 0.802912164 0.95007553 0.494892944 1.211973208 0.774548381 1 21.05564694 4.434795031 1.440000004 0.878758793 1.304843539 0.345318461 0.181462864 0.796284509 2.248025093 0.046748926 0.415907616 27214.16612 -4.434795031 0.426084746 LSGINEIPRPFS(ph)PPVTSNT(ph)SPPPAAPLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 2 LSGINEIPRPFS(1)PPVT(0.184)S(0.158)NT(0.35)S(0.308)PPPAAPLAR;LSGINEIPRPFS(0.99)PPVT(0.014)S(0.101)NT(0.475)S(0.42)PPPAAPLAR 134.73 1.69E-05 454026000 323740 336050 377670 346890 413470 349810 452990 387820 594020 TRUE FALSE 303477.6913 360931.4917 386628.5107 355791.7847 380997.7341 450794.4683 385068.3549 436240.1807 494874.2245 0.613242065 0.729339848 0.781266212 0.718953963 0.769888014 0.910927355 0.778113581 0.881517281 1 18.91670238 4.782325905 0.061908188 1.369528357 1.03E-11 0.793056068 0.049623835 70.51922253 0.677429419 4.626156699 11.44845183 60579.53074 -4.782325905 -1.369528357 LSGINEIPRPFS(ph)PPVTSNTS(ph)PPPAAPLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 2 LSGINEIPRPFS(0.821)PPVT(0.175)S(0.054)NT(0.071)S(0.878)PPPAAPLAR 139.31 6.65E-08 395580000 175300 191100 202320 191700 226420 180060 231970 194010 308270 TRUE FALSE 164328.2859 205249.2428 207119.1259 196619.3465 208637.8865 232040.399 197188.252 218232.5756 256817.7455 0.639863439 0.799201949 0.806482923 0.765598756 0.812396691 0.903521673 0.767813967 0.849756605 1 17.97038537 -5 0.077349006 1.65453475 0.586078653 0.671312489 0.053688904 173.6343414 0.955914962 19.79529693 1.999663458 1.00E-05 5 -1.068456097 LSGINEIPRPFS(ph)PPVTSNTSPPPAAPLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 LSGINEIPRPFS(0.648)PPVT(0.346)S(0.005)NTSPPPAAPLAR;LSGINEIPRPFS(0.995)PPVT(0.004)S(0.001)NTSPPPAAPLAR;LSGINEIPRPFS(0.629)PPVT(0.2)S(0.053)NT(0.053)S(0.065)PPPAAPLAR 229.8 3.01E-35 1393738000 610927 637052 621322 664873 720584 558950 753931 591423 738497 TRUE FALSE 572690.1696 684219.9929 636060.0512 681934.7668 663992.2393 720309.7912 640886.0457 665263.4634 615237.0798 0.930844691 1.112124115 1.033845443 1.108409732 1.079246133 1.170784101 1.041689564 1.081312368 1 19.23078293 4.745903224 24.81920332 1.081061025 0.930844613 0.489701434 0.047277866 637.4609309 2154662.097 0.010070339 0.10456107 55706.16025 -4.745903224 -0.150216413 LSGINEIPRPFSPPVTSNT(ph)SPPPAAPLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 LSGINEIPRPFS(0.189)PPVT(0.189)S(0.241)NT(0.309)S(0.072)PPPAAPLAR 95.586 0.001867 109760000 56572 48899 50176 50564 54860 44641 65142 50387 68311 TRUE FALSE 53031.2595 52519.53284 51366.19841 51861.55784 50551.51689 57528.13201 55374.56185 56677.92787 56909.45279 0.931853267 0.922861322 0.902595191 0.911299535 0.888279792 1.010871291 0.973029244 0.995931696 1 15.79638069 2.236880467 24.99968786 0.991250396 0.91174256 0.886626431 0.014824555 13.83535626 205856.9721 0.005175577 0.004024776 172.5362946 -2.236880467 -0.079507836 LSGLANVVLHELS(ph)GDDDTDQNMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSGLANVVLHELSGDDDTDQNMR 23 0 Q14789;Q14789-2;E7EU81;F8WF12;C9J8Q0 Q14789 GOLGB1 Golgin subfamily B member 1 1 LSGLANVVLHELS(0.997)GDDDT(0.003)DQNMR 62.683 0.028044 6298800 8016.1 8666 9319.5 10436 11159 9443 12637 10499 12051 TRUE FALSE 7514.38661 9307.639657 9540.562941 10703.80543 10282.61715 12169.04081 10742.19917 11809.82326 10039.61025 0.748473937 0.927091732 0.950292163 1.066157467 1.024204815 1.212102911 1.069981693 1.176322882 1 13.29341564 4.489650991 0.531403996 1.118840811 0.611674484 0.709719322 0.070385778 1.626933022 0.42435352 0.037159366 0.496726871 30878.12999 -4.489650991 -0.507166327 LSGLS(ph)FK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSGLSFK 7 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 LSGLS(1)FK;LSGLS(1)FK 105.52 0.0082946 1173960000 3562000 3055500 2575900 2379900 3116500 1343760 4460500 2206000 5142700 TRUE FALSE 3339060.778 3281732.399 2637001.564 2440972.263 2871742.661 1731681.698 3791689.434 2481423.956 4284350.147 0.779362252 0.765981371 0.615496277 0.569741543 0.670286639 0.404187715 0.885009232 0.579183277 1 22.03064496 -1.366065996 6.209980311 1.000038527 0.66697252 0.39339 0.132854 6.57E-05 6.71E-06 0.119296822 0.028115286 0.043046119 1.366065996 -0.333066007 LSGLS(ph)FKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LSGLSFKR 8 1 P49006 P49006 MARCKSL1 MARCKS-related protein 1 LSGLS(1)FKR;LSGLS(1)FKR;LSGLS(1)FKR;LSGLS(1)FKR;LSGLS(1)FKR 121.9 0.0008658 6544300000 11148650 12247820 7431217 7220907 11502690 3276530 12875290 7422476 24752050 TRUE FALSE 10450875.9 13154661.34 7607488.977 7406207.699 10599315.13 4222411.021 10944759.79 8349188.467 20620772.95 0.506813005 0.637932505 0.36892356 0.359162468 0.514011534 0.204764925 0.530763799 0.40489212 1 24.29759508 -1.152533676 5.627569185 1.000009401 0.447488634 0.687990029 0.11825187 1.34E-05 2.02E-06 0.110001099 0.025927067 0.070382765 1.152533676 -0.552520767 LSGLTTNVVDIILAHHFGQEELQANLDLIQTYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSGLTTNVVDIILAHHFGQEELQANLDLIQTYR 33 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 0 ; 384.8 1.91E-166 1319090000 783820 872240 740950 578950 1003090 648220 804090 960290 504970 FALSE TRUE 734762.1054 936821.5572 758525.6839 593806.8372 924311.3577 835350.591 683524.1693 1080184.32 420687.2448 1.746575668 2.226883674 1.803063186 1.411516143 2.197146144 1.985680815 1.624779876 2.567665965 1 18.68238855 -1.194019316 4.295021749 0.999690505 1.928580783 0.446687836 0.330207614 0.000920885 0.000172811 0.290346907 0.068412506 0.063970638 1.194019316 0.928890278 LSGPDDDPLHKQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSGPDDDPLHKQPR 14 1 Q86TI2;Q86TI2-4;Q86TI2-2;M0R1L4 Q86TI2 DPP9 Dipeptidyl peptidase 9 0 105.14 0.0006111 131580000 75496 238790 148050 207870 278220 151140 215070 158240 449230 FALSE TRUE 70770.84012 256470.2601 151561.8159 213204.2961 256369.7235 194771.6644 182822.2501 177996.6123 374250.6109 0.189100133 0.685290157 0.404974131 0.569683228 0.685021523 0.52043112 0.488502209 0.475608074 1 18.51364515 -2.23494797 2.16877558 2.563948004 0.516200863 0.546042385 0.142107606 7343377.342 1249375.035 56297355.53 0.030899561 0.00582173 2.23494797 -2.04774714 LSGS(ph)RQDLIPSYSLGSNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSGSRQDLIPSYSLGSNK 18 1 Q9NQT8;H0YBA8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 LS(0.188)GS(0.812)RQDLIPSYSLGSNK 176.22 8.59E-13 571690000 401470 419310 368440 396790 454970 290000 457040 423230 771110 TRUE FALSE 376342.7093 450356.1487 377179.5708 406972.3032 419238.4915 373718.2922 388511.095 476071.1971 642406.7594 0.585832424 0.701045159 0.587135122 0.633511863 0.652605978 0.581747136 0.604774295 0.74107439 1 19.29312755 0.896508676 3.158738566 0.999737133 0.624557478 0.914830966 0.036679873 0.110522293 2.382282234 0.034651293 0.009039212 7.879681731 -0.896508676 -0.375179655 LSHLLSEKPEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSHLLSEKPEDK 12 1 Q969Z0;Q969Z0-2;C9J7P5;C9J5A2;C9J347 Q969Z0 TBRG4 Protein TBRG4 0 88.087 0.0061187 123330000 309880 212700 226000 231390 270360 193150 263420 224540 401220 FALSE TRUE 290485.164 228448.5293 231360.8267 237327.8591 249127.0162 248909.2695 223922.6165 252574.3133 334253.79 0.869055707 0.683458307 0.69217114 0.710022941 0.745322936 0.744671495 0.669917958 0.755636348 1 18.35058439 0.962338571 22.14007135 1.000000001 0.719809818 0.689730286 0.055989748 737.1881025 433372.8008 0.049468271 0.012367068 9.169350437 -0.962338571 -0.280190183 LSHPLLEQLLPALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSHPLLEQLLPALR 14 0 H0Y6U5;Q86XI2;Q86XI2-2 H0Y6U5 NCAPG2 Condensin-2 complex subunit G2 0 62.287 0.078232 19918000 111280 117490 102970 109490 135170 75454 125080 111050 162610 FALSE TRUE 104315.1834 126189.0818 105412.497 112299.6988 124554.2934 97236.34491 106325.4152 124914.837 135469.3405 0.770027986 0.931495506 0.778128074 0.828967635 0.919427916 0.717773812 0.784867002 0.922089356 1 17.04760685 1.029246769 4.582770461 0.999257978 0.823164251 0.470537822 0.065482032 0.148758694 7.688743884 0.061492382 0.01562412 10.69662495 -1.029246769 -0.176093728 LSHSQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSHSQER 7 0 P12270;P12270-2;Q5SWX9 P12270 TPR Nucleoprotein TPR 0 97.093 0.01225 84369000 86817 91430 84457 85577 108420 72831 88554 93227 112820 FALSE TRUE 81383.27894 98199.57233 86460.35992 87773.0507 99905.13055 93856.12739 75276.1498 104866.5962 93989.61315 0.865875241 1.044791749 0.91989271 0.933859048 1.062937991 0.998579782 0.800898602 1.115725373 1 16.52021371 3.337969235 0.003370824 1.92217697 9.78E-08 0.023921712 0.093390931 322703.5073 294.0670867 82684.412 85005.2332 2177.555511 -3.337969235 -1.922176872 LSIPTYGLQCTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSIPTYGLQCTR 12 0 P49327;A0A0U1RQF0;J3KTF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 181.4 4.24E-05 1106110000 346950 409170 401090 487030 406650 347993 424610 367120 776750 FALSE TRUE 325235.0188 439465.3725 410604.0442 499528.0143 374713.3493 448452.9299 360943.6724 412955.7401 647105.407 0.502599755 0.679124866 0.634524205 0.771942266 0.579060761 0.693013727 0.557781883 0.638158383 1 19.30364121 -2.228685431 2.258281892 2.195733877 0.635959525 0.703189752 0.075093033 4714614.192 840347.1917 28789346.35 0.016527564 0.005906287 2.228685431 -1.559774352 LSIVPVRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSIVPVRR 8 1 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 ; 147.19 0.00086801 1129410000 634830 2121310 634230 649140 2188560 455560 722840 1708960 1628270 FALSE TRUE 595097.1235 2278374 649274.2351 665798.0314 2016679.326 587072.7766 614456.8525 1922327.418 1356501.218 0.438700029 1.679595985 0.478638888 0.490820076 1.486677121 0.432784555 0.45297184 1.417121778 1 20.37145891 3.941389346 19.85639478 0.771209295 1.139198572 0.025261144 0.488101975 66.08857277 36725.27156 0.115741106 0.208705533 8737.543402 -3.941389346 0.367989277 LSIYEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSIYEAR 7 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 81.297 0.064172 104370000 69808 117400 83288 91555 108400 61282 97428 95638 92182 FALSE TRUE 65438.84189 126092.4182 85263.63069 93904.4563 99886.70126 78973.11857 82819.57588 107578.6148 76796.22868 0.852110097 1.641908988 1.110258045 1.22277432 1.30067196 1.028346312 1.078432851 1.400832003 1 16.22874784 2.988097472 1.089252568 1.137277193 1.296121074 0 0.227009353 1.353815006 3.429318581 0.096321807 0.116856723 972.9655701 -2.988097472 0.158843881 LSKDPNIVIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSKDPNIVIAK 11 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 101.47 0.0024949 0 574810 540400 550320 576690 597680 417200 693260 509470 562360 FALSE TRUE 538833.6682 580411.7783 563373.8503 591488.8417 550740.6237 537638.8673 589312.0989 573078.451 468498.483 1.15012895 1.238876537 1.202509444 1.262520292 1.175544092 1.147578673 1.257874081 1.223223707 1 18.83768485 -1.123966879 3.929432669 0.999924428 1.211195635 0.719428304 0.04061574 6165091.197 13538574.53 6256.760649 0.009091921 0.075168022 1.123966879 0.211271207 LSKEDIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 LSKEDIER 8 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;;;; 128.27 0.0010404 65358280000 51073280 46396450 47318950 44410230 50167490 37525660 57813100 43724140 64126200 FALSE TRUE 47876694.57 49831691.43 48441377.84 45549871.69 46227537.7 48358708.86 49144562.37 49183195.13 53423122.95 0.896179256 0.932773838 0.906749272 0.852624653 0.865309535 0.905201834 0.919911822 0.920634969 1 25.67096098 0.675118033 1.080562815 0.999662216 0.897713942 0.673178315 0.022814846 0.755076998 1.469634133 0.024324217 0.007660243 4.732798699 -0.675118033 -0.101948274 LSKEEIER ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;;; 156.83 0.00035268 17187300000 26023680 24150880 24074570 24193150 29976600 18381810 28048190 23699270 32652800 FALSE TRUE 24394904.32 25939036.28 24645630.17 24813987.19 27622358.76 23688340.14 23842624.3 26658176.03 27202836.73 0.896777956 0.953541593 0.905994857 0.912183808 1.015421995 0.870804041 0.876475661 0.979977797 1 24.69725377 1.07429464 6.767908083 0.999692899 0.919554178 0.344837245 0.041296253 0.21662234 14.68299505 0.038897964 0.00976262 11.86573485 -1.07429464 -0.080138721 LSKS(ph)DEQLSSLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSKSDEQLSSLDR 13 1 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 LS(0.426)KS(0.574)DEQLSSLDR 100.39 0.0014681 342860000 358740 566740 771150 398990 486790 317940 458060 329490 503380 TRUE FALSE 336287.1038 608702.0193 789442.0422 409228.7589 448559.477 409724.1167 389378.1554 370627.5518 419362.626 0.80190051 1.451493246 1.882480682 0.975835073 1.069621967 0.977016289 0.928499898 0.88378775 1 18.67783877 3.16149684 14.24658012 0.970713091 1.466169752 0.325917136 0.26558581 1.046427555 191.4557497 0.077683293 0.092857516 1450.430222 -3.16149684 0.495456661 LSLCEDS(ph)PMVTLTVDNVHLEHGVVYEYVSTAGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSLCEDSPMVTLTVDNVHLEHGVVYEYVSTAGVR 34 0 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 1 LS(0.463)LCEDS(0.537)PMVTLTVDNVHLEHGVVYEYVSTAGVR 145.57 3.71E-10 21161000 6568.4 5010.9 4380.2 5406 4830.2 4942.1 6383.7 3951.9 4442.8 TRUE FALSE 6157.295569 5381.91225 4484.100412 5544.727112 4450.855576 6368.804042 5426.523448 4445.303414 3701.267978 1.663563839 1.454072572 1.211503852 1.498061514 1.202521839 1.720708708 1.466125522 1.201021769 1 11.85380388 1.036717062 3.664531448 1.003311716 1.440537389 0.472705175 0.164105014 0.177996215 5.353868769 0.152355392 0.039374247 10.88220899 -1.036717062 0.437225673 LSLCGEESFGTGSDHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSLCGEESFGTGSDHIR 17 0 A0A3B3ITK7;P36871;P36871-2;P36871-3 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 0 ; 214.53 5.91E-15 376570000 146672 200886 188942 190954 206305 159440 226775 188755 190288 FALSE TRUE 137492.0613 215759.8085 193423.7935 195854.2029 190102.6375 205467.7397 192772.194 212321.4773 158527.7035 0.867306208 1.361022734 1.220126131 1.235457265 1.199176127 1.296099894 1.216015812 1.339333584 1 17.27437545 4.749334769 24.93555689 1.247145331 0.867305984 0.569045286 0.099488053 972.909465 2251644.521 0.020373596 0.300369339 56148.06178 -4.749334769 -0.379839346 LSLDELHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LSLDELHR 8 0 P05023-4;P05023;P05023-3;P05023-2;Q5TC02;Q5TC01 P05023-4 ATP1A1 Sodium/potassium-transporting ATPase subunit alpha-1 0 ;;;;; 198.07 0.00013893 1071854000 1611544 1837220 1557323 1372338 2387650 1450536 1789420 2205030 2456530 FALSE TRUE 1510680.338 1973249.68 1594263.437 1407554.516 2200133.6 1869282.196 1521113.083 2480332.849 2046519.273 0.738170589 0.964197946 0.779012178 0.687779751 1.075061266 0.913395842 0.743268389 1.211976296 1 20.96474082 1.238544054 25 1.105988172 0.849378923 0.424688981 0.127093009 0.414234681 614508.4685 0.09274996 0.028821634 17.3198471 -1.238544054 -0.256609249 LSLDGNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSLDGNPK 8 0 B8ZZZ7;Q9NUQ6;Q9NUQ6-4;Q9NUQ6-3;F8VT91 B8ZZZ7 SPATS2L SPATS2-like protein 0 ; 89.298 0.014004 732100000 586430 2304100 1651400 1793150 1950700 1693460 1374980 1773170 1102370 FALSE TRUE 549726.3931 2474697.961 1690571.988 1839165.265 1797499.891 2182334.411 1168814.514 1994554.178 918377.3254 0.598584457 2.694641835 1.840825052 2.002624862 1.957256392 2.376293872 1.272695309 2.171824285 1 19.8087275 -0.180271678 0.563529329 0.913436063 1.96418308 0.151584196 0.58983753 9.301610398 3.041605978 2.334417495 0.230136444 0.660280273 0.180271678 1.050747017 LSLDLLSQMS(ph)PGDLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSLDLLSQMSPGDLAK 16 0 Q6UWE0;Q6UWE0-2;Q6UWE0-3 Q6UWE0 LRSAM1 E3 ubiquitin-protein ligase LRSAM1 1 LSLDLLS(0.077)QMS(0.923)PGDLAK 127.97 0.00034101 0 49382 41887 47386 46909 54285 37366 46993 36670 49398 TRUE FALSE 46291.26877 44988.35706 48510.0183 48112.76436 50021.67508 48152.95761 39946.83591 41248.33022 41153.15468 1.124853468 1.0931934 1.178767914 1.169114852 1.215500378 1.170091527 0.970687089 1.002312716 1 15.32871541 1.73761177 7.126493946 0.991514371 1.156032383 0.846722752 0.033551042 0.0523979 7.952630363 0.018171317 0.0095901 54.65271863 -1.73761177 0.164518013 LSLEGDHST(ph)PPSAYGSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.039)T(0.96)PPS(0.001)AYGSVK;LSLEGDHS(0.052)T(0.948)PPSAYGSVK;LSLEGDHS(0.204)T(0.796)PPSAYGSVK 145.77 3.75E-07 688900000 650910 574950 581830 508560 808620 418020 792040 657080 1859730 TRUE FALSE 610170.705 617519.8962 595631.2824 521610.5106 745114.247 538695.588 673280.9549 739117.8844 1549329.049 0.393828997 0.398572464 0.384444662 0.336668644 0.480927049 0.347696048 0.43456292 0.477056752 1 20.56321215 0.275336271 1.040457308 1.002596615 0.390234923 0.959058469 0.038933839 0.558798856 0.664443774 0.035010846 0.010234831 1.885108149 -0.275336271 -0.612361692 LSLFSDGDS(ph)SESEDTLSSSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSLFSDGDSSESEDTLSSSER 21 0 M0QXD7;M0R025;M0QYG0;M0QYA8;Q8IV63-2;Q8IV63;M0QZ79 M0QXD7 VRK3 Inactive serine/threonine-protein kinase VRK3 1 LSLFSDGDS(0.802)S(0.198)ES(0.001)EDTLSSSER 248.18 1.87E-30 41429000 58391 67032 63224 67707 74409 52523 77129 59434 55479 TRUE FALSE 54736.41154 71995.11903 64723.70314 69444.47625 68565.21729 67685.53746 65564.22248 66854.46573 46219.19649 1.184278735 1.557688677 1.400364092 1.502502889 1.483479214 1.464446433 1.418549595 1.446465339 1 15.49620456 -1.0877442 5.227333016 0.99999837 1.443791916 0.651388095 0.099050229 7.58E-06 1.32E-06 0.08331978 0.019638326 0.081706348 1.0877442 0.443793545 LSLLSS(ph)TSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.338)S(0.653)T(0.007)S(0.002)K;LSLLS(0.012)S(0.898)T(0.087)S(0.003)K;LSLLS(0.124)S(0.859)T(0.014)S(0.002)K 108.77 0.0026829 92755000 710358 956780 524844 626741 836779 281225 781900 617100 1030860 TRUE FALSE 665897.9608 1027620.987 537293.5475 642824.2351 771061.7527 362410.0922 664661.3538 694146.2934 858802.8064 0.775379349 1.196573857 0.625630871 0.748512034 0.897833294 0.421994536 0.773939429 0.808272037 1 19.71196738 3.924182497 6.415161468 0.733785964 1.002564766 0.209571862 0.183615332 0.226826856 20.87934939 0.042297578 0.077999974 8398.128139 -3.924182497 0.268778802 LSLPNTAWGSPSPEAAGYPGAGAEDEQQQLAANRHS(ph)LVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSLPNTAWGSPSPEAAGYPGAGAEDEQQQLAANRHSLVEK 40 1 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 LSLPNTAWGSPSPEAAGYPGAGAEDEQQQLAANRHS(1)LVEK 179.6 3.81E-24 129530000 61786 50659 60562 52069 66583 47337 65240 58679 55110 TRUE FALSE 57918.92455 54409.84507 61998.55924 53405.17869 61353.83976 61002.42345 55457.86766 66005.20232 45911.78498 1.261526307 1.185095398 1.350384422 1.16321286 1.336341852 1.328687688 1.207922273 1.437652715 1 15.4865769 -0.982589464 4.869649859 0.999996938 1.275869498 0.526596961 0.08427927 2.48E-06 5.18E-07 0.07222264 0.01702285 0.104090366 0.982589464 0.27587256 LSLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSLSPK 6 0 Q5FBB7-6;Q5FBB7;Q5FBB7-5;Q5FBB7-4;Q5FBB7-3;Q5FBB7-2 Q5FBB7-6 SGOL1 Shugoshin-like 1 1 LS(0.004)LS(0.996)PK 73.208 0.08766 115900000 615750 400810 454530 389560 483590 297100 508350 359020 527010 TRUE FALSE 577211.3066 430486.3894 465311.6662 399556.7691 445610.7921 382867.947 432127.6368 403844.4373 439048.6264 1.314686511 0.980498204 1.059818066 0.910051291 1.01494633 0.872039961 0.984236394 0.919817107 1 18.74402121 7.294427247 1.201568081 0.963707468 199.9997818 0.774376482 0.057959808 389.4582351 1.298387416 0.015056134 212791.5073 19698231.96 -7.294427247 199.0360743 LSLS(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LSLSPLR 7 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR 163.69 0.0012856 564563000 217419 1515440 232214 270516 1574580 300049 271454 1171560 1386000 TRUE FALSE 203811.1329 1627644.754 237722.2257 277457.8985 1450918.838 386668.2754 230751.9928 1317831.845 1154667.646 0.176510647 1.40962186 0.205879351 0.240292433 1.256568367 0.334874088 0.19984278 1.141308366 1 20.13904622 1.21222564 24.81959962 1.070655074 0.581756433 0.190565011 0.444676053 428.1823562 403531.9773 0.414327767 0.103715889 16.3014276 -1.21222564 -0.488898641 LSLSPALQDALHTFPQLQVEQSGEGS(ph)PEEGAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LSLSPALQDALHTFPQLQVEQSGEGSPEEGAVR 33 0 Q9ULL5;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 LSLSPALQDALHTFPQLQVEQS(0.329)GEGS(0.671)PEEGAVR;LSLSPALQDALHTFPQLQVEQS(0.05)GEGS(0.95)PEEGAVR;LSLSPALQDALHTFPQLQVEQS(0.003)GEGS(0.997)PEEGAVR 211.94 6.03E-28 197644000 144214 166445 157156 152410 175127 144024 179846 146885 186297 TRUE FALSE 135187.9032 178768.761 160883.8145 156321.0986 161373.2318 185601.3908 152879.7619 165223.9156 155202.8272 0.87104021 1.151839591 1.036603633 1.007205226 1.039757038 1.195863466 0.985032069 1.064567692 1 17.24379531 0.627954494 1.362834483 1.000614433 1.055021474 0.008644756 0.088840905 5.555333817 14.96895845 0.076426114 0.022633283 4.245750741 -0.627954494 0.054407041 LSLTRS(ph)PVSPLAAQGIPLPAQLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSLTRSPVSPLAAQGIPLPAQLTK 24 1 K7EIF1;K7EPF0;K7EQS3;K7EM48;K7EN63;Q96SI1-2;Q96SI1 K7EIF1 KCTD15 BTB/POZ domain-containing protein KCTD15 1 LS(0.047)LT(0.201)RS(0.712)PVS(0.04)PLAAQGIPLPAQLTK 142.79 1.55E-07 156860000 145960 270240 217220 282220 466810 107470 224410 226660 1099800 TRUE FALSE 136824.6241 290248.8508 222372.561 289462.243 430148.6256 138494.8444 190761.8038 254958.9999 916236.275 0.149333341 0.316783846 0.242702201 0.315925325 0.469473472 0.151156255 0.20820154 0.278267743 1 19.80536016 -1.554984675 2.467056601 1.058519525 0.266850702 0.86085283 0.092680081 1646264.009 1448672.816 634123.9547 0.022929609 0.027862195 1.554984675 -0.791668823 LSLTRSPVS(ph)PLAAQGIPLPAQLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSLTRSPVSPLAAQGIPLPAQLTK 24 1 K7EIF1;K7EPF0;K7EQS3;K7EM48;K7EN63;Q96SI1-2;Q96SI1 K7EIF1 KCTD15 BTB/POZ domain-containing protein KCTD15 1 LS(0.022)LT(0.088)RS(0.3)PVS(0.59)PLAAQGIPLPAQLTK 119.42 0.00021003 110520000 121520 238490 158820 214780 380790 86749 183240 179200 920640 TRUE FALSE 113914.2801 256148.0477 162587.2854 220291.6184 350884.2894 111792.028 155764.8631 201573.5145 766979.2364 0.148523291 0.33396999 0.211983946 0.287219794 0.457488642 0.145756264 0.203088761 0.262814826 1 19.548828 -1.440418283 2.669187109 1.02381726 0.257262847 0.865870135 0.091981651 2463011.982 2584403.575 440139.2777 0.022258368 0.036272853 1.440418283 -0.766554413 LSLTS(ph)DPEEGDPLALGPESPGEPQPPQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSLTSDPEEGDPLALGPESPGEPQPPQLK 29 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 LS(0.095)LT(0.095)S(0.81)DPEEGDPLALGPESPGEPQPPQLK 113.6 0.00016064 48095000 37281 34463 35376 27182 30646 27621 44729 36766 50678 TRUE FALSE 34947.64876 37014.67638 36215.13543 27879.53614 28239.18678 35594.73431 38022.30169 41356.31603 42219.51441 0.827760557 0.876719614 0.857781903 0.660347153 0.668865741 0.84308725 0.900585955 0.979554517 1 15.36562237 1.554684329 2.151374369 0.98959242 0.796249734 0.575233064 0.072639722 0.259370633 2.5189624 0.064977722 0.022802217 35.8661144 -1.554684329 -0.193342685 LSMEDSKS(ph)PPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 LSMEDSKSPPPK 12 1 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 1 LSMEDSKS(1)PPPK;LSMEDS(0.02)KS(0.98)PPPK;LSMEDSKS(1)PPPK;LSMEDS(0.003)KS(0.997)PPPK;LSMEDS(0.003)KS(0.997)PPPK;LSMEDSKS(1)PPPK;LSMEDS(0.02)KS(0.98)PPPK;LSMEDSKS(1)PPPK;LSMEDS(0.008)KS(0.992)PPPK;LS(0.002)MEDS(0.018)KS(0.98)PPPK 156.5 3.60E-05 14214420000 19992710 9566060 13172540 12652650 13067450 9042270 16431870 11192740 14401240 TRUE FALSE 18741401.97 10274341.04 13484998.87 12977338.42 12041185.19 11652626.56 13968063.64 12590178.23 11997580.01 1.56209852 0.856367787 1.123976574 1.081663003 1.003634498 0.971248081 1.164240091 1.049393146 1 23.5162401 4.751117905 24.98938625 1.037911904 1.562098848 0.792629648 0.085262033 952.2251708 1894922.978 0.020385112 0.369928842 56379.0696 -4.751117905 0.524186944 LSMEDSKS(ph)PPPKATEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSMEDSKSPPPKATEEK 17 2 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 1 LS(0.001)MEDS(0.108)KS(0.889)PPPKAT(0.002)EEK;LS(0.001)MEDS(0.007)KS(0.991)PPPKATEEK 87.326 0.0023848 666400000 1669620 768790 1047610 1140300 1339720 640250 1511990 867060 2437510 TRUE FALSE 1565121.465 825712.0115 1072459.804 1169562.029 1234503.795 825079.7814 1285281.136 975314.3496 2030673.834 0.770739957 0.406619713 0.528130016 0.575947751 0.607928154 0.406308373 0.632933322 0.480290992 1 20.9535271 -1.411280426 2.888561231 1.009157606 0.539072658 0.62378496 0.109201945 18656263.27 22027658.26 1413887.739 0.024662127 0.038789982 1.411280426 -0.470084948 LSMPQSAAVST(ph)TPPHNRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LSMPQSAAVSTTPPHNRR 18 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 LSMPQSAAVS(0.009)T(0.616)T(0.375)PPHNRR;LSMPQSAAVS(0.01)T(0.607)T(0.383)PPHNRR;LS(0.001)MPQS(0.007)AAVS(0.153)T(0.42)T(0.42)PPHNRR 120.24 3.86E-05 569861000 236208 314898 271961 315681 342493 259133 370036 285113 376647 TRUE FALSE 221424.1629 338213.3756 278412.0433 323781.9089 315594.9813 333940.4904 314552.537 320709.9857 313782.1825 0.705662002 1.077860358 0.887278051 1.031868369 1.005777252 1.064242997 1.002455062 1.022078383 1 18.25940391 4.746918618 24.97837665 1.006834826 0.705661849 0.778786047 0.051164457 488.7743813 1460698.092 0.011883653 0.134700155 55836.5554 -4.746918618 -0.301172976 LSMPQSAAVSTT(ph)PPHNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LSMPQSAAVSTTPPHNR 17 0 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 LSMPQSAAVS(0.001)T(0.174)T(0.825)PPHNR;LSMPQSAAVS(0.008)T(0.198)T(0.793)PPHNR;LSMPQSAAVST(0.416)T(0.584)PPHNR;LSMPQSAAVST(0.007)T(0.993)PPHNR;LSMPQSAAVS(0.011)T(0.358)T(0.631)PPHNR 173.43 5.44E-09 2562530000 687351 778610 744450 848174 833272 679490 926770 765323 654328 TRUE FALSE 644330.9279 836259.0945 762108.7056 869939.5808 767830.1784 875647.7324 787809.4422 860875.2612 545116.4297 1.182006068 1.534092625 1.398065925 1.595878483 1.408561798 1.606349919 1.445213168 1.579250256 1 19.05620488 -1.067996166 5.059450906 0.999990869 1.474214679 0.576563683 0.126146096 1.12E-05 2.06E-06 0.105155976 0.024785024 0.085507426 1.067996166 0.474223811 LSMWDRPDDLIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LSMWDRPDDLIGR 13 1 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 ;;; 249.04 1.58E-17 342456000 324424 409188 388147 376066 432239 336260 443487 369649 455722 FALSE TRUE 304118.881 439484.7053 397354.0301 385716.4902 398292.6925 433332.8033 376990.2415 415800.4913 379659.0541 0.801031551 1.157577307 1.046607544 1.015954937 1.049079926 1.141373552 0.992970502 1.095194456 1 18.53434489 4.751352122 24.8612476 1.065022745 0.801031371 0.686232612 0.055504312 1087.922852 2114418.54 0.012609589 0.226874871 56409.48335 -4.751352122 -0.263991374 LSNHISSLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSNHISSLFR 10 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 174.4 3.12E-06 675540000 138990 1383880 267970 265780 1283980 230240 308850 1184110 731340 FALSE TRUE 130290.864 1486343.915 274326.3749 272600.3648 1183141.39 296706.5504 262540.8097 1331948.74 609274.6294 0.213845871 2.439530293 0.450250776 0.447417883 1.941885208 0.486983268 0.430907176 2.186122113 1 19.21673314 3.863234838 10.64558686 0.924436834 1.479908567 0.015542799 0.819479994 0.925360335 80.70513124 0.193002212 0.348223293 7298.520604 -3.863234838 0.555471733 LSNIFVIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSNIFVIGK 9 0 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 99.815 0.011822 55294000 185770 226080 206720 215310 261440 184910 226000 192240 257980 FALSE TRUE 174142.9873 242819.1984 211623.496 220835.2191 240907.557 238290.5152 192113.3981 216241.5872 214921.4714 0.810263331 1.129804281 0.984654975 1.027515854 1.120909677 1.108732942 0.893877177 1.006142317 1 17.71345009 1.737205777 24.99999962 0.959518787 1.039902367 0.081407886 0.096288503 0.365801582 6476.527269 0.040841311 0.022648554 54.60165132 -1.737205777 0.080383579 LSNKVEAIDVEEAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSNKVEAIDVEEAKR 15 2 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ; 97.579 0.0018332 500780000 861520 622400 688660 685610 827360 509650 910600 649420 1071090 FALSE TRUE 807599.0011 668483.1436 704995.3404 703203.9133 762382.483 656777.6815 774063.9836 730501.5165 892318.1595 0.905057229 0.749153356 0.790071717 0.788064107 0.85438414 0.736035319 0.867475323 0.818655889 1 19.76719867 0.149192553 0.666091731 1.007202169 0.797402501 0.551920364 0.052428984 2.249013088 1.236913831 0.086678207 0.017724251 1.409913772 -0.149192553 -0.209799668 LSNLALVKPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSNLALVKPEK 11 1 O14737;K7EQA1;O14737-2 O14737 PDCD5 Programmed cell death protein 5 0 103.76 0.0021383 0 438910 388170 398750 410830 445560 284880 502500 359200 491460 FALSE TRUE 411439.4066 416910.5107 408208.5383 421372.5933 410567.5149 367120.2314 427154.79 404046.9107 409432.151 1.004902535 1.018265199 0.99701144 1.029163421 1.002773021 0.896657066 1.043285899 0.986847051 1 18.64326487 2.462954495 24.9997167 0.983521481 1.011289726 0.135893734 0.03653401 511.1935138 902083.4847 0.011945402 0.009998689 290.3718391 -2.462954495 0.027768246 LSNNNKTAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSNNNKTAER 10 1 I3L100;I3L2W2;Q96JN8-2;Q96JN8;K7EPS7;I3L2Z9 I3L100 NEURL4 Neuralized-like protein 4 0 51.762 0.092836 393960000 1087000 466930 595650 494010 628940 425670 606400 485780 680520 FALSE TRUE 1018966.61 501501.983 609779.0993 506687.133 579545.5894 548554.0188 515475.9495 546430.7023 566936.8157 1.797319529 0.88458179 1.075568004 0.893727694 1.022240175 0.967575228 0.90922998 0.963829985 1 19.11282843 4.741896188 24.99999021 0.964309751 1.797319838 0.951539891 0.059058547 60.01594589 449797.1783 0.013097201 0.095266587 55194.54886 -4.741896188 0.833010087 LSNRPAFMPSEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSNRPAFMPSEGK 13 1 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 143.38 3.72E-05 676810000 965790 1141100 706660 654540 1059400 461700 905040 1199800 1269800 FALSE TRUE 905342.9279 1225588.231 723422.3089 671336.6045 976198.9974 594985.2949 769337.654 1349597.671 1057862.177 0.855823138 1.158551897 0.683853081 0.634616323 0.922803574 0.562441222 0.727256982 1.275778358 1 20.01272025 -0.742065259 6.224746232 1.000000002 0.839161468 0.037748928 0.224839273 7.84E-09 1.51E-09 0.210471449 0.049608595 0.181106793 0.742065259 -0.160838535 LSPAT(ph)PTSEGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSPATPTSEGPK 12 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 LS(0.001)PAT(0.98)PT(0.014)S(0.005)EGPK 138.02 0.00091496 91737000 163430 125190 134810 134000 163780 110290 214720 156240 254360 TRUE FALSE 153201.208 134459.1979 138007.7569 137438.6669 150917.3795 142128.9326 182524.7294 175746.9079 211905.6728 0.722968885 0.634523824 0.651269761 0.648584179 0.712191314 0.670717922 0.861348953 0.829363866 1 17.69306268 1.369473782 0.856239528 0.990479182 0.654052568 0.873591471 0.0415592 0.152960306 0.238826839 0.034682384 0.013294534 23.41390124 -1.369473782 -0.336426614 LSPDAIPGKWTSQDSLLGMEFSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 94.08 0.0070371 68161000 45576 80866 70300 72831 120120 55956 95623 51600 330000 FALSE TRUE 42723.47952 86853.40278 71967.5492 74699.96676 110686.2597 72109.58883 81285.21887 58042.37359 274920.8681 0.155402825 0.315921463 0.261775505 0.271714429 0.402611342 0.262292162 0.295667693 0.211123928 1 18.06865689 -1.772474846 2.64626556 1.180030729 0.27970978 0.926158884 0.06456342 23530817.98 17827008.47 27497437.01 0.015511598 0.016885937 1.772474846 -0.900320948 LSPFFTLDLS(ph)PTEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LSPFFTLDLSPTEDK 15 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 LSPFFTLDLS(0.998)PT(0.002)EDK;LSPFFTLDLS(0.999)PT(0.001)EDK;LSPFFTLDLS(0.977)PT(0.022)EDK 207.05 3.76E-09 188190000 528959 357582 396801 386775 362225 304371 460104 315901 355682 TRUE FALSE 495852.4004 384057.7433 406213.3071 396700.3013 333777.3096 392237.9666 391115.6766 355341.9352 296316.3764 1.673388445 1.296107046 1.370877007 1.338772788 1.126422082 1.323713429 1.319925957 1.199197761 1 18.17677884 8 0.05446267 0.533981523 2.810638332 0.627811506 0.107012228 303.1890334 1.240341929 11.40753781 56.34059267 100000000 -8 2.276656809 LSPFFTLDLS(ph)PTEDKSSKPSSFTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSPFFTLDLSPTEDKSSKPSSFTEK 25 2 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 LSPFFTLDLS(0.985)PT(0.014)EDKSSKPSSFTEK;LSPFFTLDLS(0.976)PT(0.024)EDKSSKPSSFTEK 134.69 2.48E-05 375220000 916060 531130 609610 639570 797490 384750 815450 487140 1111560 TRUE FALSE 858725.4398 570455.4178 624070.2371 655982.449 734858.3523 495821.0791 693180.8428 547960.5013 926033.455 0.927315784 0.616020312 0.673917593 0.70837878 0.793554864 0.535424586 0.74854838 0.591728623 1 19.82070479 -1.192261203 5.322464465 1.00001558 0.689747832 0.419551611 0.110618876 1.78E-05 2.70E-06 0.093227721 0.021972882 0.064230129 1.192261203 -0.310267747 LSPLEACAHSFFDELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LSPLEACAHSFFDELR 16 0 P49840;A8MT37 P49840 GSK3A Glycogen synthase kinase-3 alpha 0 ;; 226.65 5.76E-15 138843000 102878 136658 129531 127713 149969 105133 146668 129305 145873 FALSE TRUE 96439.04962 146776.3005 132603.5365 130990.3318 138191.0397 135483.1904 124676.495 145449.0139 121525.8539 0.793568171 1.207778393 1.091154945 1.077880365 1.137132842 1.114850758 1.025925686 1.196856547 1 16.89090375 4.749882324 24.96558941 1.108701875 0.793567984 0.693945341 0.065285183 916.4653124 2020866.836 0.014587514 0.226381029 56218.89738 -4.749882324 -0.315133891 LSPQDPRPLS(ph)PGALQLAGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSPQDPRPLSPGALQLAGEK 20 1 Q8TEK3;Q8TEK3-1 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 LSPQDPRPLS(1)PGALQLAGEK 67.778 0.013255 162810000 315690 277780 305680 311440 363040 242370 449050 282280 507590 TRUE FALSE 295931.5264 298347.1202 312930.874 319432.0777 334528.3028 312338.2845 381719.1213 317523.2794 422869.9498 0.699816874 0.705529254 0.740016816 0.755390819 0.79109027 0.738615465 0.902686799 0.750876906 1 18.68985452 -5 0.087982663 1.822082846 0.546635929 0.769032115 0.045270887 89.73929411 0.551154889 13.75411492 1.024619771 1.00E-05 5 -1.275446917 LSPQFPNEEDSFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSPQFPNEEDSFHK 14 0 P49770 P49770 EIF2B2 Translation initiation factor eIF-2B subunit beta 0 ; 150.37 7.23E-06 325510000 168397 217838 208891 207929 228751 173972 235662 195055 258042 FALSE TRUE 157857.3324 233966.9522 213845.9932 213264.8102 210785.8192 224194.8922 200326.6709 219408.0461 214973.1232 0.734311946 1.088354436 0.994756879 0.992053365 0.980521733 1.042897311 0.931868449 1.020630127 1 17.71379677 4.749560067 24.99832917 1.005318194 0.734311791 0.815674233 0.040643681 716.3576986 1628027.29 0.009937539 0.151196323 56177.19713 -4.749560067 -0.271006403 LSPS(ph)FR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSPSFR 6 0 B4DF95;Q15735 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 LS(0.007)PS(0.993)FR 160.52 0.0092162 319320000 595630 648810 693920 676960 775310 491290 592480 490330 1086200 TRUE FALSE 558350.5815 696848.5675 710380.1101 694331.9397 714420.2801 633117.4476 503643.1243 551548.7798 904906.2029 0.617025919 0.770078231 0.785031761 0.767297138 0.7894965 0.699649804 0.556569424 0.609509337 1 19.78740873 2.012893692 12.50583545 0.661599247 0.754538952 0 0.128981323 1.451418562 1397.971375 0.04354357 0.03186069 103.0133931 -2.012893692 0.092939706 LSPS(ph)PSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LSPSPSSR 8 0 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 1 LS(0.055)PS(0.788)PS(0.157)S(0.001)R;LSPS(1)PSSR;LSPS(0.991)PS(0.009)SR;LS(0.025)PS(0.945)PS(0.029)SR;LS(0.251)PS(0.608)PS(0.141)SR 237.52 1.26E-08 6822670000 5148410 5460700 5310330 5129850 5274510 4227080 5784760 4763820 4396020 TRUE FALSE 4826180.208 5865015.91 5436293.535 5261490.636 4860271.261 5447369.375 4917388.941 5358593.413 3662295.863 1.317801835 1.601458792 1.484394964 1.43666455 1.327110491 1.487419253 1.342706631 1.463178731 1 21.80431691 -3.267724158 0.241806138 1.41E-19 1.500723234 0.691790549 0.08949549 34.93596 0.739395606 17.65716527 0.135313655 0.000539853 3.267724158 1.500723234 LSPS(ph)PTSQR ddPTM_SK-BR-3_Pertuzumab_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(1)PTSQR;LSPS(1)PTSQR;LSPS(1)PTSQR;LSPS(1)PTSQR;LSPS(1)PTSQR;LSPS(0.955)PT(0.045)SQR;LSPS(1)PTSQR;LS(0.001)PS(0.999)PTSQR 257.66 5.28E-15 99394370000 15929550 16846940 16266290 15106820 16455250 14492380 18167130 14253930 17211900 TRUE FALSE 14932547.9 18094304.97 16652134.08 15494486.58 15162921.04 18676094.84 15443137.51 16033564.54 14339122.7 1.041385043 1.261883683 1.161307734 1.080574238 1.057451098 1.302457287 1.076993191 1.118169143 1 23.77345342 0.880720659 1.385347624 1.001854721 1.157077518 0.198434821 0.085968932 0.811462253 3.040560943 0.076912927 0.022956633 7.598373876 -0.880720659 0.155222797 LSPS(ph)PTTEDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSPSPTTEDPR 11 0 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2 Q9BTC8 MTA3 Metastasis-associated protein MTA3 1 LSPS(0.977)PT(0.018)T(0.005)EDPR;LS(0.005)PS(0.933)PT(0.031)T(0.031)EDPR 115.14 0.0012206 669150000 539275 575624 567297 529260 552369 617488 743550 639839 755950 TRUE FALSE 505522.7404 618243.7999 580753.5527 542841.7076 508988.1669 795746.7615 632061.5803 719724.3076 629777.0614 0.802701101 0.981686755 0.922157361 0.861958526 0.808203725 1.263537227 1.003627504 1.142823948 1 19.26448169 2.252728758 24.99985395 1.097914564 0.895618785 0.605072128 0.090335943 165.6365033 292267.2501 0.029334113 0.024432645 178.9487867 -2.252728758 -0.202295779 LSPSPS(ph)SR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSPSPSSR 8 0 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 1 LSPS(0.137)PS(0.862)S(0.001)R 136.52 0.00082622 2613100000 2995300 3068200 2694600 2842000 2975600 2510600 3341400 2616300 2561500 TRUE FALSE 2807829.52 3295372.72 2758517.184 2914930.531 2741908.379 3235369.464 2840388.09 2942950.814 2133969.102 1.315777964 1.544245752 1.292669693 1.365966606 1.284886635 1.516127605 1.331035247 1.3790972 1 21.02510786 -2.962672594 0.422096958 1.21E-13 1.393157916 0.64613153 0.087872346 82.02912591 2.801218419 73.69405801 0.04748425 0.001089751 2.962672594 1.393157916 LSPSPT(ph)TEDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSPSPTTEDPR 11 0 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2 Q9BTC8 MTA3 Metastasis-associated protein MTA3 1 LSPS(0.348)PT(0.546)T(0.106)EDPR 142.1 0.00042273 517780000 461040 478000 441790 430780 497080 473280 599670 522050 600990 TRUE FALSE 432184.3294 513391.6174 452269.4674 441834.5441 458041.3419 609908.2529 509755.0506 587229.0917 500680.8865 0.863193186 1.025386891 0.903308833 0.882467368 0.914836884 1.218157652 1.018123648 1.172861013 1 18.93353186 2.263788444 24.9982366 1.098701082 0.928915124 0.58737754 0.076479245 156.8894868 155461.1255 0.024314018 0.020335181 183.5643935 -2.263788444 -0.169785958 LSPT(ph)SLVHPVMSTLPELSCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSPTSLVHPVMSTLPELSCK 20 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 LS(0.338)PT(0.579)S(0.083)LVHPVMSTLPELSCK;LS(0.261)PT(0.37)S(0.37)LVHPVMSTLPELSCK 226.08 1.72E-24 1070830000 4611800 3674900 4724100 4542100 4135800 2926900 4187300 2899900 2246400 TRUE FALSE 4323155.67 3946993.42 4836157.883 4658657.976 3810990.951 3771848.516 3559453.238 3261958.898 1871461.328 2.310042749 2.109043538 2.584161271 2.489315652 2.036371735 2.015456296 1.901964623 1.743000964 1 20.83573381 0.999518948 0.601037816 0.991903417 2.360357985 0.879350311 0.153686592 0.289961119 0.251601335 0.167834139 0.072870814 9.988929508 -0.999518948 1.368454568 LSPWIRPDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSPWIRPDSK 10 1 O14744-2;O14744;G3V580;O14744-4;G3V5L5;G3V2L6;G3V2X6;C9JSX3 O14744-2 PRMT5 "Protein arginine N-methyltransferase 5;Protein arginine N-methyltransferase 5, N-terminally processed" 0 ; 163.9 5.77E-06 1907820000 3141000 2978500 3048000 2878200 3497200 2462100 4050500 3070500 4467400 FALSE TRUE 2944410.417 3199031.239 3120299.999 2952059.485 3222544.019 3172868.301 3443165.128 3453858.684 3721762.079 0.791133435 0.859547486 0.838393195 0.793188662 0.865865133 0.852517768 0.925143804 0.928017055 1 21.8275544 1.426928844 0.885334069 0.995461955 0.829238819 0.850831163 0.02469509 0.188028113 0.305164302 0.021744141 0.008314927 26.7256849 -1.426928844 -0.166223136 LSQELEYLTEDVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LSQELEYLTEDVKR 14 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ;; 254.2 4.82E-24 279653000 310481 278819 315903 296411 367049 235224 396474 294774 421348 FALSE TRUE 291048.5484 299463.0489 323396.3683 304017.4081 338222.4521 303129.3503 337026.4044 331577.1828 351022.2968 0.829145473 0.853116886 0.921298651 0.866091445 0.963535522 0.863561526 0.960128195 0.944604334 1 18.42120315 8 0.102362001 1.049194426 0.423030892 0.672714036 0.032276168 68.06242038 0.491581544 0.331975788 5.994730599 100000000 -8 -0.626163533 LSQLEGVNVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSQLEGVNVER 11 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 105.65 0.0040519 0 69796 76437 83566 82524 91165 80144 85511 70372 82267 FALSE TRUE 65427.59295 82096.47501 85548.22498 84641.70555 84005.26864 103280.2718 72689.4194 79158.09911 68536.10623 0.954644151 1.197857298 1.248221261 1.234994373 1.225708218 1.506946885 1.060600367 1.154983898 1 16.06457661 1.600224012 25 1.080820979 1.231129613 0.225658463 0.135977537 1.012431867 3301.766657 0.06723858 0.032051936 39.83125701 -1.600224012 0.150308634 LSQSSQDSS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LSQSSQDSSPVR 12 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 LSQSSQDS(0.001)S(0.999)PVR;LSQSSQDS(0.001)S(0.999)PVR;LSQSSQDS(0.245)S(0.754)PVR;LSQSSQDS(0.003)S(0.997)PVR 278.45 6.48E-28 2249260000 2605780 2743740 2848170 2531960 2691260 2431640 3530850 2795730 2807790 TRUE FALSE 2442688.881 2946889.364 2915729.937 2596934.38 2479899.296 3133614.994 3001431.821 3144783.045 2339151.71 1.0442627 1.259811132 1.246490309 1.110203485 1.060170354 1.339637348 1.283128327 1.34441175 1 21.157554 2.222346715 24.99616337 1.269940814 1.17236005 0.097810031 0.119929337 483.5174919 745410.0399 0.042280385 0.03132444 166.8578774 -2.222346715 -0.097580764 LSQTSNVDKEEEAVTIEMNEPVQLTFALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSQTSNVDKEEEAVTIEMNEPVQLTFALR 29 1 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ; 53.55 0.06418 35412400 41504 28109 32671 33531 35881 28988 39351 28787 35317 FALSE TRUE 38906.33873 30190.21961 33445.97155 34391.46223 33063.051 37356.36502 33450.68287 32381.12032 29422.36454 1.322338953 1.026097667 1.136753353 1.168888455 1.123738745 1.269658833 1.13691348 1.100561455 1 14.84462557 -1.082536038 6.906798799 0.999999939 1.149522362 0.257477793 0.083859038 8.33E-08 1.09E-08 0.075653429 0.017831676 0.082692089 1.082536038 0.149522423 LSQYLDSSQVKPLFQFFVPDALNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSQYLDSSQVKPLFQFFVPDALNDR 25 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 162.77 1.73E-11 171349000 314010 322640 297890 313220 380210 281410 374660 366490 277550 FALSE TRUE 294356.6746 346528.6013 304956.0915 321257.7555 350349.8403 362648.4987 318483.2112 412247.0832 231225.112 1.273030737 1.498663352 1.318870986 1.389372256 1.515189407 1.568378519 1.377372935 1.782881971 1 17.81893856 -1.107800724 5.982465122 0.999997916 1.453456813 0.504332734 0.144585606 3.61E-06 5.39E-07 0.125869302 0.029667543 0.078018802 1.107800724 0.453458898 LSS(ph)AGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSSAGPR 7 0 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 LS(0.152)S(0.848)AGPR 80.684 0.041134 0 526650 492250 498990 474690 541950 376530 589750 422180 549400 TRUE FALSE 493687.9166 528696.7022 510826.2784 486871.349 499387.4331 485228.0985 501322.4625 474890.1023 457701.5907 1.078623991 1.155112224 1.116068392 1.063730952 1.091076464 1.06014073 1.095304173 1.03755397 1 18.80404778 1.244545167 0.255419356 0.980174217 1.141669571 0.613543652 0.026298508 1.298637681 0.335657071 0.082713421 0.062712427 17.56083519 -1.244545167 0.161495354 LSS(ph)AGPRS(ph)PYCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSSAGPRSPYCK 12 1 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 2 LS(0.022)S(0.978)AGPRS(1)PYCK 131.45 0.00011297 512490000 879880 795090 834420 837780 1045000 447370 1060700 646790 978280 TRUE FALSE 824809.8814 853959.2909 854212.8364 859278.8532 962929.9153 576518.4566 901657.8821 727543.1553 814998.7481 1.012038219 1.04780442 1.04811552 1.054331501 1.181510913 0.707385696 1.106330389 0.892692359 1 19.63643832 LSS(ph)ATANALYSSNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LSSATANALYSSNLR 15 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 LSS(1)ATANALYSSNLR;LSS(1)ATANALYSSNLR;LSS(1)ATANALYSSNLR;LSS(1)ATANALYSSNLR 321.48 1.25E-56 982470000 736887 918240 896110 1377320 1395230 571076 683819 474272 578612 TRUE FALSE 690766.5581 986227.445 917366.1524 1412664.363 1285654.264 735936.3706 581286.6892 533485.9032 482037.9192 1.433012903 2.045954075 1.903099561 2.930608375 2.667122674 1.526718835 1.205894113 1.106730159 1 18.87878711 2.039257207 5.415968753 1.178961798 2.168908023 0.602282176 0.408064865 0.141538493 10.35380368 0.167027811 0.118820333 109.4604443 -2.039257207 0.989946226 LSS(ph)GFDDIDLPSAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LSSGFDDIDLPSAVK 15 0 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 LS(0.081)S(0.919)GFDDIDLPSAVK;LS(0.091)S(0.909)GFDDIDLPSAVK;LS(0.021)S(0.979)GFDDIDLPSAVK;LS(0.45)S(0.55)GFDDIDLPSAVK;LS(0.018)S(0.982)GFDDIDLPSAVK;LSS(1)GFDDIDLPSAVK;LSS(1)GFDDIDLPSAVK 455.31 7.86E-166 1710002000 2923230 1818090 2061226 1771618 1834752 1204485 2129204 1182534 2388971 TRUE FALSE 2740270.252 1952703.275 2110119.254 1817080.717 1690657.979 1552200.266 1809949.627 1330175.973 1990236.307 1.37685673 0.98114142 1.060235534 0.912997472 0.849476001 0.779907522 0.909414435 0.668350772 1 20.92450831 8 0.46119322 0.839109052 12.77058047 0.669387121 0.108284171 52.12228569 0.610437531 0.057471818 589.7432941 100000000 -8 11.93147141 LSS(ph)LRAS(ph)TSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LSSLRASTSK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 LS(0.423)S(0.577)LRAS(0.947)T(0.047)S(0.005)K;LS(0.434)S(0.566)LRAS(0.776)T(0.195)S(0.029)K;LS(0.421)S(0.579)LRAS(0.945)T(0.046)S(0.009)K;LS(0.434)S(0.566)LRAS(0.909)T(0.04)S(0.051)K 112.24 0.00093752 4273900000 11407200 8298500 8485200 8059900 11457900 5860280 19900900 10713600 20933100 TRUE FALSE 10693243.71 8912929.575 8686472.951 8266730.679 10558042.75 7552047.702 16916944.8 12051216.54 17439230.38 0.613171768 0.51108503 0.498099558 0.474030706 0.605419077 0.433049369 0.970051111 0.691040618 1 24.05583304 1.74067605 10.36612393 0.86880582 0.519698601 0.755633508 0.097489637 0.039433749 21.43597177 0.03989369 0.021678712 55.03969901 -1.74067605 -0.349107219 LSS(ph)LRAS(ph)TSKSESSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSSLRASTSKSESSQK 16 2 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 LS(0.449)S(0.551)LRAS(0.876)T(0.124)SKSESSQK;LS(0.448)S(0.552)LRAS(0.98)T(0.017)S(0.003)KS(0.001)ESSQK 133.38 1.82E-05 793280000 771390 644420 599040 664080 1255650 358534 1492170 844110 3997100 TRUE FALSE 723110.0769 692133.5273 613249.5117 681121.4171 1157036.314 462036.9455 1268432.961 949498.9916 3329958.188 0.2171529 0.207850516 0.184161325 0.204543534 0.347462715 0.138751576 0.380915582 0.285138413 1 21.66707263 -3.757733129 0.278012181 3.513901003 0.183793637 0.931012562 0.065227201 21.57664441 0.392621215 30.94835549 0.066875692 0.00017469 3.757733129 -3.330107366 LSS(ph)PISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSSPISK 7 0 A0A494C142;Q99728-3;Q99728-2;Q99728 A0A494C142 BARD1 BRCA1-associated RING domain protein 1 1 LS(0.004)S(0.996)PISK;LS(0.002)S(0.998)PISK 119.75 0.0049431 323070000 2512900 2033400 2251700 2075600 2375400 1580380 2673200 2008750 1804520 TRUE FALSE 2355622.075 2183955.052 2305111.387 2128863.41 2188845.666 2036610.051 2272378.477 2259546.859 1503333.954 1.566931997 1.452741119 1.533332884 1.41609481 1.455994298 1.354728964 1.511559338 1.503023897 1 20.5197341 -1.925975155 2.676255334 0.700355803 1.472903468 0.859152046 0.060350342 7441706.435 4445690.629 13965967.25 0.013604832 0.011858366 1.925975155 0.772547665 LSS(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LSSPVK 6 0 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 LS(0.224)S(0.776)PVK;LS(0.002)S(0.998)PVK;LS(0.003)S(0.997)PVK 125.5 0.018774 2952960000 12693200 7699400 9868800 8501300 8618000 7350900 11499800 8058300 9196600 TRUE FALSE 11898755.27 8269471.587 10102892.6 8719457.751 7941177.043 9472985.498 9775511.749 9064396.494 7661628.048 1.553032227 1.07933608 1.318635221 1.138068528 1.036486892 1.236419393 1.275905289 1.183090126 1 22.86921956 7.999987954 0.020979867 1.40E-07 2.769775833 0.280498618 0.135942005 4791.857001 7.743347167 373.3133457 694.9968266 99997226.39 -7.999987954 2.769775693 LSS(ph)PVKRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSSPVKRPR 9 2 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 LS(0.02)S(0.98)PVKRPR 57.401 0.091059 217670000 147070 145320 157630 152340 174590 130310 208090 139620 243650 TRUE FALSE 137865.1512 156079.644 161369.058 156249.3023 160878.4057 167928.3816 176888.8363 157051.8643 202983.241 0.679194748 0.768928722 0.7949871 0.769764546 0.792569893 0.827301706 0.871445522 0.77371838 1 17.63100109 -5 0.088401803 1.682134013 0.611043108 0.800567236 0.037191079 91.74038227 0.565667208 11.86208275 0.873174169 1.00E-05 5 -1.071090905 LSS(ph)PVLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LSSPVLHR 8 0 Q16643;Q16643-3;Q16643-2;D6R9W4;D6RCR4 Q16643 DBN1 Drebrin 1 LS(0.077)S(0.923)PVLHR;LS(0.032)S(0.968)PVLHR;LS(0.002)S(0.998)PVLHR;LS(0.035)S(0.965)PVLHR;LS(0.203)S(0.797)PVLHR;LS(0.267)S(0.733)PVLHR 162.8 0.00021874 10328750000 2491390 2758370 2436640 2640870 2520250 1921330 2769340 1993840 1724490 TRUE FALSE 2335458.347 2962602.585 2494438.251 2708639.195 2322319.731 2475986.781 2354103.176 2242775.313 1436661.478 1.625614929 2.062143817 1.736274195 1.885370518 1.616469688 1.723430897 1.638592815 1.561102143 1 20.45428873 -0.220522321 0.302046728 0.74045409 1.901562435 0.797482042 0.122817701 2.623961398 0.313619098 0.866757038 0.132774351 0.601835331 0.220522321 1.161108345 LSS(ph)SPPSGSGGGGGASSSSHCSGESQCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSSSPPSGSGGGGGASSSSHCSGESQCR 28 0 Q9Y4X0-2;Q9Y4X0-3;Q9Y4X0 Q9Y4X0-2 AMMECR1 AMME syndrome candidate gene 1 protein 1 LS(0.026)S(0.481)S(0.481)PPS(0.006)GS(0.006)GGGGGASSSSHCSGESQCR 89.145 0.0020717 120110000 26189 34372 34110 36815 35499 32650 42558 28101 31057 TRUE FALSE 24549.87724 36916.93864 34919.10531 37759.73523 32711.05174 42075.52497 36176.82299 31609.47171 25873.38606 0.94884671 1.426830588 1.349614821 1.459404468 1.264274094 1.626208679 1.3982253 1.221698298 1 14.65918125 0.964078359 3.650901671 1.000877037 1.374189757 0.295940385 0.172580884 0.253211317 9.212756105 0.149931429 0.03864089 9.206156617 -0.964078359 0.373312721 LSS(ph)SSATLLNSPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSSSSATLLNSPDR 14 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 LSS(0.767)S(0.161)S(0.072)ATLLNSPDR 263.9 1.25E-24 495820000 208740 528190 290170 296830 552440 234390 562790 412780 1145500 TRUE FALSE 195675.336 567297.7372 297052.9694 304447.1603 509053.5908 302054.588 478404.8642 464316.4916 954308.6498 0.205044077 0.594459389 0.311275571 0.319023788 0.533426571 0.316516662 0.501310414 0.486547504 1 19.86409642 0.135138908 0.759054935 1.014215148 0.397883413 0.729268972 0.11547159 1.864129632 1.237300769 0.170920865 0.036231019 1.365019664 -0.135138908 -0.616331734 LSS(ph)TDDGYIDLQFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LSSTDDGYIDLQFK 14 0 Q96A57;Q96A57-2;Q5JWB9;A0A087WTT2 Q96A57 TMEM230 Transmembrane protein 230 1 LS(0.132)S(0.864)T(0.004)DDGYIDLQFK;LS(0.001)S(0.998)T(0.001)DDGYIDLQFK;LS(0.038)S(0.961)TDDGYIDLQFK;LS(0.025)S(0.975)TDDGYIDLQFK;LSS(0.999)T(0.001)DDGYIDLQFK 308.2 1.25E-55 841110000 3315780 2145490 2176840 2211300 2582410 1529490 3310590 2200730 3861140 TRUE FALSE 3108251.249 2304344.312 2228475.673 2268045.702 2379597.936 1971028.934 2814197.764 2475495.985 3216690.79 0.966288478 0.716371098 0.692785169 0.70508664 0.739765831 0.612750514 0.874873573 0.769578473 1 21.61714583 0.723445818 1.033891758 0.997498898 0.735839883 0.365097447 0.098918293 0.925936163 1.754808531 0.086827147 0.027811801 5.28987997 -0.723445818 -0.261659015 LSS(ph)TS(ph)SEETQLFHIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 2 LS(0.095)S(0.884)T(0.142)S(0.666)S(0.213)EETQLFHIPR;LS(0.072)S(0.927)T(0.111)S(0.623)S(0.267)EETQLFHIPR 159.26 4.86E-09 92399000 109988 111881 102771 113067 162501 89686 118419 110084 149268 TRUE FALSE 103104.0474 120164.7857 105208.7767 115968.4906 149738.827 115576.8923 100663.1703 123828.2297 124354.2065 0.829115881 0.966310582 0.846041156 0.932565885 1.204131579 0.929416829 0.809487456 0.995770334 1 16.92409578 4.746203531 23.05098656 0.943425219 0.829115717 0.112975641 0.106546498 814.0234781 2454902.745 0.025806422 0.260034619 55744.69342 -4.746203531 -0.114309502 LSS(ph)TSS(ph)EETQLFHIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 2 LS(0.111)S(0.887)T(0.018)S(0.257)S(0.727)EETQLFHIPR;LS(0.093)S(0.907)T(0.006)S(0.202)S(0.792)EETQLFHIPR 174.02 2.12E-09 73564000 93738 98055 84769 88190 136141 70074 101223 94451 120869 TRUE FALSE 87871.10591 105315.0942 86779.76071 90453.10471 125449.035 90303.22624 86045.55086 106243.4153 100695.1831 0.872644582 1.045880161 0.861806475 0.898286313 1.245829554 0.896797876 0.854515065 1.055099281 1 16.61963515 6.780808491 5.699981514 0.961611642 0.875681023 0 0.12276962 0 0 0.025663888 0 6036823.679 -6.780808491 -0.085930619 LSS(ph)TSSEETQLFHIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 1 LS(0.153)S(0.795)T(0.043)S(0.008)SEETQLFHIPR;LS(0.116)S(0.874)T(0.009)SSEETQLFHIPR 306.4 8.15E-47 138464000 44820 61328 62268 65713 80511 71392 71041 66083 71156 TRUE FALSE 42014.79621 65868.78893 63745.02637 67399.30683 74187.99083 92001.71145 60389.06156 74333.60802 59279.60391 0.708756359 1.111154336 1.075328142 1.136972962 1.251492688 1.551996056 1.018715672 1.253949134 1 15.85524819 5.235720819 0.953761838 1.200487776 2.33E-25 0.45343232 0.159308825 4.302505433 1.608319468 0.046673314 6.670008803 172076.205 -5.235720819 -1.200487776 LSSAGPRS(ph)PYCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LSSAGPRSPYCK 12 1 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 LSSAGPRS(1)PYCK;LS(0.001)S(0.01)AGPRS(0.988)PYCK;LSSAGPRS(1)PYCK;LSSAGPRS(1)PYCK;LS(0.016)S(0.1)AGPRS(0.882)PY(0.002)CK;LS(0.008)S(0.046)AGPRS(0.92)PY(0.026)CK;LS(0.002)S(0.017)AGPRS(0.981)PYCK;LSSAGPRS(1)PYCK 166.23 3.18E-05 15228030000 11739890 10925800 10710110 10707330 13279350 7202020 12451170 10156150 14451460 TRUE FALSE 11005111.24 11734757.6 10964158.87 10982098.22 12236443.42 9281126.259 10584232.65 11424167.68 12039417.97 0.914089973 0.97469476 0.910688448 0.9121785 1.016365031 0.770894929 0.879131589 0.948897008 1 23.52126231 2.267578173 24.99993867 0.884288774 0.943289868 0.085242292 0.066380867 364.4824654 314016.8325 0.021173139 0.017711998 185.1732177 -2.267578173 0.059001094 LSSAGPRS(ph)PYCKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSSAGPRSPYCKR 13 2 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 LS(0.019)S(0.019)AGPRS(0.961)PY(0.002)CKR;LSSAGPRS(1)PYCKR 135.57 4.30E-05 844450000 379844 498580 402450 433780 565010 250528 506320 422000 875720 TRUE FALSE 356070.2421 535495.382 411996.3041 444911.5292 520636.3937 322851.3666 430402.0164 474687.6289 729556.6746 0.488063854 0.734001073 0.564721451 0.6098382 0.713633926 0.442530893 0.589950077 0.650652164 1 19.47666053 0.779807258 3.774381933 0.999983838 0.60051585 0.675716224 0.088017419 1.238008665 20.60817419 0.079394514 0.020363009 6.022922265 -0.779807258 -0.399467988 LSSAHNGGSAFGAAGYGGAQPT(ph)PPMPTRPVSFHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSSAHNGGSAFGAAGYGGAQPTPPMPTRPVSFHER 35 1 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 LSSAHNGGSAFGAAGYGGAQPT(0.907)PPMPT(0.056)RPVS(0.037)FHER 250.22 3.82E-48 501440000 43984 84252 60847 64080 103320 57081 85763 70885 127340 TRUE FALSE 41231.11995 90490.10574 62290.31957 65724.40129 95205.66397 73559.35807 72903.63433 79735.14829 106086.1314 0.388657023 0.85298714 0.587167416 0.61953811 0.89743742 0.693392785 0.687211735 0.751607654 1 16.69487654 -5 0.149760997 2.084025022 0.598048155 0.405764949 0.132991895 146.2842798 1.302978342 47.24304178 0.627856298 1.00E-05 5 -1.485976867 LSSAHNGGSAFGAAGYGGAQPTPPMPT(ph)RPVSFHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSSAHNGGSAFGAAGYGGAQPTPPMPTRPVSFHER 35 1 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 LSSAHNGGSAFGAAGYGGAQPT(0.212)PPMPT(0.493)RPVS(0.296)FHER 69.264 0.0098144 66923000 17431 41252 24104 23325 35848 17589 30885 23203 45653 TRUE FALSE 16340.02483 44306.341 24675.75826 23923.55899 33032.64268 22666.65877 26254.08097 26099.94563 38033.21937 0.429625078 1.16493796 0.648794887 0.629017459 0.868520815 0.595970027 0.690293417 0.686240767 1 15.21497244 3.732006691 24.93294904 0.710528421 0.866922645 0 0.21431434 470.7117375 2402265.764 0.049241433 0.085379607 5395.189342 -3.732006691 0.156394225 LSSANGHEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSSANGHEER 10 0 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23;F8WF24;F2Z2Z5;A8MYG5;H0Y6I9;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 0 ; 152.85 1.73E-05 1509290000 526790 819550 836330 872840 915950 708830 924190 786800 906970 FALSE TRUE 493819.1542 880230.3347 856168.1425 895238.5521 844014.9818 913457.7141 785616.2893 885033.712 755590.8477 0.653553647 1.164956322 1.13311079 1.184819211 1.117026476 1.208931682 1.039737699 1.171313436 1 19.5272457 4.740923055 24.98969026 1.132456456 0.653553479 0.841614883 0.064581065 70.71354891 747956.1693 0.013508697 0.090389252 55071.01173 -4.740923055 -0.478902977 LSSCDSFTSTINELNHCLSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSSCDSFTSTINELNHCLSLR 21 0 P07814;V9GYZ6;V9GZ76 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 321.67 4.84E-67 1146000000 821930 886570 956330 898000 926990 840600 1050390 847800 787100 FALSE TRUE 770486.8685 952212.5653 979014.5992 921044.2003 854187.9447 1083267.574 892893.7708 953649.6962 655727.9251 1.175009999 1.45214582 1.493019531 1.404613354 1.302656044 1.652007689 1.361683309 1.454337477 1 19.32273781 -0.940983818 5.370797214 0.999999127 1.425316803 0.516760071 0.124593305 1.17E-06 2.30E-07 0.107867625 0.025424591 0.114555563 0.940983818 0.425317676 LSSERPSS(ph)DGEGVVENGITTCNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSSERPSSDGEGVVENGITTCNGK 24 1 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 LSSERPS(0.12)S(0.88)DGEGVVENGITTCNGK;LSSERPS(0.121)S(0.879)DGEGVVENGITTCNGK 255.56 4.66E-44 810130000 431710 350510 398810 418820 377000 327660 514010 373350 320330 TRUE FALSE 404690.0417 376462.1251 408269.9615 429567.6303 347391.9407 422250.1229 436938.9723 419963.5693 266864.8536 1.516460621 1.410684547 1.529875351 1.609682296 1.301752314 1.582262022 1.6373043 1.573693814 1 18.02574979 -1.014635891 11.32604983 1.000009448 1.519024814 0.73155864 0.099031825 0 0 0.096401683 0.022722095 0.096686115 1.014635891 0.519015365 LSSESHHGGS(ph)PIHWVLPAGMSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 LSSESHHGGSPIHWVLPAGMSAK 23 0 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 LSSESHHGGS(1)PIHWVLPAGMSAK;LSSESHHGGS(0.999)PIHWVLPAGMSAK;LS(0.007)S(0.007)ES(0.04)HHGGS(0.947)PIHWVLPAGMSAK;LS(0.023)S(0.023)ES(0.196)HHGGS(0.758)PIHWVLPAGMSAK;LSSESHHGGS(1)PIHWVLPAGMSAK;LS(0.039)S(0.009)ES(0.039)HHGGS(0.909)PIHWVLPAGMS(0.002)AK;LS(0.001)S(0.001)ES(0.006)HHGGS(0.992)PIHWVLPAGMSAK;LS(0.001)S(0.001)ES(0.012)HHGGS(0.986)PIHWVLPAGMSAK;LS(0.004)S(0.004)ES(0.024)HHGGS(0.969)PIHWVLPAGMSAK 233.83 5.37E-37 11457837000 3483919 7245425 6874355 6891265 7637061 5837462 8622053 7266694 7952496 TRUE FALSE 3265866.729 7781883.806 7037417.947 7068106.527 7037277.035 7522642.516 7329256.196 8173956.742 6625173.043 0.49294814 1.174593291 1.062224021 1.066856138 1.062202752 1.135463552 1.106273927 1.233772566 1 22.65952671 4.742363423 24.99993077 1.107586959 0.492947905 0.896297665 0.06544122 103.1002477 677761.4506 0.014196065 0.107096424 55253.96178 -4.742363423 -0.614639054 LSSEVEALRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSSEVEALRR 10 1 P15924 P15924 DSP Desmoplakin 0 93.096 0.014461 306470000 84800 105960 92819 83450 120350 80650 100500 78365 99933 FALSE TRUE 79492.51937 113805.3887 95020.71051 85591.46828 110898.1965 103932.3458 85430.958 88149.04275 83253.53671 0.954824534 1.366973622 1.141341428 1.028082069 1.332053878 1.248383551 1.0261541 1.058802379 1 16.34522394 1.683430451 6.576203528 1.03162261 1.195903139 0.23295343 0.125544057 0.174354622 15.67557632 0.060228235 0.030677263 48.24257169 -1.683430451 0.164280529 LSSGPEQITLEASS(ph)TEGHPGAPSPQHTDQTEAFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 35 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 LSSGPEQITLEAS(0.003)S(0.967)T(0.03)EGHPGAPSPQHTDQTEAFQK;LSSGPEQITLEAS(0.118)S(0.837)T(0.045)EGHPGAPSPQHTDQTEAFQK 331.57 1.96E-117 645720000 188300 249310 211360 249710 237590 172497 297860 215150 169501 TRUE FALSE 176514.6391 267769.1718 216373.559 256117.9814 218930.6398 222294.0836 253198.6582 242011.9511 141210.1881 1.250013484 1.896245416 1.532280085 1.813735856 1.550388416 1.574207121 1.793062254 1.713842 1 17.10748465 -1.288096201 8.931445795 0.99999971 1.662916416 0.541921227 0.184031052 9.28E-07 7.42E-08 0.155401743 0.036628526 0.051511453 1.288096201 0.662916707 LSSGPEQITLEASSTEGHPGAPS(ph)PQHTDQTEAFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 35 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 LSSGPEQITLEASSTEGHPGAPS(1)PQHTDQTEAFQK 328.3 2.43E-117 605330000 47149 54903 56805 54285 51713 36327 72607 47690 55167 TRUE FALSE 44198.02825 58968.07525 58152.44143 55678.045 47651.66958 46814.01518 61720.2544 53644.20148 45959.27131 0.961678177 1.283050701 1.265303817 1.211464921 1.036823871 1.018597855 1.342933703 1.16721175 1 15.4880683 2.908327752 24.99980427 1.141510839 1.211680632 0.013140226 0.13241113 194.6554852 53075.55703 0.040406505 0.042857589 809.706735 -2.908327752 0.070169793 LSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 35 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ; 238.36 1.45E-47 324197000 59284 81942 87992 77000 99544 74013 100173 78477 102514 FALSE TRUE 55573.52026 88009.07094 90079.21179 78975.95036 91726.21578 95379.3516 85152.98861 88275.0262 85403.75113 0.650715215 1.030505918 1.054745378 0.924736318 1.074030292 1.116805179 0.9970638 1.033620011 1 16.38201182 4.738549025 9.211809436 1.032041094 0.64922644 0.845454024 0.050805053 0.028026369 53.03595752 0.01145192 0.066767789 54770.79251 -4.738549025 -0.382814655 LSSLRAS(ph)TSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LSSLRASTSK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 1 LSSLRAS(0.974)T(0.025)SK;LSSLRAS(0.333)T(0.333)S(0.333)K;LSSLRAS(0.994)T(0.005)S(0.001)K 109.6 0.0012095 840980000 972450 1203970 901650 952710 1519330 709500 965680 1571590 1718050 TRUE FALSE 911586.0904 1293113.192 923037.5638 977158.1515 1400007.95 914321.1322 820885.2489 1767806.471 1431296.356 0.636895418 0.903455938 0.644896188 0.682708474 0.978139813 0.638806302 0.573525703 1.235108623 1 20.44889099 1.235246547 24.99999972 1.117554407 0.728115187 0.587667685 0.137468039 61.83960073 466455.3589 0.111135788 0.032220379 17.18883914 -1.235246547 -0.38943922 LSSPAAFLPACNS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSSPAAFLPACNSPSK 16 0 Q86YS7;Q86YS7-5;H0YFE9;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 LSSPAAFLPACNS(1)PSK;LSSPAAFLPACNS(1)PSK 269.87 4.10E-28 609180000 1055370 715680 812670 863710 913120 604730 987470 698680 776090 TRUE FALSE 989316.2756 768669.6919 831946.9162 885874.2609 841407.2385 779305.734 839408.0407 785911.736 646555.5653 1.530133416 1.188868727 1.286736919 1.37014405 1.301368798 1.205319041 1.298276723 1.215536264 1 19.30241484 -4.487041246 0.187145993 3.19E-16 1.347121558 0.567242373 0.089414138 87.05614405 1.009963855 32.576754 0.243471343 3.26E-05 4.487041246 1.347121558 LSSS(ph)LGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LSSSLGR 7 0 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 1 LS(0.003)S(0.025)S(0.971)LGR;LS(0.006)S(0.227)S(0.766)LGR;LSS(0.002)S(0.998)LGR;LSS(0.002)S(0.998)LGR;LSS(0.02)S(0.98)LGR;LSS(0.013)S(0.987)LGR 170.05 0.0010378 10189620000 16673300 19553300 18419600 18847600 20727700 15232700 22650400 17886400 17991600 TRUE FALSE 15629747.92 21001046.68 18856521.61 19331261.32 19099830.05 19630133.21 19254182.8 20119556.41 14988685.73 1.04276974 1.401126627 1.258050369 1.289723574 1.274283176 1.309663406 1.284581126 1.342316249 1 23.83737055 -1.908824533 2.588721681 0.833447204 1.286806347 0.462016478 0.09263068 6649384.972 3519219.71 6720950.928 0.01952639 0.012336031 1.908824533 0.453359143 LSSS(ph)SATLLNSPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSSSSATLLNSPDR 14 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 LS(0.001)S(0.059)S(0.9)S(0.032)AT(0.007)LLNSPDR 124.78 9.97E-05 84767000 57032 74754 69145 71606 90148 60749 103830 61555 158470 TRUE FALSE 53462.46893 80288.86394 70785.15205 73443.53119 83068.13972 78286.25012 88261.65541 69240.27725 132020.3332 0.404956325 0.608155289 0.536168561 0.556304695 0.629207166 0.592986309 0.668545922 0.524466766 1 17.01040062 -5 0.212628577 3.06585295 0.515577779 0.807268403 0.067660604 58.36398741 0.58276861 51.46994088 0.12596252 1.00E-05 5 -2.550275171 LSSSGAPPADFPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSSSGAPPADFPSPR 15 0 Q8NG08 Q8NG08 HELB DNA helicase B 1 LSSSGAPPADFPS(1)PR 158.76 1.89E-06 150390000 221810 199330 219730 218630 234760 196730 247280 187430 194630 TRUE FALSE 207927.308 214088.6006 224942.0994 224240.4159 216322.8966 253522.7574 210202.6596 210831.0481 162144.9956 1.28235415 1.32035281 1.387289805 1.382962299 1.334132427 1.563555855 1.29638697 1.300262443 1 17.30692497 -0.563417378 7.260753708 1.000000002 1.361894833 0.660397854 0.080738916 0 0 0.072974029 0.017200144 0.273264126 0.563417378 0.361894832 LSSSSATLLNS(ph)PDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LSSSSATLLNSPDR 14 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 LSSSSATLLNS(1)PDR;LSSSSATLLNS(1)PDR;LSSSSATLLNS(1)PDR;LSSSSATLLNS(1)PDR;LSSSSATLLNS(1)PDR;LSSSSATLLNS(1)PDR 350.81 6.88E-82 2792000000 1902777 1798653 2079963 1900900 1831924 2177810 2078000 1765920 1519893 TRUE FALSE 1783685.584 1931827.14 2129300.705 1949680.312 1688052.079 2806508.393 1766423.191 1986398.999 1266213.039 1.408677315 1.525673074 1.681629108 1.539772733 1.33315013 2.216458294 1.395044227 1.568771555 1 20.27208873 0.510814078 1.726467157 1.000360719 1.599478913 0.357506859 0.245939412 3.220918434 10.18872152 0.212095556 0.059785423 3.24200797 -0.510814078 0.599118194 LSST(ph)PPLSALGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSSTPPLSALGR 12 0 Q8N201 Q8N201 INTS1 Integrator complex subunit 1 1 LS(0.003)S(0.441)T(0.555)PPLS(0.001)ALGR 107.12 0.0020072 0 223110 231740 217750 209260 246210 200460 321900 259970 300500 TRUE FALSE 209145.9434 248898.2707 222915.1328 214629.9659 226873.6598 258329.5478 273634.0834 292427.8268 250344.6087 0.835432185 0.994222612 0.890433127 0.857338079 0.906245439 1.03189579 1.093029663 1.168101156 1 17.93355586 2.096275878 2.94362361 1.093602043 0.906701402 0.701898157 0.057739581 0.14467719 2.483587725 0.025082094 0.016216828 124.8176145 -2.096275878 -0.186900641 LSSTSS(ph)EETQLFHIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 1 LS(0.013)S(0.013)T(0.091)S(0.091)S(0.728)EET(0.066)QLFHIPR 57.159 0.082833 0 21597 22482 22048 20941 24274 18057 27493 24979 27811 TRUE FALSE 20245.28232 24146.59067 22570.98897 21478.38151 22367.61796 23269.76277 23370.67988 28097.68314 23169.16443 0.873802868 1.042186512 0.97418226 0.927024433 0.965404601 1.004341906 1.008697571 1.21271888 1 14.4999184 1.428707787 5.82588754 1.110002723 0.976148715 0.415109932 0.067558213 0.17373779 11.00781998 0.039838589 0.015227771 26.83538234 -1.428707787 -0.133854008 LSSWDQAET(ph)PGHT(ph)PSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LSSWDQAETPGHTPSLR 17 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 LSSWDQAET(1)PGHT(0.998)PS(0.002)LR;LSSWDQAET(1)PGHT(0.997)PS(0.003)LR;LSSWDQAET(1)PGHT(0.994)PS(0.006)LR 230.54 1.28E-15 754763000 630095 669219 654319 641397 634172 517802 831898 673517 529585 TRUE FALSE 590658.4787 718768.6711 669839.7557 657856.3329 584366.6892 667283.0316 707162.6179 757607.08 441193.8423 1.33877317 1.629144839 1.518243664 1.491082309 1.324512342 1.512448651 1.602838821 1.7171751 1 18.75105313 -0.654024363 6.863610424 1 1.526005191 0.645128714 0.120280207 0 0 0.112018788 0.026403082 0.221807199 0.654024363 0.526005191 LSSWDQAET(ph)PGHTPSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LSSWDQAETPGHTPSLR 17 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 LSSWDQAET(1)PGHTPSLR;LSSWDQAET(1)PGHTPSLR;LSSWDQAET(1)PGHTPSLR;LSSWDQAET(1)PGHTPSLR 273.27 4.32E-35 1418017000 888349 854563 907397 872294 790382 747211 1061985 798893 659324 TRUE FALSE 832748.8218 917835.7337 928920.8853 894678.5408 728308.586 962918.6857 902750.2082 898636.5496 549278.565 1.516077406 1.670984073 1.691165366 1.628824786 1.32593666 1.753060737 1.64351982 1.636030617 1 19.06717847 -1.368614802 4.734606446 0.999363018 1.621566634 0.725533172 0.117305704 0.000746411 9.95E-05 0.107485722 0.025309933 0.042794228 1.368614802 0.622203616 LSSWDQAETPGHTPSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSSWDQAETPGHTPSLR 17 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 265.77 1.40E-27 274990000 158640 175640 184610 188090 180420 157150 208550 166260 140810 FALSE TRUE 148711.0056 188644.5684 188989.0364 192916.7078 166250.541 202516.6539 177279.8636 187017.927 117307.9013 1.267698117 1.608114766 1.61105121 1.64453294 1.417215201 1.7263684 1.511235489 1.59424834 1 16.83994066 -0.800803436 6.022496674 0.999999966 1.561896688 0.639156802 0.128897328 5.07E-08 1.03E-08 0.109684883 0.025852973 0.158196388 0.800803436 0.561896722 LST(ph)GSFPEDLLESDSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSTGSFPEDLLESDSSR 17 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 LS(0.118)T(0.528)GS(0.354)FPEDLLESDSSR;LS(0.07)T(0.514)GS(0.416)FPEDLLESDSSR 209.13 5.09E-11 28620100 50995 44293.4 43588.6 44821.4 47229.8 43585.2 50673 37611.6 55293 TRUE FALSE 47803.31398 47572.92942 44622.54218 45971.59301 43520.56202 56167.53969 43075.05408 42307.49105 46064.24109 1.037753208 1.032751833 0.968702428 0.99798872 0.944779747 1.219330621 0.935108298 0.918445416 1 15.49135962 1.587635135 25 0.945057468 1.025197737 0.200023566 0.076106666 1.481945 1825.569367 0.038085285 0.017665483 38.69324339 -1.587635135 0.080140269 LST(ph)PQKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LSTPQKK 7 1 B5MC51;P53671-3;F5GXC4;F5H2U0;Q96C90 B5MC51;Q96C90 LIMK2;PPP1R14B LIM domain kinase 2;Protein phosphatase 1 regulatory subunit 14B 1 LS(0.091)T(0.909)PQKK;LS(0.109)T(0.891)PQKK;LS(0.071)T(0.929)PQKK;LS(0.183)T(0.817)PQKK 93.111 0.0088929 5667880000 4733770 2432600 3308260 2827650 3315240 1850040 4174240 2609770 3754180 TRUE FALSE 4437491.786 2612712.235 3386733.489 2900212.286 3054874.423 2384116.515 3548351.464 2935605.529 3127583.105 1.41882458 0.835377398 1.082859632 0.92730143 0.976752438 0.762287183 1.134534669 0.938617914 1 21.57661679 4.748739745 24.809847 0.964010206 1.418824859 0.645333293 0.1074411 799.0028774 1947387.252 0.023619242 0.324436316 56071.18634 -4.748739745 0.454814652 LSTCEAEDIATYEQNLQQWHLDLVQLIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSTCEAEDIATYEQNLQQWHLDLVQLIQR 29 0 Q92552;Q92552-2;G5EA06 Q92552 MRPS27 "28S ribosomal protein S27, mitochondrial" 0 ; 302.16 3.87E-81 111884000 152936 142263 131229 130923 179594 144551 138776 146746 168162 FALSE TRUE 143364.0088 152796.3005 134341.8139 134282.7058 165489.4117 186280.5271 117967.8271 165067.5611 140094.6758 1.023336597 1.090664578 0.958935899 0.958513984 1.181268387 1.329675992 0.84205789 1.178257205 1 17.0960426 5.115729365 8.600615997 1.056391684 0.696493523 0.004303314 0.139244426 65016.49582 187683.1005 0.031635697 404505.7394 130535.7187 -5.115729365 -0.35989816 LSTDHIPILYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSTDHIPILYR 11 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 120.09 0.00049858 702560000 1022070 1680490 1332360 1409280 1572910 1096500 1584610 1384980 1347670 FALSE TRUE 958100.4631 1804915.228 1363964.208 1445444.511 1449379.993 1413041.75 1347012.441 1557897.802 1122735.171 0.85336283 1.607605493 1.21485836 1.287431398 1.290936662 1.258570843 1.199759726 1.38759152 1 20.09858624 -2.063746079 2.504691277 0.589397443 1.284260159 0.154896251 0.186658807 19045554.54 10104364.4 44498304.63 0.044397846 0.008634833 2.063746079 0.694862715 LSTGS(ph)FPEDLLESDSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSTGSFPEDLLESDSSR 17 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 LS(0.013)T(0.113)GS(0.873)FPEDLLESDSSR;LSTGS(1)FPEDLLESDSSR 247.38 1.01E-20 43600000 78876 58893 62323 52793 58622 57136 64887 59726 68864 TRUE FALSE 73939.29196 63253.499 63801.33099 54147.75776 54018.06459 73630.23567 55157.79673 67182.92257 57370.15352 1.288811122 1.102550632 1.112099708 0.943831495 0.941570857 1.283424066 0.961437147 1.171043103 1 15.80801276 6.179981426 1.004457894 1.058457984 4.822225556 0.300334752 0.1087664 35.93763752 2.703900239 0.029661564 269.3964175 1513496.517 -6.179981426 3.763767572 LSTIFEECDEELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSTIFEECDEELER 14 0 Q5T5P2;Q5T5P2-3;A0A0U1RRK8 Q5T5P2 KIAA1217 Sickle tail protein homolog 0 ; 120.06 0.00035174 20767000 24787 25675 26776 21843.5 29715 26551 26470 22337.8 30022 FALSE TRUE 23235.62592 27576.00371 27411.13936 22404.04119 27381.30376 34215.84268 22501.06924 25126.7235 25011.13425 0.929011283 1.102549106 1.095957468 0.895762702 1.094764575 1.36802443 0.899642096 1.004621512 1 14.61028286 1.61170949 25 0.96409789 1.082569026 0.146838096 0.128140906 0.657932967 4250.495355 0.059067536 0.031192405 40.89869867 -1.61170949 0.118471136 LSTTPS(ph)PT(ph)SSLHEDGVEDFRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSTTPSPTSSLHEDGVEDFRR 21 1 O94842-3;O94842-2;O94842;C9J919;C9JNL1 O94842-3 TOX4 TOX high mobility group box family member 4 2 LS(0.013)T(0.043)T(0.065)PS(0.891)PT(0.686)S(0.175)S(0.128)LHEDGVEDFRR;LS(0.003)T(0.004)T(0.023)PS(0.788)PT(0.574)S(0.395)S(0.212)LHEDGVEDFRR 124.91 2.08E-05 746860000 544230 689600 630190 608640 740670 451010 767750 586990 778000 TRUE FALSE 510167.6158 740658.7015 645138.4044 624258.7328 682500.7659 581209.2655 652633.0149 660276.9936 648146.7739 0.787117419 1.142732991 0.995358506 0.963144087 1.053003414 0.896724768 1.006921644 1.018715236 1 19.30596103 3.494011976 24.62570858 0.987059357 1.016985474 0 0.096203906 1854.855768 2704259.556 0.023585024 0.03619634 3118.975591 -3.494011976 0.029926117 LSTTPS(ph)PTSSLHEDGVEDFRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSTTPSPTSSLHEDGVEDFRR 21 1 O94842-3;O94842-2;O94842;C9J919;C9JNL1 O94842-3 TOX4 TOX high mobility group box family member 4 1 LS(0.001)T(0.001)T(0.007)PS(0.695)PT(0.226)S(0.056)S(0.012)LHEDGVEDFRR 88.571 0.0011462 132520000 34906 34695 45710 38427 42078 55352 32871 34106 24414 TRUE FALSE 32721.29577 37263.8539 46794.26279 39413.10188 38773.36361 71331.22384 27942.29871 38364.20918 20339.14568 1.608784178 1.832124834 2.300699524 1.937795348 1.906341801 3.507090463 1.373818702 1.886225202 1 14.31197146 4.483050889 2.675888241 2.058841062 1.611865888 0.025341963 0.651062514 1.042660416 13.46370712 0.148977255 0.79583551 30412.41363 -4.483050889 -0.446975174 LSTTPSPT(ph)SSLHEDGVEDFRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LSTTPSPTSSLHEDGVEDFRR 21 1 O94842-3;O94842-2;O94842;C9J919;C9JNL1 O94842-3 TOX4 TOX high mobility group box family member 4 1 LSTTPS(0.134)PT(0.77)S(0.095)S(0.001)LHEDGVEDFRR;LSTTPS(0.074)PT(0.676)S(0.24)S(0.009)LHEDGVEDFRR;LSTT(0.003)PS(0.304)PT(0.655)S(0.03)S(0.007)LHEDGVEDFRR 235.76 4.83E-30 463460000 255486 298887 377696 375089 300160 410670 267599 266000 224548 TRUE FALSE 239495.5873 321016.9045 386655.1275 384714.4188 276586.6444 529223.7623 227475.0142 299210.6855 187069.4882 1.280249332 1.716030271 2.066906428 2.056532161 1.478523553 2.829022346 1.21599207 1.59946279 1 17.51321474 -0.685596032 13.15148357 0.999993011 1.802653783 0.215265416 0.466505343 0 0 0.409878038 0.09660918 0.206254754 0.685596032 0.802660772 LSVACFYGGTPYGGQFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSVACFYGGTPYGGQFER 18 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 223.39 1.20E-18 145943000 195147 210460 204168 169260 204878 191593 214450 174677 227853 FALSE TRUE 182933.0976 226042.6774 209010.9614 173603.4982 188787.7083 246902.7888 182295.2134 196485.808 189822.8623 0.963704242 1.190808497 1.101084236 0.914555265 0.994546737 1.300701011 0.960343823 1.03510086 1 17.53429424 1.605751514 25 0.998290317 1.087215446 0.095643702 0.112029747 0.465429469 5408.895756 0.05522258 0.027515906 40.34145088 -1.605751514 0.088925128 LSVAS(ph)TPISQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSVASTPISQR 11 0 H0YMD2;Q9BXS6-7;Q9BXS6-4;Q9BXS6-6;Q9BXS6-3;Q9BXS6-5;Q9BXS6-2;Q9BXS6 H0YMD2 NUSAP1 Nucleolar and spindle-associated protein 1 1 LSVAS(0.5)T(0.5)PISQR;LS(0.011)VAS(0.494)T(0.494)PISQR 142.71 3.94E-05 364920000 449750 481480 460810 415170 442730 365100 498730 394460 446190 TRUE FALSE 421600.9503 517129.2802 471740.6308 425823.9651 407959.7717 470498.4431 423950.0665 443709.1993 371718.0065 1.134195662 1.391187059 1.269081999 1.145556464 1.097498008 1.265740252 1.140515281 1.193671524 1 18.50384905 -1.255992597 0.111227072 0.669996073 1.412064345 0.370573744 0.08532098 45.75891381 0.93602525 5.643640605 1.423159887 0.055463517 1.255992597 0.742068272 LSVEEFFMDLHNFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSVEEFFMDLHNFR 14 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 245.03 1.25E-17 674310000 799380 1056270 888580 790220 1134730 689520 877880 1048700 771050 FALSE TRUE 749348.2327 1134477.33 909657.5372 810498.383 1045612.883 888573.2306 746250.0438 1179632.503 642356.7738 1.166560801 1.766117174 1.416125079 1.261757354 1.627775912 1.383301721 1.161737642 1.83641327 1 19.29301529 -2.152403878 2.262273762 2.94E-05 1.452081211 0.27273615 0.232203538 3280912.534 724574.545 16856270.21 0.05339021 0.00704038 2.152403878 1.452051809 LSVHDMKPLDS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSVHDMKPLDSPGR 14 1 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 1 LSVHDMKPLDS(1)PGR 121.26 7.00E-05 140910000 291260 344750 341090 361200 395100 281470 469380 351070 371080 TRUE FALSE 273030.5565 370275.6487 349180.8159 370469.0035 364070.4398 362725.8197 399000.8265 394901.8623 309144.3507 0.883181452 1.197743539 1.129507348 1.198368991 1.177671333 1.173321844 1.290661872 1.27740281 1 18.23792112 4.739384202 24.46406703 1.190609421 0.88318133 0.572170021 0.080406165 35.08255485 1041864.008 0.017951387 0.108370948 54876.22164 -4.739384202 -0.307428091 LSVHDMKPLDS(ph)PGRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 182.39 2.86E-07 2188750000 1947150 2434450 2309290 2476550 2676440 1717600 3015510 2255700 2852760 TRUE FALSE 1825281.357 2614699.211 2364067.449 2540102.466 2466243.199 2213443.237 2563362.27 2537329.11 2376615.926 0.768016968 1.100177434 0.994720023 1.068789634 1.03771214 0.931342424 1.078576577 1.067622699 1 21.18047734 4.747086365 24.92118287 1.035920429 0.768016828 0.742386747 0.049397992 515.7383877 1507494.112 0.011008394 0.128881741 55858.12642 -4.747086365 -0.267903601 LSVNSVTAGDYSRPLHISTFINELDSGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSVNSVTAGDYSRPLHISTFINELDSGFR 29 1 E9PGT1;Q15631 E9PGT1 TSN Translin 0 158.83 4.51E-12 72422000 36624 55542 37980 44981 56222 46194 48249 42531 61948 FALSE TRUE 34331.76922 59654.38747 38880.90354 46135.28861 51806.55091 59529.4579 41014.51037 47841.08897 51608.4786 0.665235057 1.155902849 0.753382091 0.893947852 1.00383798 1.153482132 0.794724268 0.927000568 1 15.65532048 LSVPT(ph)S(ph)DEEDEVPAPKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LSVPTSDEEDEVPAPKPR 18 1 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 2 LSVPT(1)S(1)DEEDEVPAPKPR;LSVPT(1)S(1)DEEDEVPAPKPR;LS(0.037)VPT(0.963)S(1)DEEDEVPAPKPR;LS(0.001)VPT(0.999)S(1)DEEDEVPAPKPR;LS(0.003)VPT(0.999)S(0.998)DEEDEVPAPKPR 189.11 7.89E-14 2690620000 5351910 4476960 4582290 4394770 5184040 3590430 6166080 4272660 5728600 TRUE FALSE 5016943.507 4808438.777 4690984.083 4507547.239 4776906.41 4626928.855 5241533.547 4806111.006 4772459.652 1.051228061 1.007538906 0.982927971 0.944491429 1.000931754 0.969506123 1.098287661 1.007051155 1 22.18630157 1.762037654 25 1.044818112 0.991795962 0.202694101 0.037962959 15.47511114 16491.21947 0.016439078 0.009116322 57.81461708 -1.762037654 -0.05302215 LSVPT(ph)SDEEDEVPAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LSVPTSDEEDEVPAPK 16 0 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 LSVPT(0.5)S(0.5)DEEDEVPAPK 144.8 1.43E-05 52549000 112360 68243 87981 83406 82478 81642 116520 74015 67014 TRUE FALSE 105327.5882 73295.78273 90067.95087 85546.33917 76000.51058 105210.7201 99048.90772 83255.93568 55828.93047 1.886613039 1.312863816 1.613284548 1.532294071 1.361310524 1.884519713 1.774150192 1.491268684 1 15.7687253 LSVPTS(ph)DEEDEVPAPKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LSVPTSDEEDEVPAPKPR 18 1 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 LSVPT(0.166)S(0.834)DEEDEVPAPKPR;LSVPT(0.183)S(0.817)DEEDEVPAPKPR;LSVPT(0.112)S(0.888)DEEDEVPAPKPR;LSVPT(0.036)S(0.964)DEEDEVPAPKPR;LSVPT(0.002)S(0.998)DEEDEVPAPKPR;LSVPT(0.028)S(0.972)DEEDEVPAPKPR;LSVPT(0.029)S(0.971)DEEDEVPAPKPR;LSVPT(0.093)S(0.907)DEEDEVPAPKPR 284.44 2.41E-39 7590200000 5148570 3898080 4482810 4083670 4306710 3704410 5426670 3617060 4601980 TRUE FALSE 4826330.194 4186697.899 4589144.37 4188463.886 3968478.369 4773813.031 4612991.212 4068657.903 3833879.808 1.258863198 1.092026383 1.196997454 1.092487009 1.035107663 1.245165021 1.203217483 1.06123773 1 21.87037368 1.04385765 5.069208605 1.000686609 1.156987657 0.381973163 0.070886467 0.173192685 9.790297418 0.065517957 0.0165715 11.06261122 -1.04385765 0.156301048 LSYFEHNLETWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LSYFEHNLETWR 12 0 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 0 ; 206.69 8.72E-08 386130000 247690 370080 261320 276390 411010 203046 283640 373300 312860 FALSE TRUE 232187.525 397481.1083 267518.6338 283482.6353 378730.9325 261662.084 241110.8152 419907.3267 260641.6448 0.890830493 1.525009975 1.026384843 1.087633695 1.453071449 1.003915104 0.92506635 1.61105232 1 17.99170809 LSYLEEAVMHLDHSDPITR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LSYLEEAVMHLDHSDPITR 19 0 Q6P2E9;Q6P2E9-2;I3L0V0;I3L3M2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 ;;;; 182.7 1.66E-14 105741900 65866.8 74359.8 67872.7 75871.1 82045.8 65935.7 83458.4 79128 83413.4 FALSE TRUE 61744.31456 79865.47696 69482.6725 77818.08088 75602.25382 84970.26621 70944.58771 89007.30498 69491.16467 0.888520359 1.149289659 0.999877795 1.119826977 1.08794052 1.222749203 1.020915221 1.280843477 1 16.08454194 3.21736628 23.24030371 1.121417277 1.04004917 0.181075089 0.10443452 205.1586452 224962.0859 0.027043801 0.03236551 1649.553024 -3.21736628 -0.081368107 LSYLPATVEPAS(ph)PTPAHSLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LSYLPATVEPASPTPAHSLPR 21 0 M0R344;Q9NRA0-4;Q9NRA0-2;Q9NRA0;Q9NRA0-5;E9PCV4 M0R344 SPHK2 Sphingosine kinase 2 1 LSYLPATVEPAS(0.958)PT(0.042)PAHSLPR;LSYLPATVEPAS(0.627)PT(0.372)PAHS(0.001)LPR;LSYLPATVEPAS(0.743)PT(0.257)PAHSLPR;LSYLPATVEPAS(0.945)PT(0.055)PAHSLPR 145.2 7.76E-08 391840000 281682 295290 298118 311819 331361 242644 346920 278445 353254 TRUE FALSE 264052.0264 317153.5788 305189.4997 319820.8034 305337.2437 312691.3838 294902.5666 313209.4712 294293.6253 0.897240048 1.077677366 1.037023821 1.086740507 1.03752585 1.062514975 1.002069163 1.064275418 1 18.16689677 4.745860263 24.8678633 1.046856448 0.897239972 0.724528117 0.028818295 413.7894385 1409628.358 0.006377242 0.065956205 55700.64996 -4.745860263 -0.149616476 LT(ph)ATPTPLGGMTGFHMQTEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTATPTPLGGMTGFHMQTEDR 21 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 LT(0.536)AT(0.354)PT(0.11)PLGGMTGFHMQTEDR 82.8 0.013529 119600000 84013 96113 82536 93066 101380 67404 103930 88553 100370 TRUE FALSE 78754.7763 103229.3065 84493.7929 95454.23112 93418.02375 86862.44059 88346.66134 99609.03698 83617.59859 0.941844512 1.234540435 1.010478587 1.141556715 1.117205293 1.038805731 1.056555831 1.191244889 1 16.35151899 LT(ph)PPPADLPLALPAHGLWSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTPPPADLPLALPAHGLWSR 20 0 Q15742 Q15742 NAB2 NGFI-A-binding protein 2 1 LT(1)PPPADLPLALPAHGLWSR;LT(1)PPPADLPLALPAHGLWSR 205.73 3.07E-21 397460000 523430 485460 583050 610680 384800 322630 499350 318140 212747 TRUE FALSE 490669.4506 521403.9635 596880.2213 626351.0827 354579.3602 415768.0435 424477.1032 357860.4793 177238.1513 2.768418916 2.941826913 3.367673477 3.533951794 2.000581464 2.345815731 2.394953345 2.019093952 1 17.43532966 2.728969768 24.79782694 2.099302192 3.153561917 0.638042164 0.441780528 407.5932316 1053859.398 0.132399581 0.126326416 535.7593611 -2.728969768 1.054259726 LT(ph)PVRPAAAS(ph)PIVSGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTPVRPAAASPIVSGAR 17 1 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 2 LT(1)PVRPAAAS(1)PIVSGAR;LT(1)PVRPAAAS(1)PIVSGAR 129.07 7.98E-05 437540000 474010 406400 424640 383840 476270 376940 552840 376760 745340 TRUE FALSE 444342.5602 436490.2789 434712.6613 393689.9842 438865.6754 485756.4589 469946.7743 423799.3154 620937.9389 0.715598987 0.702953148 0.700090354 0.63402469 0.706778645 0.7822947 0.756833727 0.682514771 1 19.24408956 -5 0.266418445 2.944823554 0.690238079 0.839985253 0.039739288 79.06942265 0.771620891 84.36461359 0.050618323 1.00E-05 5 -2.254585475 LT(ph)QTSSTEQLNVLETETEVLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTQTSSTEQLNVLETETEVLNK 22 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 LT(0.503)QT(0.199)S(0.109)S(0.094)T(0.094)EQLNVLETETEVLNK 277.76 5.95E-45 181900000 128190 120800 113790 109810 125090 102790 155350 102720 151460 TRUE FALSE 120166.8167 129744.1577 116489.1525 112627.9105 115265.936 132463.8043 132056.7097 115544.8181 126180.3475 0.95234178 1.028243781 0.923195686 0.892594708 0.913501494 1.049797428 1.046571136 0.915711681 1 16.9451277 2.239477338 24.99997774 1.012683377 0.948933886 0.246084574 0.051081532 35.56861547 970026.3746 0.019156945 0.015183135 173.5710688 -2.239477338 -0.063749491 LTAEDLFEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LTAEDLFEAR 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 172.59 8.54E-06 383160000 511489 631356 607291 643442 648913 561271 672350 571857 458085 FALSE TRUE 479475.8165 678102.2552 621696.2293 659953.8111 597949.9906 723300.8262 571537.3593 643254.6053 381627.6542 1.256396939 1.776868756 1.629064934 1.729313387 1.566841355 1.895305066 1.497630879 1.685555536 1 18.54180619 -0.766179322 1.006276506 0.962944311 1.646382257 0.565531115 0.172776005 48.72713844 24.13577281 6.718884138 0.045904173 0.171324975 0.766179322 0.683437947 LTAEEMDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTAEEMDER 9 0 P46940;H0YLE8;A0A0J9YXZ5;A0A087X225 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 93.178 0.022276 622340000 972890 976610 865110 917580 1033360 725990 1039740 815240 959920 FALSE TRUE 911998.5516 1048919.221 885630.8177 941126.6563 952204.074 935571.5275 883840.6395 917024.5086 799703.1507 1.140421356 1.311635723 1.107449454 1.176845002 1.190696914 1.169898514 1.105210901 1.146706134 1 19.60910505 -4.999999988 0.098254997 0.407258422 1.303055274 0.53212881 0.053625976 133.6046323 0.897234605 16.05017253 0.893109263 1.00E-05 4.999999988 0.895796852 LTAIIEEAEEAPGARPQLQDAWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LTAIIEEAEEAPGARPQLQDAWR 23 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;; 292.68 1.32E-61 9672166400 2468218.9 2829152 2680828.4 2868667 2685561 2233627.9 3264646.5 2458126.7 2264134.9 FALSE TRUE 2313737.485 3038625.358 2744418.916 2942281.852 2474647.872 2878440.015 2775143.065 2765029.229 1886236.158 1.226642526 1.610946405 1.454971003 1.559869287 1.311950182 1.526023135 1.471259605 1.465897691 1 20.84707888 0.567218063 4.674473973 1.000000005 1.470250625 0.60967528 0.113321504 48.99840514 528.5907111 0.096358562 0.024418366 3.691629119 -0.567218063 0.47025062 LTALDYHNPAGFNCKDETEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LTALDYHNPAGFNCKDETEFR 21 1 Q9Y224;G3V4C6;G3V4E7 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ;; 191.8 7.90E-18 668910000 941350 928260 964730 952320 1146560 780150 1125950 907910 1413560 FALSE TRUE 882432.5839 996989.3363 987613.8512 976758.1435 1056513.803 1005366.64 957124.2503 1021264.562 1177627.704 0.749330693 0.846608256 0.838646924 0.829428639 0.897154337 0.853721967 0.812756228 0.867221923 1 20.16745209 -5 0.22132812 1.823506962 0.817607469 0.697792747 0.035197883 90.51251301 0.906035542 33.27713864 0.064712795 1.00E-05 5 -1.005899493 LTATEGPGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTATEGPGSPR 11 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 LTATEGPGS(1)PR;LTATEGPGS(1)PR 175.34 1.04E-05 448610000 637270 643860 665370 700900 720990 587960 766460 579790 689900 TRUE FALSE 597384.4083 691532.0643 681152.8906 718886.2806 664366.3537 757694.5073 651536.4385 652178.0578 574751.2331 1.039379081 1.203185003 1.185126454 1.250778144 1.155919841 1.318299925 1.133597287 1.13471363 1 19.13257813 0.8920993 1.757648819 1.001537209 1.192788168 0.393955375 0.072127939 0.447887001 2.764243514 0.061497546 0.017493883 7.800084371 -0.8920993 0.191250959 LTDCVVMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTDCVVMR 8 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ; 89.752 0.031832 407550000 360710 417830 368280 406680 448910 317900 393550 360350 414240 FALSE TRUE 338133.805 448766.568 377015.7755 417116.0973 413654.4194 409672.5693 334540.831 405340.4907 345100.6679 0.979812085 1.300393218 1.092480573 1.208679484 1.198648562 1.187110335 0.969400706 1.174557248 1 18.39665774 1.758305362 25 1.047952967 1.172589425 0.222952672 0.098095963 10.97077275 13903.55338 0.040382384 0.022394302 57.3198918 -1.758305362 0.124636458 LTDCVVMRDPASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LTDCVVMRDPASK 13 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;; 186.56 7.02E-06 7032050000 7708140 7540030 8129260 8193480 10137400 6539770 10652350 8363780 12181420 FALSE TRUE 7225701.277 8098301.667 8322089.886 8403738.568 9341249.496 8427695.435 9055129.009 9408016.344 10148262.31 0.712013649 0.797998852 0.820050727 0.82809631 0.920477734 0.830456996 0.892283697 0.927056875 1 23.27472938 8 0.096318432 1.091194988 0.082088349 0.858506802 0.030199958 46.85903353 0.321311336 0.403249334 6.246948471 99999999.99 -8 -1.009106639 LTDCVVMRDPASKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTDCVVMRDPASKR 14 2 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 83.692 0.004741 2905700000 2300100 2930300 2640400 2849900 4287100 2296400 3585400 2916600 6674600 FALSE TRUE 2156140.847 3147262.461 2703031.535 2923033.259 3950408.459 2959333.401 3047802.555 3280743.93 5560566.14 0.387755634 0.565996768 0.486107254 0.52567188 0.71043278 0.532200018 0.548110117 0.590001782 1 22.40680035 -5 0.226293565 3.407716952 0.488834276 0.803779237 0.072931352 66.37727591 0.664606716 73.0264902 0.124603375 1.00E-05 5 -2.918882676 LTDDHVQFLIYQILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTDDHVQFLIYQILR 15 0 Q16539-2;Q16539;B4E0K5;Q16539-5;Q16539-3;Q16539-4;E7EX54;B5TY33 Q16539-2 MAPK14 Mitogen-activated protein kinase 14 0 ; 176.32 8.06E-07 240636000 255710 385260 280080 294140 451010 252310 303430 353360 330170 FALSE TRUE 239705.5676 413785.0513 286723.6299 301688.1304 415589.4939 325147.8011 257933.4884 397477.7738 275062.494 0.871458569 1.504331053 1.042394496 1.096798498 1.510891172 1.18208701 0.937726858 1.445045335 1 18.06939991 -1.582350864 5.763506268 0.999223538 1.198264249 0.070710151 0.226531198 0.002093056 0.000151672 0.203122064 0.047694633 0.026160686 1.582350864 0.19904071 LTDEDFS(ph)PFGSGGGLFSGGK ddPTM_SK-BR-3_Pertuzumab_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 243.99 7.56E-30 66619000 538200 467660 531340 638210 720190 443630 570640 450350 682500 TRUE FALSE 504515.0227 502286.033 543943.6357 654587.5491 663629.1825 571698.7793 485077.8296 506577.1888 568586.3409 0.887314707 0.883394477 0.956659695 1.151254439 1.167156393 1.005473994 0.853129586 0.890941538 1 19.11701992 -2.183197354 8.193869697 1.999000149 0.968488411 0.002789324 0.109306686 0.203046437 0.004539684 0.010772715 0.026979423 0.006558472 2.183197354 -1.030511738 LTDEGAVHVNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LTDEGAVHVNDR 12 0 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 0 ;; 121.28 0.00023087 700140000 1991020 1726110 1760080 1721020 1906620 1398460 2096710 1673540 1866520 FALSE TRUE 1866405.612 1853912.98 1801829.929 1765184.287 1756881.756 1802172.7 1782327.8 1882485.153 1554985.754 1.20027184 1.19223792 1.158743689 1.135177144 1.129837847 1.158964123 1.146202012 1.210612476 1 20.56846993 -1.7070539 2.669185778 0.972844334 1.164390339 0.787534036 0.027159786 7110388.615 6269624.652 1301584.055 0.00669619 0.019631166 1.7070539 0.191546005 LTDIFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTDIFR 6 0 O75340-2;O75340;A0A024QZ42;H0Y9X3;A0A087WZ38 O75340-2 PDCD6 Programmed cell death protein 6 0 ; 132.94 0.034151 207367000 746184 1002000 823354 849720 886680 633400 979920 825760 1005190 FALSE TRUE 699481.6754 1076189.123 842884.3457 871525.2538 817043.7295 816252.2976 832990.0931 928857.9537 837417.2952 0.835284486 1.285128846 1.006528466 1.040729943 0.975670952 0.974725865 0.994713266 1.109193659 1 19.67558719 3.714400763 24.38953199 1.010383039 1.108385479 0 0.11515758 553.5625386 1061370.413 0.027715622 0.043270509 5180.846954 -3.714400763 0.098002441 LTEDKADVQSIIGLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTEDKADVQSIIGLQR 16 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 260.24 8.10E-27 1658660000 2378200 1989980 2237800 2216800 2540900 1779630 3007500 2170500 3432000 FALSE TRUE 2229352.707 2137320.19 2290881.673 2273686.841 2341347.963 2293380.291 2556553.295 2441491.703 2859177.028 0.779718319 0.747529855 0.801238136 0.795224227 0.818888771 0.80211203 0.894157049 0.853914143 1 21.44716852 0.790195427 0.299563293 1.036133198 0.747072638 0.910761806 0.021309635 0.597054426 0.144244281 0.059309004 0.028447908 6.168725247 -0.790195427 -0.28906056 LTEDLEYHELLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LTEDLEYHELLDR 13 0 P22059;H0YCV6 P22059 OSBP Oxysterol-binding protein 1 0 ;;;;; 228.8 6.82E-12 2699830000 3201950 4151460 3905360 4049530 4117540 3325320 4678960 3539290 4120390 FALSE TRUE 3001545.665 4458838.418 3997996.983 4153447.796 3794165.018 4285285.902 3977393.385 3981178.147 3432670.29 0.874405466 1.298941652 1.164690065 1.209975746 1.105310064 1.248382612 1.158687858 1.159790429 1 21.71089986 -1.280184278 6.640868758 0.999997173 1.170445172 0.134714121 0.113683393 4.16E-06 4.51E-07 0.096164406 0.022665792 0.052458482 1.280184278 0.170447999 LTEEELLDREFDLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTEEELLDREFDLLR 15 1 H0Y9P1;Q9NSY1;Q9NSY1-2;Q9NSY1-3 H0Y9P1 BMP2K BMP-2-inducible protein kinase 0 ; 108.34 0.00099108 28038000 53317 68666 62973 61534 74338 46411 63085 64875 96003 FALSE TRUE 49979.98414 73750.10209 64466.7493 63113.06662 68499.79335 59809.10228 53625.9899 72974.78656 79979.4791 0.624910098 0.922112808 0.806041125 0.78911575 0.85646711 0.747805599 0.670496864 0.912418878 1 16.28734226 1.0166918 9.182694691 0.999989198 0.787862826 0.454651394 0.084982034 0.170142459 80.82997595 0.082317083 0.020597434 10.3918244 -1.0166918 -0.212126372 LTEEETVCLDLDKVEAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTEEETVCLDLDKVEAYR 18 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 246.49 2.47E-24 321520000 213345 171032 179029 192689 210233 148484 255031 165018 204890 FALSE TRUE 199992.1173 183695.3872 183275.6524 197633.726 193722.1482 191348.9204 216791.4691 185620.8605 170692.5354 1.17165122 1.076177039 1.073718028 1.157834615 1.134918688 1.121015163 1.270070004 1.087457399 1 17.38104044 3.229077806 24.89056239 1.150250191 1.095757573 0 0.073523311 404.5277197 1061805.132 0.020066537 0.024283435 1694.641375 -3.229077806 -0.054492618 LTEGCS(ph)FR ddPTM_SK-BR-3_Pertuzumab_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 118.03 0.0020606 790380000 1718750 1674690 1351320 1218460 1596380 992280 1810800 955850 2060720 TRUE FALSE 1611176.506 1798685.79 1383373.949 1249727.746 1471006.754 1278735.128 1539287.351 1075189.977 1716772.519 0.938491552 1.047713526 0.805799215 0.727951859 0.856844304 0.744848321 0.896616956 0.62628564 1 20.71126746 3.860806111 3.480566922 0.804420557 0.992674288 0.352795815 0.103718053 0.219698391 5.000527932 0.023863394 0.046837013 7257.818624 -3.860806111 0.188253732 LTEGCSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LTEGCSFR 8 0 P42677;C9J1C5;H0YMV8;Q71UM5 P42677;H0YMV8 RPS27;RPS27L 40S ribosomal protein S27;40S ribosomal protein S27-like 0 ;;; 190.54 0.00043248 4999700000 1996170 2502490 2201820 2419140 2636560 1970140 2405560 2222260 2559690 FALSE TRUE 1871233.283 2687776.963 2254048.21 2481219.228 2429495.213 2538887.435 2044868.61 2499714.053 2132461.203 0.877499333 1.260410722 1.057017219 1.163547184 1.139291636 1.190590212 0.95892418 1.172220179 1 21.02408806 1.747313679 25 1.042712074 1.127700065 0.072419952 0.113627183 4.382177694 12545.90086 0.04676654 0.025934264 55.88737086 -1.747313679 0.084987991 LTELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTELLR 6 0 Q9NSD9;Q9NSD9-2;Q9Y5X3;Q5QPE5;A0A087WUY5 Q9NSD9;Q9Y5X3 FARSB;SNX5 Phenylalanine--tRNA ligase beta subunit;Sorting nexin-5 0 105.27 0.077053 109290000 378180 398090 377510 401650 444910 317690 441480 355010 437320 FALSE TRUE 354510.3889 427564.9978 386464.7155 411957.019 409968.5633 409401.9457 375284.1725 399333.78 364328.4668 0.973051576 1.173570107 1.060759042 1.130729703 1.125271837 1.123716599 1.030070957 1.09608174 1 18.4748802 0.888836412 0.854925799 1.002971159 1.102214713 0.175289724 0.057630011 1.083540501 1.663572442 0.049728858 0.017421417 7.741701319 -0.888836412 0.099243554 LTEVQDDKEEEEEENPLLVPLEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTEVQDDKEEEEEENPLLVPLEEK 24 1 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 0 121.5 0.0001156 23161000 151130 65911 98506 87828 92437 72759 124440 75855 119420 FALSE TRUE 141671.0431 70791.11902 100842.6088 90081.81517 85177.37089 93763.34216 105781.3772 85325.66373 99488.03052 1.424000881 0.71155413 1.01361549 0.905453799 0.856156971 0.942458522 1.063257325 0.857647531 1 16.60223534 -0.082296855 7.485338305 0.999999996 0.953649575 0 0.187563204 21681545.72 2896534.075 0.159790616 0.038754917 0.82737643 0.082296855 -0.046350421 LTEYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LTEYSR 6 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;; 189.49 0.003225 2749890000 2598210 3086230 2794500 2766900 3225760 2311080 2960530 2787280 3339300 FALSE TRUE 2435592.674 3314737.68 2860786.86 2837903.338 2972421.822 2978251.279 2516626.011 3135278.044 2781949.257 0.875498598 1.191516226 1.028338979 1.020113264 1.068467304 1.070562761 0.904626856 1.127007632 1 21.40766467 LTFDTTFS(ph)PNTGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTFDTTFSPNTGKK 14 1 Q5JSD2;Q5JSD1;A0A0A0MR02;P45880-2;P45880;P45880-1 Q5JSD2 VDAC2 Voltage-dependent anion-selective channel protein 2 1 LTFDT(0.004)T(0.024)FS(0.967)PNT(0.004)GKK 73.498 0.021847 248780000 265680 173440 160940 169750 256610 144900 211100 227650 513280 TRUE FALSE 249051.5631 186281.6781 164757.5728 174106.0724 236456.8857 186730.2777 179447.5148 256072.6036 427610.2521 0.582426548 0.435634265 0.385298463 0.40716066 0.552972911 0.436683351 0.41965204 0.5988458 1 18.70593692 0.866035875 3.086040088 0.999792446 0.449493781 0.877647775 0.063271117 0.171862864 3.143782905 0.058956542 0.015406455 7.345745461 -0.866035875 -0.550298665 LTFNHDGSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTFNHDGSSR 10 0 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ; 92.866 0.0091754 889020000 770820 960840 866330 922810 979880 718450 978400 731910 1078680 FALSE TRUE 722575.7522 1031981.593 886879.7567 946490.8669 902924.1774 925854.8519 831698.003 823290.5746 898641.3395 0.804075798 1.148379835 0.986911817 1.053246524 1.004765904 1.030282952 0.925506057 0.916150347 1 19.7773859 1.744470316 8.526898933 0.941583414 1.021046912 0.06461185 0.088307423 0.206395081 56.88960709 0.038451489 0.020662446 55.52266667 -1.744470316 0.079463498 LTFSCLGGSDNFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTFSCLGGSDNFK 13 0 A0A087WYT3;Q15185-4;Q15185;Q15185-3;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ; 199.68 2.70E-07 228230000 226164 224521 207292 222772 231810 177444 247140 194726 221595 FALSE TRUE 212008.799 241144.7685 212209.0641 228488.7067 213604.5777 228669.2022 210083.6513 219037.9697 184609.3629 1.148418453 1.306243435 1.149503258 1.237687531 1.157062536 1.238665247 1.13799023 1.18649437 1 17.4941162 -5 0.186248147 0.137273282 1.239002708 0.590774849 0.051792355 83.12009479 0.809183437 26.43899907 0.130729394 1.00E-05 5 1.101729427 LTGGAAGHQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTGGAAGHQDR 11 0 O95274 O95274 LYPD3 Ly6/PLAUR domain-containing protein 3 0 75.479 0.037977 85504000 103550 119090 81441 83522 131040 67047 102590 122210 108670 FALSE TRUE 97068.99034 127907.5475 83372.81898 85665.31592 120748.647 86402.38048 87207.5819 137468.1875 90532.27496 1.072203149 1.412839206 0.920918192 0.946240619 1.333763534 0.954382076 0.963276157 1.518443976 1 16.46614459 3.976394699 24.99938804 1.075665646 1.254355636 0.078842399 0.20942454 68.71625657 2364549.799 0.048895356 0.095364551 9470.975186 -3.976394699 0.17868999 LTGIKHELQANCYEEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTGIKHELQANCYEEVK 17 1 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 113.53 0.00024493 599790000 1036800 701940 839680 855190 971900 695010 1232100 790910 1217300 FALSE TRUE 971908.5387 753912.368 859597.6061 877135.6232 895570.8945 895648.1045 1047358.043 889656.8545 1014124.766 0.958371762 0.74341185 0.8476251 0.864918847 0.883097351 0.883173486 1.032770403 0.877265682 1 19.95180372 2.2633972 1.225919603 0.973978757 0.830119645 0.321905297 0.067573683 0.418357093 1.222654362 0.040114155 0.023462976 183.3991 -2.2633972 -0.143859112 LTGIKHELQANCYEEVKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTGIKHELQANCYEEVKDR 19 2 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 219.87 1.82E-19 6992200000 8571800 7702200 7864300 8408700 10880900 5737600 10989700 6793700 18820400 FALSE TRUE 8035306.339 8272478.902 8050844.91 8624481.478 10026358.01 7393951.978 9341896.508 7641908.4 15679153.66 0.512483423 0.527610041 0.513474457 0.550060397 0.639470613 0.471578514 0.595816376 0.487392915 1 23.90234435 -1.906116597 2.543467182 1.266010766 0.538982038 0.895807874 0.04959574 6415177.815 3514332.786 10196381.82 0.010775614 0.01241319 1.906116597 -0.727028729 LTGMAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 138.85 0.0063879 4748800000 1756639 7716750 1742433 1681693 6986380 1226743 1355086 5843510 3934030 FALSE TRUE 1646694.101 8288106.199 1783764.334 1724848.089 6437697.897 1580883.79 1151903.434 6573085.087 3277414.978 0.502436863 2.528854678 0.544259529 0.526283092 1.96426084 0.482356919 0.351467068 2.005569978 1 21.64412692 3.839624608 7.001049748 0.913542124 1.638714303 0.068080311 0.758453937 0.412648448 23.14525189 0.180291026 0.327232492 6912.332299 -3.839624608 0.725172179 LTGS(ph)QLSITQVASIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTGSQLSITQVASIK 15 0 Q9UJF2;Q9UJF2-2;H0Y638 Q9UJF2 RASAL2 Ras GTPase-activating protein nGAP 1 LT(0.004)GS(0.996)QLSITQVASIK;LT(0.003)GS(0.996)QLSITQVASIK 151.03 1.49E-08 0 138402 131502 143017 133219 168806 110619 177466 142755 207891 TRUE FALSE 129739.6659 141238.5449 146409.4308 136637.6251 155548.6577 142552.9096 150856.6208 160578.276 173192.6491 0.749106077 0.815499651 0.845355918 0.788934321 0.898125056 0.823088684 0.871033624 0.927165655 1 17.40201817 -5 0.067054655 1.623699046 0.606590664 0.79749723 0.032359632 141.665979 0.687324674 13.63140422 1.854017464 1.00E-05 5 -1.017108382 LTGS(ph)T(ph)SSLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 2 LTGS(0.995)T(0.886)S(0.096)S(0.022)LNK;LTGS(0.998)T(0.766)S(0.136)S(0.099)LNK;LTGS(0.994)T(0.638)S(0.186)S(0.182)LNK 170.4 2.30E-05 1386940000 8418500 6661900 7035900 7287500 8469700 5402400 10404800 7629700 9391600 TRUE FALSE 7891601.112 7155154.008 7202794.871 7474509.588 7804523.927 6961985.179 8844696.833 8582284.84 7824081.288 1.008629745 0.914504048 0.920593052 0.955321055 0.997500363 0.889815037 1.130445417 1.0969064 1 22.89948993 1.733590178 10.81039261 1.083630432 0.942990114 0.60727073 0.04827764 0.050021927 27.10541076 0.02097303 0.011414906 54.14896728 -1.733590178 -0.140640318 LTGS(ph)TS(ph)SLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 2 LTGS(0.991)T(0.13)S(0.83)S(0.048)LNK;LTGS(0.997)T(0.18)S(0.77)S(0.054)LNK 179.98 2.99E-06 898460000 4315300 3565500 3725300 3773700 4235800 2894300 5333700 3909000 4611200 TRUE FALSE 4045213.076 3829493.33 3813665.875 3870539.531 3903137.354 3729837.425 4533961.201 4397047.255 3841560.931 1.053012864 0.996858673 0.992738614 1.007543444 1.016029011 0.970917159 1.180239304 1.144599119 1 21.87326121 1.745705512 25 1.123040562 1.003986971 0.470342586 0.050230139 1.01908348 3576.233886 0.020484325 0.011359584 55.68080591 -1.745705512 -0.119053591 LTGS(ph)TSS(ph)LNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 2 LTGS(0.954)T(0.11)S(0.065)S(0.871)LNK 174.89 4.34E-06 417010000 1676700 1267200 1322600 1378800 1541000 966550 1925100 1387900 1699200 TRUE FALSE 1571758.34 1361024.807 1353972.697 1414182.342 1419976.076 1245577.294 1636449.127 1561182.37 1415592.543 1.110318324 0.961452371 0.956470634 0.999003809 1.003096607 0.879898175 1.156017058 1.102847269 1 20.43297464 1.71269879 12.66652566 1.096178267 0.980275859 0.324863846 0.068047701 0.112347736 43.04964256 0.02896791 0.015886089 51.60583273 -1.71269879 -0.115902408 LTGS(ph)TSSLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 1 LTGS(0.926)T(0.068)S(0.005)SLNK;LTGS(0.49)T(0.49)S(0.019)SLNK;LTGS(0.938)T(0.06)S(0.002)SLNK;LTGS(0.962)T(0.033)S(0.005)SLNK 250.26 3.54E-13 2127740000 3076530 2594510 3076920 2815960 3022710 2447380 3218870 2739740 3449150 TRUE FALSE 2883975.479 2786610.22 3149905.995 2888222.301 2785318.55 3153898.876 2736230.326 3081802.57 2873464.583 1.003657918 0.969773644 1.096204914 1.005135862 0.969324128 1.097594484 0.952240839 1.072504108 1 21.45435984 4.218151683 24.79346345 1.025854654 0.98671578 0.102486763 0.050064882 650.3612722 1797723.314 0.011481774 0.025418026 16525.38869 -4.218151683 -0.039138874 LTGSTSS(ph)LNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 1 LTGSTS(0.05)S(0.95)LNK;LTGST(0.369)S(0.188)S(0.443)LNK;LTGSTS(0.068)S(0.932)LNK;LTGST(0.01)S(0.041)S(0.949)LNK 199.82 2.85E-07 1022800000 3825010 2913510 3195290 3079570 3602610 2404930 3857030 2909000 4175010 TRUE FALSE 3585609.452 3129229.312 3271083.788 3158596.98 3319675.543 3099194.25 3278704.158 3272195.053 3478173.859 1.030888506 0.899675933 0.940460115 0.908119349 0.954430594 0.891040637 0.942651026 0.940779612 1 21.72989862 0.644809925 2.079682932 0.999969895 0.932423659 0.186633451 0.039034393 2.805619245 14.62029378 0.032575233 0.008926745 4.413772306 -0.644809925 -0.067546236 LTGVFAPRPSTGPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTGVFAPRPSTGPHK 15 1 P62701;C9JEH7;P22090;Q8TD47 P62701 RPS4X;RPS4Y1;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1;40S ribosomal protein S4, Y isoform 2" 0 149.22 2.04E-06 973150000 276080 957400 286980 284810 1083300 219880 520700 776890 1366800 FALSE TRUE 258800.6456 1028286.892 293787.3011 292118.7068 998221.9878 283355.7865 442625.8689 873886.4266 1138672.25 0.227282825 0.903057831 0.25800866 0.256543274 0.876654356 0.248847538 0.388721047 0.767460897 1 20.11892112 1.034715525 4.156234739 0.9971431 0.471765536 0.359034489 0.249390301 0.197530713 7.835769027 0.224911551 0.057506635 10.83217144 -1.034715525 -0.525377563 LTHDVELNLDYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTHDVELNLDYER 13 0 P02786;G3V0E5;H7C3V5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ; 203.87 8.24E-08 544600000 321430 453980 354970 345950 492820 306690 374070 441080 488530 FALSE TRUE 301312.2701 487593.1516 363390.056 354827.6627 454115.9051 395226.4243 317981.6762 496149.8089 406991.187 0.740341019 1.198043513 0.892869594 0.871831317 1.115788056 0.971093323 0.781298678 1.219067697 1 18.63463803 1.995834382 24.76827141 0.950915491 0.987003009 0 0.165722726 1189.362415 7071826.071 0.059350252 0.042790723 99.04541633 -1.995834382 0.036087518 LTHVNTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LTHVNTGR 8 0 Q99470;K7ELI9 Q99470 SDF2 Stromal cell-derived factor 2 0 ;;; 111.06 0.003306 416025000 410304 536557 450732 450733 613211 376043 517212 512635 602880 FALSE TRUE 384623.8051 576284.2386 461423.5759 462299.5719 565051.8816 484600.5096 439660.8622 576638.6082 502255.4332 0.765793219 1.147392742 0.918703005 0.92044713 1.125028908 0.964848715 0.875373033 1.148098298 1 18.93806174 4.764660112 24.28303036 1.000933869 0.765792762 0.373847634 0.099339888 6977.192901 6491438.868 0.022801292 1.774638444 58164.78296 -4.764660112 -0.235141107 LTIAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LTIAEER 7 0 P62701;Q8TD47 P62701 RPS4X;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 2" 0 ;;;;;;; 188.89 0.0013099 4585720000 6135130 6960880 6838930 6589590 7021940 5910660 7347950 5991160 7029710 FALSE TRUE 5751143.165 7476270.798 7001152.649 6758690.036 6470465.158 7616971.59 6246193.113 6739169.514 5856405.987 0.982026037 1.276597083 1.195469143 1.154067879 1.104852562 1.300622192 1.066557395 1.150734688 1 22.48158414 0.768504218 0.900101085 1.001291028 1.178962233 0.192806804 0.094200186 1.216411832 1.88493512 0.08239938 0.027809897 5.86819069 -0.768504218 0.177671205 LTIFDEEVDPDEGLFGPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTIFDEEVDPDEGLFGPGR 19 0 Q53T59;H7BZZ1;H7C0Y9;F8WDN8 Q53T59 HS1BP3 HCLS1-binding protein 3 0 ; 135.58 1.20E-06 14948000 28238 34647 34223 32355 35111 27452 31538 30226 30954 FALSE TRUE 26470.63399 37212.29993 35034.78572 33185.28408 32353.52369 35376.94675 26809.16968 33999.78264 25787.57743 1.026487814 1.443032019 1.358591586 1.286870943 1.254616638 1.37186003 1.039615674 1.318455862 1 14.65438863 1.076951004 0.57788623 1.00954924 1.324090109 0.224628939 0.138971612 0.978120608 0.810286465 0.134639937 0.061682525 11.9385341 -1.076951004 0.314540868 LTIFGNSAVSQPASSSNHS(ph)SR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTIFGNSAVSQPASSSNHSSR 21 0 P46934-4;H0Y8X6;P46934-3;P46934-2;P46934 P46934-4 NEDD4 E3 ubiquitin-protein ligase NEDD4 1 LTIFGNSAVSQPAS(0.002)S(0.031)S(0.138)NHS(0.415)S(0.415)R;LTIFGNSAVSQPAS(0.004)S(0.037)S(0.089)NHS(0.435)S(0.435)R 139.67 1.11E-07 253986000 107736 197217 169536 161820 202120 171269 242305 215764 269561 TRUE FALSE 100992.9961 211819.1519 173557.474 165972.5752 186246.3105 220711.58 205973.6147 242702.6104 224569.5277 0.449718166 0.943223037 0.772845166 0.739069886 0.829348097 0.982820698 0.917193071 1.080745963 1 17.77680265 2.328778213 2.8695054 0.984275629 0.770016333 0.480426314 0.12827709 0.272183169 4.561991964 0.0477593 0.037109721 213.1955881 -2.328778213 -0.214259296 LTIQMMSPLQIERSLS(ph)VHS(ph)GT(ph)T(ph)GSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTIQMMSPLQIERSLSVHSGTTGSLK 26 1 Q8WUJ0 Q8WUJ0 STYX Serine/threonine/tyrosine-interacting protein 4 LT(0.105)IQMMS(0.117)PLQIERS(0.731)LS(0.755)VHS(0.755)GT(0.753)T(0.741)GS(0.044)LK 45.836 0.079427 69864000 16144 53863 41357 45122 47690 39657 50749 44434 40245 TRUE FALSE 15133.57586 57851.07256 42338.00757 46279.90691 43944.61977 51105.33212 43139.65858 49981.68271 33527.84951 0.451373294 1.725463262 1.262771344 1.380342241 1.310690081 1.524265137 1.286681347 1.490751225 1 15.03307233 4.75136817 24.97506236 1.393419639 0.451372692 0.69657574 0.190643148 1069.263642 2085054.441 0.040555021 0.74742539 56411.56787 -4.75136817 -0.942046947 LTISPDYAYGATGHPGIIPPHATLVFDVELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTISPDYAYGATGHPGIIPPHATLVFDVELLK 32 0 P62942;Q5W0X3;Q1JUQ5;Q5VVH2 P62942 FKBP1A;FKBP12-Exip2;FKBP1C Peptidyl-prolyl cis-trans isomerase FKBP1A;Peptidyl-prolyl cis-trans isomerase 0 166.2 2.83E-14 146330000 260960 285130 203010 154110 277690 173240 260510 347630 144170 FALSE TRUE 244626.9794 306241.3219 207825.4931 158064.7235 255881.3475 223251.5757 221448.944 391032.3707 120107.0956 2.036740445 2.54973547 1.730334848 1.316031519 2.13044322 1.858770912 1.843762376 3.255697498 1 16.87396186 -0.171169866 9.769741788 1.000000009 2.051355469 0.300663585 0.519532918 0 0 0.470111211 0.110806275 0.67426425 0.171169866 1.05135546 LTKEEIVDKYDLFVGSQATDFGEALVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTKEEIVDKYDLFVGSQATDFGEALVR 27 2 O43852;O43852-3;O43852-15;O43852-6;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 91.655 0.0035163 43370000 29034 30190 26435 30224 34267 17122 33102 25772 45595 FALSE TRUE 27216.81377 32425.29901 27062.05068 30999.59901 31575.80805 22064.84345 28138.6624 28989.69093 37984.89995 0.716516663 0.853636552 0.712442332 0.816103216 0.83127264 0.580884601 0.740785482 0.763189872 1 15.2131384 0.90803607 14.65257666 1 0.752559143 0.508691828 0.076717007 238.725891 38038.02945 0.071997472 0.018000086 8.091631011 -0.90803607 -0.247440857 LTLDDIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTLDDIER 8 0 Q5HY81;P11441 Q5HY81 UBL4A Ubiquitin-like protein 4A 0 ; 93.267 0.026033 70430000 178319 207846 199654 204523 213226 167619 213285 201088 226805 FALSE TRUE 167158.3321 223235.1341 204389.8872 209771.4064 196480.0901 216007.8842 181304.8943 226194.2794 188949.7803 0.884670688 1.181452203 1.0817154 1.110196615 1.039853499 1.143202622 0.959540117 1.197113218 1 17.52764332 -0.789411552 6.048249977 0.999999996 1.079067784 0.054713694 0.09610263 4.29E-09 9.12E-10 0.082218589 0.019379106 0.162400906 0.789411552 0.079067788 LTLDKLDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTLDKLDVK 9 1 P00558 P00558 PGK1 Phosphoglycerate kinase 1 0 113.47 0.0020798 0 8302100 8874700 5468100 6184000 10413000 3094800 9185700 7799400 12458000 FALSE TRUE 7782486.381 9531792.022 5597805.914 6342691.909 9595204.984 3988218.52 7808389.561 8773172.259 10378679.32 0.749853246 0.918401246 0.539356284 0.611127073 0.924511172 0.384270329 0.752349053 0.845307191 1 23.30711954 1.044942606 2.74886095 0.995152229 0.694716711 0.280507854 0.161868375 0.31453587 5.118462204 0.145443981 0.038987654 11.09028244 -1.044942606 -0.300435519 LTLEDLEDSWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LTLEDLEDSWDR 12 0 Q6P2Q9;I3L3Z8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;;;; 246.59 3.44E-16 416842000 631806 757823 715259 747151 813389 638438 775392 662153 619661 FALSE TRUE 592262.3903 813933.0034 732225.2812 766324.1596 749508.709 822744.6864 659129.168 744824.2596 516235.5759 1.147271552 1.576669725 1.418393686 1.484446627 1.451873416 1.593738837 1.276799195 1.442799168 1 18.97767004 0.167761757 0.814564263 0.99308811 1.449961187 0.49525154 0.132910392 2.760642019 2.092992076 0.168025291 0.039434463 1.471505049 -0.167761757 0.456873076 LTLEGLEEDDDDRVS(ph)PTVLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTLEGLEEDDDDRVSPTVLHK 21 1 Q9NPB8 Q9NPB8 GPCPD1 Glycerophosphocholine phosphodiesterase GPCPD1 1 LTLEGLEEDDDDRVS(0.882)PT(0.118)VLHK 219.51 3.04E-25 134020000 70786 62484 58203 72393 53222 43283 86540 52198 39629 TRUE FALSE 66355.63062 67110.38037 59583.60265 74250.72694 49042.15881 55778.09946 73564.1304 58715.0352 33014.66389 2.009883573 2.032744619 1.804761752 2.249022652 1.485465943 1.689494694 2.228225938 1.778453217 1 15.01081934 0.969684766 23.41734325 0.999999992 1.930266638 0.612051178 0.230650288 1083.065607 836627.6314 0.209381255 0.052345314 9.325771409 -0.969684766 0.930266646 LTLHVGDGFEFMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTLHVGDGFEFMK 13 0 P19623;K7EQ47 P19623 SRM Spermidine synthase 0 145.71 4.19E-05 151790000 275350 286800 287130 287810 299360 246490 322370 241330 250220 FALSE TRUE 258116.335 308034.9704 293940.8592 295195.6919 275849.4732 317647.6616 274033.6112 271460.5817 208456.6655 1.238225385 1.477693072 1.410081364 1.416100997 1.323294088 1.52380669 1.314583108 1.302239873 1 17.66938798 0.732512152 1.297620995 1.000847006 1.405429168 0.69142137 0.081015725 0.44778075 1.275829079 0.068347433 0.020559824 5.401472284 -0.732512152 0.404582163 LTLNS(ph)PIFDKPLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTLNSPIFDKPLSR 14 1 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;E5RIY8;E5RIU4;H0YBX5 E5RJM2 CDK16 Cyclin-dependent kinase 16 1 LT(0.001)LNS(0.999)PIFDKPLSR;LTLNS(1)PIFDKPLSR 197.1 1.45E-08 1819920000 2357000 2416300 2417600 2406600 2639300 1963400 3302300 2213260 2443000 TRUE FALSE 2209479.577 2595205.366 2474946.614 2468357.43 2432020.024 2530201.707 2807150.772 2489590.383 2035247.518 1.085607307 1.275130098 1.216042075 1.21280454 1.194950493 1.243191152 1.379267508 1.223237155 1 20.95677283 2.018333431 14.97923999 1.260036142 1.211583085 0 0.107183756 8.486685206 6928.853766 0.03658055 0.026947225 104.3117979 -2.018333431 -0.048453057 LTLSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTLSLR 6 0 P20594-2;P20594 P20594-2 NPR2 Atrial natriuretic peptide receptor 2 0 106.76 0.074087 172960000 269610 381600 351690 387080 473540 271150 430560 356930 665280 FALSE TRUE 252735.5914 409854.0611 360032.2529 397013.1281 436350.0786 349426.6032 366001.5251 401493.4962 554240.4701 0.456003495 0.739487791 0.649595748 0.716319268 0.787293787 0.630460282 0.660365933 0.724403067 1 19.08015253 -5 0.260169744 3.086163681 0.649891 0.608454035 0.085509344 134.2972026 1.31973285 149.7928324 0.105619048 1.00E-05 5 -2.436272681 LTLYDIAHT(ph)PGVAADLSHIETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTLYDIAHTPGVAADLSHIETK 22 0 P40926;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial" 1 LTLYDIAHT(1)PGVAADLSHIETK 75.326 0.022613 10043000 24545 22278 21328 21042 31549 19497 21303 22491 42216 TRUE FALSE 23008.77226 23927.4863 21833.91023 21581.97334 29071.2688 25125.46739 18108.81292 25299.05086 35169.87687 0.654218164 0.680340349 0.620812814 0.613649386 0.826595695 0.714403052 0.514895545 0.719338625 1 15.10205266 0.972978471 23.87088256 1.000000004 0.655783281 0.642579581 0.078927682 1025.368719 905814.5489 0.076148232 0.019037058 9.396767276 -0.972978471 -0.344216723 LTLYDIAHTPGVAADLSHIETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTLYDIAHTPGVAADLSHIETK 22 0 P40926;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial" 0 ; 312.74 1.75E-67 332460000 776420 613950 653430 573460 818490 588020 676430 676390 1162910 FALSE TRUE 727825.2581 659407.4968 668929.6682 588175.9545 754209.097 757771.8283 575005.6012 760838.7804 968812.8083 0.751254785 0.680634578 0.690463279 0.607110011 0.77848795 0.78216537 0.593515689 0.78533105 1 19.88585841 0.983866016 22.97034995 1.000000003 0.693886883 0.694961161 0.063274933 174.6388544 248638.7048 0.057233644 0.014308411 9.635317193 -0.983866016 -0.306113119 LTMHYPCLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTMHYPCLEK 10 0 P78412 P78412 IRX6 Iroquois-class homeodomain protein IRX-6 0 65.347 0.08236 0 58938 220870 154170 181560 215590 307250 130100 184620 131810 FALSE TRUE 55249.17579 237223.4446 157826.9852 186219.137 198658.431 395948.0872 110592.7128 207670.2134 109810.0595 0.503134012 2.160307041 1.437272559 1.695829488 1.809109584 3.605754237 1.007127337 1.891176586 1 16.7446507 4.746869438 24.57392656 1.849516209 0.503133154 0.243815714 0.730995719 1172.327811 3467142.231 0.159608682 1.80801441 55830.23271 -4.746869438 -1.346383055 LTNEDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTNEDFR 7 0 Q13123;E7EQZ7;D6REL4;D6RAY9;D6RCQ4 Q13123 IK Protein Red 0 89.296 0.041823 134450000 413480 495680 455440 466390 535190 438430 523990 455440 509730 FALSE TRUE 387601.0249 532380.663 466243.2519 478358.357 493158.3363 564997.6237 445422.564 512302.6865 424652.77 0.912748137 1.253684658 1.097939975 1.126469414 1.161321369 1.330493202 1.048910064 1.206403732 1 18.69592414 -1.033056516 4.329442383 0.999990279 1.149294203 0.131340839 0.11368858 9.35E-06 2.09E-06 0.096467981 0.022736241 0.092670922 1.033056516 0.149303924 LTPAEEENNSFQRLS(ph)P ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTPAEEENNSFQRLSP 16 1 Q5HYI7-5;Q5HYI7 Q5HYI7-5 MTX3 Metaxin-3 1 LTPAEEENNS(0.008)FQRLS(0.992)P;LTPAEEENNS(0.005)FQRLS(0.995)P 101.67 0.0043052 79057000 171878 204429 183987 196465 225350 130156 166016 154565 229830 TRUE FALSE 161120.4628 219565.1359 188351.2585 201506.6245 207651.92 167729.9243 141123.442 173862.7805 191469.8882 0.841492437 1.146734549 0.983712166 1.052419398 1.084514761 0.876012024 0.737052929 0.908042419 1 17.546758 2.150895587 5.80883075 0.842277675 1.034663973 0.287192864 0.103237523 0.17991067 9.432993995 0.035777754 0.026326877 141.5453437 -2.150895587 0.192386297 LTPEEEEILNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LTPEEEEILNK 11 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;; 148.56 8.09E-05 240851000 336217 259561 301549 298049 298529 229148 364916 239923 383848 FALSE TRUE 315173.7781 278779.1665 308701.8847 305697.4419 275083.7365 295299.3077 310200.2335 269877.9147 319781.289 0.985591681 0.871780733 0.965353181 0.955957876 0.860224616 0.923441483 0.970038724 0.843945296 1 18.286726 -2.104699785 4.827003145 1.243079377 0.924079001 0.197250644 0.04927275 0.059665752 0.001294176 0.022084307 0.010123868 0.007857786 2.104699785 -0.319000376 LTPEELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LTPEELER 8 0 Q5H8X8;O95399;O95399-2 Q5H8X8 UTS2 Urotensin-2 0 ;;; 183.04 0.00052435 2115350000 2179040 2380720 2127170 2202380 2127130 1684940 2444100 1903800 2190740 FALSE TRUE 2042657.776 2556990.986 2177627.477 2258896.799 1960073.79 2171354.825 2077629.895 2141493.621 1825091.341 1.119208518 1.40102083 1.193160818 1.237689725 1.073959284 1.18972392 1.138370364 1.173362435 1 20.79953724 1.499336262 0.197239233 0.941098167 1.346436023 0.377589948 0.083406261 2.501142178 0.518058695 0.420820954 0.405729812 31.57448402 -1.499336262 0.405337855 LTPGCEAEAETEAICFFVQQFTDMEHNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 327.05 8.72E-96 13505520000 991106 1031833 1069754 1071897 1213869 1171429 1491273 1086328 1031951 FALSE TRUE 929074.4446 1108230.989 1095129.07 1099403.692 1118536.625 1509601.536 1267670.458 1221958.442 859711.7114 1.080681387 1.289072807 1.273832909 1.278805066 1.301060123 1.755939248 1.474529707 1.421358376 1 19.71349343 2.455353906 24.99814257 1.473548499 1.251787865 0.129583998 0.193964772 317.9847299 365179.1438 0.059890011 0.050111001 285.3342503 -2.455353906 -0.221760634 LTPHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LTPHEK 6 0 O00148;O00148-2;O00148-3;K7EQN7 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ;;;; 124.89 0.018161 927030000 3446890 3166590 3411370 3343290 3654750 2652760 3939510 3211650 4354120 FALSE TRUE 3231155.308 3401047.618 3492289.307 3429084.482 3367720.678 3418568.748 3348817.048 3612631.572 3627389.243 0.890766083 0.937602058 0.9627556 0.94533127 0.928414474 0.942432289 0.923203115 0.9959316 1 21.79050013 -4.999999997 0.129456366 1.206918294 0.914477185 0.499696367 0.023144494 144.4106764 1.182103267 7.68339092 0.178573504 1.00E-05 4.999999997 -0.292441109 LTPIHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 LTPIHDR 7 0 P28072;A0A087X2I4;I3L3X7 P28072 PSMB6 Proteasome subunit beta type-6;Proteasome subunit beta type 0 ;;;;;;;; 157.58 0.0014664 4572970000 6621769 7618941 6968484 6223430 7457107 5655036 7519499 6837739 6635427 FALSE TRUE 6207324.298 8183055.319 7133779.731 6383133.75 6871455.897 7287553.091 6392019.933 7691445.766 5527931.367 1.122901839 1.480310586 1.29049716 1.15470568 1.243042911 1.318314684 1.156313186 1.391378665 1 22.39830827 -4.428214634 0.209958929 6.34E-14 1.321737633 0.31022385 0.115793993 124.0740371 1.538955061 52.67999604 0.239259214 3.73E-05 4.428214634 1.321737633 LTPLEACAHSFFDELRDPNVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTPLEACAHSFFDELRDPNVK 21 1 A0A3B3ITW1;P49841;P49841-2 A0A3B3ITW1 GSK3B Glycogen synthase kinase-3 beta 0 128.05 1.13E-05 45937000 83652 73290 88788 78476 91458 69186 90193 69422 87390 FALSE TRUE 78416.37064 78716.46786 90894.09329 80489.82702 84275.2576 89158.87506 76669.39696 78089.48952 72804.04444 1.07708811 1.081210096 1.248475878 1.105568072 1.157562856 1.224641787 1.053092552 1.072598234 1 16.15173098 1.613416068 7.777086575 1.045008346 1.151247264 0.432267935 0.05790204 0.112161497 15.65343361 0.029798877 0.014685479 41.059728 -1.613416068 0.106238917 LTPLSHEVISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 244.06 7.44E-16 1600870000 1453490 1812430 1650350 1675960 1856540 1479360 1830810 1544310 1756120 FALSE TRUE 1362518.655 1946624.203 1689497.081 1718967.971 1710734.837 1906427.217 1556297.037 1737120.503 1463012.227 0.931310505 1.33055908 1.154807219 1.174951199 1.169323677 1.303083584 1.063762153 1.187358841 1 20.4805104 0.487188578 0.824305681 0.999690826 1.186324616 0.151763485 0.113248205 2.664534429 2.76393575 0.104700727 0.033941508 3.0703549 -0.487188578 0.18663379 LTPPES(ph)QSPLHWLADLAEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTPPESQSPLHWLADLAEQK 20 0 A0A1W2PNZ9;Q15652-3;Q15652;H7BXU7 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 LT(0.007)PPES(0.497)QS(0.497)PLHWLADLAEQK 120 1.48E-05 0 94050 79290 88017 85462 100050 91334 104900 79558 77366 TRUE FALSE 88163.57838 85160.7141 90104.8048 87655.09961 92192.47658 117700.6431 89171.21884 89490.99143 64453.1148 1.367871493 1.321281592 1.39798992 1.359982367 1.430380469 1.8261436 1.38350519 1.388466511 1 15.97596246 0.690724843 2.669645619 1.000099069 1.436867183 0.486371369 0.141339427 2.100884373 16.98557807 0.13708807 0.036319349 4.905969493 -0.690724843 0.436768115 LTPPESQS(ph)PLHWLADLAEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTPPESQSPLHWLADLAEQK 20 0 A0A1W2PNZ9;Q15652-3;Q15652;H7BXU7 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 LTPPES(0.232)QS(0.768)PLHWLADLAEQK 213.05 7.23E-23 56832000 96437 73065 93139 83686 96081 81234 95435 78939 69205 TRUE FALSE 90401.18031 78474.80862 95348.30106 85833.52444 88535.18583 104684.9371 81125.40773 88794.70792 57654.23842 1.567988457 1.36112818 1.653795171 1.488763477 1.535623195 1.815737055 1.407102235 1.540124549 1 15.81513905 0.18683858 1.327276436 0.999426731 1.544425063 0.652153839 0.125423215 4.629510282 6.892779622 0.117789689 0.033341922 1.537583041 -0.18683858 0.544998332 LTPPS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTPPSPVR 8 0 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 1 LT(0.012)PPS(0.988)PVR 90.696 0.013651 170660000 247850 262140 253140 252060 276500 216230 296720 247080 181930 TRUE FALSE 232337.5109 281549.1184 259144.6003 258528.2863 254784.8053 278652.0908 252229.5906 277928.4819 151564.7077 1.532926197 1.857616609 1.709795138 1.705728796 1.6810299 1.838502479 1.664170996 1.833728222 1 17.20957433 -1.083981991 4.058241512 0.999864724 1.735490838 0.84577143 0.097643161 12549036.31 23088321.06 23248.15917 0.020561277 0.082417229 1.083981991 0.735626114 LTPPVLEEMGHCDSVYLSEVGDTQVVVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LTPPVLEEMGHCDSVYLSEVGDTQVVVFK 29 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;; 138.92 7.34E-07 54363000 39687 42558 43361 39004.4 44849.5 37612 47610 39409 37776 FALSE TRUE 37203.06151 45709.0386 44389.5434 40005.31894 41327.20118 48469.97382 40471.32249 44329.3004 31470.94156 1.182140085 1.452420434 1.41049302 1.271182779 1.313186042 1.540150101 1.285990202 1.408578778 1 14.94173272 -1.286836395 3.400017679 0.998614612 1.36918706 0.545588103 0.102232463 608370773.8 799624051.1 8434998.828 0.022494384 0.051661095 1.286836395 0.370572449 LTPS(ph)PDIIVLS(ph)DNEASSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 LTPS(1)PDIIVLS(1)DNEASSPR 244.89 2.23E-24 37552000 60595 66540 67709 66867 72969 55934 67849 57813 74056 TRUE FALSE 56802.46712 71466.69083 69315.08945 68582.92043 67238.30908 72081.23779 57675.67233 65031.08031 61695.57518 0.920689481 1.158376279 1.123501795 1.111634347 1.089840056 1.168337236 0.934842931 1.054063928 1 15.9128794 1.738075616 25 0.995303757 1.106317256 0.279642865 0.073590232 0.086646133 3742.165774 0.031000158 0.017191157 54.71112128 -1.738075616 0.111013499 LTPS(ph)PDIIVLSDNEASSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LT(0.002)PS(0.998)PDIIVLSDNEASSPR;LTPS(1)PDIIVLSDNEASSPR;LTPS(1)PDIIVLSDNEASSPR;LTPS(1)PDIIVLSDNEASSPR 332.61 2.66E-75 481542000 78627 112073 102056 99637 82473 82403.6 91914 78644 97132 TRUE FALSE 73705.87642 120371.0015 104476.8165 102193.8541 75995.90326 106192.1816 78132.34899 88462.87652 80920.0417 0.910848226 1.487530147 1.291111748 1.262899177 0.939148098 1.312310021 0.965550034 1.093213432 1 16.30420944 2.876008144 6.814988498 1.073396897 1.291676295 0.17231559 0.175124133 0.320577822 16.49591382 0.049471713 0.052608119 751.6369888 -2.876008144 0.218279398 LTPSPDIIVLS(ph)DNEAS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 LTPSPDIIVLS(0.999)DNEAS(0.535)S(0.466)PR 70.335 0.031644 103860000 33313 33954 32398 31549 36580 37628 37705 32501 40671 TRUE FALSE 31227.9988 36467.98949 33166.49586 32358.60075 33707.15436 48490.59276 32051.48529 36558.82139 33882.74736 0.921648958 1.076299661 0.978860879 0.95501703 0.994817628 1.431129308 0.945952964 1.078980432 1 15.04826324 LTPSPDIIVLS(ph)DNEASS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 LTPSPDIIVLS(1)DNEAS(0.434)S(0.566)PR;LTPSPDIIVLS(1)DNEAS(0.19)S(0.81)PR 129.2 2.92E-05 58573000 106591 113592 113102 106694 119499 117002 125515 104326 126489 TRUE FALSE 99919.65958 122002.4699 115784.8329 109431.9487 110114.0306 150778.578 106695.191 117351.3307 105377.1687 0.948209757 1.15776948 1.098765835 1.038478733 1.0449515 1.430846737 1.012507664 1.113631464 1 16.6852028 4.746912321 23.61844465 1.119519418 0.948209566 0.146371562 0.12325111 890.8539492 2519187.473 0.026900183 0.293787444 55835.74581 -4.746912321 -0.171309852 LTPSPDIIVLS(ph)DNEASSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LTPSPDIIVLS(1)DNEASSPR;LTPSPDIIVLS(1)DNEASSPR;LTPSPDIIVLS(1)DNEASSPR;LTPSPDIIVLS(1)DNEASSPR 295.17 1.21E-49 552888000 521609 587564 561881 599203 553359 451613 546716 440676 495813 TRUE FALSE 488962.4238 631067.8499 575209.0827 614579.5634 509900.4163 581986.3418 464741.0113 495695.3686 413058.6072 1.183760404 1.527792519 1.392560457 1.487874971 1.234450529 1.408967957 1.125121237 1.200060621 1 18.65598697 1.521541189 0.795932056 1.015354877 1.41648336 0.543846839 0.113428007 0.366552152 0.479700965 0.093612066 0.03916283 33.23083002 -1.521541189 0.401128483 LTPSPDIIVLSDNEAS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LTPSPDIIVLSDNEAS(0.719)S(0.281)PR 258.9 5.03E-31 281100000 172550 159320 182290 176430 184820 183370 217600 180670 236550 TRUE FALSE 161750.4035 171116.2186 186614.0049 180957.4925 170304.9827 236305.9422 184972.9001 203227.0472 197068.2768 0.820783569 0.868309305 0.946951016 0.918247703 0.864192784 1.199106959 0.938623421 1.031251962 1 17.58833603 LTPSPDIIVLSDNEASS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LTPSPDIIVLSDNEAS(0.209)S(0.791)PR 237.39 3.38E-24 264390000 271550 261470 265790 264270 286980 297760 341340 273710 348900 TRUE FALSE 254554.1702 280829.5109 272094.6643 271051.6156 264441.7484 383718.4783 290159.2358 307883.296 290666.336 0.875760756 0.966157673 0.936106561 0.932518087 0.909777692 1.320133881 0.998255387 1.059232728 1 18.14900447 LTPVRPAAAS(ph)PIVSGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LTPVRPAAASPIVSGAR 17 1 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 LTPVRPAAAS(1)PIVSGAR;LTPVRPAAAS(1)PIVSGAR;LTPVRPAAAS(1)PIVSGAR;LTPVRPAAAS(1)PIVSGAR;LTPVRPAAAS(1)PIVSGAR;LTPVRPAAAS(1)PIVSGAR 191.5 1.45E-10 3049420000 1583390 1947880 1696970 1670350 2298040 1648960 2116900 2054080 3329610 TRUE FALSE 1484288.446 2092103.062 1737222.93 1713214.009 2117561.208 2124987.983 1799490.497 2310536.41 2773876.581 0.535095345 0.754216347 0.626279821 0.617624454 0.763394169 0.766071569 0.648727672 0.832962946 1 21.40347217 -5 0.159333398 2.198059369 0.602135116 0.68764002 0.073205647 77.27901797 0.70955994 28.99904442 0.296784095 1.00E-05 5 -1.595924253 LTPVS(ph)LSNSPIKGADCQEVPQDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTPVSLSNSPIKGADCQEVPQDK 23 1 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 LT(0.014)PVS(0.369)LS(0.337)NS(0.28)PIKGADCQEVPQDK 63.085 0.024587 175960000 121110 60900 83523 78441 80623 73601 112400 77702 96982 TRUE FALSE 113529.9413 65409.09937 85504.205 80453.92886 74291.1948 94848.41389 95546.66347 87403.26574 80795.07767 1.405159133 0.809567875 1.05828483 0.995777604 0.919501496 1.173938025 1.182580254 1.081789488 1 16.30197978 2.224928693 24.991633 1.132738792 1.007464016 0.020212271 0.160616183 472.8224976 866828.0906 0.054933456 0.040790566 167.8528398 -2.224928693 -0.125274776 LTPVS(ph)PESSSTEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LTPVSPESSSTEEK 14 0 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 LTPVS(0.995)PES(0.001)S(0.002)S(0.002)TEEK;LTPVS(1)PESSSTEEK;LTPVS(1)PESSSTEEK;LTPVS(0.998)PES(0.002)SSTEEK;LTPVS(1)PESSSTEEK;LTPVS(0.986)PES(0.012)S(0.002)STEEK 382.3 1.02E-98 6021650000 8379520 5391570 7029940 6306300 6064920 4962510 7005620 4588130 6117130 TRUE FALSE 7855060.801 5790767.453 7196693.497 6468130.335 5588605.648 6395106.077 5955192.318 5160968.13 5096141.485 1.54137416 1.136304294 1.412184791 1.269221107 1.096634712 1.254891784 1.168568874 1.012720731 1 22.2809739 2.074220178 0.305718504 0.962946297 1.403265466 0.534434438 0.115800401 1.442974116 0.39317323 0.170353056 0.229637726 118.637006 -2.074220178 0.440319169 LTPVSLSNS(ph)PIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTPVSLSNSPIK 12 0 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 LTPVSLS(0.001)NS(0.999)PIK;LTPVSLS(0.001)NS(0.999)PIK 194.77 1.15E-06 77617000 402920 250030 329640 276010 310980 277520 405100 313180 293720 TRUE FALSE 377701.9564 268542.4814 337459.2165 283092.8839 286556.8852 357635.5188 344359.0158 352281.2124 244696.2345 1.543554429 1.097452447 1.37909444 1.156915571 1.171071904 1.461548926 1.407291847 1.439667485 1 17.90063238 2.240723038 24.99948717 1.369609197 1.25594649 0 0.179940418 138.7193639 1603741.844 0.057301761 0.045741438 174.0696428 -2.240723038 -0.113662707 LTPYEVDELRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LTPYEVDELRR 11 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;; 228.06 5.68E-12 5693380000 3380290 3955400 3697360 3682440 4184740 3125650 4097410 3618280 4461840 FALSE TRUE 3168723.683 4248261.932 3785063.125 3776937.645 3856087.401 4027974.414 3483041.409 4070030.223 3717130.079 0.852465105 1.142887615 1.018275671 1.016089715 1.037382959 1.08362482 0.937024353 1.094938874 1 21.82575774 LTQEPESIRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LTQEPESIRK 10 1 P09497-2;P09497;H0Y9Q6 P09497-2 CLTB Clathrin light chain B 0 ;; 106.67 0.0038259 836810000 1183190 1223740 1231790 1261630 1459840 996120 1544470 1234560 2221810 FALSE TRUE 1109136.25 1314346.983 1261008.64 1294005.562 1345190.055 1283683.673 1312891.062 1388697.534 1850975.558 0.599217124 0.710083381 0.681267041 0.699093814 0.726746525 0.693517355 0.709296812 0.750251686 1 20.81985441 -5 0.230013143 2.647556644 0.662090365 0.91738516 0.029671703 40.16927389 0.402056902 30.74946932 0.047581028 1.00E-05 5 -1.985466279 LTQT(ph)SSTEQLNVLETETEVLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTQTSSTEQLNVLETETEVLNK 22 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 LT(0.272)QT(0.34)S(0.185)S(0.102)T(0.102)EQLNVLETETEVLNK 196.89 7.62E-22 52529000 57199 46882 50003 51523 57353 46665 63312 49571 68667 TRUE FALSE 53619.01669 50353.19206 51189.09477 52845.16741 52848.72673 60136.42796 53818.95336 55760.04847 57206.03409 0.93729652 0.880207706 0.894819849 0.923769114 0.923831333 1.051225258 0.940791548 0.974723198 1 15.80387971 2.457341693 24.62399398 0.984554294 0.904048128 0.612681105 0.031346301 129.5330176 161257.2422 0.010349833 0.00866041 286.6432325 -2.457341693 -0.080506166 LTQTS(ph)STEQLNVLETETEVLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTQTSSTEQLNVLETETEVLNK 22 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 LT(0.037)QT(0.092)S(0.431)S(0.22)T(0.22)EQLNVLETETEVLNK 191.78 8.40E-18 93032000 74130 63016 71196 65029 66445 57857 88928 62238 78754 TRUE FALSE 69490.33563 67681.77021 72884.80274 66697.75423 61226.67773 74559.37667 75594.07197 70008.5513 65609.44863 1.059151343 1.031585719 1.110888817 1.016587635 0.93319909 1.136412182 1.152182705 1.067049835 1 16.00161598 LTQTSS(ph)TEQLNVLETETEVLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LTQTSSTEQLNVLETETEVLNK 22 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 LT(0.23)QT(0.147)S(0.095)S(0.263)T(0.263)EQLNVLETETEVLNK;LTQT(0.003)S(0.011)S(0.493)T(0.493)EQLNVLETETEVLNK;LT(0.002)QT(0.037)S(0.018)S(0.471)T(0.471)EQLNVLETETEVLNK 349.58 3.51E-96 393637000 392655 311295 351040 338176 347800 292895 478282 340655 452915 TRUE FALSE 368079.4245 334343.6057 359366.8346 346854.1687 320485.191 377449.0317 406568.0543 383186.5266 377320.5606 0.975508528 0.886099621 0.952417843 0.919255946 0.84937113 1.000340483 1.07751365 1.015546373 1 18.52543119 2.0440373 7.485649981 1.039543135 0.917657397 0.651630067 0.039169075 0.111305494 15.71892059 0.013629103 0.009988538 110.6718833 -2.0440373 -0.121885739 LTQYHGGS(ph)LPNVSQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LTQYHGGSLPNVSQLR 16 0 Q6UUV7;Q6UUV7-3;H0YK33 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 LTQYHGGS(1)LPNVSQLR;LTQYHGGS(1)LPNVSQLR;LTQYHGGS(1)LPNVSQLR;LTQYHGGS(1)LPNVSQLR 198.1 2.68E-11 1158990000 1183230 1447210 1324350 1410850 1465880 988858 1536660 1279060 1116320 TRUE FALSE 1109173.746 1554362.934 1355764.207 1447054.8 1350755.698 1274325.252 1306252.099 1438753.457 929998.9803 1.19266125 1.671359826 1.457812574 1.555974609 1.452427074 1.370243709 1.404573689 1.547048424 1 19.82686961 -2.88346054 0.354512894 1.02E-09 1.489888874 0.536883938 0.130167143 59.82876551 1.960887145 45.1521309 0.090920927 0.001307794 2.88346054 1.489888873 LTQYIDGQGRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTQYIDGQGRPR 12 1 Q13555-8;Q13555-9;Q13555-10;Q13555-3;Q13555-7;Q13555-4;Q13555-2;A0A2Q3DQE3;Q13555;Q8WU40;Q5SWX3;Q13555-6;Q13555-11;Q13555-5;H0Y6G2;H7C394 Q13555-8 CAMK2G;CAMK2B Calcium/calmodulin-dependent protein kinase type II subunit gamma 0 69.229 0.048375 0 93308 143670 138880 135450 186140 145420 133380 139850 181420 FALSE TRUE 87468.01884 154307.4763 142174.2992 138925.8763 171521.3153 187400.3933 113380.9072 157310.5803 151139.83 0.578722491 1.020958382 0.940680555 0.919187724 1.134851847 1.239914014 0.750172256 1.040828089 1 17.20552438 4.740856789 24.67094135 0.993914072 0.578722317 0.515753058 0.129604827 149.1169048 1602043.437 0.030243326 0.20222315 55062.60947 -4.740856789 -0.415191755 LTRDETNYGIPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 146.77 3.87E-05 633460000 1206850 744030 957950 949190 918780 658630 1045080 721970 996160 FALSE TRUE 1131315.413 799118.7554 980673.0264 973547.8224 846622.725 848765.789 888379.956 812109.5438 829894.4606 1.363203957 0.962916122 1.181684025 1.17309835 1.020157099 1.022739432 1.070473414 0.978569664 1 19.66256835 2.728849531 23.72748441 1.027006183 1.137583767 0.34201664 0.09980499 498.2960405 1217502.614 0.030374337 0.029007176 535.6110534 -2.728849531 0.110577584 LTRPAAS(ph)PAVGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTRPAASPAVGEK 13 1 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 LT(0.001)RPAAS(0.999)PAVGEK;LT(0.001)RPAAS(0.999)PAVGEK 117.37 0.00030985 3409000000 4691100 3492200 3992300 3566200 4306300 3195500 5022900 3738600 5417400 TRUE FALSE 4397492.425 3750766.122 4086999.241 3657714.73 3968100.569 4117988.975 4269762.775 4205372.44 4513200.942 0.974362206 0.831065616 0.905565538 0.810448012 0.879220894 0.912432003 0.946060862 0.931793752 1 22.10571958 1.55154156 1.049584986 0.984900887 0.873860182 0.398703117 0.045606436 0.426183148 0.907278985 0.037412891 0.013816333 35.60750632 -1.55154156 -0.111040705 LTS(ph)DEEGEPSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LTSDEEGEPSGK 12 0 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 LT(0.002)S(0.998)DEEGEPSGK;LT(0.003)S(0.997)DEEGEPSGK;LT(0.008)S(0.992)DEEGEPSGK 289.34 4.65E-36 724690000 2977060 1735400 2238840 2061120 2018080 1778810 2818370 1918580 2067270 TRUE FALSE 2790731.129 1863890.822 2291946.342 2114011.829 1859588.137 2292323.57 2395781.583 2158118.936 1722229.282 1.620417884 1.08225475 1.330802098 1.227485708 1.079756428 1.331021133 1.391093281 1.253096181 1 20.71584579 -2.318281765 1.752115549 4.47E-05 1.276901836 0.252619233 0.155148508 2336238.593 287969.8594 9214030.902 0.03872149 0.004805275 2.318281765 1.276857151 LTSS(ph)CPDLPSQTDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LTSSCPDLPSQTDKK 15 1 P56962 P56962 STX17 Syntaxin-17 1 LT(0.015)S(0.085)S(0.9)CPDLPSQTDKK;LTS(0.007)S(0.993)CPDLPSQTDKK;LT(0.001)S(0.006)S(0.994)CPDLPSQTDKK 234.49 7.21E-18 795100000 1077170 678300 869370 740610 878120 638910 1118060 739730 1481210 TRUE FALSE 1009751.853 728522.0378 889991.8669 759615.3064 809155.9974 823352.9452 950417.2826 832086.9188 1233986.482 0.818284371 0.59038089 0.721233077 0.615578305 0.655725171 0.667230117 0.770200725 0.674307969 1 20.23489516 -0.35914142 0.550032793 1.040619107 0.671405371 0.66677652 0.068618013 4.23530458 1.171186052 0.409837943 0.027269263 0.437379657 0.35914142 -0.369213737 LTSTATKDPEGFVGHPVNAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTSTATKDPEGFVGHPVNAFK 21 1 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 149.94 4.57E-08 267980000 299360 309240 272700 371210 391400 173810 361030 301750 355220 FALSE TRUE 280623.592 332136.4514 279168.5728 380735.8771 360661.0228 223986.1254 306896.9031 339424.1517 295931.4872 0.948272165 1.122342386 0.943355421 1.286567647 1.218731492 0.756885073 1.037053901 1.146968695 1 18.17490368 LTTPTYGDLNHLVSATMSGVTTCLR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 292.44 7.09E-63 10083730000 2932740 3522920 3432490 3230620 3755860 3149680 3806110 3539750 3505550 FALSE TRUE 2749185.038 3783760.662 3513910.284 3313523.179 3460889.906 4058941.485 3235419.14 3981695.579 2920451.058 0.941356312 1.295608311 1.203208071 1.134592949 1.185053212 1.389833763 1.107849122 1.363383772 1 21.47775978 4.748911164 24.17228545 1.218042589 0.941356065 0.337911176 0.117667184 953.0577233 2225664.114 0.024331303 0.330387421 56093.32237 -4.748911164 -0.276686524 LTTTGQVTS(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LTTTGQVTSPVK 12 0 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 LTTTGQVT(0.016)S(0.984)PVK;LTTTGQVT(0.018)S(0.982)PVK;LTTTGQVT(0.026)S(0.974)PVK;LTTTGQVT(0.027)S(0.973)PVK;LTTTGQVT(0.022)S(0.978)PVK;LTTTGQVT(0.001)S(0.999)PVK 244 2.36E-16 4310090000 15430600 10061140 11778120 10453720 11916350 9580710 15501270 11757470 12189540 TRUE FALSE 14464826.29 10806077.27 12057502.57 10721980.15 10980487.94 12346505.45 13176998.47 13225416.01 10155027.03 1.424400571 1.064111129 1.187343228 1.0558298 1.08128594 1.215802323 1.297583791 1.302351631 1 23.27569074 2.026046947 17.97440594 1.238955697 1.147756873 0 0.134379446 22.30257464 15388.47901 0.045671176 0.033719831 106.1810332 -2.026046947 -0.091198823 LTTTGQVTS(ph)PVKGASFVTSTNPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTTTGQVTSPVKGASFVTSTNPR 23 1 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 LTTTGQVT(0.145)S(0.855)PVKGASFVTSTNPR;LTTTGQVT(0.151)S(0.849)PVKGASFVTSTNPR 174.1 1.86E-12 2704800000 1408520 1259930 1300260 1360800 1673420 998230 1784760 1320120 2338440 TRUE FALSE 1320363.247 1353216.528 1331102.781 1395720.432 1541996.343 1286402.796 1517151.807 1484939.888 1948139.257 0.677756091 0.694620019 0.683268805 0.716437712 0.791522648 0.660323841 0.778769691 0.76223498 1 20.89366538 -4.999999938 0.187925832 2.231677264 0.662780981 0.866348501 0.035961288 41.72993728 0.407254636 19.13125745 0.090432749 1.00E-05 4.999999938 -1.568896284 LTVAS(ph)PK ddPTM_SK-BR-3_Pertuzumab_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 114.51 0.0061763 1540130000 6954000 4590040 5528630 4914570 5827000 4206670 6796600 4950190 7121790 TRUE FALSE 6518761.553 4929891.338 5659771.714 5040686.187 5369370.925 5421067.339 5777512.927 5568232.118 5933117.24 1.098707693 0.830910824 0.953928851 0.849584794 0.904983116 0.913696312 0.973773599 0.938500268 1 22.50035886 1.751592659 6.809626964 0.966689533 0.913950912 0.063274999 0.073650028 0.333345074 45.35777269 0.032315757 0.017244516 56.44073474 -1.751592659 -0.05273862 LTVEDLEKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LTVEDLEKER 10 1 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 89.301 0.010585 111100000 301950 341910 317240 343940 473470 192340 301550 276170 677730 FALSE TRUE 283051.4885 367225.3722 324765.0826 352766.0827 436285.5761 247865.4356 256335.377 310650.4324 564612.4847 0.501319925 0.650402501 0.575199967 0.624793274 0.772716842 0.439000983 0.454002318 0.550201139 1 19.1069015 -1.473410108 6.041267982 1.00028234 0.571409323 0.654676604 0.097927149 0.000387036 3.37E-05 0.098545043 0.023212359 0.033619395 1.473410108 -0.428873017 LTVENS(ph)PKQEAGISEGQGTAGEEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTVENSPKQEAGISEGQGTAGEEEEK 26 1 O43583;F8VVL1 O43583 DENR Density-regulated protein 1 LTVENS(1)PKQEAGISEGQGTAGEEEEK;LTVENS(1)PKQEAGISEGQGTAGEEEEK 263.16 3.88E-53 397060000 541890 234460 344076 336789 416490 199694 361330 256635 505470 TRUE FALSE 507974.0722 251819.6624 352237.6452 345431.5759 383780.5554 257342.416 307151.9209 288676.4447 421103.7915 1.206291851 0.597999038 0.836462773 0.820300322 0.911368083 0.611113985 0.729397187 0.685523262 1 18.68381634 2.251544038 24.99433878 0.729082346 0.829134159 0.05700288 0.180054308 641.0930802 1234165.262 0.057782531 0.048059748 178.4612943 -2.251544038 0.100051813 LTVIDTPGFGDHINNENCWQPIMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 303.94 1.88E-62 319880000 560610 548070 585430 562830 611280 527420 744920 541450 688460 FALSE TRUE 525522.4208 588649.6731 599316.6761 577273.1707 563272.5346 679677.5921 633226.1615 609051.2244 573551.5784 0.91626009 1.026323866 1.044922024 1.006488679 0.982078257 1.185033078 1.10404397 1.061894426 1 19.12956371 2.264922836 24.99937011 1.100395842 1.006747487 0.376256634 0.057131056 214.028057 202962.7231 0.018651904 0.015600852 184.0444967 -2.264922836 -0.093648355 LTVNADVGYYSWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTVNADVGYYSWR 13 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 ; 213.06 2.09E-08 450570000 128565 214080 176238 174244 204950 162607 206920 190867 190973 FALSE TRUE 120518.3461 229930.706 180418.4486 178715.396 188854.0537 209549.0012 175894.267 214697.1651 159098.3726 0.757508353 1.445210924 1.13400562 1.12330122 1.187026936 1.317103361 1.105569241 1.34946173 1 17.27955955 -1.06946326 4.546003364 0.999988482 1.195697724 0.075463558 0.185560699 1.89E-05 3.87E-06 0.156920591 0.036984362 0.08521906 1.06946326 0.195709242 LTWASHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTWASHEK 8 0 P06702 P06702 S100A9 Protein S100-A9 0 ; 123.35 0.0013512 1246930000 1206980 1975060 980530 899530 1863780 688030 1183730 1738520 2768410 FALSE TRUE 1131437.276 2121295.497 1003788.635 922613.4627 1717406.237 886653.0918 1006240.676 1955578.049 2306344.486 0.49057601 0.919765243 0.435229273 0.400032809 0.744644283 0.384440875 0.436292445 0.847912383 1 21.13717659 1.064587853 4.970351034 0.996883986 0.559818025 0.475801389 0.168861249 0.165570741 7.428162834 0.165546618 0.041926994 11.60346919 -1.064587853 -0.437065961 LTWFVNEGLVDGWDDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTWFVNEGLVDGWDDPR 17 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 152.99 4.47E-07 217020000 357380 375250 387340 347030 364080 343520 420510 382320 221180 FALSE TRUE 335012.2237 403033.9004 396527.8877 355935.3773 335486.6254 442688.6474 357458.4293 430053.4936 184263.6291 1.818113674 2.187267788 2.151959611 1.931663774 1.820688255 2.402474376 1.939929388 2.333903308 1 17.49141181 -0.87734397 5.392820283 0.999999044 2.082821383 0.738144433 0.200820541 2.05E-06 4.27E-07 0.172979339 0.040771585 0.132634355 0.87734397 1.082822338 LTWFVNEGLVDGWDDPRFPTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LTWFVNEGLVDGWDDPRFPTVR 22 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 195.09 1.21E-18 668140000 133004 126611 173642 173096 143570 139785 171417 120563 219846 FALSE TRUE 124679.5171 135985.4102 177760.8702 177537.9364 132294.5913 180138.6603 145714.6122 135615.5559 183152.2823 0.680742361 0.74247183 0.970563227 0.969346023 0.72232019 0.983545812 0.795592664 0.740452449 1 17.48268415 4.308378264 3.089542857 0.87566154 0.692580789 0.334470918 0.10187963 0.293517573 5.384342816 0.02402298 0.080564453 20341.27935 -4.308378264 -0.18308075 LTWHS(ph)CPEDEAQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LTWHSCPEDEAQ 12 0 Q13185 Q13185 CBX3 Chromobox protein homolog 3 1 LTWHS(1)CPEDEAQ;LTWHS(1)CPEDEAQ;LTWHS(1)CPEDEAQ;LT(0.002)WHS(0.998)CPEDEAQ;LTWHS(1)CPEDEAQ;LTWHS(1)CPEDEAQ;LTWHS(1)CPEDEAQ 259.4 2.98E-21 6114182000 3849310 4133050 3833640 3584790 4204680 3943340 5388740 3500040 4955530 TRUE FALSE 3608388.558 4439065.322 3924575.751 3676781.78 3874461.394 5081718.243 4580748.464 3937027.699 4128420.029 0.874036201 1.075245564 0.950624143 0.890602641 0.938485272 1.230911149 1.109564538 0.953640296 1 21.97715833 2.290611679 24.99999582 1.090838191 0.96159953 0.315577394 0.090261426 115.2270929 55342.70081 0.030776626 0.025749556 195.2592778 -2.290611679 -0.12923866 LTWHSCPEDEAQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LTWHSCPEDEAQ 12 0 Q13185 Q13185 CBX3 Chromobox protein homolog 3 0 ;;;;;; 188.04 2.26E-05 7872870000 4169220 4976940 4476520 4284150 5069910 3941470 5228230 4088340 5366360 FALSE TRUE 3908275.962 5345437.816 4582705.168 4394088.542 4671739.72 5079308.405 4444305.448 4598778.249 4470679.848 0.874201709 1.195665536 1.025057782 0.982868085 1.044972997 1.136137808 0.994100584 1.028653002 1 22.09206281 1.612415048 25 1.00853066 1.057035961 0.020254965 0.085802814 1.231559416 6731.861613 0.038960355 0.020688549 40.96519704 -1.612415048 0.048505301 LVAFGTSHGFGLFDHQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVAFGTSHGFGLFDHQQR 18 0 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 0 278.85 1.97E-39 188990000 169960 88169 101700 87487 112730 89278 107720 71378 116590 FALSE TRUE 159322.507 94697.1245 104112.372 89732.06454 103876.6405 115051.1093 91568.38602 80289.70042 97130.3758 1.640295383 0.974948606 1.071882726 0.923831127 1.069455767 1.184501845 0.942736865 0.82661783 1 16.56763492 4.740384689 24.96798665 1.008069154 1.640295599 0.812015735 0.096850407 65.8039007 900655.2644 0.022268318 0.143565918 55002.78618 -4.740384689 0.632226445 LVAIVDVIDQNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LVAIVDVIDQNR 12 0 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ;;; 180.36 4.55E-05 269063000 338731 422346 376334 435132 468327 430205 432011 349246 382635 FALSE TRUE 317530.4314 453616.9373 385260.8202 446298.2238 431546.4866 554398.1997 367234.9611 392850.1319 318770.7466 0.996109068 1.42301934 1.208582733 1.400060164 1.353783216 1.739175271 1.152034699 1.232390789 1 18.28215971 1.037030803 1.869008541 1.012686121 1.343502673 0.225854719 0.193182642 0.467374788 3.354954263 0.167802743 0.047739981 10.89007331 -1.037030803 0.330816552 LVALTLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVALTLAR 8 0 Q5SZD4 Q5SZD4 GLYATL3 Glycine N-acyltransferase-like protein 3 0 60.682 0.09075 2496100000 968190 1069100 1133000 1068700 1022100 1008100 1089300 953830 1200000 FALSE TRUE 907592.7162 1148257.276 1159875.295 1096124.651 941828.389 1299122.105 925969.5776 1072917.775 999712.2477 0.907853953 1.148587785 1.160209148 1.096440154 0.94209948 1.299496038 0.926236104 1.073226599 1 19.93115337 1.632538345 25 0.999784248 1.101966844 0.122819472 0.114821845 1.449507153 1464.186203 0.048406902 0.026827437 42.90800725 -1.632538345 0.102182596 LVDLDWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVDLDWR 7 0 Q9P000;Q9P000-2 Q9P000 COMMD9 COMM domain-containing protein 9 0 ; 91.906 0.037363 78899000 321820 467000 374730 382200 501040 306380 373870 416660 481880 FALSE TRUE 301677.8607 501577.1659 383618.7726 392007.8991 461690.3395 394826.9323 317811.6643 468680.9182 401451.1149 0.751468484 1.24941032 0.955580289 0.976477296 1.150053698 0.983499404 0.791657197 1.167466974 1 18.61486479 2.00658193 24.8169902 0.94431371 1.040582189 0 0.158716045 399.8452637 1507597.534 0.055150802 0.040632025 101.5270881 -2.00658193 0.09626848 LVDMMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LVDMMER 7 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;;; 138.33 0.0065044 222439000 244243 404859 290887 309574 450640 229721 277857 358004 421824 FALSE TRUE 228956.2666 434835.1816 297786.977 317518.1929 415248.5522 296037.7235 236194.9223 402701.5875 351418.8493 0.651519596 1.237370114 0.847384759 0.903532049 1.181634261 0.842407071 0.672117966 1.145930528 1 18.42283205 LVDQNIFSFYLSR ddPTM_SK-BR-3_Pertuzumab_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 ; 134.98 0.00020778 264840000 117738 209133 118287 113414 243969 80004 122293 191617 156524 FALSE TRUE 110368.9887 224617.4249 121092.8235 116324.3952 224808.6589 103099.856 103956.3 215540.8043 130399.1332 0.846393577 1.722537715 0.92863212 0.892064175 1.724004242 0.790648323 0.797216188 1.652931265 1 16.99257475 3.809503576 8.807057007 1.082925641 1.342404988 0.023917197 0.388827079 0.829337645 81.39718592 0.09332792 0.168570247 6449.166308 -3.809503576 0.259479347 LVDQSGPPHEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVDQSGPPHEPK 12 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 124.51 0.00032164 404750000 1359900 1015000 1148400 1148500 1273500 949300 1437300 1107600 1655000 FALSE TRUE 1274786.286 1090151.656 1175640.59 1177972.454 1173484.447 1223347.499 1221790.208 1245886.298 1378769.808 0.924582391 0.790669805 0.852673581 0.854364846 0.851109765 0.88727465 0.886145172 0.903621686 1 20.39495018 0.716915016 0.498770736 1.006169864 0.840207818 0.631160092 0.033357717 0.801121357 0.429894075 0.042115866 0.016732204 5.210927317 -0.716915016 -0.165962046 LVDVS(ph)PDRGS(ph)PPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVDVSPDRGSPPSR 14 1 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 2 LVDVS(0.999)PDRGS(0.892)PPS(0.109)R 98.552 0.03028 235170000 472990 542210 659400 443380 466580 433210 547010 380170 446550 TRUE FALSE 443386.4002 582355.7926 675041.2794 454757.8814 429936.6889 558270.6944 464990.9287 427635.0614 372017.9202 1.191841511 1.565397152 1.814539684 1.222408537 1.155688115 1.500655383 1.249915403 1.149501242 1 18.50501259 3.210831398 24.94046135 1.243907391 1.574329031 0.341728093 0.196265568 205.3069578 184658.4396 0.055787401 0.066692401 1624.917808 -3.210831398 0.33042164 LVDVS(ph)PDRGS(ph)PPSRVPQALNFSPEESDSTFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVDVSPDRGSPPSRVPQALNFSPEESDSTFSK 32 2 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 2 LVDVS(0.729)PDRGS(0.805)PPS(0.466)RVPQALNFSPEESDSTFSK 82.311 0.00023426 85669000 35541 35857 32085 38361 43207 29777 46222 34601 65047 TRUE FALSE 33316.55225 38511.88959 32846.07135 39345.40821 39813.69651 38373.13651 39291.4402 38921.01102 54190.23548 0.614807298 0.710679502 0.606125274 0.726060846 0.734702408 0.708119021 0.725064947 0.718229228 1 15.7257453 -5 0.195431913 2.38561611 0.637063333 0.872527395 0.038100363 44.16835088 0.435204092 23.79524968 0.092007734 1.00E-05 5 -1.748552777 LVDVS(ph)PDRGSPPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LVDVSPDRGSPPSR 14 1 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 1 LVDVS(1)PDRGSPPSR;LVDVS(1)PDRGSPPSR;LVDVS(0.999)PDRGS(0.001)PPSR 155.94 3.46E-06 947210000 483345 562411 574848 561973 616710 513076 604844 519818 615850 TRUE FALSE 453093.2992 604052.4956 588483.666 576394.1786 568276.0843 661192.7121 514153.2573 584718.4216 513060.6565 0.883118387 1.177351036 1.147006029 1.123442562 1.107619688 1.288722306 1.002129574 1.139667239 1 18.96876987 0.57423913 1.074648796 1.001194314 1.122735812 0.074721777 0.107545154 3.249948343 5.610078332 0.093024511 0.029118211 3.751795256 -0.57423913 0.121541498 LVEALCAEHQINLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LVEALCAEHQINLIK 15 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 ;; 251.91 1.24E-24 3671032000 6084947 5879759 6037343 5786902 6805067 5194922 7328363 5764611 7267854 FALSE TRUE 5704101.029 6315102.474 6180551.627 5935403.703 6270624.488 6694611.649 6229543.001 6484335.373 6054802.215 0.942078837 1.042990712 1.020768542 0.980280361 1.03564481 1.10566975 1.028859867 1.070940906 1 22.5296484 2.482990156 24.9867327 1.055169416 1.008277912 0.297291952 0.038096449 343.8417913 1463905.264 0.011984713 0.010327744 304.0816099 -2.482990156 -0.046891505 LVEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVEALR 6 0 O75688;O75688-3 O75688 PPM1B Protein phosphatase 1B 0 ; 106.76 0.074087 615490000 439230 556600 530190 567440 581880 442970 542140 516030 552040 FALSE TRUE 411739.3783 597811.2431 542766.3572 582001.4711 536181.492 570848.248 460851.14 580457.4814 459900.9577 0.895278367 1.299869533 1.180180967 1.265493062 1.16586296 1.241241703 1.002066059 1.26213584 1 18.81096368 -0.867691328 7.952718947 0.999996087 1.171525575 0.140511063 0.126275117 0 0 0.111511082 0.026283414 0.135615295 0.867691328 0.171529488 LVEDEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVEDEER 7 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 135.6 0.0071227 176980000 488340 473000 475730 492190 557100 383410 632190 447080 592110 FALSE TRUE 457775.6711 508021.4122 487014.5403 504820.4287 513347.6132 494094.2429 537398.9785 502898.9221 493283.0158 0.928018311 1.029878175 0.987292334 1.023389033 1.04067563 1.001644547 1.08943337 1.01949369 1 18.91205609 5.739059092 1.322784382 1.028204513 1.84E-32 0.498310084 0.02913022 14.52372639 2.806814061 0.008105343 36.95665935 548351.5704 -5.739059092 -1.028204513 LVEDEERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVEDEERR 8 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 147.36 0.00086344 484740000 646970 896390 756270 803330 956530 611960 892490 808000 907750 FALSE TRUE 606477.3026 962759.6483 774209.0815 823944.8078 881407.9923 788622.9177 758669.41 908880.5786 756240.6607 0.801963362 1.273086331 1.023760189 1.089527251 1.165512565 1.042820042 1.003211609 1.201840401 1 19.5284859 -0.377685497 6.539277811 1.000000002 1.083972325 0.029024297 0.128108903 0 0 0.110220541 0.025979231 0.419096953 0.377685497 0.083972323 LVEDKPGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LVEDKPGSR 9 1 Q08170;A0A0D9SEM4 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 0 ;;;; 127.42 0.00040659 1249150000 2271700 2075000 2108680 2138000 2417040 1693070 2458250 2054180 2609130 FALSE TRUE 2129518.352 2228635.159 2158698.885 2192864.7 2227215.428 2181831.824 2089658.234 2310648.895 2173649.347 0.979697279 1.025296542 0.993121953 1.008840134 1.024643386 1.003764396 0.961359401 1.063027437 1 21.05168779 1.995448218 24.94816016 0.998517136 1.00780422 0 0.028167468 999.1388727 5476225.511 0.009976701 0.007167625 98.95738668 -1.995448218 0.009287084 LVEEHLDSEIQKLDQMDEDELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVEEHLDSEIQKLDQMDEDELER 23 1 F8WCJ3;B8ZZX4;O14530-2;O14530;F8WBV5;G3XAJ4 F8WCJ3 TXNDC9 Thioredoxin domain-containing protein 9 0 ; 196.55 1.88E-24 54464000 64472 55447 53834 55337 61506 40980 65714 48795 73487 FALSE TRUE 60436.81261 59552.35357 55110.9679 56757.04111 56675.56686 52810.26075 55860.79576 54887.16316 61221.54496 0.987182088 0.972735229 0.900189107 0.927076263 0.925745453 0.862609083 0.912436885 0.896533454 1 15.90175183 4.154231178 2.229967563 0.911503665 0.985535735 0.342922331 0.035082522 0.296422529 2.827660701 0.008240493 0.026669813 14263.66658 -4.154231178 0.07403207 LVEGILHAPDAGWGNLVYVVNYPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVEGILHAPDAGWGNLVYVVNYPK 24 0 Q13148;A0A087WYY0;A0A087X260;G3V162;B1AKP7;K7EN94;A0A0A0N0M3;K7EJM5;A0A087WX29;A0A1W2PNU8;K7EJ99;A0A0A0MSV7 Q13148 TARDBP;TDP43 TAR DNA-binding protein 43 0 253.36 8.84E-44 159810000 238910 253780 229080 171230 289700 183570 260470 271820 210580 FALSE TRUE 223957.0496 272570.1353 234513.8858 175624.0517 266948.1306 236563.679 221414.9416 305757.3253 175432.8376 1.276597088 1.553700772 1.336773029 1.001089956 1.521654294 1.348457234 1.262106597 1.742873966 1 17.42055929 3.697687448 6.793898649 1.320407672 1.438163729 0.029417624 0.227890115 0.572213402 92.25217467 0.055059275 0.087843769 4985.255802 -3.697687448 0.117756057 LVEHGLNETIHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVEHGLNETIHIR 13 0 Q7Z3B4-2;Q7Z3B4-3;Q7Z3B4 Q7Z3B4-2 NUP54 Nucleoporin p54 0 ; 152.99 2.63E-05 164107000 69887 82352 83137 86274 78979 76664 90778 81551 69184 FALSE TRUE 65512.89742 88449.42777 85109.0489 88487.9369 72776.30793 98795.65226 77166.68164 91732.82187 57636.74345 1.136651613 1.53460141 1.476645692 1.535269545 1.262672101 1.714108854 1.338845275 1.59156844 1 15.8147012 -1.03475843 6.194642577 0.999999522 1.458918006 0.414852083 0.167124656 9.48E-07 1.47E-07 0.137963652 0.032518311 0.092308474 1.03475843 0.458918484 LVEIVHPSQEEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LVEIVHPSQEEDR 13 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PK08 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 ;;; 163.99 3.78E-05 781290000 708320 1006980 1005350 977370 926800 974200 1108840 907080 727490 FALSE TRUE 663987.5156 1081537.847 1029197.377 1002450.969 854012.8665 1255435.725 942579.736 1020330.935 606067.2192 1.095567446 1.784517975 1.698157142 1.65402605 1.409105854 2.071446343 1.555239594 1.683527672 1 19.20911829 -0.838306721 8.576106806 0.999963836 1.648921944 0.36776909 0.252333599 0 0 0.215290335 0.050744419 0.145108643 0.838306721 0.648958108 LVEKPSPLTLAPHDFANIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVEKPSPLTLAPHDFANIK 19 1 P53618 P53618 COPB1 Coatomer subunit beta 0 ; 205.68 2.40E-16 691520000 2390000 2096900 2223200 2303900 2454600 1719680 3122300 2115100 2802500 FALSE TRUE 2240414.166 2252156.658 2275935.354 2363021.974 2261825.617 2216123.699 2654140.101 2379174.891 2334744.645 0.95959709 0.964626544 0.974811253 1.01211153 0.968767879 0.949193182 1.136801023 1.019030024 1 21.15483334 1.759014419 25 1.064727807 0.972558176 0.473481305 0.039204966 6.42005067 7853.933924 0.016195106 0.008981197 57.41355239 -1.759014419 -0.092169631 LVELLMHNDYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVELLMHNDYK 11 0 C9JYI4;P52294;Q5TFJ7;O60684;O15131 C9JYI4;O60684;O15131 KPNA1;KPNA6;KPNA5 "Importin subunit alpha-5;Importin subunit alpha-5, N-terminally processed;Importin subunit alpha-7;Importin subunit alpha-6" 0 ; 178.1 7.69E-06 224730000 859900 859160 806760 789980 1029460 588280 909420 837890 1080300 FALSE TRUE 806080.394 922773.1004 825896.7282 810252.2242 948610.3642 758106.8861 773060.9136 942502.4109 899990.951 0.895653887 1.025313754 0.917672258 0.900289301 1.054022113 0.842349454 0.858965207 1.04723543 1 19.77955097 3.740104299 23.34941966 0.93180192 0.970269591 0 0.078888554 644.0668009 1158308.633 0.01936313 0.034580992 5496.728656 -3.740104299 0.038467671 LVEPHS(ph)PS(ph)PSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVEPHSPSPSSK 12 0 O15014 O15014 ZNF609 Zinc finger protein 609 2 LVEPHS(0.999)PS(0.959)PS(0.023)S(0.018)K 66.335 0.030811 153570000 852770 613070 757900 688420 776030 671210 952960 725460 960760 TRUE FALSE 799396.6479 658462.3407 775877.7459 706086.0227 715083.7342 864977.4308 810072.4948 816035.2779 800402.9493 0.998742757 0.822663561 0.969358929 0.882163195 0.893404672 1.080677466 1.012080847 1.019530574 1 19.61036696 2.24970682 24.9997357 1.029100538 0.907146801 0.546987658 0.05174607 142.1471859 318820.6327 0.016529106 0.013710664 177.7079347 -2.24970682 -0.121953737 LVEPHS(ph)PSPSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LVEPHSPSPSSK 12 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 LVEPHS(0.991)PS(0.009)PSSK;LVEPHS(0.981)PS(0.019)PSSK;LVEPHS(0.992)PS(0.008)PSSK;LVEPHS(0.999)PS(0.001)PSSK 194.48 9.52E-07 2240990000 4694100 4190310 4591300 4462400 4738800 3844030 5505200 4050860 5315300 TRUE FALSE 4400304.66 4500564.912 4700207.804 4576912.739 4366633.763 4953739.058 4679746.368 4556618.788 4428142.092 0.993713519 1.016355126 1.06144015 1.033596629 0.986109676 1.118694693 1.056819377 1.02901368 1 22.07827009 2.265766141 24.99991471 1.058212914 1.024574013 0.144665352 0.036272557 379.0224774 348293.4268 0.012009652 0.010046167 184.4022182 -2.265766141 -0.033638901 LVEPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVEPLR 6 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 103.71 0.080148 38576000 69500 103880 104430 102630 100790 100090 109680 88778 91566 FALSE TRUE 65150.11906 111571.3833 106907.1289 105263.6596 92874.35997 128984.3582 93234.50222 99862.12872 76283.04306 0.854057684 1.462597437 1.401453385 1.379909025 1.217496789 1.690865401 1.22221792 1.309099961 1 16.21907478 -0.612340579 7.425084068 0.999991785 1.344291496 0.168920927 0.213747605 0 0 0.183384356 0.043224107 0.244151514 0.612340579 0.34429971 LVEQANS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LVEQANSPK 9 0 O95391 O95391 SLU7 Pre-mRNA-splicing factor SLU7 1 LVEQANS(1)PK;LVEQANS(1)PK;LVEQANS(1)PK;LVEQANS(1)PK 177.04 5.52E-05 2712280000 4378120 2669900 3078620 2776430 2963510 2332020 3929070 2623950 3601020 TRUE FALSE 4104101.284 2867582.174 3151646.32 2847677.894 2730767.879 3005236.317 3339942.429 2951555.934 2999986.499 1.368039918 0.955865027 1.050553501 0.949230237 0.910260056 1.001749947 1.113319154 0.983856406 1 21.51652458 4.743077226 24.99442106 1.003038428 1.368040065 0.81155592 0.056299643 213.8568413 1183419.453 0.014299482 0.11378084 55344.85145 -4.743077226 0.365001637 LVEQLKEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LVEQLKEER 9 1 O95232;J3KPP4 O95232 LUC7L3 Luc7-like protein 3 0 ;; 177.57 4.74E-05 570740000 1624970 1500130 1508760 1471310 1816390 1166800 1755680 1461420 2283790 FALSE TRUE 1523266.028 1611201.186 1544548.5 1509066.306 1673738.056 1503636.219 1492432.083 1643881.504 1902610.695 0.800618872 0.846837028 0.811804803 0.793155588 0.879706006 0.79030157 0.784412748 0.864013594 1 20.85954896 0.916543631 5.480994195 0.999988146 0.816848846 0.802900336 0.028804929 0.263783702 16.65888583 0.02696091 0.006795434 8.251703814 -0.916543631 -0.1831393 LVES(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LVESPK 6 0 Q96S94;Q96S94-3 Q96S94 CCNL2 Cyclin-L2 1 LVES(1)PK;LVES(1)PK;LVES(1)PK;LVES(1)PK 101.43 0.038321 1141700000 5728230 3068450 3989610 3530350 3601860 3459630 5573510 3636090 4401310 TRUE FALSE 5369710.309 3295641.231 4084245.433 3620944.758 3318984.445 4458369.019 4737813.917 4090063.841 3666702.927 1.464451966 0.898802356 1.113874103 0.987520623 0.905168624 1.215906799 1.29211829 1.115460925 1 21.80605195 2.191692515 24.99918496 1.193479303 1.051590568 0.023785245 0.175428431 237.6593214 126764.6268 0.060276393 0.044517208 155.4864382 -2.191692515 -0.141888735 LVES(ph)PKEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVESPKEGK 9 1 Q96S94;Q96S94-3 Q96S94 CCNL2 Cyclin-L2 1 LVES(1)PKEGK;LVES(1)PKEGK 78.324 0.018225 1325030000 1861640 957350 1165220 1227340 1529690 767660 1629360 1083070 2773300 TRUE FALSE 1745123.276 1028233.19 1192859.569 1258835.622 1409554.318 989270.9801 1385052.594 1218293.674 2310418.314 0.75532784 0.445042001 0.516295929 0.54485182 0.610086195 0.428178297 0.599481309 0.52730437 1 21.13972265 -1.077364624 0.881309043 1.070837119 0.539315116 0.694459135 0.092680536 50.76546315 16.82994276 9.822887525 0.026551446 0.083682641 1.077364624 -0.531522004 LVEVDSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVEVDSGR 8 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ; 152.47 0.0010622 241630000 334160 412630 428210 404800 429270 345240 439880 363340 399500 FALSE TRUE 313245.5221 443181.5545 438367.3434 415187.8533 395556.8658 444905.1835 373924.0776 408703.7988 332820.8691 0.941183535 1.331591843 1.317126972 1.247481429 1.188497785 1.336770692 1.123499493 1.227999313 1 18.34438637 0.463367592 0.760906028 0.998198132 1.245726002 0.215050257 0.119936532 2.322528573 2.073893332 0.121069047 0.038842811 2.906481697 -0.463367592 0.247527869 LVEVNGENVEKETHQQVVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVEVNGENVEKETHQQVVSR 20 1 O14745;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ; 274.8 1.03E-44 678670000 251160 338090 305410 310670 498940 185386 317860 260210 872410 FALSE TRUE 235440.3439 363122.5354 312654.4694 318642.3182 459755.265 238903.9287 270199.8439 292697.7913 726799.135 0.32394142 0.499618833 0.430180024 0.438418681 0.632575416 0.328706952 0.371766876 0.402721711 1 19.47119718 -1.596235967 2.929735008 1.037243032 0.432407166 0.801877139 0.089257965 20533826.91 21869389.82 5916448.205 0.021320105 0.025337516 1.596235967 -0.604835865 LVFGFLNGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVFGFLNGR 9 0 P00491;G3V5M2;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 149.4 0.00020407 82140000 145000 216440 118570 107570 231360 114370 136770 196880 127320 FALSE TRUE 135924.7088 232465.4428 121382.5364 110330.4283 213189.9189 147386.7624 116262.6082 221460.9014 106069.4695 1.281468735 2.191633879 1.14436828 1.040171398 2.009908411 1.389530494 1.096098706 2.087885444 1 16.69464993 -3.717313183 0.14444483 2.24E-23 1.690538618 0.081919084 0.43880018 215.5978841 2.672577083 70.57290933 2.512727412 0.000191729 3.717313183 1.690538618 LVFLGLDNAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVFLGLDNAGK 11 0 Q9Y6B6;D6RD69;D6RDB2;D6RAA2;Q9NR31;Q5SQT8;X1WI22 Q9Y6B6;Q9NR31 SAR1B;SAR1A GTP-binding protein SAR1b;GTP-binding protein SAR1a 0 114.5 0.0029071 47193000 149900 142160 150210 133300 157150 126400 172640 142660 137510 FALSE TRUE 140518.0266 152685.6743 153773.0521 136720.7037 144808.0729 162889.6281 146754.2347 160471.415 114558.6927 1.226602917 1.332816138 1.342308022 1.193455516 1.264051375 1.42188798 1.281039713 1.400779036 1 16.80572741 -1.319407131 3.630853271 0.998949823 1.311309242 0.647224314 0.071391086 3806981.657 2767052.612 28923.6347 0.015487427 0.047928393 1.319407131 0.312359419 LVFVHSAEGNEFWSALLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LVFVHSAEGNEFWSALLEK 19 0 P07384;E9PRM1;E9PL37 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;; 285.5 5.04E-40 481457000 779480 820400 803955 746927 985989 634267 1007275 831642 938196 FALSE TRUE 730693.7382 881143.2696 823025.1923 766094.4114 908553.4012 817369.5864 856243.4648 935474.3344 781605.0266 0.934863151 1.127351078 1.05299373 0.980155431 1.16242011 1.045757843 1.095493805 1.196863253 1 19.57608022 2.736087677 24.98968205 1.10049868 1.045951368 0.181142163 0.074227276 472.4723241 4774435.169 0.022025528 0.021623416 544.6125902 -2.736087677 -0.054547312 LVGATATSS(ph)PPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LVGATATSSPPPK 13 0 H9KVD1;Q96QD9-4;Q96QD9 H9KVD1 FYTTD1 UAP56-interacting factor 1 LVGATAT(0.026)S(0.015)S(0.959)PPPK;LVGATAT(0.008)S(0.023)S(0.969)PPPK;LVGAT(0.001)AT(0.333)S(0.19)S(0.476)PPPK;LVGATAT(0.029)S(0.174)S(0.797)PPPK 161.04 4.49E-05 1381000000 2652210 2017730 2404270 2244410 2472470 2119310 2812660 2193550 2818930 TRUE FALSE 2486212.91 2167124.829 2461300.42 2302005.36 2278292.18 2731120.393 2390927.744 2467419.546 2348432.372 1.058669153 0.922796353 1.048061017 0.980230637 0.970133186 1.162954669 1.018095208 1.050666639 1 21.16326662 LVGIISS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LVGIISSR 8 0 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 1 LVGIIS(0.04)S(0.96)R;LVGIIS(0.028)S(0.972)R;LVGIIS(0.004)S(0.996)R;LVGIIS(0.002)S(0.998)R;LVGIIS(0.007)S(0.993)R;LVGIIS(0.004)S(0.996)R 125.57 0.0013179 476873000 1618030 1837160 1781070 1715680 1781210 1593120 2037480 1589920 1748190 TRUE FALSE 1516760.391 1973185.238 1823317.821 1759707.253 1641320.952 2053027.882 1731978.789 1788425.012 1456405.795 1.041440782 1.354832042 1.251929804 1.2082534 1.126966782 1.409653744 1.189214431 1.227971639 1 20.47398096 0.463669698 1.672937025 1.000060554 1.243697462 0.306283614 0.104639837 4.0590391 11.44417724 0.090617298 0.025665301 2.908504219 -0.463669698 0.243636908 LVGLNLS(ph)PPMSPVQLPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVGLNLSPPMSPVQLPLR 18 0 Q8N0Z3 Q8N0Z3 SPICE1 Spindle and centriole-associated protein 1 1 LVGLNLS(0.989)PPMS(0.011)PVQLPLR;LVGLNLS(0.997)PPMS(0.003)PVQLPLR 193.72 1.15E-14 280116000 444670 624230 480620 529690 607200 416790 487170 419670 426090 TRUE FALSE 416838.8985 670448.6387 492020.5334 543282.7422 559512.9613 537110.507 414123.3812 472066.7233 354972.8264 1.174283966 1.888732289 1.386079432 1.530491074 1.576213501 1.513103165 1.166634036 1.329867213 1 18.43734906 1.448989265 0.860826589 1.030778957 1.563121428 0.405075978 0.194129567 0.455855085 0.699625128 0.165076072 0.06449093 28.11831325 -1.448989265 0.532342471 LVGS(ph)PPWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVGSPPWK 8 0 Q86UA6-6;Q86UA6-5;Q86UA6-7;Q86UA6-3;Q86UA6-4;Q86UA6-9;Q86UA6-2;Q86UA6;Q86UA6-8 Q86UA6-6 RPAIN RPA-interacting protein 1 LVGS(1)PPWK;LVGS(1)PPWK 70.552 0.053535 666540000 1807200 1411310 1613010 1528910 1696000 1327570 1849570 1375810 1933420 TRUE FALSE 1694090.578 1515804.861 1651271.359 1568144.419 1562803.001 1710817.908 1572244.149 1547582.907 1610719.712 1.051760009 0.941073018 1.025176104 0.973567535 0.970251367 1.062145012 0.976112813 0.960802116 1 20.61927404 LVGSQEELASWGHEYVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVGSQEELASWGHEYVR 17 0 Q13200;Q13200-3;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 198.51 1.41E-11 96640000 51589 59510 67645 63652 66993 53999 68463 58218 67964 FALSE TRUE 48360.13658 63916.18232 69249.57134 65285.41808 61731.64002 69587.6347 58197.60873 65486.64545 56620.36934 0.854111994 1.128854917 1.223050506 1.153037659 1.090272648 1.229021208 1.027856395 1.156591633 1 15.78903354 -0.674420729 7.598563673 0.999995982 1.11946084 0.081060716 0.108003074 0 0 0.096917804 0.022843746 0.211630993 0.674420729 0.119464858 LVGYLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 143.02 0.0056997 353560000 390200 829060 387670 356560 888260 296566 346930 745200 826840 FALSE TRUE 365778.0785 890444.465 396865.7155 365709.9333 818499.6427 382179.7899 294911.0672 838239.8604 688835.0624 0.531009669 1.292681679 0.57614041 0.530910741 1.188237486 0.554820465 0.428130163 1.21689488 1 19.39379905 5.00942119 17.46819215 0.808962219 0.125014426 0.077174939 0.320048336 2408030.439 64438347.43 0.074679182 38756211.82 102193.0098 -5.00942119 -0.683947792 LVHDS(ph)LEDLQMTR ddPTM_SK-BR-3_Pertuzumab_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 142.01 2.58E-05 125879000 60160 86652 74200 84558 87231 79374 88590 74303 86438 TRUE FALSE 56394.69299 93067.80424 75960.05904 86727.90144 80380.22913 102287.9853 75306.75193 83579.89311 72010.93939 0.783140638 1.292412028 1.054840552 1.204371199 1.116222477 1.420450645 1.04576822 1.160655503 1 16.13592847 4.750557965 24.37910239 1.167623462 0.783140306 0.477496782 0.12436555 1065.406733 2164893.263 0.026397445 0.428595092 56306.42645 -4.750557965 -0.384483156 LVHLWSSDSHQPLWSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVHLWSSDSHQPLWSR 16 0 O95834;O95834-2;O95834-3;K7EIK7;A0A0C4DGQ7;C9JRL6;K7ELI8 O95834 EML2 Echinoderm microtubule-associated protein-like 2 0 ; 232.28 3.24E-16 298080000 151761 367220 214651 250684 319740 177134 238630 272590 219959 FALSE TRUE 142262.5499 394409.3509 219742.6231 257116.9758 294628.9102 228269.7103 202849.6468 306623.4615 183246.4219 0.776345581 2.152344077 1.199164605 1.403121399 1.607828994 1.245698049 1.106977395 1.67328485 1 17.4834255 0.305656813 0.250951409 0.878394441 1.560153998 0.046459647 0.379845413 11.09796255 1.423103456 2.245910264 0.720813611 2.021421184 -0.305656813 0.681759557 LVIASTLYEDGTLDDGEYNPTDDRPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LVIASTLYEDGTLDDGEYNPTDDRPSR 27 1 C9JLU1;P52434;P52434-3;P52434-4 C9JLU1 POLR2H "DNA-directed RNA polymerases I, II, and III subunit RPABC3" 0 ;; 168.57 6.38E-12 225721000 32678.9 33267 34976 35402.4 37565.8 26108.7 36602 32411 39969 FALSE TRUE 30633.58598 35730.12329 35805.64724 36310.88552 34615.5336 33645.85785 31113.8699 36457.5847 33297.91569 0.919985091 1.073043839 1.075311968 1.090485238 1.039570582 1.010449368 0.934408934 1.094890895 1 15.02314425 2.234298144 4.010054362 0.996128467 1.052043676 0.019421686 0.061111492 0.395977069 14.32144484 0.022146281 0.016855661 171.5134345 -2.234298144 0.055915209 LVIEEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LVIEEAER 8 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;; 221.56 1.27E-05 1008790000 1026900 1240410 1150940 1177770 1246160 972750 1150000 1148950 990390 FALSE TRUE 962628.1621 1332251.247 1178240.84 1207993.572 1148291.62 1253567.134 977568.1761 1292398.937 825087.5108 1.166698259 1.614678721 1.42801924 1.464079333 1.391721006 1.519314154 1.184805446 1.566378014 1 19.65418762 -3.18576804 0.289410172 2.13E-07 1.45589018 0.41192107 0.150347905 67.51969865 1.661501457 40.8580144 0.149709637 0.000651977 3.18576804 1.455889967 LVIGDHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LVIGDHK 7 0 E9PM92;O00193;E9PRZ9 E9PM92 C11orf58;SMAP Small acidic protein 0 ;;;;; 158.12 0.0014326 3225490000 4912180 4577570 4705030 4674100 5352620 3736210 5550670 4668440 6429980 FALSE TRUE 4604735.422 4916498.046 4816635.533 4794045.319 4932246.817 4814793.175 4718398.563 5251305.011 5356774.799 0.859609671 0.917809359 0.899167076 0.894949946 0.920749332 0.898823146 0.880828248 0.980310953 1 22.35293322 1.161061 5.341460518 0.996811137 0.898548619 0.831061385 0.01767795 0.076133275 3.585531754 0.015689144 0.004011274 14.48975358 -1.161061 -0.098262519 LVIIEGDLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LVIIEGDLER 10 0 P06753-2;A0A087WWU8;P06753-6;P06753-5;P06753-7;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;;; 237.08 8.52E-12 546604000 683005 816251 740704 742028 781630 645246 773347 726285 571928 FALSE TRUE 640256.9362 876687.0733 758273.8487 761069.6947 720243.9327 831518.0455 657390.7968 816963.281 476469.522 1.343752132 1.839964642 1.591442503 1.597310341 1.511626451 1.745165235 1.379712167 1.71461813 1 18.86202441 -2.599122405 0.336997548 5.22E-09 1.63390115 0.566952032 0.158640071 40.16976313 1.494779228 29.39809558 0.119004177 0.002516967 2.599122405 1.633901145 LVIIEGDLERTEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 72.321 0.035524 21242000 11360 14638 12197 13384 18254 9873.4 12084 12282 29873 FALSE TRUE 10648.99788 15721.81275 12486.3186 13727.4561 16820.40447 12723.6903 10272.11638 13815.43474 24887.00331 0.427893939 0.631727836 0.501720454 0.551591364 0.675871026 0.511258432 0.412750232 0.555126488 1 14.6031049 0.944552506 23.48615396 1 0.532945205 0.771433756 0.079903678 5900.406478 2499265.381 0.077380085 0.019345021 8.80141513 -0.944552506 -0.467054795 LVIIESDLER ddPTM_SK-BR-3_Pertuzumab_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 ; 147.2 6.35E-05 76821000 87569 119978 109772 104222 122083 83788 99206 103610 94906 FALSE TRUE 82088.21261 128861.296 112375.8437 106896.513 112495.0936 107976.2354 84330.98128 116545.9366 79065.57548 1.038229496 1.629802796 1.421299257 1.351998165 1.422807498 1.365654202 1.066595427 1.474041463 1 16.27076207 0.932282635 0.44858257 0.99839952 1.433891045 0.206512373 0.185030699 1.514377356 0.774426516 0.238108354 0.115549262 8.556233646 -0.932282635 0.435491525 LVIIESDLERAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVIIESDLERAEER 14 1 H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;H0YL42;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 ; 169.3 3.06E-06 60644000 42296 80898 62120 76681 114586 32542 52639 59788 142330 FALSE TRUE 39648.76886 86887.77209 63593.51574 78648.76428 105586.8778 41936.34712 44746.27063 67252.66341 118574.2035 0.334379382 0.73277129 0.536318304 0.663287308 0.8904709 0.353671759 0.377369354 0.567177863 1 16.85543065 -1.925623337 2.532686909 1.284284389 0.561147124 0.386089645 0.175511434 16683942.81 8274539.252 28067826.49 0.04258415 0.011867976 1.925623337 -0.723137265 LVILEGELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LVILEGELER 10 0 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;;; 193.1 1.42E-06 257264000 289630 332300 315489 311716 329130 284208 327533 281438 285882 FALSE TRUE 271502.5753 356903.8378 322972.5481 319715.1603 303281.4574 366254.2359 278422.4673 316576.1538 238166.4473 1.139969875 1.498547935 1.356079127 1.342402189 1.273401274 1.537807865 1.169024732 1.329222304 1 17.86161066 0.470286184 0.701232343 0.994891104 1.36741388 0.405347288 0.124587329 1.550922879 1.221028146 0.129000761 0.041396059 2.953154605 -0.470286184 0.372522776 LVILEGELERAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LVILEGELERAEER 14 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;; 210.14 5.16E-09 166235000 116130 241220 172812 203505 308518 108119 144848 167323 433631 FALSE TRUE 108861.6306 259080.1798 176911.1822 208727.2828 284288.2408 139331.2001 123129.3871 188213.6449 361255.1847 0.301342749 0.717166675 0.489712507 0.577783494 0.786945773 0.385686368 0.340837702 0.520999152 1 18.46265877 -1.779041514 2.582296033 1.128527029 0.521594828 0.495497637 0.15365499 23728124.7 16539616.44 19222054.75 0.037487795 0.016632537 1.779041514 -0.606932201 LVILFS(ph)Y(ph)MAGPLCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVILFSYMAGPLCK 14 0 Q9H617;Q5U3C3-2;Q5U3C3 Q9H617 RP13-360B22.2;TMEM164 Transmembrane protein 164 2 LVILFS(1)Y(1)MAGPLCK 46.926 0.086542 540510000 59374 342220 270580 234380 291590 239880 143380 187550 205380 TRUE FALSE 55657.88733 367558.3249 276998.2854 240394.5876 268689.6976 309129.4619 121881.5001 210966.0303 171100.7512 0.325293062 2.148198195 1.618919166 1.404988499 1.570359544 1.806710138 0.712337609 1.232993011 1 17.38448657 1.741219377 18.96865991 0.980429578 1.573080364 0.173149608 0.484049026 0.134646851 884.2078091 0.207324734 0.114813888 55.10859991 -1.741219377 0.592650786 LVINGNPITIFQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVINGNPITIFQER 14 0 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 395.04 6.37E-114 3955200000 1392770 1587480 1551140 1487360 1457990 1414800 1718720 1257470 1124130 FALSE TRUE 1305599.012 1705018.671 1587933.773 1525528.176 1343485.347 1823229.793 1461013.892 1414467.898 936505.4408 1.394117914 1.820618009 1.695594819 1.628958156 1.434572922 1.94684378 1.560069838 1.510368051 1 19.83692785 0.762846684 1.747842272 1.001100755 1.669508659 0.59735421 0.163805448 0.522906585 2.647834562 0.141931721 0.040172041 5.792241812 -0.762846684 0.668407904 LVINGNPITIFQERDPS(ph)K ddPTM_SK-BR-3_Pertuzumab_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 124.66 1.90E-05 2110083000 3096683 1810156 2214171 2147118 1838964 1727170 2873860 1771439 1700706 TRUE FALSE 2902867.139 1944181.834 2266692.182 2202216.683 1694539.185 2225775.941 2442951.373 1992607.059 1416847.182 2.048821621 1.3721888 1.599814159 1.55430784 1.195992911 1.570935786 1.724216559 1.406366956 1 20.43425273 -2.592663122 0.428965804 1.63E-22 1.561024313 0.388058286 0.223834464 105.9530346 4.750042383 98.64453916 0.118725175 0.002554682 2.592663122 1.561024313 LVINGNPITIFQERDPS(ph)KIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVINGNPITIFQERDPSKIK 20 2 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 LVINGNPITIFQERDPS(1)KIK 119.76 3.64E-05 1471900000 117640 82746 95302 92881 102520 62687 110540 78954 107670 TRUE FALSE 110277.1224 88872.59994 97562.60844 95264.48371 94468.49275 80783.71926 93965.5532 88811.5807 89699.18143 1.229410577 0.990784961 1.087664423 1.06204407 1.053170065 0.900607096 1.047563107 0.990104695 1 16.4528072 2.45696305 24.99333443 0.9898633 1.073013735 0.337178558 0.069085509 315.8626042 391622.9348 0.022008757 0.018415571 286.3934295 -2.45696305 0.083150435 LVINGNPITIFQERDPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LVINGNPITIFQERDPSK 18 1 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;; 277.07 3.65E-39 39761866000 14999370 14430730 15202142 15452044 14822701 11741941 15894898 11685359 14422310 FALSE TRUE 14060586.21 15499196.26 15562743.99 15848569.61 13658585.86 15131648.75 13511605.61 13144301.79 12015133.29 1.170239719 1.289972894 1.295261868 1.319050669 1.136781884 1.259382513 1.124548957 1.093978858 1 23.51834932 1.418056796 0.80452938 1.000973839 1.270818229 0.695516838 0.05678781 0.283001422 0.391051933 0.049100232 0.019773718 26.18525428 -1.418056796 0.26984439 LVKPGNQNTQVTEAWNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVKPGNQNTQVTEAWNK 17 1 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 263.59 1.88E-27 2659400000 4257100 3184000 3860200 3631400 3840900 2947500 4716000 3263400 4913900 FALSE TRUE 3990655.71 3419746.673 3951765.767 3724587.872 3539251.207 3798395.401 4008879.581 3670842.674 4093738.345 0.974819437 0.835360344 0.965319577 0.909825582 0.864552375 0.927854953 0.979271083 0.896696946 1 21.96498746 0.47915786 0.392981039 1.008427313 0.904074393 0.205190148 0.047282503 3.492641267 1.042061135 0.109460236 0.034735874 3.014101411 -0.47915786 -0.104352919 LVLEVAQHLGESTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVLEVAQHLGESTVR 15 0 P06576 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 ; 228.9 5.35E-13 1750260000 1426600 1670770 1456180 1493430 2075520 1651800 1442990 1687480 2319100 FALSE TRUE 1337311.653 1794475.549 1490721.277 1531753.942 1912517.031 2128647.845 1226627.046 1898165.593 1932027.228 0.692180541 0.928804482 0.77158399 0.79282213 0.989901697 1.101769072 0.634891179 0.982473521 1 20.881684 2.764311295 24.60629356 0.909277122 0.814296594 0.199032184 0.1344699 1500.194964 1433521.882 0.040926942 0.043394245 581.1808483 -2.764311295 -0.094980527 LVLTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 103.29 0.080996 233870000 152780 405980 159810 180290 388780 138970 226490 369410 393880 FALSE TRUE 143217.7725 436039.1816 163600.7687 184916.5466 358246.7871 179088.383 192529.9271 415531.6517 328138.8834 0.436454744 1.328825091 0.498571724 0.563531346 1.091753538 0.545770075 0.586733048 1.266328596 1 18.32394703 1.235852627 24.99999047 1.133164364 0.749723393 0.255405565 0.289031678 107.5907165 993175.0142 0.229956905 0.067521181 17.21284376 -1.235852627 -0.383440972 LVNACLAEELPHIHAFEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LVNACLAEELPHIHAFEQK 19 0 Q9H3K6;A0A087WZT3 Q9H3K6 BOLA2 BolA-like protein 2 0 ;;; 277.11 9.86E-40 2117069000 3102920 2707740 3114540 2771430 3054490 2528000 3680630 2614820 3418050 FALSE TRUE 2908713.776 2908223.887 3188418.36 2842549.586 2814602.677 3257792.561 3128753.701 2941286.033 2847555.374 1.021477511 1.021305473 1.119703725 0.998242075 0.988427724 1.144066448 1.098750785 1.032916185 1 21.44129247 2.247914042 24.9998491 1.081865037 1.039488158 0.084069276 0.052334361 409.3314742 1094062.95 0.018197623 0.015030865 176.9758642 -2.247914042 -0.042376879 LVNHFVEEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVNHFVEEFK 10 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 157.38 9.28E-06 3160100000 8244000 6941300 6215000 5326500 8926400 4177600 8692200 7941500 10355700 FALSE TRUE 7728022.756 7455241.074 6362422.735 5463187.008 8225356.551 5383605.302 7388885.304 8933013.756 8627266.77 0.895767218 0.864148666 0.737478382 0.63324656 0.953413957 0.62402212 0.856457265 1.035439612 1 23.04047214 1.352397092 4.472101753 1.015950974 0.786057917 0.448145258 0.105159644 0.182471588 5.519224289 0.071832503 0.024539874 22.51111942 -1.352397092 -0.229893058 LVNHFVEEFKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVNHFVEEFKR 11 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 213.16 2.25E-09 2167410000 3013300 3469100 2619800 2240130 4123100 1631640 3151200 3817600 4579400 FALSE TRUE 2824702.932 3725955.774 2681942.893 2297615.528 3799288.358 2102667.981 2678706.814 4294235.764 3815068.556 0.74040686 0.976641892 0.702986815 0.602247507 0.995863718 0.551148151 0.702138579 1.125598584 1 21.86327755 1.239087587 24.99999364 1.062799384 0.760350862 0.444583065 0.143749477 12.78564122 606829.9294 0.107903574 0.033928431 17.34153702 -1.239087587 -0.302448522 LVNLQHLDLLNNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVNLQHLDLLNNK 13 0 Q96AG4 Q96AG4 LRRC59 Leucine-rich repeat-containing protein 59 0 ; 217.09 2.64E-11 184680000 783140 786590 653290 635600 989410 599320 906970 873540 856760 FALSE TRUE 734124.6653 844829.942 668786.3473 651910.5721 911705.7297 772333.9549 770978.2684 982603.3919 713761.2211 1.028529771 1.183631048 0.936988908 0.913345462 1.27732595 1.082062085 1.080162729 1.376655614 1 19.445082 2.740291145 24.99976324 1.154006613 1.030519195 0.245159129 0.126952319 269.5501639 3894027.795 0.038305699 0.038832675 549.9094013 -2.740291145 -0.123487417 LVNWSCTLNSAISDIEVDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVNWSCTLNSAISDIEVDKK 20 1 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 161.8 3.53E-11 84013000 223620 114330 153650 160230 152840 155940 215100 133130 210550 FALSE TRUE 209624.0234 122795.1122 157294.6506 164341.7731 140836.5629 200957.3465 182847.7519 149751.5736 175407.8448 1.19506641 0.700054848 0.896736692 0.936912333 0.802909146 1.145657691 1.042414905 0.853733616 1 17.42035375 2.25080098 24.99917319 1.021734645 0.878287517 0.095507814 0.14378081 356.1183059 727319.6594 0.0469305 0.038994882 178.156216 -2.25080098 -0.143447128 LVPDSDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVPDSDVR 8 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 100.45 0.014179 279350000 405160 515260 453050 443090 511180 356950 460940 454750 608270 FALSE TRUE 379801.7588 553410.3865 463796.5599 454460.4395 471033.9848 459995.6704 391826.3262 511526.5385 506745.8074 0.749491665 1.092086759 0.915244987 0.896821311 0.929527147 0.907744403 0.773220657 1.00943418 1 18.95090272 3.541287653 7.279283986 0.899386622 0.962678341 0 0.106108669 0.695333668 67.28701367 0.02645886 0.040978101 3477.664269 -3.541287653 0.06329172 LVPGWTKPITIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVPGWTKPITIGR 13 1 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 89.466 0.0049003 0 2005600 2121800 1804800 1729400 2764100 1356300 2144700 1898600 3086300 FALSE TRUE 1880073.076 2278900.28 1847610.708 1773779.332 2547018.736 1747841.792 1823122.145 2135644.389 2571176.592 0.731211183 0.886325851 0.718585691 0.689870675 0.990604358 0.679782866 0.709061428 0.830609767 1 21.29399727 0.977499498 21.33435463 1.000000005 0.774543306 0.352958806 0.09696707 287.0852603 272208.1943 0.088064116 0.022016029 9.495099009 -0.977499498 -0.225456699 LVPLLDRPFDETTYEETED ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LVPLLDRPFDETTYEETED 19 1 O15270 O15270 SPTLC2 Serine palmitoyltransferase 2 0 ;;; 165.73 1.74E-10 209359000 214712 207495 213926 185424 280698 205833 229237 210276 265240 FALSE TRUE 201273.5592 222858.1457 219000.4257 190182.2938 258653.1114 265253.6457 194865.04 236529.4215 220969.7305 0.910864844 1.008546036 0.991087898 0.860671248 1.170536393 1.200407156 0.881863048 1.070415486 1 17.75348923 2.74434777 24.99994518 1.054163033 0.961800666 0.270323012 0.096424792 870.0261628 3758434.869 0.030384883 0.031436026 555.0700184 -2.74434777 -0.092362366 LVPLLDTGDIIIDGGNSEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVPLLDTGDIIIDGGNSEYR 20 0 P52209-2;P52209;K7EM49;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 226.19 1.07E-24 29288000 32941 38480 30450 32079 37048 35373 37603 33699 38405 FALSE TRUE 30879.28161 41329.09924 31172.28838 32902.20145 34138.39952 45584.61087 31964.77924 37906.39433 31994.95739 0.965129637 1.291737905 0.974287541 1.028355845 1.066993123 1.424743603 0.999056784 1.184761519 1 14.96555692 -1.534522019 5.583127085 0.999696826 1.120371682 0.057452535 0.148184891 0.000509841 4.25E-05 0.130809534 0.030755106 0.029206397 1.534522019 0.120674856 LVPLLDTGDIIIDGGNSEYRDTTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LVPLLDTGDIIIDGGNSEYRDTTR 24 1 P52209-2;P52209;K7EM49;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;;; 229.59 2.43E-33 620159000 108969.5 200840.6 147833.5 163750.7 195698.1 128832.6 195097.9 145694.7 343506.7 FALSE TRUE 102149.2935 215711.047 151340.1804 167952.8202 180328.7606 166024.4802 165844.7811 163885.004 286173.2126 0.35694918 0.753777913 0.528841183 0.586892179 0.630138506 0.580153812 0.579525874 0.572677654 1 18.12652911 -1.61919051 2.48150879 1.046808502 0.587522275 0.649418206 0.097981577 3999920.361 3354487.572 1207678.383 0.022126428 0.024033083 1.61919051 -0.459286227 LVPS(ph)QEETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVPSQEETK 9 0 P49321;P49321-3;P49321-4 P49321 NASP Nuclear autoantigenic sperm protein 1 LVPS(1)QEETK;LVPS(1)QEETK 160.88 6.81E-05 750230000 2011680 1207220 1485930 1378530 1331760 1245000 1865710 1296790 991140 TRUE FALSE 1885772.54 1296603.825 1521176.961 1413905.414 1227168.942 1604411.289 1585964.106 1458697.086 825712.331 2.283812981 1.570285166 1.842260197 1.71234625 1.486194278 1.943063254 1.920722322 1.766592349 1 19.65527972 -1.926313506 2.175318673 0.448290835 1.798011372 0.577135809 0.218955591 4568315.785 1982200.012 12809850.62 0.048770717 0.011849131 1.926313506 1.349720537 LVPS(ph)QEETKLSVEESEAAGDGVDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVPSQEETKLSVEESEAAGDGVDTK 25 1 P49321;P49321-3;P49321-4 P49321 NASP Nuclear autoantigenic sperm protein 1 LVPS(1)QEETKLSVEESEAAGDGVDTK;LVPS(1)QEETKLSVEESEAAGDGVDTK 307.16 1.63E-64 456870000 914400 515360 598210 639080 753170 408600 822240 542250 993550 TRUE FALSE 857169.3363 553517.7906 612399.8237 655479.8748 694019.0663 526556.1869 698952.7453 609951.1061 827720.0864 1.035578755 0.668725817 0.739863432 0.791910074 0.838470732 0.636152481 0.844431296 0.736905043 1 19.65878344 -1.350191112 2.945999717 1.002769462 0.772154676 0.259551637 0.110997317 18121171.42 22395116.2 434097.1035 0.023873732 0.044648707 1.350191112 -0.230614786 LVPTGPTHREPS(ph)PVRYDNLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LVPTGPTHREPSPVRYDNLSR 21 2 Q9C0B5;Q9C0B5-2 Q9C0B5 ZDHHC5 Palmitoyltransferase ZDHHC5 1 LVPT(0.027)GPT(0.027)HREPS(0.945)PVRYDNLS(0.001)R;LVPTGPTHREPS(1)PVRYDNLSR;LVPTGPTHREPS(1)PVRYDNLSR;LVPTGPTHREPS(1)PVRYDNLSR 177.41 3.38E-17 820708000 204191 254476 216367 224788 334459 172854 232301 255678 412583 TRUE FALSE 191411.0498 273317.6678 221499.3274 230556.4406 308191.9393 222754.1437 197469.6216 287599.9611 343720.2319 0.55688037 0.795174803 0.644417485 0.670767733 0.896636016 0.648068176 0.574506832 0.836726891 1 18.39087525 0.993085215 6.558798378 0.999919702 0.690433206 0.525202436 0.099505899 0.093038804 23.92723981 0.092043464 0.023107762 9.84204203 -0.993085215 -0.309486496 LVPVHYDETEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVPVHYDETEAER 13 0 Q8NEJ9-2;Q8NEJ9;H0YJ17 Q8NEJ9-2 NGDN Neuroguidin 0 ; 188.09 6.40E-06 273640000 182412 226908 208178 214252 233795 194547 232344 195381 236109 FALSE TRUE 170995.1585 243708.5044 213116.0805 219750.069 215433.6838 250709.5607 197506.1742 219774.7479 196700.8826 0.869315665 1.238980228 1.083452589 1.117178867 1.095234963 1.274572627 1.004093991 1.117304331 1 17.58564391 0.893861928 1.229983884 1.004211657 1.118191688 0.052167869 0.113344823 1.425025484 4.270000703 0.095427826 0.029378099 7.831806129 -0.893861928 0.113980031 LVPVS(ph)PLPPK ddPTM_SK-BR-3_Pertuzumab_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 121.08 0.0005503 265730000 1848340 1660290 1839740 1749910 1844320 1466490 2132030 1523320 2474640 TRUE FALSE 1732655.699 1783219.599 1883379.502 1794815.653 1699474.547 1889841.857 1812351.894 1713509.855 2061606.597 0.840439539 0.864965994 0.913549415 0.870590759 0.824344736 0.916684036 0.879096864 0.831152683 1 20.97533763 -1.473154189 3.412196606 1.002024442 0.872936723 0.634790155 0.031328645 3369610.6 2910288.939 46450.43384 0.007012455 0.033639212 1.473154189 -0.129087719 LVQAEYWHDPIKEDVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LVQAEYWHDPIKEDVYR 17 1 A0A2C9F2P4;A0A286YFF7;P50897;Q5T0S4;A0A286YFE3;A0A286YFL8;P50897-2 A0A2C9F2P4 PPT1 Palmitoyl-protein thioesterase 1 0 ;;;; 306.26 2.92E-47 4008980000 5584780 4893310 5396830 4682900 6128080 4516700 6564790 5342950 8566280 FALSE TRUE 5235238.589 5255615.764 5524845.356 4803071.142 5646805.316 5820597.968 5580460.684 6010029.069 7136512.528 0.733585006 0.736440347 0.774166 0.673027774 0.791255574 0.815608176 0.781959068 0.842152108 1 22.7667878 0.392765379 0.440386646 1.023266819 0.733492654 0.856025126 0.032827432 0.862970794 0.292185429 0.070366785 0.019682927 2.470389192 -0.392765379 -0.289774165 LVQAFQFTDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVQAFQFTDK 10 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ; 244.61 4.10E-12 2640900000 2429110 2595300 2122130 2044400 2835700 1668400 2572860 2416130 2986800 FALSE TRUE 2277076.341 2787458.712 2172467.926 2096862.765 2612995.561 2150039.996 2187083.528 2717789.149 2488283.785 0.91511923 1.120233444 0.873078842 0.842694382 1.050119595 0.864065429 0.878952611 1.092234401 1 21.2467196 3.96179915 21.20634142 0.930695073 1.027868394 0.080434371 0.096944752 102.4450925 141789.4084 0.022780821 0.04138993 9157.96859 -3.96179915 0.097173321 LVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSK 34 2 P32119 P32119 PRDX2 Peroxiredoxin-2 0 ; 227.4 8.20E-37 1639640000 2493700 1020620 1538700 1350680 1418890 1109270 2189600 1324540 1443840 FALSE TRUE 2337623.768 1096187.767 1575198.691 1385340.735 1307456.103 1429498.242 1861289.807 1489911.735 1202853.776 1.943398121 0.911322547 1.30955127 1.151711673 1.086961797 1.188422292 1.547394907 1.238647427 1 20.19802984 LVQAFQYTDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVQAFQYTDK 10 0 Q13162;H7C3T4 Q13162 PRDX4 Peroxiredoxin-4 0 ; 143.04 8.07E-05 299350000 289180 316430 266356 273730 359550 220874 326570 294064 387890 FALSE TRUE 271080.74 339858.8064 272674.0901 280754.3752 331312.3934 284636.7382 277603.8602 330778.5377 323148.6531 0.838873185 1.051710422 0.843803889 0.868808743 1.025263111 0.880822914 0.859059314 1.023611067 1 18.30183845 1.221112264 24.96000842 1.011805641 0.915483213 0.247852297 0.073377829 410.9756331 587887.7997 0.066988344 0.016907784 16.63842692 -1.221112264 -0.096322428 LVQS(ph)PNSYFMDVK ddPTM_SK-BR-3_Pertuzumab_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(0.965)PNS(0.034)YFMDVK;LVQS(0.712)PNS(0.287)Y(0.001)FMDVK 103.88 0.00090472 0 142865 150668 151747 149460 161066 119743 171768 120962 177640 TRUE FALSE 133923.3347 161823.6155 155346.5105 153295.3966 148416.5261 154310.8602 146012.983 136064.372 147990.7364 0.904944039 1.09347125 1.049704287 1.035844542 1.002877137 1.042706212 0.986635965 0.919411412 1 17.17514735 1.56915556 4.088674871 0.957626101 1.032763571 0.174812009 0.052352188 0.220148528 8.284019525 0.029743048 0.012787233 37.08135194 -1.56915556 0.07513747 LVREDENDAS(ph)DDEDDDEKRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 207.6 3.59E-21 1055710000 284466 201417 219344 235389 292864 161317 257479 219720 423220 TRUE FALSE 266661.7808 216330.1243 224546.9433 241429.4803 269863.6428 207886.5991 218872.4143 247152.5257 352581.8479 0.756311712 0.613560016 0.63686473 0.684747334 0.765392899 0.589612314 0.620770512 0.700979155 1 18.42759868 0.873087206 6.554120315 0.999999265 0.656987872 0.759747502 0.058244963 1.441977425 74.39753419 0.054226231 0.013612651 7.465986599 -0.873087206 -0.343011393 LVRLS(ph)SDSFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVRLSSDSFAR 11 1 A0A087WSV0;Q9HB09-3;Q9HB09 A0A087WSV0 BCL2L12 Bcl-2-like protein 12 1 LVRLS(0.9)S(0.1)DSFAR 212.46 3.54E-09 229860000 112850 140100 123190 131560 131540 116930 139500 121760 113270 TRUE FALSE 105786.9199 150473.1498 126112.125 134936.0523 121209.379 150685.7928 118583.2701 136962.004 94364.50525 1.121045669 1.594594804 1.336436032 1.429944999 1.284480628 1.596848226 1.256651214 1.451414424 1 16.52595668 -2.73240194 0.544783071 3.39E-06 1.399085456 0.395929351 0.147663003 237.229991 10.91952524 279.3708078 0.055967721 0.001851817 2.73240194 1.399082061 LVRLSS(ph)DSFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVRLSSDSFAR 11 1 A0A087WSV0;Q9HB09-3;Q9HB09 A0A087WSV0 BCL2L12 Bcl-2-like protein 12 1 LVRLS(0.25)S(0.629)DS(0.122)FAR 187.97 2.03E-06 233910000 73600 88327 76711 79642 85564 72396 86415 76995 85905 TRUE FALSE 68993.50738 94866.82298 78530.62115 81685.74855 78844.14859 93295.54995 73457.87299 86607.99524 71566.90053 0.964042132 1.325568416 1.09730365 1.141390055 1.10168455 1.303613112 1.026422444 1.210168312 1 16.12700488 -4.468215451 0.315914459 0.028495171 1.16148445 0.127363648 0.11312534 393.8306332 4.885125001 252.0432199 0.092549308 3.40E-05 4.468215451 1.132989279 LVRPPVQVYGIEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVRPPVQVYGIEGR 14 1 A0A494C0K9;H7C0C1;P48047;H7C086 A0A494C0K9 ATP5O "ATP synthase subunit O, mitochondrial" 0 145.49 7.81E-06 938150000 729860 740820 625410 637900 920420 601260 722310 792150 1154800 FALSE TRUE 684179.3654 795671.0836 640245.0205 654269.594 848133.926 774834.0014 614006.3211 891051.6712 962056.4197 0.711163453 0.827052413 0.665496334 0.680074038 0.881584394 0.805393515 0.638222778 0.926194819 1 19.87576198 1.072261612 5.823179709 0.998656095 0.745334781 0.59532232 0.076281903 0.12242671 6.665384609 0.071808748 0.018082842 11.81031856 -1.072261612 -0.253321314 LVS(ph)PEPPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 72.2 0.045984 82613000 394890 341860 403330 405570 456710 309580 372870 335660 509050 TRUE FALSE 370174.5398 367171.6701 412897.1781 415977.6128 420841.8389 398950.7204 316961.6051 377567.8899 424086.2664 0.872875566 0.865794767 0.973616009 0.980879707 0.992349605 0.940730111 0.747398891 0.890309165 1 18.69399824 1.873930473 19.93933856 0.849367457 0.937334289 0.076379572 0.074751058 5.240828841 811.4087561 0.029689539 0.019150249 74.80497335 -1.873930473 0.087966832 LVS(ph)PETEASEESLQFNLEKPATGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LVSPETEASEESLQFNLEKPATGER 25 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LVS(0.949)PET(0.051)EASEESLQFNLEKPATGER;LVS(0.91)PET(0.09)EASEESLQFNLEKPATGER;LVS(0.876)PET(0.124)EASEESLQFNLEKPATGER 229.7 1.91E-34 320228000 239117 214159 189023 209467 222093 149446 206769 190246 229504 TRUE FALSE 224151.0938 230015.5552 193506.7148 214842.2778 204650.7117 192588.6341 175765.908 213998.6319 191198.2997 1.172348782 1.203020924 1.012073408 1.123662073 1.070358429 1.007271688 0.919285936 1.119249659 1 17.54471017 4.157977523 0.49692393 0.99739433 1.271760208 0.485367969 0.062530173 2.129282405 0.61306162 0.042462513 0.32162915 14387.24113 -4.157977523 0.274365877 LVS(ph)PGSANETSSILVESVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LVSPGSANETSSILVESVTR 20 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;A0A0A0MT44 O75369-8 FLNB Filamin-B 1 LVS(0.98)PGS(0.02)ANETSSILVESVTR;LVS(1)PGSANETSSILVESVTR;LVS(1)PGSANETSSILVESVTR;LVS(1)PGSANETSSILVESVTR;LVS(1)PGSANETSSILVESVTR;LVS(0.5)PGS(0.5)ANETSSILVESVTR;LVS(0.899)PGS(0.098)ANET(0.003)SSILVESVTR;LVS(0.995)PGS(0.004)ANETSSILVESVTR 399.62 1.01E-131 3293655000 247523 259703 252422 250726 278973 216337 264346 244398 286282 TRUE FALSE 232030.9773 278931.6803 258409.569 257160.0536 257063.5859 278789.98 224709.7714 274911.6283 238499.6847 0.972877501 1.169526411 1.083479709 1.078240644 1.077836166 1.168932279 0.94218058 1.152670825 1 17.86362783 1.746563118 24.99999998 1.028231489 1.098760993 0.120453044 0.074950198 3.051153485 9556.782739 0.03086849 0.017117977 55.79086791 -1.746563118 0.070529504 LVSDSLSEHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVSDSLSEHEK 11 0 Q96KR1;H0Y8W1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 ; 209.85 1.48E-08 390780000 630110 691900 739860 702000 820540 615650 893420 744780 1290110 FALSE TRUE 590672.5399 743128.9959 757409.8286 720014.5085 756098.0983 793378.1608 759459.9651 837767.4225 1074782.307 0.54957412 0.691422804 0.70470999 0.6699166 0.703489529 0.738175681 0.70661748 0.779476381 1 20.03561305 -5 0.154143695 2.136900505 0.602223966 0.881829355 0.038837374 43.45872335 0.392783572 15.03285283 0.17723091 1.00E-05 5 -1.53467654 LVSELS(ph)GGTGGDEEEEWLYGGPWDVHVHSDLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVSELSGGTGGDEEEEWLYGGPWDVHVHSDLAK 33 0 Q6UN15;A0A0B4J203 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 LVS(0.039)ELS(0.789)GGT(0.172)GGDEEEEWLYGGPWDVHVHSDLAK 94.48 0.00032365 35172000 26644 29687 33226 28980 30695 24523 36765 26004 36140 TRUE FALSE 24976.3996 31885.05637 34014.13641 29723.67586 28284.33852 31602.392 31252.42956 29250.65664 30108.00053 0.829560222 1.059022712 1.129737472 0.987235132 0.939429322 1.049634365 1.038010795 0.971524383 1 14.87785928 LVSFHDDS(ph)DEDLLHI ddPTM_SK-BR-3_Pertuzumab_2h_R1 18 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;LVS(0.004)FHDDS(0.996)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVS(0.002)FHDDS(0.998)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI 337.89 2.38E-69 5932363100 1388958.6 2141803.5 1893569.9 1896565.8 2080308.1 1604330.8 2533475.8 1955267.1 1709827.3 TRUE FALSE 1302026.161 2300384.86 1938486.272 1945234.889 1916929.093 2067475.058 2153604.623 2199386.502 1424446.078 0.914057879 1.614932917 1.360870238 1.365607951 1.34573651 1.451423883 1.511889188 1.544029315 1 20.44196958 2.237771149 24.64611761 1.430533003 1.368028815 0 0.229225906 101.2542046 3160864.711 0.075632582 0.059141016 172.8905074 -2.237771149 -0.062504187 LVSFHDDSDEDLLHI ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LVSFHDDSDEDLLHI 15 0 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 0 ;;; 262.24 5.45E-25 132555000 91047 146622 138458 135377 151581 146404 151549 145337 137466 FALSE TRUE 85348.53079 157478.0454 141742.2891 138851.003 139676.4397 188668.4581 128825.6344 163482.6444 114522.0365 0.745258584 1.375089461 1.237685719 1.212439171 1.219646838 1.647442395 1.124898214 1.427521282 1 16.80526571 4.744043191 24.41562863 1.2915559 0.745258257 0.47612067 0.17614125 340.2742464 1515283.498 0.036686787 0.316611995 55468.08733 -4.744043191 -0.546297643 LVSPET(ph)EASEESLQFNLEKPATGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVSPETEASEESLQFNLEKPATGER 25 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LVS(0.002)PET(0.998)EASEESLQFNLEKPATGER 185.48 2.76E-17 208950000 154840 140410 143610 147600 153880 104100 147000 140540 149620 TRUE FALSE 145148.8408 150806.1025 147016.497 151387.6659 141794.8855 134151.9801 124958.7147 158086.7284 124647.4554 1.164474961 1.20986106 1.17945847 1.214526726 1.13756743 1.076251253 1.002497117 1.268270803 1 16.92749391 2.451027877 3.367754405 1.07801035 1.192506534 0.303953661 0.074421983 0.258695792 6.172499122 0.024778363 0.021046098 282.5061306 -2.451027877 0.114496184 LVSPGS(ph)ANETSSILVESVTR ddPTM_SK-BR-3_Pertuzumab_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(0.002)PGS(0.998)ANETSSILVESVTR 144.72 1.61E-07 39235000 17351 17871 17705 19494 23483 15662 18986 17183 21880 TRUE FALSE 16265.03188 19194.18743 18124.97096 19994.24904 21638.73991 20183.36515 16139.22556 19328.33537 18228.08665 0.892306044 1.053000669 0.994343033 1.096892363 1.187109779 1.107267347 0.885404259 1.060360078 1 14.15387551 -1.873727551 2.145030042 0.983169974 1.03140266 0.012494168 0.092874398 13546331.47 6305837.767 1156877.768 0.02270693 0.013374343 1.873727551 0.048232685 LVSS(ph)PELGHDEFSTQALAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LVSSPELGHDEFSTQALAR 19 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 1 LVS(0.235)S(0.765)PELGHDEFSTQALAR;LVS(0.023)S(0.977)PELGHDEFSTQALAR 232.79 1.41E-21 104235000 40151 54820 49509 47802 56245 48585 51278 39080 62246 TRUE FALSE 37638.02058 58878.92984 50683.37686 49028.68025 51827.74458 62610.70079 43589.33994 43959.22403 51856.74048 0.725807682 1.135415171 0.977372978 0.94546398 0.999440846 1.207378254 0.840572306 0.847705113 1 15.66224391 1.615992861 25 0.883101625 1.010858389 0.110263969 0.132349273 1.077848122 3305.931511 0.056957469 0.030895807 41.30407125 -1.615992861 0.127756764 LVTDQNISENWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LVTDQNISENWR 12 0 P24666;F2Z2Q9;G5E9R5;P24666-4 P24666 ACP1 Low molecular weight phosphotyrosine protein phosphatase 0 ;;; 213.13 2.83E-08 565764000 251838 281671 269123 285490 308685 210019 260380 240753 281897 FALSE TRUE 236075.9091 302526.2139 275506.7246 292816.1567 284442.1253 270648.0759 221338.4362 270811.542 234846.5696 1.00523465 1.288186642 1.173134976 1.246840255 1.211182798 1.152446367 0.942481028 1.153142422 1 17.84135899 1.934859497 6.439147782 1.029235279 1.198877121 0.375126727 0.08966405 0.206654973 16.39075613 0.035000161 0.021624832 86.07152478 -1.934859497 0.169641842 LVTSGAESGNLNT(ph)SPSSNQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVTSGAESGNLNTSPSSNQTR 21 0 Q8NHV4-2;Q8NHV4;Q8NHV4-3 Q8NHV4-2 NEDD1 Protein NEDD1 1 LVTSGAESGNLNT(0.778)S(0.222)PSSNQTR 281.71 5.41E-44 233020000 284440 299170 333600 337840 326050 290710 346080 282280 268410 TRUE FALSE 266637.4081 321320.8581 341513.1495 346509.5464 300443.3482 374633.2577 294188.5168 317523.2794 223610.637 1.192418266 1.43696589 1.527267012 1.549611195 1.343600431 1.675382096 1.315628455 1.419982894 1 17.77062929 0.40739254 1.169029932 0.999838059 1.453985448 0.505940295 0.134066728 2.004660915 3.236645481 0.117382816 0.035484086 2.555009619 -0.40739254 0.454147389 LVTSGAESGNLNTS(ph)PSSNQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVTSGAESGNLNTSPSSNQTR 21 0 Q8NHV4-2;Q8NHV4;Q8NHV4-3 Q8NHV4-2 NEDD1 Protein NEDD1 1 LVTSGAESGNLNT(0.004)S(0.996)PSSNQTR 231.93 2.55E-35 0 114690 116730 129170 131790 127650 108590 126810 103830 106510 TRUE FALSE 107511.7576 125372.8107 132233.9734 135171.9545 117624.8839 139938.1702 107796.0177 116793.4041 88732.79292 1.211635001 1.412925329 1.490249197 1.523359629 1.325607817 1.577073882 1.214838553 1.316237213 1 16.43717976 0.90002291 1.008848782 1.005976924 1.426637731 0.539108755 0.116760405 0.458654318 0.953165805 0.101033317 0.033144092 7.943701376 -0.90002291 0.420660807 LVTSIGDVVNHDPVVGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LVTSIGDVVNHDPVVGDR 18 0 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;;; 284.46 1.53E-39 2876340000 2979630 3471020 3366880 3465780 3558700 3202130 3878400 3327610 3381830 FALSE TRUE 2793140.277 3728017.932 3446743.984 3554717.782 3279214.057 4126532.949 3296869.925 3743069.433 2817380.726 0.991396105 1.32322121 1.223385946 1.261710123 1.16392294 1.464669972 1.170189707 1.328563584 1 21.4259231 -1.113389511 4.749033111 0.999985065 1.249142014 0.268545118 0.124274721 1.74E-05 3.24E-06 0.103520714 0.024398565 0.077021237 1.113389511 0.249156949 LVVADTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LVVADTR 7 0 P22314;P22314-2;Q5JRR9;Q5JRS0 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 103.29 0.019566 419597000 832560 1443150 946850 1003440 1530330 771410 1084080 1310120 1347270 FALSE TRUE 780451.5558 1550002.328 969309.7291 1029189.969 1410144.055 994103.5442 921532.2681 1473691.366 1122401.933 0.695340531 1.380969046 0.863603047 0.916953133 1.256362817 0.885693008 0.821035888 1.312980067 1 20.09815797 LVVEEYYEVLDHCSSILNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVVEEYYEVLDHCSSILNK 19 0 O00170;E9PMH2;V9GYQ3 O00170 AIP AH receptor-interacting protein 0 141.13 1.68E-07 221990000 102550 123020 122650 118450 124880 142900 144580 116470 99446 FALSE TRUE 96131.57856 132128.5288 125559.3159 121489.6275 115072.4285 184152.9102 122901.5712 131011.5359 82847.82015 1.160339263 1.594834101 1.515541576 1.46641912 1.388961452 2.222785221 1.483461737 1.581351635 1 16.33817612 LVVHLY(ph)HLCQMFPES(ph)AS(ph)DAIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVVHLYHLCQMFPESASDAIK 21 0 P78316;E9PFK5;P78316-2 P78316 NOP14 Nucleolar protein 14 3 LVVHLY(1)HLCQMFPES(1)AS(1)DAIK 48.685 0.053888 86366000 82588 197840 175750 165220 241700 163250 170030 171730 254880 TRUE FALSE 77418.9645 212488.2795 179918.873 169459.8249 222717.857 210377.6249 144535.58 193170.8685 212338.8814 0.364600981 1.000703583 0.847319491 0.798063095 1.048879298 0.990763554 0.680683533 0.909729143 1 17.69600904 4.745715515 24.71883582 0.894311393 0.36460069 0.698684044 0.112066551 439.3516276 1517833.588 0.026780709 0.272634433 55682.08836 -4.745715515 -0.529710702 LVVLDEELEGISPDELKDELPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LVVLDEELEGISPDELKDELPER 23 1 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 ;;;; 266.35 3.66E-44 311581000 409070 268047 325871 301259 304984 245583 419332 287949 463692 FALSE TRUE 383467.0389 287893.4788 333600.814 308989.816 281031.7869 316478.8254 356457.0595 323900.0665 386298.8096 0.992669481 0.745261108 0.863582299 0.799872555 0.727498454 0.819259127 0.922749567 0.838470268 1 18.55935771 0.844991126 0.875789877 0.995875034 0.819310738 0.289397689 0.07822834 0.902621809 1.408891338 0.069436006 0.02392722 6.99827696 -0.844991126 -0.176564296 LVWFDLDLSTKPYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LVWFDLDLSTKPYR 14 1 Q14137;Q14137-2 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 113.35 0.00049324 36138000 225490 272000 236570 263530 304470 211940 297860 271220 295090 FALSE TRUE 211376.9834 292139.163 242181.5521 270292.626 280558.1544 273123.6374 253198.6582 305082.414 245837.5726 0.859823749 1.188342204 0.985128309 1.099476468 1.141233829 1.110992248 1.029942882 1.240991809 1 17.9073459 4.753654086 24.49873644 1.094189659 0.859823527 0.467831299 0.080161455 1863.548542 3024722.457 0.017291455 0.399467116 56709.27382 -4.753654086 -0.234366132 LWDFQGFECIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LWDFQGFECIR 11 0 P43034;I3L3N5;P43034-2 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ; 149.23 8.02E-05 145470000 159393 220678 169099 164337 247111 159018 194008 200775 217888 FALSE TRUE 149416.8767 237017.2287 173110.1081 168554.1656 227703.8989 204923.9152 164918.3015 225842.2007 181521.0852 0.823137855 1.305728359 0.953663912 0.928565216 1.254421207 1.128926234 0.908535233 1.244165109 1 17.46977761 -1.471119165 6.118222975 0.999958565 1.071314446 0.016485443 0.164648488 8.48E-05 7.33E-06 0.145223216 0.034209575 0.033797209 1.471119165 0.071355881 LWDMFDSWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LWDMFDSWR 9 0 A0A0B4J2E5;Q15269 A0A0B4J2E5 PWP2 Periodic tryptophan protein 2 homolog 0 110.12 0.0058046 0 96548 141400 95247 106950 170520 62458 102760 127000 129370 FALSE TRUE 90505.23302 151869.4031 97506.30382 109694.5181 157128.047 80488.61068 87352.09198 142856.2296 107777.3112 0.83974291 1.409103654 0.90470158 1.017788594 1.457895407 0.746804775 0.810486836 1.325475909 1 16.71769398 2.206604005 24.99999779 0.931994628 1.129405264 0.080553603 0.24528973 395.4317664 309348.2988 0.086696371 0.064034917 160.9177698 -2.206604005 0.197410636 LWDVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LWDVDR 6 0 Q9BZK7;A0A0D9SF63 Q9BZK7 TBL1XR1 F-box-like/WD repeat-containing protein TBL1XR1 0 ;;;;; 129.2 0.037913 698664000 1689380 2011160 1945600 1939800 2104870 1709760 2005900 1749630 1910030 FALSE TRUE 1583644.721 2160068.379 1991750.551 1989578.552 1939562.001 2203339.956 1705133.917 1968075.157 1591233.654 0.995230787 1.357480326 1.251702128 1.25033715 1.218904588 1.384674055 1.071579848 1.236823487 1 20.60171426 0.741472246 0.827868787 1.002843241 1.250764792 0.241341804 0.11762183 1.185871282 1.556194756 0.103199092 0.035795868 5.514069637 -0.741472246 0.247921551 LWDWDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LWDWDKK 7 1 P35606;P35606-2;D6RBT6 P35606 COPB2 Coatomer subunit beta 0 ; 112.17 0.010285 652300000 2541200 2473900 2519900 2784600 3577900 1898130 3450200 2954000 3254500 FALSE TRUE 2382150.828 2657070.13 2579673.218 2856057.55 3296906.167 2446089.317 2932874.54 3322813.403 2711302.925 0.878600029 0.979997515 0.951451494 1.053389322 1.215985914 0.902182229 1.081721453 1.225541186 1 21.37055488 3.198675526 4.590897857 1.079302895 0.947205289 0.329763333 0.096420256 0.244702209 11.44800879 0.026556348 0.03315321 1580.067085 -3.198675526 -0.132097606 LWEAGWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LWEAGWK 7 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 119.89 0.01089 443730000 948350 1059160 924220 936750 1193780 754370 1078940 984710 1296700 FALSE TRUE 888994.4664 1137581.308 946142.9348 960788.5909 1100025.334 972144.3728 917162.9634 1107653.211 1080272.393 0.822935467 1.05305043 0.875837373 0.889394746 1.018285149 0.899906708 0.849010832 1.025346217 1 20.04296371 1.209226608 24.98800447 1.012673289 0.923218159 0.237955263 0.071267192 375.1437269 319555.0974 0.065783184 0.016456326 16.18924547 -1.209226608 -0.08945513 LWELIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LWELIK 6 0 G3V529;Q9GZR7;Q9GZR7-2;A0A1W2PRR2;F5GYL3;A0A087WXU8 G3V529 DDX24 ATP-dependent RNA helicase DDX24 0 ; 101.52 0.084748 42151000 185436 186006 203531 185147 200171 164663 208910 157018 221130 FALSE TRUE 173829.8918 199778.0778 208358.8514 189898.1855 184450.3771 212198.535 177585.8849 176622.0429 184221.9744 0.943589343 1.08444217 1.131020618 1.030811802 1.001239823 1.15186332 0.963977753 0.958745793 1 17.49108563 1.620061529 12.51218615 0.970803066 1.065361965 0.28488036 0.060881677 0.098252282 58.65975584 0.028497724 0.015041828 41.69284482 -1.620061529 0.094558899 LWGIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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" 0 104.25 0.079083 83422000 94638 117280 109630 101830 119590 109580 122030 105950 140400 FALSE TRUE 88714.77651 125963.5332 112230.4754 104443.1302 110197.8838 141213.9671 103732.7344 119178.0907 116966.333 0.758464203 1.076921282 0.959510934 0.89293327 0.942133356 1.207304389 0.886859763 1.018909354 1 16.83573381 LWLDNTENDLNQGDDHGFSPLHWACR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LWLDNTENDLNQGDDHGFSPLHWACR 26 0 A0A0A0MTH3;Q13418;Q13418-2;A0A087WWY6 A0A0A0MTH3 ILK Integrin-linked protein kinase 0 ; 215.68 2.39E-34 349820000 107431 152487 146692 156017 196887 125308 162356 143885 137556 FALSE TRUE 100707.0855 163777.2961 150171.6035 160020.6604 181424.2892 161482.3854 138012.225 161849.359 114597.015 0.87879327 1.429158484 1.31043207 1.396377213 1.583150218 1.409132563 1.204326527 1.412334859 1 16.80620994 -1.281692475 3.773918465 0.999341735 1.338720274 0.232805617 0.186196175 268.2431639 42953330.87 46828.998 0.039974976 0.052276623 1.281692475 0.339378539 LWLFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LWLFGK 6 0 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 0 100.78 0.086717 21265000 68388 92249 71656 69534 103930 57933 79651 83069 90956 FALSE TRUE 64107.71716 99079.21195 73355.71416 71318.36016 95767.75703 74657.31664 67708.07199 93440.34751 75774.856 0.846028888 1.307547347 0.96807461 0.94118767 1.263846111 0.985251844 0.893542734 1.233131311 1 16.20943158 LWPSGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 LWPSGDR 7 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;;;;;; 196.94 0.0010086 5178130000 2386490 3006850 2619660 2794610 3289440 2359830 2879160 2784660 3123250 FALSE TRUE 2237123.851 3229480.303 2681799.572 2866324.424 3031100.651 3041074.612 2447456.687 3132330.931 2601959.398 0.859784304 1.241172443 1.030684635 1.101602287 1.164930035 1.168763285 0.940620629 1.203835438 1 21.31116702 -1.722049278 2.626491453 0.982839705 1.092249423 0.051943167 0.118638279 32554234.7 22387427.95 3626281.518 0.02577768 0.018964907 1.722049278 0.109409718 LWSLDSDEPVADIEGHTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LWSLDSDEPVADIEGHTVR 19 0 O43172-2;O43172 O43172-2 PRPF4 U4/U6 small nuclear ribonucleoprotein Prp4 0 ; 199.09 7.10E-16 169123000 224420 292630 284090 280960 282660 266590 306590 243230 268260 FALSE TRUE 210373.9528 314296.6297 290828.749 288169.9093 260461.0238 343550.2053 260619.6757 273597.8009 223485.673 0.941330824 1.406339053 1.301330618 1.289433481 1.165448417 1.537235925 1.166158315 1.224229711 1 17.76982282 -0.923891141 5.8444225 0.999999859 1.274823878 0.1933196 0.157980644 2.59E-07 4.74E-08 0.135634919 0.031969441 0.119154064 0.923891141 0.274824019 LWSLGQDDMAIPSKPPAAS(ph)PEKPSALLGNSLALPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LWSLGQDDMAIPSKPPAASPEKPSALLGNSLALPR 35 2 Q8TEH3;Q8TEH3-7;Q8TEH3-6 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 LWS(0.001)LGQDDMAIPS(0.034)KPPAAS(0.901)PEKPS(0.046)ALLGNS(0.018)LALPR 44.178 0.056618 34899000 56676 41739 45674 42911 56908 29631 52134 36004 52303 TRUE FALSE 53128.75033 44829.39899 46757.40885 44012.16891 52438.67524 38184.98868 44316.99069 40499.17865 43573.29141 1.219296239 1.028827466 1.073074981 1.010072168 1.203459127 0.876339323 1.017067778 0.929449609 1 15.41115647 2.229625834 24.99734182 0.960672106 1.087271344 0.477816287 0.076971269 184.0806546 515008.4173 0.026052055 0.019523765 169.6781164 -2.229625834 0.126599238 LWSWGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LWSWGR 6 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 206.72 0.00025101 908380000 979340 1236170 1171720 1120170 1390700 957490 1205490 1166870 1074800 FALSE TRUE 918044.8576 1327697.313 1199513.752 1148915.459 1281480.032 1233901.819 1024737.966 1312556.288 895408.9365 1.025279981 1.482783183 1.339626737 1.283118151 1.431167347 1.378031611 1.144435714 1.465873563 1 19.77218719 -2.993751597 0.484622761 3.42E-15 1.330597441 0.318998557 0.143792609 255.8280033 8.960696544 265.364618 0.064785522 0.001014491 2.993751597 1.330597441 LYANMFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LYANMFER 8 0 Q02790;H0YFG2 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 96.111 0.02134 251900000 1094860 1205330 963310 888970 1413160 775750 1128600 1182970 1428640 FALSE TRUE 1026334.667 1294573.887 986160.1681 911782.4752 1302176.114 999696.4318 959376.9074 1330666.409 1190190.755 0.862327877 1.08770286 0.828573205 0.766080959 1.094090262 0.839946393 0.80606987 1.118027848 1 20.18276139 1.229606355 24.99908593 1.059013943 0.904137438 0.255425056 0.114017056 312.8818008 873491.5128 0.101158112 0.026769501 16.96705058 -1.229606355 -0.154876506 LYAVHQEGNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LYAVHQEGNK 10 0 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 77.677 0.032282 361080000 286450 549830 213620 236680 647770 119120 287370 528070 677500 FALSE TRUE 268521.6058 590539.9853 218687.1673 242753.6095 596896.7572 153508.0102 244281.5363 594000.7019 564420.8732 0.475747122 1.04627595 0.387454075 0.430093253 1.057538418 0.271974368 0.432800323 1.052407397 1 19.10641182 1.226714542 24.81797324 1.02620415 0.598488574 0.321243852 0.26554678 284.3403065 595683.2509 0.240884566 0.062205752 16.85444834 -1.226714542 -0.427715576 LYDDIDFDIEEFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LYDDIDFDIEEFAK 14 0 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ;; 236.69 6.62E-17 381710000 1345623 1082816 1171264 1177714 1266075 884994 1519670 1117310 1140799 FALSE TRUE 1261402.858 1162988.823 1199046.935 1207936.135 1166642.577 1140477.401 1291809.591 1256808.613 950392.2771 1.327244433 1.22369347 1.261633711 1.270986901 1.227537939 1.200007017 1.359238309 1.322410381 1 19.85816359 -1.381329759 3.582576112 0.998359884 1.270301921 0.744440179 0.050426524 4096883.598 1580022.446 51801.85844 0.01196594 0.041559493 1.381329759 0.271942037 LYDIDVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LYDIDVAK 8 0 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3;K7EMA7 P62750 RPL23A 60S ribosomal protein L23a 0 ; 133.55 0.002128 144753000 343790 311570 330270 323830 365410 265793 395220 308210 406570 FALSE TRUE 322272.7976 334638.967 338104.1604 332140.026 336712.1726 342523.1243 335960.43 346690.697 338710.8405 0.951468802 0.98797832 0.998208855 0.980600519 0.994099191 1.011255276 0.991879769 1.023559495 1 18.36969464 6.709849871 0.767392171 1.000185968 7.18E-16 0.6439716 0.011337065 29.75065369 1.02888966 0.003640578 46.54959503 5126841.265 -6.709849871 -1.000185968 LYDLNHNEIGELIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LYDLNHNEIGELIR 14 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;; 214.45 6.87E-12 1213140000 738120 916210 865260 857040 881620 780680 978060 795080 877240 FALSE TRUE 691922.3868 984047.1417 885784.3758 879033.0974 812381.1215 1006049.643 831408.9829 894347.4882 730822.9768 0.946771528 1.346491795 1.212036846 1.202798934 1.111597674 1.376598266 1.137633886 1.223753928 1 19.47916247 -0.22105349 1.162759094 0.998206144 1.211338716 0.193059861 0.120767886 33.04722377 28.98924291 0.387624867 0.031351106 0.601099698 0.22105349 0.213132572 LYEEGSNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LYEEGSNKR 9 1 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;;;; 137.69 0.00025254 7405170000 5168213 4558370 4322920 4270143 4833290 3237383 4922860 4115421 4817510 FALSE TRUE 4844743.774 4895876.458 4425461.704 4379722.099 4453702.9 4171962.918 4184722.845 4629240.371 4013436.459 1.207131052 1.219871426 1.10266146 1.091264841 1.109698122 1.039498933 1.042678235 1.15343557 1 21.93640663 3.827693104 0.958704013 1.065205892 1.233123049 0.65835982 0.041485161 0.406240406 0.656646208 0.01410461 0.052813198 6725.01263 -3.827693104 0.167917157 LYEIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LYEIAR 6 0 Q7Z5M8-2;Q7Z5M8 Q7Z5M8-2 ABHD12B Abhydrolase domain-containing protein 12B 0 ;;;;; 130.84 0.036268 1938928000 2022130 2689360 1885400 2038630 3161560 2235410 1920840 1721590 2928080 FALSE TRUE 1895568.493 2888483.013 1930122.578 2090944.697 2913263.831 2880736.578 1632827.874 1936534.301 2439364.532 0.777074713 1.184112901 0.791239912 0.857167787 1.19427162 1.180937306 0.66936608 0.793868352 1 21.21807394 1.728791125 24.99993889 0.798385111 0.997381346 0.180592373 0.174906738 1.212595104 3087.425827 0.078190446 0.043360589 53.55390268 -1.728791125 0.198996235 LYELDGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LYELDGLR 8 0 Q5LJB0;Q5LJA5;Q5LJA9;Q9Y5K5-2;Q9Y5K5-4;Q9Y5K5-3;Q9Y5K5;H0Y4E0;H0Y6Y4 Q5LJB0 UCHL5 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L5 0 ;; 100.15 0.014677 158556000 281581 530736 302661 305243 557815 199852 263861 453936 503657 FALSE TRUE 263957.3478 570032.2457 309840.2618 313076.0522 514006.46 257546.0281 224297.4926 510610.9088 419593.393 0.629078895 1.358534846 0.738429792 0.74614152 1.225010853 0.613799055 0.534559162 1.216918372 1 18.67863244 2.215757374 24.99960269 0.767080608 0.960392142 0 0.292051544 586.5179423 643005.9812 0.10444501 0.077190474 164.3453323 -2.215757374 0.193311534 LYENFISEFEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 LYENFISEFEHR 12 0 Q9UNM6;J3KNQ3;A0A087WUL9;E9PQG3;E9PPD2 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ;;;;;; 232.42 1.12E-12 971115100 1397394 1605972 1564311 1586257 1612880 1297132 1553533 1581635 1004656.3 FALSE TRUE 1309933.604 1724879.838 1601417.196 1626963.04 1486210.911 1671592.951 1320595.149 1779105.611 836972.6732 1.565085272 2.060855621 1.913344661 1.94386638 1.77569825 1.9971894 1.577823496 2.125643606 1 19.67482099 -1.815028078 2.668167264 0.719505546 1.873917456 0.682661409 0.186384084 15466010.85 11183873.28 27986157.56 0.041214718 0.015309885 1.815028078 1.15441191 LYFHSDTCLPLRPQEMEVDS(ph)EDEKDPEWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LYFHSDTCLPLRPQEMEVDSEDEKDPEWLR 30 2 J3QQW9;Q15022 J3QQW9 SUZ12 Polycomb protein SUZ12 1 LYFHSDTCLPLRPQEMEVDS(0.999)EDEKDPEWLR;LY(0.001)FHS(0.007)DT(0.022)CLPLRPQEMEVDS(0.97)EDEKDPEWLR;LYFHSDTCLPLRPQEMEVDS(1)EDEKDPEWLR;LYFHSDT(0.001)CLPLRPQEMEVDS(0.999)EDEKDPEWLR 85.239 0.0012078 509830000 282592 203092 206842 217447 244069 183433 282469 220820 268051 TRUE FALSE 264905.0712 218129.143 211748.3899 223027.0582 224900.8053 236387.1293 240115.3958 248389.8631 223311.5564 1.18625778 0.976792901 0.948219579 0.998726003 1.007116734 1.058553051 1.075248409 1.112301876 1 17.76869839 2.192635947 3.96422651 1.069941981 1.005330691 0.03170072 0.069587087 0.40977425 13.47866195 0.02627623 0.019344258 155.8245737 -2.192635947 -0.06461129 LYFLQCETCHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LYFLQCETCHSR 12 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ; 250.69 2.69E-17 1210610000 1252980 1978710 1208660 1219180 2082150 972950 1390550 1703740 1743240 FALSE TRUE 1174558.218 2125215.747 1237329.986 1250466.223 1918626.338 1253824.87 1182049.937 1916455.689 1452281.982 0.808767328 1.46336302 0.851990179 0.861035417 1.321111438 0.863348087 0.813925912 1.319616791 1 20.46989017 3.855013407 8.279621333 0.985084626 1.178848743 0.038149399 0.240419409 0.54808095 35.61617869 0.057014132 0.103123492 7161.655178 -3.855013407 0.193764117 LYGDADYLEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LYGDADYLEER 11 0 P17812;B4E1E0;P17812-2;A0A3B3IRI2 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ;; 152.54 7.65E-05 675420000 1237980 1035090 1092110 1058260 1101820 925650 1169980 962320 1223010 FALSE TRUE 1160497.042 1111729.141 1118015.365 1085416.743 1015287.502 1192870.128 994552.3606 1082467.77 1018881.73 1.138990923 1.091126779 1.097296508 1.065301998 0.996472379 1.170764077 0.976121498 1.062407675 1 19.95855517 7.999999762 0.12054019 0.973680028 1.4651402 0.309735918 0.051953768 104.695455 0.866220783 0.309285961 8.652419925 99999945.09 -7.999999762 0.491460173 LYGPTNFAPIINHVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LYGPTNFAPIINHVAR 16 0 Q99829;B0QZ18;F2Z2V0;A6PVH9;E7ENH5;Q5JX45;H0Y524 Q99829 CPNE1 Copine-1 0 ; 189.86 9.50E-10 545420000 257590 417070 258420 251950 435260 219034 318510 345250 296230 FALSE TRUE 241467.9017 447950.2968 264549.8444 258415.4636 401076.4354 282265.5601 270752.3824 388355.2225 246787.2993 0.978445416 1.815127027 1.071975119 1.047118163 1.625190747 1.143760481 1.097108251 1.573643472 1 17.91290862 -4.999999999 0.135721783 0.039573513 1.412908066 0.053154027 0.291462842 356.1394348 3.001721519 94.15574993 1.840335479 1.00E-05 4.999999999 1.373334553 LYHEADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LYHEADK 7 0 O75663 O75663 TIPRL TIP41-like protein 0 ; 66.682 0.068362 83537000 841770 600320 688090 676740 639190 488070 780970 605240 671690 FALSE TRUE 789085.1183 644768.3174 704411.8197 694106.2941 588990.5958 628967.8858 663870.7987 680805.5463 559580.5997 1.410136661 1.152234938 1.258821017 1.2404045 1.052557212 1.123998734 1.186372078 1.216635363 1 19.09398642 8 0.059443065 0.781949453 2.021402606 0.480308813 0.082091482 336.4464588 1.494273211 6.360748597 36.20129081 100000000 -8 1.239453153 LYKDDQLLDDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LYKDDQLLDDGK 12 1 B8ZZU8;Q15370;Q15370-2 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 ;;; 182.33 1.55E-05 2043480000 5769070 3407950 4231260 4152150 4307780 3122140 5348210 3638190 4959840 FALSE TRUE 5407994.207 3660278.164 4331627.485 4258701.199 3969464.336 4023451.134 4546295.561 4092426.03 4132010.662 1.308804514 0.885834637 1.048309852 1.030660748 0.960661688 0.973727191 1.100262301 0.990420007 1 21.97841255 4.752565336 24.91263116 1.00261168 1.308804731 0.747697916 0.056565771 1254.249639 2231112.094 0.013831529 0.287371556 56567.28515 -4.752565336 0.306193051 LYKEELEQTYHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LYKEELEQTYHAK 13 1 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ; 119.01 0.00022956 1020408000 805280 732640 729040 693200 785280 458140 945880 667270 957730 FALSE TRUE 754878.9623 786885.4279 746333.1731 710988.6856 723607.2765 590397.5807 804054.0751 750580.1283 797878.6758 0.946107454 0.986221905 0.935396816 0.891098744 0.906913919 0.739959092 1.007739772 0.940719625 1 19.60580986 1.60238386 25 0.980674067 0.91170189 0.241162119 0.066622142 0.901875108 4095.793099 0.035280681 0.017059267 40.02984053 -1.60238386 -0.068972177 LYLEDDDPVQAEAYINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LYLEDDDPVQAEAYINR 17 0 D6RFN0;Q9BT78;D6RAX7;Q9BT78-2;D6RD63 D6RFN0 COPS4 COP9 signalosome complex subunit 4 0 ;;;;; 241.51 5.35E-20 172288000 306107 324126 323754 331553 364906 302209 355346 298343 330933 FALSE TRUE 286948.3093 348124.6263 331433.5978 340061.2113 336247.7547 389451.8323 302065.1662 335591.7803 275698.1444 1.040806096 1.262702101 1.202161148 1.233454843 1.219622843 1.412602298 1.095637284 1.217243522 1 18.07273003 -0.305574843 7.246259368 1.000003169 1.215509882 0.311889949 0.09802693 0 0 0.085144643 0.020068785 0.494794835 0.305574843 0.215506713 LYNLDVFQYELYNPMALYGSVPVLLAHNPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LYNLDVFQYELYNPMALYGSVPVLLAHNPHR 31 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 203.19 4.89E-26 1262110000 80923 365880 32107 31676 341760 42361 52206 275690 34073 FALSE TRUE 75858.17388 392970.1359 32868.5932 32488.85979 314919.5482 54589.93303 44378.19496 310110.5034 28385.99618 2.672380191 13.84380289 1.15791579 1.144538299 11.09418694 1.92312902 1.563383391 10.92477084 1 14.79289175 3.945446311 12.86561633 4.039181747 8.861182247 0.116391413 4.676617778 2.334669256 947.2988867 1.09752164 1.986702782 8819.547647 -3.945446311 4.8220005 LYNNHEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 LYNNHEIR 8 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;;; 154.49 0.0004242 2788400000 1809940 2697790 1919640 1973260 2414590 1646580 2202020 2164380 2761430 FALSE TRUE 1696659.086 2897537.179 1965174.767 2023897.192 2224957.841 2121920.916 1871847.544 2434607.607 2300529.493 0.737508078 1.259508816 0.854227156 0.879752769 0.967150322 0.92236197 0.813659442 1.058281415 1 21.13353452 3.739837063 24.65880009 0.913495918 1.042116372 0.013214109 0.143785179 637.3231016 1235903.028 0.033114443 0.059184029 5493.347383 -3.739837063 0.128620454 LYNSEESRPYTNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LYNSEESRPYTNK 13 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 0 ; 225.32 1.15E-11 537550000 504690 432780 528500 507080 537320 431910 605590 469100 632480 FALSE TRUE 473102.3538 464823.4815 541036.2696 520092.5313 495121.0546 556595.4055 514787.4015 527668.1676 526915.002 0.897872241 0.882160272 1.026799897 0.987052047 0.939660197 1.056328636 0.976983763 1.001429387 1 19.00721073 4.05138462 3.618119599 0.996789501 0.890606445 0.681585217 0.030666895 0.122486332 3.112062306 0.007229469 0.016828671 11256.01389 -4.05138462 -0.106183055 LYPLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LYPLRK 6 1 P42766 P42766 RPL35 60S ribosomal protein L35 0 ; 120.78 0.031965 2848900000 1796500 1862450 1884390 1809480 2137650 1520740 2252300 1681720 2404500 FALSE TRUE 1684060.272 2000347.736 1929088.621 1855914.32 1969767.592 1959752.951 1914588.524 1891686.444 2003173.416 0.840696196 0.998589398 0.963016285 0.926487095 0.983323548 0.97832416 0.955777722 0.944344822 1 20.93385589 4.74719026 24.9575198 0.967722292 0.840696131 0.753589044 0.023002646 529.6299168 1531691.811 0.005263596 0.061403069 55871.49086 -4.74719026 -0.127026162 LYPPGDEEEAELADSSGLYHEGSPSPGS(ph)PWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 LYPPGDEEEAELADSSGLYHEGSPSPGSPWK 31 0 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 LYPPGDEEEAELADSSGLYHEGS(0.016)PS(0.05)PGS(0.934)PWK;LYPPGDEEEAELADSSGLYHEGSPS(0.001)PGS(0.999)PWK;LYPPGDEEEAELADSSGLYHEGSPSPGS(1)PWK;LYPPGDEEEAELADSSGLYHEGSPS(0.001)PGS(0.999)PWK 407.93 1.93E-175 661070000 258985 229758 255626 230273 274302 238149 315556 237239 318169 TRUE FALSE 242775.5912 246769.5214 261689.5694 236182.195 252759.4274 306898.7503 268241.3073 266858.8114 265064.5384 0.915911244 0.930979009 0.987267369 0.891036562 0.953576925 1.157826513 1.011984888 1.006769193 1 18.01598415 2.445172188 24.99962912 1.04687637 0.938746721 0.537989217 0.050050684 144.3884219 112980.885 0.016220044 0.013570767 278.7226022 -2.445172188 -0.108129649 LYPPSAEYPDLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LYPPSAEYPDLRK 13 1 P12532;F8WCN3;C9JSQ1;C9J8F6;C9JJX8;C9J995 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ; 168.61 4.80E-05 756120000 841970 890170 751040 831240 1120660 669170 1009210 898760 1340420 FALSE TRUE 789272.6007 956079.113 768855.0235 852571.0257 1032647.884 862348.5159 857888.3295 1010972.164 1116695.243 0.706793197 0.856168341 0.688509267 0.763476903 0.924735635 0.772232641 0.768238546 0.905325039 1 20.09080408 1.045301816 3.398249099 0.998808064 0.783545908 0.543430909 0.067650988 0.15536868 3.882882431 0.061595785 0.01605696 11.09945912 -1.045301816 -0.215262156 LYQAGEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LYQAGEGR 8 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;;;; 171.38 0.00079201 978040000 1446520 2045030 1615190 1495120 1880610 739460 1926840 1684670 2670870 FALSE TRUE 1355984.895 2196446.149 1653503.07 1533487.31 1732914.477 952930.0979 1637928.23 1895004.758 2225084.543 0.609408258 0.987129301 0.743119211 0.689181593 0.778808375 0.428266917 0.736119549 0.851655172 1 21.08542872 0.993240326 3.395800337 0.998394402 0.729641335 0.314014457 0.139825537 0.299948895 8.793534507 0.138410695 0.035957617 9.845557789 -0.993240326 -0.268753067 LYQPEYQEVSTEEQREEISGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LYQPEYQEVSTEEQREEISGK 21 1 A0A494C039;Q9Y4L1;A0A087X054 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 244.91 3.17E-30 274530000 155780 172780 145870 187570 204470 101130 161320 155120 203910 FALSE TRUE 146030.0079 185572.811 149330.1053 192383.3638 188411.751 130324.5893 137131.5636 174487.0735 169876.1037 0.859626544 1.092400914 0.879053039 1.132492208 1.109112741 0.767174349 0.807244578 1.027143134 1 17.3741234 2.240456093 24.99996532 0.871884636 1.012041375 0.168192439 0.118774519 70.01447068 923454.5319 0.040591271 0.032359892 173.9626815 -2.240456093 0.140156739 LYQTDPSGTYHAWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LYQTDPSGTYHAWK 14 0 O14818;H0Y586;O14818-2;Q8TAA3-2;Q8TAA3-5;Q8TAA3;A0A087WYS6 O14818 PSMA7;PSMA8 Proteasome subunit alpha type-7;Proteasome subunit alpha type-7-like 0 ; 212.39 2.50E-09 3006300000 4002400 6296100 3875700 3661600 7110200 2714800 4322600 5987300 6094400 FALSE TRUE 3751896.928 6762269.795 3967633.434 3755562.855 6551793.573 3498518.689 3674466.259 6734827.585 5077205.269 0.738968927 1.331888202 0.781460119 0.739690963 1.290433068 0.689063866 0.723718279 1.326483218 1 22.27560316 3.861569321 8.69307486 0.905049977 1.074585811 0.008894169 0.265864109 0.733814216 51.05960649 0.063404563 0.114604994 7270.584417 -3.861569321 0.169535833 LYSGS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LYSGSPTR 8 0 Q6PJI9-4;Q6PJI9-3;Q6PJI9;H3BMH3 Q6PJI9-4 WDR59 WD repeat-containing protein 59 1 LYSGS(0.646)PT(0.354)R;LYSGS(0.947)PT(0.052)R 147.41 0.00056407 896600000 543610 698030 624100 669810 835170 568890 808150 702530 819950 TRUE FALSE 509586.4205 749712.8675 638903.9467 686998.4586 769579.1171 733119.3078 686975.41 790242.417 683095.0479 0.745996362 1.0975235 0.935307537 1.005714301 1.126606201 1.073231771 1.00568056 1.156855725 1 19.38172681 4.74507833 24.7756602 1.042944059 0.74599621 0.671175133 0.066729909 404.8126828 1538760.52 0.015330285 0.146347212 55600.453 -4.74507833 -0.296947849 LYSILQGDS(ph)PTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LYSILQGDSPTK 12 0 O15042-2;O15042;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 LY(0.006)S(0.007)ILQGDS(0.98)PT(0.007)K 52.928 0.09351 16853000 34813 44626 45329 46892 47053 35058 53340 44017 62309 TRUE FALSE 32634.11647 47930.15547 46404.22529 48095.32811 43357.64718 45178.67548 45342.16218 49512.61934 51909.22537 0.628676622 0.923345612 0.893949485 0.926527564 0.835258991 0.870340005 0.873489478 0.953830827 1 15.66370334 4.741527187 24.91583215 0.900287821 0.628676518 0.777170363 0.047038409 118.6457362 996437.5812 0.01014608 0.071670246 55147.67237 -4.741527187 -0.271611303 LYSLLGIDLTAPS(ph)NNSSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LYSLLGIDLTAPSNNSSPR 19 0 A3KN83-3;A3KN83-2;A3KN83;A3KN83-4 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 1 LYSLLGIDLTAPS(0.333)NNS(0.333)S(0.333)PR 140.46 1.83E-07 99072000 83617 94240 98282 102320 118210 104470 115480 90535 102460 TRUE FALSE 78383.56123 101217.6277 100613.2955 104945.7044 108926.2634 134628.7931 98164.84606 101838.494 85358.76408 0.918283694 1.185790689 1.178710781 1.229466072 1.276099351 1.577211134 1.150026563 1.193064299 1 16.38125167 5.492421309 0.946271929 1.253298371 6.65E-14 0.292005449 0.145896761 8.724684726 2.198390377 0.042204316 15.7628739 310757.278 -5.492421309 -1.253298371 LYSLLGIDLTAPSNNS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LYSLLGIDLTAPSNNSSPR 19 0 A3KN83-3;A3KN83-2;A3KN83;A3KN83-4 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 1 LYSLLGIDLTAPS(0.086)NNS(0.457)S(0.457)PR 148.36 1.01E-07 58966000 95911 94720 111250 106740 112020 103380 114030 101980 101920 TRUE FALSE 89908.10172 101733.1674 113888.9025 109479.1291 103222.4011 133224.1278 96932.2601 114712.4275 84908.89357 1.058877321 1.198145013 1.341307109 1.289371755 1.215684208 1.569024423 1.141603147 1.351006033 1 16.37362805 -1.182016248 4.205001602 0.999902994 1.272944829 0.27601349 0.137699048 0.000115994 2.26E-05 0.120783161 0.02845855 0.065763323 1.182016248 0.273041835 LYSNWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LYSNWR 6 0 Q9Y5B9;G3V5A4;G3V401;G3V2X0 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 99.919 0.088987 371060000 227480 345530 261290 254120 392440 196090 302380 300640 366380 FALSE TRUE 213242.4329 371113.4007 267487.9222 260641.1494 361619.3454 252697.9997 257040.9262 338175.5658 305228.8111 0.698631404 1.215853115 0.876352141 0.853920534 1.1847484 0.827896943 0.842125372 1.107941169 1 18.21953162 LYTDFDEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 LYTDFDEIR 9 0 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;F8VZ52;B4DDQ3;B4DPZ9;F8VUJ9;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 0 ;;;; 180.03 0.00011427 330955000 639049 764207 697022 633954 720804 591404 737202 742960 558674 FALSE TRUE 599052.0638 820789.6814 713555.691 650222.3329 664194.9614 762132.7342 626665.4039 835720.1915 465427.7002 1.287100152 1.763517043 1.533118228 1.397042618 1.427063669 1.637488989 1.346429109 1.79559616 1 18.82819755 -1.332910211 3.797241332 0.998447384 1.530510729 0.485484515 0.169201772 8989380.712 3156279.19 114645.0446 0.037627314 0.046461132 1.332910211 0.532063345 LYTLQDK ddPTM_SK-BR-3_Pertuzumab_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 ;; 124.83 0.0095567 1163200000 3552340 3654970 3312900 3354030 4022440 2666460 4301100 3849470 4501650 FALSE TRUE 3330005.381 3925587.782 3391483.552 3440100.088 3706533.788 3436223.716 3656189.984 4330084.803 3750295.533 0.887931458 1.046740916 0.904324345 0.917287733 0.988331121 0.916254115 0.974907165 1.154598288 1 21.83857286 1.39119096 7.296893296 1.07618395 0.951497499 0.459699998 0.058771674 0.192943875 13.34218005 0.035720138 0.01312444 24.6144967 -1.39119096 -0.124686451 LYTWVEWVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LYTWVEWVK 9 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 152.59 0.00018634 165957000 451110 539750 455360 441490 595590 357810 555270 534440 523780 FALSE TRUE 422875.8304 579713.6516 466161.3542 452819.3808 548814.7639 461103.9384 472012.4184 601166.0104 436357.7343 0.969103552 1.328528421 1.068300886 1.037725117 1.257717512 1.056710818 1.081709756 1.377690741 1 18.73515184 3.756023238 24.68505367 1.124013354 1.181666844 0 0.141903164 1349.269919 1152396.353 0.033014755 0.059504526 5701.947814 -3.756023238 0.05765349 LYVELHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 LYVELHR 7 0 A0A087WTZ5;Q04323;E9PJ81;E9PRQ7;Q04323-2 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 0 ; 107.43 0.0074794 175417000 190125 286310 223010 214911 306750 183545 233980 247120 270520 FALSE TRUE 178225.4156 307508.6903 228299.9025 220425.9801 282659.0924 236531.4619 198896.8712 277973.476 225368.4644 0.7908179 1.364470806 1.013007313 0.978069317 1.254208716 1.049532207 0.882540828 1.233417802 1 17.78192613 2.007444349 24.87541894 1.010710504 1.108998611 0 0.176411298 489.1643231 1634541.26 0.061730025 0.045505397 101.7289002 -2.007444349 0.098288107 LYVYNTDTDNCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 LYVYNTDTDNCR 12 0 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 0 ;; 231.38 8.33E-12 298630000 405130 402310 398760 400980 406210 368770 485490 333920 438990 FALSE TRUE 379773.6365 432097.451 408218.7755 411269.8257 374307.9052 475227.9125 412695.2816 375610.647 365719.733 1.03842807 1.181498869 1.116206588 1.124549179 1.023482933 1.299431968 1.128446852 1.027045065 1 18.48037895 1.217104726 5.205643946 1.007988377 1.138425599 0.288443331 0.075912357 0.204886537 14.48208243 0.061295584 0.017098598 16.48559879 -1.217104726 0.130437221 MADKDGDLIATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MADKDGDLIATK 12 1 O43852;O43852-3;O43852-15;O43852-6;O43852-10;O43852-2;O43852-4;O43852-8 O43852;O43852-2 CALU Calumenin 0 150.12 6.19E-05 423670000 2460700 1782500 1856500 1845700 2087600 1071000 2144500 1882100 2801100 FALSE TRUE 2306689.179 1914478.155 1900537.057 1893063.787 1923648.317 1380180.314 1822952.134 2117084.328 2333578.314 0.988477295 0.820404502 0.814430373 0.811227879 0.824334159 0.591443752 0.781183182 0.907226604 1 21.15411245 MAGNEALS(ph)PTSPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 MAGNEALSPTSPFR 14 0 Q86WR7;Q86WR7-2;D3DRR9 Q86WR7 PROSER2;C10orf47 Proline and serine-rich protein 2 1 MAGNEALS(0.942)PT(0.057)SPFR;MAGNEALS(0.755)PT(0.142)S(0.103)PFR;MAGNEALS(0.757)PT(0.121)S(0.121)PFR;MAGNEALS(0.867)PT(0.133)SPFR;MAGNEALS(0.79)PT(0.207)S(0.002)PFR 157.54 5.53E-06 603441000 680929 845759 870984 1049333 1187505 568180 608856 544749 712078 TRUE FALSE 638310.8694 908379.8764 891644.1518 1076260.661 1094243.147 732204.3424 517563.6951 612762.1118 593227.5816 1.075996614 1.531250239 1.503038934 1.814245822 1.844558786 1.234272251 0.872453863 1.032929235 1 19.17822615 2.011518133 5.944046332 0.97548244 1.556165244 0.619784725 0.210561597 0.101706051 13.46077175 0.083545569 0.058044041 102.6876306 -2.011518133 0.580682804 MAGNEALSPTS(ph)PFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MAGNEALSPTSPFR 14 0 Q86WR7;Q86WR7-2;D3DRR9 Q86WR7 PROSER2;C10orf47 Proline and serine-rich protein 2 1 MAGNEALSPTS(1)PFR;MAGNEALSPT(0.005)S(0.995)PFR;MAGNEALSPT(0.006)S(0.994)PFR 199.33 2.18E-08 450440000 1167170 1467780 1466540 1968400 2194980 984810 1056040 918110 1135370 TRUE FALSE 1094118.913 1576455.958 1501327.021 2018912.476 2022595.125 1269108.66 897696.6058 1032738.055 945869.4122 1.156733582 1.666674002 1.587245556 2.134451596 2.138344996 1.341737711 0.949070341 1.091839995 1 19.85128149 2.012003892 6.914335148 1.03981746 1.727329085 0.587229845 0.278197098 0.105732041 25.20108798 0.110906516 0.078474068 102.8025511 -2.012003892 0.687511624 MAGTAFDFENMKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MAGTAFDFENMKR 13 1 P31150 P31150 GDI1 Rab GDP dissociation inhibitor alpha 0 68.83 0.079148 139940000 216710 249740 201820 210880 301630 139250 205740 233690 423790 FALSE TRUE 203146.5079 268231.0095 206607.2657 216291.5378 277941.1965 179449.2145 174891.197 262866.7109 353056.7112 0.575393418 0.759739161 0.58519569 0.612625482 0.787242354 0.508273059 0.495362902 0.744545289 1 18.42954042 0.984645041 20.79887798 1.000000006 0.622103732 0.628292765 0.093611983 65.0412993 88102.23285 0.092856796 0.023214199 9.652616248 -0.984645041 -0.377896274 MAKPEEVLVVENDQGEVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MAKPEEVLVVENDQGEVVR 19 1 O14980 O14980 XPO1 Exportin-1 0 182.34 2.69E-14 61441000 169000 153820 148280 142380 157800 75332 150180 162340 193490 FALSE TRUE 158422.5917 165208.9928 151797.2716 146033.7118 145407.0245 97079.12549 127661.9032 182608.5064 161195.269 0.982799264 1.024899762 0.941698057 0.905942915 0.902055162 0.602245501 0.791970534 1.132840359 1 17.29844988 3.228507114 1.627945381 0.845486254 0.999204711 0.065248059 0.138614476 0.63377555 3.46187057 0.045716941 0.065588918 1692.415965 -3.228507114 0.153718458 MALIQLGSVEEAIQALIELHNHDLGENHHLR ddPTM_SK-BR-3_Pertuzumab_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 ;; 287.87 2.95E-73 662724000 658289 765906 658423 649984 745187 404608 596363 714149 604982 FALSE TRUE 617087.8666 822614.4772 674041.1045 666663.6899 686663.019 521411.7613 506943.9045 803312.0747 504006.5959 1.224364664 1.632150222 1.337365642 1.322728106 1.362408795 1.034533607 1.005827917 1.593852305 1 18.94308309 2.720815944 1.43286744 1.14597108 1.440669784 0.185180531 0.202143124 0.514854167 2.140420162 0.08251697 0.077911915 525.7943852 -2.720815944 0.294698704 MALIQMGSVEEAVQALIDLHNHDLGENHHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 19 MALIQMGSVEEAVQALIDLHNHDLGENHHLR 31 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ;;;;;;;;;;;;;;;;;; 277.01 3.62E-72 10994390200 5476797.1 6859311 5818424 5558838 6315816 3577999.3 5125476.8 6373437 5618139 FALSE TRUE 5134014.146 7367181.524 5956439.765 5701487.194 5819797.288 4610909.614 4356959.136 7169174.639 4680435.306 1.096909541 1.574037678 1.272625167 1.218153189 1.243430772 0.985145465 0.930887589 1.53173245 1 22.15821128 2.998724417 1.397735378 1.09473325 1.376192747 0.123812076 0.20373049 0.551432817 2.222962631 0.074491863 0.08970081 997.0671705 -2.998724417 0.281459497 MALLQEFASRPLGAAPQAEHQGLPVPGS(ph)PGGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MALLQEFASRPLGAAPQAEHQGLPVPGSPGGQK 33 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 MALLQEFASRPLGAAPQAEHQGLPVPGS(1)PGGQK;MALLQEFASRPLGAAPQAEHQGLPVPGS(1)PGGQK 144.97 2.18E-10 303660000 464590 454760 407890 470080 595860 228150 378120 436990 686420 TRUE FALSE 435512.1412 488430.9036 417565.3434 482143.0486 549063.5592 294013.2013 321424.4163 491549.1634 571852.0676 0.761581825 0.854121077 0.730198188 0.843125479 0.960149644 0.514142062 0.562076164 0.85957399 1 19.12528246 2.243987542 24.99996214 0.676402726 0.820164154 0.030933292 0.15292267 225.9844027 1041035.26 0.050532234 0.04114185 175.3830192 -2.243987542 0.143761428 MALPPQEDATAS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 MALPPQEDATASPPR 15 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MALPPQEDATAS(1)PPR;MALPPQEDATAS(1)PPR;MALPPQEDATAS(1)PPR;MALPPQEDATAS(1)PPR;MALPPQEDATAS(1)PPR;MALPPQEDAT(0.004)AS(0.996)PPR;MALPPQEDATAS(1)PPR;MALPPQEDAT(0.002)AS(0.998)PPR;MALPPQEDATAS(1)PPR;MALPPQEDATAS(1)PPR;MALPPQEDAT(0.002)AS(0.998)PPR;MALPPQEDATAS(1)PPR;MALPPQEDAT(0.101)AS(0.899)PPR;MALPPQEDAT(0.02)AS(0.98)PPR 240.17 1.31E-17 9778830000 7042002 7464512 7451467 7345629 7271706 6404263 7940741 6516604 6460935 TRUE FALSE 6601255.665 8017192.235 7628219.316 7534130.276 6700615.543 8253069.764 6750100.605 7330216.354 5382563.209 1.22641489 1.489474795 1.417209426 1.399729085 1.244874474 1.533297324 1.254068061 1.361844918 1 22.35986193 -0.346772618 0.480803628 0.936040467 1.401315162 0.551715501 0.102924383 4.763762935 1.07734248 0.618345155 0.047787874 0.450015406 0.346772618 0.465274695 MALPPQEDATAS(ph)PPRQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MALPPQEDATASPPRQK 17 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MALPPQEDAT(0.483)AS(0.517)PPRQK;MALPPQEDAT(0.159)AS(0.841)PPRQK 105.22 0.00049179 1180390000 914580 916600 839130 890460 1151960 587400 1125370 734310 1789920 TRUE FALSE 857338.0704 984466.0177 859034.5599 913310.7111 1061489.708 756972.8444 956631.2159 825990.2199 1491170.789 0.574942909 0.660196689 0.576080598 0.612478945 0.711849854 0.507636583 0.641530282 0.553920601 1 20.50801407 -1.43991257 3.348574948 1.005192259 0.608731962 0.823111678 0.057546175 14839337.41 22500724.55 745846.4691 0.012142335 0.036315116 1.43991257 -0.396460298 MANS(ph)SPVLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MANSSPVLSK 10 0 Q9NXE8 Q9NXE8 CWC25 Pre-mRNA-splicing factor CWC25 homolog 1 MANS(0.504)S(0.496)PVLSK 92.925 0.0063347 0 218400 183370 204760 198090 216780 174030 249170 198130 251620 TRUE FALSE 204730.7339 196946.9056 209617.0039 203173.3248 199754.9732 224269.6359 211809.2717 222866.9666 209622.9965 0.976661613 0.939529102 0.999971413 0.969232041 0.952924901 1.069871339 1.010429558 1.063179949 1 17.67743747 2.248943224 24.99996876 1.035103724 0.968304121 0.633582646 0.025768634 124.3572443 299436.0391 0.008209349 0.00680025 177.3957553 -2.248943224 -0.066799603 MANSS(ph)PVLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 MANSSPVLSK 10 0 Q9NXE8 Q9NXE8 CWC25 Pre-mRNA-splicing factor CWC25 homolog 1 MANS(0.029)S(0.97)PVLSK;MANS(0.006)S(0.994)PVLSK;MANS(0.265)S(0.735)PVLSK;MANS(0.001)S(0.999)PVLSK;MANS(0.019)S(0.981)PVLSK 246.51 1.35E-12 1131523000 2734860 2337780 2484390 2369040 2711630 2039360 3069350 2498280 3118780 TRUE FALSE 2563689.994 2510871.664 2543320.904 2429833.577 2498669.518 2628090.126 2609129.462 2810195.757 2598235.47 0.986704255 0.966375716 0.978864669 0.935186054 0.961679396 1.011490358 1.004192842 1.081578552 1 21.30910075 1.880093646 1.803509922 1.03552621 0.966740209 0.55916808 0.025829527 0.240466273 1.466943672 0.015675742 0.007130723 75.87411639 -1.880093646 -0.068786002 MAPALSGANLTS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 MAPALSGANLTSPR 14 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MAPALSGANLTS(1)PR;MAPALSGANLT(0.001)S(0.999)PR;MAPALSGANLTS(1)PR;MAPALSGANLT(0.061)S(0.939)PR;MAPALSGANLT(0.021)S(0.979)PR;MAPALSGANLT(0.146)S(0.853)PR;MAPALSGANLT(0.004)S(0.996)PR 179.9 1.90E-06 2425120000 2251350 2409250 2572620 2445310 2620810 2367270 2798550 2255500 2479450 TRUE FALSE 2110442.022 2587633.377 2633643.761 2508060.794 2414982.154 3050662.42 2378933.408 2537104.14 2065613.777 1.021702143 1.25271888 1.274993317 1.214196392 1.169135383 1.476879392 1.15168355 1.228256786 1 20.9781391 0.476126351 1.671033439 1.00012936 1.236965309 0.268661335 0.114426605 4.274176154 12.2655476 0.099051096 0.028065303 2.993135312 -0.476126351 0.236835949 MAPPVDDLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MAPPVDDLSPK 11 0 Q92576-2;Q92576;E7EVH3;E7ER40 Q92576-2 PHF3 PHD finger protein 3 1 MAPPVDDLS(1)PK;MAPPVDDLS(1)PK;MAPPVDDLS(1)PK;MAPPVDDLS(1)PK 141.73 3.99E-05 338640000 861233 534252 644404 645589 673952 491950 787583 544991 738445 TRUE FALSE 807329.9639 573808.574 659689.5672 662155.9067 621022.5285 633967.9789 669492.2407 613034.326 615193.759 1.312318196 0.932728211 1.07232812 1.076337165 1.009474689 1.030517572 1.088262407 0.996489833 1 19.23068134 4.751297698 24.85882641 1.030973501 1.312318388 0.790266794 0.046323882 904.6092438 1765481.983 0.011010093 0.201751526 56402.41473 -4.751297698 0.281344886 MAPTPIPT(ph)RSPSDSSTASTPVAEQIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 MAPTPIPTRSPSDSSTASTPVAEQIER 27 1 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 MAPTPIPT(0.657)RS(0.291)PS(0.051)DSSTASTPVAEQIER;MAPT(0.004)PIPT(0.537)RS(0.397)PS(0.062)DSSTASTPVAEQIER;MAPTPIPT(0.662)RS(0.329)PS(0.008)DSSTASTPVAEQIER;MAPT(0.004)PIPT(0.575)RS(0.419)PS(0.002)DSSTASTPVAEQIER;MAPT(0.001)PIPT(0.608)RS(0.307)PS(0.074)DS(0.005)S(0.005)T(0.001)ASTPVAEQIER 215.3 1.09E-33 1737088000 530060 628342 599624 652964 676620 483012 623217 518185 559374 TRUE FALSE 496884.4908 674865.0955 613847.3644 669720.1617 623480.9946 622449.7234 529771.3965 582881.5379 466010.8657 1.06625087 1.448174592 1.317238308 1.437134219 1.337910852 1.335697876 1.136821983 1.250789586 1 18.83000407 1.169543816 0.850196241 1.01566988 1.346308507 0.407708113 0.115368905 0.478397486 0.772750539 0.098977833 0.036413002 14.77555546 -1.169543816 0.330638627 MAPTPIPTRS(ph)PSDSSTASTPVAEQIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 MAPTPIPTRSPSDSSTASTPVAEQIER 27 1 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 MAPTPIPT(0.071)RS(0.658)PS(0.265)DS(0.005)S(0.001)TASTPVAEQIER;MAPTPIPT(0.247)RS(0.751)PS(0.001)DSSTASTPVAEQIER;MAPTPIPT(0.01)RS(0.483)PS(0.483)DS(0.024)STASTPVAEQIER;MAPT(0.002)PIPT(0.245)RS(0.605)PS(0.143)DS(0.005)STASTPVAEQIER;MAPTPIPT(0.032)RS(0.9)PS(0.067)DS(0.001)STASTPVAEQIER 239.34 2.43E-45 3998790000 1093610 1372930 1182180 1363190 1345110 1032720 1309000 1100290 1092300 TRUE FALSE 1025162.902 1474583.166 1210221.868 1398171.763 1239470.487 1330849.499 1112727.602 1237663.629 909988.0735 1.126567405 1.620442299 1.329931571 1.536472624 1.362073331 1.462491145 1.222793611 1.360087747 1 19.79548811 0.612957962 0.618880644 0.993716074 1.431097294 0.413797629 0.141629603 1.195973462 0.861711704 0.146384768 0.052151566 4.101643986 -0.612957962 0.43738122 MAPTPIPTRSPS(ph)DSSTASTPVAEQIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MAPTPIPTRSPSDSSTASTPVAEQIER 27 1 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 MAPTPIPT(0.113)RS(0.226)PS(0.655)DS(0.006)STASTPVAEQIER 163.22 1.75E-11 842800000 320230 335510 352520 339930 431070 290090 383570 293570 324690 TRUE FALSE 300187.3759 360351.5095 360881.9409 348653.1793 397215.5011 373834.2738 326057.2394 330222.8607 270497.1414 1.109761731 1.33218232 1.33414327 1.288934802 1.46846469 1.382026708 1.205399945 1.220799817 1 18.04525382 0.934491868 1.311937285 1.004830186 1.322254832 0.51443037 0.094231352 0.397649083 1.37912224 0.084695148 0.025708633 8.59986963 -0.934491868 0.317424646 MAQYLEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MAQYLEEER 9 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 101.65 0.0089381 58572000 73717 121740 87920 94886 119000 62440 79457 129520 159110 FALSE TRUE 69103.18456 130753.7563 90005.50392 97320.9354 109654.22 80465.41437 67543.16049 145690.8571 132553.5131 0.52132292 0.986422413 0.679012587 0.734201102 0.827244918 0.607040979 0.509553907 1.099109738 1 17.01621538 1.221334375 24.99563304 1.049555204 0.713344986 0.512523503 0.142896042 250.131044 362935.5327 0.140396805 0.035443263 16.64693848 -1.221334375 -0.336210218 MASNIFGT(ph)PEENQASWAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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;MASNIFGT(1)PEENQASWAK;MASNIFGT(1)PEENQASWAK 285.1 1.47E-38 486758000 1133960 1080320 1021040 1026510 1258220 655646 1135670 1159750 1894050 TRUE FALSE 1062987.468 1160308.017 1045259.551 1052851.984 1159404.477 844920.3567 965386.8265 1304547.34 1577920.819 0.673663377 0.735339824 0.662428392 0.667240062 0.734767209 0.535464357 0.611809423 0.826750826 1 20.58959338 1.000675249 4.091952012 0.999035467 0.662778596 0.793130008 0.057558921 0.083314005 3.885977125 0.05888489 0.015056553 10.01556028 -1.000675249 -0.336256871 MAT(ph)PGPRDIPLLPGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MATPGPRDIPLLPGSPR 17 1 F5GXT3;Q9NQ90 F5GXT3 ANO2 Anoctamin;Anoctamin-2 2 MAT(1)PGPRDIPLLPGS(1)PR 47.281 0.094631 207120000 83451 194680 188840 185380 184990 190080 195000 172310 170370 TRUE FALSE 78227.95087 209094.3098 193319.374 190137.1646 170461.6316 244953.0103 165761.5603 193823.2828 141934.1464 0.551156666 1.473178337 1.362035697 1.339615375 1.200990995 1.725821563 1.167876544 1.365585997 1 17.11486219 4.743840159 24.95304955 1.352553163 0.551156319 0.614046348 0.193125524 327.1237175 1546057.273 0.040170109 0.342503281 55442.16221 -4.743840159 -0.801396844 MAVERELEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MAVERELEK 9 1 H0Y8N5;F5H7P7;Q96BP3-2;Q96BP3 H0Y8N5 PPWD1 Peptidylprolyl isomerase domain and WD repeat-containing protein 1 0 64.297 0.064237 486380000 554630 585400 620420 634360 768280 594570 809980 671120 1026000 FALSE TRUE 519916.6983 628743.6251 635136.6554 650638.7516 707942.3879 766212.707 688531.0185 754910.8093 854753.9718 0.608264735 0.735584327 0.743063708 0.761200033 0.828241121 0.896413158 0.80553123 0.883190759 1 19.7051497 6.584385901 0.105712855 1.109287786 4.01E-12 0.879971384 0.036933745 27.28985824 0.278873774 0.42703812 4.355669486 3840483.477 -6.584385901 -1.109287786 MCDLVSDFDGFSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 MCDLVSDFDGFSER 14 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ;;;;; 274.2 1.15E-32 509300000 650763 772324 757764 733608 823332 695287 837861 695490 901469 FALSE TRUE 610032.9055 829507.6726 775738.5199 752433.6233 758670.8259 896005.0699 712231.5214 782323.4575 751008.0002 0.812285495 1.104525747 1.032929769 1.001898279 1.010203388 1.19306994 0.948367422 1.041697901 1 19.51846875 4.748005278 24.86894296 1.043486567 0.812285363 0.538732987 0.066659755 887.2300156 2336132.608 0.014754658 0.185373931 55976.44039 -4.748005278 -0.231201204 MCEDLWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MCEDLWR 7 0 Q14376;Q14376-2;Q5QPP9 Q14376 GALE UDP-glucose 4-epimerase 0 ; 81.784 0.061099 174681000 426090 683860 442670 474200 656870 333350 496620 543450 607380 FALSE TRUE 399421.7875 734493.706 453170.3414 486368.7748 605282.0799 429582.7335 422156.4414 611300.9288 506004.3542 0.789364329 1.451556098 0.895585854 0.961194841 1.196199351 0.848970429 0.834294088 1.208094207 1 18.94879027 3.741860341 24.07813351 0.974984671 1.169503113 0.048342436 0.20279407 476.491211 778400.5093 0.047956718 0.085940167 5518.99933 -3.741860341 0.194518442 MCHNVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 MCHNVNR 7 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;;;;;;;;;; 170.43 0.00097502 1471618000 593292 855919 621242 591242 852408 522171 661878 733030 765501 FALSE TRUE 556158.9128 919292.1333 635978.1536 606414.2707 785463.3141 672913.291 562635.5385 824550.4091 637733.9378 0.872086116 1.441497902 0.997246839 0.950889132 1.231647349 1.055163056 0.882241802 1.292937948 1 19.28259513 3.734741876 24.65545901 1.046202459 1.204036734 0.03034143 0.183311082 507.8976085 1643218.493 0.043261316 0.076114199 5429.275446 -3.734741876 0.157834275 MCINTEWGAFGDDGSLEDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MCINTEWGAFGDDGSLEDIR 20 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;; 284.53 1.26E-44 180929000 236010 238660 245314 223644 225100 201996 246733 223419 204448 FALSE TRUE 221238.5554 256330.6347 251132.9639 229383.0837 207421.554 260308.9661 209737.6772 251313.354 170324.308 1.298925315 1.504956267 1.474439948 1.346743083 1.217803591 1.528313657 1.231401904 1.475499046 1 17.37792482 -3.515415271 0.2424032 1.45E-10 1.438903348 0.509487411 0.1151123 58.46158089 1.116059587 29.34015684 0.169410314 0.0003052 3.515415271 1.438903348 MCINTEWGAFGDDGSLEDIRTEFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MCINTEWGAFGDDGSLEDIRTEFDR 25 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 219.07 1.25E-33 289220000 62064 72101 62760 63207 87829 54219.5 66003 59674 100062 FALSE TRUE 58179.52503 77439.43306 64248.69684 64828.99863 80931.26463 69871.78947 56106.46289 67124.43026 83361.00577 0.697922542 0.928964716 0.770728427 0.777689737 0.970852785 0.838183139 0.673054054 0.805225772 1 16.34708506 -0.137500227 8.314369219 1 0.810427647 0.304766173 0.091141764 0 0 0.087224681 0.020559055 0.728617794 0.137500227 -0.189572353 MCIVLRPS(ph)RVHNSEENTMRALTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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)MRALT(0.001)LK 59.469 0.075115 1448616000 66156 142435 136448 131188 135626 130657 147400 132242 84838 TRUE FALSE 62015.41405 152981.0356 139684.611 134554.5062 124974.481 168375.5549 125298.7384 148752.7048 70677.98973 0.877436021 2.164479157 1.976352349 1.903768156 1.768223481 2.382291227 1.772811294 2.104653873 1 16.10897339 -1.511245041 6.685034262 0.999505451 1.915277719 0.312328649 0.39985635 0.002586934 0.000189135 0.339825903 0.080059141 0.030814488 1.511245041 0.915772268 MCTLIDKFDEHDGPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MCTLIDKFDEHDGPVR 16 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1;A0A3B3ITX2;A0A3B3IS23 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;;; 204.05 1.57E-11 1787424000 2373870 2193480 2281550 2414190 2500720 1739450 2714660 2107600 2417520 FALSE TRUE 2225293.714 2355887.542 2335669.443 2476142.203 2304323.539 2241600.977 2307621.935 2370738.499 2014020.294 1.104901336 1.169743695 1.159705019 1.229452459 1.144141171 1.112998208 1.145778889 1.177117483 1 20.94164679 -1.155730231 4.658753344 0.999981771 1.156316641 0.666430603 0.034564909 6.31E-06 1.14E-06 0.032256242 0.007601983 0.069866626 1.155730231 0.15633487 MCVGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MCVGNR 6 0 P56537;B7ZBH1 P56537 EIF6 Eukaryotic translation initiation factor 6 0 109.15 0.069328 134530000 203940 167490 172580 165770 175540 154330 185300 146880 188860 FALSE TRUE 191175.7594 179891.1339 176673.6791 170023.9388 161753.7965 198882.5657 157515.9852 165218.2913 157338.0459 1.215063771 1.143341605 1.122892293 1.08062826 1.028065371 1.264046242 1.001130936 1.050084805 1 17.26350805 8 0.100940833 0.940792557 1.65690433 0.364351784 0.070497069 139.1222792 0.992957173 0.792612281 13.81062359 99999999.97 -8 0.716111773 MDADGFLPITLIASFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MDADGFLPITLIASFHR 17 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 0 ; 144.33 5.16E-07 183596000 205710 372170 293020 265190 393490 234420 319570 372190 233920 FALSE TRUE 192834.9783 399725.854 299970.5728 271995.2244 362586.8827 302093.2485 271653.4452 418658.7408 194877.2408 0.989520262 2.051167455 1.539279659 1.395725962 1.860591217 1.550172033 1.393972144 2.148320343 1 17.57220609 -1.390147281 3.98416979 0.997663793 1.62844706 0.245299645 0.339000906 0.006273704 0.00096031 0.292724115 0.068772487 0.040724215 1.390147281 0.630783266 MDAEHPELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MDAEHPELR 9 0 Q12765;Q12765-2;Q12765-3;C9K052 Q12765 SCRN1 Secernin-1 0 ;;; 119.75 0.00077709 2004830000 1460410 1553360 1620200 1613760 1686210 1446260 1746110 1460560 2107870 FALSE TRUE 1369005.545 1668372.391 1658631.909 1655171.814 1553781.868 1863771.784 1484297.016 1642914.131 1756052.88 0.779592438 0.950069562 0.944522758 0.942552376 0.884814966 1.061341492 0.845246195 0.935572129 1 20.74390486 4.740793179 24.55776013 0.939957676 0.779592367 0.442667513 0.058213354 144.125628 1585218.774 0.012374884 0.082476685 55054.54518 -4.740793179 -0.160365309 MDDPTVNWSNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MDDPTVNWSNER 12 0 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ;; 161.93 0.000149 641530000 466955 487642 486495 474603 493434 435872 467761 442899 497655 FALSE TRUE 437729.1201 523747.5211 498034.8911 486782.1165 454681.6841 561701.1706 397624.5805 498195.9151 414593.1655 1.055803994 1.263280644 1.201261701 1.174119973 1.096693631 1.354824964 0.95907172 1.201650091 1 18.66133681 1.238439506 0.764374124 1.012133345 1.194549151 0.158756165 0.110707967 0.872344487 1.162624882 0.094352659 0.037457103 17.31567821 -1.238439506 0.182415807 MDEFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MDEFSR 6 0 O00422;O00422-2;H7BZW6;U3KQ12;U3KPY7 O00422 SAP18 Histone deacetylase complex subunit SAP18 0 144.9 0.026088 133160000 161230 199020 172710 172140 199300 158140 204770 182490 238150 FALSE TRUE 151138.9021 213755.6479 176806.7628 176557.4038 183647.7819 203792.4508 174066.6395 205274.2782 198401.2265 0.761784112 1.077390758 0.89115761 0.889900768 0.92563834 1.027173342 0.87734659 1.034642184 1 17.59806142 1.219613732 24.88477816 1.017321166 0.935285577 0.162429659 0.086150456 513.470934 674372.1157 0.074264639 0.018694014 16.58111503 -1.219613732 -0.082035588 MDELQLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 MDELQLFR 8 0 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;;; 174.73 0.00062874 1530709000 2265309 2631486 2187129 2122771 2637746 1680542 2503098 2356886 3063651 FALSE TRUE 2123527.353 2826323.961 2239008.733 2177244.898 2430588.069 2165687.194 2127781.693 2651148.405 2552307.856 0.832002828 1.107360131 0.877248694 0.853049483 0.952309912 0.848521149 0.833669687 1.038725951 1 21.28337092 5.049611984 18.72110399 0.930022252 4.84E-05 0.115007697 0.090243464 346.4273417 102574.6669 0.021281029 22172.47987 112101.6446 -5.049611984 -0.92997385 MDGPGYGDEEEPLHTILGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MDGPGYGDEEEPLHTILGK 19 0 E5RHM4;A0A087X1F8;B3KME9;A0A087WT20;Q9NV06 E5RHM4 DCAF13 DDB1- and CUL4-associated factor 13 0 202.41 5.54E-16 45959000 67508 60339 61431 70826 61146 55652 72195 57756 78665 FALSE TRUE 63282.79479 64806.56234 62888.17233 72643.51507 56343.83981 71717.82897 61370.02998 64966.96374 65535.3033 0.965629082 0.988880177 0.959607557 1.108463857 0.859747906 1.094338858 0.936442297 0.991327734 1 15.99998466 5.049158682 0.972740686 0.990514164 0.94277849 0.011389788 0.071370222 24.94433836 12.53129525 0.019182555 1.437000327 111984.6976 -5.049158682 -0.047735673 MDIDAPDVDVHGPDWHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 MDIDAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;;;;;; 241.32 3.16E-24 2926678000 4090020 3539460 3791950 3651939 4491000 2962776 4407190 3508808 5190630 FALSE TRUE 3834032.949 3801525.301 3881896.845 3745653.937 4138294.976 3818081.335 3746372.774 3946890.403 4324280.32 0.886629142 0.879111672 0.89769778 0.866191287 0.956990451 0.882940293 0.86635752 0.912727693 1 22.04402862 0.970657679 19.99172762 1.000000001 0.890129281 0.641764979 0.025497588 131.2527189 89426.99258 0.023092406 0.005773101 9.346686572 -0.970657679 -0.10987072 MDIDAPDVEVQGPDWHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MDIDAPDVEVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 282.19 2.29E-39 1340650000 1857090 1636510 1721090 1676060 2073160 1384100 2103630 1631260 2407020 FALSE TRUE 1740858.052 1757678.903 1761915.068 1719070.537 1910342.376 1783667.201 1788210.211 1834926.402 2005272.812 0.868140256 0.876528566 0.878641079 0.857275143 0.952659591 0.889488548 0.891754079 0.915050756 1 20.93536709 -5 0.158555034 1.419425409 0.857579229 0.71483615 0.023159937 69.34807832 0.635298804 9.104014122 0.095168572 1.00E-05 5 -0.56184618 MDIDVPDVEVQGPDWHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MDIDVPDVEVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 251.75 1.82E-30 653010000 998370 930890 998820 949490 1129410 787010 1105540 890930 1356070 FALSE TRUE 935883.8038 999814.0642 1022512.482 973855.5209 1040710.694 1014207.011 939774.5403 1002164.572 1129733.156 0.828411381 0.885000195 0.905092035 0.862022607 0.921200452 0.897740325 0.831855324 0.887080782 1 20.10755062 -1.303310113 2.613588781 1.00182737 0.878748821 0.626214082 0.029773044 1460162.534 1620498.37 20853.72846 0.007577196 0.04973818 1.303310113 -0.123078549 MDKEETKDWILPSDYDHAEAEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 MDKEETKDWILPSDYDHAEAEAR 23 2 O43852;O43852-3;O43852-15;H0Y875;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;;; 239.32 1.96E-37 2894830000 2023800 1641810 1789350 1826060 2181750 1207230 2281970 1575140 2820170 FALSE TRUE 1897133.971 1763371.321 1831794.227 1872919.791 2010404.156 1555737.703 1939809.783 1771799.696 2349465.408 0.80747474 0.750541512 0.779664268 0.79716849 0.855685787 0.662166678 0.825638793 0.754128871 1 21.1639011 -1.099997444 3.690787423 1.000104954 0.777728501 0.641037895 0.051950664 15034530.3 22405642.18 18436.78937 0.011003135 0.079433291 1.099997444 -0.222376454 MDKHEPHQDS(ph)GEEAEGCPSAPEETPVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MDKHEPHQDSGEEAEGCPSAPEETPVDK 28 1 Q96JQ2 Q96JQ2 CLMN Calmin 1 MDKHEPHQDS(0.996)GEEAEGCPS(0.004)APEETPVDK 96.887 0.0024749 146060000 214980 151520 160260 157780 171220 133650 208580 168390 145100 TRUE FALSE 201524.7856 162738.6985 164061.4429 161828.9019 157773.0719 172232.5854 177305.3654 189413.8622 120881.8726 1.667121639 1.346262222 1.357204677 1.338735895 1.305183883 1.424800772 1.466765542 1.566933553 1 16.88323839 4.741629299 24.18692381 1.371465669 1.667121814 0.305538885 0.146978549 226.5924023 1785825.747 0.031125025 0.218234564 55160.64034 -4.741629299 0.295656145 MDMMSLNSQLLDAIQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 MDMMSLNSQLLDAIQQK 17 0 H0YHW1;H0YHP2;Q6ZP65-2;Q6ZP65 H0YHW1 CCDC64 Bicaudal D-related protein 1 0 ;;;;;; 71.692 0.022737 29310000000 3917302 17256001 13674767 14374522 15403684 20811330 12238880 14435823 12186431 FALSE TRUE 3672125.06 18533653.27 13999138.93 14743396.57 14193940.79 26819223.13 10403773.56 16238167.28 10152436.94 0.361698879 1.825537394 1.378894448 1.452202723 1.398082143 2.641653752 1.024756285 1.599435424 1 23.27532273 4.746548298 24.21506926 1.562473558 0.36169795 0.391321283 0.461109856 618.6842217 1875504.18 0.09888412 1.064340968 55788.96419 -4.746548298 -1.200775608 MDMT(ph)SPEQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MDMTSPEQSR 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 MDMT(0.5)S(0.5)PEQSR 54.471 0.052341 86516000 92771 96063 99177 93259 102310 88932 107220 94766 119920 TRUE FALSE 86964.62871 103175.6045 101529.5253 95652.18383 94274.9853 114605.2247 91143.35638 106597.7437 99904.57729 0.87047692 1.032741515 1.016265 0.957435449 0.94365031 1.147146886 0.912304109 1.066995593 1 16.60826316 MDNVLIDDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MDNVLIDDRR 10 1 Q8WUA2 Q8WUA2 PPIL4 Peptidyl-prolyl cis-trans isomerase-like 4 0 126.71 0.00060192 106800000 60617 75579 67096 61468 77178 49295 66149 63577 75673 FALSE TRUE 56823.09017 81174.9478 68687.54881 63045.37295 71116.7512 63525.66626 56230.57155 71514.7284 63042.68743 0.901343082 1.287618772 1.089540304 1.000042598 1.128072963 1.00766114 0.891944393 1.134385784 1 15.94404142 2.918094069 1.109448534 0.997020413 1.135325544 0.009140452 0.117358879 0.805219673 2.099747648 0.051955287 0.058461252 828.1215175 -2.918094069 0.138305131 MDPMNIWDDIITNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MDPMNIWDDIITNR 14 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;; 111.39 0.0027061 12015800 69264.5 77319.5 75440.8 78939.7 83652.7 75301.8 86626.5 70016.8 72891.7 FALSE TRUE 64929.35859 83044.31623 77230.2914 80965.42635 77082.95438 97040.20724 73637.66053 78758.55161 60725.60437 1.069225399 1.367533796 1.271791235 1.333299638 1.26936496 1.598011386 1.212629521 1.296957888 1 15.89001732 0.519774709 1.691243306 1.000218524 1.315500715 0.338138648 0.132388746 3.008933404 9.400147797 0.113509407 0.032116958 3.309593914 -0.519774709 0.315282191 MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(ph)PTMGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFSPTMGR 38 2 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 MDRDPLGGLADMFGQMPGS(0.036)GIGT(0.096)GPGVIQDRFS(0.793)PT(0.074)MGR;MDRDPLGGLADMFGQMPGS(0.009)GIGT(0.019)GPGVIQDRFS(0.815)PT(0.156)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.991)PT(0.009)MGR;MDRDPLGGLADMFGQMPGS(0.04)GIGT(0.004)GPGVIQDRFS(0.729)PT(0.227)MGR;MDRDPLGGLADMFGQMPGS(0.008)GIGT(0.019)GPGVIQDRFS(0.903)PT(0.07)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.999)PT(0.001)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.998)PT(0.002)MGR 399.91 1.12E-180 3229267000 1224956 1480561 1342584 1403562 1647443 1117352 1785944 1416232 1892262 TRUE FALSE 1148288.191 1590183.277 1374430.726 1439579.777 1518059.472 1439913.384 1518158.277 1593051.683 1576431.248 0.72840994 1.00872352 0.871862143 0.913189065 0.962972203 0.913400686 0.96303488 1.010543076 1 20.58823082 4.748598351 24.7924235 0.947589991 0.728409805 0.704544121 0.045958205 711.0618196 1756227.773 0.010479165 0.141898401 56052.93409 -4.748598351 -0.219180186 MDRT(ph)PEKDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MDRTPEKDK 9 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 MDRT(1)PEKDK;MDRT(1)PEKDK 122.39 0.00094395 368360000 1168180 530830 730450 723080 760120 480240 915890 622620 1032740 TRUE FALSE 1095065.699 570133.2055 747776.6189 741635.457 700423.2414 618877.492 778560.7972 700355.4776 860369.0222 1.272786061 0.662661243 0.869134755 0.861996931 0.814096304 0.719316335 0.904914958 0.814017543 1 19.71459606 -1.308150078 2.970196858 1.00137613 0.843597652 0.050154725 0.162918631 38607252.02 48802978.84 471017.2749 0.034939013 0.049186953 1.308150078 -0.157778478 MDRT(ph)PPPPTLS(ph)PAAITVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 MDRTPPPPTLSPAAITVGR 19 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;H7C4H9 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 2 MDRT(1)PPPPT(0.312)LS(0.688)PAAITVGR;MDRT(1)PPPPT(0.008)LS(0.992)PAAITVGR;MDRT(1)PPPPT(0.01)LS(0.99)PAAITVGR;MDRT(1)PPPPT(0.019)LS(0.981)PAAITVGR;MDRT(1)PPPPT(0.001)LS(0.999)PAAITVGR;MDRT(1)PPPPT(0.001)LS(0.999)PAAITVGR;MDRT(1)PPPPTLS(1)PAAITVGR 162.02 6.51E-11 2910590000 2420280 2527810 2646910 2769160 2709440 2068070 2772190 2197370 2668130 TRUE FALSE 2268798.995 2714971.683 2709695.955 2840221.334 2496651.512 2665088.237 2356525.845 2471716.482 2222801.866 1.02069331 1.221418663 1.219045204 1.277766308 1.123200205 1.198976966 1.060160098 1.111982367 1 21.08394793 1.489080407 1.040254312 1.018370945 1.19387737 0.353830866 0.074126069 0.450565215 0.956683594 0.062487744 0.022641009 30.83758834 -1.489080407 0.175506425 MDRT(ph)PPPPTLSPAAITVGR ddPTM_SK-BR-3_Pertuzumab_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(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR 143.54 2.33E-07 5724640000 1007512 915514 933662 946456 969010 837092 1077264 878222 1060932 TRUE FALSE 944453.6224 983299.6092 955808.9035 970743.6633 892907.8634 1078746.871 915738.264 987869.9499 883855.5953 1.068561004 1.112511608 1.081408443 1.098305728 1.010241795 1.220501264 1.03607226 1.117682521 1 19.75345116 -1.768195623 2.59672584 0.976752038 1.092974836 0.215420924 0.055872911 11130631.82 8171098.78 1648060.692 0.011770679 0.017053141 1.768195623 0.116222798 MDS(ph)DEDEKEGEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MDSDEDEKEGEEEK 14 1 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 1 MDS(1)DEDEKEGEEEK;MDS(1)DEDEKEGEEEK 225.86 1.59E-12 388000000 1642030 363860 665450 597070 635830 434130 918940 467360 738790 TRUE FALSE 1539258.273 390800.573 681234.7882 612391.827 585894.4766 559456.2835 781153.478 525710.9248 615481.1762 2.500902274 0.6349513 1.106832856 0.994980595 0.951929156 0.908973832 1.269175254 0.854146228 1 19.23135521 4.746511537 24.99602482 0.977549334 2.500903017 0.897026927 0.163479089 304.9518844 958682.735 0.039277413 0.434896646 55784.24207 -4.746511537 1.523353683 MDS(ph)DEDEKEGEEEKVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 MDSDEDEKEGEEEKVAK 17 2 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 1 MDS(1)DEDEKEGEEEKVAK;MDS(1)DEDEKEGEEEKVAK;MDS(1)DEDEKEGEEEKVAK;MDS(1)DEDEKEGEEEKVAK;MDS(1)DEDEKEGEEEKVAK 187.83 3.95E-10 1366620000 1984180 457099 859837 889391 1155116 467996 1143668 574392 1913300 TRUE FALSE 1859993.716 490943.0856 880232.7397 912214.2788 1064397.849 603098.8479 972185.6007 646106.1056 1593957.87 1.166902684 0.308002548 0.552230869 0.5722951 0.667770378 0.378365614 0.609919258 0.405347041 1 20.60418207 -1.167957418 4.978295909 1.000032247 0.55265591 0.225877457 0.237146857 7.42E-05 1.24E-05 0.200640064 0.047287915 0.067927023 1.167957418 -0.447376337 MDS(ph)FDEDLARPSGLLAQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 MDSFDEDLARPSGLLAQER 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER 254.61 3.99E-31 1207367000 594087 482625 542144 494784 441982 400382 659401 406105 909384 TRUE FALSE 556904.1551 518359.0572 555003.9117 507480.9951 407270.5166 515965.7837 560529.9416 456808.1032 757601.9356 0.735088084 0.684210313 0.732579849 0.669851767 0.537578506 0.681051301 0.739873957 0.602965861 1 19.53108049 -1.185346207 4.115619919 1.000141569 0.67996282 0.726130667 0.062999096 9038256.773 2603130.146 11471.99258 0.014501138 0.06526101 1.185346207 -0.320178749 MDS(ph)T(ph)EPPYSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MDSTEPPYSQK 11 0 P68104;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 2 MDS(0.995)T(0.995)EPPY(0.002)S(0.009)QK 40.589 0.092261 240400000 63376 278110 270680 236800 240710 531910 249760 285520 93081 TRUE FALSE 59409.40929 298701.5538 277100.6574 242876.6889 221805.6076 685463.7822 212310.8067 321167.8005 77545.17977 0.766126398 3.851968035 3.573409182 3.132066875 2.860340362 8.839540822 2.737898181 4.141686194 1 16.24274949 4.739485775 5.590838222 3.945777814 0.65472547 0.176885753 2.002860572 0.232697375 29.35378645 0.434906187 2.926357056 54889.05766 -4.739485775 -3.291052344 MDSFDEDLARPSGLLAQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MDSFDEDLARPSGLLAQER 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;; 73.783 0.017576 479200000 329570 379870 321330 344230 378350 331468 347480 297548 375340 FALSE TRUE 308942.802 407995.9701 328952.0993 353063.5246 348635.9172 427157.4307 295378.5998 334697.5228 312693.3292 0.988005733 1.304779898 1.051995897 1.129104754 1.11494517 1.366058661 0.944627123 1.070369885 1 18.25438892 1.623733275 25 1.005634376 1.160363974 0.291265204 0.113336113 1.000160189 1572.127566 0.048061757 0.026540319 42.04683154 -1.623733275 0.154729598 MDSNFGLAGLPGS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MDSNFGLAGLPGSPK 15 0 O43463;O43463-2 O43463 SUV39H1 Histone-lysine N-methyltransferase SUV39H1 1 MDSNFGLAGLPGS(1)PK 196.3 9.44E-09 79240000 232770 138010 160390 158160 190040 122390 214980 147950 215010 TRUE FALSE 218201.3412 148228.404 164194.5265 162218.6534 175115.025 157722.0062 182745.7448 166421.8832 179123.442 1.218161837 0.827520967 0.916655714 0.905624923 0.977622041 0.880521301 1.020222383 0.929090472 1 17.45059463 1.726808547 24.99999997 0.981861487 0.9343878 0 0.106690675 3.166123798 6704.951747 0.045397926 0.025175495 53.30998332 -1.726808547 -0.047473686 MDSTEPPYSQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MDSTEPPYSQKR 12 1 P68104;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 96.745 0.008517 58379000 152310 191920 179840 209530 238310 118320 229050 150320 172770 FALSE TRUE 142777.189 206129.9565 184105.8897 214906.8945 219594.0939 152477.0632 194706.0789 169087.7829 143933.5709 0.991965864 1.432118687 1.279103191 1.493097776 1.525662794 1.05935719 1.352749589 1.174762648 1 17.1350436 0.862858756 0.92828335 1.000577232 1.333819435 0.240035695 0.172001831 0.969330698 1.696799466 0.150172252 0.050651697 7.292203103 -0.862858756 0.333242203 MDTEEARPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MDTEEARPAK 10 1 Q9NRX1;F8WBJ6 Q9NRX1 PNO1 RNA-binding protein PNO1 0 ; 114.83 0.0024868 241530000 476770 437980 464520 441970 498930 347670 576410 420070 531850 FALSE TRUE 446929.8168 470408.4949 475538.6338 453311.6985 459746.0504 448036.685 489982.6716 472516.6642 443080.7991 1.008686943 1.061676552 1.073254889 1.023090369 1.037612217 1.011185061 1.105853995 1.066434531 1 18.75721028 1.747213108 24.99999978 1.068122209 1.042769594 0.029411955 0.033211576 4.522804072 13099.44117 0.014652797 0.008125572 55.87443028 -1.747213108 -0.025352614 MDYEDDRLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 MDYEDDRLR 9 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;; 166.19 5.56E-05 5717690000 3877530 5153360 4012350 4143900 5455320 3144220 4193790 4533400 5812630 FALSE TRUE 3634842.319 5534920.136 4107524.837 4250239.49 5026881.173 4051905.272 3564970.123 5099404.969 4842464.502 0.750618268 1.142996533 0.848230242 0.877701734 1.038083226 0.836744445 0.736189211 1.053059856 1 22.20731004 2.203083683 24.99941669 0.86691611 0.94655799 0 0.137488417 499.0993573 351695.965 0.048728642 0.035989837 159.6186683 -2.203083683 0.07964188 MDYVEINIDHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MDYVEINIDHK 11 0 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7C0A4 Q00341 HDLBP Vigilin 0 ;; 182.35 5.83E-06 441260000 638810 592400 636150 609410 626660 485640 711240 558170 731700 FALSE TRUE 598828.0224 636261.9124 651239.7784 625048.4923 577444.6514 625836.3843 604596.1648 627858.7532 609574.543 0.982370457 1.043780321 1.068351338 1.025384835 0.947291284 1.026677363 0.991833028 1.029995036 1 19.21744313 2.990082355 24.91673198 0.998983243 1.040330388 0.181087152 0.030928848 571.5711343 1435999.084 0.008696812 0.009816087 977.4225506 -2.990082355 0.041347145 MEANKENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 MEANKENR 8 1 P16949;P16949-2 P16949 STMN1 Stathmin 0 ;;;;;;;;; 156.35 0.00054464 4339760000 5468330 6054400 5192550 5261960 7121620 4105557 6135000 5626640 8762880 FALSE TRUE 5126076.987 6502674.076 5315719.738 5396990.802 6562316.692 5290764.658 5215113.705 6329138.39 7300298.718 0.702173594 0.890740821 0.72815099 0.739283557 0.898910708 0.724732626 0.714369905 0.866969782 1 22.79952407 0.970981889 5.709954934 0.999932473 0.776930881 0.530287699 0.069834708 0.145622255 19.49231048 0.064581586 0.016261163 9.353666668 -0.970981889 -0.223001592 MECCDVPAETLYDVLHDIEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 18 MECCDVPAETLYDVLHDIEYR 21 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;F5GWK5;F5GY07 Q9Y365 STARD10 PCTP-like protein 0 ;;;;;;;;;;;;;;;;; 250.22 5.43E-31 2999641500 814656.3 923872.2 845829.8 861108.5 951508.5 897986.2 1183840.1 821311.1 959136.8 FALSE TRUE 763668.4164 992276.659 865893.2823 883206.002 876780.8606 1157220.238 1006334.267 923853.5988 799050.6718 0.955719635 1.241819441 1.08365253 1.105319141 1.097278172 1.448243871 1.259412329 1.156189002 1 19.60792747 MEDGEFWMSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 MEDGEFWMSFR 11 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;;;; 285.88 2.02E-27 412368000 355879 506108 420364 401555 509111 317630 429353 421709 418519 FALSE TRUE 333605.1687 543580.7629 430335.2326 411859.5811 469127.4757 409324.6247 364975.5036 474360.2969 348665.4752 0.956805857 1.559032372 1.234235286 1.181245665 1.34549449 1.173975211 1.046778444 1.360502633 1 18.41148399 1.158458322 0.348904907 0.994844151 1.323146401 0.08574356 0.174653143 2.337041184 0.88944356 0.290947501 0.186760738 14.4031778 -1.158458322 0.32830225 MEDLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MEDLDR 6 0 H3BRP2 H3BRP2 TGFB1I1 0 ; 109.63 0.068384 1244740000 3317300 2726100 3625600 3657000 2584500 3669900 4719300 3502300 2778700 FALSE TRUE 3109676.115 2927943.281 3711600.944 3750844.811 2381523.795 4729340.554 4011684.777 3939569.865 2314917.019 1.343320771 1.264815653 1.603340817 1.620293419 1.028772857 2.042984917 1.732971309 1.701819042 1 21.14252905 2.235339656 24.99930241 1.69908895 1.400290633 0.110579639 0.308653137 135.346976 1050471.753 0.1019856 0.078484349 171.9252465 -2.235339656 -0.298798317 MEDSVGCLETAEEVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MEDSVGCLETAEEVKR 16 1 P35579 P35579 MYH9 Myosin-9 0 ;; 250.19 1.47E-20 342400000 1172240 680280 812550 798570 830010 602690 1069040 701150 958080 FALSE TRUE 1098871.591 730648.639 831824.0697 819062.6582 764824.3627 776676.8191 908747.3765 788690.1209 798170.2586 1.376738333 0.915404491 1.0421637 1.026175367 0.958222077 0.973071611 1.138538259 0.988122662 1 19.606337 4.747858326 24.985058 1.010963091 1.376738526 0.795511504 0.059133584 592.4888497 1592118.76 0.01467924 0.185745164 55957.50289 -4.747858326 0.365775435 MEEADALIESLCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MEEADALIESLCR 13 0 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;; 165.66 8.13E-05 64839400 117992 128937 125900 124918 135637 125064 149299 120652 133019 FALSE TRUE 110607.0913 138483.6296 128886.4075 128123.6074 124984.6172 161167.9466 126913.001 135715.6678 110817.2696 0.99810338 1.249657478 1.163053448 1.156170043 1.127844222 1.454357675 1.145245696 1.224679766 1 16.7578232 4.747038827 24.16235496 1.202357803 0.998103213 0.208772819 0.115316164 957.5798904 2728940.831 0.024513191 0.277096344 55852.01252 -4.747038827 -0.20425459 MEEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MEEEER 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 ; 143.37 0.02654 317560000 553880 717300 653140 682410 692540 558210 782110 593970 617550 FALSE TRUE 519213.6395 770409.6383 668632.7892 699921.7959 638150.702 719356.1652 664839.8663 668128.462 514476.9155 1.009206874 1.497462015 1.299636134 1.360453258 1.240387436 1.398228266 1.292263746 1.298655862 1 18.97274682 0.313367888 1.408795572 0.999850745 1.323274929 0.345291155 0.126570735 5.065435963 9.372521737 0.107983707 0.031346429 2.057632865 -0.313367888 0.323424184 MEEFKDQLPADECNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 MEEFKDQLPADECNK 15 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;;; 220.61 1.50E-12 1989310000 3858410 1650970 2093270 1834890 2656630 1959610 2731370 2241170 3720290 FALSE TRUE 3616919.006 1773209.537 2142923.353 1881976.384 2447988.996 2525317.595 2321826.425 2520985.008 3099349.565 1.166992922 0.572123118 0.691410668 0.607216561 0.789839592 0.814789536 0.749133448 0.813391634 1 21.56353405 0.544774791 0.720870965 1.002975277 0.728034302 0.132702728 0.163868702 2.415651526 2.124599283 0.16327285 0.055033852 3.505700345 -0.544774791 -0.274940976 MEEIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 114.6 0.058509 702469000 1807160 1664880 1605930 1416110 1569140 1298280 1794000 1474890 1915890 FALSE TRUE 1694053.081 1788149.448 1644023.418 1452449.78 1445906.074 1673072.36 1525006.355 1659033.263 1596115.582 1.061359904 1.120313258 1.030015267 0.909990352 0.905890582 1.048215041 0.955448573 1.039419251 1 20.6061337 3.564777138 3.457840599 0.974418074 1.089079621 0.474633642 0.049164728 0.183261064 4.190705655 0.013045561 0.020869979 3670.938747 -3.564777138 0.114661547 MEELHNQEMQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MEELHNQEMQK 11 0 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 142.08 3.78E-05 1054610000 843930 812800 828120 802970 976800 611740 979850 900230 1187460 FALSE TRUE 791109.9278 872980.5577 847763.3975 823575.5696 900086.0682 788339.4072 832930.589 1012625.697 989265.2547 0.799694444 0.882453471 0.856962673 0.832512378 0.90985311 0.79689386 0.841968911 1.023613932 1 19.91599788 1.239502676 24.99987636 1.011807035 0.849372633 0.800740189 0.034399098 9.658313092 256369.2212 0.024439961 0.00775776 17.35811958 -1.239502676 -0.162434402 MEELHNQEVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 MEELHNQEVQK 11 0 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;;;;; 160.22 2.10E-05 3827270000 6694530 5459630 5956260 5527450 6058020 4755050 6952040 5405860 6516370 FALSE TRUE 6275531.317 5863866.686 6097545.3 5669293.725 5582247.546 6127755.743 5909646.142 6080793.521 5428745.75 1.155981806 1.080151283 1.123195961 1.044310046 1.028275739 1.128760864 1.08858407 1.120110206 1 22.37218749 -2.569370287 1.798708786 4.66E-05 1.094592777 0.376592701 0.03883918 514168.4834 34975.22457 2086345.118 0.009069231 0.00269544 2.569370287 1.09454617 MEELHNQEVQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MEELHNQEVQKR 12 1 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 116.01 0.0005763 607820000 454820 475730 440710 470450 578180 353790 505370 405240 829770 FALSE TRUE 426353.6281 510953.5442 451163.8493 482522.5435 532772.0751 455923.4297 429594.4601 455835.106 691276.0265 0.61676322 0.739145471 0.65265369 0.698017181 0.770708161 0.659538899 0.621451408 0.65941113 1 19.39890237 -2.287807445 2.265637671 2.441265487 0.678892418 0.814925978 0.048337216 2044636.811 273204.8858 15133195.91 0.011948028 0.005154571 2.287807445 -1.762373069 MEGGGAEVHAQLPSLEGDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MEGGGAEVHAQLPSLEGDLR 20 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 143.33 1.69E-07 201893000 275030 279970 309960 290720 319910 278930 316620 269020 265610 FALSE TRUE 257816.3632 300699.2701 317312.3976 298180.3674 294785.5591 359452.5629 269145.7704 302607.7392 221277.9751 1.165124379 1.358920923 1.433999012 1.347537491 1.332195664 1.624438956 1.216324265 1.367545681 1 17.75550033 -0.598100412 7.347911584 1 1.36317281 0.453021748 0.122612884 0 0 0.107853223 0.025421248 0.252289739 0.598100412 0.36317281 MEGMDDDPEDR ddPTM_SK-BR-3_Pertuzumab_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 ; 83 0.017257 376350000 417440 415540 438730 416210 451040 379870 443860 398400 521940 FALSE TRUE 391313.1756 446307.014 449136.8828 426890.6532 415617.1378 489532.3023 377307.3136 448141.117 434824.8421 0.899932887 1.02640643 1.032914496 0.981753138 0.955826571 1.125814937 0.867722533 1.030624457 1 18.73007484 MEGMDDDPEDRMS(ph)YLTAMGADYLSCDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.999)YLT(0.001)AMGADYLSCDSR;MEGMDDDPEDRMS(0.999)YLTAMGADYLSCDSR;MEGMDDDPEDRMS(1)YLTAMGADYLSCDSR;MEGMDDDPEDRMS(1)YLTAMGADYLSCDSR;MEGMDDDPEDRMS(0.998)YLT(0.002)AMGADYLSCDSR 250.03 2.43E-46 432685000 415980 500304 420891 458775 500468 397565 613151 482734 637191 TRUE FALSE 389944.5543 537347.0287 430874.7333 470547.9432 461163.2621 512335.5616 521214.6998 543004.4025 530839.7057 0.734580609 1.012258546 0.811685201 0.886421905 0.868742969 0.965141748 0.981868338 1.022915951 1 19.01791676 2.067187313 2.25128985 1.001136466 0.876377737 0.455709245 0.070091388 0.310660585 3.025911183 0.034220544 0.019662256 116.7312975 -2.067187313 -0.124758729 MEIATKDPLNPIKQDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MEIATKDPLNPIKQDVK 17 2 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 211.49 1.36E-12 804390000 2987600 1975600 2559700 2582100 3083000 1881900 3788600 2146000 4857000 FALSE TRUE 2800611.449 2121875.48 2620417.293 2648361.057 2840873.616 2425173.98 3220534.602 2413932.824 4046335.323 0.692135284 0.524394374 0.647602604 0.654508548 0.702085564 0.599350718 0.795913918 0.59657261 1 21.94818445 -5 0.179765014 2.454587517 0.573670599 0.68640412 0.073465604 67.89874719 0.653904639 35.16530989 0.206983994 1.00E-05 5 -1.880916918 MEISAELPQT(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MEISAELPQTPQR 13 0 Q8IWV7;H3BS20;H3BNQ6;A0A087WTJ9;Q8IWV7-2 Q8IWV7 UBR1 E3 ubiquitin-protein ligase UBR1 1 MEISAELPQT(1)PQR 139.21 0.00044849 90020000 602930 762340 776160 841950 817590 644050 844640 707910 929180 TRUE FALSE 565193.6876 818784.4468 794570.8817 863555.8624 753379.7794 829976.7797 717994.0733 796294.1218 774093.8553 0.730135866 1.057732782 1.026452899 1.115569975 0.973240873 1.072191407 0.927528449 1.028679037 1 19.56214897 4.742595706 24.8451293 1.02396852 0.730135741 0.760729719 0.05199694 178.5797055 1099517.056 0.011970621 0.091553579 55283.52233 -4.742595706 -0.293832779 MEISMPPPQIYVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MEISMPPPQIYVEK 14 0 P56597 P56597 NME5 Nucleoside diphosphate kinase homolog 5 0 ; 70.412 0.044282 887100000 835410 2893800 2329080 2422650 2643030 2474310 2261680 2436280 2148280 FALSE TRUE 783123.1793 3108059.963 2384326.877 2484819.301 2435457.085 3188603.13 1922562.08 2740454.921 1789718.19 0.437567872 1.736619754 1.33223593 1.388385789 1.36080479 1.781623022 1.07422615 1.531221472 1 20.77130101 -0.984217995 4.445295342 0.999992008 1.367828104 0.062455223 0.378190996 0.296024354 98124777.34 2576.555818 0.077528597 0.103700776 0.984217995 0.367836096 MEITIRNS(ph)PYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MEITIRNSPYR 11 1 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;Q9UQ88-9;A0A087X1I0;A0A087WYI9 P21127-2 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 MEITIRNS(0.996)PY(0.004)R;MEITIRNS(1)PYR;MEITIRNS(1)PYR;MEITIRNS(0.994)PY(0.006)R 169.17 1.04E-05 2417980000 1478050 4149800 1280300 1463710 4580800 1039190 1363790 3401990 5466300 TRUE FALSE 1385541.489 4457055.51 1310669.321 1501271.277 4221042.446 1339187.283 1159302.35 3826735.94 4553939.216 0.304251204 0.978725297 0.287810016 0.32966432 0.926899163 0.294072279 0.254571327 0.840313355 1 22.1186836 1.051787732 6.551305294 0.998961905 0.501217746 0.329421608 0.263973726 0.207168793 18.17381259 0.249245968 0.062584706 11.26646657 -1.051787732 -0.497744158 MEITIRNS(ph)PYRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MEITIRNSPYRR 12 2 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;Q9UQ88-9;A0A087X1I0;A0A087WYI9 P21127-2 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 MEITIRNS(1)PYRR;MEITIRNS(1)PYRR;MEITIRNS(1)PYRR 207.79 3.88E-08 1104630000 661300 908500 825430 857230 1000500 666640 932870 778660 1397510 TRUE FALSE 619910.4135 975766.2853 845009.5894 879227.9731 921924.7658 859088.146 792994.8038 875877.415 1164256.553 0.532451728 0.838102464 0.725793286 0.755184045 0.791857056 0.737885601 0.681116891 0.752306193 1 20.15097757 0.946804676 21.69503423 1.000000001 0.734936131 0.531442566 0.080472215 2599.522933 1060184.633 0.070199753 0.017549938 8.847176183 -0.946804676 -0.26506387 MEIVDHALHALTDEVIIPHSGWER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MEIVDHALHALTDEVIIPHSGWER 24 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30 O60716-13 CTNND1 Catenin delta-1 0 ; 312.56 5.74E-74 404590000 156042 194983 193572 189986 231237 153288 209244 200741 216326 FALSE TRUE 146275.6098 209419.7442 198163.6193 194861.3624 213076.5788 197539.7572 177869.8047 225803.9557 180219.7931 0.811651191 1.162024107 1.099566345 1.081242848 1.182315078 1.096104672 0.986960431 1.252936494 1 17.45939794 4.745497144 24.47897583 1.105332742 0.811651008 0.578404968 0.079395487 431.9828094 1524412.665 0.017537594 0.173528253 55654.09741 -4.745497144 -0.293681735 MEIVELEDHPFFVGVQYHPEFLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MEIVELEDHPFFVGVQYHPEFLSR 24 0 P17812;B4E1E0;P17812-2;A0A3B3IRI2 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ; 251.32 2.20E-39 642970000 380060 556570 401400 358890 568040 330610 428190 479340 255030 FALSE TRUE 356272.723 597779.0219 410921.3976 368099.725 523428.4298 426051.74 363986.8846 539186.6542 212463.8454 1.67686282 2.813556446 1.934076815 1.732528771 2.463611767 2.005290543 1.713170934 2.537780736 1 17.69685784 -1.854483776 0.346186818 2.91E-16 2.190738305 0.414144697 0.397468927 31.27656959 1.797262979 26.60653112 0.303839195 0.013980291 1.854483776 2.190738305 MEKGEHSIVYLKPSYAFGSVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MEKGEHSIVYLKPSYAFGSVGK 22 2 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 203.64 7.59E-23 1203700000 2997480 2843020 3039300 3207460 4049600 2499200 3850600 2922470 5035200 FALSE TRUE 2809873.077 3053520.159 3111393.631 3289768.854 3731560.751 3220678.469 3273238.277 3287346.813 4194792.591 0.669847916 0.727931141 0.741727645 0.784250659 0.889569787 0.767780146 0.780309921 0.783673267 1 22.00016805 -5 0.10872167 1.721479892 0.631996068 0.742856658 0.046339572 91.11818688 0.661150902 14.81517113 0.613807015 1.00E-05 5 -1.089483824 MELAGSNTTASS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MELAGSNTTASSPAR 15 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9;A0A0C4DGI9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 MELAGS(0.012)NT(0.012)T(0.012)AS(0.229)S(0.736)PAR;MELAGSNTTAS(0.007)S(0.993)PAR 211.54 1.27E-11 0 316030 327390 351180 310480 322810 307870 391680 308800 365300 TRUE FALSE 296250.2464 351630.2962 359510.1554 318447.4424 297457.8048 396747.0711 332951.2202 347354.3598 304329.0701 0.973453658 1.155427893 1.181320455 1.046391797 0.977421594 1.303677861 1.094050004 1.141377522 1 18.21527262 2.288408013 24.99999024 1.14316844 1.093576831 0.066163814 0.100193738 357.047382 179068.4941 0.033652012 0.028155231 194.2710166 -2.288408013 -0.049591609 MELATRYQQDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MELATRYQQDVR 12 1 C9IZR6 C9IZR6 CDCA7L 0 ; 74.76 0.037398 409450000 699160 1134270 1050430 1007570 1332370 411240 514460 1138360 725760 FALSE TRUE 655400.8236 1218252.531 1075346.696 1033425.952 1227731.035 529958.3121 437321.499 1280486.752 604625.9674 1.0839773 2.014886222 1.778532107 1.709198757 2.030562862 0.87650604 0.723292618 2.117816337 1 19.20568342 2.236636378 24.99999821 1.099952074 1.770042082 0.252503196 0.452169813 55.72997097 724035.0691 0.153882344 0.119426297 172.4393502 -2.236636378 0.670090008 MELGAPEEMGQVPPLDS(ph)RPSSPALYFTHDASLVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 MELGAPEEMGQVPPLDSRPSSPALYFTHDASLVHK 35 1 Q9Y3Q8;Q9Y3Q8-2 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 MELGAPEEMGQVPPLDS(0.173)RPS(0.173)S(0.173)PALY(0.16)FT(0.173)HDAS(0.149)LVHK;MELGAPEEMGQVPPLDS(0.32)RPS(0.32)S(0.32)PALY(0.012)FT(0.021)HDAS(0.007)LVHK;MELGAPEEMGQVPPLDS(0.301)RPS(0.301)S(0.301)PALY(0.048)FT(0.046)HDAS(0.002)LVHK;MELGAPEEMGQVPPLDS(0.294)RPS(0.294)S(0.294)PALY(0.01)FT(0.086)HDAS(0.022)LVHK;MELGAPEEMGQVPPLDS(0.413)RPS(0.293)S(0.293)PALYFTHDASLVHK;MELGAPEEMGQVPPLDS(0.312)RPS(0.313)S(0.313)PALY(0.015)FT(0.032)HDAS(0.015)LVHK;MELGAPEEMGQVPPLDS(0.286)RPS(0.286)S(0.286)PALY(0.045)FT(0.048)HDAS(0.048)LVHK 179.18 5.22E-20 1755550000 1144373 1080597 1321176 1138361 1266912 1254374 1422118 1285435 1601045 TRUE FALSE 1072748.737 1160605.526 1352514.919 1167573.271 1167413.842 1616491.411 1208884.608 1445924.389 1333820.246 0.804267846 0.870136384 1.014015886 0.875360285 0.875240757 1.211925981 0.906332477 1.084047414 1 20.34713282 MELGAPEEMGQVPPLDSRPS(ph)SPALYFTHDASLVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MELGAPEEMGQVPPLDSRPSSPALYFTHDASLVHK 35 1 Q9Y3Q8;Q9Y3Q8-2 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 MELGAPEEMGQVPPLDS(0.077)RPS(0.349)S(0.349)PALY(0.071)FT(0.077)HDAS(0.077)LVHK;MELGAPEEMGQVPPLDS(0.003)RPS(0.592)S(0.405)PALYFTHDASLVHK;MELGAPEEMGQVPPLDS(0.085)RPS(0.442)S(0.442)PALY(0.014)FT(0.003)HDAS(0.012)LVHK;MELGAPEEMGQVPPLDS(0.074)RPS(0.442)S(0.442)PALY(0.011)FT(0.016)HDAS(0.016)LVHK 254.37 5.37E-60 816810000 904531 811716 988481 869753 962081 926597 1142700 962182 1231830 TRUE FALSE 847918.0193 871816.2972 1011928.236 892072.3345 886523.0391 1194090.512 971362.7433 1082312.541 1026229.615 0.826245907 0.849533364 0.986064153 0.869271673 0.863864213 1.163570505 0.946535482 1.054649491 1 19.96892213 2.27228061 24.99969675 1.031599481 0.889136401 0.57743872 0.06842191 143.3207956 106256.2108 0.022680655 0.018974951 187.1891232 -2.27228061 -0.14246308 MELLAHLLGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MELLAHLLGEK 11 0 Q9Y2Q3-3;Q9Y2Q3;Q9Y2Q3-2;Q9Y2Q3-4 Q9Y2Q3-3 GSTK1 Glutathione S-transferase kappa 1 0 ; 121.68 0.00040657 219640000 962400 1110550 858910 849640 1374920 619260 985060 1062570 1331270 FALSE TRUE 902165.1019 1192776.278 879283.7508 871443.2008 1266939.329 798030.3092 837359.3978 1195234.204 1109072.437 0.813441099 1.075471933 0.792810029 0.785740563 1.142341372 0.719547509 0.755008753 1.077688133 1 20.08092216 3.961315743 24.17619224 0.872903032 0.959544002 0 0.155242499 835.2495096 1277604.748 0.037473718 0.067871223 9147.780672 -3.961315743 0.086640971 MELSLNIPVNHGPQEESCGSSQLHENSGS(ph)PETSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MELSLNIPVNHGPQEESCGSSQLHENSGSPETSR 34 0 O43353-2;O43353 O43353-2 RIPK2 Receptor-interacting serine/threonine-protein kinase 2 1 MELSLNIPVNHGPQEESCGSSQLHENS(0.065)GS(0.935)PETSR;MELSLNIPVNHGPQEESCGSSQLHENS(0.093)GS(0.907)PETSR;MELSLNIPVNHGPQEESCGSSQLHENS(0.05)GS(0.949)PETSR 280.03 9.78E-74 510010000 168122 224429 237420 242510 222333 216358 280667 206423 237170 TRUE FALSE 157599.5441 241045.9567 243051.7145 248733.2172 204871.863 278817.0423 238583.5889 232195.3659 197584.7948 0.79762992 1.219962077 1.230113455 1.258868211 1.036880713 1.411126006 1.207499743 1.175168191 1 17.5921124 4.739299425 24.95372418 1.211185506 0.797629789 0.532934861 0.114977028 40.83914471 1379105.956 0.023900897 0.143759583 54865.51052 -4.739299425 -0.413555717 MEQELKEPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MEQELKEPGR 10 1 C9JVE2;Q96GG9 C9JVE2 DCUN1D1 DCN1-like protein;DCN1-like protein 1 0 105.03 0.002374 222620000 328030 282560 343350 327490 365720 228950 392820 289500 511460 FALSE TRUE 307499.1879 303481.0364 351494.4241 335893.9478 336997.8264 295044.1483 333920.2878 325644.7123 426094.0218 0.721669801 0.712239602 0.824922215 0.788309459 0.790900152 0.69243907 0.783677476 0.764255529 1 18.70081228 0.107484399 1.649710745 1.000077202 0.760999898 0.775493713 0.040621363 9.831176822 17.36445418 0.039924037 0.010963333 1.280809083 -0.107484399 -0.239077304 MEREDS(ph)S(ph)EEEEEEIDDEEIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MEREDSSEEEEEEIDDEEIER 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 MEREDS(1)S(1)EEEEEEIDDEEIER;MEREDS(1)S(1)EEEEEEIDDEEIER;MEREDS(1)S(1)EEEEEEIDDEEIER;MEREDS(1)S(1)EEEEEEIDDEEIER 223.76 1.95E-25 2352500000 1228220 1346000 1305540 1303970 1375430 1098360 1440350 1167140 1475900 TRUE FALSE 1151347.903 1445659.241 1336508.025 1337432.078 1267409.276 1415438.702 1224382.889 1312859.998 1229562.755 0.936388076 1.175750676 1.086978293 1.087729823 1.030780471 1.151172395 0.995787229 1.067745418 1 20.22971394 1.689286739 11.06816424 1.024402779 1.088913706 0.121820428 0.067805203 0.202279284 36.9244066 0.029399182 0.015986068 48.8975094 -1.689286739 0.064510927 MES(ph)EGGADDS(ph)AEEGDLLDDDDNEDRGDDQLELIKDDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 MESEGGADDSAEEGDLLDDDDNEDRGDDQLELIKDDEK 38 2 P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 2 MES(1)EGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(1)EGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(1)EGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(1)EGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(1)EGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK 201.3 1.11E-30 1322950000 862531 247815 438311 366846 344107 342465 610725 350858 334275 TRUE FALSE 808546.7244 266163.4805 448707.9439 376259.8894 317082.2243 441329.086 519152.4559 394663.3936 278482.343 2.903403913 0.955764296 1.611261738 1.351108603 1.138608002 1.584765057 1.864220368 1.417193598 1 18.08722633 4.749614749 24.90707825 1.412985118 2.903404818 0.740328035 0.285028701 874.6686114 1970756.517 0.069673606 1.063861658 56184.2709 -4.749614749 1.4904197 MES(ph)GALDDFDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MESGALDDFDK 11 0 Q5QNY5;E9PS71 Q5QNY5 PEX19 1 MES(1)GALDDFDK;MES(1)GALDDFDK 68.893 0.036066 217369000 102805 480060 358010 396670 472440 703530 293340 351770 270680 TRUE FALSE 96370.61856 515604.1419 366502.1663 406849.2238 435336.4681 906627.6901 249356.3902 395689.2588 225501.7593 0.427360828 2.28647503 1.625274088 1.804195342 1.930523599 4.02049054 1.105784678 1.754705861 1 17.78277916 2.813760533 3.712550289 2.067848689 1.663357858 0.03673918 0.937751774 0.937333338 25.05078753 0.283754143 0.298276149 651.2691895 -2.813760533 -0.40449083 MES(ph)HS(ph)EDEDLAGAVGGLGWNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MESHSEDEDLAGAVGGLGWNSR 22 0 Q96MH2;K7ESM2;K7ELS4;K7EJA3;K7ERG7;K7EIM4 Q96MH2 HEXIM2 Protein HEXIM2 2 MES(1)HS(1)EDEDLAGAVGGLGWNSR;MES(1)HS(1)EDEDLAGAVGGLGWNSR;MES(1)HS(1)EDEDLAGAVGGLGWNSR;MES(1)HS(1)EDEDLAGAVGGLGWNSR 235.68 1.69E-30 254785000 314200 247757 247028 246582 252371 195329 367688 230581 338127 TRUE FALSE 294534.7829 266101.1861 252887.6208 252909.7116 232550.7997 251717.3114 312556.5978 259369.5454 281691.4193 1.045593734 0.944654923 0.897746979 0.897825401 0.825551592 0.8935924 1.109570886 0.920757707 1 18.10375609 1.765469704 25 1.020210844 0.914056765 0.270256615 0.070949334 20.69078722 19234.89607 0.031511893 0.017476794 58.27331219 -1.765469704 -0.106154078 MESEGGADDS(ph)AEEGDLLDDDDNEDRGDDQLELIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MESEGGADDSAEEGDLLDDDDNEDRGDDQLELIK 34 1 P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 MES(0.009)EGGADDS(0.991)AEEGDLLDDDDNEDRGDDQLELIK;MES(0.006)EGGADDS(0.994)AEEGDLLDDDDNEDRGDDQLELIK 151.96 1.36E-10 98342000 74963 36599 49839 42267 39740 42612 70662 49605 42905 TRUE FALSE 70271.19964 39308.82804 51021.20462 43351.64278 36618.9807 54913.39265 60066.88909 55798.29344 35743.87832 1.965964605 1.099735952 1.427410986 1.212841046 1.024482581 1.536302025 1.68048046 1.561058734 1 15.12540856 MESEGGADDS(ph)AEEGDLLDDDDNEDRGDDQLELIKDDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 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;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(0.106)EGGADDS(0.894)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(0.001)EGGADDS(0.999)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(0.001)EGGADDS(0.999)AEEGDLLDDDDNEDRGDDQLELIKDDEK 366.89 1.50E-161 14123750000 12421642 3547654 6476851 5246226 4917841 5222476 9023327 5042450 4811397 TRUE FALSE 11644193.6 3810325.993 6630484.964 5380853.041 4531613.605 6730120.041 7670362.885 5672010.982 4008343.758 2.904988769 0.950598607 1.654170741 1.342413068 1.130545153 1.67902766 1.913599069 1.415051035 1 21.93457481 4.750730537 24.65565905 1.438100677 2.904989863 0.701265905 0.309964037 975.5655294 1976403.983 0.075841913 1.281797828 56328.80495 -4.750730537 1.466889186 MESEGGADDS(ph)AEEGDLLDDDDNEDRGDDQVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MESEGGADDSAEEGDLLDDDDNEDRGDDQVK 31 1 B4DY08 B4DY08 HNRNPC 1 MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQVK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQVK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQVK 329.84 7.35E-106 1987670000 1905730 1214170 1529810 1405700 1736730 1098960 1937710 1460750 2618020 TRUE FALSE 1786453.761 1304068.41 1566097.816 1441772.642 1600334.231 1416211.912 1647168.374 1643127.853 2181055.549 0.819077608 0.597907014 0.718045818 0.661043522 0.733742995 0.649324091 0.75521615 0.753363597 1 21.05659508 0.426861697 0.797770922 1.003351724 0.685991225 0.70040019 0.060332395 0.942792226 0.877499357 0.057407242 0.018032419 2.672155313 -0.426861697 -0.317360498 MESMNRPYTSLVPPLS(ph)PQPK ddPTM_SK-BR-3_Pertuzumab_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 83.059 0.0018903 361760000 800240 571190 738830 856870 935290 485000 577650 439010 829640 TRUE FALSE 750154.4069 613481.5019 756355.3965 878858.7349 861836.0962 625011.6267 491036.7451 493821.3649 691167.7243 1.085343514 0.88760149 1.094315272 1.271556388 1.246927578 0.904283584 0.710445132 0.714473995 1 19.39867632 2.026287615 6.836091864 0.783209021 1.089452978 0.537883735 0.131592922 0.136417321 22.96280429 0.053448416 0.038530488 106.2398907 -2.026287615 0.306243958 MESSFGS(ph)PSKQESSESLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MESSFGSPSKQESSESLPK 19 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4;A8MV73 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 MES(0.005)S(0.021)FGS(0.501)PS(0.469)KQES(0.002)S(0.002)ESLPK;MESS(0.001)FGS(0.971)PS(0.028)KQESSESLPK 161.84 1.74E-11 725380000 1115290 545450 758580 700930 752670 533910 955450 592320 955100 TRUE FALSE 1045485.99 585835.6855 776573.8758 718917.0505 693558.3343 688041.1497 812189.1425 666272.4559 795687.6398 1.313940217 0.736263398 0.975978307 0.903516675 0.871646485 0.864712627 1.020738669 0.837354286 1 19.60184266 -0.883792561 7.419254856 1 0.925923775 0.006716777 0.153862348 9.68E-10 1.30E-10 0.12989775 0.030617193 0.130679493 0.883792561 -0.074076226 METEADAPS(ph)PAPSLGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 METEADAPSPAPSLGER 17 0 Q12873-3;Q12873;Q12873-2 Q12873-3 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 METEADAPS(1)PAPSLGER 233.37 4.36E-20 452150000 533810 506760 551290 518660 604930 503350 618610 555770 665380 TRUE FALSE 500399.785 544281.0377 564366.8591 531969.6937 557421.238 648658.9738 525855.1734 625159.1079 554323.7795 0.902721123 0.981882896 1.018117714 0.959673233 1.005587815 1.170180674 0.94864264 1.12778692 1 19.08036937 2.467399143 24.98963657 1.054518505 0.977622376 0.30436536 0.067097241 288.37272 741225.0852 0.021265004 0.017811338 293.3588153 -2.467399143 -0.076896129 METVSNASSSS(ph)NPSS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 METVSNASSSSNPSSPGR 18 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 METVSNASSS(0.021)S(0.979)NPS(0.005)S(0.995)PGR;METVSNASSS(0.004)S(0.995)NPS(0.004)S(0.996)PGR 237.66 1.08E-23 429780000 723030 745200 755270 662150 662190 515310 754890 646440 944160 TRUE FALSE 677776.8429 800375.3834 773185.3611 679141.89 610184.2685 664071.6316 641701.2526 727149.457 786573.5965 0.861682678 1.01754672 0.982979043 0.863418112 0.775749747 0.844258738 0.81581845 0.924451902 1 19.58522223 3.210331767 6.806223093 0.851935909 0.971914986 0.182803273 0.073636006 0.170126156 26.36792275 0.019429199 0.023816341 1623.049507 -3.210331767 0.119979077 METVSNASSSSNPSS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 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(0.035)S(0.965)PGR;METVSNASSSSNPS(0.002)S(0.998)PGR;METVSNASSSSNPS(0.011)S(0.989)PGR;METVSNASSSSNPS(0.2)S(0.8)PGR;METVSNASSSSNPS(0.048)S(0.952)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPS(0.001)S(0.999)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPS(0.002)S(0.998)PGR;METVSNASSSSNPSS(1)PGR 431.38 5.18E-169 13692710000 8577560 9387060 9572820 9640540 10509030 9024200 11811770 9189860 11407140 TRUE FALSE 8040705.831 10082087.69 9799891.811 9887932.578 9683693.175 11629340.04 10040704.74 10337234.25 9503214.641 0.84610378 1.060913393 1.031218612 1.040482926 1.018991314 1.223726969 1.056558767 1.087761841 1 23.17998418 5.377502828 1.513549764 1.071779906 3.74E-11 0.540377169 0.062487652 5.294309814 2.792781504 0.015798631 13.68416262 238507.9329 -5.377502828 -1.071779906 MEVDRS(ph)PGLPMSDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 MEVDRSPGLPMSDLK 15 1 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK;MEVDRS(1)PGLPMSDLK 197.84 4.98E-09 2344870000 4198070 3965070 4605400 5237210 5327610 2201458 2796529 2233187 3973330 TRUE FALSE 3935320.292 4258647.908 4714642.263 5371605.675 4909201.001 2836983.187 2377215.438 2512005.313 3310155.554 1.188862646 1.286540115 1.424296286 1.622765331 1.483072599 0.857054341 0.718158225 0.758878328 1 21.65846758 2.20178239 6.727597728 0.797573136 1.398832614 0.810834321 0.135815544 0.077198726 9.836635056 0.052228144 0.039014098 159.1411126 -2.20178239 0.601259477 MEVEELS(ph)PLALGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MEVEELSPLALGR 13 0 P30305;G8JLH2;B4DIG0;P30305-3;P30305-2;P30305-4 P30305 CDC25B M-phase inducer phosphatase 2 1 MEVEELS(1)PLALGR 94.717 0.019652 20974000 55620 58165 66102 65488 76268 53197 61485 48245 46932 TRUE FALSE 52138.84348 62471.59712 67669.97066 67168.53295 70278.21893 68554.11032 52265.89505 54268.49445 39098.74601 1.333517026 1.5977903 1.730745294 1.717920389 1.79745455 1.753358287 1.336766531 1.387985549 1 15.25483472 1.167277376 1.275121305 1.028337443 1.66028051 0.657032075 0.148307626 0.246633793 0.805603961 0.136305145 0.042719207 14.69864755 -1.167277376 0.631943067 MEVGPFSTGQES(ph)PTAENAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MEVGPFSTGQESPTAENAR 19 0 Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2 Q9Y4W2-3 LAS1L Ribosomal biogenesis protein LAS1L 1 MEVGPFST(0.012)GQES(0.974)PT(0.014)AENAR;MEVGPFSTGQES(0.999)PTAENAR;MEVGPFST(0.001)GQES(0.959)PT(0.04)AENAR;MEVGPFSTGQES(0.996)PT(0.003)AENAR 189.55 1.44E-14 480848000 580492 509953 581390 519601 445339 522254 725592 493556 350534 TRUE FALSE 544160.0419 547710.4507 595180.8454 532934.8413 410363.8714 673020.2517 616796.2157 555177.5531 292027.6109 1.86338559 1.875543374 2.038097848 1.824946757 1.405222849 2.304645954 2.11211609 1.901113225 1 18.15574526 2.198527683 24.99997226 1.956158962 1.84488112 0 0.379377959 823.345735 514162.616 0.129312371 0.095504762 157.9529286 -2.198527683 -0.111277842 MEWWSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MEWWSR 6 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 ; 144.9 0.026088 927780000 1350800 1757510 1336320 1365050 1809930 1005460 1370150 1598940 1570720 FALSE TRUE 1266255.839 1887637.869 1368018.141 1400079.494 1667785.399 1295719.98 1164708.727 1798571.179 1308556.685 0.967673662 1.442534275 1.04544049 1.069941799 1.274522853 0.99019018 0.890071283 1.374469444 1 20.31954499 3.733224876 24.15589269 1.0764937 1.240512066 0.050838754 0.180221775 318.7423695 1261448.42 0.043645561 0.076148125 5410.343961 -3.733224876 0.164018366 MFADYLAHESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MFADYLAHESR 11 0 O14579;M0QXB4;O14579-3;O14579-2;M0R061 O14579 COPE Coatomer subunit epsilon 0 ;;; 209.8 1.49E-08 864300000 801110 2412250 1532470 1670090 2311670 1358800 1518290 2075960 1489330 FALSE TRUE 750969.9551 2590855.5 1568820.912 1712947.337 2130120.763 1751063.502 1290636.51 2335148.176 1240751.202 0.605254264 2.088134589 1.264412164 1.380572781 1.716799275 1.411293013 1.04020573 1.882043856 1 20.24278242 -1.826995542 2.636758176 0.844312042 1.445517032 0.089386482 0.419737201 68313181.83 47102035.01 67539267.69 0.094865292 0.014893764 1.826995542 0.60120499 MFDYTDDPEGPVMPGSHSVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MFDYTDDPEGPVMPGSHSVER 21 0 Q09161 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 ;;; 217.42 5.82E-25 646495000 905801 1131019 1052019 1086630 1136444 929758 1185761 939173 1034066 FALSE TRUE 849108.5323 1214760.824 1076973.387 1114514.765 1047192.272 1198164.041 1007967.146 1056430.816 861473.7043 0.985646489 1.410096231 1.250152363 1.293730453 1.215582399 1.390830661 1.170049812 1.226306515 1 19.71644723 0.628595632 1.075816793 1.000684838 1.270901456 0.282910447 0.118883725 1.348173899 2.476778864 0.100725106 0.031654461 4.252023266 -0.628595632 0.270216618 MFEELGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 MFEELGQR 8 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;;; 161.68 0.00080522 445538000 634512 874165 702589 689008 904306 578732 703135 731330 830780 FALSE TRUE 594799.0266 938889.0862 719254.7429 706689.1118 833285.4546 745802.5335 597706.4343 822638.1604 692117.451 0.859390304 1.356545894 1.039209085 1.02105374 1.203965387 1.077566434 0.863591047 1.188581735 1 19.40065736 1.988998766 24.69703684 0.99432046 1.122097661 0.032056265 0.150045816 884.6893921 1986068.296 0.055217701 0.038032692 97.49868671 -1.988998766 0.127777201 MFEFYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MFEFYER 7 0 O75306;O75306-2 O75306 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" 0 ;; 143.56 0.0056153 208171000 250833 338186 237211 224423 425580 194543 206450 335014 436260 FALSE TRUE 235133.8103 363225.6433 242837.7569 230182.0741 392156.6635 250704.406 175494.7391 376841.2354 363445.3877 0.64695775 0.999395386 0.668154736 0.63333332 1.078997497 0.689799388 0.482864125 1.036857938 1 18.47137907 3.944621569 23.78893397 0.758076434 0.846528793 0 0.212520219 780.341235 571189.3947 0.052060307 0.093865526 8802.814886 -3.944621569 0.088452359 MFFDALYDEDVVKEDAFYSWESSKDPAEQQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MFFDALYDEDVVKEDAFYSWESSKDPAEQQGK 32 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 342.02 6.94E-118 326280000 1068400 512370 730450 724260 786580 501900 1048400 566290 988390 FALSE TRUE 1001530.751 550306.4079 747776.6189 742845.7378 724805.1797 646790.3823 891202.1529 636992.5531 823421.3238 1.216304123 0.668316926 0.908133658 0.902145374 0.880236106 0.785491417 1.082316096 0.773592491 1 19.65127128 1.755548838 25 0.958388808 0.868984947 0.013957586 0.157009347 18.32452592 26996.42718 0.065909201 0.036550368 56.95722706 -1.755548838 -0.089403862 MFGIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 MFGIDR 6 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;;;; 149.11 0.024845 3794260000 2138380 3974150 2242190 1943630 4686150 1893290 2473750 3914010 4026890 FALSE TRUE 2004542.613 4268400.201 2295375.806 1993506.836 4318118.682 2439852.088 2102834.153 4402682.764 3354776.044 0.597519055 1.272335364 0.684211338 0.594229484 1.287155573 0.727277188 0.626818042 1.312362645 1 21.67778503 1.231054687 24.99948163 1.156181283 0.848462688 0.205422465 0.266521413 316.237637 1053227.215 0.227302303 0.061267027 17.02372859 -1.231054687 -0.307718595 MFGIDRDAIAQAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MFGIDRDAIAQAVR 14 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 297.16 1.03E-43 2783400000 1941860 2131600 3810800 3362100 3088800 3809200 3910300 1586470 2334200 FALSE TRUE 1820322.449 2289425.882 3901193.976 3448377.178 2846218.108 4908854.203 3323986.816 1784544.272 1944606.94 0.936087603 1.177320637 2.006160677 1.773302926 1.463646996 2.524342632 1.709336086 0.917688935 1 20.89104714 4.288216824 2.760820786 1.71565561 0.976779029 0.195615626 0.46665388 0.363297055 5.347678127 0.110856895 0.385135212 19418.55117 -4.288216824 -0.73887658 MFLGDNAHLSIINEYLSQSYQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MFLGDNAHLSIINEYLSQSYQK 22 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 150.58 5.49E-08 16903000 11562 19423 15445 18634 18060 13573 19475 20095 14330 FALSE TRUE 10838.35506 20861.09913 15811.36269 19112.17999 16641.64045 17491.30476 16554.90455 22603.90498 11938.23042 0.907869481 1.747419709 1.32443102 1.600922357 1.393978828 1.465150541 1.386713437 1.893404984 1 13.54330138 -1.197482753 4.501073483 0.999884431 1.473184273 0.235073239 0.263234397 0.000261776 4.67E-05 0.218553936 0.051501155 0.06346251 1.197482753 0.473299842 MFLQYYLNEQGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MFLQYYLNEQGDR 13 0 Q9NPE3;H0YM60 Q9NPE3 NOP10 H/ACA ribonucleoprotein complex subunit 3 0 ; 227.37 2.14E-11 264300000 220111 241620 224122 198185 273120 176477 253530 229498 249840 FALSE TRUE 206334.6454 259509.7962 229438.2797 203270.7626 251670.2569 227423.045 215515.5302 258151.3305 208140.09 0.99132582 1.246803517 1.102326225 0.976605529 1.209138792 1.092644118 1.035434981 1.240276828 1 17.66719534 -1.481349187 4.238319515 0.999270634 1.115120961 0.116811008 0.096248619 0.000617543 7.56E-05 0.086758312 0.020321409 0.033010402 1.481349187 0.115850327 MFLYADNEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MFLYADNEDR 10 0 A0A087WY55;Q9NP79;Q5TGM0;Q9NP79-2 A0A087WY55 VTA1 Vacuolar protein sorting-associated protein VTA1 homolog 0 ;; 104.39 0.0062524 352079000 636340 726480 653420 625230 779770 542990 735510 664110 647590 FALSE TRUE 596512.6153 780269.3351 668919.431 641274.4603 718530.0096 699742.3983 625227.1036 747025.5954 539503.0454 1.105670525 1.446274199 1.239880732 1.188639185 1.3318368 1.297012879 1.158894484 1.384655011 1 19.04127158 -2.130902602 2.435369014 0.428123326 1.274452438 0.400866624 0.103209259 3101378.317 1456370.999 9724049.827 0.023472876 0.007397712 2.130902602 0.846329112 MFNGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MFNGEK 6 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41;A0A2R8YF08;K7ELR7;K7ENA0;K7ERK8;A0A0J9YXM3;A0A0J9YXH9 P06744 GPI Glucose-6-phosphate isomerase 0 97.068 0.09653 185350000 335210 332210 307030 326880 368110 254300 395680 305430 423420 FALSE TRUE 314229.8045 356807.1741 314312.8966 335268.2942 339200.1255 327712.2818 336351.4573 343563.6078 352748.4666 0.890804168 1.011505954 0.891039725 0.950445788 0.961592062 0.92902539 0.953516426 0.973962016 1 18.42828029 1.075102147 1.991256381 0.999564921 0.943028486 0.254118002 0.034556318 0.442862604 3.513661555 0.029960532 0.008470649 11.88781799 -1.075102147 -0.056536435 MFVGGLSWDTSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MFVGGLSWDTSKK 13 1 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ; 174.72 3.13E-05 1121930000 1252980 1278540 1149330 1100870 1544950 759220 1337430 1206610 1866840 FALSE TRUE 1174558.218 1373204.432 1176592.65 1129120.188 1423615.859 978394.4891 1136894.788 1357257.915 1555252.344 0.755220349 0.882946383 0.756528453 0.726004492 0.915360047 0.629090509 0.731003423 0.872693052 1 20.56871725 0.977982636 4.647000264 0.99971994 0.775308575 0.46595327 0.080159628 0.15924587 11.65526189 0.075307909 0.019105889 9.505667864 -0.977982636 -0.224411365 MFVLDEADEMLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 MFVLDEADEMLSR 13 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;J3QR64;J3QLN6;Q14240;Q14240-2;E7EQG2;J3KTN0 P60842;Q14240;J3KTN0 EIF4A1;EIF4A2 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ;;;;;;;;;;;;; 329.49 5.11E-62 1790229000 1449980 1681026 1611609 1633503 1748870 1452764 1827544 1492050 1766892 FALSE TRUE 1359228.34 1805490.914 1649837.127 1675421.452 1611520.805 1872153.383 1553520.743 1678335.727 1471986.311 0.923397405 1.226567734 1.120823689 1.138204507 1.094793337 1.271855159 1.055390755 1.140184331 1 20.48933282 0.332340042 1.14577111 0.999951018 1.134202119 0.127561843 0.094284279 5.883971371 8.485365762 0.081722985 0.024441166 2.149512832 -0.332340042 0.1342511 MFVSSSGLPPS(ph)PVPSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MFVSSSGLPPSPVPSPR 17 0 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3;Q7Z309-5 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 MFVSSS(0.001)GLPPS(0.999)PVPSPR 103.17 0.001746 0 32342 32569 33951 35568 36988 30259 39714 31080 34451 TRUE FALSE 30317.77195 34980.44265 34756.33375 36480.7351 34083.11168 38994.28209 33759.25439 34960.40642 28700.90554 1.056335031 1.218792299 1.210983873 1.271065648 1.187527398 1.358642919 1.176243528 1.218094195 1 14.80880864 0.210635224 1.857759308 0.999987714 1.217867086 0.435993875 0.075605778 16.74486025 37.90265999 0.065732344 0.01821515 1.624183984 -0.210635224 0.217879372 MFVVAEADAGSCLLHEFTISGTTYTPEGEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MFVVAEADAGSCLLHEFTISGTTYTPEGEVR 31 0 Q93084-4;Q93084-2;Q93084-3;Q93084-7;Q93084;Q93084-6;Q93084-5 Q93084-4 ATP2A3 Sarcoplasmic/endoplasmic reticulum calcium ATPase 3 0 73.616 0.0037107 5379100 5222.1 6351 4314.9 5378 5911.9 3631.4 4859.7 4932.1 3973.3 FALSE TRUE 4895.258083 6821.234648 4417.251466 5516.008585 5447.603221 4679.726229 4131.0331 5547.883542 3310.130562 1.478871601 2.060714682 1.334464422 1.66640212 1.645736662 1.413758806 1.247997027 1.676031636 1 11.69267241 -1.260752711 0.091577158 1.09E-09 2.220447308 0.419383311 0.218942929 60.44035638 1.001245999 20.20167791 6.389033785 0.054858925 1.260752711 2.220447307 MFYEEHLHLDDEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MFYEEHLHLDDEIR 14 0 Q9BV57;Q9BV57-2;A0A0G2JQN5 Q9BV57 ADI1 "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase" 0 ;; 211.06 2.52E-09 79498000 45539 59053 47334 45557 53612 40822 53786 50272 58297 FALSE TRUE 42688.79528 63425.34556 48456.78483 46726.06975 49401.52978 52606.64871 45721.28862 56548.56986 48566.85409 0.878969743 1.305938932 0.997733655 0.962097929 1.017186118 1.083180076 0.941409311 1.164344921 1 15.56768442 3.726988527 24.99999923 1.017516669 1.131617392 0.030044816 0.120023577 10.83982295 2042353.492 0.028086318 0.046806783 5333.208057 -3.726988527 0.114100724 MGAGLGHGMDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 MGAGLGHGMDR 11 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;;;;;;;; 170.89 1.52E-05 6158723000 3933910 4929280 4412520 4428130 5158820 3762623 4664064 4259042 5350530 FALSE TRUE 3687693.595 5294249.02 4517187.058 4541763.313 4753667.087 4848831.179 3964730.902 4790792.769 4457491.977 0.827302352 1.187719248 1.013392078 1.01890555 1.066444339 1.087793585 0.88945329 1.074773167 1 22.08780077 1.767565644 25 0.97707973 1.04974449 0.023958468 0.100146806 49.26744301 42488.75664 0.042235167 0.023425043 58.55522363 -1.767565644 0.07266476 MGANS(ph)LER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MGANSLER 8 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 1 MGANS(1)LER 70.675 0.052054 0 167030 203850 211790 212080 193240 174990 229640 185990 215340 TRUE FALSE 156575.8905 218943.2661 216813.7588 217522.3319 178063.7099 225506.7723 195207.6139 209211.2609 179398.3629 0.872783274 1.220430681 1.208560409 1.212510128 0.992560395 1.257016891 1.08812372 1.166182665 1 17.4528072 -1.01865934 4.795872462 0.999997186 1.143121748 0.088650294 0.118955613 3.21E-06 6.56E-07 0.103211416 0.024326686 0.095794519 1.01865934 0.143124562 MGANSLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MGANSLER 8 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;; 153.04 0.0016546 0 951740 1355280 1053980 1164740 1460880 848490 1166500 1203760 1344440 FALSE TRUE 892172.2923 1455626.341 1078980.903 1194629.2 1346148.378 1093435.289 991594.1543 1354052.086 1120044.279 0.796550913 1.299614997 0.963337722 1.066591047 1.201870679 0.976242913 0.885316923 1.208927282 1 20.09512434 MGAPESGLAEYLFDKHTLGDS(ph)DNES ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MGAPESGLAEYLFDKHTLGDSDNES 25 1 G3V192;P02794;G3V1D1 G3V192 FTH1 "Ferritin;Ferritin heavy chain;Ferritin heavy chain, N-terminally processed" 1 MGAPESGLAEYLFDKHTLGDS(0.97)DNES(0.03);MGAPESGLAEYLFDKHT(0.026)LGDS(0.947)DNES(0.026) 171.05 4.67E-12 92329000 48429 77885 64173 79579 99816 46002 67653 52075 161940 TRUE FALSE 45397.91534 83651.68644 65695.21386 81621.13187 91976.854 59282.03062 57509.06071 58576.67838 134911.1678 0.336502278 0.620050125 0.486951636 0.604999076 0.681758638 0.439415295 0.426273537 0.434187023 1 17.04165025 -1.897766844 2.739364924 1.256129369 0.511749516 0.687615973 0.104991248 16208481.55 8842847.121 26713854.28 0.02486998 0.012654155 1.897766844 -0.744379852 MGEMGRLKS(ph)Y(ph)ENQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MGEMGRLKSYENQK 14 2 E7EMD0 E7EMD0 POR 2 MGEMGRLKS(1)Y(1)ENQK 41.912 0.082417 181030000 47399 107790 82311 107060 162720 65266 113210 97276 192810 TRUE FALSE 44432.3812 115770.8838 84263.45579 109807.3409 149940.6276 84107.2347 96235.21149 109421.1227 160628.7654 0.276615344 0.720735688 0.524585093 0.683609443 0.933460624 0.523612533 0.599115677 0.681205029 1 17.29337075 -5 0.143442129 2.242871535 0.498594656 0.403208345 0.159302365 153.9963643 1.340218852 55.32596227 0.874349937 1.00E-05 5 -1.744276879 MGESDDSILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 MGESDDSILR 10 0 Q8WVC2;P63220 Q8WVC2 RPS21 40S ribosomal protein S21 0 ;;;;; 219.54 1.46E-08 5400320000 5183490 5481760 5248920 5078600 5608530 4064300 5571240 4774500 5047950 FALSE TRUE 4859064.614 5887635.214 5373426.861 5208925.474 5168058.678 5237597.432 4735884.283 5370606.835 4205414.534 1.155430594 1.400013047 1.277740118 1.238623549 1.228905887 1.245441416 1.126139705 1.277069547 1 22.00381659 -0.161484993 0.234507628 0.883572708 1.33079142 0.506193268 0.074568518 6.046681734 0.517899086 0.728428162 0.156747453 0.689469418 0.161484993 0.447218712 MGGAGGEGS(ph)DDDTSLT ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 MGGAGGEGSDDDTSLT 16 0 Q9Y365;F5H8H3;F5GY11 Q9Y365 STARD10 PCTP-like protein 1 MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(1)DDDTSLT;MGGAGGEGS(0.999)DDDT(0.001)SLT;MGGAGGEGS(0.995)DDDT(0.005)SLT;MGGAGGEGS(1)DDDTSLT 285.31 8.33E-36 8534350000 7060150 7422530 6760830 6660100 7063020 6176780 8402360 6108950 7643980 TRUE FALSE 6618267.814 7972101.844 6921200.08 6831009.442 6508318.9 7959916.114 7142504.122 6871665.855 6368150.356 1.039276312 1.251870857 1.08684621 1.072683442 1.022010872 1.249957314 1.121597909 1.079067778 1 22.60244297 0.96047579 2.988602893 1.000600953 1.131015304 0.187868636 0.077804532 0.408278127 8.928691174 0.071175539 0.018730455 9.130105375 -0.96047579 0.130414351 MGGEEAEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MGGEEAEIR 9 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 124.08 0.0012556 345052000 669770 768080 716240 761050 842500 571610 850320 728550 909870 FALSE TRUE 627850.2913 824949.4424 733229.551 780579.8315 776333.4485 736624.5277 722822.41 819511.0712 758006.819 0.828291086 1.088314012 0.967312605 1.029779432 1.024177394 0.971791426 0.953582991 1.081139444 1 19.5318513 4.75509418 24.48760133 1.009484092 0.828290898 0.624786248 0.045203855 1708.288973 2530064.433 0.010542611 0.280943773 56897.63049 -4.75509418 -0.181193195 MGIGGLDKEFSDIFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MGIGGLDKEFSDIFR 15 1 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 ; 187.37 3.13E-07 291110000 528140 632710 546180 590370 714180 393730 656780 550800 933760 FALSE TRUE 495084.6602 679556.5067 559135.6475 605519.8937 658091.1837 507393.4593 558301.9362 619568.5925 777909.4237 0.636429699 0.873567649 0.718767032 0.778393827 0.845974047 0.652252619 0.717695299 0.796453383 1 19.56924266 0.903153685 7.0295784 0.999999102 0.754041812 0.528965452 0.07460389 1.647271637 119.4165636 0.068019051 0.017057536 8.001173446 -0.903153685 -0.24595729 MGIISIS(ph)T(ph)IQKM ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MGIISISTIQKM 12 1 X6RDV4;Q8WWT9-4 X6RDV4 SLC13A3 2 MGIIS(0.001)IS(1)T(1)IQKM 83.647 0.028095 209130000 54794 108010 120660 134540 111600 129260 108670 104640 58831 TRUE FALSE 51364.54135 116007.1728 123522.1122 137992.5242 102835.3862 166575.2636 92375.94234 117704.5343 49011.72604 1.048005151 2.3669269 2.520256318 2.815500194 2.098179242 3.398681848 1.884772274 2.401558644 1 15.58083933 0.193676062 1.34911904 0.998863707 2.372821999 0.31162891 0.609418517 8.688095352 13.29347829 0.546601432 0.15526366 1.561982135 -0.193676062 1.373958292 MGLAMGGGGGAS(ph)FDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 MGLAMGGGGGASFDR 15 0 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 1 MGLAMGGGGGAS(1)FDR;MGLAMGGGGGAS(1)FDR;MGLAMGGGGGAS(1)FDR;MGLAMGGGGGAS(1)FDR;MGLAMGGGGGAS(1)FDR;MGLAMGGGGGAS(1)FDR;MGLAMGGGGGAS(1)FDR;MGLAMGGGGGAS(1)FDR;MGLAMGGGGGAS(1)FDR 198.89 8.07E-09 1191492000 2013270 2194800 2009460 2118630 1347391 1345648 2605010 1624840 2302850 TRUE FALSE 1887263.024 2357305.276 2057125.34 2172997.633 1241572.346 1734114.733 2214412.934 1827704.851 1918489.458 0.983723427 1.228729856 1.072263041 1.132660711 0.647161412 0.903895888 1.154248164 0.952679121 1 20.87153941 MGLGHEQGFGAPCLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MGLGHEQGFGAPCLK 15 0 Q9UGI8-2;Q9UGI8;F8WDI4 Q9UGI8-2 TES Testin 0 ; 155.98 2.21E-06 1014380000 1937420 1835330 1800530 1892570 2141860 1528690 2135800 1850300 2093950 FALSE TRUE 1816160.341 1971219.743 1843239.422 1941136.55 1973646.955 1969997.987 1815556.618 2081314.028 1744456.218 1.041103997 1.129990952 1.056626932 1.112745927 1.131382339 1.129290587 1.040757916 1.1931019 1 20.73434596 -1.202807258 3.927118896 0.999925884 1.100133729 0.318387311 0.047636398 2.74E-05 5.56E-06 0.040836642 0.009618174 0.062689202 1.202807258 0.100207845 MGLS(ph)MER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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;MGLS(1)MER 100.76 0.010028 3043080000 2485110 2443790 2322630 2520100 1933143 1598502 3151810 1910509 3066650 TRUE FALSE 2329571.401 2624730.754 2377723.88 2584770.033 1781321.747 2059963.578 2679225.35 2149040.254 2554806.304 0.911838756 1.027369766 0.930686556 1.011728376 0.697243366 0.806309103 1.048699992 0.841175416 1 21.28478248 MGLVDQLVEPLGPGLKPPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MGLVDQLVEPLGPGLKPPEER 21 1 H0YFD6;P40939;A0A2R8Y4F5;A0A2R8YG21;A0A2R8Y688 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 139.69 1.57E-07 61564000 109930 95714 103750 87792 127120 93923 103400 105860 141380 FALSE TRUE 103049.6775 102800.7642 106210.999 90044.89135 117136.508 121037.0454 87896.12992 119076.854 117782.7647 0.874913047 0.872799721 0.901753319 0.764499726 0.994513147 1.027629516 0.746256298 1.010987086 1 16.84576892 2.717046295 24.95227264 0.930291277 0.864753122 0.216970726 0.088460232 1816.76572 2107079.02 0.028440752 0.026835208 521.2502723 -2.717046295 -0.065538156 MGPGAASGGERPNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MGPGAASGGERPNLK 15 1 Q9H0U4;E9PLD0 Q9H0U4 RAB1B Ras-related protein Rab-1B 0 154.65 2.23E-06 504740000 229940 237000 208680 201500 271020 183750 308750 233680 314680 FALSE TRUE 215548.4659 254547.7266 213629.9881 206670.8311 249735.1824 236795.6421 262455.8038 262855.4624 262157.8751 0.822208624 0.970971124 0.8148906 0.788344928 0.952613696 0.90325588 1.001136448 1.002660944 1 18.00007636 1.983461559 1.490183493 1.006343332 0.868051059 0.547195143 0.055687907 0.331162143 1.370024979 0.037845323 0.017867743 96.26348028 -1.983461559 -0.138292272 MGPGIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MGPGIDR 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;; 100.82 0.022129 516410000 553650 694220 666230 634870 738330 538950 727250 635490 821780 FALSE TRUE 518998.0348 745620.7711 682033.2902 651161.839 680344.5401 694536.1159 618205.614 714832.3254 684619.6091 0.758082339 1.089102271 0.996222254 0.951129401 0.993755556 1.014484696 0.902991392 1.044130662 1 19.38494309 4.75290524 25 0.996070895 0.758082176 0.700664541 0.049450317 1596.41906 2782212.821 0.012395483 0.269544354 56611.57535 -4.75290524 -0.23798872 MGPLGLDHMASSIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 MGPLGLDHMASSIER 15 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;;; 202.25 6.01E-09 1677172000 1888800 2665800 2351360 2308010 3001660 1807184 2360940 2510040 2867040 FALSE TRUE 1770583.38 2863178.606 2407135.37 2367237.444 2765921.732 2328888.684 2006938.965 2823424.019 2388512.502 0.741291234 1.19872875 1.007796847 0.991092758 1.158010155 0.975037259 0.840246372 1.182084673 1 21.187681 2.042596425 24.99967659 0.96917984 1.043103201 0 0.147334539 434.0563417 254744.137 0.051010633 0.037673826 110.3053114 -2.042596425 0.073923361 MGPLINRPHLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MGPLINRPHLER 12 1 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ; 108.56 0.0010168 973610000 183491 307530 242821 262296 373300 203653 275680 295160 380450 FALSE TRUE 172006.6259 330299.8412 248580.8288 269026.9594 343982.5238 262444.3151 234344.3433 332011.3757 316950.4372 0.542692502 1.04211827 0.784289276 0.848798196 1.085288056 0.82802951 0.739372204 1.047518277 1 18.27389773 4.753394008 24.74715157 0.899644314 0.542692213 0.481456292 0.121750362 2215.898024 3696801.195 0.028101263 0.636573631 56675.32357 -4.753394008 -0.356952101 MGPPVGGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 MGPPVGGHR 9 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;;;; 109.86 0.0023803 613861000 564834 874432 619344 621400 845371 523419 634140 726014 789993 FALSE TRUE 529482.0482 939175.8551 634035.1322 637346.176 778978.9717 674521.5683 539056.5941 816658.4461 658138.0648 0.804515157 1.427019505 0.963377088 0.968408014 1.183610269 1.024893718 0.819063086 1.240861895 1 19.32803074 3.732738238 24.84717925 1.012986875 1.170721854 0.012442099 0.189502412 462.2385268 2044728.873 0.045167295 0.078628853 5404.284931 -3.732738238 0.157734979 MGPSGGEGMEPERRDS(ph)QDGSSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 MGPSGGEGMEPERRDSQDGSSYR 23 2 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 1 MGPSGGEGMEPERRDS(0.998)QDGS(0.001)S(0.001)YR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(0.823)QDGS(0.094)S(0.083)YR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(0.493)QDGS(0.268)S(0.238)YR;MGPSGGEGMEPERRDS(0.478)QDGS(0.478)S(0.043)YR 192.5 7.95E-18 10726000000 1921813 2304742 2111943 2129541 2602160 2030950 2599801 2315552 5544910 TRUE FALSE 1801530.155 2475387.496 2162039.285 2184188.627 2397796.85 2617252.295 2209984.975 2604653.764 4619428.7 0.389989817 0.535864423 0.468031747 0.47282657 0.519067834 0.566574887 0.478410886 0.563847595 1 22.13928301 -5 0.291109889 4.945605278 0.470911352 0.929268033 0.044086216 56.32064852 0.529766698 134.9234405 0.042980178 1.00E-05 5 -4.474693927 LRGWLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LRGWLK 6 1 P60174;P60174-3;P60174-4;U3KPZ0 P60174 TPI1 Triosephosphate isomerase 0 77.944 0.064831 159180000 89040 137500 84489 103860 146150 87166 157690 172090 311200 FALSE TRUE 83467.14534 147680.6431 86493.11898 106525.2234 134671.9685 112329.4092 134045.8484 193575.8153 259258.7096 0.321945386 0.569626545 0.333617023 0.410883876 0.519450123 0.433271497 0.517035083 0.746651156 1 17.98403293 1.054476665 1.653343812 1.000320001 0.436233722 0.868907516 0.07384051 0.115111105 0.635087943 0.064685894 0.018845755 11.33643926 -1.054476665 -0.56408628 MGQAPSQSLLPPAQDQPRS(ph)PVPSAFSDQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 MGQAPSQSLLPPAQDQPRSPVPSAFSDQSR 30 1 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MGQAPSQSLLPPAQDQPRS(0.996)PVPS(0.004)AFSDQSR;MGQAPSQS(0.001)LLPPAQDQPRS(0.993)PVPS(0.002)AFS(0.003)DQS(0.001)R;MGQAPSQSLLPPAQDQPRS(0.988)PVPS(0.012)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.499)PVPS(0.499)AFS(0.001)DQSR;MGQAPSQSLLPPAQDQPRS(0.998)PVPS(0.002)AFSDQSR;MGQAPSQSLLPPAQDQPRS(1)PVPSAFSDQSR;MGQAPSQSLLPPAQDQPRS(0.994)PVPS(0.006)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.942)PVPS(0.056)AFS(0.002)DQSR;MGQAPSQSLLPPAQDQPRS(0.891)PVPS(0.104)AFS(0.005)DQS(0.001)R;MGQAPSQSLLPPAQDQPRS(0.943)PVPS(0.055)AFS(0.002)DQSR;MGQAPSQSLLPPAQDQPRS(0.983)PVPS(0.017)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.885)PVPS(0.113)AFS(0.002)DQSR;MGQAPSQSLLPPAQDQPRS(0.977)PVPS(0.022)AFS(0.001)DQSR;MGQAPSQSLLPPAQDQPRS(0.999)PVPS(0.001)AFSDQSR 178.41 4.92E-18 15204220000 3087001 3848679 3430402 3591410 4601193 2845346 4144335 3396267 5412362 TRUE FALSE 2893791.118 4133639.198 3511772.755 3683571.661 4239833.862 3666751.2 3522930.441 3820298.411 4509003.817 0.641780587 0.916752206 0.778835614 0.816936913 0.940303897 0.813206497 0.781310148 0.847259964 1 22.1043773 -2.813418502 1.20576653 2.693969526 0.82294543 0.330187613 0.081508944 96104.26237 3493.187162 440922.5979 0.021155022 0.001536673 2.813418502 -1.871024095 MGS(ph)KSPGNTSQPPAFFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MGSKSPGNTSQPPAFFSK 18 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 MGS(0.647)KS(0.338)PGNT(0.015)SQPPAFFSK 132.72 8.60E-06 236250000 228440 275560 259580 287560 425960 110170 261070 229640 675280 TRUE FALSE 214142.3482 295962.7491 265737.3602 294939.2764 392506.8198 141974.2905 221924.9772 258311.0595 562571.4055 0.380649187 0.526089215 0.472362011 0.524269939 0.697701334 0.252366703 0.394483216 0.459161374 1 19.1016767 -1.261633127 3.461075743 1.00148612 0.463981443 0.683057609 0.114874617 56999025.41 87876563.56 900288.6987 0.028113047 0.054747825 1.261633127 -0.537504677 MGS(ph)PAPLLPGDLLGGGSDSI ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MGSPAPLLPGDLLGGGSDSI 20 0 Q9UPQ9-1;Q9UPQ9;Q9UPQ9-2 Q9UPQ9-1 TNRC6B Trinucleotide repeat-containing gene 6B protein 1 MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI 147.12 1.32E-07 49032000 136963 98789 114404 91151 116779 100371 148834 106311 126776 TRUE FALSE 128390.7303 106103.4403 117117.7169 93490.08898 107607.6484 129346.4783 126517.7234 119584.1624 105616.2666 1.215634054 1.004612677 1.108898474 0.885186458 1.018854878 1.224683304 1.197899978 1.132251368 1 16.68847252 2.250328795 24.99907753 1.162256829 1.042058147 0.150061613 0.101948043 296.6270706 630122.8964 0.033186832 0.027556717 177.9626215 -2.250328795 -0.120198681 MGSCDGEGLLT(ph)SPDQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MGSCDGEGLLTSPDQPR 17 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 MGSCDGEGLLT(0.75)S(0.25)PDQPR 264 2.17E-26 263250000 292820 279520 295820 291620 353410 248000 288030 248840 248090 TRUE FALSE 274492.9189 300215.9516 302836.9901 299103.4629 325654.6042 319593.5741 244842.5754 279908.2218 206682.1763 1.328091874 1.452548822 1.465230314 1.447166216 1.575629839 1.546304475 1.184633237 1.354292986 1 17.65705445 1.045093359 1.001129483 1.016726029 1.463971679 0.65596456 0.10129212 0.319397823 0.68672644 0.092031979 0.030782191 11.09413276 -1.045093359 0.44724565 MGSCDGEGLLTS(ph)PDQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MGSCDGEGLLTSPDQPR 17 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 MGSCDGEGLLT(0.138)S(0.862)PDQPR;MGSCDGEGLLT(0.001)S(0.999)PDQPR 316.37 2.79E-58 274270000 761030 753340 820220 797340 930810 620840 786480 681470 681280 TRUE FALSE 713398.4908 809118.0774 839676.0057 817801.0943 857707.9373 800066.4295 668554.6253 766553.0296 567569.9668 1.256934885 1.425582967 1.479422899 1.440881551 1.511193311 1.409634893 1.177924599 1.350587724 1 19.11443872 1.008577447 0.781726377 1.012841749 1.433812049 0.636011545 0.094320099 0.410624459 0.565141312 0.088198798 0.032930948 10.1994663 -1.008577447 0.420970301 MGSGIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MGSGIER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 83.364 0.051959 224980000 131820 179690 158600 172400 183090 148090 161930 140690 179490 FALSE TRUE 123569.6215 192994.4346 162362.0669 176824.0759 168710.8499 190841.179 137650.0998 158255.4562 149531.9595 0.826375993 1.290656762 1.085801774 1.182516945 1.128259474 1.276256793 0.920539665 1.058338677 1 17.19009434 1.708205857 11.75481556 0.993475781 1.146477867 0.193045639 0.131248165 0.157599114 46.00596412 0.055108785 0.03010589 51.07470379 -1.708205857 0.153002086 MGVMS(ph)SPTENSFTLDADF ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MGVMSSPTENSFTLDADF 18 0 P31350;P31350-2 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 MGVMS(0.548)S(0.389)PT(0.063)ENSFTLDADF 141.73 7.85E-08 14062000 24793 31761 32870 40446 42324 22007 25390 24591 29157 TRUE FALSE 23241.25039 34112.61749 33649.69192 41483.91283 39000.04377 28360.06365 21583.00521 27661.24048 24290.50834 0.956803788 1.404359967 1.385302088 1.707823989 1.605567213 1.167536852 0.88853658 1.13876746 1 14.56810506 2.030326581 6.239613853 1.003322681 1.419671338 0.46031829 0.201403476 0.146116438 17.58578196 0.076857607 0.055158559 107.2325369 -2.030326581 0.416348657 MGVMSS(ph)PTENSFTLDADF ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MGVMSSPTENSFTLDADF 18 0 P31350;P31350-2 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 MGVMS(0.142)S(0.761)PT(0.097)ENSFTLDADF;MGVMS(0.007)S(0.832)PT(0.16)ENSFTLDADF 230.14 1.57E-19 16894700 39183 50798 45862 55164 68422 37840 36024 38373 53406 TRUE FALSE 36730.60597 54559.13678 46949.8683 56579.60163 63048.41212 48763.79372 30622.53563 43163.95352 44492.19358 0.825551698 1.226263135 1.055238335 1.271674806 1.417066839 1.096007856 0.688267607 0.970146672 1 15.44126461 1.930867571 8.036621009 0.859924635 1.167177682 0.341559379 0.172362234 0.315062506 33.55940244 0.069317594 0.043544819 85.28400182 -1.930867571 0.307253047 MHAPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 MHAPGK 6 0 P62277;J3KMX5;E9PS50 P62277 RPS13 40S ribosomal protein S13 0 ;;;;;;;; 78.002 0.065696 4229776000 12487560 13197070 13090320 12455950 14703070 9938050 14856830 12629630 14669700 FALSE TRUE 11705985.91 14174194.79 13400828.57 12775590.76 13548350.19 12807003.7 12629186.27 14206467.11 12221232.3 0.957840063 1.159800783 1.09652024 1.045360276 1.108591168 1.047930633 1.033380755 1.162441459 1 23.54288643 3.267464031 23.8136084 1.066229623 1.093923323 0 0.066793422 480.2841728 395702.9594 0.017088459 0.023132244 1851.245565 -3.267464031 0.0276937 MHDLNTDQENLVGTHDAPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 MHDLNTDQENLVGTHDAPIR 20 0 O43684;O43684-2;J3QT28;J3QSX4 O43684 BUB3 Mitotic checkpoint protein BUB3 0 ;;;;; 290.94 1.07E-54 2220910000 531888 646119 639577 609383 660238 528659 714486 570017 719321 FALSE TRUE 498598.0795 693958.323 654748.0685 625020.7995 608385.5708 681274.2712 607355.4573 641184.8772 599261.6781 0.832020631 1.158022194 1.092591254 1.042984763 1.015225223 1.136856062 1.013506252 1.069958084 1 19.19282659 0.069515471 0.851750305 0.999064929 1.060711423 0 0.090270158 19.11738387 14.18869242 0.136936082 0.026876588 1.173587488 -0.069515471 0.061646493 MHEGDEGPGHHHKPGLGEGT(ph)P ddPTM_SK-BR-3_Pertuzumab_2h_R1 17 MHEGDEGPGHHHKPGLGEGTP 21 1 P06702 P06702 S100A9 Protein S100-A9 1 MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P;MHEGDEGPGHHHKPGLGEGT(1)P 233.91 5.10E-30 29000049000 14518192 12020763 12792425 11462024 11019378 7362928 16450743 9719532 19925544 TRUE FALSE 13609524.28 12910792.8 13095867.36 11756158.94 10153960.5 9488485.786 13984106.81 10933036.97 16599841.98 0.819858664 0.777766006 0.788915182 0.708209087 0.61169019 0.57160097 0.842424092 0.658622954 1 23.98466617 -1.138035339 4.310828632 1.000042956 0.73112961 0.487868874 0.088988863 4.43E-05 8.86E-06 0.086322093 0.020342404 0.072772059 1.138035339 -0.268913346 MHEGDEGPGHHHKPGLGEGTP ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MHEGDEGPGHHHKPGLGEGTP 21 1 P06702 P06702 S100A9 Protein S100-A9 0 ;;; 118.46 5.30E-05 1877040000 1398340 1214050 1284900 1232200 1257380 744773 1594400 1117320 2162140 FALSE TRUE 1310820.396 1303939.525 1315378.435 1263820.338 1158630.447 959776.8747 1355334.522 1256819.862 1801264.866 0.72772218 0.723902159 0.730252646 0.701629373 0.643231581 0.53283495 0.752434885 0.69774295 1 20.78057891 0.31947434 1.644913139 1.00000799 0.689937518 0.711247658 0.062381408 4.210368217 9.489984452 0.060624275 0.017172333 2.086768824 -0.31947434 -0.310070472 MHIAQDINQDNLQLFLNSYNGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MHIAQDINQDNLQLFLNSYNGR 22 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 0 ; 400.29 6.86E-133 1913950000 625440 653750 649930 654800 766010 609220 788980 657080 789100 FALSE TRUE 586294.8268 702154.3302 665346.6465 671603.2766 705850.6645 785091.9241 670679.7735 739117.8844 657394.1122 0.891846787 1.068087342 1.012097057 1.021614377 1.073710049 1.194248487 1.020209584 1.124314731 1 19.32639901 2.729880922 4.193663541 1.088531387 1.011541514 0.26105662 0.068798131 0.308356703 13.38638011 0.020556599 0.02038822 536.8845688 -2.729880922 -0.076989873 MIDLS(ph)AFSRK ddPTM_SK-BR-3_Pertuzumab_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 83178000 43630 132100 105440 104020 106980 139440 90941 107610 62887 TRUE FALSE 40899.27618 141880.8214 107941.0866 106689.3293 98578.22234 179694.0644 77305.2413 121045.3454 52390.75343 0.780658294 2.708127144 2.060307965 2.036415251 1.881595814 3.429881279 1.475551242 2.310433377 1 15.67702459 4.753077492 23.88517651 2.178112498 0.780656443 0.285153652 0.655639581 1603.003791 2637399.315 0.137600318 2.860880417 56634.03328 -4.753077492 -1.397456055 MIDQVFGVLES(ph)PELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MIDQVFGVLESPELSR 16 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 MIDQVFGVLES(0.971)PELS(0.029)R;MIDQVFGVLES(0.995)PELS(0.005)R;MIDQVFGVLES(0.963)PELS(0.037)R 123.14 9.39E-05 31002000 53018.4 56462.7 55201.4 54639.3 55385.2 50974.7 57081.2 47280.4 52009.4 TRUE FALSE 49700.07298 60643.25706 56510.80328 56041.43694 51035.46981 65690.26838 48522.40398 53183.46202 43328.69515 1.147047536 1.399609586 1.304235059 1.293402369 1.177867684 1.516091545 1.119867649 1.227442041 1 15.40303517 0.96882802 1.120611696 1.006044755 1.307657361 0.372415768 0.116098741 0.508437854 1.321009717 0.097435231 0.031032148 9.307392316 -0.96882802 0.301612606 MIEAVQNHIGSLNWGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MIEAVQNHIGSLNWGYR 17 0 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881;E9PKD3 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 ;; 216.26 5.35E-15 1311187000 1144656 1639305 1356749 1270551 1734884 1199958 1513596 1526726 1262489 FALSE TRUE 1073014.024 1760680.848 1388931.727 1303155.49 1598633.209 1546366.395 1286646.331 1717341.102 1051771.43 1.020196968 1.674014713 1.320564229 1.239010162 1.519943557 1.470249477 1.223313635 1.632808282 1 20.00438978 -1.255005245 3.495537756 0.999016408 1.397406998 0.271623887 0.198840278 34748083.03 55930758.42 370989.9465 0.042998988 0.055589754 1.255005245 0.398390589 MIFDVESMKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MIFDVESMKK 10 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 112.15 0.0026606 229950000 894930 792520 763730 777350 1071700 490680 977900 828750 1318900 FALSE TRUE 838917.9288 851199.0054 781846.0363 797298.1171 987533.005 632331.3505 831272.9734 932221.2618 1098767.07 0.763508438 0.774685581 0.71156668 0.725629789 0.898764654 0.57549172 0.75655068 0.848424828 1 20.06745415 0.969438386 2.855446446 0.998802141 0.740759145 0.529315031 0.078345939 0.19658472 3.852683763 0.068151969 0.018048806 9.320482298 -0.969438386 -0.258042997 MIIEEAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MIIEEAKR 8 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ; 121.09 0.0023219 1178780000 478330 545450 414420 400230 697910 311070 451990 515140 597560 FALSE TRUE 448392.1791 585835.6855 424250.2381 410500.5794 643098.9638 400870.8592 384218.2956 579456.363 497823.3756 0.900705353 1.176794249 0.85221036 0.824590808 1.291821548 0.80524716 0.771796413 1.16397982 1 18.92527445 MIKPFFHSLSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MIKPFFHSLSEK 12 1 P10599 P10599 TXN Thioredoxin 0 ;;; 174.84 1.76E-05 6175270000 12453600 16021000 10334500 9767800 17794200 8691130 16872200 15895500 18920600 FALSE TRUE 11674151.41 17207211.51 10579639.22 10018458.28 16396715.31 11200118.14 14342370.24 17880088.17 15762629.63 0.740622071 1.091645995 0.671184915 0.635582928 1.040227151 0.710548836 0.909897053 1.134334092 1 23.9100049 1.416174721 5.201076795 1.061700764 0.830834976 0.312817537 0.151828043 0.255548377 11.69518509 0.099746075 0.036816002 26.07202244 -1.416174721 -0.230865789 MILIQDGSQNTNVDKPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MILIQDGSQNTNVDKPLR 18 1 A0A087WTP3;Q92945;M0R0I5;M0QYH3 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ; 90.385 0.0024766 433690000 168076 183039 191256 187444 209591 182110 189743 169152 238768 FALSE TRUE 157556.4232 196591.398 195792.6826 192254.1304 193130.5683 234682.2007 161292.7986 190270.9995 198916.0783 0.792074852 0.988313261 0.984297923 0.966508751 0.97091482 1.179805085 0.810858529 0.956539065 1 17.60180037 4.740646503 24.27497701 0.977515007 0.792074754 0.313442856 0.088171887 157.0901213 1827976.264 0.01984473 0.129987385 55035.95447 -4.740646503 -0.185440253 MIMATNRPDTLDPALLRPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MIMATNRPDTLDPALLRPGR 20 2 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ; 103.71 0.00015827 993140000 1179790 1235370 1248520 1088680 1367310 1057710 1337370 1136590 1123690 FALSE TRUE 1105949.05 1326838.08 1278135.484 1116617.372 1259926.988 1363053.707 1136843.784 1278495.763 936138.8797 1.181394208 1.417351751 1.365326782 1.192790297 1.345876147 1.456037919 1.214396505 1.365711639 1 19.83636305 -3.042715468 0.46097978 0.000533767 1.330480477 0.519654434 0.094920605 151.8202001 5.035007451 149.1597032 0.046174492 0.000906326 3.042715468 1.32994671 MINTDLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MINTDLSR 8 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 81.296 0.054036 106560000 238370 425400 197080 185240 446090 266900 335070 382390 430400 FALSE TRUE 223450.8472 456897.0586 201754.8307 189993.572 411055.8908 343949.6972 284829.3641 430132.2332 358563.4595 0.623183543 1.274243224 0.56267538 0.529874328 1.146396488 0.959243582 0.794362495 1.199598626 1 18.45186895 2.71300651 24.99859842 0.98464304 0.804482425 0.226754854 0.234966325 1732.326184 1694666.168 0.077730256 0.073309404 516.4241105 -2.71300651 -0.180160615 MIPCDFLIPVQTQHPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MIPCDFLIPVQTQHPIR 17 0 P06744;A0A2U3TZU2;P06744-2;K7EQ48;K7ESF4 P06744;K7ESF4 GPI Glucose-6-phosphate isomerase 0 ;; 174.78 1.31E-09 2233640000 1407840 1827350 1442440 1476360 1750060 1145202 1710110 1591540 1291300 FALSE TRUE 1319725.807 1962648.895 1476655.358 1514245.897 1612617.347 1475803.227 1453694.881 1790247.272 1075773.688 1.226768996 1.824406859 1.372644985 1.40758778 1.499030293 1.371852875 1.351301763 1.664148596 1 20.03694318 -3.067838552 0.289333641 1.06E-14 1.510767317 0.381613481 0.176256713 69.23468075 1.805917347 42.62059788 0.182583831 0.000855385 3.067838552 1.510767317 MIPCDFLIPVQTQHPIRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MIPCDFLIPVQTQHPIRK 18 1 P06744;A0A2U3TZU2;P06744-2;K7EQ48;K7ESF4 P06744;K7ESF4 GPI Glucose-6-phosphate isomerase 0 ;; 151.48 3.07E-08 4955750000 5677210 7380200 5751590 6178350 7801600 4434200 7382300 6335340 9535900 FALSE TRUE 5321883.56 7926637.687 5888020.431 6336896.921 7188893.806 5714281.557 6275392.649 7126321.145 7944296.686 0.669899901 0.997777148 0.74116321 0.797666196 0.904912554 0.719293574 0.789924256 0.897036129 1 22.92148807 0.982244811 4.038133697 0.999593844 0.814463612 0.322832724 0.093154775 0.233495143 11.13437842 0.08357787 0.021380883 9.599415971 -0.982244811 -0.185130231 MISTPS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MISTPSPK 8 0 Q53F19;Q53F19-2 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 MIST(0.004)PS(0.996)PK;MIST(0.001)PS(0.999)PK;MIST(0.003)PS(0.997)PK;MISTPS(1)PK 113.93 0.0028895 1139120000 4125450 2381860 2988930 2634080 2990180 2476620 3972800 2591590 3509770 TRUE FALSE 3867245.449 2558215.393 3059828.831 2701674.952 2755343.325 3191579.989 3377115.522 2915155.716 2923966.713 1.322602419 0.874912625 1.046465002 0.923975961 0.942330606 1.09152405 1.154977417 0.996986629 1 21.47949546 2.213818117 24.85259208 1.08311932 1.000862205 0 0.129253849 533.0213085 535389.3282 0.044471457 0.032859268 163.6131163 -2.213818117 -0.082257115 MITNSLNHDS(ph)PPS(ph)TPPRRPDTSTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MITNSLNHDSPPSTPPRRPDTSTSK 25 2 J3QKZ5;J3QS16;Q8N9M1-2;Q8N9M1;Q8N9M1-3 J3QKZ5 C19orf47 Uncharacterized protein C19orf47 2 MIT(0.001)NS(0.001)LNHDS(0.958)PPS(0.546)T(0.491)PPRRPDT(0.001)S(0.001)T(0.001)S(0.001)K 63.706 0.028411 288880000 89731 82418 82475 83703 82375 87028 101430 79727 126790 TRUE FALSE 84114.89688 88520.31448 84431.34595 85850.96069 75905.59978 112151.5708 86221.51313 89681.09145 105627.9299 0.796331964 0.838038903 0.799327848 0.812767615 0.718612964 1.061760568 0.816275707 0.849028202 1 16.68863183 2.263927207 24.99999906 0.910911848 0.800913928 0.440211641 0.075860578 242.543487 239037.5258 0.024399442 0.020406731 183.6230544 -2.263927207 -0.10999792 MITNSLNHDS(ph)PPST(ph)PPRRPDTSTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MITNSLNHDSPPSTPPRRPDTSTSK 25 2 J3QKZ5;J3QS16;Q8N9M1-2;Q8N9M1;Q8N9M1-3 J3QKZ5 C19orf47 Uncharacterized protein C19orf47 2 MITNSLNHDS(0.983)PPS(0.048)T(0.969)PPRRPDTSTSK 161.26 3.97E-11 229170000 195180 199070 223980 194610 217830 210480 288920 214630 306410 TRUE FALSE 182964.0322 213809.3499 229292.9114 199604.0221 200722.5105 271242.1591 245599.1282 241427.028 255268.1915 0.716752178 0.837587122 0.898243177 0.781938482 0.786320102 1.062577196 0.962121942 0.945777954 1 17.96165425 2.246791195 24.99951884 0.989144628 0.820543283 0.735489131 0.055660707 103.726245 315057.8804 0.019828905 0.016327411 176.5188928 -2.246791195 -0.168601345 MITNSLNHDS(ph)PPSTPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MITNSLNHDSPPSTPPR 17 0 J3QKZ5;J3QS16;Q8N9M1-2;Q8N9M1;Q8N9M1-3 J3QKZ5 C19orf47 Uncharacterized protein C19orf47 1 MITNSLNHDS(0.994)PPS(0.004)T(0.001)PPR;MITNSLNHDS(1)PPSTPPR 167.51 1.43E-09 463740000 211092 321520 286160 288050 282250 249450 282450 235190 294130 TRUE FALSE 197880.1285 345325.6753 292947.8503 295441.8507 260083.2235 321462.1655 240099.2446 264553.9892 245037.8028 0.807549391 1.409275105 1.195521046 1.205699069 1.061400406 1.311888051 0.979845729 1.079645614 1 17.90264481 1.685738022 9.04435466 1.023864225 1.194205847 0.136698356 0.160987024 0.184831358 25.42772628 0.071784202 0.038302307 48.49958495 -1.685738022 0.170341622 MIVDPVEPHGEMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MIVDPVEPHGEMK 13 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 113.99 0.00034934 0 203320 165730 189800 177970 196000 136270 199830 165030 193270 FALSE TRUE 190594.5641 178000.8216 194302.1456 182537.0115 180606.9506 175608.9368 169867.3466 185634.3588 161011.9884 1.183729025 1.105512846 1.206755767 1.133685841 1.121698778 1.090657525 1.05499813 1.15292259 1 17.29680859 2.443455357 1.714591522 1.074208928 1.158032364 0.435971507 0.045101326 0.342495103 2.046856103 0.018892302 0.014395108 277.6229451 -2.443455357 0.083823436 MKDTDSEEEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MKDTDSEEEIR 11 1 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ;; 106.49 0.0021197 738700000 3034330 1939020 2405510 1947920 1967400 1286290 2905910 2673090 2445660 FALSE TRUE 2844416.702 2082587.058 2462569.833 1997906.925 1812888.34 1657621.042 2470195.773 3006831.171 2037463.546 1.396057714 1.022146905 1.208644855 0.98058536 0.889777068 0.813570895 1.212387715 1.475771763 1 20.95834282 -0.18134725 13.30967169 0.999999991 1.10585806 0.026833899 0.210235125 0 0 0.195338747 0.046041784 0.658647049 0.18134725 0.105858069 MKDTDSEEEIREAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 MKDTDSEEEIREAFR 15 2 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ;;;;;;;; 233.14 7.15E-18 6089620000 7995530 7657940 7438610 7335270 8803450 3856797 9394190 8048140 14277130 FALSE TRUE 7495104.05 8224941.846 7615057.342 7523505.447 8112062.548 4970191.684 7985618.421 9052967.995 11894184.77 0.630148614 0.691509507 0.640233651 0.632536453 0.682019214 0.417867368 0.671388462 0.761125556 1 23.50375306 0.928810594 2.406736346 0.998450327 0.625635797 0.715509237 0.076309898 0.191915646 2.457220451 0.070603756 0.019108646 8.488102086 -0.928810594 -0.372814531 MKEEEQAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MKEEEQAGK 9 1 Q9H446-2;Q9H446 Q9H446-2 RWDD1 RWD domain-containing protein 1 0 ; 85.958 0.01319 136841000 449510 343192 420931 392142 371681 318769 420631 338633 383460 FALSE TRUE 421375.9715 368602.2928 430915.6821 402205.0276 342490.6735 410792.4355 357561.2865 380912.0755 319458.0488 1.319033824 1.153836299 1.348895994 1.25902299 1.072099059 1.285904165 1.119274621 1.19236963 1 18.28526696 0.238127082 0.27922979 0.936411533 1.278059704 0.470391441 0.081180821 4.160436437 0.597807582 0.420334335 0.117106195 1.730322607 -0.238127082 0.341648171 MKEIAEAYLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MKEIAEAYLGK 11 1 P11142;E9PKE3;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;; 143.86 3.37E-05 8185970000 18543400 19006900 15974400 15002200 23561400 10056310 22368300 20243700 33448400 FALSE TRUE 17382801.69 20414190.65 16353320.31 15387181.85 21710982.69 12959403.45 19014381.07 22771170.51 27865645.96 0.623807599 0.732593484 0.586863134 0.552191823 0.779130788 0.465067398 0.682359243 0.817177199 1 24.73198426 1.040124238 2.43823187 0.996494428 0.631266294 0.664308094 0.087783933 0.15108558 1.91939223 0.076073871 0.020748316 10.96791908 -1.040124238 -0.365228134 MKEIAEAYLGYPVTNAVITVPAYFNDSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MKEIAEAYLGYPVTNAVITVPAYFNDSQR 29 1 A0A0G2JIW1;P0DMV9;P0DMV8 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 215.86 2.50E-34 450380000 582050 743910 494430 483040 923350 360330 721220 737070 957760 FALSE TRUE 545620.5295 798989.8704 506158.1131 495435.6242 850833.8156 464351.4215 613079.7565 829094.812 797903.6686 0.683817547 1.001361319 0.634359927 0.620921602 1.066336513 0.581964264 0.768363125 1.039091365 1 19.60585505 1.240854679 24.93475883 1.019545772 0.771602662 0.307664852 0.158338932 66.27477026 720428.9713 0.110347489 0.035898815 17.41224138 -1.240854679 -0.24794311 MKETAEAYLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MKETAEAYLGK 11 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 138.42 5.28E-05 2278700000 5879500 5525700 4722900 4955300 5721500 2730900 6755700 4966200 5057700 FALSE TRUE 5511512.59 5934828.577 4834929.418 5082461.387 5272156.469 3519266.498 5742745.502 5586241.002 4213537.196 1.308048875 1.408514581 1.147475196 1.206222029 1.251242418 0.835228535 1.362927449 1.325784191 1 22.00660043 3.931703664 3.867361697 1.173732702 1.357394161 0.213838467 0.155206443 0.334949775 10.45677132 0.038227663 0.077138825 8544.834671 -3.931703664 0.183661459 MKETAEAYLGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MKETAEAYLGKK 12 2 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 81.904 0.0092192 216630000 555340 439140 513060 498550 552430 384660 634280 470140 721430 FALSE TRUE 520582.2607 471654.3825 525230.0255 511343.637 509044.3762 495705.0976 539175.6024 528838.0139 601018.6724 0.866166535 0.784758285 0.87389968 0.850794926 0.84696932 0.82477487 0.897102914 0.879902802 1 19.19705029 -0.084011027 0.353081957 1.036491399 0.827512673 0.759173641 0.027357401 2.403429547 0.399499165 0.144155365 0.022692106 0.824117191 0.084011027 -0.208978726 MKETIMNQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MKETIMNQEK 10 1 P20290-2;D6RDG3 P20290-2 BTF3 Transcription factor BTF3 0 ; 133.32 0.00018262 918630000 968440 1031210 892730 835620 1310330 551630 971450 1094620 1425320 FALSE TRUE 907827.0691 1107561.861 913905.9772 857063.4239 1207421.967 710876.626 825790.091 1231285.717 1187424.884 0.764534314 0.932742674 0.769653718 0.721783277 1.016840714 0.598670817 0.695446173 1.036937774 1 20.17940482 1.226483485 24.98906903 1.018469099 0.790187616 0.404721597 0.117279024 261.6405587 541349.5799 0.108085496 0.027850862 16.84548369 -1.226483485 -0.228281483 MKFNPFVTSDR ddPTM_SK-BR-3_Pertuzumab_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 ; 177.83 7.12E-06 2079800000 2217700 3584600 2688300 3118500 4876200 2508400 4228200 3349000 6996000 FALSE TRUE 2078898.116 3850007.514 2752067.746 3198525.99 4493242.922 3232534.36 3594220.663 3767130.022 5828322.404 0.356688936 0.660568727 0.47218866 0.548790161 0.770932459 0.554625179 0.616681853 0.646348942 1 22.47464925 -4.999999999 0.166954509 2.626080486 0.475426039 0.672981621 0.099014051 77.8545768 0.729559567 41.82366839 0.347988933 1.00E-05 4.999999999 -2.150654447 MKGDYDVTVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MKGDYDVTVPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 137.59 6.86E-05 267500000 897070 671080 765850 732200 872110 567810 875450 692740 1037300 FALSE TRUE 840923.99 720767.4615 784016.3237 750989.4916 803617.9985 731727.5294 744184.3998 779230.1139 864167.9288 0.973102521 0.834059489 0.907249966 0.869031894 0.929932681 0.846742288 0.861157161 0.901711447 1 19.72095216 0.964057766 19.8352736 1.000000001 0.882689352 0.408363155 0.041253839 284.6234241 157075.2229 0.035270816 0.008817704 9.2057201 -0.964057766 -0.117310649 MKGDYFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 81.548 0.024536 4310400000 1435660 3361500 972720 945530 3612500 691230 1191620 2859100 2979700 FALSE TRUE 1345804.603 3610388.958 995793.3778 969793.9006 3328788.822 890776.8798 1012947.643 3216064.929 2482368.82 0.542145306 1.454412788 0.401146425 0.390672769 1.340972701 0.358841471 0.408056867 1.295562892 1 21.24328605 5.0161399 17.61227576 0.787440765 0.070172345 0.033726385 0.433191831 57428984.14 1295429948 0.100316737 1076512020 103786.269 -5.0161399 -0.71726842 MKGDYYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 94.302 0.013042 4497800000 2079110 7908790 1854690 1896190 9409560 1309160 2464190 8118420 8721490 FALSE TRUE 1948982.216 8494365.041 1898684.123 1944849.446 8670571.114 1687093.24 2094707.586 9132022.608 7265816.976 0.268239927 1.169086019 0.261317362 0.267671131 1.193337397 0.232195945 0.288296222 1.256847322 1 22.79269359 1.230473432 24.99992243 1.128423925 0.549168397 0.311256612 0.371451037 250.2613487 773602.5301 0.322252687 0.086177667 17.00095945 -1.230473432 -0.579255528 MKGYTLLSEGIDEMVGIIYKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MKGYTLLSEGIDEMVGIIYKPK 22 2 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 149.84 3.40E-08 31524000 42885 50111 45188 51400 80569 30202 66520 46839 120690 FALSE TRUE 40200.9044 53821.27058 46259.8807 52719.01102 74241.43574 38920.82711 56545.94354 52686.95226 100546.0593 0.399825758 0.535289707 0.460086462 0.524326974 0.738382352 0.387094506 0.562388461 0.524008127 1 16.61749701 -5 0.320884946 5.600387259 0.496342167 0.716004677 0.096188807 166.3164585 1.470731622 519.7369822 0.077913388 1.00E-05 5 -5.104045092 MKLDYILGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MKLDYILGLK 10 1 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 134.2 0.0041194 0 1273700 1711200 1290200 1243900 2078900 886730 1456100 1758400 1787600 FALSE TRUE 1193981.391 1837899.029 1320804.153 1275820.58 1915631.58 1142714.556 1237771.323 1977940.111 1489238.012 0.801739803 1.234120412 0.886899302 0.856693537 1.286316603 0.767314927 0.831144057 1.328155805 1 20.50614291 MKLPGR ddPTM_SK-BR-3_Pertuzumab_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 1682770000 2070830 2445000 2402400 2398300 2723800 1916940 2811900 2402100 2639000 FALSE TRUE 1941220.447 2626030.344 2459386.062 2459844.438 2509883.735 2470329.459 2390281.699 2702007.473 2198533.851 0.882961363 1.194446173 1.118648258 1.118856749 1.141617053 1.123625846 1.087216236 1.229004262 1 21.06811032 4.74776703 24.75555134 1.130853941 0.882961214 0.613561512 0.060704629 655.8550116 1763515.894 0.012681424 0.158514564 55945.74097 -4.74776703 -0.247892727 MKQDVLNCT(ph)EGPIHSNGT(ph)S(ph)MIS(ph)LIIPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MKQDVLNCTEGPIHSNGTSMISLIIPPK 28 1 B7Z7P8 B7Z7P8 ETF1 4 MKQDVLNCT(0.991)EGPIHS(0.107)NGT(0.969)S(0.969)MIS(0.965)LIIPPK 44.968 0.046325 1037300000 77387 385190 298890 301980 343610 270730 352480 375680 240630 TRUE FALSE 72543.48581 413709.8684 305979.8119 309729.3181 316624.2567 348885.3561 299628.8963 422584.475 200467.2985 0.361871918 2.063727459 1.526332795 1.545036624 1.579430955 1.740360441 1.494652238 2.107997056 1 17.61300739 4.749953685 24.74747588 1.657373668 0.361871039 0.62175029 0.3108334 896.9614299 1948294.379 0.065158194 1.019150462 56228.13579 -4.749953685 -1.295502629 MKS(ph)IS(ph)SDPLEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MKSISSDPLEEK 12 1 Q8IY92-2;Q8IY92 Q8IY92-2 SLX4 Structure-specific endonuclease subunit SLX4 2 MKS(0.667)IS(0.667)S(0.667)DPLEEK 66.262 0.077691 35455000 87774 49412 69849 59504 67821 55381 84120 58251 94775 TRUE FALSE 82280.38202 53070.51589 71505.85127 61030.97338 62494.61224 71368.59566 71506.98693 65523.76558 78956.44023 1.042098425 0.672149298 0.905636716 0.772970174 0.79150747 0.903898345 0.9056511 0.829872337 1 16.26876933 2.2259257 24.52839971 0.902453053 0.820882478 0.09704956 0.103384666 359.5356016 697966.9743 0.034886888 0.025945814 168.2386209 -2.2259257 -0.081570575 MKS(ph)LEQDALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MKSLEQDALR 10 1 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 MKS(1)LEQDALR;MKS(1)LEQDALR 114.33 0.0008297 326150000 797680 885950 660630 683570 1142330 510700 800450 830630 1138780 TRUE FALSE 747754.6327 951546.6598 676300.4556 701111.5635 1052616.01 658130.7995 680429.9535 934335.9839 948710.2612 0.788180189 1.002989742 0.712863013 0.739015474 1.109523163 0.693711058 0.717215763 0.984848612 1 19.85560803 1.145159306 8.663845061 0.99711468 0.825224 0.214521833 0.134530304 0.457962122 37.54900511 0.124972364 0.031295319 13.96880663 -1.145159306 -0.17189068 MKVVEVLAGHGHLYSR ddPTM_SK-BR-3_Pertuzumab_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 0 106.67 0.00076642 63298000 89144 215010 178050 211650 265020 108300 180180 133550 490850 FALSE TRUE 83564.63617 230929.5641 182273.4301 217081.2973 244206.3982 139564.4519 153163.6817 150224.0115 408923.964 0.204352504 0.564724948 0.445739174 0.530859809 0.597192681 0.341296828 0.374552961 0.367364167 1 18.64147309 -1.398488255 3.436633002 1.004781948 0.441278381 0.700522578 0.117207712 53744264.28 77641758.89 2549098.235 0.026796541 0.039949537 1.398488255 -0.563503567 MKYNTEGRVS(ph)PSPSQESLSSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MKYNTEGRVSPSPSQESLSSSK 22 2 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 MKYNT(0.011)EGRVS(0.978)PS(0.011)PSQESLSSSK 188.38 1.31E-17 220960000 446620 258130 318840 300190 413940 216530 495750 265310 608910 TRUE FALSE 418666.8514 277242.2138 326403.0354 307893.3836 381430.8222 279038.6959 421416.8898 298434.5375 507278.9873 0.825318734 0.546528086 0.643438904 0.606950793 0.751915281 0.550069494 0.830739889 0.588304552 1 18.95241988 -2.403432225 0.30983871 1.48225787 0.6371269 0.474316935 0.106900969 36.18264584 1.389549316 11.96702062 0.093052847 0.003949733 2.403432225 -0.84513097 MLAEDELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 MLAEDELR 8 0 P61204;F5H423;P61204-2;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 ;;;;; 159.04 0.00084097 4820900000 6599930 7975720 7122360 7012250 7545260 5992440 7364330 6743870 6432500 FALSE TRUE 6186852.163 8566250.608 7291305.743 7192196.207 6952685.716 7722360.149 6260117.084 7585857.015 5358874.194 1.154505954 1.598516833 1.360604015 1.342109545 1.297415364 1.441041508 1.168177654 1.415569155 1 22.35349852 -1.744073706 0.224032741 0.62236703 1.437084207 0.380444648 0.132669515 24.41640595 0.904609575 5.229057423 0.255658242 0.018027118 1.744073706 0.814717177 MLAEDELRDAVLLVFANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MLAEDELRDAVLLVFANK 18 1 P61204;F5H423;P61204-2;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 ;; 266.7 3.23E-31 643950000 474368 673333 583401 669009 857761 414430 624904 550964 1059215 FALSE TRUE 444678.1537 723187.2759 597239.5472 686176.9036 790395.9111 534069.2133 531205.4465 619753.0682 882425.1737 0.503927321 0.819545155 0.67681608 0.7776035 0.895708707 0.605228896 0.601983559 0.702329315 1 19.75111442 -2.344341456 2.082674535 2.546344841 0.703461815 0.40996626 0.113726788 3792400.167 423330.0169 27611526.38 0.029371072 0.004525416 2.344341456 -1.842883026 MLAES(ph)DES(ph)GDEESVSQTDKTELQNTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 MLAESDESGDEESVSQTDKTELQNTLR 27 1 P22059 P22059 OSBP Oxysterol-binding protein 1 2 MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(0.998)GDEES(0.001)VSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(0.995)GDEES(0.004)VS(0.001)QT(0.001)DKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR 199.59 2.95E-25 7262275000 3195433 2934873 2991522 2998489 3165496 2330538 3814080 2797286 3624568 TRUE FALSE 2995436.553 3152174.051 3062482.315 3075435.304 2916890.713 3003326.487 3242194.112 3146533.315 3019604.185 0.991996424 1.043903061 1.014199917 1.018489549 0.965984458 0.994609327 1.073714935 1.042035022 1 21.52592802 1.752080839 25 1.045512736 1.009474201 0.233164417 0.027050608 5.607733712 10384.2711 0.012477992 0.006919755 56.50421414 -1.752080839 -0.036038535 MLAESDES(ph)GDEESVSQTDKTELQNTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MLAESDESGDEESVSQTDKTELQNTLR 27 1 P22059 P22059 OSBP Oxysterol-binding protein 1 1 MLAESDES(1)GDEESVSQTDKTELQNTLR;MLAES(0.003)DES(0.991)GDEES(0.006)VSQTDKTELQNTLR 189.63 4.26E-18 374140000 240036 230513 243248 229560 263150 180361 263516 197839 365571 TRUE FALSE 225012.5752 247580.4224 249017.9574 235450.8982 242483.2605 232428.2928 224004.2222 222539.6346 304554.8384 0.738824497 0.812925592 0.817645711 0.773098531 0.796189158 0.763173864 0.735513589 0.730704644 1 18.2163425 -1.071160232 4.646892027 1.000007649 0.776354809 0.840823168 0.031234899 3.95E-06 7.89E-07 0.034180222 0.008055967 0.084886723 1.071160232 -0.22365284 MLDAEDIVGTARPDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MLDAEDIVGTARPDEK 16 1 P12814-3;P12814;P12814-2;P12814-4;H9KV75;G3V2N5;G3V2W4 P12814-3 ACTN1 Alpha-actinin-1 0 ; 230.82 1.74E-15 466250000 997100 741230 797920 765330 976050 612480 872060 890170 1112420 FALSE TRUE 934693.2909 796111.4404 816847.0392 784969.6635 899394.9702 789293.0332 741302.6988 1001309.684 926749.9155 1.008571218 0.859035892 0.881410428 0.847013472 0.970482927 0.85167856 0.799895081 1.080452954 1 19.82182055 1.229633295 24.99999406 1.040226543 0.880326828 0.491649497 0.063827347 162.9698677 456362.448 0.054558737 0.014444482 16.96810312 -1.229633295 -0.159899715 MLDAEDIVNTARPDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 MLDAEDIVNTARPDEK 16 1 O43707 O43707 ACTN4 Alpha-actinin-4 0 ;;;; 205.18 2.12E-11 1014320000 2475770 1965920 1871556 1772570 2379230 1526155 2219990 2225805 1975130 FALSE TRUE 2320815.975 2111478.762 1915950.192 1818057.147 2192374.873 1966731.173 1887123.109 2503701.654 1645468.043 1.410429078 1.283208611 1.164380068 1.104887545 1.33237159 1.195241185 1.14686099 1.521574159 1 20.65006658 4.65234788 2.013929014 1.210711693 1.447209666 0.177083325 0.138892498 1.005508445 5.150062155 0.031747254 0.410218738 44910.49894 -4.65234788 0.236497973 MLDEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 MLDEQK 6 0 H3BV99 H3BV99 SNAP23 Synaptosomal-associated protein 0 ;;;; 95.445 0.032873 5056970000 728759 4816810 3179780 3425980 4134390 5586650 1872510 3234460 1759580 FALSE TRUE 683147.2751 5173451.624 3255205.883 3513896.447 3809691.687 7199425.163 1591744.509 3638289.451 1465894.731 0.466027513 3.529210874 2.220627317 2.397100128 2.598884904 4.911283882 1.085851853 2.481958203 1 20.48335007 2.794839115 12.97259099 2.517518254 2.39376902 0 1.296402447 31.85137102 7322.287729 0.372504784 0.395078879 623.5038142 -2.794839115 -0.123749234 MLDHEYTTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MLDHEYTTK 9 0 P11387;E5RJ33;H0YBR3;H0YC03;E5RGE7;E5RGR4;E5RFE3;E5RGR2;E5RJ95;E5RFS0;E5RIC7;Q969P6-2;Q969P6 P11387;Q969P6-2 TOP1;TOP1MT "DNA topoisomerase 1;DNA topoisomerase I, mitochondrial" 0 ; 143.03 0.00010291 404410000 881940 776520 783170 660920 923750 566490 888480 636560 1116110 FALSE TRUE 826740.9497 834014.3488 801747.1622 677880.3261 851202.4012 730026.4668 755260.6722 716035.9172 929824.0307 0.889137001 0.89695934 0.862256874 0.729041522 0.915444614 0.785123252 0.812261941 0.770076803 1 19.82659819 3.4686041 24.99702541 0.822955299 0.886328159 0.072039437 0.076870422 347.9931071 1021323.714 0.018543211 0.02523884 2941.738742 -3.4686041 0.06337286 MLDLLEDFLEHEGYKYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MLDLLEDFLEHEGYKYER 18 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ; 256.96 7.88E-31 415030000 801990 890360 830130 793800 958480 629390 1000170 769050 1128400 FALSE TRUE 751794.8775 956283.1808 849821.0756 814170.2519 883204.8471 811084.6757 850203.7936 865067.5854 940062.7503 0.799728398 1.017254625 0.904004627 0.86608075 0.939516907 0.862798441 0.904411746 0.920223235 1 19.84239754 0.817047227 4.744920438 0.999998726 0.909530743 0.222489788 0.056459848 4.242925283 108.8508732 0.051484262 0.013040268 6.562166218 -0.817047227 -0.090467983 MLDMGFEPQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MLDMGFEPQIR 11 0 P17844;P17844-2;J3KTA4;J3QSF1;J3KRZ1;A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2;A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;O15523-2;O15523 P17844;A0A1X7SBZ2;A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX5;DDX17;DDX3X;DDX3Y Probable ATP-dependent RNA helicase DDX5;Probable ATP-dependent RNA helicase DDX17;ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;;; 114.5 0.0029071 204601000 291638 350499 325289 339937 365326 293294 366130 325383 375412 FALSE TRUE 273384.8982 376450.3107 333005.0087 348660.3589 336634.7696 377963.2166 311232.2055 366007.7838 312753.3119 0.874123111 1.203665305 1.064752941 1.114809486 1.076358768 1.208502683 0.995136402 1.170276284 1 18.25466564 -1.208815118 7.619842981 0.999999911 1.094997027 0.067897049 0.100427613 1.30E-07 1.36E-08 0.083897976 0.019774924 0.061827955 1.208815118 0.094997116 MLEQLDMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MLEQLDMR 8 0 O00148;O00148-2;O00148-3;K7EQN7;K7EPJ3;Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;F6S4E6;A0A0A0MT12;F6TRA5;A0A140T9K1;A0A140T973;A0A140T9L4 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ;; 143.28 0.0014049 517565000 792600 1365510 917400 966260 1353470 746620 926450 1168210 1075490 FALSE TRUE 742992.5808 1466613.781 939161.1612 991055.8675 1247173.926 962157.0736 787537.4232 1314063.59 895983.7711 0.829247811 1.636875386 1.048189924 1.106109172 1.391960397 1.07385547 0.878963937 1.466615392 1 19.77311308 2.11877985 14.22110455 1.070427467 1.236279899 0.017535271 0.258477196 1.592462232 189.0350828 0.090907341 0.067139901 131.4558294 -2.11877985 0.165852432 MLEVHFVGDDDVLNHILDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MLEVHFVGDDDVLNHILDR 19 0 Q13416;C9JK08;B8ZZ80 Q13416 ORC2 Origin recognition complex subunit 2 0 ;;; 187.47 1.28E-14 59462000 51963 60951.4 57690.9 52850.7 61190.6 51793.3 70315.1 53518.8 60429 FALSE TRUE 48710.72859 65464.30508 59059.35539 54206.93844 56384.93711 66745.18492 59772.00353 60200.73999 50343.00951 0.967576811 1.300365348 1.17313915 1.076752045 1.120015225 1.3258084 1.187295001 1.195811307 1 15.61950384 -0.797694699 4.762859497 0.999999655 1.183736687 0.194808599 0.103434688 6117235.506 1284362.026 21.83258417 0.0224323 0.159332842 0.797694699 0.183737032 MLFKDDYPSSPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MLFKDDYPSSPPK 13 1 P63279;H3BQQ9;B0QYN7;H3BPC4 P63279 UBE2I SUMO-conjugating enzyme UBC9 0 92.935 0.0053307 365170000 386600 322730 368320 356400 407190 267010 457720 332210 486370 FALSE TRUE 362403.3961 346625.265 377056.7243 365545.8274 375210.9399 344091.4525 389089.1353 373687.1498 405191.7049 0.89439984 0.855459924 0.930563779 0.902155259 0.926008443 0.849206556 0.96025938 0.922247779 1 18.62824511 -5 0.111549942 1.327259188 0.847617371 0.53660043 0.030569445 120.2159839 0.888875439 8.850157342 0.338708067 1.00E-05 5 -0.479641817 MLGEDS(ph)DEEEEMDTSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 MLGEDSDEEEEMDTSER 17 0 A0A087X0M4;A0A087WWF4;Q9BWU0;H7C256 A0A087X0M4 SLC4A1AP Kanadaptin 1 MLGEDS(1)DEEEEMDTSER;MLGEDS(1)DEEEEMDTSER;MLGEDS(1)DEEEEMDTSER;MLGEDS(1)DEEEEMDTSER;MLGEDS(1)DEEEEMDTSER;MLGEDS(1)DEEEEMDTSER;MLGEDS(1)DEEEEMDTSER;MLGEDS(1)DEEEEMDTSER 343.22 2.81E-72 3015090000 2966530 2709550 2878490 2797920 2930450 2476780 3203060 2589240 3211550 TRUE FALSE 2780860.183 2910167.901 2946769.142 2869719.364 2700304.278 3191786.179 2722790.889 2912512.314 2675521.558 1.039371249 1.08770116 1.101381199 1.072583159 1.009262762 1.192958498 1.017667333 1.088577405 1 21.35138872 0.225744262 0.943554383 0.99952965 1.080105282 0.171300929 0.051663664 5.927958288 5.856141174 0.052054451 0.014270209 1.681683497 -0.225744262 0.080575632 MLISAVS(ph)PEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MLISAVSPEIR 11 0 A0AVK6;E9PMT9 A0AVK6 E2F8 Transcription factor E2F8 1 MLISAVS(1)PEIR;MLISAVS(1)PEIR;MLIS(0.01)AVS(0.99)PEIR;MLISAVS(1)PEIR 170 1.70E-05 76102000 434607 479382 509799 483406 538920 498374 564690 463662 469121 TRUE FALSE 407405.7237 514875.9421 521891.673 495811.0164 496595.3971 642246.4834 480019.9768 521551.2213 390821.6745 1.042433801 1.317419109 1.335370342 1.26863746 1.270644464 1.643323606 1.228232742 1.334499224 1 18.57615095 -1.004376971 4.569219961 0.999991974 1.315413883 0.29612608 0.147045847 8568511.54 1883476.111 764.3604421 0.031411275 0.098997227 1.004376971 0.315421909 MLKHDD ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MLKHDD 6 1 Q9UII2 Q9UII2 ATPIF1 "ATPase inhibitor, mitochondrial" 0 ; 99.919 0.034885 891680000 1711250 1608290 1588440 1447460 2302300 1399590 1645510 1600340 3595100 FALSE TRUE 1604145.917 1727369.465 1626118.547 1484604.274 2121486.645 1803628.913 1398781.052 1800145.972 2995054.585 0.535598224 0.576740562 0.542934528 0.495685214 0.708329877 0.602202351 0.467030237 0.601039454 1 21.51415087 0.958307692 23.54646517 1.000000001 0.559427113 0.817129317 0.064757276 1819.044317 1027338.622 0.060661838 0.015165459 9.084639376 -0.958307692 -0.440572888 MLLS(ph)PGGVSQPLTASLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MLLSPGGVSQPLTASLAR 18 0 Q6PK04;I3L0U5 Q6PK04 CCDC137 Coiled-coil domain-containing protein 137 1 MLLS(0.564)PGGVS(0.002)QPLT(0.42)AS(0.014)LAR;MLLS(1)PGGVSQPLTASLAR 128.74 2.78E-05 0 95812 123501 111447 117639 147935 93518 113684 121183 104601 TRUE FALSE 89815.29795 132645.1425 114090.5755 120657.8159 136316.7818 120515.1285 96638.13959 136312.9643 87142.41735 1.030672555 1.522165055 1.309242719 1.384604875 1.564298834 1.38296747 1.108967854 1.564255026 1 16.41108751 -1.668159421 2.89721186 0.960886613 1.358097807 0.286086623 0.177925921 38451338.14 33135334.76 11024443.27 0.039785161 0.021470422 1.668159421 0.397211194 MLLS(ph)WDGGESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MLLSWDGGESR 11 0 Q658Y4;E7ER68 Q658Y4 FAM91A1 Protein FAM91A1 1 MLLS(1)WDGGESR;MLLS(1)WDGGESR;MLLS(1)WDGGESR 122.33 0.00041237 60721000 123096 127149 121229 112477 128748 100631 126818 108382 162152 TRUE FALSE 115391.6411 136563.2443 124104.6091 115363.3502 118636.6514 129681.5361 107802.8182 121913.7313 135087.7837 0.854197456 1.010922236 0.918696019 0.85398803 0.878218949 0.959979745 0.798020482 0.902477841 1 17.04353769 3.47554942 6.187167003 0.885851404 0.949060324 0.006770659 0.067016086 0.258358167 40.96763741 0.016823866 0.024288277 2989.161778 -3.47554942 0.06320892 MLLYTEVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MLLYTEVTR 9 0 P50395;V9GYF8;Q5SX90;V9GYJ7;Q5SX86;G5E9U5;P31150 P50395;Q5SX86;G5E9U5;P31150 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 ; 171.09 0.00013311 449330000 414330 534840 417510 476210 539610 368740 455900 435790 443490 FALSE TRUE 388397.8249 574440.1101 427413.5344 488430.3548 497231.2073 475189.252 387542.0274 490199.3408 369468.6539 1.051233496 1.554773602 1.156833008 1.321980497 1.345800792 1.286142267 1.048917204 1.326768416 1 18.49509244 0.917698522 0.437770343 0.992548902 1.324886504 0.203253817 0.152531568 1.701279616 0.828517287 0.201927138 0.097779195 8.27367623 -0.917698522 0.332337602 MLMRRDQVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 2266690000 5704100 5196630 5034580 5284020 6583440 4924970 5829160 4414810 7317030 FALSE TRUE 5347090.563 5581393.892 5154002.615 5419616.899 6066403.179 6346728.889 4955131.573 4966008.747 6095770.423 0.877180437 0.91561747 0.845504712 0.88907825 0.995182357 1.041169278 0.812880281 0.814664661 1 22.53937714 MLNS(ph)SFEDDPFFSESILAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MLNSSFEDDPFFSESILAHR 20 0 A0A494C175;A0A0S2Z4A4;P58340 A0A494C175 MLF1 Myeloid leukemia factor 1 1 MLNS(0.5)S(0.5)FEDDPFFSESILAHR 103.92 0.00017925 24432000 13460 16831 13624 17442 15389 14935 16013 11800 14154 TRUE FALSE 12617.56263 18077.18475 13947.16771 17889.59125 14180.41002 19246.49205 13611.99931 13273.25598 11791.60596 1.070046156 1.533055363 1.182804765 1.517146291 1.202585132 1.632219743 1.154380442 1.125652945 1 13.5254726 1.549533915 7.68782663 1.08907414 1.359453446 0.338387481 0.175859817 0.127839562 13.52072923 0.0835461 0.038836927 35.4432808 -1.549533915 0.270379306 MLPDKDCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 15 MLPDKDCR 8 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;;;;;;;;;;;;; 97.635 0.0073798 43570950000 50017760 86618650 41321590 39064150 97735050 29481940 52525270 78260260 97656000 FALSE TRUE 46887237.69 93031984.97 42301757.63 40066602.22 90059333.42 37992897.48 44649593.38 88031225.73 81356582.72 0.576317688 1.143509005 0.519954947 0.492481381 1.106970455 0.466992297 0.54881353 1.082041831 1 26.27775575 1.225552053 24.98981391 1.041021199 0.708708447 0.258184071 0.243796847 380.9443741 731782.8346 0.223081985 0.057174495 16.80939385 -1.225552053 -0.332312752 MLPHAPGVQMQAIPEDAIPEES(ph)GDEDEDDPDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 30 MLPHAPGVQMQAIPEDAIPEESGDEDEDDPDKR 33 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 1 MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR 310.24 1.85E-104 41624344000 13543579 8771173 9735451 10063548 10537640 7370587 12626431 8627988 12449746 TRUE FALSE 12695910.57 9420599.775 9966380.495 10321795.68 9710056.261 9498355.815 10733214.89 9705211.294 10371802.96 1.224079421 0.908289505 0.96091109 0.995178535 0.936197525 0.915786373 1.034845622 0.935730396 1 23.30616337 4.745514877 24.99044132 0.960361737 1.224079543 0.812395782 0.039750123 341.5207488 1227238.65 0.009337385 0.09347214 55656.3699 -4.745514877 0.263717806 MLPHAPGVQMQAIPEDAVHEDS(ph)GDEDGEDPDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 32 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 340.4 5.17E-118 45283503000 11409930 7503382 8727878 8787320 8925222 6533361 10683646 7496263 11986806 TRUE FALSE 10695802.85 8058940.211 8934907.388 9012817.508 8224271.067 8419436.26 9081732.464 8432187.937 9986130.641 1.071065784 0.807013297 0.894731674 0.902533507 0.823569345 0.84311297 0.909434574 0.844389908 1 23.25149435 -1.981041839 6.64617507 1.09025544 0.87936519 0.180890841 0.074020757 0.052442521 0.000149592 0.037968436 0.014810295 0.010446196 1.981041839 -0.210890251 MLQEDELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MLQEDELR 8 0 P84085 P84085 ARF5 ADP-ribosylation factor 5 0 ; 101.64 0.012211 1184682000 1372500 1578320 1517630 1606540 1609880 1371080 1787180 1504600 1687190 FALSE TRUE 1286597.675 1695180.455 1553628.9 1647766.536 1483446.519 1766888.538 1519208.95 1692452.622 1405587.089 0.915345399 1.206030183 1.105323827 1.172297717 1.055392818 1.257046647 1.080835874 1.204089476 1 20.42274141 4.748990156 24.81576883 1.140777402 0.91534526 0.438124218 0.077986583 1117.417608 2658696.601 0.015637435 0.221844614 56103.52592 -4.748990156 -0.225432142 MLQEDELRDAVLLVFANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MLQEDELRDAVLLVFANK 18 1 P84085 P84085 ARF5 ADP-ribosylation factor 5 0 ; 260.31 8.96E-31 464410000 609150 884090 808900 952670 1151290 597130 815020 731830 1353310 FALSE TRUE 571024.3889 949548.9435 828087.49 977117.1251 1060872.327 769511.7374 692815.3173 823200.5865 1127433.818 0.506481515 0.842221448 0.73448878 0.866673599 0.940961953 0.682533844 0.614506418 0.730154243 1 20.10461132 -2.315373221 2.181233181 2.238828842 0.745886066 0.298328464 0.125118071 5829992.476 703936.4207 35664744.7 0.029937665 0.004837565 2.315373221 -1.492942776 MLQHEPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MLQHEPDR 8 0 Q9BRX2 Q9BRX2 PELO Protein pelota homolog 0 ; 78.934 0.022256 126250000 91806 111394 106332 100519 110938 88252 107473 102470 120267 FALSE TRUE 86060.02634 119641.7277 108854.2453 103098.4877 102225.377 113728.9197 91358.42138 115263.6051 100193.6607 0.85893684 1.194104764 1.086438448 1.028992123 1.020277892 1.135090972 0.91181838 1.150408162 1 16.61243171 3.240126599 23.65578936 1.033737399 1.083830824 0 0.106893091 72.38316104 1093385.915 0.027951042 0.035911855 1738.307481 -3.240126599 0.050093425 MLQHIDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 127.56 0.0011709 1006510000 522450 1294140 509524 546020 1346600 460687 595960 1084390 898500 FALSE TRUE 489750.7871 1389959.472 521610.1499 560031.7976 1240843.468 593679.8583 506601.3306 1219778.479 748534.5455 0.654279472 1.856907581 0.696841786 0.748170944 1.657696997 0.793122858 0.676790849 1.629555357 1 19.51370937 3.947586149 23.60685947 0.995277793 1.333417909 0.03107377 0.455683416 415.879174 332404.3491 0.108040678 0.194823856 8863.110196 -3.947586149 0.338140116 MLRPVS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MLRPVSR 7 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 MLRPVS(1)R;MLRPVS(1)R 60.828 0.057626 465070000 136099 175805 155233 153494 179664 134023 181981 117502 247285 TRUE FALSE 127580.8065 188821.7851 158915.2001 157432.9159 165553.9142 172713.2644 154694.6385 132172.3834 206011.536 0.619289623 0.91655928 0.771389812 0.764194661 0.803614775 0.838366956 0.750902797 0.641577583 1 17.6523656 1.701255036 19.29683342 0.772214286 0.798918821 0 0.115014136 1.747093072 868.1762532 0.047715954 0.026427785 50.26376727 -1.701255036 0.026704535 MLS(ph)QDAPTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MLSQDAPTVK 10 0 O60934;A0A0C4DG07 O60934 NBN Nibrin 1 MLS(1)QDAPTVK 91.939 0.010287 198460000 419700 407440 376650 399110 471520 405450 489010 394570 576680 TRUE FALSE 393431.7262 437607.2815 385584.3159 409351.8383 434488.7212 522496.8331 415687.4902 443832.9331 480428.3825 0.818918575 0.910868919 0.802584381 0.852055901 0.904377712 1.087564457 0.865243406 0.923827462 1 18.87396186 2.476530565 24.99983663 0.958046179 0.852503832 0.456066065 0.062667542 20.58350682 871085.5319 0.02072494 0.017487101 299.5922436 -2.476530565 -0.105542346 MLS(ph)SSDAITQEFMDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MLSSSDAITQEFMDLR 16 0 H3BQK9;H3BPE1;Q9UPN3;Q9UPN3-2;Q9UPN3-3;Q9UPN3-4;A0A590UJG2;H0Y390;E9PNZ4;E9PLY5;A0A5F9ZGX0;A0A669KBB0 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 1 MLS(0.983)S(0.017)SDAITQEFMDLR;MLS(0.855)S(0.073)S(0.073)DAITQEFMDLR;MLS(0.842)S(0.081)S(0.076)DAIT(0.001)QEFMDLR 157.42 7.21E-08 25616700 50685 64658 63554 107563 101006 45871.4 42460.6 36118.8 35977.2 TRUE FALSE 47512.71633 69445.3456 65061.53089 110323.2487 93073.3962 59113.72852 36094.02721 40628.31169 29972.3729 1.585217043 2.316978567 2.170716717 3.680831313 3.105306227 1.972273891 1.204243232 1.355525364 1 14.87134569 1.904859685 3.464137535 1.221986906 2.534356836 0.556822267 0.560543138 0.204895356 4.269896388 0.293135481 0.162006606 80.32665556 -1.904859685 1.31236993 MLSELKDEYDDLAESEQFGVVMGTVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MLSELKDEYDDLAESEQFGVVMGTVPR 27 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 338.73 1.31E-95 287190000 510230 432530 464280 490960 553540 371850 551670 465120 623700 FALSE TRUE 478295.6151 464554.9712 475292.9408 503558.8648 510067.2013 479197.0585 468952.205 523191.2559 519600.4407 0.920506562 0.894061927 0.914727748 0.969127093 0.981652749 0.92224144 0.902524648 1.006910724 1 18.98704313 1.097428285 0.011924962 1.911935671 4.84E-07 0.386482724 0.0322017 992.6597684 8.810237636 714.4253294 696.6376445 12.51492598 -1.097428285 -1.911935187 MLTEAIMHDCVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 135.79 7.99E-05 591840000 1507720 1408350 1494330 1493270 1657350 1329330 1919060 1422200 1783350 FALSE TRUE 1413354.497 1512625.699 1529776.213 1531589.836 1527188.416 1713085.991 1631314.769 1599764.801 1485697.364 0.951307131 1.018125047 1.029668794 1.030889516 1.027926988 1.153051781 1.098012831 1.076777034 1 20.50270884 2.402781197 9.226993993 1.093171091 1.014593361 0.383838956 0.043552036 0.278885507 31.95962007 0.013871322 0.0115965 252.8024028 -2.402781197 -0.07857773 MLVDLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MLVDLAK 7 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41;A0A2R8YF08;K7ELR7;K7ENA0;K7ERK8;A0A0J9YXM3;A0A0J9YXH9;K7EIL4 P06744 GPI Glucose-6-phosphate isomerase 0 ; 81.958 0.059999 184292000 1003020 1042760 796940 867610 1192740 568010 949380 977050 1125110 FALSE TRUE 940242.7686 1119967.035 815843.7931 889874.3415 1099067.012 731985.2661 807029.2826 1099036.843 937321.8725 1.003116215 1.194858531 0.870398757 0.949379682 1.172560935 0.780932663 0.860994826 1.17252875 1 19.83818502 3.97554067 24.49094484 0.956044311 1.102676441 0.125018241 0.133817833 90.86076956 1407927.825 0.03239056 0.062667582 9452.369058 -3.97554067 0.146632129 MLVLVLGDLHIPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MLVLVLGDLHIPHR 14 0 Q9UBQ0 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ; 101.53 0.0007806 64011000 53863 73988 58028 56810 78861 45441 65119 59784 62005 FALSE TRUE 50491.81098 79466.1485 59404.45156 58267.84078 72667.57517 58559.07903 55355.01049 67248.164 51655.96493 0.97746332 1.538373131 1.150001779 1.127998303 1.40676058 1.13363634 1.071609263 1.30184702 1 15.65664733 0.631587919 0.283784115 0.956730576 1.296854941 0.094860752 0.169231613 5.504091775 1.084076305 0.61220234 0.255336082 4.281420846 -0.631587919 0.340124365 MLVQCMQDQEHPSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MLVQCMQDQEHPSIR 15 0 H0Y8C6;O00410-2;O00410;O00410-3;H0Y3V4 H0Y8C6 IPO5 Importin-5 0 ; 251.68 1.26E-24 371320000 135211 249616 268850 269470 277450 238720 307790 256528 211964 FALSE TRUE 126748.3849 268097.8284 275227.249 276385.0564 255660.1962 307634.5887 261639.7469 288556.0855 176585.8391 0.717772079 1.51822949 1.558603172 1.565159799 1.447795574 1.742124908 1.48165758 1.63408395 1 17.43001013 4.73855256 7.616381097 1.526536431 0.709520746 0.603264509 0.196078145 0.055282635 32.88637979 0.038879967 0.232485098 54771.23837 -4.73855256 -0.817015685 MLVTFDEELRPLPVSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MLVTFDEELRPLPVSVR 17 1 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 258.34 3.35E-27 604410000 456300 592840 536710 549640 521250 440950 548900 502920 545740 FALSE TRUE 427740.9975 636734.4904 549441.0147 563744.6929 480313.1276 568245.1068 466597.5407 565710.6691 454652.4684 0.9408087 1.400486162 1.208485718 1.239946403 1.056440163 1.249844983 1.026272974 1.244270533 1 18.79440466 2.759219122 23.63709636 1.120607549 1.233116499 0.053081561 0.138911354 774.6744921 886366.6478 0.038573957 0.040860026 574.4062044 -2.759219122 0.11250895 MLWGSDPYPHAEPQQAT(ph)TPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MLWGSDPYPHAEPQQATTPK 20 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 MLWGSDPYPHAEPQQAT(0.583)T(0.417)PK 150.18 3.33E-07 139050000 115380 89088 102180 100310 115360 79190 106430 78419 128160 TRUE FALSE 108158.5718 95684.16822 104603.7579 102884.1244 106300.0909 102050.8675 90471.80955 88209.78477 106769.2681 1.013012206 0.896177055 0.979717851 0.96361178 0.995605691 0.955807503 0.847358151 0.826172047 1 16.70413692 1.754001391 25 0.876949902 0.961488425 0.285059482 0.054821676 5.636621091 9137.5576 0.023058865 0.012787502 56.7546423 -1.754001391 0.084538523 MLWGSDPYPHAEPQQATT(ph)PK ddPTM_SK-BR-3_Pertuzumab_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(0.182)T(0.818)PK;MLWGSDPYPHAEPQQAT(0.017)T(0.983)PK;MLWGSDPYPHAEPQQAT(0.081)T(0.919)PK 214.16 1.07E-23 957330000 665772 416777 582857 596019 647620 416283 567937 438949 668560 TRUE FALSE 624102.519 447635.6027 596682.6433 611313.8566 596758.5376 536457.1443 482780.1193 493752.7489 556973.0169 1.120525591 0.803693517 1.071295422 1.097564582 1.071431684 0.96316541 0.866792654 0.886493122 1 19.08724791 1.996354321 22.66433621 0.905965554 1.010444217 0.218508587 0.094652715 73.38471929 456219.1531 0.037168789 0.026775274 99.16406482 -1.996354321 0.104478662 MMDKVEFVHMLNATMCATTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MMDKVEFVHMLNATMCATTR 20 1 P49591 P49591 SARS "Serine--tRNA ligase, cytoplasmic" 0 ;; 131.09 9.00E-06 170579000 386377 384960 386775 370275 428740 294816 422451 368211 320640 FALSE TRUE 362194.3533 413462.839 395949.4856 379776.8834 395068.4899 379924.5933 359108.3944 414182.9539 267123.1126 1.355907955 1.547836258 1.482273405 1.421729777 1.478975316 1.422282743 1.344355383 1.550532074 1 18.02714528 -2.935810997 0.353277457 5.51E-19 1.471780894 0.782894647 0.073431243 37.48783781 1.18841259 28.14007579 0.053057194 0.001159282 2.935810997 1.471780894 MMEIMTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MMEIMTR 7 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;H0Y9Y4;D6RB09;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 90.777 0.039293 63095000 79806 108650 96112 84926 117180 81429 100470 94594 93175 FALSE TRUE 74811.08492 116694.5591 98391.82203 87105.34494 107977.1555 104936.2304 85405.45622 106404.2691 77623.49057 0.963768627 1.503340783 1.267552146 1.122151868 1.391037104 1.351861784 1.100252715 1.370774083 1 16.24420569 -2.955022355 0.336676169 0.40075266 1.28636492 0.180234077 0.162237222 124.0551882 3.778178296 52.95320322 0.124929201 0.001109118 2.955022355 0.88561226 MMNGGHYTYSENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 MMNGGHYTYSENR 13 0 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ;;;;;;;;;;;;; 190.27 4.55E-06 3664517000 1544135 3919317 1634675 1679793 3705348 1432987 1905548 3511645 2792193 FALSE TRUE 1447490.347 4209507.309 1673450.263 1722899.332 3414344.915 1846667.084 1619828.768 3950081.608 2326157.95 0.622266578 1.8096395 0.719405259 0.740663089 1.467804417 0.793870031 0.696353731 1.698114098 1 21.14951763 3.883080992 10.43917195 0.980637207 1.295897438 0.022819767 0.436110058 0.934571954 97.23223846 0.102494473 0.184958263 7639.782462 -3.883080992 0.315260231 MMNGGHYTYSENRVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 MMNGGHYTYSENRVEK 16 1 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ;;;;;; 141.86 9.40E-07 1961780000 1880590 2590920 2359430 2508880 2958280 1877170 2804060 2401800 3751260 FALSE TRUE 1762887.229 2782754.413 2415396.794 2573262.108 2725948.622 2419078.506 2383617.235 2701670.017 3125150.472 0.564096751 0.890438537 0.772889759 0.823404227 0.872261559 0.77406785 0.762720789 0.864492779 1 21.57549422 -5 0.206904257 1.946489663 0.767294542 0.395279926 0.087840819 161.1012556 1.603554497 63.27147245 0.180231022 1.00E-05 5 -1.179195121 MMS(ph)PNKLHTNFHIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MMSPNKLHTNFHIPK 15 1 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 MMS(0.995)PNKLHT(0.005)NFHIPK 82.765 0.0060729 224690000 852420 571130 724400 617100 747910 454360 908790 571380 1092100 TRUE FALSE 799068.5538 613417.0595 741583.1101 632935.8307 689172.1655 585526.3561 772525.3763 642718.0508 909821.4548 0.878269632 0.674216964 0.815086417 0.695670373 0.75748067 0.643561825 0.849095581 0.706422175 1 19.79522393 -1.224518611 3.732170021 1.000314762 0.751904272 0.509431626 0.07633385 33603427.19 71834264.85 131688.1633 0.016042148 0.059632277 1.224518611 -0.24841049 MNDIVKEFEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MNDIVKEFEDR 11 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 82.362 0.017461 88347000 64443 109274 76344 114593 159330 49820 98958 78670 308266 FALSE TRUE 60409.62766 117364.7607 78154.91573 117533.6504 146816.8645 64202.22524 84120.16658 88492.12267 256814.4131 0.235226781 0.457002235 0.304324492 0.457659868 0.571684676 0.249994634 0.327552358 0.344576154 1 17.97036665 -1.293860089 3.17488771 1.003599813 0.370868363 0.788125571 0.10289355 24015867.58 32936493.25 825800.5683 0.024785106 0.050832318 1.293860089 -0.63273145 MNEAFGDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MNEAFGDTK 9 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 115.23 0.0043785 0 146230 119160 124360 136260 152860 88166 164410 120100 197750 FALSE TRUE 137077.7253 127982.7304 127309.8779 139756.6623 140854.9922 113618.0929 139758.2468 135094.7494 164744.2475 0.832063804 0.776857052 0.772772827 0.848324991 0.85499187 0.689663492 0.848334609 0.820027111 1 17.32986856 0.512803093 1.340887289 0.999887056 0.796502476 0.606263563 0.049502343 1.331407473 2.983064895 0.043889574 0.012992593 3.256890017 -0.512803093 -0.20338458 MNESDAWFEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MNESDAWFEEK 11 0 O60749;O60749-2 O60749 SNX2 Sorting nexin-2 0 81.709 0.048697 55507000 109800 95582 104600 115690 124080 79067 104410 89742 103960 FALSE TRUE 102927.814 102658.9907 107081.1614 118658.8013 114335.2573 101892.3594 88754.68979 100946.4862 86608.40439 1.188427552 1.185323658 1.236383029 1.370061048 1.320140443 1.176471961 1.024781491 1.165550699 1 16.40221941 1.963372279 5.062394005 1.071833797 1.251811987 0.622335428 0.069620641 0.145956144 9.269522586 0.031611729 0.019603708 91.91201314 -1.963372279 0.17997819 MNGFIDQIDGIVHFETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 MNGFIDQIDGIVHFETR 17 0 D6RFN0;Q9BT78;D6RD63 D6RFN0 COPS4 COP9 signalosome complex subunit 4 0 ;;;; 210.43 3.38E-12 326962100 535943 555198 581165 549704 609559 482972 628062 549882 608074 FALSE TRUE 502399.2843 596305.4376 594950.5082 563810.3353 561686.695 622398.176 533889.9337 618535.9781 506582.5211 0.99174224 1.177114118 1.174439471 1.112968395 1.108776303 1.228621498 1.053905162 1.220997473 1 18.95043777 -1.05523997 4.177351737 0.99998442 1.137772072 0.2471145 0.072943454 9.35E-06 2.12E-06 0.062408377 0.014708133 0.088056218 1.05523997 0.137787652 MNGVMFPGNS(ph)PSYTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 18 MNGVMFPGNSPSYTER 16 0 Q9NY27-2;Q9NY27;Q9NY27-3 Q9NY27-2 PPP4R2 Serine/threonine-protein phosphatase 4 regulatory subunit 2 1 MNGVMFPGNS(0.999)PS(0.001)YTER;MNGVMFPGNS(0.671)PS(0.328)YT(0.001)ER;MNGVMFPGNS(0.9)PS(0.1)YTER;MNGVMFPGNS(1)PSYTER;MNGVMFPGNS(0.999)PS(0.001)YTER;MNGVMFPGNS(0.969)PS(0.031)YTER;MNGVMFPGNS(0.945)PS(0.055)YTER;MNGVMFPGNS(1)PSYTER;MNGVMFPGNS(0.942)PS(0.058)YTER;MNGVMFPGNS(0.999)PS(0.001)YTER;MNGVMFPGNS(0.989)PS(0.011)YTER;MNGVMFPGNS(0.998)PS(0.002)YTER;MNGVMFPGNS(1)PSYTER;MNGVMFPGNS(0.973)PS(0.026)YTER;MNGVMFPGNS(1)PSYTER;MNGVMFPGNS(0.999)PS(0.001)YTER;MNGVMFPGNS(0.947)PS(0.053)YTER;MNGVMFPGNS(0.957)PS(0.042)Y(0.001)TER 377.56 4.26E-104 4674127000 6261226 6677808 6831205 6864075 7014497 5744866 7402360 5879852 6786420 TRUE FALSE 5869347.041 7172239.853 6993244.409 7040218.785 6463606.701 7403315.554 6292444.838 6613964.465 5653722.66 1.038138479 1.268587139 1.236927389 1.245235964 1.143247925 1.309458564 1.112973737 1.169842396 1 22.43076968 0.761749759 0.957157999 1.001329972 1.214706559 0.361997187 0.079679377 0.832216472 1.427508485 0.068249381 0.022508715 5.777630441 -0.761749759 0.213376587 MNLAIS(ph)IALLLT(ph)VLQVS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MNLAISIALLLTVLQVSR 18 0 E9PIM6;E9PNQ8;P04216 E9PIM6 THY1 Thy-1 membrane glycoprotein 3 MNLAIS(1)IALLLT(1)VLQVS(1)R 43.454 0.089437 67011000 11484 26749 21200 21259 28134 21620 20132 23964 19664 TRUE FALSE 10765.23694 28729.52379 21702.87401 21804.54193 25924.46913 27861.34303 17113.3935 26955.95815 16381.95137 0.657140087 1.753730258 1.324803958 1.331010052 1.582501898 1.700734083 1.044649268 1.645466865 1 13.9998196 -1.498248658 9.823365251 0.999995278 1.400887453 0.111211326 0.332990871 3.05E-05 1.56E-06 0.285642974 0.067325902 0.031750556 1.498248658 0.400892175 MNLASEPQEVLHIGSAHNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MNLASEPQEVLHIGSAHNR 19 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 0 ; 168.09 9.68E-12 338820000 175371 319860 283760 290990 327640 262250 337580 284290 359000 FALSE TRUE 164394.8422 343542.7672 290490.9212 298457.296 301908.476 337957.3177 286963.0129 319784.2323 299080.5808 0.54966739 1.1486629 0.971279782 0.997915997 1.009455295 1.1299875 0.959483936 1.069224326 1 18.19017471 4.746908682 24.99100312 1.034419317 0.549667147 0.853184014 0.063367165 367.3252816 1099610.872 0.014179843 0.161970747 55835.27787 -4.746908682 -0.484752169 MNLSEEVDLEDYVARPDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MNLSEEVDLEDYVARPDK 18 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ; 229.46 1.70E-19 671560000 738110 639590 657720 597860 698270 472670 814720 597320 796990 FALSE TRUE 691913.0127 686945.9091 673321.429 613202.0998 643430.6909 609122.1558 692560.2995 671896.7169 663967.2202 1.042089115 1.034608168 1.014088359 0.923542731 0.969069965 0.917397934 1.043063992 1.011942603 1 19.34075249 3.464524693 24.88627053 0.978562895 1.031348466 0.315219264 0.037592286 270.0420154 533504.3352 0.010680439 0.014489557 2914.235827 -3.464524693 0.052785571 MNLSLY(ph)LGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MNLSLYLGER 10 0 Q7Z589-4;Q7Z589-6;Q7Z589-7 Q7Z589-4;Q7Z589-7 EMSY Protein EMSY 1 MNLS(0.002)LY(0.998)LGER;MNLS(0.002)LY(0.998)LGER 42.743 0.093886 317040000 59471 81523 83241 85715 82926 86648 88249 63942 80786 TRUE FALSE 55748.81627 87559.04774 85215.51583 87914.59202 76413.32647 111661.871 75016.88171 71925.29945 67302.2947 0.828334554 1.30098161 1.26616063 1.306264406 1.135374757 1.659109418 1.114625914 1.06869015 1 16.03836807 1.506538935 13.32351824 1.053479589 1.264191485 0.16550745 0.202414399 0.18911641 69.83299631 0.099688951 0.046233049 32.10250595 -1.506538935 0.210711896 MNS(ph)DQDVALKLAQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MNSDQDVALKLAQER 15 1 Q92738 Q92738 USP6NL USP6 N-terminal-like protein 1 MNS(1)DQDVALKLAQER;MNS(1)DQDVALKLAQER;MNS(1)DQDVALKLAQER 65.107 0.037762 1745790000 2634170 2437940 2439930 2691060 3389910 1487370 3052160 2255870 5034870 TRUE FALSE 2469302.002 2618447.614 2497806.292 2760117.156 3123680.143 1916749.574 2594516.943 2537520.335 4194517.67 0.588697485 0.624254758 0.595493091 0.658029688 0.744705444 0.456965431 0.618549532 0.604961174 1 22.00007349 -0.843802175 5.799075549 1.000000077 0.610243624 0.749555523 0.070579122 6.50E-08 1.28E-08 0.063193865 0.014894934 0.143284042 0.843802175 -0.389756453 MNS(ph)LTFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MNSLTFK 7 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 MNS(1)LTFK;MNS(0.999)LT(0.001)FK 107.83 0.0077509 308010000 1230420 861650 1013280 994470 1074210 685040 1240550 887560 1059200 TRUE FALSE 1153410.209 925447.4625 1037315.48 1019989.784 989845.8798 882799.9273 1054541.044 998373.8198 882412.6773 1.307109744 1.048769455 1.175544625 1.155910165 1.121749387 1.000438854 1.19506561 1.131413731 1 19.75109399 0.474629033 0.015272666 1.28E-05 2.172049297 0.279760489 0.079296564 1642.811779 10.57318582 779.5297522 722.4540711 2.982833642 -0.474629033 2.17203647 MNS(ph)TGGQTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MNSTGGQTPR 10 0 Q96ST2;Q96ST2-3;Q96ST2-2;A0A1B0GW95 Q96ST2 IWS1 Protein IWS1 homolog 1 MNS(0.872)T(0.119)GGQT(0.009)PR;MNS(0.883)T(0.117)GGQTPR;MNS(0.885)T(0.115)GGQTPR 109.47 0.0078759 331863000 444060 550920 460620 590770 746650 309058 693170 458430 655140 TRUE FALSE 416267.0773 591710.69 471546.1239 605930.1584 688011.1208 398278.0275 589235.5936 515665.9946 545792.9016 0.762683201 1.084130424 0.863965293 1.110183288 1.260571764 0.729723722 1.079595561 0.944801578 1 19.05799411 4.7511102 23.79399015 1.004217679 0.7626829 0.222857778 0.144368255 1553.800014 2945895.801 0.031602096 0.527933501 56378.06937 -4.7511102 -0.241534779 MNSEEEDEVWQVIIGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MNSEEEDEVWQVIIGAR 17 0 Q9NR28-2;Q9NR28;Q9NR28-3;H7BZK7;A0A2U3TZH2;H7BZQ7 Q9NR28-2 DIABLO "Diablo homolog, mitochondrial" 0 ; 140.1 1.57E-06 15218300 19517.8 18778 17048.6 18330.4 20622.4 15721.8 17329.8 12355.9 12996.8 FALSE TRUE 18296.21574 20168.34266 17453.00084 18800.7891 19002.79989 20260.42844 14731.35737 13898.56131 10827.55012 1.689783519 1.862687537 1.611906724 1.736384398 1.755041508 1.871192303 1.36054391 1.283629368 1 13.40241923 1.383907785 1.682384406 1.053327747 1.750587912 0.869624223 0.101058451 0.109677647 0.566266439 0.085705064 0.026680665 24.20515038 -1.383907785 0.697260165 MNTNPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MNTNPSR 7 0 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ;; 98.458 0.026167 244927000 220034 256139 222183 218261 262293 177287 239609 222956 244071 FALSE TRUE 206262.4647 275103.7981 227453.2857 223861.9468 241693.5658 228466.8789 203681.8549 250792.5474 203333.9733 1.014402371 1.35296524 1.118619196 1.100956929 1.18865314 1.123604064 1.001710887 1.233402089 1 17.63349176 1.799619171 0.291695895 1.000564824 1.222999654 0.092184649 0.106022038 2.575848095 0.761605908 0.184547453 0.209893522 63.04043064 -1.799619171 0.22243483 MNTS(ph)RFADHHDLLT(ph)ET(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MNTSRFADHHDLLTETK 17 1 C9J4A2;C9JYK8;A2RUB1-1;A2RUB1-2 C9J4A2 C17orf104 3 MNT(0.489)S(0.522)RFADHHDLLT(0.99)ET(1)K 42.612 0.088162 939450000 131960 331340 293660 272990 366400 245990 296450 235010 416280 TRUE FALSE 123700.8592 355872.7584 300625.7539 279995.3856 337624.422 317003.3197 252000.0746 264351.5158 346800.1787 0.356692028 1.026160827 0.866855822 0.807368054 0.973541661 0.914080612 0.726643439 0.76225888 1 18.40374512 4.748726693 24.96870001 0.878007536 0.356691739 0.736116664 0.099265502 795.9458165 1954867.826 0.02450945 0.340924785 56069.50125 -4.748726693 -0.521315797 MPDMHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MPDMHFK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 77.674 0.037406 178710000 536900 755890 530300 526410 881300 337540 490890 705700 817910 FALSE TRUE 503296.3874 811856.8821 542878.9664 539918.5718 812086.253 434982.3185 417285.6017 793808.1984 681395.5371 0.738625893 1.191461989 0.796716352 0.792371747 1.191798609 0.638369779 0.612398495 1.164974167 1 19.37813297 2.216539057 24.99998433 0.792672137 0.949537911 0.004509355 0.223024332 554.6460726 629658.2469 0.079305283 0.058617375 164.6414026 -2.216539057 0.156865774 MPEFYNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 MPEFYNR 7 0 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ;;;;;; 154.92 0.0038296 2159350000 1230485 1654280 1349310 1353560 1639480 1050225 1373550 1374390 1493620 FALSE TRUE 1153471.14 1776764.612 1381316.27 1388294.641 1510721.854 1353407.909 1167598.929 1545985.617 1244325.173 0.926985297 1.427894132 1.110092684 1.11570084 1.214089281 1.087664172 0.938339073 1.242428949 1 20.24693212 2.104004961 5.115701019 1.044195712 1.186440559 0.071004362 0.145262782 0.357689526 14.87405933 0.05287627 0.038432948 127.0588619 -2.104004961 0.142244848 MPEMHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MPEMHFK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 92.925 0.015312 854610000 1712600 2125300 1501990 1493080 2551400 990170 1402800 2170800 2428300 FALSE TRUE 1605411.423 2282659.423 1537617.912 1531394.961 2351023.336 1276016.005 1192463.163 2441829.159 2023001.043 0.793579138 1.128353063 0.76006778 0.756991681 1.162146379 0.630754003 0.58945257 1.20703307 1 20.94806563 3.892386186 6.831612942 0.833561407 0.979128851 0.00222274 0.222077889 0.603586316 40.51058957 0.054801069 0.09983305 7805.238641 -3.892386186 0.145567444 MPFGELMFESSSSCGWVHGVCFSASGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MPFGELMFESSSSCGWVHGVCFSASGSR 28 0 A0A1W2PNV4;C9JEY1;C9K057;O15143 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 143.9 1.07E-07 23351000 7826.7 11991 7917.1 7109 11017 7082.7 9183.9 10501 7940.8 FALSE TRUE 7336.840818 12878.82612 8104.897351 7291.428976 10151.76926 9127.360512 7806.859454 11812.07297 6615.42918 1.109049862 1.946786182 1.225150649 1.102185327 1.534559434 1.379707992 1.180098712 1.785533885 1 12.69161904 -2.17259506 2.209333909 3.60E-05 1.41559945 0.170257753 0.282524927 5596697.762 1386719.03 27930086.51 0.065563966 0.006720552 2.17259506 1.41556346 MPFLSISS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MPFLSISSPK 10 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 MPFLSISS(1)PK;MPFLSIS(0.002)S(0.998)PK 205.12 1.83E-07 335820000 1589400 1167890 1234140 1331670 1731120 831370 1334870 1236350 1908900 TRUE FALSE 1489922.291 1254361.791 1263414.384 1365842.907 1595164.818 1071373.023 1134718.636 1390711.019 1590292.258 0.936885836 0.788761804 0.794454213 0.858862828 1.00306394 0.673695679 0.713528366 0.874500276 1 20.60086049 2.21358722 24.99976736 0.7789888 0.852481835 0.000795137 0.110858944 567.0293953 567624.3649 0.039692527 0.029327117 163.5261529 -2.21358722 0.073493036 MPGGPKPGGGPGLS(ph)TPGGHPKPPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MPGGPKPGGGPGLSTPGGHPKPPHR 25 2 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 1 MPGGPKPGGGPGLS(0.766)T(0.234)PGGHPKPPHR 86.141 0.0080194 1501900000 1533700 1264300 1448100 1385800 1539000 846690 1818700 1293800 2552900 TRUE FALSE 1437708.455 1357910.088 1482449.616 1421361.974 1418133.148 1091115.658 1546002.819 1455333.778 2126804.498 0.675994647 0.638474335 0.697031447 0.668308712 0.666790553 0.513030539 0.726913461 0.684281879 1 21.02025599 0.44865554 1.396557605 0.999926918 0.653610192 0.791940296 0.05530603 1.203995864 2.618439499 0.0492217 0.014416779 2.809671463 -0.44865554 -0.346316726 MPGGPKPGGGPGLST(ph)PGGHPKPPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MPGGPKPGGGPGLSTPGGHPKPPHR 25 2 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 1 MPGGPKPGGGPGLS(0.002)T(0.998)PGGHPKPPHR 141.38 3.37E-07 813270000 1137000 1037700 1106100 1086000 1387100 748200 1418100 1144200 1904400 TRUE FALSE 1065837.2 1114532.388 1132337.214 1113868.599 1278162.761 964193.194 1205469.07 1287055.889 1586543.337 0.671798352 0.702490983 0.713713384 0.702072596 0.805627386 0.607732024 0.759808473 0.811232734 1 20.5974555 0.900613252 1.71555951 0.99889985 0.705933352 0.78005149 0.04982946 0.196043488 1.157757814 0.041953289 0.011993672 7.954506695 -0.900613252 -0.292966498 MPLDLS(ph)PLATPIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 125.22 9.70E-05 83082000 115490 118860 117000 117980 165260 124270 128200 128510 134800 TRUE FALSE 108261.6871 127660.5181 119775.2953 121007.5665 152281.1462 160144.7316 108977.6002 144554.7564 112301.0092 0.964031293 1.13677089 1.066555823 1.077528755 1.356008707 1.4260311 0.970406241 1.287207991 1 16.77701137 5.65431232 0.590026679 1.183989992 0.517157182 0.150315753 0.15012179 19.80256355 2.322593187 0.06598837 11.44645998 451141.0234 -5.65431232 -0.66683281 MPLLELGGET(ph)TPPLSTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MPLLELGGETTPPLSTER 18 0 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 MPLLELGGET(0.634)T(0.366)PPLSTER 101.96 0.0064651 61591000 83436 102140 107980 120220 109020 81821 90248 71354 115090 TRUE FALSE 78213.8897 109702.5519 110541.3366 123305.0487 100458.009 105441.3944 76716.15022 80262.70397 95880.73549 0.815741445 1.144156345 1.152904554 1.28602527 1.04773924 1.099714076 0.800120586 0.837109807 1 16.54895336 1.766925005 9.758490062 0.86478259 1.110256229 0.370449716 0.12818111 0.192727057 59.02929666 0.056618209 0.031281054 58.46891096 -1.766925005 0.24547364 MPLLELGGETT(ph)PPLSTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MPLLELGGETTPPLSTER 18 0 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 MPLLELGGET(0.168)T(0.832)PPLSTER;MPLLELGGET(0.008)T(0.934)PPLS(0.029)T(0.029)ER;MPLLELGGET(0.162)T(0.838)PPLSTER 150.28 6.27E-07 131830000 203852 228729 239636 229151 245307 181278 201498 183617 239042 TRUE FALSE 191093.2672 245664.3332 245320.2791 235031.4026 226041.5777 233610.0158 171285.2455 206541.9866 199144.3459 0.959571643 1.233599337 1.231871675 1.180206254 1.135063999 1.173068784 0.860105994 1.037147129 1 17.60345499 1.755088128 25 0.956839891 1.171224295 0.48455473 0.089085939 4.265960891 6460.217345 0.038837085 0.021537287 56.89683757 -1.755088128 0.214384404 MPLLELGGETT(ph)PPLSTERS(ph)PEAVGSECPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MPLLELGGETTPPLSTERSPEAVGSECPSR 30 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 2 MPLLELGGET(0.485)T(0.51)PPLS(0.151)T(0.144)ERS(0.709)PEAVGS(0.001)ECPSR;MPLLELGGET(0.469)T(0.53)PPLS(0.078)T(0.069)ERS(0.853)PEAVGSECPSR 101.78 0.00092284 145857000 47091 63650 61951 59693 68754 47071 62439 58819 75057 TRUE FALSE 44143.65837 68362.71223 63420.50698 61224.82344 63354.33818 60659.63357 53076.85161 66162.68163 62529.50181 0.705965298 1.093287332 1.014249356 0.979134995 1.013191155 0.970096223 0.848828954 1.05810345 1 15.9322494 1.991249414 24.34337466 0.941501167 0.987604875 0 0.114276615 1205.140795 3352600.826 0.041578361 0.029121557 98.00526655 -1.991249414 0.046103708 MPLLELGGETTPPLS(ph)TERSPEAVGSECPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MPLLELGGETTPPLSTERSPEAVGSECPSR 30 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 MPLLELGGET(0.001)TPPLS(0.383)T(0.383)ERS(0.232)PEAVGSECPSR 88.683 0.00070409 66676000 8979.5 10132 9681.7 8888.1 10417 7121.6 9152.5 8738.6 10427 TRUE FALSE 8417.489124 10882.18382 9911.354496 9116.183694 9598.89084 9177.49031 7780.167593 9829.633446 8686.666339 0.969012599 1.252745691 1.140984828 1.049445591 1.105014336 1.056503145 0.895644807 1.131577185 1 13.08458691 2.603725903 1.175130628 0.998857797 1.147833753 0.116307625 0.093723269 0.573073383 1.620031353 0.047254701 0.038664695 401.5373077 -2.603725903 0.148975956 MPLLELGGETTPPLSTERS(ph)PEAVGSECPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 MPLLELGGETTPPLSTERSPEAVGSECPSR 30 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 MPLLELGGETTPPLS(0.019)T(0.019)ERS(0.962)PEAVGSECPSR;MPLLELGGETTPPLS(0.001)T(0.02)ERS(0.979)PEAVGSECPSR;MPLLELGGETTPPLS(0.002)T(0.002)ERS(0.997)PEAVGSECPSR;MPLLELGGETTPPLST(0.003)ERS(0.996)PEAVGSECPSR;MPLLELGGETTPPLS(0.001)T(0.005)ERS(0.994)PEAVGSECPSR;MPLLELGGETTPPLS(0.175)T(0.175)ERS(0.65)PEAVGSECPSR 278.37 1.16E-71 1147440000 157350 176004 174197 169368 197270 137620 189643 148431 219504 TRUE FALSE 147501.7444 189035.5193 178329.0351 173714.2696 181777.2099 177348.6599 161207.7927 166962.9371 182867.3643 0.806605076 1.033730212 0.975182399 0.949946811 0.994038551 0.969821272 0.881555838 0.913027525 1 17.4804381 1.770756033 24.99999684 0.919100819 0.967642182 0 0.066133924 65.21079383 50661.99583 0.02801187 0.015538934 58.98696244 -1.770756033 0.048541363 MPQDGS(ph)DDEDEEWPTLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 MPQDGSDDEDEEWPTLEK 18 0 Q13895;F8WBL2 Q13895 BYSL Bystin 1 MPQDGS(1)DDEDEEWPTLEK;MPQDGS(1)DDEDEEWPTLEK;MPQDGS(1)DDEDEEWPTLEK;MPQDGS(1)DDEDEEWPTLEK;MPQDGS(1)DDEDEEWPTLEK 199.85 5.29E-15 638912000 923106 807531 842848 839169 867583 644810 1063540 734783 953390 TRUE FALSE 865330.4433 867321.4355 862840.7526 860703.4972 799446.5308 830956.1794 904072.0504 826522.275 794263.0499 1.08947589 1.091982607 1.086341298 1.083650432 1.006526151 1.046197704 1.138252687 1.040615291 1 19.59925736 2.973353034 24.60859439 1.059994019 1.088876363 0.181713564 0.03824602 1400.04932 1292952.409 0.012001609 0.012771841 940.4875125 -2.973353034 0.028882344 MPS(ph)VMEKPSAGSGILSRS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MPSVMEKPSAGSGILSRSR 19 2 Q8IZ40 Q8IZ40 RCOR2 REST corepressor 2 2 MPS(0.943)VMEKPS(0.056)AGS(0.032)GILS(0.08)RS(0.889)R 47.331 0.093813 855210000 324560 718690 693290 843770 789670 395120 441170 358200 496690 TRUE FALSE 304246.369 771902.5554 709735.1662 865422.5667 727652.5036 509184.7298 375020.6541 402922.0585 413789.2303 0.735268941 1.865448637 1.715209373 2.091457446 1.75851001 1.230541282 0.906308397 0.973737422 1 18.65853657 2.073183661 3.507833783 0.966717689 1.69607042 0.429396244 0.353143562 0.199009892 4.874510793 0.143473074 0.095722794 118.3541963 -2.073183661 0.72935273 MPSARPPS(ph)PPLSSWER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MPSARPPSPPLSSWER 16 1 O43896 O43896 KIF1C Kinesin-like protein KIF1C 1 MPSARPPS(0.759)PPLS(0.183)S(0.058)WER;MPSARPPS(0.546)PPLS(0.193)S(0.261)WER;MPSARPPS(1)PPLSSWER;MPSARPPS(0.995)PPLS(0.002)S(0.003)WER 139.26 1.31E-06 2395630000 944540 1180710 1074120 1073350 1114640 847250 1087970 978610 1307400 TRUE FALSE 885422.9275 1268130.997 1099598.634 1100893.978 1027100.671 1091837.321 924838.9987 1100791.613 1089186.494 0.812921325 1.164291886 1.009559556 1.010748834 0.942997986 1.002433768 0.849109867 1.01065485 1 20.05481957 2.854908481 1.858162285 0.944089913 1.034490793 0 0.097983676 0.658875677 4.520873594 0.033221237 0.035541814 715.9925134 -2.854908481 0.09040088 MPSGEFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MPSGEFAR 8 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ; 110.14 0.0081051 450010000 875480 741520 699640 652580 809680 591140 814170 745490 789040 FALSE TRUE 820685.2696 796422.9124 716235.7912 669326.3076 746090.9989 761792.5216 692092.7669 838566.0675 657344.1266 1.248486503 1.211576829 1.089590311 1.018228171 1.135008238 1.158894544 1.052862175 1.275688081 1 19.32628931 4.177134042 2.293642453 1.104847991 1.241491407 0.31341388 0.077979412 0.359874849 3.63508895 0.018649149 0.061295532 15036.05972 -4.177134042 0.136643416 MPSHQGAEQQQQQHHVFISQVVTEKEFLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MPSHQGAEQQQQQHHVFISQVVTEKEFLSR 30 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 D6REX3 SEC31A Protein transport protein Sec31A 0 60.029 0.010798 102110000 183150 80124 99437 77657 99709 60559 119540 77021 131680 FALSE TRUE 171686.9684 86056.46433 101795.6926 79649.81009 91878.25735 78041.40021 101616.0868 86637.24139 109701.7573 1.565033894 0.784458394 0.927931285 0.726057741 0.837527671 0.711396081 0.926294065 0.789752539 1 16.74322711 4.740999124 24.99897415 0.835569952 1.56503415 0.860895855 0.091849076 69.61677716 713651.0421 0.019216753 0.13029008 55080.6586 -4.740999124 0.729464198 MPTQSEEEKLS(ph)PSPTTEDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MPTQSEEEKLSPSPTTEDPR 20 1 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2 Q9BTC8 MTA3 Metastasis-associated protein MTA3 1 MPTQSEEEKLS(0.882)PS(0.109)PT(0.005)T(0.005)EDPR;MPTQSEEEKLS(0.945)PS(0.052)PT(0.002)TEDPR;MPTQS(0.001)EEEKLS(0.972)PS(0.017)PT(0.008)T(0.001)EDPR;MPT(0.001)QS(0.003)EEEKLS(0.767)PS(0.226)PT(0.003)TEDPR 101.86 0.00018936 1845660000 3991920 2617620 3065450 2966130 3141000 2165600 3484310 2584850 4704300 TRUE FALSE 3742072.853 2811431.308 3138163.922 3042245.917 2894318.53 2790773.564 2961870.062 2907574.212 3919121.939 0.954824298 0.71736255 0.800731381 0.77625702 0.738511987 0.712091537 0.755748381 0.741894296 1 21.90209903 -1.179728606 8.986687733 1.00000001 0.767189539 0.506545428 0.06954275 1.25E-08 1.09E-09 0.059771693 0.014088322 0.066110645 1.179728606 -0.232810471 MPWSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MPWSFR 6 0 P05186-2 P05186-2 0 ; 107.73 0.072163 419890000 514980 364030 551100 543140 400890 399350 620000 353200 974270 FALSE TRUE 482748.3211 390983.16 564172.3522 557077.8919 369405.7165 514635.8621 527036.7558 397297.7975 811658.043 0.594768111 0.481709217 0.695086258 0.686345557 0.455124815 0.634055027 0.649333497 0.48948914 1 19.63051251 -1.7227166 2.689442677 1.073294285 0.591777997 0.697672064 0.085619824 17153254.92 14199582.22 8451134.652 0.01955002 0.018935789 1.7227166 -0.481516287 MQAS(ph)IEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 MQASIEK 7 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK 133.81 0.0033942 12073290000 9426170 6310450 8111640 7286840 7752810 5995110 9771160 6908800 10833370 TRUE FALSE 8836202.846 6777682.284 8304051.931 7473832.651 7143935.576 7725800.935 8306065.269 7771378.888 9025210.561 0.979057806 0.750972206 0.920095091 0.828106181 0.791553341 0.856024453 0.92031817 0.861074524 1 23.10552916 0.568880286 0.715303782 1.000592829 0.848436688 0.289664328 0.066199146 1.671693595 1.482268378 0.065067269 0.022233647 3.705785569 -0.568880286 -0.152156141 MQASIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MQASIEK 7 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ; 94.302 0.033268 144207000 336570 427300 403810 410660 484780 337410 478310 468330 495170 FALSE TRUE 315504.6845 458937.7366 413388.5639 421198.2308 446707.3343 434814.7896 406591.8559 526802.0314 412522.9281 0.76481733 1.112514494 1.002098394 1.021029868 1.082866682 1.054037873 0.985622442 1.277024853 1 18.65411478 4.745059958 24.91260533 1.058409338 0.764817191 0.554847353 0.084731681 520.4488467 1994875.531 0.018072224 0.173053085 55598.10094 -4.745059958 -0.293592147 MQEHSDQVPVGNIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MQEHSDQVPVGNIPR 15 0 P33993;P33993-3;P33993-2;C9J8M6 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 162.46 1.59E-06 636430000 661410 664610 715900 679970 719550 648210 746030 643210 707010 FALSE TRUE 620013.5288 713818.4159 732881.4861 697419.1814 663039.4455 835337.7042 634169.7273 723516.1844 589005.4635 1.052644784 1.211904575 1.244269419 1.18406233 1.125693201 1.418217242 1.076678854 1.228369224 1 19.16792149 -0.974782334 6.845933272 0.999999981 1.197856094 0.260754891 0.101658274 2.59E-08 3.98E-09 0.087018214 0.020510388 0.105978475 0.974782334 0.197856113 MQES(ph)PKLPQQSYNFDPDTCDESVDPFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MQESPKLPQQSYNFDPDTCDESVDPFK 27 1 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 MQES(0.975)PKLPQQS(0.014)Y(0.011)NFDPDTCDESVDPFK;MQES(1)PKLPQQSYNFDPDTCDESVDPFK 117.36 0.00031292 97993000 355750 155481 227860 270370 342310 136598 191721 101015 173862 TRUE FALSE 333484.2425 166992.975 233264.9468 277308.1519 315426.3534 176031.6251 162974.2159 113626.9451 144843.309 2.302379342 1.152921569 1.610464083 1.914538917 2.177707452 1.215324521 1.125176006 0.784481837 1 17.14413352 2.052098917 7.962964468 1.029497973 1.713068956 0.581540839 0.333065118 0.214590549 28.7936256 0.130140206 0.095735616 112.7454222 -2.052098917 0.683570984 MQFS(ph)FEEYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MQFSFEEYEK 10 0 A0A1W2PR28;Q5JU85-3;Q5JU85;A0A1W2PR18 A0A1W2PR28 IQSEC2 IQ motif and SEC7 domain-containing protein 2 1 MQFS(1)FEEYEK;MQFS(1)FEEYEK 148.41 2.64E-05 89224000 180530 155962 151693 181772 145354 117459 193778 142025 159286 TRUE FALSE 169230.9496 167509.5888 155291.2296 186436.5773 133938.4832 151367.5065 164722.7878 159757.1339 132700.1376 1.275288426 1.262316617 1.170241662 1.404946375 1.009331909 1.14067332 1.241315878 1.203895767 1 17.01781034 -4.999999999 0.134714333 0.294008841 1.295559657 0.349921993 0.098049257 164.719099 1.382103542 31.47502205 0.632543675 1.00E-05 4.999999999 1.001550816 MQFS(ph)FEGPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 MQFSFEGPEK 10 0 A0A0C4DGT3;A0A3B3IU98;Q6DN90-2;A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90;A0A2R8Y695 A0A0C4DGT3;A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 MQFS(1)FEGPEK;MQFS(1)FEGPEK;MQFS(1)FEGPEK;MQFS(1)FEGPEK;MQFS(1)FEGPEK 135.58 0.0001472 708958000 1464620 1275427 1128208 1396400 1035639 899977 1755650 1051737 1077629 TRUE FALSE 1372952.049 1369860.942 1154969.627 1432233.988 954304.0905 1159785.75 1492406.581 1183048.68 897765.7582 1.529298747 1.525855636 1.286493293 1.595331494 1.062976708 1.291857859 1.662356319 1.317769885 1 19.77597955 -2.204333325 1.567766009 0.128482215 1.416802717 0.342656307 0.177735019 251217.1448 41138.82456 773504.6441 0.046760113 0.006246931 2.204333325 1.288320503 MQHLIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 MQHLIAR 7 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;; 146.94 0.0021848 7112960000 2819085 11538168 2552183 2684267 12095740 1357261 2682848 9439630 9497926 FALSE TRUE 2642643.502 12392465.96 2612721.986 2753149.836 11145789.37 1749080.217 2280579.849 10618188.58 7912660.792 0.333976594 1.566156605 0.330195121 0.347942356 1.408601944 0.2210483 0.288219084 1.341923894 1 22.91573148 4.990236633 23.35403143 0.759554405 0.082367733 0.071989297 0.509330477 15196.44278 49805.22196 0.11477156 205399.9674 97776.98306 -4.990236633 -0.677186672 MQHLIAREAEAAIYHLQLFEELRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MQHLIAREAEAAIYHLQLFEELRR 24 2 P14618;P14618-3;B4DNK4 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 146.64 6.15E-08 20507000 5647.1 12762 4805 10066 5666.8 3410 3851.5 3018.9 6887.1 FALSE TRUE 5293.658091 13706.91176 4918.976869 10324.3106 5221.752387 4394.411643 3274.003331 3395.81631 5737.598518 0.922626091 2.388963208 0.857323295 1.799413216 0.910093721 0.765897375 0.570622591 0.591853247 1 12.48623131 2.576602708 4.061355109 0.69686621 1.534364336 0.398807608 0.442867231 0.206811898 6.014280827 0.140653893 0.130111444 377.2269465 -2.576602708 0.837498125 MQKS(ph)PCY(ph)IPIVS(ph)S(ph)ATLWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MQKSPCYIPIVSSATLWDR 19 1 F8VX61;F8W1Y6;Q96LP6-3;Q96LP6 F8VX61 C12orf42 Uncharacterized protein C12orf42 4 MQKS(0.914)PCY(0.987)IPIVS(0.99)S(0.99)AT(0.119)LWDR 53.266 0.041199 114390000 11200 31585 24237 23217 31052 26978 26771 23447 22724 TRUE FALSE 10499.01199 33923.58626 24811.91309 23812.78753 28613.30118 34766.11065 22756.93708 26374.40956 18931.2176 0.554587255 1.791938954 1.310634826 1.257858212 1.511434805 1.836443455 1.202085231 1.393170272 1 14.20847958 0.557944012 1.491991024 1.000943314 1.408508822 0.075466186 0.35654343 4.321030015 12.05272119 0.305436892 0.08855684 3.613632735 -0.557944012 0.407565508 MQLLETEFSHTVGELIEVHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MQLLETEFSHTVGELIEVHLR 21 0 Q9Y6D9;Q9Y6D9-3 Q9Y6D9 MAD1L1 Mitotic spindle assembly checkpoint protein MAD1 0 111.57 0.00017171 5630500 3391.5 3575.7 3788.2 5960.8 4593 4242.3 4528.1 3732.8 3305.1 FALSE TRUE 3179.232069 3840.448549 3878.057893 6113.76422 4232.284307 5466.983142 3849.153442 4198.848297 2753.457458 1.154632718 1.394773156 1.408432108 2.22039538 1.53707997 1.985497588 1.397934597 1.524936688 1 11.4270286 3.45556491 24.99997509 1.651521773 1.338152413 0.142252493 0.331654137 384.0783876 445434.0288 0.083311676 0.112835008 2854.729153 -3.45556491 -0.31336936 MQMELSHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MQMELSHK 8 0 Q9Y6D9;C9JJ38 Q9Y6D9 MAD1L1 Mitotic spindle assembly checkpoint protein MAD1 0 ;; 90.709 0.0070166 994530000 2584320 1550330 1866260 1727440 1732830 1855430 1980080 1517660 1337900 FALSE TRUE 2422572.024 1665118.046 1910528.569 1771769.035 1596740.522 2391062.521 1683185.386 1707143.192 1114595.847 2.173498162 1.493920914 1.714099845 1.589606708 1.432573543 2.14522827 1.510130682 1.531625294 1 20.08808925 0.798149613 1.659057286 1.002714664 1.702412542 0.450056329 0.252972162 0.639170051 3.117771213 0.216217358 0.06187991 6.282747597 -0.798149613 0.699697877 MQMLEDEDDLAYAETEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MQMLEDEDDLAYAETEKK 18 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 205.02 1.62E-15 363966000 446999 318648 368372 371847 426200 260094 503126 357178 552513 FALSE TRUE 419022.1305 342241.0295 377109.9578 381389.2236 392727.9712 335178.9155 427686.9271 401772.4595 460295.0109 0.910333852 0.743525394 0.81927883 0.828575619 0.853209272 0.728182812 0.929158294 0.872858602 1 18.81219928 1.108803546 1.032427084 0.994831094 0.809050494 0.461766292 0.06009169 0.390037799 0.887866001 0.050979466 0.016993559 12.84705388 -1.108803546 -0.1857806 MQNGFGSPEPSLPGTPHS(ph)PAPPSGGTWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MQNGFGSPEPSLPGTPHSPAPPSGGTWK 28 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 MQNGFGSPEPSLPGT(0.001)PHS(0.999)PAPPSGGTWK 115.92 0.00021098 353960000 142150 119000 132180 148490 150510 118950 183240 140160 171180 TRUE FALSE 133253.0852 127810.8838 135315.372 152300.5048 138689.5517 153288.934 155764.8631 157659.2845 142608.9521 0.934394954 0.896233244 0.948856085 1.067958936 0.972516449 1.074889982 1.092251649 1.105535678 1 17.12170502 3.222146395 0.986419323 1.072013004 0.904753594 0.635962395 0.043770028 0.285812036 0.600720083 0.018000796 0.029033166 1667.809313 -3.222146395 -0.16725941 MQQENMKPQEQLTLEPYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MQQENMKPQEQLTLEPYER 19 1 P22087;M0QXL5;M0R299 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 218.88 2.98E-19 646210000 329740 274050 327780 305650 285010 253900 396910 292850 355160 FALSE TRUE 309102.162 294340.9471 335555.0964 313493.4965 262626.4643 327196.8083 337397.0302 329412.9671 295881.5016 1.044682281 0.99479334 1.134086094 1.059523812 0.887606906 1.105837325 1.140311336 1.113327347 1 18.17465998 MQQHEQALADCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MQQHEQALADCR 12 0 Q9UNE7;Q9UNE7-2 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ;;; 107.37 0.0013814 539053000 474356 556297 504718 524569 564449 516398 542398 509158 515067 FALSE TRUE 444666.9047 597485.8087 516690.1493 538030.3286 520119.4524 665473.7196 461070.4553 572727.4971 429098.9902 1.036280473 1.392419517 1.204128094 1.253860626 1.212119964 1.550862935 1.074508367 1.334721149 1 18.71095098 -1.207633951 4.271824132 0.999891854 1.262358114 0.228803127 0.148238865 0.000133252 2.47E-05 0.125256036 0.029510999 0.06199634 1.207633951 0.26246626 MQQNIQELEEQLEEEESAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MQQNIQELEEQLEEEESAR 19 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 267.46 2.79E-31 152986000 135477 141712 130891 130744 161903 115356.6 151960 130919 144673 FALSE TRUE 126997.7364 152204.5039 133995.7963 134099.1124 149187.7915 148658.1778 129175.0087 147264.5253 120526.1417 1.053694532 1.262833953 1.111757121 1.11261433 1.237804425 1.233410244 1.071759263 1.221847172 1 16.87898657 -1.207385417 3.211795026 0.999538679 1.164468573 0.323761765 0.074111341 9254689.137 12973972.67 43100.02814 0.01645511 0.062031829 1.207385417 0.164929895 MQQQLDEYQELLDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MQQQLDEYQELLDIK 15 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 75.045 0.025507 0 24543 22524 23287 24253 26636 20571 24938 24370 28381 FALSE TRUE 23006.89744 24191.7004 23839.37864 24875.37304 24544.116 26509.51376 21198.77841 27412.64814 23644.02775 0.973053224 1.023163255 1.008262166 1.052078491 1.038068313 1.121192803 0.896580677 1.15938995 1 14.5291882 6.450537801 0.853042636 1.031955041 1.89E-06 0.071236768 0.070433931 117.3880389 5.794592409 0.020722353 207.3677233 2821875.19 -6.450537801 -1.03195315 MQRPS(ph)LPDLSRPNTTSSTGMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MQRPSLPDLSRPNTTSSTGMK 21 2 Q8TF74;Q8TF74-2 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 1 MQRPS(1)LPDLSRPNTTSSTGMK 136.16 2.82E-06 499620000 349200 300070 294390 246610 345540 182370 403240 314650 668940 TRUE FALSE 327344.1953 322287.495 301373.0698 252938.4301 318402.6822 235017.2585 342777.9055 353934.7451 557289.5925 0.587386163 0.578312424 0.540783596 0.453872517 0.571341519 0.421714781 0.6150804 0.635100224 1 19.08806769 0.682466902 1.41798036 0.999354335 0.534219008 0.865745571 0.057228709 0.356913498 1.108866188 0.051115537 0.015035035 4.81356568 -0.682466902 -0.465135328 MQS(ph)LSLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MQSLSLNK 8 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 MQS(0.981)LS(0.019)LNK;MQS(0.645)LS(0.355)LNK 81.09 0.024926 275490000 542750 531680 394840 421960 769520 282920 524860 450930 903220 TRUE FALSE 508780.2463 571046.1404 404205.7913 432788.208 709085.0033 364594.4112 446162.1156 507229.6031 752466.747 0.676149808 0.758898839 0.537174291 0.575159248 0.942347295 0.484532257 0.592932668 0.674089061 1 19.5212683 0.947518845 20.50847613 1.000000002 0.646780236 0.418444618 0.127871479 1468.253202 573763.2119 0.116020087 0.029005022 8.861736765 -0.947518845 -0.353219765 MQSLDKDIVALMVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MQSLDKDIVALMVR 14 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 ; 179.56 1.69E-06 361670000 486450 538830 498100 502510 653520 330552 585040 550600 682350 FALSE TRUE 456003.9628 578725.5339 509915.1672 515405.2573 602195.1754 425976.9963 497318.6832 619343.622 568461.3769 0.802172287 1.018056032 0.897009345 0.906667152 1.059342288 0.749350816 0.874850436 1.089508711 1 19.11670281 1.241414392 24.99956562 1.044754378 0.908432886 0.292795828 0.092289776 91.00170176 797250.9514 0.065187598 0.021443781 17.43469653 -1.241414392 -0.136321492 MQVDQEEGHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MQVDQEEGHQK 11 0 O95757;E9PDE8;D6RJ96 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 ; 117.79 0.0006122 514900000 643830 553720 626530 595990 691490 479390 736670 567620 770720 FALSE TRUE 603533.8296 594718.0049 641391.5875 611284.1124 637183.1647 617782.1108 626213.1724 638488.6065 642081.853 0.939964004 0.926233941 0.998924957 0.952034557 0.992370617 0.962154759 0.97528558 0.994403756 1 19.2923977 4.057994024 4.324201665 0.979054967 0.933709306 0.605246503 0.016287437 0.134579566 4.623644593 0.003643691 0.008247684 11428.62609 -4.057994024 -0.045345661 MQYAPNTQVEILPQGHES(ph)PIFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MQYAPNTQVEILPQGHESPIFK 22 0 P40121-2;P40121;H7C0X8 P40121-2 CAPG Macrophage-capping protein 1 MQYAPNTQVEILPQGHES(1)PIFK 142.2 7.51E-08 74602000 96223 75268 84413 81355 100600 64829 97554 82019 136420 TRUE FALSE 90200.57419 80840.92104 86415.31622 83442.70703 92699.2818 83544.07989 82926.68335 92259.2527 113650.6207 0.793665478 0.711310863 0.760359386 0.734203707 0.815651347 0.735095676 0.729663268 0.811779576 1 16.79424604 0.870674111 3.683164358 0.99994502 0.750464994 0.859075728 0.031169775 0.204632917 5.140489704 0.027980634 0.007194041 7.424617948 -0.870674111 -0.249480026 MRDAGDPS(ph)PPNK ddPTM_SK-BR-3_Pertuzumab_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 70.134 0.029129 278620000 461180 321730 345100 355150 392530 258290 478670 372000 529440 TRUE FALSE 432315.567 345551.224 353285.935 364263.7503 361702.2772 332854.13 406897.8773 418445.0189 441073.0437 0.980145065 0.783433105 0.800969227 0.82585811 0.820050743 0.754646276 0.922518125 0.948697783 1 18.75065807 1.562025832 4.52940625 0.964122312 0.819151087 0.508154691 0.060954967 0.121728641 5.504841991 0.033372795 0.014651004 36.47756436 -1.562025832 -0.144971225 MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDK ddPTM_SK-BR-3_Pertuzumab_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 0 205.84 1.50E-31 520310000 63339 83066 77268 78842 107680 83191 152450 94324 141650 FALSE TRUE 59374.72505 89216.29307 79100.83345 80865.2192 99223.24716 107206.8912 129591.5378 106100.559 118007.6999 0.503142804 0.756020947 0.670302307 0.685253753 0.84082011 0.908473695 1.098161712 0.899098611 1 16.84852147 2.42595466 1.679311832 1.008509624 0.668870029 0.780488388 0.08104646 0.157882173 0.905086463 0.035476 0.026437377 266.6580262 -2.42595466 -0.339639595 MREDYDS(ph)VEQDGDEPGPQR ddPTM_SK-BR-3_Pertuzumab_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 190.87 6.60E-15 958620000 501020 588230 534750 544260 656880 484780 642910 546070 698600 TRUE FALSE 469662.0525 631783.1613 547434.5225 558226.633 605291.2945 624728.1163 546511.614 614248.0415 581999.1469 0.806980655 1.085539669 0.940610524 0.959153696 1.040020931 1.073417581 0.939024768 1.055410553 1 19.15065751 2.749841069 23.89964752 1.015628322 0.969739121 0.159371042 0.076369123 1097.493653 2325230.816 0.022159583 0.023291653 562.1355724 -2.749841069 -0.045889201 MREDYDSVEQDGDEPGPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MREDYDSVEQDGDEPGPQR 19 1 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ;; 182.22 3.12E-14 1629010000 279784 327848 305433 291197 344646 275139 332525 301448 360785 FALSE TRUE 262272.8189 352122.207 312678.015 298669.608 317578.8934 354567.1628 282665.9633 339084.4464 300567.6527 0.872591633 1.171523961 1.040291635 0.993685133 1.056597044 1.179658422 0.940440399 1.128146836 1 18.19733023 -1.59683302 3.130844688 0.997035747 1.054308966 0.019713183 0.097049862 0.001893372 0.000243814 0.088466045 0.019778514 0.025302707 1.59683302 0.057273219 MREEFDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MREEFDK 7 1 O43809;H3BND3;H3BV41 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 ;;; 130.56 0.0032387 1663940000 2528370 2160000 2271400 2308730 2689330 1802570 2550600 2171340 2866820 FALSE TRUE 2370123.835 2319928.647 2325278.681 2367975.92 2478120.87 2322942.697 2168161.209 2442436.579 2388329.222 0.992377355 0.971360492 0.973600565 0.991478017 1.03759601 0.972622483 0.907815049 1.022654899 1 21.18757029 -2.128867371 8.959632885 1.316868912 0.977803976 0 0.034913449 0.080195375 0.001153459 0.012267722 0.008086042 0.007432461 2.128867371 -0.339064935 MRPGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MRPGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVK 41 2 A0A2R8Y5Y7;P32969;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ;;; 318.68 2.71E-114 431863000 473283 377970 440451 440917 468594 298975.6 559037 377032 677435 FALSE TRUE 443661.0619 405955.2921 450898.7057 452231.6767 431792.5175 385285.0023 475214.5917 424105.2751 564366.7221 0.786121939 0.719311179 0.798946302 0.80130819 0.765092094 0.682685543 0.84203156 0.751471089 1 19.1062734 -4.99999326 0.370348662 4.060452697 0.762949044 0.724630934 0.044765722 271.8249152 2.096379532 665.6943739 0.029166952 1.00E-05 4.99999326 -3.297503653 MRS(ph)PQPARPGSAAVPGAAFAPIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MRSPQPARPGSAAVPGAAFAPIPR 24 2 Q8N3V7-2 Q8N3V7-2 SYNPO Synaptopodin 1 MRS(0.998)PQPARPGS(0.002)AAVPGAAFAPIPR;MRS(0.995)PQPARPGS(0.005)AAVPGAAFAPIPR 127.28 4.47E-05 986480000 166413.8 163635 159353 163869 198225 137584.9 180528 155057 230125 TRUE FALSE 155998.2573 175750.7057 163132.9284 168074.156 182657.2081 177303.4271 153459.5023 174416.2078 191715.6508 0.813695995 0.916725916 0.850910855 0.876684586 0.952750635 0.924825002 0.800453701 0.909765097 1 17.54860859 -2.940319401 1.613868763 4.971581508 0.879392951 0.374162214 0.048451159 2008515.055 31212.00271 29376243.45 0.011532482 0.00114731 2.940319401 -4.092188557 MRTETSRCTSARAWPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MRTETSRCTSARAWPR 16 3 A0A096LNX7;A0A096LNT2 A0A096LNX7 0 84.566 0.023108 22266000 56315 35258 40790 43626 48265 33297 59503 40164 67998 FALSE TRUE 52790.34468 37868.53901 41757.55806 44745.51702 44474.46159 42909.30337 50581.07755 45178.56381 56648.69452 0.931889872 0.668480348 0.737131869 0.789877285 0.785092436 0.757463234 0.892890436 0.797521712 1 15.78975509 0.770806646 0.518314659 1.005051997 0.75096768 0.416332873 0.074922453 1.060361912 0.63127383 0.088828764 0.036520994 5.899383735 -0.770806646 -0.254084317 MS(ph)ADMSEIEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MSADMSEIEAR 11 0 O43318;O43318-3;Q9UG54;O43318-2;O43318-4 O43318 MAP3K7;DKFZp586F0420 Mitogen-activated protein kinase kinase kinase 7 1 MS(0.999)ADMS(0.001)EIEAR;MS(0.999)ADMS(0.001)EIEAR 216.83 1.24E-11 131570000 337690 352890 333690 319790 400170 252140 378670 326270 380890 TRUE FALSE 316554.5857 379018.3428 341605.2844 327996.3528 368742.2624 324928.7248 321891.9489 367005.5277 317316.9984 0.997597315 1.194447019 1.076542657 1.03365516 1.162062746 1.023987768 1.014417603 1.156589561 1 18.27556528 0.075712835 0.186252834 0.95557476 1.125779779 0.06089469 0.070828233 19.86034436 1.435596407 0.88859444 0.292968528 1.190454594 -0.075712835 0.170205019 MS(ph)DEFVDSFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MSDEFVDSFK 10 0 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 MS(1)DEFVDSFK;MS(1)DEFVDSFK 122.7 0.0005052 33079000 216125 137160 157018 171785 159558 130913 215241 147481 117703 TRUE FALSE 202598.122 147315.4691 160742.5411 176193.2939 147026.9583 168705.4579 182967.6102 165894.3275 98057.60891 2.06611322 1.50233593 1.639266375 1.796834492 1.499393672 1.720472891 1.865919558 1.691804739 1 16.58134196 -1.324212119 6.21621362 0.999955721 1.703137943 0.645456566 0.167786122 9.77E-05 1.06E-05 0.154193796 0.036341552 0.047401041 1.324212119 0.703182222 MS(ph)FVLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MSFVLSR 7 0 F8VV96;Q8N9I9 F8VV96 DTX3 Probable E3 ubiquitin-protein ligase DTX3 1 MS(1)FVLSR 86.838 0.020751 217700000 33319 47288 32559 44203 40862 38319 48346 34593 53020 TRUE FALSE 31233.62327 50789.25272 33331.31486 45337.32382 37652.86335 49381.07324 41096.96612 38912.0122 44170.61948 0.707113091 1.149842437 0.754603745 1.026413583 0.852441369 1.117961981 0.930414076 0.880947849 1 15.43079945 MS(ph)GFIYQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 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 168.3 6.22E-05 8888850000 17866410 16605160 14976160 15004090 16946000 11112940 21170390 16375310 21610210 TRUE FALSE 16748183.29 17834623.32 15331401.59 15389120.35 15615129.52 14321065.37 17996086.56 18419803.5 18003326.34 0.930282714 0.990629342 0.851587162 0.854793168 0.867346912 0.795467743 0.999597864 1.023133345 1 24.10176015 1.603954249 8.417042108 1.011063733 0.889210685 0.565859568 0.051769437 0.089836328 15.71822321 0.02910804 0.014217069 40.1748486 -1.603954249 -0.121853048 MS(ph)GFIYQGKLPTTGMTITK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MSGFIYQGKLPTTGMTITK 19 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E9PDQ5;E7EUY6;F6SJA5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 1 MS(1)GFIYQGKLPTTGMTITK;MS(1)GFIYQGKLPTTGMTITK 201.17 3.71E-16 442540000 819010 825070 991520 1248240 1581180 785590 1145490 954430 1748040 TRUE FALSE 767749.6261 886159.0413 1015039.323 1280271.952 1457000.501 1012377.08 973734.4087 1073592.686 1456280.831 0.527198882 0.608508347 0.697007954 0.879138092 1.000494183 0.695179843 0.668644665 0.737215421 1 20.47385716 3.763403626 1.86216279 0.800281848 0.571114292 0.43828813 0.118168268 0.381987145 2.598445568 0.035503046 0.078513296 5799.674579 -3.763403626 -0.229167557 MS(ph)GGSTMSSGGGNTNNSNSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MSGGSTMSSGGGNTNNSNSK 20 0 Q86U70-2;Q86U70;A0A6E1WJ75;Q86U70-3 Q86U70-2 LDB1 LIM domain-binding protein 1 1 MS(0.996)GGS(0.003)T(0.001)MSSGGGNTNNSNSK;MS(1)GGSTMSSGGGNTNNSNSK 291.02 1.12E-40 27832000 215030 154771 174363 165154 173780 134334 204128 166791 216241 TRUE FALSE 201571.6561 166230.4059 178498.9727 169392.1312 160132.0198 173114.0451 173520.9014 187615.2235 180148.9801 1.118916443 0.922738534 0.990840873 0.940289149 0.88888663 0.960949348 0.963207792 1.041444827 1 17.45883096 -0.439177593 5.889772545 1.000000005 0.969477175 0 0.064645316 0 0 0.056276005 0.013264382 0.363766254 0.439177593 -0.03052283 MS(ph)PMGTASGSNSPTSDSASVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 MSPMGTASGSNSPTSDSASVQR 22 0 Q5QPB1;O76080 Q5QPB1 ZFAND5 AN1-type zinc finger protein 5 1 MS(1)PMGTASGSNSPTSDSASVQR;MS(0.998)PMGT(0.002)ASGSNSPTSDSASVQR;MS(1)PMGTASGSNSPTSDSASVQR;MS(1)PMGTASGSNSPTSDSASVQR;MS(1)PMGTASGSNSPTSDSASVQR;MS(1)PMGTASGSNSPTSDSASVQR;MS(1)PMGTASGSNSPTSDSASVQR;MS(1)PMGTASGSNSPTSDSASVQR;MS(1)PMGTASGSNSPTSDSASVQR;MS(1)PMGTASGSNSPTSDSASVQR 503.51 3.10E-277 2925172000 1656335 1571058 1762337 1628974 1742933 1434847 1901449 1511007 1850102 TRUE FALSE 1552667.949 1687380.769 1804140.466 1670776.231 1606050.073 1849064.036 1616344.375 1699659.55 1541308.024 1.007370315 1.094771936 1.170525578 1.083998918 1.042004614 1.199671972 1.048683553 1.102738404 1 20.55572378 0.326917444 1.064871432 0.999827281 1.102180467 0.194862722 0.057741046 4.651835118 6.026660067 0.053995001 0.016196884 2.122840888 -0.326917444 0.102353186 MS(ph)PSKSPFLPSMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MSPSKSPFLPSMK 13 1 A0A3F2YNW7;Q8NFD5;Q8NFD5-2;Q8NFD5-3;A0A1B0GV63;A0A1B0GWJ2;A0A1B0GTJ8;A0A1B0GVK1;H0Y7H8;Q8NFD5-4 A0A3F2YNW7 ARID1B AT-rich interactive domain-containing protein 1B 1 MS(0.938)PS(0.061)KSPFLPSMK 112.91 0.00052273 362730000 680030 432650 485950 485070 531200 393180 787040 484080 830160 TRUE FALSE 637468.1362 464683.8562 497476.9635 497517.7174 489481.6948 506684.6833 669030.6585 544518.4536 691600.933 0.921728277 0.671895936 0.719312164 0.719371091 0.70775164 0.732625795 0.967365176 0.787330421 1 19.39958029 1.750925744 24.9997491 0.908153974 0.73149236 0.464483608 0.086372333 2.812747252 5696.006811 0.035856303 0.019884241 56.35412923 -1.750925744 -0.176661614 MS(ph)QPGS(ph)PSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 2 MS(1)QPGS(0.999)PS(0.001)PK;MS(1)QPGS(0.995)PS(0.005)PK 139.61 9.10E-05 236799000 1233330 659390 909340 750530 630760 581310 1063790 673320 767020 TRUE FALSE 1156138.077 708211.9217 930909.9742 769789.8704 581222.654 749124.7602 904284.5652 757385.4842 638999.4069 1.809294444 1.108313895 1.456824473 1.204680102 0.909582462 1.172340306 1.415157128 1.185267899 1 19.28545507 4.744985026 24.89854676 1.216301934 1.809294727 0.573859041 0.167647145 550.806291 2134653.618 0.039927526 0.376125628 55588.50909 -4.744985026 0.592992792 MS(ph)SHTETSSFLQTLTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MSSHTETSSFLQTLTGR 17 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 MS(0.999)S(0.001)HTETSSFLQTLTGR;MS(0.471)S(0.471)HT(0.058)ETSSFLQTLTGR 278.64 4.99E-36 107920000 58295 70647 69210 65044 77315 50201 73826 63092 67026 TRUE FALSE 54646.42001 75877.77739 70851.69388 66713.13916 71242.99177 64693.21375 62756.47667 70969.17508 55838.9276 0.978643795 1.358868815 1.268858428 1.194742486 1.275866046 1.158568342 1.123883989 1.270962358 1 15.76898361 -0.339348186 0.377054932 0.946117676 1.240933436 0.217591923 0.107976617 8.858596394 1.377761063 0.760220099 0.077025289 0.457774729 0.339348186 0.29481576 MS(ph)SVYLKEIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MSSVYLKEIAK 11 1 Q09MP3 Q09MP3 RAD51AP2 RAD51-associated protein 2 1 MS(0.333)S(0.333)VY(0.333)LKEIAK;MS(0.359)S(0.359)VY(0.282)LKEIAK 79.693 0.015972 311270000 479290 877620 632630 679640 1005640 555710 909650 921160 782550 TRUE FALSE 449292.0945 942599.898 647636.2823 697080.713 926661.091 716134.4558 773256.4273 1036168.854 651937.3495 0.689164526 1.445844296 0.993402637 1.069244941 1.421395923 1.098471282 1.186090086 1.589368755 1 19.3143738 2.797680666 24.99757605 1.249940563 1.106150491 0.135701042 0.244368101 687.1616746 290549.0181 0.069216848 0.073415533 627.596721 -2.797680666 -0.143790072 MS(ph)TSQNSIPFEHHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MSTSQNSIPFEHHGK 15 0 P48730-2 P48730-2 CSNK1D Casein kinase I isoform delta 1 MS(0.547)T(0.09)S(0.09)QNS(0.273)IPFEHHGK 110.74 0.00099031 0 198200 141520 153690 139400 150130 151460 206640 134260 206580 TRUE FALSE 185795.0158 151998.2881 157335.5994 142977.24 138339.3954 195184.0433 175656.2504 151022.6565 172100.4634 1.079573013 0.883195112 0.914207877 0.830777774 0.803829302 1.134128516 1.020661112 0.877526147 1 17.39289146 2.245916011 24.99977718 1.015404601 0.898078923 0.234374814 0.094401646 221.1943505 751804.2779 0.031834229 0.026128103 176.1635327 -2.245916011 -0.117325677 MSAEINEIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MSAEINEIIR 10 0 P18206;P18206-2;P18206-3 P18206 VCL Vinculin 0 ; 102.52 0.0068296 84077000 59690 75938 65913 69491 87863 58158 64486 60441 78759 FALSE TRUE 55954.10945 81560.52853 67476.48749 71274.25671 80962.5944 74947.27048 54816.92296 67987.1919 65613.6141 0.852782006 1.243042769 1.028391568 1.086272379 1.23392981 1.142251826 0.835450443 1.036175081 1 16.00170757 1.755996641 25 0.943917134 1.111327732 0.22419285 0.120697207 7.948149569 11408.40389 0.050829745 0.028188072 57.01598619 -1.755996641 0.167410599 MSATFIGNSTAIQELFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MSATFIGNSTAIQELFK 17 0 P68371;Q13885;Q9BVA1 P68371;Q13885;Q9BVA1 TUBB4B;TUBB2A;TUBB2B Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-2B chain 0 110.77 0.0025953 0 41556 44133 34708 33646 48554 28314 38070 38603 45536 FALSE TRUE 38955.08414 47400.65324 35531.29015 34509.41332 44740.7647 36487.79216 32361.75692 43422.66953 37935.74743 1.026870084 1.249498335 0.936617638 0.909680596 1.179382712 0.961831376 0.853067598 1.144637248 1 15.21127034 3.904394611 5.439968266 0.986139336 1.146026352 0.204804802 0.112674325 0.252960907 13.47743066 0.027693125 0.051482102 8024.068202 -3.904394611 0.159887016 MSCFSRPS(ph)MS(ph)PTPLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 MS(0.004)CFS(0.002)RPS(0.991)MS(0.942)PT(0.061)PLDR;MS(0.001)CFS(0.001)RPS(0.997)MS(0.875)PT(0.126)PLDR;MSCFSRPS(0.985)MS(0.864)PT(0.151)PLDR;MSCFS(0.078)RPS(0.922)MS(0.99)PT(0.01)PLDR 129.05 0.00068697 840530000 952910 1498060 827900 876570 1260480 369834 747960 1349490 2632310 TRUE FALSE 893269.0641 1608977.921 847538.179 899064.2702 1161486.985 476599.072 635810.3417 1517976.797 2192960.456 0.40733478 0.733701293 0.386481287 0.40997742 0.529643379 0.217331357 0.289932424 0.692204364 1 21.06444837 0.985489257 5.18107014 0.999525824 0.438412332 0.65231536 0.137999544 0.105880947 11.05861277 0.145579134 0.03676841 9.671398019 -0.985489257 -0.561113492 MSCFSRPS(ph)MSPT(ph)PLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 MSCFSRPS(1)MS(0.002)PT(0.998)PLDR 249.47 3.50E-19 233500000 541210 922820 473100 521540 761380 175110 369730 792400 1739900 TRUE FALSE 507336.6322 991146.553 484322.1554 534923.5994 701584.2861 225661.4143 314292.4189 891332.8843 1449499.45 0.350008158 0.683785394 0.334130624 0.369040222 0.484018318 0.155682304 0.216828243 0.61492461 1 20.46712336 0.962863204 5.888003882 0.999880218 0.383711254 0.667765559 0.142967194 0.156774702 20.33871448 0.151331034 0.038073826 9.180433817 -0.962863204 -0.616168964 MSCFSRPSMS(ph)PTPLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MSCFSRPS(0.004)MS(0.964)PT(0.032)PLDR;MSCFSRPSMS(0.777)PT(0.223)PLDR;MSCFSRPSMS(0.996)PT(0.004)PLDR;MSCFSRPS(0.002)MS(0.989)PT(0.009)PLDR;MS(0.006)CFS(0.005)RPS(0.316)MS(0.665)PT(0.008)PLDR;MS(0.008)CFS(0.008)RPS(0.064)MS(0.892)PT(0.028)PLDR;MSCFSRPS(0.022)MS(0.968)PT(0.01)PLDR;MSCFSRPS(0.124)MS(0.741)PT(0.135)PLDR;MSCFSRPS(0.063)MS(0.911)PT(0.026)PLDR;MSCFSRPS(0.028)MS(0.908)PT(0.064)PLDR 175.85 2.04E-09 8264160000 2005600 2751960 1983570 2071610 2745440 1238541 2140070 2376540 4518560 TRUE FALSE 1880073.076 2955717.982 2030621.217 2124771.02 2529824.217 1596087.681 1819186.371 2673256.25 3764383.145 0.499437226 0.7851799 0.539430005 0.56444069 0.67204217 0.423997138 0.483262809 0.71014457 1 21.84398204 0.941497797 5.787434573 0.999955349 0.577955066 0.648395096 0.101302601 0.268761304 24.72686919 0.102036984 0.025681581 8.739725589 -0.941497797 -0.422000284 MSCFSRPSMSPT(ph)PLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MSCFSRPS(0.006)MS(0.157)PT(0.837)PLDR;MSCFSRPS(0.002)MS(0.034)PT(0.964)PLDR 92.492 0.013132 1096480000 497020 635910 465710 483810 603010 283760 509070 542900 1042750 TRUE FALSE 465912.4054 682993.4381 476756.8611 496225.3837 555652.027 365676.9055 432739.6795 610682.2601 868708.2886 0.5363278 0.786217246 0.548811226 0.571222112 0.639630166 0.420943268 0.498141534 0.702977361 1 19.72851228 0.931012797 5.60704893 0.999959938 0.581830757 0.67003474 0.095065931 0.318209415 24.415963 0.098693818 0.024860256 8.531252516 -0.931012797 -0.418129181 MSDT(ph)GSPGMQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 MSDTGSPGMQR 11 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;A0A0U1RQL3 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 MSDT(0.901)GS(0.099)PGMQR;MS(0.002)DT(0.562)GS(0.436)PGMQR;MS(0.001)DT(0.5)GS(0.5)PGMQR;MS(0.002)DT(0.707)GS(0.291)PGMQR;MSDT(0.714)GS(0.286)PGMQR 167.84 0.00020976 1457490000 1748230 1966060 1916150 1936470 2005280 1604010 2136190 1639930 1980540 TRUE FALSE 1638811.405 2111629.128 1961601.983 1986163.099 1847793.398 2067061.648 1815888.141 1844678.87 1649975.079 0.993234035 1.279794559 1.188867643 1.203753392 1.119891701 1.252783557 1.100554889 1.11800408 1 20.6540128 0.997292571 1.063870184 1.002171735 1.186501927 0.281579219 0.081052048 0.587015971 1.396719582 0.068918014 0.022404192 9.937853066 -0.997292571 0.184330192 MSDTGS(ph)PGMQR ddPTM_SK-BR-3_Pertuzumab_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 MS(0.002)DT(0.18)GS(0.818)PGMQR;MSDT(0.151)GS(0.849)PGMQR 98.105 0.0038416 202049000 458270 527020 497240 515100 537600 412450 557640 436490 526350 TRUE FALSE 429587.6987 566041.1092 509034.7676 528318.3381 495379.0646 531517.6194 474027.0589 490986.7373 438498.7846 0.979678197 1.290861295 1.160857876 1.204834213 1.129715935 1.2121302 1.081022515 1.119699198 1 18.74221332 1.048249503 0.806098453 1.002646693 1.180702176 0.241652867 0.082699489 0.733113537 1.074466383 0.071044894 0.026287109 11.17505073 -1.048249503 0.178055483 MSES(ph)PTPCSGSSFEETEALVNTAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 MSESPTPCSGSSFEETEALVNTAAK 25 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;O95359-2;Q4VXL4;H0Y911 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 MS(0.065)ES(0.479)PT(0.432)PCS(0.01)GS(0.013)SFEETEALVNTAAK;MS(0.025)ES(0.486)PT(0.486)PCS(0.001)GS(0.001)SFEETEALVNTAAK;MS(0.171)ES(0.826)PT(0.004)PCSGSSFEETEALVNTAAK;MS(0.084)ES(0.871)PT(0.045)PCSGSSFEETEALVNTAAK;MS(0.053)ES(0.852)PT(0.095)PCSGSSFEETEALVNTAAK;MS(0.034)ES(0.669)PT(0.274)PCS(0.009)GS(0.012)S(0.002)FEETEALVNTAAK;MS(0.054)ES(0.944)PT(0.002)PCSGSSFEETEALVNTAAK 330.44 4.95E-88 2921963000 1753794 1515936 1698255 1507402 1893084 1310899 1982187 1627615 1674793 TRUE FALSE 1644027.164 1628177.479 1738538.411 1546084.487 1744408.819 1689334.261 1684976.461 1830826.316 1395259.229 1.178295137 1.166935466 1.246032547 1.108098377 1.250239943 1.210767308 1.207644018 1.31217646 1 20.41210176 -0.954604789 4.85976235 0.999998277 1.207585309 0.595008772 0.054421216 3138759.853 645892.4269 57.88564298 0.011490664 0.111018463 0.954604789 0.207587033 MSESPT(ph)PCSGSSFEETEALVNTAAK ddPTM_SK-BR-3_Pertuzumab_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(0.013)ES(0.103)PT(0.854)PCS(0.01)GS(0.01)S(0.01)FEETEALVNTAAK;MS(0.04)ES(0.36)PT(0.6)PCS(0.001)GSSFEETEALVNTAAK;MS(0.021)ES(0.421)PT(0.547)PCS(0.004)GS(0.004)S(0.004)FEETEALVNTAAK;MS(0.05)ES(0.311)PT(0.636)PCS(0.002)GSSFEETEALVNTAAK 264 8.74E-45 1096731000 392133 341814 385730 356114 411809 284686 427921 347702 371705 TRUE FALSE 367590.0955 367122.2642 394879.6978 365252.4881 379467.1823 366870.2267 363758.2187 391113.3601 309665.0342 1.187057158 1.185546393 1.275183357 1.179508333 1.225411785 1.184732489 1.174682894 1.263020738 1 18.24034896 -1.717858322 2.945371449 0.969150196 1.209065133 0.776224756 0.0353323 1073554.677 1217080.738 200226.1783 0.008040578 0.019148805 1.717858322 0.239914937 MSESPTPCS(ph)GSSFEETEALVNTAAK ddPTM_SK-BR-3_Pertuzumab_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(0.006)ES(0.02)PT(0.072)PCS(0.277)GS(0.277)S(0.277)FEET(0.072)EALVNTAAK 50.202 0.060966 0 12094 13240 13752 14264 14946 11389 18048 12246 15623 TRUE FALSE 11337.05813 14220.30338 14078.20393 14630.03839 13772.20145 14676.81942 15341.86995 13774.94006 13015.42037 0.871048172 1.092573499 1.081655723 1.124054235 1.058144959 1.127648512 1.178745635 1.058355371 1 13.66793429 4.739775104 5.23888741 1.101012981 0.86105878 0.66011673 0.048898918 0.09035575 8.596316402 0.011165931 0.078232654 54925.63725 -4.739775104 -0.239954201 MSESPTPCSGSSFEET(ph)EALVNTAAK ddPTM_SK-BR-3_Pertuzumab_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(0.013)ES(0.072)PT(0.072)PCS(0.084)GS(0.084)S(0.084)FEET(0.589)EALVNTAAK 93.006 0.033278 66573000 28873 26095 28935 25285 34129 20652 37256 25777 31449 TRUE FALSE 27065.89047 28027.10095 29621.35186 25933.85591 31448.64601 26613.89714 31669.80867 28995.31519 26199.95873 1.033050882 1.069738363 1.13058773 0.989843388 1.200331891 1.015799201 1.208773227 1.106693163 1 14.67727692 2.739043633 24.99977419 1.118912458 1.07059108 0.072573026 0.075392083 108.0818319 5594215.571 0.021384936 0.021389658 548.3320529 -2.739043633 -0.048321378 MSGY(ph)S(ph)S(ph)DRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MSGYSSDRDR 10 1 P17844;P17844-2;J3QRQ7;J3KRX8;J3QR02;X6RLV5;J3QKN9;J3QS79 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 3 MS(0.427)GY(0.883)S(0.771)S(0.919)DRDR 41.684 0.074635 0 12114 16069 16086 14244 13579 11248 13811 11684 14145 TRUE FALSE 11355.80636 17258.76548 16467.56752 14609.52516 12512.56012 14495.115 11740.16877 13142.77312 11784.10812 0.963654292 1.464579695 1.397438597 1.23976503 1.061816472 1.230056179 0.996271304 1.115296379 1 13.52455495 2.909612965 3.502811516 1.08598767 1.332932012 0.253171498 0.147707167 0.250696558 5.796114824 0.044348013 0.04842074 812.1064599 -2.909612965 0.246944342 MSKDEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MSKDEER 7 1 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5;P08651-4;Q14938-6;Q14938-4;A0A1B0GTC1;K7EN08;K7ESG9;C9JWJ8;Q5W0Y9;K7EKH0;K7EJB0;U3KPY9;Q14938-3;O00712-2;A0A087WXP2;Q14938;Q14938-2;Q14938-5;K7EMQ5;A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A1B0GWJ4;Q5VW27;O00712-5;Q5VW26;A0A2R8Y7V8;Q5VW30;A0A1B0GWI9;A0A1B0GVN4 P08651-3;A0A1B0GW37 NFIC;NFIX;NFIB Nuclear factor 1 C-type;Nuclear factor 1 X-type;Nuclear factor 1;Nuclear factor 1 B-type 0 63.486 0.083054 30968000 57620 71568 66780 65441 79720 47115 62861 59078 78709 FALSE TRUE 54013.66705 76866.96919 68364.05314 67120.32685 73459.11278 60716.33565 53435.57662 66454.01835 65571.95942 0.823731173 1.172253656 1.042580605 1.023613255 1.120282411 0.925949692 0.814915051 1.01345177 1 16.00079139 2.153860629 7.333433668 0.910083224 1.055025752 0.140749319 0.105715319 0.271704972 20.00025655 0.036865149 0.027207771 142.515017 -2.153860629 0.144942528 MSLQTDEDEHSIEMHLPYTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MSLQTDEDEHSIEMHLPYTAK 21 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 ;; 165.46 8.49E-12 297418000 436220 445480 443580 428710 470230 342835 542700 430550 595860 FALSE TRUE 408917.7689 478463.8027 454101.9271 439711.4244 433300.0326 441805.899 461327.1732 484305.1153 496407.1166 0.823754848 0.963853633 0.91477723 0.885787914 0.872872322 0.890007182 0.929332312 0.975620814 1 18.92116427 1.261989082 2.250566549 0.998255202 0.902041293 0.541986209 0.035684026 0.252812399 2.15779944 0.032800709 0.009529394 18.28054258 -1.261989082 -0.096213909 MSQPGS(ph)PSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 16 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(0.998)PS(0.002)PK;MSQPGS(0.967)PS(0.033)PK;MSQPGS(1)PSPK;MS(0.001)QPGS(0.994)PS(0.005)PK;MSQPGS(1)PSPK;MSQPGS(0.944)PS(0.056)PK;MSQPGS(0.998)PS(0.002)PK;MSQPGS(0.998)PS(0.002)PK;MSQPGS(0.983)PS(0.017)PK;MSQPGS(0.996)PS(0.004)PK;MSQPGS(0.997)PS(0.003)PK;MSQPGS(0.975)PS(0.025)PK;MSQPGS(0.998)PS(0.002)PK;MSQPGS(0.998)PS(0.002)PK;MSQPGS(0.963)PS(0.037)PK;MSQPGS(0.985)PS(0.015)PK 225.79 3.49E-09 26862310000 25298700 18789640 20309920 20554490 21478960 14875350 26337900 18071420 21691440 TRUE FALSE 23715299.53 20180844.5 20791680.89 21081953.01 19792089.12 19169622.06 22388776.4 20327676.57 18070998.53 1.312340294 1.116753148 1.150555176 1.166618047 1.095240481 1.060794844 1.238934106 1.124878436 1 24.10717289 -5 0.215347598 0.262301898 1.174696041 0.359355194 0.070057921 184.6627402 1.845845342 59.29176041 0.135029955 1.00E-05 5 0.912394144 MSS(ph)PLADAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MSSPLADAK 9 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 MS(0.007)S(0.993)PLADAK 119.27 0.00089554 198740000 677910 499520 616550 558990 634320 460640 734790 523100 951050 TRUE FALSE 635480.8232 536504.9806 631174.8572 573334.6298 584503.0659 593619.2901 624615.061 588410.1865 792313.611 0.802057183 0.67713715 0.79662251 0.723620826 0.737716805 0.749222633 0.788343217 0.742648086 1 19.59571206 -4.999999999 0.327928861 3.497176469 0.740566528 0.809605939 0.037682152 133.0939989 1.157037152 231.3869473 0.029065693 1.00E-05 4.999999999 -2.756609941 MSSCVPRPPS(ph)HGGPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MSSCVPRPPSHGGPTR 16 1 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 MSSCVPRPPS(1)HGGPTR 75.912 0.017015 128800000 83521 98300 84341 92061 105990 77292 99991 81674 130310 TRUE FALSE 78293.5697 105578.2343 86341.60835 94423.44112 97665.97294 99604.94567 84998.27782 91871.17869 108560.4192 0.721198115 0.972529722 0.795332304 0.869777787 0.89964624 0.917507011 0.782958269 0.846267723 1 16.72813867 -2.2605418 2.20611036 1.540364677 0.856175493 0.295197186 0.072075812 7497192.71 1241439.723 20181750.98 0.015947516 0.005488557 2.2605418 -0.684189184 MSSEGPPRMS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MSSEGPPRMSPK 12 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;F8W0B5;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 MSSEGPPRMS(1)PK;MSSEGPPRMS(1)PK 93.237 0.004412 744600000 1694340 1257940 1296310 1352090 1452190 990650 1769770 1283060 1646530 TRUE FALSE 1588294.284 1351079.186 1327059.085 1386786.918 1338140.855 1276634.573 1504409.418 1443252.865 1371713.506 1.15789068 0.984957267 0.967446248 1.010988747 0.975525027 0.930686012 1.096737337 1.052153281 1 20.38754776 1.718596963 20.30215079 1.055778369 0.997161961 0.089561235 0.063897633 0.629825888 628.160503 0.027715194 0.0153565 52.31147467 -1.718596963 -0.058616408 MSSPEDDSDTKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MSSPEDDSDTKR 12 1 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 82.543 0.015394 274010000 281040 186490 200560 192540 211710 145090 254400 190650 290570 FALSE TRUE 263450.2081 200297.9136 205317.3779 197480.9024 195083.1506 186975.1277 216255.0817 214453.0722 242071.9898 1.088313473 0.827431186 0.848166605 0.815794105 0.805888987 0.772394723 0.893350288 0.885906181 1 17.88507663 -0.455099896 14.1109077 1 0.857005025 0.179184383 0.086975523 0 0 0.076795794 0.018100942 0.350671204 0.455099896 -0.142994975 MSTSQNS(ph)IPFEHHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MSTSQNSIPFEHHGK 15 0 P48730-2 P48730-2 CSNK1D Casein kinase I isoform delta 1 MSTS(0.001)QNS(0.999)IPFEHHGK;MS(0.001)TS(0.001)QNS(0.998)IPFEHHGK;MSTSQNS(1)IPFEHHGK;MS(0.001)T(0.001)S(0.001)QNS(0.998)IPFEHHGK 123.55 0.00017055 815120000 1042320 832440 907800 888180 1024820 715739 1148170 855290 1206840 TRUE FALSE 977083.0518 894074.7238 929333.4447 910972.2025 944334.7711 922361.2302 976012.5676 962074.8392 1005410.608 0.971824889 0.889263269 0.924332246 0.906069814 0.939252843 0.917397552 0.970760165 0.956897443 1 19.93935338 1.402115886 0.870857066 0.996797714 0.917391287 0.510030345 0.023679076 0.361355374 0.574696964 0.019671398 0.007536394 25.24154219 -1.402115886 -0.079406427 MSVQPTVSLGGFEITPPVVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MSVQPTVSLGGFEITPPVVLR 21 0 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 0 230.38 2.19E-25 29353000 60877 58820 56616 65808 64863 49985 69640 51712 60856 FALSE TRUE 57066.81724 63175.094 57958.95826 67496.74469 59768.92162 64414.85806 59198.12851 58168.35703 50698.74046 1.125606213 1.246088038 1.14320312 1.331329814 1.178903481 1.270541585 1.167644955 1.147333376 1 15.62966229 0.840662961 1.491734074 1.000840347 1.213309609 0.547185133 0.060765588 0.430833272 1.804769696 0.051192189 0.014996647 6.928878747 -0.840662961 0.212469262 MSWFVDLAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MSWFVDLAGK 10 0 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 0 ;; 100.45 0.0093162 1987690000 2389550 2116170 2189940 2200260 2438760 1811380 2701100 2068780 3109220 FALSE TRUE 2239992.331 2272853.429 2241886.411 2256722.397 2247229.627 2334296.001 2296095.131 2327071.737 2590271.096 0.864771388 0.877457743 0.865502617 0.871230197 0.867565418 0.901178261 0.886430434 0.898389262 1 21.30467167 -0.734636637 0.363250276 1.046126894 0.866724747 0.959021449 0.008125674 1.865108389 0.214471335 0.103454944 0.005977849 0.184231277 0.734636637 -0.179402147 SRNTDEMVELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRNTDEMVELR 11 1 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ; 152.38 3.01E-05 446440000 335010 350130 213510 303260 432770 182281 428310 540570 1023310 FALSE TRUE 314042.3221 376053.9895 218574.558 311042.165 398781.9899 234902.5656 364088.8917 608061.3544 852512.9502 0.368372495 0.441112348 0.256388549 0.364853302 0.467772354 0.275541346 0.427077256 0.713257616 1 19.70136222 1.061463102 2.256206451 0.996812307 0.361259576 0.916826388 0.064257635 0.069587262 0.72771759 0.058244348 0.016119943 11.52028179 -1.061463102 -0.635552731 MT(ph)KRLYDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MTKRLYDEK 9 2 Q00987-8 Q00987-8 MDM2 E3 ubiquitin-protein ligase Mdm2 1 MT(0.999)KRLY(0.001)DEK 49.35 0.080149 0 49135 82324 77941 75924 77804 85148 87153 78658 58980 TRUE FALSE 46059.72806 88419.35462 79789.79733 77872.33838 71693.58769 109728.8453 74085.21674 88478.62445 49135.85697 0.937395436 1.799487382 1.623860908 1.584837289 1.459088985 2.233172516 1.507762789 1.800693626 1 15.5844886 MT(ph)VKT(ph)LHGPAMVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MTVKTLHGPAMVK 13 1 Q96PD4 Q96PD4 IL17F Interleukin-17F 2 MT(1)VKT(1)LHGPAMVK 67.136 0.014789 0 457120 398920 396320 408670 469360 387270 543260 433250 626770 TRUE FALSE 428509.6752 428456.4519 405720.8976 419157.1641 432498.3589 499068.5622 461803.2064 487342.2162 522158.0379 0.820651305 0.820549375 0.777007856 0.80274004 0.828290149 0.955780676 0.884412712 0.93332321 1 18.994127 2.33660444 4.879261654 0.92903062 0.804311214 0.80931195 0.031977352 0.089482626 3.549500105 0.010709774 0.008814031 217.072316 -2.33660444 -0.124719406 MTDFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MTDFDR 6 0 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ;;; 136.89 0.050377 2474350000 4852500 6275400 5921800 6116400 6884600 6028500 6061300 5373400 6002700 FALSE TRUE 4548790.687 6740037.146 6062267.892 6273357.179 6343911.287 7768830.085 5152464.335 6044280.818 5000810.591 0.909610673 1.347788928 1.21225705 1.254468064 1.268576598 1.553514164 1.030325832 1.208660218 1 22.25373053 1.614364077 25 1.08961484 1.265209344 0.20387906 0.165006955 0.836732564 3207.670899 0.07136291 0.038390071 41.14945398 -1.614364077 0.175594504 MTDLSDNPIHESMWELEVEDLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MTDLSDNPIHESMWELEVEDLHR 23 0 Q96E14;Q96E14-2 Q96E14 RMI2 RecQ-mediated genome instability protein 2 0 152.88 3.30E-08 15745000 16436 28557 23518 25681 26883 24138 26977 23704 23388 FALSE TRUE 15407.3001 30671.38999 24075.85807 26340.01794 24771.71762 31106.24875 22932.04929 26663.49658 19484.39171 0.790750891 1.574151785 1.235648432 1.351852207 1.271362124 1.596470099 1.176944584 1.368454144 1 14.25003127 -0.592620017 7.261789929 1.00000021 1.319071789 0.139080066 0.22462007 0 0 0.188179636 0.044354366 0.255493575 0.592620017 0.319071579 MTDQEAIQDLWQWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 16 MTDQEAIQDLWQWR 14 0 P06748;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;;;;;;;;;;;;; 325.79 9.96E-57 18253837000 6928687 8170722 7783492 7462250 8477518 6477211 8161158 6975806 7927098 FALSE TRUE 6495032.849 8775690.759 7968120.106 7653743.969 7811727.933 8347076.667 6937468.122 7846750.735 6604014.133 0.983497721 1.328841911 1.206557095 1.158953299 1.182875714 1.263939855 1.050492622 1.188178974 1 22.65491178 0.840977278 0.609293891 1.000439633 1.20693024 0.194960722 0.099593617 1.311855188 1.08208092 0.098656551 0.039953775 6.93389527 -0.840977278 0.206490607 MTEEEVEMLVAGHEDS(ph)NGCINYEELVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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(0.999)NGCINY(0.001)EELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR 351.32 2.12E-110 418815000 359782 380615 371641 360166 432146 382655 498652 384353 513195 TRUE FALSE 337263.8868 408796.1306 380456.5 369408.4693 398206.9964 493121.2866 423883.7619 432340.3181 427539.4391 0.788848597 0.956160048 0.88987463 0.864033667 0.931392428 1.153393679 0.991449497 1.01122909 1 18.70569798 2.459567464 24.33258018 1.038020289 0.89151404 0.617319356 0.060663303 117.7889782 163274.4845 0.019477592 0.016299702 288.1160581 -2.459567464 -0.146506249 MTEEEVEMLVAGHEDSNGCINYEAFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MTEEEVEMLVAGHEDSNGCINYEAFVR 27 0 P60660;J3KND3;G3V1Y7 P60660 MYL6 Myosin light polypeptide 6 0 272.35 8.75E-61 44135000 38832 44321 36654 42090 40615 35281 54315 37545 25488 FALSE TRUE 36401.57444 47602.57296 37523.45019 43170.10066 37425.26173 45466.05196 46170.96999 42232.5759 21233.88814 1.71431507 2.24182084 1.767149282 2.033075637 1.762525143 2.141202386 2.17440017 1.988923348 1 14.37408095 0.904748938 20.94997228 1 1.998903007 0.737213371 0.183121025 13877.52454 3052294.69 0.165879126 0.041469782 8.030617449 -0.904748938 0.998903007 MTEEEVEMLVAGHEDSNGCINYEELVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 MTEEEVEMLVAGHEDSNGCINYEELVR 27 0 P60660-2;G8JLA2;F8VZU9;F8W180;F8VXL3 P60660-2 MYL6 Myosin light polypeptide 6 0 ;;;;;;;;;;;; 367.56 9.24E-127 1621976400 1092317.4 1236150.6 1247547.2 1249851.2 1346307.9 1193857.5 1519642 1172133.4 1446551.7 FALSE TRUE 1023951.204 1327676.477 1277139.609 1281924.498 1240574.308 1538504.78 1291785.79 1318476.835 1205112.876 0.849672445 1.101703005 1.059767623 1.063738114 1.029425818 1.276647864 1.071920992 1.094069163 1 20.20073685 4.739818025 24.67511023 1.093013675 0.84967235 0.504853594 0.073711415 71.32658135 1399506.305 0.016319598 0.101810815 54931.06579 -4.739818025 -0.243341325 MTELETAMGMIIDVFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MTELETAMGMIIDVFSR 17 0 P25815 P25815 S100P Protein S100-P 0 110.29 0.002683 0 197610 117660 123580 139170 160210 118360 135460 87298 138650 FALSE TRUE 185241.9428 126371.6688 126511.376 142741.3378 147627.7529 152528.6106 115149.0305 98197.34747 115508.4193 1.603709444 1.094047253 1.09525675 1.235765658 1.278069198 1.320497774 0.996888636 0.850131515 1 16.81763849 1.603733565 4.879168581 0.925282519 1.228679646 0.499706597 0.148919536 0.140098539 7.283629689 0.082812077 0.03808256 40.15443922 -1.603733565 0.303397127 MTEQHFPHPIQSFSPESMPEPLNGPINILGEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MTEQHFPHPIQSFSPESMPEPLNGPINILGEGR 33 0 O15067 O15067 PFAS Phosphoribosylformylglycinamidine synthase 0 44.267 0.065375 42412000 29537 36226 31393 34058 38443 28353 31342 35811 33464 FALSE TRUE 27688.3319 38908.21073 32137.65678 34931.98594 35423.84185 36538.05083 26642.55806 40282.08218 27878.64221 0.993173616 1.395627894 1.152769799 1.253001695 1.270644445 1.310610845 0.955661967 1.444908323 1 14.76687268 -3.802395934 0.361756127 3.77E-11 1.225207978 0.148718524 0.157701938 348.9176184 6.442076859 264.9826246 0.10483553 0.000157617 3.802395934 1.225207978 MTGSAPPPS(ph)PTPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MTGSAPPPSPTPNK 14 0 Q9UBW7 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1 MTGSAPPPS(0.988)PT(0.012)PNK 107.74 0.0016952 0 224230 194650 222790 220740 211760 133580 213370 166250 195050 TRUE FALSE 210195.8446 209062.0885 228074.684 226404.5621 195129.2238 172142.3775 181377.1493 187006.6785 162494.8949 1.293553528 1.286576348 1.403580612 1.393302616 1.200832949 1.059370989 1.116202139 1.150846484 1 17.31003487 2.511673383 3.744341879 1.09415099 1.343489993 0.839334045 0.053953865 0.088532755 2.627210113 0.018688407 0.016651126 324.842903 -2.511673383 0.249339003 MTGSEFDFEEMKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 MTGSEFDFEEMKR 13 1 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;;;;;;;;;; 208.27 7.57E-08 7792160000 7251040 7293630 7189872 7319888 8229270 5256097 8662450 7033259 9612130 FALSE TRUE 6797210.35 7833657.954 7360419.159 7507728.719 7582976.329 6773446.878 7363596.041 7911376.868 8007803.406 0.84882333 0.978253031 0.919155827 0.937551578 0.946948363 0.84585579 0.91955255 0.987958428 1 22.93297513 1.220686589 6.267044518 0.995808474 0.91906744 0.396979443 0.040768655 0.174994424 24.27750464 0.034086195 0.009568125 16.62212672 -1.220686589 -0.076741034 MTNGFSGADLTEICQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MTNGFSGADLTEICQR 16 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 172.82 1.03E-08 98792000 91277 82964 87997 97192 117950 77236 105150 82297 127600 FALSE TRUE 85564.1355 89106.74088 90084.3304 99686.11127 108686.6828 99532.77938 89383.73366 92571.96161 106302.7357 0.804910005 0.838235633 0.847431911 0.937756781 1.022426018 0.936314374 0.84084133 0.870833295 1 16.6978192 3.310651806 5.017028612 0.925120664 0.832381026 0.44908967 0.054037135 0.228678759 10.61156874 0.016371327 0.022186211 2044.804567 -3.310651806 -0.092739638 MTNHCVFSANEDHETIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MTNHCVFSANEDHETIR 17 0 E7ETZ4;Q9Y6E2;Q75MG1;B5MCH7;E9PFE3;C9JF98;F8WDX8;E7EMS9;Q9Y6E2-2 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 ; 212.55 8.49E-13 782390000 252780 296040 283650 319420 317810 264270 319250 251890 302070 FALSE TRUE 236958.951 317959.1096 290378.3119 327616.858 292850.4846 340560.4589 271381.4263 283339.021 251652.5656 0.941611505 1.263484475 1.15388576 1.301861784 1.163709513 1.353296193 1.078397217 1.1259135 1 17.94107378 1.172151783 1.688670237 1.014143354 1.199237506 0.201988421 0.114937959 0.468405246 2.500625474 0.095337209 0.028079731 14.86455059 -1.172151783 0.185094152 MTNNEDS(ph)LSPTSSTLSNLELDAAEKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MTNNEDSLSPTSSTLSNLELDAAEKDR 27 1 Q9ULH7-4;Q9ULH7;Q9ULH7-5 Q9ULH7-4 MKL2 MKL/myocardin-like protein 2 1 MTNNEDS(0.605)LS(0.37)PT(0.018)S(0.004)S(0.001)T(0.001)LSNLELDAAEKDR 87.749 0.011647 91366000 137290 113320 131060 128500 132720 88287 133260 95655 156020 TRUE FALSE 128697.264 121710.3307 134168.8051 131797.5275 122296.7066 113774.0237 113278.9001 107597.7373 129979.2541 0.990136964 0.936382745 1.032232459 1.013988951 0.940894048 0.875324485 0.871515235 0.827807007 1 16.98792185 2.436822299 3.516466606 0.881754912 0.989835695 0.460058568 0.049885331 0.180600881 4.689919155 0.016762125 0.014131145 273.4149764 -2.436822299 0.108080783 MTNNEDSLS(ph)PTSSTLSNLELDAAEKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MTNNEDSLSPTSSTLSNLELDAAEKDR 27 1 Q9ULH7-4;Q9ULH7;Q9ULH7-5 Q9ULH7-4 MKL2 MKL/myocardin-like protein 2 1 MTNNEDS(0.172)LS(0.735)PT(0.066)S(0.018)S(0.007)T(0.002)LSNLELDAAEKDR 78.221 0.021055 120360000 71283 56236 64439 61060 71171 47683 66653 56654 81028 TRUE FALSE 66821.52427 60399.77195 65967.52351 62626.90297 65581.51675 61448.30803 56659.00143 63727.37661 67503.90334 0.989891265 0.894759695 0.977240133 0.927752321 0.971521845 0.910292664 0.839344077 0.944054691 1 16.04268331 2.093023306 7.471773371 0.901327964 0.94652506 0 0.049317313 0.400582964 27.7680015 0.017057156 0.012569632 123.8863068 -2.093023306 0.045197096 MTNYDVEHTIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MTNYDVEHTIK 11 0 E5RK69;P08133;P08133-2;E7EMC6 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 113.65 0.0013634 226490000 496010 373850 361140 299550 547720 256930 499940 432050 654930 FALSE TRUE 464965.6195 401530.243 369706.4113 307236.9601 504704.2806 331101.5201 424978.6382 485992.3936 545617.952 0.852181674 0.735918313 0.677592095 0.563099068 0.925014067 0.606837658 0.778894163 0.890719214 1 19.05753159 1.131488417 2.344928434 0.995600705 0.721740236 0.432876113 0.105415539 0.232476331 2.389140479 0.089217413 0.02484448 13.53593988 -1.131488417 -0.273860469 MTPHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 107.74 0.031005 1446280000 3656610 3538700 3612220 3740630 3724260 2743500 4168830 3375280 3974930 FALSE TRUE 3427749.307 3800709.03 3697903.564 3836620.899 3431771.643 3535503.913 3543752.643 3796691.138 3311488.504 1.035108322 1.147734327 1.116689235 1.158578957 1.036322982 1.06764795 1.070138893 1.146521008 1 21.65904842 2.734730089 24.98014029 1.068817315 1.1204224 0.201927183 0.048679196 479.2764526 3125501.867 0.014142228 0.013824042 542.9128098 -2.734730089 0.051605085 MTSACHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MTSACHR 7 0 P62072 P62072 TIMM10 Mitochondrial import inner membrane translocase subunit Tim10 0 82.305 0.02485 15730000 10766 36450 16050 20174 40239 14291 14158 28437 29180 FALSE TRUE 10092.17528 39148.79593 16430.71358 20691.69899 37078.79126 18416.5797 12035.13934 31987.42205 24309.66949 0.415150658 1.61042074 0.675892101 0.851171547 1.525269246 0.75758248 0.495076222 1.315831219 1 14.56924266 MTSHHFEGAQILSQLQCSGMVSVLDLMQGGYPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 208.58 8.75E-28 174632000 75400 157190 70796 54378 159991 70090 97648 134749 54483 FALSE TRUE 70680.84859 168828.5112 72475.31455 55773.43154 147425.9522 90323.84518 83006.58892 151572.7093 45389.43533 1.557209251 3.719555221 1.596744133 1.22877562 3.248023492 1.98997508 1.82876452 3.339383012 1 15.47006892 -1.388818354 3.687012733 0.992646279 2.319662836 0.190759577 0.850165896 63164.71539 97913060.24 1010551.95 0.186543376 0.04084902 1.388818354 1.327016556 MTSSDKDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 1979690000 6286500 8324800 6067420 6097200 9180360 3983170 7115650 7951950 10365610 FALSE TRUE 5893039.187 8941176.854 6211342.068 6253664.475 8459371.557 5133046.518 6048724.341 8944768.462 8635522.727 0.682418352 1.035394977 0.719278064 0.72417903 0.979601563 0.594410632 0.700446809 1.035810888 1 23.04185208 1.227685393 24.99918918 1.017905645 0.788039817 0.354059714 0.134845095 285.5247581 656322.5155 0.123854779 0.032178946 16.89216805 -1.227685393 -0.229865828 MVDKMDQDLKIS(ph)QK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MVDKMDQDLKISQK 14 2 O95721;C9JAF7 O95721 SNAP29 Synaptosomal-associated protein 29;Synaptosomal-associated protein 1 MVDKMDQDLKIS(1)QK 47.201 0.08902 344240000 137770 283600 234440 284550 376280 283250 320380 234230 641190 TRUE FALSE 129147.2216 304598.0391 240001.0275 291852.0347 346728.4866 365019.6768 272341.9933 263474.1311 534171.2468 0.241771197 0.570225449 0.449296043 0.546364179 0.649096126 0.68333831 0.509840234 0.493239074 1 19.0269428 -5 0.159598571 2.704571173 0.398953578 0.665227744 0.111854436 83.12509205 0.763820548 45.1603043 0.458858854 1.00E-05 5 -2.305617594 MVEGFFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MVEGFFDR 8 0 P00367;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ;;; 127.46 0.0027343 285797000 353654 439277 368384 369135 554049 346052 378760 452596 626270 FALSE TRUE 331519.4274 471801.5261 377122.2424 378607.629 510536.2265 445951.5947 321968.4542 509103.6069 521741.4911 0.635409361 0.904282167 0.722814361 0.725661339 0.97852334 0.854736689 0.617103412 0.975777498 1 18.99297564 1.096901283 9.427786851 0.999622684 0.784776902 0.376274695 0.112788766 0.290528984 24.27218302 0.103604737 0.025921833 12.49974873 -1.096901283 -0.214845783 MVEKDQDGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 MVEKDQDGGR 10 1 P39019;A0A075B6E2 P39019 RPS19 40S ribosomal protein S19 0 ;;;;;;;;; 184.24 1.44E-06 6373060000 5188320 5786510 5400070 5576050 7142290 4287840 6257710 4706870 8897320 FALSE TRUE 4863592.313 6214949.221 5528162.21 5719140.883 6581363.354 5525669.801 5319424.479 5294533.081 7412299.813 0.656151591 0.83846436 0.74580931 0.771574414 0.887897619 0.745473057 0.717648316 0.714290195 1 22.82148981 -1.394557169 3.427132892 1.001954815 0.765459722 0.573416845 0.064975405 23755456.41 28343482.22 445978.6733 0.014944726 0.040312788 1.394557169 -0.236495093 MVEPENAVTITPLRPEDDYS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 273.53 1.35E-45 1230230000 1466841 1605715 1582998 1882030 2115928 1095710 1011621 1031590 1183563 TRUE FALSE 1375034.04 1724603.809 1620547.46 1930326.076 1949751.55 1412023.69 859937.8225 1160386.282 986018.6892 1.394531417 1.749057932 1.643526109 1.95769725 1.977398169 1.432045564 0.872131362 1.176840049 1 19.91125547 1.961956085 4.531925973 1.023475084 1.740655895 0.778123847 0.177266433 0.092868422 4.284133527 0.077727411 0.047441368 91.61278494 -1.961956085 0.717180811 MVHNGIEYGDMQLICEAYHLMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MVHNGIEYGDMQLICEAYHLMK 22 0 P52209-2;P52209;K7EM49;K7EPF6;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 296.69 8.36E-56 208460000 389440 317490 319860 361960 396280 321080 341520 349000 153070 FALSE TRUE 365065.6456 340997.2899 327447.2302 371248.5064 365157.7673 413770.5837 290312.2465 392573.4182 127521.6281 2.862774346 2.674034946 2.567777992 2.911259147 2.863496747 3.244709072 2.276572616 3.078484991 1 16.96038243 -0.948984395 7.724967609 0.999999987 2.763778317 0.815324901 0.269911231 5.79E-08 7.97E-09 0.243043227 0.057285839 0.112464538 0.948984395 1.763778331 MVIENDLSGLIDFTRLPS(ph)PTPENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MVIENDLSGLIDFTRLPSPTPENK 24 1 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 MVIENDLSGLIDFT(0.004)RLPS(0.958)PT(0.038)PENK;MVIENDLSGLIDFT(0.005)RLPS(0.957)PT(0.039)PENK 134.21 2.22E-05 270360000 314890 272000 323730 353270 442340 208222 287040 246509 559860 TRUE FALSE 295181.597 292139.163 331409.0285 362335.5063 407600.4007 268332.3112 244001.0167 277286.1913 466415.7492 0.632872277 0.626349268 0.71054425 0.776850925 0.873899309 0.575307141 0.523140604 0.594504349 1 18.83125698 MVINHLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MVINHLEK 8 0 P50990-2;P50990;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;; 103.56 0.0047486 2060330000 4811500 5091300 4723000 4790600 5574100 3588180 5381800 4841800 5693400 FALSE TRUE 4510356.804 5468265.149 4835031.79 4913534.906 5136332.671 4624029.317 4574849.052 5446309.388 4743134.759 0.950923183 1.152879989 1.019374746 1.035925639 1.082898322 0.974888877 0.964520151 1.148251033 1 22.17740943 2.247631124 24.99442798 1.011551783 1.05812252 0.014240229 0.071067172 475.4582091 1310159.755 0.023454482 0.019353513 176.8606122 -2.247631124 0.046570737 MVIQGPS(ph)SPQGEAMVTDVLEDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MVIQGPSSPQGEAMVTDVLEDQK 23 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.5)S(0.5)PQGEAMVT(0.001)DVLEDQK;MVIQGPS(0.646)S(0.354)PQGEAMVTDVLEDQK 266.17 2.71E-44 196081000 551791 385274 469303 429432 423669 356207 543324 389743 407088 TRUE FALSE 517255.3863 413800.0878 480435.0888 440451.9521 390395.7457 459038.1784 461857.6102 438403.2715 339142.3829 1.525186507 1.220136759 1.41661766 1.298722821 1.151126386 1.353526429 1.361839845 1.292682052 1 18.37153156 -3.274060971 0.376804584 2.44E-18 1.333731361 0.514333297 0.10095819 109.2483381 2.883412821 86.71613652 0.064083636 0.000532034 3.274060971 1.333731361 MVIQGPS(ph)SPQGEAMVTDVLEDQKEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 MVIQGPSSPQGEAMVTDVLEDQKEGR 26 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.5)S(0.5)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.545)S(0.454)PQGEAMVT(0.001)DVLEDQKEGR;MVIQGPS(0.5)S(0.5)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.5)S(0.5)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.558)S(0.441)PQGEAMVT(0.002)DVLEDQKEGR;MVIQGPS(0.499)S(0.499)PQGEAMVT(0.001)DVLEDQKEGR 115.77 0.0017082 2765770000 1058106 937626 1064200 1127020 1263348 820759 1317280 891260 1792190 TRUE FALSE 991881.0342 1007048.805 1089443.327 1155941.241 1164129.744 1057698.799 1119766.093 1002535.773 1493061.911 0.664326795 0.674485631 0.729670564 0.774208513 0.779692882 0.708409204 0.749979679 0.671462962 1 20.50984256 -2.440576268 2.315423457 3.921070733 0.721128934 0.822046704 0.041073223 1488712.663 266478.5668 22574116.94 0.010204961 0.003625966 2.440576268 -3.199941799 MVIQGPSS(ph)PQGEAMVTDVLEDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MVIQGPSSPQGEAMVTDVLEDQK 23 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.188)S(0.812)PQGEAMVTDVLEDQK;MVIQGPS(0.156)S(0.844)PQGEAMVTDVLEDQK;MVIQGPS(0.257)S(0.743)PQGEAMVTDVLEDQK;MVIQGPS(0.217)S(0.783)PQGEAMVTDVLEDQK 284.29 2.23E-52 323771000 826917 546715 670366 622508 606101 539030 797175 591390 592510 TRUE FALSE 775161.7411 587194.3475 686267.3981 638482.6092 558500.2724 694639.2106 677646.0094 665226.3433 493616.2532 1.570373212 1.189576607 1.390285254 1.293479712 1.131446278 1.407245418 1.372819483 1.347658913 1 18.91303037 -2.244012319 1.982792222 1.89E-05 1.328224566 0.436082109 0.120300721 1315521.241 211514.0436 5888396.746 0.029507342 0.005701481 2.244012319 1.328205647 MVIQGPSS(ph)PQGEAMVTDVLEDQKEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 16 MVIQGPSSPQGEAMVTDVLEDQKEGR 26 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.127)S(0.873)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.18)S(0.82)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.036)S(0.961)PQGEAMVT(0.003)DVLEDQKEGR;MVIQGPS(0.144)S(0.856)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.056)S(0.944)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.205)S(0.779)PQGEAMVT(0.017)DVLEDQKEGR;MVIQGPS(0.406)S(0.594)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.209)S(0.791)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.052)S(0.948)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.007)S(0.993)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.132)S(0.868)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.304)S(0.694)PQGEAMVT(0.002)DVLEDQKEGR;MVIQGPS(0.005)S(0.995)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.003)S(0.997)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.457)S(0.542)PQGEAMVT(0.001)DVLEDQKEGR;MVIQGPS(0.329)S(0.671)PQGEAMVTDVLEDQKEGR 257.07 7.19E-53 6357137300 4269036.8 3901811.1 3815264.8 4058037.8 4852179.9 2893117.6 4765682.6 3448310.7 6292936.2 TRUE FALSE 4001845.407 4190705.254 3905764.683 4162173.92 4471109.263 3728313.685 4051112.737 3878839.882 5242604.494 0.763331549 0.799355599 0.745004642 0.793913393 0.85284123 0.711156771 0.77272904 0.739868874 1 22.32185228 -1.048391514 5.364585751 1.000001786 0.772583233 0.776042922 0.038445798 7.61E-07 1.35E-07 0.034510309 0.008134094 0.089455796 1.048391514 -0.227418553 MVIQLRPGRS(ph)PEPDGPAPAFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MVIQLRPGRSPEPDGPAPAFLR 22 2 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 MVIQLRPGRS(1)PEPDGPAPAFLR;MVIQLRPGRS(1)PEPDGPAPAFLR 165.39 6.72E-12 802910000 434110 608560 518400 580820 682710 461750 572520 500520 658820 TRUE FALSE 406939.83 653618.4156 530696.6928 595724.8245 629092.7105 595049.7291 486675.941 563011.0238 548858.6859 0.741429152 1.19086831 0.966909528 1.085388352 1.146183392 1.084158353 0.886705364 1.02578503 1 19.06607522 1.755947373 25 0.960961888 1.051912315 0.043489269 0.127026496 15.25664134 21960.80281 0.053308467 0.02956254 57.0095185 -1.755947373 0.090950426 MVMISLEGEDGLDEIYSFSESLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MVMISLEGEDGLDEIYSFSESLRK 24 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 182.39 4.94E-17 146019000 199468 184021 192631 195465 242362 153338 235401 170929 262203 FALSE TRUE 186983.6539 197646.1063 197200.2983 200480.9628 223327.8662 197604.1914 200104.8054 192269.8619 218439.6254 0.855996954 0.90480885 0.902767975 0.917786608 1.022377995 0.904616967 0.916064588 0.880196812 1 17.73687506 5.817661423 0.584459253 0.934207433 0.636645724 0.257784819 0.043815627 17.81690697 1.767489882 0.01895307 4.747653587 657145.3254 -5.817661423 -0.297561709 MVNHFIAEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MVNHFIAEFK 10 0 P11142;E9PKE3;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;; 175.15 2.89E-06 11893800000 29103500 35181800 23419200 19972100 38997400 14682400 30788700 35034000 40005400 FALSE TRUE 27281963.89 37786697.08 23974714.48 20484617.9 35934701.51 18920970.53 26172220.26 39408072.02 33328240.3 0.818583989 1.133774143 0.719351345 0.614632447 1.078205786 0.567715858 0.785286593 1.182422824 1 24.99024181 1.245251489 24.99288574 1.091211439 0.826074008 0.280145794 0.18240822 190.012479 709786.8356 0.125813982 0.043622811 17.58941879 -1.245251489 -0.265137431 MVNHFIAEFKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MVNHFIAEFKR 11 1 P11142;E9PKE3;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 129.82 0.00015389 220330000 294400 794860 246890 230370 939150 153550 265470 695150 933630 FALSE TRUE 275974.0295 853712.2615 252746.3474 236281.6842 865392.9473 197877.3923 225665.238 781941.0077 777801.1215 0.354813103 1.097597108 0.324949837 0.303781619 1.112614682 0.254406155 0.290132312 1.005322551 1 19.56904179 1.215101199 24.57464964 1.002662434 0.553616563 0.26887806 0.319997847 315.9196712 330927.3785 0.299522222 0.075077127 16.40972106 -1.215101199 -0.449045871 MVPTSDKGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MVPTSDKGR 9 1 P13639 P13639 EEF2 Elongation factor 2 0 75.294 0.035266 350380000 242470 408040 253790 312390 553900 218180 398200 432190 679320 FALSE TRUE 227294.2355 438251.7062 259810.0186 320406.4563 510398.9283 281165.0241 338493.6067 486149.8729 565937.1034 0.401624552 0.774382354 0.459079317 0.566152059 0.901865111 0.496813201 0.598111707 0.859017495 1 19.1102822 1.097401475 3.486639149 0.995047872 0.605926015 0.478910388 0.146692948 0.177789113 4.002663204 0.127921984 0.03347639 12.51415341 -1.097401475 -0.389121858 MVQEAEK ddPTM_SK-BR-3_Pertuzumab_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 ; 119.41 0.011141 278870000 532950 664880 389740 388020 802100 282120 493110 717290 873380 FALSE TRUE 499593.6108 714108.407 398984.8168 397977.2501 739106.3015 363563.4642 419172.7333 806845.2355 727607.2357 0.686625402 0.981447644 0.548351909 0.546967142 1.015803946 0.49966994 0.576097533 1.10890216 1 19.47280036 1.231924683 24.99603001 1.054451276 0.69783473 0.413821141 0.178509787 169.8054212 639588.5676 0.154890253 0.042276535 17.05786541 -1.231924683 -0.356616547 MVQFEENGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MVQFEENGR 9 0 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;E9PQ35;Q5SZW8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;; 182.98 0.0001063 1030871000 685977 824400 754422 755306 716957 640264 742732 638801 589887 FALSE TRUE 643042.9241 885439.4338 772317.2461 774688.4307 660650.0893 825097.823 631366.2318 718556.711 491431.0489 1.308510981 1.801757206 1.571567869 1.576392929 1.344339335 1.678969664 1.28475039 1.462171983 1 18.90662949 0.442692729 0.375077886 0.928874756 1.625289981 0.504201019 0.160566592 1.905571392 0.511345649 0.399478921 0.12258745 2.771358626 -0.442692729 0.696415224 MVQFEENGRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MVQFEENGRK 10 1 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;E9PQ35;Q5SZW8 P49368 CCT3 T-complex protein 1 subunit gamma 0 104.82 0.0065163 0 257540 256040 266620 237440 298210 197950 284980 232570 318970 FALSE TRUE 241421.0311 274997.468 272944.3523 243533.1124 274789.7895 255094.9516 242249.8946 261606.8764 265731.8464 0.908513731 1.034868315 1.027142046 0.916461898 1.034086781 0.959971321 0.911632903 0.984476946 1 18.01961161 2.023430547 24.013327 0.950614053 0.994157078 0 0.050350235 275.1842292 282026.868 0.018018048 0.013306331 105.5432705 -2.023430547 0.043543025 MVSDEYEQLSSEALEAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MVSDEYEQLSSEALEAAR 18 0 F8W7C6 F8W7C6 RPL10 0 ; 261.17 2.09E-30 53271000 31321 30295 35879 31801 24974 32219 37712 28755 22723 FALSE TRUE 29360.67452 32538.07332 36730.06682 32617.0675 23012.64278 41520.10227 32057.4357 32345.12505 18930.3845 1.550981414 1.718827915 1.940270511 1.723000792 1.215645819 2.193304751 1.693438171 1.708635397 1 14.20841609 0.564332231 2.824609454 1.000013439 1.743866545 0.447740384 0.249509599 6.848229994 43.27931951 0.22086363 0.05808378 3.667180031 -0.564332231 0.743853107 MVSDINNGWQHLEQAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MVSDINNGWQHLEQAEK 17 0 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 ; 343.55 5.98E-73 592540000 1018890 672600 748130 686760 643520 570660 928060 780610 701950 FALSE TRUE 955119.4937 722400.0038 765875.9969 704383.4243 592980.535 735400.2781 788906.0187 878070.8768 584790.0102 1.633269168 1.235315226 1.30965985 1.204506595 1.014005925 1.257545897 1.349041545 1.501514837 1 19.15755914 4.739902104 24.37984901 1.249759254 1.633269333 0.414852174 0.147987355 83.68841941 1520697.398 0.033642789 0.209595857 54941.70133 -4.739902104 0.383510079 MVSQSQPGS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 MVSQSQPGSR 10 0 E3W994;J3KR49;O75122;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 MVSQSQPGS(1)R;MVSQSQPGS(1)R;MVSQSQPGS(1)R;MVSQSQPGS(1)R;MVSQSQPGS(1)R 145.06 3.26E-05 1397090000 1510880 1659210 1778240 1937650 1658210 1786120 1761680 1680080 1202500 TRUE FALSE 1416316.718 1782059.635 1820420.693 1987373.379 1527980.875 2301743.849 1497532.439 1889841.686 1001794.982 1.413779011 1.778866602 1.817158926 1.983812473 1.525243092 2.297619664 1.494849212 1.886455533 1 19.93415586 -0.767203988 6.510715294 0.999999994 1.779834395 0.469535895 0.258736373 1.93E-08 4.94E-09 0.215789148 0.050861989 0.170921231 0.767203988 0.779834401 MVSSCLDAHTGISHEDLIQNFLNAGSFPEIQGFLQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MVSSCLDAHTGISHEDLIQNFLNAGSFPEIQGFLQLR 37 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ;; 164.29 6.25E-18 213357000 86390 145065 82666 61015 154397 69986 80535 115743 57806 FALSE TRUE 80983.00411 155805.7635 84626.87656 62580.7482 142271.2824 90189.82207 68459.5244 130193.7683 48157.80516 1.681617421 3.235316955 1.757282673 1.299493363 2.954272562 1.872797603 1.421566539 2.703482185 1 15.55548202 -1.27676235 0.161184057 1.48E-11 2.592375248 0.175294572 0.672309734 44.96450529 1.38186392 24.04241152 3.466559736 0.05287345 1.27676235 2.592375248 MVVNEGSDGGQSVYHVHLHVLGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MVVNEGSDGGQSVYHVHLHVLGGR 24 0 P49773 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ; 172 2.08E-12 1325180000 412770 654360 570560 582050 593730 507390 640530 560900 562270 FALSE TRUE 386935.4625 702809.4953 584093.9526 596986.3884 547100.8408 653865.2562 544488.4729 630929.5997 468423.5046 0.826037675 1.500371968 1.246935619 1.274458652 1.167961973 1.395884813 1.162385037 1.346921308 1 18.83745394 -1.68167138 2.78211986 0.965922305 1.262416787 0.139619182 0.179912592 18744026.54 15947140.7 4494253.151 0.042336999 0.020812709 1.68167138 0.296494482 MVVPGLDGAQIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MVVPGLDGAQIPR 13 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 77.379 0.060741 46792000 36341 44194 45436 49703 46012 44920 51973 44929 49205 FALSE TRUE 34066.48168 47466.16974 46513.76338 50978.46313 42398.40312 57887.67478 44180.13114 50538.48455 40992.36762 0.831044501 1.157927012 1.134693263 1.243608654 1.034299934 1.412157388 1.077764806 1.232875471 1 15.3230677 4.739414817 5.581000429 1.168073835 0.819179555 0.436978717 0.117802982 0.121335747 15.19053228 0.024006878 0.161528915 54880.09028 -4.739414817 -0.34889428 MWDPHNDPNAQGDAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MWDPHNDPNAQGDAFK 16 0 P08621;P08621-2;M0QYR1;P08621-3 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;;; 160.93 8.61E-09 1652840000 4065570 3317640 3613860 3521870 3842990 2834300 4282720 3208240 4681810 FALSE TRUE 3811113.231 3563281.518 3699582.466 3612247.147 3541177.067 3652516.399 3640565.895 3608795.826 3900385.665 0.977111896 0.913571586 0.948517091 0.926125634 0.907904338 0.936450062 0.933386133 0.925240767 1 21.89518535 -1.270316394 4.458556245 1.000037771 0.932315526 0.54085199 0.019215313 6.36E-06 1.04E-06 0.01640293 0.003864052 0.05366407 1.270316394 -0.067722244 MWSESS(ph)LDEPYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MWSESSLDEPYEK 13 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 MWS(0.005)ES(0.105)S(0.888)LDEPY(0.002)EK 63.283 0.073668 66241000 98052 74639 77232 87463 74586 55948 111620 75109 84813 TRUE FALSE 91915.10035 80165.34922 79063.97951 89707.44865 68728.31643 72099.27936 94883.61723 84486.52399 70657.16239 1.300860341 1.134567912 1.118980395 1.269615784 0.972701338 1.020410061 1.342873306 1.195724837 1 16.10854819 4.740958078 23.61096521 1.144729802 1.300860464 0.162275653 0.117482885 206.5212799 2033597.856 0.027452882 0.182982446 55075.45306 -4.740958078 0.156130663 MWVFEETVNGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 MWVFEETVNGR 11 0 Q8N335;C9K0P5;C9JFA7;C9JM46 Q8N335 GPD1L Glycerol-3-phosphate dehydrogenase 1-like protein;Glycerol-3-phosphate dehydrogenase [NAD(+)] 0 162.88 5.73E-05 21697000 24797 36769 30240 30544 31576 25661 37264 30019 32106 FALSE TRUE 23245.00003 39491.41502 30957.30708 31327.81075 29096.14833 33068.91413 31676.60914 33766.93823 26747.30119 0.869059643 1.476463541 1.157399278 1.17125128 1.08781623 1.236345824 1.184291788 1.262442816 1 14.70710571 3.691836956 24.77158349 1.168190648 1.246382802 0 0.164644981 945.641618 663893.551 0.039733242 0.061557006 4918.548475 -3.691836956 0.078192155 MYEEHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 MYEEHLK 7 0 P84090;G3V279 P84090 ERH Enhancer of rudimentary homolog 0 ;;;; 126.54 0.0039421 3315080000 5609740 5012500 4941210 4920460 5194470 3900620 5886970 4922640 5799670 FALSE TRUE 5258636.387 5383630.716 5058417.835 5046727.334 4786517.28 5026665.673 5004273.5 5537242.44 4831667.61 1.088368822 1.114238634 1.046930013 1.044510455 0.990655332 1.040358336 1.035723875 1.146031327 1 22.20408978 3.833946853 2.774959037 1.041711768 1.101206738 0.249092802 0.041678736 0.346564891 5.235216545 0.010581444 0.021536054 6822.551982 -3.833946853 0.05949497 MYEEHLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MYEEHLKR 8 1 P84090;G3V279 P84090 ERH Enhancer of rudimentary homolog 0 ;;; 186.3 0.00013517 1984630000 2339540 2546770 2415520 2410090 2952530 1636920 2698800 2289211 3883550 FALSE TRUE 2193112.368 2735335.501 2472817.275 2471936.99 2720650.204 2109472.231 2294139.994 2575024.033 3235360.416 0.677857205 0.845450011 0.764309677 0.764037594 0.840911013 0.652005328 0.709083286 0.795900209 1 21.62549501 0.966031146 21.22913866 1.000000002 0.757111934 0.611216459 0.061968752 453.3667476 283336.8605 0.060131065 0.015032766 9.247644919 -0.966031146 -0.242888068 MYFPDVEFDIKS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 MYFPDVEFDIKSPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 MYFPDVEFDIKS(1)PK;MYFPDVEFDIKS(1)PK;MYFPDVEFDIKS(1)PK 209.73 3.77E-09 739980000 3496730 1667790 2600740 3506360 3554800 1341920 2418920 1442290 3010110 TRUE FALSE 3277875.911 1791274.907 2662430.781 3596339.134 3275620.347 1729310.52 2056225.402 1622363.081 2507703.195 1.307122756 0.714308978 1.061700917 1.434116741 1.306223302 0.689599361 0.819963625 0.646951794 1 21.25793517 2.22532398 24.99969016 0.776018033 1.10148022 0.409281419 0.216683388 285.1493943 538550.6769 0.086535702 0.064286349 168.0056859 -2.22532398 0.325462187 MYLETDPSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 MYLETDPSGR 10 0 Q9Y6U3;Q9Y6U3-3 Q9Y6U3 SCIN Adseverin 0 ; 116.37 0.0025569 178642000 240610 261210 259730 244050 357460 244840 277140 319460 630270 FALSE TRUE 225550.6496 280550.2602 265890.9183 250312.7362 329386.5335 315521.3334 235585.4298 359345.2842 525073.8653 0.429559848 0.534306273 0.506387645 0.476719092 0.62731466 0.600908471 0.448671026 0.68437092 1 19.00216086 -4.999999982 0.238113482 3.678249128 0.482097617 0.831953316 0.067932932 64.49849443 0.644092655 83.4031499 0.104374584 1.00E-05 4.999999982 -3.196151511 MYPIDFEKDDDSNFHMDFIVAASNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 MYPIDFEKDDDSNFHMDFIVAASNLR 26 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;;; 243.88 4.38E-45 620834000 1041473 967162 932350 897362 1163159 686486 1137492 931887 1078378 FALSE TRUE 976289.064 1038771.681 954465.7823 920389.8282 1071809.184 884663.364 966935.6346 1048235.143 898389.7452 1.086709938 1.156259504 1.062418385 1.02448835 1.193033636 0.984721129 1.076298611 1.166793309 1 19.77698193 1.522354761 0.009756276 2.68E-07 2.14613117 0.1052647 0.066846713 2152.628225 21.34917621 2348.163385 2344.549938 33.29314033 -1.522354761 2.146130902 MYPPRS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 MYPPRSPK 8 1 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 1 MYPPRS(1)PK;MYPPRS(1)PK;MYPPRS(1)PK;MYPPRS(1)PK 93.096 0.013542 1360920000 1455235 1303080 1230912 1328267 1675083 589241 1036659 932545 1504098 TRUE FALSE 1364154.439 1399561.399 1260109.814 1362352.58 1543528.738 759345.3112 881221.6068 1048975.296 1253054.327 1.088663444 1.116919968 1.005630631 1.08722547 1.231813103 0.605995522 0.703258899 0.83713473 1 20.25701753 2.239087156 24.99999964 0.75002231 1.092983421 0.646633562 0.115728191 7.622765387 361951.5511 0.038721105 0.030584257 173.4151979 -2.239087156 0.342961111 NAAEELKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NAAEELKPR 9 1 P78406 P78406 RAE1 mRNA export factor 0 ;;; 125.75 0.00044953 1523840000 2109920 1661130 1795750 1775930 1856620 1303750 2402470 1585740 2051400 FALSE TRUE 1977863.874 1784121.794 1838346.038 1821503.37 1710808.554 1680121.46 2042241.927 1783723.13 1709008.087 1.15731686 1.043951639 1.075680128 1.065824898 1.001053516 0.983097431 1.194986695 1.043718367 1 20.70472779 -0.178730308 8.124429494 1 1.071799311 0.107074377 0.064097288 0 0 0.059822805 0.01410037 0.66262786 0.178730308 0.07179931 NAATEDLWESLENASGKPIAAVMNTWTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NAATEDLWESLENASGKPIAAVMNTWTK 28 1 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 180.71 1.33E-17 56369000 75239 65113 72467 66255 76549 56373 93290 65734 101590 FALSE TRUE 70529.9253 69934.03427 74185.95146 67955.21547 70537.15032 72646.96996 79302.03056 73941.0346 84633.9727 0.833352412 0.82631161 0.876550504 0.802930706 0.83343778 0.858366536 0.936999978 0.873656668 1 16.36894927 1.073712365 0.611420278 0.997864396 0.833693866 0.746278024 0.029396147 0.400070535 0.364592274 0.029764332 0.013116331 11.84983669 -1.073712365 -0.16417053 NAAVIDPLQFHMGVERPGVTNVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NAAVIDPLQFHMGVERPGVTNVAR 24 1 O75582-3;O75582;O75582-2 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 0 64.377 0.024104 106260000 101730 103840 93604 109360 115130 82572 127140 106120 132200 FALSE TRUE 95362.90089 111528.4216 95824.33108 112166.3627 106088.1542 106409.196 108076.5373 119369.3156 110134.966 0.865873068 1.012652255 0.870062748 1.018444613 0.963255886 0.966170871 0.981309944 1.083845757 1 16.74891305 1.939141641 0.819749097 1.031281607 0.938585566 0.308422592 0.054696897 0.779201664 0.977543996 0.043600544 0.021437453 86.92438794 -1.939141641 -0.092696041 NACDHLSGFNVCNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NACDHLSGFNVCNR 14 0 Q9Y3B4 Q9Y3B4 SF3B6 Splicing factor 3B subunit 6 0 ;; 183.06 1.45E-06 692220000 313191 685170 636720 702960 700670 525660 831500 670330 664160 FALSE TRUE 293588.9344 735900.6997 651823.2991 720999.1437 645642.2046 677409.5086 706824.2943 754022.1761 553307.4054 0.530607275 1.330003345 1.178049115 1.30307156 1.166877939 1.224291419 1.277453162 1.362754535 1 19.07772171 4.742891947 24.99519598 1.241814029 0.530606992 0.819083967 0.103219868 156.7424546 904495.0258 0.021224893 0.168050943 55321.24526 -4.742891947 -0.711207037 NADGFIDLEEYIGDMYSHDGNTDEPEWVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 NADGFIDLEEYIGDMYSHDGNTDEPEWVK 29 0 O43852;O43852-3;O43852-15;H0Y875;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;;;;; 328.19 4.62E-105 324133000 446490.4 317632.3 367125.6 341030.2 307859 266357.5 422713.7 313585.6 259814.8 FALSE TRUE 418545.3629 341150.126 375833.9926 349781.6123 283680.996 343250.5863 359331.705 352737.4524 216450.0314 1.93368123 1.576114929 1.73635453 1.61599243 1.310607322 1.585819064 1.660113896 1.629648423 1 17.72367448 -2.720266624 0.254572268 5.71E-14 1.699486829 0.649562234 0.148383699 32.79078726 0.912474779 18.50728623 0.211716255 0.001904291 2.720266624 1.699486829 NADGTICYDSTHYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NADGTICYDSTHYK 14 0 P14550;Q5T621 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ;;; 223.96 3.33E-12 5970300000 5136500 5047100 5132300 5043600 5917300 3452800 6051700 5098900 6718800 FALSE TRUE 4815015.634 5420792.536 5254040.58 5173027.315 5452579.127 4449567.308 5144303.766 5735508.889 5597388.875 0.86022532 0.968450229 0.938659203 0.9241858 0.974129054 0.794936248 0.919054202 1.024675794 1 22.41632255 1.244082835 24.57005448 1.012337917 0.916548393 0.386902623 0.052524155 106.8923856 475618.5277 0.036716904 0.012548236 17.54215058 -1.244082835 -0.095789524 NADGYKLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NADGYKLDK 9 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ; 97.734 0.0059196 310290000 790160 522860 602450 620960 735550 415650 843460 529680 1077760 FALSE TRUE 740705.2961 561573.0984 616740.3985 636894.8849 677782.8701 535641.4075 716991.0033 595811.714 897874.8934 0.82495379 0.625446933 0.686889012 0.709335888 0.75487451 0.596565748 0.798542212 0.66357988 1 19.77615491 -4.999997778 0.387938018 5.443312068 0.695211511 0.612482687 0.07240708 395.3025 2.879164475 1481.661206 0.042176999 1.00E-05 4.999997778 -4.748100557 NADHLLHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NADHLLHLK 9 0 A0A0J9YWM9;H3BSH7;Q969X6;A0A0J9YWK2;Q969X6-3;H3BRM8 A0A0J9YWM9 CIRH1A Cirhin 0 107.55 0.001593 1680000000 693770 788180 756880 767340 761970 640620 874870 649460 683560 FALSE TRUE 650348.1741 846537.6673 774833.551 787031.2435 702127.9498 825556.5944 743691.3654 730546.5106 569469.42 1.142024754 1.486537534 1.360623633 1.382043031 1.232951103 1.449694339 1.305937315 1.28285468 1 19.11925885 0.614528259 1.295969782 1.000062379 1.359026963 0.520969671 0.09977276 0.967757212 2.363184553 0.08590655 0.02572168 4.116501325 -0.614528259 0.358964585 NADHSMNYQYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NADHSMNYQYR 11 0 Q12906;K7ELV3;Q12906-7 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;;;;; 187.85 3.41E-06 1365603000 242059 299885 247150 234605 351397 170868 247602 271898 367949 FALSE TRUE 226908.9593 322088.7974 253012.5147 240625.3615 323799.6971 220194.8178 210476.3787 305845.0638 306535.9349 0.740236082 1.050737486 0.825392673 0.784982555 1.056318886 0.718332805 0.686628727 0.997746199 1 18.22569668 2.205405284 24.99976391 0.805990201 0.899381108 0 0.144440663 474.2136707 357563.5971 0.050812245 0.037529745 160.474224 -2.205405284 0.093390907 NADNDWFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NADNDWFR 8 0 Q9Y3C8 Q9Y3C8 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 0 ;;;; 141.2 0.0014829 2123690000 3475130 3840200 3634100 3602630 3981390 2764270 3928560 3343590 3984700 FALSE TRUE 3257627.817 4124532.404 3720302.568 3695079.585 3668707.69 3562269.875 3339508.899 3761044.572 3319627.828 0.981323204 1.242468318 1.120698693 1.113100557 1.105156325 1.073093148 1.005988946 1.132971757 1 21.66259008 2.456152444 1.328592535 1.04448131 1.141159591 0.11076193 0.072986913 0.608225076 2.167861784 0.036211884 0.026124143 285.8593778 -2.456152444 0.096678281 NADSELMPPPPERGDPPRLS(ph)PDPVAGSAVSQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NADSELMPPPPERGDPPRLSPDPVAGSAVSQELR 34 2 Q9BUR4;E9PMG4;E9PMR3 Q9BUR4 WRAP53 Telomerase Cajal body protein 1 1 NADSELMPPPPERGDPPRLS(1)PDPVAGSAVSQELR 157.09 8.81E-12 183400000 145430 178230 166670 181220 209250 119390 198250 147910 343010 TRUE FALSE 136327.7959 191426.3346 170623.4911 185870.412 192816.3491 153855.9549 168524.253 166376.8891 285759.4151 0.477071931 0.669886361 0.597087907 0.650443703 0.674750643 0.538410799 0.589741734 0.582227147 1 18.12444151 -1.835275869 2.48506843 1.154252116 0.604081895 0.814843555 0.060231156 6673019.005 4127867.594 6131454.028 0.014391351 0.014612487 1.835275869 -0.550170221 NADSELMPPPPERGDPPRLSPDPVAGS(ph)AVSQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NADSELMPPPPERGDPPRLSPDPVAGSAVSQELR 34 2 Q9BUR4;E9PMG4;E9PMR3 Q9BUR4 WRAP53 Telomerase Cajal body protein 1 1 NADSELMPPPPERGDPPRLS(0.381)PDPVAGS(0.595)AVS(0.024)QELR 127.01 3.46E-08 266340000 153500 196970 179860 197370 211910 146840 235820 150220 372380 TRUE FALSE 143892.709 211553.8637 184126.3641 202434.8483 195267.4434 189230.3243 200460.9802 168975.2977 310227.3723 0.463829829 0.68193165 0.59352069 0.652537031 0.629433315 0.609973011 0.646174381 0.544682103 1 18.24296646 -1.535771626 3.177308522 1.012922091 0.614026913 0.798362375 0.06251196 38258963.43 50912751.15 4321650.389 0.013140495 0.029122481 1.535771626 -0.398895179 NADSGVHLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 106.29 0.0024361 163460000 572280 735650 657810 679490 732130 538410 765120 630500 741140 FALSE TRUE 536462.0163 790118.2914 673413.5638 696926.8638 674631.4631 693840.2266 650397.359 709219.3129 617438.9461 0.868850305 1.279670316 1.090656118 1.128738102 1.092628619 1.123739005 1.053379226 1.14864687 1 19.23593696 -1.159888471 0.367548806 0.942109751 1.119722054 0.050655709 0.102882547 40.18601263 3.665393943 2.438821908 0.069914888 0.069200866 1.159888471 0.177612303 NAEAVLQS(ph)PGLSGK ddPTM_SK-BR-3_Pertuzumab_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 339.56 8.32E-69 3248630000 9759230 6884760 8134370 7976400 7906240 6017980 11276180 7152080 10376280 TRUE FALSE 9148417.215 7394514.794 8327321.098 8181087.928 7285315.803 7755273.132 9585421.492 8045032.932 8644411.835 1.058304184 0.855409823 0.963318414 0.946401917 0.842777501 0.89714295 1.108857569 0.930662847 1 23.04333638 1.763153475 25 1.023039335 0.920593318 0.225837659 0.073589637 16.83500714 17125.70058 0.030935903 0.017156466 57.96334962 -1.763153475 -0.102446017 NAEEES(ph)ES(ph)EAEEGD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NAEEESESEAEEGD 14 0 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;H0Y503 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 2 NAEEES(1)ES(1)EAEEGD 150.55 4.46E-07 0 83053 145600 137000 144640 133230 129470 110060 110590 103450 TRUE FALSE 77854.86098 156380.3755 140249.7047 148351.7073 122766.6532 166845.8872 93557.52475 124397.4049 86183.52669 0.90336128 1.81450425 1.62733773 1.721346445 1.42447934 1.935937106 1.085561572 1.44340119 1 16.39512452 1.67571413 9.601445752 1.201557505 1.605211187 0.272181133 0.299325654 0.139313759 19.55991195 0.128753076 0.069026193 47.3929923 -1.67571413 0.403653682 NAEIGNKDFELDVLEEAYTTEHWLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NAEIGNKDFELDVLEEAYTTEHWLVR 26 1 P46977;P46977-2 P46977 STT3A Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A 0 163.16 9.14E-12 16936000 32527 30290 27750 27720 44715 19978 38528 34162 46331 FALSE TRUE 30491.19313 32532.70312 28408.2431 28431.34213 41203.26427 25745.32428 32751.08408 38427.2009 38598.05679 0.789967052 0.842858574 0.736001899 0.73660035 1.06749582 0.667010892 0.848516397 0.995573459 1 15.2362406 1.285668408 4.473969152 1.001615383 0.806496344 0.353920792 0.105097178 0.201580106 7.736177954 0.07529652 0.024167662 19.30493786 -1.285668408 -0.19511904 NAEPADRDSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NAEPADRDSPR 11 1 Q3KQV9;Q3KQV9-2 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 ;; 182.35 5.31E-06 1609774000 2044680 2045690 1896220 2043640 2318960 1267352 2232180 1593601 1547580 FALSE TRUE 1916707.129 2197155.016 1941199.234 2096083.262 2136838.236 1633215.949 1897485.332 1792565.593 1289278.9 1.486650505 1.704173562 1.505647252 1.625779544 1.657390217 1.266766988 1.471741553 1.390362933 1 20.29813295 0.512417786 0.381416939 0.935643587 1.626227385 0.729739461 0.107197811 1.165419994 0.339113847 0.245932391 0.081733328 3.254001782 -0.512417786 0.690583798 NAEQYKDQADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NAEQYKDQADK 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 187.44 3.27E-06 4304000000 3211900 1659960 2118150 2218920 2387010 1436580 2911900 1659840 2849200 FALSE TRUE 3010872.912 1782865.166 2168393.518 2275861.244 2199543.863 1851297.325 2475287.628 1867074.678 2373650.113 1.26845692 0.751106979 0.913527022 0.958802323 0.926650415 0.779936906 1.04281908 0.78658378 1 21.17867586 -1.232258432 4.309283813 1.000041784 0.914998835 0.014859645 0.150893633 5.32E-05 9.48E-06 0.128282646 0.030221659 0.058578948 1.232258432 -0.085042948 NAFACFDEEATGTIQEDYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NAFACFDEEATGTIQEDYLR 20 0 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ; 385.68 2.08E-130 101476000 141853 137931 128608 130796 137156 109451 174788 119682 137775 FALSE TRUE 132974.6739 148143.5548 131658.6425 134152.4468 126384.321 141047.7269 148580.1621 134624.5612 114779.4624 1.158523233 1.290679984 1.147057494 1.168784414 1.101105706 1.228858577 1.294483864 1.172897645 1 16.808505 3.952835877 18.95097497 1.180531104 1.232144502 0.049291803 0.08457993 64.12749362 50041.96782 0.021079827 0.038089949 8970.897132 -3.952835877 0.051613399 NAFMMLIHADQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NAFMMLIHADQDR 13 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ; 172.1 2.40E-05 957690000 1101270 1543740 1002920 1154770 1627800 622270 1242420 1358680 1616840 FALSE TRUE 1032343.477 1658040.116 1026709.736 1184403.353 1499959.154 801909.2473 1056130.655 1528314.189 1346978.959 0.766413959 1.230932454 0.762231458 0.87930353 1.113572817 0.595339105 0.78407361 1.134623655 1 20.36129588 3.915275177 10.08659961 0.871717295 1.027304988 0.030220836 0.197121234 1.011065236 160.1936865 0.047275679 0.085393086 8227.638029 -3.915275177 0.155587693 NAHVTDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NAHVTDPR 8 0 R4GN43;A0A2Y9D025;P56556 R4GN43 NDUFA6 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 0 ;; 94.302 0.010456 231781000 623830 558840 561470 511570 676950 470440 558150 540830 782420 FALSE TRUE 584785.5939 600217.0951 574788.3335 524697.7523 623785.0777 606248.391 474460.5891 608353.816 651829.0474 0.897145649 0.920819803 0.881808406 0.804962213 0.956976496 0.930072683 0.727891141 0.933302709 1 19.31413412 3.719505373 4.11960933 0.872066646 0.908677784 0 0.079097785 0.811212869 32.20605139 0.020548647 0.035485496 5242.100861 -3.719505373 0.036611139 NAKPLSFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NAKPLSFK 8 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 62.823 0.07041 246840000 226280 227780 172990 213440 267470 140260 230140 224370 349500 FALSE TRUE 212117.5387 244645.0682 177093.4045 218917.2318 246463.9851 180750.7851 195632.6435 252383.0884 291166.1921 0.728510193 0.840224843 0.608221041 0.751863498 0.846471849 0.620782185 0.671893402 0.8668008 1 18.15148333 1.014695584 4.287811034 0.999068948 0.722261747 0.576349997 0.079171856 0.12154082 5.941907342 0.075322842 0.019206633 10.34416844 -1.014695584 -0.276807201 NALFPEVFS(ph)PTPDENSDQNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NALFPEVFSPTPDENSDQNSR 21 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 NALFPEVFS(0.999)PT(0.001)PDENSDQNSR;NALFPEVFS(1)PTPDENSDQNSR;NALFPEVFS(1)PTPDENSDQNSR 265.39 4.34E-37 272184000 425340 352390 413220 382060 438190 320889 452100 318916 385130 TRUE FALSE 398718.7287 378481.3223 423021.7735 391864.3064 403776.325 413524.4451 384311.8021 358733.3646 320849.315 1.242697771 1.179623283 1.318443749 1.221334403 1.258460923 1.28884316 1.197795302 1.118074273 1 18.29153638 1.071992409 1.787619142 1.002059098 1.249967067 0.828331289 0.037741856 0.128548317 0.821034174 0.034633619 0.009965943 11.80300005 -1.071992409 0.247907969 NALLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NALLHK 6 0 A0A1B0GVP4;A8MVM7 A0A1B0GVP4 Putative uncharacterized protein ENSP00000382790 0 69.39 0.09363 486950000 1751200 1287100 1418900 1427800 1536000 985050 1853700 1404400 1744600 FALSE TRUE 1641595.518 1382398.223 1452556.978 1464439.765 1415368.756 1269417.944 1575754.894 1579742.431 1453414.989 1.12947474 0.951137998 0.999409658 1.007585429 0.97382287 0.873403641 1.084174104 1.086917668 1 20.47101526 1.61376814 25 1.064162221 0.98553678 0.182236956 0.066938905 0.710864667 2999.195621 0.029278985 0.015694131 41.0930276 -1.61376814 -0.078625441 NALPPVLTTVNGQS(ph)PPEHSAPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 NALPPVLTTVNGQSPPEHSAPAK 23 0 Q6PKG0;A0A0B4J210;H0YBM7 Q6PKG0 LARP1 La-related protein 1 1 NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK 240.57 1.88E-37 12185320000 6840460 4777260 5650570 5797390 5600330 4076480 7200820 4636530 5894300 TRUE FALSE 6412327.819 5130973.301 5784604.189 5946160.842 5160502.672 5253293.6 6121123.89 5215410.977 4910503.251 1.305839237 1.044897649 1.178006386 1.210906609 1.050911161 1.06980758 1.246536979 1.062092969 1 22.22743946 -5 0.261846771 0.062602217 1.154992287 0.236936889 0.088310408 317.9576308 3.119031376 160.450384 0.108332619 1.00E-05 5 1.09239007 NALVSHLDGTTPVCEDIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NALVSHLDGTTPVCEDIGR 19 0 P31930 P31930 UQCRC1 "Cytochrome b-c1 complex subunit 1, mitochondrial" 0 ;; 201.52 5.96E-16 1076560000 339643 319853 230422 242904 385050 263949 268747 363700 424810 FALSE TRUE 318385.3509 343535.2489 235887.7187 249137.3279 354809.7262 340146.7914 228450.8823 409108.7456 353906.4666 0.899631346 0.970695032 0.666525596 0.703963763 1.002552255 0.961120588 0.645512032 1.155979854 1 18.4330086 2.733082421 24.93103254 0.90838639 0.813006062 0.140500186 0.154977821 1224.533783 5572784.69 0.050147327 0.048533816 540.8569577 -2.733082421 -0.095380328 ERVYFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 ERVYFFK 7 1 P04004 P04004 VTN Vitronectin;Vitronectin V65 subunit;Vitronectin V10 subunit;Somatomedin-B 0 ; 133.12 0.0030123 580470000 692920 736120 357560 645340 1028840 435180 1036330 1520730 2204800 FALSE TRUE 649551.3741 790623.0907 366041.4921 661900.517 948039.0565 560809.4014 880941.9373 1710596.488 1836804.636 0.353631171 0.430433959 0.199281668 0.360354337 0.516134943 0.305317937 0.47960568 0.931289291 1 20.80876676 1.269072477 2.943724801 1.007382628 0.357285683 0.903310655 0.080962354 0.071034653 1.032067008 0.072407454 0.021120223 18.58114519 -1.269072477 -0.650096945 NAPAAVDEGSIS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 358.65 2.75E-82 3166710000 2188510 1920370 2097610 2028150 2059450 1665860 2325780 1700720 2480730 TRUE FALSE 2051535.066 2062556.193 2147366.3 2080195.763 1897709.104 2146766.739 1977050.88 1913058.636 2066680.137 0.992671788 0.998004556 1.039041437 1.006539776 0.918240356 1.038751329 0.956631288 0.9256675 1 20.97888369 2.969506117 24.98760353 0.969617833 1.012926952 0.241276436 0.036143786 892.9482958 731709.1155 0.010271369 0.010905915 932.1935998 -2.969506117 0.043309118 NAPWTLTPEFLAEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NAPWTLTPEFLAEHR 15 0 P49585;C9JEJ2;C9J050;H7C1T3;C9J2E1;H7BZN1 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 0 ;;; 171.91 1.06E-06 565134000 647976 733732 623096 621080 783063 443099 705933 663551 961370 FALSE TRUE 607420.3388 788058.2807 637876.1314 637017.9643 721564.3907 571014.4882 600084.9002 746396.803 800911.1363 0.758411653 0.983952208 0.796438085 0.795366596 0.900929402 0.71295611 0.749252786 0.931934604 1 19.61128265 3.738416984 23.86742121 0.819211342 0.88816295 0 0.102930108 551.8240982 1165968.574 0.024272573 0.043202706 5475.41428 -3.738416984 0.068951608 NAS(ph)AS(ph)FQELEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NASASFQELEDK 12 0 Q99543;Q99543-2;H7C3L7;F2Z3H0;F2Z3N9 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 2 NAS(1)AS(1)FQELEDK 185.71 1.86E-05 154550000 2582600 1243000 1734400 1738800 1703400 1350000 2464200 1383400 1331300 TRUE FALSE 2420959.676 1335033.013 1775540.787 1783420.552 1569621.835 1739723.085 2094716.087 1556120.535 1109097.429 2.182819662 1.203711214 1.600888019 1.607992683 1.415224482 1.568593559 1.888667335 1.40305125 1 20.08095467 0.986842572 24.04200716 0.999999977 1.59759754 0.372722269 0.261740551 458.8671012 838470.7712 0.236997952 0.059249488 9.701582294 -0.986842572 0.597597562 NAS(ph)AS(ph)FQELEDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NASASFQELEDKK 13 1 Q99543;Q99543-2;H7C3L7;F2Z3H0;F2Z3N9 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 2 NAS(1)AS(1)FQELEDKK;NAS(1)AS(1)FQELEDKK 175.56 6.32E-05 235753000 1741330 610470 970520 1031930 960110 786120 1525570 733020 885700 TRUE FALSE 1632343.264 655669.834 993541.1927 1058411.071 884706.8335 1013060.082 1296824.941 824539.1606 737870.9482 2.212234087 0.888596896 1.346497237 1.434412174 1.198999413 1.372950222 1.7575227 1.117457142 1 19.49300899 1.996647522 24.58318038 1.423180934 1.331410988 0 0.392235314 775.7882813 5688760.425 0.138553683 0.100259283 99.23103525 -1.996647522 -0.091769946 NAS(ph)ASFQELEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NASASFQELEDK 12 0 Q99543;Q99543-2;H7C3L7;F2Z3H0;F2Z3N9 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 1 NAS(0.99)AS(0.01)FQELEDK 318.82 1.42E-46 298800000 519120 227020 322580 278390 236080 222290 392880 222260 233060 TRUE FALSE 486629.2059 243828.797 330231.7499 285533.9587 217539.2291 286461.5144 333971.2913 250009.6503 194160.7804 2.506320818 1.255808699 1.700815939 1.470605743 1.120407678 1.475382999 1.720075963 1.287642385 1 17.56689229 4.74446227 24.95046158 1.435604737 2.506321297 0.689437907 0.235085911 372.1081334 1573118.583 0.052818182 0.476210581 55521.63791 -4.74446227 1.07071656 NAS(ph)ASFQELEDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.725)AS(0.275)FQELEDKK;NAS(0.978)AS(0.022)FQELEDKK;NAS(0.985)AS(0.015)FQELEDKK;NAS(0.988)AS(0.012)FQELEDKK 235.45 6.70E-17 978050000 1813269 580550 1016605 869154 701403 627973 1229896 600192 765201 TRUE FALSE 1699779.73 623534.5261 1040719.351 891457.9631 646317.6377 809258.6108 1045484.513 675127.2924 637484.0097 2.666388026 0.978117908 1.632541891 1.398400508 1.013857019 1.269457113 1.640016842 1.059049768 1 19.28202963 4.746977149 24.90643357 1.30131382 2.666388746 0.755316657 0.251979169 513.3254315 1519011.202 0.057440129 0.662781646 55844.08112 -4.746977149 1.365074926 NAS(ph)ILLEELDLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NASILLEELDLEK 13 0 O75179-6;O75179-2;O75179;H0YM23;O75179-7;H0YLQ3 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 NAS(1)ILLEELDLEK 146.76 4.45E-05 5538700 26891 23181 23068 22989 25985 16856 32010 19471 37978 TRUE FALSE 25207.94031 24897.34536 23615.18385 23578.93666 23944.24292 21722.05357 27210.39767 21901.99721 31639.22645 0.796730614 0.786913846 0.746389419 0.745243778 0.75678977 0.686554508 0.860020952 0.692241868 1 14.94942671 -1.340831448 3.450108285 1.001238216 0.763735604 0.694469053 0.050173176 20372079.97 32125228.58 264222.1796 0.010987353 0.045621394 1.340831448 -0.237502612 NAS(ph)SPEKAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NASSPEKAK 9 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 NAS(0.5)S(0.5)PEKAK;NAS(0.5)S(0.5)PEKAK;NAS(0.5)S(0.5)PEKAK 140.24 0.00028822 538087000 1927540 875114 1234080 1253300 1345830 630452 1382600 902810 2178940 TRUE FALSE 1806898.712 939908.3511 1263352.96 1285461.8 1240133.941 812453.2579 1175291.965 1015527.816 1815260.838 0.99539343 0.517781429 0.695962219 0.708141647 0.683171209 0.447568328 0.647450736 0.55943906 1 20.79174544 -1.143320037 5.189372783 1.000012855 0.641312425 0.346061821 0.146861942 1.94E-05 3.20E-06 0.126362552 0.029782872 0.0718919 1.143320037 -0.35870043 NASAS(ph)FQELEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NASASFQELEDK 12 0 Q99543;Q99543-2;H7C3L7;F2Z3H0;F2Z3N9 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 1 NAS(0.019)AS(0.981)FQELEDK 274.61 8.83E-28 196040000 544010 272750 380550 322130 272620 278660 442930 244510 267270 TRUE FALSE 509961.3852 292944.6938 389576.8257 330396.4012 251209.5249 359104.6183 376516.7585 275037.6117 222660.9104 2.29030495 1.315653894 1.749641754 1.483854533 1.128215655 1.612786985 1.690987241 1.235230788 1 17.76448878 7.999998082 0.044176687 3.69E-08 4.144398166 0.403544528 0.285354411 787.7801166 2.63989646 63.65076314 233.7781239 99999558.48 -7.999998082 4.144398129 NASEMIDKLTLTFNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NASEMIDKLTLTFNR 15 1 P36542-2;P36542 P36542-2 ATP5C1 "ATP synthase subunit gamma, mitochondrial" 0 140.22 4.54E-06 69978000 120120 122880 107740 104510 156420 92009 101630 121840 203620 FALSE TRUE 112601.9036 131978.1631 110295.6437 107191.9035 144135.4042 118570.5047 86391.52499 137051.9922 169634.5066 0.663791265 0.778014837 0.6501958 0.631899168 0.849682102 0.698976329 0.509280374 0.807925197 1 17.37207014 0.992350199 24.68041272 1.000000014 0.683568325 0.569467279 0.089008231 191.1127144 616585.8094 0.0871337 0.021783425 9.825399065 -0.992350199 -0.316431689 NASGVVNSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NASGVVNSSPR 11 0 Q8N5G2;A0A3B3ITD2 Q8N5G2 TMEM57 Macoilin 1 NASGVVNS(0.271)S(0.729)PR 86.729 0.010013 0 109800 102340 92573 97033 112500 96837 130280 108140 113840 TRUE FALSE 102927.814 109917.3601 94768.87528 99523.03106 103664.7038 124792.2699 110745.7235 121641.517 94839.36857 1.085285737 1.15898452 0.999256709 1.049385214 1.093055609 1.315827718 1.167718903 1.282605725 1 16.53319844 2.415713867 12.85094567 1.205370619 1.074794795 0.275195115 0.091475878 1.033930322 214.3809414 0.028471255 0.023818033 260.4437064 -2.415713867 -0.130575824 NASYYGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NASYYGNR 8 0 Q99615;A0A6I8PUD4;A0A6I8PU73;A0A6I8PS32;A0A6I8PIK4;A0A6I8PR89;A0A6I8PLE7;A0A6I8PU89;A0A6I8PRZ0;K7EIH8;K7EK03;Q99615-2;K7ESP1;K7ER44;K7EPP7;A0A6I8PUC2;K7ELJ8;K7EJV7;K7EN19;K7EJL5;K7EJE9;A0A6I8PR93 Q99615 DNAJC7 DnaJ homolog subfamily C member 7 0 ; 134.48 0.0020353 148601000 132465 162409 113685 124370 191023 79352 126135 154835 152626 FALSE TRUE 124174.2521 174433.9313 116381.6619 127561.5448 176020.8241 102259.6342 107222.2277 174166.4906 127151.7346 0.976583233 1.371856482 0.915297477 1.003223001 1.38433679 0.804233104 0.843262013 1.369753163 1 16.95619162 2.215780346 24.9993722 0.968715583 1.128117275 0.067975536 0.214350136 524.5243614 575616.3583 0.076963112 0.056879254 164.3540256 -2.215780346 0.159401692 NATTGRIVSPGFPGNYSNNLTCHWLLEAPEGQRLHLHFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NATTGRIVSPGFPGNYSNNLTCHWLLEAPEGQRLHLHFEK 40 2 H0YGK0;H0YFX0;H0YF95;A0A0A0MSU7;C9JFF1;Q53EL9-4;Q53EL9-2;Q53EL9-3;Q53EL9 H0YGK0 SEZ6 Seizure protein 6 homolog 0 22.801 0.090307 4489400000 14904000 558430 2492800 2463900 3546100 1175000 3413300 941380 2013200 FALSE TRUE 13971185.24 599776.7382 2551930.393 2527127.845 3267603.61 1514203.425 2901507.353 1058913.365 1677183.914 8.330145028 0.357609403 1.521556683 1.506768473 1.948267917 0.902824915 1.729987587 0.631363893 1 20.67760947 4.742915257 24.9998824 1.24144901 8.33014784 0.953294971 0.495923457 84.13087161 482975.8533 0.113457008 0.89425115 55324.21463 -4.742915257 7.088698831 NAVEEYVYDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NAVEEYVYDFR 11 0 O95757;E9PDE8 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 ;;;; 246.14 1.25E-15 895489000 1007830 1072835 1105416 1100233 1258409 809402 1196868 999517 1220102 FALSE TRUE 944751.7193 1152268.82 1131636.99 1128466.841 1159578.633 1043063.218 1017408.755 1124308.898 1016459.094 0.929453753 1.133610616 1.113312868 1.110194053 1.140802065 1.026173334 1.000934283 1.106103437 1 19.95512073 2.214421514 24.92655796 1.029646786 1.09695839 0.119468909 0.066103569 354.1589366 365709.5666 0.023118776 0.017082694 163.8405941 -2.214421514 0.067311604 NAVEEYVYEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 NAVEEYVYEFR 11 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;;;;; 220.82 2.06E-11 1796352000 1322356 1394261 1371280 1331286 1506647 1123926 1604029 1243096 1444895 FALSE TRUE 1239592.098 1497493.535 1403807.409 1365449.053 1388321.022 1448385.191 1363519.743 1398299.272 1203732.69 1.029790176 1.244041594 1.166211918 1.134345743 1.153346614 1.203244875 1.13274297 1.161636037 1 20.19908362 -0.500753686 0.71537505 0.986085684 1.164671761 0.415745813 0.055737197 12.63469273 4.693166342 0.518137113 0.018103752 0.315679452 0.500753686 0.178586078 NAVEEYVYEMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NAVEEYVYEMR 11 0 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 117.42 0.0019927 238880000 245040 243540 233440 228150 242330 235790 306230 294730 277780 FALSE TRUE 229703.3838 261571.955 238977.307 234004.7153 223298.3793 303858.7453 260313.6544 331527.6893 231416.7235 0.992596301 1.130307054 1.032670861 1.011183253 0.964918939 1.313037108 1.124869674 1.432600394 1 17.8201336 2.241913519 24.99986129 1.220015307 1.040688463 0.384793432 0.119408345 88.49905164 659870.4135 0.037932396 0.030536479 174.5474544 -2.241913519 -0.179326844 NAYAVLYDIILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NAYAVLYDIILK 12 0 Q06323;H0YKK6 Q06323 PSME1 Proteasome activator complex subunit 1 0 ; 170.62 0.00017039 26296000 233246 219582 242020 260680 298480 201058 263340 226046 214363 FALSE TRUE 218647.5492 235840.0798 247760.8287 267369.4901 275038.5848 259100.1807 223854.6117 254268.3407 178584.4305 1.224337131 1.320608292 1.387359626 1.497160136 1.540103939 1.450855374 1.253494558 1.42379904 1 17.44624678 -0.990296581 6.580428936 0.999999913 1.382342822 0.596867187 0.099937852 1.31E-07 2.01E-08 0.099677829 0.023494284 0.102259442 0.990296581 0.382342908 NCASPSS(ph)AGQLILPECMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NCASPSSAGQLILPECMK 18 0 P53992;G5EA31;P53992-2 P53992 SEC24C Protein transport protein Sec24C 1 NCASPS(0.009)S(0.991)AGQLILPECMK;NCASPS(0.114)S(0.886)AGQLILPECMK 273.01 1.38E-27 46029000 234650 170483 204666 216492 189955 132640 245670 160654 143644 TRUE FALSE 219963.6754 183105.7387 209520.7742 222047.5512 175036.7005 170931.0148 208834.0642 180712.0055 119668.8884 1.838102436 1.530103113 1.750837473 1.855516118 1.462675077 1.428366362 1.745099056 1.510100143 1 16.8686886 -2.569762595 0.274790654 3.73E-10 1.705693289 0.679482265 0.143523302 28.35783087 0.901964755 17.09408186 0.173170863 0.002693007 2.569762595 1.705693289 NCCFEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NCCFEHR 7 0 Q9BTY7 Q9BTY7 HGH1 Protein HGH1 homolog 0 ; 90.37 0.017188 146349000 122096 142985 128932 135243 153446 109416 140957 135266 166140 FALSE TRUE 114454.2293 153571.7582 131990.3279 138713.5643 141394.9701 141002.623 119821.8064 152154.2579 138410.1607 0.826920717 1.109541073 0.95361733 1.002192062 1.021564959 1.018730289 0.865700942 1.09929977 1 17.07859033 NCEQCKPFYYQHPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NCEQCKPFYYQHPER 15 1 P07942;G3XAI2;E7EPA6 P07942 LAMB1 Laminin subunit beta-1 0 119.23 0.00013732 81338000 144140 135910 124850 133780 160050 94527 171030 127790 156680 FALSE TRUE 135118.5347 145972.9178 127811.501 137213.0213 147480.3186 121815.4104 145385.6393 143744.8628 130529.0958 1.035160275 1.118317084 0.97918016 1.051206403 1.129865473 0.933243348 1.113817868 1.101247671 1 16.9940119 1.619500307 25 1.080654091 1.04505617 0.039156672 0.064607322 2.296006695 4921.698992 0.027745553 0.015223575 41.63900152 -1.619500307 -0.035597921 NCGSFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NCGSFTR 7 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;; 126.28 0.0092303 775030000 656660 597910 599750 608057 582730 435660 674120 547342 629390 FALSE TRUE 615560.8228 642179.8785 613976.3532 623660.7721 536964.7364 561427.9697 573041.9642 615678.8535 524340.743 1.173970993 1.224737706 1.170949161 1.189418866 1.024075935 1.070731156 1.092880864 1.174196096 1 19.00014513 2.759858712 23.07798787 1.079108401 1.192460638 0.597661649 0.047660739 203.2343129 220217.8648 0.01365364 0.014463766 575.2527613 -2.759858712 0.113352237 NCHLNENIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NCHLNENIEK 10 0 Q13907;Q13907-2;Q9BXS1 Q13907 IDI1;IDI2 Isopentenyl-diphosphate Delta-isomerase 1;Isopentenyl-diphosphate delta-isomerase 2 0 ; 96.229 0.0068825 426100000 627530 549530 596360 597960 583300 466000 745880 533030 721130 FALSE TRUE 588254.0175 590217.773 610505.9408 613304.6659 537489.9709 600526.6351 634042.2184 599579.9688 600768.7443 0.979168812 0.982437549 1.016207895 1.020866468 0.89467033 0.999597001 1.055384829 0.998021243 1 19.19645023 1.992752627 24.99585761 1.024839655 0.982963476 0.174347836 0.037448375 521.7712018 1799565.348 0.014153315 0.010039433 98.34507746 -1.992752627 -0.041876179 NCLTNFHGMDLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NCLTNFHGMDLTR 13 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;D6RB09;D6RAS7;D6RED7 P61247 RPS3A 40S ribosomal protein S3a 0 ;;;;; 229.9 5.00E-12 4767290000 3058440 4302930 2580830 2704500 4699640 1592650 2839670 3792470 4186780 FALSE TRUE 2867017.7 4621523.414 2642048.506 2773902.049 4330549.232 2052422.2 2413887.846 4265968.228 3487979.37 0.821970945 1.32498588 0.757472515 0.795274786 1.241563889 0.588427276 0.692059095 1.223048583 1 21.73396008 3.893765723 6.62247056 0.86796989 1.099806757 0.066733387 0.244419983 0.401483013 26.16711783 0.059251907 0.108128633 7830.071409 -3.893765723 0.231836867 NCPAVTLTS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NCPAVTLTSPAK 12 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 NCPAVTLT(0.003)S(0.997)PAK 184.32 0.00011478 0 1073300 657060 766090 747340 748100 527740 1023400 613160 804740 TRUE FALSE 1006124.069 705709.4061 784262.0166 766518.0096 689347.2437 680089.9709 869950.6708 689714.3757 670423.6952 1.500728683 1.052631957 1.169800564 1.143333708 1.028226253 1.014418159 1.297613251 1.028773864 1 19.35471361 4.743763059 24.93149248 1.110478798 1.500728852 0.651991554 0.092998492 347.0739638 1663216.509 0.021274562 0.181437959 55432.32051 -4.743763059 0.390250054 NCPHIVVGTPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 119.39 0.00052319 554340000 387830 409810 401030 415260 417290 307220 444080 321920 431560 FALSE TRUE 363556.4126 440152.7588 410542.621 425916.2746 384517.7267 395909.4267 377494.3266 362112.4206 359529.848 1.011199528 1.224245389 1.141887449 1.184647887 1.069501541 1.101186533 1.049966585 1.007183194 1 18.45575202 1.884916589 0.926873853 0.998975758 1.153389696 0.429908546 0.057910358 0.440493841 0.699184565 0.045399554 0.0204918 76.72141236 -1.884916589 0.154413938 NCPS(ph)PVLIDCPHPNCNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NCPSPVLIDCPHPNCNK 17 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 NCPS(1)PVLIDCPHPNCNK 217.11 3.27E-15 238620000 497190 322850 371680 349030 339970 338700 505390 310520 363040 TRUE FALSE 466071.7654 346754.1499 380496.4251 357986.7007 313270.1276 436477.1917 429611.4613 349289.1055 302446.2787 1.541006778 1.146498318 1.258062843 1.183637313 1.035787674 1.443156099 1.420455438 1.154879826 1 18.20631938 2.214153591 24.99928253 1.309156343 1.222377055 0 0.180921943 765.800645 784378.6443 0.062697946 0.046326038 163.7395493 -2.214153591 -0.086779288 NCPS(ph)PVLIDCPHPNCNKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NCPSPVLIDCPHPNCNKK 18 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 NCPS(1)PVLIDCPHPNCNKK;NCPS(1)PVLIDCPHPNCNKK;NCPS(1)PVLIDCPHPNCNKK;NCPS(1)PVLIDCPHPNCNKK;NCPS(1)PVLIDCPHPNCNKK 248.03 8.92E-25 3752240000 4171243 2595519 3231337 3130871 3301316 2353425 4501908 2699905 4411482 TRUE FALSE 3910172.347 2787693.927 3307985.84 3211214.45 3042043.958 3032820.593 3826888.689 3036994.082 3675177.155 1.063941188 0.758519606 0.900088812 0.873757731 0.827727163 0.825217524 1.04128006 0.826353113 1 21.80938236 1.757015116 25 0.957741011 0.8625024 0.130067196 0.095193539 12.1637215 16494.49701 0.039427041 0.021864496 57.14985277 -1.757015116 -0.095238611 NCQHANAERPTVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NCQHANAERPTVAR 14 1 Q9Y5J1;F6VJE8 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 0 ;;; 215.87 3.81E-12 374082000 156645 207020 192801 202731 208494 174206 195985 180212 181221 FALSE TRUE 146840.8691 222347.9762 197374.3308 207933.4207 192119.7223 224496.4442 166598.8687 202711.8649 150974.0444 0.972623272 1.472756308 1.307339494 1.377279264 1.27253478 1.486987019 1.103493447 1.342693479 1 17.20394102 0.386900914 0.712720754 0.996144473 1.323788831 0.231237285 0.158593607 2.649220858 1.989028635 0.172254894 0.051482784 2.437254683 -0.386900914 0.327644357 NCS(ph)ASTSQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NCSASTSQGR 10 0 F5GYV5;F8WCT1;Q66PJ3-2;A0A0C4DH18;Q66PJ3-5;A0A0A0MTG7;Q66PJ3-6;Q66PJ3 F5GYV5;Q66PJ3 ARL6IP4 ADP-ribosylation factor-like protein 6-interacting protein 4 1 NCS(0.963)AS(0.033)T(0.004)SQGR;NCS(0.955)AS(0.04)T(0.005)S(0.001)QGR 130.77 0.0002809 120089000 311190 282410 289130 320480 347550 222900 344840 307990 307950 TRUE FALSE 291713.1734 303319.9302 295988.3001 328704.0594 320254.8249 287247.6115 293134.4433 346443.2295 256551.1556 1.137056556 1.182298047 1.153720393 1.281241781 1.248307864 1.11965043 1.142596465 1.350386548 1 17.968887 -0.917123521 7.618705011 1 1.192204056 0.422797199 0.073365421 1.99E-09 1.31E-10 0.066869346 0.015761256 0.121025387 0.917123521 0.192204056 NCSASTS(ph)QER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 NCSASTSQER 10 0 H7BZV4;A0A0C4DG62;Q66PJ3-4;Q66PJ3-3;F8WEP2 H7BZV4 ARL6IP4 ADP-ribosylation factor-like protein 6-interacting protein 4 1 NCSAST(0.002)S(0.998)QER;NCSAST(0.007)S(0.993)QER;NCSAS(0.002)T(0.006)S(0.991)QER;NCSAS(0.001)T(0.023)S(0.976)QER;NCSAST(0.004)S(0.996)QER;NCSAST(0.006)S(0.993)QER;NCSAST(0.043)S(0.957)QER 158.25 8.44E-06 1514715000 3367445 3305255 3171946 3379407 3370356 2373224 3929093 2841902 2918167 TRUE FALSE 3156682.629 3549979.519 3247186.057 3466128.305 3105661.835 3058335.243 3339961.981 3196719.72 2431106.076 1.298455325 1.46023226 1.335682589 1.425741287 1.277468666 1.258001563 1.373844611 1.314923998 1 21.21318141 -3.714846448 0.239282148 8.12E-09 1.394042524 0.759569049 0.061262687 38.97287377 0.679083163 19.11540679 0.094362292 0.000192821 3.714846448 1.394042516 NCSETQYESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NCSETQYESK 10 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;; 202.56 5.15E-07 454134000 531493 347395 432681 440050 423446 309837 513800 367870 457485 FALSE TRUE 498227.8019 373116.4873 442944.3976 451342.428 390190.2593 399281.9121 436760.4599 413799.3793 381127.798 1.307246033 0.978979988 1.162193889 1.184228572 1.023778012 1.047632616 1.145968523 1.085723428 1 18.53991531 2.735814069 24.99827151 1.074759889 1.128970392 0.187428357 0.089784648 680.2555268 6191445.392 0.02755731 0.02712972 544.2695892 -2.735814069 0.054210503 NCVAIAADRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NCVAIAADRR 10 1 P49720;A0A087WXQ8;A0A087WY10;A0A087WUL2 P49720 PSMB3 Proteasome subunit beta type-3 0 ;;; 195.51 5.62E-07 1814490000 971360 1457890 737770 717030 1490480 467461 788030 1275670 1159940 FALSE TRUE 910564.3115 1565833.693 755270.2528 735430.2037 1373423.713 602409.4021 669872.2172 1434940.208 966338.5205 0.94228295 1.620378014 0.781579371 0.761048213 1.421265617 0.623393758 0.693206576 1.484924979 1 19.88216915 3.897854259 6.005382142 0.930421822 1.311994656 0.126407811 0.331130226 0.3126537 18.3815864 0.079608998 0.146319347 7904.13335 -3.897854259 0.381572834 NCVVLSDIHIDIMDYIQPATCTDAEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NCVVLSDIHIDIMDYIQPATCTDAEFR 27 0 P53618 P53618 COPB1 Coatomer subunit beta 0 ;;; 219.65 2.96E-34 297760900 388487 377971 404923 420245 377938 311629 497161 352172 329383 FALSE TRUE 364172.2921 405956.3661 414527.9648 431029.1982 348256.274 401591.2334 422616.3235 396141.4494 274406.8494 1.327125372 1.479395893 1.510632718 1.570766907 1.269123838 1.463488372 1.540108508 1.443628139 1 18.06595697 0.93961667 22.1059391 1 1.464148037 0.701450729 0.092099574 3797.435597 1390218.222 0.083995369 0.020998842 8.701951728 -0.93961667 0.464148037 NCWQNYLDFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NCWQNYLDFHR 11 0 P14854;A0A494C160 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 ;;;; 188.06 3.32E-06 1980030000 1872349 2569190 1280466 1157423 3119610 843003 1645591 2434625 2518260 FALSE TRUE 1755162.018 2759415.501 1310839.258 1187124.434 2874608.415 1086364.281 1398849.906 2738593.291 2097946.137 0.836609666 1.315293778 0.624820263 0.565850768 1.370201247 0.51782277 0.666771125 1.305368733 1 21.00054621 5.069542738 14.91403498 0.892639243 0.226802905 0 0.326359685 11098940.7 51435250.54 0.074572327 227420288.5 117366.1175 -5.069542738 -0.665836338 NDEELNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 147.04 0.0050682 18214340000 17111950 10476490 11828560 11524320 11222650 7846120 14804840 9106060 12636360 FALSE TRUE 16040943.6 11252180.22 12109139.03 11820053.56 10341268.34 10111167.47 12584991.68 10242971.64 10527269.88 1.523751531 1.068860241 1.150263949 1.122803319 0.982331455 0.960473854 1.195465854 0.972994114 1 23.327628 4.738881111 25 1.073017666 1.523751665 0.762674898 0.081433567 12.74512081 993759.7551 0.018652937 0.109438967 54812.68933 -4.738881111 0.450734 NDEELNKLLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 171.57 1.31E-05 2005150000 2065410 1920310 1747090 1984200 2511720 1057580 2637440 1410060 5024280 FALSE TRUE 1936139.675 2062491.75 1788531.8 2035117.931 2314459.643 1362886.178 2241980.357 1586109.095 4185695.21 0.462561075 0.492747715 0.427296234 0.486207865 0.552945097 0.32560569 0.535629147 0.37893564 1 21.99703583 -1.503276443 3.325757135 1.012001158 0.461459767 0.86179885 0.06822918 50769634.96 62931770.95 5528599.471 0.0140937 0.031385103 1.503276443 -0.550541391 NDEELNKLLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NDEELNKLLGR 11 1 Q7L7L0;P04908 Q7L7L0 HIST3H2A;HIST1H2AB Histone H2A type 3;Histone H2A type 1-B/E 0 ;;; 197.31 5.24E-08 1714250000 2003850 2673830 2172540 2585750 3950270 1158840 3214020 1753570 8834300 FALSE TRUE 1878432.605 2871803.155 2224073.675 2652104.723 3640031.729 1493378.296 2732107.538 1972507.075 7359798.258 0.255228817 0.390201342 0.302192206 0.360350193 0.494583085 0.202910222 0.371220439 0.268011025 1 22.81123479 -1.631626717 2.892784905 1.057054836 0.336072842 0.869154888 0.081600985 20312903.36 20021080.47 8691818.822 0.017205203 0.023354646 1.631626717 -0.720981995 NDEWAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NDEWAR 6 0 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 108.24 0.07115 633280000 635040 883980 863530 971790 1021500 1000800 986490 865670 901470 FALSE TRUE 595293.98 949430.799 884013.3394 996727.7766 941275.5105 1289714.713 838574.9826 973750.8051 751008.8333 0.792659092 1.264207233 1.177101121 1.327185157 1.253348122 1.717309646 1.116598028 1.296590349 1 19.51847035 4.740401566 5.313204024 1.279563883 0.772244964 0.393342449 0.185620785 0.153223548 15.44997595 0.040517261 0.283770315 55004.92364 -4.740401566 -0.507318919 NDHQEDFWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NDHQEDFWK 9 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ;;;;; 155.11 7.41E-05 4268900000 7468840 5721690 6273440 6372190 7200190 4123200 7843670 5983410 8204000 FALSE TRUE 7001378.637 6145329.881 6422248.959 6535711.183 6634716.122 5313500.905 6667584.501 6730451.91 6834699.4 1.024387208 0.89913682 0.939653463 0.956254372 0.970740004 0.777430081 0.975549049 0.984747319 1 22.70444646 1.508158025 19.29212558 0.988296672 0.924989466 0.164219627 0.063031956 0.421706096 253.9811061 0.031422368 0.014551641 32.22241039 -1.508158025 -0.063307205 NDIASHPPVEGSYAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NDIASHPPVEGSYAPR 16 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 202.03 3.18E-12 7029700000 3951540 3709710 3838950 3746490 3829990 2842260 4528660 3273130 4265160 FALSE TRUE 3704220.165 3984380.788 3930011.707 3842631.276 3529198.035 3662774.322 3849629.475 3681787.486 3553277.242 1.042479917 1.121325615 1.106024506 1.081433002 0.993223381 1.0308158 1.083402508 1.036166681 1 21.76071883 2.961213717 10.53398113 1.037984688 1.098324371 0.436271557 0.032095151 0.686102628 184.6174865 0.00973567 0.010400929 914.5631878 -2.961213717 0.060339683 NDIHTLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NDIHTLLK 8 0 O43324;H0YAL7;D6RBD7;C9J1V9;O43324-2;H0YAH9 O43324 EEF1E1;EEF1E1-BLOC1S5 Eukaryotic translation elongation factor 1 epsilon-1 0 ; 147.2 0.00054111 643860000 1754730 1199200 1520950 1464900 1317600 1060180 1768880 1304530 1149840 FALSE TRUE 1644904.582 1287990.016 1557027.652 1502491.814 1214121.011 1366236.755 1503652.865 1467403.442 957924.2757 1.717155127 1.344563499 1.625418305 1.568487042 1.267449883 1.426247137 1.569699092 1.531857454 1 19.86955209 -1.325330855 3.451252927 0.997665848 1.49894815 0.591270963 0.132180376 14316381.1 24900210.02 355840.3498 0.029531352 0.047279094 1.325330855 0.501282302 NDKS(ph)EEEQSSSSVK ddPTM_SK-BR-3_Pertuzumab_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(1)EEEQSSSSVK;NDKS(1)EEEQSSSSVK;NDKS(0.443)EEEQS(0.425)S(0.123)S(0.008)S(0.001)VK;NDKS(0.903)EEEQS(0.089)S(0.008)S(0.001)SVK;NDKS(0.999)EEEQS(0.001)SSSVK 274.17 1.31E-32 11606010000 9600295 3172104 4999527 4514298 4740028 3129658 6841375 3755375 6290769 TRUE FALSE 8999429.673 3406969.881 5118118.141 4630142.529 4367765.321 4033139.459 5815574.331 4224241.835 5240799.014 1.717186568 0.650085964 0.976591189 0.88348027 0.833415918 0.769565757 1.109673223 0.806030116 1 22.32135535 4.748474747 24.87247613 0.881232374 1.717187055 0.80726134 0.128767355 548.6417898 1376397.731 0.029964593 0.402259663 56036.98329 -4.748474747 0.835954681 NDKS(ph)EEEQSSSSVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.997)EEEQS(0.001)S(0.001)S(0.001)S(0.001)VKK;NDKS(1)EEEQSSSSVKK;NDKS(1)EEEQSSSSVKK;NDKS(1)EEEQSSSSVKK 139.98 2.62E-06 1073560000 1298984 380169 658259 632184 721036 408554 1041340 493043 1150413 TRUE FALSE 1217682.91 408317.1083 673873.2143 648406.9117 664408.7411 526496.9075 885200.7343 554600.5039 958401.6383 1.270535088 0.42603966 0.703121935 0.676550296 0.693246667 0.549348923 0.923621892 0.578672325 1 19.87027085 -1.576831082 0.527588838 1.179527189 0.69936674 0.104478715 0.23359958 98.09958822 11.09838785 23.39080258 0.094471389 0.026495305 1.576831082 -0.480160449 NDKSEEEQS(ph)SSS(ph)VKKDETNVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NDKSEEEQSSSSVKKDETNVK 21 3 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 2 NDKSEEEQS(0.971)S(0.064)S(0.227)S(0.738)VKKDETNVK 108.44 0.00045849 218850000 479120 80997 182530 154310 196210 98020 209930 98714 281580 TRUE FALSE 449132.7345 86994.10216 186859.6978 158269.8558 180800.4581 126316.7828 178452.9454 111038.6602 234582.4789 1.914604776 0.370846546 0.796562892 0.674687456 0.770733001 0.538474925 0.760725806 0.473345924 1 17.83973574 4.746724312 24.97825765 0.660072315 1.914605401 0.82511021 0.179528819 365.8676762 1119410.795 0.037852912 0.426863496 55811.57932 -4.746724312 1.254533086 NDKSEEEQSSS(ph)SVKKDETNVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NDKSEEEQSSSSVKKDETNVK 21 3 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 NDKSEEEQS(0.001)S(0.054)S(0.551)S(0.394)VKKDETNVK;NDKSEEEQS(0.001)S(0.011)S(0.494)S(0.494)VKKDETNVK 144.4 9.13E-08 2154200000 1694680 316150 682140 543430 700350 359990 921950 464310 1152190 TRUE FALSE 1588613.004 339558.075 698320.6829 557375.3338 645347.3361 463913.2691 783712.1565 522280.1256 959882.0456 1.655008562 0.353749793 0.727506766 0.580670653 0.672319416 0.483302372 0.816467148 0.544108652 1 19.87249761 -0.565600214 7.933037922 0.999774105 0.687841437 0.043299488 0.355804142 0 0 0.29917717 0.070516735 0.271894101 0.565600214 -0.311932667 NDKSEEEQSSSSVK ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;; 245.39 1.08E-17 6073265000 7020672 3008311 4132280 3877204 4492773 2686930 5416890 3482468 5953257 FALSE TRUE 6581260.672 3231049.477 4230299.633 3976699.619 4139928.732 3462603.072 4604677.632 3917261.796 4959619.947 1.326968748 0.651471183 0.852948346 0.801815393 0.83472701 0.698158954 0.928433566 0.789831043 1 22.24179814 -0.72004022 5.418520212 1.000000019 0.838088502 0.041584065 0.184224821 20784532.53 3835831.613 4.59222593 0.037743282 0.190528426 0.72004022 -0.161911517 NDKSEEEQSSSSVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NDKSEEEQSSSSVKK 15 2 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 185.61 2.34E-07 172150000 426090 165410 257160 235620 297390 165860 390430 212380 467460 FALSE TRUE 399421.7875 177657.1285 263259.9566 241666.4081 274034.189 213741.0895 331888.6461 238896.1105 389437.9061 1.025636645 0.456188588 0.675999826 0.620551837 0.703665937 0.548845108 0.852224811 0.613438257 1 18.57103379 -0.221832118 0.517189525 1.040451306 0.651696563 0.247610182 0.161399671 7.28674532 2.019227357 0.732226531 0.068939834 0.600022977 0.221832118 -0.388754743 NDLAVVDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NDLAVVDVR 9 0 P19338 P19338 NCL Nucleolin 0 ;;;; 155.06 0.00017267 2422730000 4752480 4494790 4692030 4722050 4674510 3531580 5555810 3948330 4944020 FALSE TRUE 4455030.76 4827588.928 4803327.167 4843225.797 4307392.841 4551089.816 4722767.868 4441287.692 4118831.122 1.081625012 1.172077413 1.166186965 1.175873847 1.045780396 1.104946933 1.146628188 1.078288369 1 21.97380354 -0.09965447 0.325091082 0.963801793 1.15326259 0.468788685 0.042577277 4.866850376 0.703478216 0.26489272 0.043902401 0.794960464 0.09965447 0.189460797 NDLGHPFCNNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NDLGHPFCNNLR 12 0 P35573-2;P35573-3;P35573 P35573-2 AGL "Glycogen debranching enzyme;4-alpha-glucanotransferase;Amylo-alpha-1,6-glucosidase" 0 72.29 0.034602 0 135240 170970 129750 141280 203110 111280 145850 162900 199110 FALSE TRUE 126775.5698 183628.7967 132827.7313 144905.484 187158.5599 143404.7295 123981.1465 183238.4236 165877.2547 0.764273378 1.107016131 0.800759161 0.873570546 1.128295499 0.864523167 0.747427046 1.104662745 1 17.33975655 3.94083952 24.94803572 0.909984999 0.959346866 0 0.147297748 1476.885459 1015535.556 0.035936881 0.064788799 8726.488481 -3.94083952 0.049361867 NDLQDTEIS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NDLQDTEISPR 11 0 Q9NS91 Q9NS91 RAD18 E3 ubiquitin-protein ligase RAD18 1 NDLQDTEIS(1)PR;NDLQDTEIS(1)PR 153.18 3.42E-05 872440000 1219640 985340 1048040 1031740 1053810 854730 1207100 950600 953430 TRUE FALSE 1143304.91 1058295.599 1072900.004 1058216.195 971048.0135 1101476.676 1026106.561 1069284.503 794296.3736 1.439393339 1.332368665 1.350755259 1.332268698 1.222526057 1.3867326 1.291843442 1.34620343 1 19.59931789 -3.553701598 0.292494459 2.50E-11 1.356894089 0.791594957 0.054828402 41.07845226 0.843695366 24.91130972 0.053059335 0.000279446 3.553701598 1.356894089 NDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK 41 0 P68104;A0A087WVQ9;A0A087WV01 P68104 EEF1A1 Elongation factor 1-alpha 1;Elongation factor 1-alpha 0 ;; 338.03 9.02E-134 3168240000 932180 730500 768730 794000 804810 598100 1006710 706090 830100 FALSE TRUE 873836.5178 784586.9801 786964.6386 814375.3842 741603.469 770761.7607 855763.1813 794246.8908 691550.9473 1.263589503 1.134532435 1.137970589 1.177607214 1.072377201 1.114540821 1.237455005 1.148500908 1 19.39947601 -2.414866537 1.930703325 1.20E-05 1.158129559 0.449337059 0.0558799 1179335.596 74188.10623 5176078.982 0.014438115 0.0038471 2.414866537 1.158117581 NDPYHPDHFNCANCGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NDPYHPDHFNCANCGK 16 0 P48059;P48059-4;P48059-2;P48059-5;P48059-3;A0A0J9YXC7 P48059 LIMS1 LIM and senescent cell antigen-like-containing domain protein 1 0 ; 123.97 4.92E-05 588920000 609430 393060 477510 462350 463100 548180 860270 424620 569490 FALSE TRUE 571286.8642 422162.5714 488836.7627 474214.6838 426729.9941 706430.667 731280.4999 477634.7417 474438.44 1.204132752 0.889815276 1.030348137 0.999528377 0.899442284 1.48898278 1.541360139 1.006737021 1 18.85586138 2.244659832 24.99995142 1.336366549 0.992264484 0.253151982 0.197938104 134.8418387 552701.7899 0.065451266 0.053466008 175.6547232 -2.244659832 -0.344102065 NDQDTWDYTNPNLSGQGDPGSNPNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NDQDTWDYTNPNLSGQGDPGSNPNKR 26 1 A0A3B3ITJ4;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;;; 218.61 5.51E-34 6111380000 1207633 876299 973978 994336 1007695 691259 1185411 900607 1154409 FALSE TRUE 1132049.406 941181.0897 997081.2181 1019852.345 928554.6995 890814.2516 1007669.625 1013049.766 961730.6801 1.177096072 0.978632697 1.036757211 1.06043445 0.965503876 0.926261655 1.047766954 1.053361182 1 19.87527342 4.744993676 24.73298251 1.009071743 1.17709616 0.602824289 0.042983189 464.687011 1786511.163 0.010186495 0.09822662 55589.6163 -4.744993676 0.168024417 NDRGDQVPNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NDRGDQVPNR 10 1 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6;F5H3E1 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 106.35 0.0022142 438230000 194730 127760 169040 158120 161810 102450 166350 124620 195250 FALSE TRUE 182542.1969 137219.4833 173049.7086 162177.6269 149102.0953 132025.6519 141407.3618 140179.0813 162661.5136 1.122221187 0.843589121 1.063863878 0.997025192 0.916640279 0.811658818 0.869335091 0.861783947 1 17.31151342 2.567739317 4.078690514 0.871075319 0.988395713 0.297999694 0.085054221 0.278175954 8.332095561 0.026717032 0.024646211 369.6062592 -2.567739317 0.117320394 NDRGPGGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NDRGPGGPR 9 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 61.161 0.082978 27969000 15838 19757 16696 17521 20921 13117 14067 14837 21821 FALSE TRUE 14846.72785 21219.82884 17092.037 17970.61852 19277.94905 16903.66496 11957.78394 16689.43211 18178.93413 0.816699579 1.167275743 0.940211174 0.988540824 1.06045541 0.929849068 0.657782456 0.918064392 1 14.14997999 1.992321374 21.44883541 0.813897452 1.009202378 0.165952899 0.124594844 56.47038177 157739.4467 0.044087228 0.031045544 98.24746975 -1.992321374 0.195304926 NDS(ph)GEENVPLDLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NDSGEENVPLDLTR 14 0 Q6R327-3;Q6R327;Q6R327-4 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 NDS(1)GEENVPLDLTR;NDS(1)GEENVPLDLTR 175.48 2.49E-06 140089000 230616 168944 181416 185643 176863 146003 212475 137677 182436 TRUE FALSE 216182.1562 181452.7895 185719.2732 190406.9137 162972.8934 188151.6959 180616.3463 154866.2765 151986.253 1.422379669 1.193876327 1.221947837 1.252790367 1.072287067 1.237952066 1.188372913 1.018949237 1 17.21358131 7.999999987 0.073802684 0.798727316 2.145853568 0.618631514 0.07684359 166.0874819 0.90021542 2.71078377 23.04925995 99999997.05 -7.999999987 1.347126252 NDS(ph)PTQIPVSSDVCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NDSPTQIPVSSDVCR 15 0 Q8TC07-2;Q8TC07-3;Q8TC07 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 NDS(0.994)PT(0.006)QIPVSSDVCR;NDS(0.999)PT(0.001)QIPVSSDVCR 346.37 3.30E-82 1617220000 1106160 782550 843220 826690 883980 715670 1186660 732570 938970 TRUE FALSE 1036927.42 840490.8162 863221.5766 847904.265 814555.7766 922272.3111 1008731.349 824032.9771 782249.841 1.325570637 1.074453163 1.103511348 1.083930249 1.041298744 1.178999678 1.289525797 1.053414055 1 19.57726993 NDS(ph)WGSFDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 NDSWGSFDLR 10 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 NDS(0.999)WGS(0.001)FDLR;NDS(0.998)WGS(0.002)FDLR;NDS(1)WGSFDLR;NDS(0.999)WGS(0.001)FDLR;NDS(0.998)WGS(0.002)FDLR;NDS(0.98)WGS(0.02)FDLR;NDS(1)WGSFDLR 251.85 5.05E-17 5014490000 4551530 4259270 4094340 4020450 4478180 2786260 4380100 3468550 4455020 TRUE FALSE 4266657.862 4574630.783 4191459.678 4123621.554 4126481.807 3590608.031 3723344.668 3901606.103 3711448.381 1.14959375 1.232572924 1.129332608 1.111054534 1.111825191 0.967441188 1.003205295 1.051235448 1 21.82355087 2.824651712 0.997994059 1.001462122 1.190713823 0.779880919 0.037722281 0.211351724 0.448829647 0.019105417 0.019521705 667.8081452 -2.824651712 0.189251701 NDSWGSFDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NDSWGSFDLR 10 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 0 ; 103.31 0.0065865 211283000 377000 371750 331990 362640 426520 269104 407820 347800 449400 FALSE TRUE 353404.243 399274.7568 339864.9596 371945.9563 393022.8397 346789.9563 346671.177 391223.5956 374392.2368 0.943941162 1.0664611 0.907777796 0.993465996 1.049762258 0.926274431 0.925957173 1.044956485 1 18.51419099 3.983621361 24.98054073 0.970964732 1.010598417 0.02349076 0.056384104 717.5761041 2757682.142 0.013378335 0.027870866 9629.890778 -3.983621361 0.039633686 NDSYTLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NDSYTLHK 8 0 P62195-2;P62195;J3QSA9;J3KRP2;J3QQM1;J3QLH6;J3QRW1;J3QSE0 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ; 79.986 0.026619 829970000 1303450 1289280 1100450 1386250 1725980 762440 1303160 1116130 2267500 FALSE TRUE 1221869.391 1384739.633 1126553.194 1421823.522 1590428.493 982544.0508 1107763.256 1255481.287 1889039.601 0.646820422 0.733038964 0.596362931 0.752670045 0.841924379 0.520128879 0.586416111 0.664613535 1 20.84922152 -0.217882694 9.22449369 1 0.662637764 0.563105742 0.091876003 0 0 0.089302999 0.021048919 0.605504403 0.217882694 -0.337362236 NDTKEDVFVHQTAIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 2310790000 4688870 3610620 4469890 4447290 4792200 2911990 5858610 3903670 5568300 FALSE TRUE 4395401.997 3877954.062 4575917.902 4561414.991 4415839.943 3752634.241 4980165.819 4391051.793 4638914.757 0.947506524 0.835961483 0.986419915 0.983293557 0.951912284 0.808946583 1.073562693 0.946568761 1 22.14535591 4.664118505 0.188281166 1.013674253 0.794527675 0.105942008 0.07262693 29.60701103 1.049947662 0.180459433 1.565676323 46144.34706 -4.664118505 -0.219146578 NDTKEDVFVHQTAIKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NDTKEDVFVHQTAIKK 16 2 P67809;P16989;P16989-3;P16989-2 P67809;P16989;P16989-2 YBX1;YBX3 Nuclease-sensitive element-binding protein 1;Y-box-binding protein 3 0 145.55 7.26E-07 486700000 866430 749790 885040 971120 1121300 562850 1344200 763080 1807600 FALSE TRUE 812201.6929 805305.2318 906033.5667 996040.5833 1033237.621 725335.6579 1142649.689 858352.2177 1505899.882 0.539346408 0.53476678 0.601655912 0.6614255 0.686126371 0.481662603 0.758781976 0.569992884 1 20.52219443 -4.999999997 0.194959357 2.744944328 0.537801126 0.71600056 0.079111761 68.54382263 0.675023333 46.45921949 0.181923437 1.00E-05 4.999999997 -2.207143202 NDTSGEYKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NDTSGEYKK 9 1 E5RK69;P08133;P08133-2 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ; 99.752 0.0082166 1123190000 2315590 1294740 1704520 1448870 2298690 819610 2546960 2018390 4168460 FALSE TRUE 2170661.355 1390603.897 1744952.019 1486050.457 2118160.16 1056218.102 2165066.993 2270390.435 3472717.097 0.625061384 0.40043685 0.502474567 0.427921543 0.609943195 0.304147465 0.623450437 0.653779266 1 21.72763346 0.883734325 1.352921878 0.997146522 0.476523972 0.721025248 0.100144895 0.259441603 0.929603601 0.082029143 0.024625957 7.651284054 -0.883734325 -0.520622551 NDWLDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NDWLDLR 7 0 E9PS41;Q6RFH5-2;Q6RFH5 E9PS41 WDR74 WD repeat-containing protein 74 0 79.906 0.072942 35427000 133040 122440 127860 114080 145290 89378 140760 118830 162150 FALSE TRUE 124713.2639 131505.585 130892.8996 117007.4859 133879.5095 115179.9777 119654.3448 133666.1871 135086.1175 0.92321303 0.973494445 0.968958928 0.866169582 0.991067861 0.852641114 0.885763445 0.989488702 1 17.04351989 NDYEARPQYYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NDYEARPQYYK 11 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 124.6 0.00031534 1188340000 2294580 1932260 2065000 1987730 2483580 1337670 2508360 2028650 2604790 FALSE TRUE 2150966.334 2075326.541 2113982.775 2038738.517 2288529.645 1723833.614 2132254.704 2281931.418 2170033.721 0.991213322 0.956356816 0.974170472 0.939496238 1.054605568 0.794381026 0.982590585 1.051564958 1 21.04928603 1.472224946 25 1.022882655 0.952146318 0.17662284 0.065763147 1.311405948 6699.76156 0.03235715 0.01497945 29.66367443 -1.472224946 -0.070736337 NDYEMTFNNETSVMPCEDDHHLPTVQFDFTGIDDLENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NDYEMTFNNETSVMPCEDDHHLPTVQFDFTGIDDLENK 38 0 P27694;I3L4R8 P27694 RPA1 "Replication protein A 70 kDa DNA-binding subunit;Replication protein A 70 kDa DNA-binding subunit, N-terminally processed" 0 117.09 2.45E-06 20496000 13578 13428 13036 10727 11591 11485 15760 10719 16340 FALSE TRUE 12728.17722 14422.22309 13345.22008 11002.27298 10680.68962 14800.53306 13396.93431 12057.29075 13612.74844 0.935018911 1.059464454 0.980347219 0.808233035 0.784609343 1.087255312 0.984146175 0.885735221 1 13.73267076 3.466986296 24.99528585 0.929765638 1.008573786 0.099510271 0.09337647 435.6793275 1074489.271 0.026548241 0.036065419 2930.800762 -3.466986296 0.078808148 NECDPALALLSDYVLHNSNTMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NECDPALALLSDYVLHNSNTMR 22 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 119.32 5.33E-05 28194000 59003 71418 87569 79766 85127 68924 100973 74595 86948 FALSE TRUE 55310.10755 76705.86303 89646.17803 81812.9306 78441.46881 88821.23991 85833.03604 83908.34995 72435.81709 0.763574013 1.058949372 1.237594627 1.1294541 1.082909974 1.226206088 1.184952962 1.158382045 1 16.14441562 4.74651868 2.168154555 1.158528186 0.652716976 0.74648732 0.069431039 0.298349489 1.572447721 0.01583729 0.295133768 55785.15965 -4.74651868 -0.50581121 NECQFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NECQFK 6 0 Q9Y3Q7-2;Q9Y3Q7 Q9Y3Q7-2 ADAM18 Disintegrin and metalloproteinase domain-containing protein 18 0 98.03 0.093984 93473000 71595 329940 259830 256070 301860 357170 234450 298290 228060 FALSE TRUE 67113.99675 354369.1009 265993.2903 262641.1897 278153.1332 460279.1808 199296.399 335532.1631 189995.3127 0.353240276 1.865146544 1.399999224 1.382356154 1.463999976 2.42258177 1.048954294 1.766002321 1 17.5356043 4.747557231 24.82855608 1.56117724 0.353239588 0.452497134 0.411104144 935.6532092 2582123.688 0.087558443 1.072316843 55918.72124 -4.747557231 -1.207937652 NEDEDS(ph)PNKLYTLVTYVPVTTFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NEDEDSPNKLYTLVTYVPVTTFK 23 1 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 1 NEDEDS(1)PNKLYTLVTYVPVTTFK;NEDEDS(1)PNKLYTLVTYVPVTTFK 197.36 1.80E-24 267410000 2548210 1043670 1505740 1404710 1293770 1038550 2023470 1105650 1148650 TRUE FALSE 2388722.085 1120944.413 1541456.864 1440757.237 1192162.523 1338362.526 1720069.458 1243692.836 956932.8944 2.496227373 1.171392915 1.610830679 1.505599029 1.245816222 1.398596007 1.797481797 1.299665675 1 19.86805823 7.999999996 0.039730858 4.40E-11 3.958376915 0.29736587 0.349678593 1356.529949 4.103464661 112.3946643 362.7829677 99999999.08 -7.999999996 3.958376915 NEDEDSPNKLYTLVTYVPVTTFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NEDEDSPNKLYTLVTYVPVTTFK 23 1 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 0 142.32 1.58E-07 68531000 307140 206890 236880 232230 256730 179160 336190 199130 336080 FALSE TRUE 287916.6557 222208.3509 242498.9055 238189.415 236567.4614 230880.5836 285781.4305 223991.8188 279986.0768 1.028324904 0.793640717 0.866110587 0.850718784 0.844925805 0.824614517 1.020698721 0.800010563 1 18.09499556 1.760998842 25 0.940545588 0.857688534 0.131951144 0.08452786 18.87327072 21044.55756 0.034799632 0.019299012 57.6764926 -1.760998842 -0.082857054 NEDEEEEEEEKDEAEDLLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NEDEEEEEEEKDEAEDLLGR 20 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 300.51 7.23E-55 866220000 1561720 809490 1015860 920290 984830 693140 1392440 828910 1215710 FALSE TRUE 1463974.733 869425.4819 1039956.679 943906.1994 907485.4244 893238.2658 1183656.549 932401.2382 1012800.147 1.445472473 0.858437357 1.026813317 0.93197676 0.896016284 0.881949186 1.168697054 0.920617202 1 19.94991809 4.746736246 24.91825821 0.968338105 1.445472719 0.740866451 0.090022622 539.7756744 1645127.596 0.021743275 0.246403754 55813.11304 -4.746736246 0.477134614 NEDEMMVAIFEYIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NEDEMMVAIFEYIDR 15 0 Q9H0D6 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 73.022 0.047381 0 33330 29501 45221 34063 38651 40296 40852 20052 43253 FALSE TRUE 31243.9348 31685.28474 46293.66347 34937.11425 35615.50637 51928.80105 34726.62185 22555.53634 36033.79487 0.867073116 0.879321338 1.284729062 0.96956522 0.988391772 1.441113855 0.963723692 0.625955063 1 15.13706298 1.471480704 25 0.806930781 1.077062191 0.226215188 0.196723714 1.286519899 5705.795704 0.100827318 0.046677038 29.61288389 -1.471480704 0.27013141 NEEDAAELVALAQAVNAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NEEDAAELVALAQAVNAR 18 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 253.06 3.94E-30 182875000 271832 263449 281953 285750 318158 231164 349764 253988 324023 FALSE TRUE 254818.5204 282955.0381 288641.0583 293082.8288 293171.1541 297897.2942 297320.1352 285698.9609 269941.468 0.943976938 1.048208859 1.069272759 1.085727328 1.08605453 1.103562548 1.101424458 1.058373739 1 18.04228709 5.842137604 0.995726548 1.080722707 3.85E-08 0.62513396 0.030294582 8.079173994 1.171518478 0.008078769 15.51102914 695244.5681 -5.842137604 -1.080722669 NEEDEGHS(ph)NSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 2 NEEDEGHS(1)NS(0.005)S(0.995)PR;NEEDEGHS(1)NS(0.049)S(0.951)PR 211.43 3.21E-08 99520000 491510 354080 413390 400450 386710 365780 499780 371410 358010 TRUE FALSE 460747.2665 380296.4516 423195.806 410726.225 356339.3565 471374.7481 424842.6287 417781.3561 298255.8182 1.544805628 1.275068007 1.418902098 1.377093756 1.194744024 1.580437729 1.424423608 1.400748387 1 18.18619076 -0.958443429 5.179939378 0.999998408 1.395392595 0.559000417 0.112082727 1.91E-06 3.83E-07 0.100440729 0.023674012 0.110041518 0.958443429 0.395394187 NEEDEGHSNS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 NEEDEGHS(0.001)NS(0.499)S(0.499)PR;NEEDEGHS(0.009)NS(0.752)S(0.239)PR;NEEDEGHS(0.014)NS(0.493)S(0.493)PR;NEEDEGHS(0.251)NS(0.375)S(0.375)PR 137.61 3.78E-05 440324400 454858 354001 409222 390097 366624 352348 480848 328514 312452 TRUE FALSE 426389.2497 380211.6024 418928.9391 400107.5495 337830.8299 454065.1477 408749.3064 369529.696 260301.7427 1.638057607 1.460657153 1.609397366 1.537091321 1.297843136 1.744379976 1.570290318 1.419620523 1 17.98982544 0.855470218 3.420657166 1.000182384 1.548571167 0.688855537 0.116180467 0.37704476 7.808651871 0.103449156 0.026756346 7.169192113 -0.855470218 0.548388783 NEEDEGHSNS(ph)SPRHS(ph)EAATAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NEEDEGHSNSSPRHSEAATAQR 22 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 2 NEEDEGHS(0.009)NS(0.542)S(0.45)PRHS(0.999)EAAT(0.001)AQR 117.33 0.00017867 91125000 93912 84062 95773 86913 86833 67116 133440 103270 85845 TRUE FALSE 88034.21556 90286.03795 98044.78079 89143.33472 80013.48645 86491.29966 113431.9108 116163.4868 71516.91492 1.23095656 1.26244313 1.370931351 1.246465047 1.118805062 1.20938242 1.586085067 1.624279892 1 16.12599688 1.752794456 25 1.461495093 1.253166836 0.127692301 0.17933897 6.428458703 11306.29973 0.075369251 0.041796054 56.59713608 -1.752794456 -0.208328257 NEEDEGHSNSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 NEEDEGHSNS(0.02)S(0.98)PR;NEEDEGHSNS(0.014)S(0.986)PR;NEEDEGHSNS(0.042)S(0.958)PR;NEEDEGHSNS(0.041)S(0.959)PR;NEEDEGHSNS(0.052)S(0.948)PR;NEEDEGHSNS(0.044)S(0.956)PR;NEEDEGHSNS(0.045)S(0.954)PR 224.55 1.46E-11 35155960000 32256780 25177840 28676560 27967890 25303490 24464990 32966160 23089200 21407910 TRUE FALSE 30237885.72 27042033.47 29356781.55 28685593.41 23316255.96 31527635.46 28023190.35 25971937.45 17834791.52 1.695443745 1.516251729 1.646040073 1.608406433 1.307346707 1.767760247 1.571265373 1.45625125 1 24.08819102 0.8029505 2.615896959 1.000273487 1.585421712 0.698077056 0.121053722 0.444700556 4.91618797 0.104809385 0.027892446 6.352585217 -0.8029505 0.585148225 NEEDEGHSNSS(ph)PRHS(ph)EAATAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NEEDEGHSNSSPRHSEAATAQR 22 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 2 NEEDEGHS(0.007)NS(0.438)S(0.556)PRHS(0.999)EAATAQR 161.05 2.36E-11 115920000 120080 101600 104540 105430 104440 65728 161880 118540 100660 TRUE FALSE 112564.4071 109122.5697 107019.7382 108135.5123 96237.70369 84702.6066 137607.5968 133339.9799 83859.19571 1.342302489 1.301259436 1.276183694 1.289489022 1.147610621 1.010057464 1.640936282 1.590046015 1 16.35568137 1.729720202 24.99999997 1.465970169 1.241157122 0.141025129 0.1951352 1.080322495 3038.627497 0.082415937 0.045703825 53.66859199 -1.729720202 -0.224813047 NEEDEGHSNSSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;;;;; 269.4 4.76E-25 2429297000 3206658 2776156 2979359 2835966 2661797 2534887 3379963 2428152 2233864 FALSE TRUE 3005959 2981705.479 3050030.802 2908741.689 2452750.201 3266667.726 2873168.926 2731312.122 1861017.667 1.615223247 1.602190851 1.638904808 1.562984458 1.317961803 1.755312582 1.543869775 1.467644381 1 20.82766032 -2.663705742 0.329729761 1.99E-16 1.605683933 0.727638337 0.109784782 30.94139616 1.092269894 21.99081139 0.089377479 0.002169173 2.663705742 1.605683933 NEEKLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NEEKLR 6 1 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 0 71.029 0.081451 716970000 1620400 1366200 1449500 1388300 1612400 1064500 1926400 1322400 1629100 FALSE TRUE 1518982.056 1467354.87 1483882.825 1423926.128 1485768.608 1371803.869 1637554.204 1487504.551 1357192.686 1.119208844 1.081169155 1.093347201 1.049170205 1.094736675 1.01076574 1.206574587 1.096015744 1 20.37219413 1.753056907 25 1.122296568 1.077409322 0 0.058027126 9.732853171 16807.6369 0.023775293 0.013184702 56.63134903 -1.753056907 -0.044887246 NEEPS(ph)EEEIDAPKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 NEEPSEEEIDAPKPK 15 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK 192.96 1.25E-07 22345151000 16208290 6249990 9883980 8770480 8067600 6538680 12569090 6426334 10220120 TRUE FALSE 15193842.06 6712745.763 10118432.67 8995545.365 7434003.239 8426290.769 10684471.64 7228675.946 8514315.948 1.784505315 0.788406938 1.188402302 1.056520033 0.873118085 0.989661509 1.254883153 0.849002549 1 23.0214592 4.749523893 24.8363289 1.020392435 1.784505796 0.740285432 0.145587017 786.8569665 1782517.153 0.033845147 0.511615797 56172.51808 -4.749523893 0.76411336 NEEPVRS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NEEPVRSPER 10 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 1 NEEPVRS(1)PER 84.954 0.038328 93278000 237540 216630 247730 221270 245640 202400 276530 225020 222860 TRUE FALSE 222672.7954 232669.5106 253606.2726 226948.1628 226348.4253 260829.5943 235066.8937 253114.2423 185663.2263 1.1993371 1.25318037 1.365947785 1.22236464 1.219134396 1.40485329 1.266092906 1.363297662 1 17.50232857 -1.02474327 5.390844253 0.999998395 1.290389449 0.623410762 0.069997353 1.25E-06 2.26E-07 0.062697486 0.014777857 0.094461912 1.02474327 0.290391054 NEEPVRS(ph)PERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 NEEPVRSPERR 11 2 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 1 NEEPVRS(1)PERR;NEEPVRS(1)PERR;NEEPVRS(1)PERR;NEEPVRS(1)PERR;NEEPVRS(1)PERR;NEEPVRS(1)PERR;NEEPVRS(1)PERR 154.65 1.66E-05 7849203000 3858167 3741628 3761486 3876836 4000399 2943748 4094549 3344519 4582107 TRUE FALSE 3616691.214 4018662.03 3850710.224 3976322.175 3686223.799 3793560.26 3480609.389 3762089.559 3817323.74 0.947441574 1.05274331 1.008746045 1.041651808 0.965656583 0.993774832 0.911793085 0.985530653 1 21.86413011 2.718550512 21.4120093 0.963356088 1.01867867 0.212961982 0.036946462 137.1954391 146806.0595 0.011136236 0.010522338 523.0587986 -2.718550512 0.055322582 NEEVQFGQHLDAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NEEVQFGQHLDAAR 14 0 Q9H6W3;Q9H6W3-2 Q9H6W3 NO66 Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 0 66.387 0.065314 0 45412 60600 66354 53268 69349 58822 57113 60461 59923 FALSE TRUE 42569.74398 65086.88705 67927.94821 54634.94706 63902.60928 75802.9565 48549.43586 68009.68894 49921.46418 0.852734283 1.303785618 1.360696232 1.094417961 1.280062801 1.518444175 0.972516264 1.362333619 1 15.60737263 -0.591210553 12.51938428 1 1.230884892 0.104054379 0.198025961 0 0 0.174510236 0.041132457 0.256324103 0.591210553 0.230884892 NEGGFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NEGGFTR 7 0 Q8HWS3 Q8HWS3 RFX6 DNA-binding protein RFX6 0 84.097 0.050705 558690000 729370 406550 847410 866150 492140 653700 1037100 519310 2580800 FALSE TRUE 683720.0337 436651.385 867510.9654 888376.8754 453489.3096 842412.5781 881596.483 584146.9966 2150047.807 0.318002247 0.203089152 0.4034845 0.413189359 0.21092057 0.391811091 0.410035758 0.271690236 1 21.03593731 -5 0.339825652 8.22329064 0.306950004 0.871839616 0.080759491 127.5239055 1.075044045 668.2287716 0.062348258 1.00E-05 5 -7.916340637 NEGIDLTHNPEFTTCEFYMAYADYHDLMEITEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NEGIDLTHNPEFTTCEFYMAYADYHDLMEITEK 33 0 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 227.58 1.18E-36 23540000 23715 16890 20560 19838 20371 16141 24943 16012 18049 FALSE TRUE 22230.72048 18140.55317 21047.69291 20347.07667 18771.14383 20800.64467 21203.02871 18011.13345 15036.5053 1.478449948 1.206434129 1.399772919 1.353178565 1.248371444 1.383343021 1.410103497 1.197827094 1 13.87618168 0.973535379 4.417673699 1.000380206 1.34441956 0.683882846 0.078512701 0.105681627 6.612000286 0.071024781 0.018065486 9.408824734 -0.973535379 0.344039353 NEGNLENEGKPEDEVEPDDEGKS(ph)DEEEKPDVEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NEGNLENEGKPEDEVEPDDEGKSDEEEKPDVEGK 34 3 Q969E4 Q969E4 TCEAL3 Transcription elongation factor A protein-like 3 1 NEGNLENEGKPEDEVEPDDEGKS(1)DEEEKPDVEGK;NEGNLENEGKPEDEVEPDDEGKS(1)DEEEKPDVEGK 187.24 3.21E-20 273230000 1191490 118442 280700 292700 374750 194957 402650 179455 243690 TRUE FALSE 1116916.768 127211.5689 287358.3366 300211.1775 345318.6467 251237.921 342276.3705 201860.3518 203016.5647 5.501604115 0.626606844 1.415442809 1.47875213 1.700938281 1.237524245 1.685952922 0.994304835 1 17.63123792 4.744168479 24.99990611 1.299087253 5.501605911 0.9411861 0.332554754 139.4075408 621462.0502 0.080210689 0.708261145 55484.09141 -4.744168479 4.202518657 NEGS(ph)ESAPEGQAQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NEGSESAPEGQAQQR 15 0 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NEGS(0.794)ES(0.206)APEGQAQQR;NEGS(0.998)ES(0.002)APEGQAQQR;NEGS(0.974)ES(0.026)APEGQAQQR;NEGS(0.999)ES(0.001)APEGQAQQR 350 2.61E-82 368428700 869112 573077.2 742872.2 685001.6 563344.7 642455 922684 589381 497057.9 TRUE FALSE 814715.8313 615508.4322 760493.4794 702579.9008 519101.8797 827921.3291 784336.1 662966.5152 414095.7254 1.967457719 1.486391659 1.836516131 1.696660597 1.253579421 1.999347683 1.894093689 1.60099821 1 18.65960478 0.968718527 21.89073009 0.999999994 1.725187042 0.508985053 0.224853903 618.6449159 432928.3328 0.207240214 0.051814521 9.305046049 -0.968718527 0.725187049 NEGSES(ph)APEGQAQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NEGSESAPEGQAQQR 15 0 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NEGSES(1)APEGQAQQR;NEGSES(1)APEGQAQQR 338.36 3.62E-69 1049690000 1316960 917930 1048030 1021740 735830 912160 1486910 857770 565390 TRUE FALSE 1234533.824 985894.4923 1072889.767 1047959.578 678040.88 1175485.784 1263961.649 964864.4727 471022.7564 2.62096429 2.093093123 2.277787542 2.224859763 1.43950769 2.495602958 2.68344073 2.048445557 1 18.84543724 0.969941061 23.23961792 0.999999987 2.258330297 0.566718504 0.344446941 1107.916791 856570.919 0.329464643 0.08236616 9.331276545 -0.969941061 1.25833031 NEHFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NEHFQK 6 0 P15924 P15924 DSP Desmoplakin 0 81.958 0.060507 197010000 204220 175680 170950 208650 213220 143020 255380 170450 203390 FALSE TRUE 191438.2347 188687.53 175005.0147 214004.3122 196474.5613 184307.5523 217088.1398 191731.0577 169442.8951 1.129809749 1.113575933 1.032825924 1.262987818 1.159532604 1.087726648 1.281187622 1.1315379 1 17.37043962 3.255022748 24.99996041 1.171045906 1.088215337 0.083257459 0.084273382 391.8357588 595051.6766 0.021435237 0.028942766 1798.96514 -3.255022748 -0.082830569 NEKDNALLSAIEESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NEKDNALLSAIEESR 15 1 H3BVG0;Q8N1F7;H3BM93;H3BNN5;H3BV11;H3BRI8 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 ;;; 309.15 3.78E-56 709044000 1064470 958100 941860 1024110 1068580 729120 1249050 905470 1155910 FALSE TRUE 997846.7228 1029038.721 964201.364 1050390.396 984658.0372 939605.1077 1061766.548 1018519.923 962981.1535 1.036205869 1.068596947 1.001267118 1.090769422 1.022510185 0.975725334 1.102582895 1.057673786 1 19.87714804 1.709951611 25 1.062255333 1.034917111 0.03988571 0.040233245 1.926948178 1675.245162 0.01718625 0.009530648 51.28042442 -1.709951611 -0.027338222 NELDS(ph)PHEEKQDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NELDSPHEEKQDK 13 1 Q8TBZ6 Q8TBZ6 TRMT10A tRNA methyltransferase 10 homolog A 1 NELDS(1)PHEEKQDK;NELDS(1)PHEEKQDK 153.21 2.75E-05 194347000 843800 368070 520650 458020 415300 395290 700750 431880 422800 TRUE FALSE 790988.0642 395322.2858 533000.0639 469773.5686 382684.0132 509403.806 595679.0429 485801.1687 352231.9486 2.245645426 1.122335118 1.513207606 1.333705164 1.086454578 1.446216926 1.69115563 1.379208134 1 18.42616625 4.748414439 24.56339396 1.362309317 2.245646041 0.64862887 0.211871563 719.8777183 1794448.452 0.050384796 0.662600227 56029.20232 -4.748414439 0.883336724 NELDS(ph)PHEEKQDKENHTESTVNSLPH ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NELDSPHEEKQDKENHTESTVNSLPH 26 2 Q8TBZ6 Q8TBZ6 TRMT10A tRNA methyltransferase 10 homolog A 1 NELDS(1)PHEEKQDKENHTESTVNSLPH 90.944 0.0048595 171610000 171800 97781 134060 122310 137740 78071 166390 93032 190890 TRUE FALSE 161047.3447 105020.807 137239.9665 125448.6817 126922.456 100608.8303 141441.3642 104647.25 159029.2258 1.012690239 0.660386834 0.862985818 0.788840422 0.79810774 0.632643653 0.889404847 0.658037851 1 17.2789324 -0.842141299 7.639098376 0.999997235 0.784412164 0.243569332 0.117332278 7.25E-10 9.50E-11 0.097363826 0.022948874 0.143833054 0.842141299 -0.215585072 NELHNLLDKPQLQGIPVLVLGNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NELHNLLDKPQLQGIPVLVLGNKR 24 2 Q96BM9;Q9NVJ2 Q96BM9;Q9NVJ2 ARL8A;ARL8B ADP-ribosylation factor-like protein 8A;ADP-ribosylation factor-like protein 8B 0 94.449 0.0045148 67294000 223320 286460 196500 187120 303000 169490 249060 249430 264460 FALSE TRUE 209342.7998 307669.7965 201161.0728 191921.816 279203.6022 218419.0116 211715.7652 280571.8846 220319.9175 0.950176462 1.396468372 0.913040796 0.871105155 1.267264464 0.991372065 0.960947006 1.273474898 1 17.7492404 3.958318289 23.41310759 1.033114373 1.198894651 0.090885712 0.170687278 325.0232339 404713.7679 0.040087754 0.072471615 9084.861045 -3.958318289 0.165780278 NELMYQLEQDHDLQAILQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 NELMYQLEQDHDLQAILQER 20 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;;; 340.46 2.61E-80 2589414000 2039510 2159773 2146278 2013782 2248641 1549513 2553077 1960590 1807836 FALSE TRUE 1911860.71 2319684.84 2197188.728 2065459.055 2072041.806 1996832.249 2170266.805 2205373.977 1506096.493 1.269414489 1.540196695 1.458863186 1.371398888 1.375769625 1.325832879 1.440987889 1.464297931 1 20.52238277 -1.767778891 2.738186028 0.903183598 1.418773666 0.728900561 0.077428479 17279724.59 12883996.45 11216943.98 0.01884207 0.017069512 1.767778891 0.515590068 NENEEILERPAQLANAR ddPTM_SK-BR-3_Pertuzumab_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 ; 328.67 5.58E-72 1213280000 723340 691110 739210 673780 769550 550740 765950 694370 1011780 FALSE TRUE 678067.4406 742280.5035 756744.4103 691070.3355 709112.6472 709729.6975 651102.9082 781063.623 842907.3817 0.804438845 0.880619294 0.897778839 0.819865089 0.841269946 0.842001996 0.772448934 0.926630422 1 19.68501459 -1.827772605 4.803856768 1.022546938 0.848489302 0.529665223 0.044974017 0.011837541 0.000424398 0.047464414 0.010339952 0.014867139 1.827772605 -0.174057636 NENESEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NENESEKR 8 1 P47813;O14602;A6NJH9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 ; 148.69 0.0008293 1214640000 1184530 721420 851910 751960 831170 573740 863700 697990 765360 FALSE TRUE 1110392.382 774834.6874 872117.7075 771256.5667 765893.261 739369.4241 734196.2032 785135.588 637616.4716 1.741473803 1.215204942 1.367777883 1.209593229 1.201181737 1.159583319 1.151469945 1.231360266 1 19.28232937 7.327363101 1.105210515 1.194832066 199.9999937 0.755292299 0.096330706 300.1639936 1.296407456 0.026334317 150145.833 21250203.85 -7.327363101 198.8051616 NENLAANFLLQQNFDED ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NENLAANFLLQQNFDED 17 0 P54727;P54727-2 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ;;; 244.36 3.84E-20 434305000 1262940 1104450 1075310 1035340 1116330 837930 1334620 1025200 926250 FALSE TRUE 1183894.84 1186224.627 1100816.861 1061908.577 1028657.945 1079826.788 1134506.121 1153198.477 771652.8912 1.534232364 1.537251581 1.426569995 1.376147993 1.333057851 1.399368551 1.470228563 1.49445235 1 19.55759251 -1.958933045 2.677656241 0.653050243 1.446922849 0.818673757 0.066025593 2483239.823 1521446.633 5348516.321 0.017404512 0.010991753 1.958933045 0.793872606 NENLAANFLLSQNFDDE ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NENLAANFLLSQNFDDE 17 0 P54725-2;P54725;K7EQ16;P54725-3 P54725-2;P54725-3 RAD23A UV excision repair protein RAD23 homolog A 0 101.42 0.0025394 14289000 33599 27536 30345 26211 31650 21832 32494 26480 23858 FALSE TRUE 31496.09857 29574.79409 31064.79773 26883.61864 29164.33667 28134.54399 27621.82636 29786.08629 19875.94567 1.584633963 1.487969155 1.562934325 1.352570543 1.467318192 1.415507189 1.389711303 1.498599703 1 14.27873588 -3.30647452 0.212136054 2.22E-20 1.549392787 0.830746324 0.06751823 24.05420482 0.457415688 10.78383711 0.136963064 0.000493771 3.30647452 1.549392787 NENQLIIFADDTYPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NENQLIIFADDTYPR 15 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 195.1 5.61E-08 22486000 50940 45010 51696 53639 52250 37326 62402 45603 50028 FALSE TRUE 47751.75633 48342.58723 52922.25353 55015.46755 48146.49577 48101.41026 53045.39941 51296.63493 41678.00361 1.145730414 1.159906499 1.269788592 1.320012064 1.155201584 1.154119826 1.27274329 1.230784359 1 15.34699855 NENTEGS(ph)PQEDGVELEGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NENTEGSPQEDGVELEGLK 19 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 NENTEGS(1)PQEDGVELEGLK;NENTEGS(1)PQEDGVELEGLK;NENTEGS(1)PQEDGVELEGLK;NENTEGS(1)PQEDGVELEGLK 413.5 7.01E-148 530320000 2193430 1286140 1575740 1466030 1578550 1051018 2170940 1395940 2047490 TRUE FALSE 2056147.132 1381367.144 1613117.297 1503650.812 1454577.051 1354429.835 1845427.701 1570226.182 1705750.692 1.205420664 0.80982945 0.945693474 0.881518512 0.852748914 0.794037394 1.081885946 0.920548466 1 20.70197537 1.728053064 24.99999771 1.002731169 0.902636732 0.096413754 0.120139142 1.604066242 3798.165661 0.050478668 0.02799293 53.46296782 -1.728053064 -0.100094436 NENTFLDLTVQQIEHLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NENTFLDLTVQQIEHLNK 18 0 A0A087WYS1;E7EUC7;Q16851;Q16851-2;C9JVG3;C9JQU9;C9JNZ1;C9JWG0 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 ;;; 313.12 3.21E-61 788793000 2014050 1526094 1733460 1858849 1917390 1270701 2212940 1573983 2098770 FALSE TRUE 1887994.206 1639087.588 1774578.49 1906550.212 1766805.924 1637531.751 1881130.191 1770498.242 1748471.728 1.079796816 0.937440143 1.014931189 1.090409517 1.01048584 0.936550316 1.075871094 1.012597581 1 20.73766304 3.492717066 23.83581937 1.024503024 0.992402053 0 0.054073303 670.3144563 1024464.764 0.013639445 0.020855738 3109.689779 -3.492717066 -0.03210097 NEPT(ph)TRSPVSSQQSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NEPTTRSPVSSQQSLK 16 1 Q8IWJ2 Q8IWJ2 GCC2 GRIP and coiled-coil domain-containing protein 2 1 NEPT(0.359)T(0.359)RS(0.279)PVS(0.002)SQQSLK 72.086 0.024129 0 22748 19785 32518 35140 28864 11909 26688 23481 36028 TRUE FALSE 21324.24329 21249.90199 33289.34232 36041.75189 26597.13787 15346.93497 22686.38216 26412.65454 30014.69405 0.710460125 0.707983295 1.109101504 1.200803574 0.886137231 0.511314057 0.755842526 0.879990797 1 14.87338134 2.459449213 24.78073099 0.749009771 0.936162079 0.098434029 0.19426447 401.5019554 563004.9339 0.068756778 0.057536733 288.0376195 -2.459449213 0.187152308 NEQLPLQYLADVDT(ph)SDEESIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NEQLPLQYLADVDTSDEESIR 21 0 Q9BV36-2;H7C2D8;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 NEQLPLQYLADVDT(0.5)S(0.5)DEESIR 133.38 3.68E-05 18409000 48361 46996 46725 49030 51356 34848 55183 41105 47842 TRUE FALSE 45334.17134 50475.63274 47833.33907 50288.19281 47322.70692 44908.05189 46908.82144 46237.04973 39856.86113 1.137424525 1.266422676 1.200128101 1.261719849 1.187316451 1.12673328 1.176932155 1.160077548 1 15.28254048 0.176710013 0.380602463 0.968175879 1.226095026 0.679229975 0.042583269 1.960868244 0.441964251 0.144846695 0.031264644 1.502138625 -0.176710013 0.257919147 NES(ph)SPIRFDILLDDLDTVPVSTLQR ddPTM_SK-BR-3_Pertuzumab_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 166.74 8.22E-12 44501000 39755 33122 37957 37625 37320 27738 40958 32354 42242 TRUE FALSE 37266.80551 35574.38734 38857.35796 38590.5212 34389.03774 35745.51031 34816.72814 36393.46812 35191.53731 1.058970661 1.010879037 1.104167676 1.096585263 0.977196234 1.015741654 0.989349452 1.034153973 1 15.10294092 2.734639625 24.99925266 1.00257278 1.064274892 0.549392052 0.028888453 274.3654712 1749280.104 0.00944882 0.009214179 542.7997324 -2.734639625 0.061702112 NESEDNKFS(ph)DDS(ph)DDDFVQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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;NESEDNKFS(1)DDS(1)DDDFVQPR 198.99 8.54E-22 697300000 2183700 1122320 1402870 1464370 1623320 1063130 2032460 1283120 2007190 TRUE FALSE 2047026.115 1205417.741 1436146.739 1501948.213 1495830.995 1370038.373 1727711.491 1443320.356 1672177.022 1.224168308 0.720867303 0.858848507 0.89819929 0.894541054 0.819314196 1.033210879 0.863138494 1 20.67329615 1.743121019 24.99993998 0.964855423 0.876142086 0.021632613 0.13574485 2.123775238 11693.75789 0.057912873 0.032115812 55.3504325 -1.743121019 -0.088713336 NESS(ph)PAPPDSDADKLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NESSPAPPDSDADKLK 16 1 Q8ND04;Q8ND04-2;J3KTD7 Q8ND04 SMG8 Protein SMG8 1 NES(0.441)S(0.559)PAPPDSDADKLK 74.324 0.019742 133280000 264320 166770 198430 197660 200850 155140 247600 173820 202940 TRUE FALSE 247776.683 179117.8243 203136.8533 202732.2902 185076.0512 199926.3995 210474.6786 195521.8096 169068.003 1.465544507 1.05944248 1.201509746 1.199116845 1.094684079 1.182520619 1.244911367 1.15646844 1 17.36724412 -2.530007547 1.219828293 0.165980712 1.188209317 0.244341096 0.108929965 61585.35459 4385.625946 139809.5642 0.028326955 0.002951158 2.530007547 1.022228605 NESSFASHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NESSFASHK 9 0 E5RH53;Q96DB5-3;Q96DB5-2;Q96DB5;H0YC67;H0YB03;H0YB83 E5RH53 RMDN1 Regulator of microtubule dynamics protein 1 0 ; 142.83 0.0001034 554080000 1029470 1100380 978100 1005530 1318440 701870 1067560 1042070 1119890 FALSE TRUE 965037.3104 1181853.28 1001300.994 1031333.602 1214895.041 904488.4751 907489.2887 1172174.733 932973.1242 1.034367749 1.266760263 1.073236697 1.105426915 1.302175817 0.96946895 0.972685349 1.256386388 1 19.831476 2.212363236 24.99993556 1.036576441 1.157787396 0.175065882 0.113571209 337.3289069 321908.0113 0.03980103 0.029404212 163.0659316 -2.212363236 0.121210955 NETLDATHLAEFHQIEGVVADHGLTLGHLMGVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NETLDATHLAEFHQIEGVVADHGLTLGHLMGVLR 34 0 K7ER00;Q9Y285;Q9Y285-2;K7EPH2 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ; 309.47 8.16E-105 294040000 359510 355220 371720 346710 391770 273900 414130 342350 304260 FALSE TRUE 337008.9108 381520.8584 380537.3739 355607.1656 361001.9645 352970.4836 352035.0511 385093.1511 253477.0404 1.329544129 1.50514957 1.501269596 1.402916671 1.424199856 1.392514616 1.388824213 1.519242731 1 17.95149555 -1.791272146 2.81909177 0.886829168 1.438838629 0.835059412 0.060421586 17765662.43 14142023.77 13821043.19 0.014784086 0.016170664 1.791272146 0.552009461 NFAADHFNQEILPVFLNANR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NFAADHFNQEILPVFLNANR 20 0 Q6PI48;A0A3B3ITK9;A0A3B3ITS3 Q6PI48 DARS2 "Aspartate--tRNA ligase, mitochondrial" 0 151.87 7.10E-08 93739000 138050 127750 116940 96370 163360 105970 127330 130060 159830 FALSE TRUE 129409.6969 137208.7429 119713.872 98843.01735 150530.3646 136561.8187 108238.0486 146298.2773 133153.3405 0.971884719 1.030456633 0.899067734 0.742324729 1.130503854 1.025598143 0.812882713 1.098720293 1 17.0227291 NFDEALVDYFCDEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NFDEALVDYFCDEFK 15 0 O95757;E9PDE8;D6RJ96 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 ; 231.26 5.07E-13 28658400 58590 43970 55663 49093 54195 46348 64958 49207 62534 FALSE TRUE 54922.95649 47225.58455 56983.35265 50352.80949 49938.74331 59727.9152 55218.15094 55350.60227 52096.67141 1.05425078 0.906499077 1.093800258 0.966526423 0.958578388 1.146482368 1.059917063 1.062459477 1 15.66890358 2.255847787 24.97411671 1.073543639 0.995744966 0.245152673 0.061711665 300.2601622 433773.522 0.020108555 0.016787306 180.2385925 -2.255847787 -0.077798673 NFDEILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 NFDEILR 7 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;;;;;;; 191.63 0.001217 8594350000 8496960 9201640 8828720 8816560 9608460 7284320 10391070 8275720 10769480 FALSE TRUE 7965150.441 9882939 9038141.408 9042807.856 8853850.31 9387184.933 8833025.519 9308961.859 8971984.215 0.887780256 1.101533258 1.007373753 1.007893866 0.986833024 1.046277469 0.984511933 1.037558876 1 23.09699565 NFDFEGS(ph)LSPVIAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NFDFEGSLSPVIAPK 15 0 Q9H1A4;H0Y564 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 NFDFEGS(0.5)LS(0.5)PVIAPK 173.37 1.02E-06 155710000 197280 159480 164250 220770 159980 99196 159180 100300 113510 TRUE FALSE 184932.597 171288.0651 168146.0876 226435.332 147415.8161 127832.2749 135312.4368 112822.6758 94564.4477 1.955624989 1.811336811 1.778111031 2.394508057 1.558892583 1.351800576 1.430901782 1.193077087 1 16.52901027 2.494228465 5.878414108 1.313800962 1.928162925 0.735443236 0.206521771 0.096589595 12.04460419 0.067315033 0.06025612 312.0530736 -2.494228465 0.614361963 NFDFEGSLS(ph)PVIAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NFDFEGSLSPVIAPK 15 0 Q9H1A4;H0Y564 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 NFDFEGS(0.008)LS(0.992)PVIAPK;NFDFEGS(0.001)LS(0.999)PVIAPK 237.4 1.03E-17 231347000 589350 542510 582770 701850 524790 344214 549310 327597 419270 TRUE FALSE 552463.6355 582678.0049 596593.5796 719860.6592 483575.1103 443582.994 466946.065 368498.2066 349291.1284 1.581670963 1.668172929 1.708012403 2.060918817 1.384447159 1.269952077 1.336839178 1.054988737 1 18.41407047 2.524979579 5.973498302 1.22362243 1.733766952 0.748935539 0.159569207 0.110205381 9.618455114 0.050744041 0.046894987 334.9496888 -2.524979579 0.510144521 NFDLRPGVIVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NFDLRPGVIVR 11 1 P31153;P31153-2;Q00266 P31153 MAT2A;MAT1A S-adenosylmethionine synthase isoform type-2;S-adenosylmethionine synthase isoform type-1 0 ; 115.29 0.0010429 1163430000 2953100 3133600 2965800 2890500 3406300 2159590 3209100 2951300 3670000 FALSE TRUE 2768270.742 3365615.005 3036150.177 2964675.124 3138782.938 2783028.575 2727925.247 3319776.302 3057453.291 0.905417182 1.100790326 0.993032399 0.969655083 1.026600455 0.91024402 0.892221397 1.08579788 1 21.54389903 3.149178788 1.490933754 0.962104911 1.023523614 0 0.073328458 0.87968763 4.048884467 0.025075536 0.034188614 1409.869087 -3.149178788 0.061418703 NFEATLGWLQEHACSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NFEATLGWLQEHACSR 16 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 245.97 3.68E-20 1846070000 1027340 1213580 1106780 1102030 1284760 813890 1327720 1066860 1224050 FALSE TRUE 963040.6233 1303434.726 1133033.344 1130309.956 1183860.132 1048846.831 1128640.712 1200059.819 1019748.147 0.944390657 1.278192786 1.111091349 1.1084207 1.16093384 1.028535167 1.106783783 1.176819808 1 19.95978146 2.269297607 24.99133177 1.086974418 1.14024369 0.021994724 0.093762895 553.7811309 450260.8843 0.030344698 0.025385163 185.9077982 -2.269297607 0.053269272 NFEDVAFDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NFEDVAFDEK 10 0 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 129.7 0.00068886 171500000 419300 309760 352770 351590 340880 263790 453030 284600 314850 FALSE TRUE 393056.7615 332694.9527 361137.871 360612.3946 314108.6598 339941.8907 385102.3572 320132.9365 262299.501 1.498503657 1.268378138 1.376814937 1.374811592 1.19751909 1.296006624 1.468178002 1.220486258 1 18.00085554 0.974774263 9.611556611 1.000001064 1.346633147 0.623228228 0.088484721 0.395985999 150.1808347 0.080385473 0.020110156 9.435703015 -0.974774263 0.346632083 NFEDVAFDEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NFEDVAFDEKK 11 1 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ;;;;; 182.02 9.57E-06 7619210000 16271400 9171320 11535760 12121430 12165650 7541370 16474800 9167730 14307900 FALSE TRUE 15253002.12 9850374.076 11809393.67 12432486.42 11210208.92 9718441.095 14004556.68 10312341.27 11919819.06 1.279633696 0.826386208 0.990735985 1.043009659 0.940468045 0.815317837 1.174896751 0.865142434 1 23.506859 -1.515570575 5.521282001 1.000035144 0.983384299 0 0.14786166 5.73E-05 5.03E-06 0.128310565 0.030179261 0.030509102 1.515570575 -0.016650844 NFEES(ph)PERK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NFEESPERK 9 1 Q6MZP7-3;Q6MZP7;Q6MZP7-4;Q6MZP7-2 Q6MZP7-3 LIN54 Protein lin-54 homolog 1 NFEES(1)PERK 102.97 0.0021427 95898000 267620 172940 211400 205480 208640 172710 260690 195350 281470 TRUE FALSE 250870.1419 185744.6575 216414.5078 210752.9647 192254.256 222568.5733 221601.9546 219739.8775 234490.8386 1.069850504 0.792119038 0.922912422 0.898768438 0.819879604 0.949156797 0.945034595 0.937093657 1 17.83917203 2.049218209 24.99697678 0.952725748 0.888478632 0.112215548 0.075067888 197.8097589 100462.768 0.02562892 0.018928209 112.000048 -2.049218209 -0.064247116 NFEHLNSDFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NFEHLNSDFDR 11 0 P48163 P48163 ME1 NADP-dependent malic enzyme 0 ;;;;; 170.07 1.61E-05 2694300000 2395040 3020830 2539480 2596050 3150280 1964320 2602340 2739400 3405140 FALSE TRUE 2245138.722 3244495.396 2599717.665 2662669.038 2902869.716 2531387.296 2212143.276 3081420.12 2836800.136 0.791433522 1.143716596 0.916426093 0.938617072 1.023290178 0.892338965 0.779802302 1.086230955 1 21.43583308 2.22336487 24.78568611 0.905056546 0.979977072 0 0.119104763 561.0593421 915133.7688 0.042006049 0.03114504 167.2495161 -2.22336487 0.074920525 NFESLSEAFSVASAAAVLSHNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NFESLSEAFSVASAAAVLSHNR 22 0 P04844-2;P04844;F2Z3K5;Q5JYR4;Q5JYR7 P04844-2 RPN2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 0 104.41 0.00055203 17589000 19493 17800 18002 15648 21547 15922 21100 18374 12648 FALSE TRUE 18272.96793 19117.93052 18429.01594 16049.55417 19854.78554 20518.42293 17936.25088 20668.03435 10536.96709 1.734177185 1.814367489 1.748986761 1.523166394 1.884297955 1.947279777 1.702221401 1.961478495 1 13.36317205 -1.345431363 5.464885327 0.999792441 1.783942407 0.789591468 0.128052076 0.00030036 3.60E-05 0.115001996 0.027099243 0.045140736 1.345431363 0.784149966 NFEWVAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NFEWVAER 8 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;;;; 126.82 0.0027977 1680186000 1957270 2602450 1941112 2008350 2823060 1351977 1819567 2277850 1996631 FALSE TRUE 1834767.965 2795138.106 1987156.093 2059887.661 2601348.255 1742270.812 1546739.82 2562244.587 1663380.387 1.103035709 1.680396214 1.194649227 1.238374383 1.563892586 1.047427772 0.929877394 1.540384031 1 20.6656867 2.219156202 24.99812611 1.100105281 1.372934347 0.182566893 0.233179502 336.9978214 434141.5559 0.082086781 0.06071231 165.6365598 -2.219156202 0.272829067 NFFLTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NFFLTNR 7 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ; 101.6 0.020798 385880000 481390 868770 464850 496960 941140 287530 557760 764310 1027390 FALSE TRUE 451260.6592 933094.6348 475876.4615 509712.835 867226.6608 370535.2433 474129.066 859735.786 855911.9718 0.527227886 1.090175936 0.555987622 0.595520161 1.013219454 0.432912794 0.553946062 1.004467532 1 19.7071029 1.220718079 24.57554975 1.002234339 0.697952772 0.281500464 0.211875166 320.6149928 441586.7198 0.198066524 0.049970282 16.623332 -1.220718079 -0.304281567 NFGEDMDDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 NFGEDMDDER 10 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YBN4 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ;;;;;;;;; 271.74 2.23E-23 10097140000 9298540 7946350 9013280 8680680 8324660 7363800 10565490 7802160 8013910 FALSE TRUE 8716560.98 8534706.022 9227079.258 8903440.945 7670874.784 9489609.519 8981292.86 8776276.851 6676336.649 1.305590392 1.278351658 1.382057218 1.333581785 1.148964647 1.42137972 1.345242658 1.314534798 1 22.67062527 0.9144808 19.6111529 1 1.321146711 0.657540103 0.071656643 3761.224173 862522.371 0.065050581 0.016262645 8.212602437 -0.9144808 0.321146711 NFGEDMDDERLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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 ;;;;;;;; 210.41 4.01E-08 2995890000 3377610 2884470 2917680 3143530 3831470 1659480 3392400 2573900 5703460 FALSE TRUE 3166211.419 3098039.16 2986888.747 3224198.302 3530561.802 2138544.937 2883741.113 2895257.081 4751515.68 0.666358196 0.65201072 0.628618098 0.678562067 0.743039072 0.450076372 0.606909733 0.609333374 1 22.17995636 -1.799296158 7.169631856 1.013586411 0.626683316 0.708023805 0.074782211 0.015564607 0.000435709 0.069393818 0.016575923 0.015874638 1.799296158 -0.386903095 NFGEEVDDESLKELFSQFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NFGEEVDDESLKELFSQFGK 20 1 B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0YCC8 B1ANR0 PABPC4 Polyadenylate-binding protein;Polyadenylate-binding protein 4 0 ; 294.33 1.34E-54 280140000 891200 552180 655550 647990 701350 448860 908910 587490 937930 FALSE TRUE 835421.3828 593063.9817 671099.9556 664618.5204 646268.8001 578438.5954 772627.3834 660839.4197 781383.4237 1.069156777 0.758992274 0.858861265 0.850566444 0.827082813 0.740274976 0.988794182 0.845730021 1 19.57567112 0.978754334 1.004527588 0.992321837 0.846497445 0.124459242 0.099333617 0.981741356 2.093590502 0.084961462 0.028151519 9.522573503 -0.978754334 -0.145824392 NFGIWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NFGIWLR 7 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 138.07 0.0065628 439360000 582480 1266090 528200 573290 1291470 338210 549300 1131880 712160 FALSE TRUE 546023.6166 1359832.621 540729.1534 588001.592 1190043.156 435845.7366 466937.5645 1273197.71 593295.8953 0.920322593 2.291997352 0.911398777 0.991076454 2.005817275 0.734617819 0.787023083 2.145974243 1 19.17839228 3.863293521 7.023553808 1.185671325 1.688088365 0.06163403 0.583046766 0.454129863 25.31353542 0.139109256 0.252670374 7299.506857 -3.863293521 0.50241704 NFGSYVTHETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NFGSYVTHETK 11 0 P63167;Q96FJ2 P63167;Q96FJ2 DYNLL1;DYNLL2 "Dynein light chain 1, cytoplasmic;Dynein light chain 2, cytoplasmic" 0 ;;; 180.2 6.77E-06 1842940000 6217610 3770710 4991350 5091710 4596650 4232470 6665900 3810500 4136020 FALSE TRUE 5828460.889 4049897.292 5109747.179 5222371.899 4235647.651 5454315.381 5666410.178 4286249.313 3445691.542 1.691521373 1.175351085 1.482938074 1.515623739 1.22925909 1.582937797 1.64449142 1.243944578 1 21.71636213 0.991977114 8.128009526 1.000021034 1.453672554 0.476051099 0.164056836 0.105946923 66.7771899 0.156705065 0.039240026 9.816962094 -0.991977114 0.453651521 NFHEVMLALTVLETCVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NFHEVMLALTVLETCVK 17 0 O60784;O60784-4;O60784-2;O60784-3;V9GYF4;B0QY02;V9GZ68;Q6UW50;H7BYN7 O60784 TOM1 Target of Myb protein 1 0 ; 149.57 3.20E-07 173467000 224716 219828 234169 238859 295240 180613 276540 226437 290320 FALSE TRUE 210651.4267 236104.2939 239723.5993 244988.5263 272053.0413 232753.0411 235075.3943 254708.1579 241863.7165 0.870950921 0.976187323 0.991151557 1.012919713 1.124819569 0.962331368 0.971933276 1.053106111 1 17.88383483 5.867649604 0.907875087 1.013854337 2.27E-11 0.496741609 0.046050138 12.71559863 1.691976167 0.014385532 20.49055345 737309.1166 -5.867649604 -1.013854337 NFHIFYQLLEGGEEETLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NFHIFYQLLEGGEEETLR 18 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 193.8 1.05E-14 92117000 112110 111550 103050 104160 127630 65391 100070 89528 93291 FALSE TRUE 105093.2352 119809.2781 105494.3947 106832.9219 117606.4546 84268.32017 85065.4325 100705.7679 77720.12942 1.352200981 1.541547588 1.357362571 1.374584972 1.513204565 1.084253472 1.094509661 1.295748844 1 16.24600068 2.233520245 24.99998412 1.121566866 1.431273531 0.723716743 0.094894253 61.7751941 306398.4751 0.032449604 0.02470653 171.2064983 -2.233520245 0.309706665 NFHIFYQLLEGGEEETLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NFHIFYQLLEGGEEETLRR 19 1 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 109.03 0.00017098 141910000 56925 39162 52206 53317 58933 61175 60887 42481 71692 FALSE TRUE 53362.16586 42061.59523 53444.35097 54685.20449 54304.6399 78835.22941 51757.5596 47784.84636 59726.14205 0.893447392 0.704240954 0.894823425 0.915599143 0.909227317 1.319945114 0.86658133 0.800065846 1 15.86607491 3.335677951 1.572101074 0.986046994 0.789579098 0.195220957 0.143894955 0.532768219 2.704455416 0.046202676 0.073221166 2166.09725 -3.335677951 -0.196467896 NFHQYSVEGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NFHQYSVEGGK 11 0 Q9HCY8 Q9HCY8 S100A14 Protein S100-A14 0 ;; 151.1 3.36E-05 931150000 2260060 1782880 1751390 1770580 2505030 1425280 2390850 2121040 2993840 FALSE TRUE 2118606.879 1914886.29 1792933.798 1816016.08 2308295.049 1836735.199 2032364.238 2385856.513 2494148.763 0.84943084 0.767751434 0.718855998 0.728110571 0.92548411 0.736417661 0.814852854 0.956581479 1 21.25011609 1.224275805 3.001981 0.998204049 0.779866938 0.6154852 0.061985182 0.154258664 2.402042798 0.054498093 0.015390048 16.7600691 -1.224275805 -0.218337111 NFLIEPFVPHSQAEEFYVCIYATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NFLIEPFVPHSQAEEFYVCIYATR 24 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ;;; 302.57 2.56E-62 1087116000 1756157 1820811 1601798 1435145 1899081 1302726 1835081 1734635 1214997 FALSE TRUE 1646242.268 1955625.741 1639793.405 1471973.25 1749934.839 1678801.848 1559927.64 1951207.998 1012206.152 1.626390302 1.932042932 1.620019205 1.454222787 1.728832448 1.658557247 1.541116538 1.927678463 1 19.94907172 -1.815420479 2.639797588 0.777064244 1.684623574 0.67206451 0.15061708 9617720.482 7188525.094 13711615.72 0.035569689 0.015296058 1.815420479 0.907559331 NFLNAIATDIIHLHSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NFLNAIATDIIHLHSQR 17 0 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 ; 135.09 8.55E-06 67035000 110991 102731 122812 110677 108819 86960 121110 107559 91027 FALSE TRUE 104044.2714 110337.3101 125725.1586 113517.1592 100272.7947 112063.9403 102950.6798 120987.9779 75834.00564 1.372000207 1.454984597 1.657899482 1.496916301 1.322266889 1.477753145 1.357579347 1.595431718 1 16.21055731 -2.815206121 0.389767398 6.40E-13 1.485809398 0.647565898 0.106523861 61.91911666 2.244006817 51.67043123 0.069839223 0.001530361 2.815206121 1.485809398 NFMPALEETPFHSCTAGPNPTLGRPLS(ph)PKPSSPGSVLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NFMPALEETPFHSCTAGPNPTLGRPLSPKPSSPGSVLAR 39 2 F8VWK5;F8VUY0;F8VVS9;Q15583-4;Q15583-2;Q15583-3;Q15583 F8VWK5 TGIF1 Homeobox protein TGIF1 1 NFMPALEETPFHSCTAGPNPT(0.001)LGRPLS(0.999)PKPSSPGSVLAR;NFMPALEETPFHSCTAGPNPT(0.067)LGRPLS(0.933)PKPSSPGSVLAR;NFMPALEETPFHSCTAGPNPT(0.129)LGRPLS(0.87)PKPSS(0.001)PGSVLAR 246.34 7.03E-51 818870000 594470 458834 503505 473449 483285 261267 520406 377417 326472 TRUE FALSE 557263.1839 492806.5468 515448.3764 485598.5029 445329.7456 336690.5416 442375.9515 424538.3432 271981.7141 2.048899448 1.811910585 1.895158202 1.785408642 1.637351787 1.237916096 1.62649152 1.560907669 1 18.05315013 1.898743817 0.079154566 3.30E-15 3.118527477 0.79120569 0.141086556 7.967304887 0.535678253 9.454233762 10.69679895 79.2033986 -1.898743817 3.118527477 NFPNAIEHTLQWAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NFPNAIEHTLQWAR 14 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 266.2 7.67E-25 4709400000 2904100 3573800 2836300 2721200 3616300 1721800 3008200 3089800 3524600 FALSE TRUE 2722337.565 3838407.871 2903578.375 2791030.599 3332290.385 2218855.709 2557148.337 3475568.331 2936321.49 0.927125171 1.30721649 0.988848934 0.95051942 1.134852024 0.755658301 0.87086797 1.183647071 1 21.4855785 3.685035941 4.696634443 0.961742423 1.146348438 0.102277184 0.151131997 0.282245768 14.18916405 0.038460629 0.062947358 4842.124384 -3.685035941 0.184606015 NFQAATESVPNSGNIHNGSLEQTEEPETSSHS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NFQAATESVPNSGNIHNGSLEQTEEPETSSHSPSR 35 0 E7EUR8;A0A1B0GVL4;P78312-4;P78312-6;P78312-2;P78312-5;P78312 E7EUR8 FAM193A Protein FAM193A 1 NFQAATESVPNSGNIHNGSLEQTEEPET(0.044)S(0.023)S(0.074)HS(0.685)PS(0.174)R 160.38 2.79E-14 158260000 27851 42312 39733 47774 45414 29636 49591 42491 32621 TRUE FALSE 26107.85563 45444.82451 40675.48552 48999.96172 41847.36763 38191.4321 42155.28993 47796.09488 27176.34436 0.960683132 1.672219924 1.496723952 1.803037269 1.539845355 1.405318964 1.551175882 1.758738933 1 14.73006378 NFQDFDCQEHDIETTHGVVHVTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NFQDFDCQEHDIETTHGVVHVTIR 24 0 Q5TH30;Q9UGV2 Q5TH30 NDRG3 Protein NDRG3 0 156.92 6.52E-09 116580000 18647 47014 30745 33932 36967 40290 34972 37536 32819 FALSE TRUE 17479.91756 50494.96548 31474.28592 34802.75257 34063.76094 51921.06895 29728.27326 42222.45223 27341.29688 0.639322913 1.846838711 1.151162875 1.272900577 1.245872172 1.898998031 1.087302969 1.544273939 1 14.73879406 -1.062368486 4.383948128 0.999977879 1.364987459 0.071065561 0.368416834 1.644165497 94214782.14 5755.7748 0.075480985 0.08662266 1.062368486 0.36500958 NFQLLVITHDEDFVELLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NFQLLVITHDEDFVELLGR 19 0 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494BZX8 Q92878-2 RAD50 DNA repair protein RAD50 0 ;; 181.14 3.21E-14 61666000 199178 197607 197770 207674 208881 160805 220521 171995 194719 FALSE TRUE 186711.8045 212238.0279 202461.1978 213003.2664 192476.3288 207226.793 187455.9233 193468.9544 162219.141 1.15098504 1.308341461 1.248072185 1.313058774 1.186520454 1.277449701 1.155572161 1.192639495 1 17.30758453 0.66291183 0.624713265 0.995998798 1.260996541 0.654600473 0.054474714 0.689180833 0.524834456 0.054164884 0.01989785 4.601631421 -0.66291183 0.264997743 NFQTAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NFQTAHR 7 0 O75475;O75475-3;O75475-2;V9GYT7 O75475 PSIP1 PC4 and SFRS1-interacting protein 0 ; 98.997 0.010852 178619000 232670 500420 346980 371790 468260 348590 383090 383980 331440 FALSE TRUE 218107.6 537471.6175 355210.5295 381330.7608 431484.7485 449222.2741 325649.2109 431920.7482 276120.5228 0.789899997 1.946510937 1.286432916 1.381030128 1.562668157 1.626906503 1.17937344 1.564247177 1 18.0749386 -0.951663432 0.498489161 0.862405791 1.460692788 0.136539982 0.308200572 31.19239834 4.971450971 6.635335153 0.134761228 0.111772913 0.951663432 0.598286996 NFRNPLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NFRNPLAK 8 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 129.47 0.00099363 4338900000 972880 1102110 987590 1318030 1805400 1067680 1483600 1044900 2114690 FALSE TRUE 911989.1774 1183711.371 1011016.101 1351852.881 1663611.167 1375901.884 1261147.953 1175358.065 1761734.578 0.517665481 0.671901083 0.573875381 0.76734197 0.944302954 0.780992722 0.715855821 0.66715956 1 20.74856515 3.174742591 5.632708756 0.798892281 0.603958329 0.500443898 0.105171387 0.180667844 10.97193744 0.029392684 0.0357198 1495.349092 -3.174742591 -0.194933952 NFRPDDPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NFRPDDPTR 9 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7EMQ3 P50570-2 DNM2 Dynamin-2 0 ; 71.451 0.045555 304420000 831840 728780 770720 824020 815070 700060 875780 788070 828680 FALSE TRUE 779776.6193 782739.6295 789001.8424 845165.7483 751057.69 902155.9575 744464.9193 886462.2743 690367.9545 1.129508712 1.133800641 1.142871475 1.224225057 1.087909259 1.306775541 1.078359612 1.284043195 1 19.39700597 3.456049251 24.6781591 1.168958586 1.134995325 0.018372186 0.093480874 820.568939 960993.5801 0.022252317 0.030138904 2857.914625 -3.456049251 -0.033963262 NFS(ph)AAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NFSAAK 6 0 Q13555-8;Q13555-9;Q13555-10;Q13555-3;Q13555-7;Q13555-4;Q13555-2;A0A2Q3DQE3;Q13555;Q8WU40;H0Y6G2;E9PF82;E9PBG7;Q13557;Q13557-8;Q13557-6;Q13557-11;Q13557-12;Q13557-10;Q13557-3;Q13557-4;Q13557-9;Q13557-5;H0Y9J2 Q13555-8;E9PF82;Q13557 CAMK2G;CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit gamma;Calcium/calmodulin-dependent protein kinase type II subunit delta 1 NFS(1)AAK 82.645 0.061571 285010000 457520 245710 282820 259230 278910 150490 405720 302250 461790 TRUE FALSE 428884.6399 263902.6241 289528.624 265882.2807 257005.5337 193934.02 344886.0525 339986.5778 384714.2657 1.114813455 0.685970466 0.752580941 0.69111625 0.66804264 0.504098853 0.896473261 0.883737901 1 18.5534278 1.578566925 10.0899038 0.9224025 0.72586898 0.252467326 0.154530718 0.147329371 31.44082341 0.077168973 0.036299503 37.89369235 -1.578566925 -0.19653352 NFSDNQLQEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NFSDNQLQEGK 11 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ;;; 260.59 2.78E-20 1667130000 2125500 1614220 1805420 1813400 1884710 1263250 2210980 1522120 2180000 FALSE TRUE 1992468.749 1733738.528 1848245.415 1859934.914 1736692.479 1627929.768 1879464.075 1712160.033 1816143.917 1.097087478 0.954626179 1.017675636 1.024112074 0.956252675 0.89636606 1.034865165 0.942744689 1 20.7924471 4.746882471 24.14322529 0.981008337 1.097087573 0.43209633 0.04268873 636.2887516 1845921.644 0.009641875 0.107198642 55831.90821 -4.746882471 0.116079236 NFTKPQDGDVIAPLIT(ph)PQKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NFTKPQDGDVIAPLITPQKK 20 2 Q9Y3Z3-4;Q9Y3Z3;Q9Y3Z3-3 Q9Y3Z3-4 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 1 NFTKPQDGDVIAPLIT(1)PQKK 98.491 0.037746 1452800000 576170 319090 378010 356970 426010 251440 519540 322480 632770 TRUE FALSE 540108.5482 342715.7556 386976.5757 366130.4545 392552.893 324026.6462 441639.8002 362742.3379 527156.5991 1.024569453 0.650121342 0.734082768 0.694538312 0.744660872 0.614668671 0.837777239 0.688111158 1 19.00787207 -1.104560635 4.753230504 1.000014514 0.738162418 0.316616671 0.115191195 1.55E-05 2.93E-06 0.097820934 0.023055338 0.078603044 1.104560635 -0.261852096 NFVFHTLS(ph)PVKAEAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NFVFHTLSPVKAEAAK 16 1 E7ESG2;Q9HAW4-2;Q9HAW4-3;Q9HAW4 E7ESG2 CLSPN Claspin 1 NFVFHT(0.033)LS(0.967)PVKAEAAK;NFVFHT(0.002)LS(0.998)PVKAEAAK 125.09 4.78E-05 559010000 626580 420510 492360 504730 609730 372640 686830 465810 871190 TRUE FALSE 587363.4763 451644.9979 504039.0117 517682.2263 561844.2653 480215.1187 583846.2177 523967.4039 725782.7609 0.809282761 0.622286753 0.694476418 0.713274349 0.774121811 0.661651316 0.804436602 0.72193421 1 19.46917826 -1.459157105 0.300737383 1.215231713 0.68561563 0.673006428 0.059853383 11.19837408 0.670010408 1.895346443 0.059140069 0.034741046 1.459157105 -0.529616083 NFWNGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NFWNGR 6 0 P47755;P52907 P47755;P52907 CAPZA2;CAPZA1 F-actin-capping protein subunit alpha-2;F-actin-capping protein subunit alpha-1 0 ;; 148.4 0.025056 3803210000 1455020 1333540 1402100 1331750 1432620 1049360 1528640 1172600 1231840 FALSE TRUE 1363952.895 1432276.689 1435358.474 1365924.96 1320107.804 1352293.197 1299434.623 1319001.691 1026237.946 1.329080552 1.395657503 1.398660496 1.331002196 1.286356453 1.317718958 1.266211826 1.28527862 1 19.96893385 -1.756853055 0.215710782 0.637511641 1.411407828 0.925662058 0.030367649 6.77797724 0.239365795 1.338500068 0.071110622 0.017504389 1.756853055 0.773896186 NFWSHETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NFWSHETR 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 169.77 0.00029906 1301140000 900890 1050840 833600 953680 978200 584140 1054560 906970 905430 FALSE TRUE 844504.903 1128645.287 853373.3857 978153.0434 901376.1179 752771.7353 896438.5181 1020207.201 754307.8837 1.119575867 1.496266062 1.13133298 1.296755694 1.194971095 0.997963499 1.188425227 1.352507674 1 19.52479398 3.775454443 7.278122911 1.171039551 1.329754155 0.141725187 0.142354658 0.359404352 45.30975893 0.033657825 0.060574368 5962.857669 -3.775454443 0.158714604 NFYES(ph)DDDQKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NFYESDDDQKEK 12 1 O00203;O00203-3 O00203 AP3B1 AP-3 complex subunit beta-1 1 NFYES(1)DDDQKEK;NFYES(1)DDDQKEK;NFYES(1)DDDQKEK;NFYES(1)DDDQKEK;NFYES(1)DDDQKEK;NFYES(1)DDDQKEK 199.08 1.07E-07 4483141000 10553750 3642413 5639440 5575970 5358990 4099037 7740020 4341429 5460570 TRUE FALSE 9893209.626 3912101.048 5773210.18 5719058.83 4938116.543 5282362.44 6579475.856 4883465.967 4549165.59 2.174730603 0.859960134 1.269070133 1.257166554 1.085499405 1.161171721 1.446303883 1.073486087 1 22.11717052 4.749523014 24.9571685 1.167214345 2.174731195 0.800518198 0.161321518 732.512912 1667618.392 0.039175685 0.586750913 56172.40437 -4.749523014 1.00751685 NFYNEHEEITNLTPQQLIDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NFYNEHEEITNLTPQQLIDLR 21 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ;; 252.01 2.51E-36 608830000 487400 518000 485810 489900 509950 392298 584150 437605 553260 FALSE TRUE 456894.504 556353.259 497333.6426 502471.6634 469900.584 505548.0642 496562.1305 492240.9475 460917.3318 0.991272127 1.207056495 1.079008335 1.090155715 1.019489942 1.096830232 1.077334472 1.067959292 1 18.81414849 3.533357175 3.519355313 1.064952741 1.122682543 0.034845458 0.060115357 0.412662034 10.19400669 0.015179127 0.023811218 3414.736332 -3.533357175 0.057729801 NFYQEHPDLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 NFYQEHPDLAR 11 0 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4;X6RLV5 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;;;;;; 208.79 1.84E-08 19490810000 7298730 7449710 7227430 7119130 7958160 5320720 7915860 6735740 9597090 FALSE TRUE 6841915.518 8001294.28 7398868.053 7301818.928 7333158.215 6856725.489 6728950.28 7576711.966 7995273.679 0.855745005 1.00075302 0.925405227 0.913266915 0.917186642 0.857597346 0.841616003 0.947648857 1 22.93071599 3.082626983 1.765969825 0.893292295 0.94449525 0 0.057640598 0.706860165 4.500867776 0.018522963 0.023416275 1209.558793 -3.082626983 0.051202956 NFYVEHPEVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 NFYVEHPEVAR 11 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;;;; 168.02 1.86E-05 5484160000 3765020 3751830 3613500 3787370 4288880 2828100 4360630 3601820 4574760 FALSE TRUE 3529374.119 4029619.397 3699213.926 3884560.326 3952048.665 3644526.56 3706794.014 4051515.156 3811203.002 0.926052513 1.057309043 0.97061582 1.019247813 1.036955697 0.956266711 0.972604716 1.063054147 1 21.86181502 4.767440038 23.76061058 1.005198314 0.926052276 0.335856147 0.036436188 6763.866988 5564804.317 0.008413377 0.791213839 58538.29077 -4.767440038 -0.079146038 NGAAGPHS(ph)PDPLLDEQAFGDLTDLPVVPK ddPTM_SK-BR-3_Pertuzumab_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 165.8 2.95E-12 525787000 551802 349667 501034 608318 662839 301089 350954 224954 379044 TRUE FALSE 517265.6978 375556.7085 512918.7631 623928.4698 610782.2987 388008.5065 298331.7058 253040.0021 315779.1077 1.638061814 1.18930195 1.624296068 1.975838346 1.934207438 1.228733938 0.94474808 0.801319644 1 18.2685562 1.986239855 3.927353012 0.932073312 1.61440981 0.706017815 0.222503244 0.150602542 5.072750421 0.114223138 0.070412137 96.88127701 -1.986239855 0.682336498 NGALDQQKDELDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NGALDQQKDELDVR 14 1 P12270 P12270 TPR Nucleoprotein TPR 0 93.909 0.0039899 183050000 441890 280120 353980 348410 376100 237100 428900 289330 428750 FALSE TRUE 414232.8937 300860.3763 362376.5728 357350.7905 346562.6231 305546.921 364590.4267 325453.4874 357188.8552 1.159702739 0.84230057 1.014523739 1.00045336 0.970250382 0.855421205 1.020721731 0.911152413 1 18.44632754 2.462014102 24.97849455 0.947942055 0.979605918 0.055775923 0.088733052 1068.426733 1766549.725 0.028670394 0.023996355 289.7437669 -2.462014102 0.031663863 NGDECAYHHPIS(ph)PCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 223.51 2.10E-12 1059170000 2018120 1014970 1318570 1217950 1384170 1527490 2519840 1147070 1612050 TRUE FALSE 1891809.472 1090119.435 1349847.103 1249204.659 1275462.872 1968451.566 2142013.385 1290284.215 1342988.441 1.408656556 0.811711703 1.005107015 0.930167841 0.949719918 1.465724876 1.594960403 0.960756009 1 20.35701546 2.247296872 24.97315989 1.341756241 0.986214185 0.134191266 0.248367518 207.4417339 592986.1019 0.081484914 0.067195876 176.7245448 -2.247296872 -0.355542056 NGDGFVSLEEFLGDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NGDGFVSLEEFLGDYR 16 0 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 ;; 142.85 3.42E-06 61909000 102310 73137 84169 85212 76368 68121 109126 80131 71269 FALSE TRUE 95906.59973 78552.13958 86165.52843 87398.68418 70370.36533 87786.42685 92763.56938 90135.53174 59373.74348 1.615303232 1.323011401 1.451239611 1.47200899 1.185210182 1.478539531 1.562366863 1.51810424 1 15.85753746 4.753811941 23.21050987 1.404474407 1.615303653 0.141720492 0.172687223 2116.503778 3220890.908 0.037431714 0.804525522 56729.88988 -4.753811941 0.210829246 NGDLDEVKDYVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NGDLDEVKDYVAK 13 1 P58546;C9JL85 P58546 MTPN Myotrophin 0 ;; 210.34 2.80E-08 1784950000 4040340 1996510 2740960 2697490 2763130 1756380 3639980 2151870 3840290 FALSE TRUE 3787462.332 2144333.678 2805976.866 2766712.16 2546124.916 2263418.394 3094198.791 2420535.706 3199320.79 1.183833251 0.670246536 0.877053928 0.864781103 0.795832954 0.70746841 0.967142401 0.756577994 1 21.60933423 -1.271234188 4.013421274 1.000189877 0.840288439 0.085775116 0.145909292 0.000218023 3.96E-05 0.124245041 0.029250153 0.053550781 1.271234188 -0.159901438 NGEELHGGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NGEELHGGKR 10 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;;; 115.57 0.00078214 313498000 649890 465107 519688 537585 514509 373349 676990 477507 513548 FALSE TRUE 609214.545 499544.0062 532015.2448 551380.3412 474101.5386 481128.7955 575481.6344 537124.8001 427833.5212 1.423952343 1.167613059 1.24350996 1.288773118 1.108144909 1.124570123 1.345106463 1.255452819 1 18.70669 -1.482433875 2.968847525 0.993114473 1.237535467 0.386800001 0.096434793 39774149.93 45102561.81 2248204.308 0.021851763 0.032928059 1.482433875 0.244420994 NGEFELMHVDEFIDELLHSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NGEFELMHVDEFIDELLHSER 21 0 Q8NAV1 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 0 ;;;; 182.17 3.34E-17 128819000 69254.8 65529.8 68537.2 66971 68800.8 52802.7 80498 57853.5 70440 FALSE TRUE 64920.26569 70381.69458 70162.93475 68689.58924 63397.4627 68045.98231 68428.07221 65076.63683 58683.10894 1.106285384 1.199351838 1.195624022 1.170517215 1.080335787 1.159549716 1.166060787 1.108950054 1 15.84065768 -1.150010577 0.308570836 0.903883773 1.176066664 0.605706409 0.038179609 10.74133087 0.77940622 0.904345454 0.040024348 0.070792854 1.150010577 0.272182891 NGESAS(ph)PERDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NGESASPERDR 11 1 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 NGES(0.008)AS(0.992)PERDR;NGESAS(1)PERDR 103.79 0.0016272 99811000 173236 141235 170375 147435 164245 149416 172023 134517 117233 TRUE FALSE 162393.468 151692.1864 174416.3755 151218.4317 151345.8602 192549.9736 146229.7481 151311.7436 97666.05495 1.662742169 1.553172046 1.785844381 1.548321285 1.549626022 1.971513785 1.497242294 1.549276703 1 16.5755696 0.645548752 1.426589233 1.001126474 1.662326575 0.689267253 0.137572941 0.686257067 2.040336236 0.1197912 0.035144293 4.421287458 -0.645548752 0.661200101 NGGS(ph)FEDDLSLGAEANHLHESDAQIENCNNILAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NGGSFEDDLSLGAEANHLHESDAQIENCNNILAK 34 0 E9PHV5;P28290-3;P28290 E9PHV5 SSFA2 Sperm-specific antigen 2 1 NGGS(0.515)FEDDLS(0.419)LGAEANHLHES(0.066)DAQIENCNNILAK 107.09 2.42E-05 21302000 9474.7 8812.3 9576 10470 7954.9 5921.2 13935 7556.9 11286 TRUE FALSE 8881.69544 9464.771861 9803.147242 10738.67793 7330.154243 7630.554317 11845.57612 8500.3956 9402.29369 0.944630718 1.006644993 1.042633592 1.142133854 0.77961341 0.811563068 1.259860254 0.904076801 1 13.19879703 1.745669837 24.99999939 1.078728648 0.971200358 0.090117694 0.1366191 3.366222007 11872.41615 0.061545785 0.034130094 55.67623212 -1.745669837 -0.10752829 NGGSFEDDLS(ph)LGAEANHLHESDAQIENCNNILAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NGGSFEDDLSLGAEANHLHESDAQIENCNNILAK 34 0 E9PHV5;P28290-3;P28290 E9PHV5 SSFA2 Sperm-specific antigen 2 1 NGGS(0.409)FEDDLS(0.491)LGAEANHLHES(0.101)DAQIENCNNILAK 86.544 0.00098203 79932000 11568 15235 18292 15189 13027 12115 22729 13784 20524 TRUE FALSE 10843.97953 16363.01525 18725.89488 15578.77545 12003.91197 15612.40383 19320.99746 15504.96274 17098.41181 0.634209753 0.956990359 1.095183289 0.911124122 0.70204836 0.913090877 1.129987842 0.906807189 1 14.06157471 1.936737062 14.41309161 1.025447068 0.899232854 0.166488136 0.140097044 6.12704066 1393.455228 0.060060655 0.038621205 86.4444393 -1.936737062 -0.126214214 NGHDGDTHQEDDGEKS(ph)D ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NGHDGDTHQEDDGEKSD 17 1 K7EQH5;Q08117;Q08117-2 K7EQH5 AES Amino-terminal enhancer of split 1 NGHDGDTHQEDDGEKS(1)D;NGHDGDTHQEDDGEKS(1)D;NGHDGDTHQEDDGEKS(1)D 292.36 3.05E-46 370090000 1124150 483431 677770 598782 585410 467058 873680 523065 584415 TRUE FALSE 1053791.458 519224.7342 693847.0245 614147.7599 539434.26 601890.0625 742679.7948 588370.8167 486872.361 2.164410105 1.066449394 1.425110727 1.261414303 1.107958272 1.236237895 1.525409644 1.208470358 1 18.89318408 4.746279414 24.92139718 1.262901065 2.16441056 0.769228191 0.160075028 445.1000454 1437042.813 0.037042083 0.400259758 55754.43432 -4.746279414 0.901509495 NGHRDS(ph)ITTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NGHRDSITTVR 11 1 Q8TF74;Q8TF74-2;A8MWR2;J3KSA3 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 1 NGHRDS(0.998)IT(0.001)T(0.001)VR;NGHRDS(0.93)IT(0.065)T(0.005)VR 166.64 1.22E-05 1356290000 663890 601160 619610 489090 687820 291740 762640 581620 1178300 TRUE FALSE 622338.31 645670.5119 634307.4418 501640.8774 633801.3917 375960.602 648289.212 654236.5373 981634.1179 0.633981948 0.657750683 0.646175016 0.511026327 0.645659498 0.382994636 0.660418378 0.666476975 1 19.90482587 0.712504097 1.954965434 0.999574847 0.594832322 0.690225462 0.085744807 0.680771099 3.758835183 0.078690122 0.021810507 5.158270313 -0.712504097 -0.404742525 NGIDILVGT(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NGIDILVGTPGR 12 0 Q9NR30;Q9NR30-2;Q9BQ39;A0A087WVC1 Q9NR30;Q9BQ39 DDX21;DDX50 Nucleolar RNA helicase 2;ATP-dependent RNA helicase DDX50 1 NGIDILVGT(1)PGR;NGIDILVGT(1)PGR 121.99 0.0040961 103619000 253280 236020 240750 237870 238860 178815 298150 204116 258940 TRUE FALSE 237427.6569 253495.1664 246460.7037 243974.1469 220100.8991 230435.9877 253445.1754 229600.3319 215721.2412 1.100622524 1.175105265 1.142496225 1.130969512 1.020302395 1.068211857 1.174873527 1.064338081 1 17.71880871 2.979128632 23.63141456 1.083697546 1.146152894 0.297987841 0.050416603 529.2512521 599240.7723 0.01535833 0.016479587 953.0784104 -2.979128632 0.062455348 NGIHDLDNISFPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NGIHDLDNISFPK 13 0 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 ;;; 158.81 3.99E-05 865660000 3746930 2746450 3105160 2823510 3188000 2133850 3913390 2867360 3072530 FALSE TRUE 3512416.34 2949800.016 3178815.862 2895966.047 2937627.34 2749857.855 3326613.5 3225356.208 2559704.894 1.372195814 1.152398475 1.241868103 1.131367156 1.147642975 1.074287064 1.299608212 1.260050022 1 21.28754606 4.743526987 24.40230114 1.179162603 1.372195926 0.337784009 0.089488813 455.8613509 2239772.635 0.01985657 0.164101383 55402.19703 -4.743526987 0.193033323 NGIS(ph)FTIWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NGISFTIWDR 10 0 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 1 NGIS(0.96)FT(0.04)IWDR;NGIS(0.972)FT(0.028)IWDR;NGIS(0.672)FT(0.328)IWDR;NGIS(0.786)FT(0.214)IWDR;NGIS(0.735)FT(0.265)IWDR 148.62 2.60E-05 142229000 262428 267578 270707 275187 284788 220497 334786 243122 382633 TRUE FALSE 246003.0999 287389.7535 277128.2979 282248.7643 262421.8993 284150.9044 284587.9473 273476.3169 318769.0804 0.771728235 0.901560946 0.86937007 0.885433317 0.823235111 0.891400459 0.892771491 0.857913561 1 18.28215217 -5 0.233852708 1.724816027 0.8539625 0.572147539 0.038174627 122.2134105 1.222228735 41.99013798 0.058749304 1.00E-05 5 -0.870853527 NGIS(ph)PTNPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NGISPTNPTK 10 0 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q9UJF2;Q9UJF2-2 Q5VWQ8;Q9UJF2 DAB2IP;RASAL2 Disabled homolog 2-interacting protein;Ras GTPase-activating protein nGAP 1 NGIS(0.979)PT(0.021)NPTK 86.772 0.013826 0 213340 89356 127840 123570 135170 93649 166330 105240 212800 TRUE FALSE 199987.4302 95972.01121 130872.4252 126741.0154 124554.2934 120683.946 141390.3606 118379.4457 177282.3053 1.128073272 0.541351327 0.738214821 0.714910691 0.702576003 0.680744454 0.797543559 0.66774541 1 17.43568902 -1.514472318 4.272295339 1.002297662 0.727351092 0.207938726 0.151552252 0.002938477 0.000333945 0.130004778 0.030402015 0.030586352 1.514472318 -0.274946569 NGLEGS(ph)SEETSFHDESLQDDREEIENNSYHMHPAGIILTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NGLEGSSEETSFHDESLQDDREEIENNSYHMHPAGIILTK 40 1 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 NGLEGS(0.42)S(0.42)EET(0.15)S(0.009)FHDESLQDDREEIENNSYHMHPAGIILTK 96.221 7.91E-05 112660000 20278 23668 26252 27242 27661 20454 38461 22883 27352 TRUE FALSE 19008.83618 25420.40335 26874.70984 27941.07584 25488.61664 26358.73776 32694.1301 25739.99292 22786.7745 0.834204779 1.115577079 1.179399473 1.226197057 1.118570627 1.156755984 1.434785345 1.129602302 1 14.4759091 5.338224213 1.059771809 1.208703341 1.51E-16 0.45793138 0.112455904 4.581673748 1.713954874 0.032287431 8.472591264 217883.4346 -5.338224213 -1.208703341 NGMVLKPHFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NGMVLKPHFHK 11 1 P26373;P26373-2;J3QSB4;H3BTH3 P26373 RPL13 60S ribosomal protein L13 0 ;; 110.38 0.0011626 1128310000 3587170 4008030 2942400 2976530 4622460 1854760 3949930 3822750 4792220 FALSE TRUE 3362655.433 4304788.712 3012195.118 3052912.799 4259430.638 2390199.102 3357674.666 4300028.752 3992367.523 0.842271012 1.078254616 0.754488433 0.764687314 1.066893419 0.598692152 0.841023439 1.077062351 1 21.92881311 -2.023262958 6.789765678 1.183804368 0.872236803 0.054710633 0.157909437 0.109233193 0.000374253 0.038012668 0.033689074 0.009478444 2.023262958 -0.311567565 NGNYCVLQMDQSYKPDENEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NGNYCVLQMDQSYKPDENEVR 21 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 171.79 5.88E-12 476970000 282680 167356 205833 224706 229661 140975 286907 183376 262503 FALSE TRUE 264987.5634 179747.2124 210715.456 230472.3364 211624.3515 181672.194 243887.9589 206270.8973 218689.5535 1.211706546 0.821928663 0.963536907 1.053879039 0.967693006 0.830731012 1.11522455 0.943213309 1 17.73852478 1.715975266 24.99999697 1.026362274 0.958697513 0.017876155 0.117266939 2.538810625 2798.53922 0.050309727 0.027899347 51.9966383 -1.715975266 -0.067664761 NGPFKPNYYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 71.349 0.046599 0 144390 168190 114130 122400 224800 80895 155210 181370 215240 FALSE TRUE 135352.8876 180642.9626 116837.2175 125540.9912 207145.1148 104248.0733 131937.7014 204014.4437 179315.0535 0.754832821 1.007405452 0.651575064 0.700114066 1.155202036 0.581368219 0.73578709 1.137742982 1 17.45213708 1.239293771 24.99996607 1.068871559 0.798963892 0.301263615 0.171471291 23.06989856 786912.3835 0.124825801 0.039424588 17.34977195 -1.239293771 -0.269907667 NGPLNES(ph)QEDEEDSEHGTSLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NGPLNESQEDEEDSEHGTSLNR 22 0 Q9H2K8 Q9H2K8 TAOK3 Serine/threonine-protein kinase TAO3 1 NGPLNES(1)QEDEEDSEHGTSLNR;NGPLNES(1)QEDEEDSEHGTSLNR 353.03 2.66E-96 529280000 194922 193720 190242 229538 195177 142324 269820 208434 224481 TRUE FALSE 182722.18 208063.2304 194754.6301 235428.3337 179848.5857 183410.6284 229362.9959 234457.4437 187013.6709 0.977052528 1.112556261 1.041392478 1.258883014 0.961686837 0.980733801 1.226450424 1.253691469 1 17.51278421 1.71034518 10.96376223 1.178841471 1.064637694 0.160965635 0.108409738 0.174149227 47.28070695 0.047328025 0.025747917 51.3269171 -1.71034518 -0.114203777 NGS(ph)EADIDEGLYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NGSEADIDEGLYSR 14 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 NGS(1)EADIDEGLYSR;NGS(1)EADIDEGLYSR 340.52 6.90E-69 486200000 417185 310679 356270 382653 309914 209684 346843 219695 259452 TRUE FALSE 391074.1355 333681.9964 364720.8926 392472.5238 285574.6046 270216.3669 294837.1121 247124.4044 216147.7851 1.809290507 1.543767827 1.68736817 1.8157601 1.321200698 1.250146361 1.364053358 1.143312222 1 17.72165853 2.620584346 4.937528286 1.242105843 1.680053772 0.79809652 0.124145761 0.108120726 3.944967979 0.038873841 0.036476581 417.4306618 -2.620584346 0.437947929 NGS(ph)GTLDLEEFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NGSGTLDLEEFLR 13 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 1 NGS(0.997)GT(0.003)LDLEEFLR;NGS(0.95)GT(0.05)LDLEEFLR;NGS(0.977)GT(0.023)LDLEEFLR 161.24 4.46E-05 58206000 124984 100192 95031 100285 102954 78796 130958 96369 144491 TRUE FALSE 117161.4745 107610.3199 97285.1802 102858.4829 94868.40814 101543.1261 111322.0637 108400.8818 120374.5187 0.973307938 0.893962619 0.808187491 0.854487179 0.788110384 0.843559976 0.924797581 0.900530137 1 16.8771705 1.031571698 1.199827981 0.995339126 0.857590675 0.386251773 0.052755003 0.489396554 1.460654151 0.049566486 0.01555062 10.75404126 -1.031571698 -0.13774845 NGS(ph)PPPGAPSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NGSPPPGAPSSR 12 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 NGS(1)PPPGAPSSR;NGS(1)PPPGAPSSR 164.3 6.05E-05 584480000 626600 453250 491650 489770 501620 376280 568890 405480 630350 TRUE FALSE 587382.2245 486809.1016 503312.1702 502338.3274 462224.7886 484905.9276 483590.2258 456105.0706 525140.5128 1.118523919 0.927007324 0.95843333 0.956578887 0.880192591 0.923383201 0.920877773 0.868539104 1 19.00234397 4.73877659 24.94873228 0.928187996 1.118523977 0.712665892 0.037737773 8.7639431 1011736.325 0.008273734 0.048225556 54799.49928 -4.73877659 0.190335981 NGS(ph)PTPAGSLGGGAVATAGGPGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NGSPTPAGSLGGGAVATAGGPGSR 24 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 NGS(0.867)PT(0.133)PAGSLGGGAVATAGGPGSR;NGS(1)PTPAGSLGGGAVATAGGPGSR;NGS(0.997)PT(0.003)PAGSLGGGAVATAGGPGSR 230.54 1.71E-45 287708000 183304 130278 147981 141649 140782 113227 182225 111961 161286 TRUE FALSE 171831.3298 139923.9187 151491.1792 145283.9532 129725.5496 145913.7968 154902.0529 125939.5773 134366.3247 1.278827342 1.04136151 1.127449006 1.081252714 0.96546177 1.085940225 1.152833892 0.937285273 1 17.03581208 4.742398494 24.68467091 1.064633314 1.278827441 0.510074346 0.069303604 276.0833106 1775639.446 0.015627578 0.118912492 55258.42399 -4.742398494 0.214194127 NGSEADIDEGLYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NGSEADIDEGLYSR 14 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 234.49 7.60E-17 295340000 515450 501260 531430 567730 628050 396460 643590 447070 894950 FALSE TRUE 483188.9046 538373.812 544035.7706 582298.913 578725.4864 510911.566 547089.6543 502887.6736 745577.0634 0.648073725 0.722090094 0.729684156 0.781004327 0.776211494 0.68525655 0.733780157 0.67449456 1 19.50799795 -1.820669202 2.856046431 1.085182631 0.722962749 0.816655595 0.04182835 19320917.21 15404867.06 11361665.32 0.009704557 0.015112308 1.820669202 -0.362219882 NGSGTLDLEEFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NGSGTLDLEEFLR 13 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ;;; 250.69 1.44E-17 381112000 674085 690960 634054 684186 728170 500569 817400 612329 645500 FALSE TRUE 631895.2231 742119.3973 649094.0603 701743.3711 670982.4655 645075.1442 694838.4584 688779.6236 537761.8799 1.175046515 1.380014882 1.20702877 1.304933275 1.247731553 1.199555358 1.292093182 1.28082642 1 19.03660797 -1.646845304 2.816901314 0.973000329 1.266806991 0.6531375 0.059615109 107663149.3 106147067.2 21186454.58 0.013051886 0.022550423 1.646845304 0.293806662 NGSLDSPGKQDT(ph)EEDEEEDEKDKGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NGSLDSPGKQDTEEDEEEDEKDKGK 25 3 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 1 NGS(0.006)LDS(0.202)PGKQDT(0.792)EEDEEEDEKDKGK;NGSLDS(0.018)PGKQDT(0.982)EEDEEEDEKDKGK 198.7 3.98E-25 786140000 1060420 121218 334110 303510 309890 170694 438570 165451 400070 TRUE FALSE 994050.2051 130193.1068 342035.247 311298.5804 285552.4894 219970.5868 372810.5 186107.9216 333295.7324 2.982487048 0.390623384 1.026221501 0.934001099 0.856754112 0.659986209 1.118557676 0.558386752 1 18.34644332 4.745664864 24.99996563 0.825606822 2.98248805 0.901049952 0.225400043 237.2331502 834806.8044 0.050753249 0.517171751 55675.59459 -4.745664864 2.156881229 NGSLDSPGKQDTEEDEEEDEKDKGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NGSLDSPGKQDTEEDEEEDEKDKGK 25 3 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 191.18 3.21E-18 167120000 392660 145140 206660 197980 235230 147580 282840 181430 311450 FALSE TRUE 368084.1115 155886.3166 211562.0728 203060.502 216755.9847 190183.9502 240430.7678 204081.9349 259466.983 1.418616378 0.600794424 0.815371846 0.782606325 0.835389467 0.732979387 0.926633381 0.786542983 1 17.98519144 -1.686239023 6.830960763 1.001202408 0.832759714 0.0228187 0.216221313 0.003515144 0.000161458 0.18586327 0.043511201 0.020594961 1.686239023 -0.168442694 NGSTAVAESVAS(ph)PQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NGSTAVAESVASPQK 15 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 NGSTAVAESVAS(1)PQK 174.02 9.83E-07 199890000 547120 296240 392350 345130 369140 271520 502290 318920 461430 TRUE FALSE 512876.7358 318173.9178 401656.7273 353986.6201 340149.2334 349903.4162 426976.2775 358737.864 384414.352 1.334176867 0.827684805 1.04485362 0.920846525 0.884850505 0.910224643 1.110718877 0.933206219 1 18.55230267 -0.801890774 7.455637286 0.999998658 0.985142573 0 0.144704782 0 0 0.124588485 0.029365788 0.157800809 0.801890774 -0.014856084 NGTLPWLRPDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NGTLPWLRPDSK 12 1 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 116.19 0.0007922 232240000 739190 498470 600970 610780 641660 396520 754860 477650 750790 FALSE TRUE 692925.4174 535377.2375 615225.2922 626453.6488 591266.6119 510988.887 641675.7508 537285.6539 625478.2987 1.107832868 0.855948541 0.983607734 1.001559367 0.945303159 0.81695702 1.025896106 0.858999673 1 19.2546003 2.479478368 24.99962263 0.927564847 0.965618849 0.081783634 0.085452317 346.5998857 3676111.494 0.027318898 0.023209117 301.6326631 -2.479478368 0.038054002 NGVAAEVS(ph)PAKEENPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NGVAAEVSPAKEENPR 16 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 NGVAAEVS(1)PAKEENPR 193.59 2.12E-10 221440000 305990 140580 193220 207920 212070 150390 281120 180430 285800 TRUE FALSE 286838.6321 150988.6895 197803.2696 213255.5792 195414.8776 193805.1516 238968.6658 202957.0827 238098.1337 1.204707604 0.634144784 0.830763629 0.89566254 0.820732505 0.813971738 1.00365619 0.852409381 1 17.86119679 1.749526687 25 0.948071349 0.835041004 0.041623276 0.147682872 6.371137758 14551.64323 0.063516318 0.035223054 56.17287954 -1.749526687 -0.113030345 NGVAAEVS(ph)PAKEENPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NGVAAEVSPAKEENPRR 17 2 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 NGVAAEVS(1)PAKEENPRR;NGVAAEVS(1)PAKEENPRR;NGVAAEVS(1)PAKEENPRR 208.69 2.58E-12 1443790000 1538160 914710 1093590 1112480 1216750 804060 1561050 992310 1888250 TRUE FALSE 1441889.311 982436.0802 1119530.471 1141028.12 1121191.363 1036179.069 1326985.045 1116202.088 1573088.876 0.916597487 0.624526748 0.711676554 0.725342438 0.71273237 0.658690736 0.843553765 0.709560728 1 20.58516875 -0.060354481 0.580857102 1.020458584 0.714761689 0.461315695 0.086703863 3.828648491 1.437159975 0.261142597 0.033370097 0.870252979 0.060354481 -0.305696895 NGVMPSHFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NGVMPSHFSR 10 0 P39019;A0A075B6E2 P39019 RPS19 40S ribosomal protein S19 0 ;;;; 147.91 1.98E-05 1007830000 597264 1212990 978180 979560 1225470 713695 1176460 1043730 1155750 FALSE TRUE 559882.3124 1302801.042 1001382.892 1004697.168 1129226.53 919727.1606 1000060.745 1174041.988 962847.8586 0.581485753 1.353070509 1.040021933 1.043464094 1.172798505 0.955215461 1.038648771 1.219343199 1 19.87694833 4.756869891 24.58753495 1.104105934 0.581485191 0.658905734 0.117877969 2079.499595 2792504.585 0.027988975 0.931214631 57130.74552 -4.756869891 -0.522620743 NGYGFINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 93.262 0.02604 445910000 385420 686480 342190 350820 724760 237779 368960 605020 575550 FALSE TRUE 361297.2502 737307.6935 350306.9084 359822.6351 667840.2731 306421.9373 313637.8733 680558.0788 479486.9868 0.753507937 1.537701155 0.730586894 0.750432535 1.39282252 0.639062051 0.654111335 1.419346296 1 18.87113214 3.891586339 7.684374901 0.904582686 1.192160121 0.048473185 0.335265086 0.496427856 38.84439364 0.080242241 0.145520519 7790.876849 -3.891586339 0.287577435 NGYGFVEFDDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NGYGFVEFDDLR 12 0 Q08170;A0A0D9SEM4 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 0 82.505 0.024842 0 263700 145890 169960 169280 203800 132310 203270 160230 195880 FALSE TRUE 247195.4877 156691.8474 173991.5315 173624.0114 187794.3701 170505.7491 172791.5506 180235.0682 163186.3626 1.514804815 0.960201851 1.066213676 1.063961526 1.150796961 1.04485293 1.058860237 1.104473838 1 17.31616097 4.745902706 24.99671093 1.055774006 1.514805032 0.886448605 0.051586654 281.0913023 956973.8907 0.012246633 0.127210677 55706.09372 -4.745902706 0.459031025 NGYGFVEFEDS(ph)RDADDAVYELNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NGYGFVEFEDSRDADDAVYELNGK 24 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 NGYGFVEFEDS(1)RDADDAVYELNGK;NGYGFVEFEDS(1)RDADDAVYELNGK;NGYGFVEFEDS(1)RDADDAVYELNGK 329.02 5.45E-87 384305000 507723 337634 388161 376488 361717 287183 536315 356374 385333 TRUE FALSE 475945.5237 362632.7727 397368.3622 386149.3195 333309.2059 370088.0701 455899.5447 400868.0784 321018.433 1.482611199 1.129632244 1.23783659 1.202888307 1.038286814 1.152856136 1.420166252 1.248738506 1 18.29229661 4.747644419 24.11809292 1.199554816 1.482611443 0.385170295 0.118069888 871.3365973 2313373.961 0.028472826 0.342315705 55929.94846 -4.747644419 0.283056627 NGYGFVEFEDSRDADDAVYELNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NGYGFVEFEDSRDADDAVYELNGK 24 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;; 319.52 7.52E-74 1053070000 1063693 949346 946403 1034049 1218442 694468 1272993 872628 1795460 FALSE TRUE 997118.3539 1019636.566 968852.1261 1060584.448 1122750.48 894949.6379 1082119.518 981577.5267 1495786.127 0.666618266 0.681672699 0.647721027 0.709048191 0.750608967 0.598313904 0.72344535 0.656228527 1 20.51247248 -1.332480072 3.282780209 1.002062082 0.679302593 0.849754919 0.04239165 6339473.838 9101663.116 127668.8676 0.009768046 0.046507172 1.332480072 -0.322759489 NGYHGDLNETFFVGEVDDGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NGYHGDLNETFFVGEVDDGAR 21 0 P53582;H0Y903 P53582 METAP1 Methionine aminopeptidase 1 0 ; 239.19 6.45E-30 248407000 190238 164183 172086 167855 186076 142559 197037 151006 206839 FALSE TRUE 178331.3432 176339.2802 176167.9612 172162.4435 171462.3416 183713.469 167493.1311 169859.4315 172316.2347 1.034907381 1.023346874 1.022352662 0.999107506 0.995044616 1.066141385 0.972010161 0.985742474 1 17.39469911 1.621980217 25 0.98415951 1.021150291 0.423261806 0.020516567 0.754488436 1333.274115 0.008870235 0.004888542 41.8774489 -1.621980217 0.036990781 NHAAPFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NHAAPFSK 8 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;P34932;A0A087WYC1;A0A087WTS8 Q92598-2;P34932 HSPH1;HSPA4 Heat shock protein 105 kDa;Heat shock 70 kDa protein 4 0 ; 112.84 0.0029633 807530000 1336800 1274600 1296530 1296030 1529030 926600 1656720 1174730 1694380 FALSE TRUE 1253132.074 1368972.71 1327284.304 1329288.324 1408946.152 1194094.378 1408310.216 1321397.626 1411577.032 0.887753233 0.969817927 0.940284713 0.941704416 0.998136212 0.845929305 0.997685698 0.936114428 1 20.42887643 0.501210913 0.990048051 0.999798949 0.941798694 0.14064686 0.046275663 3.437379048 4.81873567 0.039560868 0.012516501 3.171107122 -0.501210913 -0.058000256 NHAVLTANFSVTNLS(ph)QTDEIPVLTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NHAVLTANFSVTNLSQTDEIPVLTLK 26 0 O60934;E5RGU1 O60934 NBN Nibrin 1 NHAVLTANFSVTNLS(0.992)QT(0.008)DEIPVLTLK;NHAVLTANFSVTNLS(0.999)QT(0.001)DEIPVLTLK;NHAVLT(0.001)ANFS(0.001)VT(0.007)NLS(0.929)QT(0.062)DEIPVLTLK 245.62 1.54E-45 279615000 499592 375080 405896 403158 463918 311808 593086 445388 625374 TRUE FALSE 468323.4285 402851.3135 415524.0448 413503.7168 427483.7516 401821.9078 504158.2602 500995.6722 520995.0393 0.898901896 0.773234452 0.797558544 0.793680718 0.820514054 0.771258606 0.967683418 0.961613133 1 18.99091011 1.681248498 5.445329201 0.975827113 0.803662872 0.816653669 0.037239762 0.053918831 3.586498497 0.017998425 0.008879333 48.00080246 -1.681248498 -0.172164241 NHAVVCQGCHNAIDPEVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NHAVVCQGCHNAIDPEVQR 19 0 Q9UGI8-2;Q9UGI8 Q9UGI8-2 TES Testin 0 ;;; 232.84 6.28E-22 5677700000 954150 812000 787145 841708 839850 641350 1005210 729274 976870 FALSE TRUE 894431.4547 872121.3249 805816.4511 863307.6523 773891.5688 826497.3336 854488.0924 820325.4642 813824.0862 1.099047656 1.07163371 0.990160484 1.060803762 0.950932249 1.015572465 1.04996658 1.007988677 1 19.63435745 4.298087832 2.30058461 1.014511466 1.096796595 0.514591891 0.030472342 0.268848398 2.652925816 0.00753452 0.030412071 19864.96626 -4.298087832 0.08228513 NHDDWSHDYDNRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NHDDWSHDYDNRR 13 1 J3KPD3;Q9Y580;G3V1T9 J3KPD3 RBM7 RNA-binding protein 7 0 138.77 1.84E-05 304570000 174100 250660 183090 194520 227690 156830 238340 172800 228530 FALSE TRUE 163203.3918 269219.1272 187432.9813 199511.7125 209808.1459 202104.2751 202603.1296 194374.4604 190386.8666 0.8572198 1.414063543 0.984484826 1.047927917 1.102009553 1.061545256 1.064165471 1.020944689 1 17.53857444 3.73976856 24.86552195 1.047919314 1.182573636 0.05220385 0.13738263 640.3431457 1258952.81 0.031384936 0.056101244 5492.480962 -3.73976856 0.134654322 NHDEESLECLCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 239.03 3.71E-16 4553720000 2569990 2363200 2584270 2434610 2672820 2429110 3586690 2190710 3020670 FALSE TRUE 2409138.913 2538173.787 2645570.105 2497086.214 2462907.499 3130354.624 3048899.132 2464224.966 2516500.663 0.957336888 1.008612406 1.051289254 0.992285141 0.978703298 1.243931571 1.211563016 0.97922683 1 21.26298755 2.261341387 24.99461857 1.139645581 1.006212295 0.258137054 0.08606199 243.7965364 267487.9741 0.028616417 0.023926539 182.5329981 -2.261341387 -0.133433286 NHEGDEDDSHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NHEGDEDDSHVR 12 0 Q9UNE7;Q9UNE7-2;H3BTA3;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ;; 216.34 2.27E-11 1168090000 350677 386550 382621 410432 383239 269082 417928 283041 444552 FALSE TRUE 328728.7525 415170.5642 391696.9508 420964.38 353140.9549 346761.6052 355263.5763 318379.2919 370353.3993 0.887608304 1.12101189 1.05763023 1.13665591 0.95352427 0.936299237 0.959255611 0.85966348 1 18.49854305 2.613283518 6.835388683 0.938958496 1.063327605 0.340708516 0.074603267 0.23816916 12.26712384 0.022213637 0.020896742 410.4719813 -2.613283518 0.124369109 NHELSGLNKEELAVLLLQSDPFFMPEICK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NHELSGLNKEELAVLLLQSDPFFMPEICK 29 1 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 0 137.98 1.33E-06 36539000 75530 60410 64241 82790 81031 54141 100820 59024 99988 FALSE TRUE 70802.71212 64882.81926 65764.82686 84914.53156 74667.15212 69770.62779 85702.97697 66393.27633 83299.35685 0.849979097 0.778911407 0.789499815 1.019390002 0.896371292 0.837589033 1.028855206 0.797044285 1 16.34601774 3.263342467 24.9347207 0.93012011 0.797921696 0.364014788 0.07685007 202.5900651 203838.3529 0.019334605 0.026167761 1833.759882 -3.263342467 -0.132198414 NHET(ph)DGGSAHGDDDDDGPHFEPVVPLPDKIEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NHETDGGSAHGDDDDDGPHFEPVVPLPDKIEVK 33 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 NHET(0.538)DGGS(0.462)AHGDDDDDGPHFEPVVPLPDKIEVK 54.998 0.028326 342050000 29842 24130 26576 26614 26402 17773 39517 21317 37137 TRUE FALSE 27974.24249 25916.61031 27206.39527 27296.9603 24328.49342 22903.77658 33591.79271 23978.47437 30938.59479 0.904185943 0.837678973 0.879367517 0.882294768 0.786347718 0.740297895 1.085756898 0.775034372 1 14.91712005 1.746320895 25 0.95811362 0.842703165 0.268322403 0.089408689 2.161971853 6983.652377 0.037428912 0.02075634 55.75975995 -1.746320895 -0.115410455 NHETDGGS(ph)AHGDDDDDGPHFEPVVPLPDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NHETDGGSAHGDDDDDGPHFEPVVPLPDK 29 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 NHET(0.074)DGGS(0.926)AHGDDDDDGPHFEPVVPLPDK;NHET(0.204)DGGS(0.796)AHGDDDDDGPHFEPVVPLPDK;NHET(0.155)DGGS(0.845)AHGDDDDDGPHFEPVVPLPDK 174.63 1.49E-12 416985000 464700 318983 395303 362442 317289 297913 563140 298293 353358 TRUE FALSE 435615.2565 342600.8332 404679.7738 371742.8753 292370.4018 383915.6469 478702.3849 335535.5377 294380.267 1.479770573 1.163803664 1.374683765 1.262798214 0.993172555 1.304148715 1.626136119 1.139803089 1 18.16732144 NHETDGGS(ph)AHGDDDDDGPHFEPVVPLPDKIEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NHETDGGSAHGDDDDDGPHFEPVVPLPDKIEVK 33 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 NHET(0.065)DGGS(0.935)AHGDDDDDGPHFEPVVPLPDKIEVK;NHET(0.06)DGGS(0.94)AHGDDDDDGPHFEPVVPLPDKIEVK;NHET(0.141)DGGS(0.859)AHGDDDDDGPHFEPVVPLPDKIEVK;NHET(0.054)DGGS(0.946)AHGDDDDDGPHFEPVVPLPDKIEVK;NHET(0.015)DGGS(0.985)AHGDDDDDGPHFEPVVPLPDKIEVK;NHET(0.001)DGGS(0.999)AHGDDDDDGPHFEPVVPLPDKIEVK 311.83 1.78E-104 6031620000 3289547 2106074 2494115 2710370 2650634 1734759 3743843 1934638 3562351 TRUE FALSE 3083660.125 2262009.91 2553276.586 2779922.683 2442463.898 2235555.762 3182488.498 2176181.813 2967771.604 1.039049003 0.762191372 0.860334596 0.936703714 0.822995912 0.753277563 1.072349534 0.733271324 1 21.50094864 -4.11302192 0.290238037 1.559033876 0.863152471 0.085551875 0.116949497 328.834111 5.034059534 109.7873694 0.116266902 7.71E-05 4.11302192 -0.695881405 NHKPS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NHKPSR 6 1 P84103 P84103 SRSF3 Serine/arginine-rich splicing factor 3 1 NHKPS(1)R;NHKPS(1)R;NHKPS(1)R 79.596 0.040413 14800200000 5475100 2939530 4569580 3882890 2659980 3408380 5065740 3314630 2452520 TRUE FALSE 5132423.264 3157175.86 4677972.596 3982531.531 2451075.901 4392323.976 4306179.315 3728468.852 2043178.568 2.511979787 1.545227573 2.289556414 1.949184273 1.199638612 2.149750415 2.107588334 1.824837491 1 20.96238387 0.959308894 20.29246482 0.999999992 1.947952592 0.399183227 0.368659517 602.8222047 300626.4297 0.327341537 0.081835384 9.105606821 -0.959308894 0.9479526 NHLEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NHLEGK 6 0 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 128.75 0.016489 205926000 647840 471080 564390 585840 548960 392960 674380 462350 554200 FALSE TRUE 607292.8508 505959.2534 577777.5973 600873.6462 505846.896 506401.1728 573262.9796 520075.4153 461700.4397 1.315339555 1.095860454 1.251412274 1.301436158 1.095617098 1.09681761 1.241634034 1.126434741 1 18.81659758 2.718433849 24.89297375 1.135045665 1.218553539 0.331620096 0.085022164 1323.106319 1636427.964 0.027015903 0.0255016 522.9183104 -2.718433849 0.083507873 NHLGSYECK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NHLGSYECK 9 0 Q15428;K7EMT0 Q15428 SF3A2 Splicing factor 3A subunit 2 0 ; 134.84 0.0013958 521180000 673120 577720 631370 632850 652630 486520 815660 654340 858930 FALSE TRUE 630990.6208 620494.9899 646346.3946 649090.0024 601375.0724 626970.426 693359.3552 736035.7894 715569.0341 0.88180258 0.86713505 0.903262109 0.907096271 0.840415171 0.876184402 0.968962214 1.02860207 1 19.44873143 1.601407178 3.28076172 1.011622785 0.88011193 0.89172422 0.020087776 0.060768117 1.533228317 0.012853035 0.005337497 39.93991884 -1.601407178 -0.131510855 NHLS(ph)PQQGGATPQVPSPCCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NHLSPQQGGATPQVPSPCCR 20 0 A0A087X0R7;Q9H4L4 A0A087X0R7 SENP3-EIF4A1;SENP3 Sentrin-specific protease 3 1 NHLS(1)PQQGGATPQVPSPCCR;NHLS(1)PQQGGATPQVPSPCCR;NHLS(1)PQQGGATPQVPSPCCR;NHLS(1)PQQGGATPQVPSPCCR 229.77 1.37E-25 1637820000 577278 548557 553669 592726 602962 442886 790790 483604 684121 TRUE FALSE 541147.2005 589172.7311 566802.2901 607936.3526 555607.7968 570739.9985 672218.3808 543983.0239 569936.7855 0.949486354 1.033751016 0.994500275 1.066673301 0.974858635 1.001409302 1.179461298 0.954462035 1 19.12044239 NHPWLELSDVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NHPWLELSDVHR 12 0 B4DEM9;Q9Y2S7 B4DEM9 POLDIP2 Polymerase delta-interacting protein 2 0 141.34 3.50E-05 76011000 42730 48055 33750 34654 57102 36179 44399 38970 62099 FALSE TRUE 40055.60558 51613.0422 34550.56594 35543.28031 52617.43926 46623.28998 37741.78213 43835.49028 51734.27573 0.774256622 0.997656611 0.667846712 0.687035429 1.017071149 0.901206972 0.729531468 0.847320073 1 15.65883281 2.757462829 24.95183918 0.870057144 0.798716469 0.163081967 0.11995742 2382.817757 3145431.42 0.038136609 0.040386041 572.0879882 -2.757462829 -0.071340675 NHSDSSTSESEVSSVS(ph)PLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NHSDSSTSESEVSSVSPLK 19 0 Q9NY27-2;Q9NY27;Q9NY27-3;H7C559;C9IZ04 Q9NY27-2 PPP4R2 Serine/threonine-protein phosphatase 4 regulatory subunit 2 1 NHSDSSTSESEVSS(0.006)VS(0.994)PLK;NHSDSSTSESEVS(0.001)S(0.003)VS(0.997)PLK;NHSDSSTSESEVS(0.131)S(0.006)VS(0.863)PLK;NHSDSSTSESEVSS(0.006)VS(0.994)PLK;NHSDSSTSESEVSS(0.001)VS(0.999)PLK;NHSDSSTSESEVSS(0.001)VS(0.999)PLK 362.96 6.90E-92 8526610000 5222220 3680230 4679850 4364470 4384390 3468450 6139970 4050640 4967580 TRUE FALSE 4895370.572 3952718.058 4790858.252 4476469.689 4040057.695 4469735.209 5219338.499 4556371.321 4138458.806 1.182897016 0.955118377 1.157643093 1.081675546 0.976222764 1.080048254 1.26117928 1.100982644 1 21.98066217 1.972682791 24.53125199 1.15495888 1.064037549 0.01254187 0.094858933 976.9412158 877305.9313 0.035849414 0.023189004 93.90371864 -1.972682791 -0.090921331 NHSGNDERDEEDEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NHSGNDERDEEDEER 15 1 A0A0D9SGE8;Q8IWS0-3;Q8IWS0-5;Q8IWS0 A0A0D9SGE8;Q8IWS0-5 PHF6 PHD finger protein 6 0 162.26 9.65E-07 193320000 51709 44436 47639 52954 46685 38090 51793 30707 42271 FALSE TRUE 48472.62599 47726.08768 48769.01958 54312.88929 43018.54842 49085.96466 44027.12047 34540.83654 35215.69702 1.376449427 1.355250406 1.384865946 1.542292043 1.221573107 1.393866055 1.25021295 0.980836373 1 15.10393102 1.375539153 2.588998938 0.978637752 1.377240948 0.805348428 0.077805373 0.108124846 1.234483509 0.061212534 0.018980884 23.74319465 -1.375539153 0.398603195 NHSGNDERDEEDEERESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NHSGNDERDEEDEERESK 18 2 A0A0D9SGE8;Q8IWS0-3;Q8IWS0-5;Q8IWS0 A0A0D9SGE8;Q8IWS0-5 PHF6 PHD finger protein 6 0 69.763 0.015794 108880000 63291 62403 76585 68995 81305 44706 74380 66783 107090 FALSE TRUE 59329.72929 67023.38305 78401.63237 70765.52851 74919.63327 57611.89646 63227.40951 75121.00456 89215.98717 0.665012305 0.751248573 0.878784564 0.793193359 0.839755695 0.645757541 0.708700442 0.842012816 1 16.44501464 0.947235789 5.640290817 0.99996183 0.762970851 0.541091331 0.072007939 0.280677154 26.77409158 0.07336979 0.018478949 8.855962907 -0.947235789 -0.236990979 NHSGS(ph)RT(ph)PPVALNSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NHSGSRTPPVALNSSR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 NHS(0.102)GS(0.898)RT(1)PPVALNSSR 98.135 0.0065003 928510000 520030 421730 465200 440330 539690 392520 613170 398720 783300 TRUE FALSE 487482.2506 452955.328 476234.7637 451629.6133 497304.9244 505834.152 521230.8509 448501.0697 652562.1697 0.747028058 0.694118276 0.729792173 0.692086723 0.76208053 0.775150898 0.798745124 0.687292477 1 19.31575583 -5 0.235787825 2.469244341 0.708575356 0.818768687 0.038710664 64.24752355 0.64214299 45.14409184 0.06004017 1.00E-05 5 -1.760668985 NHSGS(ph)RTPPVALNSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NHSGSRTPPVALNSSR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 NHS(0.023)GS(0.489)RT(0.489)PPVALNSSR 148.52 5.58E-07 332110000 49038 82623 72325 83562 128820 39777 66938 74261 186100 TRUE FALSE 45968.79912 88740.49289 74040.58315 85706.34239 118702.9968 51259.97417 56901.26832 83532.64932 155038.7077 0.296498854 0.572376371 0.477561921 0.552806094 0.765634586 0.330626944 0.367013304 0.538785769 1 17.24226893 0.957624058 22.12403074 1.000000003 0.485531443 0.589589411 0.13513963 1463.342025 763997.1592 0.127480959 0.03187024 9.070350258 -0.957624058 -0.51446856 NHSGSRT(ph)PPVALNSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NHSGSRTPPVALNSSR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 NHS(0.056)GS(0.33)RT(0.614)PPVALNSSR;NHS(0.056)GS(0.339)RT(0.605)PPVALNSSR 172.83 6.50E-09 773940000 159694 213449 164516 204727 253900 121467 167023 145109 460930 TRUE FALSE 149699.0376 229252.9861 168418.3972 209980.6414 233959.7182 156532.551 141979.4517 163226.1781 383997.8053 0.389843472 0.597016397 0.438592083 0.546827712 0.609273582 0.407639182 0.369740269 0.425070602 1 18.55073854 -1.351035486 4.228216975 1.000944124 0.476409613 0.791962551 0.084869061 28784626.69 9198600.297 251605.9768 0.020617826 0.044561984 1.351035486 -0.524534511 NHSVNEEEQEEQGEGS(ph)EDEWEQVGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NHSVNEEEQEEQGEGSEDEWEQVGPR 26 0 Q14694;Q14694-3;Q14694-2;H3BNA1 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 NHSVNEEEQEEQGEGS(1)EDEWEQVGPR;NHSVNEEEQEEQGEGS(1)EDEWEQVGPR 445.95 7.87E-211 4833700000 883080 883950 846250 846410 931260 749780 1048100 703840 921400 TRUE FALSE 827809.5991 949398.5777 866323.4496 868130.3136 858122.5961 966229.3143 890947.1351 791715.9733 767612.3875 1.078421366 1.236820293 1.128594931 1.130948807 1.117911344 1.25874638 1.160673212 1.031400725 1 19.55001847 1.20367785 4.716552565 1.006515409 1.166422447 0.546997136 0.054161431 0.134755276 6.524923773 0.045889492 0.012466439 15.98371952 -1.20367785 0.159907038 NHVENLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NHVENLQK 8 0 C9J674;Q8WXG1 C9J674 RSAD2 Radical S-adenosyl methionine domain-containing protein 2 0 77.923 0.031959 224710000 536250 318460 368980 400600 389470 600090 893750 243890 261350 FALSE TRUE 502687.0697 342039.1098 377732.3798 410880.0742 358882.5972 773326.2414 759740.4847 274340.2034 217728.9966 2.308774107 1.570939632 1.734874021 1.887116923 1.648299505 3.551783425 3.489385872 1.260007659 1 17.73217403 2.280821751 24.9998642 2.671637404 1.784297979 0.008268922 0.855216016 216.8741378 128292.504 0.2788808 0.233326648 190.9069552 -2.280821751 -0.887339426 NHVQPYIPSILEALMVPTSQGFTEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NHVQPYIPSILEALMVPTSQGFTEVR 26 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 148.87 1.65E-07 165842000 151137 140886 150272 138167 156995 109418 183748 123635 137512 FALSE TRUE 141677.605 151317.346 153836.5228 141712.5991 144665.246 141005.2003 156196.6932 139071.1019 114560.3588 1.236707063 1.320852584 1.342842536 1.237012528 1.26278625 1.230837628 1.363444518 1.213954838 1 16.80574839 0.94336957 7.676608522 1.000002205 1.292541761 0.788379153 0.046255315 0.39360807 53.09793978 0.044353644 0.011111839 8.777474373 -0.94336957 0.292539556 NHYNEEMSNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NHYNEEMSNLR 11 0 P15924;P15924-3 P15924 DSP Desmoplakin 0 111.94 0.00093045 0 112010 193490 171290 177700 191070 172580 188450 144390 181130 FALSE TRUE 104999.494 207816.2009 175353.0797 182260.0828 176064.1329 222401.0444 160193.672 162417.4093 150898.2329 0.695829845 1.377194398 1.16206185 1.207834442 1.166773988 1.473847905 1.061600716 1.076337385 1 17.20321639 1.580112695 16.54659196 1.050872949 1.206317677 0.080542474 0.202262128 0.391927339 217.0279981 0.097869337 0.045488782 38.02880647 -1.580112695 0.155444728 NICFTVWDVGGQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NICFTVWDVGGQDR 14 0 P18085;C9JPM4;C9JAK5 P18085 ARF4 ADP-ribosylation factor 4 0 ;;; 198.14 5.23E-08 477987000 528763 481318 495412 539083 503912 431285 591099 428511 490059 FALSE TRUE 495668.6677 516955.2855 507163.4066 552916.7824 464336.7842 555789.9782 502469.1924 482011.5416 408264.987 1.214085664 1.266224883 1.242240757 1.354308599 1.137341675 1.361346174 1.230742798 1.180634042 1 18.63914632 0.861243245 2.06883471 1.000560713 1.261085041 0.618628496 0.064302006 0.305882844 2.550486734 0.052626127 0.014531243 7.265127574 -0.861243245 0.260524327 NIDDASQMDLFHRDS(ph)DDDQTEEQLDESEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NIDDASQMDLFHRDSDDDQTEEQLDESEAR 30 1 E7ESG2;Q9HAW4-2;Q9HAW4-3;Q9HAW4 E7ESG2 CLSPN Claspin 1 NIDDASQMDLFHRDS(1)DDDQTEEQLDESEAR;NIDDAS(0.006)QMDLFHRDS(0.994)DDDQTEEQLDESEAR 289.22 4.95E-81 185327000 111664 93809 119793 108734 123420 96535 140842 104860 129680 TRUE FALSE 104675.1496 100754.716 122634.5465 111524.2985 113727.0911 124403.0874 119724.0496 117952.0018 108035.5702 0.968895238 0.932606879 1.1351312 1.032292404 1.052681916 1.151501187 1.108191028 1.09178858 1 16.72114687 4.0398397 4.053758655 1.088427518 0.952482373 0.571336016 0.04670721 0.138968135 4.540081976 0.011204697 0.025313592 10960.73556 -4.0398397 -0.135945146 NIDDCPNHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NIDDCPNHR 9 0 Q04721;D2WEZ3 Q04721 NOTCH2 Neurogenic locus notch homolog protein 2;Notch 2 extracellular truncation;Notch 2 intracellular domain 0 94.692 0.0085502 53835000 77397 90088 85443 90036 88386 64189 103810 86953 84483 FALSE TRUE 72552.85993 96758.20926 87469.74831 92346.47619 81444.52009 82719.32228 88244.65422 97809.27346 70382.24152 1.030840427 1.374753165 1.242781509 1.31207069 1.157174286 1.175286841 1.253791472 1.389686821 1 16.10292384 2.742932677 24.77012219 1.212512624 1.262996739 0.005818482 0.129917627 1364.706749 7731828.901 0.036982095 0.038025427 553.2643373 -2.742932677 0.050484115 NIDDGTSDRPYSHALVAGIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 NIDDGTSDRPYSHALVAGIDR 21 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;;;;;;; 258.4 9.79E-37 20842110000 9312530 9484440 9972480 9961910 9114150 7698530 11267830 8238330 7642100 FALSE TRUE 8729675.371 10186677.81 10209031.93 10217549.48 8398361.424 9920970.636 9578323.497 9266903.635 6366584.14 1.371170973 1.60002249 1.603533655 1.604871506 1.319131459 1.558287838 1.504468218 1.45555347 1 22.6020881 -1.879341181 0.365769635 0.506008455 1.547101784 0.720094123 0.098270088 17.90890244 1.079528723 7.658873888 0.068867385 0.01320258 1.879341181 1.041093329 NIDDGTSDRPYSHALVAGIDRYPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NIDDGTSDRPYSHALVAGIDRYPR 24 2 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;;;; 277.15 2.69E-52 5750840000 1547810 2017720 1804290 1982020 2119200 1480665 2358160 1647070 2891640 FALSE TRUE 1450935.335 2167114.088 1847088.611 2032881.989 1952766.58 1908108.949 2004575.8 1852710.315 2409006.603 0.602296122 0.899588272 0.766742859 0.843867338 0.810610721 0.792072943 0.832117188 0.769076479 1 21.20000692 -5 0.34870253 3.258765096 0.795458881 0.416636348 0.077512744 415.8713955 3.421191945 702.076152 0.052524298 1.00E-05 5 -2.463306216 NIDEHANEDVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NIDEHANEDVER 12 0 P61026 P61026 RAB10 Ras-related protein Rab-10 0 ; 182.02 1.74E-05 694680000 1368460 1452650 1165890 1240410 1450080 1059840 1531600 1426180 1455710 FALSE TRUE 1282810.531 1560205.717 1193545.461 1272241.021 1336196.566 1365798.603 1301950.799 1604241.712 1212742.597 1.057776427 1.286510197 0.984170478 1.049061049 1.101797339 1.126206506 1.073559057 1.322821279 1 20.20984194 NIDLATPLHHTWTYQALVHDVLDFHLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NIDLATPLHHTWTYQALVHDVLDFHLNR 28 0 Q8WVM8;Q8WVM8-2;Q8WVM8-3 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 ;; 269.83 1.59E-55 462756000 144915 307221.4 126720.6 85802.8 290923.3 98220.1 175798.1 249126.3 79805.7 FALSE TRUE 135845.0288 329968.3921 129726.4725 88004.64511 268075.3575 126574.6484 149438.8069 280230.2669 66485.61311 2.043224428 4.963004426 1.951196152 1.323664489 4.032080702 1.903790046 2.247686378 4.214900846 1 16.02075457 -1.280587714 0.199932135 1.13E-33 3.292661787 0.127751188 1.2359871 45.99205974 1.817228995 35.91012738 3.489667057 0.052409774 1.280587714 3.292661787 NIDNPALADIYTEHAHQVVVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NIDNPALADIYTEHAHQVVVAK 22 0 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ; 235.83 1.03E-30 389780000 791660 637980 719190 746280 760010 559860 915470 645000 802830 FALSE TRUE 742111.4138 685216.703 736249.5264 765430.8082 700321.8803 721482.4934 778203.7723 725529.6698 668832.4865 1.109562452 1.024496741 1.100798094 1.144428274 1.047081137 1.078719273 1.163525678 1.084770379 1 19.3512854 3.73073756 18.45681677 1.09909122 1.061461447 0 0.050590383 12.1543556 61999.9638 0.012226497 0.020844091 5379.446097 -3.73073756 -0.037629773 NIDPKPCTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NIDPKPCTPR 10 1 K7EQ55;K7EK33;Q96EP5;Q96EP5-2 K7EQ55 DAZAP1 DAZ-associated protein 1 0 ; 92.866 0.0083681 639480000 2321100 1673390 1889050 1922060 2196300 1347690 2452900 1735990 2725100 FALSE TRUE 2175826.494 1797289.537 1933859.158 1971383.314 2023811.457 1736746.225 2085110.417 1952732.173 2270263.205 0.958402748 0.791665712 0.851821566 0.868350114 0.891443535 0.764997742 0.918444351 0.860134705 1 21.11442814 0.343826722 0.8669242 1.001062259 0.851333291 0.359988369 0.05624418 2.397323531 2.343894637 0.054852444 0.016416965 2.207123945 -0.343826722 -0.149728968 NIEDVIAQGIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NIEDVIAQGIGK 12 0 P05387;H0YDD8 P05387 RPLP2 60S acidic ribosomal protein P2 0 ; 215.46 9.63E-11 145074000 908410 769200 779720 707410 775400 618280 961110 692370 891140 FALSE TRUE 851554.2397 826152.3684 798215.3266 725563.3382 714503.2118 796767.3991 817000.478 778813.9186 742402.977 1.147024279 1.112808534 1.075177971 0.977317388 0.962419648 1.073227646 1.100481145 1.049044714 1 19.50184297 3.826913223 1.995470828 1.037352453 1.129117366 0.464790981 0.043815942 0.362847409 2.832265899 0.013784909 0.031530554 6712.947076 -3.826913223 0.091764913 NIEDYIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NIEDYIHR 8 0 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ;;; 175.51 0.00026568 1661070000 1465210 1695140 1542390 1505150 1753680 1243850 1751440 1478970 1722460 FALSE TRUE 1373505.122 1820649.929 1578976.219 1543774.697 1615953.047 1602929.303 1488827.832 1663622.66 1434970.298 0.957166238 1.268771856 1.100354635 1.07582345 1.126122993 1.117047025 1.037532159 1.159342923 1 20.45258945 -0.781402094 0.236466939 0.930388701 1.14264955 0.084320225 0.082868014 24.51379086 1.510628141 1.357951879 0.155968187 0.165423767 0.781402094 0.212260849 NIETIINTFHQYSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NIETIINTFHQYSVK 15 0 P06702 P06702 S100A9 Protein S100-A9 0 ; 273.88 1.84E-33 981370000 1869720 2179190 1851830 1504170 2126900 911750 2129300 2000940 3154200 FALSE TRUE 1752697.563 2340539.495 1895756.282 1542769.549 1959861.854 1174957.424 1810031.232 2250761.764 2627743.643 0.666997166 0.890703133 0.721438823 0.587108089 0.745834495 0.447135483 0.688815759 0.856537802 1 21.32539311 1.037533836 3.489527073 0.997242251 0.691742677 0.479193853 0.113093327 0.19977153 5.415429883 0.114710306 0.029795803 10.90269433 -1.037533836 -0.305499574 NIGNGIISS(ph)PLTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NIGNGIISSPLTGK 14 0 Q9P275;A0A075B784;E9PEW0;K7EMM6 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 NIGNGIIS(0.015)S(0.985)PLTGK;NIGNGIIS(0.034)S(0.966)PLTGK;NIGNGIIS(0.182)S(0.818)PLTGK;NIGNGIIS(0.128)S(0.872)PLTGK 267.47 5.55E-25 383692000 1835840 1247900 1586430 1444740 1601010 1127760 2005210 1372590 1773570 TRUE FALSE 1720938.051 1340295.814 1624060.869 1481814.474 1475273.133 1453326.004 1704547.376 1543960.883 1477549.709 1.1647243 0.907107088 1.099158193 1.002886377 0.998459222 0.983605489 1.153631154 1.044946829 1 20.49477524 1.761716582 25 1.081795325 1.018767742 0.038050884 0.078417515 25.10917361 27129.24756 0.032739959 0.018157001 57.77189084 -1.761716582 -0.063027584 NIGRDT(ph)PTSAGPNSFNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NIGRDTPTSAGPNSFNK 17 1 Q8WW12;Q8WW12-3 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 1 NIGRDT(0.985)PT(0.015)SAGPNSFNK;NIGRDT(0.993)PT(0.007)SAGPNSFNK;NIGRDT(0.929)PT(0.07)S(0.001)AGPNSFNK;NIGRDT(0.998)PT(0.002)SAGPNSFNK 265.7 2.29E-27 3991150000 1891950 1493220 1654480 1719210 1831330 1215530 2526470 1745220 2475890 TRUE FALSE 1773536.227 1603779.562 1693725.047 1763327.839 1687504.729 1566433.779 2147649.278 1963114.559 2062647.964 0.859834668 0.77753431 0.821141114 0.854885501 0.818125419 0.759428563 1.041209802 0.951744841 1 20.97606618 1.731689012 9.289962281 0.99495265 0.813191758 0.843426984 0.037015592 0.034022368 10.5686944 0.016369477 0.008813291 53.91244306 -1.731689012 -0.181760892 NIHESCMSQIGWNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 NIHESCMSQIGWNR 14 0 P11413;P11413-3;P11413-2;E9PD92 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;; 266.2 7.67E-25 2437830000 1050974 1852450 1684330 1795140 1883730 1448940 2030780 1655040 1954640 FALSE TRUE 985195.4134 1989607.325 1724283.103 1841206.332 1735789.444 1867225.456 1726283.392 1861675.387 1628397.957 0.605008996 1.221818854 1.058883116 1.13068573 1.065949166 1.146664087 1.060111495 1.143255787 1 20.63502189 4.746581397 24.95862028 1.107920634 0.605008745 0.865330033 0.061769791 308.1718032 958929.5959 0.013201169 0.14712688 55793.21623 -4.746581397 -0.502911889 NIHLWTPTDGGSWHVDQRPFVGHTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NIHLWTPTDGGSWHVDQRPFVGHTR 25 1 Q9BQ67;M0QX71 Q9BQ67 GRWD1 Glutamate-rich WD repeat-containing protein 1 0 ; 213.2 1.59E-26 492410000 81227 87298 69043 89408 94746 62567 91011 81401 118638 FALSE TRUE 76143.14706 93761.63475 70680.73256 91702.36065 87305.03135 80629.07721 77364.74545 91564.09404 98836.55137 0.770394616 0.948653443 0.715127466 0.927818296 0.883327374 0.815781976 0.7827544 0.926419354 1 16.59275705 1.019497223 5.315201863 0.999701483 0.835794118 0.38279236 0.071166432 0.146593332 12.50159336 0.064130649 0.016186687 10.45917003 -1.019497223 -0.163907365 NIIEATHMYDNAAEACSTTEEVFNS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NIIEATHMYDNAAEACSTTEEVFNSPR 27 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 NIIEATHMYDNAAEACS(0.045)T(0.045)T(0.008)EEVFNS(0.901)PR;NIIEATHMYDNAAEACSTTEEVFNS(1)PR;NIIEATHMYDNAAEACSTTEEVFNS(1)PR;NIIEATHMYDNAAEACSTTEEVFNS(1)PR;NIIEATHMYDNAAEACSTTEEVFNS(1)PR 315.94 2.29E-82 2285973000 834142 881143 908014 877796.2 1013515 871417 1197284 897654 1287397 TRUE FALSE 781934.5412 946383.7445 929552.5209 900321.9366 933917.6202 1122980.942 1017762.379 1009728.078 1072522.124 0.729061456 0.882390884 0.866697759 0.839443697 0.870767697 1.047046878 0.948943016 0.941451981 1 20.03257598 2.375992879 6.483219344 0.978648352 0.845516349 0.677010074 0.05041514 0.134191545 7.451500863 0.016687941 0.013905998 237.6801316 -2.375992879 -0.133132003 NIIGSS(ph)PVADFSAIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NIIGSSPVADFSAIK 15 0 P42566;B1AUU8 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 NIIGS(0.002)S(0.998)PVADFSAIK;NIIGSS(1)PVADFSAIK;NIIGS(0.27)S(0.73)PVADFSAIK 288 1.31E-34 556570000 3091440 2360380 2636720 2662290 2912950 1901780 2950830 2436710 3865080 TRUE FALSE 2897952.289 2535144.991 2699264.244 2730608.869 2684178.657 2450793.013 2508380.436 2740938.607 3219973.179 0.899992679 0.787318667 0.838287804 0.84802224 0.8336028 0.761122182 0.779006624 0.85123026 1 21.61861724 0.968078977 19.55843382 1.000000001 0.815909757 0.664264625 0.039575442 120.6624797 73932.37898 0.037184373 0.009296093 9.291353351 -0.968078977 -0.184090244 NIIHGSDSVESAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 NIIHGSDSVESAEK 14 0 P15531;P15531-2 P15531 NME1 Nucleoside diphosphate kinase A 0 ;;;;;; 230.86 7.56E-13 12063000000 14212230 20001920 19086260 18982690 21361390 14266880 27079400 19602570 23046940 FALSE TRUE 13322711.89 21482882.97 19538995.1 19469817.96 19683752.6 18385496.65 23019095.36 22049994.02 19200256.83 0.693881963 1.118885188 1.017642383 1.014039455 1.025181735 0.957565142 1.19889518 1.148421827 1 24.19462227 1.745691295 25 1.131915588 0.997322626 0.218512438 0.121135038 2.26221684 7954.589545 0.051553207 0.028588585 55.67898317 -1.745691295 -0.134592962 NIIHGSDSVESAEKEIGLWFHPEELVDYTSCAQNWIYE ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NIIHGSDSVESAEKEIGLWFHPEELVDYTSCAQNWIYE 38 1 P15531;P15531-2 P15531 NME1 Nucleoside diphosphate kinase A 0 ;; 241.41 2.97E-50 455938000 250977.9 749017 474845 615988 1072774 337689 607806 563155 1526866 FALSE TRUE 235269.6412 804474.998 486108.5476 631795.2949 988522.6574 435174.3324 516671.1329 633466.1414 1272022.201 0.184957182 0.63243786 0.382154138 0.496685745 0.77712689 0.342112215 0.406180908 0.497999281 1 20.27869242 0.934506248 19.3454818 1.000000001 0.47085803 0.524677064 0.16018809 1292.560611 381797.5355 0.14125044 0.035312537 8.600154401 -0.934506248 -0.529141971 NIIHGSDSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 9028080000 8168820 17387830 11932430 12749270 18648600 7990470 16734990 16327580 22752400 FALSE TRUE 7657548.138 18675243.03 12215472.87 13076437.85 17184014.18 10297188.97 14225733.61 18366114.3 18954877.45 0.403988269 0.985247363 0.644450111 0.689871928 0.906574797 0.543247457 0.750505174 0.968938699 1 24.17606579 1.238124548 5.108718059 0.992883744 0.72373588 0.331052795 0.164767229 0.201164824 14.25775613 0.124698603 0.03705083 17.30312511 -1.238124548 -0.269147864 NIIIALIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NIIIALIDR 9 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 101.11 0.0097903 55833000 177999 200998 181929 190050 230280 144024 189875 183501 173463 FALSE TRUE 166858.3603 215880.1011 186244.4418 194927.0048 212194.7377 185601.3908 161405.0065 206411.5038 144510.9047 1.154642002 1.493867203 1.288791612 1.348874019 1.468364883 1.284341768 1.116905377 1.428345523 1 17.14081884 -0.166587831 0.368135272 0.927458837 1.36623964 0.365439838 0.126879391 5.690562991 0.955571732 0.716171662 0.09657675 0.681415753 0.166587831 0.438780802 NIILEEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NIILEEGK 8 0 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 120.15 0.0083355 294590000 1294640 851040 1029870 910250 958880 779530 1265280 889350 940510 FALSE TRUE 1213610.793 914051.8871 1054299.003 933608.556 883573.4327 1004567.656 1075563.01 1000387.305 783532.8051 1.548895956 1.166577687 1.345570978 1.191537291 1.127678927 1.282100315 1.372709609 1.276765055 1 19.57963415 -2.068668637 2.40116799 0.588009932 1.281835951 0.364208616 0.119661425 4064497.174 1304728.154 9180265.655 0.027101563 0.008537513 2.068668637 0.693826019 NIILEEGKEILVGDVGQTVDDPYATFVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NIILEEGKEILVGDVGQTVDDPYATFVK 28 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ;; 342.12 1.33E-96 975586000 1469887 1074957 1220198 1239826 1460480 775314 1519785 1065098 2057864 FALSE TRUE 1377889.396 1154547.935 1249141.673 1271642.034 1345779.792 999134.5656 1291907.348 1198077.83 1714393.204 0.80371842 0.673444069 0.72862029 0.741744677 0.784988991 0.582791954 0.753565369 0.698834915 1 20.70926661 -1.777057601 2.609405199 1.074243381 0.716504281 0.666835682 0.061913234 12612468.82 9119510.798 5974989.325 0.013157739 0.01670869 1.777057601 -0.3577391 NIIS(ph)PPWDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NIISPPWDFR 10 0 Q5T8C6;Q13042-4;Q13042-3;Q13042-2;Q13042 Q5T8C6 CDC16 Cell division cycle protein 16 homolog 1 NIIS(1)PPWDFR 92.295 0.010033 45306000 40452 43361 48784 49647 44364 39515 49504 33232 45287 TRUE FALSE 37920.18153 46571.49356 49941.17952 50921.02607 40879.8304 50922.33903 42081.33477 37381.08835 37728.30713 1.005085688 1.234391286 1.323705814 1.349676939 1.083532061 1.349711739 1.115378292 0.990796863 1 15.20335975 1.467710794 3.924072202 1.002325248 1.236663209 0.417154894 0.111028209 0.184911108 5.602415443 0.072337259 0.027094821 29.35694058 -1.467710794 0.234337961 NILFVITKPDVYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NILFVITKPDVYK 13 1 F8VZJ2;H0YHX9;Q13765;E9PAV3-2;E9PAV3;F8W0W4;F8W1N5;F8VZ58;F8VNW4;Q9BZK3 F8VZJ2 NACA;NACAP1 "Nascent polypeptide-associated complex subunit alpha;Nascent polypeptide-associated complex subunit alpha, muscle-specific form;Putative nascent polypeptide-associated complex subunit alpha-like protein" 0 ; 173.68 1.94E-05 709680000 3468400 2537400 2756600 2892000 3183100 1867770 3840100 2758800 3935900 FALSE TRUE 3251319.035 2725271.736 2821987.854 2966213.616 2933112.166 2406964.878 3264312.655 3103242.253 3278972.863 0.991566314 0.831135801 0.860631659 0.904616702 0.894521635 0.734060628 0.995529024 0.946406812 1 21.64481253 1.612819613 25 0.978231785 0.866195107 0.390411205 0.065407805 0.421842739 2118.700669 0.028634026 0.015250484 41.00337577 -1.612819613 -0.112036678 NILGGTVFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NILGGTVFR 9 0 O75874;C9J4N6;P48735;P48735-2 O75874;P48735 IDH1;IDH2 "Isocitrate dehydrogenase [NADP] cytoplasmic;Isocitrate dehydrogenase [NADP], mitochondrial" 0 90.906 0.020468 0 210350 179950 190730 187050 230190 149130 181620 187520 251620 FALSE TRUE 197184.569 193273.6852 195254.2057 191850.0197 212111.8059 192181.4101 154387.7671 210932.2848 209622.9965 0.940662868 0.922006118 0.931454129 0.915214566 1.011872788 0.916795453 0.736502052 1.006245919 1 17.67743747 1.988178914 24.94441372 0.870391022 0.94032896 0 0.081202866 1052.558123 2221067.739 0.029612834 0.020297887 97.31480445 -1.988178914 0.069937938 NINDAWVCTNDMFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NINDAWVCTNDMFR 14 0 P61970 P61970 NUTF2 Nuclear transport factor 2 0 ; 125.03 0.00021775 271430000 142517 141127 126923 130200 168896 86095 146678 121633 193510 FALSE TRUE 133597.1154 151576.1899 129933.6735 133541.1524 155631.5895 110949.2289 124684.9956 136819.1478 161211.9309 0.82870489 0.940229356 0.805980505 0.828357751 0.965385059 0.688219713 0.773422878 0.848691205 1 17.29859899 2.247849908 24.99996454 0.800619163 0.871498157 0.022845092 0.092472577 397.2785362 1069183.145 0.029569595 0.024427387 176.9497316 -2.247849908 0.070878994 NINDGLSSLFSVVEHSGS(ph)TESVWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NINDGLSSLFSVVEHSGSTESVWK 24 0 O94964-2;H0YDM2;O94964;O94964-3 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 NINDGLSSLFSVVEHS(0.005)GS(0.773)T(0.18)ES(0.042)VWK 131.95 6.70E-10 0 38809 37052 42263 41776 43421 35873 45591 34118 44129 TRUE FALSE 36380.01397 39795.36863 43265.49832 42848.04289 40010.88981 46228.95275 38755.0528 38377.7074 36763.58482 0.989566555 1.082467034 1.17685744 1.165502306 1.088329389 1.257465859 1.054169581 1.043905473 1 15.16598983 1.539843413 9.096786757 1.03127955 1.129238054 0.28949963 0.070346954 0.147018337 19.09807489 0.036510001 0.016973797 34.66118557 -1.539843413 0.097958504 NINMDNDLEVLTSS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NINMDNDLEVLTSSPTR 17 0 Q9Y5T5-4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5 Q9Y5T5-4 USP16 Ubiquitin carboxyl-terminal hydrolase 16 1 NINMDNDLEVLT(0.031)S(0.35)S(0.615)PT(0.003)R;NINMDNDLEVLTS(0.003)S(0.994)PT(0.003)R;NINMDNDLEVLTS(0.016)S(0.984)PTR;NINMDNDLEVLTS(0.002)S(0.996)PT(0.002)R;NINMDNDLEVLTS(0.025)S(0.966)PT(0.009)R 446.54 1.50E-182 1023392000 1460511 1451070 1565067 1491638 1487260 1212903 1600360 1202342 1302970 TRUE FALSE 1369100.224 1558508.733 1602191.128 1529915.956 1370456.599 1563048.406 1360400.875 1352457.045 1085495.889 1.261267073 1.435757378 1.475999259 1.409416628 1.262516618 1.439939498 1.253252903 1.245934746 1 20.04992283 0.862666335 0.669444426 0.99629383 1.409005959 0.708807805 0.075929215 0.459055731 0.451984332 0.073622746 0.028791948 7.288972898 -0.862666335 0.412712129 NINPDVLFEVHNYNITTVENFQHFMDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NINPDVLFEVHNYNITTVENFQHFMDR 27 0 Q9GZZ9-2;Q9GZZ9;E7EWE1;E7EQ61;C9JRV9;C9J5W5 Q9GZZ9-2 UBA5 Ubiquitin-like modifier-activating enzyme 5 0 ; 267.51 8.01E-54 232356000 282600 342780 294520 299830 339230 237880 347550 301360 307610 FALSE TRUE 264912.5705 368159.7879 301506.1535 307524.1454 312588.2442 306552.0943 295438.104 338985.4594 256267.9038 1.033732928 1.436620749 1.176527177 1.200010383 1.219771339 1.196217278 1.152848639 1.322777665 1 17.96729327 -4.359643966 0.263038983 2.94E-09 1.245414148 0.254440155 0.108255188 172.3095665 2.311660087 92.83335307 0.131363855 4.37E-05 4.359643966 1.245414145 NINPSTANS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NINPSTANSPK 11 0 P46937-6;P46937-7;P46937;P46937-9;P46937-4;H0YCI3 P46937-6 YAP1 Transcriptional coactivator YAP1 1 NINPS(0.001)T(0.001)ANS(0.999)PK;NINPSTANS(1)PK;NINPSTANS(1)PK 169.17 1.80E-05 169120000 1010435 621327 756660 728012 891221 612326 1051931 787763 1289140 TRUE FALSE 947193.677 667330.6976 774608.3325 746694.0204 821228.0977 789094.5759 894203.7122 886116.9446 1073974.206 0.88195198 0.621365666 0.721254131 0.695262527 0.764662776 0.734742577 0.832611908 0.825082148 1 20.03452791 0.993046575 0.658342834 1.00008484 0.709090687 0.590184175 0.067921687 0.477744254 0.484477138 0.061872845 0.02538467 9.841166405 -0.993046575 -0.290994154 NINTFVET(ph)PVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NINTFVETPVQK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 NINTFVET(1)PVQK;NINTFVET(1)PVQK;NINTFVET(1)PVQK 203.04 1.45E-06 237230000 752570 552950 679730 644310 644630 520850 927970 588700 878240 TRUE FALSE 705467.9871 593890.9933 695853.5166 660844.0854 594003.3601 671210.9397 788829.5134 662200.4909 731656.0704 0.964207113 0.811707874 0.951066416 0.903216842 0.811861453 0.917385869 1.078142512 0.905070726 1 19.48080611 1.982347753 23.77854796 1.001756268 0.885290255 0.362419353 0.06400341 351.9990581 474161.2423 0.023758961 0.015720604 96.01691617 -1.982347753 -0.116466012 NIPS(ph)PGQLDPDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NIPSPGQLDPDTR 13 0 Q9P2D1 Q9P2D1 CHD7 Chromodomain-helicase-DNA-binding protein 7 1 NIPS(1)PGQLDPDTR;NIPS(1)PGQLDPDTR 171.26 6.53E-07 129490000 273780 243340 269940 243810 235850 192608 268080 226619 197157 TRUE FALSE 256644.5985 261357.1468 276343.1043 250066.5774 217327.2924 248210.8029 227883.8927 254912.881 164250.223 1.56252207 1.591213345 1.682451927 1.52247329 1.323147624 1.51117483 1.387419076 1.551978903 1 17.3255358 -3.078245927 0.169620434 9.04E-11 1.682010013 0.755703571 0.094326032 29.3807195 0.504876279 10.95910647 0.371363505 0.00083513 3.078245927 1.682010013 NIQVSHQEFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NIQVSHQEFSK 11 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 198.32 5.41E-08 1001900000 3089800 2990700 2891100 2909700 3457800 1873520 3626900 2989000 3905500 FALSE TRUE 2896414.933 3212134.54 2959678.257 2984367.828 3186238.336 2414374.81 3083080.015 3362183.23 3253646.82 0.890205697 0.987241307 0.909649517 0.917237793 0.979282176 0.742051902 0.947576731 1.033358387 1 21.63362623 1.468143004 25 1.007943053 0.911539726 0.317091978 0.06687144 2.405619671 6702.371548 0.034883983 0.016149006 29.38617119 -1.468143004 -0.096403326 NIRDDEGFIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 200.93 4.12E-08 176940000 186870 208520 220690 226250 221830 176650 228870 206880 230460 FALSE TRUE 175174.1403 223959.0378 225924.871 232055.958 204408.3666 227645.9873 194553.0682 232709.4234 191994.7372 0.912390323 1.166485296 1.176724291 1.208657911 1.064656092 1.185688684 1.013325006 1.21206147 1 17.55070724 1.746817206 24.99999848 1.078900977 1.132567688 0.028562083 0.101685311 5.86875897 17814.87362 0.043149151 0.023928499 55.82351848 -1.746817206 0.053666711 NISFNDKK ddPTM_SK-BR-3_Pertuzumab_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 ; 111.06 0.0053021 5734200000 4874700 3018300 3410600 3105600 4325300 2243300 4341000 3314500 5511600 FALSE TRUE 4569601.229 3241778.073 3491501.043 3185294.954 3985608.385 2890904.293 3690107.35 3728322.621 4591678.354 0.995191927 0.706011576 0.760397566 0.693710384 0.868006876 0.629596429 0.803651098 0.811973822 1 22.13059015 0.747582539 1.981960738 0.999687382 0.764721454 0.310450423 0.100982233 1.034719751 6.303226932 0.084659667 0.023436339 5.592197994 -0.747582539 -0.234965927 NISFTVWDVGGQDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NISFTVWDVGGQDK 14 0 P61204;F5H423;F5H0C7;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 ; 236.92 6.52E-17 334080000 1208890 935210 1024630 1006030 1077070 749070 1295920 889070 1105630 FALSE TRUE 1133227.733 1004453.921 1048934.707 1031846.433 992481.2669 965314.3489 1101608.827 1000072.347 921093.2104 1.230307335 1.090501928 1.138793225 1.120241059 1.077503618 1.048009407 1.195979749 1.085744999 1 19.81298763 -5 0.218295833 0.397508403 1.1383988 0.374004534 0.053249683 176.9558509 1.770334019 47.01216957 0.099039102 1.00E-05 5 0.740890396 NISLHGDGPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NISLHGDGPLR 11 0 E7EV54;C9JFV4;Q8IZL8;I3L445 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 0 88.338 0.013053 227490000 52551 92945 76427 89873 93009 56195 83257 85811 92991 FALSE TRUE 49261.92672 99826.74451 78239.88453 92179.29333 85704.44832 72417.58425 70773.38577 96524.69224 77470.20136 0.63588226 1.288582484 1.009935216 1.189867739 1.106289216 0.934779864 0.913556239 1.245958969 1 16.24135387 2.25962419 24.79839816 1.002440374 1.080776897 0 0.191621806 824.7457119 970980.0814 0.061163554 0.051120747 181.812689 -2.25962419 0.078336523 NISSS(ph)PSVESLPGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NISSSPSVESLPGGR 15 0 Q92609;Q92609-2;C9J3F6 Q92609 TBC1D5 TBC1 domain family member 5 1 NIS(0.008)S(0.029)S(0.849)PS(0.114)VESLPGGR 118.2 0.00032497 99493000 204010 289060 213680 274110 270050 231050 315050 226520 274330 TRUE FALSE 191241.3783 310462.3032 218748.5905 281144.1267 248841.3623 297750.3842 267811.1773 254801.5206 228542.5508 0.83678675 1.358444203 0.95714601 1.230160973 1.088818522 1.30282253 1.171821949 1.114897509 1 17.80210327 4.764355799 23.90007351 1.160689101 0.836785986 0.38917843 0.124173856 4475.556312 4146624.349 0.026829365 1.890391716 58124.04075 -4.764355799 -0.323903115 NIVHNYSEAEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NIVHNYSEAEIK 12 0 Q9H201;I6L9I8;Q9H201-2;D6RFG3;D6REL6;D6RBR6;D6R907;D6RBI9;Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9H201;Q9Y6I3 EPN3;EPN1 Epsin-3;Epsin-1 0 160.69 6.74E-05 167420000 200840 179090 169310 161380 185880 111700 192560 158440 222230 FALSE TRUE 188269.7829 192350.0099 173326.1132 165521.284 171281.7346 143945.9767 163687.4156 178221.5828 185138.3773 1.016913865 1.038952662 0.936197647 0.894040914 0.925155211 0.777504798 0.884135521 0.962639866 1 17.49824446 3.701135779 1.640243453 0.891309312 1.029861523 0.390511376 0.059128385 0.318724847 1.68495856 0.016820493 0.03713355 5024.996677 -3.701135779 0.138552212 NIVQS(ph)TEHLHEDNGDVEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NIVQSTEHLHEDNGDVEVR 19 0 Q6PL18 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 NIVQS(0.977)T(0.023)EHLHEDNGDVEVR;NIVQS(0.965)T(0.035)EHLHEDNGDVEVR;NIVQS(0.835)T(0.165)EHLHEDNGDVEVR 222.47 4.06E-19 786912000 483135 469645 518550 436675 549769 372599 618370 510761 735860 TRUE FALSE 452896.4428 504418.0045 530850.2509 447880.8198 506592.3604 480162.2827 525651.1592 574530.6352 613040.2122 0.738771183 0.822813895 0.865930555 0.730589627 0.826360735 0.783247613 0.857449721 0.937182625 1 19.22562218 1.21141185 1.87720022 0.998002169 0.80464639 0.754728312 0.041085738 0.161574453 1.016812539 0.037480062 0.010933796 16.27091027 -1.21141185 -0.193355779 NIVQSTEHLHEDNGDVEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NIVQSTEHLHEDNGDVEVR 19 0 Q6PL18 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 237.76 1.82E-24 222050000 108170 124190 144230 131130 128420 126300 158610 131080 133110 FALSE TRUE 101399.8328 133385.1568 147651.2037 134495.0178 118334.4112 162760.7597 134827.903 147445.6265 110893.0811 0.914392781 1.202826682 1.331473544 1.21283507 1.067103647 1.467726914 1.215836927 1.329619712 1 16.75880983 4.737456165 3.256503981 1.250544372 0.867572338 0.351035973 0.132926507 0.321619292 5.511687908 0.028492385 0.311136712 54633.14038 -4.737456165 -0.382972034 NIYAFMGT(ph)PVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NIYAFMGTPVQK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 NIYAFMGT(1)PVQK;NIYAFMGT(1)PVQK 198.74 2.01E-06 282320000 1039320 782560 924220 831940 892230 607040 1272700 752990 1303160 TRUE FALSE 974270.8164 840501.5567 946142.9348 853288.9889 822157.8549 782282.5935 1081870.45 847002.459 1085654.177 0.897404382 0.774189032 0.871495689 0.785967582 0.757292582 0.720563334 0.996514795 0.780177037 1 20.05013319 0.736324253 0.766189504 0.995819719 0.812937563 0.297069189 0.082079134 1.241281972 1.420112556 0.077116127 0.027501966 5.449093413 -0.736324253 -0.182882156 NIYSEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NIYSEELR 8 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;; 219.56 1.49E-05 7189940000 6450820 8891310 6313600 6706060 9267420 4291250 7145800 7647370 10044200 FALSE TRUE 6047074.691 9549631.844 6463361.573 6878148.853 8539594.216 5530064.212 6074353.628 8602160.978 8367758.132 0.722663657 1.141241381 0.772412571 0.821982273 1.020535498 0.660877636 0.725923662 1.028012622 1 22.99640972 3.75166213 21.41003035 0.836072203 0.960344142 0.006979542 0.161256494 166.3620659 145132.9275 0.038546184 0.069401082 5644.97639 -3.75166213 0.124271939 NKAISEMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NKAISEMK 8 1 M9MMK7;Q0VDD8-2;Q0VDD8;Q0VDD8-4 M9MMK7 DNAH14 "Dynein heavy chain 14, axonemal" 0 64.265 0.062091 711720000 1428400 1040600 1121200 1201300 1319200 911380 1435400 1076200 1524900 FALSE TRUE 1338998.994 1117647.107 1147795.393 1232127.392 1215595.353 1174480.611 1220175.096 1210565.939 1270384.339 1.054010942 0.879770848 0.903502474 0.969885533 0.956872118 0.9245081 0.960477124 0.952913148 1 20.2768336 0.64817062 0.565341946 1.001608139 0.933540022 0.046795659 0.047522609 2.848747271 1.806055925 0.05718531 0.02110405 4.448059829 -0.64817062 -0.068068117 NKAPGEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NKAPGEYR 8 1 A0A1B0GWF2;A0A1B0GVQ5;A0A2R8Y5D4;A0A0D9SG72;A0A1B0GTP9;P61764;P61764-2;A0A096LP52 A0A1B0GWF2 STXBP1 Syntaxin-binding protein 1 0 ; 71.223 0.044961 258667000 273360 260390 216608 242510 303420 168298 282990 238483 324650 FALSE TRUE 256250.8856 279669.5465 221746.044 248733.2172 279590.6171 216882.9005 240558.2767 268258.1275 270463.8177 0.947449784 1.034036822 0.819873231 0.919654316 1.033744992 0.801892476 0.889428681 0.991844787 1 18.04507608 4.069284006 7.20287965 0.91067429 0.989664025 0.104502257 0.077520118 0.422946441 28.35869366 0.0181248 0.039480693 11729.62172 -4.069284006 0.078989735 NKAS(ph)PQSEFMPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NKASPQSEFMPSK 13 1 Q9NQW6;Q9NQW6-2;H7C1K5 Q9NQW6 ANLN Actin-binding protein anillin 1 NKAS(0.991)PQS(0.009)EFMPSK;NKAS(0.995)PQS(0.005)EFMPSK;NKAS(0.933)PQS(0.067)EFMPSK;NKAS(0.939)PQS(0.061)EFMPSK 176.44 1.00E-05 1215800000 3106780 1886060 2307810 2144140 2489230 1333430 2537070 2067220 4017190 TRUE FALSE 2912332.186 2025705.845 2362552.343 2199162.262 2293735.917 1718369.595 2156659.907 2325316.968 3346695.037 0.870211404 0.60528546 0.705935951 0.657114627 0.685373448 0.513452698 0.644414828 0.694809937 1 21.67430566 0.790825971 4.387912438 0.999995184 0.658481054 0.570354704 0.089366795 1.953832546 40.45003741 0.07840987 0.019930682 6.177688005 -0.790825971 -0.34151413 NKDEMSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NKDEMSTK 8 1 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ; 89.08 0.014859 253710000 544580 340500 403580 382810 417870 264500 504490 366670 487130 FALSE TRUE 510495.7099 365710.9743 413153.1082 392633.5527 385052.1758 340856.8562 428846.408 412449.5566 405824.856 1.257921249 0.901154695 1.018057672 0.967495083 0.948813682 0.839911235 1.056727802 1.016324039 1 18.6304977 4.746812669 24.82300606 0.968233239 1.257921408 0.680275952 0.06234256 553.3489218 1664488.006 0.014333533 0.161177861 55822.93535 -4.746812669 0.289688169 NKDQEVNFQEYVTFLGALALIYNEALKG ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NKDQEVNFQEYVTFLGALALIYNEALKG 28 2 P06703 P06703 S100A6 Protein S100-A6 0 ;; 222.36 8.65E-34 4267040000 2008030 1292420 1366790 1596710 1656420 1195440 1915630 1174650 1579350 FALSE TRUE 1882350.987 1388112.122 1399210.904 1637684.282 1526331.455 1540544.122 1628399.065 1321307.638 1315746.282 1.430633711 1.054999843 1.063435195 1.244680912 1.160049985 1.170851966 1.237623915 1.004226769 1 20.32744989 1.223210626 24.66618349 1.002113106 1.170611758 0.343275103 0.106750887 295.9277264 475516.0887 0.098632352 0.025043525 16.71901265 -1.223210626 0.168498652 NKDQGTYEDYVEGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 266.17 2.55E-25 20799190000 16871820 14961520 14819960 15688490 16950080 11224440 18259090 13157660 19250940 FALSE TRUE 15815842.9 16069286.51 15171496.45 16091083.21 15618889.09 14464753.61 15521308.96 14800422.81 16037833.75 0.986158302 1.00196116 0.945981651 1.003320241 0.973877728 0.901914426 0.967793357 0.92284426 1 23.93497595 2.454499294 24.99875272 0.945243046 0.981664534 0.244792957 0.029926392 297.3933808 328637.3112 0.009298588 0.007780312 284.7733169 -2.454499294 0.036421488 NKDQSEQETSDADQHVTSNAS(ph)DSESSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NKDQSEQETSDADQHVTSNASDSESSYR 28 1 A0A590UJD9;A0A0C4DFT3;A0A590UJ08;Q12959-4;Q12959-2 A0A590UJD9;A0A590UJ08 DLG1 Disks large homolog 1 1 NKDQSEQETSDADQHVTS(0.062)NAS(0.895)DS(0.042)ESSYR;NKDQSEQETSDADQHVTS(0.016)NAS(0.928)DS(0.041)ES(0.012)S(0.003)YR 208.33 1.14E-25 559810000 803470 624100 681970 654160 790680 560930 871480 675660 850730 TRUE FALSE 753182.2469 670309.0134 698146.6504 670946.8531 728583.1822 722861.3851 740809.6644 760017.6383 708737.6671 1.062709493 0.945778734 0.985056507 0.9466787 1.028001214 1.019927991 1.045252283 1.072353952 1 19.4348922 2.599297877 6.079243874 1.036574524 0.978638716 0.289413504 0.036808502 0.24065273 11.00435403 0.011072068 0.010397703 397.4640718 -2.599297877 -0.057935808 NKDSGSDTASAIIPSTTPSVDS(ph)DDESVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NKDSGSDTASAIIPSTTPSVDSDDESVVK 29 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 NKDSGSDTASAIIPSTT(0.001)PS(0.1)VDS(0.898)DDES(0.001)VVK;NKDSGSDTASAIIPS(0.003)T(0.001)T(0.001)PS(0.036)VDS(0.959)DDESVVK;NKDSGSDTASAIIPSTTPS(0.002)VDS(0.997)DDESVVK;NKDSGSDTASAIIPSTTPS(0.001)VDS(0.999)DDESVVK;NKDSGSDTASAIIPST(0.001)T(0.006)PS(0.431)VDS(0.562)DDESVVK 200.73 2.03E-25 2145150000 2914760 1523050 1945360 1951910 2204420 1365460 3084910 1660980 3169890 TRUE FALSE 2732330.375 1635818.207 1991504.858 2001999.315 2031293.745 1759646.136 2622356.384 1868357.009 2640814.881 1.034654263 0.619436909 0.754125127 0.758099074 0.769192025 0.666326954 0.993010303 0.707492609 1 21.33255174 0.74173123 0.58032204 0.998406582 0.750804107 0.154022634 0.135383185 1.785312734 1.268390189 0.143015357 0.055994057 5.517358837 -0.74173123 -0.247602475 NKDSGSDTASAIIPSTTPSVDS(ph)DDESVVKDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NKDSGSDTASAIIPSTTPSVDSDDESVVKDK 31 2 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 NKDSGSDTASAIIPSTTPS(0.273)VDS(0.72)DDES(0.007)VVKDK 146.12 8.99E-09 354470000 740150 285400 426610 432010 511630 260780 654070 302280 811460 TRUE FALSE 693825.3327 306531.313 436729.3907 443096.108 471448.6436 336062.9526 555998.2756 340020.3234 676022.0838 1.026335307 0.453433875 0.64602829 0.655446203 0.697386454 0.497118305 0.822455788 0.502972213 1 19.36671085 -1.570329269 3.004733411 1.017930136 0.648793483 0.278932285 0.169162706 31406367.78 32828137.37 4484685.336 0.035570115 0.026894949 1.570329269 -0.369136653 NKEDFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NKEDFEK 7 1 O15042-2;O15042;E7ET15;E7EW00;H0Y8D9 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 ;; 88.417 0.016984 496970000 1632320 952970 1201260 1228350 1244090 881790 1608860 1028400 1480290 FALSE TRUE 1530156.005 1023528.89 1229754.454 1259871.541 1146384.19 1136348.458 1367626.379 1156798.004 1233220.036 1.240781013 0.829964532 0.997189811 1.021611313 0.929586089 0.921448262 1.108988128 0.938030497 1 20.2339988 1.762186351 25 1.026521976 0.971323119 0 0.113211751 43.9870752 46579.97244 0.047935688 0.026583145 57.83441551 -1.762186351 -0.055198857 NKEEAAEYAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 NKEEAAEYAK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ;;;;;; 147.71 2.41E-05 10790420000 16166240 9837500 12190120 12007330 12752270 8870530 16076810 10342520 15792140 FALSE TRUE 15154423.9 10565878.74 12479275.4 12315458.42 11750758.15 11431308.01 13666241.59 11633806.39 13156329.81 1.151873213 0.8031023 0.948537744 0.936086172 0.893163847 0.868882749 1.038757905 0.884274456 1 23.64925374 1.746396589 25 0.976166531 0.918811518 0.022944936 0.097164806 4.794777948 15338.18216 0.040675917 0.022556917 55.76947922 -1.746396589 -0.057355012 NKEES(ph)S(ph)DDEDKES(ph)EEEPPKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NKEESSDDEDKESEEEPPKK 20 3 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;A0A494C198 H0Y993 DEK Protein DEK 3 NKEES(1)S(1)DDEDKES(1)EEEPPKK 115.63 0.0002081 308480000 1315800 172270 411020 396650 400400 234860 643280 257330 385210 TRUE FALSE 1233446.427 185025.05 420769.5885 406828.7105 368954.1991 302660.2694 546826.1359 289458.217 320915.9624 3.843518463 0.576552966 1.311151945 1.267711046 1.149691017 0.943113789 1.703954306 0.90197513 1 18.29183603 4.745901344 24.99617125 1.139440312 3.843519737 0.893090703 0.297384815 276.1386028 940266.6011 0.071146634 0.738694968 55705.91907 -4.745901344 2.704079425 NKEFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NKEFER 6 1 Q32MZ4-2;Q32MZ4;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ;;; 100.19 0.034606 916280000 1183920 1033570 1091550 1078520 1202680 755210 1324720 1035830 1445900 FALSE TRUE 1109820.561 1110096.598 1117442.081 1106196.649 1108226.364 973226.8672 1126090.534 1165155.656 1204569.949 0.92134173 0.921570888 0.927668901 0.918333261 0.920018273 0.807945498 0.934848603 0.967279365 1 20.20008674 1.207660033 3.11715521 0.994104687 0.906892173 0.462855888 0.035661859 0.22064694 3.765788319 0.03205703 0.008934853 16.13095325 -1.207660033 -0.087212514 NKEGLHNAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NKEGLHNAK 9 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 113.12 0.0011131 423490000 437020 332910 411690 417930 470500 288520 495030 405560 769030 FALSE TRUE 409667.6983 357559.0028 421455.4812 428654.7914 433548.8279 371811.0403 420804.8471 456195.0587 640673.9249 0.639432451 0.55809826 0.657831488 0.669068577 0.676707465 0.580343644 0.656815941 0.71205498 1 19.28923075 0.688812233 1.591212475 0.999866215 0.627767475 0.903727268 0.037422778 0.326108462 1.238322107 0.036167755 0.010391991 4.884411361 -0.688812233 -0.37209874 NKEIFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NKEIFLR 7 1 P14625;Q96GW1;A0A1W2PRR1;F8W026 P14625 HSP90B1 Endoplasmin 0 ; 145.63 0.0020733 2473900000 2941700 3469500 2952000 3548000 3791300 2172300 4308200 2638400 3412800 FALSE TRUE 2757584.248 3726385.39 3022022.834 3639047.687 3493546.591 2799407.746 3662225.405 2967810.048 2843181.632 0.969893804 1.310639232 1.062901786 1.279920933 1.228745484 0.984603908 1.288072969 1.043834138 1 21.43907484 1.046083022 9.907410349 1.000017892 1.169080365 0.183858423 0.122486557 0.463377763 94.53276013 0.102816449 0.025719148 11.11944272 -1.046083022 0.169062473 NKEPGAEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NKEPGAEEK 9 1 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ;;; 108.35 0.0023948 1040480000 2054330 1113310 1488410 1393110 1254700 997780 2159770 1319750 1753780 FALSE TRUE 1925753.152 1195740.631 1523715.788 1428859.561 1156160.923 1285822.888 1835932.539 1484523.693 1461062.788 1.318049551 0.818404685 1.042881798 0.97795904 0.791315016 0.88005998 1.256573334 1.016057424 1 20.47858675 1.754210827 25 1.114275776 0.955351352 0.097676509 0.161247975 9.115600776 14579.31038 0.068336023 0.037896115 56.78201853 -1.754210827 -0.158924424 NKESKDPADETEAD ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NKESKDPADETEAD 14 2 P16949 P16949 STMN1 Stathmin 0 ; 90.367 0.022966 2169950000 4043400 1997550 2684300 2701800 2974300 1705080 3572100 2133870 4542400 FALSE TRUE 3790330.812 2145450.68 2747972.864 2771132.762 2740710.476 2197308.916 3036496.767 2400288.367 3784244.095 1.001608437 0.566942995 0.726161631 0.732281717 0.724242519 0.580646719 0.802405101 0.634284762 1 21.85157372 -1.427389231 3.540108072 1.002733893 0.708848405 0.330484674 0.123684048 12501659.3 10483591.19 240939.4949 0.025359866 0.037377545 1.427389231 -0.293885488 NKEVTWEVLEGEVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NKEVTWEVLEGEVEK 15 1 P05455 P05455 SSB Lupus La protein 0 126.63 7.58E-05 107410000 288360 193490 212880 232770 260040 167780 298060 190190 302800 FALSE TRUE 270312.0623 207816.2009 217929.6141 238743.2723 239617.5074 216215.3623 253368.6701 213935.6402 252260.7238 1.07155826 0.82381513 0.863906243 0.946414759 0.949880361 0.857110687 1.004392068 0.848073521 1 17.94455608 -1.532101219 0.297949501 1.068774007 0.902704143 0.049455504 0.078807248 52.72962137 3.006337325 2.812798689 0.081750937 0.029369651 1.532101219 -0.166069865 NKFDVDAADEKFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NKFDVDAADEKFR 13 2 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 115.68 0.00036273 76724000 199770 142550 171850 174540 175290 118100 217820 131520 299320 FALSE TRUE 187266.7523 153104.5503 175926.3632 179018.9919 161523.4305 152193.5528 185159.9131 147940.5615 249361.5583 0.750984849 0.613986179 0.705507153 0.717909341 0.647747919 0.610332859 0.742535916 0.593277338 1 17.92787955 -1.772358468 2.632584514 1.082166516 0.673411693 0.770192826 0.056170762 7476415.602 5629863.484 3965944.138 0.012499944 0.016890462 1.772358468 -0.408754823 NKFEEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NKFEEAER 8 1 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;; 122.94 0.0012485 5877120000 8472310 8298810 7069000 7565370 9378760 4550550 8525260 7438870 9485120 FALSE TRUE 7942043.241 8913262.527 7236680.018 7759510.202 8642190.022 5864219.913 7246976.408 8367629.294 7901992.196 1.005068474 1.12797663 0.915804501 0.981968852 1.093672305 0.742119173 0.917107513 1.058926545 1 22.91378499 NKGNECFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NKGNECFQK 9 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 137.46 0.00014963 2432200000 1887150 1880650 1754740 1798510 1939640 1387220 1984200 1683390 1850040 FALSE TRUE 1769036.65 2019895.283 1796363.261 1844662.811 1787308.499 1787687.894 1686687.63 1893564.947 1541256.372 1.147788701 1.310551132 1.16551879 1.196856568 1.159643866 1.159890026 1.094358901 1.228585316 1 20.55567543 -5 0.095261588 0.385644742 1.328785959 0.505229002 0.056834171 137.8487542 0.903281585 16.8949831 1.023295258 1.00E-05 5 0.943141217 NKHEAMITDLEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 NKHEAMITDLEER 13 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;; 240.73 4.43E-17 7303830000 8099340 7038030 7390520 7628730 8066440 5447260 9417360 6504040 8214790 FALSE TRUE 7592416.767 7559133.064 7565826.624 7824496.127 7432934.341 7019795.533 8005314.294 7316083.711 6843688.479 1.109404204 1.104540788 1.105518851 1.143315648 1.086100626 1.025732769 1.169736805 1.069026408 1 22.70634266 -4.359349452 0.412436078 2.17E-05 1.106496759 0.409799038 0.038594012 455.875427 5.2554496 404.7389247 0.021404294 4.37E-05 4.359349452 1.106475088 NKHEMVIYEAASAIIHLPNCTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NKHEMVIYEAASAIIHLPNCTAR 23 1 Q9UBF2;Q9UBF2-2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 127.16 3.05E-05 111110000 216340 214550 204790 218620 247590 167080 265730 214280 276070 FALSE TRUE 202799.6656 230435.5052 209647.7155 224230.1593 228145.2801 215313.2837 225886.2534 241033.3297 229992.1335 0.881767835 1.001927769 0.911542983 0.974947081 0.991969928 0.936176731 0.982147737 1.048006843 1 17.81122499 1.457071445 4.49882649 1.023191592 0.954189144 0.394109158 0.037604339 0.190226335 7.578437669 0.022735643 0.008703431 28.64649191 -1.457071445 -0.069002448 NKKS(ph)PEIHR ddPTM_SK-BR-3_Pertuzumab_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 138.45 7.11E-05 25615650000 21927370 11236150 13967650 14309460 15108140 8861600 17454200 11241540 19291330 TRUE FALSE 20554975.05 12068086.24 14298969.25 14676664.97 13921607.63 11419800.06 14837104.75 12645071.01 16071482.4 1.278971942 0.750900629 0.889710663 0.913211651 0.866230462 0.710562958 0.923194537 0.786801784 1 23.93799967 4.746569751 24.99503229 0.848413063 1.278972153 0.703709408 0.086345539 510.2025161 1592211.768 0.018428504 0.204685057 55791.72004 -4.746569751 0.430559089 NKKS(ph)PEIHRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NKKSPEIHRR 10 3 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 NKKS(1)PEIHRR;NKKS(1)PEIHRR 139.46 2.93E-05 1025300000 935550 576600 637540 673950 770150 410710 915750 573690 1471020 TRUE FALSE 876995.5955 619292.064 652662.7499 691244.698 709665.5256 529275.3097 778441.7889 645316.4593 1225497.259 0.715624282 0.505339412 0.532569735 0.564052423 0.579083732 0.431886164 0.635204839 0.526575196 1 20.22493583 -1.64571659 0.858599912 1.221390855 0.553972741 0.766228123 0.076037867 146.0788256 29.24817824 69.20906869 0.021922345 0.022609107 1.64571659 -0.667418114 NKNPAPPIDAVEQILPTLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NKNPAPPIDAVEQILPTLVR 20 1 P52292 P52292 KPNA2 Importin subunit alpha-1 0 121.63 2.91E-05 64379000 255150 219460 218760 224160 243620 165870 275190 195780 252900 FALSE TRUE 239180.617 235709.0467 223949.0905 229912.3251 224487.0679 213753.9763 233927.8142 220223.564 210689.3562 1.135228762 1.118751564 1.062934998 1.091238443 1.065488414 1.014545681 1.110297257 1.045252441 1 17.68475791 8 0.096170451 0.971238861 1.411943351 0.608827469 0.027455519 103.6924306 0.710077506 0.390580741 6.027758988 100000000 -8 0.44070449 NKPEWFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NKPEWFFK 8 1 Q5TA02;P78417-3;P78417;Q5TA01;P78417-2 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 ; 109.29 0.0033258 620410000 2658900 2218400 2891400 3052200 2970500 2036300 3590000 2279730 3927600 FALSE TRUE 2492484.195 2382652.644 2959985.373 3130524.619 2737208.912 2624146.753 3051712.828 2564359.309 3272058.187 0.761748127 0.728181624 0.904624919 0.956744789 0.836540415 0.80198658 0.932658484 0.783714458 1 21.64176697 3.986615342 3.577508963 0.883300479 0.74654974 0.432182168 0.067803507 0.202286871 5.539478936 0.016086155 0.035203017 9696.507593 -3.986615342 -0.136750739 NKPGPNIES(ph)GNEDDDASFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 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 301.09 3.69E-50 76065670000 19903460 9111222 12972820 12167520 12781640 8092359 16794220 10196586 16658880 TRUE FALSE 18657737.97 9785826.357 13280541.42 12479759.16 11777821.55 10428491.67 14276082.62 11469652.21 13878405.31 1.34437189 0.705111729 0.956921283 0.899221408 0.848643723 0.751418585 1.028654395 0.82643877 1 23.72633847 -0.859532524 5.817784634 1.000000022 0.903196483 0.011777884 0.177769962 4.48E-08 8.85E-09 0.150285449 0.035422612 0.138187092 0.859532524 -0.09680354 NKPLS(ph)PIKLTPTSVLDYFGTGSVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NKPLSPIKLTPTSVLDYFGTGSVQR 25 2 P35251-2;P35251;A0A1W2PP02 P35251-2 RFC1 Replication factor C subunit 1 1 NKPLS(0.956)PIKLT(0.043)PT(0.001)S(0.001)VLDYFGTGSVQR;NKPLS(0.997)PIKLT(0.003)PTSVLDYFGTGSVQR 228.53 2.25E-34 733030000 887120 533780 596530 680280 707710 366430 828030 486470 977980 TRUE FALSE 831596.7428 573301.6266 610679.9733 697737.1365 652129.3114 472212.3925 703874.5886 547206.8504 814748.82 1.020678671 0.703654442 0.749531584 0.85638312 0.800405346 0.579580333 0.863916058 0.671626441 1 19.63599583 -1.169687416 3.856421523 1.000141445 0.771745421 0.243856371 0.120429411 6887933.004 3133765.022 7908.531017 0.024963613 0.067656976 1.169687416 -0.228396024 NKPRS(ph)PVVELSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NKPRSPVVELSK 12 2 P25098 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 1 NKPRS(1)PVVELSK;NKPRS(1)PVVELSK;NKPRS(1)PVVELSK 154.46 3.68E-05 1935910000 5375440 3011990 3741330 3906840 4225500 2468320 5248660 3260040 6194250 TRUE FALSE 5039000.806 3235000.874 3830076.114 4007096.129 3893646.275 3180883.914 4461672.159 3667063.17 5160389.659 0.976476805 0.626890814 0.742206765 0.776510379 0.754525633 0.616403823 0.864599857 0.710617495 1 22.29904858 -0.610990602 0.658023382 1.031164519 0.743247728 0.326782855 0.106282329 16.42590396 4.987439477 1.281727649 0.035924496 0.244911624 0.610990602 -0.287916791 NKPSDLGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NKPSDLGTK 9 1 P31948;P31948-2;P31948-3;F5H783 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;; 126.03 0.00044239 2232060000 4112820 2378750 2991790 2904160 2979190 1932550 3720320 2485340 3502960 FALSE TRUE 3855405.938 2554875.125 3062756.672 2978685.662 2745216.435 2490445.813 3162492.554 2795640.17 2918293.346 1.321116653 0.87546892 1.049502675 1.020694395 0.940692422 0.853391184 1.083678773 0.957970923 1 21.47669348 4.749045927 24.95300608 0.976303361 1.321116851 0.699582048 0.071723954 841.4827298 2002525.837 0.016449305 0.236116799 56110.73103 -4.749045927 0.344813489 NKPYPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NKPYPK 6 1 P27635;X1WI28;A0A087WV22;Q96L21;A6QRI9 P27635 RPL10;RPL10L 60S ribosomal protein L10;60S ribosomal protein L10-like 0 ; 79.027 0.062227 3216700000 2515800 1903080 2155700 1950140 1947980 1019580 1991040 1848460 2096700 FALSE TRUE 2358340.569 2043986.023 2206834.222 2000183.894 1794993.509 1313916.195 1692502.036 2079244.3 1746747.225 1.350132713 1.170167036 1.263396438 1.145090638 1.027620644 0.752207403 0.968945026 1.190352142 1 20.73623942 2.82508544 2.640145883 0.961203045 1.239703016 0.541046333 0.114623444 0.207104062 2.827570069 0.037342342 0.039307556 668.4754157 -2.82508544 0.278499971 NKQDDDLNCEPLS(ph)PHNITPEPVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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;NKQDDDLNCEPLS(1)PHNITPEPVSK;NKQDDDLNCEPLS(1)PHNITPEPVSK 252.21 5.70E-44 3458892000 4152170 2006075 2757925 2826110 3029523 2435395 4574610 2386974 3978700 TRUE FALSE 3892293.092 2154606.88 2823344.283 2898632.767 2791596.484 3138454.001 3888689.699 2684992.958 3314629.267 1.174277054 0.650029523 0.851782826 0.874496824 0.842204741 0.946849179 1.173189937 0.810043218 1 21.66041609 2.07933586 4.574481204 1.023889861 0.844526688 0.071479455 0.155185902 0.304104472 11.8269483 0.057334891 0.040814321 120.0427289 -2.07933586 -0.179363172 NKQEMAFYSLPEFEEWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NKQEMAFYSLPEFEEWK 17 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 127.97 3.51E-05 170680000 839750 565170 646900 638910 796950 411100 953100 623070 1048800 FALSE TRUE 787191.5465 607015.7749 662244.7735 655305.5123 734360.7617 529777.8963 810191.5031 700861.661 873748.5045 0.900936073 0.694725967 0.75793523 0.749993286 0.840471552 0.606327672 0.927259388 0.802132029 1 19.73685856 0.937420655 0.949806816 0.995016403 0.75738176 0.356492674 0.092698269 0.611446643 1.160335208 0.077787079 0.026223402 8.658061265 -0.937420655 -0.237634643 NKS(ph)EDEDEDEGDATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NKSEDEDEDEGDATR 15 1 Q9BZI1 Q9BZI1 IRX2 Iroquois-class homeodomain protein IRX-2 1 NKS(1)EDEDEDEGDATR;NKS(1)EDEDEDEGDATR 190.64 1.26E-07 568580000 882160 446500 582030 556310 586340 356840 655750 442880 525500 TRUE FALSE 826947.1803 479559.3246 595836.0265 570585.8564 540291.2216 459853.9152 557426.3752 498174.5429 437790.6551 1.888910077 1.09540786 1.361006727 1.30333037 1.234131463 1.050396827 1.273271525 1.137928681 1 18.73988163 4.744146596 24.86735255 1.204014471 1.888910393 0.783626444 0.116235793 250.4477269 1114893.729 0.025703463 0.224887483 55481.29586 -4.744146596 0.684895922 NKS(ph)NEDQSMGNWQIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NKSNEDQSMGNWQIK 15 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 NKS(1)NEDQSMGNWQIK;NKS(1)NEDQSMGNWQIK;NKS(1)NEDQSMGNWQIK;NKS(1)NEDQSMGNWQIK;NKS(1)NEDQSMGNWQIK 264.96 2.19E-25 3365390000 5432640 2634640 3555810 3436960 3393460 2463450 4519300 2815650 4442570 TRUE FALSE 5092620.76 2829711.487 3640155.492 3525158.212 3126951.34 3174608.024 3841672.92 3167190.101 3701076.367 1.375983702 0.764564469 0.983539687 0.95246838 0.844876201 0.85775264 1.037988017 0.855748379 1 21.81951347 4.750141333 24.97798701 0.913220734 1.375983979 0.753010005 0.083487931 871.0551398 1878708.802 0.019263509 0.309961292 56252.43579 -4.750141333 0.462763246 NKS(ph)PAAVTEPETNKFDSTGYDKDLVEALER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NKSPAAVTEPETNKFDSTGYDKDLVEALER 30 3 B7ZBC9;B7ZBC8;O75449 B7ZBC9 KATNA1 Katanin p60 ATPase-containing subunit A1 1 NKS(1)PAAVTEPETNKFDSTGYDKDLVEALER 162.1 2.82E-12 134350000 378980 158040 230910 239680 249170 172110 290900 196740 359980 TRUE FALSE 355260.3183 169741.446 236387.2942 245830.5946 229601.1933 221795.363 247282.2456 221303.4221 299897.0124 1.184607727 0.565999123 0.78822824 0.819716717 0.765600135 0.739571766 0.824557216 0.737931399 1 18.19410762 -1.208310338 3.761590878 1.000229763 0.780482961 0.122537735 0.155122826 15732434.1 10139791.9 27197.42124 0.032284886 0.061899859 1.208310338 -0.219746802 NKS(ph)TESLQANVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NKSTESLQANVQR 13 1 P26373;J3QSB4 P26373 RPL13 60S ribosomal protein L13 1 NKS(0.987)T(0.013)ESLQANVQR;NKS(0.698)T(0.274)ES(0.028)LQANVQR;NKS(0.956)T(0.034)ES(0.01)LQANVQR 302.62 2.86E-41 1027300000 889687 561135 645860 658861 725843 375097 847200 524204 961656 TRUE FALSE 834003.0788 602682.0193 661180.1042 675768.4887 668838.2187 483381.4147 720170.225 589652.0233 801149.4011 1.041008179 0.752271697 0.825289395 0.843498713 0.834848304 0.60335989 0.898921255 0.736007569 1 19.61171178 -1.484844149 3.225721112 1.004128447 0.810249674 0.204245189 0.112903912 33687746.61 42763102.64 1240793.404 0.023955656 0.032745819 1.484844149 -0.193878773 NKTEDLEATSEHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NKTEDLEATSEHFK 14 1 C9JXZ5;Q9BV40 C9JXZ5 VAMP8 Vesicle-associated membrane protein 8 0 ; 202.82 9.56E-09 831680000 1824880 1411170 1573710 1614980 1915380 1051700 2513600 1621480 2512900 FALSE TRUE 1710664.018 1515654.495 1611039.144 1656423.121 1764953.781 1355308.717 2136709.015 1823925.347 2093480.756 0.81713864 0.723987785 0.769550491 0.791229208 0.843071414 0.647394877 1.020648988 0.871240561 1 20.99747223 1.708974632 9.800348142 0.957169672 0.765200679 0.671146713 0.065384762 0.060173726 12.81376447 0.027682581 0.014931404 51.16519482 -1.708974632 -0.191968992 NKYNTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NKYNTPK 7 1 P46777;A0A2R8Y4A2;R4GNJ2 P46777 RPL5 60S ribosomal protein L5 0 90.657 0.015484 1884100000 1657400 1114300 1255900 1354000 1407200 924120 1632900 1212600 1673900 FALSE TRUE 1553666.293 1196803.931 1285690.541 1388745.932 1296684.188 1190898.442 1388061.804 1363995.779 1394515.276 1.114126406 0.858222174 0.921962321 0.995862832 0.929845811 0.853987376 0.995372247 0.97811462 1 20.41133231 1.605685042 25 0.990064788 0.933485985 0.062205687 0.07372818 0.475138994 5358.38183 0.034843252 0.01734989 40.33527683 -1.605685042 -0.056578803 NLAPDEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLAPDEKR 8 1 O95232;J3KPP4;D6RDI2;C9JL41;O95232-2;E7EN55 O95232 LUC7L3 Luc7-like protein 3 0 104.2 0.0074175 281640000 231760 181290 218230 197060 237780 141090 233200 159400 318410 FALSE TRUE 217254.5553 194712.9002 223406.5187 202116.8932 219105.718 181820.3926 198233.8249 179301.4409 265265.314 0.819008532 0.734030761 0.842200268 0.761942412 0.825987064 0.685428448 0.74730398 0.675932478 1 18.01707652 NLDDGIDDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 249.24 1.39E-12 5896460000 3890290 3248270 3572400 3413230 3261250 2819300 4140330 3033220 3278920 FALSE TRUE 3646803.693 3488775.291 3657139.015 3500819.26 3005124.58 3633186.142 3519525.953 3411924.194 2731647.069 1.335020082 1.277169123 1.338803631 1.281578173 1.100114511 1.330034975 1.28842631 1.249035511 1 21.38133967 -3.902763416 0.277860945 3.95E-11 1.300428874 0.629673326 0.067100424 74.82094754 1.266866094 42.74275218 0.077083756 0.000125094 3.902763416 1.300428874 NLDDGIDDERLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 212.1 2.21E-08 3650170000 2067230 2452990 2298510 2492600 2839070 1644960 2546450 2008040 3789920 FALSE TRUE 1937845.764 2634611.932 2353031.743 2556564.336 2616100.894 2119833.248 2164633.463 2258748.214 3157357.868 0.613755502 0.83443564 0.745253418 0.809716365 0.828572814 0.671394671 0.685583818 0.71539189 1 21.59028636 -1.062949261 4.243955661 1.000026231 0.744742229 0.567649969 0.071641795 9479021.56 2374134.153 2356.292325 0.016642872 0.086506898 1.062949261 -0.255284001 NLDFGIDMDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NLDFGIDMDSR 11 0 Q8NE71;Q8NE71-2;H0YGW7 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ;;; 237.84 3.16E-15 405119000 697100 836580 768460 764150 840620 616230 819530 705650 848890 FALSE TRUE 653469.7554 898521.2537 786688.2341 783759.3827 774601.0961 794125.5973 696649.0846 793751.9558 707204.775 0.924017736 1.270524868 1.11239101 1.108249563 1.095299584 1.122907573 0.985074068 1.122379237 1 19.43176849 2.141644988 1.04413566 1.031970985 1.136160515 0.041024489 0.093308951 0.942931648 1.928566731 0.064622238 0.033729786 138.5622696 -2.141644988 0.10418953 NLDIERPTYTNLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 NLDIERPTYTNLNR 14 1 P68363;F8VQQ4;F8VVB9;C9JDS9;P68366-2;P68366;Q9BQE3;F5H5D3 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA1A;TUBA4A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 ;;;;;;;;;;; 318.74 4.59E-56 1.50429E+11 21518859.1 23021353.9 21713221 21835704 25084328.4 17079686.2 25473601.9 21562634.7 25517924 FALSE TRUE 20172032.12 24725878.9 22228268.86 22396045.13 23114306.43 22010314.34 21654071.78 24254777.11 21258817.63 0.948878365 1.163088151 1.045602311 1.053494391 1.087280903 1.035349883 1.01859248 1.140927851 1 24.34155802 3.7046804 24.19152468 1.05323172 1.081202352 0 0.064529417 1042.149329 1123447.811 0.015649186 0.024264779 5066.177474 -3.7046804 0.027970632 NLDKEYLPIGGLAEFCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLDKEYLPIGGLAEFCK 17 1 P00505 P00505 GOT2 "Aspartate aminotransferase, mitochondrial" 0 ; 190.51 2.69E-10 505300000 1276050 1006230 911920 1000860 1847900 796420 1080450 1269440 2262100 FALSE TRUE 1196184.308 1080732.316 933551.173 1026543.762 1702773.388 1026333.525 918446.5529 1427932.378 1884540.896 0.634735129 0.573472467 0.495373263 0.54471822 0.903548122 0.544606661 0.48735825 0.757708353 1 20.84578167 -4.999991671 0.287952883 4.124632182 0.57252331 0.481499949 0.126120769 209.2228624 1.97883235 391.9052028 0.135313969 1.00E-05 4.999991671 -3.552108872 NLDQEQLSQVLDAMFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLDQEQLSQVLDAMFER 17 0 P13861-2;P13861;H7C1L0 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 0 ; 258.81 5.50E-22 80825000 120662 122576 120437 137775 139039 103489 132934 108773 131858 FALSE TRUE 113109.9808 131651.6546 123293.8225 141310.5398 128119.4378 133364.5943 113001.7808 122353.5485 109850.048 1.029676208 1.198466974 1.122382965 1.286394884 1.166312079 1.21406041 1.028691229 1.113823351 1 16.74517597 1.719381794 8.60825935 1.054930603 1.171749097 0.393057735 0.071150953 0.111130428 22.14340311 0.031469733 0.016790733 52.40609427 -1.719381794 0.116818494 NLDSLEEDLDFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 NLDSLEEDLDFLR 13 0 P61758;P61758-2 P61758 VBP1 Prefoldin subunit 3 0 ;;;;;; 274.53 8.33E-32 446916000 371060 382366 389405 363426 364451 321605 416887 344727 325016 FALSE TRUE 347836.017 410676.7765 398641.8705 372752.1264 335828.4886 414447.1427 354378.6645 387766.9248 270768.7299 1.28462403 1.51670681 1.472259631 1.376643922 1.240277962 1.530631483 1.308787262 1.432096405 1 18.04670161 -3.201409313 0.305738276 5.87E-10 1.432899635 0.601910739 0.099385817 52.82081533 1.330100178 33.81404931 0.091873251 0.000628913 3.201409313 1.432899634 NLDSLEEDLDFLRDQFTTTEVNMAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NLDSLEEDLDFLRDQFTTTEVNMAR 25 1 P61758;P61758-2 P61758 VBP1 Prefoldin subunit 3 0 ;;; 109.39 0.0032703 623552000 100522 127621 112427 133796 131651 110905 153727 100338 153367 FALSE TRUE 94230.50746 137070.1916 115093.8215 137229.4319 121311.6615 142921.4731 130677.0635 112865.4202 127769.0569 0.73750648 1.072796457 0.900795735 1.074042771 0.949460413 1.118592221 1.022759866 0.883354882 1 16.96317896 4.747670865 24.67931867 1.005049363 0.737506314 0.548900024 0.075534688 745.8313878 2020377.675 0.016581702 0.203843768 55933.35435 -4.747670865 -0.267543049 NLDSTTVAVHGEEIYCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLDSTTVAVHGEEIYCK 17 0 P21291;E9PS42;E9PND2 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ; 289.61 5.96E-46 2328400000 4203600 3087500 3528200 3320800 3685800 3866500 5597800 3227200 5244600 FALSE TRUE 3940504.18 3316101.713 3611890.57 3406017.35 3396332.136 4982695.783 4758461.857 3630123.024 4369242.379 0.90187356 0.758964925 0.826662899 0.779544153 0.777327473 1.140402695 1.089081686 0.830835808 1 22.05895171 2.251254223 24.99996908 1.033847583 0.803161175 0.569500506 0.088342269 140.1160594 275957.3567 0.029250864 0.024321961 178.3422423 -2.251254223 -0.230686408 NLEAQHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NLEAQHK 7 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 ;;; 142.64 0.0024753 965960000 1977070 1594740 1763790 1712190 1816950 1294450 2114150 1543630 2154280 FALSE TRUE 1853328.718 1712816.209 1805627.932 1756127.694 1674254.076 1668136.701 1797152.834 1736355.603 1794716.751 1.03265806 0.954365756 1.006079612 0.978498525 0.932879283 0.929470737 1.001357364 0.967481695 1 20.77532474 -1.486107637 1.392641031 1.004811488 0.97496238 0.054620627 0.032192154 17843.39556 7969.42626 321.0129904 0.008571348 0.03265069 1.486107637 -0.029849108 NLEGANQHVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLEGANQHVSK 11 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 101.39 0.0033207 149640000 289070 465740 390310 414090 478910 280930 494420 430500 512390 FALSE TRUE 270977.6247 500223.8742 399568.3375 424716.2505 441298.3404 362029.9305 420286.311 484248.8726 426868.7988 0.634803072 1.171844547 0.936044842 0.994957354 1.033803224 0.848105862 0.984579599 1.134420866 1 18.70343319 4.75538858 24.65222948 1.006631199 0.634802717 0.62789644 0.091374216 1918.842662 2810964.404 0.021308888 0.593589481 56936.21329 -4.75538858 -0.371828482 NLEHLS(ph)S(ph)FSSDEDDPGYSQDAYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLEHLSSFSSDEDDPGYSQDAYK 23 0 A0A3B3IRW6;Q2KHR3-2;Q2KHR3;H0YCQ7 A0A3B3IRW6 QSER1 Glutamine and serine-rich protein 1 2 NLEHLS(0.649)S(0.613)FS(0.422)S(0.316)DEDDPGYSQDAYK 176.21 3.27E-13 76684000 70450 91179 101580 95689 95825 71096 124930 88940 116230 TRUE FALSE 66040.66026 97929.98803 103989.5256 98144.54174 88299.29104 91620.26105 106197.9063 100044.3548 96830.46213 0.682023599 1.011355165 1.073934001 1.013570932 0.911895793 0.946192541 1.096740674 1.033190926 1 16.56317336 4.738367455 6.698603963 1.017764272 0.676092434 0.784600855 0.05405171 0.05390143 16.14583908 0.013603066 0.083688043 54747.89875 -4.738367455 -0.341671838 NLEHLSSFS(ph)S(ph)DEDDPGYSQDAYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLEHLSSFSSDEDDPGYSQDAYK 23 0 A0A3B3IRW6;Q2KHR3-2;Q2KHR3;H0YCQ7 A0A3B3IRW6 QSER1 Glutamine and serine-rich protein 1 2 NLEHLS(0.007)S(0.577)FS(0.777)S(0.639)DEDDPGYSQDAYK 133.95 1.11E-05 60261000 54476 65629 69833 65016 67462 52763 80882 57789 84094 TRUE FALSE 51066.4444 70488.23945 71489.47174 66684.42063 62163.80665 67994.82156 68754.49497 65004.08386 70058.16813 0.728914925 1.006138775 1.020430217 0.951843624 0.887317044 0.970548094 0.981391561 0.927858744 1 16.09626564 4.743425263 24.97629299 0.972312181 0.728914825 0.784639022 0.03934321 245.9165859 1262554.54 0.010044286 0.082582813 55389.22174 -4.743425263 -0.243397356 NLEQILNGGES(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 282.69 1.64E-32 463948000 1596450 838370 1149410 1153650 1001670 714154 1200080 714723 915580 TRUE FALSE 1496531.044 900443.7871 1176674.548 1183254.612 923002.8787 920318.6665 1020139.145 803957.7398 762763.7831 1.961984926 1.180501496 1.542646064 1.551272672 1.210076959 1.206557898 1.337424728 1.054006178 1 19.54087682 7.999999999 0.109160422 0.820454419 3.279953265 0.523095173 0.196686962 99.96771803 0.762147401 1.734000164 37.03775101 99999999.68 -7.999999999 2.459498846 NLETFCEETRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 2931220000 1816850 2187920 1993020 2029270 2287810 1633500 2335280 1937830 2452680 FALSE TRUE 1703136.602 2349915.873 2040295.376 2081344.504 2108134.631 2105064.932 1985126.444 2179772.341 2043311.863 0.833517699 1.150052479 0.998523726 1.018613233 1.031724363 1.030222048 0.971523965 1.06678397 1 20.96247798 NLETLPSFS(ph)S(ph)DEEDSVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLETLPSFSSDEEDSVAK 18 0 Q9ULL5;Q9ULL5-2;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 2 NLETLPS(0.002)FS(0.998)S(1)DEEDSVAK 185.09 8.02E-14 45634000 196190 123410 148660 140840 145020 110770 195070 120080 170650 TRUE FALSE 183910.8181 132547.4048 152186.2854 144454.1928 133630.7142 142747.5008 165821.0644 135072.2523 142167.4126 1.293621476 0.932333243 1.070472358 1.016085123 0.939953199 1.004080318 1.166378859 0.950092921 1 17.11723128 4.750312494 24.68979879 1.020364047 1.293621672 0.617998372 0.069668021 1103.788379 2318923.83 0.016901882 0.269473497 56274.60997 -4.750312494 0.273257625 NLETQHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLETQHK 7 0 P17676-3;P17676-2;P17676 P17676-3 CEBPB CCAAT/enhancer-binding protein beta 0 ; 100.45 0.0097841 243670000 318320 228003 263680 259760 301400 194496 302920 237803 347820 FALSE TRUE 298396.9194 244884.5794 269934.6141 266425.8814 277729.2598 250643.8378 257499.9582 267493.228 289766.595 1.029783711 0.845109766 0.931558774 0.91944995 0.958458513 0.864985275 0.888646112 0.923133421 1 18.14453176 0.962229303 20.95231481 1.000000002 0.91070932 0.17649371 0.051478765 1040.160397 577004.6567 0.04470202 0.011175505 9.167043738 -0.962229303 -0.089290682 NLFASFPTEESSINYTFKT(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLFASFPTEESSINYTFKTPEK 22 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 NLFASFPTEESSINYT(0.013)FKT(0.987)PEK;NLFASFPTEESSINYT(0.463)FKT(0.537)PEK 172.95 6.96E-12 525310000 1299930 536230 831570 759540 801240 551130 1220420 692900 1058420 TRUE FALSE 1218569.702 575933.0271 851295.2331 779031.0823 738313.8424 710232.2842 1037429.351 779410.0903 881762.8643 1.381969859 0.653160901 0.96544691 0.883492732 0.837315646 0.805468582 1.17654008 0.883922562 1 19.75003119 1.752958079 25 1.034890158 0.890660989 0.036066753 0.199335493 10.46540047 18196.90801 0.0831927 0.046134492 56.6184634 -1.752958079 -0.144229168 NLGLEELGIELDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NLGLEELGIELDPR 14 0 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 ;;;; 148.96 1.77E-05 241668000 447311 425834 404923 392799 540604 381867 438949 440357 663260 FALSE TRUE 419314.603 457363.1924 414527.9648 402878.8873 498147.1425 492105.8038 373132.6725 495336.5408 552557.6212 0.758861315 0.827720359 0.75019862 0.729116515 0.901529765 0.890596356 0.675282827 0.896443234 1 19.07576539 -4.99999996 0.295690901 2.656695062 0.784933711 0.414934832 0.075407718 258.2351107 2.408859444 264.4341009 0.074961378 1.00E-05 4.99999996 -1.871761352 NLGS(ph)INTELQDVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NLGSINTELQDVQR 14 0 O75396;A0A087X1A9 O75396 SEC22B Vesicle-trafficking protein SEC22b 1 NLGS(1)INTELQDVQR;NLGS(0.951)INT(0.049)ELQDVQR;NLGS(1)INTELQDVQR;NLGS(0.751)INT(0.249)ELQDVQR;NLGS(1)INTELQDVQR 427.83 7.21E-153 1282213000 1101484 1090723 944086 856400 1164507 850513 1408255 1316420 2019512 TRUE FALSE 1032544.083 1171481.266 966480.1657 878376.6739 1073051.318 1096042.296 1197100.236 1480777.935 1682442.401 0.613717345 0.696297992 0.574450671 0.522084247 0.637793791 0.651459031 0.711525242 0.880135887 1 20.68212568 1.21099904 1.438650516 1.001577574 0.613738236 0.903451208 0.044388002 0.114283001 0.453530662 0.043551192 0.013329194 16.25545164 -1.21099904 -0.387839338 NLHSEISGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLHSEISGK 9 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 109.42 0.0024522 385480000 806730 759130 774490 792430 830640 544970 931790 700500 724060 FALSE TRUE 756238.2094 815336.7751 792861.2685 812765.0954 765404.885 702293.9922 792076.7398 787958.967 603209.7084 1.253690381 1.35166388 1.314404025 1.347400554 1.26888688 1.164261752 1.313103434 1.306276998 1 19.20230012 -3.876039161 0.267025054 1.03E-09 1.320061861 0.734139728 0.054568039 53.60693203 0.90917301 29.36214636 0.068403113 0.000133033 3.876039161 1.32006186 NLHSHHFTSPLSGNQEVSAFGEEGEGDYLDDWTVLCNGPYWVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLHSHHFTSPLSGNQEVSAFGEEGEGDYLDDWTVLCNGPYWVR 43 0 Q99470 Q99470 SDF2 Stromal cell-derived factor 2 0 215.15 1.31E-44 175800000 15549 23612 14054 13830 25818 13440 19254 23220 12558 FALSE TRUE 14575.81585 25360.25705 14387.36752 14184.90121 23790.35842 17319.90982 16367.04145 26119.06811 10461.98867 1.393216558 2.4240379 1.37520389 1.355851326 2.273980518 1.655508371 1.564429284 2.496568189 1 13.35286949 -1.234755775 4.504147946 0.999711667 1.806618919 0.256640472 0.436827596 0.001157999 0.000196741 0.387243593 0.091242414 0.058243066 1.234755775 0.806907252 NLIQHNNS(ph)TQTDIFYTDRLEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NLIQHNNSTQTDIFYTDRLEDR 22 1 Q8TDM6-4;Q8TDM6;Q8TDM6-3 Q8TDM6-4 DLG5 Disks large homolog 5 1 NLIQHNNS(0.996)T(0.004)QTDIFYTDRLEDR;NLIQHNNS(0.997)T(0.003)QTDIFYTDRLEDR;NLIQHNNS(0.967)T(0.014)QT(0.019)DIFYTDRLEDR;NLIQHNNS(0.996)T(0.004)QTDIFYTDRLEDR 245.62 4.08E-31 451980000 162803 215405 182093 212204 237370 140365 231613 194349 336264 TRUE FALSE 152613.4508 231353.8103 186412.332 217649.5139 218727.9177 180886.0969 196884.7808 218613.9005 280139.3661 0.544776884 0.825852552 0.665427121 0.776932985 0.780782511 0.645700386 0.702810118 0.780375509 1 18.0957852 0.84809235 3.381182906 0.999923093 0.715541411 0.572089321 0.07956288 0.517730961 10.16931965 0.06857417 0.017752871 7.048429337 -0.84809235 -0.284381682 NLKPIKPMQFLGDEETVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NLKPIKPMQFLGDEETVR 18 2 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;; 225.6 2.23E-19 4322450000 6884340 5453830 5624710 5823160 6199140 4023080 7469870 5456630 6777710 FALSE TRUE 6453461.448 5857637.248 5758130.777 5972592.144 5712284.551 5184477.887 6349832.34 6137902.267 5646466.415 1.142920364 1.037398758 1.019775972 1.05775749 1.011656518 0.918180948 1.12456745 1.087034229 1 22.42891687 -0.434416466 6.293267797 1.000002409 1.045208424 0.053957884 0.063000763 0 25145154.06 0.057861064 0.014033369 0.367776126 0.434416466 0.045206015 NLKPIKPMQFLGDEETVRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLKPIKPMQFLGDEETVRK 19 3 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 64.2 0.021109 318650000 297390 227040 245810 250530 263940 181890 327020 241960 358170 FALSE TRUE 278776.8908 243850.2778 251640.7293 256959.0239 243211.2171 234398.6903 277986.3869 272169.2386 298389.1131 0.934272996 0.817222436 0.843330799 0.861154153 0.815080733 0.785547059 0.931623758 0.912128582 1 18.18683537 1.285673385 1.587402443 0.98609756 0.841006756 0.547023101 0.044743594 0.24395502 1.123776804 0.037984603 0.011567686 19.3051591 -1.285673385 -0.145090804 NLLDEELQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLLDEELQR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 147.24 0.00021605 286520000 779800 985130 890330 972830 1040670 736630 1037100 879670 931200 FALSE TRUE 730993.71 1058070.05 911449.048 997794.4648 958939.9761 949283.1228 881596.483 989498.7359 775776.7042 0.942273345 1.363884794 1.174885818 1.286187713 1.236103083 1.223655103 1.136404945 1.275494263 1 19.56528193 -3.274903424 0.521448643 8.18E-10 1.216498641 0.238653313 0.112669582 548.3004611 14.96053457 614.8546768 0.045341819 0.000531003 3.274903424 1.21649864 NLLEDDS(ph)DEEEDFFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NLLEDDSDEEEDFFLR 16 0 O75379 O75379 VAMP4 Vesicle-associated membrane protein 4 1 NLLEDDS(1)DEEEDFFLR;NLLEDDS(1)DEEEDFFLR;NLLEDDS(1)DEEEDFFLR;NLLEDDS(1)DEEEDFFLR 359.91 1.04E-87 606778000 665210 684140 644143 673687 721190 505172 802050 654560 657024 TRUE FALSE 623575.6935 734794.4374 659422.3761 690974.949 664550.6465 651006.9556 681790.0484 736283.2569 547362.4499 1.139237253 1.342427559 1.204727099 1.262371851 1.214096156 1.189352605 1.245591561 1.345147547 1 19.06213694 -1.648325322 6.068092612 0.998195359 1.245688741 0.587885566 0.063866541 0.001421477 8.24E-05 0.056374301 0.013199057 0.022473705 1.648325322 0.247493382 NLLHVTDTGVGMTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NLLHVTDTGVGMTR 14 0 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 ;;;;; 169.37 2.94E-06 4488880000 2509580 2825010 2583970 2810920 2872510 1928590 3031900 2200990 2418220 FALSE TRUE 2352509.868 3034176.68 2645262.989 2883052.966 2646914.652 2485342.625 2577294.742 2475788.446 2014603.46 1.167728496 1.506091268 1.313044002 1.431077144 1.313863847 1.233663435 1.279306222 1.228920974 1 20.94206447 0.731915781 0.478604005 0.984685913 1.378939439 0.560706956 0.091547291 0.939653493 0.474385754 0.118964751 0.04823245 5.394060101 -0.731915781 0.394253526 NLLPAYRPNLS(ph)PPAEAGLALPPTGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLLPAYRPNLSPPAEAGLALPPTGYR 26 1 Q8N1G0;F8WCX2;Q8N1G0-2;H0Y5I5 Q8N1G0 ZNF687 Zinc finger protein 687 1 NLLPAYRPNLS(1)PPAEAGLALPPTGYR;NLLPAY(0.002)RPNLS(0.998)PPAEAGLALPPTGYR 96.842 0.0041392 769240000 891600 663940 747120 761410 828990 568300 923440 656490 1078740 TRUE FALSE 835796.3476 713098.8084 764842.0392 780949.0697 763884.4694 732358.9844 784978.7448 738454.2216 898691.3251 0.930014928 0.793485804 0.851062003 0.868984765 0.849996487 0.814917162 0.873468702 0.82169951 1 19.77746615 -1.977157701 2.337370587 1.135840168 0.846376671 0.609115827 0.037522772 5618313.511 2304818.984 4124122.894 0.008140426 0.010540041 1.977157701 -0.289463497 NLLQQS(ph)WEDMKR ddPTM_SK-BR-3_Pertuzumab_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 142.91 3.78E-05 243030000 244680 190446 204215 208620 218140 154391 270740 192676 257070 TRUE FALSE 229365.9156 204546.82 209059.0762 213973.5424 201008.1643 198961.1754 230145.0504 216732.0227 214163.3563 1.07098581 0.955097191 0.976166417 0.999113696 0.93857403 0.929015957 1.07462385 1.011993959 1 17.70835213 1.735895457 24.99999959 1.033635483 0.974551196 0.227897938 0.043373806 0.40316445 3716.199514 0.018573413 0.010299903 54.43715967 -1.735895457 -0.059084287 NLLSSWDEVIHIADQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLLSSWDEVIHIADQLR 17 0 Q15813-2;Q15813;A0A2R8Y5Q8;A0A2R8YHI9;A0A2R8Y7E7;A0A2R8Y6Q1;A0A2R8YFL4;A0A2R8YER9;A0A2R8Y897;A0A2R8Y6L2;A0A2R8Y809;A0A2R8Y4V6;A0A2R8Y784;A0A2R8Y4E7 Q15813-2 TBCE Tubulin-specific chaperone E 0 147.56 3.95E-07 77616000 91117 93496 97318 91856 119960 77788 94892 77292 83476 FALSE TRUE 85414.14962 100418.5411 99626.42892 94213.18047 110538.8255 100244.1328 80663.82553 86942.07634 69543.31632 1.228215077 1.443971131 1.432580932 1.354740979 1.589496034 1.441463222 1.159907663 1.250185941 1 16.08562425 1.705695096 5.033798719 1.150411584 1.425093078 0.5950835 0.107720378 0.106469746 6.406587961 0.052598988 0.026085549 50.78028056 -1.705695096 0.274681493 NLLSVAYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLLSVAYK 8 0 P27348;E9PG15;P31946-2;P31946;Q4VY19;A0A0J9YWE8;Q4VY20;A0A0J9YWZ2;P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;E5RGE1;P31947-2;P31947;P61981;P62258;P62258-2;B4DJF2;I3L3T1;K7EIT4;Q04917;A2IDB2 P27348;P31946-2;P63104;P31947-2;P61981;P62258;Q04917 YWHAQ;YWHAB;YWHAZ;SFN;YWHAG;YWHAE;YWHAH "14-3-3 protein theta;14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed;14-3-3 protein zeta/delta;14-3-3 protein sigma;14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed;14-3-3 protein epsilon;14-3-3 protein eta" 0 ; 130.56 0.0024255 675610000 1436880 1833050 1221800 1179730 2178230 755590 1353110 1812730 1905770 FALSE TRUE 1346948.246 1968770.929 1250781.673 1210003.869 2007160.602 973716.567 1150223.717 2039053.331 1587684.675 0.848372644 1.240026411 0.787802321 0.762118504 1.264206069 0.613293422 0.724466095 1.28429364 1 20.59849298 3.933907771 9.416885984 0.887967642 1.064775256 0.030791343 0.239623775 0.904228771 190.6903331 0.057754229 0.104774652 8588.311163 -3.933907771 0.176807614 NLNDQVLFIDQGNRPLFEDMTDSDCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLNDQVLFIDQGNRPLFEDMTDSDCR 26 1 Q14116-2;Q14116 Q14116-2 IL18 Interleukin-18 0 ; 201.82 4.38E-25 111049000 60211 54204 58793 57714 64868 63695 78963 56791 90992 FALSE TRUE 56442.50099 58217.32056 60187.59772 59195.03895 59773.52894 82082.7125 67123.23121 63881.48136 75804.84737 0.744576408 0.767989417 0.793980858 0.780887252 0.788518558 1.082816144 0.885474129 0.842709716 1 16.21000248 2.375526505 10.73180535 0.94189964 0.77589179 0.649385107 0.064683203 0.227406509 22.32763935 0.02101645 0.017575553 237.4250318 -2.375526505 -0.166007851 NLNIINTHAYNQPEDLVYS(ph)QPEMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NLNIINTHAYNQPEDLVYSQPEMR 24 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 NLNIINTHAYNQPEDLVY(0.001)S(0.999)QPEMR;NLNIINTHAYNQPEDLVYS(1)QPEMR;NLNIINTHAYNQPEDLVYS(1)QPEMR;NLNIINTHAYNQPEDLVYS(1)QPEMR;NLNIINTHAYNQPEDLVYS(1)QPEMR;NLNIINTHAYNQPEDLVYS(1)QPEMR 216.7 8.44E-33 1486020000 481688 565541 495901 509990 721731 394837 684628 576326 997121 TRUE FALSE 451540.0079 607414.2441 507664.0059 523077.2068 665049.1586 508820.0323 581974.3872 648281.5698 830695.0635 0.543568907 0.731212055 0.611131603 0.629686187 0.800593609 0.612523241 0.700587271 0.780408598 1 19.66395946 0.829417052 1.449193634 0.999998597 0.661157354 0.70634373 0.070235152 0.33194152 1.298425094 0.059978868 0.017670216 6.75176086 -0.829417052 -0.338841244 NLNNSNLFS(ph)PVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NLNNSNLFSPVNR 13 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3;H0YEN4 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR 321.82 4.31E-51 3247030000 2077850 2180640 2182710 2503550 2126010 1440750 1820640 1297846 1656610 TRUE FALSE 1947801.078 2342096.855 2234484.912 2567795.332 1959041.751 1856671.136 1547651.934 1459884.93 1380111.089 1.411336445 1.697035024 1.619061632 1.86057148 1.419481204 1.345305571 1.121396637 1.057802478 1 20.39635297 2.033643668 1.411088227 1.035091444 1.647837365 0.816428362 0.120004848 0.15743491 0.586211383 0.07594488 0.036977325 108.0547014 -2.033643668 0.612745921 NLNNYEVEY(ph)LCDY(ph)KVVKDMEY(ph)YLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLNNYEVEYLCDYKVVKDMEYYLVK 25 2 Q9H5I1-3;Q9H5I1 Q9H5I1-3 SUV39H2 Histone-lysine N-methyltransferase SUV39H2 3 NLNNY(0.006)EVEY(0.953)LCDY(0.68)KVVKDMEY(0.68)Y(0.68)LVK 41.482 0.061402 270420000 2272300 153280 330090 275810 379560 170240 343730 170870 348080 TRUE FALSE 2130080.799 164629.0107 337919.8907 282887.7515 349750.8887 219385.5244 292190.8775 192203.4956 289983.1993 7.345531756 0.567719134 1.165308513 0.975531521 1.206107421 0.756545637 1.007613125 0.662809073 1 18.14560979 4.740503042 25 0.926228074 7.345533929 0.98984699 0.204586335 14.44438787 185892.9887 0.045347452 0.296052705 55017.7774 -4.740503042 6.419305855 NLPIMSTAS(ph)VEIDDALYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NLPIMSTASVEIDDALYSR 19 0 A0AVT1;A0AVT1-4;A0AVT1-3 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 1 NLPIMSTAS(1)VEIDDALYSR;NLPIMSTAS(1)VEIDDALYSR;NLPIMSTAS(1)VEIDDALYSR 317.28 9.92E-62 305306000 100515 97552 93787 97722 87288 75060 107409 70594 120673 TRUE FALSE 94223.94557 104774.8516 96011.67193 100229.712 80432.75258 96728.6035 91304.01759 79407.8163 100531.8967 0.937254231 1.042205061 0.955036909 0.99699414 0.800071969 0.962168293 0.90820944 0.789876834 1 16.61729379 2.791034627 24.97707392 0.894152971 0.988122103 0.300053909 0.068668179 371.1374114 176656.712 0.018957069 0.020106996 618.065677 -2.791034627 0.093969132 NLPIYSEEIVEMYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLPIYSEEIVEMYK 14 0 P35579;Q5BKV1 P35579 MYH9 Myosin-9 0 191.06 1.24E-06 16746000 22673 17211 21465 20651 20934 16343 26107 17472 19865 FALSE TRUE 21253.9374 18485.32035 21974.15994 21180.93962 19289.92808 21060.95879 22192.49772 19653.41766 16549.40317 1.284272139 1.116978066 1.327791686 1.279861238 1.165596601 1.272611379 1.340984777 1.18756051 1 14.01449157 -0.724183949 7.314445745 0.999999515 1.249114284 0.543033387 0.071171104 0 6.93E-11 0.068008265 0.016029702 0.188719184 0.724183949 0.249114769 NLPLGWDGKPIPYWLYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLPLGWDGKPIPYWLYK 17 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 123.97 4.73E-05 66255000 181430 189570 159350 145340 228980 130620 197600 189640 220460 FALSE TRUE 170074.6202 203605.96 163129.8573 149069.6705 210996.8345 168327.8736 167971.7144 213316.9714 183663.8018 0.926010561 1.108579688 0.888198195 0.81164426 1.148821011 0.916499996 0.914560805 1.161453533 1 17.48670779 1.248162512 24.99999743 1.080726789 0.963760427 0.181185353 0.107073119 305.0673577 794303.1903 0.069763006 0.024758237 17.70771451 -1.248162512 -0.116966363 NLPRRGLS(ph)GYS(ph)MLAIGIGT(ph)LIYGHWSIMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLPRRGLSGYSMLAIGIGTLIYGHWSIMK 29 2 U3KQP3;B4DEZ3;K7EJE1;E7ENQ6;Q9P0J0;Q9P0J0-2 U3KQP3 NDUFA13 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 3 NLPRRGLS(0.615)GY(0.594)S(0.615)MLAIGIGT(0.616)LIY(0.545)GHWS(0.016)IMK 46.66 0.067593 984250000 1385000 441240 610050 446570 662660 383310 691600 467400 600230 TRUE FALSE 1298315.322 473909.8687 624520.6741 458029.7422 610617.3566 493965.3745 587901.0005 525755.9189 500047.7354 2.596382766 0.947729257 1.248922113 0.915972036 1.221118132 0.987836439 1.175689757 1.051411459 1 18.9317063 4.741692594 24.99915477 1.083715621 2.596383321 0.945924064 0.114749418 55.27862421 441207.74 0.023635212 0.168941184 55168.6802 -4.741692594 1.5126677 NLPT(ph)PTSAPTPGLAQGVHAPSTCSYMEATASSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLPTPTSAPTPGLAQGVHAPSTCSYMEATASSR 33 0 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 NLPT(0.947)PT(0.042)S(0.011)APTPGLAQGVHAPSTCSYMEATASSR;NLPT(0.973)PT(0.021)S(0.005)APTPGLAQGVHAPSTCSYMEATASSR 167.58 1.14E-13 319110000 23626 20317.2 30866 28869.7 29915.1 24300.7 31624 26867.7 34906.4 TRUE FALSE 22147.29083 21821.50663 31598.1561 29610.54538 27565.68872 31315.9176 26882.27478 30222.19149 29080.29634 0.761590961 0.750388042 1.086583016 1.018233963 0.947916362 1.076877527 0.924415435 1.039266971 1 14.82775435 4.09255375 3.482257794 1.00670863 0.754711245 0.81406194 0.050927618 0.090264673 2.042947482 0.012193878 0.029555489 12375.2434 -4.09255375 -0.251997385 NLQEEIDALESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLQEEIDALESR 12 0 Q9NQP4;E9PQY2 Q9NQP4 PFDN4 Prefoldin subunit 4 0 ; 306.48 7.06E-37 158404000 313086 334470 318460 327260 344240 270307 350720 278149 347430 FALSE TRUE 293490.5061 359234.5068 326014.0216 335658.0456 317204.779 348340.2428 298132.7919 312876.5149 289441.6885 1.013988371 1.241129115 1.126354753 1.159674155 1.09591946 1.203490225 1.030027131 1.080965622 1 18.1429132 1.676864833 7.6138066 1.041971824 1.149024899 0.359393443 0.063841698 0.121221724 13.0097685 0.028681146 0.014915523 47.51873091 -1.676864833 0.107053075 NLQLLMDRVDEMSQDIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLQLLMDRVDEMSQDIVK 18 1 A0A087WZK9;B3KS98;O15372;E5RJT0 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ; 205.65 8.57E-16 200267000 348620 322850 312400 346070 452960 228200 410020 294880 602360 FALSE TRUE 326800.4965 346754.1499 319810.2755 354950.7421 417386.3488 294077.6355 348541.3074 331696.4171 501822.2246 0.651227627 0.690990022 0.637297951 0.707323679 0.831741458 0.586019552 0.694551358 0.660983912 1 18.93681684 -1.707086859 2.745098729 1.050066933 0.681103984 0.713812667 0.063170949 13339202.64 11467513.37 4608244.518 0.014617077 0.019629676 1.707086859 -0.368962949 NLQYYDISAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLQYYDISAK 10 0 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 112.13 0.0038658 42151000 88553 79819 90943 104410 77488 74387 128710 81592 103510 FALSE TRUE 83010.6258 85728.88181 93100.21091 107089.3374 71402.40505 95861.31933 109411.1304 91778.94081 86233.5123 0.962626056 0.994148093 1.079629119 1.2418529 0.828012256 1.111648091 1.268777387 1.064307116 1 16.39596102 2.011723699 24.97040424 1.153222469 1.030068762 0.081101333 0.12414615 356.5306079 759374.654 0.043552479 0.032140467 102.7362474 -2.011723699 -0.123153707 NLS(ph)FEIK ddPTM_SK-BR-3_Pertuzumab_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 150.15 0.0020645 3468128000 8958540 5634082 6185990 6670500 5442200 3999867 8863880 5094074 6680590 TRUE FALSE 8397840.973 6051235.294 6332724.604 6841676.323 5014791.565 5154563.67 7534823.482 5730080.352 5565556.371 1.508895142 1.087265116 1.137842146 1.229288838 0.901040477 0.926154247 1.353831132 1.029561102 1 22.40809449 4.739889901 24.60712388 1.102563063 1.508895305 0.484469459 0.136729092 84.5896179 1565672.8 0.031801672 0.198568583 54940.15756 -4.739889901 0.406332243 NLS(ph)FNELYPSGTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLSFNELYPSGTLK 14 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 NLS(1)FNELYPSGTLK;NLS(1)FNELYPSGTLK 146.76 8.62E-06 94749000 163580 173285 168294 164804 179130 140960 216746 156694 195408 TRUE FALSE 153341.8198 186115.2017 172286.0132 169033.1497 165061.8524 181652.8637 184246.9495 176257.5908 162793.1424 0.941942747 1.143261927 1.058312473 1.038330897 1.013936152 1.115850834 1.131785693 1.082708941 1 17.3126804 2.215610133 24.9785103 1.098459005 1.055927557 0.049602966 0.061512265 558.0935582 607405.2056 0.022027037 0.016277654 164.2896229 -2.215610133 -0.042531448 NLS(ph)LEAIQLCDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLSLEAIQLCDR 12 0 Q96FC7-3;Q96FC7 Q96FC7-3 PHYHIPL Phytanoyl-CoA hydroxylase-interacting protein-like 1 NLS(1)LEAIQLCDR;NLS(1)LEAIQLCDR 190.11 7.41E-06 175549000 133767 131533 133919 127988 127742 118986 164838 121523 138212 TRUE FALSE 125394.7623 141271.8402 137095.6219 131272.3888 117709.6586 153335.3266 140122.0722 136695.4141 115143.5243 1.089030087 1.226919543 1.190649867 1.140076175 1.022286397 1.331688669 1.216934022 1.187174137 1 16.81307375 2.232811346 24.99918859 1.208254939 1.154530487 0.012137325 0.098690468 416.2416483 1809898.414 0.034075068 0.025864865 170.9272661 -2.232811346 -0.053724453 NLS(ph)LVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLSLVR 6 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L0N7 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 NLS(1)LVR 82.279 0.062583 87337000 165350 137560 164020 181660 196960 150720 198720 119490 126560 TRUE FALSE 155001.0387 147745.0855 167910.6319 186321.7031 181491.5561 194230.4173 168923.7808 134408.5895 105436.3184 1.47009153 1.401273184 1.592531249 1.767149176 1.721338139 1.842158568 1.602140357 1.274784548 1 16.68601237 1.056715744 3.043534303 1.005627087 1.620699455 0.728482952 0.130502304 0.135861275 2.648042419 0.141117945 0.037346782 11.3950371 -1.056715744 0.615072367 NLS(ph)NEELTK ddPTM_SK-BR-3_Pertuzumab_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(0.999)NEELT(0.001)K;NLS(1)NEELTK 229.4 1.35E-07 2857330000 5553890 3692450 4220500 4287970 4497000 3182860 5556350 3751900 5432790 TRUE FALSE 5206281.939 3965842.84 4320612.253 4398006.57 4143823.76 4101700.013 4723226.9 4220332.974 4526022.252 1.150299678 0.876231406 0.954615778 0.971715631 0.915555322 0.906248309 1.043571294 0.932459617 1 22.10981225 -0.838263247 4.744518348 1.00000012 0.961116786 0.006870042 0.078780052 9.01E-08 2.21E-08 0.069122712 0.016292329 0.145123169 0.838263247 -0.038883333 NLS(ph)PGAVESDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 201.3 1.57E-07 1946090000 1365120 1358520 1348300 1446560 1418880 1012860 1469770 1136520 1425410 TRUE FALSE 1279679.576 1459106.234 1380282.313 1483681.179 1307446.888 1305256.24 1249391.633 1278417.024 1187499.862 1.077625031 1.228721182 1.162343135 1.249415874 1.101008033 1.099163276 1.052119392 1.076561829 1 20.17949592 2.374766181 2.136286143 1.055924558 1.184359787 0.548053371 0.051941292 0.213663196 1.997800975 0.019932852 0.015107647 237.009733 -2.374766181 0.128435229 NLS(ph)SDEATNPISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NLSSDEATNPISR 13 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 NLS(0.5)S(0.5)DEATNPISR;NLS(0.5)S(0.5)DEATNPISR;NLS(0.498)S(0.498)DEAT(0.004)NPISR;NLS(0.902)S(0.098)DEATNPISR 298.39 9.06E-41 1405380000 1100461 1008547 1051042 977087 1065360 878769 1215426 842363 1031014 TRUE FALSE 1031585.11 1083220.869 1075973.213 1002160.707 981690.9231 1132455.345 1033184.155 947533.8748 858931.1028 1.20101031 1.261126609 1.252688614 1.166753309 1.142921615 1.318447243 1.202871978 1.10315469 1 19.71218289 1.066090822 2.598174259 1.002346986 1.228622352 0.694170583 0.049380817 0.136486752 1.90167042 0.046002301 0.012470746 11.64369503 -1.066090822 0.226275366 NLS(ph)STTDDEAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLSSTTDDEAPR 12 0 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 NLS(0.967)S(0.032)T(0.001)TDDEAPR;NLS(0.977)S(0.005)T(0.018)TDDEAPR 225.92 1.74E-11 1980600000 1496600 1497450 1591040 2005580 1981170 980130 1205700 1012120 1214200 TRUE FALSE 1402930.478 1608322.756 1628780.22 2057046.578 1825576.9 1263077.62 1024916.478 1138485.41 1011542.176 1.386922375 1.589971031 1.610195065 2.033574701 1.804746202 1.248665305 1.013221695 1.125494751 1 19.94812504 2.088405277 4.332098939 1.064206854 1.676133438 0.757975372 0.167916259 0.111457436 3.855549544 0.070179305 0.049737846 122.5759526 -2.088405277 0.611926584 NLSDIGWPVFEIPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NLSDIGWPVFEIPSPR 16 0 F5H4R1;J3KNB8;F5H538;Q9Y6R4-2;Q9Y6R4;F5H1X6 F5H4R1 MAP3K4 Mitogen-activated protein kinase kinase kinase 4 1 NLSDIGWPVFEIPS(1)PR;NLSDIGWPVFEIPS(1)PR;NLSDIGWPVFEIPS(1)PR;NLSDIGWPVFEIPS(1)PR 235.55 3.33E-16 183701000 366428 367714 392632 414136 377438 346742 413134 311568 244524 TRUE FALSE 343493.9256 394939.9272 401945.4165 424763.4309 347795.542 446840.7865 351188.392 350467.9506 203711.3647 1.686179493 1.938723093 1.973112384 2.085123879 1.707295724 2.193499548 1.723950907 1.720414328 1 17.63616694 0.66957112 1.225257384 1.001302392 1.930962847 0.757984499 0.160313576 0.469562842 1.12248806 0.133959679 0.040757165 4.672734661 -0.66957112 0.929660455 NLSDIGWPVFEIPS(ph)PRPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLSDIGWPVFEIPSPRPSK 19 1 F5H4R1;J3KNB8;F5H538;Q9Y6R4-2;Q9Y6R4;F5H1X6 F5H4R1 MAP3K4 Mitogen-activated protein kinase kinase kinase 4 1 NLSDIGWPVFEIPS(0.999)PRPS(0.001)K;NLSDIGWPVFEIPS(1)PRPSK 215.07 2.51E-19 331960000 776230 823560 849370 938860 1013100 550510 1013390 729370 837120 TRUE FALSE 727647.1499 884537.2393 869517.4575 962952.7371 933535.2126 709433.3002 861441.5774 820433.45 697399.264 1.043372409 1.268336927 1.246800079 1.380776819 1.338595064 1.017255591 1.235220084 1.176418577 1 19.41162532 2.250008401 24.99991616 1.134525751 1.261810524 0.290346548 0.111442983 307.9226031 672447.4141 0.03706106 0.030750956 177.831381 -2.250008401 0.127284773 NLSES(ph)PVITK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLSESPVITK 10 0 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 NLSES(1)PVITK;NLSES(1)PVITK 196.42 3.50E-07 673790000 1994660 1492700 1780260 1750080 1853220 1497950 2396500 1813040 2680400 TRUE FALSE 1869817.791 1603221.061 1822488.608 1794990.016 1707675.577 1930383.848 2037167.073 2039402.035 2233023.924 0.837347854 0.717959644 0.816152746 0.803838238 0.764736803 0.864470742 0.912290751 0.913291619 1 21.09056728 1.626301511 0.808660917 0.991849731 0.775458194 0.79421888 0.036632998 0.22709566 0.294998726 0.031329833 0.013460281 42.29621561 -1.626301511 -0.216391537 NLSFDIPTGSLRDS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLSFDIPTGSLRDSR 15 1 Q5THJ4-2;Q5THJ4 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 NLSFDIPT(0.002)GS(0.002)LRDS(0.996)R 77.391 0.015761 196330000 113830 141410 125470 112690 145830 89943 142640 128520 136560 TRUE FALSE 106705.5835 151880.1435 128446.2077 115581.8162 134377.1 115908.084 121252.4562 144566.0049 113767.2538 0.937928797 1.335007557 1.129026177 1.015949778 1.181157983 1.018817631 1.065793998 1.270717189 1 16.79572583 3.48388019 23.41559001 1.090673127 1.184242561 0 0.126311478 229.6020679 795425.5181 0.031182222 0.045564346 3047.054276 -3.48388019 0.093569434 NLSLCFEGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLSLCFEGSPR 11 0 Q96JQ2 Q96JQ2 CLMN Calmin 1 NLSLCFEGS(1)PR 87.082 0.014674 110520000 102160 239160 200830 215880 221010 209460 194190 194780 163600 TRUE FALSE 95765.98796 256867.6552 205593.7824 221419.8463 203652.7661 269927.7017 165073.0123 219098.7118 136294.1031 0.702642196 1.884657145 1.508456916 1.624573927 1.494215534 1.98047968 1.211153003 1.60754359 1 17.05636362 -1.670128469 9.429988602 0.999583686 1.537163879 0.158417138 0.355160757 0.002731331 9.55E-05 0.302151596 0.071168483 0.021373297 1.670128469 0.537580193 NLSS(ph)TTDDEAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLSSTTDDEAPR 12 0 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 NLS(0.068)S(0.836)T(0.066)T(0.029)DDEAPR 231.36 3.80E-12 1447100000 728140 720880 739010 985420 912450 480170 515200 432110 511750 TRUE FALSE 682567.0172 774254.7053 756539.6662 1010707.546 840789.8576 618787.2841 437950.5429 486059.8847 426335.619 1.601008658 1.81606854 1.774516678 2.370685208 1.972131392 1.451408835 1.027243616 1.140087441 1 18.70163007 2.008524932 3.101753222 1.071950307 1.896007223 0.791774853 0.199743059 0.119768051 2.271497562 0.098913817 0.0591227 101.9823306 -2.008524932 0.824056916 NLSST(ph)TDDEAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLSSTTDDEAPR 12 0 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 NLS(0.242)S(0.101)T(0.328)T(0.328)DDEAPR 115.09 0.00056535 0 99708 109490 88504 90051 111490 82541 100260 66110 104680 TRUE FALSE 93467.45426 117596.7535 90603.35667 92361.86112 102734.0251 106369.2468 85226.94377 74363.97903 87208.23174 1.071773299 1.348459327 1.038931244 1.059095676 1.178031283 1.219715669 0.977280952 0.852717427 1 16.4121767 1.612681564 4.788271238 0.923570709 1.158999056 0.515100167 0.096244347 0.118671717 5.988909089 0.053725264 0.024775636 40.99034408 -1.612681564 0.235428346 NLSTVMDEIHTVLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLSTVMDEIHTVLKK 15 1 Q8IX12-2;Q8IX12 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ; 222.27 9.24E-13 77964000 181988 152327 171632 175937 200711 124355 225314 153957 298020 FALSE TRUE 170597.6959 163605.4496 175703.1921 180451.8413 184947.9677 160254.2698 191530.2574 173178.8704 248278.5367 0.687122206 0.658959295 0.707685789 0.726812086 0.744921289 0.645461633 0.771433004 0.697518491 1 17.92160002 -5 0.261852758 2.935840146 0.681030714 0.867322946 0.036402877 61.65118889 0.604768822 64.21831244 0.043351915 1.00E-05 5 -2.254809432 NLTANDPSQEYVAS(ph)EGEEDPEVEFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLTANDPSQEYVASEGEEDPEVEFLK 26 0 Q86X95 Q86X95 CIR1 Corepressor interacting with RBPJ 1 1 NLTANDPSQEYVAS(1)EGEEDPEVEFLK;NLTANDPSQEYVAS(1)EGEEDPEVEFLK 342.14 7.86E-96 412190000 254850 193243 223220 227377 214829 155537 273571 188008 240124 TRUE FALSE 238899.3934 207550.9128 228514.8838 233211.8788 197957.1969 200438.007 232551.5683 211481.2127 200045.7531 1.19422377 1.037517216 1.142313097 1.1657927 0.989559607 1.001960821 1.162491903 1.05716422 1 17.60997048 2.751811705 24.94100444 1.05792781 1.119946179 0.314424112 0.064126837 1376.476467 2590783.361 0.019974212 0.021077071 564.6920904 -2.751811705 0.062018369 NLTELEDEHLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLTELEDEHLAK 12 0 E9PGD8;E7EWK7;E9PH71;O15381-5;O15381 E9PGD8 NVL Nuclear valosin-containing protein-like 0 ; 111.39 0.0013872 119809000 411260 325650 385510 379160 394290 291460 465610 347980 399970 FALSE TRUE 385519.9707 349761.4648 394654.4793 388889.8875 363324.0539 375599.7705 395796.103 391426.069 333212.4231 1.156979584 1.04966514 1.184393053 1.167093003 1.090367672 1.127208185 1.187819168 1.174704308 1 18.34608266 NLTEQNSYSNIPHEGKHT(ph)PLYER ddPTM_SK-BR-3_Pertuzumab_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 NLTEQNSYSNIPHEGKHT(1)PLYER;NLTEQNSYSNIPHEGKHT(1)PLYER 296.71 1.56E-61 529560000 227780 203341 237050 240240 289850 176658 263710 239380 345030 TRUE FALSE 213523.6564 218396.5792 242672.9379 246404.9651 267086.3502 227656.2968 224169.1337 269267.1199 287442.264 0.742840157 0.759792858 0.844249327 0.857232898 0.9291826 0.79200704 0.779875341 0.93676941 1 18.13291268 -5 0.074147581 1.570275948 0.629333379 0.579267719 0.054816784 241.1652585 1.279585538 23.33669932 2.585148181 1.00E-05 5 -0.940942569 NLTEQNSYSNIPHEGKHTPLY(ph)ER ddPTM_SK-BR-3_Pertuzumab_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 NLTEQNSYS(0.001)NIPHEGKHT(0.455)PLY(0.543)ER;NLTEQNSY(0.001)S(0.021)NIPHEGKHT(0.478)PLY(0.5)ER 130.25 1.32E-05 533220000 286320 267440 287510 302130 369530 210310 358720 295490 408830 TRUE FALSE 268399.7423 287241.5359 294329.873 309883.1673 340508.6044 271023.0829 304933.2662 332382.577 340593.6319 0.788035116 0.843355568 0.864167282 0.909832534 0.999750355 0.795737376 0.895299376 0.975891931 1 18.37769194 8 0.087819242 1.070255216 0.35781009 0.475647141 0.055903614 158.2561212 1.001552058 1.095415575 13.59853677 100000000 -8 -0.712445126 NLVLTGFSHIDLIDLDTIDVSNLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NLVLTGFSHIDLIDLDTIDVSNLNR 25 0 Q9UBT2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 ;;;;; 263.18 3.48E-45 494615800 389198.3 389948.4 376977.8 347862.7 419002.7 303177.8 448123.8 388818.5 414271.7 FALSE TRUE 364839.0731 418820.5853 385919.8914 356789.4458 386095.9181 390700.3092 380931.7964 437363.3456 345127.077 1.057115183 1.213525722 1.118196506 1.033791521 1.11870654 1.132047687 1.103743583 1.267253064 1 18.39676814 3.650122009 6.956197078 1.112526457 1.152173342 0.006738926 0.078958223 0.752026568 56.87090257 0.019243957 0.030022368 4468.090991 -3.650122009 0.039646885 NLVS(ph)PAYCTQESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NLVSPAYCTQESR 13 0 Q9NUQ3 Q9NUQ3 TXLNG Gamma-taxilin 1 NLVS(1)PAYCTQESR 151.44 4.69E-05 103550000 91001 93899 89732 102650 118480 73168 99747 74145 123050 TRUE FALSE 85305.40985 100851.3797 91860.48541 105284.1728 109175.0587 94290.41382 84790.86336 83402.16646 102512.1601 0.832149179 0.983799186 0.89609355 1.027040819 1.064996179 0.919797356 0.827129809 0.813583154 1 16.64543553 -0.780567932 5.011137437 1.000000029 0.924250097 0.078122207 0.084915779 5.71E-08 1.38E-08 0.084288499 0.019866974 0.165741806 0.780567932 -0.075749932 NLVTGDHIPTPQDLPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NLVTGDHIPTPQDLPQR 17 0 A6NMQ3;Q5T5H1;O43768-2;O43768;O43768-9;O43768-3;O43768-4;A0A1W2PRU0;O43768-6;O43768-5;O43768-7 A6NMQ3 ENSA Alpha-endosulfine 0 ; 87.16 0.0046114 252600000 327260 286610 295820 308630 301970 239820 327680 274630 294250 FALSE TRUE 306777.3808 307830.9026 302836.9901 316549.9683 278254.4943 309052.1408 278547.426 308918.16 245137.7741 1.251448831 1.255746503 1.235374643 1.291314525 1.135094317 1.260728348 1.136289285 1.260181795 1 17.90323329 -5 0.180092837 0.063852333 1.274103346 0.668158999 0.051110848 70.67804904 0.681074728 23.61005411 0.137748122 1.00E-05 5 1.210251013 NLVYDQS(ph)PNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NLVYDQSPNR 10 0 Q9NXR1;Q9NXR1-1;I3L533;I3L2R9;I3L2T8 Q9NXR1 NDE1 Nuclear distribution protein nudE homolog 1 1 NLVYDQS(1)PNR;NLVYDQS(1)PNR;NLVYDQS(1)PNR 187.62 1.27E-06 252640000 702060 725030 641860 634680 805460 444801 688920 701580 902080 TRUE FALSE 658119.3178 778711.9756 657085.2223 650966.9633 742202.4207 573207.828 585622.8416 789173.8074 751517.0203 0.875721108 1.036186746 0.874345097 0.866203886 0.987605604 0.762734326 0.779254263 1.050107697 1 19.51944625 3.759162483 6.214611214 0.880977992 0.964622564 0.009129527 0.100983404 0.393396321 46.67984755 0.025111032 0.044641331 5743.312968 -3.759162483 0.083644572 NLYSDDIPHALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NLYSDDIPHALR 12 0 P60228;H0YBR5;E5RIT4 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 ;; 180.47 1.94E-05 1515050000 1795690 2144830 2093460 2099370 2280910 1537630 2468240 1986040 2328890 FALSE TRUE 1683300.968 2303635.445 2143117.86 2153243.388 2101776.529 1981518.82 2098150.326 2234001.466 1940183.214 0.867598975 1.18732882 1.10459561 1.109814461 1.083287658 1.021305001 1.081418657 1.151438405 1 20.88776146 2.470078205 24.48879831 1.067579883 1.093844457 0 0.090816751 756.2166054 2629338.241 0.029359759 0.024615461 295.1740708 -2.470078205 0.026264574 NMAPGAVCS(ph)PGESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NMAPGAVCSPGESK 14 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 NMAPGAVCS(1)PGESK;NMAPGAVCS(1)PGESK;NMAPGAVCS(0.998)PGES(0.002)K;NMAPGAVCS(1)PGESK;NMAPGAVCS(0.991)PGES(0.009)K;NMAPGAVCS(1)PGESK 272.44 5.82E-33 1407830000 2845910 1739320 2165600 2296820 2324220 1610020 2843620 1585450 2359210 TRUE FALSE 2667789.573 1868101.063 2216969.055 2355760.29 2141685.137 2074806.638 2417245.58 1783396.923 1965442.61 1.357347989 0.950473473 1.127974454 1.19859022 1.089670655 1.05564346 1.229873397 0.907376747 1 20.90642281 1.225997941 24.99989429 0.953688298 1.124393782 0.32537582 0.111246327 318.4643724 633729.3472 0.096558879 0.024800569 16.82666084 -1.225997941 0.170705484 NMAPSQQS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NMAPSQQSPVR 11 0 H7C3Q7;B7Z836;E7EW77;E7EP65;A0A0C4DG21;F8WAL6;Q9NYB9-3;Q9NYB9-2;Q9NYB9-4;Q9NYB9;H0Y6B5 H7C3Q7 ABI2 Abl interactor 2 1 NMAPSQQS(1)PVR;NMAPSQQS(1)PVR 109.51 0.0075024 312200000 465430 629200 372890 404030 712030 233440 393950 538250 601400 TRUE FALSE 436299.5671 675786.6227 381735.1269 414398.0938 656110.036 300830.3384 334880.8548 605451.6973 501022.4548 0.870818389 1.348815041 0.761912212 0.827104833 1.309542177 0.600432846 0.668394902 1.20843226 1 18.93451574 2.226049462 24.99849082 0.814498932 1.023357524 0.06644252 0.252702341 460.3257172 919768.8154 0.091351558 0.067928069 168.2865711 -2.226049462 0.208858592 NMDPLNDNIATLLHQSSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NMDPLNDNIATLLHQSSDK 19 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 252.41 7.51E-31 793730000 1334340 1927570 1930440 2033570 1885080 1640960 2405360 1908200 1450920 FALSE TRUE 1250826.041 2070289.288 1976230.948 2085754.849 1737033.421 2114678.513 2044698.598 2146442.97 1208752.079 1.034807769 1.71274931 1.634934891 1.72554396 1.437046894 1.749472494 1.691578144 1.775751213 1 20.20508694 -0.890681821 5.449489342 0.999999441 1.620679211 0.411878808 0.221686619 1.34E-06 2.73E-07 0.191202348 0.045066785 0.128622865 0.890681821 0.62067977 NMDPLNDNIATLLHQSSDKFVSELWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NMDPLNDNIATLLHQSSDKFVSELWK 26 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 350.05 3.95E-110 1752040000 920217 1724780 1559810 1786620 2090300 1284860 2217610 1591440 1987930 FALSE TRUE 862622.2606 1852484.506 1596809.43 1832467.694 1926136.27 1655778.224 1885099.968 1790134.787 1656131.64 0.520865757 1.118561146 0.964180256 1.10647466 1.163033314 0.999786601 1.138254908 1.080913343 1 20.65938592 4.741486819 24.96250666 1.072297091 0.520865553 0.875985558 0.065098308 85.25035629 727206.0568 0.014680284 0.103448643 55142.54667 -4.741486819 -0.551431538 NMDPLNDNVAALLHQSTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NMDPLNDNVAALLHQSTDR 19 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 ;; 235.56 3.64E-24 442820000 74049 157025 132595 142961 163490 115701 149085 137211 131222 FALSE TRUE 69414.40527 168651.2944 135740.216 146629.6213 150650.1549 149102.0005 126731.0883 154342.0954 109320.2005 0.634964123 1.542727635 1.241675513 1.341285697 1.378063288 1.363901638 1.159265056 1.411835093 1 16.73820049 -1.076894577 4.425919065 0.999982012 1.284381324 0.091833227 0.245072721 0.748122722 63337078.38 3143.672197 0.050261849 0.083773261 1.076894577 0.284399312 NMFHPMDFEDDPLVLNEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NMFHPMDFEDDPLVLNEIR 19 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 ; 202.95 5.28E-16 153514000 150407 166690 160600 151204 168225 127505 187423 151408 169070 FALSE TRUE 140993.2944 179031.901 164409.5078 155084.1506 155013.2871 164313.6236 159320.6611 170311.6221 140851.1248 1.001009361 1.271071859 1.16725733 1.10105014 1.10054703 1.166576581 1.131128071 1.20916054 1 17.10381156 -1.458704145 2.982336376 0.996266368 1.153824237 0.272157788 0.071990162 10334180.76 12748982.65 324285.8636 0.016959604 0.034777299 1.458704145 0.157557869 NMGGPYGGGNYGPGGSGGS(ph)GGYGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 NMGGPYGGGNYGPGGSGGSGGYGGR 25 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 NMGGPYGGGNYGPGGS(0.04)GGS(0.96)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR;NMGGPYGGGNYGPGGS(0.002)GGS(0.998)GGYGGR;NMGGPYGGGNYGPGGS(0.001)GGS(0.999)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR 471.81 1.64E-230 4179700000 2225927 1985855 2054792 2060131 2340089 1642853 2445180 2072139 2787504 TRUE FALSE 2086610.202 2132889.77 2103532.637 2112997.449 2156307.849 2117117.992 2078547.959 2330850.115 2322251.574 0.898528921 0.91845767 0.905816002 0.909891707 0.928541883 0.911666081 0.895057186 1.003702674 1 21.14709284 1.233502402 24.99909194 1.001851405 0.910163056 0.943000903 0.009417534 27.56101753 136206.5426 0.008016963 0.002249527 17.11994644 -1.233502402 -0.091688349 NMGGPYGGGNYGPGGSGGSGGYGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NMGGPYGGGNYGPGGSGGSGGYGGR 25 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;; 508.67 7.62E-287 155352000 70570.8 65656.8 65019.1 68205.8 73586.4 50923.4 80795.9 56885.2 76610 FALSE TRUE 66153.8996 70518.09779 66561.38376 69956.0763 67807.22098 65624.15891 68681.30487 63987.44244 63823.29608 1.036516502 1.104895894 1.04290107 1.096089995 1.062421171 1.028216387 1.076116545 1.002571888 1 15.9617955 1.232084248 24.8405853 1.001285883 1.065621068 0.531339405 0.024397072 108.8500267 417481.3109 0.019697035 0.005402349 17.06413382 -1.232084248 0.064335186 NMITQYWPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NMITQYWPDR 10 0 O95373 O95373 IPO7 Importin-7 0 117.02 0.0023561 120360000 160760 149720 144330 146340 201830 130930 221840 154090 161520 FALSE TRUE 150698.3186 160805.4246 147753.5758 150095.3322 185979.0859 168727.3655 188577.1515 173328.4757 134561.2685 1.119923439 1.195034993 1.098039409 1.11544231 1.382114541 1.253907364 1.401422218 1.288100785 1 17.03790369 2.753160878 24.51733633 1.297836185 1.136919081 0.228688472 0.112646459 657.0727518 1103381.479 0.030485499 0.032206539 566.449083 -2.753160878 -0.160917104 NMLAFSS(ph)PAAGGVCEPLKS(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NMLAFSSPAAGGVCEPLKSPQR 22 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 2 NMLAFS(0.182)S(0.818)PAAGGVCEPLKS(1)PQR;NMLAFS(0.465)S(0.535)PAAGGVCEPLKS(1)PQR 138.08 1.15E-06 167334000 302600 184806 232020 220656 228540 217831 366800 214887 248940 TRUE FALSE 283660.8062 198489.2285 237523.624 226318.4065 210591.3903 280715.2735 311801.7452 241716.115 207390.3058 1.367763093 0.957080553 1.145297622 1.091268011 1.015435073 1.353560247 1.503453809 1.165513084 1 17.66198893 2.230794905 24.9869815 1.321642615 1.096769796 0.085154617 0.171222891 211.5090099 680546.2894 0.05838766 0.043923746 170.1354856 -2.230794905 -0.224872819 NMLAFSSPAAGGVCEPLKS(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NMLAFSSPAAGGVCEPLKSPQR 22 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 NMLAFSSPAAGGVCEPLKS(1)PQR;NMLAFSSPAAGGVCEPLKS(1)PQR;NMLAFSSPAAGGVCEPLKS(1)PQR;NMLAFSSPAAGGVCEPLKS(1)PQR;NMLAFSSPAAGGVCEPLKS(1)PQR 258.09 2.20E-37 4095550000 5229530 2861850 3655500 3351290 3506540 3435040 6687700 3155950 4263290 TRUE FALSE 4902223.052 3073744.352 3742210.186 3437289.775 3231150.493 4426680.285 5684941.471 3549977.305 3551719.357 1.380239416 0.865424332 1.053633412 0.967781919 0.909742626 1.246348554 1.600616743 0.999509519 1 21.76008616 2.128674162 6.212862099 1.303858716 1.012490622 0.072852216 0.222330219 0.263037625 13.45426243 0.077909823 0.057300507 134.4850974 -2.128674162 -0.291368095 NMPGLSAATLASLGGT(ph)SSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NMPGLSAATLASLGGTSSR 19 0 Q32MZ4-2;Q32MZ4;C9JTC6;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 NMPGLSAATLASLGGT(0.333)S(0.333)S(0.333)R 112.57 0.0021696 64439000 325140 133930 219520 195210 193760 242010 310010 151090 238820 TRUE FALSE 304790.0678 143846.3166 224727.1181 200219.4191 178542.8712 311874.3583 263526.8785 169953.9191 198959.3992 1.53192093 0.72299332 1.129512448 1.006333051 0.897383446 1.567527644 1.324525906 0.854214075 1 17.60211453 2.300886527 24.99999998 1.238159095 1.019467373 0.026526903 0.27844228 131.9430938 52923.47384 0.089977088 0.075280202 199.933941 -2.300886527 -0.218691723 NMPGLSAATLASLGGTS(ph)SR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NMPGLSAATLASLGGTSSR 19 0 Q32MZ4-2;Q32MZ4;C9JTC6;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 NMPGLSAATLASLGGT(0.003)S(0.697)S(0.3)R;NMPGLSAATLASLGGT(0.13)S(0.435)S(0.435)R;NMPGLSAATLASLGGT(0.106)S(0.447)S(0.447)R 368.61 6.73E-108 1677010000 1523240 1637930 1549030 1378290 1634410 1167768 2115190 1530120 2092390 TRUE FALSE 1427903.127 1759204.041 1585773.723 1413659.255 1506050.031 1504883.664 1798036.896 1721158.85 1743156.592 0.819147938 1.009205971 0.909713867 0.810976628 0.863978623 0.863309511 1.03148329 0.987380513 1 20.73327075 1.730038051 8.916180777 1.005595056 0.894672843 0.513981391 0.056834716 0.10413228 27.67056151 0.029551138 0.01585118 53.70788503 -1.730038051 -0.110922213 NMPGLSAATLASLGGTSS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.002)S(0.086)S(0.912)R;NMPGLSAATLASLGGT(0.047)S(0.189)S(0.764)R;NMPGLSAATLASLGGT(0.135)S(0.214)S(0.651)R;NMPGLSAATLASLGGT(0.038)S(0.16)S(0.801)R;NMPGLSAATLASLGGT(0.029)S(0.247)S(0.724)R 319.09 7.96E-62 2607552000 1715549 1716496 1577428 1534628 1739819 1305008 2182391 1614529 2205167 TRUE FALSE 1608175.85 1843587.15 1614845.337 1574009.153 1603180.634 1681742.625 1855161.73 1816106.5 1837110.382 0.875383356 1.003525519 0.879013778 0.856785291 0.872664294 0.915428186 1.009825946 0.988566892 1 20.80900688 1.773644867 5.590879838 0.999113299 0.906715376 0.562655445 0.040910998 0.1638238 11.44209461 0.021529555 0.011738012 59.38063904 -1.773644867 -0.092397923 NMQNVEHVPLSLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 NMQNVEHVPLSLDR 14 0 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ;;;;;; 119.77 0.00012737 5873530000 6203780 7220890 6558290 6450090 7594310 5113987 7605720 6660914 7125770 FALSE TRUE 5815496.484 7755532.209 6713855.736 6615610.229 6997883.527 6590312.028 6465312.894 7492543.775 5936432.953 0.979628092 1.306429681 1.130957898 1.114408313 1.178802756 1.110146797 1.089090527 1.262128931 1 22.50116488 -2.193795503 2.481553666 0.536917435 1.153002758 0.201752654 0.090719147 36902319.48 27915987.51 91883147.67 0.020680772 0.006400361 2.193795503 0.616085323 NMSVIAHVDHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 NMSVIAHVDHGK 12 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;;; 204.13 6.76E-08 9555180000 12860940 10479580 12288470 11929480 12167600 8760680 15127360 10518200 14694920 FALSE TRUE 12055996.72 11255499.01 12579958.31 12235610.65 11212005.78 11289746.1 12859152.8 11831420.42 12242242.92 0.984786595 0.919398437 1.027586072 0.999458247 0.91584572 0.922195889 1.0503919 0.96644222 1 23.54536456 1.738488155 24.99999999 1.008720528 0.964002305 0.19880651 0.041349933 0.065708512 5860.285437 0.019098035 0.010590871 54.76311643 -1.738488155 -0.044718223 NMTVADSGTNHDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NMTVADSGTNHDSR 14 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ; 118.2 0.00019656 165181000 46396 82682 85695 82411 89132 69376 87735 84714 118776 FALSE TRUE 43492.15718 88803.86131 87727.72587 84525.80578 82131.93226 89403.72497 74579.95124 95290.72938 98951.51828 0.439529963 0.897448193 0.886572813 0.854214339 0.830021951 0.903510391 0.753701939 0.963004217 1 16.59443422 4.740639214 24.74478055 0.871876273 0.439529791 0.804716502 0.068814992 65.72368466 782347.7877 0.014907435 0.098089288 55035.03083 -4.740639214 -0.432346482 NMTVEQLLT(ph)GSPTSPTVEPEKPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NMTVEQLLTGSPTSPTVEPEKPTR 24 1 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 NMTVEQLLT(0.525)GS(0.399)PT(0.062)S(0.013)PTVEPEKPTR 123.28 0.0001845 105930000 196490 158900 191080 168730 189060 148760 239770 181240 203020 TRUE FALSE 184192.0416 170665.1213 195612.5078 173059.8975 174211.9902 191704.5971 203818.7144 203868.213 169134.6504 1.089026058 1.009048831 1.156548982 1.023207823 1.030019513 1.133443659 1.20506776 1.205360418 1 17.36781273 2.074530878 5.835070393 1.161934751 1.066042727 0.185495662 0.070797579 0.243147107 14.28319296 0.024936983 0.018188159 118.7219109 -2.074530878 -0.095892024 NMTVEQLLTGS(ph)PTSPTVEPEKPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NMTVEQLLTGSPTSPTVEPEKPTR 24 1 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 NMTVEQLLT(0.002)GS(0.632)PT(0.349)S(0.015)PT(0.003)VEPEKPTR;NMTVEQLLT(0.047)GS(0.931)PT(0.022)SPTVEPEKPTR;NMTVEQLLT(0.035)GS(0.777)PT(0.165)S(0.023)PTVEPEKPTR 180.65 2.11E-17 330166000 302275 212927 263723 272731 285825 199374 336670 251598 283112 TRUE FALSE 283356.1473 228692.3366 269978.6341 279729.7392 263377.4575 256930.0372 286189.459 283010.5641 235858.7782 1.201380544 0.96961554 1.144662226 1.186005207 1.116674391 1.089338456 1.21339329 1.199915332 1 17.84756377 3.722224783 23.03574533 1.14692837 1.065402033 0.034650058 0.083161418 126.5918785 595568.498 0.019893312 0.03200762 5275.028171 -3.722224783 -0.081526338 NMTVEQLLTGSPTS(ph)PTVEPEKPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NMTVEQLLTGSPTSPTVEPEKPTR 24 1 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 NMTVEQLLTGS(0.004)PT(0.252)S(0.732)PT(0.011)VEPEKPTR;NMTVEQLLTGSPT(0.013)S(0.985)PT(0.002)VEPEKPTR 173.83 5.57E-12 498670000 579910 451980 541320 635720 578410 250420 412530 318240 439910 TRUE FALSE 543614.4683 485445.0695 554160.366 652033.6515 532984.0118 322712.1888 350674.9562 357972.9645 366486.1791 1.483315059 1.324593115 1.512090763 1.779149361 1.454308627 0.880557596 0.956857247 0.976770708 1 18.48339927 2.264045959 7.75225006 0.947983893 1.499010296 0.852523791 0.115099002 0.072133024 16.9378079 0.043174097 0.035355885 183.6732706 -2.264045959 0.551026403 NMVDLVNTHHLHSSS(ph)DDEDDRLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NMVDLVNTHHLHSSSDDEDDRLK 23 1 Q9UPN7 Q9UPN7 PPP6R1 Serine/threonine-protein phosphatase 6 regulatory subunit 1 1 NMVDLVNTHHLHS(0.011)S(0.188)S(0.802)DDEDDRLK;NMVDLVNTHHLHS(0.01)S(0.338)S(0.652)DDEDDRLK;NMVDLVNTHHLHSS(0.163)S(0.836)DDEDDRLK 323.28 3.67E-74 2021890000 1343330 1341140 1397740 1539030 1546340 1267390 2090900 1446680 1675530 TRUE FALSE 1259253.373 1440439.401 1430895.053 1578524.115 1424896.694 1633264.919 1777388.956 1627301.183 1395873.219 0.902125893 1.031927099 1.025089552 1.130850635 1.020792343 1.170066806 1.273316897 1.165794401 1 20.41273648 3.310307832 0.710516377 1.175673824 0.953903051 0.377673874 0.084106068 0.71936361 0.773481382 0.047232829 0.095218616 2043.18566 -3.310307832 -0.221770773 NNASTDYDLSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NNASTDYDLSDK 12 0 P39023;G5E9G0;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ;; 205.49 2.35E-07 814130000 2097480 1389100 1556190 1576980 1620090 1078240 2010100 1385640 1829750 FALSE TRUE 1966202.471 1491950.409 1593103.562 1617447.977 1492854.667 1389510.384 1708704.166 1558640.204 1524352.904 1.289860416 0.978743443 1.045101536 1.061071863 0.97933665 0.91154114 1.12093739 1.02249302 1 20.53976551 4.743845672 24.91373301 1.01942736 1.289860535 0.705480513 0.05576381 307.5288506 1449642.493 0.012986314 0.111113269 55442.86601 -4.743845672 0.270433174 NNCPDKTSAAAGSS(ph)SR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NNCPDKTSAAAGSSSR 16 1 A0A087X2H1;Q9ULT8;H0YJP0 A0A087X2H1 HECTD1 E3 ubiquitin-protein ligase HECTD1 1 NNCPDKTSAAAGS(0.074)S(0.463)S(0.463)R 88.176 0.0037662 66641000 51598 62666 54223 80352 84785 34124 71756 43606 135590 TRUE FALSE 48368.57329 67305.85584 55509.19517 82413.96836 78126.32811 43975.04484 60996.85395 49050.30509 112959.1531 0.428195254 0.595842426 0.491409449 0.729590884 0.691633444 0.389300412 0.539990362 0.434230461 1 16.78544165 -1.391710112 3.128072425 1.005707041 0.542152348 0.631297292 0.111024029 27635711.92 34781147.93 1418811.991 0.027716555 0.04057793 1.391710112 -0.463554693 NNCPDKTSAAAGSSS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NNCPDKTSAAAGSSSR 16 1 A0A087X2H1;Q9ULT8;H0YJP0 A0A087X2H1 HECTD1 E3 ubiquitin-protein ligase HECTD1 1 NNCPDKTSAAAGS(0.115)S(0.159)S(0.726)R 78.456 0.012771 83021000 34515 40670 33221 48461 54531 20248 46739 28450 89122 TRUE FALSE 32354.76776 43681.24912 34009.01781 49704.5913 50248.35523 26093.2689 39730.92085 32002.04513 74246.96245 0.435772275 0.58832372 0.458052649 0.669449492 0.676773212 0.351438874 0.535118469 0.431021608 1 16.18004438 -1.14311932 5.031544077 1.00002334 0.521893255 0.675277729 0.104962086 2.56E-05 4.37E-06 0.094807117 0.022345163 0.071925134 1.14311932 -0.478130084 NNDLCYWVPELVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NNDLCYWVPELVR 13 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;; 165.7 8.12E-05 135880000 225337 249415 199931 210381 255772 178385 270187 245349 269065 FALSE TRUE 211233.5594 267881.9461 204673.4577 215779.7326 235684.6989 229881.8537 229674.9676 275981.3627 224156.3133 0.942349365 1.195067595 0.913083619 0.962630628 1.051430118 1.025542624 1.02461967 1.23120049 1 17.77414561 1.399242894 24.99999646 1.119706073 1.023618236 0.157993455 0.093970835 62.00359573 19901.50054 0.058336548 0.021310023 25.07511273 -1.399242894 -0.096087837 NNFEGEVTKENLLDFIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NNFEGEVTKENLLDFIK 17 1 P07237;H7BZ94;I3L398;I3L312;I3L4M2;I3NI03 P07237 P4HB Protein disulfide-isomerase 0 ; 181.4 7.35E-10 1171230000 2976300 2334990 2444020 2686400 2717100 1565000 3459000 2035660 3686900 FALSE TRUE 2790018.696 2507875.089 2501993.309 2755337.572 2503709.926 2016790.094 2940355.062 2289816.632 3071532.572 0.908347423 0.816489824 0.814574891 0.897056277 0.81513377 0.6566071 0.957292489 0.745496451 1 21.55052725 -1.501307419 5.374778611 1.000358565 0.828236687 0.292946206 0.084727175 0.000325195 3.02E-05 0.073282365 0.017237176 0.031527721 1.501307419 -0.172121878 NNLAGAEELFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NNLAGAEELFAR 12 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 145.28 0.00014833 235430000 180913 190556 186343 190974 211001 164331 246369 184895 229301 FALSE TRUE 169589.9783 204664.9645 190763.144 195874.7162 194429.8326 211770.692 209428.2556 207979.5478 191029.1818 0.887770008 1.071380627 0.998607345 1.025365415 1.017801735 1.108577706 1.096315514 1.088731815 1 17.54343352 2.305807961 6.938111224 1.083867481 1.010364228 0.289240025 0.05474677 0.254327873 21.28732443 0.017409972 0.014463529 202.2124826 -2.305807961 -0.073503253 NNQFQALLQYADPVSAQHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NNQFQALLQYADPVSAQHAK 20 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;K7EK45;A0A087WU68;K7EKJ7 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 184.32 4.05E-17 640760000 251200 213810 225250 224890 212410 152490 268260 217350 250690 FALSE TRUE 235477.8404 229640.7149 230593.0364 230661.0581 195728.1754 196511.3875 228036.9034 244486.6259 208848.2195 1.127507053 1.099557925 1.104117799 1.104443498 0.937179048 0.940929197 1.091878609 1.170642616 1 17.67209532 2.940181521 24.99334866 1.030230012 1.106814037 0.258256261 0.067947154 382.0172515 159614.0189 0.021265792 0.022555814 871.3277006 -2.940181521 0.076584025 NNQITNNQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NNQITNNQR 9 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;; 223.88 7.68E-07 803400000 553119 601028 422295 482717 537805 247507 608353 488400 557646 FALSE TRUE 518500.2691 645528.7385 432312.0368 495104.3355 495567.9647 318958.253 517136.1153 549377.8151 464571.2801 1.116083347 1.389514949 0.930561262 1.06572308 1.066721052 0.686564725 1.113146976 1.18254795 1 18.82554044 3.927912118 5.274297472 1.004330846 1.258799284 0.324919954 0.147345378 0.195034896 12.26032403 0.035894936 0.067896872 8470.559901 -3.927912118 0.254468438 NNRPAFFS(ph)PSLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NNRPAFFSPSLKR 13 2 B0QY16;Q6ICG6-3;Q6ICG6;Q6ICG6-2 B0QY16 KIAA0930 Uncharacterized protein KIAA0930 1 NNRPAFFS(0.5)PS(0.5)LKR 119.47 0.00018042 557500000 1072700 832000 936780 1030200 1106200 680850 1297900 909700 1407900 TRUE FALSE 1005561.622 893602.1457 959000.864 1056636.676 1019323.514 877400.3423 1103291.944 1023278.047 1172912.395 0.857320313 0.761866061 0.817623608 0.900865811 0.869053408 0.74805275 0.940643094 0.872424959 1 20.16166383 0.34225148 0.260244501 1.052191942 0.788295574 0.474549098 0.05504045 3.817383875 0.530585635 0.302890792 0.098475936 2.19913292 -0.34225148 -0.263896368 NNRPAFFSPS(ph)LKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NNRPAFFSPSLKR 13 2 B0QY16;Q6ICG6-3;Q6ICG6;Q6ICG6-2 B0QY16 KIAA0930 Uncharacterized protein KIAA0930 1 NNRPAFFS(0.183)PS(0.817)LKR 120.77 0.00013277 968480000 1100000 823750 890010 972080 1019500 673880 1259300 941140 1384300 TRUE FALSE 1031152.964 884741.3071 911121.4575 997025.2185 939432.5825 868418.2165 1070479.656 1058643.401 1153251.387 0.894126792 0.767171249 0.790045837 0.864534159 0.8145948 0.753017275 0.928227503 0.917964125 1 20.1372756 1.624770816 5.481550967 0.947400659 0.808000557 0.651741115 0.046469703 0.084415419 5.43545559 0.024014781 0.011425487 42.14740266 -1.624770816 -0.139400102 NNRPSEGPLQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NNRPSEGPLQTR 12 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 189.99 6.58E-06 3257210000 1359777 1501544 1312944 1607167 1520391 1057361 1792450 1403262 1410464 FALSE TRUE 1274670.985 1612719.88 1344087.652 1648409.626 1400985.624 1362603.956 1523688.763 1578462.35 1175048.446 1.084781643 1.372470969 1.143857222 1.402843969 1.192279032 1.159615129 1.296702929 1.343316826 1 20.16428881 -1.688742721 8.120711881 0.999248858 1.253135854 0.357088301 0.10510245 0.001260527 4.83E-05 0.089746873 0.021095118 0.020476573 1.688742721 0.253886997 RSIQFVDWCPTGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSIQFVDWCPTGFK 14 1 P68363;P68363-2;P68366-2;P68366 P68363;P68366-2 TUBA1B;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 101.42 0.0022353 343550000 370170 374090 170580 236430 455410 156790 539060 887510 1271900 FALSE TRUE 347001.7205 401788.0128 174626.2382 242497.1941 419643.9356 202052.7277 458232.9574 998317.5772 1059611.673 0.327480085 0.379184208 0.164802109 0.228854778 0.396035591 0.190685638 0.432453671 0.942154189 1 20.01510421 1.283280143 3.084345924 1.009378997 0.282675568 0.933801955 0.075033484 0.055049146 0.877151792 0.063823516 0.018907898 19.19906781 -1.283280143 -0.726703429 NNS(ph)FTAPSTVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NNSFTAPSTVGK 12 0 A0A494C0Q6;A0A494C0K5;A0A494C0W0;O95453-2;O95453-3;O95453;O95453-4 A0A494C0Q6 PARN Poly(A)-specific ribonuclease PARN 1 NNS(0.961)FT(0.039)APSTVGK;NNS(1)FTAPSTVGK;NNS(0.998)FT(0.002)APSTVGK 169.3 4.64E-05 200731000 791210 502620 576920 589830 570080 410212 873800 551710 843450 TRUE FALSE 741689.5785 539834.5078 590604.8148 604966.0364 525308.2164 528633.5452 742781.802 620592.208 702672.7461 1.055526321 0.768258782 0.840511914 0.860949908 0.74758587 0.752318271 1.057080705 0.883188101 1 19.42249342 1.739439462 25 0.978273295 0.827319171 0.321161866 0.096941052 0.139914709 3942.502128 0.041059839 0.022769738 54.88320462 -1.739439462 -0.150954124 NNS(ph)NTCNIENELEDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NNSNTCNIENELEDSR 16 0 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 NNS(0.999)NT(0.001)CNIENELEDSR;NNS(0.997)NT(0.003)CNIENELEDSR;NNS(0.922)NT(0.078)CNIENELEDSR;NNS(1)NTCNIENELEDSR;NNS(0.949)NT(0.051)CNIENELEDSR 374.21 1.90E-104 864835000 717098 540723 576306 595787 643635 517693 790924 505610 649973 TRUE FALSE 672216.1162 580758.6935 589976.2505 611075.9031 593086.5034 667142.5651 672332.2888 568736.5215 541488.3073 1.241423143 1.072523055 1.089545688 1.128511724 1.095289585 1.232053502 1.241637686 1.050320965 1 19.04657066 2.322536126 23.99037564 1.163778086 1.113481462 0 0.087936989 51.50916526 14706.80234 0.02862822 0.023952075 210.1532575 -2.322536126 -0.050296624 NNS(ph)NTCNIENELEDSRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NNSNTCNIENELEDSRK 17 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 NNS(0.951)NT(0.049)CNIENELEDSRK 328.27 3.84E-72 1247400000 666460 385540 404430 437640 473230 354320 660830 379430 585600 TRUE FALSE 624747.4583 414085.7828 414023.2706 448870.5833 436064.4247 456606.4321 561744.6763 426802.6707 487859.5769 1.280588694 0.848780679 0.848652543 0.920081525 0.893831843 0.935938237 1.151447472 0.874847376 1 18.89610642 1.960447156 24.41583616 1.030117594 0.92574817 0 0.140857351 897.5689402 554064.4 0.054506766 0.035190916 91.29503436 -1.960447156 -0.104369424 NNSNT(ph)CNIENELEDSRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NNSNTCNIENELEDSRK 17 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 NNS(0.273)NT(0.727)CNIENELEDSRK;NNS(0.188)NT(0.812)CNIENELEDSRK 325.44 1.56E-59 2196250000 1248120 674400 818000 753190 771810 530550 1124120 658720 1021310 TRUE FALSE 1170002.397 724333.2777 837403.3463 772518.1305 711195.1559 683711.1722 955568.6418 740962.642 850846.7631 1.375103541 0.85130873 0.984199955 0.907940377 0.835867499 0.803565579 1.123079599 0.870853218 1 19.6985398 4.744585599 24.86692895 0.927721099 1.375103753 0.695117922 0.094218906 365.4522826 1508287.101 0.022071435 0.200856885 55537.40701 -4.744585599 0.447382654 NNSNTCNIENELEDSRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NNSNTCNIENELEDSRK 17 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 133.78 3.07E-05 278070000 1211000 499680 673330 629340 691930 466500 883640 543260 907070 FALSE TRUE 1135205.672 536676.8271 689301.7056 645489.9299 637588.6089 601170.977 751146.3853 611087.2069 755674.1571 1.502242284 0.710196084 0.912167896 0.854190823 0.843734833 0.795542591 0.994008301 0.808664953 1 19.52740476 4.746935009 24.94888374 0.861431546 1.502242613 0.83816969 0.088012285 383.957232 1143854.227 0.019827518 0.228742508 55838.66279 -4.746935009 0.640811067 NNSQIASGQNQPQAAAGS(ph)HQLSMGQPHNAAGPSPHTLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPSPHTLRR 39 1 Q68EM7;Q68EM7-3;Q68EM7-6;Q68EM7-5;Q68EM7-7;Q68EM7-2 Q68EM7;Q68EM7-2 ARHGAP17 Rho GTPase-activating protein 17 1 NNSQIASGQNQPQAAAGS(0.348)HQLS(0.348)MGQPHNAAGPS(0.263)PHT(0.041)LRR 151.38 6.94E-14 183120000 9898.8 12084 9071.2 9908.5 17546 8056.8 11095 9877.6 33237 TRUE FALSE 9279.251778 12978.71193 9286.373148 10162.76889 16168.00794 10382.66737 9431.407751 11110.8401 27689.52998 0.335117706 0.468722725 0.335374893 0.367025691 0.5839033 0.374967267 0.340612779 0.401265031 1 14.75705294 -1.662887889 2.437579608 1.090444483 0.39994923 0.859462185 0.076137646 2663754.439 2073314.992 1497953.825 0.01876659 0.021732621 1.662887889 -0.690495254 NNSQIASGQNQPQAAAGSHQLS(ph)MGQPHNAAGPSPHTLR ddPTM_SK-BR-3_Pertuzumab_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(0.007)HQLS(0.789)MGQPHNAAGPS(0.196)PHT(0.008)LR 121.37 3.60E-08 990930000 145080 162980 156960 145510 181630 133760 175020 161360 247120 TRUE FALSE 135999.7018 175047.2088 160683.1653 149244.0329 167365.5125 172374.3406 148777.3758 181506.1512 205874.0755 0.660596539 0.850263484 0.780492468 0.724928734 0.812950888 0.83728046 0.722662022 0.881636752 1 17.65140265 0.988598104 4.900528751 0.999791624 0.779797264 0.632991027 0.057692722 0.096596158 8.271473891 0.050848567 0.01287081 9.740877998 -0.988598104 -0.21999436 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(ph)PHTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPSPHTLR 38 0 Q68EM7;Q68EM7-3;Q68EM7-6;Q68EM7-5;Q68EM7-7;Q68EM7-2 Q68EM7;Q68EM7-2 ARHGAP17 Rho GTPase-activating protein 17 1 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(0.997)PHT(0.003)LR;NNSQIASGQNQPQAAAGS(0.083)HQLS(0.083)MGQPHNAAGPS(0.638)PHT(0.196)LR;NNSQIASGQNQPQAAAGS(0.001)HQLS(0.386)MGQPHNAAGPS(0.538)PHT(0.075)LR;NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(0.999)PHT(0.001)LR;NNSQIASGQNQPQAAAGS(0.193)HQLS(0.193)MGQPHNAAGPS(0.51)PHT(0.104)LR;NNSQIASGQNQPQAAAGSHQLS(0.01)MGQPHNAAGPS(0.876)PHT(0.114)LR;NNSQIASGQNQPQAAAGS(0.005)HQLS(0.256)MGQPHNAAGPS(0.618)PHT(0.121)LR;NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(0.999)PHT(0.001)LR;NNSQIASGQNQPQAAAGS(0.001)HQLS(0.004)MGQPHNAAGPS(0.871)PHT(0.124)LR;NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(1)PHTLR 354.36 4.12E-145 5814650000 962034 1039262 1172680 1097437 1330888 925592 1275873 1146703 1700050 TRUE FALSE 901822.0092 1116210.04 1200496.523 1125599.091 1226365.425 1192795.385 1084567.688 1289871.394 1416300.672 0.636744744 0.788116578 0.847628295 0.794745857 0.865893414 0.842190792 0.765775029 0.910732741 1 20.43369614 -5 0.027903275 2.154933158 1.70E-19 0.661849682 0.055369961 1234.483135 2.596943721 151.6762128 65.47766116 1.00E-05 5 -2.154933158 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(ph)PHTLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPSPHTLRR 39 1 Q68EM7;Q68EM7-3;Q68EM7-6;Q68EM7-5;Q68EM7-7;Q68EM7-2 Q68EM7;Q68EM7-2 ARHGAP17 Rho GTPase-activating protein 17 1 NNSQIASGQNQPQAAAGSHQLS(0.017)MGQPHNAAGPS(0.778)PHT(0.205)LRR 265.22 9.54E-64 237230000 10415 15534 14076 15429 22038 7553.2 17785 13607 45738 TRUE FALSE 9763.143741 16684.15352 14409.88937 15824.93426 20307.22438 9733.686224 15118.30436 15305.8639 38104.03232 0.256223374 0.437857951 0.378172295 0.415308651 0.532941611 0.255450293 0.396763897 0.401686199 1 15.21765606 0.493503898 3.150437275 0.999999462 0.387703785 0.850354431 0.081184351 7.636077776 46.93065956 0.070629183 0.018368582 3.115328854 -0.493503898 -0.612295677 NNTAAETEDDES(ph)DGEDRGGGTSGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NNTAAETEDDESDGEDRGGGTSGVR 25 1 A0A590UJS4;Q6KC79-2 A0A590UJS4 NIPBL Nipped-B-like protein 1 NNTAAETEDDES(1)DGEDRGGGTSGVR;NNTAAETEDDES(1)DGEDRGGGTSGVR 256.65 4.04E-45 605870000 182651 228216 239590 246662 233643 217372 234009 211433 212201 TRUE FALSE 171219.2 245113.3501 245273.1879 252991.7645 215293.6213 280123.7677 198921.5229 237830.8755 176783.2822 0.96852597 1.386518833 1.387422978 1.431084214 1.217839258 1.584560283 1.125228135 1.34532447 1 17.43162233 0.362173947 0.91789023 0.999106609 1.330863449 0.225118462 0.172440482 3.244040237 3.516410283 0.160301324 0.048823755 2.302363791 -0.362173947 0.33175684 NPDDITNEEYGEFYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 NPDDITNEEYGEFYK 15 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;; 358.26 2.35E-82 6263079000 4100584 3414680 3735484 3666760 3919487 3016265 4441131 3468222 3973939 FALSE TRUE 3843935.767 3667506.46 3824091.445 3760855.269 3611666.301 3887011.741 3775224.636 3901237.151 3310662.908 1.161077365 1.107786133 1.155083302 1.135982543 1.090919372 1.174088649 1.140322872 1.178385495 1 21.65868869 -1.505082879 4.850783134 0.999441563 1.140510766 0.728621567 0.027382195 0.000151975 1.55E-05 0.024365173 0.005720415 0.031254829 1.505082879 0.141069202 NPDDITNEEYGEFYKS(ph)LTNDWEDHLAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NPDDITNEEYGEFYKSLTNDWEDHLAVK 28 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 NPDDITNEEYGEFYKS(0.964)LT(0.036)NDWEDHLAVK 174.16 9.36E-13 19747000 23820 26338 26975 27921 30503 19216 31628 26030 42845 TRUE FALSE 22329.14872 28288.09292 27614.85974 28637.50013 28107.41742 24763.34725 26885.67502 29279.9028 35693.89271 0.625573369 0.792519134 0.773657834 0.802308125 0.787457329 0.693769869 0.753228997 0.820305676 1 15.12338963 0.855956419 2.854941072 0.99984218 0.754770302 0.6906365 0.05331136 0.328579312 5.037820505 0.04800892 0.012654314 7.177222642 -0.855956419 -0.245071879 NPDDITQEEYGEFYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 NPDDITQEEYGEFYK 15 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;; 347.46 6.86E-82 5760306000 3792747 3181516 3540634 3404910 3526589 2644264 4237945 3017629 3867071 FALSE TRUE 3555365.736 3417078.755 3624619.51 3492285.755 3249624.926 3407620.091 3602504.49 3394386.623 3221631.868 1.103591559 1.060667046 1.125088048 1.084011426 1.008689093 1.05773106 1.118223509 1.053623369 1 21.61936022 2.984779135 24.69798578 1.059482848 1.094332294 0.255571992 0.036164872 1070.752427 1737448.964 0.011009488 0.01207151 965.5597088 -2.984779135 0.034849446 NPDELAEALDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NPDELAEALDER 12 0 O14908;O14908-2;K7EM11 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ;;; 164.81 0.00013095 371842000 400970 413838 413938 405714 441584 350462 456423 379389 520912 FALSE TRUE 375874.0035 444478.9961 423756.8048 416125.3081 406903.7739 451634.6901 387986.6084 426756.5518 433968.422 0.866132153 1.024219675 0.976469216 0.958883843 0.937634522 1.040708649 0.894043411 0.983381578 1 18.72723054 3.240436123 24.41747413 0.962625547 0.973290042 0 0.055129587 305.9103532 3982547.19 0.014457649 0.018629248 1739.546822 -3.240436123 0.010664494 NPDTQWITKPVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NPDTQWITKPVHK 13 1 P61313;A0A2R8YEM3;E7EQV9;E7ENU7 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 231.26 1.63E-12 4651000000 8762500 7123800 8000400 7860700 7974400 5672900 10183100 7518100 9057800 FALSE TRUE 8214070.767 7651253.564 8190173.266 8062418.87 7348122.791 7310574.138 8656238.69 8456751.334 7545994.664 1.088533869 1.013948976 1.085366957 1.068436863 0.973777894 0.968801923 1.147130243 1.120694052 1 22.84727965 1.726917933 25 1.100869654 1.03602903 0.173637704 0.055608966 1.254820648 2682.263621 0.024649745 0.013669488 53.3234123 -1.726917933 -0.064840624 NPDVDTSFLPDRDREEEENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NPDVDTSFLPDRDREEEENR 20 2 Q14320;B0S8I6;Q9Y247 Q14320 FAM50A;FAM50B Protein FAM50A;Protein FAM50B 0 243.18 4.48E-30 408340000 327580 270910 320390 301120 334960 277560 384690 326030 315310 FALSE TRUE 307077.3525 290968.4583 327989.8021 308847.249 308653.5928 357687.0662 327009.3058 366735.5632 262682.724 1.169004752 1.107680223 1.24861581 1.175742524 1.175005299 1.361669548 1.244883184 1.396116035 1 18.0029618 3.457143802 0.858157101 1.259625448 1.13603649 0.070196474 0.110871566 1.268155494 1.923356248 0.044931556 0.103435312 2865.126501 -3.457143802 -0.123588959 NPDVDTSFLPDRDREEEENRLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NPDVDTSFLPDRDREEEENRLR 22 3 Q14320;B0S8I6;Q9Y247 Q14320 FAM50A;FAM50B Protein FAM50A;Protein FAM50B 0 ;;; 305.47 1.30E-56 1809800000 456208 577370 527676 543850 694530 342295 577850 500507 834040 FALSE TRUE 427654.7556 620119.0756 540192.7239 557806.1117 639984.4154 441110.0098 491206.757 562996.4007 694833.3359 0.615478178 0.892471681 0.777442152 0.802791235 0.92106176 0.6348429 0.70694184 0.810261068 1 19.40630745 2.243346124 24.99990168 0.752922401 0.810921236 0 0.12407812 395.4887986 2066075.936 0.039689922 0.032210852 175.1241837 -2.243346124 0.057998835 NPEAALS(ph)PTFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NPEAALSPTFR 11 0 Q86U44;F5H6D8;B4DTN4;B4E349 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 1 NPEAALS(0.973)PT(0.027)FR;NPEAALS(0.988)PT(0.012)FR;NPEAALS(0.919)PT(0.081)FR;NPEAALS(0.883)PT(0.117)FR 190.57 2.32E-06 696690000 762100 682570 719770 727100 764760 585320 846090 651150 943950 TRUE FALSE 714401.5214 733108.193 736843.2843 745758.617 704698.8345 754292.3821 719226.6592 732447.5109 786398.6468 0.908447038 0.93223481 0.936984425 0.948321338 0.89610891 0.959173042 0.914582778 0.931394673 1 19.58490131 -2.510318007 1.969437536 1.714086831 0.929417923 0.596134552 0.018502703 906790.2067 62198.41005 2887921.776 0.003921559 0.003088033 2.510318007 -0.784668908 NPEDKSPQLSLSPRPAS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NPEDKSPQLSLSPRPASPK 19 2 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 NPEDKSPQLSLS(0.011)PRPAS(0.989)PK;NPEDKSPQLS(0.039)LS(0.059)PRPAS(0.902)PK 123.32 1.64E-05 657930000 372870 255602 288200 280710 368420 196762 419110 225761 700970 TRUE FALSE 349532.7323 274527.038 295036.2401 287913.4938 339485.7793 253563.9952 356268.3463 253947.7578 583973.5786 0.598542032 0.470101813 0.505221899 0.493024863 0.581337567 0.434204568 0.610076139 0.434861725 1 19.15554357 -1.696911439 2.836846296 1.066884448 0.515526182 0.852782192 0.063208901 11628437.97 11128280.4 5600379.032 0.013294157 0.020095025 1.696911439 -0.551358266 NPEHFVVCNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NPEHFVVCNR 10 0 Q2TAY7;Q2TAY7-2 Q2TAY7 SMU1 "WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed" 0 ;; 122.69 0.00048184 841200000 656400 774730 745160 735420 748910 558840 812050 710400 712330 FALSE TRUE 615317.0957 832091.8153 762835.5471 754292.1223 690093.6296 720168.036 690290.6412 799095.0038 593437.5212 1.036869213 1.402155721 1.285452166 1.271055664 1.162874953 1.213553256 1.163206937 1.346552881 1 19.17873662 2.806718471 6.016818894 1.188262145 1.281298624 0.046231629 0.123309734 0.480765963 32.91378595 0.034646834 0.036679911 640.7940509 -2.806718471 0.093036479 NPEISHMLNNPDIMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NPEISHMLNNPDIMR 15 0 Q9UMX0;Q9UMX0-2 Q9UMX0 UBQLN1 Ubiquilin-1 0 ;;; 234.77 1.16E-17 984500000 656850 753730 662900 689060 789850 466451 753770 613230 787140 FALSE TRUE 615738.931 809536.9535 678624.301 706742.4462 727818.3671 601107.8315 640749.1862 689793.1154 655761.2489 0.938968157 1.23449953 1.034864903 1.077743535 1.10988316 0.916656531 0.977107426 1.051896733 1 19.32281113 2.254735753 24.95011177 0.981291346 1.094259779 0.237723717 0.079831502 264.213338 407547.7237 0.02612526 0.021794831 179.7776723 -2.254735753 0.112968433 NPEVGLKPVWYSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NPEVGLKPVWYSPK 14 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 185.26 1.09E-06 1032410000 1869370 1546120 1506300 1555290 1836000 989560 2076990 1575510 2315440 FALSE TRUE 1752369.469 1660596.334 1542030.147 1595201.374 1691807.966 1275229.908 1765564.631 1772215.892 1928978.106 0.908444457 0.86086842 0.799402618 0.826967071 0.877048817 0.661090919 0.915284951 0.918733026 1 20.87940534 1.534935802 9.160743042 0.945006572 0.823924528 0.422121577 0.068456919 0.111451522 14.80661371 0.034425663 0.015995993 34.27171221 -1.534935802 -0.121082044 NPFDTFFGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NPFDTFFGQR 10 0 P25685;P25685-2;M0R080;M0QZD0;M0QYT3;M0QXK0;M0R128;A0A1B0GX60;M0R1D6 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 129.28 0.00071486 811740000 235553 201829 189280 196718 231186 157683 228556 200949 272849 FALSE TRUE 220810.1582 216772.6292 193769.811 201766.1169 213029.5841 203203.5223 194286.1496 226037.925 227308.7392 0.971410774 0.95364846 0.852452095 0.887630267 0.937181671 0.893953849 0.854723625 0.994409303 1 17.79429363 1.215703304 23.72098277 0.997205039 0.903722888 0.478817757 0.038863523 132.3656881 137360.3435 0.038247755 0.009596263 16.43248725 -1.215703304 -0.09348215 NPGFEIIHGLLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NPGFEIIHGLLDR 13 0 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 ; 185.27 8.80E-06 324880000 488840 571660 523510 500130 571780 372530 535320 522020 468780 FALSE TRUE 458244.377 613986.3012 535927.9044 512964.1825 526874.7052 480073.3635 455053.7357 587195.3461 390537.5896 1.173368171 1.572156734 1.372282512 1.313482226 1.349101135 1.229262884 1.165198301 1.503556538 1 18.57510189 -4.444312111 0.134468836 1.21E-15 1.486305859 0.324252143 0.137684639 118.4561697 1.144061328 32.59479216 0.925773007 3.59E-05 4.444312111 1.486305859 NPHLITNWGPAAFTEAELEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NPHLITNWGPAAFTEAELEER 21 0 Q9UH65;E7EMB1 Q9UH65 SWAP70 Switch-associated protein 70 0 124.19 2.52E-05 48149000 153610 164390 180780 177020 171090 173340 184940 180630 134290 FALSE TRUE 143995.8243 176561.6066 185068.187 181562.6329 157653.2815 223380.4441 157209.9639 203182.0531 111876.1315 1.287100496 1.578188344 1.654224047 1.622889803 1.409177092 1.996676513 1.405214516 1.816134063 1 16.77154275 -0.55566027 5.973556219 0.999999999 1.598504715 0.453831899 0.205532907 11522581.99 1928931.423 0.37527587 0.041604186 0.278188857 0.55566027 0.598504717 NPISGLLEYAQFASQTCEFNMIEQSGPPHEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NPISGLLEYAQFASQTCEFNMIEQSGPPHEPR 32 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 313.47 4.30E-104 338560000 275780 301620 326000 318340 327820 236940 372200 289990 295630 FALSE TRUE 258519.4221 323952.2586 333732.8739 326509.1433 302074.3396 305340.7316 316392.0653 326195.8898 246287.4432 1.049665459 1.315342165 1.355054361 1.325723874 1.22651133 1.23977385 1.28464554 1.324451972 1 17.90998355 -1.540649292 6.730396895 0.999775091 1.277727918 0.473766393 0.086925861 0.000276247 1.89E-05 0.079256503 0.018666048 0.02879723 1.540649292 0.277952827 NPLPNIDHELQELLIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NPLPNIDHELQELLIDR 17 0 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 0 ;;; 260.65 2.97E-27 232818000 155783 149739 165214 141866 145431 138556 174516 136257 129941 FALSE TRUE 146032.8201 160825.8314 169132.9541 145506.5217 134009.4359 178554.8679 148348.9459 153268.9864 108253.0076 1.348995499 1.485647696 1.562385727 1.344133756 1.237928061 1.649421774 1.370390986 1.415840444 1 16.72404758 0.318156888 1.358867914 0.99976063 1.446392926 0.562596876 0.117736104 3.356557154 5.967278805 0.108767978 0.031761105 2.080448108 -0.318156888 0.446632295 NPPGFAFVEFEDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NPPGFAFVEFEDPR 14 0 P84103;P84103-2;A0A087X2D0;Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 P84103;Q16629 SRSF3;SRSF7 Serine/arginine-rich splicing factor 3;Serine/arginine-rich splicing factor 7 0 ;;;; 142.83 2.16E-05 1483236000 1069750 936361 1077500 998340 950900 863322 1180400 983060 937130 FALSE TRUE 1002796.257 1005690.143 1103058.809 1023959.095 876220.1497 1112549.047 1003409.978 1105797.205 780716.9489 1.2844556 1.288162303 1.41287929 1.311562527 1.122327562 1.425035089 1.2852417 1.416386831 1 19.57444006 -1.170097184 4.796144445 0.999966501 1.32016179 0.556993745 0.08918448 2.93E-05 5.07E-06 0.079248925 0.018677199 0.06759317 1.170097184 0.320195289 NPPGFAFVEFEDPRDAADAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NPPGFAFVEFEDPRDAADAVR 21 1 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;; 193.63 6.00E-18 1890100000 215571 365813 269990 299345 461466 164504 294941 251809 767200 FALSE TRUE 202078.7959 392898.1751 276394.2903 307026.6995 425224.3218 211993.6343 250717.3351 283247.9079 639149.3637 0.316168344 0.614720435 0.432440844 0.480367684 0.665297262 0.331680897 0.392267206 0.443163874 1 19.28579359 -1.264096112 3.268309317 1.002072438 0.466490493 0.702745977 0.110389113 26077667.26 37348958.72 544667.2693 0.02898456 0.054438217 1.264096112 -0.535581945 NPPGFAFVEFEDPRDAEDAVR ddPTM_SK-BR-3_Pertuzumab_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 3283914000 467079 535203 519503 542493 659850 359179 544228 458218 772689 FALSE TRUE 437845.3591 574829.987 531825.8565 556414.2888 608028.0427 462868.1465 462626.0638 515427.526 643722.2141 0.680177489 0.892978329 0.826172912 0.864370184 0.94455035 0.719049516 0.718673449 0.800698678 1 19.29607873 2.216778734 24.9999005 0.77653384 0.847571498 0 0.104030391 545.1095864 625639.2535 0.035306569 0.026097352 164.7322893 -2.216778734 0.071037658 NPPPNSDPNLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NPPPNSDPNLRR 12 1 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 0 67.153 0.09 49911000 17095 19067 20503 19942 18931 15782 21728 14924 26472 FALSE TRUE 16025.05447 20478.74052 20989.34084 20453.74548 17444.23562 20338.0072 18470.08811 16787.29425 22053.65218 0.726639485 0.928587263 0.951739905 0.927453889 0.790990784 0.922205856 0.837507001 0.761202458 1 14.42872997 2.785165531 24.99339503 0.856266187 0.902457948 0 0.090250108 1279.754373 686307.2961 0.025592311 0.027144688 609.7692666 -2.785165531 0.046191761 NPPS(ph)PRPSQLPVLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NPPSPRPSQLPVLDR 15 1 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 NPPS(1)PRPSQLPVLDR;NPPS(1)PRPSQLPVLDR;NPPS(1)PRPSQLPVLDR;NPPS(1)PRPSQLPVLDR;NPPS(1)PRPSQLPVLDR 132.65 2.80E-05 2253790000 1724660 1789450 1784030 1744810 1975920 1374210 1986040 1660050 1886960 TRUE FALSE 1616716.609 1921942.74 1826348.034 1789584.779 1820739.214 1770922.119 1688251.739 1867310.897 1572014.186 1.0284364 1.222598853 1.16178852 1.138402436 1.1582206 1.126530622 1.073941797 1.187846085 1 20.58418281 -1.725779201 0.286130549 0.869132954 1.158942827 0.329843244 0.056970677 26.86293023 1.326825841 2.498140894 0.0634828 0.018802725 1.725779201 0.289809873 NPQGFVLSLCHLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NPQGFVLSLCHLQK 14 0 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 0 126.48 0.00037128 0 115760 154680 123690 129290 187630 86478 147220 132410 183790 FALSE TRUE 108514.7882 166132.6681 126623.9852 132607.8003 172894.2967 111442.7947 125145.7277 148941.68 153114.2617 0.708717706 1.085024127 0.826990143 0.86607086 1.129184798 0.727840722 0.81733554 0.972748576 1 17.22424914 NPQMPQYSSPQPGSALS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NPQMPQYSSPQPGSALSPR 19 0 O14497;H0Y488;A0A1B0GTU5;O14497-3;O14497-2;A0A087WUV6 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 NPQMPQYSSPQPGS(0.034)ALS(0.965)PR;NPQMPQYSSPQPGSALS(1)PR;NPQMPQYSSPQPGS(0.018)ALS(0.982)PR 306.2 1.48E-50 697380000 187487 166534 175323 178698 169519 162357 247659 166621 178788 TRUE FALSE 175752.5233 178864.3506 179481.7444 183283.6932 156205.6615 209226.8303 210524.8321 187423.9986 148947.1278 1.179965844 1.200858004 1.205003057 1.23052855 1.048732284 1.40470537 1.413419884 1.258325699 1 17.18444078 2.225276265 24.99943654 1.318946782 1.183789751 0.065458719 0.12599062 337.4070177 634952.3747 0.042545779 0.031606048 167.9872284 -2.225276265 -0.135157031 NPQNSAQTADGSHCAVSDVEMQEHYDEFFEEVFTEMEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NPQNSAQTADGSHCAVSDVEMQEHYDEFFEEVFTEMEEK 39 0 Q01081-2 Q01081-2 U2AF1 Splicing factor U2AF 35 kDa subunit 0 ;;;; 237.13 2.36E-50 180558500 94131.9 72045.8 77973.4 81513.7 88684.3 61563.8 108067.5 75066.7 105509.4 FALSE TRUE 88240.35241 77380.146 79822.96587 83605.47954 81719.39281 79336.26966 91863.78162 84438.94274 87899.19952 1.003881183 0.880328222 0.908119372 0.951151774 0.929694391 0.902582391 1.045103734 0.960633808 1 16.42356241 1.748181665 25 1.003619637 0.922056108 0.431021266 0.03872515 1.887853308 4916.063724 0.016729669 0.009277516 55.9991796 -1.748181665 -0.081563529 NPSDSAVHS(ph)PFTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NPSDSAVHSPFTK 13 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 NPSDSAVHS(1)PFTK;NPSDSAVHS(1)PFTK;NPSDSAVHS(0.999)PFT(0.001)K;NPSDSAVHS(0.999)PFT(0.001)K;NPSDSAVHS(1)PFTK;NPSDSAVHS(1)PFTK 159.69 2.61E-05 5625420000 6789070 5167830 6762450 7080050 6842000 5135720 7000400 4986160 5476250 TRUE FALSE 6364154.228 5550461.51 6922858.507 7261736.069 6304656.919 6618318.993 5950755.009 5608693.052 4562228.497 1.394966129 1.216611907 1.517429149 1.591708104 1.381924847 1.45067679 1.304352689 1.229375744 1 22.12130727 1.015971726 1.323716916 1.003650655 1.416827931 0.660378341 0.098309764 0.302227579 1.085264453 0.097558421 0.029743218 10.37460871 -1.015971726 0.413177276 NPSDSAVHS(ph)PFTKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NPSDSAVHSPFTKR 14 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 NPSDSAVHS(0.998)PFT(0.002)KR;NPSDSAVHS(1)PFTKR;NPSDSAVHS(0.632)PFT(0.368)KR;NPSDSAVHS(0.896)PFT(0.104)KR;NPSDSAVHS(0.986)PFT(0.014)KR;NPSDSAVHS(1)PFTKR 228.3 8.04E-13 2238992000 1792483 1778976 1924394 2260944 2544130 1317665 2117812 1647162 2777640 TRUE FALSE 1680294.689 1910693.234 1970041.534 2318963.651 2344324.292 1698053.495 1800265.751 1852813.802 2314033.94 0.726132258 0.825698016 0.851345134 1.002130354 1.013089848 0.733806651 0.777977246 0.800685664 1 21.14197859 -2.666245949 2.090976967 4.925717974 0.841238842 0.206047134 0.097866293 3539963.266 160604.7883 66874352.21 0.025952481 0.002156523 2.666245949 -4.084479132 NPSTVEAFDLAQSNSEHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NPSTVEAFDLAQSNSEHSR 19 0 O15067 O15067 PFAS Phosphoribosylformylglycinamidine synthase 0 213.93 1.21E-17 411030000 164110 192660 176260 195940 193940 145170 229200 156920 211960 FALSE TRUE 153838.648 206924.7469 180440.9704 200968.1521 178708.7347 187078.2224 194833.5878 176511.8074 176582.5067 0.87119982 1.171830385 1.02185077 1.138097742 1.012040989 1.059438026 1.103357243 0.999599625 1 17.4299829 1.215565244 24.0972054 0.999799606 1.06590062 0.055601134 0.082075871 396.3313127 415304.7294 0.068322669 0.017135172 16.42726429 -1.215565244 0.066101014 NPTDAYQLNYDMHNPFDICAASYRPIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NPTDAYQLNYDMHNPFDICAASYRPIYR 28 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITI7 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 231.74 1.42E-35 991850000 353652 428993 321517 296876 413783 279439 451735 421313 229244 FALSE TRUE 331517.5526 460756.0881 329143.5351 304494.3408 381286.1523 360108.503 384001.5305 473914.8555 190981.6954 1.73586035 2.412566749 1.723429747 1.594364005 1.996453909 1.885565536 2.010671911 2.481467422 1 17.54307484 3.878599458 7.312704698 1.866928458 2.114514909 0.052286506 0.40745763 0.642315401 41.18999059 0.094393372 0.171333035 7561.352039 -3.878599458 0.247586451 NPVWYQALTHGLNEEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NPVWYQALTHGLNEEQR 17 0 O95373 O95373 IPO7 Importin-7 0 ;; 158.65 3.31E-09 991981000 1244752 1091358 1326578 1374560 1490533 1054693 1716072 1055094 1965449 FALSE TRUE 1166845.194 1172163.282 1358045.057 1409833.537 1373472.551 1359165.748 1458762.935 1186824.808 1637402.865 0.71261949 0.71586737 0.829389691 0.86101812 0.838811621 0.830074123 0.890900441 0.724821505 1 20.64297789 7.855254008 0.053432788 1.24939514 1.37E-18 0.558559534 0.059022736 302.6560121 1.246641531 6.629180994 30.69048909 71656238.77 -7.855254008 -1.24939514 NPWGEVEWTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NPWGEVEWTGR 11 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;; 217.02 2.71E-11 2937290000 617235 692020 665690 677470 705140 515315 749900 632180 783470 FALSE TRUE 578603.3631 743257.8808 681480.4812 694855.0272 649761.1488 664078.0751 637459.4567 711109.0646 652703.7956 0.886471577 1.138736876 1.04408843 1.064579418 0.995491605 1.017426403 0.976644323 1.089482043 1 19.3160689 2.742106282 24.29565277 1.011382419 1.052783601 0 0.06911126 552.5692823 3786343.569 0.019901913 0.020361942 552.2125619 -2.742106282 0.041401183 NPWSMDENLMHISYEAGILENPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NPWSMDENLMHISYEAGILENPK 23 0 P00966 P00966 ASS1 Argininosuccinate synthase 0 ; 267.57 2.78E-44 601390000 533010 764310 803910 810100 888730 595980 1043480 789580 877280 FALSE TRUE 499649.8556 820900.3077 822979.1248 830888.5375 818932.7308 768029.7511 887019.8612 888160.8011 730856.3006 0.683649926 1.123203436 1.126047794 1.136869911 1.120511283 1.050862872 1.213672045 1.215233146 1 19.47922825 4.738681142 6.563321832 1.131446878 0.675017515 0.819538952 0.064748619 0.043760827 11.79440786 0.014270242 0.088794673 54787.45694 -4.738681142 -0.456429363 NPYLLS(ph)EEEDDDVDGDVNVEKNETEPPKGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NPYLLSEEEDDDVDGDVNVEKNETEPPKGK 30 2 O60524-4;O60524-3;O60524;G3V5V3;O60524-5 O60524-4 NEMF Nuclear export mediator factor NEMF 1 NPYLLS(1)EEEDDDVDGDVNVEKNETEPPKGK 182.15 3.31E-18 129440000 161190 108220 127030 140860 178390 88722 161520 94076 309320 TRUE FALSE 151101.4056 116232.7214 130043.2116 144474.7061 164379.969 114334.6011 137301.5755 105821.5957 257692.4937 0.58636324 0.451052026 0.504644934 0.560647708 0.637891956 0.443686192 0.532811699 0.410650672 1 17.97529099 -1.113088615 4.575122567 1.000042691 0.512400955 0.829246957 0.069010019 2.79E-05 5.41E-06 0.062104632 0.014636924 0.077074619 1.113088615 -0.487641736 NPYYGGESASITPLEDLYKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NPYYGGESASITPLEDLYKR 20 1 P50395;P50395-2;Q5SX87;V9GYF8;Q5SX90;V9GYJ7 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;; 285.27 7.25E-45 1402940000 1596179 1387686 1381995 1484181 1722681 928507 1898865 1326972 2350751 FALSE TRUE 1496277.006 1490431.715 1414776.574 1522267.597 1587388.583 1196551.898 1614147.821 1492647.375 1958395.472 0.7640321 0.761047366 0.722416179 0.777303471 0.810555685 0.610985838 0.824219543 0.762178731 1 20.9012407 0.327295371 1.159970373 1.000320511 0.748329689 0.643097137 0.057747125 2.008926917 2.929782376 0.050545739 0.015080425 2.124689009 -0.327295371 -0.251990821 NQALNTDNYGHDLASVQALQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NQALNTDNYGHDLASVQALQR 21 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 337.91 2.21E-80 719210000 430470 394450 415770 409710 466360 308310 455280 373380 525930 FALSE TRUE 403527.6511 423655.4884 425632.2607 420223.8522 429733.9668 397314.092 387014.9906 419997.3149 438148.8854 0.920982946 0.966921297 0.971432942 0.959089173 0.980794386 0.906801558 0.883295618 0.958572141 1 18.74106166 2.235744088 24.99641823 0.92197484 0.962355188 0.01633547 0.035463894 103.7067964 920373.1675 0.012002946 0.009263617 172.0854246 -2.235744088 0.040380348 NQAS(ph)DS(ph)ENEELPKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NQASDSENEELPKPR 15 1 Q96ST2;Q96ST2-3 Q96ST2 IWS1 Protein IWS1 homolog 2 NQAS(1)DS(1)ENEELPKPR;NQAS(1)DS(1)ENEELPKPR 74.776 0.019231 1026510000 1797460 892070 1209570 1120110 980090 871930 1386490 936000 924360 TRUE FALSE 1684960.187 958119.791 1238261.572 1148853.919 903117.6849 1123642.036 1178598.696 1052861.66 770078.3444 2.188037359 1.244184826 1.607968307 1.491866285 1.172760787 1.459126912 1.530491936 1.367213697 1 19.5546457 7.999999992 0.04008514 6.10E-10 3.840992907 0.404808954 0.244848575 940.2434052 2.868757574 75.16695573 245.137228 99999998.15 -7.999999992 3.840992907 NQDDFECVTTLEGHENEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NQDDFECVTTLEGHENEVK 19 0 O76071 O76071 CIAO1 Probable cytosolic iron-sulfur protein assembly protein CIAO1 0 189.51 1.39E-14 66697000 29093 45302 46529 44296 42788 41606 40919 40038 36125 FALSE TRUE 27272.12106 48656.20722 47632.68985 45432.71035 39427.60308 53616.97678 34783.57582 45036.83243 30095.50412 0.906185886 1.616726771 1.582717793 1.509617854 1.310082826 1.781561012 1.155773157 1.496463799 1 14.87726036 0.321741519 0.759045748 0.99450037 1.467973808 0.193850837 0.25260949 3.448518074 2.697170404 0.281039998 0.079772158 2.09769102 -0.321741519 0.473473437 NQDECVIALHDCNGDVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NQDECVIALHDCNGDVNR 18 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;Q5VU81;Q5VU80;Q5VU79;Q5VU78;Q5VU77 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 0 ;;; 290.94 3.60E-49 2152900000 1755090 1490870 1620030 1538490 1604500 1620750 2307320 1460130 1748450 FALSE TRUE 1645242.05 1601255.566 1658457.877 1577970.258 1478489.042 2088634.214 1961358.786 1642430.445 1456622.4 1.129491109 1.099293521 1.138564035 1.083307698 1.015011881 1.433888573 1.346511482 1.127560887 1 20.47419551 2.255336169 24.9999841 1.271936186 1.099722055 0.187677555 0.123118731 270.8367797 403617.3639 0.039721492 0.033148552 180.0263883 -2.255336169 -0.172214131 NQEDNTGKYPDIISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NQEDNTGKYPDIISR 15 1 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28 P18858 LIG1 DNA ligase 1;DNA ligase 0 189.81 1.09E-11 0 269800 204440 229300 222580 212170 155980 283230 186810 293340 FALSE TRUE 252913.6996 219576.9503 234739.1043 228291.7796 195507.0241 201008.8939 240762.2909 210133.6397 244379.659 1.03492124 0.898507475 0.960550912 0.934168501 0.800013491 0.822527107 0.985197753 0.859865509 1 17.89876468 4.741438855 24.12383997 0.908591968 1.034921311 0.26841673 0.066038858 232.7104067 1950277.587 0.015172818 0.10564897 55136.4569 -4.741438855 0.126329343 NQEIPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 65.252 0.071089 299920000 540040 546960 615370 616000 580130 464630 639010 521640 628080 FALSE TRUE 506239.8604 587457.4875 629966.867 631807.6029 534568.9299 598761.1384 543196.3828 586767.9023 523249.3904 0.967492499 1.122710314 1.203951459 1.207469353 1.021633163 1.144313112 1.038121387 1.121392424 1 18.9971392 2.728038296 24.93038537 1.071564081 1.138047568 0.116265208 0.078170177 1351.608637 3202338.333 0.024300528 0.023158266 534.6114991 -2.728038296 0.066483487 NQESLGS(ph)PHICDLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NQESLGSPHICDLGK 15 0 A4D1E1;A0A087WUA7 A4D1E1 ZNF804B Zinc finger protein 804B 1 NQESLGS(1)PHICDLGK;NQES(0.002)LGS(0.998)PHICDLGK;NQES(0.007)LGS(0.993)PHICDLGK;NQES(0.004)LGS(0.996)PHICDLGK 99.283 0.0032727 187006000 1519850 899630 1037410 1063650 1044440 660540 1367020 802080 933740 TRUE FALSE 1424725.302 966239.5413 1062017.855 1090945.06 962413.8955 851227.175 1162048.042 902221.4536 777892.7618 1.831518908 1.24212435 1.365249694 1.402436317 1.23720639 1.094273166 1.493840924 1.159827547 1 19.56921176 4.741089888 24.81550471 1.28178022 1.831519124 0.594808559 0.148879391 144.1186519 1413904.033 0.03181405 0.216984522 55092.17121 -4.741089888 0.549738904 NQGGYDRYS(ph)GGNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NQGGYDRYSGGNYR 14 1 P98179 P98179 RBM3 RNA-binding protein 3 1 NQGGYDRYS(1)GGNYR;NQGGYDRYS(1)GGNYR 150.91 4.29E-06 440480000 193082 175680 195046 198824 163847 174311 217991 138366 174394 TRUE FALSE 180997.3423 188687.53 199672.5832 203926.1604 150979.1175 224631.756 185305.2733 155641.2997 145286.5148 1.245795885 1.298727072 1.374336658 1.403613823 1.039181907 1.546129428 1.275447164 1.07127148 1 17.14854128 1.215545806 3.871276407 1.012491113 1.322410953 0.452793603 0.127810897 0.174826054 5.067978385 0.102794685 0.028692112 16.42652906 -1.215545806 0.30991984 NQGGYGGSSSS(ph)SSYGSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.005)S(0.89)S(0.1)S(0.005)YGSGR;NQGGYGGSSS(0.009)S(0.901)S(0.089)SYGSGR;NQGGYGGSSS(0.007)S(0.73)S(0.239)S(0.024)YGSGR 300.33 1.67E-49 643484000 642890 763470 543830 607910 888500 360340 990560 695220 1202500 TRUE FALSE 602652.6625 819998.1132 556729.9044 623509.9998 818720.794 464364.3084 842034.7239 782019.7474 1001794.982 0.60157285 0.818528869 0.555732375 0.622392816 0.817253838 0.463532276 0.840525995 0.780618551 1 19.93415586 1.04020901 1.306433805 0.992008462 0.664352272 0.457751626 0.118237058 0.384466318 1.345715451 0.100589998 0.030842624 10.97006018 -1.04020901 -0.32765619 NQGGYGGSSSSSS(ph)YGSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NQGGYGGSSSSSSYGSGR 18 0 F8W6I7;P09651-2;P09651;P09651-3;A0A2R8Y4L2;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 NQGGYGGSSSSS(0.041)S(0.958)YGSGR 197.38 1.84E-18 0 141910 128450 131760 119740 146060 103440 161720 116660 175530 TRUE FALSE 133028.1064 137960.5717 134885.4094 122812.7311 134589.0368 133301.4488 137471.5873 131225.2578 146232.909 0.909700199 0.943430399 0.922401191 0.839843315 0.920374474 0.911569425 0.940086525 0.897371588 1 17.15790849 -1.083734413 5.193378283 1.000001487 0.91471151 0.481637282 0.028868999 4.92E-07 8.68E-08 0.02767784 0.006523616 0.082464226 1.083734413 -0.085289977 NQGGYGGSSSSSSYGSGR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 491.18 7.79E-240 1046490000 118495 105134 96731 107589 101601 70070 124757 85791 105556 FALSE TRUE 111078.6095 112918.2308 99025.505 110349.9159 93621.6673 90298.07151 106050.846 96502.1952 87938.02168 1.263146559 1.28406608 1.126082929 1.254860114 1.064632403 1.02683765 1.205972616 1.097388744 1 16.42419946 8 0.140023406 0.990918338 2.030189442 0.568866859 0.066789123 56.84929714 0.530165836 0.275698652 11.83787847 100000000 -8 1.039271104 NQIGDKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NQIGDKEK 8 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 127.4 0.0010744 2375080000 6591500 3678150 4068930 4193240 4295040 2381560 5230910 3380230 4640890 FALSE TRUE 6178949.781 3950484.053 4165446.941 4300845.638 3957724.884 3069077.711 4446583.607 3802259.156 3866295.478 1.598157672 1.021774998 1.077374185 1.112394452 1.023647806 0.793803197 1.150088924 0.983437292 1 21.88252047 4.738963929 24.9999582 1.028388358 1.598157844 0.782835198 0.095562992 14.59231077 904226.2051 0.021404656 0.12589991 54823.14286 -4.738963929 0.569769486 NQIHVKSPPREGS(ph)QGELTPANSQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NQIHVKSPPREGSQGELTPANSQSR 25 2 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4 Q13098-7 GPS1 COP9 signalosome complex subunit 1 1 NQIHVKS(0.382)PPREGS(0.617)QGELT(0.001)PANSQSR 72.152 0.018894 88635000 17561 22568 21375 27142 40847 9737 26478 22701 73604 TRUE FALSE 16461.88836 24238.9582 21882.02509 27838.50967 37639.04139 12547.91383 22507.86971 25535.26982 61319.0169 0.268463018 0.395292675 0.356855446 0.453994716 0.613823301 0.204633317 0.367061816 0.416433125 1 15.90404695 0.727404526 4.419613147 0.999998637 0.380504747 0.764108659 0.107646552 3.369121959 54.29170686 0.097922656 0.024879539 5.33831905 -0.727404526 -0.619493891 NQKDPGVLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NQKDPGVLDR 10 1 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;;;; 157.38 8.46E-06 23332000000 16298200 17374100 16211000 17962500 21124600 11092500 22281300 15178500 34291400 FALSE TRUE 15278124.76 18660496.44 16595532.58 18423448.16 19465559.13 14294724.68 18940425.91 17073569.14 28567943.81 0.534799594 0.653197044 0.580914492 0.644899342 0.681377675 0.500376393 0.66299577 0.597647813 1 24.76789387 NQKPEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NQKPEVR 7 1 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 0 ;;;; 121.62 0.0040315 3117640000 8456650 6768730 7362060 7347290 7359950 5519410 8750330 5903510 8307420 FALSE TRUE 7927363.372 7269893.812 7536691.54 7535833.9 6781929.216 7112774.067 7438299.251 6640576.219 6920857.934 1.145430732 1.050432458 1.088982264 1.088858343 0.979926084 1.027730107 1.074765487 0.959501883 1 22.72251946 2.760721589 24.41353399 1.019682198 1.085519762 0.528744742 0.038775887 576.2179231 634786.1691 0.011475685 0.012163077 576.3968375 -2.760721589 0.065837564 NQKPSQVNGAPGS(ph)PTEPAGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NQKPSQVNGAPGSPTEPAGQK 21 1 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 NQKPSQVNGAPGS(0.987)PT(0.013)EPAGQK;NQKPSQVNGAPGS(0.968)PT(0.032)EPAGQK;NQKPSQVNGAPGS(0.845)PT(0.155)EPAGQK;NQKPSQVNGAPGS(0.983)PT(0.017)EPAGQK 193.26 4.78E-18 5710700000 6044590 3282823 4431670 4233600 4029470 2778346 6334270 3689060 5103750 TRUE FALSE 5666269.902 3525886.631 4536791.305 4342241.343 3713011.68 3580409.388 5384505.018 4149647.262 4251901.154 1.332643845 0.829249435 1.067003004 1.021247011 0.873259172 0.842072583 1.266375869 0.975951019 1 22.01967663 NQKPSQVNGAPGSPT(ph)EPAGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NQKPSQVNGAPGSPTEPAGQK 21 1 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 NQKPSQVNGAPGS(0.471)PT(0.529)EPAGQK 218.19 8.93E-25 1712000000 2445700 1305900 1741300 1653100 1600800 1191800 2621400 1502200 2027700 TRUE FALSE 2292628.003 1402590.195 1782604.458 1695521.345 1475079.625 1535853.313 2228345.406 1689752.977 1689263.771 1.357175855 0.830296736 1.055255248 1.00370432 0.873208584 0.909185019 1.319122238 1.000289597 1 20.68796319 1.767091594 25 1.139142854 0.985386271 0.055882579 0.16895809 37.30996089 32711.51934 0.070709856 0.039217158 58.4913431 -1.767091594 -0.153756583 NQLRGELDTMSKKT(ph)T(ph)ALDQLS(ph)EK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NQLRGELDTMSKKTTALDQLSEK 23 3 P49454 P49454 CENPF Centromere protein F 3 NQLRGELDT(0.05)MS(0.053)KKT(0.949)T(0.949)ALDQLS(0.999)EK 51.296 0.08193 3759800000 6414200 1362400 3029400 2627300 2184300 2409900 4401600 1979600 2062500 TRUE FALSE 6012746.672 1463273.514 3101258.799 2694720.966 2012753.889 3105599.009 3741620.942 2226757.418 1718255.426 3.499332277 0.851604186 1.804888116 1.568288932 1.171393879 1.807414056 2.177569694 1.295940862 1 20.71251308 4.751078098 24.96052271 1.530702949 3.499333528 0.709360135 0.408062253 1181.055739 2355044.928 0.098954147 1.75234152 56373.90221 -4.751078098 1.968630579 NQLS(ph)QNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NQLSQNR 7 0 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 1 NQLS(1)QNR;NQLS(1)QNR 68.915 0.039393 1570220000 69916.3 84651 76120.3 69548 76619 71900 78830 73164 84393.6 TRUE FALSE 65540.36359 90918.64812 77925.90946 71332.71942 70601.65281 92656.3628 67010.17332 82298.68645 70307.76296 0.932192418 1.293152339 1.108354272 1.014578141 1.004180048 1.317868169 0.953097788 1.170549069 1 16.10139637 -4.480331342 0.150484116 0.656704777 1.147775482 0.020038338 0.133951944 330.7937104 3.413388909 34.35831173 0.638620772 3.31E-05 4.480331342 0.491070704 NQLTSNPENTVFDAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NQLTSNPENTVFDAKR 16 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 218.12 2.19E-14 252960000 150683 175545 153492 172032 208713 95696 222178 132023 284660 FALSE TRUE 141252.02 188542.5345 157132.9027 176446.6324 192321.5229 123321.8817 188864.4715 148506.3622 237148.407 0.595627109 0.795040274 0.662593119 0.744034651 0.810975394 0.520019861 0.796397808 0.626216992 1 17.85543065 -1.774803119 2.47701109 1.081848576 0.704212502 0.4975393 0.09618566 7445158.295 5170919.815 3695836.617 0.021701601 0.016795653 1.774803119 -0.377636075 NQMPS(ph)PTSTGTPSPGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NQMPSPTSTGTPSPGPR 17 0 Q9Y572;H0YJN5 Q9Y572 RIPK3 Receptor-interacting serine/threonine-protein kinase 3 1 NQMPS(0.961)PT(0.019)S(0.019)T(0.001)GTPSPGPR;NQMPS(0.429)PT(0.251)S(0.251)T(0.068)GT(0.001)PSPGPR 159.4 3.38E-09 179316000 147561 155941 164009 188007 170289 93890 140490 107930 115082 TRUE FALSE 138325.4204 167487.0339 167899.3709 192831.5779 156915.1889 120994.5188 119424.8287 121405.2981 95874.07074 1.442782385 1.746948185 1.751249004 2.01130062 1.636680154 1.262015036 1.245642621 1.266299607 1 16.54885307 2.269251117 3.627033202 1.210308105 1.748525423 0.744143501 0.153734158 0.111304534 3.091299239 0.055678877 0.043085855 185.8878984 -2.269251117 0.538217318 NQPTVYIAAS(ph)PPNTDELMSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NQPTVYIAASPPNTDELMSR 20 0 A0A1B0GV57;Q9NYJ8;Q9NYJ8-2 A0A1B0GV57 TAB2 TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 1 NQPTVYIAAS(1)PPNTDELMSR 207.56 6.86E-22 104870000 105360 95653 88075 113100 137930 84591 133480 92124 124630 TRUE FALSE 98765.70567 102735.2476 90164.18059 116002.3375 127097.5342 109011.0485 113465.9132 103625.8842 103828.4479 0.951239354 0.989471092 0.868395728 1.11725004 1.224110894 1.049915035 1.092821048 0.998049054 1 16.66384225 3.22862525 25 1.089885211 0.938037372 0.47869399 0.070359821 155.3522802 390906.7409 0.019721366 0.023838203 1692.876397 -3.22862525 -0.151847839 NQQFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NQQFHK 6 0 Q15233;Q15233-2;H7C367 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;; 122.17 0.019338 2502230000 5144320 4253760 4551950 4368630 5080460 3138660 5500750 4248530 5744300 FALSE TRUE 4822346.194 4568712.816 4659924.404 4480736.442 4681461.165 4044740.19 4675963.604 4778968.323 4785539.22 1.007691291 0.954691333 0.973751168 0.936307537 0.978251551 0.84520051 0.977102765 0.998626926 1 22.19025006 1.483862484 25 0.995499563 0.949935898 0.197899129 0.042048268 0.955159446 3529.390388 0.021439143 0.009925149 30.46930048 -1.483862484 -0.045563664 NQS(ph)PTEAEKPASSSLPSSPPPQLLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NQSPTEAEKPASSSLPSSPPPQLLTR 26 1 Q99567;I3L2W3 Q99567 NUP88 Nuclear pore complex protein Nup88 1 NQS(0.936)PT(0.064)EAEKPASSSLPSSPPPQLLTR;NQS(0.969)PT(0.031)EAEKPASSSLPSSPPPQLLTR 231.94 1.38E-35 909210000 718440 475060 550400 527210 544040 344278 664460 442740 706810 TRUE FALSE 673474.1229 510233.9367 563455.7479 540739.1012 501313.293 443665.4697 564830.3915 498017.0636 588838.8448 1.143732498 0.866508623 0.956892965 0.918314248 0.851359073 0.753458223 0.959227464 0.845761226 1 19.16751332 4.742234789 24.89030771 0.892829142 1.1437326 0.553683634 0.07047472 249.9348052 1693083.554 0.015636843 0.115982997 55237.59854 -4.742234789 0.250903457 NQSFCPTVNLDKLWTLVSEQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NQSFCPTVNLDKLWTLVSEQTR 22 1 P46776;E9PLL6;E9PJD9 P46776 RPL27A 60S ribosomal protein L27a 0 ; 350.85 4.53E-96 1383200000 794550 847780 789560 837570 985340 551140 1120510 700330 1534320 FALSE TRUE 744820.5338 910550.5133 808288.7361 859063.4642 907955.3711 710245.171 952499.9278 787767.7421 1278232.08 0.582695854 0.71235148 0.632348968 0.672071588 0.71032122 0.555646492 0.745169788 0.616294767 1 20.28571837 -1.751877991 2.522483152 1.080230385 0.66093302 0.766931818 0.059924847 9124950.989 6570762.57 4553829.69 0.012626442 0.017706063 1.751877991 -0.419297366 NQSPTEAEKPASSSLPS(ph)SPPPQLLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NQSPTEAEKPASSSLPSSPPPQLLTR 26 1 Q99567;I3L2W3 Q99567 NUP88 Nuclear pore complex protein Nup88 1 NQSPTEAEKPASSS(0.012)LPS(0.59)S(0.397)PPPQLLTR;NQSPTEAEKPASSSLPS(0.969)S(0.03)PPPQLLTR 155.32 2.95E-08 456660000 683680 493160 580870 599320 574160 381360 701900 456180 619220 TRUE FALSE 640889.6892 529674.0795 594648.5107 614699.5658 529067.7897 491452.4411 596656.6111 513135.0772 515868.1817 1.242351655 1.026762453 1.152714069 1.191582632 1.025587172 0.952670582 1.156606731 0.994701932 1 18.97664294 2.719682717 24.77815331 1.039401213 1.13214789 0.390029863 0.076162885 1004.852244 1318915.812 0.024075058 0.022732023 524.4241914 -2.719682717 0.092746677 NQTAEKEEFEHQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NQTAEKEEFEHQQK 14 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;; 219.52 2.99E-12 21536220000 30347870 11958640 17664310 15911010 13542030 12182820 25780610 14423840 19683920 FALSE TRUE 28448450.99 12844070.15 18083315.77 16319313.45 12478493.59 15699802.36 21915046.87 16224688.17 16398546.59 1.73481539 0.783244422 1.102738933 0.995168283 0.760951193 0.957389868 1.336401781 0.989397938 1 23.96706462 -2.983313946 9.541942527 1.006516285 1.057144269 0 0.283568577 0 0 0 0.05745856 0.001039169 2.983313946 0.050627984 NQTYSFS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NQTYSFSPSK 10 0 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 NQTYS(0.003)FS(0.993)PS(0.004)K;NQTYS(0.029)FS(0.971)PSK 120.84 0.00055692 480640000 489548 436198 341552 370254 510137 203875 438767 507672 620830 TRUE FALSE 458908.0645 468494.5538 349653.7747 379755.3445 470072.8978 262730.4029 372977.9617 571055.9667 517209.4623 0.887277009 0.905812032 0.676039014 0.734238973 0.908863685 0.507976791 0.721135224 1.104109666 1 18.98038914 1.240355855 24.99834386 1.052054921 0.758010983 0.484787142 0.123779504 38.23695355 532507.8201 0.092808639 0.029932735 17.39225344 -1.240355855 -0.294043938 NQVAMNPTNTVFDAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NQVAMNPTNTVFDAKR 16 1 P11142;E9PKE3;E9PNE6;P11142-2;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 209.89 1.78E-11 456870000 369630 342960 339670 380150 425460 261510 481780 293450 767430 FALSE TRUE 346495.5181 368353.1152 347727.1328 389905.2926 392046.0878 337003.6917 409541.5616 330087.8785 639340.9752 0.541957315 0.576145014 0.543883696 0.609855003 0.613203444 0.527111048 0.6405683 0.516293952 1 19.28622603 -1.817242933 2.602036999 1.142344607 0.574507921 0.917226171 0.040477883 5581675.883 3782657.817 4986662.645 0.008834603 0.015232005 1.817242933 -0.567836686 NQVEEDAEDS(ph)GEADDEEKPEIHKPGQNSFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NQVEEDAEDSGEADDEEKPEIHKPGQNSFSK 31 2 O75717;O75717-2 O75717 WDHD1 WD repeat and HMG-box DNA-binding protein 1 1 NQVEEDAEDS(1)GEADDEEKPEIHKPGQNSFSK;NQVEEDAEDS(1)GEADDEEKPEIHKPGQNSFSK;NQVEEDAEDS(1)GEADDEEKPEIHKPGQNSFSK;NQVEEDAEDS(1)GEADDEEKPEIHKPGQNSFSK 363.05 5.18E-122 1785250000 2895470 1095240 1709790 1674100 1689750 1199560 2617870 1416240 2104050 TRUE FALSE 2714247.701 1176332.709 1750347.026 1717060.24 1557043.851 1545853.499 2225344.697 1593060.682 1752870.462 1.548458805 0.671089356 0.998560398 0.979570526 0.888282326 0.88189831 1.269543155 0.908829669 1 20.74128795 NQVGDENWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NQVGDENWR 9 0 Q92973-2;Q92973;Q92973-3;S4R398 Q92973-2 TNPO1 Transportin-1 0 ; 211.45 1.20E-05 742650000 875770 936470 886360 927480 912940 682030 1063900 799430 917270 FALSE TRUE 820957.119 1005807.213 907384.8778 951280.707 841241.375 878920.9892 904378.0718 899240.5953 764171.7112 1.074309749 1.316205767 1.187409668 1.244852031 1.100853856 1.150161641 1.183474942 1.176752008 1 19.54353733 -5 0.176042761 0.217618508 1.233915931 0.386584749 0.068932717 119.9468061 1.146988791 32.64572861 0.212433678 1.00E-05 5 1.016297423 NQVIIPLVLS(ph)PDRDEDLMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NQVIIPLVLSPDRDEDLMR 19 1 Q96G25-2;Q96G25 Q96G25-2 MED8 Mediator of RNA polymerase II transcription subunit 8 1 NQVIIPLVLS(1)PDRDEDLMR;NQVIIPLVLS(1)PDRDEDLMR;NQVIIPLVLS(1)PDRDEDLMR 161.16 1.82E-11 107443000 84200 74912 73610 78541 81144 64132 90746 66600 88144 TRUE FALSE 78930.0723 80458.56243 75356.06396 80556.49503 74771.27756 82645.8673 77139.47974 74915.1566 73432.19697 1.074870092 1.095685077 1.02619923 1.097018724 1.018235606 1.125471806 1.050485794 1.020194951 1 16.16412514 1.234904771 3.126896939 1.003718142 1.070061009 0.390733069 0.032078387 0.236254534 4.011554381 0.025861432 0.007361242 17.1753174 -1.234904771 0.066342867 NQYDNDVTVWSPQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NQYDNDVTVWSPQGR 15 0 P25786;P25786-2;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ;;; 310.51 8.89E-56 1209860000 598582 587492 555521 578541 627604 436514 669460 533494 644240 FALSE TRUE 561117.8211 630990.519 568698.2205 593387.3415 578314.5135 562528.5056 569080.688 600101.9003 536712.1821 1.04547249 1.175659022 1.059596259 1.105596931 1.077513298 1.048100871 1.060308871 1.118107471 1 19.03378911 -4.999999699 0.099311938 0.716330151 1.150759164 0.28331405 0.040482685 202.7611959 1.373147457 11.94364955 0.645032602 1.00E-05 4.999999699 0.434429013 NRDEAIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NRDEAIK 7 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 120.46 0.0041522 1822280000 2492900 3822100 3529600 3786600 3810000 2858700 3386600 3430200 3316200 FALSE TRUE 2336873.839 4105092.261 3613323.779 3883770.567 3510777.969 3683960.283 2878810.77 3858468.021 2762704.797 0.845864474 1.485896092 1.307893548 1.405785581 1.270775645 1.333461428 1.042026196 1.396626967 1 21.39764998 1.760953211 24.99999994 1.154575023 1.30796015 0.069759911 0.197750198 24.07968678 26904.718 0.082575926 0.045794546 57.67043285 -1.760953211 0.153385127 NRDSDKTDTDWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NRDSDKTDTDWR 12 2 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 96.059 0.0032045 643840000 966170 978120 898300 961620 1408060 643030 1463170 818950 2827860 FALSE TRUE 905699.1444 1050541.023 919608.1002 986296.7972 1297476.647 828662.3223 1243781.242 921197.7102 2355871.897 0.384443291 0.44592451 0.390347243 0.418654681 0.550741595 0.351743371 0.527949437 0.391021987 1 21.16782966 -5 0.372564221 8.571617772 0.421471977 0.886260023 0.063787592 151.8729592 1.163127471 926.5571908 0.038443354 1.00E-05 5 -8.150145795 NRDVITLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NRDVITLR 8 1 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 155.84 0.00036705 113280000 50328 66589 57360 58233 70037 44472 68070 57572 82509 FALSE TRUE 47178.06032 71519.31885 58720.60629 59727.35737 64536.57654 57310.34446 57863.53543 64759.99093 68737.71487 0.686348978 1.040466925 0.854270562 0.868916831 0.938881612 0.833753996 0.841801848 0.942131857 1 16.06881427 -2.087991986 3.570566848 1.236678292 0.885190676 0.146899615 0.091604805 0.101391808 0.00249867 0.052106464 0.018972947 0.008165974 2.087991986 -0.351487616 NREEEWDPEYT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NREEEWDPEYTPK 13 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 NREEEWDPEY(0.003)T(0.997)PK;NREEEWDPEY(0.002)T(0.998)PK;NREEEWDPEYT(1)PK 111.77 0.0015415 1682340000 2951850 1656110 2116430 1999940 2222220 1412730 2580710 1704020 2861300 TRUE FALSE 2767098.978 1778730.108 2166632.719 2051261.846 2047695.805 1820562.217 2193756.494 1916770.648 2383730.545 1.160827084 0.746195962 0.908925182 0.860525889 0.859029897 0.763744971 0.92030389 0.804105419 1 21.18478973 -1.611081849 2.795486534 1.010891714 0.866729758 0.092289615 0.115613208 27399338.97 28366789.14 2198879.021 0.023857274 0.024486017 1.611081849 -0.144161956 NREEEWDPEYTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NREEEWDPEYTPK 13 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;; 101.36 0.0018056 991210000 3674180 3408100 3694460 3708540 4026360 3327710 4461580 3495280 4527780 FALSE TRUE 3444219.632 3660439.27 3782094.336 3803707.415 3710145.927 4288365.856 3792607.498 3931673.402 3772064.267 0.913086148 0.970407451 1.00265904 1.008388815 0.983585025 1.136875077 1.005446151 1.042313472 1 21.84692283 5.082362123 0.514543656 1.039900259 0.788927369 0.457215928 0.041744087 5.136722404 0.803522512 0.021851043 0.836800955 120882.1354 -5.082362123 -0.250972889 NREELDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NREELDK 7 1 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 151.04 0.0017405 16468660000 16467550 8210280 11119630 10087050 9120780 10049440 14015630 9557000 9285370 FALSE TRUE 15436875.44 8818177.674 11383392.87 10345900.78 8404470.73 12950550.19 11914116.4 10750212.49 7735581.761 1.995567485 1.139950161 1.471562608 1.337443143 1.086469123 1.674153359 1.540170703 1.389709633 1 22.88307836 -2.038464372 2.074817311 0.481745869 1.431255207 0.228497059 0.259314891 4431837.185 1388416.46 10909248.9 0.061032224 0.009152413 2.038464372 0.949509338 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 18 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR 38 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;;;;;; 314.65 3.46E-110 6802014000 1663151 1229017 1414742 1305485.1 1390908 1148274 1735546 1277368 1709792 FALSE TRUE 1559057.348 1320014.697 1448300.348 1338986.058 1281671.696 1479762.063 1475316.989 1436850.207 1424416.67 1.09452338 0.926705455 1.01676734 0.940024142 0.899787066 1.038854778 1.035734151 1.008728862 1 20.44193979 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR 39 3 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;; 200.03 5.80E-31 2876266000 829476 801766 800656 837678 973864 606715 985250 748435 1568102 FALSE TRUE 777560.5778 861129.5889 819647.9384 859174.2357 897380.6498 781863.7713 837520.9091 841878.7573 1306375.646 0.595204435 0.659174558 0.627421325 0.657677781 0.686923897 0.598498429 0.641102666 0.644438497 1 20.31713837 0.462868769 3.424562646 0.999999962 0.639555081 0.944932238 0.027404939 8.794958977 55.66849728 0.024016431 0.006201073 2.903145276 -0.462868769 -0.36044488 NREELGFRPEYSASQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NREELGFRPEYSASQLK 17 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;; 186.98 2.77E-10 3090320000 1051400 883840 847560 895040 1054090 557611 1023440 862380 1164160 FALSE TRUE 985594.7508 949280.4332 867664.5234 918008.2417 971306.0234 718584.2436 869984.6732 970050.0413 969854.1752 1.016229837 0.978786768 0.894634003 0.946542547 1.001496976 0.740919885 0.89702627 1.000201954 1 19.88740832 NRENS(ph)PSSQSAGLSSINK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NRENSPSSQSAGLSSINK 18 1 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2 H3BSS6 ZNF106 Zinc finger protein 106 1 NRENS(0.993)PS(0.006)S(0.001)QSAGLSSINK;NRENS(0.999)PS(0.001)SQSAGLSSINK;NRENS(0.909)PS(0.089)S(0.001)QSAGLSSINK;NRENS(0.993)PS(0.006)S(0.001)QSAGLSSINK;NRENS(0.996)PS(0.004)SQSAGLSSINK 312.01 9.16E-61 1825952000 2424400 1698920 1994610 1973800 2080310 1515490 2462430 1783400 2354710 TRUE FALSE 2272661.132 1824709.805 2041923.091 2024451.05 1916930.844 1952987.361 2093211.482 2006061.416 1961693.689 1.158519877 0.930170604 1.040898027 1.031991417 0.977181532 0.995561831 1.067042981 1.022617051 1 20.90366836 1.760174323 25 1.036731194 1.01251337 0 0.060815023 43.77594227 50676.24296 0.025681583 0.01424253 57.56709618 -1.760174323 -0.024217824 NREPVQLETLSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NREPVQLETLSIR 13 1 P62314;J3QLI9 P62314 SNRPD1 Small nuclear ribonucleoprotein Sm D1 0 ;; 205.37 6.42E-08 3207230000 1350930 1739620 1161860 1237050 1812510 1019940 1494370 1548290 1647880 FALSE TRUE 1266377.703 1868423.275 1189419.868 1268794.797 1670162.776 1314380.121 1270303.092 1741597.415 1372838.182 0.922452274 1.360993086 0.866394804 0.924212929 1.216576577 0.957418097 0.925311597 1.268610851 1 20.38873015 3.965458932 24.89495824 1.012352097 1.165627891 0.076215181 0.164821971 641.128941 1368588.573 0.038610758 0.070340035 9235.468517 -3.965458932 0.153275794 NRES(ph)FQIFLDELHEHGQLHSMSSWMELYPTISSDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NRESFQIFLDELHEHGQLHSMSSWMELYPTISSDIR 36 1 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 NRES(0.25)FQIFLDELHEHGQLHS(0.25)MS(0.25)S(0.25)WMELYPTISSDIR 48.388 0.037793 67411000 25844 36132 24190 23214 37968 21610 35643 30298 21678 TRUE FALSE 24226.47017 38807.25088 24763.79822 23809.71054 34986.14644 27848.45619 30298.66304 34080.77199 18059.80175 1.341458256 2.148819317 1.371210967 1.318381612 1.937238676 1.542013394 1.677685251 1.88710665 1 14.14049444 -1.048615499 4.982529845 0.99998788 1.666519076 0.355574449 0.275733156 3.44E-05 6.57E-06 0.247627066 0.058365198 0.089409672 1.048615499 0.666531196 NRHS(ph)LEISSALNMFNIAPHGPDISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NRHSLEISSALNMFNIAPHGPDISK 25 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 NRHS(1)LEISSALNMFNIAPHGPDISK 264.56 1.70E-45 258680000 137500 115070 115050 131030 148570 73051 157900 101640 137900 TRUE FALSE 128894.1204 123589.9025 117779.0403 134392.4516 136901.9115 94139.63782 134224.3609 114329.9777 114883.5991 1.12195406 1.075783693 1.02520326 1.169814078 1.191657578 0.819434963 1.168350939 0.995181023 1 16.80981333 NRHS(ph)PDHPGMGSSQASSSSSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NRHSPDHPGMGSSQASSSSSLR 22 1 J3KR33;A0JLT2 J3KR33 MED19 Mediator of RNA polymerase II transcription subunit 19 1 NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR;NRHS(1)PDHPGMGSSQASSSSSLR 280.7 7.22E-46 3667940000 481549 630954 608238 609054 594774 441533 659440 514183 559228 TRUE FALSE 451409.7077 677670.4907 622665.6926 624683.3568 548062.8492 568996.4094 560563.0939 578379.8794 465889.234 0.968920668 1.454574266 1.336510155 1.340840936 1.176380155 1.221312638 1.203211092 1.241453627 1 18.82962747 2.734411778 24.32178175 1.187059395 1.315321743 0.087024074 0.1414148 428.8163721 2513845.942 0.041649361 0.04056678 542.5150343 -2.734411778 0.128262347 NRLEEVSPNLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NRLEEVSPNLVR 12 1 P28331-4;P28331;P28331-2;B4DJ81;P28331-3;P28331-5 P28331-4 NDUFS1 "NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial" 0 86.405 0.01015 257310000 227890 191330 202450 180720 242510 155880 221220 183090 381410 FALSE TRUE 213626.7717 205496.2723 207252.2096 185357.5812 223464.2428 200880.0255 188050.1147 205949.1895 317750.207 0.672310409 0.646722702 0.652248858 0.583343699 0.703270172 0.63219479 0.591817442 0.648148089 1 18.27753354 -1.695197104 2.438618621 1.065205684 0.638931459 0.912745303 0.034851651 2022194.386 1519962.59 809943.4225 0.008299376 0.020174505 1.695197104 -0.426274226 NRLENDGATALAEAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NRLENDGATALAEAFR 16 1 P46060 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ;; 235.4 9.66E-20 680231000 414428 483334 439338 435799 518644 306315 436268 405861 621078 FALSE TRUE 388489.6913 519120.5523 449759.3048 446982.3401 477911.7923 394743.1679 370853.6635 456533.6393 517416.0695 0.75082649 1.003294221 0.869241083 0.863874098 0.92365085 0.762912463 0.716741681 0.882333708 1 18.98096534 2.243807935 24.99656905 0.804233854 0.896097288 0 0.099386953 221.1806827 1053638.774 0.032524808 0.026461781 175.3105029 -2.243807935 0.091863433 NRNEQESAVHPR ddPTM_SK-BR-3_Pertuzumab_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 3.99E-05 3064120000 1607582 1991252 1794938 1982562 2070499 1344599 2095173 1642338 2313505 FALSE TRUE 1506966.312 2138686.37 1837514.777 2033437.897 1907890.361 1732762.904 1781021.259 1847387.515 1927366.07 0.781878615 1.109642015 0.953381304 1.055034604 0.989895169 0.899031549 0.924070049 0.958503703 1 20.87819918 2.350703222 7.981356399 0.936200128 0.996584934 0.004541704 0.088361009 0.550726072 36.56540737 0.027934666 0.023320305 224.2349074 -2.350703222 0.060384806 NRPDYVS(ph)EEEEDDEDFETAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NRPDYVSEEEEDDEDFETAVK 21 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 NRPDYVS(1)EEEEDDEDFETAVK;NRPDYVS(1)EEEEDDEDFETAVK 316.44 6.14E-67 273790000 326930 216374 242461 250615 276404 186582 315480 245221 288347 TRUE FALSE 306468.0349 232394.5561 248212.2894 257046.2052 254696.3448 240445.1945 268176.7028 275837.3816 240220.0229 1.275780558 0.967423753 1.033270609 1.070044878 1.060262761 1.000937356 1.116379474 1.148269733 1 17.87399688 1.657441491 11.69862241 1.098995795 1.052236425 0 0.090111935 0.366268422 70.67113557 0.039116245 0.02127727 45.44033146 -1.657441491 -0.04675937 NRPEDYQGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NRPEDYQGGR 10 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;;;; 230.61 9.77E-10 11138840000 3732420 4038530 3918050 3936230 3886010 2692550 4190180 3264360 3449950 FALSE TRUE 3498814.495 4337546.963 4010987.996 4037240.326 3580818.45 3469845.475 3561901.409 3671922.532 2874131.057 1.217346887 1.50916812 1.395548051 1.404682057 1.245878625 1.20726766 1.239296795 1.277576582 1 21.45469442 2.668959999 3.138411606 1.206372599 1.407040511 0.444207674 0.103001416 0.217397809 4.218983689 0.031986535 0.030572705 466.6164007 -2.668959999 0.200667912 NRPLLDFVSMEELNDMDDYDS(ph)EDDNDWRPTVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NRPLLDFVSMEELNDMDDYDSEDDNDWRPTVVK 33 2 A0A0U1RRH6;O94880 A0A0U1RRH6 PHF14 PHD finger protein 14 1 NRPLLDFVSMEELNDMDDYDS(1)EDDNDWRPTVVK;NRPLLDFVSMEELNDMDDYDS(1)EDDNDWRPTVVK;NRPLLDFVSMEELNDMDDYDS(1)EDDNDWRPTVVK;NRPLLDFVSMEELNDMDDYDS(1)EDDNDWRPTVVK;NRPLLDFVSMEELNDMDDYDS(1)EDDNDWRPTVVK;NRPLLDFVSMEELNDMDDYDS(1)EDDNDWRPTVVK 317.12 1.18E-104 432455000 311576 230430 244513 214890 203451 126784 275802 236855 293971 TRUE FALSE 292075.0143 247491.277 250312.9638 220404.4412 187472.7791 163384.4826 234448.0505 266426.8681 244905.341 1.192603694 1.01055892 1.022080461 0.899957675 0.765490774 0.667133195 0.957300684 1.08787692 1 17.90186471 4.215084292 0.897304681 0.883247343 1.194951767 0.3242939 0.124221754 1.348736184 1.415923677 0.044937931 0.352623943 16409.08224 -4.215084292 0.311704424 NRPT(ph)SISWDGLDSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NRPTSISWDGLDSGK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 1 NRPT(0.333)S(0.333)IS(0.333)WDGLDS(0.001)GK 176.44 5.09E-06 130800000 255050 166580 171080 170380 187500 126730 222750 164770 347040 TRUE FALSE 239086.8758 178913.7565 175138.0984 174752.2393 172774.5063 163314.8937 189350.7054 185341.8972 289116.782 0.826956063 0.61882868 0.605769396 0.604434782 0.59759418 0.564875178 0.654928102 0.641062397 1 18.14129283 0.233697206 1.689596713 1.000054779 0.628906747 0.713546066 0.071616532 6.075515904 12.69806426 0.063523555 0.017853873 1.712762736 -0.233697206 -0.371148031 NRPTS(ph)ISWDGLDSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NRPTSISWDGLDSGK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 1 NRPT(0.175)S(0.65)IS(0.175)WDGLDSGK 191.4 1.45E-11 0 199440 133240 142350 129380 158620 99062 184310 138580 283710 TRUE FALSE 186957.4064 143105.2282 145726.6092 132700.1098 146162.625 127659.5913 156674.4266 155882.0181 236356.9682 0.790995958 0.605462277 0.616553048 0.561439381 0.618397783 0.540113508 0.662872044 0.659519452 1 17.85060787 0.459472414 1.478757623 0.999977382 0.618608511 0.747804687 0.067369614 1.36299586 3.250054549 0.058687564 0.017003602 2.880530078 -0.459472414 -0.381368871 NRPTSISWDGLDSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NRPTSISWDGLDSGK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ;; 203.53 4.89E-09 1280810000 2944230 1929670 2101780 1937370 2252640 1427320 2733540 2111420 4180600 FALSE TRUE 2759955.9 2072544.775 2151635.214 1987086.194 2075726.741 1839364.113 2323671.054 2375035.435 3482830.852 0.79244615 0.595074772 0.617783437 0.570537668 0.595988387 0.528123297 0.667178842 0.681926724 1 21.73182898 0.629860347 1.525787865 0.999693553 0.613286007 0.738849852 0.069787101 0.671798937 2.167537192 0.060894364 0.01761048 4.264423688 -0.629860347 -0.386407546 NRS(ph)AEEGELAESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NRSAEEGELAESK 13 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 NRS(1)AEEGELAESK;NRS(1)AEEGELAESK;NRS(1)AEEGELAESK;NRS(1)AEEGELAESK;NRS(1)AEEGELAESK;NRS(1)AEEGELAESK 224.12 8.87E-12 5364640000 7314310 5109350 5607730 6446910 6288060 3177710 5550320 3661380 5497290 TRUE FALSE 6856520.394 5487651.59 5740748.004 6612348.625 5794221.132 4095063.291 4718101.043 4118511.353 4579756.785 1.497136358 1.198240834 1.253504994 1.443820914 1.26518097 0.894166106 1.030207774 0.899286042 1 22.12683955 2.298839185 6.069231526 0.964145064 1.3106545 0.787346428 0.096776427 0.094953658 6.876793443 0.033298734 0.027477455 198.9936347 -2.298839185 0.346509436 NRS(ph)PHHSTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NRSPHHSTVK 10 1 Q8TAD8;A0A1W2PRA0 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 NRS(0.99)PHHS(0.006)T(0.003)VK 73.466 0.027194 26331000 7399.7 13650 12168 13776 11826 9669.9 17727 13427 14956 TRUE FALSE 6936.565986 14660.6602 12456.63071 14129.51548 10897.23366 12461.44315 15069.00092 15103.39051 12459.74698 0.556718045 1.176641887 0.999749893 1.134013035 0.874595101 1.000136132 1.209414681 1.212174736 1 13.60498715 1.760049624 15.36296764 1.158047907 0.990894842 0.171499626 0.178801956 1.028264763 740.8879862 0.076360649 0.04220732 57.55056926 -1.760049624 -0.167153065 NRSAEEGELAES(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NRSAEEGELAESK 13 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 NRS(0.183)AEEGELAES(0.817)K 221.03 5.21E-11 1030900000 2068800 1360800 1463600 1775900 1633000 819490 1442400 910590 1399100 TRUE FALSE 1939317.501 1461555.048 1498317.283 1821472.601 1504750.767 1056063.46 1226125.511 1024279.166 1165581.171 1.663820203 1.253928155 1.285467988 1.562716218 1.290987538 0.906040253 1.051943477 0.878771201 1 20.15261805 2.338656501 4.761722148 0.971646901 1.387564673 0.744317529 0.132258739 0.116381783 4.446497075 0.046211608 0.0379979 218.1004196 -2.338656501 0.415917772 NRT(ph)PSDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NRTPSDVK 8 1 P39687;H0YN26;H7BZ09;O95626 P39687 ANP32A;ANP32D Acidic leucine-rich nuclear phosphoprotein 32 family member A;Acidic leucine-rich nuclear phosphoprotein 32 family member D 1 NRT(0.999)PS(0.001)DVK 74.944 0.03666 0 260640 194250 208280 218390 222150 145550 225740 176160 209780 TRUE FALSE 244327.0077 208632.4721 213220.5 223994.2571 204703.2351 187567.9222 191892.3827 198153.9638 174766.3628 1.398020785 1.193779334 1.220031684 1.281678314 1.171296535 1.073249561 1.097993799 1.133822096 1 17.41506801 2.457614375 3.283804 1.085673846 1.250799493 0.668947767 0.064217899 0.162335096 3.6685366 0.02207913 0.018813482 286.8232648 -2.457614375 0.165125647 NRTPSDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NRTPSDVK 8 1 P39687;H0YN26;H7BZ09;O95626 P39687 ANP32A;ANP32D Acidic leucine-rich nuclear phosphoprotein 32 family member A;Acidic leucine-rich nuclear phosphoprotein 32 family member D 0 ; 118.67 0.00168 402900000 337340 359140 257050 283300 455520 184237 362440 330540 547690 FALSE TRUE 316226.4916 385731.0993 263147.3474 290569.9576 419745.2967 237423.2311 308095.4867 371808.6466 456277.0008 0.693058145 0.845387996 0.576727179 0.636827973 0.91993525 0.52034889 0.675237819 0.814874837 1 18.79955041 0.955438819 3.605526208 0.999402981 0.695193628 0.416561032 0.116282245 0.234672544 8.186864688 0.105207491 0.027137562 9.024825621 -0.955438819 -0.304209353 NRVPS(ph)AGDVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NRVPSAGDVEK 11 1 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 1 NRVPS(1)AGDVEK 97.904 0.0035845 584890000 939780 617840 764480 809280 769040 475120 834680 613830 769820 TRUE FALSE 880960.8474 663585.5165 782613.8266 830047.4949 708642.7006 612279.4311 709527.4828 690468.0267 641332.0688 1.373642283 1.034698791 1.220294236 1.294255403 1.104954415 0.95469954 1.106334015 1.07661547 1 19.29071202 2.484536622 24.6204941 1.044736605 1.196643061 0.468180382 0.09577796 304.3588387 1010537.929 0.031415305 0.027339565 305.1663351 -2.484536622 0.151906456 NRVPSAGDVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NRVPSAGDVEK 11 1 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 ; 75.102 0.035575 556110000 756060 631210 632770 589230 687560 487060 796730 579900 820700 FALSE TRUE 708739.5542 677945.4452 647779.6032 604350.6394 633561.8111 627666.3152 677267.733 652301.7915 683719.8681 1.036593475 0.991554402 0.947434225 0.883915574 0.926639463 0.918016785 0.990563189 0.95404832 1 19.38304582 -4.327187688 7.322907879 0.999791298 0.958611852 0 0.045087205 0 0 0 0.009977527 4.71E-05 4.327187688 -0.041179446 NS(ph)EEEEEEKKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NSEEEEEEKKK 11 2 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 NS(1)EEEEEEKKK;NS(1)EEEEEEKKK;NS(1)EEEEEEKKK 140.02 2.02E-05 872300000 3125590 487170 1108860 984480 909070 705887 1541010 666049 974040 TRUE FALSE 2929964.901 523240.5737 1135162.683 1009743.424 837675.3092 909665.1178 1309949.857 749206.6838 811466.4315 3.610703767 0.644808649 1.398902824 1.244344047 1.032298166 1.121013861 1.614299502 0.923275018 1 19.63017189 4.745963539 24.99797954 1.159325397 3.610704926 0.896366537 0.265636127 274.3568948 926418.402 0.063305882 0.660817713 55713.89725 -4.745963539 2.451379529 NS(ph)FTPLSSSNTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NSFTPLSSSNTIR 13 0 O60825 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 NS(0.997)FT(0.003)PLSSSNTIR;NS(0.752)FT(0.248)PLSSSNTIR;NS(0.943)FT(0.057)PLSSSNTIR;NS(0.745)FT(0.255)PLSSSNTIR 258.79 6.29E-24 993840000 1114560 1221740 784130 980700 1384640 713730 1512780 987820 1236060 TRUE FALSE 1044801.679 1312198.901 802729.9339 1005866.422 1275895.96 919772.2646 1285952.683 1111151.501 1029753.601 1.014613281 1.274284353 0.779535933 0.976803015 1.239030346 0.893196454 1.248796491 1.079045998 1 19.97386774 NS(ph)IEVAGLSHGLEGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSIEVAGLSHGLEGLR 16 0 Q16825 Q16825 PTPN21 Tyrosine-protein phosphatase non-receptor type 21 1 NS(1)IEVAGLSHGLEGLR 93.388 0.0028657 95489000 127680 125000 130590 119350 130020 107390 144660 106260 147590 TRUE FALSE 119688.7367 134255.1301 133687.6565 122412.7231 119808.7537 138391.7497 122969.576 119526.7949 122956.2755 0.973425197 1.091893272 1.087278025 0.995579303 0.974401291 1.125536286 1.000108172 0.972108129 1 16.90778584 1.548586296 8.97815214 0.986430107 1.049100382 0.171048232 0.051312406 0.173570446 22.32487696 0.027387347 0.012749223 35.3660288 -1.548586296 0.062670275 NS(ph)LESISSIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NSLESISSIDR 11 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 NS(1)LESISSIDR;NS(1)LESISSIDR;NS(0.999)LES(0.001)ISSIDR 212.03 7.68E-09 458695000 599040 470288 481793 493573 562340 410206 531374 451383 439064 TRUE FALSE 561547.1557 505108.6129 493221.3575 506238.9188 518176.0848 528625.8131 451699.4017 507739.1612 365781.3819 1.535198847 1.380903014 1.348404763 1.383993128 1.416627828 1.445196063 1.234888991 1.3880946 1 18.48062212 -3.686579066 0.213175548 2.89E-13 1.442160245 0.774375489 0.068484176 37.35473654 0.617560219 16.32803521 0.140924788 0.000205788 3.686579066 1.442160245 NS(ph)LIELPDDYSCLLNQASHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSLIELPDDYSCLLNQASHFR 21 0 Q8IWV7 Q8IWV7 UBR1 E3 ubiquitin-protein ligase UBR1 1 NS(1)LIELPDDYSCLLNQASHFR;NS(1)LIELPDDYSCLLNQASHFR 222.71 2.46E-25 48085000 69902 53527 62446 61117 60218 52103 72641 61678 76851 TRUE FALSE 65526.9586 57490.19477 63927.24861 62685.36569 55488.72119 67144.29028 61749.15642 69378.63407 64024.07162 1.02347378 0.897946558 0.998487709 0.979090584 0.866685292 1.048735086 0.964467814 1.083633582 1 15.96632681 2.194933943 24.99998252 1.016146171 0.9529743 0.2907642 0.054513554 185.8913911 106522.7004 0.018683085 0.013798451 156.6512782 -2.194933943 -0.063171871 NS(ph)PATLFEVPDTW ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NSPATLFEVPDTW 13 0 A0A494C0Q6;A0A494C0K5;A0A494C0W0;O95453-2;O95453-3;O95453;O95453-4 A0A494C0Q6 PARN Poly(A)-specific ribonuclease PARN 1 NS(0.988)PAT(0.012)LFEVPDTW;NS(0.886)PAT(0.114)LFEVPDTW;NS(0.5)PAT(0.5)LFEVPDTW 94.692 0.0052853 27661500 106358 74667 82760 74248 81640 84309 118994 87764 85163 TRUE FALSE 99701.24263 80195.42237 84723.10628 76153.32938 75228.32372 108647.6397 101151.9544 98721.52859 70948.74513 1.405257309 1.130328975 1.19414524 1.07335696 1.060319299 1.53135393 1.42570463 1.391448551 1 16.11448955 2.245383493 24.99992005 1.383961424 1.165318319 0.16953734 0.166685749 186.9938839 685171.5747 0.052896095 0.043338044 175.9476589 -2.245383493 -0.218643105 NS(ph)PEDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NSPEDKR 7 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 NS(1)PEDKR;NS(1)PEDKR;NS(1)PEDKR;NS(1)PEDKR 87.806 0.011681 3726320000 7772180 2987251 4716950 4041942 4061622 3520614 5165702 3510403 4955162 TRUE FALSE 7285733.128 3208430.172 4828838.282 4145665.075 3742638.592 4536958.109 4391152.941 3948684.542 4128113.451 1.764906225 0.777214631 1.169744567 1.00425173 0.906622029 1.099039104 1.063719056 0.956534889 1 21.97705119 4.749390208 24.99804821 1.006287385 1.764906658 0.834813793 0.107261922 608.9174613 1405543.034 0.024596 0.362360565 56155.22966 -4.749390208 0.758619273 NS(ph)PEDLGLSLTGDSCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 NSPEDLGLSLTGDSCK 16 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 NS(1)PEDLGLSLTGDSCK;NS(1)PEDLGLSLTGDSCK;NS(1)PEDLGLSLTGDSCK;NS(1)PEDLGLSLTGDSCK;NS(1)PEDLGLSLTGDSCK;NS(1)PEDLGLSLTGDSCK;NS(1)PEDLGLSLTGDSCK 397.5 6.98E-122 4126326000 7460440 4341961 5217972 5346247 5371042 3825291 7248612 4359744 5997162 TRUE FALSE 6993504.378 4663444.31 5341744.76 5483440.749 4949222.027 4929590.413 6161749.923 4904067.635 4996196.919 1.39976556 0.93339882 1.069162174 1.097522944 0.99059787 0.986668559 1.233288044 0.981560118 1 22.25239891 4.750286195 24.77335268 1.047124222 1.399765801 0.645254034 0.084317924 1100.744993 2325563.084 0.020455852 0.331034106 56271.20236 -4.750286195 0.352641579 NS(ph)PGSQVASNPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 NSPGSQVASNPR 12 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 1 NS(1)PGSQVASNPR;NS(0.999)PGS(0.001)QVASNPR;NS(1)PGSQVASNPR;NS(0.998)PGS(0.002)QVASNPR;NS(0.918)PGS(0.082)QVASNPR;NS(0.977)PGS(0.023)QVASNPR;NS(0.997)PGS(0.002)QVASNPR 306.92 2.08E-37 3877601000 1694337 1259742 1426127 1387927 1483413 1236756 1920692 1275560 1948649 TRUE FALSE 1588291.472 1353014.608 1459955.406 1423543.557 1366911.727 1593787.38 1632702.065 1434816.474 1623406.893 0.978369304 0.833441458 0.899315761 0.87688648 0.842001924 0.98175472 1.005725719 0.883830468 1 20.63059321 2.227145648 24.92095245 0.972794622 0.880236496 0.383657134 0.051073421 184.7664591 403375.9766 0.017452449 0.013002686 168.7118735 -2.227145648 -0.092558126 NS(ph)PGVPTGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSPGVPTGAK 10 0 Q08379;B7ZC06;R4GND7 Q08379 GOLGA2 Golgin subfamily A member 2 1 NS(1)PGVPTGAK;NS(1)PGVPTGAK 98.337 0.0057122 164740000 1143100 728840 864170 893720 815300 585690 1069780 674440 988960 TRUE FALSE 1071555.411 782804.072 884668.5205 916654.3683 751269.6268 754769.1951 909376.4204 758645.3186 823896.1871 1.300595182 0.950124645 1.073762125 1.112584792 0.911849865 0.916097449 1.103751218 0.920802075 1 19.65210304 4.74546341 24.81984714 1.007247383 1.300595332 0.602742 0.076761172 520.209004 1870423.284 0.017512743 0.173898808 55649.7746 -4.74546341 0.293347949 NS(ph)PQALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSPQALR 7 0 Q7L7X3-3;Q7L7X3 Q7L7X3-3 TAOK1 Serine/threonine-protein kinase TAO1 1 NS(1)PQALR;NS(1)PQALR 109.83 0.0072799 507550000 1585500 1337490 1447980 1338840 1507430 1197650 1646910 1442300 1208560 TRUE FALSE 1486266.385 1436519.151 1482326.769 1373196.901 1389042.528 1543392.113 1399971.135 1622374.33 1006843.528 1.476164213 1.426755112 1.472251375 1.363863264 1.379601189 1.532901657 1.390455513 1.611347031 1 19.94140806 -1.051441005 4.438044539 0.999973245 1.449333146 0.785106218 0.074997286 4394336.592 1041086.026 1181.836304 0.015502766 0.088829864 1.051441005 0.449359901 NS(ph)PQALRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NSPQALRR 8 1 Q7L7X3-3;Q7L7X3 Q7L7X3-3 TAOK1 Serine/threonine-protein kinase TAO1 1 NS(1)PQALRR;NS(1)PQALRR;NS(1)PQALRR 93.839 0.0066053 1230810000 321901 298830 283934 265290 415617 221958 316077 325041 427550 TRUE FALSE 301753.791 320955.6841 290669.0486 272097.7905 382976.1173 286033.6714 268684.1882 365623.0844 356189.1429 0.847172905 0.901082165 0.816052522 0.763913769 1.075204354 0.803038714 0.75433009 1.026485764 1 18.44228402 1.219099674 24.96665181 1.013243111 0.850279966 0.355864111 0.090431695 298.9660605 383536.5219 0.082734102 0.020806164 16.56150019 -1.219099674 -0.162963145 NS(ph)PSNLSSSSDTGSVGGTYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSPSNLSSSSDTGSVGGTYR 20 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 NS(0.992)PS(0.008)NLSSSSDTGSVGGTYR 102.98 0.0007497 0 85060 59370 62148 64518 68132 45611 89549 58242 70803 TRUE FALSE 79736.24644 63765.81657 63622.17991 66173.64111 62781.18755 58778.15527 76121.95878 65513.64191 58985.5219 1.351793523 1.081041831 1.078606713 1.121862433 1.064349107 0.996484449 1.290519374 1.11067326 1 15.84807327 4.741833263 24.64895113 1.103992702 1.351793635 0.492893569 0.081834163 238.3542222 1795137.499 0.019497533 0.139282742 55186.55228 -4.741833263 0.247800933 NS(ph)PVT(ph)KTPPRDLPTIPGVTSPSSDEPPMEASQSHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NSPVTKTPPRDLPTIPGVTSPSSDEPPMEASQSHLR 36 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 NS(0.999)PVT(0.543)KT(0.458)PPRDLPTIPGVTSPSSDEPPMEASQSHLR;NS(0.996)PVT(0.502)KT(0.502)PPRDLPTIPGVTSPSSDEPPMEASQSHLR;NS(0.998)PVT(0.628)KT(0.374)PPRDLPT(0.001)IPGVTSPSSDEPPMEASQSHLR;NS(0.997)PVT(0.656)KT(0.347)PPRDLPTIPGVTSPSSDEPPMEASQSHLR;NS(0.985)PVT(0.596)KT(0.404)PPRDLPT(0.015)IPGVTSPSSDEPPMEASQSHLR;NS(0.99)PVT(0.55)KT(0.455)PPRDLPT(0.004)IPGVTSPSSDEPPMEASQSHLR 185.22 8.27E-23 2004160000 366811 333735 343744 470539 756847 293727 544258 457681 1413920 TRUE FALSE 343852.9543 358445.0867 351897.77 482613.8274 697407.2896 378521.2166 462651.5655 514823.4803 1177927.618 0.291913484 0.304301454 0.298743119 0.409714332 0.592062941 0.321345056 0.392767398 0.437058672 1 20.16781946 -4.999999999 0.228664287 4.366722208 0.298107647 0.853543747 0.08201941 58.74210325 0.588058801 91.39593032 0.146524133 1.00E-05 4.999999999 -4.068614561 NS(ph)PVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSPVTK 6 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 NS(1)PVTK 109.48 0.030969 860530000 2124000 977480 1910000 1764800 1857500 1620000 2623500 1761600 2525000 TRUE FALSE 1991062.631 1049853.636 1955306.102 1810087.756 1711619.443 2087667.701 2230130.53 1981539.638 2103561.188 0.946519951 0.499083955 0.929521857 0.860487333 0.813677041 0.992444486 1.060169081 0.941992869 1 21.00440235 2.964011236 0.749381308 1.016556391 0.70529486 0.337117564 0.126829229 0.610583324 0.760585475 0.076306038 0.096809386 920.4733867 -2.964011236 -0.311261531 NS(ph)PVTKT(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NSPVTKTPPR 10 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 NS(1)PVT(0.012)KT(0.988)PPR;NS(1)PVT(0.038)KT(0.962)PPR;NS(1)PVT(0.45)KT(0.55)PPR 126.48 0.00087387 1922170000 3499210 1781300 2347480 2639070 3670350 2085350 3578100 2889240 4829300 TRUE FALSE 3280200.692 1913189.305 2403163.334 2706793.004 3382095.516 2687356.692 3041597.122 3249967.974 4023258.632 0.815309428 0.475532269 0.597317636 0.672786229 0.840635869 0.667955242 0.75600338 0.807794942 1 21.93993305 1.081186506 0.343421532 1.030883082 0.576748877 0.506970406 0.101532292 1.118090014 0.401953615 0.189405749 0.114589875 12.0555355 -1.081186506 -0.454134205 NS(ph)PVTKT(ph)PPRDLPTIPGVTSPSSDEPPMEASQSHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NSPVTKTPPRDLPTIPGVTSPSSDEPPMEASQSHLR 36 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 NS(0.966)PVT(0.471)KT(0.563)PPRDLPT(0.001)IPGVTSPSSDEPPMEASQSHLR;NS(0.992)PVT(0.457)KT(0.552)PPRDLPTIPGVTSPSSDEPPMEASQSHLR;NS(0.924)PVT(0.259)KT(0.816)PPRDLPT(0.001)IPGVTSPSSDEPPMEASQSHLR;NS(0.978)PVT(0.093)KT(0.913)PPRDLPT(0.016)IPGVTSPSSDEPPMEASQSHLR 184.67 1.86E-22 931130000 271182 265414 250677 318306 513097 207251 396128 328755 1029877 TRUE FALSE 254209.2027 285065.5287 256623.1768 326474.2709 472800.4314 267080.9993 336732.2839 369800.7854 857983.8754 0.29628669 0.33225045 0.299100233 0.380513294 0.55105981 0.311289066 0.392469245 0.431011347 1 19.71059101 -5 0.260652521 5.119522927 0.31564592 0.892399453 0.069185537 58.64043214 0.575967937 129.303795 0.090040713 1.00E-05 5 -4.803877007 NS(ph)QEDSEDS(ph)EDKDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 NS(0.67)QEDS(0.33)EDS(1)EDKDVK 200.45 8.26E-08 1478700000 14609000 3583500 5848400 6463000 7970300 4196400 8401500 4464500 7395100 TRUE FALSE 13694648.77 3848826.069 5987126.81 6628851.522 7344344.789 5407832.557 7141773.071 5021902.653 6160810.036 2.222864962 0.624727276 0.971808378 1.075970771 1.192107003 0.877779468 1.159226308 0.815136747 1 22.55468862 4.748190353 24.98825901 0.964645891 2.222865636 0.849801856 0.166245504 512.2177033 1329129.461 0.040968763 0.539014906 56000.29995 -4.748190353 1.258219745 NS(ph)QKHSPTSEPTPPGDALPPVSSPHTHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 NSQKHSPTSEPTPPGDALPPVSSPHTHR 28 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 NS(0.615)QKHS(0.318)PT(0.033)S(0.033)EPT(0.001)PPGDALPPVSSPHTHR;NS(0.539)QKHS(0.376)PT(0.042)S(0.042)EPT(0.001)PPGDALPPVSSPHTHR;NS(0.465)QKHS(0.465)PT(0.053)S(0.013)EPT(0.005)PPGDALPPVSSPHTHR;NS(0.486)QKHS(0.486)PT(0.014)S(0.014)EPTPPGDALPPVSSPHTHR;NS(0.455)QKHS(0.455)PT(0.044)S(0.044)EPT(0.002)PPGDALPPVSSPHTHR;NS(0.441)QKHS(0.441)PT(0.1)S(0.017)EPTPPGDALPPVSSPHTHR;NS(0.433)QKHS(0.433)PT(0.112)S(0.021)EPTPPGDALPPVSSPHTHR;NS(0.424)QKHS(0.424)PT(0.117)S(0.033)EPT(0.002)PPGDALPPVSSPHTHR 136.87 3.43E-06 29404156000 2866438 3657031 4128928 4126935 4031985 3234590 5839270 3597251 4537757 TRUE FALSE 2687032.762 3927801.38 4226868.122 4232839.139 3715329.162 4168363.624 4963725.673 4046375.706 3780376.042 0.710784518 1.038997533 1.118107848 1.119687325 0.982793543 1.102632007 1.313024318 1.070363282 1 21.85009832 5.174467187 1.348840501 1.121242938 4.24E-14 0.6343315 0.091054946 2.428120643 1.770094034 0.025763551 4.951932514 149440.1129 -5.174467187 -1.121242938 NS(ph)RPKFDEIVNMLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSRPKFDEIVNMLDK 15 2 F8W9W0;F8VP57;B7ZKW7;B7ZKJ3;P54756-3;P54756-2;P54756 F8W9W0 EPHA5 Receptor protein-tyrosine kinase;Ephrin type-A receptor 5 1 NS(1)RPKFDEIVNMLDK 62.765 0.040913 344100000 4192300 962480 1175800 955220 1252000 732410 1334400 1095100 1448900 TRUE FALSE 3929911.426 1033743.021 1203690.531 979732.5624 1153672.97 943844.8773 1134319.108 1231825.646 1207069.23 3.255746505 0.8564074 0.997200907 0.811662279 0.955763714 0.781931023 0.939729951 1.020509524 1 20.20307699 4.73941873 24.99988706 0.914225827 3.255747236 0.987919211 0.081157183 6.302159656 183575.0701 0.017405052 0.105495353 54880.58471 -4.73941873 2.341521409 NS(ph)SEASSGDFLDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.993)S(0.007)EASSGDFLDLK;NS(0.995)S(0.005)EASSGDFLDLK;NS(0.795)S(0.205)EASSGDFLDLK;NS(0.999)S(0.001)EASSGDFLDLK;NS(0.956)S(0.044)EASSGDFLDLK 273.44 5.47E-33 645210000 2029240 982654 1419259 1274105 1126842 1147337 1831940 1102809 918404 TRUE FALSE 1902233.491 1055410.725 1452924.494 1306800.691 1038344.375 1478554.566 1557257.604 1240497.131 765116.4393 2.486201306 1.379411904 1.898958667 1.70797623 1.357106345 1.932456931 2.035321062 1.621318099 1 19.5453198 0.974564637 22.14020584 0.999999984 1.791199982 0.38987017 0.323027398 547.6311088 476687.232 0.287163154 0.071790789 9.431149675 -0.974564637 0.791199998 NS(ph)SEKLPTELSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSSEKLPTELSK 12 1 P38432 P38432 COIL Coilin 1 NS(0.924)S(0.075)EKLPTELSK 68.41 0.031941 194540000 258930 161330 214450 192880 203680 125640 232050 152210 217020 TRUE FALSE 242724.0335 173275.0411 219536.8553 197829.6273 187683.7944 161910.2284 197256.2567 171213.7536 180797.96 1.342515333 0.958390466 1.214266219 1.094202763 1.038085797 0.895531279 1.09103143 0.94698941 1 17.46401887 2.733215254 3.153444752 0.996276202 1.133113425 0.350493192 0.107383742 0.33472662 6.876064822 0.0333189 0.033173656 541.0224092 -2.733215254 0.136837223 NS(ph)SPEKHILENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSSPEKHILENK 12 1 E7EVA0;B5MEG9 E7EVA0 MAP4 Microtubule-associated protein 1 NS(0.5)S(0.5)PEKHILENK 94.569 0.003947 293590000 155720 96011 128460 127690 140360 79465 133650 100030 219210 TRUE FALSE 145973.7632 103119.7543 131507.1319 130966.7416 129336.6918 102405.2555 113610.4232 112518.9657 182622.4348 0.799319992 0.564660932 0.720103924 0.717144866 0.708219074 0.560748495 0.622105512 0.616128932 1 17.47850448 -1.972199323 2.712815815 1.289480416 0.655592783 0.661100088 0.07551322 6052809.406 2918614.897 10985663.63 0.017958473 0.010661067 1.972199323 -0.633887633 NS(ph)TELAPPLPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSTELAPPLPVR 12 0 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 NS(0.755)T(0.245)ELAPPLPVR;NS(0.767)T(0.233)ELAPPLPVR 169.54 4.57E-05 129686000 290060 271430 269520 310530 285340 229417 334090 266360 153572 TRUE FALSE 271905.6624 291526.9596 275913.1417 318498.7255 262930.5474 295645.9636 283996.306 299615.6323 127939.8411 2.125261842 2.278625307 2.156584996 2.489441309 2.055110786 2.310820157 2.219764411 2.341847776 1 16.96510607 -0.908483585 5.333824162 0.999998125 2.244394278 0.911963167 0.121777242 2.32E-06 4.74E-07 0.100592358 0.023709811 0.123457198 0.908483585 1.244396153 NS(ph)TGSGHSAQELPTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSTGSGHSAQELPTIR 16 0 O94763-3;O94763;O94763-2;O94763-4;I3L280 O94763-3 URI1 Unconventional prefoldin RPB5 interactor 1 1 NS(0.938)T(0.043)GS(0.02)GHSAQELPTIR 130.37 6.56E-05 0 234040 167740 257870 298400 247890 421860 265390 164410 217940 TRUE FALSE 219391.8542 180159.6441 263986.7982 306057.4492 228421.7193 543644.1337 225597.2333 184936.9504 181564.4061 1.208341761 0.99226301 1.453956774 1.685668771 1.258075436 2.994221971 1.24251905 1.01857492 1 17.47012188 3.687602046 2.269433068 1.611894832 1.099177552 0.075742258 0.570773917 0.629873452 6.405108761 0.15431863 0.293606461 4870.819616 -3.687602046 -0.51271728 NS(ph)WDSPAFSNDVIR ddPTM_SK-BR-3_Pertuzumab_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(0.998)WDS(0.002)PAFSNDVIR;NS(1)WDSPAFSNDVIR;NS(1)WDSPAFSNDVIR;NS(0.995)WDS(0.005)PAFSNDVIR;NS(1)WDSPAFSNDVIR;NS(0.998)WDS(0.002)PAFSNDVIR 330.74 2.14E-68 1233553000 1180493 1197732 1129705 1199960 1221445 884085 1381633 1041563 991421 TRUE FALSE 1106608.05 1286413.324 1156502.136 1230753.005 1125517.637 1139305.988 1174469.958 1171604.433 825946.4303 1.339806082 1.557502129 1.400214461 1.490112385 1.362700528 1.379394529 1.421968684 1.4184993 1 19.65568869 -3.098525119 0.314102269 4.74E-11 1.45549169 0.811883215 0.063567465 30.4000632 0.820795448 20.08659495 0.054885141 0.00079703 3.098525119 1.45549169 NSASATTPLS(ph)GNSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSASATTPLSGNSSR 15 0 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 NSASATT(0.058)PLS(0.942)GNSSR;NSASATT(0.001)PLS(0.999)GNSSR 235.79 1.14E-17 626160000 716880 581250 644940 616430 640180 525060 690310 575370 753470 TRUE FALSE 672011.7605 624286.3548 660238.2814 632248.6374 589902.8452 676636.2984 586804.424 647206.211 627710.9894 1.070575108 0.994544249 1.051818898 1.007228881 0.93976823 1.077942413 0.934832166 1.03105764 1 19.25974094 3.009390433 22.54449988 0.992589632 1.031070856 0.145090355 0.045056858 112.3873048 269810.7278 0.011634473 0.013879549 1021.857726 -3.009390433 0.038481224 NSASATTPLSGNS(ph)SR ddPTM_SK-BR-3_Pertuzumab_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 NSASATT(0.002)PLS(0.032)GNS(0.483)S(0.483)R 67.997 0.056581 161400000 176060 180440 182380 186340 194880 118630 216920 172140 233540 TRUE FALSE 165040.7189 193799.9653 186706.1397 191121.7999 179574.9109 152876.5552 184394.8598 193632.0579 194560.6653 0.848273821 0.996090166 0.959629427 0.982324971 0.922976444 0.785752634 0.947749945 0.995227158 1 17.56986054 1.288051926 5.400146526 0.998234459 0.927596517 0.205188829 0.062671308 0.33325732 20.21762166 0.047524816 0.016073662 19.41117953 -1.288051926 -0.070637943 NSASATTPLSGNSS(ph)R ddPTM_SK-BR-3_Pertuzumab_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(0.118)S(0.882)R;NSASATTPLSGNS(0.496)S(0.504)R;NSASATTPLS(0.027)GNS(0.246)S(0.727)R 199.99 7.49E-09 1304230000 2131720 2010670 1981740 2002090 2153240 1398400 2529690 1865440 2414510 TRUE FALSE 1998299.45 2159542.099 2028747.809 2053467.019 1984133.216 1802095.379 2150386.469 2098344.29 2011512.683 0.993431196 1.073591093 1.008568241 1.020857108 0.986388618 0.895890637 1.069039478 1.043167318 1 20.9398494 6.601529204 8.457227187 1.014288407 0.567209281 0 0.050398368 0 0 0.010965432 0 3995114.258 -6.601529204 -0.447079125 NSATCHS(ph)EDS(ph)DLEID ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSATCHSEDSDLEID 15 0 Q13371-2;Q13371 Q13371-2 PDCL Phosducin-like protein 2 NSAT(0.002)CHS(0.998)EDS(1)DLEID;NSAT(0.001)CHS(0.999)EDS(1)DLEID 157.37 2.87E-06 303170000 492720 516590 523810 533560 538470 434960 681300 431280 477280 TRUE FALSE 461881.5347 554838.8611 536235.0206 547252.0529 496180.7383 560525.891 579145.3899 485126.2574 397618.8847 1.161618707 1.395403696 1.348615575 1.376323092 1.247880213 1.409706411 1.456533913 1.220078513 1 18.60102675 0.965470453 6.188772791 1.000050347 1.353995729 0.625344648 0.08444519 0.137831396 20.77233824 0.076671974 0.019268913 9.235713513 -0.965470453 0.353945381 NSATCHSEDS(ph)DLEID ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSATCHSEDSDLEID 15 0 Q13371-2;Q13371 Q13371-2 PDCL Phosducin-like protein 1 NSATCHSEDS(1)DLEID;NSATCHS(0.251)EDS(0.749)DLEID 191.89 1.64E-07 911160000 1337150 1263590 1299580 1344050 1520070 1107720 1606800 1291410 1906380 TRUE FALSE 1253460.168 1357147.518 1330406.651 1378540.598 1400689.834 1427500.782 1365875.257 1452645.381 1588192.862 0.789236747 0.854523119 0.837685827 0.867993196 0.881939383 0.898820802 0.860018509 0.91465301 1 20.59895469 -5 0.086659759 1.466908902 0.735341085 0.867931479 0.019961721 75.72093356 0.459235397 6.560920173 0.507559778 1.00E-05 5 -0.731567817 NSATFKS(ph)FEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 NSATFKSFEDR 11 1 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;O43399-6 O43399 TPD52L2 Tumor protein D54 1 NSAT(0.001)FKS(0.999)FEDR;NSAT(0.001)FKS(0.999)FEDR;NSATFKS(1)FEDR;NSATFKS(1)FEDR;NSATFKS(1)FEDR;NSAT(0.007)FKS(0.993)FEDR;NSATFKS(1)FEDR;NSAT(0.001)FKS(0.999)FEDR;NS(0.002)AT(0.082)FKS(0.916)FEDR 182.17 3.58E-06 22108050000 17850470 18373740 14340190 19636050 18625390 7097120 21007920 14046140 29959370 TRUE FALSE 16733240.95 19734150.83 14680346.08 20139944.29 17162627 9145943.332 17857977.42 15799831.5 24958957.6 0.670430281 0.790664063 0.588179455 0.806922493 0.687633966 0.366439315 0.71549372 0.633032507 1 24.57305435 -1.055820553 4.836548542 1.000009234 0.659607436 0.436530688 0.122319796 1.16E-05 2.26E-06 0.112389052 0.026489635 0.08793858 1.055820553 -0.340401799 NSDDAPWS(ph)PK ddPTM_SK-BR-3_Pertuzumab_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 172.09 4.01E-06 171680000 1683500 963800 1214500 1155100 1213600 846180 1525700 988640 1418000 TRUE FALSE 1578132.74 1035160.755 1243308.514 1184741.822 1118288.751 1090458.429 1296935.449 1112073.88 1181326.639 1.335898716 0.876269713 1.052468024 1.002890972 0.946638054 0.923079522 1.097863542 0.941377129 1 20.1719765 4.749804442 24.94335366 0.985603281 1.335898926 0.752595205 0.064045724 832.215702 1846155.137 0.014873027 0.231359517 56208.81666 -4.749804442 0.350295645 NSDGGS(ph)DPETQKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSDGGSDPETQKEK 14 1 O75554-2;O75554 O75554-2 WBP4 WW domain-binding protein 4 1 NSDGGS(0.999)DPET(0.001)QKEK;NS(0.019)DGGS(0.913)DPET(0.068)QKEK 150.61 4.34E-06 658040000 1665580 713650 945790 997940 1119470 582970 1264380 830810 1355570 TRUE FALSE 1561334.321 766489.3886 968224.5854 1023548.83 1031551.342 751263.9753 1074797.957 934538.4573 1129316.61 1.382547912 0.678719663 0.857354419 0.906343554 0.913429709 0.665237692 0.951724209 0.827525646 1 20.10701858 4.749214121 24.78638822 0.839042577 1.382548259 0.705036105 0.108036454 719.3357715 1673565.955 0.024036586 0.347095275 56132.46585 -4.749214121 0.543505682 NSDLLTS(ph)PDVGLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NSDLLTSPDVGLLK 14 0 P05412 P05412 JUN Transcription factor AP-1 1 NSDLLT(0.203)S(0.797)PDVGLLK;NSDLLT(0.05)S(0.95)PDVGLLK;NSDLLT(0.168)S(0.832)PDVGLLK;NSDLLT(0.004)S(0.996)PDVGLLK 277.92 3.90E-33 338461000 1600420 1350090 1332170 1539800 1622890 693314 1317740 990561 1692110 TRUE FALSE 1500252.569 1450052.068 1363769.701 1579313.875 1495434.766 893462.4968 1120157.12 1114234.721 1409685.91 1.064245985 1.02863486 0.967428058 1.120330326 1.060828342 0.633802531 0.794614682 0.790413463 1 20.42694232 2.257388028 24.99991245 0.782852137 1.037860142 0.610272531 0.09582127 139.7231326 185530.443 0.030325335 0.025332436 180.8789497 -2.257388028 0.255008005 NSGSSQGLGGS(ph)PGSHSHTTMANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSGSSQGLGGSPGSHSHTTMANK 23 0 Q9Y3L3;Q6ZT62-2;Q6ZT62;Q9Y3L3-2 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 NSGSSQGLGGS(0.92)PGS(0.038)HS(0.038)HT(0.002)T(0.002)MANK 120.13 0.00013509 60608000 37640 46381 55965 57416 58159 41287 71085 49699 44166 TRUE FALSE 35284.17959 49815.0975 57292.51623 58889.39177 53591.42674 53205.88666 60426.46417 55904.02955 36794.40928 0.958954914 1.353876811 1.557098411 1.600498362 1.456510046 1.446031821 1.64227298 1.519362062 1 15.16719895 4.799076805 1.793686308 1.499096826 0.723254255 0.421086477 0.179213191 0.834077349 2.417736847 0.040161557 1.151046072 62961.75214 -4.799076805 -0.775842571 NSHLINVLMWELEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSHLINVLMWELEK 14 0 A0A087WZK9;B3KS98;O15372;E5RJT0 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ; 151.9 6.81E-06 254860000 718880 483080 599930 590000 611680 389050 709900 455620 591450 FALSE TRUE 673886.584 518847.7458 614160.6229 605140.3989 563641.1202 501362.4193 603457.0854 512505.1599 492733.1741 1.367650119 1.052999419 1.24643652 1.228130012 1.143907392 1.017513019 1.224713734 1.040127166 1 18.91044708 -4.999999998 0.053758464 0.29981759 1.487037753 0.360901799 0.096020644 604.9813079 2.395359466 57.71051672 11.57132016 1.00E-05 4.999999998 1.187220163 NSKYEYDPDIS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NSKYEYDPDISPPR 14 1 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 NSKYEYDPDIS(1)PPR;NSKYEYDPDIS(1)PPR;NSKYEYDPDIS(1)PPR 118.37 0.00015108 925440000 1716710 1723310 1681820 1807640 2231110 1085040 1993770 1417870 3020410 TRUE FALSE 1609264.186 1850905.666 1721713.565 1854027.103 2055887.62 1398273.434 1694822.698 1594894.191 2516284.058 0.639539952 0.735571034 0.684228618 0.736811528 0.817033202 0.555689819 0.673541881 0.633829152 1 21.26286336 -1.560997259 6.377107895 1.000495359 0.687760241 0.666141103 0.070154107 0.000472055 3.25E-05 0.064898287 0.015273254 0.027479115 1.560997259 -0.312735118 NSLDASRPAGLS(ph)PTLTPGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.471)PT(0.471)LT(0.058)PGER;NSLDASRPAGLS(0.94)PT(0.06)LTPGER;NSLDAS(0.028)RPAGLS(0.914)PT(0.058)LT(0.001)PGER 139.47 1.29E-07 899730000 744750 586962 702670 690180 686919 646620 792640 603159 772340 TRUE FALSE 698137.4269 630421.2772 719337.6642 707891.1873 632971.1526 833288.697 673790.9905 678464.7289 643431.4645 1.085022206 0.979779995 1.117970917 1.100181179 0.983742928 1.295069861 1.047183776 1.054447546 1 19.29542696 3.908152667 5.936454086 1.093545427 1.028079304 0.051690032 0.089022424 0.468801746 30.15395726 0.020945537 0.038642091 8093.803705 -3.908152667 -0.065466124 NSLESYAFNMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSLESYAFNMK 11 0 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 223.14 1.67E-11 570590000 863070 850540 824330 761350 826600 648630 1196500 944390 1020550 FALSE TRUE 809051.9893 913514.8666 843883.4969 780887.53 761682.1703 835878.9514 1017095.933 1062299.17 850213.612 0.951586728 1.074453353 0.992554677 0.918460395 0.895871531 0.98313993 1.196282815 1.249449733 1 19.69746583 1.759186668 7.30850171 1.165585079 0.979131906 0.527706077 0.078975723 0.115576181 18.84816204 0.037387359 0.020246042 57.43632817 -1.759186668 -0.186453173 NSLFTGDTLGAGQFSFQRPLLVLVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSLFTGDTLGAGQFSFQRPLLVLVDR 26 1 Q8WVM8;Q8WVM8-2;Q8WVM8-3;H0YJY1 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 98.632 0.0052922 67920000 37012 92142 38194 30361 68274 26549 44135 63312 27084 FALSE TRUE 34695.48499 98964.28955 39099.97972 31140.11466 62912.03544 34213.26531 37517.36648 71216.64257 22563.50543 1.537681505 4.386033449 1.732885869 1.380109786 2.788220812 1.51630984 1.662745472 3.156275641 1 14.4617036 3.736838547 17.39073273 1.896511242 3.133575755 0.181199912 0.930595331 9.110603604 16297.65403 0.214440396 0.375897475 5455.55008 -3.736838547 1.237064512 NSLLAGGDDDTMSVIS(ph)GIS(ph)SR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSLLAGGDDDTMSVISGISSR 21 0 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 2 NSLLAGGDDDTMS(0.001)VIS(0.998)GIS(0.547)S(0.454)R 124.81 5.39E-05 83083000 175150 203150 157690 165750 214750 102100 264740 182680 298680 TRUE FALSE 164187.6742 218191.4374 161430.4813 170003.4256 197884.4013 131574.6125 225044.6947 205488.0001 248828.3785 0.659843042 0.876875213 0.648762341 0.683215583 0.795264602 0.528776554 0.904417318 0.825822205 1 17.92479151 1.608892336 25 0.898860773 0.716663756 0.486822461 0.100940614 0.099085753 2258.367714 0.046432544 0.023891786 40.63425823 -1.608892336 -0.182197017 NSLLAGGDDDTMSVIS(ph)GISSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NSLLAGGDDDTMSVISGISSR 21 0 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 1 NSLLAGGDDDTMSVIS(0.973)GIS(0.013)S(0.013)R;NSLLAGGDDDTMS(0.001)VIS(0.733)GIS(0.133)S(0.133)R;NSLLAGGDDDTMSVIS(0.998)GIS(0.001)S(0.001)R;NSLLAGGDDDT(0.012)MS(0.007)VIS(0.937)GIS(0.022)S(0.022)R 253.84 2.36E-36 281032000 333601 341727 275781 312709 354669 196266 433280 309671 425352 TRUE FALSE 312721.5089 367028.8226 282322.6556 320733.6424 326814.7274 252924.8081 368313.6864 348334.106 354358.0033 0.882501611 1.035757113 0.7967159 0.905111891 0.922272742 0.713755032 1.039383005 0.983000533 1 18.43484811 1.613700818 25 1.008398197 0.88736176 0.346818914 0.084072146 0.606448962 2588.049322 0.038808917 0.020793449 41.08665805 -1.613700818 -0.121036436 NSLLAGGDDDTMSVISGIS(ph)SR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 278.52 7.29E-45 121139000 85243 87080 80868 92709 93417 53790 111094 82876 100863 TRUE FALSE 79907.79279 93527.49381 82786.22715 95088.0699 86080.40565 69318.29979 94436.48605 93223.25103 84028.3137 0.950962709 1.113047373 0.985218238 1.1316194 1.024421434 0.824939794 1.123865063 1.109426655 1 16.35858791 -1.08573074 4.230019446 0.999995143 1.035789222 0.01076075 0.095842313 6034440.133 1549022.945 269.5931411 0.020806075 0.082086031 1.08573074 0.03579408 NSLLAGGDDDTMSVISGISS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSLLAGGDDDTMSVISGISSR 21 0 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 1 NSLLAGGDDDTMSVISGIS(0.226)S(0.774)R;NSLLAGGDDDTMSVISGIS(0.2)S(0.8)R 409.78 1.12E-151 142823000 99373 105169 93028 112443 126543 63551 125029 100348 129560 TRUE FALSE 93153.42132 112955.8222 95234.66809 115328.4777 116604.8232 81897.14204 106282.0622 112876.6687 107935.599 0.863046318 1.046511283 0.88232862 1.068493424 1.080318489 0.758759323 0.984680338 1.045777943 1 16.71981124 4.769512196 22.5147973 0.97321377 0.863045604 0.122477949 0.097915795 7304.346399 5312977.442 0.022089518 2.281039683 58818.26315 -4.769512196 -0.110168167 NSLS(ph)PVQATQKPLVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSLSPVQATQKPLVSK 16 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 NSLS(1)PVQATQKPLVSK;NSLS(1)PVQATQKPLVSK 295.4 7.05E-46 1802600000 2409210 1541470 1934480 1793880 1879560 1344270 2249390 1608040 1916580 TRUE FALSE 2258421.847 1655602.043 1980366.779 1839913.998 1731946.939 1732338.927 1912114.852 1808807.334 1596690.416 1.414439408 1.036896086 1.240294774 1.152329831 1.08471055 1.08495605 1.1975489 1.132847868 1 20.60665318 7.245769273 0.018218565 8.34E-07 2.54537184 0.314847212 0.097324959 4867.133124 7.748049935 425.3436372 685.1293453 17610402.14 -7.245769273 2.545371006 NSMDRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSMDRPK 7 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 61.962 0.080551 45024000 142110 121500 121670 122850 140870 98003 135740 106600 163400 FALSE TRUE 133215.5888 130495.9864 124556.0699 126002.539 129806.6384 126294.8752 115387.0471 119909.2447 136127.4844 0.978609054 0.958630706 0.914995751 0.925621593 0.953566717 0.927769111 0.847639605 0.880859917 1 17.05459885 1.983057544 23.04568239 0.891354255 0.942587852 0.083145478 0.042881767 356.9074166 485475.8348 0.01578607 0.010481834 96.17397007 -1.983057544 0.051233598 NSMPTVSFLDQDQS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NSMPTVSFLDQDQSPPR 17 0 A7KAX9;A7KAX9-2 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 NSMPTVSFLDQDQS(1)PPR;NSMPTVSFLDQDQS(1)PPR;NSMPTVSFLDQDQS(1)PPR 369.41 1.04E-104 298170000 213030 195664 184625 191715 197853 164869 233979 172429 212723 TRUE FALSE 199696.8326 210151.1661 189004.3922 196634.7315 182314.4235 212464.0039 198896.0211 193957.1402 177218.1571 1.126841831 1.185833154 1.066506928 1.109563121 1.028757022 1.198883948 1.122323042 1.094454109 1 17.4351669 -4.123261405 0.431674114 3.29E-12 1.12134209 0.351787548 0.049892342 517.6764062 7.032916426 480.6107088 0.027030412 7.53E-05 4.123261405 1.12134209 NSNFSVQHPSST(ph)SPTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSNFSVQHPSSTSPTEK 17 0 Q03468 Q03468 ERCC6 DNA excision repair protein ERCC-6 1 NSNFSVQHPSS(0.002)T(0.982)S(0.015)PT(0.001)EK 138.46 1.32E-05 339810000 192780 177290 193160 230190 203950 124220 286320 166700 244970 TRUE FALSE 180714.2439 190416.7361 197741.8464 236097.0651 187932.5897 160080.2975 243388.9741 187512.862 204082.9244 0.88549419 0.933036101 0.968928914 1.156868296 0.920863861 0.784388493 1.192598424 0.918807208 1 17.63879595 4.0676056 1.78668245 1.001935714 0.899872959 0.079178173 0.116765375 0.953243316 5.72185368 0.031381911 0.104630949 11684.37804 -4.0676056 -0.102062754 NSNILEDLETLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NSNILEDLETLR 12 0 B0YIW6;P48444;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 ;;;;; 228.83 2.24E-11 212408000 438491 412471 403172 428931 430314 317809 487691 358410 434272 FALSE TRUE 411046.631 443010.782 412735.4302 439938.0956 396518.8742 409555.2991 414566.2621 403158.2775 361789.1977 1.136149541 1.22449975 1.140817451 1.21600672 1.095994233 1.132027439 1.145877944 1.114345812 1 18.46478981 -2.550423669 0.1709358 0.743575249 1.207592294 0.667843982 0.035888118 26.2393634 0.540404112 2.645450689 0.131199589 0.002815635 2.550423669 0.464017045 NSNLVGAAHEELQQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 ;;;;;; 276.14 2.75E-35 18301200000 9281360 9738300 9028930 9459670 10115190 6964400 11279680 8471030 10875700 FALSE TRUE 8700456.245 10459333.86 9243100.483 9702421.147 9320783.78 8974909.222 9588396.699 9528656.743 9060475.41 0.96026487 1.154391286 1.020156235 1.07085122 1.028730101 0.990556104 1.058266401 1.051672932 1 23.11115532 3.729531032 24.9860726 1.034299248 1.076018106 0.011268519 0.05278302 235.688282 2443732.23 0.012417617 0.021134047 5364.522017 -3.729531032 0.041718858 NSNPVIAELSQAINSGTLLSKPS(ph)PPLPPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSNPVIAELSQAINSGTLLSKPSPPLPPKR 30 2 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 NSNPVIAELSQAINSGTLLS(0.002)KPS(0.998)PPLPPKR 160.52 2.28E-12 248290000 289400 167750 218780 212470 227510 162150 257040 173350 238720 TRUE FALSE 271286.9706 180170.3845 223969.5649 217922.3399 209642.2823 208960.0727 218499.2382 194993.1291 198876.0898 1.364100485 0.905942915 1.12617643 1.095769432 1.054135178 1.050704853 1.098670225 0.980475477 1 17.60151031 NSNS(ph)DGGEGGEGTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NSNSDGGEGGEGTKK 15 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 NS(0.036)NS(0.964)DGGEGGEGTKK;NS(0.007)NS(0.993)DGGEGGEGTKK;NS(0.009)NS(0.991)DGGEGGEGTKK;NS(0.002)NS(0.998)DGGEGGEGTKK 174.63 1.17E-11 0 754160 348997 482070 474125 473756 268809 575900 354796 488538 TRUE FALSE 706958.4718 374837.101 493504.928 486291.8502 436549.1148 346409.7946 489549.1414 399093.0616 406997.8517 1.737007871 0.920980539 1.212549221 1.194826577 1.072607909 0.851134209 1.202829792 0.980577809 1 18.63466165 4.74640016 24.91044936 1.06874521 1.737008211 0.751695967 0.12304384 459.7580607 1460863.434 0.027775246 0.303918483 55769.93777 -4.74640016 0.668263001 NSNS(ph)PPS(ph)PSSMNQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NSNSPPSPSSMNQR 14 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 2 NSNS(1)PPS(0.999)PS(0.001)SMNQR;NS(0.008)NS(0.992)PPS(0.994)PS(0.005)S(0.001)MNQR;NS(0.009)NS(0.991)PPS(0.938)PS(0.049)S(0.013)MNQR;NS(0.098)NS(0.902)PPS(0.979)PS(0.018)S(0.002)MNQR 207 2.25E-08 358423000 383747 334552 368170 392100 497235 369596 551936 412545 325795 TRUE FALSE 359728.9603 359322.5782 376903.1663 402161.9498 458184.1688 476292.3653 469178.3207 464052.1514 271417.7098 1.325370259 1.323873002 1.388646181 1.481708582 1.68811449 1.754831568 1.728620881 1.709734239 1 18.05015533 3.044252217 2.416771896 1.643524824 1.342349585 0.146576242 0.222000925 0.34839735 4.119341202 0.062756909 0.075442287 1107.266644 -3.044252217 -0.301175238 NSNS(ph)PPSPSSMNQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSNSPPSPSSMNQR 14 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 NSNS(1)PPSPSSMNQR 122.16 0.00043144 144230000 90232 78824 90343 79067 105910 74638 124290 91552 88432 TRUE FALSE 84584.54019 84660.21098 92485.97862 81095.99308 97592.25582 96184.77895 105653.8684 102982.4687 73672.12791 1.148121313 1.149148442 1.255372707 1.10076898 1.324683548 1.305578944 1.434109091 1.397848435 1 16.16883129 2.71529463 21.75008212 1.3294613 1.17632213 0.175889317 0.123943031 189.9122557 177537.1137 0.03615614 0.034126027 519.152118 -2.71529463 -0.15313917 NSNSPPS(ph)PSSMNQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 NSNSPPSPSSMNQR 14 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 NSNSPPS(1)PSSMNQR;NSNS(0.008)PPS(0.992)PSSMNQR;NSNSPPS(0.995)PS(0.005)SMNQR;NSNSPPS(1)PSSMNQR;NSNSPPS(0.923)PS(0.076)S(0.001)MNQR;NSNSPPS(0.998)PS(0.002)SMNQR;NS(0.001)NS(0.018)PPS(0.629)PS(0.278)S(0.075)MNQR;NSNSPPS(1)PSSMNQR;NSNS(0.012)PPS(0.987)PS(0.002)SMNQR 413.74 8.06E-133 2293301000 2185280 2225534 2075356 2158856 2195810 1618121 2168650 1739429 1796242 TRUE FALSE 2048507.226 2390314.853 2124584.424 2214255.9 2023359.94 2085246.265 1843481.065 1956600.54 1496437.606 1.368922578 1.597336797 1.419761449 1.479684747 1.352117811 1.393473578 1.231913083 1.307505593 1 20.5131007 1.072799075 0.382303332 0.971305174 1.519697957 0.798558107 0.07070649 0.49322371 0.208055227 0.101164606 0.058383586 11.82494352 -1.072799075 0.548392784 NSPEDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSPEDKR 7 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 0 ; 127.84 0.0061177 500720000 743530 478880 577980 528450 653560 358300 583050 531330 1099560 FALSE TRUE 696993.7845 514336.7735 591689.9585 542010.9217 602232.0339 461735.3935 495627.0653 597667.7201 916036.3326 0.760880065 0.561480757 0.645924116 0.591691511 0.657432476 0.504057947 0.541056122 0.652449798 1 19.8050453 0.959516928 20.40801145 1.000000001 0.600590681 0.745811869 0.071063751 297.267503 149857.029 0.064383009 0.016095752 9.109969601 -0.959516928 -0.399409321 NSPGS(ph)QVASNPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSPGSQVASNPR 12 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 1 NS(0.433)PGS(0.567)QVASNPR 258.68 3.17E-21 496590000 248410 189430 225770 207220 226720 175330 270730 204540 319470 TRUE FALSE 232862.4615 203455.5943 231125.371 212537.616 208914.3257 225944.9248 230136.5498 230077.2692 266148.3931 0.874934689 0.764444196 0.868407914 0.798568098 0.7849543 0.848943411 0.864692614 0.864469879 1 18.02187133 0.579214721 0.693764242 1.002209735 0.817055056 0.702229501 0.035476915 0.739882523 0.628959189 0.035844201 0.01235874 3.795025701 -0.579214721 -0.185154679 NSPLDCGSAS(ph)PNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NSPLDCGSASPNK 13 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 NSPLDCGSAS(1)PNK;NSPLDCGSAS(1)PNK;NSPLDCGSAS(1)PNK 220.72 2.13E-11 301169000 1414300 580124 893630 781210 765200 690102 1124590 713280 748300 TRUE FALSE 1325781.488 623076.9846 914827.3256 801257.1712 705104.2787 889323.2445 955968.1697 802334.5781 623403.8958 2.126681428 0.999475603 1.4674713 1.285293814 1.131055297 1.426560293 1.533465184 1.287022079 1 19.24980765 4.751847721 24.83821829 1.299477896 2.126682016 0.678561524 0.184852115 1287.987095 2407649.474 0.043324209 0.83986308 56473.89223 -4.751847721 0.82720412 NSPLDELEEGEIRS(ph)DSETSKPQESFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSPLDELEEGEIRSDSETSKPQESFEK 27 2 Q9UKL3;A0A087WTW5 Q9UKL3 CASP8AP2 CASP8-associated protein 2 1 NSPLDELEEGEIRS(0.995)DS(0.005)ETSKPQESFEK;NSPLDELEEGEIRS(0.955)DS(0.041)ET(0.003)SKPQESFEK 193.49 1.24E-18 87460000 186562 84323 125289 108512 109534 76139 153250 95143 110067 TRUE FALSE 174885.4174 90566.36266 128260.9142 111296.6016 100931.6415 98119.09329 130271.5852 107021.813 91696.10664 1.907228386 0.987679477 1.398760743 1.213754931 1.100718942 1.070046449 1.420688293 1.167135846 1 16.48457286 4.749251519 24.77841614 1.197625281 1.907228842 0.704430505 0.149146682 780.9947612 1810080.111 0.033991374 0.492420768 56137.2997 -4.749251519 0.709603561 NSPMAQT(ph)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSPMAQTPPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 43 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 NS(0.007)PMAQT(0.993)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 206.29 5.23E-36 165080000 265420 189210 214920 251550 316990 211730 367510 259110 387750 TRUE FALSE 248807.836 203219.3053 220018.0039 258005.1989 292094.8841 272853.0139 312405.2873 291460.4539 323032.02 0.770226543 0.629099571 0.681102771 0.798698528 0.904228887 0.844662439 0.96710316 0.902264902 1 18.30131765 2.924841896 1.567497071 0.928918442 0.672759266 0.796911952 0.05324682 0.140979849 0.701704545 0.018527664 0.020879802 841.0888883 -2.924841896 -0.256159176 NSPNNISGISNPPGT(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSPNNISGISNPPGTPR 17 0 Q9BWW4-2;Q9BWW4;Q9NW25;A0A087WVT6;Q9BWW4-3 Q9BWW4-2 SSBP3 Single-stranded DNA-binding protein 3 1 NSPNNISGISNPPGT(1)PR 188.26 2.28E-17 0 138620 97513 124110 121360 132350 106510 134770 104140 123800 TRUE FALSE 129944.0216 104732.964 127053.9478 124474.3031 121955.7649 137257.708 114562.4896 117142.1082 103136.9802 1.259916873 1.015474408 1.23189517 1.206883339 1.182463987 1.33082923 1.110779949 1.135791527 1 16.65420218 -0.719181666 7.586590059 0.999998547 1.175743145 0.307016075 0.086157 0 0 0.079970779 0.018849293 0.190905453 0.719181666 0.175744598 NSPT(ph)PAT(ph)STESLSPLHNVALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSPTPATSTESLSPLHNVALR 21 0 G5EA48;Q7Z6B7-2;Q7Z6B7 G5EA48 SRGAP1 SLIT-ROBO Rho GTPase-activating protein 1 2 NS(0.002)PT(0.998)PAT(0.498)S(0.409)T(0.093)ESLSPLHNVALR;NSPT(1)PAT(0.506)S(0.415)T(0.079)ESLSPLHNVALR 131.42 2.25E-05 395810000 186168 236473 210093 234694 240442 195999 287770 221229 258820 TRUE FALSE 174516.0772 253981.707 215076.5052 240716.6454 221558.6552 252580.7295 244621.56 248849.9276 215621.27 0.809363924 1.177906554 0.997473511 1.116386363 1.027536176 1.171409154 1.134496425 1.154106586 1 17.71813997 4.748011512 24.9556313 1.100689861 0.809363767 0.640492216 0.06778215 774.9322247 2046209.724 0.015159348 0.194739516 55977.24389 -4.748011512 -0.291326095 NSPTFKS(ph)FEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 NSPTFKSFEEK 11 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 1 NSPTFKS(1)FEEK;NSPTFKS(1)FEEK;NSPTFKS(1)FEEK;NSPTFKS(1)FEEK;NSPTFKS(1)FEEK;NSPTFKS(1)FEEK;NSPTFKS(1)FEEK;NSPTFKS(1)FEEK 226.39 2.89E-12 21203970000 21453800 10404640 12284840 14124740 11582830 5812540 20096200 10230770 16894830 TRUE FALSE 20111044.95 11175010.37 12576242.21 14487204.74 10673161.25 7490525.939 17082961.37 11508104.16 14074973.73 1.428851332 0.793963142 0.893517988 1.029288226 0.758307721 0.532187561 1.213711777 0.81762882 1 23.74662889 4.744400597 24.31022377 0.882483899 1.428851686 0.475602019 0.181158183 390.0852771 1623746.596 0.04120301 0.3651036 55513.75411 -4.744400597 0.546367788 NSPTFKS(ph)FEEKVENLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NSPTFKSFEEKVENLK 16 2 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 1 NSPT(0.001)FKS(0.999)FEEKVENLK;NSPTFKS(1)FEEKVENLK;NSPTFKS(1)FEEKVENLK;NSPT(0.024)FKS(0.976)FEEKVENLK 222.51 7.54E-15 6809125000 7146907 3724639 4049956 5255155 5235402 1550642 6258454 3154508 10820930 TRUE FALSE 6699594.848 4000415.147 4146022.869 5390011.174 4824234.646 1998287.173 5320056.923 3548355.268 9014846.877 0.743173449 0.443758524 0.459910515 0.597903797 0.535143271 0.221666236 0.590143903 0.393612373 1 23.10387156 -1.188404599 4.928202146 1.000051124 0.489106931 0.564397063 0.138350205 6.93E-05 1.14E-05 0.119510939 0.02816619 0.064803043 1.188404599 -0.510944193 NSPTFKS(ph)FEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NSPTFKSFEER 11 1 Q16890-5;E9PPQ1;J3KNE7;Q16890;E9PNK6 Q16890-5 TPD52L1 Tumor protein D53 1 NSPTFKS(1)FEER;NSPTFKS(1)FEER;NSPTFKS(1)FEER;NSPTFKS(1)FEER;NS(0.005)PT(0.089)FKS(0.906)FEER 169.37 1.03E-05 3314770000 2934150 2711910 2326650 3003040 2583660 1159420 3555480 2307330 5626370 TRUE FALSE 2750506.789 2912702.638 2381839.237 3080103.091 2380749.766 1494125.732 3022368.781 2595405.23 4687292.499 0.586800757 0.62140407 0.508148198 0.657117748 0.507915767 0.318760933 0.64480055 0.55371096 1 22.16032339 0.237373465 1.538701924 1.000114746 0.54811929 0.682614834 0.096498397 5.163827489 9.719142197 0.088840007 0.02528262 1.72732264 -0.237373465 -0.451995456 NSPTPATS(ph)TESLSPLHNVALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSPTPATSTESLSPLHNVALR 21 0 G5EA48;Q7Z6B7-2;Q7Z6B7 G5EA48 SRGAP1 SLIT-ROBO Rho GTPase-activating protein 1 1 NS(0.005)PT(0.016)PAT(0.222)S(0.535)T(0.222)ES(0.001)LSPLHNVALR;NSPT(0.004)PAT(0.164)S(0.81)T(0.021)ESLSPLHNVALR 176.53 1.86E-13 106260000 118689 119106 116798 122857 143792 97958 137112 105905 145206 TRUE FALSE 111260.4674 127924.7322 119568.5037 126009.7186 132499.1563 126236.8844 116553.3285 119127.4724 120970.1805 0.919734656 1.057489801 0.988413039 1.041659342 1.095304279 1.043537208 0.963488092 0.984767253 1 16.88429194 1.740198201 12.73718919 0.980968656 1.027424704 0.146494199 0.046876305 0.127343596 166.7325442 0.020876178 0.011459388 54.97917281 -1.740198201 0.046456048 NSQDDYDEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSQDDYDEER 10 0 O76094-2;O76094;R4GNC1;D6RDY6 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 136.5 0.00026993 161600000 138100 137910 139970 138040 132040 117310 161360 119470 151900 FALSE TRUE 129456.5675 148120.9999 143290.1545 141582.3401 121670.111 151175.4926 137165.566 134386.0925 126546.9087 1.022992729 1.170482957 1.132308612 1.118813107 0.96146253 1.194620194 1.083910839 1.061946861 1 16.94931274 2.96639413 24.89437391 1.07439022 1.12528386 0.080523428 0.071136078 1321.493897 978929.6754 0.020246398 0.021487807 925.5377354 -2.96639413 0.050893639 NSQEDS(ph)EDS(ph)EDKDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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(0.103)QEDS(0.897)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK 228.68 3.21E-13 11455070000 29548210 7044670 11650310 12572820 14799580 8666280 16066600 8449280 13455750 TRUE FALSE 27698840.28 7566264.697 11926660.85 12895459.85 13637280.69 11168094.35 13657562.49 9504191.207 11209898.4 2.47092697 0.674962826 1.063940139 1.150363669 1.216539187 0.996270792 1.218348463 0.847839193 1 23.41826987 4.747239044 24.9994998 1.028050559 2.470927699 0.883254967 0.165641469 380.4134191 1095813.719 0.040943372 0.486409238 55877.76714 -4.747239044 1.44287714 NSQEDS(ph)EDSEDKDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 NSQEDS(1)EDSEDKDVK;NSQEDS(0.888)EDS(0.112)EDKDVK;NSQEDS(0.949)EDS(0.051)EDKDVK;NSQEDS(0.998)EDS(0.002)EDKDVK;NSQEDS(0.999)EDS(0.001)EDKDVK;NSQEDS(1)EDSEDKDVK;NSQEDS(1)EDSEDKDVK 264.59 2.34E-25 6612640000 10611860 3139820 5045440 4914720 4899320 3155690 6419850 3497740 5758460 TRUE FALSE 9947682.625 3372295.54 5165120.219 5040840.036 4514547.17 4066686.475 5457253.091 3934440.538 4797335.825 2.073584795 0.702951735 1.0766643 1.050758217 0.941052979 0.847696852 1.137559114 0.820130314 1 22.193802 4.746534213 24.98757846 0.95510562 2.073585345 0.880673005 0.130283816 317.4962682 994943.7326 0.029876878 0.333068124 55787.15491 -4.746534213 1.118479725 NSQEDSEDS(ph)EDKDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 NSQEDS(0.001)EDS(0.999)EDKDVK;NSQEDS(0.057)EDS(0.943)EDKDVK 312.93 8.53E-56 652190000 1748630 543190 811710 863830 819670 513400 1123650 571990 959310 TRUE FALSE 1639186.37 583408.3528 830964.1445 885997.3403 755296.4246 661610.2456 955169.114 643404.2106 799194.9636 2.051046921 0.729995032 1.039751478 1.108612267 0.945071552 0.827845865 1.195164081 0.805065397 1 19.60818797 4.74620905 24.99645727 0.965209536 2.051047442 0.855040811 0.141600665 335.6571162 1096961.99 0.032667994 0.350006886 55745.40175 -4.74620905 1.085837905 NSQGSEMFGDDDKRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NSQGSEMFGDDDKRK 15 2 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;; 196.22 5.08E-09 620177000 640450 343847 437171 494884 512261 293452 650148 397114 566195 FALSE TRUE 600365.3777 369305.7897 447540.9026 507583.5613 472030.0874 378166.8286 552664.3431 446694.5571 471693.3967 1.272787327 0.782936103 0.9487962 1.07608791 1.000713791 0.801721693 1.171660123 0.94700193 1 18.84748988 1.724258817 24.99999991 1.051439847 0.958498923 0.018076818 0.148282119 2.393935358 4167.3859 0.063956597 0.035467134 52.99791899 -1.724258817 -0.092940924 NSQKHS(ph)PTSEPTPPGDALPPVS(ph)SPHTHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NSQKHSPTSEPTPPGDALPPVSSPHTHR 28 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 2 NS(0.297)QKHS(0.602)PT(0.07)S(0.031)EPTPPGDALPPVS(0.538)S(0.448)PHT(0.014)HR;NS(0.431)QKHS(0.473)PT(0.094)S(0.002)EPTPPGDALPPVS(0.437)S(0.353)PHT(0.209)HR;NS(0.09)QKHS(0.431)PT(0.178)S(0.301)EPT(0.001)PPGDALPPVS(0.701)S(0.295)PHT(0.004)HR;NS(0.306)QKHS(0.5)PT(0.081)S(0.112)EPT(0.001)PPGDALPPVS(0.512)S(0.47)PHT(0.018)HR;NS(0.117)QKHS(0.346)PT(0.268)S(0.268)EPT(0.002)PPGDALPPVS(0.493)S(0.493)PHT(0.015)HR 171.29 1.64E-12 4541660000 3197310 3001100 3542720 4330670 4092970 2386220 4150030 2651690 3305060 TRUE FALSE 2997196.074 3223304.567 3626754.991 4441802.324 3771524.646 3075082.977 3527771.528 2982759.334 2753424.134 1.088534104 1.170653125 1.317179924 1.613192195 1.369757968 1.116821393 1.281230699 1.083290909 1 21.39279543 1.154715174 1.311736282 0.996902835 1.292419237 0.314564511 0.147912106 0.544070142 1.873851405 0.142897284 0.04436032 14.27957147 -1.154715174 0.295516402 NSQKHS(ph)PTSEPTPPGDALPPVSSPHT(ph)HR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSQKHSPTSEPTPPGDALPPVSSPHTHR 28 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 2 NS(0.102)QKHS(0.357)PT(0.264)S(0.264)EPT(0.013)PPGDALPPVS(0.28)S(0.28)PHT(0.44)HR 68.074 0.020836 670930000 220080 199020 244030 302810 264530 159000 282760 180260 225780 TRUE FALSE 206305.5857 213755.6479 249818.5068 310580.6173 243754.8809 204900.7189 240362.763 202765.8578 188095.8594 1.096810883 1.136418678 1.328144637 1.651182638 1.295907744 1.089341996 1.27787376 1.077992139 1 17.52110857 1.164524179 1.157321532 0.998192886 1.282288626 0.265564023 0.160187857 0.676087839 1.866868498 0.154787371 0.049939259 14.60576062 -1.164524179 0.28409574 NSQKHS(ph)PTSEPTPPGDALPPVSSPHTHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NSQKHSPTSEPTPPGDALPPVSSPHTHR 28 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 NS(0.072)QKHS(0.7)PT(0.191)S(0.038)EPTPPGDALPPVSSPHTHR;NS(0.178)QKHS(0.64)PT(0.178)S(0.003)EPTPPGDALPPVSSPHTHR;NS(0.389)QKHS(0.567)PT(0.022)S(0.022)EPTPPGDALPPVSSPHTHR 157.15 3.35E-09 3372280000 1021530 1360700 1450140 1454450 1455920 1152030 2041860 1379000 1532360 TRUE FALSE 957594.2608 1461447.644 1484538.006 1491773.649 1341577.916 1484602.359 1735702.049 1551171.186 1276599.217 0.750113464 1.144797541 1.162884942 1.168552847 1.050899843 1.162935352 1.359629574 1.215080791 1 20.28387424 4.745558061 3.873200318 1.177139063 0.705622158 0.638791408 0.095792492 0.16825005 5.013964209 0.023730391 0.227310707 55661.90444 -4.745558061 -0.471516905 NSQPNRYT(ph)NR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSQPNRYTNR 10 1 P50750;P50750-2 P50750 CDK9 Cyclin-dependent kinase 9 1 NSQPNRYT(1)NR;NSQPNRYT(1)NR 137.62 0.00013942 568030000 398580 464230 338220 398890 550640 227370 592170 348020 805980 TRUE FALSE 373633.5893 498602.0722 346242.7381 409126.1927 507394.9556 293008.028 503379.6059 391471.0631 671456.7312 0.556452221 0.742567688 0.515659047 0.609311328 0.755662922 0.436376634 0.749682865 0.583017557 1 19.35693491 -2.125758756 0.543909411 1.442891395 0.621614572 0.560486125 0.105903529 81.44438841 6.321560898 44.40497299 0.040783974 0.007485852 2.125758756 -0.821276823 NSRPEANEALER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSRPEANEALER 12 1 Q9Y696 Q9Y696 CLIC4 Chloride intracellular channel protein 4 0 149.02 6.10E-05 579480000 468110 447670 463730 498400 502360 294180 599220 445020 555630 FALSE TRUE 438811.8307 480815.9526 474729.8946 511189.7878 462906.672 379104.9904 509372.5239 500581.7266 462891.7635 0.947979345 1.038722204 1.025574296 1.104339779 1.000032207 0.818992733 1.100413885 1.081422842 1 18.82031537 4.74741764 22.60190875 1.021957556 0.947979199 0.074724721 0.08091838 858.3131677 2190101.135 0.018637623 0.204622898 55900.75072 -4.74741764 -0.073978357 NSS(ph)EASSGDFLDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSSEASSGDFLDLK 14 0 Q9UK76;J3KT51;Q9UK76-2;Q9UK76-3;J3KSH8 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 NS(0.218)S(0.782)EASSGDFLDLK 251.26 6.78E-19 174830000 693020 305170 467700 430130 336940 348810 585230 331000 275710 TRUE FALSE 649645.1153 327765.1043 478794.0649 441167.864 310478.0916 449505.7845 497480.1945 372326.0786 229692.2198 2.828328777 1.426975213 2.084502754 1.920691368 1.351713575 1.956991773 2.16585566 1.620978189 1 17.80934246 -2.092599207 0.432407823 2.44E-13 1.919186032 0.336723588 0.413576457 70.39577806 4.456704059 69.60636902 0.214462916 0.008079803 2.092599207 1.919186032 NSS(ph)GPQSGWMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSSGPQSGWMK 11 0 F8VXG7;Q99590-2;Q99590 F8VXG7 SCAF11 Protein SCAF11 1 NS(0.007)S(0.992)GPQSGWMK;NS(0.075)S(0.923)GPQS(0.002)GWMK 94.059 0.0092169 119774000 498490 449460 422590 479380 611580 279970 454330 424010 618090 TRUE FALSE 467290.4007 482738.4861 432614.0344 491681.7024 563548.9738 360792.7941 386207.4343 476948.5819 514926.786 0.907489013 0.93748956 0.840146689 0.954857498 1.094425439 0.700668141 0.750023974 0.926245429 1 18.97400779 2.22229132 24.99958909 0.811157671 0.931408722 0.150232977 0.105889962 353.9822861 543929.7987 0.038077975 0.028206188 166.8365958 -2.22229132 0.120251051 NSS(ph)PAPPQPAPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NSSPAPPQPAPGK 13 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 NSS(1)PAPPQPAPGK;NS(0.003)S(0.997)PAPPQPAPGK;NS(0.056)S(0.944)PAPPQPAPGK;NSS(1)PAPPQPAPGK;NS(0.014)S(0.986)PAPPQPAPGK;NS(0.011)S(0.989)PAPPQPAPGK 249.58 1.43E-17 2773770000 7979990 4695690 5817470 5434720 5014380 4488240 7725550 5076380 5354540 TRUE FALSE 7480536.671 5043363.773 5955463.136 5574184.116 4620570.822 5783922.028 6567175.498 5710177.217 4460832.682 1.67693729 1.130587971 1.335056381 1.249583769 1.035809041 1.296601428 1.472186017 1.280069804 1 22.08888161 4.749027855 24.45838236 1.252258481 1.676937614 0.489348345 0.142695858 1039.220756 2428241.092 0.033814602 0.471361008 56108.39616 -4.749027855 0.424679134 NSS(ph)SESAIVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSSSESAIVPK 11 0 Q5THJ4-2;Q5THJ4;H3BLS7;A0A2R8YD87 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 NS(0.004)S(0.974)S(0.014)ES(0.007)AIVPK 132.09 0.000199 242900000 341390 242870 273290 271400 296480 205370 344100 233280 279100 TRUE FALSE 320023.0093 260852.3475 279772.5679 278364.5835 273195.6567 264656.9851 292505.3995 262405.5215 232516.4069 1.376345925 1.121866413 1.203237963 1.197182544 1.174952169 1.138229291 1.257998966 1.12854626 1 17.82697299 -4.798840837 0.241456856 7.70E-14 1.214443296 0.463830672 0.071417938 146.0359699 1.593950274 71.64858506 0.10260417 1.59E-05 4.798840837 1.214443296 NSS(ph)VPFGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSSVPFGSK 9 0 Q9BXT8-2 Q9BXT8-2 RNF17 RING finger protein 17 1 NSS(0.964)VPFGS(0.036)K 82.029 0.020571 467870000 613470 810560 808100 840360 854020 724330 938560 783220 757600 TRUE FALSE 575074.0078 870574.7058 827268.5136 861925.0603 786948.7142 933432.3125 797831.6412 881006.7411 631151.6657 0.911150265 1.379343117 1.310728559 1.365638573 1.246845658 1.478935038 1.264088625 1.395871688 1 19.2676272 -1.13070367 3.704744104 0.999823254 1.308864665 0.264663592 0.152284862 15122416.05 28004528.45 34094.68786 0.033215535 0.07401101 1.13070367 0.309041411 NSSLGS(ph)PSNLCGS(ph)PPGSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSSLGSPSNLCGSPPGSIR 19 0 Q9C0B0 Q9C0B0 UNK RING finger protein unkempt homolog 2 NSS(0.001)LGS(0.999)PSNLCGS(0.986)PPGS(0.014)IR;NS(0.018)S(0.14)LGS(0.839)PS(0.01)NLCGS(0.993)PPGSIR 141.08 2.47E-07 380160000 510900 485140 486030 521210 576900 385780 545190 438230 601860 TRUE FALSE 478923.681 521060.2704 497558.8611 534585.131 531592.6011 497148.4234 463443.8208 492943.9802 501405.6778 0.955162062 1.039198983 0.992327935 1.066172871 1.06020459 0.991509361 0.924289136 0.983124049 1 18.93561881 1.999992412 24.99999289 0.960018867 1.022986125 0.29522128 0.037211331 0.264372317 864504.0735 0.013271777 0.00970184 99.99825288 -1.999992412 0.062967259 NSSLGSPSNLCGS(ph)PPGSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NSSLGSPSNLCGSPPGSIR 19 0 Q9C0B0 Q9C0B0 UNK RING finger protein unkempt homolog 1 NSSLGSPSNLCGS(1)PPGSIR;NSSLGSPSNLCGS(1)PPGSIR;NSSLGSPSNLCGS(1)PPGSIR;NSSLGSPSNLCGS(0.997)PPGS(0.003)IR;NSSLGSPSNLCGS(1)PPGSIR;NSSLGSPSNLCGS(1)PPGSIR 387.26 7.19E-127 2481140000 1106640 932330 998000 1004200 1108580 800693 1268570 906114 1095310 TRUE FALSE 1037377.378 1001360.683 1021673.031 1029969.472 1021516.599 1031840.071 1078359.705 1019244.328 912495.685 1.136857297 1.09738676 1.119646973 1.128739006 1.119475539 1.130788987 1.181769649 1.116985367 1 19.79945821 0.960239347 24.21292969 1 1.129732391 0.788223972 0.021118455 3009.637274 1832772.054 0.023527553 0.005881888 9.125136016 -0.960239347 0.129732392 NSSLLS(ph)FDNEDENE ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NSSLLSFDNEDENE 14 0 Q96AT1 Q96AT1 KIAA1143 Uncharacterized protein KIAA1143 1 NSSLLS(1)FDNEDENE;NSSLLS(1)FDNEDENE;NSSLLS(1)FDNEDENE 270.61 6.46E-33 110270000 257857 238337 228871 237418 148103 146209 322124 168947 216705 TRUE FALSE 241718.1907 255983.7195 234299.9282 243510.5478 136471.5878 188417.1648 273824.4967 190040.4048 180535.5355 1.338895359 1.417913203 1.297805042 1.348823361 0.755926457 1.043656941 1.516734619 1.052648191 1 17.46192331 2.934118797 24.99998804 1.128448428 1.353744138 0.322857914 0.190449875 291.9432863 110783.3658 0.061357974 0.065079994 859.2485288 -2.934118797 0.22529571 NSSNTSVGS(ph)PSNTIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSSNTSVGSPSNTIGR 16 0 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 NSSNTS(0.001)VGS(0.998)PS(0.001)NTIGR 281.98 1.58E-35 264000000 406230 345490 373900 360490 391160 272250 414460 323510 413690 TRUE FALSE 380804.7894 371070.4391 382769.0846 369740.7837 360439.8715 350844.1554 352315.5707 363900.9356 344642.4665 1.104927066 1.076682287 1.110626582 1.072824215 1.045837082 1.017994558 1.022263955 1.055879559 1 18.39474095 2.739392788 2.192924717 1.025544015 1.09468959 0.790879922 0.016635051 0.128728744 1.221285348 0.005488458 0.005452042 548.773066 -2.739392788 0.069145574 NSSQSGGKPGS(ph)SPITK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSSQSGGKPGSSPITK 16 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 NS(0.001)S(0.001)QS(0.001)GGKPGS(0.498)S(0.498)PIT(0.001)K 55.127 0.083241 442270000 305950 198960 247980 219390 238680 164820 297670 232780 331150 TRUE FALSE 286801.1356 213691.2054 253862.2027 225019.9188 219935.0356 212400.8584 253037.1469 261843.0954 275878.9257 1.039590592 0.774583288 0.920194256 0.815647365 0.79721579 0.769906066 0.917203611 0.949123224 1 18.07367573 1.375619534 2.781473623 0.980955237 0.84811979 0.278266431 0.080807545 0.318671062 4.164197683 0.062019844 0.019436323 23.74758954 -1.375619534 -0.132835448 NSSQSGGKPGSS(ph)PITK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NSSQSGGKPGSSPITK 16 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 NSSQSGGKPGS(0.186)S(0.814)PITK;NSSQSGGKPGS(0.326)S(0.674)PITK;NSSQSGGKPGS(0.252)S(0.746)PIT(0.001)K;NSSQSGGKPGS(0.197)S(0.803)PITK;NSSQSGGKPGS(0.317)S(0.682)PIT(0.001)K 213.48 1.10E-12 7079570000 5093250 2459170 3533870 3261830 3501910 2448830 4699170 3100530 4690320 TRUE FALSE 4774472.574 2641249.506 3617695.065 3345534.08 3226884.115 3155767.468 3994573.083 3487637.996 3907475.291 1.221881706 0.675947846 0.925839524 0.85618816 0.825823294 0.807623141 1.022290043 0.892555355 1 21.89780532 1.73827696 24.99970193 0.968189694 0.862587847 0.059991362 0.142204998 0.124918387 7635.502826 0.059481777 0.032985666 54.73649196 -1.73827696 -0.105601847 NSSS(ph)PVSLDAALPESSNVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSSSPVSLDAALPESSNVYR 20 0 Q70EL1-7;Q70EL1;H7C296;H7C1E9;Q70EL1-6;R4GN32 Q70EL1-7 USP54 Inactive ubiquitin carboxyl-terminal hydrolase 54 1 NS(0.004)S(0.175)S(0.821)PVSLDAALPESSNVYR;NSS(0.015)S(0.985)PVSLDAALPESSNVYR 238.64 1.29E-29 147178000 227993 193540 210542 200528 211984 188431 241880 199655 185581 TRUE FALSE 213723.3251 207869.903 215536.1557 205673.888 195335.6317 242827.9708 205612.3395 224582.3662 154606.3322 1.382371097 1.344510927 1.394096559 1.330307013 1.263438754 1.570621121 1.329908915 1.452607814 1 17.23823988 -1.276755916 4.003122589 0.999515845 1.380384966 0.679511488 0.082742494 5731487.216 1844463.881 24091.0546 0.017300463 0.052874233 1.276755916 0.380869122 NSSS(ph)PVSPASVPGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSSSPVSPASVPGQR 15 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 NSS(0.001)S(0.999)PVSPASVPGQR;NSS(0.005)S(0.995)PVSPASVPGQR 278.24 1.38E-33 1409570000 1524830 1162760 1400890 1206760 1531970 1271140 1897760 1554560 1961000 TRUE FALSE 1429393.612 1248851.96 1434119.772 1237727.505 1411655.256 1638097.483 1613208.506 1748650.238 1633696.431 0.874944442 0.764433304 0.877837366 0.757623926 0.864086637 1.002693922 0.98745916 1.070364239 1 20.6397085 2.293903785 3.426034355 1.01362223 0.818610906 0.818781366 0.04423489 0.088669147 2.126148204 0.015415773 0.012036653 196.7450366 -2.293903785 -0.195011324 NSSTETDQQPHS(ph)PDSSSSVHSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSSTETDQQPHSPDSSSSVHSIR 23 0 Q92613 Q92613 JADE3 Protein Jade-3 1 NSSTETDQQPHS(1)PDSSSSVHSIR;NSSTETDQQPHS(1)PDSSSSVHSIR 205.73 2.50E-24 945840000 207151 356680 349840 352380 393270 280370 390590 317970 415390 TRUE FALSE 194185.7887 383088.9583 358138.37 361422.6674 362384.1606 361308.2676 332024.6556 357669.2544 346058.7255 0.561135363 1.107005633 1.034906343 1.044396921 1.047175332 1.044066342 0.959445987 1.033550748 1 18.40065736 4.743889789 24.9999405 1.034901736 0.561135164 0.941064289 0.037174218 140.9238173 661074.3399 0.009739259 0.084171225 55448.49838 -4.743889789 -0.473766572 NSSVPFGS(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSSVPFGSK 9 0 Q9BXT8-2 Q9BXT8-2 RNF17 RING finger protein 17 1 NS(0.001)S(0.404)VPFGS(0.594)K 61.78 0.09119 341490000 308420 401260 391010 368200 394570 335860 430350 392860 403850 TRUE FALSE 289116.5427 430969.7079 400284.9418 377648.6354 363582.0638 432817.3298 365823.0127 441909.4358 336444.826 0.859328248 1.280952104 1.189749138 1.122468251 1.080658806 1.286443709 1.087319478 1.313467771 1 18.36001041 -1.717915929 7.348441571 0.998608573 1.164565488 0.109298595 0.132980984 0.002678244 0.000102809 0.113757128 0.026602714 0.019146265 1.717915929 0.165956915 NSSYFVEWIPNNVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSSYFVEWIPNNVK 14 0 Q13509;A0A0B4J269;Q13509-2;Q5JP53;P07437;Q5ST81;P68371;Q13885;Q9BVA1;P04350;K7ESM5;Q9BUF5 Q13509;Q5JP53;P68371;Q13885;Q9BVA1;P04350;K7ESM5 TUBB3;TUBB;TUBB4B;TUBB2A;TUBB2B;TUBB4A;TUBB6 Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-2B chain;Tubulin beta-4A chain;Tubulin beta-6 chain 0 ; 318.47 1.21E-55 596700000 3074200 2298520 2602400 2434600 2773000 1779550 3205300 2421330 3429200 FALSE TRUE 2881791.31 2468704.812 2664130.157 2497075.958 2555219.766 2293277.196 2724695.022 2723638.381 2856844.367 1.008732342 0.864136962 0.932542979 0.874067901 0.89442036 0.802730881 0.953742897 0.953373034 1 21.44599101 1.552456012 9.096313754 0.968594049 0.894557269 0.298423549 0.053208281 0.140722038 18.66613148 0.026282792 0.012243985 35.6825606 -1.552456012 -0.07403678 NSSYVHGGLDSNGKPADAVYGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSSYVHGGLDSNGKPADAVYGQK 23 1 Q13283;E5RH42;E5RIZ6;E5RJU8;Q13283-2;E5RIF8;E5RI46 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 233.91 2.82E-37 136300000 225950 184970 217380 222760 227750 166180 312580 205270 275160 FALSE TRUE 211808.1928 198665.3713 222536.3563 228476.3987 209863.4337 214153.4683 265711.5309 230898.4114 229234.0184 0.923982375 0.866648731 0.970782425 0.996694995 0.915498647 0.934213298 1.159127832 1.007260672 1 17.80646163 1.765787553 25 1.07049453 0.932613331 0.512471862 0.054882193 12.56245184 11542.05722 0.024113517 0.013373228 58.31597664 -1.765787553 -0.137881199 NST(ph)PSEPGSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NSTPSEPGSGR 11 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 NS(0.042)T(0.927)PS(0.031)EPGSGR;NS(0.016)T(0.983)PSEPGSGR;NS(0.226)T(0.774)PSEPGSGR;NS(0.147)T(0.851)PS(0.002)EPGSGR 241.22 1.15E-14 2526060000 2293950 1706420 1916300 1807840 2222830 1640400 2373670 1890660 3232570 TRUE FALSE 2150375.764 1832765.112 1961755.541 1854232.235 2048257.898 2113956.85 2017760.22 2126713.063 2693033.184 0.798495829 0.680557939 0.728455762 0.688529293 0.760576554 0.784972448 0.749251896 0.789709193 1 21.36080058 -0.3610691 0.412706253 1.059229627 0.716997583 0.834667498 0.036095438 2.459248549 0.433812383 0.244435693 0.021579808 0.435442585 0.3610691 -0.342232044 NSTFSEIFKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSTFSEIFKK 10 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 179.19 3.42E-06 3500300000 3156700 2969900 2274420 2148150 4409200 1654120 3290900 3376900 5462700 FALSE TRUE 2959127.782 3189794.486 2328370.316 2203275.166 4062919.218 2131637.592 2797460.096 3798513.398 4550940.08 0.650223411 0.700908918 0.511624033 0.484136272 0.892764824 0.468395003 0.614699391 0.834665659 1 22.11773316 1.062377801 3.205993997 0.996393763 0.612333886 0.529565849 0.122803428 0.159856748 3.391290421 0.108145444 0.028445613 11.54457105 -1.062377801 -0.384059877 NSTGGTSVGWDS(ph)PPASPLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSTGGTSVGWDSPPASPLQR 20 0 Q13424-2;Q13424 Q13424-2 SNTA1 Alpha-1-syntrophin 1 NSTGGTSVGWDS(1)PPASPLQR 285.46 4.50E-45 115640000 193430 169260 188970 182370 185930 138890 185670 132540 208330 TRUE FALSE 181323.5616 181792.1865 193452.4576 187049.923 171327.8078 178985.2883 157830.5072 149087.9108 173558.3771 1.044741052 1.047441152 1.114624721 1.077734916 0.987148017 1.031268506 0.909379943 0.859007287 1 17.40506148 2.086789332 1.44141835 0.91428749 1.071029969 0.618198491 0.047013837 0.238125534 0.934723169 0.028769949 0.014730474 122.1207133 -2.086789332 0.156742479 NSTPSEPGS(ph)GR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NSTPSEPGSGR 11 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 NSTPS(0.125)EPGS(0.875)GR 138.19 6.57E-05 209450000 459180 412010 400990 402430 461940 336550 498620 348660 458620 TRUE FALSE 430440.7435 442515.6491 410501.6722 412757.0351 425661.0958 433706.5216 423856.56 392190.9685 382073.3592 1.126591878 1.15819551 1.074405379 1.080308337 1.114082114 1.135139394 1.109359105 1.026480803 1 18.54349014 -4.99999993 0.134027681 0.613330078 1.152308536 0.601484383 0.030804474 105.2800378 0.880627703 10.75964474 0.220372189 1.00E-05 4.99999993 0.538978458 NSTWSGESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSTWSGESK 9 0 P19338 P19338 NCL Nucleolin 0 ; 110.39 0.0053396 683500000 388290 368640 356550 376790 410440 274280 423710 331500 388120 FALSE TRUE 363987.622 395934.4892 365007.5344 386459.0693 378205.698 353460.1834 360178.619 372888.5047 323340.2646 1.125710782 1.224513407 1.128865082 1.195208613 1.16968327 1.093152391 1.113930612 1.153238695 1 18.30269365 -1.467396439 0.203051092 0.849881684 1.195574971 0.634942963 0.036974651 14.52197733 0.539766801 1.207016447 0.096345399 0.03408816 1.467396439 0.345693287 NSVLSDPGLDS(ph)PRT(ph)SPVIMAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSVLSDPGLDSPRTSPVIMAR 21 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 2 NSVLSDPGLDS(1)PRT(0.661)S(0.339)PVIMAR;NS(0.009)VLS(0.008)DPGLDS(0.977)PRT(0.573)S(0.433)PVIMAR 146.17 2.55E-07 216497000 64889 53410 68941 55787 71393 58291 71046 57046 85146 TRUE FALSE 60827.71332 57364.53197 70576.31308 57218.58887 65786.08177 75118.66542 60393.31186 64168.31867 70934.58254 0.857518451 0.808696265 0.994949298 0.806638833 0.927419031 1.058985092 0.851394478 0.904612622 1 16.11420153 4.084192451 5.209982509 0.927660183 0.834463154 0.241573391 0.073973226 0.306084611 12.41559256 0.017402504 0.038805974 12139.26666 -4.084192451 -0.093197029 NSVLSDPGLDS(ph)PRTS(ph)PVIMAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NSVLSDPGLDSPRTSPVIMAR 21 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 2 NSVLSDPGLDS(1)PRT(0.112)S(0.888)PVIMAR;NSVLSDPGLDS(1)PRT(0.04)S(0.96)PVIMAR;NSVLSDPGLDS(1)PRT(0.245)S(0.755)PVIMAR;NSVLSDPGLDS(1)PRT(0.183)S(0.817)PVIMAR 205.73 2.62E-22 1332990000 390751 327368 359109 355955 414617 279340 406447 327562 440532 TRUE FALSE 366294.5924 351606.6673 367627.2351 365089.4079 382054.6533 359980.9233 345504.0456 368458.8368 367004.3633 0.998066043 0.958044924 1.001697178 0.9947822 1.041008477 0.980862789 0.941416725 1.003963096 1 18.48543769 3.958787017 22.57304073 0.990478088 0.975781113 0.044844622 0.02641735 438.5619158 539956.7503 0.007255132 0.013125351 9094.671491 -3.958787017 -0.014696975 NSWGEPWGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NSWGEPWGER 10 0 Q9UBR2 Q9UBR2 CTSZ Cathepsin Z 0 ;;; 219.35 1.48E-08 1121100000 1614740 1627470 1553900 1647300 1716030 1164530 1827280 1438210 1106700 FALSE TRUE 1513676.306 1747969.572 1590759.242 1689572.507 1581259.926 1500710.906 1553296.328 1617773.684 921984.6204 1.641758737 1.895877147 1.725364183 1.83253871 1.715061066 1.627696247 1.684731278 1.754664501 1 19.81438316 -2.327432828 0.331713314 4.16E-11 1.787795872 0.887814243 0.08195461 13.56909618 0.577556805 10.06192114 0.065875142 0.004705082 2.327432828 1.787795872 NSYVAGQYDDAASYQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NSYVAGQYDDAASYQR 16 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 507.21 7.43E-258 1330920000 706450 635890 695360 685770 776710 530390 862670 624410 863070 FALSE TRUE 662234.5555 682971.9572 711854.2676 703368.0192 715710.3297 683504.9828 733320.6421 702368.963 719018.0414 0.921026341 0.949867622 0.990036726 0.978234173 0.995399682 0.950608947 1.019891852 0.9768447 1 19.45566845 7.126439448 0.520142691 0.991575331 3.70E-11 0.614283909 0.017845571 27.6075727 0.704992684 0.008137888 27.51286636 13379486.57 -7.126439448 -0.991575331 NT(ph)PSQHSHSIQHS(ph)PER ddPTM_SK-BR-3_Pertuzumab_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(0.982)PS(0.018)QHSHS(0.212)IQHS(0.788)PER;NT(0.998)PS(0.002)QHSHS(0.001)IQHS(0.999)PER;NT(1)PSQHSHSIQHS(1)PER;NT(0.985)PS(0.015)QHS(0.003)HS(0.017)IQHS(0.98)PER;NT(0.992)PS(0.007)QHS(0.014)HS(0.04)IQHS(0.946)PER;NT(0.999)PS(0.001)QHSHSIQHS(1)PER 191.2 1.34E-09 1249397000 407766 604178 610147 634860 695759 559818 827795 618782 756128 TRUE FALSE 382244.6539 648911.9678 624619.975 651151.5824 641116.8947 721428.3687 703674.8246 696038.2948 629925.352 0.606809446 1.030141057 0.991577769 1.033696422 1.017766459 1.145260095 1.117076527 1.104953615 1 19.26482135 5.067893881 1.753955747 1.063736805 1.61E-10 0.869905283 0.054116806 0.98909466 1.439837829 0.01529247 2.320251139 116921.366 -5.067893881 -1.063736805 NTAELQPESGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NTAELQPESGKR 12 1 O15355 O15355 PPM1G Protein phosphatase 1G 0 ; 98.531 0.0069053 680090000 804250 661330 715440 748030 774290 609490 867470 677620 1046200 FALSE TRUE 753913.4281 710295.5613 732410.5747 767225.7162 713480.3867 785439.8688 737400.9267 762222.3486 871582.4613 0.864993803 0.814949351 0.840322755 0.880267502 0.818603424 0.901165298 0.846048377 0.874526947 1 19.73327764 -5 0.212342299 1.734586317 0.82980416 0.76740654 0.025487254 61.48529105 0.613856195 19.20130536 0.047349039 1.00E-05 5 -0.904782157 NTASQEDKDDSVVLPLGADTLTHNLGIPVLVVCTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NTASQEDKDDSVVLPLGADTLTHNLGIPVLVVCTK 35 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 133.73 1.12E-08 90195000 285840 163930 198980 196330 208030 127740 254730 158600 233020 FALSE TRUE 267949.7846 176067.5478 203699.8996 201368.1602 191692.163 164616.4643 216535.6013 178401.5591 194127.4566 1.380277624 0.906968807 1.049310093 1.037298709 0.987455182 0.847981358 1.115430064 0.918991894 1 17.56664466 4.745996942 24.98411134 0.989337567 1.380277811 0.723055293 0.077192573 461.4835274 1550426.582 0.017011396 0.177306402 55718.18251 -4.745996942 0.390940245 NTCEHIYDFPPLSEELISEMIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NTCEHIYDFPPLSEELISEMIR 22 0 K7EN86;Q13432 K7EN86 UNC119 Protein unc-119 homolog A 0 63.056 0.034974 11542000 5955.8 7539.2 7725.9 9166.5 9049.8 4561.7 7485.3 7348.5 8425.6 FALSE TRUE 5583.037109 8097.410213 7909.161996 9401.727909 8339.065213 5878.588737 6362.948755 8265.976401 7019.312929 0.795382278 1.153590144 1.126771534 1.339408572 1.188017303 0.837487771 0.906491678 1.177604772 1 12.77711411 2.253519601 24.99952913 0.960694674 1.135909245 0.152824664 0.158883194 351.913109 588118.0284 0.053472128 0.044570056 179.2749462 -2.253519601 0.175214571 NTDDDRPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NTDDDRPPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 160.75 5.93E-05 797179000 1536925 1417967 1565710 1527420 1482542 1296227 1760638 1412255 1373326 FALSE TRUE 1440731.608 1522954.752 1602849.381 1566616.183 1366109.132 1670426.692 1496646.677 1588578.146 1144109.019 1.259260774 1.331127303 1.40095861 1.369289253 1.194037552 1.460024058 1.308132925 1.388484943 1 20.1257931 -1.083702106 4.377531656 0.999966551 1.343163867 0.66926823 0.074820901 2.17E-05 4.55E-06 0.06449239 0.015199523 0.082470361 1.083702106 0.343197315 NTDDDRPPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NTDDDRPPRR 10 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 169.58 2.58E-06 1774050000 2384850 2447510 2578000 2545920 2726190 2022250 3070350 2267580 3419690 FALSE TRUE 2235586.496 2628726.187 2639151.377 2611252.617 2512086.034 2606040.747 2609979.521 2550692.355 2848921.647 0.784713226 0.922709191 0.926368537 0.916575793 0.88176733 0.914746374 0.916128923 0.895318535 1 21.44198451 NTDEMVELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NTDEMVELR 9 0 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ; 112.3 0.0046196 596320000 602670 590560 616120 604360 637850 521100 684800 580330 660590 FALSE TRUE 564949.9605 634285.6769 630734.6574 619868.9008 587755.834 671533.1106 582120.5974 652785.478 550333.2614 1.026559723 1.152548322 1.146095832 1.126351875 1.067999838 1.220229918 1.057760158 1.186163955 1 19.069946 -1.384318431 3.823608641 0.999444938 1.125448842 0.298344962 0.059153733 0.000242748 3.91E-05 0.049673543 0.01165687 0.041274476 1.384318431 0.126003904 NTDKNGEELHGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NTDKNGEELHGGK 13 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 126.1 0.00011567 454290000 1052800 579570 717220 742660 729790 559970 1017840 665590 779740 FALSE TRUE 986907.1273 622481.9658 734232.7971 761717.9129 672475.2372 721624.2486 865224.3412 748690.3766 649596.3567 1.519262104 0.958259632 1.130290818 1.172601886 1.035220149 1.110880997 1.331941493 1.152547069 1 19.30918402 NTDKNGEELHGGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NTDKNGEELHGGKR 14 2 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;;; 242.79 1.01E-17 1033074000 1372110 1061560 1120900 1177620 1373460 730019 1591040 1009158 2017390 FALSE TRUE 1286232.084 1140159.007 1147488.277 1207839.723 1265593.992 940763.6344 1352478.322 1135153.598 1680674.576 0.76530704 0.678393678 0.682754588 0.718663649 0.753027391 0.559753594 0.804723497 0.675415463 1 20.68060898 -0.940171495 0.653140738 1.060991852 0.699531437 0.658946087 0.066510092 16.01401557 3.817502871 2.039036606 0.022133278 0.114770033 0.940171495 -0.361460416 NTDVAQS(ph)PEAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NTDVAQSPEAPK 12 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 NTDVAQS(1)PEAPK 293.69 3.55E-36 303240000 1060200 550470 689640 615850 593470 542610 962750 584020 435550 TRUE FALSE 993843.9745 591227.3716 705998.5865 631653.7536 546861.2601 699252.6985 818394.5752 656936.1826 362853.8912 2.738964632 1.629381373 1.945682831 1.740793661 1.507111466 1.927091635 2.255438332 1.81047027 1 18.46902922 4.745288687 24.32197458 1.803554652 2.738965266 0.461474788 0.334591377 501.3221551 1812209.137 0.07456249 0.71682867 55627.39043 -4.745288687 0.935410613 NTDVAQS(ph)PEAPKQEAPAK ddPTM_SK-BR-3_Pertuzumab_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 284.28 9.62E-40 7375660000 12750950 6476640 8572860 8315680 8957700 5379070 11682590 6866470 9429070 TRUE FALSE 11952890.8 6956177.165 8776212.288 8529074.427 8254198.376 6931920.187 9930894.085 7723763.894 7855297.303 1.521634426 0.885539642 1.117234899 1.085773599 1.050781155 0.882451665 1.264228928 0.983255451 1 22.90523445 4.750865224 24.70200214 1.04562896 1.521634774 0.65115739 0.111942146 1061.214264 2130385.347 0.025599203 0.439624538 56346.27671 -4.750865224 0.476005814 NTDVAQS(ph)PEAPKQEAPAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NTDVAQSPEAPKQEAPAKK 19 2 Q9P2E9;A0A087WVV2;Q9P2E9-3;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 NTDVAQS(1)PEAPKQEAPAKK;NTDVAQS(1)PEAPKQEAPAKK 136.34 3.14E-06 624890000 2016910 891850 1233160 1199450 1297260 751260 1717750 974280 1483180 TRUE FALSE 1890675.203 957883.502 1262411.138 1230229.918 1195378.432 968136.5663 1460189.334 1095921.003 1235627.676 1.530133421 0.775220174 1.021675997 0.995631565 0.967426075 0.783518033 1.181738935 0.886934652 1 20.23681266 4.750061644 24.84636423 0.957193727 1.530133791 0.702022383 0.118418773 900.1643345 1944639.744 0.027102562 0.427528101 56242.11503 -4.750061644 0.572940064 NTEDLTEEWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NTEDLTEEWLR 11 0 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 140.78 8.94E-05 163560000 100790 104710 110140 113160 97271 94523 124090 104410 138790 FALSE TRUE 94481.73382 112462.8374 112752.5728 116063.8772 89631.72803 121810.2556 105483.8565 117445.8183 115625.0524 0.817138949 0.972651126 0.975156945 1.00379524 0.775192972 1.053493626 0.9122924 1.015747158 1 16.81909449 1.279106707 1.495266369 1.007200383 0.937371899 0.105642907 0.084078545 0.983251341 4.094567286 0.070538376 0.021696989 19.01545437 -1.279106707 -0.069828483 NTEESSS(ph)PVRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NTEESSSPVRK 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 NTEESS(0.011)S(0.989)PVRK;NTEES(0.006)S(0.035)S(0.959)PVRK 145.52 2.22E-05 2275910000 2200550 1638900 1867570 1790300 1805840 1212710 2223240 1578540 2131230 TRUE FALSE 2062821.504 1760245.861 1911869.642 1836242.129 1664016.611 1562799.69 1889885.802 1775624.194 1775513.945 1.16181656 0.991400753 1.076797875 1.034203158 0.937202783 0.880195672 1.064416197 1.000062094 1 20.75980526 7.419469882 1.281747219 1.000147752 199.9975936 0.418473461 0.058740469 1879.676267 3.18049616 0.015862169 1099748.341 26270593.38 -7.419469882 198.9974459 NTELAVFHDETEIQNQTDLLSLSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NTELAVFHDETEIQNQTDLLSLSGK 25 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 195.63 8.99E-25 63888000 57737 50705 54350 57797 57832 44234 64455 44246 58536 FALSE TRUE 54123.34423 54459.25096 55639.20767 59280.16887 53290.108 57003.63772 54790.57112 49770.2105 48765.96344 1.109859017 1.116747155 1.140943472 1.215605408 1.092772586 1.168922619 1.123541242 1.020593196 1 15.57358694 1.229699832 3.719369399 1.001431131 1.139646698 0.716674394 0.033758421 0.109786528 2.873925911 0.027905085 0.007938147 16.97070295 -1.229699832 0.138215566 NTENCDFLFS(ph)PPEVTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NTENCDFLFSPPEVTGR 17 0 Q9Y6A5;A0A494BZT8;E7EMT0;C9JA91;C9JWI7;Q8IX09;F8WC55 Q9Y6A5 TACC3;ERIC-1s Transforming acidic coiled-coil-containing protein 3 1 NTENCDFLFS(1)PPEVTGR;NTENCDFLFS(1)PPEVTGR 165.19 2.62E-09 114140000 147863 137210 158387 141662 157052 134551 178094 135325 213123 TRUE FALSE 138608.5188 147369.1712 162144.0144 145297.2868 144717.7694 173393.6894 151390.458 152220.6241 177551.3945 0.780667024 0.830008526 0.913222985 0.818339316 0.815075375 0.97658309 0.852657105 0.857332744 1 17.43787717 -5 0.107377046 1.431933119 0.777992429 0.482111323 0.051355527 162.723948 1.169845925 15.66832304 0.674140329 1.00E-05 5 -0.65394069 NTETQPTS(ph)PQLGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NTETQPTSPQLGTK 14 0 O95696-2 O95696-2 BRD1 Bromodomain-containing protein 1 1 NTETQPT(0.203)S(0.797)PQLGTK 133.66 1.88E-05 0 157090 115590 126970 135320 138370 87964 149630 103150 169330 TRUE FALSE 147258.0173 124148.4039 129981.7884 138792.5403 127502.9784 113357.7788 127194.3706 116028.5046 141067.7291 1.043881675 0.880062398 0.921414056 0.983871657 0.903842283 0.803569885 0.901654627 0.822502108 1 17.10602847 2.478651938 24.99678695 0.871657095 0.938991636 0.192394345 0.067677008 94.37032231 1541152.052 0.02109027 0.017881518 301.0592239 -2.478651938 0.067334541 NTETSKS(ph)PEKDVPMVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NTETSKSPEKDVPMVEK 17 2 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 NT(0.164)ET(0.123)S(0.123)KS(0.591)PEKDVPMVEK;NT(0.002)ET(0.032)S(0.032)KS(0.933)PEKDVPMVEK 109.05 0.00055489 779480000 1002600 298030 515670 540800 513270 364590 727660 386010 556150 TRUE FALSE 939849.0557 320096.4513 527901.9359 554677.8436 472959.8446 469841.2144 618554.1383 434204.1982 463324.9721 2.028487805 0.690868118 1.139377257 1.197168029 1.020795064 1.014064086 1.335033023 0.937148275 1 18.82166492 4.752374898 24.74804987 1.055290339 2.028488554 0.769923545 0.169366014 1065.340248 1908500.963 0.041827145 0.848937637 56542.48589 -4.752374898 0.973198215 NTFTAWS(ph)DEES(ph)DYEIDDRDVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NTFTAWSDEESDYEIDDRDVNK 22 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 2 NTFTAWS(1)DEES(1)DYEIDDRDVNK;NT(0.002)FT(0.014)AWS(0.984)DEES(1)DYEIDDRDVNK;NTFTAWS(1)DEES(1)DYEIDDRDVNK;NTFTAWS(1)DEES(1)DYEIDDRDVNK 239.97 7.48E-31 1292142000 3930816 2602518 2958077 2920302 3222008 2003903 3866327 2480603 4101415 TRUE FALSE 3684793.243 2795211.141 3028243.983 2995241.893 2968964.489 2582397.265 3286607.16 2790311.745 3416862.34 1.07841431 0.818063727 0.886264556 0.87660596 0.868915453 0.755780306 0.961878716 0.81662984 1 21.70424069 -1.982411841 6.172216307 1.095524837 0.877348114 0.146518058 0.088005227 0.063539122 0.000181059 0.046802393 0.017538401 0.010413295 1.982411841 -0.218176723 NTFTAWS(ph)DEESDYEIDDRDVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NTFTAWSDEESDYEIDDRDVNK 22 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 NTFTAWS(1)DEESDYEIDDRDVNK;NTFTAWS(1)DEESDYEIDDRDVNK 332.9 4.91E-81 1330200000 741740 482200 595840 607230 580400 401430 673270 517050 800340 TRUE FALSE 695315.8174 517902.5897 609973.6062 622812.5498 534817.7252 517316.3243 572319.4138 581604.8307 666758.0836 1.042830728 0.776747373 0.914834962 0.934090737 0.802116597 0.775868095 0.858361418 0.872287633 1 19.34680389 0.766727324 4.648339397 0.999999302 0.861920152 0.189620986 0.080956952 7.725038487 152.9701879 0.071325452 0.018080493 5.844230335 -0.766727324 -0.138079149 NTFTAWSDEES(ph)DYEIDDRDVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NTFTAWSDEESDYEIDDRDVNK 22 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 NTFTAWSDEES(1)DYEIDDRDVNK 152.35 2.54E-08 52922000 59824 52567 50196 50191 61889 40066 68283 42264 72258 TRUE FALSE 56079.72263 56459.11538 51386.67282 51478.98603 57028.48759 51632.40378 58044.59806 47540.75343 60197.673 0.931592865 0.937895313 0.853632213 0.855165714 0.947353689 0.857714281 0.964233253 0.789744039 1 15.8774201 NTGKEEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NTGKEEQR 8 1 P23921;E9PL69 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ;; 79.906 0.024464 167105000 481580 374719 443110 443490 431990 278803 434810 369021 529120 FALSE TRUE 451438.7674 402463.5847 453620.7785 454870.7042 398063.248 359288.9001 369614.2771 415094.0842 440806.4538 1.024120141 0.913016543 1.029070184 1.031905727 0.903034074 0.815071778 0.838495612 0.941669707 1 18.74978582 2.589531365 5.457482016 0.875748161 0.989499173 0.356205869 0.062676546 0.211520813 8.809828447 0.019692937 0.018445526 388.6255639 -2.589531365 0.113751012 NTGS(ph)PDRKPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NTGSPDRKPSK 11 2 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 NT(0.15)GS(0.849)PDRKPSK;NT(0.008)GS(0.992)PDRKPSK;NT(0.064)GS(0.936)PDRKPSK 100.43 0.0021069 722520000 1935540 881810 1226470 1092150 1034290 786060 1509530 881960 1048260 TRUE FALSE 1814398.006 947100.1299 1255562.448 1120176.418 953061.0355 1012982.761 1283189.99 992074.6474 873298.634 2.077637518 1.084508887 1.437724048 1.282695718 1.091334623 1.159950012 1.469359896 1.136008473 1 19.73611556 4.745271751 24.83546128 1.242773232 2.077637936 0.754125621 0.154962252 354.8229989 1313033.023 0.035022098 0.342086796 55625.22124 -4.745271751 0.834864705 NTHATTHNAYDLEVIDIFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NTHATTHNAYDLEVIDIFK 19 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 48.848 0.090497 12750000 27298 26752 26492 24767 27145 18167 34929 19070 28133 FALSE TRUE 25589.46691 28732.74592 27120.40275 25402.56315 25013.1412 23411.51798 29691.72071 21450.93148 23437.42055 1.091820956 1.225934648 1.157141106 1.083846368 1.067230975 0.99889482 1.266851045 0.915242845 1 14.51652618 1.822266057 0.22150965 0.96943714 1.213824932 0.196379127 0.095322532 3.963007685 0.847126096 0.316681817 0.388866703 66.41498169 -1.822266057 0.244387792 NTKDEFEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NTKDEFEER 9 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ;; 127.83 0.00039617 818810000 4570280 4480410 4464860 4508910 4944390 3461760 5154680 4256690 5453740 FALSE TRUE 4284234.333 4812144.218 4570768.588 4624616.264 4556077.554 4461113.915 4381783.588 4788147.117 4543475.561 0.942942088 1.05913285 1.006007081 1.01785873 1.002773646 0.981872546 0.964412272 1.053851188 1 22.11536489 2.523435989 4.494655873 0.992887846 1.014989711 0 0.036412539 0.58344945 25.81136763 0.01160125 0.010538802 333.7613081 -2.523435989 0.022101865 NTLQLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NTLQLHR 7 0 P61313;E7ERA2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;; 147.04 0.0021785 1421200000 1157940 2312370 1170550 1187240 2425000 736880 1230400 2045400 1944740 FALSE TRUE 1085466.602 2483580.281 1198315.999 1217706.588 2234550.282 949605.2938 1045912.942 2300772.692 1620150.33 0.669978941 1.532931997 0.739632598 0.751600988 1.379224039 0.586121717 0.645565367 1.420098277 1 20.62769625 3.816330225 8.222111312 0.892191398 1.157643427 0.024221385 0.350213046 0.634962183 52.34873414 0.083735987 0.151387389 6551.341301 -3.816330225 0.265452029 NTPENLHEMAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 NTPENLHEMAK 11 0 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ;;;;;;; 169.89 1.64E-05 2069070000 4765610 3759770 3971420 4030880 4286650 2769740 4830400 3497920 4699960 FALSE TRUE 4467338.977 4038147.283 4065623.958 4134319.205 3949993.801 3569318.975 4106126.363 3934643.012 3915506.313 1.1409352 1.031321867 1.038339268 1.055883677 1.008807925 0.91158555 1.048683372 1.004887414 1 21.90076744 8 0.597051633 1.003987046 8.692775319 0.507729412 0.040033765 147.1088387 1.144150118 0.016612472 1474.495978 100000000 -8 7.688788272 NTPS(ph)QHSHSIQHS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NTPSQHSHSIQHSPER 16 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 NT(0.029)PS(0.889)QHS(0.082)HS(0.001)IQHS(1)PER;NT(0.034)PS(0.792)QHS(0.173)HS(0.001)IQHS(1)PER 158.75 4.43E-09 958170000 228880 350340 324290 304470 390660 381680 334220 338020 481230 TRUE FALSE 214554.8094 376279.5381 331982.3119 312283.2157 359979.1394 491864.8199 284106.8137 380222.5411 400909.6041 0.535170041 0.93856454 0.828072734 0.778936729 0.897906001 1.22687213 0.708655544 0.948399682 1 18.61291745 2.486865879 24.93424472 0.947602165 0.810949318 0.238414685 0.160378456 893.4165092 2286053.673 0.05146426 0.045428385 306.8074345 -2.486865879 -0.136652847 NTPSQHSHSIQHS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 NTPSQHSHSIQHSPER 16 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 NTPSQHSHSIQHS(1)PER;NTPSQHS(0.001)HS(0.002)IQHS(0.997)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER 299.51 1.30E-45 47789340000 2683155 5990098 5117658 6084990 6654824 4613051.1 6774462 5121415.1 8946778 TRUE FALSE 2515221.118 6433611.089 5239051.264 6241141.145 6132180.967 5944764.066 5758694.314 5760835.049 7453502.953 0.337454903 0.863166102 0.702897859 0.837343352 0.822724698 0.79757989 0.772615822 0.772903034 1 22.82948718 4.74300531 24.99208178 0.803843989 0.337454717 0.787001909 0.078624916 188.1789275 1058074.661 0.016323814 0.129774057 55335.68743 -4.74300531 -0.466389272 NTS(ph)LPPLWS(ph)PEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NTSLPPLWSPEAER 14 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 2 NT(0.041)S(0.959)LPPLWS(1)PEAER;NT(0.028)S(0.972)LPPLWS(1)PEAER 137.13 3.37E-05 51735000 157406 143391 151851 150471 149355 111594 179916 126858 173460 TRUE FALSE 147554.2394 154007.8188 155452.9774 154332.3406 137625.2608 143809.3762 152939.2661 142696.5005 144508.4054 1.02107721 1.065736062 1.075736577 1.067981756 0.952368552 0.995162709 1.058341663 0.987461595 1 17.14079388 2.78495542 24.99973033 1.006588949 1.062000728 0.476160397 0.029946545 392.8019117 211659.5248 0.009348645 0.009915666 609.4743318 -2.78495542 0.055411779 NTSAS(ph)DEDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NTSASDEDER 10 0 Q32MZ4-2;Q32MZ4;C9JTC6;Q32MZ4-4 Q32MZ4-2;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 NTS(0.13)AS(0.87)DEDER 159.93 7.90E-06 52451000 140580 148130 148620 151440 126530 153040 177570 143250 132760 TRUE FALSE 131781.3487 159097.6993 152145.3366 155326.2068 116592.8442 197220.1636 150945.027 161135.0778 110601.4983 1.191496957 1.43847689 1.375617319 1.404377057 1.054170567 1.783159962 1.364764757 1.456897784 1 16.7550114 2.266116133 24.9994867 1.436998057 1.329049154 0.032388884 0.218760526 659.1911256 598042.8558 0.067888917 0.056788563 184.5508853 -2.266116133 -0.107948903 NTSGLPAEPESVS(ph)SPPTLHMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NTSGLPAEPESVSSPPTLHMK 21 0 Q8IWI9-3;Q8IWI9 Q8IWI9-3 MGA MAX gene-associated protein 1 NTSGLPAEPES(0.006)VS(0.491)S(0.491)PPT(0.012)LHMK 71.735 0.0042386 0 88165 79343 85229 88873 100250 57298 116810 73700 91021 TRUE FALSE 82646.91003 85217.63828 87250.67213 91153.63164 92376.76939 73839.00244 99295.42491 82901.60723 75829.00708 1.089911542 1.123813189 1.150623956 1.202094491 1.2182247 0.973756683 1.309464923 1.093270378 1 16.21046221 -4.933767795 14.96562905 1.016457705 1.143719834 0 0.101026561 0 0 0 0.019753922 1.16E-05 4.933767795 0.12726213 NTSHETAANHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NTSHETAANHK 11 0 Q9NR09;A0A3B3IUB9 Q9NR09 BIRC6 Baculoviral IAP repeat-containing protein 6 0 ; 155.99 1.81E-05 52216000 52891 74839 59565 62557 80582 50094 79435 70039 61408 FALSE TRUE 49580.64672 80380.15743 60977.90993 64162.31853 74253.41477 64555.32459 67524.45919 78783.52332 51158.60809 0.969155506 1.57119516 1.191938409 1.254184211 1.4514354 1.261866321 1.319904151 1.539985669 1 15.64268939 -0.610798826 5.563975536 0.999999994 1.329627074 0.24593473 0.175346878 1.11E-08 2.79E-09 0.148571358 0.035018604 0.245019796 0.610798826 0.32962708 NTSLPPLWS(ph)PEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NTSLPPLWSPEAER 14 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 NTSLPPLWS(1)PEAER;NTSLPPLWS(1)PEAER;NTSLPPLWS(1)PEAER;NTSLPPLWS(1)PEAER;NTSLPPLWS(1)PEAER;NTSLPPLWS(1)PEAER 278.79 3.59E-33 1837136000 1016644 925759 967604 942956 1006216 754245 1107845 840344 1113297 TRUE FALSE 953014.0668 994303.1596 990556.0238 967153.8474 927191.8542 971983.2874 941733.927 945262.7982 927480.5385 1.027529988 1.072047464 1.068007341 1.042775355 0.999688744 1.047982407 1.015367857 1.01917265 1 19.82295748 2.985522656 5.33443851 1.019805091 1.060646291 0.500409785 0.01794121 0.127507396 11.37757228 0.005030986 0.005655033 967.2141815 -2.985522656 0.0408412 NTSSNSSPLNLKGS(ph)SEQLHGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NTSSNSSPLNLKGSSEQLHGR 21 1 Q9P219;Q9P219-2;A0A0A0MR69;Q9P219-3 Q9P219 CCDC88C Protein Daple 1 NTSSNSSPLNLKGS(0.958)S(0.042)EQLHGR;NTSSNSSPLNLKGS(0.945)S(0.055)EQLHGR 179.86 3.38E-17 229900000 206129 179974 192836 198161 201733 143899 279946 164702 217878 TRUE FALSE 193227.7538 193299.4622 197410.161 203246.1467 185889.7039 185440.3053 237970.6962 185265.4073 181512.7543 1.064540917 1.064935977 1.087582863 1.119734795 1.024113731 1.021637879 1.311041184 1.020674321 1 17.4697114 NTVDLVTTCHIHSS(ph)S(ph)DDEIDFK ddPTM_SK-BR-3_Pertuzumab_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(0.004)VDLVT(0.012)T(0.013)CHIHS(0.47)S(0.544)S(0.957)DDEIDFK 80.355 0.0031168 56798000 82761 54874 73523 76468 76142 60950 82630 57707 52457 TRUE FALSE 77581.13674 58936.92806 75267.00028 78430.29834 70162.11446 78545.27556 70240.3986 64911.84598 43701.58781 1.775247551 1.348622121 1.722294407 1.79467846 1.605482042 1.797309423 1.607273376 1.485342964 1 15.41539808 0.800046845 2.162329795 1.000550932 1.647137603 0.712961987 0.132586328 0.432533645 3.446183726 0.127512214 0.034871971 6.310254065 -0.800046845 0.646586671 NTVDLVTTCHIHSSS(ph)DDEIDFK ddPTM_SK-BR-3_Pertuzumab_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 NTVDLVT(0.001)TCHIHS(0.008)S(0.197)S(0.794)DDEIDFK;NTVDLVTTCHIHS(0.034)S(0.241)S(0.724)DDEIDFK;NTVDLVTTCHIHS(0.037)S(0.14)S(0.822)DDEIDFK;NTVDLVTTCHIHS(0.003)S(0.109)S(0.888)DDEIDFK 203.78 2.08E-22 1690790000 1896520 1678020 1951810 2018370 2006660 1724460 2931550 1846590 1670800 TRUE FALSE 1777820.199 1802262.347 1998107.855 2070164.791 1849065.018 2222283.608 2491991.293 2077140.826 1391932.686 1.277231447 1.29479131 1.435491726 1.48725927 1.328415545 1.596545314 1.790310205 1.492271032 1 20.40865801 3.636782543 0.87623625 1.531241533 1.264045285 0.019081325 0.208395689 1.292443216 1.895843032 0.08259133 0.243678892 4332.938684 -3.636782543 -0.267196248 NTVELLTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NTVELLTDR 9 0 Q9P2M7 Q9P2M7 CGN Cingulin 0 66.299 0.064123 8073000000 419410 2034900 1485400 1741700 1576200 2228500 931290 1320900 812130 FALSE TRUE 393159.8768 2185566.113 1520634.389 1786394.971 1452411.61 2871831.773 791651.7102 1485817.273 676580.2564 0.581098655 3.230313171 2.247529949 2.640329737 2.146695231 4.244628403 1.170078055 2.196069511 1 19.36790155 1.614608675 25 1.512276562 2.568153564 0.210353635 0.962081684 0.815960789 3014.941306 0.406871177 0.219182674 41.17263625 -1.614608675 1.055877002 NTVGNVPLEWYDDFPHVGYDLDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NTVGNVPLEWYDDFPHVGYDLDGR 24 0 Q14137;Q14137-2;A0A075B729 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 ;; 211.3 3.21E-25 312317000 337104 291328 313904 284136 276416 263541 328035 262061 187742 FALSE TRUE 316005.2624 312898.2282 321349.9511 291427.4108 254707.4024 339621.0085 278849.1971 294779.8927 156406.6473 2.020408133 2.00054303 2.054579883 1.863267423 1.628494739 2.171397535 1.78284748 1.884701819 1 17.2549423 -2.022234143 0.325040133 9.53E-17 2.001488678 0.80111016 0.146236649 14.53528534 0.71271692 11.0628533 0.123154095 0.009500924 2.022234143 2.001488678 NVADHKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NVADHKK 7 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 0 77.923 0.023845 261580000 732890 586800 677380 824260 722240 579690 787030 632250 880950 FALSE TRUE 687019.7231 630247.2826 693447.7735 845411.9071 665518.1838 747037.0925 669022.1579 711187.8043 733913.7538 0.936104167 0.858748428 0.944862758 1.151922692 0.906807074 1.017881309 0.911581442 0.969034577 1 19.48525101 3.4784782 24.99997861 0.986710381 0.89961592 0.241557853 0.069750526 61.81129615 1138787.772 0.018208642 0.025585113 3009.388105 -3.4784782 -0.087094461 NVAEALGHS(ph)PKDPGGGGGPVR ddPTM_SK-BR-3_Pertuzumab_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 171.63 4.02E-12 1346740000 1891970 1193908 1439730 1397960 1607450 1094180 1943500 1309930 2207250 TRUE FALSE 1773554.975 1282306.191 1473881.075 1433834.02 1481207.361 1410052.003 1652090.218 1473477.644 1838845.716 0.964493628 0.697343001 0.801525143 0.779746777 0.80550932 0.766813655 0.898438734 0.801305749 1 20.81036901 0.37714868 0.557570671 1.008224275 0.788010575 0.365673323 0.074047798 2.054698239 1.023503649 0.109668671 0.030489419 2.383135195 -0.37714868 -0.2202137 NVALLSQLYHS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NVALLSQLYHSPAR 14 0 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 1 NVALLS(0.002)QLYHS(0.998)PAR;NVALLSQLYHS(1)PAR;NVALLSQLYHS(1)PAR;NVALLSQLYHS(1)PAR 188.84 5.07E-07 1065340000 1276156 1100310 1294837 1196346 1312500 1086083 1545769 1111858 1601290 TRUE FALSE 1196283.674 1181778.097 1325551.145 1227046.264 1209421.544 1399617.531 1313995.289 1250675.919 1334024.354 0.896748002 0.885874455 0.993648385 0.919807993 0.906596301 1.0491694 0.984985982 0.937521054 1 20.34735357 2.260061044 24.99972575 0.993005665 0.925745533 0.454895379 0.039142843 235.7084426 274070.285 0.01373454 0.011481642 181.9956654 -2.260061044 -0.067260132 NVALLSQLYHS(ph)PARR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NVALLSQLYHSPARR 15 1 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 1 NVALLSQLYHS(1)PARR 99.273 0.0012254 271050000 635300 856710 668090 678550 1028800 588150 943930 764110 1854700 TRUE FALSE 595537.707 920141.6998 683937.4103 695962.7418 948002.198 757939.3572 802396.4595 859510.8155 1545138.588 0.385426726 0.595507553 0.44263823 0.450420918 0.613538621 0.490531634 0.519303877 0.556267782 1 20.55930481 -4.999999995 0.322963695 5.752393774 0.489175689 0.84843811 0.066228358 114.9868865 1.011812061 373.8234802 0.053187384 1.00E-05 4.999999995 -5.263218085 NVALLSQLYHSPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVALLSQLYHSPAR 14 0 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 0 ; 271.08 6.01E-33 945940000 1088930 1110090 1087530 1069250 1266680 736560 1258280 1008750 1266710 FALSE TRUE 1020775.815 1192282.219 1113326.725 1096688.765 1167200.062 949192.9149 1069612.595 1134694.658 1055287.918 0.967296032 1.12981699 1.054998078 1.039231803 1.106048921 0.899463454 1.013574189 1.075246517 1 20.00920524 2.278665055 24.99999895 0.996322246 1.067538739 0.205022695 0.059898663 202.2954395 126104.5897 0.019438241 0.016263016 189.9612658 -2.278665055 0.071216493 NVAQYNANHPDFPMQIEQLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVAQYNANHPDFPMQIEQLER 21 0 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 253.31 2.33E-36 383940000 229290 257230 226699 254710 272100 178339 276260 249620 205230 FALSE TRUE 214939.1482 276275.5768 232076.4073 261246.2898 250730.3636 229822.5742 234837.3777 280785.6065 170975.7872 1.257132087 1.615875449 1.357364169 1.527972435 1.466467081 1.344181992 1.373512481 1.642253626 1 17.38343251 -1.415571529 3.520789905 0.996089407 1.447735848 0.571854052 0.121849727 6300272.131 5071534.312 173494.4801 0.025750314 0.038408599 1.415571529 0.451646441 NVATETQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NVATETQLK 9 0 Q5T3J3 Q5T3J3 LRIF1 Ligand-dependent nuclear receptor-interacting factor 1 0 ;; 78.516 0.02955 3518300000 1244840 6305800 3673070 3847070 6654200 4659400 3731930 5729700 7892200 FALSE TRUE 1166927.687 6772687.993 3760196.955 3945792.329 6131605.974 6004493.141 3172361.742 6445065.658 6574940.834 0.177481093 1.030075884 0.571898219 0.600125907 0.932572038 0.913239114 0.48249282 0.980246944 1 22.64854648 -5 0.040698345 2.238910117 7.31E-11 0.209423292 0.249212573 1723.048641 5.235784248 261.7357026 77.1630111 1.00E-05 5 -2.238910117 NVDAAVS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NVDAAVSPR 9 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 NVDAAVS(1)PR 93.623 0.0097278 74100000 254930 229070 252050 230090 271140 187250 299540 246650 339500 TRUE FALSE 238974.3864 246030.5811 258028.745 235994.4989 249845.7581 241306.0353 254626.7578 277444.7954 282835.2567 0.844924318 0.869872391 0.912293425 0.834388547 0.883361434 0.853168159 0.900265267 0.980941339 1 18.10960244 1.270468565 2.765672542 0.999935152 0.871572901 0.843650838 0.021805642 0.09832382 1.25148862 0.019113812 0.005562792 18.64097248 -1.270468565 -0.128362252 NVDILKDPETVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NVDILKDPETVK 12 1 O14980 O14980 XPO1 Exportin-1 0 101.32 0.0024961 294580000 816080 512750 608000 681070 643030 411930 848880 525250 767640 FALSE TRUE 765003.0095 550714.5435 622422.0471 698547.4092 592529.0177 530847.5039 721598.3246 590828.6187 639515.9249 1.196221986 0.861142815 0.973270599 1.092306512 0.926527385 0.830077068 1.12835083 0.923868501 1 19.28662076 NVDLLSDMVQEHDEPILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 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 ;;;;;;;;;; 322.43 9.68E-62 4090413000 7254340 6092200 6757460 6535680 6919400 5103680 8285920 5922230 7640710 FALSE TRUE 6800303.809 6543272.827 6917750.142 6703396.614 6375978.236 6577029.565 7043523.219 6661633.452 6365426.14 1.068318705 1.027939479 1.086769368 1.053094713 1.00165772 1.033242617 1.106528151 1.046533776 1 22.60182567 -0.44731381 6.112664464 0.999999643 1.055203246 0.235702907 0.029767604 0 0 0.029037657 0.006844241 0.357014776 0.44731381 0.055203603 NVFEVGPGDS(ph)PTFPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NVFEVGPGDSPTFPR 15 0 Q16584;Q16584-2 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 NVFEVGPGDS(0.996)PT(0.004)FPR;NVFEVGPGDS(0.954)PT(0.046)FPR;NVFEVGPGDS(0.994)PT(0.006)FPR;NVFEVGPGDS(0.98)PT(0.02)FPR 191.43 1.84E-07 352277000 383093 400830 390321 405858 460740 347201 510885 372206 429097 TRUE FALSE 359115.893 430507.8703 399579.5984 416273.0034 424555.3389 447432.2924 434282.5371 418676.7384 357477.9386 1.004581973 1.204292136 1.117774148 1.164471869 1.187640671 1.251636098 1.214851296 1.171196019 1 18.44749468 4.744614162 24.48669515 1.175417306 1.004581872 0.335931621 0.068782346 521.110987 2107822.833 0.01490054 0.134709754 55541.05974 -4.744614162 -0.170835434 NVFIIGATNRPDIIDPAILRPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVFIIGATNRPDIIDPAILRPGR 23 2 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 206.85 7.30E-25 2626600000 2578900 2681900 2495600 2304700 2710700 1945510 2969800 2213700 2593000 FALSE TRUE 2417491.252 2880470.667 2554796.811 2363842.504 2497812.556 2507147.154 2524506.06 2490085.318 2160211.549 1.11909931 1.33342064 1.182660472 1.094264358 1.156281457 1.160602607 1.16863835 1.152704382 1 21.04274117 -5 0.099675034 0.406826622 1.311583694 0.425992146 0.062752585 161.8681572 1.099343627 19.93267082 1.065501755 1.00E-05 5 0.904757072 NVHGINFVSPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVHGINFVSPVR 12 0 P53634;H0YCY8 P53634 CTSC Dipeptidyl peptidase 1;Dipeptidyl peptidase 1 exclusion domain chain;Dipeptidyl peptidase 1 heavy chain;Dipeptidyl peptidase 1 light chain 0 ; 150.49 6.82E-05 524000000 396090 469840 364040 410750 517710 288150 493970 443800 561990 FALSE TRUE 371299.4339 504627.4425 372675.2007 421290.5404 477051.1449 371334.2273 419903.7843 499209.4069 468190.2384 0.793052489 1.077825638 0.795990967 0.899827689 1.018925868 0.793126804 0.896865739 1.066253343 1 18.83673533 1.245857324 24.91266447 1.033126683 0.903188667 0.259679446 0.095378863 196.6767306 671517.9928 0.062385812 0.021734367 17.61397292 -1.245857324 -0.129938016 NVHPQYPEGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NVHPQYPEGGK 11 0 E9PRM4;E9PIV9;E9PMI2;E9PQW2;Q6BCY4-2;Q6BCY4 E9PRM4 CYB5R2 NADH-cytochrome b5 reductase 2 0 64.55 0.080431 0 158830 147630 134600 157430 170300 86528 173600 126070 149620 FALSE TRUE 148889.1138 158560.6788 137792.7756 161469.9203 156925.325 111507.2289 147570.2916 141810.117 124647.4554 1.194481775 1.27207313 1.105459996 1.295412889 1.258953297 0.894580869 1.183901357 1.137689627 1 16.92749391 2.315120618 24.99999877 1.07535378 1.218507561 0.447867827 0.092977269 37.02402182 12088.3304 0.030524049 0.025538242 206.5953858 -2.315120618 0.143153781 NVHS(ph)EDFENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NVHSEDFENR 10 0 A0A669KBJ7;Q9H2P0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 NVHS(1)EDFENR;NVHS(1)EDFENR;NVHS(1)EDFENR;NVHS(1)EDFENR 204.17 1.24E-07 1763390000 1206390 1093570 1187480 1136230 1220470 1012500 1377110 1000990 1276940 TRUE FALSE 1130884.203 1174539.061 1215647.586 1165387.585 1124619.209 1304792.313 1170625.14 1125965.805 1063810.465 1.06305046 1.104086771 1.142729487 1.095484228 1.057161258 1.226527052 1.100407619 1.058427081 1 20.0208097 1.042077047 2.861879029 1.0016101 1.117405904 0.384555231 0.047142027 0.227784336 4.055518116 0.041937511 0.011173188 11.01734749 -1.042077047 0.115795804 NVHSEDFENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVHSEDFENR 10 0 A0A669KBJ7;Q9H2P0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 ; 180.97 1.94E-06 891720000 396300 404980 393390 425450 340140 398870 395650 346010 373990 FALSE TRUE 371496.2904 434965.1406 402721.3966 436367.7673 313426.7765 514017.2939 336325.9555 389210.1102 311568.6529 1.192341678 1.39604911 1.292560701 1.400550932 1.005963769 1.649772174 1.079460184 1.249195343 1 18.24919056 0.960831157 1.130819884 1.006939325 1.313870223 0.214180035 0.177307674 0.746407733 1.967222486 0.14465602 0.045903149 9.137579253 -0.960831157 0.306930898 NVIGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVIGAR 6 0 P62258;P62258-2;B4DJF2;I3L3T1;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 ; 107.55 0.072514 368110000 538950 501290 504940 514510 496970 359340 569520 488810 498440 FALSE TRUE 505218.0816 538406.0332 516917.4152 527713.1977 457939.9809 463075.6246 484125.7632 549839.0045 415247.144 1.216668408 1.296591779 1.244842795 1.270841246 1.102813078 1.115180758 1.165873794 1.324124711 1 18.66361072 2.751593035 24.23682731 1.150635147 1.26172981 0.3268958 0.08177193 599.5864905 1115069.768 0.023092173 0.024350044 564.4078369 -2.751593035 0.111094663 NVIHPFLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVIHPFLSR 9 0 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 ; 109.66 0.0024125 533230000 417190 877900 353410 339220 972410 162499 364980 752000 920280 FALSE TRUE 391078.8226 942900.6295 361793.0521 347924.9595 896040.8411 209409.8233 310254.6373 845888.8554 766679.3228 0.510094391 1.229850084 0.471896191 0.453807673 1.16872963 0.273138739 0.404673281 1.103315076 1 19.54826375 3.912774244 8.716620351 0.642114709 0.912109364 0.019417028 0.355536909 0.707423087 89.34912652 0.084827788 0.153570963 8180.394423 -3.912774244 0.269994655 NVIIWGNHSSTQYPDVNHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NVIIWGNHSSTQYPDVNHAK 20 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51;C9JF79 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic;Malate dehydrogenase" 0 234.28 9.49E-30 1342700000 269250 461880 345020 416810 476600 265420 594590 385960 529550 FALSE TRUE 252398.1231 496078.0758 353204.0373 427506.0503 439169.7585 342042.4453 505436.7494 434147.9556 441164.684 0.572117697 1.12447368 0.800617207 0.969039603 0.995478048 0.775316923 1.145687241 0.984094991 1 18.75095778 4.752702108 24.82180513 0.971371563 0.572117396 0.538891575 0.116899167 1782.841837 3129267.805 0.026368804 0.556284364 56585.10268 -4.752702108 -0.399254166 NVIPHDIGDPDDEPWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NVIPHDIGDPDDEPWLR 17 0 Q9HCG7-3;Q9HCG7-2;Q9HCG7 Q9HCG7-3 GBA2 Non-lysosomal glucosylceramidase 0 91.317 0.0035854 23809000 26769 32861 28275 29290 35983 24340 39255 34486 33809 FALSE TRUE 25093.57607 35294.06263 28945.69635 30041.63099 33157.04033 31366.56287 33369.07718 38791.65301 28166.05949 0.890915397 1.253070656 1.027680012 1.066589773 1.177198406 1.113629789 1.184726504 1.377248139 1 14.78167012 2.179936169 1.473765934 1.199342572 1.090307146 0.122061151 0.128635133 0.884319684 3.718623651 0.071157422 0.03993385 151.3338807 -2.179936169 -0.109035426 NVKLPDAYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NVKLPDAYER 10 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 62.14 0.079366 147170000 214020 337850 270960 323750 476900 206590 334460 267790 890370 FALSE TRUE 200624.8702 362864.7655 277387.2992 332057.9731 439446.1977 266229.1793 284310.828 301224.171 741761.495 0.270470861 0.489193316 0.373957534 0.447661378 0.592435979 0.358914801 0.383291435 0.406093027 1 19.50059585 -1.869217317 2.595724072 1.26578183 0.419227934 0.823793031 0.084973428 18590368.41 11472701.88 30449607.9 0.019316228 0.013513962 1.869217317 -0.846553897 NVLFSHLDDNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 183.89 1.50E-05 864709000 1136426 1179647 1208216 1109343 1224273 1054677 1311877 1108586 1091991 FALSE TRUE 1065299.125 1266989.291 1236875.454 1137810.619 1128123.537 1359145.129 1115173.223 1246995.402 909730.6476 1.171004987 1.392708155 1.359606228 1.25071154 1.240063243 1.494008289 1.225827915 1.370730343 1 19.79507993 -1.167887692 3.422481987 0.999546563 1.321313396 0.513224019 0.095525109 11587302.56 19378761.5 58548.50901 0.021219326 0.06793793 1.167887692 0.321766833 NVLGWQDANSTEFDPTTSHPVVVDMPEHNPGQMGGTMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NVLGWQDANSTEFDPTTSHPVVVDMPEHNPGQMGGTMR 38 0 P17812;B4E1E0;P17812-2;A0A3B3IRI2 P17812 CTPS1 CTP synthase 1;CTP synthase 0 217.37 2.25E-39 31654000 4277.2 5348.2 6608.7 5777.9 5227.4 3874.1 6028 4488.1 6453.5 FALSE TRUE 4009.497687 5744.186293 6765.461485 5926.170696 4816.86109 4992.489779 5124.157361 5048.449165 5376.369159 0.745763092 1.068413668 1.258369968 1.102262609 0.895931985 0.928598768 0.953088824 0.939007166 1 12.39241649 2.744953556 24.64042517 0.940305579 1.083598834 0.095634507 0.129568281 666.3779052 2568432.587 0.040476733 0.041986216 555.8448109 -2.744953556 0.143293255 NVLLDPQLVPGGGASEMAVAHALTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVLLDPQLVPGGGASEMAVAHALTEK 26 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 151.42 1.19E-07 209730000 543840 435190 455550 458820 505640 348180 550110 424490 574660 FALSE TRUE 509802.0252 467411.9204 466355.8611 470594.098 465929.0741 448693.9138 467626.1125 477488.5109 478745.5336 1.064870562 0.976326436 0.974120547 0.982973344 0.973229078 0.937228407 0.976773838 0.997374341 1 18.8688995 4.738694968 6.311606554 0.974380051 1.066900701 0.718711046 0.017147518 0.06158597 13.68421252 0.003868084 0.024401105 54789.20106 -4.738694968 0.09252065 NVLS(ph)DSRPAMAPGSSHLGAPASTTTAADATPSGSLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVLSDSRPAMAPGSSHLGAPASTTTAADATPSGSLAR 37 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 1 NVLS(0.984)DS(0.016)RPAMAPGSSHLGAPASTTTAADATPSGSLAR;NVLS(0.596)DS(0.203)RPAMAPGS(0.101)S(0.101)HLGAPASTTTAADATPSGSLAR 216.35 2.96E-39 396700000 119971 145617 149175 152230 154480 109615 172965 126436 158035 TRUE FALSE 112462.2293 156398.6342 152713.5014 156136.4795 142347.7639 141259.071 147030.504 142221.8129 131657.9376 0.854200144 1.187916483 1.159926278 1.185925303 1.081193938 1.072924836 1.11676141 1.080237284 1 17.00643498 2.555873485 24.99989556 1.080762821 1.12372767 0 0.099902407 408.7478576 129753.5377 0.030508505 0.028763692 359.6445513 -2.555873485 0.042964849 NVLSDSRPAMAPGSSHLGAPASTTTAADATPSGSLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NVLSDSRPAMAPGSSHLGAPASTTTAADATPSGSLAR 37 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;; 174.92 9.55E-19 421560000 257226 305025 316052 319609 288997 238438 368957 274804 333325 FALSE TRUE 241126.6838 327609.3684 323548.9027 327810.708 266300.3414 307271.1799 313635.3231 309113.8843 277690.9041 0.868327627 1.179762691 1.165140442 1.180487741 0.958981146 1.106522307 1.12944039 1.113158118 1 18.0831204 NVMEEGKDFQPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NVMEEGKDFQPSR 13 1 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 0 ;; 148.57 3.95E-05 2017070000 2044840 1720090 1738900 1911260 1924070 1257570 2350610 1553860 2237360 FALSE TRUE 1916857.115 1847447.253 1780147.529 1960306.167 1772961.304 1620610.044 1998157.852 1747862.841 1863930.162 1.028395352 0.991156906 0.955050551 1.051705803 0.951195136 0.869458565 1.072013262 0.937729791 1 20.82991638 -1.058391994 3.885720387 1.000003196 0.983218346 0.008651272 0.05916874 7098535.085 1933625.49 218.3818985 0.012651625 0.087419437 1.058391994 -0.01678485 NVMLLPVGSADDGAHSQNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NVMLLPVGSADDGAHSQNEK 20 0 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ;; 355.78 2.59E-95 677580000 1035000 757890 859268 919566 931724 591286 1076600 808053 965350 FALSE TRUE 970221.1975 814004.9642 879650.2427 943163.6204 858550.1554 761980.6695 915173.8247 908940.1958 804226.8486 1.206402397 1.012158405 1.093783731 1.172758186 1.067547244 0.947469822 1.137954827 1.130203745 1 19.61724297 2.506652366 24.4898613 1.061282748 1.100671998 0.127187749 0.075715189 1746.753856 1448563.242 0.024202289 0.022779507 321.108917 -2.506652366 0.03938925 NVMVEPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVMVEPHR 8 0 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R2U2;M0R1H0;M0R2B0;M0QXC9 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ; 110.87 0.0060005 352410000 464510 405650 474420 469580 400210 353660 535890 430180 400570 FALSE TRUE 435437.1483 435684.7481 485673.4664 481630.2178 368779.121 455755.9008 455538.2695 483888.9199 333712.2792 1.304828067 1.305570023 1.455365885 1.443249913 1.105081065 1.365715106 1.365062953 1.450018324 1 18.34824525 NVMVEPHRHEGVFICR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVMVEPHRHEGVFICR 16 1 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ; 189.81 5.76E-10 294060000 259220 299780 276200 268600 304240 204544 318800 243280 382790 FALSE TRUE 242995.8829 321976.0231 282751.5944 275492.7307 280346.2176 263592.5323 270998.8996 273654.0435 318899.8761 0.761981741 1.009646122 0.886646925 0.863884722 0.879104191 0.826568312 0.849793054 0.858119002 1 18.28274401 4.798072084 22.60348021 0.891407167 0.761978219 0.320409899 0.06123568 37983.46641 14424953.94 0.014989795 30.65272025 62816.26119 -4.798072084 -0.129428948 NVNANLLAEAGTS(ph)QDGGDAGTSHDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVNANLLAEAGTSQDGGDAGTSHDFK 26 0 Q96DT7-3;Q96DT7-2;Q96DT7;Q96DT7-4 Q96DT7-3 ZBTB10 Zinc finger and BTB domain-containing protein 10 1 NVNANLLAEAGT(0.198)S(0.802)QDGGDAGTSHDFK;NVNANLLAEAGT(0.061)S(0.939)QDGGDAGTSHDFK 161.04 1.13E-11 221610000 190705 121114 140108 123853 129597 97089 178366 140629 175526 TRUE FALSE 178769.1145 130081.4066 143431.4279 127031.2777 119418.9744 125117.0182 151621.6742 158186.8402 146229.5767 1.222523641 0.889569741 0.980864687 0.868711245 0.816654039 0.855620464 1.036874192 1.081770486 1 17.15787562 -0.918753345 7.395191691 1 0.956390284 0 0.122681697 0 2.26E-10 0.111981875 0.026394381 0.120572053 0.918753345 -0.043609716 NVNIFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVNIFK 6 0 P00338;P00338-3;P00338-2;P00338-5;F5GXY2;F5GYU2 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 122.51 0.044642 3309700000 5737700 5093100 5371300 5433200 5575300 3625000 6565900 4551700 5300500 FALSE TRUE 5378587.599 5470198.423 5498709.773 5572625.11 5137438.428 4671478.653 5581404.25 5119989.765 4415812.307 1.218029034 1.238775121 1.245231769 1.261970555 1.163418658 1.05789792 1.26395867 1.159467253 1 22.07424742 2.661775913 5.684766344 1.14792319 1.2412018 0.369878656 0.07046306 0.279762668 15.80577355 0.021618436 0.020399543 458.9611374 -2.661775913 0.09327861 NVNVQNFHISWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVNVQNFHISWK 12 0 O43707 O43707 ACTN4 Alpha-actinin-4 0 ; 107.12 0.0018486 917730000 1466810 2116200 1605410 1616900 2249900 1247380 2141490 2083710 1730560 FALSE TRUE 1375004.98 2272885.65 1643491.083 1658392.391 2073201.93 1607478.356 1820393.455 2343865.78 1441718.356 0.953726485 1.576511557 1.139952943 1.15028874 1.438007584 1.114973913 1.262655391 1.625744564 1 20.45935793 NVPHEDICEDS(ph)DIDGDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NVPHEDICEDSDIDGDYR 18 0 O00629 O00629 KPNA4 Importin subunit alpha-3 1 NVPHEDICEDS(1)DIDGDYR;NVPHEDICEDS(1)DIDGDYR;NVPHEDICEDS(1)DIDGDYR;NVPHEDICEDS(1)DIDGDYR 314.45 1.86E-61 2235940000 927860 846390 912120 843140 880580 935220 1359230 714152 910380 TRUE FALSE 869786.8989 909057.5963 933755.9171 864776.3998 811422.7989 1205202.832 1155426.08 803315.4492 758431.6967 1.14682298 1.198601799 1.23116679 1.140216586 1.069869314 1.589072341 1.523441181 1.05917969 1 19.53265973 2.264111697 24.99913383 1.365587316 1.172252504 0.055197105 0.188185424 348.3458822 340819.8258 0.061830728 0.051714042 183.7010745 -2.264111697 -0.193334811 NVPHEDICEDSDIDGDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NVPHEDICEDSDIDGDYR 18 0 O00629 O00629 KPNA4 Importin subunit alpha-3 0 ;; 228.01 2.66E-19 1254840000 563678 577515 508414 543115 601358 494383 784303 454210 652429 FALSE TRUE 528398.4002 620274.8115 520473.8202 557052.2504 554129.7684 637103.3465 666704.0463 510919.1183 543534.385 0.972152664 1.141187804 0.957572942 1.024870304 1.019493492 1.172149111 1.226608775 0.939994106 1 19.05201178 2.256675596 24.69631589 1.119203753 1.030317441 0.040053902 0.09532323 365.2115578 497894.785 0.031795985 0.02655059 180.5824728 -2.256675596 -0.088886312 NVPNWHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NVPNWHR 7 0 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ;;;;; 138.62 0.0033602 6353000000 4875150 4964360 4633950 4669130 5280090 3617970 5126410 4428920 4799840 FALSE TRUE 4570023.064 5331926.38 4743869.482 4788947.781 4865413.03 4662419.206 4357752.412 4981880.411 3998715.696 1.142872715 1.333409721 1.186348279 1.197621473 1.216743925 1.16597917 1.089788008 1.245870122 1 21.93110528 -2.608197274 0.131358129 0.634782659 1.310674136 0.472904437 0.064709593 49.37552013 0.771568994 5.747387058 0.523839862 0.002464919 2.608197274 0.675891478 NVPQEESLEDS(ph)DVDADFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NVPQEESLEDSDVDADFK 18 0 O00505 O00505 KPNA3 Importin subunit alpha-4 1 NVPQEESLEDS(1)DVDADFK;NVPQEESLEDS(1)DVDADFK;NVPQEESLEDS(1)DVDADFK;NVPQEESLEDS(1)DVDADFK;NVPQEESLEDS(1)DVDADFK 367.55 1.69E-107 1662216000 1561951 927890 1148048 1035663 1092808 873808 1431989 942676 1227392 TRUE FALSE 1464191.275 996591.9411 1175280.241 1062239.866 1006983.268 1126062.185 1217275.543 1060371.174 1022532.346 1.431926609 0.974631213 1.149381969 1.038832532 0.984793559 1.101248473 1.19045187 1.037005018 1 19.96371505 4.748405659 24.77471869 1.072884433 1.43192683 0.727437621 0.071220479 674.7066898 1697837.848 0.017195363 0.225123324 56028.06949 -4.748405659 0.359042397 NVQNINLFVVDEVHLIGGENGPVLEVICSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NVQNINLFVVDEVHLIGGENGPVLEVICSR 30 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 115.76 0.00011672 12703000 8619.5 9286.9 7569 8962.4 8702 5535 9751.8 6966.9 6082.3 FALSE TRUE 8080.020881 9974.511739 7748.540254 9192.390357 8018.580022 7132.864647 8289.608121 7836.732801 5067.124837 1.594596767 1.968475627 1.529178874 1.814123522 1.582471378 1.407674939 1.635958929 1.546583724 1 12.30695166 -2.473925853 0.172710884 7.13E-13 1.858898268 0.692092209 0.140459554 24.7631273 0.528748573 10.06330689 0.514774019 0.003357949 2.473925853 1.858898268 NVQRPESVSDHMYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVQRPESVSDHMYR 14 1 Q7Z4H3-2;Q7Z4H3;V9GYS5;V9GZ04;Q7Z4H3-3 Q7Z4H3-2 HDDC2 HD domain-containing protein 2 0 ; 194.48 8.38E-08 485490000 288600 289480 279830 291970 342290 187628 292410 261810 344070 FALSE TRUE 270537.0412 310913.4004 286467.6997 299462.4445 315407.9241 241793.1577 248565.8351 294497.5548 286642.4942 0.943813449 1.084673092 0.9993902 1.044724528 1.100352985 0.843535633 0.867163244 1.027403685 1 18.12889298 2.240764996 24.99949787 0.914570259 1.037080779 0.320317194 0.069736969 53.47955535 606511.0326 0.023389613 0.018689431 174.0864606 -2.240764996 0.12251052 NVRS(ph)DIS(ph)DQEEDEESEGCPVSINLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NVRSDISDQEEDEESEGCPVSINLSK 26 1 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;H0YBA1 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 2 NVRS(1)DIS(0.994)DQEEDEES(0.006)EGCPVSINLSK;NVRS(1)DIS(1)DQEEDEESEGCPVSINLSK;NVRS(0.999)DIS(0.975)DQEEDEES(0.026)EGCPVSINLSK 197.66 3.65E-25 570379000 617623 515014 542565 561141 616907 468434 728828 470454 610670 TRUE FALSE 578967.0789 553146.1724 555434.898 575540.8281 568457.6127 603663.2914 619547.0075 529191.2175 508745.2319 1.138029494 1.087275394 1.09177416 1.131294786 1.117371873 1.186572873 1.217794229 1.040189046 1 18.95658384 3.074595795 2.870464441 1.138957448 1.099814605 0 0.066471502 0.773455802 12.92422204 0.019591105 0.023768036 1187.396584 -3.074595795 -0.039142843 NVS(ph)ES(ph)PNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVSESPNR 8 0 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 NVS(1)ES(1)PNR;NVS(1)ES(1)PNR 88.803 0.020988 292300000 853190 785470 863760 875580 789160 716470 957040 685000 648930 TRUE FALSE 799790.3609 843627.0161 884248.7951 898048.8652 727182.5569 923303.2581 813540.7367 770523.7579 540619.3908 1.479396364 1.560482348 1.635621678 1.661148084 1.345091518 1.707861897 1.504830849 1.425261045 1 19.04425373 0.746065624 1.635959945 1.000475537 1.569453054 0.747973738 0.101464901 0.399311228 1.748072073 0.08713402 0.024951733 5.572699486 -0.746065624 0.568977517 NVS(ph)ES(ph)PNRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NVSESPNRK 9 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 NVS(1)ES(1)PNRK;NVS(1)ES(1)PNRK;NVS(1)ES(1)PNRK 120.59 0.00042812 444360000 3311710 2033140 2416010 2418590 2244690 1824780 3098200 1968160 1976000 TRUE FALSE 3104435.983 2183675.801 2473318.898 2480655.114 2068401.102 2351564.363 2633653.672 2213889.108 1646192.835 1.885827661 1.326500611 1.502447858 1.506904332 1.256475583 1.428486574 1.59984518 1.344854055 1 20.65070191 -3.102391763 0.275824582 2.97E-17 1.512319844 0.469674579 0.168305593 63.88571581 1.588457122 37.32489309 0.191680302 0.000789966 3.102391763 1.512319844 NVS(ph)ES(ph)PNRKNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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;NVS(1)ES(1)PNRKNEK 131.18 0.00099966 1868370000 4249580 2621230 2844580 3546110 4005890 1926880 3760820 2526990 5527600 TRUE FALSE 3983606.374 2815308.597 2912054.781 3637109.186 3691283.558 2483138.976 3196919.955 2842490.264 4605007.85 0.865059627 0.611358045 0.632366953 0.789816066 0.801580297 0.539225786 0.69422682 0.617260677 1 22.13477219 -1.157681608 5.058425891 1.000017492 0.681101664 0.471846827 0.100989771 1.86E-05 3.10E-06 0.091374117 0.021535906 0.069553404 1.157681608 -0.318915829 NVS(ph)ESPNRKNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NVSESPNRKNEK 12 2 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 NVS(0.579)ES(0.421)PNRKNEK 55.885 0.064812 83483000 78962 71047 60097 80201 107160 38401 80829 56717 264060 TRUE FALSE 74019.90937 76307.3938 61522.52922 82259.09344 98744.08586 49486.74531 68709.44183 63798.2423 219986.6801 0.336474505 0.346872791 0.279664792 0.37392761 0.44886393 0.224953371 0.312334555 0.290009569 1 17.74705665 -1.544288586 3.146768843 1.024884138 0.323888169 0.926785167 0.059474217 40215954.73 47529534.18 8493149.05 0.013564284 0.028556923 1.544288586 -0.700995969 NVS(ph)ESPSKHENSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NVSESPSKHENSK 13 1 Q8NEV8-2;Q8NEV8;E9PPH6 Q8NEV8-2 EXPH5 Exophilin-5 1 NVS(0.585)ES(0.409)PS(0.005)KHENSK 100.35 0.0014739 64611000 232510 157540 188520 207320 195770 135000 238540 166490 171440 TRUE FALSE 217957.6141 169204.4255 192991.7834 212640.1822 180395.0139 173972.3085 202773.1415 187276.643 142825.5565 1.526040714 1.18469292 1.35124125 1.488810459 1.263044362 1.218075482 1.419725899 1.311226419 1 17.12389463 0.949563892 22.01636882 0.999999999 1.335358966 0.492642761 0.110031304 2921.989825 1275509.532 0.098855639 0.02471391 8.903564156 -0.949563892 0.335358967 NVS(ph)PEFVPCEGEGGFGLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NVSPEFVPCEGEGGFGLHK 19 0 O94986-3;O94986 O94986-3 CEP152 Centrosomal protein of 152 kDa 1 NVS(1)PEFVPCEGEGGFGLHK 130.78 1.09E-05 134660000 539600 314490 382120 362070 359030 261380 513700 294870 422130 TRUE FALSE 505827.3992 337775.1668 391184.0669 371361.3292 330833.2321 336836.1629 436675.454 331685.1686 351673.7759 1.438342674 0.960478688 1.112349267 1.055982432 0.940738988 0.957808588 1.241706046 0.943161507 1 18.42387823 4.745914534 24.69381448 1.042128856 1.438342897 0.648706654 0.094621959 499.4367164 1677016.148 0.022197601 0.230235091 55707.61102 -4.745914534 0.396214041 NVS(ph)TGSAENEEKSEVQAIIESTPELDMDKDLSGYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NVSTGSAENEEKSEVQAIIESTPELDMDKDLSGYK 35 2 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 NVS(0.379)T(0.329)GS(0.286)AENEEKS(0.006)EVQAIIESTPELDMDKDLSGYK 62.179 0.014678 42122000 15741 6801.5 10975 12426 12171 10184 12846 7557.2 13533 TRUE FALSE 14755.79891 7305.090137 11235.33218 12744.8722 11215.13876 13123.95548 10919.86156 8500.733055 11274.25487 1.308804801 0.647944385 0.996547649 1.130440312 0.994756539 1.164064111 0.968566143 0.753995111 1 13.46074447 4.791100019 22.73872934 0.957270107 1.308811029 0.338799084 0.154436691 23716.11743 10263212.86 0.03800013 38.61181079 61815.87476 -4.791100019 0.351540922 NVSES(ph)PNRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 NVSESPNRK 9 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 NVS(0.001)ES(0.999)PNRK;NVS(0.002)ES(0.998)PNRK;NVS(0.007)ES(0.993)PNRK;NVS(0.021)ES(0.979)PNRK 118.88 0.00056191 2805550000 3806680 2781760 3126370 3054790 2981340 2503120 3687910 2709360 3296780 TRUE FALSE 3568426.694 2987724.405 3200528.973 3133181.083 2747197.583 3225730.109 3134942.132 3047629.56 2746526.12 1.299250958 1.087819403 1.165300759 1.140779642 1.000244477 1.1744764 1.141420833 1.109630649 1 21.38917658 -2.682788539 0.018444019 6.22E-08 2.027958593 0.365345047 0.069123615 3194.776201 6.903309099 453.0423741 316.2030866 0.002075924 2.682788539 2.027958531 NVSES(ph)PNRKNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NVSESPNRKNEK 12 2 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 NVS(0.02)ES(0.98)PNRKNEK 64.52 0.032989 84061000 147700 142460 135120 173660 237330 77336 177320 110420 542060 TRUE FALSE 138455.7207 153007.8866 138325.1102 178116.4096 218691.0591 99661.64775 150732.5122 124206.1801 451586.6842 0.306598324 0.338822848 0.306309099 0.39442352 0.484272603 0.220692176 0.333784227 0.275043938 1 18.78464342 -1.4824842 3.284357277 1.013311555 0.332206416 0.899868268 0.069976807 36787761.38 46335172.12 4444626.713 0.016816267 0.032924243 1.4824842 -0.681105139 NVSES(ph)PSKHENSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NVSESPSKHENSK 13 1 Q8NEV8-2;Q8NEV8;E9PPH6 Q8NEV8-2 EXPH5 Exophilin-5 1 NVS(0.062)ES(0.935)PS(0.003)KHENSK 128.99 9.60E-05 93585000 215990 139710 186970 188670 182870 131330 248030 144320 160350 TRUE FALSE 202471.5715 150054.2738 191405.0167 193511.5916 168508.1279 169242.839 210840.2041 162338.6697 133586.5491 1.515658371 1.123273823 1.432816537 1.448585901 1.261415382 1.266915271 1.578304145 1.215232153 1 17.02741522 0.99329985 24.65350659 0.999999977 1.362369015 0.456317108 0.132912409 195.7111299 720131.3587 0.124861357 0.031215339 9.846907312 -0.99329985 0.362369037 NVSKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NVSKPR 6 1 Q9Y3U8;J3QSB5;J3KTD3 Q9Y3U8 RPL36 60S ribosomal protein L36 0 ;;;;; 125.86 0.018813 807440000 4596040 3915620 4217880 4308000 4294910 3030120 4825070 3820800 4417380 FALSE TRUE 4308382.061 4205536.579 4317930.105 4418550.573 3957605.093 3904866.454 4101595.547 4297835.291 3680090.741 1.170727127 1.142780675 1.173321641 1.200663485 1.075409649 1.061078851 1.114536525 1.167861228 1 21.81130991 2.730211476 24.95438032 1.090812128 1.167265874 0.489621581 0.044260765 565.616402 1690543.283 0.013337677 0.012773202 537.2933628 -2.730211476 0.076453746 NVSS(ph)FPDDATSPLQENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVSSFPDDATSPLQENR 17 0 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 1 NVS(0.001)S(0.999)FPDDATSPLQENR;NVSS(1)FPDDATSPLQENR 253.26 5.50E-27 245200000 278296 267302 293754 260570 302514 253786 309918 257300 300666 TRUE FALSE 260877.9501 287093.3182 300721.9836 267256.6673 278755.7707 327049.8983 263448.673 289424.4714 250482.9022 1.04150003 1.146159341 1.200568905 1.066965709 1.112873447 1.305677535 1.051763097 1.155465977 1 17.9343526 0.201619533 1.118857472 0.999664525 1.142511956 0.219803852 0.078448341 7.219115979 8.785791379 0.076086309 0.021327826 1.590814471 -0.201619533 0.142847431 NVSSFPDDATS(ph)PLQENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 NVSSFPDDATSPLQENR 17 0 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 1 NVSSFPDDAT(0.003)S(0.997)PLQENR;NVSSFPDDATS(1)PLQENR;NVSSFPDDATS(1)PLQENR;NVSSFPDDAT(0.002)S(0.998)PLQENR;NVSSFPDDAT(0.004)S(0.996)PLQENR;NVSSFPDDAT(0.021)S(0.979)PLQENR 530.16 1.81E-287 7244980000 3548380 3313910 3524360 3652670 3694600 3000830 4270130 3075250 4156170 TRUE FALSE 3326293.23 3559275.345 3607959.484 3746403.696 3404441.019 3867120.907 3629863.648 3459201.732 3462478.377 0.960668304 1.027955977 1.042016466 1.082000604 0.983238204 1.116864998 1.048342619 0.999053671 1 21.72337363 5.008146306 1.531218193 1.044672812 0.873321758 0.258274326 0.040165367 2.758698031 3.588735314 0.009618294 0.865225697 101893.4591 -5.008146306 -0.171351055 NVTELNEPLSNEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVTELNEPLSNEER 14 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ; 305.06 6.67E-44 977010000 771140 744440 783450 785360 795010 641350 830460 673070 875930 FALSE TRUE 722875.7239 799559.1122 802033.804 805513.6672 732573.1215 826497.3336 705940.2326 757104.2711 729731.6243 0.990604902 1.095689272 1.099080508 1.103849197 1.003893894 1.132604517 0.967397066 1.037510567 1 19.47700645 1.715741992 12.19789359 1.002474535 1.075723801 0.322821576 0.046961688 0.116473963 45.92295329 0.020066052 0.010985577 51.96871668 -1.715741992 0.073249266 NVTFHGVLLDAFFNESSADWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 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 ;;;;;;;;;;;; 289.31 1.11E-54 5747734500 4679725 5099882 4796256 4599606 5887456 4089060 5414449 5265827 2587896 FALSE TRUE 4386829.366 5477482.57 4910025.457 4717639.677 5425078.955 5269505.242 4602602.638 5923277.092 2155959.439 2.034745778 2.540624128 2.277420144 2.188185729 2.516317727 2.444157875 2.134828028 2.747397277 1 21.03989861 -0.978542943 6.056616102 0.999999119 2.355915923 0.80157622 0.212711405 2.23E-06 3.76E-07 0.18109924 0.042685472 0.105064756 0.978542943 1.355916804 NVVFIDMGHSAYQVLVCAFNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVVFIDMGHSAYQVLVCAFNK 21 0 O95757;E9PDE8;D6RJ96 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 ; 234.11 9.10E-30 181107000 455330 431690 408250 356210 529520 301330 508180 457720 406200 FALSE TRUE 426831.7081 463652.7768 417933.8828 365350.9517 487933.6352 388319.0793 431983.1267 514867.3496 338402.5958 1.261313339 1.370121809 1.235019731 1.07963401 1.441873204 1.147506207 1.27653609 1.521463948 1 18.36838111 3.856648332 5.279375781 1.251791687 1.32021392 0.033449612 0.156222013 0.817917691 32.92604042 0.036452569 0.067230929 7188.666436 -3.856648332 0.068422233 NVVGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NVVGAR 6 0 P31946-2;P31946;Q4VY19;A0A0J9YWE8;Q4VY20;A0A0J9YWZ2;P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;P61981;Q04917;A2IDB2 P31946-2;P63104;P61981;Q04917 YWHAB;YWHAZ;YWHAG;YWHAH "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed;14-3-3 protein zeta/delta;14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed;14-3-3 protein eta" 0 ;;;; 141.59 0.027066 1615960000 1521710 1553100 1605400 1578580 1667210 1213330 1813660 1396220 1570300 FALSE TRUE 1426468.887 1668093.14 1643480.846 1619089.035 1536274.052 1563598.674 1541718.52 1570541.14 1308206.785 1.090400159 1.275098982 1.256285218 1.237639992 1.174335792 1.195222874 1.178497572 1.200529731 1 20.31915917 -0.618437783 0.401308638 0.937284384 1.227482956 0.581109343 0.052529429 6.34924359 0.908639221 0.566357106 0.033434958 0.240747739 0.618437783 0.290198572 NVVHELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NVVHELR 7 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 85.064 0.021085 155859000 556940 588110 611620 598940 628830 481870 694420 598290 570590 FALSE TRUE 522082.1196 631654.2763 626127.9152 614309.8144 579444.2284 620978.0465 590298.1677 672987.8235 475354.8428 1.098299781 1.328805809 1.317180049 1.292318409 1.218971968 1.306346313 1.241805309 1.415758845 1 18.85864533 -1.199237072 6.643440966 0.999998647 1.282548337 0.526286891 0.082593668 1.47E-06 1.77E-07 0.070949676 0.016722919 0.063206673 1.199237072 0.28254969 NVVHQLS(ph)VTLEDLYNGATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVVHQLSVTLEDLYNGATR 19 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 1 NVVHQLS(0.999)VT(0.001)LEDLYNGATR;NVVHQLS(1)VTLEDLYNGATR 275.67 1.23E-39 56597000 73967 66591 74816 69237 75561 59827 80278 67167 79734 TRUE FALSE 69337.5375 71521.46693 76590.67085 71013.73864 69626.74386 77098.08369 68241.05916 75552.9478 66425.8803 1.043833175 1.076710863 1.153024552 1.069067332 1.048186995 1.160663334 1.02732638 1.137402282 1 16.01945782 -1.759069862 2.746803095 0.980244776 1.09067823 0.265864872 0.046718608 13302426.88 7859356.361 1745903.437 0.010340823 0.017415267 1.759069862 0.110433454 NVVHQLSVTLEDLYNGATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NVVHQLSVTLEDLYNGATR 19 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ; 261.97 3.50E-31 570610000 654910 579160 663630 581690 657560 553740 751490 626950 675580 FALSE TRUE 613920.3521 622041.609 679371.617 596617.1502 605917.8901 713595.7488 638811.051 705226.0876 562821.3336 1.090790835 1.105220381 1.207082206 1.060047149 1.076572358 1.26789037 1.135015702 1.253019467 1 19.10231749 NWDDMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NWDDMK 6 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ; 107.67 0.072273 1040910000 1751570 1423430 1492050 1530290 1663560 1082210 1858060 1306620 1823950 FALSE TRUE 1641942.36 1528822.238 1527442.131 1569559.832 1532910.708 1394626.459 1579461.152 1469754.383 1519520.962 1.080565785 1.00612119 1.005212938 1.032930688 1.008811821 0.91780666 1.039446768 0.967248508 1 20.53518515 2.467411608 24.99977772 0.984852788 1.022511843 0.278878464 0.03660867 329.2322602 847679.513 0.011863141 0.009934491 293.3672353 -2.467411608 0.037659055 NWEDEDFYDS(ph)DDDTFLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NWEDEDFYDSDDDTFLDR 18 0 A0A087X0M4;A0A087WWF4;Q9BWU0 A0A087X0M4 SLC4A1AP Kanadaptin 1 NWEDEDFY(0.041)DS(0.757)DDDT(0.202)FLDR;NWEDEDFY(0.001)DS(0.962)DDDT(0.037)FLDR 113.54 0.00015724 35808000 77671 77426 74176 76092 84246 67745 88894 67121 88345 TRUE FALSE 72809.71076 83158.7016 75935.48975 78044.64954 77629.65899 87301.88175 75565.16995 75501.2046 73599.64877 0.989267095 1.129879055 1.031737121 1.06039432 1.054755835 1.186172532 1.026705578 1.02583648 1 16.16741126 1.544311212 12.07881575 1.017623136 1.077375157 0.208562648 0.05335275 0.178018155 31.61565636 0.02642428 0.012271218 35.01960247 -1.544311212 0.059752021 NWQNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NWQNVR 6 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ; 104.94 0.077699 210050000 257400 486700 274890 294790 465930 222830 279090 430980 283040 FALSE TRUE 241289.7935 522735.7744 281410.5206 302354.8105 429337.7373 287157.4037 237243.0454 484788.8017 235798.7955 1.023286794 2.216872115 1.193434937 1.282257655 1.820780027 1.217806915 1.006124925 2.055942655 1 17.84719682 -3.143180657 0.092755197 1.92E-10 1.884703492 0.04818875 0.438260033 293.4230064 2.830647107 71.25947784 10.11698641 0.00071915 3.143180657 1.884703492 NWQWWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NWQWWR 6 0 P35579;P35579-2;P35749;P35749-2;P35749-4;P35749-3 P35579;P35749 MYH9;MYH11 Myosin-9;Myosin-11 0 107.55 0.072514 773650000 1016100 1745700 912310 950000 1795000 670500 1157000 1450900 1431000 FALSE TRUE 952504.1148 1874953.444 933950.424 974378.6083 1654027.941 864062.4653 983518.5911 1632048.059 1192156.855 0.798975496 1.572740563 0.783412367 0.817324167 1.387424761 0.724789243 0.824990929 1.368987689 1 20.18514264 3.912272919 9.412329919 0.965223777 1.23290111 0.064886785 0.294143395 0.699025379 96.80362061 0.069344177 0.125350673 8170.956878 -3.912272919 0.267677333 NWRDPDQTDGLGLSYLSSHIANVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NWRDPDQTDGLGLSYLSSHIANVER 25 1 P06396-2;A0A0A0MS51;A0A0A0MT01;P06396-4;P06396-3;P06396 P06396-2 GSN Gelsolin 0 ;; 299.66 2.25E-63 1095270000 272434 438360 376534 377929 456106 250716 452930 358818 474310 FALSE TRUE 255382.8422 470816.6305 385465.5643 387627.298 420285.2746 323093.6392 385017.3513 403617.2172 395144.5968 0.646302251 1.191504665 0.975505087 0.980975828 1.063623995 0.817659261 0.974370786 1.021441823 1 18.59202116 NWTEDMEGGISS(ph)PVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NWTEDMEGGISSPVKK 16 1 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5;P08651-4 P08651-3 NFIC Nuclear factor 1 C-type 1 NWTEDMEGGIS(0.07)S(0.93)PVKK;NWTEDMEGGIS(0.002)S(0.998)PVKK;NWTEDMEGGIS(0.023)S(0.977)PVKK 215.65 9.75E-15 1168870000 1937460 964750 1341470 1198570 1224430 840860 1735950 1004360 1400660 TRUE FALSE 1816197.837 1036181.094 1373290.302 1229327.335 1128268.207 1083602.632 1475660.413 1129756.557 1166880.797 1.55645533 0.887992241 1.176889966 1.053515782 0.966909567 0.928631814 1.264619674 0.968185062 1 20.15422576 4.749945523 24.78672097 1.047700265 1.556455668 0.672308061 0.114788175 963.1174994 2096813.075 0.026649585 0.420957966 56227.07902 -4.749945523 0.508755403 NY(ph)EY(ph)KKPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NYEYKKPEER 10 2 O95373;E9PLB2 O95373 IPO7 Importin-7 2 NY(1)EY(1)KKPEER;NY(1)EY(1)KKPEER 67.726 0.040999 431750000 51398 35069 40380 44511 50893 42198 44665 40675 59513 TRUE FALSE 48181.09093 37665.54525 41337.83267 45653.22762 46896.06907 54379.87757 37967.8979 45753.36329 49579.89583 0.971786853 0.759693917 0.833761991 0.920801201 0.945868649 1.096813066 0.765792208 0.922820884 1 15.59746762 3.221981945 5.159347218 0.930781008 0.830991625 0.130353949 0.097063352 0.300747553 21.99808562 0.027391 0.034570009 1667.177901 -3.221981945 -0.099789384 NYAGAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NYAGAYR 7 0 Q8NFU3;Q8NFU3-4;R4GNF9;Q8NFU3-2 Q8NFU3 TSTD1 Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1 0 ;; 148.07 0.0049053 374020000 313962 595790 330251 293823 605230 207681 294860 474190 460599 FALSE TRUE 294311.6789 639902.9115 338084.7097 301362.9956 557697.6772 267635.1333 250648.4803 533393.6653 383722.0513 0.766991831 1.667620897 0.881066669 0.785367936 1.4533897 0.69747134 0.653203222 1.390052158 1 18.54970215 3.734411009 23.73322585 0.942293301 1.279449166 0.062341056 0.341599598 270.7322999 881408.6773 0.082502825 0.144740014 5425.14074 -3.734411009 0.337155865 NYDYYASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NYDYYASR 8 0 O95861-3;O95861-4;O95861 O95861-3 BPNT1 "3(2),5-bisphosphate nucleotidase 1" 0 ; 160.56 0.00082038 769600000 495880 530410 397260 356760 631430 253530 481900 502940 717890 FALSE TRUE 464843.756 569682.1083 406683.1948 365915.0656 581840.0349 326719.9953 409643.5687 565733.1661 598069.5213 0.777240337 0.952534928 0.679993179 0.611826974 0.972863545 0.546290997 0.684943061 0.945932113 1 19.18995367 1.132924813 5.556257899 0.993444611 0.750679056 0.332500398 0.134051741 0.245315392 10.43618415 0.12586376 0.031846178 13.58078309 -1.132924813 -0.242765555 NYEIKNEADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NYEIKNEADR 10 1 O15145;C9JZD1;F8VR50 O15145 ARPC3 Actin-related protein 2/3 complex subunit 3 0 ; 106.49 0.0021974 421260000 470070 421020 412020 483480 529860 303070 528570 372620 671910 FALSE TRUE 440649.1578 452192.7589 421793.309 495886.9153 488246.933 390561.3891 449315.8355 419142.4272 559763.8803 0.787205415 0.807827684 0.753520053 0.885885876 0.872237295 0.697725242 0.802688154 0.748784339 1 19.09445887 -1.137801314 4.620959479 1.000021424 0.793419356 0.574181735 0.055613798 1.17E-05 2.18E-06 0.051174004 0.012060578 0.072811283 1.137801314 -0.206602068 NYFESTDGLIWVVDSADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NYFESTDGLIWVVDSADR 18 0 V9GYD0;P36404-2;P36404 V9GYD0 ARL2-SNX15;ARL2 ADP-ribosylation factor-like protein 2 0 ; 178.03 2.11E-13 38085000 43284 46315 48175 43757 54713 37470 46697 43234 41334 FALSE TRUE 40574.9317 49744.21079 49317.73375 44879.8787 50416.06168 48286.98073 39695.21836 48631.86007 34435.08837 1.178301948 1.444579153 1.432194197 1.303318238 1.464089801 1.402260979 1.152754944 1.412276325 1 15.07159176 0.153447247 0.507440309 0.972236885 1.385759047 0.471186022 0.112127183 2.663991052 0.948843425 0.272561418 0.052955019 1.42379429 -0.153447247 0.413522162 NYGFVHIEDK ddPTM_SK-BR-3_Pertuzumab_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 0 103.34 0.0045821 0 420430 304060 332130 344450 369610 224100 418740 313620 461260 FALSE TRUE 394116.0368 326572.9188 340008.2804 353289.1702 340582.3215 288794.032 355953.8244 352776.1474 384272.7261 1.025615429 0.849846727 0.884809817 0.919370921 0.886303655 0.751534034 0.9263052 0.918035872 1 18.55177106 -0.937554555 4.958668187 1.000000608 0.887171478 0.178611787 0.068705955 4.21E-07 9.01E-08 0.060594761 0.014282245 0.115463693 0.937554555 -0.11282913 NYGS(ph)PLISGSTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NYGSPLISGSTPK 13 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 NYGS(0.971)PLIS(0.029)GSTPK;NYGS(0.957)PLIS(0.043)GSTPK;NYGS(0.778)PLIS(0.212)GS(0.008)T(0.002)PK 166.7 7.83E-07 223970000 846750 706520 684030 682680 859920 622320 1036760 706720 1437650 TRUE FALSE 793753.429 758831.4759 700255.5146 700198.7246 792385.352 801973.6815 881307.4628 794955.5477 1197696.927 0.662733126 0.633575539 0.584668374 0.584620958 0.66159087 0.669596509 0.73583512 0.663736818 1 20.19183146 -0.22489328 0.40211802 1.07359656 0.610521793 0.90048134 0.037358988 1.716070655 0.318438902 0.22662411 0.025767711 0.595808534 0.22489328 -0.463074767 NYGYNPS(ph)PVKPEGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NYGYNPSPVKPEGLR 15 1 E9PRF4;Q15047-3;Q15047 E9PRF4 SETDB1 Histone-lysine N-methyltransferase SETDB1 1 NYGYNPS(1)PVKPEGLR;NYGYNPS(1)PVKPEGLR;NYGYNPS(1)PVKPEGLR;NY(0.001)GY(0.001)NPS(0.999)PVKPEGLR;NYGYNPS(1)PVKPEGLR 164.99 8.78E-07 2685800000 3116370 1826770 2263870 2188430 2289380 1672760 3011180 1997500 2876890 TRUE FALSE 2921321.965 1962025.952 2317570.065 2244588.819 2109581.33 2155658.657 2559681.513 2246892.272 2396718.474 1.218884069 0.818630128 0.966976343 0.936525855 0.880195715 0.899420888 1.067994235 0.937486942 1 21.19262902 -0.837128095 5.063849216 1.000000058 0.954750012 0.000645102 0.110814634 6.70E-08 1.53E-08 0.097793869 0.023050206 0.145502986 0.837128095 -0.045250047 NYHIFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NYHIFYR 7 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 93.262 0.015064 118590000 122990 152070 140590 129570 162960 93252 136770 151090 158020 FALSE TRUE 115292.2754 163329.421 143924.8612 132894.9856 150161.7789 120172.3386 116262.6082 169953.9191 131645.4412 0.875778716 1.24067662 1.093276455 1.009491741 1.140653088 0.912848463 0.88314952 1.290997376 1 17.00629804 2.251688188 24.98818222 0.994663136 1.095044581 5.64E-05 0.143627675 527.7882427 1004638.309 0.047609973 0.039609379 178.5205384 -2.251688188 0.100381446 NYILSAS(ph)ASALWNDEVDKAEQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NYILSASASALWNDEVDKAEQELR 24 1 B7ZC38;Q9NR46;Q9NR46-2 B7ZC38 SH3GLB2 Endophilin-B2 1 NYILS(0.077)AS(0.915)AS(0.007)ALWNDEVDKAEQELR;NYILS(0.151)AS(0.681)AS(0.167)ALWNDEVDKAEQELR 83.647 0.0080738 43135000 39878 33909 32835 33871 36423 20714.7 44650 33127 48539 TRUE FALSE 37382.10716 36419.65764 33613.86171 34740.1872 33562.4845 26694.69761 37955.14701 37262.97887 40437.52733 0.924440974 0.900640075 0.831254133 0.859107604 0.8299836 0.660146636 0.938611966 0.921494991 1 15.30340716 1.571378631 13.31772916 0.949146215 0.839385946 0.375266394 0.072288036 0.152245103 46.16542483 0.038283968 0.017809933 37.271651 -1.571378631 -0.109760269 NYIVEDGDIIFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NYIVEDGDIIFFK 13 0 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 176.8 1.22E-06 36768000 153318 147080 157660 171508 199854 126720 179200 152595 168116 FALSE TRUE 143722.1001 157969.9562 161399.7697 175909.1856 184158.273 163302.0069 152330.6236 171646.8217 140056.3535 1.026173368 1.127902821 1.152391631 1.255988616 1.314886961 1.165973572 1.087638081 1.225555409 1 17.09564791 -1.495786986 3.070338176 0.995353421 1.165259608 0.293418864 0.082453617 23072861.52 27983539.95 913964.802 0.020152377 0.031931036 1.495786986 0.169906187 NYLHYSLYDQAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NYLHYSLYDQAEK 13 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 213.67 4.07E-09 66554000 59597 98750 94544 104420 105600 72792 123890 99672 105140 FALSE TRUE 55866.93015 106061.5527 96786.62833 107099.594 97306.60197 93805.86872 105313.8446 112116.2686 87591.45477 0.637812562 1.210866437 1.104977975 1.222717379 1.110914326 1.070947719 1.202330124 1.279990941 1 16.41850251 4.742284586 24.984992 1.155611184 0.637812363 0.792299337 0.082430883 147.6364472 990487.1588 0.017656354 0.132714942 55243.93255 -4.742284586 -0.517798821 NYLPAINGIVFLVDCADHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NYLPAINGIVFLVDCADHER 20 0 Q9Y6B6;D6RD69;D6RDB2;Q9H029;D6R9R5 Q9Y6B6 SAR1B;DKFZp434B2017 GTP-binding protein SAR1b 0 ; 203.06 1.10E-21 226770000 299850 326940 342040 348420 366180 299510 380150 308310 321460 FALSE TRUE 281082.9237 351146.9778 350153.3503 357361.0471 337421.6999 385973.6749 323150.0366 346803.1822 267806.2493 1.049575671 1.311197848 1.307487601 1.334401449 1.259947073 1.441242226 1.206656071 1.294977929 1 18.0308301 -0.482889913 8.116899767 1 1.284593469 0.42572602 0.100152377 0 0 0.08635991 0.020355226 0.328935 0.482889913 0.284593469 NYLPAINGIVFLVDCADHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NYLPAINGIVFLVDCADHSR 20 0 Q9NR31;Q5SQT8;Q9NR31-2 Q9NR31 SAR1A GTP-binding protein SAR1a 0 ; 192.6 1.04E-17 1203120000 601620 653670 623400 635560 674820 537390 783890 580780 528460 FALSE TRUE 563965.6781 702068.4069 638187.3424 651869.5456 621822.3593 692525.7692 666352.9718 653291.6615 440256.612 1.280993091 1.594679984 1.44958037 1.480658161 1.412408905 1.573004812 1.513555853 1.483888359 1 18.74798515 0.887046899 19.05032863 1 1.487287534 0.740903625 0.08768669 8469.549856 1428454.942 0.075303442 0.01882586 7.70986722 -0.887046899 0.487287534 NYQQNYQNS(ph)ESGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NYQQNYQNSESGEK 14 0 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NYQQNYQNS(0.999)ES(0.001)GEK;NYQQNYQNS(1)ESGEK 396.97 1.99E-114 481890000 1210820 647360 819140 801490 690240 641700 1149990 656330 623630 TRUE FALSE 1135036.938 695291.208 838570.3876 822057.5903 636031.3347 826948.3729 977559.6755 738274.2453 519542.1242 2.184687025 1.33827687 1.614056587 1.582273221 1.224215141 1.591686861 1.881579241 1.421009406 1 18.9868812 4.747855261 24.51635583 1.511058301 2.184687492 0.452739378 0.245150477 932.219594 2458834.423 0.055650437 0.69368162 55957.10794 -4.747855261 0.673629191 NYQQNYQNS(ph)ESGEKNEGSESAPEGQAQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NYQQNYQNS(0.992)ES(0.008)GEKNEGSESAPEGQAQQR;NYQQNYQNS(0.999)ES(0.001)GEKNEGSESAPEGQAQQR;NYQQNYQNS(0.999)ES(0.001)GEKNEGSESAPEGQAQQR;NYQQNYQNS(0.999)ES(0.001)GEKNEGSESAPEGQAQQR;NYQQNYQNS(0.993)ES(0.007)GEKNEGSESAPEGQAQQR 447.85 2.68E-220 9104590000 3161130 2001550 2413500 2422890 2417110 1680410 2976150 1978440 2898700 TRUE FALSE 2963280.516 2149746.845 2470749.36 2485065.459 2227279.931 2165517.088 2529903.937 2225452.589 2414888.244 1.227088054 0.89020552 1.023131967 1.029060233 0.922311803 0.896735944 1.04762775 0.921555105 1 21.20352499 4.749597115 24.96430993 0.969330507 1.227088205 0.671314067 0.057307457 978.7301873 2213822.983 0.013066146 0.200077941 56181.98961 -4.749597115 0.257757698 NYQQNYQNSESGEKNEGS(ph)ES(ph)APEGQAQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 2 NYQQNYQNSESGEKNEGS(1)ES(1)APEGQAQQR;NYQQNYQNSESGEKNEGS(1)ES(1)APEGQAQQR 300.4 2.89E-81 649080000 990240 546480 661940 696860 660080 446290 969270 593980 792540 TRUE FALSE 928262.646 586941.9478 677641.5294 714742.6074 608239.9794 575126.6781 823936.9618 668139.7105 660259.954 1.405904811 0.888955849 1.026325352 1.082516974 0.921212889 0.871060973 1.247897827 1.011934324 1 19.33267462 1.017549482 24.97938263 0.999999231 1.044690199 0.01118577 0.164379105 1433.40051 2040247.427 0.146558579 0.036639645 10.41236735 -1.017549482 0.044690968 NYQQNYQNSESGEKNEGS(ph)ESAPEGQAQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NYQQNYQNSESGEKNEGS(0.689)ES(0.311)APEGQAQQR;NYQQNYQNSESGEKNEGS(0.997)ES(0.003)APEGQAQQR 451.33 1.71E-220 3948730000 1457720 931480 1012680 1086680 985010 714747 1461600 821420 1205280 TRUE FALSE 1366483.907 1000447.748 1036701.248 1114566.049 907651.2879 921082.856 1242446.649 923976.0952 1004110.982 1.360889316 0.996351765 1.032456837 1.110002847 0.903935227 0.917311804 1.237359885 0.920193198 1 19.9374873 4.741879537 24.29913074 1.02724159 1.360889504 0.535073146 0.100813905 177.5447759 1299784.208 0.023288675 0.167882114 55192.43276 -4.741879537 0.333647915 NYQQNYQNSESGEKNEGSESAPEGQAQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;; 386.59 1.03E-154 1354110000 788550 515840 614730 627550 638520 456220 768650 545490 750410 FALSE TRUE 739196.0631 554033.3303 629311.6859 643653.9954 588373.2149 587923.3079 653398.0683 613595.6273 625161.7232 1.182407745 0.886224012 1.006638223 1.029579982 0.941153614 0.940433949 1.045166465 0.981499034 1 19.25386992 0.73163632 0.001901628 1.47E-05 1.976530298 0.002472679 0.079141996 677117.5694 691.3716465 360520.78 358061.3069 5.390590236 -0.73163632 1.976515609 NYS(ph)SPPPCHLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NYSSPPPCHLSR 12 0 Q12986;Q12986-2;Q12986-3 Q12986 NFX1 Transcriptional repressor NF-X1 1 NY(0.003)S(0.584)S(0.413)PPPCHLSR;NYS(0.7)S(0.3)PPPCHLSR 99.451 0.0024405 628050000 301710 687180 582020 589130 689510 497420 698740 620090 664770 TRUE FALSE 282826.5097 738059.5222 595825.7892 604248.0732 635358.6659 641017.0791 593970.4238 697509.6015 553815.5924 0.510687156 1.332681008 1.07585593 1.091063671 1.147238674 1.157455817 1.07250578 1.259461834 1 19.07904615 4.749097131 24.99414711 1.145807895 0.510686799 0.811081053 0.095742645 611.8041983 1451260.404 0.021380133 0.30913497 56117.34692 -4.749097131 -0.635121096 NYSEVIEVDES(ph)DVEEDIFPTTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NYSEVIEVDESDVEEDIFPTTSK 23 0 F8W7U8;P49959-2;P49959;P49959-3 F8W7U8 MRE11A Double-strand break repair protein MRE11A 1 NYSEVIEVDES(1)DVEEDIFPTTSK;NYSEVIEVDES(1)DVEEDIFPTTSK 123.32 4.00E-05 74962000 285280 238000 258910 260880 285100 185636 337900 235600 313600 TRUE FALSE 267424.834 255621.7676 265051.4675 267574.6225 262709.396 239226.0997 287235.0319 265015.1786 261258.1341 1.023603858 0.978426063 1.014519484 1.024177193 1.005554897 0.91566948 1.099430006 1.014380584 1 17.99511643 1.718452095 25 1.044850992 0.995935634 0.203445725 0.040372128 1.214333382 1503.679894 0.016952785 0.009401131 52.29402795 -1.718452095 -0.048915358 NYSS(ph)PPPCHLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NYSSPPPCHLSR 12 0 Q12986;Q12986-2;Q12986-3 Q12986 NFX1 Transcriptional repressor NF-X1 1 NYS(0.06)S(0.94)PPPCHLSR;NYS(0.007)S(0.715)PPPCHLS(0.278)R 125.93 0.00031105 355840000 293600 556980 490060 506000 553110 402740 588300 520690 553180 TRUE FALSE 275224.1001 598219.3787 501684.4546 518984.8167 509670.9717 519004.5001 500089.8765 585699.2927 460850.6843 0.597208835 1.29807636 1.088605207 1.126145266 1.105935152 1.126187977 1.085145132 1.270909022 1 18.81393987 4.748907577 24.9253916 1.141153114 0.597208521 0.790018676 0.087542627 606.0191708 1459844.656 0.019337121 0.275060556 56092.85916 -4.748907577 -0.543944593 NYSVGSRPLKPLS(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NYSVGSRPLKPLSPLR 16 2 O60825 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 NYSVGSRPLKPLS(1)PLR;NYSVGS(0.001)RPLKPLS(0.999)PLR 136.46 9.03E-06 1829330000 1851070 2635820 1421650 1425530 3264500 1002210 1803630 2630660 4966200 TRUE FALSE 1735214.833 2830978.855 1455372.209 1462111.513 3008119.338 1291531.757 1533192.426 2959103.692 4137309.137 0.419406618 0.684256061 0.351767818 0.353396728 0.727071446 0.312167091 0.370577198 0.715224218 1 21.98026133 0.991021815 4.291560413 0.998952423 0.466138928 0.616854219 0.140381175 0.115003225 6.40495279 0.130908972 0.033362033 9.795391865 -0.991021815 -0.532813495 NYTEEEDRFLICMLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NYTEEEDRFLICMLHK 16 1 O60264;A0A0A0MRP6;B7ZLQ5;P28370-2;P28370 O60264 SMARCA5;SMARCA1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5;Probable global transcription activator SNF2L1 0 ; 170.91 3.07E-09 112657000 186372 160816 167782 161129 210820 120391 204251 166301 213300 FALSE TRUE 174707.3092 172722.984 171761.8683 165263.8429 194263.0476 155145.9273 173625.4587 187064.0459 177698.852 0.983165098 0.971998311 0.966589634 0.930022007 1.093214984 0.873083453 0.977076986 1.052702613 1 17.43907484 1.329556669 7.890623701 1.025774582 0.968462246 0.147710563 0.055569637 0.383492189 28.19207697 0.033483433 0.01217303 21.35780756 -1.329556669 -0.057312335 NYVPSYDPSS(ph)PQTSQSWYLG ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NYVPSYDPSSPQTSQSWYLG 20 0 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;Q5VW31 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 NYVPSYDPS(0.106)S(0.42)PQT(0.117)S(0.085)QS(0.145)WY(0.127)LG;NYVPSYDPS(0.189)S(0.744)PQT(0.032)S(0.008)QS(0.015)WY(0.012)LG 87.566 0.0024598 49085000 114094 110778 108381 101594 132651 112203 159593 122000 145306 TRUE FALSE 106953.0602 118980.1184 110951.8485 104201.074 122233.1255 144594.1846 135663.5112 137231.9686 121053.4899 0.883519015 0.98287227 0.91655225 0.860785378 1.009744747 1.19446523 1.120690625 1.133647354 1 16.88528515 2.452618026 5.411661819 1.12364693 0.924435453 0.728076299 0.05748791 0.083443863 7.039314512 0.018395234 0.015665575 283.5424094 -2.452618026 -0.199211477 NYYEQWGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 NYYEQWGK 8 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;; 263.91 5.08E-13 21456000000 12639303 10805277 11324110 10792765 11859663 8486505 13627670 10141760 13263191 FALSE TRUE 11848231.59 11605310.95 11592723.24 11069725.62 10928252.91 10936421.23 11584327.4 11407981.06 11049478.74 1.072288736 1.050303931 1.049164717 1.001832384 0.989028819 0.989768068 1.048404877 1.03244518 1 23.39747498 3.32081133 5.628769009 1.012749682 1.055416306 0.566746509 0.019319102 0.180038748 9.360990945 0.005891268 0.007994901 2093.202913 -3.32081133 0.042666624 NYYGYQGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 NYYGYQGYR 9 0 Q1KMD3 Q1KMD3 HNRNPUL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 138.83 0.00029246 485660000 164275 315620 177079 181282 299720 113958 196990 262780 329610 FALSE TRUE 153993.321 338988.8332 181279.3975 185934.003 276181.2002 146855.8246 167453.1783 295588.6615 274595.9616 0.560799657 1.234500432 0.660167748 0.67711849 1.005772986 0.534806935 0.609816609 1.076449412 1 18.06695088 5.012706729 18.01475587 0.823620984 0.115595085 0.126608542 0.229574207 50534945.48 1269361398 0.054458242 916717133.5 102969.0555 -5.012706729 -0.708025899 PAAS(ph)PRPR ddPTM_SK-BR-3_Pertuzumab_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 81.263 0.014118 86552000 169910 232330 226790 226150 232780 218100 210240 220200 171760 TRUE FALSE 159275.6364 249531.9549 232169.5659 231953.3919 214498.3978 281061.9294 178716.4638 247692.4547 143092.1464 1.11309838 1.743855 1.622517879 1.621007146 1.499022855 1.964202345 1.248960675 1.730999646 1 17.12658497 -0.697151658 6.46559738 0.999999998 1.581079045 0.347798903 0.243837109 6.20E-09 9.59E-10 0.207962545 0.049017242 0.200839135 0.697151658 0.581079047 PAGAT(ph)LERPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 PAGATLERPK 10 1 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 PAGAT(1)LERPK;PAGAT(1)LERPK;PAGAT(1)LERPK 130.1 0.00046174 1478170000 3307220 1676390 1767690 1688190 2926850 1427510 3095470 2875230 2548850 TRUE FALSE 3100227.004 1800511.66 1809620.442 1731511.813 2696987.007 1839608.963 2631333.01 3234208.795 2123430.469 1.460008721 0.847925885 0.852215539 0.815431369 1.270108462 0.866338216 1.239189627 1.523105579 1 21.01796544 1.615792546 5.677578613 1.29808449 0.982435214 0.159230109 0.242092779 0.185055252 12.71056383 0.122042114 0.057981457 41.28502448 -1.615792546 -0.315649276 PAQPQEHPFASSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 PAQPQEHPFASSR 13 0 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;; 179.5 1.37E-05 1173890000 889280 769380 806800 841990 863720 651040 975030 731030 924350 FALSE TRUE 833621.5522 826345.6957 825937.677 863596.8889 795886.9153 838984.6792 828833.3032 822300.7047 770070.0135 1.082526962 1.073078657 1.072548811 1.121452431 1.033525396 1.089491429 1.076309022 1.067825899 1 19.55463009 0.634454485 2.213703003 1.00000508 1.077744274 0.568830571 0.021283722 1.612811334 8.924699237 0.017933492 0.004867872 4.30977388 -0.634454485 0.077739194 PAS(ph)PSLQLLPWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 PASPSLQLLPWR 12 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 PAS(0.665)PS(0.335)LQLLPWR;PAS(0.98)PS(0.02)LQLLPWR;PAS(1)PSLQLLPWR;PAS(0.989)PS(0.011)LQLLPWR 199.13 1.84E-07 629012000 1142157 1001373 893475 893071 1063386 758465 1073641 933642 996706 TRUE FALSE 1070671.432 1075515.699 914668.6489 915988.7138 979871.9531 977421.5328 912658.4992 1050209.259 830349.3296 1.28942289 1.2952569 1.101546802 1.103136573 1.180071951 1.177120879 1.099125954 1.264780041 1 19.66335888 4.067616793 3.259876625 1.137692707 1.293064349 0.480270326 0.068865549 0.195063721 3.996434978 0.015783505 0.038262405 11684.67918 -4.067616793 0.155371641 PASHSHAHQHSPIS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PASHSHAHQHSPISPR 16 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 PASHSHAHQHS(0.01)PIS(0.99)PR 84.499 0.012482 27640000 19223 19898 26820 23899 25055 25772 28427 26715 17849 TRUE FALSE 18019.86674 21371.26862 27456.18307 24512.2888 23087.28137 33211.95803 24164.63525 30050.42656 14869.88659 1.211836192 1.437217997 1.846428545 1.648451631 1.552619869 2.23350446 1.625071927 2.020891442 1 13.86010602 4.419357115 1.721603296 1.747500563 1.176042116 0.197948576 0.324026496 0.699790767 3.180925065 0.075669079 0.536953466 26263.77295 -4.419357115 -0.571458447 PAT(ph)PGASSVEQLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PATPGASSVEQLRK 14 1 Q9H3U1 Q9H3U1 UNC45A Protein unc-45 homolog A 1 PAT(0.964)PGAS(0.031)S(0.005)VEQLRK;PAT(0.676)PGAS(0.162)S(0.162)VEQLRK 93.226 0.0027226 576950000 1170450 594450 840850 730650 797290 568980 1064930 740830 969760 TRUE FALSE 1097193.624 638463.6965 860795.3591 749399.716 734674.0595 733235.2894 905253.6328 833324.2563 807900.7911 1.35807965 0.790274875 1.065471613 0.927588788 0.909361728 0.907580853 1.120500986 1.031468548 1 19.62381862 -0.480751382 6.253477983 0.999995997 0.997160968 0 0.154450228 0 0 0.134155537 0.031620763 0.33055872 0.480751382 -0.002835029 PAVEASTGGEATQETGKEEAGKEEPPPLT(ph)PPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PAVEASTGGEATQETGKEEAGKEEPPPLTPPAR 33 2 Q9C0C2;E9PKK0;E9PKE7 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 PAVEASTGGEATQETGKEEAGKEEPPPLT(1)PPAR 170.7 9.78E-13 395420000 1333200 444170 794200 1093700 945220 375130 471060 238040 295350 TRUE FALSE 1249757.392 477056.809 813038.799 1121766.194 870986.234 483423.9413 400428.9261 267759.818 246054.177 5.079196002 1.93882833 3.304308056 4.559021137 3.539814868 1.964705283 1.627401457 1.088214885 1 17.90861648 2.063585924 2.612471639 1.322628489 3.437048808 0.633705865 0.854509603 0.219523885 2.917951933 0.426492734 0.256545465 115.7673052 -2.063585924 2.114420319 PAYS(ph)PASWSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PAYSPASWSSR 11 0 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 PAYS(0.983)PAS(0.017)WSSR;PAYS(0.996)PAS(0.004)WSSR 145.14 3.82E-05 810480000 579570 525060 509790 534610 567950 371170 516090 472320 726110 TRUE FALSE 543295.7483 563935.9887 521882.4595 548328.9977 523345.498 478320.7536 438707.0956 531290.1917 604917.5502 0.898131899 0.932252649 0.86273321 0.906452454 0.865151785 0.790720576 0.725234531 0.878285299 1 19.20637899 2.440183782 4.378614003 0.81408466 0.898313515 0.010460392 0.074285185 0.299321647 13.01383615 0.024354209 0.020624163 275.5394465 -2.440183782 0.084228855 PCIQAQYGTPAPS(ph)PGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 PCIQAQYGTPAPSPGPR 17 0 P22736;F8VVX9;P22736-3 P22736 NR4A1 Nuclear receptor subfamily 4 group A member 1 1 PCIQAQYGT(0.03)PAPS(0.97)PGPR;PCIQAQYGT(0.003)PAPS(0.997)PGPR;PCIQAQYGT(0.004)PAPS(0.996)PGPR;PCIQAQYGTPAPS(1)PGPR;PCIQAQY(0.001)GT(0.286)PAPS(0.714)PGPR 296.46 3.89E-46 1490870000 1590100 1300090 1462330 1348260 959180 722777 1292490 800006 751040 TRUE FALSE 1490578.479 1396350.016 1497017.158 1382858.634 883849.8719 931430.9866 1098693.123 899888.5101 625686.5721 2.382308565 2.23170846 2.392599146 2.210145935 1.412608024 1.488654269 1.755980026 1.438241686 1 19.25508062 2.790443273 4.966791882 1.494065697 2.316051671 0.832594831 0.195902796 0.08199439 4.533678494 0.056986398 0.059740036 617.2246658 -2.790443273 0.821985973 PCSEETPAIS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 PCSEETPAISPSK 13 0 P33316-2;H0YNJ9 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 1 PCSEETPAIS(0.999)PS(0.001)K;PCSEETPAIS(1)PSK;PCSEETPAIS(0.999)PS(0.001)K 202.25 1.00E-07 351828000 1378450 521335 851590 711770 790590 652480 1046010 679850 1039030 TRUE FALSE 1292175.275 559935.1858 871790.1169 730035.2232 728500.2505 840840.3839 889170.5112 764730.769 865609.1806 1.492792942 0.646868354 1.007140562 0.843377404 0.841604117 0.971385705 1.027219363 0.883459633 1 19.72335627 2.03132428 24.75966169 0.979763778 0.92140599 0 0.219493661 1024.087706 809465.5238 0.075067198 0.055440349 107.479164 -2.03132428 -0.058357788 PCSEETPAIS(ph)PSKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 PCSEETPAISPSKR 14 1 P33316-2;H0YNJ9 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 1 PCSEETPAIS(0.976)PS(0.024)KR;PCSEETPAIS(0.995)PS(0.005)KR;PCSEETPAIS(0.999)PS(0.001)KR;PCSEETPAIS(0.966)PS(0.034)KR;PCSEETPAIS(1)PSKR;PCSEETPAIS(0.999)PS(0.001)KR;PCSEETPAIS(0.993)PS(0.007)KR 214.63 4.17E-12 21619080000 12763190 4664810 7114930 6393540 7151380 4995320 8728380 6046800 10773160 TRUE FALSE 11964364.72 5010197.386 7283699.5 6557609.061 6589739.462 6437387.792 7419640.449 6801756.291 8975049.999 1.333069423 0.558236153 0.811549741 0.73064875 0.734228719 0.717253697 0.82669628 0.757851632 1 23.09748855 -1.918538348 9.418798714 1.037381077 0.781262766 0.067439321 0.201833866 0.097669324 0.000844726 0.120474483 0.040168281 0.012063176 1.918538348 -0.256118311 PEEQLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PEEQLRK 7 1 A0A590UK20;Q9BXX2 A0A590UK20 ANKRD30B Ankyrin repeat domain-containing protein 30B 0 ; 91.626 0.026081 2809600000 1848640 1607370 1785750 1740890 1839780 1477740 2178150 1559560 1511740 FALSE TRUE 1732936.922 1726381.347 1828108.833 1785564.185 1695291.1 1904339.549 1851556.628 1754274.499 1259420.828 1.375979247 1.370774017 1.451547245 1.417766123 1.34608787 1.512075636 1.470165164 1.392921619 1 20.264329 0.949038948 21.74745496 1 1.423542705 0.876533978 0.049301144 994.210155 424276.7178 0.048610557 0.012152639 8.892808661 -0.949038948 0.423542706 PEINTNHLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PEINTNHLDK 10 0 Q13907 Q13907 IDI1 Isopentenyl-diphosphate Delta-isomerase 1 0 ; 119.74 0.00065187 393670000 1318880 705170 960890 892370 940570 611530 1127000 739600 1274740 FALSE TRUE 1236333.655 757381.5205 983682.7646 915269.725 866701.4263 788068.7836 958016.8126 831940.6881 1061977.659 1.164180475 0.713180277 0.926274443 0.86185403 0.816120207 0.742076612 0.902106372 0.783388126 1 20.01832199 4.752637293 24.8290608 0.837839389 1.164180718 0.577126791 0.086262422 1524.852612 2689551.366 0.018383052 0.389102159 56576.65833 -4.752637293 0.326341329 PFDFSAT(ph)DVMDIIINS(ph)GLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PFDFSATDVMDIIINSGLIK 20 0 Q9H9P8;C9JVN9;Q9H9P8-2 Q9H9P8 L2HGDH "L-2-hydroxyglutarate dehydrogenase, mitochondrial" 2 PFDFS(0.49)AT(0.566)DVMDIIINS(0.944)GLIK 42.806 0.083442 830610000 295940 527350 470570 460090 487700 415090 509280 436580 460920 TRUE FALSE 277417.6437 566395.5427 481732.1426 471896.6883 449398.0093 534919.7446 432918.1919 491087.974 383989.4743 0.722461583 1.475028824 1.254545176 1.228931312 1.170339396 1.393058353 1.127422028 1.278909988 1 18.55070724 -1.096573892 4.487960548 0.999979302 1.234672925 0.079614596 0.200899009 3.69E-05 7.42E-06 0.17233062 0.040615137 0.08006194 1.096573892 0.234693622 PFLELDTNLPANRVPAGLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PFLELDTNLPANRVPAGLEK 20 1 P30046;B5MC82;P30046-2;A6NHG4 P30046 DDT;DDTL D-dopachrome decarboxylase;D-dopachrome decarboxylase-like protein 0 160.3 2.21E-11 166920000 241060 198010 226470 222560 268730 152780 309730 208990 464810 FALSE TRUE 225972.4849 212670.8664 231841.9753 228271.2664 247625.0298 196885.1058 263288.8619 235082.8615 387230.2082 0.583561097 0.549210423 0.598718722 0.589497569 0.639477563 0.508444594 0.679928519 0.607088126 1 18.56283198 -4.999999996 0.277083593 3.939543891 0.566138002 0.897538737 0.043376016 57.87783649 0.55688698 97.59558083 0.04450525 1.00E-05 4.999999996 -3.373405889 PFSAPKPQTS(ph)PSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PFSAPKPQTSPSPK 14 1 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 PFSAPKPQT(0.182)S(0.815)PS(0.003)PK 141.6 5.83E-06 343530000 608460 227540 367160 375420 342000 263460 467680 308670 289940 TRUE FALSE 570377.5747 244387.2984 375869.2086 385053.9128 315140.6996 339516.6251 397555.7257 347208.129 241547.1409 2.361350967 1.011758191 1.556090489 1.594114968 1.30467576 1.40559157 1.645872206 1.437434232 1 17.88194525 -2.117695738 1.66349631 0.224924235 1.493780519 0.184632403 0.344612126 643313.1959 135458.9213 1881397.97 0.083741761 0.007626131 2.117695738 1.268856284 PFVPNVHAAEFVPSFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PFVPNVHAAEFVPSFLR 17 0 P15170-2;P15170-3;Q8IYD1 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ; 115.87 0.00029391 621380000 1243210 1161680 1117470 972090 1250530 816480 1201300 1167570 1043530 FALSE TRUE 1165399.705 1247691.996 1143976.916 997035.4751 1152318.418 1052184.522 1021176.217 1313343.685 869358.1015 1.340528953 1.435187633 1.315886876 1.14686396 1.325481888 1.210300473 1.174632428 1.510705062 1 19.72959104 -5 0.116145427 0.122317951 1.447439285 0.353697054 0.118640789 165.7035579 1.261137534 35.24956481 1.186300226 1.00E-05 5 1.325121334 PGFQGQS(ph)S(ph)SQAQQVIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PGFQGQSSSQAQQVIK 16 0 Q9ULJ3 Q9ULJ3 ZBTB21 Zinc finger and BTB domain-containing protein 21 2 PGFQGQS(0.667)S(0.667)S(0.667)QAQQVIK 46.3 0.085608 0 117090 83409 77859 80562 91959 56966 104810 42088 88541 TRUE FALSE 109761.5459 89584.68915 79705.85225 82629.35731 84736.91108 73411.15943 89094.71351 47342.77945 73762.9351 1.48803116 1.214494638 1.080567796 1.120201592 1.148773581 0.995230997 1.207852065 0.641823422 1 16.17060844 8 0.405038358 1.005245251 8.508402853 0.521984391 0.147455346 63.29223142 0.832495062 0.093261169 380.4254089 100000000 -8 7.503157602 PGHLQEGFGCVVTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 PGHLQEGFGCVVTNR 15 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;;; 261.61 5.88E-25 3216350000 3525060 2826950 3292160 3177570 3194950 2775460 3601230 2890630 2927690 FALSE TRUE 3304432.787 3036260.319 3370251.59 3259111.826 2944031.515 3576690.246 3061258.994 3251531.519 2439039.625 1.35480898 1.244858955 1.381794521 1.336227502 1.207045381 1.466433841 1.255108347 1.333119595 1 21.21788177 -0.669940093 1.073240131 0.988038636 1.320129395 0.650578822 0.074219894 41.65567702 23.96531672 2.107738565 0.019523743 0.213825702 0.669940093 0.332090759 PGPTPSGTNVGSSGRS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 PGPTPSGTNVGSSGRSPSK 19 1 P60468 P60468 SEC61B Protein transport protein Sec61 subunit beta 1 PGPTPSGTNVGS(0.01)S(0.03)GRS(0.957)PS(0.003)K;PGPTPSGTNVGSS(0.001)GRS(0.998)PS(0.001)K;PGPTPSGTNVGSS(0.001)GRS(0.988)PS(0.011)K;PGPTPSGTNVGSS(0.091)GRS(0.901)PS(0.007)K;PGPTPSGTNVGS(0.001)S(0.009)GRS(0.988)PS(0.001)K;PGPTPSGTNVGSSGRS(0.954)PS(0.046)K;PGPTPSGTNVGSS(0.005)GRS(0.952)PS(0.042)K 201.61 6.62E-16 12620600000 3215230 1464280 1625730 1670480 2204180 1149585 2335040 1620070 2325140 TRUE FALSE 3013994.494 1572696.815 1664293.083 1713347.345 2031072.594 1481451.528 1984922.429 1822339.306 1937059.113 1.555964128 0.811899236 0.85918549 0.884509581 1.048534131 0.764794176 1.02470927 0.9407763 1 20.88543655 4.743706838 24.9900994 0.907252574 1.555964399 0.827217466 0.091710201 208.5142357 1012515.381 0.020894487 0.176812835 55425.14496 -4.743706838 0.648711825 PGPYDRPGTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PGPYDRPGTAR 11 1 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 66.267 0.057618 205090000 104510 76376 97463 94166 82436 80866 96132 72138 81252 FALSE TRUE 97968.90566 82030.95851 99774.86839 96582.45898 75961.80909 104210.7015 81717.89905 81144.5881 67690.51629 1.447306226 1.211853048 1.473985927 1.426824085 1.122192786 1.539517013 1.207228184 1.198758593 1 16.0466661 1.069645907 1.407523608 1.005500411 1.356657085 0.457612996 0.128286508 0.350938228 1.407632922 0.10855607 0.032770869 11.73940017 -1.069645907 0.351156673 PGSGAAAS(ph)GGRGDLPYGPGRRS(ph)SGGGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 PGSGAAASGGRGDLPYGPGRRSSGGGGR 28 3 P54826 P54826 GAS1 Growth arrest-specific protein 1 2 PGS(0.001)GAAAS(0.995)GGRGDLPY(0.014)GPGRRS(0.52)S(0.47)GGGGR;PGS(0.004)GAAAS(0.975)GGRGDLPY(0.032)GPGRRS(0.519)S(0.47)GGGGR;PGS(0.001)GAAAS(0.978)GGRGDLPY(0.032)GPGRRS(0.519)S(0.47)GGGGR 88.683 0.0047243 2599460000 498950 800910 767700 745970 864290 735660 868950 830070 1118790 TRUE FALSE 467721.6102 860210.2097 785910.2065 765112.8531 796412.1498 948033.0996 738659.0144 933706.0667 932056.7213 0.501816681 0.92291616 0.843199978 0.820886579 0.854467471 1.017140994 0.792504359 1.001769576 1 19.83005823 4.741362306 24.91083749 0.891659241 0.501816533 0.70861655 0.081073811 129.8890572 1154826.156 0.017156361 0.119441435 55126.73944 -4.741362306 -0.389842708 PGSGAAASGGRGDLPY(ph)GPGRRS(ph)SGGGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PGSGAAASGGRGDLPYGPGRRSSGGGGR 28 3 P54826 P54826 GAS1 Growth arrest-specific protein 1 2 PGS(0.002)GAAAS(0.234)GGRGDLPY(0.8)GPGRRS(0.486)S(0.478)GGGGR 48.831 0.067075 459490000 415550 628570 606410 578780 704220 584400 708250 676200 924090 TRUE FALSE 389541.4673 675109.9768 620794.3316 593632.4747 648913.4019 753106.7931 602054.4876 760625.0585 769853.4092 0.50599434 0.876933152 0.806379921 0.771098066 0.842905148 0.978247007 0.782037827 0.988012847 1 19.55422424 4.739914211 24.81614273 0.863126954 0.505994212 0.64801779 0.085924946 64.12047217 1175418.031 0.018391969 0.115226318 54943.23299 -4.739914211 -0.357132743 PGWLSS(ph)PTLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 PGWLSSPTLGR 11 0 Q5XPI4;Q5XPI4-2;C9JS59;C9J266 Q5XPI4 RNF123 E3 ubiquitin-protein ligase RNF123 1 PGWLS(0.004)S(0.992)PT(0.004)LGR;PGWLS(0.048)S(0.949)PT(0.003)LGR;PGWLSS(1)PTLGR;PGWLSS(0.999)PTLGR 261.22 1.17E-20 823230000 2291010 1751650 1882270 1933790 2074370 1327300 2367710 1791990 1828700 TRUE FALSE 2147619.774 1881343.989 1926918.333 1983414.325 1911457.348 1710469.963 2012693.866 2015723.896 1523478.156 1.409682026 1.234900534 1.264815203 1.301898762 1.254666724 1.122740064 1.32111764 1.32310653 1 20.53893738 -1.386568885 3.155556174 0.996875236 1.270594427 0.583291184 0.073829756 34607136.2 46448786.98 994699.0387 0.016467557 0.041061151 1.386568885 0.273719191 PIPEAEEAQRPEPVGTSSNADSAS(ph)PDLGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PIPEAEEAQRPEPVGTSSNADSASPDLGPR 30 1 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 PIPEAEEAQRPEPVGTSSNADSAS(1)PDLGPR;PIPEAEEAQRPEPVGTSSNADSAS(1)PDLGPR 310.71 1.89E-92 647260000 342720 243847 283010 278080 222870 216160 321460 213479 186501 TRUE FALSE 321269.767 261901.6856 289723.1308 285216.0036 205366.6892 278561.8829 273260.0573 240132.3231 155372.7783 2.067735227 1.685634308 1.864696854 1.83568838 1.321767503 1.792861569 1.758738309 1.545523777 1 17.24537424 -2.342004969 0.211598188 1.34E-17 1.89031239 0.668919863 0.174702656 24.35625688 0.666864562 12.08354583 0.388154247 0.004549829 2.342004969 1.89031239 PIPQT(ph)PESAGNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PIPQTPESAGNK 12 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 PIPQT(0.981)PES(0.019)AGNK;PIPQT(0.997)PES(0.003)AGNK 181.76 0.00019842 273490000 1257880 501450 827480 785980 763530 604760 914890 636690 569390 TRUE FALSE 1179151.536 538577.8798 847108.2164 806149.5775 703565.4337 779344.3945 777710.7379 716182.148 474355.1306 2.485799057 1.135389595 1.78581017 1.699464231 1.483204014 1.64295555 1.639511597 1.509801627 1 18.85560803 -2.64165312 0.261155868 2.51E-12 1.701655329 0.312547434 0.330505379 63.87985425 1.881038469 36.72084479 0.416573099 0.002282164 2.64165312 1.701655329 PIRPGQHPAAS(ph)PTHPSAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PIRPGQHPAASPTHPSAIR 19 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 1 PIRPGQHPAAS(0.995)PT(0.005)HPSAIR;PIRPGQHPAAS(0.933)PT(0.067)HPSAIR 124.86 1.72E-05 711460000 216874 216043 253037 261326 255592 182844 263798 248014 210402 TRUE FALSE 203300.2435 232039.0485 259039.1571 268032.0676 235518.8353 235628.0946 224243.9389 278979.0938 175284.547 1.159829814 1.323784969 1.477820844 1.529125483 1.343637186 1.344260511 1.279313795 1.591578372 1 17.41933929 2.492911306 23.86230761 1.325235613 1.387463159 0.025135184 0.171039958 1734.92995 2621873.981 0.052282402 0.047919675 311.1080911 -2.492911306 0.062227547 PIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PISPGLSYASHTVGFTPPTSLTR 23 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 PIS(0.999)PGLS(0.001)YASHTVGFTPPTSLTR;PIS(1)PGLSYASHTVGFTPPTSLTR 305.57 1.34E-62 1700430000 900920 535700 697010 676860 594750 533720 698300 572430 526590 TRUE FALSE 844533.0254 575363.7854 713543.4064 694229.3735 548040.7341 687796.2998 593596.3977 643899.1456 438698.7271 1.925086564 1.311523717 1.626499833 1.5824741 1.249241678 1.56781011 1.353084386 1.467747923 1 18.74287099 -3.303928107 0.139605336 2.03E-12 1.7021731 0.507618412 0.175011182 67.4617317 0.912754857 21.12669889 1.083619496 0.000496675 3.303928107 1.7021731 PIS(ph)PSPSAILER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 PISPSPSAILER 12 0 Q5T5P2;Q5T5P2-3;Q5T5P2-7;Q5T5P2-9;Q5T5P2-2;Q5T5P2-10;Q5T5P2-8;Q5T5P2-6;Q5T5P1;Q5T5P2-4;Q5T5P0 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 PIS(0.989)PS(0.011)PSAILER;PIS(0.934)PS(0.066)PS(0.001)AILER;PIS(0.922)PS(0.076)PS(0.003)AILER;PIS(0.791)PS(0.192)PS(0.018)AILER 190.78 6.50E-06 345184000 414971 266942 349810 328358 285173 277497 353649 283853 260132 TRUE FALSE 388998.7059 286706.6634 358107.6584 336784.2222 262776.6629 357605.8791 300622.6156 319292.6719 216714.2887 1.794984116 1.322970743 1.652441381 1.554047148 1.212548856 1.650125985 1.3871841 1.473334656 1 17.72543475 -3.09639496 0.23831556 2.00E-10 1.560698672 0.498938961 0.165230916 50.08819271 1.127088849 25.30999018 0.248537965 0.000800949 3.09639496 1.560698671 PIT(ph)PVYTVAPNVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PITPVYTVAPNVQR 14 0 B7Z8Z7;A0AV96;A0AV96-2 B7Z8Z7 RBM47 RNA-binding protein 47 1 PIT(1)PVYTVAPNVQR 156.2 6.30E-05 141420000 113620 100600 91736 87737 145720 66988 126660 73642 489680 TRUE FALSE 106508.727 108048.5287 93912.02124 89988.47996 134275.739 86326.34814 107668.5089 82836.36581 407949.2445 0.26108328 0.264857774 0.23020516 0.220587441 0.32914815 0.211610511 0.263926237 0.203055569 1 18.63803014 -1.511576786 3.213264862 1.020226528 0.249043836 0.977223187 0.03607716 21682950.37 27135063.68 3864176.103 0.0077512 0.030790959 1.511576786 -0.771182692 PKHEFSVDMTCGGCAEAVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PKHEFSVDMTCGGCAEAVSR 20 1 O00244 O00244 ATOX1 Copper transport protein ATOX1 0 ; 178.75 3.65E-17 281950000 195121 145899 171332 166010 176027 134210 195552 145169 218970 FALSE TRUE 182908.7249 156701.5138 175396.0759 170270.0977 162202.5495 172954.2483 166230.793 163293.6692 182422.4924 1.00266542 0.85900325 0.96148273 0.933383244 0.889158718 0.948097167 0.911240664 0.895139996 1 17.4769241 -2.247735634 2.347221947 1.298393959 0.921798913 0.249636385 0.040511788 9607524.453 1562233.69 15244965.6 0.009080749 0.00565281 2.247735634 -0.376595046 PKPSSS(ph)PVIFAGGQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PKPSSSPVIFAGGQDR 16 1 Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3 Q15366;Q15366-2 PCBP2 Poly(rC)-binding protein 2 1 PKPSS(0.14)S(0.859)PVIFAGGQDR;PKPSS(0.005)S(0.995)PVIFAGGQDR 151.82 3.68E-07 650670000 693050 319770 472820 432820 386480 340030 554440 386760 328680 TRUE FALSE 649673.2376 343446.1035 484035.5137 443926.894 356127.4198 438191.1411 471306.8692 435047.8374 273821.1846 2.372618607 1.254271484 1.767706594 1.621229177 1.300583884 1.600282102 1.72122135 1.5888027 1 18.06287454 -2.495323175 0.407698037 2.35E-39 1.638876827 0.316723978 0.302609436 98.254245 4.528634745 87.90300708 0.166999595 0.003196516 2.495323175 1.638876827 PKQES(ph)QFEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PKQESQFEFK 10 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 PKQES(1)QFEFK 53.683 0.086008 34397000000 782620 3192100 2207300 2734600 2967200 3752500 1843100 2068900 1269400 TRUE FALSE 733637.2112 3428446.405 2259658.198 2804774.466 2734168.081 4835785.833 1566744.266 2327206.719 1057528.939 0.693727787 3.241940979 2.136734149 2.652196419 2.585430979 4.572721987 1.481514318 2.200608071 1 20.01226571 4.752245691 23.89606708 2.567882963 0.693725443 0.248579093 0.96841136 1649.828584 2880738.84 0.20946355 3.992917652 56525.66644 -4.752245691 -1.87415752 PLELELCPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PLELELCPGR 10 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 146.81 6.51E-05 49736000 86434 74486 76447 72952 82257 54394 80941 65604 84122 FALSE TRUE 81024.25023 80001.02094 78260.35894 74824.07183 75796.86703 70096.66479 68804.64847 73794.80381 70081.49475 1.156143295 1.141542731 1.116705048 1.067672316 1.08155323 1.000216463 0.98178055 1.052985586 1 16.09674593 2.894553713 0.86739803 1.000504985 1.149209501 0.839503492 0.02410819 0.204350113 0.336134904 0.01346644 0.015126571 784.4291305 -2.894553713 0.148704516 PLENLEEEGLPKNPDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PLENLEEEGLPKNPDLR 17 1 Q15008;Q15008-4;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 89.502 0.0036786 63920000 109810 74320 91102 101110 102740 57713 102020 64555 122150 FALSE TRUE 102937.1881 79822.73013 93262.98246 103704.6538 94671.21483 74373.80621 86723.04811 72614.83385 101762.3759 1.011544662 0.784403169 0.916478037 1.019086405 0.930316475 0.730857604 0.852211314 0.713572509 1 16.63484473 2.265875003 24.99534884 0.813277195 0.913964406 0.208132137 0.100414513 343.0507965 313923.9863 0.032860221 0.027486564 184.4484472 -2.265875003 0.100687211 PLFLVHPIEGSTTVFHSLASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PLFLVHPIEGSTTVFHSLASR 21 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 237.31 4.30E-30 246250000 116970 95398 131770 118170 116500 94273 132940 114220 95600 FALSE TRUE 109649.0565 102461.3672 134895.6466 121202.4423 107350.5599 121488.0847 113006.8812 128480.6184 79643.7424 1.376744151 1.28649614 1.693738172 1.521807472 1.347884425 1.525393974 1.418904709 1.613191628 1 16.28127339 -1.307973591 3.699695524 0.998715523 1.472173044 0.593635819 0.122991036 9299934.366 3288432.084 96148.76009 0.02809447 0.049206946 1.307973591 0.473457521 PLHISTFINELDSGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PLHISTFINELDSGFR 16 0 E9PGT1;Q15631 E9PGT1 TSN Translin 0 199.37 3.83E-11 85850000 51895 112930 88237 101490 129420 87630 118780 116160 83862 FALSE TRUE 48646.98459 121291.4547 90330.02331 104094.4052 119255.8753 112927.3584 100970.0417 130662.8317 69864.89043 0.696300879 1.73608595 1.292924425 1.489938717 1.706950008 1.616367789 1.445218637 1.870221665 1 16.09228001 4.747268483 24.99877509 1.531133935 0.696300456 0.525570909 0.245648233 832.1636183 2388945.744 0.051130327 0.612585261 55881.55511 -4.747268483 -0.834833479 PLPKGT(ph)MMETLSR ddPTM_SK-BR-3_Pertuzumab_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 52.008 0.084062 867660000 1449600 993090 989090 1031700 1020600 644320 1118100 873510 1469700 TRUE FALSE 1358872.124 1066619.417 1012551.682 1058175.169 940446.1929 830324.7243 950451.2849 982569.6463 1224397.575 1.109829153 0.871138132 0.82697949 0.864241477 0.768088905 0.678149599 0.776260346 0.802492316 1 20.22364066 7.99999807 0.825914446 0.793784597 94.52720946 0.532309453 0.083720487 406.3678387 1.245693171 0.025166439 71439.77769 99999555.51 -7.99999807 93.73342486 PLS(ph)TLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PLSTLPR 7 0 D6RD84;D6RBG1;A0A0G2JP87;A0A0G2JPU2;B0S7V6;A0A0G2JII5;A0A0G2JJ47;A2ABH1;A0A494C023;A0A494C0D7;A2ABH5;A2ABH3;A0A0G2JIT9;A0A0G2JJZ1;A0A0G2JIL2;A0A0G2JI40;E9PGB6;A0A0G2JJK7;A2ABH4;E7EQE8;Q5STF0;A0A0G2JI86;B0V092;D6RDI7;D6RB88;D6R9W9;Q8TD31;Q8TD31-2 D6RD84 CCHCR1 Coiled-coil alpha-helical rod protein 1 1 PLS(0.5)T(0.5)LPR 72.485 0.060028 0 327010 413590 234380 252220 512520 151980 226200 351660 432620 TRUE FALSE 306543.0278 444212.6339 239939.6043 258692.3922 472268.7466 195854.1588 192283.4099 395565.5251 360412.9272 0.850532833 1.232510269 0.665735289 0.717766686 1.310354627 0.543416021 0.533508638 1.097534232 1 18.45929123 PLTS(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 PLTSPLR 7 0 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 PLT(0.033)S(0.967)PLR;PLT(0.283)S(0.717)PLR;PLT(0.271)S(0.729)PLR 118.07 0.0053386 407838000 1162510 1483490 842210 838490 1923500 494893 777890 1316150 1664720 TRUE FALSE 1089750.574 1593329.143 862187.6189 860007.073 1772436.069 637760.5752 661252.6161 1480474.225 1386867.477 0.785764027 1.148869066 0.621679889 0.620107607 1.278014012 0.459856897 0.47679582 1.067495091 1 20.40339851 PMMS(ph)NLKEIHLVS(ph)NEDPT(ph)VAAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PMMSNLKEIHLVSNEDPTVAAFK 23 1 Q8IXQ6-3;Q8IXQ6-2;Q8IXQ6 Q8IXQ6-3 PARP9 Poly [ADP-ribose] polymerase 9 3 PMMS(1)NLKEIHLVS(1)NEDPT(1)VAAFK 43.992 0.054798 850410000 76768 639570 464040 404100 527160 458510 279060 312870 319990 TRUE FALSE 71963.22791 686924.4283 475047.2479 414469.8901 485758.9801 590874.3937 237217.5437 351932.5082 266581.6018 0.269948216 2.576788584 1.781995624 1.554758045 1.822177438 2.216486021 0.889849645 1.320168031 1 18.02421769 1.704726799 9.07546242 1.087247925 1.811670656 0.180952839 0.605320479 0.15795684 27.21478218 0.268436264 0.143687677 50.66718763 -1.704726799 0.724422731 PPRAHELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PPRAHELK 8 1 Q9Y426-2;Q9Y426-3;Q9Y426 Q9Y426-2 C2CD2 C2 domain-containing protein 2 0 60.59 0.083296 198710000 77881 264260 189180 227260 253750 218450 161940 211250 159000 FALSE TRUE 73006.56723 283826.0854 193667.4389 233091.8764 233821.4986 281512.9688 137658.6004 237625.0275 132461.8728 0.551151555 2.14270023 1.46206176 1.759690327 1.765198495 2.125237721 1.039231874 1.793912637 1 17.01521764 -0.515059775 9.100218856 0.99999499 1.612296247 0.121554086 0.482991511 0 0 0.416316311 0.098126696 0.305450067 0.515059775 0.612301257 PPSNIKNS(ph)RMT(ph)QVFHKNT(ph)S(ph)VTSLPFVDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PPSNIKNSRMTQVFHKNTSVTSLPFVDTK 29 3 A0A0A0MTH5;Q9NR20-3;Q9NR20-4 A0A0A0MTH5 DYRK4 Dual specificity tyrosine-phosphorylation-regulated kinase 4 4 PPS(0.172)NIKNS(0.666)RMT(0.632)QVFHKNT(0.632)S(0.632)VT(0.632)S(0.632)LPFVDT(0.001)K 40.104 0.071176 251070000 117000 40859 60448 64921 79258 35893 90047 42850 128750 TRUE FALSE 109677.1789 43884.24287 61881.85511 66586.98277 73033.39639 46254.72643 76545.28831 48199.91682 107260.7932 1.022528135 0.409135916 0.576928934 0.620795174 0.680895546 0.431236102 0.713637164 0.449371251 1 16.7107633 -1.486957244 2.916577774 1.01290536 0.594567138 0.311629792 0.178861683 32307345.8 36289098.47 3359162.543 0.041628237 0.032586878 1.486957244 -0.418338222 PQRS(ph)RPNLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PQRSRPNLIK 10 2 Q9NWF9-1 Q9NWF9-1 RNF216 E3 ubiquitin-protein ligase RNF216 1 PQRS(1)RPNLIK 76.943 0.027157 619870000 1062000 869850 855180 917890 1106900 858740 1005000 768720 1210000 TRUE FALSE 995531.3157 934254.5991 875465.2734 941444.6114 1019968.539 1106644.298 854309.58 864696.3842 1008043.183 0.987587965 0.926800176 0.86847993 0.933932819 1.011830203 1.097814375 0.847493038 0.857796966 1 19.94312601 4.744986896 22.36810839 0.935373525 0.987588063 0.023182058 0.077960581 693.1214236 2412246.001 0.01883187 0.16778071 55588.74845 -4.744986896 0.052214538 PQS(ph)PSIPSS(ph)HLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PQSPSIPSSHLR 12 0 Q9P2P6;H3BN21 Q9P2P6 STARD9 StAR-related lipid transfer protein 9 2 PQS(0.499)PS(0.501)IPS(0.017)S(0.983)HLR 47.991 0.095163 14367000000 706830 2559400 1879600 2277200 2373900 2787800 1536900 1506600 1485300 TRUE FALSE 662590.772 2748900.639 1924185 2335636.807 2187463.47 3592592.604 1306456.113 1694702.326 1237393.835 0.535472825 2.221524435 1.555030376 1.887545212 1.767798908 2.903354214 1.05581269 1.369573921 1 20.23887332 1.606072367 25 1.159448049 1.841311985 0.22072254 0.591383627 0.254728306 3469.098874 0.270308667 0.135122449 40.3712658 -1.606072367 0.681863936 PQYQTWEEFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PQYQTWEEFSR 11 0 P49458;Q6P2S0;Q659G3;E9PE20;P49458-2 P49458 SRP9;DKFZp564M2223 Signal recognition particle 9 kDa protein 0 139.54 9.08E-05 152680000 320650 168080 192360 166310 187290 157210 224610 142210 231190 FALSE TRUE 300581.0889 180524.8181 196922.87 170577.7962 172580.9989 202593.9749 190931.8157 159965.2315 192602.8955 1.560626013 0.937290261 1.022429437 0.885645025 0.896045714 1.051873984 0.991323704 0.830544272 1 17.55526987 4.739848753 24.99824463 0.959562844 1.560626208 0.887345288 0.068115595 33.4357168 648800.5465 0.015447787 0.096286625 54934.95243 -4.739848753 0.601063363 PRPATS(ph)TPDLASHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PRPATSTPDLASHR 14 1 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 PRPAT(0.001)S(0.87)T(0.129)PDLASHR;PRPATS(0.956)T(0.044)PDLASHR 167.14 2.24E-06 711250000 330030 286730 282170 283400 358700 184398 377860 269390 616890 TRUE FALSE 309374.0114 307959.7875 288863.2057 290672.5238 330529.1489 237630.7091 321203.4009 303023.9345 513927.0737 0.601980373 0.599228574 0.562070419 0.565590993 0.643144068 0.462382157 0.624998015 0.589624384 1 18.97120413 0.133147772 1.438957798 1.000344354 0.577947048 0.88086045 0.048442218 3.346749296 5.189132141 0.043004545 0.011881737 1.3587757 -0.133147772 -0.422397306 PRPPGRPVS(ph)GHGMDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 PRPPGRPVSGHGMDSR 16 2 P36507;G5E9C7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(0.999)GHGMDS(0.001)R;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR 113.49 0.00034291 1426830000 693516 506138 573344 634533 678366 479949 639043 519212 507448 TRUE FALSE 650110.0715 543612.9842 586943.9904 650816.191 625089.8708 618502.485 543224.4347 584036.7611 422751.6506 1.537806111 1.285892044 1.388389589 1.539476405 1.478621952 1.463039787 1.284972948 1.381512669 1 18.68945086 0.391269731 0.849219345 0.997446017 1.421403514 0.707852803 0.086201437 1.311917483 1.300938107 0.094985869 0.029292938 2.46189616 -0.391269731 0.423957497 PS(ph)PS(ph)QWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PSPSQWK 7 0 F5H142;H3BM22;Q6IMN6-6;Q6IMN6-4;Q6IMN6-10;Q6IMN6-7;Q6IMN6-3;Q6IMN6-2;Q6IMN6-9;Q6IMN6 F5H142 CAPRIN2 Caprin-2 2 PS(1)PS(1)QWK 46.016 0.097399 70322000 56806 82936 71691 72235 91041 71954 84729 82013 90059 TRUE FALSE 53250.61386 89076.66773 73391.54437 74088.67239 83891.0071 92725.95172 72024.67304 92252.50358 75027.5711 0.709747271 1.187252452 0.978194326 0.987485951 1.118135718 1.235891691 0.959976073 1.229581369 1 16.19513323 2.737211409 24.20977022 1.10469624 1.004687795 0.174276325 0.143840949 180.1662043 3232806.302 0.042224962 0.041878658 546.0235936 -2.737211409 -0.100008445 PS(ph)SPGGLPEEDSVLFNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PSSPGGLPEEDSVLFNK 17 0 Q5R372-4;Q5R372;Q5R372-3;A0A0U1RQY6;A0A0C4DG54;Q5R372-2 Q5R372-4 RABGAP1L Rab GTPase-activating protein 1-like 1 PS(0.5)S(0.5)PGGLPEEDSVLFNK 177.84 1.05E-09 97800000 271870 129320 167290 153520 124450 136700 207970 133570 121920 TRUE FALSE 254854.142 138894.9874 171258.1978 157459.5831 114676.199 176163.0709 176786.8292 150246.5085 101570.7644 2.509128917 1.36747014 1.686097361 1.550245133 1.129027626 1.734387567 1.740528688 1.47922987 1 16.63212568 4.743741257 24.92804132 1.514304916 2.50912935 0.627544034 0.250811311 352.212622 1694710.4 0.055409489 0.470893579 55429.53777 -4.743741257 0.994824434 PSADLTNSSAPS(ph)PSHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PSADLTNSSAPSPSHK 16 0 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 PSADLTNS(0.008)S(0.041)APS(0.824)PS(0.127)HK;PSADLTNS(0.002)S(0.066)APS(0.877)PS(0.055)HK 109.83 0.00060682 584780000 605490 290630 404290 407200 412110 318420 496580 411150 463870 TRUE FALSE 567593.4617 312148.5476 413879.9497 417649.4414 379744.543 410342.6849 422122.439 462482.9826 386447.1003 1.468748145 0.807739397 1.070987334 1.080741558 0.982655951 1.061834038 1.092316228 1.19675625 1 18.55991142 1.722251949 3.565270218 1.110232941 1.042320386 0 0.170842552 0.899675147 25.31586524 0.088447128 0.042284754 52.75358139 -1.722251949 -0.067912556 PSATSHSGSGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 PSATSHSGSGSK 12 0 Q14444-2;Q14444;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ;;; 132.32 0.00018301 268003000 415907 334906 425110 403358 416547 319752 473990 384578 500470 FALSE TRUE 389876.1233 359702.7887 435193.81 413708.8492 383833.0789 412059.2117 402919.5998 432593.4099 416938.3238 0.935093037 0.862724216 1.04378462 0.992254311 0.92059918 0.98829776 0.966376984 1.037547726 1 18.66947446 4.001543888 8.053596443 0.987684261 0.900783195 0.502042493 0.038569094 0.174829108 47.86712331 0.009108157 0.019223194 10035.61261 -4.001543888 -0.086901066 PSGGFVISGVLS(ph)PDTISSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PSGGFVISGVLSPDTISSK 19 0 Q03188;H0Y8J2;H0Y9W1 Q03188 CENPC Centromere protein C 1 PSGGFVISGVLS(0.995)PDT(0.005)ISSK 164.69 1.11E-10 0 137790 68509 101610 93550 92550 69448 120880 69363 72980 TRUE FALSE 129165.9699 73581.47764 104020.2372 95950.65138 85281.49633 89496.51021 102755.1662 78023.12324 60799.16653 2.124469417 1.210238262 1.710882618 1.578157347 1.402675418 1.472002255 1.690075244 1.283292645 1 15.89176393 -2.908137555 0.231559478 1.22E-12 1.627190498 0.390108403 0.242496476 60.0366164 1.426906442 29.89449555 0.401932706 0.001235556 2.908137555 1.627190498 PSHLTNKFEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PSHLTNKFEDK 11 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 206.51 1.57E-08 206720000 894060 607120 707850 798450 770530 423160 855960 611570 683510 FALSE TRUE 838102.3805 652071.7965 724640.5363 818939.5788 710015.682 545319.4226 727616.7443 687925.8607 569427.7654 1.471832656 1.145135233 1.272576752 1.438179921 1.246893329 0.957662158 1.277803417 1.208100312 1 19.11915332 2.463315483 24.99657715 1.138037027 1.296069163 0.374818158 0.129294685 323.7049155 586092.8095 0.043348069 0.036284732 290.6132981 -2.463315483 0.158032137 PSMS(ph)PTPLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 PSMSPTPLDR 10 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 PSMS(0.998)PT(0.001)PLDR;PSMS(1)PTPLDR;PSMS(0.997)PT(0.003)PLDR;PSMS(0.996)PT(0.004)PLDR;PS(0.002)MS(0.943)PT(0.055)PLDR;PSMS(0.5)PT(0.5)PLDR;PSMS(0.787)PT(0.213)PLDR 234.29 1.71E-11 4148730000 5100800 3171780 3842270 3520010 3429560 2942580 4002310 3221580 3163800 TRUE FALSE 4781550.033 3406621.891 3933410.459 3610339.416 3160216.192 3792055.077 3402200.771 3623801.355 2635741.341 1.814119602 1.292472003 1.492335533 1.369762412 1.198985706 1.438705315 1.290794631 1.37486987 1 21.32977737 7.999999971 0.035805305 6.65E-08 3.4992016 0.541242086 0.141897295 798.9538887 2.184507214 62.29126771 179.3013388 99999993.36 -7.999999971 3.499201533 PSQMEHAMETMMFTFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PSQMEHAMETMMFTFHK 17 0 P60903 P60903 S100A10 Protein S100-A10 0 ; 150.28 1.70E-07 127110000 267260 200089 227330 192623 323900 154634 244840 242150 446340 FALSE TRUE 250532.6737 214903.7978 232722.375 197566.0323 298462.2005 199274.3255 208128.515 272382.9605 371842.9705 0.673759338 0.577942343 0.625861972 0.531315765 0.802656563 0.53590989 0.559721526 0.732521473 1 18.50433397 0.920803952 4.175710889 0.999837318 0.610556005 0.701239481 0.079461129 0.184440872 7.815282346 0.06966243 0.017766285 8.333049319 -0.920803952 -0.389281313 PSSLMNPSLSKPNIS(ph)PSHSRPPGGSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PSSLMNPSLSKPNISPSHSRPPGGSDK 27 2 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 PSSLMNPSLSKPNIS(0.993)PS(0.005)HS(0.002)RPPGGSDK 138.28 3.01E-06 250190000 967710 388460 676020 528580 627420 470140 774440 554280 623810 TRUE FALSE 907142.7585 417221.9826 692055.5136 542144.2577 578144.9641 605861.7859 658319.9115 623483.0781 519692.081 1.745538929 0.802825361 1.331664535 1.043202845 1.112475993 1.165809155 1.266749938 1.199716334 1 18.98729755 4.759419198 24.74481838 1.130566014 1.745539623 0.640137096 0.148110903 3136.62414 3720951.213 0.034199393 1.540180511 57467.0889 -4.759419198 0.614973609 PSSS(ph)PVIFAGGQDR ddPTM_SK-BR-3_Pertuzumab_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(0.022)S(0.978)PVIFAGGQDR 126.1 0.00035877 0 187720 139010 164780 163870 150210 127050 167510 142120 132080 TRUE FALSE 175970.9403 149302.445 168688.6594 168075.1816 138413.1125 163727.2725 142393.4306 159863.9948 110034.9947 1.599227052 1.356863291 1.533045554 1.527470257 1.257900842 1.487956381 1.294074044 1.452846844 1 16.7476029 -3.481420759 0.200935832 4.76E-10 1.514006069 0.660939805 0.102067912 40.8349064 0.700406243 17.08143696 0.228314767 0.00033005 3.481420759 1.514006069 PSTGPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PSTGPHK 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" 0 66.799 0.066894 49387000 82560 89889 60202 57314 105280 35525 61860 89157 80137 FALSE TRUE 77392.71697 96544.47509 61630.01987 58784.77427 97011.73348 45780.4908 52584.66728 100288.4477 66761.617 1.159239702 1.446107501 0.923135518 0.880517533 1.453106408 0.685730707 0.787648197 1.502187218 1 16.02673128 3.930934402 5.030021324 1.002537403 1.30703345 0.137961057 0.271210631 0.304504939 17.59065855 0.066628908 0.127306544 8529.712677 -3.930934402 0.304496048 PSTQPRPDS(ph)WGEDNWEGLETDSR ddPTM_SK-BR-3_Pertuzumab_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 316.51 1.39E-73 4537690000 2597220 1885930 2084790 2268890 2438630 1621090 2476680 1850620 2053110 TRUE FALSE 2434664.636 2025566.22 2134242.203 2327113.559 2247109.837 2089072.367 2105324.826 2081673.981 1710432.677 1.423420324 1.184242003 1.247779133 1.360540867 1.3137669 1.221370706 1.230872664 1.217045259 1 20.70592989 0.403454639 0.691059783 0.994532124 1.280835266 0.641208797 0.067759979 1.393431654 1.010235865 0.082862948 0.025005083 2.531947167 -0.403454639 0.286303142 PSTQPRPDSWGEDNWEGLETDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PSTQPRPDSWGEDNWEGLETDSR 23 1 E9PS17;Q96KG9-2;Q96KG9;Q96KG9-3;E9PPN3;H0YDH0 E9PS17 SCYL1 N-terminal kinase-like protein 0 116.48 0.00043063 71364000 59243 44863 52316 48020 52372 36752 63497 48393 62267 FALSE TRUE 55535.08638 48184.7032 53556.96023 49252.2745 48258.91438 47361.70578 53976.21433 54434.97258 51874.23544 1.070571661 0.928875439 1.032438546 0.94945543 0.930306037 0.913010194 1.040520672 1.049364335 1 15.66273055 1.625008753 12.06776261 1.03379827 0.97090092 0.236781846 0.049878956 0.128475809 57.91657043 0.022755032 0.012109402 42.1705003 -1.625008753 -0.062897349 PTHSGGGGGGGGGGGGGGGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PTHSGGGGGGGGGGGGGGGGR 21 0 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 0 159.95 2.18E-11 11402000 16598 8953.6 13024 12803 11155 10252 12550 10927 13114 FALSE TRUE 15559.16081 9616.53386 13332.93543 13131.54666 10278.9313 13211.58597 10668.24401 12291.26 10925.18868 1.424154883 0.88021673 1.220384912 1.201951476 0.940847028 1.209277602 0.976481443 1.125038694 1 13.41537058 2.764186119 24.91260132 1.056114088 1.137884929 0.126692914 0.15283996 2145.581985 2085887.879 0.043512358 0.0461335 581.0133596 -2.764186119 0.081770841 PTRPDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PTRPDK 6 1 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 100.19 0.034606 218870000 396080 276480 364820 368740 369750 301730 403670 354710 375360 FALSE TRUE 371290.0598 296950.8669 373473.7027 378202.4927 340711.3265 388834.5528 343143.431 398996.3243 312709.9911 1.187330339 0.949604667 1.194313304 1.209435271 1.089544102 1.243435016 1.09732161 1.275930849 1 18.25446579 3.808829675 6.167993043 1.162827457 1.05553545 0.121786952 0.098478447 0.32151242 19.30496657 0.021953263 0.039917864 6439.166794 -3.808829675 -0.107292007 PTS(ph)SPAKGPPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PTSSPAKGPPQK 12 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 PT(0.083)S(0.806)S(0.111)PAKGPPQK 70.98 0.02775 1010400000 2278800 921230 1409500 1208600 1302700 1008300 1685800 1178200 1313800 TRUE FALSE 2136173.976 989438.8277 1442934.006 1239614.722 1200391.197 1299379.842 1433029.94 1325300.864 1094518.293 1.951702398 0.903994784 1.318327903 1.132566473 1.096730137 1.187170512 1.309279114 1.210853096 1 20.06186464 4.750403896 24.93370394 1.16244087 1.951702889 0.796501353 0.127892921 798.3433129 1680723.566 0.029836274 0.491363242 56286.45484 -4.750403896 0.789262019 PTSS(ph)PAKGPPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PTSSPAKGPPQK 12 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 PTS(0.014)S(0.986)PAKGPPQK;PTS(0.015)S(0.985)PAKGPPQK 160.78 3.63E-05 1276620000 3976700 1293980 2143700 1854610 1985610 1496330 2581300 1766110 1962480 TRUE FALSE 3727805.446 1389787.626 2194549.576 1902202.432 1829668.2 1928296.18 2194258.029 1986612.721 1634929.41 2.280101773 0.850059713 1.342290109 1.163476797 1.119111436 1.179436964 1.342111785 1.215106114 1 20.64079692 4.748851958 24.99885567 1.169670344 2.280102385 0.852646351 0.147281698 544.7668632 1323275.632 0.034604637 0.486468204 56085.67587 -4.748851958 1.110432041 PTTLSEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PTTLSEER 8 0 Q6ZRI6;H3BMJ2;Q6ZRI6-2 Q6ZRI6 C15orf39 Uncharacterized protein C15orf39 0 ; 80.229 0.025989 434620000 96129 288660 247720 254360 228911 246790 187309 224420 190997 FALSE TRUE 90112.45749 310032.6868 253596.0354 260887.3082 210933.2534 318034.2667 159223.7543 252439.331 159118.3668 0.566323419 1.948440604 1.593757154 1.639580103 1.325637371 1.99872757 1.000662322 1.586487695 1 17.27974085 1.694785361 14.00891049 1.222033675 1.569498805 0.098504048 0.425629915 0.264089171 72.69502923 0.178834105 0.098431051 49.52053879 -1.694785361 0.34746513 PTVEELYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PTVEELYR 8 0 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-3;E9PQK6 Q9BZZ5-2 API5 Apoptosis inhibitor 5 0 ; 127.02 0.0027782 135574000 210348 222278 182835 205365 248330 137835 209000 209454 252866 FALSE TRUE 197182.6942 238735.6944 187171.9325 210635.0136 228827.1635 177625.7269 177662.3903 235604.793 210661.031 0.936018841 1.133269372 0.888498132 0.999876496 1.086233948 0.843182653 0.843356692 1.118407101 1 17.68456394 2.240277014 24.99998859 0.92463018 1.008948599 0.044231494 0.104247175 93.26915679 1358521.882 0.035980586 0.028663832 173.8909637 -2.240277014 0.084318419 PVLISTPTPTIVRPGSLPLHLGYDPLHPTLPS(ph)PTSVITQAPPSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PVLISTPTPTIVRPGSLPLHLGYDPLHPTLPSPTSVITQAPPSNR 45 1 P17544;K7ELQ4;P17544-2;P17544-1;P17544-3 P17544 ATF7 Cyclic AMP-dependent transcription factor ATF-7 1 PVLISTPTPTIVRPGSLPLHLGYDPLHPT(0.141)LPS(0.783)PT(0.037)S(0.037)VIT(0.001)QAPPSNR 66.137 0.00067387 45713000 42097 34010 30459 31415 42735 44110 47495 37887 30210 TRUE FALSE 39462.22392 36528.13579 31181.50186 32221.16209 39378.76548 56843.84093 40373.56567 42617.27535 25167.75584 1.567967528 1.451386291 1.238946455 1.280255669 1.564651443 2.258597918 1.604178217 1.693328385 1 14.61928896 2.479681191 24.99954514 1.726956684 1.376578627 0.100871916 0.315834074 147.1669702 1437210.743 0.097880182 0.083233634 301.7735634 -2.479681191 -0.350378056 PVS(ph)PSSLLDTAISEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PVSPSSLLDTAISEEAR 17 0 A0A0B4J2F2;P57059 A0A0B4J2F2 LOC102724428;SIK1 Serine/threonine-protein kinase SIK1 1 PVS(0.966)PS(0.028)S(0.006)LLDTAISEEAR;PVS(0.987)PS(0.012)SLLDTAISEEAR 72.417 0.015835 11792000 32666 28288 26100 26832 30980 21438.9 32761 21859 39285 TRUE FALSE 30621.49337 30382.47295 26719.10433 27520.55455 28546.95577 27627.9624 27848.79219 24588.14427 32728.07971 0.935633671 0.92833045 0.816396946 0.840885099 0.872246585 0.844166925 0.850914335 0.751285883 1 14.99824134 4.148096446 3.327625139 0.847301664 0.934123837 0.212614506 0.061654922 0.303009628 6.493050469 0.013675745 0.035373449 14063.59806 -4.148096446 0.086822174 PVS(ph)SAASVYAGAGGSGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 PVS(0.499)S(0.499)AAS(0.002)VYAGAGGSGSR;PVS(0.49)S(0.49)AAS(0.021)VYAGAGGSGSR;PVS(0.499)S(0.499)AAS(0.003)VYAGAGGSGSR 252.67 1.82E-30 487735000 380551 349200 351802 343820 439531 316222 399782 298918 473671 TRUE FALSE 356732.9922 375055.1313 360146.9096 352643.0033 405012.0082 407510.158 339838.4005 336238.5703 394612.2501 0.904008915 0.950439656 0.912660237 0.893644339 1.026354372 1.032685016 0.86119577 0.852073321 1 18.59007622 -1.257782793 7.645184788 1.000000146 0.930847228 0.117449777 0.060889868 1.51E-07 1.46E-08 0.058536693 0.013797202 0.055235362 1.257782793 -0.069152918 PVSS(ph)AASVYAGAGGSGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 PVSS(1)AASVYAGAGGSGSR;PVSS(0.995)AAS(0.005)VYAGAGGSGSR 418.68 3.35E-148 1713950000 758220 611100 577300 572580 691100 379600 794320 558080 915300 TRUE FALSE 710764.3637 656346.4798 590993.8286 587273.3722 636823.7938 489184.3577 675219.0901 627757.5165 762530.5169 0.93211268 0.86074782 0.775042855 0.770163763 0.835145322 0.641527581 0.885497793 0.823255598 1 19.54043555 0.573292513 1.509100225 0.999643676 0.808824533 0.356853159 0.078041824 1.998816215 5.803483104 0.069959407 0.020245583 3.7436265 -0.573292513 -0.190819143 PVSSAAS(ph)VYAGAGGSGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 PVSS(0.005)AAS(0.995)VYAGAGGSGSR 349.53 2.53E-90 3547000000 669180 477310 577830 483720 608690 396060 702570 526480 833650 TRUE FALSE 627297.2183 512650.529 591536.4005 496133.0741 560885.9427 510396.0925 597226.1508 592212.1869 694508.4294 0.903224773 0.73814875 0.851733939 0.714365806 0.807601346 0.73490266 0.859926425 0.852706982 1 19.40563268 0.850855884 1.23031152 0.998419094 0.791734031 0.537780347 0.058874964 0.447208978 1.301391129 0.048961358 0.015028175 7.093423411 -0.850855884 -0.206685063 PVSSAASVYAGAGGS(ph)GSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 PVSS(0.001)AASVYAGAGGS(0.998)GS(0.001)R;PVSSAASVYAGAGGS(0.975)GS(0.025)R;PVSSAASVYAGAGGS(0.848)GS(0.152)R;PVSSAASVYAGAGGS(0.931)GS(0.069)R;PVSSAASVYAGAGGS(0.999)GS(0.001)R;PVSSAASVYAGAGGS(0.998)GS(0.002)R;PVSSAASVYAGAGGS(0.998)GS(0.002)R 366.85 1.77E-107 11073350000 2156920 1715110 1830460 1783930 2019350 1655392 2309250 1790390 2596660 TRUE FALSE 2021922.227 1842098.529 1873879.376 1829708.664 1860758.397 2133276.797 1962999.401 2013924.133 2163260.671 0.934664164 0.851537937 0.866229115 0.845810534 0.860163743 0.9861395 0.907426196 0.930966924 1 21.04477609 2.254659501 24.99928855 0.945373793 0.867014901 0.568269604 0.035911294 171.5528084 266396.8444 0.011507505 0.009599312 179.7461101 -2.254659501 -0.078358892 PWIS(ph)LPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 PWISLPR 7 0 P62701;C9JEH7;P22090;Q8TD47 P62701 RPS4X;RPS4Y1;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1;40S ribosomal protein S4, Y isoform 2" 1 PWIS(1)LPR;PWIS(1)LPR;PWIS(1)LPR;PWIS(1)LPR;PWIS(1)LPR 73.248 0.031825 2482920000 990667 4827700 2558750 2813330 4408460 2530490 1966680 3603400 2465000 TRUE FALSE 928662.9209 5185147.931 2619444.758 2885524.811 4062237.334 3261001.384 1671794.592 4053292.422 2053575.575 0.452217553 2.524936503 1.275553133 1.405122288 1.978128968 1.587962685 0.814089636 1.973773194 1 20.96970661 1.963832194 23.88245452 1.231729497 1.636689991 0.027118 0.602894066 829.7479274 547900.0244 0.227626527 0.146968442 92.00939901 -1.963832194 0.404960495 PWLHPEQSPLPSLALS(ph)ELSVQHADSLENIDESAVAESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PWLHPEQSPLPSLALSELSVQHADSLENIDESAVAESR 38 0 Q9Y365;F5H8H3;F5GY11 Q9Y365 STARD10 PCTP-like protein 1 PWLHPEQSPLPS(0.002)LALS(0.347)ELS(0.347)VQHADS(0.284)LENIDES(0.019)AVAES(0.001)R 92.846 0.00066863 41330000 16513 12378 13783 11369 12441 10604 12453 11113 11651 TRUE FALSE 15479.48081 13294.48 14109.93927 11660.74779 11463.93404 13665.20266 10585.78826 12500.48251 9706.372832 1.594775008 1.369665088 1.453677858 1.201349669 1.181072914 1.407858826 1.090601859 1.28786342 1 13.24471656 7.999999999 0.116420754 0.906420271 2.870774215 0.642221101 0.10614997 57.50001372 0.462393141 0.718655576 18.2642968 99999999.78 -7.999999999 1.964353944 PWLHPEQSPLPSLALSELSVQHADS(ph)LENIDESAVAESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 PWLHPEQSPLPSLALSELSVQHADSLENIDESAVAESR 38 0 Q9Y365;F5H8H3;F5GY11 Q9Y365 STARD10 PCTP-like protein 1 PWLHPEQSPLPSLALSELSVQHADS(1)LENIDESAVAESR;PWLHPEQSPLPSLALSELSVQHADS(1)LENIDESAVAESR;PWLHPEQSPLPSLALSELSVQHADS(1)LENIDESAVAESR 383.93 4.49E-179 377223000 163036 118821 133720 122792 123382 100070 142533 128519 96377 TRUE FALSE 152831.8678 127618.6305 136891.9015 125943.0506 113692.0754 128958.5845 121161.4999 144564.8801 80291.05608 1.903473129 1.589450142 1.704945834 1.568581318 1.415999253 1.60613885 1.509028599 1.800510382 1 16.29295167 -2.675425227 0.295093472 4.14E-23 1.668722396 0.654671249 0.14347048 33.10727139 1.063418215 21.53786578 0.141808088 0.002111421 2.675425227 1.668722396 PYHPPPLFPPS(ph)PQPPDSTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 PYHPPPLFPPSPQPPDSTPR 20 0 P54259 P54259 ATN1 Atrophin-1 1 PYHPPPLFPPS(1)PQPPDSTPR;PYHPPPLFPPS(1)PQPPDSTPR 131.37 9.32E-06 436250000 318980 203325 276370 262960 241200 219600 265430 224110 184420 TRUE FALSE 299015.6112 218379.3946 282925.6269 269707.9988 222257.125 282994.9551 225631.2356 252090.6268 153639.1106 1.94622066 1.42137893 1.841494824 1.755464463 1.446618144 1.841946064 1.468579418 1.640797228 1 17.22918599 -2.501669704 0.297828575 0.002019514 1.707852475 0.598234093 0.176153385 32.08974854 1.132041906 20.89786884 0.167022959 0.003150143 2.501669704 1.70583296 PYQYPALT(ph)PEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 PYQYPALTPEQK 12 0 P04075;J3KPS3;H3BQN4;H3BUH7;H3BR04;H3BMQ8 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 1 PYQYPALT(1)PEQK 162.37 0.00070267 82581000 469280 245810 294810 261970 314380 197700 334790 261670 357920 TRUE FALSE 439908.6025 264010.0282 301803.0324 268692.5937 289689.8629 254772.7806 284591.3475 294340.0755 298180.8397 1.475308081 0.88540239 1.012147637 0.901106167 0.97152407 0.854423714 0.954425334 0.987119346 1 18.18582803 4.742300668 24.99844895 0.942530078 1.475308285 0.912604033 0.051491107 90.5940621 605504.7412 0.011090418 0.083128898 55245.97825 -4.742300668 0.532778207 QAAPPIELDAVWEDIRER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QAAPPIELDAVWEDIRER 18 1 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;;; 267.39 2.62E-31 216698000 95665.3 136362.9 103154.9 124368.6 156683.2 94885.8 147140.3 98346 265349 FALSE TRUE 89677.77964 146459.351 105601.7829 127560.1088 144377.9335 122277.7901 125077.978 110624.7146 221060.5377 0.405670685 0.662530511 0.477705266 0.577036997 0.653114911 0.553141648 0.565808712 0.500427239 1 17.75408198 -1.861030352 2.558220139 1.195014125 0.557816704 0.771230861 0.077000495 7716862.415 4688987.635 9156847.503 0.016419151 0.013771132 1.861030352 -0.637197422 QAAS(ph)PLEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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;QAAS(1)PLEPK 123.92 0.00057081 688520000 1628000 1255150 1444540 1569260 1472200 825690 1371000 923150 1555230 TRUE FALSE 1526106.386 1348082.612 1478805.171 1609529.868 1356579.351 1064053.299 1165431.278 1038407.31 1295652.066 1.177867443 1.040466532 1.141359791 1.2422547 1.047024418 0.821249259 0.899494014 0.801455373 1 20.30524692 2.392974227 4.682368281 0.874690875 1.132042504 0.751191 0.072926305 0.100208982 3.96288839 0.024535266 0.02038333 247.1577469 -2.392974227 0.257351628 QADEEFQILANSWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QADEEFQILANSWR 14 0 A0A087WU53;Q9H0U3;Q9H0U3-2 A0A087WU53 MAGT1 Magnesium transporter protein 1 0 95.981 0.0082649 27786000 29356 62819 55136 47616 57353 59808 49140 53759 40204 FALSE TRUE 27518.66036 67470.18412 56443.85196 48837.90717 52848.72673 77073.5987 41771.91319 60470.92949 33493.69267 0.821607239 2.014414618 1.685208392 1.458122508 1.577871011 2.301137693 1.247157595 1.805442299 1 15.03160182 -1.331941001 2.921970455 0.992744311 1.651037426 0.180228967 0.404601962 15566023.57 19344636.7 977651.0127 0.095831005 0.046564935 1.331941001 0.658293115 QADFEAHNILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QADFEAHNILR 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;;;; 237.49 1.39E-15 2062390000 2780360 3687180 2798110 2792510 3679490 2540620 3249730 3026260 3431790 FALSE TRUE 2606342.231 3960182.644 2864482.491 2864170.534 3390517.698 3274055.75 2762463.156 3404095.223 2859002.079 0.91162656 1.385162562 1.001916897 1.001807783 1.18590949 1.145174316 0.96623335 1.190658534 1 21.44708024 1.408399302 0.170339123 0.961380858 1.189478538 0.001158199 0.14142432 11.25970263 1.952212037 1.120782198 1.020882195 25.60939404 -1.408399302 0.22809768 QADLYISEGLHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QADLYISEGLHPR 13 0 P40227;Q92526-3;Q92526 P40227 CCT6A;CCT6B T-complex protein 1 subunit zeta;T-complex protein 1 subunit zeta-2 0 ;;;;; 212.17 1.61E-08 3943260000 5105420 6295360 5801650 5582530 6366360 5999960 7272040 5507840 6470810 FALSE TRUE 4785880.876 6761475.005 5939267.878 5725787.171 5866371.766 7732051.051 6181665.112 6195505.948 5390790.008 0.887788407 1.254264216 1.101743505 1.062142499 1.088221162 1.434307595 1.146708572 1.149276069 1 22.36206528 QADNPHVALYQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QADNPHVALYQAR 13 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2;J3QL06;J3KTF1;Q9BST8;J3QQH7;J3QLE9 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;;; 143.25 4.07E-05 1481370000 1279190 2290400 1083980 1194920 2106420 902390 1405240 1719610 1778550 FALSE TRUE 1199127.781 2459983.599 1109692.517 1225583.67 1940990.27 1162895.344 1194537.308 1934307.094 1481698.515 0.809292693 1.660245707 0.748932732 0.827147802 1.309976524 0.78483938 0.806194577 1.305466041 1 20.4988205 3.912226253 8.331955316 0.950364082 1.283531782 0.123550697 0.284541577 0.409903705 48.19520763 0.066521827 0.120559913 8170.078942 -3.912226253 0.3331677 QADVFPDRDHFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QADVFPDRDHFGR 13 1 Q9HCC0-2;Q9HCC0;D6R9R1;D6RDF7;A0A0G2JM88 Q9HCC0-2 MCCC2 "Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial" 0 ;;; 148.72 2.36E-05 1932060000 1548393 1656800 1476748 1421577 2110760 1574200 1466420 1635860 2900200 FALSE TRUE 1451481.846 1779471.196 1511777.16 1458057.073 1944989.424 2028645.985 1246543.935 1840100.722 2416137.884 0.600744625 0.736494058 0.62569987 0.603466003 0.804999349 0.839623433 0.515924171 0.761587629 1 21.20427136 0.981588763 24.18765424 1.000000009 0.676080432 0.522089313 0.09783931 651.3843973 855753.9929 0.089981468 0.022495367 9.584925968 -0.981588763 -0.323919576 QAEDCITR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QAEDCITR 8 0 O43813;E9PHS0 O43813 LANCL1 LanC-like protein 1 0 76.345 0.083848 207610000 241290 259040 258890 222550 286110 277090 321090 238020 407300 FALSE TRUE 226188.0896 278219.5911 265030.9931 228261.0098 263640.0747 357081.3848 272945.5354 267737.3209 339318.9987 0.666594239 0.8199352 0.781067356 0.672703299 0.776968209 1.05234716 0.804392139 0.789043119 1 18.37228268 2.449077108 24.99940268 0.893988599 0.753678916 0.451807167 0.091066364 226.6544154 202045.4369 0.030062376 0.025152394 281.2400121 -2.449077108 -0.140309683 QAEEECAHRGS(ph)PLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QAEEECAHRGSPLPK 15 1 H7C1J2;F2Z2A4;H7C1M5;Q9H147 H7C1J2;H7C1M5 DNTTIP1 Deoxynucleotidyltransferase terminal-interacting protein 1 1 QAEEECAHRGS(1)PLPK;QAEEECAHRGS(1)PLPK;QAEEECAHRGS(1)PLPK;QAEEECAHRGS(1)PLPK 171.3 6.61E-07 1996190000 1309240 976630 1156100 1040770 1167750 970920 1484370 1064160 1624210 TRUE FALSE 1227297.005 1048940.701 1183523.238 1067477.92 1076039.625 1251208.842 1261802.499 1197022.719 1353118.858 0.907013451 0.775202189 0.874663176 0.788901813 0.795229199 0.924685097 0.932514162 0.884639743 1 20.36785714 2.225660942 23.87741776 0.929938997 0.825523979 0.54936329 0.048121648 96.43418879 178498.4321 0.016240666 0.012080349 168.1360892 -2.225660942 -0.104415018 QAEEQIEHLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QAEEQIEHLQR 11 0 H3BP71;O75150-4;O75150;O75150-3 H3BP71 RNF40 E3 ubiquitin-protein ligase BRE1B 0 83.182 0.016902 118190000 86221 147680 128890 140650 141420 139410 120700 137780 130720 FALSE TRUE 80824.58152 158614.3809 131947.3317 144259.3171 130313.4437 179655.4039 102602.1555 154982.1363 108901.9875 0.742177286 1.456487475 1.21161546 1.324671114 1.196612171 1.649698118 0.942151359 1.423134139 1 16.73267076 -1.530723942 3.195417202 0.991932182 1.255421084 0.079502989 0.257280618 49930427.29 47750500.39 3346750.523 0.054006484 0.029462938 1.530723942 0.263488903 QAEEYLSFAFEHCHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QAEEYLSFAFEHCHR 15 0 Q5JVF3-3;Q5JVF3-2;Q5JVF3;Q5JVF3-4 Q5JVF3-3 PCID2 PCI domain-containing protein 2 0 ; 163.23 8.96E-07 134707000 88821 112112 98045 104488 116212 89986 120513 105109 112566 FALSE TRUE 83261.85216 120412.8891 100370.6737 107169.339 107085.1783 115963.4974 102443.1944 118232.09 93778.0074 0.887861178 1.284020555 1.070300772 1.14279821 1.141900764 1.236574551 1.092401057 1.260765645 1 16.516962 4.75689415 24.30605464 1.156935042 0.887860837 0.472416851 0.08819083 2229.055014 2955144.087 0.018482544 0.594950981 57133.93682 -4.75689415 -0.269074204 QAEILQESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QAEILQESR 9 0 E5RJD8;O75347;E5RIW3;O75347-2 E5RJD8 TBCA Tubulin-specific chaperone A 0 ; 124.81 0.0012082 378800000 402980 483770 384100 401190 490290 313980 484820 407690 485650 FALSE TRUE 377758.2011 519588.8342 393211.0334 411485.2146 451784.6011 404620.929 412125.7418 458590.9939 404591.8776 0.933677175 1.284229524 0.971870804 1.017037754 1.116642785 1.000071804 1.018620898 1.133465646 1 18.62610783 3.81326418 9.590596809 1.036718542 1.132735801 0.074879786 0.09771918 0.624271221 65.01638086 0.022420349 0.04047031 6505.252822 -3.81326418 0.096017258 QAENDSSNDDKTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QAENDSSNDDKTK 13 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 84.365 0.0089173 95766000 119800 66055 88888 88633 78280 66130 104100 68349 91509 FALSE TRUE 112301.9318 70945.78093 90996.46534 90907.47284 72132.20457 85220.65747 88491.17142 76882.5231 76235.55673 1.473091254 0.930612748 1.193622363 1.192455027 0.94617535 1.117859712 1.160759824 1.008486412 1 16.21817642 4.752976298 24.7637884 1.082627249 1.47309156 0.626341051 0.09762727 1558.989707 2678037.841 0.022209079 0.489064181 56620.8387 -4.752976298 0.390464311 QAEPELDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 82.749 0.040109 0 238480 264440 275140 275740 279190 229950 288590 230890 336130 FALSE TRUE 223553.9625 284019.4127 281666.4507 282815.9552 257263.5436 296332.8321 245318.6086 259717.1248 280027.7315 0.798327942 1.014254593 1.005851989 1.009956956 0.91870738 1.058226735 0.876051123 0.927469302 1 18.09521018 -0.277841738 7.578698526 0.999999999 0.96091639 0.024803377 0.07693856 0 0 0.069077176 0.016281646 0.527422025 0.277841738 -0.039083609 QAEREEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QAEREEKR 8 2 P14678-2;P14678;P14678-3 P14678-2 SNRPB Small nuclear ribonucleoprotein-associated proteins B and B 0 ;;; 159.37 0.00020224 442197000 513084 398598 627797 586837 500769 512280 551968 208300 475837 FALSE TRUE 480970.9883 428110.6107 642688.6413 601896.2309 461440.6227 660166.9198 469205.5226 234306.7135 396416.7307 1.21329639 1.079950914 1.621244997 1.518342149 1.164029132 1.665335665 1.183616851 0.591061616 1 18.59665833 1.420530345 5.622873806 0.807780799 1.371270218 0.554018968 0.213057195 0.143290126 7.916882724 0.136642293 0.051243329 26.33481942 -1.420530345 0.563489419 QAEVANQETKEDLPAENGETKTEESPAS(ph)DEAGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QAEVANQETKEDLPAENGETKTEESPASDEAGEK 34 2 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 QAEVANQETKEDLPAENGET(0.003)KT(0.015)EES(0.013)PAS(0.969)DEAGEK 94.45 0.00015407 104160000 154210 51033 68076 77575 88852 50764 97773 48159 122350 TRUE FALSE 144558.2714 54811.53642 69690.79487 79565.70583 81873.92233 65418.74272 83112.84633 54171.75716 101928.9946 1.418225226 0.537742343 0.683719045 0.780599339 0.803244677 0.641807005 0.815399452 0.531465628 1 16.63720497 4.747156828 24.8223107 0.708636101 1.418225623 0.707591399 0.139881662 512.2447448 1479115.53 0.030335479 0.355553808 55867.18999 -4.747156828 0.709589522 QAFEELRDDLVELSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QAFEELRDDLVELSK 15 1 Q15397 Q15397 KIAA0020 Pumilio domain-containing protein KIAA0020 0 ;;; 194.58 4.18E-08 116245000 306247 242730 258850 235008 248446 234308 399900 230593 342742 FALSE TRUE 287079.5469 260701.9818 264990.0442 241038.7031 228934.0533 301948.9159 339938.7075 259383.0436 285536.146 1.005405273 0.913026198 0.92804378 0.844161787 0.801769081 1.057480533 1.190527757 0.908407035 1 18.12331386 2.146781207 8.404449361 1.071000277 0.902227599 0.36072902 0.088651146 0.229307364 18.66292471 0.03210321 0.023701177 140.210716 -2.146781207 -0.168772677 QAFPNTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QAFPNTNR 8 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;; 147.36 0.0012528 476700000 569001 610343 604448 562562 690105 510183 715385 603369 734320 FALSE TRUE 533388.2431 655533.4308 618785.792 576998.2933 635906.937 657464.55 608119.6606 678700.9478 611757.2481 0.871895257 1.071558094 1.011489106 0.943181785 1.039475934 1.07471477 0.994053871 1.109428535 1 19.22259976 2.526931341 24.91013855 1.041954704 0.996308584 0.203930016 0.061350266 763.8446477 381998.4713 0.01884148 0.017763708 336.4583731 -2.526931341 -0.04564612 QAGAPGGSSGSGGS(ph)PELSALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QAGAPGGSSGSGGSPELSALR 21 0 Q9Y2J4;Q9Y2J4-2;Q9Y2J4-4 Q9Y2J4 AMOTL2 Angiomotin-like protein 2 1 QAGAPGGSSGS(0.002)GGS(0.997)PELSALR 236.77 8.09E-30 87284000 74218 73070 65182 67741 81933 64711 67821 69267 60239 TRUE FALSE 69572.82786 78480.17883 66728.14782 69479.34875 75498.31268 83392.0152 57651.87067 77915.13743 50184.72174 1.386334834 1.563826123 1.329650649 1.384472133 1.504408315 1.661701257 1.148793272 1.552566891 1 15.6149606 -3.038003953 0.331623451 8.60E-09 1.453693915 0.470181604 0.1450645 73.34964828 2.11234753 51.25993408 0.115382159 0.000916212 3.038003953 1.453693907 QAGEVTFADAHRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QAGEVTFADAHRPK 14 1 Q13243;Q13243-3 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ; 131.24 3.45E-05 728640000 1346620 1152390 1214210 1161480 1312640 1014050 1590930 1105030 1512610 FALSE TRUE 1262337.458 1237714.155 1243011.635 1191285.543 1209550.549 1306789.773 1352384.816 1242995.428 1260145.619 1.001739354 0.982199308 0.986403171 0.945355461 0.959849823 1.037014892 1.073197252 0.98639031 1 20.26515903 2.229790055 24.90936214 1.03509344 0.976263829 0.407289314 0.028029595 145.3387448 412774.6861 0.010157686 0.007616566 169.7422893 -2.229790055 -0.058829611 QAGEVTYADAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QAGEVTYADAHK 12 0 Q08170;A0A0D9SEM4;Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q08170;Q13247 SRSF4;SRSF6 Serine/arginine-rich splicing factor 4;Serine/arginine-rich splicing factor 6 0 ;;;; 203.7 1.22E-07 7861120000 7704830 6421200 7205790 6996750 7856450 5778520 8529100 6679400 9277320 FALSE TRUE 7222598.444 6896632.329 7376714.742 7176298.45 7239436.108 7446684.918 7250240.635 7513337.793 7728875.358 0.934495397 0.892320294 0.954435723 0.928504875 0.936673937 0.963488809 0.93807188 0.972112687 1 22.88182707 -2.719686261 0.0586906 1.208913888 0.810291997 0.669615906 0.016526856 136.0092671 0.926423892 5.414793561 1.729940996 0.001906838 2.719686261 -0.398621891 QAGIGGEPAAAGAGCS(ph)PRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QAGIGGEPAAAGAGCSPRPK 20 1 J3QQY0;Q68DK7;J3KSZ8 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 QAGIGGEPAAAGAGCS(1)PRPK;QAGIGGEPAAAGAGCS(1)PRPK;QAGIGGEPAAAGAGCS(1)PRPK;QAGIGGEPAAAGAGCS(1)PRPK 204.99 5.50E-22 1905070000 2141180 1436030 1765920 1526180 1788300 1661380 2491210 1622330 2089020 TRUE FALSE 2007167.366 1542355.155 1807808.456 1565344.363 1647854.132 2140993.436 2117676.188 1824881.472 1740349.066 1.153313094 0.886233219 1.038761988 0.899442757 0.946852654 1.230209202 1.216811172 1.048572098 1 20.73094527 2.248381415 24.96241204 1.153136428 0.974919957 0.291863098 0.102539435 178.6770038 454159.4623 0.032991191 0.027284216 177.1664222 -2.248381415 -0.178216472 QAGPASVPLRTEEEFKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QAGPASVPLRTEEEFKK 17 2 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;; 117.67 0.00011604 681480000 1073800 855310 878040 963480 1072540 610040 1240860 730270 1240010 FALSE TRUE 1006592.775 918638.0423 898867.5234 988204.528 988307.0348 786148.6448 1054804.563 821445.817 1033044.32 0.974394569 0.889253272 0.870115159 0.956594513 0.95669374 0.761001856 1.02106419 0.795169966 1 19.97847072 -1.900337099 2.559095892 1.053114891 0.904400517 0.125999602 0.08018575 21224034.28 10286957.2 6768151.451 0.016977559 0.012579486 1.900337099 -0.148714374 QAHLCVLASNCDEPMYVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QAHLCVLASNCDEPMYVK 18 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 226.65 3.40E-19 208930000 193720 160020 143440 126050 179940 218400 340200 141270 332550 FALSE TRUE 181595.411 171868.0473 146842.4645 129284.6564 165808.2382 281448.5346 289190.1683 158907.8705 277045.2566 0.655472009 0.620360909 0.530030603 0.466655369 0.598487916 1.015893713 1.043837284 0.57358091 1 18.07976214 2.27534976 8.42419152 0.929700021 0.568821308 0.584317948 0.139498069 0.159853377 32.7716392 0.046536891 0.038565246 188.5166702 -2.27534976 -0.360878714 QAHLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QAHLYR 6 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 104.31 0.078958 240110000 198536 220640 159528 172637 222650 141729 235870 189460 246120 FALSE TRUE 186109.9862 236976.4152 163312.0795 177067.1577 205163.9671 182643.8615 200503.4832 213114.4981 205040.982 0.907672136 1.155751464 0.796485063 0.863569595 1.000599808 0.890767591 0.977870284 1.039375134 1 17.64555277 -0.57422111 7.60336786 0.999999719 0.955499508 0.020297561 0.099936 0 0 0.094078516 0.022174519 0.266550125 0.57422111 -0.04450021 QAHTMDPQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 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 ;;;;;;;;;;;; 183.03 1.71E-06 28669737000 2367511 3098611 2573521 2318456 3062914 2192956 3211602 2631855 3519623 FALSE TRUE 2219332.713 3328035.383 2634566.133 2377951.506 2822365.09 2826026.798 2730052.095 2960447.89 2932175.184 0.756889535 1.135005644 0.898502296 0.810985482 0.962549955 0.963798757 0.931067185 1.00964223 1 21.48353987 1.236113253 24.88002699 1.00482115 0.940398583 0.083379066 0.100676789 187.572753 1906664.024 0.079006977 0.023354387 17.22317654 -1.236113253 -0.064422566 QALDYVELSPLTQAS(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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;QALDYVELSPLTQAS(1)PQR 407.7 3.10E-147 300329000 403080 404294 377512 370309 387498 397818 521081 339148 354437 TRUE FALSE 377851.9423 434228.3484 386466.7629 379811.7559 357065.4702 512661.5986 442949.7415 381491.3744 295279.1749 1.279643044 1.470568822 1.308818216 1.286280199 1.209247046 1.736192871 1.500104915 1.291968438 1 18.17172009 QALTEFNTAIQEIVVTHWHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QALTEFNTAIQEIVVTHWHR 20 0 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ;; 270.55 1.29E-44 259541000 178405 188696 132425 124351 162174 216892 349138 138860.6 323917 FALSE TRUE 167238.9495 202667.2482 135566.1835 127542.0572 149437.5082 279505.1995 296787.9981 156197.6516 269853.1601 0.619740563 0.751027885 0.502370191 0.472635033 0.553773423 1.035767746 1.099812943 0.578824615 1 18.04181506 2.242695967 24.99973374 0.957902318 0.587794077 0.546553792 0.156721961 74.97640804 453262.7665 0.054666963 0.044210745 174.8622116 -2.242695967 -0.370108241 QAPAS(ph)PQEAALDLDVVLIPPPEAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QAPASPQEAALDLDVVLIPPPEAFR 25 0 Q9BW04 Q9BW04 SARG Specifically androgen-regulated gene protein 1 QAPAS(1)PQEAALDLDVVLIPPPEAFR 50.851 0.086654 7019300 7657.5 11682 11136 13685 10233 7631.9 12956 7153 9191.1 TRUE FALSE 7178.230744 12546.94744 11400.15118 14036.18027 9429.341458 9835.105636 11013.36808 8046.067796 7657.046033 0.937467362 1.638614602 1.48884454 1.833106424 1.231459419 1.284451679 1.438331183 1.050805723 1 12.90257222 1.24565228 0.999366997 0.98205711 1.475232876 0.261752766 0.245965331 0.581972734 1.226380342 0.213206808 0.073703905 17.60565876 -1.24565228 0.493175766 QAPGVGAVGGGS(ph)PEREEVGAGYNS(ph)EDEYEAAAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QAPGVGAVGGGSPEREEVGAGYNSEDEYEAAAAR 34 1 A0A087WXV6;Q96G74-2;Q96G74-3;Q96G74-5;Q96G74;H7BZQ3 A0A087WXV6 OTUD5 OTU domain-containing protein 5 2 QAPGVGAVGGGS(1)PEREEVGAGY(0.189)NS(0.811)EDEYEAAAAR 170.53 7.75E-15 92177000 56870 59716 62852 58279 65122 51921 67899 57383 82177 TRUE FALSE 53310.60822 64137.43477 64342.87912 59774.53781 60007.58081 66909.74983 57718.17529 64547.39387 68461.12782 0.778698948 0.936844554 0.939845445 0.873116463 0.876520483 0.977339287 0.843079528 0.942832757 1 16.06299744 -5 0.266790038 1.661415665 0.894046355 0.268628803 0.056635317 309.4957859 3.01895157 112.613087 0.066922457 1.00E-05 5 -0.767369311 QAQAQES(ph)EEEEESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QAQAQESEEEEESR 14 0 H0YLQ7;Q9NVM6 H0YLQ7 DNAJC17 DnaJ homolog subfamily C member 17 1 QAQAQES(1)EEEEESR;QAQAQES(1)EEEEESR 389.78 5.29E-114 3444300000 998860 1119120 1002910 983350 1029330 956600 1157610 822800 1003890 TRUE FALSE 936343.1356 1201980.809 1026699.499 1008584.426 948490.5739 1232754.891 984037.1272 925528.3912 836334.2736 1.119580011 1.437201424 1.227618586 1.2059585 1.134104632 1.473997814 1.176607438 1.106648885 1 19.67372016 1.212385219 2.443457955 1.014280596 1.275798721 0.362858129 0.116424296 0.267844753 2.743171149 0.100335116 0.028461795 16.30741859 -1.212385219 0.261518126 QAQEEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QAQEEAER 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 203.02 0.00023032 391847000 514722 651220 541129 598580 642280 443058 638280 534572 559019 FALSE TRUE 482506.4688 699437.0064 553964.8354 613940.5762 591837.9196 570961.6522 542575.8395 601314.4909 465715.1175 1.036054984 1.50185592 1.189492921 1.318274956 1.270815349 1.225989088 1.165038065 1.291163779 1 18.82908819 -0.752963687 0.291104832 0.87135591 1.304424225 0.268418866 0.121942278 13.14923635 1.090987362 1.633228869 0.136043459 0.176618549 0.752963687 0.433068315 QAQEYEALLNIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QAQEYEALLNIK 12 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;; 234.67 1.16E-15 720200000 1657000 1540680 1455880 1397050 1668170 1358970 2079700 1456420 2516980 FALSE TRUE 1553291.328 1654753.55 1490414.161 1432900.668 1537158.657 1751282.578 1767868.292 1638257.243 2096879.778 0.740763178 0.789150417 0.710777116 0.683348985 0.733069522 0.835185019 0.843094731 0.781283343 1 20.99981272 0.676555405 0.508984872 1.006907948 0.733631782 0.761606546 0.043776475 0.758111457 0.409301543 0.063588146 0.024325814 4.748488655 -0.676555405 -0.273276166 QAQQERDELADEIANSSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QAQQERDELADEIANSSGK 19 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 351.66 8.01E-91 4471340000 4890610 4805040 4398080 4661640 5514160 3569740 6106010 4049820 7592360 FALSE TRUE 4584515.45 5160810.161 4502404.535 4781265.575 5081100.117 4600265.988 5190470.486 4555448.942 6325146.067 0.724807839 0.815919523 0.711826175 0.755913859 0.803317435 0.727297985 0.820608794 0.720212449 1 22.59266737 -1.966284401 2.912039917 1.187791087 0.764573598 0.771996035 0.040924609 1328144.367 3437778.715 1622252.775 0.008591875 0.01080726 1.966284401 -0.423217489 QAQTQTS(ph)PEHLVLQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QAQTQTSPEHLVLQQK 16 0 H0Y5D5;Q9BTG3;Q5SYW2;F5H2X7;Q9ULV3-5;Q9ULV3-2;Q9ULV3;A0A494C0L7;Q9ULV3-3;Q9ULV3-4 H0Y5D5 CIZ1 Cip1-interacting zinc finger protein 1 QAQT(0.189)QT(0.069)S(0.742)PEHLVLQQK;QAQT(0.029)QT(0.086)S(0.885)PEHLVLQQK 194.92 8.75E-11 493350000 746640 550640 510730 437550 575800 693460 1081730 518590 1060310 TRUE FALSE 699909.1352 591409.9585 522844.7568 448778.2738 530578.9907 893650.6446 919534.6288 583337.1031 883337.4111 0.792346307 0.669517617 0.591896992 0.508048531 0.600652688 1.011675305 1.040977793 0.660378578 1 19.75260509 2.242899045 24.99960264 0.946241245 0.626348999 0.574078909 0.126106231 71.79960534 413737.6118 0.043335537 0.035085876 174.9439971 -2.242899045 -0.319892246 QAREEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QAREEEAR 8 1 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 99.139 0.0064073 128290000 35456 56440 52123 59230 82673 34155 47201 49143 74362 FALSE TRUE 33236.87225 60618.87633 53359.38217 60749.94208 76180.19607 44014.99404 40123.64824 55278.61173 61950.5018 0.536506909 0.978505009 0.86132284 0.980620662 1.229694576 0.710486481 0.647672692 0.892302889 1 15.91882835 0.979729017 23.95196672 1.000000022 0.85710121 0.055953957 0.193498913 3260.808782 3852942.921 0.185406999 0.04635175 9.543968936 -0.979729017 -0.142898812 QAS(ph)DTGSNDAHNKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.853)DT(0.147)GSNDAHNKK;QAS(0.999)DT(0.001)GSNDAHNKK;QAS(0.987)DT(0.013)GSNDAHNKK;QAS(0.995)DT(0.005)GSNDAHNKK;QAS(0.942)DT(0.058)GSNDAHNKK 249.41 1.96E-18 1436770000 3201970 1395290 2200020 1756980 1767010 1497030 2032160 1301870 3122820 TRUE FALSE 3001564.413 1498598.723 2252205.513 1802067.081 1628236.162 1929198.259 1727456.474 1464411.335 2601601.168 1.153737341 0.576029386 0.865699763 0.69267615 0.625859253 0.741542663 0.663997424 0.562888483 1 21.31096838 4.749201439 24.56371644 0.706649424 1.153737665 0.516298307 0.132848884 891.3775701 2057641.516 0.027929341 0.398534927 56130.82678 -4.749201439 0.447088242 QAS(ph)ESSSRPH ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QASESSSRPH 10 1 A0A2R8Y653;Q9BZX2;Q9BZX2-2 A0A2R8Y653 UCK2 Uridine-cytidine kinase 2 1 QAS(0.992)ES(0.008)SSRPH;QAS(0.887)ES(0.111)S(0.001)S(0.001)RPH;QAS(0.996)ES(0.004)SSRPH;QAS(0.996)ES(0.004)SSRPH;QAS(0.838)ES(0.145)S(0.008)S(0.009)RPH;QAS(0.833)ES(0.145)S(0.008)S(0.015)RPH 149.58 2.04E-05 1937820000 1413070 1804056 1717039 2004821 2484320 1569031 1937341 1639720 1904665 TRUE FALSE 1324628.471 1937630.183 1757767.976 2056268.101 2289211.528 2021984.779 1646854.702 1844442.651 1586764.107 0.83479861 1.221120502 1.107768929 1.295887708 1.442691777 1.274281899 1.037869898 1.162392471 1 20.59765624 1.709434046 9.553723403 1.076625749 1.2020263 0.124606496 0.160164699 0.250656354 51.37348621 0.075360032 0.040558424 51.21934798 -1.709434046 0.125400551 QAS(ph)FLEAEGGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QASFLEAEGGAK 12 0 Q8WYP3-2;Q8WYP3 Q8WYP3-2 RIN2 Ras and Rab interactor 2 1 QAS(1)FLEAEGGAK;QAS(1)FLEAEGGAK;QAS(1)FLEAEGGAK 174.62 3.14E-05 209954000 558060 497000 451830 523720 432960 304914 693980 380170 398390 TRUE FALSE 523132.0208 533798.3971 462547.621 537159.5419 398957.0681 392937.7219 589924.1416 427635.0614 331896.1353 1.576191962 1.608329656 1.393651723 1.618456754 1.202053973 1.183917739 1.777436007 1.288460503 1 18.3403723 -3.287747971 0.228666554 4.97E-11 1.538350696 0.390050163 0.188217718 73.66449806 1.488455813 35.76514341 0.340832017 0.000515528 3.287747971 1.538350696 QAS(ph)LDGLQQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QASLDGLQQLR 11 0 Q3MII6 Q3MII6 TBC1D25 TBC1 domain family member 25 1 QAS(1)LDGLQQLR;QAS(1)LDGLQQLR;QAS(1)LDGLQQLR;QAS(1)LDGLQQLR 183.7 5.49E-06 1020630000 685010 796680 718810 773730 851750 632070 825470 685570 910830 TRUE FALSE 642136.4469 855667.0161 735860.5126 793585.2217 784856.9908 814538.3482 701698.4368 771164.9236 758806.5888 0.846245218 1.127648374 0.96976031 1.04583333 1.034330754 1.073446594 0.924739515 1.016286541 1 19.53337268 1.739996588 25 0.974689947 1.025545982 0.035348911 0.076981127 0.537037941 9390.514659 0.031909762 0.017695527 54.95365566 -1.739996588 0.050856035 QAS(ph)PQNLGTPGLLHPQTSPLLHSLVGQHILSVQQFTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QASPQNLGTPGLLHPQTSPLLHSLVGQHILSVQQFTK 37 0 F8VPD4;P27708;H7BZB3 F8VPD4;H7BZB3 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 1 QAS(1)PQNLGTPGLLHPQTSPLLHSLVGQHILSVQQFTK;QAS(0.999)PQNLGT(0.001)PGLLHPQTSPLLHSLVGQHILSVQQFTK 319.23 9.01E-110 449950000 296020 418340 378140 314520 557010 332410 546390 487770 436820 TRUE FALSE 277492.6366 449314.3289 387109.6594 322591.1157 513264.6815 428371.3708 464463.8919 548669.1582 363911.92 0.762526923 1.234678789 1.063745478 0.886453831 1.410409094 1.177129265 1.276308542 1.507697682 1 18.47322978 2.734817538 24.99832843 1.28172772 1.040971548 0.365924376 0.181784474 394.8654718 2637118.921 0.053744699 0.052497345 543.022141 -2.734817538 -0.240756172 QAS(ph)PTEVVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QASPTEVVER 10 0 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;C9JW01;A0A0C4DG68 Q8TB72-3 PUM2 Pumilio homolog 2 1 QAS(0.956)PT(0.044)EVVER;QAS(0.996)PT(0.004)EVVER;QAS(0.911)PT(0.089)EVVER;QAS(0.54)PT(0.46)EVVER 199.3 2.95E-07 2049330000 1056740 1158450 1154560 1185410 1282680 990170 1250570 1009100 1244990 TRUE FALSE 990600.5297 1244222.843 1181946.708 1215829.627 1181943.487 1276016.005 1063058.638 1135088.356 1037193.126 0.955078186 1.199605755 1.139562805 1.172230703 1.139559699 1.230258833 1.02493799 1.094384766 1 19.98425312 1.657565652 9.370733247 1.045130539 1.147386354 0.269368242 0.076219299 0.138724074 20.01665936 0.033261918 0.017687063 45.45332436 -1.657565652 0.102255814 QAS(ph)TDAGTAGALTPQHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QASTDAGTAGALTPQHVR 18 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 1 QAS(0.938)T(0.062)DAGTAGALTPQHVR;QAS(0.763)T(0.237)DAGTAGALTPQHVR;QAS(0.938)T(0.062)DAGTAGALTPQHVR;QAS(0.679)T(0.321)DAGTAGALTPQHVR;QAS(0.929)T(0.071)DAGTAGALTPQHVR 245.94 1.94E-24 4709360000 1360280 1488040 1282970 1505240 1755750 1110390 1578330 1184930 2375460 TRUE FALSE 1275142.503 1598216.03 1313402.654 1543867.007 1617860.477 1430941.567 1341674.069 1332871.119 1978980.38 0.644343176 0.807595692 0.66367644 0.780132548 0.817522242 0.723070113 0.677962289 0.673514064 1 20.91632588 -1.845953268 2.84720198 1.099613285 0.726511994 0.668881669 0.06111039 20477603.01 15668866.92 13919030.52 0.014919623 0.01425761 1.845953268 -0.373101291 QAS(ph)VHDS(ph)GEEGEA ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QASVHDSGEEGEA 13 0 Q8TE77;Q8TE77-3;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 2 QAS(1)VHDS(1)GEEGEA;QAS(1)VHDS(1)GEEGEA 181.97 1.70E-05 1470230000 1497560 1686340 1561990 1698160 1792890 1358300 1805030 1460240 1822830 TRUE FALSE 1403830.393 1811198.368 1599041.14 1741737.661 1652083.652 1750419.16 1534382.509 1642554.178 1518587.897 0.924431438 1.192685897 1.052978984 1.14694557 1.087907822 1.152662393 1.010400854 1.081632602 1 20.53429898 1.699123315 10.20865129 1.035222533 1.101668217 0.123968023 0.075234306 0.206073031 39.06254258 0.031721083 0.017154813 50.01765369 -1.699123315 0.066445684 QAS(ph)VHDSGEEGEA ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QASVHDSGEEGEA 13 0 Q8TE77;Q8TE77-3;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 QAS(0.999)VHDS(0.001)GEEGEA;QAS(1)VHDSGEEGEA;QAS(0.999)VHDS(0.001)GEEGEA;QAS(1)VHDSGEEGEA 245.56 4.30E-17 2684660000 1956490 3044590 2740500 2966600 3104380 2439030 3346170 2516560 3032510 TRUE FALSE 1834036.783 3270014.611 2805505.954 3042727.978 2860574.517 3143138.367 2844442.873 2830758.056 2526364.49 0.725958899 1.294355832 1.110491366 1.204389941 1.132288919 1.244134953 1.125903599 1.120486797 1 21.26863137 4.749090596 24.85840858 1.165705301 0.725958632 0.731261266 0.081275293 649.6796226 1533683.812 0.017149878 0.244532052 56116.50257 -4.749090596 -0.439746669 QASALIDRPAPFFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QASALIDRPAPFFER 15 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 0 ; 239.55 7.56E-18 706630000 573260 551210 503310 410870 596850 497210 625390 498490 1220930 FALSE TRUE 537380.6799 592022.1619 515248.7509 421413.6198 549975.8086 640746.4555 531618.5753 560727.5738 1017148.895 0.528320566 0.582040805 0.506561776 0.414308683 0.540703343 0.629943618 0.522655609 0.551273836 1 19.95609945 -2.507398505 0.445268527 1.796197136 0.526680032 0.881004465 0.053899731 32.84241124 1.606738672 25.36509819 0.029463958 0.003108862 2.507398505 -1.269517104 QASASERLPS(ph)VEEAEVPKPLPPASKDEDEDIQSILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QASASERLPSVEEAEVPKPLPPASKDEDEDIQSILR 36 3 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 QASAS(0.004)ERLPS(0.876)VEEAEVPKPLPPAS(0.119)KDEDEDIQSILR;QAS(0.013)AS(0.017)ERLPS(0.97)VEEAEVPKPLPPASKDEDEDIQSILR 125.7 1.45E-08 458000000 191655 159128 210563 242905 216297 81742 104239 86262 202469 TRUE FALSE 179659.6557 170910.0027 215557.6538 249138.3535 199309.9061 105339.5884 88609.32966 97032.00059 168675.6159 1.06511931 1.01324665 1.277941999 1.477026494 1.18161659 0.624509879 0.525323884 0.575258019 1 17.3638919 2.243132607 8.017924585 0.62778443 1.200527078 0.67338972 0.178847814 0.065609261 32.20338115 0.063657215 0.050473839 175.0381065 -2.243132607 0.572742648 QASASYDS(ph)EEEEEGLPMSYDEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QASASYDSEEEEEGLPMSYDEKR 23 1 Q15059 Q15059 BRD3 Bromodomain-containing protein 3 1 QASAS(0.002)YDS(0.998)EEEEEGLPMSYDEKR 121.7 4.19E-05 76694000 62849 57234 54351 59334 68738 51207 81097 52528 76910 TRUE FALSE 58915.39328 61471.66491 55640.23139 60856.61089 63339.59476 65989.62962 68937.25772 59086.23643 64073.22414 0.919500994 0.959397092 0.868385072 0.949797856 0.988550141 1.029909615 1.07591367 0.922167367 1 15.96743397 2.720406907 2.56013978 1.01932331 0.918144757 0.437807575 0.044502869 0.224930832 2.924851274 0.015052092 0.014833226 525.2994026 -2.720406907 -0.101178552 QASCSGDEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QASCSGDEYR 10 0 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A087WT27;A0A494C1E2;A0A494C1Q4;J3KN95;A0A494C099;A0A494C163;D6RIS6 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 84.817 0.03641 0 35943 47363 35696 35642 43362 33514 49153 30203 39180 FALSE TRUE 33693.39179 50869.8058 36542.72598 36556.63406 39956.52343 43188.94775 41782.96396 33973.91104 32640.60489 1.032253903 1.558482325 1.119548063 1.119974161 1.224135508 1.32316628 1.280091595 1.040848083 1 14.99438017 1.200398716 6.021343236 1.01197003 1.258145166 0.273071202 0.143760668 0.230398157 21.20376456 0.12692131 0.033568194 15.86348917 -1.200398716 0.246175136 QASDTGSNDAHNKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 337.22 7.30E-69 1022260000 1154212 848214 973011 988179 1076015 780481 1255460 914783 1404580 FALSE TRUE 1081971.931 911016.6471 996091.2804 1013537.346 991509.1223 1005793.195 1067215.428 1028995.671 1170146.524 0.924646537 0.778549206 0.851253463 0.866162763 0.847337579 0.859544659 0.91203572 0.879373352 1 20.15825776 0.618685583 0.433633797 1.010654619 0.834322615 0.563128556 0.03829732 1.189932505 0.466692954 0.06449043 0.023707621 4.156096122 -0.618685583 -0.176332005 QASEGPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QASEGPLK 8 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 109.71 0.0082939 1147660000 1106780 1887560 817300 865860 2003690 582541 851150 1605310 1653870 FALSE TRUE 1037508.615 2027316.906 836686.742 888079.4335 1846328.27 750711.1299 723527.9592 1805736.487 1377828.413 0.753002773 1.471385615 0.607250318 0.644550094 1.340027723 0.544850958 0.525121962 1.310567028 1 20.3939648 3.962692843 22.48648007 0.809940279 1.147983509 0.078011679 0.341267604 196.5840988 306375.6163 0.081894646 0.148803096 9176.833311 -3.962692843 0.338043231 QASPT(ph)EVVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QASPTEVVER 10 0 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;C9JW01;A0A0C4DG68 Q8TB72-3 PUM2 Pumilio homolog 2 1 QAS(0.313)PT(0.687)EVVER 120.9 0.0079811 0 306150 183520 236200 218970 225640 153580 231780 194390 286820 TRUE FALSE 286988.618 197108.0118 241802.7755 224589.1409 207919.1446 197916.0528 197026.7407 218660.0194 238947.8891 1.201051071 0.824899573 1.011947737 0.939908454 0.870144304 0.828281236 0.824559453 0.915095004 1 17.8663365 2.846140406 3.543144648 0.867411093 0.972598119 0.184224157 0.104840625 0.407243183 9.452179654 0.03094579 0.032954159 701.6821141 -2.846140406 0.105187026 QATENAKEEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QATENAKEEVR 11 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 73.435 0.039733 392960000 242200 361440 305920 350760 407900 254370 348290 304090 464230 FALSE TRUE 227041.1343 388201.3937 313176.5669 359761.0954 375865.1794 327802.4896 296067.1479 342056.3059 386747.014 0.587053361 1.003760545 0.809771131 0.930223331 0.971863171 0.847588935 0.765531826 0.884444594 1 18.56103063 4.752945924 24.75772835 0.887167191 0.587053123 0.599244659 0.080077509 1721.031992 2961911.518 0.019261468 0.416552449 56616.87887 -4.752945924 -0.300114067 QATENAKEEVRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QATENAKEEVRR 12 2 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;; 269.14 1.72E-22 2051180000 905870 1314160 994020 1097590 1618410 652550 1266240 816460 3055110 FALSE TRUE 849173.2137 1411461.774 1017598.624 1125756.018 1491306.607 840930.5917 1076379.067 918396.8283 2545192.404 0.333638122 0.554559951 0.399812062 0.442306843 0.585930794 0.330399616 0.422906758 0.360835914 1 21.27934329 -1.467254893 3.100338422 1.012525668 0.437094171 0.815542584 0.085291114 52958617.41 64377637.85 5736715.97 0.019715806 0.034099272 1.467254893 -0.575431497 QATINIGTIGHVAHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QATINIGTIGHVAHGK 16 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 0 138.39 3.97E-06 366480000 199350 171100 134340 144380 175160 207970 301260 157820 306860 FALSE TRUE 186873.0393 183768.422 137526.6082 148085.0352 161403.6402 268007.5629 256088.8598 177524.1744 255643.0836 0.730991962 0.718847619 0.537963344 0.579264783 0.631363219 1.04836618 1.001743744 0.694421973 1 17.96377147 2.249870705 24.99919223 0.947295576 0.633863142 0.641544342 0.109920727 126.9670939 280640.9068 0.037740755 0.031312793 177.7750073 -2.249870705 -0.313432434 QATS(ph)PASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QATSPASK 8 0 E9PKP7;P17480-2;P17480 E9PKP7 UBTF Nucleolar transcription factor 1 1 QAT(0.043)S(0.955)PAS(0.002)K;QAT(0.004)S(0.995)PAS(0.001)K 96.113 0.00962 268590000 1445060 935640 1389490 1125040 1104150 998090 1483420 1027310 1014560 TRUE FALSE 1354616.274 1004915.759 1422449.359 1153910.431 1017434.513 1286222.38 1260994.942 1155571.915 845223.3817 1.602672505 1.188935116 1.682927129 1.365213571 1.203746294 1.521754377 1.491907311 1.367179304 1 19.68897315 0.898134802 7.29453312 1.000000741 1.433486974 0.432335129 0.156097862 2.604889995 186.5072299 0.140565294 0.035234281 7.909240876 -0.898134802 0.433486233 QATVGDINTERPGMLDFTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QATVGDINTERPGMLDFTGK 20 1 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 89.47 0.0018919 177610000 132860 105470 106790 96426 90183 75820 136860 100290 157740 FALSE TRUE 124544.5298 113279.1085 109323.1092 98900.45441 83100.39096 97708.00317 116339.1135 112811.4273 131412.175 0.947739658 0.862013802 0.831910051 0.752597348 0.632364474 0.743523218 0.885299354 0.858454913 1 17.00373942 0.939720026 1.474681156 0.996044512 0.803841738 0.344023118 0.085362345 0.600484401 2.639238049 0.085288608 0.025196606 8.704022914 -0.939720026 -0.192202775 QATVSWDSGGSDEAPPKPSRPGYPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QATVSWDSGGSDEAPPKPSRPGYPSPR 27 2 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-6;B4DWJ1;E5RJQ2;E5RG80;E5RHK7 E7ESA6 PTK2 Focal adhesion kinase 1 1 QATVSWDSGGSDEAPPKPS(0.003)RPGYPS(0.997)PR;QATVSWDSGGSDEAPPKPS(0.141)RPGYPS(0.859)PR 261.78 2.20E-53 572530000 564560 439520 429240 391210 475760 457600 702460 481310 596290 TRUE FALSE 529225.1974 472062.5181 439421.7755 401249.1109 438395.7287 589701.6915 597132.6443 541402.613 496765.3468 1.065342421 0.950272641 0.88456608 0.807723633 0.882500624 1.187082986 1.202041664 1.089855837 1 18.92220501 2.240250521 24.99954058 1.1453991 0.912884345 0.568122478 0.086021402 28.17615649 416830.3441 0.030289669 0.024121228 173.8803562 -2.240250521 -0.232514755 QAVDFLSNEGHIYSTVDDDHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QAVDFLSNEGHIYSTVDDDHFK 22 0 Q5TEJ0;P15927;P15927-2;P15927-3 Q5TEJ0 RPA2 Replication protein A 32 kDa subunit 0 245.44 4.02E-31 146870000 111870 87513 81390 78257 94282 100020 157600 82062 169220 FALSE TRUE 104868.2564 93992.55358 83320.60924 80265.20711 86877.47204 128894.1503 133969.3431 92307.62134 140976.0888 0.743872647 0.666726921 0.591026535 0.569353341 0.616256791 0.914297959 0.950298339 0.65477502 1 17.10509096 2.240411521 24.99947314 0.885072082 0.63201463 0.589011719 0.100512981 31.63079919 427232.248 0.033896856 0.027025358 173.9448285 -2.240411521 -0.253057452 QAVEQQIQSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QAVEQQIQSHR 11 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 81.676 0.021022 360380000 581230 420520 432260 447270 442130 324020 538330 427910 531640 FALSE TRUE 544851.8518 451655.7384 442513.4113 458747.7054 407406.8933 417559.314 457612.4141 481335.5054 442905.8495 1.230175335 1.019755641 0.999113947 1.035767999 0.919849882 0.942772182 1.03320472 1.0867671 1 18.75664053 4.744127992 3.882953158 1.001595913 1.253520513 0.69891183 0.046644756 0.14639665 4.412289785 0.011217538 0.105701611 55478.91926 -4.744127992 0.2519246 AEDGATPS(ph)PSNETPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 AEDGATPSPSNETPK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 AEDGATPS(0.985)PS(0.015)NETPK;AEDGATPS(0.999)PS(0.001)NETPK 337.52 7.97E-58 317100000 1990240 1376910 1640110 1723150 1502430 1007280 1530470 941860 902670 TRUE FALSE 1865674.431 1478857.849 1679014.184 1767368.946 1384435.208 1298065.384 1300990.232 1059453.294 752008.5455 2.480921849 1.966543941 2.232706255 2.350197956 1.840983346 1.726131162 1.730020542 1.408831456 1 19.52038953 1.437315648 0.567428815 0.992966922 2.23921225 0.863227882 0.163284642 0.264761406 0.20726046 0.159863323 0.084777137 27.37257457 -1.437315648 1.246245328 QAWRKGPDGPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QAWRKGPDGPQK 12 2 Q9BYZ6-2;E5RI44 Q9BYZ6-2 RHOBTB2 Rho-related BTB domain-containing protein 2 0 ; 68.069 0.030182 2959000000 7139700 4966300 4411200 4260130 5699900 2534590 6080800 4402600 6621300 FALSE TRUE 6692838.922 5334010.019 4515835.747 4369452.148 5252252.846 3266284.987 5169040.491 4952274.301 5516162.255 1.213314368 0.966978449 0.818655351 0.792118133 0.952157062 0.592129969 0.937071872 0.897775314 1 22.39523346 4.824415934 1.462498777 0.844741891 1.416169237 0.498899157 0.112976939 1.09158432 1.843234396 0.027368127 0.961171176 66744.56922 -4.824415934 0.571427347 QAYS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QAYSPR 6 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 QAYS(1)PR;QAYS(1)PR;QAYS(1)PR;QAYS(1)PR;QAY(0.001)S(0.999)PR 78.113 0.0741 9492130000 8814230 9569530 9430780 8670110 10620500 8189950 10901540 9273630 10939930 TRUE FALSE 8262563.078 10278067.96 9654482.555 8892599.701 9786408.771 10554255.61 9266955.282 10431463.12 9113985.008 0.906580719 1.127724914 1.059304195 0.975709275 1.073779336 1.158028634 1.016784126 1.144555659 1 23.11965057 2.501574868 24.75373959 1.081930497 1.040926662 0.107673645 0.075161533 1989.19806 2013610.173 0.023014701 0.021586538 317.3765742 -2.501574868 -0.041003835 QAYVDKLEELMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QAYVDKLEELMK 12 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 141.46 5.52E-05 104970000 292750 201050 163920 198010 325690 283180 564440 295750 676170 FALSE TRUE 274427.3001 215935.9512 167808.2598 203091.2718 300111.6212 364929.469 479807.462 332675.0385 563312.8588 0.48716676 0.383332189 0.297895312 0.360530154 0.532761886 0.647827337 0.85176018 0.59056887 1 19.10357688 2.257486767 1.615166796 0.803354602 0.367097317 0.743583933 0.110906292 0.172798378 0.897523563 0.054601096 0.033988092 180.9200785 -2.257486767 -0.436257285 QCEGITS(ph)PEGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QCEGITSPEGSK 12 0 Q9Y570;Q9Y570-4;Q9Y570-2 Q9Y570 PPME1 Protein phosphatase methylesterase 1 1 QCEGIT(0.205)S(0.795)PEGSK 248.81 8.66E-17 123260000 528700 377430 421360 402450 521000 278580 491070 396690 728470 TRUE FALSE 495609.6108 405375.3099 431354.8582 412777.5483 480082.7616 359001.5236 417438.6124 446217.6197 606883.6509 0.816646832 0.667962153 0.710770273 0.680159282 0.791062275 0.591549176 0.687839608 0.735260571 1 19.21106043 0.788067442 4.050055192 0.999992301 0.699296886 0.679229777 0.062738481 1.235514724 23.10974972 0.05421445 0.013841539 6.138573243 -0.788067442 -0.300695416 QCQMEPNSDGHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QCQMEPNSDGHDR 13 0 Q8TBZ6;D6R954;X6REK4 Q8TBZ6 TRMT10A tRNA methyltransferase 10 homolog A 0 60.55 0.068999 54467000 23365 26371 23571 25948 26749 25266 31789 23856 28074 FALSE TRUE 21902.62636 28323.53628 24130.11525 26613.86961 24648.24144 32559.88404 27022.53456 26834.47411 23388.26804 0.936479192 1.211014695 1.031718775 1.137915367 1.053872027 1.392146011 1.155388442 1.147347639 1 14.51349741 QCVENADLPEGEKKPIDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QCVENADLPEGEKKPIDQR 19 2 A0A087WW66;Q99460-2;Q99460;C9J9M4;H7BZR6 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;; 153.25 2.68E-08 1332510000 2213490 1459260 1657050 1651000 1890170 1255880 2525300 1392750 2802240 FALSE TRUE 2074951.612 1567305.129 1696356.009 1693367.455 1741723.673 1618432.168 2146654.709 1566637.903 2334528.041 0.88880989 0.671358451 0.726637667 0.725357514 0.746071001 0.693258826 0.919524063 0.671072643 1 21.15469949 -0.654332511 0.384234105 1.079565395 0.731700765 0.41068101 0.087837534 9.052448956 1.187153926 0.969954579 0.057857443 0.221649874 0.654332511 -0.34786463 QDAKDPTSLLGVLQAEADS(ph)TSEGLEDAVHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QDAKDPTSLLGVLQAEADSTSEGLEDAVHSR 31 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 QDAKDPTSLLGVLQAEADS(0.695)T(0.258)S(0.047)EGLEDAVHSR;QDAKDPTSLLGVLQAEADS(0.977)T(0.022)S(0.001)EGLEDAVHSR;QDAKDPTSLLGVLQAEADS(0.773)T(0.183)S(0.044)EGLEDAVHSR 186.42 1.22E-18 125970000 140585 168770 133205 151984 169585 124617 264841 130782 185797 TRUE FALSE 131786.0358 181265.9064 136364.6855 155884.1667 156266.4782 160591.9049 225130.5507 147110.4206 154786.2804 0.851406439 1.171072177 0.880986901 1.007092918 1.009562849 1.037507358 1.454460629 0.950409947 1 17.23991808 1.974929229 24.90405483 1.200585383 0.998779313 0.109819582 0.160810079 924.0193552 917873.7412 0.06022839 0.039068828 94.39070475 -1.974929229 -0.20180607 QDAKDPTSLLGVLQAEADSTSEGLEDAVHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QDAKDPTSLLGVLQAEADSTSEGLEDAVHSR 31 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 126.18 3.72E-06 44641000 57175 59940 45354 53488 67704 55478 99540 50052 92795 FALSE TRUE 53596.51881 64378.01997 46429.8183 54860.59263 62386.80094 71493.59799 84614.90108 56301.10238 77306.91502 0.693295274 0.83275888 0.600590753 0.709646642 0.807001559 0.924802108 1.094532113 0.728280289 1 16.23830985 2.368151385 2.722821095 0.963045305 0.713396809 0.500447322 0.106372613 0.202586461 3.063782232 0.0399038 0.031568762 233.4271591 -2.368151385 -0.249648496 QDAQSLHGDIPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QDAQSLHGDIPQK 13 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;;; 167.55 3.17E-05 3689930000 2746380 3139060 3410230 3119510 3093410 2827190 3863060 2772150 3382530 FALSE TRUE 2574488.978 3371479.269 3491122.266 3199561.908 2850466.057 3643353.857 3283830.016 3118259.03 2817963.891 0.913598995 1.196423872 1.238881122 1.13541622 1.011533918 1.292902961 1.165320119 1.10656458 1 21.42622169 0.91826183 3.838276712 1.000140503 1.155817563 0.113183529 0.109220906 0.635304336 22.40965439 0.09806503 0.025150069 8.284414682 -0.91826183 0.15567706 QDDS(ph)PPRPIIGPALPPGFIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QDDSPPRPIIGPALPPGFIK 20 1 A0A0A0MRI1;Q8IXQ4;Q8IXQ4-4 A0A0A0MRI1 GPALPP1 GPALPP motifs-containing protein 1 1 QDDS(1)PPRPIIGPALPPGFIK 133.41 6.55E-06 483620000 540000 442920 490360 496780 486580 373780 562570 425850 537600 TRUE FALSE 506202.3639 475714.2577 501991.5708 509528.2158 448365.9696 481684.2182 478217.8511 479018.3099 447871.087 1.13024122 1.062167824 1.120839423 1.137667134 1.001104967 1.075497464 1.06775781 1.069545063 1 18.77272401 2.75070209 24.9929531 1.051353144 1.105653806 0.50512156 0.033493055 761.9131303 1568382.162 0.00984136 0.010374184 563.251154 -2.75070209 0.054300662 QDDS(ph)PSGASYGQDYDLS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QDDSPSGASYGQDYDLSPSR 20 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 QDDS(1)PSGASYGQDYDLS(0.897)PS(0.103)R 280.08 1.58E-44 160940000 85903 70722 80285 63455 76038 79316 107770 75429 70885 TRUE FALSE 80526.48457 75958.33047 82189.39811 65083.36273 70066.2822 102213.2416 91610.88899 84846.47669 59053.83557 1.36361142 1.286255664 1.391770701 1.102102211 1.18648148 1.730848481 1.551311411 1.436764875 1 15.84974315 2.267411458 24.99996184 1.492891572 1.278492981 0.104755539 0.201617347 304.8902659 264193.8322 0.064150622 0.05366405 185.1021477 -2.267411458 -0.214398592 QDDSPSGASYGQDYDLS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QDDSPSGASYGQDYDLSPSR 20 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 QDDSPSGASYGQDYDLS(0.966)PS(0.034)R;QDDSPSGASYGQDYDLS(1)PSR;QDDSPSGASYGQDYDLS(0.991)PS(0.009)R 418.92 2.18E-152 1095080000 707413 710567 735151 702999 709158 562923 818540 547086 602733 TRUE FALSE 663137.2831 763178.12 752589.1289 721039.1445 653463.5913 725429.7318 695807.526 615390.8914 502132.9685 1.320640796 1.519872559 1.498784537 1.435952606 1.301375596 1.444696479 1.385703727 1.225553648 1 18.93770993 0.819180483 0.822793415 0.99472873 1.451259092 0.782665466 0.071178526 0.374217251 0.514557817 0.068891118 0.024276848 6.594478893 -0.819180483 0.456530363 QDEESEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QDEESEFR 8 0 Q5T280 Q5T280 C9orf114 Putative methyltransferase C9orf114 0 81.338 0.053787 148830000 271380 283120 245560 269270 300390 196820 299500 257480 320520 FALSE TRUE 254394.8102 304082.4994 251384.7992 276179.9241 276798.5811 253638.7389 254592.7554 289626.9448 267023.1414 0.952706979 1.138787065 0.941434506 1.034292094 1.036608961 0.949875496 0.953448282 1.084651103 1 18.02660525 3.959437375 24.57007678 0.995064694 1.056672496 0.073965492 0.062819507 568.8226268 790326.7362 0.014786401 0.026739188 9108.301022 -3.959437375 0.061607803 QDEHGYISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 QDEHGYISR 9 0 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;; 141.71 0.00010606 54866000000 36792904 40947720 37687506 38474151 51481009 30177085 40808598 39062390 65326929 FALSE TRUE 34490101.82 43979531.79 38581471.44 39461462.85 47437898.22 38888719.56 34689727.58 43939415.38 54423442.52 0.633736129 0.808099043 0.708912734 0.725082079 0.871644571 0.714558245 0.63740414 0.807361926 1 25.69772488 0.98228828 23.30856731 1.000000005 0.732905353 0.596086074 0.070577888 331.950216 436846.7687 0.066076514 0.016519129 9.600376817 -0.98228828 -0.267094652 QDELGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QDELGER 7 0 Q15393 Q15393 SF3B3 Splicing factor 3B subunit 3 0 106.38 0.017948 140840000 246100 273820 268830 273670 288850 241050 311180 241200 270500 FALSE TRUE 230697.0403 294093.9177 275206.7746 280692.8355 266164.8862 310637.2219 264521.4479 271314.3509 225351.8025 1.023719525 1.305043556 1.221231743 1.245576172 1.181108308 1.378454569 1.17381554 1.203959089 1 17.78181946 -1.042755921 6.518324511 0.999999869 1.227957128 0.347557907 0.092112544 1.54E-07 2.27E-08 0.078222326 0.018437168 0.090624178 1.042755921 0.227957259 QDELKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 904990000 1500200 1232400 1346800 1317700 1358300 1084900 1596600 1376900 1577500 FALSE TRUE 1406305.16 1323648.178 1378746.732 1351514.413 1251624.597 1398093.018 1357204.652 1548808.996 1314205.059 1.070080464 1.007185423 1.049110809 1.028389294 0.952381509 1.063831712 1.03271909 1.178513951 1 20.32575897 1.427718073 22.59618634 1.094710924 1.02800283 0.178800719 0.053380175 41.63089362 19043.29511 0.028077785 0.011480709 26.77429678 -1.427718073 -0.066708094 QDENDDDDDWNPCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QDENDDDDDWNPCK 14 0 Q14974;Q14974-2 Q14974 KPNB1 Importin subunit beta-1 0 ;; 305.71 5.06E-44 1427240000 4106470 2764130 3189900 3086720 3439030 2661120 4842010 2712390 3995740 FALSE TRUE 3849453.373 2968789.061 3265565.934 3165930.461 3168942.456 3429342.144 4115995.552 3051037.862 3328825.181 1.15639998 0.891842888 0.980996525 0.951065403 0.951970225 1.030195927 1.236470925 0.916550944 1 21.66658168 1.998648971 20.39631538 1.091294712 0.972857093 0.022780543 0.106026686 6.906452399 104268.9618 0.037085809 0.02684989 99.68939735 -1.998648971 -0.118437619 QDFVQHFSQIVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QDFVQHFSQIVR 12 0 P14324-2;P14324;A0A087WVN4;A0A087X1D8;A0A087WTP2 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 ; 122.64 0.00035495 555630000 700760 1313900 941230 971250 1205410 827880 1188180 1108010 1292650 FALSE TRUE 656900.6825 1411182.523 963556.4201 996173.9193 1110741.961 1066875.516 1010023.44 1246347.488 1076898.364 0.609993203 1.310413842 0.894751494 0.925039867 1.031426918 0.990692856 0.937900431 1.157349225 1 20.03845067 1.250352069 24.99290987 1.078674655 0.986422146 0.058017424 0.17499781 667.4276936 1414684.801 0.109282136 0.039217143 17.79721591 -1.250352069 -0.09225251 QDGPMPKPHSVSLNDTETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QDGPMPKPHSVSLNDTETR 19 1 Q9P0L0-2;Q9P0L0 Q9P0L0-2 VAPA Vesicle-associated membrane protein-associated protein A 0 ;; 278.93 8.68E-40 615840000 604910 569960 493080 548250 725190 461950 699270 569670 851980 FALSE TRUE 567049.7629 612160.4314 504776.0904 562319.0232 668236.5027 595307.4659 594420.9552 640794.5535 709779.034 0.798910275 0.862466207 0.711173571 0.792245187 0.941471177 0.838722246 0.837473251 0.902808512 1 19.43701043 0.692948887 0.395213187 1.0164727 0.793057529 0.53128465 0.055514257 1.55631807 0.550343501 0.112343032 0.045362558 4.931157649 -0.692948887 -0.223415171 QDGS(ph)QEAPEAPLSSELEPFHPKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QDGSQEAPEAPLSSELEPFHPKPK 24 1 Q14676;Q14676-3;Q14676-2;H0Y6Z8 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 QDGS(1)QEAPEAPLSSELEPFHPKPK 127.95 4.89E-05 81354000 197890 125330 165470 155830 171390 108380 200870 136980 185460 TRUE FALSE 185504.4181 134609.5636 169395.0265 159828.8616 157929.7208 139667.5466 170751.4083 154082.2545 154505.5279 1.200632888 0.87122814 1.096368712 1.034454002 1.022162268 0.903964722 1.105147567 0.997260465 1 17.23729893 4.771503877 23.7689754 1.008786838 1.2006336 0.416730535 0.072964088 8082.32026 5831292.733 0.016550461 2.497832954 59088.6241 -4.771503877 0.191846761 QDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPK 38 2 O43809;H3BND3 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 146.01 2.04E-13 88233000 72488 79332 38942 28227 93554 43332 84208 72492 58035 FALSE TRUE 67951.10547 85205.82382 39865.72263 28951.35261 86206.64622 55841.24496 71581.79215 81542.78577 48348.58358 1.405441493 1.762323061 0.824547891 0.598804566 1.7830232 1.154971683 1.480535454 1.686559972 1 15.561186 QDHAQQLATAAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QDHAQQLATAAEER 14 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 177.04 2.14E-06 1152280000 1518340 1668470 1768740 1611230 1743140 1452940 1868090 1554670 1970130 FALSE TRUE 1423309.81 1792005.255 1810695.348 1652576.89 1606240.816 1872380.191 1587987.247 1748773.972 1641302.575 0.867183072 1.09181895 1.103206304 1.006869126 0.978637845 1.140789163 0.967516454 1.065479332 1 20.64640979 QDHPSSMGVYGQESGGFSGPGENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QDHPSSMGVYGQESGGFSGPGENR 24 0 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;Q01844-4 B0QYK0 EWSR1 RNA-binding protein EWS 0 ; 223.82 7.33E-33 1210580000 1174800 1033720 1145790 1032180 1254990 875690 1573750 1008700 2046390 FALSE TRUE 1101271.365 1110257.704 1172968.68 1058667.486 1156428.148 1128487.487 1337780.797 1134638.415 1704834.289 0.645969742 0.651240834 0.68802504 0.620979701 0.678322905 0.661933828 0.784698434 0.665541761 1 20.70120008 -4.001038909 0.226776455 2.034819316 0.635471811 0.875235373 0.039213861 29.98411456 0.452805041 14.24847627 0.067469423 9.98E-05 4.001038909 -1.399347506 QDKDDIINIFSVASGHLYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QDKDDIINIFSVASGHLYER 20 1 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 108.71 4.88E-05 67924000 223060 215740 211600 235730 207760 180000 272100 176290 138870 FALSE TRUE 209099.0728 231713.6141 216619.2519 241779.2309 191443.3677 231963.0779 231301.1311 198300.1946 115691.6999 1.8073818 2.002854261 1.87238369 2.089858055 1.654771845 2.005010543 1.999288897 1.714039942 1 16.81992584 0.86113512 3.729112117 1.000159915 1.925741487 0.845992803 0.122737978 0.24012467 5.834578324 0.105388649 0.027068069 7.263319025 -0.86113512 0.925581572 QDKPMDTSVLS(ph)EEGGEPFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QDKPMDTSVLSEEGGEPFQK 20 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 QDKPMDTSVLS(1)EEGGEPFQK;QDKPMDTSVLS(1)EEGGEPFQK 211.94 1.35E-22 385820000 649780 362280 456680 457660 478750 362560 563170 411580 569520 TRUE FALSE 609111.4297 389103.5882 467512.6653 469404.3304 441150.9062 467225.1863 478727.8867 462966.669 474463.4328 1.283790041 0.820091837 0.985350257 0.989337213 0.929789054 0.984744353 1.008987951 0.975768915 1 18.85593738 2.000962776 23.58856844 0.996154764 0.972719684 0 0.116873055 127.589374 3125836.23 0.04083081 0.029864514 100.2219334 -2.000962776 -0.02343508 QDLPALEEKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QDLPALEEKPR 11 1 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;; 174.05 1.05E-05 1544300000 2805540 2324510 2676400 2615030 2676990 2220120 3160610 2337720 2509270 FALSE TRUE 2629946.259 2496619.139 2739885.472 2682136.097 2466750.004 2861032.603 2686705.872 2629589.488 2090456.626 1.258072627 1.194293681 1.310663631 1.283038386 1.18000535 1.368616104 1.285224404 1.25790196 1 20.99538668 0.926398877 18.62982667 1 1.268868998 0.71181025 0.053478277 897.4720744 227168.7642 0.049684875 0.012421219 8.441096727 -0.926398877 0.268868998 QDLPDAMKPHEIQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QDLPDAMKPHEIQEK 15 1 P62330 P62330 ARF6 ADP-ribosylation factor 6 0 ;;;;; 215.23 1.42E-12 1094210000 4003750 2435610 2936830 2874550 2980180 2108340 3737940 2299600 3062700 FALSE TRUE 3753162.434 2615945.099 3006492.994 2948315.82 2746128.684 2716983.532 3177470.598 2586710.122 2551515.584 1.470954149 1.025251468 1.178316532 1.155515505 1.07627353 1.064850847 1.245326745 1.013793581 1 21.28292302 4.74724231 24.6430522 1.111935862 1.470954373 0.682995984 0.079765803 535.7257765 1520621.121 0.017703111 0.206539949 55878.18743 -4.74724231 0.35901851 QDLPNAMNAAEITDKLGLHSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QDLPNAMNAAEITDKLGLHSLR 22 1 P61204;P61204-2;H0YGG7;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 133.1 1.29E-05 162150000 178300 211710 198870 205140 222190 153010 251780 172910 291510 FALSE TRUE 167140.5213 227385.2287 203587.2903 210404.2397 204740.0937 197181.5031 214027.9264 194498.1941 242855.0978 0.688231471 0.936300003 0.838307667 0.866377694 0.843054544 0.811930673 0.881298883 0.800881661 1 17.88973624 -2.101812584 2.261763593 1.261806654 0.845931838 0.381627827 0.06494158 5877039.126 1709282.263 7908999.97 0.014010203 0.007910199 2.101812584 -0.415874816 QDLPPLDEKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QDLPPLDEKPR 11 1 O95757;E9PDE8;D6RJ96 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 134.56 0.0001261 133000000 222270 185020 193290 193750 220950 185670 229850 177550 185100 FALSE TRUE 208358.5175 198719.0733 197874.9301 198721.953 203597.4783 239269.9149 195386.1263 199717.5083 154205.6142 1.351173357 1.288663025 1.283188884 1.2886817 1.320298741 1.551629077 1.26704937 1.295137725 1 17.23449577 0.614321643 1.96298537 1.000176625 1.331080137 0.627020775 0.080834396 1.465220123 6.625562476 0.075893277 0.0209752 4.114543354 -0.614321643 0.330903513 QDLPSLDEKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QDLPSLDEKPR 11 1 Q92598-2;Q92598;Q92598-4;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;; 170.18 1.46E-05 2505760000 3077530 2422920 2831120 2654700 2810040 2271610 3405800 2432380 2851240 FALSE TRUE 2884912.891 2602315.518 2898275.503 2722824.096 2589350.794 2927386.93 2895131.908 2736067.997 2375349.624 1.214521375 1.095550521 1.22014691 1.146283506 1.090092493 1.232402548 1.218823485 1.151859065 1 21.17970845 0.961910867 22.44262752 0.999999999 1.173072132 0.533420928 0.050728263 1426.035497 840241.0683 0.048098992 0.012024748 9.160324676 -0.961910867 0.173072133 QDPFQESGLHLS(ph)PTAAEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QDPFQESGLHLSPTAAEAK 19 0 H3BN50;Q15599-3;H3BQS0;Q15599 H3BN50;Q15599 SLC9A3R2 Na(+)/H(+) exchange regulatory cofactor NHE-RF2 1 QDPFQESGLHLS(0.877)PT(0.123)AAEAK;QDPFQESGLHLS(0.944)PT(0.056)AAEAK;QDPFQESGLHLS(0.994)PT(0.006)AAEAK;QDPFQESGLHLS(0.858)PT(0.142)AAEAK 260.32 2.70E-31 1235550000 2342320 1546320 1995940 1847720 1758880 1720150 2603500 1621170 1760500 TRUE FALSE 2195718.372 1660811.142 2043284.639 1895135.623 1620744.66 2216729.381 2213129.345 1823576.643 1466661.177 1.497086312 1.132375472 1.393153833 1.292142762 1.105057314 1.511412053 1.508957474 1.243352365 1 20.48410419 2.223237049 24.99991543 1.379947451 1.278553485 0 0.185438919 696.3166939 1136011.592 0.063484584 0.047061788 167.2002989 -2.223237049 -0.101393966 QDPGTELLHCENEDLICFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QDPGTELLHCENEDLICFK 19 0 Q9NQE9 Q9NQE9 HINT3 Histidine triad nucleotide-binding protein 3 0 185.87 2.18E-14 56090000 88351 76985 71695 68623 87791 79751 101630 75820 111990 FALSE TRUE 82821.26862 82685.0495 73395.63926 70383.98236 80896.24899 102773.8191 86391.52499 85286.2939 93298.14552 0.887705411 0.88624537 0.786678437 0.754398514 0.867072422 1.101563364 0.925972585 0.914126357 1 16.50956078 2.458152895 24.79076575 0.978708552 0.829266271 0.579091041 0.063752323 159.535465 208504.1236 0.021793099 0.018235995 287.1791429 -2.458152895 -0.149442281 QDPQLHPEDPERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QDPQLHPEDPERR 13 1 A2IDC7;Q4TT37;A2IDC6;Q13084 A2IDC7 MRPL28 "39S ribosomal protein L28, mitochondrial" 0 82.908 0.007187 360930000 303670 242640 216790 182920 292060 207240 228720 262770 379520 FALSE TRUE 284663.8368 260605.3181 221932.3612 187614.0369 269122.7857 267066.8237 194425.5593 295577.4129 316175.6602 0.900334443 0.824242188 0.701927407 0.593385451 0.851181225 0.844678631 0.614928927 0.934851888 1 18.27036679 1.061404128 7.270057924 0.999602675 0.756742862 0.425252404 0.100936575 0.176044916 16.14725306 0.094556705 0.023705772 11.51871752 -1.061404128 -0.242859813 QDPSVLHTEEMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 QDPSVLHTEEMR 12 0 P50502;Q3KNR6;Q8NFI4;F8WAQ7 P50502 ST13;ST13P5 Hsc70-interacting protein;Putative protein FAM10A5 0 ;;;;;;; 192.86 3.54E-06 6270090000 6793110 8061380 7667610 7723230 8507680 6968090 8790740 6935370 8016280 FALSE TRUE 6367941.371 8658252.963 7849489.33 7921421.157 7839521.131 8979664.466 7472650.146 7801266.211 6678311.081 0.953525718 1.296473443 1.175370425 1.186141385 1.173877802 1.344601106 1.118943106 1.168149569 1 22.67105187 0.685913028 1.463242222 1.000758716 1.195941723 0.213774345 0.103969907 1.464021109 4.81771759 0.088022235 0.02572053 4.851913256 -0.685913028 0.195183008 QDPVVHLS(ph)PNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QDPVVHLSPNK 11 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 QDPVVHLS(1)PNK 77.222 0.021389 144490000 348900 270540 314460 296710 327330 253280 381450 290740 338760 TRUE FALSE 327062.9718 290571.0631 321919.1397 304324.0809 301622.8222 326397.8243 324255.1137 327039.529 282218.7675 1.158898732 1.02959511 1.140672332 1.078326872 1.068755366 1.156541881 1.148949507 1.158815666 1 18.1064544 2.240207282 24.99783012 1.131683275 1.091721566 0 0.058183845 98.47725354 1494999.995 0.018617846 0.014797265 173.8630451 -2.240207282 -0.039961709 QDS(ph)DSDVVDIEEAEHDFMGEAHPVVFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QDSDSDVVDIEEAEHDFMGEAHPVVFSR 28 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 QDS(0.73)DS(0.27)DVVDIEEAEHDFMGEAHPVVFSR;QDS(0.979)DS(0.021)DVVDIEEAEHDFMGEAHPVVFSR 171.23 3.77E-12 55200000 38171 33815 37725 34271 34623 30955 43547 37741 38361 TRUE FALSE 35781.94525 36318.69778 38619.85482 35150.45188 31903.84924 39891.20599 37017.53162 42453.04693 31958.30128 1.119644781 1.136440184 1.20844517 1.099884865 0.998296154 1.248226733 1.158307236 1.32838872 1 14.9639031 QDS(ph)LEPVLRDPCYLINEGICNR ddPTM_SK-BR-3_Pertuzumab_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 126.99 1.14E-05 263886000 110622 94408 89933 112503 111225 71929 119149 87832 136455 TRUE FALSE 103698.3665 101398.0666 92066.25323 115390.0174 102489.8372 92693.73463 101283.7136 98798.01854 113679.779 0.912197116 0.891962207 0.809873612 1.015044351 0.901566119 0.81539334 0.890956285 0.869090523 1 16.79461613 -0.853875684 4.172463171 1.000001854 0.883079148 0.27369837 0.056648524 12204606.93 30304471.97 378.9517079 0.013124414 0.139998801 0.853875684 -0.116922706 QDSGEWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QDSGEWR 7 0 Q96G03-2;Q96G03 Q96G03-2;Q96G03 PGM2 Phosphoglucomutase-2 0 90.308 0.040093 694310000 1499700 1281600 1269300 1245600 1366200 1015500 1373000 1080500 1355900 FALSE TRUE 1405836.454 1376490.998 1299408.395 1277564.205 1258904.163 1308658.365 1167131.396 1215402.803 1129591.531 1.244552934 1.218574113 1.150334754 1.130996622 1.114477339 1.158523528 1.033233133 1.07596664 1 20.10736975 8 0.123868301 0.942835059 1.953710705 0.880017852 0.026179853 25.9748823 0.21971408 0.150875024 4.55485219 100000000 -8 1.010875646 QDSGHLDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QDSGHLDLR 9 0 Q86U44;F5H6D8;B4DTN4;B4E349 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 0 72.2 0.044725 0 116370 139030 144250 144190 167470 112890 147730 139100 153400 FALSE TRUE 109086.6094 149323.9259 147671.6781 147890.1595 154317.5817 145479.5104 125579.258 156466.9412 127796.549 0.853595893 1.168450377 1.155521642 1.157231245 1.207525422 1.138368066 0.982649836 1.224344025 1 16.96348935 -0.294471849 6.939014974 0.999998891 1.115664137 0.086827463 0.112170843 0 0 0.100690983 0.023733092 0.507607641 0.294471849 0.115665246 T(ph)NSAEVTPPVLSVMGEATPVSIEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TNSAEVTPPVLSVMGEATPVSIEPR 25 0 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 T(0.828)NS(0.123)AEVT(0.049)PPVLSVMGEATPVSIEPR 158.65 9.02E-11 18650000 94466 81337 84125 85738 65634 47487 92873 47178 47490 TRUE FALSE 88553.54169 87359.27611 86120.48473 87938.18223 60479.37039 61195.72601 78947.55584 53068.27715 39563.6122 2.238257246 2.208071287 2.176759905 2.222703574 1.52866149 1.546767916 1.995458742 1.341340545 1 15.27188653 1.478064398 0.249302708 0.80793237 2.488432551 0.765921317 0.210592651 0.96417756 0.258072543 0.632027267 0.584647861 30.0652208 -1.478064398 1.680500181 QDWEHAANDVSFATIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QDWEHAANDVSFATIR 16 0 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224;J3KPM9;A0A669KBI6;P42224-2;A0A669KB52;E7EPD2;A0A669KB75;D2KFR9;A0A669KB17;E7ENM1;E9PH66 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta;Signal transducer and activator of transcription 0 ; 230.45 2.25E-15 266600000 314860 381790 328300 369020 386120 305270 436300 334530 353400 FALSE TRUE 295153.4746 410058.1289 336087.431 378489.6779 355795.6927 393396.4934 370880.8654 376296.8069 294415.2569 1.002507403 1.392788312 1.141542169 1.285564077 1.208482524 1.336196016 1.259720265 1.278115852 1 18.16749291 -0.834454507 7.985044946 1.000008242 1.249038404 0.321115372 0.107771345 1.34E-09 0 0.090011815 0.021215988 0.146401489 0.834454507 0.249030163 QDYDAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QDYDAGR 7 0 P52298-2;P52298;C9JQX9;B3KSB0;P52298-3 P52298-2 NCBP2 Nuclear cap-binding protein subunit 2 0 82.452 0.056881 281120000 144570 162780 147070 149660 174560 136910 174810 146550 177390 FALSE TRUE 135521.6218 174832.4006 150558.5699 153500.529 160850.7617 176433.6945 148598.8634 164847.0901 147782.463 0.917034532 1.183038887 1.01878509 1.038692453 1.088429293 1.193874367 1.005524338 1.115471259 1 17.17311555 -0.973412956 3.822313882 0.999991228 1.075549075 0.062548707 0.082949449 10736304.97 18797920.76 1220.027302 0.017777931 0.106313164 0.973412956 0.075557848 QDYINLDESEAAAFDDEWRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QDYINLDESEAAAFDDEWRR 20 1 Q15773 Q15773 MLF2 Myeloid leukemia factor 2 0 ; 203.26 1.73E-21 126748000 50396 68451 52161 46093 59596 45899 65882 48292 73254 FALSE TRUE 47241.80432 73519.18326 53398.28355 47275.82442 54915.57056 59149.29619 56003.60572 54321.3625 61027.43416 0.774107661 1.204690714 0.87498818 0.774665117 0.899850556 0.969224694 0.91767918 0.890113819 1 15.89717031 3.730263756 24.88556752 0.900081356 1.026060432 0.063573071 0.118753482 217.6344743 1723430.104 0.028272107 0.04838284 5373.580464 -3.730263756 0.125979076 QEAEDLSLSAPSSPEIS(ph)PQS(ph)SPRPHRPNNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QEAEDLSLSAPSSPEISPQSSPRPHRPNNDR 31 2 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 2 QEAEDLSLS(0.001)APS(0.377)S(0.134)PEIS(0.551)PQS(0.483)S(0.453)PRPHRPNNDR 84.362 0.00039478 184160000 23227 31785 29852 38518 34330 25181 34454 29605 35003 TRUE FALSE 21773.26353 34138.39447 30560.10354 39506.43709 31633.86028 32450.34592 29287.94256 33301.24942 29160.77317 0.746662765 1.170695793 1.047986737 1.354780165 1.084808695 1.112808146 1.004360974 1.141987876 1 14.83174135 4.744047698 24.90829661 1.113451192 0.746662601 0.566246485 0.101219903 415.7540245 1887231.97 0.022798985 0.198100294 55468.66299 -4.744047698 -0.366788592 QEAEDLSLSAPSSPEIS(ph)PQSSPRPHRPNNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QEAEDLSLSAPSSPEISPQSSPRPHRPNNDR 31 2 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 QEAEDLSLSAPS(0.007)S(0.03)PEIS(0.757)PQS(0.103)S(0.103)PRPHRPNNDR 135.82 8.73E-07 225580000 23883 35672 33186 39576 38890 26611 43475 29040 43686 TRUE FALSE 22388.20566 38313.192 33973.18759 40591.58716 35835.73627 34293.16371 36956.32735 32665.70792 36394.52438 0.615153132 1.052718579 0.933469751 1.11532127 0.984646369 0.942261626 1.01543647 0.897544575 1 15.15143379 4.744047465 24.93943285 0.993588049 0.615152966 0.786506169 0.061812249 240.7131735 1094082.443 0.013355523 0.116173846 55468.6332 -4.744047465 -0.378435083 QEAGDS(ph)PPPAPGTPK ddPTM_SK-BR-3_Pertuzumab_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 228.33 6.42E-13 100380000 484120 371070 432130 404960 404370 320090 506580 369360 496680 TRUE FALSE 453819.7934 398544.4089 442380.3277 415351.9592 372612.4114 412494.7868 430623.0319 415475.4091 413780.8993 1.096763515 0.963177395 1.069117324 1.00379684 0.900506553 0.996891803 1.040703021 1.004095186 1 18.65850752 4.754489522 23.78849951 1.002057936 1.096763655 0.325465128 0.044538228 2011.302173 3003611.591 0.010769025 0.252076003 56818.46828 -4.754489522 0.094705719 QEAKPQQAAGMLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QEAKPQQAAGMLSPK 15 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 QEAKPQQAAGMLS(1)PK;QEAKPQQAAGMLS(1)PK;QEAKPQQAAGMLS(1)PK;QEAKPQQAAGMLS(1)PK;QEAKPQQAAGMLS(1)PK 195.03 1.65E-08 3026550000 6406540 2549460 3799080 3261790 3410790 2796670 5132340 3190430 3211890 TRUE FALSE 6005566.097 2738224.671 3889195.972 3345493.054 3142920.312 3604023.229 4362793.263 3588762.209 2675804.809 2.244396182 1.023327509 1.453467741 1.250275447 1.174570096 1.346893173 1.630460207 1.341189834 1 21.35154145 4.749753668 24.77300666 1.311439593 2.244396799 0.715618077 0.190486447 864.8803284 1914153.916 0.045784837 0.704966472 56202.24549 -4.749753668 0.932957206 QEALKNDLVEALKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QEALKNDLVEALKR 14 2 P47756-2;B1AK88 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ; 197.14 1.34E-08 668490000 2191370 1386880 1510920 1490130 1854520 1500960 2761700 1521970 2948100 FALSE TRUE 2054216.063 1489566.038 1546759.736 1528369.259 1708873.48 1934262.786 2347608.723 1711991.305 2456043.065 0.836392526 0.606490195 0.629777123 0.622289275 0.695783191 0.787552472 0.955849984 0.697052641 1 21.22790443 2.141517831 2.815305632 0.878715728 0.656522904 0.459635797 0.101063925 0.205615466 3.263927621 0.040824561 0.027149336 138.5217057 -2.141517831 -0.222192824 QEARPEPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 138.25 0.00012947 657970000 605580 1542350 459560 456920 1484300 319510 602470 1225570 1509400 FALSE TRUE 567677.8288 1656547.199 470460.9802 468645.3408 1367729.065 411747.3502 512135.2166 1378585.112 1257471.389 0.451443932 1.31736373 0.374132552 0.372688671 1.087682056 0.327440731 0.407273852 1.096315292 1 20.26209414 1.220768026 24.9920239 1.048158096 0.645343993 0.22015863 0.332523296 468.5436416 658113.2375 0.315161926 0.079476085 16.62524393 -1.220768026 -0.402814103 QEASES(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QEASESPVK 9 0 Q01167;Q01167-2;E9PPI7;Q01167-3 Q01167 FOXK2 Forkhead box protein K2 1 QEAS(0.035)ES(0.965)PVK;QEAS(0.007)ES(0.993)PVK 104.17 0.0037644 0 545890 340450 393330 379440 346340 342080 502520 344150 300390 TRUE FALSE 511723.7193 365657.2722 402659.9733 389177.0728 319139.8535 440832.9428 427171.7912 387117.8851 250252.9684 2.044825772 1.461150589 1.609011777 1.555134691 1.275269003 1.761549306 1.706959937 1.546906267 1 17.93302766 0.954957267 20.82442318 0.999999997 1.609977208 0.490262878 0.199627599 952.7457402 440480.8455 0.177716262 0.04442885 9.014824299 -0.954957267 0.609977211 QECLDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QECLDSR 7 0 P25786;P25786-2;F5GX11;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 82.452 0.056881 973190000 1871900 2267200 1820500 2133100 2673600 1522700 2035100 1806600 2957900 FALSE TRUE 1754741.12 2435065.847 1863683.12 2187838.957 2463626.241 1962278.771 1729955.648 2032157.987 2464207.381 0.712091496 0.988174074 0.756301249 0.88784693 0.999764167 0.79631235 0.702033303 0.824670035 1 21.23269224 2.061555387 24.99999603 0.794133047 0.872911885 0 0.11588176 154.9806775 62942.33563 0.040000737 0.029542498 115.2273003 -2.061555387 0.078778839 QEDEWDKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QEDEWDKPR 9 1 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ;;; 180.07 4.48E-05 2007900000 3902110 3450870 3262770 3752020 3612940 2239470 4296450 2891090 2077620 FALSE TRUE 3657883.901 3706376.005 3340164.445 3848303.185 3329194.266 2885968.634 3652237.209 3252048.951 1730851.8 2.113343211 2.141359535 1.929780727 2.223357994 1.923442704 1.667369 2.110080833 1.878871981 1 20.72305077 -1.917090407 0.308659438 1.29E-16 2.091233301 0.827596439 0.146281772 12.20825087 0.597541792 9.05248521 0.140349153 0.012103461 1.917090407 2.091233301 QEDKDDLDVTELTNEDLLDQLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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" 0 189.78 1.57E-17 29983000 74634 33794 42999 39400 39949 30107 61307 38052 60010 FALSE TRUE 69962.79117 36296.14292 44018.95659 40411.0707 36811.56669 38798.40215 52114.5845 42802.87596 49993.94332 1.399425341 0.726010803 0.880485788 0.808319329 0.736320527 0.77606205 1.042417962 0.856161229 1 15.60946571 -1.991277255 11.68072237 1.092052659 0.883607686 0.014628439 0.198834464 0.108763023 8.12E-05 0.04392983 0.041000695 0.010202879 1.991277255 -0.208444973 QEEAEEQGAGS(ph)PGQPAHLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 QEEAEEQGAGSPGQPAHLAR 20 0 Q96S99 Q96S99 PLEKHF1 Pleckstrin homology domain-containing family F member 1 1 QEEAEEQGAGS(1)PGQPAHLAR;QEEAEEQGAGS(1)PGQPAHLAR;QEEAEEQGAGS(1)PGQPAHLAR;QEEAEEQGAGS(1)PGQPAHLAR;QEEAEEQGAGS(1)PGQPAHLAR;QEEAEEQGAGS(1)PGQPAHLAR;QEEAEEQGAGS(1)PGQPAHLAR;QEEAEEQGAGS(1)PGQPAHLAR 318.41 9.55E-67 11670030000 4025940 3795950 4187200 3998960 4316720 3818444 4651040 3895190 4332520 TRUE FALSE 3773963.602 4077006.088 4286522.361 4101580.084 3977702.224 4920766.796 3953659.73 4381513.046 3609394.423 1.045594679 1.12955405 1.187601536 1.136362393 1.102041439 1.363321992 1.095380351 1.21391916 1 21.78332537 4.766474403 1.775713708 1.166464855 0.99923469 0.115371243 0.093870625 1.822478352 5.495551603 0.021481161 0.525028702 58408.27809 -4.766474403 -0.167230165 QEEDSYEIFICHANVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QEEDSYEIFICHANVIR 17 0 Q96HS1;Q96HS1-2;F5GXG4 Q96HS1 PGAM5 "Serine/threonine-protein phosphatase PGAM5, mitochondrial" 0 167.05 2.27E-09 156810000 111350 106120 94441 86837 127110 93395 88871 103170 107020 FALSE TRUE 104380.8023 113977.2352 96681.18512 89065.38443 117127.2933 120356.6204 75545.61859 116051.0016 89157.67062 1.170743936 1.278378343 1.084384377 0.99896491 1.313709662 1.349930068 0.847326069 1.301637883 1 16.4440713 -5 0.079849 0.473958021 1.315991717 0.077626944 0.159394699 610.7790401 3.456181797 56.45888061 5.307959147 1.00E-05 5 0.842033697 QEELGAVVDKEMAATSAAIEDAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QEELGAVVDKEMAATSAAIEDAVR 24 1 O75146 O75146 HIP1R Huntingtin-interacting protein 1-related protein 0 ; 138.92 2.91E-06 17348200 41226 48699 46904 47359 55792 39011 63564 47294 85875 FALSE TRUE 38645.73825 52304.72463 48016.58503 48574.31212 51410.32137 50272.84241 54033.1683 53198.76001 71541.90773 0.540183222 0.731106093 0.671167244 0.678963053 0.718604284 0.702704806 0.75526597 0.74360276 1 16.12650097 -5 0.160541591 2.15611883 0.613869004 0.838072337 0.045803681 48.78850075 0.449512799 17.86488582 0.176920584 1.00E-05 5 -1.542249826 QEESES(ph)PVERPLKENPPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QEESESPVERPLKENPPNK 19 2 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;D6RBF8 H3BLV9 SRPK1 SRSF protein kinase 1 1 QEES(0.029)ES(0.971)PVERPLKENPPNK;QEES(0.121)ES(0.879)PVERPLKENPPNK;QEES(0.136)ES(0.864)PVERPLKENPPNK 152.88 2.68E-08 731970000 1229720 784260 1001680 946830 985070 839860 1308440 831390 1062310 TRUE FALSE 1152754.02 842327.4264 1025440.323 971127.2608 907706.5758 1082313.948 1112251.569 935190.8716 885003.5982 1.30254162 0.951778533 1.158684919 1.097314477 1.025652978 1.222948641 1.256776324 1.056708553 1 19.7553238 2.232695591 24.99191359 1.168765394 1.092573747 0 0.117615954 351.3746771 1497254.746 0.040047833 0.030374288 170.8817138 -2.232695591 -0.076191648 QEFAQHANAFHQWIQETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QEFAQHANAFHQWIQETR 18 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 205.24 5.69E-16 336240000 226225 214072 187735 168589 209100 178459 252892 169814 351330 FALSE TRUE 212065.9811 229922.1136 192188.1629 172915.2792 192678.1295 229977.2163 214973.1923 191015.6517 292690.7533 0.724539394 0.785546216 0.656625331 0.590778073 0.658299339 0.785734478 0.7344721 0.652619359 1 18.15901764 -1.229469467 4.611863042 1.000082644 0.704339358 0.699968104 0.061916771 5.47E-05 9.14E-06 0.062331984 0.014687696 0.058956343 1.229469467 -0.295743285 QEFEFWYPVDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QEFEFWYPVDLR 12 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRP1 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ;;;;; 205.49 2.35E-07 484613000 666710 697863 647782 644720 684063 621063 838996 636719 579135 FALSE TRUE 624981.8112 749533.5026 663147.6949 661264.6067 630339.4514 800353.806 713196.3387 716214.7687 482473.6271 1.295369894 1.553522225 1.374474495 1.370571508 1.306474418 1.658855036 1.478207924 1.484464079 1 18.88009056 -0.863913734 7.182986775 0.999999999 1.450296033 0.603001731 0.111997373 6.12E-09 8.52E-10 0.102632649 0.024190747 0.136800053 0.863913734 0.450296034 QEGGDNDLIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QEGGDNDLIER 11 0 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A096LNY6 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 0 160.67 6.33E-05 71896000 70690 86442 80002 74195 82343 73937 83623 83265 105650 FALSE TRUE 66265.63909 92842.25562 81899.68522 76098.96931 75876.11294 95281.41163 71084.50747 93660.81854 88016.33247 0.752878894 1.05482986 0.930505543 0.864600548 0.862068559 1.082542398 0.807628601 1.064129985 1 16.42548364 1.201528503 24.99951778 1.032065171 0.924471572 0.189053897 0.102549432 346.7993935 234108.6533 0.089600549 0.02240259 15.90481064 -1.201528503 -0.107593599 QEGHNLGLLHGDMDQSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QEGHNLGLLHGDMDQSER 18 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ; 140.84 7.18E-08 338190000 102998 90742 99856 89079 105364 86671 121703 89474 122268 FALSE TRUE 96551.53904 97460.6321 102224.6315 91364.91795 97089.13646 111691.5107 103454.765 100645.0259 101860.6809 0.947878398 0.956803265 1.003573023 0.896959623 0.95315617 1.096512508 1.015649651 0.988065512 1 16.63623774 2.293408587 24.99982314 1.027719131 0.956963487 0.474074331 0.038135646 79.41293609 36196.12571 0.012948366 0.010833372 196.520829 -2.293408587 -0.070755644 QEIQHLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QEIQHLFR 8 0 P04844-2;P04844;H0Y5M1 P04844-2 RPN2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 0 134.66 0.00086716 84873000 131490 173390 100600 102760 177180 103760 157300 152040 141320 FALSE TRUE 123260.2756 186227.976 102986.2795 105396.9956 163264.9975 133713.8276 133714.3253 171022.5287 117732.779 1.046949512 1.581785273 0.874746017 0.895222184 1.386742068 1.13574001 1.135744237 1.452633074 1 16.84515652 QEKPAEKPAET(ph)PVATS(ph)PTATDSTSGDSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 2 QEKPAEKPAET(1)PVAT(0.21)S(0.787)PT(0.003)ATDSTSGDSSR 127.49 3.57E-05 186120000 196740 120470 158490 174780 148600 73752 120560 85666 134000 TRUE FALSE 184426.3946 129389.7241 162249.4576 179265.1507 136929.5554 95043.00514 102483.1472 96361.58867 111634.5343 1.652055036 1.159047466 1.453398436 1.605821637 1.226587778 0.851376375 0.918023691 0.863187984 1 16.76842387 2.393537632 4.027140405 0.902859254 1.414817095 0.776477247 0.140035251 0.106810565 3.330280024 0.049739066 0.041187352 247.4785897 -2.393537632 0.51195784 QEKPAEKPAETPVAT(ph)SPTATDSTSGDSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 1 QEKPAEKPAETPVAT(0.637)S(0.361)PT(0.003)ATDSTSGDSSR 294.1 1.52E-80 2096600000 1180500 822780 1037900 1166700 1002500 533750 870650 548330 852770 TRUE FALSE 1106614.612 883699.4873 1062519.478 1196639.497 923767.6939 687834.9603 740104.1152 616790.2075 710437.1779 1.557653015 1.243881253 1.49558541 1.684370602 1.30028062 0.96818548 1.041758706 0.868184023 1 19.43834756 2.353576574 3.830190122 0.979038013 1.456780881 0.810089073 0.119466542 0.104244649 2.881804654 0.044670018 0.036375064 225.7233953 -2.353576574 0.477742867 QEKPAEKPAETPVATS(ph)PTATDSTSGDSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 1 QEKPAEKPAETPVAT(0.008)S(0.99)PT(0.001)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.084)S(0.913)PT(0.003)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.121)S(0.877)PT(0.001)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.005)S(0.833)PT(0.117)AT(0.045)DSTSGDSSR;QEKPAEKPAETPVAT(0.228)S(0.77)PT(0.001)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.101)S(0.854)PT(0.036)AT(0.008)DSTSGDSSR;QEKPAEKPAETPVAT(0.016)S(0.981)PT(0.003)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.004)S(0.992)PT(0.004)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.007)S(0.989)PT(0.004)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.136)S(0.527)PT(0.337)ATDSTSGDSSR 259.81 3.43E-58 69450470000 19949490 13255924 17701286 19781640 16091480 8682471 13903064 8590770 13707902 TRUE FALSE 18700887.03 14237406.41 18121168.86 20289270.37 14827720.07 11188959.43 11818428.62 9663346.545 11419964.6 1.637560858 1.246711956 1.586797289 1.776649148 1.298403331 0.979771814 1.034891879 0.846180079 1 23.44505484 2.382196107 3.601278219 0.974695354 1.516104038 0.790778839 0.143472968 0.114165708 2.897670909 0.053941538 0.04424875 241.0993874 -2.382196107 0.541408683 QEKPAEKPAETPVATSPTATDSTSGDSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ;; 185.65 4.07E-18 3437240000 2570500 1588010 1885200 1708340 2004890 1465970 2674470 1778170 2778090 FALSE TRUE 2409616.993 1705587.913 1929917.834 1752178.897 1847434.027 1889171.741 2273458.052 2000178.439 2314408.832 1.041137141 0.736943227 0.833870753 0.757074062 0.798231497 0.816265353 0.98230616 0.864228658 1 21.1422123 1.757310978 15.29809656 0.942252301 0.816087179 0.269456559 0.089477634 0.522288561 428.9525228 0.037517386 0.020726873 57.18879922 -1.757310978 -0.126165122 (ac)SILKIHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SILKIHAR 8 1 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 ; 65.252 0.002695 1111180000 1413920 1861540 1918090 2273600 1963790 1921120 1384820 599010 770730 FALSE TRUE 1325425.271 1999370.359 1963588.001 2331944.425 1809561.855 2475716.157 1177179.097 673797.7171 642090.1839 2.064235374 3.113846635 3.058118703 3.631802017 2.818236286 3.855714072 1.833354763 1.049381744 1 19.29241642 1.535307693 4.095877263 1.109609099 3.097289473 0.768134322 0.478747147 0.07769649 2.877527086 0.275788847 0.114626162 34.301072 -1.535307693 1.987680375 QELEQS(ph)LASWTQNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QELEQSLASWTQNLK 15 0 Q8WXH0-13 Q8WXH0-13 SYNE2 Nesprin-2 1 QELEQS(0.333)LAS(0.333)WT(0.333)QNLK 73.887 0.060905 1613200000 867460 2528200 2100200 2267900 2546500 1838500 2248700 2000700 1995900 TRUE FALSE 813167.2271 2715390.559 2150017.736 2326098.154 2346508.162 2369245.104 1911528.311 2250491.799 1662771.396 0.48904331 1.633051041 1.293032669 1.398928415 1.411203108 1.424877232 1.149603797 1.353458331 1 20.6651584 0.037694533 0.867397073 0.995207958 1.314063462 0.052526674 0.305859169 13.59540294 10.07433431 0.481089806 0.088206815 1.090672926 -0.037694533 0.318855504 QELGS(ph)PEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 149.83 9.09E-05 4413610000 2664190 2894170 2670650 2534800 2780590 2314380 2849270 2312180 3195450 TRUE FALSE 2497443.104 3108457.358 2733999.079 2599847.259 2562213.678 2982503.935 2422048.415 2600860.763 2662108.752 0.938144658 1.167667307 1.02700503 0.976611965 0.962475209 1.120353905 0.909823242 0.97699268 1 21.34413808 3.505245486 4.148769052 0.989341084 1.076941348 0.086224873 0.076123489 0.311887094 11.93751575 0.019519499 0.029706817 3200.703807 -3.505245486 0.087600263 QELQDDKRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QELQDDKRR 9 2 P12270 P12270 TPR Nucleoprotein TPR 0 114.97 0.00087298 34572000 42339 49008 49815 48018 62579 33174 49808 42381 74848 FALSE TRUE 39689.07757 52636.60331 50996.63532 49250.22317 57664.29777 42750.79527 42339.75279 47672.36114 62355.38526 0.636497993 0.844138852 0.817838509 0.78983111 0.924768527 0.685599088 0.679007156 0.764526768 1 15.92822654 2.193856195 24.999954 0.744837009 0.809773185 0 0.114615592 361.1839042 201981.8756 0.038779529 0.028640717 156.2630133 -2.193856195 0.064936176 QELSFAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 118.33 0.0044354 351280000 228010 422810 279940 288220 421950 205340 287200 382900 358710 FALSE TRUE 213739.2611 454115.2923 286580.309 295616.2132 388811.7491 264618.3246 244137.0262 430705.9079 298838.9836 0.715232191 1.51959857 0.958978998 0.989215696 1.301074392 0.885487969 0.816951735 1.44126413 1 18.18900883 2.221650786 24.99774112 0.994016822 1.130784049 0 0.267833711 775.7184433 1146734.229 0.094691105 0.070110485 166.5907124 -2.221650786 0.136767227 QELSHALYQHDAACR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QELSHALYQHDAACR 15 0 Q9UMS4;F5GY56;F5H2I0 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ;; 256.98 5.20E-25 2213780000 1108910 1164610 1167030 1259090 1290840 1327430 1564650 1220830 1389490 FALSE TRUE 1039505.303 1250838.936 1194712.503 1291400.381 1189462.633 1710637.492 1330045.258 1373253.313 1157575.143 0.89800244 1.080568241 1.03208203 1.115608252 1.0275468 1.477776629 1.148992587 1.186318937 1 20.14267442 QELVDAFVEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QELVDAFVEHR 11 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ;;;; 177.1 8.13E-06 999420000 1135630 1394140 1303249 1271940 1387237 1339169 1584790 1183597 1298043 FALSE TRUE 1064552.945 1497363.576 1334162.682 1304580.134 1278289.002 1725765.351 1347165.452 1331371.691 1081391.238 0.984429047 1.384664055 1.233746525 1.206390517 1.182078195 1.595875101 1.245770638 1.231165599 1 20.04445714 0.786581417 2.843759714 1.000179437 1.280349372 0.210505148 0.155064269 1.548301864 18.37596518 0.135989543 0.035807466 6.117604782 -0.786581417 0.280169935 QEMQEVQSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 QEMQEVQSSR 10 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;; 260.04 6.24E-17 5163250000 2169480 2348720 2021430 1961490 2288440 1635580 2442990 1892990 2544820 FALSE TRUE 2033696.119 2522621.673 2069379.274 2011825.154 2108715.154 2107745.395 2076686.329 2129333.968 2120073.102 0.959257545 1.189874854 0.976088642 0.948941408 0.994642662 0.994185244 0.979535247 1.004368183 1 21.01568258 3.739093167 9.592588178 0.983714211 1.088749268 0.290227706 0.056965043 0.198550093 140.88622 0.01307513 0.022647275 5483.945961 -3.739093167 0.105035056 QENGASVILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QENGASVILR 10 0 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PI39;E9PPR1;E9PL12;E9PMW7;E9PK06;H0YCK7;E9PIZ1;E9PK72 P29692 EEF1D Elongation factor 1-delta 0 83.883 0.035594 99296000 413380 241440 333270 307510 306550 278070 374610 272680 246330 FALSE TRUE 387507.2837 259316.4688 341175.3218 315401.2272 282474.7996 358344.2949 318440.7082 306724.6982 205215.9316 1.888290449 1.263627374 1.66251869 1.536923691 1.376475975 1.746181654 1.551734827 1.494643694 1 17.64678321 0.720236295 3.250959813 1.000022093 1.55280791 0.507993229 0.175426514 2.247651009 25.21370099 0.151663713 0.039357459 5.250930802 -0.720236295 0.552785817 QENGDLS(ph)PFSGTSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QENGDLSPFSGTSLR 15 0 P19174-2 P19174-2 PLCG1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1" 1 QENGDLS(0.986)PFS(0.009)GT(0.003)S(0.003)LR 95.662 0.0041948 63291000 82540 57810 67160 67590 61611 54294 70660 48224 67395 TRUE FALSE 77373.96874 62090.31255 68753.06692 69324.47383 56772.32059 69967.79641 60065.18898 54244.87255 56146.33911 1.378076825 1.105865735 1.224533389 1.234710489 1.011149106 1.24616845 1.069797068 0.966133739 1 15.77690434 1.713238175 0.633106898 0.974258778 1.215793901 0.462851729 0.096655751 0.675224898 0.570699945 0.084273265 0.045003255 51.6699659 -1.713238175 0.241535124 QENKRPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QENKRPSPR 9 2 Q9Y4B6-3;Q9Y4B6-2;Q9Y4B6 Q9Y4B6-3 VPRBP Protein VPRBP 1 QENKRPS(1)PR;QENKRPS(1)PR;QENKRPS(1)PR;QENKRPS(1)PR 98.368 0.0047735 1540770000 1081730 825250 919890 895950 945220 720760 1280670 801220 1478500 TRUE FALSE 1014026.45 886352.3687 941710.2252 918941.5938 870986.234 928831.7114 1088645.423 901254.0807 1231728.799 0.823254641 0.719600264 0.764543483 0.746058381 0.707125006 0.754087842 0.883835325 0.731698473 1 20.23225321 -0.129022496 0.455410494 1.033921392 0.747485533 0.647529772 0.053490017 3.065908228 0.741600506 0.237824195 0.028948236 0.742980651 0.129022496 -0.286435859 QEPCAQHNGSEPAS(ph)PKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QEPCAQHNGSEPASPKR 17 1 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 QEPCAQHNGS(0.014)EPAS(0.986)PKR;QEPCAQHNGS(0.004)EPAS(0.996)PKR 142.23 2.79E-07 612260000 565540 503170 541870 565830 570210 424820 683150 477640 543720 TRUE FALSE 530143.8609 540425.2303 554723.4123 580350.1557 525428.0067 547458.6376 580717.9996 537274.4054 452969.6194 1.17037399 1.193071692 1.224637125 1.281212096 1.159963018 1.208599019 1.282024168 1.186115762 1 18.78905477 0.968703547 23.90493508 0.999999999 1.21935352 0.739619358 0.040158893 1190.269714 909155.9296 0.037946208 0.009486552 9.3047251 -0.968703547 0.219353521 QEPES(ph)EEEEEEKQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QEPESEEEEEEKQEK 15 1 P49756 P49756 RBM25 RNA-binding protein 25 1 QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK 296.69 2.61E-44 2686730000 4078340 1403400 2303650 2123800 2014870 1707240 3295220 1724710 2405580 TRUE FALSE 3823083.979 1507309.196 2358293.666 2178300.304 1856630.238 2200092.473 2801132.352 1940043.84 2004073.157 1.907656896 0.752122841 1.176750288 1.08693652 0.926428375 1.097810459 1.39771961 0.968050409 1 20.93450374 4.752545908 24.90192204 1.070774465 1.907657492 0.71645739 0.169001033 1418.545786 2525787.621 0.042434941 0.892915645 56564.75468 -4.752545908 0.836883027 QEPGGSHGS(ph)ETEDTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QEPGGSHGSETEDTGR 16 0 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 QEPGGS(0.007)HGS(0.964)ET(0.029)EDTGR 163.56 6.10E-09 0 65374 71150 66442 67708 72973 70505 74893 65453 66813 TRUE FALSE 61282.35804 76418.02003 68018.03562 69445.50191 67241.99494 90858.64895 63663.48992 73624.95113 55661.47867 1.100983292 1.372906754 1.221994766 1.247640263 1.208052616 1.632343429 1.143762103 1.322727187 1 15.76439161 -1.129185603 3.305965033 0.999623878 1.286098587 0.264608701 0.147184566 15410333.99 24236595.15 62720.65374 0.031117557 0.074270166 1.129185603 0.286474709 QEPLGS(ph)DSEGVNCLAYDEAIMAQQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QEPLGSDSEGVNCLAYDEAIMAQQDR 26 0 J3KR44;Q96FW1;F5H6Q1;F5GYJ8;F5H3F0 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 1 QEPLGS(0.5)DS(0.5)EGVNCLAYDEAIMAQQDR;QEPLGS(0.712)DS(0.288)EGVNCLAYDEAIMAQQDR 237.01 1.96E-44 135401000 44299 55423 42064 47139 45467 43047 58130 37207 37496 TRUE FALSE 41526.40467 59526.57659 43061.77794 48348.66655 41896.20523 55473.97009 49413.94615 41852.37585 31237.67537 1.329369237 1.905601998 1.378520567 1.547767751 1.341207524 1.775867424 1.581870148 1.33980443 1 14.93099948 0.959165001 3.07222507 1.001503362 1.573086204 0.479494513 0.183834991 0.211132318 4.937342085 0.163579292 0.042901217 9.102590415 -0.959165001 0.571582842 QEPLGSDS(ph)EGVNCLAYDEAIMAQQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QEPLGSDSEGVNCLAYDEAIMAQQDR 26 0 J3KR44;Q96FW1;F5H6Q1;F5GYJ8;F5H3F0 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 1 QEPLGS(0.377)DS(0.623)EGVNCLAYDEAIMAQQDR 251.68 1.08E-52 87029000 34773 35447 33476 36116 32496 32910 42479 25978 29198 TRUE FALSE 32596.62 38071.53276 34270.06653 37042.7977 29943.89524 42410.58275 36109.66831 29221.41048 24324.66517 1.340064489 1.565141082 1.408860771 1.522849233 1.231009555 1.743521748 1.484487784 1.20130782 1 14.57013233 1.065176512 3.426787033 1.00532775 1.481282772 0.582221042 0.135930497 0.133200233 3.165888405 0.117348238 0.030624303 11.61920761 -1.065176512 0.475955022 QEPLLIGSTK ddPTM_SK-BR-3_Pertuzumab_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 ; 113.38 0.0034803 205281000 403180 387110 384080 395920 460260 379740 559450 369600 573450 FALSE TRUE 377945.6835 415772.0272 393190.559 406079.9775 424113.0362 489364.7734 475565.6662 415745.3736 477737.4904 0.791115814 0.870293907 0.823026384 0.850006511 0.887753305 1.024338226 0.995453938 0.870238116 1 18.86585857 2.434389268 4.272148726 0.97614681 0.839899292 0.676077547 0.045195381 0.11790452 4.721297784 0.015259052 0.012878365 271.8875169 -2.434389268 -0.136247518 QEPS(ph)PKPNNK ddPTM_SK-BR-3_Pertuzumab_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 66.267 0.088792 0 137930 56806 95668 80176 92028 62074 104390 72362 123260 TRUE FALSE 129297.2075 61011.97535 97937.29014 82233.4519 84800.4921 79993.75611 88737.68861 81396.55499 102687.1097 1.259137665 0.594154179 0.953744734 0.800815722 0.825814383 0.779004846 0.864156065 0.792665752 1 16.64789557 -1.105937475 4.350103649 1.000016821 0.839102898 0.05392154 0.169184373 0.752813469 84691438.78 3619.856906 0.034189592 0.078354244 1.105937475 -0.160913923 QEPVKPEEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QEPVKPEEGR 10 1 P61586 P61586 RHOA Transforming protein RhoA 0 ;; 133.05 0.00018918 1230590000 1425960 943397 1145250 1187370 1234600 1167560 1420930 1020350 881900 FALSE TRUE 1336711.709 1013247.095 1172415.871 1217839.924 1137639.496 1504615.618 1207874.738 1147742.944 734705.1927 1.819385139 1.37912064 1.595763692 1.657589924 1.548429911 2.047917496 1.644026406 1.562181614 1 19.48680595 0.770360974 3.487864061 1.000052428 1.646900785 0.586584778 0.17471794 1.492766186 21.78275628 0.170241963 0.043923729 5.893332895 -0.770360974 0.646848357 QEQEEEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QEQEEEGR 8 0 O00154-6;O00154-4;O00154-7;O00154;O00154-5;K7EKP8;O00154-2;O00154-3 O00154-6 ACOT7 Cytosolic acyl coenzyme A thioester hydrolase 0 ;; 233.89 3.51E-08 988241000 1360546 1511587 1526017 1507779 1481363 1215396 1553543 1223817 1515187 FALSE TRUE 1275391.855 1623506.474 1562214.844 1546471.162 1365022.726 1566261.095 1320603.65 1376613.246 1262292.501 1.010377431 1.286157109 1.237601303 1.22512901 1.081383851 1.240806781 1.046194641 1.09056597 1 20.26761482 1.563106073 0.864390016 1.006135299 1.208311929 0.300377571 0.087807422 0.543107737 0.80851009 0.074440876 0.030092558 36.56840958 -1.563106073 0.202176629 QEQGAENEELHQLWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QEQGAENEELHQLWR 15 0 Q6PGP7;D6RCE2;H0Y964 Q6PGP7 TTC37 Tetratricopeptide repeat protein 37 0 135.55 2.83E-05 52885000 57956 62059 60015 65163 71607 65050 77933 65360 69487 FALSE TRUE 54328.63741 66653.91293 61438.58414 66835.1929 65983.27507 83828.879 66247.67014 73520.33988 57889.1708 0.938493965 1.151405557 1.061313943 1.154537057 1.139820698 1.448092585 1.144387961 1.27001888 1 15.82100587 2.861842481 2.122144391 1.227375411 1.074781645 0.213333508 0.124847973 0.436492962 3.880371941 0.039023689 0.041987617 727.5158864 -2.861842481 -0.152593766 QEQINTEPLEDTVLS(ph)PTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QEQINTEPLEDTVLSPTK 18 0 O15446;O15446-2 O15446 CD3EAP DNA-directed RNA polymerase I subunit RPA34 1 QEQINTEPLEDTVLS(0.967)PT(0.033)K;QEQINTEPLEDTVLS(0.874)PT(0.126)K;QEQINTEPLEDTVLS(1)PTK;QEQINTEPLEDTVLS(1)PTK 249.26 1.30E-24 946000000 2460330 1557350 1904130 1659240 1805450 1545480 2487830 1508490 2161320 TRUE FALSE 2306342.337 1672657.814 1949296.863 1701818.907 1663657.24 1991634.987 2114802.987 1696828.297 1800581.729 1.280887337 0.928954119 1.082592826 0.945149492 0.923955415 1.106106407 1.174510967 0.942377827 1 20.78003166 QEQLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 123.75 0.0044197 1524260000 4479370 2674020 3477850 3197540 3457050 2301020 4318530 2686960 4107640 TRUE FALSE 4199014.228 2872007.223 3560346.244 3279594.29 3185547.238 2965287.12 3671006.518 3022432.871 3422048.348 1.22704702 0.839265531 1.040413776 0.958371699 0.930889022 0.866524029 1.072751214 0.883223311 1 21.70642871 4.754524493 24.4631811 0.954265089 1.227047298 0.577736903 0.074599584 1656.557402 2538465.368 0.016616059 0.417051515 56823.04374 -4.754524493 0.272782209 QEQLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QEQLSPR 7 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 QEQLS(1)PR;QEQLS(1)PR 89.029 0.019063 591280000 1939560 2085860 2059110 1964670 2175670 2037690 2469550 1997070 2097760 TRUE FALSE 1818166.402 2240299.245 2107953.062 2015086.758 2004801.654 2625938.024 2099263.904 2246408.586 1747630.304 1.040360995 1.281906842 1.206177907 1.153039492 1.147154321 1.502570663 1.201205941 1.285402628 1 20.7369686 QERLS(ph)PEVAPPAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QERLSPEVAPPAHR 14 1 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 QERLS(1)PEVAPPAHR;QERLS(1)PEVAPPAHR;QERLS(1)PEVAPPAHR;QERLS(1)PEVAPPAHR;QERLS(1)PEVAPPAHR;QERLS(1)PEVAPPAHR 138.75 8.23E-06 4858940000 4476360 4626170 4482280 4549750 4860830 4088680 5359010 3824470 4957200 TRUE FALSE 4196192.618 4968696.44 4588601.798 4666504.288 4479080.019 5269015.542 4555476.201 4301963.498 4129811.295 1.016073694 1.203129171 1.111092365 1.129955815 1.084572563 1.275848983 1.103071273 1.041685247 1 21.97764443 1.232664156 3.329279122 1.008674636 1.142309654 0.31918292 0.068921723 0.242619624 4.784172582 0.055592832 0.015810997 17.08693456 -1.232664156 0.133635018 QES(ph)DPEDDDVKKPALQSSVVATSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QESDPEDDDVKKPALQSSVVATSK 24 2 Q9H307 Q9H307 PNN Pinin 1 QES(1)DPEDDDVKKPALQSSVVATSK;QES(1)DPEDDDVKKPALQSSVVATSK;QES(1)DPEDDDVKKPALQSSVVATSK;QES(1)DPEDDDVKKPALQSSVVATSK 159.42 1.14E-11 10969230000 6241030 2040508 3448960 2971080 3166890 2236079 4852700 2334920 4551950 TRUE FALSE 5850415.073 2191589.335 3530770.96 3047322.943 2918175.234 2881598.708 4125082.685 2626439.902 3792200.138 1.542749554 0.577920272 0.931061345 0.803576507 0.769520365 0.759875165 1.087780849 0.692590002 1 21.85460368 -0.688488768 7.553527521 1 0.87373691 0.008971855 0.267861608 0 0 0.227825798 0.053699056 0.204885504 0.688488768 -0.12626309 QESCLGNS(ph)PPFEK ddPTM_SK-BR-3_Pertuzumab_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;QESCLGNS(1)PPFEK 133.86 0.00010727 215650000 808580 512660 660140 543290 638060 681100 934240 609370 647750 TRUE FALSE 757972.4212 550617.8798 675798.8325 557231.7412 587949.3414 877722.5133 794159.3851 685451.1859 539636.3404 1.40459855 1.020349889 1.252322688 1.032606034 1.089528813 1.626507423 1.471656606 1.270209463 1 19.04162798 2.266635042 24.99358721 1.399822739 1.14767456 0.14825982 0.195220244 252.2090285 224531.2208 0.061510171 0.051453441 184.7715244 -2.266635042 -0.252148179 QESCSPHHPQVLAQQGSGSS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QESCSPHHPQVLAQQGSGSSPK 22 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 QESCSPHHPQVLAQQGSGS(0.005)S(0.995)PK;QESCSPHHPQVLAQQGSGSS(1)PK;QESCSPHHPQVLAQQGSGS(0.049)S(0.951)PK;QESCSPHHPQVLAQQGS(0.001)GS(0.174)S(0.825)PK 201.98 2.44E-22 1057679000 505053 585139 684171 673039 628112 521875 968509 594832 663748 TRUE FALSE 473442.6343 628463.3004 700399.8592 690310.3202 578782.6172 672531.8406 823290.0666 669098.0846 552964.1708 0.856190436 1.136535301 1.266627923 1.248381643 1.046690993 1.216230411 1.488866929 1.210020685 1 19.07682648 4.974464534 1.409238359 1.241492786 0.497990252 0.392986355 0.133486389 2.115940811 2.493084877 0.036400232 2.597009588 94289.76089 -4.974464534 -0.743502534 QESDKNGES(ph)ASPERDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QESDKNGESASPERDR 16 2 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 QESDKNGES(0.684)AS(0.316)PERDR 94.632 0.0031709 177340000 199870 154040 157700 148820 191430 123190 188610 145980 222590 TRUE FALSE 187360.4935 165445.2819 161440.7185 152638.9732 176395.86 158752.9532 160329.6815 164205.9243 185438.291 1.010365726 0.892185109 0.870589982 0.823125431 0.95123752 0.85609586 0.864598571 0.885501713 1 17.50057965 -1.328179528 3.168912684 1.000829278 0.888039671 0.277790436 0.052777836 95967036.2 123412190.4 741406.9642 0.011758361 0.04696999 1.328179528 -0.112789607 QESDKNGESAS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QESDKNGESASPER 14 1 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 QESDKNGES(0.04)AS(0.96)PER 73.11 0.022257 330640000 235190 151260 214010 174200 169660 189700 241230 152160 164710 TRUE FALSE 220469.8777 162459.4478 219086.4183 178670.2669 156335.588 244463.3105 205059.801 171157.5109 137218.8369 1.606702714 1.183944212 1.596620575 1.302082651 1.139315793 1.781557955 1.494399789 1.247332471 1 17.06611902 0.977552199 4.16935115 1.000879982 1.436384473 0.352043822 0.19654786 0.213423023 11.23694757 0.179484981 0.045813196 9.496251298 -0.977552199 0.435504492 QESDKNGESAS(ph)PERDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QESDKNGESASPERDR 16 2 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 QESDKNGESAS(1)PERDR;QESDKNGES(0.007)AS(0.993)PERDR;QESDKNGESAS(1)PERDR;QESDKNGES(0.038)AS(0.962)PERDR 190.91 6.15E-10 2362373000 2602110 1954340 2242510 2063140 2508360 1698530 2823130 2096530 3225960 TRUE FALSE 2439248.58 2099041.367 2295703.396 2116083.665 2311363.524 2188868.038 2399827.865 2358286.386 2687526.436 0.907618451 0.781030966 0.854206815 0.787372224 0.860033782 0.814454514 0.892950422 0.877493279 1 21.35784751 0.766592915 0.752760624 1.000298862 0.827311406 0.625627549 0.039093516 0.550822734 0.625263979 0.033867402 0.012250736 5.842421891 -0.766592915 -0.172987456 QET(ph)VECLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QETVECLR 8 0 Q13555-8;Q13555-9;Q13555-10;Q13555-3;Q13555-7;Q13555-4;Q13555-2;A0A2Q3DQE3;Q13555;Q8WU40;Q5SWX3;Q13555-6;Q13555-11;Q13555-5;H0Y6G2 Q13555-8 CAMK2G Calcium/calmodulin-dependent protein kinase type II subunit gamma 1 QET(1)VECLR;QET(1)VECLR 126.71 0.013498 535580000 607820 636540 446130 491900 650750 324670 987180 601370 1111870 TRUE FALSE 569777.6312 683670.0839 456712.4143 504522.9868 599642.72 418396.9584 839161.5235 676452.3683 926291.714 0.615116839 0.738072114 0.493054626 0.544669653 0.647358398 0.451690274 0.905936554 0.73028006 1 19.82110708 1.687851862 7.986092604 0.861613469 0.590992498 0.645719562 0.10309554 0.078743399 9.406752505 0.047633426 0.025032174 48.73622229 -1.687851862 -0.270620971 QETHCQS(ph)TPLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QETHCQSTPLKK 12 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 QETHCQS(0.902)T(0.098)PLKK;QETHCQS(0.875)T(0.125)PLKK 151.59 3.16E-05 1783090000 4143800 2638530 3255300 2922180 3054070 2287850 4809400 2692230 5465900 TRUE FALSE 3884446.955 2833889.507 3332517.253 2997168.086 2814215.662 2948315.155 4088275.118 3028360.842 4553605.979 0.853048545 0.62233964 0.731841373 0.658196625 0.618019142 0.647468219 0.897810469 0.665046747 1 22.11857803 0.430953855 0.624609648 1.005546787 0.688687851 0.454276576 0.096889654 1.664250837 1.047240659 0.121701503 0.037003439 2.697452804 -0.430953855 -0.316858936 QETHCQST(ph)PLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QETHCQSTPLKK 12 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 QETHCQS(0.097)T(0.903)PLKK;QETHCQS(0.256)T(0.744)PLKK;QETHCQS(0.376)T(0.624)PLKK;QETHCQS(0.078)T(0.922)PLKK 166.92 3.86E-05 1553710000 2855690 1862575 2215170 1988580 2120365 1544292 3271210 1782049 3794870 TRUE FALSE 2676957.46 2000481.991 2267714.878 2039610.329 1953840.086 1990104.031 2780722.429 2004541.74 3161481.681 0.846741411 0.632767225 0.717294961 0.645143808 0.618014046 0.6294846 0.879563037 0.634051354 1 21.59216943 -0.100692289 0.575804922 1.023805886 0.686363442 0.482761611 0.095122985 4.233555664 1.520003273 0.325411369 0.038087899 0.793063042 0.100692289 -0.337442444 QETVADFT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QETVADFTPK 10 0 O75400-3;O75400;O75400-2;F5H578 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 QETVADFT(1)PK 143.98 0.00036914 159310000 508580 233370 374870 282920 283650 315440 541120 349930 289710 TRUE FALSE 476748.8856 250648.9576 383762.0934 290180.2062 261373.2732 406502.4073 459984.0795 393619.5308 241355.5294 1.975297135 1.038505139 1.590028181 1.202293591 1.082938824 1.684247335 1.905836094 1.63087016 1 17.88080035 2.200428831 24.97154883 1.662112848 1.352503585 0.018183036 0.355492398 290.352847 190143.1054 0.120829157 0.089240079 158.6458921 -2.200428831 -0.309609262 QEVGSHGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QEVGSHGR 8 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 82.749 0.019466 99345000 36791 38182 36518 37232 34402 36117 44705 32998 37962 FALSE TRUE 34488.31698 41009.03501 37384.22421 38187.43615 31700.20569 46543.39159 38001.90027 37117.87294 31625.89696 1.090508738 1.296691603 1.18207633 1.207473616 1.002349617 1.471686057 1.201607035 1.173654394 1 14.94881878 0.826265386 3.12998846 1.000141435 1.218335253 0.214769346 0.122475984 1.200206419 19.05910343 0.106297353 0.027715486 6.702940832 -0.826265386 0.218193817 QEVPSWLENMAYEHHYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 150.59 1.97E-07 98027000 100230 84509 94618 85256 88421 75229 115200 84196 120810 FALSE TRUE 93956.78322 90766.13429 96862.38364 87443.8133 81476.77133 96946.39106 97926.82946 94708.05594 100646.0305 0.933536899 0.901835212 0.962406397 0.868825257 0.809537852 0.963241079 0.97298253 0.941001403 1 16.61893075 2.043226232 24.99999833 0.968272905 0.90261471 0.4257348 0.042307588 153.0254442 88501.99954 0.016328409 0.012059324 110.4653904 -2.043226232 -0.065658195 QEYDESGPSIVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 QEYDESGPSIVHR 13 0 P60709;A0A2R8YFE2;Q9BYX7;P63261;Q6S8J3;A5A3E0;P0CG38;P0CG39 P60709;P63261;Q6S8J3 ACTB;POTEKP;ACTG1;POTEE;POTEF;POTEI;POTEJ "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Putative beta-actin-like protein 3;Putative beta-actin-like protein 3, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I;POTE ankyrin domain family member J" 0 ;;;;;;;;;; 248.68 1.98E-17 1.70101E+11 56212884 63147674 63713793 60845528 63707972 54033332 69801636 58218146 49985356 FALSE TRUE 52694619.93 67823193.49 65225114.26 62406927.26 58704604.86 69631877.79 59335528.69 65486809.68 41642477.17 1.265405507 1.628702184 1.566312062 1.498636285 1.409728932 1.672135822 1.4248799 1.5725964 1 25.31155256 -1.533670774 3.017041876 0.979678728 1.518861187 0.640789818 0.118363085 126438642.2 137883709 20865721.1 0.025614225 0.029263699 1.533670774 0.539182459 QEYDESGPSIVHRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QEYDESGPSIVHRK 14 1 P60709;A0A2R8YFE2;Q9BYX7;P63261;Q6S8J3;A5A3E0;P0CG38;P0CG39 P60709;P63261;Q6S8J3 ACTB;POTEKP;ACTG1;POTEE;POTEF;POTEI;POTEJ "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Putative beta-actin-like protein 3;Putative beta-actin-like protein 3, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I;POTE ankyrin domain family member J" 0 ;; 177.84 1.33E-06 2847570000 1332110 1975100 1845960 2083950 2659710 1666320 2633950 1726450 5080620 FALSE TRUE 1248735.613 2121338.459 1889747.043 2137427.685 2450827.105 2147359.534 2239013.65 1942001.083 4232631.7 0.295025814 0.50118664 0.446470937 0.504987874 0.579031505 0.507334369 0.528988537 0.458816458 1 22.01312353 -5 0.242892283 3.983988236 0.433890427 0.848236957 0.070198279 61.14827794 0.609235698 90.2947725 0.099738422 1.00E-05 5 -3.550097809 QFAPIHAEAPEFMEMSVEQEILVTGIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QFAPIHAEAPEFMEMSVEQEILVTGIK 27 0 P06576;H0YH81;F8W079 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ; 161.84 1.27E-11 95386000 76758 59823 58362 54212 80183 59290 64224 66400 103749 FALSE TRUE 71953.8538 64252.35717 59746.3742 55603.1717 73885.75062 76406.06051 54594.20743 74690.18616 86432.62166 0.832484916 0.743380866 0.691247969 0.643312335 0.854836394 0.883995638 0.631638916 0.864143477 1 16.3992883 0.994811828 12.73211627 0.999999915 0.747457713 0.472106046 0.084878255 0.306660066 746.5034815 0.079050768 0.019765022 9.881248652 -0.994811828 -0.252542202 QFCQEGQPHVLEALS(ph)PPQTSGLS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QFCQEGQPHVLEALSPPQTSGLSPSR 26 0 E9PR76;E9PSH4;Q9H063 E9PR76 MAF1 Repressor of RNA polymerase III transcription MAF1 homolog 2 QFCQEGQPHVLEALS(1)PPQT(0.001)SGLS(0.99)PS(0.009)R;QFCQEGQPHVLEALS(0.996)PPQT(0.003)S(0.001)GLS(0.993)PS(0.005)R;QFCQEGQPHVLEALS(0.973)PPQT(0.026)S(0.009)GLS(0.886)PS(0.107)R;QFCQEGQPHVLEALS(0.996)PPQT(0.112)S(0.029)GLS(0.683)PS(0.181)R 163.83 7.64E-12 856740000 503993 553439 486219 583290 808260 759280 881640 588460 967420 TRUE FALSE 472448.9778 594416.1994 497752.3443 598258.2089 744782.52 978471.8101 749446.2667 661930.5264 805951.3522 0.586200366 0.737533597 0.617596016 0.742300645 0.924103568 1.214058153 0.929890203 0.821303326 1 19.62033323 2.762835888 3.118674536 0.994731124 0.664958662 0.686556851 0.10472795 0.142866902 2.841652725 0.033681181 0.034216818 579.2097815 -2.762835888 -0.329772461 QFCQEGQPHVLEALSPPQTSGLS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QFCQEGQPHVLEALSPPQTSGLSPSR 26 0 E9PR76;E9PSH4;Q9H063 E9PR76 MAF1 Repressor of RNA polymerase III transcription MAF1 homolog 1 QFCQEGQPHVLEALSPPQTSGLS(0.999)PS(0.001)R;QFCQEGQPHVLEALSPPQTSGLS(0.993)PS(0.007)R;QFCQEGQPHVLEALSPPQTSGLS(0.998)PS(0.001)R;QFCQEGQPHVLEALSPPQTS(0.001)GLS(0.932)PS(0.066)R;QFCQEGQPHVLEALSPPQTS(0.005)GLS(0.775)PS(0.219)R;QFCQEGQPHVLEALSPPQT(0.001)S(0.004)GLS(0.937)PS(0.059)R 261.49 5.09E-53 2295110000 1082250 1165890 935480 924220 1127070 1285190 1656840 1015750 1854450 TRUE FALSE 1014513.904 1252213.709 957670.0274 947937.0499 1038554.469 1656203.49 1408412.223 1142568.623 1544930.315 0.656672922 0.810530868 0.619879109 0.613579163 0.67223386 1.072024721 0.91163479 0.739559974 1 20.55911034 2.259998424 24.90348833 0.927482694 0.682886141 0.62424253 0.098648889 152.306776 176928.5124 0.033672899 0.028147556 181.9694255 -2.259998424 -0.244596552 QFCTGEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QFCTGEFR 8 0 C9JQD4;O43447;A6NM32 C9JQD4 PPIH Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase H 0 ; 86.205 0.037684 114857000 217270 315710 230370 215680 280930 201351 278890 261050 416010 FALSE TRUE 203671.4585 339085.4969 235834.4852 221214.7139 258866.891 259477.765 237073.0336 293642.6671 346575.2435 0.587668803 0.978389263 0.680471239 0.638287697 0.746928397 0.748690998 0.684044917 0.847269598 1 18.40280908 0.968503306 4.772428962 0.999825663 0.741349374 0.42322459 0.104144623 0.198352411 15.47481062 0.098431558 0.024939482 9.300435942 -0.968503306 -0.258476289 QFDTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QFDTDR 6 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;U3KQE2;K7EIV0;A0A075B7C0;U3KPR7 A0A0C4DGQ5 CAPNS1 Calpain small subunit 1 0 ; 124.37 0.042768 3029100000 4484800 5398600 4770300 4692300 5593400 4220000 5409300 4930600 6445700 FALSE TRUE 4204104.374 5798317.961 4883453.769 4812712.362 5154116.927 5438245.494 4598225.682 5546196.264 5369871.029 0.782906023 1.079787192 0.909417329 0.896243566 0.959821362 1.012732981 0.856300954 1.032836028 1 22.35645601 -0.838577148 6.679534071 1.000000001 0.94649074 0.039873783 0.087294245 0 3.38E-10 0.075705838 0.017844037 0.145018314 0.838577148 -0.053509261 QFDVDILISGHTHKFEAFEHENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QFDVDILISGHTHKFEAFEHENK 23 1 Q9UBQ0;F8VXU5;Q9UBQ0-2;Q05DG7 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ;; 182.77 1.29E-17 654996000 1686307 1438894 1576580 1567392 2049180 1177067 1949800 1467920 1859841 FALSE TRUE 1580764.055 1545431.209 1613977.222 1607613.932 1888245.669 1516867.135 1657445.591 1651193.043 1549421.522 1.020228539 0.997424643 1.041664388 1.037557507 1.218677837 0.978989328 1.069718968 1.06568356 1 20.56329825 3.483408826 2.232124669 1.06673758 1.010543087 0.104292986 0.063456019 0.611443558 6.091378023 0.017460273 0.028397846 3043.748934 -3.483408826 -0.056194493 QFEDELHPDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QFEDELHPDLK 11 0 Q9Y3C6 Q9Y3C6 PPIL1 Peptidyl-prolyl cis-trans isomerase-like 1 0 ;;;; 145.17 3.64E-05 1064670000 4935800 3930490 4074820 3943010 4542570 3053530 5355500 3746990 6206120 FALSE TRUE 4626877.089 4221507.569 4171476.655 4044194.312 4185814.876 3935034.541 4552492.493 4214809.95 5170278.479 0.894899009 0.816495202 0.806818563 0.782200481 0.809591764 0.761087542 0.880512048 0.815199794 1 22.30181056 0.127055744 0.857715121 1.002519385 0.814685853 0.658690938 0.040387142 2.476077557 1.951626186 0.054534409 0.012200313 1.339848653 -0.127055744 -0.187833532 QFEEIWER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QFEEIWER 8 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;;;;; 166.3 0.0007428 570603000 933823 1032289 944580 883164 1100815 647425 1083755 867046 1291422 FALSE TRUE 875376.6854 1108720.752 966985.8837 905827.4834 1014361.43 834326.0874 921255.9988 975298.6017 1075875.325 0.813641381 1.030529027 0.898789907 0.841944659 0.942824328 0.775485847 0.856285089 0.906516377 1 20.03707947 3.541388295 5.070824195 0.873142207 0.944860894 0 0.079881411 0.381144437 19.11964147 0.019595462 0.030401755 3478.470266 -3.541388295 0.071718687 QFEGHTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QFEGHTK 7 0 H0Y8P4;Q8TED0-3;Q8TED0 H0Y8P4 UTP15 U3 small nucleolar RNA-associated protein 15 homolog 0 ; 92.439 0.015668 224710000 285490 413230 361640 346270 380740 285650 388270 336760 375260 FALSE TRUE 267621.6905 443825.9792 370218.2716 355155.8744 350838.2162 368112.5179 330052.518 378805.2273 312626.6817 0.856042386 1.419667626 1.184218409 1.136038269 1.122227362 1.177482727 1.05574008 1.211685532 1 18.25408139 3.287077174 3.392010259 1.118695181 1.218353283 0 0.149916129 0.598995254 14.02919822 0.040323604 0.054612227 1936.766098 -3.287077174 0.099658102 QFFDER ddPTM_SK-BR-3_Pertuzumab_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 ;;; 146.87 0.025507 1320740000 3170220 3737770 3632590 3464220 3935540 3165080 3935900 3263160 3542400 FALSE TRUE 2971801.589 4014518.38 3718756.75 3553117.75 3626458.564 4078787.215 3345748.334 3670572.709 2951150.555 1.006997621 1.360323137 1.260104044 1.203977121 1.228828721 1.382100689 1.13370981 1.243776839 1 21.49284609 0.299248077 0.885090255 0.998275508 1.248883629 0.29248379 0.107441015 3.137728669 3.031907853 0.10791237 0.031271237 1.991810772 -0.299248077 0.250608121 QFGFIVLTTSAGIMDHEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QFGFIVLTTSAGIMDHEEAR 20 0 P62244 P62244 RPS15A 40S ribosomal protein S15a 0 ;; 183.09 4.50E-17 409570000 706897 764658 620318 638510 752186 741103 1002719 662092 843303 FALSE TRUE 662653.5786 821274.0739 635032.2359 654895.2476 693112.3457 955047.4053 852370.5947 744755.6436 702550.2814 0.943211605 1.168989745 0.903895782 0.932168508 0.986566178 1.359400787 1.213252087 1.060074508 1 19.42224196 2.283045492 24.9993981 1.186501181 0.997968905 0.325770979 0.118758532 135.5398982 76169.48074 0.03998475 0.033453492 191.8869732 -2.283045492 -0.188532276 QFHDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QFHDSK 6 0 Q02543;M0R3D6;M0R1A7;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ;;; 98.418 0.039957 3216060000 3855830 7967960 7509300 7639180 8125250 6604970 9637460 7500540 8801850 FALSE TRUE 3614500.483 8557916.049 7687424.142 7835214.292 7487125.641 8511717.616 8192412.343 8436998.93 7332764.373 0.492924673 1.167079101 1.048366448 1.068521214 1.021050897 1.160778825 1.117233819 1.150589123 1 22.80592575 4.742598131 24.99999456 1.097174732 0.492924439 0.912260678 0.058336785 103.7726921 642528.3425 0.013080667 0.100553148 55283.83105 -4.742598131 -0.604250293 QFKEEDGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QFKEEDGLR 9 1 O95292 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 0 ; 113.63 0.0016136 1247540000 746310 692800 616750 603210 863240 542020 824130 742640 1089610 FALSE TRUE 699599.7893 744095.6329 631379.6013 618689.3898 795444.6125 698492.375 700559.3573 835360.2388 907747.0519 0.770699049 0.819716937 0.695545747 0.681565849 0.876284435 0.76947909 0.771756136 0.920256626 1 19.79193081 1.113453809 2.898979438 0.998777546 0.766262392 0.685429261 0.055132102 0.135167835 2.146777696 0.05130079 0.01381385 12.98535445 -1.113453809 -0.232515154 QFLEVELDQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QFLEVELDQAR 11 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 113.38 0.001732 0 48543 61107 47293 52156 62361 44900 53248 48429 60359 FALSE TRUE 45504.78028 65631.42586 48414.81229 53494.41126 57463.41861 57861.90111 45263.95673 54475.46726 50284.69297 0.904942988 1.30519691 0.962814118 1.063830922 1.142761648 1.150686177 0.900153786 1.083340954 1 15.61783168 1.750391902 25 0.987605048 1.100051184 0.120474902 0.116262497 5.721655368 12110.70074 0.050035937 0.027747534 56.28490037 -1.750391902 0.112446137 QFLIS(ph)PPAS(ph)PPVGWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QFLISPPASPPVGWK 15 0 V9GYW9;E9PD55;E9PDJ2;P53805-4;P53805-3;P53805-2;P53805;H0YF64;Q9UKA8-6;Q9UKA8-5;Q9UKA8-2;Q9UKA8 V9GYW9 RCAN1;RCAN3 Calcipressin-1;Calcipressin-3 2 QFLIS(1)PPAS(1)PPVGWK;QFLIS(1)PPAS(1)PPVGWK 144.72 6.12E-06 275740000 745090 616200 541170 456400 629320 485830 912250 571850 1231910 TRUE FALSE 698456.1469 661824.0892 554006.808 468111.9967 579895.7458 626081.2342 775466.5814 643246.7313 1026296.263 0.680559963 0.64486651 0.539811776 0.456117803 0.565037375 0.610039476 0.755597199 0.62676515 1 19.96901583 0.548157703 0.678971621 1.003453597 0.579464457 0.727344746 0.076585242 0.835998761 0.667646809 0.089274459 0.030259664 3.533114429 -0.548157703 -0.423989141 QFS(ph)TASDHEQPGVSG ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QFSTASDHEQPGVSG 15 0 Q66K14-2;Q66K14;G3V133 Q66K14-2 TBC1D9B TBC1 domain family member 9B 1 QFS(0.455)T(0.455)AS(0.091)DHEQPGVSG 86.488 0.0066509 0 131550 151850 132750 148990 166520 115480 161290 120660 208360 TRUE FALSE 123316.5203 163093.132 135898.8927 152813.3356 153442.1909 148817.2013 137106.0618 135724.6666 173583.3699 0.710416674 0.939566573 0.782902721 0.880345483 0.883968268 0.857324071 0.789857127 0.781899019 1 17.40526921 -2.459718972 2.289327056 2.858435533 0.835310843 0.398203478 0.06583948 1723030.804 419013.805 16405123.63 0.015455682 0.003469613 2.459718972 -2.02312469 QFSEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QFSEER 6 0 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 134.06 0.03303 607520000 1419000 1499300 1551600 1359400 1535000 1457000 1534000 1327600 1777200 FALSE TRUE 1330187.323 1610309.732 1588404.685 1394284.505 1414447.292 1877612.248 1303990.941 1493353.782 1480573.839 0.898426872 1.087625412 1.072830441 0.941718994 0.955337218 1.26816522 0.880733474 1.00863175 1 20.49772501 QFTPCQLLADHANSPNKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QFTPCQLLADHANSPNKK 18 1 H0YFD6;P40939;A0A2R8Y4F5 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 ; 215.75 6.06E-19 657780000 858590 614430 606800 553430 859620 593090 732520 674830 1368650 FALSE TRUE 804852.3845 659923.0365 621193.5826 567631.9508 792108.9127 764305.455 622685.4264 759084.011 1140213.473 0.705878683 0.578771477 0.544804633 0.497829542 0.694702292 0.67031786 0.546113023 0.665738503 1 20.12087252 0.87862799 5.662952975 0.999995723 0.597264385 0.762739613 0.06851003 0.719898642 33.29367079 0.064176281 0.016160165 7.561848805 -0.87862799 -0.402731338 QFYINVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 128.69 0.0026123 1239500000 1806200 2050040 1814553 1741985 2010290 2076750 2438580 1684560 2004470 FALSE TRUE 1693153.166 2201827.095 1857595.054 1786687.284 1852409.933 2676274.012 2072937.568 1894881.024 1669911.008 1.013918202 1.318529601 1.112391646 1.069929641 1.109286617 1.602644692 1.241346131 1.134719764 1 20.67133979 QGAIYHGLATLLNQPS(ph)PMMQR ddPTM_SK-BR-3_Pertuzumab_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 247.5 1.37E-30 3246710000 1378080 1487520 1140635 1110848 1502850 1694750 2478620 1248350 2319430 TRUE FALSE 1291828.433 1597657.529 1167691.401 1139354.24 1384822.223 2183996.813 2106973.941 1404209.245 1932302.149 0.668543702 0.826815583 0.604300627 0.589635654 0.716669608 1.13025637 1.090395693 0.726702729 1 20.88188927 2.306844772 7.338526675 1.008946413 0.684637634 0.599294932 0.123695049 0.14833272 13.38231471 0.042665643 0.035502971 202.6958105 -2.306844772 -0.32430878 QGANINEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QGANINEIR 9 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ; 143.04 0.00023938 446750000 515480 610550 578720 569330 644960 505000 636790 524180 637350 FALSE TRUE 483217.027 655755.7573 592447.5117 583939.9717 594307.4432 650785.302 541309.2512 589625.0269 530972.1676 0.910060934 1.235009662 1.115778845 1.099756272 1.119281724 1.225648615 1.019468221 1.110463152 1 19.01827671 1.062501269 1.144706482 1.006908542 1.126490589 0.084121052 0.094009152 0.91309706 2.501964945 0.080073718 0.02557811 11.54785359 -1.062501269 0.119582047 QGDDEQS(ph)DWFYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QGDDEQSDWFYEK 13 0 Q9NW75-2;Q9NW75 Q9NW75-2 GPATCH2 G patch domain-containing protein 2 1 QGDDEQS(1)DWFYEK;QGDDEQS(1)DWFYEK 191.96 3.27E-06 191940000 948730 566960 740790 704970 682770 547570 992560 642200 408151 TRUE FALSE 889350.6828 608938.3083 758361.8886 723060.7237 629147.9984 705644.5699 843734.8425 722380.0837 340027.9613 2.615522204 1.790847747 2.230292725 2.126474308 1.850283123 2.075254538 2.481369 2.12447259 1 18.37529386 2.950362498 24.87966367 2.044360008 2.131243543 0.040052531 0.432936855 2736.996176 1371855.667 0.12189965 0.129295798 891.9951596 -2.950362498 0.086883535 QGDTGDWIGTFLGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QGDTGDWIGTFLGHK 15 0 Q9Y3F4;Q9Y3F4-2 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 ; 209.66 2.27E-09 1337110000 2715500 2572600 2690400 2636800 2975600 2185100 3362500 2408700 3236400 FALSE TRUE 2545541.702 2763077.981 2754217.558 2704464.752 2741908.379 2815902.898 2858324.341 2709431.497 2696223.932 0.944113607 1.024795436 1.021509202 1.00305643 1.016943862 1.044387621 1.060121271 1.004898542 1 21.36250889 2.421037568 4.754232701 1.035612619 1.006860257 0.132540023 0.028640772 0.343291323 16.20808 0.009689768 0.008120584 263.655945 -2.421037568 -0.028752362 QGEAEFNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QGEAEFNR 8 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ; 88.177 0.034431 841800000 1339490 1181040 1217270 1130640 1183520 963180 1380610 1082220 1186450 FALSE TRUE 1255653.712 1268485.43 1246144.219 1159654.137 1090571.113 1241234.43 1173600.347 1217337.549 988423.8302 1.27035961 1.283341611 1.260738745 1.173235712 1.103343606 1.255771454 1.187345258 1.231594699 1 19.91477027 -5 0.131712268 0.267323559 1.314856089 0.656225032 0.051628498 89.89937308 0.743934801 17.48834018 0.381855152 1.00E-05 5 1.04753253 QGEEIHNEVEFEWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QGEEIHNEVEFEWLR 15 0 A0A1B0GTY1;A0A1B0GV98;A0A1B0GTC5;A0A1B0GU26;A0A1B0GTC3;A0A1B0GVH5;Q9C0B1;A0A1B0GUC3;A0A1B0GTI3;A0A1B0GUY7 A0A1B0GTY1 FTO Alpha-ketoglutarate-dependent dioxygenase FTO 0 ;; 129.05 6.82E-05 75863000 146703 183690 171567 181917 182627 166473 196229 160787 175461 FALSE TRUE 137521.1211 197290.5987 175636.6503 186585.2982 168284.2121 214531.0526 166806.2832 180861.6109 146175.4256 0.940795079 1.349683765 1.201547042 1.276447785 1.151248313 1.467627351 1.14113766 1.237291495 1 17.15734127 -0.533459089 7.348628768 1.000002083 1.234250255 0.195368282 0.138373232 0 0 0.115843085 0.027304477 0.292779666 0.533459089 0.234248172 QGFDFLCMPVFHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QGFDFLCMPVFHPR 14 0 O14744-2;O14744;G3V580;O14744-4;O14744-3;O14744-5;G3V2L6;C9JSX3 O14744-2 PRMT5 "Protein arginine N-methyltransferase 5;Protein arginine N-methyltransferase 5, N-terminally processed" 0 112.72 0.00057701 68897000 60375 136360 42346 44079 132850 35799 71187 117940 126280 FALSE TRUE 56596.23652 146456.2363 43350.46712 45210.14177 122416.4969 46133.59015 60513.17022 132665.0686 105203.0522 0.537971431 1.392129156 0.412064728 0.429741731 1.163621153 0.438519503 0.575203561 1.26103821 1 16.68281704 1.23641057 24.99699526 1.130519177 0.730446336 0.216159478 0.33294871 95.56282656 1110905.416 0.266487999 0.079162457 17.23497152 -1.23641057 -0.400072841 QGFGELLQAVPLADSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QGFGELLQAVPLADSFR 17 0 P27695;G3V3M6;G3V5Q1 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 168.5 3.03E-10 36833000 156490 223490 177743 163497 234220 145431 196840 192019 215160 FALSE TRUE 146695.5702 240037.4321 181959.1479 167692.6098 215825.306 187414.5688 167325.6694 215992.9948 179248.406 0.818392607 1.339132869 1.015122823 0.935531944 1.204057045 1.045557799 0.933484839 1.204992556 1 17.45160076 3.720567396 24.70314557 1.040687644 1.134309284 0 0.156462506 642.1125566 2420291.867 0.03794578 0.060352615 5254.93557 -3.720567396 0.09362164 QGGDVLQNEEGETTSHLMGMFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QGGDVLQNEEGETTSHLMGMFYR 23 0 P39748;F5H1Y3 P39748 FEN1 Flap endonuclease 1 0 ;;;; 380.76 2.90E-119 767386000 550882 538454 608131 529614 575646 517751 606536 499265 620493 FALSE TRUE 516403.279 578321.6944 622556.1545 543204.7919 530437.0852 667217.3087 515591.5576 561599.3343 516928.7098 0.998983553 1.118764896 1.20433658 1.050831153 1.026131989 1.290733705 0.997413276 1.086415445 1 18.9796058 1.612297769 25 1.031432986 1.12156502 0.175407214 0.088056156 0.66167854 3711.817952 0.039797254 0.021114195 40.9541361 -1.612297769 0.090132033 QGGLGPMNIPLVSDPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QGGLGPMNIPLVSDPKR 17 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ; 225.68 3.72E-15 1067940000 1360680 1287990 1361710 1291530 1415410 1059950 1688630 1125530 2067460 FALSE TRUE 1275517.468 1383354.12 1394010.404 1324672.846 1304249.408 1365940.358 1435435.608 1266054.898 1722387.57 0.740551947 0.803160766 0.809347692 0.769091039 0.757233407 0.79305052 0.833398727 0.735058079 1 20.71597838 -1.708984425 2.671854415 1.035408995 0.787766637 0.823654504 0.031800428 4828768.501 4175142.452 1151026.184 0.007500413 0.019544095 1.708984425 -0.247642358 QGGS(ph)PDEPDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QGGSPDEPDSK 11 0 Q9ULX6;Q9ULX6-2;V9GZ50 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 1 QGGS(1)PDEPDSK;QGGS(1)PDEPDSK 188.13 3.44E-06 566360000 1093400 659630 836730 773380 937040 568130 930580 730350 1259570 TRUE FALSE 1024966.046 708469.6915 856577.6307 793226.2401 863448.6582 732139.9082 791048.1681 821535.8052 1049339.63 0.976772454 0.675157662 0.816301611 0.755928984 0.822849565 0.697714913 0.753853324 0.782907442 1 20.00105027 0.929736927 18.73795456 1 0.772441313 0.391583559 0.082920475 1322.355133 352651.9788 0.069884408 0.017471102 8.506226186 -0.929736927 -0.227558687 QGIETPEDQNDLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 168.41 5.60E-06 1116120000 807550 661990 739500 653140 717100 554660 898840 588880 892030 FALSE TRUE 757006.887 711004.4284 757041.2892 669900.6782 660781.8586 714781.3378 764067.2864 662402.9643 743144.4303 1.018653785 0.956751339 1.018700078 0.901440758 0.889170169 0.961833674 1.028154495 0.891351583 1 19.5032831 -0.165184867 7.033520179 0.999999999 0.964674155 0.046493195 0.052713806 6734573.454 957496.4797 0.049748471 0.012065776 0.683620587 0.165184867 -0.035325845 QGLYELSASNFELHVAQGDHFIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QGLYELSASNFELHVAQGDHFIK 23 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 187.62 1.37E-17 121420000 56806 55888 42027 53820 71474 82146 105290 57808 109340 FALSE TRUE 53250.61386 60026.00567 43023.90029 55201.11232 65860.72035 105860.2167 89502.74196 65025.45605 91090.44764 0.584590539 0.658971464 0.472320659 0.606003305 0.723025543 1.162143994 0.982570009 0.713855928 1 16.47501215 2.441018147 5.205858486 0.972336605 0.582443825 0.706349529 0.116972896 0.09787319 6.646723426 0.040169667 0.033957848 276.0693212 -2.441018147 -0.38989278 QGPPCS(ph)DS(ph)EEEVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QGPPCSDSEEEVER 14 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 2 QGPPCS(1)DS(1)EEEVER;QGPPCS(1)DS(1)EEEVER 172.66 4.13E-06 494400000 906510 987970 941840 932060 1051260 980250 1286640 875600 1111840 TRUE FALSE 849773.1573 1061120.327 964180.8896 955978.2376 968698.2802 1263232.262 1093720.277 984920.5874 926266.7212 0.917417346 1.145588309 1.040932236 1.032076632 1.045809223 1.363788888 1.180783301 1.063322869 1 19.82106816 QGPPHINHDDPSLVPNVPYFDLPAGLMAPLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QGPPHINHDDPSLVPNVPYFDLPAGLMAPLVK 32 0 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ; 167.68 2.43E-14 357840000 693070 608660 631280 575890 718830 553060 780420 602850 694840 FALSE TRUE 649691.9859 653725.8197 646254.2597 590668.3124 662375.9914 712719.4438 663403.2661 678117.1495 578866.7152 1.122351603 1.129320105 1.116412885 1.020387417 1.144263393 1.231232381 1.146038023 1.171456454 1 19.14287168 2.49840703 24.78878741 1.15639923 1.10336329 0.054781003 0.065391465 1309.837717 1525399.162 0.019244594 0.017976952 315.0699836 -2.49840703 -0.053035939 QGPSPVS(ph)PNALDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QGPSPVSPNALDR 13 0 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 QGPS(0.005)PVS(0.995)PNALDR 105.09 0.0015524 320370000 310380 299250 359360 373360 436490 279750 357650 297800 505850 TRUE FALSE 290953.8698 321406.7814 367884.1889 382941.0497 402209.8361 360509.2836 304023.7028 334980.9855 421420.3671 0.690412454 0.762675007 0.872962528 0.908691368 0.954414802 0.855462412 0.721426221 0.79488561 1 18.68490052 -3.37172623 0.019741217 1.921001621 3.24E-06 0.300905586 0.083232619 4497.645362 8.953610681 543.1430016 347.2381766 0.000424887 3.37172623 -1.920998384 QGPVSQSATQQPVTADKQQGHEPVS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QGPVSQSATQQPVTADKQQGHEPVSPR 27 1 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 QGPVSQSATQQPVTADKQQGHEPVS(1)PR;QGPVSQSATQQPVT(0.002)ADKQQGHEPVS(0.998)PR;QGPVSQSATQQPVTADKQQGHEPVS(1)PR;QGPVSQSATQQPVTADKQQGHEPVS(1)PR;QGPVSQSATQQPVTADKQQGHEPVS(1)PR 292.78 9.17E-71 6401330000 2299098 2333302 2302213 2426933 2997980 1754515 2895930 1997098 4288010 TRUE FALSE 2155201.56 2506062.108 2356822.58 2489212.21 2762530.744 2261014.998 2461712.181 2246440.081 3572313.429 0.603306961 0.701523581 0.659746863 0.696806778 0.773317011 0.632927385 0.689108677 0.628847419 1 21.76842724 -1.82452049 2.54381445 1.115430813 0.67730144 0.822729827 0.047639583 10606812.96 6785749.645 7488910.169 0.01126755 0.014978886 1.82452049 -0.438129372 QGQDVAPPPNPVPQRT(ph)SPTGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QGQDVAPPPNPVPQRTSPTGPK 22 1 Q9UPY8-2 Q9UPY8-2 MAPRE3 Microtubule-associated protein RP/EB family member 3 1 QGQDVAPPPNPVPQRT(0.489)S(0.489)PT(0.022)GPK 63.803 0.047206 332910000 211350 266290 260150 262860 300470 199240 305430 221490 428820 TRUE FALSE 198121.9808 286006.3887 266320.8809 269605.4326 276872.2982 256757.3536 259633.607 249143.5141 357247.1717 0.554579564 0.800584053 0.745480726 0.754674785 0.775016068 0.718710669 0.726761826 0.697398143 1 18.44656306 -1.212142906 4.639975839 1.000059037 0.732846479 0.62757092 0.066895668 2.515942108 37244964.97 3988.837795 0.01409632 0.061356008 1.212142906 -0.267212557 QGQQQAGGDGKTEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QGQQQAGGDGKTEQK 15 1 Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;; 216.71 1.98E-12 497465000 532287 354629 410128 405697 499237 294241 556438 343391 941768 FALSE TRUE 498972.1068 380886.1002 419856.4298 416107.8719 460028.9398 379183.6001 473005.2876 386264.1222 784580.8367 0.635972845 0.485464445 0.535134699 0.530356915 0.586337211 0.483294496 0.602876422 0.492319088 1 19.58156257 -1.760111271 2.555997258 1.111906788 0.540719239 0.885680201 0.051477721 4271676.012 3117962.322 3006326.487 0.011830464 0.017373556 1.760111271 -0.571187549 QGQSQAASSSSVTS(ph)PIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QGQSQAASSSSVTSPIK 17 0 O60583-2;O60583 O60583-2 CCNT2 Cyclin-T2 1 QGQSQAASSSS(0.001)VT(0.001)S(0.998)PIK;QGQSQAASSSS(0.002)VT(0.142)S(0.855)PIK;QGQSQAASSSSVT(0.174)S(0.826)PIK 261.16 2.95E-27 795860000 1321220 914590 1078870 1029280 1073590 826410 1450990 909460 1253240 TRUE FALSE 1238527.199 982307.1952 1104461.306 1055693.067 989274.5721 1064981.151 1233427.52 1023008.083 1044066.148 1.186253573 0.940847663 1.057846103 1.011136191 0.947520973 1.020032259 1.181369133 0.979830718 1 19.99378169 1.948564835 24.99920657 1.080589251 1.016899161 0 0.086789297 762.080756 370395.0422 0.032554131 0.021013237 88.83105805 -1.948564835 -0.06369009 QGRPTLQEGPGLQQKPRPEAEPPS(ph)PPSGDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QGRPTLQEGPGLQQKPRPEAEPPSPPSGDLR 31 3 A0A0A0MRY0;Q8WUA7-3;Q8WUA7-4;Q8WUA7;F8WDP1;B0QYI1;Q8WUA7-2 A0A0A0MRY0 TBC1D22A TBC1 domain family member 22A 1 QGRPTLQEGPGLQQKPRPEAEPPS(0.992)PPS(0.008)GDLR 95.691 0.00027048 227160000 308830 264900 282110 297530 315830 231660 354520 245090 343570 TRUE FALSE 289500.8816 284513.4716 288801.7824 305165.1235 291025.9858 298536.4813 301363.0172 275690.026 286225.9475 1.011441779 0.994017049 1.008999306 1.06616862 1.016770102 1.043009846 1.052885037 0.963190195 1 18.12679494 3.457871043 24.93689222 1.029780702 1.002118781 0.062554499 0.029204108 386.5045476 500679.999 0.007438103 0.010076733 2869.928272 -3.457871043 -0.027661921 QGRPVVICDKEDTETIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QGRPVVICDKEDTETIK 17 2 Q06210-2;Q06210;A0A6I8PRN4 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 176.11 6.44E-10 413930000 1089060 677330 813120 857340 873020 688660 1387590 743580 1092530 FALSE TRUE 1020897.679 727480.218 832407.5904 879340.7959 804456.5308 887464.9625 1179533.761 836417.5998 910179.685 1.121644106 0.79927099 0.914553032 0.966117801 0.883843645 0.975043694 1.295935056 0.918958766 1 19.79579186 1.984137335 23.84526198 1.112257084 0.917615222 0.16013125 0.12598017 409.359956 615362.0171 0.046513845 0.031032872 96.41338587 -1.984137335 -0.194641862 QGS(ph)FSEDVISHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QGSFSEDVISHK 12 0 H3BQK9;H3BPE1;Q9UPN3;Q9UPN3-2;Q9UPN3-3;Q9UPN3-4;A0A590UJG2;H0Y390;Q9UPN3-5;E9PNZ4 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 1 QGS(0.997)FS(0.003)EDVISHK;QGS(0.997)FS(0.003)EDVISHK 176.81 1.55E-05 597240000 566770 386200 447530 441020 528440 347740 570840 420450 641480 TRUE FALSE 531296.8774 414794.6498 458145.6229 452337.3198 486938.454 448126.8929 485247.8414 472944.108 534412.8439 0.994169365 0.776168939 0.857287822 0.846419253 0.911165328 0.838540649 0.908001832 0.884978932 1 19.02759516 0.318047039 0.507153944 1.009096573 0.853721575 0.290898019 0.057742792 2.68552582 1.088158328 0.106079505 0.026750096 2.079921952 -0.318047039 -0.155374997 QGS(ph)PTPALPEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QGSPTPALPEKR 12 1 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 QGS(0.825)PT(0.175)PALPEKR;QGS(0.688)PT(0.312)PALPEKR 114.01 0.00067595 834040000 1034730 643140 843610 706020 875630 688060 1050400 820770 1782380 TRUE FALSE 969968.0963 690758.7548 863620.8276 724137.6685 806861.5519 886691.7523 892902.2714 923244.9412 1484889.263 0.65322588 0.4651921 0.581606217 0.487671159 0.543381632 0.597143352 0.601325832 0.62176013 1 20.50192391 -0.092462964 0.549881174 1.041088069 0.535976418 0.872095709 0.052657276 1.453362181 0.488186869 0.174263748 0.020982063 0.808233852 0.092462964 -0.505111651 QGS(ph)SLNLFEDVQITEPEAEPESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QGSSLNLFEDVQITEPEAEPESK 23 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 QGS(0.5)S(0.5)LNLFEDVQITEPEAEPESK;QGS(0.5)S(0.5)LNLFEDVQITEPEAEPESK;QGS(0.5)S(0.5)LNLFEDVQITEPEAEPESK 155.44 1.85E-08 125461000 478182 252239 296012 280415 311584 158885 430583 239830 416765 TRUE FALSE 448253.4422 270915.038 303033.5444 287610.9236 287113.4495 204752.5202 366021.0765 269773.3034 347204.2291 1.291036815 0.780275744 0.872781836 0.828362386 0.826929586 0.589717818 1.054195329 0.776987378 1 18.40542499 4.7431609 24.89435107 0.839470709 1.291037009 0.557024765 0.126073767 320.6192502 1734961.742 0.027226687 0.219244396 55355.51555 -4.7431609 0.451566299 QGS(ph)VVSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QGSVVSSR 8 0 Q9BZ67-2;Q9BZ67-3;Q9BZ67 Q9BZ67-2 FRMD8 FERM domain-containing protein 8 1 QGS(1)VVSSR 84.882 0.017976 164470000 275790 230320 212560 241370 246640 164930 237380 175240 240470 TRUE FALSE 258528.7962 247373.1324 217602.0236 247563.9628 227269.8893 212542.6136 201787.0727 197119.0998 200334.0035 1.290488842 1.234803519 1.086196151 1.23575608 1.134454887 1.060941277 1.007253233 0.983952281 1 17.61204779 2.733390892 0.431178 0.962917998 1.274704752 0.783940615 0.050413945 0.650707671 0.246258575 0.052799414 0.080462828 541.2412547 -2.733390892 0.311786754 QGSGRES(ph)PSLASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.5)PS(0.5)LASR;QGSGRES(0.948)PS(0.052)LASR;QGSGRES(0.998)PS(0.001)LASR;QGSGRES(0.999)PS(0.001)LASR;QGS(0.367)GRES(0.632)PS(0.001)LASR 234.78 3.00E-16 9199830000 3209170 3403150 3403460 3406980 3728030 2995520 3787690 3020100 3909510 TRUE FALSE 3008313.778 3655122.767 3484191.678 3494408.875 3435245.562 3860277.996 3219761.048 3397166.133 3256987.525 0.923649156 1.122240334 1.069758988 1.072895996 1.054730955 1.185229592 0.988570273 1.043039345 1 21.63510676 1.61519216 25 1.011852044 1.077250567 0.154171267 0.0662616 0.973768214 3312.284862 0.028295897 0.015290448 41.22798977 -1.61519216 0.065398524 QGSIT(ph)SPQANEQSVT(ph)PQRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QGSITSPQANEQSVTPQRR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QGS(0.077)IT(0.508)S(0.415)PQANEQS(0.108)VT(0.892)PQRR;QGS(0.009)IT(0.514)S(0.477)PQANEQS(0.003)VT(0.997)PQRR;QGS(0.003)IT(0.993)S(0.005)PQANEQS(0.069)VT(0.931)PQRR 259.18 3.74E-31 3942570000 1124110 1087560 1080330 1081540 1074810 939400 1277710 935680 903680 TRUE FALSE 1053753.962 1168084.074 1105955.938 1109294.147 990398.7582 1210589.53 1086129.247 1052501.708 752849.97 1.399686529 1.551549606 1.469025678 1.473459775 1.315532706 1.608009004 1.442690165 1.398023178 1 19.52200286 0.674432562 2.022848238 1.000144956 1.475615204 0.773435714 0.078531337 0.663960438 3.550877531 0.068461564 0.018853457 4.725334553 -0.674432562 0.475470247 QGSITS(ph)PQANEQSVT(ph)PQRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QGSITSPQANEQSVTPQRR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QGS(0.005)IT(0.421)S(0.575)PQANEQS(0.006)VT(0.994)PQRR;QGS(0.001)IT(0.093)S(0.906)PQANEQSVT(1)PQRR 210.31 1.58E-16 2587900000 1374850 1281410 1242430 1294290 1254450 1129080 1518140 1078480 1039280 TRUE FALSE 1288800.593 1376286.93 1271901.026 1327503.673 1155930.557 1455027.067 1290509.001 1213130.602 865817.454 1.488536165 1.589580948 1.46901754 1.533237366 1.335074214 1.680524065 1.490509339 1.401139 1 19.72370336 0.788856105 2.345490977 1.00032299 1.517576511 0.770502231 0.087566316 0.365926515 3.252539994 0.075566659 0.020407255 6.149730801 -0.788856105 0.51725352 QGSITS(ph)PQANEQSVTPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QGSITSPQANEQSVTPQR 18 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QGSIT(0.079)S(0.921)PQANEQSVTPQR;QGSIT(0.002)S(0.998)PQANEQSVTPQR 387.56 1.65E-126 377420000 506050 433490 489370 489800 389400 414360 477890 367300 280220 TRUE FALSE 474377.2338 465586.0506 500978.0875 502369.0972 358818.0948 533979.0054 406234.831 413158.2135 233449.4717 2.032033872 1.994376116 2.145980815 2.151939319 1.537026801 2.287342959 1.740140288 1.769797166 1 17.8327508 0.132992374 0.492229964 0.905288187 2.059739166 0.70584411 0.203171863 1.714110981 0.57157053 0.500526942 0.094068229 1.358289596 -0.132992374 1.154450978 QGSITSPQANEQSVT(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QGSITSPQANEQSVTPQR 18 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QGSITSPQANEQS(0.207)VT(0.793)PQR;QGSITSPQANEQS(0.065)VT(0.935)PQR 146.18 9.57E-07 226380000 213810 174229 204588 203152 198107 194574 246685 169624 182504 TRUE FALSE 200428.0138 187129.0964 209440.924 208365.2243 182548.4753 250744.3552 209696.8744 190801.9298 152042.9034 1.31823327 1.230765082 1.377512 1.370437026 1.200637921 1.649168423 1.379195409 1.254921641 1 17.21411895 0.903118242 3.823107671 1.00023581 1.358782183 0.476942202 0.119439394 0.386430577 12.42108945 0.112475478 0.028848385 8.000520488 -0.903118242 0.358546373 QGSITSPQANEQSVT(ph)PQRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 QGSITSPQANEQSVTPQRR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QGSITSPQANEQSVT(1)PQRR;QGSITSPQANEQS(0.001)VT(0.999)PQRR;QGSITSPQANEQSVT(1)PQRR;QGSITSPQANEQS(0.003)VT(0.997)PQRR;QGSIT(0.001)SPQANEQS(0.04)VT(0.959)PQRR;QGSITSPQANEQS(0.291)VT(0.709)PQRR;QGSITSPQANEQSVT(1)PQRR 304.06 1.98E-50 11707880000 918347 891401 946822 861774 905170 821022 1033418 784664 847529 TRUE FALSE 860869.3006 957401.2575 969281.065 883888.5798 834081.5995 1058037.723 878466.5647 882631.0277 706070.9347 1.219239114 1.355956194 1.372781427 1.251841049 1.181300006 1.498486443 1.244161913 1.250059993 1 19.4294536 0.739057213 1.64989219 1.000694181 1.317585508 0.520959316 0.090697555 0.685159395 3.008861842 0.080348234 0.022965609 5.483491983 -0.739057213 0.316891327 QGTEIDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QGTEIDGR 8 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;; 162.59 0.0011779 494810000 4768860 5143800 5272860 5207380 5169980 4411550 5450860 4318550 5207420 FALSE TRUE 4470385.565 5524652.304 5397934.729 5341010.187 4763950.625 5685092.869 4633554.146 4857730.474 4338267.961 1.030453998 1.273469586 1.244260331 1.23113884 1.098122723 1.310452218 1.068065456 1.11973961 1 22.04868774 1.270049364 1.180954915 1.009322007 1.20998963 0.309987187 0.089077822 0.437362369 1.220452849 0.075202045 0.024555492 18.62298801 -1.270049364 0.200667623 QGTTPPIWHLTDK ddPTM_SK-BR-3_Pertuzumab_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 0 125.28 0.00020201 459430000 993690 1016700 963880 966280 1164900 764400 1284400 984580 1429900 FALSE TRUE 931496.7167 1091977.526 986743.6888 991076.3807 1073413.453 985069.871 1091816.144 1107506.98 1191240.452 0.781955242 0.916672636 0.828332925 0.831970052 0.901088819 0.82692782 0.916537162 0.929709009 1 20.18403322 1.160104648 1.131562312 0.998407632 0.853427084 0.617423517 0.039862935 0.295665725 0.785716278 0.033812387 0.010983917 14.45788107 -1.160104648 -0.144980548 QGVLTHGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 QGVLTHGR 8 0 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ;;;;;;; 141.48 0.00063284 4655390000 4885982 7277770 5024860 5079860 7550350 4300496 5952130 6275370 7329950 FALSE TRUE 4580177.108 7816623.663 5144052.052 5210217.808 6957375.968 5541979.382 5059663.363 7058863.758 6106533.992 0.750045298 1.280042603 0.842384904 0.853220143 1.139333045 0.907549092 0.828565496 1.155952586 1 22.54192232 3.778709615 24.86117907 0.946396297 1.05539498 0 0.170818336 457.892215 220661.9302 0.040099677 0.072290627 6007.719053 -3.778709615 0.108998684 QGVSYSVHAYTGQPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QGVSYSVHAYTGQPSPR 17 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 QGVSYSVHAYT(0.001)GQPS(0.999)PR 103.88 0.00092046 75494000 14854 15016 16104 15648 18794 18197 19525 11344 14958 TRUE FALSE 13924.31466 16127.80026 16485.99448 16049.55417 17317.99505 23450.1785 16597.40751 12760.32337 12461.41317 1.11739451 1.294219207 1.322963476 1.287940136 1.389729625 1.881823368 1.331904118 1.023986862 1 13.60518006 1.252659963 5.985436016 1.006349747 1.383428716 0.376717832 0.194728935 0.15953102 19.7273833 0.152284793 0.048677494 17.89204421 -1.252659963 0.377078968 QGYACPYYHNS(ph)KDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QGYACPYYHNSKDRR 15 2 Q9C0B0 Q9C0B0 UNK RING finger protein unkempt homolog 1 QGYACPYYHNS(1)KDRR 120.4 7.13E-05 156150000 314830 177890 229680 198420 232530 197250 314840 193770 280440 TRUE FALSE 295125.3523 191061.1607 235128.1181 203511.7931 214268.0318 254192.8729 267632.6648 217962.611 233632.7523 1.263201967 0.817784146 1.006400497 0.871075614 0.917114701 1.088001877 1.145527167 0.93292832 1 17.83388301 2.23453167 24.99414094 1.064799366 0.953198193 0.033126499 0.130792543 191.5273663 1188151.541 0.044083188 0.033747204 171.6056846 -2.23453167 -0.111601172 QGYGEGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QGYGEGFR 8 0 Q9Y6B6;Q9H029;Q9NR31;Q9NR31-2;H0Y5E8 Q9Y6B6;Q9NR31 SAR1B;DKFZp434B2017;SAR1A GTP-binding protein SAR1b;GTP-binding protein SAR1a 0 ;;;; 133.05 0.0021774 3838280000 3727890 4563350 4005650 4140070 4392930 3764290 5043090 3700440 3927610 FALSE TRUE 3494568.019 4901225.182 4100665.91 4246311.205 4047926.998 4850979.415 4286925.472 4162448.08 3272066.518 1.068000299 1.497899005 1.253234275 1.297745991 1.237116353 1.482543032 1.310158412 1.272115972 1 21.64177065 0.754205256 2.734937029 1.000087905 1.324957932 0.372850458 0.122272979 1.3011773 13.12116543 0.104851083 0.027721405 5.678129011 -0.754205256 0.324870027 QGYVIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QGYVIYR 7 0 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;;;; 114.19 0.013869 1853350000 2136700 2446840 1834520 1829340 2240950 2154090 2953750 1929580 3002660 FALSE TRUE 2002967.761 2628006.58 1878035.681 1876283.961 2064954.827 2775940.814 2510862.609 2170492.311 2501496.648 0.800707753 1.050573696 0.75076482 0.750064552 0.825487745 1.109711986 1.003744143 0.867677481 1 21.25436009 2.260757587 24.99517362 1.000544113 0.849403411 0.375384124 0.101429905 275.974887 310764.0426 0.036448676 0.030473147 182.2877932 -2.260757587 -0.151140702 QHAHTVLS(ph)SPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QHAHTVLSSPPR 12 0 Q6ZNC4 Q6ZNC4 ZNF704 Zinc finger protein 704 1 QHAHTVLS(0.5)S(0.5)PPR;QHAHTVLS(0.5)S(0.5)PPR;QHAHT(0.003)VLS(0.499)S(0.499)PPR;QHAHTVLS(0.5)S(0.5)PPR 117 0.00050335 829660000 400592 415409 325022 311892 478329 493789 662930 416211 484084 TRUE FALSE 375519.6618 446166.3146 332731.6753 319895.6768 440762.9698 636337.8683 563529.8008 468175.8595 403287.2531 0.931146866 1.10632387 0.825048828 0.793220401 1.092925617 1.577877464 1.397340969 1.160899225 1 18.62144828 2.460945339 11.02806901 1.335264617 0.932334912 0.495704813 0.172129985 0.301756482 200.2506606 0.056736092 0.047850356 289.0316077 -2.460945339 -0.402929704 QHEAEEGVRR ddPTM_SK-BR-3_Pertuzumab_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 91.937 0.0063673 84254000 20101 18511 20207 20766 22275 15305 22431 18375 23870 FALSE TRUE 18842.91429 19881.5737 20686.31958 21298.89072 20525.61135 19723.30504 19067.67979 20669.1592 19885.94279 0.947549457 0.999780292 1.04024837 1.071052599 1.032166871 0.991821472 0.95885219 1.03938543 1 14.27946134 -0.191549706 7.612676326 1 1.009742727 0.006882468 0.037931661 0 0 0.038081558 0.008975909 0.643354427 0.191549706 0.009742727 QHEAPSNRPLNELLT(ph)PQGPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QHEAPSNRPLNELLTPQGPSPR 22 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 2 QHEAPSNRPLNELLT(1)PQGPS(1)PR;QHEAPSNRPLNELLT(1)PQGPS(1)PR 105.56 0.0078581 121255000 85461 168156 160448 176944 183794 145139 131175 121238 124875 TRUE FALSE 80112.14856 180606.4452 164253.9023 181484.6826 169359.5606 187038.2732 111506.5265 136374.8312 104032.5558 0.770068062 1.736056986 1.578870202 1.744498934 1.627947707 1.797882132 1.071842614 1.310886099 1 16.66667555 1.691362953 8.060080167 1.147083339 1.579520486 0.290706825 0.300548371 0.139018095 17.22834789 0.134921297 0.071054831 49.13183143 -1.691362953 0.432437147 QHEAPSNRPLNELLTPQGPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QHEAPSNRPLNELLTPQGPSPR 22 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 QHEAPSNRPLNELLT(0.05)PQGPS(0.949)PR 57.351 0.022096 0 29482 65999 62027 66017 74743 54022 57133 52084 68388 TRUE FALSE 27636.77425 70885.63463 63498.30973 67711.10799 68872.98628 69617.27443 48566.43705 58586.80205 56973.601 0.485080349 1.244183857 1.114521614 1.188464601 1.208857876 1.221921613 0.852437553 1.028314887 1 15.79800597 -1.222066468 6.273658374 0.999999097 1.068576729 0 0.230776596 2.69E-06 3.34E-07 0.206225947 0.048607282 0.059969929 1.222066468 0.068577632 QHEDFVWLHDTLIETTDYAGLIIPPAPTKPDFDGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QHEDFVWLHDTLIETTDYAGLIIPPAPTKPDFDGPR 36 1 Q9Y5X3;Q5QPE4 Q9Y5X3 SNX5 Sorting nexin-5 0 136.33 2.88E-09 170960000 338650 321050 309540 283660 358180 283160 404350 305010 403200 FALSE TRUE 317454.501 344820.8761 316882.435 290939.1958 330049.9876 364903.6953 343721.4713 343091.1699 335903.3152 0.945077011 1.026547999 0.943373943 0.866139697 0.982574368 1.086335498 1.023275019 1.021398582 1 18.35768651 2.465229343 23.73333092 1.035205822 0.955094794 0.461171148 0.04402396 121.2813571 242044.5005 0.015719547 0.013163914 291.8968063 -2.465229343 -0.080111028 QHEVEIPS(ph)PTQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QHEVEIPSPTQK 12 0 Q08499-10;A0A087WSZ7;A0A1B0GW84;Q08499-2;Q08499-9;Q08499-6;Q08499-11;Q08499;Q08499-3;Q08499-4;D6RHE0;Q08499-5;Q08499-8 Q08499-10 PDE4D "cAMP-specific 3,5-cyclic phosphodiesterase 4D" 1 QHEVEIPS(0.968)PT(0.032)QK;QHEVEIPS(0.985)PT(0.015)QK;QHEVEIPS(0.958)PT(0.042)QK;QHEVEIPS(0.874)PT(0.126)QK 77.222 0.018682 914780000 1038770 680543 820988 793580 793980 651126 1121390 675819 661827 TRUE FALSE 973755.24 730931.1118 840462.2231 813944.6063 731624.0136 839095.5061 953247.98 760196.4898 551363.7981 1.76608483 1.325678462 1.524333346 1.476238754 1.326935167 1.521854552 1.72889113 1.378756626 1 19.07264502 0.980846224 23.99521036 0.99999999 1.51020661 0.573019001 0.142370681 605.0288109 757961.4165 0.134832735 0.033708184 9.568552062 -0.980846224 0.51020662 QHFIQEEQILEIDCTMLTPEPVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QHFIQEEQILEIDCTMLTPEPVLK 24 0 P41250 P41250 GARS Glycine--tRNA ligase 0 124.81 0.00010333 87904000 110860 64088 98289 81541 64621 126410 172820 58675 116740 FALSE TRUE 103921.4705 68833.1422 100620.4615 83633.48011 59545.92733 162902.5149 146907.2454 66000.70291 97255.33983 1.068542567 0.707756945 1.034600894 0.859937154 0.612263835 1.674998156 1.510531408 0.678633204 1 16.56948984 2.24880909 24.99981977 1.300451177 0.860741608 0.23969744 0.301828266 230.1430014 561403.9765 0.100594213 0.083287633 177.3409741 -2.24880909 -0.439709568 QHFISFDTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QHFISFDTDR 10 0 C9J0K6;P30626-3;P30626-2;P30626 C9J0K6 SRI Sorcin 0 ;;; 151.98 1.88E-05 1833450000 549331 919280 548415 613495 942410 439891 605884 736560 774740 FALSE TRUE 514949.3533 987344.4477 561423.6628 629238.3203 868396.9201 566880.3907 515037.319 828521.1374 645430.889 0.797838099 1.529744647 0.869843189 0.974912002 1.345452991 0.878297584 0.797974388 1.283671345 1 19.2999031 3.81565034 8.93749074 1.003336411 1.212725655 0.042833452 0.246027279 0.647349329 59.88889348 0.05895517 0.106482849 6541.093248 -3.81565034 0.209389244 QHFPATPLLDYALEVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QHFPATPLLDYALEVEK 17 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 166.76 2.31E-09 587000000 1330820 1068640 935990 933770 1180900 966730 1576450 936770 1756470 FALSE TRUE 1247526.352 1147763.218 958192.1248 957732.1191 1088156.878 1245809.257 1340075.958 1053727.797 1463303.81 0.852540903 0.784364265 0.654814208 0.654499847 0.743630181 0.851367467 0.915787924 0.720101861 1 20.4807979 2.227477858 4.317742228 0.872117259 0.728074551 0.360138257 0.088755861 0.215198416 9.421992327 0.032437676 0.02468141 168.8409777 -2.227477858 -0.144042708 QHGDVVSAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 QHGDVVSAIR 10 0 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;;;;; 158.94 7.84E-06 3513740000 632578 1038998 753435 798401 1031475 744684 796375 844599 818936 FALSE TRUE 592986.0722 1115926.493 771306.834 818889.3213 950467.1143 959662.1819 676965.9619 950049.0443 682250.2911 0.869162065 1.635655576 1.130533536 1.200276983 1.39313552 1.406613078 0.992254559 1.392522739 1 19.37994158 -0.128045578 0.42383799 0.956209634 1.291944076 0.082428392 0.225531358 11.0132337 2.375667059 1.028778846 0.131484153 0.74465382 0.128045578 0.335734442 QHGEQLGGGGSGGGGYNNSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QHGEQLGGGGSGGGGYNNSK 20 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38;E9PMX1 Q5T1Z4 PUM1 Pumilio homolog 1 0 161.47 2.25E-11 39536000 19365 20135 21712 21964 23536 20843 25040 19660 23939 FALSE TRUE 18152.97922 21625.81635 22227.01889 22527.63342 21687.5775 26860.03574 21285.48446 22114.59428 19943.42625 0.910223699 1.084358128 1.114503527 1.129576891 1.087454945 1.346811496 1.067293262 1.10886635 1 14.28362566 5.582481074 1.052896888 1.133725017 8.11E-09 0.34859767 0.088934598 9.255935829 2.241410918 0.023811663 17.98991347 382367.5905 -5.582481074 -1.133725009 QHHHLLQSPVSHHEPES(ph)PQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QHHHLLQSPVSHHEPESPQLR 21 0 Q9Y6D6 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 QHHHLLQSPVSHHEPES(1)PQLR 135.3 3.09E-06 219800000 80883 82745 95482 108520 82838 84869 96251 53501 121520 TRUE FALSE 75820.67741 88871.5259 97746.87813 111304.8069 76332.23763 109369.3026 81819.0561 60180.71762 101237.527 0.748938459 0.877851609 0.965520209 1.099442176 0.753991528 1.080323728 0.808189004 0.594450689 1 16.62738465 1.545625581 8.180536907 0.76665286 0.923034125 0.117423073 0.150099044 0.188621913 21.53724973 0.072759311 0.033828925 35.12574799 -1.545625581 0.156381265 QHHPPYHQQHHQGPPPGGPGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 QHHPPYHQQHHQGPPPGGPGGR 22 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;;;;;;; 137.43 1.05E-06 1562186100 149182.1 155645.7 165722.6 160899.5 178332.3 125887.6 152669.61 147064.8 163495.1 FALSE TRUE 139845.0587 167169.8696 169653.6183 165028.4536 164326.8005 162229.3065 129778.2193 165426.164 136206.7116 1.026711951 1.22732476 1.245559902 1.21160295 1.206451566 1.191052222 0.95280341 1.214522853 1 17.05543827 1.771313551 25 1.052674308 1.198570007 0.309058334 0.089319836 30.59585106 23364.94634 0.037609894 0.020863474 59.06273458 -1.771313551 0.145895699 QHIAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QHIAEK 6 0 Q96TA1 Q96TA1 FAM129B Niban-like protein 1 0 ; 70.912 0.089617 300300000 822630 725880 756190 758660 808800 661030 918610 710340 931310 FALSE TRUE 771143.0567 779624.9105 774127.1839 778128.5 745280.1105 851858.6301 780872.9585 799027.5127 775868.3445 0.993909678 1.004841757 0.997755856 1.002913066 0.960575484 1.097942243 1.006450339 1.029849353 1 19.56545234 QHIPYREDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QHIPYREDK 9 1 P48729-2;A0A5F9W493;U3KPX3;A0A590UJ43;P48729;E7ETM0;P48729-3;D6REM4;Q8N752;U3KQ83 P48729-2 CSNK1A1;CSNK1A1L Casein kinase I isoform alpha;Casein kinase I isoform alpha-like 0 60.563 0.057022 335900000 792840 654950 745960 719270 728830 574100 923940 557930 868430 FALSE TRUE 743217.5597 703443.1795 763654.5235 737727.6859 671590.6318 739833.3503 785403.7744 627588.7887 723483.4227 1.027276557 0.972300342 1.055524563 1.019688444 0.928273697 1.022598897 1.085586414 0.867454276 1 19.46460043 QHLASIYEKEEDWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QHLASIYEKEEDWR 14 1 D6RFN0;Q9BT78;D6RAX7;Q9BT78-2 D6RFN0 COPS4 COP9 signalosome complex subunit 4 0 138.91 7.62E-06 182650000 174560 144810 175610 177850 186470 149370 201580 142990 239550 FALSE TRUE 163634.6012 155531.8831 179775.5521 182413.9321 171825.3984 192490.6942 171354.9504 160842.6163 199567.5574 0.819945903 0.779344524 0.900825537 0.914046022 0.860988633 0.964539009 0.858631295 0.805955729 1 17.60651768 7.999999992 0.025226952 1.510958798 9.39E-09 0.385416428 0.054282998 2094.284768 4.061073142 83.30376516 175.7817967 99999998.08 -7.999999992 -1.510958788 QHLVEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QHLVEVR 7 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 72.485 0.051478 214430000 369010 666600 378160 394560 679580 306730 486230 551270 569670 FALSE TRUE 345914.3228 715955.7576 387130.1338 404685.0776 626208.5281 395277.9717 413324.3254 620097.273 474588.3968 0.728872272 1.508582516 0.815717654 0.852707484 1.319477114 0.832885874 0.870911148 1.306600155 1 18.8563173 3.872042162 11.83952302 0.984442152 1.172779376 0.023349968 0.259866513 1.143044242 121.2004511 0.060860919 0.109763589 7448.042766 -3.872042162 0.188337225 QHLYVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QHLYVDK 7 0 P53597;A0A494C0D1;H7C233 P53597 SUCLG1 "Succinyl-CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial" 0 84.476 0.04011 0 184390 234880 172540 168370 292330 204260 226920 233280 354260 FALSE TRUE 172849.359 252270.7596 176632.7303 172690.6592 269371.581 263226.5461 192895.4526 262405.5215 295131.7174 0.58566853 0.854773461 0.598487793 0.585130805 0.912716476 0.891895146 0.653591062 0.889113254 1 18.17099945 2.734994844 24.99811032 0.834098232 0.679553641 0.420876086 0.119097513 414.1602953 2903489.183 0.037944528 0.037086567 543.2438817 -2.734994844 -0.154544591 QHMDITGEENPLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QHMDITGEENPLNK 14 0 Q9H4A4;A6NKB8;C9JMZ3 Q9H4A4 RNPEP Aminopeptidase B 0 ;; 224.34 3.18E-12 1330560000 1111685 985740 935654 950877 1130380 919587 1523530 1013950 1610720 FALSE TRUE 1042106.62 1058725.215 957848.1547 975278.1137 1041604.515 1185056.839 1295090.82 1140543.889 1341880.426 0.7766017 0.788986257 0.713810363 0.726799568 0.776227519 0.883131474 0.965131315 0.849959406 1 20.35582469 2.182794567 2.93836215 0.933294324 0.751378568 0.796259956 0.04307021 0.1057834 1.858572156 0.017081225 0.01190617 152.3332007 -2.182794567 -0.181915756 QHMENEMAHYACDCWDAESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QHMENEMAHYACDCWDAESK 20 0 P41250 P41250 GARS Glycine--tRNA ligase 0 57.496 0.047565 85217000 21178 15526 13447 10044 19321 13386 23795 14177 20520 FALSE TRUE 19852.50678 16675.56119 13765.96919 10301.74604 17803.6066 17250.3209 20227.16065 15947.02966 17095.07944 1.161299476 0.975459708 0.805259153 0.602614693 1.041446263 1.009081061 1.183215365 0.932843262 1 14.06129351 2.519379408 24.9987391 1.055533129 0.881005816 0.180773042 0.151775612 711.8559353 421112.8848 0.049229676 0.046410427 330.6582843 -2.519379408 -0.174527313 QHQETSACDS(ph)PHGEDGPGDFAHTGVPGHVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QHQETSACDSPHGEDGPGDFAHTGVPGHVPR 31 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 QHQETSACDS(1)PHGEDGPGDFAHTGVPGHVPR 281.91 2.67E-72 1264300000 151680 189050 159580 190940 218520 185070 215560 161730 160320 TRUE FALSE 142186.6196 203047.4587 163365.313 195839.8437 201358.3207 238496.7046 183238.7792 181922.3465 133561.5563 1.064577439 1.520253764 1.223146222 1.466289021 1.507606876 1.785668805 1.371942528 1.362086154 1 17.02714528 0.742371142 2.545145874 1.000243773 1.428780582 0.324171276 0.188919245 1.59618501 14.05013208 0.172324308 0.045965108 5.525494389 -0.742371142 0.42853681 QHQNTMEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QHQNTMEDK 9 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;; 134.68 0.00018372 155944000 163426 138449 145496 145942 151509 173605 224263 133690 171144 FALSE TRUE 153197.4584 148699.908 148947.2338 149687.1188 139610.0943 223721.9453 190636.8451 150381.4908 142578.9608 1.074474506 1.042930228 1.044664886 1.049854186 0.979177387 1.569109103 1.337061542 1.054724273 1 17.12140159 2.289711411 24.9999958 1.286424319 1.040269915 0.268944105 0.157487124 103.5412031 50605.33492 0.050904791 0.042589955 194.8549358 -2.289711411 -0.246154404 QHS(ph)ITK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QHSITK 6 0 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 1 QHS(0.996)IT(0.004)K;QHS(0.933)IT(0.067)K;QHS(0.961)IT(0.039)K 90.15 0.051773 390348000 1317800 820730 947390 816050 886680 580320 1013630 597180 1154450 TRUE FALSE 1235321.25 881497.7032 969862.5382 836991.2246 817043.7295 747848.9633 861645.5916 671739.2376 961764.837 1.284431706 0.916541829 1.008419627 0.870265986 0.849525475 0.777579856 0.895900493 0.698444372 1 19.87532466 8 0.647790254 0.850768593 35.50579458 0.632790283 0.095681964 134.3851842 0.867799474 0.03438742 6676.290588 100000000 -8 34.65502599 QHSITK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QHSITK 6 0 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ;;; 106.42 0.052615 471330000 1725260 1571840 1578750 1607510 1713210 1394020 2156900 1495380 1696420 FALSE TRUE 1617279.056 1688220.669 1616198.696 1648761.428 1578661.397 1796450.944 1833492.869 1682081.485 1413276.543 1.144347201 1.194543756 1.143582764 1.166623359 1.117022288 1.271124858 1.29733482 1.190199819 1 20.43061236 2.24096666 24.99957865 1.225348424 1.158152776 0 0.083523465 122.1351946 1269036.027 0.026954271 0.021540401 174.1673165 -2.24096666 -0.067195648 QHSLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QHSLLK 6 0 K7EM56;A0A0B4J2B4;S4R417;K7ELC2;P62841;K7EQJ5;S4R456;K7EJ78 K7EM56 RPS15 40S ribosomal protein S15 0 ; 95.62 0.043138 697900000 1978580 1933860 1656750 1683440 2222600 1309360 2010970 1862830 2166100 FALSE TRUE 1854744.21 2077045.007 1696048.892 1726639.92 2048045.962 1687350.976 1709443.717 2095408.426 1804563.916 1.027807435 1.150995533 0.939866345 0.956818379 1.134925697 0.93504639 0.947289094 1.161171631 1 20.78321881 3.978432907 24.98748406 1.002613794 1.091604434 0.125313522 0.084269316 101.5740579 1934946.839 0.01985192 0.039458335 9515.528337 -3.978432907 0.08899064 QHTFVETESVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QHTFVETESVR 11 0 B0YIW6;P48444;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 ;;; 172.99 1.27E-05 2582140000 423070 535580 376374 461620 526350 364747 487497 419473 549290 FALSE TRUE 396590.8039 575234.9005 385301.769 473465.9507 485012.5942 470043.5377 414401.3506 471845.1274 457609.9505 0.866656862 1.257041941 0.841987305 1.034649597 1.059882098 1.02717071 0.905577665 1.031107665 1 18.8037589 3.965763642 24.99667452 0.981852104 1.084706628 0.063239209 0.113681133 679.011922 1494423.477 0.02629041 0.047952188 9241.950575 -3.965763642 0.102854524 QHVIDGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QHVIDGEK 8 0 Q9UQ80;Q9UQ80-2;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;;;;; 118.33 0.0019065 7920080000 17109100 12528920 13975940 13101070 14607100 12156290 19133900 12007230 18356100 FALSE TRUE 16038271.97 13456574.27 14307455.9 13437265.64 13459917.29 15665613.58 16264949.33 13506359.1 15292348.33 1.048777574 0.879954732 0.935595737 0.878692098 0.880173339 1.024408629 1.0636005 0.88321027 1 23.86630663 2.230770762 24.99997902 1.006061709 0.917951087 0.187928748 0.067177712 216.8713057 695998.628 0.023284706 0.017510781 170.1260279 -2.230770762 -0.088110623 QHVLDMLFSAFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QHVLDMLFSAFEK 13 0 P13984 P13984 GTF2F2 General transcription factor IIF subunit 2 0 80.967 0.016351 20196000 43194 46150 42472 46084 47969 30208 48418 36922 39411 FALSE TRUE 40490.56464 49566.99402 43479.4559 47266.59346 44201.70824 38928.55921 41158.17039 41531.79298 32833.0495 1.233225828 1.509667691 1.324258836 1.439604124 1.346256559 1.185651647 1.253559174 1.26493864 1 15.00286113 0.94945844 0.397648756 0.98084118 1.41225383 0.616730666 0.086286044 0.834322964 0.352575932 0.129361085 0.06646379 8.901402521 -0.94945844 0.43141265 QHVPEQHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QHVPEQHPK 9 0 Q9H3U1;A0A1W2PNX8;Q9H3U1-2 Q9H3U1;Q9H3U1-2 UNC45A Protein unc-45 homolog A 0 77.379 0.018949 74198000 174730 165670 170470 169860 200070 141180 189310 168020 224210 FALSE TRUE 163793.9612 177936.3792 174513.6289 174218.8952 184357.3092 181936.3741 160924.723 188997.6669 186787.9025 0.876898123 0.952611902 0.934287641 0.932709735 0.986987416 0.974026538 0.861537181 1.01183034 1 17.5110415 QHYIDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 QHYIDLK 7 0 Q32Q12;P22392-2;J3KPD9;P22392;F6XY72;O60361 Q32Q12;O60361 NME1-NME2;NME2;NME2P1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Putative nucleoside diphosphate kinase 0 ;;;;;;; 155.75 0.0015897 13211850000 29271220 24592310 23574780 21961710 28356140 21487370 35667930 22900790 39900780 FALSE TRUE 27439186.59 26413150.22 24133984.91 22525284.66 26129163.15 27690424.9 30319855.02 25760004.04 33241082.05 0.82546009 0.794593575 0.72602886 0.677633918 0.786050319 0.833018157 0.912119978 0.774944811 1 24.98646401 2.140633745 2.660119771 0.884432947 0.756092261 0.456352468 0.066737102 0.252162455 3.569578543 0.028495959 0.018613383 138.2400062 -2.140633745 -0.128340686 QHYNCEHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QHYNCEHSK 9 0 P50454;E9PR70;E9PPV6;E9PK86;E9PMI5;E9PQ34;E9PIG2;E9PRS3;E9PNX1 P50454 SERPINH1 Serpin H1 0 51.927 0.087609 19069000 14483 32141 10913 13651 39719 6806.2 13032 28449 31949 FALSE TRUE 13576.53488 34520.75308 11171.86151 14001.30777 36599.62996 8771.039451 11077.97258 32000.92027 26616.5055 0.51007954 1.296967894 0.419734345 0.526038543 1.375072695 0.329533847 0.416206875 1.202296082 1 14.70003355 3.966550306 24.53576318 0.697166482 0.947057674 0.006902932 0.400021299 781.381945 1813638.085 0.096116684 0.175680864 9258.706271 -3.966550306 0.249891191 QIANS(ph)QDGYVWQVTDMNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QIANSQDGYVWQVTDMNR 18 0 P10155-3;P10155-5;P10155-4;P10155;D6RE09;P10155-2;D6RDN1 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 1 QIANS(1)QDGYVWQVTDMNR;QIANS(1)QDGYVWQVTDMNR;QIANS(1)QDGYVWQVTDMNR 237.16 8.05E-24 206444000 272206 260238 208307 207684 262223 344085 432911 215199 511904 TRUE FALSE 255169.1124 279506.2923 213248.1404 213013.523 241629.0633 443416.7537 368000.0145 242067.0689 426463.9154 0.598336936 0.65540432 0.500037946 0.4994878 0.566587359 1.039752105 0.862910087 0.567614422 1 18.70206415 2.262552561 24.89429169 0.863427186 0.564789768 0.569079608 0.131252463 155.5861757 161437.3083 0.043574639 0.036439501 183.0427624 -2.262552561 -0.298637418 QIAQSKEDDDVIVNKPHVS(ph)DEEEEEPPFYHHPFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QIAQSKEDDDVIVNKPHVSDEEEEEPPFYHHPFK 34 2 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;H7C1M2;H7C2G8;J3QSZ5 P18583-7 SON Protein SON 1 QIAQSKEDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK;QIAQSKEDDDVIVNKPHVS(1)DEEEEEPPFYHHPFK 215.15 2.75E-36 1844870000 626400 367323 355185 363345 506920 339131 726240 346773 1272080 TRUE FALSE 587194.7422 394519.9771 363610.1559 372669.0478 467108.548 437032.6144 617347.0541 390068.3724 1059761.63 0.554081904 0.372272373 0.343105606 0.351653652 0.44076756 0.412387656 0.58253388 0.368071802 1 20.01530837 -1.723507112 0.362758826 1.48239582 0.39051687 0.815916389 0.08468656 11.88777972 0.775148897 5.08123549 0.060702136 0.018901353 1.723507112 -1.09187895 QIATLHAQVADMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QIATLHAQVADMK 13 0 P35579 P35579 MYH9 Myosin-9 0 138.77 4.53E-05 274650000 958130 761030 627560 589120 746640 835690 1333400 623280 1179200 FALSE TRUE 898162.3536 817377.4531 642446.0196 604237.8166 688001.9062 1076940.137 1133469.049 701097.88 982383.9021 0.914268192 0.832034657 0.653966355 0.615073003 0.700339149 1.096251816 1.153794404 0.71366996 1 19.90592739 2.242982744 25 1.023125762 0.737278159 0.420268217 0.142307642 94.64157635 535048.0359 0.050171503 0.040638308 174.9777161 -2.242982744 -0.285847603 QICLVMLETLSQS(ph)PQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 QICLVMLETLSQSPQGR 17 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR 423.23 1.86E-160 2162529000 1151544 1166002 793050 741603 1089796 1836734 2441540 888628 2490963 TRUE FALSE 1079470.917 1252334.001 811861.5205 760633.7885 1004207.818 2366969.289 2075453.743 999575.1619 2075205.183 0.520175511 0.603474785 0.391219879 0.366534256 0.483907725 1.140595305 1.000119776 0.48167534 1 20.98482256 2.257897943 24.79280756 0.924126259 0.474843236 0.5869777 0.179987811 143.8566411 184441.2681 0.060629523 0.050652912 181.0914488 -2.257897943 -0.449283022 QICVVMLETLSQS(ph)PPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QICVVMLETLSQSPPK 16 0 F8VZX2;Q15366;Q15366-2;Q15366-5;Q15366-8 F8VZX2;Q15366;Q15366-2;Q15366-5 PCBP2 Poly(rC)-binding protein 2 1 QICVVMLETLSQS(1)PPK 222.51 1.00E-14 106950000 169630 93547 78797 66222 83691 164270 296460 94209 177420 TRUE FALSE 159013.1611 100473.3172 80666.10205 67921.36863 77118.24645 211692.0823 252008.5752 105971.201 147807.4558 1.075812855 0.679758113 0.545751238 0.459525998 0.521748013 1.432215182 1.704978777 0.716954368 1 17.17335952 2.238256769 24.99959434 1.324357182 0.63562917 0.420796245 0.312413644 6.159076282 506679.7001 0.108934115 0.085525293 173.0839385 -2.238256769 -0.688728012 QIDDILSVASVRPAVLQVECHPYLAQNELIAHCQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QIDDILSVASVRPAVLQVECHPYLAQNELIAHCQAR 36 1 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 344.47 1.93E-130 487660000 147290 167610 136330 135730 182930 130890 203690 149100 185200 FALSE TRUE 138071.3818 180020.0188 139563.812 139213.0616 168563.4157 168675.8182 173148.5755 167715.4632 154288.9236 0.89488849 1.166772148 0.904561447 0.902288112 1.092517932 1.093246451 1.122235942 1.087022058 1 17.23527497 2.691986238 23.58302919 1.090584907 0.989973949 0.279736555 0.084665276 312.0041607 157983.1601 0.027328805 0.025765989 492.0239443 -2.691986238 -0.100610958 QIDNPDYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QIDNPDYK 8 0 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;; 150.17 0.0011479 884410000 2351930 2038520 2042620 2060610 2094180 1622470 2679970 1694870 1946150 FALSE TRUE 2204726.9 2189454.142 2091071.911 2113488.741 1929711.55 2090850.75 2278133.378 1906478.25 1621324.992 1.35983033 1.350410406 1.289730264 1.303556505 1.190206504 1.289593857 1.40510594 1.175876681 1 20.62874188 0.981231332 5.576926537 1.000139319 1.312566458 0.76758963 0.056205876 0.072867933 9.79838081 0.055448605 0.013971079 9.577040686 -0.981231332 0.31242714 QIDSS(ph)PVGGETDETTVSQNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QIDSSPVGGETDETTVSQNYR 21 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 QIDS(0.105)S(0.895)PVGGETDETTVSQNYR;QIDS(0.002)S(0.998)PVGGETDETTVSQNYR;QIDS(0.002)S(0.998)PVGGETDETTVSQNYR;QIDS(0.004)S(0.996)PVGGETDETTVSQNYR 388.81 4.11E-131 1975170000 1916660 2180290 2155750 2128640 2194830 1903080 2345600 1800690 1943760 TRUE FALSE 1796699.672 2341720.94 2206885.408 2183264.506 2022456.905 2452468.302 1993899.055 2025510.11 1619333.899 1.109530081 1.446101352 1.362835305 1.348248504 1.248943721 1.514492041 1.231308167 1.250829191 1 20.62696906 0.838243019 1.347261227 1.002208051 1.348320765 0.447189121 0.112414305 0.515923464 1.767329604 0.095298014 0.028561043 6.89037754 -0.838243019 0.346112714 QIEEENRER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QIEEENRER 9 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 0 68.786 0.052063 149850000 232570 339910 310550 333740 358180 327020 319450 282100 302830 FALSE TRUE 218013.8588 365077.2901 317916.3927 342304.3334 330049.9876 421425.3653 271551.4381 317320.806 252285.7166 0.864154585 1.447078713 1.26014424 1.356812181 1.308238897 1.670428952 1.076364694 1.257783477 1 17.944699 1.028935801 1.49929321 1.015834137 1.318115921 0.142909348 0.21203162 0.669910328 3.065829037 0.179201853 0.053124534 10.68896858 -1.028935801 0.302281785 QIEETLAHFHLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QIEETLAHFHLTK 13 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 261.35 2.70E-24 746500000 1508520 1595530 1413650 1344330 1618570 1196700 1749540 1409650 2060890 FALSE TRUE 1414104.426 1713664.701 1447182.446 1378827.784 1491454.041 1542167.863 1487212.719 1585647.906 1716914.145 0.823631415 0.998107393 0.842897386 0.803084876 0.868682948 0.898220722 0.866212631 0.923545251 1 20.71138647 0.935084606 3.493928551 0.99991047 0.879656682 0.375602513 0.052781203 0.350250563 10.77530179 0.05117038 0.013229256 8.611615013 -0.935084606 -0.120253788 QIEHCEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QIEHCEGR 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 157.99 0.00068729 0 460680 548060 496520 483030 604480 479790 622320 494310 483460 FALSE TRUE 431846.8611 588638.9327 508297.6889 495425.3676 557006.5792 618297.5843 529008.8933 556025.6916 402767.4027 1.072199136 1.461486031 1.262012977 1.230053287 1.382948509 1.5351232 1.313435223 1.380513139 1 18.6195874 -1.439943616 6.527071463 0.999924582 1.341196838 0.393828509 0.127853797 0.000127843 1.10E-05 0.112788824 0.02657874 0.03631252 1.439943616 0.341272257 QIEIQFAQGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QIEIQFAQGDR 11 0 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 0 120.86 0.0009858 104940000 62598 69348 61636 56906 77662 60270 74092 60684 86967 FALSE TRUE 58680.10292 74482.59808 63098.03503 58366.3043 71562.73979 77668.9706 62982.59244 68260.53098 72451.64587 0.80992091 1.02803183 0.870898573 0.805589764 0.987731044 1.072011128 0.869305199 0.942152937 1 16.14473084 QIESTETSCHGCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 QIESTETSCHGCR 13 0 Q9Y508;A0A096LNV3;A0A096LP02;Q9Y508-2 Q9Y508 RNF114 E3 ubiquitin-protein ligase RNF114 0 ;;;;;; 266.35 2.06E-24 5001786000 1338087 2622410 2341721 2254163 2490880 2577859 2841659 2267315 2598551 FALSE TRUE 1254338.523 2816575.965 2397267.728 2312008.639 2295256.333 3322045.045 2415578.614 2550394.269 2164836.051 0.57941502 1.301057401 1.107366873 1.067983249 1.060244877 1.534548098 1.115825197 1.178100424 1 21.04582634 QIEYEYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QIEYEYK 7 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 117.02 0.012389 63076000 158720 171910 153400 157150 174120 123180 209890 148880 170280 FALSE TRUE 148785.9985 184638.3953 157038.7204 161182.7351 160445.3176 158740.0663 178418.943 167467.9957 141859.1679 1.048828924 1.301561245 1.107004381 1.136216555 1.131018318 1.118997585 1.257718804 1.180522896 1 17.11409987 3.760049859 24.79715356 1.149402441 1.196558043 0 0.088885361 1014.807144 764202.8142 0.021269979 0.038341466 5755.060036 -3.760049859 0.047155601 QIEYYFSVDNLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QIEYYFSVDNLER 13 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 0 145.29 9.71E-05 37811000 28971 28240 25427 24322 25159 30722 40557 26859 35536 FALSE TRUE 27157.75682 30330.91898 26030.14045 24946.1437 23183.11363 39590.94267 34475.85436 30212.40527 29604.81203 0.917342654 1.024526653 0.879253698 0.842638138 0.783085993 1.337314442 1.164535493 1.020523462 1 14.85354407 2.247504688 24.99978156 1.153365452 0.904296396 0.536689529 0.109988123 142.2415351 397582.7991 0.038024478 0.031381392 176.8091304 -2.247504688 -0.249069056 QIFDEYENETFLCHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QIFDEYENETFLCHR 15 0 S4R3N1;Q9Y3A3-2;Q9Y3A3-3;Q9Y3A3;B4DM50 S4R3N1 HSPE1-MOB4;MOB4 MOB-like protein phocein 0 ;;; 259.96 6.99E-25 713820000 750240 728690 753290 708040 801980 859040 975040 671160 720500 FALSE TRUE 703283.8176 782642.9658 771158.3945 726209.5051 738995.7258 1107030.903 828841.8038 754955.8034 600243.8954 1.171663424 1.303874928 1.284741753 1.209857377 1.231159086 1.84430181 1.380841705 1.257748407 1 19.1951893 QIFLGGVDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QIFLGGVDKR 10 1 P05141 P05141 SLC25A5 "ADP/ATP translocase 2;ADP/ATP translocase 2, N-terminally processed" 0 ; 152.7 2.82E-05 1482860000 1038900 1329780 766820 909980 1875850 907200 1035190 1643310 2227600 FALSE TRUE 973877.1035 1428238.295 785009.3325 933331.6274 1728528.308 1169093.913 879972.8697 1848480.871 1855799.169 0.524775051 0.76960822 0.423003386 0.502927064 0.931419917 0.629967904 0.474174622 0.996056525 1 20.82360916 1.226010766 24.97937375 0.998028727 0.607375758 0.540349016 0.149558737 194.7193919 387559.9013 0.136462922 0.035060468 16.82715773 -1.226010766 -0.390652969 QIGLDQIWDDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QIGLDQIWDDLR 12 0 A0A590UJ56;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;Q13616;A0A590UJC4;A0A590UK34;A0A590UJ50;A0A590UJM8;A0A590UJ59;A0A590UJ97 A0A590UJ56 CUL1 Cullin-1 0 ;;; 205.46 2.36E-07 151621000 101547 117141 94775 97341 116288 133463 172469 96951 164463 FALSE TRUE 95191.35454 125814.2415 97023.10776 99838.93486 107155.2096 171991.6015 146608.8746 109055.5458 137013.0628 0.694761161 0.918264572 0.708130347 0.72868187 0.782080244 1.255293459 1.070035744 0.795949988 1 17.06395392 2.31049798 12.92247907 1.047560881 0.777261618 0.516807196 0.126084106 0.645701433 114.395307 0.042367899 0.035440464 204.4080429 -2.31049798 -0.270299263 QIGNVAALPGIVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QIGNVAALPGIVHR 14 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 63.185 0.071092 247560000 191670 179220 166560 164870 204760 178530 249260 169470 280600 FALSE TRUE 179673.7168 192489.6353 170510.8819 169100.8433 188678.9756 230068.7128 211885.777 190628.7025 233766.0473 0.768604846 0.823428541 0.729408243 0.723376407 0.807127373 0.984183612 0.906400992 0.815467878 1 17.83470588 2.397357018 5.859121774 0.918941074 0.766135789 0.662309887 0.056034793 0.127433673 7.202390309 0.018838667 0.015704635 249.6646289 -2.397357018 -0.152805286 QIGVEHVVVYVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QIGVEHVVVYVNK 13 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 96.591 0.0041668 361390000 724820 546910 494990 469920 705860 696670 787820 572880 1218200 FALSE TRUE 679454.81 587403.7855 506731.3966 481978.9428 650424.6029 897787.3195 669693.7048 644405.3291 1014874.55 0.669496353 0.578794478 0.499304467 0.474914799 0.640891628 0.884628863 0.659878312 0.634960576 1 19.95286997 2.471772263 22.55948731 0.759746001 0.550881653 0.474969174 0.116496263 39.24697246 165517.8166 0.037397857 0.031424595 296.3277088 -2.471772263 -0.208864349 QIILEKEETEELKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QIILEKEETEELKR 14 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 122.1 6.23E-05 264600000 339640 211910 205360 202580 289170 143980 364980 179340 457460 FALSE TRUE 318382.5387 227600.0369 210231.2362 207778.5458 266459.7547 185544.6887 310254.6373 201730.9938 381106.9707 0.835415154 0.597207751 0.551633143 0.545197443 0.699173133 0.486857242 0.814088068 0.529329058 1 18.53983647 -1.872635935 0.479620332 1.328791426 0.621201741 0.475281371 0.119758527 47.85134195 3.926045049 17.79825349 0.054408491 0.013408002 1.872635935 -0.707589685 QILGVIDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QILGVIDKK 9 1 Q14444-2;Q14444;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ; 107.83 0.0051546 0 917160 830210 794660 755190 982060 882640 1118450 773430 1247790 FALSE TRUE 859756.5928 891679.6122 813509.7105 774569.4539 904932.969 1137443.84 950748.8057 869994.438 1039525.788 0.827066151 0.857775365 0.78257771 0.745118075 0.870524791 1.094194923 0.914598576 0.836914724 1 19.98749412 2.470995022 24.99622745 0.958464909 0.808715691 0.530501714 0.070172759 126.7270954 517065.8379 0.023489493 0.019702897 295.7978561 -2.470995022 -0.149749218 QILIACS(ph)PVSSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QILIACSPVSSVR 13 0 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 QILIACS(0.904)PVS(0.095)S(0.001)VR;QILIACS(0.948)PVS(0.052)SVR;QILIACS(0.81)PVS(0.19)SVR;QILIACS(0.615)PVS(0.371)S(0.014)VR;QILIACS(0.891)PVS(0.108)S(0.001)VR;QILIACS(0.494)PVS(0.453)S(0.053)VR 235.46 1.15E-16 2036800000 2603200 2343910 2080580 1719980 2275150 3361880 4154040 2003820 3229550 TRUE FALSE 2440270.359 2517455.535 2129932.34 1764117.599 2096468.897 4332400.18 3531180.266 2254001.338 2690517.241 0.906989304 0.935677161 0.791644189 0.655679723 0.779206639 1.610248065 1.312454056 0.837757626 1 21.35945212 2.275087221 24.97803174 1.240545969 0.820237674 0.424555197 0.214057144 141.3306884 96645.8075 0.072263614 0.060458413 188.4027428 -2.275087221 -0.420308295 QIQELVEAIVLPMNHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QIQELVEAIVLPMNHK 16 0 P17980;E9PM69;R4GNH3;E9PN50;E9PMD8 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ; 156.5 1.57E-07 116423000 475590 484850 457870 413830 521020 494920 699510 424500 671680 FALSE TRUE 445823.6709 520748.7985 468730.8926 424449.5784 480101.1909 637795.3696 594624.9694 477499.7594 559572.2688 0.796722239 0.930619381 0.83765926 0.758525042 0.857978884 1.139790882 1.062641955 0.85332992 1 19.09396494 2.32857065 8.636364977 1.027829145 0.844945816 0.526042733 0.083155976 0.207140601 17.74501175 0.028540561 0.023835552 213.0937196 -2.32857065 -0.18288333 QIS(ph)LPDLSQEEPQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QISLPDLSQEEPQLK 15 0 H0YBZ4;Q15390-2;Q15390 H0YBZ4 MTFR1 Mitochondrial fission regulator 1 1 QIS(1)LPDLSQEEPQLK;QIS(1)LPDLSQEEPQLK;QIS(1)LPDLSQEEPQLK;QIS(0.996)LPDLS(0.004)QEEPQLK 268.55 1.25E-25 274832000 450606 359399 399914 381725 413031 327658 514449 347076 572080 TRUE FALSE 422403.3748 386009.2759 409400.1489 391520.7098 380593.2113 422247.5455 437312.1484 390409.2026 476596.1522 0.886292037 0.809929485 0.859008507 0.821493644 0.79856543 0.885965075 0.917573812 0.819161466 1 18.86240778 -0.586221248 0.346360758 1.052487314 0.83343651 0.581766732 0.039361031 6.499564008 0.761820949 0.424497868 0.033230031 0.259285812 0.586221248 -0.219050805 QIS(ph)QDVK ddPTM_SK-BR-3_Pertuzumab_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 146.11 0.0023512 2774270000 6235590 4652880 4453480 4659150 4132400 3780330 7805070 4095930 6467660 TRUE FALSE 5845315.553 4997384.077 4559118.649 4778711.677 3807857.973 4871649.902 6634772.212 4607315.877 5388165.763 1.084843305 0.927474079 0.846135559 0.886890249 0.706707652 0.904138832 1.231360078 0.855080575 1 22.3613628 1.965777176 24.74985467 1.057827595 0.882279918 0.186567027 0.129009748 673.3618159 486972.4882 0.050098681 0.032343741 92.42238605 -1.965777176 -0.175547677 QIS(ph)QDVKLEPDILLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 233.59 7.51E-18 506160000 713431 858429 524008 719220 942237 362598 1011019 619510 2860110 TRUE FALSE 668778.6272 921987.9764 536437.7172 737676.4028 868237.5068 467274.1563 859426.0868 696857.1872 2382739.164 0.28067639 0.386944568 0.225134889 0.309591756 0.3643863 0.196107977 0.360688278 0.292460542 1 21.1841896 -1.099135312 0.960828892 1.094960053 0.303162637 0.930469907 0.059958978 33.5685958 12.35216438 9.47857737 0.016817246 0.079591133 1.099135312 -0.791797416 QIT(ph)MEELVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QITMEELVR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 QIT(1)MEELVR;QIT(1)MEELVR;QIT(1)MEELVR;QIT(1)MEELVR 179.67 0.00055368 656456000 768499 925212 727869 829345 633432 565971 1071384 676880 704967 TRUE FALSE 720400.0194 993715.6592 745134.3964 850627.3968 583684.8059 729357.6399 910739.9154 761389.958 587303.4534 1.226623162 1.691996962 1.268738319 1.448360965 0.993838539 1.241875279 1.550714388 1.29641662 1 19.1637466 -4.30494993 0.163749676 2.90E-17 1.463923758 0.224355542 0.192948641 153.349952 1.7549961 51.96235436 0.791099257 4.96E-05 4.30494993 1.463923758 QIT(ph)QEEDDSDEEVAPENFFSLPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QITQEEDDSDEEVAPENFFSLPEK 24 0 Q92733 Q92733 PRCC Proline-rich protein PRCC 1 QIT(0.54)QEEDDS(0.46)DEEVAPENFFSLPEK;QIT(0.764)QEEDDS(0.236)DEEVAPENFFSLPEK 113.54 0.0051837 93664000 73290 57716.4 66056.8 63453.3 66955.1 58074.2 85107.3 57949.2 79401 TRUE FALSE 68702.90973 61989.78231 67623.69849 65081.6191 61696.71653 74839.27878 72346.25046 65184.28518 66148.46015 1.038616917 0.937131147 1.02230193 0.98387202 0.932700722 1.131383537 1.093695156 0.985424075 1 16.01341995 2.24499447 24.9998811 1.066531284 0.982092707 0.284282385 0.052940792 153.608314 596873.8422 0.017538475 0.014345012 175.790123 -2.24499447 -0.084438578 QITQEEDDS(ph)DEEVAPENFFSLPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QITQEEDDSDEEVAPENFFSLPEK 24 0 Q92733 Q92733 PRCC Proline-rich protein PRCC 1 QIT(0.451)QEEDDS(0.548)DEEVAPENFFSLPEK;QIT(0.166)QEEDDS(0.834)DEEVAPENFFSLPEK;QIT(0.207)QEEDDS(0.793)DEEVAPENFFSLPEK;QIT(0.084)QEEDDS(0.916)DEEVAPENFFSLPEK 139.22 6.48E-07 557510000 311785 251387 266145 265962 281210 232789 357874 266627 346435 TRUE FALSE 292270.9334 269999.955 272458.0851 272787.0352 259124.9009 299991.4053 304214.116 299915.9679 288612.7604 1.012675022 0.935509416 0.944026469 0.945166232 0.897828982 1.039425301 1.054056361 1.039163921 1 18.13877556 2.219474692 24.96456818 1.039485067 0.94497238 0.652834444 0.031034266 125.5128535 164170.9298 0.010729545 0.00793668 165.7580739 -2.219474692 -0.094512688 QITT(ph)SPITVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QITTSPITVR 10 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 QIT(0.026)T(0.702)S(0.27)PIT(0.001)VR;QIT(0.029)T(0.839)S(0.133)PITVR;QIT(0.026)T(0.887)S(0.088)PITVR 163.51 7.20E-05 486386000 1120670 1211880 1116160 1131950 1158220 1094030 1360490 978940 1281390 TRUE FALSE 1050529.265 1301608.856 1142635.842 1160997.753 1067258.073 1409858.701 1156497.155 1101162.814 1067517.731 0.984086011 1.219285468 1.070367085 1.087567653 0.999756765 1.320688791 1.083351706 1.031517119 1 20.0258286 1.274397767 4.322346296 1.011530577 1.121811983 0.133361264 0.098730545 0.343993693 12.68668861 0.073035132 0.022833492 18.81038859 -1.274397767 0.110281407 QITTS(ph)PITVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QITTSPITVR 10 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 QIT(0.019)T(0.356)S(0.625)PITVR;QIT(0.025)T(0.239)S(0.736)PITVR 147.73 2.77E-05 492800000 920660 1054290 974960 991440 1044950 936640 1211630 839260 1051170 TRUE FALSE 863037.534 1132350.729 998086.5116 1016882.029 962883.8421 1207032.763 1029957.33 944043.4584 875722.9362 0.985514366 1.293046787 1.139728641 1.161191499 1.099530231 1.378327223 1.176122364 1.078016139 1 19.74011497 -0.808976233 6.229119851 0.999999993 1.180591014 0.165883098 0.110029949 1.00E-08 1.84E-09 0.096128 0.022657586 0.155247197 0.808976233 0.180591021 QITVNDLPVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QITVNDLPVGR 11 0 P32119;Q06830;A0A0A0MSI0;A0A0A0MRQ5 P32119;Q06830 PRDX2;PRDX1 Peroxiredoxin-2;Peroxiredoxin-1 0 ;;; 203.52 8.45E-08 1648240000 2413870 2715770 2301800 2228570 2662090 2820870 3532120 2185940 3536690 FALSE TRUE 2262790.186 2916848.437 2356399.783 2285758.879 2453020.19 3635209.376 3002511.397 2458859.421 2946393.591 0.767986393 0.989972435 0.7997573 0.775781921 0.83255007 1.233782678 1.019046269 0.834531893 1 21.49051873 2.342807661 23.82398101 1.030880353 0.847405537 0.40316418 0.11307464 7.564028727 1707.46649 0.038358895 0.032093333 220.1951054 -2.342807661 -0.183474816 QIVGT(ph)PVNSEDSDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QIVGTPVNSEDSDTR 15 0 Q5QJE6;J3KP30 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 QIVGT(0.999)PVNS(0.001)EDSDTR 245.32 4.83E-17 215020000 136390 135250 148230 146410 152390 151770 174230 134180 183680 TRUE FALSE 127853.5934 145264.0507 151746.0856 150167.1285 140421.9041 195583.5352 148105.829 150932.6684 153022.6214 0.835520867 0.949297884 0.991657862 0.981339407 0.917654546 1.278134785 0.967868853 0.986342196 1 17.22338542 6.318176288 0.494334863 1.037325938 4.12E-15 0.274737894 0.096038691 25.11922238 1.368686484 0.049500358 21.22479565 2080541.044 -6.318176288 -1.037325938 QIYVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QIYVGR 6 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YAP2;H0YAW6 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ; 109.8 0.068051 425430000 261511 258573 222779 235966 282690 226578 308600 234117 332920 FALSE TRUE 245143.4933 277718.014 228063.4231 242021.287 260488.6677 291987.3904 262328.2949 263347.0228 277353.5013 0.88386659 1.001314253 0.822284276 0.872609453 0.939193724 1.05276259 0.945826513 0.949499543 1 18.08136641 2.474695579 24.99741335 0.982948121 0.90114112 0.400447733 0.052733261 87.82631736 905058.8675 0.018406914 0.015487013 298.3290733 -2.474695579 -0.081807001 QIYYSDKYDDEEFEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QIYYSDKYDDEEFEYR 16 1 P61024;Q5T179 P61024 CKS1B Cyclin-dependent kinases regulatory subunit 1;Cyclin-dependent kinases regulatory subunit 0 ;; 230.82 1.74E-15 1205180000 1405750 975740 846950 757395 1064640 1291380 2051740 864320 2219820 FALSE TRUE 1317766.617 1047984.805 867040.054 776831.038 981027.469 1664180.442 1744100.634 972232.2546 1849317.701 0.712569082 0.566687273 0.468843214 0.420063593 0.530480765 0.899888884 0.943104926 0.525724841 1 20.81856166 2.244116186 24.95834251 0.85099021 0.528299353 0.516275512 0.145128846 96.65473262 434221.9273 0.048477299 0.03949656 175.4349776 -2.244116186 -0.322690857 QKAEADKNDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 138.24 3.94E-05 4334750000 6010300 2160230 3493570 3232710 3222010 2501490 4333600 2840730 3831910 FALSE TRUE 5634126.052 2320175.677 3576439.13 3315666.812 2968966.332 3223629.555 3683816.911 3195401.394 3192339.466 1.76488939 0.726794785 1.120319179 1.038632278 0.930028389 1.009801617 1.153955258 1.000959149 1 21.60618264 4.751892104 24.83271717 1.003655013 1.764889935 0.813959442 0.115255772 909.3532912 1693830.166 0.02813967 0.547209973 56479.66396 -4.751892104 0.761234922 QKDEEDKAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QKDEEDKAR 9 2 O00170 O00170 AIP AH receptor-interacting protein 0 ; 99.283 0.0030609 283470000 729920 424220 500600 506330 577140 348350 607410 496490 880890 FALSE TRUE 684235.6101 455629.6902 512474.4684 519323.285 531813.7525 448912.99 516334.5094 558477.8694 733863.7682 0.932374154 0.62086413 0.698323709 0.707656254 0.724676398 0.611711614 0.703583597 0.761010277 1 19.48515275 0.795686195 2.725484408 0.999891366 0.699097432 0.503762689 0.087522522 0.689377178 7.929970927 0.074872425 0.019818659 6.24721129 -0.795686195 -0.300793934 QKDFLDGVYAFEYYPST(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.25)T(0.75)PGR 163.67 3.12E-11 69016000 164660 196210 121690 140660 227710 108710 177720 168000 323500 TRUE FALSE 154354.2245 210737.5926 124576.5443 144269.5737 209826.5751 140092.8122 151072.5359 188975.1698 269505.7601 0.572730707 0.781940959 0.462240748 0.535311652 0.778560633 0.519813796 0.560554015 0.70119158 1 18.03995658 0.887413061 4.258628758 0.999933103 0.603878284 0.592326237 0.103819599 0.437503481 15.17945184 0.096358186 0.024540248 7.716370302 -0.887413061 -0.396054819 QKDFLDGVYAFEYYPSTPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 143.91 1.48E-07 186530000 473000 638700 362290 391500 676510 311420 601340 575000 971390 FALSE TRUE 443395.7743 685990.0126 370883.6899 401546.5528 623379.6335 401321.8985 511174.6496 646790.0157 809258.7336 0.547903601 0.847676996 0.458300509 0.496190571 0.77030943 0.495912966 0.631657872 0.79923761 1 19.6262415 1.009784931 2.666854745 0.997976653 0.611995286 0.53080988 0.122725606 0.204431493 3.301813585 0.112495982 0.03017254 10.22786369 -1.009784931 -0.385981367 QKDYDFEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QKDYDFEER 9 1 Q96NC0 Q96NC0 ZMAT2 Zinc finger matrin-type protein 2 0 ;; 88.338 0.011721 1778460000 3884420 3529340 3635420 3444610 3867740 2989990 4355620 3281820 4560560 FALSE TRUE 3641301.086 3790656.006 3721653.879 3533004.524 3563983.302 3853151.575 3702535.217 3691562.451 3799373.074 0.958395245 0.997705656 0.979544206 0.929891447 0.938045102 1.014154572 0.974512148 0.971624102 1 21.85732995 2.234869043 24.99903267 0.987445001 0.966926638 0.266105188 0.022788095 200.0265561 1354542.544 0.009076623 0.006956227 171.7390446 -2.234869043 -0.020518363 QKEDVEVVGGS(ph)DGEGAIGLSSDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QKEDVEVVGGSDGEGAIGLSSDPK 24 1 Q8NHZ8 Q8NHZ8 CDC26 Anaphase-promoting complex subunit CDC26 1 QKEDVEVVGGS(1)DGEGAIGLSSDPK;QKEDVEVVGGS(1)DGEGAIGLSSDPK;QKEDVEVVGGS(1)DGEGAIGLSSDPK 243.73 6.51E-38 1238240000 2178620 1085620 1419630 1387790 1422340 1062180 1991200 1202750 1744430 TRUE FALSE 2042264.063 1166000.434 1453304.294 1423403.041 1310635.154 1368814.123 1692638.045 1352915.985 1453273.364 1.405285554 0.802326984 1.000021283 0.979446178 0.901850393 0.941883446 1.164707266 0.930943908 1 20.47087467 QKEECTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QKEECTIR 8 1 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 0 ; 98.048 0.0071125 281350000 495220 464720 457220 457780 502590 390120 628840 421020 469740 FALSE TRUE 464225.0642 499128.3523 468065.4743 469527.4098 463118.6088 502741.3109 534551.2799 473585.2738 391337.3594 1.186252866 1.275442634 1.19606642 1.199802162 1.183425496 1.284674971 1.365960257 1.210171384 1 18.57805332 2.232901746 24.99599414 1.259975566 1.21533173 0 0.098882535 481.730276 2127842.278 0.033380706 0.025324733 170.962849 -2.232901746 -0.044643836 QKEEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QKEEEAR 7 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 ;;; 120.07 0.0042307 2661200000 4483080 3670140 4210510 4167170 3897230 3020010 4670880 3666630 3769640 FALSE TRUE 4202492.025 3941880.984 4310385.286 4274106.637 3591157.276 3891837.861 3970524.906 4124416.827 3140462.731 1.338176054 1.255191136 1.372531902 1.360979895 1.143512146 1.239256184 1.26431206 1.313315005 1 21.58254572 2.751227807 24.92972555 1.216713921 1.325767006 0.354902603 0.090056018 961.1423613 1891580.696 0.025386172 0.02676181 563.9333864 -2.751227807 0.109053085 QKEELQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QKEELQR 7 1 P80303-2;P80303;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 81.594 0.024421 200320000 221730 371060 273800 275760 359820 231620 327370 317620 275140 FALSE TRUE 207852.3151 398533.6685 280294.6653 282836.4685 331561.1886 298484.934 278283.9077 357275.5562 229217.3565 0.906791345 1.738671428 1.222833513 1.233922565 1.446492507 1.302191677 1.214061238 1.558675842 1 17.80635676 -1.414018655 3.393193987 0.996456451 1.34511919 0.171889728 0.223416674 6901637.066 4427901.353 169979.7516 0.047438254 0.03854618 1.414018655 0.34866274 QKEIEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QKEIEER 7 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 0 ; 78.516 0.04403 295100000 654580 793350 692340 694760 805580 617120 852280 660080 842390 FALSE TRUE 613611.0063 852090.4595 708762.6317 712588.7178 742312.9964 795272.5259 724488.5262 742492.441 701789.667 0.874351726 1.214167862 1.009935975 1.015387874 1.057742841 1.133206377 1.032344248 1.057998537 1 19.42067918 0.623331098 1.531719773 1.000185588 1.06288918 0.011012753 0.087786794 5.355928641 17.20388899 0.07620632 0.022017613 4.200791228 -0.623331098 0.062703592 QKETS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QKETSPR 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QKET(0.114)S(0.886)PR 78.334 0.021569 2646500000 4189200 2724000 3751200 3399600 3327000 2669800 3705100 3055300 3544200 TRUE FALSE 3927005.45 2925687.794 3840180.235 3486839.492 3065710.84 3440527.919 3149554.651 3436760.931 2952650.124 1.329993492 0.990868431 1.300587633 1.180918614 1.038291268 1.165233866 1.066687389 1.163958067 1 21.49357898 2.772999044 20.58317545 1.095393443 1.182304252 0.221260429 0.102857001 140.2000734 83793.3363 0.029314905 0.031087665 592.9240192 -2.772999044 0.086910809 QKFNDS(ph)EGDDT(ph)EETEDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QKFNDSEGDDTEETEDYR 18 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 2 QKFNDS(1)EGDDT(1)EETEDYR;QKFNDS(1)EGDDT(0.999)EET(0.001)EDYR;QKFNDS(1)EGDDT(1)EETEDYR;QKFNDS(1)EGDDT(0.999)EET(0.001)EDYR 192.2 4.27E-14 968780000 1624920 1028170 1200300 1171900 1384080 1046400 1772560 1184610 2261150 TRUE FALSE 1523219.158 1104296.777 1228771.683 1201972.938 1275379.94 1348478.693 1506781.084 1332511.166 1883749.457 0.80861027 0.586222744 0.652301015 0.638074736 0.677043295 0.715848218 0.799884017 0.707371758 1 20.84517567 0.46180859 0.466396572 1.021167668 0.648012388 0.676753685 0.066361176 1.127717826 0.444259896 0.117957969 0.035974829 2.896066898 -0.46180859 -0.37315528 QKFNDS(ph)EGDDTEETEDYR ddPTM_SK-BR-3_Pertuzumab_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(0.999)EGDDT(0.001)EETEDYR;QKFNDS(1)EGDDTEETEDYR 280.89 1.65E-39 17497550000 17114430 11959770 13253510 12873870 14099230 11030980 17154110 11333360 20166010 TRUE FALSE 16043268.38 12845283.81 13567889.52 13204235.3 12991933.35 14215444.85 14582010.46 12748354.94 16800172.65 0.954946637 0.764592369 0.807604171 0.78595831 0.773321419 0.846148736 0.867967893 0.758822853 1 24.00197272 -1.561319928 3.907678063 1.003543845 0.816474982 0.476264602 0.059249203 0.001718813 0.000192956 0.05390381 0.01247727 0.027458706 1.561319928 -0.187068864 QKGESRPET(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QKGESRPETPK 11 2 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 QKGES(0.01)RPET(0.99)PK;QKGES(0.205)RPET(0.795)PK 70.98 0.068952 34749000 172930 85752 105017 107535 109581 84849 169332 109663 132576 TRUE FALSE 162106.62 92101.1673 107508.0528 110294.5302 100974.9503 109343.5289 143942.2386 123354.6669 110448.2091 1.467716147 0.833885565 0.973379774 0.998608588 0.91422895 0.989998206 1.303255523 1.116855293 1 16.7530105 1.77034412 25 1.171016835 0.994926275 0.044532003 0.184434823 48.30650536 38015.82623 0.078075706 0.043309831 58.93104194 -1.77034412 -0.17609056 QKIDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QKIDDR 6 1 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 0 ; 74.335 0.073505 320205000 1188300 1191880 1211870 1178070 1231280 898220 1423310 1159740 1281950 FALSE TRUE 1113926.424 1280128.035 1240616.129 1208301.271 1134580.236 1157521.533 1209897.879 1304536.092 1067984.263 1.043017638 1.198639418 1.161642705 1.131384902 1.062356698 1.08383763 1.132879875 1.22149374 1 20.02645896 2.996605726 21.76042577 1.107670087 1.151383208 0.031492775 0.068221044 67.34991612 431803.8155 0.018788045 0.021936544 992.214858 -2.996605726 0.043713121 QKIDDRDS(ph)DEEGASDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QKIDDRDSDEEGASDR 16 2 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 QKIDDRDS(1)DEEGASDR;QKIDDRDS(1)DEEGASDR;QKIDDRDS(1)DEEGASDR;QKIDDRDS(1)DEEGASDR 279.47 1.07E-35 992500000 2140200 1553020 1741820 1686630 1776770 1422230 2235520 1410720 2362350 TRUE FALSE 2006248.702 1668007.217 1783136.793 1729911.781 1637229.651 1832804.713 1900324.53 1586851.497 1968058.524 1.019405002 0.847539439 0.9060385 0.878994075 0.831900897 0.931275514 0.965583344 0.806303003 1 20.90834169 QKIPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QKIPAR 6 1 A0A3B3ISL2;A0A3B3IRU6;Q9GZU2-2;Q9GZU2-4;Q9GZU2 A0A3B3ISL2 PEG3 Paternally-expressed gene 3 protein 0 ;; 98.03 0.036843 3881800000 3492160 3957550 3378910 3913090 4001290 3001430 5697800 3522550 6269300 FALSE TRUE 3273591.939 4250571.12 3459059.341 4013506.514 3687044.824 3867894.117 4843467.786 3962348.122 5222913.329 0.626775084 0.813831449 0.662285419 0.768442105 0.705936437 0.74056257 0.92734983 0.758647114 1 22.31642333 1.102817214 0.525603139 0.99877014 0.709769204 0.582382824 0.073427149 0.622517073 0.442209532 0.075540007 0.037289874 12.67118449 -1.102817214 -0.289000936 QKLDILDQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QKLDILDQER 10 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 142.97 3.17E-05 418000000 1165350 1032360 1021260 1042920 1292630 850950 1313490 1041490 1547510 FALSE TRUE 1092412.824 1108797.009 1045484.769 1069683.093 1191112.054 1096605.451 1116544.368 1171522.319 1289220.584 0.84734361 0.860052207 0.810943281 0.829713011 0.923900897 0.850595674 0.866061543 0.908705875 1 20.2980677 0.187537924 0.409226841 1.020622416 0.838408185 0.735996567 0.028098346 1.77178969 0.453656772 0.090462864 0.019270933 1.540061002 -0.187537924 -0.18221423 QKLDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QKLDPK 6 1 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 0 ;; 95.62 0.039342 5885050000 5493220 4189840 4426500 4352020 4920400 3527320 6438200 3616000 7313700 FALSE TRUE 5149409.166 4500060.113 4531498.67 4463700.201 4533971.632 4545600.023 5472851.679 4067465.56 6092996.222 0.845135788 0.738562761 0.743722547 0.732595268 0.744128417 0.746036902 0.898220101 0.667564103 1 22.53872042 -5 0.322449033 3.242965053 0.757600015 0.546894166 0.065784139 247.7228691 2.182490381 379.4695416 0.054693449 1.00E-05 5 -2.485365038 QKLDSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QKLDSQR 7 1 O15371-2;O15371;O15371-3 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 67.993 0.058057 40795000 64291 186750 58812 58268 183760 60278 60705 142450 186630 FALSE TRUE 60267.14107 200577.1643 60207.04841 59763.25553 169328.2309 77679.28007 51602.84881 160235.1961 155480.2473 0.387619277 1.290049172 0.38723278 0.384378444 1.08906587 0.499608673 0.331893277 1.030582333 1 17.24637178 1.196265476 24.98968016 1.015293224 0.651940058 0.198982331 0.322471264 295.0428148 174316.659 0.306444751 0.076613568 15.7132303 -1.196265476 -0.363353165 QKLEAQLTENNIVKEELALLDGSNVVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QKLEAQLTENNIVKEELALLDGSNVVFK 28 2 O15212;A2AB88 O15212 PFDN6 Prefoldin subunit 6 0 ; 132.77 1.01E-05 30739000 78487 57272 72980 73906 81794 39146 60450 51273 68058 FALSE TRUE 73574.63877 61512.47847 74711.12006 75802.55308 75370.22918 50446.81472 51386.08369 57674.54692 56698.68013 1.297642884 1.084901418 1.317687112 1.33693682 1.329311882 0.889735257 0.906301233 1.017211455 1 15.79102753 2.236017077 24.99998963 0.939311713 1.256551957 0.789882858 0.081611988 31.60211381 310605.7129 0.031549607 0.024384594 172.1936281 -2.236017077 0.317240244 QKLPDGSEIPLPPILLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QKLPDGSEIPLPPILLGR 18 1 Q96KP4;J3QKT2;A0A087WYZ1;J3KSV5;J3QRD0;J3QKQ0;J3QLU1;J3QR27;A0A087WVS2;J3QL02;J3KRD5;J3QQN6 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 175.33 3.31E-12 442380000 1551100 1387060 1190880 1147090 1417490 1399720 2311700 1220390 2166710 FALSE TRUE 1454019.42 1489759.366 1219128.236 1176526.271 1306166.053 1803796.441 1965082.046 1372758.378 1805072.104 0.805518747 0.82531848 0.675390326 0.651789072 0.723608797 0.99929329 1.088644626 0.760500578 1 20.78362504 2.239020121 24.99998147 0.983326725 0.736308694 0.567383149 0.097185374 8.253742656 449088.3274 0.03453289 0.027262396 173.3884327 -2.239020121 -0.247018031 QKLYTLQDK ddPTM_SK-BR-3_Pertuzumab_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 ; 131.82 0.00029406 1404610000 1451920 2001090 1313640 1440200 2732800 1717810 3695090 2142680 6456900 FALSE TRUE 1361046.919 2149252.786 1344800.161 1477157.97 2518176.912 2213713.861 3141045.558 2410198.315 5379201.677 0.253020244 0.399548653 0.249999952 0.274605426 0.468132088 0.411532044 0.583924111 0.448058738 1 22.35896065 -0.018929918 0.316821708 1.167766479 0.269282782 0.881452015 0.075625077 1.662081084 0.243536873 0.43016609 0.080825765 0.957348546 0.018929918 -0.898483698 QKPELLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QKPELLNK 8 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 75.378 0.030632 0 499370 427750 466060 460220 494610 360870 568660 464210 593280 FALSE TRUE 468115.3231 459421.0551 477115.1633 472030.0244 455765.3258 465047.3108 483394.7122 522167.6404 494257.7353 0.947107733 0.929517178 0.965316533 0.955028097 0.922120775 0.94090042 0.978021542 1.056468322 1 18.91490402 1.473457724 3.732301461 1.027507492 0.944361318 0.781501463 0.01833642 0.086964091 2.399247386 0.011897523 0.004425236 29.74799666 -1.473457724 -0.083146174 QKPQAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 QKPQAER 7 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;;;;;;; 116.25 0.0050141 14059530000 7702710 7978280 6433940 6405310 8282460 5667220 8725520 7359040 9447710 FALSE TRUE 7220611.131 8569000.153 6586556.095 6569681.099 7631989.001 7303254.414 7417209.28 8277832.343 7870826.166 0.917389227 1.088704028 0.836831605 0.834687612 0.969655388 0.927889177 0.94236731 1.051710731 1 22.90808365 1.281463623 8.331631956 1.025675121 0.935429182 0.230188464 0.071724279 0.367605862 64.44355071 0.050324746 0.018082074 19.11893174 -1.281463623 -0.090245938 QKQPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QKQPER 6 1 Q9Y5P6;Q9Y5P6-2 Q9Y5P6 GMPPB Mannose-1-phosphate guanyltransferase beta 0 69.344 0.0855 90591000 145430 142870 141170 133130 137720 110400 141390 122610 155700 FALSE TRUE 136327.7959 153448.2435 144518.6191 136546.3412 126904.0267 142270.6878 120189.8821 137918.1284 129712.6641 1.050998349 1.182985829 1.114144251 1.052683191 0.978347238 1.096814168 0.926585564 1.063258775 1 16.98495981 3.147448415 2.617750413 1.008581316 1.132850914 0.406698753 0.055670362 0.207089927 2.88144123 0.015693573 0.019967932 1404.262878 -3.147448415 0.124269598 QKS(ph)AEPS(ph)PTVMSTSLGSNLSELDR ddPTM_SK-BR-3_Pertuzumab_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(0.936)PT(0.063)VMS(0.001)TSLGSNLSELDR 62.213 0.031224 57744000 48612 41358 43454 48581 39496 27737 38514 30586 45594 TRUE FALSE 45569.46169 44420.18935 44484.7494 49827.67071 36394.14348 35744.22163 32739.18325 34404.72943 37984.06685 1.199699386 1.169442691 1.171142352 1.311804523 0.958142361 0.94103198 0.861918851 0.905767399 1 15.21310676 2.621958868 5.539923987 0.915657958 1.198027982 0.870131852 0.0534997 0.07396372 3.097804876 0.016983558 0.015955472 418.7539035 -2.621958868 0.282370024 QKS(ph)DAEEDGGTVS(ph)QEEEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QKSDAEEDGGTVSQEEEDR 19 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 2 QKS(1)DAEEDGGT(0.098)VS(0.902)QEEEDR;QKS(1)DAEEDGGT(0.001)VS(0.999)QEEEDR 187.08 1.09E-14 1798170000 1555190 824650 902430 899550 950040 781240 1434600 976070 665280 TRUE FALSE 1457853.434 885707.944 923836.0658 922633.9759 875427.6907 1006771.306 1219495.048 1097934.488 554240.4701 2.630362654 1.598057146 1.66685061 1.664681714 1.579508783 1.816488257 2.200299534 1.980971342 1 19.08015253 1.993201976 24.58825322 1.897441137 1.761407701 0 0.439349442 1312.318879 4746624.306 0.154570333 0.109824054 98.44688433 -1.993201976 -0.136033436 QKS(ph)DAEEDGGTVS(ph)QEEEDRKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 2 QKS(1)DAEEDGGT(0.017)VS(0.983)QEEEDRKPK;QKS(1)DAEEDGGTVS(1)QEEEDRKPK;QKS(1)DAEEDGGT(0.193)VS(0.807)QEEEDRKPK;QKS(1)DAEEDGGTVS(1)QEEEDRKPK;QKS(1)DAEEDGGT(0.208)VS(0.792)QEEEDRKPK 291.68 1.01E-55 9374720000 8453160 2065120 3133920 3084250 3915490 2208960 5600660 2636590 4226080 TRUE FALSE 7924091.805 2218023.634 3208258.062 3163397.077 3607983.21 2846650.893 4760893.027 2965774.065 3520719.946 2.250702108 0.629991498 0.911250571 0.898508579 1.02478563 0.808542269 1.352249852 0.842377159 1 21.74743904 4.746905477 24.95211864 0.938634811 2.250702779 0.834391644 0.184413639 440.5726268 1317334.139 0.04677906 0.537449099 55834.86582 -4.746905477 1.312067968 QKS(ph)DAEEDGGTVSQEEEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QKSDAEEDGGTVSQEEEDR 19 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 QKS(1)DAEEDGGTVSQEEEDR;QKS(1)DAEEDGGTVSQEEEDR 315.18 7.03E-62 1235600000 1104849 521731 641832 589412 694049 530756 886793 654955 676480 TRUE FALSE 1035698.473 560360.5061 657056.5581 604537.3098 639541.1912 683976.6411 753826.6222 736727.5735 563571.1178 1.837742284 0.994303094 1.165880467 1.072690368 1.134801219 1.213647434 1.337589167 1.307248633 1 19.10423815 4.747443109 24.94727029 1.16284307 1.837742643 0.779174719 0.114414917 582.0724035 1634766.26 0.029326414 0.351711289 55904.02901 -4.747443109 0.674899572 QKS(ph)DAEEDGGTVSQEEEDRKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 QKS(0.999)DAEEDGGT(0.001)VSQEEEDRKPK;QKS(1)DAEEDGGTVSQEEEDRKPK;QKS(1)DAEEDGGTVSQEEEDRKPK;QKS(1)DAEEDGGTVSQEEEDRKPK 237.7 1.12E-30 7789650000 6261700 1647070 2600300 2428620 3432850 1737364 4103540 2345090 4841240 TRUE FALSE 5869791.374 1769020.777 2661980.344 2490942.501 3163247.808 2238912.783 3488252.272 2637879.649 4033205.768 1.455366205 0.438614065 0.660016001 0.617608583 0.784301122 0.5551199 0.86488329 0.654040433 1 21.94349558 -1.114701247 4.605154403 1.00002263 0.716181577 0.057944214 0.277461449 6.01E-05 1.15E-05 0.238230472 0.056146761 0.076788954 1.114701247 -0.283841052 QKS(ph)PAQSDSTTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QKSPAQSDSTTQR 13 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 QKS(1)PAQSDSTTQR;QKS(1)PAQSDSTTQR 192.85 1.43E-06 625290000 123328 118747 115879 119266 147545 91958.5 152943 122942 153321 TRUE FALSE 115609.1206 127539.1514 118627.7046 122326.5675 135957.4109 118505.4261 130010.617 138291.5793 127730.7346 0.905100256 0.998500101 0.928732658 0.957690941 1.064406396 0.927775343 1.017849129 1.082680529 1 16.96274618 2.402292028 0.702588183 1.030057547 0.949548707 0.302349549 0.048916634 0.962381281 0.945694569 0.037434733 0.027660118 252.5178181 -2.402292028 -0.08050884 QKS(ph)PEIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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 115.92 0.0014359 79120840000 29604540 20032210 25055760 22333380 22787170 18969200 27172070 18681900 30328890 TRUE FALSE 27751644.69 21515415.67 25650094.46 22906492.34 20997557.59 24445300.1 23097870.36 21014376.34 25266802.33 1.098344156 0.85152903 1.015169792 0.906584539 0.831033437 0.967486894 0.914158826 0.831699084 1 24.59073976 4.751850894 24.67253348 0.916935225 1.098344298 0.439726057 0.06510026 1732.946818 3217034.211 0.014357923 0.272183697 56474.3049 -4.751850894 0.181409073 QKS(ph)PEIHRR ddPTM_SK-BR-3_Pertuzumab_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 130.1 0.00019345 18108840000 7907637 6663408 6669125 6985132 7844367 5212266 8857331 6085002 13534400 TRUE FALSE 7412712.116 7156773.662 6827319.794 7164382.313 7228302.058 6716962.58 7529256.444 6844727.894 11275421.2 0.657422191 0.634723398 0.605504634 0.635398198 0.641067143 0.595717221 0.667758331 0.607048532 1 23.42667799 -1.671678803 2.770231905 1.045517794 0.63039 0.963072812 0.022733483 6324377.022 5503715.227 2025674.779 0.005404126 0.021297136 1.671678803 -0.415127794 QKSDAEEDGGT(ph)VSQEEEDRKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 QKSDAEEDGGT(0.841)VS(0.159)QEEEDRKPK 50.857 0.068432 639180000 223770 223690 210580 226930 276620 177130 261790 213170 279390 TRUE FALSE 209764.6351 240252.2403 215575.057 232753.408 254895.381 228264.5555 222537.0198 239784.7437 232758.0041 0.901213413 1.032197545 0.926176773 0.999980254 1.095108983 0.980694763 0.956087507 1.030189036 1 17.82847125 4.753190642 23.98449896 0.995899415 0.901213295 0.315390055 0.046003329 2033.148537 3333047.329 0.010934594 0.232310086 56648.79049 -4.753190642 -0.09468612 QKSDAEEDGGTVS(ph)QEEEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QKSDAEEDGGTVSQEEEDR 19 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 QKSDAEEDGGT(0.001)VS(0.999)QEEEDR 147.87 6.12E-08 332950000 264320 135350 164660 143360 186210 153200 258270 200790 175520 TRUE FALSE 247776.683 145371.4548 168565.813 147038.8603 171585.8177 197426.353 219544.8112 225859.0735 146224.5781 1.694494087 0.994165664 1.152787138 1.00556871 1.173440334 1.350158472 1.501422087 1.544604036 1 17.1578263 2.184126411 4.123191698 1.408055426 1.158387205 0.04550852 0.243164973 0.345269123 12.05064334 0.086677206 0.063664178 152.8010754 -2.184126411 -0.249668221 QKSDAEEDGGTVS(ph)QEEEDRKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 QKSDAEEDGGT(0.002)VS(0.998)QEEEDRKPK;QKSDAEEDGGT(0.011)VS(0.989)QEEEDRKPK;QKSDAEEDGGT(0.009)VS(0.991)QEEEDRKPK;QKSDAEEDGGTVS(1)QEEEDRKPK 213.37 6.97E-24 2884880000 3153790 1190010 1558200 1526410 2019670 1187110 2376650 1453130 2734860 TRUE FALSE 2956399.914 1278119.579 1595161.24 1565580.265 1861053.265 1529809.386 2020293.396 1634556.479 2278394.198 1.297580514 0.560973856 0.70012522 0.687141964 0.816826722 0.671441925 0.88671811 0.717416012 1 21.11958595 -0.270979779 0.650744938 1.017652064 0.757400187 0.069744573 0.202432009 16.86602946 6.436417609 0.94537904 0.069968403 0.535821605 0.270979779 -0.260251876 QKSPEIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QKSPEIHR 8 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 98.033 0.0071224 235150000 269170 197810 223480 229140 235130 191510 293210 196310 290470 FALSE TRUE 252323.1302 212456.0582 228781.0511 235020.1203 216663.8383 246795.8281 249245.8825 220819.7356 241988.6805 1.042706335 0.877958662 0.945420466 0.97120295 0.895346997 1.019865175 1.029989841 0.912520929 1 17.88458004 2.225863103 24.98351444 0.998002505 0.938147567 0.124450894 0.054103755 331.6278226 652503.5504 0.018855354 0.014016775 168.2143737 -2.225863103 -0.059854938 QKT(ph)VDIDDAQILPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QKTVDIDDAQILPR 14 1 Q6GYQ0-2;A0A1B0GUI1;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5 Q6GYQ0-2 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 1 QKT(1)VDIDDAQILPR 99.021 0.0037931 280960000 68992 75275 59734 70552 73501 56670 129230 67230 112580 TRUE FALSE 64673.91387 80848.43932 61150.91869 72362.48376 67728.52795 73029.70904 109853.1612 75623.81349 93789.67071 0.68956329 0.862018586 0.652000569 0.771540013 0.722132058 0.778654072 1.171271425 0.806312816 1 16.51714142 1.886640879 7.882694161 1.005579789 0.746245584 0.564980095 0.102182893 0.180583423 11.38331137 0.03915159 0.024460582 77.02662669 -1.886640879 -0.259334205 QKVDLQSLPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QKVDLQSLPTR 11 1 Q9C005 Q9C005 DPY30 Protein dpy-30 homolog 0 ; 128.31 0.0002448 333320000 527200 532370 451980 435770 608290 465460 668690 515730 847360 FALSE TRUE 494203.4931 571787.2287 462701.179 446952.596 560517.3571 599830.7459 568426.1423 580120.0258 705930.1418 0.70007422 0.809977071 0.655448962 0.63313998 0.794012501 0.849702698 0.805215854 0.821781068 1 19.4291659 2.505862183 5.350634645 0.84546706 0.710357649 0.548150771 0.070832172 0.167662973 13.6216078 0.023002796 0.020800341 320.5252025 -2.505862183 -0.135109411 QKVDSLLENLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QKVDSLLENLEK 12 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;G3V576;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4;A0A0G2JNQ3;O60812;B2RXH8;A0A0G2JPF8;P0DMR1;B7ZW38 B4DY08;P07910;P07910-2 HNRNPC;HNRNPCL1;HNRNPCL2;HNRNPCL4;HNRNPCL3 Heterogeneous nuclear ribonucleoproteins C1/C2;Heterogeneous nuclear ribonucleoprotein C-like 1;Heterogeneous nuclear ribonucleoprotein C-like 2;Heterogeneous nuclear ribonucleoprotein C-like 4;Heterogeneous nuclear ribonucleoprotein C-like 3 0 ; 203.74 1.11E-07 3209400000 8730000 5245300 6376900 5685500 7341400 5275600 9875500 6148100 10741900 FALSE TRUE 8183604.883 5633667.47 6528163.079 5831399.556 6764836.058 6798580.078 8394760.455 6915703.819 8949007.495 0.91447067 0.629529864 0.729484592 0.651625285 0.755931433 0.759702133 0.938066088 0.772790035 1 23.09329626 1.89744592 3.792314729 0.893358996 0.71879572 0.390777006 0.094619387 0.216710181 5.237209982 0.041927111 0.023489839 78.96705107 -1.89744592 -0.174563276 QKVEEELNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QKVEEELNR 9 1 P15924 P15924 DSP Desmoplakin 0 117.7 0.0010118 316090000 755280 585430 644910 682290 738360 500090 784520 640710 900030 FALSE TRUE 708008.373 628775.8463 660207.5697 699798.7165 680372.184 644457.8647 666888.5091 720704.0539 749809.1786 0.944251409 0.838581154 0.880500784 0.933302414 0.907393779 0.859495833 0.88941097 0.961183291 1 19.51616396 1.115391847 3.25720919 0.998496655 0.886469761 0.574661656 0.031744978 0.150482202 2.938903423 0.029687963 0.007870522 13.04343104 -1.115391847 -0.112026894 QKWDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QKWDQK 6 1 O15371-2;O15371;B0QYA5;B0QYA6 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ; 105.12 0.030325 821640000 873970 731190 780770 797530 944550 714200 1105330 759600 1229800 FALSE TRUE 819269.7778 785328.0684 799290.2331 817995.97 870368.8531 920377.9459 939596.0279 854437.7321 1024538.435 0.799647675 0.766518894 0.780146655 0.798404376 0.849522891 0.89833423 0.917092025 0.833973332 1 19.96654268 2.533491697 1.469212371 0.911700867 0.777203909 0.689775324 0.040093907 0.208428907 0.911693991 0.0169008 0.013488302 341.5794206 -2.533491697 -0.134496958 QKYNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QKYNVR 6 1 P61254;E5RIT6;J3QRI7;J3QQQ9;J3QQV1;J3QRC4;J3KSS0;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 ; 109.88 0.026612 1714470000 1399390 2017250 1218130 1143240 2064050 1034590 1941310 1788370 2723600 FALSE TRUE 1311804.678 2166609.289 1247024.619 1172577.474 1901947.839 1333259.338 1650228.588 2011651.931 2269013.565 0.578138755 0.954868372 0.549588878 0.516778521 0.838226738 0.587594256 0.727288992 0.886575542 1 21.1136338 1.127104005 2.695923537 0.995761741 0.687626839 0.412381611 0.135335639 0.257990315 3.500460797 0.123216614 0.033632879 13.39997552 -1.127104005 -0.308134902 QKYPEQQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QKYPEQQGR 9 1 A0A0G2JKR7;P28702;P28702-3 A0A0G2JKR7 RXRB Retinoic acid receptor RXR-beta 0 ; 79.974 0.023188 54175000 87434 93704 89531 85287 106210 73990 108586 91238 129038 FALSE TRUE 81961.66201 100641.9417 91654.7176 87475.60881 97868.69503 95349.71187 92304.53736 102629.2651 107500.7242 0.762428929 0.936197802 0.852596281 0.813721112 0.910400332 0.886968089 0.858641075 0.954684407 1 16.71398685 1.096929276 3.480047388 0.999009415 0.867626901 0.506036864 0.048686247 0.174270222 3.91504939 0.042296736 0.011070384 12.50055443 -1.096929276 -0.131382514 QLAAEEERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLAAEEERR 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 107.45 0.0044428 406840000 343830 556460 426040 514900 489440 396380 430810 393570 393130 FALSE TRUE 322310.2941 597660.8774 436145.87 528113.2057 451001.3567 510808.4713 366214.0399 442708.0809 327514.0633 0.984111311 1.824840349 1.33168593 1.612490164 1.377044247 1.559653549 1.118162794 1.351722355 1 18.32119733 1.318996246 0.840934077 1.028063223 1.491632289 0.227236057 0.236154131 0.645486669 0.992487442 0.196971746 0.07530577 20.84472864 -1.318996246 0.463569066 QLAAENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLAAENR 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 85.212 0.048802 68665000 119960 218500 118040 127330 193860 106310 152700 172920 164060 FALSE TRUE 112451.9177 234677.9673 120839.9645 130597.5034 178635.0176 136999.9712 129804.0526 194509.4426 136677.3261 0.822754739 1.717021938 0.884125904 0.955516961 1.306983555 1.002360633 0.949711677 1.423128826 1 17.0604144 3.854461613 8.346291197 1.065967025 1.328513042 0.072940507 0.270725621 0.447883238 29.33381127 0.062615526 0.113239285 7152.561699 -3.854461613 0.262546017 QLAEDFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QLAEDFLR 8 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;; 122.13 0.0032649 226569000 387732 789470 354045 339157 847310 256936 347628 682350 737740 FALSE TRUE 363464.5462 847923.1802 362443.1146 347860.3428 780765.6905 331109.2522 295504.4086 767542.8995 614606.428 0.591377717 1.379619772 0.589715789 0.565988781 1.270350675 0.538733793 0.480802665 1.248836433 1 19.22930333 3.895312356 8.402071664 0.767237543 1.033986433 0.024204747 0.343334774 0.620928006 57.49355224 0.082149556 0.148674529 7858.005994 -3.895312356 0.26674889 QLAPIWDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLAPIWDK 8 0 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ; 120.15 0.0036205 668100000 2489160 2874600 2458500 2269880 2830600 1783750 3044200 2300190 2547210 FALSE TRUE 2333367.919 3087438.375 2516816.781 2328128.964 2608296.094 2298689.668 2587750.471 2587373.785 2122064.195 1.099574614 1.454922232 1.186022924 1.097105813 1.229131569 1.08323286 1.219449664 1.219272155 1 21.01703687 -4.999998477 0.062144588 0.238506436 1.528973105 0.226477529 0.108164669 457.2981251 2.070699674 52.61567421 8.254819141 1.00E-05 4.999998477 1.290466669 QLCAEHGISPEGIVEEFATEGTDR ddPTM_SK-BR-3_Pertuzumab_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 ;; 155.49 4.27E-08 51186700 42835 45638 44835.9 44235.5 45103 45189 57757 41513.6 53026.9 FALSE TRUE 40154.03381 49017.08501 45899.42872 45370.65782 41560.79232 58234.33072 49096.87404 46696.66434 44176.36782 0.908948286 1.109577075 1.039004132 1.02703459 0.940792427 1.318223602 1.111383223 1.057050786 1 15.43098718 QLCAEHGISPEGIVEEFATEGTDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLCAEHGISPEGIVEEFATEGTDRK 25 1 P23258;K7EIS0;Q9NRH3;K7EKE5 P23258 TUBG1;TUBG2 Tubulin gamma-1 chain;Tubulin gamma chain;Tubulin gamma-2 chain 0 175.48 1.11E-12 38999000 64590 49309 55176 52916 57828 49041 84122 52808 93612 FALSE TRUE 60547.4272 52959.88967 56484.80078 54273.91415 53286.42215 63198.34059 71508.68705 59401.19504 77987.55244 0.776372963 0.679081315 0.724279696 0.695930472 0.683268297 0.810364457 0.916924366 0.761675334 1 16.25095625 2.050428595 3.949572962 0.880718952 0.708784433 0.627862736 0.063671787 0.130270242 4.239584788 0.023523656 0.01586246 112.3126295 -2.050428595 -0.171934519 QLDDLKVELSQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QLDDLKVELSQLR 13 1 P42766;F2Z388 P42766 RPL35 60S ribosomal protein L35 0 ;;; 189.86 4.47E-06 4313229000 2781200 2972780 2620990 2631120 3311740 2118750 3171960 2573070 3811410 FALSE TRUE 2607129.657 3192887.724 2683161.121 2698638.994 3051649.299 2730398.73 2696354.045 2894323.454 3175261.048 0.82107569 1.005551253 0.845020639 0.849895159 0.961070366 0.859897403 0.849175549 0.911522993 1 21.59844377 0.972541179 22.40178639 1.000000003 0.890060213 0.283067217 0.057118427 1006.452751 821098.8316 0.052998681 0.01324967 9.387310403 -0.972541179 -0.10993979 QLEAIDQLHLEYAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QLEAIDQLHLEYAK 14 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ;; 160.81 4.70E-06 1075100000 1415980 1004110 1090200 982880 984590 903070 1455930 1024690 1369010 FALSE TRUE 1327356.339 1078455.349 1116060.059 1008102.365 907264.273 1163771.649 1237626.813 1152624.802 1140513.387 1.163823551 0.945587629 0.978559368 0.883902264 0.795487614 1.020392801 1.08514887 1.010619266 1 20.12125195 -0.336323804 7.81652205 1.000000789 0.981829336 0.000916102 0.1009675 0 0 0.097835677 0.02306009 0.460973751 0.336323804 -0.018171453 QLEDLVEELSFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLEDLVEELSFSR 13 0 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;A0A0A0MRE9;A0A087WX84;Q99996-4 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 0 ; 114.82 0.0016591 8642400 29427 27183 26414.2 26550 27626 22608.1 33288 23883 29521 FALSE TRUE 27585.2166 29195.6576 27040.7573 27231.31795 25456.3654 29134.69146 28296.77343 26864.84512 24593.75439 1.121635036 1.187116743 1.099496924 1.107245259 1.035074393 1.184637815 1.150567456 1.092344207 1 14.58600437 0.920791407 4.87468403 1.000025273 1.129811985 0.452645769 0.043718195 0.406276393 22.63392117 0.041761807 0.010568759 8.332808607 -0.920791407 0.129786712 QLEDTVALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLEDTVALR 9 0 Q9Y5S2 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 0 66.299 0.077366 0 319410 437190 416330 415220 399630 379490 375240 381980 342850 FALSE TRUE 299418.6983 469560.0025 426205.5442 425875.2482 368244.6718 489042.6025 318976.2456 429671.0438 285626.1201 1.048288925 1.643967304 1.492179861 1.491023468 1.289254189 1.712177452 1.116761469 1.504312854 1 18.12376839 0.23215083 0.548133349 0.976078796 1.464540021 0.242555311 0.215282367 3.468869572 1.492930153 0.39618678 0.088441078 1.706675011 -0.23215083 0.488461225 QLEEAEEEAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QLEEAEEEAQR 11 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 202.96 8.90E-08 1793940000 1390687 1390475 1359448 1480752 1393806 1177219 1626855 1214120 1243890 FALSE TRUE 1303646.383 1493427.216 1391694.749 1518750.603 1284342.099 1517063.015 1382923.196 1365705.555 1036276.723 1.258009906 1.441147121 1.342975981 1.465584018 1.239381403 1.463955506 1.334511492 1.317896585 1 19.98297788 0.539167944 1.492180086 1.000044688 1.37323555 0.679618626 0.077803588 1.067849878 2.895739175 0.063504206 0.018402944 3.460731801 -0.539167944 0.373190862 QLEEEDGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLEEEDGSR 9 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 133.99 0.00060807 274990000 162650 216540 203250 225340 229750 192180 212990 210850 178300 FALSE TRUE 152470.0268 232572.8469 208071.186 231122.6059 211706.3618 247659.2462 181054.1268 237175.0866 148540.5781 1.026453705 1.565719279 1.400770002 1.555956014 1.425242613 1.667283441 1.218886644 1.596702326 1 17.18049757 -0.832476466 10.5116825 0.999999999 1.438884731 0.336200706 0.190613746 0 0 0.160226428 0.037765731 0.147069811 0.832476466 0.438884732 QLEEEDGSRDSPLFDFIESCLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QLEEEDGSRDSPLFDFIESCLR 22 1 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ;; 158.89 1.85E-11 64624000 32348.7 57250 38540.4 42035 58586 29336.6 57674 43419 94613 FALSE TRUE 30324.05261 61488.84957 39454.59649 43113.68927 53984.89188 37805.60018 49026.31912 48839.95773 78821.47908 0.384718137 0.780102712 0.500556409 0.546978942 0.684900772 0.479635762 0.621991869 0.619627522 1 16.2663012 0.425091558 1.62669375 1.000002341 0.584565157 0.594919114 0.109981099 2.844467983 7.308951665 0.094687542 0.02693403 2.661286055 -0.425091558 -0.415437183 QLEEPGAGTPS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLEEPGAGTPSPVR 14 0 Q96P11-2;Q63ZY6;Q96P11-5;Q96P11;Q96P11-4;Q63ZY6-5;Q63ZY6-4 Q96P11-2 NSUN5;NSUN5P2 Probable 28S rRNA (cytosine-C(5))-methyltransferase;Putative methyltransferase NSUN5C 1 QLEEPGAGTPS(1)PVR;QLEEPGAGTPS(1)PVR 295.93 1.33E-43 909490000 1204050 1256830 1464610 1330570 1314950 1232420 1401560 1060450 1337680 TRUE FALSE 1128690.66 1349887.001 1499351.241 1364714.679 1211679.131 1588199.647 1191409.089 1192849.517 1114412.566 1.012812215 1.211299156 1.345418462 1.224604532 1.087280571 1.425145135 1.069091578 1.070384123 1 20.087852 1.585780898 10.68956278 1.048984504 1.228520844 0.323189413 0.116452136 0.116678733 32.96764944 0.058234148 0.027566821 38.52839329 -1.585780898 0.179536339 QLEEQLR ddPTM_SK-BR-3_Pertuzumab_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 ; 160.78 0.0031029 329340000 551540 742410 603370 625440 768960 478620 654340 608460 679460 FALSE TRUE 517020.0959 797378.8089 617682.2213 641489.8493 708568.9834 616789.8243 556227.7916 684427.5704 566053.7365 0.91337635 1.408662742 1.091207745 1.133266699 1.251769819 1.089631221 0.982641321 1.209121195 1 19.11057949 2.063616902 7.317172278 1.055613006 1.18262808 0.082320941 0.137907189 0.393968916 37.92159051 0.048336743 0.035539284 115.775563 -2.063616902 0.127015073 QLEES(ph)VSEKEQQLLSTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLEESVSEKEQQLLSTLK 18 1 O95239;O95239-2 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 QLEES(0.988)VS(0.012)EKEQQLLSTLK 81.144 0.004502 28140000 56175 39553 47679 41643 48822 30590 63715 43240 70214 TRUE FALSE 52659.10703 42481.54527 48809.9684 42711.62988 44987.71706 39420.83641 54161.52725 48638.60918 58494.8298 0.900235238 0.726244446 0.834432181 0.730177864 0.769088776 0.673920012 0.925919905 0.831502705 1 15.83602149 1.09521257 1.184205239 0.989016224 0.776803556 0.441249796 0.075234727 0.385403053 1.120644737 0.063768286 0.020230577 12.45123901 -1.09521257 -0.212212668 QLFHPEQLITGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 168.61 4.61E-05 11212200000 5720800 4657200 4229200 3797000 5119200 5796900 8885800 4547800 8740600 FALSE TRUE 5362745.34 5002023.934 4329518.621 3894437.448 4717158.682 7470370.925 7553456.782 5115602.841 7281737.394 0.736465084 0.686927262 0.5945722 0.534822562 0.647806756 1.025905017 1.037315186 0.702525038 1 22.79585128 2.247601463 24.6483916 0.957391158 0.635504587 0.661528987 0.10679953 88.76680708 242008.3358 0.036268543 0.029926909 176.8485335 -2.247601463 -0.321886571 QLFHPEQLITGKEDAANNYAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLFHPEQLITGKEDAANNYAR 21 1 P68363;P68363-2;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;F8VWV9;F8VX09;P68366-2;P68366;C9JEV8;C9JQ00;C9JJQ8;C9JDL2;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA1A;TUBA1C;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 ; 197.68 5.39E-22 1590670000 1055210 1654370 1129810 1166700 2247400 1332680 2618200 1205300 7283600 FALSE TRUE 989166.2897 1776861.276 1156609.627 1196639.497 2070898.27 1717403.082 2225625.216 1355784.358 6067920.106 0.163015708 0.29282872 0.190610556 0.197207524 0.341286344 0.283029943 0.366785517 0.223434774 1 22.53277066 -5 0.288503151 6.709867977 0.218702464 0.931642942 0.063411113 54.16245163 0.511785725 185.8907977 0.063287073 1.00E-05 5 -6.491165513 QLGEAHGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QLGEAHGR 8 0 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ;; 134.77 0.00086256 169277000 208369 250271 250333 240040 273690 226465 252595 227365 280732 FALSE TRUE 195327.5562 268801.3252 256271.017 246199.8328 252195.4914 291841.7691 214720.7247 255752.0207 233876.0156 0.835175662 1.149332584 1.09575587 1.052693805 1.078329861 1.247848217 0.918096386 1.093536762 1 17.83538439 1.687548462 24.99999967 1.003445467 1.086351364 0.083251214 0.110471503 0.891434946 423.7358932 0.046464925 0.025767079 48.70218676 -1.687548462 0.082905897 QLHDDYFYHDEL ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLHDDYFYHDEL 12 0 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 ; 166.04 5.30E-05 430570000 423830 554200 485960 465070 532650 475170 615800 439600 564010 FALSE TRUE 397303.2369 595233.5446 497487.2007 477004.4836 490817.8176 612343.8653 523466.5068 494485.0277 469873.0874 0.845554358 1.266796419 1.058769302 1.015177282 1.044575292 1.30321119 1.114059351 1.052379974 1 18.84191161 QLHDEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLHDEAR 7 0 P18206;P18206-2 P18206 VCL Vinculin 0 106.36 0.0077204 64027000 31870 37996 35021 38709 34944 24022 39549 32774 38128 FALSE TRUE 29875.31359 40809.26337 35851.71466 39702.33847 32199.6392 30956.76144 33618.9946 36865.90604 31764.19048 0.940534392 1.284756915 1.128683405 1.249908714 1.013708793 0.974580525 1.058392929 1.16061217 1 14.95511363 2.723002579 24.64665317 1.040540902 1.16955396 0.209558425 0.102901832 843.7691444 1336675.519 0.030723053 0.029059309 528.4483902 -2.723002579 0.129013058 QLHLEGASLELS(ph)DDDTESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLHLEGASLELSDDDTESK 19 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 1 QLHLEGASLELS(1)DDDTESK;QLHLEGASLELS(1)DDDTESK 292.75 8.85E-50 413860000 288810 204900 205873 210804 251847 247530 356860 217668 329390 TRUE FALSE 270733.8976 220071.0092 210756.4048 216213.5875 232067.9525 318987.8927 303352.1559 244844.3289 274412.6811 0.986593974 0.801970989 0.768027206 0.787913979 0.845689607 1.1624386 1.105459685 0.892248594 1 18.06598763 2.324390912 7.059424166 1.058351328 0.819466401 0.535726069 0.092041108 0.143846005 9.933128692 0.031161166 0.025945873 211.0526995 -2.324390912 -0.238884927 QLICDPSYIPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLICDPSYIPDR 12 0 P31150 P31150 GDI1 Rab GDP dissociation inhibitor alpha 0 ; 107.18 0.0016209 0 131900 149881 128122 119629 149180 126232 175310 120992 182450 FALSE TRUE 123644.6144 160978.3452 131161.1143 122698.8827 137464.0046 162673.1292 149023.893 136098.1175 151997.9163 0.813462562 1.059082579 0.862913897 0.807240557 0.904380849 1.070232626 0.980433789 0.895394627 1 17.21369202 2.338755846 24.99999999 0.987469311 0.905200698 0.250292148 0.080976425 20.48951603 5082.554001 0.028554741 0.023890603 218.1503156 -2.338755846 -0.082268612 QLLCGAAIGTHEDDKYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLLCGAAIGTHEDDKYR 17 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 112.82 0.00026579 85500000 76584 57543 52485 44738 50658 52279 70180 44572 61871 FALSE TRUE 71790.74415 61803.54359 53729.96899 45886.05282 46679.52502 67371.09862 59657.16052 50136.91232 51544.3304 1.392796135 1.199036696 1.042403084 0.890225025 0.905619001 1.307051583 1.157395199 0.972694997 1 15.65352613 4.624169998 1.574422156 1.059009403 1.469610567 0.465048161 0.12260481 0.879505638 2.471467511 0.035055358 0.519999903 42089.13479 -4.624169998 0.410601163 QLLDS(ph)DEEQEEDEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLLDSDEEQEEDEGR 15 0 Q9UNS1-2;Q9UNS1 Q9UNS1-2 TIMELESS Protein timeless homolog 1 QLLDS(1)DEEQEEDEGR;QLLDS(1)DEEQEEDEGR 422.16 3.92E-153 1424950000 486220 505270 604420 510240 511670 557720 640030 474340 644400 TRUE FALSE 455788.3581 542680.7165 618757.1278 523333.6222 471485.5022 718724.7102 544063.4432 533562.3932 536845.477 0.849012197 1.010869496 1.152579568 0.974831017 0.878251792 1.338792522 1.013445147 0.99388449 1 19.03414736 QLLEEELAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLLEEELAR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 134.26 0.00059066 169474000 277200 358700 325150 335130 374130 291800 378640 309090 315140 FALSE TRUE 259850.5468 385258.5212 332862.7115 343730.0032 344747.339 376037.923 321866.4471 347680.5669 262541.0981 0.989751885 1.467421764 1.267849925 1.309242651 1.313117609 1.432301174 1.225965951 1.324290061 1 18.00218375 -1.100243297 3.563896331 0.999819329 1.306426807 0.328459181 0.129263149 93097310.14 164069164.1 210178.1406 0.027365037 0.079388337 1.100243297 0.306607477 QLLEELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QLLEELER 8 0 Q9NWB6;Q9NWB6-2;Q9NWB6-3 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 ;; 178.27 0.00058276 199915000 352568 431000 383760 410050 431600 363290 450350 375810 431380 FALSE TRUE 330501.3982 462911.6885 392862.9684 420572.5772 397703.877 468165.9255 382824.1983 422730.7058 359379.8912 0.919643548 1.288084558 1.093169034 1.170272983 1.106639205 1.302704845 1.065235445 1.176278128 1 18.45515016 -0.815764106 1.00892008 0.990398044 1.150439708 0.132174772 0.110037687 154.9768517 74.45375566 5.40332433 0.029167293 0.152839601 0.815764106 0.160041664 QLLGHMEDLEGDAQSVLDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLLGHMEDLEGDAQSVLDAR 20 0 Q9NX46 Q9NX46 ADPRHL2 Poly(ADP-ribose) glycohydrolase ARH3 0 ; 238.63 1.23E-29 117568000 120493 125792 102401 103952 130381 136497 159653 105174 166505 FALSE TRUE 112951.5582 135105.7706 104830.0001 106619.5843 120141.4022 175901.4681 135714.5148 118305.2054 138714.2398 0.814275148 0.97398631 0.755726306 0.768627536 0.866107202 1.268085153 0.978374787 0.85286994 1 17.08175637 2.446227973 24.99997334 1.032010191 0.83808579 0.395337282 0.116603534 201.0807115 162720.8639 0.039431007 0.032990645 279.4010109 -2.446227973 -0.1939244 QLLHSCTVIATNILLVDEIMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 269.08 1.68E-37 629224000 465463 487312.4 368283.3 349655.5 497802 718321 947314 385137.6 682590 FALSE TRUE 436330.5017 523393.5171 377019.1538 358628.2521 458706.639 925688.6117 805273.0601 433222.8772 568661.3193 0.767294147 0.920395848 0.662994195 0.630653501 0.806642941 1.627838188 1.41608552 0.761829339 1 19.11721015 2.359333008 8.580870392 1.268397981 0.756899043 0.442535567 0.243030763 0.203022862 14.38249002 0.081966341 0.068474397 228.7352023 -2.359333008 -0.511498938 QLLLTADDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 QLLLTADDR 9 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;; 237.65 6.75E-10 1912127000 3809130 4485700 2817070 3102090 3928530 3948090 5545750 3315570 4176880 FALSE TRUE 3570723.353 4817825.895 2883892.231 3181694.881 3619999.101 5087839.491 4714216.272 3729526.213 3479731.744 1.02614903 1.384539456 0.82876855 0.914350621 1.040309819 1.462135551 1.35476428 1.071785553 1 21.73054466 2.279358354 24.99606909 1.270288349 1.051664664 0.161084319 0.193369014 223.882003 137167.7413 0.067649235 0.056598848 190.2647583 -2.279358354 -0.218623685 QLLLTADDRVNPCIGGVILFHETLYQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QLLLTADDRVNPCIGGVILFHETLYQK 27 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;; 311.77 2.98E-82 2031020000 2128260 1628330 2129200 2442400 1524640 3799040 6427920 1097189 3844470 FALSE TRUE 1995056.006 1748893.247 2179705.629 2505076.119 1404900.925 4895761.176 5464113.07 1234175.462 3202803.121 0.622909349 0.546050813 0.680561854 0.782151142 0.438647295 1.528586364 1.706040885 0.385342282 1 21.61090369 2.242169523 24.99999333 1.277807451 0.621497717 0.33162078 0.363374953 84.19567542 583253.1258 0.123239074 0.099352091 174.6503752 -2.242169523 -0.656309735 QLLSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLLSER 6 0 A0A087X1E4;P53365;P53365-2;P53365-3;E9PRV8;E9PPY7 A0A087X1E4 ARFIP2 Arfaptin-2 0 ; 116.54 0.05464 529420000 464670 597080 540500 586320 629650 686390 700340 534160 602020 FALSE TRUE 435587.1342 641288.4245 553320.9152 601365.9638 580199.8289 884539.6504 595330.5186 600851.0518 501538.9728 0.868501069 1.278641261 1.103246099 1.199041344 1.15683897 1.763650879 1.187007493 1.19801468 1 18.93600229 2.434294807 24.99998375 1.325990669 1.142489561 0.109485161 0.219052425 261.2605399 152509.8199 0.069487655 0.058137574 271.8283862 -2.434294807 -0.183501108 QLLTLS(ph)SELSQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLLTLSSELSQAR 13 0 P15311;E7EQR4 P15311 EZR Ezrin 1 QLLT(0.001)LS(0.897)S(0.1)ELS(0.001)QAR 211.17 2.53E-08 49270000 41430 40626 41058 36000 44443 43510 45446 31891 57302 TRUE FALSE 38836.97025 43633.99131 42031.91515 36923.82095 40952.62605 56070.63067 38631.7942 35872.66155 47737.92601 0.813545403 0.914031986 0.880472167 0.773469315 0.857863537 1.174551041 0.809247435 0.751449938 1 15.54284827 QLLTLSSELS(ph)QAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLLTLSSELSQAR 13 0 P15311;E7EQR4 P15311 EZR Ezrin 1 QLLTLS(0.003)S(0.02)ELS(0.978)QAR;QLLTLS(0.06)S(0.336)ELS(0.604)QAR 127.05 0.00019033 142105000 122534 108448 117512 97884 140645 128682 135009 93894 169969 TRUE FALSE 114864.8157 116477.6028 120299.4401 100395.8692 129599.309 165830.4044 114765.6538 105616.8726 141600.0759 0.811191766 0.8225815 0.849571862 0.709009996 0.915248867 1.171118048 0.810491471 0.745881469 1 17.11146251 2.51300786 23.64056476 0.930039172 0.81088916 0.2327044 0.117014611 504.20058 332145.0043 0.037279795 0.03513076 325.8425981 -2.51300786 -0.119150012 QLMEQDAS(ph)SSPSAQVIGLK ddPTM_SK-BR-3_Pertuzumab_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 QLMEQDAS(0.439)S(0.279)S(0.261)PS(0.021)AQVIGLK 106.13 0.00033571 28590000 70948 60412 70161 67754 81491 57747 86927 71502 102710 TRUE FALSE 66507.49133 64884.96734 71825.25205 69492.68235 75091.02558 74417.62146 73893.10334 80429.1821 85567.03747 0.777255977 0.758293956 0.839403282 0.812143138 0.877569538 0.869699637 0.863569729 0.939955203 1 16.38476752 2.625334342 0.117044822 1.124273997 0.571708555 0.912135571 0.021263609 3.884539015 0.208954724 0.340273588 0.587712797 422.0212716 -2.625334342 -0.552565442 QLMEQDASS(ph)SPSAQVIGLK ddPTM_SK-BR-3_Pertuzumab_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(0.714)S(0.286)PSAQVIGLK 223.93 2.19E-19 76677000 238360 202090 223670 205150 269580 203740 314390 240210 344120 TRUE FALSE 223441.4731 217052.9539 228975.558 210414.4963 248408.2742 262556.4306 267250.1382 270200.7473 286684.1489 0.779399468 0.757115295 0.798703238 0.733959297 0.866487649 0.915838673 0.932211073 0.942503268 1 18.12910261 2.412007533 1.994466831 0.946582702 0.770169729 0.905502042 0.02739673 0.087171867 0.708145859 0.010721792 0.008253284 258.2304979 -2.412007533 -0.176412973 QLMEQDASSS(ph)PSAQVIGLK ddPTM_SK-BR-3_Pertuzumab_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(0.022)S(0.977)PSAQVIGLK 327.16 3.82E-75 83569000 210570 174960 199790 162830 213400 164980 260100 182960 269990 TRUE FALSE 197390.7996 187914.2204 204529.1131 167008.4935 196640.4248 212607.0478 221100.4197 205802.9587 224926.9248 0.877577461 0.835445648 0.909313606 0.74250112 0.874241379 0.945227202 0.982987785 0.914976982 1 17.77909684 2.254341718 3.808462673 0.963443981 0.848138689 0.590161641 0.047404547 0.154384962 4.87432162 0.017124758 0.013181863 179.6146343 -2.254341718 -0.115305292 QLNENKQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLNENKQER 9 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 129.89 0.0012743 0 239240 268300 236690 255040 327230 177226 271060 241150 448080 FALSE TRUE 224266.3955 288165.2112 242304.3986 261584.7582 301530.6758 228388.2692 230417.0694 271258.1083 373292.5533 0.600779184 0.771955424 0.649100542 0.700750004 0.807759686 0.611821123 0.617256003 0.726663594 1 18.5099472 0.964320071 22.45263052 1.000000001 0.683455249 0.68547215 0.067587267 859.7033912 540994.5727 0.063472259 0.015868065 9.211281847 -0.964320071 -0.316544752 QLNVNAKPFVPNVHAAEFVPSFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLNVNAKPFVPNVHAAEFVPSFLR 24 1 P15170-2;P15170-3 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 165.32 8.65E-12 206780000 457960 488550 326400 279550 521820 393080 642320 436030 795290 FALSE TRUE 429297.1011 524722.7503 334142.3621 286723.7263 480838.3621 506555.8149 546010.079 490469.3053 662550.9612 0.647945783 0.791973419 0.504327035 0.432757241 0.725737928 0.764553739 0.824102765 0.740274083 1 19.3376719 2.352707696 2.942541964 0.820678007 0.610706322 0.475834708 0.115939852 0.264466704 4.636739136 0.045373757 0.035941162 225.2722497 -2.352707696 -0.209971685 QLPAHDQDPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QLPAHDQDPSK 11 0 Q9UGI8-2;Q9UGI8;F8W7T0 Q9UGI8-2 TES Testin 0 ;;;;; 147.33 3.54E-05 5439980000 3133526 2456287 2509696 2493195 2830335 2079392 3442221 2363956 3787992 FALSE TRUE 2937404.201 2638153.045 2569227.174 2557174.605 2608051.906 2679678.714 2926091.917 2659101.11 3155751.664 0.930809682 0.835982462 0.814141114 0.810321875 0.826443961 0.849141187 0.927225026 0.842620521 1 21.58955225 0.586838321 0.625474255 1.001165845 0.838086804 0.52286382 0.042945384 1.115160167 0.801057437 0.049262682 0.017216116 3.862231675 -0.586838321 -0.163079041 QLPDKWQHDLFDSGFGGGAGVETGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLPDKWQHDLFDSGFGGGAGVETGGK 26 1 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 ; 263.57 3.63E-53 989790000 1845650 1376690 1308990 1200720 1627440 1629080 2686000 1249780 3047200 FALSE TRUE 1730134.061 1478621.56 1340039.861 1231532.508 1499627.427 2099368.95 2283259.236 1405817.784 2538602.634 0.681530082 0.582454907 0.52786515 0.485122205 0.590729485 0.826978166 0.899415767 0.553776225 1 21.27560316 2.263583825 5.578653831 0.822530221 0.562836268 0.506032664 0.120964718 0.131756882 11.66060749 0.040054785 0.032167092 183.4779269 -2.263583825 -0.259693953 QLPLEPES(ph)PSGQVGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLPLEPESPSGQVGPR 16 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 QLPLEPES(0.995)PS(0.005)GQVGPR;QLPLEPES(0.949)PS(0.051)GQVGPR 233.09 1.27E-19 134155000 174966 165124 176440 173254 166439 145098 157301 119333 125966 TRUE FALSE 164015.1904 177349.9528 180625.2401 177699.991 153367.5523 186985.4371 133715.1754 134231.9877 104941.4608 1.562920785 1.689989365 1.721199978 1.693324922 1.461458142 1.781807073 1.274188241 1.279113009 1 16.67922525 1.362482268 1.152432674 1.018037377 1.669582813 0.796553293 0.112199721 0.165310309 0.433583831 0.092049033 0.030959297 23.03998905 -1.362482268 0.651545436 QLPS(ph)PEPCEIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLPSPEPCEIQK 12 0 A0A590UK32;A0A590UJW2;A0A590UJD8;Q5VVJ2;Q5VVJ2-2 A0A590UK32 MYSM1 Histone H2A deubiquitinase MYSM1 1 QLPS(1)PEPCEIQK;QLPS(1)PEPCEIQK 207.31 8.38E-08 358120000 655970 571160 597420 586310 655520 498960 829950 523720 701870 TRUE FALSE 614914.0086 613449.2807 611591.0845 601355.7072 604038.1034 643001.6521 705506.7024 589107.5948 584723.3627 1.051632358 1.049127365 1.045949458 1.028444809 1.033032271 1.099668139 1.206564929 1.00749796 1 19.15739471 2.195479761 6.719760787 1.108198275 1.042651524 0 0.059626857 0.295904287 33.67574483 0.021000862 0.015630648 156.8482802 -2.195479761 -0.06554675 QLPTAAPDKTEVTGDHIPTPQDLPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLPTAAPDKTEVTGDHIPTPQDLPQR 26 1 P56211;H3BMD8;P56211-2;H3BQ52 P56211 ARPP19 cAMP-regulated phosphoprotein 19 0 ; 125.82 6.52E-05 317040000 540780 478110 498940 437540 529660 423970 628660 426140 678320 FALSE TRUE 506933.5451 513509.7619 510775.0924 448768.0172 488062.6401 546363.2564 534398.2692 479344.517 565104.0099 0.897062375 0.908699554 0.903860322 0.794133486 0.86366869 0.96683663 0.945663559 0.848241224 1 19.1081569 2.246862385 24.99986344 0.937842962 0.878822105 0.306017418 0.049495049 258.7156656 779094.5308 0.017204419 0.014169432 176.5478306 -2.246862385 -0.059020858 QLPTAAPDKTEVTGDHIPTPQDLPQRKPS(ph)LVASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLPTAAPDKTEVTGDHIPTPQDLPQRKPSLVASK 34 3 P56211;H3BMD8;P56211-2;H3BQ52 P56211 ARPP19 cAMP-regulated phosphoprotein 19 1 QLPTAAPDKTEVTGDHIPTPQDLPQRKPS(1)LVASK 155.53 3.18E-11 243600000 397520 263160 266350 233560 308380 181310 420320 247770 953930 TRUE FALSE 372639.9328 282644.6402 272667.9478 239553.545 284161.0787 233651.2537 357296.9181 278704.6299 794712.9204 0.468898798 0.355656279 0.343102447 0.301434064 0.357564438 0.294007116 0.449592436 0.350698501 1 19.60007427 -0.781353252 0.719773169 1.085333182 0.356537238 0.926353123 0.056212311 6.062320424 1.862005872 1.304070212 0.018378713 0.165442372 0.781353252 -0.728795944 QLQDKLNES(ph)DEQHQENEGTNQLVMGIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLQDKLNESDEQHQENEGTNQLVMGIQK 28 1 Q15545 Q15545 TAF7 Transcription initiation factor TFIID subunit 7 1 QLQDKLNES(1)DEQHQENEGTNQLVMGIQK 195.89 3.57E-25 73597000 162860 111820 129410 126370 147500 90293 178360 117930 224890 TRUE FALSE 152666.8833 120099.2691 132479.6663 129612.8681 135915.945 116359.1233 151616.5738 132653.8201 187354.4062 0.814856114 0.641027193 0.707107289 0.691805818 0.725448351 0.621064248 0.80925011 0.708036831 1 17.51541038 -0.057151028 0.628317706 1.017744597 0.697465618 0.674264302 0.06199651 2.595786331 1.104482155 0.169070269 0.021706699 0.876695893 0.057151028 -0.320278979 QLQEERPELSESELTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLQEERPELSESELTR 16 1 E9PKP7;P17480-2;P17480;E9PLT2 E9PKP7 UBTF Nucleolar transcription factor 1 0 ; 172.2 4.24E-09 405090000 167503 206571 186427 178444 226444 184599 231450 174305 201860 FALSE TRUE 157019.2862 221865.7318 190849.1365 183023.1751 208660.0017 237889.7346 196746.2212 196067.3629 168168.2619 0.933703449 1.319307991 1.134870125 1.088333631 1.240781104 1.414593526 1.169936699 1.165899919 1 17.35954593 0.777475183 2.622056855 1.000178629 1.201586638 0.15962564 0.129409461 1.760820865 18.00940059 0.114805273 0.030525726 5.990667047 -0.777475183 0.201408009 QLRDELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLRDELR 7 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 0 83.753 0.0384 0 35983 69426 53834 43064 82586 45407 63880 52882 91263 FALSE TRUE 33730.88826 74566.37328 55110.9679 44169.09515 76100.0287 58515.26378 54301.78703 59484.43411 76030.61572 0.443648758 0.98074141 0.724852316 0.58093828 1.000912961 0.769627646 0.714209487 0.782374752 1 16.21429285 -2.160944325 1.849631706 1.461415897 0.767514203 0.178566089 0.164832217 2914467.514 587521.3672 5626898.51 0.039431077 0.006903283 2.160944325 -0.693901694 QLS(ph)EEQPSGNGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QLSEEQPSGNGVK 13 0 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 1 QLS(0.919)EEQPS(0.081)GNGVK;QLS(1)EEQPSGNGVK;QLS(1)EEQPSGNGVK 244.05 5.37E-17 498460000 1989560 1664950 1857040 1828120 1982770 1344180 2154730 1589230 2104230 TRUE FALSE 1865036.991 1788224.63 1901089.866 1875032.654 1827051.242 1732222.945 1831648.24 1787648.864 1753020.419 1.063899183 1.020082031 1.084465329 1.069601149 1.04223044 0.988136205 1.04485277 1.019753589 1 20.74141137 2.468709943 24.7137793 1.01842464 1.056980839 0.494477387 0.021810099 163.0767677 479141.4655 0.007457702 0.006250403 294.2455766 -2.468709943 0.038556199 QLS(ph)ESESSLEMDDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QLSESESSLEMDDER 15 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.993)ES(0.007)ESSLEMDDER;QLS(0.982)ES(0.018)ESSLEMDDER;QLS(0.731)ES(0.268)ESSLEMDDER 363.51 6.94E-84 1739460000 982170 910490 865420 866090 777870 798300 999120 736610 729470 TRUE FALSE 920697.7329 977903.627 885948.1711 888315.3357 716779.228 1028756.251 849311.2314 828577.38 607716.7444 1.515011297 1.609143793 1.457830773 1.46172595 1.179462693 1.69282196 1.397544562 1.363426938 1 19.21303952 -3.285826 0.205383277 2.23E-15 1.559580894 0.569352601 0.131099726 45.94382855 0.859568674 19.92418855 0.292695418 0.000517814 3.285826 1.559580894 QLS(ph)ESESSLEMDDERYFNEMSAQGLRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.939)ES(0.042)ES(0.008)S(0.011)LEMDDERYFNEMSAQGLRPR;QLS(0.965)ES(0.035)ESSLEMDDERYFNEMSAQGLRPR;QLS(0.993)ES(0.007)ESSLEMDDERYFNEMSAQGLRPR;QLS(0.817)ES(0.183)ESSLEMDDERYFNEMSAQGLRPR;QLS(0.77)ES(0.223)ES(0.003)S(0.003)LEMDDERYFNEMSAQGLRPR;QLS(0.984)ES(0.008)ES(0.003)S(0.004)LEMDDERYFNEMSAQGLRPR;QLS(0.898)ES(0.082)ES(0.011)S(0.01)LEMDDERYFNEMSAQGLRPR;QLS(0.553)ES(0.202)ES(0.108)S(0.137)LEMDDERYFNEMSAQGLRPR 337.42 1.95E-96 1688583000 154636.8 222074.8 183847.5 191201.8 242367.2 184994.9 205702.5 177120.3 266683.1 TRUE FALSE 144958.3587 238517.4493 188208.4495 196108.3619 223332.6578 238399.9245 174859.3198 199234.1593 222171.9678 0.652460165 1.073571304 0.847129597 0.882687244 1.005224286 1.073042323 0.787044925 0.896756514 1 17.76131727 4.757332771 24.27060399 0.936764329 0.652459791 0.483542641 0.094838231 2618.625348 3385550.86 0.022349874 0.7521807 57191.66909 -4.757332771 -0.284304538 QLS(ph)EVFETEDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLSEVFETEDSK 12 0 Q99618;F5GX58;F8WDL1 Q99618 CDCA3 Cell division cycle-associated protein 3 1 QLS(1)EVFETEDSK 79.022 0.013639 0 100790 81115 90891 81608 99245 75345 106160 77637 108670 TRUE FALSE 94481.73382 87120.839 93046.97744 83702.19944 91450.69804 97095.87838 90242.29354 87330.15035 90532.27496 1.043624871 0.962318013 1.027776862 0.924556458 1.010144703 1.072500149 0.996796928 0.964630022 1 16.46614459 QLS(ph)LEGSGLGVEDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLSLEGSGLGVEDLK 15 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 QLS(1)LEGSGLGVEDLK 170.5 2.94E-11 0 54183 35956 44849 39538 38178 36157 49005 37371 44184 TRUE FALSE 50791.78275 38618.21965 45912.83946 40552.61202 35179.65388 46594.93894 41657.15519 42036.85161 36809.40496 1.379858838 1.049140014 1.247312732 1.101691594 0.955724601 1.265843308 1.131698685 1.142013886 1 15.16778681 7.99999994 0.01645611 3.90E-11 2.546045159 0.213745685 0.113792001 8735.589828 11.0920324 670.9123238 1092.718119 99999986.19 -7.99999994 2.546045159 QLS(ph)LEGSGLGVEDLKDNTPSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.793)LEGS(0.207)GLGVEDLKDNTPSGK;QLS(1)LEGSGLGVEDLKDNTPSGK;QLS(0.996)LEGS(0.004)GLGVEDLKDNTPSGK;QLS(1)LEGSGLGVEDLKDNTPSGK 247.61 2.73E-31 490151000 1032290 606291 714686 753476 864498 526750 1024530 653619 1426030 TRUE FALSE 967680.8116 651181.4165 731638.6894 772811.4698 796603.8143 678814.1739 870911.2378 735224.7709 1188016.38 0.814534907 0.548124948 0.615848991 0.650505736 0.670532686 0.571384524 0.73308016 0.618867537 1 20.1801233 -1.658889128 0.453121706 1.256577002 0.633471672 0.652450095 0.078639246 22.15224153 1.9608328 6.348806666 0.038385706 0.021933648 1.658889128 -0.62310533 QLS(ph)LPLTQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QLSLPLTQSK 10 0 Q9C0I1-3;Q9C0I1-2;Q9C0I1 Q9C0I1-3 MTMR12 Myotubularin-related protein 12 1 QLS(0.998)LPLT(0.002)QSK;QLS(1)LPLTQSK;QLS(0.992)LPLT(0.008)QSK;QLS(0.927)LPLT(0.073)QSK;QLS(0.979)LPLT(0.021)QSK;QLS(0.999)LPLT(0.001)QSK 209.67 9.56E-08 1247240000 4155070 4483820 3785130 4126500 4387890 2640900 5546850 4066000 6317200 TRUE FALSE 3895011.586 4815806.698 3874915.071 4232392.976 4043282.819 3403284.959 4715151.337 4573649.05 5262818.509 0.740099925 0.915062279 0.736281341 0.804206523 0.768273276 0.646665841 0.895936527 0.869049359 1 22.32740421 1.11269373 1.663352914 0.99043692 0.785742813 0.481522738 0.074355011 0.312662892 1.686602823 0.067555651 0.019786689 12.96264807 -1.11269373 -0.204694107 QLS(ph)LSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLSLSSSR 8 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 QLS(0.998)LS(0.002)SSR 117.25 0.0022186 182710000 125440 148320 120200 161030 106680 94609 172360 112790 139410 TRUE FALSE 117588.9343 159301.7671 123051.2008 165162.3024 98301.78313 121921.0825 146516.2181 126872.0798 116141.5704 1.012462066 1.371617127 1.059493172 1.4220774 0.846396194 1.049762648 1.26153123 1.092391634 1 16.82552492 2.746422654 24.99405475 1.082150952 1.216126658 0.198026811 0.159257509 1170.953177 3722554.224 0.046731003 0.048793517 557.7282648 -2.746422654 0.133975706 QLS(ph)MTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLSMTLR 7 0 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;E5RIY8;E5RIU4;E5RJQ8;E5RGV7 E5RJM2 CDK16 Cyclin-dependent kinase 16 1 QLS(0.779)MT(0.221)LR 76.282 0.043198 102050000 121500 157380 129900 141890 158170 114750 182630 122130 157870 TRUE FALSE 113895.5319 169032.579 132981.2893 145531.1376 145747.9662 147876.4622 155246.327 137378.1993 131520.4771 0.865990866 1.285218718 1.011107109 1.106528358 1.108176988 1.124360749 1.180396622 1.044538481 1 17.00492791 1.013852324 13.32810539 1.000000096 1.1126858 0.071452044 0.108383856 1.588823311 1521.467006 0.092256541 0.023066072 10.32410289 -1.013852324 0.112685704 QLS(ph)PQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QLSPQSK 7 0 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 QLS(0.51)PQS(0.49)K;QLS(0.955)PQS(0.045)K;QLS(0.987)PQS(0.013)K;QLS(0.999)PQS(0.001)K;QLS(0.74)PQS(0.26)K;QLS(0.997)PQS(0.003)K 136.36 0.0031339 8930340000 9291900 7419090 8169570 7867210 8311960 6543910 9720700 6917170 9546700 TRUE FALSE 8710336.566 7968407.143 8363356.058 8069095.928 7659172.19 8433030.585 8263171.278 7780793.901 7953294.096 1.095186027 1.001900225 1.051558758 1.014560235 0.963018857 1.060319219 1.038962118 0.978310849 1 22.92312109 4.74678649 24.31177213 1.019112668 1.095186084 0.396474495 0.030980856 789.9150369 2334533.817 0.007061105 0.080444699 55819.57042 -4.74678649 0.076073415 QLS(ph)SGVSEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 QLSSGVSEIR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 QLS(0.77)S(0.23)GVSEIR;QLS(0.5)S(0.5)GVSEIR;QLS(0.5)S(0.5)GVSEIR;QLS(0.5)S(0.5)GVS(0.001)EIR;QLS(0.808)S(0.192)GVSEIR;QLS(0.499)S(0.499)GVS(0.002)EIR;QLS(0.872)S(0.127)GVSEIR;QLS(0.5)S(0.5)GVSEIR;QLS(0.498)S(0.498)GVS(0.004)EIR;QLS(0.676)S(0.302)GVS(0.022)EIR;QLS(0.491)S(0.491)GVS(0.018)EIR;QLS(0.851)S(0.134)GVS(0.015)EIR 218.56 7.05E-09 1.51797E+11 17186250 18040140 15231230 15585010 20022890 13034160 17533200 16838880 34431960 TRUE FALSE 16110593.29 19375850.74 15592521.97 15984947.74 18450372.99 16796910.4 14904259.43 18941251.23 28685043.44 0.561637403 0.675468761 0.543576725 0.557257226 0.643205336 0.585563359 0.519582948 0.660318025 1 24.77379537 0.915597539 7.874399883 0.999999402 0.586813628 0.889244393 0.045874518 0.760973634 71.0066828 0.044485636 0.011142268 8.233747386 -0.915597539 -0.413185775 QLS(ph)TCQRANSLGDLYAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLSTCQRANSLGDLYAQK 18 1 Q13009;Q13009-2 Q13009 TIAM1 T-lymphoma invasion and metastasis-inducing protein 1 1 QLS(0.811)T(0.183)CQRANS(0.005)LGDLY(0.001)AQK 51.31 0.085402 541130000 325070 584410 534480 669630 646310 377610 414300 288290 282960 TRUE FALSE 304724.449 627680.3245 547158.118 686813.8395 595551.4197 486619.877 352179.5612 324283.6411 235732.148 1.292672432 2.662684448 2.321100973 2.913534897 2.526390332 2.064291532 1.493981895 1.375644535 1 17.84678899 1.717482354 1.859405111 1.184418617 2.409350141 0.561663685 0.429672614 0.218111304 1.530967606 0.292711662 0.11679246 52.17739033 -1.717482354 1.224931524 QLSES(ph)ESSLEMDDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLSESESSLEMDDER 15 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.204)ES(0.796)ESSLEMDDER 354.93 1.68E-82 271870000 201760 179800 171650 174230 164940 184100 195990 145920 145770 TRUE FALSE 189132.2018 193112.5791 175721.6191 178701.0368 151986.2777 237246.6814 166603.119 164138.4332 121440.0453 1.557412148 1.590188629 1.44698249 1.471516552 1.251533441 1.953611602 1.371896054 1.35160056 1 16.88988471 0.926887213 1.949680078 1.004589007 1.527283284 0.464535296 0.179676712 0.343158702 2.72942709 0.154798506 0.043330756 8.45059353 -0.926887213 0.522694277 QLSES(ph)ESSLEMDDERYFNEMSAQGLRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.188)ES(0.811)ES(0.001)SLEMDDERYFNEMSAQGLRPR;QLS(0.334)ES(0.496)ES(0.137)S(0.033)LEMDDERYFNEMSAQGLRPR;QLS(0.158)ES(0.825)ES(0.007)S(0.01)LEMDDERYFNEMSAQGLRPR 331.75 3.37E-96 686420000 30800.7 34630.7 33578 33980.1 37081.1 25468.4 41724 23045.5 52145 TRUE FALSE 28872.93917 37194.79306 34374.48602 34852.08689 34168.89998 32820.71364 35467.87355 25922.7814 43441.66263 0.664637065 0.856200956 0.791279245 0.80227332 0.786546783 0.755512373 0.816448345 0.596726272 1 15.4067917 2.476629588 22.33411441 0.779187341 0.793721631 0 0.107829467 50.83742138 2308239.758 0.032866678 0.027825907 299.6605608 -2.476629588 0.01453429 QLSES(ph)FK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QLSESFK 7 0 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 1 QLSES(1)FK;QLSES(1)FK;QLSES(1)FK;QLSES(1)FK;QLS(0.022)ES(0.978)FK 132.25 0.003553 2783780000 4400210 2902730 3394800 3310920 4007790 2685540 4940310 2928630 5398470 TRUE FALSE 4124808.711 3117651.149 3475326.259 3395883.813 3693034.34 3460811.802 4199556.379 3294275.902 4497430.482 0.917147853 0.693207191 0.77273596 0.755071996 0.821143174 0.769508682 0.933767936 0.73247956 1 22.10066955 -0.075035486 0.339429959 1.048711537 0.762051309 0.357449318 0.079034527 5.110177735 0.803148754 0.421185197 0.069398725 0.841326394 0.075035486 -0.286660228 QLSESES(ph)SLEMDDERYFNEMSAQGLRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.004)ES(0.004)ES(0.413)S(0.351)LEMDDERY(0.001)FNEMS(0.228)AQGLRPR 61.583 0.024809 184400000 26040 31579 29901 33582 41537 26729 31687 27851 46277 TRUE FALSE 24410.20288 33917.14202 30610.26584 34443.77097 38274.85157 34445.22839 26935.82852 31328.25866 38553.06974 0.633158476 0.879752047 0.793977394 0.893411892 0.992783502 0.893449695 0.69866884 0.812600887 1 15.23455812 -4.816253007 0.01758804 1.968100237 6.11E-07 0.216132303 0.102954793 9314.640498 12.77487611 922.6625767 550.9661551 1.53E-05 4.816253007 -1.968099626 QLSESESS(ph)LEMDDERYFNEMSAQGLRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.003)ES(0.358)ES(0.094)S(0.388)LEMDDERY(0.01)FNEMS(0.148)AQGLRPR;QLS(0.159)ES(0.237)ES(0.29)S(0.313)LEMDDERYFNEMS(0.001)AQGLRPR 93.172 0.0020199 269487000 48343 74050 59119 74666 76401 45059 64176 52734 121146 TRUE FALSE 45317.29792 79532.73905 60521.3306 76582.05597 70400.77365 58066.80183 54553.40458 59317.95598 100925.95 0.449015322 0.788030621 0.599660747 0.758794502 0.697548784 0.575340652 0.540529018 0.587737406 1 16.62293764 -1.407834751 3.664733827 1.002471963 0.63399228 0.572412903 0.101681896 11692901.13 8987979.367 213768.1124 0.023199578 0.039098964 1.407834751 -0.368479683 QLSILVHPDKNQDDADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QLSILVHPDKNQDDADR 17 1 O75937 O75937 DNAJC8 DnaJ homolog subfamily C member 8 0 ;;; 189.48 2.12E-10 1354320000 1893430 1779680 1686750 1703290 2127880 1564070 2421480 1649090 2986070 FALSE TRUE 1774923.596 1911449.359 1726760.507 1746999.305 1960764.888 2015591.618 2058401.554 1854982.517 2487675.626 0.713486749 0.768367603 0.69412607 0.702261696 0.788191542 0.810230883 0.827439692 0.745668968 1 21.24636695 -2.46051992 0.195987614 1.368438583 0.697747289 0.804159308 0.039219746 18.68524949 0.453700803 3.084093286 0.111792094 0.00346322 2.46051992 -0.670691293 QLSSGVSEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLSSGVSEIR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ; 145.99 0.010299 0 374160 424290 334330 336550 475040 289220 449740 382410 530210 FALSE TRUE 350741.9935 455704.8731 342260.4655 345186.4428 437732.2746 372713.1189 382305.6622 430154.7303 441714.5257 0.794046772 1.031672826 0.774845393 0.78146953 0.990984559 0.843787327 0.86550394 0.973829714 1 18.75275475 1.170414342 4.79839654 0.995954108 0.875007601 0.250751681 0.084683601 0.301617087 12.44655407 0.075771645 0.019679247 14.80520217 -1.170414342 -0.120946507 QLSSTS(ph)PLAPYPTSQMVSSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLSSTSPLAPYPTSQMVSSDR 21 0 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 QLS(0.005)S(0.018)T(0.121)S(0.857)PLAPYPTSQMVSSDR;QLS(0.007)S(0.033)T(0.16)S(0.8)PLAPYPTSQMVSSDR 139.81 1.79E-07 99625000 97356 117692 95242 107654 135541 92382 99002 69502 93804 TRUE FALSE 91262.66175 126406.0381 97501.18522 110416.5839 124896.1566 119051.1837 84157.56919 78179.47769 78147.5064 1.167825641 1.617531307 1.247655744 1.412925236 1.598210389 1.523416283 1.076906648 1.000409115 1 16.25391222 1.644804352 4.850751308 1.013486191 1.434373838 0.648140049 0.140067623 0.092001623 4.82338077 0.073420885 0.034693884 44.13715663 -1.644804352 0.420887647 QLT(ph)QPETHFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QLTQPETHFGR 11 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 1 QLT(1)QPETHFGR;QLT(1)QPETHFGR;QLT(1)QPETHFGR;QLT(1)QPETHFGR;QLT(1)QPETHFGR;QLT(1)QPETHFGR 204.52 1.21E-07 13886170000 7945970 9411830 6772950 7366320 6396910 4393590 12303950 7167280 9729370 TRUE FALSE 7448645.922 10108691.69 6933607.572 7555352.242 5894522.492 5661948.109 10459086.92 8062130.685 8105475.293 0.918964731 1.247143606 0.855422702 0.932129452 0.727227248 0.698533757 1.290373056 0.994652429 1 22.95046536 1.728633326 24.99999998 1.114011961 0.927123982 0.218213332 0.169379969 1.368287476 3428.652585 0.082290406 0.045634261 53.53444768 -1.728633326 -0.186887978 QLT(ph)QPETHFGREPAAAISRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.999)QPET(0.001)HFGREPAAAISRPR;QLT(1)QPETHFGREPAAAISRPR;QLT(1)QPETHFGREPAAAISRPR 258.83 7.49E-35 1731510000 942663 701034 609795 713732 795433 628273 1067743 482171 1790690 TRUE FALSE 883663.4055 752939.2868 624259.6254 732047.5715 732962.9008 809645.2159 907644.8496 542371.1107 1491812.271 0.592342229 0.504714502 0.418457227 0.490710249 0.491323818 0.542725939 0.608417605 0.363565256 1 20.50863457 -1.576142712 2.990041051 1.026810682 0.50342924 0.82278394 0.072697588 21991268.38 25489853.96 4729042.113 0.017298006 0.026537334 1.576142712 -0.523381442 QLTACPELPHNVQEILGLAPPAEPHS(ph)PSPTASPLPLSPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLTACPELPHNVQEILGLAPPAEPHSPSPTASPLPLSPTR 40 0 Q9HA65-2;Q9HA65 Q9HA65-2 TBC1D17 TBC1 domain family member 17 1 QLTACPELPHNVQEILGLAPPAEPHS(0.979)PS(0.019)PT(0.002)ASPLPLSPTR;QLTACPELPHNVQEILGLAPPAEPHS(0.865)PS(0.118)PT(0.017)ASPLPLSPTR 244.27 1.03E-50 336060000 244780 248450 194433 169455 244210 270460 394950 223210 394290 TRUE FALSE 229459.6567 266845.4965 199045.0426 173803.5022 225030.7317 348537.4114 335730.914 251078.2598 328480.4518 0.698548895 0.8123634 0.605957041 0.529113685 0.685065825 1.061059827 1.022072736 0.764362867 1 18.32544799 2.250978403 24.34800753 0.973442697 0.67169179 0.659821941 0.105303565 99.2089508 194522.3759 0.037442059 0.031105065 178.2290136 -2.250978403 -0.301750907 QLTEMLPSILNQLGADS(ph)LTSLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLTEMLPSILNQLGADSLTSLRR 23 1 P20290-2;D6RDG3;H0Y9Y1;P20290 P20290-2;P20290 BTF3 Transcription factor BTF3 1 QLTEMLPSILNQLGADS(0.95)LT(0.03)S(0.02)LRR;QLTEMLPSILNQLGADS(0.978)LT(0.021)S(0.001)LRR 150.44 5.15E-08 324320000 94385 120306 82613 100971 126596 103308 158619 100277 239890 TRUE FALSE 88477.61133 129213.5814 84572.61937 103562.0868 116653.6608 133131.3425 134835.5535 112796.8042 199850.8093 0.442718304 0.646550204 0.423178769 0.518196985 0.58370372 0.666153632 0.674681048 0.564405041 1 17.60856389 -2.827269982 0.2016826 1.764471629 0.476140162 0.776331179 0.076382283 23.92837217 0.521640487 8.044833237 0.192128115 0.001488435 2.827269982 -1.288331467 QLTQPETHFGR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 168.82 1.76E-05 2966380000 1625490 1795260 1499260 1407430 1885150 2260040 2431040 1462640 2195120 FALSE TRUE 1523753.482 1928182.918 1534823.155 1443547.037 1737097.923 2912476.859 2066528.121 1645253.824 1828740.291 0.83322574 1.054377665 0.839278908 0.78936689 0.949887708 1.59261371 1.130028212 0.899665104 1 20.80241877 2.450399289 24.99999909 1.189425063 0.898448403 0.31381827 0.19145626 237.2801462 221988.4902 0.063436902 0.053076274 282.0975336 -2.450399289 -0.290976659 QLVAGNS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QLVAGNSPK 9 0 Q96EU6-2;Q96EU6 Q96EU6-2 RRP36 Ribosomal RNA processing protein 36 homolog 1 QLVAGNS(1)PK;QLVAGNS(1)PK;QLVAGNS(1)PK;QLVAGNS(1)PK 131.69 0.00034197 1514510000 4188600 2264980 2789390 2429000 2847120 2488740 3896140 2268260 3493060 TRUE FALSE 3926443.003 2432681.476 2855555.648 2491332.252 2623518.68 3207198.837 3311949.977 2551457.254 2910045.72 1.349271929 0.835959882 0.981275184 0.856114471 0.901538647 1.102112869 1.138109259 0.876775659 1 21.47261039 2.235661425 24.99894176 1.053380208 0.958195455 0 0.158337915 202.8925605 1749456.262 0.053745606 0.041459169 172.0526733 -2.235661425 -0.095184753 QLVARPDVVEMHDVTAQDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QLVARPDVVEMHDVTAQDPK 20 1 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ;;; 164.35 1.10E-11 662691000 1000931 705023 709666 654699 802270 754754 1237420 736795 1308520 FALSE TRUE 938284.5154 757223.6365 726499.6126 671499.6847 739262.9504 972639.2274 1051880.359 828785.4776 1090119.559 0.860717073 0.694624393 0.666440306 0.615987191 0.678148506 0.8922317 0.964922013 0.760270258 1 20.05605494 2.218290295 7.151724943 0.908877702 0.692878489 0.565255408 0.087397738 0.109532018 23.17575801 0.030492047 0.023110183 165.3066387 -2.218290295 -0.215999214 QLVEILTTHCDSYWVEMASLQVFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 52.483 0.084136 0 16181 18280 14592 19830 18049 15692 18962 13196 17744 FALSE TRUE 15168.26009 19633.47022 14938.12913 20338.87137 16631.50435 20222.02566 16118.82413 14843.54965 14782.41177 1.026101852 1.328164208 1.010533962 1.375883157 1.125087341 1.367978783 1.09040557 1.004135853 1 13.85159405 1.502889348 6.352809884 1.015230181 1.202532016 0.306984822 0.128061202 0.153875167 14.16317564 0.064954054 0.029137874 31.83386337 -1.502889348 0.187301835 QLVHELDEAEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QLVHELDEAEYR 12 0 Q06323;Q06323-3;Q06323-2;H0YKK6 Q06323 PSME1 Proteasome activator complex subunit 1 0 187.74 1.01E-05 1325900000 834420 923510 862470 789420 955610 928320 1275000 807190 942320 FALSE TRUE 782195.1417 991887.6413 882928.1957 809677.8537 880560.2453 1196310.914 1083825.587 907969.4483 785040.7044 0.996375267 1.26348562 1.124690976 1.031383276 1.121674635 1.52388393 1.380597949 1.156589007 1 19.58240793 2.35993344 21.92890015 1.315184651 1.12762748 0.166147877 0.155394146 4.434742307 817.9869029 0.050646239 0.042373625 229.0516579 -2.35993344 -0.18755717 QLYLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QLYLER 6 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ; 99.139 0.09105 400970000 364410 565310 372080 399900 536750 357850 465460 474980 590000 FALSE TRUE 341602.2286 607166.1406 380905.9133 410162.111 494595.8201 461155.4858 395668.5941 534282.2986 491525.1885 0.694984177 1.235269636 0.774946884 0.834468143 1.00624715 0.938213334 0.804981318 1.086988645 1 18.90690582 1.217306393 24.9985417 1.043494376 0.917296499 0.12998617 0.149963561 634.1820746 745885.3614 0.135750148 0.034070971 16.49325572 -1.217306393 -0.126197877 QMDTVLSSS(ph)PDVLFDPINGLTPDEEALSNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QMDTVLSSSPDVLFDPINGLTPDEEALSNER 31 0 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 QMDTVLS(0.02)S(0.13)S(0.85)PDVLFDPINGLTPDEEALSNER;QMDT(0.002)VLS(0.193)S(0.151)S(0.654)PDVLFDPINGLTPDEEALSNER;QMDTVLS(0.001)S(0.005)S(0.994)PDVLFDPINGLTPDEEALSNER;QMDTVLS(0.023)S(0.159)S(0.818)PDVLFDPINGLTPDEEALSNER;QMDTVLSS(0.005)S(0.995)PDVLFDPINGLTPDEEALSNER 172.03 3.81E-13 128911000 77710.3 84208.2 77274.5 84674.7 95985 89204 100750 75926.6 105236 TRUE FALSE 72846.55104 90443.06275 79107.48763 86847.59616 88446.72528 114955.7467 85643.47282 85406.20315 87671.43175 0.830904088 1.031613844 0.902317734 0.990603147 1.008843172 1.311211011 0.976868646 0.974162295 1 16.41981919 2.723168124 3.218562048 1.070694414 0.945353558 0.22337827 0.108838845 0.375529282 8.06853253 0.034707482 0.034316175 528.6498628 -2.723168124 -0.125340856 QMEKDETVSDCSPHIANIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 QMEKDETVSDCSPHIANIGR 20 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;;;;;; 223.93 3.68E-25 4786931000 4180880 3811519 3807495 3743313 4519265 3257888 4991470 3545256 5836075 FALSE TRUE 3919206.184 4093727.833 3897810.579 3839372.749 4164340.157 4198387.378 4243045.412 3987889.016 4861996.38 0.806089902 0.841984961 0.801689322 0.789670014 0.85650828 0.863511005 0.872696127 0.820216369 1 22.21311739 -5 0.19378004 1.745860234 0.803108704 0.815840182 0.025625802 57.09151011 0.561470861 16.39335835 0.066248227 1.00E-05 5 -0.942751531 QMEQISQFLQAAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QMEQISQFLQAAER 14 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ; 203.87 3.36E-08 114815000 84072 116377 76671 76363 100470 70485 113025 94205 147118 FALSE TRUE 78810.08359 124993.6742 78489.67233 78322.60386 92579.49148 90832.87527 96077.95052 105966.7016 122563.0554 0.643016636 1.019831578 0.64040238 0.639039257 0.755362137 0.741111381 0.783906294 0.864589262 1 16.90316464 0.968270501 1.850514019 0.999323892 0.757263087 0.363279877 0.110575916 0.462557602 3.323410527 0.105491279 0.029883927 9.295451753 -0.968270501 -0.242060805 QMEVIS(ph)LR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QMEVISLR 8 0 C4P092;C4P0A0;C4P093;C4P0B0;C4P0B1;A0A087WYX6;Q9NRI5-7;Q9NRI5-6;Q9NRI5-9;Q9NRI5-3;Q9NRI5-8;Q9NRI5-5;Q9NRI5-2;Q9NRI5 C4P092 DISC1 Disrupted in schizophrenia 1 protein 1 QMEVIS(1)LR 83.456 0.070946 45937000 100770 120880 126590 121470 103900 58834 101320 116850 88026 TRUE FALSE 94462.98558 129830.081 129592.7746 124587.1258 95740.11311 75818.42071 86128.00661 131438.9797 73333.89193 1.28812181 1.77039671 1.767160738 1.698902412 1.305537052 1.03387968 1.174463871 1.792336071 1 16.16219249 2.692945696 4.938918419 1.240015593 1.677804659 0.337611238 0.253871311 0.19961776 11.50921488 0.07862724 0.075277568 493.1121412 -2.692945696 0.437789066 QMFLTQTDTGDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QMFLTQTDTGDDR 13 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;; 171.62 5.77E-05 355673000 254924 276483 267538 283054 291846 240846 311620 226672 316146 FALSE TRUE 238968.7619 296954.089 273884.1277 290317.6448 268925.5924 310374.3304 264895.4739 254972.4982 263379.1902 0.907318311 1.127477417 1.039885222 1.102280118 1.02105862 1.178431486 1.005757037 0.968081411 1 18.00678184 1.537387259 9.139104588 0.985312564 1.069071426 0.181636794 0.071734701 0.161027913 21.14749059 0.03429834 0.015941088 34.46571231 -1.537387259 0.083758862 QMGFPLIYVEAEQVEDDRLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QMGFPLIYVEAEQVEDDRLLR 21 1 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 54.764 0.092657 9192700 4019.1 3755.3 3987.2 3889.9 6395.4 2817.3 3608.9 3977.4 6999.3 FALSE TRUE 3767.551705 4033.346319 4081.778267 3989.72142 5893.131082 3630.608775 3067.778948 4473.987145 5831.071613 0.646116521 0.691698986 0.700004826 0.684217531 1.010642893 0.622631485 0.526108947 0.767266712 1 12.50954533 -2.394486705 1.696668489 2.418501777 0.696256804 0.350361514 0.125142385 1374827.269 132519.1251 7448247.461 0.03383285 0.004031933 2.394486705 -1.722244974 QMGYTEAIEVIQAASS(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QMGYTEAIEVIQAASSPVK 19 0 P19838;P19838-2;P19838-3 P19838 NFKB1 Nuclear factor NF-kappa-B p105 subunit;Nuclear factor NF-kappa-B p50 subunit 1 QMGYTEAIEVIQAAS(0.049)S(0.951)PVK 91.589 0.0019094 0 40411 26287 26391 24097 26893 32979 50221 22143 43300 TRUE FALSE 37881.74765 28233.31683 27017.00698 24715.36982 24780.93226 42499.50193 42690.82728 24907.60229 36072.95027 1.050142762 0.782672796 0.748954737 0.685149666 0.686967162 1.178154313 1.183458158 0.690478658 1 15.1386298 2.243158223 24.99930947 1.05028543 0.779167883 0.286558388 0.169236191 119.0691625 647436.7567 0.057806976 0.046871292 175.0484313 -2.243158223 -0.271117547 QMKEMELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QMKEMELLR 9 1 Q6ZUX3 Q6ZUX3 FAM179A Protein FAM179A 0 65.305 0.061045 239650000 269610 436770 288600 345890 491350 277670 298980 336610 430700 FALSE TRUE 252735.5914 469108.9053 295445.7283 354766.123 452761.353 357828.8214 254150.7246 378636.4995 358813.3876 0.704364999 1.307389639 0.823396614 0.988720419 1.261829599 0.99725605 0.708308924 1.0552463 1 18.45287419 1.981124553 24.71382319 0.87977682 1.037386189 0.028045878 0.19916049 1366.403181 1789044.5 0.075104735 0.049409849 95.74686271 -1.981124553 0.157609368 QMLDDFGPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QMLDDFGPHR 10 0 A0A1B0GVZ4;A0A494C085;P06132;A0A494BZY8;A0A494C0Q8 A0A1B0GVZ4 UROD Uroporphyrinogen decarboxylase 0 84.479 0.018197 0 127280 165510 129880 129690 170620 125730 157320 143760 188590 FALSE TRUE 119313.772 177764.5326 132960.8149 133018.065 157220.1934 162026.2099 133731.3265 161708.7525 157113.1107 0.759413212 1.131443021 0.846274473 0.84663886 1.000681565 1.031271097 0.851178657 1.02925053 1 17.26144405 QMNPHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QMNPHIR 7 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 102.72 0.0085375 617950000 253758 581509 313601 344853 645166 238104 344173 449047 680379 FALSE TRUE 237875.7398 624564.5314 321039.7638 353702.5118 594497.2648 306840.7595 292567.4538 505111.5064 566819.3495 0.419667642 1.101875813 0.566388152 0.624012769 1.048830223 0.541337835 0.516156433 0.891133139 1 19.11252948 1.009603288 23.11966299 1.000000062 0.709587347 0.191384792 0.22275593 108.6165224 261488.2395 0.205883193 0.051470798 10.22358679 -1.009603288 -0.290412716 QMQVLHPAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QMQVLHPAAR 10 0 P50991 P50991 CCT4 T-complex protein 1 subunit delta 0 ; 88.681 0.012029 391654000 447892 650720 424057 456929 730620 323816 601608 533000 815930 FALSE TRUE 419859.2392 698899.9859 434115.8323 468654.5717 673240.0524 417296.4225 511402.4655 599546.2233 679746.0119 0.617670765 1.028178134 0.638644177 0.689455419 0.990428838 0.613900509 0.752343458 0.882015066 1 19.37463626 1.000528964 3.833146233 0.999112142 0.773239204 0.229759885 0.144340672 0.289302838 11.32480035 0.128772237 0.033089276 10.01218726 -1.000528964 -0.225872938 QMVEILHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QMVEILHK 8 0 O76003 O76003 GLRX3 Glutaredoxin-3 0 ; 90.629 0.014736 238900000 858530 827340 807450 778640 976130 709290 1089570 837900 1080270 FALSE TRUE 804796.1398 888597.1144 826603.0953 798621.2206 899468.6873 914050.5086 926199.0936 942513.6594 899965.9582 0.894251758 0.987367474 0.918482625 0.887390477 0.999447456 1.015650092 1.029149031 1.047277012 1 19.77951091 2.553696311 5.151784216 1.023743275 0.932405112 0.721685872 0.029724789 0.126610366 6.017131565 0.009891179 0.009188244 357.8461183 -2.553696311 -0.091338164 QMVIDVLHPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QMVIDVLHPGK 11 0 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4 E7ETK0 RPS24 40S ribosomal protein S24 0 ; 131.69 0.00019805 1922590000 3635400 3217600 2859600 2740200 3172100 3618900 5398800 2922200 4803700 FALSE TRUE 3407866.803 3455834.452 2927431.062 2810518.171 2922976.062 4663617.682 4589300.06 3287043.103 4001931.437 0.851555519 0.863541644 0.731504552 0.702290435 0.730391339 1.165341725 1.146771286 0.821364172 1 21.93226502 2.24562179 24.99966697 1.060716481 0.778421768 0.585396227 0.106576025 104.8146156 371090.625 0.037329076 0.030611617 176.0442278 -2.24562179 -0.282294714 QNAQCLHGDIAQSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QNAQCLHGDIAQSQR 15 0 Q9BQ39;A0A087WVC1 Q9BQ39 DDX50 ATP-dependent RNA helicase DDX50 0 125.52 8.99E-05 149150000 52685 58843 47439 45111 53529 62636 77933 47838 59827 FALSE TRUE 49387.5399 63199.79695 48564.27548 46268.62463 49325.04827 80717.99639 66247.67014 53810.6796 49841.4872 0.99089218 1.268015874 0.974374526 0.92831549 0.989638372 1.619494139 1.329167203 1.079636316 1 15.6050595 QNDAGEFVDLYVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QNDAGEFVDLYVPR 14 0 Q8WVC2;P63220;Q9BYK1;Q9BYK2 Q8WVC2 RPS21 40S ribosomal protein S21 0 ; 139.78 2.36E-05 73657000 134903 111255 143799 138397 118110 131209 170218 89571 133020 FALSE TRUE 126459.662 119492.436 147209.9802 141948.5013 108834.117 169086.9083 144695.3911 100754.1365 110818.1027 1.141146248 1.078275418 1.328392895 1.280914381 0.982096918 1.525805841 1.305701755 0.909184818 1 16.75783405 1.235992507 24.9984345 0.954592286 1.239289946 0.376203891 0.149816072 72.01505449 700936.6794 0.12055206 0.035497444 17.21838869 -1.235992507 0.284697659 QNEEFRPFIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QNEEFRPFIR 10 1 O15258;Q5T092;A0A0A0MR06;Q5T091 O15258 RER1 Protein RER1 0 ;; 152.69 1.60E-05 2654970000 1738110 2227730 1868240 2022900 2025060 1668980 2572670 1678640 1697850 FALSE TRUE 1629324.798 2392673.447 1912555.535 2074811.039 1866019.956 2150787.432 2186922.017 1888221.899 1414467.866 1.151899478 1.691571441 1.352137847 1.466849186 1.319238139 1.52056295 1.546109367 1.334934461 1 20.43182797 0.924102506 5.720075061 1.000027235 1.457624044 0.463257973 0.145452864 0.46351872 33.65132972 0.126218793 0.03177642 8.396581475 -0.924102506 0.457596809 QNEQHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QNEQHIK 7 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 0 75.38 0.043628 25722000 87146 69684 78904 83580 103080 76241 88267 76012 89145 FALSE TRUE 81691.68742 74843.47587 80775.64014 85724.8043 94984.5126 98250.53903 75032.18278 85502.26552 74266.1236 1.099985881 1.0077741 1.087651223 1.154292161 1.278974962 1.3229523 1.010315055 1.151295656 1 16.18041666 3.373150375 3.202680445 1.161175641 1.049160615 0.144453193 0.10177698 0.408576525 8.262704528 0.029249298 0.041628659 2361.295691 -3.373150375 -0.112015026 QNGDDPLLTYR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 237.93 3.14E-15 1475130000 1638580 1836850 1662900 1654610 1841000 1450850 1853130 1634900 1839470 FALSE TRUE 1536024.203 1972852.285 1702344.773 1697070.094 1696415.286 1869686.842 1575270.36 1839020.864 1532450.574 1.00233197 1.287383958 1.110864391 1.107422401 1.106995107 1.22006339 1.027942034 1.200052319 1 20.54740911 -5 0.193774812 0.383006909 1.164091727 0.150462605 0.087730254 216.2539812 2.126754439 51.44528672 0.207928621 1.00E-05 5 0.781084818 QNGSNDS(ph)DRYS(ph)DNEEDSKIELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QNGSNDSDRYSDNEEDSKIELK 22 2 P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 2 QNGS(0.22)NDS(0.78)DRY(0.002)S(0.998)DNEEDSKIELK 138.09 1.07E-06 329730000 393290 148130 175440 166550 197470 141300 343770 170790 231160 TRUE FALSE 368674.6809 159097.6993 179601.5196 170823.955 181961.5028 182091.0162 292224.8799 192113.5075 192577.9026 1.914418404 0.826147222 0.932617487 0.887038194 0.94487218 0.945544705 1.517437234 0.997588533 1 17.55508265 QNGSNDSDRY(ph)S(ph)DNEEDSKIELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QNGSNDSDRYSDNEEDSKIELK 22 2 P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 2 QNGS(0.047)NDS(0.356)DRY(0.604)S(0.993)DNEEDSKIELK 79.635 0.012112 196190000 875630 317670 370740 375870 449970 312840 712790 372600 532600 TRUE FALSE 820825.8813 341190.6173 379534.1279 385515.4605 414631.1713 403151.8295 605913.7567 419119.9302 443705.6193 1.849933482 0.76895717 0.855373724 0.868854132 0.934473564 0.908602037 1.365576027 0.944590089 1 18.7592433 QNGSNDSDRYS(ph)DNEEDSKIELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QNGSNDSDRYSDNEEDSKIELK 22 2 P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 QNGSNDSDRYS(1)DNEEDSKIELK;QNGSNDSDRYS(1)DNEEDSKIELK;QNGSNDSDRYS(0.83)DNEEDS(0.17)KIELK;QNGSNDSDRYS(0.922)DNEEDS(0.078)KIELK;QNGSNDSDRYS(1)DNEEDSKIELK 217.84 6.41E-26 4076150000 4678770 1955070 2149250 2200550 2362820 1590070 3641530 1963300 2527090 TRUE FALSE 4385934.138 2099825.417 2200231.225 2257019.839 2177253.648 2049097.396 3095516.383 2208422.327 2105302.353 2.083279929 0.997398504 1.045090375 1.072064464 1.034176229 0.973303142 1.470342907 1.048981075 1 21.00559601 4.742104209 24.82349914 1.096946781 2.083280342 0.829355435 0.142816928 136.3569513 955159.351 0.03635855 0.267379523 55220.99265 -4.742104209 0.986333561 QNGSNDSDRYS(ph)DNEEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QNGSNDSDRYSDNEEGK 17 1 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 QNGSNDSDRYS(1)DNEEGK;QNGSNDSDRYS(1)DNEEGK;QNGSNDSDRYS(1)DNEEGK;QNGSNDSDRYS(1)DNEEGK;QNGSNDSDRYS(1)DNEEGK;QNGSNDSDRYS(1)DNEEGK 289.26 3.68E-46 3678570000 3414230 1790976 2361964 2131097 2051654 1877471 3065470 1907546 2335898 TRUE FALSE 3200539.439 1923581.727 2417990.901 2185784.557 1890525.371 2419466.4 2605831.232 2145707.317 1946021.533 1.644657772 0.988468881 1.242530393 1.123206768 0.971482246 1.243288606 1.339055703 1.10261232 1 20.89209624 4.750389217 24.52749396 1.148344851 1.644658162 0.633655424 0.12284868 1000.756681 2075094.125 0.029837608 0.483663139 56284.55247 -4.750389217 0.496313311 QNGSNDSDRYS(ph)DNEEGKKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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(0.001)DRYS(0.999)DNEEGKKK;QNGSNDS(0.011)DRYS(0.989)DNEEGKKK;QNGSNDS(0.008)DRY(0.001)S(0.991)DNEEGKKK;QNGSNDSDRYS(1)DNEEGKKK;QNGSNDSDRYS(1)DNEEGKKK 199.89 4.80E-16 3682580000 3291260 1176132 1740399 1737104 1972645 1112835 2603899 1257835 3719142 TRUE FALSE 3085265.912 1263214.037 1781682.086 1781681.03 1817721.419 1434092.399 2213468.518 1414878.469 3098393.174 0.995763203 0.407699722 0.575034215 0.575033874 0.586665835 0.462850361 0.714392394 0.456649105 1 21.5630888 -1.337340073 3.086801183 1.003767171 0.58090067 0.363643941 0.166468527 24318649.54 31501695.03 833669.6717 0.035544137 0.045989631 1.337340073 -0.4228665 QNLFQEAEEFLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QNLFQEAEEFLYR 13 0 A0A087X1Z3;Q9UL46 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;; 293.71 3.02E-40 177597000 79746 78166 41125.8 39311.6 67840 169085 267793 56056.6 252363 FALSE TRUE 74754.84021 83953.49197 42101.3234 40320.40221 62512.12005 217897.0946 227639.9257 63055.38991 210241.985 0.355565708 0.399318395 0.20025174 0.191780924 0.297334141 1.036410946 1.082751981 0.299918163 1 17.68169128 2.247699981 24.8937044 0.891594908 0.287420067 0.609049558 0.224438647 110.8211625 301853.6352 0.074809543 0.061761859 176.8886553 -2.247699981 -0.604174841 QNLNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QNLNDR 6 0 K7EMD9 K7EMD9 KRT13 0 ; 116.11 0.05549 2827400000 3081100 1550460 3802800 3869100 1463170 3477600 3987300 1339640 1696980 FALSE TRUE 2888259.451 1665257.672 3893004.212 3968387.656 1348258.53 4481526.666 3389441.381 1506897.003 1413743.075 2.042987514 1.177906864 2.753685787 2.807007671 0.953680024 3.169972497 2.397494595 1.065891695 1 20.43108853 QNPEQS(ph)ADEDAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QNPEQSADEDAEK 13 0 Q99613-2;Q99613;B5ME19;H3BPE3 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 1 QNPEQS(1)ADEDAEK;QNPEQS(1)ADEDAEK 218.78 2.47E-11 353870000 671740 430070 569450 482770 452760 546380 754630 461410 346240 TRUE FALSE 629696.9925 461912.8303 582957.6229 495158.6955 417202.0559 704111.0363 641480.2371 519018.0542 288450.3072 2.18303457 1.601360161 2.020998447 1.716616981 1.446356775 2.4410133 2.223884742 1.799332645 1 18.13796327 2.251987147 24.99978002 2.012350897 1.794945293 0 0.430189543 702.5417794 1308109.735 0.135755007 0.112984203 178.6434703 -2.251987147 -0.217405604 QNPHDGVVT(ph)PAAS(ph)PSLPQPGLQMPGQWGPVQGGPQPSGQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.96)PS(0.04)LPQPGLQMPGQWGPVQGGPQPSGQHR;QNPHDGVVT(1)PAAS(0.982)PS(0.018)LPQPGLQMPGQWGPVQGGPQPSGQHR;QNPHDGVVT(1)PAAS(0.994)PS(0.006)LPQPGLQMPGQWGPVQGGPQPSGQHR;QNPHDGVVT(1)PAAS(0.994)PS(0.006)LPQPGLQMPGQWGPVQGGPQPSGQHR;QNPHDGVVT(1)PAAS(0.988)PS(0.012)LPQPGLQMPGQWGPVQGGPQPSGQHR 235.44 4.69E-54 1476360000 185171 237443 224587 222680 236271 188429.5 295015 185751 188554.8 TRUE FALSE 173581.4776 255023.5268 229914.3097 228394.3458 217715.2287 242826.0378 250780.2395 208942.4212 157083.7858 1.105024792 1.623487272 1.463641257 1.453965122 1.385981549 1.545837698 1.59647438 1.330133599 1 17.26117475 0.945524284 6.337488283 1.000026662 1.47878761 0.48759963 0.144717872 0.330488077 36.80141055 0.126770819 0.031843943 8.821131249 -0.945524284 0.478760948 QNPHDGVVTPAAS(ph)PSLPQPGLQMPGQWGPVQGGPQPSGQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QNPHDGVVTPAASPSLPQPGLQMPGQWGPVQGGPQPSGQHR 41 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 QNPHDGVVTPAAS(0.995)PS(0.005)LPQPGLQMPGQWGPVQGGPQPSGQHR 170.28 1.05E-19 195130000 9875.3 10072 12819 10835 10292 11359 11874 7146.8 7991 TRUE FALSE 9257.222601 10817.74136 13123.07273 11113.04444 9483.707836 14638.1589 10093.60393 8039.093712 6657.250476 1.390547439 1.624956339 1.971245153 1.669314454 1.424568276 2.198829525 1.516182089 1.207569663 1 12.70071073 1.241471108 2.925652936 1.034849761 1.726860416 0.520488655 0.23988085 0.185030004 2.695439536 0.202606489 0.057915975 17.43697352 -1.241471108 0.692010655 QNRDEVLDNLLAFVCDIRPEIHENYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QNRDEVLDNLLAFVCDIRPEIHENYR 26 2 O75348 O75348 ATP6V1G1 V-type proton ATPase subunit G 1 0 ; 146.57 1.24E-07 325000000 207312 244300 171139 157289 230070 234570 368210 185857 596000 FALSE TRUE 194336.712 262388.2262 175198.4979 161325.302 212001.2303 302286.5511 313000.3288 209061.6556 496523.7497 0.391394595 0.528450505 0.352850187 0.324909538 0.426970976 0.608805825 0.630383399 0.421050666 1 18.9215032 -0.702876691 0.320028134 1.226469836 0.398693647 0.760638204 0.096690448 5.436091805 0.53030885 1.33143034 0.100535997 0.198208972 0.702876691 -0.827776189 QNSPAGNKENIKPNET(ph)SPSFSK ddPTM_SK-BR-3_Pertuzumab_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 QNSPAGNKENIKPNET(0.886)S(0.113)PSFSK;QNSPAGNKENIKPNET(0.568)S(0.43)PS(0.002)FSK 113.6 0.012163 342500000 290710 159860 228465 223406 222903 133892 282310 149035 271460 TRUE FALSE 272514.98 171696.2007 233884.2977 229138.9762 205397.0975 172544.4468 239980.2363 167642.3478 226151.5723 1.205010327 0.759208521 1.034192667 1.013209742 0.90822759 0.762959307 1.061147769 0.741283141 1 17.7869305 2.602329286 8.164848655 0.900331436 0.967330621 0.100591794 0.143895449 1.005396005 62.3212742 0.043524164 0.040983835 400.2481067 -2.602329286 0.066999185 QNVAYEYLCHLEEAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QNVAYEYLCHLEEAKR 16 1 P46940;A0A0J9YXZ5;A0A087X225 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 185.33 1.09E-09 622830000 1148860 1020990 871520 871640 1133320 973500 1600040 938640 1762210 FALSE TRUE 1076954.903 1096585.162 892192.866 894007.7581 1044313.619 1254533.647 1360128.856 1055831.27 1468085.767 0.733577648 0.746948977 0.607725302 0.608961532 0.711343739 0.854537027 0.926464166 0.719189092 1 20.48550482 2.261188422 3.825532322 0.877550836 0.674278921 0.584087168 0.08175234 0.151413369 4.796302161 0.029525942 0.022862591 182.4687186 -2.261188422 -0.203271916 QPAQELS(ph)PTPGGTAHQALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QPAQELSPTPGGTAHQALK 19 0 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 QPAQELS(0.907)PT(0.093)PGGTAHQALK;QPAQELS(0.811)PT(0.189)PGGTAHQALK 243.35 1.21E-24 1242400000 1039630 821660 1014140 939970 926810 821850 1159930 834190 981880 TRUE FALSE 974561.4141 882496.5613 1038195.88 964091.2216 854022.0812 1059104.753 986009.2648 938340.4578 817997.8848 1.191398452 1.078849442 1.269191399 1.178598673 1.044039474 1.294752435 1.205393416 1.14711844 1 19.64173759 0.890809246 5.804162337 1.000003532 1.181175927 0.360534744 0.074999697 1.443566096 75.96527361 0.068894839 0.017337753 7.776948916 -0.890809246 0.181172394 QPAQSQNLS(ph)PLSGFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QPAQSQNLSPLSGFSR 16 0 Q9P2M7;Q9P2M7-2;A6PVU7 Q9P2M7 CGN Cingulin 1 QPAQSQNLS(0.999)PLS(0.001)GFSR;QPAQSQNLS(0.999)PLS(0.001)GFSR 233.79 1.22E-19 518500000 909080 1516270 1365720 1383040 1198760 613570 714210 931440 1112880 TRUE FALSE 852182.3056 1628536.208 1398115.523 1418531.148 1104614.225 790697.6985 607120.8409 1047732.334 927133.1385 0.919158501 1.756528961 1.507998652 1.530018817 1.191429989 0.852841588 0.654836739 1.130077538 1 19.822417 2.460879189 2.843452774 0.855012655 1.495027672 0.483451677 0.245219548 0.17579782 2.910112102 0.086548693 0.073184364 288.9875873 -2.460879189 0.640015017 QPDISCILGTGGKS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 163.04 4.76E-09 1086860000 2330720 2194080 2536750 2904010 2755170 1468350 2261990 1639900 2088680 TRUE FALSE 2184844.396 2356531.966 2596922.908 2978531.813 2538790.062 1892238.808 1922825.599 1844645.125 1740065.815 1.255610206 1.354277491 1.49242798 1.711735147 1.459019562 1.087452436 1.105030386 1.060100779 1 20.73071044 2.23429068 7.785622812 1.075133458 1.458187855 0.73253682 0.117442908 0.07021957 29.80390777 0.044927223 0.034950269 171.510487 -2.23429068 0.383054397 QPDKEFSFMDEEEEDEIRV ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPDKEFSFMDEEEEDEIRV 19 2 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 0 164.35 9.51E-11 73654000 114770 97386 120360 100090 134590 83287 115820 103360 160900 FALSE TRUE 107586.7506 104596.5608 123214.996 102658.4789 124019.8443 107330.6048 98453.86622 116264.7235 134044.7505 0.802618156 0.780310757 0.919207918 0.765852288 0.925212243 0.800707259 0.734485057 0.867357528 1 17.0323552 0.981472164 24.13342072 1.000000004 0.81998331 0.468710742 0.060924175 739.3865749 963089.4469 0.057827021 0.014456755 9.582352973 -0.981472164 -0.180016694 QPEDDSSQAFISTQNGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QPEDDSSQAFISTQNGSPR 19 0 Q5TCQ9;Q5TCQ9-1;Q5TCQ9-3;Q5TCQ9-2 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 QPEDDSSQAFISTQNGS(1)PR;QPEDDSSQAFISTQNGS(1)PR;QPEDDSSQAFISTQNGS(1)PR;QPEDDSSQAFISTQNGS(1)PR 478.45 6.70E-240 970496000 406920 453564 432134 412791 510312 415916 499675 419478 455977 TRUE FALSE 381451.6036 487146.3505 442384.4225 423383.9159 470234.154 535984.1974 424753.3725 471850.7517 379871.493 1.004159592 1.282397757 1.164563361 1.114545113 1.237876921 1.410961884 1.118150165 1.242132564 1 18.53515193 -1.060088403 4.553188185 0.999989305 1.203596825 0.239188527 0.109747257 0.07850667 30248000.25 700.1099372 0.023332697 0.087078632 1.060088403 0.20360752 QPEKEEEEEAGES(ph)VEDIFSEVVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPEKEEEEEAGESVEDIFSEVVGR 24 1 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 QPEKEEEEEAGES(1)VEDIFSEVVGR 131.81 3.25E-05 47028000 51430 36587 44345 44112 46240 35711 54177 38710 52593 TRUE FALSE 48211.08811 39295.93955 45396.88434 45243.9886 42608.49692 46020.18598 46053.6618 43543.02871 43814.88854 1.100335747 0.896862707 1.036106352 1.032616768 0.972466172 1.050332148 1.051096176 0.993795264 1 15.41913357 3.727157881 24.99999376 1.023752318 0.978791164 0 0.055037966 3.586040016 2443930.896 0.013129988 0.021917945 5335.288166 -3.727157881 -0.044961154 QPEKEEEEEAGESVEDIFSEVVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QPEKEEEEEAGESVEDIFSEVVGR 24 1 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 0 ;; 100.88 0.0036995 69875000 72030 58370 66885 59931 65616 49221 77536 53519 66794 FALSE TRUE 67521.77088 62691.77553 68471.54379 61468.93092 60462.78404 63430.30366 65910.19661 60200.96496 55645.64989 1.213424068 1.126624914 1.230492301 1.104649349 1.086568027 1.139896897 1.184462698 1.081862914 1 15.76398129 -4.999999992 0.155917374 0.433593725 1.19645398 0.548872687 0.045817265 106.197122 0.965181524 18.52787447 0.20811651 1.00E-05 4.999999992 0.762860255 QPEWLEEQQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPEWLEEQQGR 11 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 125.23 0.00077404 212590000 147140 153850 168000 150530 176290 124330 162490 119480 157290 FALSE TRUE 137930.7701 165241.2141 171985.0393 154392.8546 162444.8945 160222.0527 138126.133 134397.341 131037.2829 1.052607067 1.261024423 1.312489359 1.178236081 1.239684546 1.222721115 1.054097963 1.025642001 1 16.99961782 1.684013825 3.259309499 1.018295937 1.229770536 0.612209225 0.068689931 0.128801599 3.156569545 0.040504064 0.018264376 48.30741799 -1.684013825 0.211474599 QPEYLDATGGTLHPYQMEGLNWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QPEYLDATGGTLHPYQMEGLNWLR 24 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 ; 310.16 1.94E-73 276380000 135784 148157 144077 142680 164386 127820 162158 146568 136278 FALSE TRUE 127285.5218 159126.6984 147494.5745 146341.4104 151475.7867 164719.559 137843.9133 164867.3374 113532.3214 1.121139075 1.40159821 1.299141713 1.288984569 1.334208486 1.450860486 1.214138067 1.452162128 1 16.79274355 -1.319586761 3.600277878 0.998854272 1.322881859 0.493160593 0.102010053 5063649.626 3712257.342 41458.23533 0.020720464 0.047908573 1.319586761 0.324027587 QPEYSPES(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QPEYSPESPR 10 0 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 QPEYSPES(1)PR;QPEYSPES(1)PR;QPEYSPES(1)PR;QPEYSPES(1)PR;QPEYS(0.007)PES(0.993)PR;QPEYSPES(1)PR 179.59 2.19E-06 3526700000 1997560 1831864 1954620 1774620 1904030 1764790 2253320 1753681 2223090 TRUE FALSE 1872536.285 1967497.117 2000984.509 1820159.754 1754495.164 2274256.224 1915455.585 1972631.933 1852041.917 1.011065823 1.062339409 1.080420746 0.982785398 0.947330159 1.227972328 1.034239866 1.065111926 1 20.82068532 QPGQVIGATTPSTGS(ph)PTNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QPGQVIGATTPSTGSPTNK 19 0 Q9ULM3 Q9ULM3 YEATS2 YEATS domain-containing protein 2 1 QPGQVIGATT(0.006)PS(0.019)T(0.096)GS(0.875)PT(0.004)NK;QPGQVIGATT(0.003)PS(0.026)T(0.288)GS(0.68)PT(0.003)NK 175.52 6.41E-15 0 160051 114646 136363 131421 142530 114237 178958 116284 142924 TRUE FALSE 150033.6936 123134.5091 139597.5948 134793.4854 131336.2687 147215.3674 152124.9093 130802.3134 119069.0611 1.260056074 1.034143614 1.17240863 1.132061378 1.103025988 1.236386397 1.277619122 1.098541571 1 16.86143907 3.71536581 24.19146497 1.167070928 1.122657104 0 0.095279434 929.9758193 1913798.48 0.024310095 0.038011193 5192.372132 -3.71536581 -0.044413824 QPGS(ph)PMYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPGSPMYR 8 0 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 QPGS(1)PMYR 83.499 0.070826 284200000 272470 315790 306760 325500 315490 227220 330960 276860 249970 TRUE FALSE 255416.5891 339171.4202 314036.4921 333852.8811 290712.688 292814.7254 281335.6205 311426.5804 208248.3921 1.226499693 1.628686861 1.507989996 1.603147461 1.395990072 1.406083967 1.350961789 1.495457311 1 17.66794583 -0.932842555 0.342307271 0.782015604 1.512675635 0.566342086 0.121600138 8.907605559 0.838401839 2.045890596 0.098059875 0.11672327 0.932842555 0.730660032 QPGTCS(ph)PDLAAPLDENGAVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPGTCSPDLAAPLDENGAVDR 21 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 QPGT(0.216)CS(0.784)PDLAAPLDENGAVDR 75.358 0.012927 68334000 42655 39209 40917 41476 41981 45816 56015 41156 32130 TRUE FALSE 39985.29969 42112.07516 41887.57056 42540.34438 38683.9816 59042.33544 47616.07077 46294.4172 26767.29543 1.493811722 1.573265975 1.564878703 1.589265695 1.44519575 2.205763955 1.778889873 1.729514187 1 14.70818376 QPGTCSPDLAAPLDENGAVDRGEGGS(ph)EDGSEDGLPEGIHLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPGTCSPDLAAPLDENGAVDRGEGGSEDGSEDGLPEGIHLDK 42 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 QPGTCSPDLAAPLDENGAVDRGEGGS(0.997)EDGS(0.003)EDGLPEGIHLDK 132.28 2.52E-09 27296000 22124 18131 19578 18353 21631 16595 19390 14079 19039 TRUE FALSE 20739.29833 19473.43811 20042.39941 18823.96905 19932.18852 21385.7071 16482.64951 15836.79414 15861.2679 1.307543537 1.227735275 1.263606386 1.186788419 1.256657957 1.348297452 1.039176036 0.998457011 1 13.95322048 1.630967509 5.576750008 1.006037098 1.256760104 0.881018241 0.043777343 0.043937036 2.919592716 0.022566628 0.010814771 42.75309002 -1.630967509 0.250723006 QPGVDSLS(ph)PVASLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QPGVDSLSPVASLPK 15 0 Q9UBW7;Q9UBW7-2;A0A087X151 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1 QPGVDS(0.001)LS(0.999)PVASLPK;QPGVDSLS(1)PVASLPK 256.89 9.51E-25 247160000 464350 385630 394820 394230 430800 321300 501800 368400 526660 TRUE FALSE 435287.1624 414182.4464 404185.3168 404346.6092 396966.7058 414054.0941 426559.7485 414395.5509 438757.0436 0.992091566 0.943990421 0.921205306 0.921572919 0.904752896 0.943697885 0.972200343 0.944476122 1 18.74306276 0.967802286 0.91594911 0.997443404 0.935890977 0.334929678 0.025138049 0.707791509 1.273666388 0.023762556 0.00816437 9.285435672 -0.967802286 -0.061552427 QPGYQPPNPHPGPS(ph)SPPAAPASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPGYQPPNPHPGPSSPPAAPASK 23 0 Q9BUL9 Q9BUL9 RPP25 Ribonuclease P protein subunit p25 1 QPGYQPPNPHPGPS(0.68)S(0.32)PPAAPASK 166.2 7.89E-12 553230000 431240 345670 346590 382860 385620 245880 441580 367180 395180 TRUE FALSE 404249.4582 371263.7665 354811.2785 392684.8358 355334.9607 316861.5645 375369.1784 413023.2313 329221.905 1.227893564 1.127700681 1.077726825 1.192766428 1.079317492 0.962455899 1.140170726 1.254543592 1 18.3287008 4.752925744 2.469177205 1.102517131 1.258743552 0.181369021 0.084302216 0.997177521 7.38271607 0.019801412 0.334567354 56614.24808 -4.752925744 0.156226421 QPGYQPPNPHPGPSS(ph)PPAAPASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QPGYQPPNPHPGPSSPPAAPASK 23 0 Q9BUL9 Q9BUL9 RPP25 Ribonuclease P protein subunit p25 1 QPGYQPPNPHPGPS(0.427)S(0.573)PPAAPASK;QPGYQPPNPHPGPS(0.423)S(0.576)PPAAPASK 140.45 1.25E-07 1098370000 716810 648550 699350 670640 687790 498860 792120 636920 749220 TRUE FALSE 671946.1416 696569.3168 715938.9123 687849.7578 633773.7478 642872.7837 673348.9597 716440.864 624170.3419 1.076542887 1.115992334 1.147024881 1.102022496 1.015385874 1.029963682 1.078790379 1.147829072 1 19.25158028 2.982417676 22.58494064 1.058761824 1.11935966 0.286011556 0.043599 252.7772456 324699.8687 0.012816408 0.013898596 960.323763 -2.982417676 0.060597836 QPHVGDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QPHVGDYR 8 0 Q06323;Q06323-3;Q06323-2;H0YKK6 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;;;;; 103.7 0.0047222 5777970000 4552190 5156840 4770940 4818540 5170300 3835330 5138280 4672940 4928800 FALSE TRUE 4267276.554 5538657.799 4884108.95 4942191.894 4764245.494 4942527.51 4367842.615 5256366.845 4106151.439 1.039239935 1.34886837 1.189461476 1.203606825 1.160270284 1.203688559 1.063731497 1.280120065 1 21.96935541 -3.320239049 0.182179655 0.588156041 1.241135151 0.234719327 0.094021506 79.66650641 1.342258439 12.66511976 0.28004411 0.000478367 3.320239049 0.652979111 QPLLLS(ph)EDEEDTKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 QPLLLSEDEEDTKR 14 1 Q99613-2;Q99613;B5ME19;H3BPE4 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 1 QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR 264.69 6.42E-25 61031110000 14344970 10130940 12379650 12275830 12863010 9608030 15720890 10954700 15003290 TRUE FALSE 13447143.93 10881045.34 12673301.14 12590848.58 11852801.08 12381712.29 13363688.49 12322418.41 12499143.97 1.075845191 0.870543244 1.013933528 1.007336871 0.948289027 0.990604822 1.069168298 0.985860987 1 23.57532596 1.986803971 23.54557558 1.026992997 0.972812688 0.052197452 0.056527485 507.0384361 904704.1828 0.021231538 0.014409671 97.00720038 -1.986803971 -0.054180309 QPPGPVPT(ph)PPLPSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QPPGPVPTPPLPSER 15 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QQI0 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 QPPGPVPT(1)PPLPSER;QPPGPVPT(1)PPLPSER 115.87 0.0055182 361290000 384810 395240 403570 445810 434340 328230 396560 321920 417780 TRUE FALSE 360725.429 424503.9808 413142.871 457250.2394 400228.6884 422984.6726 337099.5095 362112.4206 348049.819 1.036418953 1.219664421 1.187022226 1.313749395 1.149917818 1.215299217 0.968538097 1.040403991 1 18.4089343 1.744335496 8.382479349 1.005607008 1.194265547 0.598849482 0.070753636 0.071807323 18.67910527 0.031351257 0.016826462 55.50543311 -1.744335496 0.188658538 QPPGTQQSHSS(ph)PGEITS(ph)SPQGLDNPALLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPPGTQQSHSSPGEITSSPQGLDNPALLR 29 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 2 QPPGT(0.153)QQS(0.098)HS(0.085)S(0.663)PGEIT(0.074)S(0.498)S(0.428)PQGLDNPALLR 75.141 0.0030592 96979000 49605 61256 47110 47388 60238 34730 46375 53953 87701 TRUE FALSE 46500.3116 65791.45798 48227.47145 48604.05631 55507.15047 44755.98721 39421.49927 60689.15082 73063.13653 0.636440123 0.900474043 0.660079402 0.665233641 0.759714859 0.612565917 0.539553886 0.830639823 1 16.15685607 -0.907445504 12.49786071 1 0.699679097 0.440864333 0.105964458 0 0 0.106407391 0.025080462 0.123752647 0.907445504 -0.300320903 QPPGTQQSHSS(ph)PGEITSSPQGLDNPALLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QPPGTQQSHSSPGEITSSPQGLDNPALLR 29 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 1 QPPGTQQS(0.035)HS(0.166)S(0.799)PGEITSSPQGLDNPALLR;QPPGT(0.002)QQS(0.115)HS(0.18)S(0.703)PGEITSSPQGLDNPALLR;QPPGTQQS(0.004)HS(0.252)S(0.744)PGEITSSPQGLDNPALLR 250.66 1.14E-46 2647730000 347152 386660 398350 422690 443690 406000 451980 366949 343956 TRUE FALSE 325424.376 415288.7087 407799.0501 433536.941 408844.3772 523205.6091 384209.795 412763.3904 286547.5216 1.135673323 1.449283897 1.423146318 1.512966989 1.426794323 1.825894729 1.340824003 1.440470984 1 18.12841489 0.441543523 1.836583922 1.000085594 1.456820648 0.40418265 0.16923327 4.962198095 15.18492854 0.149332707 0.041618527 2.764034901 -0.441543523 0.456735054 QPPGTQQSHSSPGEITSS(ph)PQGLDNPALLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPPGTQQSHSSPGEITSSPQGLDNPALLR 29 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 1 QPPGTQQSHSSPGEIT(0.004)S(0.236)S(0.76)PQGLDNPALLR 111.38 0.00020547 214620000 15839 30565 24072 32882 29057 17418 24770 23438 18072 TRUE FALSE 14847.66526 32828.0644 24642.99921 33725.80779 26774.98043 22446.29384 21055.96845 26364.28589 15055.66645 0.986184525 2.180445782 1.636792319 2.240074055 1.778398885 1.490886765 1.398541109 1.751120482 1 13.87801895 0.836098668 0.577304109 1.009638309 1.810809566 0.236387516 0.367462222 1.322700329 0.990169374 0.377359617 0.155927126 6.856439814 -0.836098668 0.801171257 QPPGVPNGPS(ph)SPTNESAPELPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QPPGVPNGPSSPTNESAPELPQR 23 0 Q8TF74;Q8TF74-2 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 1 QPPGVPNGPS(0.6)S(0.398)PT(0.002)NESAPELPQR;QPPGVPNGPS(0.577)S(0.408)PT(0.015)NESAPELPQR 138.35 2.56E-06 1020460000 733470 824690 861160 990570 1091450 719010 758330 667450 1039700 TRUE FALSE 687563.422 885750.9057 881587.1219 1015989.703 1005731.92 926576.5148 644625.4565 750782.6017 866167.3533 0.793799742 1.022609433 1.017802297 1.172971597 1.161128869 1.06974306 0.744227376 0.866787 1 19.72428627 1.753460559 25 0.848421134 1.044980972 0.301746252 0.11971544 5.301635679 8906.957964 0.053913358 0.029897995 56.68400915 -1.753460559 0.196559838 QPPGVPNGPSS(ph)PTNESAPELPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QPPGVPNGPSSPTNESAPELPQR 23 0 Q8TF74;Q8TF74-2 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 1 QPPGVPNGPS(0.185)S(0.804)PT(0.011)NESAPELPQR;QPPGVPNGPS(0.177)S(0.817)PT(0.006)NESAPELPQR 137.7 4.18E-06 1343700000 955090 1062120 1121910 1176800 1332780 938720 948030 774210 1222420 TRUE FALSE 895312.6218 1140760.47 1148522.235 1206998.68 1228108.835 1209713.225 805881.7026 870871.8227 1018390.205 0.879144966 1.120160489 1.127782091 1.185202562 1.205931507 1.187868088 0.791329 0.855145521 1 19.95785902 1.742611249 11.00520452 0.870153517 1.125113873 0.529018715 0.104353313 0.06168471 43.43182705 0.046875011 0.025566041 55.28550099 -1.742611249 0.254960357 QPPLLGDHPAEYGGPHGGYHSHYHDEGYGPPPPHYEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPPLLGDHPAEYGGPHGGYHSHYHDEGYGPPPPHYEGR 38 0 P14866;M0QXS5;P14866-2 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 57.184 0.00886 505210000 14016 11788 16758 12204 16452 15532 19075 15349 18158 FALSE TRUE 13138.76358 12660.79579 17155.50767 12517.1753 15159.92628 20015.83626 16214.88083 17265.35644 15127.31249 0.86854579 0.836949444 1.13407505 0.827455327 1.002155954 1.323158774 1.071894353 1.141336668 1 13.88486808 2.463770593 24.99353124 1.142237507 0.937188068 0.429659019 0.117131591 219.5126448 410942.9275 0.038516441 0.032240757 290.9179999 -2.463770593 -0.205049439 QPPPAS(ph)SPTKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPPPASSPTKR 11 1 A0A0J9YWL0;Q9Y4K1;A0A494C1M5 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 QPPPAS(0.499)S(0.499)PT(0.003)KR 55.314 0.077249 73458000 74069 55609 68352 62911 68036 54309 64620 57490 74481 TRUE FALSE 69433.15351 59726.34822 69973.34172 64525.40277 62692.727 69987.12667 54930.8309 64667.75305 62049.63993 1.118993657 0.962557531 1.1276994 1.039899713 1.010364074 1.12792156 0.885272356 1.042193849 1 15.92113522 1.742986737 25 0.967425221 1.057052164 0.282277147 0.065535433 0.958718501 5439.561454 0.027427501 0.015209999 55.33332106 -1.742986737 0.089626943 QPPTAAGRPVDAS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QPPTAAGRPVDASPR 15 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 QPPTAAGRPVDAS(1)PR;QPPTAAGRPVDAS(1)PR 114.99 0.00034097 1259290000 833710 825450 934500 868810 844810 832890 1088490 771000 922830 TRUE FALSE 781529.5793 886567.1769 956666.7813 891105.1355 778462.0304 1073331.822 925281.0295 867261.0472 768803.7113 1.016552818 1.153177546 1.244357652 1.159080169 1.012562789 1.396106453 1.203533511 1.128065636 1 19.55225577 4.723966004 3.028936512 1.184673216 0.992443702 0.119300641 0.113635358 0.612771964 8.591922085 0.025540673 0.279398222 52962.19845 -4.723966004 -0.192229514 QPPTAAGRPVDASPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPPTAAGRPVDASPR 15 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 126.71 7.54E-05 221650000 138400 154560 142200 143710 145710 119430 159180 123970 173990 FALSE TRUE 129737.7911 166003.7832 145573.0512 147397.8419 134266.5244 153907.5022 135312.4368 139447.9274 144949.945 0.895052365 1.145249025 1.004298768 1.016887878 0.926295794 1.06179759 0.933511474 0.962041948 1 17.14519526 3.267960356 2.166412042 0.977119836 1.046501463 0.015487501 0.07185045 0.54843793 5.247085673 0.020422494 0.028681877 1853.362432 -3.267960356 0.069381628 QPQSGEEAVALLEELWGPAAS(ph)PDGSSATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPQSGEEAVALLEELWGPAASPDGSSATR 29 0 Q8N0Y2-2;Q8N0Y2 Q8N0Y2-2 ZNF444 Zinc finger protein 444 1 QPQSGEEAVALLEELWGPAAS(0.894)PDGS(0.035)S(0.035)AT(0.035)R 79.395 0.0025118 18052000 24264 25327 27167 23305 24871 25586 27942 23914 35640 TRUE FALSE 22745.35955 27202.23743 27811.41407 23903.04576 22917.73198 32972.26285 23752.3565 26899.71554 29691.45376 0.766057457 0.916163879 0.93668078 0.80504801 0.771862913 1.110496748 0.799972837 0.905975024 1 14.85776011 QPS(ph)ATRLPK ddPTM_SK-BR-3_Pertuzumab_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(0.965)AT(0.035)RLPK;QPS(0.985)AT(0.015)RLPK 92.247 0.0061806 640974000 376944 555453 443724 495999 744401 328678 692771 458028 1498460 TRUE FALSE 353351.7479 596579.3181 454249.3428 508727.1741 685938.7482 423562.003 588896.4199 515213.804 1248357.346 0.283053365 0.477891463 0.363877654 0.407517267 0.549473074 0.339295479 0.471737057 0.4127134 1 20.25159954 -5 0.373867207 8.873796983 0.403947973 0.860788593 0.074323775 176.2547733 1.34428439 1122.653092 0.045111437 1.00E-05 5 -8.46984901 QPS(ph)EEEIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 QPSEEEIIK 9 0 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 1 QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK 152.47 8.43E-05 31179479000 9927030 7279210 7659410 8042570 6739760 5948909 10746300 6524710 9811890 TRUE FALSE 9305714.913 7818170.282 7841094.822 8248955.962 6210446.436 7666262.456 9134992.079 7339334.406 8174222.172 1.138422068 0.956442108 0.9592466 1.009142618 0.759759927 0.937858342 1.117536554 0.897863338 1 22.96265003 -0.046023007 7.146392421 0.999999986 0.973483674 0.00658216 0.106659383 6527765.555 1370152.595 0.098695379 0.023937146 0.899449931 0.046023007 -0.026516312 QPS(ph)LTLELFPNHTDNLNSSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QPSLTLELFPNHTDNLNSSQR 21 0 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 QPS(0.724)LT(0.276)LELFPNHTDNLNSSQR;QPS(0.999)LT(0.001)LELFPNHTDNLNSSQR;QPS(0.998)LT(0.002)LELFPNHTDNLNSSQR;QPS(0.997)LT(0.003)LELFPNHTDNLNSSQR 204.41 3.42E-22 393649000 112220 106065 104827 110619 88477 81539 134024 81617 113724 TRUE FALSE 105196.3505 113918.163 107313.5459 113457.6708 81528.37332 105077.9856 113928.3454 91807.06211 94742.72971 1.110336918 1.202394773 1.132683703 1.197534324 0.860523795 1.109087588 1.202502248 0.969014323 1 16.53172762 4.324133234 0.112350219 0.935102814 1.367695164 0.163694593 0.103272536 72.55566191 1.537671988 1.382962371 5.345666011 21092.75137 -4.324133234 0.43259235 QPS(ph)SPSHNTNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPSSPSHNTNLR 12 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 QPS(0.614)S(0.385)PSHNTNLR 87.519 0.006765 375410000 141610 178330 202510 210460 189970 177430 250470 169410 176340 TRUE FALSE 132746.8829 191533.7388 207313.6328 215860.7599 175050.5225 228651.1607 212914.3487 190561.2114 146907.7148 0.903607296 1.303769098 1.411182749 1.469362996 1.191567936 1.556427183 1.449306791 1.297149109 1 17.16455063 4.768738933 2.65799934 1.373842151 0.788218425 0.40839775 0.159384964 0.44833816 3.933730411 0.034582641 0.601387374 58713.63014 -4.768738933 -0.585623725 QPS(ph)SPYEDKDK ddPTM_SK-BR-3_Pertuzumab_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(0.492)S(0.492)PY(0.015)EDKDK 121.56 0.0011698 0 304200 108400 166310 161100 144640 117670 203650 128220 115280 TRUE FALSE 285160.665 116426.0488 170254.9517 165234.0987 133280.5578 151639.4188 173114.5731 144228.5492 96039.02326 2.96921663 1.21227856 1.772768464 1.720489163 1.387775024 1.578935454 1.802544083 1.501770263 1 16.55133311 4.746956985 24.97325046 1.548693325 2.969217349 0.764328066 0.2554765 496.3709136 1476318.685 0.055890169 0.646029354 55841.48837 -4.746956985 1.420524024 QPS(ph)SPYEDKDKDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPSSPYEDKDKDKK 14 3 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QPS(0.594)S(0.406)PYEDKDKDKK 87.287 0.038696 724040000 1541800 303210 608990 576360 565710 331340 773770 363650 712540 TRUE FALSE 1445301.49 325659.9839 623435.5304 591150.3734 521281.4186 426992.4791 657750.3718 409052.503 593612.4708 2.434755941 0.548607046 1.050239948 0.995852349 0.878151057 0.719311841 1.108046755 0.689090144 1 19.17916188 4.746097975 24.99772362 0.880556449 2.434756681 0.885173175 0.176685468 280.2136542 929309.2712 0.039830264 0.422485159 55731.14621 -4.746097975 1.554200232 QPS(ph)VETLDSPTGSHVEWCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPSVETLDSPTGSHVEWCK 19 0 F8WA39;Q13613;Q13613-2;E9PPP8;Q8NEC6 F8WA39 MTMR1 Myotubularin-related protein 1 1 QPS(0.998)VET(0.002)LDSPTGSHVEWCK 96.317 0.00083457 213920000 139580 183610 168300 197130 178180 155920 261430 185890 187810 TRUE FALSE 130843.937 197204.6754 172292.1555 202188.6895 164186.4615 200931.5729 222230.9985 209098.7757 156463.2977 0.836259614 1.260389359 1.101166587 1.292243565 1.049360866 1.284208986 1.420339477 1.336407827 1 17.25546475 2.121432241 6.883556387 1.311683405 1.136580576 0.131194046 0.166103917 0.326661696 18.40802168 0.056363384 0.041520752 132.2611337 -2.121432241 -0.17510283 QPSKEEEEEEEEEQLNQTLAEMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPSKEEEEEEEEEQLNQTLAEMK 23 1 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 0 93.583 0.0041231 28832000 33746 20361 27295 25223 23302 18380 31258 19584 31085 FALSE TRUE 31633.8981 21868.54963 27942.45029 25870.26488 21471.95492 23686.00763 26571.15309 22029.10551 25896.71268 1.221541069 0.844452726 1.078996034 0.99897872 0.829138245 0.914633757 1.026043475 0.850652582 1 14.66048135 4.753173292 24.59505938 0.950581075 1.221541307 0.516177358 0.084497895 1794.186614 3019787.85 0.019327991 0.425665998 56646.52746 -4.753173292 0.270960232 QPSS(ph)PGPTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPSSPGPTPR 10 0 Q13424-2;Q13424 Q13424-2 SNTA1 Alpha-1-syntrophin 1 QPS(0.19)S(0.81)PGPTPR 116.03 0.0024854 0 536470 482580 537850 570560 594390 488750 624550 463170 742110 TRUE FALSE 502893.3003 518310.7253 550608.056 585201.5356 547709.0071 629844.1908 530904.5255 520997.7941 618247.0468 0.813418039 0.83835536 0.890595529 0.946549666 0.885906386 1.018758107 0.858725534 0.84270163 1 19.23782392 3.935997511 1.463804852 0.919119807 0.818315484 0.340668321 0.056020186 0.529852574 2.11606097 0.01565063 0.049974084 8629.736014 -3.935997511 -0.100804323 QPSS(ph)PSHNTNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QPSSPSHNTNLR 12 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 QPS(0.283)S(0.715)PS(0.002)HNTNLR;QPS(0.243)S(0.754)PS(0.003)HNTNLR 100.68 0.0019945 825600000 237802 306950 306520 352730 336440 298510 376520 251880 260400 TRUE FALSE 222918.3973 329676.8974 313790.7991 361781.649 310017.3595 384684.9911 320064.3214 283327.7725 216937.5578 1.027569406 1.519685668 1.44645677 1.667676417 1.429062642 1.773252152 1.475375333 1.306033752 1 17.72692032 0.945891684 2.880839666 1.001592163 1.495914784 0.38347054 0.192561123 0.282812204 5.602437651 0.168210398 0.044437098 8.828596826 -0.945891684 0.49432262 QPSS(ph)PYEDKDK ddPTM_SK-BR-3_Pertuzumab_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(0.004)S(0.996)PYEDKDK;QPS(0.003)S(0.997)PYEDKDK;QPS(0.028)S(0.972)PYEDKDK;QPS(0.283)S(0.716)PYEDKDK;QPS(0.016)S(0.984)PYEDKDK 228.19 2.09E-12 4484410000 10094230 3422620 5429900 4787080 4258670 3856740 6852920 4225360 3772990 TRUE FALSE 9462450.163 3676034.346 5558699.792 4909924.577 3924211.237 4970118.229 5825388.265 4752905.497 3143253.595 3.010399854 1.169499767 1.768454127 1.562051686 1.248455181 1.581201796 1.853298848 1.512097371 1 21.58382724 4.746772455 24.98241969 1.516032201 3.0104006 0.766597542 0.267045062 495.8364828 1508421.698 0.060513157 0.685100633 55817.76658 -4.746772455 1.494368398 QPSS(ph)PYEDKDKDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QPSSPYEDKDKDK 13 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QPS(0.063)S(0.937)PYEDKDKDK;QPS(0.004)S(0.996)PYEDKDKDK;QPS(0.014)S(0.986)PYEDKDKDK 183.6 5.33E-06 1236350000 3659500 798680 1577080 1443970 1308070 1044890 2018840 1042340 1273980 TRUE FALSE 3430458.427 857815.0982 1614489.082 1481024.715 1205339.459 1346532.781 1716133.684 1172478.443 1061344.508 3.232181824 0.808234359 1.521173446 1.395423167 1.135672206 1.268704714 1.616943105 1.10471052 1 20.01746159 4.746941211 24.91564117 1.270855404 3.232182851 0.869710971 0.242948878 351.9161917 1046228.024 0.056759685 0.653495185 55839.4602 -4.746941211 1.961327448 QPSS(ph)PYEDKDKDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QPSSPYEDKDKDKK 14 3 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QPS(0.128)S(0.872)PYEDKDKDKK;QPS(0.024)S(0.976)PYEDKDKDKK 144.68 4.86E-05 2802000000 4836200 939000 2054070 1886950 1815870 1120500 2698510 1190460 2394020 TRUE FALSE 4533510.875 1008524.537 2102793.51 1935372.332 1673258.895 1443970.16 2293893.477 1339091.552 1994442.596 2.273071626 0.505667367 1.054326414 0.97038257 0.838960669 0.723996852 1.150142642 0.671411428 1 20.92755417 4.747934668 24.9130217 0.873225674 2.2730724 0.840645181 0.192718359 449.5392464 1194695.438 0.043838972 0.556111247 55967.34026 -4.747934668 1.399846726 QPSSS(ph)PSSIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QPSSSPSSIIR 11 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 QPSS(0.001)S(0.999)PSSIIR;QPSS(0.16)S(0.675)PS(0.16)S(0.004)IIR 197.25 6.05E-08 483320000 235870 266600 264130 270080 246660 229520 291490 212330 231560 TRUE FALSE 221107.3177 286339.3414 270395.2883 277010.71 227288.3186 295778.6981 247783.7806 238839.8679 192911.1401 1.14616148 1.484306926 1.401657199 1.435949785 1.178202143 1.533238039 1.284445162 1.2380823 1 17.55757693 0.920455603 1.560098801 1.0019394 1.377836429 0.448748853 0.123684864 0.381377843 1.867338421 0.104959842 0.030603198 8.326368037 -0.920455603 0.375897028 QPSVETLDS(ph)PTGSHVEWCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QPSVETLDSPTGSHVEWCK 19 0 F8WA39;Q13613;Q13613-2;E9PPP8;Q8NEC6 F8WA39 MTMR1 Myotubularin-related protein 1 1 QPS(0.001)VET(0.102)LDS(0.823)PT(0.061)GS(0.013)HVEWCK 106.99 0.00024604 0 69300 74215 80706 78266 87735 65798 98595 70597 101370 TRUE FALSE 64962.6367 79709.95582 82620.38443 80274.43806 80844.64701 84792.81446 83811.59506 79411.19085 84450.69212 0.769237469 0.943863855 0.978326907 0.950548019 0.957299993 1.004051149 0.992432305 0.94032611 1 16.36582163 4.819856346 2.253309688 0.97440489 0.68745012 0.901652916 0.021131183 0.243459973 1.196654452 0.00525239 0.149961331 66047.49433 -4.819856346 -0.286954771 QPT(ph)PPSEAAASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QPTPPSEAAASK 12 0 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 1 QPT(0.978)PPS(0.022)EAAASK;QPT(0.805)PPS(0.195)EAAASK 101.2 0.031359 348950000 970670 734230 711930 702380 868460 624250 1046060 822010 677530 TRUE FALSE 909917.4974 788593.1532 728817.3158 720404.2599 800254.6548 804460.8411 889213.0141 924639.758 564445.866 1.612054498 1.397110335 1.291208528 1.276303545 1.417770424 1.42522231 1.57537342 1.638137178 1 19.1064757 2.217225902 3.256616142 1.472803089 1.376592901 0 0.193393445 0.813343799 17.96796891 0.071158145 0.052059584 164.9019919 -2.217225902 -0.096210188 QPVSEPPADQVASDMPHS(ph)PTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QPVSEPPADQVASDMPHSPTLR 22 0 H7BYY2;Q6W2J9-4;Q6W2J9-2;Q6W2J9;H7C2V9;H7C231 H7BYY2 BCOR BCL-6 corepressor 1 QPVSEPPADQVASDMPHS(0.999)PT(0.001)LR;QPVSEPPADQVAS(0.001)DMPHS(0.986)PT(0.013)LR 184.46 1.31E-16 696740000 375880 453980 465350 490810 479470 431800 537140 399410 364630 TRUE FALSE 352354.3418 487593.1516 476388.3218 503405.0155 441814.3603 556453.6503 456600.8436 449277.2177 303770.8974 1.159934493 1.605134513 1.568248722 1.657186452 1.454432811 1.831820148 1.503109243 1.479000199 1 18.21262413 0.688190829 2.219068881 1.000225331 1.56120528 0.493014956 0.169867643 1.251553584 7.875193258 0.145450596 0.039503626 4.877427572 -0.688190829 0.560979949 QPYAVSELAGHQTSAESWGTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QPYAVSELAGHQTSAESWGTGR 22 0 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 ;;;;; 325.6 1.87E-68 7305990000 1731850 2544290 2510800 2546660 2585630 2294000 2983490 2226160 2334870 FALSE TRUE 1623456.6 2732671.879 2570357.362 2612011.607 2382565.05 2956240.56 2536143.372 2504100.976 1945165.113 0.834611205 1.404853429 1.321408319 1.342822565 1.224865197 1.519789009 1.303819072 1.287346231 1 20.89146119 0.705662239 3.898654548 1.000002833 1.306972109 0.18319219 0.178338542 8.597305003 112.5405597 0.15291366 0.039125515 5.077643888 -0.705662239 0.306969276 QQAAYYAQTS(ph)PQGMPQHPPAPQGQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QQAAYYAQTSPQGMPQHPPAPQGQ 24 0 Q96AE4 Q96AE4 FUBP1 Far upstream element-binding protein 1 1 QQAAYYAQT(0.008)S(0.992)PQGMPQHPPAPQGQ;QQAAYYAQT(0.001)S(0.999)PQGMPQHPPAPQGQ;QQAAYYAQT(0.011)S(0.989)PQGMPQHPPAPQGQ 161.49 1.24E-11 1148770000 418736 414920 394159 357600 430920 488660 629190 385952 744290 TRUE FALSE 392528.0612 445641.1085 403508.6376 366776.6214 397077.2814 629728.2093 534848.8006 434138.9568 620063.1907 0.633045256 0.718702731 0.650754058 0.591514908 0.64038196 1.015587151 0.862571442 0.700152764 1 19.24205572 2.257681899 24.99048741 0.885654016 0.654685486 0.648142446 0.090479134 151.6605722 198211.7328 0.02994892 0.025020256 181.0013855 -2.257681899 -0.23096853 QQALTVSTDPEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QQALTVSTDPEHR 13 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ; 134.4 9.60E-05 404000000 415240 383890 303390 319040 371350 460200 608060 366080 445940 FALSE TRUE 389250.8696 412313.615 310586.5541 327227.1065 342185.669 593052.2693 516887.048 411785.8938 371509.7331 1.047754163 1.109832605 0.83601189 0.88080359 0.921067844 1.596330369 1.391314956 1.108412128 1 18.50304048 2.264479107 24.99859102 1.326044707 0.959306573 0.424337559 0.177729938 175.0968794 168881.7801 0.059342862 0.049634252 183.8565502 -2.264479107 -0.366738135 QQASKS(ph)PYNGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QQASKSPYNGVR 12 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 1 QQAS(0.001)KS(0.999)PYNGVR;QQASKS(1)PYNGVR;QQAS(0.201)KS(0.798)PY(0.001)NGVR;QQAS(0.001)KS(0.999)PYNGVR 220.34 1.80E-11 1283908000 1546710 1481122 1229625 1281350 1600251 1062864 2079800 1203503 2089190 TRUE FALSE 1449904.182 1590785.814 1258792.286 1314231.61 1474573.742 1369695.583 1767953.298 1353762.999 1740490.692 0.833043341 0.91398697 0.723239884 0.755092582 0.847217252 0.786959441 1.015778657 0.777805365 1 20.73106267 1.758629149 25 0.929788949 0.811254062 0.331671292 0.081128053 10.4664394 13050.14709 0.035382006 0.019621408 57.36264236 -1.758629149 -0.118534887 QQDAQEFFLHLINMVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQDAQEFFLHLINMVER 17 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 187.39 4.69E-10 177060000 203070 243530 182940 171770 239280 273660 351830 191990 309840 FALSE TRUE 190360.2112 261561.2146 187279.4232 176177.909 220487.914 352661.1995 299076.3577 215960.3741 258125.7024 0.737470966 1.013309454 0.725535743 0.682527572 0.854188142 1.366238218 1.158646175 0.836648083 1 17.97771428 2.401090441 10.47192178 1.118555558 0.811508885 0.445661778 0.158718341 0.365677959 47.96627761 0.054247348 0.04536607 251.8201281 -2.401090441 -0.307046673 QQDLHLES(ph)PQRQPEYS(ph)PESPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQDLHLESPQRQPEYSPESPR 21 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 2 QQDLHLES(1)PQRQPEY(0.001)S(0.992)PES(0.007)PR 161.8 2.58E-11 475910000 210960 211440 231240 203100 222540 201700 256520 193460 267240 TRUE FALSE 197756.3902 227095.2376 236725.122 208311.8898 205062.6061 259927.5157 218057.2074 217613.9069 222635.9176 0.888250163 1.020029652 1.063283609 0.935661649 0.921067042 1.167500368 0.97943409 0.977442945 1 17.76432683 QQDLHLES(ph)PQRQPEYSPES(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QQDLHLESPQRQPEYSPESPR 21 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 2 QQDLHLES(1)PQRQPEYS(0.026)PES(0.974)PR;QQDLHLES(1)PQRQPEYS(0.001)PES(0.999)PR;QQDLHLES(0.999)PQRQPEY(0.001)S(0.018)PES(0.982)PR;QQDLHLES(1)PQRQPEY(0.007)S(0.409)PES(0.584)PR 196.01 5.62E-22 800544000 611300 476105 540712 501087 559555 510706 720297 488352 700900 TRUE FALSE 573039.8242 511356.3096 553537.944 513945.7408 515609.8074 658138.5316 612295.1518 549323.8222 583915.262 0.981374973 0.875737188 0.947976496 0.880171789 0.883021632 1.127113084 1.048602754 0.940759487 1 19.15539949 2.256581142 24.99856514 1.038177833 0.911643577 0.508949045 0.056023384 170.9912498 237203.2188 0.01837267 0.01534308 180.5432028 -2.256581142 -0.126534256 QQDLHLES(ph)PQRQPEYSPESPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QQDLHLESPQRQPEYSPESPR 21 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 QQDLHLES(1)PQRQPEYSPESPR;QQDLHLES(1)PQRQPEYSPESPR 178.7 3.63E-17 545340000 417860 435790 407230 410880 400180 338530 447050 329500 435970 TRUE FALSE 391706.8885 468056.345 416889.6879 421423.8764 368751.477 436258.1154 380019.0027 370638.8003 363203.7905 1.078476874 1.288687941 1.147812051 1.16029592 1.015274308 1.201138663 1.046296907 1.020470628 1 18.47041973 2.130589866 0.483912059 0.996000636 1.207734158 0.386501401 0.073022654 0.848421155 0.433223784 0.067374104 0.058825892 135.0796311 -2.130589866 0.211733522 QQDS(ph)QPEEVMDVLEMVENVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 QQDSQPEEVMDVLEMVENVK 20 0 Q9H307 Q9H307 PNN Pinin 1 QQDS(1)QPEEVMDVLEMVENVK;QQDS(1)QPEEVMDVLEMVENVK;QQDS(1)QPEEVMDVLEMVENVK;QQDS(1)QPEEVMDVLEMVENVK;QQDS(1)QPEEVMDVLEMVENVK;QQDS(1)QPEEVMDVLEMVENVK;QQDS(1)QPEEVMDVLEMVENVK;QQDS(1)QPEEVMDVLEMVENVK 142.98 5.80E-07 81665000 147050.1 106776.9 128781.2 124251.9 121460 107055.3 160385.8 115175.8 125330.4 TRUE FALSE 137846.4967 114682.7728 131835.9509 127440.4141 111921.0215 137960.4272 136337.4382 129555.7522 104411.9466 1.320217669 1.098368305 1.262651978 1.220553953 1.071917776 1.321308832 1.30576474 1.240813493 1 16.67192727 2.195296656 24.99999679 1.252051804 1.192032828 0 0.11390575 407.5009214 235471.0342 0.038433663 0.028385328 156.7821646 -2.195296656 -0.060018976 QQDTPGS(ph)PDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QQDTPGSPDHR 11 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;H0Y954 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 QQDTPGS(1)PDHR;QQDT(0.036)PGS(0.964)PDHR;QQDT(0.001)PGS(0.999)PDHR 138.73 3.32E-05 932630000 940420 976010 1079100 1240740 1265860 765250 906450 788650 763640 TRUE FALSE 881560.7909 1048274.796 1104696.762 1272579.489 1166444.462 986165.2522 770536.2376 887114.6885 636183.5507 1.385701957 1.647755266 1.736443453 2.000333846 1.833503021 1.550126927 1.211185415 1.39443198 1 19.27908354 1.873749771 3.075735631 1.222107655 1.724986577 0.631903043 0.179973502 0.172095212 2.841421849 0.094494791 0.049690168 74.77385492 -1.873749771 0.502878922 QQDTPGSPDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQDTPGSPDHR 11 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;H0Y954 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 67.519 0.059751 6236400000 134770 166450 182770 165530 187770 153180 191870 157690 161310 FALSE TRUE 126334.9863 178774.1312 187105.3907 169777.78 173023.3016 197400.5793 163100.8747 177377.9436 134386.3189 0.940088153 1.330300083 1.392294932 1.263356132 1.287506817 1.468903836 1.21367172 1.319910725 1 17.03602675 -0.488401756 8.367709685 1 1.294563333 0.272974515 0.139477387 0 0 0.122757074 0.02893412 0.324786705 0.488401756 0.294563333 QQDVIYELIQTELHHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QQDVIYELIQTELHHVR 17 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 0 ; 130.01 1.83E-05 90056000 127648 130939 123718 116842 130533 159380 209717 117461 169309 FALSE TRUE 119658.7395 140633.8598 126652.6494 119840.3635 120281.4647 205390.4187 178271.8828 132126.2644 141050.2341 0.848341304 0.997048042 0.897925836 0.849628959 0.852756222 1.456150853 1.263889308 0.936731975 1 17.10584954 2.266707081 24.99997988 1.204151234 0.903256799 0.448650738 0.148148054 169.6099709 150648.7722 0.049314065 0.041251335 184.802176 -2.266707081 -0.300894435 QQEEEKAEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQEEEKAEAR 10 1 O43818 O43818 RRP9 U3 small nucleolar RNA-interacting protein 2 0 72.652 0.040048 0 310870 289280 288870 268870 324830 224830 323510 254060 406710 FALSE TRUE 291413.2016 310698.5922 295722.1328 275769.6594 299319.1621 289734.7712 275002.6788 285779.9503 338827.4736 0.860063674 0.916981698 0.872780857 0.813894034 0.883396966 0.85511003 0.811630403 0.843437952 1 18.37019133 3.477571268 24.94087534 0.854342546 0.891701991 0 0.055055738 32.76683304 1816021.091 0.013381203 0.018701918 3003.11019 -3.477571268 0.037359445 QQEEIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQEEIRR 7 1 Q92828 Q92828 CORO2A Coronin-2A 0 93.992 0.023295 106110000 105450 87934 93378 106500 112670 114130 141670 85028 142470 FALSE TRUE 98850.07273 94444.72486 95592.97026 109232.9703 103821.3527 147077.4783 120427.8987 95643.93297 118690.8366 0.832836599 0.795720441 0.805394696 0.92031511 0.874720877 1.239164559 1.014635183 0.80582407 1 16.85684903 2.787134504 1.933784007 1.019678193 0.810879503 0.340279227 0.111129534 0.325088236 2.4046692 0.039276232 0.040105478 612.5400707 -2.787134504 -0.208798689 QQEEIS(ph)KLEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQEEISKLEER 11 1 B4DDJ5;P21757-2;P21757-3;P21757 B4DDJ5 MSR1 Macrophage scavenger receptor types I and II 1 QQEEIS(1)KLEER 64.439 0.041361 709760000 258650 758660 554780 555720 848140 822520 471170 735780 774920 TRUE FALSE 242461.5582 814831.9758 567939.6436 569980.716 781530.5056 1059968.172 400522.4326 827643.7527 645580.8458 0.375571177 1.26216876 0.879734347 0.882895953 1.210585027 1.641882931 0.620406314 1.282014109 1 19.30023825 4.748198861 24.4088328 1.076762472 0.375570647 0.394969873 0.279748127 1002.031013 2537567.724 0.062685136 0.804874184 56001.39699 -4.748198861 -0.701191824 QQEGFKPNYMENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QQEGFKPNYMENR 13 1 Q8WXF1 Q8WXF1 PSPC1 Paraspeckle component 1 0 ;; 159.22 4.19E-05 663380000 512240 556680 482770 446950 623070 368080 601260 532450 817020 FALSE TRUE 480179.8128 597897.1664 494221.5324 458419.4937 574136.5955 474338.7207 511106.6448 598927.5546 680654.0838 0.705468202 0.878415601 0.726097946 0.673498484 0.843507163 0.696886615 0.750905132 0.879929422 1 19.37656226 1.013104136 3.255118875 0.998890028 0.760354092 0.621733511 0.06406257 0.143295284 3.617031541 0.059006231 0.015418794 10.30633219 -1.013104136 -0.238535935 QQEIILWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QQEIILWR 8 0 O75436 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ; 147.19 0.0012594 340510000 282510 300860 255069 231799 275460 255278 363360 254966 399140 FALSE TRUE 264828.2034 323135.9874 261119.3571 237747.3548 253826.4828 328972.6145 308877.5413 286799.0663 332520.9555 0.796425606 0.971776311 0.785271884 0.714984577 0.763339809 0.98932897 0.928896469 0.862499225 1 18.34308574 2.235861325 24.99984504 0.939934263 0.821887441 0.446402057 0.075628846 84.4228092 781879.9014 0.02968479 0.02292224 172.1318849 -2.235861325 -0.118046822 QQEKEDKDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QQEKEDKDEK 10 2 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;; 117.98 0.00049852 676600000 3862880 1049149 2019960 1772910 1855140 1031283 2403240 1398268 2520080 FALSE TRUE 3621109.236 1126829.084 2067874.405 1818405.872 1709444.788 1328997.661 2042896.473 1572844.838 2099462.368 1.724779302 0.536722687 0.984954261 0.866129301 0.814229783 0.633018091 0.973056962 0.74916553 1 21.0015885 4.749625653 24.99759339 0.81654902 1.724779826 0.779893216 0.151106988 725.9229623 1639938.725 0.033433895 0.511840269 56185.68154 -4.749625653 0.908230806 QQELDNLLHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQELDNLLHEK 11 0 Q12788;J3KNP2 Q12788 TBL3 Transducin beta-like protein 3 0 136.93 8.89E-05 86597000 263530 215870 231870 242300 234260 210160 311960 216970 254050 FALSE TRUE 247036.1277 231853.2394 237370.0659 248517.8282 215862.1646 270829.7803 265184.4941 244059.1821 211647.4138 1.167205983 1.095469277 1.121535395 1.17420678 1.01991402 1.279627166 1.252954096 1.153140394 1 17.69130333 2.230760248 24.99986122 1.202097391 1.116373414 0.044509265 0.086624438 277.2926915 888704.0758 0.028898026 0.02174105 170.121909 -2.230760248 -0.085723977 QQELTHQEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQELTHQEHR 10 0 P18206;P18206-2;P18206-3 P18206 VCL Vinculin 0 134.13 0.0001034 1646500000 430590 468960 514060 428120 553540 459820 582590 487100 480860 FALSE TRUE 403640.1405 503682.2864 526253.746 439106.284 510067.2013 592562.5694 495236.038 547915.5072 400601.3595 1.007585548 1.257315469 1.313659411 1.096117808 1.273253795 1.479182622 1.236231546 1.367732521 1 18.61180779 4.738267958 4.882848417 1.2716107 0.993675055 0.241523279 0.133299251 0.218531888 15.58359269 0.028588047 0.206325181 54735.35733 -4.738267958 -0.277935644 QQEQADSLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQEQADSLER 10 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 140.49 9.12E-05 49187000 100890 129070 110650 119680 122390 106980 130150 104630 130670 FALSE TRUE 94575.47499 138626.4771 113274.6703 122751.1914 112777.9831 137863.3893 110635.2158 117693.2858 108860.3328 0.868778117 1.273434257 1.040550468 1.127602573 1.035987859 1.26642447 1.016304221 1.081140235 1 16.73211883 1.605235239 25 1.036535818 1.115236868 0.064812686 0.11755525 0.623393033 5854.745708 0.053371065 0.026458125 40.29352283 -1.605235239 0.07870105 QQGHEPVS(ph)PR ddPTM_SK-BR-3_Pertuzumab_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 149.02 2.45E-05 2371320000 2072570 2063970 2165350 1980570 2128000 1822610 2346280 1891700 2184610 TRUE FALSE 1942851.543 2216788.486 2216713.125 2031394.779 1960875.464 2348767.919 1994477.096 2127882.909 1819984.478 1.067509952 1.21802604 1.217984632 1.116160497 1.07741329 1.29054283 1.095875882 1.169176405 1 20.79549472 -0.918367559 0.474550411 0.947415825 1.171602508 0.306826361 0.071816571 18.18585325 2.756937032 1.416271851 0.034545843 0.120679205 0.918367559 0.224186683 QQHGEANKENIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QQHGEANKENIR 12 1 O75934 O75934 BCAS2 Pre-mRNA-splicing factor SPF27 0 ; 146.79 3.91E-05 245290000 369870 294440 312880 303060 357180 256930 409990 278190 385770 FALSE TRUE 346720.4969 316240.644 320301.6614 310837.0327 329128.5236 331101.5201 348515.8057 312922.6339 321382.4948 1.078840642 0.984000837 0.996636925 0.967187192 1.024102211 1.030241303 1.084426847 0.973676659 1 18.29393182 2.494140945 21.73811319 1.034097891 1.000659967 0 0.040671618 264.0204233 337217.6006 0.012608352 0.011587479 311.9901943 -2.494140945 -0.033437924 QQHVIETLIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QQHVIETLIGK 11 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ; 155.15 3.17E-05 977110000 2705900 2069040 2043310 1959920 2332010 2305350 3172200 2029050 2802900 FALSE TRUE 2536542.549 2222233.874 2091778.278 2010214.865 2148863.341 2970867.121 2696558.059 2282381.359 2335077.883 1.086277493 0.951674414 0.895806643 0.86087701 0.920253392 1.27227753 1.154804334 0.977432648 1 21.15503924 2.269219206 24.99863522 1.124049557 0.933999318 0.370197311 0.100165306 172.1965363 140406.3631 0.033552335 0.028068924 185.8742403 -2.269219206 -0.190050239 QQITEKEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQITEKEEK 9 1 P12270 P12270 TPR Nucleoprotein TPR 0 99.522 0.0048153 144620000 399680 290750 336130 338820 400830 229540 451130 305250 613430 FALSE TRUE 374664.7422 312277.4325 344103.1623 347514.6948 369350.4287 295804.4717 383487.2446 343361.1344 511044.5701 0.733135159 0.611057138 0.673332978 0.680008585 0.722736235 0.578823236 0.750398824 0.671880995 1 18.96308959 -2.097074406 0.3955003 1.369480486 0.661702785 0.785818914 0.05277018 20.04718047 1.155885391 6.680611544 0.030265224 0.007996972 2.097074406 -0.707777701 QQLPQT(ph)PPSCLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQLPQTPPSCLK 12 0 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 1 QQLPQT(1)PPSCLK 138.02 0.00071861 0 231350 181370 216760 188370 211980 173610 266730 160860 285960 TRUE FALSE 216870.2165 194798.8235 221901.6496 193203.8931 195331.9459 223728.3887 226736.3127 180943.7251 238231.4286 0.910334198 0.817687341 0.931454136 0.810992463 0.819925175 0.939122054 0.951748113 0.759529195 1 17.86200423 2.228139786 24.99468803 0.914294955 0.860436217 0.123127658 0.072082959 451.1706704 1082139.148 0.024945278 0.018622281 169.0985121 -2.228139786 -0.053858738 QQLQMLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQLQMLDR 8 0 Q6ZU80;H0YJE3;Q6ZU80-1 Q6ZU80 CEP128 Centrosomal protein of 128 kDa 0 60.973 0.06744 100380000 35657 57274 47313 46865 48026 29008 48189 56183 68168 FALSE TRUE 33425.29202 61514.62655 48435.2867 48067.63524 44254.23169 37382.13869 40963.50681 63197.57122 56790.32042 0.588573753 1.08318858 0.852879264 0.846405424 0.779256594 0.65824842 0.721311423 1.112822938 1 15.79335743 1.233084057 24.99877139 1.056411559 0.815399862 0.388411424 0.136115581 174.2378536 795298.8488 0.124668788 0.034675841 17.10346316 -1.233084057 -0.241011697 QQLS(ph)AEELDAQLDAYNAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QQLSAEELDAQLDAYNAR 18 0 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 1 QQLS(1)AEELDAQLDAYNAR;QQLS(1)AEELDAQLDAYNAR 259.64 1.10E-30 138735000 91793 109739 113479 106256 109227 97499 130830 85858 135628 TRUE FALSE 86047.83999 117864.1897 116170.7755 108982.7089 100648.752 125645.3785 111213.2561 96577.5603 112990.8106 0.76154724 1.043130756 1.028143571 0.964527188 0.89076936 1.111996435 0.984268149 0.854738184 1 16.78584592 4.746171962 24.64701415 0.993746316 0.761547104 0.473363619 0.073420634 653.5887255 2116385.353 0.016735185 0.177207684 55740.64149 -4.746171962 -0.232199212 QQLS(ph)PSPGQEAGILPETEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QQLSPSPGQEAGILPETEK 19 0 E5RJM0;B7ZLQ8;Q17RY0-2;Q17RY0 E5RJM0 CPEB4 Cytoplasmic polyadenylation element-binding protein 4 1 QQLS(0.925)PS(0.075)PGQEAGILPETEK;QQLS(0.999)PS(0.001)PGQEAGILPETEK;QQLS(1)PSPGQEAGILPETEK 259.16 4.91E-31 368112000 718040 573061 690854 682095 681270 412278 519883 381463 806260 TRUE FALSE 673099.1581 615491.0327 707241.3831 699598.7125 627765.8023 531295.9658 441931.3705 429089.4953 671689.9974 1.002097933 0.916331991 1.052928264 1.041549994 0.934606448 0.790983888 0.657939484 0.638820731 1 19.35743602 2.241183783 2.954004289 0.727299998 0.996095405 0.509973443 0.105271745 0.167926016 3.029716682 0.039104801 0.028635339 174.254412 -2.241183783 0.268795408 QQLSAEELDAQLDAYNAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQLSAEELDAQLDAYNAR 18 0 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 180.06 3.10E-14 0 54161 65902 58465 54315 74063 66640 80445 58160 101600 FALSE TRUE 50771.15969 70781.45265 59851.81741 55708.81486 68246.39074 85877.88619 68383.01906 65421.40403 84642.30364 0.599831969 0.83624204 0.707114703 0.658167517 0.806291745 1.014597695 0.80790593 0.772916157 1 16.36909127 2.478056748 24.99985413 0.883388288 0.724929901 0.480736733 0.095178405 35.05691331 936898.9178 0.031092408 0.026319996 300.6469126 -2.478056748 -0.158458387 QQMLEQHLQDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QQMLEQHLQDVR 12 0 P40763;P40763-2;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 ; 125.61 0.00022733 1047100000 1470630 1630160 1731450 1777950 1810290 1752490 2671100 1536280 2988500 FALSE TRUE 1378585.893 1750858.743 1772520.812 1823575.207 1668117.126 2258405.414 2270593.352 1728087.94 2489700.044 0.553715656 0.703240837 0.711941511 0.732447755 0.670007269 0.907099399 0.911994743 0.694094835 1 21.24754051 5.673789655 0.105529481 1.137425286 1.67E-10 0.617235622 0.083363979 43.92356426 0.566195961 1.097079393 7.336003249 471834.459 -5.673789655 -1.137425286 QQNAS(ph)ESKLELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QQNASESKLELR 12 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 QQNAS(0.993)ES(0.007)KLELR;QQNAS(0.961)ES(0.039)KLELR;QQNAS(0.985)ES(0.015)KLELR;QQNAS(0.976)ES(0.024)KLELR;QQNAS(0.937)ES(0.063)KLELR 177.76 1.38E-05 1584930000 4601550 2989640 3372910 3110840 2822410 2214040 4796880 3185130 2959230 TRUE FALSE 4313547.2 3210996.056 3452917.018 3190669.421 2600749.304 2853197.406 4077632.376 3582800.492 2465315.396 1.749693855 1.302468667 1.400598489 1.294223622 1.054935733 1.157335654 1.654000289 1.453282812 1 21.2333408 -2.195215743 2.176739162 0.000210598 1.375805074 0.251907379 0.207236506 2731296.626 491363.8204 13482326.63 0.049815051 0.006379465 2.195215743 1.375594476 QQNDQNRPSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QQNDQNRPSEK 11 1 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 0 ;; 123.84 0.00032982 232222000 356700 271876 310604 298730 299160 260370 374721 270221 294698 FALSE TRUE 334374.7837 292005.9819 317971.6736 306395.9175 275665.1804 335534.5922 318535.0648 303958.6867 245511 1.361954388 1.189380443 1.295142269 1.247992626 1.122822115 1.366678447 1.297437039 1.23806545 1 17.90542814 0.951585057 19.63668186 0.999999999 1.264714164 0.56828187 0.072981859 495.6370807 201027.5064 0.065701609 0.016425402 8.945097044 -0.951585057 0.264714165 QQPGPSEHIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQPGPSEHIER 11 0 P50552;K7EQD0 P50552 VASP Vasodilator-stimulated phosphoprotein 0 123.64 0.0010639 0 99916 105260 110750 102010 109640 76349 111810 75827 104420 FALSE TRUE 93662.43592 113053.5599 113377.0423 104627.7493 101029.3167 98389.71688 95045.12849 85294.16787 86991.62742 1.076683339 1.299591274 1.30330982 1.202733555 1.161368279 1.131025132 1.092577887 0.980487093 1 16.40858893 1.907584592 0.907512818 0.989367569 1.249477832 0.626020872 0.066958946 0.330960207 0.503774595 0.056273405 0.025933022 80.83223591 -1.907584592 0.260110263 QQPPEPEWIGDGESTS(ph)PSDKVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QQPPEPEWIGDGESTSPSDKVVK 23 1 Q5STZ8;Q8NE71;Q8NE71-2;A0A0G2JIC2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 QQPPEPEWIGDGES(0.007)T(0.233)S(0.757)PS(0.003)DKVVK;QQPPEPEWIGDGES(0.055)T(0.206)S(0.735)PS(0.005)DKVVK;QQPPEPEWIGDGES(0.021)T(0.226)S(0.747)PS(0.006)DKVVK;QQPPEPEWIGDGES(0.002)T(0.401)S(0.561)PS(0.036)DKVVK;QQPPEPEWIGDGES(0.005)T(0.208)S(0.765)PS(0.022)DKVVK 176 5.29E-13 3010710000 2463560 1698900 2007530 1968180 2230290 1349950 2550850 1503670 2812970 TRUE FALSE 2309370.177 1824688.324 2055149.56 2018686.831 2055132.02 1739658.65 2168373.723 1691406.509 2343467.135 0.985450209 0.778627657 0.876969653 0.861410344 0.876962168 0.74234395 0.925284461 0.721753885 1 21.16021313 -1.26092488 5.075805085 1.000027384 0.845508292 0.264250385 0.080699077 2.13E-05 3.10E-06 0.066485568 0.015668023 0.054837181 1.26092488 -0.154519093 QQPPLGPSSS(ph)LLSLPGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QQPPLGPSSSLLSLPGLK 18 0 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 QQPPLGPS(0.033)S(0.163)S(0.804)LLSLPGLK;QQPPLGPS(0.004)S(0.262)S(0.734)LLSLPGLK 264.37 6.12E-31 790930000 987800 1142270 975930 1011240 1304120 761690 1660480 1178030 1879000 TRUE FALSE 925975.3613 1226844.859 999079.5205 1037190.13 1201699.676 981577.538 1411506.439 1325109.639 1565382.761 0.591532872 0.783734745 0.638233373 0.662579247 0.767671464 0.627052733 0.901700513 0.846508389 1 20.57808403 1.459263885 1.270938125 0.975304961 0.685013648 0.688305988 0.073528957 0.222935891 0.69105012 0.059654931 0.020107254 28.79147303 -1.459263885 -0.290291313 QQQEELEAEHGTGDKPAAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQQEELEAEHGTGDKPAAPR 20 1 Q13895;F8WBL2 Q13895 BYSL Bystin 0 134.07 5.78E-06 295990000 186100 174910 175520 176980 181700 151880 252510 171160 210840 FALSE TRUE 174452.3332 187860.5184 179683.4173 181521.6064 167430.0149 195725.2904 214648.4697 192529.7028 175649.4419 0.993184671 1.069519586 1.022966059 1.033431159 0.953205505 1.114294975 1.222027621 1.09610199 1 17.42233947 2.072249696 7.931712011 1.139965353 1.024329376 0.299736945 0.063609994 0.217134693 20.80499814 0.022056265 0.016254255 118.0999453 -2.072249696 -0.115635977 QQQQQQHGS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQQQQQHGSPTR 12 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 QQQQQQHGS(0.98)PT(0.02)R 64.394 0.041163 18819000 17808 15797 18989 16862 13920 19185 22828 18030 23547 TRUE FALSE 16693.42907 16966.62632 19439.42805 17294.70747 12826.77935 24723.39806 19405.15332 20281.08519 19616.85358 0.850973832 0.864900492 0.990955454 0.881624945 0.653865274 1.260314145 0.989208246 1.033860252 1 14.25980604 2.234014817 24.9999993 1.068094639 0.871643316 0.490761259 0.111163264 107.8576773 593164.9451 0.039271651 0.029981753 171.4015783 -2.234014817 -0.196451323 QQQQQQQHQQPNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 197.73 1.31E-07 233264000 20285.9 38404.3 24152.1 32150.6 49793 17431.4 21409.6 24716.6 74072 FALSE TRUE 19016.24173 41247.79433 24724.99922 32975.63883 45882.45864 22463.5622 18199.42924 27802.52192 61708.90468 0.308160416 0.66842532 0.400671497 0.534374075 0.743530595 0.364024646 0.294923874 0.450543111 1 15.91319107 -1.396224648 4.006480394 1.0020045 0.4739584 0.565080457 0.145938958 48857382.21 17034287.75 856002.4115 0.034458648 0.040158303 1.396224648 -0.5280461 QQQQQQQQHSENKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QQQQQQQQHSENKR 14 1 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 0 ;; 193.06 1.96E-07 164590000 172152 126111 145553 138475 138283 127434 193758 134244 177866 FALSE TRUE 161377.3136 135448.3897 149005.5859 142028.5029 127422.811 164222.1271 164705.7867 151004.6589 148179.0155 1.089069954 0.914086176 1.005578188 0.958492688 0.859924805 1.108268445 1.111532467 1.01906912 1 17.17698163 2.212701446 24.99999117 1.074969704 0.963588185 0.309698818 0.068249834 219.710988 212409.5875 0.023646287 0.017469826 163.1929697 -2.212701446 -0.111381519 QQS(ph)GSELEELMNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QQSGSELEELMNK 13 0 Q9H6S3;Q9H6S3-3;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 QQS(0.938)GS(0.062)ELEELMNK;QQS(0.999)GS(0.001)ELEELMNK;QQS(0.995)GS(0.005)ELEELMNK 280.5 2.21E-32 155935000 635050 356710 422750 375710 417990 397290 412930 270985 605640 TRUE FALSE 595303.3541 383121.1796 432777.8296 385351.3547 385162.7515 511981.1735 351014.98 304818.0738 504554.7714 1.179858735 0.759325253 0.857742022 0.763745338 0.763371537 1.014718723 0.695692519 0.604132774 1 18.94465136 4.742528942 24.60264016 0.801661388 1.179858919 0.462906604 0.125971656 271.3144935 1681999.797 0.027380356 0.208055954 55275.02429 -4.742528942 0.37819753 QQS(ph)LGGFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QQSLGGFFK 9 0 O75363;G3XAF7;O75363-2;H0Y542;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 QQS(1)LGGFFK;QQS(1)LGGFFK 129.34 0.00041113 655030000 1791700 1511340 1321270 1389970 1468390 948010 2215830 1385750 2460410 TRUE FALSE 1679560.695 1623241.186 1352611.148 1425638.983 1353068.573 1221685.097 1883586.862 1558763.938 2049751.676 0.819397157 0.791920897 0.659890251 0.695517901 0.660113412 0.596016147 0.918934173 0.76046477 1 20.96701771 1.050401067 1.095854616 0.985777876 0.714247446 0.475477579 0.089688955 0.435082092 1.101191067 0.08243759 0.026682643 11.23055107 -1.050401067 -0.27153043 QQS(ph)LPLRPIIPLVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQSLPLRPIIPLVAR 15 1 Q9NU19 Q9NU19 TBC1D22B TBC1 domain family member 22B 1 QQS(1)LPLRPIIPLVAR 103.66 0.00088119 111850000 109110 141640 108430 128950 110190 77154 162010 84707 144200 TRUE FALSE 102280.9999 152127.173 111002.0108 132259.0753 101536.1219 99427.10731 137718.1045 95282.85541 120132.0884 0.851404493 1.266332542 0.923999676 1.100947108 0.845204002 0.827648205 1.146388998 0.793150745 1 16.87426203 3.735967517 24.25521968 0.960215851 1.090504232 0.072847773 0.150612475 454.4687882 1246076.677 0.035549837 0.062862711 5444.61928 -3.735967517 0.130288381 QQS(ph)PQEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 QQSPQEPK 8 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK;QQS(1)PQEPK 199.59 0.00013289 20224798000 15549208 10374122 12620979 11837429 13249060 8668389 12016711 8758722 16187160 TRUE FALSE 14576010.83 11142232.79 12920354.58 12141197.47 12208532.27 11170812.18 10214916.74 9852267.722 13485418.42 1.080871974 0.826243016 0.95809816 0.900320412 0.905313568 0.828362297 0.757478665 0.730586728 1 23.68489695 2.222512454 3.166590458 0.800350375 0.923154085 0.207357855 0.095839011 0.316671437 6.600167563 0.034895846 0.025512636 166.9215673 -2.222512454 0.122803709 QQS(ph)PS(ph)PIR ddPTM_SK-BR-3_Pertuzumab_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 55.314 0.065872 615930000 0 12480 0 13000 8277.1 0 14138 10845 0 TRUE FALSE 0 13404.03219 0 13333.60201 7627.049954 0 12018.13815 12199.02212 0 0 QQSGS(ph)ELEELMNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQSGSELEELMNK 13 0 Q9H6S3;Q9H6S3-3;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 QQS(0.065)GS(0.935)ELEELMNK 318.62 7.30E-51 64202000 274520 156770 177800 161580 196090 166540 177480 122760 261390 TRUE FALSE 257338.2832 168377.4139 182017.5 165726.4164 180689.8824 214617.3944 150868.5216 138086.8562 217762.3204 1.18173926 0.773216476 0.83585397 0.761042664 0.829757334 0.985557989 0.692812794 0.634117307 1 17.73239482 4.741600368 24.70490038 0.805654097 1.181739423 0.50588868 0.113934267 192.1598593 1561644.395 0.025066556 0.177737807 55156.96583 -4.741600368 0.376085326 QQSHFAMMHGGTGFAGIDSS(ph)SPEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QQSHFAMMHGGTGFAGIDSSSPEVK 25 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 QQSHFAMMHGGTGFAGIDS(0.118)S(0.525)S(0.357)PEVK;QQSHFAMMHGGTGFAGIDS(0.005)S(0.498)S(0.498)PEVK;QQSHFAMMHGGTGFAGIDS(0.012)S(0.558)S(0.43)PEVK 88.79 0.016968 640390000 315361 236171 205866 186980 319620 443830 764401 282748 879823 TRUE FALSE 295623.1179 253657.3466 210749.2387 191778.2234 294518.3345 571956.516 649786.1664 318049.7102 732974.8574 0.403319589 0.346065549 0.287525877 0.261643659 0.401812329 0.780322149 0.886505396 0.433916262 1 19.48340419 2.286428635 4.33116807 0.781878562 0.323650977 0.687845774 0.146275513 0.107784355 4.267152176 0.04884919 0.039049315 193.3876051 -2.286428635 -0.458227584 QQSHFAMMHGGTGFAGIDSSS(ph)PEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QQSHFAMMHGGTGFAGIDSSSPEVK 25 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 QQSHFAMMHGGTGFAGIDS(0.044)S(0.23)S(0.726)PEVK;QQSHFAMMHGGTGFAGIDS(0.002)S(0.053)S(0.945)PEVK;QQSHFAMMHGGTGFAGIDS(0.001)S(0.156)S(0.843)PEVK;QQSHFAMMHGGTGFAGIDS(0.006)S(0.128)S(0.866)PEVK 128.17 0.00012985 899370000 576655 381493 330658 347983 584015 741113 1344622 526558 1520413 TRUE FALSE 540563.1929 409739.1387 338501.3639 356912.8329 538148.8177 955060.2921 1143008.414 592299.9254 1266646.248 0.426767295 0.323483482 0.267242227 0.281777831 0.424861179 0.754007122 0.90238961 0.467612742 1 20.27258223 2.29553662 3.376475673 0.792344474 0.317695141 0.708888363 0.140234305 0.116244658 2.703899975 0.048856401 0.038107841 197.4861392 -2.29553662 -0.474649333 QQSNEHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQSNEHLR 8 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 174.02 0.00027436 117700000 171880 171750 136370 120510 148360 106480 162210 172080 159260 FALSE TRUE 161122.3376 184466.5487 139604.7608 123602.4906 136708.4041 137219.0474 137888.1164 193564.5668 132678.4771 1.214381873 1.3903276 1.052203521 0.931594131 1.03037363 1.034222358 1.039265142 1.458899521 1 17.01757483 3.874132993 3.926371976 1.067781305 1.303608127 0.282615087 0.147427286 0.252236247 7.037167239 0.03632762 0.070086081 7483.986461 -3.874132993 0.235826822 QQSS(ph)SSKGDSPELKPR ddPTM_SK-BR-3_Pertuzumab_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(0.137)S(0.415)S(0.096)S(0.06)KGDS(0.291)PELKPR 140.2 8.99E-07 324330000 913720 451600 620470 426620 684670 515190 938140 649130 1911600 TRUE FALSE 856531.8962 485036.9339 635187.8414 437567.7915 630898.78 663916.9896 797474.6163 730175.3094 1592541.611 0.537839571 0.304567825 0.398851645 0.274760665 0.396158427 0.416891455 0.500755906 0.458496848 1 20.60289964 -0.025162309 0.564606903 1.047496841 0.367920703 0.863996888 0.074270067 1.377296204 0.507795477 0.213239263 0.029456541 0.943708119 0.025162309 -0.679576138 QQSSSSKGDS(ph)PELKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QQSSSSKGDSPELKPR 16 2 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 QQS(0.01)S(0.057)S(0.019)S(0.013)KGDS(0.9)PELKPR;QQS(0.004)S(0.002)S(0.002)S(0.001)KGDS(0.991)PELKPR;QQS(0.001)S(0.001)S(0.001)S(0.002)KGDS(0.995)PELKPR 185.87 8.30E-10 2316340000 3440280 1781590 2284650 1827400 2552650 2004650 3842690 2428240 7255100 TRUE FALSE 3224959.016 1913500.777 2338842.977 1874294.178 2352175.166 2583359.912 3266514.308 2731411.109 6044176.94 0.533564627 0.316585831 0.386958059 0.310099158 0.38916385 0.427413019 0.540439888 0.451907867 1 22.52711446 -0.053293408 0.507699457 1.063108037 0.369958454 0.868157437 0.071891425 1.415087631 0.430850134 0.246165547 0.032807881 0.884517831 0.053293408 -0.693149583 QQTEKPES(ph)EDEWER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QQTEKPESEDEWER 14 1 O60231;A0A140T947;A2AB15 O60231 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 1 QQTEKPES(1)EDEWER;QQTEKPES(1)EDEWER;QQTEKPES(1)EDEWER 214.26 4.20E-12 3813240000 4383900 2568520 3149100 2788470 3194890 2367200 4250260 2639220 4096520 TRUE FALSE 4109519.524 2758695.893 3223798.139 2860026.861 2943976.227 3050572.212 3612972.97 2968732.427 3412784.347 1.204154469 0.808341698 0.94462404 0.83803328 0.862631777 0.893866093 1.058658445 0.869885737 1 21.70251782 1.781429867 25 0.982051644 0.908250607 0.026057711 0.117782437 183.7107911 107172.1261 0.049205457 0.027383948 60.45467164 -1.781429867 -0.073801038 QQVSWEQEFLVGSS(ph)PGGSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QQVSWEQEFLVGSSPGGSGR 20 0 Q9BUA3 Q9BUA3 C11orf84 Uncharacterized protein C11orf84 1 QQVSWEQEFLVGS(0.048)S(0.952)PGGSGR 212.65 1.59E-22 42954000 70882 72985 64596 57091 66311 80696 99469 69288 95930 TRUE FALSE 66445.62215 78388.88534 66128.24762 58556.05171 61103.20155 103991.6252 84554.54687 77938.75932 79918.66327 0.831415585 0.980858314 0.827444366 0.732695585 0.764567362 1.301218276 1.058007522 0.975226013 1 16.28624483 2.258512048 24.99974474 1.092784609 0.844024853 0.578709428 0.107985708 177.8917635 222903.1984 0.03780079 0.031588502 181.3476982 -2.258512048 -0.248759756 QRDEKDEHGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QRDEKDEHGR 10 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 96.113 0.0039155 84986000 32337 27847 31193 28697 30495 20652 28989 27884 50702 FALSE TRUE 30313.08489 29908.82085 31932.91269 29433.4136 28100.04571 26613.89714 24642.36857 31365.37878 42239.50865 0.717647668 0.708076912 0.75599631 0.696821875 0.665255033 0.630071182 0.583396194 0.742560219 1 15.36630543 0.973719225 23.78841323 1.000000002 0.681536746 0.816154535 0.047529649 717.3171144 649290.7245 0.055274548 0.013818637 9.412808544 -0.973719225 -0.318463256 QRDELNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QRDELNR 7 1 P43034;I3L495 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ;;; 187.34 0.0005342 1402490000 606671 640980 602630 600520 612640 562555 663350 578200 694970 FALSE TRUE 568700.545 688438.8261 616924.6682 615930.3599 564525.7257 724955.4962 563886.8257 650389.5428 578975.0173 0.982254032 1.189064822 1.065546267 1.063828907 0.975043324 1.252136059 0.973939823 1.123346471 1 19.14314157 -4.999999909 0.21095388 0.594803106 1.095343889 0.049333849 0.092552748 399.915645 3.990018826 68.46998115 0.175169633 1.00E-05 4.999999909 0.500540783 QREEHYFCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QREEHYFCK 9 1 Q9BQ69 Q9BQ69 MACROD1 O-acetyl-ADP-ribose deacetylase MACROD1 0 83 0.010131 167940000 341200 451670 329600 316430 519720 254700 353100 405830 590440 FALSE TRUE 319844.9011 485112.1168 337418.2676 324550.1295 478903.2876 328227.7553 300155.933 456498.7688 491891.7496 0.650234328 0.986217226 0.685960413 0.659799905 0.973594877 0.667276399 0.610207293 0.928047216 1 18.90798133 1.046326944 8.097058363 0.999874034 0.758552966 0.324584568 0.131313879 0.252726113 37.28206116 0.125154743 0.031341462 11.12568971 -1.046326944 -0.241321068 QREEKS(ph)PDDLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QREEKSPDDLKK 12 3 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 QREEKS(1)PDDLKK 123.02 0.0019237 313660000 1222800 311630 535120 480990 531220 321530 831720 359580 900650 TRUE FALSE 1146267.131 334703.4095 547813.2991 493333.0177 489500.124 414350.4914 707011.3073 404474.3545 750325.6966 1.527692755 0.446077498 0.730100677 0.657491833 0.652383527 0.55222751 0.94227255 0.539065044 1 19.51715744 -1.059022151 8.305653807 1.000000004 0.726787964 0.05194175 0.306003023 1.83E-08 2.57E-09 0.260059336 0.061296572 0.087292684 1.059022151 -0.27321204 QREESYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QREESYSR 8 1 P23246;P23246-2;H0Y9K7;H0Y9U2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 174.02 0.00025021 1878940000 430540 544170 411790 416100 551130 320280 393330 473670 551290 FALSE TRUE 403593.2699 584460.913 421557.8533 426777.8305 507846.473 412739.6367 334353.818 532808.7422 459276.1375 0.878759502 1.272569736 0.917874496 0.929240158 1.105754102 0.898674246 0.72800172 1.160105433 1 18.8090023 3.734051385 21.43679088 0.939306157 1.101222611 0.066398214 0.151236324 74.00434774 228902.8834 0.0374228 0.065302474 5420.65023 -3.734051385 0.161916454 QRELEIEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QRELEIEER 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 160.77 5.93E-05 508830000 288640 421310 368480 383200 459090 302540 481540 391060 573860 FALSE TRUE 270574.5376 452504.2308 377220.5196 393033.5608 423034.9233 389878.3867 409337.5474 439884.7018 478079.0587 0.565961911 0.946505024 0.789033765 0.82210997 0.884863948 0.815510279 0.856213088 0.920108701 1 18.86688969 1.823864876 0.030459543 1.738728187 5.32E-08 0.405106243 0.090559075 137.5715653 3.757656265 104.4888206 108.475552 66.65993348 -1.823864876 -1.738728134 QRELEQLGR ddPTM_SK-BR-3_Pertuzumab_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 87.895 0.011994 180630000 229300 158560 239280 242360 232800 224660 297830 177130 250630 FALSE TRUE 214948.5223 170299.9474 244955.8346 248579.3679 214516.8271 289515.6949 253173.1564 199245.0704 208798.2339 1.029455654 0.815619674 1.173170051 1.190524284 1.02738813 1.386581149 1.212525373 0.954246914 1 17.67174998 3.849115535 3.928057181 1.160047828 0.918868196 0.284573665 0.135023266 0.226571258 6.23255425 0.033256164 0.063412338 7065.054805 -3.849115535 -0.241179632 QRESDITK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QRESDITK 8 1 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 110.88 0.0030464 410610000 415180 394140 367360 395930 517530 287280 516270 455240 695460 FALSE TRUE 389194.6249 423322.5357 376073.9527 406090.2341 476885.2814 370213.0724 438860.1063 512077.7161 579383.2332 0.671739537 0.730643401 0.649093607 0.700900908 0.82309127 0.638977884 0.757460833 0.883832474 1 19.14415841 1.123058228 2.113767952 0.997645758 0.703148586 0.794766468 0.051428476 0.118186997 1.001752024 0.04495649 0.012682639 13.2757244 -1.123058228 -0.294497173 QRIDEFEAL ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QRIDEFEAL 9 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 127.56 0.0036036 1085830000 1228290 1956550 1074040 1060290 2322400 769880 1135960 1653320 2422600 FALSE TRUE 1151413.521 2101414.998 1099516.736 1087498.836 2140008.072 992131.858 965633.3437 1859740.641 2018252.409 0.570500259 1.041205247 0.544786535 0.538831928 1.060327272 0.491579672 0.478450237 0.92146088 1 20.94467518 1.055556332 8.593260323 0.999830224 0.687424069 0.242627769 0.211442278 0.353562931 47.97872523 0.200923861 0.050294359 11.36465698 -1.055556332 -0.312406155 QRLEAEAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QRLEAEAGR 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 160.18 5.97E-05 804370000 537720 857490 519640 564850 901900 458180 656890 681080 843400 FALSE TRUE 504065.0651 920979.4518 531966.1062 579345.0073 831068.4121 590449.1281 558395.4428 766114.3372 702631.0914 0.717396471 1.310758182 0.757105845 0.824536538 1.182794815 0.840340166 0.794720657 1.09035075 1 19.42240789 3.944998884 24.71662371 0.911258091 1.053644356 0.019648852 0.195148242 662.4008912 509685.7348 0.045996417 0.082929894 8810.466097 -3.944998884 0.142386265 QRPDLGS(ph)AQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QRPDLGSAQK 10 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RFR3 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 1 QRPDLGS(1)AQK;QRPDLGS(1)AQK;QRPDLGS(1)AQK;QRPDLGS(1)AQK 143.56 2.04E-05 1630140000 1629510 1149569 1331403 1220303 1412900 1190233 2074270 1256922 2037770 TRUE FALSE 1527521.878 1234684.285 1362984.508 1251618.041 1301936.533 1533833.945 1763252.47 1413851.479 1697653.023 0.899784501 0.72728895 0.802864007 0.737263754 0.766903788 0.903502615 1.038641257 0.832827121 1 20.69511019 2.114446224 4.19119276 0.963492064 0.778854568 0.558981309 0.070081215 0.135824177 4.293854406 0.025159824 0.017946079 130.1506149 -2.114446224 -0.184637496 QRS(ph)DDESPSTSSGSSDADQRDPAAPEPEEQEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QRSDDESPSTSSGSSDADQRDPAAPEPEEQEER 33 2 R4GN77;R4GND1;A0A1B0GX65;Q969T4;R4GMM6;R4GNG6 R4GN77 UBE2E3 Ubiquitin-conjugating enzyme E2 E3 1 QRS(1)DDESPSTSSGSSDADQRDPAAPEPEEQEER;QRS(0.999)DDES(0.001)PSTSSGSSDADQRDPAAPEPEEQEER 303.21 2.41E-90 1156480000 90220 96238 108471 131789 145928 89801 125091 110739 123511 TRUE FALSE 84573.29125 103363.5617 111043.9833 135170.9289 134467.4035 115725.0909 106334.7658 124565.0079 102896.2162 0.821928098 1.004541911 1.079184322 1.313662775 1.306825542 1.124677808 1.033417649 1.21058881 1 16.65083041 4.533260584 1.158779932 1.156134826 0.749322561 0.515636264 0.104411694 1.002965623 1.452689163 0.032110084 0.453138456 34139.76943 -4.533260584 -0.406812265 QRS(ph)PIALPVKQEPPQIDAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QRSPIALPVKQEPPQIDAVK 20 2 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 QRS(1)PIALPVKQEPPQIDAVK 156.69 8.12E-09 310330000 255080 193560 220620 214910 294990 139200 247200 180720 464730 TRUE FALSE 239114.9981 207891.3838 225853.2106 220424.9544 271822.6753 179384.7803 210134.6549 203283.2898 387163.5607 0.617607188 0.536960099 0.58335348 0.569332904 0.702087445 0.463330743 0.542754216 0.525057909 1 18.56258365 -1.769033929 2.704894438 1.103435784 0.564047074 0.825260316 0.062517138 10217834.8 8014538.081 7022993.339 0.014333906 0.017020255 1.769033929 -0.539388711 QRS(ph)PLLNQPVPELSHASLIANQSPFR ddPTM_SK-BR-3_Pertuzumab_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 291.4 1.82E-70 1511080000 260157 528642 506845 566260 581179 428020 525343 489634 458645 TRUE FALSE 243874.2378 567783.2037 518867.6027 580791.1903 535535.5457 551582.4257 446572.6942 550765.8827 382094.1865 0.638256865 1.48597708 1.357957334 1.520021007 1.401579936 1.443577121 1.168750298 1.441440101 1 18.54356878 -1.150898816 3.441812169 0.999618081 1.33092569 0.117441786 0.257448041 274263036.6 436364862.4 1197381.797 0.055627132 0.070648213 1.150898816 0.331307609 QRS(ph)PS(ph)PAPAPAPAAAAGPPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QRSPSPAPAPAPAAAAGPPTR 21 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 QRS(1)PS(1)PAPAPAPAAAAGPPTR;QRS(1)PS(1)PAPAPAPAAAAGPPTR;QRS(1)PS(1)PAPAPAPAAAAGPPTR;QRS(1)PS(1)PAPAPAPAAAAGPPTR 197.7 1.07E-20 3978190000 1072210 1221210 1221000 1218610 1187800 1039870 1211130 1010990 1134510 TRUE FALSE 1005102.29 1311629.659 1249962.697 1249881.596 1094514.979 1340063.588 1029532.3 1137214.327 945152.9518 1.063428187 1.387743282 1.322497797 1.32241199 1.158029478 1.417827226 1.089275866 1.203206661 1 19.85018829 1.137045513 0.864124786 1.007289564 1.296116637 0.323949093 0.11704175 0.555770344 0.925406368 0.099647036 0.036129851 13.71025437 -1.137045513 0.288827073 QRS(ph)SPVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QRSSPVTK 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QRS(0.668)S(0.328)PVT(0.004)K;QRS(0.869)S(0.131)PVTK 86.243 0.0097938 1421382000 607530 453919 466610 519460 556430 413594 635270 495550 658370 TRUE FALSE 569505.7818 487527.6351 477678.2095 532790.223 512730.2323 532991.8737 540017.1611 557420.5083 548483.7938 1.038327455 0.888864248 0.870906698 0.971387357 0.934813823 0.971755008 0.984563568 1.016293489 1 19.06508947 2.102462615 1.097046237 1.006261651 0.920092763 0.211536447 0.047038546 0.585426272 1.315899964 0.034520938 0.017408847 126.6084275 -2.102462615 -0.086168888 QRS(ph)VSPYS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QRSVSPYSR 9 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 QRS(0.972)VS(0.038)PY(0.001)S(0.99)R;QRS(0.998)VS(0.004)PYS(0.998)R 117.63 0.013397 716650000 1341020 1478910 1375380 1432000 1553850 1105710 1416940 1234320 1681180 TRUE FALSE 1257087.952 1588410.035 1408004.663 1468747.544 1431816.889 1424910.527 1204483.001 1388427.569 1400580.197 0.897547998 1.134108592 1.005300993 1.048670792 1.02230268 1.017371608 0.859988599 0.991323147 1 20.41759316 1.933245636 10.08497259 0.93564418 1.034612426 0.164438575 0.069009205 0.687300842 101.2645264 0.02639501 0.016797233 85.75227202 -1.933245636 0.098968246 QRSS(ph)PVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QRSSPVTK 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QRS(0.237)S(0.763)PVTK;QRS(0.066)S(0.934)PVTK;QRS(0.236)S(0.764)PVTK;QRS(0.174)S(0.826)PVTK 89.805 0.0082639 6948800000 6410200 4905680 5302870 5102170 5426280 4336600 6244720 4772220 5884370 TRUE FALSE 6008997.025 5268901.652 5428656.581 5233100.32 5000121.857 5588506.021 5308382.209 5368042.172 4902230.633 1.225767916 1.07479677 1.107384982 1.067493701 1.019968711 1.139992473 1.082850361 1.095020323 1 22.22500693 QRSSPVT(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QRSSPVTK 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QRS(0.019)S(0.487)PVT(0.494)K 118.04 0.019775 0 445720 334650 368810 368470 410520 279790 447110 319590 409980 TRUE FALSE 417823.1808 359427.8342 377558.3474 377925.564 378279.4152 360560.831 380070.0063 359491.515 341551.6894 1.223308781 1.052338036 1.105420816 1.106495959 1.107531969 1.055655241 1.112774488 1.052524482 1 18.3817444 1.018447615 0.013130722 1.81E-06 2.131663597 0.467329798 0.042975776 877.1710582 7.913448 651.9759405 631.112227 10.4339227 -1.018447615 2.131661782 QRT(ph)LEDEEEQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QRTLEDEEEQER 12 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 QRT(1)LEDEEEQER;QRT(1)LEDEEEQER 216.26 6.38E-11 2414100000 684620 608270 575210 530740 472260 534140 591110 365290 544700 TRUE FALSE 641770.8563 653306.9437 588854.2528 544359.6869 435170.6046 688337.547 502478.5431 410897.2606 453786.0511 1.414258668 1.439680533 1.297647319 1.19959546 0.958977482 1.516876831 1.107302752 0.905486759 1 18.79165274 4.543708983 0.195546631 0.934995802 1.873498108 0.444135962 0.158459368 12.93904658 0.507069945 0.366778291 3.026166954 34971.07502 -4.543708983 0.938502306 QRT(ph)LEDEEEQERER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QRTLEDEEEQERER 14 2 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 QRT(1)LEDEEEQERER;QRT(1)LEDEEEQERER 264.96 4.76E-23 2596900000 440390 403690 394450 411860 400400 320700 418620 303250 551190 TRUE FALSE 412826.776 433579.6276 403806.5403 422429.0249 368954.1991 413280.8839 355851.8173 341111.43 459192.8282 0.899027055 0.944221253 0.879383378 0.919938202 0.803484237 0.900015981 0.77495073 0.742850082 1 18.80874058 2.746781234 24.38383968 0.830627993 0.911029091 0.157607509 0.072548732 614.9589442 1824078.312 0.020242126 0.021121562 558.1889486 -2.746781234 0.080401097 QRWDEAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QRWDEAFR 8 1 P27695;G3V3M6;G3V5Q1;H7C4A8 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 140.83 0.00058659 175710000 25342 113920 32344 31107 121040 28053 33068 108390 115370 FALSE TRUE 23755.88946 122354.7553 33111.21495 31905.25828 111534.0067 36151.4457 28109.76039 121922.7301 96114.00168 0.247163671 1.273016971 0.34449939 0.331952241 1.160434533 0.376130897 0.292462699 1.268522046 1 16.55245899 1.226166445 24.97127591 1.13426127 0.60702522 0.283328879 0.36700083 348.6013021 702326.0003 0.332505267 0.085515652 16.83319075 -1.226166445 -0.52723605 QS(ph)HPLTQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSHPLTQSR 9 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7 E9PGF5 TNS1 Tensin-1 1 QS(1)HPLTQSR 56.956 0.062551 0 81250 85242 83583 73592 110890 80092 89903 93627 166780 TRUE FALSE 76164.70754 91553.40637 85565.62823 75480.49531 102181.1467 103213.2602 76422.87977 105316.537 138943.3406 0.548170983 0.658926193 0.615831085 0.543246585 0.735415935 0.74284424 0.550029094 0.757981898 1 17.08413716 -4.999999999 0.233471353 3.003948684 0.599318867 0.713474155 0.074196281 88.73902804 0.887550497 83.99619432 0.11870136 1.00E-05 4.999999999 -2.404629817 QS(ph)LGELIGTLNAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QSLGELIGTLNAAK 14 0 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 1 QS(1)LGELIGTLNAAK;QS(1)LGELIGTLNAAK;QS(1)LGELIGTLNAAK;QS(1)LGELIGTLNAAK 207.16 1.03E-08 677095000 1406280 970940 1102175 1013743 999793 839480 1428810 923976 1203339 TRUE FALSE 1318263.445 1042829.408 1128319.111 1039757.362 921273.2908 1081824.248 1214573.205 1039336.438 1002493.947 1.314983945 1.040235117 1.125512144 1.037170713 0.9189814 1.079132948 1.211551659 1.036750836 1 19.9351621 4.743002659 24.64648054 1.070845345 1.314984065 0.516292312 0.077581883 344.4978621 1911349.096 0.019295172 0.150607154 55335.34968 -4.743002659 0.24413872 QS(ph)LLDMS(ph)LVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSLLDMSLVK 10 0 Q9BXL8 Q9BXL8 CDCA4 Cell division cycle-associated protein 4 2 QS(1)LLDMS(1)LVK 51.445 0.082698 478340000 166840 589580 475400 436410 506510 614600 522550 498770 452900 TRUE FALSE 156397.7822 633233.1167 486676.7125 447609.0194 466730.7478 792025.0428 444198.4786 561042.5324 377308.0642 0.414509514 1.678292029 1.289865653 1.18632243 1.237001782 2.099146872 1.177283289 1.486961414 1 18.52538341 QS(ph)PALQHRPMGQSQANHIPGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QSPALQHRPMGQSQANHIPGDR 22 1 Q5TCQ9;Q5TCQ9-1;Q5TCQ9-3;Q5TCQ9-2 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 QS(1)PALQHRPMGQSQANHIPGDR;QS(1)PALQHRPMGQSQANHIPGDR;QS(1)PALQHRPMGQSQANHIPGDR;QS(1)PALQHRPMGQSQANHIPGDR;QS(0.996)PALQHRPMGQS(0.004)QANHIPGDR;QS(1)PALQHRPMGQSQANHIPGDR 198.48 1.14E-22 1957700000 504956 524356 563107 579352 643211 517073 630525 468899 527620 TRUE FALSE 473351.7053 563179.8638 576464.164 594219.1532 592695.8026 666343.5811 535983.6298 527442.0723 439556.8134 1.076884013 1.28124476 1.311466792 1.351859725 1.348394074 1.515944153 1.219372817 1.199940613 1 18.74569012 0.958905917 1.925866591 1.003618063 1.312373969 0.440198964 0.109028721 0.33849564 2.655023338 0.099074729 0.027853262 9.097161755 -0.958905917 0.308755906 QS(ph)PECENFLDVGLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QSPECENFLDVGLGR 15 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36;A0A087X047 Q12802-2 AKAP13 A-kinase anchor protein 13 1 QS(1)PECENFLDVGLGR;QS(1)PECENFLDVGLGR 218.14 2.07E-12 66925000 66405 56561 57270 56191 62551 55251 77116 56459 57893 TRUE FALSE 62248.82959 60748.83529 58628.47144 57632.95619 57638.49678 71201.06677 65553.17171 63508.03043 48230.2843 1.290658566 1.259557893 1.215594565 1.19495369 1.195068568 1.476273006 1.359170336 1.316766661 1 15.55765169 2.341038221 21.07996616 1.329073702 1.231265665 0.003248677 0.123929341 7.376598614 1494.760737 0.038299054 0.032043205 219.2997924 -2.341038221 -0.097808037 QS(ph)PGHQS(ph)PLASPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSPGHQSPLASPK 13 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 2 QS(1)PGHQS(1)PLASPK 120.71 0.00013474 368260000 441320 320130 371160 355290 381220 304040 510370 333260 395630 TRUE FALSE 413698.569 343832.7583 379964.0905 364407.3429 351280.519 391811.4123 433844.7565 374868.2446 329596.7971 1.255165622 1.043192049 1.152814875 1.105615546 1.06578863 1.188759769 1.316289358 1.137354027 1 18.3303427 2.10538744 7.683424376 1.202608124 1.116664283 0 0.09823298 0.422454338 27.66570966 0.033711597 0.024858702 127.4639696 -2.10538744 -0.085943841 QS(ph)PGPALAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSPGPALAR 9 0 P85037 P85037 FOXK1 Forkhead box protein K1 1 QS(1)PGPALAR 84.479 0.016221 363510000 561120 580080 593010 618810 772950 530730 715780 577200 623920 TRUE FALSE 526000.5008 623029.7268 607076.4772 634689.7122 712245.6249 683943.1353 608455.434 649264.6906 519783.7213 1.01196032 1.198632626 1.167940534 1.221065005 1.37027305 1.315822538 1.170593478 1.249105472 1 18.98755193 5.669837639 1.026014253 1.228667263 2.11E-17 0.272037967 0.099142537 13.01982498 2.633316511 0.027130311 27.59217479 467560.3113 -5.669837639 -1.228667263 QS(ph)PLHGNHITISHTQATGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSPLHGNHITISHTQATGSR 20 0 Q86VQ1;H7C2L5 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 QS(1)PLHGNHITISHTQATGSR 79.426 0.012674 111980000 54215 46678 47670 52414 52604 45286 57730 43140 56022 TRUE FALSE 50821.77993 50134.08769 48800.75491 53759.03198 48472.69403 58359.33304 49073.92244 48526.12396 46671.56628 1.088923813 1.074189098 1.045620681 1.151858321 1.038591543 1.250425852 1.051473656 1.03973635 1 15.51025626 1.490101363 24.99999945 1.028446123 1.100106211 0.266163549 0.061246675 1.189288951 2285.29669 0.031245715 0.014465043 30.9101678 -1.490101363 0.071660089 QS(ph)PNSSSAAASVASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSPNSSSAAASVASR 15 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 QS(0.983)PNS(0.01)S(0.004)S(0.004)AAASVASR 107.15 0.0012383 282980000 236010 266000 327550 267110 302330 265520 302490 280740 274590 TRUE FALSE 221238.5554 285694.9168 335319.6407 273964.4948 278586.2213 342171.3136 257134.4327 315791.007 228759.1551 0.967124377 1.248889544 1.465819545 1.197611063 1.217814523 1.495771015 1.124039965 1.380451886 1 17.80346996 -1.051462077 5.319492682 0.999997523 1.275163196 0.210729578 0.15769979 4.27E-06 7.62E-07 0.140818465 0.033190932 0.088825554 1.051462077 0.275165672 QS(ph)PPISTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QSPPISTSK 9 0 P33981-2;P33981 P33981-2 TTK Dual specificity protein kinase TTK 1 QS(0.999)PPIS(0.001)TSK;QS(1)PPISTSK 117.25 0.0012398 92421000 553400 403720 487240 474650 467660 431960 655070 431360 405900 TRUE FALSE 518763.6818 433611.8489 498797.5629 486830.3226 430931.87 556659.8397 556848.3349 485216.2455 338152.6678 1.534110865 1.282296105 1.475066177 1.439676125 1.274370754 1.646179057 1.646736483 1.434902906 1 18.36731521 2.243237171 24.99911135 1.508813282 1.396741979 0 0.199211428 321.5735386 1719017.409 0.063509105 0.051523261 175.080255 -2.243237171 -0.112071303 QS(ph)PSFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QSPSFK 6 0 Q6IN85-2;Q6IN85;Q6IN85-4 Q6IN85-2 SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3A 1 QS(0.985)PS(0.015)FK;QS(0.997)PS(0.003)FK;QS(1)PSFK;QS(0.997)PS(0.003)FK 106.36 0.033768 3822850000 14535200 11980600 12754100 12580200 12608000 9093390 16942000 10782200 16005400 TRUE FALSE 13625467.78 12867656.09 13056633.27 12903029.23 11617818.54 11718504.07 14401704.38 12128381.4 13333995.34 1.021859347 0.965026293 0.979198878 0.967679146 0.87129313 0.87884417 1.080074202 0.909583444 1 23.66860579 -0.425337341 6.282234732 1 0.964188205 0.034452938 0.063147546 0 0 0.059136327 0.013938566 0.375545583 0.425337341 -0.035811795 QS(ph)PSPS(ph)TRPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSPSPSTRPIR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 QS(0.949)PS(0.158)PS(0.857)T(0.035)RPIR 107.6 0.026008 167890000 342380 335870 357610 376800 401470 337760 406520 315460 342350 TRUE FALSE 320951.047 360738.1643 366092.6781 386469.3259 369940.1657 435265.8289 345566.0999 354845.8754 285209.5733 1.125316529 1.264817867 1.28359183 1.355036303 1.297081866 1.526126293 1.211621671 1.244158361 1 18.12166288 0.753013559 1.776511884 1.00097005 1.300911027 0.45287479 0.101666783 0.797716983 4.082665844 0.091839915 0.025909025 5.662569678 -0.753013559 0.299940977 QS(ph)PSPSTRPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QSPSPSTRPIR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QS(0.992)PS(0.008)PSTRPIR;QS(0.99)PS(0.01)PSTRPIR;QS(0.955)PS(0.045)PSTRPIR 119.62 0.00034055 1760610000 2008790 2054410 2125990 2028320 2264240 1822120 2257510 1702990 2145490 TRUE FALSE 1883063.42 2206520.654 2176419.487 2080370.125 2086415.724 2348136.464 1919017.333 1915612.05 1787393.859 1.053524611 1.234490453 1.217649639 1.16391254 1.167294894 1.313720786 1.073639883 1.071734716 1 20.76942614 1.584400603 7.36291457 1.048734956 1.197946731 0.502334868 0.067522294 0.092753682 10.52346562 0.033446632 0.015831693 38.40613492 -1.584400603 0.149211775 QS(ph)PSSS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QSPSSSPTR 9 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 QS(0.999)PS(0.014)S(0.052)S(0.933)PT(0.002)R;QS(0.758)PS(0.242)S(0.044)S(0.955)PTR 97.594 0.0096273 214083000 760370 697380 787180 783010 717030 640400 762720 647020 722430 TRUE FALSE 712779.799 749014.7408 805852.2813 803103.3622 660717.3562 825273.084 648357.2167 727801.8713 601851.7659 1.18431122 1.244516978 1.338954751 1.334387315 1.097807456 1.371223166 1.077270606 1.209270974 1 19.19904867 1.031630523 0.672603859 1.003852694 1.272123523 0.405266978 0.094147924 0.672708251 0.716043699 0.084477091 0.034581464 10.75549797 -1.031630523 0.26827083 QS(ph)RPANKQSPSPSEVSQSPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSRPANKQSPSPSEVSQSPGR 21 2 A0A5F9ZH11;P55201-3;P55201;P55201-2;P55201-4;A0A5F9ZHX4;A0A5F9ZHW9;C9JHC0 A0A5F9ZH11 BRPF1 Peregrin 1 QS(0.545)RPANKQS(0.45)PS(0.006)PSEVSQSPGR 84.524 0.0015829 38628000 43264 39861 44236 39967 42357 33582 52717 40059 52977 TRUE FALSE 40556.18347 42812.34992 45285.29881 40992.62088 39030.45208 43276.57824 44812.57525 45060.45433 44134.79646 0.918916291 0.970036193 1.02606792 0.928805029 0.884346484 0.980554613 1.015357016 1.020973426 1 15.42962892 1.996254477 24.99544923 1.009851324 0.956938928 0.377911313 0.037577059 216.2393908 1443061.328 0.015913542 0.011499028 99.1412697 -1.996254477 -0.052912396 QS(ph)SFEIPDDVPLPAGWEMAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QSSFEIPDDVPLPAGWEMAK 20 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 1 QS(0.5)S(0.5)FEIPDDVPLPAGWEMAK;QS(0.5)S(0.5)FEIPDDVPLPAGWEMAK 83.453 0.0018871 54905000 192340 161770 150858 161813 142846 117382 232235 129296 182637 TRUE FALSE 180301.7827 173747.6191 154436.423 165965.3955 131627.4514 151268.2779 197413.5177 145438.8902 152153.7048 1.184997651 1.141921712 1.015002712 1.090774594 0.865095277 0.994180707 1.29746113 0.955868215 1 17.21516994 4.288582469 2.350461556 1.051406359 1.180454685 0.181278579 0.112228196 0.668072584 6.938527103 0.030364469 0.118342983 19434.90711 -4.288582469 0.129048325 QS(ph)SPSGSEQLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 QS(0.801)S(0.199)PSGSEQLVR 118.08 0.00069675 217170000 220310 243470 251370 219260 248140 206690 261330 190190 219400 TRUE FALSE 206521.1904 261496.7721 257332.6151 224886.5828 228652.0853 266358.0477 222145.9926 213935.6402 182780.7226 1.129884965 1.430658378 1.407876123 1.230362697 1.250963899 1.457254594 1.215368828 1.17044969 1 17.4797544 1.09874799 1.549520381 1.00550081 1.334937771 0.482423633 0.103189014 0.288044899 1.37019093 0.093329969 0.027671514 12.55301333 -1.09874799 0.329436961 QSAGPNS(ph)PTGGGGGGGSGGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.981)PT(0.019)GGGGGGGSGGTR;QSAGPNS(0.996)PT(0.004)GGGGGGGSGGTR;QSAGPNS(0.994)PT(0.006)GGGGGGGSGGTR 389.28 3.95E-131 247830000 192183 206224 223409 232242 224697 164381 205852 163273 174231 TRUE FALSE 180154.6091 221493.0395 228708.367 238201.7229 207050.204 211835.1262 174986.4036 183657.9935 145150.7205 1.241155459 1.52595205 1.575661259 1.641064695 1.426449716 1.459414913 1.205549673 1.265291642 1 17.14719221 1.442606432 0.990981022 1.034321013 1.514964182 0.646063498 0.116103104 0.276996842 0.545316431 0.101439449 0.036935704 27.70807996 -1.442606432 0.480643169 QSAPS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QSAPSPTR 8 0 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 QS(0.002)APS(0.849)PT(0.149)R;QS(0.001)APS(0.946)PT(0.053)R 81.642 0.022829 0 945760 1125220 1071140 1112080 1241510 994300 1211100 1038200 986460 TRUE FALSE 886566.5698 1208532.46 1096547.947 1140617.856 1144006.813 1281338.269 1029506.798 1167821.555 821813.4532 1.078792963 1.47056787 1.334302745 1.387927943 1.392051698 1.55915952 1.252725657 1.42102998 1 19.64845142 -0.228304071 8.349490155 0.999999935 1.370967223 0.437073966 0.128783315 0 0 0.109348362 0.025773656 0.591147598 0.228304071 0.370967288 QSDEVGDRDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QSDEVGDRDHR 11 1 P40222 P40222 TXLNA Alpha-taxilin 0 ;;;; 136.7 5.63E-05 784945000 420982 501917 492527 497379 532898 409312 507098 438630 580862 FALSE TRUE 394633.4881 539079.4569 504209.973 510142.5872 491046.3407 527473.7298 431063.3626 493393.921 483912.3797 0.815506081 1.114002203 1.04194477 1.054204456 1.014742258 1.090019086 0.890788045 1.019593509 1 18.88438632 1.746232965 25 0.961233556 1.03569436 0.054320639 0.087087537 3.220457422 10522.35396 0.036570064 0.020279969 55.74847151 -1.746232965 0.074460804 QSDS(ph)VKGK ddPTM_SK-BR-3_Pertuzumab_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 88.596 0.0087829 164970000 890400 458560 545990 471820 538750 249710 525970 270660 962110 TRUE FALSE 834671.4534 492512.2595 558941.1406 483927.7 496438.7482 321797.2233 447105.6814 304452.4968 801527.6255 1.041350824 0.61446698 0.697344824 0.603756732 0.619365737 0.40147989 0.557816932 0.379840304 1 19.61239272 7.550721401 1.036758922 0.577294708 199.9792768 0.360700001 0.173751762 714.626698 2.320275656 0.045280279 336834.6204 35540325.53 -7.550721401 199.4019821 QSEPFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSEPFFK 7 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 77.058 0.090912 50847000 217080 193220 224090 196120 210170 180730 247010 187730 238060 FALSE TRUE 203493.3503 207526.2098 229405.5206 201152.7712 193664.096 232903.8171 209973.1436 211168.5037 198326.2481 1.026053547 1.046388019 1.156707813 1.014251886 0.976492511 1.174346913 1.058725941 1.064753182 1 17.5975161 4.450581039 9.024745203 1.07327936 1.031052614 0.01907804 0.062987001 0.769586896 250.3112575 0.014612439 0.041109303 28221.56147 -4.450581039 -0.042226746 QSETVDQNS(ph)DSDEMLAILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSETVDQNSDSDEMLAILK 19 0 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 QS(0.014)ET(0.077)VDQNS(0.455)DS(0.455)DEMLAILK 54.805 0.069725 15142000 31127 30810 34714 34658 34709 30532 33565 31862 32844 TRUE FALSE 29178.81663 33091.20446 35537.43247 35547.38296 31983.09515 39346.09275 28532.23985 35840.04084 27362.12422 1.066394422 1.209379951 1.298781929 1.299145588 1.168882024 1.437976542 1.042764064 1.309841317 1 14.73989262 -1.147189598 4.496697765 0.999966455 1.229330159 0.271682794 0.11790771 3.56E-05 6.75E-06 0.102424718 0.02413821 0.071254189 1.147189598 0.229363704 QSFDDNDS(ph)EELEDKDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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;QSFDDNDS(1)EELEDKDSK 277.2 5.34E-36 7855970000 13549800 4984326 7304950 6601320 7113280 4988608 9239550 5389437 8470760 TRUE FALSE 12701742.21 5353370.683 7478226.864 6770721.047 6554631.682 6428738.146 7854165.253 6062320.073 7056935.433 1.799894916 0.75859709 1.059698921 0.959442114 0.928821263 0.910981574 1.112971109 0.859058458 1 22.75061038 4.74683828 24.99984406 0.955946059 1.799895334 0.879158122 0.09914408 339.516079 1025369.092 0.022919691 0.260894495 55826.2273 -4.74683828 0.843949275 QSFTMVADT(ph)PENLR ddPTM_SK-BR-3_Pertuzumab_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 307.19 6.49E-44 474202000 794780 643970 692300 632800 731380 765970 1052840 607740 1275160 TRUE FALSE 745036.1385 691650.2089 708721.6829 649038.7193 673940.365 987093.1045 894976.4161 683617.6768 1062327.558 0.701324307 0.65107057 0.667140448 0.610959129 0.634399776 0.929179608 0.842467476 0.643509313 1 20.01879724 2.251231945 24.99993748 0.844016264 0.652739735 0.538590056 0.092160362 170.2829424 335960.0262 0.029491802 0.024521975 178.3330942 -2.251231945 -0.191276529 QSGLSSLVNGKS(ph)PIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QSGLSSLVNGKSPIR 15 1 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 1 QSGLSSLVNGKS(1)PIR;QSGLSSLVNGKS(1)PIR 223.93 7.27E-13 823630000 934330 718070 949200 801190 1117560 792110 1402450 1125620 1641740 TRUE FALSE 875851.9531 771236.65 971715.4722 821749.8918 1029791.346 1020779.298 1192165.642 1266156.135 1367722.988 0.640372327 0.563883664 0.710462192 0.600816027 0.752923914 0.746334826 0.871642615 0.925740187 1 20.38334463 1.796157229 0.689360326 1.006251969 0.614997046 0.91236008 0.041662491 0.16395886 0.155210231 0.034986413 0.018013782 62.53990677 -1.796157229 -0.391254923 QSGT(ph)PPGMGAPGVPGAAGVGGAGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSGTPPGMGAPGVPGAAGVGGAGGR 25 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 QS(0.268)GT(0.732)PPGMGAPGVPGAAGVGGAGGR 56.882 0.030483 0 36334 31921 36265 30701 41687 27576 42836 33320 50075 TRUE FALSE 34059.9198 34284.46405 37125.22293 31488.83964 38413.07118 35536.74354 36413.13947 37480.07535 41717.159 0.81644869 0.821831229 0.889926922 0.754817451 0.920797871 0.85184956 0.872857604 0.898433073 1 15.34835329 -5 0.141609658 1.533994208 0.799112511 0.6037586 0.041690162 90.45000744 0.781512234 13.47560473 0.223961489 1.00E-05 5 -0.734881697 QSHAASAAPQASS(ph)PPDYTMAWAEYYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QSHAASAAPQASSPPDYTMAWAEYYR 26 0 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 1 QSHAASAAPQAS(0.129)S(0.871)PPDYTMAWAEYYR;QSHAASAAPQAS(0.286)S(0.712)PPDY(0.002)TMAWAEYYR;QSHAASAAPQAS(0.058)S(0.942)PPDYTMAWAEYYR 181.9 1.25E-17 1282130000 560706 579045 570246 559453 590181 468405 661245 485465 593030 TRUE FALSE 525612.4123 621918.0943 583772.5044 573809.5111 543830.5649 603625.9196 562097.4509 546076.3739 494049.4619 1.063886216 1.258817471 1.181607409 1.161441425 1.100761375 1.221792485 1.137735175 1.105307092 1 18.91429596 0.913027576 1.367297685 1.000279906 1.175830292 0.452647481 0.055719339 0.431466981 1.607536297 0.049838113 0.014952414 8.185167599 -0.913027576 0.175550386 QSHSES(ph)PSLQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 QSHSESPSLQSK 12 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHSES(0.999)PSLQSK;QSHS(0.003)ES(0.996)PSLQSK;QSHSES(1)PSLQSK;QSHSES(1)PSLQSK;QSHS(0.002)ES(0.998)PSLQSK;QSHSES(1)PSLQSK;QSHSES(0.979)PS(0.021)LQSK;QSHS(0.172)ES(0.802)PS(0.025)LQS(0.001)K 213.7 3.59E-09 21978489000 14781768 11556778 12286620 12104028 13009078 10533811 16948944 11082804 14939318 TRUE FALSE 13856603.53 12412453.87 12578064.43 12414637.85 11987397.49 13574751.23 14407607.19 12466516.48 12445849.31 1.113351381 0.99731674 1.01062323 0.997492219 0.96316428 1.090705093 1.157623464 1.001660567 1 23.56916135 2.214570279 24.74212738 1.084955655 1.012143436 0.074410031 0.060136894 276.4389001 285099.6309 0.021182594 0.015652619 163.8967264 -2.214570279 -0.072812219 QSHSGSIS(ph)PYPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 QSHSGSISPYPK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHSGS(0.001)IS(0.999)PYPK;QSHSGS(0.002)IS(0.998)PYPK;QSHSGS(0.003)IS(0.997)PYPK;QSHSGSIS(1)PYPK;QSHSGS(0.002)IS(0.998)PYPK;QSHSGS(0.095)IS(0.904)PYPK;QSHSGSIS(1)PYPK;QSHSGS(0.001)IS(0.998)PYPK 176.98 2.50E-05 16541400000 15477840 10960250 12498660 11291740 11577750 10445790 17626190 10408050 12913600 TRUE FALSE 14509109.62 11771758.31 12795134.12 11581505.17 10668480.22 13461320 14983306.44 11707517.95 10758236.73 1.348651269 1.094208894 1.189333757 1.076524476 0.991656949 1.251257091 1.392728828 1.088237621 1 23.35893831 QSHSS(ph)SS(ph)PHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QSHSSSSPHPK 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QS(0.005)HS(0.082)S(0.894)S(0.03)S(0.989)PHPK;QS(0.001)HS(0.083)S(0.907)S(0.306)S(0.703)PHPK;QS(0.022)HS(0.099)S(0.878)S(0.291)S(0.711)PHPK;QS(0.003)HS(0.109)S(0.858)S(0.05)S(0.98)PHPK 122.63 0.0002043 2305020000 7546030 5245070 6625530 6316140 6360900 5114600 7520730 5457740 6250920 TRUE FALSE 7073737.452 5633420.44 6782690.7 6478222.846 5861340.573 6591101.991 6393066.356 6139150.853 5207601.07 1.358348567 1.081768815 1.302459733 1.243993685 1.125535634 1.265669529 1.22764134 1.178882708 1 22.3121875 0.809242944 3.214241536 1.000035468 1.220881554 0.44785715 0.079308953 0.959361973 14.75287049 0.068751343 0.017874309 6.445297139 -0.809242944 0.220846086 QSHSSS(ph)SPHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSHSSSSPHPK 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHS(0.001)S(0.018)S(0.811)S(0.17)PHPK 140.27 6.46E-05 1596100000 495770 808820 740780 780550 803340 720250 1045400 788700 868560 TRUE FALSE 464740.6407 868705.8744 758351.6514 800580.2345 740248.9169 928174.4827 888651.975 887170.9311 723591.7249 0.642269148 1.200547 1.048038038 1.10639772 1.023020153 1.282732307 1.228112407 1.226065612 1 19.46481638 4.74224077 24.89206276 1.147463098 0.642268943 0.726235229 0.095801565 181.8725834 1230107.214 0.022896523 0.170155893 55238.35925 -4.74224077 -0.505194155 QSHSSSS(ph)PHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QSHSSSSPHPK 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHS(0.001)S(0.005)S(0.273)S(0.72)PHPK;QSHSSS(0.014)S(0.985)PHPK;QSHSS(0.01)S(0.045)S(0.945)PHPK;QS(0.004)HS(0.002)S(0.002)S(0.048)S(0.943)PHPK;QSHSSS(0.21)S(0.79)PHPK 133.47 0.00010371 5009813000 3050690 4766841 4898780 4952870 5226300 4592820 6641520 5006280 5797910 TRUE FALSE 2859752.759 5119782.868 5014981.375 5079969.029 4815847.48 5918692.576 5645685.733 5631325.078 4830201.365 0.592056633 1.059952263 1.038255136 1.051709576 0.997028305 1.225351104 1.168830305 1.165857208 1 22.2036519 4.750209179 3.733905652 1.096266708 0.532529482 0.810337312 0.075573296 0.128545273 3.348895154 0.019551074 0.203414532 56261.22431 -4.750209179 -0.563737226 QSIRNS(ph)QK ddPTM_SK-BR-3_Pertuzumab_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 106.67 0.0025141 696070000 698130 606620 478620 467700 544000 383380 607210 391810 929050 TRUE FALSE 654435.2895 651534.776 489973.0924 479701.9738 501276.4344 494055.5823 516164.4976 440728.341 773985.5531 0.845539412 0.841791909 0.633051987 0.61978156 0.647656061 0.63832662 0.666891644 0.56942709 1 19.56194711 -0.910352185 4.580394967 1.000002916 0.686224644 0.544878931 0.091056499 10689319.16 4667422.117 323.578123 0.022350683 0.122927151 0.910352185 -0.313778272 QSKPVTTPEEIAQVATISANGDKEIGNIISDAMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSKPVTTPEEIAQVATISANGDKEIGNIISDAMK 34 2 P10809;E7EXB4;E7ESH4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 92.817 0.00020002 67822000 130900 75111 111160 107640 127960 43107 73228 104850 86673 FALSE TRUE 122707.2027 80672.29659 113796.7677 110402.2246 117910.5378 55551.29112 62248.14122 117940.7533 72206.71637 1.699387659 1.117240897 1.575985911 1.528974453 1.632958036 0.769336897 0.862082426 1.633376495 1 16.13984542 2.245595571 24.9999981 1.023875843 1.466922545 0.382378095 0.275410605 167.9189957 596731.9522 0.093983092 0.077067844 176.0336 -2.245595571 0.443046702 QSLGHPPPEPGPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSLGHPPPEPGPDR 14 0 P13861-2;P13861;C9J830 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 0 65.943 0.056756 417930000 138810 255450 224980 208180 254420 213930 280690 216780 305470 FALSE TRUE 130122.1299 274363.7838 230316.6318 213522.2512 234438.8795 275688.1181 238603.1403 243845.4602 254485.0836 0.511315351 1.07811342 0.905029987 0.839036411 0.921228373 1.083317396 0.93759185 0.958191564 1 17.95722157 2.465710352 24.49509529 0.98921793 0.885509016 0.176303132 0.14615706 404.1080602 867466.731 0.047863422 0.040079785 292.2202795 -2.465710352 -0.103708914 QSMAFSILNT(ph)PK ddPTM_SK-BR-3_Pertuzumab_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 167.29 0.00055477 292890000 390640 407000 246900 222630 445210 143232 1040990 260610 1989720 TRUE FALSE 366190.5397 437134.7035 252756.5846 228343.0627 410245.0025 184580.7532 884903.2136 293147.7322 1657622.878 0.220913058 0.263711794 0.152481356 0.137753325 0.24748995 0.111352682 0.533838683 0.176848266 1 20.66068439 -0.627724622 0.4292489 1.206889305 0.188994122 0.810444456 0.117142677 3.966081748 0.624426224 1.250073762 0.065222698 0.235654305 0.627724622 -1.017895184 QSMDMS(ph)PIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QSMDMSPIK 9 0 Q14562;F5H658 Q14562 DHX8 ATP-dependent RNA helicase DHX8 1 QSMDMS(1)PIK;QSMDMS(1)PIK 98.531 0.0062425 257100000 490850 837470 292600 293900 986380 185249 340710 826080 1220040 TRUE FALSE 460128.5747 899477.1502 299540.6102 301441.9716 908913.6937 238727.379 289623.6985 929217.9064 1016407.442 0.452700911 0.884957265 0.294705251 0.296575919 0.894241478 0.234873702 0.284948424 0.914217929 1 19.95504741 1.138142463 6.464509945 0.987662118 0.486413765 0.415739047 0.236802391 0.219969453 11.63657815 0.225705888 0.056803706 13.74492781 -1.138142463 -0.501248352 QSNASS(ph)DVEVEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QSNASSDVEVEEK 13 0 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 QSNAS(0.028)S(0.972)DVEVEEK;QSNASS(1)DVEVEEK;QSNASS(1)DVEVEEK;QSNAS(0.002)S(0.998)DVEVEEK;QSNASS(1)DVEVEEK;QSNAS(0.005)S(0.995)DVEVEEK 405.46 2.84E-126 3877520000 11631060 6580360 8398660 7685710 7445500 7028680 11061580 6491780 6166760 TRUE FALSE 10903092.72 7067576.701 8597880.181 7882938.33 6860760.464 9057745.815 9402998.77 7302293.023 5137487.917 2.122261481 1.375687265 1.673557256 1.534395498 1.335430968 1.763069025 1.830271705 1.421374248 1 22.29263167 0.96373222 8.160531936 1.000007198 1.634431068 0.464929463 0.226270057 0.481660392 107.0492531 0.204542105 0.051216853 9.198822097 -0.96373222 0.63442387 QSNASS(ph)DVEVEEKETSVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSNASSDVEVEEKETSVSK 19 1 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 QSNAS(0.062)S(0.938)DVEVEEKETSVSK 217.89 2.12E-19 292300000 312140 197470 246030 257420 252220 169200 334500 205260 293030 TRUE FALSE 292603.7146 212090.8843 251865.9478 264025.833 232411.6586 218045.2933 284344.8303 230887.1628 244121.4 1.1985992 0.868792676 1.031724166 1.081534978 0.952033122 0.893183856 1.164768146 0.945788296 1 17.89723924 1.74609233 25 1.05253454 0.992796257 0.005511124 0.108247132 4.926905929 16399.34076 0.046097446 0.025563219 55.73042181 -1.74609233 -0.059738283 QSPGPGHRS(ph)PDSGHVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSPGPGHRSPDSGHVAK 17 1 O15169-2;O15169 O15169-2 AXIN1 Axin-1 1 QS(0.327)PGPGHRS(0.67)PDS(0.002)GHVAK 90.464 0.0022924 28516000 23877 30474 34819 30215 54254 23223 33555 34665 91969 TRUE FALSE 22382.58119 32730.32667 35644.92312 30990.36805 49993.10969 29927.10311 28523.73926 38993.00156 76618.77976 0.292129179 0.427184129 0.465224365 0.404474832 0.652491593 0.390597491 0.372281304 0.508922247 1 16.22541043 -4.779160383 0.431374449 9.999985515 0.430009489 0.782654368 0.093297833 382.6371685 2.914053026 3254.563558 0.050130511 1.66E-05 4.779160383 -9.569976026 QSPGS(ph)TSPKPPHTLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSPGSTSPKPPHTLSR 16 1 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 1 QS(0.016)PGS(0.326)T(0.326)S(0.326)PKPPHT(0.002)LS(0.002)R 58.848 0.064573 237050000 173620 125950 153560 136620 129850 100330 171790 113040 124580 TRUE FALSE 162753.4341 135275.4691 157202.5157 140125.9005 119652.1048 129293.6423 146031.6843 127153.2928 103786.7932 1.56815168 1.303397715 1.514667819 1.350132288 1.152864455 1.245761993 1.407035325 1.225139432 1 16.66326335 -4.146453018 0.085275382 5.78E-13 1.69363383 0.59926389 0.105856462 141.5555717 1.005691302 28.14754723 3.153109546 7.14E-05 4.146453018 1.69363383 QSPGST(ph)SPKPPHTLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSPGSTSPKPPHTLSR 16 1 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 1 QS(0.001)PGS(0.021)T(0.671)S(0.307)PKPPHTLSR 114.88 0.00080422 351880000 218940 176340 191960 208070 216650 163560 259370 216380 239870 TRUE FALSE 205236.9362 189396.3971 196513.3819 213409.4285 199635.1829 210777.1168 220479.8764 243395.5193 199834.1474 1.027036364 0.947767934 0.983382392 1.06793274 0.999004352 1.054760258 1.10331432 1.217987629 1 17.6084436 2.003486489 1.794294896 1.120798044 0.99435985 0.359986543 0.060610241 0.314664135 1.891863568 0.034498842 0.017384927 100.8060249 -2.003486489 -0.126438194 QSPGSTS(ph)PKPPHTLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QSPGSTSPKPPHTLSR 16 1 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 1 QSPGS(0.012)T(0.082)S(0.906)PKPPHTLSR;QSPGS(0.012)T(0.322)S(0.665)PKPPHTLSR 156.51 9.42E-08 1073410000 825510 557190 680090 665640 640360 455750 797700 564130 672270 TRUE FALSE 773842.8027 598444.9274 696222.056 682721.4493 590068.7087 587317.6265 678092.2905 634562.8723 560063.794 1.381704747 1.068529931 1.243112059 1.219006579 1.053574102 1.048662015 1.210741165 1.133018915 1 19.09523164 8 0.019515509 8.32E-15 2.62283068 0.351287236 0.092922716 4297.878193 6.464341679 324.3486372 578.2790109 100000000 -8 2.62283068 QSPS(ph)PS(ph)TRPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSPSPSTRPIR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 QS(0.128)PS(0.881)PS(0.962)T(0.029)RPIR 122.1 0.0047574 779860000 594660 531880 614190 592630 579840 507320 665100 474740 512470 TRUE FALSE 557441.2921 571260.9486 628758.8768 607837.8891 534301.7054 653775.0483 565374.4295 534012.334 426935.4463 1.305680512 1.338049941 1.472725871 1.423723175 1.251481248 1.531320611 1.324262097 1.250803461 1 18.70365842 0.904230757 1.866361406 1.001472717 1.388669181 0.690159409 0.081118335 0.23764126 1.686813895 0.071237451 0.020062829 8.021041375 -0.904230757 0.387196464 QSPS(ph)SSPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSPSSSPTR 9 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 QS(0.001)PS(0.333)S(0.333)S(0.333)PT(0.001)R 87.066 0.013036 0 102370 135550 104350 120050 156990 91559 115310 121890 142360 TRUE FALSE 95962.84444 145586.263 106825.2313 123130.6862 144660.6387 117990.597 98020.33599 137108.2348 118599.1963 0.809135706 1.227548479 0.900724749 1.038208437 1.219743836 0.994868436 0.826483982 1.156063777 1 16.85573471 -1.200282844 5.042991214 0.999998147 1.019989355 0.001979717 0.148544615 2.92E-06 4.62E-07 0.13554718 0.031945816 0.063054655 1.200282844 0.019991207 QSQEGAGLPSHHGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QSQEGAGLPSHHGR 14 0 Q92754;A2A2R7 Q92754 TFAP2C Transcription factor AP-2 gamma 0 ; 86.497 0.0042309 119256000 33958 51040 52355 49578 47167 49263 54817 44050 41775 FALSE TRUE 31832.6294 54819.05471 53596.88532 50850.25542 43462.69408 63484.42838 46597.69975 49549.73947 34802.48262 0.914665478 1.575147822 1.540030517 1.461110001 1.248838899 1.82413505 1.338918842 1.423741519 1 15.0869026 -0.544352951 7.292936212 1.000000004 1.447740247 0.224507272 0.236349665 0 0 0.203631028 0.047996294 0.285526913 0.544352951 0.447740243 QSQQPMKPIS(ph)PVKDPVS(ph)PASQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QSQQPMKPISPVKDPVSPASQK 22 2 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 QS(0.033)QQPMKPIS(0.967)PVKDPVS(0.978)PAS(0.022)QK;QSQQPMKPIS(1)PVKDPVS(0.999)PAS(0.001)QK;QS(0.028)QQPMKPIS(0.973)PVKDPVS(0.976)PAS(0.024)QK 166.28 6.37E-12 457000000 1250090 458056 649680 596360 703380 529656 1104380 485488 1108680 TRUE FALSE 1171849.098 491970.9428 665090.7164 611663.6072 648139.3721 682559.089 938788.4716 546102.2455 923634.1457 1.268737307 0.532646985 0.720080261 0.662235811 0.701727383 0.738992914 1.016407282 0.591253851 1 19.81696198 1.951123548 23.87796741 0.872707766 0.729892492 0.020500244 0.223804397 583.721563 285167.8459 0.084133988 0.05429902 89.35596475 -1.951123548 -0.142815274 QSQQPMKPIS(ph)PVKDPVSPASQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSQQPMKPISPVKDPVSPASQK 22 2 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 QSQQPMKPIS(1)PVKDPVSPASQK 165.48 6.67E-12 496940000 882440 330250 447310 407310 514910 396820 836870 404600 892960 TRUE FALSE 827209.6556 354702.0536 457920.4044 417762.2642 474471.0456 511375.4922 711389.1126 455115.2006 743919.2073 1.111961686 0.476801849 0.615551259 0.561569402 0.63779916 0.687407298 0.956272006 0.611780414 1 19.50478642 1.919747375 6.613361414 0.846274901 0.640459997 0.130977698 0.196276791 0.394531463 27.05586012 0.077945667 0.048052033 83.12800827 -1.919747375 -0.205814904 QSS(ph)PSGSEQLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 QSSPSGSEQLVR 12 0 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 1 QSS(0.998)PS(0.002)GSEQLVR;QSS(1)PSGSEQLVR;QSS(0.995)PS(0.004)GS(0.002)EQLVR;QS(0.01)S(0.989)PS(0.001)GSEQLVR;QS(0.051)S(0.945)PS(0.004)GSEQLVR 270.16 4.04E-23 2863960000 2699920 2682530 2650460 2721900 2646250 2423100 3053810 2239430 2442110 TRUE FALSE 2530936.827 2881147.312 2713330.163 2791748.562 2438424.199 3122609.634 2595919.541 2519027.765 2034506.064 1.244005546 1.416140931 1.33365548 1.372199676 1.198533758 1.534824442 1.275945836 1.238152006 1 20.95624715 0.88478747 1.834738027 1.001631107 1.351576692 0.575093201 0.092690738 0.310547138 2.083718675 0.077373307 0.021831819 7.669860586 -0.88478747 0.349945585 QSS(ph)TPSAPELGQQPDVNISEWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QSSTPSAPELGQQPDVNISEWK 22 0 Q93100-4;Q93100-2;I3L213;Q93100-3;Q93100 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 1 QS(0.174)S(0.787)T(0.039)PS(0.001)APELGQQPDVNISEWK;QS(0.177)S(0.783)T(0.04)PSAPELGQQPDVNISEWK 271.18 1.65E-45 312170000 263590 221107 245662 250840 273160 202091 335120 220285 295820 TRUE FALSE 247092.3724 237477.9923 251489.2186 257276.9791 251707.1155 260431.391 284871.8671 247788.0672 246445.7309 1.00262387 0.963611711 1.020464902 1.043949831 1.021349059 1.056749452 1.15592129 1.005446782 1 17.91091046 3.168085006 0.99996385 1.071435041 0.981025434 0.187461986 0.046150977 0.571065565 1.236515526 0.020273318 0.030543722 1472.60071 -3.168085006 -0.090409607 QSSGASSSS(ph)FSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QSSGASSSSFSSSR 14 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8Y7T2;A0A087WVZ1;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 1 QSSGASS(0.001)S(0.03)S(0.969)FSSSR;QSSGAS(0.013)S(0.1)S(0.061)S(0.825)FS(0.001)SSR 189.45 7.52E-07 544390000 796230 833380 717050 635410 762120 536900 787720 489810 1060140 TRUE FALSE 746395.3856 895084.3223 734058.7646 651715.6963 702266.1694 691894.3142 669608.6988 550963.8567 883195.7852 0.845107504 1.013460817 0.831139343 0.737906257 0.79514212 0.783398569 0.758165641 0.623829808 1 19.75237376 3.605133792 3.030562114 0.771324544 0.937406896 0.253920417 0.100391675 0.257735815 4.573260186 0.024677173 0.041131885 4028.411177 -3.605133792 0.166082352 QSSGASSSSFSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSSGASSSSFSSSR 14 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8Y7T2;A0A087WVZ1;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 0 99.941 0.0046092 10258000 6093.4 6214.6 7042.5 4772.9 5763.8 5839.7 7677.7 6327.6 7155.9 FALSE TRUE 5712.024971 6674.73545 7209.551426 4895.380695 5311.134398 7525.52659 6526.500161 7117.614789 5961.534061 0.958146831 1.11963387 1.209345003 0.821161239 0.890900621 1.262347328 1.094768577 1.193923362 1 12.54146791 2.229408768 24.99998349 1.144372306 1.036620926 0.190419381 0.129193049 426.8210169 1165931.686 0.050637796 0.037918391 169.5933299 -2.229408768 -0.107751381 QSSLAEPVS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QSSLAEPVSPSK 12 0 E7EMD6;O43572 E7EMD6 AKAP10 "A-kinase anchor protein 10, mitochondrial" 1 QSSLAEPVS(0.999)PS(0.001)K;QSSLAEPVS(0.975)PS(0.025)K 228.11 1.19E-11 230620000 1174490 839270 938700 1088170 1099460 704290 1046980 630180 987370 TRUE FALSE 1100980.767 901410.4241 960966.4073 1116094.284 1013112.847 907607.0898 889995.0687 708859.3602 822571.5683 1.338461977 1.095844372 1.168246563 1.356835475 1.231640973 1.103377657 1.081966728 0.861760104 1 19.64978168 1.638028251 1.822988035 0.937623413 1.210594774 0.635989078 0.089764904 0.225153492 1.542432172 0.070016557 0.025867404 43.45384902 -1.638028251 0.272971361 QSST(ph)PSAPELGQQPDVNISEWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSSTPSAPELGQQPDVNISEWK 22 0 Q93100-4;Q93100-2;I3L213;Q93100-3;Q93100 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 1 QS(0.052)S(0.341)T(0.584)PS(0.023)APELGQQPDVNISEWK 276.9 6.41E-45 208980000 207420 163650 183400 188580 215180 135800 261370 168840 229260 TRUE FALSE 194437.9525 175766.8163 187750.3346 193419.2821 198280.6308 175003.2555 222179.9949 189920.0457 190995.0249 1.018026268 0.920269082 0.98301165 1.012692776 1.038145527 0.916271277 1.163276347 0.99437169 1 17.54317553 2.803900993 0.893160561 1.04783492 0.959785857 0.069565967 0.065935083 0.883947962 1.518268685 0.036481528 0.03679685 636.6503659 -2.803900993 -0.088049064 QSTIVCHNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QSTIVCHNR 9 0 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 ;;; 140.45 0.00010908 1410930000 814050 1329900 662800 643320 1345470 495610 917220 1098690 1500790 FALSE TRUE 763100.0636 1428367.18 678521.929 659828.6803 1239802.214 638684.5614 779691.3761 1235863.865 1250298.454 0.610334326 1.142420976 0.542687969 0.52773694 0.991605012 0.510825683 0.623604207 0.988455086 1 20.25384109 1.224136972 24.50289049 0.994228018 0.722623727 0.246847583 0.20717069 327.7218064 556713.3189 0.192576326 0.049085874 16.75471217 -1.224136972 -0.271604291 QSVDHFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QSVDHFAK 8 0 E7ETZ4;Q9Y6E2;Q75MG1;B5MCH7;B5MCE7;E9PFD4 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 ; 103.55 0.0047518 703540000 740280 954900 876340 871780 1062090 755760 1158370 924130 1176350 FALSE TRUE 693947.1962 1025601.79 897127.1986 894151.3507 978677.7357 973935.6433 984683.1723 1039509.665 980009.5855 0.708102458 1.046522202 0.915426963 0.912390413 0.998640983 0.99380216 1.004768919 1.060713773 1 19.90243633 4.746134382 24.98457248 0.986758191 0.708102324 0.777773323 0.047551647 453.2413072 1495130.539 0.01145212 0.122742191 55735.81829 -4.746134382 -0.278655867 QSVENDIHGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QSVENDIHGLR 11 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;; 225.15 5.69E-12 1413420000 1615220 1792770 2675840 2575510 2308040 3076920 2604480 1098840 1743170 FALSE TRUE 1514126.263 1925508.556 2739312.188 2641601.947 2126775.849 3965176.854 2213962.403 1236032.593 1452223.666 1.042626077 1.325903579 1.886288079 1.819004888 1.464496068 2.730417461 1.524532656 0.851131008 1 20.46983224 4.409504183 2.203027583 1.695417348 1.042211827 0.100812818 0.516969135 0.688963163 5.827544103 0.125272141 0.669220986 25674.62939 -4.409504183 -0.653205521 QSVSGLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSVSGLHR 8 0 Q8N1G4;J3KRP5 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 74.269 0.041416 38275000 155720 157790 138560 148170 182470 105800 150150 162470 166350 FALSE TRUE 145973.7632 169472.9358 141846.7086 151972.2931 168139.5422 136342.7425 127636.4014 182754.7371 138585.1103 1.053314911 1.222879827 1.023534984 1.096598997 1.21325835 0.983819561 0.920996499 1.318718416 1 17.08041274 2.22010248 24.99408722 1.033214616 1.121118421 0.054961373 0.120745203 544.0442552 736683.2049 0.042733319 0.031618182 165.9978565 -2.22010248 0.087903806 QSVTSFPDADAFHHQVHDDDLLS(ph)SSEEECKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QSVTSFPDADAFHHQVHDDDLLSSSEEECKDR 32 1 P50402;Q5HY57 P50402 EMD Emerin 1 QSVTSFPDADAFHHQVHDDDLLS(0.631)S(0.166)S(0.203)EEECKDR 82.713 0.00016819 111930000 117810 88756 91922 97644 126440 49573 94723 111250 84634 TRUE FALSE 110436.4824 95327.58659 94102.43325 100149.7104 116509.9124 63883.92035 80520.16552 125139.8074 70508.03864 1.566296333 1.352010188 1.334634108 1.420401309 1.652434455 0.906051588 1.141999793 1.774830357 1 16.10550013 2.249359237 24.9996545 1.198333561 1.429893736 0.20841316 0.245774893 364.413616 843645.8319 0.081697574 0.067718508 177.5657651 -2.249359237 0.231560175 QTDDLRGEIAVLEATVQNNQDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QTDDLRGEIAVLEATVQNNQDER 23 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ;;;;; 302.83 4.31E-62 273811000 179378 215858 203905 222852 226253 180506 221495 183111 279342 FALSE TRUE 168151.0512 231840.3509 208741.7229 228570.7596 208484.002 232615.1519 188283.881 205972.8114 232718.0156 0.722552789 0.996228635 0.896972769 0.982179051 0.895865331 0.99955799 0.809064483 0.88507463 1 17.82822337 -0.886087318 0.006967355 1.876494464 2.61E-06 0.088410828 0.087205009 46208.64286 64.68008321 9054.267828 8372.369731 0.12999082 0.886087318 -1.87649185 QTDFEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QTDFEHR 7 0 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ;; 131.06 0.0035026 2058040000 3925180 4956440 4316010 4422820 4635830 3449630 4736260 3810200 3047440 FALSE TRUE 3679509.99 5323419.975 4418387.795 4536317.049 4271750.612 4445482.181 4026101.782 4285911.857 2538802.577 1.449309223 2.096823134 1.740343198 1.786793936 1.682584794 1.75101531 1.585827043 1.688162718 1 21.27571678 -1.069909136 0.299327992 0.555838531 1.849028415 0.656165967 0.164185947 8.232539309 0.598515269 3.200231337 0.168583913 0.085131613 1.069909136 1.293189884 QTDKPSHCSQFVT(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QTDKPSHCSQFVTPPR 16 1 O60333-3 O60333-3 KIF1B Kinesin-like protein KIF1B 1 QTDKPSHCSQFVT(1)PPR 138.04 1.28E-05 134620000 73281 122370 123290 129010 125830 99236 156750 119330 139270 TRUE FALSE 68694.47302 131430.4021 126214.497 132320.615 115947.8194 127883.8222 133246.7927 134228.6132 116024.9373 0.592066453 1.132777187 1.087822153 1.140449787 0.999335333 1.102209794 1.148432361 1.156894512 1 16.82407539 4.740598551 24.99923986 1.102851916 0.592066279 0.886582704 0.056595852 52.88763588 648724.4795 0.012469377 0.082152552 55029.87817 -4.740598551 -0.510785637 QTDPST(ph)PQQESSKPLGGIQPSSQTIQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QTDPSTPQQESSKPLGGIQPSSQTIQPK 28 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 QT(0.003)DPS(0.099)T(0.675)PQQES(0.185)S(0.037)KPLGGIQPSSQTIQPK 149.37 1.06E-07 203200000 146110 94302 104670 103860 114510 97457 152220 104220 170280 TRUE FALSE 136965.2359 101284.2182 107152.8218 106525.2234 105516.8465 125591.2538 129396.0241 117232.0964 141859.1679 0.965501475 0.713977247 0.755346471 0.750922376 0.74381408 0.885323491 0.912144248 0.826397744 1 17.11409987 2.181010925 6.156739672 0.901172978 0.770416362 0.346400309 0.080406119 0.20029417 15.40017447 0.027915804 0.020674763 151.7088529 -2.181010925 -0.130756616 QTDVGITHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QTDVGITHFR 10 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 84.507 0.014874 338760000 361020 447850 333380 347200 424460 354970 481340 381160 513590 FALSE TRUE 338424.4026 481009.28 341287.931 356109.7398 391124.6238 457444.0765 409167.5355 428748.665 427868.5111 0.790954216 1.124198831 0.797646759 0.832287795 0.914123413 1.069123024 0.956292704 1.002057066 1 18.70680798 2.350489117 9.324712247 1.000417718 0.907441108 0.248305187 0.097144789 0.506123801 39.59494825 0.033861082 0.028300199 224.1243882 -2.350489117 -0.092976609 QTELKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QTELKR 6 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YAP2;H0YAW6 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ;; 132.29 0.023993 1013550000 1415450 1373820 1379970 1263580 1481880 1162540 1765520 1271630 1895960 FALSE TRUE 1326859.511 1475539.062 1412703.54 1296005.602 1365499.122 1498146.426 1500796.666 1430395.805 1579512.028 0.840043943 0.934173996 0.894392392 0.820510119 0.864506948 0.948486874 0.95016476 0.905593487 1 20.59104749 2.230829242 24.95693636 0.947313638 0.880322339 0.513965415 0.038113683 172.8712778 558025.0287 0.014413845 0.010846727 170.1489379 -2.230829242 -0.066991299 QTEPVS(ph)PVLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QTEPVSPVLKR 11 1 Q8IYH5-2;Q8IYH5;Q8IYH5-4 Q8IYH5-2 ZZZ3 ZZ-type zinc finger-containing protein 3 1 QTEPVS(1)PVLKR 105.17 0.0015322 273230000 560400 266780 402630 335420 321530 241720 488220 324280 353730 TRUE FALSE 525325.5643 286532.6688 412180.5737 344027.4451 296278.3308 311500.64 415015.9434 364767.0718 294690.1778 1.78263683 0.972318355 1.398691252 1.167420807 1.005389229 1.057044528 1.408312779 1.23779854 1 18.16883945 4.75128922 24.72822825 1.181199876 1.782637273 0.60453793 0.158136686 1321.001266 2566294.425 0.037186289 0.673408903 56401.3138 -4.75128922 0.601437396 QTFPFPTIYEGEKQHES(ph)EEPFMPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QTFPFPTIYEGEKQHESEEPFMPEER 26 1 H7BZ15;Q9BSF0 H7BZ15 C2orf88 Small membrane A-kinase anchor protein 1 QT(0.003)FPFPT(0.009)IY(0.003)EGEKQHES(0.985)EEPFMPEER 43.622 0.085667 1107900000 406870 80400 138730 154750 171060 100820 181620 95569 176100 TRUE FALSE 381404.733 86352.89966 142020.7411 158721.147 157625.6376 129925.0973 154387.7671 107501 146707.7724 2.599758192 0.588604804 0.968051923 1.081886423 1.074419133 0.885604731 1.052348929 0.732755997 1 17.16258578 4.74555882 24.99625592 0.921998999 2.599758968 0.918324641 0.157155755 224.4560832 801694.519 0.038269347 0.384400139 55662.00172 -4.74555882 1.677759969 QTGIET(ph)PNKSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QTGIETPNKSGK 12 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 QTGIET(1)PNKSGK;QTGIET(1)PNKSGK;QTGIET(1)PNKSGK 144.33 0.00010179 682520000 1610960 844506 1278320 944600 1439240 1036060 1907670 1121960 2542060 TRUE FALSE 1510132.889 907034.1029 1308642.354 968840.0352 1326207.896 1335153.703 1621632.593 1262039.176 2117773.764 0.713075643 0.428296034 0.617933028 0.457480422 0.626227371 0.630451527 0.765725131 0.595927288 1 21.01411705 0.342519593 0.375104387 1.056467512 0.527716231 0.627873145 0.097722509 1.748998184 0.435216491 0.272261168 0.07370278 2.200490984 -0.342519593 -0.528751281 QTGIVLNRPVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QTGIVLNRPVLR 12 1 Q13435;E9PPJ0;H0YCG1;E9PJ04;E9PJT3 Q13435 SF3B2 Splicing factor 3B subunit 2 0 109.16 0.0014848 450910000 446720 630470 586510 619150 656830 613200 706310 517350 737110 FALSE TRUE 418760.5926 677150.6548 600422.2942 635038.4372 605245.2213 790220.8855 600405.3726 581942.2863 614081.5791 0.681929905 1.102704718 0.977756563 1.034127156 0.98561045 1.286833724 0.977729007 0.947662829 1 19.2280708 4.744364569 24.85458861 1.043243037 0.681929734 0.56872036 0.09767454 420.037275 1798692.611 0.021751044 0.193781901 55509.14891 -4.744364569 -0.361313302 QTHTKHPT(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QTHTKHPTPER 11 1 Q8IYW5 Q8IYW5 RNF168 E3 ubiquitin-protein ligase RNF168 1 QTHT(0.001)KHPT(0.999)PER 78.505 0.043532 17243000 9666.1 14419 11197 13701 13526 7896.7 13174 11589 23909 TRUE FALSE 9061.116055 15486.59776 11462.59813 14052.59086 12463.72252 10176.3491 11198.681 13035.91216 19918.43344 0.454911079 0.777500791 0.57547689 0.705506831 0.625738091 0.510901077 0.562226996 0.65446473 1 14.28181657 0.953524872 19.88666438 1.000000001 0.613333696 0.646914497 0.091430478 447.9077742 191660.5478 0.084780491 0.021195123 8.985140498 -0.953524872 -0.386666305 QTLENER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QTLENER 7 0 P35579 P35579 MYH9 Myosin-9 0 ; 99.7 0.024045 553880000 947230 1254090 1035660 975150 1119090 984410 1213260 1048810 984600 FALSE TRUE 887944.5652 1346944.128 1060226.344 1000174 1031201.186 1268593.186 1031342.926 1179756.237 820263.8992 1.082510843 1.642086321 1.292542979 1.219331975 1.257157832 1.546567132 1.257330631 1.438264244 1 19.64572861 -1.299896787 3.756143039 0.999156703 1.35974808 0.294571074 0.164279171 377.9527148 38063171.34 51780.93331 0.035591537 0.050130636 1.299896787 0.360591377 QTPEVPAERS(ph)PRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QTPEVPAERSPRR 13 2 Q9UJF2 Q9UJF2 RASAL2 Ras GTPase-activating protein nGAP 1 QTPEVPAERS(1)PRR 52.254 0.080297 247630000 28749 131710 95713 104530 112320 101880 72275 82744 63861 TRUE FALSE 26949.65141 141461.9454 97983.35756 107212.4168 103498.8403 131291.1021 61438.03472 93074.77054 53202.18654 0.506551575 2.658949841 1.84171674 2.015188167 1.945386966 2.467776433 1.154802814 1.749453859 1 15.69919792 1.687184404 9.412165276 1.345276598 1.990315919 0.174004024 0.598468325 0.175274595 25.59830853 0.258606332 0.13862062 48.66137808 -1.687184404 0.645039321 QTPMAS(ph)SPRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QTPMASSPRPK 11 1 Q5SSJ5;Q5SSJ5-2;Q5SWC8;B0QZK4 Q5SSJ5 HP1BP3 Heterochromatin protein 1-binding protein 3 1 QT(0.027)PMAS(0.562)S(0.411)PRPK 64.394 0.041533 221090000 196510 103980 142990 116520 138640 131630 183510 122080 158880 TRUE FALSE 184210.7899 111678.7874 146381.7903 119510.1005 127751.7736 169629.4442 155994.3791 137321.9567 132361.9016 1.391720636 0.843738161 1.105920877 0.902904076 0.96517028 1.281557927 1.178544409 1.037473435 1 17.0141284 2.263530329 24.99995071 1.148562068 1.017283779 0.038024023 0.165655061 440.1851419 440716.6314 0.052525762 0.043929812 183.4553278 -2.263530329 -0.131278289 QTPS(ph)PDVVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 QTPS(1)PDVVLR;QT(0.004)PS(0.996)PDVVLR;QT(0.007)PS(0.993)PDVVLR;QT(0.061)PS(0.939)PDVVLR 190.26 9.66E-07 1706390000 1409040 1506260 1498440 1516020 1669470 1343100 1660860 1373750 1674290 TRUE FALSE 1320850.702 1617785.058 1533983.704 1554923.64 1538356.561 1730831.167 1411829.462 1545265.711 1394840.183 0.946954868 1.159835426 1.099755889 1.114768315 1.102890912 1.240881348 1.01218009 1.107844275 1 20.4116684 0.850395948 1.222754276 1.003080211 1.110070606 0.119285539 0.078756716 1.183981084 3.404228212 0.066812374 0.020541125 7.085915152 -0.850395948 0.106990396 QTS(ph)IETDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QTSIETDR 8 0 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 QT(0.018)S(0.982)IETDR;QT(0.008)S(0.992)IETDR;QT(0.011)S(0.988)IETDR;QT(0.013)S(0.987)IETDR 174.42 0.00028536 1720640000 2882870 2995890 3007510 3134830 3045510 2542690 3420700 2507430 3274660 TRUE FALSE 2702436.313 3217708.813 3078849.557 3215275.045 2806327.93 3276723.326 2907797.791 2820488.155 2728098.091 0.990593528 1.179469618 1.128569962 1.178577506 1.028675596 1.201101726 1.065869956 1.033866108 1 21.37946409 1.443745193 3.599956341 1.01912545 1.125618535 0.276606953 0.066583097 0.255289243 6.083138782 0.043526214 0.01542853 27.78082845 -1.443745193 0.106493085 QTSDGNWLMVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QTSDGNWLMVHR 12 0 O75131;A0A087WYQ3 O75131 CPNE3 Copine-3 0 ; 162.32 6.30E-05 360900000 399360 562670 427040 397700 750410 425890 496860 573690 807970 FALSE TRUE 374364.7705 604330.6723 437169.5905 407905.6553 691475.8256 548837.5293 422360.4556 645316.4593 673114.5873 0.556167965 0.897812473 0.649472762 0.605997349 1.027278028 0.815370131 0.62747185 0.958702235 1 19.3604926 -4.999999972 0.144046328 1.866038986 0.677732591 0.25886617 0.150686683 214.2297905 1.868779166 52.70702733 0.819255174 1.00E-05 4.999999972 -1.188306395 QVAEQGGDLS(ph)PAANR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QVAEQGGDLSPAANR 15 0 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 QVAEQGGDLS(1)PAANR;QVAEQGGDLS(1)PAANR;QVAEQGGDLS(1)PAANR;QVAEQGGDLS(1)PAANR;QVAEQGGDLS(1)PAANR;QVAEQGGDLS(1)PAANR 335.1 5.36E-69 5684180000 3361950 3821790 3500220 3451320 4192650 3223710 4115480 3348630 3948480 TRUE FALSE 3151531.551 4104759.308 3583246.871 3539886.714 3863376.181 4154342.744 3498401.98 3766713.827 3289453.18 0.958071563 1.247854608 1.089313839 1.076132269 1.17447368 1.262928067 1.063520831 1.145088141 1 21.64941635 0.2602439 1.230645551 0.999902131 1.137105532 0.155476478 0.090152222 8.231183943 12.05976349 0.081062003 0.023633157 1.820723091 -0.2602439 0.137203401 QVAGDAPVEQATAETAS(ph)PVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QVAGDAPVEQATAETASPVHR 21 0 Q92766;Q92766-2;A0A087X055;Q92766-4 Q92766 RREB1 Ras-responsive element-binding protein 1 1 QVAGDAPVEQATAET(0.004)AS(0.996)PVHR 214.16 9.61E-25 564750000 270850 280660 260050 239060 219850 223980 330560 194860 232760 TRUE FALSE 253897.982 301440.3584 266218.5088 245194.6843 202583.8678 288639.39 280995.5968 219188.6999 193910.8523 1.309354164 1.554530625 1.372891231 1.26447118 1.044726819 1.488515916 1.449096806 1.130358086 1 17.56503402 -4.230913993 0.153964425 4.05E-10 1.471053511 0.3471343 0.150522791 118.2923883 1.329635353 37.23262415 0.755203427 5.88E-05 4.230913993 1.471053511 QVALWDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QVALWDTK 8 0 P31146;H3BRY3;H3BTU6 P31146 CORO1A Coronin-1A;Coronin 0 93.649 0.022822 0 219370 295890 239800 238790 312720 210310 324890 249670 304460 FALSE TRUE 205640.0233 317798.0035 245488.1692 244917.7557 288160.2327 271023.0829 276175.7606 280841.8491 253643.6591 0.810743797 1.252931 0.967846664 0.965597786 1.136082935 1.068519055 1.088833687 1.107229923 1 17.95244357 2.723353122 24.27422313 1.084825523 1.036316142 0.070300772 0.114552587 2131.390696 3402122.531 0.035299134 0.033416933 528.8751016 -2.723353122 -0.048509381 QVAPEKPVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QVAPEKPVKK 10 2 P53999;D6RC37;D6R970 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 54.471 0.076995 700000000 1234800 873930 1075900 1071200 1147900 753390 1345200 969710 1428000 FALSE TRUE 1157516.072 938636.6865 1101420.856 1098688.806 1057748.564 970881.4627 1143499.748 1090780.428 1189657.575 0.97298256 0.788997361 0.925830154 0.923533653 0.889120186 0.816101611 0.961200746 0.916886045 1 20.18211494 1.104831657 1.187648461 0.995308128 0.882780633 0.24717395 0.057161165 0.564975233 1.649439187 0.050118215 0.015904834 12.73009537 -1.104831657 -0.112527496 QVDGDNSHVEMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QVDGDNSHVEMK 12 0 P02786;F8WBE5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ; 145.43 6.39E-05 308860000 1164890 936730 988730 927600 1287810 796440 1304860 1041900 1697010 FALSE TRUE 1091981.614 1006086.464 1012183.143 951403.7864 1186670.597 1026359.299 1109208.357 1171983.509 1413768.068 0.772390917 0.711634735 0.715947096 0.672956058 0.839367237 0.725974311 0.784575902 0.828978625 1 20.43111403 0.514684387 0.554939446 1.01124234 0.722167175 0.783933526 0.04311861 0.729455593 0.403239278 0.055862234 0.018271719 3.271028943 -0.514684387 -0.289075165 QVDVPTLTGAFGILAAHVPTLQVLRPGLVVVHAEDGTTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QVDVPTLTGAFGILAAHVPTLQVLRPGLVVVHAEDGTTSK 40 1 P30049 P30049 ATP5D "ATP synthase subunit delta, mitochondrial" 0 254.78 3.57E-63 106500000 111690 99971 74912 76333 132290 94624 100820 95843 104890 FALSE TRUE 104699.5223 107372.9569 76688.94802 78291.83401 121900.477 121940.4127 85702.97697 107809.2095 87383.18138 1.198165604 1.228759987 0.8776168 0.895959986 1.395010746 1.395467764 0.980771993 1.233752397 1 16.41506801 2.748814816 24.98233501 1.19778558 1.051146542 0.156258259 0.174113714 1445.116228 3520741.627 0.054839808 0.05758817 560.8087947 -2.748814816 -0.146639037 QVEDLQATFSSIHSFQDLSSSILAQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QVEDLQATFSSIHSFQDLSSSILAQSR 27 0 O60664-4;O60664;O60664-3;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 0 ; 285.17 2.02E-61 401730000 75327 118931 96776 101750 110713 94267 116690 97895 102274 FALSE TRUE 70612.41753 127736.775 99071.57242 104361.0773 102018.0476 121480.3526 99193.4178 110117.4062 85203.80868 0.828747196 1.499190904 1.162759904 1.224840519 1.1973414 1.425761999 1.16418995 1.292400046 1 16.3786303 -0.611906998 6.640569824 1 1.245634665 0.124661873 0.179191049 0 0 0.151188521 0.035635476 0.244395385 0.611906998 0.245634665 QVEEALHQLHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QVEEALHQLHAR 12 0 F5H169;F5H5V4;F5GX23;J3KN29;O00233-2;O00233 F5H169 PSMD9 26S proteasome non-ATPase regulatory subunit 9 0 ; 161.48 3.77E-05 607670000 267430 324530 314150 283960 337390 247330 335160 276380 325250 FALSE TRUE 250692.0337 348558.5389 321601.7864 291246.8943 310892.7504 318730.1559 284905.8695 310886.6514 270963.6738 0.925186872 1.286366301 1.186881554 1.074855866 1.147359519 1.176283712 1.051454114 1.14733701 1 18.04773993 0.718406209 0.491520892 0.995928299 1.161508437 0.084829782 0.098344989 2.475387811 1.296381164 0.130140019 0.051900432 5.228850303 -0.718406209 0.165580138 QVEELFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QVEELFER 8 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 ;;; 165.26 0.00075678 692630000 779350 1079000 974330 969160 1120900 1021350 969140 929910 1084460 FALSE TRUE 730571.8747 1158890.283 997441.5677 994030.2864 1032869.035 1316197.165 823826.4541 1046011.31 903456.6201 0.80864079 1.282729305 1.10402818 1.100252369 1.143241427 1.456846002 0.911860554 1.157788085 1 19.78509581 -0.30617481 7.596398368 0.999990621 1.132356855 0.040072229 0.177612006 0 0 0.153850094 0.036262815 0.49411176 0.30617481 0.132366234 QVEELYHSLLELGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QVEELYHSLLELGEK 15 0 A0A0D9SGF6;Q13813;Q13813-2 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 168.07 1.28E-06 65891000 446980 307210 359580 333250 387220 292580 426040 299110 429380 FALSE TRUE 419004.3197 329956.1481 368109.4074 341801.7592 356809.3032 377043.0964 362159.2572 336454.5419 357713.7041 1.171339859 0.922402872 1.029061518 0.955517654 0.997471719 1.054035929 1.012427685 0.940569338 1 18.44844586 4.752828471 24.98939481 0.992104793 1.171339982 0.669522885 0.040219269 1591.425027 2787249.616 0.009362932 0.203868663 56601.56915 -4.752828471 0.17923519 QVELALWDTAGQEDYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 278.93 1.75E-35 618442000 592413 662825 574308 611190 710770 701894 789576 620234 670045 FALSE TRUE 555334.9278 711901.2527 587930.857 626874.1701 654948.9913 904519.4035 671186.4089 697671.5802 558210.1608 0.994849193 1.275328367 1.053242843 1.123007452 1.173301809 1.620392223 1.202390168 1.249836762 1 19.09044886 2.457802944 24.99998172 1.301732668 1.131065225 0.147120293 0.166878713 370.4661362 479420.423 0.052467002 0.043902613 286.9478293 -2.457802944 -0.170667443 QVELS(ph)TMYRHMEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QVELSTMYRHMEK 13 1 Q5VSF9;Q05586-2;Q05586-3;Q05586-7;Q05586-4;Q05586;Q05586-6;Q05586-5 Q5VSF9 GRIN1 "Glutamate receptor ionotropic, NMDA 1" 1 QVELS(0.999)T(0.001)MY(0.001)RHMEK 104.87 0.00090715 421430000 81653 462440 357630 353990 404730 722480 154980 295460 125140 TRUE FALSE 76542.48448 496679.5388 366113.1525 363073.9827 372944.1384 931048.2475 131742.1878 332348.8314 104253.3256 0.734197054 4.764160146 3.511764737 3.48261296 3.577287692 8.930633555 1.26367372 3.187896689 1 16.66973388 4.749174907 23.72738125 3.877433469 0.73419336 0.153782813 2.16763122 1309.365643 2926859.774 0.47126612 6.473709017 56127.39766 -4.749174907 -3.143240109 QVEPPAKKPATPAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLR ddPTM_SK-BR-3_Pertuzumab_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 225.8 6.10E-40 766330000 320560 365120 262310 430610 836900 205273 585300 257560 3201900 TRUE FALSE 300496.7218 392153.8647 268532.1171 441660.1816 771173.2499 264531.9828 497539.6987 289716.933 2667482.205 0.112651819 0.147012739 0.100668757 0.165571932 0.289101554 0.099169165 0.186520344 0.108610634 1 21.34704722 -1.541398193 3.224440351 1.028186336 0.151130372 0.956612011 0.05681244 76232473.76 91104344.73 18667332.59 0.013410987 0.028747614 1.541398193 -0.877055964 QVETEEAGVVTTATASVNLKVS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QVETEEAGVVTTATASVNLKVSPK 24 1 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 QVETEEAGVVT(0.009)T(0.008)AT(0.008)AS(0.039)VNLKVS(0.937)PK;QVETEEAGVVT(0.004)T(0.003)AT(0.003)AS(0.001)VNLKVS(0.989)PK 84.962 0.007645 31560000 239550 126374 164809 162383 174761 113522 198171 122926 195991 TRUE FALSE 224556.9931 135730.8625 168718.3473 166550.0227 161035.976 146293.9585 168457.0983 138273.5817 163278.8359 1.375297612 0.831282644 1.033314246 1.020034359 0.986263621 0.895976246 1.031714229 0.846855509 1 17.31697828 4.74971712 24.85820706 0.959658192 1.375297873 0.758259404 0.074429693 735.3769694 1638486.189 0.016560232 0.254980879 56197.51603 -4.74971712 0.415639681 QVHPDTGISS(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QVHPDTGISSK 11 0 Q16778;P33778;P23527;P06899;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053;Q99880;Q96A08 Q16778;P58876;Q99880 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS;HIST1H2BL;HIST1H2BA Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S;Histone H2B type 1-L;Histone H2B type 1-A 1 QVHPDTGIS(0.007)S(0.993)K;QVHPDTGIS(0.042)S(0.958)K;QVHPDTGIS(0.057)S(0.943)K;QVHPDTGIS(0.027)S(0.973)K 184 3.29E-06 1834260000 4237590 2687550 3124270 3082220 3718250 2598920 3712700 2135860 3469490 TRUE FALSE 3972366.806 2886538.998 3198379.16 3161314.983 3426233.644 3349186.014 3156015.102 2402526.823 2890409.705 1.374326553 0.998660845 1.10654872 1.093725563 1.185379926 1.158723626 1.091891954 0.831206323 1 21.46284257 1.358673064 5.859790445 0.918440982 1.127746528 0.450787178 0.10430008 0.188521669 8.354353027 0.067060154 0.024002523 22.83878858 -1.358673064 0.209305546 QVHPDTGISSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 16 QVHPDTGISSK 11 0 Q16778;P33778;P23527;P06899;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053;Q99880;Q96A08 Q16778;P58876;Q99880 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS;HIST1H2BL;HIST1H2BA Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S;Histone H2B type 1-L;Histone H2B type 1-A 0 ;;;;;;;;;;;;;;; 179.67 7.00E-06 1.94473E+11 76679559 75482254 76169417 69688704 76469069 61235841 101911856 67206950 88911315 FALSE TRUE 71880322.28 81071038.63 77976191.54 71477034.13 70463496.78 78913634.22 86631119.3 75597885.65 74071442.14 0.970418831 1.09449791 1.05271599 0.964974247 0.951291007 1.065371916 1.169561666 1.02060772 1 26.14241409 2.009237274 24.80008705 1.09103919 1.021873862 0.094660335 0.063689455 293.8470975 788911.4631 0.024233496 0.017872951 102.1497419 -2.009237274 -0.069165328 QVHQCIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QVHQCIER 8 0 E7EQY1;Q96C01;C9JF51 E7EQY1 FAM136A Protein FAM136A 0 ;;; 149.72 0.00050068 1382870000 387772 539750 327991 306477 608490 333827 431487 438668 700150 FALSE TRUE 363502.0427 579713.6516 335771.1014 314341.7187 560701.6499 430197.4357 366789.5301 493436.6654 583290.4419 0.623192181 0.993867909 0.575649929 0.538911143 0.961273509 0.737535548 0.628828288 0.845953628 1 19.15385491 -1.246506448 4.933144001 1.000050073 0.738965239 0.218416472 0.155660592 8.13E-05 1.24E-05 0.142947471 0.033686591 0.056688316 1.246506448 -0.261084834 TRDELDQFLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TRDELDQFLDK 11 1 Q14137;Q14137-2;A0A075B729 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 ; 120.59 0.0003937 450230000 280640 232680 251980 236000 205417 162560 220942 126744 130661 FALSE TRUE 263075.2434 249907.8693 257957.0846 242056.1595 189284.3774 209488.4331 187813.7982 142568.2674 108852.835 2.416797352 2.295832436 2.369778285 2.223701014 1.738901678 1.924510584 1.725391886 1.309734077 1 16.73201946 1.657945482 0.467838699 0.961693561 2.435907863 0.932991257 0.120914963 0.209957055 0.116766189 0.127758147 0.090143078 45.49309481 -1.657945482 1.474214302 up QVLGQMVIDEELLGDGHSYSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QVLGQMVIDEELLGDGHSYSPR 22 0 P28070 P28070 PSMB4 Proteasome subunit beta type-4 0 ;;; 260.56 2.90E-37 449754000 475812 523823 379423 315195 471197 524446 766800 391233 723340 FALSE TRUE 446031.7763 562607.4 388423.0927 323283.4373 434191.0883 675845.0465 651825.4586 440079.3013 602609.881 0.740166715 0.933617947 0.644568078 0.536472181 0.720517705 1.121529978 1.081670711 0.73028889 1 19.2008648 2.25322853 24.89024311 1.004672168 0.72713894 0.465295659 0.141778968 200.1651932 339663.3625 0.050844604 0.042365637 179.1548337 -2.25322853 -0.277533228 QVLIRPCSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QVLIRPCSK 9 1 P62244;I3L3P7;I3L246;H3BN98;H3BV27;H3BT37;I3L303 P62244 RPS15A 40S ribosomal protein S15a 0 ; 114.5 0.0014854 855680000 709490 832100 625430 593550 992530 859090 1550250 704540 1777170 FALSE TRUE 665084.2874 893709.5498 640265.4949 608781.4979 914580.6975 1107095.337 1317804.404 792503.3699 1480548.846 0.449214688 0.603633951 0.43245145 0.411186365 0.61773085 0.747760089 0.890078303 0.535276747 1 20.49770066 2.358768121 2.780685511 0.799025455 0.489678617 0.583917348 0.126800675 0.184278453 2.901969718 0.045514551 0.035896753 228.4378797 -2.358768121 -0.309346838 QVQEFLKDGDDVIIIGVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QVQEFLKDGDDVIIIGVFK 19 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 172.2 8.02E-12 34813000 83956 51834 41962 41553 61533 74808 141570 42536 113050 FALSE TRUE 78701.34383 55671.84329 42957.35846 42619.32033 56700.44639 96403.85519 120342.8928 47846.71323 94181.22467 0.835637295 0.59111403 0.456113823 0.452524593 0.602035561 1.023599508 1.27778008 0.508028149 1 16.52315186 2.258859831 6.231019465 1.010714833 0.561933002 0.397431441 0.217071927 0.131838796 17.6327095 0.074368704 0.059848318 181.4929799 -2.258859831 -0.448781831 QVQPEGPYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QVQPEGPYR 9 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 160.74 0.00015137 3480170000 2035770 3960210 1985270 2194570 4136370 1389910 2246370 3481480 3818370 FALSE TRUE 1908354.79 4253428.069 2032361.542 2250886.382 3811516.186 1791154.454 1909547.673 3916150.442 3181059.379 0.599911716 1.337110554 0.638894563 0.707590181 1.198190832 0.563068538 0.600286711 1.231083729 1 21.60107587 3.938545053 20.38605287 0.810547161 1.017021898 0.009669599 0.295328166 85.53332288 45200.51595 0.0703158 0.126779034 8680.506235 -3.938545053 0.206474738 QVS(ph)ASELHTSGILGPETLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 QVSASELHTSGILGPETLR 19 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 QVS(0.999)AS(0.001)ELHTSGILGPETLR;QVS(1)ASELHTSGILGPETLR;QVS(1)ASELHTSGILGPETLR;QVS(0.869)AS(0.131)ELHTSGILGPETLR;QVS(0.998)AS(0.002)ELHTSGILGPETLR;QVS(0.847)AS(0.153)ELHTSGILGPETLR;QVS(0.5)AS(0.5)ELHTSGILGPETLR;QVS(1)ASELHTSGILGPETLR;QVS(0.475)AS(0.475)ELHT(0.044)S(0.005)GILGPETLR;QVS(0.568)AS(0.431)ELHT(0.001)SGILGPETLR;QVS(0.991)AS(0.009)ELHTSGILGPETLR;QVS(0.999)AS(0.001)ELHTSGILGPETLR;QVS(0.996)AS(0.004)ELHTSGILGPETLR;QVS(0.998)AS(0.002)ELHTSGILGPETLR 269.06 5.49E-32 97025359900 4438413.3 13033476.8 10103681.6 12719647 7631480.1 9507514.4 13293731 8643812.5 7799263.7 TRUE FALSE 4160620.934 13998488.98 10343345.7 13046054.68 7032134.437 12252179.47 11300459.45 9723011.518 6497516.203 0.640340217 2.154436949 1.591892252 2.007852581 1.0822804 1.885671245 1.739196809 1.496419742 1 22.6314569 0.895295738 4.617050885 1.000087491 1.65726704 0.128368519 0.446992543 1.058826906 43.7160756 0.378317397 0.095956678 7.857705323 -0.895295738 0.657179549 QVS(ph)DLGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QVSDLGSK 8 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 QVS(1)DLGSK;QVS(1)DLGSK;QVS(1)DLGSK;QVS(1)DLGSK 135.1 0.00088986 1102980000 2784770 1414320 1851060 1620940 1760750 1438140 1888680 1449360 1697540 TRUE FALSE 2610476.217 1519037.724 1894968.017 1662536.065 1622467.798 1853307.672 1605489.968 1630315.786 1414209.607 1.845890597 1.07412488 1.339948482 1.175593813 1.14726119 1.310490087 1.135256018 1.152810572 1 20.43156453 4.74448818 24.90658738 1.185331776 1.8458909 0.81664032 0.100772136 243.7422476 1024132.146 0.021651638 0.196306352 55524.95043 -4.74448818 0.660559124 QVSASELHTSGILGPETLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QVSASELHTSGILGPETLR 19 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 247.89 8.41E-25 1570160000 384287 1395470 1128360 1129130 1411100 1496000 1591330 1250860 1127700 FALSE TRUE 360235.1626 1498792.051 1155125.232 1158105.387 1300277.898 1927870.914 1352724.84 1407032.624 939479.5848 0.383441182 1.595342863 1.229537343 1.232709477 1.384040611 2.052062595 1.439866136 1.497672379 1 19.84150229 2.475395695 24.9975493 1.564412678 1.220724127 0.144089353 0.396923372 105.4980808 1528264.29 0.125775996 0.105929407 298.8103907 -2.475395695 -0.343688551 QVSDDLTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QVSDDLTER 9 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0 P35232 PHB Prohibitin 0 ; 121.93 0.001396 329770000 594720 652070 614700 627090 819440 561070 635670 623880 868930 FALSE TRUE 557497.5368 700349.9413 629280.9743 643182.1911 755084.4879 723041.8008 540357.1848 701772.7913 723899.9695 0.770130626 0.967467842 0.869292721 0.88849595 1.043078491 0.99881452 0.746452835 0.969433376 1 19.46543083 4.750643865 23.41516173 0.920230862 0.770130399 0.2534702 0.085688631 1218.307592 2360752.967 0.020373867 0.319330953 56317.56446 -4.750643865 -0.150100463 QVTDAETKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QVTDAETKPK 10 1 O43684;O43684-2 O43684 BUB3 Mitotic checkpoint protein BUB3 0 63.091 0.088112 0 191680 146040 185780 156770 187190 135600 198170 141830 227780 FALSE TRUE 179683.091 156852.9536 190186.7893 160792.9836 172488.8525 174745.5187 168456.2482 159537.7877 189762.0465 0.946886347 0.826577055 1.002238292 0.847340059 0.908974453 0.920866538 0.887723606 0.84072548 1 17.53383195 -1.472736293 3.965871081 1.000813695 0.899649024 0.270785022 0.052686715 0.000347458 4.62E-05 0.046761302 0.010933688 0.033671596 1.472736293 -0.101164671 QVVESAYEVIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QVVESAYEVIK 11 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 170.62 3.61E-05 157090000 330610 323410 270920 293540 331960 216560 350080 253310 328370 FALSE TRUE 309917.7103 347355.6129 277346.3503 301072.7334 305889.2007 279077.3564 297588.754 284936.3111 273562.9256 1.132893683 1.269746666 1.013830181 1.100561169 1.118167602 1.020157815 1.087825601 1.041575025 1 18.0615132 3.954383864 5.985343854 1.062729752 1.203004745 0.587907448 0.050688031 0.097140876 11.97298834 0.011458004 0.021957374 9002.929799 -3.954383864 0.140274993 QVVPPFKPNISGEFGLDNFDSQFTNEPVQLT(ph)PDDDDIVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QVVPPFKPNISGEFGLDNFDSQFTNEPVQLTPDDDDIVR 39 1 P41743 P41743 PRKCI Protein kinase C iota type 1 QVVPPFKPNISGEFGLDNFDSQFTNEPVQLT(1)PDDDDIVR;QVVPPFKPNISGEFGLDNFDSQFTNEPVQLT(1)PDDDDIVR;QVVPPFKPNISGEFGLDNFDSQFTNEPVQLT(1)PDDDDIVR 285.29 4.73E-77 209167000 187344 201523 193762 181264 230677 179059 249969 203184 262985 TRUE FALSE 175618.4735 216443.9726 198358.1261 185915.5411 212560.5589 230750.4265 212488.469 228551.9697 219091.1046 0.80157738 0.987917666 0.905368233 0.848576402 0.970192557 1.053216775 0.969863516 1.043182333 1 17.74117138 2.50048581 8.445340862 1.010914013 0.906340718 0.560711482 0.053337617 0.218144404 71.05718929 0.016870105 0.015413942 316.581702 -2.50048581 -0.104573295 QVVSVVQDEEVGLPFEASPES(ph)PPPASPDGVTEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QVVSVVQDEEVGLPFEASPESPPPASPDGVTEIR 34 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 QVVSVVQDEEVGLPFEAS(0.003)PES(0.996)PPPAS(0.001)PDGVTEIR;QVVSVVQDEEVGLPFEAS(0.012)PES(0.987)PPPAS(0.001)PDGVTEIR 173.01 5.27E-15 707060000 145568 159314 145563 153475 168530 148563 149584 96135 149030 TRUE FALSE 136457.1587 171109.7743 149015.8231 157413.4283 155294.3336 191450.7264 127155.2679 108137.6664 124155.9302 1.099078864 1.378184465 1.200231216 1.267868784 1.250800774 1.54201838 1.024157828 0.870982692 1 16.92179365 1.565544899 6.679659915 0.940790941 1.2879615 0.630005952 0.118605871 0.074069608 6.539091347 0.058834297 0.027384135 36.774341 -1.565544899 0.347170559 QVVSVVQDEEVGLPFEASPESPPPAS(ph)PDGVTEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QVVSVVQDEEVGLPFEASPESPPPASPDGVTEIR 34 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 QVVSVVQDEEVGLPFEASPES(0.003)PPPAS(0.995)PDGVT(0.002)EIR;QVVSVVQDEEVGLPFEASPES(0.048)PPPAS(0.952)PDGVTEIR 237.22 3.76E-47 131586000 114147 133981 126517 162235 176656 113046 89462 55621 92986 TRUE FALSE 107002.743 143901.0926 129518.043 166398.2248 162782.1504 145680.5451 76048.00362 62565.40429 77466.03589 1.381285899 1.85760238 1.671933274 2.148015228 2.101335747 1.880573123 0.981694787 0.807649489 1 16.2412763 1.697037825 4.64434348 0.902495096 1.846046995 0.795347047 0.217677614 0.071351339 3.615353849 0.117511761 0.057230865 49.77804372 -1.697037825 0.943551899 QWADDWLVHLISPNVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QWADDWLVHLISPNVYR 17 0 Q9H7Z7;A6NHH0;X6RJ95 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 89.261 0.0040928 21163000 49357 93831 71277 90853 142070 92098 65182 82296 87334 FALSE TRUE 46267.83347 100778.3449 72967.7241 93184.44179 130912.3953 118685.1975 55408.56422 92570.83676 72757.3912 0.635919358 1.38512862 1.00289088 1.280755677 1.799300293 1.63124592 0.761552377 1.2723221 1 16.15080619 1.725602427 24.99999962 1.005909073 1.286537208 0.130763716 0.337636182 1.864767244 3582.222173 0.153663935 0.085214449 53.16213654 -1.725602427 0.280628134 QWGWTQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QWGWTQGR 8 0 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2;J3KRB3;A0A087WWH0;J3QS96;A0A087WY81 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 0 142.19 0.0014458 2448100000 1809100 990390 715390 686210 1029500 615240 879790 701980 1069100 FALSE TRUE 1695871.66 1063719.506 732359.3886 703819.3104 948647.2228 792849.8004 747873.6571 789623.7482 890660.3034 1.904061126 1.194304385 0.822265667 0.790221937 1.065105539 0.890182034 0.839684506 0.886559944 1 19.76451577 4.868103975 1.494254143 0.892827099 2.54788265 0.934210046 0.084138443 0.351190297 0.575452131 0.021888923 0.938685561 73808.09144 -4.868103975 1.655055551 QWLQEIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 QWLQEIDR 8 0 Q9H0U4;E9PLD0;Q92928;P62820;E7END7;P62820-2 Q9H0U4;P62820 RAB1B;RAB1C;RAB1A Ras-related protein Rab-1B;Putative Ras-related protein Rab-1C;Ras-related protein Rab-1A 0 ;;;;;;; 186.33 0.000484 2204957000 1853621 2981040 1792720 1828220 2945220 1722910 2377070 2752250 2957070 FALSE TRUE 1737606.17 3201759.303 1835244.165 1875135.22 2713914.302 2220286.148 2020650.421 3095874.471 2463515.914 0.705335882 1.29967064 0.744969478 0.761162211 1.101642692 0.901267224 0.82023031 1.256689455 1 21.23228736 1.242693651 24.99996069 1.128344726 0.924431467 0.188238137 0.189564967 173.0840633 1047004.438 0.131539811 0.044147064 17.48612791 -1.242693651 -0.203913259 QWTEILHFTEHSGLTTGVAFGHHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QWTEILHFTEHSGLTTGVAFGHHAK 25 0 Q9UMS4;H0YGZ5 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ; 115.88 0.00043834 104011000 79293 84807 85698 86225 89915 84731 108516 91031 78284 FALSE TRUE 74330.19267 91086.19852 87730.79703 88437.67948 82853.4386 109191.4642 92245.03321 102396.4207 65217.89467 1.139720824 1.396644264 1.345195172 1.356033953 1.270409587 1.674256196 1.414412926 1.570066333 1 15.99298025 QWTSLS(ph)LR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QWTSLSLR 8 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 QWTSLS(1)LR;QWTSLS(1)LR 115.41 0.0025897 458190000 484970 531660 356920 350520 373340 203393 539880 413380 659210 TRUE FALSE 454616.5934 571024.6596 365386.3109 359514.9366 344019.3824 262109.2573 458930.006 464991.403 549183.5923 0.827804399 1.039770065 0.665326343 0.654635247 0.626419629 0.477270736 0.835658626 0.846695731 1 19.066929 -0.623050667 8.212627042 0.999995727 0.753392754 0.210239294 0.153802347 0 0 0.157416803 0.037103496 0.238204155 0.623050667 -0.246602973 QWYESHYALPLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QWYESHYALPLGR 13 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;; 184.76 9.23E-06 5528710000 5890570 6756090 4848470 4104150 5840020 4962790 7567260 5844360 6731450 FALSE TRUE 5521889.739 7256317.933 4963477.998 4209469.437 5381368.387 6395466.909 6432619.614 6574041.211 5607927.508 0.984657831 1.293939325 0.885082411 0.750628362 0.959600205 1.140433235 1.147058268 1.172276425 1 22.41903627 2.231743866 24.70481358 1.129797607 0.995882633 0.182381768 0.142114773 276.2391246 1001117.494 0.057200312 0.043198182 170.5076488 -2.231743866 -0.133914974 QY(ph)T(ph)FKMNEDT(ph)QEEPGKSEEEK ddPTM_SK-BR-3_Pertuzumab_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(0.989)T(0.98)FKMNEDT(0.707)QEEPGKS(0.324)EEEK 72.569 0.016466 110780000 685930 89068 166130 149050 187030 159790 171000 110130 129140 TRUE FALSE 642998.8657 95662.6874 170070.6821 152874.8753 172341.4182 205918.779 145360.1375 123879.9729 107585.6997 5.976620196 0.889176607 1.580792638 1.420959066 1.601898939 1.913997674 1.351110211 1.151453894 1 16.7151268 4.74243485 24.99994109 1.397662555 5.976621954 0.958338746 0.302190923 70.18443764 452873.4226 0.07070858 0.534674669 55263.05002 -4.74243485 4.578959399 QYADKLEFMHILTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QYADKLEFMHILTR 14 1 P42574 P42574 CASP3 Caspase-3;Caspase-3 subunit p17;Caspase-3 subunit p12 0 136.01 1.78E-05 77538000 171620 171020 139780 129750 184310 176670 241520 166380 242070 FALSE TRUE 160878.6106 183682.4987 143095.6476 133079.6047 169835.0361 227671.761 205306.3182 187152.9092 201666.9532 0.797744043 0.910821014 0.709564187 0.659897929 0.842156007 1.128949277 1.018046412 0.928029637 1 17.62161517 2.393235634 6.147090008 1.022515786 0.780036072 0.685236889 0.080165428 0.125722143 7.348999371 0.029088979 0.024250336 247.3065588 -2.393235634 -0.242479713 QYAENYTRPS(ph)SR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QYAENYTRPSSR 12 1 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 QYAENYT(0.006)RPS(0.613)S(0.381)R 67.102 0.034077 628470000 500370 467180 417060 393170 458020 417380 560990 386850 465620 TRUE FALSE 469052.7349 501770.4933 426952.8601 403259.4078 422048.9568 537870.8304 476874.7575 435149.0741 387905.014 1.209194823 1.293539591 1.100663422 1.03958287 1.088021401 1.386604481 1.229359612 1.121792857 1 18.5653439 QYAENYTRPSS(ph)R ddPTM_SK-BR-3_Pertuzumab_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(0.042)S(0.958)R;QYAENYT(0.001)RPS(0.04)S(0.959)R;QYAENYT(0.001)RPS(0.218)S(0.78)R 70.134 0.029129 1178600000 1388140 1137580 1263730 1124710 1167930 1098430 1478760 1094390 1254570 TRUE FALSE 1301258.795 1221807.607 1293706.272 1153571.963 1076205.489 1415528.909 1257033.666 1231027.001 1045174.162 1.24501623 1.168999054 1.23779014 1.103712668 1.029690101 1.3543474 1.202702585 1.17781997 1 19.99531193 -2.077908724 1.676334316 0.739124983 1.193119261 0.325657707 0.085825112 394073.3113 91646.63582 392524.9534 0.022264329 0.008357787 2.077908724 0.453994278 QYDISDPQRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 QYDISDPQRPR 11 1 Q13228;Q13228-4;Q13228-2;Q13228-3;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ;;;;;; 169.89 1.49E-05 20510820000 10337660 12700100 10684900 10874900 12533550 8635790 12540650 9987520 13804650 FALSE TRUE 9690644.314 13640428.62 10938350.87 11153968.35 11549215.54 11128802.38 10660295.95 11234483.86 11500564.73 0.842623344 1.186065983 0.951114239 0.969862664 1.004230297 0.967674426 0.926936738 0.976863669 1 23.45520137 3.72486458 24.98902804 0.966653557 1.047790433 0.008483732 0.085421923 180.8604932 2002766.946 0.020258545 0.033112232 5307.189321 -3.72486458 0.081136877 QYDPPAESQQSES(ph)PPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QYDPPAESQQSESPPRR 17 1 Q6P597;Q6P597-3;K7ENJ3;K7EL76 Q6P597 KLC3 Kinesin light chain 3 1 QYDPPAESQQS(0.014)ES(0.986)PPRR;QYDPPAESQQS(0.029)ES(0.971)PPRR;QYDPPAESQQS(0.268)ES(0.732)PPRR;QYDPPAES(0.042)QQS(0.294)ES(0.664)PPRR 155.17 6.76E-08 2846670000 924310 1008540 996170 1041160 1089770 902060 1016140 783180 850740 TRUE FALSE 866459.087 1083213.351 1019799.623 1067877.928 1004183.86 1162470.078 863779.2404 880961.747 708745.998 1.222524133 1.528351982 1.438878845 1.506714579 1.416845898 1.640178684 1.218743023 1.242986556 1 19.43490916 1.232432519 1.533008086 1.026036487 1.461813051 0.597438416 0.119619151 0.218050666 0.95779833 0.098602855 0.029884176 17.07782344 -1.232432519 0.435776564 QYEMGECTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 157.59 0.00015861 1069980000 447928 519178 442927 449116 518494 391236 495893 424063 549102 FALSE TRUE 419892.9861 557618.4793 453433.4376 460641.0769 477773.5727 504179.482 421538.4483 477008.199 457453.3289 0.917892514 1.218962557 0.991212456 1.006968466 1.044420365 1.102144088 0.92148952 1.042747246 1 18.80326504 3.731877169 24.94484583 1.012895198 1.094479038 0.042906631 0.085346253 364.7148331 1912914.78 0.020226149 0.035055467 5393.58055 -3.731877169 0.08158384 QYHES(ph)EEES(ph)EEEEAA ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QYHESEEESEEEEAA 15 0 Q8N9N8;E9PNH5 Q8N9N8 EIF1AD Probable RNA-binding protein EIF1AD 2 QYHES(1)EEES(1)EEEEAA 136.39 3.38E-05 88874000 188010 187960 214110 196060 192850 179960 216940 177400 223050 TRUE FALSE 176242.7897 201876.754 219188.7903 201091.2315 177704.3389 231911.5306 184411.861 199548.7805 185821.514 0.948452017 1.086401405 1.179566271 1.08217411 0.956317356 1.248033802 0.99241394 1.073873397 1 17.50355802 1.610083267 25 1.024856947 1.092131691 0.085840823 0.091437134 0.491852896 5454.714974 0.041839701 0.021779926 40.74583919 -1.610083267 0.067274744 QYPEFPWTDVQAEIFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QYPEFPWTDVQAEIFR 16 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 83.877 0.017865 37776000 18459 23198 14830 18004 22594 17433 24743 18994 32352 FALSE TRUE 17303.68414 24915.60406 15181.7746 18466.01312 20819.55838 22465.6241 21033.01685 21365.44271 26952.2422 0.642012787 0.924435298 0.56328429 0.68513829 0.77246109 0.833534514 0.780380968 0.792714853 1 14.71811768 0.428479724 0.51884262 1.012635186 0.725186415 0.431029104 0.096491568 2.158626866 0.992994234 0.161981575 0.04761384 2.682129382 -0.428479724 -0.287448771 QYPWGVAEVENGEHCDFTILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 QYPWGVAEVENGEHCDFTILR 21 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4 E7EPK1 7-Sep Septin-7 0 ;;; 313.4 1.32E-66 539942000 365573 388517 309492 297715 362524 460942 589322 313926 602737 FALSE TRUE 342692.4385 417283.2029 316833.2964 305354.8709 334052.8274 594008.4726 500958.6371 353120.3521 502136.3009 0.682468959 0.831015806 0.630970706 0.608111524 0.66526325 1.182962617 0.997654693 0.703236057 1 18.9377195 2.262839921 24.99838484 0.981227045 0.6930709 0.549792575 0.128921861 170.5463087 175596.8412 0.044143063 0.036916101 183.1639164 -2.262839921 -0.288156146 QYQDFLEDLEEDEAIRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 QYQDFLEDLEEDEAIRK 17 1 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 0 ;;;;; 396.36 4.84E-122 724339000 916916 782254 839329 825632 869880 706173 1142792 741629 916437 FALSE TRUE 859527.8643 840172.9001 859238.2802 846819.1149 801563.1337 910033.6813 971440.9488 834223.0132 763477.7443 1.125806051 1.100454999 1.125426755 1.109160183 1.049884086 1.191958362 1.272389347 1.092661861 1 19.54222658 2.216909256 24.99543117 1.174855821 1.105409153 0 0.075331923 412.1628498 475818.7024 0.026133918 0.019318202 164.7818051 -2.216909256 -0.069446668 QYTS(ph)PEEIDAQLQAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QYTSPEEIDAQLQAEK 16 0 Q13442;F8WBW6 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 QYT(0.019)S(0.981)PEEIDAQLQAEK;QYT(0.028)S(0.972)PEEIDAQLQAEK 280.38 1.94E-35 170756000 697590 530190 629250 568980 699380 491710 684030 531710 969040 TRUE FALSE 653929.0871 569445.8193 644176.1072 583580.9901 644453.516 633658.6948 581466.0517 598095.1639 807300.9638 0.81001896 0.705369924 0.797937989 0.722879095 0.798281614 0.784910118 0.720259331 0.740857736 1 19.62274709 -1.204496032 5.017011741 1.00002481 0.756962285 0.804555095 0.037136814 9.34E-06 1.48E-06 0.03259283 0.00768142 0.062445906 1.204496032 -0.243062525 QYVETHWCAQSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 QYVETHWCAQSEK 13 0 Q96P70 Q96P70 IPO9 Importin-9 0 191.06 3.89E-06 369570000 398970 367840 363340 347230 422160 287120 432290 355210 462420 FALSE TRUE 373999.1799 395075.2563 371958.5964 356140.5097 389005.2565 370006.883 367472.1277 399558.7504 385239.1147 0.970823485 1.025532562 0.965526558 0.92446612 1.009776115 0.960460319 0.953880626 1.037170773 1 18.55539467 1.236263031 24.99935864 1.018585389 0.975322761 0.291576927 0.029405515 85.56234919 930873.9978 0.024108133 0.007127607 17.22911744 -1.236263031 -0.043262628 QYYTLLNQAPDMLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QYYTLLNQAPDMLHR 15 0 Q13283;E5RH42;E5RJU8;Q13283-2;E5RIF8;E5RI46;E5RH00 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ; 180.74 6.17E-07 1031340000 677790 750400 529580 464670 736730 907080 1203120 590230 1260180 FALSE TRUE 635368.3338 805960.3968 542141.8877 476594.2189 678870.1976 1168939.271 1022723.325 663921.5148 1049847.817 0.605200414 0.767692597 0.516400452 0.453965052 0.646636766 1.113436873 0.974163406 0.632397862 1 20.00174878 2.350976788 7.032097676 0.938278529 0.599698542 0.569540306 0.143852229 0.162070689 9.410949546 0.049845231 0.041547339 224.3761998 -2.350976788 -0.338579987 RAAATQPDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RAAATQPDAK 10 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 140.09 6.40E-05 1291000000 1403710 1271700 1199570 1272930 1478030 862550 1533670 1266200 2080270 FALSE TRUE 1315854.297 1365857.991 1228024.367 1305595.539 1361951.486 1111554.183 1303710.421 1424287.857 1733059.498 0.75926666 0.788119504 0.70858754 0.753347211 0.785865394 0.641382586 0.752259471 0.821834368 1 20.72488975 0.886159412 2.58873754 0.999575896 0.740217849 0.793353173 0.041901024 0.189995973 2.643723145 0.038561953 0.01030455 7.694128089 -0.886159412 -0.259358046 RAADEDWDS(ph)ELEDDLLGEDLLSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RAADEDWDSELEDDLLGEDLLSGK 24 1 Q96EV2;A8MTF7;Q96EV2-2 Q96EV2 RBM33 RNA-binding protein 33 1 RAADEDWDS(1)ELEDDLLGEDLLSGK;RAADEDWDS(1)ELEDDLLGEDLLSGK;RAADEDWDS(1)ELEDDLLGEDLLSGK;RAADEDWDS(1)ELEDDLLGEDLLSGK;RAADEDWDS(1)ELEDDLLGEDLLSGK 158.41 1.42E-11 144996700 167023.2 155996 166625.2 156621.6 175460.9 134048.8 181982.1 133126.3 203768.7 TRUE FALSE 156569.5161 167546.1062 170577.6284 160640.7754 161680.9087 172746.5125 154695.5735 149747.4116 169758.3876 0.922307983 0.986968058 1.004825923 0.946290653 0.952417792 1.017602222 0.911269103 0.882120841 1 17.37312333 1.663579562 9.345718641 0.92280226 0.975476674 0.168058173 0.040485348 0.147611547 20.44270787 0.018019044 0.009600118 46.08711922 -1.663579562 0.052674414 RAAEDDEDDDVDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RAAEDDEDDDVDTK 14 1 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;; 292.82 2.56E-43 10498580000 14250158 9769439 10877149 11431737 12303269 8352300 14371252 10059618 13675297 FALSE TRUE 13358266.05 10492778.43 11135160.11 11725094.73 11337019.88 10763473.42 12216416.18 11315583.45 11392801.58 1.172518098 0.921000717 0.977385591 1.029166938 0.995103776 0.944760895 1.072292543 0.9932222 1 23.44161923 1.734000945 24.99999998 1.027736172 0.993815946 0 0.070797053 1.750487824 9505.125824 0.030412224 0.016865375 54.20020699 -1.734000945 -0.033920226 RAAEDDEDDDVDTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RAAEDDEDDDVDTKK 15 2 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;; 172.24 5.84E-07 9732940000 3250270 2117350 2450510 2369070 2737650 1695420 3134430 2003020 3123490 FALSE TRUE 3046841.403 2274120.797 2508637.254 2429864.347 2522646.012 2184860.231 2664451.32 2253101.456 2602159.34 1.170889636 0.873936028 0.964059816 0.933787685 0.969443328 0.839633529 1.023938572 0.865858374 1 21.31127788 4.747714617 24.8888472 0.934545625 1.170889767 0.61126458 0.059408809 714.2888306 1942038.137 0.012398725 0.153980866 55938.9895 -4.747714617 0.236344142 RAAEEAEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RAAEEAEEAR 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 119.55 0.0010864 160530000 538180 543780 492890 514980 637940 383730 616250 528970 726400 FALSE TRUE 504496.2745 584042.037 504581.5836 528195.2587 587838.7657 494506.6217 523849.0335 595013.0689 605159.1473 0.833658843 0.965104865 0.833799813 0.872820416 0.971378799 0.817151362 0.865638462 0.983234033 1 19.20695507 1.211429876 8.459140489 0.992688327 0.882614013 0.443740601 0.051926049 0.235198232 61.38741532 0.04458618 0.011776857 16.27158564 -1.211429876 -0.110074314 RAAGEVLEPANLLAEEKDEDLLFE ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RAAGEVLEPANLLAEEKDEDLLFE 24 2 G3V2V6;H0YJH8;G3V2S6;Q9Y5K8 G3V2V6 ATP6V1D V-type proton ATPase subunit D 0 103.03 0.013124 17677000 50793 34854 41951 37529 45436 32451 51334 36638 63707 FALSE TRUE 47613.9568 37434.62643 42946.09753 38492.05768 41867.63984 41819.0769 43636.94326 41212.33495 53073.89014 0.897125812 0.705330367 0.809175612 0.725254124 0.788855683 0.787940677 0.82219229 0.776508653 1 15.69571468 -1.173602218 0.457949108 1.093476649 0.776073323 0.605590602 0.052950019 13.14918514 1.609169265 1.593136538 0.025066635 0.067049846 1.173602218 -0.317403325 RAAS(ph)SDQLR ddPTM_SK-BR-3_Pertuzumab_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(0.903)S(0.097)DQLR 132.14 0.00019192 1027100000 207650 249190 225900 235880 221210 207020 293690 249150 203690 TRUE FALSE 194653.5572 267640.2869 231258.4547 241933.0801 203837.0589 266783.3133 249653.911 280256.9259 169692.8231 1.147093634 1.577204516 1.362806337 1.425711917 1.201212021 1.572154369 1.471210782 1.651554384 1 17.37256602 4.759427469 23.37099115 1.432105093 1.147092949 0.142332982 0.192995257 3401.648015 3809715.078 0.040400492 1.565958213 57468.18335 -4.759427469 -0.285012145 RAAS(ph)SDQLRDNS(ph)PPPAFKPEPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RAASSDQLRDNSPPPAFKPEPPK 23 3 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 2 RAAS(0.745)S(0.257)DQLRDNS(0.999)PPPAFKPEPPK;RAAS(0.965)S(0.036)DQLRDNS(1)PPPAFKPEPPK;RAAS(0.958)S(0.05)DQLRDNS(0.992)PPPAFKPEPPK;RAAS(0.818)S(0.186)DQLRDNS(0.996)PPPAFKPEPPK;RAAS(0.801)S(0.199)DQLRDNS(1)PPPAFKPEPPK 119.65 0.00023812 3264973000 1512990 951990 1097350 1117420 1137370 756666 1655490 1124720 2206980 TRUE FALSE 1418294.657 1022476.33 1123379.66 1146094.889 1048045.548 975103.1908 1407264.643 1265143.768 1838620.78 0.771390529 0.556110505 0.610990408 0.623344901 0.570017243 0.53034492 0.76539146 0.688093913 1 20.81019252 0.724097458 0.932822408 0.998024809 0.607067469 0.692305158 0.077552828 0.498538139 0.791679064 0.068322386 0.022642998 5.297823161 -0.724097458 -0.39095734 RAASSDQLRDNS(ph)PPPAFKPEPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RAASSDQLRDNSPPPAFKPEPPK 23 3 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 RAAS(0.003)S(0.015)DQLRDNS(0.982)PPPAFKPEPPK;RAAS(0.015)S(0.015)DQLRDNS(0.97)PPPAFKPEPPK;RAAS(0.001)S(0.007)DQLRDNS(0.992)PPPAFKPEPPK 114.31 0.0037674 568680000 492160 447694 456245 484641 747092 304644 531974 458578 1575330 TRUE FALSE 461356.5841 480841.7296 467067.3469 497077.7086 688418.4079 392589.7773 452209.4373 515832.4728 1312397.246 0.3515373 0.366384287 0.355888698 0.378755525 0.52455033 0.29913944 0.344567499 0.393045988 1 20.32377304 0.922877678 18.82967248 1 0.371640199 0.919868916 0.05783241 573.340951 139983.9965 0.053296343 0.013324086 8.372934195 -0.922877678 -0.628359801 RAAVAASSS(ph)S ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RAAVAASSSS 10 1 P61927 P61927 RPL37 60S ribosomal protein L37 1 RAAVAASS(0.009)S(0.865)S(0.125);RAAVAASS(0.015)S(0.958)S(0.027) 100.88 0.0039333 403840000 629980 755960 605780 677730 806890 483120 676070 782180 978030 TRUE FALSE 590550.6763 811932.065 620149.3877 695121.6992 743520.1142 622588.9012 574699.5798 879836.8948 814790.4747 0.72478839 0.996491847 0.761115166 0.853129388 0.912529217 0.764109204 0.70533419 1.079832082 1 19.63606959 1.225061209 24.99995303 1.039916193 0.824848026 0.512682467 0.090174303 228.1142294 422439.0445 0.085139138 0.02176306 16.79040642 -1.225061209 -0.215068167 RADAGEKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RADAGEKPK 9 2 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RQX9 P47897 QARS Glutamine--tRNA ligase 0 ;;; 88.681 0.0070979 490111000 1227090 819303 984038 951384 1043131 693452 1178570 910243 1336470 FALSE TRUE 1150288.627 879965.0466 1007379.846 975798.1241 961207.699 893640.3351 1001854.37 1023888.842 1113404.523 1.033127317 0.79033723 0.904774343 0.876409341 0.863305007 0.802619638 0.899811658 0.919601835 1 20.08654642 0.955238864 1.996998143 0.998931047 0.870469948 0.237122111 0.066090539 0.450472703 3.830419231 0.055786784 0.015583255 9.020671419 -0.955238864 -0.128461099 RADAGSHTEGS(ph)PSQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RADAGSHTEGSPSQPR 16 1 Q86V15;Q86V15-2 Q86V15 CASZ1 Zinc finger protein castor homolog 1 1 RADAGS(0.003)HT(0.303)EGS(0.682)PS(0.012)QPR;RADAGSHTEGS(0.97)PS(0.03)QPR 86.748 0.0041061 246075000 101227 117547 106633 95819 120276 105371 124277 109517 151096 TRUE FALSE 94891.38277 126250.3022 109162.3851 98277.87776 110830.0081 135789.8971 105642.8176 123190.4385 125877.1015 0.753841498 1.002964802 0.867214003 0.780744684 0.880462029 1.078749793 0.839253656 0.97865646 1 16.94165634 2.43372724 24.99992905 0.955418837 0.874301516 0.279821341 0.088882139 250.6981458 144429.5267 0.030059218 0.025149363 271.4733739 -2.43372724 -0.081117321 RADDFPVRDDPS(ph)DVT(ph)DEDEGPAEPPPPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 224.29 1.53E-34 733920000 780807 603776 630343 639188 611942 532853 747574 592322 612860 TRUE FALSE 731937.6837 648480.2033 645295.0336 655590.6462 563882.5438 686679.011 635482.2188 666274.7056 510569.7068 1.433570527 1.270111005 1.263872543 1.284037493 1.104418332 1.344927053 1.244653199 1.304963253 1 18.96174842 -3.979121335 0.274532482 2.24E-23 1.29523589 0.541651933 0.08174422 91.15074485 1.48174111 51.56312263 0.090497907 0.000104925 3.979121335 1.29523589 RADDFPVRDDPS(ph)DVT(ph)DEDEGPAEPPPPPKLPLPAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RADDFPVRDDPSDVTDEDEGPAEPPPPPKLPLPAFR 36 3 Q3YEC7;Q3YEC7-2 Q3YEC7 RABL6 Rab-like protein 6 2 RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPKLPLPAFR;RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPKLPLPAFR;RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPKLPLPAFR 210.52 2.08E-30 371851000 224647 248374 224224 232780 254075 159420 283793 222382 384340 TRUE FALSE 210586.7453 266763.8694 229542.6992 238753.5289 234120.9744 205441.966 241240.8743 250146.8822 320191.1711 0.657690668 0.833139366 0.716892656 0.745659314 0.731191224 0.641622832 0.753427627 0.781242285 1 18.288574 0.729092978 2.220284593 0.999869105 0.733076655 0.726791078 0.052492401 0.665021935 4.633428308 0.048905621 0.013293197 5.359113786 -0.729092978 -0.26679245 RADDFPVRDDPSDVT(ph)DEDEGPAEPPPPPKLPLPAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RADDFPVRDDPSDVTDEDEGPAEPPPPPKLPLPAFR 36 3 Q3YEC7;Q3YEC7-2 Q3YEC7 RABL6 Rab-like protein 6 1 RADDFPVRDDPS(0.221)DVT(0.779)DEDEGPAEPPPPPKLPLPAFR 57.811 0.018576 35606000 32443 36855 35625 31434 42907 26110 34212 31582 62454 TRUE FALSE 30412.45054 39583.78255 36470.04182 32240.64966 39537.2573 33647.53314 29082.22821 35525.08222 52030.02393 0.584517328 0.760787322 0.700942246 0.619654715 0.759893122 0.646694554 0.55895089 0.682780432 1 15.66705675 0.942105425 22.95916773 1 0.667919319 0.716000354 0.066486534 6147.512129 2437913.127 0.067307227 0.016826807 8.751962028 -0.942105425 -0.332080681 RADLNQGIGEPQS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RADLNQGIGEPQSPSR 16 1 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 RADLNQGIGEPQS(0.992)PS(0.008)R;RADLNQGIGEPQS(0.975)PS(0.025)R;RADLNQGIGEPQS(0.944)PS(0.056)R;RADLNQGIGEPQS(0.999)PS(0.001)R;RADLNQGIGEPQS(0.999)PS(0.001)R;RADLNQGIGEPQS(1)PSR 207.34 1.08E-11 7101020000 2933500 2792410 2872310 3038880 3198640 2668270 3253320 2514790 3114000 TRUE FALSE 2749897.471 2999162.942 2940442.55 3116862.806 2947431.717 3438556.233 2765514.868 2828767.067 2594253.283 1.059995757 1.156079463 1.133444668 1.20144892 1.136138764 1.325451241 1.066015754 1.090397413 1 21.30688791 1.589889738 18.38852809 1.058389182 1.165535329 0.378114368 0.070288282 0.256647244 251.9665 0.034633007 0.016189807 38.89463837 -1.589889738 0.107146147 RADLNQGIGEPQS(ph)PSRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RADLNQGIGEPQSPSRR 17 2 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 RADLNQGIGEPQS(0.849)PS(0.151)RR;RADLNQGIGEPQS(0.89)PS(0.11)RR;RADLNQGIGEPQS(0.832)PS(0.168)RR;RADLNQGIGEPQS(0.607)PS(0.393)RR 179.19 7.32E-10 2643900000 232834 275977 284609 281931 362922 243351 303806 266886 377088 TRUE FALSE 218261.3356 296410.6242 291360.0599 289165.8268 334419.5701 313602.4832 258253.1107 300207.3046 314149.5767 0.694768835 0.943533419 0.927456478 0.920471801 1.064523383 0.998258494 0.822070535 0.955619001 1 18.26109211 4.73857431 9.65081096 0.944243992 0.694020644 0.618356046 0.063592552 0.055208904 142.4022555 0.015462492 0.089883028 54773.98141 -4.73857431 -0.250223348 RADS(ph)GEEENTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RADSGEEENTK 11 1 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 1 RADS(1)GEEENTK;RADS(1)GEEENTK;RADS(0.999)GEEENT(0.001)K;RADS(1)GEEENTK 201.3 2.69E-08 1000110000 2348770 1692910 1906870 1841780 1801580 1525920 2185620 1563360 2098220 TRUE FALSE 2201764.678 1818254.818 1952101.857 1889043.193 1660091.174 1966428.333 1857906.571 1758548.937 1748013.527 1.25958103 1.040183494 1.116754434 1.080679963 0.94970156 1.124950295 1.062867388 1.006027076 1 20.73728492 4.741526058 24.88458355 1.05732642 1.259581108 0.596725802 0.054237852 184.9125245 1551616.422 0.012031827 0.085341528 55147.529 -4.741526058 0.202254688 RAEAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RAEAEK 6 1 P39748;P39748-2;F5H1Y3;F5GYN0;Q96PX6;A6NE01 P39748 FEN1;FAM186A;CCDC85A Flap endonuclease 1;Coiled-coil domain-containing protein 85A;Protein FAM186A 0 84.244 0.089907 41233000 59391 61895 77802 58135 72875 76829 72869 66787 87184 FALSE TRUE 55673.82333 66477.7702 79647.50018 59626.84252 67151.69146 99008.28509 61942.96993 75125.50397 72632.42717 0.766514703 0.915262959 1.096583211 0.820939694 0.924541477 1.363141629 0.852828032 1.03432457 1 16.14832617 RAEATAASTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RAEATAASTSR 11 1 O95721 O95721 SNAP29 Synaptosomal-associated protein 29 0 ;;; 160.56 4.38E-05 224912000 57417.3 80756 67871.9 69518 81654 51722.2 62994.6 66960 75349 FALSE TRUE 53823.65369 86735.25827 69481.85352 71301.94957 75241.22422 66653.5595 53549.14454 75320.1034 62772.76513 0.857436399 1.381733911 1.106878969 1.135873964 1.198628483 1.0618229 0.853063338 1.199885066 1 15.93785114 2.044717039 5.810698895 0.990733012 1.164034921 0.090593521 0.152602903 0.26943919 21.92583772 0.054639295 0.039374034 110.8452376 -2.044717039 0.173301908 RAEDGSVIDYELIDQDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RAEDGSVIDYELIDQDAR 18 1 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;H0YL33;H0YNP5;H0YN28;H0YNA0 P07355-2 ANXA2 Annexin A2;Annexin 0 ;;; 248.94 2.27E-24 2828840000 1649200 1642790 1667000 1470750 2064290 984850 1898050 1784940 3818990 FALSE TRUE 1545979.516 1764423.881 1706542.027 1508491.935 1902168.99 1269160.207 1613455.023 2007793.688 3181575.897 0.485916277 0.554575449 0.536382624 0.474133569 0.597870066 0.398909298 0.50712448 0.631068927 1 21.60131011 0.838105887 2.884922371 0.999775399 0.512082001 0.896202032 0.052601602 0.196615228 2.876061915 0.048062815 0.012647185 6.888202202 -0.838105887 -0.487693399 RAEHQDKVDEVPGLSGQSDDVPAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RAEHQDKVDEVPGLSGQSDDVPAGK 25 2 O75363;G3XAF7;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 76.826 0.017395 321280000 364180 234860 266750 302070 338010 221320 406230 285730 437950 FALSE TRUE 341386.6239 252249.2788 273077.436 309821.6276 311464.0581 285211.4912 345319.5828 321404.0195 364853.3157 0.935681846 0.691371759 0.748458145 0.849167636 0.853669255 0.781715497 0.946461408 0.880912974 1 18.47695704 1.605125483 0.607034369 0.993853392 0.769580206 0.39088334 0.073626841 0.597185308 0.490244816 0.067905082 0.036072151 40.28334106 -1.605125483 -0.224273186 RAELEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RAELEK 6 1 Q9UH65;E7EMB1;Q5JVD5;Q5JVD6;Q7Z7A1-3;Q7Z7A1-2;Q7Z7A1-5;Q7Z7A1 Q9UH65 SWAP70;CNTRL Switch-associated protein 70;Centriolin 0 91.626 0.076449 291250000 443920 404320 334260 366930 409750 284500 445020 328610 486840 FALSE TRUE 416135.8396 434256.2735 342188.805 376346.045 377569.8879 366630.5315 378293.3824 369637.6819 405583.2589 1.026018285 1.070695755 0.843695585 0.927913164 0.930930653 0.90395874 0.93271449 0.911373124 1 18.62963858 4.086317774 4.646679267 0.918034144 1.046823233 0.637774979 0.039572025 0.114203248 3.985561551 0.008835313 0.020009773 12198.81861 -4.086317774 0.128789089 RAELGS(ph)WSSQEHLEWEPACQTPQPSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RAELGSWSSQEHLEWEPACQTPQPSAR 27 1 B7Z896;F5H3M2;Q9BVG8-5;Q9BVG8-2;Q9BVG8;Q9BVG8-6;H3BTL6 B7Z896 KIFC3 Kinesin-like protein;Kinesin-like protein KIFC3 1 RAELGS(0.474)WS(0.315)S(0.211)QEHLEWEPACQTPQPSAR 157.75 1.72E-09 278300000 254770 284130 261860 268370 302330 221030 332780 254150 387160 TRUE FALSE 238824.4005 305167.2808 268071.4429 275256.8285 278586.2213 284837.7729 282882.7284 285881.187 322540.4949 0.740447802 0.946136332 0.83112492 0.853402388 0.86372479 0.883107013 0.87704562 0.886341999 1 18.29912078 -5 0.208573595 1.644039124 0.84662666 0.468069674 0.049527067 134.246668 1.337648168 36.04971245 0.098237155 1.00E-05 5 -0.797412464 RAELYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RAELYEK 7 1 Q99614;H0YB37 Q99614 TTC1 Tetratricopeptide repeat protein 1 0 ; 109.71 0.028194 293630000 294060 370380 250020 267510 445350 198625 302150 366120 444080 FALSE TRUE 275655.3095 397803.3206 255950.5925 274374.7595 410374.0075 255964.8131 256845.4125 411830.8879 369960.1791 0.74509454 1.075259833 0.691832816 0.741633222 1.10923832 0.691871254 0.694251509 1.113176258 1 18.49701047 1.226476501 24.9996315 1.056588242 0.827464936 0.284506131 0.154877218 341.0293629 705500.1597 0.140796983 0.036280605 16.84521277 -1.226476501 -0.229123306 RAEPPKPEVVDSTESIPVS(ph)DEDS(ph)DAMVDDPNDEDFVPFRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RAEPPKPEVVDSTESIPVSDEDSDAMVDDPNDEDFVPFRPR 41 3 A6NHN7;A6NHB5;Q14202-2;Q14202;A6NL54;Q14202-3 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 2 RAEPPKPEVVDS(0.001)T(0.001)ES(0.002)IPVS(0.998)DEDS(1)DAMVDDPNDEDFVPFRPR 75.14 0.00081921 99013000 48854 41357 40399 42752 42864 32797 49551 33956 49820 TRUE FALSE 45796.31535 44419.11531 41357.28336 43849.0887 39497.63435 42264.96149 42121.28756 38195.48135 41504.72015 1.103400172 1.070218403 0.99644771 1.056484384 0.951641987 1.018316985 1.014855356 0.920268374 1 15.3409878 8 0.35496837 0.98219486 2.539260289 0.570859041 0.035312644 44.55608284 0.625688034 0.026358622 46.64396438 99999999.99 -8 1.557065429 RAEPPKPEVVDSTESIPVS(ph)DEDSDAMVDDPNDEDFVPFRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RAEPPKPEVVDSTESIPVSDEDSDAMVDDPNDEDFVPFRPR 41 3 A6NHN7;A6NHB5;Q14202-2;Q14202;A6NL54;Q14202-3 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 1 RAEPPKPEVVDSTESIPVS(0.961)DEDS(0.038)DAMVDDPNDEDFVPFRPR 56.049 0.014203 166550000 36533 30578 33781 31449 37942 30277 37404 25075 32183 TRUE FALSE 34246.46474 32842.02694 34582.30127 32256.03458 34962.18837 39017.47839 31795.61744 28205.66895 26811.44939 1.277307476 1.224925458 1.289833338 1.203069409 1.304002177 1.455254351 1.185897002 1.052000902 1 14.71056159 1.320076929 3.274055441 1.014961121 1.283129424 0.716638395 0.068410217 0.130690677 2.303090182 0.056209702 0.017361045 20.89666251 -1.320076929 0.268168302 RAETFAGYDCTNS(ph)PTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RAETFAGYDCTNSPTK 16 1 M0QZS0;A0A590UK10;A0A3B3IPE9;A0A087WZG4;Q6ZSZ5-2;Q6ZSZ5-1;Q6ZSZ5-6;Q6ZSZ5-5;Q6ZSZ5 M0QZS0 ARHGEF18 Rho guanine nucleotide exchange factor 18 1 RAETFAGYDCT(0.027)NS(0.971)PT(0.002)K;RAETFAGYDCTNS(0.982)PT(0.017)K 178.56 1.70E-09 462340000 301440 223298 268625 248524 296739 224803 350320 250359 293130 TRUE FALSE 282573.4085 239831.2163 274996.9119 254901.5466 273434.3159 289699.9767 297792.7682 281616.8723 244204.7093 1.15711695 0.982090873 1.126091764 1.043802748 1.119693051 1.186299714 1.219439089 1.153200006 1 17.8977315 2.486767599 4.385358781 1.165066569 1.069969449 0.092145001 0.074539039 0.257857752 12.26984897 0.02349529 0.020676446 306.7380126 -2.486767599 -0.09509712 RAEVLGHKT(ph)PEPAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 121.48 0.0054688 1571560000 1735770 1393870 1536710 1553630 1792170 1265150 1968360 1534880 2428500 TRUE FALSE 1627131.254 1497073.585 1573161.487 1593498.776 1651420.197 1630378.267 1673222.691 1726513.147 2023167.661 0.804249339 0.739965161 0.777573464 0.787625666 0.816254742 0.805854254 0.827031157 0.853371265 1 20.94818445 -0.071096297 0.317146393 1.059143243 0.757030582 0.936201183 0.017492609 1.197256925 0.169717654 0.103902888 0.018267836 0.848992205 0.071096297 -0.302112662 RAGAES(ph)PTMSVDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RAGAESPTMSVDGR 14 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 RAGAES(0.78)PT(0.206)MS(0.014)VDGR;RAGAES(0.943)PT(0.055)MS(0.002)VDGR;RAGAES(0.94)PT(0.052)MS(0.008)VDGR 117.78 0.00040462 0 717599 656971 677848 697054 699020 689447 871813 562507 598970 TRUE FALSE 672685.7595 705613.8164 693926.8747 714941.5857 644121.7889 888479.1567 741092.7342 632737.2372 498998.0375 1.348072956 1.414061306 1.390640489 1.432754304 1.290830305 1.780526355 1.485161621 1.268015482 1 18.92867462 0.963382176 3.770659997 1.000965135 1.450518198 0.55541673 0.129870499 0.169668927 6.724827059 0.1230587 0.031629544 9.191410776 -0.963382176 0.449553063 RAGAESPT(ph)MSVDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RAGAESPTMSVDGR 14 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 RAGAES(0.046)PT(0.671)MS(0.282)VDGR 152.88 3.02E-07 0 117820 151630 126810 140150 176860 108680 150640 107820 175800 TRUE FALSE 110445.8565 162856.843 129817.9931 143746.4863 162970.129 140054.1517 128052.9305 121281.5643 146457.8443 0.754113629 1.111970777 0.886384705 0.98148711 1.112744284 0.956276206 0.874333028 0.828098795 1 17.16012594 1.851035605 5.118728261 0.889301729 0.982008395 0.063440511 0.111296565 0.451387605 16.50913943 0.047090561 0.027392377 70.96359434 -1.851035605 0.092706666 RAGDLLEDS(ph)PK ddPTM_SK-BR-3_Pertuzumab_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 239.31 1.29E-15 24647620000 41950140 20559780 26995050 25480390 25213130 22648180 37326840 23097860 27150740 TRUE FALSE 39324555.62 22082047.5 27635385.33 26134259.95 23232992.47 29186341.9 31730026.87 25981678.67 22619106.09 1.738554807 0.976256418 1.221771772 1.1554064 1.02714017 1.290340201 1.402797561 1.148660719 1 24.43103858 4.751360963 24.78569174 1.173823492 1.738555212 0.653211637 0.133350019 1331.484891 2578142.111 0.033677053 0.617862485 56410.63164 -4.751360963 0.56473172 RAGDLLEDS(ph)PKRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 RAGDLLEDSPKRPK 14 3 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK;RAGDLLEDS(1)PKRPK 161.86 7.15E-06 29851070000 12622200 7493440 8849330 9244050 11507010 5735630 10952310 7935810 18108240 TRUE FALSE 11832199.03 8048262.095 9059240.287 9481267.973 10603295.85 7391413.271 9310112.792 8926613.347 15085857.76 0.784323916 0.533497148 0.600512111 0.628487165 0.702863305 0.489956447 0.617141759 0.591720636 1 23.84669339 -1.531128414 2.786827772 1.019384962 0.607129852 0.679339761 0.082024133 9802797.622 10081972.67 1430659.992 0.018648146 0.029435511 1.531128414 -0.412255109 RAGDLLEDSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RAGDLLEDSPK 11 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ; 86.288 0.023382 343900000 612050 524830 557060 575360 618730 442270 646510 500250 870260 FALSE TRUE 573742.883 563688.9593 570273.7263 590124.7117 570137.4416 569946.1693 549571.8274 562707.3137 725007.9839 0.791360779 0.777493451 0.786575788 0.813956156 0.786387811 0.78612399 0.758021759 0.776139472 1 19.46763736 -1.037895846 5.25492502 1.000001907 0.783193602 0.959111346 0.013980705 3.30E-07 6.05E-08 0.014321902 0.003375675 0.091644025 1.037895846 -0.216808304 RAGELTEDEVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RAGELTEDEVER 12 1 P62269 P62269 RPS18 40S ribosomal protein S18 0 ;;;;; 202.15 2.25E-07 7822570000 4784570 5669190 5319510 5185400 5778440 4371140 5858180 4749570 5838750 FALSE TRUE 4485112.304 6088942.726 5445691.289 5318466.143 5324624.632 5633017.158 4979800.294 5342564.27 4864224.905 0.922061046 1.251780673 1.119539371 1.093384094 1.094650172 1.15805031 1.023760289 1.09833825 1 22.2137785 1.227208192 0.659089262 1.003703192 1.128398786 0.069526708 0.086402829 1.200390468 1.248356717 0.07825204 0.034257402 16.87361718 -1.227208192 0.124695595 RAGSSASSPPS(ph)ASSSPHPSAAVPAADPADSASGSSNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RAGSSASSPPSASSSPHPSAAVPAADPADSASGSSNKR 38 2 G4U4J3;Q8NDF8-4;Q8NDF8-2;Q8NDF8;Q8NDF8-3;Q8NDF8-5 G4U4J3 PAPD5 Non-canonical poly(A) RNA polymerase PAPD5 1 RAGS(0.002)S(0.002)AS(0.005)S(0.125)PPS(0.547)AS(0.125)S(0.097)S(0.097)PHPSAAVPAADPADSASGSSNKR 132.13 4.50E-09 234120000 53281 122810 107830 126140 127960 97255 152690 117450 175850 TRUE FALSE 49946.23732 131902.9802 110387.7785 129376.966 117910.5378 125330.9397 129795.552 132113.891 146499.499 0.340931114 0.900364719 0.753502772 0.883122242 0.80485284 0.855504221 0.885979494 0.901804388 1 17.16053621 4.741347696 24.99794622 0.85890618 0.340930927 0.865635562 0.065683704 84.39320243 756901.728 0.014293087 0.098916825 55124.885 -4.741347696 -0.517975253 RAHT(ph)PTPGIYMGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RAHTPTPGIYMGR 13 1 Q13595;Q13595-3;Q13595-4;Q13595-2 Q13595 TRA2A Transformer-2 protein homolog alpha 1 RAHT(0.949)PT(0.051)PGIYMGR;RAHT(0.97)PT(0.03)PGIYMGR;RAHT(0.982)PT(0.018)PGIYMGR 55.851 0.061466 382401000 186567 214386 195938 209346 265742 150292 221030 201013 354583 TRUE FALSE 174890.1045 230259.3625 200585.7419 214718.1728 244871.6953 193678.8606 187888.6034 226109.9155 295400.8066 0.592043422 0.779481157 0.679029093 0.726870638 0.82894728 0.655647704 0.636046345 0.76543432 1 18.17231424 0.971753027 20.81001402 1.000000003 0.704840171 0.654080935 0.068313819 194.2395654 143100.5053 0.063108171 0.015777043 9.370289894 -0.971753027 -0.295159832 RAHT(ph)PTPGIYMGRPTHSGGGGGGGGGGGGGGGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RAHTPTPGIYMGRPTHSGGGGGGGGGGGGGGGGR 34 2 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 RAHT(0.993)PT(0.007)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;RAHT(0.995)PT(0.005)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;RAHT(0.908)PT(0.059)PGIY(0.011)MGRPT(0.02)HS(0.001)GGGGGGGGGGGGGGGGR;RAHT(0.94)PT(0.06)PGIYMGRPTHSGGGGGGGGGGGGGGGGR 221.48 2.85E-36 784880000 67261.5 73705.2 65679.6 75899.3 79570.5 60744.5 71058 82308.4 123447.7 TRUE FALSE 63051.72278 79162.4097 67237.55113 77847.00454 73321.3539 78280.45105 60403.51257 92584.78492 102843.4814 0.61308429 0.769736775 0.65378525 0.756946415 0.712941189 0.761161038 0.587334382 0.900249425 1 16.65009083 1.061367517 5.447378974 0.998584368 0.698506318 0.755035366 0.062053163 0.077456784 4.19924554 0.054920069 0.013856873 11.51774653 -1.061367517 -0.300078051 RALPNNTSS(ph)SPQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RALPNNTSSSPQPK 14 1 P04637-7;P04637;P04637-4;A0A087WZU8;A0A0U1RQC9;A0A087X1Q1;A0A087WT22;J3KP33;A0A087WXZ1;E7ESS1;P04637-5;P04637-9;P04637-8;P04637-6;P04637-2;P04637-3 P04637-7 TP53 Cellular tumor antigen p53 1 RALPNNT(0.003)S(0.014)S(0.633)S(0.351)PQPK 74.12 0.0089403 0 166090 149720 143810 159170 187360 101370 188080 141000 187040 TRUE FALSE 155694.7234 160805.4246 147221.2411 163254.5717 172645.5014 130633.8734 159879.15 158604.1604 155821.8157 0.999184374 1.031982742 0.944805068 1.047700355 1.10796746 0.838354199 1.026038295 1.017855938 1 17.24953771 RALPNNTSSS(ph)PQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RALPNNTSSSPQPK 14 1 P04637-7;P04637;P04637-4;A0A087WZU8;A0A0U1RQC9;A0A087X1Q1;A0A087WT22;J3KP33;A0A087WXZ1;E7ESS1;P04637-5;P04637-9;P04637-8;P04637-6;P04637-2;P04637-3 P04637-7 TP53 Cellular tumor antigen p53 1 RALPNNTS(0.006)S(0.15)S(0.844)PQPK;RALPNNTSS(0.064)S(0.935)PQPK;RALPNNTS(0.002)S(0.062)S(0.936)PQPK 134.08 2.50E-05 688890000 561360 470634 446291 467891 596160 324268 610880 452556 592470 TRUE FALSE 526225.4797 505480.2311 456877.2333 479897.8752 549339.9984 417878.9075 519284.2151 509058.6128 493582.9295 1.066133872 1.024103957 0.925634186 0.972274053 1.112963933 0.8466235 1.052070856 1.031353765 1 18.91293297 RALS(ph)SAGPIPIRPPIVPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RALSSAGPIPIRPPIVPVK 19 2 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 RALS(0.825)S(0.175)AGPIPIRPPIVPVK 95.71 0.00072677 174710000 352970 442150 337990 351240 499550 226570 601920 404880 620680 TRUE FALSE 330878.2378 474887.2461 346007.2824 360253.413 460317.3581 291977.0809 511667.684 455430.1593 517084.4983 0.639892008 0.918393894 0.669150368 0.696701244 0.890216898 0.564660287 0.989524315 0.880765447 1 18.98004053 1.641646596 10.70379228 0.95104973 0.750091678 0.469861084 0.112048567 0.098677211 21.83972232 0.049013692 0.026264482 43.81739914 -1.641646596 -0.200958052 RALS(ph)SDSILSPAPDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RALSSDSILSPAPDAR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 RALS(0.647)S(0.333)DS(0.02)ILSPAPDAR;RALS(0.895)S(0.083)DS(0.019)ILS(0.003)PAPDAR;RALS(0.959)S(0.036)DS(0.004)ILS(0.001)PAPDAR;RALS(0.5)S(0.5)DSILSPAPDAR 311.58 1.19E-57 1754730000 804178 1106840 853106 902783 1095450 660484 1084540 811267 1818340 TRUE FALSE 753845.9345 1188791.585 873342.0772 925949.9402 1009417.776 851155.0087 921923.2954 912555.4708 1514847.307 0.497638231 0.784760008 0.576521523 0.611249686 0.66634952 0.561875118 0.608591566 0.60240756 1 20.53074095 -1.494968576 2.987995913 1.011648571 0.623719861 0.722917117 0.074936147 29601540.45 32993813.02 2820465.911 0.016937106 0.031991266 1.494968576 -0.38792871 RALSS(ph)DSILSPAPDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RALSSDSILSPAPDAR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 RALS(0.384)S(0.611)DS(0.006)ILSPAPDAR 133.84 1.93E-05 370660000 122240 181020 130170 140460 175980 111040 165910 125370 276530 TRUE FALSE 114589.2166 194422.9092 133257.6939 144064.4414 162159.2407 143095.4454 141033.3357 141022.7205 230375.3565 0.497402232 0.843939699 0.578437277 0.62534658 0.703891437 0.621140419 0.612189332 0.612143254 1 17.81362687 -1.798478018 2.478030188 1.111323748 0.648389541 0.614415732 0.090005282 20090996.6 13101552.57 13440734.27 0.020477348 0.015904572 1.798478018 -0.462934207 RALSSDS(ph)ILSPAPDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RALSSDSILSPAPDAR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 RALS(0.057)S(0.011)DS(0.913)ILS(0.019)PAPDAR 136.34 1.90E-05 159960000 114910 150090 123200 121910 162140 102230 160480 107880 226630 TRUE FALSE 107717.9882 161202.8198 126122.3622 125038.417 149406.1784 131742.1414 136417.5138 121349.0555 188803.9889 0.570528138 0.853810455 0.668006873 0.662265759 0.791329565 0.697772024 0.722535125 0.642725062 1 17.52652972 -1.571447619 3.752394287 1.007054739 0.71386006 0.581157441 0.07908535 0.004302854 0.000491419 0.070591344 0.016299046 0.026825781 1.571447619 -0.293194679 RALVEFESNPEETREPGS(ph)PPSVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RALVEFESNPEETREPGSPPSVQR 24 2 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 RALVEFESNPEET(0.001)REPGS(0.999)PPSVQR;RALVEFESNPEET(0.002)REPGS(0.998)PPSVQR;RALVEFESNPEETREPGS(0.998)PPS(0.002)VQR;RALVEFESNPEET(0.004)REPGS(0.993)PPS(0.004)VQR 141.84 1.42E-07 1186180000 313790 374017 378745 378268 364531 292259.4 461807 368947 537743 TRUE FALSE 294150.444 401709.6078 387729.0103 387974.9973 335902.2057 376629.9443 392563.3276 415010.8451 447990.2193 0.656600147 0.896692808 0.865485436 0.866034526 0.749798079 0.840710194 0.876276558 0.926383718 1 18.77310771 1.155717566 1.477361464 0.997502101 0.828213633 0.450424388 0.069519237 0.373195063 1.584438798 0.061970089 0.018694155 14.31256809 -1.155717566 -0.169288467 RAPAPPPPQPPPPS(ph)PLIPNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RAPAPPPPQPPPPSPLIPNR 20 1 H7C1N2;J3KR05;O75128-2;O75128-3;O75128;O75128-7;A0A0J9YWK3;A0A3B3IU00;O75128-5;O75128-4 H7C1N2;O75128-3 COBL Protein cordon-bleu 1 RAPAPPPPQPPPPS(1)PLIPNR;RAPAPPPPQPPPPS(1)PLIPNR 146.39 8.21E-08 675110000 140151 143124 171652 155455 168477 151843 181381 150950 131453 TRUE FALSE 131379.1991 153721.0499 175723.6665 159444.2385 155245.496 195677.6091 154184.6029 169796.4398 109512.6451 1.199671499 1.403683107 1.604597043 1.455943634 1.417603382 1.786803789 1.407915979 1.550473369 1 16.74073794 -0.943037119 5.257123665 0.999998645 1.488290514 0.491656195 0.152558367 2.24E-06 4.51E-07 0.136545274 0.03218394 0.114015233 0.943037119 0.488291869 RAPDQAAEIGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RAPDQAAEIGSR 12 1 M0QXC3;M0R2Z3;M0R303;M0R2D2;M0R1Y4;M0R003;Q3ZCQ8;Q3ZCQ8-2 M0QXC3 TIMM50 Mitochondrial import inner membrane translocase subunit TIM50 0 83.087 0.021171 323900000 35053 47662 42058 36806 58158 46870 36853 40686 62854 FALSE TRUE 32859.0953 51190.94407 43055.63562 37750.50427 53590.50528 60400.60813 31327.23478 45765.73666 52363.26135 0.627521939 0.977611836 0.82224893 0.720934932 1.023437118 1.153492097 0.598267449 0.874004703 1 15.67626734 4.753494041 23.91603583 0.879477658 0.627521608 0.214011972 0.158984367 2542.312166 4071412.384 0.036966377 0.799400447 56688.3793 -4.753494041 -0.25195605 RAPEEELPPLDPEEIRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RAPEEELPPLDPEEIRK 17 2 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67;K7EKR9;Q8IY67-3 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 0 55.589 0.06617 32358000 50505 49225 52417 51968 55356 41856 65121 52815 72352 FALSE TRUE 47343.9822 52869.67022 53660.35599 53301.58686 51008.56306 53939.14772 55356.7106 59409.06901 60275.98379 0.785453496 0.877126625 0.890244383 0.884292275 0.846250195 0.894869637 0.918387509 0.985617576 1 15.87929567 1.423095934 1.4721412 1.003064425 0.865419241 0.758639961 0.030432654 0.186128647 0.759146884 0.026264791 0.008468042 26.49085244 -1.423095934 -0.137645184 RAPFDLFENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RAPFDLFENK 10 1 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ; 169.81 7.25E-06 3215500000 3714500 6129700 2712100 2747000 6878000 1427020 2540000 5699600 4966200 FALSE TRUE 3482016.076 6583549.366 2776432.293 2817492.671 6337829.625 1838977.508 2159150.58 6411207.606 4137309.137 0.841613706 1.591263584 0.671071994 0.68099641 1.531872387 0.444486367 0.521873157 1.549608065 1 21.98026133 3.927519128 7.629866826 0.862848539 1.252091014 0.070966149 0.419362328 0.44779906 60.45734535 0.101668331 0.185539463 8462.898423 -3.927519128 0.389242476 RAPFDLFENKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RAPFDLFENKK 11 2 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ; 189.24 1.57E-06 4790000000 12753100 9958400 10016000 10491100 12528100 8029600 13904700 11181800 13140300 FALSE TRUE 11954906.24 10695730.3 10253584.25 10760319.39 11544193.56 10347615.17 11819819.32 12577872.34 10947099.04 1.092061576 0.977037867 0.936648532 0.982937977 1.05454363 0.945238107 1.079721603 1.148968535 1 23.38404527 1.635117445 6.579870104 1.087593489 0.990394351 0.270029979 0.058772887 0.134200658 12.08846176 0.028797878 0.014217957 43.16357873 -1.635117445 -0.097199138 RAPFDLFENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RAPFDLFENR 10 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;; 260.08 4.28E-17 5629730000 2176397 9602180 1475988 1807097 10266450 848842 1329189 7926690 6176940 FALSE TRUE 2040180.197 10313135.4 1510999.132 1853470.168 9460164.43 1093888.906 1129889.449 8916354.695 5145968.809 0.396461827 2.004119298 0.293627728 0.360179052 1.838364122 0.212572005 0.219567877 1.732687279 1 22.29501128 RAPFDLFENRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RAPFDLFENRK 11 2 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 107.09 0.0012619 645920000 470920 592390 419240 335460 506520 129260 448360 493590 791710 FALSE TRUE 441445.9578 636251.172 429184.5708 344068.4715 466739.9624 166575.2636 381132.5804 555215.798 659568.4864 0.669295103 0.964647622 0.650705089 0.52165693 0.707644425 0.252551884 0.577851411 0.841786425 1 19.33116294 -1.231980761 7.307686197 1.00000085 0.651589792 0.25609256 0.18832227 2.74E-06 2.88E-07 0.191540609 0.045146444 0.058616413 1.231980761 -0.348411059 RAPS(ph)PDGFSPYSPEETNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RAPSPDGFSPYSPEETNR 18 1 Q13233 Q13233 MAP3K1 Mitogen-activated protein kinase kinase kinase 1 1 RAPS(1)PDGFSPYSPEETNR;RAPS(1)PDGFSPYSPEETNR 203.33 7.32E-16 438540000 168301 206882 202948 192703 208764 177957 216970 187012 264413 TRUE FALSE 157767.3408 222199.7585 207762.0224 197648.0852 192368.5176 229330.297 184437.3628 210360.8599 220280.7621 0.716210255 1.008711593 0.943169165 0.897255318 0.87328787 1.041081821 0.837283115 0.954967006 1 17.74898398 7.999949928 0.011480586 1.725412431 9.01E-05 0.135058451 0.088639674 29758.81072 26.39989685 1671.434992 2349.400187 99988471.12 -7.999949928 -1.725322288 RAPS(ph)PGAYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RAPSPGAYK 9 1 P54259 P54259 ATN1 Atrophin-1 1 RAPS(1)PGAYK;RAPS(1)PGAYK;RAPS(1)PGAYK;RAPS(1)PGAYK 114.72 0.00097529 4657870000 4803520 4298540 4610950 4489120 4732900 3497470 5188070 4064790 5210220 TRUE FALSE 4502876.258 4616808.374 4720323.911 4604318.419 4361197.126 4507132.812 4410167.067 4572287.979 4340600.623 1.037385525 1.063633533 1.087481739 1.060756061 1.004745081 1.038366163 1.016026917 1.053376797 1 22.04946326 2.856826149 6.137659006 1.024299766 1.067344532 0.501862606 0.019470876 0.174664032 8.161480763 0.005584323 0.005939752 719.1610347 -2.856826149 0.043044766 RAPS(ph)PLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RAPSPLPK 8 1 Q9BSL1 Q9BSL1 UBAC1 Ubiquitin-associated domain-containing protein 1 1 RAPS(1)PLPK;RAPS(1)PLPK;RAPS(1)PLPK;RAPS(1)PLPK 84.198 0.010794 4933910000 6552600 5517480 5993400 5813100 5992700 4770540 7045700 5371750 7053000 TRUE FALSE 6142484.463 5925999.96 6135566.278 5962273.988 5522057.515 6147717.455 5989262.694 6042424.812 5875808.736 1.045385365 1.008542011 1.044207964 1.014715464 0.939795314 1.046275965 1.019308654 1.02835628 1 22.486356 -0.308019466 6.585053704 1.000006687 1.018616871 0.033609606 0.030842572 0 0 0.027972375 0.006593152 0.492017482 0.308019466 0.018610184 RAPS(ph)PVVSPTEMNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 145.88 5.18E-06 1524440000 1453840 975550 1127860 1028520 1250970 946860 1228120 1029910 1343610 TRUE FALSE 1362846.75 1047780.737 1154613.372 1054913.564 1152723.862 1220203.111 1043974.807 1158496.531 1119352.811 1.217531002 0.936059415 1.031500846 0.942431693 1.029812809 1.090096973 0.932659298 1.034969957 1 20.0942334 4.748447072 24.92998602 0.997007428 1.217531126 0.644691946 0.050788908 794.1735816 2002570.397 0.011192601 0.149878562 56033.41248 -4.748447072 0.220523698 RAPS(ph)TSPSFEGTQETYTVAHEENVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RAPSTSPSFEGTQETYTVAHEENVR 25 1 Q9BUT9 Q9BUT9 FAM195A Protein FAM195A 1 RAPS(0.333)T(0.333)S(0.333)PS(0.002)FEGTQETYTVAHEENVR;RAPS(0.32)T(0.32)S(0.32)PS(0.04)FEGTQETYTVAHEENVR;RAPS(0.318)T(0.318)S(0.318)PS(0.045)FEGTQETYTVAHEENVR;RAPS(0.315)T(0.315)S(0.315)PS(0.055)FEGTQETYTVAHEENVR 298.9 1.93E-63 932790000 68495.1 88428 74871.7 83840 97037 58546 87358 77083.3 72921 TRUE FALSE 64208.11396 94975.30113 76647.69208 85991.47634 89416.10545 75447.27979 74259.47889 86707.31969 60750.01401 1.056923443 1.563379082 1.261690114 1.415497226 1.471869709 1.241930245 1.222377971 1.427280653 1 15.89059712 -1.711584564 0.351747314 0.714335769 1.36301487 0.314770372 0.148137821 32.22671615 2.039992989 7.950568728 0.107447458 0.019427434 1.711584564 0.648679101 RAPS(ph)VANVGSHCDLSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RAPSVANVGSHCDLSLK 17 1 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 1 RAPS(1)VANVGSHCDLSLK;RAPS(1)VANVGSHCDLSLK;RAPS(1)VANVGSHCDLSLK 161.04 1.42E-09 728000000 590480 468380 515760 492510 604280 444091 693510 537160 764940 TRUE FALSE 553522.9108 503059.3425 527994.0708 505148.6404 556822.2863 572292.8625 589524.6137 604225.6084 637266.5723 0.868589276 0.789401742 0.828529369 0.792680273 0.873766663 0.898043123 0.925083222 0.948152052 1 19.28153746 1.825563117 0.793669809 0.990705882 0.813085475 0.852392144 0.025629762 0.195351536 0.23400521 0.020997734 0.009923934 66.9211071 -1.825563117 -0.177620407 RAPS(ph)WR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RAPSWR 6 1 Q13136-2;A0A2R8Y7R9;Q13136;O75335;B1APN9;M0QZB5;O75335-1;O75335-2 Q13136-2 PPFIA1;PPFIA4 Liprin-alpha-1;Liprin-alpha-4 1 RAPS(1)WR;RAPS(1)WR 68.95 0.058059 2272370000 520790 637850 567460 586300 693470 447670 596370 557280 855770 TRUE FALSE 488194.6835 685077.0777 580920.4192 601345.4506 639007.6635 576905.0617 506949.8549 626857.6347 712936.4585 0.684766051 0.960923052 0.814827762 0.843476923 0.896303809 0.809195623 0.711072984 0.879261577 1 19.44341397 3.700812474 24.18650139 0.830525876 0.856161712 0 0.100505904 1731.313278 1591650.848 0.025267884 0.039160769 5021.257272 -3.700812474 0.025635835 RAPSS(ph)PVAKPGPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RAPSSPVAKPGPVK 14 2 Q9GZR2;A0A0C4DG31;Q9GZR2-2 Q9GZR2 REXO4 RNA exonuclease 4 1 RAPS(0.03)S(0.97)PVAKPGPVK;RAPS(0.392)S(0.608)PVAKPGPVK 111.33 0.0003434 2259550000 4316000 3680600 3436900 3068300 4884600 2215700 4357200 4096400 5756400 TRUE FALSE 4045869.264 3953115.454 3518424.891 3147037.773 4500983.22 2855336.621 3703878.31 4607844.557 4795619.652 0.84365933 0.824317969 0.733674717 0.656231728 0.938561343 0.595405146 0.772346136 0.960844456 1 22.19328581 1.216879499 5.21383967 0.989629702 0.762311664 0.467549368 0.095302559 0.146840664 10.41804661 0.076592851 0.02135143 16.47705148 -1.216879499 -0.227318037 RAQS(ph)IER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RAQSIER 7 1 O14681-3;O14681;E9PLB8;E9PL33;E9PM05;E9PS58;E9PK61 O14681-3 EI24 Etoposide-induced protein 2.4 homolog 1 RAQS(1)IER 86.18 0.021467 437500000 666280 736920 667710 678650 819270 639830 834860 777960 786060 TRUE FALSE 624578.7241 791482.3236 683548.3965 696065.308 754927.839 824538.5342 709680.4935 875090.0185 654861.5079 0.953756965 1.208625509 1.043806039 1.062919869 1.152805334 1.25910368 1.083710807 1.33629784 1 19.32083031 2.611857669 5.384911872 1.173659357 1.087304215 0.159291695 0.109104619 0.457472562 18.21015306 0.032248898 0.030261917 409.1265553 -2.611857669 -0.086355142 RAQTGSAPPRPAAPHPRPASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RAQTGSAPPRPAAPHPRPASR 21 3 A6NKF1;A6NKF1-2 A6NKF1 SAC3D1 SAC3 domain-containing protein 1 0 58.071 0.04427 11362000 9738 11275 8684.5 8795.9 10940 7355.7 10765 10136 8667.2 FALSE TRUE 9128.515963 12109.81273 8890.500441 9021.617685 10080.81653 9479.17118 9150.888187 11401.50191 7220.588328 1.264234374 1.677122719 1.231270921 1.249429725 1.396121212 1.312797621 1.267332767 1.579026721 1 12.81790068 -2.194987662 2.194445177 2.43E-05 1.373340793 0.384036458 0.148119452 3060580.407 517681.1026 15242048.44 0.037846889 0.006382816 2.194987662 1.373316493 RAS(ph)AGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RASAGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK 35 1 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 RAS(1)AGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK;RAS(1)AGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK;RAS(1)AGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK 245.2 5.69E-48 2935300000 584780 841540 840530 791180 980130 679350 1169800 995400 1342370 TRUE FALSE 548179.6637 903848.4972 860467.7685 811483.0183 903154.5435 875467.3167 994399.3499 1119677.881 1118319.775 0.490181499 0.808220079 0.769429092 0.725626995 0.807599547 0.782841667 0.889190527 1.001214417 1 20.09290134 6.161274616 0.128949504 1.10061522 1.07E-12 0.696407789 0.080205023 32.94715982 0.458484974 0.50900114 6.265499124 1449688.241 -6.161274616 -1.10061522 RAS(ph)APHGPLDMAPFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RASAPHGPLDMAPFAR 16 1 Q8N4B1-2;Q8N4B1;Q8N4B1-4 Q8N4B1-2 FAM109A Sesquipedalian-1 1 RAS(1)APHGPLDMAPFAR 89.816 0.003468 195290000 151640 137670 138530 135020 154840 120240 153860 105770 152610 TRUE FALSE 142149.1231 147863.23 141815.997 138484.8418 142679.491 154951.3361 130790.1214 118975.6173 127138.4051 1.118065961 1.163009949 1.115445777 1.089244762 1.12223754 1.21876105 1.02872237 0.93579605 1 16.95604037 1.541394578 5.17497496 0.97161483 1.135558806 0.783966509 0.037943872 0.062609905 3.608570242 0.020734213 0.009224578 34.78520591 -1.541394578 0.163943976 RAS(ph)CTSSTSGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RASCTSSTSGSK 12 1 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 1 RAS(0.997)CT(0.003)SSTSGSK;RAS(0.997)CT(0.003)SSTSGSK;RAS(0.995)CT(0.002)S(0.002)STSGSK;RAS(0.899)CT(0.04)S(0.003)S(0.028)T(0.028)S(0.001)GSK;RAS(0.993)CT(0.003)S(0.003)STSGSK;RAS(0.999)CT(0.001)SSTSGSK;RAS(0.886)CT(0.084)S(0.014)S(0.014)T(0.002)SGSK 196.74 2.15E-07 1127889000 2212905 1684801 1949552 1886245 1966223 1527228 2288244 1884605 1957091 TRUE FALSE 2074403.226 1809545.419 1995796.294 1934649.24 1811803.777 1968113.931 1945143.055 2119902.083 1630439.869 1.272296676 1.109851061 1.224084575 1.186581166 1.111236183 1.207106112 1.193017352 1.300202555 1 20.6368298 -2.309944556 2.313415142 9.86E-05 1.191832052 0.517714148 0.06031197 670756.1438 308838.1651 3630880.855 0.013673079 0.004898414 2.309944556 1.191733435 RAS(ph)CTSSTSGSKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RASCTSSTSGSKR 13 2 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 1 RAS(0.997)CT(0.003)SSTSGSKR 165.58 2.76E-05 139220000 93630 101230 86363 90081 124560 63124 127630 81325 144940 TRUE FALSE 87769.86543 108725.1745 88411.57114 92392.63097 114777.5601 81346.87407 108493.0664 91478.60527 120748.5777 0.726881154 0.90042613 0.732195549 0.765165377 0.950549996 0.673688052 0.898503887 0.757595717 1 16.88164667 -1.377461177 3.128800348 1.002164656 0.807927494 0.327167976 0.089310451 22358906.97 31433211.42 446345.7913 0.018712895 0.041931348 1.377461177 -0.194237162 RAS(ph)DDGKLTDPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RASDDGKLTDPSK 13 2 P04049;P04049-2;A0A0B4J1W9 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 RAS(0.999)DDGKLTDPSK 83.418 0.0080428 478020000 720980 466690 526610 542580 657520 375880 719960 417650 1156300 TRUE FALSE 675855.1488 501244.2132 539101.4379 556503.5214 605881.0315 484390.4541 612008.6818 469794.5219 963306.06 0.701599602 0.520337444 0.559636714 0.577701672 0.628960054 0.502841697 0.635321117 0.487689781 1 19.87763472 -1.659030602 2.823743822 1.04649513 0.573094826 0.804279522 0.065592788 20683052.03 20560114.71 7004508.612 0.014396265 0.021926504 1.659030602 -0.473400304 RAS(ph)DGGANIQLHAQQLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RASDGGANIQLHAQQLLK 18 1 H0Y4E8;Q9Y2K2-8;Q9Y2K2-7;Q9Y2K2;H7C3X8 H0Y4E8 SIK3 Serine/threonine-protein kinase SIK3 1 RAS(1)DGGANIQLHAQQLLK 258.47 5.47E-31 217800000 469960 459090 405170 449820 538890 328770 522390 450380 705340 TRUE FALSE 440546.0425 493081.5013 414780.8237 461363.1427 496567.7532 423680.5619 444062.4691 506610.9344 587614.1973 0.749719875 0.839124554 0.705872706 0.785146351 0.845057447 0.721018253 0.755704119 0.862148901 1 19.16450973 0.953555275 3.396593205 0.999612016 0.771824727 0.731962888 0.044596407 0.128797041 3.849191974 0.041134557 0.010668903 8.985769519 -0.953555275 -0.227787288 RAS(ph)DTSLTQGIVAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RASDTSLTQGIVAFR 15 1 Q9H0K1 Q9H0K1 SIK2 Serine/threonine-protein kinase SIK2 1 RAS(0.999)DT(0.001)SLTQGIVAFR;RAS(0.999)DT(0.001)SLTQGIVAFR 183.06 3.19E-07 392070000 142564 188717 169175 157331 202866 152399 163216 165349 179273 TRUE FALSE 133641.1737 202689.803 173187.9109 161368.3798 186933.7227 196394.1173 138743.276 185993.1866 149351.1782 0.894811647 1.357135615 1.159601906 1.080462718 1.251638755 1.314982043 0.928973429 1.245341275 1 17.18834909 1.740615041 24.99999963 1.057385971 1.194547661 0.113487186 0.15032819 0.585736427 7172.785419 0.063438734 0.035180026 55.03196766 -1.740615041 0.137161691 RAS(ph)EELDGLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RASEELDGLFR 11 1 Q14814-4;Q14814;Q05BX2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 RAS(1)EELDGLFR;RAS(1)EELDGLFR 212.43 3.64E-09 134786000 160027 175676 175292 178015 219557 160551 200503 169360 327475 TRUE FALSE 150011.1957 188683.2338 179450.009 182583.1663 202313.8789 206899.4674 170439.4365 190504.9688 272817.3069 0.549859528 0.691610206 0.657766221 0.669250673 0.741572744 0.75838102 0.624738359 0.698287696 1 18.05757564 -5 0.274456393 3.283542529 0.65299576 0.778082378 0.055565431 100.9287585 0.974750551 130.9624547 0.06388897 1.00E-05 5 -2.630546769 RAS(ph)FAEK ddPTM_SK-BR-3_Pertuzumab_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 117.25 0.0032298 32051400000 19021930 17384640 16936280 17484440 18856390 12939380 22294400 16611460 18611510 TRUE FALSE 17831381.36 18671816.83 17338016.56 17933120.33 17375485.19 16674768.95 18951561.69 18685437.35 15505128.75 1.15003117 1.204234879 1.118211712 1.156592804 1.120628244 1.075435698 1.222276964 1.205113331 1 23.88624217 3.97328318 22.97397911 1.140009933 1.178532042 0.06843783 0.064444351 169.2979184 1013417.279 0.015332272 0.029155727 9403.362539 -3.97328318 0.038522109 RAS(ph)FAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RASFAK 6 1 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;F6UYG0;K7ENT7;Q96J92-2;Q96J92-3;Q96J92;Q9Y3S1;Q9Y3S1-4;Q9Y3S1-2;H0Y7T5;F8W9F9;A6PVV2;Q9Y3S1-3 F5GWT4;Q9Y3S1 WNK1;WNK4;WNK2 Serine/threonine-protein kinase WNK1;Serine/threonine-protein kinase WNK4;Serine/threonine-protein kinase WNK2 1 RAS(1)FAK;RAS(1)FAK 86.67 0.032655 2735780000 4583600 3903700 4091800 4082500 4118700 2877150 4725200 3107800 5992900 TRUE FALSE 4296720.658 4192734.01 4188859.428 4187263.862 3795233.916 3707736.498 4016700.127 3495815.671 4992646.274 0.860609869 0.839781907 0.839005849 0.838686266 0.760164792 0.742639533 0.804523274 0.70019294 1 22.25137327 2.814124564 7.383285152 0.786056801 0.843099013 0.049176296 0.079154646 0.584327817 50.40070497 0.020986077 0.022264858 651.8153205 -2.814124564 0.057042212 RAS(ph)GQAFELILS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RASGQAFELILSPR 14 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 2 RAS(1)GQAFELILS(1)PR;RAS(1)GQAFELILS(1)PR;RAS(1)GQAFELILS(1)PR;RAS(1)GQAFELILS(1)PR;RAS(1)GQAFELILS(1)PR;RAS(1)GQAFELILS(1)PR 182.02 5.50E-06 2670240000 597029 663425 682234 705803 820915 576626 764509 625702 1001190 TRUE FALSE 559662.0206 712545.6773 698416.9127 723915.0999 756443.6473 743088.5655 649877.9728 703822.272 834084.9211 0.670989256 0.854284329 0.837345089 0.867915342 0.906914426 0.890902769 0.779150847 0.843825676 1 19.66983475 -4.777568846 0.020216212 2.037164852 8.49E-07 0.464281932 0.062208647 3531.616966 5.596279513 377.2518616 209.3748591 1.67E-05 4.777568846 -2.037164004 RAS(ph)GQAFELILSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 RASGQAFELILSPR 14 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(0.883)GQAFELILS(0.117)PR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR 219.06 3.16E-12 4819902000 1232813 1799939 1361788 1396587 2155794 1145589 1432366 1575595 1510052 TRUE FALSE 1155653.435 1933208.356 1394090.254 1432425.787 1986486.635 1476301.947 1217596.016 1772311.504 1258014.566 0.918632794 1.53671381 1.108167021 1.138640065 1.579064893 1.173517372 0.967871159 1.408816362 1 20.2627172 0.321739387 0.424459589 0.980900634 1.263480046 0.060004224 0.225417919 6.952829734 2.094269224 0.552707603 0.141098634 2.097680721 -0.321739387 0.282579412 RAS(ph)HTLLPSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RASHTLLPSHR 11 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 RAS(0.885)HT(0.115)LLPSHR;RAS(0.666)HT(0.334)LLPSHR;RAS(0.592)HT(0.408)LLPSHR 85.909 0.0069897 1000480000 409700 527950 442490 408870 514950 389430 491090 490590 770690 TRUE FALSE 384057.6083 567039.9673 452986.0718 419362.2964 474507.9042 501852.1191 417455.6136 551841.2414 642056.8602 0.598167596 0.883161605 0.705523295 0.653154452 0.73904343 0.781631893 0.650184804 0.859489674 1 19.29234154 0.994810451 5.257692771 0.999764471 0.729932462 0.58433344 0.079284357 0.102419446 10.88481735 0.073144263 0.018465314 9.881217327 -0.994810451 -0.26983201 RAS(ph)ISEPSDTDPEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RASISEPSDTDPEPR 15 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 RAS(0.618)IS(0.373)EPS(0.008)DT(0.001)DPEPR;RAS(0.776)IS(0.215)EPS(0.008)DT(0.001)DPEPR;RAS(0.998)IS(0.002)EPSDTDPEPR;RAS(0.923)IS(0.066)EPS(0.011)DTDPEPR 171.25 1.16E-06 957140000 889670 1051720 1011354 1098875 1011308 905205 1243969 973586 1239287 TRUE FALSE 833987.1428 1129590.443 1035343.794 1127073.993 931883.9491 1166522.989 1057447.397 1095140.355 1032441.994 0.807781113 1.094095794 1.002810619 1.091658417 0.902601749 1.129867824 1.024219669 1.060728217 1 19.9776293 4.746813979 24.90184932 1.040122982 0.807780992 0.565769563 0.063433915 658.1739467 1985779.029 0.01313603 0.147690859 55823.10373 -4.746813979 -0.232341991 RAS(ph)LSDIGFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RASLSDIGFGK 11 1 Q07002;A0A0A0MSJ6;Q07002-3;D6R9B0;D6RA44 Q07002 CDK18 Cyclin-dependent kinase 18 1 RAS(0.993)LS(0.007)DIGFGK;RAS(0.975)LS(0.025)DIGFGK 132.84 0.0001067 262780000 864130 913070 906390 920750 1102300 669310 1154170 929490 2062800 TRUE FALSE 810045.6458 980674.6528 927889.9988 944378.0038 1015729.804 862528.9317 981112.9233 1045538.873 1718505.354 0.471366379 0.57065557 0.539940127 0.549534514 0.591054198 0.501906456 0.5709106 0.608400125 1 20.71272292 0.472173919 1.407790179 1.000103675 0.543640798 0.946768137 0.03388956 0.4900407 1.112496363 0.028812314 0.008432109 2.966018936 -0.472173919 -0.456462877 RAS(ph)LSDLTDLEDIEGLTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RASLSDLTDLEDIEGLTVR 19 1 J3KSI3;J3KSU7;K7EN88;Q8WZ73-3;Q8WZ73-2;Q8WZ73 J3KSI3 RFFL;hCG_2039718 E3 ubiquitin-protein ligase rififylin 1 RAS(0.833)LS(0.167)DLTDLEDIEGLTVR;RAS(0.999)LS(0.001)DLTDLEDIEGLTVR;RAS(0.467)LS(0.182)DLT(0.35)DLEDIEGLTVR;RAS(0.5)LS(0.5)DLTDLEDIEGLTVR 313.24 8.34E-62 143959000 69200.6 83386 87352.3 85278.4 105117 72467.7 93089 85144.4 112095 TRUE FALSE 64869.45797 89559.9862 89424.33781 87466.78812 96861.53484 93387.94858 79131.16865 95774.86577 93385.62034 0.694640757 0.959034013 0.957581451 0.936619447 1.037221089 1.000024931 0.847359244 1.025584725 1 16.5109128 4.738581423 8.027936962 0.961107284 0.692517369 0.716106541 0.054291991 0.051616959 41.52012671 0.012671665 0.075127632 54774.87855 -4.738581423 -0.268589914 RAS(ph)LSEIGFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RASLSEIGFGK 11 1 Q00537;Q00537-2;F5H6Z0 Q00537 CDK17 Cyclin-dependent kinase 17 1 RAS(0.994)LS(0.006)EIGFGK;RAS(0.995)LS(0.005)EIGFGK;RAS(1)LSEIGFGK;RAS(1)LSEIGFGK 177.39 4.90E-06 705620000 2821360 2558537 2565057 2453418 3044803 1971735 2795184 2369574 4340450 TRUE FALSE 2644776.114 2747973.742 2625901.363 2516376.86 2805676.455 2540942.886 2376072.108 2665420.53 3616000.855 0.731409151 0.759948311 0.726189365 0.695900516 0.775905916 0.702694216 0.657099432 0.737118335 1 21.78596359 0.948643091 23.57057097 1 0.720928484 0.875436859 0.032855951 3394.672819 1558007.929 0.034254535 0.008563634 8.884706607 -0.948643091 -0.279071516 RAS(ph)LTLEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RASLTLEEK 9 1 Q6P3W7;A0A0U1RQQ9 Q6P3W7 SCYL2 SCY1-like protein 2 1 RAS(1)LTLEEK;RAS(1)LTLEEK;RAS(0.999)LT(0.001)LEEK;RAS(0.999)LT(0.001)LEEK;RAS(1)LTLEEK 170.66 3.52E-05 932250000 1480180 1251830 1353300 1373800 1614120 1104670 1676400 1309840 2330940 TRUE FALSE 1387538.176 1344516.796 1385400.915 1409054.034 1487353.526 1423570.296 1425039.383 1473376.407 1941891.056 0.714529361 0.692374988 0.713428753 0.72560921 0.765930469 0.733084532 0.733841056 0.758732784 1 20.88903083 -5 0.247650497 2.651746613 0.700163692 0.970020972 0.01516453 28.88774196 0.286966167 24.09326424 0.023509499 1.00E-05 5 -1.951582921 RAS(ph)MQPIQIAEGTGITTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RASMQPIQIAEGTGITTR 18 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 RAS(1)MQPIQIAEGTGITTR;RAS(1)MQPIQIAEGTGITTR;RAS(1)MQPIQIAEGTGITTR;RAS(1)MQPIQIAEGTGITTR 174.03 4.19E-12 1071010000 372081 398829 423775 408552 478862 319166 576030 468509 647454 TRUE FALSE 348793.1144 428358.7141 433827.1431 419036.136 441254.1102 411304.043 489659.6491 527003.38 539389.7447 0.646643949 0.794154354 0.804292531 0.776870788 0.818061735 0.762535897 0.907803038 0.977036336 1 19.04096857 1.534347198 2.15409205 0.994108978 0.775258206 0.793590284 0.047799104 0.127062895 1.214826957 0.03612021 0.012431922 34.22529485 -1.534347198 -0.218850771 RAS(ph)PNLFSEAQYQEAPVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RASPNLFSEAQYQEAPVEK 19 1 F6VUX8;Q9HC77-2;Q9HC77 F6VUX8 CENPJ Centromere protein J 1 RAS(0.999)PNLFS(0.001)EAQYQEAPVEK 157.68 2.19E-09 82922000 117190 106010 99208 100780 110830 81741 120280 94234 107620 TRUE FALSE 109855.2871 113859.0907 101561.2606 103366.1854 102125.8589 105338.2997 102245.1306 105999.3223 89657.52675 1.225276796 1.269933433 1.13276893 1.152900255 1.139066206 1.174896337 1.14039651 1.182269087 1 16.45213708 -5 0.074968281 0.443746704 1.364987449 0.720553818 0.037055218 153.9759651 0.82489865 14.72693365 1.593239069 1.00E-05 5 0.921240745 RAS(ph)PS(ph)PPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RASPSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RAS(1)PS(1)PPPK;RAS(1)PS(1)PPPK;RAS(1)PS(1)PPPK 116.24 0.00089976 845770000 1558690 1250600 1355020 1303520 1416240 1096320 1601500 1212930 1624610 TRUE FALSE 1461134.375 1343195.725 1387161.714 1336970.53 1305014.223 1412809.787 1361369.943 1364366.98 1353452.096 1.079561205 0.992422066 1.0249064 0.987822572 0.964211609 1.043856514 1.005850112 1.008064478 1 20.36821239 4.744591506 24.7629349 1.005100259 1.079561242 0.558347392 0.021241545 457.3570374 1877854.891 0.004821017 0.043811749 55538.16238 -4.744591506 0.074460983 RAS(ph)PS(ph)PPPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RASPSPPPKR 10 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RAS(1)PS(1)PPPKR 48.704 0.093531 192100000 62660 62607 59835 61082 63056 51736 71310 59341 71698 TRUE FALSE 58738.22245 67242.48742 61254.31446 62649.46753 58103.83612 66671.34334 60617.72751 66749.85448 59731.14061 0.983376876 1.12575261 1.025500498 1.048857713 0.972756179 1.116190695 1.014842959 1.117505104 1 15.86619565 0.083058614 19.61828143 1 1.052808729 0.076615463 0.05472725 0 0 0.046443175 0.010946761 1.210761531 -0.083058614 0.052808729 RAS(ph)PSKPASAPASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RASPSKPASAPASR 14 2 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;B5MEG9;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 RAS(0.999)PS(0.001)KPASAPASR;RAS(0.813)PS(0.181)KPAS(0.006)APASR;RAS(0.937)PS(0.063)KPASAPASR;RAS(0.845)PS(0.145)KPAS(0.002)APAS(0.008)R;RAS(0.786)PS(0.214)KPASAPASR;RAS(0.994)PS(0.006)KPASAPASR;RAS(0.974)PS(0.026)KPASAPASR 185.96 5.83E-07 7429020000 3994240 3179580 3435330 3262850 3284370 2519220 4066430 2789440 2429260 TRUE FALSE 3744247.648 3414999.412 3516817.65 3346580.255 3026428.829 3246477.918 3456706.572 3137707.724 2023800.812 1.850106802 1.687418737 1.737729142 1.653611479 1.495418329 1.604148935 1.70802707 1.550403432 1 20.94863587 -2.548984756 0.252315584 6.90E-12 1.751501024 0.875708926 0.081052372 15.34634607 0.456539107 8.632173742 0.124203822 0.002824979 2.548984756 1.751501024 RAS(ph)PSPPPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RASPSPPPKR 10 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RAS(0.955)PS(0.045)PPPKR 97.463 0.0031523 71212000 103230 95990 98723 93899 103000 72699 99365 88409 126190 TRUE FALSE 96769.01857 103097.1995 101064.7562 96308.60731 94910.79548 93686.02113 84466.14071 99447.05826 105128.0738 0.920486936 0.980681903 0.961348882 0.916107409 0.902811134 0.891160827 0.803459415 0.945961004 1 16.68178846 2.997407297 1.993710224 0.886383555 0.961594522 0.05022228 0.053373299 0.411882678 3.295349661 0.017110047 0.02017049 994.0478664 -2.997407297 0.075210966 RAS(ph)QEANLLTLAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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;RAS(1)QEANLLTLAQK 299.38 9.48E-44 3377390000 5594900 4843800 4734360 4859130 5458300 3594940 5690140 4488250 4802460 TRUE FALSE 5244725.196 5202439.992 4846661.255 4983823.502 5029627.136 4632740.819 4836956.332 5048617.892 4000898.401 1.310886874 1.300317946 1.211393235 1.245676096 1.257124433 1.157925135 1.208967549 1.261871057 1 21.93189256 -5 0.147710677 0.153935827 1.319287191 0.801009194 0.039586566 58.00165279 0.512902762 14.43858544 0.20296851 1.00E-05 5 1.165351364 RAS(ph)SASVPAVGASAEGTRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RASSASVPAVGASAEGTRR 19 2 V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23;A0A2R8YFI4 V9GYZ0 PANK2 "Pantothenate kinase 2, mitochondrial" 1 RAS(0.877)S(0.089)AS(0.034)VPAVGASAEGTRR 127.48 1.84E-05 307070000 140880 104770 111090 108240 132510 79417 165860 92407 174200 TRUE FALSE 132062.5723 112527.2798 113725.1073 111017.6216 122103.1991 102343.3987 140990.8328 103944.2174 145124.8946 0.909992546 0.775382336 0.783636106 0.764979861 0.841366324 0.705209116 0.971513765 0.716239744 1 17.14693549 -1.699966394 0.382751371 1.1520233 0.800881438 0.323532171 0.083754668 35.12689432 2.473596556 5.017368878 0.051789349 0.019954167 1.699966394 -0.351141861 RAS(ph)SKGGGGY(ph)TCQSGSGWDEFTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RASSKGGGGYTCQSGSGWDEFTK 23 2 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 2 RAS(0.972)S(0.135)KGGGGY(0.811)T(0.082)CQS(0.001)GSGWDEFTK 93.147 0.0076454 391820000 610530 437560 529910 853220 879510 218920 367710 208740 316700 TRUE FALSE 572318.0171 469957.3977 542479.7154 875115.0697 810436.8324 282118.6501 312575.2992 234801.6485 263840.724 2.169179982 1.781216298 2.056087882 3.316830913 3.071689692 1.069276364 1.184712103 0.889937099 1 18.00930774 2.217171165 24.95600027 1.066298935 2.364261636 0.702483434 0.463122569 164.0573425 191411.5874 0.196871653 0.145535846 164.8812096 -2.217171165 1.297962702 RAS(ph)SLNFLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RASSLNFLNK 10 1 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 RAS(0.5)S(0.5)LNFLNK 80.287 0.025909 224070000 293320 343160 269650 262190 402900 185050 379380 343930 656510 TRUE FALSE 274961.6248 368567.9235 276046.2253 268918.2393 371257.8592 238470.931 322495.491 386870.4176 546934.2398 0.502732513 0.673879777 0.504715568 0.491682948 0.678797984 0.4360139 0.589642168 0.70734357 1 19.06100786 0.891861356 2.236101892 0.999128346 0.55731799 0.773111324 0.077242003 0.194480962 2.01012691 0.067883209 0.018541731 7.795811979 -0.891861356 -0.441810355 RAS(ph)SLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RASSLSR 7 1 Q9Y259;Q9Y259-2 Q9Y259 CHKB Choline/ethanolamine kinase 1 RAS(0.38)S(0.38)LS(0.24)R 90.263 0.018291 244420000 401130 483200 441510 398680 467690 404000 519890 467160 464980 TRUE FALSE 376023.9893 518976.6308 451982.8257 408910.8038 430959.514 520628.2416 441937.3209 525485.9543 387371.8341 0.97070555 1.33973765 1.16679321 1.055602828 1.112521552 1.344001282 1.140860749 1.356541462 1 18.56335953 RAS(ph)VCAEAYNPDEEEDDAESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RASVCAEAYNPDEEEDDAESR 21 1 P31323 P31323 PRKAR2B cAMP-dependent protein kinase type II-beta regulatory subunit 1 RAS(1)VCAEAYNPDEEEDDAESR 150.24 4.49E-08 135100000 135560 113210 130060 123620 116480 103060 175100 118080 105640 TRUE FALSE 127075.5416 121592.1862 133145.0846 126792.2985 107332.1307 132811.749 148845.3805 132822.5479 88008.00154 1.443908956 1.381603764 1.512874765 1.440690577 1.219572411 1.509087204 1.691270997 1.509209908 1 16.42534708 RASEDTTSGS(ph)PPKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RASEDTTSGSPPKK 14 2 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 RASEDT(0.002)T(0.009)S(0.041)GS(0.948)PPKK;RASEDTT(0.004)S(0.007)GS(0.988)PPKK;RASEDT(0.002)T(0.002)S(0.051)GS(0.944)PPKK;RASEDTTS(0.044)GS(0.956)PPKK 143.46 4.76E-06 3105430000 3098550 1549900 1950650 2062550 2071580 1359390 2872860 1809900 2724660 TRUE FALSE 2904617.287 1664656.209 1996920.339 2115478.525 1908886.463 1751823.825 2442101.313 2035869.999 2269896.644 1.27962535 0.733362117 0.879740646 0.931971299 0.840957437 0.771763697 1.075864542 0.896899867 1 21.11419518 1.7302534 24.99999888 0.991812629 0.88171061 0.048016523 0.153754053 1.689359856 5055.365602 0.065124995 0.036115017 53.73452331 -1.7302534 -0.110102019 RASGQAFELILS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RASGQAFELILSPR 14 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 RASGQAFELILS(1)PR 153.19 3.96E-06 154130000 84297 106680 97959 129570 144460 66896 74252 78336 119240 TRUE FALSE 79021.00124 114578.6982 100282.6337 132894.9856 133114.6943 86207.78923 63118.60192 88116.42204 99338.07368 0.795475474 1.153421784 1.00950854 1.33780514 1.340016868 0.867822236 0.635391845 0.887035743 1 16.60005915 2.062544147 8.288295954 0.788187025 1.123619555 0.362107559 0.180225377 0.237532187 28.17946895 0.065452545 0.048237682 115.4899378 -2.062544147 0.33543253 RASHT(ph)LLPSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RASHTLLPSHR 11 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 RAS(0.239)HT(0.761)LLPSHR;RAS(0.201)HT(0.799)LLPSHR;RAS(0.207)HT(0.793)LLPSHR 106.32 0.0017888 2046530000 501610 615210 512510 491810 700190 447920 636820 660700 1166550 TRUE FALSE 470215.1255 660760.7885 524666.9792 504430.6772 645199.9018 577227.2326 541334.7529 743189.8494 971845.2688 0.483837439 0.679903283 0.539866783 0.519044228 0.663891591 0.593949728 0.557017429 0.764720345 1 19.89036711 0.971136838 3.091610536 0.99924111 0.583839763 0.837557465 0.060853577 0.090094986 2.142430688 0.05414507 0.014198362 9.357004499 -0.971136838 -0.415401347 RASLS(ph)DLTDLEDIEGLTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RASLSDLTDLEDIEGLTVR 19 1 J3KSI3;J3KSU7;K7EN88;Q8WZ73-3;Q8WZ73-2;Q8WZ73 J3KSI3 RFFL;hCG_2039718 E3 ubiquitin-protein ligase rififylin 1 RAS(0.07)LS(0.93)DLTDLEDIEGLTVR 146.06 7.30E-08 23292000 11209 13683 14483 14769 15414 11847 17742 13301 14406 TRUE FALSE 10507.4487 14696.10356 14826.5436 15147.99754 14203.44662 15267.03658 15081.75181 14961.65913 12001.54553 0.875507964 1.224517585 1.235386189 1.262170568 1.183468127 1.27208921 1.256650801 1.246644367 1 13.55093258 4.738557131 8.707780378 1.22638563 0.873652035 0.627317055 0.080186693 0.045358407 59.78581294 0.016044955 0.09407407 54771.81485 -4.738557131 -0.352733595 RASNGETLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RASNGETLEK 10 1 Q9BRT3 Q9BRT3 MIEN1 Migration and invasion enhancer 1 0 ; 78.043 0.050007 626950000 704660 635660 589690 567320 702660 495250 741310 611570 845410 FALSE TRUE 660556.5885 682724.9278 603677.7253 581878.3917 647475.918 638220.6353 630157.4475 687925.8607 704305.6094 0.937883469 0.969358924 0.857124687 0.826173161 0.919311034 0.90617003 0.894721608 0.976743407 1 19.42584205 1.152703816 4.218742008 0.998087445 0.901690298 0.458970707 0.039501929 0.204224218 6.196305264 0.039081609 0.010174207 14.21359104 -1.152703816 -0.096397147 RASS(ph)LNFLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RASSLNFLNK 10 1 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 RAS(0.12)S(0.88)LNFLNK 86.288 0.01447 150270000 380330 447280 341100 317080 524790 231070 444490 467350 893010 TRUE FALSE 356525.8242 480397.0766 349191.0531 325216.8096 483575.1103 297776.1579 377842.8509 525699.6763 743960.8619 0.479226586 0.645728964 0.469367504 0.437142364 0.650000739 0.400257827 0.507880011 0.706622758 1 19.5048672 0.947049287 2.993094657 0.999015417 0.51794107 0.791526454 0.080724314 0.123273534 2.679214486 0.073604519 0.019353249 8.852160657 -0.947049287 -0.481074347 RASS(ph)LNVLNVGGK ddPTM_SK-BR-3_Pertuzumab_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(0.132)S(0.868)LNVLNVGGK;RAS(0.016)S(0.984)LNVLNVGGK 110.57 0.00111 133503000 510350 683020 483620 509270 690470 298410 855310 506940 1065820 TRUE FALSE 478408.1045 733591.5115 495091.6948 522338.7304 636243.2714 384556.1227 727064.2058 570232.5749 887927.7565 0.538791699 0.826183781 0.557581054 0.58826715 0.716548465 0.433093931 0.818832614 0.642206047 1 19.76008278 0.309817173 0.901291744 1.002019017 0.641547075 0.462852624 0.122177879 2.465502069 2.471687346 0.121398779 0.035628594 2.040878607 -0.309817173 -0.360471941 RASS(ph)PFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RASSPFR 7 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 RAS(0.024)S(0.976)PFR 79.148 0.020464 364670000 215520 303070 225750 263460 305070 233980 269580 300150 272360 TRUE FALSE 202030.9879 325509.6181 231104.8966 270220.8296 281111.0328 301526.2277 229158.9817 337624.3882 226901.3565 0.890391274 1.434586479 1.018525848 1.190917647 1.238912967 1.328886845 1.009949809 1.487978712 1 17.79170571 RASSDLS(ph)IASSEEDKLSQNACILESVSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RASSDLSIASSEEDKLSQNACILESVSEK 29 2 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 RAS(0.163)S(0.163)DLS(0.223)IAS(0.223)S(0.223)EEDKLS(0.007)QNACILESVSEK 142.37 3.98E-08 92879000 91844 56007 67814 69447 88433 52414 89952 71943 122180 TRUE FALSE 86095.64799 60153.81656 69422.5801 71229.12759 81487.8289 67545.07093 76464.53267 80925.24192 101787.3687 0.845838232 0.590975259 0.682035315 0.699783564 0.800569166 0.663589911 0.751218286 0.795042086 1 16.63519902 0.304568868 0.533376839 1.018856436 0.685882598 0.592805151 0.072280824 1.597185841 0.696502801 0.129658923 0.032258644 2.016363688 -0.304568868 -0.332973837 RASSLS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RASSLSR 7 1 Q9Y259;Q9Y259-2 Q9Y259 CHKB Choline/ethanolamine kinase 1 RASS(0.003)LS(0.997)R 122.44 0.0045977 232380000 372540 466770 353950 383670 443760 377710 501160 423100 405960 TRUE FALSE 349223.3864 501330.1365 362345.8611 393515.6218 408908.8796 486748.7454 426015.7105 475924.9664 338202.6534 1.032586181 1.482336497 1.071386808 1.163549776 1.20906467 1.439222136 1.259646269 1.40721831 1 18.36752845 RATASEQPLAQEPPASGGS(ph)PATTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RATASEQPLAQEPPASGGSPATTK 24 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 RATASEQPLAQEPPAS(0.007)GGS(0.991)PAT(0.001)T(0.001)K;RATASEQPLAQEPPAS(0.002)GGS(0.996)PAT(0.001)TK 165.58 8.62E-12 1167420000 772060 630580 700360 651790 709940 552930 785910 598840 909540 TRUE FALSE 723738.1428 677268.7993 716972.8699 668516.0349 654184.1762 712551.9149 668070.0915 673606.4922 757731.8981 0.955137489 0.893810596 0.946209169 0.882259327 0.863345172 0.940374711 0.881670804 0.888977347 1 19.53132796 -0.976888394 4.874943622 1.000000962 0.906548798 0.474111131 0.030955994 0.00045837 18744781.02 42.45742592 0.006752501 0.105465789 0.976888394 -0.093452164 RATS(ph)LPSIPNPFPELCSPPSQS(ph)PILGGPSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 RAT(0.11)S(0.864)LPS(0.026)IPNPFPELCSPPS(0.378)QS(0.617)PILGGPS(0.003)S(0.003)AR;RAT(0.124)S(0.875)LPS(0.001)IPNPFPELCSPPS(0.14)QS(0.86)PILGGPSSAR;RAT(0.229)S(0.723)LPS(0.048)IPNPFPELCS(0.021)PPS(0.248)QS(0.731)PILGGPSSAR;RAT(0.181)S(0.807)LPS(0.012)IPNPFPELCS(0.003)PPS(0.474)QS(0.523)PILGGPSSAR 230.65 4.12E-36 1301640000 474581 732766 545028 679662 911920 594723 932030 649440 788118 TRUE FALSE 444877.8224 787020.7571 557956.3215 697103.2776 840301.4817 766409.8756 792280.754 730524.0136 656576.0144 0.677572456 1.198674243 0.849796991 1.061725166 1.279823605 1.16728278 1.206685497 1.112626714 1 19.32460252 2.998541352 24.38049544 1.170422133 0.961579342 0.344084045 0.14721367 45.80286333 765603.502 0.039112511 0.04610878 996.6469732 -2.998541352 -0.208842792 RATS(ph)LPSIPNPFPELCSPPSQSPILGGPSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 RAT(0.112)S(0.885)LPS(0.003)IPNPFPELCSPPSQSPILGGPSSAR;RAT(0.112)S(0.881)LPS(0.008)IPNPFPELCSPPSQSPILGGPSSAR 303.67 3.47E-90 2481700000 392130 564210 457040 510370 647590 463210 711420 523440 674120 TRUE FALSE 367587.2833 605984.6955 467881.2046 523466.9583 596730.8937 596931.2074 604749.1755 588792.6362 561605.017 0.654529914 1.079022938 0.833114361 0.932090958 1.062545518 1.062902199 1.076822958 1.04841057 1 19.0991963 2.807093582 4.143586091 1.058124419 0.898758305 0.398392198 0.105717562 0.247959044 8.378412309 0.030939028 0.032511708 641.3477592 -2.807093582 -0.159366114 RATVVESSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RATVVESSEK 10 1 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;; 158.3 1.29E-05 1093400000 924990 787090 786850 736110 956970 557174 899160 846300 1085480 FALSE TRUE 867096.5271 845366.9626 805514.4536 754999.8288 881813.4364 718021.0888 764339.3054 951962.4179 904306.3755 0.958852608 0.934823623 0.890753925 0.834893847 0.97512686 0.79400202 0.845221626 1.052699001 1 19.78645211 1.234140516 24.99998421 1.02634956 0.888956633 0.491616562 0.057405278 98.88128826 559234.8822 0.048343132 0.013708662 17.14511946 -1.234140516 -0.137392926 RAVS(ph)PSNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RAVSPSNPK 9 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 RAVS(0.916)PS(0.084)NPK;RAVS(0.999)PS(0.001)NPK;RAVS(0.999)PS(0.001)NPK;RAVS(0.999)PS(0.001)NPK;RAVS(0.994)PS(0.006)NPK;RAVS(0.717)PS(0.283)NPK 158.02 7.11E-05 9480900000 3940580 3552690 3767010 3347270 4350310 3122846 3939030 3666880 5801290 TRUE FALSE 3693946.132 3815734.864 3856365.256 3433166.615 4008654.201 4024360.945 3348409.02 4124698.04 4833017.221 0.764314705 0.789514022 0.79792086 0.710356793 0.829430978 0.832680862 0.692819592 0.853441619 1 22.2044927 0.988170098 23.46958228 1.000000002 0.776109329 0.722198372 0.044843747 130.135278 258179.2417 0.040907478 0.010226869 9.731282892 -0.988170098 -0.223890673 RAVSEGCAS(ph)EDEVEGEA ddPTM_SK-BR-3_Pertuzumab_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 220.55 4.21E-15 799590000 509620 535540 515760 458100 608790 573260 746940 537680 719940 TRUE FALSE 477723.7939 575191.9388 527994.0708 469855.6216 560978.0891 738750.8559 634943.2813 604810.5316 599777.363 0.796501874 0.959009083 0.88031677 0.783383386 0.93531054 1.231708466 1.05863162 1.008391728 1 19.19406755 2.46053542 23.30158469 1.082853157 0.874715235 0.627533186 0.07940711 68.61441942 96395.54853 0.026244458 0.021965551 288.7589277 -2.46053542 -0.208137921 RCDDLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RCDDLTR 7 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 110.12 0.027891 0 133330 187240 137070 119680 207020 113850 158470 174720 218840 FALSE TRUE 124985.1133 201103.4444 140321.3651 122751.1914 190761.4843 146716.6468 134708.8947 196534.1766 182314.1902 0.685547917 1.103059746 0.769667819 0.673294773 1.046333717 0.804746173 0.738883213 1.077997145 1 17.47606733 1.225343534 24.99962537 1.038998696 0.847432975 0.261308936 0.143035312 386.3479294 730741.3682 0.128988669 0.033020817 16.80132507 -1.225343534 -0.191565721 RCDELTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RCDELTR 7 1 P17844;P17844-2;J3KTA4;J3QSF1 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ; 120.87 0.0072048 283890000 94553 128498 120675 134047 129098 113057 121668 110295 115651 FALSE TRUE 88635.09651 138012.1256 123537.468 137486.873 118959.1638 145694.7206 103425.0129 124065.5735 96348.10097 0.919946482 1.432432235 1.282199304 1.426980621 1.23468094 1.512170132 1.073451494 1.287680528 1 16.55596861 0.848190271 0.974334027 1.00732574 1.307225082 0.176758989 0.175810596 1.062824711 2.009586031 0.148135089 0.048968127 7.050018738 -0.848190271 0.299899342 RCDIIIISGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RCDIIIISGR 10 1 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 153.54 0.0088029 0 37787 44293 42369 46897 45492 35943 43339 39579 63222 FALSE TRUE 35421.97912 47572.49981 43374.01269 48100.45642 41919.24183 46319.16061 36840.71929 44520.52527 52669.83977 0.672528705 0.903220895 0.823507588 0.913244783 0.79588702 0.879424749 0.699465186 0.845275502 1 15.68468945 -2.413774346 2.054963688 2.268583581 0.82096612 0.344073053 0.079387319 3370901.552 263041.5618 19928355.62 0.018290812 0.003856787 2.413774346 -1.447617461 RCEAFGWHAIIVDGHSVEELCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RCEAFGWHAIIVDGHSVEELCK 22 1 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 191.4 5.84E-18 750660000 243210 335700 222970 214320 508850 247520 325290 330460 542040 FALSE TRUE 227987.9202 360555.5773 228258.9537 219819.814 468886.9736 318975.0058 276515.7843 371718.6584 451570.0223 0.504878333 0.798448877 0.505478536 0.486790095 1.038348319 0.706368869 0.612343093 0.823169476 1 18.78459019 2.772928556 24.99925119 0.785061312 0.599920556 0.385935659 0.155632641 879.1804918 639514.7668 0.047182024 0.050041647 592.8277935 -2.772928556 -0.185140756 RCPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTGSQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RCPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTGSQDR 38 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 136.92 1.17E-09 201440000 114930 154020 85604 74101 252210 102580 107030 124830 74960 FALSE TRUE 107736.7365 165423.8011 87634.56731 76002.55711 232402.444 132193.1808 90981.84512 140415.3003 62448.69174 1.725204059 2.64895543 1.403305095 1.217040021 3.721494198 2.116828665 1.456905543 2.248490663 1 15.93038373 0.030775324 0.791416176 0.976377826 2.071723448 0.169774921 0.729940435 9.355496065 6.046088654 1.389239602 0.23750348 1.073433942 -0.030775324 1.095345622 RCPS(ph)QSSSRPAAMISQPPTPPTGQPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RCPSQSSSRPAAMISQPPTPPTGQPVR 27 2 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 RCPS(0.232)QS(0.232)S(0.232)S(0.232)RPAAMIS(0.073)QPPTPPTGQPVR 54.05 0.045716 128630000 56248 71110 69792 81596 91617 53064 79765 61375 69350 TRUE FALSE 52727.53809 76375.05839 71447.4992 83689.8915 84421.77039 68382.71538 67804.97875 69037.80385 57775.03698 0.912635298 1.321938719 1.236649995 1.448547606 1.461215341 1.183603143 1.173603381 1.194941751 1 15.81815866 1.024608773 1.065912996 1.009975978 1.276760014 0.205516419 0.15376031 0.784684867 1.883542292 0.138469499 0.0451212 10.58299943 -1.024608773 0.266784036 RCPS(ph)QSSSRPAAMISQPPTPPTGQPVREDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RCPSQSSSRPAAMISQPPTPPTGQPVREDAK 31 3 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 RCPS(0.587)QS(0.125)S(0.125)S(0.125)RPAAMIS(0.038)QPPTPPTGQPVREDAK 71.735 0.0030603 146630000 53158 55713 47083 64263 81342 35924 67811 43294 86488 TRUE FALSE 49830.93567 59838.04849 48199.83099 65912.09738 74953.72744 46294.67562 57643.37008 48699.3512 72052.59407 0.69159114 0.830477365 0.668953445 0.914777576 1.040264107 0.642512268 0.800017971 0.675886161 1 16.13676275 -2.359129263 2.245881179 2.386219863 0.783627434 0.231751627 0.12412753 4323418.754 636335.1886 30387923.71 0.028685234 0.004373919 2.359129263 -1.602592429 RCPSQSS(ph)SRPAAMISQPPTPPTGQPVREDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RCPSQSSSRPAAMISQPPTPPTGQPVREDAK 31 3 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 RCPS(0.277)QS(0.277)S(0.366)S(0.08)RPAAMISQPPTPPTGQPVREDAK 127.78 3.01E-05 97167000 27311 28262 28736 32636 43935 20717 30867 26314 48735 TRUE FALSE 25601.65326 30354.54789 29417.63149 33473.49501 40484.52233 26697.66159 26238.77991 29599.36082 40600.81366 0.630569955 0.747633979 0.724557683 0.824453798 0.997135739 0.657564693 0.646262415 0.729033686 1 15.30922102 -2.317754254 2.115897649 2.21350218 0.741994534 0.364137071 0.105992073 4193775.349 469639.375 24387550.86 0.026142517 0.004811115 2.317754254 -1.471507646 RCPSQSSSRPAAMIS(ph)QPPTPPTGQPVREDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RCPSQSSSRPAAMISQPPTPPTGQPVREDAK 31 3 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 RCPS(0.102)QS(0.102)S(0.102)S(0.102)RPAAMIS(0.594)QPPTPPTGQPVREDAK 63.085 0.0097571 70525000 56020 53088 50450 53614 74327 32164 63762 46574 81322 TRUE FALSE 52513.8082 57018.69076 51646.69782 54989.82601 68489.65724 41449.22466 54201.48004 52388.86642 67748.83284 0.775124914 0.841618791 0.762326016 0.811671932 1.010934866 0.611807214 0.800035628 0.773280723 1 16.04790847 -2.330679598 2.23614931 2.111096733 0.797573369 0.299534425 0.096904001 6834928.229 807628.2998 38455837.81 0.021719382 0.004670038 2.330679598 -1.313523364 RCPT(ph)PEIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RCPTPEIQK 9 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 RCPT(1)PEIQK;RCPT(1)PEIQK;RCPT(1)PEIQK;RCPT(1)PEIQK 130.1 0.00021725 2735400000 3589500 2953160 3299900 3248810 3429400 2786720 4071940 3247370 3593940 TRUE FALSE 3364839.602 3171815.039 3378175.186 3332179.965 3160068.758 3591200.825 3461390.399 3652811.293 2994088.196 1.123827817 1.059359254 1.128281789 1.112919776 1.055436096 1.199430541 1.156074962 1.220007913 1 21.51368529 2.238783345 24.99999998 1.158317349 1.096150779 0.106889203 0.062942976 9.166414434 1029037.757 0.019846456 0.015648305 173.2939277 -2.238783345 -0.06216657 RCQYVTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RCQYVTEK 8 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;P09972 H3BPS8;P04075;P09972 ALDOA;ALDOC Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase C 0 ;;;;; 194.84 0.00026176 2645930000 4462600 5253140 3893010 4333910 5689360 3086850 5163410 5118950 4099980 FALSE TRUE 4183293.832 5642087.951 3985354.036 4445125.468 5242540.615 3977973.484 4389204.605 5758062.176 3415666.851 1.224737076 1.651826187 1.166786519 1.301393157 1.534851273 1.164625725 1.285021285 1.685779798 1 21.70373584 -1.205463668 4.190715641 0.999830207 1.369351039 0.280369762 0.189413573 25.86408474 49017086.09 15503.58168 0.041081202 0.062306927 1.205463668 0.369520832 RCS(ph)DPSLNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.989)DPS(0.011)LNEK;RCS(0.98)DPS(0.02)LNEK 176.83 1.47E-06 1005190000 1689080 1489450 1515040 1535260 1582080 1116780 1827050 1324870 1828460 TRUE FALSE 1583363.498 1599730.428 1550977.464 1574657.371 1457829.819 1439176.257 1553100.814 1490282.936 1523278.214 1.039444721 1.050189265 1.018183973 1.033729332 0.95703451 0.94478884 1.019577908 0.978339296 1 20.53874803 2.757828933 23.48021871 0.981408319 1.034986768 0.614256884 0.02181223 264.4143915 322212.4595 0.006787669 0.007186444 572.5704534 -2.757828933 0.053578449 RCS(ph)QVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RCSQVK 6 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 1 RCS(1)QVK 110.41 0.017597 240220000 341730 231710 270020 219570 262100 228710 364380 319670 436590 TRUE FALSE 320341.7293 248866.0495 276425.0019 225204.5379 241515.7233 294734.8642 309744.6017 359581.5032 363720.3085 0.880736439 0.684223684 0.759993312 0.619169545 0.664014952 0.810333812 0.851601064 0.988620912 1 18.47246996 1.538531137 1.608279086 1.002888435 0.719618357 0.690934602 0.071933396 0.189857578 0.959406003 0.058094781 0.019689966 34.55661043 -1.538531137 -0.283270079 RCS(ph)SSLGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RCSSSLGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR 36 2 Q96HP0 Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 1 RCS(0.333)S(0.333)S(0.333)LGVPLT(0.002)EVVEPLDFEDVLLSRPPDAEPGPLR;RCS(0.333)S(0.333)S(0.333)LGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR 97.509 0.00015145 56810000 13220.1 18677.7 15209 15113 19396.9 11235.8 19917.8 15647.1 24509 TRUE FALSE 12392.67754 20060.61634 15569.76466 15500.82517 17873.54572 14479.39306 16931.3108 17600.67488 20418.28957 0.606940043 0.982482704 0.762540105 0.759163745 0.875369392 0.709138394 0.829222778 0.862005352 1 14.3175744 0.859420064 2.179062813 0.999538098 0.804328695 0.306628408 0.099458349 0.677722282 6.256120689 0.086818097 0.023771572 7.23469228 -0.859420064 -0.195209403 RCS(ph)VTSMESTVSSGTQTTVQDDPEQFEVIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RCSVTSMESTVSSGTQTTVQDDPEQFEVIK 30 1 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 RCS(0.999)VT(0.001)SMESTVSSGTQTTVQDDPEQFEVIK 282.32 7.40E-72 319810000 216980 195500 211570 215740 216740 191560 283730 218790 311980 TRUE FALSE 203399.6091 209975.0234 216588.5403 221276.2536 199718.1147 246860.2623 241187.3205 246106.4131 259908.5225 0.78258153 0.807880486 0.833326042 0.851362054 0.768416952 0.94979672 0.927970034 0.94689628 1 17.98764442 2.226835896 24.94734744 0.947772367 0.813894676 0.857024843 0.029797504 77.5479517 165001.9673 0.010370673 0.007721447 168.591586 -2.226835896 -0.133877692 RDDASMDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDDASMDR 8 1 A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5;H0YIX9;H7C0E9;V9GYY9 A0A0U1RRA6 R3HDM2 R3H domain-containing protein 2 0 71.379 0.05131 129360000 142840 137310 149240 153100 133690 116470 165290 132430 172600 FALSE TRUE 133899.8994 147476.5753 152780.0433 157028.8052 123190.5267 150092.9983 140506.299 148964.177 143791.945 0.931205843 1.025624734 1.062507662 1.092055645 0.856727591 1.043820628 0.97715 1.035970249 1 17.13362333 RDDGLSAAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RDDGLSAAAR 10 1 F8WBN3;B9A031;C9JQZ0;B8ZZY7;F8WBV6;P84101-4;P84101;P84101-3;P84101-2 F8WBN3 SERF2 Small EDRK-rich factor 2 0 ;;; 219.93 9.75E-09 1555380000 608891 843126 596823 578900 918992 480267 565677 713725 773125 FALSE TRUE 570781.5992 905551.9263 610979.9234 593755.5541 846818.0754 618912.2864 480858.9853 802835.1374 644085.4429 0.886189256 1.405949997 0.948600733 0.921858366 1.314760463 0.960916433 0.746576391 1.246473036 1 19.29689256 3.738594136 23.07583248 0.998538109 1.181419512 0.048748944 0.20339314 288.6402573 580542.7991 0.050000487 0.088968658 5477.648198 -3.738594136 0.182881402 RDDGTGQLLLPLSDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RDDGTGQLLLPLSDAR 16 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;;; 202.03 5.04E-11 2373650000 1644160 2099280 1955900 2136570 2166440 1736810 2237230 1918500 1927720 FALSE TRUE 1541254.961 2254712.875 2002294.872 2191398.003 1996296.541 2238198.852 1901778.131 2158028.948 1605971.078 0.959702812 1.40395609 1.246781401 1.364531425 1.243046384 1.3936732 1.184192017 1.343753307 1 20.61501448 -1.002162825 5.249361445 0.999998395 1.278602501 0.289686731 0.130584313 2.12E-06 4.03E-07 0.108787776 0.025641377 0.099503229 1.002162825 0.278604106 RDDMESLGYVLMYFNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RDDMESLGYVLMYFNR 16 1 P48729-2;A0A5F9W493;U3KPX3;A0A590UJ43;P48729;E7ETM0;P48729-3;D6REM4;H0Y9X2;U3KQK7 P48729-2 CSNK1A1 Casein kinase I isoform alpha 0 ; 137.79 1.62E-05 171988000 168558 249290 194231 202969 259630 158525 178228 214890 200740 FALSE TRUE 158008.2557 267747.691 198838.251 208177.5282 239239.7071 204288.5941 151504.366 241719.4895 167235.1972 0.944826558 1.601024757 1.188973699 1.244818864 1.430558346 1.221564584 0.905935883 1.445386459 1 17.35151899 1.994233878 24.42336545 1.095929456 1.312397676 0.096962731 0.215920935 305.3448435 1293340.125 0.075687675 0.054099961 98.68107629 -1.994233878 0.21646822 RDEFLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RDEFLGR 7 1 Q9H078-5;Q9H078-3;Q9H078-2;H0YGM0;Q9H078-4;Q9H078;A0A2R8Y602;A0A2U3TZY2 Q9H078-5 CLPB Caseinolytic peptidase B protein homolog 0 ; 126.52 0.0063237 227790000 277060 260080 268810 265780 317530 222870 291230 275030 298370 FALSE TRUE 259719.3092 279336.5938 275186.3001 272600.3648 292592.4747 287208.951 247562.7651 309368.1009 248570.1195 1.044853298 1.123773825 1.107077153 1.09667391 1.177102362 1.155444394 0.995947404 1.244590869 1 17.92329336 -1.252776252 5.108484536 0.999982964 1.111826498 0.223141169 0.068392744 1.20E-05 1.76E-06 0.059883309 0.014112482 0.055875799 1.252776252 0.111843534 RDELLAQHAAGALGLPDLVAVLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RDELLAQHAAGALGLPDLVAVLTR 24 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 170.16 5.39E-12 2843596000 482741 604302 494771 490361 550469 421383 626587 503427 370575 FALSE TRUE 452527.1025 649045.1489 506507.2018 502944.4934 507237.3852 543029.4315 532636.0963 566280.9691 308723.6385 1.465799978 2.102350024 1.640649236 1.629109115 1.643014405 1.75894996 1.725284461 1.834265014 1 18.23595643 -1.1874761 4.12796968 0.999702152 1.745861777 0.65039804 0.166402052 84.62733479 43689808.11 26976.8878 0.037172989 0.064941737 1.1874761 0.746159626 RDELTLEGIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RDELTLEGIK 10 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ;;; 216.04 1.27E-08 1478870000 2283520 2369450 2059210 2026570 2924460 1418840 2222590 2436960 2727670 FALSE TRUE 2140598.559 2544886.543 2108055.434 2078575.217 2694784.708 1828436.075 1889333.263 2741219.82 2272404.256 0.94199725 1.119909249 0.927676239 0.9147031 1.185873817 0.804626233 0.831424804 1.206308171 1 21.11578808 2.217492505 24.99991383 0.929139584 1.014906412 0.019182291 0.137483925 633.5717389 751806.3991 0.049026637 0.036242625 165.0032524 -2.217492505 0.085766827 RDEQDDDDKGDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RDEQDDDDKGDSK 13 2 Q9H4A6;D6REM1 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 0 ;;; 198.23 7.17E-08 2752950000 5824400 2104090 3281710 3079480 3028650 2096190 3971140 2495070 4366270 FALSE TRUE 5459861.201 2259879.013 3359553.711 3158504.67 2790792.046 2701326.024 3375704.423 2806584.982 3637511.33 1.500988095 0.621270646 0.923585772 0.868314731 0.767225664 0.742630271 0.928025817 0.771567351 1 21.79452031 4.749155956 24.99457445 0.822079698 1.500988477 0.789200217 0.109299979 653.967988 1542690.883 0.024222824 0.352871564 56124.94854 -4.749155956 0.678908779 RDFNHINVELSLLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDFNHINVELSLLGK 15 1 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 64.394 0.04223 73915000 105560 101890 116530 101440 135160 85236 112040 104780 128170 FALSE TRUE 98953.18803 109434.0416 119294.1466 104043.1221 124545.0788 109842.2495 95240.64213 117862.0136 106777.599 0.926722355 1.024878276 1.117220726 0.974390913 1.166397072 1.02870125 0.891953397 1.103808428 1 16.70424949 1.986294966 24.70567289 0.980018399 1.051025591 0.031878977 0.083784714 1082.948146 1952200.475 0.031182195 0.021050564 96.89357192 -1.986294966 0.071007192 RDGFVMGEGAAVLVLEEYEHAVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RDGFVMGEGAAVLVLEEYEHAVQR 24 1 Q9NWU1 Q9NWU1 OXSM "3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial" 0 ;; 136.44 1.35E-05 49460000 33911.5 33562.1 34860.4 34474 47932.9 35901.6 35120.3 37188.5 57862.1 FALSE TRUE 31789.03975 36047.07281 35687.30515 35358.6612 44168.44339 46265.80911 29854.33706 41831.56609 48204.54171 0.659461508 0.747794119 0.740330763 0.733513066 0.91627141 0.959781122 0.619326229 0.867793046 1 15.55688146 -5 0.084329325 1.684459873 0.575288529 0.392421637 0.099457987 275.6004452 1.633697015 35.28567414 2.917692449 1.00E-05 5 -1.109171343 RDGPGLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDGPGLER 8 1 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 0 83.862 0.028638 149760000 97726 119670 94888 101110 128270 94747 113530 101460 147860 FALSE TRUE 91609.50411 128530.4913 97138.78817 103704.6538 118196.1916 122098.9208 96507.23046 114127.5043 123181.2108 0.743697058 1.043426108 0.788584457 0.841886949 0.95953101 0.991213839 0.783457395 0.926500914 1 16.91042269 2.752230501 24.46091455 0.912642988 0.874934194 0.101592033 0.098344736 2578.973204 4614811.896 0.029648963 0.031279084 565.2368931 -2.752230501 -0.037708794 RDGSYGSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDGSYGSGR 9 1 Q08170;A0A0D9SEM4;A0A0D9SGD2 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 0 141.1 0.00017242 55192000 28402 50091 35434 36489 57091 34317 35007 40843 45153 FALSE TRUE 26624.36952 53799.78976 36274.51121 37425.36952 52607.30315 44223.76081 29758.02534 45942.33846 37616.6726 0.70778109 1.430211288 0.96432004 0.994914407 1.398510275 1.175642548 0.791086061 1.221329142 1 15.19908462 RDHHSTHYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RDHHSTHYR 9 1 P05060 P05060 CHGB Secretogranin-1;PE-11;GAWK peptide;CCB peptide 0 ;;;; 104.2 0.0052892 2554840000 1623030 2316480 1543050 1656800 2762400 1554620 1433260 1761540 2310820 FALSE TRUE 1521447.449 2487994.589 1579651.875 1699316.293 2545452.247 2003413.557 1218355.969 1981472.147 1925129.214 0.790309263 1.292377972 0.820543298 0.88270246 1.322224103 1.040664462 0.632869711 1.029267092 1 20.87652385 RDHRPPCAQEAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RDHRPPCAQEAPR 13 2 Q13501;Q13501-2;E7EMC7;C9JRJ8;E9PFW8;E3W990 Q13501 SQSTM1 Sequestosome-1 0 ;;; 148.52 2.21E-05 217863000 36833.4 50587.7 36427.1 37853.9 52082.3 32115.4 42886 40887.7 45064.2 FALSE TRUE 34528.06324 54333.26594 37291.16801 38825.29516 47991.96625 41386.59463 36455.64243 45992.61935 37542.69389 0.91970127 1.447239404 0.993300271 1.034163805 1.278330383 1.102387451 0.971044927 1.225075097 1 15.19624455 1.966902373 0.246797386 0.992957282 1.211485134 0.009268309 0.163324101 6.267066579 1.39002058 0.385372646 0.523216671 92.66215016 -1.966902373 0.218527852 RDIEDIPYV ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDIEDIPYV 9 1 Q96EI5;Q96EI5-2;A2RQR6 Q96EI5 TCEAL4 Transcription elongation factor A protein-like 4 0 119.29 0.0017827 0 45154 58647 50320 52018 58320 37003 52983 50903 52421 FALSE TRUE 42327.89174 62989.2849 51513.61416 53352.86995 53739.78245 47685.16541 45038.69102 57258.3516 43671.59645 0.96923161 1.442339874 1.17956792 1.221683526 1.230543118 1.091903417 1.031303975 1.311111941 1 15.41440765 2.248550699 10.98168484 1.101917681 1.237203657 0.09251147 0.140131986 0.452376817 472.9086233 0.046107156 0.03731312 177.2354937 -2.248550699 0.135285977 RDINVSVGSQQPDTKDS(ph)PVCPHFTTNGNENSSIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDINVSVGSQQPDTKDSPVCPHFTTNGNENSSIEK 35 2 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 RDINVSVGSQQPDT(0.005)KDS(0.995)PVCPHFTTNGNENSSIEK 109.99 7.10E-06 382640000 108230 67398 80722 96093 101400 60960 131280 80198 91596 TRUE FALSE 101456.0775 72388.21805 82636.76396 98558.90907 93436.45303 78558.1624 111595.7827 90210.89684 76308.03587 1.329559546 0.948631651 1.082936587 1.291592792 1.224464134 1.029487412 1.462438149 1.18219393 1 16.21954737 3.257129021 23.57531602 1.227059973 1.078224954 0.008085974 0.160611307 218.9773703 278020.3996 0.041699778 0.056337074 1807.711086 -3.257129021 -0.148835019 RDLEIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDLEIER 7 1 Q92597;Q92597-3;Q92597-2;Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q92597;Q5TH30 NDRG1;NDRG3 Protein NDRG1;Protein NDRG3 0 116.05 0.0088873 87105000 54583 78619 49333 56856 73623 39788 54638 57596 30653 FALSE TRUE 51166.74746 84440.03256 50503.20206 58315.02122 67840.94656 51274.1497 46445.53913 64786.98738 25536.81627 2.003646301 3.306599838 1.977662427 2.28356662 2.656593752 2.007852081 1.818767799 2.537003309 1 14.64029105 -0.932031303 0.194409297 1.53E-14 2.794847275 0.471405869 0.437505537 15.11772622 0.674096459 9.903947309 1.365258984 0.11694151 0.932031303 2.794847275 RDNYVPEVSALDQEIIEVDPDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RDNYVPEVSALDQEIIEVDPDTK 23 1 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ;;;;; 206.46 2.19E-24 1007017000 1497700 1139760 1241620 1275240 1259130 1010500 1552440 1014770 1326690 FALSE TRUE 1403961.63 1224149.016 1271071.813 1307964.817 1160243.009 1302214.946 1319666.034 1141466.268 1105256.868 1.270258228 1.107569698 1.150023899 1.183403474 1.049749648 1.17820118 1.193990349 1.032761072 1 20.07595027 -4.999999998 0.17035968 0.412079231 1.182444126 0.410624192 0.064047398 146.0593375 1.379803442 28.85759115 0.218951196 1.00E-05 4.999999998 0.770364894 RDPEVGKDELSKPS(ph)SDAESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDPEVGKDELSKPSSDAESR 20 3 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 RDPEVGKDELS(0.026)KPS(0.487)S(0.487)DAESR 102.73 0.0016339 380280000 486980 244340 307320 317350 359670 226190 410430 273520 349370 TRUE FALSE 456500.7911 262431.1878 314609.7755 325493.7383 331422.969 291487.3811 348889.8317 307669.5741 291057.89 1.568419228 0.901646019 1.080918217 1.118312712 1.138684023 1.001475621 1.198695668 1.057073471 1 18.1509466 4.750559208 24.89057658 1.06742392 1.568419549 0.78712425 0.082708775 861.066673 1786212.253 0.020329676 0.342674423 56306.58753 -4.750559208 0.50099563 RDPEVGKDELSKPSSDAESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RDPEVGKDELSKPSSDAESR 20 3 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 ; 128.55 8.55E-06 904680000 829260 491810 636390 548490 691760 456700 752270 558040 694640 FALSE TRUE 777358.0969 528224.1241 651485.4713 562565.182 637431.96 588541.8761 639474.0972 627712.5224 578700.0965 1.343283165 0.912776976 1.125773912 0.972118694 1.101489293 1.017006701 1.105018128 1.084694 1 19.14245636 4.755055374 24.99941749 1.04474036 1.343283395 0.668561808 0.0670619 1938.945302 2938613.105 0.014807728 0.402546981 56892.54656 -4.755055374 0.298543035 RDPHLACVAYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 85.837 0.0074322 905560000 309500 496860 340600 384180 561680 301230 529180 452790 611220 FALSE TRUE 290128.9475 533648.0314 348679.1928 394038.7092 517567.9185 388190.2109 449834.3717 509321.8282 509203.4334 0.569770211 1.048005564 0.684754206 0.773833567 1.016426608 0.762347984 0.883407971 1.00023251 1 18.95788262 1.34502533 3.410353772 1.003312773 0.828628436 0.227850426 0.140940622 0.372158521 7.028984231 0.104247573 0.033196833 22.13223791 -1.34502533 -0.174684337 RDPMYNEYLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDPMYNEYLDR 11 1 Q7L5D6;Q7L5D6-2 Q7L5D6 GET4 Golgi to ER traffic protein 4 homolog 0 136.01 0.00017324 102660000 109110 197450 154940 151200 201200 129580 143040 167080 201870 FALSE TRUE 102280.9999 212069.4034 158615.25 155080.048 185398.5636 166987.6424 121592.4799 187940.3058 168176.5929 0.608176192 1.260992388 0.943147006 0.922126233 1.102404089 0.992930345 0.723004776 1.11751762 1 17.3596174 1.965783215 24.82952528 0.901539551 1.005850747 0 0.191984392 1714.428565 1244078.491 0.072931321 0.047089157 92.42367111 -1.965783215 0.104311196 RDPSEEIEILLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RDPSEEIEILLR 12 1 E9PGT3;Q15418-4;Q15418;Q15418-2;Q15418-3;Q5SVM6;B7Z3B5;F2Z2J1;Q15349;Q15349-3;Q15349-2 E9PGT3 RPS6KA1;RPS6KA2 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1;Ribosomal protein S6 kinase alpha-2 0 ;; 179.5 3.31E-05 110876000 94989 109557 103814 105177 108493 91569 118717 96268 102207 FALSE TRUE 89043.80805 117668.7143 106276.5171 107876.0199 99972.39742 118003.4838 100916.488 108287.2717 85147.99142 1.045753477 1.381931767 1.248138862 1.266923836 1.174101652 1.385863387 1.185189296 1.271753683 1 16.37768488 -0.685997937 0.775880644 0.975221342 1.259380815 0.364600335 0.099927898 25.00076541 9.152217454 1.794494198 0.029955285 0.20606397 0.685997937 0.284159473 RDPSSNDINGGMEPTPSTVS(ph)TPS(ph)PSADLLGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDPSSNDINGGMEPTPSTVSTPSPSADLLGLR 32 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 2 RDPSSNDINGGMEPTPS(0.005)T(0.006)VS(0.823)T(0.179)PS(0.98)PS(0.007)ADLLGLR 115.41 7.04E-06 45257000 53245 52452 56422 55517 66495 58139 67942 52563 79071 TRUE FALSE 49912.4905 56335.60066 57760.35648 56941.66021 61272.75093 74922.78549 57754.72784 59125.60626 65873.53928 0.757701667 0.855208347 0.876836999 0.864408696 0.930157262 1.137373008 0.876751553 0.897562313 1 16.00741145 2.695125081 3.65698151 0.970461058 0.846310452 0.422885801 0.076320137 0.253287511 7.102011785 0.024841739 0.02405029 495.5929053 -2.695125081 -0.124150607 RDPSSNDINGGMEPTPSTVS(ph)TPSPSADLLGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RDPSSNDINGGMEPTPSTVSTPSPSADLLGLR 32 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 1 RDPSSNDINGGMEPTPST(0.001)VS(0.561)T(0.069)PS(0.367)PS(0.002)ADLLGLR;RDPSSNDINGGMEPT(0.007)PS(0.035)T(0.035)VS(0.659)T(0.116)PS(0.143)PS(0.005)ADLLGLR;RDPSSNDINGGMEPT(0.001)PS(0.048)T(0.048)VS(0.691)T(0.121)PS(0.083)PS(0.007)ADLLGLR;RDPSSNDINGGMEPTPS(0.002)T(0.022)VS(0.512)T(0.328)PS(0.136)PSADLLGLR 218.37 4.68E-36 1152842000 212384 222661 232973 245785 236069 213610 302983 228321 305877 TRUE FALSE 199091.2646 239147.0521 238499.2296 252092.2592 217529.093 275275.7393 257553.5119 256827.3794 254824.1527 0.781288832 0.938478749 0.935936516 0.989279299 0.853643937 1.080257646 1.010710756 1.007861212 1 17.9591425 6.703275719 0.377544874 1.01188866 1.20E-14 0.535454984 0.058309944 20.21520134 0.692666966 0.042642761 12.59904796 5049817.923 -6.703275719 -1.01188866 RDPSSNDINGGMEPTPSTVSTPS(ph)PSADLLGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 RDPSSNDINGGMEPTPSTVSTPSPSADLLGLR 32 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 1 RDPSSNDINGGMEPTPSTVS(0.001)T(0.003)PS(0.996)PSADLLGLR;RDPSSNDINGGMEPTPSTVS(0.075)T(0.142)PS(0.777)PS(0.005)ADLLGLR;RDPSSNDINGGMEPTPST(0.001)VS(0.013)T(0.007)PS(0.979)PS(0.001)ADLLGLR;RDPSSNDINGGMEPTPS(0.001)T(0.001)VS(0.227)T(0.176)PS(0.594)PS(0.002)ADLLGLR;RDPSSNDINGGMEPTPSTVSTPS(0.998)PS(0.002)ADLLGLR;RDPSSNDINGGMEPTPSTVS(0.165)T(0.165)PS(0.638)PS(0.032)ADLLGLR;RDPSSNDINGGMEPTPS(0.001)T(0.001)VS(0.013)T(0.018)PS(0.967)PSADLLGLR;RDPSSNDINGGMEPTPSTVS(0.006)T(0.003)PS(0.99)PS(0.001)ADLLGLR;RDPSSNDINGGMEPTPS(0.001)T(0.005)VS(0.436)T(0.006)PS(0.552)PSADLLGLR;RDPSSNDINGGMEPTPSTVS(0.001)T(0.001)PS(0.996)PS(0.002)ADLLGLR 309.49 3.44E-104 9166600000 1218541 1379700 1407388 1371782 1409814 1309346 1702453 1391696 1833510 TRUE FALSE 1142274.694 1481854.424 1440771.908 1406984.249 1299092.895 1687332.935 1447185.977 1565452.309 1527485.336 0.747813853 0.970126775 0.943231253 0.92111146 0.850478145 1.10464755 0.947430357 1.024855867 1 20.5427271 2.251559173 24.99851782 1.010835804 0.907248642 0.437311248 0.072432218 256.4742477 493244.8646 0.023889216 0.019870664 178.4675135 -2.251559173 -0.103587161 RDPTEEIEILLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RDPTEEIEILLR 12 1 B4DG22;B1AXG1;B7ZB17;P51812;A0A2R8Y603 B4DG22 RPS6KA3 Ribosomal protein S6 kinase alpha-3 0 ; 156.81 0.00010722 34036000 35803 44214 45215 42457 43697 32195 44823 39548 47325 FALSE TRUE 33562.15414 47487.65056 46287.52115 43546.5185 40265.21389 41489.17386 38102.20727 44485.65486 39426.15177 0.851266295 1.204470851 1.174030918 1.104508468 1.021281867 1.052326235 0.966419637 1.128328606 1 15.26686528 2.793938567 4.792335458 1.027606992 1.119968623 0.001994289 0.104168351 0.404087238 20.00831761 0.031079324 0.03260122 622.2122641 -2.793938567 0.092361631 RDPYGFGDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDPYGFGDSR 10 1 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 0 86.014 0.022202 303760000 254890 347410 317500 300530 347170 285380 346540 318960 404070 FALSE TRUE 238936.8899 373132.5979 325031.2499 308242.1086 319904.6686 367764.5732 294579.5441 358782.8581 336628.1066 0.709794831 1.108441602 0.965549945 0.915675496 0.950320732 1.092495148 0.875088973 1.065813731 1 18.36079611 4.754183284 24.41218159 0.991945624 0.70979454 0.588132655 0.075354624 1546.401207 2416370.343 0.017219048 0.415189523 56778.41748 -4.754183284 -0.282151084 RDQALTEEHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RDQALTEEHAR 11 1 P12814-3;P12814;P12814-2;P12814-4;H9KV75;H0YJ11 P12814-3 ACTN1 Alpha-actinin-1 0 ; 174.9 6.79E-06 260270000 336510 320600 301180 278220 257930 231920 310170 316210 349170 FALSE TRUE 315448.4398 344337.5576 308324.1318 285359.5962 237673.2182 298871.5391 263662.888 355689.5146 290891.2713 1.084420438 1.183732864 1.059929129 0.980983702 0.817051736 1.027433851 0.906396699 1.222757606 1 18.15012048 3.48540126 2.676233696 0.977098657 1.135533543 0.228907689 0.10495165 0.314975018 4.524478503 0.028068265 0.044097595 3057.744967 -3.48540126 0.158434885 RDRS(ph)PIRGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RDRSPIRGSPR 11 3 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 2 RDRS(1)PIRGS(1)PR;RDRS(1)PIRGS(1)PR 88.768 0.018278 1023690000 462250 512800 514780 512330 621090 513620 543130 505070 629880 TRUE FALSE 433318.5976 550768.2456 526990.8247 525477.2552 572312.0968 661893.7561 461692.6987 568129.1013 524748.9588 0.825763616 1.049584256 1.004272264 1.001387895 1.090639795 1.261353157 0.879835378 1.082668373 1 19.00126787 4.739935844 24.21355606 1.041319255 0.825763512 0.340294181 0.096250144 91.12194151 1604110.2 0.02167286 0.136312596 54945.96991 -4.739935844 -0.215555743 RDS(ph)ASYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RDSASYR 7 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 1 RDS(0.998)AS(0.002)YR;RDS(1)ASYR;RDS(1)ASYR;RDS(1)ASYR;RDS(0.999)AS(0.001)YR 150.06 0.0012091 1699656000 338255 313401 343229 346967 423882 336808 387814 304051 462930 TRUE FALSE 317084.2234 336605.5361 351370.554 355870.7606 390592.0176 434039.002 329664.891 342012.4366 385663.9924 0.822177413 0.872794823 0.911079491 0.922748215 1.012778028 1.125433047 0.854798212 0.886814542 1 18.55698493 3.724062361 1.167944131 0.966682476 0.84136695 0.313692124 0.074410643 0.729772195 1.904601742 0.025753172 0.072171047 5297.395051 -3.724062361 -0.125315526 RDS(ph)DGVDGFEAEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RDSDGVDGFEAEGK 14 1 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 RDS(1)DGVDGFEAEGK;RDS(1)DGVDGFEAEGK;RDS(1)DGVDGFEAEGK;RDS(1)DGVDGFEAEGK;RDS(1)DGVDGFEAEGK 247.44 8.40E-18 900860000 2804000 1728860 2065370 2038110 2074120 1467290 2129330 1619940 2482730 TRUE FALSE 2628502.645 1856866.593 2114361.552 2090411.353 1911226.982 1890872.804 1810056.734 1822193.075 2068346.324 1.270823273 0.897754197 1.022247352 1.010667957 0.92403625 0.914195452 0.875122659 0.880990313 1 20.98004634 2.708257295 2.576750099 0.904242807 1.022745733 0.283867654 0.098796137 0.409985453 5.396793148 0.032347142 0.031632574 510.8075347 -2.708257295 0.118502926 RDS(ph)DGVDGFEAEGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDSDGVDGFEAEGKK 15 2 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 RDS(1)DGVDGFEAEGKK 130 4.92E-05 306660000 839230 411290 547880 530830 592410 380980 629300 426420 945600 TRUE FALSE 786704.0924 441742.3395 560875.9723 544451.9965 545884.5083 490962.7413 534942.3071 479659.4757 787773.2512 0.998642809 0.560748082 0.711976411 0.691127803 0.692946235 0.6232285 0.679056196 0.608880125 1 19.58742091 -1.603207868 5.018569057 1.003249076 0.681515257 0.392062436 0.117843965 0.003752746 0.00029671 0.099952487 0.023354127 0.02493401 1.603207868 -0.32173382 RDS(ph)DTYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RDSDTYR 7 1 H3BUL5;H3BVF8;P49761-3;P49761-1;P49761;H3BRT8;H3BQR7;H3BV35;H3BRK0;H3BQG1;P49761-2 H3BUL5 CLK3 Dual specificity protein kinase CLK3 1 RDS(0.923)DT(0.077)YR;RDS(0.995)DT(0.005)YR 94.465 0.0086857 468890000 257190 179339 223051 219577 191615 180904 232918 194381 206455 TRUE FALSE 241092.937 192617.4462 228341.8751 225211.7176 176566.3308 233128.0481 197994.1082 218649.8957 171996.3267 1.401733058 1.11989279 1.327597393 1.309398415 1.026570359 1.355424575 1.15115312 1.271247473 1 17.39201823 -4.456473757 0.240937146 1.35E-16 1.260868152 0.314789403 0.115132631 155.8987721 1.979854906 76.2566104 0.161289013 3.50E-05 4.456473757 1.260868152 RDS(ph)FDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDSFDDR 7 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RDS(1)FDDR 123.96 0.0049924 0 940840 816440 807070 834330 840800 857310 920620 760680 860100 TRUE FALSE 881954.5038 876890.0671 826214.0815 855740.3203 774766.9596 1104801.48 782581.5776 855652.5725 716543.7535 1.23084529 1.223777422 1.153054615 1.194261085 1.081255619 1.541847897 1.092161607 1.194138625 1 19.45069528 0.721700839 1.659881894 1.001202647 1.216516569 0.225109946 0.126379126 1.485974219 6.400875052 0.108721829 0.031021375 5.268668075 -0.721700839 0.215313921 RDS(ph)FDDRGPSLNPVLDYDHGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 RDSFDDRGPSLNPVLDYDHGSR 22 2 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(0.987)FDDRGPS(0.013)LNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(0.986)FDDRGPS(0.014)LNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(0.989)FDDRGPS(0.011)LNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(0.999)FDDRGPS(0.001)LNPVLDYDHGSR;RDS(0.994)FDDRGPS(0.006)LNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR 301.65 3.78E-56 24229870000 2405950 3625107 3292030 3703735 4369284 3125781 3862995 3302704 5734537 TRUE FALSE 2255365.884 3893513.694 3370118.506 3798779.111 4026138.059 4028143.232 3283774.762 3715053.865 4777405.728 0.472090087 0.814984934 0.705428573 0.795155222 0.842745684 0.843165404 0.687355219 0.777629968 1 22.18779597 -4.999999994 0.033648098 2.140694887 4.40E-08 0.476540026 0.09825996 1225.09558 3.095671001 161.8314736 58.84288426 1.00E-05 4.999999994 -2.140694843 RDS(ph)FDNCSLGESSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RDSFDNCSLGESSK 14 1 Q5UIP0-2;Q5UIP0 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 RDS(1)FDNCSLGESSK;RDS(1)FDNCSLGESSK;RDS(1)FDNCSLGESSK 217.76 3.45E-12 1019940000 1708890 1340160 1303280 1279790 934630 758890 2201710 909640 1650510 TRUE FALSE 1601933.625 1439386.841 1334194.417 1312631.578 861227.9299 977969.2235 1871584.025 1023210.556 1375029.218 1.16501788 1.046804549 0.970302594 0.954620862 0.626334276 0.711235231 1.361123095 0.744137319 1 20.39103084 4.43602952 1.173802524 0.92806331 1.198894721 0.149005944 0.202016908 2.283553315 3.805426173 0.062082125 0.66589516 27291.63286 -4.43602952 0.27083141 RDS(ph)FIGTPYWMAPEVVMCETMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RDSFIGTPYWMAPEVVMCETMK 22 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 RDS(1)FIGTPYWMAPEVVMCETMK;RDS(1)FIGTPYWMAPEVVMCETMK;RDS(0.343)FIGT(0.343)PY(0.313)WMAPEVVMCETMK;RDS(1)FIGTPYWMAPEVVMCETMK;RDS(1)FIGTPYWMAPEVVMCETMK;RDS(0.809)FIGT(0.102)PY(0.088)WMAPEVVMCETMK 287.2 1.61E-46 1181882700 1464196 1101842 1183942 1030734 1328777 901997 1729417 1172025 1353580 TRUE FALSE 1372554.586 1183423.528 1212025.663 1057184.379 1224420.214 1162388.891 1470106.976 1318354.901 1127658.754 1.217171934 1.049451817 1.074815993 0.937503811 1.085807396 1.030798446 1.30368072 1.169108028 1 20.10489912 1.76622105 25 1.188924431 1.060875407 0.131240176 0.10041822 24.55552444 22207.13639 0.042026648 0.023308068 58.37421452 -1.76622105 -0.128049025 RDS(ph)FIGTPYWMAPEVVMCETSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 RDSFIGTPYWMAPEVVMCETSK 22 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 RDS(1)FIGTPYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(0.993)FIGT(0.007)PYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(0.999)FIGT(0.001)PYWMAPEVVMCETSK;RDS(0.996)FIGT(0.004)PYWMAPEVVMCETSK;RDS(0.989)FIGT(0.009)PY(0.001)WMAPEVVMCETSK 336.19 3.63E-81 3329786000 2833044 2245306 2292646 2218044 2816001 1836194 3760224 2362229 4066454 TRUE FALSE 2655728.833 2411550.792 2347028.646 2274962.764 2594843.641 2366273.4 3196413.319 2657158.491 3387736.557 0.783924248 0.711847203 0.692801405 0.671528829 0.765952015 0.698482116 0.943524759 0.784346258 1 21.69189026 1.473644609 0.860678935 0.972407393 0.707568929 0.624024944 0.066517619 0.309765999 0.471332763 0.05578363 0.021956116 29.76080055 -1.473644609 -0.264838465 RDS(ph)GDNSAPSGQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RDSGDNSAPSGQER 14 1 Q8IXQ3 Q8IXQ3 C9orf40 Uncharacterized protein C9orf40 1 RDS(1)GDNSAPSGQER;RDS(1)GDNSAPSGQER;RDS(1)GDNSAPSGQER;RDS(1)GDNSAPSGQER;RDS(0.99)GDNS(0.01)APSGQER;RDS(1)GDNSAPSGQER;RDS(1)GDNSAPSGQER 211.11 2.63E-09 1821187000 790880 698113 746850 698018 708681 615132 766945 609964 697089 TRUE FALSE 741380.2326 749802.0129 764565.6347 715930.3236 653024.0529 792710.6226 651948.7172 686119.3481 580740.3425 1.276612245 1.291114045 1.316536116 1.23278903 1.124468209 1.365000095 1.122616546 1.18145632 1 19.14753373 0.485441447 0.291619955 0.940597231 1.316091504 0.598007378 0.069044866 2.22066166 0.408631011 0.261227521 0.09256907 3.058027923 -0.485441447 0.375494274 RDS(ph)GDNSAPSGQEREDHGLETGDPPLPPPPVLPGPGEELPGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDSGDNSAPSGQEREDHGLETGDPPLPPPPVLPGPGEELPGAR 43 2 Q8IXQ3 Q8IXQ3 C9orf40 Uncharacterized protein C9orf40 1 RDS(0.25)GDNS(0.25)APS(0.25)GQEREDHGLET(0.25)GDPPLPPPPVLPGPGEELPGAR 47.871 0.014595 29920000 10501 20538 13350 19570 24775 7187.2 14960 17307 60689 TRUE FALSE 9843.761155 22058.65489 13666.6683 20072.19933 22829.27144 9262.027966 12716.88688 19467.81705 50559.61383 0.19469613 0.436290019 0.270308004 0.397000646 0.45153176 0.183190243 0.251522627 0.385046791 1 15.62569782 0.917758165 11.69762046 0.999999998 0.317951244 0.841235859 0.093173461 9.540759992 1357.404124 0.087167734 0.021796513 8.274812555 -0.917758165 -0.682048754 RDS(ph)GVGASLTRPNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RDSGVGASLTRPNR 14 2 H3BRG5;Q9Y3M8-5;Q9Y3M8-3;Q9Y3M8-4;Q9Y3M8-2;Q9Y3M8 H3BRG5;Q9Y3M8-3 STARD13 StAR-related lipid transfer protein 13 1 RDS(0.998)GVGAS(0.001)LTRPNR;RDS(0.774)GVGAS(0.16)LT(0.066)RPNR;RDS(0.759)GVGAS(0.199)LT(0.042)RPNR 116.96 0.00026073 533900000 418780 325121 389270 351564 388507 316654 432390 349532 444487 TRUE FALSE 392569.3073 349193.2971 398503.6682 360585.7274 357995.2274 408066.8694 367557.1336 393171.8396 370299.2482 1.060140708 0.943002987 1.07616656 0.973768457 0.966772763 1.101992163 0.992594869 1.061767858 1 18.49833209 2.291161522 24.99999964 1.035827314 1.004128797 0.106715483 0.050092975 239.6969368 113921.1211 0.016016461 0.013400318 195.5066445 -2.291161522 -0.031698517 RDS(ph)IVAELDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RDSIVAELDR 10 1 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 1 RDS(1)IVAELDR;RDS(1)IVAELDR;RDS(1)IVAELDR;RDS(1)IVAELDR 134 0.00011162 2480070000 1202400 1241520 1155040 1282160 1379890 968470 1438160 1198600 1619070 TRUE FALSE 1127143.93 1333443.433 1182438.094 1315062.396 1271519.006 1248051.567 1222521.259 1348247.848 1348836.757 0.83564147 0.988587704 0.876635433 0.974960379 0.942678199 0.92527992 0.906352272 0.999563395 1 20.36328433 -4.999999999 0.10828546 1.233145251 0.887569179 0.266976953 0.046877553 262.8346751 1.901444984 13.49626766 0.566054575 1.00E-05 4.999999999 -0.345576072 RDS(ph)IVAELDREMSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RDSIVAELDREMSR 14 2 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 1 RDS(1)IVAELDREMSR;RDS(1)IVAELDREMSR;RDS(0.998)IVAELDREMS(0.002)R 130.01 5.08E-05 83868000 18246.3 33678.5 31153.1 36971.1 55071.6 25194.5 33178.7 28784.3 98226.2 TRUE FALSE 17104.29665 36172.09118 31892.06624 37919.84102 50746.49868 32467.74315 28203.86195 32378.08322 81831.61265 0.209018203 0.442030775 0.389727945 0.463388656 0.620133186 0.396762841 0.344657291 0.395667178 1 16.32037066 -1.997884233 3.077844009 1.579580996 0.411659548 0.769137908 0.101964618 29563028.93 38078918.79 121338278.2 0.023647968 0.010048836 1.997884233 -1.167921448 RDS(ph)LASLFPSEEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RDSLASLFPSEEEER 15 1 Q6P597;Q6P597-3;Q6P597-2;K7ENJ3;K7EL76 Q6P597 KLC3 Kinesin light chain 3 1 RDS(1)LASLFPSEEEER;RDS(1)LASLFPSEEEER 194.08 4.08E-08 216230000 139037 124947 135633 131835 131778 114423 166506 130771 116329 TRUE FALSE 130334.9224 134198.2059 138850.2788 135218.1093 121428.6874 147455.0626 141539.9711 147098.0472 96912.93839 1.344866068 1.384729512 1.432732111 1.395253426 1.252966729 1.521520914 1.460485807 1.517837037 1 16.56440167 2.218315489 24.99956478 1.422250356 1.376330909 0 0.155837257 1248.264894 1541401.029 0.051428069 0.03802452 165.3162286 -2.218315489 -0.045919447 RDS(ph)LDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RDSLDK 6 1 Q96C24-2;Q96C24 Q96C24-2 SYTL4 Synaptotagmin-like protein 4 1 RDS(1)LDK;RDS(1)LDK;RDS(1)LDK;RDS(1)LDK 108.57 0.018559 1448290000 2109880 1222060 1559180 1410060 1478500 1144019 1808030 1373700 1379420 TRUE FALSE 1977826.377 1312542.594 1596164.486 1446244.527 1362384.574 1474278.714 1536932.686 1545209.469 1149185.891 1.721067404 1.142149938 1.388952387 1.258494852 1.185521494 1.282889675 1.337409986 1.344612287 1 20.13218075 -4.317103044 0.205355454 3.47E-30 1.362406808 0.326892847 0.154331522 136.7385198 1.753069018 57.47209584 0.323279358 4.82E-05 4.317103044 1.362406808 RDS(ph)LDKSGLFPEWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RDSLDKSGLFPEWK 14 2 Q96C24-2;Q96C24 Q96C24-2 SYTL4 Synaptotagmin-like protein 4 1 RDS(0.999)LDKS(0.001)GLFPEWK;RDS(0.843)LDKS(0.157)GLFPEWK;RDS(0.85)LDKS(0.15)GLFPEWK 227.25 1.65E-12 1048815000 949740 686930 717773 754047 898795 455726 969377 649496 1278860 TRUE FALSE 890297.4687 737791.012 734798.9145 773397.1226 828207.2663 587286.6981 824027.9181 730587.0053 1065410.004 0.83563836 0.692494917 0.689686517 0.725915018 0.777360136 0.551230696 0.773437376 0.685733194 1 20.0229773 -1.334754694 5.078252182 1.000120851 0.711242988 0.582849336 0.075277229 9.06E-05 1.19E-05 0.064125534 0.015108241 0.046264227 1.334754694 -0.288877862 RDS(ph)LEEGELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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;RDS(1)LEEGELR;RDS(1)LEEGELR 202.25 1.39E-07 2886540000 2301370 1882180 1966610 1918740 1852130 1854360 2340040 1852760 1823070 TRUE FALSE 2157331.36 2021538.566 2013258.918 1967978.117 1706671.181 2389683.629 1989172.726 2084081.164 1518787.84 1.420429703 1.331021037 1.325569553 1.295755777 1.123706114 1.57341504 1.309710727 1.372200323 1 20.53448892 -1.692198422 2.433039312 0.939210832 1.341084948 0.484400407 0.111492739 6714890.229 5107296.977 2507476.58 0.025344484 0.020314287 1.692198422 0.401874117 RDS(ph)LGAYASQDANEQGQDLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RDSLGAYASQDANEQGQDLGK 21 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RDS(1)LGAYASQDANEQGQDLGK;RDS(1)LGAYASQDANEQGQDLGK;RDS(1)LGAYASQDANEQGQDLGK;RDS(1)LGAYASQDANEQGQDLGK 389.52 2.26E-131 3498340000 3652680 2253490 2873220 2558330 2571040 2389230 3687530 2625160 2156980 TRUE FALSE 3424065.279 2420340.744 2941374.135 2623981.079 2369120.889 3078961.915 3134619.11 2952917.005 1796966.103 1.905470155 1.346903951 1.636855659 1.460228478 1.318400433 1.713422367 1.744395236 1.643279191 1 20.77713176 -1.372190304 5.863215728 0.999878587 1.58244155 0.516300745 0.180900915 0.000278253 2.98E-05 0.169754147 0.040003206 0.042443354 1.372190304 0.582562963 RDS(ph)LGAYASQDANEQGQDLGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RDSLGAYASQDANEQGQDLGKR 22 2 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RDS(0.999)LGAYAS(0.001)QDANEQGQDLGKR;RDS(0.993)LGAYAS(0.007)QDANEQGQDLGKR;RDS(0.997)LGAYAS(0.003)QDANEQGQDLGKR;RDS(1)LGAYASQDANEQGQDLGKR 213.54 6.09E-24 4369370000 1596050 1215100 1336490 1215740 1413990 1058850 1701100 1200380 1508270 TRUE FALSE 1496156.08 1305067.268 1368192.174 1246937.947 1302940.929 1364522.806 1446035.847 1350250.085 1256529.993 1.190704629 1.038628027 1.088865512 0.992366241 1.036935796 1.085945273 1.150816817 1.074586435 1 20.26101368 2.010052082 23.72957969 1.098514143 1.064176181 0 0.063406595 333.6695128 787675.2305 0.022121836 0.016316619 102.3415717 -2.010052082 -0.034337962 RDS(ph)LGTYSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RDSLGTYSSR 10 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RDS(0.698)LGT(0.142)YS(0.142)S(0.017)R;RDS(1)LGTYSSR;RDS(1)LGTYSSR;RDS(1)LGTYSSR;RDS(1)LGTYSSR;RDS(1)LGTYSSR 185.95 8.54E-07 6181640000 1122783 1259272 1260361 1208767 1203540 1088423 1281817 1093166 1131064 TRUE FALSE 1052510.016 1352509.809 1290257.358 1239786.008 1109018.823 1402633.051 1089620.441 1229650.181 942282.1114 1.116979728 1.435355498 1.369289879 1.315726992 1.176949886 1.488548954 1.156363288 1.304970313 1 19.84579953 0.138598376 0.520916399 0.975308091 1.334922347 0.359006396 0.121033565 3.218290625 1.182889302 0.28016146 0.053059463 1.375936451 -0.138598376 0.359614256 RDS(ph)LTGSSDLYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RDSLTGSSDLYK 12 1 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;Q14671-4;E9PR38;H0YDK8 Q5T1Z4 PUM1 Pumilio homolog 1 1 RDS(0.633)LT(0.34)GS(0.009)S(0.019)DLYK;RDS(0.982)LT(0.017)GSSDLYK;RDS(1)LTGSSDLYK;RDS(0.994)LT(0.006)GSSDLYK;RDS(0.898)LT(0.1)GS(0.001)S(0.001)DLYK 220.24 1.84E-11 4209760000 8089990 5664660 6278130 5756070 6842100 4854210 7910650 6549710 7573450 TRUE FALSE 7583651.967 6084077.32 6427050.208 5903780.501 6304749.066 6255541.625 6724521.471 7367455.711 6309392.269 1.201962351 0.964288962 1.018648062 0.935713021 0.999264081 0.991465003 1.065795434 1.16769657 1 22.58906962 1.58789718 4.874107289 1.09339183 1.008696543 0.096538004 0.081308237 0.252837259 13.06096942 0.041902148 0.01905393 38.7165972 -1.58789718 -0.084695287 RDS(ph)LTGSSDLYKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RDSLTGSSDLYKR 13 2 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;Q14671-4;E9PR38;H0YDK8 Q5T1Z4 PUM1 Pumilio homolog 1 1 RDS(0.935)LT(0.043)GS(0.016)S(0.006)DLYKR;RDS(0.999)LT(0.001)GSSDLYKR;RDS(0.838)LT(0.071)GS(0.071)S(0.021)DLYKR;RDS(0.742)LT(0.089)GS(0.07)S(0.099)DLYKR;RDS(0.831)LT(0.137)GS(0.017)S(0.015)DLYKR 147.49 2.23E-05 4232640000 2090520 1834110 1847800 1895950 2420720 1467030 2585970 1854320 3824500 TRUE FALSE 1959678.085 1969909.413 1891630.689 1944603.287 2230606.416 1890537.746 2198227.805 2085835.934 3186166.243 0.615058329 0.618269501 0.59370119 0.610327001 0.700091033 0.593358162 0.689928785 0.65465383 1 21.60339011 -5 0.25346503 3.302788502 0.599666424 0.927935601 0.032407101 40.41615975 0.399689085 48.2266244 0.040457167 1.00E-05 5 -2.703122078 RDS(ph)PPPPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RDSPPPPAR 9 1 O96013;O96013-4;O96013-2;M0R2X4 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 RDS(1)PPPPAR;RDS(1)PPPPAR;RDS(1)PPPPAR;RDS(1)PPPPAR;RDS(1)PPPPAR;RDS(1)PPPPAR 108.72 0.0015718 9043360000 2620920 2474250 2500040 2660809 2478420 2186213 2966520 2412799 2459980 TRUE FALSE 2456881.296 2657446.044 2559342.129 2729089.864 2283774.891 2817337.203 2521717.866 2714042.266 2049393.446 1.198833392 1.296698811 1.248829079 1.331657359 1.114366251 1.374717582 1.230470348 1.324314895 1 20.96676555 -1.174945481 4.149543231 0.999900301 1.26612563 0.557477289 0.074189662 5.79E-05 1.15E-05 0.060386065 0.014227781 0.066842782 1.174945481 0.266225329 RDS(ph)PRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDSPRK 6 2 Q8N8S7 Q8N8S7 ENAH Protein enabled homolog 1 RDS(1)PRK 69.598 0.073305 90713000 82079 49997 83137 66817 64512 54550 70797 54896 75263 TRUE FALSE 76941.82191 53698.8299 85109.0489 68531.63734 59445.48775 70297.69945 60181.6471 61749.88644 62701.11908 1.227120393 0.856425383 1.357376872 1.092989062 0.948076982 1.121155419 0.959817751 0.984829096 1 15.93620357 2.984691777 24.63256288 1.008199049 1.128572708 0.200499561 0.131425979 1061.349992 1707829.933 0.038788848 0.042408068 965.365507 -2.984691777 0.120373659 RDS(ph)PTYDPYKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RDSPTYDPYKR 11 2 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 RDS(0.901)PT(0.099)YDPYKR;RDS(0.998)PT(0.002)YDPYKR;RDS(0.794)PT(0.206)YDPYKR;RDS(0.993)PT(0.007)YDPYKR;RDS(0.992)PT(0.008)YDPYKR;RDS(0.997)PT(0.003)YDPYKR;RDS(1)PTYDPYKR 106.55 0.0018243 4277830000 3353200 2118670 2645350 2387840 2373070 2099550 3142950 2222550 2210070 TRUE FALSE 3143329.198 2275538.531 2708098.951 2449116.017 2186698.655 2705656.002 2671693.825 2500040.26 1841195.039 1.707222282 1.235903032 1.470837632 1.330177393 1.187651828 1.469510803 1.451065079 1.357835648 1 20.81221103 -2.278422794 1.462009399 2.84E-05 1.391685484 0.433297301 0.143850727 125137.1789 16502.45595 410683.7774 0.03631936 0.005267168 2.278422794 1.391657052 RDS(ph)QDGSSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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(0.561)QDGS(0.219)S(0.219)YR;RDS(1)QDGSSYR;RDS(0.998)QDGS(0.002)SYR;RDS(1)QDGSSYR;RDS(1)QDGSSYR 217.57 4.40E-09 6521658000 1700274 1422504 1697356 1407003 1353448 1711313 1951131 1723809 2277120 TRUE FALSE 1593856.885 1527827.676 1737618.086 1443109.079 1247153.654 2205341.282 1658577.02 1939030.348 1897053.961 0.840174775 0.805368591 0.915956067 0.760710612 0.657416014 1.162508462 0.874290903 1.022127144 1 20.85532929 2.240822334 24.99997503 0.995982914 0.811980143 0.560206291 0.095106822 51.23120449 566293.3929 0.032814496 0.026233067 174.1094462 -2.240822334 -0.184002772 RDS(ph)SDDWEIPDGQITVGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RDSSDDWEIPDGQITVGQR 19 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 RDS(0.796)S(0.204)DDWEIPDGQITVGQR;RDS(0.498)S(0.498)DDWEIPDGQIT(0.004)VGQR 232.32 8.15E-21 1822840000 623344 696363 764598 701891 732848 600352 874203 633672 760624 TRUE FALSE 584330.0117 747922.4411 782734.6256 719902.7114 675293.0742 773663.8765 743124.3759 712787.3441 633670.9406 0.922134777 1.180300994 1.235238316 1.136082887 1.065684145 1.220923711 1.172729138 1.124854082 1 19.27337433 -0.664785803 7.871934343 1.000001537 1.149595482 0.151671892 0.090354006 0 0 0.082002061 0.019328071 0.216378545 0.664785803 0.149593945 RDS(ph)SDTTPLLNGSSQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RDSSDTTPLLNGSSQDR 17 1 B4DQA8;E9PCW1 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 1 RDS(0.943)S(0.055)DT(0.002)TPLLNGSSQDR;RDS(0.748)S(0.245)DT(0.002)T(0.001)PLLNGS(0.004)SQDR;RDS(0.556)S(0.136)DT(0.223)T(0.083)PLLNGS(0.001)S(0.001)QDR;RDS(0.874)S(0.066)DT(0.049)T(0.01)PLLNGSSQDR;RDS(0.79)S(0.209)DT(0.001)TPLLNGSSQDR;RDS(0.989)S(0.009)DT(0.002)TPLLNGSSQDR 305.1 9.20E-47 3847160000 1590482 1739217 1683444 1575221 1711091 1584247 2325220 1784962 2138219 TRUE FALSE 1490936.571 1867990.436 1723376.087 1615643.838 1576708.815 2041593.391 1976574.847 2007818.435 1781336.435 0.836976408 1.0486455 0.967462436 0.906984108 0.88512691 1.146102078 1.109602211 1.12714162 1 20.76452859 2.232947398 24.99963136 1.10682818 0.949586088 0.583768727 0.068441581 101.6705538 452806.6066 0.024761167 0.018798054 170.9808211 -2.232947398 -0.157242092 RDS(ph)SESQLASTESDKPTTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RDSSESQLASTESDKPTTGR 20 2 Q96B23-2;Q96B23;A0A087WVF1;K7EQH1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 RDS(0.799)S(0.201)ESQLASTESDKPTTGR;RDS(0.885)S(0.113)ES(0.001)QLASTESDKPTTGR 235.68 7.87E-30 1296580000 824610 577260 686010 665940 695740 533420 791320 545160 863810 TRUE FALSE 772999.1321 620000.931 702282.4812 683029.1478 641099.3869 687409.6946 672668.9123 613224.426 719634.5306 1.074155143 0.861549724 0.975887692 0.949133371 0.890868017 0.955220554 0.934736847 0.852133131 1 19.45690489 4.75537339 24.722174 0.927030144 1.074155278 0.48569118 0.047445003 2405.988866 3537794.401 0.010214396 0.28330213 56934.22193 -4.75537339 0.147125134 RDS(ph)SSHEETPGSHPLYGHGECK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDSSSHEETPGSHPLYGHGECK 22 1 B7ZBM3;Q8IVH2-3;Q8IVH2-2;Q8IVH2 B7ZBM3 FOXP4 Forkhead box protein P4 1 RDS(0.333)S(0.333)S(0.333)HEETPGSHPLYGHGECK 202.03 5.50E-23 240970000 349020 352020 334620 383150 497010 299940 441380 322410 607760 TRUE FALSE 327175.4612 378083.9271 342557.3444 392982.2777 457976.8394 386527.8089 375199.1666 362663.5982 506320.9297 0.646181981 0.746727826 0.676561691 0.776152544 0.904518878 0.763404762 0.741030332 0.716272184 1 18.9496926 -5 0.192233875 2.073533467 0.701093585 0.58577732 0.067576573 103.8517606 1.019414356 42.94322339 0.180867646 1.00E-05 5 -1.372439881 RDS(ph)TEAPKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDSTEAPKPK 10 2 Q8N201 Q8N201 INTS1 Integrator complex subunit 1 1 RDS(0.997)T(0.003)EAPKPK 117.07 0.00052498 153490000 248620 148180 158220 195610 142190 81502 179050 116830 148180 TRUE FALSE 233059.318 159151.4014 161973.0531 200629.6838 131022.971 105030.3043 152203.1147 131416.4827 123447.8007 1.887917943 1.289220225 1.312077268 1.625218777 1.061363347 0.850807416 1.232935004 1.064551024 1 16.91354161 2.720812489 23.73745636 1.05486209 1.452621936 0.594829751 0.194998431 347.8727872 465265.6819 0.06156426 0.058184754 525.7902022 -2.720812489 0.397759847 RDSAS(ph)YR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDSASYR 7 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 1 RDS(0.495)AS(0.505)YR 62.869 0.087774 496970000 417690 402420 412350 410730 556840 374210 489900 455720 734150 TRUE FALSE 391547.5285 432215.5955 422131.1367 421270.0272 513108.0326 482238.3522 416444.043 512617.6452 611615.6222 0.640185624 0.706678476 0.690190246 0.68878232 0.838938729 0.788466374 0.680891769 0.838136939 1 19.22226573 -5 0.138405533 1.960503033 0.623148988 0.756398543 0.053064641 70.4227315 0.600494645 18.56614869 0.337008853 1.00E-05 5 -1.337354044 RDSFDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDSFDDR 7 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 78.113 0.058072 140780000 361380 330020 362500 378770 344990 340400 371650 338690 308440 FALSE TRUE 338761.8709 354455.0242 371098.6712 388489.8795 317895.877 438667.9541 315924.5327 380976.192 256959.3714 1.31834799 1.379420498 1.44419201 1.511872781 1.237144515 1.707149078 1.229472702 1.482632021 1 17.97118074 -1.343857288 2.924392443 0.995053395 1.410693198 0.462350659 0.140192884 10748950.21 13338389.7 458095.4327 0.028933824 0.045304643 1.343857288 0.415639803 RDSFDDRGPSLNPVLDYDHGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RDSFDDRGPSLNPVLDYDHGSR 22 2 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 206.85 5.28E-23 507070000 124240 258270 232190 242900 264230 181714 244050 208148 297170 FALSE TRUE 116464.0402 277392.5795 237697.6564 249133.2252 243478.4417 234171.8819 207456.9681 234135.736 247570.4072 0.470427954 1.120459358 0.960121442 1.00631262 0.983471508 0.94587994 0.837971592 0.945733937 1 17.91747935 4.749230595 24.9966212 0.971313742 0.470427672 0.838248355 0.069639288 700.0756741 1640039.598 0.01890825 0.277063384 56134.59517 -4.749230595 -0.50088607 RDSIVAELDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDSIVAELDR 10 1 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 0 135.5 0.0070484 0 62655 127320 79613 99440 127070 113700 84892 111210 74884 FALSE TRUE 58733.53539 136746.9053 81501.45796 101991.7988 117090.4348 146523.3442 72163.2327 125094.8133 62385.37663 0.941463185 2.191970501 1.306419266 1.634867084 1.876889122 2.348680927 1.156733142 2.005194487 1 15.92892028 -1.293831926 3.712847046 0.998366868 1.689123136 0.185767852 0.449056987 13561037.96 7090234.392 171839.3649 0.093747034 0.050835614 1.293831926 0.690756268 RDSLT(ph)GSSDLYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDSLTGSSDLYK 12 1 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;Q14671-4;E9PR38;H0YDK8 Q5T1Z4 PUM1 Pumilio homolog 1 1 RDS(0.294)LT(0.697)GS(0.01)SDLYK 199.8 3.24E-07 285490000 728350 535150 619830 559330 658510 461640 777070 626130 711010 TRUE FALSE 682763.8736 574773.0628 634532.6603 573683.3547 606793.2809 594907.9739 660555.5675 704303.7088 592337.8377 1.152659564 0.970346694 1.071234387 0.968507021 1.024404052 1.00433897 1.115166929 1.189023669 1 19.17606072 1.687677165 6.379738733 1.114166993 1.026735876 0.170145057 0.069614537 0.173026158 15.10119078 0.031369781 0.015931085 48.71662179 -1.687677165 -0.087431116 RDSS(ph)DDWEIPDGQITVGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RDSSDDWEIPDGQITVGQR 19 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 RDS(0.379)S(0.621)DDWEIPDGQITVGQR;RDS(0.382)S(0.618)DDWEIPDGQITVGQR;RDS(0.393)S(0.607)DDWEIPDGQITVGQR;RDS(0.393)S(0.607)DDWEIPDGQITVGQR 187.21 1.16E-14 3389400000 1827950 1975350 1935100 1919140 1975340 1644390 2293050 1706560 2127410 TRUE FALSE 1713541.872 2121606.969 1981001.486 1968388.381 1820204.765 2119098.699 1949228.44 1919627.773 1772331.527 0.9668292 1.197071167 1.117737542 1.110620869 1.027011446 1.195655929 1.099810284 1.083108743 1 20.75721706 0.854948806 2.400601564 1.000243247 1.114620833 0.158382345 0.069186269 0.828075406 9.162302209 0.059957282 0.01617385 7.160589978 -0.854948806 0.114377586 RDSSDT(ph)TPLLNGSSQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDSSDTTPLLNGSSQDR 17 1 B4DQA8;E9PCW1 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 1 RDS(0.086)S(0.086)DT(0.634)T(0.194)PLLNGSSQDR 174.87 2.51E-09 408300000 179460 173680 164650 156970 184030 155330 236070 170590 211680 TRUE FALSE 168227.9189 186539.4479 168555.5758 160998.1159 169577.0261 200171.2494 200673.4951 191888.537 176349.2405 0.95394751 1.057784243 0.95580551 0.912950436 0.961597712 1.135084273 1.13793229 1.088116606 1 17.42807584 2.242162541 24.99997115 1.106840892 0.97636253 0.555058264 0.053044597 64.40555589 447024 0.018803862 0.015158036 174.6475673 -2.242162541 -0.130478362 RDSSESQLAS(ph)TESDKPTTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDSSESQLASTESDKPTTGR 20 2 Q96B23-2;Q96B23;A0A087WVF1;K7EQH1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 RDS(0.019)S(0.005)ES(0.278)QLAS(0.347)T(0.347)ES(0.004)DKPTTGR 246.5 3.81E-30 1107400000 401100 267580 361210 335260 362130 293000 354990 260430 474710 TRUE FALSE 375995.867 287391.9016 369778.0718 343863.3392 333689.7706 377584.3435 301762.5451 292945.2588 395477.8343 0.950738156 0.726695346 0.935015922 0.869488273 0.843763523 0.954754757 0.763032764 0.740737491 1 18.59323731 -0.303191193 7.550690466 1 0.844188287 0.24307276 0.084037442 0 0 0.075695641 0.017841634 0.49751801 0.303191193 -0.155811713 RDTDS(ph)DTQDANDSSCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RDTDSDTQDANDSSCK 16 1 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49;A0A087X246;A0A087WWE6 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 RDT(0.001)DS(0.994)DT(0.005)QDANDSSCK;RDT(0.016)DS(0.807)DT(0.177)QDANDSSCK 151.64 3.82E-07 483100000 481260 374820 391710 393820 395820 285670 534450 347320 452140 TRUE FALSE 451138.7957 402572.0628 401001.5462 403926.0879 364733.8939 368138.2915 454314.1841 390683.6665 376674.9131 1.197687396 1.06875199 1.064582568 1.072346668 0.968298873 0.977336899 1.206117446 1.037190567 1 18.52296043 4.743898919 4.0608101 1.05917183 1.210404871 0.316650717 0.06727968 0.330356464 11.64797023 0.016440958 0.147776066 55449.664 -4.743898919 0.151233041 RDTDSDTQDANDSSCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDTDSDTQDANDSSCK 16 1 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49;A0A087X246;A0A087WWE6 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 0 205.52 3.21E-12 0 99064 67091 73281 75320 88968 63544 102440 79525 86853 FALSE TRUE 92863.76107 72058.48745 75019.25993 77252.83872 81980.81216 81888.12125 87080.07301 89453.87131 72356.67321 1.283416677 0.995878946 1.036798081 1.06766709 1.133009694 1.131728666 1.203483648 1.23629055 1 16.14283846 2.506575437 2.201200536 1.164728718 1.069344539 0 0.098350204 0.555413866 5.41925385 0.036120543 0.030585151 321.0520423 -2.506575437 -0.095384179 RDTFNHLTTWLEDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RDTFNHLTTWLEDAR 15 1 P61019;P61019-2;E9PKL7 P61019 RAB2A Ras-related protein Rab-2A 0 ; 174.17 6.02E-07 345250000 217269 391890 273910 306330 419680 245780 335800 349470 363510 FALSE TRUE 203670.5211 420905.9434 280407.2745 314190.9464 386720.0257 316732.6961 285449.9074 393102.0988 302837.8326 0.672539885 1.389872394 0.925932114 1.037489087 1.276987166 1.045882192 0.942583378 1.298061393 1 18.20818592 4.767472431 23.8844703 1.104344762 0.672538672 0.433791435 0.158335365 5939.266902 4906362.598 0.036118779 3.56666064 58542.65729 -4.767472431 -0.43180609 RDVEQLEQLIESHDVVFLLMDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RDVEQLEQLIESHDVVFLLMDTR 23 1 O95352-3;O95352-2;O95352 O95352-3 ATG7 Ubiquitin-like modifier-activating enzyme ATG7 0 ; 151.94 3.22E-08 62420000 65762 72162 71041 69251 83218 58354 83013 63787 113766 FALSE TRUE 61646.07381 77504.94956 72726.12607 71028.0979 76682.39397 75199.8525 70565.9713 71750.94736 94777.71964 0.650427907 0.817754952 0.767333571 0.749417671 0.809076165 0.793433866 0.744541772 0.757044458 1 16.53226033 -1.027440846 4.306880596 1.000012908 0.767565437 0.719924707 0.046669857 0.121371244 24121922.05 813.102756 0.009835649 0.093876989 1.027440846 -0.232447471 RDVTQLDPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RDVTQLDPNK 10 1 Q9UNN5;B1ANM7;Q9UNN5-2 Q9UNN5 FAF1 FAS-associated factor 1 0 ; 113.67 0.0023367 604130000 965110 881120 811840 771500 1057770 575950 900870 846310 1216930 FALSE TRUE 904705.4879 946359.0416 831097.2282 791297.9961 974697.011 742217.4152 765792.9068 951973.6665 1013816.521 0.892375956 0.933461846 0.819770847 0.780514008 0.961413619 0.732102308 0.755356507 0.938999954 1 19.95136515 3.953128079 4.249479112 0.834656224 0.912229473 0.026770766 0.091372135 0.42609572 17.90951574 0.02210492 0.044730743 8976.934962 -3.953128079 0.077573249 RDVYLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RDVYLSPR 8 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 1 RDVYLS(1)PR;RDVYLS(1)PR 132.56 0.00058605 577510000 428870 798260 407020 436400 961180 239440 388440 712920 910230 TRUE FALSE 402027.7923 857364.001 416674.7066 447598.7628 885692.8 308562.441 330197.0281 801929.6313 758306.7327 0.530165136 1.130629551 0.549480426 0.590260832 1.16798752 0.4069098 0.435439927 1.057526719 1 19.53242201 2.191596737 24.99999562 0.642263916 0.797103381 0 0.302349864 386.3286943 205649.585 0.107262784 0.079219021 155.4521516 -2.191596737 0.154839464 RDWGDHGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RDWGDHGR 8 1 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 ; 88.294 0.023598 150071000 192673 196534 258640 232460 228860 216451 275470 202432 256090 FALSE TRUE 180613.9409 211085.5819 264775.0629 238425.3172 210886.2588 278936.8899 234165.8308 227706.0808 213346.9246 0.846573913 0.989400631 1.241054041 1.117547476 0.988466364 1.307433376 1.097582406 1.067304257 1 17.70284179 4.496003497 2.331073657 1.12895744 0.839003673 0.450098525 0.097803449 0.307186825 2.794411224 0.022917455 0.145873389 31333.10954 -4.496003497 -0.289953767 RDYDDMS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 RDYDDMSPR 9 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR 138.24 0.00015071 16173480000 12604190 14550570 13204100 14165570 16511500 12028600 17047160 13342810 17372380 TRUE FALSE 11815316.25 15627909.34 13517307.49 14529082.51 15214753.39 15501061.55 14491096.62 15008689.2 14472817.55 0.816379824 1.079811121 0.933978988 1.00388763 1.051264092 1.071046567 1.001262993 1.037026077 1 23.78684248 3.00281847 22.38488442 1.032333923 0.970985459 0.233617582 0.067499241 42.00104306 333553.4742 0.018190223 0.021580436 1006.510872 -3.00281847 -0.061348464 RDYDDMSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RDYDDMSPR 9 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;; 160.77 0.00010429 1161380000 489290 622429 598132 582581 680317 584804 620664 620920 714848 FALSE TRUE 458666.2123 668514.2908 612319.9735 597531.0148 626887.6471 753627.4213 527601.1952 698443.2288 595535.2507 0.770174749 1.122543611 1.028184264 1.003351211 1.052645744 1.265462322 0.885927734 1.172799138 1 19.18382738 4.746110293 24.46285318 1.061511526 0.770174559 0.445333036 0.103757758 613.7159877 1988529.166 0.02227265 0.232301147 55732.72697 -4.746110293 -0.291336967 RDYEVDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RDYEVDGR 8 1 A0A590UJD9;A0A0C4DFT3;A0A590UJ18;F8VYC1;E9PIW2;E9PN83;A0A3B3ISW2;B7Z2T4;A0A3B3ITF1;F8W750;Q15700-2;Q15700-4;Q15700;Q15700-3;B5MCC5;H7C325;Q15700-5;A0A590UJ08;Q12959-4;Q12959-2;A0A590UJC5;Q12959;Q12959-3;Q12959-5;Q12959-7;Q12959-6;A0A590UKA8;A0A590UJR5;A0A590UJ68;A0A590UJS9;A0A590UK48;A0A590UJ81;C9JUA9;Q12959-8;A0A590UJX2;A0A590UK81;A0A590UJ29;Q12959-9;A0A590UJR4 A0A590UJD9;A0A590UJ08;Q12959 DLG1;DLG2 Disks large homolog 2;Disks large homolog 1 0 128.27 0.0018291 327550000 368230 365280 379030 352190 449930 309860 370280 392440 567560 FALSE TRUE 345183.1416 392325.7113 388020.7706 361227.7917 414594.3127 399311.5518 314759.9515 441436.9979 472830.5694 0.730035586 0.829738466 0.82063385 0.763968777 0.876834832 0.844512977 0.665692897 0.93360503 1 18.85096379 1.034183843 9.325837886 0.999978692 0.795461142 0.605233307 0.060509284 0.172577887 43.58768086 0.057508404 0.014388826 10.81891833 -1.034183843 -0.20451755 RDYYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RDYYDR 6 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 ;;; 135.6 0.021696 1589420000 1281400 1326630 1388830 1463470 1365940 1285390 1537470 1182830 1533450 FALSE TRUE 1201199.461 1424855.066 1421773.703 1501025.118 1258664.582 1656461.226 1306940.647 1330508.929 1277507.289 0.940268186 1.115340068 1.112928056 1.174964035 0.985250412 1.296635441 1.023039679 1.041488327 1 20.28490009 1.584073158 25 1.024154447 1.10860049 0.138529182 0.096759721 1.644656731 1721.849051 0.04632207 0.021463071 38.37718871 -1.584073158 0.084446043 READGSETPEPFAAEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 READGSETPEPFAAEAK 17 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 135.09 2.37E-05 587570000 593160 486570 527940 540170 598020 400010 667280 465350 683130 FALSE TRUE 556035.1744 522596.1491 540462.9861 554031.6767 551053.9215 515486.3934 567227.5587 523449.9719 569111.1898 0.977023795 0.918267218 0.9496615 0.973503397 0.968271107 0.905774482 0.996690223 0.919767492 1 19.11835102 -5 0.256414917 1.309646299 0.946406237 0.188458583 0.029707381 292.9018527 2.888981176 47.73081864 0.037091713 1.00E-05 5 -0.363240062 REALEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 REALEK 6 1 O43707;O43707-2;F5GXS2;O43707-3;Q9Y2J4;Q9Y2J4-2;Q9Y2J4-4;Q9Y2J4-3;Q4VCS5;E7ERM3;Q4VCS5-2;A6NP16 O43707;Q9Y2J4;Q4VCS5 ACTN4;AMOTL2;AMOT Alpha-actinin-4;Angiomotin-like protein 2;Angiomotin 0 100.39 0.060474 211530000 628000 512410 526050 551900 461340 388940 620780 504610 802380 FALSE TRUE 588694.601 550349.3696 538528.1544 566062.6884 425108.2174 501220.6641 527699.802 567611.6693 668457.5944 0.880676061 0.823312315 0.805627999 0.846819145 0.635953905 0.749816695 0.789428988 0.849136391 1 19.35047652 0.864205505 2.778761941 0.999833028 0.789938145 0.507830288 0.065143099 0.454441796 6.822137065 0.062031791 0.016408835 7.314851351 -0.864205505 -0.209894883 RECPSDECGAGVFMASHFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RECPSDECGAGVFMASHFDR 20 1 P62979 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ; 240.31 6.94E-30 2689400000 831050 1058160 1105010 1094140 1163910 1058790 1268640 907310 1385340 FALSE TRUE 779036.064 1136507.267 1131221.359 1122217.485 1072501.204 1364445.485 1078419.209 1020589.651 1154117.804 0.675005672 0.984741127 0.980161085 0.972359564 0.929282262 1.182241085 0.934409993 0.884302839 1 20.13835906 4.738569368 9.034821098 0.986064845 0.673654013 0.605102712 0.078280114 0.05339631 88.93462986 0.017404361 0.101691682 54773.35813 -4.738569368 -0.312410831 REDIVDTMVFKPSDVMLVHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 REDIVDTMVFKPSDVMLVHFR 21 2 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7;H3BSK9;H3BUE3;H3BSQ5 Q8WWM7 ATXN2L Ataxin-2-like protein 0 ; 188.98 1.40E-17 323630000 287560 289400 276620 265810 348830 213300 323820 277740 339910 FALSE TRUE 269562.1329 310827.4771 283181.557 272631.1346 321434.2989 274876.2474 275266.1972 312416.4504 283176.8251 0.951921588 1.097644474 1.00001671 0.962759345 1.135101006 0.970687652 0.972064706 1.103255714 1 18.11134368 REDLVEEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 REDLVEEIK 9 1 B3KWE1;P12081-4;P12081;B4DDD8;P12081-3;P12081-2;B4E1C5 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 ;;; 166.69 9.71E-05 1632890000 2579620 1998820 2236970 2185600 2407910 1938190 2694950 1838260 2619440 FALSE TRUE 2418166.189 2146814.713 2290031.985 2241686.196 2218802.462 2497713.989 2290867.266 2067770.808 2182238.542 1.108112675 0.983767206 1.049395811 1.027241593 1.016755235 1.144565061 1.049778575 0.947545728 1 21.05737738 1.250889424 24.93821663 0.973772871 1.049182817 0.333605299 0.046855328 230.8647592 466989.8603 0.031146668 0.011196448 17.81925013 -1.250889424 0.075409946 REDLVEEIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 REDLVEEIKR 10 2 B3KWE1;P12081-4;P12081;B4DDD8;P12081-3;P12081-2;B4E1C5 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 67.385 0.035508 633060000 1361000 1560500 1419100 1462200 1707800 1286000 1690900 1393900 1619100 FALSE TRUE 1275817.439 1676041.044 1452761.722 1499722.527 1573676.277 1657247.324 1437365.243 1567931.483 1348861.75 0.945847445 1.242559546 1.077027888 1.111843024 1.166669806 1.228626524 1.065613464 1.162410813 1 20.36331106 -0.482446065 8.019571383 1.000004186 1.131834574 0.169893134 0.085736666 0 0 0.073179421 0.017248555 0.329271343 0.482446065 0.131830388 REDS(ph)MEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 REDSMEDR 8 1 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;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)MEDR 52.693 0.060641 96483000 27829 27029 29228 26384 24238 32951 31287 23117 19456 TRUE FALSE 26087.23257 29030.25528 29921.30196 27061.05811 22334.44525 42463.41879 26595.8048 26003.20834 16208.66791 1.609461845 1.791032764 1.846006231 1.669542387 1.377932189 2.619796952 1.640838405 1.604277938 1 13.98447791 0.847809275 2.326017314 1.002499465 1.812107422 0.376090677 0.321275207 0.572209172 5.85354892 0.281234052 0.076197452 7.043836629 -0.847809275 0.809607957 REDS(ph)MEDRGEEDDSLAIKPPQQMSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 REDSMEDRGEEDDSLAIKPPQQMSR 25 3 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;Q9UQ88-9;A0A087X1I0;A0A087WYI9;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;J3KS35;E7ESP2;E9PFJ2 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 REDS(1)MEDRGEEDDSLAIKPPQQMSR;REDS(1)MEDRGEEDDSLAIKPPQQMSR;REDS(1)MEDRGEEDDSLAIKPPQQMSR;REDS(1)MEDRGEEDDSLAIKPPQQMSR;REDS(1)MEDRGEEDDSLAIKPPQQMSR;REDS(1)MEDRGEEDDSLAIKPPQQMSR 168.87 5.90E-11 1597350000 733012 650672 624032 623987 737170 487513 798057 599996 1212267 TRUE FALSE 687134.0874 698848.4319 638834.3337 639999.5628 679275.6418 628250.089 678395.7616 674906.8214 1009931.806 0.680376718 0.691975862 0.63255195 0.63370572 0.672595553 0.622071793 0.671724326 0.668269696 1 19.94582645 0.1271006 1.558162622 1.000163294 0.657185877 0.957797517 0.0224982 2.82063986 4.766620157 0.022000059 0.006086425 1.339987045 -0.1271006 -0.342977416 REDS(ph)PGPEVQPMDK ddPTM_SK-BR-3_Pertuzumab_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 233.09 2.53E-16 14774712000 10681661 8885650 9635195 9096434 10029742 7711049 12138899 8655312 12591438 TRUE FALSE 10013114.91 9543552.772 9863746.375 9329863.897 9242046.521 9937103.668 10318783.79 9735946.756 10489845.65 0.954553121 0.909789628 0.940313776 0.889418606 0.88104695 0.947306948 0.983692623 0.928130601 1 23.32249011 2.007210645 24.25662689 0.967971809 0.916393697 0.459715369 0.027707288 107.1854943 360570.0336 0.009833607 0.007244986 101.6741721 -2.007210645 -0.051578112 REEAAVDAQQQK ddPTM_SK-BR-3_Pertuzumab_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 ;;; 187.74 1.62E-05 1075230000 2219335 2045660 2091986 2187190 2401400 1591286 2620880 2125380 2445010 FALSE TRUE 2080430.784 2197122.795 2141608.896 2243316.998 2212803.731 2050664.436 2227903.375 2390738.372 2036922.036 1.021360046 1.078648449 1.051394633 1.101326884 1.086346798 1.00674665 1.093759769 1.173701462 1 20.95795933 4.741856776 22.74964671 1.074101407 1.02135998 0.101639471 0.049172885 214.5311563 1480392.593 0.010681868 0.07600149 55189.54024 -4.741856776 -0.052741427 REEDEENDNDNES(ph)DHDEADS ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 REEDEENDNDNESDHDEADS 20 1 H0YBP8;Q9NRG0 H0YBP8 CHRAC1 Chromatin accessibility complex protein 1 1 REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(0.998)DHDEADS(0.002);REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS 322.26 4.74E-67 4195290000 2714802 2872805 2847994 2842031 2987444 2491728 3102409 2663126 3139641 TRUE FALSE 2544887.389 3085510.471 2915549.763 2914962.327 2752822.199 3211049.424 2637231.572 2995623.143 2615614.634 0.972959608 1.179650255 1.114670993 1.114446405 1.052457102 1.227646222 1.008264573 1.145284594 1 21.31871857 -0.497794959 0.550058496 0.983677852 1.111254373 0.132623148 0.076756635 17.40282721 4.365284085 0.622088141 0.029940965 0.31783743 0.497794959 0.127576521 REEDEPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 REEDEPEER 9 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;; 199.68 3.90E-05 189060000 363020 404538 385127 373919 386003 335324 412291 373915 416792 FALSE TRUE 340299.2262 434490.4144 394262.3943 383514.3946 355687.8814 432126.5953 350471.7921 420599.1108 347226.7226 0.980049069 1.251316175 1.135460979 1.104507141 1.024367822 1.244508464 1.009345679 1.211309739 1 18.40551846 -5 0.247801906 0.245056339 1.138688443 0.103241577 0.097477436 350.2831335 3.479296726 133.888558 0.130131697 1.00E-05 5 0.893632104 REEDEPEERS(ph)GDETPGSEVPGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 REEDEPEERSGDETPGSEVPGDK 23 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 REEDEPEERS(0.995)GDET(0.005)PGSEVPGDK 151.65 3.69E-08 633250000 423770 372340 367130 401980 461130 222860 395020 376440 683190 TRUE FALSE 397246.9922 399908.441 375838.497 412295.4874 424914.7099 287196.0642 335790.4182 423439.3626 569161.1754 0.697951669 0.702627759 0.660337551 0.724391447 0.746563062 0.504595318 0.589974216 0.743970919 1 19.11847773 0.92723388 6.576681162 0.999992865 0.659073444 0.69880129 0.069905162 0.499335965 44.58979381 0.071264808 0.017889271 8.457341755 -0.92723388 -0.340919422 REEDGHLFSQLLDMLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 REEDGHLFSQLLDMLK 16 1 O60306;H0YH15 O60306 AQR Intron-binding protein aquarius 0 74.816 0.020273 16233000 32588 43707 28370 32966 48019 19924 27060 40725 46225 FALSE TRUE 30548.37525 46943.11176 29042.9498 33811.96337 44247.78144 25675.73536 23002.60421 45809.6059 38509.74888 0.793263424 1.218992934 0.754171363 0.878010487 1.149002077 0.666733389 0.597318988 1.189558676 1 15.23293609 2.226639869 24.99786524 0.799106996 0.962628397 0.008201859 0.218786745 494.1431087 1036213.322 0.078260034 0.058252115 168.515506 -2.226639869 0.163521401 REEGDPS(ph)PHSGGVCKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 REEGDPSPHSGGVCKPK 17 2 O75376;O75376-2;E7EVK1;J3KRE4 O75376 NCOR1 Nuclear receptor corepressor 1 1 REEGDPS(1)PHSGGVCKPK;REEGDPS(0.999)PHS(0.001)GGVCKPK 90.316 0.0019997 274390000 455670 258710 386870 336820 399860 290050 489560 368550 554350 TRUE FALSE 427150.4281 277865.1576 396046.7391 345463.3714 368456.6086 373782.7264 416155.0229 414564.2788 461825.4038 0.924917565 0.601667113 0.857568111 0.74803891 0.797826637 0.809359389 0.901108989 0.897664519 1 18.81698801 1.470627171 0.670088211 0.998390944 0.755681373 0.413426492 0.083938021 0.543068655 0.544981917 0.072991433 0.033960033 29.55474193 -1.470627171 -0.242709571 REEQT(ph)DT(ph)SDGESVTHHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 2 REEQT(1)DT(0.556)S(0.444)DGESVTHHIR;REEQT(1)DT(0.544)S(0.456)DGESVTHHIR;REEQT(1)DT(0.919)S(0.081)DGESVTHHIR 187.79 1.82E-14 2626090000 574633 774363 698448 728735 792424 583961 790806 708805 929631 TRUE FALSE 538667.7463 831697.6422 715015.5164 747435.5738 730190.2155 752541.0609 672231.9818 797300.8645 774469.5805 0.695531187 1.073893234 0.923232538 0.96509352 0.942826205 0.971685757 0.867990169 1.029479898 1 19.56284905 4.753678087 24.98772051 0.963985641 0.695530993 0.698637088 0.056813931 1694.947574 2801537.734 0.013401626 0.321043638 56712.40796 -4.753678087 -0.268454647 REEQT(ph)DTS(ph)DGESVTHHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 2 REEQT(0.999)DT(0.108)S(0.892)DGESVTHHIR;REEQT(1)DT(0.305)S(0.695)DGESVTHHIR;REEQT(0.999)DT(0.148)S(0.853)DGESVTHHIR 193.77 1.15E-14 1594190000 445607 642080 568140 629890 678070 466920 647420 575600 763080 TRUE FALSE 417717.2533 689620.2713 581616.5491 646054.0438 624817.1174 601712.2242 550345.3814 647464.9271 635717.0183 0.657080495 1.084791269 0.914898504 1.01626042 0.982854162 0.946509543 0.865708115 1.018479777 1 19.27802518 4.751946867 24.90918852 0.970174487 0.657080281 0.733616673 0.060711845 1223.59313 2276824.973 0.014766321 0.290313714 56486.78634 -4.751946867 -0.313094206 REEQTDT(ph)SDGESVTHHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 1 REEQT(0.028)DT(0.486)S(0.486)DGESVTHHIR;REEQT(0.022)DT(0.489)S(0.489)DGESVTHHIR;REEQT(0.101)DT(0.449)S(0.449)DGESVTHHIR 172.69 7.75E-12 4248780000 661520 835260 837900 813560 843670 677720 826650 658360 996210 TRUE FALSE 620116.644 897103.5195 857775.3837 834437.327 777411.5614 873366.7621 702701.5067 740557.6952 829936.1152 0.747185997 1.080930813 1.033543869 1.005423564 0.936712534 1.052330108 0.846693491 0.892306868 1 19.66264076 1.737322615 24.99999994 0.901310967 0.994382494 0.057853422 0.099855263 0.30715191 5919.350963 0.042930155 0.023806998 54.61634267 -1.737322615 0.093071527 REEQTDTS(ph)DGESVTHHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 1 REEQT(0.019)DT(0.187)S(0.794)DGESVTHHIR;REEQT(0.001)DT(0.357)S(0.642)DGESVTHHIR;REEQTDT(0.043)S(0.957)DGESVTHHIR 223.97 2.29E-19 5328740000 788320 1152650 1103430 1100860 1160850 947650 1074160 897030 1320120 TRUE FALSE 738980.4584 1237993.405 1129603.881 1129109.931 1069681.524 1221221.171 913099.68 1009026.17 1099783.444 0.6719327 1.12567016 1.027114826 1.026665693 0.97262923 1.110419672 0.83025407 0.917477141 1 20.06878804 1.72974815 24.99999987 0.904361481 1.010036889 0.047272296 0.131038744 1.540922353 4347.849431 0.05534246 0.030690166 53.67204583 -1.72974815 0.105675408 REERPENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 REERPENK 8 2 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 ;; 134.05 0.00050234 323451000 324812 262835 286276 261196 286954 239099 340681 252507 281807 FALSE TRUE 304482.5967 282295.5769 293066.6019 267898.7316 264417.7904 308122.9999 289599.0468 284033.0548 234771.5912 1.29693118 1.202426475 1.248305216 1.141103701 1.126276774 1.312437328 1.233535307 1.209827192 1 17.84089832 0.833839222 7.331923325 1.000000019 1.222513134 0.587359595 0.058408168 9.613983472 424.5105881 0.054095755 0.013558843 6.820861355 -0.833839222 0.222513114 REES(ph)KPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 REESKPR 7 2 O75363;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 REES(1)KPR;REES(1)KPR 82.645 0.018844 416810000 630500 409210 445390 452790 500910 307830 409610 371340 648390 TRUE FALSE 591038.1305 439508.3342 455954.8611 464409.358 461570.5492 396695.5238 348192.7831 417702.6164 540169.5202 1.094171567 0.813648897 0.84409587 0.859747432 0.854492029 0.734390796 0.644599094 0.773280611 1 19.04305271 2.302785778 4.799789245 0.745280731 0.875958503 0.110967135 0.119647548 0.30517916 13.74463089 0.039736604 0.032342727 200.8102042 -2.302785778 0.130677772 REESPMDVDQPS(ph)PSAQDTQSIASDGTPQGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 REESPMDVDQPSPSAQDTQSIASDGTPQGEK 31 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 REESPMDVDQPS(0.967)PS(0.033)AQDTQSIASDGTPQGEK 168.69 6.19E-13 186020000 282720 233130 251720 254050 242020 193250 324540 226590 259830 TRUE FALSE 265025.0599 250391.1878 257690.9173 260569.3531 223012.7255 249038.1378 275878.2399 254880.2603 216462.6944 1.224345195 1.156740603 1.19046341 1.203761017 1.030259399 1.150489873 1.274483996 1.177478923 1 17.72375888 REFDRHS(ph)GSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 REFDRHSGSDR 11 2 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 REFDRHS(0.998)GS(0.002)DR 145.86 1.88E-05 166670000 91493 97006 118040 99395 116190 90523 92810 89137 127240 TRUE FALSE 85766.61645 104188.4252 120839.9645 101945.644 107064.9061 116655.5206 78894.00211 100265.9507 106002.822 0.809097483 0.982883505 1.139969317 0.961725755 1.010019394 1.100494481 0.744263224 0.945880013 1 16.69374315 1.749496487 25 0.87370814 1.013572528 0.151204717 0.108984487 3.857468734 8834.8173 0.047801918 0.026508589 56.16897343 -1.749496487 0.139864388 REFEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 REFEER 6 1 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 ; 120.62 0.032078 509110000 226580 351110 309040 318820 352750 301220 290130 282140 299500 FALSE TRUE 212398.7623 377106.5497 316370.5747 327001.461 325046.4379 388177.3241 246627.6999 317365.8001 249511.5152 0.851258356 1.511379343 1.267959816 1.310566612 1.30273121 1.555749136 0.988442156 1.271948511 1 17.92874687 1.689165878 11.80381611 1.099429945 1.321019274 0.192413904 0.202048795 0.174438298 34.47843986 0.085260139 0.046554118 48.88390354 -1.689165878 0.221589329 REFITGDVEPTDAESEWHS(ph)ENEEEEKLAGDMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 REFITGDVEPTDAESEWHSENEEEEKLAGDMK 32 2 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 REFITGDVEPTDAES(0.025)EWHS(0.975)ENEEEEKLAGDMK 144.92 2.58E-10 190430000 81233 50613 57882 67153 74397 49827 68113 49444 88146 TRUE FALSE 76148.77154 54360.43918 59254.98837 68876.25967 68554.15972 64211.24603 57900.08798 55617.19224 73433.86316 1.036970796 0.740263917 0.806916398 0.937935943 0.933549684 0.874409207 0.788465777 0.757377998 1 16.16415788 3.83558111 0.006852061 1.690633255 8.70E-05 0 0.103168571 61760.21199 90.77428744 10798.41854 11603.59019 6848.27372 -3.83558111 -1.690546286 REFQLDLDEIENDNGTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 REFQLDLDEIENDNGTVR 18 1 Q14008;Q14008-3;Q14008-2;H0YEK7;H0YCF6 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 127.37 4.10E-05 55188000 31212 32785 31368 35861 41547 27249 39740 30276 39657 FALSE TRUE 29258.49664 35212.43551 32112.06377 36781.25397 38284.06621 35115.34395 33781.35593 34056.02525 33037.99051 0.885601581 1.065816503 0.971973879 1.11330179 1.158789189 1.062877718 1.022500322 1.030814064 1 15.01183832 4.741627695 24.63955089 1.051424514 0.885601506 0.490626874 0.05365793 227.2163543 1825243.856 0.013228672 0.094868817 55160.43665 -4.741627695 -0.165823007 REGDVAACYANPSLAQEELGWTAALGLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 REGDVAACYANPSLAQEELGWTAALGLDR 29 1 Q14376;Q14376-2;Q5QPP4;Q5QPP9 Q14376 GALE UDP-glucose 4-epimerase 0 ;; 207.48 2.68E-25 204852000 100554 110020 117580 108448 101744 85245 133151 97238 114800 FALSE TRUE 94260.50463 118165.9953 120369.0531 111230.9593 93753.43666 109853.8477 113186.2437 109378.3783 95639.13836 0.985585047 1.235540149 1.258575257 1.163027618 0.980283159 1.14862858 1.183472014 1.143657087 1 16.54531351 2.989799085 24.88183101 1.10965281 1.192779705 0.063087041 0.097736641 943.2685851 2300806.209 0.02852125 0.032182225 976.7852319 -2.989799085 0.083126895 REGGDGEEQDVGDAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 REGGDGEEQDVGDAGR 16 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 198.49 6.51E-11 1482160000 885240 908630 901240 876650 955060 774230 996570 885490 1172430 FALSE TRUE 829834.4086 975905.9106 922617.8384 899146.3232 880053.4401 997737.6324 847143.5802 996045.3757 976743.8588 0.849592655 0.9991421 0.944585246 0.920554877 0.901007395 1.021493633 0.867313956 1.019761083 1 19.89762075 1.197176875 24.99012357 1.009880846 0.937406965 0.275990959 0.053084728 229.2715868 138443.6518 0.046049703 0.011512885 15.74624032 -1.197176875 -0.072473881 REGS(ph)YDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 96.113 0.0079442 402784000 510722 555840 542646 563874 614574 460746 578099 519554 705550 TRUE FALSE 478756.8217 596994.972 555517.8194 578343.9615 566307.8371 593755.8906 491418.4218 584421.4606 587789.147 0.814504358 1.015661781 0.945097102 0.983930997 0.963454055 1.010151163 0.836045416 0.994270588 1 19.1649392 4.752690161 24.27480186 0.960740396 0.814504208 0.457260043 0.052134542 1654.444182 2842290.495 0.012447531 0.253035251 56583.54603 -4.752690161 -0.146236188 REGT(ph)PPPPPPSR ddPTM_SK-BR-3_Pertuzumab_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 68.257 0.03115 835300000 378170 429310 416990 413850 447490 393090 481610 375770 402840 TRUE FALSE 354501.0148 461096.5591 426881.1997 424470.0916 412345.9405 506568.7017 409397.0515 422685.7117 335603.4016 1.056309361 1.373932913 1.271981147 1.26479675 1.228670325 1.509426601 1.219883498 1.25947982 1 18.35639781 -0.412335164 7.417633861 1 1.286069421 0.352164881 0.115196139 0 0 0.098980727 0.023329981 0.386958896 0.412335164 0.286069421 REHY(ph)VAVQLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 REHYVAVQLLK 11 1 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;A0A0A0MRE9;H7BYL6 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 1 REHY(1)VAVQLLK 92.062 0.010783 197340000 319990 264680 277660 240660 283460 261770 388620 274560 477390 TRUE FALSE 299962.3971 284277.1826 284246.2263 246835.743 261198.195 337338.7495 330350.0388 308839.4204 397710.5249 0.754222929 0.714784158 0.714706322 0.620641717 0.656754545 0.848201715 0.83062936 0.776543242 1 18.60135922 2.229769062 24.99531902 0.847628413 0.695111007 0.617648113 0.066534559 133.9244132 380758.3564 0.023045805 0.017276217 169.7340845 -2.229769062 -0.152517406 REPAEQPGDGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 REPAEQPGDGER 12 1 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 ;;; 157.22 0.00011841 1177700000 701370 749130 735920 675320 772630 634220 806750 676470 927700 FALSE TRUE 657472.5037 804596.3647 753376.3699 692649.8545 711950.7564 817309.0183 685785.327 760928.7686 772860.8768 0.850699684 1.041062355 0.974789115 0.896215445 0.921188765 1.057511181 0.887333474 0.984561118 1 19.55984921 REPAPNAPGDIAAAFPAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 REPAPNAPGDIAAAFPAER 19 1 O95359-3;E9PBC6;E7EMZ9;O95359;H0Y954 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 123.84 4.88E-05 246750000 173680 206770 217180 192360 224840 178190 193040 207340 173000 FALSE TRUE 162809.6788 222079.4659 222331.6122 197296.2833 207181.9734 229630.5603 164095.4441 233226.8554 144125.1824 1.129640748 1.540878993 1.542628488 1.368923043 1.437514041 1.593271603 1.138561918 1.618224182 1 17.13696291 -2.928471933 0.384056633 1.38E-12 1.441334537 0.350508172 0.174735113 110.231165 3.679875329 89.95644621 0.108178368 0.001179039 2.928471933 1.441334537 REPGS(ph)GT(ph)ESDTSPDFHNQENEPSQEDPEDLDGSVQGVKPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 REPGSGTESDTSPDFHNQENEPSQEDPEDLDGSVQGVKPQK 41 2 Q9HAF1-3;Q9HAF1-2;Q9HAF1;Q9HAF1-4;B1AK63 Q9HAF1-3 MEAF6 Chromatin modification-related protein MEAF6 2 REPGS(0.622)GT(0.38)ES(0.316)DT(0.356)S(0.325)PDFHNQENEPSQEDPEDLDGSVQGVKPQK 151.89 2.35E-12 328940000 158910 104570 112740 119240 130120 95029 157110 98402 160270 TRUE FALSE 148964.1068 112312.4716 115414.246 122299.9003 119900.9001 122462.3296 133552.814 110687.7063 133519.9016 1.115669686 0.841166525 0.864397327 0.915967573 0.898000213 0.917184091 1.000246498 0.828997812 1 17.02669527 1.981412193 23.7452831 0.947010443 0.906393633 0 0.087905122 1419.804692 1813746.996 0.033392866 0.022007888 95.81029852 -1.981412193 -0.040616811 REPLPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 REPLPSR 7 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39;Q8IZ40 P38159;Q96E39;Q8IZ40 RBMX;RBMXL1;RCOR2 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1;REST corepressor 2" 0 ;;;;;; 128.93 0.0059481 4862910000 2353000 2823230 2607850 2417720 2715750 2114170 2536830 2491670 2586270 FALSE TRUE 2205729.93 3032264.887 2669709.434 2479762.788 2502465.95 2724496.558 2156455.892 2802760.484 2154604.829 1.023728296 1.407341544 1.239071498 1.150913037 1.161450079 1.264499421 1.00085912 1.300823449 1 21.03899186 1.045617093 0.299636586 0.980614585 1.274871757 0.12552556 0.127172585 2.771128115 0.798471284 0.303386573 0.185402332 11.10751973 -1.045617093 0.294257172 REPWLLPSQHNDIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 REPWLLPSQHNDIIR 15 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 240.92 4.77E-18 422390000 74490 298950 104227 122273 301280 66176 140258 240327 254150 FALSE TRUE 69827.80387 321084.5691 106699.3137 125410.7322 277618.6841 85279.93692 119227.615 270332.355 211730.7231 0.329795331 1.516476042 0.503938739 0.592312397 1.311187531 0.402775448 0.563109658 1.276774343 1 17.6918711 4.987965603 23.91355672 0.855727798 0.058689311 0.170168519 0.383849058 10965.16712 40583.86373 0.086045458 163383.6328 97267.01826 -4.987965603 -0.797038487 REPYGHLGPAELLEAS(ph)PAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 REPYGHLGPAELLEASPAAR 20 1 Q9H6W3 Q9H6W3 NO66 Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 1 REPYGHLGPAELLEAS(1)PAAR;REPYGHLGPAELLEAS(1)PAAR 94.594 0.00063293 110090000 41912 49210 43857 49818 56557 42545 57482 43277 58432 TRUE FALSE 39288.80274 52853.5596 44897.30875 51096.41422 52115.24136 54827.05084 48863.10774 48680.22871 48679.32171 0.807094293 1.085749713 0.922307608 1.049653373 1.070582735 1.126290361 1.003775443 1.000018632 1 15.57102145 4.747393956 24.90733208 1.030372533 0.807094173 0.612643714 0.056258097 790.4371531 2228742.598 0.013450919 0.161721165 55897.70227 -4.747393956 -0.22327836 REQEEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 REQEEELR 8 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WT54 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 0 ; 137.05 0.0012265 318430000 75895 95065 98158 102000 119869 89400 108157 84114 116181 FALSE TRUE 71144.86743 102103.7115 100486.3541 104617.4927 110454.9723 115208.3287 91939.86193 94615.81806 96789.64054 0.735046303 1.054903303 1.038193277 1.080874896 1.141185892 1.19029607 0.949893619 0.977540753 1 16.56256502 4.738577019 9.19868076 1.056112582 0.733781907 0.659130483 0.072096829 0.050924276 95.29154973 0.017450747 0.101817051 54774.32301 -4.738577019 -0.322330675 REQEVAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 REQEVAEER 9 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 145.28 0.00015643 49155000 67583 72871 74420 74067 78515 69364 79324 64263 67598 FALSE TRUE 63353.10067 78266.44466 76185.27754 75967.68462 72348.74861 89388.26077 67430.10261 72286.37701 56315.4571 1.12496824 1.389786192 1.35283067 1.348966847 1.284704988 1.58727755 1.197364029 1.283597448 1 15.78124334 -0.648101608 5.620466389 0.999999992 1.331787131 0.402553549 0.122365489 1.11E-08 2.82E-09 0.10644766 0.025089953 0.224852848 0.648101608 0.331787139 REQGGSGLGSGSS(ph)GGGGSTSGLGSGYIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 REQGGSGLGSGSSGGGGSTSGLGSGYIGR 29 1 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 REQGGS(0.001)GLGS(0.008)GS(0.087)S(0.903)GGGGSTSGLGSGYIGR 77.026 0.0030341 140220000 72371 75437 73599 92278 88868 38559 45110 48111 81904 TRUE FALSE 67841.4283 81022.43397 75344.80304 94646.00971 81888.66576 49690.35735 38346.17428 54117.76426 68233.69328 0.994251154 1.187425597 1.104216985 1.387086132 1.200120671 0.728237839 0.56198298 0.793123773 1 16.05819669 2.23567689 23.76524814 0.715650541 1.176423488 0.643351267 0.14685245 21.00779915 173123.5373 0.050563951 0.039030861 172.0588 -2.23567689 0.460772948 REQS(ph)PLLHLDLFNFDCPEAEGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 REQSPLLHLDLFNFDCPEAEGSR 23 1 Q9NQR7 Q9NQR7 CCDC177 Coiled-coil domain-containing protein 177 1 REQS(1)PLLHLDLFNFDCPEAEGSR;REQS(1)PLLHLDLFNFDCPEAEGSR;REQS(0.999)PLLHLDLFNFDCPEAEGS(0.001)R;REQS(1)PLLHLDLFNFDCPEAEGSR;REQS(1)PLLHLDLFNFDCPEAEGSR 210.8 2.81E-25 187104000 77232.8 77911.7 86214.7 72804 110395 82192.3 88268 89768.3 208778 TRUE FALSE 72398.93691 83680.36334 88259.7534 74672.2739 101725.022 105919.8827 75033.03284 100976.0699 173931.603 0.416249466 0.481110746 0.507439429 0.429319759 0.584856462 0.608974337 0.431393902 0.580550447 1 17.40816057 -5 0.276633789 4.580004169 0.467785327 0.867412277 0.061925905 74.16704551 0.714083139 152.1086263 0.070169468 1.00E-05 5 -4.112218841 RES(ph)AAS(ph)GLGGLLEEEGAGAGAAQEEVLEPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RESAASGLGGLLEEEGAGAGAAQEEVLEPGR 31 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 RES(1)AAS(1)GLGGLLEEEGAGAGAAQEEVLEPGR 191.69 2.95E-18 162970000 73435 77009 70138 67120 74068 52546 101430 76419 75488 TRUE FALSE 68838.83444 82710.82649 71801.70648 68842.41283 68250.99806 67715.17719 86221.51313 85960.08037 62888.56513 1.094616077 1.315196591 1.141729126 1.094672977 1.085268807 1.076748643 1.371020518 1.366863438 1 15.9405101 1.742395011 25 1.28086209 1.152900157 0.121637863 0.123842963 1.122565859 7355.809831 0.054786687 0.030381897 55.25798076 -1.742395011 -0.127961933 RES(ph)AASGLGGLLEEEGAGAGAAQEEVLEPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RESAASGLGGLLEEEGAGAGAAQEEVLEPGR 31 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RES(1)AASGLGGLLEEEGAGAGAAQEEVLEPGR;RES(1)AASGLGGLLEEEGAGAGAAQEEVLEPGR;RES(1)AASGLGGLLEEEGAGAGAAQEEVLEPGR;RES(1)AASGLGGLLEEEGAGAGAAQEEVLEPGR;RES(0.998)AAS(0.002)GLGGLLEEEGAGAGAAQEEVLEPGR;RES(0.941)AAS(0.059)GLGGLLEEEGAGAGAAQEEVLEPGR 360.69 2.58E-121 4840670000 939932 959237 966446 954492 960871 854295 1151310 942802 886080 TRUE FALSE 881103.3339 1030259.906 989370.5555 978985.8807 885408.0676 1100916.098 978681.7537 1060512.905 738187.5237 1.193603665 1.395661499 1.34026995 1.32620215 1.199435156 1.491377276 1.325790158 1.436644309 1 19.49362783 -1.250616187 3.793962587 0.999506843 1.344775707 0.568210319 0.092630578 9420194.719 20829476.19 54474.26311 0.019841793 0.056154403 1.250616187 0.345268864 RES(ph)CGSSVLTDFEGK ddPTM_SK-BR-3_Pertuzumab_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(0.933)CGS(0.053)S(0.014)VLTDFEGK;RES(0.938)CGS(0.062)SVLTDFEGK;RES(1)CGSSVLTDFEGK;RES(0.929)CGS(0.007)S(0.06)VLT(0.004)DFEGK;RES(0.859)CGS(0.139)S(0.002)VLTDFEGK;RES(0.997)CGS(0.003)SVLTDFEGK 235.35 6.85E-18 2592489000 3938650 2910830 3164370 3028330 2919306 2557643 4253010 2955970 3095380 TRUE FALSE 3692136.927 3126350.882 3239430.351 3106042.075 2690035.483 3295993.014 3615310.634 3325029.361 2578741.081 1.431759456 1.21235548 1.256206129 1.204480007 1.043158424 1.278140345 1.401967286 1.289400237 1 21.2982355 4.742439712 23.27424085 1.232947649 1.431759668 0.238773307 0.118254375 241.027763 1445980.675 0.027875313 0.208112088 55263.66859 -4.742439712 0.198812019 RES(ph)CGSSVLTDFEGKDVATK ddPTM_SK-BR-3_Pertuzumab_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(0.998)CGS(0.002)SVLTDFEGKDVATK;RES(0.999)CGS(0.001)SVLTDFEGKDVATK;RES(0.983)CGS(0.012)S(0.005)VLTDFEGKDVATK;RES(0.977)CGS(0.022)SVLTDFEGKDVATK;RES(0.969)CGS(0.031)SVLTDFEGKDVATK 263.92 8.31E-37 2459050000 2106820 1666940 1687610 1911260 2167420 1313030 2748480 1642840 3981550 TRUE FALSE 1974957.897 1790361.972 1727640.906 1960306.167 1997199.576 1692080.446 2336370.94 1847952.19 3317003.583 0.59540421 0.5397528 0.520843847 0.590987051 0.602109562 0.510123189 0.704361898 0.557114921 1 21.66144914 -4.611435716 0.251102788 3.098775085 0.535842978 0.857979568 0.054088815 47.53320113 0.564980965 50.90702587 0.070957402 2.45E-05 4.611435716 -2.562932107 RES(ph)DESGESAPDEGGEGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RESDESGESAPDEGGEGAR 19 1 Q7Z3C6;H7C152;Q7Z3C6-2 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 RES(1)DESGESAPDEGGEGAR;RES(0.999)DES(0.001)GESAPDEGGEGAR 206.67 2.16E-16 1377590000 753020 712960 666840 693550 835100 624420 929610 806290 1224000 TRUE FALSE 705889.8224 765748.3002 682657.7597 711347.6672 769514.6146 804679.9174 790223.6106 906957.0814 1019706.493 0.692248041 0.750949715 0.669464954 0.69760041 0.754643243 0.789128953 0.774952024 0.889429545 1 19.95972252 1.100749958 0.729966102 1.003039422 0.706282531 0.91763711 0.028487433 0.174429465 0.216468141 0.027289957 0.010802603 12.61101255 -1.100749958 -0.296756892 RES(ph)EDDPES(ph)EPDDHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RESEDDPESEPDDHEK 16 1 P16383-3;P16383-4;P16383 P16383-3 GCFC2 GC-rich sequence DNA-binding factor 2 2 RES(1)EDDPES(1)EPDDHEK;RES(1)EDDPES(1)EPDDHEK 192.58 1.79E-09 1472510000 2501700 1503540 1862740 1799130 1825200 1406840 2300200 1524720 2252640 TRUE FALSE 2345123.063 1614863.666 1906925.072 1845298.722 1681856.155 1812971.87 1955306.364 1715084.648 1876659.831 1.249626077 0.860498871 1.016127185 0.983288868 0.896196597 0.96606313 1.041907719 0.913902786 1 20.83973574 4.75159412 24.8776579 0.962843655 1.249626274 0.725647819 0.055986833 1105.967514 2110971.801 0.013145621 0.246544595 56440.92467 -4.75159412 0.286782619 RES(ph)ES(ph)ESDETPPAAPQLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RESESESDETPPAAPQLIK 19 1 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 2 RES(0.996)ES(0.992)ES(0.012)DETPPAAPQLIK 122.39 0.00011647 66349000 170510 125040 158690 155510 141930 106810 186420 134540 142970 TRUE FALSE 159838.0835 134298.0917 162454.2017 159500.6499 130783.3903 137644.3131 158468.0516 151337.6152 119107.3834 1.341966207 1.127537923 1.363930574 1.339133187 1.098029246 1.155632079 1.330463714 1.270598101 1 16.86190332 -1.392939663 9.769825644 0.999999705 1.251473567 0.40673669 0.0961571 5.96E-07 3.70E-08 0.089789185 0.021163489 0.04046321 1.392939663 0.251473862 RES(ph)FLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RESFLYR 7 1 Q08499-10;A0A087WSZ7;A0A1B0GW84;Q08499-2;Q08499-9;Q08499-6;Q08499-11;Q08499;A0A1W2PQN6;Q08499-7;Q08499-12;P27815 Q08499-10;P27815 PDE4D;PDE4A "cAMP-specific 3,5-cyclic phosphodiesterase 4D;cAMP-specific 3,5-cyclic phosphodiesterase 4A" 1 RES(1)FLYR;RES(1)FLYR;RES(1)FLYR;RES(1)FLYR 152.27 0.0011178 649940000 202272 252043 202941 210057 201458 134603 224985 189468 244886 TRUE FALSE 189612.1566 270704.526 207754.8564 215447.4182 185636.3013 173460.701 191250.5879 213123.4969 204012.9446 0.929412381 1.326898774 1.018341541 1.056047785 0.909924131 0.850243603 0.937443398 1.044656736 1 17.63830117 3.310163395 1.676733603 0.94047616 1.155802315 0.247158825 0.112454615 0.342514853 1.975145321 0.034057099 0.051923514 2042.506252 -3.310163395 0.215326155 RES(ph)INDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RESINDR 7 1 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 RES(1)INDR 112.89 0.0038294 59148000 200950 167810 237060 224890 231660 196970 249620 198200 272430 TRUE FALSE 188372.8982 180234.827 242683.1751 230661.0581 213466.3581 253832.0415 212191.7984 222945.7063 226959.673 0.829984004 0.7941271 1.069278837 1.016308558 0.940547522 1.118401512 0.934931724 0.982314185 1 17.79207645 4.055106814 3.840316575 1.00607929 0.813695239 0.683814468 0.055441445 0.119374656 3.360865437 0.013110361 0.030224446 11352.90005 -4.055106814 -0.192384051 RES(ph)PLKIDPFEDLSFNLLAVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RESPLKIDPFEDLSFNLLAVSK 22 2 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 RES(1)PLKIDPFEDLSFNLLAVSK 89.668 0.0013019 194990000 163030 99382 132770 127770 133530 115460 176940 123160 145180 TRUE FALSE 152826.2433 106740.3467 135919.3671 131048.7945 123043.0924 148791.4277 150409.4896 138536.7971 120948.5201 1.263564392 0.8825271 1.12377867 1.083508871 1.017317883 1.230204615 1.24358272 1.14541953 1 16.88403359 2.24069137 24.99310157 1.184405699 1.05520531 0.070219999 0.116091436 79.87243349 936891.6536 0.038321796 0.030609309 174.0569504 -2.24069137 -0.129200389 RES(ph)PPAGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RESPPAGQK 9 1 J3KPC5;P47736-3;P47736;P47736-4;F2Z357;X6R8W7;P47736-2;A0A0A0MQY8 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 RES(1)PPAGQK;RES(1)PPAGQK;RES(1)PPAGQK;RES(1)PPAGQK 118.76 0.00057426 1363160000 1600630 1358710 1492540 1399880 1561270 1030250 1593180 1276120 1742210 TRUE FALSE 1500449.426 1459310.302 1527943.754 1435803.291 1438654.152 1327666.45 1354297.449 1435446.391 1451423.896 1.033777541 1.005433565 1.052720544 0.989237737 0.99120192 0.914733769 0.933081957 0.988991841 1 20.4690375 2.746030397 2.084686527 0.951399679 1.027085479 0.478214485 0.029584086 0.222184544 1.905705439 0.010147036 0.010103642 557.2247482 -2.746030397 0.0756858 RES(ph)PS(ph)PAPKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RESPSPAPKPR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RES(1)PS(1)PAPKPR 114.7 0.032078 127830000 487870 413100 458030 462910 504300 367680 517380 424730 627770 TRUE FALSE 457335.0876 443686.3538 468894.6879 474789.0543 464694.3122 473823.2472 439803.6721 477758.4754 522991.1315 0.874460502 0.848363055 0.896563364 0.907833854 0.888531916 0.905987155 0.840939063 0.913511619 1 18.99642696 0.98255694 23.04456817 1.000000001 0.879235926 0.745865566 0.022016948 199.7015957 263832.992 0.021357992 0.005339498 9.606317582 -0.98255694 -0.120764075 RES(ph)PSEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RESPSEER 8 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 RES(0.99)PS(0.01)EER;RES(0.998)PS(0.002)EER 156.01 0.00024486 478900000 257550 263540 256430 244400 217763 250360 295450 238657 194096 TRUE FALSE 241430.4052 283052.7758 262512.6407 250671.7178 200660.7724 322634.8677 251150.0153 268453.8518 161700.1237 1.493074957 1.750479649 1.623453555 1.550225888 1.24094384 1.995266673 1.553183817 1.660195711 1 17.30296126 -1.051869934 4.319524611 0.999960421 1.621925032 0.498862068 0.191192859 2.704973233 49992285.35 5448.087059 0.040649098 0.088742174 1.051869934 0.621964611 RES(ph)PSEERLEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RESPSEERLEPK 12 2 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 RES(0.953)PS(0.047)EERLEPK;RES(0.998)PS(0.002)EERLEPK;RES(0.998)PS(0.002)EERLEPK 163.02 3.73E-05 2012190000 1869800 1661390 1734620 1770520 2053170 1242140 2003620 1459620 2577930 TRUE FALSE 1752772.556 1784401.044 1775766.006 1815954.541 1891922.31 1600725.654 1703195.782 1641856.77 2147656.829 0.816132509 0.830859484 0.826838805 0.845551541 0.880923938 0.745335862 0.793048386 0.764487486 1 21.03433205 2.256546708 24.99967912 0.804564538 0.837252946 0 0.071502357 785.4688431 1091756.333 0.021752219 0.01816447 180.5288882 -2.256546708 0.032688408 RES(ph)PSPAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RESPSPAPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RES(1)PSPAPK;RES(1)PSPAPK;RES(0.979)PS(0.021)PAPK;RES(0.997)PS(0.003)PAPK;RES(0.997)PS(0.003)PAPK;RES(0.943)PS(0.057)PAPK 109 0.0015439 3037650000 6044870 4281340 4893310 4603850 4354440 4071890 5328030 4125570 3534550 TRUE FALSE 5666532.377 4598334.868 5009381.624 4721992.585 4012459.847 5247378.541 4529141.365 4640656.496 2944610.771 1.92437399 1.561610422 1.701203321 1.60360501 1.362645239 1.782027898 1.538112069 1.575982993 1 21.48964552 -2.669533139 0.255929904 7.93E-12 1.69783183 0.676413375 0.141537643 27.87799105 0.796804073 15.69935126 0.186488867 0.002140262 2.669533139 1.69783183 RES(ph)PSPAPKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 RESPSPAPKPR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RES(0.895)PS(0.105)PAPKPR;RES(0.785)PS(0.215)PAPKPR;RES(0.65)PS(0.35)PAPKPR;RES(0.973)PS(0.027)PAPKPR;RES(0.869)PS(0.131)PAPKPR;RES(0.927)PS(0.073)PAPKPR;RES(0.987)PS(0.013)PAPKPR;RES(0.981)PS(0.019)PAPKPR;RES(0.892)PS(0.108)PAPKPR;RES(0.857)PS(0.143)PAPKPR 131.53 0.00010505 67385470000 12680460 11695180 11895940 11725640 12053890 9815690 14050060 10132250 12871870 TRUE FALSE 11886812.64 12561103.3 12178117.31 12026539.77 11107226.1 12649320.36 11943383.94 11397283.72 10723471.74 1.108485473 1.171365356 1.135650618 1.1215155 1.035786392 1.179591896 1.113760937 1.062835245 1 23.35426872 -4.947477496 0.151531429 0.54238604 1.16321591 0.483594888 0.040675144 107.1500567 0.974358161 14.6222301 0.191965932 1.13E-05 4.947477496 0.620829869 RES(ph)QEEPR ddPTM_SK-BR-3_Pertuzumab_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 169.82 0.00018301 3441590000 3694600 3887550 3682920 3628730 3711100 3491000 4433760 3637970 4827570 TRUE FALSE 3463361.581 4175388.247 3770280.602 3721849.355 3419645.176 4498795.028 3768958.849 4092178.563 4021817.38 0.861143422 1.038184446 0.937456937 0.925414807 0.850273608 1.11859754 0.937128291 1.017494873 1 21.93941614 2.248897156 24.99998607 1.008698702 0.940443599 0.307091824 0.067954523 339.1395702 820244.091 0.022946758 0.018995273 177.3769392 -2.248897156 -0.068255103 RES(ph)VNLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RESVNLGK 8 1 P46013 P46013 MKI67 Antigen KI-67 1 RES(1)VNLGK 117.14 0.001309 220410000 174880 166540 165220 147120 198370 99562 259330 166210 351050 TRUE FALSE 163934.573 178870.7949 169139.0964 150895.3483 182790.8204 128303.9331 220445.874 186961.6844 292457.4871 0.560541549 0.611612979 0.578337378 0.515956523 0.625016724 0.438709689 0.753770663 0.63927816 1 18.1578674 0.608296116 0.851660617 1.000189262 0.569311475 0.760104448 0.074717901 0.571194881 0.700192237 0.066122126 0.022135512 4.057851182 -0.608296116 -0.430877787 RESSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RESSLK 6 1 O43684;O43684-2;J3QT28 O43684 BUB3 Mitotic checkpoint protein BUB3 0 83.753 0.090802 57828000 141260 224490 216420 204650 211690 183350 198370 199710 185020 FALSE TRUE 132418.7888 241111.4732 221553.5846 209901.6655 195064.7213 236280.1686 168626.2601 224644.2331 154138.9667 0.859087041 1.564247369 1.437362591 1.361768993 1.26551206 1.532903545 1.09398852 1.457413644 1 17.2338721 -0.44659896 0.492413817 0.939443718 1.362702608 0.150349345 0.216773933 13.30398539 2.915052156 1.612110052 0.099125117 0.357602906 0.44659896 0.42325889 RESWER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RESWER 6 1 E9PH64;Q9Y6M9;A0A3B3IT57;E7EWZ0;E9PF49 E9PH64 NDUFB9 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 0 ; 120.62 0.032078 309310000 182060 303710 284460 279620 323000 301660 256530 297190 289140 FALSE TRUE 170665.1896 326197.0044 291207.5255 286795.5226 297632.8829 388744.345 218065.708 334294.8257 240880.6661 0.708505138 1.354185081 1.208928596 1.190612461 1.235603038 1.613846189 0.905285225 1.387802646 1 17.87795908 -1.306684893 3.243722236 0.998810201 1.211495667 0.05842471 0.249692819 30991888.97 47765129.89 366364.3929 0.05321854 0.049353176 1.306684893 0.212685466 RET(ph)DDEGEDD ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RETDDEGEDD 10 1 Q92688 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 1 RET(1)DDEGEDD;RET(1)DDEGEDD;RET(1)DDEGEDD;RET(1)DDEGEDD 173.6 6.50E-06 447799500 766261 714054 765273 729207 688649 622097 784967 628240 685264 TRUE FALSE 718302.0918 766923.3011 783425.6369 747919.6862 634565.2854 801686.305 667268.4856 706677.1469 570889.0114 1.258216707 1.343384241 1.372290623 1.310096483 1.111538798 1.404276994 1.168823488 1.237853826 1 19.12285077 0.046043637 0.311147351 0.922226619 1.343938675 0.537923791 0.084585474 3.60981752 0.537267378 0.440480818 0.091001443 1.111843436 -0.046043637 0.421712055 RET(ph)PS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RETPSPR 7 1 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RET(1)PS(1)PR;RET(1)PS(1)PR 64.82 0.062548 153577000 191226 337780 212486 194460 437580 161508 231044 406900 403220 TRUE FALSE 179257.506 362789.5827 217526.2683 199450.1728 403214.2319 208132.7377 196401.0971 457702.3607 335919.9771 0.533631574 1.079988114 0.647553832 0.593743113 1.200328231 0.619590236 0.584666321 1.362533913 1 18.35775807 1.238424891 24.99999998 1.181266983 0.767549568 0.361163156 0.236946899 3.906847999 718321.4957 0.174514114 0.054133486 17.31509549 -1.238424891 -0.413717415 REVLYDS(ph)EGLS(ph)GEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 REVLYDSEGLSGEER 15 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 REVLY(0.001)DS(0.999)EGLS(1)GEER;REVLY(0.001)DS(0.999)EGLS(1)GEER 123.6 6.80E-05 398990000 520920 535490 524450 535630 562790 462210 635440 493670 555050 TRUE FALSE 488316.5471 575138.2368 536890.2017 549375.1726 518590.7436 595642.5236 540161.6711 555305.7862 462408.5692 1.056028325 1.243788016 1.16107321 1.188073079 1.12149899 1.288130375 1.168148056 1.200898563 1 18.81880861 -1.386466522 3.12766517 0.99777529 1.184989925 0.438052923 0.063136193 9056955.237 11492305.65 181324.2978 0.013279524 0.04107083 1.386466522 0.187214636 REVS(ph)PAPAVAGQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 REVSPAPAVAGQSK 14 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 REVS(1)PAPAVAGQSK;REVS(1)PAPAVAGQSK 142.74 5.71E-06 793040000 1530330 1233560 1422990 1359260 1317430 1171020 1709750 1304730 1629280 TRUE FALSE 1434549.377 1324894.066 1456743.995 1394140.913 1213964.362 1509074.464 1453388.86 1467628.413 1357342.642 1.056880799 0.976094042 1.073232321 1.027110524 0.894368396 1.111785939 1.070760481 1.081251238 1 20.37235352 RFDAMPFTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RFDAMPFTLR 10 1 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 181.66 2.99E-06 197640000 62930 326830 64147 75107 373280 43604 58348 279650 258500 FALSE TRUE 58991.32363 351028.8333 65668.59713 77034.37278 343964.0945 56191.76695 49599.25908 314564.9181 215354.68 0.27392636 1.630003273 0.304932296 0.357709304 1.597198141 0.260926612 0.230314285 1.460682991 1 17.71635515 4.986095818 24.50342242 0.792392151 0.037325938 0.085796447 0.564109147 20435.872 56694.80484 0.126422055 272376.9441 96849.15097 -4.986095818 -0.755066214 RFDAQTGADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RFDAQTGADR 10 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;; 204 3.13E-07 1104950000 505080 824340 544660 594090 858180 487344 538410 689660 847330 FALSE TRUE 473467.9444 885374.9913 557579.5924 609335.3552 790782.0045 628032.3014 457680.4189 775765.5691 705905.149 0.670724594 1.254240733 0.789878914 0.86319721 1.120238329 0.889683695 0.648359655 1.098965732 1 19.42911482 2.010463028 24.97612579 0.849783383 0.962513231 0 0.20000484 605.2722758 1444829.744 0.07042509 0.0519612 102.438457 -2.010463028 0.112729848 RFDDAVVQSDMK ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;;;;;;;;;;;; 269.44 3.63E-22 43835420000 22508920 22944170 17873810 15664460 26501310 11557160 23424020 23351100 31755350 FALSE TRUE 21100126.88 24642980.22 18297785.21 16066436.56 24420004.01 14893524.48 19911805.66 26266536.24 26455176.94 0.797580259 0.931499354 0.691652347 0.607307848 0.923070901 0.562972023 0.752661973 0.992869422 1 24.65704673 1.236955925 14.35378139 0.996485061 0.75541734 0.427540931 0.117360186 0.223707412 1839.480933 0.090609422 0.027645683 17.25662751 -1.236955925 -0.241067721 RFDEATQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RFDEATQLR 9 1 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ;; 180.09 7.86E-05 751020000 331700 696360 607090 363920 486660 277377 402220 415140 553800 FALSE TRUE 310939.4891 747919.219 621490.4615 373258.8033 448439.6867 357451.2371 341910.845 466971.1428 461367.2023 0.673952304 1.621093167 1.34706251 0.809027606 0.971979986 0.774765166 0.741081818 1.012146378 1 18.81555592 3.240365484 24.99222367 0.85971975 1.32026639 0.233390955 0.255671985 43.16073572 597644.5425 0.067959827 0.087495623 1739.263905 -3.240365484 0.460546641 RFDEILEASDGIMVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 27 RFDEILEASDGIMVAR 16 1 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;;;;;;;;;;;;;;;;;; 334.04 1.90E-71 10626873000 4707405.4 5927376.1 5253688.3 5474218.8 6123444.1 4598961.8 5625418.9 4833448.5 5732616.4 FALSE TRUE 4412777.299 6366245.194 5378308.267 5614696.522 5642533.501 5926607.414 4781939.56 5436915.185 4775805.689 0.923985938 1.333020145 1.126157264 1.175654306 1.181483056 1.240964939 1.001284364 1.138428893 1 22.18731271 1.733260403 12.64153936 1.053447977 1.179931728 0.191039832 0.109744871 0.113930863 108.9873468 0.046328171 0.025415503 54.1078657 -1.733260403 0.126483751 RFDGVQDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RFDGVQDPR 9 1 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 0 85.731 0.023437 978260000 753830 1319400 617630 701290 1663600 461340 733090 1370800 1441200 FALSE TRUE 706649.1259 1417089.749 632280.4753 719286.2887 1532947.567 594521.3688 623169.9602 1541947.398 1200654.409 0.588553309 1.180264477 0.526613212 0.599078538 1.276760036 0.49516444 0.519025254 1.284255807 1 20.19538952 1.230281956 24.9993292 1.142127964 0.752316681 0.257354535 0.282916505 288.8040714 872076.6568 0.247074752 0.065904041 16.99346558 -1.230281956 -0.389811282 RFDSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RFDSEK 6 1 P17980;E9PM69;E9PKD5;R4GNH3 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ;; 143.02 0.018363 789250000 1278900 1368260 1104620 1147950 1451790 849840 1334710 1223780 1731540 FALSE TRUE 1198855.932 1469567.394 1130822.108 1177408.34 1337772.27 1095175.012 1134582.626 1376571.627 1442534.788 0.831075924 1.018739656 0.783913232 0.816207935 0.927376089 0.759201803 0.786520114 0.954272742 1 20.46017468 3.966731121 24.30134906 0.843442934 0.933689103 0.049978646 0.092028681 422.5715685 988351.4226 0.021361976 0.039081202 9262.561842 -3.966731121 0.090246169 RFDSELSQAHEEAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RFDSELSQAHEEAQR 15 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 163.91 9.81E-07 600930000 248573 327510 283834 300288 367104 257978 319015 312992 366040 FALSE TRUE 233015.2596 351759.1812 290566.6765 307993.8985 338273.1327 332452.0607 271181.6623 352069.7402 304945.5593 0.764120849 1.153514686 0.952847706 1.009996339 1.10929024 1.090201351 0.889278935 1.154533094 1 18.21819218 4.754730881 24.86744577 1.035951336 0.764120625 0.510538937 0.086016541 2507.577806 3856210.432 0.01955248 0.508497845 56850.05388 -4.754730881 -0.27183071 RFDVSGYPTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RFDVSGYPTLK 11 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 173.72 1.90E-05 1200210000 1987940 2295220 2106410 2295530 2565400 1601580 2694100 2063220 2357310 FALSE TRUE 1863518.384 2465160.477 2156375.04 2354437.186 2363923.832 2063930.147 2290144.716 2320817.559 1963859.732 0.948906051 1.255263009 1.098029052 1.198882561 1.203713174 1.050955989 1.16614475 1.181763402 1 20.90526046 -1.474438454 6.269169083 0.999925821 1.146256715 0.18957754 0.088169518 7.99E-05 6.70E-06 0.074619911 0.017579186 0.033539883 1.474438454 0.146330894 RFEEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RFEEGK 6 1 O00154-6;O00154-4;O00154-7;O00154;O00154-5 O00154-6 ACOT7 Cytosolic acyl coenzyme A thioester hydrolase 0 ;; 128.86 0.026366 869740000 1658580 1409570 1588710 1446320 1681760 1226910 1885760 1407310 1922890 FALSE TRUE 1554772.438 1513936.029 1626394.951 1483435.02 1549681.353 1581099 1603007.795 1583015.751 1601947.237 0.970551591 0.945059859 1.015261248 0.9260199 0.96737353 0.986985691 1.000662043 0.988182204 1 20.6113952 2.122866147 3.839847069 0.995818966 0.967275681 0.292923023 0.022641994 0.32292432 8.946369306 0.009029933 0.006375809 132.6985406 -2.122866147 -0.028543285 GWSQEGPVKS(ph)PAECR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 GWSQEGPVKSPAECR 15 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR 257.2 5.36E-25 5610270000 4858750 3925460 4707470 5769060 5271730 3098540 3752480 2574630 2683390 TRUE FALSE 4554649.511 4216105.143 4819133.411 5917103.847 4857709.591 3993038.197 3189830.46 2896078.223 2235514.874 2.037405147 1.885966044 2.155715208 2.646864003 2.172971269 1.786182791 1.426888498 1.295486001 1 21.09217571 1.740502177 1.621093348 1.13817327 2.156166396 0.817056977 0.205410013 0.166049946 0.854889653 0.169257525 0.066938714 55.01766783 -1.740502177 1.017993126 up RFEKPLEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RFEKPLEEK 9 2 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;; 201.75 1.18E-05 4768160000 12716920 8063670 9471390 9248280 9914880 7169830 13093950 8331520 12181150 FALSE TRUE 11920990.68 8660712.517 9696055.844 9485606.522 9136205.32 9239643.529 11130633.76 9371728.612 10148037.37 1.174708985 0.853437192 0.955461188 0.934723255 0.900292833 0.910485761 1.096826248 0.923501586 1 23.2746974 1.766804102 25 1.016143093 0.940347593 0.045786344 0.094626561 41.30153384 36579.98164 0.039621343 0.02197465 58.45263619 -1.766804102 -0.075795501 RFELYFQGPSSNKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RFELYFQGPSSNKPR 15 2 P33993;P33993-2;C9J8M6 P33993 MCM7 DNA replication licensing factor MCM7 0 114.73 0.00032822 189640000 238590 154270 154750 163610 189230 105590 170200 141280 155450 FALSE TRUE 223657.0778 165692.3113 158420.7431 167808.5096 174368.6391 136072.1189 144680.0901 158919.119 129504.3908 1.727023126 1.279433928 1.223284725 1.295774673 1.346430326 1.050714328 1.117182894 1.227133058 1 16.98264149 7.883324222 0.890782646 1.176406134 200 0.721045249 0.105760085 370.0665871 1.068627928 0.032702477 149181.0163 76440623.65 -7.883324222 198.8235939 RFES(ph)IPDMLELDHLTVSGDVTFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RFESIPDMLELDHLTVSGDVTFGK 24 1 A0A087WYS1;E7EUC7;Q16851;Q16851-2 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 1 RFES(1)IPDMLELDHLTVSGDVTFGK 99.866 0.0021639 64127000 138290 149010 141560 150640 177710 127240 181820 137670 175910 TRUE FALSE 129634.6758 160042.8554 144917.87 154505.6774 163753.3734 163972.1224 154557.7789 154858.4025 146549.4846 0.884579541 1.09207382 0.98886646 1.054290146 1.117393036 1.118885699 1.054645667 1.056697013 1 17.16102837 4.744707036 24.81240127 1.061350837 0.884579454 0.62421371 0.042855407 425.7782515 1718765.442 0.010275583 0.094027316 55552.93851 -4.744707036 -0.176771384 RFESIPDMLELDHLTVSGDVTFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RFESIPDMLELDHLTVSGDVTFGK 24 1 A0A087WYS1;E7EUC7;Q16851;Q16851-2 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 90.193 0.0063669 68397000 73411 76326 73018 79436 93723 67518 81381 67232 83572 FALSE TRUE 68816.33655 81977.25646 74750.02144 81474.46224 86362.37364 87009.35054 69178.67455 75626.0632 69623.2933 0.988409673 1.177440086 1.073635243 1.170218448 1.240423564 1.249716099 0.993613937 1.086217839 1 16.08728244 1.676606481 9.902027164 1.030899199 1.148416555 0.347759297 0.079409185 0.137797036 20.05761471 0.037055536 0.01993272 47.49047149 -1.676606481 0.117517355 RFFPYYVYNIIGGLDEEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RFFPYYVYNIIGGLDEEGK 19 1 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 135.43 1.25E-05 97562000 325630 356880 308710 317550 415480 165070 301720 356390 425490 FALSE TRUE 305249.3996 383303.7665 316032.747 325698.8706 382849.8768 212723.0293 256479.887 400886.076 354472.9702 0.861135898 1.081334259 0.891556687 0.918825688 1.080053795 0.60011072 0.723552735 1.130935529 1 18.4353161 2.270522892 24.99935404 0.819480366 0.969828013 0.063325247 0.160569136 332.8480228 260336.5347 0.053004935 0.0443437 186.4330448 -2.270522892 0.150347647 RFNDGSDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RFNDGSDEK 9 1 P25705;P25705-2;P25705-3;K7EK77;K7ENJ4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 84.658 0.024601 163240000 275390 249550 215110 197300 309820 202870 227930 222850 327790 FALSE TRUE 258153.8315 268026.9417 220212.5108 202363.052 285487.987 261435.2757 193754.0125 250673.3131 273079.7314 0.945342337 0.981497017 0.806403718 0.741040175 1.045438215 0.95735877 0.709514439 0.917949171 1 18.05896271 RFPEAEALS(ph)PEQAAHYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RFPEAEALSPEQAAHYLR 18 1 Q2NKX8 Q2NKX8 ERCC6L DNA excision repair protein ERCC-6-like 1 RFPEAEALS(1)PEQAAHYLR;RFPEAEALS(1)PEQAAHYLR 143.15 5.06E-08 65166000 48542 61146 53137 59280 63495 53289 63379 55116 79725 TRUE FALSE 45503.84287 65673.31346 54397.43473 60801.22516 58508.35883 68672.66923 53875.90733 61997.35393 66418.38246 0.68510917 0.988782187 0.819011736 0.915427671 0.880906109 1.033940706 0.811159582 0.933436673 1 16.01929497 4.751436038 24.43732329 0.910521686 0.685108972 0.499920562 0.073813942 1290.609359 2449493.922 0.015878561 0.286785977 56420.38406 -4.751436038 -0.225412714 RFPEEPHVPLEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RFPEEPHVPLEQR 13 1 Q8TCD5;J3KSX6;J3KRC4;Q8TCD5-2 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 0 ; 84.566 0.0062872 411614000 503672 620360 582100 604500 577670 487960 635500 491660 546410 FALSE TRUE 472148.0686 666292.0999 595907.6869 620012.4934 532302.1284 628826.1306 540212.6747 553044.8333 455210.6411 1.03720789 1.463700625 1.309081188 1.362034271 1.169353439 1.381395938 1.18673121 1.214920706 1 18.79617476 0.75195828 0.67789602 0.996981354 1.316239397 0.322991452 0.121653075 1.060316348 0.993582028 0.113960338 0.04270013 5.648827073 -0.75195828 0.319258043 RFPELESLVPNALDYIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RFPELESLVPNALDYIR 17 1 Q8WWY3-4;Q8WWY3;E7EVX8;Q8WWY3-3;Q8WWY3-2;E7EU94;E7ESX0;E7EN72 Q8WWY3-4 PRPF31 U4/U6 small nuclear ribonucleoprotein Prp31 0 125.51 7.48E-05 65243000 90823 114710 107100 95299 123090 74495 109310 100030 126100 FALSE TRUE 85138.55055 123203.2478 109640.4626 97744.53368 113423.0079 96000.49717 92919.98028 112518.9657 105053.0954 0.810433527 1.172771229 1.04366713 0.93042983 1.079673165 0.913828354 0.884504925 1.07106759 1 16.68075915 3.301086055 8.805856477 0.968243355 1.049370317 0 0.109415249 0.671560578 86.82568497 0.028818313 0.039002116 2000.258178 -3.301086055 0.081126962 RFPGYDSESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 RFPGYDSESK 10 1 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;;;; 214.67 1.37E-08 13585070000 19190050 17222830 17728770 17647770 19782730 13635100 21792800 16967290 22188580 FALSE TRUE 17988979.03 18498026.25 18149304.8 18100641.66 18229074.19 17571332.02 18525171.95 19085693.51 18485162.65 0.973157735 1.000695888 0.981830949 0.979198398 0.986146269 0.950564101 1.002164401 1.032487182 1 24.1398644 1.50447662 7.186597942 1.016651799 0.981522512 0.535464125 0.014728964 0.090212242 10.55911042 0.007735796 0.003532082 31.95042359 -1.50447662 -0.035129287 RFPQHTIMAGNVVTGEMVEELILSGADIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RFPQHTIMAGNVVTGEMVEELILSGADIIK 30 1 A0A087WWM4;Q9P2T1;Q9P2T1-3;F8WAN9;H0YNJ6;Q9P2T1-2;H0YNH0;H0YLB8 A0A087WWM4 GMPR2 GMP reductase;GMP reductase 2 0 122.68 1.10E-05 82998000 159200 139770 151790 154260 183220 139440 161390 145760 142180 FALSE TRUE 149235.9562 150118.7162 155390.5305 158218.5728 168830.6403 179694.0644 137191.0678 163958.4569 118449.2395 1.259914853 1.267367498 1.311874446 1.335750009 1.425341699 1.517055451 1.158226666 1.384208608 1 16.85390941 -0.786300898 19.78956007 1 1.323588474 0.53077206 0.097924442 0 0 0.092123889 0.021713809 0.163568286 0.786300898 0.323588474 RFS(ph)ADEQFFSVGQAASSSAHSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RFSADEQFFSVGQAASSSAHSSK 23 1 P46019 P46019 PHKA2 "Phosphorylase b kinase regulatory subunit alpha, liver isoform" 1 RFS(1)ADEQFFSVGQAASSSAHSSK 248.82 3.46E-38 175890000 55852 158700 146170 159940 157990 136600 222390 162540 195770 TRUE FALSE 52356.32302 170450.3131 149637.2214 164044.3312 145582.1027 176034.2025 189044.6841 182833.4768 163094.7223 0.321017886 1.045100116 0.917486595 1.005822438 0.892623015 1.07933721 1.159109758 1.121026323 1 17.31535057 4.739452334 24.92041151 1.027041248 0.321017654 0.879862706 0.082048924 26.1581804 730912.3469 0.021867439 0.132683429 54884.83138 -4.739452334 -0.706023593 RFS(ph)DFLGLHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RFSDFLGLHSK 11 1 O60749;O60749-2;D6RC15 O60749 SNX2 Sorting nexin-2 1 RFS(1)DFLGLHSK;RFS(1)DFLGLHSK 140.22 1.82E-05 1398600000 1000140 1040620 917825 848643 1314750 688936 1014670 1048800 1583200 TRUE FALSE 937543.0227 1117668.588 939596.2424 870420.6161 1211494.838 887820.6393 862529.6532 1179744.989 1318953.692 0.710823305 0.847390317 0.712380009 0.659932658 0.918527197 0.673124951 0.653949914 0.8944552 1 20.33096248 1.03103998 5.480008297 0.999410627 0.743697041 0.532464233 0.084063315 0.117900827 9.375415477 0.078744651 0.019857074 10.74088284 -1.03103998 -0.255713586 RFS(ph)DFLGLYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RFSDFLGLYEK 11 1 Q13596-2;Q13596;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 1 RFS(1)DFLGLYEK 62.088 0.088123 54427000 202560 213430 193650 183750 244080 131460 203290 233790 330820 TRUE FALSE 189882.1312 229232.5793 198243.4694 188465.3361 224910.9414 169410.3679 172808.5518 262979.1961 275604.0048 0.688967242 0.831746184 0.719305474 0.683826551 0.816065578 0.614687613 0.627017564 0.954192216 1 18.07223733 1.156681223 6.475850799 0.990409802 0.717853206 0.713002589 0.070051402 0.130832828 8.070683997 0.071541328 0.018055162 14.34436153 -1.156681223 -0.272556596 RFS(ph)DGAASIQAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RFSDGAASIQAFK 13 1 H0Y4E8;Q9Y2K2-8;Q9Y2K2-7;Q9Y2K2 H0Y4E8 SIK3 Serine/threonine-protein kinase SIK3 1 RFS(0.962)DGAAS(0.038)IQAFK 136.1 2.31E-06 0 256840 293100 260140 265220 373010 192850 306480 312220 481900 TRUE FALSE 240764.8429 314801.429 266310.6436 272025.9942 343715.2992 248522.6643 260526.1692 351201.3543 401467.7768 0.599711501 0.784126267 0.663342512 0.67757865 0.856146668 0.619035147 0.648934197 0.874793382 1 18.61492467 1.046190397 4.162420271 0.99813988 0.698380844 0.65444553 0.076678651 0.107469897 3.975112076 0.069181615 0.017695331 11.12219222 -1.046190397 -0.299759036 RFS(ph)DQAAGPAIPTSNSYSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RFSDQAAGPAIPTSNSYSK 19 1 Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7 Q7KZI7-12 MARK2 Serine/threonine-protein kinase MARK2 1 RFS(1)DQAAGPAIPTSNSYSK;RFS(1)DQAAGPAIPTSNSYSK;RFS(1)DQAAGPAIPTSNSYSK 137.26 2.58E-06 722420000 936280 843590 908620 898780 983870 679610 1042710 809050 1518380 TRUE FALSE 877679.9061 906050.2814 930172.8955 921844.2164 906600.8189 875802.3745 886365.3155 910061.6734 1264952.569 0.693844123 0.716272138 0.735342113 0.728757931 0.716707362 0.692359853 0.700710317 0.719443318 1 20.27065186 -1.904414282 1.958418528 1.185907864 0.713914779 0.976467642 0.014004629 173953.7237 69740.57399 148684.2362 0.004041531 0.012461942 1.904414282 -0.471993085 RFS(ph)DQAGPAIPTSNSYSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 247.64 1.29E-24 2908910000 2998950 2730970 2826500 2931650 3437110 2250460 3253680 2530990 4313830 TRUE FALSE 2811251.073 2933173.86 2893545.915 3006881.102 3167173.245 2900131.269 2765820.89 2846989.673 3593823.905 0.782245081 0.816170725 0.805144045 0.836680144 0.881282258 0.806976453 0.769603899 0.792189531 1 21.77708829 -1.144254561 4.043566506 1.000060359 0.810757154 0.786898058 0.030862031 1.377866172 17465361.05 2256.751841 0.007585197 0.071737368 1.144254561 -0.189303205 RFS(ph)DSEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RFSDSEER 8 1 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 RFS(0.845)DS(0.155)EER;RFS(0.756)DS(0.244)EER 115.65 0.0014845 469770000 276360 301040 279350 302440 314220 259060 327330 265760 311370 TRUE FALSE 259063.1209 323329.3148 285976.3139 310201.1224 289542.4287 333846.4165 278249.9053 298940.721 259400.3355 0.998700023 1.246449101 1.102451596 1.195839326 1.11619913 1.286993002 1.072665942 1.152429971 1 17.98482082 0.500478245 1.126844611 1.000338232 1.157168396 0.225861244 0.083686706 2.447693817 4.177037934 0.069928673 0.021502743 3.165761874 -0.500478245 0.156830164 RFS(ph)DSEGEETVPEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RFSDSEGEETVPEPR 15 1 A0A1B0GWH8;H3BQ48;A0A1B0GWD3;A0A1B0GV71;A0A1B0GW34;A0A0D9SFH9;H3BPL0;Q9UBD8;A0A1B0GV41;H3BR84;O95090;H3BR00;Q9UP10;Q9UBH5;A0A0D9SF04;Q13286-5;Q13286-4;Q13286-6;Q13286-2;Q13286-7;Q13286-3;Q13286 A0A1B0GWH8 CLN3 Battenin 1 RFS(0.999)DS(0.001)EGEETVPEPR;RFS(0.999)DS(0.001)EGEETVPEPR;RFS(1)DSEGEETVPEPR;RFS(0.997)DS(0.003)EGEETVPEPR 221.81 9.10E-13 861550000 653180 519590 668730 614680 593880 738560 756260 565420 716120 TRUE FALSE 612298.6298 558060.9842 684592.5914 630453.7295 547239.0604 951770.2825 642865.8338 636013.9316 596594.9457 1.026322188 0.935410178 1.147499818 1.056753387 0.917270695 1.595337489 1.077558297 1.066073282 1 19.18639223 RFS(ph)EGVLQS(ph)PSQDQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RFSEGVLQSPSQDQEK 16 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 RFS(1)EGVLQS(0.998)PS(0.002)QDQEK;RFS(1)EGVLQS(0.996)PS(0.004)QDQEK 232.44 1.43E-15 403570000 736670 543680 609460 574680 683980 473540 780720 619840 856050 TRUE FALSE 690563.1397 583934.6329 623916.679 589427.2617 630262.9698 610243.3107 663658.2838 697228.3884 713169.7247 0.968301255 0.818787748 0.874850204 0.826489462 0.883748914 0.855677533 0.930575515 0.977647206 1 19.44388593 1.445695956 1.92948422 0.996786119 0.863633775 0.581314661 0.041119064 0.197187963 1.371873587 0.03201224 0.010191763 27.90589498 -1.445695956 -0.133152345 RFS(ph)EGVLQSPSQDQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RFSEGVLQSPSQDQEK 16 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RFS(1)EGVLQSPSQDQEK;RFS(1)EGVLQSPSQDQEK;RFS(0.974)EGVLQS(0.024)PS(0.002)QDQEK 314.74 5.42E-58 6742660000 3496220 2594370 3041460 2253930 2533530 2107540 3951510 3063080 4279280 TRUE FALSE 3277397.831 2786459.854 3113604.867 2311769.66 2334556.774 2715952.585 3359017.76 3445512.281 3565040.523 0.91931573 0.781606783 0.873371522 0.648455367 0.654847191 0.761829373 0.94221026 0.966472122 1 21.76548704 1.66216867 4.214784908 0.974000813 0.776331939 0.555261376 0.083152398 0.142743602 5.897622492 0.0491308 0.022910469 45.93763894 -1.66216867 -0.197668874 RFS(ph)FCCSPEPEAEAEAAAGPGPCER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RFSFCCSPEPEAEAEAAAGPGPCER 25 1 Q13501;E7EMC7;E3W990;D6RBF1;C9J6J8 Q13501 SQSTM1 Sequestosome-1 1 RFS(0.853)FCCS(0.147)PEPEAEAEAAAGPGPCER;RFS(1)FCCSPEPEAEAEAAAGPGPCER;RFS(1)FCCSPEPEAEAEAAAGPGPCER;RFS(0.996)FCCS(0.004)PEPEAEAEAAAGPGPCER;RFS(0.984)FCCS(0.016)PEPEAEAEAAAGPGPCER;RFS(0.997)FCCS(0.003)PEPEAEAEAAAGPGPCER 268.75 4.66E-46 8935210000 1945184 1858930 1998660 1785627 2235240 2128780 2783530 1860684 2827920 TRUE FALSE 1823438.406 1996567.111 2046069.159 1831449.212 2059693.267 2743324.228 2366165.518 2092994.493 2355921.883 0.773980843 0.84746745 0.868479203 0.777381128 0.874262123 1.164437687 1.004348037 0.888397238 1 21.16786027 2.453870146 22.15387434 1.018959 0.830070444 0.628722712 0.07186673 40.09353878 38200.50972 0.023806009 0.019919975 284.3610741 -2.453870146 -0.188888556 RFS(ph)FSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 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(0.989)FS(0.011)QR;RFS(1)FSQR;RFS(0.761)FS(0.239)QR;RFS(0.748)FS(0.252)QR;RFS(1)FSQR;RFS(0.997)FS(0.003)QR 174.86 0.00049633 22517070000 2836772 3528494 3172228 2936338 3732858 2218803 3752354 2791347 4850949 TRUE FALSE 2659223.504 3789747.367 3247474.746 3011689.404 3439694.39 2859335.407 3189723.353 3139852.817 4041294.274 0.658012836 0.937755855 0.803572946 0.745228929 0.851136828 0.707529621 0.789282625 0.776942387 1 21.94638598 -1.147173171 3.84785893 1.000090665 0.79620109 0.431789003 0.076801026 4698452.466 2102849.699 3996.036754 0.017257128 0.071256884 1.147173171 -0.203889575 RFS(ph)IPESGQGGTEMDGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RFSIPESGQGGTEMDGFR 18 1 Q9Y572 Q9Y572 RIPK3 Receptor-interacting serine/threonine-protein kinase 3 1 RFS(1)IPESGQGGTEMDGFR;RFS(1)IPESGQGGTEMDGFR;RFS(1)IPESGQGGTEMDGFR;RFS(1)IPESGQGGTEMDGFR;RFS(0.999)IPES(0.001)GQGGTEMDGFR;RFS(1)IPESGQGGTEMDGFR 288.45 1.18E-40 1472499000 555752 565143 590670 601360 571678 520121 727429 580599 522207 TRUE FALSE 520968.4744 606986.7758 604680.9713 616791.9157 526780.7159 670271.4892 618357.7746 653088.0632 435047.2781 1.197498526 1.395220258 1.389920135 1.41775836 1.210858549 1.540686548 1.421357645 1.501188712 1 18.73081267 2.23726262 24.99999159 1.408102542 1.345770336 0 0.164225275 139.5287654 2687280.748 0.052649526 0.041028391 172.6881828 -2.23726262 -0.062332206 RFS(ph)IPESGQGGTEMDGFRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RFSIPESGQGGTEMDGFRR 19 2 Q9Y572 Q9Y572 RIPK3 Receptor-interacting serine/threonine-protein kinase 3 1 RFS(1)IPESGQGGTEMDGFRR;RFS(1)IPESGQGGTEMDGFRR;RFS(0.999)IPES(0.001)GQGGT(0.001)EMDGFRR 147.26 5.59E-08 591010000 620718 712370 536485 616561 663095 364969 705020 554924 885205 TRUE FALSE 581868.3684 765114.616 549210.6775 632382.9991 611018.1935 470329.6255 599308.7961 624207.4829 737458.5669 0.789018386 1.037501835 0.744734284 0.857516649 0.828545794 0.637770916 0.812667752 0.846430581 1 19.49220247 3.907614027 6.777460099 0.802753499 0.925616367 0.101693986 0.108709744 0.321234485 25.65808858 0.025139706 0.045920601 8083.771454 -3.907614027 0.122862867 RFS(ph)LS(ph)PSLGPQASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RFSLSPSLGPQASR 14 1 Q9NYF3 Q9NYF3 FAM53C Protein FAM53C 2 RFS(0.997)LS(0.857)PS(0.146)LGPQASR 69.07 0.068671 0 94877 114620 111120 124640 116090 90728 126360 105840 124960 TRUE FALSE 88938.81793 123106.5841 113755.8189 127838.4734 106972.7597 116919.7008 107413.4911 119054.357 104103.3687 0.854331796 1.182541791 1.092719864 1.227995549 1.027562902 1.123111597 1.031796496 1.143616757 1 16.66765723 0.002504752 7.60894774 1.000000003 1.094348119 0.058168973 0.102674217 1981348.372 260397.1442 0.087564414 0.02123749 1.005784068 -0.002504752 0.094348116 RFS(ph)LSVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RFSLSVPR 8 1 Q07002;A0A0A0MSJ6;Q07002-3;D6R9B0;D6R9X1 Q07002 CDK18 Cyclin-dependent kinase 18 1 RFS(1)LSVPR;RFS(1)LSVPR 138.25 0.00043703 312890000 154031 193716 171492 162547 224190 121688 202249 161593 361210 TRUE FALSE 144390.4747 208058.9342 175559.8712 166718.2312 206583.0217 156817.3502 171923.64 181768.2418 300921.7175 0.479827365 0.691405512 0.583407116 0.554025255 0.686500873 0.521123405 0.571323471 0.604038297 1 18.1990287 0.920130929 19.17957564 1 0.592406904 0.79814386 0.065326996 1427.234314 342734.5501 0.058161391 0.014540348 8.320145648 -0.920130929 -0.407593096 RFS(ph)MEDVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RFSMEDVSK 9 1 Q07002 Q07002 CDK18 Cyclin-dependent kinase 18 1 RFS(1)MEDVSK 108.17 0.0016261 240960000 383650 314350 362930 393170 449080 345330 476260 357320 650350 TRUE FALSE 359638.0313 337624.8011 371538.871 403259.4078 413811.0683 445021.165 404849.2344 401932.1886 541802.3836 0.663780822 0.623151192 0.685746099 0.744292421 0.76376753 0.821371737 0.74722675 0.741842784 1 19.04740721 -4.999999993 0.081041088 1.939049634 0.437544995 0.859293963 0.038610584 86.1339668 0.493630292 14.39002557 1.307378634 1.00E-05 4.999999993 -1.501504638 RFS(ph)PSQVPIQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RFSPSQVPIQTR 12 1 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 RFS(0.94)PS(0.06)QVPIQTR;RFS(0.979)PS(0.021)QVPIQTR;RFS(0.993)PS(0.007)QVPIQTR;RFS(1)PSQVPIQTR 173.19 2.07E-05 1860000000 706244 760818 743992 746783 812446 606611 716194 627666 888930 TRUE FALSE 662041.4487 817149.7564 761639.8416 765946.7161 748639.7684 781729.7482 608807.3585 706031.4818 740561.8403 0.893971864 1.103418664 1.028462176 1.034277861 1.010907837 1.055590102 0.822088481 0.953372755 1 19.49826069 1.758122293 24.99999995 0.908731874 1.031566041 0.282962577 0.069077755 7.772018109 9941.968654 0.028758902 0.01594839 57.29573476 -1.758122293 0.122834167 RFS(ph)TEEFVLL ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RFSTEEFVLL 10 1 Q96DT6 Q96DT6 ATG4C Cysteine protease ATG4C 1 RFS(0.5)T(0.5)EEFVLL 76.522 0.037862 54098000 140330 180710 150500 156020 195950 134810 168460 154780 193320 TRUE FALSE 131546.9958 194089.9564 154069.9311 160023.7373 180560.8774 173727.4585 143200.9869 174104.6237 161053.6431 0.816789942 1.205126147 0.956637354 0.9936052 1.12112259 1.078693131 0.88915087 1.081034992 1 17.29718177 RFS(ph)WWS(ph)SLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RFSWWSSLK 9 1 C9JVG2;C9JAM7;Q96BV0 C9JVG2 ZNF775 Zinc finger protein 775 2 RFS(0.844)WWS(0.638)S(0.518)LK 66.056 0.043317 8300000 12210 37431 28794 26008 34599 26532 26384 26496 36717 TRUE FALSE 11445.7979 40202.43019 29477.00728 26675.40931 31881.73411 34191.35769 22427.96414 29804.08392 30588.6955 0.374183917 1.314290444 0.963656893 0.872067569 1.04227178 1.117777569 0.733210873 0.974349623 1 14.90071096 1.744599331 25 0.878142663 0.992344307 0 0.250421319 4.389331116 18234.33054 0.106772712 0.059210757 55.53916312 -1.744599331 0.114201644 RFSDIQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RFSDIQIR 8 1 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ; 156.62 0.00062547 595670000 378250 527030 390380 414010 530890 358000 458060 465090 676680 FALSE TRUE 354576.0077 566051.8496 399639.998 424634.1975 489196.0409 461348.7884 389378.1554 523157.5103 563737.7365 0.628973341 1.004104946 0.708911205 0.753247778 0.867772386 0.818374855 0.690707984 0.928015771 1 19.10466462 1.039356401 6.899648625 0.999795373 0.795325955 0.352451859 0.103958169 0.183742011 22.54958596 0.094326124 0.023663706 10.94854483 -1.039356401 -0.204469418 RFSEGVLQS(ph)PSQDQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RFSEGVLQSPSQDQEK 16 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RFSEGVLQS(0.736)PS(0.264)QDQEK 300.3 7.43E-46 594440000 675440 484940 536780 398060 451750 404140 706650 506650 749270 TRUE FALSE 633165.4161 520845.4622 549512.6751 408274.8935 416271.3773 520808.6573 600694.3927 569906.3678 624211.9965 1.014343556 0.834404762 0.880330205 0.654064478 0.666875003 0.8343458 0.962324332 0.913001306 1 19.25167656 1.78227808 4.916586659 0.953091742 0.811225152 0.302951238 0.103417459 0.274914184 13.28034393 0.052401502 0.028407128 60.57286001 -1.78227808 -0.141866589 RFTDEESR ddPTM_SK-BR-3_Pertuzumab_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 ; 117.01 0.0034643 495420000 1042780 1313010 1135720 1132110 1174730 1044620 1277400 1136460 1195280 FALSE TRUE 977514.2612 1410226.627 1162659.815 1161161.859 1082471.444 1346184.836 1085865.729 1278349.533 995780.0462 0.981656808 1.416202938 1.167586978 1.166082674 1.087058782 1.351889748 1.090467451 1.28376697 1 19.92546758 -3.760418447 0.386058546 3.02E-11 1.210644293 0.161917122 0.130974827 358.6692448 6.779891698 292.1967697 0.078445892 0.000173613 3.760418447 1.210644293 RFVEVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RFVEVGR 7 1 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ;;; 143.61 0.0038644 1262250000 630720 899330 682280 796010 1066570 641270 722150 804520 904200 FALSE TRUE 591244.3611 965917.329 698464.0038 816436.9642 982805.8945 826394.2389 613870.3116 904966.093 753283.1786 0.784889903 1.282276515 0.927226339 1.08383804 1.304696457 1.097056542 0.81492635 1.201362407 1 19.52283279 RFVNVVPTFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RFVNVVPTFGK 11 1 P62861;E9PR30 P62861 FAU 40S ribosomal protein S30 0 ; 120.77 0.00068227 677150000 2261900 2407900 2280800 2144670 2887600 1731620 2884300 2579800 3024000 FALSE TRUE 2120331.717 2586183.421 2334901.653 2199705.863 2660819.544 2231510.583 2451825.992 2901893.709 2519274.864 0.84164366 1.026558657 0.926814968 0.873150403 1.056184691 0.885774957 0.97322687 1.151876578 1 21.2645771 1.397856604 7.347050131 1.074336766 0.945817349 0.365931434 0.074805121 0.235325661 17.57068034 0.044323659 0.016369605 24.99519928 -1.397856604 -0.128519417 RGAAAADLLS(ph)SSPESQHGGTQSPGGGQPLLQPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 34 1 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 RGAAAADLLS(0.39)S(0.303)S(0.303)PES(0.002)QHGGT(0.002)QSPGGGQPLLQPTK;RGAAAADLLS(0.379)S(0.307)S(0.307)PES(0.003)QHGGT(0.003)QSPGGGQPLLQPTK 146.06 1.00E-10 700180000 209335 312940 278580 334580 394910 279880 428320 339520 440170 TRUE FALSE 196233.096 336110.4032 285188.0492 343165.8892 363895.3616 360676.8125 364097.3923 381909.8194 366702.7834 0.535128461 0.916574453 0.777708984 0.935814793 0.992344149 0.983567153 0.992895088 1.04146965 1 18.48425169 5.6280088 0.40669945 1.01601991 1.64E-15 0.726195848 0.078618105 6.165351917 0.460427858 0.054972608 3.52106829 424628.1683 -5.6280088 -1.01601991 RGAAAADLLSSS(ph)PESQHGGTQSPGGGQPLLQPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 34 1 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 RGAAAADLLS(0.03)S(0.227)S(0.743)PESQHGGTQSPGGGQPLLQPTK 176.94 4.76E-20 495060000 126990 172180 176460 181990 202900 145110 240780 187980 226420 TRUE FALSE 119041.9226 184928.3864 180645.7145 186660.1715 186965.0525 187000.9013 204677.2743 211449.7168 188629.0393 0.631090118 0.980381319 0.957677117 0.989562223 0.991178523 0.991368572 1.085078284 1.120981783 1 17.52519227 5.139415948 1.539023343 1.018878451 2.39E-14 0.846909966 0.051067083 1.372841138 1.339434899 0.014521246 2.860700412 137852.9131 -5.139415948 -1.018878451 RGAAGDWGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGAAGDWGER 10 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 93.839 0.013649 222480000 278130 289800 308730 325780 322000 234430 312800 258210 285180 FALSE TRUE 260722.3398 311257.0935 316053.2214 334140.0663 296711.4189 302106.1353 265898.5439 290448.0869 237581.6157 1.097401156 1.310105972 1.330293257 1.406422233 1.248882065 1.271588858 1.119188213 1.222519201 1 17.85806368 1.171613056 0.789279884 1.014265041 1.297314264 0.465987758 0.088518009 0.480170213 0.682036771 0.080074826 0.030715321 14.84612304 -1.171613056 0.283049223 RGADDDRPSWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RGADDDRPSWR 11 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;; 163.51 1.34E-05 1500540000 555308 525018 628753 678892 621467 538139 721651 507145 660556 FALSE TRUE 520552.2635 563890.879 643667.3181 696313.5181 572659.4887 693490.9933 613446.132 570463.1696 550304.9362 0.945934207 1.024688026 1.169655723 1.265323046 1.040622119 1.260194026 1.11473856 1.036631024 1 19.06987174 4.353892055 2.019535453 1.139606243 0.947260016 0.310977172 0.089579008 0.412311796 2.931188983 0.021377833 0.109174176 22588.7425 -4.353892055 -0.192346227 RGAEDDRGPWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RGAEDDRGPWR 11 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 91.961 0.0058218 1005348000 239006 444920 351540 327953 404900 265227 317404 348295 511040 FALSE TRUE 224047.0411 477862.3397 359878.6948 336368.8292 373100.7873 341793.7293 269812.2168 391780.3974 425744.1226 0.526248113 1.122416763 0.845293395 0.790072749 0.876349825 0.80281491 0.63374267 0.920225029 1 18.69962709 3.486133903 20.74075978 0.807079499 0.904093823 0 0.174993323 102.9715695 236959.3493 0.044043822 0.065203033 3062.907654 -3.486133903 0.097014324 RGAEGPEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGAEGPEAER 10 1 Q9Y446;Q9Y446-2;E9PQ15 Q9Y446 PKP3 Plakophilin-3 0 ; 116.13 0.0018126 385770000 196557 199180 220822 199413 217273 183339 226767 179440 232661 FALSE TRUE 184254.8482 213927.4944 226060.0021 204530.2752 200209.255 236265.993 192765.3936 201843.479 193828.3761 0.950608224 1.103695438 1.166289512 1.055213273 1.032920252 1.218944294 0.994515857 1.041351546 1 17.56442027 1.61139859 24.99999972 1.013445766 1.096237334 0.187446393 0.073211288 0.494813582 3474.878565 0.033522603 0.017657006 40.8694309 -1.61139859 0.082791569 RGAS(ph)SS(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGASSSPQR 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RGAS(0.905)S(0.186)S(0.909)PQR;RGAS(0.54)S(0.508)S(0.952)PQR 92.969 0.0064939 675340000 1716050 1561060 1611700 1630040 1644630 1415640 1713510 1440840 1487490 TRUE FALSE 1608645.494 1676642.507 1649930.285 1671869.586 1515467.394 1824312.287 1456585.083 1620732.046 1239218.309 1.298113078 1.352983969 1.331428266 1.349132411 1.222922049 1.472147622 1.17540636 1.307866446 1 20.24099893 0.033352193 0.537798448 0.973489026 1.336133667 0.625083432 0.077279488 2.313321098 0.825275484 0.198335742 0.030925273 1.079822054 -0.033352193 0.362644641 RGAYGGGYGGYDDYNGYNDGYGFGSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RGAYGGGYGGYDDYNGYNDGYGFGSDR 27 1 P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7 P31943 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 ;; 289.16 3.02E-70 766480000 278156 364717 288118 322923 404037 276319 381404 286441 411909 FALSE TRUE 260746.7125 391721.0262 294952.295 331209.7509 372305.5638 356087.8096 324216.011 322203.7894 343158.7269 0.759842872 1.14151556 0.859521475 0.965179449 1.084936896 1.037676684 0.944798968 0.938935146 1 18.38851652 2.981165596 24.1583244 0.999383592 0.953183141 0.085396459 0.103838374 1804.93501 2315139.758 0.030129561 0.032484066 957.5591178 -2.981165596 -0.04620045 RGDDS(ph)FGDKYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGDDSFGDKYR 11 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 RGDDS(1)FGDKYR;RGDDS(1)FGDKYR 105.14 0.0013076 510240000 634840 516550 536890 516960 628310 384900 635560 493380 819240 TRUE FALSE 595106.4976 554795.8995 549625.2843 530226.0688 578965.0671 496014.3817 540263.6782 554979.5791 682503.5515 0.871946375 0.812883535 0.805307581 0.77688397 0.84829605 0.726757217 0.791591014 0.813152661 1 19.38047703 0.845043833 7.859631878 0.999999991 0.801843723 0.711699983 0.038833277 8.098794986 411.0766623 0.034966835 0.008758221 6.999126349 -0.845043833 -0.198156268 RGDDSFGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RGDDSFGDK 9 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;; 166.86 9.69E-05 2865500000 3947600 3030610 3266670 2943340 3293730 2569760 3536770 3197500 2935140 FALSE TRUE 3700526.763 3254999.518 3344156.955 3018871.087 3035053.732 3311607.995 3006464.172 3596714.914 2445246.172 1.513355508 1.33115412 1.367615659 1.234587798 1.2412058 1.354304541 1.229513906 1.470900948 1 21.22154828 -4.128989658 0.213011473 1.24E-21 1.37904994 0.535317812 0.097923562 76.59363425 1.070317064 33.52677334 0.189237776 7.43E-05 4.128989658 1.37904994 RGDDSFGDKYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RGDDSFGDKYR 11 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;; 196.38 3.41E-08 3822720000 1015154 1714097 996571 1006134 2023763 639282 987608 1452744 2239427 FALSE TRUE 951617.3232 1841010.525 1020210.135 1031953.102 1864824.817 823832.3355 839525.3489 1634122.286 1865652.166 0.51007221 0.986791943 0.546838341 0.553132637 0.999556536 0.441578741 0.449990284 0.875898689 1 20.8312486 1.028083363 8.937636438 0.999960473 0.655046027 0.285116207 0.199856994 0.285634113 81.14323471 0.190899649 0.047773608 10.66800874 -1.028083363 -0.344914446 RGDDWNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGDDWNDR 8 1 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;A0A087X0F4 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 70.439 0.082301 557060000 374060 328420 349740 295980 372390 333270 413910 312490 294520 FALSE TRUE 350648.2523 352736.5585 358035.998 303575.3479 343143.9915 429479.6388 351848.0381 351505.0644 245362.7093 1.429101648 1.437612747 1.459211137 1.237251368 1.398517291 1.750386764 1.433991494 1.432593671 1 17.90455648 0.617893156 3.326201149 1.000004177 1.453572048 0.561215412 0.12435624 6.518763495 55.85372245 0.11745201 0.030405586 4.14851969 -0.617893156 0.453567871 RGDDWNDREWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RGDDWNDREWDR 12 2 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;;; 170.79 2.26E-05 5124210000 1271530 1421060 1374190 1442610 1629060 1150020 1531250 1396060 1971800 FALSE TRUE 1191947.207 1526276.761 1406786.436 1479629.815 1501120.199 1482012.105 1301653.278 1570361.164 1642693.842 0.725605208 0.929130385 0.856389913 0.900733769 0.913816172 0.902184003 0.792389455 0.955967037 1 20.64763219 -5 0.224229169 1.657655762 0.857443954 0.312456417 0.065622514 210.4151064 2.10678872 62.6618673 0.112888245 1.00E-05 5 -0.800211808 RGDIIGVQGNPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGDIIGVQGNPGK 13 1 Q15046;Q15046-2;H3BVA8;J3KRL2;H3BPV7 Q15046 KARS Lysine--tRNA ligase 0 164.53 5.91E-05 192210000 317630 290310 286170 318480 343390 239110 370350 298930 431540 FALSE TRUE 297750.1053 311804.8545 292958.0875 326652.736 316421.5346 308137.1754 314819.4557 336252.0685 359513.1861 0.828203573 0.867297408 0.814874388 0.908597372 0.880138884 0.857095615 0.875682639 0.935298291 1 18.45568516 0.291165983 0.344603198 1.027265994 0.839513781 0.756046864 0.026371574 1.709824706 0.356196306 0.095227386 0.024983273 1.955086526 -0.291165983 -0.187752213 RGDLIIEFEVIFPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGDLIIEFEVIFPER 15 1 P25685;P25685-2 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 79.771 0.030391 7683700 6369.4 11654 8560.7 12442 10975 11682 7567.5 7886.6 9077.7 FALSE TRUE 5970.750624 12516.87429 8763.763847 12761.28278 10113.06777 15054.40376 6432.823628 8871.259371 7562.573226 0.789513099 1.655107847 1.158833585 1.687426013 1.337252212 1.990645685 0.85061307 1.173047732 1 12.88466149 1.622794631 25 1.008897954 1.434474782 0.273530667 0.329225418 1.024347351 1711.402947 0.136797669 0.075468246 41.95605353 -1.622794631 0.425576828 RGDLPFVVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RGDLPFVVPR 10 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 199.68 4.40E-07 9738818000 2941753 3866796 3250208 3319682 3740116 2613392 3572463 3004926 3656285 FALSE TRUE 2757633.931 4153097.599 3327304.469 3404870.66 3446382.376 3367835.846 3036805.338 3380097.626 3046027.413 0.905321442 1.363447217 1.09234226 1.117806966 1.131435115 1.105648567 0.996972426 1.109674066 1 21.53849749 2.263243928 0.825052934 1.024827396 1.168077951 0.051984509 0.116452551 1.07532898 1.403041966 0.085676467 0.05209468 183.3343857 -2.263243928 0.143250555 RGDPFTDLCFLNS(ph)PIFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGDPFTDLCFLNSPIFK 17 1 Q5FBB7-6;Q5FBB7;Q5FBB7-5;Q5FBB7-4;Q5FBB7-3;Q5FBB7-2 Q5FBB7-6 SGOL1 Shugoshin-like 1 1 RGDPFTDLCFLNS(1)PIFK 111.11 0.00032188 121210000 379810 346740 355810 364410 412540 308160 456520 333660 486960 TRUE FALSE 356038.3701 372412.9904 364249.9812 373761.3775 380140.7725 397120.7894 388069.0641 375318.1855 405683.2301 0.877626541 0.91798961 0.897867977 0.921313354 0.937038419 0.978893777 0.956581479 0.925150851 1 18.62999414 2.714202659 1.92399714 0.961564151 0.902398161 0.64347948 0.021679824 0.213104855 1.562116257 0.007481499 0.007250358 517.8484241 -2.714202659 -0.05916599 RGDQGPK ddPTM_SK-BR-3_Pertuzumab_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 67528000 152770 124770 150360 140680 152300 76827 124430 154210 181180 FALSE TRUE 143208.3984 134008.1006 153926.6102 144290.087 140338.9723 99005.70772 105772.8767 173463.458 150939.8875 0.948777694 0.887824304 1.019787498 0.955944047 0.929767304 0.655928061 0.700761597 1.149222123 1 17.20361458 2.450226658 24.99115878 0.823956133 0.952277446 0.004739171 0.144889706 405.5163318 376814.1095 0.048212608 0.040338453 281.9854228 -2.450226658 0.128321313 RGDS(ph)ES(ph)EEDEQDSEEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGDSESEEDEQDSEEVR 17 1 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 2 RGDS(1)ES(0.995)EEDEQDS(0.005)EEVR 197.05 1.03E-11 367780000 681720 604710 594310 617090 630900 503530 689180 536770 705250 TRUE FALSE 639052.3621 649483.3576 608407.3139 632925.5741 581351.6589 648890.9369 585843.857 603786.9161 587539.2189 1.087676093 1.105429794 1.035517791 1.077248214 0.989468686 1.104421485 0.99711447 1.027653809 1 19.16432563 8 0.157347678 0.990052597 1.424508195 0.411137359 0.034121101 55.79977383 0.56916683 0.092115152 5.602363293 100000000 -8 0.434455599 RGDS(ph)ESEEDEQDS(ph)EEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGDSESEEDEQDSEEVR 17 1 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 2 RGDS(0.999)ES(0.006)EEDEQDS(0.995)EEVR 236.6 2.29E-20 378790000 987340 876090 892960 876870 887030 738280 1024200 757580 1016200 TRUE FALSE 925544.1519 940956.6152 914141.4329 899371.9687 817366.2419 951409.451 870630.7182 852165.5306 846589.6551 1.093261826 1.111467178 1.079792822 1.062346986 0.965481018 1.123814171 1.028397539 1.006586279 1 19.69130333 3.227406699 2.587335561 1.033812231 1.099249591 0.366933203 0.041158922 0.299962019 4.094948417 0.011697739 0.015640962 1688.133153 -3.227406699 0.06543736 RGDSQECS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGDSQECSPR 10 1 Q13111;Q13111-2;Q13111-3 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 RGDS(0.018)QECS(0.982)PR 51.979 0.093777 121840000 135710 141220 135040 123160 144650 140030 170030 117790 155650 TRUE FALSE 127216.1533 151676.0757 138243.2126 126320.4941 133289.7725 180454.3878 144535.58 132496.3408 129671.0095 0.981068582 1.169699198 1.066107321 0.974161415 1.027907263 1.391632475 1.114632951 1.021788458 1 16.98449645 RGDTVATLSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGDTVATLSER 11 1 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 134.56 0.00022171 409900000 41657 58867 38123 37756 55730 35219 47685 43114 55045 FALSE TRUE 39049.76273 63225.57393 39027.29556 38724.88288 51353.1906 45386.15357 40535.07694 48496.87781 45857.6339 0.85154334 1.37873607 0.851053407 0.844458809 1.119839517 0.989718608 0.883933023 1.057552989 1 15.4848743 3.866045254 7.178751119 0.958107222 1.146934886 0.137065709 0.152656551 0.313174873 18.08040659 0.035610149 0.064640972 7345.9041 -3.866045254 0.188827663 RGDTWHDRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGDTWHDRDR 10 2 Q9UBU9;Q9UBU9-2;E9PIN3;E9PMV7;E9PLA7 Q9UBU9 NXF1 Nuclear RNA export factor 1 0 ; 94.791 0.0044225 39777000 13355.5 36999 19400.6 19056.1 40094 12050.9 15172.4 27648 43886 FALSE TRUE 12519.6031 39738.44446 19860.79139 19545.11179 36945.17897 15529.7992 12897.43947 31099.91366 36561.14309 0.342429203 1.086903776 0.543221292 0.534587 1.010503935 0.424762409 0.352763573 0.850627498 1 15.15802356 1.006152032 24.9391291 1.000000086 0.637960556 0.215970312 0.252571168 193.6863304 785161.3575 0.242231255 0.060557814 10.14266384 -1.006152032 -0.36203953 RGEAHLAVNDFELAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RGEAHLAVNDFELAR 15 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;;; 211.57 8.52E-10 7355980000 2656720 3045830 2906750 3070440 3550870 2481640 3083910 2682340 3399490 FALSE TRUE 2490440.638 3271346.422 2975699.483 3149232.689 3271998.994 3198049.182 2621506.325 3017236.054 2832093.157 0.879363954 1.155098452 1.05070678 1.111980614 1.155328872 1.12921751 0.925642689 1.065373166 1 21.43343729 1.748649334 25 0.992609861 1.08960843 0.167138376 0.085782226 3.696248278 9178.031366 0.036159317 0.020052234 56.05951467 -1.748649334 0.096998569 RGEDVETSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGEDVETSK 9 1 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ; 176.65 8.50E-05 494920000 744120 595540 631280 674480 663070 554730 755660 563970 616050 FALSE TRUE 697546.8575 639634.4013 646254.2597 691788.2987 610995.1569 714871.5457 642355.7982 634382.896 513227.2752 1.359138322 1.246298535 1.259197028 1.347918032 1.19049627 1.392894689 1.251601053 1.236066216 1 18.96923832 0.679069401 1.820049604 1.000192005 1.287047571 0.69661453 0.060373394 0.701848183 3.240034486 0.051032079 0.01430305 4.7760559 -0.679069401 0.286855566 RGEDVETSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RGEDVETSKK 10 2 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ;;;; 138.75 3.17E-05 2912262000 3405220 2491950 2787120 2695340 3150130 2084960 3630840 2437930 3460450 FALSE TRUE 3192093.359 2676456.571 2853231.803 2764506.988 2902731.497 2686854.106 3086429.249 2742310.927 2882878.54 1.107259052 0.928397272 0.989716273 0.958939806 1.006886505 0.932003922 1.070606759 0.951240536 1 21.45907862 1.747670076 24.99999969 1.013742294 0.980375659 0.013343034 0.057464415 6.004037102 16515.03042 0.023677701 0.01313051 55.9332527 -1.747670076 -0.033366636 RGEEGHDPKEPEQLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGEEGHDPKEPEQLRK 16 3 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 132.59 2.30E-05 443870000 476760 356970 369710 433690 511250 276710 493300 346570 755720 FALSE TRUE 446920.4426 383400.4302 378479.6958 444819.2196 471098.4873 356591.685 419334.2446 389840.0274 629585.4499 0.70986463 0.608972825 0.601156993 0.70652716 0.748267749 0.566391242 0.666048182 0.619201139 1 19.26404267 -1.781766373 2.609949858 1.095192546 0.646643927 0.786141494 0.056733842 10031520.08 7336322.908 6089683.418 0.013461081 0.016528507 1.781766373 -0.448548619 RGEFCIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGEFCIAK 8 1 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 91.085 0.020424 847000000 730910 1811850 642270 644300 2127850 394510 657600 1597020 1595890 FALSE TRUE 685163.6478 1946001.259 657504.9477 660833.8288 1960737.244 508398.6327 558998.9849 1796411.462 1329525.649 0.515344438 1.46368087 0.494541003 0.497044814 1.474764511 0.382390993 0.420449944 1.35116721 1 20.34248018 3.954813265 23.74313573 0.747544498 1.047483436 0.014387041 0.444775114 551.6819604 587174.0814 0.106659315 0.192522618 9011.835702 -3.954813265 0.299938938 RGEGDAPFSEPGTTST(ph)QRPSSPETATK ddPTM_SK-BR-3_Pertuzumab_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(0.006)EPGT(0.127)T(0.076)S(0.178)T(0.249)QRPS(0.214)S(0.129)PET(0.021)AT(0.001)K;RGEGDAPFSEPGT(0.008)T(0.168)S(0.087)T(0.614)QRPS(0.08)S(0.043)PETATK 268.3 1.60E-53 4759200000 2793450 2144920 2281880 2159100 2303310 1833270 2746600 2017140 2395540 TRUE FALSE 2618612.951 2303732.109 2336007.271 2214506.161 2122417.324 2362505.288 2334772.828 2268984.369 1995708.898 1.312121699 1.154342755 1.170515035 1.109633857 1.063490435 1.183792531 1.169896487 1.136931529 1 20.92846987 7.658603746 0.017168271 3.45E-07 2.554345873 0.524467572 0.056199145 3879.558754 5.426550432 316.5108699 512.4769115 45562101.32 -7.658603746 2.554345528 RGEGDAPFSEPGTTSTQRPS(ph)S(ph)PETATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RGEGDAPFS(0.095)EPGT(0.021)T(0.078)S(0.042)T(0.049)QRPS(0.789)S(0.923)PET(0.003)ATK;RGEGDAPFSEPGTTST(0.001)QRPS(0.964)S(0.947)PET(0.085)AT(0.003)K 167.15 4.40E-12 913080000 1482310 1056730 1243610 1136610 1139190 895240 1480490 1021550 1183850 TRUE FALSE 1389534.863 1134971.389 1273109.016 1165777.337 1049722.613 1153681.255 1258504.269 1149092.766 986257.787 1.408896215 1.150785731 1.290848126 1.18202092 1.064349125 1.169756295 1.27603988 1.165103872 1 19.91160526 -5 0.103549481 0.381289447 1.340567864 0.431390535 0.087074266 199.1805967 1.393207756 27.063887 1.296866176 1.00E-05 5 0.959278416 RGEGDAPFSEPGTTSTQRPS(ph)SPETATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RGEGDAPFSEPGTTS(0.003)T(0.003)QRPS(0.72)S(0.274)PETATK;RGEGDAPFSEPGTT(0.011)S(0.107)T(0.078)QRPS(0.402)S(0.402)PETATK 256.12 3.66E-53 6486210000 1634750 1159717 1229368 1219784 1256700 965956 1653810 1035786 1364813 TRUE FALSE 1532433.916 1245583.653 1258529.19 1251085.723 1158003.851 1244811.816 1405836.544 1165106.162 1137016.893 1.34776706 1.095483858 1.106869385 1.100322898 1.018457912 1.094805032 1.236425379 1.024704355 1 20.11682226 4.739176179 24.8426284 1.099848059 1.347767144 0.592897363 0.067484924 35.07532885 1415210.566 0.015815688 0.094182918 54849.9428 -4.739176179 0.247919085 RGEGDAPFSEPGTTSTQRPSS(ph)PETATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RGEGDAPFSEPGTTS(0.002)T(0.002)QRPS(0.197)S(0.799)PETATK;RGEGDAPFSEPGTTSTQRPS(0.023)S(0.977)PETATK;RGEGDAPFSEPGTTSTQRPS(0.049)S(0.951)PETATK;RGEGDAPFSEPGTTS(0.001)T(0.004)QRPS(0.285)S(0.707)PET(0.002)ATK 303 2.51E-71 8170520000 2874540 2087390 2390700 2326880 2481930 1982210 3031940 2137360 2649170 TRUE FALSE 2694627.673 2241942.528 2447408.533 2386591.68 2287009.229 2554441.849 2577328.744 2404214.101 2207006.413 1.220942385 1.015829639 1.108926788 1.081370524 1.036249472 1.157423845 1.167793954 1.089355286 1 21.07365939 2.225406433 24.97568943 1.124422562 1.08389073 0 0.071491392 640.2511811 1215628.243 0.024309931 0.018059199 168.0375855 -2.225406433 -0.040531832 RGEIIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGEIIAK 7 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 105.81 0.012577 673720000 1391330 1247700 1238070 1213780 1340000 1009080 1524290 1147160 1579650 FALSE TRUE 1304249.139 1340081.006 1267437.605 1244927.65 1234761.805 1300385.015 1295736.865 1290385.451 1315996.21 0.991073628 1.01830157 0.963101258 0.945996379 0.938271551 0.988137356 0.984605317 0.980538881 1 20.3277239 -0.995259564 7.098491321 1.000000002 0.977840932 0.091646324 0.0230176 7.12E-10 5.01E-11 0.023876718 0.005627796 0.101097505 0.995259564 -0.02215907 RGEIIDNDTEEEFYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGEIIDNDTEEEFYLR 16 1 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 176.08 5.28E-09 61085000 39052 49179 45612 43234 59412 33635 50636 45641 65174 FALSE TRUE 36607.80503 52820.26433 46693.93818 44343.45763 54746.02118 43344.87848 43043.60188 51339.37932 54296.03836 0.674226079 0.972819858 0.85998794 0.816697847 1.008287581 0.798306466 0.792757689 0.945545584 1 15.72855932 1.031247398 6.636200638 0.999862412 0.858980423 0.241593053 0.093845325 0.221023902 29.13080235 0.083868601 0.021052859 10.74601391 -1.031247398 -0.140881988 RGERPDYKGEEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGERPDYKGEEELR 14 3 Q9UQ35;Q9UQ35-2;I3L4D8;I3L0N7 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 81.904 0.0053466 202760000 159150 176460 123760 131860 211710 85135 171260 163270 241910 FALSE TRUE 149189.0856 189525.282 126695.6456 135243.7508 195083.1506 109712.0924 145581.1529 183654.6189 201533.6582 0.740268831 0.940415034 0.6286575 0.671072773 0.967992902 0.544385952 0.722366448 0.911285095 1 17.62066128 1.08714548 4.157417125 0.99617056 0.747160629 0.3284409 0.128309285 0.229405272 6.926852075 0.117244454 0.030076257 12.22209007 -1.08714548 -0.249009931 RGES(ph)LDNLDSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGESLDNLDSPR 12 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 RGES(1)LDNLDSPR;RGES(1)LDNLDSPR 180.49 2.05E-05 830390000 499550 565560 437690 589750 522400 375100 589220 450610 493040 TRUE FALSE 468284.0572 607434.6509 448072.2135 604883.9834 481372.8113 483385.2808 500871.9311 506869.6504 410748.4388 1.140075075 1.47884835 1.090867721 1.472638545 1.171940696 1.176840214 1.219412866 1.234014795 1 18.64789557 -4.999983876 0.146090029 0.06764846 1.342300394 0.281142828 0.128477439 159.071554 1.398363152 42.72050498 0.627824333 1.00E-05 4.999983876 1.274651933 RGEVPAELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RGEVPAELR 9 1 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ;;;; 150.15 0.00013777 1423310000 1270070 1696900 1440770 1399800 1595800 1205830 1427860 1478730 1464540 FALSE TRUE 1190578.586 1822540.242 1474945.745 1435721.238 1470472.305 1553933.546 1213765.649 1663352.696 1220098.813 0.975805052 1.493764458 1.20887401 1.176725379 1.205207554 1.273612866 0.994809302 1.36329343 1 20.21856656 0.341060124 0.246233462 0.934293536 1.297116727 0.086936293 0.159289616 8.77250054 1.121623208 0.950819637 0.319851578 2.193108529 -0.341060124 0.362823191 RGFGFVTFDDHDPVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RGFGFVTFDDHDPVDK 16 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;; 147.92 6.37E-07 2342180000 6600370 5156930 5254680 5083600 6325920 4145950 6826590 5539390 7576290 FALSE TRUE 6187264.624 5538754.463 5379323.491 5214053.783 5829107.761 5342818.461 5803006.204 6230995.035 6311758.254 0.980275919 0.877529563 0.852270203 0.826085787 0.92353153 0.846486549 0.919396145 0.987204323 1 22.58961052 1.337916636 2.800350059 0.9989918 0.879140244 0.511446992 0.04338567 0.196378876 2.542440988 0.034943307 0.010660602 21.77291795 -1.337916636 -0.119851556 RGFS(ph)DSGGGPPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGFSDSGGGPPAK 13 1 Q9H307;G3V5F0;G3V579 Q9H307 PNN Pinin 1 RGFS(0.977)DS(0.023)GGGPPAK 111.34 0.00019403 0 170520 143520 150150 135350 168960 134100 209760 149880 311180 TRUE FALSE 159847.4576 154146.3701 153711.6289 138823.3101 155690.5632 172812.4931 178308.4353 168592.8479 259242.0477 0.616595413 0.594604045 0.592927074 0.535496889 0.600560613 0.666606728 0.687806769 0.650329873 1 17.98394021 -0.216304289 0.426163856 1.071397038 0.581976983 0.933470463 0.032874665 1.385548423 0.283523635 0.190712427 0.02090393 0.607709061 0.216304289 -0.489420055 RGGADVNIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RGGADVNIR 9 1 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;;;;; 133.23 0.0004536 1679270000 1473660 1726940 1514680 1577100 1952580 1301140 1683670 1508790 2342360 FALSE TRUE 1381426.251 1854804.434 1550608.925 1617571.056 1799232.243 1676757.996 1431219.314 1697165.753 1951404.984 0.707913664 0.950496924 0.794611543 0.828926373 0.922018883 0.859256797 0.733430183 0.869714778 1 20.89608179 0.976068378 23.67087796 1.000000006 0.834364977 0.343523023 0.074219734 1273.46877 1259596.106 0.068182005 0.017045501 9.463861543 -0.976068378 -0.165635028 RGGDGYDGGYGGFDDYGGYNNYGYGNDGFDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RGGDGYDGGYGGFDDYGGYNNYGYGNDGFDDR 32 1 P31942;P31942-3;P31942-4;P31942-5 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;;;; 289.97 3.96E-89 1503590000 602377 687264 639559 666146 852138 595089 740838 638329 824533 FALSE TRUE 564675.2988 738149.7417 654729.6415 683240.4341 785214.5188 766881.5338 629756.2195 718025.7808 686913.1156 0.82204763 1.074589675 0.953147679 0.994653354 1.143106022 1.116417079 0.916791666 1.04529345 1 19.38976811 4.747365127 24.6976687 1.024852451 0.822047506 0.468047119 0.069608393 954.5115571 2677446.196 0.016673719 0.199552697 55893.9918 -4.747365127 -0.202804944 RGGGS(ph)GGGEES(ph)EGEEVDED ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGGGSGGGEESEGEEVDED 19 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 2 RGGGS(1)GGGEES(1)EGEEVDED;RGGGS(1)GGGEES(1)EGEEVDED 137.87 2.03E-06 969880000 842140 774020 780580 779140 863530 629210 922880 705460 919000 TRUE FALSE 789431.9607 831329.2462 799095.7262 799134.0515 795711.8371 810852.7126 784502.7116 793538.2339 765612.963 1.031111017 1.085834862 1.043733276 1.043783334 1.039313433 1.059089582 1.024672713 1.036474397 1 19.54625573 0.752104797 0.274918348 0.988991372 1.065112444 0.48922579 0.015835548 2.135552507 0.439281031 0.055329822 0.026307998 5.650733123 -0.752104797 0.076121072 RGGGSGGGEES(ph)EGEEVDED ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RGGGSGGGEESEGEEVDED 19 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED 285.82 4.86E-40 8442063000 4737119 4511657 4244766 4368589 5098459 3595736 5178669 4063242 5815456 TRUE FALSE 4440631.178 4845704.779 4345453.854 4480694.39 4698046.596 4633766.611 4402175.66 4570546.708 4844818.824 0.916573217 1.000182866 0.89692804 0.924842507 0.969705322 0.956437543 0.908635765 0.943388571 1 22.20801129 0.945792312 22.24306994 1 0.939865611 0.279573371 0.030532999 6913.831013 2836961.152 0.028685538 0.007171385 8.826576947 -0.945792312 -0.060134389 RGGIPAS(ph)PIDPFQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RGGIPASPIDPFQSR 15 1 Q96LD4;Q96LD4-2 Q96LD4 TRIM47 Tripartite motif-containing protein 47 1 RGGIPAS(1)PIDPFQSR;RGGIPAS(1)PIDPFQSR;RGGIPAS(1)PIDPFQSR 115.42 0.000324 660430000 235803 327793 295496 449740 413830 162215 215158 165111 284187 TRUE FALSE 221044.5112 352063.1348 302505.3047 461281.0898 381329.4611 209043.8372 182897.0553 185725.4718 236754.3538 0.933644968 1.487039749 1.277718022 1.948353145 1.610654482 0.882956676 0.772518234 0.784464863 1 17.85303143 2.202020672 8.672064018 0.833347488 1.455084636 0.560268178 0.2599278 0.195413256 42.07050706 0.095504418 0.07101377 159.2284517 -2.202020672 0.621737148 RGGPNYQEGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RGGPNYQEGLR 11 1 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ;;;;; 192.6 2.12E-06 4637030000 1511420 2409330 1625340 1630730 2533570 1164674 1845710 1962420 3262230 FALSE TRUE 1416822.92 2587719.3 1663893.832 1672577.293 2334593.632 1500896.477 1568962.92 2207432.457 2717742.738 0.521323413 0.952157562 0.612233752 0.615428852 0.859019362 0.552258481 0.577303693 0.8122301 1 21.37397747 0.976289879 7.187629252 0.999978236 0.68565226 0.37930822 0.136608629 0.230856143 60.62833033 0.128831507 0.032299576 9.468689582 -0.976289879 -0.314325976 RGGS(ph)DTNLNFDVPDGILDFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGGSDTNLNFDVPDGILDFHK 21 1 G3V207;Q9ULS5;F8VQF2 G3V207 TMCC3 Transmembrane and coiled-coil domains protein 3 1 RGGS(0.999)DT(0.001)NLNFDVPDGILDFHK 190.19 8.90E-18 31156000 30489 31300 22585 25909 40993 25379 35993 33788 62133 TRUE FALSE 28580.74791 33617.48457 23120.72687 26573.8688 37773.57514 32705.50531 30596.18379 38006.50618 51762.60091 0.552150538 0.649455089 0.446668569 0.513379705 0.729746467 0.631836591 0.591086678 0.734246454 1 15.65962249 0.236924318 0.485330887 1.036718693 0.554362553 0.755992001 0.075336934 1.473105119 0.52017114 0.183110598 0.040772069 1.725537168 -0.236924318 -0.48235614 RGHT(ph)ASESDEQQWPEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGHTASESDEQQWPEEK 17 1 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 RGHT(0.585)AS(0.242)ES(0.173)DEQQWPEEK 97.57 0.0011966 103810000 206250 178220 175800 237340 274300 154810 234510 166270 237640 TRUE FALSE 193341.1807 191415.5942 179970.059 243430.5462 252757.5845 199501.1339 199347.4026 187029.1755 197976.3488 0.976587263 0.966860918 0.909048278 1.229594079 1.27670596 1.007701855 1.006925341 0.944704641 1 17.59496856 3.285587858 24.99980097 1.077385754 0.948297652 0.244994154 0.104878154 179.2210462 95273.068 0.030703012 0.041571942 1930.135765 -3.285587858 -0.129088101 RGILTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGILTLK 7 1 C9JTX5;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6;Q6S8J3;A5A3E0;P0CG38;P0CG39 C9JTX5;P60709;P63261;P68133;Q6S8J3 ACTB;ACTG1;ACTA1;ACTC1;ACTG2;ACTA2;POTEE;POTEF;POTEI;POTEJ "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, gamma-enteric smooth muscle;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I;POTE ankyrin domain family member J" 0 ; 157.58 0.0023513 7970200000 4246900 9140200 3253900 2957300 10482800 1983510 4353000 8932500 9323000 FALSE TRUE 3981094.11 9816949.918 3331084.045 3033189.325 9659523.174 2556117.137 3700308.061 10047742.29 7766931.071 0.512569775 1.263941939 0.428880341 0.390526103 1.243673091 0.329102591 0.476418295 1.293656683 1 22.88891323 1.234058706 24.99834694 1.146828442 0.683008863 0.257092701 0.340269723 173.5847085 963826.729 0.282127098 0.07990677 17.14189009 -1.234058706 -0.463819579 RGKNENESEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGKNENESEKR 11 3 P47813;O14602;A6NJH9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 69.01 0.024388 25241000 24085 19129 20568 24110 31453 11999 28390 18433 56255 FALSE TRUE 22577.56284 20545.33106 21055.88267 24728.70342 28982.80826 15462.91651 24133.18306 20734.40063 46865.67708 0.481750489 0.438387586 0.449281521 0.527650617 0.618422907 0.329941174 0.514943655 0.442421873 1 15.51624411 -1.539955296 2.867394551 1.025290064 0.47221531 0.832631942 0.073911524 18293515.61 19365726.92 3576240.315 0.016254109 0.028843284 1.539955296 -0.553074755 RGLDEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGLDEDR 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 153.04 0.0028434 1094790000 751880 898550 834360 850580 938650 759380 993110 809900 1018540 FALSE TRUE 704821.1729 965079.5769 854151.4132 872407.3228 864932.2153 978600.6785 844202.3751 911017.7978 848539.094 0.830628993 1.137342503 1.006614096 1.028128614 1.019319229 1.153277068 0.994889194 1.073630908 1 19.6946216 4.752535392 24.85713654 1.052903486 0.830628831 0.610606181 0.055460973 1451.512053 2581777.357 0.012123599 0.248421627 56563.38502 -4.752535392 -0.222274655 RGLEVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RGLEVNK 7 1 P31146;H3BRY3 P31146 CORO1A Coronin-1A;Coronin 0 ;; 110.12 0.011024 549860000 2057130 2419810 1558440 1858170 1730820 1056470 2898530 1962370 1808300 FALSE TRUE 1928377.905 2598975.25 1595406.933 1905853.788 1594888.379 1361455.739 2463922.335 2207376.214 1506483.048 1.280052841 1.725193824 1.059027471 1.265101383 1.058683256 0.903731204 1.635546008 1.46525128 1 20.52275301 3.972084237 23.84870493 1.227907341 1.516630584 0.203801192 0.244390763 183.8355076 870416.9028 0.06217123 0.116851043 9377.438766 -3.972084237 0.288723243 RGLEVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGLEVSK 7 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ; 111.74 0.01044 732660000 1396040 1993860 1307040 1332080 1982440 891690 1682000 1755980 2177770 FALSE TRUE 1308664.348 2141487.469 1338043.606 1366263.428 1826747.159 1149106.428 1429799.715 1975217.968 1814286.118 0.721310898 1.180347161 0.737504186 0.753058415 1.006868289 0.633365607 0.788078408 1.088702575 1 20.79097056 5.050879093 12.86851834 0.881080072 5.45E-05 0.086334025 0.173092104 1661103.691 14316151.52 0.040260771 34292511.38 112429.1929 -5.050879093 -0.88102554 RGLKPSCTIIPLMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 80.967 0.0083353 480330000 1554500 1514500 1364100 1406100 1879800 942850 1919800 1425000 2582900 FALSE TRUE 1457206.62 1626635.156 1396457.096 1442182.907 1732168.091 1215035.489 1631943.813 1602914.387 2151797.304 0.677204408 0.755942557 0.648972417 0.670222471 0.804986644 0.564660754 0.758409637 0.744918856 1 21.03711075 0.604044762 1.423708389 0.999721584 0.695301571 0.675524259 0.065815752 0.822648628 2.293108816 0.055671331 0.016318324 4.01832225 -0.604044762 -0.304420014 RGLLEDVQEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGLLEDVQEGR 11 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 112.95 0.0012852 231470000 212621 301720 268900 298680 313400 274600 310630 269110 275830 FALSE TRUE 199313.4311 324059.6627 275278.435 306344.6345 288786.8282 353872.5622 264053.9152 302708.9759 229792.1911 0.867363813 1.410229222 1.197945125 1.333137706 1.256730383 1.539967745 1.149098731 1.3173162 1 17.80997025 -1.145213843 3.844694031 0.999877132 1.27256823 0.171234751 0.176817192 10800736.97 3217209.179 12584.25245 0.036063614 0.071579087 1.145213843 0.272691098 RGLLYDS(ph)DEEDEERPAR ddPTM_SK-BR-3_Pertuzumab_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 255.63 3.55E-27 2798850000 521574 550128 504312 568524 638492 382939 666412 522012 763828 TRUE FALSE 488929.6144 590860.0495 516274.5188 583113.2883 588347.4139 493487.2728 566489.7073 587186.3473 636340.1723 0.768346296 0.9285286 0.811318445 0.91635467 0.924580027 0.775508595 0.890230936 0.922755427 1 19.27943868 1.006738492 2.22436245 0.998582579 0.861620661 0.388940869 0.0583022 0.303117928 3.255648293 0.049972845 0.013775715 10.15636949 -1.006738492 -0.136961918 RGLLYDS(ph)DEEDEERPARK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGLLYDSDEEDEERPARK 18 3 P49736 P49736 MCM2 DNA replication licensing factor MCM2 1 RGLLYDS(1)DEEDEERPARK 110.91 0.0017681 243760000 143790 114530 128340 125750 159730 91366 173950 113690 218060 TRUE FALSE 134790.4406 123009.9204 131384.2854 128976.9579 147185.4501 117741.881 147867.8124 127884.4468 181664.3773 0.741975078 0.677127361 0.723225364 0.709973853 0.810205349 0.648128614 0.813961518 0.703959954 1 17.47091602 -5 0.254357726 2.706625527 0.703896232 0.726025353 0.052261489 86.45789505 0.854351303 76.81128994 0.06296116 1.00E-05 5 -2.002729294 RGNDPLT(ph)SSPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGNDPLTSSPGR 12 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RGNDPLT(0.333)S(0.333)S(0.333)PGR 90.367 0.0052157 246240000 94435 126920 105160 92048 117830 87430 110670 94547 115880 TRUE FALSE 88524.48192 136317.2889 107654.4449 94410.10752 108576.1071 112669.6217 94076.06091 106351.4011 96538.87939 0.916982696 1.412045486 1.115140817 0.977949072 1.124687875 1.167090631 0.974488843 1.101643211 1 16.55882246 3.541871849 5.346040178 1.060093527 1.217010663 0.07038352 0.134644637 0.29548575 16.34726678 0.033256451 0.051572926 3482.34543 -3.541871849 0.156917136 RGNDPLTS(ph)SPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGNDPLTSSPGR 12 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RGNDPLT(0.324)S(0.396)S(0.28)PGR 80.534 0.0123 252210000 88121 101210 107370 114640 108340 100950 150400 96057 123530 TRUE FALSE 82605.66391 108703.6937 109916.8671 117581.8565 99831.41342 130092.6262 127848.9162 108049.9279 102912.045 0.802682173 1.056277657 1.068066106 1.14254708 0.970065394 1.264114674 1.242312465 1.049924991 1 16.65105232 5.51583626 0.835907353 1.132884154 3.83E-11 0.461948137 0.097633668 6.566315169 1.376665552 0.031863583 9.329253326 327971.6161 -5.51583626 -1.132884154 RGNDPLTSS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RGNDPLTSSPGR 12 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RGNDPLT(0.07)S(0.363)S(0.567)PGR;RGNDPLT(0.013)S(0.239)S(0.748)PGR;RGNDPLT(0.019)S(0.127)S(0.854)PGR 124.09 0.00020157 7256000000 1978650 1897320 2173330 1957970 2186950 1826540 2535270 1949260 2257960 TRUE FALSE 1854809.828 2037799.547 2224882.414 2008214.825 2015195.769 2353832.447 2155129.8 2192629.402 1881091.889 0.986028295 1.083306753 1.182761154 1.067579333 1.071290446 1.251311784 1.145680236 1.165615255 1 20.84313889 4.661841305 2.060833339 1.137279437 0.957406605 0.277303947 0.069965497 0.682191182 3.657325272 0.016512921 0.216361535 45903.02487 -4.661841305 -0.179872831 RGNGLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGNGLIK 7 1 P62249;M0R210;M0R3H0;M0R1M5;Q6IPX4 P62249 RPS16 40S ribosomal protein S16 0 ; 143.02 0.0039283 2111710000 3163400 3131600 3045600 2890800 3437600 2473810 3710200 2877600 3750600 FALSE TRUE 2965408.441 3363466.922 3117843.07 2964982.822 3167624.763 3187958.788 3153889.954 3236874.694 3124600.63 0.949051988 1.076446983 0.997837304 0.948915773 1.013769482 1.020277202 1.009373782 1.035932293 1 21.57524037 2.497337981 24.59512955 1.016523112 1.00511472 0.045567875 0.036753745 3560.608506 4331728.093 0.012238873 0.011387012 314.295368 -2.497337981 -0.011408392 RGNVAGDSK ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;;; 163.43 0.00010106 15342881000 19399490 16878160 16126300 15807660 19057020 12016540 19374120 16774870 19385320 FALSE TRUE 18185310.55 18127836.53 16508823.45 16213311.32 17560358.52 15485520.03 16469150.57 18869249.45 16149784.86 1.126040422 1.122481611 1.022231788 1.003933579 1.087343186 0.958868503 1.01977523 1.168390143 1 23.94501161 4.0540329 2.772102604 1.033274117 1.125759752 0.285568714 0.056819688 0.318981871 4.809567029 0.013947337 0.035328291 11324.86152 -4.0540329 0.092485634 RGNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK 50 2 P68104;A0A087WVQ9;A0A087WV01 P68104 EEF1A1 Elongation factor 1-alpha 1;Elongation factor 1-alpha 0 191.08 2.29E-30 140760000 184730 226490 157730 169680 284690 132020 277360 194510 586960 FALSE TRUE 173168.0791 243259.5553 161471.4301 174034.2761 262331.5958 170132.0308 235772.4429 218795.0017 488992.5841 0.354132322 0.497470848 0.330212431 0.355903713 0.536473567 0.34792354 0.482159547 0.447440327 1 18.89945306 -1.537888195 0.450157174 1.369823476 0.402809231 0.87712703 0.068726862 10.15006252 0.963201221 4.286663134 0.03394901 0.028980896 1.537888195 -0.967014245 RGNVCGDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RGNVCGDSK 9 1 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ;;; 157.75 0.00010873 1062690000 1129267 1467190 855860 884644 1633300 562561 1040390 1300870 1564510 FALSE TRUE 1058588.194 1575822.274 876161.4034 907345.4627 1505027.206 724963.2283 884393.178 1463286.483 1303383.174 0.812184947 1.209024565 0.672220895 0.696146368 1.154708175 0.556216501 0.678536593 1.12268327 1 20.31382984 3.969388017 24.12095273 0.80842497 1.026659484 0.077917937 0.222677099 330.9928974 1032416.43 0.052913724 0.097816169 9319.401392 -3.969388017 0.218234514 RGPAEESSSWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RGPAEESSSWR 11 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 96.551 0.011108 906030000 637297 890420 733823 897100 1011520 569824 1055460 892023 1281980 FALSE TRUE 597409.7184 956347.6233 751229.6281 920121.1048 932079.2995 734322.9385 897203.5714 1003394.035 1068009.256 0.559367548 0.895448815 0.703392432 0.861529148 0.872725863 0.687562336 0.84007097 0.939499381 1 20.02649272 -4.999999966 0.066503132 1.756561772 0.510760417 0.416860031 0.100634053 366.1901614 1.763476587 42.87443899 5.925490718 1.00E-05 4.999999966 -1.245801356 RGPCIIYNEDNGIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGPCIIYNEDNGIIK 15 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ; 176.43 1.28E-06 2294900000 1155410 1106080 1103310 1148980 1181510 824570 1419390 957020 1311310 FALSE TRUE 1083094.951 1187975.314 1129481.034 1178464.772 1088718.971 1062609.973 1206565.646 1076506.054 1092443.89 0.991442179 1.087447443 1.033903018 1.078741694 0.996590288 0.972690665 1.104464639 0.985410843 1 20.05912775 2.737297567 24.99309971 1.022092607 1.052147465 0.114629521 0.044323358 275.11374 5443918.83 0.013566817 0.013385545 546.1319274 -2.737297567 0.030054858 RGPEEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGPEEDR 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 163.9 0.0019527 149923000 236720 275170 286130 279780 272480 246450 318320 264050 310080 FALSE TRUE 221904.1178 295543.8731 292917.1387 286959.6285 251080.5199 317596.1142 270590.8711 297017.2237 258325.6448 0.859009248 1.144074849 1.133906542 1.110844526 0.971953521 1.229440904 1.047479709 1.149778312 1 17.97883135 4.744007913 24.91348088 1.105822445 0.859009138 0.492707617 0.076021915 438.4115334 2005033.212 0.015950459 0.140273769 55463.58185 -4.744007913 -0.246813308 RGPEVTSQGVQTS(ph)SPACK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGPEVTSQGVQTSSPACK 18 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB05;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 RGPEVTSQGVQT(0.046)S(0.539)S(0.414)PACK 55.705 0.064866 665500000 464180 403170 420750 396660 459120 343830 531730 389830 467010 TRUE FALSE 435127.8024 433021.1263 430730.3887 406838.9671 423062.5672 443088.1394 452002.0228 438501.1336 389063.014 1.1183993 1.112984557 1.107096725 1.045689136 1.087388294 1.138859577 1.161770733 1.127069698 1 18.56964431 2.243807918 24.98150386 1.125496903 1.096391227 0 0.04804206 334.2949012 1591526.403 0.015675504 0.012758912 175.3104957 -2.243807918 -0.029105676 RGPEVTSQGVQTSS(ph)PACK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGPEVTSQGVQTSSPACK 18 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB05;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 RGPEVTSQGVQT(0.017)S(0.305)S(0.678)PACK 110.16 0.0002092 927620000 548120 372550 472730 463980 440820 407640 653490 429750 486100 TRUE FALSE 513814.1476 400133.9896 483943.3788 475886.5123 406199.7754 525319.0505 555505.2412 483405.2335 404966.7697 1.268781011 0.988066231 1.195019975 1.175124845 1.003044708 1.29719051 1.37173043 1.193691112 1 18.627444 2.216423209 24.97586762 1.261839856 1.118840594 0.057556636 0.128449724 333.9688433 376787.8347 0.044136737 0.032622324 164.5974903 -2.216423209 -0.142999262 RGPEVTSQGVQTSS(ph)PACKQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.045)S(0.045)S(0.91)PACKQEK;RGPEVTSQGVQT(0.044)S(0.021)S(0.934)PACKQEK 142.21 7.75E-08 273900000 333549 219179 260312 251252 326022 185654 365347 227297 465080 TRUE FALSE 312672.7635 235407.2412 266486.7236 257699.5517 300417.5472 239249.296 310566.6091 255675.5308 387455.1435 0.80699087 0.60757289 0.687787291 0.665108093 0.775360844 0.617489018 0.801555004 0.659884209 1 18.56366977 -5 0.281079871 3.243861637 0.677593338 0.61355011 0.073046261 136.2610375 1.303230137 178.3113628 0.073394655 1.00E-05 5 -2.566268299 RGPGLYYVDSEGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RGPGLYYVDSEGNR 14 1 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;;;;; 268.93 4.14E-25 7714040000 3698640 4149070 3716100 3719900 4464800 3290010 4375900 3839610 4507930 FALSE TRUE 3467148.725 4456271.46 3804247.647 3815358.932 4114152.618 4239782.478 3719774.419 4318993.761 3755527.361 0.923212213 1.186590066 1.012972955 1.015931603 1.095492649 1.128944638 0.990479914 1.150036558 1 21.84058408 -1.148294147 4.593252663 0.999992796 1.066408662 0.055925313 0.080185568 5.95E-06 1.10E-06 0.06918837 0.016305859 0.071073197 1.148294147 0.066415866 RGPGYTSGTNSEASNAS(ph)ETESDHRDELSDWSLAPTEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGPGYTSGTNSEASNASETESDHRDELSDWSLAPTEEER 39 2 Q06787;Q06787-2;R9WNI0;G3V0J0;Q06787-9;Q06787-7;A0A087WXC0 Q06787 FMR1 Fragile X mental retardation protein 1 1 RGPGYTSGTNSEASNAS(0.982)ET(0.014)ES(0.004)DHRDELSDWSLAPTEEER 157.33 9.42E-15 52765000 37140 59718 57368 57563 60805 48190 64949 54718 68262 TRUE FALSE 34815.4737 64139.58286 58728.79605 59040.16403 56029.62058 62101.6707 55210.50041 61549.66275 56868.63121 0.612208751 1.127855225 1.032709858 1.038185073 0.985246513 1.09201979 0.970842787 1.082313069 1 15.79534546 4.745590671 24.99728738 1.042056625 0.612208552 0.883100195 0.049044451 257.3933126 915209.9008 0.011211291 0.112742577 55666.08408 -4.745590671 -0.429848073 RGPGYTSGTNSEASNAS(ph)ETESDHRDELSDWSLAPTEEERESFLR ddPTM_SK-BR-3_Pertuzumab_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 RGPGYTSGTNSEASNAS(0.796)ET(0.192)ES(0.012)DHRDELSDWSLAPTEEERESFLR 134.85 8.35E-10 58310000 10366 17231 12236 14851 16955 7952.3 15068 11499 22647 TRUE FALSE 9717.210564 18506.80117 12526.2437 15232.1018 15623.42269 10247.99992 12808.69328 12934.67546 18867.06939 0.515035502 0.980904919 0.663921006 0.807337986 0.828078933 0.543168613 0.678891513 0.685568871 1 14.20358273 -0.945543203 4.143851932 1.000011285 0.727516623 0.298751859 0.136622224 35171852.27 72573524.2 5937.17621 0.031647519 0.113359207 0.945543203 -0.272494662 RGPNYTSGYGTNSELS(ph)NPS(ph)ETESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGPNYTSGYGTNSELSNPSETESER 25 1 B4DXZ6;P51114;P51114-3;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 2 RGPNYTSGYGTNS(0.001)ELS(0.999)NPS(0.994)ET(0.005)ES(0.001)ER 89.634 0.049929 170480000 81127 65753 85304 69123 77728 76824 85605 74348 56927 TRUE FALSE 76049.40589 70621.42054 87327.45116 70896.8132 71623.55642 99001.84167 72769.32497 83630.51146 47425.51594 1.603554635 1.489101787 1.841360066 1.494908633 1.510232519 2.087522712 1.534391846 1.76340752 1 15.53337585 -1.616501296 7.323884761 0.998967079 1.664923043 0.548609941 0.189728268 0.002916702 0.000152727 0.167441705 0.039417161 0.024182361 1.616501296 0.665955964 RGPNYTSGYGTNSELSNPS(ph)ETESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.978)ET(0.021)ESER;RGPNYTSGYGTNSELSNPS(0.994)ET(0.006)ESER;RGPNYTSGYGTNSELSNPS(0.978)ET(0.022)ESER;RGPNYTSGYGTNSELSNPS(0.954)ET(0.046)ESER;RGPNYTSGYGTNSELSNPS(0.99)ET(0.01)ESER;RGPNYTSGYGTNSELSNPS(0.998)ET(0.002)ESER 322.13 2.95E-75 3567170000 824294 905021 926224 941414 905737 791408 1138446 929013 792651 TRUE FALSE 772702.9099 972029.6965 948194.4707 965572.2771 834604.0696 1019874.642 967746.5911 1045002.318 660352.4274 1.170137154 1.471986255 1.43589155 1.462207508 1.263876735 1.544439908 1.465500165 1.582491825 1 19.33287666 2.219632284 24.99840915 1.443804634 1.390824408 0 0.184188098 1299.651823 1716422.995 0.061257846 0.04531367 165.8182335 -2.219632284 -0.052980226 RGPNYTSGYGTNSELSNPSETESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RGPNYTSGYGTNSELSNPSETESER 25 1 B4DXZ6;P51114;P51114-3;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 ;;; 291.5 1.21E-62 948590000 280028 282449 305589 303013 317769 253142 352601 260432 263730 FALSE TRUE 262501.5473 303361.8178 312837.7154 310788.8266 292812.7046 326219.986 299731.7534 292947.5085 219711.7592 1.194754201 1.380726361 1.423855129 1.414529781 1.33271294 1.484763433 1.364204422 1.333326489 1 17.74525256 0.658390834 2.325721997 1.00005307 1.381684612 0.70079808 0.075325246 1.129163851 7.042383748 0.066351844 0.017890741 4.553977012 -0.658390834 0.381631542 RGPPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RGPPEK 6 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 124.37 0.029477 289078000 634350 519500 598910 578350 599510 472000 718800 602220 633440 FALSE TRUE 594647.1658 557964.3205 613116.428 593191.4401 552426.9029 608258.7377 611022.613 677408.4926 527714.7718 1.126834414 1.057321777 1.161832984 1.124075868 1.046828576 1.15262784 1.157865282 1.283664072 1 19.00939884 2.02743564 24.99128185 1.162349444 1.10548654 0.070264669 0.075152812 430.937956 392542.2515 0.025334074 0.018710036 106.5210994 -2.02743564 -0.056862905 RGPPEKEWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGPPEKEWR 9 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 73.499 0.024605 169510000 277990 337360 294960 326610 393260 223770 404800 295430 598610 FALSE TRUE 260591.1021 362338.4854 301956.5905 334991.3655 362374.9459 288368.7664 344103.998 332315.0858 498698.1238 0.522542776 0.726568776 0.605489726 0.671731754 0.726641887 0.578243135 0.690004597 0.666365222 1 18.92780725 -5 0.359545868 5.26464304 0.643779175 0.754014993 0.063448241 217.7902209 1.736115155 718.584226 0.041095098 1.00E-05 5 -4.620863865 RGPPPPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 119.17 0.0027981 202052000 85787 91414 86567 94991 91050 78095 93462 91157 107700 FALSE TRUE 80417.7448 98182.38768 88620.41012 97428.62988 83899.30028 100639.7587 79448.24076 102538.1521 89724.17423 0.896277347 1.094269059 0.987698253 1.085868226 0.935080217 1.121657119 0.885471964 1.142815222 1 16.45320912 2.771652806 24.94074359 1.008402071 1.024346668 0 0.093017923 5541.696256 4176640.441 0.025190482 0.026716033 591.088903 -2.771652806 0.015944597 RGQAALDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RGQAALDR 8 1 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ;;;;; 145.72 0.0009056 2886030000 1814170 3072870 1872230 1878640 3415460 1574870 1966310 2757960 2931110 FALSE TRUE 1700624.338 3300388.492 1916640.18 1926849.083 3147223.549 2029509.403 1671480.07 3102297.377 2441888.805 0.696438075 1.351571982 0.784900678 0.789081419 1.288848019 0.831122776 0.684502941 1.270449895 1 21.21956608 3.840644253 13.69451734 0.92241725 1.07042706 0 0.25428661 2.080340347 240.356846 0.060980486 0.109948596 6928.580281 -3.840644253 0.14800981 RGQPAS(ph)PSAHMVSHSHSPSVVS ddPTM_SK-BR-3_Pertuzumab_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(0.963)PS(0.037)AHMVSHSHSPSVVS;RGQPAS(0.96)PS(0.04)AHMVSHSHSPSVVS;RGQPAS(0.98)PS(0.02)AHMVSHSHSPSVVS;RGQPAS(0.92)PS(0.08)AHMVSHSHSPSVVS 134.28 3.34E-06 1708430000 243198 546107 465281 498761 557726 514357 597170 514895 532117 TRUE FALSE 227976.6713 586541.3305 476317.685 511560.0517 513924.4497 662843.516 507629.9024 579180.7742 443303.2351 0.514268007 1.323115385 1.07447374 1.153973197 1.159306788 1.495237263 1.145107597 1.306511499 1 18.75793437 4.744075144 24.87576433 1.213580395 0.514267687 0.707743585 0.139888505 291.0342176 1312799.163 0.030442385 0.267154093 55472.16851 -4.744075144 -0.699312707 RGQS(ph)SPPPAPPICLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.573)S(0.427)PPPAPPICLR 94.313 0.002768 1504780000 527040 596860 576490 594380 704290 481720 626300 546810 725130 TRUE FALSE 494053.5072 641052.1354 590164.615 609632.7971 648977.9044 620784.7439 532392.1293 615080.4322 604101.1185 0.817832466 1.06116694 0.976930181 1.009156875 1.074286878 1.027617273 0.881296381 1.018174629 1 19.20443053 0.055500036 6.580988019 1.000000007 0.987271856 0.002167633 0.078980478 604940.8143 86177.33503 0.071504998 0.017342509 1.136318393 -0.055500036 -0.01272815 RGQSS(ph)PPPAPPICLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGQSSPPPAPPICLR 15 1 O43379-4;O43379;H7C3R4;O43379-3;O43379-2 O43379-4 WDR62 WD repeat-containing protein 62 1 RGQS(0.149)S(0.851)PPPAPPICLR;RGQS(0.15)S(0.85)PPPAPPICLR 106.44 0.00075729 1449490000 1451540 929360 1078830 1008990 1201720 777020 1308980 858830 1329580 TRUE FALSE 1360690.702 998170.7814 1104420.357 1034882.392 1107341.759 1001333.06 1112710.601 966056.816 1107664.509 1.228432158 0.901149015 0.997071179 0.934292273 0.999708621 0.904003922 1.004555614 0.872156514 1 20.07908955 4.745345638 24.92678355 0.953932905 1.228432289 0.764286393 0.048296933 328.1162854 1205400.462 0.009878131 0.097845158 55634.68552 -4.745345638 0.274499384 RGRS(ph)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RGRSPQPPAEEDEDDFDDTLVAIDTYNCDLHFK 33 2 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0;M0R0K8;M0QYI8 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 1 RGRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;RGRS(0.831)PQPPAEEDEDDFDDT(0.169)LVAIDTYNCDLHFK;RGRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;RGRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;RGRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK 294.69 6.94E-90 671950000 191117.3 266277 194322.6 215167 423398 136031.9 230692 220632 1073673 TRUE FALSE 179155.6093 285992.4261 198932.0238 220688.5495 390146.029 175302.1012 196101.8762 248178.3909 894470.0401 0.200292465 0.319733936 0.22240211 0.246725479 0.436175625 0.195984319 0.21923806 0.277458584 1 19.77067364 0.91821216 20.86182858 1 0.263249867 0.91360068 0.071071709 3106.121673 792288.0123 0.064481655 0.016120414 8.283467268 -0.91821216 -0.736750133 RGRS(ph)PS(ph)PKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGRSPSPKPR 10 3 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RGRS(1)PS(1)PKPR 70.412 0.077606 195720000 265510 182420 174730 207580 208250 133060 195920 160950 322810 TRUE FALSE 248892.203 195926.5666 178874.6781 212906.8542 191894.885 171472.262 166543.6148 181044.9618 268930.9256 0.925487474 0.728538625 0.665132423 0.791678584 0.713547111 0.637607079 0.619280265 0.673202464 1 18.03687614 -1.106446074 4.269978247 1.000044804 0.707063116 0.492933612 0.088698562 12056536.03 3124116.911 5023.130229 0.020420639 0.078262538 1.106446074 -0.292981687 RGS(ph)ALGPDEAGGELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGSALGPDEAGGELER 16 1 O75145-2;O75145;R4GN36;R4GNF1 O75145-2 PPFIA3 Liprin-alpha-3 1 RGS(1)ALGPDEAGGELER;RGS(1)ALGPDEAGGELER 96.708 0.0020342 234220000 114339 103218 102307 98630 127149 95418 131989 94652 134803 TRUE FALSE 107182.7261 110860.3681 104733.7704 101161.0128 117163.2304 122963.6276 112198.4748 106469.5106 112303.5084 0.954402294 0.987149642 0.932595711 0.900782301 1.043273109 1.094922406 0.999064734 0.948051508 1 16.77704347 2.724971153 24.91602023 1.02199893 0.949112549 0.417626425 0.042598903 775.287874 1421473.289 0.014037232 0.013303997 530.8491822 -2.724971153 -0.072886381 RGS(ph)ASGSEPAGDSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.997)AS(0.003)GSEPAGDSDR;RGS(0.956)AS(0.044)GSEPAGDSDR;RGS(0.981)AS(0.015)GS(0.004)EPAGDSDR;RGS(1)ASGSEPAGDSDR;RGS(0.997)AS(0.003)GSEPAGDSDR;RGS(0.999)AS(0.001)GSEPAGDSDR 227.57 4.37E-13 872625000 631118 588493 605423 642169 645440 468458 677437 516247 688767 TRUE FALSE 591617.451 632065.634 619783.9195 658648.1437 594749.746 603694.2198 575861.6109 580701.5743 573807.3381 1.031038489 1.101529367 1.080125468 1.147855909 1.036497281 1.05208522 1.003580074 1.012014897 1 19.13020689 2.16910154 1.681644355 1.006616274 1.089108699 0.545476733 0.031588759 0.256928683 1.417574453 0.016331048 0.009422204 147.6051599 -2.16910154 0.082492425 RGS(ph)CVTQVGLLESVYEMFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGSCVTQVGLLESVYEMFR 19 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 1 RGS(0.995)CVT(0.005)QVGLLESVYEMFR;RGS(0.985)CVT(0.015)QVGLLESVYEMFR 225.88 9.99E-20 292630000 289930 253990 260140 274370 282930 223420 313060 208501 294470 TRUE FALSE 271783.7988 272795.6839 266310.6436 281410.7987 260709.8191 287917.7271 266119.5593 234532.8088 245321.0547 1.107869845 1.111994583 1.085559672 1.147112298 1.062729082 1.173636431 1.084780757 0.956023971 1 17.90431153 1.325914569 5.103626181 0.978850774 1.111412507 0.748170089 0.032255935 0.085130136 3.42184182 0.020381324 0.007039793 21.17944471 -1.325914569 0.132561733 RGS(ph)DAS(ph)DFDISEIQSVCSDVETVPQTHRPTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGSDASDFDISEIQSVCSDVETVPQTHRPTPR 32 2 F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A0U1RQJ2;A0A494C073;H0YC65;A0A494C1U5 F6QMI7 DST Dystonin 2 RGS(1)DAS(1)DFDISEIQSVCSDVETVPQTHRPTPR;RGS(1)DAS(1)DFDISEIQSVCSDVETVPQTHRPTPR 156.18 3.75E-11 339820000 26161 25786 30292 31048 23242.1 23748.7 25848 21256.6 32889 TRUE FALSE 24523.62971 27695.22227 31010.54054 31844.74424 21416.75922 30604.56416 21972.33236 23910.5333 27399.61343 0.89503561 1.010788796 1.13178752 1.162233341 0.781644576 1.116970655 0.801921254 0.872659513 1 14.74186792 2.74439776 24.99948451 0.911102618 1.05707026 0.243678809 0.118077839 635.7580844 2722843.648 0.034554845 0.035744558 555.1339143 -2.74439776 0.145967642 RGS(ph)DASDFDISEIQSVCSDVETVPQTHRPTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGSDASDFDISEIQSVCSDVETVPQTHRPTPR 32 2 F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A0U1RQJ2;A0A494C073;H0YC65;A0A494C1U5 F6QMI7 DST Dystonin 1 RGS(1)DASDFDISEIQSVCSDVETVPQTHRPTPR 257.45 1.70E-59 254830000 11202 7168.2 9669.7 7193 10501 6227.6 4884 11350 7203.8 TRUE FALSE 10500.88682 7698.940987 9899.06985 7377.584558 9676.293819 8025.407023 4151.689541 12767.07248 6001.439242 1.749728089 1.282849109 1.649449316 1.229302549 1.612328881 1.337247067 0.691782316 2.127335123 1 12.55109281 1.998756503 24.95217305 1.182723241 1.481114517 0.053991448 0.392587978 95.18990817 1910114.819 0.134573024 0.098072671 99.71408368 -1.998756503 0.298391276 RGS(ph)DPASGEVEASQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RGSDPASGEVEASQLR 16 1 Q8WWA1-3;Q8WWA1-2;Q8WWA1 Q8WWA1-3 TMEM40 Transmembrane protein 40 1 RGS(0.959)DPAS(0.041)GEVEASQLR;RGS(1)DPASGEVEASQLR;RGS(1)DPASGEVEASQLR 166.3 7.12E-09 1018300000 618220 572970 518751 507690 593490 456120 695330 572392 492811 TRUE FALSE 579526.7138 615393.295 531056.0187 520718.1849 546879.6894 587794.4395 591071.7216 643856.4012 410557.6604 1.41155986 1.498920503 1.293499233 1.268319252 1.332041129 1.431697655 1.439680168 1.568248417 1 18.64722533 -1.407712763 3.7536433 0.997601105 1.401562921 0.663722368 0.090669384 0.001870111 0.000295084 0.090091317 0.021117781 0.039109948 1.407712763 0.403961816 RGS(ph)FDATGSGFSMTFSSSSYSSSGYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.915)FDAT(0.042)GS(0.042)GFSMTFSSSSYSSSGYGR 72.725 0.00040454 0 39591 97682 76358 82515 86772 71600 82211 74597 77502 TRUE FALSE 37113.06998 104914.4769 78169.24782 84632.4746 79957.27714 92269.75767 69884.22376 83910.59966 64566.41552 0.574804559 1.624907873 1.210679688 1.31078168 1.238372558 1.429067371 1.082361832 1.299601333 1 15.97849632 0.235957208 0.764240031 0.996157962 1.266890468 0.036699256 0.273996906 7.868897289 5.760716555 0.332686108 0.084586372 1.721698923 -0.235957208 0.270732506 RGS(ph)FSSENYWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RGSFSSENYWR 11 1 Q6P6C2-3;Q6P6C2;Q6P6C2-1;K7ER58 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 RGS(0.999)FS(0.001)SENYWR;RGS(0.999)FS(0.001)SENYWR;RGS(0.984)FS(0.016)SENYWR;RGS(0.999)FS(0.001)SENYWR;RGS(0.989)FS(0.011)SENYWR;RGS(1)FSSENYWR 217.39 6.97E-12 4111420000 789246 924608 847587 994579 1169821 672068 1125080 836523 1398114 TRUE FALSE 739848.5017 993066.9384 867692.1639 1020101.581 1077947.977 866083.1215 956384.6987 940964.738 1164759.741 0.635194088 0.852593804 0.744953773 0.875804292 0.925468094 0.743572336 0.821100408 0.80786166 1 20.15160097 -5 0.157856354 1.687975722 0.751546848 0.422105312 0.077440577 138.4284487 1.265531829 30.11786555 0.320885567 1.00E-05 5 -0.936428873 RGS(ph)GDTSISIDTEASIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 20 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(0.994)GDT(0.006)SISIDTEASIR;RGS(0.868)GDT(0.077)S(0.054)IS(0.001)IDTEASIR;RGS(0.971)GDT(0.025)S(0.003)ISIDTEASIR;RGS(0.916)GDT(0.078)S(0.006)IS(0.001)IDTEASIR;RGS(0.882)GDT(0.105)S(0.013)IS(0.001)IDTEASIR;RGS(0.996)GDT(0.003)S(0.001)ISIDTEASIR;RGS(0.939)GDT(0.054)S(0.005)IS(0.002)IDTEASIR;RGS(0.972)GDT(0.027)S(0.001)ISIDTEASIR;RGS(1)GDTSISIDTEASIR;RGS(0.964)GDT(0.033)S(0.002)ISIDTEASIR;RGS(0.997)GDT(0.003)SISIDTEASIR;RGS(0.903)GDT(0.091)S(0.006)ISIDTEASIR;RGS(0.986)GDT(0.013)S(0.001)ISIDTEASIR;RGS(0.985)GDT(0.012)S(0.003)ISIDTEASIR;RGS(0.951)GDT(0.042)S(0.006)ISIDTEASIR;RGS(0.991)GDT(0.008)S(0.001)ISIDTEASIR;RGS(0.943)GDT(0.053)S(0.004)ISIDTEASIR;RGS(0.996)GDT(0.004)SISIDTEASIR;RGS(0.966)GDT(0.025)S(0.009)ISIDTEASIR;RGS(0.995)GDT(0.005)SISIDTEASIR 173.18 5.84E-14 677123700 434402.1 457118.6 448694.3 438508.2 494385.7 377991.6 491834.3 390566.3 537298.3 TRUE FALSE 407213.648 490964.1368 459337.5407 449761.0628 455558.6414 487111.6387 418088.3127 439329.3623 447619.7427 0.909731205 1.096833071 1.026178019 1.004783793 1.01773581 1.088226439 0.934025631 0.981478966 1 18.77191414 1.714816811 13.5790796 0.968711605 1.031608666 0.164377469 0.053337559 0.173671393 81.62776273 0.022916106 0.012602702 51.85812505 -1.714816811 0.062897061 RGS(ph)GDTSSLIDPDTSLSELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RGSGDTSSLIDPDTSLSELR 20 1 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 RGS(0.988)GDT(0.01)S(0.001)SLIDPDTSLSELR;RGS(0.992)GDT(0.007)S(0.001)SLIDPDTSLSELR;RGS(0.975)GDT(0.025)SSLIDPDTSLSELR;RGS(0.999)GDT(0.001)SSLIDPDTSLSELR;RGS(0.867)GDT(0.082)S(0.035)S(0.016)LIDPDTSLSELR 243.19 4.88E-30 6194180000 6111090 5267700 5745960 5724260 5674850 4562270 6261200 4884290 5867950 TRUE FALSE 5728607.786 5657725.989 5882256.885 5871154.203 5229170.172 5879323.287 5322391.186 5494104.358 4888551.237 1.171841617 1.157342066 1.203272012 1.201000853 1.069676867 1.202671917 1.088746119 1.123871694 1 22.22097554 0.665412081 0.42904589 0.988115333 1.182357864 0.615841358 0.041427242 1.083571759 0.431993373 0.06623891 0.025624493 4.628199602 -0.665412081 0.194242531 RGS(ph)GDTSSLIDPDTSLSELRDIYDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RGSGDTSSLIDPDTSLSELRDIYDLK 26 2 C9JSU1;Q9Y608-4;Q9Y608 C9JSU1 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 RGS(0.857)GDT(0.14)S(0.003)SLIDPDTSLSELRDIYDLK;RGS(0.999)GDT(0.001)SSLIDPDTSLSELRDIYDLK;RGS(0.999)GDT(0.001)SSLIDPDTSLSELRDIYDLK 160.45 9.52E-12 145932000 209257 203008 193964 231152 309179 114167 240996 165077 541970 TRUE FALSE 196159.9779 218038.9235 198564.9177 237083.7517 284897.3285 147125.1596 204860.8871 185687.2268 451511.7057 0.434451589 0.482908684 0.439778006 0.525088826 0.630985476 0.325850156 0.453722206 0.411256728 1 18.78440387 -1.556457935 2.76604379 1.031859376 0.462759445 0.822281061 0.078456486 12503584.1 12552663.09 2945993.891 0.018835085 0.027767838 1.556457935 -0.569099931 RGS(ph)GHLPSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGSGHLPSAR 10 1 Q8N4Y2 Q8N4Y2 CRACR2B EF-hand calcium-binding domain-containing protein 4A 1 RGS(0.998)GHLPS(0.002)AR 68.14 0.037284 93014000 226730 100810 120370 111360 101820 87905 166250 110550 138410 TRUE FALSE 212539.374 108274.0773 123225.2332 114217.6861 93823.46792 113281.7465 141322.3559 124352.4109 115308.4768 1.843224192 0.938994949 1.068657193 0.990540238 0.813673639 0.982423405 1.225602486 1.078432517 1 16.81513905 4.74204742 24.99500683 1.021199697 1.843224501 0.859735591 0.105422988 131.4501386 942254.0171 0.027160599 0.198598534 55213.77236 -4.74204742 0.822024804 RGS(ph)GVFCANCLTTK ddPTM_SK-BR-3_Pertuzumab_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 224.4 1.94E-12 3234620000 4289770 3663380 3257450 3382970 4530350 2012950 5088290 3079300 5999240 TRUE FALSE 4021280.953 3934620.467 3334718.252 3469782.738 4174554.586 2594055.987 4325348.152 3463757.383 4997928.087 0.804589598 0.787250316 0.667220135 0.69424423 0.835257033 0.519026273 0.865428249 0.69303866 1 22.25289871 -0.674203694 0.862863657 1.019168683 0.732634876 0.412235969 0.099802424 31.70444576 13.59169706 2.004313384 0.028535123 0.211736781 0.674203694 -0.286533806 RGS(ph)IDSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGSIDSPK 8 1 F5H212;P15822 F5H212 HIVEP1 Zinc finger protein 40 1 RGS(1)IDSPK;RGS(1)IDSPK 79.82 0.016567 292000000 440160 358400 380650 366680 338220 276365 510130 355880 402500 TRUE FALSE 412611.1713 384936.3089 389679.1978 376089.6296 311657.5655 356147.0891 433640.7423 400312.4014 335320.1498 1.230499186 1.14796653 1.16211089 1.121583746 0.929432859 1.062110611 1.29321409 1.193821492 1 18.35517965 5.495217873 0.927247172 1.12300081 1.530755785 0.11459427 0.101090749 20.70888993 5.071591176 0.033275517 11.89240352 312764.8021 -5.495217873 0.407754975 RGS(ph)IGENQIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RGSIGENQIK 10 1 Q05682-5;Q05682-4;C9J813;E9PGZ1 Q05682-5 CALD1 Caldesmon 1 RGS(1)IGENQIK;RGS(1)IGENQIK;RGS(1)IGENQIK 138.19 4.36E-05 651390000 705880 495000 550940 507010 602100 458644 661260 585530 763460 TRUE FALSE 661700.2308 531650.315 564008.557 520020.735 554813.4948 591047.0773 562110.2018 658634.7094 636033.5939 1.040354216 0.835884016 0.886759068 0.817599479 0.872302187 0.929270219 0.883774391 1.035534468 1 19.27874344 1.242506474 24.99475047 1.017767268 0.886725881 0.405128808 0.061122055 79.65657972 504605.3957 0.040621148 0.013607532 17.47859318 -1.242506474 -0.131041386 RGS(ph)IGENQIKDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGSIGENQIKDEK 13 2 Q05682-5;Q05682-4;C9J813;E9PGZ1 Q05682-5 CALD1 Caldesmon 1 RGS(1)IGENQIKDEK 136.26 3.88E-05 530360000 193090 87126 130950 134550 163670 102340 169260 126290 282550 TRUE FALSE 181004.8416 93576.89969 134056.1958 138002.7808 150816.0184 131883.8966 143881.0343 142057.5845 235390.5797 0.768955333 0.397538847 0.569505356 0.586271468 0.640705412 0.560276868 0.611243808 0.603497322 1 17.84469706 -5 0.272290361 3.9882954 0.543980996 0.648835347 0.09293069 120.546692 1.167666353 202.5573865 0.104474569 1.00E-05 5 -3.444314404 RGS(ph)IS(ph)S(ph)MSSVSSVLDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGSISSMSSVSSVLDEK 17 1 Q9H1K0 Q9H1K0 RBSN Rabenosyn-5 3 RGS(0.553)IS(0.641)S(0.415)MS(0.392)S(0.375)VS(0.326)S(0.297)VLDEK 67.227 0.014634 168520000 134730 179590 192080 174060 205370 161600 204710 170440 228090 TRUE FALSE 126297.4898 192887.0305 196636.2283 178526.6743 189241.0686 208251.2966 174015.6359 191719.8092 190020.3055 0.664652598 1.015086414 1.034816926 0.939513668 0.995899192 1.095942332 0.915773898 1.0089438 1 17.53579407 4.740060395 24.94084925 1.000626869 0.664652484 0.823706549 0.048864715 49.40346198 821484.8161 0.011125573 0.070397928 54961.73005 -4.740060395 -0.335974385 RGS(ph)KGHMNYEGPGMAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGSKGHMNYEGPGMAR 16 2 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 RGS(1)KGHMNYEGPGMAR;RGS(1)KGHMNYEGPGMAR 150.63 3.76E-07 190300000 174616 132558 125501 140786 162374 87866 161401 139973 271901 TRUE FALSE 163687.0963 142372.7322 128477.943 144398.8071 149621.801 113231.4878 137200.4184 157448.9372 226518.9666 0.722619826 0.628524553 0.567184042 0.637468947 0.660526592 0.49987641 0.605690643 0.695080591 1 17.78927233 0.823545916 3.019514172 0.999872054 0.610258874 0.808705706 0.05809646 0.331661053 4.933833772 0.053462225 0.01399172 6.661099423 -0.823545916 -0.38961318 RGS(ph)LEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 96.034 0.026135 4638670000 5391250 3336420 4062920 4093160 4209170 2978060 4887340 3611120 5441960 TRUE FALSE 5053821.286 3583452.008 4159294.381 4198197.415 3878598.767 3837777.577 4154528.739 4061976.281 4533661.72 1.11473277 0.790410099 0.917424951 0.926005881 0.855511286 0.846507264 0.916373783 0.895959278 1 22.11224532 -0.870681346 5.138581934 1.000000164 0.895958156 0.089949666 0.084895067 1.40E-07 3.08E-08 0.072306406 0.017042756 0.134684821 0.870681346 -0.104042008 RGS(ph)LLGSMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGSLLGSMK 9 1 Q9HDC5 Q9HDC5 JPH1 Junctophilin-1 1 RGS(1)LLGSMK;RGS(1)LLGSMK 95.98 0.0025996 0 746030 682420 439908 440728 804450 299440 597192 675420 946330 TRUE FALSE 699337.314 732947.0869 450342.8255 452037.8266 741271.742 385883.467 507648.6037 759747.6738 788381.4095 0.887054547 0.929685908 0.571224562 0.573374538 0.940245081 0.48946292 0.643912448 0.963680351 1 19.58853423 1.221176111 16.87633961 0.981870637 0.713166259 0.32333812 0.157716577 7.549618661 7315.563424 0.145661536 0.037617609 16.64087317 -1.221176111 -0.268704379 RGS(ph)LPAGASWQNTDLFEMIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RGSLPAGASWQNTDLFEMIEK 21 1 J3KPC5;P47736-3 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 RGS(1)LPAGASWQNTDLFEMIEK;RGS(1)LPAGASWQNTDLFEMIEK;RGS(0.999)LPAGAS(0.001)WQNTDLFEMIEK;RGS(1)LPAGASWQNTDLFEMIEK 279.15 4.00E-45 1412204000 2644890 1705897 2062290 1843549 2349740 1384633 2261510 1888574 3398040 TRUE FALSE 2479351.056 1832203.389 2111208.493 1890857.588 2165200.899 1784354.069 1922417.57 2124366.621 2830885.172 0.875821839 0.647219254 0.745776803 0.667938639 0.764849426 0.630316654 0.679087089 0.750424864 1 21.4328218 0.85456887 5.192275558 0.999995739 0.706814321 0.60815425 0.070822871 1.095992989 38.71647813 0.060102181 0.015172724 7.154328373 -0.85456887 -0.293181417 RGS(ph)LPDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RGSLPDQK 8 1 X6RKU3;Q6P3S6 X6RKU3 FBXO42 F-box only protein 42 1 RGS(1)LPDQK;RGS(1)LPDQK;RGS(1)LPDQK;RGS(1)LPDQK 139.76 0.00040452 1281390000 3164500 2089170 2360050 2398900 2328950 1739850 3200500 2026930 2535730 TRUE FALSE 2966439.594 2243854.321 2416031.5 2460459.835 2146043.662 2242116.451 2720614.737 2279996.672 2112500.282 1.404231573 1.062179418 1.143683398 1.16471456 1.015878521 1.061356758 1.287864793 1.079288222 1 21.0105201 4.745405305 24.75546897 1.1174293 1.404231724 0.55452624 0.084147397 574.3840986 2077337.94 0.019799517 0.195269121 55642.32964 -4.745405305 0.286802424 RGS(ph)LQAYTFEEQPTLPVLLPTSSGLPPGWEEKQDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGSLQAYTFEEQPTLPVLLPTSSGLPPGWEEKQDER 36 2 P46934-4;H0Y8X6;P46934-3;P46934-2;P46934 P46934-4 NEDD4 E3 ubiquitin-protein ligase NEDD4 1 RGS(1)LQAYTFEEQPTLPVLLPTSSGLPPGWEEKQDER 137.88 1.12E-09 109520000 152490 121580 116600 136750 169380 89156 174500 128570 249200 TRUE FALSE 142945.9231 130581.9097 119365.8071 140259.2365 156077.578 114893.8899 148335.345 144622.2475 207606.9101 0.688541258 0.628986336 0.574960665 0.675600039 0.751793753 0.553420355 0.714501 0.69661577 1 17.66349494 -0.469429669 0.479122981 1.067859463 0.63292549 0.769032985 0.0590271 3.774645593 0.780535967 0.477654728 0.028955567 0.339289431 0.469429669 -0.434933974 RGS(ph)LSNAGDPEIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RGSLSNAGDPEIVK 14 1 O43847;O43847-2;F5H7V1 O43847 NRD1 Nardilysin 1 RGS(0.998)LS(0.002)NAGDPEIVK;RGS(0.999)LS(0.001)NAGDPEIVK;RGS(0.997)LS(0.003)NAGDPEIVK;RGS(0.996)LS(0.004)NAGDPEIVK;RGS(0.961)LS(0.039)NAGDPEIVK;RGS(1)LSNAGDPEIVK;RGS(0.716)LS(0.284)NAGDPEIVK 210.66 3.02E-09 34353710000 28455620 20777220 23761270 22687680 23577270 19378350 34800460 22430100 29098230 TRUE FALSE 26674633.54 22315586.99 24324898.55 23269884.28 21725606.32 24972565.06 29582454.09 25230547.36 24241547.43 1.100368432 0.920551258 1.003438358 0.959917445 0.896213675 1.030155568 1.220320369 1.040797723 1 24.53097846 1.993693649 24.58780393 1.114949057 0.970821783 0.270704036 0.078791846 199.9915046 779747.0425 0.027392541 0.019518719 98.55840102 -1.993693649 -0.144127273 RGS(ph)LTLTISGESPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RGSLTLTISGESPK 14 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(0.889)LT(0.11)LT(0.001)ISGESPK;RGS(0.997)LT(0.003)LTISGESPK;RGS(1)LTLTISGESPK;RGS(0.958)LT(0.042)LTISGESPK;RGS(0.966)LT(0.034)LTISGESPK;RGS(0.94)LT(0.06)LTISGESPK 246.48 5.99E-18 2496600000 4645920 3001560 3687390 3531700 3666590 2706700 4869000 3162480 5113940 TRUE FALSE 4355140.16 3223798.626 3774856.632 3622329.401 3378630.812 3488080.35 4138938.652 3557322.589 4260390.377 1.022239695 0.756690899 0.886035386 0.850234152 0.793033153 0.818723178 0.971492818 0.834975736 1 22.0225542 0.718238578 0.713016892 0.997768215 0.848926893 0.183831388 0.081059792 1.578839722 1.574333931 0.076127178 0.027701187 5.226832447 -0.718238578 -0.148841322 RGS(ph)MFYDEDGDLAHEFYEETIVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RGSMFYDEDGDLAHEFYEETIVTK 24 1 O75896 O75896 TUSC2 Tumor suppressor candidate 2 1 RGS(0.612)MFY(0.375)DEDGDLAHEFY(0.012)EET(0.001)IVTK;RGS(0.538)MFY(0.46)DEDGDLAHEFY(0.001)EETIVTK;RGS(1)MFYDEDGDLAHEFYEETIVTK;RGS(0.542)MFY(0.458)DEDGDLAHEFYEETIVTK;RGS(0.531)MFY(0.456)DEDGDLAHEFY(0.013)EETIVTK 151.37 6.85E-08 385139000 525178 459740 395955 420456 512652 279766 586660 437976 584521 TRUE FALSE 492308.0464 493779.628 405347.2396 431245.6128 472390.3799 360529.9026 498695.7793 492658.2677 486960.669 1.010981128 1.0140031 0.832402421 0.885586127 0.970079125 0.740367602 1.024098682 1.011700326 1 18.89344573 1.601455272 25 1.01344075 0.911413623 0.25983176 0.081884387 0.811674355 3154.053475 0.041530775 0.019948408 39.94434202 -1.601455272 -0.102027127 RGS(ph)MNNELLSPEFGPVRDPLADGVEGLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RGSMNNELLSPEFGPVRDPLADGVEGLGR 29 2 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 RGS(1)MNNELLSPEFGPVRDPLADGVEGLGR;RGS(1)MNNELLSPEFGPVRDPLADGVEGLGR;RGS(0.857)MNNELLS(0.143)PEFGPVRDPLADGVEGLGR;RGS(1)MNNELLSPEFGPVRDPLADGVEGLGR 164.83 4.43E-12 524705000 211504 192049 197374 198654 183213 159589 237069 177056 173544 TRUE FALSE 198266.3422 206268.5078 202055.8045 203751.798 168824.19 205659.7536 201522.7043 199161.8313 144578.3853 1.371341517 1.426689802 1.397551952 1.409282567 1.167700066 1.422479254 1.393864677 1.377535314 1 17.14149236 -1.559853693 2.399408335 0.966882984 1.376872909 0.708710759 0.074619557 1533535.9 1292681.15 323990.8408 0.017969729 0.027551567 1.559853693 0.409989925 RGS(ph)MSYLAAVEEEVEESSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGSMSYLAAVEEEVEESSVK 20 1 Q8WXH0;Q8WXH0-2;G3V5X4;A0A0A0MRE3;A0A0C4DGK3;Q8WXH0-7 Q8WXH0 SYNE2 Nesprin-2 1 RGS(0.635)MS(0.336)Y(0.03)LAAVEEEVEESSVK;RGS(0.981)MS(0.019)YLAAVEEEVEESSVK 192.85 5.82E-18 101198000 124865 95959 87010 93735 114585 67452 130013 92535 138105 TRUE FALSE 117049.9225 103063.9042 89073.91829 96140.39879 105585.9563 86924.29741 110518.7576 104088.1984 115054.3833 1.017344313 0.895784248 0.774189698 0.83560831 0.91770477 0.755506178 0.960578419 0.904686944 1 16.81195642 1.218655465 1.503353437 0.987750483 0.861787172 0.188340884 0.078586464 0.542871047 2.316850174 0.069678349 0.021149284 16.54456928 -1.218655465 -0.125963311 RGS(ph)PSAAFTFPDTDDFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGSPSAAFTFPDTDDFGK 18 1 Q9ULT0;Q9ULT0-4;H7C055;Q9ULT0-3 Q9ULT0 TTC7A Tetratricopeptide repeat protein 7A 1 RGS(0.991)PS(0.009)AAFTFPDTDDFGK 208.69 3.70E-16 152460000 281180 258270 268420 268640 317870 235290 351360 280970 390550 TRUE FALSE 263581.4457 277392.5795 274787.0492 275533.7572 292905.7724 303214.4034 298676.8299 316049.723 325364.682 0.810110809 0.852558974 0.844550944 0.846845932 0.900238375 0.931921687 0.917975572 0.971370713 1 18.31169813 1.990325769 0.500115501 1.001470575 0.824571543 0.930567033 0.015858881 0.216827823 0.119790293 0.015398522 0.011954558 97.79705315 -1.990325769 -0.176899032 RGS(ph)PTTGFIEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RGSPTTGFIEQK 12 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(0.799)PT(0.195)T(0.006)GFIEQK;RGS(0.984)PT(0.015)T(0.001)GFIEQK;RGS(0.964)PT(0.036)TGFIEQK;RGS(0.637)PT(0.326)T(0.037)GFIEQK;RGS(0.591)PT(0.363)T(0.047)GFIEQK;RGS(0.847)PT(0.076)T(0.076)GFIEQK 177.04 1.46E-05 10670280000 20620600 13404300 16273500 14974600 16573900 13154900 20464400 13758400 20979600 TRUE FALSE 19329993.45 14396768.32 16659515.1 15358873.59 15272252.75 16952506.08 17395953.2 15476166.53 17477969.23 1.105963353 0.823709444 0.953172242 0.878756187 0.873800185 0.969935686 0.995307463 0.885467089 1 24.05903423 2.207576667 24.82986924 0.966097701 0.914345693 0.032732318 0.080186529 453.1738922 363160.9417 0.027371193 0.020217213 161.2785711 -2.207576667 -0.051752008 RGS(ph)PVPPVPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RGSPVPPVPER 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(1)PVPPVPER;RGS(1)PVPPVPER;RGS(1)PVPPVPER;RGS(1)PVPPVPER;RGS(1)PVPPVPER;RGS(1)PVPPVPER 97.417 0.0038478 9613450000 3589280 2934610 3205720 3109320 3236120 2789200 3721980 2851750 3361650 TRUE FALSE 3364633.372 3151891.578 3281761.192 3189110.415 2981968.189 3594396.761 3163903.652 3207797.265 2800568.898 1.201410676 1.125446898 1.171819481 1.138736639 1.064772301 1.28345236 1.129736053 1.145409159 1 21.41728849 0.572528358 2.132059921 1.000035583 1.157782845 0.436988874 0.056466682 3.023645311 13.99317183 0.048601934 0.013254252 3.737045265 -0.572528358 0.157747262 RGS(ph)PVPPVPERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RGSPVPPVPERR 12 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(1)PVPPVPERR;RGS(1)PVPPVPERR;RGS(1)PVPPVPERR;RGS(1)PVPPVPERR 67.646 0.04316 3160790000 462328 463654 465482 443838 488215 391130 515076 432620 633420 TRUE FALSE 433391.7158 497983.4246 476523.4529 455227.6345 449872.5633 504042.8815 437845.1355 486633.5593 527698.11 0.821287224 0.943689991 0.903022853 0.86266679 0.852518807 0.955172801 0.829726556 0.922181736 1 19.00935329 -1.382570395 3.357659098 1.000930722 0.889811111 0.376998845 0.045741664 603237141 970754548.7 5627745.978 0.010160026 0.041440941 1.382570395 -0.111119611 RGS(ph)QNSSEHRPPASSTSEDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGSQNSSEHRPPASSTSEDVK 21 2 O15014 O15014 ZNF609 Zinc finger protein 609 1 RGS(0.905)QNS(0.094)S(0.002)EHRPPASSTSEDVK;RGS(0.998)QNS(0.002)SEHRPPASSTSEDVK 201.08 3.72E-22 370710000 304450 277270 296180 370970 409610 282350 340810 218417 416230 TRUE FALSE 285395.018 297799.3593 303205.5295 380489.7183 377440.8829 363859.8614 289708.7044 245686.8432 346758.5241 0.823036777 0.858809052 0.874399643 1.097275746 1.088483359 1.049317713 0.835476807 0.708524308 1 18.40357182 -2.197423275 4.799924128 1.725343047 0.918167333 0.040908428 0.126299712 0.155792009 0.006407804 0.019433532 0.029700245 0.00634712 2.197423275 -0.807175714 RGS(ph)QVGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGSQVGHK 8 1 Q5JTH9-2;Q5JTH9-3;Q5JTH9 Q5JTH9-2 RRP12 RRP12-like protein 1 RGS(1)QVGHK;RGS(1)QVGHK 97.163 0.0051616 254732000 237041 143274 161600 123987 174404 99812 185648 133857 283380 TRUE FALSE 222205.0269 153882.156 165433.2283 127168.7163 160707.0134 128626.1041 157811.8059 150569.3411 236082.0473 0.941219502 0.651816425 0.700744636 0.538663222 0.680725261 0.544836448 0.668461697 0.637783952 1 17.84892881 -0.812084939 7.522987348 1 0.662728722 0.467404446 0.110247813 7.18E-10 9.54E-11 0.096322535 0.022703439 0.154139896 0.812084939 -0.337271278 RGS(ph)RS(ph)SPEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGSRSSPEPK 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RGS(0.978)RS(0.608)S(0.414)PEPK;RGS(0.971)RS(0.916)S(0.112)PEPK 111.72 0.04507 708450000 2305030 1177110 1480510 1442880 1518230 1029440 1833980 1168330 1877680 TRUE FALSE 2160762.287 1264264.449 1515628.396 1479906.744 1398994.34 1326622.616 1558991.725 1314198.572 1564283.078 1.381311553 0.808206946 0.968896498 0.9460607 0.894335789 0.848070682 0.996617394 0.840128357 1 20.57707018 4.746474549 24.912178 0.912767601 1.381311793 0.831169781 0.066360962 347.0444484 1092430.605 0.014535587 0.159864529 55779.49126 -4.746474549 0.468544191 RGS(ph)RSS(ph)PEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGSRSSPEPK 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RGS(0.996)RS(0.058)S(0.947)PEPK 120.54 0.0026853 1419200000 2288200 1201500 1525400 1482700 1561500 1053500 1918700 1189000 1918400 TRUE FALSE 2144985.647 1290460.31 1561583.208 1520748.592 1438866.089 1357628.348 1631008.747 1337449.267 1598206.647 1.342120339 0.807442713 0.977084666 0.951534393 0.900300403 0.849469842 1.020524318 0.836843765 1 20.60802253 4.747999026 24.91191035 0.919208532 1.342120573 0.777844388 0.07124553 545.3610198 1439404.718 0.015714881 0.202932151 55975.63463 -4.747999026 0.422912042 RGS(ph)S(ph)PGSLEIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGSSPGSLEIPK 12 1 Q6GYQ0-2;A0A1B0GUI1;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5;Q6GYQ0-6;Q6GYQ0-3 Q6GYQ0-2 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 2 RGS(0.989)S(0.975)PGS(0.036)LEIPK 138.91 0.00023147 119700000 557550 313020 413040 412150 440730 288760 511740 321260 463990 TRUE FALSE 522653.9408 336196.3265 422837.5039 422726.4668 406116.8436 372120.3244 435009.3378 361370.0182 386547.0715 1.352109431 0.869742268 1.093883604 1.093596351 1.050627138 0.962677903 1.125372225 0.934866785 1 18.56028458 4.756583729 24.58332636 1.023973682 1.352109778 0.637222579 0.079432764 2070.760867 2824436.766 0.018258624 0.583785565 57093.11372 -4.756583729 0.328136096 RGS(ph)SDPTVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGSSDPTVQR 10 1 H7BXG1;A0A2R8YDG4;H7BZJ9;H7BZI2;Q2KHT3;Q2KHT3-2 H7BXG1;Q2KHT3 CLEC16A Protein CLEC16A 1 RGS(0.944)S(0.053)DPT(0.003)VQR;RGS(0.994)S(0.006)DPTVQR 126.83 0.00022794 1315370000 988160 826770 845210 744080 947210 727370 1131160 915990 1322960 TRUE FALSE 926312.8295 887984.9111 865258.7803 763174.3525 872819.9475 937349.9111 961553.0592 1030353.368 1102149.429 0.84046029 0.805684681 0.785064854 0.692441816 0.791925236 0.850474433 0.872434385 0.934858142 1 20.07188841 1.419923158 1.115257148 0.994130567 0.783577699 0.786798742 0.038943248 0.207404603 0.507449193 0.036498786 0.012615558 26.29802648 -1.419923158 -0.210552868 RGS(ph)SGSVDETLFALPAASEPVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RGSSGSVDETLFALPAASEPVIR 23 1 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 RGS(0.671)S(0.121)GS(0.177)VDET(0.031)LFALPAASEPVIR;RGS(0.683)S(0.124)GS(0.18)VDET(0.013)LFALPAASEPVIR;RGS(0.632)S(0.166)GS(0.166)VDET(0.036)LFALPAASEPVIR;RGS(0.741)S(0.128)GS(0.128)VDET(0.003)LFALPAASEPVIR 184.75 1.99E-17 684940000 642430 470002 509260 497341 517477 444481 633010 502556 425978 TRUE FALSE 602221.4531 504801.4371 521339.8877 510103.6121 476836.4438 572795.4492 538096.0271 565301.2229 354879.5199 1.69697438 1.422458634 1.469061635 1.437399409 1.343657261 1.614056087 1.516278052 1.592938423 1 18.43696979 -1.13267076 3.989688884 0.99983115 1.498496344 0.70594279 0.103461852 16054152.63 25906257.56 33664.6746 0.0234672 0.073676543 1.13267076 0.498665194 RGS(ph)SPGSLEIPK ddPTM_SK-BR-3_Pertuzumab_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(0.981)S(0.019)PGSLEIPK;RGS(0.982)S(0.018)PGSLEIPK 162.14 3.89E-05 2804400000 4418300 3013860 3412200 3699500 3770600 2449940 4990300 3292000 4390400 TRUE FALSE 4141766.49 3237009.33 3493138.995 3794435.433 3474472.286 3157197.907 4242050.843 3703013.447 3657613.877 1.132368432 0.885005755 0.955032191 1.037407326 0.94992867 0.863185129 1.159786403 1.012412346 1 21.80247135 1.736514323 24.99999998 1.068794035 0.960623436 0.174331231 0.086243289 0.348300033 4153.75631 0.036678994 0.020340435 54.51478738 -1.736514323 -0.1081706 RGS(ph)SSSSPEHSASSDSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGSSSSSPEHSASSDSTK 18 1 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 RGS(0.215)S(0.215)S(0.215)S(0.215)S(0.138)PEHSASSDSTK;RGS(0.198)S(0.198)S(0.198)S(0.198)S(0.198)PEHS(0.009)ASSDSTK 129.85 1.24E-05 344729000 113174 116708 117585 115855 142476 103996 171314 121139 181804 TRUE FALSE 106090.6414 125349.1818 120374.1717 118828.0354 131286.5097 134017.957 145627.0561 136263.4708 151459.7379 0.70045441 0.82760728 0.794760201 0.784551968 0.866807981 0.884842129 0.961490216 0.899667943 1 17.20857481 2.171997535 0.565758722 0.991373424 0.765434339 0.806918648 0.038347861 0.35178691 0.229253742 0.034032945 0.025655051 148.592721 -2.171997535 -0.225939084 RGS(ph)WREEEDREVAAAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGSWREEEDREVAAAVR 17 3 Q86UK7-2 Q86UK7-2 ZNF598 Zinc finger protein 598 1 RGS(1)WREEEDREVAAAVR 141.1 3.52E-06 314690000 110440 110710 110110 109490 137220 82746 100740 92829 179070 TRUE FALSE 103527.7575 118907.0836 112721.8612 112299.6988 126443.2947 106633.4269 85634.97222 104418.905 149182.0602 0.693969217 0.797060206 0.755599306 0.752769459 0.847577079 0.714787199 0.574029961 0.699942774 1 17.18671453 2.017815659 24.54568969 0.694097812 0.77141827 0 0.115988815 445.4246322 613684.8788 0.038906364 0.028728238 104.1875101 -2.017815659 0.077320458 RGSLPAGAS(ph)WQNTDLFEMIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGSLPAGASWQNTDLFEMIEK 21 1 J3KPC5;P47736-3 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 RGS(0.415)LPAGAS(0.542)WQNT(0.043)DLFEMIEK 53.625 0.067739 238730000 35166 25228 30170 30495 33629 24327 44192 27817 39703 TRUE FALSE 32965.02283 27095.90737 30885.64665 31277.55333 30987.91399 31349.80998 37565.81986 31290.01368 33076.31281 0.996635357 0.819193709 0.933769336 0.945617896 0.936861196 0.94780244 1.135731787 0.945994611 1 15.0135108 1.952096517 9.747078848 1.042354701 0.916017781 0.326412751 0.064376443 0.498493258 99.0363839 0.025589114 0.016327216 89.55637727 -1.952096517 -0.12633692 RGSMNNELLS(ph)PEFGPVRDPLADGVEGLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGSMNNELLSPEFGPVRDPLADGVEGLGR 29 2 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 RGS(0.443)MNNELLS(0.557)PEFGPVRDPLADGVEGLGR;RGS(0.044)MNNELLS(0.956)PEFGPVRDPLADGVEGLGR 186.56 5.17E-18 367470000 222650 199814 207479 198230 208670 150849 249950 180951 175983 TRUE FALSE 208714.7339 214608.4365 212400.4999 203316.9174 192281.8999 194396.6575 212472.3179 203543.1307 146610.3004 1.423602116 1.463801901 1.448742 1.386784672 1.31151699 1.325941335 1.449231857 1.388327628 1 17.16162694 -3.233581714 0.300301329 2.18E-12 1.434018076 0.863640875 0.050013037 30.93922206 0.758747163 19.47995978 0.055553304 0.000584007 3.233581714 1.434018076 RGSQNS(ph)SEHRPPASSTSEDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGSQNSSEHRPPASSTSEDVK 21 2 O15014 O15014 ZNF609 Zinc finger protein 609 1 RGS(0.166)QNS(0.411)S(0.411)EHRPPAS(0.004)S(0.004)T(0.004)SEDVK 93.767 0.00087247 53528000 41147 33313 35255 45670 45719 31079 38452 27955 42827 TRUE FALSE 38571.68272 35779.52918 36091.26525 46841.96952 42128.41416 40051.00277 32686.47957 31445.24329 35678.89703 1.081078339 1.002820495 1.011557763 1.312876053 1.180765597 1.122540384 0.916129205 0.881340117 1 15.1227834 1.718391835 6.251485506 0.924772063 1.102779462 0.465690732 0.092657592 0.145083281 14.23505087 0.051890659 0.026684386 52.28677251 -1.718391835 0.178007399 RGSQNSSEHRPPASSTSEDVKAS(ph)PSSANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGSQNSSEHRPPASSTSEDVKASPSSANK 29 3 O15014 O15014 ZNF609 Zinc finger protein 609 1 RGSQNSSEHRPPAS(0.005)S(0.005)T(0.005)S(0.026)EDVKAS(0.717)PS(0.114)S(0.125)ANK;RGSQNSSEHRPPASSTSEDVKAS(0.991)PS(0.005)S(0.005)ANK 140.94 5.94E-08 128784000 56263 42896 60620 43607 44602 45114 84430 55937 69757 TRUE FALSE 52741.59926 46072.06447 62057.93503 44726.02945 41099.13884 58137.67944 71770.50531 62920.85758 58114.10605 0.907552449 0.792786255 1.06786354 0.769624322 0.707214507 1.00040564 1.234992847 1.082712303 1 15.82660077 2.000789659 24.97276188 1.128433852 0.866429857 0.523419887 0.11172951 19.69942198 622973.4804 0.042014848 0.03076164 100.181991 -2.000789659 -0.262003996 RGSS(ph)GSVDETLFALPAASEPVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGSSGSVDETLFALPAASEPVIR 23 1 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 RGS(0.253)S(0.359)GS(0.359)VDET(0.03)LFALPAASEPVIR 110.01 0.00067248 33675000 50898 37757 40109 37290 38490 31898 50563 37595 32281 TRUE FALSE 47712.38504 40552.56757 41060.40442 38246.92453 35467.15066 41106.43478 42981.54755 42288.81851 26893.09256 1.774150181 1.507917599 1.526801142 1.422183947 1.318820087 1.528512747 1.598237446 1.572478822 1 14.71494805 -2.01832466 2.684376827 0.412633455 1.52446747 0.670353923 0.116969621 172556651 146446466.4 622840315 0.027513649 0.009586837 2.01832466 1.111834015 RGSS(ph)SSSPEHSASSDSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGSSSSSPEHSASSDSTK 18 1 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 RGS(0.037)S(0.232)S(0.232)S(0.232)S(0.145)PEHS(0.121)ASSDSTK;RGS(0.144)S(0.232)S(0.232)S(0.232)S(0.144)PEHS(0.016)ASSDSTK 171.58 7.91E-12 483150000 495235 451273 485240 430101 585250 463134 799370 574770 836060 TRUE FALSE 464239.1254 484685.7225 496750.1219 441138.1198 539286.8258 596833.2674 679511.8895 646531.2997 696516.1848 0.666515919 0.695871443 0.713192504 0.633349417 0.774263165 0.856883559 0.975586647 0.92823586 1 19.40979735 2.168110248 1.745479797 0.968113095 0.68607198 0.942600265 0.03143391 0.072951694 0.434848804 0.016019132 0.0093434 147.2686305 -2.168110248 -0.282041115 RGSSGSVDET(ph)LFALPAASEPVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGSSGSVDETLFALPAASEPVIR 23 1 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 RGS(0.25)S(0.25)GS(0.25)VDET(0.251)LFALPAASEPVIR 85.945 0.0040698 39987000 51750 37716 41681 37191 37080 39023 44077 35370 33786 TRUE FALSE 48511.05988 40508.53188 42669.693 38145.38402 34167.88637 50288.30661 37468.06304 39786.02236 28146.89833 1.723495758 1.439182797 1.515964299 1.355225132 1.21391302 1.78663759 1.331161345 1.413513556 1 14.78068833 -3.250983643 0.229622795 1.68E-10 1.533183051 0.459636004 0.167468213 59.44761187 1.222613273 28.78275938 0.280019538 0.000561069 3.250983643 1.533183051 RGT(ph)GQSDDS(ph)DIWDDTALIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGTGQSDDSDIWDDTALIK 19 1 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 2 RGT(0.55)GQS(0.55)DDS(0.901)DIWDDTALIK 81.157 0.005433 64829000 58870 45496 50891 54987 55356 38012 64915 46731 61145 TRUE FALSE 55185.43179 48864.57118 52098.15855 56398.05951 51008.56306 48985.44733 55181.59839 52565.46822 50939.50449 1.083352348 0.959266716 1.022745688 1.1071576 1.001355698 0.961639651 1.083277094 1.031919504 1 15.63649731 3.482506357 24.98149299 1.034914988 1.00615786 0 0.051032873 582.3356321 2701458.026 0.013197106 0.019140725 3037.430553 -3.482506357 -0.028757128 RGT(ph)GQSDDSDIWDDTALIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGTGQSDDSDIWDDTALIK 19 1 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 1 RGT(0.69)GQS(0.307)DDS(0.003)DIWDDTALIK;RGT(0.805)GQS(0.195)DDSDIWDDTALIK 197.33 4.65E-16 373610000 248470 206865 202039 210285 257896 159158 265346 193248 288878 TRUE FALSE 232918.7062 222181.4998 206831.4605 215681.2691 237641.8885 205104.3309 225559.8307 217375.4382 240662.3956 0.967823434 0.923208212 0.859425753 0.896198463 0.987449194 0.852249187 0.937245846 0.903238072 1 17.87665121 -1.38240991 2.749088838 1.001755627 0.912043122 0.275690152 0.042465463 7395949.939 8271409.608 103305.3768 0.010161307 0.041456257 1.38240991 -0.089712505 RGT(ph)SPRPPEGGLGYSQLGDDDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RGTSPRPPEGGLGYSQLGDDDLK 23 2 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12;Q9UQ88-8;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;Q9UQ88-5;Q9UQ88-10 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 RGT(0.495)S(0.495)PRPPEGGLGY(0.01)SQLGDDDLK;RGT(0.82)S(0.174)PRPPEGGLGYS(0.006)QLGDDDLK;RGT(0.5)S(0.5)PRPPEGGLGYSQLGDDDLK;RGT(0.5)S(0.5)PRPPEGGLGYSQLGDDDLK 204.82 7.90E-23 1271910000 1166540 664475 879560 745716 749431 666511 1061660 737821 818140 TRUE FALSE 1093528.344 713673.4204 900423.5786 764852.3351 690573.7123 858921.9058 902473.939 829939.576 681587.1486 1.604385215 1.047075817 1.321068891 1.122163668 1.013184761 1.260179139 1.324077106 1.217657313 1 19.37853861 4.750721441 24.54129391 1.185570245 1.604385547 0.562441766 0.120873807 1186.006989 2393378.48 0.028292979 0.473993261 56327.62511 -4.750721441 0.418815301 RGTFS(ph)DQELDAQS(ph)LDDEDDNMHHAVYPAVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGTFSDQELDAQSLDDEDDNMHHAVYPAVNR 31 1 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 2 RGT(0.446)FS(0.554)DQELDAQS(1)LDDEDDNMHHAVYPAVNR 119.99 6.10E-06 147640000 22897 27314 24663 22913 27766 24458 30976 20902 25678 TRUE FALSE 21463.91764 29336.35698 25248.01801 23500.98637 25585.37036 31518.62756 26331.43637 23511.66071 21392.17591 1.003353643 1.371359188 1.180245437 1.098578586 1.196015331 1.473371745 1.23089098 1.09907757 1 14.38479561 1.074582219 3.503007838 1.003857492 1.239375299 0.241820977 0.130511291 0.266999717 6.407942021 0.117828642 0.030706522 11.87359466 -1.074582219 0.235517807 RGTGGVDTAATGGVFDISNLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGTGGVDTAATGGVFDISNLDR 22 1 P12532;P12532-2 P12532 CKMT1A "Creatine kinase U-type, mitochondrial" 0 162.98 2.50E-11 364860000 269170 337620 286740 283750 367090 268760 377810 311920 424820 FALSE TRUE 252323.1302 362617.7361 293541.6082 291031.5054 338260.2322 346346.649 321160.8979 350863.8986 353914.7976 0.7129488 1.024590491 0.82941321 0.822320817 0.955767418 0.978615903 0.907452585 0.991379567 1 18.43304256 2.706915857 20.67567617 0.957566923 0.873879569 0.324441351 0.081069013 129.2987222 84478.34005 0.025183259 0.023749718 509.2321998 -2.706915857 -0.083687355 RGTGQS(ph)DDS(ph)DIWDDTALIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RGTGQSDDSDIWDDTALIK 19 1 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 2 RGT(0.003)GQS(0.997)DDS(1)DIWDDTALIK;RGT(0.262)GQS(0.742)DDS(0.996)DIWDDTALIK;RGT(0.383)GQS(0.663)DDS(0.954)DIWDDTALIK 252.28 2.65E-30 410642000 315206 223006 250568 266908 312912 202841 312759 234817 327372 TRUE FALSE 295477.8191 239517.5963 256511.5913 273757.3112 288337.1537 261397.9039 265863.6915 264134.4193 272731.4983 1.083401884 0.878217579 0.940527929 1.003761256 1.05721985 0.958444131 0.974818432 0.968477866 1 18.0571218 3.244513787 24.95818195 0.99182258 0.944439332 0 0.057875014 285.4347614 1196653.672 0.015514671 0.02046345 1755.956637 -3.244513787 -0.047383248 RGTGQS(ph)DDSDIWDDTALIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RGTGQSDDSDIWDDTALIK 19 1 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 1 RGT(0.044)GQS(0.955)DDS(0.001)DIWDDTALIK;RGT(0.094)GQS(0.905)DDS(0.001)DIWDDTALIK 264.74 1.43E-31 382187000 694110 522780 568370 574610 699270 459300 721860 509020 787720 TRUE FALSE 650666.8941 561487.1752 581852.0048 589355.4654 644352.1549 591892.4539 613623.7944 572572.2675 656244.4431 0.991500806 0.85560675 0.886639134 0.898073076 0.981878265 0.901938996 0.9350537 0.872498462 1 19.32387378 2.955806958 24.95388584 0.932230125 0.895378123 0.052132316 0.04994307 926.4292648 523114.4102 0.013962297 0.014810016 903.2478954 -2.955806958 -0.036852001 RGVMLAVDAVIAELKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RGVMLAVDAVIAELKK 16 2 P10809;E7EXB4;E7ESH4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;;; 188.04 6.99E-10 453200000 1524710 1180535 1131436 1060323 1858330 961022 1318016 1368394 2496050 FALSE TRUE 1429281.123 1267943.04 1158274.196 1087532.683 1712384.258 1238453.451 1120391.737 1539241.003 2079443.13 0.687338404 0.609751246 0.557011721 0.52299227 0.82348213 0.595569762 0.538794123 0.740217889 1 20.9877658 0.937770332 4.82208871 0.999890334 0.611794595 0.661261452 0.086375164 0.182484229 11.69720075 0.079764258 0.020196731 8.665035206 -0.937770332 -0.388095739 RGVTIKPTVDDD ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 169.57 0.00017273 3088940000 3369670 2965840 3306410 3189280 3480010 2473980 3951350 2993920 3889790 FALSE TRUE 3158768.37 3185433.88 3384839.607 3271122.324 3206704.052 3188177.864 3358881.75 3367717.502 3240558.92 0.974760357 0.982989033 1.044523396 1.009431522 0.989552769 0.983835796 1.036513093 1.039239707 1 21.62781123 1.70083294 9.560425341 1.028103815 1.001438578 0.243095833 0.022142336 0.177006202 31.19940813 0.011009621 0.005920642 50.21493902 -1.70083294 -0.026665237 RGYFDEEMNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RGYFDEEMNR 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 Q15149-3;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 PLEC;EPPK1 Plectin;Epiplakin 0 72.321 0.050726 175250000 83598 159730 82563 111390 167590 93541 92823 126560 120260 FALSE TRUE 78365.75041 171556.5754 84521.43335 114248.456 154428.1574 120544.7682 78905.05288 142361.2946 100187.8291 0.782188327 1.712349464 0.843629751 1.140342665 1.541386402 1.203187745 0.787571241 1.420944 1 16.61234773 1.969344938 24.2540824 1.03327124 1.233856037 0.029842666 0.31628425 1231.189223 974106.4528 0.121878618 0.078798007 93.18477 -1.969344938 0.200584797 RHEDGEFWMSFSDFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RHEDGEFWMSFSDFLR 16 1 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;; 197.88 2.74E-11 396165000 210068 437703 260301 285526 519121 174605 262001 376880 497355 FALSE TRUE 196920.2189 470110.9855 266475.4626 292853.0806 478351.3307 225010.629 222716.3823 423934.2976 414343.2375 0.475258677 1.134593118 0.643127336 0.706788609 1.154480844 0.543053702 0.537516634 1.023147621 1 18.66046685 RHEGLPGLAVQWGAIGDVGILVETMSTNDTIVSGTLPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 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 11177424000 1942498 2596177 1953945.4 2045122 2875592 1988583.5 2466383 2337528 1972349 FALSE TRUE 1820920.518 2788400.646 2000293.908 2097603.293 2649754.604 2562655.274 2096571.766 2629373.516 1643151.21 1.108188039 1.696983594 1.217352302 1.276573501 1.612605455 1.55959796 1.275945727 1.600201795 1 20.64803382 -1.422813127 5.872403329 0.999827754 1.422327584 0.310395426 0.19592924 0.000400132 3.93E-05 0.171789033 0.040474776 0.037773469 1.422813127 0.422499829 RHEHPPNPPVS(ph)PGK ddPTM_SK-BR-3_Pertuzumab_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 136.04 1.38E-05 761208000 1199830 785225 923680 854760 956760 681118 1097850 839620 958690 TRUE FALSE 1124734.782 843363.876 945590.1258 876694.5887 881619.929 877745.7096 933237.5844 944448.4052 798678.4456 1.408244818 1.055949213 1.183943464 1.097681543 1.103848406 1.098997618 1.168477238 1.182513952 1 19.60725525 7.999999976 0.015749668 2.97E-11 2.527835488 0.284482892 0.092564555 8154.534708 9.911921594 628.5878048 1002.615743 99999994.44 -7.999999976 2.527835488 RHES(ph)EEGDSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RHESEEGDSHR 11 1 Q6UN15;Q6UN15-5;Q6UN15-3;H0Y8P7 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 RHES(1)EEGDSHR;RHES(1)EEGDSHR;RHES(1)EEGDSHR;RHES(1)EEGDSHR 168.45 8.49E-06 604460000 449078.5 482390 474444.1 478298 500167 417280 511920 401926.6 379288 TRUE FALSE 420971.4783 518106.6575 485698.1381 490571.9364 460885.9014 537741.962 435162.3484 452108.0208 315982.3825 1.332262498 1.639669444 1.53710512 1.552529393 1.458581006 1.701809948 1.377172819 1.430801354 1 18.2694846 0.625603375 1.007390087 1.000351903 1.543519022 0.691590596 0.107867765 0.609713127 1.002223896 0.091625346 0.02932846 4.222827828 -0.625603375 0.543167119 RHES(ph)EEGDSHRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RHESEEGDSHRR 12 2 Q6UN15;Q6UN15-5;Q6UN15-3;H0Y8P7 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 RHES(1)EEGDSHRR;RHES(1)EEGDSHRR;RHES(1)EEGDSHRR 79.652 0.010665 84267700 19667.8 25045.7 21734.4 25019.6 22283 19920.2 27119.1 22124.1 24230.4 TRUE FALSE 18436.82751 26900.10969 22249.95023 25661.64529 20532.98307 25670.83836 23052.84272 24886.34259 20186.18971 0.913338662 1.332599667 1.102236259 1.271247604 1.017179734 1.271703018 1.142010605 1.232840023 1 14.301081 -0.922040205 5.534335691 0.999999814 1.172360635 0.129518591 0.127363824 2.50E-07 4.85E-08 0.104676471 0.024672454 0.119662975 0.922040205 0.172360822 RHGAPAAPS(ph)PPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RHGAPAAPSPPPR 13 1 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 RHGAPAAPS(1)PPPR;RHGAPAAPS(1)PPPR;RHGAPAAPS(1)PPPR 126.42 0.0001156 1065650000 290499 304666 322262 289536 359090 278057 351107 295028 393356 TRUE FALSE 272317.1861 327223.7876 329906.2068 296965.9839 330888.5199 358327.542 298461.7649 331862.8952 327702.3424 0.83098944 0.998539666 1.006725202 0.906206473 1.009722779 1.09345432 0.910770923 1.012696134 1 18.32202646 4.740460784 24.15788955 0.990136458 0.830989352 0.476568165 0.0530758 92.51921842 1176098.06 0.011877986 0.077045718 55012.42428 -4.740460784 -0.159147106 RHNS(ph)ISEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RHNSISEAK 9 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 RHNS(0.989)IS(0.011)EAK;RHNS(0.998)IS(0.002)EAK 126.34 0.00029164 664860000 635280 515330 507830 421970 593000 338280 738760 434530 1364510 TRUE FALSE 595518.9588 553485.5694 519875.9674 432798.4646 546428.172 435935.9445 627989.7963 488782.027 1136764.466 0.523871898 0.486895558 0.457329537 0.380728355 0.480687239 0.383488363 0.55243616 0.429976518 1 20.11650193 -1.688808633 0.68560073 1.328845291 0.462518471 0.904333942 0.054957681 36.12764573 5.221708311 19.98751792 0.018484177 0.020473466 1.688808633 -0.86632682 RHNS(ph)SDGFDSAIGRPNGGNFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RHNSSDGFDSAIGRPNGGNFGR 22 2 D4PHA4;Q86WP2-3;Q86WP2;Q86WP2-2 D4PHA4 GPBP1 Vasculin 1 RHNS(0.793)S(0.207)DGFDSAIGRPNGGNFGR;RHNS(0.971)S(0.029)DGFDSAIGRPNGGNFGR 166.79 5.89E-12 524410000 130394 149791 153568 168839 178153 145719 178179 156743 147225 TRUE FALSE 122232.8723 160881.6815 157210.7055 173171.6946 164161.582 187785.7097 151462.7131 176312.7086 122652.1964 0.996581194 1.311690179 1.281760214 1.411892324 1.338431653 1.531042372 1.234896052 1.437501437 1 16.90421354 4.747313778 3.996753086 1.332529015 0.963416175 0.336025023 0.141225413 0.255188239 8.448778813 0.029238135 0.276330181 55887.38356 -4.747313778 -0.36911284 RHNS(ph)WSSSSR ddPTM_SK-BR-3_Pertuzumab_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(1)WSSSSR;RHNS(1)WSSSSR 179.83 1.26E-06 1778030000 254269 381695 343076 332824 469178 323635 404626 323816 435821 TRUE FALSE 238354.7572 409956.095 351213.9247 341364.8273 432330.6525 417063.1707 343956.0877 364245.1404 363079.6596 0.656480612 1.129107853 0.967319197 0.94019265 1.190732229 1.148682279 0.947329542 1.003209987 1 18.46992658 4.746799735 24.92695333 1.040063726 0.656480414 0.654678039 0.087722279 651.8695916 1972145.713 0.020785444 0.237208416 55821.27286 -4.746799735 -0.383583312 RHPKGEEGS(ph)DDDETENGPKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RHPKGEEGSDDDETENGPKPK 21 3 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 RHPKGEEGS(1)DDDETENGPKPK;RHPKGEEGS(1)DDDETENGPKPK 224.93 2.14E-25 508250000 687070 310260 428020 454450 545930 316090 698650 328790 1083690 TRUE FALSE 644067.5152 333231.9732 438172.8365 466111.9564 503054.86 407340.0517 593893.9184 369840.1553 902815.1381 0.713399109 0.369103219 0.485340595 0.516287263 0.557206939 0.45118877 0.657824502 0.409652142 1 19.78407108 -4.999999993 0.350403716 6.654411035 0.496211358 0.654065899 0.108004055 247.6612991 2.027596909 1052.102259 0.075456458 1.00E-05 4.999999993 -6.158199677 RHPTGTT(ph)PPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RHPTGTTPPVK 11 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 RHPT(0.222)GT(0.162)T(0.615)PPVK;RHPT(0.001)GT(0.042)T(0.957)PPVK 66.538 0.036588 525120000 610510 553260 603020 580690 708790 531670 836510 651090 748540 TRUE FALSE 572299.2689 594223.9461 617323.9192 595591.4885 653124.4925 685154.4981 711083.0913 732380.0197 623603.8382 0.917728907 0.952886929 0.989929634 0.955079895 1.047338795 1.098701541 1.140280171 1.174431546 1 19.25027028 2.49267548 1.978434072 1.120319434 0.957699608 0.678561788 0.048073614 0.167195803 1.323915596 0.018067808 0.014860067 310.9392026 -2.49267548 -0.162619827 RHQDGLPYIDDS(ph)PSSS(ph)PHLSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHQDGLPYIDDSPSSSPHLSSK 22 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 2 RHQDGLPYIDDS(0.98)PS(0.05)S(0.046)S(0.924)PHLSSK 99.614 0.0010002 36441000 33650 66584 57391 67568 78693 48812 78083 61352 79265 TRUE FALSE 31543.90657 71513.94864 58752.34162 69301.90927 72512.76921 62903.232 66375.17904 69011.93225 66035.15943 0.477683507 1.082967759 0.889713028 1.049469856 1.098093347 0.95257182 1.005149069 1.045078604 1 16.01094675 4.743462999 24.96977056 1.008632317 0.477683287 0.883327682 0.061369839 159.4205238 811964.7603 0.014073842 0.11648025 55394.03473 -4.743462999 -0.53094903 RHQYSDYDYHS(ph)S(ph)SEKLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHQYSDYDYHSSSEKLK 17 2 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 RHQYSDY(0.002)DY(0.189)HS(0.805)S(0.822)S(0.182)EKLK 49.973 0.08763 125940000 53772 41000 39236 43790 50955 34151 49913 32906 73951 TRUE FALSE 50406.50651 44035.68266 40166.69645 44913.72554 46953.19984 44009.8393 42429.00902 37014.38654 61608.10036 0.818179853 0.714770986 0.651971027 0.729023055 0.762127051 0.714351507 0.688692051 0.600803893 1 15.91083243 -1.897205732 2.88599553 1.148360469 0.706233106 0.708707043 0.058387379 14253079.75 7800384.645 14285237.42 0.013843272 0.012670515 1.897205732 -0.442127363 RHQYSDYDYHSS(ph)SEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHQYSDYDYHSSSEK 15 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 RHQYSDYDYHS(0.041)S(0.918)S(0.041)EK 108.71 0.00049706 180050000 214890 187920 204330 201260 239720 184290 256240 190740 336720 TRUE FALSE 201440.4185 201833.7923 209176.8041 206424.6723 220893.3582 237491.5313 217819.1908 214554.3089 280519.2567 0.718098361 0.719500667 0.745677165 0.735866317 0.787444544 0.846614005 0.776485698 0.764846989 1 18.09774028 -5 0.15166203 1.869243237 0.686237584 0.86880718 0.030336828 45.0094227 0.403510775 11.75752279 0.148339391 1.00E-05 5 -1.183005653 RHS(ph)AQLSSDHIIPLMHLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RHSAQLSSDHIIPLMHLAK 19 1 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2;H3BNX5 H3BSS6 ZNF106 Zinc finger protein 106 1 RHS(0.957)AQLS(0.022)S(0.022)DHIIPLMHLAK;RHS(0.997)AQLS(0.001)S(0.001)DHIIPLMHLAK 165.96 7.86E-12 960900000 1021120 1389810 1248950 1201370 1602350 1211650 1865390 1508310 2502400 TRUE FALSE 957209.922 1492712.978 1278575.684 1232199.188 1476507.895 1561433.686 1585692.087 1696625.824 2084733.274 0.459152225 0.716021084 0.613304205 0.591058436 0.708247867 0.748984873 0.760621086 0.813833522 1 20.99143138 1.007340987 0.304287724 1.054594326 0.563440431 0.802685477 0.063750498 0.859942705 0.247538978 0.155346638 0.091270819 10.17046915 -1.007340987 -0.491153895 RHS(ph)ASNLHALAHPAPSPGSCSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RHSASNLHALAHPAPSPGSCSPK 23 1 P47974 P47974 ZFP36L2 "Zinc finger protein 36, C3H1 type-like 2" 1 RHS(0.5)AS(0.5)NLHALAHPAPSPGSCSPK;RHS(0.5)AS(0.5)NLHALAHPAPSPGSCSPK 112.9 0.00030884 1033850000 727350 755560 787030 845020 1021420 757840 1132570 851740 1124520 TRUE FALSE 681826.4619 811502.4486 805698.7233 866704.6438 941201.7934 976616.1055 962751.6428 958081.6139 936830.3473 0.727801425 0.86622135 0.860026285 0.925145782 1.004666209 1.042468477 1.027669146 1.022684221 1 19.83742829 3.31851272 0.755861752 1.036596901 0.781204589 0.874331416 0.035422401 0.238772313 0.291818548 0.018618478 0.037111758 2082.15339 -3.31851272 -0.255392312 RHS(ph)DENDGGQPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 RHSDENDGGQPHK 13 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK 172.6 1.09E-05 13581258000 1775814 1739233 1605509 1830128 1450683 993570 1553823 1114632 1230693 TRUE FALSE 1664668.972 1868007.621 1643592.432 1877092.183 1336752.209 1280397.53 1320841.666 1253796.259 1025282.388 1.623619982 1.821944513 1.603063167 1.83080506 1.303789302 1.24882427 1.288271097 1.222878959 1 19.96758989 2.648622356 4.924189209 1.230174544 1.71676714 0.845553445 0.107845603 0.078697485 3.202110448 0.031875273 0.030040836 445.2688931 -2.648622356 0.486592596 RHS(ph)DENDGGQPHKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RHSDENDGGQPHKR 14 2 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RHS(1)DENDGGQPHKR;RHS(1)DENDGGQPHKR;RHS(1)DENDGGQPHKR;RHS(1)DENDGGQPHKR;RHS(1)DENDGGQPHKR 211.09 2.05E-09 7141959000 2508136 2506507 2224759 2703685 2403412 1301742 2226936 1522781 1989947 TRUE FALSE 2351156.245 2692091.386 2277531.334 2773066.134 2214657.716 1677533.783 1893027.621 1712903.56 1657811.99 1.41822852 1.623882203 1.373817627 1.672726552 1.335891965 1.011896279 1.141883176 1.033231494 1 20.66084897 2.413911059 4.028669404 1.067623117 1.514765095 0.845136048 0.095753078 0.076238845 2.51105808 0.031193639 0.026045569 259.3648142 -2.413911059 0.447141977 RHS(ph)EVETDSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RHSEVETDSKK 11 2 Q9NX58 Q9NX58 LYAR Cell growth-regulating nucleolar protein 1 RHS(1)EVETDSKK;RHS(1)EVETDSKK 95.981 0.0038366 172788000 256611 157828 179559 215756 277518 140756 237363 154221 276067 TRUE FALSE 240550.1756 169513.7493 183818.2243 221292.6642 255722.8557 181389.9722 201772.6217 173475.8313 229989.6342 1.045917467 0.737049519 0.799245692 0.962185383 1.111888614 0.788687598 0.877311807 0.754276739 1 17.81120931 4.771885368 23.0386904 0.865122276 1.045918471 0.154552614 0.119036322 9592.901387 6631602.445 0.028638414 4.008319044 59140.55124 -4.771885368 0.180796195 RHS(ph)GSYLVTSV ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHSGSYLVTSV 11 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 RHS(0.737)GS(0.263)YLVTSV 63.611 0.077903 97366000 73174 83660 79679 85175 97206 67824 100620 78407 103550 TRUE FALSE 68594.16996 89854.27345 81569.02351 87360.7347 89571.83287 87403.68777 85532.96511 88196.28655 86266.83604 0.795139513 1.04158536 0.945543238 1.012680408 1.038311325 1.013178317 0.991493012 1.022366075 1 16.39651842 4.744728118 24.9304023 1.004846042 0.795139416 0.858625674 0.027133562 242.1749616 978896.6276 0.006377008 0.05938432 55555.63523 -4.744728118 -0.209706625 RHS(ph)HS(ph)HS(ph)PMSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHSHSHSPMSTR 12 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 3 RHS(1)HS(0.999)HS(0.977)PMS(0.018)T(0.007)R 51.786 0.072064 326420000 146460 139370 128520 140380 193770 98125 138110 115660 174250 TRUE FALSE 137293.33 149689.0998 131568.5551 143982.3885 178552.0858 126452.0946 117401.6877 130100.4056 145166.5493 0.945764232 1.031154219 0.906328322 0.991842743 1.22998092 0.871082871 0.808737882 0.89621477 1 17.14734953 2.080408901 24.99999989 0.870201606 1.009190759 0.277893895 0.097432346 34.1619112 10618.81558 0.035234172 0.026022158 120.3396934 -2.080408901 0.138989153 RHS(ph)HSHS(ph)PMSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHSHSHSPMSTR 12 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 2 RHS(0.999)HS(0.002)HS(1)PMSTR 108.77 0.00070062 252840000 87897 89139 70964 86751 101540 82052 94695 73865 97917 TRUE FALSE 82395.68367 95738.94431 72647.29959 88977.17753 93565.45799 105739.0804 80496.36386 83087.20785 81574.02013 1.010072613 1.173645042 0.890569074 1.090753862 1.147000698 1.29623476 0.986789222 1.018549873 1 16.31582213 1.593063828 24.99999996 1.001984655 1.0906528 0.161555197 0.105074615 1.997809128 3365.054678 0.05748832 0.026787786 39.17994553 -1.593063828 0.088668144 RHS(ph)HTIGGLPESDDQSELPSPPALPMSLSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHSHTIGGLPESDDQSELPSPPALPMSLSAK 31 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6;H7BZD9 Q8NEY1-5 NAV1 Neuron navigator 1 1 RHS(0.409)HT(0.409)IGGLPES(0.089)DDQS(0.089)ELPS(0.004)PPALPMSLSAK 75.954 0.0014074 126330000 51075 42778 51363 43432 61244 49263 70742 48715 88771 TRUE FALSE 47878.30692 45945.32763 52581.35462 44546.53865 56434.14329 63484.42838 60134.89384 54797.17498 73954.54662 0.647401804 0.621264408 0.710995564 0.602350237 0.763092276 0.858424955 0.813133155 0.740957487 1 16.17435122 1.256431238 0.18844235 1.106578509 0.524519126 0.7644323 0.058087024 1.60769548 0.289163619 0.390573778 0.315540798 18.04808959 -1.256431238 -0.582059383 RHS(ph)LAMPGETVLNGNQEWVVQADLPLTAAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHSLAMPGETVLNGNQEWVVQADLPLTAAIR 31 1 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-2;Q674X7;Q674X7-5 A0A1B0GWK2 KAZN Kazrin 1 RHS(0.798)LAMPGET(0.202)VLNGNQEWVVQADLPLTAAIR 63.403 0.0056586 17254000 51669 27988 37408 37891 41409 24921 45868 31440 45561 TRUE FALSE 48435.12952 30060.26064 38295.33543 38863.34721 38156.90418 32115.28814 38990.51922 35365.35321 37956.57476 1.276066922 0.791964523 1.008924953 1.023889733 1.005277858 0.846106066 1.027240194 0.931731944 1 15.21206219 RHS(ph)LENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RHSLENK 7 1 O14578-4 O14578-4 CIT Citron Rho-interacting kinase 1 RHS(1)LENK;RHS(1)LENK 119.6 0.0029062 507770000 580810 389900 483490 480440 505510 414260 644890 401360 508230 TRUE FALSE 544458.1389 418768.6017 494958.6111 492768.9038 465809.2837 533850.1371 548194.7314 451470.6795 423403.1297 1.285909576 0.989054101 1.169000833 1.163829148 1.100155504 1.260855434 1.294734717 1.066290369 1 18.69167241 3.656288779 7.000737625 1.175581966 1.10528184 0 0.113633627 0.633970403 52.47797796 0.028750663 0.044879141 4531.988288 -3.656288779 -0.070300125 RHS(ph)LSSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RHSLSSTK 8 1 P42858;A0A3B3IU44 P42858 HTT Huntingtin 1 RHS(1)LSSTK;RHS(0.985)LS(0.007)S(0.007)T(0.002)K 87.667 0.0092865 283140000 126279 128766 130476 124968 144469 122654 201013 155769 219500 TRUE FALSE 118375.4228 138299.9686 133570.9523 128174.8905 133122.9875 158062.2187 170872.9668 175217.1025 182864.032 0.647341205 0.75629946 0.730438626 0.700930025 0.727988911 0.864370193 0.934426333 0.95818243 1 17.48041181 1.990199413 1.680227765 0.972546143 0.717002151 0.931986114 0.031426688 0.089356363 0.470441818 0.019580681 0.00957424 97.76860371 -1.990199413 -0.255543992 RHS(ph)PESPSIAVVESELVAEYITTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RHSPESPSIAVVESELVAEYITTER 25 1 Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-7 EMSY Protein EMSY 1 RHS(0.333)PES(0.333)PS(0.333)IAVVESELVAEYITTER;RHS(0.448)PES(0.448)PS(0.102)IAVVES(0.002)ELVAEYITTER;RHS(0.333)PES(0.333)PS(0.333)IAVVES(0.001)ELVAEYITTER;RHS(0.333)PES(0.333)PS(0.333)IAVVESELVAEYITTER 185.45 8.04E-18 105170000 45613.9 55636 54092.3 52735.8 57155.5 42523.9 53785.1 47856.6 50255.6 TRUE FALSE 42759.00742 59755.34733 55375.3949 54089.08991 52666.73758 54799.85961 45720.52357 53831.60186 41867.6157 1.021290721 1.427245052 1.322630725 1.291907576 1.257934963 1.308884175 1.092025968 1.285757523 1 15.35354714 0.849164954 0.54232405 1.000015736 1.305460962 0.273268617 0.119380228 1.192444431 0.806776559 0.129113839 0.05507013 7.065858797 -0.849164954 0.305445226 RHS(ph)PPIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RHSPPIEK 8 1 Q8IZD4;Q8IZD4-2;F5GZK9 Q8IZD4 DCP1B mRNA-decapping enzyme 1B 1 RHS(1)PPIEK;RHS(1)PPIEK;RHS(1)PPIEK;RHS(1)PPIEK 164.9 0.00020053 2052890000 2882960 2675340 2711930 2991520 3120790 2439560 3610530 2664510 3075110 TRUE FALSE 2702520.68 2873424.957 2776258.26 3068287.468 2875695.742 3143821.369 3069164.545 2997179.939 2561854.275 1.054908043 1.121619206 1.083690937 1.197682279 1.122505589 1.227166354 1.19802464 1.169926006 1 21.28875698 3.247719606 24.99917547 1.168374152 1.093778132 0.155635587 0.065011619 262.9023618 717579.4251 0.016077173 0.021462928 1768.96649 -3.247719606 -0.07459602 RHS(ph)PS(ph)PRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHSPSPRPR 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RHS(1)PS(1)PRPR 67.385 0.032742 20189000 21235 21972 21896 27295 25077 21002 23838 19363 27849 TRUE FALSE 19905.93926 23598.82974 22415.38346 27995.43591 23107.55358 27064.93646 20263.7132 21780.51317 23200.82199 0.857984224 1.017154899 0.96614609 1.206657071 0.995979952 1.166550757 0.873404969 0.938781961 1 14.5018883 -0.459831158 5.675486829 0.999999999 1.004273842 0 0.111453879 0 2.85E-18 0.100777813 0.023753558 0.346871678 0.459831158 0.004273843 RHS(ph)SDINHLVTQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RHSSDINHLVTQGR 14 1 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 RHS(0.5)S(0.5)DINHLVTQGR;RHS(0.957)S(0.043)DINHLVTQGR;RHS(0.824)S(0.176)DINHLVTQGR;RHS(0.922)S(0.078)DINHLVTQGR;RHS(0.795)S(0.205)DINHLVTQGR;RHS(0.744)S(0.256)DINHLVTQGR 197.84 1.08E-08 15906880000 2414600 5105310 4533330 4771220 5155980 5039940 6044690 5089370 5377500 TRUE FALSE 2263474.496 5483312.464 4640862.728 4893657.583 4751050.129 6494888.861 5138344.851 5724789.048 4479960.51 0.505244296 1.223964464 1.03591599 1.092343911 1.060511609 1.449764757 1.146962086 1.277865962 1 22.09505458 4.741672934 24.97417648 1.165075628 0.505244051 0.707772606 0.132380464 156.3013635 1254147.923 0.029953271 0.212975345 55166.18282 -4.741672934 -0.659831577 RHS(ph)SDINHLVTQGRES(ph)PEGSYTDDANQEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RHSSDINHLVTQGRESPEGSYTDDANQEVR 30 2 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 2 RHS(0.777)S(0.223)DINHLVT(0.037)QGRES(0.946)PEGS(0.006)Y(0.009)T(0.002)DDANQEVR;RHS(0.922)S(0.078)DINHLVT(0.014)QGRES(0.984)PEGS(0.002)YTDDANQEVR;RHS(0.84)S(0.16)DINHLVT(0.065)QGRES(0.927)PEGS(0.006)Y(0.001)T(0.002)DDANQEVR;RHS(0.628)S(0.372)DINHLVT(0.322)QGRES(0.676)PEGS(0.002)YTDDANQEVR;RHS(0.947)S(0.053)DINHLVTQGRES(1)PEGSYTDDANQEVR 285.81 3.11E-72 4564200000 887184 1100003 1026581 1082356 1263806 990602 1272411 966134 1452711 TRUE FALSE 831656.7371 1181448.367 1050931.986 1110131.087 1164551.775 1276572.716 1081624.783 1086757.957 1210244.149 0.687180961 0.976206634 0.868363616 0.917278624 0.962245325 1.054805939 0.893724447 0.897965883 1 20.20686669 4.743564529 24.90540703 0.940156457 0.687180851 0.678608511 0.055903562 305.9622206 1522779.247 0.013009418 0.108502451 55406.98634 -4.743564529 -0.252975607 RHS(ph)VADPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHSVADPR 8 1 A0A0D9SGD0;A0A0D9SF89;Q9H2X9 A0A0D9SGD0 SLC12A5 Solute carrier family 12 member 5 1 RHS(1)VADPR 73.499 0.026587 316340000 533450 626140 552550 496450 734170 365600 670430 589880 831690 TRUE FALSE 500062.3167 672500.0571 565656.7469 509189.7475 676511.2497 471142.785 569905.2455 663527.8165 692875.5661 0.721720236 0.970592831 0.816390092 0.734893497 0.976382027 0.679981815 0.822521782 0.95764355 1 19.40223676 1.163551182 4.607206211 0.993229699 0.827868129 0.322927266 0.096972124 0.252343685 9.298120509 0.08547718 0.02218236 14.57307439 -1.163551182 -0.16536157 RHS(ph)VSEMTSCPEPQGFSDPPGQGPTGTFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RHSVSEMTSCPEPQGFSDPPGQGPTGTFR 29 1 P85299;P85299-5;P85299-2;P85299-4;P85299-3 P85299 PRR5 Proline-rich protein 5 1 RHS(0.433)VS(0.433)EMT(0.055)S(0.08)CPEPQGFSDPPGQGPTGTFR;RHS(0.449)VS(0.449)EMT(0.042)S(0.059)CPEPQGFSDPPGQGPTGTFR 189.78 1.97E-18 419180000 116529 123074 125842 118149 139904 114762 153610 117303 162533 TRUE FALSE 109235.6579 132186.527 128827.0317 121180.9034 128916.5042 147891.9264 130577.6065 131948.5378 135405.1923 0.806731677 0.976229381 0.951418697 0.894950196 0.952079473 1.092217543 0.964347115 0.974471773 1 17.04692354 2.464520814 24.83589696 1.005898941 0.925898178 0.397166581 0.05631546 247.2766055 487386.9218 0.018593087 0.015565063 291.4209798 -2.464520814 -0.080000762 RHS(ph)VTDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RHSVTDKR 8 2 Q17R89-3;Q17R89 Q17R89-3 ARHGAP44 Rho GTPase-activating protein 44 1 RHS(0.988)VT(0.012)DKR;RHS(0.972)VT(0.028)DKR 77.744 0.016916 64876000 91065 84460 90290 83927 110531 75260 117947 81073 129440 TRUE FALSE 85365.40421 90713.50628 92431.72144 86080.70891 101850.3411 96986.34026 100261.9423 91195.14251 107835.6278 0.791625235 0.841220181 0.857153831 0.798258522 0.944496204 0.89939051 0.92976639 0.845686573 1 16.71847438 2.735861853 24.99920707 0.918417822 0.831105296 0.577010172 0.042862601 180.6030735 1672953.762 0.012256609 0.012043115 544.3294761 -2.735861853 -0.087312526 RHS(ph)VTLPSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RHSVTLPSSK 10 1 Q07352;G3V2D5;G3V515;G3V2P5 Q07352 ZFP36L1 "Zinc finger protein 36, C3H1 type-like 1" 1 RHS(0.993)VT(0.007)LPSSK;RHS(0.997)VT(0.003)LPSSK;RHS(0.961)VT(0.039)LPSSK;RHS(0.996)VT(0.004)LPSSK;RHS(0.997)VT(0.003)LPSSK;RHS(0.997)VT(0.003)LPSSK 134.88 9.73E-05 3395410000 4517370 4238090 3843240 3842990 5737820 3094160 5159200 4376370 8154760 TRUE FALSE 4234635.875 4551882.593 3934403.468 3941607.63 5287194.762 3987393.763 4385625.856 4922769.428 6793677.874 0.623320086 0.670017431 0.579127174 0.580187595 0.778252202 0.586927116 0.645545158 0.724610369 1 22.69576138 0.782550844 2.119257547 0.999855087 0.634984323 0.792906027 0.058125885 0.343098367 2.532125641 0.051617924 0.014152462 6.061091549 -0.782550844 -0.364870764 RHS(ph)VVAGGGGGEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RHSVVAGGGGGEGR 14 1 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 RHS(1)VVAGGGGGEGR;RHS(1)VVAGGGGGEGR;RHS(1)VVAGGGGGEGR;RHS(1)VVAGGGGGEGR;RHS(1)VVAGGGGGEGR;RHS(1)VVAGGGGGEGR 192.25 2.42E-07 3175215000 893750 946730 860312 732115 1007591 661448 1064376 958395 1790535 TRUE FALSE 837811.7829 1016826.874 880719.0069 750902.3104 928458.8673 852397.2999 904782.7 1078052.725 1491683.141 0.561655327 0.681664119 0.590419629 0.503392637 0.622423651 0.57143322 0.606551536 0.722708929 1 20.50850968 0.854225 2.157525281 0.999699837 0.596164548 0.890972249 0.045440355 0.171273637 1.533878567 0.044008632 0.012065995 7.148665897 -0.854225 -0.403535289 RHS(ph)WGPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RHSWGPGK 8 1 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36;H0YLH1 Q12802-2 AKAP13 A-kinase anchor protein 13 1 RHS(1)WGPGK;RHS(1)WGPGK 138.99 0.0004175 1029420000 1631400 1509960 1540960 1591660 1882710 1298570 2047600 1587260 2288600 TRUE FALSE 1529293.586 1621759.01 1577512.299 1632504.69 1734849.551 1673446.078 1740581.389 1785432.905 1906617.875 0.802097581 0.850594674 0.827387763 0.856230665 0.909909413 0.87770397 0.912915698 0.936439823 1 20.8625843 1.629114207 0.282406914 1.019387338 0.797419018 0.910256041 0.017156875 0.43523129 0.131813452 0.034510821 0.034940002 42.57103476 -1.629114207 -0.22196832 RHSHTIGGLPES(ph)DDQSELPSPPALPMSLSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHSHTIGGLPESDDQSELPSPPALPMSLSAK 31 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6;H7BZD9 Q8NEY1-5 NAV1 Neuron navigator 1 1 RHS(0.092)HT(0.092)IGGLPES(0.406)DDQS(0.406)ELPS(0.005)PPALPMSLSAK 91.086 0.00024648 128180000 25478 22453 21523 19930 23489 19988 30710 25933 34850 TRUE FALSE 23883.37746 24115.44348 22033.53572 20441.43754 21644.26869 25758.21112 26105.3206 29170.79214 29033.30986 0.822619866 0.830612961 0.758905403 0.704068452 0.745497802 0.88719513 0.89915069 1.004735329 1 14.82542143 1.700751352 1.518759546 0.999741756 0.777265008 0.812655005 0.043733556 0.167992652 0.756594864 0.036824902 0.013998589 50.20550638 -1.700751352 -0.222476748 RHSHTIGGLPESDDQS(ph)ELPSPPALPMSLSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHSHTIGGLPESDDQSELPSPPALPMSLSAK 31 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6;H7BZD9 Q8NEY1-5 NAV1 Neuron navigator 1 1 RHS(0.142)HT(0.142)IGGLPES(0.192)DDQS(0.261)ELPS(0.261)PPALPMSLSAK 142.45 1.06E-08 113270000 32968 31176 35438 28780 37216 31526 44462 33172 56020 TRUE FALSE 30904.59173 33484.30348 36278.6061 29518.54352 34293.20548 40627.04442 37795.33586 37313.59722 46669.9001 0.662195369 0.717471077 0.777344842 0.632496394 0.73480349 0.870519207 0.809843942 0.799521686 1 15.51020476 0.263641419 0.234854108 1.097139256 0.663080625 0.742781267 0.053308256 3.198008565 0.361224624 0.403885785 0.130339506 1.835022606 -0.263641419 -0.434058631 RHSLAMPGET(ph)VLNGNQEWVVQADLPLTAAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHSLAMPGETVLNGNQEWVVQADLPLTAAIR 31 1 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-2;Q674X7;Q674X7-5 A0A1B0GWK2 KAZN Kazrin 1 RHS(0.464)LAMPGET(0.536)VLNGNQEWVVQADLPLTAAIR 66.825 0.0044176 48525000 29508 33768 31568 29702 41157 29940 32099 31512 45771 TRUE FALSE 27661.14695 36268.21786 32316.80787 30464.20361 37924.69524 38583.19196 27286.05294 35446.34257 38131.52441 0.725414139 0.951134748 0.847508941 0.798924357 0.994575901 1.011844991 0.715577291 0.929581052 1 15.21869659 4.752328317 24.0337455 0.890954385 0.725413948 0.245693494 0.096304356 2141.045949 3737429.921 0.022166756 0.425162611 56536.4216 -4.752328317 -0.165540437 RHSS(ph)DINHLVT(ph)QGRESPEGSYTDDANQEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHSSDINHLVTQGRESPEGSYTDDANQEVR 30 2 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 2 RHS(0.382)S(0.618)DINHLVT(0.891)QGRES(0.082)PEGS(0.026)Y(0.001)TDDANQEVR 167.6 4.78E-11 760020000 36199 47330 48874 46712 48588 36583 54471 40900 82450 TRUE FALSE 33933.36921 50834.36245 50033.31436 47910.709 44772.09447 47143.91822 46303.57923 46006.45503 68688.56235 0.494017753 0.740070264 0.728408233 0.697506359 0.65181295 0.686343062 0.674109017 0.669783345 1 16.06778227 -1.506042295 3.010842384 1.010386826 0.680435968 0.697942061 0.068238485 17289731.93 19670847.41 1479864.662 0.015108834 0.031185859 1.506042295 -0.329950858 RHSS(ph)DINHLVTQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHSSDINHLVTQGR 14 1 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 RHS(0.409)S(0.591)DINHLVTQGR 74.732 0.015152 394940000 155100 237610 206960 194190 217080 229920 280480 202740 243470 TRUE FALSE 145392.5679 255202.8916 211869.1889 199173.2442 200031.4125 296294.1716 238424.6278 228052.5353 202833.2841 0.716808232 1.258190404 1.044548432 0.981955427 0.986186332 1.460776878 1.175470924 1.124334876 1 17.62993489 RHSVSEMT(ph)SCPEPQGFSDPPGQGPTGTFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHSVSEMTSCPEPQGFSDPPGQGPTGTFR 29 1 P85299;P85299-5;P85299-2;P85299-4;P85299-3 P85299 PRR5 Proline-rich protein 5 1 RHS(0.203)VS(0.275)EMT(0.375)S(0.147)CPEPQGFSDPPGQGPTGTFR 97.469 0.00075765 541530000 56688 64163 56772 71159 74107 66463 84448 72844 77053 TRUE FALSE 53139.99927 68913.69528 58118.65865 72985.06041 68286.93515 85649.78916 71785.80638 81938.73375 64192.35652 0.827824404 1.073549859 0.905382849 1.136974312 1.063786078 1.33426772 1.118292119 1.276456235 1 15.9701139 2.996052538 1.938135081 1.181145449 0.960509294 0.42257008 0.11571978 0.290849274 2.200662773 0.035020803 0.041308331 990.9518159 -2.996052538 -0.220636156 RHSVSEMTS(ph)CPEPQGFSDPPGQGPTGTFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHSVSEMTSCPEPQGFSDPPGQGPTGTFR 29 1 P85299;P85299-5;P85299-2;P85299-4;P85299-3 P85299 PRR5 Proline-rich protein 5 1 RHS(0.121)VS(0.182)EMT(0.276)S(0.421)CPEPQGFSDPPGQGPTGTFR 182.54 4.48E-18 246640000 172990 156860 161820 156440 212050 144260 215610 160030 203430 TRUE FALSE 162162.8647 168474.0776 165658.4468 160454.5153 195396.4484 185905.5201 183281.2821 180010.0978 169476.2188 0.956847314 0.994086833 0.977473111 0.946767142 1.152943167 1.096941633 1.08145723 1.062155499 1 17.37072332 2.75183415 24.99834441 1.084974896 0.97445572 0.65466761 0.039423519 435.1417628 819512.1334 0.011035769 0.011642981 564.7212756 -2.75183415 -0.110519176 RHT(ph)MDKDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RHTMDKDSR 9 2 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;F6UYG0 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 RHT(1)MDKDSR;RHT(1)MDKDSR;RHT(1)MDKDSR 155.86 0.0034463 452080000 685820 679880 525930 630410 1156600 509542 783880 793160 996780 TRUE FALSE 642895.7504 730219.0226 538405.308 646587.3879 1065765.301 656638.5037 666344.4712 892187.772 830410.9786 0.774189849 0.879346542 0.648360055 0.778635404 1.283419089 0.790739189 0.802427338 1.074393035 1 19.66346599 2.953168792 24.9999668 0.955358393 0.766714685 0.33582809 0.149451947 547.1577172 292089.7527 0.045243398 0.047989192 897.7776557 -2.953168792 -0.188643708 RHT(ph)PLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RHTPLSK 7 1 P61956;P61956-2;A8MUA9;A8MU27;P55854;P55854-2 P61956;A8MUA9 SUMO2;SUMO3 Small ubiquitin-related modifier 2;Small ubiquitin-related modifier 3 1 RHT(1)PLSK;RHT(1)PLSK;RHT(1)PLSK;RHT(1)PLSK;RHT(1)PLSK;RHT(1)PLSK 125.48 0.0023705 2968140000 3437970 2912380 3145240 2901490 3326260 2548910 3744710 3124930 4545100 TRUE FALSE 3222793.595 3128015.646 3219846.578 2975947.146 3065028.957 3284738.939 3183225.5 3515084.389 3786493.448 0.851128792 0.826098259 0.850350495 0.785937487 0.80946369 0.867488346 0.840678993 0.928321794 1 21.852431 1.049846231 1.652552729 1.000912622 0.829827226 0.86203821 0.022834749 0.122226077 0.675197519 0.020707626 0.00603081 11.21621256 -1.049846231 -0.171085396 RHT(ph)VEDAVVSQGPEAAGPLSTPQEVSASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RHTVEDAVVSQGPEAAGPLSTPQEVSASR 29 1 Q96NW4 Q96NW4 ANKRD27 Ankyrin repeat domain-containing protein 27 1 RHT(0.999)VEDAVVS(0.001)QGPEAAGPLSTPQEVSASR;RHT(0.986)VEDAVVS(0.014)QGPEAAGPLSTPQEVSASR;RHT(0.992)VEDAVVS(0.008)QGPEAAGPLSTPQEVSASR;RHT(0.967)VEDAVVS(0.033)QGPEAAGPLSTPQEVSASR 170.44 2.01E-12 427088000 152192 166356 151753 181417 162589 131608 210250 160041 185582 TRUE FALSE 142666.5744 178673.1713 155352.6528 186072.4674 149819.9158 169601.0931 178724.9644 180022.4711 154607.1653 0.922768192 1.15565906 1.004821817 1.203517748 0.969036044 1.096980808 1.155994058 1.164386339 1 17.23824766 2.003400578 24.92705732 1.124716474 1.06326608 0.056144114 0.093302296 228.5876521 1675586.39 0.031254068 0.022965935 100.7860855 -2.003400578 -0.061450394 RHT(ph)VGGGEMAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHTVGGGEMAR 11 1 Q9BWN1 Q9BWN1 PRR14 Proline-rich protein 14 1 RHT(1)VGGGEMAR 59.68 0.026006 0 61177 65586 64398 77765 81608 53830 69535 55090 70188 TRUE FALSE 57348.04077 70442.05568 65925.55097 79760.58156 75198.83687 69369.84714 59108.87228 61968.10777 58473.16937 0.980758207 1.204690227 1.127449592 1.364054359 1.286040037 1.186353466 1.010871703 1.05976995 1 15.83548717 1.759455746 5.855286519 1.027220368 1.196453164 0.385329045 0.099825782 0.18041137 15.46887141 0.048523121 0.025946075 57.47192525 -1.759455746 0.169232796 RHVFGESDELIGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHVFGESDELIGQK 14 1 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3;U3KPS5 P60174 TPI1 Triosephosphate isomerase 0 77.078 0.016666 551230000 474180 528200 528540 523310 569570 419910 702270 501990 879580 FALSE TRUE 444501.9202 567308.4776 541077.2184 536739.0206 524838.2697 541131.2003 596971.1331 564664.5565 732772.4157 0.606602965 0.774194641 0.738397362 0.732477109 0.71623639 0.73847103 0.81467468 0.770586535 1 19.48300567 -5 0.172556211 2.038874817 0.682673716 0.798774712 0.044291382 58.32168931 0.55366099 20.63004724 0.147498543 1.00E-05 5 -1.356201101 RHVTLPS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RHVTLPSSPR 10 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 RHVT(0.002)LPS(0.778)S(0.22)PR;RHVT(0.011)LPS(0.574)S(0.415)PR;RHVTLPS(0.621)S(0.379)PR;RHVTLPS(0.5)S(0.5)PR 92.925 0.0055954 1036120000 534876 767820 648240 690180 824670 567240 834790 776750 810920 TRUE FALSE 501399.0659 824670.1917 663616.5589 707891.1873 759903.7448 730992.9796 709620.9893 873728.9473 675572.2133 0.742184264 1.220698802 0.982302922 1.047839407 1.124829781 1.082035296 1.050399906 1.29331688 1 19.36575046 4.751758221 24.65724657 1.094538153 0.742183986 0.58042227 0.095549044 1266.730378 2366597.438 0.020813712 0.388616693 56462.25519 -4.751758221 -0.352354167 RHYNGEAYEDDEHHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RHYNGEAYEDDEHHPR 16 1 P31689 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 166.3 2.02E-09 189380000 67317 77785 64077 74931 85879 60334 66644 50446 156610 FALSE TRUE 63103.74913 83544.28234 65596.9367 76853.85632 79134.40976 77751.44636 56651.35089 56744.29415 130470.7793 0.483661932 0.64032945 0.502771096 0.589050336 0.606529755 0.595929961 0.434207193 0.434919562 1 16.99336721 -1.138337475 4.374220568 1.000075591 0.540735903 0.80315852 0.072166938 5.60E-05 1.10E-05 0.071089605 0.01675314 0.072721449 1.138337475 -0.459339688 RIACDEEFS(ph)DS(ph)EDEGEGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RIACDEEFSDSEDEGEGGR 19 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 2 RIACDEEFS(1)DS(1)EDEGEGGR;RIACDEEFS(1)DS(1)EDEGEGGR 156.43 5.60E-08 662800000 678870 934810 986750 1009300 977060 898250 924530 777400 757010 TRUE FALSE 636380.7385 1004024.305 1010156.176 1035200.347 900325.6489 1157560.193 785905.3094 874460.1013 630660.1405 1.009070809 1.592021186 1.601744127 1.641455168 1.42759244 1.835473845 1.246162963 1.386578991 1 19.26650323 0.964488548 1.277495975 1.011848223 1.528802368 0.308480761 0.225322064 0.533974079 1.776501193 0.192575092 0.058996584 9.214855902 -0.964488548 0.516954145 RIDFIPVS(ph)PAPS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RIDFIPVSPAPSPTR 15 1 Q96E09 Q96E09 FAM122A Protein FAM122A 2 RIDFIPVS(1)PAPS(0.979)PT(0.021)R;RIDFIPVS(1)PAPS(0.987)PT(0.013)R;RIDFIPVS(1)PAPS(0.984)PT(0.016)R;RIDFIPVS(1)PAPS(0.677)PT(0.323)R;RIDFIPVS(1)PAPS(0.99)PT(0.01)R 166.77 9.01E-07 794485000 648709 701138 689595 630958 675386 682481 881210 679874 839779 TRUE FALSE 608107.4617 753050.9871 705952.5191 647149.4505 622343.9079 879502.1855 749080.7413 764757.7655 699614.4597 0.869203678 1.076379964 1.00905936 0.925008684 0.889552666 1.257124082 1.070705059 1.093113149 1 19.41620058 2.254457397 24.99999988 1.112010878 0.976770003 0.41266962 0.087234686 254.2635443 399865.906 0.029444271 0.024559418 179.662483 -2.254457397 -0.135240875 RIDFTPVS(ph)PAPS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RIDFTPVSPAPSPTR 15 1 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3;Q7Z309-5 G1UD79 SPACIA2;FAM122B Protein FAM122B 2 RIDFTPVS(1)PAPS(0.908)PT(0.092)R;RIDFT(0.014)PVS(0.986)PAPS(0.964)PT(0.036)R;RIDFT(0.001)PVS(0.999)PAPS(0.897)PT(0.103)R;RIDFTPVS(1)PAPS(0.994)PT(0.006)R 130.47 0.00015153 1412880000 1834100 2067470 1935780 1812510 2006420 1879530 2399930 1833230 2111230 TRUE FALSE 1719306.955 2220547.63 1981697.616 1859022.075 1848843.867 2422119.799 2040082.776 2062112.801 1758852.074 0.977516518 1.26249823 1.126699422 1.056951919 1.051165072 1.37710262 1.15989446 1.172419689 1 20.74620272 RIDIS(ph)PSTFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 RIDISPSTFR 10 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 RIDIS(0.971)PS(0.027)T(0.002)FR;RIDIS(0.819)PS(0.152)T(0.029)FR;RIDIS(0.747)PS(0.199)T(0.053)FR;RIDIS(0.998)PS(0.001)T(0.001)FR;RIDIS(0.989)PS(0.006)T(0.006)FR;RIDIS(0.975)PS(0.018)T(0.008)FR;RIDIS(0.937)PS(0.056)T(0.007)FR;RIDIS(0.99)PS(0.01)TFR;RIDIS(0.984)PS(0.013)T(0.003)FR 141.54 2.29E-05 21883593000 738617 1250742 1089171 1065185 1323588 1032584 1033313 932516 1397191 TRUE FALSE 692388.2804 1343348.239 1115006.65 1092519.45 1219638.738 1330674.238 878377.3085 1048942.675 1163990.796 0.594839996 1.154088369 0.957917068 0.938598015 1.047807888 1.143199966 0.754625648 0.901160627 1 20.15064822 1.728062918 24.9999999 0.867072541 0.993531992 0.04550155 0.165274932 1.750724276 4149.308091 0.069631785 0.038614387 53.46418091 -1.728062918 0.126459451 RIDIS(ph)PSTFRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RIDISPSTFRK 11 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 RIDIS(0.94)PS(0.025)T(0.035)FRK;RIDIS(0.956)PS(0.035)T(0.009)FRK 98.582 0.0028245 1387620000 1225590 1322200 1114270 1212720 1616760 936810 1494670 1093570 2672890 TRUE FALSE 1148882.51 1420097.064 1140701.011 1243840.448 1489786.191 1207251.839 1270558.109 1230104.622 2226767.391 0.51594186 0.637739294 0.5122677 0.558585712 0.66903539 0.542154445 0.570584119 0.552417206 1 21.08651943 -1.347586467 3.313104908 1.002948684 0.572041978 0.882445292 0.04933518 12553144.4 18113463.5 362698.3974 0.010832489 0.044917289 1.347586467 -0.430906705 RIDIS(ph)PSTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 RIDISPSTLR 10 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 RIDIS(0.981)PS(0.017)T(0.002)LR;RIDIS(0.992)PS(0.007)T(0.001)LR;RIDIS(0.939)PS(0.053)T(0.008)LR;RIDIS(0.966)PS(0.024)T(0.01)LR;RIDIS(0.953)PS(0.035)T(0.012)LR;RIDIS(0.942)PS(0.058)T(0.001)LR;RIDIS(0.988)PS(0.01)T(0.002)LR;RIDIS(0.772)PS(0.209)T(0.019)LR 139.05 2.97E-05 30326430000 1023955 1173126 1095797 1019235 1238071 1016432 1106381 988150 1440172 TRUE FALSE 959867.4844 1259985.47 1121789.822 1045390.296 1140837.898 1309859.418 940489.4402 1111522.703 1199797.989 0.800024248 1.050164678 0.934982249 0.871305257 0.950858318 1.0917333 0.783873159 0.926424875 1 20.19436009 1.721051482 24.99999734 0.885253071 0.95673102 0.03465682 0.096871857 2.039645232 2900.708768 0.041161673 0.022826246 52.60796251 -1.721051482 0.071477949 RIDIS(ph)PSTLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RIDISPSTLRK 11 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 RIDIS(0.816)PS(0.154)T(0.03)LRK;RIDIS(0.995)PS(0.004)T(0.001)LRK;RIDIS(0.984)PS(0.016)TLRK 116.96 0.00047936 1825340000 729210 838130 790490 785210 1060780 627350 1033720 730460 1708640 TRUE FALSE 683570.0478 900186.0173 809240.7961 805359.818 977470.6178 808455.7608 878723.2826 821659.5389 1423456.946 0.480218281 0.632394271 0.56850388 0.565777434 0.68668787 0.56795238 0.617316376 0.577228234 1 20.44096743 -5 0.3903604 7.159930185 0.583693261 0.857104268 0.053039077 216.8245663 1.566358238 1134.783854 0.030447268 1.00E-05 5 -6.576236924 RIDISPS(ph)TLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RIDISPSTLR 10 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 RIDIS(0.32)PS(0.548)T(0.132)LR 51.829 0.084493 0 191470 189360 179550 173100 217900 165250 188170 160310 243470 TRUE FALSE 179486.2345 203380.4114 183809.0108 177542.0391 200787.013 212954.9924 159955.6554 180325.0564 202833.2841 0.884895372 1.002697424 0.90620734 0.875310183 0.989911561 1.049901614 0.788606545 0.889030896 1 17.62993489 1.732337252 24.99999996 0.874073888 0.950721194 0.106911764 0.074132977 1.005808644 4011.515966 0.031913681 0.017697745 53.99297424 -1.732337252 0.076647306 RIDISPS(ph)TLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.346)PS(0.549)T(0.106)LRK 82.109 0.015624 1575900000 1142600 1272000 1386500 1327700 1633700 1002400 1567200 1167500 3021300 TRUE FALSE 1071086.706 1366180.204 1419388.435 1361771.03 1505395.792 1291776.607 1332212.909 1313264.945 2517025.512 0.42553669 0.542775668 0.563914997 0.541023928 0.598085234 0.51321554 0.529280654 0.521752735 1 21.26328841 -1.422639661 3.110147854 1.00743857 0.534971178 0.917930545 0.044190244 9770493.299 12474423.55 644207.6502 0.010657011 0.03778856 1.422639661 -0.472467392 RIDT(ph)PSLEEPSDLEELEQFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.971)PS(0.029)LEEPSDLEELEQFAK;RIDT(0.975)PS(0.025)LEEPSDLEELEQFAK;RIDT(0.95)PS(0.05)LEEPS(0.001)DLEELEQFAK;RIDT(0.982)PS(0.018)LEEPSDLEELEQFAK 266.86 2.77E-37 378645000 236262 199980 234566 214648 251823 183729 306264 262738 383872 TRUE FALSE 221474.7832 214786.7273 240130.0163 220156.2311 232045.8374 236768.5797 260342.5564 295541.4177 319801.2833 0.692538757 0.671625595 0.750872585 0.688415721 0.725593828 0.740361569 0.814076022 0.924140812 1 18.2868162 1.321845397 1.218802009 1.002269338 0.704642661 0.962382169 0.020797405 0.072057265 0.209974532 0.019039191 0.006227069 20.98192824 -1.321845397 -0.297626677 RIEELNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 91.064 0.026743 261400000 209850 257780 225730 241470 330070 194500 264430 261350 357340 FALSE TRUE 196715.8631 276866.2994 231084.4222 247666.529 304147.6336 250648.9926 224781.1763 293980.1228 297697.6455 0.660790793 0.930025157 0.776238663 0.831939831 1.021666238 0.841958263 0.755065348 0.987512422 1 18.18348829 -5 0.064773283 1.509297408 0.644645911 0.279863759 0.10010984 581.7606273 2.735595981 46.30200583 6.729083393 1.00E-05 5 -0.864651497 RIENAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RIENAK 6 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;;;; 119.56 0.033528 4651010000 4958660 4401730 4424430 4262640 4778960 3393890 4777580 4345690 5155180 FALSE TRUE 4648306.322 4727638.669 4529379.569 4372026.559 4403639.759 4373650.948 4061226.232 4888258.963 4294747.154 1.082323628 1.100795576 1.054632416 1.017993936 1.025354835 1.018372163 0.945626386 1.13819482 1 22.03414177 3.50479798 1.685839348 1.014858754 1.091773485 0.236740929 0.047812897 0.424261458 2.422837205 0.013924903 0.025057611 3197.407433 -3.50479798 0.076914732 RIEQHYFEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RIEQHYFEDR 10 1 C9JNK6;O75431-2;O75431 C9JNK6 MTX2 Metaxin-2 0 ;;; 128.28 0.00021663 1855480000 1380420 1663690 1402190 1263010 2086300 1031630 1607730 1704670 2358140 FALSE TRUE 1294021.976 1786871.339 1435450.609 1295420.975 1922450.414 1329444.834 1366665.812 1917501.802 1964551.2 0.658685799 0.909557022 0.7306761 0.65939792 0.978569769 0.676716817 0.695663117 0.976050816 1 20.90576834 1.223787339 23.32503336 0.988026187 0.767032411 0.44102821 0.10710563 113.8409028 179727.4964 0.094798046 0.02419998 16.74122906 -1.223787339 -0.220993776 RIESLIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RIESLIDR 8 1 Q13619;A0A0A0MR50;Q13619-2;A0A669KAX4;Q13620-1;K4DI93;Q13620;Q13620-3 Q13619;A0A669KAX4 CUL4A;CUL4B Cullin-4A;Cullin-4B 0 ;; 129.85 0.0017205 869120000 340537 441300 397370 390060 430300 365720 446690 424860 414810 FALSE TRUE 319223.397 473974.3112 406795.8041 400069.6 396505.9737 471297.427 379712.9814 477904.7062 345575.5312 0.923744213 1.371550554 1.177154536 1.157690762 1.147378613 1.363804391 1.098784338 1.38292403 1 18.39864154 -0.995319366 4.415849295 0.999992262 1.211470733 0.16520578 0.142161796 9.39E-06 2.14E-06 0.119258118 0.02810838 0.101083585 0.995319366 0.211478471 RIEYIEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RIEYIEAR 8 1 Q8WUW1;Q8WUW1-2 Q8WUW1 BRK1 Protein BRICK1 0 116.3 0.0073752 0 30498 50375 27848 39876 62118 28173 28507 44686 55878 FALSE TRUE 28589.18462 54104.81742 28508.56771 40899.28567 57239.50285 36306.08775 24232.64 50265.14547 46551.60081 0.614139667 1.162254712 0.612407892 0.878579575 1.229592578 0.779910618 0.520554386 1.079772652 1 15.50654316 RIKEDEDDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RIKEDEDDK 9 2 P14625;H0YIV0;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 56.258 0.069245 439580000 201120 408280 444840 506000 413450 169890 225940 440880 209300 FALSE TRUE 188532.2582 438509.476 455391.8149 518984.8167 380979.3048 218934.4851 192062.3945 495924.8385 174366.4779 1.08124142 2.514872591 2.611693603 2.976402477 2.184934337 1.25559963 1.101486919 2.844152411 1 17.41176318 2.360965134 5.431639113 1.503581095 2.40223436 0.201258366 0.700209241 0.271043843 11.85195043 0.233387403 0.193590765 229.5964316 -2.360965134 0.898653265 RIPSIVSS(ph)PLNSPLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RIPSIVSSPLNSPLDR 16 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 RIPSIVS(0.072)S(0.928)PLNSPLDR;RIPSIVS(0.342)S(0.657)PLNSPLDR 123.61 5.33E-05 240400000 143880 173850 172163 182539 220090 149820 181045 149238 251330 TRUE FALSE 134874.8076 186722.0349 176246.7877 187223.2598 202805.0192 193070.6019 153898.983 167870.6928 209381.3993 0.644158498 0.891779477 0.841749975 0.894173314 0.968591383 0.922100065 0.735017454 0.801745969 1 17.67577376 4.742095614 24.5599126 0.869345303 0.644158387 0.474705633 0.07760181 264.4787005 1837400.601 0.018672757 0.137353733 55219.89973 -4.742095614 -0.225186916 RIPVLS(ph)PKPAVAPPAPPSSSQLCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RIPVLSPKPAVAPPAPPSSSQLCR 24 2 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;G3V411;Q6PJT7-8 Q6PJT7-5 ZC3H14 Zinc finger CCCH domain-containing protein 14 1 RIPVLS(1)PKPAVAPPAPPSSSQLCR 71.881 0.015248 205150000 198730 144840 167020 150140 175910 127130 205170 155280 235800 TRUE FALSE 186291.844 155564.1043 170981.7933 153992.8466 162094.7382 163830.3672 174406.6632 174667.0498 196443.4567 0.948322979 0.791902703 0.870386808 0.783904179 0.825147047 0.833982307 0.887821189 0.889146693 1 17.58375459 0.866391978 1.034531725 0.998671285 0.837213102 0.518779509 0.046557552 0.491215529 1.047508855 0.039548807 0.012817645 7.35177113 -0.866391978 -0.161458183 RIPVLS(ph)PKPVAPPAPPSSSQLCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RIPVLSPKPVAPPAPPSSSQLCR 23 2 Q6PJT7-9;Q6PJT7-2;H0YJA2;Q6PJT7-3;Q6PJT7-11;Q6PJT7-6 Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 1 RIPVLS(1)PKPVAPPAPPSSSQLCR 52.237 0.06257 181380000 221710 172370 175470 170620 210940 128130 231810 140340 249720 TRUE FALSE 207833.5669 185132.4542 179632.2313 174998.3981 194373.6233 165119.051 197052.2425 157861.7579 208040.1187 0.999007154 0.889888235 0.863449955 0.841176207 0.934308365 0.793688506 0.947183859 0.758804402 1 17.66650224 4.749588875 3.199819528 0.874975896 1.018745609 0.22140993 0.071296612 0.490885794 7.793805242 0.014588647 0.178799036 56180.92367 -4.749588875 0.143769714 RIPVS(ph)PEQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RIPVSPEQAR 10 1 C9J7L6;Q9H981-2;Q9H981 C9J7L6 ACTR8 Actin-related protein 8 1 RIPVS(1)PEQAR;RIPVS(1)PEQAR;RIPVS(1)PEQAR 85.837 0.0085552 407891000 259193 277964 297434 296360 315633 269141 317018 279768 342043 TRUE FALSE 242970.5728 298544.7438 304489.2749 303965.0993 290844.4574 346837.6376 269484.094 314697.6506 284953.8136 0.852666507 1.047695204 1.068556588 1.066717078 1.020672276 1.217171419 0.945711484 1.104381256 1 18.12036858 4.739758396 4.637420795 1.059355508 0.839802993 0.457308929 0.070716361 0.159756607 9.274483508 0.014964978 0.114324129 54923.52416 -4.739758396 -0.219552516 RIQEIIEQLDVTTSEYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RIQEIIEQLDVTTSEYEK 18 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 93.684 0.0026818 0 110310 116160 109880 109680 170420 106260 110990 137940 172270 FALSE TRUE 103405.894 124760.6073 112486.4055 112494.5745 157035.9006 136935.537 94348.07988 155162.1126 143517.0241 0.720513087 0.869308767 0.783784406 0.783841326 1.094197024 0.954141419 0.657399918 1.081140817 1 17.13086236 7.999999991 0.067977251 1.149279248 0.206051705 0.205682843 0.13278393 523.6543914 2.633356252 6.568378028 47.5256206 99999997.86 -7.999999991 -0.943227543 RIQLVEEELDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RIQLVEEELDR 11 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;H0YL80;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5;H0YKP3;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2 TPM3;TPM1;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain 0 ;;;;; 256.47 2.73E-20 4391810000 3368260 4630900 4067230 4249810 4697960 3755180 4305810 3759810 4170340 FALSE TRUE 3157446.619 4973776.654 4163706.616 4358867.32 4329001.172 4839239.506 3660193.764 4229230.555 3474283.313 0.908805165 1.431597889 1.198436121 1.25460906 1.246012712 1.392874176 1.053510446 1.21729582 1 21.72828397 1.03307233 1.027941642 1.011048304 1.2509817 0.146619204 0.15130871 0.821382129 1.84882603 0.127916749 0.042284761 10.79126432 -1.03307233 0.239933396 RIQPQPPDEDGDHS(ph)DKEDEQPQVVVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RIQPQPPDEDGDHSDKEDEQPQVVVLK 27 2 Q96AT1 Q96AT1 KIAA1143 Uncharacterized protein KIAA1143 1 RIQPQPPDEDGDHS(1)DKEDEQPQVVVLK 56.625 0.034429 251550000 123050 67727 74571 82064 104590 55812 111650 71932 150110 TRUE FALSE 115348.5202 72741.57755 76339.85933 84169.90117 96375.9233 71924.01837 94909.11901 80912.86854 125055.6713 0.922377362 0.58167356 0.610447 0.673059449 0.770664156 0.575135999 0.758934945 0.647014787 1 16.93221096 -2.23351762 0.503929676 1.428209845 0.673371228 0.443320469 0.10630439 88.99713753 5.908708702 42.91562978 0.045970115 0.005840935 2.23351762 -0.754838617 RIS(ph)FSASHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RISFSASHR 9 1 E9PKY8;E9PJM0;Q03393 E9PKY8 PTS 6-pyruvoyl tetrahydrobiopterin synthase 1 RIS(1)FSASHR;RIS(1)FSASHR;RIS(1)FSASHR;RIS(1)FSASHR;RIS(1)FSASHR;RIS(1)FSASHR 174.05 3.37E-05 3092950000 863357 1371435 1049311 1061556 1368506 929604 1117351 1182956 1498804 TRUE FALSE 809321.0265 1472977.474 1074201.152 1088797.324 1261029.059 1197965.584 949814.5905 1330650.661 1248643.93 0.648159982 1.179661743 0.860294217 0.871983836 1.009918864 0.959413293 0.760676897 1.065676634 1 20.2519307 3.731867364 24.92901947 0.915638698 0.972306075 0 0.155449942 943.366794 4954999.892 0.037041547 0.064139666 5393.458781 -3.731867364 0.056667377 RIS(ph)GLIYEETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RISGLIYEETR 11 1 P62805 P62805 HIST1H4A Histone H4 1 RIS(1)GLIYEETR;RIS(1)GLIYEETR 101.3 0.0020728 136005000 101265 114852 114584 105406 140033 107190 116087 99342 152064 TRUE FALSE 94927.00441 123355.7616 117301.9866 108110.8964 129035.373 138134.0129 98680.83205 111745.0674 126683.536 0.749323925 0.973731595 0.925944999 0.853393423 1.018564662 1.090386464 0.77895546 0.882080426 1 16.95086952 4.746404093 24.35063775 0.933805756 0.749323794 0.311782247 0.088731432 899.2148321 2791582.081 0.020919181 0.224005441 55770.44279 -4.746404093 -0.184481962 RIS(ph)HEGSPVKPVAIR ddPTM_SK-BR-3_Pertuzumab_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 145.48 2.11E-06 364000000 206160 152950 164050 170510 211030 135350 237830 219970 371360 TRUE FALSE 193256.8136 164274.5771 167941.3435 174885.5753 194456.5551 174423.3478 202169.5994 247433.7387 309377.6169 0.624663205 0.530984041 0.542836114 0.565281926 0.628541124 0.56378787 0.653471965 0.799779057 1 18.2390093 1.046806218 1.294847236 1.000798959 0.564403212 0.950266362 0.032052483 0.08491053 0.292134047 0.029606783 0.009105318 11.13797447 -1.046806218 -0.436395747 RIS(ph)HSLYSGIEGLDESPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RISHSLYSGIEGLDESPSR 19 1 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3;B1AP52 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 RIS(0.808)HS(0.192)LYSGIEGLDESPSR;RIS(0.794)HS(0.198)LYS(0.008)GIEGLDESPSR 319.68 4.27E-62 675720000 150654 184859 173698 159761 228508 128734 195417 204609 217164 TRUE FALSE 141224.8351 198546.1527 177818.1986 163860.7377 210561.9034 165897.416 166116.035 230154.884 180917.9255 0.780601672 1.097437704 0.982866668 0.905718642 1.163853183 0.916976113 0.9181845 1.272150802 1 17.46497583 4.75097714 23.78251641 1.019280454 0.780601374 0.303169504 0.118431325 1262.83728 2418740.544 0.025970745 0.428073093 56360.7988 -4.75097714 -0.23867908 RIS(ph)LDQQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RISLDQQ 7 1 Q96PM5-2;Q96PM5;Q96PM5-8;Q96PM5-7;Q96PM5-6 Q96PM5-2 RCHY1 RING finger and CHY zinc finger domain-containing protein 1 1 RIS(1)LDQQ;RIS(1)LDQQ;RIS(1)LDQQ 76.619 0.042654 1302930000 1429170 1623360 1698750 1519480 1739670 1619160 1900700 1624430 2103650 TRUE FALSE 1339720.801 1743555.264 1739045.152 1558472.429 1603043.336 2086585.207 1615707.68 1827243.661 1752537.225 0.764446416 0.994874881 0.992301406 0.889266377 0.914698594 1.190608209 0.921924885 1.042627589 1 20.74101366 RIS(ph)LSDMPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 RISLSDMPR 9 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 RIS(1)LSDMPR;RIS(1)LSDMPR;RIS(1)LSDMPR;RIS(1)LSDMPR;RIS(1)LSDMPR;RIS(1)LSDMPR;RIS(1)LSDMPR;RIS(1)LSDMPR;RIS(1)LSDMPR;RIS(1)LSDMPR;RIS(1)LSDMPR 191.23 2.21E-05 4763070000 1820862 2051030 2008970 2707130 3105560 1911549 2070730 1776358 2607170 TRUE FALSE 1706897.498 2202890.395 2056623.717 2776599.539 2861661.845 2463382.165 1760243.26 1998140.207 2172016.484 0.785858446 1.0142144 0.946872978 1.278351044 1.317513871 1.134145244 0.810418923 0.919947073 1 21.05060362 1.743785656 24.99999503 0.897367468 1.073461486 0.200416381 0.158492037 1.702030307 8175.64583 0.077354558 0.04289707 55.43520481 -1.743785656 0.176094018 RIS(ph)MEDLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RISMEDLNK 9 1 Q00537;Q00537-2;F5H6Z0;F8VQZ9;F8VZY6 Q00537 CDK17 Cyclin-dependent kinase 17 1 RIS(1)MEDLNK 70.009 0.032846 152530000 229320 249130 234960 222800 297140 192630 265270 245040 402260 TRUE FALSE 214967.2705 267575.8444 240533.3622 228517.4252 273803.823 248239.1539 225495.2261 275633.7834 335120.2073 0.64146317 0.798447359 0.717752487 0.681896884 0.817031671 0.740746599 0.672878631 0.82249228 1 18.35431916 0.94525616 5.18470042 0.999939852 0.731059915 0.727752453 0.053839155 0.149777124 11.9306199 0.048437572 0.012231053 8.81568695 -0.94525616 -0.268879937 RIS(ph)QSQPVR ddPTM_SK-BR-3_Pertuzumab_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(1)QSQPVR;RIS(0.919)QS(0.081)QPVR;RIS(0.999)QS(0.001)QPVR;RIS(1)QSQPVR 209.67 4.92E-06 4990650000 1757100 2363310 2126890 2200480 2271450 1849140 2074030 1607606 2685180 TRUE FALSE 1647126.248 2538291.931 2177340.835 2256948.042 2093059.48 2382956.7 1763048.456 1808319.148 2237006.111 0.736308336 1.134682609 0.973328068 1.008914563 0.935652106 1.065243715 0.788128583 0.808365761 1 21.09313777 1.7335651 13.17438195 0.849752824 0.993491427 0.149196859 0.117053994 0.10520248 119.829018 0.049478919 0.027188345 54.14584049 -1.7335651 0.143738602 RIS(ph)QVSSGETEYNPTEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RISQVSSGETEYNPTEAR 18 1 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 RIS(0.96)QVS(0.011)S(0.029)GETEYNPTEAR;RIS(0.843)QVS(0.085)S(0.072)GETEYNPTEAR 373.33 1.05E-107 748290000 410140 552890 433090 502660 469390 408700 668200 464380 513830 TRUE FALSE 384470.0695 593826.5509 443363.0993 515559.1066 432526.0028 526685.0553 568009.6133 522358.8652 428068.4535 0.898150906 1.387223342 1.035729439 1.204384725 1.010413169 1.230375775 1.326913041 1.220269471 1 18.70748199 2.05758216 24.99991109 1.233701957 1.138405553 0.026583976 0.154342914 200.7743148 87167.06155 0.053320904 0.039380094 114.1779286 -2.05758216 -0.095296405 RIS(ph)SSSVQPCSEEVSTPQDSLAQCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RISSSSVQPCSEEVSTPQDSLAQCK 25 1 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 RIS(0.816)S(0.179)S(0.002)S(0.003)VQPCSEEVSTPQDSLAQCK;RIS(0.826)S(0.162)S(0.011)S(0.001)VQPCSEEVSTPQDSLAQCK;RIS(0.762)S(0.144)S(0.086)S(0.009)VQPCSEEVSTPQDSLAQCK 300.15 2.15E-63 3172020000 1411760 1334730 1371190 1337450 1580990 1225970 2002110 1500980 2308710 TRUE FALSE 1323400.462 1433554.798 1403715.274 1371771.231 1456825.423 1579887.637 1701912.192 1688380.657 1923371.386 0.688062883 0.745334369 0.729820192 0.713211833 0.757433241 0.821415795 0.88485885 0.877823529 1 20.87520593 1.589184316 0.695903093 0.991217124 0.716052499 0.946829284 0.022206224 0.133813002 0.13685472 0.020891549 0.009826484 38.83151329 -1.589184316 -0.275164626 RIS(ph)YVQDENRDPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RISYVQDENRDPIR 14 2 Q9NQS7-2;Q9NQS7;E9PM67 Q9NQS7-2 INCENP Inner centromere protein 1 RIS(1)YVQDENRDPIR 90.718 0.0029435 84270000 71513 74313 82067 77447 79340 62993 87916 61235 69068 TRUE FALSE 67037.12898 79815.21184 84013.66799 79434.42114 73108.95644 81178.05649 74733.81197 68880.32454 57540.1046 1.165050523 1.387123162 1.460088899 1.380505331 1.270573923 1.410808288 1.298812584 1.197083756 1 15.81228022 0.978036177 1.517563952 1.000762526 1.363453044 0.638876527 0.082535395 0.253973129 1.194854919 0.075588107 0.022255936 9.50683982 -0.978036177 0.362690517 RIS(ph)YVQDENRDPIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RISYVQDENRDPIRR 15 3 Q9NQS7-2;Q9NQS7;E9PM67 Q9NQS7-2 INCENP Inner centromere protein 1 RIS(1)YVQDENRDPIRR 89.831 0.034527 422370000 403490 265120 326780 324920 334070 327760 407560 247580 386840 TRUE FALSE 378236.2812 284749.7607 334531.3759 333257.9973 307833.4898 422378.9913 346450.1616 278490.908 322273.9049 1.173648488 0.883564435 1.038034327 1.034083096 0.955192105 1.310621136 1.07501773 0.864143524 1 18.29792785 RISQVS(ph)SGETEYNPTEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RISQVSSGETEYNPTEAR 18 1 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 RIS(0.333)QVS(0.333)S(0.333)GETEYNPTEAR 329.64 7.78E-75 162360000 94563 121930 93091 118440 93732 85293 144080 105970 121060 TRUE FALSE 88644.47063 130957.8241 95299.16248 121479.3709 86370.66682 109915.7045 122476.5416 119200.5878 100854.3039 0.878935922 1.29848523 0.944919144 1.204503588 0.856390491 1.089846444 1.214390827 1.181908785 1 16.62191313 1.98641361 24.5254129 1.154970483 1.059610716 0.063644291 0.14659971 1264.429663 2282478.736 0.054034411 0.036528194 96.92004568 -1.98641361 -0.095359768 RISQVSS(ph)GETEYNPTEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RISQVSSGETEYNPTEAR 18 1 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 RIS(0.006)QVS(0.256)S(0.737)GETEYNPTEAR 173.06 9.79E-12 174060000 65278 83574 76395 81998 71126 64246 107080 81858 85037 TRUE FALSE 61192.3665 89761.90592 78207.12548 84102.2075 65540.05087 82792.77725 91024.34808 92078.15149 70843.77534 0.8637649 1.267040124 1.103937856 1.187150277 0.925134926 1.168666927 1.28486021 1.299735242 1 16.11235348 2.002586693 24.99958688 1.226578125 1.1014571 0.115323764 0.142376932 147.8207777 1428625.502 0.049689854 0.036484852 100.5973853 -2.002586693 -0.125121025 RITEAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RITEAEK 7 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;; 99.136 0.017237 494090000 503870 699510 595800 585060 744620 537200 673920 638910 771460 FALSE TRUE 472333.6761 751302.4482 609932.6574 600073.6301 686140.5489 692280.9193 572871.9524 718679.3199 642698.3422 0.734922817 1.168981463 0.949018563 0.933678509 1.067593463 1.077147511 0.891354333 1.118221836 1 19.29378223 2.738679509 24.99989446 1.017058802 0.984100235 0.064889211 0.121350965 63.48200566 13349722.1 0.036452381 0.036454271 547.8725084 -2.738679509 -0.032958568 RITEAEKNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RITEAEKNER 10 2 P15311;E7EQR4 P15311 EZR Ezrin 0 ;; 147.26 1.53E-05 858550000 825930 1047510 835260 865550 1355960 632650 909710 875270 2006350 FALSE TRUE 774236.5156 1125068.73 855072.7616 887761.4784 1249468.371 815285.7848 773307.4308 984549.3862 1671477.223 0.463204945 0.673098451 0.511567103 0.531123886 0.74752342 0.487763622 0.462649099 0.589029496 1 20.67269227 -1.835274627 2.131858267 1.196512986 0.558855292 0.69528389 0.091906638 1561983.962 793026.6476 1565885.261 0.023038081 0.014612529 1.835274627 -0.637657694 RIVDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 RIVDGK 6 1 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;; 117.62 0.036181 33213370000 71387200 68351010 69647720 70729670 79447850 62530760 88331720 72444000 111552250 FALSE TRUE 66919202.58 73411789.9 71299796.81 72544713.08 73208336.34 80582375.31 75087198.62 81488792.87 92933458.82 0.72007653 0.789939284 0.76721342 0.780609201 0.787750045 0.867097559 0.80796733 0.876850963 1 26.46969477 -0.89503279 0.184757307 1.177474085 0.716851437 0.890368295 0.025701371 5.589737807 0.238061747 0.587747631 0.090565274 0.127340693 0.89503279 -0.460622649 RIVNAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RIVNAK 6 1 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 130.01 0.025572 1421630000 2769600 2937700 2585700 2615600 3318500 2084160 2961900 3067500 3558900 FALSE TRUE 2596255.68 3155210.365 2647034.025 2682720.724 3057878.396 2685823.158 2517790.592 3450484.127 2964896.599 0.875664831 1.064189006 0.892791346 0.904827752 1.03136089 0.905874141 0.849200135 1.163778909 1 21.49955036 1.236926683 24.99999998 1.081889438 0.937858296 0.391352676 0.077450581 46.11764099 705515.1269 0.060376233 0.018152641 17.25546562 -1.236926683 -0.144031142 RKAENPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKAENPSPR 9 2 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 1 RKAENPS(1)PR;RKAENPS(1)PR 64.55 0.054397 49373000 144423 123665 135443 131066 146598 115584 173762 130431 166349 TRUE FALSE 135383.8222 132821.2853 138655.7719 134429.3755 135084.7844 148951.2245 147708.0012 146715.5975 138584.2772 0.976906074 0.958415254 1.000515893 0.970018953 0.97474827 1.074806085 1.065835203 1.05867419 1 17.08040406 2.245417138 24.99982138 1.057138394 0.976755703 0.72025712 0.022620772 69.73471368 254262.6634 0.007230003 0.005923527 175.9612904 -2.245417138 -0.080382691 RKAS(ph)PEPPDSAEGALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RKASPEPPDSAEGALK 16 2 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 RKAS(0.926)PEPPDS(0.074)AEGALK;RKAS(1)PEPPDSAEGALK;RKAS(1)PEPPDSAEGALK 168.79 3.05E-09 1114690000 2180840 1386870 1740910 1619600 1879160 1275040 2092270 1584950 3099230 TRUE FALSE 2044345.117 1489555.298 1782205.207 1661161.678 1731578.354 1643123.349 1778553.537 1782834.496 2581948.491 0.79178385 0.576911314 0.690255911 0.64337522 0.670647908 0.636388896 0.688841603 0.690499637 1 21.30002879 0.083417548 0.990890478 1.002899834 0.659823581 0.780131437 0.054397244 2.356812665 2.181978063 0.06565389 0.014637074 1.211762611 -0.083417548 -0.343076253 RKAS(ph)VHSSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKASVHSSGR 10 2 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 1 RKAS(1)VHSSGR 73.466 0.02343 15082000 3731 11151 9026.9 11094 12815 3914.1 10859 7082.1 21222 TRUE FALSE 3497.48337 11976.63164 9241.022331 11378.69082 11808.56159 5044.03713 9230.79376 7966.315775 17679.9111 0.197822452 0.677414698 0.522684887 0.643594346 0.667908426 0.285297652 0.522106345 0.450585737 1 14.1098234 -1.369752737 3.14208359 1.005058749 0.515201596 0.49877373 0.157755576 28505982.79 37692315.42 1323548.6 0.034699225 0.042682246 1.369752737 -0.489857153 RKDDAQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKDDAQQR 8 2 Q9NZQ3-5;Q9NZQ3-4;Q9NZQ3-3;Q9NZQ3-2;Q9NZQ3;H7C2K2 Q9NZQ3-5 NCKIPSD NCK-interacting protein with SH3 domain 0 52.58 0.079872 10024000 4519.2 6632.9 4987.1 3216.1 7356 2879.1 4259.3 6497.6 7833.9 FALSE TRUE 4236.351339 7124.006818 5105.396367 3298.630571 6778.289433 3710.249432 3620.657506 7308.839663 6526.371481 0.649112811 1.091572375 0.7822718 0.505431016 1.038600002 0.56850111 0.554773432 1.119893295 1 12.67206539 5.029595482 16.26295483 0.806597285 0.172106032 0.048399736 0.231419042 17233810.89 258619181.7 0.053979557 299434171.7 107052.1717 -5.029595482 -0.634491253 RKDDSYFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKDDSYFDR 9 2 Q9HCD5;Q5JY17 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 0 ; 143.5 5.73E-05 872630000 312310 427220 361270 340210 499230 283440 399670 406330 569570 FALSE TRUE 292763.0746 458851.8133 369839.495 348940.3646 460022.4896 365264.5267 339743.1939 457061.1949 474505.0874 0.616986166 0.967011367 0.779421559 0.735377499 0.969478519 0.769780001 0.715994839 0.963237712 1 18.85606403 1.108775776 6.488968025 0.99781468 0.807716242 0.342589127 0.107477731 0.237692862 11.82286132 0.096680437 0.024294625 12.84623245 -1.108775776 -0.190098438 RKDGVFLYFEDNAGVIVNNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKDGVFLYFEDNAGVIVNNK 20 2 J3KTJ3;P62829;J3KT29 J3KTJ3 RPL23 60S ribosomal protein L23 0 ; 115.98 5.71E-05 115237000 126520 106220 103769 110261 123311 92457 134861 91854 126072 FALSE TRUE 118601.339 114084.6393 106230.4497 113090.4839 113626.6515 119147.835 114639.845 103322.1741 105029.7687 1.129216416 1.08621242 1.011431816 1.076746957 1.081851868 1.134419664 1.091498595 0.983741803 1 16.68043877 1.238039276 24.99994522 0.99187086 1.082016946 0.577591317 0.033703886 11.3909748 545977.0887 0.029030164 0.008932193 17.29972805 -1.238039276 0.090146086 RKDNPIEDELVFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKDNPIEDELVFR 13 2 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 0 128.95 8.96E-05 48020000 42172 54354 41980 53975 58110 38574 67177 54838 68402 FALSE TRUE 39532.5298 58378.42672 42975.78542 55360.08988 53546.275 49709.6876 57104.43249 61684.64501 56985.26431 0.693732499 1.024447766 0.754156113 0.971480795 0.939651253 0.872325297 1.002091211 1.082466595 1 15.79830128 1.629651779 3.730202499 1.042051218 0.88497604 0.347548812 0.098579213 0.201857565 6.590963692 0.053513467 0.02366892 42.62376212 -1.629651779 -0.157075178 RKDPELWGSVLLESNPYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKDPELWGSVLLESNPYR 18 2 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 155.11 1.19E-08 1002160000 814150 1391670 1082450 1199540 1691020 785730 1368200 1244840 2351100 FALSE TRUE 763193.8048 1494710.695 1108126.225 1230322.227 1558214.11 1012557.496 1163051.112 1400261.014 1958686.221 0.389645772 0.763119012 0.565749742 0.628136459 0.795540446 0.516957481 0.59379144 0.714898078 1 20.90145487 0.873772951 3.701231067 0.999890429 0.620616826 0.534326576 0.114948111 0.46244156 11.90701941 0.099477152 0.025567605 7.477784593 -0.873772951 -0.379273603 RKDREDS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RKDREDSPER 10 3 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 1 RKDREDS(1)PER;RKDREDS(1)PER;RKDREDS(1)PER;RKDREDS(1)PER;RKDREDS(1)PER;RKDREDS(1)PER 150.11 0.00012241 4272989000 893165 830615 907685 916576 1160447 621569.9 903411 707587.8 1571030 TRUE FALSE 837263.397 892114.5989 929215.7168 940096.8919 1069310.174 801007.0398 767952.9074 795931.6944 1308814.944 0.639711062 0.68162012 0.709967227 0.718280989 0.817006391 0.612009393 0.586754385 0.608131576 1 20.3198297 -1.652619098 3.02241635 1.029175081 0.672649803 0.701861394 0.067244935 24119371.22 27481024.84 5535557.568 0.017849688 0.022252607 1.652619098 -0.356525279 RKDS(ph)AQDDQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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 184.44 2.56E-06 6351860000 4581520 2612160 3304730 3480430 3552410 2270971 4124060 2890290 4531340 TRUE FALSE 4294770.841 2805567.044 3383119.756 3569743.726 3273418.048 2926563.462 3505695.489 3251149.069 3775030.08 1.137678575 0.743190646 0.896183523 0.945619942 0.867123699 0.775242422 0.928653657 0.861224679 1 21.84805671 -1.31448513 3.033395718 1.000996035 0.880003204 0.073954859 0.107259724 70479508.45 90274672.24 634343.8805 0.022813916 0.048474671 1.31448513 -0.120992832 RKDS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKDSPSR 7 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;Q7Z6E9-4 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 RKDS(0.5)PS(0.5)R 73.499 0.038374 722770000 388020 317740 363280 341190 327720 308600 355640 307220 368280 TRUE FALSE 363734.5208 341265.8002 371897.1732 349945.513 301982.1932 397687.8103 302315.0836 345577.0933 306811.6888 1.185530194 1.112297258 1.212134957 1.140587291 0.984259088 1.296195109 0.985344088 1.126349177 1 18.22699392 1.178469337 0.384176815 0.991226757 1.168880455 0.207397024 0.091542159 1.808680306 0.798284885 0.123398957 0.077083949 15.0823612 -1.178469337 0.177653697 RKDSPS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RKDSPSR 7 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;Q7Z6E9-4 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 RKDS(0.14)PS(0.86)R;RKDS(0.178)PS(0.822)R;RKDS(0.224)PS(0.776)R;RKDS(0.022)PS(0.978)R 102.06 0.00684 2024490000 1235480 988890 1180590 1127690 1050110 815560 1163210 1049700 1220200 TRUE FALSE 1158153.512 1062108.445 1208594.152 1156628.435 967638.5965 1050998.932 988797.4592 1180757.356 1016540.737 1.13930851 1.044826248 1.1889284 1.137808247 0.951893575 1.033897506 0.972708149 1.161544552 1 19.9552366 2.758105397 24.92933249 1.019041553 1.12410435 0.381577745 0.065364076 786.7485352 1003495.32 0.018866917 0.019981709 572.935057 -2.758105397 0.105062797 RKEDEVEEWQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RKEDEVEEWQHR 12 2 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;;; 196.38 1.24E-07 40799300000 26946860 20081570 23643480 21332730 27030190 17763190 26330250 20300380 29543240 FALSE TRUE 25260304.13 21568430.34 24204314.51 21880163.97 24907347.91 22891134.59 22382273.45 22834927.13 24612282.39 1.026329202 0.876327924 0.983424216 0.888993699 1.011988548 0.930069558 0.909394468 0.927785842 1 24.55287511 4.769269259 23.36403143 0.936954533 1.026329566 0.253939983 0.04549862 6598.751334 5020312.246 0.009724377 1.096680384 58785.37037 -4.769269259 0.089375033 RKEDQDRS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RKEDQDRSPR 10 3 O60318 O60318 MCM3AP Germinal-center associated nuclear protein 1 RKEDQDRS(1)PR;RKEDQDRS(1)PR;RKEDQDRS(1)PR 117.93 0.0049294 795850000 857420 761240 798750 714170 946470 750760 1076280 805620 981630 TRUE FALSE 803755.6127 817603.0017 817696.7272 732496.8113 872138.0641 967492.2244 914901.8057 906203.4304 817789.6114 0.982839109 0.999771812 0.99988642 0.895703248 1.066457744 1.183057612 1.118749606 1.10811316 1 19.64137021 2.486990921 23.96639946 1.116729971 0.979786859 0.573431337 0.053734255 171.9912256 417646.7632 0.016382136 0.014483812 306.895783 -2.486990921 -0.136943112 RKEEEEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKEEEEEAR 9 2 B1AK53;A0A0J9YY76;H0Y7L4;A0A2R8YG57;A0A0J9YWQ8;A0A0A0MSQ4;B1AK53-2;A0A1B0GUS9 B1AK53;A0A1B0GUS9 ESPN Espin 0 ; 115.57 0.00081775 68947000 79372 73169 73264 77257 86234 63482 84693 63861 93106 FALSE TRUE 74404.2482 78586.50889 75001.85668 79239.54542 79461.52949 81808.22286 71994.0709 71834.18643 77566.00711 0.959237828 1.013156559 0.966942343 1.021575667 1.02443754 1.054691686 0.928165231 0.926103961 1 16.24313692 1.672463737 9.898291495 0.945792225 1.00399656 0.363036277 0.034028429 0.116694823 16.87938894 0.015588182 0.008378494 47.03961266 -1.672463737 0.058204334 RKEEEVQQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKEEEVQQQK 10 2 Q96CS3 Q96CS3 FAF2 FAS-associated factor 2 0 129.16 0.00017468 31088000 74531 55632 46307 57629 70546 40408 75961 65111 84573 FALSE TRUE 69866.23775 59751.05117 47405.42391 59107.85771 65005.60173 52073.13363 64571.35324 73240.25168 70457.21994 0.991612184 0.848047244 0.672825637 0.838918393 0.92262513 0.739074486 0.916461837 1.039499596 1 16.10445993 1.467700775 4.078187888 1.014501769 0.821627438 0.418004611 0.088334693 0.18592428 6.126492259 0.060706843 0.022995041 29.35626336 -1.467700775 -0.192874331 RKEEQEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKEEQEQR 8 2 Q9P2K8-2;Q9P2K8;Q9P2K8-3 Q9P2K8-2 EIF2AK4 Eukaryotic translation initiation factor 2-alpha kinase 4 0 58.981 0.057096 636410000 180120 425500 621550 705120 500360 1211700 556470 271660 452380 FALSE TRUE 168846.6107 457004.4627 636293.4595 723214.573 461063.744 1561498.12 473032.4895 305577.349 376874.8555 0.448017713 1.212615955 1.688341502 1.918978044 1.223386854 4.143280181 1.255144732 0.810819147 1 18.52372602 4.629109967 1.062270709 1.84237439 1.99E-11 0.152695549 0.93289434 2.63083897 2.749823107 0.269060115 5.247986762 42570.61918 -4.629109967 -1.84237439 RKEEWER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKEEWER 7 2 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 0 ; 121.09 0.002515 290910000 403410 360680 414960 384460 491040 327540 480830 371780 557410 FALSE TRUE 378161.2882 387385.1225 424803.0472 394325.8945 452475.6992 422095.4808 408734.0053 418197.5514 464374.67 0.81434521 0.834208124 0.914785139 0.849154616 0.974376357 0.908954575 0.880181525 0.900560643 1 18.82492975 8 0.071795994 1.083923676 0.431467122 0.594564899 0.037014419 184.4191096 0.974882194 1.505263026 12.1097811 100000000 -8 -0.652456554 RKEPEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKEPEPK 7 2 P39748;P39748-2 P39748 FEN1 Flap endonuclease 1 0 ; 94.114 0.0081206 278930000 984530 638800 807420 713070 792990 497880 843100 660840 1067950 FALSE TRUE 922910.0247 686097.4167 826572.3837 731368.5834 730711.7642 641609.8736 716684.982 743347.3287 889702.2458 1.037324598 0.771153967 0.929043832 0.82203747 0.821299224 0.721151235 0.80553352 0.835501239 1 19.76296307 4.748714256 24.38481673 0.828985243 1.037324762 0.386174742 0.07812397 996.4553033 2393002.873 0.017236833 0.234037758 56067.89555 -4.748714256 0.208339519 RKEPPEDVAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKEPPEDVAQR 11 2 Q9NXH9-2;Q9NXH9 Q9NXH9-2 TRMT1 tRNA (guanine(26)-N(2))-dimethyltransferase 0 96.067 0.0040994 35642000 18466 22496 21804 15576 23590 13083 28793 18679 36200 FALSE TRUE 17310.24602 24161.62725 22321.20118 15975.70653 21737.33656 16859.84972 24475.75695 21011.11427 30157.98614 0.573985476 0.801168458 0.740142298 0.529733864 0.720782099 0.559050914 0.811584594 0.696701503 1 14.88025247 0.335824917 0.947327259 1.001189496 0.685899136 0.519087665 0.097391239 2.285828359 2.52852989 0.097577192 0.029335332 2.166830385 -0.335824917 -0.31529036 RKEQEEEEQKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RKEQEEEEQKER 12 3 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ;;; 207.97 3.16E-08 482260000 464938 278932 321955 335947 379622 220317 384032 281115 502582 FALSE TRUE 435838.3605 299584.4155 329591.9246 344567.9688 349808.0194 283918.9414 326449.9668 316212.8266 418697.8174 1.040937742 0.715514634 0.787183288 0.822951433 0.835466546 0.678099884 0.77967917 0.755229221 1 18.67554987 4.747583642 24.57699635 0.780579923 1.040937914 0.42674125 0.087162548 779.3832788 2122833.037 0.018102432 0.22143102 55922.12195 -4.747583642 0.26035799 RKEQEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKEQEEK 7 2 P21127-2;P21127;P21127-3;P21127-8;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;A0A087X1I0;A0A087WYI9;A0A590UK33;Q5QPQ9;A0A590UJH0;Q9P2H0;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;J3KS35;E7ESP2;E9PFJ2 P21127-2;Q5QPR3 CDK11B;CDK11A;CEP126 Cyclin-dependent kinase 11B;Centrosomal protein of 126 kDa;Cyclin-dependent kinase 11A 0 ; 76.478 0.022864 72097000 128191 98849 134423 129513 145244 94455 145094 118124 174803 FALSE TRUE 120167.7541 106167.8828 137611.577 132836.5228 133837.1221 121722.6252 123338.5017 132872.0414 145627.25 0.825173545 0.729038575 0.944957602 0.912168037 0.919038999 0.835850606 0.846946582 0.912411938 1 17.15192081 7.999999237 0.029534669 1.472802882 3.50E-06 0.437927164 0.056471008 1537.818811 3.482783825 55.726279 133.4769398 99999824.26 -7.999999237 -1.472799377 RKGAAEEEQQDS(ph)GSEPRGDEDDIPLGPQSNVSLLDQHQHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKGAAEEEQQDSGSEPRGDEDDIPLGPQSNVSLLDQHQHLK 41 3 Q9UJV9;D6RGI7;A0A499FJW5 Q9UJV9 DDX41 Probable ATP-dependent RNA helicase DDX41 1 RKGAAEEEQQDS(0.5)GS(0.5)EPRGDEDDIPLGPQSNVSLLDQHQHLK 60.606 0.0012298 104550000 39140 32934 36617 42842 45648 26191 56849 38371 80069 TRUE FALSE 36690.29727 35372.46763 37485.57253 43941.39825 42062.99022 33751.91652 48325.02021 43161.70381 66704.96663 0.550038462 0.530282367 0.561960742 0.658742527 0.630582584 0.505988058 0.724459102 0.647053825 1 16.02550656 -5 0.171827667 2.631092862 0.500489396 0.850133902 0.054920212 44.63800142 0.423082795 24.66809384 0.179877599 1.00E-05 5 -2.130603466 RKGS(ph)DDAPYSPTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKGSDDAPYSPTAR 14 2 O75151;E7ET14;A0A087WW48 O75151 PHF2 Lysine-specific demethylase PHF2 1 RKGS(1)DDAPYSPTAR 76.768 0.020901 194850000 111800 131900 104720 120780 106720 58541 104400 72762 155830 TRUE FALSE 104802.6376 141666.0132 107204.0079 123879.4193 98338.64169 75440.83637 88746.1892 81846.49587 129820.9663 0.807285915 1.091241402 0.825783469 0.954232762 0.757494298 0.581114426 0.683604442 0.630456684 1 16.98616387 2.625561438 3.978327547 0.689631642 0.932684056 0.309727485 0.135510667 0.210464442 5.817886049 0.040757104 0.038208802 422.2420075 -2.625561438 0.243052414 RKGS(ph)GS(ph)EQEGEDEEGGER ddPTM_SK-BR-3_Pertuzumab_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 164.83 1.46E-10 3963520000 4929950 3312080 3791840 3803000 4178550 2681780 4788880 3252730 5292840 TRUE FALSE 4621393.23 3557309.849 3881784.235 3900591.418 3850383.538 3455966.351 4070831.902 3658840.501 4409430.811 1.048070245 0.80675035 0.880336806 0.884602024 0.873215547 0.783766998 0.923210291 0.829776145 1 22.07216101 -1.950049923 6.192086106 1.062794325 0.871998347 0.210527017 0.072784787 0.045611932 0.00036794 0.050945446 0.014470332 0.011218895 1.950049923 -0.190795979 RKGS(ph)QITQQSTNQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKGSQITQQSTNQSR 15 2 P50750;P50750-2 P50750 CDK9 Cyclin-dependent kinase 9 1 RKGS(0.999)QITQQSTNQSR 85.855 0.0061284 45793000 10381 13929 10256 14520 16265 8645.2 17337 12327 29797 TRUE FALSE 9731.271741 14960.31765 10499.27716 14892.60778 14987.61251 11140.9289 14737.4778 13866.05309 24823.6882 0.392015548 0.60266297 0.422953957 0.599935338 0.603762519 0.448802322 0.593686066 0.558581504 1 14.59942986 -5 0.275962864 4.370661153 0.497560385 0.795886288 0.076157098 89.45655707 0.862121295 172.2141259 0.080824593 1.00E-05 5 -3.873100768 RKHDNEGS(ph)GSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKHDNEGSGSK 11 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 1 RKHDNEGS(0.894)GS(0.106)K;RKHDNEGS(0.974)GS(0.026)K 83.729 0.0086044 13312200 25024 10865.7 15165.6 15149.8 15599.2 14073.3 19694.7 13212.6 16702.6 TRUE FALSE 23457.79251 11670.20773 15525.33519 15538.56952 14374.10176 18136.03325 16741.66257 14862.22219 13914.82816 1.685812591 0.838688599 1.115740347 1.116691442 1.033006056 1.303360203 1.203152664 1.068085213 1 13.76433547 4.211549013 0.009979069 9.47E-07 2.308161073 0.054788398 0.218722309 35049.49094 64.80527485 7045.785003 7959.660521 16276.04991 -4.211549013 2.308160126 RKHDNEGSGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKHDNEGSGSK 11 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 164.13 1.30E-05 16987000 25952 16952 22798 23332 28252 18414 28984 22376 34236 FALSE TRUE 24327.71065 18207.14372 23338.77933 23930.73862 26033.20188 23729.82287 24638.11827 25169.69286 28521.79043 0.852951736 0.638359074 0.818278901 0.839033534 0.912747815 0.831989245 0.86383491 0.8824724 1 14.79977693 2.674592278 0.172282271 1.050534805 0.605920576 0.51618553 0.063038702 5.113104982 0.425498451 0.313125631 0.671531848 472.7072666 -2.674592278 -0.444614229 RKHS(ph)PS(ph)PPPPTPTESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RKHSPSPPPPTPTESR 16 2 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 2 RKHS(1)PS(1)PPPPTPTESR;RKHS(1)PS(1)PPPPTPTESR;RKHS(1)PS(1)PPPPTPTESR 184.35 9.85E-10 478730000 717190 562890 629530 601750 666870 492070 697200 527830 919320 TRUE FALSE 672302.3581 604566.9613 644462.7489 617191.9238 614496.7202 634122.6209 592661.3325 593730.7374 765879.553 0.877817348 0.78937603 0.841467495 0.805860297 0.802341201 0.82796651 0.77383099 0.775227299 1 19.546758 -1.359249186 6.864270451 1.000007595 0.809970023 0.778987449 0.031502225 3.40E-06 3.17E-07 0.028304564 0.006671183 0.043727114 1.359249186 -0.190037572 RKLESTESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RKLESTESR 9 2 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;; 135.55 0.00012245 820990000 368114 541640 344698 387724 604990 310821 448465 516430 730960 FALSE TRUE 345074.4018 581743.5892 352874.3993 397673.6543 557476.5258 400549.9769 381221.8366 580907.4223 608958.0538 0.566663664 0.955309788 0.579472424 0.653039486 0.915459648 0.657762837 0.626023146 0.953936677 1 19.21598333 1.154562621 6.413678484 0.990912385 0.717839256 0.421601215 0.130950845 0.215960585 12.86358562 0.11901155 0.030032701 14.2745564 -1.154562621 -0.273073129 RKLS(ph)GDQPAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RKLSGDQPAAR 11 2 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 RKLS(1)GDQPAAR;RKLS(1)GDQPAAR;RKLS(1)GDQPAAR;RKLS(1)GDQPAAR 150.9 2.65E-05 1048520000 630428 804864 694893 774832 1091260 450500 741741 628979 1406370 TRUE FALSE 590970.6368 864456.968 711376.1901 794715.5009 1005556.842 580552.0367 630523.823 707508.4127 1171637.762 0.504397055 0.737819313 0.607163932 0.678294544 0.858248918 0.495504716 0.538155942 0.60386276 1 20.16009517 -1.182650806 5.074008858 1.000026261 0.631402269 0.528667962 0.110364116 3.22E-05 5.19E-06 0.105024169 0.024752673 0.065667305 1.182650806 -0.368623992 RKNS(ph)TGSGHSAQELPTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKNSTGSGHSAQELPTIR 18 2 O94763-3;O94763;O94763-2;O94763-4;I3L280 O94763-3 URI1 Unconventional prefoldin RPB5 interactor 1 1 RKNS(0.704)T(0.148)GS(0.148)GHSAQELPTIR 140.45 6.63E-08 102890000 37660 82845 76514 94533 99816 84818 64273 69200 119080 TRUE FALSE 35302.92783 88978.93 78328.94821 96958.87682 91976.854 109303.5797 54635.86033 77839.77233 99204.77871 0.355859146 0.896921813 0.789568297 0.977360951 0.927141365 1.101797525 0.550738191 0.784637326 1 16.598122 4.741265932 24.74979949 0.85826733 0.355858938 0.539418587 0.150750462 183.9274739 1682568.954 0.035746815 0.246577574 55114.50767 -4.741265932 -0.502408391 RKPDTIEVQQMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKPDTIEVQQMK 12 2 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 ; 155.99 4.09E-05 1253730000 2274710 1754840 1780600 1597610 2154510 1063720 2192660 1858870 3028860 FALSE TRUE 2132339.962 1884770.18 1822836.673 1638607.377 1985303.475 1370798.696 1863890.989 2090954.011 2523323.699 0.845052088 0.746939515 0.722395099 0.649384531 0.786781132 0.543251227 0.738665035 0.828650725 1 21.26689386 0.959205489 2.689053033 0.998682752 0.714434949 0.563568233 0.07984551 0.204222697 3.46317702 0.071134387 0.018980681 9.103439063 -0.959205489 -0.284247802 RKPEEES(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RKPEEESPR 9 2 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33 P49321 NASP Nuclear autoantigenic sperm protein 1 RKPEEES(1)PR;RKPEEES(1)PR;RKPEEES(1)PR;RKPEEES(1)PR;RKPEEES(1)PR 123.95 0.00042795 3346329000 8232800 4918210 6328420 5284530 5349150 6193000 8211080 5576590 4376270 TRUE FALSE 7717523.744 5282359.386 6478533.111 5420139.986 4929049.336 7980818.565 6979904.782 6272839.537 3645842.265 2.116801327 1.448872168 1.776964728 1.486663326 1.351964506 2.189019158 1.914483478 1.720546058 1 21.79782071 0.926548661 21.34849362 1 1.740021381 0.425740023 0.273843076 10345.08683 3006786.113 0.260311547 0.065077887 8.444008485 -0.926548661 0.74002138 RKPEEESPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKPEEESPR 9 2 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33 P49321 NASP Nuclear autoantigenic sperm protein 0 ; 123.79 0.00030809 196802000 212773 183052 195120 209399 183028 133262 209500 180180 188627 FALSE TRUE 199455.9177 196605.3605 199748.3385 214772.5329 168653.7192 171732.5761 178087.4199 202675.8696 157143.9351 1.269256224 1.251116439 1.271117071 1.366724924 1.073243578 1.092836169 1.133275807 1.289746686 1 17.26172707 2.730501657 24.9959412 1.124430581 1.280074696 0.541276489 0.078211303 488.2611099 1514403.949 0.023538932 0.022552709 537.6524839 -2.730501657 0.155644115 RKPGQADNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKPGQADNER 10 2 Q9NU22 Q9NU22 MDN1 Midasin 0 ; 149.33 1.32E-05 42119000 57040 71271 59104 62341 67907 45076 66414 66690 72974 FALSE TRUE 53469.96822 76547.979 60505.97479 63940.7756 62573.85814 58088.70945 56455.83726 75016.3933 60794.16797 0.879524632 1.25913359 0.995259526 1.05175838 1.029274028 0.955498058 0.928639031 1.23394062 1 15.89164531 3.726860759 24.99999769 1.016114844 1.105669798 0 0.122748846 28.23602925 2710171.887 0.029530861 0.049059209 5331.639278 -3.726860759 0.089554954 RKPNAGGS(ph)PAPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RKPNAGGSPAPVR 13 2 Q3KQU3-4;Q3KQU3;Q3KQU3-2 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 RKPNAGGS(1)PAPVR;RKPNAGGS(1)PAPVR;RKPNAGGS(1)PAPVR;RKPNAGGS(1)PAPVR;RKPNAGGS(1)PAPVR 141.99 3.16E-05 2576940000 1451230 1430220 1427020 1330630 1605280 1175340 1682570 1341440 1857090 TRUE FALSE 1360400.105 1536114.977 1460869.588 1364776.219 1479207.784 1514641.578 1430284.249 1508921.737 1547129.682 0.879305801 0.992880555 0.944245079 0.882134339 0.956098123 0.979001047 0.924475993 0.97530398 1 20.5611627 1.024331391 5.195406052 0.999897104 0.943228959 0.249664896 0.036653832 0.226138919 17.00351479 0.033210588 0.008389661 10.57624228 -1.024331391 -0.056668145 RKPQEESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RKPQEESER 9 2 P26358;P26358-2;K7EJL0;K7ENQ6;K7ERQ1;K7ELB1 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ;; 172.88 3.14E-05 216276000 214034 222514 203197 201265 259663 157222 238681 222247 309922 FALSE TRUE 200637.994 238989.1681 208016.9288 206429.8006 239270.1154 202609.4391 202892.9999 249995.0272 258194.016 0.777082277 0.92561854 0.805661308 0.799514272 0.926706665 0.784717796 0.785816042 0.968244853 1 17.97809604 1.141798704 5.83774336 0.995511688 0.834358923 0.578514744 0.055005569 0.151817896 7.180555265 0.05116804 0.012933567 13.86113215 -1.141798704 -0.161152766 RKPS(ph)PEPEGEVGPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RKPSPEPEGEVGPPK 15 2 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK 189.84 1.90E-07 9449310000 8589010 5259060 6155090 6167780 6206110 4133960 7697380 5291460 5333100 TRUE FALSE 8051439.196 5648446.274 6301091.641 6326055.677 5718707.155 5327367.143 6543229.328 5952110.429 4442971.157 1.812174536 1.271321842 1.418215743 1.423834514 1.287135782 1.199055082 1.472714789 1.339668933 1 22.08309334 -4.453508102 0.087589063 1.62E-21 1.703299692 0.477307928 0.151209814 201.9000613 1.378286128 41.17984952 3.855992248 3.52E-05 4.453508102 1.703299692 RKPS(ph)SEEGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKPSSEEGKR 10 3 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 RKPS(0.957)S(0.043)EEGKR 121.45 0.0028445 423460000 544890 334880 424310 450550 434330 271690 472420 364300 619200 TRUE FALSE 510786.3076 359674.8636 434374.8336 462111.8758 400219.4738 350122.4925 401585.0067 409783.6569 515851.5198 0.990180872 0.697244943 0.842053996 0.895823426 0.775842386 0.678727268 0.778489529 0.794382959 1 18.97659634 -1.345688741 3.121752727 1.001846486 0.79478093 0.302107639 0.090818148 28868503.82 37366875.99 490700.72 0.020068352 0.045113992 1.345688741 -0.207065556 RKPS(ph)VPDSASPADDSFVDPGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RKPSVPDSASPADDSFVDPGER 22 2 P16333-2;P16333;C9JAB9;C9K098;C9JVV5;H7C5C7;C9J869 P16333-2 NCK1 Cytoplasmic protein NCK1 1 RKPS(0.989)VPDS(0.005)AS(0.005)PADDSFVDPGER;RKPS(0.997)VPDS(0.003)ASPADDSFVDPGER;RKPS(1)VPDSASPADDSFVDPGER;RKPS(0.995)VPDS(0.001)AS(0.004)PADDSFVDPGER;RKPS(0.997)VPDS(0.002)AS(0.002)PADDSFVDPGER;RKPS(0.999)VPDS(0.001)ASPADDSFVDPGER;RKPS(1)VPDSASPADDSFVDPGER 276.27 9.56E-46 8010760000 5359800 4733660 5077570 5323920 6150860 3996460 5548780 4664020 7616790 TRUE FALSE 5024339.686 5084145.112 5198012.358 5460540.801 5667796.267 5150173.125 4716791.951 5246333.164 6345498.543 0.791795893 0.801220752 0.819165322 0.860537713 0.893199522 0.81162624 0.743328821 0.826780296 1 22.59730209 -2.46146979 2.024010728 2.590930183 0.81482278 0.67225033 0.039765233 3145428.223 181789.6241 23019518.03 0.010849677 0.003455654 2.46146979 -1.776107403 RKPSVPDSASPADDSFVDPGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKPSVPDSASPADDSFVDPGER 22 2 P16333-2;P16333;C9JAB9;C9K098;C9JVV5;H7C5C7;C9J869 P16333-2 NCK1 Cytoplasmic protein NCK1 0 77.959 0.0051869 120610000 34129 38965 34551 30527 34130 30711 39358 32758 40030 FALSE TRUE 31992.92681 41850.00914 35370.56604 31310.3745 31449.56747 39576.76715 33456.63328 36847.90841 33348.7344 0.959344557 1.254920461 1.060626938 0.938877444 0.943051304 1.186754696 1.003235472 1.104926741 1 15.02534439 3.602012707 5.184975436 1.032182815 1.136232282 0.072911397 0.10175496 0.358291786 14.13385277 0.025574587 0.040190078 3999.56452 -3.602012707 0.104049467 RKPVLPALTINPTIAEGPS(ph)PTSEGASEANLVDLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKPVLPALTINPTIAEGPSPTSEGASEANLVDLQK 35 2 P36507 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 RKPVLPALTINPTIAEGPS(0.702)PT(0.297)S(0.002)EGASEANLVDLQK;RKPVLPALTINPTIAEGPS(0.754)PT(0.123)S(0.123)EGASEANLVDLQK 385.77 4.87E-167 1913160000 625210 482339 557420 566070 647720 340408 606100 459215 863680 TRUE FALSE 586079.2221 518051.8814 570642.2656 580596.3146 596850.684 438678.2635 515220.9318 516549.0036 719526.2284 0.814534897 0.719990267 0.793080562 0.806914733 0.829505111 0.609676543 0.716055804 0.717901562 1 19.45668775 -0.990538633 4.655475484 1.000005047 0.747312919 0.588634695 0.065365416 11979110.49 40647899.9 1035.145964 0.01577756 0.102202464 0.990538633 -0.252692128 RKPYHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKPYHK 6 2 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 104.94 0.018784 608340000 651900 575610 552400 554110 680480 450830 794880 655150 931610 FALSE TRUE 611098.7427 618228.7633 565503.1889 568329.4007 627037.8457 580977.3024 675695.1233 736946.9197 776118.2726 0.787378373 0.796565144 0.72863017 0.732271641 0.807915324 0.748567999 0.870608446 0.949529145 1 19.565917 1.389867328 1.729502029 0.99617552 0.764496165 0.907359896 0.027683695 0.091962099 0.500660713 0.024303201 0.007561187 24.53959144 -1.389867328 -0.231679356 RKQEEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 182.39 0.00012869 459115000 525610 463281 473216 457406 531746 356134 554350 450554 637136 FALSE TRUE 492713.0083 497582.8073 484440.907 469143.8123 489984.8141 458944.1044 471230.3638 506806.6587 530793.8855 0.928256752 0.93743131 0.912672358 0.883853083 0.923116915 0.864637135 0.887784085 0.954808773 1 19.01779223 -1.836779353 6.733634324 1.007183375 0.909760504 0.515272914 0.026903696 0.003109473 7.54E-05 0.027918563 0.006169987 0.014561987 1.836779353 -0.09742287 RKQEELQQLEQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 232.37 4.84E-13 264640000 228140 246050 228650 253580 315680 179100 292130 257380 320900 FALSE TRUE 213861.1246 264267.798 234073.686 260087.2921 290887.7662 230803.2626 248327.8185 289514.4596 267339.7169 0.799960167 0.988509306 0.875566447 0.972871877 1.088082869 0.863333235 0.928884871 1.082945935 1 18.02831466 4.744763354 23.89587637 0.96124907 0.799960031 0.334177692 0.075463937 470.2127139 1811384.9 0.017126435 0.155860813 55560.14287 -4.744763354 -0.161289039 RKQQDTPGS(ph)PDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RKQQDTPGSPDHR 13 2 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;H0Y954 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 RKQQDT(0.022)PGS(0.978)PDHR;RKQQDT(0.026)PGS(0.974)PDHR;RKQQDT(0.019)PGS(0.981)PDHR 134.85 4.73E-05 221307000 203421 269648 262059 302247 379382 226908 284754 196832 356279 TRUE FALSE 190689.2427 289613.0185 268275.1632 310003.1697 349586.8681 292412.6561 242057.7812 221406.9085 296813.7332 0.642454244 0.975739954 0.903850237 1.044436746 1.177798831 0.985172259 0.815520827 0.745945634 1 18.17919832 -1.336756051 7.950633683 1.000000406 0.923620078 0.026993686 0.152172193 1.07E-06 8.96E-08 0.143958245 0.033931103 0.046051518 1.336756051 -0.076380328 RKRET(ph)DDEGEDD ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RKRETDDEGEDD 12 3 Q92688 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 1 RKRET(1)DDEGEDD;RKRET(1)DDEGEDD;RKRET(1)DDEGEDD;RKRET(1)DDEGEDD;RKRET(1)DDEGEDD;RKRET(1)DDEGEDD 115.63 0.0021779 14536570000 10407890 7617700 8126530 8327740 9396890 5919368 10477310 7596380 13655780 TRUE FALSE 9756478.744 8181722.434 8319295.129 8541443.907 8658896.165 7628193.449 8906334.632 8544804.765 11376542.1 0.857596153 0.719174804 0.731267468 0.750794383 0.761118457 0.670519511 0.78286834 0.751089803 1 23.43955878 0.095882397 1.309778462 1.000440195 0.745350683 0.722193303 0.047965005 4.990523205 6.662147685 0.046658733 0.01222175 1.247045781 -0.095882397 -0.255089512 RKS(ph)ELPQDVYTIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKSELPQDVYTIK 13 2 E9PFR3;Q14738;H0Y8C4;Q14738-2;Q14738-3 E9PFR3 PPP2R5D Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform 1 RKS(1)ELPQDVYTIK;RKS(1)ELPQDVYTIK 174.23 1.60E-05 661690000 992470 833120 765700 759460 1041220 411880 1441230 896000 1992760 TRUE FALSE 930353.0743 894805.0717 783862.7656 778949.0294 959446.7813 530783.0697 1225130.941 1007867.572 1660155.482 0.56040117 0.538988716 0.472162261 0.469202456 0.577925858 0.319718891 0.737961567 0.607092277 1 20.66288693 0.78171096 0.947315201 0.996344914 0.500803601 0.709108469 0.097705775 0.420493701 0.720045168 0.083321939 0.027638987 6.049381312 -0.78171096 -0.495541314 RKS(ph)HEAEVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 RKSHEAEVLK 10 2 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 RKS(1)HEAEVLK;RKS(1)HEAEVLK;RKS(1)HEAEVLK;RKS(1)HEAEVLK;RKS(1)HEAEVLK;RKS(1)HEAEVLK;RKS(1)HEAEVLK;RKS(1)HEAEVLK 166.86 2.83E-06 23085130000 14447680 10289090 10673690 11087560 14386340 7561210 14377990 11970640 20347630 TRUE FALSE 13543425.5 11050904.93 10926874.97 11372085.56 13256494.89 9744008.581 12222143.88 13465200.75 16951479.1 0.798952435 0.651913905 0.644597141 0.670860961 0.782025852 0.574817603 0.721007518 0.794337808 1 24.01490783 0.906027377 1.999889817 0.999010588 0.679809194 0.69073334 0.065546905 0.220284089 1.820575091 0.056793409 0.015808582 8.054292121 -0.906027377 -0.319201394 RKS(ph)ISGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 79.148 0.026312 359410000 353610 337040 300000 298110 432610 204690 438070 303170 861100 TRUE FALSE 331478.1813 361994.7923 307116.1417 305760.0073 398634.5557 263780.6801 372385.4703 341021.4419 717376.8471 0.462069807 0.504608971 0.428109916 0.426219509 0.555683609 0.367701692 0.519093238 0.475372802 1 19.45237166 -0.403932574 0.916816418 1.018442729 0.463685651 0.910617728 0.052478909 4.83056899 2.727196294 0.375324635 0.014477998 0.394518548 0.403932574 -0.554757078 RKS(ph)LS(ph)DSESDDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 RKS(1)LS(0.999)DS(0.001)ESDDSK 181.94 6.23E-06 256620000 674630 330260 438320 427330 401030 250250 449790 274210 523760 TRUE FALSE 632406.1125 354712.794 448717.1574 438296.0113 369534.7215 322493.1125 382348.1651 308445.7221 436341.0724 1.449338952 0.812925522 1.028363328 1.0044803 0.846894196 0.739084934 0.876259856 0.706891333 1 18.73509675 2.733095212 3.84977443 0.820110126 1.025073539 0.297414829 0.176393976 0.319114785 10.85418198 0.053426433 0.053173998 540.8728878 -2.733095212 0.204963413 RKS(ph)LSDS(ph)ESDDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 RKS(0.995)LS(0.242)DS(0.669)ES(0.093)DDS(0.001)K 86.258 0.043821 660040000 2355000 1085000 1554300 1426700 1301200 792870 1665700 934520 1749400 TRUE FALSE 2207604.754 1165334.529 1591168.73 1463311.537 1199009.001 1021758.698 1415943.749 1051196.879 1457413.838 1.514741178 0.799590685 1.091775505 1.004046688 0.822696319 0.701076572 0.971545426 0.721275489 1 20.47497916 4.744137467 24.94023491 0.89758086 1.51474145 0.698586378 0.129062554 339.5349279 1518387.622 0.029944494 0.263339786 55480.12955 -4.744137467 0.61716059 RKS(ph)LSDSES(ph)DDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 RKS(0.992)LS(0.051)DS(0.245)ES(0.394)DDS(0.317)K;RKS(0.75)LS(0.255)DS(0.282)ES(0.64)DDS(0.072)K 101.48 0.0094672 4901010000 15505130 6303490 9160770 8928370 9196860 5438950 10347710 6092130 11949320 TRUE FALSE 14534691.59 6770206.958 9378067.79 9157487.09 8474575.714 7009086.571 8796166.949 6852745.841 9954901.296 1.460053812 0.680087804 0.942055326 0.919897327 0.85129681 0.704083985 0.883601624 0.688379085 1 23.24697558 4.747027021 24.95572406 0.830319753 1.460054136 0.758138 0.111171368 485.1766592 1430083.229 0.024173414 0.281014606 55850.49433 -4.747027021 0.629734383 RKS(ph)LSDSESDDS(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 RKS(0.927)LS(0.073)DSES(0.003)DDS(0.997)K 262.68 1.04E-22 192520000 1890300 827990 1202500 1131300 1070900 633860 1274800 765770 1459900 TRUE FALSE 1771989.497 889295.2411 1231023.868 1160331.073 986795.8338 816845.0921 1083655.575 861378.0702 1216233.259 1.456948726 0.731188063 1.012160997 0.954036625 0.811354094 0.671618776 0.89099321 0.708234267 1 20.21398852 4.745350166 24.89349199 0.848174089 1.456949022 0.719428002 0.119619569 397.7411556 1458255.399 0.027237941 0.267822489 55635.26566 -4.745350166 0.608774933 RKS(ph)LSDSESDDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 RKS(0.965)LS(0.026)DS(0.008)ES(0.001)DDSK;RKS(0.985)LS(0.005)DS(0.01)ESDDSK;RKS(0.972)LS(0.014)DS(0.014)ES(0.001)DDSK;RKS(0.989)LS(0.005)DS(0.003)ES(0.003)DDSK;RKS(0.493)LS(0.493)DS(0.013)ESDDSK;RKS(0.764)LS(0.233)DS(0.003)ESDDSK;RKS(0.999)LS(0.001)DSESDDSK;RKS(0.998)LS(0.002)DSESDDSK;RKS(0.991)LS(0.008)DS(0.001)ESDDSK;RKS(0.943)LS(0.057)DSESDDSK;RKS(0.825)LS(0.003)DS(0.155)ES(0.017)DDSK 220.64 1.07E-11 16547617000 14183550 7873580 9976590 10299350 10436130 6021520 10443070 6662920 14321920 TRUE FALSE 13295826.92 8456548.056 10213239.43 10563648.76 9616518.447 7759835.073 8877228.602 7494800.229 11931499.03 1.11434673 0.708758224 0.855989629 0.885358054 0.80597739 0.650365478 0.744016203 0.62815244 1 23.50827197 2.468538651 22.0343291 0.731822917 0.853946869 0.13996791 0.141157584 83.79493909 215120.1473 0.044074906 0.036966375 294.1295446 -2.468538651 0.122123952 RKS(ph)LVGTPYWMAPELISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKSLVGTPYWMAPELISR 18 2 O96013;O96013-4;O96013-2;O96013-3;M0R1R1 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 RKS(0.849)LVGT(0.15)PYWMAPELISR;RKS(0.831)LVGT(0.169)PYWMAPELISR 173.27 4.55E-12 1745320000 624280 864880 651310 676480 1060370 374510 807660 670160 1705300 TRUE FALSE 585207.4292 928916.6151 666759.3808 693839.6221 977092.8175 482624.9573 686558.8809 753830.9512 1420674.413 0.41192227 0.653856089 0.469325959 0.488387498 0.687766886 0.339715386 0.483262649 0.530614857 1 20.43814453 0.923404925 18.18924869 1.000000001 0.51166924 0.696374063 0.102136616 804.6683584 191088.5804 0.092080215 0.02302124 8.383105361 -0.923404925 -0.488330761 RKS(ph)PENTEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 RKSPENTEGK 10 2 Q15651;A0A087WZE9;Q15651-2 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 RKS(0.992)PENT(0.008)EGK;RKS(0.994)PENT(0.006)EGK;RKS(0.998)PENT(0.002)EGK;RKS(0.992)PENT(0.008)EGK;RKS(0.901)PENT(0.099)EGK;RKS(0.999)PENT(0.001)EGK;RKS(1)PENTEGK;RKS(1)PENTEGK 210.07 6.60E-08 13557040000 11341990 5997870 7605850 7228130 7419390 5233100 9088320 5804680 9543920 TRUE FALSE 10632115.09 6441958.536 7786264.354 7413616.053 6836701.038 6743811.018 7725610.788 6529407.076 7950978.096 1.33720845 0.810209569 0.979283839 0.932415605 0.859856606 0.848173764 0.971655398 0.821208032 1 22.92270091 4.746163144 24.97845988 0.903539718 1.337208659 0.803630754 0.067476714 368.7309714 1211453.99 0.014649428 0.155841277 55739.50965 -4.746163144 0.433668941 RKS(ph)PENTEGKDGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RKSPENTEGKDGSK 14 3 Q15651;A0A087WZE9;Q15651-2 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 RKS(0.988)PENT(0.012)EGKDGSK;RKS(1)PENTEGKDGSK;RKS(0.793)PENT(0.207)EGKDGSK;RKS(1)PENTEGKDGSK;RKS(1)PENTEGKDGSK 133.93 0.00023041 1359330000 2011420 1187018 1346160 1562060 2107960 855713 1952630 1067419 5437010 TRUE FALSE 1885528.813 1274906.048 1378091.551 1602145.104 1942409.325 1102743.452 1659851.259 1200688.612 4529537.907 0.416273989 0.281464925 0.304245506 0.353710497 0.428831674 0.24345606 0.366450462 0.265079714 1 22.11093245 -1.731406757 2.635200814 1.131719976 0.327764502 0.92102254 0.061420588 14932622.51 11699361.25 12889637.62 0.013421564 0.018560653 1.731406757 -0.803955474 RKS(ph)PPKEYIDEEGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RKSPPKEYIDEEGVR 15 3 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3;Q9H0E3-2 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 RKS(1)PPKEYIDEEGVR;RKS(1)PPKEYIDEEGVR;RKS(1)PPKEYIDEEGVR 128.29 0.00040284 4185960000 3944070 2160760 2493960 2796490 3200350 1804720 3396900 2448410 3824480 TRUE FALSE 3697217.699 2320744.919 2553117.909 2868252.668 2949007.421 2325713.367 2887566.38 2754099.378 3186149.581 1.160403052 0.728385426 0.801317654 0.900225365 0.925570927 0.729944815 0.906287137 0.864397389 1 21.60338257 0.510574245 1.409682517 0.999852677 0.853354097 0.062723757 0.123773173 4.899866645 11.75706138 0.108597981 0.031810298 3.240218112 -0.510574245 -0.14649858 RKS(ph)QEALHEQSSYILSSAETPARPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKSQEALHEQSSYILSSAETPARPR 25 3 Q9NVE5;Q9NVE5-3 Q9NVE5 USP40 Ubiquitin carboxyl-terminal hydrolase 40 1 RKS(1)QEALHEQSSYILSSAETPARPR;RKS(1)QEALHEQSSYILSSAETPARPR 176.25 4.80E-13 636200000 265330 167778 184986 179819 205100 145105 277770 170108 242350 TRUE FALSE 248723.4689 180200.4577 189373.9553 184433.46 188992.2733 186994.4579 236120.9672 191346.3583 201900.2194 1.231912822 0.892522347 0.937958145 0.91348816 0.936067697 0.926172634 1.169493366 0.947727342 1 17.62328295 RKS(ph)QMEEVQDELIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKSQMEEVQDELIHR 15 2 A0A2R8Y4W2;A0A2R8YE63;Q12929-2;Q12929 A0A2R8Y4W2 EPS8 Epidermal growth factor receptor kinase substrate 8 1 RKS(1)QMEEVQDELIHR 56.488 0.06778 205600000 228240 192370 200160 210660 226870 175920 198880 150050 214380 TRUE FALSE 213954.8658 206613.275 204907.8897 216065.8922 209052.5453 226705.2482 169059.7903 168784.0728 178598.5931 1.197965013 1.156858357 1.147309652 1.209784963 1.170516194 1.269356294 0.946590829 0.945047046 1 17.44636119 1.679843872 6.960108966 0.959478902 1.182238899 0.886867146 0.03819143 0.039187398 3.770988425 0.018759736 0.009628958 47.8458057 -1.679843872 0.222759997 RKS(ph)QVNGEAGSYEMTNQHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RKSQVNGEAGSYEMTNQHVK 20 2 Q05D32-2;Q05D32;H0YMH7 Q05D32-2 CTDSPL2 CTD small phosphatase-like protein 2 1 RKS(1)QVNGEAGSYEMTNQHVK;RKS(1)QVNGEAGSYEMTNQHVK;RKS(1)QVNGEAGSYEMTNQHVK;RKS(1)QVNGEAGSYEMTNQHVK;RKS(1)QVNGEAGSYEMTNQHVK 267.27 3.95E-37 1752740000 941170 918830 841080 887454 1161630 366709 1301860 742851 1574980 TRUE FALSE 882263.8497 986861.1292 861030.8148 910227.5721 1070400.266 472571.9353 1106658.179 835597.5826 1312105.663 0.67240305 0.752120166 0.656220637 0.693715146 0.815788161 0.360163018 0.84342154 0.636837113 1 20.32345247 -1.514142377 2.995825748 1.010985138 0.685425849 0.369806117 0.131509666 38381322.66 43070035.84 3447731.404 0.029475494 0.030609598 1.514142377 -0.325559289 RKS(ph)TDSVPISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.871)T(0.128)DS(0.001)VPISK;RKS(0.939)T(0.058)DS(0.002)VPISK;RKS(0.787)T(0.211)DS(0.002)VPISK;RKS(0.977)T(0.023)DSVPISK;RKS(0.983)T(0.017)DSVPISK;RKS(0.935)T(0.032)DS(0.032)VPISK 182.57 4.51E-06 22307380000 31350100 21004790 25150470 24095820 28751010 18203550 32126030 24245200 31239880 TRUE FALSE 29387953.2 22560006.51 25747051.03 24714159.54 26493021.65 23458619.38 27309030.04 27272266.59 26025742.21 1.1291879 0.866834318 0.98929171 0.949604408 1.01795451 0.901362166 1.049308405 1.047895824 1 24.63343597 1.64198557 10.52651781 1.036349893 0.965544598 0.110989521 0.071387762 0.176878855 37.696976 0.030969009 0.016566455 43.85161268 -1.64198557 -0.070805295 RKS(ph)TITALLFGEDDLEALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKSTITALLFGEDDLEALK 19 2 Q96HU1;Q96HU1-2 Q96HU1 SGSM3 Small G protein signaling modulator 3 1 RKS(0.341)T(0.341)IT(0.318)ALLFGEDDLEALK 96.317 0.0010204 66817000 151540 130470 123830 126580 137240 84304 166400 114700 172750 TRUE FALSE 142055.3819 140130.1346 126767.3061 129828.2571 126461.724 108641.1962 141449.8648 129020.5475 143916.909 0.987065265 0.973687773 0.880836776 0.902105653 0.878713453 0.754888338 0.982857857 0.89649332 1 17.13487658 0.372411387 1.405398112 0.999893163 0.907213032 0.154001784 0.067897646 8.115071477 16.10677837 0.063754344 0.018590362 2.357281168 -0.372411387 -0.092680131 RKS(ph)VEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKSVEDR 7 2 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 RKS(1)VEDR 73.067 0.039298 98966000 259560 202330 252890 236710 261000 187870 255560 236310 218920 TRUE FALSE 243314.6029 217310.7237 258888.6702 242784.3793 240502.1128 242105.0192 217241.1505 265813.8237 182380.8377 1.334101795 1.191521689 1.419494907 1.331194562 1.318680821 1.327469608 1.191140216 1.457465746 1 17.47659463 -1.192220879 4.361371736 0.999906988 1.310144115 0.589287858 0.083854773 3.700410722 22899628.37 3961.662079 0.018441201 0.064236093 1.192220879 0.310237127 RKSLS(ph)DSES(ph)DDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 RKS(0.198)LS(0.814)DS(0.28)ES(0.589)DDS(0.119)K 182.35 0.00029607 159660000 1003200 437550 618600 582600 558290 330280 668690 374160 736970 TRUE FALSE 940411.5028 469946.6573 633273.4841 597550.5023 514444.1554 425626.4744 568426.1423 420874.6996 613964.946 1.531702272 0.765429135 1.031448926 0.973264852 0.837904768 0.693242305 0.925828333 0.685502816 1 19.22779676 4.744006144 24.98913295 0.86849036 1.531702555 0.747374519 0.121960405 290.7135465 1334023.128 0.027592048 0.239775706 55463.35596 -4.744006144 0.663212195 RKSNTQGPAYS(ph)HLTEFAPPPTPMVDHLVASNPFEDDFGAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKSNTQGPAYSHLTEFAPPPTPMVDHLVASNPFEDDFGAPK 41 2 Q9BRQ0;Q5T171 Q9BRQ0 PYGO2 Pygopus homolog 2 1 RKS(0.202)NT(0.202)QGPAY(0.187)S(0.407)HLT(0.001)EFAPPPTPMVDHLVASNPFEDDFGAPK 246.55 3.28E-55 151400000 231750 183320 173010 215400 296880 131920 218040 163300 223350 TRUE FALSE 217245.1812 196893.2035 177113.8789 220927.5287 273564.2424 170003.1625 185346.9262 183688.3645 186071.4421 1.167536397 1.058159174 0.951859549 1.187326363 1.470210792 0.913644569 0.996106249 0.987192674 1 17.50549712 RKST(ph)DSVPISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.344)T(0.65)DS(0.006)VPISK;RKS(0.365)T(0.633)DS(0.002)VPISK 132.76 0.0083734 3227200000 6189200 4173000 4526400 4769300 6270000 3553600 6457800 4793900 6752100 TRUE FALSE 5801829.02 4481973.262 4633768.346 4891688.312 5777579.492 4579466.632 5489512.841 5392428.968 5625130.89 1.03141227 0.796776706 0.823761871 0.869613242 1.027101343 0.814108458 0.975890686 0.958631732 1 22.42345524 1.752522477 0.657958216 0.997947788 0.862202094 0.122007565 0.084425891 1.042133223 0.925149815 0.074912381 0.039327951 56.56170302 -1.752522477 -0.135745693 RKT(ph)DTVVESSVSGDHSGTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RKTDTVVESSVSGDHSGTLR 20 2 Q9NXL2-1;Q9NXL2 Q9NXL2-1 ARHGEF38 Rho guanine nucleotide exchange factor 38 1 RKT(0.994)DT(0.006)VVESSVSGDHSGTLR;RKT(0.993)DT(0.007)VVESSVSGDHSGTLR;RKT(0.994)DT(0.006)VVESSVSGDHSGTLR;RKT(0.999)DT(0.001)VVESSVSGDHSGTLR;RKT(0.962)DT(0.038)VVESSVSGDHSGTLR;RKT(0.993)DT(0.007)VVESSVSGDHSGTLR 309 1.53E-64 3237740000 821921 985808 1026800 1060005 1088940 834443 1194455 1001631 1221156 TRUE FALSE 770478.4318 1058798.25 1051156.181 1087206.523 1003419.045 1075333.148 1015357.562 1126686.835 1017337.175 0.757348155 1.040754507 1.033242672 1.068678654 0.986319059 1.057007622 0.998054123 1.107486154 1 19.95636648 4.739276281 24.95971545 1.035044412 0.757348067 0.85364802 0.036313229 18.21187488 635039.2455 0.007427843 0.044459696 54862.58684 -4.739276281 -0.277696345 RKT(ph)SDANETEDHLESLICK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RKTSDANETEDHLESLICK 19 2 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RKT(0.71)S(0.29)DANETEDHLESLICK;RKT(0.492)S(0.492)DANET(0.016)EDHLESLICK;RKT(0.497)S(0.497)DANET(0.007)EDHLESLICK 121.47 0.0016724 847130000 758990 707510 633510 1152860 1170580 347034 509470 253420 724060 TRUE FALSE 711486.1707 759894.7766 648537.1564 1182444.339 1078647.369 447217.0822 433079.7032 285060.0448 603209.7084 1.17950053 1.259752232 1.075143764 1.960254159 1.788179722 0.741395697 0.717958775 0.472572044 1 19.20230012 2.176894261 10.33736735 0.709978005 1.397632665 0.59205166 0.294595627 0.351621138 56.80000107 0.117027757 0.086464481 150.2776035 -2.176894261 0.68765466 RKT(ph)SQSEEEEAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RKTSQSEEEEAPR 13 2 Q7RTP6;A0A5F9ZHV5;Q7RTP6-2;Q7RTP6-4;Q7RTP6-3;J3KSK6;Q7RTP6-5 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 RKT(0.465)S(0.465)QS(0.07)EEEEAPR;RKT(0.982)S(0.017)QS(0.001)EEEEAPR;RKT(0.694)S(0.306)QSEEEEAPR 153.18 5.06E-06 366760000 271146 349956 328430 406890 444930 328023 306856 239106 336793 TRUE FALSE 254175.4559 375867.1064 336220.5147 417331.4863 409986.9926 422717.9151 260845.7915 268958.9104 280580.0725 0.905892758 1.339607275 1.198305039 1.48738819 1.461212084 1.506585665 0.929666135 0.958581656 1 18.09805302 1.666828249 7.543948764 0.958171517 1.31690426 0.47667933 0.174245962 0.10667853 11.2128233 0.084992386 0.04394592 46.43316094 -1.666828249 0.358732743 RKTS(ph)DANETEDHLESLICK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKTSDANETEDHLESLICK 19 2 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RKT(0.326)S(0.666)DANET(0.008)EDHLESLICK 217.29 1.90E-19 203310000 292810 290290 256700 469590 517340 166490 233080 126100 331720 TRUE FALSE 274483.5448 311783.3736 262789.0452 481640.4744 476710.2032 214552.9603 198131.8178 141843.8626 276353.789 0.993232428 1.128203723 0.950915297 1.742840133 1.7249997 0.776370612 0.716949887 0.513269107 1 18.07615687 2.071072687 13.13261313 0.720627761 1.254535498 0.470497306 0.290069827 0.881418269 160.8867334 0.114893 0.084852461 117.7803083 -2.071072687 0.533907738 RKVDEGAGDSAAVASGGAQTLALAGS(ph)PAPSGHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKVDEGAGDSAAVASGGAQTLALAGSPAPSGHPK 34 2 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 1 RKVDEGAGDSAAVASGGAQTLALAGS(0.991)PAPS(0.009)GHPK 107.29 6.76E-06 127590000 51156 43860 53489 52649 59764 41625 71648 48666 85158 TRUE FALSE 47954.23728 47107.44004 54757.78434 54000.06247 55070.37652 53641.46177 60905.04755 54742.05723 70944.57966 0.675939409 0.664003371 0.771838872 0.761158396 0.776245018 0.756103737 0.858487679 0.77161719 1 16.11440484 -5 0.062275351 1.924326216 0.378666724 0.870490424 0.033906972 114.0190334 0.517284804 15.73810504 2.45974274 1.00E-05 5 -1.545659492 RKVDWLTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKVDWLTEK 9 2 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3QL52;Q14240;Q14240-2;E7EQG2;P38919;I3L3H2;J3KTN0 P60842;Q14240;P38919;J3KTN0 EIF4A1;EIF4A2;EIF4A3 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed;Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ; 173.32 3.12E-05 2829400000 2352000 3418500 1704810 2019390 4042900 986540 2292100 3707200 4862600 FALSE TRUE 2204792.518 3671609.297 1745248.898 2071210.966 3725386.942 1271338.083 1948420.884 4170052.081 4051000.646 0.544258743 0.906346263 0.43081921 0.511283791 0.919621414 0.313833098 0.480972741 1.029388155 1 21.94984688 1.230460531 24.99897012 1.014694434 0.592375502 0.462315104 0.191800653 180.8010606 557977.094 0.169622914 0.04535617 17.00045447 -1.230460531 -0.422318932 RKVMDS(ph)DEDDDY ddPTM_SK-BR-3_Pertuzumab_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 106.36 0.001334 3695950000 4180190 3513530 3483710 3679490 4317210 2859530 5191850 3223310 5536640 TRUE FALSE 3918559.37 3773675.417 3566345.246 3773911.943 3978153.741 3685029.89 4413380.291 3625747.349 4612539.016 0.849544981 0.818134091 0.773184841 0.81818537 0.86246506 0.798915712 0.956822322 0.786063237 1 22.13712968 0.165260367 0.331430704 1.034265527 0.801503699 0.488342215 0.052603027 3.266516352 0.583478559 0.222451861 0.050938366 1.463054039 -0.165260367 -0.232761828 RKVMDSDEDDDY(ph) ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RKVMDSDEDDDY 12 2 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 RKVMDS(0.003)DEDDDY(0.997);RKVMDSDEDDDY(1) 117.7 0.00069581 1336710000 3402360 3049640 2893460 3173340 3691100 2440800 4320250 2845190 4996550 TRUE FALSE 3189412.361 3275438.519 2962094.238 3254773.277 3401215.895 3145419.337 3672468.62 3200418.235 4162593.526 0.766207976 0.786874457 0.711598243 0.781909945 0.817090565 0.755639319 0.88225492 0.76885197 1 21.98905126 -0.829674838 0.275677173 1.119104433 0.745592176 0.732024891 0.04187821 6.17080061 0.45573844 0.648831301 0.054227013 0.148021623 0.829674838 -0.373512257 RKYQEDS(ph)DPERS(ph)DYEEQQLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RKYQEDSDPERSDYEEQQLQK 21 3 Q6P6C2-3;Q6P6C2;Q6P6C2-1 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 2 RKYQEDS(1)DPERS(0.919)DY(0.081)EEQQLQK 127.63 2.80E-05 104310000 122020 71900 86600 81385 111190 64286 138300 85704 165810 TRUE FALSE 114382.986 77223.55081 88654.1929 83473.47688 102457.5859 82844.3246 117563.1989 96404.33306 138135.2398 0.828050729 0.559043086 0.641792732 0.604288066 0.741719391 0.599733455 0.851073188 0.697898184 1 17.07572189 0.722288456 0.546702095 1.006687607 0.637799221 0.521071845 0.094518026 0.896075381 0.566092894 0.104685127 0.041045183 5.275801611 -0.722288456 -0.368888386 RLAAAEETAVS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RLAAAEETAVSPR 13 1 Q9BUH6 Q9BUH6 C9orf142 Protein PAXX 1 RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR;RLAAAEET(0.005)AVS(0.995)PR;RLAAAEETAVS(1)PR 170 1.69E-05 9219830000 4100504 4644150 4540380 4917660 5165020 4125260 4796810 4215200 4321910 TRUE FALSE 3843860.774 4988007.698 4648079.958 5043855.481 4759380.164 5316155.594 4077572.872 4741476.999 3600555.3 1.06757443 1.385344004 1.290934195 1.400854885 1.321846151 1.47648214 1.132484445 1.316873816 1 21.77978799 0.512631192 0.898800484 1.000624177 1.319768417 0.365868441 0.121934087 1.593548311 1.943177947 0.108795967 0.035163735 3.255601143 -0.512631192 0.319144241 RLAEDEAFQR ddPTM_SK-BR-3_Pertuzumab_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 ; 154.15 3.08E-05 255950000 229369 420800 375290 379430 461780 356930 405760 419830 483310 FALSE TRUE 215013.2037 451956.4698 384192.056 389166.8162 425513.6615 459969.8967 344920.0549 472246.6997 402642.4387 0.534005319 1.12247599 0.954176756 0.966532036 1.056802812 1.142378082 0.856641083 1.172868665 1 18.61913972 4.7457142 24.87035337 1.02357686 0.534005072 0.725415219 0.096482988 406.3052342 1412534.853 0.021180623 0.214531143 55681.91975 -4.7457142 -0.489571789 RLAPEYEAAATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RLAPEYEAAATR 12 1 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;; 166.86 8.14E-05 1020897000 478260 780090 571931 652096 827030 511814 642660 588096 684030 FALSE TRUE 448326.5603 837848.6753 585497.4734 668829.8874 762078.3999 659566.3932 546299.0992 661521.0802 569860.974 0.786729713 1.470268563 1.027439148 1.173672032 1.337305825 1.157416323 0.958653293 1.160846435 1 19.12025047 1.917409249 7.618177056 1.039652777 1.189313079 0.07060189 0.186251053 0.601238589 49.35432262 0.072688531 0.045389716 82.68167173 -1.917409249 0.149660302 RLAVPTEVSTEVPEMDT(ph)ST ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLAVPTEVSTEVPEMDTST 19 1 O00488 O00488 ZNF593 Zinc finger protein 593 1 RLAVPTEVSTEVPEMDT(0.333)S(0.333)T(0.333);RLAVPTEVSTEVPEMDT(0.333)S(0.333)T(0.333) 93.754 0.0031852 106970000 176282 132189 144870 138787 154226 130322 181863 136796 150338 TRUE FALSE 165248.8243 141976.4111 148306.3848 142348.5094 142113.7121 167943.8458 154594.3315 153875.2817 125245.6166 1.319398066 1.133583873 1.184124354 1.136554821 1.134680127 1.340915957 1.234329278 1.228588161 1 16.93440059 -1.034314264 4.895594595 0.999996121 1.207168907 0.457334779 0.072928358 3.07E-06 6.05E-07 0.070130351 0.016529573 0.092402929 1.034314264 0.207172786 RLAVPTEVSTEVPEMDTS(ph)T ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RLAVPTEVSTEVPEMDTST 19 1 O00488 O00488 ZNF593 Zinc finger protein 593 1 RLAVPTEVSTEVPEMDT(0.069)S(0.465)T(0.465);RLAVPTEVSTEVPEMDT(0.153)S(0.507)T(0.339);RLAVPTEVSTEVPEMDT(0.089)S(0.747)T(0.164) 166.67 2.06E-11 428158000 802370 584370 656500 605190 649890 628110 773250 587660 641110 TRUE FALSE 752151.094 627637.3628 672072.49 620720.2 598850.2609 809435.1605 657308.341 661030.6446 534104.5993 1.408246802 1.175120686 1.258316238 1.162169734 1.121222812 1.515499327 1.230673433 1.237642674 1 19.02676278 0.662091542 2.872399817 1.000024748 1.259038456 0.333264502 0.117485632 4.189605195 34.20993825 0.105358014 0.027671616 4.592948147 -0.662091542 0.259013708 RLAVPTEVSTEVPEMDTST(ph) ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLAVPTEVSTEVPEMDTST 19 1 O00488 O00488 ZNF593 Zinc finger protein 593 1 RLAVPTEVSTEVPEMDT(0.299)S(0.073)T(0.628) 157.74 5.73E-09 128220000 134280 135520 139020 138950 150960 129670 163960 128660 150140 TRUE FALSE 125875.6545 145554.0418 142317.62 142515.6922 139104.2105 167103.624 139375.7201 144723.4842 125080.6641 1.006355822 1.163681396 1.13780672 1.139390275 1.112116022 1.335966876 1.114286698 1.157041221 1 16.93249926 4.740728898 24.01605819 1.154788942 1.006355735 0.211611254 0.082230121 156.8805612 1737406.292 0.017371641 0.115607414 55046.39695 -4.740728898 -0.148433207 RLDECEEAFQGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RLDECEEAFQGTK 13 1 K7ESG5;K9J957;P61289;P61289-2;B3KQ25;P61289-3;K7ENH2;K7EMD0;K7EPX6;K7EKR3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 ;;; 202.92 1.44E-07 1395660000 1974870 1862660 1969020 1921900 2133620 1841390 2396700 1820020 2516620 FALSE TRUE 1851266.412 2000573.284 2015726.084 1971219.208 1966054.092 2372969.401 2037337.085 2047253.503 2096579.864 0.882993509 0.954208003 0.961435392 0.940207068 0.937743477 1.131828766 0.971743133 0.97647294 1 20.99960636 RLDEEEEDNEGGEWER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLDEEEEDNEGGEWER 16 1 Q99613-2;Q99613 Q99613-2 EIF3C Eukaryotic translation initiation factor 3 subunit C 0 ; 258.92 1.61E-26 1392700000 385020 445470 409760 440530 421920 401870 472450 409770 475250 FALSE TRUE 360922.2855 478453.0623 419479.7007 451834.7456 388784.1051 517883.3452 401610.5085 460930.6865 395927.7048 0.911586335 1.20843542 1.059485597 1.141205175 0.981957313 1.308025023 1.014353135 1.164178917 1 18.5948775 -1.990962264 2.363038116 0.899719581 1.105347963 0.064837955 0.115279406 15616611.38 6304533.9 8534567.911 0.024938762 0.010210282 1.990962264 0.205628382 RLDEELEDAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RLDEELEDAEK 11 1 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ;; 173.19 2.00E-05 774780000 1603180 1296270 1329120 1318620 1410870 1001330 1702780 1187270 1642070 FALSE TRUE 1502839.826 1392247.18 1360647.354 1352458.022 1300065.961 1290397.716 1447463.947 1335503.273 1367997.909 1.098568803 1.017726102 0.994626779 0.988640416 0.950342068 0.943274626 1.058089298 0.976246575 1 20.38363459 5.255370726 1.167251583 0.989953204 1.315599651 0.555419877 0.031215784 3.798032683 1.889157752 0.009119613 2.017985812 180040.7138 -5.255370726 0.325646447 RLDEVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RLDEVSR 7 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;; 127.02 0.0062459 879540000 2956170 2468080 3358110 3158050 2465640 2654800 3646070 2279790 2540830 FALSE TRUE 2771148.597 2650819.211 3437765.955 3239090.91 2271998.58 3421197.663 3099375.652 2564426.8 2116749.059 1.309153102 1.252306786 1.624078178 1.530219606 1.073343376 1.616250943 1.464214967 1.211493063 1 21.01341882 1.007597508 3.819324439 1.001661913 1.419591456 0.392272143 0.168494343 0.186184837 7.01896897 0.154994751 0.039849366 10.17647824 -1.007597508 0.417929543 RLDGESSELQEQMVEQQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLDGESSELQEQMVEQQQR 19 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ; 216.35 6.17E-19 346980000 129167 155197 141979 155218 174652 121432 151321 144886 190105 FALSE TRUE 121082.668 166687.9474 145346.8089 159201.1567 160935.5364 156487.4471 128631.8208 162975.336 158375.2474 0.764530254 1.052487369 0.917736902 1.005214889 1.016165967 0.988080206 0.812196495 1.029045503 1 17.27298735 4.754897139 24.25656788 0.966322346 0.764530019 0.477320292 0.069184568 2103.919166 3123834.144 0.016867643 0.436095584 56871.82157 -4.754897139 -0.201792327 RLDIDEKPLVVQLNWNKDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLDIDEKPLVVQLNWNKDDR 20 3 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;E9PFY5;F8W9I4;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 0 202.95 4.86E-22 110260000 155490 151330 158460 157970 185040 119150 176980 131890 205090 FALSE TRUE 145758.1585 162534.6307 162218.746 162023.7776 170507.7048 153546.6708 150443.492 148356.7568 170859.1541 0.853089548 0.951278447 0.949429645 0.948288539 0.997943047 0.898673949 0.880511746 0.868298556 1 17.38244802 -0.192313665 8.358484388 1 0.923338516 0.240605769 0.04479151 0 0 0.044306228 0.010443078 0.64222371 0.192313665 -0.076661484 RLDINEGAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLDINEGAAR 10 1 Q9BUP0;H7C0I0 Q9BUP0 EFHD1 EF-hand domain-containing protein D1 0 118.77 0.001253 183060000 104460 128320 78572 87734 139260 76919 86379 99877 85224 FALSE TRUE 97922.03507 137820.9463 80435.76494 89985.40297 128323.0813 99124.26662 73427.27085 112346.8633 70999.56383 1.379192065 1.941152014 1.132905057 1.267407828 1.807378446 1.396125008 1.034193267 1.582359908 1 16.11552254 4.331521523 0.04788455 8.46E-10 3.104896746 0.210290982 0.277063395 321.1713774 2.755735283 64.79706345 118.8684826 21454.65442 -4.331521523 3.104896745 RLDINEGAARPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RLDINEGAARPR 12 2 Q9BUP0;H7C0I0 Q9BUP0 EFHD1 EF-hand domain-containing protein D1 0 ;;;;; 179.67 1.15E-05 2728290000 1247390 1516040 1383130 1432160 1678760 1027840 1405060 1290770 1339230 FALSE TRUE 1169318.087 1628289.179 1415938.497 1468911.65 1546916.961 1324560.722 1194384.297 1451925.476 1115703.861 1.048054172 1.459427753 1.269098859 1.316578441 1.386494226 1.187197399 1.070520896 1.301353815 1 20.08952272 2.068777917 5.74231087 1.130923417 1.314781654 0.269707876 0.12878714 0.223664828 13.52056542 0.044600537 0.032446808 117.15961 -2.068777917 0.183858237 RLDLPIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RLDLPIER 8 1 P17812;B4E1E0;P17812-2;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6;A0A3B3ITB8;A0A3B3ISY3 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ;;;;; 156.83 0.00062006 2168010000 1172684 1450088 1369850 1342125 1551987 1298173 1493928 1304769 1539911 FALSE TRUE 1099287.802 1557454.024 1402343.489 1376566.2 1430100.201 1672934.471 1269927.365 1467672.282 1282889.906 0.856883975 1.214020016 1.093112887 1.073019745 1.11474897 1.304035883 0.989895828 1.144036035 1 20.29096594 -0.113068799 1.052203309 0.998935961 1.109569781 0.054435023 0.120166327 33.91784322 28.66275472 0.256033783 0.032290927 0.770781355 0.113068799 0.11063382 RLDPDAIPSPIQVIEDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RLDPDAIPSPIQVIEDDR 18 1 P53992;G5EA31 P53992 SEC24C Protein transport protein Sec24C 0 ;;; 168.79 3.18E-11 146424000 107049 105124 104614 115980 110554 101207 138804 108209 131296 FALSE TRUE 100348.9942 112907.4903 107095.4935 118956.2432 101871.5348 130423.8179 117991.6288 121719.1318 109381.8494 0.917419067 1.032232413 0.979097483 1.087531833 0.931338566 1.192371666 1.078713054 1.112790948 1 16.73901383 2.24601365 24.99998883 1.103185394 0.998380899 0.381734263 0.066506284 162.0466071 543559.5177 0.02055679 0.016885883 176.2031425 -2.24601365 -0.104804495 RLDPNKYPVPENWLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLDPNKYPVPENWLHK 16 2 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 111.59 0.00048325 921630000 1234100 1087400 1153800 1026900 1430500 802950 1530100 1155500 2044600 FALSE TRUE 1156859.884 1167912.227 1181168.681 1053251.993 1318154.3 1034748.63 1300675.71 1299766.719 1703343.051 0.679170225 0.685658844 0.693441453 0.618344022 0.77386308 0.607481053 0.763601735 0.763068084 1 20.69993759 0.651567378 0.965470911 1.000312125 0.680090663 0.804135735 0.049013465 0.423583219 0.666209635 0.040211215 0.013070183 4.482985952 -0.651567378 -0.320221462 RLDQELDFILSQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLDQELDFILSQQK 14 1 P37198;M0QXN5 P37198 NUP62 Nuclear pore glycoprotein p62 0 198.74 3.47E-08 86920000 232520 281340 227670 224820 322090 161530 250250 268880 351460 FALSE TRUE 217966.9883 302170.7063 233070.4399 230589.2618 296794.3506 208161.0888 212727.3357 302450.2599 292799.0555 0.744425175 1.032007108 0.796008169 0.787534172 1.013645178 0.710934974 0.72653013 1.03296187 1 18.15955137 1.217168819 24.99887712 1.016481199 0.839833669 0.324814353 0.111003306 355.7508501 415726.6478 0.106605777 0.026752193 16.4880319 -1.217168819 -0.17664753 RLDQLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLDQLER 7 1 Q96CT7;M0R2F5 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 170.24 0.0015748 198970000 128570 171670 151260 160470 178860 118790 150510 151510 173350 FALSE TRUE 120523.0332 184380.6254 154847.9586 164587.9319 164813.0571 153082.7446 127942.4228 170426.357 144416.7651 0.834550151 1.276725907 1.072229796 1.139673304 1.141232162 1.060006741 0.885925001 1.180100917 1 17.13987871 1.998171004 15.87105887 1.000241419 1.115877676 0.033900973 0.130617886 1.212083849 10475.29522 0.045743398 0.032782003 99.57974376 -1.998171004 0.115636256 RLDQVEQELNELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RLDQVEQELNELR 13 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ;;; 209.39 6.13E-08 243357000 158031 174390 177864 174715 178171 168823 197149 165128 159965 FALSE TRUE 148140.1218 187302.0171 182083.0181 179198.4827 164178.1684 217559.4595 167588.3377 185744.5943 133265.8081 1.111613879 1.405476917 1.366314591 1.344669614 1.231960176 1.63252272 1.257549405 1.393790327 1 17.02394715 -1.717150374 8.616839538 0.998709404 1.353232078 0.386195491 0.135344674 0.002942407 9.66E-05 0.114907558 0.027003079 0.019180045 1.717150374 0.354522673 RLDS(ph)SGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLDSSGER 8 1 A0A087X2H1;Q9ULT8;G3V4V5;A0A087WVU6 A0A087X2H1 HECTD1 E3 ubiquitin-protein ligase HECTD1 1 RLDS(0.953)S(0.047)GER;RLDS(0.989)S(0.011)GER 119.05 0.0010835 369850000 146096 176385 165492 177907 188023 158946 185136 170388 226027 TRUE FALSE 136952.1121 189444.7289 169417.5484 182472.3948 173256.432 204831.1299 157376.5755 191661.3169 188301.6335 0.727301774 1.006070555 0.899713642 0.96904308 0.920100526 1.087782013 0.835768509 1.01784203 1 17.52268599 4.746227153 24.72106281 0.956778853 0.727301645 0.529854015 0.070383029 625.3996234 2016571.25 0.014889385 0.159897564 55747.7255 -4.746227153 -0.229477209 RLDVFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLDVFEK 7 1 A0A087WW66;Q99460-2;Q99460;C9J9M4;H7BZR6 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 120.87 0.0072048 151730000 173620 171060 180230 184890 185630 143280 211830 158950 202030 FALSE TRUE 162753.4341 183725.4604 184505.1407 189634.5904 171051.3686 184642.61 180068.058 178795.2574 168309.8878 0.966986766 1.091590415 1.096222825 1.126699048 1.016288293 1.097039588 1.069860246 1.062298001 1 17.36076041 -1.985757412 7.502906092 0.943366104 1.072433128 0.156988255 0.045781774 0.035866416 6.81E-05 0.036657794 0.009440553 0.010333384 1.985757412 0.129067024 RLDVT(ph)VQSFGWSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLDVTVQSFGWSDR 14 1 Q52LJ0;Q52LJ0-1;Q8NCA5;E9PH82 Q52LJ0;Q8NCA5 FAM98B;FAM98A Protein FAM98B;Protein FAM98A 1 RLDVT(0.333)VQS(0.333)FGWS(0.333)DR 59.871 0.074278 255190000 90910 210790 157790 177110 175350 172100 175250 170710 127870 TRUE FALSE 85220.10538 226397.1109 161532.8533 181654.9424 161578.7183 221782.4762 148972.8894 192023.5193 106527.6709 0.799980931 2.125242286 1.516346428 1.705237154 1.516776974 2.081923638 1.398443129 1.802569394 1 16.7008687 -1.070918888 5.561400682 0.999995536 1.655703704 0.206442934 0.374658149 1.79E-05 2.99E-06 0.313158989 0.073811779 0.084933909 1.070918888 0.655708168 RLDVTVQSFGWSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLDVTVQSFGWSDR 14 1 Q52LJ0;Q52LJ0-1;Q8NCA5;E9PH82 Q52LJ0;Q8NCA5 FAM98B;FAM98A Protein FAM98B;Protein FAM98A 0 ; 156.57 8.87E-06 1190700000 492050 514660 529690 563450 567250 430390 561080 522040 577310 FALSE TRUE 461253.4688 552765.9619 542254.4969 577909.0809 522700.4732 554636.6062 476951.2628 587217.8432 480953.2314 0.95904017 1.149313334 1.127457851 1.201591014 1.086801042 1.153202786 0.99167909 1.220945832 1 18.87553709 RLEAAYLDLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLEAAYLDLQR 11 1 E5RJD8;O75347;E5RIW3;E5RHG6;O75347-2 E5RJD8 TBCA Tubulin-specific chaperone A 0 ; 114.79 0.0019413 205394000 166501 471080 176979 209048 514260 158746 225138 388510 429570 FALSE TRUE 156079.9996 505959.2534 181177.0255 214412.5256 473872.094 204573.3932 191380.647 437016.3287 357871.9919 0.436133599 1.413799528 0.506262098 0.599131898 1.324138532 0.571638457 0.534774029 1.221152643 1 18.44908411 3.946118018 24.86208302 0.780544583 0.990453937 0 0.37065549 945.9462138 758572.2638 0.088037652 0.158733816 8833.199065 -3.946118018 0.209909354 RLEAEQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLEAEQAR 8 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 140.83 0.0010313 62835000 25597 123780 22309 14313 115700 16159 10434 82187 91870 FALSE TRUE 23994.92946 132944.8 22838.18002 14680.29581 106613.3887 20823.84098 8869.518565 92448.22787 76536.3035 0.313510431 1.737016212 0.298396695 0.191808268 1.392978023 0.272077956 0.115886425 1.207900351 1 16.2238566 3.852491759 6.751904175 0.567477397 1.108960504 0.060003819 0.558915967 0.397434287 20.85425933 0.133237131 0.242231966 7120.192894 -3.852491759 0.541483107 RLEAGAMVLADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLEAGAMVLADR 12 1 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 94.532 0.0032738 0 56740 95767 78208 65619 90445 60068 69622 76368 97379 FALSE TRUE 53188.74468 102857.6883 80063.13069 67302.89463 83341.81454 77408.65648 59182.82744 85902.71291 81125.81581 0.655632787 1.267878631 0.986900777 0.829611314 1.02731558 0.954180315 0.729519042 1.058882577 1 16.30787346 3.472486765 23.98148085 0.912392571 1.044572717 0 0.178114558 165.2088119 854882.2047 0.045920776 0.062981498 2968.156288 -3.472486765 0.132180146 RLEDELGGQFLDLSLHDTVTTLILGGHNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLEDELGGQFLDLSLHDTVTTLILGGHNK 29 1 Q9H269-2;Q9H269 Q9H269-2 VPS16 Vacuolar protein sorting-associated protein 16 homolog 0 207.01 7.28E-26 67053000 57725 108890 86015 90187 107060 80440 110240 99656 91597 FALSE TRUE 54112.09529 116952.3289 88055.31642 92501.35111 98651.93946 103661.7222 93710.53542 112098.271 76308.86896 0.709119347 1.532617774 1.153932926 1.212196595 1.29279782 1.358449202 1.228042516 1.469007109 1 16.21956312 4.754013426 24.90363248 1.290615898 0.709118897 0.581952935 0.152096218 1860.79072 2998783.8 0.032464605 0.796351129 56756.21514 -4.754013426 -0.581497001 RLEDELGGQFLDLSLHDTVTTLILGGHNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLEDELGGQFLDLSLHDTVTTLILGGHNKR 30 2 Q9H269-2;Q9H269 Q9H269-2 VPS16 Vacuolar protein sorting-associated protein 16 homolog 0 119.18 1.54E-05 35419000 105770 250230 163950 146740 223350 123440 215050 187200 267010 FALSE TRUE 99150.0445 268757.2896 167838.9714 150505.5968 205808.992 159075.1241 182805.2489 210572.3321 222444.306 0.445729748 1.208200355 0.75452132 0.676599008 0.925215824 0.715123381 0.82180233 0.946629454 1 17.76308464 1.125969317 3.979346438 0.995935855 0.826134321 0.11480275 0.19451735 0.523364835 13.9925419 0.173654007 0.045042895 13.36501088 -1.125969317 -0.169801535 RLEDLSESIVNDFAYMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLEDLSESIVNDFAYMK 17 1 P49755 P49755 TMED10 Transmembrane emp24 domain-containing protein 10 0 130.56 4.79E-05 50294000 79099 120050 77241 87298 154240 67339 91170 104240 92973 FALSE TRUE 74148.33479 128938.6269 79073.193 89538.21448 142126.6126 86778.67614 77499.90488 117254.5935 77455.20567 0.957306021 1.664686393 1.02088933 1.155999958 1.834952362 1.120372419 1.000577098 1.513837481 1 16.24107458 -2.480973916 0.271978225 0.586875092 1.309077942 0.064650618 0.301077486 124.6047343 4.091343148 31.00977551 0.364749095 0.003303894 2.480973916 0.722202849 RLEEALMADMLAHVEELAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLEEALMADMLAHVEELAR 19 1 O95983-2;O95983;K7EIE8 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 0 ; 181.26 2.07E-14 130169000 169272 210507 196303 197348 227184 179852 209779 185883 233698 FALSE TRUE 158677.5677 226093.1573 200959.3999 202412.2838 209341.8851 231772.3527 178324.5864 209090.9017 194692.2941 0.815017196 1.161284572 1.032189799 1.039652261 1.075244843 1.190454681 0.915930378 1.073955714 1 17.57083626 1.707732136 25 0.993847362 1.062969466 0.051324385 0.106231776 1.871150237 1508.688759 0.044435241 0.024641582 51.01902278 -1.707732136 0.069122105 RLEEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLEEELR 7 1 Q07065 Q07065 CKAP4 Cytoskeleton-associated protein 4 0 99.305 0.017038 335730000 195600 267500 196410 220080 273030 164060 224240 207120 280250 FALSE TRUE 183357.7452 287305.9783 201068.938 225727.6254 251587.3252 211421.4587 190617.2937 232979.3879 233474.4645 0.785343894 1.23056703 0.861203123 0.96681933 1.077579622 0.905544249 0.816437438 0.997879526 1 17.83290524 2.156665096 12.39269709 0.903658854 1.00028664 0.016348863 0.129716307 1.394706836 205.2762168 0.045806115 0.033830818 143.4382891 -2.156665096 0.096627786 RLEELEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RLEELEAK 8 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ;; 117.31 0.0033725 876100000 662173 641454 644920 641380 725540 467705 718170 643721 776670 FALSE TRUE 620728.7739 688947.9216 660217.807 657838.8967 668559.0151 602723.8409 610487.0757 724090.9839 647038.7595 0.959337852 1.064770713 1.02036825 1.016691639 1.033259608 0.931511184 0.943509282 1.119084403 1 19.30349261 RLEEPEEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLEEPEEPK 9 1 O75822;O75822-2 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 ; 139.43 0.00017878 796090000 1873390 1355310 1488890 1499850 1614560 1138310 1776280 1344860 1845030 FALSE TRUE 1756137.864 1455658.563 1524207.174 1538338.69 1487758.97 1466921.618 1509943.304 1512768.731 1537082.574 1.142513678 0.947026912 0.991623482 1.000817208 0.967910896 0.954354466 0.982343649 0.984181824 1 20.55176324 4.744861204 24.99915461 0.976759367 1.142513751 0.892017082 0.017920881 213.9483689 848870.4655 0.004133505 0.038945485 55572.66243 -4.744861204 0.165754384 RLEEPSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RLEEPSLR 8 1 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;O00429-7;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 0 ;;; 155.84 0.00064533 1147030000 648550 751530 737990 701010 775330 674080 780890 657860 761150 FALSE TRUE 607958.4132 807174.0632 755495.4713 718999.1034 714438.7093 868675.9532 663802.7939 739995.2691 634109.1478 0.958759884 1.272926066 1.191428122 1.133872782 1.126680969 1.369915505 1.046827342 1.166984062 1 19.27437166 0.764409577 1.156949133 1.002526302 1.179299381 0.147043029 0.113213242 1.339099516 3.21935592 0.097077131 0.0301475 5.813123868 -0.764409577 0.176773079 RLEEQAAQHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RLEEQAAQHK 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 155.26 8.45E-06 1606560000 1266850 1466180 1204210 1271720 1601020 899300 1447710 1435990 1458240 FALSE TRUE 1187560.12 1574737.493 1232774.43 1304354.488 1475282.347 1158913.311 1230639.325 1615276.513 1214850.323 0.97753616 1.296239926 1.014754169 1.073675055 1.214373754 0.953955634 1.012996664 1.329609485 1 20.21234715 3.834876448 10.29105892 1.078862103 1.158947838 0.016814299 0.134699237 1.055555232 93.85765087 0.031869765 0.057507942 6837.171098 -3.834876448 0.080085734 RLEESDVLQEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLEESDVLQEAR 12 1 O43615;M0QXU7;M0R301;M0R124 O43615 TIMM44 Mitochondrial import inner membrane translocase subunit TIM44 0 ; 127.02 0.00044447 418940000 431920 493540 460990 428770 604320 420340 428040 461210 728990 FALSE TRUE 404886.8982 530082.2151 471924.9005 439772.9641 556859.1449 541685.3344 363859.3757 518793.0837 607316.8595 0.666681473 0.872826444 0.777065371 0.724124412 0.916916987 0.891931989 0.59912609 0.854237908 1 19.21208989 -2.309641596 1.752509815 1.74276818 0.78708769 0.299384372 0.101980485 2058176.042 259037.715 6031850.666 0.026556117 0.004901832 2.309641596 -0.95568049 RLEEWLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RLEEWLGR 8 1 P56192;P56192-2 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;; 203.35 0.00015448 1571998000 1101916 1433750 1271645 1297042 1397110 1155852 1454050 1260550 1611740 FALSE TRUE 1032949.045 1539906.342 1301809.02 1330326.294 1287386.616 1489527.709 1236028.701 1417932.442 1342730.182 0.769290107 1.146847194 0.969523913 0.990762189 0.95878281 1.109327644 0.920533938 1.056006979 1 20.356738 RLEIS(ph)PDS(ph)SPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLEISPDSSPER 12 1 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 2 RLEIS(0.999)PDS(0.763)S(0.238)PER;RLEIS(0.999)PDS(0.807)S(0.194)PER 120.77 0.00025945 302770000 642210 685630 601570 672270 774800 539700 675460 579000 748930 TRUE FALSE 602015.2225 736394.7586 615839.5245 689521.5864 713950.3334 695502.6287 574181.0437 651289.4245 623928.7447 0.964878165 1.18025458 0.987035026 1.105128738 1.144281842 1.114714837 0.920267015 1.043852251 1 19.25102175 1.750540473 25 0.983009048 1.08616011 0.27934176 0.071390425 3.887326395 8125.840135 0.03053454 0.016932974 56.30415863 -1.750540473 0.103151062 RLEIS(ph)PDSS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLEISPDSSPER 12 1 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 2 RLEIS(1)PDS(0.002)S(0.998)PER 173.19 2.25E-05 359600000 292370 376380 330830 353390 419670 284900 375500 317340 414710 TRUE FALSE 274071.0836 404247.5668 338677.4438 362458.5857 386710.8111 367146.005 319197.261 356960.5976 345492.2219 0.793277146 1.170062714 0.980275162 1.049107803 1.119303957 1.062675168 0.923891309 1.033194309 1 18.39829371 1.760407194 25 0.978844562 1.04398204 0.02361373 0.102890587 28.01435665 32084.10701 0.043152629 0.023931502 57.5979722 -1.760407194 0.065137479 RLEQTSVRDPS(ph)PEADAPVLGSPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLEQTSVRDPSPEADAPVLGSPEK 24 2 O15234 O15234 CASC3 Protein CASC3 1 RLEQT(0.005)S(0.022)VRDPS(0.973)PEADAPVLGSPEK;RLEQT(0.001)S(0.006)VRDPS(0.994)PEADAPVLGSPEK 193.6 2.29E-18 279320000 248402 193900 209056 189652 198521 189307 293376 187349 187883 TRUE FALSE 232854.9622 208256.5578 214014.907 194518.7914 182929.9615 243956.8578 249386.9924 210739.9351 156524.1135 1.487661913 1.330507824 1.36729672 1.242740093 1.168701469 1.558589614 1.593281615 1.346373605 1 17.25602541 2.225682627 24.99409023 1.446945191 1.323948965 0 0.183537522 543.4201142 1054683.354 0.063258964 0.047022809 168.1444849 -2.225682627 -0.122996226 RLFDANKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 72.321 0.026481 319740000 284700 516830 310240 321090 639250 221450 358360 401860 689050 FALSE TRUE 266881.1352 555096.631 317599.0393 329329.713 589045.8836 285379.0201 304627.2449 452033.1056 574043.1036 0.464914801 0.966994686 0.553266884 0.573702063 1.026135285 0.497138661 0.530669636 0.787454989 1 19.13079954 -1.958120301 3.930865748 1.219919329 0.678717643 0.214675557 0.195218806 0.120469493 0.00128349 0.060521512 0.041834111 0.011012342 1.958120301 -0.541201686 RLFDDEAS(ph)VDEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 118.24 0.00027151 403940000 324720 392960 358260 332640 435100 300640 391860 325340 507150 TRUE FALSE 304396.3548 422055.1673 366758.0964 341176.1056 400929.0011 387429.8875 333104.2308 365959.4152 422503.3887 0.720458967 0.998939129 0.868059538 0.807510933 0.94893677 0.916986462 0.788406057 0.866169183 1 18.68860339 RLGDKHAT(ph)LQKS(ph)T(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLGDKHATLQKSTK 14 3 Q13263;Q13263-2;M0R3C0 Q13263 TRIM28 Transcription intermediary factor 1-beta 3 RLGDKHAT(1)LQKS(1)T(1)K 68.809 0.042298 24761000 5627.7 5678 6189.7 6496.3 7242.8 5321.4 4841.9 4753.4 11397 TRUE FALSE 5275.472303 6098.405028 6336.522607 6663.006056 6673.979704 6857.601794 4115.902045 5346.872454 9494.767073 0.555618928 0.642291167 0.66736999 0.70175561 0.702911367 0.722250661 0.433491629 0.563138876 1 13.21291689 -2.010306752 3.00235827 1.403671956 0.624090005 0.646639389 0.087442538 2296886.344 13697606.14 6541048.965 0.022401761 0.009765472 2.010306752 -0.77958195 RLGDSS(ph)LSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RLGDSSLSR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 RLGDS(0.043)S(0.957)LSR;RLGDS(0.029)S(0.969)LS(0.001)R;RLGDS(0.033)S(0.885)LS(0.082)R 140.63 0.00011508 1063820000 857050 1128000 1057000 1079980 1559920 917790 1269450 1225340 1889840 TRUE FALSE 803408.7704 1211518.294 1082072.539 1107694.115 1437410.176 1182741.074 1079107.757 1378326.396 1574413.495 0.510290831 0.769504515 0.687286118 0.703559845 0.912981361 0.751226458 0.685403016 0.875453876 1 20.58638306 -5 0.056475918 1.980423186 0.291155442 0.569241261 0.090348009 371.6592889 1.540820586 52.1960599 9.66406716 1.00E-05 5 -1.689267744 RLGGLRPES(ph)PESLTSVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLGGLRPESPESLTSVSR 18 2 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 RLGGLRPES(0.999)PES(0.001)LTSVSR;RLGGLRPES(0.92)PES(0.078)LT(0.002)SVSR 185.62 4.11E-14 1075990000 144080 201001 176568 175212 250600 110798 196361 152308 527320 TRUE FALSE 135062.29 215883.3232 180756.2763 179708.2366 230918.8869 142783.5839 166918.491 171323.9891 439306.8854 0.307444054 0.491418028 0.411457872 0.409072206 0.525643678 0.325020137 0.379958741 0.389987034 1 18.74486959 -1.404840742 3.59339592 1.004278095 0.411132663 0.889265945 0.065953274 62488595.56 100671531.5 2801652.283 0.015064024 0.039369442 1.404840742 -0.593145432 RLGRPPKIT(ph)T(ph)T(ph)NENQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLGRPPKITTTNENQK 16 3 J3KNV1;O60281-2;O60281 J3KNV1 ZNF292 Zinc finger protein 292 3 RLGRPPKIT(1)T(1)T(1)NENQK 87.18 0.011106 27658000 57261 93319 74029 85853 111230 64737 87031 84211 110570 TRUE FALSE 53677.13622 100228.4359 75785.00284 88056.13333 102494.4445 83425.52098 73981.50951 94724.92872 92115.15269 0.582717769 1.088077617 0.822720265 0.955935378 1.112677355 0.905665556 0.803141583 1.028331669 1 16.49115087 4.752925227 24.4609551 0.947909683 0.582717427 0.574225578 0.102445499 1500.460098 2555017.598 0.02432824 0.517316468 56614.18079 -4.752925227 -0.365192256 RLGS(ph)VEAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLGSVEAPK 9 1 P46087-2;P46087;P46087-4;P46087-3;F5H359;F5GWB7;F5H709;F5H5X6 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 RLGS(1)VEAPK 61.038 0.056224 114960000 87606 73531 83602 80332 101270 67549 83873 68278 136460 TRUE FALSE 82122.89684 78975.31175 85585.07892 82393.45512 93316.6627 87049.29973 71297.02229 76802.6586 113683.9444 0.722379024 0.694691868 0.752833475 0.724758941 0.820842936 0.765713225 0.627151201 0.675580523 1 16.79466899 -0.945801307 8.562507689 1 0.721013315 0.735163748 0.052238243 7.92E-10 0 0.053130668 0.012523019 0.113291856 0.945801307 -0.278986686 RLGYDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLGYDTR 7 1 A0A2R8Y891;P08237;P08237-3 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 75.692 0.068596 102590000 228210 322520 252630 258930 317590 203190 256380 299080 357440 FALSE TRUE 213926.7435 346399.7164 258622.5029 265574.5822 292647.7625 261847.6545 217938.1991 336420.7964 297780.9548 0.718403041 1.163270218 0.868499139 0.891845425 0.982761851 0.879329756 0.731874203 1.129759277 1 18.18389196 3.728851772 24.99357083 0.902903706 0.985594405 0 0.149570187 250.6541615 3620086.811 0.036142512 0.061159211 5356.138169 -3.728851772 0.082690699 RLHPPS(ph)PVPQGVCPAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLHPPSPVPQGVCPAHR 17 1 Q96F44-3;Q96F44;Q96F44-2 Q96F44-3 TRIM11 E3 ubiquitin-protein ligase TRIM11 1 RLHPPS(1)PVPQGVCPAHR;RLHPPS(1)PVPQGVCPAHR 70.99 0.014795 329210000 168851 205090 209821 205074 227590 154129 227630 175643 232200 TRUE FALSE 158282.9173 220275.077 214798.0532 210336.546 209715.9995 198623.5402 193498.9947 197572.4152 193444.3199 0.818235022 1.138700155 1.110386975 1.087323454 1.084115571 1.026773701 1.000282638 1.021339966 1 17.56155884 2.092027809 4.502454948 1.008520878 1.070327038 0.007354506 0.088599629 0.519592231 18.85403209 0.033179575 0.023697651 123.6026577 -2.092027809 0.06180616 RLHPPS(ph)PVPQGVCPAHREPLAAFCGDELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLHPPSPVPQGVCPAHREPLAAFCGDELR 29 2 Q96F44-3;Q96F44;Q96F44-2 Q96F44-3 TRIM11 E3 ubiquitin-protein ligase TRIM11 1 RLHPPS(1)PVPQGVCPAHREPLAAFCGDELR;RLHPPS(1)PVPQGVCPAHREPLAAFCGDELR 143.72 3.31E-08 379630000 58252 80058 84055 80751 100940 70686 89795 74488 129643 TRUE FALSE 54606.1113 85985.57762 86048.82429 82823.20737 93012.57957 91091.90071 76331.07337 83787.99077 108004.7458 0.505589925 0.796127772 0.796713364 0.766847853 0.861189746 0.843406464 0.706738142 0.77578064 1 16.72073518 -5 0.030116794 2.100802116 6.37E-12 0.47655563 0.090330313 1617.279118 3.666890645 199.7471119 80.7049884 1.00E-05 5 -2.100802116 RLIELYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLIELYK 7 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ; 155.75 0.002549 901900000 1501080 2323100 1243620 1424840 2621400 837000 1460030 2503700 2867500 FALSE TRUE 1407130.082 2495104.741 1273119.254 1461403.807 2415525.818 1078628.312 1241112.056 2816292.456 2388895.725 0.589029512 1.044459461 0.532932116 0.61174868 1.011147449 0.451517536 0.519533792 1.178909748 1 21.18791245 1.231371718 24.99942242 1.089455045 0.690398542 0.411527956 0.20324031 186.6251274 648961.8009 0.179504029 0.048595618 17.0361603 -1.231371718 -0.399056503 RLKEDILENEDEQNS(ph)PPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLKEDILENEDEQNSPPK 18 2 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 RLKEDILENEDEQNS(1)PPK 134.29 5.66E-06 399830000 342850 161210 196990 215250 222470 147820 322840 173460 347650 TRUE FALSE 321391.6305 173146.1561 201662.6958 220773.6794 204998.1036 190493.2343 274433.1391 195116.8628 289624.9691 1.109682054 0.597828829 0.696289054 0.762274331 0.707805353 0.657723797 0.947546546 0.673687988 1 18.14382646 0.125138249 0.570977852 1.013360124 0.738034256 0.145449129 0.155656409 5.486645978 2.316497382 0.335145429 0.062476295 1.333945999 -0.125138249 -0.275325868 RLKEDILENEDEQNS(ph)PPKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLKEDILENEDEQNSPPKK 19 3 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 RLKEDILENEDEQNS(1)PPKK 162.65 1.94E-11 355410000 738470 298870 410570 386830 472420 291140 683210 397350 819410 TRUE FALSE 692250.4809 320998.6458 420308.9143 396756.7127 435318.0389 375187.3917 580769.0031 446960.0222 682645.1774 1.014070712 0.470227662 0.615706268 0.581204886 0.637692982 0.549608207 0.850762625 0.654747205 1 19.38077637 0.727218993 0.724594107 0.997488788 0.621442348 0.278850114 0.158447999 1.177723192 1.215618176 0.146038211 0.053003108 5.336038973 -0.727218993 -0.376046441 RLKS(ph)EDELRPEVDEHTQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 181.69 5.15E-14 911370000 653060 432620 479930 760510 712760 299470 487630 235760 448420 TRUE FALSE 612186.1403 464651.6349 491314.1662 780025.9741 656782.7047 385922.1275 414514.4084 265195.155 373575.8051 1.638719992 1.243794776 1.315165917 2.087999178 1.758097542 1.033049042 1.1095858 0.709883112 1 18.5110415 2.172719898 7.6142498 0.985044726 1.540183626 0.604875577 0.255797404 0.211950728 20.97184499 0.105791375 0.078191402 148.840081 -2.172719898 0.555138901 RLLAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLLAEK 6 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;B5MCA1;Q96G28;Q96G28-2;P02545-2;Q3BDU5;Q5TCI8;A0A3B3ISJ8 P02545;P02545-2;A0A3B3ISJ8 LMNA;CFAP36 Prelamin-A/C;Lamin-A/C;Cilia- and flagella-associated protein 36 0 ; 139.27 0.019153 1667960000 1806150 3037700 1488080 1518020 3437700 906210 1843300 2926100 3859600 FALSE TRUE 1693106.296 3262614.469 1523377.96 1556974.963 3167716.909 1167818.116 1566914.277 3291430.026 3215407.826 0.526560358 1.014681386 0.473774415 0.484223168 0.985168004 0.3631944 0.48731432 1.023643097 1 21.6165703 1.225869258 24.91984369 1.011821978 0.631727186 0.360882235 0.216688568 285.2215659 560023.0499 0.199450926 0.051211527 16.82167578 -1.225869258 -0.380094793 RLLEDGEDFNLGDALDSSNSMQTIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 RLLEDGEDFNLGDALDSSNSMQTIQK 26 1 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;; 332.63 8.12E-95 4745450000 1891767 2287844 2021464 2253536 2909012 1603028 2664024 2017528 5461710 FALSE TRUE 1773364.68 2457238.35 2069414.081 2311365.549 2680549.932 2065796.161 2264578.333 2269420.812 4550115.317 0.389740601 0.540038698 0.454804755 0.507979554 0.589116922 0.454009628 0.49769691 0.498761164 1 22.11747168 -4.166159234 0.5764698 10 0.492310199 0.90105569 0.052966043 570.9591573 5.370236719 6581.275345 0.019696944 6.82E-05 4.166159234 -9.507689801 RLLGPAPEDDGGHNDHSQPQASQDQDSHTLS(ph)PQV ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLLGPAPEDDGGHNDHSQPQASQDQDSHTLSPQV 34 1 Q92610 Q92610 ZNF592 Zinc finger protein 592 1 RLLGPAPEDDGGHNDHSQPQASQDQDSHT(0.002)LS(0.997)PQV;RLLGPAPEDDGGHNDHSQPQAS(0.021)QDQDS(0.042)HT(0.035)LS(0.902)PQV 96.886 7.75E-05 541290000 84874 87310 84483 88097 107833 80825 120101 95656 137740 TRUE FALSE 79561.88784 93774.52325 86486.97666 90357.71817 99364.23116 104157.8654 102092.97 107598.8622 114750.3042 0.693347947 0.817205008 0.753697145 0.787429008 0.865916931 0.90769141 0.889696727 0.937678231 1 16.80813845 2.140112558 0.44398348 1.000020193 0.7355749 0.859960674 0.033966917 0.377070627 0.168683099 0.034381374 0.033385208 138.074207 -2.140112558 -0.264445293 RLNHS(ph)PPQSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RLNHSPPQSSSR 12 1 A0A087X0H9;Q5T8P6-3;Q5T8P6-2;Q5T8P6 A0A087X0H9 RBM26 RNA-binding protein 26 1 RLNHS(0.998)PPQS(0.002)SSR;RLNHS(0.999)PPQSSSR;RLNHS(0.955)PPQS(0.044)S(0.001)SR;RLNHS(0.998)PPQS(0.002)SSR;RLNHS(0.978)PPQS(0.01)S(0.01)S(0.002)R;RLNHS(1)PPQSSSR 169.94 2.60E-05 6070010000 619519 802515 668641 704404 844972 668104 715775 638791 845622 TRUE FALSE 580744.4117 861934.0456 684501.4803 722480.1992 778611.3076 860974.779 608451.1837 718545.4625 704482.2253 0.824356372 1.223500061 0.971637688 1.025547804 1.105224915 1.222138399 0.863685643 1.019962515 1 19.42620378 1.718600644 24.99999874 0.955717272 1.070516541 0.128409659 0.122270245 1.582872334 1974.632563 0.051802745 0.02872722 52.31191806 -1.718600644 0.114799269 RLNKHEENLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLNKHEENLK 10 2 P42766 P42766 RPL35 60S ribosomal protein L35 0 84.17 0.0090711 459270000 411120 974270 305710 284470 1290300 113880 387520 978570 1800700 FALSE TRUE 385388.7331 1046405.965 312961.5856 291769.9818 1188965.043 146755.3073 329414.9736 1100746.619 1500151.537 0.256899869 0.697533508 0.208619981 0.194493673 0.792563293 0.097826989 0.219587799 0.733756951 1 20.51667681 1.038131211 4.602199305 0.996980889 0.36391241 0.49520429 0.224307896 0.141011469 6.816076087 0.207274932 0.052663725 10.91770137 -1.038131211 -0.633068479 RLNLEEWILEQLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLNLEEWILEQLTR 14 1 Q96C90 Q96C90 PPP1R14B Protein phosphatase 1 regulatory subunit 14B 0 ; 140.84 1.58E-05 198897000 83370 127024 109505 116272 161681 97389 113431 113964 113151 FALSE TRUE 78152.02052 136428.9891 112102.5103 119255.7364 148983.2264 125503.6233 96423.07459 128192.6563 94265.36712 0.829063981 1.447286456 1.189222657 1.265106582 1.580466199 1.331386353 1.022889716 1.359912555 1 16.5244402 0.370958815 0.77500471 0.99984138 1.273749967 0.104317182 0.213125555 4.643172987 3.922290034 0.228613167 0.068560632 2.349410014 -0.370958815 0.273908588 RLPDAHSDYAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RLPDAHSDYAR 11 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ;; 150.51 2.20E-05 688020000 585043 734120 627056 627604 800560 493965 627753 693570 829660 FALSE TRUE 548426.203 788475.0087 641930.0644 643709.3812 737687.2469 636564.6766 533627.2654 780163.7412 691184.3862 0.793458611 1.140759289 0.928739244 0.931313545 1.067279964 0.920976644 0.772047627 1.128734614 1 19.3987111 2.053115975 24.9955262 0.917827045 0.988030015 0 0.127664058 272.8162882 128381.4781 0.044813835 0.033097203 113.0097659 -2.053115975 0.07020297 RLPDGLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLPDGLTR 8 1 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 123.21 0.0053619 0 72752 107830 108910 110870 105880 87898 103600 98028 107510 FALSE TRUE 68198.58219 115813.8454 111493.3966 113715.1119 97564.6119 113272.7257 88066.14178 110267.0116 89565.88646 0.761434793 1.293057547 1.244819887 1.26962526 1.089305491 1.264686034 0.983255403 1.23112734 1 16.45066173 1.741654071 25 1.075033939 1.18236024 0.032801748 0.168260312 1.354253216 11007.219 0.071757393 0.039793005 55.16378676 -1.741654071 0.107326301 RLPEYPQVDDLLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLPEYPQVDDLLLR 14 1 A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2;A0A087WW69;F8W8L6 A0A087WTA5 EIF2B4 Translation initiation factor eIF-2B subunit delta 0 ; 179.17 3.04E-06 134525000 107366 146921 125177 129172 147862 114300 145020 127586 165289 FALSE TRUE 100646.1537 157799.1837 128146.2576 132486.7722 136249.515 147296.5545 123275.5973 143515.393 137701.1981 0.730902527 1.1459536 0.930611057 0.962132313 0.989457731 1.069682447 0.895239831 1.04222327 1 17.07118159 4.759935332 24.8449069 0.999525127 0.730902231 0.594045142 0.070954491 3823.079003 4443678.801 0.016434937 0.783462439 57535.42582 -4.759935332 -0.268622896 RLPIFSRLS(ph)ISDD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 RLPIFSRLS(0.997)IS(0.002)DD 75.911 0.023708 59470000 53319 75849 60426 73615 121130 35915 60779 53668 134600 TRUE FALSE 49981.85897 81464.93888 61859.33326 75504.08553 111616.9384 46283.07747 51665.75319 60368.56794 112134.3905 0.445731758 0.726493795 0.551653538 0.673335675 0.99538543 0.412746503 0.460748509 0.538359086 1 16.77486928 3.219974077 24.17909668 0.636731878 0.603887487 0.020787042 0.209636372 1755.423243 2283610.976 0.060019903 0.071880373 1659.487851 -3.219974077 -0.032844391 RLPLNFLSGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLPLNFLSGEK 11 1 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 101.3 0.0054302 149050000 499340 667470 449990 454950 717250 315160 494930 562640 694370 FALSE TRUE 468087.2007 716890.1733 460663.9753 466624.7872 660920.0782 406141.5758 420719.8412 632886.8425 578475.1612 0.809174243 1.239275636 0.796341842 0.806646194 1.142521101 0.702089913 0.727291108 1.094060532 1 19.14189549 3.840681268 6.355249107 0.870697935 1.048531584 0.064222857 0.180411347 0.388888687 19.53153093 0.043586958 0.07938199 6929.170828 -3.840681268 0.177833649 RLPQDHADSCVVS(ph)S(ph)DDEELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLPQDHADSCVVSSDDEELSR 21 1 D6RA71;P78317 D6RA71 RNF4 E3 ubiquitin-protein ligase RNF4 2 RLPQDHADSCVVS(1)S(1)DDEELSR;RLPQDHADS(0.003)CVVS(0.999)S(0.998)DDEELSR 133.29 3.55E-05 353710000 444100 465150 516240 487250 507480 479690 642920 376700 418830 TRUE FALSE 416304.5737 499590.19 528485.4566 499753.6599 467624.5679 618168.7159 546520.1146 423731.8242 348924.5673 1.193107659 1.431799985 1.514612344 1.432268481 1.340188143 1.771639987 1.566298753 1.21439378 1 18.41255565 1.02875031 4.374143179 1.002248078 1.478750006 0.521359589 0.149408952 0.131260774 6.095246606 0.141747416 0.036112509 10.68440422 -1.02875031 0.476501928 RLPS(ph)SPASPSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 140.22 3.64E-05 314800000 782520 667010 706090 723180 996230 603390 800990 771410 1553900 TRUE FALSE 733543.47 716396.1144 722838.7882 741738.0231 917990.1144 777578.8978 680888.9855 867722.2366 1294544.051 0.56664234 0.553396475 0.558373265 0.572972409 0.709122346 0.600658507 0.525968185 0.67029178 1 20.30401263 -5 0.306421657 4.603076375 0.565105692 0.858295153 0.052323831 102.4029747 0.935162167 237.6349819 0.051308156 1.00E-05 5 -4.037970683 RLPSS(ph)PASPSPK ddPTM_SK-BR-3_Pertuzumab_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(0.03)S(0.96)PAS(0.01)PSPK;RLPS(0.187)S(0.813)PASPSPK 223.9 2.26E-11 589140000 881390 767320 830680 787660 1135740 682250 927200 855110 1829550 TRUE FALSE 826225.3732 824133.1712 850384.1219 807872.6891 1046543.562 879204.4996 788174.9677 961872.3658 1524186.286 0.542076373 0.540703705 0.557926633 0.530035401 0.686624445 0.57683533 0.517111967 0.631072707 1 20.53960781 -4.999999999 0.351686859 6.065924108 0.553135186 0.884643663 0.048789334 137.1459404 1.118699764 524.1199123 0.036412278 1.00E-05 4.999999999 -5.512788922 RLPSSPAS(ph)PSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.088)S(0.088)PAS(0.491)PS(0.332)PK 52.887 0.089101 375360000 765310 614780 696170 626520 722500 528770 836590 632410 924520 TRUE FALSE 717410.6132 660298.9509 712683.4812 642597.5639 665757.7644 681417.3151 711151.096 711367.7806 770211.6394 0.931446081 0.857295472 0.925308636 0.834312975 0.864382892 0.884714383 0.923319072 0.923600403 1 19.5548954 0.95506088 1.062047197 0.998364511 0.882627668 0.595813315 0.030083524 0.387083904 0.906409639 0.02673612 0.008658535 9.0169753 -0.95506088 -0.115736843 RLPTEEEWEFAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLPTEEEWEFAAR 13 1 A8MXB9;C9J660;J3KQJ1;Q8NBJ7;A0A494C1B1;H7C3B2;C9JL30;Q8NBJ7-3;Q8NBJ7-2;F8WA42 A8MXB9 SUMF2 Sulfatase-modifying factor 2 0 ; 190.24 7.35E-06 494810000 207579 284770 244503 253930 309470 214603 271410 242258 293930 FALSE TRUE 194587.0009 305854.6671 250302.7266 260446.2737 285165.4745 276555.4023 230714.5901 272504.4446 244871.1841 0.794650467 1.249043117 1.022181224 1.063605236 1.16455301 1.129391371 0.942187587 1.112848151 1 17.90166349 1.754326371 25 1.01431011 1.088927268 0.023635687 0.124634998 15.07809436 23938.60811 0.05233021 0.029019412 56.79712739 -1.754326371 0.074617158 RLPVTNEMVHNLVAIELAYINTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLPVTNEMVHNLVAIELAYINTK 23 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 51.526 0.081216 52028000 107260 89213 92734 93503 102020 80309 113990 93092 89060 FALSE TRUE 100546.7881 95818.42335 94933.69427 95902.44528 94007.76073 103492.9046 96898.25773 104714.7411 74195.31065 1.355163651 1.291435031 1.279510705 1.292567474 1.267031028 1.394871235 1.305988975 1.411339075 1 16.17904039 -1.360097153 3.471841262 0.998096066 1.317317681 0.811611576 0.04905307 2613091.428 2047863.859 34043.22187 0.010891281 0.043641819 1.360097153 0.319221615 RLQLS(ph)PWESSVVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLQLSPWESSVVNR 14 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 RLQLS(1)PWESSVVNR 145.43 5.26E-06 120920000 64447 80473 74311 71567 95434 58273 75505 57731 112430 TRUE FALSE 60413.37731 86431.30465 76073.69201 73403.53038 87938.9986 75095.46912 64183.7262 64938.84243 93664.70667 0.644996173 0.922773451 0.812191643 0.783683983 0.938870165 0.801747764 0.68524985 0.693311758 1 16.51521792 1.993707368 24.83490869 0.754285917 0.834864306 0 0.118597291 609.0242841 2403619.648 0.04085726 0.029150623 98.5615144 -1.993707368 0.080578389 RLQQQQRPEDAEDGAEGGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLQQQQRPEDAEDGAEGGGK 20 2 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 105.79 0.00014113 82315000 73803 62046 77241 72379 75753 60900 93111 76083 95994 FALSE TRUE 69183.80197 66639.9504 79073.193 74236.36768 69803.66495 78480.84137 79149.86995 85582.13003 79971.98126 0.865100513 0.833291227 0.988761211 0.928279711 0.872851514 0.981354221 0.989720008 1.070151429 1 16.28720701 3.863774417 0.299566396 1.032705882 0.769512989 0.584259759 0.047188674 3.381111561 0.372064149 0.058246232 0.314740556 7307.594108 -3.863774417 -0.263192893 RLQSIGTENTEENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 RLQSIGTENTEENR 14 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;;; 334.4 2.44E-68 20613450000 8277009 9083474 7931960 7967772 8273466 6959875 8759928 7840066 5368983 FALSE TRUE 7758965.782 9756023.866 8120109.837 8172238.519 7623701.354 8969077.928 7446458.12 8818915.498 4472865.052 1.734674686 2.181157659 1.815415789 1.827070216 1.704433571 2.005219881 1.664807239 1.971648014 1 22.0927678 -2.131765142 0.327836402 3.79E-11 1.93163673 0.734230165 0.161184629 18.98134638 0.886458531 14.3960156 0.132153278 0.007383034 2.131765142 1.93163673 RLQSIGTENTEENRR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;; 287.91 7.61E-35 18551200000 2469708 2782671 3022069 3809915 2961646 2388941 3323773 1588764 4711290 FALSE TRUE 2315133.385 2988702.856 3093753.904 3907683.869 2729050.27 3078589.485 2825404.095 1787124.683 3924945.263 0.589851127 0.761463576 0.788228548 0.995602131 0.695309128 0.784364948 0.719858216 0.45532474 1 21.9042411 1.58696014 5.502353823 0.684975054 0.775698873 0 0.164008727 0.435548444 27.90282836 0.082172872 0.03806842 38.63315174 -1.58696014 0.090723818 RLQTQVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLQTQVFK 8 1 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 122.33 0.0056183 0 399500 1030800 328860 403240 1177400 202210 470250 896950 1047900 FALSE TRUE 374496.0081 1107121.505 336660.7145 413587.8211 1084931.753 260584.7444 399740.3781 1008936.182 872998.7203 0.428976583 1.268182277 0.385637123 0.473755358 1.242764426 0.298493845 0.45789343 1.155713243 1 19.73562001 1.226516995 24.98453152 1.077856869 0.67123962 0.209586811 0.342996743 418.7025723 868572.6306 0.309204199 0.079689506 16.84678351 -1.226516995 -0.406617249 RLREEFSFIPSAALDLLDHMLTLDPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLREEFSFIPSAALDLLDHMLTLDPSK 27 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 0 64.722 0.014745 452180000 291170 530210 446200 480560 575230 228530 366040 434090 432290 FALSE TRUE 272946.1895 569467.3001 456784.0747 492891.9832 530053.7562 294502.9011 311155.7001 488287.092 360138.0063 0.757893321 1.581247439 1.268358426 1.368619736 1.471807326 0.817750129 0.863990178 1.355833274 1 18.45819033 2.240310413 24.99967823 0.977255083 1.330055282 0.21331316 0.257760429 54.20243897 774414.3767 0.085603636 0.068193984 173.904337 -2.240310413 0.352800199 RLS(ph)AEGGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RLSAEGGDK 9 1 S4R3H3;S4R393;S4R410;A7E2V4-5;A7E2V4;A7E2V4-3;A7E2V4-4;A7E2V4-2;H7BZ52;H0YCW2 S4R3H3 ZSWIM8 Zinc finger SWIM domain-containing protein 8 1 RLS(1)AEGGDK;RLS(1)AEGGDK;RLS(1)AEGGDK 121.56 0.00037393 529240000 1071380 839100 1020220 1004440 1146110 820240 1294980 1001170 1698420 TRUE FALSE 1004324.238 901227.8371 1044420.1 1030215.631 1056099.144 1057029.973 1100809.771 1126168.278 1414942.73 0.709798508 0.636935911 0.738135953 0.728097052 0.746390028 0.747047884 0.777988923 0.795910855 1 20.43231223 -5 0.130267396 1.951605879 0.610600608 0.941203002 0.022652684 28.83102364 0.236937534 7.086284297 0.161038758 1.00E-05 5 -1.341005272 RLS(ph)APLPSSCGDPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RLSAPLPSSCGDPEK 15 1 H0YKX0;Q96EP0-3;Q96EP0 H0YKX0 RNF31 E3 ubiquitin-protein ligase RNF31 1 RLS(1)APLPSSCGDPEK;RLS(1)APLPSSCGDPEK;RLS(0.909)APLPS(0.045)S(0.045)CGDPEK;RLS(1)APLPSSCGDPEK 204.81 2.89E-09 3626320000 4725170 3440890 3857860 3823560 4271960 3337520 5352810 4173720 5924890 TRUE FALSE 4429430.044 3695657.076 3949370.261 3921679.023 3936457.494 4301007.844 4550205.834 4694818.129 4935987.583 0.897374633 0.74871685 0.800117544 0.794507473 0.797501499 0.871357104 0.921843047 0.951140588 1 22.23490733 1.715966697 1.160993988 0.988590233 0.795137121 0.762883355 0.038827309 0.191475327 0.48449497 0.03039134 0.011785784 51.99561228 -1.715966697 -0.193453112 RLS(ph)AQAHPAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 116.58 0.00059441 1177550000 1668160 1530350 1562940 1309970 1917290 1114830 1690380 1728990 2598030 TRUE FALSE 1563752.843 1643658.706 1600013.675 1343586.048 1766713.777 1436663.323 1436923.212 1944858.207 2164402.009 0.722487244 0.759405461 0.739240524 0.620765478 0.816259535 0.663769169 0.663889243 0.89856607 1 21.04553705 1.072261136 4.342916781 0.997432433 0.715677483 0.769025607 0.055371809 0.085396964 2.929106545 0.051313134 0.013102836 11.8103056 -1.072261136 -0.28175495 RLS(ph)ASSTGSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLSASSTGSTR 11 1 A0A2R8Y5E4;A0A2R8YFK2;A0A2R8Y6M6;A0A2R8Y4C2;A0A2R8YFS8;A0A2R8Y8C4;A0A2R8Y5C9;A0A2R8Y596;P56945-4;P56945-5;P56945-8;P56945;P56945-7;P56945-3;P56945-2;P56945-6 A0A2R8Y5E4 BCAR1 Breast cancer anti-estrogen resistance protein 1 1 RLS(0.906)AS(0.024)S(0.058)T(0.002)GS(0.009)TR;RLS(0.298)AS(0.118)S(0.117)T(0.117)GS(0.117)T(0.234)R 114.54 0.0013169 215270000 277760 305390 310670 288180 333230 294050 333240 281940 421840 TRUE FALSE 260375.4974 328001.3934 318039.2391 295575.1867 307059.46 378937.4615 283273.7556 317140.8296 351432.1788 0.740898282 0.933327718 0.904980415 0.841058971 0.873737462 1.078266261 0.806055258 0.902423992 1 18.42288677 RLS(ph)DEHEPEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RLSDEHEPEQR 11 1 Q9UK59;Q9UK59-2 Q9UK59 DBR1 Lariat debranching enzyme 1 RLS(1)DEHEPEQR;RLS(1)DEHEPEQR;RLS(1)DEHEPEQR;RLS(1)DEHEPEQR 143.97 2.26E-05 2596350000 1125580 1237080 1330920 1269200 1212340 1084240 1314150 1046590 1323560 TRUE FALSE 1055131.957 1328674.69 1362490.051 1301769.821 1117127.707 1397242.487 1117105.407 1177259.065 1102649.285 0.956906218 1.204983949 1.235651325 1.180583743 1.013130577 1.267168541 1.013110354 1.067664108 1 20.07254256 1.63680401 10.32938673 1.030244706 1.156955104 0.232820548 0.096968861 0.137646514 31.24238725 0.04451111 0.023647236 43.33152861 -1.63680401 0.126710398 RLS(ph)DPLLPSPEDETGSLVHLEDPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSDPLLPSPEDETGSLVHLEDPER 25 1 Q8WYL5-2;Q8WYL5-5;Q8WYL5-4;Q8WYL5 Q8WYL5-2 SSH1 Protein phosphatase Slingshot homolog 1 1 RLS(0.99)DPLLPS(0.009)PEDETGSLVHLEDPER 71.44 0.017546 28537000 6143.5 4930 5864.7 6913.1 6801.9 5295.5 8249.5 5152.5 6005.7 TRUE FALSE 5758.989301 5295.02233 6003.813454 7090.50185 6267.706212 6824.224885 7012.56406 5795.800967 5003.309872 1.151035904 1.058303896 1.199968342 1.417162245 1.252711979 1.363942082 1.401584999 1.158393367 1 12.28866709 3.532950678 3.731408605 1.300119759 1.109118321 0.175431892 0.127370835 0.252526424 7.045886608 0.031624405 0.049378866 3411.54165 -3.532950678 -0.191001438 RLS(ph)DSPVFDAPPSPPDSLSDRDSYLSGSLSSGSLSGSESPSLDPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSDSPVFDAPPSPPDSLSDRDSYLSGSLSSGSLSGSESPSLDPGR 46 2 P47974 P47974 ZFP36L2 "Zinc finger protein 36, C3H1 type-like 2" 1 RLS(0.766)DS(0.233)PVFDAPPSPPDSLSDRDSYLSGSLSSGSLSGSESPSLDPGR 69.766 0.00042198 102610000 8377.8 13515 11029 11860 14828 8292 12074 11854 18927 TRUE FALSE 7853.448453 14515.66466 11290.61309 12164.34768 13663.46869 10685.76579 10263.61579 13333.99799 15767.96143 0.498063652 0.920579666 0.716047736 0.771459756 0.86653362 0.677688479 0.650915836 0.845638674 1 13.94470853 0.978714753 8.771690497 0.999997099 0.745249506 0.360724369 0.116216486 0.370392166 148.3062377 0.104718774 0.026208863 9.521705668 -0.978714753 -0.254747593 RLS(ph)ELGITQADDNLMSQEMFVGIVGNQFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLSELGITQADDNLMSQEMFVGIVGNQFK 29 1 Q8NEM2 Q8NEM2 SHCBP1 SHC SH2 domain-binding protein 1 1 RLS(0.971)ELGIT(0.029)QADDNLMSQEMFVGIVGNQFK;RLS(0.842)ELGIT(0.155)QADDNLMS(0.002)QEMFVGIVGNQFK 144.55 4.42E-08 82563000 139713 133394 147515 137810 153964 122103 181216 138736 169009 TRUE FALSE 130968.6127 143270.6306 151014.1255 141346.4379 141872.2885 157352.1539 154044.3431 156057.495 140800.3061 0.930172784 1.01754488 1.072541173 1.003878769 1.007613495 1.117555482 1.094062559 1.108360481 1 17.10329094 2.247776591 24.93555305 1.089562123 1.016790456 0.357292145 0.047188629 199.1033318 538711.8067 0.015790401 0.013040246 176.9198616 -2.247776591 -0.072771667 RLS(ph)EQLAHTPTAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RLSEQLAHTPTAFK 14 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;F8W860;Q9UBF8-3 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 RLS(0.943)EQLAHT(0.057)PTAFK;RLS(0.997)EQLAHT(0.003)PTAFK;RLS(1)EQLAHTPTAFK;RLS(1)EQLAHTPTAFK;RLS(1)EQLAHTPTAFK;RLS(0.999)EQLAHT(0.001)PTAFK 218.79 3.22E-12 4366310000 3750060 3896070 3761570 3672410 4387470 3127300 4802230 4189480 5350870 TRUE FALSE 3515350.439 4184539.077 3850796.217 3766650.258 4042895.804 4030100.743 4082180.193 4712545.8 4457775.229 0.788588535 0.938705713 0.86383813 0.844961907 0.906931282 0.904061003 0.915743837 1.057151955 1 22.08789244 1.383309907 3.354954535 1.028208133 0.881942791 0.671150117 0.043445292 0.137854068 2.572151671 0.031592179 0.010356133 24.17185091 -1.383309907 -0.146265342 RLS(ph)EQLAHTPTAFKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSEQLAHTPTAFKR 15 2 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;F8W860;Q9UBF8-3 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 RLS(1)EQLAHTPTAFKR 70.907 0.023633 891810000 240970 255430 251600 216130 309340 215110 314480 256480 404710 TRUE FALSE 225888.1178 274342.303 257568.0708 221676.2617 285045.6842 277208.765 267326.6435 288502.0926 337161.2865 0.669970506 0.813682691 0.763931332 0.657478396 0.845428273 0.822184444 0.792874669 0.855679772 1 18.36307937 0.19926061 0.353985128 1.043139683 0.740609119 0.669452741 0.055664306 2.39717607 0.487897921 0.211399045 0.048704847 1.582197193 -0.19926061 -0.302530565 RLS(ph)ESQLSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSESQLSFR 10 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 1 RLS(0.774)ES(0.222)QLS(0.004)FR 111.53 0.0018439 134030000 114970 168570 131510 129870 210060 99708 146390 171120 266730 TRUE FALSE 107774.2329 181051.0982 134629.4793 133202.6841 193562.7349 128492.081 124440.1785 192484.7087 222211.0399 0.485008454 0.814770942 0.605863144 0.599442243 0.87107614 0.578243462 0.560008983 0.866224778 1 17.76157097 1.045594671 4.918879315 0.998447473 0.65669745 0.527682759 0.116577821 0.129920426 6.768343521 0.105482803 0.026715835 11.10694626 -1.045594671 -0.341750023 RLS(ph)ESSALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RLSESSALK 9 1 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 RLS(0.983)ES(0.017)SALK;RLS(0.994)ES(0.006)S(0.001)ALK;RLS(0.883)ES(0.089)S(0.028)ALK 156 4.41E-05 504390000 584190 501510 476610 550140 643940 388230 572210 498520 537160 TRUE FALSE 547626.5907 538642.3222 487915.4143 564257.5238 593367.5499 500305.6986 486412.4226 560761.3194 447504.5258 1.223734195 1.203657821 1.090302748 1.260897916 1.325947595 1.117990254 1.086944142 1.253085247 1 18.77154275 -4.678557323 0.263786532 1.72E-05 1.197078678 0.365743577 0.078858831 205.4644901 2.359898681 110.8796309 0.10498231 2.10E-05 4.678557323 1.197061462 RLS(ph)EVIYEPFQLLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RLSEVIYEPFQLLSK 15 1 A0A087WVA8;Q8IWB9;Q8IWB9-2 A0A087WVA8 TEX2 Testis-expressed sequence 2 protein 1 RLS(1)EVIYEPFQLLSK;RLS(1)EVIYEPFQLLSK;RLS(1)EVIYEPFQLLSK 251.13 1.96E-19 874420000 1519517 1323252 1256249 1183762 1624708 1109691 1574230 1340758 2108080 TRUE FALSE 1424413.143 1421226.955 1286047.82 1214139.337 1497109.987 1430040.777 1338188.826 1508154.588 1756227.829 0.811063986 0.809249763 0.732278465 0.691333617 0.852457729 0.814268373 0.761967669 0.858746549 1 20.74404858 0.921999518 3.054219746 0.999862166 0.779752303 0.698042308 0.045806194 0.188778832 4.10774484 0.043607493 0.01142687 8.356020909 -0.921999518 -0.220109863 RLS(ph)FAVPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLSFAVPFR 9 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 1 RLS(1)FAVPFR;RLS(1)FAVPFR 145.31 5.97E-05 514090000 252666 333990 269173 270000 317730 215953 352160 295860 389690 TRUE FALSE 236852.0861 358718.9671 275557.9107 276928.6571 292776.7675 278295.1254 299356.8773 332798.7723 324648.2215 0.729565328 1.104946657 0.84878922 0.853011471 0.901827726 0.857220545 0.922096157 1.025105792 1 18.30851778 1.303920898 5.105820231 1.012654261 0.903174829 0.223587923 0.093619036 0.319205637 14.80689009 0.066435041 0.022567243 20.13357503 -1.303920898 -0.109479432 RLS(ph)FEASNPPFDVGRPFDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLSFEASNPPFDVGRPFDLR 20 2 Q92545;H7BZ05 Q92545 TMEM131 Transmembrane protein 131 1 RLS(1)FEASNPPFDVGRPFDLR;RLS(1)FEASNPPFDVGRPFDLR 92.819 0.00083396 173355000 226638 283500 225105 229050 306330 196067 259895 271699 293280 TRUE FALSE 212453.1321 304490.635 230444.5969 234927.8108 282272.0775 252668.36 220926.1575 305621.2182 244329.6733 0.869534712 1.246228634 0.943170732 0.961519768 1.155291838 1.034128833 0.904213371 1.25085592 1 17.89846956 RLS(ph)FLVSYIASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RLSFLVSYIASK 12 1 P47897;A0A1B0GVU9;A0A0U1RQT0;C9J165;A0A0U1RQE9;A0A0U1RQL2;A0A0U1RRI9;A0A0U1RQM8;A0A0U1RQU2 P47897 QARS Glutamine--tRNA ligase 1 RLS(1)FLVSYIASK;RLS(1)FLVSYIASK;RLS(0.972)FLVS(0.025)Y(0.003)IASK 171.29 2.38E-05 325850000 1050294 1662189 1081653 1035976 1917684 681376 1114552 1697943 2225889 TRUE FALSE 984557.9734 1785259.203 1107310.32 1062560.898 1767076.834 878078.19 947435.2746 1909934.921 1854373.746 0.530938262 0.962728903 0.597134382 0.573002557 0.952923777 0.473517376 0.510919267 1.029962231 1 20.82250062 1.22285057 24.99397774 1.014981544 0.671427027 0.427693253 0.17140627 279.0285896 443909.5917 0.161464127 0.040925168 16.70515733 -1.22285057 -0.343554517 RLS(ph)GEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSGEER 7 1 Q99549-2;Q99549;A0A0A0MT47 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 RLS(1)GEER 64.906 0.076297 522130000 691360 893900 756090 840180 939910 654210 872860 708390 928600 TRUE FALSE 648089.0117 960085.2861 774024.8119 861740.4412 866093.26 843069.8068 741982.7462 796834.0509 773610.661 0.837745709 1.241044539 1.000535348 1.113920069 1.119546697 1.089785663 0.959116496 1.03001948 1 19.56124815 1.750646565 25 0.995093523 1.083305442 0.079980275 0.103742745 6.544960074 13560.86452 0.04331279 0.024019475 56.31791465 -1.750646565 0.088211919 RLS(ph)GGSHSYGGESPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSGGSHSYGGESPR 15 1 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 RLS(0.957)GGS(0.042)HS(0.001)YGGESPR 92.563 0.0031815 311750000 68316 99308 90102 97438 101470 73085 105490 90130 90046 TRUE FALSE 64040.22351 106660.8676 92239.26199 99938.42404 93500.95551 94183.45306 89672.75382 101382.9289 75016.74088 0.853679096 1.421827533 1.229582369 1.332214955 1.246401195 1.255499132 1.195369897 1.351470721 1 16.19492497 -1.236741925 6.093041753 0.999994372 1.251740389 0.185818967 0.151846403 1.01E-05 1.27E-06 0.128240691 0.030225945 0.057977312 1.236741925 0.251746017 RLS(ph)GLSSVGHNWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSGLSSVGHNWR 13 1 Q14D93;A0A0G2JR24;Q8WYQ4 Q14D93 C22orf15 Uncharacterized protein C22orf15 1 RLS(0.97)GLS(0.015)S(0.015)VGHNWR 54.234 0.065299 69495000 187610 61348 68689 64138 86462 47019 68966 59897 117510 TRUE FALSE 175867.825 65890.26975 70318.33552 65783.88967 79671.62329 60592.62201 58625.18855 67375.2723 97896.82186 1.796461026 0.673058313 0.718290279 0.671971658 0.813832582 0.618943709 0.598846698 0.688227371 1 16.5789744 4.739378189 24.99687185 0.698877508 1.796461368 0.893027612 0.11650744 18.04787258 551712.5725 0.024571056 0.148643383 54875.4619 -4.739378189 1.09758386 RLS(ph)IIGPTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RLSIIGPTSR 10 1 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 1 RLS(1)IIGPTSR;RLS(1)IIGPTSR;RLS(1)IIGPTSR;RLS(1)IIGPTSR;RLS(1)IIGPTSR 191.19 5.02E-07 1633590000 488879 586914 538224 528115 688401 449266 706625 547516 787712 TRUE FALSE 458280.9361 630369.7232 550990.9274 541667.325 634336.7623 578961.801 600673.1412 615874.5778 656237.7784 0.698345861 0.960581277 0.839620859 0.825413201 0.966626402 0.882243937 0.9153285 0.938493025 1 19.32385912 7.999999965 0.077063263 1.096632696 0.371882438 0.413004555 0.067286472 239.3129569 1.348684275 1.995204999 18.55044555 99999992.02 -7.999999965 -0.724750259 RLS(ph)LGQGDSTEAATEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RLSLGQGDSTEAATEER 17 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RLS(1)LGQGDSTEAATEER;RLS(1)LGQGDSTEAATEER;RLS(1)LGQGDSTEAATEER 242.63 1.25E-20 4962210000 971820 1010210 970730 900030 1078680 1142050 1180660 1017110 1151840 TRUE FALSE 910995.5209 1085007 993756.174 923126.2935 993964.824 1471741.295 1003630.994 1144098.422 959590.4628 0.949358665 1.130697982 1.035604471 0.96200028 1.035821908 1.533718135 1.045895132 1.192277817 1 19.87205929 RLS(ph)LGQGDSTEAATEERGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLSLGQGDSTEAATEERGPR 20 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RLS(1)LGQGDSTEAATEERGPR;RLS(1)LGQGDSTEAATEERGPR 354.46 1.57E-95 412810000 66898 107070 80980 96154 135203 78103 118873 88480 286050 TRUE FALSE 62710.9736 114997.5742 82900.88384 98621.47443 124584.7018 100650.0682 101049.0972 99526.92277 238306.407 0.263152696 0.482561823 0.347875178 0.413843151 0.522792078 0.422355695 0.424030132 0.417642664 1 17.86245821 -5 0.361170494 8.257759948 0.39963227 0.880680781 0.068251603 146.1231722 1.159164736 824.8305617 0.045315066 1.00E-05 5 -7.858127679 RLS(ph)LPADIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 110.38 0.0014066 2276330000 2610650 3259660 2825210 2747030 3305980 2331170 3224360 2728370 3207230 TRUE FALSE 2447254.077 3501008.618 2892225.315 2817523.441 3046341.666 3004140.936 2740897.151 3069013 2671922.594 0.915915035 1.310295675 1.082451012 1.054492914 1.140130958 1.124336814 1.025814579 1.148615985 1 21.34944678 0.491248028 0.302035108 0.979664538 1.142231122 0.032106869 0.103440679 7.304232609 1.426897152 0.372258579 0.130645637 3.099188761 -0.491248028 0.162566584 RLS(ph)LPADIRLPEGYLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLSLPADIRLPEGYLEK 17 2 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;E5RIY8;E5RIU4;H0YBX5 E5RJM2 CDK16 Cyclin-dependent kinase 16 1 RLS(1)LPADIRLPEGYLEK;RLS(1)LPADIRLPEGYLEK 115.96 0.00015096 289970000 138909 177966 139378 181031 215225 105103 187037 134308 289180 TRUE FALSE 130214.9336 191142.7878 142684.112 185676.5619 198322.0967 135444.5299 158992.5382 151076.6494 240913.9898 0.540503828 0.793406759 0.592261629 0.770717226 0.823207058 0.562211144 0.659955606 0.627097868 1 17.87815865 -1.830936325 2.669313562 1.114450697 0.676450514 0.528848007 0.09742811 15317264.01 9667037.713 11203623.28 0.021980536 0.014759229 1.830936325 -0.438000183 RLS(ph)LPGLLSQVS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RLSLPGLLSQVSPR 14 1 Q96Q42;Q96Q42-3 Q96Q42 ALS2 Alsin 2 RLS(1)LPGLLS(0.077)QVS(0.923)PR;RLS(1)LPGLLS(0.186)QVS(0.814)PR;RLS(1)LPGLLS(0.011)QVS(0.989)PR;RLS(1)LPGLLS(0.006)QVS(0.994)PR 147.02 2.85E-05 354860000 280725 348962 313136 328854 400672 263018 367765 360655 461836 TRUE FALSE 263154.9234 374799.5096 320563.7338 337292.9504 369204.8374 338947.0269 312622.0524 405683.5706 384752.588 0.683958813 0.974131224 0.833168493 0.876648945 0.959590264 0.88094801 0.812527484 1.054401148 1 18.55357151 7.972714392 0.026338428 1.535836719 3.95E-11 0.2935122 0.089708303 2873.251766 5.838832352 114.8503337 249.5878364 93910551.77 -7.972714392 -1.535836719 RLS(ph)LPMDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 84.169 0.007686 143185000 185791 294915 206801 218840 329678 142921 204635 262797 488729 TRUE FALSE 174162.673 316750.8135 211706.4174 224455.8049 303786.4197 184179.9726 173951.8815 295607.7839 407156.9726 0.427753139 0.777957483 0.519962647 0.551275847 0.746116216 0.452356179 0.427235423 0.726029035 1 18.63522558 0.969553096 7.982074652 0.999991997 0.569573335 0.580086917 0.120881558 0.283733434 72.31911707 0.116478893 0.029171208 9.322944442 -0.969553096 -0.430418662 RLS(ph)LPNTAWGSPSPEAAGYPGAGAEDEQQQLAANRHS(ph)LVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSLPNTAWGSPSPEAAGYPGAGAEDEQQQLAANRHSLVEK 41 2 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 2 RLS(0.807)LPNT(0.074)AWGS(0.111)PS(0.008)PEAAGYPGAGAEDEQQQLAANRHS(1)LVEK 84.836 0.00018519 127940000 14279 12179 14247 14701 14542 10378 16521 12318 21529 TRUE FALSE 13385.30288 13080.74583 14584.94557 15078.25255 13399.92998 13373.96013 14043.82942 13855.92942 17935.67082 0.74629508 0.729314558 0.813180935 0.840685174 0.747110611 0.745662667 0.783011105 0.772534775 1 14.13054408 -0.2383584 1.676090596 1.000253353 0.772723728 0.816943261 0.033883998 48.2394143 63.38168851 0.117079657 0.009393781 0.577619172 0.2383584 -0.227529625 RLS(ph)LTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSLTLR 7 1 Q00537;Q00537-2;F8VQZ9;F8VZY6;F8VUX2;F8W1S5 Q00537 CDK17 Cyclin-dependent kinase 17 1 RLS(0.999)LT(0.001)LR 140.05 0.0016235 245470000 31649 31166 29121 29062 35899 30091 34705 30249 48838 TRUE FALSE 29668.14559 33473.56307 29811.76387 29807.78012 33079.63735 38777.78321 29501.30744 34025.65424 40686.62229 0.729186743 0.822716686 0.732716608 0.732618695 0.813034739 0.953084356 0.725086178 0.83628604 1 15.3122669 2.48236523 24.94291824 0.849921648 0.763183469 0.329762458 0.078526922 338.6010807 1610564.799 0.0252511 0.02171232 303.644368 -2.48236523 -0.086738179 RLS(ph)MEIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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;RLS(1)MEIEK 120.55 0.00090656 762850000 1260410 1095900 1138230 1128570 1398580 1018940 1329290 1036380 1560460 TRUE FALSE 1181523.188 1177041.576 1165229.353 1157531.017 1288741.168 1313091.437 1129975.305 1165774.324 1300009.145 0.908857597 0.905410228 0.896323966 0.890402211 0.991332387 1.010063231 0.869205659 0.896743172 1 20.31009034 2.783579346 24.99062607 0.943896853 0.90045469 0.247001773 0.044461233 784.0895407 435259.4402 0.013987197 0.014835556 607.5462518 -2.783579346 -0.043442164 RLS(ph)MSEVKDDNSATK ddPTM_SK-BR-3_Pertuzumab_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(0.844)MS(0.156)EVKDDNSATK 148.2 1.87E-06 289090000 791910 460950 543950 550900 675230 383950 708590 515000 893130 TRUE FALSE 742345.7667 495079.2176 556852.7509 565037.0267 622200.1595 494790.1321 602343.5077 579298.8837 744060.8332 0.997694992 0.665374652 0.748396806 0.759396277 0.836222163 0.664986128 0.809535297 0.778563873 1 19.50506105 0.301575282 1.323121785 1.000155038 0.764745289 0.329072422 0.095056505 4.879657094 8.221983564 0.082497548 0.024128422 2.002512714 -0.301575282 -0.235409749 RLS(ph)PGSDIYVTVSSMALAR ddPTM_SK-BR-3_Pertuzumab_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(0.868)PGS(0.132)DIYVTVSSMALAR 66.853 0.016287 22242000 35191 42249 40159 37136 49988 36111 48703 41354 40849 TRUE FALSE 32988.45813 45377.15992 41111.59044 38088.97263 46062.14412 46535.65949 41400.43729 46517.13793 34031.03801 0.969363853 1.333405108 1.208061607 1.119242164 1.353533328 1.367447548 1.216549354 1.366903294 1 15.05456354 4.74814792 24.48278723 1.257404189 0.969363646 0.341727836 0.11952035 1007.014167 2571508.243 0.025273952 0.320953603 55994.82861 -4.74814792 -0.288040543 RLS(ph)PISGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSPISGSR 9 1 E9PQ01 E9PQ01 PCF11 1 RLS(0.998)PIS(0.002)GSR 52.071 0.092214 153110000 61911 123310 114580 111560 141310 88923 119390 103290 178730 TRUE FALSE 58036.10102 132440.0007 117297.8917 114422.8185 130212.0826 114593.6266 101488.5779 116185.9839 148898.8084 0.389768741 0.889463134 0.787769177 0.76846027 0.874500502 0.769607412 0.681594292 0.780301637 1 17.18397268 -2.7529437 1.796102046 6.404857887 0.759929084 0.244596967 0.139210968 3404899.635 86414.79472 75314023.62 0.033377723 0.001766267 2.7529437 -5.644928804 RLS(ph)PPFPLEPAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLSPPFPLEPAQK 13 1 Q8NEV8-2;Q8NEV8;E9PPH6 Q8NEV8-2 EXPH5 Exophilin-5 1 RLS(1)PPFPLEPAQK;RLS(1)PPFPLEPAQK 138.97 2.63E-05 315380000 386950 362450 378420 386840 432830 317240 465630 364850 487630 TRUE FALSE 362731.4902 389286.1751 387396.3011 396766.9693 398837.2778 408822.038 395813.1042 410402.3256 406241.4028 0.89289641 0.958263172 0.953611076 0.976677824 0.981774076 1.006352467 0.974329799 1.010242488 1 18.63197776 7.99717649 0.333081664 0.998768786 2.89E-14 0.822278102 0.014281963 23.04514764 0.32898571 0.011640173 14.20642818 99351971.73 -7.99717649 -0.998768786 RLS(ph)PPSSSAASSYSFSDLNSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RLSPPSSSAASSYSFSDLNSTR 22 1 P50402 P50402 EMD Emerin 1 RLS(0.981)PPS(0.012)S(0.006)S(0.001)AASSYSFSDLNSTR;RLS(0.949)PPS(0.031)S(0.01)S(0.01)AASSYSFSDLNSTR;RLS(0.977)PPS(0.017)S(0.005)S(0.001)AASSYSFSDLNSTR;RLS(0.993)PPS(0.006)SSAASSYSFSDLNSTR;RLS(0.958)PPS(0.026)S(0.011)S(0.005)AASSYSFSDLNSTR;RLS(0.918)PPS(0.062)S(0.016)S(0.003)AASSYSFSDLNSTR 240.68 7.56E-31 5861240000 988349 1005569 874046 968185 1050320 767164 1061294 890108 857121 TRUE FALSE 926490.0003 1080022.375 894778.7839 993030.2662 967832.104 988631.7929 902162.8173 1001239.943 714061.9679 1.297492433 1.51250511 1.253082819 1.390677996 1.355389515 1.384518203 1.263423705 1.402175145 1 19.44568975 -3.441386965 0.293063284 4.42E-19 1.382237205 0.678208042 0.076752208 50.41467257 1.097733037 30.67680923 0.075106785 0.00036192 3.441386965 1.382237205 RLS(ph)PS(ph)ASPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSPSASPPR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RLS(0.835)PS(0.606)AS(0.56)PPR 112.33 0.0010928 2421500000 663420 719930 675500 658350 686130 643920 806690 613970 666240 TRUE FALSE 621897.7264 773234.3663 691523.179 675244.3756 632244.1175 829809.2508 685734.3234 690625.506 555040.2399 1.120455206 1.393114068 1.245897377 1.216568326 1.139096001 1.495043406 1.235467763 1.244280065 1 19.08223284 0.669272428 2.300835721 1.000107931 1.277650612 0.350271281 0.110990558 2.060358669 13.00715207 0.097301098 0.026279885 4.669522024 -0.669272428 0.277542681 RLS(ph)PSAS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLSPSASPPR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RLS(0.996)PS(0.019)AS(0.985)PPR;RLS(1)PS(0.001)AS(1)PPR 96.707 0.022946 3336500000 556910 608880 561160 596830 578240 515950 613460 496720 575220 TRUE FALSE 522053.9972 653962.1087 574470.9802 612145.6682 532827.3629 664896.3893 521477.3681 558736.5854 479212.0659 1.089400777 1.364661191 1.198782378 1.277400366 1.111882193 1.387478397 1.088197492 1.165948492 1 18.87030471 1.053296324 1.00358537 1.004474131 1.244475948 0.318041587 0.103146464 0.546728756 1.181754302 0.085475554 0.028592163 11.3056705 -1.053296324 0.240001816 RLS(ph)QIGVENTEENRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSQIGVENTEENRR 15 2 P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5;J3QKK1 P09972 ALDOC Fructose-bisphosphate aldolase C;Fructose-bisphosphate aldolase 1 RLS(1)QIGVENTEENRR 163.79 7.92E-07 63307000 19558 28452 27779 30063 31628 24439 30240 19509 24708 TRUE FALSE 18333.89969 30558.61568 28437.931 30834.46748 29144.06446 31494.14257 25705.79273 21944.74159 20584.07518 0.890683673 1.484575596 1.381550094 1.49797682 1.415854937 1.530024657 1.248819415 1.066102868 1 14.32924101 1.33951508 2.83731611 1.015189116 1.388976092 0.359603234 0.180393478 0.25208603 3.348387671 0.14064312 0.043036986 21.85320199 -1.33951508 0.373786976 RLS(ph)QPAGGLLDSITNIFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLSQPAGGLLDSITNIFGR 19 1 Q676U5-3;Q676U5;Q676U5-4 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 1 RLS(1)QPAGGLLDSITNIFGR;RLS(1)QPAGGLLDSITNIFGR 185.18 1.43E-14 188499000 116891 145007 130980 117249 151792 111296 149585 115831 158440 TRUE FALSE 109575.001 155743.4692 134086.9075 120257.8078 139870.8686 143425.3485 127156.1179 130292.7553 131995.3404 0.830142947 1.179916417 1.015845764 0.91107616 1.059665198 1.086594027 0.963337929 0.987101173 1 17.01012748 1.652708175 12.14720169 0.981627923 1.030950643 0.000902298 0.095305916 0.385183923 84.33349929 0.043126087 0.023499199 44.94777264 -1.652708175 0.049322721 RLS(ph)QPESAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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;RLS(0.998)QPES(0.002)AEK;RLS(1)QPESAEK;RLS(0.999)QPES(0.001)AEK 226.42 3.22E-09 7497140000 10220570 8535175 8329799 9525462 11950162 7107528 8731590 7401614 14386095 TRUE FALSE 9580882.768 9167128.238 8527385.766 9769901.481 11011644.48 9159355.953 7422369.14 8325721.801 11984962.81 0.799408636 0.764885831 0.71150707 0.815179958 0.918788373 0.764237328 0.619306815 0.694680654 1 23.5147221 4.735604881 6.455466586 0.763441746 0.800107141 0 0.111040778 0.950430294 238.6176571 0.025752755 0.15401218 54400.74925 -4.735604881 0.036665395 RLS(ph)QRPTPEELEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RLSQRPTPEELEQR 14 2 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 RLS(0.998)QRPT(0.002)PEELEQR;RLS(1)QRPTPEELEQR;RLS(0.996)QRPT(0.004)PEELEQR;RLS(1)QRPTPEELEQR 211.09 3.40E-09 1601450000 557567 747890 544463 518333 753761 296901 642538 569620 1038210 TRUE FALSE 522669.8768 803264.5538 557377.9195 531634.3023 694563.6516 382611.4989 546195.3919 640738.3109 864926.0439 0.604294298 0.928708945 0.644422634 0.614658682 0.803032417 0.442363254 0.631493751 0.740801269 1 19.72221725 -0.931414138 9.132104813 0.999999988 0.683574746 0.380362841 0.129571474 0 0 0.126108084 0.029723961 0.117107811 0.931414138 -0.316425242 RLS(ph)QRPTTEELEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RLSQRPTTEELEQR 14 2 J3KP75;O75167-5;O75167-2;O75167;O75167-4 J3KP75 PHACTR2 Phosphatase and actin regulator;Phosphatase and actin regulator 2 1 RLS(0.981)QRPT(0.014)T(0.005)EELEQR;RLS(0.999)QRPT(0.001)TEELEQR;RLS(1)QRPTTEELEQR;RLS(0.996)QRPT(0.003)TEELEQR 203.26 1.20E-08 2523000000 1058220 1421410 1177750 1211180 1466740 682179 1144250 1015190 1572430 TRUE FALSE 991987.8992 1526652.675 1205686.786 1242260.929 1351548.157 879113.003 972680.3352 1141938.706 1309981.275 0.757253495 1.16540038 0.920384749 0.948304341 1.031730898 0.671088221 0.742514686 0.871721397 1 20.32111476 2.251846247 24.99997266 0.789128826 0.985221898 0.197835492 0.133149223 245.0034784 461029.9141 0.042854447 0.03565979 178.5855219 -2.251846247 0.196093072 RLS(ph)QSDEDVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RLSQSDEDVIR 11 1 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y917;Q9H7D7-3;Q9H7D7-4 A0A499FIZ0 WDR26 WD repeat-containing protein 26 1 RLS(1)QSDEDVIR;RLS(1)QSDEDVIR;RLS(1)QSDEDVIR;RLS(1)QSDEDVIR;RLS(0.999)QS(0.001)DEDVIR;RLS(0.999)QS(0.001)DEDVIR 198.38 3.30E-08 2821380000 1708960 1899710 1937030 1936565 2114710 1724750 2073250 1760460 2406810 TRUE FALSE 1601999.244 2040366.505 1982977.266 1986260.536 1948629.207 2222657.326 1762385.41 1980257.306 2005097.862 0.79896312 1.017589487 0.988967822 0.990605284 0.971837457 1.108503165 0.878952316 0.9876113 1 20.93524122 4.743672952 24.80435729 0.989907684 0.798963031 0.547692234 0.055354713 380.6549676 1846820.581 0.012401012 0.105712742 55420.82066 -4.743672952 -0.190944653 RLS(ph)S(ph)LRAS(ph)TSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RLSSLRASTSK 11 2 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 3 RLS(1)S(1)LRAS(0.803)T(0.17)S(0.026)K;RLS(1)S(1)LRAS(0.808)T(0.166)S(0.027)K;RLS(1)S(1)LRAS(0.852)T(0.147)S(0.001)K 99.044 0.0033471 1742650000 2707150 2001210 2368650 2748930 3168270 2104510 3474700 2040980 2743000 TRUE FALSE 2537714.314 2149381.671 2424835.497 2819472.198 2919446.854 2712047.873 2953700.993 2295800.846 2285175.58 1.110511742 0.94057616 1.061115618 1.233809876 1.277559099 1.186800654 1.292548817 1.00464965 1 21.12387359 3.374146024 4.519558697 1.193886575 1.012434285 0.210575484 0.108972915 0.209163191 7.381514862 0.027962004 0.038589914 2366.715331 -3.374146024 -0.18145229 RLS(ph)S(ph)LRAS(ph)TSKSESSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSSLRASTSKSESSQK 17 3 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 3 RLS(1)S(1)LRAS(0.746)T(0.12)S(0.089)KS(0.015)ES(0.015)S(0.016)QK 66.383 0.080411 294690000 163470 147950 158400 239820 292410 93232 261680 188560 554200 TRUE FALSE 153238.7045 158904.3719 162157.3228 245974.1872 269445.2981 120146.5649 222443.5133 212102.1311 461700.4397 0.331900712 0.344172018 0.351217605 0.5327571 0.583593332 0.26022623 0.481791859 0.459393392 1 18.81659758 -5 0.248977689 4.563332639 0.356470102 0.791320576 0.095037538 79.61326016 0.790121207 144.2045529 0.135933834 1.00E-05 5 -4.206862537 RLS(ph)S(ph)LRAST(ph)SK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSSLRASTSK 11 2 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 3 RLS(1)S(1)LRAS(0.14)T(0.84)S(0.02)K 95.197 0.012705 435620000 1102300 816500 957540 1123300 1286700 795560 1407800 889190 1183600 TRUE FALSE 1033309.011 876954.5096 980253.301 1152125.78 1185647.772 1025225.257 1196713.459 1000207.329 986049.5137 1.047928118 0.889361536 0.994121783 1.168425889 1.202422146 1.039729996 1.213644389 1.014358118 1 19.91130057 3.363786023 4.989850105 1.122826362 0.954976608 0.33210016 0.084072403 0.168341277 6.653904151 0.021215355 0.029059872 2310.925915 -3.363786023 -0.167849754 RLS(ph)SAS(ph)TGKPPLSVEDDFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSSASTGKPPLSVEDDFEK 20 2 O75152;A0A1B0GTU1;A0A494C0C4 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 2 RLS(0.822)S(0.179)AS(0.906)T(0.093)GKPPLSVEDDFEK 148.02 6.18E-08 67233000 93958 66115 66755 67946 87541 50930 98152 64757 131900 TRUE FALSE 88077.3365 71010.22339 68338.46012 69689.60939 80665.88298 65632.66422 83435.0188 72842.054 109885.0379 0.801540757 0.646222859 0.621908691 0.634204717 0.734093417 0.597284812 0.759293716 0.662893287 1 16.74563543 -0.665645515 0.572826588 1.057111401 0.666934828 0.693487195 0.065890946 7.109795585 1.68861633 0.83852789 0.025287897 0.215950635 0.665645515 -0.390176573 RLS(ph)SASTGKPPLSVEDDFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLSSASTGKPPLSVEDDFEK 20 2 O75152;A0A1B0GTU1;A0A494C0C4 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 RLS(0.896)S(0.069)AS(0.015)T(0.02)GKPPLSVEDDFEK;RLS(0.979)S(0.021)ASTGKPPLSVEDDFEK 299.97 4.45E-55 633450000 767100 444739 577506 587956 739549 427900 756001 513890 956870 TRUE FALSE 719088.5803 477667.9383 591204.715 603043.9464 681467.8047 551427.7836 642645.6684 578050.2977 797162.2154 0.902060542 0.599210461 0.74163665 0.756488372 0.854867167 0.691738486 0.806166745 0.725135094 1 19.6045138 -5 0.251917981 2.556970329 0.724671994 0.412560811 0.086537645 163.2583633 1.616595965 130.9258119 0.114335173 1.00E-05 5 -1.832298334 RLS(ph)SDCSVTQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSSDCSVTQER 12 1 E7EX48;P51957-3;P51957-2;P51957 E7EX48 NEK4 Serine/threonine-protein kinase Nek4 1 RLS(0.552)S(0.058)DCS(0.285)VT(0.106)QER 72.286 0.013955 0 98065 124450 107710 138990 142760 119570 135510 109680 151440 TRUE FALSE 91927.2867 133664.4075 110264.9321 142556.7187 131548.2055 154087.9179 115191.5335 123373.7894 126163.6857 0.728635076 1.059452304 0.873983123 1.12993464 1.04267884 1.221333359 0.913032406 0.977886694 1 16.94493719 4.743385857 24.46022839 1.020086844 0.728634913 0.468098719 0.099787567 349.4652767 1771436.156 0.023129014 0.188614904 55384.19621 -4.743385857 -0.291451931 RLS(ph)SQFENSVYKGDDDDEDVIILEENSTPKPAVDHDIDMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSSQFENSVYKGDDDDEDVIILEENSTPKPAVDHDIDMK 40 3 Q14149 Q14149 MORC3 MORC family CW-type zinc finger protein 3 1 RLS(0.684)S(0.158)QFENS(0.158)VYKGDDDDEDVIILEENSTPKPAVDHDIDMK 138.24 7.12E-10 105840000 212600 80348 118530 136530 173510 78343 167850 94030 280040 TRUE FALSE 199293.7455 86297.04952 121341.5876 140033.5909 159883.2245 100959.3523 142682.4507 105769.8525 233299.5149 0.854239862 0.36989811 0.520110758 0.600230956 0.685313146 0.432745659 0.611584858 0.453365077 1 17.83182378 -1.305510917 3.6721245 1.001257879 0.547669906 0.486087274 0.13914097 44410412.77 66565233.95 611239.5968 0.030510251 0.049486767 1.305510917 -0.453587973 RLS(ph)STSLASGHSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RLSSTSLASGHSVR 14 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3;M0QZ82 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 RLS(0.595)S(0.386)T(0.019)SLASGHSVR;RLS(0.687)S(0.291)T(0.021)SLASGHSVR;RLS(0.738)S(0.249)T(0.013)SLASGHSVR;RLS(0.775)S(0.208)T(0.018)SLASGHSVR 173.18 1.68E-06 5187220000 720894 1198140 940560 1018390 1311760 829530 1176420 1128330 1352150 TRUE FALSE 675774.5314 1286851.532 962870.5274 1044523.612 1208739.661 1069001.845 1000026.742 1269204.484 1126467.43 0.599905966 1.142377931 0.854769967 0.927255936 1.073035606 0.948986022 0.887754689 1.126712101 1 20.10337417 4.754470257 24.51922044 0.981614697 0.599905591 0.619121145 0.096903553 1616.63536 2491431.526 0.021980877 0.553572417 56815.94789 -4.754470257 -0.381709106 RLS(ph)TIFEECDEELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RLSTIFEECDEELER 15 1 Q5T5P2;Q5T5P2-3;A0A0U1RRK8 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 RLS(0.991)T(0.009)IFEECDEELER;RLS(0.992)T(0.008)IFEECDEELER;RLS(0.985)T(0.015)IFEECDEELER;RLS(0.948)T(0.052)IFEECDEELER 301.57 1.48E-44 667026000 144652 164566 157215 158929 183283 110995 197991 138313 201309 TRUE FALSE 135598.4895 176750.6379 160944.214 163007.3872 168888.6925 143037.4546 168304.0876 155581.6825 167709.2274 0.808533267 1.053911228 0.959662247 0.971964332 1.007032798 0.852889593 1.003546974 0.927687074 1 17.35560254 RLS(ph)TSPDVIQGHQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RLSTSPDVIQGHQPR 15 1 Q9Y385 Q9Y385 UBE2J1 Ubiquitin-conjugating enzyme E2 J1 1 RLS(0.936)T(0.062)S(0.002)PDVIQGHQPR;RLS(0.987)T(0.013)SPDVIQGHQPR;RLS(0.963)T(0.03)S(0.008)PDVIQGHQPR;RLS(0.862)T(0.104)S(0.034)PDVIQGHQPR;RLS(0.671)T(0.299)S(0.03)PDVIQGHQPR;RLS(0.709)T(0.236)S(0.056)PDVIQGHQPR;RLS(0.843)T(0.078)S(0.078)PDVIQGHQPR 228.94 3.24E-13 8902850000 1920146 2216832 1851557 1629515 2347815 1869418 2297246 2201614 2874734 TRUE FALSE 1799967.489 2380968.548 1895476.806 1671331.114 2163427.081 2409088.629 1952795.289 2476490.354 2394922.324 0.751576563 0.9941736 0.791456486 0.697864435 0.903339143 1.005915142 0.815389823 1.034058737 1 21.19154743 2.48928298 24.62634113 0.938548604 0.833165353 0.337468544 0.097314581 769.4932235 1558154.241 0.032316371 0.029012254 308.5197564 -2.48928298 -0.105383252 RLS(ph)YNTASNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSYNTASNK 10 1 P49207 P49207 RPL34 60S ribosomal protein L34 1 RLS(0.716)Y(0.246)NT(0.037)AS(0.001)NK 61.657 0.055227 288600000 692790 560770 455800 397580 638110 339550 490530 428170 756960 TRUE FALSE 649429.5106 602289.9943 466611.7912 407782.5759 587995.4146 437572.5729 416979.5804 481627.967 630618.4859 1.029829485 0.955078241 0.739927233 0.646639109 0.932410685 0.693878443 0.661223211 0.763739056 1 19.26640794 4.177632443 1.98512337 0.753660892 1.020931249 0.37463575 0.114250278 0.323430332 2.383054781 0.028258641 0.103565951 15053.32519 -4.177632443 0.267270357 RLSELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLSELLR 7 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 179.21 0.0011295 2089120000 512150 1531020 492970 501430 1526770 294140 500510 1407450 1164220 FALSE TRUE 480095.4457 1644378.314 504663.4812 514297.5427 1406863.643 379053.443 425463.172 1583173.231 969904.1609 0.494992665 1.695402886 0.52032304 0.530256043 1.450518205 0.390815359 0.438665168 1.632298628 1 19.88748267 5.000029578 24.99933151 0.910574131 0.078718855 0.071920035 0.497344507 54553.20518 657341.2778 0.112024526 1307247.653 100006.8108 -5.000029578 -0.831855276 RLSLGQGDST(ph)EAATEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSLGQGDSTEAATEER 17 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RLS(0.39)LGQGDS(0.164)T(0.445)EAATEER 200.19 2.44E-11 642140000 367240 420430 384720 427680 480500 412910 478490 385770 446910 TRUE FALSE 344255.1039 451559.0747 393845.7401 438654.9929 442763.4682 532110.414 406744.8666 433934.2337 372317.8339 0.924626952 1.212832246 1.057821314 1.178173466 1.189208327 1.429183256 1.092466784 1.165494087 1 18.5061752 4.744657646 24.36207971 1.171087958 0.924626795 0.305137959 0.114040602 586.553787 2343613.85 0.025478369 0.232658831 55546.62106 -4.744657646 -0.246461162 RLSPS(ph)AS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSPSASPPR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RLS(0.331)PS(0.7)AS(0.969)PPR 111.72 0.0011471 2002300000 691470 733840 685910 680550 644130 622250 721380 599550 645710 TRUE FALSE 648192.127 788174.2772 702180.1091 698014.0652 593542.6281 801883.4736 613215.766 674405.1373 537936.8296 1.204959563 1.465179987 1.305320756 1.297576271 1.10336864 1.490664758 1.139940105 1.253688352 1 19.03707724 -0.954635074 0.211947585 0.771328785 1.383478192 0.362392325 0.121300497 16.36084263 0.804260329 2.46330024 0.288010355 0.111010722 0.954635074 0.612149407 RLSQPESAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSQPESAEK 10 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 73.848 0.070167 86376000 149800 129850 136660 122530 151050 98488 153960 132480 188960 FALSE TRUE 140424.2854 139464.2291 139901.6397 125674.3272 139187.1423 126919.8868 130875.1273 149020.4196 157421.3553 0.892028182 0.885929542 0.888708139 0.798330868 0.884169381 0.806243134 0.831368318 0.946634079 1 17.26427174 1.063626936 4.362974513 0.998810442 0.85733511 0.683519548 0.034357042 0.111970844 4.057035231 0.034256715 0.008740397 11.57782381 -1.063626936 -0.141475332 RLSS(ph)AS(ph)TGKPPLSVEDDFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSSASTGKPPLSVEDDFEK 20 2 O75152;A0A1B0GTU1;A0A494C0C4 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 2 RLS(0.381)S(0.62)AS(0.893)T(0.106)GKPPLSVEDDFEK 142.22 9.76E-08 35189000 92716 50642 61326 73789 82703 55265 85114 56670 122660 TRUE FALSE 86913.07106 54391.58637 62780.68168 75682.55066 76207.83999 71219.10835 72351.94586 63745.37425 102187.2536 0.850527517 0.532273688 0.614369009 0.740626135 0.745766593 0.696947083 0.708032982 0.623809448 1 16.64085573 -5 0.303510392 3.766042607 0.65743746 0.523604779 0.089915452 213.3481585 1.960041152 376.1601351 0.087431928 1.00E-05 5 -3.108605146 RLSS(ph)LR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLSSLR 6 1 P62753;A2A3R5;Q9Y253-2;Q9Y253 P62753 RPS6;POLH 40S ribosomal protein S6;DNA polymerase eta 1 RLS(0.01)S(0.99)LR;RLSS(1)LR 110.55 0.030301 5140600000 4125800 4767400 4563200 5675500 4998000 4360600 3634700 3838700 2827600 TRUE FALSE 3867573.543 5120383.256 4671441.259 5821142.939 4605477.241 5619434.432 3089710.478 4317970.145 2355655.293 1.641824911 2.173655573 1.983075059 2.471135296 1.955072652 2.385507951 1.311614007 1.833022921 1 21.16769701 1.197831512 0.992631734 1.066382467 2.099927623 0.520091949 0.315001395 0.354935296 0.746627008 0.265269102 0.091140481 15.76999342 -1.197831512 1.033545156 RLSS(ph)LRAS(ph)TSKSESSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLSSLRASTSKSESSQK 17 3 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 RLS(0.489)S(0.548)LRAS(0.738)T(0.153)S(0.069)KS(0.003)ESSQK 66.3 0.059454 259780000 93894 93310 68690 91705 195220 51063 183750 124040 797870 TRUE FALSE 88017.34215 100218.7695 70319.35924 94058.30556 179888.2087 65804.05916 156198.3934 139526.667 664700.3426 0.132416574 0.150772857 0.105791068 0.141504825 0.270630534 0.098998082 0.234990692 0.209909125 1 19.34234457 -5 0.319442397 8.918319322 0.127905752 0.96691352 0.048611678 46.9175051 0.416297023 250.9579119 0.039010942 1.00E-05 5 -8.790413571 T(ph)SDANETEDHLESLICK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSDANETEDHLESLICK 17 0 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 T(0.5)S(0.5)DANETEDHLESLICK 174.63 4.89E-09 62027000 172420 125480 132030 191180 180570 88970 107100 49864 74739 TRUE FALSE 161628.54 134770.6698 135161.8139 196086.0025 166388.7606 114654.1947 91041.34927 56089.63016 62264.57807 2.595834502 2.164483787 2.170765757 3.149238436 2.672286005 1.841403222 1.462169216 0.900827275 1 15.92612404 1.759674517 1.849079163 0.987101517 2.464704495 0.821605876 0.305429353 0.149803153 1.016061996 0.233771802 0.096738004 57.50088336 -1.759674517 1.477602978 up RLTAEDLFEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLTAEDLFEAR 11 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 185.57 7.07E-06 173681000 188834 291720 230760 264300 316560 179308 249000 233100 271730 FALSE TRUE 177015.217 313319.2523 236233.7362 271082.3855 291698.6545 231071.3088 211664.7616 262203.0481 226376.5076 0.781950472 1.384062577 1.043543514 1.197484617 1.288555326 1.020738906 0.935012046 1.158260859 1 17.78836472 2.115670482 10.85418515 1.012434762 1.162073401 0.085439228 0.167495425 0.613675308 55.49412948 0.057288485 0.042307379 130.5180216 -2.115670482 0.149638638 RLTAIIEEAEEAPGARPQLQDAWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLTAIIEEAEEAPGARPQLQDAWR 24 2 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 110.94 0.0010559 90914000 24853.4 54004 40139 49584 78473 35025 42085 33088 148244 FALSE TRUE 23297.87006 58002.51235 41091.11604 50856.40939 72310.04712 45136.14892 35774.74495 37219.10964 123501.1187 0.188645012 0.469651716 0.332718573 0.411789058 0.585501151 0.365471579 0.289671424 0.301366579 1 16.91416458 -1.976952929 2.865652771 1.536548988 0.375312008 0.773234106 0.107480164 36241385.38 22623401 128941593.5 0.026127883 0.010545012 1.976952929 -1.16123698 RLTDADAMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLTDADAMK 9 1 P25705;P25705-2;P25705-3;K7ENJ4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 73.841 0.068594 261040000 251170 316100 239610 207210 407520 147020 208720 329620 460150 FALSE TRUE 235449.7181 339504.3729 245293.6624 212527.3594 375515.0231 189462.2873 177424.3737 370773.7826 383347.9923 0.614193169 0.885629714 0.639872041 0.554397998 0.979566949 0.494230545 0.462828493 0.967198968 1 18.5482951 1.133291906 8.284781443 0.995858334 0.670253428 0.408000572 0.161173455 0.273860093 19.06690206 0.156851276 0.039285041 13.59226728 -1.133291906 -0.325604907 RLTLEDLEDSWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLTLEDLEDSWDR 13 1 Q6P2Q9;I3L3Z8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 194.48 1.58E-06 144533000 111660 156974 136216 150298 179440 128456 162767 128691 191971 FALSE TRUE 104671.3999 168596.5183 139447.1078 154154.9011 165347.5062 165539.1619 138361.5994 144758.3546 159929.7999 0.654483404 1.054190766 0.871926982 0.96389104 1.033875527 1.035073901 0.865139577 0.905136846 1 17.28707926 4.749801707 24.78375946 0.959561551 0.654483204 0.675082658 0.067815738 954.5899529 2104584.367 0.016175974 0.251751361 56208.46262 -4.749801707 -0.305078347 RLVELLMHNDYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RLVELLMHNDYK 12 1 C9JYI4;P52294;Q5TFJ7;O60684;O15131 C9JYI4;O60684;O15131 KPNA1;KPNA6;KPNA5 "Importin subunit alpha-5;Importin subunit alpha-5, N-terminally processed;Importin subunit alpha-7;Importin subunit alpha-6" 0 ; 142.1 3.97E-05 236190000 560050 625710 543210 538830 768130 396800 649590 642500 901350 FALSE TRUE 524997.4702 672038.2195 556095.1977 552657.29 707804.1683 511349.7185 552190.01 722717.5393 750908.8621 0.699149386 0.894966425 0.740562838 0.735984509 0.942596637 0.680974409 0.735362223 0.962457065 1 19.51827829 1.175311118 6.266919553 0.990118371 0.781344126 0.514247104 0.083050123 0.173689307 12.48959666 0.074288823 0.018933387 14.97307908 -1.175311118 -0.208774245 RLVEVDSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLVEVDSSR 9 1 Q03252 Q03252 LMNB2 Lamin-B2 0 96.113 0.012166 121880000 67763 93995 81567 70734 103700 65942 92255 73669 103540 FALSE TRUE 63521.83479 100954.4876 83501.80776 72549.15419 95555.82031 84978.38492 78422.2192 82866.73682 86258.50511 0.736412423 1.170371403 0.968041443 0.841066676 1.10778433 0.98515949 0.90915347 0.960679028 1 16.39637909 1.968051924 22.49602229 0.946676646 0.992511546 0 0.124047694 878.1105387 618311.0582 0.048165558 0.031131193 92.90774612 -1.968051924 0.0458349 RLVIQDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLVIQDK 7 1 P46777;A0A2R8Y4A2;R4GNJ2 P46777 RPL5 60S ribosomal protein L5 0 113.7 0.0097347 349710000 332360 311370 302130 321670 369780 247830 346930 306660 449900 FALSE TRUE 311558.1809 334424.1588 309296.6663 329924.5968 340738.9704 319374.4978 294911.0672 344947.176 374808.7835 0.831245677 0.892252726 0.825211894 0.880247772 0.909100815 0.852099822 0.786830726 0.920328421 1 18.51579524 0.996449423 22.5387375 1.000000002 0.85406661 0.652548533 0.035040165 20.03746565 127199.7297 0.034526762 0.008631691 9.918578227 -0.996449423 -0.145933392 RLVPDSDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RLVPDSDVR 9 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 83.862 0.025466 218670000 200000 307950 225760 237200 322020 210450 224820 266690 339670 FALSE TRUE 187482.357 330750.9384 231115.1338 243286.9536 296729.8482 271203.4986 191110.3281 299986.8336 282976.8826 0.662535947 1.168826709 0.816727966 0.859741444 1.048601021 0.958394538 0.675356681 1.060110744 1 18.11032467 RMDEISDHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RMDEISDHAK 10 1 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 100.09 0.0027611 881830000 422160 565060 513770 478370 626480 418000 598000 538240 606900 FALSE TRUE 395737.7592 606897.6303 525956.867 490645.7841 577278.7879 538669.8143 508335.4516 605440.4488 505604.4693 0.782702257 1.200340715 1.040253595 0.970414254 1.141759662 1.065397652 1.00540142 1.197458657 1 18.94764969 4.754388517 24.60005441 1.076714528 0.782701983 0.572110169 0.080153573 1786.383868 2776377.747 0.018080215 0.451592028 56805.25538 -4.754388517 -0.294012545 RMEDEGGFPVPQENGQPES(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RMEDEGGFPVPQENGQPESPR 21 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR 213.54 2.15E-23 5398400000 2301902 2681156 2668164 2873131 2904793 2405519 2612988 2214503 2920265 TRUE FALSE 2157830.063 2879671.58 2731454.11 2946860.406 2676662.275 3099953.285 2221194.707 2490988.574 2432853.906 0.88695423 1.183659887 1.122736595 1.211277175 1.100214965 1.274204455 0.912999626 1.023895668 1 21.21421826 1.694658796 10.61487371 0.977918624 1.137100783 0.316067903 0.10411 0.12217054 22.79133124 0.044425621 0.024091809 49.50610926 -1.694658796 0.159182159 RMEDEGGFPVPQENGQPES(ph)PRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RMEDEGGFPVPQENGQPESPRR 22 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RMEDEGGFPVPQENGQPES(1)PRR;RMEDEGGFPVPQENGQPES(1)PRR;RMEDEGGFPVPQENGQPES(1)PRR;RMEDEGGFPVPQENGQPES(1)PRR 171.14 3.32E-12 1253300000 332456 346508 373518 392185 406394 295498 357146 310142 371448 TRUE FALSE 311648.1724 372163.8129 382378.0233 402249.1311 374477.4546 380803.4756 303595.2729 348863.9114 309450.9292 1.007100458 1.202658573 1.235666102 1.299880185 1.210135176 1.230577903 0.98107727 1.127364239 1 18.23935113 1.750288052 16.50989222 1.041070514 1.207040519 0.451216019 0.083487345 0.262550104 370.7849389 0.036657553 0.020267441 56.27144294 -1.750288052 0.165970005 RMEEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 162.25 0.0020506 303940000 480380 571930 556540 575560 596790 474960 568320 545970 516360 FALSE TRUE 450313.8733 614276.2923 569741.3916 590329.844 549920.5207 612073.2417 483105.692 614135.5563 430176.1802 1.046812664 1.427964449 1.32443733 1.372297843 1.27836116 1.422843174 1.123041475 1.427637291 1 18.71456812 -3.198400366 0.418450559 1.87E-08 1.315457311 0.338245684 0.13031704 179.6151702 5.146471223 159.1573024 0.068884577 0.000633286 3.198400366 1.315457292 RMEEEQHHWDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RMEEEQHHWDDR 12 1 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 ;; 153.81 2.89E-05 1299370000 580153 537336 596287 586700 667511 500086 572310 547318 797120 FALSE TRUE 543842.2593 577120.9165 610431.2092 601755.7153 615087.3787 644452.71 486497.4286 615651.8571 664075.5224 0.818946401 0.869059161 0.91921956 0.906155543 0.926231065 0.970450933 0.732593526 0.927081087 1 19.3409878 -2.747865984 1.807563858 3.68932321 0.880377593 0.228360962 0.0669263 2252751.109 45903.46957 25022158.93 0.016621372 0.001787039 2.747865984 -2.808945617 RMEEEQHHWDDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RMEEEQHHWDDRR 13 2 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 ;;; 106.13 0.00083976 1909630000 446284 654013 588298 653395 768510 472717 587365 561338 1314280 FALSE TRUE 418351.8811 702436.803 602252.7064 670162.2219 708154.3246 609182.724 499295.0711 631422.285 1094918.177 0.382085063 0.641542736 0.550043573 0.61206603 0.646764607 0.556372829 0.456011309 0.576684448 1 20.06239163 -1.301455553 2.549614376 1.007321776 0.557580201 0.749080605 0.081315756 798147.7252 861556.8547 44471.06978 0.020022481 0.04995103 1.301455553 -0.449741575 RMEELHNQEMQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 RMEELHNQEMQK 12 1 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;;;;;; 118.88 0.00027568 1673947000 1028480 1039026 1004536 952100 1336756 745959 1109326 1036042 1833764 FALSE TRUE 964109.2727 1115956.566 1028364.068 976532.4979 1231772.576 961305.2537 942992.8648 1165394.124 1527696.942 0.631086733 0.730482948 0.673146643 0.639218729 0.806293802 0.629251278 0.617264353 0.762843789 1 20.54292695 0.922536216 5.786211223 0.999983474 0.678710454 0.764097135 0.05682607 0.295462207 21.37395877 0.05265808 0.013253146 8.366353594 -0.922536216 -0.32127302 RMEELHNQEVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RMEELHNQEVQK 12 1 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;;; 145.31 2.83E-05 1891510000 1128333 1724713 1469033 1554229 1913667 1422423 1575528 1626686 1791141 FALSE TRUE 1057712.652 1852412.545 1503879.156 1594113.147 1763375.313 1833053.429 1339292.203 1829781.328 1492187.996 0.708833374 1.241406948 1.007834911 1.068305838 1.181738037 1.228433303 0.897535838 1.226240482 1 20.50899788 4.751813193 24.83523505 1.099921708 0.708833095 0.539601013 0.115281103 1609.170167 3015515.747 0.025892573 0.497855129 56469.40254 -4.751813193 -0.391088612 RMGESDDSILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RMGESDDSILR 11 1 Q8WVC2;P63220 Q8WVC2 RPS21 40S ribosomal protein S21 0 ;;;; 222.25 1.25E-11 3108620000 927483 1392100 1074820 1198860 1494070 900480 1210860 1233520 1751470 FALSE TRUE 869433.4946 1495172.532 1100315.238 1229624.777 1376731.769 1160433.958 1029302.784 1387527.687 1459138.342 0.595854053 1.024695527 0.754085618 0.842706097 0.943523811 0.795287139 0.705418228 0.950922642 1 20.47668524 1.044645505 9.282662856 0.999966879 0.823796752 0.252658382 0.118649942 0.386410782 74.22997748 0.106792855 0.02672061 11.08269816 -1.044645505 -0.176170127 RMKVT(ph)NEDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RMKVTNEDFK 10 2 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 1 RMKVT(1)NEDFK 75.294 0.063391 595960000 150050 568170 477130 495250 620960 1125400 306010 454270 238140 TRUE FALSE 140658.6383 610237.898 488447.7489 507958.9535 572192.3064 1450284.711 260126.6414 510986.6095 198392.8956 0.708990299 3.075906001 2.46202238 2.560368667 2.88413708 7.310164543 1.311169136 2.575629576 1 17.59800084 4.739919758 23.1550778 2.993051431 0.708988519 0.138154517 1.702958943 80.47838297 1370627.913 0.375844482 2.338047274 54943.93472 -4.739919758 -2.284062912 RMS(ph)DEFVDSFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 RMSDEFVDSFK 11 1 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 RMS(0.996)DEFVDS(0.004)FK;RMS(1)DEFVDSFK;RMS(1)DEFVDSFK;RMS(1)DEFVDSFK;RMS(1)DEFVDSFK;RMS(1)DEFVDSFK;RMS(0.995)DEFVDS(0.005)FK;RMS(1)DEFVDSFK 211.7 5.17E-09 1499020000 4738510 3893070 4101410 4386450 4653160 3209020 5039180 3688820 3636950 TRUE FALSE 4441935.118 4181316.954 4198697.382 4499013.733 4287719.584 4135411.98 4283601.74 4149377.297 3029919.549 1.466024112 1.380009233 1.3857455 1.484862439 1.415126545 1.364858674 1.413767485 1.369467812 1 21.53084806 -0.373194153 0.729290401 0.973066628 1.413732326 0.926781641 0.036455547 2.765302981 1.15892884 0.244675436 0.01254868 0.423453617 0.373194153 0.440665698 RMS(ph)DEFVDSFKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RMSDEFVDSFKK 12 2 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 RMS(1)DEFVDSFKK;RMS(1)DEFVDSFKK;RMS(1)DEFVDSFKK;RMS(0.999)DEFVDS(0.001)FKK 151.48 3.28E-05 650067000 2231450 1784630 1820600 2017790 2388970 1316890 2450090 1748280 2671770 TRUE FALSE 2091787.528 1916765.862 1863785.492 2069569.908 2201349.933 1697054.765 2082721.75 1966556.606 2225834.327 0.93977683 0.861144893 0.837342416 0.929795126 0.988999903 0.762435346 0.93570385 0.883514367 1 21.08591478 0.150071534 1.107038002 1.000435097 0.884849034 0.21394264 0.063474717 8.511183187 9.707692884 0.066063228 0.017500541 1.412770228 -0.150071534 -0.115586063 RMS(ph)DPESVSSVFSDTPIVV ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RMSDPESVSSVFSDTPIVV 19 1 Q86WK6 Q86WK6 AMIGO1 Amphoterin-induced protein 1 1 RMS(0.705)DPES(0.072)VS(0.105)S(0.105)VFS(0.013)DTPIVV 72.819 0.019191 21006000 38501 44371 33466 36363 47673 33825 47207 41800 38302 TRUE FALSE 36091.29114 47656.27501 34259.82932 37296.13614 43928.95488 43589.7284 40128.7486 47018.82201 31909.14876 1.131064053 1.493498788 1.073667918 1.16882266 1.376688398 1.366057388 1.25759383 1.473521665 1 14.9616825 -1.049377145 4.59342757 0.999987505 1.290634054 0.30160916 0.13990575 1.67E-05 3.46E-06 0.126612773 0.029841635 0.089253007 1.049377145 0.290646549 RMS(ph)GEPIQTVESIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RMSGEPIQTVESIR 14 1 Q5VT52-2;Q5VT52-3;Q5VT52 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 RMS(1)GEPIQTVESIR;RMS(1)GEPIQTVESIR;RMS(1)GEPIQTVESIR;RMS(1)GEPIQTVESIR;RMS(1)GEPIQTVESIR;RMS(1)GEPIQTVESIR 143.57 5.57E-06 1089990000 497415 551113 550427 553552 617008 489375 550138 519738 715819 TRUE FALSE 466282.6831 591917.98 563483.3884 567757.0815 568550.6806 630649.6182 467649.9141 584628.4334 596344.1845 0.781901954 0.992577769 0.944896258 0.952062745 0.953393519 1.057526232 0.784194642 0.980354045 1 19.18578571 4.748200443 24.02920869 0.949032122 0.781901797 0.377320378 0.070287263 874.7577654 2180430.414 0.016288182 0.205737689 56001.60098 -4.748200443 -0.167130325 RMS(ph)PKPELTEEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RMSPKPELTEEQK 13 2 P41208 P41208 CETN2 Centrin-2 1 RMS(1)PKPELTEEQK;RMS(1)PKPELTEEQK 178.51 7.59E-06 235720000 712120 319030 408700 393120 371280 302210 534740 328750 321640 TRUE FALSE 667549.6804 342651.3132 418394.557 403208.1248 342121.1665 389453.121 454560.7013 369795.1612 267956.2061 2.491264114 1.278758638 1.561428873 1.50475382 1.276780155 1.453420791 1.696399228 1.380058206 1 18.03163771 4.743863782 24.99324391 1.438213707 2.491264557 0.759804013 0.19246953 270.3878748 1274269.429 0.04226128 0.362813436 55445.17798 -4.743863782 1.05305085 RNAET(ph)PEATTQQETDTDLPEAPPPPLEPAVIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RNAETPEATTQQETDTDLPEAPPPPLEPAVIAR 33 1 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 1 RNAET(0.838)PEAT(0.048)T(0.048)QQET(0.065)DT(0.002)DLPEAPPPPLEPAVIAR;RNAET(0.997)PEAT(0.001)T(0.001)QQETDTDLPEAPPPPLEPAVIAR 203.75 2.56E-27 409300000 252110 294880 285030 292260 340390 245720 339620 313060 373080 TRUE FALSE 236330.8851 316713.222 291791.0462 299759.8864 313657.1425 316655.3751 288697.1339 352146.2301 310810.5378 0.760369603 1.018991262 0.938806799 0.964445699 1.009158649 1.018805145 0.928852464 1.132993214 1 18.24567589 4.742710781 24.90607751 0.991603115 0.760369507 0.634492455 0.057079427 249.2232452 1495585.624 0.012284046 0.095060338 55298.17274 -4.742710781 -0.231233608 RNALFPEVFS(ph)PTPDENSDQNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RNALFPEVFSPTPDENSDQNSR 22 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 RNALFPEVFS(0.996)PT(0.004)PDENSDQNSR;RNALFPEVFS(0.984)PT(0.016)PDENSDQNSR;RNALFPEVFS(0.996)PT(0.004)PDENSDQNSR;RNALFPEVFS(0.938)PT(0.062)PDENSDQNSR;RNALFPEVFS(0.995)PT(0.005)PDENSDQNSR 208.58 4.12E-23 568241000 277167 355358 311467 342604 412895 260766 379936 331927 486024 TRUE FALSE 259819.6122 381669.0761 318855.1443 351395.7987 380467.8922 336044.911 322968.124 373368.8166 404903.4546 0.641682874 0.942617485 0.787484376 0.867850829 0.939650892 0.829938365 0.797642303 0.922118131 1 18.62721843 -5 0.15348888 1.550539309 0.798870453 0.315172487 0.084748472 186.4166281 1.681306827 31.41330157 0.377030698 1.00E-05 5 -0.751668856 RNDDISELEDLS(ph)ELEDLKDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RNDDISELEDLSELEDLKDAK 21 2 D6RAY8;Q9H4L7;Q9H4L7-2 D6RAY8 SMARCAD1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 1 RNDDISELEDLS(1)ELEDLKDAK;RNDDISELEDLS(1)ELEDLKDAK;RNDDISELEDLS(1)ELEDLKDAK 303.37 1.37E-55 131560000 365686 165673 233968 225106 249434 171594 337603 194425 385880 TRUE FALSE 342798.366 177939.6013 239517.8314 230882.6011 229844.4598 221130.4022 286982.5643 218699.3892 321474.1351 1.066332649 0.553511408 0.745060972 0.718199618 0.714970303 0.687863744 0.8927081 0.680301665 1 18.29434314 -0.255583224 0.497247356 1.035434094 0.727381326 0.199674903 0.140477263 8.566118224 2.177517082 0.70510223 0.063606432 0.555158222 0.255583224 -0.308052768 RNDFQLIGIQDGYLSLLQDSGEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RNDFQLIGIQDGYLSLLQDSGEVR 24 1 P63241;P63241-2;I3L397;I3L504 P63241 EIF5A Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A 0 ;;;;;; 347.35 1.31E-101 3921206000 1338867 1719487 1377273 1353360 1804284 1304659 1724941 1427535 1985315 FALSE TRUE 1255069.704 1846799.607 1409942.566 1388089.509 1662582.813 1681292.874 1466302.111 1605765.887 1653953.101 0.758830286 1.116597324 0.852468287 0.839255665 1.005217628 1.016529957 0.886543947 0.970865429 1 20.6574869 RNDS(ph)IYEASSLYGISAMDGVPFTLHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RNDSIYEASSLYGISAMDGVPFTLHPR 27 1 E9PLZ8;Q96EY5;M0QZK6;E9PQA6;Q96EY5-2;Q96EY5-3 E9PLZ8 MVB12A Multivesicular body subunit 12A 1 RNDS(1)IYEASSLYGISAMDGVPFTLHPR;RNDS(0.953)IY(0.047)EASSLYGISAMDGVPFTLHPR;RNDS(0.7)IY(0.217)EAS(0.027)S(0.027)LY(0.025)GIS(0.004)AMDGVPFTLHPR 200.33 2.32E-25 170378000 43629.2 71652.7 35595.6 38008.8 55097 25232.4 73353 45341.7 120901 TRUE FALSE 40898.52625 76957.94046 36439.94444 38984.17016 50769.90387 32516.58427 62354.39863 51002.71105 100721.842 0.406054193 0.764064069 0.361787907 0.387047828 0.504060518 0.32283548 0.619075241 0.506371905 1 16.62001705 0.209261779 1.093722268 1.001670588 0.489025571 0.608560951 0.130360077 3.348569047 3.985192747 0.135565712 0.038071865 1.619055659 -0.209261779 -0.512645017 RNEDEDSPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RNEDEDSPNK 10 1 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 0 ;; 193.3 9.43E-07 712771000 3268560 2142390 2703830 2447430 2367460 2118870 2819790 2139790 1876940 FALSE TRUE 3063986.664 2301014.785 2767966.124 2510235.197 2181529.241 2730553.372 2396988.667 2406947.492 1563666.589 1.959488478 1.471550778 1.770176676 1.605351944 1.395137082 1.746250378 1.532928237 1.53929713 1 20.5765015 -2.672608668 0.242699759 4.63E-17 1.704388851 0.648578017 0.151811491 29.02760287 0.791195282 15.4883884 0.224254666 0.002125159 2.672608668 1.704388851 RNEES(ph)DDDLDFDIDLEDTGGDHQMN ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RNEESDDDLDFDIDLEDTGGDHQMN 25 1 Q96MD7-1 Q96MD7-1 1 RNEES(1)DDDLDFDIDLEDTGGDHQMN;RNEES(1)DDDLDFDIDLEDTGGDHQMN 154.42 4.93E-08 167785000 122413 128765 127610 127474 124256 102914 130265 106698 92722 TRUE FALSE 114751.3888 138298.8946 130636.9695 130745.1987 114497.435 132623.6011 110732.9726 120019.4802 77246.09919 1.485529885 1.790367359 1.691178853 1.692579949 1.48224229 1.716897067 1.433508924 1.553728686 1 16.23717446 -0.110029517 0.381103697 0.868964982 1.700619621 0.75747208 0.110061436 2.234659892 0.411885246 0.529284956 0.075384167 0.77619436 0.110029517 0.831654639 RNEIDAEPPAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RNEIDAEPPAKR 12 2 Q8TDN6 Q8TDN6 BRIX1 Ribosome biogenesis protein BRX1 homolog 0 ;;; 143.42 3.50E-05 1871290000 1358530 1285550 1362230 1261880 1412820 1043960 1543760 1185410 1602620 FALSE TRUE 1273502.032 1380733.46 1394542.739 1294261.977 1301862.816 1345334.305 1312287.52 1333411.048 1335132.369 0.953839531 1.034154734 1.044497738 0.96938851 0.975081458 1.007641142 0.98288945 0.998710749 1 20.34855135 3.233300319 24.99989279 0.98840458 1.020638263 0.094458009 0.026654774 176.2370066 837577.4161 0.007444952 0.009159183 1711.198218 -3.233300319 0.032233684 RNELVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 RNELVIR 7 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;; 143.12 0.0039174 10418660000 3312577 4827590 3883220 3935650 5167750 3222780 4045354 4440800 5409190 FALSE TRUE 3105248.719 5185029.787 3975331.812 4036645.442 4761895.761 4153144.269 3438790.723 4995243.655 4506361.244 0.689081179 1.150602339 0.882160039 0.895766057 1.056705289 0.92161814 0.763096995 1.108487177 1 22.10353154 2.018172209 24.91043928 0.908743466 0.958138378 0 0.148417879 1100.766095 1508922.424 0.051792284 0.038243894 104.2730816 -2.018172209 0.049394912 RNES(ph)PGAPPAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RNESPGAPPAGK 12 1 P49796-1;P49796-4;P49796-6;P49796;C9J582;P49796-2;H7BXY1;A0A087WUY2;P49796-7;P49796-8;P49796-9 P49796-1 RGS3 Regulator of G-protein signaling 3 1 RNES(1)PGAPPAGK;RNES(1)PGAPPAGK;RNES(1)PGAPPAGK 116.19 9.10E-05 896300000 1552734 1337692 1478896 1327587 1591257 1277951 1856520 1532031 2434680 TRUE FALSE 1455551.151 1436736.108 1513976.112 1361655.13 1466286.094 1646874.708 1578152.061 1723308.443 2028316.179 0.717615511 0.708339322 0.746420172 0.671322915 0.72290805 0.811941809 0.778060185 0.849625152 1 20.95185113 0.896115953 0.618868589 1.003839758 0.711596946 0.911371534 0.027975771 0.249698308 0.218183005 0.028396881 0.011675388 7.872559519 -0.896115953 -0.292242812 RNGAAGPHS(ph)PDPLLDEQAFGDLTDLPVVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RNGAAGPHSPDPLLDEQAFGDLTDLPVVPK 30 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;RNGAAGPHS(0.827)PDPLLDEQAFGDLT(0.173)DLPVVPK;RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK 147.76 1.51E-08 633906000 441454 360635 449064 614192 758373 322162 339209 240366 433345 TRUE FALSE 413824.1822 387336.7906 459716.0101 629953.2065 698813.4437 415164.9395 288347.7595 270376.2242 361016.92 1.146273649 1.072904812 1.273391868 1.744940948 1.935680587 1.149987484 0.798709821 0.748929508 1 18.46170693 1.997022044 24.9655382 0.86372274 1.391211439 0.501406998 0.265150263 116.9856692 980747.499 0.113005801 0.081894196 99.31664577 -1.997022044 0.527488699 RNLDIERPTYTNLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 310.74 2.12E-56 5939900000 793234 897345 824361 863679 993619 669129 912861 875802 1210199 FALSE TRUE 743586.8999 963785.3575 843915.2322 885842.4653 915584.1718 862295.6799 775985.9676 985147.8076 1008208.969 0.737532519 0.955938092 0.837043964 0.878629821 0.908129366 0.855274756 0.769667789 0.977126606 1 19.94336326 1.101952404 7.499023401 0.999143312 0.857378644 0.460259636 0.062588463 0.199399658 12.06270012 0.057758632 0.01447719 12.64597749 -1.101952404 -0.141764668 RNPDTQWITKPVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RNPDTQWITKPVHK 14 2 P61313;A0A2R8YEM3;E7EQV9;E7ENU7 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 196.95 1.45E-08 6101100000 4473100 3927900 4195200 4453500 4639600 3271700 5590500 4278100 5459100 FALSE TRUE 4193136.656 4218725.803 4294712.125 4567784.35 4275224.531 4216186.678 4752256.425 4812230.202 4547940.943 0.921985731 0.927612266 0.944320117 1.004363163 0.940035191 0.927053964 1.044924832 1.058111849 1 22.11678209 1.712407335 6.657611714 1.038099562 0.944513336 0.70702825 0.027242154 0.068661144 7.38979093 0.013497714 0.006973591 51.57121169 -1.712407335 -0.093586226 RNPGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RNPGVK 6 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 92.785 0.074337 511800000 963480 1454200 1323800 1281000 1410400 1084200 1277800 1099000 1106000 FALSE TRUE 903177.5067 1561870.481 1355201.161 1313872.629 1299632.873 1397190.939 1086205.753 1236212.569 921401.455 0.98022149 1.69510312 1.470804234 1.425950243 1.41049579 1.516375877 1.178862641 1.341665528 1 19.81347035 1.035332915 0.741933117 1.008743702 1.462169604 0.265960576 0.193167401 0.750480564 0.948659003 0.171662111 0.066336992 10.84758132 -1.035332915 0.453425902 RNPPGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RNPPGGK 7 1 Q9UK76;Q9UK76-3 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 0 ;; 108.24 0.011701 167211000 315620 301823 314971 312168 319570 250541 331160 273959 333980 FALSE TRUE 295865.9076 324170.289 322442.2609 320178.7594 294472.2613 322868.1195 281505.6323 308163.3842 278236.5804 1.063360925 1.165088676 1.158878032 1.150742864 1.058352072 1.160408596 1.011749181 1.10755884 1 18.08595258 1.604479301 0.662923133 1.011106905 1.143393081 0.360224262 0.049727478 0.591838861 0.55710395 0.042631308 0.020965189 40.22344847 -1.604479301 0.132286176 RNPS(ph)PDHSYKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RNPSPDHSYKR 11 2 Q15696 Q15696 ZRSR2 U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 1 RNPS(0.964)PDHS(0.036)YKR;RNPS(1)PDHSYKR;RNPS(1)PDHSYKR;RNPS(1)PDHSYKR 142.95 1.95E-05 2200550000 1542610 1547060 1547680 1521450 1683310 1120550 1711560 1249840 2358610 TRUE FALSE 1446060.794 1661605.932 1584391.7 1560492.983 1551109.623 1444034.594 1454927.467 1405885.275 1964942.754 0.735930241 0.845625619 0.8063297 0.794167148 0.789391762 0.734899066 0.740442674 0.715484089 1 20.90605585 2.713793178 2.623870999 0.770657073 0.806846623 0 0.084717056 1.076865419 14.72992954 0.026108522 0.025630549 517.3603935 -2.713793178 0.03618955 RNPSNQSSLES(ph)DSNYPSISTSEIGDTEDALQQVEEIGLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RNPSNQSSLESDSNYPSISTSEIGDTEDALQQVEEIGLEK 40 1 Q9ULV0;A0A0A0MR36;Q9ULV0-2 Q9ULV0 MYO5B Unconventional myosin-Vb 1 RNPS(0.225)NQS(0.225)S(0.225)LES(0.273)DS(0.044)NY(0.007)PSISTSEIGDTEDALQQVEEIGLEK 90.672 0.00014019 7654800 8443.1 6589.7 7041.3 7805.5 6532.3 6432.2 8035.1 4065.7 8616.4 TRUE FALSE 7914.661442 7077.608245 7208.322961 8005.802345 6019.279508 8289.071722 6830.311349 4573.311595 7178.267176 1.102586634 0.985977266 1.004187053 1.115283417 0.838542138 1.1547455 0.951526487 0.637105235 1 12.80941991 1.448637282 10.03652708 0.810092609 1.021769904 0.339920994 0.122073336 0.199416319 59.19968756 0.059425033 0.026057742 28.09553342 -1.448637282 0.211677295 RNPSPDHS(ph)YK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RNPSPDHSYK 10 1 Q15696 Q15696 ZRSR2 U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 1 RNPS(0.398)PDHS(0.601)Y(0.001)K;RNPS(0.447)PDHS(0.552)Y(0.001)K 80.312 0.014936 848200000 1493970 1116490 1240740 1181440 1227640 1087990 1468610 1063340 1154910 TRUE FALSE 1400465.085 1199156.081 1270170.939 1211757.751 1131226.106 1402075.051 1248405.564 1196100.34 962148.06 1.455560888 1.246332172 1.32014083 1.259429604 1.175729759 1.457234192 1.297519183 1.243156214 1 19.87589939 0.808377534 2.769364824 1.000160776 1.308929255 0.564723673 0.086824617 0.621779313 7.655193844 0.076227498 0.020143266 6.432466515 -0.808377534 0.30876848 RNQKPEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RNQKPEVR 8 2 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 0 ;;; 136.57 0.00044177 2907500000 2960280 3178150 2948790 2983220 3367340 2390280 3449960 2652480 3473980 FALSE TRUE 2775001.359 3413463.533 3018736.691 3059774.476 3102882.7 3080315.033 2932670.526 2983647.967 2894150.295 0.958831117 1.179435477 1.043047659 1.057227222 1.072122172 1.064324489 1.013309686 1.030923643 1 21.46470841 1.794271771 0.745683861 1.001244528 1.081703388 0.099884461 0.054744071 0.988363999 1.068013903 0.046162637 0.022396796 62.26898269 -1.794271771 0.08045886 RNQSFCPTVNLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RNQSFCPTVNLDK 13 1 P46776;E9PLL6;E9PJD9 P46776 RPL27A 60S ribosomal protein L27a 0 ; 138.21 8.29E-05 369520000 707380 569720 601370 647090 676690 457640 777900 619370 698680 FALSE TRUE 663106.3485 611902.6616 615634.7804 663695.4249 623545.497 589753.2388 661261.1167 696699.7079 582065.7944 1.139229199 1.0512603 1.05767215 1.140241243 1.071262911 1.013207174 1.136059056 1.196943223 1 19.15082271 1.615391841 25 1.124876926 1.075217917 0.040020936 0.061446905 1.217649249 4032.247847 0.026359081 0.014258112 41.24695005 -1.615391841 -0.049659009 RNS(ph)CNVGGGGGGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RNSCNVGGGGGGFK 14 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 RNS(1)CNVGGGGGGFK;RNS(1)CNVGGGGGGFK;RNS(1)CNVGGGGGGFK 173.18 1.68E-06 1662570000 2148370 1636310 1768740 1971480 2708980 1460640 2733060 1975770 2970640 TRUE FALSE 2013907.357 1757464.095 1810695.348 2022071.515 2496227.638 1882303.056 2323263.025 2222449.234 2474820.993 0.813758798 0.710137865 0.731646997 0.817057686 1.008649775 0.760581497 0.938760028 0.898024237 1 21.23889275 3.000705318 5.034984602 0.907009307 0.742449548 0.529038779 0.07296062 0.128210361 9.590902279 0.019836879 0.02272271 1001.625374 -3.000705318 -0.164559759 RNS(ph)CNVGGGGGGFKHPAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RNSCNVGGGGGGFKHPAFK 19 2 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 RNS(1)CNVGGGGGGFKHPAFK 97.623 0.00056708 495160000 287250 274730 249920 329040 473740 227170 502980 282450 870570 TRUE FALSE 269271.5353 295071.2951 255848.2204 337483.7235 436534.3714 292750.2912 427562.8184 317714.5042 725266.2429 0.371272671 0.406845483 0.352764551 0.465323909 0.601895339 0.403645274 0.589525326 0.438066031 1 19.46815118 -5 0.183484719 3.307914184 0.339817883 0.842605241 0.075712988 46.2086378 0.447887899 38.81140483 0.206691007 1.00E-05 5 -2.968096301 RNS(ph)FSENEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RNSFSENEK 9 1 Q9HCG8 Q9HCG8 CWC22 Pre-mRNA-splicing factor CWC22 homolog 1 RNS(0.999)FS(0.001)ENEK;RNS(0.985)FS(0.015)ENEK;RNS(0.999)FS(0.001)ENEK 218.01 3.34E-07 2524730000 1735950 1425320 1435230 1582120 1633110 1214090 1914060 1452820 1870810 TRUE FALSE 1627299.988 1530852.176 1469274.333 1622719.878 1504852.128 1564578.074 1627064.472 1634207.775 1558559.725 1.044104991 0.982222337 0.942712884 1.04116631 0.965540238 1.003861481 1.04395388 1.048537152 1 20.57178201 1.914518256 4.662109517 1.034289555 0.988037737 0.172635959 0.033421183 0.288804988 10.58904811 0.014925624 0.008770937 82.13310777 -1.914518256 -0.046251818 RNS(ph)FTPLSSSNTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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(0.996)FT(0.004)PLSSSNTIR;RNS(0.998)FT(0.002)PLSSSNTIR;RNS(0.999)FT(0.001)PLSSSNTIR;RNS(0.999)FT(0.001)PLSSSNTIR;RNS(0.919)FT(0.073)PLS(0.001)S(0.004)S(0.004)NTIR;RNS(0.956)FT(0.005)PLSS(0.012)S(0.012)NT(0.016)IR;RNS(0.855)FT(0.105)PLS(0.013)S(0.013)S(0.013)NTIR 276.1 4.58E-33 6990180000 3449030 4648050 3205890 3497360 5001570 2803310 4860420 3742930 4733220 TRUE FALSE 3233161.369 4992196.458 3281935.225 3587108.179 4608766.868 3612580.089 4131645.143 4210243.05 3943215.004 0.819930277 1.266021876 0.832299335 0.909691248 1.168784066 0.916150929 1.047785915 1.067718358 1 21.91094095 RNS(ph)GSSLVSSSSASSNLSHLEEDSWILWGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RNSGSSLVSSSSASSNLSHLEEDSWILWGR 30 1 O60447-2;O60447 O60447-2 EVI5 Ecotropic viral integration site 5 protein homolog 1 RNS(0.999)GS(0.001)SLVSSSSASSNLSHLEEDSWILWGR 263.2 9.19E-59 79128000 15369 20039 16884 17307 22071 14472 23648 17611 23217 TRUE FALSE 14407.08172 21522.70841 17284.49645 17751.12692 20337.63269 18649.83147 20102.20194 19809.77212 19341.93271 0.744862571 1.112748593 0.893628197 0.917753525 1.051478825 0.964217576 1.039306787 1.024187831 1 14.23944434 2.742407403 24.88525659 1.01567591 0.945894946 0.193013487 0.092246244 667.1075444 4315591.216 0.026995503 0.027653321 552.5955751 -2.742407403 -0.069780964 RNS(ph)GSSLVSSSSASSNLSHLEEDTWILWGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RNSGSSLVSSSSASSNLSHLEEDTWILWGR 30 1 Q96CN4;Q96CN4-2 Q96CN4 EVI5L EVI5-like protein 1 RNS(0.975)GS(0.024)S(0.002)LVSSSSASSNLSHLEEDTWILWGR 170.37 8.09E-13 58320000 44178 40838 48552 45924 64582 37898 57124 43460 83826 TRUE FALSE 41412.97784 43861.68801 49703.67637 47102.48759 59509.99023 48838.53738 48558.78651 48886.07667 69834.89906 0.59301264 0.628076916 0.711731198 0.674483506 0.852152592 0.699342851 0.695336961 0.700023589 1 16.09166056 -5 0.166123689 2.143986846 0.61774187 0.723873912 0.0615312 73.51360135 0.687459249 27.84433946 0.23695416 1.00E-05 5 -1.526244976 RNS(ph)IEVAGLSHGLEGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RNSIEVAGLSHGLEGLR 17 1 Q16825 Q16825 PTPN21 Tyrosine-protein phosphatase non-receptor type 21 1 RNS(1)IEVAGLSHGLEGLR;RNS(1)IEVAGLSHGLEGLR;RNS(1)IEVAGLSHGLEGLR 200.98 7.29E-12 952910000 233078 279847 274247 293349 288170 211299 289802 258902 278387 TRUE FALSE 218490.064 300567.1631 280752.2683 300876.832 265538.2906 272297.5911 246348.8805 291226.4846 231922.4113 0.942082582 1.295981537 1.210543935 1.297316764 1.144944506 1.174089169 1.06220386 1.255706523 1 17.82328271 2.24114086 2.250860372 1.116178664 1.207817466 0.044412011 0.118285654 0.675984603 6.975152409 0.049286677 0.033615819 174.2371906 -2.24114086 0.091638802 RNS(ph)IPIVTEQPLISAGENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RNSIPIVTEQPLISAGENR 19 1 Q9NZI5-3;Q9NZI5;B7Z1S6 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 RNS(1)IPIVTEQPLISAGENR;RNS(1)IPIVTEQPLISAGENR 123.79 1.87E-05 404180000 285740 299910 304260 324720 341270 289490 377880 291680 436370 TRUE FALSE 267856.0435 322115.6485 311477.1909 333052.8649 314468.0308 373061.0635 321220.4021 328096.8901 363537.0279 0.736805395 0.886060081 0.856796329 0.916145645 0.865023386 1.026198255 0.883597481 0.90251299 1 18.47174279 7.073302329 0.327118805 0.94686854 6.88E-34 0.543297573 0.053449566 25.62973241 0.640013913 0.044963099 13.09000334 11838654.03 -7.073302329 -0.94686854 RNS(ph)LDGGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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;RNS(1)LDGGGR 177.12 3.22E-05 3740760000 910252 1001873 1034931 1072969 1124136 1012899 1268644 963431 1358210 TRUE FALSE 853280.9522 1076052.719 1059480.052 1100503.201 1035850.893 1305306.498 1078422.61 1083717.481 1131515.977 0.754104202 0.950983231 0.936336803 0.972591836 0.915454059 1.153590869 0.953077669 0.957757118 1 20.10982552 5.598020672 0.912838446 0.989415682 4.37E-29 0.533713704 0.06599777 6.914118748 1.421973031 0.019491397 9.875815118 396296.8975 -5.598020672 -0.989415682 RNS(ph)LIELPDDYSCLLNQASHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RNSLIELPDDYSCLLNQASHFR 22 1 Q8IWV7 Q8IWV7 UBR1 E3 ubiquitin-protein ligase UBR1 1 RNS(1)LIELPDDYSCLLNQASHFR;RNS(1)LIELPDDYSCLLNQASHFR;RNS(1)LIELPDDYSCLLNQASHFR;RNS(1)LIELPDDYSCLLNQASHFR 282.29 4.55E-46 395042000 191359 213127 215893 216820 271587 202755 223442 226897 357250 TRUE FALSE 179382.1818 228907.1448 221014.0839 222383.9683 250257.6525 261287.077 189938.9464 255225.5899 297622.6671 0.602716801 0.769118653 0.742598291 0.747201046 0.840855487 0.877913902 0.638187099 0.857547553 1 18.18312488 -5 0.159086407 1.885271902 0.690105243 0.520043139 0.080490611 117.5872582 1.078890346 32.97870456 0.33979023 1.00E-05 5 -1.195166659 RNS(ph)LILKPKPDPAQQTDSQNSDTEQYFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RNSLILKPKPDPAQQTDSQNSDTEQYFR 28 3 Q9NXD2 Q9NXD2 MTMR10 Myotubularin-related protein 10 1 RNS(0.998)LILKPKPDPAQQT(0.002)DSQNSDTEQYFR 218.29 2.16E-34 241750000 239990 179560 220870 200300 222120 160900 296660 186250 367810 TRUE FALSE 224969.4543 192854.8092 226109.1407 205440.0371 204675.5912 207349.218 252178.5871 209503.7225 306420.1349 0.734186265 0.629380342 0.737905624 0.670452146 0.667957382 0.676682745 0.822983082 0.683713956 1 18.22515157 -0.900874785 0.348303362 1.133399752 0.675571894 0.761049358 0.052500524 5.919920114 0.581467295 0.85299675 0.041386372 0.125639215 0.900874785 -0.457827859 RNS(ph)LPQIPMLNLEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RNSLPQIPMLNLEAR 15 1 Q14289;Q14289-2;H0YB74 Q14289 PTK2B Protein-tyrosine kinase 2-beta 1 RNS(1)LPQIPMLNLEAR;RNS(1)LPQIPMLNLEAR 156.87 1.26E-06 143321000 123887 133959 167435 164834 163845 168332 224475 149667 162006 TRUE FALSE 116133.1338 143877.4637 171406.6373 169063.9195 150977.2746 216926.7158 190817.0577 168353.2544 134966.152 0.860461176 1.066026271 1.269997216 1.252639399 1.118630652 1.607267545 1.413814166 1.247373893 1 17.04223812 5.039902357 0.660010889 1.331181549 0.37671506 0.389233874 0.165006691 4.088657434 1.016833893 0.06531738 3.20456116 109623.17 -5.039902357 -0.954466489 RNS(ph)LQHHQDDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RNSLQHHQDDTK 12 1 Q6ZU80;H0YJH2 Q6ZU80 CEP128 Centrosomal protein of 128 kDa 1 RNS(1)LQHHQDDTK 94.544 0.0030798 112290000 79657 56151 62928 55478 70597 43756 73140 50755 64585 TRUE FALSE 74671.41056 60308.47847 64420.68188 56901.6594 65052.59639 56387.64688 62173.336 57091.87348 53805.34626 1.387806524 1.120864053 1.197291465 1.05754657 1.209035921 1.047993383 1.155523388 1.061081796 1 15.71546191 7.253085836 1.271720479 1.115085603 199.9999999 0.608013802 0.069561018 675.8441253 1.980973291 0.016635342 391121.8202 17909597.92 -7.253085836 198.8849143 RNS(ph)LTGEEGQLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RNSLTGEEGQLAR 13 1 Q9BX95 Q9BX95 SGPP1 Sphingosine-1-phosphate phosphatase 1 1 RNS(1)LTGEEGQLAR;RNS(0.999)LT(0.001)GEEGQLAR;RNS(0.999)LT(0.001)GEEGQLAR;RNS(1)LTGEEGQLAR 193.3 1.21E-06 2130900000 818300 1037100 988720 961090 1178560 855460 1074990 949010 1185900 TRUE FALSE 767084.0637 1113887.963 1012172.905 985753.1965 1086000.652 1102417.415 913805.2292 1067495.988 987965.6288 0.776427885 1.127456189 1.024502144 0.997760618 1.099229184 1.115845919 0.924936255 1.080499115 1 19.91410133 4.749705065 24.82224863 1.044770776 0.776427713 0.648226679 0.062464479 986.0833683 2196276.808 0.014721094 0.225407501 56195.95612 -4.749705065 -0.268343063 RNS(ph)PAFLSTDLGDEDVGLGPPAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RNSPAFLSTDLGDEDVGLGPPAPR 24 1 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 RNS(1)PAFLSTDLGDEDVGLGPPAPR;RNS(0.997)PAFLS(0.001)T(0.002)DLGDEDVGLGPPAPR;RNS(0.946)PAFLS(0.027)T(0.027)DLGDEDVGLGPPAPR;RNS(1)PAFLSTDLGDEDVGLGPPAPR 185.38 1.45E-17 407488000 112274 117354 125143 106260 139688 118268 124085 138433 185480 TRUE FALSE 105246.9708 126043.0123 128111.4511 108986.8115 128717.468 152410.0517 105479.6062 155716.6648 154522.1898 0.681112343 0.815695225 0.829081255 0.705314956 0.833003132 0.986331167 0.682617858 1.00773012 1 17.2374545 -4.999999998 0.085538855 1.666771342 0.630272163 0.376716344 0.099869184 265.5324727 1.592973287 32.19735387 2.571846294 1.00E-05 4.999999998 -1.03649918 RNS(ph)PMAQT(ph)PPCHLPNIPGVTSPGTLIEDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSK 30 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 RNS(0.937)PMAQT(0.942)PPCHLPNIPGVT(0.087)S(0.026)PGT(0.008)LIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK 251.16 4.84E-47 1591290000 736092 521675 554842 730650 1026876 861432 1300205 901871 841388 TRUE FALSE 690021.3157 560300.3598 568003.1143 749399.716 946229.3012 1110113.434 1105251.331 1014471.58 700954.9072 0.984401862 0.799338665 0.810327609 1.06911259 1.349914654 1.583715904 1.576779504 1.447270815 1 19.41896211 2.84173546 2.262388672 1.467611164 0.843972963 0.65131783 0.174419467 0.144482529 1.454691985 0.054467306 0.057867704 694.6010895 -2.84173546 -0.623638202 RNS(ph)PMAQT(ph)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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;RNS(0.999)PMAQT(0.997)PPCHLPNIPGVT(0.003)S(0.001)PGT(0.001)LIEDSKVEVNNLNNLNNHDR 114.95 2.20E-05 615524000 125146 113439 118597 156217 228590 149782 229943 163145 235220 TRUE FALSE 117313.3353 121838.1416 121410.1768 160225.7927 210637.4635 193021.6319 195465.1818 183514.0124 195960.2624 0.598658798 0.621749227 0.61956529 0.817644306 1.074898864 0.985003947 0.997473566 0.936485847 1 17.5802016 3.045056491 3.00688617 0.996621688 0.614746078 0.959010433 0.036339424 0.042034956 0.777402521 0.010699533 0.01273819 1109.319101 -3.045056491 -0.38187561 RNS(ph)PMAQTPPCHLPNIPGVTSPGTLIEDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSK 30 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 RNS(0.5)PMAQT(0.5)PPCHLPNIPGVTSPGTLIEDSK 65.155 0.003874 332070000 151650 104320 117020 119060 106690 97380 161670 102800 110910 TRUE FALSE 142158.4972 112043.9613 119795.7697 122115.2812 98310.99777 125492.0252 137429.0844 115634.8063 92398.40449 1.538538441 1.212617923 1.296513401 1.321616773 1.06399021 1.358162252 1.487353436 1.251480552 1 16.49558032 4.747804241 23.80174567 1.277388636 1.538538716 0.274094722 0.141531822 920.8417243 2371007.249 0.03268831 0.393209519 55950.53463 -4.747804241 0.261150079 RNS(ph)PMAQTPPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 44 2 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 RNS(0.974)PMAQT(0.026)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR;RNS(0.971)PMAQT(0.029)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR;RNS(0.749)PMAQT(0.251)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 152.43 1.83E-14 524424000 149005 195922 195229 204165 229611 174442 206725 176642 212315 TRUE FALSE 139679.043 210428.2687 199859.9241 209404.2196 211578.2783 224800.5736 175728.5054 198696.1425 176878.2549 0.789690305 1.189678567 1.129929308 1.183888996 1.196180268 1.270933918 0.993499769 1.123349745 1 17.43239717 1.650427277 15.33166512 1.044073758 1.139031815 0.083423968 0.132568592 0.32763944 104.5802192 0.057272248 0.031563502 44.71232739 -1.650427277 0.094958056 RNS(ph)SEASSGDFLDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 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(0.992)S(0.007)EAS(0.001)SGDFLDLK;RNS(0.982)S(0.018)EASSGDFLDLK;RNS(0.992)S(0.007)EAS(0.001)SGDFLDLK;RNS(1)SEASSGDFLDLK;RNS(0.999)S(0.001)EASSGDFLDLK;RNS(1)SEASSGDFLDLK;RNS(1)SEASSGDFLDLK;RNS(1)SEASSGDFLDLK;RNS(1)SEASSGDFLDLK;RNS(0.46)S(0.46)EAS(0.04)S(0.04)GDFLDLK;RNS(0.933)S(0.067)EASSGDFLDLK;RNS(0.997)S(0.003)EASSGDFLDLK;RNS(0.998)S(0.002)EASSGDFLDLK;RNS(0.876)S(0.121)EAS(0.003)SGDFLDLK 285.2 2.85E-34 83538215500 47500339 27273516 35589480 32023122 28026495 29796450 45103530 28402815 24620061 TRUE FALSE 44527377.57 29292875.5 36433679.27 32844889.53 25825407.14 38398201.41 38340674.4 31948968.98 20510813.77 2.170922035 1.428167397 1.776315639 1.601345022 1.259111775 1.872095464 1.869290747 1.557664622 1 24.2898814 -1.933755761 1.334472128 0.443396973 1.68224015 0.420943279 0.254803533 16417.62947 4005.22419 28418.24387 0.067277651 0.011647809 1.933755761 1.238843178 RNS(ph)SIVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RNSSIVGR 8 1 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GUE9;Q96N67-7;A0A0U1RQT6 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 RNS(0.995)S(0.005)IVGR;RNS(0.981)S(0.019)IVGR;RNS(0.997)S(0.003)IVGR;RNS(0.997)S(0.003)IVGR 136.49 0.00048314 748090000 336990 343454 350874 285223 375343 272686 375945 363524 499800 TRUE FALSE 315898.3974 368883.6915 359196.897 292542.3051 345865.0748 351406.0215 319575.5374 408910.7716 416380.1512 0.758677849 0.885930058 0.862665754 0.702584655 0.830647364 0.843954786 0.767509057 0.982061154 1 18.66754177 1.226026782 24.37214673 0.991030891 0.817253873 0.658148798 0.054657126 123.2679075 239685.4345 0.051541616 0.013269991 16.8277783 -1.226026782 -0.173777017 RNS(ph)SS(ph)PVS(ph)PASVPGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 3 RNS(0.881)S(0.119)S(0.997)PVS(0.937)PAS(0.066)VPGQR 175.56 6.81E-12 0 182290 193140 182120 201640 203270 157810 206020 150680 219830 TRUE FALSE 170880.7943 207440.2866 186439.9724 206814.4238 187305.9942 203367.1852 175129.2136 169492.7297 183138.9528 0.93306635 1.132693419 1.018024672 1.129275998 1.022753441 1.110452921 0.956264142 0.925487053 1 17.48257915 1.655362783 6.708363854 0.954647527 1.062947795 0.346076959 0.06236525 0.119564596 10.74324017 0.028050102 0.014118311 45.22335551 -1.655362783 0.108300267 RNS(ph)SS(ph)PVSPASVPGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 2 RNS(0.516)S(0.505)S(0.979)PVSPASVPGQR;RNS(0.998)S(0.008)S(0.81)PVS(0.183)PAS(0.002)VPGQR 228.26 2.85E-15 309190000 826430 855100 833460 807080 867930 608820 806500 655230 903190 TRUE FALSE 774705.2215 918412.4937 853230.0648 827791.0392 799766.2789 784576.4506 685572.8122 737036.9078 752441.7542 1.029588293 1.220576196 1.133948322 1.100139691 1.062894602 1.042707221 0.91113074 0.979526859 1 19.52122038 2.383432943 1.260042648 0.955581379 1.1464284 0.59288252 0.054615698 0.248603285 0.787658185 0.029996348 0.019859575 241.7869979 -2.383432943 0.190847022 RNS(ph)SSPVS(ph)PASVPGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 2 RNS(0.995)S(0.004)S(0.037)PVS(0.963)PASVPGQR 278.76 3.58E-23 0 408880 389120 388680 397920 422480 289690 399270 316570 456280 TRUE FALSE 383288.9307 417930.8497 397899.6731 408131.3009 389300.125 373318.8003 339403.1701 356094.4614 380123.9203 1.008326259 1.099459485 1.046763047 1.073679606 1.024140035 0.982097627 0.892875065 0.936785196 1 18.53611029 2.214056742 2.346787521 0.93245654 1.061411477 0.656223268 0.035769107 0.140468024 1.571032668 0.014803318 0.009969458 163.7030391 -2.214056742 0.128954937 RNS(ph)SSSSSPSERPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RNSSSSSSPSERPR 14 2 G3V1D0;B7WPE2;H0Y3M3;Q32P44;Q32P44-2 G3V1D0 EML3 Echinoderm microtubule-associated protein-like 3 1 RNS(0.98)S(0.02)SSSSPSERPR 185.02 6.39E-07 335150000 29667 36118 28619 40853 41508 31142 41116 38150 56432 TRUE FALSE 27810.19543 38792.2143 29297.85619 41901.35714 38248.12912 40132.18985 34951.0375 42913.11148 47013.13464 0.591540973 0.825135669 0.623184487 0.891269163 0.813562623 0.853637822 0.743431336 0.912789837 1 15.52077626 -1.356313636 0.039918659 1.92552068 6.43E-12 0.527997762 0.086397862 288.7184726 1.963282796 61.00274647 35.83249465 0.044023682 1.356313636 -1.92552068 RNS(ph)TDSRPVSVTYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RNSTDSRPVSVTYR 14 2 A0A088AWN2;Q8TBZ3-4;Q8TBZ3-5;Q8TBZ3-6;Q8TBZ3;Q8TBZ3-2;Q8TBZ3-7 A0A088AWN2 WDR20 WD repeat-containing protein 20 1 RNS(0.5)T(0.5)DS(0.001)RPVSVTYR;RNS(0.991)T(0.009)DSRPVSVTYR;RNS(0.938)T(0.062)DSRPVSVTYR;RNS(0.996)T(0.004)DSRPVSVTYR 197.28 1.24E-08 2282870000 760603 842690 741644 730166 917500 633417 828850 763910 999210 TRUE FALSE 712998.2159 905083.6444 759236.1459 748903.2957 845443.251 816274.2052 704571.6372 859285.8451 832435.3959 0.856520782 1.087271936 0.912066149 0.899653354 1.015626264 0.980585652 0.84639798 1.032255295 1 19.66697879 3.748274161 23.952092 0.944688732 0.99176574 0 0.079731553 748.4660949 847503.5635 0.018964015 0.034137044 5601.110758 -3.748274161 0.047077008 RNS(ph)TIVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RNSTIVLR 8 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6 Q8NEY1-5 NAV1 Neuron navigator 1 1 RNS(0.983)T(0.017)IVLR;RNS(0.999)T(0.001)IVLR;RNS(0.982)T(0.018)IVLR;RNS(0.982)T(0.018)IVLR;RNS(0.982)T(0.018)IVLR;RNS(0.986)T(0.014)IVLR 190.26 0.00011477 2653590000 953791 1005999 998623 808778 1039301 704339 1086763 961113 1675747 TRUE FALSE 894094.9239 1080484.213 1022310.809 829532.6127 957678.4918 907670.2353 923812.9772 1081110.074 1396054 0.64044437 0.773955888 0.732286007 0.594198085 0.685989576 0.650168429 0.66173155 0.774404195 1 20.41292332 0.889007401 3.6131404 0.999881186 0.687542715 0.804997277 0.050108277 0.236875113 6.363549207 0.052544626 0.013533362 7.744749956 -0.889007401 -0.312338471 RNS(ph)TTFPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RNSTTFPSR 9 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 RNS(0.993)T(0.007)TFPSR;RNS(0.997)T(0.003)TFPSR;RNS(0.958)T(0.041)T(0.001)FPSR 132.79 0.00018079 2714220000 415270 450030 409110 393870 454240 359216 519220 434870 550940 TRUE FALSE 389278.992 483350.6895 418814.2824 403977.371 418565.8227 462915.8278 441367.7812 489164.4768 458984.5548 0.848130918 1.053087047 0.912480122 0.880154608 0.911938797 1.008565153 0.961617938 1.065753677 1 18.80808608 1.719862796 1.598016928 1.023499677 0.938709251 0.301944565 0.06054898 0.543444222 2.727277527 0.046339387 0.01798347 52.4641687 -1.719862796 -0.084790426 RNS(ph)TTIMSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RNSTTIMSR 9 1 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 RNS(0.967)T(0.03)T(0.003)IMSR;RNS(0.988)T(0.011)T(0.001)IMSR 69.352 0.023811 418079000 325963 352016 306212 332313 348926 278239 383334 296388 423237 TRUE FALSE 305561.5577 378079.6309 313475.4932 340840.7142 321522.7595 358562.0825 325856.6254 333392.6942 352596.0105 0.866605261 1.072274273 0.889050029 0.966660722 0.911872936 1.016920418 0.924164244 0.945537341 1 18.42765663 RNS(ph)VDTATSSSLSTPSEPLSPTSSLGEERN ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RNSVDTATSSSLSTPSEPLSPTSSLGEERN 30 2 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 1 RNS(0.98)VDT(0.016)AT(0.001)S(0.001)S(0.001)S(0.001)LSTPSEPLSPTSSLGEERN;RNS(0.999)VDT(0.001)ATSSSLSTPSEPLSPTSSLGEERN;RNS(0.78)VDT(0.065)AT(0.065)S(0.065)S(0.013)S(0.013)LSTPSEPLSPTSSLGEERN 209.11 6.46E-26 1022110000 237750 223785 212953 198671 253468 277929 385563 307301 419227 TRUE FALSE 222869.6519 240354.2742 218004.3457 203769.2342 233561.6457 358162.5905 327751.4075 345668.2063 349255.3054 0.638128179 0.688190761 0.624197664 0.583439195 0.668741869 1.02550365 0.938429288 0.989729292 1 18.41392251 2.266015619 7.645696891 0.980104689 0.641343472 0.961348685 0.034648231 0.033213205 7.143147689 0.012063675 0.009892248 184.5081775 -2.266015619 -0.338761217 RNS(ph)VERPAEPVAGAATPSLVEQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RNSVERPAEPVAGAATPSLVEQQK 24 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK;RNS(1)VERPAEPVAGAATPSLVEQQK 236.65 1.06E-37 4321070000 1978624 1411245 1608976 1735825 1948060 1404120 1851601 1377226 3129610 TRUE FALSE 1854785.456 1515735.048 1647141.671 1780369.208 1795067.226 1809466.65 1573970.619 1549175.698 2607257.873 0.711393175 0.58135218 0.631752497 0.682851216 0.688488563 0.694011386 0.603688126 0.594178165 1 21.31410185 -1.308220462 5.3411756 1.000072203 0.642334365 0.853156408 0.045770943 3.95E-05 5.12E-06 0.044512619 0.010489616 0.049178982 1.308220462 -0.357737839 RNS(ph)VTPLASPEPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RNSVTPLASPEPTK 14 1 Q5W015;Q5VX20;A0A1W2PR17;Q16875-3;Q16875-2;Q16875;Q16875-4;Q9H178 Q5W015 PFKFB3 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 RNS(0.996)VT(0.004)PLASPEPTK;RNS(0.999)VT(0.001)PLASPEPTK 153.68 3.87E-06 473650000 893610 774120 750350 813220 850970 571400 955670 700210 1178960 TRUE FALSE 837680.5452 831436.6503 768148.6563 834088.602 784138.2488 736353.9041 812376.1555 787632.7599 982183.9596 0.852875408 0.846518254 0.782082266 0.84921831 0.798361897 0.749710782 0.827112017 0.801919795 1 19.90563374 -1.146883024 4.945917986 1.000011314 0.812475671 0.764405412 0.032539029 3.89E-06 6.71E-07 0.030184208 0.007114057 0.071304506 1.146883024 -0.187535643 RNS(ph)YPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RNSYPR 6 1 Q14134-2;Q14134 Q14134-2 TRIM29 Tripartite motif-containing protein 29 1 RNS(1)YPR;RNS(0.996)Y(0.004)PR;RNS(1)YPR;RNS(1)YPR 71.692 0.053633 1154360000 434070 598737 528370 557685 683359 590064 560641 648749 1091189 TRUE FALSE 406902.3335 643068.1105 540903.1859 571996.1413 629690.7407 760405.8979 476578.0868 729746.7407 909062.5065 0.447606551 0.707397023 0.595012094 0.629215414 0.692681456 0.836472621 0.524252275 0.802746495 1 19.79401997 -5 0.162480439 2.32744588 0.558079326 0.574220433 0.104187082 98.68477598 0.914117167 42.10378896 0.395553003 1.00E-05 5 -1.769366554 RNSPMAQT(ph)PPCHLPNIPGVTSPGTLIEDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSK 30 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 RNS(0.447)PMAQT(0.553)PPCHLPNIPGVTSPGTLIEDSK;RNS(0.431)PMAQT(0.568)PPCHLPNIPGVTSPGTLIEDSK;RNS(0.449)PMAQT(0.551)PPCHLPNIPGVTSPGTLIEDSK 118.14 3.13E-05 657440000 331163 219815 258938 261347 248127 236764 330661 216524 244862 TRUE FALSE 310436.099 236090.3313 265080.1316 268053.6065 228640.1063 305113.9233 281081.4528 243557.498 203992.9503 1.521798172 1.15734554 1.299457316 1.314033676 1.120823567 1.495708174 1.377897875 1.193950564 1 17.63815977 0.958189623 5.075741968 1.000144241 1.311032753 0.409256989 0.126068344 0.231264277 20.016802 0.115750797 0.029252293 9.08216993 -0.958189623 0.310888512 RNSPMAQT(ph)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDRK 45 3 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 RNS(0.424)PMAQT(0.576)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDRK 103.53 8.48E-07 225450000 219810 152550 175190 203790 261600 163070 250830 156100 383460 TRUE FALSE 206052.4845 163844.9607 179345.5895 209019.5964 241054.9912 210145.6618 213220.3701 175589.4286 319458.0488 0.645006395 0.512884122 0.561405763 0.65429435 0.754574794 0.657819274 0.667444038 0.549647847 1 18.28526696 -5 0.208322776 2.790781434 0.56277706 0.712573099 0.073239797 79.53335767 0.792359972 59.57481362 0.163428486 1.00E-05 5 -2.228004373 RNSS(ph)EASSGDFLDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RNSSEASSGDFLDLK 15 1 Q9UK76;J3KT51;Q9UK76-2;Q9UK76-3;J3KSH8 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 RNS(0.396)S(0.525)EAS(0.036)S(0.044)GDFLDLK 71.558 0.026557 8424600 20602 18886 22628 25555 25880 18453 24974 24609 18990 TRUE FALSE 19312.5576 20284.33909 23164.74685 26210.78456 23847.48919 23780.08154 21229.38055 27681.48782 15820.44632 1.220734055 1.282159724 1.464228403 1.656766442 1.507384097 1.503123304 1.341895173 1.749728627 1 13.94950268 4.084333095 2.109393006 1.477949271 1.236471536 0.158401095 0.198688223 0.52268226 4.477145921 0.047284795 0.143561931 12143.19851 -4.084333095 -0.241477735 RNSS(ph)IVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.2)S(0.8)IVGR 83.397 0.011142 94873000 18882 26273 27067 24483 27473 19681 25682 26275 32308 TRUE FALSE 17700.20933 28218.28026 27709.04202 25111.27523 25315.3814 25362.58521 21831.22252 29555.49159 26915.58608 0.657619317 1.04839925 1.029479423 0.932964088 0.940547285 0.942301057 0.811099653 1.098080922 1 14.71615422 4.747930955 24.61137433 0.967898938 0.657619112 0.616871087 0.078499907 774.1891755 2033369.326 0.020037821 0.251246888 55966.86171 -4.747930955 -0.310279826 RNSS(ph)S(ph)PVS(ph)PASVPGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 3 RNS(0.459)S(0.541)S(0.998)PVS(0.995)PAS(0.007)VPGQR 164.93 1.12E-07 153140000 273330 263740 263670 270630 294730 209210 274100 219510 311130 TRUE FALSE 256222.7632 283267.584 269924.3769 277574.824 271583.0947 269605.5308 233001.2496 246916.3067 259200.393 0.988512248 1.092851676 1.041373332 1.070888901 1.047772696 1.040143217 0.898923211 0.952607764 1 17.98370838 1.833543158 6.60149162 0.942498278 1.053256571 0.611217165 0.035926556 0.126207583 7.209115134 0.014259094 0.00861413 68.16213078 -1.833543158 0.110758294 RNSS(ph)SPVS(ph)PASVPGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 2 RNS(0.122)S(0.876)S(0.453)PVS(0.548)PAS(0.002)VPGQR 268.38 1.14E-27 193900000 337810 319430 306190 319740 369890 251450 325220 263890 398300 TRUE FALSE 316667.0751 343080.9296 313452.9714 327945.0697 340840.3315 324039.5331 276456.2802 296837.2474 331821.1569 0.954330574 1.033933257 0.944644321 0.988318746 1.02718083 0.976548741 0.833148443 0.894569985 1 18.34004635 1.89190487 7.724809945 0.893073669 0.990462065 0.348404437 0.049084507 0.231095136 14.78690834 0.019019481 0.011865322 77.96593111 -1.89190487 0.097388396 RNSSS(ph)PVSPASVPGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 RNS(0.013)S(0.043)S(0.944)PVSPASVPGQR 148.69 5.56E-07 327570000 74595 97062 80439 92350 150950 92127 129330 112710 251170 TRUE FALSE 69926.23211 104248.5715 82347.05107 94719.85735 139094.9959 118722.5693 109938.1671 126782.0916 209248.1044 0.334178569 0.498205572 0.393537859 0.452667696 0.664737185 0.567377036 0.525396239 0.605893621 1 17.67485503 -4.999999999 0.141033396 2.776651022 0.316667431 0.85601555 0.069505526 49.35067344 0.425414878 24.48909215 0.413504116 1.00E-05 4.999999999 -2.45998359 RNT(ph)RDETDTWAYIAAEGDQEVLDSVCQADENSDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RNTRDETDTWAYIAAEGDQEVLDSVCQADENSDGR 35 2 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 RNT(0.345)RDET(0.279)DT(0.345)WAY(0.031)IAAEGDQEVLDSVCQADENSDGR 136.91 3.86E-07 21691000 10334 9677.1 10528 10984 18864 9547.6 11022 9492.1 17187 TRUE FALSE 9687.213387 10393.60255 10777.72913 11265.86804 17382.49753 12303.83713 9369.353423 10677.20958 14318.37867 0.676557983 0.725892421 0.75271994 0.786811712 1.21399901 0.859303795 0.654358544 0.745699623 1 13.80558052 2.993746082 24.80239411 0.867287268 0.730509944 0.216392997 0.149604313 522.6592241 2072826.302 0.046659626 0.053982207 985.7030074 -2.993746082 -0.136777324 RNVSSFPDDATS(ph)PLQENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RNVSSFPDDATSPLQENR 18 1 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 1 RNVSSFPDDAT(0.24)S(0.76)PLQENR;RNVSSFPDDAT(0.182)S(0.818)PLQENR;RNVSSFPDDAT(0.146)S(0.854)PLQENR;RNVSSFPDDAT(0.034)S(0.966)PLQENR 205.13 6.10E-16 753320000 613664 593597 634991 678411 675107 528375 764790 571287 786990 TRUE FALSE 575255.8657 637547.5395 650053.2864 695820.1748 622086.8195 680908.285 650116.8395 642613.4395 655636.2849 0.877400899 0.972410396 0.99148461 1.061289912 0.948829151 1.038545762 0.991581544 0.980137089 1 19.32253617 5.228962381 1.204855631 1.00233082 0.640424512 0.614636119 0.030736976 2.654054506 1.454575264 0.00770808 1.598284337 169419.104 -5.228962381 -0.361906307 RPAAAAAAGSAS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RPAAAAAAGSASPR 14 1 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 RPAAAAAAGSAS(1)PR;RPAAAAAAGS(0.002)AS(0.998)PR;RPAAAAAAGSAS(1)PR;RPAAAAAAGS(0.002)AS(0.998)PR;RPAAAAAAGS(0.001)AS(0.999)PR;RPAAAAAAGSAS(1)PR 192.72 2.09E-07 4434660000 1387819 1712944 1468091 1576378 1635858 1405216 1701551 1483359 1599141 TRUE FALSE 1300957.886 1839772.156 1502914.812 1616830.528 1507384.311 1810879.047 1446419.224 1668559.636 1332234.036 0.976523532 1.380967687 1.12811621 1.213623496 1.131471101 1.359279975 1.085709556 1.25245234 1 20.34541612 -3.259064735 0.552673785 7.12E-13 1.201500569 0.188907118 0.12220559 809.3802179 22.22598462 966.0871527 0.045951747 0.000550726 3.259064735 1.201500569 RPAEATS(ph)SPT(ph)SPERPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 RPAEAT(0.02)S(0.933)S(0.051)PT(0.72)S(0.276)PERPR;RPAEAT(0.069)S(0.724)S(0.209)PT(0.498)S(0.499)PERPR 155.54 2.75E-07 8867500000 1493790 1622410 1517110 1627070 1689060 1459220 1627750 1404530 1594450 TRUE FALSE 1400296.35 1742534.925 1553096.566 1668823.371 1556408.041 1880473.126 1383683.999 1579888.662 1328325.994 1.054181245 1.311827768 1.16921341 1.256335702 1.171706379 1.415671404 1.041675014 1.18938323 1 20.34117782 1.061134895 1.209115273 1.011830656 1.224784514 0.252313418 0.110272931 0.559099294 1.692768165 0.091279773 0.028661882 11.51157892 -1.061134895 0.212953858 RPAEATSS(ph)PT(ph)SPERPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 RPAEAT(0.022)S(0.103)S(0.874)PT(0.635)S(0.367)PERPR 104.86 0.0014663 788000000 391750 409830 379380 420390 388660 351080 444920 368110 405270 TRUE FALSE 367231.0668 440174.2396 388379.0728 431177.9191 358136.2114 452431.0967 378208.3764 414069.3438 337627.8189 1.087680121 1.303726219 1.150317157 1.277080546 1.060742603 1.340029084 1.120193169 1.226407662 1 18.36507425 -3.651036577 0.418093549 1.50E-06 1.204171507 0.298727451 0.093325133 287.8847126 5.842122371 255.2762383 0.04666115 0.000223338 3.651036577 1.204170012 RPAEATSS(ph)PTS(ph)PERPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 RPAEAT(0.104)S(0.106)S(0.787)PT(0.262)S(0.74)PERPR 121.35 0.00048789 6452700000 410140 439340 443380 450780 486530 399480 501210 426300 470760 TRUE FALSE 384470.0695 471869.1907 453897.183 462347.778 448319.8964 514803.391 426058.2135 479524.4934 392187.1148 0.980323053 1.20317362 1.157348536 1.178895891 1.143127552 1.312647386 1.086364639 1.222693136 1 18.58118261 -0.948611754 4.232620731 0.999994366 1.165060945 0.251833584 0.086672411 0.017235227 21305040.64 301.9828718 0.017678968 0.112561079 0.948611754 0.16506658 RPAEATSSPT(ph)SPERPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 RPAEATS(0.001)S(0.017)PT(0.941)S(0.041)PERPR;RPAEATSSPT(0.5)S(0.5)PERPR;RPAEAT(0.001)SS(0.007)PT(0.622)S(0.37)PERPR;RPAEATSS(0.004)PT(0.498)S(0.498)PERPR;RPAEATSSPT(0.604)S(0.396)PERPR;RPAEAT(0.006)S(0.012)S(0.023)PT(0.479)S(0.479)PERPR 208.08 2.54E-11 10452470000 653222 720448 689967 741324 769907 662601 794093 672440 733810 TRUE FALSE 612338.0011 773790.7195 706333.3431 760347.6289 709441.6099 853883.1523 675026.1266 756395.6142 611332.3704 1.001644982 1.265744719 1.155399873 1.243754896 1.160484287 1.396757629 1.104188424 1.237290304 1 19.22159744 -1.021555804 3.953075269 0.999974537 1.200529883 0.255783946 0.104591949 4870137.831 2518028.544 1050.767879 0.021214904 0.095157757 1.021555804 0.200555346 RPAEDMEEEQAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RPAEDMEEEQAFK 13 1 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;; 240.42 1.22E-16 1925360000 2494350 1844960 2142170 2112750 2084780 1794220 2467890 1980220 1887680 FALSE TRUE 2338233.086 1981562.758 2192983.284 2166966.742 1921049.788 2312182.187 2097852.805 2227454.826 1572614.013 1.486844875 1.260043941 1.394482858 1.377939357 1.221564715 1.470279527 1.333990914 1.416402758 1 20.58473318 -1.390444976 5.228887618 0.999765604 1.36078133 0.659051512 0.083435152 0.000199689 2.33E-05 0.070758773 0.016667308 0.040696309 1.390444976 0.361015726 RPAEDMEEEQAFKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RPAEDMEEEQAFKR 14 2 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;; 249.41 2.35E-18 11255000000 6768590 6370540 6771320 6582720 7350930 4953030 7943460 6508610 8841550 FALSE TRUE 6344956.034 6842221.41 6931938.908 6751643.74 6773617.61 6382889.355 6752411.916 7321224.286 7365838.186 0.861403125 0.928912805 0.941093021 0.916615811 0.919599024 0.866553024 0.9167201 0.993943133 1 22.81241827 1.238791855 5.938746895 0.998657862 0.911442671 0.681687026 0.025397254 0.091389568 11.6661741 0.020921909 0.00633137 17.32973232 -1.238791855 -0.087215191 RPAEPGPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPAEPGPAR 9 1 A0A0A0MTR2;Q8N543;H3BR79;H3BR02 A0A0A0MTR2 OGFOD1 Prolyl 3-hydroxylase OGFOD1 0 ; 101.97 0.0058682 84832000 48455 112112 47200 44937 116568 35960 52264 99348 91783 FALSE TRUE 45422.28804 120412.8891 48319.60629 46090.1595 107413.2195 46341.06824 44427.4984 111751.8165 76463.82436 0.59403631 1.574769378 0.631927669 0.602770786 1.404758661 0.60605219 0.581026371 1.461499179 1 16.22248974 3.901946403 10.17211883 0.855659596 1.14777077 0.022636335 0.398619531 1.011230971 131.3241113 0.094504965 0.170607598 7978.962116 -3.901946403 0.292111174 RPAETNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RPAETNLR 8 1 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ;;;; 210.01 6.82E-05 1431440000 640695 1011300 660050 646837 1195500 509127 590286 988650 1421300 FALSE TRUE 600595.0436 1086177.704 675706.6977 663435.9325 1101610.252 656103.6999 501778.0942 1112085.129 1184075.848 0.507226834 0.917321053 0.570661667 0.560298509 0.930354465 0.554106142 0.423771919 0.939200922 1 20.17533007 1.089984412 7.78768035 0.998786042 0.6508352 0.411811936 0.165148206 0.225933426 15.77668555 0.158947651 0.03982107 12.30224614 -1.089984412 -0.347950842 RPAGGRPS(ph)PSAMGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RPAGGRPSPSAMGK 14 2 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 RPAGGRPS(0.997)PS(0.003)AMGK;RPAGGRPS(1)PSAMGK;RPAGGRPS(0.955)PS(0.045)AMGK;RPAGGRPS(0.971)PS(0.029)AMGK 124.68 8.48E-05 1700730000 1556830 1412750 1519710 1435700 1606630 1299920 1830680 1496970 1665690 TRUE FALSE 1459390.789 1517351.48 1555758.239 1472542.493 1480451.761 1675185.802 1556186.529 1683870 1387675.578 1.051680099 1.093448284 1.121125329 1.061157605 1.066857257 1.207188357 1.121433967 1.213446447 1 20.40423889 2.270342957 24.99960172 1.145241918 1.085803814 0.162459868 0.061090235 298.2517602 234599.9893 0.018673466 0.01562203 186.3558186 -2.270342957 -0.059438104 RPAMLDNEADGNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPAMLDNEADGNK 13 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 113.52 0.0013071 275180000 483210 352770 389200 383970 418930 315400 469870 358120 475220 FALSE TRUE 452966.7487 378889.4579 398432.0078 393823.3203 386028.9277 406450.8599 399417.3556 402832.0703 395902.712 1.144136514 0.95702668 1.00638868 0.99474772 0.975060074 1.026643283 1.008877544 1.01750268 1 18.59478642 -0.505269983 7.548271011 0.999999969 1.008704505 0 0.050270122 0 0 0.043055219 0.010148212 0.312413662 0.505269983 0.008704536 RPAPAVS(ph)PGSWKPGPPGS(ph)PRPWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPAPAVSPGSWKPGPPGSPRPWK 23 3 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 RPAPAVS(0.998)PGS(0.002)WKPGPPGS(1)PRPWK;RPAPAVS(1)PGSWKPGPPGS(1)PRPWK 159.89 2.81E-11 2181060000 1746590 1192000 1455770 1357860 1566620 1101900 1974050 1425270 2123900 TRUE FALSE 1637274.05 1280256.92 1490301.552 1392704.986 1443583.985 1420000.642 1678059.529 1603218.097 1769407.369 0.925323404 0.723551254 0.842260283 0.787102513 0.815857337 0.802528952 0.948373765 0.906076308 1 20.75483481 1.725487913 5.299805145 0.945975631 0.807061348 0.56789034 0.055122133 0.10415014 7.181200107 0.025627342 0.013011316 53.14812071 -1.725487913 -0.138914283 RPAPAVSPGSWKPGPPGS(ph)PRPWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPAPAVSPGSWKPGPPGSPRPWK 23 3 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 RPAPAVSPGSWKPGPPGS(1)PRPWK;RPAPAVSPGSWKPGPPGS(1)PRPWK 128.89 2.90E-05 1762340000 3968000 3037800 3382800 3294700 3753200 2548400 4120600 2964500 4729400 TRUE FALSE 3719649.963 3262721.873 3463041.613 3379247.58 3458438.812 3284081.71 3502754.284 3334624.351 3940032.587 0.944065787 0.828095149 0.878937302 0.857669957 0.877769088 0.833516383 0.889016577 0.846344358 1 21.90977613 -1.804349834 2.578647954 1.041752782 0.866544339 0.60502521 0.033082619 5979831.034 4174311.569 1560987.549 0.006847646 0.015690983 1.804349834 -0.175208444 RPAS(ph)PS(ph)SPEHLPATPAESPAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 2 RPAS(0.979)PS(0.674)S(0.347)PEHLPATPAESPAQR;RPAS(0.966)PS(0.579)S(0.455)PEHLPATPAESPAQR 163.14 5.40E-11 2200280000 656900 784340 777950 711420 842180 652860 881360 733050 732640 TRUE FALSE 615785.8016 842413.3497 796403.3414 729676.2416 776038.58 841330.0837 749208.2501 824572.9061 610357.651 1.008893393 1.380196264 1.304814219 1.195489629 1.271448926 1.378421459 1.227490552 1.350966773 1 19.21929534 -1.095214247 4.192427332 0.999956685 1.278097006 0.35952089 0.109753684 1.104556833 27406210.14 2556.059727 0.022959756 0.080312982 1.095214247 0.278140321 RPAS(ph)PSHNGSSGGGYGASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RPASPSHNGSSGGGYGASK 19 1 K7ELX9;K7EQ79;K7ENM4;K7ENP7;Q6PI98;Q6PI98-3;Q6PI98-4 K7ELX9 INO80C INO80 complex subunit C 1 RPAS(0.962)PS(0.035)HNGS(0.003)SGGGYGASK;RPAS(0.933)PS(0.067)HNGSSGGGYGASK;RPAS(0.499)PS(0.499)HNGS(0.001)SGGGYGASK;RPAS(0.828)PS(0.171)HNGS(0.001)SGGGYGASK;RPAS(0.383)PS(0.102)HNGS(0.332)S(0.183)GGGYGASK 233.8 2.48E-24 1153260000 491827 493744 556682 511028 514029 511565 645352 522091 533291 TRUE FALSE 461044.426 530301.3195 569886.7599 524141.8436 473659.2358 659245.5109 548587.4588 587275.2106 444281.2869 1.037730914 1.193616151 1.282716101 1.179752241 1.06612466 1.483847126 1.234775074 1.321854483 1 18.76111385 2.283937487 24.99997412 1.282166826 1.176753313 0.111448448 0.136301091 253.3222213 139564.5566 0.043126875 0.036082366 192.2814937 -2.283937487 -0.105413514 RPAS(ph)PSSPEHLPATPAESPAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 1 RPAS(0.969)PS(0.012)S(0.019)PEHLPATPAESPAQR;RPAS(0.975)PS(0.011)S(0.015)PEHLPATPAESPAQR;RPAS(0.985)PS(0.014)S(0.001)PEHLPATPAESPAQR;RPAS(0.958)PS(0.033)S(0.009)PEHLPATPAESPAQR 156.52 5.26E-09 1742050000 574330 746540 676530 786650 765180 629390 772630 701760 739520 TRUE FALSE 538383.7105 801814.5984 692577.6111 806836.7708 705085.8494 811084.6757 656781.3042 789376.2808 616089.3345 0.873872798 1.301458333 1.124151275 1.309610028 1.144453913 1.316504978 1.066048814 1.281269187 1 19.23278003 -1.1629726 4.823071037 0.999983107 1.183968896 0.138103582 0.138173377 2.14E-05 3.72E-06 0.114274751 0.026932345 0.068711179 1.1629726 0.183985788 RPAS(ph)VSSSAAVEHEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RPASVSSSAAVEHEQR 16 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 RPAS(0.788)VS(0.094)S(0.056)S(0.061)AAVEHEQR;RPAS(0.943)VS(0.057)SSAAVEHEQR;RPAS(0.984)VS(0.016)SSAAVEHEQR;RPAS(0.977)VS(0.023)SSAAVEHEQR;RPAS(0.945)VS(0.043)S(0.01)S(0.003)AAVEHEQR 198.64 2.46E-11 6441800000 519180 732381 669248 748604 746847 512378 629875 522683 470143 TRUE FALSE 486685.4506 786607.2513 685122.8786 767814.446 688192.6493 660293.2108 535431.0912 587941.1231 391673.0961 1.242580753 2.008325972 1.749221189 1.960345129 1.757058772 1.685827333 1.367035665 1.50110163 1 18.57929051 1.227290876 0.823813527 1.030875598 1.797852349 0.512569849 0.220882001 0.39419889 0.598244088 0.189903135 0.071924108 16.87683 -1.227290876 0.766976751 RPASPS(ph)S(ph)PEHLPATPAESPAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 2 RPAS(0.469)PS(0.669)S(0.862)PEHLPATPAESPAQR 129.22 5.42E-05 1741600000 467070 570460 529980 579610 581050 594940 552490 475750 539060 TRUE FALSE 437836.9224 612697.452 542551.3759 594483.7739 535416.6768 766689.52 469649.2536 535148.4348 449087.4035 0.974948126 1.364316717 1.208119782 1.323759627 1.192232676 1.707216711 1.045785853 1.191635371 1 18.77663673 1.601593594 25 1.089010247 1.296361787 0.227062982 0.187511039 0.831980514 3304.022867 0.087966878 0.042292719 39.95706623 -1.601593594 0.207351539 RPASVSSSAAVEHEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RPASVSSSAAVEHEQR 16 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 ;;; 168.68 3.82E-09 560900000 304063 415704 387957 450832 413519 321886 417611 369866 255222 FALSE TRUE 285032.2396 446483.1567 397159.5232 462401.1124 381042.8858 414809.2628 354994.1075 416044.5843 212623.7994 1.340547203 2.099873852 1.867897782 2.174738264 1.792098941 1.95090702 1.669587828 1.956716912 1 17.69794356 -1.114060439 0.535497132 0.700030698 1.895827807 0.560816277 0.235553116 17.21165271 2.73017747 8.064783056 0.093895104 0.076902341 1.114060439 1.195797109 RPATADS(ph)PKPSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RPATADSPKPSAK 13 2 Q03111 Q03111 MLLT1 Protein ENL 1 RPAT(0.003)ADS(0.997)PKPSAK;RPAT(0.001)ADS(0.998)PKPS(0.001)AK;RPATADS(1)PKPSAK;RPATADS(1)PKPSAK;RPATADS(1)PKPSAK;RPATADS(1)PKPSAK 159.4 2.38E-05 2527543000 7498400 3388860 5014660 4125050 5555910 3848590 7076780 5165080 7670790 TRUE FALSE 7029088.529 3639774.721 5133610.103 4230905.767 5119571.24 4959615.456 6015682.537 5809951.608 6390485.594 1.099930268 0.569561525 0.803320816 0.662063266 0.801123978 0.776093676 0.941349831 0.909156514 1 22.60749413 1.759859326 2.052168341 0.959475893 0.75291623 0.219610325 0.138102958 0.371780878 3.139926986 0.084912378 0.036189562 57.52535749 -1.759859326 -0.206559664 RPDADLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RPDADLK 7 1 P27824;P27824-2;P27824-3;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ;;; 122.52 0.006948 6189200000 11616700 10092500 8687400 9483800 11920200 6799300 12751200 11052700 9606600 FALSE TRUE 10889631.48 10839759.2 8893469.23 9727170.364 10984035.58 8762147.533 10839275.94 12432653.92 8003196.399 1.360660284 1.354428738 1.111239658 1.215410678 1.372456082 1.094831002 1.354368354 1.553461055 1 22.93214488 1.604005013 25 1.340446966 1.248611261 0.003577147 0.164717311 1.08701339 6993.333049 0.076445977 0.037463002 40.17954486 -1.604005013 -0.091835705 RPDDVPLS(ph)LSPSKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPDDVPLSLSPSKR 14 2 Q9UFC0;F8WDB4 Q9UFC0 LRWD1 Leucine-rich repeat and WD repeat-containing protein 1 1 RPDDVPLS(0.498)LS(0.498)PS(0.003)KR 215.67 5.05E-12 1390100000 1911600 1351500 1529300 1401400 1665200 1260300 2054200 1416000 2098200 TRUE FALSE 1791956.368 1451566.466 1565575.718 1437362.297 1534421.909 1624128.151 1746191.78 1592790.717 1747996.865 1.025148502 0.830417088 0.895639889 0.822291118 0.877817312 0.929136764 0.998967341 0.911209138 1 20.73727117 2.054750309 3.857412228 0.969200323 0.880054562 0.26043416 0.059983351 0.249757647 7.644499916 0.02307497 0.015531041 113.4358447 -2.054750309 -0.089145761 RPDDVPLSLS(ph)PSKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RPDDVPLSLSPSKR 14 2 Q9UFC0;F8WDB4 Q9UFC0 LRWD1 Leucine-rich repeat and WD repeat-containing protein 1 1 RPDDVPLS(0.003)LS(0.989)PS(0.008)KR;RPDDVPLS(0.002)LS(0.976)PS(0.022)KR;RPDDVPLS(0.435)LS(0.556)PS(0.009)KR;RPDDVPLS(0.017)LS(0.979)PS(0.003)KR 183.53 1.06E-06 4720690000 2209090 1576570 1917690 1645790 1956710 1609720 2447320 1822430 2332550 TRUE FALSE 2070827 1693300.883 1963178.512 1688023.758 1803037.89 2074420.032 2080367.086 2049964.397 1943232.336 1.065661044 0.871383649 1.010264432 0.868668006 0.927855026 1.067510042 1.070570434 1.054925013 1 20.89002697 2.23734453 24.98536147 1.056371271 0.94295948 0.388334446 0.061428915 27.47716871 564516.2244 0.020256426 0.015798581 172.7207559 -2.23734453 -0.113411791 RPDDVPLSLSPS(ph)KR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPDDVPLSLSPSKR 14 2 Q9UFC0;F8WDB4 Q9UFC0 LRWD1 Leucine-rich repeat and WD repeat-containing protein 1 1 RPDDVPLSLS(0.164)PS(0.836)KR 176.68 1.72E-06 1668600000 1167600 791460 899380 812870 919640 790990 1220300 805760 1168400 TRUE FALSE 1094522 850060.5219 920713.7183 833729.6204 847415.184 1019335.972 1037327.344 906360.9097 973386.4918 1.124447493 0.873302156 0.945887092 0.856524749 0.870584492 1.047205792 1.065689068 0.931141861 1 19.89265323 2.228072714 24.99836971 1.022852565 0.923924108 0.162650505 0.08300169 286.2316961 682240.6353 0.028925006 0.02158886 169.0723987 -2.228072714 -0.098928457 RPDHSGGS(ph)PS(ph)PPTSEPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RPDHSGGSPSPPTSEPAR 18 1 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 2 RPDHS(0.001)GGS(0.999)PS(0.985)PPT(0.013)S(0.002)EPAR;RPDHS(0.006)GGS(0.994)PS(0.899)PPT(0.046)S(0.055)EPAR;RPDHS(0.405)GGS(0.597)PS(0.942)PPT(0.03)S(0.025)EPAR;RPDHS(0.053)GGS(0.947)PS(0.63)PPT(0.298)S(0.071)EPAR 194.68 2.12E-14 2329250000 788141 859464 825280 826141 850430 706508 929272 760769 803266 TRUE FALSE 738812.6617 923099.6088 844856.0313 847341.1767 783640.6583 910465.3904 789936.2905 855752.6843 669195.7153 1.104030771 1.379416496 1.262494681 1.266208311 1.171018643 1.36053679 1.180426402 1.278777889 1 19.35206868 -3.711999426 0.330356644 7.61E-08 1.272105975 0.4503518 0.085004633 113.5533733 2.209179184 77.94621918 0.064807224 0.000194089 3.711999426 1.272105899 RPDHSGGS(ph)PSPPTSEPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RPDHSGGSPSPPTSEPAR 18 1 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 RPDHS(0.016)GGS(0.984)PSPPTSEPAR;RPDHS(0.008)GGS(0.992)PSPPTSEPAR;RPDHS(0.013)GGS(0.987)PSPPTSEPAR;RPDHS(0.009)GGS(0.982)PS(0.01)PPTSEPAR 168.75 1.22E-11 2346950000 420767 516740 479860 493590 512540 463882 509040 430103 466651 TRUE FALSE 394431.9446 554999.9673 491242.5058 506256.355 472287.1759 597797.2029 432714.1777 483802.3063 388763.9334 1.01457957 1.427601481 1.263601028 1.302220478 1.214843084 1.537686888 1.113051239 1.244462937 1 18.56853486 0.865248844 1.218774069 1.005118516 1.29604982 0.243586784 0.145886119 0.768769098 2.221273033 0.122188708 0.037636888 7.33244551 -0.865248844 0.290931304 RPDLLTMVVDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPDLLTMVVDYR 12 1 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ; 161.63 0.00010399 424130000 372300 987260 345630 358130 1108180 213880 346920 890360 917880 FALSE TRUE 348998.4076 1060357.758 353828.5068 367320.2221 1021148.013 275623.6839 294902.5666 1001523.406 764679.8983 0.456398041 1.386668801 0.462714539 0.480358151 1.335392777 0.360443219 0.385654922 1.309728957 1 19.54449642 5.001963812 21.28828582 0.791332967 0.087668571 0.068635951 0.410641534 262696645 10160283857 0.094902885 4731451699 100453.2083 -5.001963812 -0.703664396 RPDPDS(ph)DEDEDYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RPDPDSDEDEDYER 14 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 1 RPDPDS(1)DEDEDYER;RPDPDS(1)DEDEDYER;RPDPDS(1)DEDEDYER 174.2 1.58E-06 7031650000 780160 2090420 1719020 1766120 1745070 2276880 1415430 1775650 975900 TRUE FALSE 731331.1782 2245196.872 1759795.966 1811441.629 1608019.241 2934178.294 1203199.412 1997343.811 813015.9854 0.899528658 2.76156547 2.164528125 2.228051676 1.977844557 3.609004431 1.479920977 2.456709151 1 19.63292419 4.75197122 23.90529009 2.275552746 0.899526964 0.252669569 0.700031545 1512.51213 2696064.85 0.145784499 2.692714977 56489.95382 -4.75197122 -1.376025782 RPDPDS(ph)DEDEDYERER ddPTM_SK-BR-3_Pertuzumab_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 251.12 2.44E-21 6117230000 1134723 1744724 1406771 1517726 1923472 1030902 1563708 1299345 2220219 TRUE FALSE 1063702.713 1873905.18 1440140.272 1556673.419 1772410.268 1328506.672 1329244.502 1461571.083 1849650.106 0.575083206 1.013113331 0.77860146 0.841604265 0.958240838 0.718247558 0.718646461 0.790187873 1 20.81882095 2.21016314 24.99751003 0.77407044 0.850758224 0 0.140115351 607.4147382 534686.8964 0.04754702 0.035122529 162.2419435 -2.21016314 0.076687785 RPDQQLQGEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RPDQQLQGEGK 11 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;;;;; 198.32 8.67E-08 10096732000 5486780 4752250 4972690 4680510 5426970 3908931 5780500 4477930 6015940 FALSE TRUE 5143372.234 5104111.535 5090644.555 4800619.811 5000757.668 5037375.924 4913767.689 5037009.418 5011840.75 1.026244147 1.018410558 1.015723525 0.957855616 0.99778862 1.005094969 0.980431728 1.005021841 1 22.25690914 3.444913126 24.99266537 0.990361149 1.019697225 0.489331649 0.014062625 143.0537459 111005.4178 0.003590117 0.004861092 2785.5639 -3.444913126 0.029336076 RPDS(ph)PTRPTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RPDSPTRPTLR 11 2 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 RPDS(0.992)PT(0.004)RPT(0.004)LR;RPDS(0.977)PT(0.022)RPT(0.002)LR;RPDS(0.879)PT(0.119)RPT(0.002)LR;RPDS(0.976)PT(0.011)RPT(0.013)LR;RPDS(0.945)PT(0.054)RPT(0.001)LR;RPDS(0.976)PT(0.024)RPTLR;RPDS(0.969)PT(0.025)RPT(0.006)LR 144.27 2.90E-05 8409908000 3723810 4037123 3823320 3973726 4095362 3261870 4193037 3483315 3688790 TRUE FALSE 3490743.379 4336035.788 3914010.956 4075698.537 3773728.788 4203518.917 3564330.028 3918214.545 3073107.119 1.135900327 1.410961486 1.273633103 1.326246818 1.227984786 1.367840025 1.159845684 1.275000966 1 21.55126662 0.144977064 0.491637307 0.974233337 1.306885498 0.496874827 0.085359519 2.436608499 0.818405057 0.20526946 0.03936947 1.396294617 -0.144977064 0.332652162 RPDSTWHSAEVIQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPDSTWHSAEVIQSR 15 1 Q9H7Z6;Q9H7Z6-2 Q9H7Z6 KAT8 Histone acetyltransferase KAT8 0 ; 176.23 5.26E-07 400140000 115084 222988 179739 184015 216890 151028 186681 169700 182716 FALSE TRUE 107881.0979 239498.2635 184002.494 188737.1364 199856.3343 194627.3319 158689.9171 190887.4186 152219.5192 0.708720527 1.573374195 1.208796972 1.239901015 1.312948138 1.278596417 1.042507018 1.254027207 1 17.21579384 1.181867282 0.775451125 1.01863568 1.264253812 0.031450561 0.223807242 1.35756571 1.868896678 0.194748255 0.075654696 15.20082931 -1.181867282 0.245618132 RPDTTAPLTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPDTTAPLTDR 11 1 Q96JB2;Q96JB2-2;A0A087WYY9 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 0 80.31 0.039702 136280000 71448 107420 92718 88347 111450 80199 105270 98779 107510 FALSE TRUE 66976.19722 115373.4886 94917.31474 90614.13359 102697.1666 103351.1494 89485.74078 111111.7756 89565.88646 0.747786907 1.288140978 1.05974851 1.011703643 1.146610285 1.15391198 0.999105176 1.240559101 1 16.45066173 -0.573374115 6.122795901 1 1.09370314 0.021867239 0.149918743 0 0 0.127731002 0.030106486 0.267070479 0.573374115 0.09370314 RPDTTESLNSSLSNGTSDADLFDSHDDRDDDAEAGSVEEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPDTTESLNSSLSNGTSDADLFDSHDDRDDDAEAGSVEEHK 41 2 Q96SU4-7;Q96SU4-2;Q96SU4;Q96SU4-6;Q96SU4-5;Q96SU4-4;Q96SU4-3 Q96SU4-7 OSBPL9 Oxysterol-binding protein-related protein 9 0 198.06 1.13E-35 92625000 58324 52256 61870 64704 66947 50571 77557 59426 70806 FALSE TRUE 54673.60495 56125.08861 63337.58562 66364.41418 61689.25267 65170.02675 65928.04785 66845.46691 58988.02118 0.926859451 0.951465865 1.073736402 1.125048999 1.045792882 1.104801033 1.117651458 1.133204091 1 15.84813439 3.99629888 1.675144346 1.095308844 0.927925616 0.694876055 0.040339394 0.19395769 1.027073703 0.010400388 0.032721745 9915.14067 -3.99629888 -0.167383229 RPDYAPMES(ph)S(ph)DEEDEEFQFIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RPDYAPMESSDEEDEEFQFIK 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 RPDYAPMES(1)S(1)DEEDEEFQFIK;RPDY(0.001)APMES(1)S(1)DEEDEEFQFIK;RPDY(0.006)APMES(0.997)S(0.997)DEEDEEFQFIK;RPDYAPMES(1)S(1)DEEDEEFQFIK;RPDY(0.001)APMES(0.999)S(0.999)DEEDEEFQFIK;RPDY(0.001)APMES(0.999)S(0.999)DEEDEEFQFIK 184 1.44E-16 1395280000 780375 636805 698095 668638 707353 574784 797752 608538 709404 TRUE FALSE 731532.7218 683954.7048 714654.1431 685796.3831 651800.3487 740714.81 678136.4936 684515.3089 590999.8895 1.237788255 1.157283981 1.209228895 1.160400188 1.102877277 1.253324786 1.14743929 1.15823255 1 19.17279834 0.382609932 1.123732562 0.999670433 1.181819003 0.627803382 0.043708353 1.681845446 2.496668214 0.038244796 0.011590274 2.413292327 -0.382609932 0.18214857 RPDYAPMES(ph)S(ph)DEEDEEFQFIKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPDYAPMESSDEEDEEFQFIKK 22 2 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 RPDYAPMES(1)S(1)DEEDEEFQFIKK;RPDYAPMES(1)S(1)DEEDEEFQFIKK 146.57 5.91E-08 152733000 313691 276638 295154 314240 328394 211945 345679 251811 485500 TRUE FALSE 294057.6403 297120.5654 302155.1923 322303.9304 302603.2599 273130.0809 293847.6431 283250.1577 404466.9136 0.727025204 0.73459795 0.747045511 0.796861052 0.748153309 0.675284113 0.726506009 0.700304891 1 18.62566217 -2.228912792 2.427887395 1.960218076 0.7329575 0.87663769 0.031596356 3498222.883 506563.6137 18556806.63 0.00835426 0.005903196 2.228912792 -1.227260575 RPEDYEAVFVGNIDDHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPEDYEAVFVGNIDDHFR 18 1 Q68CQ4;H7C2R4 Q68CQ4 DIEXF Digestive organ expansion factor homolog 0 ; 211.16 2.16E-16 238540000 153916 196040 179078 190127 203222 164175 198917 191573 173554 FALSE TRUE 144282.6723 210555.0056 183325.8147 195005.9807 187261.7639 211569.6573 169091.2425 215491.3108 144586.7162 0.997897152 1.456254151 1.267929859 1.348712979 1.295151925 1.463271751 1.16947979 1.490394944 1 17.14157549 -0.831722586 6.073743145 0.999999975 1.316730602 0.30199633 0.148439298 4.40E-08 8.44E-09 0.122902502 0.028968395 0.147325327 0.831722586 0.316730628 RPEGACGDGQSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RPEGACGDGQSSR 13 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 ;;;;; 207.64 8.38E-08 2345868000 779486.2 901544 872960.2 851712.3 974091 770075.6 832321 830103.3 747366.5 FALSE TRUE 730699.5502 968295.2558 893667.2282 873568.6796 897589.8222 992383.9246 707522.1929 933743.5243 622626.203 1.173576613 1.555179097 1.435319015 1.403038734 1.441619093 1.59386791 1.136351457 1.499685557 1 19.24800677 -0.083413442 0.52074591 0.958383063 1.437563255 0.397898011 0.151008693 4.43315135 1.374623086 0.526297799 0.065584086 0.825251947 0.083413442 0.479180192 RPEGACGDGQSSRVS(ph)PPAADVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RPEGACGDGQSSRVSPPAADVLK 23 2 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 RPEGACGDGQS(0.039)S(0.039)RVS(0.922)PPAADVLK;RPEGACGDGQS(0.004)S(0.018)RVS(0.978)PPAADVLK;RPEGACGDGQS(0.001)S(0.003)RVS(0.997)PPAADVLK 146.37 6.73E-08 1691600000 848840 639770 724990 732220 871220 542017 773070 641330 865730 TRUE FALSE 795712.6196 687139.2365 742187.1052 751010.0048 802797.8955 698488.509 657155.3303 721401.4622 721234.0702 1.103265434 0.952727089 1.029051643 1.041284703 1.113089257 0.968462997 0.911154031 1.000232091 1 19.46010802 2.027685409 24.99568653 0.955394793 1.032767841 0.328390368 0.051501416 238.2833008 215132.384 0.019167557 0.014155924 106.5823788 -2.027685409 0.077373048 RPEGPGAQAPSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RPEGPGAQAPSSPR 14 1 P40222 P40222 TXLNA Alpha-taxilin 1 RPEGPGAQAPS(0.005)S(0.995)PR;RPEGPGAQAPS(0.008)S(0.992)PR;RPEGPGAQAPS(0.059)S(0.941)PR;RPEGPGAQAPS(0.083)S(0.917)PR;RPEGPGAQAPS(0.004)S(0.996)PR;RPEGPGAQAPS(0.004)S(0.996)PR;RPEGPGAQAPS(0.049)S(0.951)PR 214.73 7.17E-12 30884680000 8800600 10189230 10302760 10756020 11313380 7280530 7616090 6580770 7768920 TRUE FALSE 8249786.156 10943651.19 10547146.33 11032037.68 10424872.77 9382300.821 6474128.009 7402393.621 6472237.063 1.274642149 1.690860685 1.629598272 1.704516935 1.610706263 1.449622554 1.000292163 1.143714847 1 22.62583302 1.877447995 3.20615774 1.050301146 1.60669825 0.78628055 0.126797017 0.101336413 1.799456055 0.061814014 0.032920615 75.41330855 -1.877447995 0.556397103 RPEILK ddPTM_SK-BR-3_Pertuzumab_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 94.006 0.072111 734060000 977980 911120 1016000 1034000 1085000 899040 1215300 1023900 1204400 FALSE TRUE 916769.9775 978580.2728 1040100 1060534.191 999788.4767 1158578.253 1033077.047 1151736.169 1003377.859 0.913683683 0.975285894 1.036598516 1.056963915 0.996422701 1.154677914 1.029599206 1.147858863 1 19.93643358 5.027428771 0.544660768 1.074964433 0.754663721 0.48646124 0.05264352 4.165230311 0.749133543 0.024256734 0.905044994 106519.4147 -5.027428771 -0.320300712 RPELEDSTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RPELEDSTLR 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;; 211.46 9.36E-08 4650410000 2452710 3126120 2712830 3031310 3236710 2388170 3170840 2758510 2563260 FALSE TRUE 2299199.259 3357581.178 2777179.609 3109098.547 2982511.853 3077595.91 2695401.979 3102916.046 2135435.347 1.076688771 1.572316944 1.300521513 1.455955364 1.39667626 1.441203039 1.262225983 1.453060169 1 21.02609879 -1.529641033 2.659707166 0.978742289 1.379568355 0.423849051 0.13508567 7850477.378 7842296.893 1204476.99 0.030478699 0.029536496 1.529641033 0.400826066 RPELLTHSTTEVTQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RPELLTHSTTEVTQPR 16 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 ;;; 174.52 2.49E-09 1707760000 482725 588409 619197 577805 681350 557989 645330 564611 663130 FALSE TRUE 452512.1039 631975.4146 633884.6452 592632.4545 627839.5194 719071.3661 548568.7575 635103.9262 552449.319 0.819101569 1.143951839 1.147407777 1.072736329 1.136465369 1.301606032 0.992975715 1.149614823 1 19.07548259 4.74089727 24.64943438 1.123777966 0.819101438 0.536413184 0.087211209 127.0881994 1340554.343 0.018897466 0.126142988 55067.74209 -4.74089727 -0.304676528 RPENPKPQDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPENPKPQDGK 11 2 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 96.23 0.0040314 192190000 486420 346590 611900 580340 477830 327870 535110 387410 444070 FALSE TRUE 455975.8405 372251.8842 626414.557 595232.5069 440303.1593 422520.7465 454875.2232 435778.9913 369951.8482 1.232527538 1.006217123 1.693232673 1.608945893 1.190163426 1.142096596 1.229552509 1.177934354 1 18.49697798 2.512562245 24.08076897 1.16412116 1.376011476 0.26512261 0.195538043 643.8535605 437472.4192 0.067794616 0.063886221 325.5084338 -2.512562245 0.211890316 RPENSLLEETLHFDHAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RPENSLLEETLHFDHAVR 18 1 O00566;U3KQ48 O00566 MPHOSPH10 U3 small nucleolar ribonucleoprotein protein MPP10 0 ;;;; 285.47 4.84E-40 394868000 235184 277613 267386 262192 270560 237252 291683 237978 254308 FALSE TRUE 220464.2533 298167.7554 273728.5222 268920.2906 249311.309 305742.8009 247947.842 267690.0772 211862.3519 1.040601368 1.407365455 1.292011156 1.269316083 1.176760792 1.443120017 1.170325165 1.263509419 1 17.69276772 0.295511594 0.886004024 0.997789821 1.282233195 0.313651243 0.116690813 3.007515542 2.900153693 0.11645416 0.033641854 1.974747596 -0.295511594 0.284443374 RPEPSTLENITDDKYATVSS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPEPSTLENITDDKYATVSSPSK 23 2 Q01804-5;Q01804-3;Q01804 Q01804-5 OTUD4 OTU domain-containing protein 4 1 RPEPSTLENITDDKYAT(0.021)VS(0.153)S(0.709)PS(0.117)K;RPEPSTLENITDDKYATVS(0.036)S(0.964)PSK 255.84 7.66E-44 1155100000 1250489 576939 808735 741903 702325 616890 1087095 771098 927479 TRUE FALSE 1172223.126 619656.1639 827918.5761 760941.487 647167.2275 794976.1286 924095.1968 867371.2827 772676.7632 1.517093799 0.801960397 1.071494078 0.984812179 0.837565277 1.028859889 1.195966077 1.12255386 1 19.55950549 1.928607352 8.942778896 1.124542051 1.004699449 0.001795281 0.199182545 1.13038398 134.2452188 0.076591255 0.048425926 84.84130732 -1.928607352 -0.119842602 RPES(ph)PSEIS(ph)PIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPESPSEISPIK 12 1 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 2 RPES(0.992)PS(0.008)EIS(1)PIK 109.42 0.0055983 123680000 252560 151970 196740 194230 190580 172780 259560 181810 183370 TRUE FALSE 236752.7204 163222.0169 201406.7657 199214.2706 175612.6156 222658.7812 220641.3876 204509.3787 152764.3624 1.549790257 1.068456114 1.3184146 1.304062463 1.149565336 1.457530917 1.444325 1.338724396 1 17.2209485 2.235057586 24.99949179 1.361522756 1.256160956 0 0.178349303 239.7628886 1711052.214 0.059034219 0.045364998 171.8136192 -2.235057586 -0.1053618 RPES(ph)PSEIS(ph)PIKGSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPESPSEISPIKGSVR 16 2 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 2 RPES(0.996)PS(0.023)EIS(0.98)PIKGS(0.001)VR;RPES(0.989)PS(0.054)EIS(0.956)PIKGS(0.001)VR 120.8 0.00050273 1682820000 2209030 1873040 2014820 2040000 2145510 1538570 2455000 1784800 2617600 TRUE FALSE 2070770.756 2011721.83 2062612.482 2092349.854 1977010.299 1982730.182 2086895.541 2007636.209 2180705.65 0.949587468 0.92250957 0.945846351 0.959482933 0.906592001 0.909214952 0.956981765 0.920636038 1 21.05636362 -1.42806545 3.01838404 1.001229818 0.934443688 0.545367366 0.018972388 7963306.159 9510085.606 83480.50622 0.004313639 0.037319391 1.42806545 -0.06678613 RPES(ph)PSEISPIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RPESPSEISPIK 12 1 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 1 RPES(0.994)PS(0.006)EISPIK;RPES(1)PSEISPIK;RPES(0.978)PS(0.022)EISPIK;RPES(0.984)PS(0.011)EIS(0.005)PIK;RPES(0.97)PS(0.03)EISPIK 197.75 1.17E-07 2745880000 3195980 3177670 3096350 3351500 3483900 2445830 4191640 3132550 4074990 TRUE FALSE 2995949.317 3412947.993 3169796.884 3437505.164 3210288.547 3151901.416 3563142.495 3523655.763 3394847.844 0.88249885 1.005331653 0.933708087 1.012565311 0.945635473 0.928436726 1.049573548 1.037942178 1 21.69491548 1.718052199 8.800572655 1.031860834 0.957729089 0.459085717 0.03931944 0.095370285 19.50115366 0.017218523 0.009205042 52.24589814 -1.718052199 -0.074131744 RPEVDGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPEVDGEK 8 1 E5RGC7;E5RK86;E5RFH3;H0YAT2;Q9Y2Q9;H7C5V3 E5RGC7 MRPS28 "28S ribosomal protein S28, mitochondrial" 0 ; 110.76 0.0053949 658720000 1415330 1255120 1253530 1170790 1472860 1087830 1192150 1286280 1780030 FALSE TRUE 1326747.022 1348050.391 1283264.324 1200834.454 1357187.517 1401868.862 1013398.175 1446874.889 1482931.494 0.894678566 0.909044279 0.865356444 0.809770686 0.915205809 0.945336226 0.683374909 0.97568559 1 20.50002052 3.869720654 3.431134043 0.862942737 0.901290051 0 0.092015158 1.05470143 23.51980493 0.023165893 0.04587099 7408.335707 -3.869720654 0.038347314 RPFDPNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RPFDPNDR 8 1 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2;F8WEA1 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ;;;;;; 98.249 0.012277 5604140000 838706 1404810 1548110 1082690 997399 1061920 1192910 918333 1192910 FALSE TRUE 786212.8886 1508823.594 1584831.9 1110473.658 919067.3059 1368479.065 1014044.22 1032988.897 993805.6145 0.79111335 1.518228084 1.59471015 1.117395235 0.924795848 1.377008788 1.020364753 1.039427511 1 19.92260417 3.12064196 8.45086038 1.087457232 1.389083575 0.122329948 0.245270545 0.340314939 23.72507981 0.068693366 0.082239941 1320.206783 -3.12064196 0.301626343 RPGAPSLS(ph)PAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPGAPSLSPAPR 12 1 Q5QP82-2;Q5QP82 Q5QP82-2 DCAF10 DDB1- and CUL4-associated factor 10 1 RPGAPS(0.023)LS(0.977)PAPR;RPGAPS(0.098)LS(0.902)PAPR 112.03 0.00080706 936230000 255245 304140 300820 329270 356730 234705 335660 277800 312320 TRUE FALSE 239269.6711 326658.8421 307955.5925 337719.6257 328713.8648 302460.5234 285330.8991 312483.9415 260191.7743 0.919589682 1.255454147 1.183571592 1.297964267 1.263352255 1.162452288 1.096617677 1.200975482 1 17.98921583 0.447244949 0.745714857 0.999461185 1.191639919 0.182840095 0.107839151 2.813522716 2.397060925 0.112422155 0.035637864 2.800560437 -0.447244949 0.192178733 RPGFS(ph)PTSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RPGFSPTSHR 10 1 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 RPGFS(0.957)PT(0.036)S(0.007)HR;RPGFS(0.72)PT(0.236)S(0.044)HR;RPGFS(0.629)PT(0.292)S(0.078)HR;RPGFS(0.97)PT(0.025)S(0.004)HR 97.69 0.0036059 923910000 339494 364140 373879 377095 371774 309685 381259 329899 364615 TRUE FALSE 318245.6766 391101.3045 382747.5864 386771.8961 342576.3697 399086.0322 324092.7524 371087.6163 303758.401 1.047693415 1.287540701 1.260039509 1.273287899 1.127792247 1.313827143 1.066942515 1.221653838 1 18.21256478 0.658194284 0.593167948 0.997730075 1.231568735 0.293232121 0.093649928 1.444990735 1.00290406 0.100040797 0.03695825 4.55191647 -0.658194284 0.23383866 RPGFSPTS(ph)HR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPGFSPTSHR 10 1 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 RPGFS(0.107)PT(0.297)S(0.596)HR;RPGFS(0.162)PT(0.266)S(0.573)HR 88.42 0.0074768 888690000 367790 409220 436510 407940 398880 356530 475140 386990 377800 TRUE FALSE 344770.6804 439519.0746 446864.2233 418408.431 367553.5738 459454.4232 403897.168 435306.5534 314742.7393 1.095404714 1.396439122 1.419776114 1.329366428 1.167790477 1.459777672 1.283261272 1.383055108 1 18.26381357 -1.290075921 5.074901675 0.99991717 1.331895417 0.429603838 0.113573301 9.74E-05 1.36E-05 0.100575946 0.023700085 0.051277174 1.290075921 0.331978247 RPGGS(ph)SPLNAVPCEGPPGSEPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPGGSSPLNAVPCEGPPGSEPPR 23 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 RPGGS(0.587)S(0.413)PLNAVPCEGPPGSEPPR;RPGGS(0.5)S(0.5)PLNAVPCEGPPGSEPPR 86.492 0.0041474 612530000 184436 167709 210550 198865 187022 211560 208840 192287 207020 TRUE FALSE 172892.48 180126.3489 215544.3454 203968.2126 172334.0465 272633.9376 177526.3808 216294.4552 172467.0246 1.00246688 1.044410369 1.249771346 1.182650498 0.999228965 1.580788781 1.029335209 1.25412064 1 17.39596102 4.207300014 2.781181374 1.193235181 1.011116196 0.135826995 0.169762708 0.483667118 7.376131248 0.038954925 0.118752336 16117.58667 -4.207300014 -0.182118985 RPGHGS(ph)LTNISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RPGHGSLTNISR 12 1 G5EA48;Q7Z6B7-2;Q7Z6B7 G5EA48 SRGAP1 SLIT-ROBO Rho GTPase-activating protein 1 1 RPGHGS(0.992)LT(0.008)NISR;RPGHGS(0.986)LT(0.014)NISR;RPGHGS(0.998)LT(0.001)NIS(0.001)R 196.78 1.24E-07 885210000 481340 462818 467970 478750 501660 415000 541500 470740 481300 TRUE FALSE 451213.7886 497085.5263 479070.4694 491035.5355 462261.6472 534803.763 460307.102 529512.9252 400967.9207 1.125311441 1.239713954 1.194785031 1.224625488 1.152864415 1.33378192 1.147989847 1.320586755 1 18.61312729 -1.231951899 3.607017888 0.999649927 1.215850303 0.495725599 0.068910057 7432020.397 13975593.73 31313.63995 0.014002889 0.058620309 1.231951899 0.216200376 RPGQSFHVNSEVNSVLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 271.38 1.19E-39 2025160000 403580 718530 680460 818690 922130 785380 836150 694930 779690 TRUE FALSE 378320.6482 771730.7088 696600.8325 839698.9714 849709.6295 1012106.456 710777.0699 781693.5402 649554.702 0.582430775 1.188091944 1.072428281 1.292730187 1.308141758 1.558154307 1.094252828 1.203429885 1 19.3090915 4.746882101 4.18151153 1.221234578 0.526004976 0.624514948 0.154176812 0.155889677 6.064317144 0.036368531 0.328178879 55831.86054 -4.746882101 -0.695229601 RPGRS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 83.948 0.017252 8539150000 5427740 3626110 4221425 3987440 4160850 3153749 4635420 3682370 4545160 TRUE FALSE 5088027.442 3894590.957 4321559.195 4089764.461 3834073.625 4064185.139 3940381.804 4142122 3786543.433 1.343712949 1.028534606 1.141293972 1.080078582 1.012552396 1.073323259 1.040627653 1.093905847 1 21.85245005 4.743074093 24.99908553 1.064590735 1.34371306 0.819701189 0.041916747 186.6118951 1033563.782 0.009548927 0.076099812 55344.45221 -4.743074093 0.279122325 RPGS(ph)VSSTDQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPGSVSSTDQER 12 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 RPGS(0.991)VS(0.005)S(0.002)T(0.002)DQER 134.37 0.00015528 489530000 215770 255360 219950 246560 290520 188990 233720 215540 242630 TRUE FALSE 202265.3409 274267.1201 225167.3179 252887.147 267703.7311 243548.345 198675.8558 242450.6435 202133.4856 1.000652318 1.35686138 1.11395357 1.251089825 1.324390812 1.204888662 0.982894325 1.199458085 1 17.62494881 1.762791547 25 1.06238396 1.220901432 0.264075118 0.115137645 16.30169045 16831.09171 0.048030002 0.026636809 57.91506485 -1.762791547 0.158517473 RPGTQGHLGPEKEEEES(ph)DGEPEDSSTS ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 RPGTQGHLGPEKEEEESDGEPEDSSTS 27 2 Q8IYB7;H7C1Q8 Q8IYB7 DIS3L2 DIS3-like exonuclease 2 1 RPGTQGHLGPEKEEEES(1)DGEPEDSSTS;RPGTQGHLGPEKEEEES(0.993)DGEPEDSS(0.002)T(0.002)S(0.002);RPGTQGHLGPEKEEEES(1)DGEPEDSSTS;RPGTQGHLGPEKEEEES(0.881)DGEPEDS(0.002)S(0.032)T(0.043)S(0.043);RPGTQGHLGPEKEEEES(0.993)DGEPEDS(0.002)S(0.002)T(0.002)S(0.002);RPGTQGHLGPEKEEEES(0.964)DGEPEDS(0.009)S(0.009)T(0.009)S(0.009);RPGTQGHLGPEKEEEES(1)DGEPEDSSTS;RPGTQGHLGPEKEEEES(0.929)DGEPEDS(0.018)S(0.018)T(0.018)S(0.018) 183.98 7.24E-18 4208590000 3430030 2424341 2763743 2857948 3087550 1958144 3459120 2404508 3244990 TRUE FALSE 3215350.545 2603841.73 2829300.289 2931287.784 2845066.278 2523428.385 2940457.069 2704716.117 2703380.206 1.189381552 0.963179994 1.046578755 1.084304671 1.052410709 0.933434513 1.087696456 1.000494163 1 21.366333 RPHS(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RPHSPEK 7 1 Q53F19;Q53F19-2 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 RPHS(1)PEK;RPHS(1)PEK;RPHS(1)PEK;RPHS(1)PEK;RPHS(1)PEK;RPHS(1)PEK;RPHS(1)PEK 103.01 0.0051899 6429370000 5788700 3935870 4636370 4339230 4846350 3337620 5081600 4105320 5760630 TRUE FALSE 5426395.6 4227285.91 4746346.886 4450581.988 4465737.22 4301136.712 4319661.255 4617878.239 4799143.638 1.13070081 0.880841714 0.988998714 0.927370032 0.930527935 0.896230044 0.900090012 0.962229637 1 22.19434556 4.747412247 24.91612502 0.930588585 1.130700917 0.708181857 0.039195569 584.400828 1644970.385 0.008767232 0.106733593 55900.05656 -4.747412247 0.200112332 RPHT(ph)PTPGIYMGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 17 RPHTPTPGIYMGR 13 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 1 RPHT(0.957)PT(0.043)PGIYMGR;RPHT(0.975)PT(0.025)PGIYMGR;RPHT(0.826)PT(0.174)PGIYMGR;RPHT(0.974)PT(0.026)PGIYMGR;RPHT(0.974)PT(0.026)PGIYMGR;RPHT(0.982)PT(0.018)PGIYMGR;RPHT(0.941)PT(0.059)PGIYMGR;RPHT(0.887)PT(0.113)PGIYMGR;RPHT(0.964)PT(0.036)PGIYMGR;RPHT(0.752)PT(0.248)PGIYMGR;RPHT(0.998)PT(0.002)PGIYMGR;RPHT(0.994)PT(0.006)PGIYMGR;RPHT(0.944)PT(0.056)PGIYMGR;RPHT(0.957)PT(0.043)PGIYMGR;RPHT(0.779)PT(0.221)PGIYMGR;RPHT(0.986)PT(0.014)PGIYMGR;RPHT(0.577)PT(0.423)PGIYMGR 189.52 3.04E-06 47363290000 3346378 3374747 3493601 3388797 3483507 2953462 3486335 3561869 2760433 TRUE FALSE 3136934.174 3624616.779 3576470.866 3475759.268 3209926.412 3806078.534 2963591.432 4006576.185 2299698.899 1.364062998 1.576126675 1.555190928 1.511397544 1.395802908 1.65503342 1.28868672 1.742217725 1 21.13301355 -1.524348569 2.980948871 0.980651783 1.507527138 0.58476765 0.135312761 18420448.85 21007753.31 2896706.577 0.029610681 0.02989864 1.524348569 0.526875355 RPHT(ph)PTPGIYMGRPT(ph)YGSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPHTPTPGIYMGRPTYGSSR 20 2 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 2 RPHT(0.999)PT(0.001)PGIYMGRPT(0.592)YGS(0.406)S(0.002)R 96.887 0.0011817 247210000 31046 31045 35333 19572 21872 25342 29195 30878 36725 TRUE FALSE 29102.88628 33343.6041 36171.11545 20074.25066 20154.26135 32657.82401 24817.48078 34733.18627 30595.36025 0.951218944 1.089825511 1.182241855 0.656120748 0.658735873 1.067410998 0.811151775 1.135243579 1 14.90102527 3.262796043 24.99999829 0.876078099 1.093129953 0.214614959 0.165682678 292.104846 301318.0245 0.044069603 0.059641471 1831.454116 -3.262796043 0.217051855 RPHTPT(ph)PGIYMGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPHTPTPGIYMGR 13 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 1 RPHT(0.025)PT(0.975)PGIYMGR 112.51 0.00040661 171350000 65526 68075 68632 74745 77548 63283 71344 68608 64139 TRUE FALSE 61424.84463 73115.34383 70259.98345 76663.08324 71457.69289 81551.77479 60646.62953 77173.85982 53433.78655 1.149550661 1.36833544 1.314898082 1.434730499 1.337312916 1.526221143 1.134986559 1.444289556 1 15.70546464 -1.017456327 6.10675065 0.999999665 1.335542129 0.431435411 0.122176056 4.97E-07 8.00E-08 0.105425019 0.024848891 0.096060241 1.017456327 0.335542464 RPILQLS(ph)PPGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RPILQLSPPGPR 12 1 Q8N3X1-2;Q8N3X1;F5GXL1 Q8N3X1-2 FNBP4 Formin-binding protein 4 1 RPILQLS(1)PPGPR;RPILQLS(1)PPGPR;RPILQLS(1)PPGPR;RPILQLS(1)PPGPR;RPILQLS(1)PPGPR;RPILQLS(1)PPGPR 129.92 0.00013827 3021950000 1470140 1816730 1590910 1612230 1780670 1287890 1606910 1533430 1820410 TRUE FALSE 1378126.562 1951242.58 1628647.136 1653602.551 1640823.361 1659682.936 1365968.763 1724882.111 1516571.811 0.908711709 1.286614037 1.073900441 1.09035559 1.081929223 1.094364885 0.900695077 1.137356041 1 20.53238238 1.965471362 21.47494472 1.000619635 1.111363643 0.077591711 0.107068964 181.625702 112959.7229 0.041346499 0.026708088 92.35732857 -1.965471362 0.110744008 RPIS(ph)DDDCPSASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPISDDDCPSASK 13 1 Q96PU4 Q96PU4 UHRF2 E3 ubiquitin-protein ligase UHRF2 1 RPIS(1)DDDCPSASK 210.37 3.22E-08 127630000 475690 385200 366630 404380 407990 307880 495830 335530 445410 TRUE FALSE 445917.412 413720.6088 375326.6367 414757.0754 375948.1112 396759.958 421484.8946 377421.6591 371068.1935 1.201712838 1.114944951 1.011476174 1.117738148 1.013150999 1.069237312 1.135869099 1.017122097 1 18.50132482 4.62475445 2.232819856 1.062369569 1.219444001 0.51268199 0.046566478 0.4083533 2.856820892 0.011193474 0.114978736 42145.81438 -4.62475445 0.157074432 RPKEEDPATGTGDPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RPKEEDPATGTGDPPR 16 2 P45974-2;P45974;F5H571 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;; 114.63 0.00031981 219763000 441020 492740 446220 500950 618280 304433 487850 429060 888950 FALSE TRUE 413417.3454 529222.9823 456804.5491 513805.2251 569722.7828 392317.865 414701.4215 482629.0855 740578.5022 0.558235682 0.714607541 0.616821239 0.693789009 0.769294249 0.529745144 0.559969565 0.651692 1 19.49829315 -1.314637087 2.67524008 1.005322952 0.637065941 0.696868446 0.075287679 2089561.553 2359259.433 88361.54323 0.019390276 0.048457713 1.314637087 -0.368257011 RPLDS(ph)PEAEELPAMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RPLDSPEAEELPAMK 15 1 Q5VWG9 Q5VWG9 TAF3 Transcription initiation factor TFIID subunit 3 1 RPLDS(1)PEAEELPAMK;RPLDS(1)PEAEELPAMK;RPLDS(1)PEAEELPAMK;RPLDS(1)PEAEELPAMK 201.27 3.98E-09 910300000 2236530 1905970 2065740 2002470 2296120 1638630 2420620 1995560 2727490 TRUE FALSE 2096549.58 2047090.002 2114740.328 2053856.77 2115791.997 2111675.88 2057670.503 2244710.059 2272254.299 0.922673831 0.900907087 0.930679427 0.903885085 0.931142257 0.929330789 0.905563477 0.987878012 1 21.11569287 1.197162551 6.506550385 0.996217274 0.917320856 0.883396946 0.011515206 0.058435273 6.20396605 0.009860709 0.002572275 15.74572096 -1.197162551 -0.078896419 RPLEDGDQPDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RPLEDGDQPDAK 12 1 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 ;;; 169.6 6.96E-05 2217790000 4333370 3312240 3726160 3600750 3796320 2898690 4375820 3286180 4473500 FALSE TRUE 4062152.107 3557481.696 3814546.275 3693151.341 3498172.341 3735494.747 3719706.414 3696466.807 3726843.95 1.089971075 0.954556119 1.023532599 0.99095948 0.938642022 1.002321212 0.998084831 0.991849097 1 21.82952298 4.750674992 24.9085033 0.988465927 1.08997114 0.637787454 0.02426053 1181.897197 2430065.779 0.005561435 0.094129002 56321.60107 -4.750674992 0.101505213 RPLEEDFRRS(ph)PTEDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RPLEEDFRRSPTEDFR 16 3 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 RPLEEDFRRS(0.994)PT(0.006)EDFR;RPLEEDFRRS(0.999)PT(0.001)EDFR;RPLEEDFRRS(0.997)PT(0.003)EDFR 175.32 1.97E-08 1359830000 573210 879430 727220 880640 1146340 530820 771120 731000 1573520 TRUE FALSE 537333.8093 944543.9122 744470.0018 903238.7133 1056311.081 684059.1169 655497.7147 822266.9591 1310889.347 0.409900203 0.720536722 0.567912161 0.689027427 0.805797288 0.521828268 0.500040462 0.627258861 1 20.32211448 0.938866494 20.97643429 1.000000001 0.607805942 0.539958027 0.114634436 2886.473791 990424.0184 0.107029769 0.026757442 8.686933451 -0.938866494 -0.392194059 RPLEEDFRRSPT(ph)EDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPLEEDFRRSPTEDFR 16 3 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 RPLEEDFRRS(0.426)PT(0.574)EDFR 61.815 0.08439 72681000 89939 100030 96739 89295 118170 58558 86224 86845 143380 TRUE FALSE 84309.87854 107436.3253 99033.69476 91586.46088 108889.4049 75462.74399 73295.51166 97687.78942 119448.9517 0.705823511 0.899432969 0.829088019 0.766741437 0.911597827 0.631757273 0.613613687 0.817820399 1 16.86603467 2.240121655 24.99984557 0.717106216 0.831379798 0 0.12435672 71.28007024 1141565.233 0.040785147 0.032436087 173.8287693 -2.240121655 0.114273582 RPLEMEQQQAYRPEMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPLEMEQQQAYRPEMK 16 2 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0QYZ0;M0R0K8;M0QZV6;M0R203 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 152.89 2.83E-07 82687000 145020 135460 137320 134460 137670 110160 150760 121930 173720 FALSE TRUE 135943.4571 145489.5993 140577.2952 137910.4712 126857.9535 141961.4037 128154.9376 137153.2289 144725.0097 0.939322494 1.005283051 0.971340721 0.952913885 0.876544792 0.980904434 0.885506505 0.947681601 1 17.14295473 3.116642624 3.654491102 0.929763995 0.979250689 0.093652347 0.040935334 0.305735727 7.830120847 0.010853114 0.013289719 1308.105056 -3.116642624 0.049486694 RPLEQQQPHHIPTSAPVYQQPQQQPVAQSYGGYKEPAAPVSIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPLEQQQPHHIPTSAPVYQQPQQQPVAQSYGGYKEPAAPVSIQR 44 2 Q14847;Q14847-2;C9J9W2;Q14847-3;J3KSN1 Q14847 LASP1 LIM and SH3 domain protein 1 0 100.41 5.11E-06 253580000 50668 46491 52316 54170 60837 41771 58141 50200 92169 FALSE TRUE 47496.78032 49933.24201 53556.96023 55560.09391 56059.10742 53829.6096 49423.2968 56467.5805 76785.39847 0.618565265 0.650296059 0.697488862 0.723576292 0.730075099 0.70103966 0.643654885 0.735394771 1 16.22854437 -5 0.307559349 3.755799906 0.669104439 0.88472243 0.035887222 97.00972794 0.883798511 172.9659949 0.036285642 1.00E-05 5 -3.086695467 RPLFLAPDFDRWLDES(ph)DAEMELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 249.97 2.25E-38 440004000 285778 364874 360341 355548 509669 429361 409421 294526 467418 TRUE FALSE 267891.6651 391889.6506 368888.4587 364671.9636 469641.6526 553310.5506 348032.1219 331298.2194 389402.9162 0.687954954 1.006386019 0.947318172 0.936490068 1.206055818 1.420920408 0.893758386 0.850785153 1 18.57090416 5.315170484 1.049144917 1.049272501 3.25E-31 0.282463224 0.168737399 7.5253856 2.883267406 0.050665841 11.79808444 206619.109 -5.315170484 -1.049272501 RPLILQLVHVSQEDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPLILQLVHVSQEDKR 16 2 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;F8VZ52;B4DDQ3;B4DPZ9;F8W1W3;H0YHY4;F8VR28;F8VYL3;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 0 94.544 0.002436 101990000 42767 83546 64675 68848 82594 52372 76441 68478 86910 FALSE TRUE 40090.28981 89731.83277 66209.12154 70614.75624 76107.40041 67490.94621 64979.38169 77027.62904 72404.15954 0.553701473 1.239318754 0.914438093 0.975285905 1.051146797 0.932141836 0.897453711 1.063856407 1 16.14378496 4.759070763 24.70230499 1.00326929 0.553700961 0.680087048 0.098106075 2761.930289 3326390.333 0.023935028 1.0105535 57421.0015 -4.759070763 -0.449568328 RPLLAFACDDKDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPLLAFACDDKDGK 14 2 Q96J01;D6REC9 Q96J01 THOC3 THO complex subunit 3 0 106.42 0.00053012 146920000 392740 244920 258790 276630 299430 216600 350690 255170 327040 FALSE TRUE 368159.1045 263054.1316 264928.621 283728.7941 275913.9756 279128.9038 298107.2901 287028.5362 272454.9112 1.35126617 0.965496017 0.972376016 1.041378894 1.012695915 1.024495769 1.094152749 1.053490043 1 18.05565797 4.744280382 24.99846682 1.019605193 1.351266313 0.883723527 0.037703581 248.2882714 1085122.046 0.010897538 0.098156617 55498.38968 -4.744280382 0.33166112 RPLRPQVVTDDDGQAPEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPLRPQVVTDDDGQAPEAK 19 2 Q9HDC9;Q9HDC9-2 Q9HDC9 APMAP Adipocyte plasma membrane-associated protein 0 114.4 8.90E-05 262080000 595920 437660 403960 385300 556000 338420 587420 498010 590590 FALSE TRUE 558622.4309 470064.8018 413542.122 395187.4503 512334.0028 436116.3602 499341.8243 560187.6448 492016.7136 1.135372875 0.955383809 0.840504216 0.80319924 1.0412939 0.886385255 1.014887931 1.138554096 1 18.9083478 1.537256998 4.77237557 1.072089178 0.931915369 0.209169695 0.100409905 0.212561438 10.5881953 0.057610239 0.025074247 34.45537636 -1.537256998 -0.140173809 RPLS(ph)ASLGQLNEVGLPSAAILPDEGAVDLPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPLSASLGQLNEVGLPSAAILPDEGAVDLPSR 32 1 Q5TC82-2;Q5TC82 Q5TC82-2 RC3H1 Roquin-1 1 RPLS(0.56)AS(0.44)LGQLNEVGLPSAAILPDEGAVDLPSR 142.3 3.63E-10 384640000 23692 28675 32418 25568 28332 22033 32051 26990 34644 TRUE FALSE 22209.16001 30798.12684 33186.97027 26224.11817 26106.91901 28393.56942 27245.2501 30359.76091 28861.69259 0.769503034 1.067093579 1.149862232 0.908613314 0.904552598 0.983780467 0.943993496 1.051905075 1 14.81686829 3.187531 24.99999603 0.959942874 1.032887227 0 0.10583617 248.7160605 121847.8196 0.030169813 0.036059858 1540.03645 -3.187531 0.072944353 RPLS(ph)GPDVGTPQPAGLASGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPLSGPDVGTPQPAGLASGAK 21 1 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 RPLS(1)GPDVGTPQPAGLASGAK 182.95 2.75E-17 198930000 133030 117730 114850 127680 137780 96492 146450 113790 125910 TRUE FALSE 124703.8898 126446.8517 117574.2962 130956.485 126959.3146 124347.674 124491.1821 127996.932 104894.8076 1.188847119 1.205463403 1.120878134 1.248455362 1.210348896 1.185451185 1.1868193 1.220240877 1 16.67858374 -1.473437824 6.060743176 0.999876948 1.191182409 0.777651372 0.032822612 5.38E-05 4.68E-06 0.03135513 0.007385743 0.033617249 1.473437824 0.191305461 RPLS(ph)SSHEASEGQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RPLSSSHEASEGQAK 15 1 Q8IZ21-3;Q8IZ21;Q8IZ21-2;A0A0J9YVR0 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 RPLS(0.795)S(0.135)S(0.066)HEAS(0.004)EGQAK;RPLS(0.753)S(0.222)S(0.024)HEASEGQAK;RPLS(0.554)S(0.223)S(0.223)HEASEGQAK 260.98 3.86E-25 830603000 657848 772730 705123 745032 962130 434305 1007830 835800 1143310 TRUE FALSE 616674.468 829943.7332 721848.8505 764150.7825 886568.1908 559681.8031 856715.2477 940151.4698 952484.1749 0.64743802 0.87134648 0.757859154 0.802271368 0.930795717 0.587602207 0.899453524 0.987052063 1 19.8613356 1.500620127 6.992156689 0.978202411 0.782464129 0.478994769 0.098704433 0.105918277 12.07272922 0.049804662 0.022619222 31.66796283 -1.500620127 -0.195738282 RPLSAS(ph)LGQLNEVGLPSAAILPDEGAVDLPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPLSASLGQLNEVGLPSAAILPDEGAVDLPSR 32 1 Q5TC82-2;Q5TC82 Q5TC82-2 RC3H1 Roquin-1 1 RPLS(0.225)AS(0.775)LGQLNEVGLPSAAILPDEGAVDLPSR 220.14 4.11E-36 260410000 76934 81280 87681 72982 84943 75149 99070 81274 94199 TRUE FALSE 72118.83827 87298.05577 89760.83473 74854.84168 78271.91942 96843.29636 84215.37322 91421.23781 78476.57835 0.918985509 1.112409047 1.143791391 0.953849457 0.997392102 1.23404076 1.073127486 1.164949336 1 16.25997452 2.277752579 24.99994431 1.122585859 1.050078822 0.178224681 0.090418106 324.6605848 207094.7132 0.03082244 0.025787504 189.562566 -2.277752579 -0.072507037 RPLSSSHEAS(ph)EGQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPLSSSHEASEGQAK 15 1 Q8IZ21-3;Q8IZ21;Q8IZ21-2;A0A0J9YVR0 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 RPLS(0.147)S(0.147)S(0.147)HEAS(0.559)EGQAK 160.55 1.04E-06 141240000 96865 113280 102440 113100 120790 64760 128080 107030 146420 TRUE FALSE 90802.39256 121667.3691 104869.9252 116002.3375 111303.6406 83455.16071 108875.593 120392.9311 121981.5561 0.744394443 0.997424307 0.859719523 0.950982601 0.912462869 0.684162126 0.89255783 0.986976515 1 16.8963035 1.253545391 5.672465759 0.995798579 0.872142351 0.256937508 0.091643255 0.231336617 23.0989161 0.069373693 0.022019503 17.92855927 -1.253545391 -0.123656228 RPMEEDGEEKS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 17 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(0.999)PS(0.001)K;RPMEEDGEEKS(0.989)PS(0.011)K;RPMEEDGEEKS(0.966)PS(0.034)K;RPMEEDGEEKS(0.981)PS(0.019)K;RPMEEDGEEKS(0.987)PS(0.013)K;RPMEEDGEEKS(0.994)PS(0.006)K;RPMEEDGEEKS(0.978)PS(0.022)K;RPMEEDGEEKS(0.965)PS(0.035)K;RPMEEDGEEKS(0.5)PS(0.5)K;RPMEEDGEEKS(0.992)PS(0.008)K;RPMEEDGEEKS(0.985)PS(0.015)K;RPMEEDGEEKS(0.5)PS(0.5)K;RPMEEDGEEKS(0.782)PS(0.218)K;RPMEEDGEEKS(0.692)PS(0.308)K;RPMEEDGEEKS(0.641)PS(0.359)K;RPMEEDGEEKS(0.5)PS(0.5)K;RPMEEDGEEKS(0.545)PS(0.455)K 196.71 1.28E-08 34601263000 29833130 10988720 16184369 15250818 16342135 11437718 22324150 13231183 20538039 TRUE FALSE 27965927.65 11802336.26 16568269.88 15642179.81 15058689.64 14739601.51 18976850.95 14883125.32 17110107.61 1.63446825 0.689787378 0.968332301 0.91420698 0.880104905 0.861455804 1.109101789 0.869844051 1 24.0283455 4.749635883 24.9949901 0.912421217 1.634468667 0.81632976 0.107756432 720.822616 1626743.159 0.026398857 0.403964593 56187.00496 -4.749635883 0.72204745 RPMEEDGEEKS(ph)PSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPMEEDGEEKSPSKK 15 3 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 RPMEEDGEEKS(0.997)PS(0.003)KK;RPMEEDGEEKS(0.991)PS(0.009)KK 126.22 6.11E-05 2288230000 3004770 791210 1383780 1390840 1503570 962450 1987390 1085670 1941910 TRUE FALSE 2816706.809 849792.0117 1416603.915 1426531.309 1385485.677 1240293.691 1689399.32 1221218.289 1617792.676 1.741080209 0.525278686 0.875639961 0.881776343 0.856404963 0.766657996 1.044261941 0.754866991 1 20.6255953 4.750784213 24.96267227 0.832087093 1.741080778 0.798740105 0.142417826 857.7649032 1751670.132 0.034408922 0.592115686 56335.76717 -4.750784213 0.908993685 RPMEEDGEEKSPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPMEEDGEEKSPSK 14 2 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ; 89.541 0.0034355 170418000 227140 173446 199129 205345 237870 141605 249890 186971 399520 FALSE TRUE 212923.7129 186288.1223 203852.4339 210614.5003 219188.6497 182484.0647 212421.3144 210314.7409 332837.531 0.639722667 0.559696864 0.612468291 0.632784709 0.658545474 0.548267691 0.638213226 0.631884092 1 18.3444586 -0.06669782 0.996539055 1.004656079 0.60614927 0.923856623 0.03475657 2.20691754 1.806893797 0.068926371 0.010027421 0.857634375 0.06669782 -0.398506809 RPMS(ph)DPSWNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(1)DPSWNR;RPMS(1)DPSWNR 64.224 0.03153 306850000 294360 527080 444900 460470 541430 437850 517340 304830 550520 TRUE FALSE 275936.533 566105.5516 455453.2381 472286.4398 498908.2718 564250.1871 439769.6697 342888.6965 458634.6555 0.601647803 1.234327901 0.993063286 1.029766142 1.087811978 1.230282492 0.958867073 0.747629278 1 18.80698585 1.481816308 8.431650071 0.866742212 1.053640691 0.099148831 0.184244963 0.176939901 39.00727404 0.091197067 0.041690712 30.32608222 -1.481816308 0.18689848 RPMS(ph)SPEMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.618)S(0.382)PEMK;RPMS(0.5)S(0.5)PEMK;RPMS(0.5)S(0.5)PEMK;RPMS(0.5)S(0.5)PEMK;RPMS(0.5)S(0.5)PEMK 62.338 0.029867 693585000 1478570 1074052 1273570 1269867 1268351 900474 1503490 1081429 1308790 TRUE FALSE 1386028.943 1153575.928 1303779.682 1302453.937 1168739.829 1160426.226 1278055.632 1216447.791 1090344.494 1.271184429 1.057992161 1.195750232 1.194534337 1.071899602 1.064274853 1.172157643 1.115654546 1 20.0563526 2.736151267 24.94100485 1.099931463 1.162200592 0.294327464 0.068649867 383.3323983 3968125.518 0.020934314 0.020658051 544.6923395 -2.736151267 0.062269129 RPMSS(ph)PEMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.409)S(0.591)PEMK 46.88 0.079211 493410000 683040 420570 517330 512500 522160 361480 580340 468950 556640 TRUE FALSE 640289.7457 451709.4404 529601.3119 525651.6177 481151.6599 465833.4079 493323.4046 527499.4398 463733.188 1.380728752 0.974071842 1.14203884 1.13352167 1.037561409 1.00452894 1.06380871 1.137506337 1 18.82293545 4.748793723 24.94375218 1.064434462 1.380728931 0.73408663 0.060335559 731.7464967 1783635.483 0.013932358 0.192331558 56078.15576 -4.748793723 0.316294469 RPNEDS(ph)DEDEEK ddPTM_SK-BR-3_Pertuzumab_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 199.33 1.06E-07 1287990000 2687960 1401960 1779910 1695820 1566680 1465890 2379810 1522920 1364360 TRUE FALSE 2519725.382 1505762.577 1822130.306 1739337.612 1443639.272 1889068.646 2022979.584 1713059.914 1136639.502 2.216820177 1.324749469 1.603085501 1.530245614 1.27009423 1.661976944 1.779789969 1.507126852 1 20.11634333 4.747838397 24.55981851 1.506845334 2.216820657 0.519719326 0.224716279 817.2037566 2163214.512 0.050418084 0.626620962 55954.93515 -4.747838397 0.709975323 RPNEDS(ph)DEDEEKGAVVPPVHDIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 189.39 6.79E-18 16040320000 5076170 3584750 3789110 4103630 4274620 2828900 5167260 3562840 5250830 TRUE FALSE 4758461.581 3850168.62 3878989.479 4208936.093 3938908.588 3645557.507 4392477.333 4007668.417 4374432.551 1.08778945 0.8801527 0.886741179 0.962167331 0.900438752 0.833378379 1.004125057 0.916157323 1 22.06066445 1.651164821 17.41845323 0.970012224 0.916053405 0.08284412 0.071346993 0.381247975 141.5176605 0.030769828 0.017012257 44.78832498 -1.651164821 -0.053958819 RPNKQEESES(ph)PVERPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPNKQEESESPVERPLK 17 3 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;D6RBF8 H3BLV9 SRPK1 SRSF protein kinase 1 1 RPNKQEES(0.018)ES(0.982)PVERPLK;RPNKQEES(0.007)ES(0.993)PVERPLK 209.01 2.57E-11 1539510000 1013140 605680 783350 677270 802520 562200 892290 727210 856630 TRUE FALSE 949729.3759 650525.1774 801931.4319 694649.8948 739493.3164 724498.0134 758499.3981 818003.7693 713652.919 1.3308001 0.911542796 1.123699505 0.973372176 1.036208634 1.015196595 1.062840742 1.146220729 1 19.44486307 4.754069667 24.90305506 1.035026626 1.330800329 0.653173391 0.06804546 1668.323279 2678797.8 0.015067923 0.362896393 56763.56549 -4.754069667 0.295773703 RPNPDILDHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPNPDILDHER 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L0N7 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ; 166.04 1.36E-05 831100000 394490 546750 416900 461800 525990 331550 458910 492370 444900 FALSE TRUE 369799.5751 587231.9389 426789.0649 473650.5698 484680.8671 427263.1027 390100.7058 553843.4783 370643.3158 0.997723578 1.584358638 1.151481887 1.277914776 1.307674647 1.152760847 1.052496266 1.494276181 1 18.49967197 2.690555703 0.908833951 1.165789053 1.314976593 0.008960441 0.1974189 1.515918367 2.639131586 0.112468565 0.100016827 490.4059189 -2.690555703 0.14918754 RPNT(ph)SPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RPNTSPDR 8 1 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RPNT(0.5)S(0.5)PDR;RPNT(0.861)S(0.139)PDR;RPNT(0.847)S(0.153)PDR 86.463 0.0093852 3252202000 1996157 2272216 2116897 2239857 2213053 1802464 2028486 2075625 1944646 TRUE FALSE 1871221.097 2440453.237 2167110.797 2297335.523 2039248.744 2322806.096 1724333.356 2334771.35 1620072.02 1.155023403 1.506385647 1.337663246 1.418045306 1.258739562 1.433767183 1.064355988 1.441152814 1 20.62762652 0.105610234 0.344276604 0.933968213 1.388441144 0.318506254 0.141177207 4.42369829 0.805131904 0.582654343 0.120713215 1.275293759 -0.105610234 0.454472931 RPNT(ph)SPDRGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPNTSPDRGSR 11 2 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RPNT(0.722)S(0.058)PDRGS(0.22)R;RPNT(0.885)S(0.106)PDRGS(0.008)R 105.19 0.0040178 1586150000 232283 389240 278790 309310 456190 223083 369730 281860 773450 TRUE FALSE 217744.8217 418059.7346 285403.0305 317247.4183 420362.6776 287483.4407 314292.4189 317050.8415 644356.1983 0.337926169 0.648802224 0.442927423 0.492347896 0.652376246 0.446156088 0.487761924 0.492042821 1 19.2974989 -1.871983399 2.594751928 1.228695565 0.508599287 0.738069206 0.093477483 12380467.73 8277207.959 17473600.15 0.020903726 0.013428163 1.871983399 -0.720096278 RPNTATPSPIPSPTPAS(ph)EPES(ph)EPELESASSCHRPLLIPPVRPVGPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPNTATPSPIPSPTPASEPESEPELESASSCHRPLLIPPVRPVGPGR 47 3 Q5SY16 Q5SY16 NOL9 Polynucleotide 5-hydroxyl-kinase NOL9 2 RPNTATPS(0.001)PIPS(0.009)PT(0.112)PAS(0.844)EPES(0.864)EPELES(0.059)AS(0.056)S(0.054)CHRPLLIPPVRPVGPGR 47.806 0.0094163 79096000 9227.9 11078 10050 10682 10154 8624.3 13183 9284.7 8105.1 TRUE FALSE 8650.342211 11898.22665 10288.39075 10956.1182 9356.545799 11113.99541 11206.33153 10443.91523 6752.306449 1.281094434 1.762098142 1.523685399 1.622574196 1.385681451 1.645955421 1.659630175 1.546718194 1 12.72116467 0.941711004 21.17278694 0.999999999 1.578602669 0.604528427 0.139623138 2079.350012 755301.2493 0.121066112 0.030266528 8.74401722 -0.941711004 0.57860267 RPNTS(ph)PDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPNTSPDR 8 1 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RPNT(0.105)S(0.895)PDR;RPNT(0.115)S(0.885)PDR 107.58 0.0042117 2092887000 1237465 1362910 1234269 1284034 1408090 1021340 1299836 1265673 1249566 TRUE FALSE 1160014.275 1463821.275 1263546.444 1316984.486 1297504.291 1316184.278 1104937.659 1423695.06 1041005.362 1.114321133 1.406161128 1.213775154 1.265108264 1.246395397 1.264339576 1.061413994 1.367615492 1 19.98954607 -5 0.169733972 0.035164154 1.303228968 0.305380453 0.106048269 141.2636624 1.332579148 45.72052782 0.352820518 1.00E-05 5 1.268064813 RPNTS(ph)PDRGS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPNTSPDRGSR 11 2 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 2 RPNT(0.362)S(0.638)PDRGS(1)R 92.8 0.047836 563650000 336390 352250 343920 386500 391400 371330 400200 392890 489990 TRUE FALSE 315335.9504 378330.9565 352077.9448 396418.2443 360661.0228 478526.943 340193.7253 441943.1814 408207.5035 0.772489353 0.926810392 0.862497484 0.971119445 0.883523746 1.172263956 0.833384302 1.082643453 1 18.63894318 7.315108516 0.267212053 1.010757431 2.95E-15 0.315041531 0.098482282 44.26270565 0.856838934 0.104505784 19.12795858 20658962.92 -7.315108516 -1.010757431 RPNTSPDRGS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RPNTSPDRGSR 11 2 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RPNT(0.101)S(0.091)PDRGS(0.808)R;RPNT(0.056)S(0.117)PDRGS(0.827)R;RPNT(0.218)S(0.16)PDRGS(0.622)R 94.63 0.0065846 1531192000 319644 538683 404213 384004 628228 316426 411104 421197 1001655 TRUE FALSE 299638.0526 578567.6498 413801.1232 393858.1928 578889.507 407773.0495 349462.7717 473784.3726 834472.3096 0.35907489 0.693333551 0.495883588 0.471984736 0.693719253 0.488659773 0.418782945 0.567765242 1 19.67050465 0.95448821 22.72075019 1.000000001 0.527805408 0.668042356 0.105908863 2213.53506 1105059.954 0.097723854 0.024430963 9.005093152 -0.95448821 -0.472194593 RPPDEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RPPDEQR 7 1 B8ZZU8;Q15370;Q15370-2;I3L0M9;A0A0B4J296 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 ;;;;; 160.54 0.0021528 3223141000 648489 835034 788510 796707 837121 707324 827993 714597 797515 FALSE TRUE 607901.2311 896860.7862 807213.8296 817151.8504 771376.8934 911516.9564 703843.1364 803816.0085 664404.5944 0.914956393 1.34987144 1.214943178 1.229900963 1.161004755 1.371930544 1.059359225 1.209829094 1 19.34170252 0.689069825 0.887021186 1.002080211 1.217278352 0.144606946 0.133157952 1.67092641 2.360416319 0.115379616 0.038720922 4.887309304 -0.689069825 0.215198141 RPPEEDFRHS(ph)PEEDFR ddPTM_SK-BR-3_Pertuzumab_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 155.76 1.19E-07 2133850000 1377950 1574580 1576640 1543810 1627720 1387880 1625490 1374780 1643290 TRUE FALSE 1291706.569 1691163.542 1614038.645 1583426.778 1499885.437 1788538.426 1381762.865 1546424.309 1369014.283 0.943530382 1.235314754 1.178978675 1.156618158 1.095595171 1.306442488 1.009312234 1.129589609 1 20.38470607 1.623936917 25 1.05209678 1.162879557 0.197164085 0.099637434 1.217513075 1889.52094 0.041819384 0.023097479 42.0665521 -1.623936917 0.110782777 RPPEEDFRHS(ph)PEEDFRQS(ph)PQEHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPPEEDFRHSPEEDFRQSPQEHFR 24 3 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 2 RPPEEDFRHS(1)PEEDFRQS(1)PQEHFR 148.02 8.06E-08 658920000 65304 73319 72701 78883 86197 64363 71859 64081 81319 TRUE FALSE 61216.73921 78747.61505 74425.50205 80907.27133 79427.43532 82943.55325 61084.41006 72081.65391 67746.33356 0.903617008 1.162389327 1.098590848 1.194267897 1.172424117 1.224325346 0.901663704 1.063993431 1 16.04785525 1.736544364 25 0.98614674 1.131403133 0.3152062 0.095208523 0.28403111 3436.206998 0.040674547 0.022556043 54.51855841 -1.736544364 0.145256393 RPPES(ph)PPIVEEWNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RPPESPPIVEEWNSR 15 1 Q9BTL3;A0A3B3IU46 Q9BTL3 FAM103A1 RNMT-activating mini protein 1 RPPES(1)PPIVEEWNSR;RPPES(1)PPIVEEWNSR;RPPES(1)PPIVEEWNSR;RPPES(1)PPIVEEWNSR 162.44 9.77E-07 1645400000 318939 435557 365851 311781 516480 299713 369494 393521 488810 TRUE FALSE 298977.1773 467806.0935 374529.1585 319781.8283 475917.7442 386235.2777 314091.8049 442652.9631 407224.4532 0.734182771 1.148767197 0.919711858 0.785271675 1.168686557 0.948457969 0.771298979 1.086999957 1 18.63546467 1.993154972 24.98153339 0.910485932 0.974071385 0 0.157439055 1276.057777 4657088.615 0.056841705 0.040377236 98.43622982 -1.993154972 0.063585453 RPPGPTT(ph)SPASTSLSSPGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPPGPTTSPASTSLSSPGQR 20 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 RPPGPT(0.197)T(0.523)S(0.28)PASTSLSSPGQR;RPPGPT(0.3)T(0.349)S(0.349)PAS(0.001)T(0.001)SLSSPGQR 99.387 0.00038946 823880000 73051 71775 75367 66630 77950 73021 84316 63351 74596 TRUE FALSE 68478.86831 77089.29568 77154.74083 68339.8386 71828.12144 94100.9773 71673.59855 71260.5118 62145.44569 1.1019129 1.24046573 1.241518827 1.099675734 1.155806683 1.514205526 1.153320211 1.146673115 1 15.92336105 0.960358171 2.328420146 1.00273546 1.226169406 0.253102709 0.117501017 0.428118123 5.180171679 0.10540251 0.028732971 9.127633029 -0.960358171 0.223433946 RPPGPTTS(ph)PASTSLSSPGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPPGPTTSPASTSLSSPGQR 20 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 RPPGPTT(0.014)S(0.985)PASTSLSSPGQR;RPPGPT(0.062)T(0.298)S(0.635)PAS(0.002)T(0.002)S(0.002)LSSPGQR 134.56 5.36E-06 801690000 92504 100915 108821 106934 105562 91891 111081 97331 93808 TRUE FALSE 86714.33976 108386.8516 111402.2855 109678.1075 97271.58634 118418.44 94425.43528 109482.9896 78150.83878 1.109576572 1.386893005 1.425477797 1.403415615 1.244664649 1.515254882 1.208245961 1.400918932 1 16.25397374 -1.225424012 0.632375264 0.88681072 1.349836974 0.432400448 0.119978352 39.36521931 7.313101435 7.969389297 0.041584892 0.059508087 1.225424012 0.463026254 RPPPAPHDGDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPPPAPHDGDRK 12 2 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 0 60.401 0.055378 10586000 35360 26395 33841 29627 32028 23468 33911 27380 39247 FALSE TRUE 33146.88072 28349.31326 34643.7245 30387.27898 29512.65007 30242.83063 28826.36036 30798.45327 32696.42215 1.013776999 0.867046343 1.059557047 0.929376273 0.902626285 0.924958409 0.881636536 0.941951787 1 14.99684516 3.023737377 24.99928493 0.918852487 0.970645474 0.122488391 0.057059882 413.808709 435804.3253 0.015620885 0.018669584 1056.178633 -3.023737377 0.051792987 RPPPPPVPLLPPGT(ph)SPPVDPFTTLASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPPPPPVPLLPPGTSPPVDPFTTLASK 27 1 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 RPPPPPVPLLPPGT(0.5)S(0.5)PPVDPFTTLASK 85.866 0.0049025 71790000 84955 69238 82755 71787 92991 88110 106410 85226 104000 TRUE FALSE 79637.8182 74364.45356 84717.98768 73629.17596 85687.86197 113545.9267 90454.80836 95866.65371 86641.72813 0.919162393 0.858298365 0.977796606 0.84981195 0.988990684 1.310522413 1.044009743 1.106472086 1 16.4027744 2.468512321 24.99790693 1.121738243 0.908114762 0.575274915 0.08666214 124.5522648 361661.5481 0.026947628 0.022578007 294.1117131 -2.468512321 -0.213623482 RPPS(ph)PDVIVLS(ph)DNEQPS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JHD7;C9JJK9;C9JMI3;C9JGN4 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 3 RPPS(1)PDVIVLS(1)DNEQPS(0.727)S(0.273)PR 133.94 4.02E-06 867410000 128010 154510 154730 154990 157860 152540 174150 135010 153240 TRUE FALSE 119998.0826 165950.0812 158400.2687 158967.3058 145462.3124 196575.8217 148037.8242 151866.2957 127663.254 0.939957888 1.299904835 1.240766342 1.245208004 1.139421938 1.539799555 1.1595962 1.189585029 1 16.9619838 0.822933496 2.083080362 1.001111328 1.242149406 0.173584492 0.149053098 0.992941117 7.785301202 0.127476639 0.035099686 6.651712904 -0.822933496 0.241038078 RPPS(ph)PDVIVLS(ph)DNEQPSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JHD7;C9JJK9;C9JMI3;C9JGN4 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 3 RPPS(1)PDVIVLS(1)DNEQPS(0.085)S(0.915)PR;RPPS(1)PDVIVLS(1)DNEQPS(0.29)S(0.71)PR;RPPS(1)PDVIVLS(1)DNEQPS(0.051)S(0.949)PR 215.47 4.85E-25 5555920000 1468090 1556580 1597170 1476320 1708930 1487580 1848970 1534170 1648420 TRUE FALSE 1376204.868 1671830.803 1635055.627 1514204.871 1574717.531 1917020.197 1571734.113 1725714.502 1373288.053 1.002123964 1.217392665 1.190613741 1.102612717 1.146676786 1.395934519 1.144504323 1.256629662 1 20.38920284 4.74312662 24.03490449 1.193357999 1.002123828 0.223798504 0.103179234 370.9150437 1952330.353 0.021926142 0.174017567 55351.14633 -4.74312662 -0.191234171 RPPS(ph)PDVIVLS(ph)DNEQPSSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JHD7;C9JJK9;C9JMI3;C9JGN4 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 2 RPPS(1)PDVIVLS(1)DNEQPSSPR;RPPS(1)PDVIVLS(1)DNEQPSSPR;RPPS(1)PDVIVLS(1)DNEQPSSPR;RPPS(1)PDVIVLS(0.738)DNEQPS(0.148)S(0.113)PR 269.62 6.06E-37 1862242000 883600 1102190 1009080 1100240 963460 736710 863100 667650 857920 TRUE FALSE 828297.0533 1183797.294 1033015.854 1128474.021 887793.738 949386.2175 733686.1676 751007.5722 714727.6096 1.158898918 1.656291542 1.445328039 1.578886846 1.242142777 1.328318935 1.026525571 1.050760544 1 19.44703399 2.041635543 1.185401121 0.999314047 1.487535885 0.609384142 0.143093987 0.26895501 0.702278135 0.095669471 0.045968202 110.0615292 -2.041635543 0.488221838 RPPS(ph)PDVIVLSDNEQPSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JHD7;C9JJK9;C9JMI3;C9JGN4 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 2 RPPS(1)PDVIVLSDNEQPS(0.02)S(0.98)PR;RPPS(1)PDVIVLSDNEQPS(0.016)S(0.984)PR;RPPS(1)PDVIVLSDNEQPS(0.443)S(0.557)PR 273.67 6.47E-44 1449410000 538470 571990 542560 542440 620110 534540 571760 510700 708010 TRUE FALSE 504768.1239 614340.7348 555429.7794 556359.9287 571409.062 688853.0205 486029.896 574462.0192 589838.5571 0.85577336 1.041540482 0.941664075 0.943241031 0.968755018 1.167867058 0.824004959 0.973930938 1 19.16996061 -2.88583359 1.967243263 2.80796895 0.967326494 0.013010823 0.094277208 3258625.065 284438.0167 26711875.57 0.022222672 0.001300668 2.88583359 -1.840642456 RPPS(ph)PDVIVLSDNEQPSSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JHD7;C9JJK9;C9JMI3;C9JGN4 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 1 RPPS(1)PDVIVLSDNEQPSSPR 237.41 8.23E-30 355490000 181880 201370 208600 222870 207540 153380 184390 149340 167350 TRUE FALSE 170496.4555 216279.6443 213548.0905 228589.2215 191240.6456 197658.3161 156742.4313 167985.4277 139418.2039 1.222913872 1.551301324 1.531708805 1.639593792 1.371704987 1.417736785 1.124260871 1.204903112 1 17.08905942 1.782097215 1.352895355 1.067827105 1.501338151 0.642152909 0.12166848 0.23424269 0.809573338 0.089605613 0.035845975 60.54763926 -1.782097215 0.433511045 RPPS(ph)PEPSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RPPSPEPSTK 10 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 RPPS(1)PEPSTK;RPPS(0.885)PEPS(0.113)T(0.002)K;RPPS(0.984)PEPS(0.012)T(0.003)K;RPPS(0.998)PEPS(0.002)TK;RPPS(0.999)PEPS(0.001)TK;RPPS(0.955)PEPS(0.037)T(0.008)K;RPPS(0.989)PEPS(0.01)T(0.001)K 104.24 0.002868 21465890000 5181630 4616911 4732560 4869580 5672560 3974734 5853360 4565106 5926660 TRUE FALSE 4857321.028 4958751.894 4844818.558 4994541.667 5227060.02 5122175.181 4975703.008 5135069.533 4937462.158 0.983768761 1.004311878 0.981236595 1.011560495 1.058653181 1.037410519 1.007745042 1.040022054 1 22.23533826 3.00741518 8.499088944 1.028863001 0.992192352 0.512348642 0.017327517 0.105176801 66.75112689 0.004864239 0.00566826 1017.220677 -3.00741518 -0.036670649 RPPSAFFLFCSEYRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPPSAFFLFCSEYRPK 16 2 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ; 203.89 1.50E-11 2000600000 1083250 1506200 1013430 923430 1692960 685270 1195250 1291290 1442510 FALSE TRUE 1015451.316 1617720.615 1037469.038 947126.7772 1560001.751 883096.3246 1016033.359 1452510.399 1201745.762 0.844980152 1.346142143 0.863301599 0.788125748 1.298112962 0.734844551 0.845464482 1.208666962 1 20.19670029 3.813045246 7.137882249 0.943227902 1.12594582 0.052776569 0.21359286 0.47898772 33.92521506 0.050654908 0.091790769 6501.974268 -3.813045246 0.182717918 RPPSPEPS(ph)TK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPPSPEPSTK 10 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 RPPS(0.096)PEPS(0.452)T(0.452)K 125.36 0.00043554 956740000 478220 424810 398920 403060 457250 329410 484670 372110 472520 TRUE FALSE 448289.0638 456263.3744 408382.5708 413403.202 421339.4295 424505.3195 411998.233 418568.7526 393653.3594 1.138791409 1.159048598 1.037416704 1.050170644 1.070331091 1.07837342 1.046601593 1.063292723 1 18.58656626 3.999435507 3.464146607 1.053793307 1.148086101 0.771128565 0.022358365 0.09836224 2.470341266 0.005228848 0.011694656 9987.010514 -3.999435507 0.094292794 RPPT(ph)PCS(ph)DPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RPPTPCSDPER 11 1 Q9BW71;Q9BW71-2;Q9BW71-3 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 RPPT(1)PCS(1)DPER;RPPT(1)PCS(1)DPER;RPPT(1)PCS(1)DPER;RPPT(1)PCS(1)DPER 91.307 0.024013 1073550000 888010 993410 981400 955720 1148590 1040610 1114420 848110 1355800 TRUE FALSE 832431.0392 1066963.11 1004679.271 980245.3932 1058384.375 1341017.214 947323.0668 953998.4004 1129508.221 0.736985374 0.944626245 0.889483806 0.86785149 0.937031139 1.187257595 0.838704003 0.84461395 1 20.10726334 2.631389214 5.483697723 0.962613053 0.879180425 0.171023997 0.108596483 0.510291155 21.89036524 0.034755565 0.03267603 427.9462387 -2.631389214 -0.083432628 RPQGESYDQAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPQGESYDQAIR 12 1 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ; 119.52 0.00081541 411610000 275170 293230 281500 270610 306020 298780 325590 302540 275950 FALSE TRUE 257947.6009 314941.0543 288177.3129 277554.3107 281986.4236 385032.9357 276770.8021 340312.785 229892.1623 1.122037386 1.369951247 1.25353257 1.207323938 1.226603033 1.674841508 1.203915781 1.480314864 1 17.81059776 -1.154943795 5.558753749 0.999993621 1.317833087 0.277901118 0.160746351 1.14E-05 1.73E-06 0.139136324 0.032794088 0.069993257 1.154943795 0.317839465 RPQHNSSGAS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RPQHNSSGASPR 12 1 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 1 RPQHNS(0.001)S(0.001)GAS(0.998)PR;RPQHNSSGAS(0.999)PR;RPQHNS(0.013)S(0.348)GAS(0.638)PR;RPQHNS(0.064)S(0.064)GAS(0.873)PR 124.25 0.00019988 2886214000 316104 799206 698574 727792 715095 876696 697976 674583 444655 TRUE FALSE 296319.6149 858380.0438 715144.5052 746468.3749 658934.3233 1129783.903 593320.9785 758806.1725 370439.2079 0.799914287 2.317195441 1.930531353 2.015090085 1.778792064 3.049849689 1.601668954 2.048395948 1 18.49887728 4.747083625 24.22875029 2.030099548 0.799913312 0.326102416 0.520747516 733.1854789 2084187.864 0.107784098 1.228259825 55857.77404 -4.747083625 -1.230186236 RPQLDLDILSSLIDLCDSPVS(ph)PAEASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPQLDLDILSSLIDLCDSPVSPAEASR 27 1 Q9BQ89 Q9BQ89 FAM110A Protein FAM110A 1 RPQLDLDILSSLIDLCDS(0.006)PVS(0.994)PAEASR 162.81 7.29E-12 87493000 46841 57268 49798 60634 69092 49930 51709 45583 45210 TRUE FALSE 43909.30542 61508.18231 50979.23208 62189.97109 63665.79302 64343.98045 43955.71549 51274.13789 37664.15893 1.165811389 1.633069317 1.353521053 1.65117111 1.690354831 1.708361006 1.167043596 1.361350933 1 15.20090469 1.671457903 7.542050978 1.198618122 1.534268402 0.445681575 0.186984853 0.117998606 12.4068114 0.087596282 0.045386758 46.93079416 -1.671457903 0.33565028 RPQS(ph)PGAS(ph)PSQAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPQSPGASPSQAER 14 1 Q96T58;A0A669KB49 Q96T58 SPEN Msx2-interacting protein 2 RPQS(1)PGAS(0.978)PS(0.022)QAER;RPQS(1)PGAS(0.997)PS(0.003)QAER 156.51 1.94E-05 1674970000 740580 752410 741670 700010 758770 720480 814940 700550 737280 TRUE FALSE 694228.4198 808119.2193 759262.7626 717973.4417 699179.2649 928470.88 692747.3125 788015.2096 614223.205 1.130254302 1.315676797 1.236134937 1.168912923 1.138314637 1.511618044 1.127842952 1.282946009 1 19.22840349 -1.442951591 3.627772401 0.997674831 1.244022195 0.293695638 0.116225563 8751417.917 3621801.483 159222.0195 0.024248748 0.036061884 1.442951591 0.246347364 RPQS(ph)PSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPQSPSPR 8 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 RPQS(0.931)PS(0.069)PR;RPQS(0.979)PS(0.021)PR 105.98 0.0026243 403730000 174416 170775 175782 174557 162398 159006 162702 131387 145474 TRUE FALSE 163499.6139 183419.3587 179951.6321 179036.4281 149643.9162 204908.451 138306.3456 147790.9562 121193.4496 1.349079628 1.513442841 1.484829689 1.477278093 1.234752511 1.690755166 1.141203143 1.219463235 1 16.8869522 1.621905139 8.237958948 1.130898962 1.45927817 0.611110992 0.127031209 0.06887735 10.85797929 0.057592389 0.028976933 41.87021003 -1.621905139 0.328379208 RPQT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPQTPK 6 1 P46013;P46013-2 P46013;REV__Q8N3K9 MKI67 Antigen KI-67 1 RPQT(1)PK 57.047 0.086809 121270000 482030 281870 388120 341980 316680 277490 425130 299800 480700 TRUE FALSE 451860.6027 302739.9481 397326.3897 350755.7858 291809.2302 357596.8583 361385.7032 337230.6899 400468.0646 1.128331177 0.755965269 0.992154993 0.875864562 0.728670414 0.892947253 0.902408295 0.842091342 1 18.61132767 -1.516264942 3.126757399 1.003557296 0.883323258 0.083876857 0.112656484 421877804.1 632257293.8 13409447.41 0.024145414 0.030460362 1.516264942 -0.120234038 RPQYSNPPVQGEVMEGADNQGAGEQGRPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 RPQYSNPPVQGEVMEGADNQGAGEQGRPVR 30 2 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;;;;;;;;;; 304.15 8.95E-82 11725650000 1750052 1940255 1995552 1933342 2089075 1660587 2147828 1736473 2114007 FALSE TRUE 1640519.369 2083913.499 2042887.436 1982954.829 1925007.476 2139971.51 1825781.131 1953275.476 1761165.575 0.931496387 1.183258138 1.159963302 1.125933221 1.093030379 1.215088201 1.036689087 1.109081113 1 20.74809912 0.904017857 1.039365578 1.003042385 1.12677074 0.125591556 0.080529808 1.046113455 2.300417071 0.069623136 0.022606268 8.017110278 -0.904017857 0.123728355 RPRPPNAPS(ph)QDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPRPPNAPSQDGK 13 2 P16989;P16989-2 P16989;P16989-2 YBX3 Y-box-binding protein 3 1 RPRPPNAPS(1)QDGK 87.388 0.0066079 88374000 118430 61963 95815 78067 60276 67091 72276 50029 65973 TRUE FALSE 111017.6777 66550.80499 98087.77705 80070.33139 55542.1661 86459.08257 61438.88478 56275.23078 54961.6801 2.019910554 1.210858272 1.784657545 1.456839224 1.01056165 1.573079324 1.117849467 1.023899391 1 15.74613849 2.507253848 0.361492822 0.946843157 1.742440178 0.46206082 0.258266079 1.515063895 0.434780533 0.281610239 0.439354777 321.5539493 -2.507253848 0.795597021 RPRPTPGDGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPRPTPGDGEK 11 2 I3L4Q4;Q9BUL5-4;Q9BUL5;I3L410;I3L1N0;Q9BUL5-3 I3L4Q4 PHF23 PHD finger protein 23 0 ; 110.39 0.0010131 48946000 60075 62972 65215 67113 70861 51786 71036 56484 64715 FALSE TRUE 56315.01299 67634.5124 66761.9306 68835.2332 65295.8629 66735.77752 60384.81127 63536.15174 53913.64843 1.04454094 1.254497041 1.238312237 1.276768225 1.211119351 1.237827145 1.120028287 1.178479914 1 15.71836292 0.771238684 0.815456169 1.001859142 1.220618279 0.447141354 0.068594152 0.76549301 1.001433607 0.061794542 0.021675295 5.905255376 -0.771238684 0.218759136 RPS(ph)ADSESPGTPSPDGAAWEPPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPSADSESPGTPSPDGAAWEPPAR 24 1 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 RPS(0.969)ADS(0.004)ES(0.026)PGTPSPDGAAWEPPAR;RPS(0.995)ADS(0.002)ES(0.003)PGTPSPDGAAWEPPAR 204.88 6.35E-25 632190000 71926 74727 70862 84279 85934 61006 72043 66001 85066 TRUE FALSE 67424.28005 80259.86483 72542.8801 86441.74182 79185.09028 78617.44185 61240.82096 74241.37014 70867.93505 0.951407431 1.132527211 1.023634738 1.219758157 1.117361332 1.109351384 0.864154161 1.047601713 1 16.11284539 1.761976265 25 0.958619069 1.094912644 0.320224104 0.08296042 12.84354876 13722.78231 0.035285469 0.019568324 57.80644548 -1.761976265 0.136293575 TS(ph)DANETEDHLESLICK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSDANETEDHLESLICK 17 0 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 T(0.169)S(0.831)DANETEDHLESLICK 292.31 3.27E-46 64581000 195950 136940 145390 232500 203770 95795 114140 50202 72861 TRUE FALSE 183685.8393 147079.1801 148838.7195 238466.3436 187766.7262 123449.4614 97025.76662 56469.83021 60700.0284 3.026124437 2.423049609 2.452037065 3.928603493 3.093354832 2.033762828 1.598446808 0.930309782 1 15.88940957 1.781592341 1.846199017 1.02442105 2.866195429 0.774423495 0.446981709 0.176697719 1.17996026 0.337217617 0.142179995 60.47729259 -1.781592341 1.841774379 up RPS(ph)ASSPNNNTAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPSASSPNNNTAAK 14 1 O75151;E7ET14;A0A087WW48 O75151 PHF2 Lysine-specific demethylase PHF2 1 RPS(0.725)AS(0.115)S(0.16)PNNNTAAK 145.69 5.21E-06 467410000 342940 272660 280010 253230 271800 226960 393010 272230 297360 TRUE FALSE 321475.9976 292848.0301 286651.9694 259728.3105 250453.9244 292479.6676 334081.799 306218.5148 247728.695 1.297693824 1.18213205 1.157120573 1.048438537 1.011000863 1.180645091 1.348579336 1.236104339 1 17.91840146 1.993252151 24.9896565 1.241372257 1.139458331 0 0.116303755 592.8097759 2195387.458 0.042904678 0.030534982 98.45825882 -1.993252151 -0.101913925 RPS(ph)DSGPPAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RPSDSGPPAER 11 1 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 1 RPS(0.923)DS(0.077)GPPAER;RPS(0.5)DS(0.5)GPPAER;RPS(0.875)DS(0.125)GPPAER;RPS(0.993)DS(0.007)GPPAER;RPS(0.983)DS(0.017)GPPAER;RPS(0.997)DS(0.003)GPPAER;RPS(0.728)DS(0.272)GPPAER 170.95 9.25E-06 6089195000 2945349 3564243 3385191 3838786 3939937 2807650 3378924 2898735 3290478 TRUE FALSE 2761004.864 3828143.26 3465489.329 3937295.748 3630510.241 3618172.977 2872285.715 3260648.446 2741275.964 1.007196977 1.396482262 1.26418842 1.436300394 1.324386996 1.319886441 1.047791522 1.189463771 1 21.38641614 1.751223733 8.432069018 1.091286967 1.307316834 0.391316926 0.123365234 0.117432733 31.22179496 0.053442801 0.02883869 56.39280961 -1.751223733 0.216029867 RPS(ph)GPAELGTWHALHSVTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPSGPAELGTWHALHSVTPR 20 1 A0A5E8;Q99501;Q99501-4 A0A5E8 GAS2L1 GAS2-like protein 1 1 RPS(1)GPAELGTWHALHSVTPR 197 7.98E-22 188580000 82948 92018 89892 88653 95046 76135 102420 81572 126760 TRUE FALSE 77756.43275 98831.10846 92024.28069 90927.98607 87581.47056 98113.93855 87063.07182 91756.44376 105602.9371 0.736309376 0.935874618 0.871417815 0.861036526 0.829346919 0.929083426 0.824437977 0.868881551 1 16.68829043 -1.199560284 2.886805328 1.000657213 0.864892926 0.381375153 0.056436815 3755022.333 4885673.9 22435.49127 0.012468103 0.06315965 1.199560284 -0.135764287 RPS(ph)GRSPTSTEK ddPTM_SK-BR-3_Pertuzumab_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(0.577)GRS(0.412)PT(0.01)S(0.002)TEK;RPS(0.91)GRS(0.087)PT(0.002)S(0.001)TEK 69.729 0.03874 184745000 116935 136602 109329 134753 169927 66622 118284 120930 307000 TRUE FALSE 109616.2471 146716.1542 111922.3355 138210.9901 156581.6189 85854.68988 100548.4123 136028.3767 255759.7167 0.428590743 0.573648408 0.437607364 0.540393897 0.612221584 0.335684958 0.393136236 0.531860054 1 17.96442953 0.958690269 22.25830614 1.000000001 0.475542942 0.794535944 0.083337412 921.1278488 496318.6641 0.081817311 0.020454328 9.0926457 -0.958690269 -0.524457059 RPS(ph)ILPEGSSDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPSILPEGSSDSR 13 1 A0A2R8YF49;H0Y895;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 RPS(1)ILPEGSSDSR;RPS(1)ILPEGSSDSR 109.87 0.00067567 483110000 488990 576350 497500 428980 539040 316830 595000 507980 667290 TRUE FALSE 458384.9888 619023.5537 509300.9349 439988.3531 496705.9728 408293.6777 505785.2737 571402.4212 555914.9881 0.824559507 1.113521972 0.916148954 0.791466973 0.89349268 0.734453444 0.909824855 1.027859355 1 19.08450475 3.581792326 4.80142052 0.877387163 0.996046264 0.049108502 0.110629463 0.342268097 12.67250091 0.027723282 0.043584752 3817.61674 -3.581792326 0.118659101 RPS(ph)LGELLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPSLGELLLR 10 1 Q8N612;Q8N612-2 Q8N612 FAM160A2 FTS and Hook-interacting protein 1 RPS(1)LGELLLR;RPS(1)LGELLLR 175.01 1.80E-06 176528000 82100 106603 103285 90438 100677 72549 118355 94726 106115 TRUE FALSE 76961.50755 114495.997 105734.969 92758.79219 92770.23453 93492.71857 100608.7665 106552.7496 88403.72097 0.870568645 1.29514907 1.19604659 1.049263438 1.049392871 1.057565423 1.138060315 1.205297112 1 16.43181947 3.244550464 24.99262724 1.089983148 1.168773811 0 0.121884786 368.5388328 1537719.331 0.032479603 0.04287706 1756.104936 -3.244550464 0.078790664 RPS(ph)LPV ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPSLPV 6 1 Q15053 Q15053 KIAA0040 Uncharacterized protein KIAA0040 1 RPS(1)LPV 77.058 0.077774 247740000 167920 201300 161780 150650 288050 161670 194110 268050 290880 TRUE FALSE 157410.1869 216204.4615 165617.498 154515.934 265427.7149 208341.5045 165005.0075 301516.6326 242330.2488 0.649568874 0.892189326 0.683437164 0.63762545 1.095314003 0.859742048 0.680909661 1.24423853 1 17.88661497 1.239964652 24.99999989 1.122119312 0.789598619 0.462672981 0.150746647 30.85706575 549523.9536 0.107797615 0.034508135 17.37659394 -1.239964652 -0.332520693 RPS(ph)PGEMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPSPGEMR 8 1 A0A0G2JHC2;Q6NYC8-2;Q6NYC8;Q6NYC8-3 A0A0G2JHC2 PPP1R18 Phostensin 1 RPS(1)PGEMR 56.404 0.050561 74398000 123250 96717 140050 149580 104780 119150 143670 95135 82498 TRUE FALSE 115536.0025 103878.0273 143372.0521 153418.476 96551.00146 153546.6708 122128.0173 107012.8142 68728.55084 1.681048139 1.511424671 2.086062493 2.232237901 1.404816489 2.234103133 1.776961914 1.5570358 1 16.06862192 -0.173985952 8.567918945 1 1.824281855 0.430323243 0.292672942 0 0 0.263365621 0.062075872 0.669906279 0.173985952 0.824281855 RPS(ph)PPEPWDEEDGASCSTFFGSEER ddPTM_SK-BR-3_Pertuzumab_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 247.77 3.00E-39 1200860000 275642 258003 272359 282028 289980 280607 320164 255672 230716 TRUE FALSE 258390.0593 277105.8106 278819.4841 289265.316 267206.1405 361613.6856 272158.3805 287593.212 192208.0091 1.344325143 1.441697523 1.450613246 1.504959743 1.390192541 1.881366376 1.415957544 1.496260293 1 17.55230893 0.159760306 2.335979495 0.999996274 1.492367296 0.524429856 0.146827578 54.69091816 149.4127774 0.131835461 0.035412856 1.444642229 -0.159760306 0.492371022 RPS(ph)PPPQPS(ph)SVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPSPPPQPSSVK 12 1 H0YAU4;H3BLZ3;Q8IX03-2 H0YAU4 WWC1 Protein KIBRA 2 RPS(0.996)PPPQPS(0.998)S(0.006)VK;RPS(0.919)PPPQPS(0.961)S(0.119)VK 58.098 0.072535 557770000 1124500 903640 1006570 867800 1011200 758240 1223440 928270 1332180 TRUE FALSE 1054119.552 970546.4458 1030446.316 890069.2172 931784.431 977131.579 1039996.53 1044166.553 1109830.552 0.949802247 0.874499665 0.928471751 0.801986588 0.839573599 0.880433123 0.937076861 0.940834212 1 20.08190799 1.30014215 1.472754013 0.991187187 0.880345367 0.46889132 0.042296558 0.346235422 1.401218262 0.039106109 0.012126697 19.95915495 -1.30014215 -0.11084182 RPS(ph)PQPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPSPQPSPR 9 1 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RPS(1)PQPS(1)PR 59.155 0.069597 272930000 348420 360830 350290 336740 313950 289180 360580 279370 304640 TRUE FALSE 326613.0141 387546.2286 358599.0442 345381.3185 289293.6334 372661.5716 306514.3765 314249.9595 253793.616 1.28692368 1.527013306 1.412955337 1.36087473 1.139877504 1.46836464 1.207730838 1.238210655 1 17.95329625 0.769763224 0.278024185 0.923109738 1.472556703 0.541466623 0.106855867 1.918619245 0.406910709 0.36087275 0.173861588 5.885227066 -0.769763224 0.549446965 RPS(ph)PQPSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RPSPQPSPR 9 1 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RPS(1)PQPSPR;RPS(0.999)PQPS(0.001)PR;RPS(0.999)PQPS(0.001)PR;RPS(0.993)PQPS(0.007)PR;RPS(0.998)PQPS(0.002)PR;RPS(1)PQPSPR 104.59 0.0019815 2791850000 973234 871394 800794 765637 814216 636844 909489 870894 1394002 TRUE FALSE 912321.0212 935912.9184 819789.2118 785284.5416 750270.7597 820690.5245 773119.5677 979627.033 1161334.061 0.785580181 0.80589466 0.705903012 0.676191777 0.646042155 0.706679114 0.665716777 0.843535952 1 20.1473516 0.982819249 4.19909247 0.999561946 0.716079637 0.780677874 0.049857731 0.09377493 5.00595511 0.053409266 0.013627714 9.612121432 -0.982819249 -0.283482309 RPS(ph)PTSGDSRPAAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RPSPTSGDSRPAAGR 15 2 Q8N1G1 Q8N1G1 REXO1 RNA exonuclease 1 homolog 1 RPS(0.941)PT(0.038)S(0.021)GDSRPAAGR;RPS(0.889)PT(0.076)S(0.035)GDSRPAAGR;RPS(0.966)PT(0.026)S(0.008)GDSRPAAGR;RPS(0.857)PT(0.072)S(0.072)GDSRPAAGR 128.1 5.83E-05 1282150000 273109 313410 283897 289421 305285 265220 316941 257416 263131 TRUE FALSE 256015.5952 336615.2025 290631.1709 296848.0328 281309.1476 341784.7085 269418.6394 289554.9542 219212.7362 1.1678865 1.535564075 1.325795097 1.354155046 1.283270089 1.559146218 1.229028222 1.320885635 1 17.7419721 0.552488588 0.968723101 0.999843814 1.376796434 0.449260334 0.120887915 1.212537348 1.733711872 0.104998895 0.033662665 3.568523723 -0.552488588 0.376952619 RPS(ph)QEQSASASSGQPQAPLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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(1)QEQSASASSGQPQAPLNR;RPS(1)QEQSASASSGQPQAPLNR;RPS(0.505)QEQS(0.436)AS(0.008)AS(0.044)S(0.008)GQPQAPLNR;RPS(1)QEQSASASSGQPQAPLNR 378.37 4.69E-113 17245210000 1476414 1675501 1657234 1731909 1655674 1527736 1930874 1563059 1815807 TRUE FALSE 1384007.883 1799556.837 1696544.373 1776352.717 1525644.043 1968768.582 1641357.369 1758210.357 1512737.081 0.914903125 1.189603177 1.121506436 1.174264014 1.008532191 1.301461177 1.085024879 1.162270945 1 20.52872983 4.746691346 24.66761108 1.138801891 0.914902991 0.36663414 0.08836442 817.5325016 2480222.419 0.017967743 0.201879939 55807.34292 -4.746691346 -0.2238989 RPS(ph)QGPPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 RPSQGPPAR 9 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RPS(1)QGPPAR;RPS(1)QGPPAR;RPS(1)QGPPAR;RPS(1)QGPPAR;RPS(1)QGPPAR;RPS(1)QGPPAR;RPS(1)QGPPAR;RPS(1)QGPPAR;RPS(1)QGPPAR;RPS(1)QGPPAR 120.87 0.00038574 14073057000 2440216 2830031 2718220 2617041 2830075 2276844 3120646 2708403 3397022 TRUE FALSE 2287487.236 3039569.44 2782697.462 2684198.703 2607812.325 2934131.901 2652734.103 3046553.076 2830037.083 0.808288786 1.074038732 0.983272438 0.948467679 0.92147638 1.036782139 0.937349591 1.076506416 1 21.43238953 1.240009443 24.99995917 1.038253204 0.972878201 0.147172747 0.073742654 77.64505191 1340004.17 0.051369919 0.016477268 17.37838616 -1.240009443 -0.065375004 RPS(ph)QGPPARS(ph)PSQDFSFIEDTEILDSAMYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPSQGPPARSPSQDFSFIEDTEILDSAMYR 30 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 RPS(0.5)QGPPARS(0.5)PS(0.5)QDFS(0.5)FIEDTEILDSAMYR 64.315 0.0050021 11202000 6454.7 10729 6317.7 7242.9 10621 4763.2 5328.1 5665.1 10194 TRUE FALSE 6050.711849 11523.38632 6467.558827 7428.765076 9786.869503 6138.258516 4529.200869 6372.400205 8492.555544 0.712472449 1.35688089 0.761556259 0.874738474 1.15240571 0.722781086 0.533314247 0.750351313 1 13.05198303 2.139113575 7.552136514 0.690119277 0.990593449 0.175846891 0.218113657 0.278524889 18.61913632 0.077599769 0.05725174 137.7569678 -2.139113575 0.300474173 RPS(ph)QGPPARSPSQDFSFIEDTEILDSAMYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPSQGPPARSPSQDFSFIEDTEILDSAMYR 30 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RPS(0.489)QGPPARS(0.489)PS(0.018)QDFS(0.004)FIEDTEILDSAMYR;RPS(0.371)QGPPARS(0.371)PS(0.129)QDFS(0.129)FIEDTEILDSAMYR 102.42 0.0002011 101308000 11715.1 22695.8 17663.4 22821.7 27138 11044.6 13592 11918.7 22157.3 TRUE FALSE 10981.8728 24376.22065 18082.38419 23407.34346 25006.69095 14232.99673 11554.00578 13406.77593 18459.10349 0.594929911 1.320552792 0.97959168 1.268065021 1.354707771 0.771055687 0.625924536 0.726296157 1 14.17204487 2.134853971 7.872845975 0.732479151 1.123135996 0.30825514 0.234897145 0.229574023 15.63610936 0.080953504 0.059736809 136.4124379 -2.134853971 0.390656845 RPS(ph)QNAISFFNVGHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPSQNAISFFNVGHSK 16 1 Q9BXB4 Q9BXB4 OSBPL11 Oxysterol-binding protein-related protein 11 1 RPS(1)QNAISFFNVGHSK;RPS(1)QNAISFFNVGHSK 254.56 8.50E-27 1748160000 1715170 1709720 1852020 1718190 2189800 1430240 2377410 2129920 3616800 TRUE FALSE 1607820.571 1836309.448 1895950.789 1762281.664 2017821.941 1843127.07 2020939.441 2395845.201 3013132.715 0.533604299 0.609435303 0.629229101 0.584866925 0.66967576 0.611697939 0.670710398 0.79513431 1 21.52283279 0.950398709 1.202480253 1.000978865 0.606678903 0.936711938 0.033387943 0.113870089 0.335740404 0.029153558 0.009071981 8.920695369 -0.950398709 -0.394299962 RPS(ph)RHDNSAIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RPSRHDNSAIGR 12 2 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 RPS(1)RHDNSAIGR;RPS(1)RHDNSAIGR;RPS(0.999)RHDNS(0.001)AIGR;RPS(1)RHDNSAIGR;RPS(1)RHDNSAIGR 162.7 3.23E-05 1028291000 82137.2 140539.5 118543.3 117147.9 134916.5 82484 103343.8 117575.5 185641.2 TRUE FALSE 76996.37927 150945.1908 121355.2031 120154.1134 124320.7023 106295.7918 87848.35659 132255.06 154656.4844 0.497854193 0.976002987 0.784675816 0.776909639 0.803850565 0.687302522 0.568022459 0.855153668 1 17.2387078 2.252628473 24.0350587 0.721081673 0.798946644 0 0.164336322 491.0778345 839009.0824 0.053251473 0.044322912 178.9074696 -2.252628473 0.077864971 S(ph)PDPFGAVAAQK ddPTM_SK-BR-3_Pertuzumab_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 166.7 5.37E-05 764570000 2115800 1548090 2070730 2328960 2112480 1250010 1132460 734210 949670 TRUE FALSE 1983375.855 1662712.194 2119848.693 2388725.057 1946574.342 1610867.595 962658.1362 825877.7347 791163.9419 2.506908808 2.101602596 2.679405091 3.019254203 2.460393149 2.036073068 1.216761894 1.043876864 1 19.59361715 1.838619844 2.069337677 1.019881839 2.531842019 0.89955468 0.224307907 0.101218582 0.821330625 0.157178345 0.071917958 68.96358733 -1.838619844 1.51196018 up RPS(ph)SMYSTGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RPSSMYSTGGK 11 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 RPS(0.492)S(0.492)MY(0.014)S(0.001)TGGK;RPS(0.466)S(0.466)MY(0.012)S(0.051)T(0.005)GGK;RPS(0.839)S(0.153)MY(0.008)STGGK;RPS(0.693)S(0.303)MY(0.003)S(0.001)TGGK;RPS(0.691)S(0.309)MYSTGGK;RPS(0.612)S(0.388)MYSTGGK 117.83 0.00049162 2103390000 2807120 3118820 2596410 2481530 3687390 1653104 3729760 2711590 5220540 TRUE FALSE 2631427.37 3349740.678 2657998.071 2545210.261 3397797.264 2130328.289 3170517.113 3050137.98 4349198.148 0.605037361 0.770197302 0.611146694 0.585213682 0.781246829 0.489820932 0.728988886 0.70131042 1 22.05231801 0.566761705 1.498708057 0.999745556 0.656462915 0.600775829 0.088496345 1.231777417 3.505131936 0.075904141 0.021992493 3.687751978 -0.566761705 -0.343282641 RPS(ph)SPVISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPSSPVISK 9 1 Q96T17-5;Q96T17-4;Q96T17;Q96T17-2 Q96T17-5 MAP7D2 MAP7 domain-containing protein 2 1 RPS(0.588)S(0.412)PVISK 62.924 0.048655 208000000 224920 207950 224450 212100 222880 186220 272750 190350 220150 TRUE FALSE 210842.6587 223346.8344 229774.06 217542.8451 205375.9039 239978.691 231853.6696 214115.6165 183405.5428 1.149598074 1.217775815 1.252819607 1.186130156 1.119791151 1.308459316 1.264158466 1.167443542 1 17.48467771 0.924120271 6.530232993 1.000004287 1.220840497 0.597132324 0.054854874 0.602447794 51.27091408 0.052378367 0.013149831 8.396924937 -0.924120271 0.220836211 RPS(ph)STSVPLGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPSSTSVPLGDK 12 1 Q9NXR1;Q9NXR1-1;I3L533;I3L2R9;I3L2T8 Q9NXR1 NDE1 Nuclear distribution protein nudE homolog 1 1 RPS(0.942)S(0.049)T(0.008)S(0.002)VPLGDK;RPS(0.998)S(0.002)TSVPLGDK 152.16 7.37E-05 530230000 431880 336570 360380 334180 407120 269650 454140 371250 647240 TRUE FALSE 404849.4017 361489.993 368928.3838 342755.6246 375146.4374 347493.5776 386045.923 417601.3797 539211.4627 0.750817499 0.670404875 0.684199816 0.635660865 0.69573157 0.644447683 0.71594532 0.774466807 1 19.04049164 0.788032839 1.516535831 0.999620784 0.678425161 0.907496511 0.031826381 0.182360783 0.740454633 0.027124866 0.007898749 6.13808417 -0.788032839 -0.321195623 RPS(ph)TFGIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RPSTFGIPR 9 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 RPS(0.976)T(0.024)FGIPR;RPS(0.975)T(0.025)FGIPR;RPS(0.925)T(0.075)FGIPR 151.55 5.06E-05 407390000 98751 122343 108980 108403 126889 93570 122448 116216 212968 TRUE FALSE 92570.35119 131401.403 111565.0571 111184.8045 116923.6498 120582.14 104088.0592 130725.8234 177422.265 0.521751603 0.740613942 0.628810917 0.62666771 0.659013398 0.679633641 0.586668529 0.736806192 1 17.43682754 0.909850909 5.034907936 0.999969192 0.644963663 0.799531764 0.057524449 0.240371489 12.67738883 0.050746111 0.012825934 8.125515228 -0.909850909 -0.355005529 RPS(ph)TSQTVSTPAPVPVIESTEAIEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPSTSQTVSTPAPVPVIESTEAIEAK 26 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 RPS(0.619)T(0.089)S(0.121)QT(0.164)VS(0.003)T(0.003)PAPVPVIESTEAIEAK 170.6 4.21E-12 49616000 43552 35688 35567 46128 48817 22110 35453 26687 50294 TRUE FALSE 40826.15806 38330.37665 36410.66604 47311.72257 44983.10974 28492.79807 30137.15178 30018.9307 41899.60649 0.974380465 0.914814717 0.868997804 1.129168661 1.073592654 0.680025434 0.719270521 0.716448989 1 15.35464907 2.233265265 24.99994955 0.748958831 0.971066782 0.444924676 0.114897519 115.1452411 543607.8369 0.041607874 0.031636644 171.1060103 -2.233265265 0.222107951 RPS(ph)TSS(ph)ASGQWSPTPEWVLSWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RPSTSSASGQWSPTPEWVLSWK 22 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 2 RPS(0.647)T(0.268)S(0.323)S(0.76)AS(0.002)GQWSPTPEWVLSWK;RPS(0.787)T(0.207)S(0.142)S(0.863)AS(0.001)GQWSPTPEWVLSWK;RPS(0.875)T(0.275)S(0.169)S(0.554)AS(0.124)GQWS(0.003)PTPEWVLSWK 226.07 1.95E-25 503562000 627645 690302 590374 636220 643373 465575 839552 588154 608141 TRUE FALSE 588361.8198 741412.6783 604377.9501 652546.4823 592845.0798 599978.9445 713668.9716 661586.3216 506638.3384 1.161305364 1.463396317 1.192917915 1.287992702 1.170154398 1.184235181 1.408635939 1.305835488 1 18.95059673 -2.258821835 2.107888899 0.000155926 1.284679243 0.404804951 0.10252904 1462411.197 234280.6746 6965413.602 0.024228993 0.005510337 2.258821835 1.284523317 RPS(ph)TSSASGQWSPTPEWVLSWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPSTSSASGQWSPTPEWVLSWK 22 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 RPS(0.317)T(0.317)S(0.125)S(0.192)AS(0.05)GQWSPTPEWVLSWK;RPS(0.372)T(0.056)S(0.163)S(0.282)AS(0.127)GQWSPTPEWVLSWK 274.57 1.27E-45 4896300000 738980 805280 718860 695780 813520 553440 980180 735120 671740 TRUE FALSE 692728.5609 864903.7691 735911.6987 713634.8928 749629.4208 713209.1437 833211.1085 826901.3502 559622.2544 1.237850274 1.545513536 1.315015071 1.275208209 1.339527538 1.27444743 1.488881298 1.477606267 1 19.09409381 -1.153757585 4.175288636 0.999888605 1.380342912 0.553372745 0.103830529 0.000104543 2.12E-05 0.097616575 0.023001738 0.070184695 1.153757585 0.380454307 RPS(ph)VGSQSNQAGQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RPSVGSQSNQAGQGK 15 1 Q9UPP1-4;Q9UPP1-3;Q9UPP1-2;Q9UPP1;H0Y3N9 Q9UPP1-4 PHF8 Histone lysine demethylase PHF8 1 RPS(1)VGSQSNQAGQGK;RPS(1)VGSQSNQAGQGK;RPS(1)VGSQSNQAGQGK;RPS(1)VGSQSNQAGQGK;RPS(1)VGSQSNQAGQGK 259.23 4.58E-25 1705660000 1377660 1257710 1208700 1337740 1852190 1109910 1934200 1308420 2162750 TRUE FALSE 1291434.72 1350832.157 1237370.935 1372068.673 1706726.469 1430322.999 1644184.666 1471779.117 1801773.053 0.716757706 0.749723809 0.686751826 0.761510264 0.947248304 0.793841931 0.91253705 0.816850443 1 20.78098587 2.903250849 5.203755623 0.881799836 0.720460425 0.648002224 0.0608332 0.130470432 5.496552722 0.016348508 0.017512518 800.2963739 -2.903250849 -0.161339411 RPS(ph)VNGEPGSVPPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPSVNGEPGSVPPPR 15 1 Q8N3D4 Q8N3D4 EHBP1L1 EH domain-binding protein 1-like protein 1 1 RPS(1)VNGEPGSVPPPR;RPS(1)VNGEPGSVPPPR 108.71 0.00099742 169650000 327460 236410 241972 240147 247532 238177 281710 211048 225490 TRUE FALSE 306964.8631 253914.0424 247711.6901 246309.5786 228091.8352 306934.8334 239470.2008 237397.8074 187854.2623 1.634058548 1.351654412 1.318637582 1.311173756 1.214195688 1.633898692 1.274765863 1.263733942 1 17.51925432 -3.840123529 0.20451598 1.81E-10 1.431465295 0.458697813 0.137729527 82.04539279 1.250201901 34.35311217 0.306996139 0.000144503 3.840123529 1.431465295 RPS(ph)VSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPSVSK 6 1 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5;A0FGR8-4 A0A499FIX8 ESYT2 Extended synaptotagmin-2 1 RPS(0.993)VS(0.007)K;RPS(0.998)VS(0.002)K 108.81 0.018435 3003900000 4616200 3657400 3450300 3344100 4440200 3126500 5208600 4043200 5133400 TRUE FALSE 4327280.282 3928197.702 3532142.745 3429915.268 4091484.603 4029069.796 4427618.784 4548002.42 4276602.377 1.011850039 0.918532366 0.825922645 0.802018744 0.956713821 0.942119337 1.035312239 1.063461603 1 22.02803365 2.021479557 1.775911896 1.038279382 0.886781119 0.484527617 0.060951473 0.289276062 1.709705503 0.037453589 0.019118527 105.0701996 -2.021479557 -0.151498263 RPSASS(ph)PNNNTAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RPSASSPNNNTAAK 14 1 O75151;E7ET14;A0A087WW48 O75151 PHF2 Lysine-specific demethylase PHF2 1 RPS(0.172)AS(0.061)S(0.768)PNNNTAAK;RPS(0.258)AS(0.167)S(0.575)PNNNTAAK;RPS(0.002)AS(0.085)S(0.913)PNNNTAAK;RPS(0.104)AS(0.254)S(0.642)PNNNTAAK;RPS(0.156)AS(0.156)S(0.689)PNNNTAAK 188.44 8.83E-07 879062000 755520 635321 678462 582832 593737 541316 891374 617551 703381 TRUE FALSE 708233.3518 682360.8279 694555.439 597788.4559 547107.291 697585.1417 757720.7438 694653.6017 585982.1671 1.208626118 1.16447371 1.18528426 1.020147864 0.933658602 1.190454558 1.293078162 1.185451778 1 19.16049723 2.029491408 24.99881575 1.204497536 1.113754453 0.03001895 0.109501298 419.9670939 355989.6529 0.041171756 0.030406882 107.0265209 -2.029491408 -0.090743083 RPSDLTISINQMGSPGMGHLKS(ph)PTLSQVHSPLVTSPSANLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPSDLTISINQMGSPGMGHLKSPTLSQVHSPLVTSPSANLK 41 2 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 RPSDLTISINQMGS(0.009)PGMGHLKS(0.941)PT(0.039)LS(0.009)QVHS(0.001)PLVTSPSANLK 150.19 7.38E-14 209760000 139290 147870 145280 138270 195420 108680 192470 149440 198880 TRUE FALSE 130572.0875 158818.4487 148726.1102 141818.2423 180072.5015 140054.1517 163610.9103 168097.913 165685.6432 0.788071223 0.958552869 0.897640298 0.855947682 1.086832257 0.845300468 0.987477896 1.014559317 1 17.33808907 8 0.200924773 1.00410923 0.26530271 0.30794768 0.075511782 71.58489221 0.867489902 0.125187831 16.69018376 100000000 -8 -0.738806521 RPSDSSRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RPSDSSRPK 9 2 Q13573;G3V4X8 Q13573 SNW1 SNW domain-containing protein 1 0 ;;; 93.667 0.0051993 252057000 269954 279360 255640 252300 296410 198322 277394 257428 308061 FALSE TRUE 253058.061 300044.1051 261703.9015 258774.4451 273131.1543 255574.3419 235801.3449 289568.4525 256643.6289 0.986029001 1.169107943 1.019717117 1.008302626 1.064242878 0.995833573 0.918789007 1.128290048 1 17.96940692 3.693235006 5.207260521 1.009797064 1.092093795 0.09140616 0.06894452 0.267325881 18.85119447 0.017386584 0.028305245 4934.407433 -3.693235006 0.082296731 RPSGSQHS(ph)PSLQTFAPEADGTIFFPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPSGSQHSPSLQTFAPEADGTIFFPER 27 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 RPS(0.174)GS(0.174)QHS(0.221)PS(0.215)LQT(0.215)FAPEADGTIFFPER 108.56 0.00077702 54371000 11978 20315 20745 21285 24711 16312 19162 15573 12531 TRUE FALSE 11228.31836 21819.14374 21237.0812 21831.20914 22770.29774 21021.0096 16288.83599 17517.32333 10439.49515 1.075561433 2.090057367 2.034301554 2.091213112 2.181168478 2.013604039 1.560308785 1.677985677 1 13.34976432 0.938969036 1.059599679 1.017392522 1.956141006 0.410422211 0.326444602 0.528849656 1.225248716 0.287973755 0.09318761 8.688984767 -0.938969036 0.938748484 RPSGVPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPSGVPDR 8 1 P01709;P01706 P01709 Ig lambda chain V-II region MGC;Ig lambda chain V-II region BOH 0 ; 85.533 0.026737 260950000 404510 581720 362820 341180 460580 294710 492000 382920 584950 FALSE TRUE 379192.4412 624791.1541 371426.2617 349935.2564 424407.9047 379787.9928 418229.1675 430728.4049 487318.0661 0.778121042 1.282101358 0.76218447 0.718083898 0.870905337 0.779343142 0.858226273 0.883875306 1 18.89450418 3.808126856 6.144334278 0.82805998 1.057400123 0.228613568 0.142598686 0.222705553 13.38697695 0.032573847 0.059230779 6428.75471 -3.808126856 0.229340143 RPSNDCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPSNDCR 7 1 Q9UGT4 Q9UGT4 SUSD2 Sushi domain-containing protein 2 0 ; 105.14 0.012819 181857000 177955 252980 151153 141514 329870 125242 184146 289080 367880 FALSE TRUE 166817.1142 271710.9024 154738.4205 145145.4888 303963.3408 161397.3323 156535.0168 325172.2743 306478.4514 0.544302914 0.886557933 0.504891681 0.473591171 0.991793516 0.526618859 0.510753745 1.060995554 1 18.22542612 1.229462743 24.99950756 1.030498087 0.640978807 0.473766235 0.173577304 188.2433256 517243.8435 0.151545951 0.040050895 16.96144089 -1.229462743 -0.38951928 RPSPDEPMTNLELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPSPDEPMTNLELK 14 1 Q9UHD1-2;Q9UHD1;E9PPQ5 Q9UHD1-2 CHORDC1 Cysteine and histidine-rich domain-containing protein 1 0 190.34 9.85E-07 540340000 523970 417200 448400 440160 505400 398690 510330 505630 636180 FALSE TRUE 491175.653 448089.9221 459036.2597 451455.2508 465707.9227 513785.3308 433810.7542 568759.0185 529997.4481 0.926750977 0.845456754 0.866110321 0.851806461 0.878698425 0.969410952 0.818514798 1.073135391 1 19.01562589 1.234122233 24.99999663 1.036567756 0.875541897 0.668949434 0.045859313 62.26256764 350683.324 0.035529193 0.01007198 17.1443977 -1.234122233 -0.161025859 RPSQGPPARS(ph)PS(ph)QDFSFIEDTEILDSAMYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPSQGPPARSPSQDFSFIEDTEILDSAMYR 30 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 RPS(0.178)QGPPARS(0.974)PS(0.841)QDFS(0.007)FIEDTEILDSAMYR;RPS(0.442)QGPPARS(0.519)PS(0.519)QDFS(0.519)FIEDT(0.001)EILDSAMYR 233.58 1.19E-45 83554000 26626 39581 34362 37574 54270 19712.2 33267 31229 69012 TRUE FALSE 24959.52619 42511.61842 35177.08287 38538.21245 50007.85311 25402.79214 28278.92219 35128.00939 57493.45137 0.434128159 0.739416706 0.611845037 0.670306122 0.869800854 0.44183801 0.49186336 0.610991488 1 15.81111002 -1.176035984 4.16087169 1.000142782 0.613802134 0.45726405 0.13384994 20.21921479 53634251.17 14654.27644 0.03201303 0.066675152 1.176035984 -0.386340648 RPSS(ph)EDFVFL ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPSSEDFVFL 10 1 Q86TL0;K7EQ67;K7EN30;Q86TL0-2 Q86TL0 ATG4D "Cysteine protease ATG4D;Cysteine protease ATG4D, mitochondrial" 1 RPS(0.372)S(0.628)EDFVFL 68.536 0.063221 8110800 31667 35081 32851 32829 25947 24886 43084 32979 25545 TRUE FALSE 29685.019 37678.43374 33630.24123 33671.44772 23909.22729 32070.18421 36623.95417 37096.50075 21281.37447 1.394882602 1.770488734 1.58026641 1.58220268 1.123481348 1.506960194 1.720939323 1.743144024 1 14.37730371 2.980444331 24.46500392 1.477602388 1.616961418 0.063979125 0.24907139 1732.311118 2167200.602 0.073451028 0.079004403 955.9701487 -2.980444331 0.13935903 RPSS(ph)MYSTGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RPSSMYSTGGK 11 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 RPS(0.411)S(0.587)MY(0.001)STGGK;RPS(0.001)S(0.999)MYSTGGK;RPS(0.327)S(0.673)MY(0.001)STGGK 153.39 1.99E-05 1230270000 1396920 1506660 1231370 1261790 1710450 828044 1865580 1306410 2572360 TRUE FALSE 1309489.271 1618214.674 1260578.678 1294169.668 1576118.157 1067086.861 1585853.598 1469518.164 2143016.498 0.611049552 0.755110694 0.588226306 0.603900935 0.735467113 0.497936839 0.740009981 0.685724149 1 21.03121153 0.455408879 1.181807526 1.000046383 0.647246144 0.664205995 0.078654474 1.293516508 2.244825014 0.068488685 0.020763409 2.853703703 -0.455408879 -0.352800239 RPSS(ph)TSVPLGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPSSTSVPLGDK 12 1 Q9NXR1;Q9NXR1-1;I3L533;I3L2R9;I3L2T8 Q9NXR1 NDE1 Nuclear distribution protein nudE homolog 1 1 RPS(0.382)S(0.596)T(0.016)S(0.006)VPLGDK 112.3 0.0007894 365920000 860720 647230 755640 702210 820630 514290 931800 786660 1408300 TRUE FALSE 806849.0716 695151.5826 773564.1376 720229.8974 756181.0301 662757.1742 792085.2404 884876.2327 1173245.632 0.687706862 0.592503022 0.6593369 0.613878184 0.644520644 0.564892087 0.67512311 0.754212254 1 20.16207366 0.865672342 1.697159194 0.999185825 0.626955524 0.916599596 0.035287629 0.124702497 0.696084337 0.029743323 0.008503457 7.339599163 -0.865672342 -0.3722303 RPST(ph)FGIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPSTFGIPR 9 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 RPS(0.271)T(0.729)FGIPR 132.86 0.00017178 176640000 45216 50869 52765 42874 55361 44521 62078 58336 109660 TRUE FALSE 42386.01127 54635.39369 54016.61072 43974.21943 51013.17038 57373.48996 52769.9802 65619.37801 91357.03757 0.463960001 0.598042528 0.59126929 0.48134463 0.558393439 0.628013906 0.577623592 0.718273926 1 16.47922825 0.736302248 1.104148306 1.001005243 0.555616216 0.893792212 0.049118272 0.26806305 0.576888875 0.044838753 0.014089662 5.44881732 -0.736302248 -0.445389026 RPSVGS(ph)QSNQAGQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPSVGSQSNQAGQGK 15 1 Q9UPP1-4;Q9UPP1-3;Q9UPP1-2;Q9UPP1;H0Y3N9 Q9UPP1-4 PHF8 Histone lysine demethylase PHF8 1 RPS(0.45)VGS(0.5)QS(0.05)NQAGQGK 104.84 0.00083446 110480000 121880 102190 119460 116590 158590 99677 165560 115830 176530 TRUE FALSE 114251.7484 109756.2539 122293.6476 119581.8968 146134.9811 128452.1318 140735.815 130291.6305 147066.0026 0.776873964 0.746306094 0.831556209 0.813117204 0.993669363 0.873431857 0.956956826 0.885939838 1 17.16610425 3.081244849 1.432705128 0.936516363 0.769799434 0.702283417 0.047585794 0.198953946 0.845600938 0.015548347 0.020091812 1205.715515 -3.081244849 -0.166716929 RPTEICADPQFIIGGATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPTEICADPQFIIGGATR 18 1 P17655 P17655 CAPN2 Calpain-2 catalytic subunit 0 ; 208.86 9.40E-16 924820000 570480 687150 642080 629470 724530 613540 786270 639510 882560 FALSE TRUE 534774.6751 738027.301 657310.4408 645623.2659 667628.3364 790659.038 668376.1129 719354.2312 735255.0344 0.727332218 1.003770483 0.893989718 0.878094315 0.908022802 1.07535345 0.909039832 0.978373758 1 19.48788523 2.440103137 24.97785688 0.98012217 0.899447806 0.304313392 0.078537068 260.8213852 175987.1227 0.025484878 0.021322217 275.4882859 -2.440103137 -0.080674364 RPTELLSNPQFIVDGATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPTELLSNPQFIVDGATR 18 1 P07384;E9PRM1;E9PJJ3;E9PLC9;E9PMC6;E9PJA6;E9PSA6;E9PQB3;E9PLX0 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 179.87 1.31E-13 1751250000 451925 552490 472972 516322 553297 432634 578640 452568 510258 FALSE TRUE 423639.821 593396.9345 484191.1192 529571.6967 509843.2855 557528.4126 491878.3038 509072.111 425092.6434 0.996582339 1.395923791 1.139024932 1.24577949 1.199369816 1.311545662 1.157108483 1.197555683 1 18.69741777 0.480702269 1.082214259 0.999933732 1.224860513 0.262407903 0.106009397 2.277320079 3.575115335 0.090392987 0.027985608 3.024839033 -0.480702269 0.224926781 RPTETNPVTSNS(ph)DEECNETVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RPTETNPVTSNSDEECNETVK 21 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 RPTETNPVTSNS(1)DEECNETVK;RPTETNPVTSNS(1)DEECNETVK;RPTETNPVTSNS(1)DEECNETVK 387.14 2.72E-131 1877580000 1422800 1012950 1192250 1131070 1174200 1037300 1506990 1042150 1247740 TRUE FALSE 1333749.488 1087949.872 1220530.733 1160095.171 1081983.068 1336751.671 1281030.84 1172264.722 1039484.133 1.283087875 1.046624799 1.174169662 1.116029705 1.040884641 1.285976022 1.232371711 1.127737003 1 19.98743631 2.244647361 24.99999249 1.190155105 1.12549107 0 0.100936125 352.1645975 1446446.695 0.032346582 0.026418399 175.6496791 -2.244647361 -0.064664035 RPTETNPVTSNS(ph)DEECNETVKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPTETNPVTSNSDEECNETVKEK 23 2 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 RPTETNPVTSNS(1)DEECNETVKEK;RPTETNPVTSNS(1)DEECNETVKEK 229.7 2.58E-33 369470000 413230 288400 345170 394080 496270 241230 480990 257560 764580 TRUE FALSE 387366.6719 309753.4361 353357.5954 404192.76 457294.9561 310869.185 408870.0148 289716.933 636966.6586 0.608142776 0.486294584 0.554750536 0.634558739 0.717926048 0.488046243 0.641901753 0.454838458 1 19.28085833 -2.027046384 2.666053713 1.505991668 0.571439481 0.730047282 0.081535831 10849138.39 3807923.598 33586536.29 0.018978226 0.00939623 2.027046384 -0.934552187 RPTPNDDTLDEGVGLVHSNIATEHIPS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPTPNDDTLDEGVGLVHSNIATEHIPSPAK 30 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 1 RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAK;RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAK 173.23 4.47E-13 1136400000 797090 478514 691530 632370 669470 625200 809910 536102 812860 TRUE FALSE 747201.5597 513943.6745 707933.4182 648597.6848 616892.5267 805685.0907 688471.5143 603035.5148 677188.4147 1.103387984 0.758937488 1.045400959 0.957780244 0.91096143 1.189750257 1.016661684 0.890498865 1 19.36919777 3.739234215 24.10323712 1.008776213 0.905242121 0.047273981 0.115977423 490.5703665 976162.3862 0.027743675 0.049514736 5485.727309 -3.739234215 -0.103534092 RPTPNDDTLDEGVGLVHSNIATEHIPS(ph)PAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPTPNDDTLDEGVGLVHSNIATEHIPSPAKK 31 2 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 1 RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAKK 247.21 1.27E-46 401190000 187280 84969 137960 122490 122330 114840 170230 97098 191530 TRUE FALSE 175558.4791 91260.19317 141232.4763 125633.3008 112722.6953 147992.4437 144705.5918 109220.899 159562.4057 1.100249638 0.571940444 0.885123759 0.787361536 0.706448958 0.927489424 0.906890262 0.68450271 1 17.28376125 2.226346533 24.99311979 0.877686959 0.786905771 0.035681322 0.154965419 606.3213195 1240679.001 0.052951949 0.039393274 168.4017238 -2.226346533 -0.090781188 RPTPQDS(ph)PIFLPVDDTSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 RPTPQDSPIFLPVDDTSFR 19 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPT(0.003)PQDS(0.997)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR 206.03 2.35E-16 9334796000 1626810 1892563 1861153 1928080 2019171 1603407 2035780 1723270 1749006 TRUE FALSE 1524990.866 2032690.334 1905300.428 1977557.797 1860593.455 2066284.572 1730533.688 1938424.053 1457085.6 1.046603485 1.39503838 1.307610499 1.357200838 1.276928037 1.418094155 1.187667827 1.330343292 1 20.4746542 -1.08811187 4.584753401 0.999980228 1.299912385 0.414148074 0.107793874 1.93E-05 3.84E-06 0.092381885 0.021773184 0.081637206 1.08811187 0.299932157 RPTPQDSPIFLPVDDTSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 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 28487215000 7577651 9580744 9298506 9308504 10080989 8156623 10765758 9586280 9883028 FALSE TRUE 7103379.35 10290112.25 9519070.953 9547375.972 9289268.789 10511307.65 9151532.532 10783148.16 8233486.78 0.862742546 1.249787912 1.156140917 1.159578709 1.128230243 1.276653249 1.111501455 1.3096697 1 22.97307209 4.746366618 24.8275816 1.180124342 0.862742378 0.544371157 0.089316576 592.0523108 1883019.479 0.018100841 0.195617937 55765.63071 -4.746366618 -0.317381964 RPTSNGVVS(ph)SPNSTSRPTLPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPTSNGVVSSPNSTSRPTLPVK 22 2 Q7Z422-5;Q7Z422;Q7Z422-4;Q7Z422-2;Q7Z422-3 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 RPTSNGVVS(0.538)S(0.431)PNS(0.01)T(0.01)S(0.01)RPTLPVK 75.71 0.0061015 230840000 127410 110940 131670 118070 129240 98923 145660 99268 133270 TRUE FALSE 119435.6355 119154.113 134793.2746 121099.8761 119090.0117 127480.4642 123819.6352 111661.8283 111026.376 1.075741097 1.073205461 1.214065336 1.090730693 1.072628109 1.148199813 1.115227207 1.005723435 1 16.76054293 1.236852632 6.561772523 1.001206208 1.118643229 0.52564237 0.043184473 0.105229996 20.6679534 0.035509924 0.010739697 17.25252368 -1.236852632 0.117437021 RPVS(ph)PGKDITAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RPVSPGKDITAR 12 2 P31629 P31629 HIVEP2 Transcription factor HIVEP2 1 RPVS(0.998)PGKDIT(0.002)AR 62.861 0.058885 254190000 384450 288740 315500 310720 315720 190010 365040 275830 296080 TRUE FALSE 360387.9608 310118.61 322983.809 318693.6012 290924.6248 244862.8024 310305.6409 310267.9827 246662.3353 1.461057929 1.257259685 1.309416813 1.292023774 1.179444865 0.992704469 1.258017932 1.257865261 1 17.91217791 8 0.10917372 0.94534216 2.283961036 0.538868593 0.095279626 91.74740798 0.69954743 0.865984727 18.50317592 100000000 -8 1.338618877 RPWRPEEAVEDPDEEDEDNT(ph)SEAENGFSLEEVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RPWRPEEAVEDPDEEDEDNTSEAENGFSLEEVLR 34 2 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 RPWRPEEAVEDPDEEDEDNT(0.5)S(0.5)EAENGFSLEEVLR;RPWRPEEAVEDPDEEDEDNT(0.559)S(0.441)EAENGFSLEEVLR;RPWRPEEAVEDPDEEDEDNT(0.5)S(0.5)EAENGFSLEEVLR 287.65 4.26E-73 689198000 130158 122800 124751 106712 96836 82129 134198 108477 113296 TRUE FALSE 122011.6431 131892.2398 127710.1526 109450.4106 89230.89118 105838.309 114076.2557 122020.5922 94386.16568 1.292685663 1.397368341 1.353060077 1.159602255 0.945381037 1.121332859 1.208612035 1.292780476 1 16.5262878 3.214194537 4.938395323 1.126731403 1.360616522 0.534627265 0.099693942 0.141695558 8.71608323 0.02901742 0.036455179 1637.549877 -3.214194537 0.233885119 RPWRPEEAVEDPDEEDEDNTS(ph)EAENGFSLEEVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPWRPEEAVEDPDEEDEDNTSEAENGFSLEEVLR 34 2 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 RPWRPEEAVEDPDEEDEDNT(0.439)S(0.561)EAENGFSLEEVLR;RPWRPEEAVEDPDEEDEDNT(0.159)S(0.841)EAENGFSLEEVLR 280.03 3.05E-74 396997000 87160 96042 95691 86749 74310 54529 109159 86910 89051 TRUE FALSE 81704.81119 103153.0496 97960.83571 88975.12621 68473.99235 70270.6371 92791.62133 97760.90481 74187.81281 1.101323898 1.3904312 1.320443776 1.199322676 0.922981683 0.947199202 1.25076637 1.317748847 1 16.17889459 3.012150331 6.145084484 1.099320018 1.299562562 0.250588032 0.142540078 0.199957351 29.70316403 0.043037669 0.050070519 1028.372208 -3.012150331 0.200242544 RPYDLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 80.438 0.047962 415440000 207050 388160 232780 212463 411610 163594 211650 373610 382640 FALSE TRUE 194091.1101 416899.7703 238301.6515 217915.1603 379283.811 210820.9321 179915.0474 420256.0309 318774.9121 0.6088657 1.307818635 0.747554599 0.683601978 1.189817004 0.661347315 0.564395254 1.318347257 1 18.28217857 5.011652784 18.83873447 0.901946331 0.123081807 0.112878911 0.273647337 177547468.8 4732513172 0.064018034 3679850579 102719.4732 -5.011652784 -0.778864524 RPYGVGLLIAGYDDMGPHIFQTCPSANYFDCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RPYGVGLLIAGYDDMGPHIFQTCPSANYFDCR 32 1 P25786;P25786-2;F5GX11 P25786 PSMA1 Proteasome subunit alpha type-1 0 ; 270.23 1.31E-61 686130000 335700 685800 167391 72061 648320 136138 272520 670610 124533 FALSE TRUE 314689.1362 736577.3456 171361.5936 73910.20726 597403.5624 175438.8306 231658.156 754337.1347 103747.6378 3.033217362 7.099702329 1.651715617 0.71240376 5.758237731 1.691015182 2.232900535 7.270884916 1 16.66271896 RPYPDPEDEIPDEMIQCVVCEDWFHGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RPYPDPEDEIPDEMIQCVVCEDWFHGR 27 1 E9PCJ7;Q8N806;H0YJA0;H0YJM2 E9PCJ7 UBR7 Putative E3 ubiquitin-protein ligase UBR7 0 ;;;; 237.13 3.07E-45 249231400 90110.9 104945.7 97846 96685 100187.3 108538 129933.8 98046.5 112364.9 FALSE TRUE 84471.01962 112715.9888 100166.9533 99166.10079 92318.99359 139871.1586 110451.4329 110287.8214 93610.47229 0.902367198 1.204095931 1.070040038 1.059348365 0.986203694 1.494182811 1.179904665 1.178156873 1 16.51438231 RQAVDVSPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RQAVDVSPLR 10 1 M0R0F0;M0R0R2;P46782;M0QZN2 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;; 220.1 9.63E-09 1376330000 739800 1169360 707690 725290 1195040 534400 816490 1060480 1021060 FALSE TRUE 693497.2386 1255940.631 724476.741 743902.1693 1101186.379 688672.6047 694064.9044 1192883.262 850638.4897 0.815266705 1.476468143 0.851685822 0.874522113 1.294540974 0.809594926 0.815934046 1.402338687 1 19.69818661 3.852461616 7.913551744 0.983759421 1.18839755 0.037337844 0.254340738 0.52667672 32.61769602 0.060218289 0.10900488 7119.698722 -3.852461616 0.204638129 RQCEEVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RQCEEVAR 8 1 P51570;P51570-2;K7EII7 P51570 GALK1 Galactokinase 0 ;; 162.97 0.00054297 538349000 162912 208780 210787 197313 243313 147278 218918 184681 236385 FALSE TRUE 152715.6287 224238.2884 215786.9672 202376.3856 224204.1785 189794.7677 186093.2782 207738.8294 196930.8164 0.775478574 1.138665307 1.095750128 1.027652194 1.138492099 0.963763677 0.944967789 1.054882284 1 17.58732936 2.196166606 24.99925592 0.981081541 1.057228101 0.014927331 0.106659341 321.9046156 189821.4463 0.037443666 0.027654202 157.096535 -2.196166606 0.07614656 RQDEDYDEQVEESLQDEDDNDVYILTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RQDEDYDEQVEESLQDEDDNDVYILTK 27 1 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ;; 352.86 4.63E-110 448292000 217371 226596 221241 233106 253290 190721 306445 236568 280755 FALSE TRUE 203766.1371 243373.4036 226488.941 239087.8946 233397.6251 245779.0566 260496.4171 266104.0356 233895.1768 0.871185716 1.040523396 0.968335235 1.022201047 0.997872758 1.050808572 1.113731462 1.137706383 1 17.83550259 2.120222846 2.466788973 1.095373224 0.986909173 0.411525212 0.056985723 0.259868473 3.128677441 0.02463097 0.015391743 131.8933338 -2.120222846 -0.108464052 RQDLEDSLQAQQYFADANEAESWMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RQDLEDSLQAQQYFADANEAESWMR 25 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 205.65 6.63E-25 515206000 113176 96391 105318 100232 121087 79164 113029 88181 130575 FALSE TRUE 106092.5162 103527.8899 107816.1927 102804.1228 111577.3155 102017.3617 96081.35076 99190.59196 108781.189 0.975283661 0.951707652 0.991129015 0.94505423 1.025704136 0.93782172 0.883253361 0.911835887 1 16.73106957 2.009945542 24.82627455 0.916677805 0.975155264 0.231838445 0.037042699 185.3912103 462775.4194 0.012355154 0.009113718 102.3164685 -2.009945542 0.058477459 RQDLLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 RQDLLSR 7 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;;;; 125.5 0.0064834 4533860000 1590022 3525720 2321950 2588170 3375760 2183920 2246220 2869260 2700620 FALSE TRUE 1490505.361 3786767.977 2377027.751 2654586.824 3110641.427 2814382.251 1909420.164 3227493.427 2249869.075 0.662485376 1.683105928 1.056518255 1.179885022 1.382587752 1.250909345 0.848680568 1.434524996 1 21.10140962 RQDSDLVQCGVTS(ph)PSSAEATGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQDSDLVQCGVTSPSSAEATGK 22 1 Q9HC52 Q9HC52 CBX8 Chromobox protein homolog 8 1 RQDSDLVQCGVT(0.004)S(0.993)PS(0.001)S(0.002)AEATGK 162.07 1.02E-11 281860000 520850 401630 460600 467380 493040 400780 571280 419670 674390 TRUE FALSE 488250.9282 431367.1031 471525.6495 479373.7621 454318.6272 516478.6799 485621.8675 472066.7233 561829.9523 0.869036843 0.767789438 0.839267553 0.853236393 0.808640809 0.919279362 0.864357383 0.84023061 1 19.09977401 -5 0.138927937 1.562556854 0.780893135 0.625887279 0.038234722 80.51444621 0.688059603 12.46378838 0.22300846 1.00E-05 5 -0.781663719 RQEAIAQNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RQEAIAQNR 9 1 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;; 212.21 6.24E-06 212901000 73132 108103 67189 68430 98777 56996 76846 86630 87283 FALSE TRUE 68554.79866 116107.0586 68782.75481 70186.02965 91019.45287 73449.81995 65323.6557 97445.9462 72714.90343 0.942788829 1.596743626 0.945923759 0.965222071 1.251730369 1.010106821 0.898353056 1.340109683 1 16.14996346 3.817631532 6.606670135 1.047039753 1.307714354 0.14386356 0.207472577 0.302692881 18.42916372 0.048417207 0.087932838 6571.000974 -3.817631532 0.260674602 RQEELDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RQEELDR 7 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ; 157.68 0.0023406 389730000 350800 432430 408140 419120 436810 340030 419220 400550 500210 FALSE TRUE 328844.0542 464447.5671 417821.2735 429875.3288 402504.7046 438191.1411 356361.8528 450559.5492 416721.7195 0.789121466 1.114526902 1.002638581 1.031564492 0.965883672 1.051519805 0.855155458 1.081200063 1 18.66872477 RQEELQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQEELQR 7 1 Q9NYJ1;Q9NYJ1-2 Q9NYJ1 COA4 "Cytochrome c oxidase assembly factor 4 homolog, mitochondrial" 0 167.24 0.0017534 172900000 88110 99652 76625 84618 115470 70231 81062 94409 131030 FALSE TRUE 82595.35238 107030.3378 78442.58118 86789.44114 106401.452 90505.54959 68907.50564 106196.1715 109160.2465 0.756643146 0.980488238 0.718600257 0.79506454 0.974727113 0.82910723 0.631250916 0.972846571 1 16.73608803 1.995044656 24.95584237 0.802840057 0.848863919 0 0.132812007 1003.254939 5052549.346 0.048140746 0.034564195 98.86547479 -1.995044656 0.046023862 RQEENDKLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQEENDKLR 9 2 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 121.9 0.000338 80778000 381230 394280 335600 338150 467660 267750 369220 372100 676230 FALSE TRUE 357369.4948 423472.9014 343560.5905 346827.5015 430931.87 345045.0784 313858.8887 418557.5041 563362.8444 0.634350487 0.751687666 0.609838923 0.61563787 0.764927745 0.612473971 0.557116771 0.742962565 1 19.10370489 0.978369035 20.78862547 1.000000003 0.651697308 0.749531846 0.063819599 90.0146275 86510.18099 0.062603119 0.01565078 9.514128992 -0.978369035 -0.348302694 RQEIEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQEIEQK 7 1 Q9H307 Q9H307 PNN Pinin 0 124.08 0.0067043 330370000 306450 285860 303690 273360 345160 279970 327170 281040 371430 FALSE TRUE 287269.8415 307025.3718 310893.6702 280374.8804 318052.5259 360792.7941 278113.8958 316128.4626 309435.9335 0.928366135 0.99220982 1.004710948 0.90608378 1.027846127 1.165969285 0.898776986 1.021628158 1 18.23928121 RQEQIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RQEQIAK 7 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ;;;;;; 143.89 0.0038344 4663490000 3624600 4103257 3606488 3607649 4186797 2721418 4058759 3731631 4554904 FALSE TRUE 3397742.756 4407066.418 3692035.598 3700227.381 3857982.852 3507047.198 3450185.768 4197533.345 3794661.097 0.895400846 1.161386038 0.972955293 0.975114058 1.016687065 0.924205643 0.909221056 1.106168176 1 21.85553961 3.7218852 24.16871109 0.975546766 1.053325873 0.010885059 0.083673748 262.5373169 1211835.834 0.020433926 0.032743401 5270.905135 -3.7218852 0.077779107 RQEQIQAMPLADSQAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RQEQIQAMPLADSQAVR 17 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 133.95 2.98E-05 651880000 238570 326400 256170 318600 296780 239670 302080 276410 286240 FALSE TRUE 223638.3296 350566.9956 262246.4734 326775.8154 273472.096 308858.8383 256785.9084 310920.397 238464.6948 0.937825743 1.4701002 1.099728719 1.370332055 1.146803287 1.295197339 1.076829879 1.303842471 1 17.86341616 -1.677605054 0.333439624 0.815373098 1.238494301 0.133940553 0.157415321 46.62721249 2.822506565 7.121857235 0.120707963 0.021008495 1.677605054 0.423121203 RQEQPSIES(ph)TSPISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQEQPSIESTSPISR 15 1 Q5T5P2;Q5T5P2-3 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 RQEQPSIES(0.452)T(0.096)S(0.452)PISR 106.75 0.00074228 1222000000 1341200 595370 771390 807090 760260 556380 938430 547210 668320 TRUE FALSE 1257256.686 639451.8143 789687.7351 827801.2958 700552.2463 716997.8739 797721.1335 615530.3731 556773.0745 2.258113303 1.148496297 1.418329605 1.486783995 1.258236575 1.287773973 1.432758102 1.105531861 1 19.08672992 4.74416459 24.85384254 1.300714389 2.258113748 0.797330703 0.156190189 237.1298187 1051646.275 0.033680882 0.297693086 55483.59464 -4.74416459 0.957399359 RQEQTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RQEQTLR 7 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;; 183.26 0.0010347 6353090000 1868180 2588510 1848420 1897910 2433380 1574730 2187780 2127590 2174180 FALSE TRUE 1751253.949 2780165.974 1892265.395 1946613.584 2242272.151 2029328.987 1859742.699 2393224.295 1811295.312 0.966851698 1.534904858 1.044702861 1.074708012 1.237938472 1.120374449 1.026747371 1.321277805 1 20.78859035 3.743657715 23.56299337 1.116820143 1.290958725 0.088524438 0.166591548 336.2825225 479167.1363 0.038240356 0.068634486 5541.887626 -3.743657715 0.174138582 RQEVS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQEVSSPR 8 1 E7EV32;E7EMT6;E7ENY2;E7EVA2;E7EW82;H7C3L4;E7EQA9;Q92844 E7EV32 TANK TRAF family member-associated NF-kappa-B activator 1 RQEVS(0.836)S(0.164)PR 63.624 0.044182 178110000 235090 251590 248020 231270 267990 209950 254200 220070 279100 TRUE FALSE 220376.1365 270217.9854 253903.1515 237204.7797 246943.1464 270559.1567 216085.0699 247546.2239 232516.4069 0.947787468 1.162145884 1.091979507 1.020163621 1.062046114 1.163613185 0.929332569 1.064639813 1 17.82697299 1.733417165 24.99999999 0.9957626 1.084146487 0.199756373 0.0705622 0.731113397 3523.212718 0.03037569 0.016844888 54.1273998 -1.733417165 0.088383887 RQGLEQFINK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQGLEQFINK 10 1 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 0 93.821 0.013669 91615000 246490 292690 217310 213440 315820 119240 192050 263310 343160 FALSE TRUE 231062.6309 314361.0721 222464.6958 218917.2318 291016.7712 153662.6523 163253.8854 296184.8331 285884.3791 0.808238042 1.099609126 0.778163174 0.765754437 1.017952684 0.537499295 0.571048638 1.036030139 1 18.12507227 3.757078142 4.735810654 0.773880497 0.96783497 0.052138768 0.18837983 0.344299604 19.07509637 0.048320244 0.086131203 5715.814707 -3.757078142 0.193954473 RQGSVVS(ph)SR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQGSVVSSR 9 1 Q9BZ67-2;Q9BZ67-3;Q9BZ67 Q9BZ67-2 FRMD8 FERM domain-containing protein 8 1 RQGS(0.417)VVS(0.506)S(0.077)R 125.3 0.00064842 0 175220 234540 170980 199600 207000 125440 222620 180550 270090 TRUE FALSE 164253.293 251905.5856 175035.7263 204722.0739 190743.055 161652.4917 189240.1977 203092.0649 225010.2342 0.729981432 1.119529459 0.777901179 0.9098345 0.847708353 0.718422841 0.841029291 0.902590345 1 17.7796311 RQIQAAYSILSEVQQAVSQGSSDSQILDLSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RQIQAAYSILSEVQQAVSQGSSDSQILDLSNR 32 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 216.83 1.36E-35 213340000 130578 163095 140281 142693 176888 138094 181833 143854 178527 FALSE TRUE 122405.3561 175170.7235 143608.5316 146354.744 162995.93 177959.496 154568.8297 161814.4886 148729.6904 0.823005519 1.177779118 0.96556734 0.984031793 1.09592059 1.196529728 1.039260079 1.087977042 1 17.18233315 2.724337166 23.04173911 1.091778188 1.015621706 0.161645838 0.099490518 594.9710687 963839.3849 0.03028871 0.028711298 530.0748092 -2.724337166 -0.076156481 RQLEEAEEEAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RQLEEAEEEAQR 12 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 234.52 8.09E-16 1760600000 851003 1121193 1085458 1158564 1154428 996962 1108329 1024944 1059370 FALSE TRUE 797740.2413 1204207.296 1111205.576 1188294.714 1063763.882 1284768.745 942145.3557 1152910.515 882554.3032 0.903899328 1.364456886 1.259078985 1.34642674 1.205323998 1.45573903 1.067521117 1.306333798 1 19.75132552 0.034177054 0.784393356 0.994187865 1.25725988 0.16913416 0.158645625 7.664156198 4.903072291 0.278217857 0.047752802 1.081874923 -0.034177054 0.263072014 RQLHLEGASLELS(ph)DDDTESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQLHLEGASLELSDDDTESK 20 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 1 RQLHLEGAS(0.084)LELS(0.914)DDDT(0.003)ESK 79.36 0.0036042 94733000 84292 80150 74795 83088 102120 72105 96774 84380 105850 TRUE FALSE 79016.31419 86084.3894 76569.17272 85220.17875 94099.90713 92920.54297 82263.63711 94915.02874 88182.95118 0.896049782 0.976202182 0.86829905 0.966401981 1.067098638 1.053724577 0.93287462 1.076342167 1 16.42821214 2.998479189 24.30048156 1.016819707 0.920097404 0.525470541 0.048501601 35.22678403 562901.2345 0.013847111 0.016325027 996.504328 -2.998479189 -0.096722303 RQLS(ph)PQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RQLSPQSK 8 1 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RQLS(0.963)PQS(0.037)K;RQLS(1)PQSK 103.21 0.0029498 574175000 657870 576750 614000 579010 675220 474590 700280 574580 944440 TRUE FALSE 616695.091 619453.1701 628564.37 593868.3769 622190.9449 611596.4287 595279.5151 646317.5778 786806.8627 0.783794754 0.787300162 0.798880132 0.754782914 0.790779764 0.777314558 0.756576415 0.821443747 1 19.58565002 0.863941733 4.63756137 0.999990675 0.78005655 0.961024112 0.01393768 0.203748121 6.73472739 0.013950167 0.003537234 7.310409966 -0.863941733 -0.219934125 RQPQT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQPQTPK 7 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 RQPQT(1)PK 71.349 0.03197 48043000 167740 110070 132320 121160 130750 100440 167100 110760 176010 TRUE FALSE 157241.4528 118219.6973 135458.6929 124269.1707 120481.4224 129435.3975 142044.9063 124588.6298 146632.7939 1.072348474 0.80622959 0.923795348 0.847485528 0.821654005 0.882717938 0.968711722 0.849664161 1 17.16184827 -0.88863571 4.988685259 1.000000308 0.892302524 0.144192331 0.078574047 2.43E-07 5.42E-08 0.068866297 0.016231896 0.129230281 0.88863571 -0.107697784 RQQEELLAEENQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQQEELLAEENQR 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 0 117.48 0.00080683 290810000 354470 328040 364580 336420 394330 312070 445600 337390 418700 FALSE TRUE 332284.3554 352328.4229 373228.0098 345053.1068 363360.9125 402159.543 378786.4167 379513.8842 348816.2651 0.95260568 1.01006879 1.069984537 0.989211632 1.041697159 1.152926578 1.085919593 1.088005125 1 18.41210779 2.464931685 24.85847736 1.091652511 1.01683403 0.349369392 0.047093154 216.679302 441875.995 0.015236383 0.012756729 291.6968136 -2.464931685 -0.074818481 RQQEGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RQQEGFK 7 1 Q15233;Q15233-2;H7C367;Q8WXF1;Q8WXF1-2;A0A0U1RQF9 Q15233;Q8WXF1 NONO;PSPC1 Non-POU domain-containing octamer-binding protein;Paraspeckle component 1 0 ;;; 141.52 0.004091 1300620000 1050650 1503560 884530 866920 1804610 636938 1153090 1478630 1989460 FALSE TRUE 984891.692 1614885.147 905511.4693 889166.6349 1662883.21 820811.6608 980194.8593 1663240.21 1657406.274 0.594236735 0.974344777 0.546342489 0.536480795 1.003304523 0.495238659 0.591402889 1.00351992 1 20.66049586 1.227962168 24.8717276 1.001760309 0.686120692 0.368652559 0.17621485 244.3419351 573384.9384 0.156370298 0.04075992 16.90293682 -1.227962168 -0.315639617 RQQELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQQELK 6 1 P35221-2;P35221;G3XAM7;P26232;P26232-5;P26232-2;P26232-3;E5RIB1;E5RJ41 P35221-2;REV__E7EW15 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 0 100.07 0.061064 85886000 87762 89102 83430 87256 92112 61080 95374 101100 119570 FALSE TRUE 82269.13308 95699.20479 85408.999 89495.13668 84877.89508 78712.80445 81073.55411 113722.5575 99612.99455 0.825887561 0.960710048 0.857408206 0.898428333 0.852076533 0.790186108 0.813885322 1.141643799 1 16.60404633 1.242246787 24.99994518 1.07082193 0.862709776 0.702391921 0.057785006 50.36015401 341566.5109 0.043390824 0.014453774 17.46814494 -1.242246787 -0.208112155 RQQEQQVPILEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 ;;;;;; 173.06 5.47E-05 17463550000 9657500 9639660 10184320 10351810 11517010 8812610 13926980 10294070 14282090 FALSE TRUE 9053054.314 10353390.46 10425896.88 10617454.97 10612510.49 11356667.45 11838758.64 11579307.3 11898316.91 0.760868481 0.870155883 0.876249721 0.892349317 0.891933756 0.954476799 0.994994395 0.973188677 1 23.50425417 4.948665046 0.232269886 1.024919619 0.578538538 0.86963601 0.026046013 4.350498652 0.189616973 0.044053384 0.57172991 88851.55775 -4.948665046 -0.446381081 RQQVLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RQQVLDR 7 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3;A0A0D9SFF6 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 128.61 0.016145 0 168339 351640 159399 157129 374650 102537 157196 304810 353680 FALSE TRUE 157802.9625 377675.7915 163180.0196 161161.1962 345226.5003 132137.7674 133625.9191 342866.1995 294648.5231 0.535563392 1.281784098 0.553812447 0.546960814 1.171655288 0.44845895 0.45350955 1.163644724 1 18.16863551 5.014697545 17.2989655 0.789636602 0.079328905 0.065571338 0.319055973 25893439.85 600484935.5 0.074644966 461295625.9 103442.1516 -5.014697545 -0.710307697 RQS(ph)FASLALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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;RQS(1)FASLALR 208.23 7.20E-08 994660000 245359 654350 240283 249388 665320 182743 238514 490373 651000 TRUE FALSE 230002.4182 702798.7549 245982.6262 255787.7183 613068.451 235497.9375 202751.04 551597.1485 542343.8944 0.424089624 1.295854461 0.453554707 0.471633812 1.130405371 0.434222529 0.37384221 1.017061599 1 19.04884841 3.890406092 9.010185937 0.647851306 0.915730774 0.016445836 0.34463042 0.681381692 64.81446434 0.081895386 0.148012551 7769.732949 -3.890406092 0.267879468 RQS(ph)FAVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 165.66 0.00019782 2356600000 686170 1235755 617043 801628 954387 378044 1268456 700942 1904521 TRUE FALSE 643223.8445 1327251.586 631679.5513 822199.1316 879433.2948 487179.1658 1078262.799 788456.1517 1586644.141 0.405398935 0.836514976 0.398123016 0.518200087 0.55427255 0.307050052 0.679587042 0.496933201 1 20.59754716 -1.534369551 2.861425263 1.021281678 0.542338022 0.494211841 0.150212722 26312128.72 28762699.45 4347107.752 0.033600308 0.029216652 1.534369551 -0.478943656 RQS(ph)GLYDSQNPPTVNNCAQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQSGLYDSQNPPTVNNCAQDR 21 1 Q96RU3-5;Q96RU3-2;Q96RU3;H0Y7W6;Q96RU3-3;B7ZL14;Q96RU3-4 Q96RU3-5 FNBP1 Formin-binding protein 1 1 RQS(1)GLYDSQNPPTVNNCAQDR 293.46 5.27E-55 508750000 242380 275430 269500 272400 313190 223800 281810 234360 340600 TRUE FALSE 227209.8685 295823.1238 275892.6673 279390.2452 288593.3207 288407.4269 239555.2067 263620.3619 283751.6596 0.800734941 1.042542356 0.972303273 0.984629466 1.017063023 1.016407894 0.844242487 0.92905311 1 18.11426931 -0.40740714 5.483157383 0.999999999 0.958399363 0.030647894 0.077113812 4859230.818 886210.3051 0.072708636 0.017634434 0.391374801 0.40740714 -0.041600635 RQS(ph)HLLLQSSIPDQQLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RQSHLLLQSSIPDQQLLK 18 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 1 RQS(0.809)HLLLQS(0.095)S(0.095)IPDQQLLK;RQS(0.971)HLLLQS(0.013)S(0.016)IPDQQLLK 69.605 0.012489 209518000 349190 357370 334500 336630 449990 280750 374490 299580 421340 TRUE FALSE 327334.8212 383830.0466 342434.498 345268.4957 414649.6006 361797.9674 318338.7011 336983.2225 351015.632 0.932536307 1.093484197 0.975553413 0.983627121 1.181285284 1.030717536 0.906907477 0.960023406 1 18.42117576 1.758911987 25 0.947649993 1.037063001 0.201304434 0.071602229 12.66720423 15574.43259 0.031337093 0.017378525 57.40001251 -1.758911987 0.089413008 RQS(ph)ILFSTEV ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQSILFSTEV 10 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 RQS(1)ILFSTEV 75.115 0.04233 47784000 87868 99757 72836 80139 107990 51711 86039 91575 111720 TRUE FALSE 82368.49873 107143.1121 74563.70432 82195.50242 99508.90101 66639.12624 73138.2507 103008.3403 93073.21026 0.884986115 1.151170265 0.801129607 0.883127402 1.069146543 0.715986115 0.785814205 1.106745325 1 16.50607835 3.967676968 23.30104399 0.887639822 1.029473666 0.079009929 0.140079845 241.2508839 595221.6958 0.033791387 0.062093506 9282.756706 -3.967676968 0.141833845 RQS(ph)IPEEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RQSIPEEFK 9 1 F5H4N6;Q9Y3R0-3;Q9Y3R0-2;Q9Y3R0;F5H3G9 F5H4N6 GRIP1 Glutamate receptor-interacting protein 1 1 RQS(1)IPEEFK;RQS(1)IPEEFK 82.529 0.011144 542260000 688890 481120 558710 528120 595490 422060 645590 494630 670090 TRUE FALSE 645773.6046 516742.6254 571962.865 541672.4533 548722.6175 543901.8704 548789.7729 556385.6443 558247.6501 1.156786965 0.925651233 1.024568334 0.970308524 0.982937622 0.974302123 0.983057918 0.996664552 1 19.09054575 4.75002943 24.97844677 0.981465368 1.156787069 0.825479593 0.025228126 658.7721135 1434742.387 0.005566891 0.08879509 56237.9434 -4.75002943 0.175321701 RQS(ph)LATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RQSLATK 7 1 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 1 RQS(1)LATK;RQS(1)LATK;RQS(1)LATK;RQS(1)LATK;RQS(1)LATK;RQS(1)LATK 135.56 0.0018777 4505610000 3371790 2803660 3181890 2806870 3726930 2274370 3863800 3199330 5316440 TRUE FALSE 3160755.683 3011245.904 3257365.933 2878899.036 3434231.952 2930943.698 3284459.06 3598773.393 4429091.818 0.713635168 0.679878862 0.735447822 0.649997596 0.775380618 0.661748236 0.741564906 0.812530772 1 22.07857948 0.877998442 1.600320474 0.999560143 0.703869406 0.869891918 0.036334083 0.152720269 0.764703225 0.029492107 0.008533349 7.550895193 -0.877998442 -0.295690737 RQS(ph)LELQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RQSLELQK 8 1 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 RQS(1)LELQK;RQS(1)LELQK 152.55 0.00027888 2544800000 3098000 2187200 2428500 1968160 2168200 1858220 3115100 1965420 3308800 TRUE FALSE 2904101.71 2349142.564 2486105.167 2018666.318 1997918.318 2394657.948 2648019.674 2210807.013 2756539.904 1.053531533 0.852206986 0.901893407 0.732318917 0.72479209 0.868718768 0.960631722 0.802022496 1 21.39442706 -0.391354647 7.63976198 0.999999997 0.864233819 0.161873646 0.098559046 0 0 0.092913043 0.021899814 0.406111561 0.391354647 -0.135766178 RQS(ph)LTSPDSQSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQSLTSPDSQSAR 13 1 Q15751 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 RQS(0.998)LT(0.002)SPDSQSAR 85.636 0.0056317 397270000 144450 165550 141990 158680 156890 134390 176620 137410 174950 TRUE FALSE 135409.1324 177807.4943 145358.0699 162751.9974 144568.4923 173186.2114 150137.4707 154565.941 145749.7148 0.929052469 1.21995089 0.997312894 1.116653969 0.991895541 1.188243913 1.03010473 1.060488806 1 17.15313353 0.9460806 1.618760993 1.001780493 1.079687125 0.043564234 0.089541087 1.191326237 6.374802216 0.074591149 0.021625402 8.832438049 -0.9460806 0.077906632 RQS(ph)LTSPDSQSARPANR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RQSLTSPDSQSARPANR 17 2 Q15751 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 RQS(0.983)LT(0.017)S(0.001)PDSQSARPANR;RQS(0.999)LT(0.001)SPDSQSARPANR;RQS(0.999)LT(0.001)SPDSQSARPANR;RQS(0.983)LT(0.015)S(0.002)PDSQSARPANR 136.14 5.89E-06 397295000 191699 220915 219655 244193 233670 186467 250340 218449 289808 TRUE FALSE 179700.9018 237271.7765 224865.3203 250459.4058 215318.5008 240296.9959 212803.841 245722.8385 241437.1726 0.744296745 0.982747495 0.931361637 1.037368866 0.891820006 0.995277543 0.881404627 1.017750647 1 17.88128829 4.742468261 24.94694311 0.958776152 0.74429666 0.640411569 0.052155989 228.3437279 1457719.775 0.010923111 0.083124813 55267.3016 -4.742468261 -0.214479492 RQS(ph)MLF ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RQSMLF 6 1 Q00537 Q00537 CDK17 Cyclin-dependent kinase 17 1 RQS(1)MLF;RQS(1)MLF 99.305 0.041258 115650000 168706 222390 199219 177923 259240 146635 230240 217190 401980 TRUE FALSE 158146.9926 238855.987 203944.5688 182488.8054 238880.3361 188966.1441 195717.6494 244306.6496 334886.9411 0.472239951 0.713243658 0.608995287 0.54492661 0.713316367 0.564268477 0.584429028 0.729519786 1 18.35331459 0.898420519 3.383841007 0.999773021 0.611655854 0.751121418 0.072879756 0.19942274 4.965125116 0.064326219 0.016665973 7.914445971 -0.898420519 -0.388117167 RQS(ph)NLQEVLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQSNLQEVLER 11 1 A6NF31;O75665-3;O75665 A6NF31 OFD1 Oral-facial-digital syndrome 1 protein 1 RQS(1)NLQEVLER 112.03 0.00039219 0 33830 36468 38701 31240 42857 34871 39619 39026 52775 TRUE FALSE 31712.64069 39168.12866 39619.006 32041.67129 39491.1841 44937.69162 33678.49875 43898.48201 43966.51156 0.721290809 0.890862779 0.901117796 0.728774473 0.89821054 1.022089086 0.766003432 0.998452696 1 15.42411745 -4.999999988 0.030691259 1.814516708 0.326236736 0.298287717 0.092846326 2116.547203 4.888550723 186.6645971 74.13553865 1.00E-05 4.999999988 -1.488279973 RQS(ph)PEPSPVTLGR ddPTM_SK-BR-3_Pertuzumab_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 148.41 2.55E-05 3940990000 2116660 2256850 2357570 2179920 2238490 1969770 2454250 1900790 2186170 TRUE FALSE 1984182.029 2423949.522 2413492.674 2235860.438 2062688.025 2538410.622 2086257.997 2138107.816 1821284.104 1.089441249 1.330901377 1.325159907 1.227628591 1.132545999 1.39374775 1.145487402 1.173956227 1 20.79652456 0.921683639 1.081089285 1.001756218 1.262611688 0.374811283 0.095570301 0.568294381 1.355666645 0.084593972 0.027143458 8.349945464 -0.921683639 0.26085547 RQS(ph)PLPPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 15 RQSPLPPQK 9 1 Q01105;B2REB7 Q01105 SET Protein SET 1 RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK 117.14 0.0012718 28543830000 12396030 11574420 11249230 11629110 12979590 8886130 14206880 10857210 13833670 TRUE FALSE 11620184.61 12431402.1 11516067.05 11927532.65 11960225.36 11451411.48 12076690.23 12212756.57 11524741.11 1.008281618 1.078670834 0.999247353 1.03495016 1.037786901 0.993637199 1.04789254 1.059698995 1 23.45823101 -0.266779236 7.489544924 1 1.033254877 0.128450565 0.026560854 0 0 0.023801204 0.005609998 0.541029274 0.266779236 0.033254877 RQS(ph)PLPPQKK ddPTM_SK-BR-3_Pertuzumab_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 0.014046 8987410000 12692200 10444210 11138250 11050680 11855930 8059990 14027100 10901010 13281820 TRUE FALSE 11897817.86 11217510.18 11402454.55 11334259.16 10924813.08 10386778.27 11923866.58 12262025.09 11064998.44 1.075266113 1.013783259 1.030497619 1.024334456 0.987330739 0.938705805 1.077620267 1.108181367 1 23.39949991 -0.934629089 4.374568696 0.999999385 1.028160447 0.036422083 0.048263821 2.81E-07 6.86E-08 0.0454079 0.010702511 0.116244098 0.934629089 0.028161062 RQS(ph)PS(ph)PSTRPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQSPSPSTRPIR 12 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RQS(1)PS(0.992)PS(0.007)T(0.001)RPIR 68.481 0.028186 791410000 0 45100 40620 46522 38573 38004 50095 55766 42039 TRUE FALSE 0 48439.25093 41583.52558 47715.83328 35543.63218 48975.13786 42583.71981 62728.50786 35022.41932 0 1.383092655 1.187340178 1.362436811 1.014882263 1.398393909 1.215898862 1.791095792 1 15.09599113 4.741036183 24.99999908 1.291243672 3.87E-07 0.766886853 0.224229385 96.50964507 974564.7126 0.046616573 0.315321309 55085.35888 -4.741036183 -1.291243285 RQS(ph)PSPS(ph)TRPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RQSPSPSTRPIR 12 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RQS(1)PS(0.021)PS(0.724)T(0.256)RPIR;RQS(0.994)PS(0.049)PS(0.936)T(0.022)RPIR 96.208 0.027613 13593700000 3790700 4487600 3955300 4012500 4442200 3869800 4643400 3650700 4604400 TRUE FALSE 3553446.854 4819866.573 4049121.584 4115467.543 4093327.531 4986948.439 3947165.277 4106497.931 3835895.894 0.926366865 1.256516523 1.055586933 1.072883013 1.067111216 1.300073979 1.029007404 1.070544677 1 21.87113214 1.593551238 25 1.037310988 1.12289302 0.107702643 0.10571496 1.848842092 3220.232659 0.05172419 0.024119683 39.22394202 -1.593551238 0.085582033 RQS(ph)PSPSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RQSPSPSTR 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RQS(0.998)PS(0.002)PSTR;RQS(1)PSPSTR;RQS(0.999)PS(0.001)PSTR 73.435 0.026907 359769000 75611 77439 88962 89940 92320 67156 87485 66596 84307 TRUE FALSE 70878.64248 83172.66414 91072.22065 92248.01267 85069.5596 86542.84701 74367.43642 74910.6572 70235.61706 1.009155261 1.184194966 1.296667196 1.313407877 1.211202566 1.232178923 1.058827978 1.066562242 1 16.0999152 1.68732632 4.396074385 1.042127096 1.219807214 0.462395806 0.083755889 0.150894983 6.821160478 0.046156849 0.022116736 48.67728197 -1.68732632 0.177680118 RQS(ph)PSPSTRPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQSPSPSTRPIR 12 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RQS(0.837)PS(0.161)PS(0.001)T(0.001)RPIR 57.328 0.089774 43770000 42253 54416 49947 49227 58366 49162 53353 46514 59133 TRUE FALSE 39608.46015 58445.01726 51131.76643 50490.24816 53782.1698 63354.27132 45353.21295 52321.37529 49263.32029 0.804015237 1.186379987 1.037927735 1.024905505 1.09172848 1.28603332 0.920628425 1.062075698 1 15.58822625 RQS(ph)S(ph)TPSAPELGQQPDVNISEWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RQSSTPSAPELGQQPDVNISEWK 23 1 Q93100-4;Q93100-2;I3L213;Q93100-3;Q93100 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 2 RQS(0.981)S(0.956)T(0.061)PS(0.002)APELGQQPDVNISEWK;RQS(0.931)S(0.825)T(0.185)PS(0.059)APELGQQPDVNISEWK 136.66 3.68E-05 174257000 121265 116450 124783 115511 133972 93044 155178 117992 188665 TRUE FALSE 113675.2401 125072.0792 127742.9117 118475.2078 123450.3795 119904.2924 131910.4995 132723.5609 157175.5927 0.723237229 0.795747463 0.81274013 0.753776116 0.785429706 0.762868397 0.83925562 0.84442857 1 17.26201768 0.731332233 0.919534683 0.999963358 0.778736194 0.868324984 0.027524506 0.329149271 0.513174493 0.025839257 0.008613732 5.386817139 -0.731332233 -0.221227164 RQS(ph)SGS(ph)ATNVASTPDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQSSGSATNVASTPDNR 17 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 2 RQS(0.995)S(0.102)GS(0.884)AT(0.019)NVASTPDNR 166.29 1.58E-09 166490000 132740 153730 148660 162880 183260 123850 166300 150860 271260 TRUE FALSE 124432.0403 165112.3292 152186.2854 167059.7766 168867.4988 159603.4845 141364.8589 169695.2031 225984.9536 0.550620908 0.730634171 0.673435479 0.739251768 0.747251072 0.706257129 0.625549872 0.750913724 1 17.78586719 0.951412605 12.29823341 0.999999994 0.687991268 0.740118305 0.058947104 4.259291169 1078.487455 0.052715612 0.01318088 8.941545789 -0.951412605 -0.312008726 RQS(ph)SGSATNVASTPDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RQSSGSATNVASTPDNR 17 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 RQS(0.809)S(0.103)GS(0.088)AT(0.001)NVASTPDNR;RQS(0.616)S(0.267)GS(0.117)ATNVASTPDNR;RQS(0.632)S(0.338)GS(0.03)ATNVASTPDNR 225.15 2.64E-15 2660970000 703430 983470 899370 1073880 1153910 774040 1066400 1016360 1210400 TRUE FALSE 659403.572 1056287.142 920703.4811 1101437.579 1063286.563 997492.7825 906503.22 1143254.783 1008376.421 0.653926013 1.047512735 0.913055346 1.092288114 1.054454013 0.989206771 0.898973044 1.13375795 1 19.94360286 4.743026409 24.9766224 1.002938835 0.653925871 0.702403508 0.073652881 261.6238024 1463176.923 0.016858551 0.135621485 55338.37583 -4.743026409 -0.349012964 RQS(ph)SPSCGPVAETSSIGNGDGISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RQSSPSCGPVAETSSIGNGDGISK 24 1 Q9Y4K4 Q9Y4K4 MAP4K5 Mitogen-activated protein kinase kinase kinase kinase 5 1 RQS(0.764)S(0.236)PSCGPVAETSSIGNGDGISK;RQS(0.982)S(0.018)PSCGPVAETSSIGNGDGISK;RQS(0.997)S(0.003)PSCGPVAETSSIGNGDGISK 304.33 1.03E-62 1161510000 533360 481610 521020 446250 602840 407930 654920 525760 910950 TRUE FALSE 499977.9497 517268.9055 533378.8404 457701.5305 555495.3781 525692.7688 556720.826 591402.2933 758906.56 0.658813583 0.681597621 0.702825445 0.603106568 0.731968081 0.692697621 0.733582835 0.779282094 1 19.53356274 0.544149544 0.703168749 1.005204989 0.673653691 0.911662984 0.031480247 0.38647693 0.326031791 0.031721761 0.010706669 3.500656867 -0.544149544 -0.331551297 RQS(ph)SSYDDPWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RQSSSYDDPWK 11 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;H0YCF0;H7C1V2;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 RQS(0.985)S(0.012)S(0.003)YDDPWK;RQS(0.9)S(0.097)S(0.003)YDDPWK 164.92 2.35E-05 208650000 745200 505460 564210 512100 524330 394090 866530 550080 914050 TRUE FALSE 698559.2622 542884.7843 577593.3276 525241.353 483151.2368 507857.3855 736601.871 618758.6989 761489.15 0.917359443 0.712925173 0.758505 0.689755531 0.634482102 0.666926621 0.967317618 0.812564038 1 19.53846396 1.732913507 9.720934212 0.915006292 0.726129984 0.517260199 0.089190725 0.076937431 28.37884684 0.039951613 0.021589019 54.06466389 -1.732913507 -0.188876308 RQS(ph)STPSAPELGQQPDVNISEWK ddPTM_SK-BR-3_Pertuzumab_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(0.446)S(0.446)T(0.094)PS(0.013)APELGQQPDVNISEWK 176.85 3.45E-17 119430000 114140 134840 116830 142100 170480 105850 184400 123030 222140 TRUE FALSE 106996.1811 144823.6939 119601.2628 145746.5266 157091.1885 136407.1767 156750.9319 138390.5663 185063.3989 0.578159602 0.782562596 0.646271837 0.787549172 0.848850661 0.737083494 0.847012066 0.747800846 1 17.49766007 -4.999999917 0.055064309 1.967877573 0.304997251 0.633217613 0.069631982 286.5624268 1.16035239 38.92247523 7.510866624 1.00E-05 4.999999917 -1.662880322 RQS(ph)VS(ph)PPYKEPSAYQSSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RQSVSPPYKEPSAYQSSTR 19 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 RQS(1)VS(0.997)PPY(0.002)KEPS(0.001)AYQSSTR;RQS(0.999)VS(0.975)PPY(0.025)KEPS(0.001)AYQSSTR;RQS(1)VS(0.999)PPY(0.001)KEPSAYQSSTR;RQS(0.837)VS(0.632)PPY(0.099)KEPS(0.35)AY(0.066)QS(0.007)S(0.003)T(0.005)R;RQS(1)VS(0.999)PPY(0.001)KEPSAYQSSTR;RQS(1)VS(0.998)PPY(0.002)KEPSAYQSSTR;RQS(1)VS(1)PPYKEPSAYQSSTR 109.97 0.00013136 5051680000 3503730 2397770 2960830 2739290 2532860 2663080 3768700 2487200 2504220 TRUE FALSE 3284437.794 2575303.386 3031062.286 2809584.819 2333939.393 3431867.965 3203618.422 2797732.395 2086249.504 1.574326459 1.234417734 1.452876216 1.346715632 1.11872496 1.644994023 1.535587386 1.341034421 1 20.99248028 2.229288337 24.99994667 1.444736541 1.344990007 0 0.20671007 640.6352216 1727268.958 0.069760439 0.052204825 169.5463081 -2.229288337 -0.099746534 RQS(ph)VSGLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RQSVSGLHR 9 1 Q8N1G4;J3KRP5 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 RQS(1)VSGLHR;RQS(1)VSGLHR;RQS(0.992)VS(0.008)GLHR;RQS(1)VSGLHR;RQS(0.99)VS(0.01)GLHR;RQS(1)VSGLHR 165.58 3.76E-05 4491260000 700989 932160 782916 756983 971383 568846 951829 723716 1229260 TRUE FALSE 657115.3498 1001178.096 801487.1372 776408.4653 895094.4976 733062.6058 809111.0778 814073.5357 1024088.565 0.641658712 0.977628431 0.782634593 0.758145821 0.874040125 0.71581954 0.790079204 0.794924935 1 19.96590906 -1.097886559 3.557910019 1.00011128 0.804630457 0.34022921 0.089531959 7396015175 11975008333 10303582.91 0.020933645 0.079820316 1.097886559 -0.195480823 RQSHLLLQS(ph)SIPDQQLLK ddPTM_SK-BR-3_Pertuzumab_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(0.277)HLLLQS(0.362)S(0.362)IPDQQLLK 91.957 0.0011399 117770000 273670 254900 239090 235010 309960 185270 266210 200390 313890 TRUE FALSE 256541.4832 273773.0612 244761.3277 241040.7545 285616.9919 238754.4414 226294.2819 225409.1326 261499.7312 0.981039185 1.046934389 0.935990743 0.921762915 1.092226713 0.913019835 0.865370992 0.861986097 1 17.99644994 2.023794164 24.99242224 0.892919011 0.992068639 0.309110455 0.061853987 224.7634523 236081.3373 0.021575895 0.015934136 105.6316744 -2.023794164 0.099149628 RQSS(ph)TPSAPELGQQPDVNISEWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RQSSTPSAPELGQQPDVNISEWK 23 1 Q93100-4;Q93100-2;I3L213;Q93100-3;Q93100 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 1 RQS(0.055)S(0.472)T(0.472)PS(0.002)APELGQQPDVNISEWK;RQS(0.094)S(0.799)T(0.106)PSAPELGQQPDVNISEWK 251.13 7.66E-39 902820000 551770 566720 562790 585360 718050 424730 727630 567110 996900 TRUE FALSE 517235.7006 608680.5385 576139.6446 600381.3286 661657.2495 547342.6561 618528.6365 637914.9319 830510.9498 0.622792151 0.732898872 0.693717096 0.722905976 0.796686967 0.659043275 0.744756751 0.768099363 1 19.66363966 -4.999999993 0.229745568 2.53056396 0.685332527 0.811751732 0.04426451 63.71287483 0.637731909 45.25394165 0.0705186 1.00E-05 4.999999993 -1.845231432 RQSVS(ph)PPYKEPS(ph)AYQSSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQSVSPPYKEPSAYQSSTR 19 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 RQS(0.237)VS(0.602)PPY(0.24)KEPS(0.525)AY(0.095)QS(0.159)S(0.027)T(0.115)R 101.04 0.0026552 1750400000 1232000 846990 1019400 961680 905730 965120 1334300 890830 918110 TRUE FALSE 1154891.319 909702.0209 1043580.649 986358.3369 834597.6193 1243734.477 1134234.102 1002052.086 764871.5098 1.509915462 1.189352733 1.364386876 1.289573901 1.091160553 1.626069818 1.482908028 1.310092053 1 19.54485789 2.243772186 24.99999507 1.412679607 1.285634648 0 0.192903513 301.6562387 1447055.195 0.061708072 0.05017446 175.2960724 -2.243772186 -0.127044959 RQT(ph)IEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RQTIEER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 RQT(1)IEER;RQT(1)IEER;RQT(1)IEER;RQT(1)IEER 166.66 0.00065354 741870000 685690 780340 572350 601370 598050 551820 618720 481817 971050 TRUE FALSE 642773.8869 838117.1855 585926.4123 616802.1723 551081.5654 711121.476 525948.6799 541972.9131 808975.4818 0.794552989 1.036022975 0.72428204 0.762448537 0.68120923 0.87903959 0.650141681 0.669949739 1 19.62573645 3.833991408 4.68819083 0.749799445 0.924214276 0.196381048 0.120496713 0.246857288 8.817340125 0.027626064 0.051264591 6823.251958 -3.833991408 0.174414831 RQTEPVS(ph)PVLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RQTEPVSPVLKR 12 2 Q8IYH5-2;Q8IYH5;Q8IYH5-4 Q8IYH5-2 ZZZ3 ZZ-type zinc finger-containing protein 3 1 RQTEPVS(1)PVLKR;RQT(0.001)EPVS(0.999)PVLKR 86.578 0.0057564 419460000 383930 365370 375810 385810 431650 300780 429530 337900 505170 TRUE FALSE 359900.5066 392422.375 384724.3907 395710.5378 397749.9502 387610.3032 365125.9641 380087.5588 420853.8635 0.855167406 0.932443323 0.914151975 0.940256398 0.94510229 0.921009255 0.867583729 0.903134299 1 18.68295984 RQTIEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RQTIEER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 121.58 0.0070939 1050180000 864360 1292170 1114980 1091170 1285220 1057790 1187040 1107040 1149570 FALSE TRUE 810261.2505 1387843.611 1141427.852 1119171.27 1184284.006 1363156.801 1009054.372 1245256.381 957699.3405 0.846049711 1.44914333 1.191843623 1.168603989 1.236592692 1.423366127 1.053623334 1.300258159 1 19.86921328 -1.275578832 0.646157006 0.922725445 1.227214156 0.114007445 0.174473276 101.9319852 18.8184707 14.15376865 0.059247244 0.053017735 1.275578832 0.30448871 RQVEEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 176.38 0.00041792 1336368000 693699 1408766 671533 675639 1524006 470408 661867 1245285 1290857 FALSE TRUE 650281.6179 1513072.5 687462.0799 692977.0406 1404316.716 606207.1532 562626.1878 1400761.573 1075404.627 0.604685531 1.406979719 0.639258994 0.644387259 1.305849613 0.563701455 0.523176276 1.302543747 1 20.03644815 3.872274511 8.255110598 0.809706739 1.057260887 0.015585233 0.341798267 0.621033924 43.63617525 0.082025271 0.148407802 7452.028572 -3.872274511 0.247554149 RQVEEEILALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 93.623 0.01461 223700000 274310 296590 279910 300350 331810 241150 393680 289950 376290 FALSE TRUE 257141.4268 318549.8322 286549.5974 308057.4895 305750.9811 310766.0903 334651.3387 326150.8958 313484.7681 0.820267691 1.016157289 0.914078215 0.982687265 0.975329624 0.99132756 1.067520252 1.040404284 1 18.25803582 2.387195285 1.136462827 1.04220923 0.938674885 0.414709389 0.052891125 0.47774188 1.224548159 0.03028628 0.019789368 243.8907253 -2.387195285 -0.103534346 RQVS(ph)ASELHTSGILGPETLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RQVSASELHTSGILGPETLR 20 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 RQVS(0.862)AS(0.138)ELHTSGILGPETLR;RQVS(0.983)AS(0.017)ELHTSGILGPETLR;RQVS(0.849)AS(0.151)ELHTSGILGPETLR;RQVS(0.532)AS(0.467)ELHT(0.001)SGILGPETLR;RQVS(0.716)AS(0.231)ELHT(0.053)SGILGPETLR;RQVS(0.954)AS(0.046)ELHTSGILGPETLR;RQVS(0.819)AS(0.181)ELHTSGILGPETLR 287.26 1.30E-45 13025630000 539913 2102705 1409579 1933278 1485705 1144500 1928258 1390311 2115900 TRUE FALSE 506120.8091 2258391.466 1443014.88 1982889.187 1369023.722 1474898.571 1639133.614 1563894.389 1762742.621 0.287121218 1.281180496 0.818619158 1.124888661 0.776644138 0.836706705 0.929876883 0.887193837 1 20.74939041 4.757275555 24.80142307 0.954848028 0.287120569 0.658342115 0.151627613 2407.581702 3190519.658 0.034917787 1.232847144 57184.13491 -4.757275555 -0.667727458 RQWTSLS(ph)LR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RQWTSLSLR 9 1 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 RQWT(0.001)S(0.013)LS(0.987)LR;RQWTSLS(1)LR 145.01 6.01E-05 220452000 93014 244210 55417 71691 193491 40345 72314 194881 307100 TRUE FALSE 87192.41977 262291.5625 56731.51741 73530.71243 178294.9974 51991.94655 61471.18703 219212.3218 255843.0261 0.340804364 1.025205051 0.221743458 0.287405577 0.696892153 0.20321815 0.240269152 0.856823519 1 17.96489938 1.088376607 5.737898685 0.99495419 0.4525446 0.398622001 0.255901116 0.207554406 9.709697896 0.252308349 0.063582831 12.25678609 -1.088376607 -0.54240959 RQYEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQYEEK 6 1 Q32MZ4-2;Q32MZ4;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 104.45 0.054232 348500000 523390 425450 446240 468520 488860 360080 603010 406890 557940 FALSE TRUE 490631.9542 456950.7607 456825.0235 480543.0164 450466.9076 464029.2506 512594.2486 457691.1122 464816.2096 1.055539682 0.983078368 0.982807859 1.033834463 0.969129084 0.998306946 1.102789098 0.984671151 1 18.82630086 1.892796835 22.9952825 1.043069209 0.998785292 0.036557092 0.040363808 23.11067014 4940.268282 0.015213393 0.009817223 78.12622411 -1.892796835 -0.044283917 RQYHES(ph)EEES(ph)EEEEAA ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RQYHESEEESEEEEAA 16 1 Q8N9N8;E9PNH5 Q8N9N8 EIF1AD Probable RNA-binding protein EIF1AD 2 RQY(0.012)HES(0.99)EEES(0.998)EEEEAA 69.398 0.048235 0 68544 80399 94070 79707 78990 76536 92713 80374 86231 TRUE FALSE 64253.95339 86351.82562 96301.38482 81752.41656 72786.44403 98630.70074 78811.54636 90408.87082 71838.48903 0.894422395 1.202027309 1.340526313 1.138003007 1.013195642 1.372950657 1.097065757 1.258501843 1 16.13246939 -1.774502043 6.634910665 0.99421211 1.181417463 0.10394669 0.14454224 0.011693101 0.000397409 0.132238698 0.030440934 0.0168073 1.774502043 0.187205353 RRAS(ph)PS(ph)PPPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRASPSPPPKR 11 3 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRAS(1)PS(1)PPPKR 68.044 0.083714 279600000 161360 145180 143510 161580 157980 131620 166670 156680 197830 TRUE FALSE 151260.7656 155929.2783 146914.125 165726.4164 145572.8881 169616.5573 141679.3808 176241.8429 164810.895 0.917783777 0.946110257 0.891410274 1.005554981 0.883272238 1.029158645 0.859648149 1.069357963 1 17.33045209 1.225032276 24.99998542 1.03467901 0.932294181 0.372709923 0.054679555 246.0700999 454717.1463 0.043756231 0.011186041 16.78928787 -1.225032276 -0.102384829 RRAS(ph)QEANLLTLAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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;RRAS(1)QEANLLTLAQK 229.07 4.03E-13 2278810000 1552850 1661500 1549610 1756220 2246380 1180180 1898810 1472760 2519530 TRUE FALSE 1455659.89 1784519.189 1586367.481 1801287.578 2069958.376 1520878.807 1614101.068 1656637.328 2099004.166 0.693500239 0.8501742 0.755771478 0.858162936 0.986162109 0.7245716 0.768984214 0.789249185 1 21.0012736 -2.439179875 2.217946628 2.844665903 0.804200217 0.362186726 0.082016231 4785137.371 392850.1014 44482187.47 0.019033983 0.003637643 2.439179875 -2.040465686 RRDEDMLYS(ph)PELAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 RRDEDMLYSPELAQR 15 2 Q9Y2W2 Q9Y2W2 WBP11 WW domain-binding protein 11 1 RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLY(0.001)S(0.999)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLY(0.057)S(0.943)PELAQR;RRDEDMLYS(1)PELAQR 199.61 3.83E-09 3239579000 1316884 1679650 1494593 1621008 1789745 1469222 1682456 1550322 1967352 TRUE FALSE 1234462.581 1804013.034 1530045.452 1662605.81 1649185.647 1893362.541 1430187.342 1743883.114 1638988.242 0.753185746 1.10068699 0.933530463 1.014409846 1.006221769 1.155202028 0.872603784 1.063999771 1 20.64437407 4.751469989 24.39146742 1.011084511 0.753185513 0.521522942 0.079545661 1212.657907 2291185.299 0.017465986 0.316282488 56424.79484 -4.751469989 -0.257898999 RRDELSEEINNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRDELSEEINNLR 13 2 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7;A0A087WYS2;B4DSP0;A0A087WZG9;Q86TG7-2 A0A087WXK2;B4DSP0 PEG10 Retrotransposon-derived protein PEG10 0 142.91 2.28E-05 57877000 34942 42812 40549 36743 53050 46369 37528 34186 64475 FALSE TRUE 32755.04259 45981.84503 41510.84143 37685.88759 48883.66699 59754.97756 31901.02479 38454.19735 53713.70598 0.609807907 0.856054227 0.772816559 0.701606543 0.910078091 1.112471696 0.593908467 0.715910337 1 15.71300264 4.745467821 23.84399902 0.817184096 0.609807724 0.170085818 0.151361098 828.2765774 2859104.256 0.034621335 0.334649087 55650.33991 -4.745467821 -0.207376372 RRDS(ph)DGVDGFEAEGK ddPTM_SK-BR-3_Pertuzumab_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 242.34 5.02E-18 7432930000 8210150 5907720 6715040 6838320 7604910 5098010 6912920 5627670 9478850 TRUE FALSE 7696291.367 6345133.736 6874323.92 7013802.868 7007651.045 6569722.728 5876391.822 6330296.988 7896768.699 0.974612738 0.803510142 0.870523651 0.888186439 0.887407408 0.831950761 0.744151443 0.801631304 1 22.912831 2.075598604 6.016171175 0.812502043 0.871523568 0 0.078708902 0.436675431 26.61320615 0.027337264 0.019979845 119.0141512 -2.075598604 0.059021525 RRDS(ph)DGVDGFEAEGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RRDSDGVDGFEAEGKK 16 3 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 RRDS(1)DGVDGFEAEGKK;RRDS(1)DGVDGFEAEGKK;RRDS(1)DGVDGFEAEGKK 190.83 4.38E-09 4572280000 5711410 3608940 4262580 4565540 5389780 2902770 4798090 3438670 8654280 TRUE FALSE 5353943.043 3876149.673 4363690.411 4682699.486 4966488.42 3740752.576 4078660.948 3867995.519 7209824.759 0.742589899 0.537620511 0.605242229 0.649488669 0.688850088 0.518840985 0.565708749 0.536489533 1 22.78153276 -1.964456265 2.58146816 1.32618732 0.59705423 0.746622827 0.072052317 15742671.96 7739647.916 30730036.05 0.016306687 0.010852848 1.964456265 -0.72913309 RRDS(ph)EEFGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RRDSEEFGVK 10 2 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 RRDS(1)EEFGVK;RRDS(1)EEFGVK;RRDS(1)EEFGVK;RRDS(1)EEFGVK 182.89 1.36E-06 4850140000 4074810 3376870 3481290 3540630 4182370 2758560 4182320 3547570 5217100 TRUE FALSE 3819774.916 3626896.968 3563867.843 3631488.56 3853903.531 3554911.491 3555219.943 3990491.924 4346332.306 0.878850177 0.834473002 0.819971321 0.835529431 0.886702456 0.817910652 0.81798162 0.918128583 1 22.05136705 1.004964969 3.773846284 0.999493774 0.838259135 0.822854802 0.024259199 0.072398965 2.676269325 0.022875556 0.005886694 10.11497861 -1.004964969 -0.161234639 RRDS(ph)GDNSAPSGQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RRDSGDNSAPSGQER 15 2 Q8IXQ3 Q8IXQ3 C9orf40 Uncharacterized protein C9orf40 1 RRDS(1)GDNSAPSGQER;RRDS(0.978)GDNS(0.022)APSGQER;RRDS(1)GDNSAPSGQER;RRDS(0.999)GDNS(0.001)APSGQER;RRDS(0.829)GDNS(0.171)APSGQER;RRDS(0.987)GDNS(0.013)APSGQER;RRDS(1)GDNSAPSGQER 190.31 1.75E-07 5908128000 982497 1254900.6 1055397.2 1105594.2 1245900.3 942173.2 1146206.1 1011169.4 1380984.5 TRUE FALSE 921004.2666 1347814.746 1080431.72 1133965.619 1148052.316 1214163.308 974343.1362 1137416.125 1150489.265 0.80053269 1.171514404 0.939106302 0.985637722 0.997881815 1.055345186 0.846894591 0.988636887 1 20.13381609 1.755686644 25 0.930463751 1.006363103 0.025127855 0.101252447 14.27392344 20859.47529 0.042893413 0.023786695 56.9753031 -1.755686644 0.075899353 RRDS(ph)GIGEETATGLGSHVEVTPHTAPPGVSAGPDAISEVLSTLSLEVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RRDSGIGEETATGLGSHVEVTPHTAPPGVSAGPDAISEVLSTLSLEVNK 49 2 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 RRDS(0.204)GIGEET(0.204)AT(0.204)GLGS(0.204)HVEVT(0.054)PHT(0.054)APPGVS(0.061)AGPDAIS(0.005)EVLS(0.005)T(0.005)LS(0.001)LEVNK;RRDS(0.199)GIGEET(0.199)AT(0.199)GLGS(0.199)HVEVT(0.069)PHT(0.069)APPGVS(0.056)AGPDAIS(0.006)EVLS(0.002)T(0.002)LSLEVNK;RRDS(0.155)GIGEET(0.155)AT(0.155)GLGS(0.155)HVEVT(0.155)PHT(0.155)APPGVS(0.052)AGPDAIS(0.006)EVLS(0.005)T(0.005)LSLEVNK 53.256 0.0042318 278724000 25905 26194.8 29178.5 27942 29718.5 26349.1 35989 27268.5 29733.2 TRUE FALSE 24283.65229 28134.29025 29870.6278 28659.03903 27384.52889 33955.65743 30592.78356 30673.03225 24770.53684 0.980344207 1.135796549 1.205893437 1.156980941 1.105528276 1.370808297 1.235047256 1.23828694 1 14.59633752 5.776656953 0.826293562 1.209917766 6.85E-17 0.291126972 0.097110662 12.59256409 1.812214707 0.029654498 20.77676485 597939.1 -5.776656953 -1.209917766 RRDS(ph)YYDR ddPTM_SK-BR-3_Pertuzumab_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(1)YYDR 138.99 0.00053681 4054370000 1225780 1484150 1374630 1341640 1852300 1064020 1708310 1562640 3422030 TRUE FALSE 1149060.618 1594038.01 1407236.873 1376068.754 1706827.83 1371185.301 1452164.775 1757739.044 2850871.086 0.403055972 0.559140684 0.493616453 0.482683612 0.598703967 0.480970644 0.509375812 0.616562093 1 21.44297137 0.770114944 2.317938056 0.999890282 0.509154057 0.901740934 0.05128612 0.254379555 2.107725462 0.043940393 0.011880509 5.889995245 -0.770114944 -0.490736225 RRDYYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRDYYDR 7 2 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 94.262 0.056932 63520000 25162 31457 23188 25436 41642 19903 37934 41722 61482 FALSE TRUE 23587.15534 33786.10901 23738.03031 26088.73082 38371.6053 25648.673 32246.14886 46931.08354 51220.25701 0.460504431 0.659623965 0.463450043 0.509344005 0.749149019 0.500752524 0.629558513 0.916260212 1 15.64442687 1.224295943 2.967430786 0.997784146 0.563171938 0.774175521 0.089092246 0.107436446 1.630625318 0.075034281 0.021195131 16.76084629 -1.224295943 -0.434612208 RREDQMDGDGPRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RREDQMDGDGPRPR 14 3 Q15527 Q15527 SURF2 Surfeit locus protein 2 0 ; 92.939 0.0031229 454680000 105884 125031 123233 113717 119647 106350 127611 107817 140252 FALSE TRUE 99256.90945 134288.4253 126156.145 116635.1707 110250.4073 137051.5186 108476.9152 121278.1898 116843.0351 0.849489311 1.149306205 1.079706161 0.998220995 0.943577057 1.172954112 0.928398643 1.037958229 1 16.83421221 3.234500333 24.91940597 1.01215145 1.06020257 0 0.100720797 333.5841356 2047326.571 0.026883192 0.033249588 1715.933026 -3.234500333 0.04805112 RREDS(ph)YHVR ddPTM_SK-BR-3_Pertuzumab_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 112.5 0.0010189 405665000 90998.2 161196 128588 149274 175966 116870 157080 149201 166266 TRUE FALSE 85302.7851 173131.1196 131638.1681 153104.6236 162146.3402 150608.4718 133527.3123 167829.0733 138515.1305 0.615837308 1.249907638 0.950352266 1.105327794 1.170603815 1.087307006 0.963990806 1.211629897 1 17.07968405 4.751411858 24.84682361 1.084855847 0.615836983 0.688817674 0.100549427 1124.450581 2173990.986 0.022596568 0.418496629 56417.24282 -4.751411858 -0.469018864 RREEEGLQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RREEEGLQLR 10 2 C9JYI4;P52294;C9J352;C9JWD9;F2Z3G4;C9J4U1 C9JYI4 KPNA1 "Importin subunit alpha-5;Importin subunit alpha-5, N-terminally processed" 0 ;;; 226.71 1.63E-09 735970000 251918 341391 309204 312983 369201 249137 326612 299640 403007 FALSE TRUE 236150.9021 366667.9449 316538.4649 321014.6737 340205.4427 321058.8075 277639.5627 337050.7136 335742.5282 0.703369047 1.092110514 0.942801219 0.956133485 1.01329267 0.956264937 0.826941896 1.003896395 1 18.35699577 1.972414112 24.47509879 0.916188921 0.964731146 0 0.110619791 2066.75477 1833688.002 0.041696229 0.026967605 93.84564241 -1.972414112 0.048542225 RREEEMMIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RREEEMMIR 9 2 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;;; 134.59 0.00013755 1422901000 383839 496136 424442 375833 580049 323043 427988 466220 569223 FALSE TRUE 359815.2022 532870.4257 434509.9647 385477.5111 534494.2913 416300.2699 363815.1726 524428.5933 474216.004 0.758758033 1.123687141 0.916270141 0.812873264 1.127111457 0.877870562 0.767192945 1.10588548 1 18.85518483 RREEGPPPPS(ph)PDGAS(ph)SDAEPEPPSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RREEGPPPPSPDGASSDAEPEPPSGR 26 2 Q9NTJ3;E9PD53;Q9NTJ3-2;C9JR83;C9JWF0;C9IYK2;C9JJ64;F8WCB7 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 2 RREEGPPPPS(1)PDGAS(0.623)S(0.377)DAEPEPPSGR 108.8 0.012445 195360000 82008 85796 89435 89383 89224 71870 94720 75079 102180 TRUE FALSE 76875.26567 92148.42511 91556.44043 91676.71911 82216.70695 92617.70229 80517.61534 84452.77842 85125.49789 0.903081539 1.082500865 1.075546607 1.076959564 0.965829381 1.088013634 0.945869538 0.992097321 1 16.37730371 1.722628262 12.95106314 0.977228189 1.042020626 0.130113139 0.060493458 0.16670347 98.45131779 0.026534262 0.014567685 52.79931178 -1.722628262 0.064792437 RREEGPPPPS(ph)PDGASS(ph)DAEPEPPSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.106)S(0.894)DAEPEPPSGR;RREEGPPPPS(1)PDGAS(0.257)S(0.743)DAEPEPPSGR 152.82 4.60E-07 1314080000 441910 533290 495230 490560 538520 416650 533930 407180 516060 TRUE FALSE 414251.6419 572775.3465 506977.0895 503148.6001 496226.8115 536930.0913 453872.1533 458017.3193 429926.2521 0.963541165 1.332264182 1.179218731 1.17031374 1.154213796 1.248888824 1.055697695 1.065339269 1 18.71372968 1.641028027 5.790901279 1.041649636 1.192175118 0.301338526 0.094068657 0.149482365 10.61092429 0.046518046 0.022596241 43.75503411 -1.641028027 0.150525482 RREEGPPPPSPDGASS(ph)DAEPEPPSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RREEGPPPPSPDGASSDAEPEPPSGR 26 2 Q9NTJ3;E9PD53;Q9NTJ3-2;C9JR83;C9JWF0;C9IYK2;C9JJ64;F8WCB7 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 1 RREEGPPPPSPDGAS(0.108)S(0.892)DAEPEPPSGR;RREEGPPPPSPDGAS(0.152)S(0.848)DAEPEPPSGR;RREEGPPPPS(0.007)PDGAS(0.217)S(0.776)DAEPEPPSGR;RREEGPPPPS(0.002)PDGAS(0.114)S(0.885)DAEPEPPSGR 185.3 7.60E-18 5051950000 447509 413731 466707 454983 498862 409068 517351 411098 560661 TRUE FALSE 419500.2105 444364.0737 477777.5104 466658.6341 459683.3908 527159.2909 439779.0204 462424.4902 467083.0571 0.898127654 0.951359864 1.022896256 0.999091333 0.984157708 1.128620024 0.941543509 0.990026256 1 18.83331959 4.524295134 1.491165675 1.00905386 0.879173822 0.380602208 0.047506124 0.802459864 2.239351833 0.012259174 0.13685048 33442.22268 -4.524295134 -0.129880038 RRES(ph)EKS(ph)LENETLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RRESEKSLENETLNK 15 3 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 RRES(1)EKS(1)LENETLNK;RRES(1)EKS(1)LENETLNK;RRES(0.531)EKS(0.976)LENET(0.493)LNK 203.2 7.94E-09 1367240000 1862530 701540 1065590 1033460 967990 873670 1455630 827220 1015730 TRUE FALSE 1745957.572 753482.7516 1090866.298 1059980.333 891967.9701 1125884.346 1237371.795 930500.2379 846198.1011 2.06329649 0.890433045 1.289138201 1.252638516 1.054088834 1.330521003 1.462272006 1.099624588 1 19.69063592 4.751647588 24.70482009 1.198312302 2.063297146 0.726944988 0.170948893 1074.133449 2027644.002 0.042080157 0.790615829 56447.87373 -4.751647588 0.864984844 RRES(ph)EKSLENET(ph)LNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRESEKSLENETLNK 15 3 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 RRES(0.784)EKS(0.245)LENET(0.972)LNK 196.1 1.72E-08 685350000 813620 357510 495280 477660 459890 408190 632220 388670 461910 TRUE FALSE 762696.9766 383980.4124 507028.2755 489917.5643 423772.0945 526027.8266 537424.4802 437196.3051 384814.2369 1.98198742 0.997833176 1.3175923 1.27312744 1.101238088 1.366965606 1.396581594 1.136122999 1 18.55380265 4.749299615 24.96703908 1.224502789 1.981987855 0.744106679 0.143651827 813.4678197 1891189.963 0.033664709 0.493118354 56143.51709 -4.749299615 0.757485066 RRES(ph)QEEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 141.37 8.42E-05 11712210000 6516480 6906420 6996940 6204960 7074160 6500000 7873850 6187430 9771990 TRUE FALSE 6108625.149 7417778.523 7162910.721 6364189.779 6518584.009 8376444.481 6693239.29 6959944.256 8140981.74 0.750354852 0.91116511 0.879858345 0.781747212 0.800712275 1.028923138 0.82216611 0.854926897 1 22.95677135 RRET(ph)PS(ph)PR ddPTM_SK-BR-3_Pertuzumab_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 78.342 0.034073 775000000 331570 340950 383550 344930 291824 323620 354650 301920 220438 TRUE FALSE 310817.6256 366194.2928 392647.9871 353781.4878 268905.3202 417043.8405 301473.5249 339615.3766 183645.4737 1.692487265 1.994028414 2.13807604 1.926437285 1.464263261 2.270918156 1.641606073 1.849298922 1 17.48656381 -0.980882157 0.389080456 0.616090715 1.958740911 0.573262091 0.236133449 9.846544021 1.079084998 4.427326387 0.149295276 0.104500374 0.980882157 1.342650196 RRET(ph)PS(ph)PRPMR ddPTM_SK-BR-3_Pertuzumab_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 88.009 0.010594 14008510000 5756430 6929030 6105540 6267710 7345300 5385710 6395560 5491730 7805550 TRUE FALSE 5396145.322 7442062.591 6250366.292 6428550.05 6768429.768 6940477.047 5436605.151 6177384.579 6502753.279 0.829824705 1.144447939 0.961187673 0.988588952 1.040856 1.067313605 0.836046659 0.949964471 1 22.63261926 1.748415368 25 0.914574523 1.017039061 0.124167985 0.09007552 3.531752849 8978.261835 0.037870796 0.02100122 56.02932211 -1.748415368 0.102464538 RRFS(ph)DSEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRFSDSEER 9 2 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 RRFS(0.99)DS(0.01)EER 110.38 0.0018086 445390000 158110 201090 166920 194970 212450 167320 215090 175130 248780 TRUE FALSE 148214.1773 215978.9128 170879.4212 199973.2603 195765.034 215622.5678 182839.2513 196995.366 207257.0108 0.715122624 1.042082543 0.824480777 0.964856434 0.944552048 1.040363204 0.882186087 0.95048831 1 17.66106138 3.154976713 25 0.957177865 0.894287079 0.193472684 0.090343096 58.39086067 17458.00631 0.024272823 0.029011584 1428.817341 -3.154976713 -0.062890786 RRGDDWNDREWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RRGDDWNDREWDR 13 3 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;;; 161.21 1.86E-05 2533140000 102109 321384 234774 185121 247628 144919 220309 214859 380839 FALSE TRUE 95718.17996 345179.6058 240342.9501 189871.5183 228180.2958 186754.7627 187275.7107 241684.6191 317274.5106 0.301688843 1.087952528 0.757523665 0.598445548 0.719188867 0.588622018 0.590263965 0.761752398 1 18.2753721 0.973155495 22.67585071 1.000000007 0.703101894 0.206555867 0.196992374 1480.980555 1251004.24 0.189592644 0.047398161 9.400598305 -0.973155495 -0.296898112 RRGDS(ph)ES(ph)EEDEQDSEEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRGDSESEEDEQDSEEVR 18 2 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 2 RRGDS(1)ES(0.973)EEDEQDS(0.027)EEVR 208.99 2.81E-15 2894300000 513090 530010 548640 548680 546790 429440 589260 425120 674700 TRUE FALSE 480976.6128 569252.4919 561653.9999 562760.0577 503847.319 553412.3566 500905.9334 478197.1678 562088.2113 0.855695962 1.01274583 0.999227503 1.001195269 0.896384783 0.984564959 0.891151822 0.850751107 1 19.10043703 2.740492236 24.98881493 0.920738055 0.98013965 0.088280775 0.061535907 287.3608305 3717526.618 0.018029821 0.018253286 550.1640855 -2.740492236 0.059401595 RRGDS(ph)ESEEDEQDS(ph)EEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRGDSESEEDEQDSEEVR 18 2 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 2 RRGDS(0.994)ES(0.292)EEDEQDS(0.713)EEVR 215.07 4.78E-18 2565600000 447140 447170 458030 439180 471270 360870 497750 385040 546610 TRUE FALSE 419154.3056 480278.9321 468894.6879 450450.1023 434258.3552 465047.3108 423117.0084 433113.0916 455377.2598 0.920455066 1.05468361 1.029684021 0.989180054 0.953623278 1.021235252 0.929157087 0.9511083 1 18.79670272 3.02691346 4.717282032 0.967934494 1.016694974 0.058972309 0.043138021 0.289925943 16.05903902 0.012254417 0.014378284 1063.930991 -3.02691346 0.04876048 YWGPAS(ph)PTHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 YWGPASPTHK 10 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 YWGPAS(0.985)PT(0.015)HK;YWGPAS(0.741)PT(0.259)HK;YWGPAS(0.893)PT(0.107)HK;YWGPAS(0.957)PT(0.043)HK;YWGPAS(0.99)PT(0.01)HK;YWGPAS(0.882)PT(0.118)HK;YWGPAS(0.952)PT(0.048)HK;YWGPAS(0.905)PT(0.095)HK;YWGPAS(0.961)PT(0.039)HK 203.03 2.23E-07 35408290000 21302960 16888200 20378120 23977150 23394740 12775320 13884710 10380670 11062630 TRUE FALSE 19969645.76 18138619.9 20861498.63 24592444.26 21557411.49 16463347.49 11802826.63 11676719.5 9216205.586 2.166796907 1.968122318 2.263566978 2.668391458 2.339076672 1.786347683 1.280660086 1.266976891 1 23.13574147 1.886492455 2.246195023 1.16792564 2.252569029 0.874371963 0.189919977 0.113571144 1.054979032 0.123967481 0.060463486 77.00030673 -1.886492455 1.084643389 up RRGS(ph)DIDNPTLTVMDISPPS(ph)RSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RRGSDIDNPTLTVMDISPPSRSPR 24 3 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 2 RRGS(1)DIDNPTLTVMDIS(0.036)PPS(0.556)RS(0.408)PR;RRGS(1)DIDNPTLTVMDIS(0.015)PPS(0.642)RS(0.343)PR 106.18 0.0039274 475780000 85296 115763 91792 99589 111016 76582 115181 83116 105366 TRUE FALSE 79957.47562 124334.213 93969.34959 102144.6223 102297.2512 98689.9802 97910.67834 93493.21556 87779.73391 0.910887651 1.416434152 1.070513038 1.163646981 1.165385752 1.124291175 1.115413251 1.065088847 1 16.42160028 1.263236746 0.555115542 0.996807682 1.184778064 0.094756765 0.124945728 1.359667627 1.064640752 0.118684206 0.060094466 18.3331354 -1.263236746 0.187970381 RRGS(ph)QEK ddPTM_SK-BR-3_Pertuzumab_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 110.53 0.0053412 1692800000 1292780 841720 1359560 1167790 1112000 886030 1372570 995710 1529400 TRUE FALSE 1211867.207 904041.8246 1391809.405 1197757.468 1024668.006 1141812.478 1166765.871 1120026.585 1274133.26 0.951130659 0.709534751 1.092357801 0.940056669 0.804207878 0.896148396 0.915732999 0.879049799 1 20.28108474 -2.358056965 2.097456866 1.571989152 0.898559837 0.094835743 0.098520997 10452271.62 1127495.836 28350546.83 0.023708706 0.004384732 2.358056965 -0.673429315 RRGS(ph)SGSVDETLFALPAASEPVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RRGSSGSVDETLFALPAASEPVIR 24 2 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 RRGS(0.672)S(0.164)GS(0.164)VDETLFALPAASEPVIR;RRGS(0.25)S(0.25)GS(0.25)VDET(0.25)LFALPAASEPVIR 199.3 1.31E-24 138473000 83891 116073 104102 115403 146076 93120 129420 101723 199832 TRUE FALSE 78640.41206 124667.1657 106571.3486 118364.4364 134603.7802 120002.2323 110014.6725 114423.3405 166478.7482 0.47237508 0.748847327 0.640149867 0.710988265 0.808534312 0.720826133 0.660833131 0.687314998 1 17.3449785 -5 0.234158813 2.697274485 0.654013163 0.593182423 0.084860679 118.5604088 1.18559332 95.74978524 0.132895168 1.00E-05 5 -2.043261321 RRGSS(ph)GSVDETLFALPAASEPVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRGSSGSVDETLFALPAASEPVIR 24 2 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 RRGS(0.19)S(0.398)GS(0.398)VDET(0.014)LFALPAASEPVIR 196.32 1.57E-24 99418000 46291 61959 51426 56896 74174 44791 62277 50955 98407 TRUE FALSE 43393.72894 66546.50883 52645.84901 58356.04768 68348.67324 57721.43458 52939.142 57316.84392 81982.23597 0.529306482 0.811718637 0.642161663 0.711813321 0.833701014 0.70407246 0.645739182 0.699137359 1 16.32302372 -1.01174399 3.775503438 1.000052852 0.703071173 0.551126087 0.085733711 21291859.5 39542099.37 15163.41872 0.01892338 0.097332081 1.01174399 -0.296981679 RRHEGLPGLAVQWGAIGDVGILVETMSTNDTIVSGTLPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 ;;;;;; 242.67 4.52E-51 313730500 66978 101796.2 56333.1 53675.5 133334.8 57700.8 79705.8 96013.2 84537.5 FALSE TRUE 62785.96654 109333.2966 57669.34773 55052.9042 122863.2227 74358.08427 67754.65524 108000.6594 70427.64512 0.891496037 1.552420167 0.818845322 0.781694519 1.744531177 1.055808186 0.962046298 1.533498091 1 16.10385422 -1.12389211 4.534272707 0.999983283 1.156940822 0.023098301 0.336196485 5.23E-05 1.01E-05 0.299856091 0.070669232 0.075180964 1.12389211 0.156957539 RRHS(ph)DENDGGQPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRHSDENDGGQPHK 14 2 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RRHS(1)DENDGGQPHK 108.45 0.00039187 1045700000 69068 56143 58374 73957 56561 32332 61917 44926 49105 TRUE FALSE 64745.15717 60299.88614 59758.65885 75854.86183 52118.92722 41665.72353 52633.12066 50535.10999 40909.05827 1.58266066 1.473998393 1.460768382 1.854231435 1.274019237 1.018496277 1.28658842 1.235303674 1 15.32013271 2.49405609 24.02975163 1.164962457 1.552376428 0.704047667 0.139433157 260.4438135 369558.2449 0.043517748 0.040078478 311.9292424 -2.49405609 0.387413972 RRHS(ph)DENDGGQPHKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RRHSDENDGGQPHKR 15 3 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RRHS(1)DENDGGQPHKR;RRHS(1)DENDGGQPHKR;RRHS(1)DENDGGQPHKR;RRHS(1)DENDGGQPHKR 108.45 0.00043874 1192837000 34605.4 81054 55738.5 85757 102113 35745.9 51906.7 49580.3 142437 TRUE FALSE 32439.50979 87055.3225 57060.64354 87957.66981 94093.45688 46065.16104 44123.77221 55770.50959 118663.3445 0.273374309 0.733632807 0.480861582 0.74123707 0.792944588 0.388200427 0.371839951 0.469989362 1 16.85651483 -1.040631955 4.888579204 1.00000939 0.540161268 0.416215373 0.17410154 0.248120118 113181434.9 2347.393119 0.040658043 0.091068471 1.040631955 -0.459848122 RRHS(ph)EVETDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RRHSEVETDSK 11 2 Q9NX58 Q9NX58 LYAR Cell growth-regulating nucleolar protein 1 RRHS(1)EVETDSK;RRHS(1)EVETDSK 102.28 0.001508 304543000 100622 93966 90997 110716 134762 77152 103777 78353 124841 TRUE FALSE 94324.24864 100923.3404 93155.49181 113557.16 124178.3361 99424.52994 88216.60227 88135.54453 104004.2306 0.906927036 0.970377261 0.895689447 1.091851354 1.193973893 0.955966208 0.848202056 0.847422687 1 16.66628269 1.992402043 24.94702896 0.886777372 1.000685346 0.219730363 0.095604075 539.7789654 1772303.818 0.038909351 0.027509978 98.26572059 -1.992402043 0.113907974 RRHT(ph)MDKDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RRHTMDKDSR 10 3 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;F6UYG0 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 RRHT(1)MDKDSR;RRHT(1)MDKDSR;RRHT(1)MDKDSR;RRHT(1)MDKDSR;RRHT(1)MDKDSR 143.94 1.75E-05 237028000 88313.8 139657.8 68631.3 90721.9 219648 60868.3 95061.3 152926 247682 TRUE FALSE 82786.3969 149998.2088 70259.26685 93049.97755 202397.7321 78439.9901 80807.74057 172019.1477 206342.2741 0.401209094 0.726938818 0.340498655 0.450949656 0.9808835 0.380145031 0.391619899 0.833659261 1 17.6546799 1.061573549 4.972918486 0.996943534 0.526607725 0.42317126 0.195341921 0.165237291 7.604483291 0.178939264 0.045314103 11.52321193 -1.061573549 -0.470335809 RRKDS(ph)AQDDQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RRKDSAQDDQAK 12 3 Q13045-3;Q13045;Q13045-2;J3KS54 Q13045-3 FLII Protein flightless-1 homolog 1 RRKDS(1)AQDDQAK;RRKDS(1)AQDDQAK;RRKDS(1)AQDDQAK 156.49 0.00040465 523700000 450914 290763 302956 350499 413852 209234 510799 365592 814625 TRUE FALSE 422692.0976 312291.3951 310142.2594 359493.3977 381349.7333 269636.4592 434209.432 411236.966 678658.8248 0.622834453 0.460159632 0.456992893 0.52971152 0.561916709 0.397307821 0.639805181 0.60595538 1 19.37232696 0.547558388 0.863274312 1.002195826 0.49704173 0.816396791 0.071111136 0.546330099 0.646381584 0.064816431 0.021308569 3.528242179 -0.547558388 -0.505154096 RRKEDEVEEWQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRKEDEVEEWQHR 13 3 P15311;E7EQR4 P15311 EZR Ezrin 0 167.98 1.86E-05 151540000 66688 77841 57636 64391 111280 47519 78367 61669 169160 FALSE TRUE 62514.11712 83604.42863 59003.15314 66043.38207 102540.5177 61236.96389 66616.59587 69368.5104 140926.1032 0.443595017 0.593250127 0.418681506 0.46863839 0.727619053 0.434532443 0.472705868 0.492233226 1 17.10457934 -1.415658345 4.287365732 1.001542972 0.50609396 0.740106667 0.091922355 0.001266818 0.00017266 0.083166829 0.019546174 0.038400922 1.415658345 -0.495449012 RRLS(ph)EQLAHTPTAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRLSEQLAHTPTAFK 15 2 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;F8W860;Q9UBF8-3 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 RRLS(0.999)EQLAHT(0.001)PTAFK 131.31 2.84E-05 301920000 508140 573730 495090 546910 661330 400790 702000 608430 986310 TRUE FALSE 476336.4245 616209.5662 506833.7686 560944.6365 609391.8095 516491.5667 596741.617 684393.8248 821688.4892 0.57970439 0.749930873 0.616819848 0.68267311 0.741633621 0.628573448 0.726238258 0.83291154 1 19.64823203 1.014870671 1.719452082 0.998969036 0.673098896 0.809203616 0.05288908 0.141087119 0.858132966 0.044836449 0.01291931 10.34833956 -1.014870671 -0.325870139 RRNDLDDPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RRNDLDDPER 10 2 Q15393 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ;;; 139.32 2.32E-05 639784000 173180 203910 168478 202786 221181 170246 226431 181308 273499 FALSE TRUE 162340.9729 219007.7086 172474.3777 207989.8321 203810.3365 219393.2565 192479.7736 203944.7029 227850.25 0.712489773 0.961191434 0.756963741 0.912835654 0.894492485 0.962883545 0.844764373 0.895082199 1 17.79772643 -4.06044821 0.019355637 2.060254296 2.35E-06 0.324946341 0.074384878 3801.390219 6.509762924 443.5214197 269.0197377 8.70E-05 4.06044821 -2.060251947 RRNDS(ph)YTEEEPEWFSAGPTSQSETIELTGFDDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RRNDSYTEEEPEWFSAGPTSQSETIELTGFDDK 33 2 B1AKL4;Q9NRA8;Q9NRA8-3 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 RRNDS(0.353)Y(0.295)T(0.353)EEEPEWFSAGPTSQSETIELTGFDDK;RRNDS(0.41)Y(0.177)T(0.41)EEEPEWFS(0.001)AGPTSQSETIELTGFDDK;RRNDS(0.356)Y(0.287)T(0.356)EEEPEWFSAGPTSQSETIELTGFDDK 206 1.79E-27 332851000 174084 121306 137151 167748 198998 134577 179499 138394 153410 TRUE FALSE 163188.3932 130287.6225 140404.2865 172052.6977 183369.4998 173427.1952 152584.7913 155672.7955 127804.8799 1.276855729 1.019426039 1.098583141 1.346213836 1.434761332 1.356968492 1.193888617 1.218050482 1 16.9635834 5.066889511 21.05816391 1.206547458 3.078178849 0.021945073 0.142921849 3005.440787 1111681.063 0.035908526 45918.26578 116651.2805 -5.066889511 1.871631391 RRNES(ph)PGAPPAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RRNESPGAPPAGK 13 2 P49796-1;P49796-4;P49796-6;P49796;C9J582;P49796-2;H7BXY1;A0A087WUY2;P49796-7;P49796-8;P49796-9 P49796-1 RGS3 Regulator of G-protein signaling 3 1 RRNES(1)PGAPPAGK;RRNES(1)PGAPPAGK;RRNES(1)PGAPPAGK;RRNES(1)PGAPPAGK 97.823 0.0028366 353288000 283938 278176 268064 248917 332578 226442 356994 301458 586810 TRUE FALSE 266166.8274 298772.4405 274422.6047 255304.6316 306458.6654 291812.1294 303466.0639 339095.6949 488867.6201 0.544455833 0.611152034 0.561343385 0.522236739 0.626874542 0.596914415 0.620753045 0.693635007 1 18.89908433 0.455218092 0.788492642 1.0050354 0.572622564 0.95493298 0.028731844 0.332668619 0.312079683 0.029238299 0.009341241 2.852450336 -0.455218092 -0.432412836 RRPDLDEIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRPDLDEIHR 10 2 O00488;A9J4F5 O00488 ZNF593 Zinc finger protein 593 0 83.045 0.0091075 104300000 50625 47950 54804 52460 69800 44847 57156 61603 59456 FALSE TRUE 47456.47162 51500.26789 56103.97676 53806.21241 64318.18956 57793.60087 48585.98841 69294.27015 49532.4095 0.958089301 1.039728703 1.132672069 1.08628296 1.298507184 1.166783556 0.980892892 1.398968289 1 15.59608518 4.511026858 0.993739285 1.148928364 0.902953371 0.223099347 0.124494713 2.215592157 2.2524584 0.036945756 0.536850861 32435.96762 -4.511026858 -0.245974993 RRPEAS(ph)PVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RRPEASPVQK 10 2 Q3KQU3-4;Q3KQU3;Q3KQU3-2 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 RRPEAS(1)PVQK;RRPEAS(1)PVQK 110.55 0.0014738 335089000 653420 434344 524340 502850 568680 425556 640420 498120 652590 TRUE FALSE 612523.6086 466503.2817 536777.5924 515753.9823 524018.1667 548407.1089 544394.9664 560311.3785 543668.5131 1.12664904 0.85806566 0.987325143 0.948655237 0.963856015 1.008715965 1.001336206 1.030612156 1 19.05236775 2.247895307 5.632170141 1.009525543 0.960604612 0.027922359 0.06628739 0.364638883 37.29469388 0.022318848 0.017613881 176.9682301 -2.247895307 -0.048920931 RRPENPKPQDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RRPENPKPQDGK 12 3 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;; 105.65 0.0024541 602600000 1283920 813970 1014730 1017640 1034950 816520 1291140 949260 1213190 FALSE TRUE 1203561.739 874237.1857 1038799.875 1043754.365 953669.2018 1052236.069 1097545.543 1067777.201 1010700.751 1.19081908 0.864981236 1.027801625 1.03270366 0.943572269 1.041095564 1.085925326 1.056472155 1 19.94692448 2.018049705 23.34651924 1.058637435 0.99480637 0.011256006 0.084730316 233.082161 301479.2127 0.029407188 0.02171287 104.2436729 -2.018049705 -0.063831066 RRPES(ph)APAESSPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRPESAPAESSPSK 14 2 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 RRPES(0.715)APAES(0.132)S(0.152)PSK 111.18 0.00052499 206670000 144470 105430 131820 120880 143440 79800 129680 102580 133230 TRUE FALSE 135427.8806 113236.1469 134946.8326 123981.9854 132174.801 102836.9646 110235.6879 115387.3388 110993.0523 1.220147368 1.020209324 1.215813331 1.117024741 1.19083851 0.926517133 0.99317647 1.039590645 1 16.76010985 2.241216112 24.9999948 0.987432315 1.141690575 0.618258308 0.063292441 46.50158062 437791.2147 0.021386086 0.017139209 174.267384 -2.241216112 0.15425826 RRPESAPAESS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRPESAPAESSPSK 14 2 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 RRPESAPAES(0.004)S(0.995)PS(0.001)K 100.77 0.00086153 214730000 209980 150610 201280 206790 214760 122820 204030 175040 233740 TRUE FALSE 196837.7266 161761.3211 206054.4567 212096.5815 197893.6159 158276.1402 173437.5956 196894.1293 194727.284 1.01083794 0.830707017 1.058169417 1.089198068 1.01626034 0.812809263 0.890669207 1.01112759 1 17.57109551 2.301963747 24.99999882 0.912629313 0.989606711 0.12647375 0.087439875 125.4226836 49453.26325 0.031483834 0.026341256 200.4304709 -2.301963747 0.076977398 RRPGAQPLPPPPPSQS(ph)PEPTEPHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RRPGAQPLPPPPPSQSPEPTEPHPR 25 2 K7EPZ6;A0A0A0MS90;Q9UIS9-4;Q9UIS9-11;Q9UIS9-7;Q9UIS9-10;Q9UIS9-6;Q9UIS9-5;Q9UIS9;Q9UIS9-9;Q9UIS9-12 K7EPZ6;Q9UIS9-6 MBD1 Methyl-CpG-binding domain protein 1 1 RRPGAQPLPPPPPS(0.003)QS(0.997)PEPTEPHPR;RRPGAQPLPPPPPS(0.005)QS(0.995)PEPTEPHPR;RRPGAQPLPPPPPS(0.026)QS(0.974)PEPTEPHPR;RRPGAQPLPPPPPSQS(1)PEPTEPHPR 176.93 1.65E-17 603460000 144602 134877 129917 122890 164664 114883 179052 142298 260295 TRUE FALSE 135551.6189 144863.4334 132998.6926 126043.5655 151731.9537 148047.8571 152204.8148 160064.2185 216850.0829 0.625093692 0.668034946 0.613320921 0.581247486 0.699708995 0.682719855 0.701889586 0.738133075 1 17.72633847 0.250954984 0.510133739 1.025846249 0.628900322 0.933869455 0.029693262 0.65308984 0.253349237 0.064603907 0.01472585 1.782194028 -0.250954984 -0.396945927 RRPPS(ph)PEPSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RRPPSPEPSTK 11 2 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 RRPPS(0.999)PEPST(0.001)K;RRPPS(1)PEPSTK 86.467 0.011379 275070000 335510 298590 300700 303820 356090 229400 389900 274980 463410 TRUE FALSE 314511.028 320697.9143 307832.746 311616.5356 328124.1278 295624.056 331438.1147 309311.8583 386063.8773 0.814660595 0.830686146 0.797362209 0.807163151 0.849921858 0.765738712 0.858505895 0.801193472 1 18.55848005 -4.999991275 0.462798707 5.526374577 0.814897462 0.824138278 0.02672527 549.8709804 3.02018338 2558.62012 0.011994355 1.00E-05 4.999991275 -4.711477115 RRPS(ph)DENTIAPSEVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRPSDENTIAPSEVQK 16 2 F5GZP6;Q86W92-3;Q86W92-4;Q86W92;Q86W92-2 F5GZP6;Q86W92-2 PPFIBP1 Liprin-beta-1 1 RRPS(0.5)DENT(0.5)IAPSEVQK 121.79 5.05E-05 157610000 137360 121850 134780 137920 156020 122300 161880 127670 264770 TRUE FALSE 128762.8828 130871.9008 137977.0452 141459.2607 143766.8186 157606.0246 137607.5968 143609.8805 220578.1765 0.583751688 0.593313005 0.625524462 0.641311225 0.651772631 0.714513227 0.623849553 0.651061147 1 17.75093054 -5 0.244773157 3.156246424 0.598220982 0.934428387 0.030714792 41.18106207 0.409850207 44.29087822 0.046581289 1.00E-05 5 -2.558025443 RRPS(ph)PQPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 103.76 0.013633 1100810000 298978 354780 317301 317860 335880 297770 350106 277779 332406 TRUE FALSE 280265.5007 381048.2803 324827.5296 326016.8257 309501.3397 383731.3651 297610.8555 312460.3196 276925.2912 1.012061771 1.375996677 1.172978922 1.177273568 1.11763479 1.385685516 1.074697274 1.12831991 1 18.07913729 1.605405894 24.99999997 1.076108815 1.218829066 0.242446804 0.114448253 0.321653112 3225.815244 0.053161851 0.026398446 40.30935915 -1.605405894 0.142720251 RRQEIEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RRQEIEQK 8 2 Q9H307 Q9H307 PNN Pinin 0 ;;; 122.52 0.00078014 92678000 107457 137749 81026 85518 156872 63466 106802 128834 187014 FALSE TRUE 100731.4582 147948.0793 82947.97498 87712.53666 144551.9059 81787.60392 90788.0316 144919.2085 155800.1552 0.646542733 0.949601617 0.532399822 0.562981061 0.92780335 0.524952005 0.58272106 0.930160874 1 17.24933715 1.122475521 5.614611977 0.993564278 0.681266181 0.391698201 0.15094761 0.213594748 8.963765075 0.142379556 0.035966301 13.25792387 -1.122475521 -0.312298097 RRS(ph)EVVESTTESQDKENSHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRSEVVESTTESQDKENSHQK 21 3 Q5UIP0-2;Q5UIP0 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 RRS(0.999)EVVESTTESQDKENSHQK 195.03 1.09E-18 83233000 83636 60669 72105 68380 84740 50412 105370 64655 154050 TRUE FALSE 78401.37205 65160.99589 73815.36465 70134.74657 78084.86222 64965.12603 89570.74671 72727.31907 128338.0598 0.610897283 0.50772932 0.575163477 0.546484392 0.608431064 0.506203118 0.697928166 0.566685512 1 16.96958955 -2.817023457 0.290636987 1.791113789 0.541611108 0.857165957 0.054379259 18.36211704 0.543561206 9.008034548 0.052560492 0.00152397 2.817023457 -1.24950268 RRS(ph)LEPAENVHGAGGGAFPASQTPSKPASADGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 142.37 1.99E-10 4164660000 644730 895595 756660 811578 993224 549702 973293 840892 1037548 TRUE FALSE 604377.5002 961905.7857 774608.3325 832404.4655 915220.1935 708392.0437 827356.7503 945879.2172 864374.536 0.699207895 1.112834478 0.89614895 0.963013637 1.058823641 0.819542935 0.957173905 1.094293247 1 19.72129705 4.757107781 24.60236144 0.978343957 0.699207594 0.507462216 0.088903747 2836.948901 3763067.882 0.020151469 0.674496187 57162.0481 -4.757107781 -0.279136362 RRS(ph)PGLCSDSLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RRSPGLCSDSLEK 13 2 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 RRS(1)PGLCSDSLEK;RRS(0.996)PGLCS(0.004)DSLEK 172.2 1.87E-05 657920000 579740 520470 511500 490980 648090 325450 654550 517330 1058600 TRUE FALSE 543455.1083 559006.1403 523633.0215 503579.378 597191.6257 419402.1318 556406.304 581919.7893 881912.8212 0.616223163 0.633856462 0.59374692 0.571008115 0.677154942 0.475559626 0.63090851 0.659838224 1 19.75027652 0.663949398 2.053447467 0.999874586 0.599397699 0.851760168 0.052120175 0.565591189 3.019786462 0.044962407 0.012350111 4.612638273 -0.663949398 -0.400476887 RRS(ph)PPADAIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 RRSPPADAIPK 11 2 P18754-2;C9JW69;P18754;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4;M0R1Q8 P18754-2 RCC1 Regulator of chromosome condensation 1 RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK;RRS(1)PPADAIPK 115.26 0.00090352 58370410800 13188141 11013362 11854505 11399890 12737926 9153831 13879781 10786753 17279848 TRUE FALSE 12362718.8 11828802.78 12135699.46 11692430.48 11737540.67 11796393.41 11798636.69 12133502.86 14395729.74 0.858776806 0.821688306 0.843006897 0.812215198 0.81534878 0.819436988 0.819592817 0.84285431 1 23.77913759 0.754636145 4.00498892 0.999998687 0.826703077 0.936809628 0.014004408 0.760673229 12.22294628 0.012820578 0.003275163 5.68376541 -0.754636145 -0.173295609 RRS(ph)PPPGPDGHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 RRSPPPGPDGHAK 13 2 P57081;P57081-2;P57081-3 P57081 WDR4 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 1 RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK;RRS(1)PPPGPDGHAK 182.49 5.82E-06 35508549000 1719643 1509336 1605793 1587170 1675065 1201137 1820183 1484263 1980316 TRUE FALSE 1612013.614 1621088.808 1643883.168 1627899.469 1543512.152 1547885.753 1547263.457 1669576.503 1649788.466 0.977103215 0.982604037 0.996420573 0.98673224 0.935581854 0.938232861 0.937855664 1.011994287 1 20.65384963 2.775679921 20.90606307 0.956832372 0.986980849 0.095217675 0.02639406 115.9863723 65323.92866 0.007610678 0.008071551 596.5954284 -2.775679921 0.030148477 RRS(ph)PPPGPDGHAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RRSPPPGPDGHAKK 14 3 P57081;P57081-2;P57081-3 P57081 WDR4 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 1 RRS(1)PPPGPDGHAKK;RRS(1)PPPGPDGHAKK;RRS(1)PPPGPDGHAKK 143.99 6.41E-06 573220000 346732 384910 335785 365724 469970 246885 491560 319199 1043800 TRUE FALSE 325030.6631 413409.1369 343749.9788 375109.097 433060.452 318156.6917 417855.1414 359051.6978 869583.0368 0.373777603 0.475410765 0.395304375 0.431366622 0.498009314 0.365872698 0.480523566 0.412900991 1 19.72996427 -4.028727435 0.591047836 10 0.430859605 0.940894339 0.044950769 406.2145624 4.361935104 4793.181764 0.015754679 9.36E-05 4.028727435 -9.569140395 RRS(ph)PPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRSPPPR 7 2 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 1 RRS(1)PPPR 56.432 0.095802 356950000 8722.6 10654 9131.4 10125 10067 9059.2 7851.3 10863 8662.1 TRUE FALSE 8176.668036 11442.83325 9348.00112 10384.82464 9276.378428 11674.44398 6674.070453 12219.26946 7216.339551 1.133076954 1.585683873 1.295393746 1.439070954 1.285468673 1.617779193 0.924855379 1.693278064 1 12.81705151 -3.520757339 0.272865537 2.00E-11 1.392805154 0.169985684 0.236611858 142.7054977 2.891286883 80.71132079 0.259403303 0.000301469 3.520757339 1.392805154 RRS(ph)PQEGPTWSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RRSPQEGPTWSR 12 2 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 RRS(1)PQEGPTWSR;RRS(1)PQEGPTWSR;RRS(1)PQEGPTWSR 105.63 0.0015825 1004930000 639738 509290 606280 533030 625770 430021 692560 522504 775890 TRUE FALSE 599697.9405 546998.3615 620661.2479 546708.4522 576624.5484 554161.0819 588717.0574 587739.7746 646388.9466 0.927766392 0.846237183 0.960197805 0.845788677 0.892070558 0.857318314 0.910778349 0.909266437 1 19.302043 0.629647048 1.495939143 0.999876307 0.890852101 0.472737402 0.035932795 1.208225885 3.779515828 0.03139232 0.009114683 4.262329779 -0.629647048 -0.109024206 RRS(ph)PS(ph)LSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RRSPSLSSK 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRS(0.998)PS(0.878)LS(0.124)S(0.001)K;RRS(1)PS(0.785)LS(0.212)S(0.004)K;RRS(1)PS(0.992)LS(0.008)SK 118.76 0.0046071 6925200000 6958700 5680500 5815400 5951500 6972300 5086200 7219700 5148800 7265800 TRUE FALSE 6523167.389 6101090.131 5953344.034 6104225.566 6424723.683 6554503.372 6137173.009 5791639.014 6053091.041 1.077658893 1.007929682 0.983521311 1.008447672 1.061395515 1.082835749 1.013890749 0.956806857 1 22.52924062 1.463400457 25 0.980718424 1.028952073 0.320555363 0.033662128 5.404921112 9852.063442 0.019531729 0.009041552 29.0670165 -1.463400457 0.048233648 RRS(ph)PS(ph)PAPPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRSPSPAPPPR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRS(1)PS(1)PAPPPR 91.076 0.054161 6489300000 2093700 2212500 2388100 2262300 2209400 2193900 2160300 1840100 2060900 TRUE FALSE 1962659.054 2376315.802 2444746.86 2320354.448 2035882.636 2827243.315 1836383.07 2069840.536 1716922.476 1.143126193 1.384055387 1.4239122 1.351461397 1.185774352 1.646692471 1.069578327 1.205552705 1 20.71139347 1.612695679 25 1.103159768 1.36010248 0.426953931 0.143984541 0.389610762 2006.717589 0.061984042 0.032983172 40.99167634 -1.612695679 0.256942712 RRS(ph)PS(ph)PKPTK ddPTM_SK-BR-3_Pertuzumab_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(0.999)PKPT(0.001)K;RRS(0.999)PS(0.996)PKPT(0.005)K;RRS(1)PS(0.974)PKPT(0.026)K;RRS(1)PS(0.999)PKPT(0.001)K;RRS(1)PS(0.995)PKPT(0.005)K;RRS(0.999)PS(0.753)PKPT(0.248)K 119.17 0.0010453 8700000000 5825200 2956660 3777740 3491280 3818840 2627630 4200970 3040460 4863140 TRUE FALSE 5460611.13 3175574.183 3867349.777 3580872.156 3518923.711 3386184.125 3571073.548 3420068.124 4051450.517 1.347816321 0.783811667 0.954559302 0.883849412 0.868558976 0.835795504 0.881430869 0.844158928 1 21.95000709 4.745475987 24.99259263 0.876396293 1.347816539 0.854819608 0.060359344 262.6421547 949181.7969 0.012837215 0.128154672 55651.38622 -4.745475987 0.471420246 RRS(ph)PS(ph)PYYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.621)PS(0.748)PY(0.405)Y(0.054)S(0.172)R;RRS(0.992)PS(0.986)PY(0.021)YSR 104.97 0.012844 16412900000 2860300 3135400 2822000 3294300 3137600 2642900 2973700 2876700 3365600 TRUE FALSE 2681278.929 3367548.278 2888939.173 3378837.315 2891185.552 3405862.326 2527821.291 3235862.327 2803859.617 0.956281446 1.201040258 1.030343729 1.205066507 1.031144903 1.214705011 0.90155059 1.154074301 1 21.41898269 1.740714038 24.99999998 1.012655891 1.109466787 0.136205297 0.103796999 0.572350478 6686.83752 0.04150503 0.023016732 55.0445135 -1.740714038 0.096810896 RRS(ph)PSLSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 RRSPSLSSK 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RRS(0.994)PS(0.006)LSSK;RRS(0.984)PS(0.016)LSSK;RRS(0.996)PS(0.004)LSSK;RRS(0.996)PS(0.004)LSSK;RRS(0.992)PS(0.008)LSSK;RRS(0.998)PS(0.002)LSSK;RRS(0.904)PS(0.096)LSSK;RRS(0.991)PS(0.009)LSSK 143.55 8.01E-05 24950710000 5335580 6127610 4661680 4437210 6192730 3341250 5311080 5668300 7404950 TRUE FALSE 5001635.572 6581304.62 4772257.251 4551076.321 5706377.966 4305814.634 4514732.86 6375999.732 6169016.007 0.810767157 1.066832152 0.773584838 0.73773132 0.925006186 0.697974301 0.73184003 1.033552146 1 22.55660896 5.081364258 15.55560677 0.8547464 0.000132167 0.006944301 0.134556928 11195040.9 33860680.33 0.031849379 319913305.7 120604.707 -5.081364258 -0.854614233 RRS(ph)PSPYY(ph)SR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRSPSPYYSR 10 2 P62995;P62995-3;H7BXF3;Q13595;Q13595-3 P62995;Q13595 TRA2B;TRA2A Transformer-2 protein homolog beta;Transformer-2 protein homolog alpha 2 RRS(0.525)PS(0.525)PY(0.285)Y(0.507)S(0.158)R 90.759 0.017413 1288800000 688380 721330 609820 778930 741740 642350 664080 652610 773300 TRUE FALSE 645295.5246 774738.0237 624285.2184 798918.6625 683486.7324 827786.0173 564507.369 734089.7951 644231.2343 1.001652032 1.202577557 0.969039042 1.240111656 1.060933864 1.284920652 0.876249612 1.139481844 1 19.29721908 1.725844786 25 1.000388635 1.118988565 0.190139423 0.117176051 1.373841673 2689.35652 0.048081013 0.026663444 53.19181216 -1.725844786 0.118599931 KT(ph)SDANETEDHLESLICK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTSDANETEDHLESLICK 18 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 KT(0.62)S(0.38)DANETEDHLESLICK;KT(0.5)S(0.5)DANETEDHLESLICK 307.49 4.11E-51 1891610000 3977770 2690930 2884600 4642980 4175640 1816830 2285730 1111900 1684430 TRUE FALSE 3728808.476 2890169.257 2953024.074 4762126.727 3847702.078 2341319.327 1943006.006 1250723.163 1403287.751 2.657194487 2.059569931 2.104361042 3.3935497 2.741919521 1.668452764 1.384609824 0.89128061 1 20.42037944 1.896083887 2.150075514 1.051428298 2.480482355 0.743763476 0.401270586 0.186491305 1.591302584 0.262944171 0.127600078 78.71978271 -1.896083887 1.429054056 up RRS(ph)S(ph)DEDAAGEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRSSDEDAAGEPK 13 2 E9PHH9;Q9BUI4 E9PHH9 POLR3C DNA-directed RNA polymerase III subunit RPC3 2 RRS(1)S(1)DEDAAGEPK 125.18 0.00099962 176010000 410590 301920 347270 340000 315380 185380 322640 222130 380740 TRUE FALSE 384891.9048 324274.4709 355507.4084 348724.9756 290611.327 238896.1966 274263.1272 249863.4195 317192.0343 1.213434964 1.022328545 1.120795512 1.099412778 0.916199953 0.753159508 0.864659568 0.78773548 1 18.27499702 2.634629074 3.503921021 0.839126232 1.10075178 0.711657541 0.079316566 0.119733066 2.739574949 0.02401667 0.022570324 431.1506788 -2.634629074 0.261625548 RRS(ph)SDEDAAGEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RRSSDEDAAGEPK 13 2 E9PHH9;Q9BUI4 E9PHH9 POLR3C DNA-directed RNA polymerase III subunit RPC3 1 RRS(0.767)S(0.233)DEDAAGEPK;RRS(0.5)S(0.5)DEDAAGEPK 137.81 4.44E-05 1553400000 1952880 1298310 1443980 1512130 2009920 1253420 2117700 1485780 2294700 TRUE FALSE 1830652.727 1394438.223 1478231.887 1550933.816 1852068.991 1615262.006 1800170.545 1671282.904 1911699.746 0.957604734 0.72942324 0.773255262 0.811285255 0.968807468 0.84493499 0.941659666 0.874239225 1 20.86642452 2.848124955 5.937740207 0.916940897 0.794021942 0.325256285 0.073534083 0.225360885 10.51241849 0.020824972 0.022144988 704.8958528 -2.848124955 -0.122918955 RRS(ph)SS(ph)PFLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RRSSSPFLSK 10 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 RRS(0.995)S(0.127)S(0.878)PFLSK;RRS(0.994)S(0.106)S(0.897)PFLS(0.003)K 123.72 0.002236 1041220000 1799300 1541240 1718850 1608350 1756640 1142100 1795950 1448510 1927050 TRUE FALSE 1686685.025 1655355.013 1759621.934 1649622.984 1618680.58 1471805.73 1526663.97 1629359.662 1605412.906 1.050623811 1.031108575 1.09605568 1.027538136 1.008264338 0.916777064 0.950947862 1.01491626 1 20.61451297 2.6578087 2.577336899 0.963605382 1.057373278 0.567294667 0.03260356 0.176602927 2.305738066 0.011197134 0.010609912 454.7876888 -2.6578087 0.093767896 RRSPS(ph)PY(ph)YSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.019)PS(0.988)PY(0.732)Y(0.231)S(0.03)R;RRS(0.224)PS(0.949)PY(0.823)Y(0.002)S(0.001)R 107.69 0.0036932 13263400000 3829170 4333550 3970710 4235820 4651910 3631130 4086090 3844060 4863600 TRUE FALSE 3589509.085 4654410.551 4064897.116 4344518.312 4286567.754 4679378.285 3473418.738 4323999.353 4051833.74 0.885897427 1.148717062 1.003224065 1.072235089 1.057932785 1.154879145 0.857246116 1.067170973 1 21.95014355 1.742713429 25 0.963656735 1.059794973 0.138656274 0.090619012 1.118546942 6765.588309 0.03717172 0.020613511 55.29850992 -1.742713429 0.096138238 RRSPS(ph)PYYS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRSPSPYYSR 10 2 P62995;P62995-3;H7BXF3;Q13595;Q13595-3 P62995;Q13595 TRA2B;TRA2A Transformer-2 protein homolog beta;Transformer-2 protein homolog alpha 2 RRS(0.034)PS(0.976)PY(0.429)Y(0.069)S(0.493)R 103.14 0.01404 1205500000 529430 660970 603230 643100 613460 540230 673210 534780 655110 TRUE FALSE 496293.9214 709908.9065 617538.9005 659603.0348 565281.3262 696185.6311 572268.4103 601548.4602 545767.9088 0.909349768 1.30075238 1.131504602 1.208577903 1.035754058 1.275607488 1.048556357 1.102205627 1 19.05792804 1.166734253 1.250778496 1.006665915 1.157651017 0.09844138 0.116568018 0.745744374 2.355873935 0.096887599 0.030529874 14.6802771 -1.166734253 0.150985101 RRSS(ph)PSARPPDVPGQQPQAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRSSPSARPPDVPGQQPQAAK 21 3 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 RRS(0.207)S(0.637)PS(0.156)ARPPDVPGQQPQAAK 160.43 1.17E-10 324490000 178180 164640 138420 152180 198990 115430 199910 166900 308760 TRUE FALSE 167028.0319 176830.1169 141703.3878 156085.1964 183362.1281 148752.7672 169935.3514 187737.8324 257225.9613 0.6493436 0.687450505 0.550890692 0.606801878 0.712844563 0.578296088 0.66064619 0.729855693 1 17.97267673 0.763336758 1.660677216 0.999768662 0.629559586 0.853717338 0.047592284 0.286314692 1.324356118 0.043824088 0.012521973 5.798781678 -0.763336758 -0.370209076 RRT(ph)AS(ph)PPPPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRTASPPPPPK 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRT(1)AS(1)PPPPPK 71.354 0.054365 358180000 511500 442230 481000 447420 479000 320910 513910 398530 476830 TRUE FALSE 479486.1281 474973.1693 492409.5471 458901.5547 441381.2722 413551.5075 436853.9664 448287.3478 397243.9926 1.207031792 1.19567112 1.23956449 1.155213328 1.11110874 1.041051634 1.099711952 1.128493712 1 18.59966588 2.842187722 2.253747843 1.077597442 1.213322946 0.746822689 0.03711488 0.143214044 1.43114884 0.011730218 0.012465852 695.3248043 -2.842187722 0.135725504 RRT(ph)AS(ph)PPPPPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRTASPPPPPKR 12 3 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRT(1)AS(1)PPPPPKR 77.191 0.05509 908870000 235550 182080 216950 213080 233890 170940 216010 181310 247960 TRUE FALSE 220807.346 195561.3927 222096.1565 218547.9935 215521.2229 220287.603 183621.3058 203946.9526 206573.8741 1.068902575 0.946689863 1.075141556 1.057965314 1.04331307 1.06638656 0.888889297 0.98728338 1 17.65629828 1.751322076 25 0.949503472 1.036229751 0.410249838 0.046764633 3.5367404 6939.374228 0.020959759 0.011623246 56.40558087 -1.751322076 0.086726279 RRT(ph)PS(ph)PPPR ddPTM_SK-BR-3_Pertuzumab_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 69.352 0.061232 10138000000 120020 152060 133880 125180 143520 137750 124540 108550 155850 TRUE FALSE 112508.1624 163318.6806 137055.6968 128392.3307 132248.5181 177516.1888 105866.3832 122102.7064 129837.6282 0.866529711 1.257868639 1.055593042 0.988868424 1.0185685 1.367216818 0.815375209 0.940426194 1 16.98634903 1.628473052 24.9999563 0.908449831 1.099825052 0.239535654 0.145237731 1.044186621 1263.489541 0.062143552 0.034410498 42.50823293 -1.628473052 0.191375221 RRT(ph)SS(ph)KSEAGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RRTSSKSEAGAR 12 3 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 2 RRT(0.994)S(0.096)S(0.862)KS(0.047)EAGAR;RRT(0.996)S(0.156)S(0.424)KS(0.424)EAGAR 83.894 0.023756 336383000 171187 137163 136238 171679 193381 99520 174042 135194 221939 TRUE FALSE 160472.7112 147318.6912 139469.6297 176084.5738 178193.6363 128249.8084 147946.0178 152073.2685 184895.9471 0.867908214 0.796765389 0.754314153 0.952344151 0.963750905 0.69363234 0.800158252 0.82248027 1 17.49635408 -2.153735713 2.194391877 1.388771569 0.821228852 0.284358724 0.082654007 7657734.212 1651622.282 14816135.62 0.020124075 0.007018823 2.153735713 -0.567542717 RRTCET(ph)GEPMEAESGDTSSEGPAQVYLPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRTCETGEPMEAESGDTSSEGPAQVYLPGR 30 2 Q9BQ67 Q9BQ67 GRWD1 Glutamate-rich WD repeat-containing protein 1 1 RRT(0.438)CET(0.537)GEPMEAES(0.02)GDT(0.004)S(0.001)SEGPAQVYLPGR 71.974 0.0076277 215190000 45233 48465 55991 44370 55792 44475 48956 39326 70343 TRUE FALSE 42401.94727 52053.39903 57319.13296 45508.60932 51410.32137 57314.21051 41615.50229 44235.93767 58602.29887 0.723554333 0.888248414 0.97810383 0.776566964 0.877274823 0.978019832 0.710134297 0.75484987 1 15.83866964 1.733848032 24.99999991 0.79491113 0.881470623 0.017086121 0.108278998 1.073900096 5643.859198 0.046488399 0.025780121 54.18112671 -1.733848032 0.086559493 QELASGLPS(ph)PAATQELPVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 QELASGLPSPAATQELPVER 20 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 QELASGLPS(1)PAATQELPVER;QELASGLPS(1)PAATQELPVER;QELASGLPS(1)PAATQELPVER 379.2 1.17E-112 831030000 1402140 1397420 1699780 2071220 1938990 989280 958990 749470 710810 TRUE FALSE 1314382.56 1500886.431 1740099.584 2124371.012 1786709.547 1274869.076 815198.3523 843042.9793 592171.219 2.219598856 2.534548088 2.938507527 3.587426987 3.017217807 2.152872405 1.376626094 1.423647338 1 19.17565485 1.906448737 2.445884859 1.267794501 2.856091675 0.79648752 0.366828876 0.136745445 1.487753263 0.219478772 0.111501323 80.62110326 -1.906448737 1.588297175 up RRVS(ph)EVEEEKEPVPQPLPSDDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RRVSEVEEEKEPVPQPLPSDDTR 23 3 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 1 RRVS(1)EVEEEKEPVPQPLPSDDTR;RRVS(1)EVEEEKEPVPQPLPSDDTR;RRVS(1)EVEEEKEPVPQPLPSDDTR;RRVS(1)EVEEEKEPVPQPLPSDDTR;RRVS(1)EVEEEKEPVPQPLPSDDTR;RRVS(1)EVEEEKEPVPQPLPSDDTR 232.54 3.00E-33 8637420000 4621320 3507740 3612890 4821880 5450790 3002000 4477160 3386000 5104860 TRUE FALSE 4332079.83 3767456.719 3698589.457 4945617.604 5022706.941 3868628.667 3805851.422 3808749.554 4252825.887 1.018635596 0.885871376 0.869678081 1.1629015 1.181028115 0.909660722 0.89489942 0.895580881 1 22.01999036 -2.105106205 7.811876996 1.245231812 0.962974575 0 0.114155797 0.196080848 0.002638203 0.0444516 0.02754996 0.007850436 2.105106205 -0.282257237 RRVS(ph)GPDPKPGSNCSPAQSVLSEVPSVPTNGMAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRVSGPDPKPGSNCSPAQSVLSEVPSVPTNGMAK 34 3 P22314;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 RRVS(0.522)GPDPKPGS(0.118)NCS(0.118)PAQS(0.118)VLS(0.118)EVPS(0.006)VPTNGMAK 52.92 0.042509 246660000 140390 138630 127700 145570 181450 79989 147490 110150 269320 TRUE FALSE 131603.2405 148894.3094 130729.1043 149305.5726 167199.6489 103080.5258 125375.2437 123902.47 224368.7521 0.586548881 0.663614287 0.582652901 0.665447266 0.745200244 0.459424607 0.558791019 0.552226942 1 17.77551224 -1.906100705 2.577885694 1.227844718 0.60214672 0.72449283 0.077182423 23968092.9 13987026.93 33105031.8 0.020437229 0.012413644 1.906100705 -0.625697998 RRVS(ph)HS(ph)PPPK ddPTM_SK-BR-3_Pertuzumab_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 86.467 0.0072606 584225000 689632 548322 565090 587006 650835 476974 697871 548075 704004 TRUE FALSE 646469.1641 588920.3314 578494.2017 602069.5678 599721.0444 614668.6508 593231.7223 616503.3702 586501.1844 1.102246988 1.00412471 0.986347883 1.026544505 1.02254021 1.048026274 1.011475745 1.051154519 1 19.1617745 3.040030886 24.99494703 1.02747031 1.017257583 0 0.033943287 839.9624733 524458.582 0.009454445 0.011300223 1096.556178 -3.040030886 -0.010212728 RRYS(ph)DFEWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RRYSDFEWLR 10 2 O60493-4;O60493;O60493-3 O60493-4 SNX3 Sorting nexin-3 1 RRYS(1)DFEWLR 119.88 0.00049905 93824000 41921 59121 45217 47142 68562 35738 52873 49827 115040 TRUE FALSE 39297.23944 63498.38036 46289.56859 48351.74353 63177.41709 46054.98044 44945.1845 56048.01063 95839.08081 0.410033559 0.662552059 0.482992618 0.504509675 0.659203078 0.480544889 0.468965104 0.584813733 1 16.54832645 0.956028239 20.34619331 1.000000001 0.53190565 0.773600922 0.080186165 352.8200645 163254.4019 0.072671578 0.018167894 9.037082343 -0.956028239 -0.468094351 RS(ph)AS(ph)PERMD ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RSASPERMD 9 2 Q16629;Q16629-4;C9JAB2;H7BZZ6 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 2 RS(1)AS(1)PERMD;RS(1)AS(1)PERMD;RS(1)AS(1)PERMD;RS(1)AS(1)PERMD 89.663 0.0067795 2212104000 1624380 1517780 1627460 1537130 1547540 1429400 1820670 1395630 1437930 TRUE FALSE 1522712.955 1630158.01 1666064.12 1576575.358 1426002.451 1842044.576 1547677.436 1569877.478 1197930.194 1.27111994 1.36081219 1.390785647 1.316082829 1.190388604 1.537689412 1.291959618 1.310491618 1 20.19211241 0.569509725 1.869515286 1.000111108 1.346229882 0.578598809 0.089640232 1.718011548 6.67876951 0.077824156 0.021663461 3.711160399 -0.569509725 0.346118773 RS(ph)ASASHQADIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RSASASHQADIK 12 1 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 RS(0.52)AS(0.256)AS(0.224)HQADIK;RS(0.719)AS(0.211)AS(0.07)HQADIK;RS(0.451)AS(0.451)AS(0.098)HQADIK 166.48 3.17E-05 898890000 1624020 1480670 1221280 1326790 1861810 1024840 2033200 1656250 1567940 TRUE FALSE 1522375.487 1590300.347 1250249.338 1360837.678 1715590.953 1320694.671 1728340.535 1863036.458 1306240.685 1.16546323 1.217463494 0.957135506 1.041797039 1.31338043 1.011065332 1.323140946 1.426258177 1 20.31698932 1.69431499 9.062826162 1.279288691 1.115491479 0.140987981 0.147274111 0.174902194 26.11666777 0.065804969 0.035169078 49.46693364 -1.69431499 -0.163797212 RS(ph)ASPHDVDLCLVSPCEFEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSASPHDVDLCLVSPCEFEHR 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 RS(0.5)AS(0.5)PHDVDLCLVSPCEFEHR 96.317 0.00060961 376680000 63990 61361 58918 62743 69636 54631 69978 56680 92308 TRUE FALSE 59984.98013 65904.23229 60315.56278 64353.0916 64167.06946 70402.08284 59485.44854 63756.62277 76901.19847 0.780026597 0.856998767 0.784325394 0.836828201 0.834409226 0.91548746 0.773530839 0.829071901 1 16.23071846 -2.221242684 2.21475733 1.537885942 0.825952867 0.629616314 0.041859475 2808681.226 494553.9671 7571646.334 0.009277646 0.006008379 2.221242684 -0.711933075 RS(ph)DSASSEPVGIYQGFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RSDSASSEPVGIYQGFEK 18 1 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 RS(0.508)DS(0.132)AS(0.309)S(0.052)EPVGIYQGFEK;RS(0.81)DS(0.146)AS(0.034)S(0.01)EPVGIYQGFEK;RS(0.924)DS(0.071)AS(0.006)SEPVGIYQGFEK;RS(0.801)DS(0.091)AS(0.102)S(0.006)EPVGIYQGFEK 271.11 3.67E-39 2289897000 2679290 2465540 2659670 3126650 3436840 2033160 2708610 1989330 3255190 TRUE FALSE 2511598.022 2648091.147 2722758.628 3206885.132 3166924.45 2620100.286 2302479.076 2237702.23 2711877.76 0.92614721 0.976478802 1.004012301 1.18253307 1.167797641 0.966157223 0.849034979 0.825148634 1 21.37086072 1.998569678 24.98886709 0.882864493 1.042869519 0.397104154 0.089969708 55.78605989 974635.8974 0.035778365 0.026060792 99.671198 -1.998569678 0.160005026 RS(ph)DSMTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSDSMTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR 38 1 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 RS(0.541)DS(0.371)MT(0.087)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR;RS(0.553)DS(0.378)MT(0.069)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR 274.11 1.04E-76 1204180000 197440 299980 227070 250646 314120 217930 302030 224499 347490 TRUE FALSE 185082.5828 322190.8313 232456.2076 257078.0007 289450.2823 280842.8532 256743.4054 252528.1943 289491.6741 0.639336462 1.112953705 0.802980633 0.88803245 0.999857019 0.970124112 0.886876647 0.872315914 1 18.14316233 RS(ph)EEKEAGEI ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSEEKEAGEI 10 2 Q9NQ29-3;Q9NQ29;B8ZZ08 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 1 RS(1)EEKEAGEI 100.31 0.0032306 240090000 295250 210370 246500 267460 325590 175700 293940 211850 403230 TRUE FALSE 276770.8295 225946.0137 252347.0964 274323.4764 300019.4748 226421.7377 249866.4258 238299.9388 335928.308 0.823898501 0.672601886 0.751193306 0.816613158 0.893105664 0.674018034 0.743808782 0.709377368 1 18.35779385 -1.496376196 3.118303837 1.00662584 0.752930653 0.537716193 0.06944539 58705651.8 69955390.83 3338464.215 0.01644096 0.031887745 1.496376196 -0.253695187 RS(ph)ET(ph)PPHWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSETPPHWR 9 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 RS(1)ET(1)PPHWR 65.043 0.05858 405180000 258790 298340 269310 264080 295260 215270 302450 226640 254360 TRUE FALSE 242592.7959 320429.404 275698.1604 270856.7399 272071.4706 277414.9544 257100.4303 254936.5029 211905.6728 1.144815015 1.512132261 1.301041906 1.278194851 1.283927264 1.309143596 1.213277714 1.203065966 1 17.69306268 0.755768005 0.417032329 0.975619991 1.360557437 0.511523768 0.091387203 1.155391555 0.468039792 0.146602877 0.06240675 5.698597785 -0.755768005 0.384937447 RS(ph)FSSQRPVDR ddPTM_SK-BR-3_Pertuzumab_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(0.495)FS(0.341)S(0.164)QRPVDR;RS(0.575)FS(0.397)S(0.029)QRPVDR 67.646 0.046784 586570000 286791 431970 290395 339400 555290 198183 584930 393280 687420 TRUE FALSE 268841.2632 463953.5083 297283.3065 348109.5786 511679.7633 255395.2149 497225.1767 442381.8737 572685.1611 0.469439897 0.810137122 0.51910426 0.60785507 0.893474806 0.445960944 0.868234783 0.772469594 1 19.1273827 1.048756773 0.799802903 0.999032199 0.636854101 0.381589224 0.150853777 0.65856298 0.952093328 0.129091442 0.047970003 11.18811117 -1.048756773 -0.362178098 RS(ph)LSMDSQVPVYSPSIDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSLSMDSQVPVYSPSIDLK 19 1 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 RS(0.416)LS(0.411)MDS(0.173)QVPVYSPSIDLK 185.5 9.70E-15 119250000 260820 256520 220130 252560 290080 164970 326250 224820 372430 TRUE FALSE 244495.7418 275513.0077 225351.5876 259041.1172 267298.2869 212594.1609 277331.8413 252889.2719 310269.027 0.788012081 0.887981022 0.726310292 0.834891964 0.861504899 0.685192986 0.89384314 0.815064508 1 18.24316016 0.356427746 0.961846728 1.000641795 0.807338074 0.449184667 0.065920512 2.272403849 2.62390447 0.061297015 0.018639829 2.272101593 -0.356427746 -0.193303721 RS(ph)LSVEHLETK ddPTM_SK-BR-3_Pertuzumab_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(0.604)LS(0.396)VEHLETK 129.01 0.00015557 264060000 423790 394710 331350 374350 443530 269180 528050 376780 493890 TRUE FALSE 397265.7404 423934.7391 339209.7785 383956.4548 408696.9429 346887.8962 448873.8047 423821.8124 411456.5683 0.965510751 1.030326824 0.824412112 0.933163994 0.993293033 0.843072934 1.090938483 1.030052368 1 18.65038063 1.702675274 10.81929783 1.04423155 0.9331401 0.379659003 0.065348806 0.117482655 26.08243104 0.030187768 0.016401915 50.4284099 -1.702675274 -0.111091451 RS(ph)NSPDKFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RSNSPDKFK 9 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 RS(0.893)NS(0.107)PDKFK;RS(0.907)NS(0.093)PDKFK;RS(0.623)NS(0.377)PDKFK;RS(0.914)NS(0.086)PDKFK 120.84 0.00049672 27764100000 44747600 24109640 29365200 27833100 30703700 20243690 37457300 25166200 39312300 TRUE FALSE 41946927.59 25894742.83 30061756.41 28547344.47 28292355.25 26087714.67 31840925.6 28308255.47 32750823.16 1.280790024 0.790659297 0.917893155 0.871652731 0.863866997 0.796551419 0.972217567 0.864352487 1 24.96502783 4.746494911 24.89679379 0.880219699 1.280790231 0.77762808 0.066536749 402.7553413 1263763.538 0.014510516 0.159890442 55782.10654 -4.746494911 0.400570532 RS(ph)PERPTGDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RSPERPTGDLR 11 2 Q5T200;Q5T200-2;Q5T9K0 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 RS(1)PERPTGDLR;RS(0.998)PERPT(0.002)GDLR;RS(1)PERPTGDLR 94.09 0.0069016 3534660000 2906880 3149210 3128650 3233890 3374830 2621760 3226810 2759950 3171860 TRUE FALSE 2724943.57 3382380.785 3202863.055 3316877.092 3109784.465 3378619.551 2742979.797 3104535.833 2642456.075 1.031216222 1.280014006 1.212078068 1.255225063 1.176853797 1.27859062 1.038041776 1.174867527 1 21.33344806 1.285627364 0.954624436 1.017687379 1.215629166 0.303684967 0.086988976 0.507108465 0.977998202 0.072760746 0.025879982 19.3031135 -1.285627364 0.197941786 RS(ph)PESCSKPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSPESCSKPEK 11 2 Q03111 Q03111 MLLT1 Protein ENL 1 RS(0.997)PES(0.003)CSKPEK;RS(0.902)PES(0.097)CS(0.001)KPEK 157.68 2.40E-05 2235710000 1731180 1106050 1355140 1342980 1454790 987930 1702210 1182400 1830770 TRUE FALSE 1622828.534 1187943.093 1387284.561 1377443.14 1340536.662 1273129.353 1446979.413 1330025.243 1525202.66 1.064008461 0.778875571 0.909573919 0.903121386 0.878923632 0.834727992 0.948712883 0.872031814 1 20.54056952 -0.288847744 0.651355629 1.00853457 0.886746618 0.133054601 0.075151994 13.76206928 5.190113447 0.364563521 0.025691659 0.514223897 0.288847744 -0.121787952 RS(ph)PGGGSEANGLALVSGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSPGGGSEANGLALVSGFK 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 RS(0.999)PGGGS(0.001)EANGLALVSGFK;RS(0.992)PGGGS(0.008)EANGLALVSGFK 189.02 9.14E-15 386450000 659350 552980 614470 601360 676650 444180 664340 585600 674040 TRUE FALSE 618082.4605 593923.2146 629045.5186 616791.9157 623508.6385 572407.5553 564728.3844 658713.4491 561538.3695 1.100694973 1.057671651 1.12021823 1.098396742 1.110358031 1.019356087 1.005680849 1.17305154 1 19.09902508 2.245192798 24.99961614 1.044153256 1.095185697 0.177833358 0.050513036 247.5419196 933096.7015 0.016662291 0.013654045 175.870419 -2.245192798 0.051032441 RS(ph)PLGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RSPLGQK 7 1 A0A2R8Y6S3;C9J167;Q68D20;P54278-3;P54278 A0A2R8Y6S3 PMS2;PMS2CL Protein PMS2CL;Mismatch repair endonuclease PMS2 1 RS(1)PLGQK;RS(1)PLGQK;RS(1)PLGQK;RS(1)PLGQK;RS(1)PLGQK;RS(1)PLGQK 98.048 0.0070738 2435313000 5523620 4627040 4860410 5142470 5290230 3676350 5963810 4437140 5426610 TRUE FALSE 5177906.484 4969630.856 4975701.22 5274434.486 4874756.676 4737652.564 5069592.056 4991126.696 4520873.734 1.145333134 1.099263361 1.100606103 1.16668476 1.078277555 1.047950649 1.121374397 1.104018159 1 22.10817019 RS(ph)PLSDPPSQDPTPAAT(ph)PETPPVISAVVHATDEEK ddPTM_SK-BR-3_Pertuzumab_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 2 RS(0.896)PLS(0.092)DPPS(0.012)QDPTPAAT(0.573)PET(0.381)PPVIS(0.046)AVVHATDEEK 158.36 2.02E-14 33510000 40046 27560 38697 34738 34691 24371 41819 29156 21958 TRUE FALSE 37539.59234 29600.57108 39614.91111 35629.43589 31966.5088 31406.51207 35548.62918 32796.19078 18293.06795 2.052121189 1.618130494 2.165569561 1.947701501 1.747465701 1.716853191 1.94328416 1.792820695 1 14.15900943 -2.11254082 0.411490315 5.89E-18 1.901338209 0.749905201 0.159644988 27.05666004 1.608431596 25.34526566 0.093902127 0.00771719 2.11254082 1.901338209 RS(ph)PLSDPPSQDPTPAATPETPPVISAVVHATDEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSPLSDPPSQDPTPAATPETPPVISAVVHATDEEK 35 1 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911;H0Y9Y7 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 RS(0.994)PLS(0.006)DPPSQDPTPAATPETPPVISAVVHATDEEK;RS(0.972)PLS(0.028)DPPSQDPTPAATPETPPVISAVVHATDEEK 148.17 3.84E-11 279153000 263940 176562 228078 215246 215236 183037 285550 193975 140199 TRUE FALSE 247420.4665 189634.8342 233488.1179 220769.5768 198332.2328 235876.8105 242734.4284 218193.2057 116798.8812 2.118346204 1.623601462 1.999061254 1.890168592 1.698066204 2.019512586 2.07822563 1.868110409 1 16.83366693 0.939541874 22.35056006 0.999999999 1.906767992 0.771411389 0.15613659 4015.671416 1484542.154 0.148602518 0.037150629 8.700453169 -0.939541874 0.906767993 RS(ph)PPAPGLQPMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RSPPAPGLQPMR 12 1 P15408;P15408-3;P15408-2;C9JCN8 P15408 FOSL2 Fos-related antigen 2 1 RS(1)PPAPGLQPMR;RS(1)PPAPGLQPMR;RS(1)PPAPGLQPMR 110.38 0.00091613 1009440000 1203690 1492760 1302710 1308540 1662100 845770 1151410 1242030 1735020 TRUE FALSE 1128353.192 1603285.504 1333610.896 1342119.352 1531565.371 1089930.069 978766.7597 1397100.18 1445433.953 0.780632826 1.109207031 0.922637035 0.928523471 1.059588622 0.754050413 0.677143883 0.966561064 1 20.46307126 2.231228187 24.99969344 0.804510771 0.973901031 0.107594824 0.129501074 208.158243 709702.9171 0.044687133 0.033674294 170.3053091 -2.231228187 0.16939026 RS(ph)PPPGPDGHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSPPPGPDGHAK 12 1 P57081;P57081-2;P57081-3 P57081 WDR4 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 1 RS(1)PPPGPDGHAK 63.128 0.034268 102530000 138180 133880 155790 159500 154070 140270 164780 140900 132240 TRUE FALSE 129531.5605 143792.6145 159485.4124 163593.04 141969.9637 180763.6719 140072.7687 158491.6752 110168.2897 1.175760837 1.305208739 1.447652612 1.484937639 1.288664498 1.640795844 1.271443617 1.438632438 1 16.7493495 -1.127899544 3.830761649 0.999852416 1.384202157 0.455805727 0.131024277 3319257.355 1956963.148 4442.934514 0.027833458 0.074490426 1.127899544 0.384349741 RS(ph)PPWEP ddPTM_SK-BR-3_Pertuzumab_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 125.16 0.0043178 3833400000 4594120 4826920 4877030 4710000 4866060 4037840 5331550 4271210 4802840 TRUE FALSE 4306582.23 5184310.179 4992715.455 4830866.574 4483899.276 5203498.859 4532133.573 4804479.971 4001214.976 1.076318632 1.295683988 1.247799852 1.207349918 1.120634433 1.300479702 1.132689346 1.20075527 1 21.93200671 -0.326574346 0.445343693 0.960106217 1.224251285 0.398594764 0.074214242 6.060533666 1.232468881 0.45499072 0.039392472 0.471439159 0.326574346 0.264145069 RS(ph)PRPDHPGTPPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSPRPDHPGTPPHK 14 2 P30291 P30291 WEE1 Wee1-like protein kinase 1 RS(1)PRPDHPGTPPHK 53.403 0.070704 94194000 107170 142950 138590 129000 152610 119590 111900 98880 118500 TRUE FALSE 100462.421 153534.1667 141877.4202 132310.3584 140624.6262 154113.6916 95121.63383 111225.3857 98721.58446 1.017633799 1.555223891 1.437146912 1.340237387 1.424456738 1.561094187 0.963534311 1.126657218 1 16.59107793 1.710657768 8.242908986 1.038154158 1.413126816 0.534663775 0.156528246 0.080388185 12.75937869 0.070074168 0.037155716 51.36387354 -1.710657768 0.374972657 RS(ph)PS(ph)PKPTK ddPTM_SK-BR-3_Pertuzumab_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(1)PS(0.998)PKPT(0.002)K 55.782 0.067701 246720000 347660 219410 252500 255270 257780 198230 316280 214560 327990 TRUE FALSE 325900.5812 235655.3447 258489.4192 261820.6604 237534.9986 255455.783 268856.7502 241348.2883 273246.3501 1.192698754 0.862428152 0.945994042 0.958185389 0.869307124 0.93489184 0.983935376 0.883262624 1 18.0598427 4.747444682 24.94439653 0.928427082 1.192698894 0.760687954 0.04634492 537.5156447 1509186.513 0.010465948 0.127462417 55904.23158 -4.747444682 0.264271812 RS(ph)PSPYYSR ddPTM_SK-BR-3_Pertuzumab_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 1 RS(1)PSPYYSR 84.352 0.0095248 132920000 62154 77870 66238 87914 84613 75763 54218 83272 57888 TRUE FALSE 58263.89209 83635.57582 67809.19664 90170.02208 77967.83629 97634.54819 46088.51424 93668.6925 48226.11883 1.20813977 1.734238165 1.40606788 1.869734166 1.616713892 2.024515979 0.955675376 1.942281377 1 15.55752709 -0.488258447 8.477233486 0.999998735 1.572372964 0.237125208 0.333082373 0 0 0.289994838 0.068352439 0.324893897 0.488258447 0.57237423 RS(ph)PVPAQIAITVPK ddPTM_SK-BR-3_Pertuzumab_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 106.19 0.00058573 1867580000 3200080 2879100 3320800 3142690 3555410 2696490 3911670 3199470 4594390 TRUE FALSE 2999792.705 3092271.56 3399570.944 3223336.746 3276182.44 3474922.889 3325151.398 3598930.872 3827556.628 0.783735682 0.807897011 0.888183056 0.842139532 0.855946171 0.907869753 0.868739961 0.940268485 1 21.86799229 4.981397665 0.030439684 1.606681049 1.47E-09 0.857543897 0.023674494 258.4740068 1.139816482 23.50866696 37.93269422 95807.09341 -4.981397665 -1.606681048 RS(ph)PVSTRPLPSASQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSPVSTRPLPSASQK 15 2 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 RS(1)PVSTRPLPSASQK;RS(1)PVSTRPLPSASQK 162.79 8.22E-07 294430000 464380 412650 409740 420740 491370 333610 464800 398110 544300 TRUE FALSE 435315.2847 443203.0354 419459.2263 431536.9007 452779.7823 429917.7913 395107.555 447814.9098 453452.8137 0.960001287 0.977396152 0.925033903 0.951668812 0.998515763 0.948098189 0.871331135 0.987566724 1 18.79059291 1.99435294 24.98362922 0.931430726 0.960142528 0 0.040193405 579.3800091 2563285.553 0.014538252 0.010409466 98.70813344 -1.99435294 0.028711802 RS(ph)S(ph)VKRSDSGDEQLPT(ph)ICR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSVKRSDSGDEQLPTICR 19 3 Q01668-3 Q01668-3 3 RS(0.5)S(0.5)VKRS(0.5)DS(0.5)GDEQLPT(1)ICR;RS(0.5)S(0.5)VKRS(0.5)DS(0.5)GDEQLPT(0.999)ICR 64.507 0.023638 635650000 578380 447500 495200 474900 423660 594520 709990 501670 391580 TRUE FALSE 542180.2282 480633.3656 506946.3779 487086.738 390387.4526 766148.2728 603533.5907 564304.6038 326222.7683 1.66199383 1.473328695 1.553988339 1.493110798 1.196689779 2.348543226 1.850065812 1.729813669 1 18.31549795 2.267220766 24.99999949 1.827479996 1.486927251 0.091188079 0.347352926 323.0413492 281785.0646 0.107530675 0.089951898 185.02089 -2.267220766 -0.340552744 RS(ph)SAIGIENIQEVQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RSSAIGIENIQEVQEK 16 1 J3KPC5;P47736-3;P47736;P47736-4;F2Z357;X6R8W7;P47736-2;A0A0A0MQY8 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 RS(0.5)S(0.5)AIGIENIQEVQEK;RS(0.5)S(0.5)AIGIENIQEVQEK;RS(0.677)S(0.323)AIGIENIQEVQEK;RS(0.687)S(0.313)AIGIENIQEVQEK 299.85 4.56E-46 7062010000 6425863 4821305 5713756 4887282 6763167 3799324 5953391 5472432 9471630 TRUE FALSE 6023679.705 5178279.439 5849288.991 5012697.93 6232015.145 4896127.162 5060735.288 6155677.182 7890753.764 0.763384575 0.656246487 0.741283934 0.635262242 0.789787051 0.620489158 0.641350046 0.780112695 1 22.91173169 0.919139094 4.702955797 0.999933942 0.689788144 0.742487419 0.057142748 0.199606334 10.33695075 0.050457665 0.012788805 8.301165913 -0.919139094 -0.310145798 RS(ph)SDGS(ph)LSHEEDLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSDGSLSHEEDLAK 15 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 2 RS(0.648)S(0.403)DGS(0.436)LS(0.513)HEEDLAK 114.84 0.0020105 594070000 580310 419660 495890 498890 567590 388370 587270 477820 703480 TRUE FALSE 543989.433 450732.0631 507652.745 511692.362 523013.7709 500486.1143 499214.3154 537476.8788 586064.6433 0.928207219 0.769082503 0.866206059 0.873098843 0.892416522 0.853977663 0.851807597 0.917094872 1 19.16070028 -0.985644596 0.288452046 1.083107672 0.837632237 0.492418502 0.04258406 10.98913935 0.794779099 0.787043862 0.049891578 0.103360691 0.985644596 -0.245475435 RS(ph)SDGSLSHEEDLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSDGSLSHEEDLAK 15 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 1 RS(0.349)S(0.349)DGS(0.048)LS(0.254)HEEDLAK 89.917 0.0038068 265840000 237570 287000 284630 260060 320280 253140 346000 320000 413880 TRUE FALSE 222700.9178 308249.7786 291381.558 266733.5799 295126.5007 326217.4086 294120.5121 359952.7044 344800.7542 0.645882919 0.893993922 0.845072276 0.773587577 0.855933455 0.946104104 0.853015861 1.043944075 1 18.3954034 1.673286111 0.69697413 1.016541972 0.809288126 0.528555049 0.077300554 0.584292307 0.582600755 0.068051463 0.032995979 47.1287706 -1.673286111 -0.207253847 RS(ph)SDPALIGLSTSVSDSNFSSEEPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.498)S(0.498)DPALIGLS(0.001)T(0.002)SVSDSNFSSEEPSR;RS(0.5)S(0.5)DPALIGLSTSVSDSNFSSEEPSR;RS(0.616)S(0.384)DPALIGLSTSVSDSNFSSEEPSR 233.58 4.42E-45 2093460000 322318 337629 357104 356350 405213 259752 398032 322306 351683 TRUE FALSE 302144.6917 362627.4025 365574.6755 365494.5443 373389.2055 334738.1857 338350.7967 362546.6136 292984.8353 1.031263927 1.237700245 1.247759718 1.247486218 1.274431849 1.142510278 1.154840647 1.237424501 1 18.16046647 -0.854682778 4.636841387 0.999999008 1.202761587 0.420785511 0.072205003 7.10E-07 1.75E-07 0.067028639 0.015798724 0.139738868 0.854682778 0.202762579 RS(ph)SDPLGDTASNLGSAVDELMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RSSDPLGDTASNLGSAVDELMR 22 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 RS(0.5)S(0.5)DPLGDTASNLGSAVDELMR;RS(0.5)S(0.5)DPLGDTASNLGSAVDELMR;RS(0.5)S(0.5)DPLGDTASNLGSAVDELMR;RS(0.5)S(0.5)DPLGDT(0.001)ASNLGSAVDELMR;RS(0.5)S(0.5)DPLGDTASNLGSAVDELMR;RS(0.5)S(0.5)DPLGDTASNLGSAVDELMR;RS(0.5)S(0.5)DPLGDTASNLGSAVDELMR 193.23 4.84E-18 565848000 386798 431743 452559 474171 478225 375402 530528 424204 592606 TRUE FALSE 362589.0036 463709.7009 463293.9132 486339.0306 440667.1376 483774.4633 450980.2516 477166.8032 493696.2302 0.734437457 0.939261174 0.938418981 0.98509772 0.892587609 0.979903094 0.913477203 0.966519033 1 18.9132641 4.739314113 5.391416264 0.946703303 0.726077931 0.808618953 0.033185069 0.056631504 6.097313634 0.006752539 0.046239781 54867.36623 -4.739314113 -0.220625372 RS(ph)SDSWEVWGSASTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RSSDSWEVWGSASTNR 16 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 RS(0.497)S(0.497)DS(0.007)WEVWGSASTNR;RS(0.492)S(0.492)DS(0.016)WEVWGSASTNR;RS(0.499)S(0.499)DS(0.002)WEVWGSASTNR;RS(0.5)S(0.5)DS(0.001)WEVWGSASTNR;RS(0.5)S(0.5)DS(0.001)WEVWGSASTNR;RS(0.481)S(0.481)DS(0.037)WEVWGSASTNR 220.74 6.87E-15 4880420000 1510599 1810149 1585293 1567310 1755583 1369248 1900974 1613918 2595080 TRUE FALSE 1416053.305 1944174.315 1622896.899 1607529.828 1617706.593 1764527.67 1615940.596 1815419.215 2161944.383 0.654990626 0.899271198 0.750665425 0.743557439 0.748264667 0.816176255 0.747447811 0.839715965 1 21.04389798 0.903070815 4.167967091 0.999954582 0.777484597 0.582059071 0.062374197 0.340075918 12.71723401 0.055814151 0.014233883 7.999646842 -0.903070815 -0.222469986 RS(ph)SDSYPLAPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSDSYPLAPVR 12 1 Q52LW3 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 RS(0.5)S(0.5)DSYPLAPVR;RS(0.675)S(0.325)DSYPLAPVR 186.77 6.94E-06 321380000 276800 332480 276460 287970 375070 213318 315970 321730 445520 TRUE FALSE 259475.5821 357097.1651 283017.7618 295359.7977 345613.5152 274899.4437 268593.2318 361898.6987 371159.8338 0.699093917 0.962111556 0.762522601 0.795775218 0.931171651 0.740649765 0.723659209 0.975048121 1 18.50168107 1.147310072 7.26642957 0.995270658 0.81092415 0.448859277 0.085071101 0.22928391 15.2189089 0.07990765 0.020065684 14.03815625 -1.147310072 -0.184346508 RS(ph)SDTEEESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSDTEEESR 10 1 Q96IZ7-2;Q96IZ7;C9J713;C9J8Q2;C9JVB3;F8WDM0;C9J367 Q96IZ7-2 RSRC1 Serine/Arginine-related protein 53 1 RS(0.5)S(0.5)DTEEESR 129.37 0.00018679 476610000 107850 126500 114530 134730 143510 100050 156970 114710 172900 TRUE FALSE 101099.861 135866.1916 117246.7057 138187.3999 132239.3035 128932.8108 133433.8057 129031.796 144041.873 0.701878273 0.943240939 0.813976542 0.959355755 0.918061538 0.895106458 0.926354281 0.895793656 1 17.13612874 4.744322409 24.79305826 0.909412992 0.701878172 0.654768809 0.049108387 349.1977324 1502552.743 0.010822732 0.096175135 55503.76053 -4.744322409 -0.207534821 RS(ph)SGFISELPSEEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RSSGFISELPSEEGK 15 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 RS(0.499)S(0.499)GFIS(0.001)ELPSEEGK;RS(0.499)S(0.499)GFIS(0.002)ELPSEEGK;RS(0.5)S(0.5)GFISELPSEEGK;RS(0.5)S(0.5)GFISELPSEEGK;RS(0.5)S(0.5)GFISELPSEEGK;RS(0.5)S(0.5)GFISELPSEEGK 220.63 1.01E-12 3311840000 6099280 4859330 5237120 5431020 6840240 4405350 7292000 5408730 8048560 TRUE FALSE 5717536.952 5219119.849 5361346.96 5570389.168 6303035.143 5677103.03 6198632.296 6084021.847 6705203.34 0.852701501 0.778368617 0.79958007 0.830756188 0.940021476 0.84667127 0.924451054 0.907358291 1 22.67684965 1.88252813 0.395537962 0.998048745 0.78405567 0.691048455 0.03780109 0.576692798 0.23889852 0.042609342 0.040510778 76.30063103 -1.88252813 -0.213993075 RS(ph)SGREEDDEELLR ddPTM_SK-BR-3_Pertuzumab_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(0.671)S(0.329)GREEDDEELLR 159.18 2.58E-06 216450000 110530 127090 122170 112630 135580 95546 150890 119510 173450 TRUE FALSE 103612.1246 136499.8758 125067.9301 115520.2765 124932.0937 123128.5791 128265.4453 134431.0866 144500.0745 0.717038555 0.944635332 0.865521562 0.799447868 0.864581518 0.852100455 0.887649683 0.930318459 1 17.14071071 1.062890926 1.393782781 0.999333352 0.854248168 0.448953333 0.0580598 0.41217514 1.625486402 0.051852298 0.015678744 11.55821919 -1.062890926 -0.145085184 RS(ph)SITEPEGPNGPNIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSITEPEGPNGPNIQK 17 1 Q13625-2;Q13625;Q13625-3 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 RS(0.497)S(0.497)IT(0.006)EPEGPNGPNIQK;RS(0.5)S(0.5)IT(0.001)EPEGPNGPNIQK 175.33 4.96E-14 0 223824 215878 197982 181626 247610 123282 274870 176213 328440 TRUE FALSE 209815.2554 231861.8317 202678.2265 186286.8307 228163.7094 158871.5121 233655.7953 198213.5809 273621.2422 0.766809089 0.847382425 0.740725482 0.68082006 0.833866945 0.580625652 0.8539388 0.7244086 1 18.06182071 -1.475251189 4.004762588 1.001897524 0.760292427 0.463444568 0.083050526 0.001268989 0.000166277 0.07252338 0.016964925 0.033477176 1.475251189 -0.241605098 RS(ph)SLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 49 3 Q93052;A0A087WZF1;C9JUT4 Q93052 LPP Lipoma-preferred partner 1 RS(0.5)S(0.5)LDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK;RS(0.208)S(0.208)LDAEIDS(0.195)LT(0.195)S(0.195)ILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 305.23 2.19E-103 3100000000 809610 676930 723610 748890 766350 554867 893870 627517 688194 TRUE FALSE 758937.9553 727050.6015 740774.3709 768107.7853 706163.9623 715048.0954 759842.4918 705863.8788 573329.9755 1.323736745 1.268118941 1.292055889 1.339730728 1.231688543 1.247184215 1.325314434 1.231165139 1 19.12900618 0.882924798 5.250088268 1.000007252 1.287038417 0.874002339 0.034383653 0.348869408 15.34437959 0.030999117 0.007823153 7.637035303 -0.882924798 0.287031165 RS(ph)SLLSLMTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RSSLLSLMTGK 11 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 RS(0.832)S(0.168)LLSLMTGK;RS(0.5)S(0.5)LLSLMTGK;RS(0.495)S(0.495)LLS(0.01)LMTGK 209.6 9.55E-09 3007830000 6111610 5855840 5283310 4595380 7007720 3517420 6375000 6516470 9315710 TRUE FALSE 5729095.24 6289412.487 5408632.608 4713305.231 6457361.939 4532842.053 5419127.933 7330065.624 7760857.819 0.738203865 0.810401715 0.696911699 0.60731756 0.832042293 0.584064566 0.69826404 0.944491678 1 22.88778469 1.187854535 5.096859367 0.988212584 0.711790511 0.66994647 0.076917657 0.116035178 6.16211473 0.068763906 0.018079295 15.41184155 -1.187854535 -0.276422073 RS(ph)SLPLDHGSPAQENPESEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RSSLPLDHGSPAQENPESEK 20 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5;A0A0A0MRX3 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 RS(0.498)S(0.498)LPLDHGS(0.004)PAQENPESEK;RS(0.49)S(0.49)LPLDHGS(0.02)PAQENPESEK;RS(0.5)S(0.5)LPLDHGSPAQENPESEK;RS(0.362)S(0.362)LPLDHGS(0.277)PAQENPESEK;RS(0.419)S(0.419)LPLDHGS(0.162)PAQENPESEK 223.97 2.87E-25 2388460000 729760 1204801 1199500 1208470 1290600 1049280 1635460 1225623 1687740 TRUE FALSE 684085.6243 1294005.72 1227952.706 1239481.386 1189241.482 1352190.102 1390237.956 1378644.729 1406045.291 0.486531713 0.920315816 0.873337946 0.881537312 0.845805956 0.961697401 0.988757592 0.98051232 1 20.42321164 4.738736516 7.166758494 0.925594311 0.480637912 0.875970781 0.052581672 0.038055204 16.16238349 0.013474982 0.081890035 54794.44291 -4.738736516 -0.444956399 RS(ph)SLPLDHGSPAQENPESEKSS(ph)PAVSR ddPTM_SK-BR-3_Pertuzumab_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(0.754)S(0.246)LPLDHGSPAQENPES(0.008)EKS(0.244)S(0.748)PAVSR 198.92 2.91E-25 238760000 62149 108420 102090 124440 138660 95265 175270 137340 142370 TRUE FALSE 58259.20503 116447.5296 104511.623 127633.3411 127770.2029 122766.459 148989.8906 154487.2013 118607.5273 0.491193151 0.981788697 0.881155062 1.076098154 1.077252059 1.035064653 1.256158813 1.302507563 1 16.85583605 5.17925962 0.456370708 1.173053649 2.93E-14 0.670324987 0.127288519 4.380587813 0.524548064 0.079761019 3.014342777 151098.3147 -5.17925962 -1.173053649 RS(ph)SLPSFETLDYGDEEDIETQLSSSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSLPSFETLDYGDEEDIETQLSSSGK 27 1 K7EQI2;A0A0C4DGP8;K7EJF0;Q96ST8-3;Q96ST8;K7EPU8 K7EQI2 CEP89 Centrosomal protein of 89 kDa 1 RS(0.483)S(0.483)LPS(0.016)FET(0.016)LDY(0.002)GDEEDIETQLSSSGK 61.014 0.028629 53297000 20522 20855 20940 21282 22682 16317 22396 21071 27721 TRUE FALSE 19237.56465 22399.1259 21436.70669 21828.13215 20900.64721 21027.45302 19037.92771 23701.76073 23094.18602 0.833004664 0.969903243 0.928229584 0.945178676 0.905017704 0.910508515 0.824360196 1.026308557 1 14.49524208 1.20908989 24.99961616 1.013154503 0.909234532 0.50082448 0.045599252 221.831607 188171.4836 0.045082013 0.011277297 16.18414982 -1.20908989 -0.10391997 RS(ph)SLS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSLSPGR 8 1 Q9BUQ8;F8VVA2;F8W1J5 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 2 RS(0.61)S(0.398)LS(0.992)PGR 79.697 0.018291 262950000 530690 582820 539030 594680 633650 469840 622180 518620 592940 TRUE FALSE 497475.0602 625972.5992 551816.0461 609940.4956 583885.685 605475.1808 528889.885 583370.8486 493974.4835 1.007086554 1.267216466 1.117094232 1.234761139 1.182015883 1.225721573 1.070682602 1.18097365 1 18.91407699 0.391900129 0.720393449 0.998085306 1.17498311 0.274593329 0.079532836 2.429384361 1.863675887 0.084995985 0.025589766 2.465472309 -0.391900129 0.176897805 RS(ph)SLSSHSHQSQIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.499)S(0.499)LS(0.001)S(0.001)HSHQSQIYR;RS(0.495)S(0.495)LS(0.004)S(0.005)HSHQSQIYR;RS(0.492)S(0.492)LS(0.006)S(0.01)HSHQSQIYR 199.15 3.56E-09 389363000 34702 105482 68189 66401 101736 56964.4 83996 89250 120345 TRUE FALSE 32530.06376 113291.997 69806.47528 68104.96208 93746.06494 73409.09754 71401.57958 100393.059 100258.642 0.324461444 1.129997322 0.696263922 0.679292684 0.935042237 0.732197206 0.712173815 1.001340702 1 16.61336707 1.227943517 24.5280824 1.000670648 0.777748786 0.200322546 0.204667483 321.1717417 741953.3394 0.171676563 0.044792515 16.90221094 -1.227943517 -0.222921862 RS(ph)SLTTAALPFTQSILTQVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSLTTAALPFTQSILTQVGR 21 1 Q3MII6;C9JMI8 Q3MII6 TBC1D25 TBC1 domain family member 25 1 RS(0.408)S(0.408)LT(0.144)T(0.04)AALPFTQSILTQVGR;RS(0.482)S(0.482)LT(0.018)T(0.018)AALPFTQSILTQVGR 131.42 8.10E-06 210490000 142497 154099 159387 155491 201837 156155 216858 151845 245980 TRUE FALSE 133578.3671 165508.6503 163167.7349 159481.1623 185985.5362 201234.4135 184342.1561 170803.1825 204924.3489 0.65184234 0.807657319 0.796234004 0.778244084 0.907581443 0.98199367 0.899561995 0.83349384 1 17.64473189 2.725200742 4.497890966 0.923012802 0.771991071 0.639203314 0.061732121 0.138676349 7.408842673 0.019046357 0.018786543 531.1298891 -2.725200742 -0.151021731 RS(ph)SLYGIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSLYGIAK 9 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 RS(0.499)S(0.499)LY(0.002)GIAK;RS(0.633)S(0.365)LY(0.001)GIAK 91.62 0.0065107 770530000 505873 621650 454759 452589 705900 307541 475660 518830 840050 TRUE FALSE 474211.3119 667677.6128 465546.0982 464203.2 650461.4615 396323.0942 404339.1988 583607.0676 699840.2281 0.67759939 0.954042917 0.665217688 0.663298824 0.9294428 0.566305105 0.577759298 0.83391472 1 19.41666607 3.851060885 6.343774267 0.715478392 0.831283376 0 0.158454246 0.518458556 25.48056364 0.038046497 0.069338984 7096.77253 -3.851060885 0.115804984 RS(ph)SMIETGQGAEGGLSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RSSMIETGQGAEGGLSLR 18 1 P49796-1;P49796-4;P49796-6;P49796 P49796-1 RGS3 Regulator of G-protein signaling 3 1 RS(0.5)S(0.5)MIETGQGAEGGLSLR;RS(0.664)S(0.336)MIETGQGAEGGLSLR;RS(0.5)S(0.5)MIETGQGAEGGLSLR 249.12 8.06E-25 1176230000 264302 287638 302750 233904 329428 235486 301162 253907 483480 TRUE FALSE 247759.8096 308935.0168 309931.373 239906.3726 303556.0537 303466.9854 256005.554 285607.8479 402784.0646 0.615118202 0.766999104 0.769472778 0.595620318 0.753644646 0.753423514 0.635590075 0.709084279 1 18.61964708 -2.074156847 2.460102944 1.445025299 0.70762916 0.677644913 0.064858801 4448666.887 1574386.614 11099649.38 0.015539827 0.008430302 2.074156847 -0.737396139 RS(ph)SNVSYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSNVSYK 8 1 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 1 RS(0.5)S(0.5)NVSYK;RS(0.878)S(0.122)NVSYK 73.841 0.016247 193230000 367660 350700 315080 284219 372720 229543 357740 356100 480130 TRUE FALSE 344648.8169 376666.1929 322553.8464 291512.5407 343448.0747 295808.3378 304100.2081 400559.8689 399993.2012 0.861636687 0.941681488 0.806398322 0.728793739 0.858634781 0.739533414 0.760263442 1.001416693 1 18.60961595 1.227368172 24.98531409 1.000708544 0.817880903 0.598042241 0.063621731 189.7562103 423586.1844 0.064812743 0.016806665 16.87983401 -1.227368172 -0.182827641 RS(ph)SPAAFINPPIGTVTPALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSPAAFINPPIGTVTPALK 20 1 F6VRR5;Q9BY77-2;Q9BY77;Q6R954;F8WEE2;Q8WUT1;F8WCX5 F6VRR5 POLDIP3;PDIP46 Polymerase delta-interacting protein 3 1 RS(0.638)S(0.362)PAAFINPPIGTVTPALK;RS(0.5)S(0.5)PAAFINPPIGTVTPALK 198.67 9.39E-22 854860000 1201310 1156830 1137830 1100890 1394920 1005620 1547690 1170090 1528120 TRUE FALSE 1126122.151 1242482.897 1164819.865 1129140.701 1285368.61 1295926.169 1315628.253 1316178.312 1273066.9 0.884574213 0.975976123 0.914971448 0.886945298 1.009663051 1.017956063 1.033432141 1.033864216 1 20.2798768 2.629001055 5.691146472 1.023408063 0.925818362 0.777190366 0.027275841 0.112273289 4.981517528 0.008868458 0.008337786 425.5994473 -2.629001055 -0.097589701 RS(ph)SPAQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSPAQTR 8 1 Q9UNN5;B3KT28 Q9UNN5 FAF1 FAS-associated factor 1 1 RS(0.5)S(0.5)PAQTR 60.255 0.057239 197440000 15800 21097 13058 26310 20997 15547 18374 12441 23908 TRUE FALSE 14811.1062 22659.04383 13367.74193 26985.15914 19347.98032 20035.16652 15618.98928 13994.28624 19917.60035 0.743619008 1.137639245 0.671152232 1.354839874 0.971401172 1.005902627 0.784180273 0.702609049 1 14.28175622 1.730137186 7.64647654 0.80951767 0.977147261 0.108864722 0.201653903 0.239024426 41.4516704 0.091398249 0.048338945 53.72014616 -1.730137186 0.167629591 RS(ph)SPPGHYYQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.597)S(0.398)PPGHY(0.003)Y(0.002)QK;RS(0.894)S(0.106)PPGHYYQK 147.07 2.17E-05 236230000 357570 363174 338832 310592 471930 357784 393750 482600 885970 TRUE FALSE 335190.332 390063.7808 346869.255 318562.3166 434866.5215 461070.4327 334710.8429 542853.6723 738095.8834 0.45412844 0.528473047 0.469951483 0.431600181 0.589173482 0.624675524 0.45347881 0.735478526 1 19.49344872 0.985609741 3.366889714 0.999207547 0.509260206 0.870447043 0.062434217 0.07157948 2.081863835 0.05818661 0.015124225 9.674081491 -0.985609741 -0.489947341 RS(ph)SPSARPPDVPGQQPQAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RSSPSARPPDVPGQQPQAAK 20 2 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 RS(0.555)S(0.381)PS(0.064)ARPPDVPGQQPQAAK;RS(0.377)S(0.377)PS(0.245)ARPPDVPGQQPQAAK;RS(0.498)S(0.498)PS(0.003)ARPPDVPGQQPQAAK;RS(0.494)S(0.494)PS(0.011)ARPPDVPGQQPQAAK 173.98 2.13E-12 11057500000 2281440 1878720 1975940 1978940 2087630 1598820 2487230 1835020 2332840 TRUE FALSE 2138648.743 2017822.384 2022810.23 2029722.951 1923675.961 2060373.379 2114292.952 2064126.286 1943473.933 1.100425741 1.03825544 1.040821899 1.044378788 0.989813101 1.060149737 1.08789365 1.062080767 1 20.89020633 2.031641077 24.99984781 1.063323606 1.040527446 0 0.034632905 460.4581879 363810.0252 0.012011926 0.008871197 107.5575936 -2.031641077 -0.022796161 RS(ph)SPSSSSTQPQEESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RSSPSSSSTQPQEESR 16 1 Q4G0A6 Q4G0A6 FAM188B Protein FAM188B 1 RS(0.489)S(0.489)PS(0.021)S(0.001)SSTQPQEESR;RS(0.651)S(0.065)PS(0.037)S(0.196)S(0.037)S(0.007)T(0.007)QPQEESR;RS(0.499)S(0.499)PS(0.001)SSSTQPQEESR;RS(0.472)S(0.472)PS(0.042)S(0.013)S(0.001)STQPQEESR 153.1 2.96E-07 739431000 293552.2 408413 326106 319604 415178 252397 432010 359645 563792 TRUE FALSE 275179.2918 438652.3235 333841.3883 327805.5797 382571.5946 325259.9166 367234.1111 404547.4699 469691.473 0.585872445 0.933915876 0.710767403 0.697916821 0.814516798 0.692496959 0.781862419 0.861304693 1 18.84135388 0.968356586 2.238324679 0.999026483 0.758300261 0.455776602 0.090813974 0.303833419 3.358116716 0.080237125 0.022022307 9.297294465 -0.968356586 -0.240726222 RS(ph)SPVPPVPER ddPTM_SK-BR-3_Pertuzumab_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(0.888)S(0.112)PVPPVPER;RS(0.891)S(0.109)PVPPVPER 89.43 0.0033904 2854850000 2545200 2299350 2513930 2429670 2542290 2127630 2906990 2316290 2764170 TRUE FALSE 2385900.475 2469596.266 2573561.607 2492019.446 2342628.799 2741842.242 2471113.837 2605483.905 2302812.17 1.036081234 1.07242627 1.117573392 1.082163573 1.017290437 1.190649536 1.073085278 1.131435703 1 21.13496531 RS(ph)SQPPADRDPAPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSQPPADRDPAPFR 15 2 Q10570 Q10570 CPSF1 Cleavage and polyadenylation specificity factor subunit 1 1 RS(0.5)S(0.5)QPPADRDPAPFR 64.203 0.03476 134500000 84220 86492 77665 82201 71957 63248 95926 78771 83693 TRUE FALSE 78948.82054 92895.95767 79507.25048 84310.41683 66305.78748 81506.67085 81542.78683 88605.73275 69724.09762 1.132303224 1.332336464 1.140312362 1.209200545 0.950973763 1.168988537 1.169506521 1.270805012 1 16.08936974 -5 0.092898809 0.534349292 1.29616123 0.174804635 0.102478477 337.4163151 2.166746861 32.57434522 2.109797456 1.00E-05 5 0.761811938 RS(ph)SQPSPTAVPASDSPPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RSSQPSPTAVPASDSPPTK 19 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 RS(0.496)S(0.496)QPS(0.006)PT(0.003)AVPASDSPPTK;RS(0.5)S(0.5)QPS(0.001)PTAVPASDSPPTK;RS(0.5)S(0.5)QPSPTAVPASDSPPTK 156.2 1.12E-08 1649750000 1218890 1008310 1078570 909830 1151730 868270 1434080 1116660 2026040 TRUE FALSE 1142601.851 1082966.322 1104154.19 933177.7781 1061277.772 1118925.454 1219053.017 1256077.459 1687880.835 0.67694462 0.641613021 0.654165962 0.552869467 0.628763447 0.662917328 0.722238793 0.744174253 1 20.68678162 0.71762573 0.840504117 1.000329715 0.632300979 0.915297806 0.034511633 0.273766552 0.361630933 0.03391077 0.011647934 5.219461879 -0.71762573 -0.368028737 RS(ph)SQPSPTAVPASDSPPTKQEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSQPSPTAVPASDSPPTKQEVK 23 2 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 RS(0.593)S(0.406)QPS(0.001)PTAVPASDSPPTKQEVK 171.15 3.39E-12 230080000 213450 177380 174920 181030 270580 130610 258450 180730 762050 TRUE FALSE 200090.5455 190513.3998 179069.185 185675.5363 249329.7383 168314.9867 219697.8218 203294.5383 634858.932 0.315173238 0.300087768 0.282061378 0.292467392 0.392732504 0.265121869 0.3460577 0.320220018 1 19.27607653 -4.536774272 0.437762191 9.99999983 0.30196608 0.974334696 0.034990989 93.42830483 0.869506301 802.3158928 0.017384525 2.91E-05 4.536774272 -9.69803375 RS(ph)SSSGDQSSDSLNSPTLLAL ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RSSSSGDQSSDSLNSPTLLAL 21 1 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 1 RS(0.377)S(0.377)S(0.154)S(0.063)GDQS(0.014)S(0.014)DSLNSPTLLAL;RS(0.434)S(0.434)S(0.111)S(0.019)GDQSSDSLNSPTLLAL;RS(0.785)S(0.138)S(0.038)S(0.038)GDQS(0.001)S(0.001)DSLNSPTLLAL 158.44 2.52E-11 226550000 253479 294211 276287 285463 324238 229173 274770 257136 416843 TRUE FALSE 237614.2019 315994.6886 282840.6581 292788.4639 298773.6554 295331.5248 233570.7893 289239.9956 347269.2104 0.684236306 0.909941564 0.814470876 0.84311668 0.8603517 0.850439705 0.672592854 0.832898475 1 18.40569498 RS(ph)STAKPEVEHPEPDHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSTAKPEVEHPEPDHSK 18 2 Q9NZI5-3;Q9NZI5;B7Z1S6;F8WFB0 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 RS(0.457)S(0.457)T(0.086)AKPEVEHPEPDHSK;RS(0.436)S(0.436)T(0.128)AKPEVEHPEPDHSK 195.13 1.78E-15 395460000 669940 388870 501240 545830 614050 404360 659360 471730 684620 TRUE FALSE 628009.6513 417662.3394 513129.6495 559836.9219 565824.99 521092.1678 560495.0892 530626.5289 570352.4992 1.101090382 0.732288085 0.899671081 0.981563021 0.99206191 0.913631778 0.982716986 0.930348389 1 19.12149431 3.391036487 4.738833143 0.964164724 0.86648343 0.015305773 0.09400793 0.330336788 13.0856185 0.024300732 0.033581891 2460.574318 -3.391036487 -0.097681294 RS(ph)STAKPEVEHPEPDHSKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSTAKPEVEHPEPDHSKR 19 3 Q9NZI5-3;Q9NZI5;B7Z1S6;F8WFB0 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 RS(0.492)S(0.492)T(0.016)AKPEVEHPEPDHSKR 122.3 1.36E-05 451040000 100890 72560 96136 98602 133170 70167 113510 79520 145910 TRUE FALSE 94575.47499 77932.4179 98416.39132 101132.2943 122711.3654 90423.07383 96490.22928 89448.24705 121556.6784 0.778036026 0.641120002 0.809633766 0.831976454 1.009499165 0.74387582 0.793787972 0.735856295 1 16.89126963 -5 0.060904822 1.628097427 0.51072524 0.297988967 0.095013526 509.5676318 2.265169364 50.00185001 8.133547263 1.00E-05 5 -1.117372186 RS(ph)STSGDT(ph)EEEEEEEVVPFSSDEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSTSGDTEEEEEEEVVPFSSDEQK 25 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;O15231-2;H7BZT5;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 2 RS(0.377)S(0.378)T(0.4)S(0.219)GDT(0.625)EEEEEEEVVPFSSDEQK;RS(0.316)S(0.318)T(0.324)S(0.096)GDT(0.947)EEEEEEEVVPFSSDEQK 131.43 7.00E-05 827940000 961320 682210 721530 827590 841670 544150 923090 635850 767280 TRUE FALSE 901152.6972 732721.5382 738645.0323 848827.3605 775568.6333 701237.2715 784681.224 715237.2722 639216.0112 1.409778043 1.146281578 1.15554839 1.327919429 1.213312276 1.097027076 1.227568162 1.118928906 1 19.28594402 -5 0.122058637 0.316289158 1.301500453 0.460374638 0.085580439 160.7594296 1.266146159 26.9028195 0.767795314 1.00E-05 5 0.985211295 RS(ph)STSGDTEEEEEEEVVPFSSDEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSTSGDTEEEEEEEVVPFSSDEQK 25 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;O15231-2;H7BZT5;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 1 RS(0.427)S(0.427)T(0.114)S(0.031)GDT(0.002)EEEEEEEVVPFSSDEQK 168.87 6.54E-12 198360000 237990 179070 184080 213750 218680 142510 250310 181050 246380 TRUE FALSE 223094.6307 192328.5291 188446.4645 219235.1869 201505.7549 183650.3235 212778.3393 203654.491 205257.5863 1.08690078 0.937010576 0.91809744 1.068097851 0.981721351 0.894730991 1.03664056 0.992189837 1 17.64707602 1.627191471 25 1.010814874 0.971646651 0.031136388 0.061284601 2.289187915 2953.969159 0.027671495 0.015315016 42.38297826 -1.627191471 -0.039168224 RS(ph)STSSEPTPTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RSSTSSEPTPTVK 13 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 RS(0.469)S(0.469)T(0.041)S(0.02)S(0.001)EPTPTVK;RS(0.684)S(0.305)T(0.011)SSEPTPTVK;RS(0.483)S(0.483)T(0.028)S(0.005)S(0.001)EPTPTVK;RS(0.494)S(0.494)T(0.009)S(0.003)SEPTPTVK 172.56 1.42E-05 4431590000 5399600 4665270 4891840 4750100 5493420 4144730 6283930 4992480 7588290 TRUE FALSE 5061648.675 5010691.445 5007876.755 4871995.608 5061988.953 5341246.267 5341713.034 5615802.118 6321755.377 0.800671392 0.792610778 0.792165539 0.770671327 0.800725218 0.844899233 0.844973068 0.888329551 1 22.59189378 0.946386663 0.67378078 1.001394651 0.788001033 0.964871051 0.012548896 0.136564007 0.14171928 0.012542817 0.005011259 8.838664784 -0.946386663 -0.213393618 RS(ph)STVAPAQPDGAESEWTDVETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSTVAPAQPDGAESEWTDVETR 23 1 Q02241;H7BYN4;A0A2U3TZL8;Q02241-2;Q02241-3 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 RS(0.439)S(0.439)T(0.121)VAPAQPDGAESEWTDVETR 206.16 8.70E-25 307840000 63685 62917 58732 60277 75053 57105 80772 63938 81668 TRUE FALSE 59699.06953 67575.44015 60125.15078 61823.80987 69158.64013 73590.28648 68660.98845 71920.80004 68037.0832 0.877448984 0.993214832 0.883711469 0.908678135 1.016484495 1.081620243 1.009170076 1.057082354 1 16.05403367 2.661882141 4.823259578 1.037234883 0.923385853 0.693209446 0.03868137 0.125989207 5.392946608 0.012101495 0.011443389 459.0734125 -2.661882141 -0.11384903 RS(ph)SWECTGSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSWECTGSGR 11 1 Q8NEV8-2;Q8NEV8;E9PPH6 Q8NEV8-2 EXPH5 Exophilin-5 1 RS(0.905)S(0.094)WECTGSGR 108.72 0.0021457 181180000 277650 356960 301070 336050 377550 271820 379460 292620 428050 TRUE FALSE 260272.3821 383389.6898 308211.5226 344673.6119 347898.746 350290.0214 322563.4957 329154.2511 356605.6897 0.72986043 1.075108168 0.864292218 0.966539856 0.975583834 0.982289491 0.904538276 0.923020189 1 18.4439702 4.759000215 24.99987791 0.955709195 0.729860214 0.616547783 0.057233158 3620.851513 4428628.107 0.013060503 0.570815659 57411.67469 -4.759000215 -0.225848981 RS(ph)TPLKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSTPLKER 8 2 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 RS(0.758)T(0.242)PLKER 60.691 0.071426 103010000 135960 120580 118440 120220 144020 88706 143250 111820 171670 TRUE FALSE 127450.5063 129507.8687 121249.4527 123305.0487 132709.2501 114313.9822 121770.9924 125780.9731 143017.168 0.891155293 0.905540716 0.847796488 0.86216956 0.927925312 0.799302516 0.851443181 0.879481638 1 17.12582881 0.948777937 19.95819719 1 0.868033786 0.576932106 0.034915043 725.92596 282851.827 0.032817499 0.008204375 8.887465679 -0.948777937 -0.131966215 RS(ph)WGQQAQEYQEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RSWGQQAQEYQEQK 14 1 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 RS(1)WGQQAQEYQEQK;RS(1)WGQQAQEYQEQK;RS(1)WGQQAQEYQEQK;RS(1)WGQQAQEYQEQK 260.24 1.15E-24 1410790000 1251020 834340 952110 964570 1167770 758830 1141700 890800 1478000 TRUE FALSE 1172720.891 896115.4017 974694.4988 989322.4992 1076058.055 977891.9024 970512.684 1002018.341 1231312.252 0.952415514 0.727772667 0.791590027 0.803470036 0.873911596 0.794186772 0.788193801 0.813780858 1 20.23176523 0.92818316 19.22749513 1 0.806048131 0.462723196 0.060397812 1805.978923 483516.7805 0.053780393 0.013445098 8.475847999 -0.92818316 -0.19395187 RS(ph)YDVPPPPMEPDHPFYSNISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RSYDVPPPPMEPDHPFYSNISK 22 1 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 1 RS(0.549)Y(0.451)DVPPPPMEPDHPFYSNISK;RS(0.949)Y(0.051)DVPPPPMEPDHPFYSNISK;RS(0.921)Y(0.079)DVPPPPMEPDHPFYSNISK;RS(0.539)Y(0.461)DVPPPPMEPDHPFYSNISK 167.06 5.17E-12 504277000 858080 782360 844880 881850 957320 615893 987260 729560 936820 TRUE FALSE 804374.3045 840286.7484 864920.9526 904479.764 882135.9488 793691.3109 839229.5283 820647.172 780458.6899 1.030643024 1.07665756 1.108221311 1.158907929 1.130278848 1.016954928 1.075302946 1.051493414 1 19.57396275 1.249318105 0.891658109 1.005732764 1.096076113 0.332258876 0.040983592 0.634302783 1.097689541 0.038792765 0.01414947 17.75489488 -1.249318105 0.090343349 RS(ph)YSSPDITQAIQEEEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSYSSPDITQAIQEEEKR 18 2 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 RS(0.56)Y(0.001)S(0.336)S(0.103)PDITQAIQEEEKR 93.397 0.0011254 214700000 131920 117300 126900 130700 151830 85871 158260 117210 215260 TRUE FALSE 123663.3627 125985.0141 129910.1279 134053.9833 139905.8843 110660.5637 134530.3822 131843.9265 179331.7154 0.689578876 0.702525004 0.724412454 0.747519662 0.780151375 0.617071908 0.750176186 0.735195814 1 17.45227113 0.396559864 1.605399171 1.000003838 0.715187028 0.807960483 0.043298767 1.864891499 4.526535828 0.038115367 0.010861333 2.492067862 -0.396559864 -0.28481681 RSAPGGGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RSAPGGGSK 9 1 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 0 ;;; 145.28 0.00015643 592810000 857890 852710 723635 816890 881130 549438 866310 883220 1026780 FALSE TRUE 804196.1963 915845.5356 740799.9639 837852.7804 811929.6041 708051.8312 736414.8579 993491.9612 855403.7847 0.940136355 1.070658737 0.866023716 0.979482199 0.949177007 0.827739886 0.860897358 1.161430402 1 19.70624606 1.241282931 24.99999067 1.080715203 0.929812756 0.397860357 0.078211519 71.45644512 656262.7525 0.059421805 0.019490422 17.42941981 -1.241282931 -0.150902447 RSAS(ph)PDDDLGSSNWEAADLGNEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RSASPDDDLGSSNWEAADLGNEER 24 1 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 RS(0.178)AS(0.822)PDDDLGSSNWEAADLGNEER;RS(0.087)AS(0.913)PDDDLGSSNWEAADLGNEER;RS(0.06)AS(0.94)PDDDLGSSNWEAADLGNEER;RS(0.004)AS(0.996)PDDDLGSSNWEAADLGNEER;RS(0.241)AS(0.759)PDDDLGSSNWEAADLGNEER;RS(0.004)AS(0.996)PDDDLGSSNWEAADLGNEER 361.16 8.24E-103 7075280000 1502165 1642350 1578740 1613801 1863310 1385435 1755360 1435695 2049090 TRUE FALSE 1408147.174 1763951.303 1616188.458 1655213.866 1716973.149 1785387.594 1492160.064 1614944.681 1707083.641 0.824884698 1.033312756 0.946754113 0.969614977 1.005793218 1.045870015 0.874098977 0.946025515 1 20.70310232 -0.710320915 5.857891399 1.000000001 0.961353446 0.035021375 0.067535576 9.02E-10 1.54E-10 0.060526608 0.014266258 0.194840433 0.710320915 -0.038646555 RSAS(ph)PHDVDLCLVSPCEFEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RSASPHDVDLCLVSPCEFEHR 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 RS(0.156)AS(0.844)PHDVDLCLVSPCEFEHR;RS(0.145)AS(0.855)PHDVDLCLVSPCEFEHR;RS(0.149)AS(0.851)PHDVDLCLVSPCEFEHR 188.41 1.19E-17 539340000 160790 206466 174605 184795 245314 169857 211471 190350 289111 TRUE FALSE 150726.4409 221752.9575 178746.7131 189537.1526 226048.028 218891.9585 179762.8868 214115.6165 240856.5064 0.62579352 0.920684937 0.742129477 0.786929759 0.938517424 0.9088065 0.746348477 0.888975846 1 17.87781437 -5 0.11003628 1.547498283 0.722360964 0.346525383 0.091773906 221.0245576 1.61802225 27.57607991 1.101124636 1.00E-05 5 -0.825137319 RSATSTSAS(ph)PTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSATSTSASPTLR 13 1 O75061-4;O75061;O75061-2 O75061-4 DNAJC6 Putative tyrosine-protein phosphatase auxilin 1 RS(0.011)AT(0.009)S(0.007)T(0.005)S(0.161)AS(0.784)PT(0.022)LR 62.203 0.048037 172820000 70746 74094 71189 65947 78334 60816 75086 73688 83495 TRUE FALSE 66318.13415 79579.99685 72877.6367 67639.31167 72181.96362 78372.59193 63827.55136 82888.10901 69559.1451 0.9534064 1.144062319 1.047707481 0.972399985 1.037706308 1.126704358 0.917601147 1.191620583 1 16.08595258 3.485684219 24.38744222 1.032498769 1.072309641 0 0.089055219 777.8459832 2215304.687 0.021810042 0.032292695 3059.737852 -3.485684219 0.039810873 RSCFES(ph)SPDPELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSCFESSPDPELK 13 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RS(0.011)CFES(0.494)S(0.494)PDPELK 101.96 0.0010581 167480000 493180 387890 391320 414100 457180 313400 532080 348090 521750 TRUE FALSE 462312.7442 416609.7792 400602.2952 424726.5071 421274.927 403873.4924 452299.5436 391549.8027 434666.5544 1.063603214 0.958458329 0.921631285 0.977131787 0.969191033 0.929157048 1.040566703 0.900804994 1 18.72954957 RSCFESS(ph)PDPELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSCFESSPDPELK 13 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RS(0.01)CFES(0.166)S(0.824)PDPELK 113.88 0.00048194 190060000 483630 333160 357430 363090 409930 303870 481620 316770 466400 TRUE FALSE 453360.4616 357827.5131 365908.4084 372407.5041 377735.7514 391592.3361 409405.5521 356319.4318 388554.8269 1.166786333 0.920918975 0.941716286 0.958442614 0.972155601 1.007817453 1.053662247 0.917037718 1 18.56775866 2.239480548 23.66632654 1.005258332 0.973927625 0 0.075604901 49.12438564 1263851.269 0.025741633 0.020385003 173.5723517 -2.239480548 -0.031330707 RSDAEEVDFAGWLCSTIGLNQPS(ph)TPTHAAGV ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSDAEEVDFAGWLCSTIGLNQPSTPTHAAGV 31 1 Q02750;Q02750-2;H3BRW9 Q02750 MAP2K1 Dual specificity mitogen-activated protein kinase kinase 1 1 RSDAEEVDFAGWLCSTIGLNQPS(0.333)T(0.333)PT(0.333)HAAGV 47.507 0.057615 19473000 6841.5 9087.1 8517.3 11212 9856.7 5031.2 6073.6 4685.9 7180.5 TRUE FALSE 6413.302727 9759.918339 8719.334378 11499.7189 9082.594542 6483.625765 5162.920065 5270.94493 5982.028162 1.072095041 1.631540019 1.45758832 1.922377928 1.518313571 1.083850759 0.863071842 0.881130076 1 12.54641899 2.150465913 3.457818902 0.913505964 1.547924934 0.646762122 0.20935233 0.135890553 3.206118912 0.081433914 0.057340258 141.4053735 -2.150465913 0.634418969 RSDAEEVDFAGWLCSTIGLNQPST(ph)PTHAAGV ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RSDAEEVDFAGWLCSTIGLNQPSTPTHAAGV 31 1 Q02750;Q02750-2;H3BRW9 Q02750 MAP2K1 Dual specificity mitogen-activated protein kinase kinase 1 1 RSDAEEVDFAGWLCSTIGLNQPS(0.246)T(0.737)PT(0.018)HAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.121)T(0.77)PT(0.109)HAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.204)T(0.69)PT(0.106)HAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.233)T(0.748)PT(0.019)HAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.005)T(0.966)PT(0.029)HAAGV 175.83 6.76E-14 260984000 241103 253570 290568 326203 310192 173631 196766 165986 227827 TRUE FALSE 226012.7936 272344.5866 297460.4102 334573.9212 285830.7716 223755.451 167262.765 186709.7175 189801.2019 1.190786946 1.434893899 1.567220899 1.762759761 1.505948164 1.178893752 0.881252402 0.983711987 1 17.5341296 2.067409636 3.16888323 0.951928186 1.507380752 0.748075427 0.143332542 0.122466371 2.447786911 0.06564116 0.04221994 116.7910696 -2.067409636 0.555452567 RSDEDYLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSDEDYLYR 9 1 E7EMD0;P16435;H0Y4R2 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 80.037 0.034984 0 207330 175990 245990 196260 218030 164470 227960 180530 231310 FALSE TRUE 194353.5854 189020.4827 251824.999 201296.3639 200906.8033 211949.8191 193779.5143 203069.5679 192702.8667 1.008566135 0.980890871 1.306804633 1.044594548 1.042572987 1.09987891 1.005587087 1.0537963 1 17.55601851 1.979866359 1.226693736 1.017634818 1.098976083 0.062723677 0.090442941 1.140661195 3.176840469 0.07065842 0.032420294 95.46987622 -1.979866359 0.081341264 RSDLDLGYEPEGSAS(ph)PTPPYLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSDLDLGYEPEGSASPTPPYLK 22 1 O15169-2;O15169 O15169-2 AXIN1 Axin-1 1 RSDLDLGYEPEGS(0.259)AS(0.733)PT(0.008)PPYLK;RSDLDLGYEPEGS(0.001)AS(0.987)PT(0.013)PPYLK 189.34 1.33E-17 386750000 336810 317270 362040 337930 404620 260240 352690 292450 505680 TRUE FALSE 315729.6633 340761.0009 370627.7598 346601.8559 372842.7774 335367.0634 299807.4087 328963.0263 421278.7412 0.749455485 0.808873004 0.879768485 0.822737589 0.885026328 0.796069278 0.711660427 0.780867853 1 18.68441559 2.026191777 24.64268861 0.787569957 0.833639195 0 0.084011476 527.9099172 496684.6929 0.028689349 0.021187708 106.2164487 -2.026191777 0.046069238 RSDLDLGYEPEGSASPT(ph)PPYLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSDLDLGYEPEGSASPTPPYLK 22 1 O15169-2;O15169 O15169-2 AXIN1 Axin-1 1 RSDLDLGYEPEGS(0.001)AS(0.155)PT(0.844)PPYLK;RSDLDLGYEPEGS(0.027)AS(0.36)PT(0.613)PPYLK 163.38 8.88E-12 287270000 439040 371210 404910 433830 522100 326530 478340 385060 596180 TRUE FALSE 411561.2701 398694.7746 414514.6564 444962.8123 481096.3721 420793.9102 406617.3577 433135.5886 496673.7065 0.828635107 0.802729779 0.834581438 0.895885581 0.968636684 0.847224052 0.818681062 0.872072717 1 18.92193885 -5 0.17443234 1.563077098 0.820274079 0.48501096 0.046496806 128.7553679 1.227186183 25.30335158 0.171969929 1.00E-05 5 -0.742803018 RSDS(ph)ASSEPVGIYQGFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.09)DS(0.838)AS(0.058)S(0.014)EPVGIYQGFEK;RS(0.05)DS(0.855)AS(0.078)S(0.017)EPVGIYQGFEK;RS(0.055)DS(0.887)AS(0.055)S(0.003)EPVGIYQGFEK 290.33 2.29E-49 1465400000 1380940 1336700 1465480 1755670 1969370 1086270 1386740 1032730 1659430 TRUE FALSE 1294509.43 1435670.659 1500241.878 1800723.465 1814703.624 1399858.515 1178811.211 1161668.614 1382460.413 0.936380831 1.038489526 1.085196989 1.30254975 1.312662271 1.012584883 0.852690753 0.84029069 1 20.39880674 1.999248169 24.97210077 0.894129019 1.126028947 0.455225436 0.118842921 25.93455314 861434.6517 0.047733533 0.034831612 99.82703433 -1.999248169 0.231899928 RSDS(ph)IKFQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSDSIKFQHR 10 2 Q8TDM6-4;Q8TDM6;Q8TDM6-3;A0A0J9YYG8 Q8TDM6-4 DLG5 Disks large homolog 5 1 RS(0.043)DS(0.957)IKFQHR;RS(0.488)DS(0.512)IKFQHR 157.43 4.79E-06 896430000 594200 802810 509060 530740 1054570 236790 820280 631780 1609820 TRUE FALSE 557010.0827 862250.8877 521135.1436 544359.6869 971748.3261 305147.429 697286.6291 710659.1237 1341130.642 0.415328727 0.642928333 0.388578955 0.405896092 0.724573949 0.227529981 0.519924463 0.529895524 1 20.35501835 0.625284502 2.415023208 0.999941971 0.479596543 0.58738003 0.137245742 2.05706027 12.44135708 0.118771241 0.031847027 4.219728436 -0.625284502 -0.520345428 RSDS(ph)LLSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RSDSLLSFR 9 1 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 RS(0.02)DS(0.98)LLSFR;RSDS(1)LLSFR;RSDS(1)LLSFR;RSDS(1)LLSFR;RSDS(1)LLSFR;RSDS(1)LLSFR 196.11 1.85E-05 1860140000 613459 862838 713498 656863 925824 474648 923617 836340 1105015 TRUE FALSE 575063.6962 926723.4233 730422.5095 673719.2166 853113.5176 611671.1723 785129.2053 940758.89 920580.8578 0.624674836 1.006672489 0.79343656 0.731841436 0.926712206 0.664440464 0.85286284 1.021918805 1 19.81218492 1.291989809 5.162441121 1.012165113 0.815014978 0.370953205 0.113643168 0.203335126 10.65670058 0.079156672 0.026613868 19.58798708 -1.291989809 -0.197150135 RSDS(ph)PEIPFQAAAGPSDGLDAS(ph)SPGNSFVGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 32 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 RS(0.001)DS(0.999)PEIPFQAAAGPSDGLDAS(0.698)S(0.302)PGNSFVGLR 221.62 2.08E-35 127860000 78656 89728 80900 88093 102250 90529 102950 88284 110410 TRUE FALSE 73733.06136 96371.55448 82818.9862 90353.61552 94219.69746 116663.2527 87513.60324 99306.45174 91981.85772 0.801604394 1.047723506 0.900383926 0.982298224 1.024329143 1.268328946 0.951422437 1.079630855 1 16.48906172 2.738313289 3.302283864 1.071843482 0.943916645 0.299576284 0.101670799 0.329780544 7.559432574 0.031400926 0.031380869 547.4107082 -2.738313289 -0.127926837 RSDS(ph)PEIPFQAAAGPSDGLDASS(ph)PGNSFVGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 32 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 RS(0.204)DS(0.796)PEIPFQAAAGPS(0.001)DGLDAS(0.405)S(0.586)PGNS(0.007)FVGLR 99.099 0.00013356 15082000 18102 20310 20408 18392 21152 19337 23668 19819 21515 TRUE FALSE 16969.02813 21813.77353 20892.0874 18863.96986 19490.80724 24919.27799 20119.20312 22293.44578 17924.00751 0.946720655 1.217014305 1.165592426 1.052441528 1.087413472 1.390273798 1.122472366 1.243775744 1 14.12960562 RSDS(ph)PEIPFQAAAGPSDGLDASSPGNSFVGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RSDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 32 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 RS(0.037)DS(0.963)PEIPFQAAAGPSDGLDASSPGNSFVGLR;RS(0.236)DS(0.764)PEIPFQAAAGPSDGLDASSPGNSFVGLR;RS(0.032)DS(0.968)PEIPFQAAAGPSDGLDASSPGNSFVGLR;RS(0.017)DS(0.983)PEIPFQAAAGPSDGLDASSPGNSFVGLR;RS(0.037)DS(0.963)PEIPFQAAAGPSDGLDASSPGNSFVGLR 253.23 2.64E-59 3522640000 1005467 1249857 1053258 1147269 1276117 995430 1344938 1017980 1439339 TRUE FALSE 942536.6153 1342397.713 1078241.777 1176709.865 1175895.918 1282794.482 1143277.033 1145077.044 1199104.022 0.78603407 1.119500634 0.899206205 0.981324258 0.980645462 1.069794161 0.953442747 0.954943877 1 20.19352539 2.788680095 3.939555654 0.992685999 0.966838966 0.041239635 0.088053505 1.297898598 42.38544297 0.02638518 0.027419368 614.7238949 -2.788680095 -0.025847033 RSDS(ph)PENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSDSPENK 8 1 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5;Q9BTA9-3;A0A494C0B7;A0A494C0C1;A0A494C0S5;C9JVK6;C9JD58;J3QTA0;E9PMZ7;C9JMU2 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 RS(0.006)DS(0.994)PENK 84.06 0.010853 438450000 754520 505520 619250 583140 623790 473240 676120 558510 632620 TRUE FALSE 707295.9401 542949.2268 633938.9024 598104.3597 574800.0496 609856.7056 574742.0828 628241.2029 527031.6351 1.342036973 1.030202346 1.202847913 1.13485476 1.090636712 1.157153888 1.090526725 1.192036988 1 19.00753004 -5 0.162991995 0.48829608 1.178152453 0.263041516 0.083080452 194.3724083 1.802956831 32.46473176 0.300787167 1.00E-05 5 0.689856373 RSDS(ph)PENKYSDSTGHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RSDSPENKYSDSTGHSK 17 2 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5;Q9BTA9-3;A0A494C0B7;A0A494C0C1;A0A494C0S5;C9JVK6;C9JD58;J3QTA0;E9PMZ7;C9JMU2 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 RS(0.005)DS(0.93)PENKY(0.003)S(0.036)DS(0.013)T(0.013)GHSK;RS(0.001)DS(0.999)PENKYSDSTGHSK;RS(0.008)DS(0.992)PENKYSDSTGHSK;RSDS(0.998)PENKYS(0.001)DSTGHSK;RS(0.029)DS(0.968)PENKYS(0.001)DS(0.001)T(0.001)GHSK;RS(0.002)DS(0.998)PENKYSDSTGHSK 219.13 2.31E-15 2146890000 794183 844102 812122 902750 1158983 552853 1160786 769332 2357760 TRUE FALSE 744476.5037 906600.1904 831385.9174 925916.0934 1067961.15 712452.6863 986736.9155 865384.7937 1964234.624 0.379016078 0.46155392 0.423262021 0.471387726 0.543703454 0.36271262 0.502351859 0.44057099 1 20.90553584 -4.779932349 0.434651567 10 0.442447183 0.914407159 0.053086043 214.4290684 1.614363767 1839.404624 0.026235055 1.66E-05 4.779932349 -9.557552817 RSDS(ph)QQAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RSDSQQAVK 9 1 Q15036-2;Q15036 Q15036-2 SNX17 Sorting nexin-17 1 RS(0.018)DS(0.982)QQAVK;RS(0.004)DS(0.996)QQAVK;RS(0.009)DS(0.991)QQAVK;RSDS(1)QQAVK;RS(0.047)DS(0.953)QQAVK 126.5 0.00028897 1784370000 1827690 1427910 1543943 1469938 1543520 1069212 1926140 1357268 2112350 TRUE FALSE 1713298.145 1533633.942 1580566.057 1507659.098 1422298.165 1377876.147 1637333.188 1526725.898 1759785.139 0.973583711 0.871489313 0.898158544 0.856729077 0.808222626 0.782979761 0.930416533 0.867563809 1 20.74696786 0.314813733 1.286416363 1.000005274 0.871558003 0.344983908 0.0545135 5.008792719 8.264720079 0.051356891 0.015105549 2.064494514 -0.314813733 -0.12844727 RSDS(ph)VSASER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RSDSVSASER 10 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 RS(0.008)DS(0.99)VS(0.002)AS(0.001)ER;RS(0.005)DS(0.994)VS(0.001)ASER;RS(0.01)DS(0.987)VS(0.004)ASER;RSDS(1)VSASER 170.26 2.68E-06 492015000 163679 228103 186199 207845 229625 156082 206255 145564.4 333727 TRUE FALSE 153434.6236 244991.9835 190615.7282 213178.6546 211591.1788 201140.3396 175328.9775 163738.4358 278025.8077 0.551871874 0.881184324 0.68560444 0.766758512 0.761048697 0.72345924 0.630621232 0.588932506 1 18.08485928 -1.056783943 4.657586767 1.000011596 0.712732164 0.489783969 0.095699205 12477790.37 2831149.919 1483.423576 0.021802532 0.087743723 1.056783943 -0.287279432 RSDSMT(ph)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSDSMTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR 38 1 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 RS(0.054)DS(0.412)MT(0.534)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR 89.193 0.00025087 146590000 28390 38424 24811 30318 34423 22904 40585 26477 34145 TRUE FALSE 26613.12058 41268.95294 25399.52864 31096.01121 31719.55644 29516.01298 34499.65602 29782.71173 28445.97891 0.93556705 1.450783363 0.89290401 1.093160172 1.115080502 1.037616356 1.212813105 1.046991978 1 14.79593711 1.697070597 0.014279287 5.02E-07 2.185847793 0.018846587 0.155291092 1683.46284 23.56193161 1792.200364 1808.805566 49.78180015 -1.697070597 2.185847291 RSDSVS(ph)ASER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSDSVSASER 10 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 RSDS(0.238)VS(0.737)AS(0.025)ER 157.22 1.01E-05 179250000 186890 255680 202900 211170 245060 150690 247730 184350 354210 TRUE FALSE 175192.8885 274610.8132 207712.8838 216588.9797 225813.9761 194191.7568 210585.1863 207366.5033 295090.0627 0.593692945 0.930600003 0.703896573 0.73397585 0.765237481 0.658076233 0.71363022 0.70272276 1 18.17079581 -1.008311172 4.30217791 1.000013259 0.738316365 0.491066282 0.087007043 9330290.222 4373522.461 1168.137074 0.019820522 0.098104477 1.008311172 -0.261696894 RSDSVSAS(ph)ER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSDSVSASER 10 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 RSDS(0.044)VS(0.37)AS(0.586)ER 151.85 2.02E-05 159580000 228220 295630 263870 266920 318850 194960 305110 231520 454080 TRUE FALSE 213936.1176 317518.7528 270129.121 273769.6191 293808.8072 251241.7871 259361.588 260425.7816 378291.1145 0.565533023 0.83935028 0.714077362 0.723700897 0.776673826 0.664149322 0.685613746 0.688426906 1 18.52913736 -2.250031377 2.217963196 2.011696645 0.717874776 0.619417753 0.071697188 4881779.629 715842.8636 24811270.23 0.016596493 0.005623007 2.250031377 -1.293821869 RSECNMCNTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RSECNMCNTPK 11 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 0 ;; 154.85 5.10E-05 417196000 556414 451320 487570 505551 539084 368456 581576 425168 569357 FALSE TRUE 521589.041 484736.2024 499135.3906 518524.2946 496746.5172 474823.2658 494374.0779 478251.1607 474327.6385 1.099638728 1.021943828 1.052300878 1.093177484 1.047264542 1.001044905 1.042262853 1.008271755 1 18.85552441 2.405483147 6.652891493 1.018922455 1.05816689 0.489831357 0.025016314 0.234799426 17.44755077 0.008612919 0.007191624 254.3801078 -2.405483147 0.039244435 RSEKDTAAVVS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSEKDTAAVVSR 12 2 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 RSEKDTAAVVS(1)R 64.04 0.052305 82663000 35557 47137 35538 44435 53339 22439 55169 35215 124530 TRUE FALSE 33331.55084 50627.07253 36380.97814 45575.27733 49149.9701 28916.77503 46896.92061 39611.67027 103745.1385 0.321283015 0.48799465 0.350676462 0.439300366 0.473756851 0.278728965 0.452039694 0.381817123 1 16.66268421 -1.262996499 3.126081988 1.00294743 0.403723736 0.886169471 0.067758093 8182694.187 11172182.67 230566.6262 0.014694852 0.054576226 1.262996499 -0.599223694 RSELIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RSELIAK 7 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;; 111.74 0.01044 2352670000 3362030 3452010 3017160 3064780 3905580 2492980 3763620 3246210 3997210 FALSE TRUE 3151606.544 3707600.412 3088728.46 3143427.443 3598851.501 3212662.856 3199300.121 3651506.464 3330049.828 0.94641423 1.113376857 0.927532205 0.94395808 1.080720015 0.964749184 0.960736411 1.09653208 1 21.66711233 1.247782221 24.9997637 1.048266054 0.99525296 0.116560344 0.06467136 402.941476 1092394.738 0.042758351 0.015150272 17.69221551 -1.247782221 -0.053013094 RSES(ph)PPAELPSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RSESPPAELPSLR 13 1 Q14669-3;Q14669;Q14669-2;G5E9G6;H7C1L9 Q14669-3;H7C1L9 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 RS(0.112)ES(0.888)PPAELPSLR;RS(0.005)ES(0.995)PPAELPSLR;RS(0.017)ES(0.983)PPAELPSLR 125.51 0.00012206 592350000 492280 612560 577190 576460 576590 521390 616110 514340 500590 TRUE FALSE 461469.0735 657914.5798 590881.2194 591252.9395 531306.9473 671906.8289 523730.0252 578556.4812 417038.2951 1.106538845 1.577587928 1.416851225 1.417742559 1.274000382 1.611139401 1.255831974 1.387298212 1 18.66982034 0.178954713 0.767022126 0.991678646 1.414720333 0.380131869 0.149769062 3.151749485 2.206866077 0.198767233 0.046072616 1.509922695 -0.178954713 0.423041687 RSES(ph)VK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSESVK 6 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 RS(0.001)ES(0.999)VK 66.546 0.061939 866220000 633780 578720 592510 570760 621180 301780 678610 515410 779640 TRUE FALSE 594112.8411 621569.031 606564.617 585406.6679 572395.0285 388898.987 576858.7304 579760.0731 649513.0473 0.914705014 0.956976975 0.933875954 0.90130086 0.881267945 0.598754696 0.888140327 0.892607278 1 19.30899898 2.687165711 3.455176167 0.824977412 0.934630154 0.099510605 0.101988454 0.380842946 9.252681213 0.03201643 0.03088331 486.5928368 -2.687165711 0.109652743 RSET(ph)PPHWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RSETPPHWR 9 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 RS(0.077)ET(0.923)PPHWR;RS(0.204)ET(0.796)PPHWR;RS(0.326)ET(0.674)PPHWR;RS(0.041)ET(0.959)PPHWR;RS(0.048)ET(0.952)PPHWR 84.954 0.0088738 2774120000 884410 1253970 1106170 1156240 1236320 1123080 1064190 996100 1051780 TRUE FALSE 829056.3568 1346815.244 1132408.875 1185911.076 1139224.414 1447294.964 904624.589 1120465.278 876231.1232 0.946161732 1.537054788 1.292363219 1.353422681 1.300141463 1.651727411 1.032404083 1.278732572 1 19.74095193 1.633275451 16.21049211 1.116944252 1.359975831 0.253532746 0.19522986 0.202833993 120.4102933 0.081413166 0.044758084 42.98089463 -1.633275451 0.243031578 RSFS(ph)KEVEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSFSKEVEER 10 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 RS(0.098)FS(0.902)KEVEER;RS(0.017)FS(0.983)KEVEER 104.94 0.0013648 1276410000 1395920 1128440 1100430 1251270 1594270 988850 1697670 1290250 2181540 TRUE FALSE 1308551.859 1211990.872 1126532.719 1283379.707 1469062.465 1274314.942 1443120.144 1451340.553 1817426.881 0.720002479 0.666871875 0.619850367 0.706152044 0.808319983 0.701164353 0.794045779 0.798568882 1 20.79346589 0.625431804 0.35874956 1.037615585 0.652105996 0.819369676 0.044527217 0.898040533 0.256810173 0.110874805 0.042523004 4.2211599 -0.625431804 -0.38550959 RSFS(ph)SQRPVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSFSSQRPVDR 11 2 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;H7C5N8 E7EPN9 PRRC2C Protein PRRC2C 1 RS(0.135)FS(0.823)S(0.042)QRPVDR 69.258 0.043311 150870000 73568 134770 85998 95605 159060 55070 170900 98525 172120 TRUE FALSE 68963.5102 144748.511 88037.91317 98058.38616 146568.0692 70967.81501 145275.1316 110826.0631 143392.0601 0.480943716 1.009459736 0.613966444 0.683848088 1.022149128 0.494921511 1.013132328 0.772888423 1 17.12960562 1.013833681 0.658659254 0.997609059 0.747907716 0.145532164 0.199934978 1.579297587 1.613215649 0.179037222 0.073871184 10.32365972 -1.013833681 -0.249701343 RSGS(ph)FGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RSGSFGK 7 1 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 RS(0.079)GS(0.921)FGK;RS(0.158)GS(0.842)FGK;RS(0.104)GS(0.896)FGK 63.415 0.048736 390290000 1322000 1053960 1173080 1084650 1207580 929630 1362960 1132340 1846620 TRUE FALSE 1239258.38 1131996.295 1200906.012 1112483.955 1112741.538 1197999.09 1158596.801 1273715.142 1538407.192 0.805546403 0.735823585 0.780616483 0.723140116 0.72330755 0.778726917 0.753114524 0.827944089 1 20.55300598 0.822592878 2.056087361 0.999972454 0.755051333 0.893861256 0.026416735 0.176204583 1.347078313 0.023007756 0.006348294 6.646497997 -0.822592878 -0.244921121 RSGS(ph)PLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSGSPLEK 8 1 B1AKL4;Q9NRA8;Q9NRA8-3;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 RS(0.201)GS(0.799)PLEK 89.403 0.0085323 404030000 331080 249720 291250 283670 314480 238010 358650 306050 296540 TRUE FALSE 310358.2938 268209.5286 298158.5875 290949.4525 289782.0094 306719.6232 304873.762 344261.0162 247045.5583 1.256279595 1.085668289 1.20689718 1.17771578 1.172990162 1.241550851 1.234079107 1.393512268 1 17.91441759 2.242947695 21.69577386 1.236671422 1.170639281 0.011983603 0.10358438 50.22050445 248364.5217 0.032608584 0.026316911 174.9635954 -2.242947695 -0.066032141 KTS(ph)DANETEDHLESLICK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 KTSDANETEDHLESLICK 18 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 KT(0.125)S(0.874)DANET(0.002)EDHLESLICK;KT(0.057)S(0.943)DANETEDHLESLICK 219.13 4.59E-19 1009360000 1938160 1279650 1425500 2240690 2011890 862400 1094320 570690 969900 TRUE FALSE 1816854.025 1374396.617 1459313.533 2298189.899 1853884.275 1111360.88 930236.8752 641941.9027 808017.4242 2.248533226 1.700949232 1.806042159 2.844233095 2.294361754 1.375416973 1.151258435 0.794465421 1 19.62402688 2.039095987 3.098789352 1.021640201 2.090837471 0.738502828 0.327450165 0.160370921 3.063729558 0.167989264 0.10401812 109.4198177 -2.039095987 1.069197271 up RSLS(ph)MDSQVPVYSPSIDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSLSMDSQVPVYSPSIDLK 19 1 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 RS(0.199)LS(0.747)MDS(0.053)QVPVYSPSIDLK 120.85 1.56E-05 146350000 141000 152420 130730 157570 165700 103230 200080 143360 225540 TRUE FALSE 132175.0617 163705.3354 133830.9773 161613.513 152686.5904 133030.8252 170079.8615 161258.8116 187895.917 0.703448291 0.871255417 0.712261232 0.860122538 0.812612604 0.708002746 0.905181253 0.858234783 1 17.51957419 1.040554685 1.015902617 0.996128743 0.786222008 0.513419587 0.066928857 0.418101675 0.92232257 0.05692129 0.018918788 10.97879522 -1.040554685 -0.209906734 RSLS(ph)VEHLETK ddPTM_SK-BR-3_Pertuzumab_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(0.08)LS(0.92)VEHLETK 183.41 3.28E-06 277210000 481570 463230 450380 485870 545190 355530 664050 492050 627310 TRUE FALSE 451429.3933 497528.0312 461063.2263 498338.2468 502372.9766 458165.7395 564481.8672 553483.5256 522607.9084 0.863801305 0.952010146 0.882235456 0.953560478 0.961280854 0.876691171 1.080125 1.059079889 1 18.99536943 1.724549017 8.692160639 1.050471766 0.918758156 0.712542905 0.03922891 0.052927531 11.84453624 0.017272037 0.009233127 53.03334462 -1.724549017 -0.13171361 RSNEETDDYGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSNEETDDYGK 11 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 0 84.605 0.025394 157180000 82316 70258 82469 84986 86917 74946 104480 77337 109870 FALSE TRUE 77163.9885 75459.97542 84425.20362 87166.88464 80090.88943 96581.69355 88814.19394 86992.69469 91531.98721 0.843027567 0.824410982 0.922357377 0.952310633 0.875004377 1.055168761 0.970307721 0.950407583 1 16.48198838 3.609666349 0.610533248 0.989519651 0.803939735 0.630164132 0.042927285 0.720135791 0.480020972 0.024731203 0.080472625 4070.674243 -3.609666349 -0.185579916 RSNS(ph)PDKFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSNSPDKFK 9 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 RS(0.198)NS(0.802)PDKFK;RS(0.037)NS(0.963)PDKFK 115.57 0.001145 5116500000 3162430 1732570 2108790 2205400 2483050 1527150 2812490 1988310 3036710 TRUE FALSE 2964499.151 1860851.286 2158811.495 2261994.298 2288041.269 1968013.414 2390783.234 2236554.88 2529863.483 1.171802025 0.735554032 0.853331221 0.894117138 0.904412939 0.77791289 0.945024603 0.88406149 1 21.27062811 0.664762066 1.042230614 0.999179952 0.871331783 0.042940105 0.117508594 2.60029349 4.710762935 0.102079561 0.032464189 4.621277693 -0.664762066 -0.127848169 RSNVSSPATPTAS(ph)SSSSTTPTRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSNVSSPATPTASSSSSTTPTRK 23 2 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 RSNVSSPATPT(0.014)AS(0.138)S(0.138)S(0.138)S(0.138)S(0.138)T(0.138)T(0.138)PT(0.018)RK 50.055 0.070892 85777000 25912 19141 19344 21219 22894 14609 28688 18049 26020 TRUE FALSE 24290.21417 20558.21956 19802.84881 21763.51546 21095.99759 18826.38114 24386.50073 20302.45738 21677.0939 1.120547537 0.948384486 0.913537991 1.003986769 0.973193071 0.868491931 1.124989394 0.936585756 1 14.40388374 1.738359779 24.99999989 1.030643023 0.963359206 0.067943939 0.079476537 0.095591087 6846.665224 0.033819018 0.018754357 54.74693101 -1.738359779 -0.067283817 RSPES(ph)CSKPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSPESCSKPEK 11 2 Q03111 Q03111 MLLT1 Protein ENL 1 RS(0.127)PES(0.867)CS(0.005)KPEK 115.68 0.00085878 807330000 936650 564440 700050 647780 706490 482720 840130 572640 838600 TRUE FALSE 878026.7485 606231.7249 716655.5166 664403.1315 651005.1252 622073.4277 714160.3059 644135.3645 698632.2424 1.256779598 0.867740834 1.025797942 0.951005538 0.931828057 0.890416144 1.022226377 0.9219949 1 19.4141737 4.748720813 24.86201161 0.953527313 1.256779778 0.768838562 0.052616194 611.2337019 1495657.344 0.011720351 0.160897684 56068.74213 -4.748720813 0.303252465 RSPQQTVPYVVPLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSPQQTVPYVVPLSPK 16 1 Q9UQR0;H0Y6S1;B4DRC2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 1 RSPQQTVPYVVPLS(1)PK 84.573 0.0045588 392070000 346850 217780 283300 268300 289440 207580 349670 218910 342470 TRUE FALSE 325141.2776 233904.6578 290020.0098 275185.0322 266708.5499 267504.9762 297240.2297 246241.3954 285309.5446 1.139608835 0.819827665 1.016510016 0.964513938 0.934804163 0.937595609 1.041816635 0.8630675 1 18.12216849 RSPTGS(ph)TTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSPTGSTTSR 10 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 RS(0.09)PT(0.09)GS(0.38)T(0.38)T(0.024)S(0.035)R;RS(0.002)PT(0.02)GS(0.287)T(0.287)T(0.287)S(0.116)R 83.214 0.01669 237160000 187060 205743 204386 217443 222635 171676 199049 184746 227176 TRUE FALSE 175352.2485 220976.4258 209234.1324 223022.9555 205150.1452 221236.0743 169203.4503 207811.9448 189258.858 0.926520694 1.167588287 1.105544727 1.178401676 1.083965883 1.168960209 0.894031868 1.098030216 1 17.5300013 1.750678386 25 0.990170645 1.114412245 0.251542005 0.086396789 3.827559992 7909.675918 0.035516236 0.01969562 56.32204123 -1.750678386 0.1242416 RSQAGVSSGAPPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSQAGVSSGAPPGR 14 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 156.17 9.05E-06 50557000 29273 38182 33044 33387 39590 27107 37738 28150 42648 FALSE TRUE 27440.85518 41009.03501 33827.81928 34243.76694 36480.7611 34932.35085 32079.53724 31664.58947 35529.77328 0.772334092 1.154216062 0.952097809 0.963804826 1.026765941 0.983185301 0.902891696 0.891212821 1 15.11674086 1.83647644 5.574119732 0.922593893 0.995596783 0.014882467 0.097920139 0.506954877 22.10514759 0.041365125 0.02428701 68.62406503 -1.83647644 0.07300289 RSQS(ph)FSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSQSFSK 7 1 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 RS(0.029)QS(0.971)FSK 60.434 0.05974 110920000 77622 75987 74748 82768 93887 58213 94728 76358 123830 TRUE FALSE 72763.77758 81613.15654 76521.05786 84891.96701 86513.49374 75018.14809 80524.41581 85891.46438 103161.973 0.705335265 0.79111667 0.74175644 0.8228998 0.838618061 0.727187993 0.780562968 0.832588422 1 16.65455175 -5 0.242168365 2.29575687 0.755646688 0.754250206 0.040816044 84.66658872 0.843885074 54.01243638 0.060799186 1.00E-05 5 -1.540110182 RSQS(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSQSPVK 7 1 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3;Q7Z309-5 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 RS(0.021)QS(0.979)PVK 58.592 0.066536 79086000 100350 190760 62500 55568 252540 33520 67574 195130 251550 TRUE FALSE 94069.27263 204884.0689 63982.52951 56993.96896 232706.5271 43196.67985 57441.90603 219492.41 209564.6799 0.448879423 0.977665077 0.305311609 0.27196362 1.110428185 0.206125764 0.274101084 1.047373107 1 17.67703606 1.221723029 24.98611849 1.023687213 0.522971457 0.32722874 0.30389545 335.7042521 498154.352 0.282296952 0.071335302 16.66184266 -1.221723029 -0.500715757 RSRHGPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSRHGPGR 8 2 P55198 P55198 MLLT6 Protein AF-17 0 0 0.098121 78714000 0 0 2699.9 0 0 0 0 0 2458.8 FALSE TRUE 0 0 2763.942903 0 0 0 0 0 2048.410396 0 0 1.349311109 0 0 0 0 0 1 11.00028907 -1.629092982 3.333635362 1.044936107 0.224885185 0.266850092 0.424047571 470686830.5 536008383.4 182951974.6 0.114501184 0.023491298 1.629092982 -0.820050922 RSS(ph)AIGIENIQEVQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSAIGIENIQEVQEK 16 1 J3KPC5;P47736-3;P47736;P47736-4;F2Z357;X6R8W7;P47736-2;A0A0A0MQY8 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 RS(0.107)S(0.893)AIGIENIQEVQEK 225.39 4.24E-15 905490000 1214600 1038200 1052800 1002200 1315200 753690 1259800 1009200 1980700 TRUE FALSE 1138580.354 1115069.408 1077772.913 1027918.149 1211909.497 971268.0679 1070904.685 1135200.842 1650108.374 0.690003379 0.675755257 0.653152805 0.622939781 0.734442365 0.588608653 0.648990516 0.687955324 1 20.65412935 0.737834435 3.84327733 0.999996444 0.657899363 0.88413171 0.038504809 1.095857568 15.79371991 0.033822182 0.008662699 5.468074657 -0.737834435 -0.342097081 RSS(ph)DGS(ph)LSHEEDLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSDGSLSHEEDLAK 15 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 2 RS(0.604)S(0.665)DGS(0.66)LS(0.071)HEEDLAK;RS(0.46)S(0.548)DGS(0.875)LS(0.118)HEEDLAK 98.269 0.010475 317050000 470620 393770 434740 442290 558940 352080 550910 415700 772250 TRUE FALSE 441164.7343 422925.1405 445052.2381 453639.9102 515043.1071 453719.7805 468306.1599 467601.0601 643356.4861 0.685723613 0.657372933 0.691766148 0.705114381 0.80055633 0.705238527 0.72791084 0.726814869 1 19.29525884 -5 0.212281822 2.420930009 0.667277788 0.883913501 0.033292136 46.54680452 0.464700878 28.16296516 0.069559283 1.00E-05 5 -1.753652221 RSS(ph)DPALIGLSTSVSDSNFSSEEPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.202)S(0.798)DPALIGLSTSVSDSNFSSEEPSR;RS(0.221)S(0.779)DPALIGLSTSVSDSNFSSEEPSR;RS(0.208)S(0.792)DPALIGLSTSVSDSNFSSEEPSR;RS(0.451)S(0.549)DPALIGLSTSVSDSNFSSEEPSR 328.65 4.08E-95 7419000000 1191480 1382900 1281320 1302200 1531030 1172080 1524120 1282140 1405090 TRUE FALSE 1116907.394 1485291.355 1311713.515 1335616.657 1410789.08 1510440.469 1295592.355 1442218.001 1170571.402 0.954155716 1.268860108 1.120575399 1.140995461 1.205214033 1.290344584 1.106803355 1.232063246 1 20.15878151 -1.09537312 4.897633802 0.999993636 1.171502139 0.22219782 0.096238033 5.86E-06 1.08E-06 0.081607894 0.019234451 0.080283608 1.09537312 0.171508503 RSS(ph)DSWEVWGSASTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSDSWEVWGSASTNR 16 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 RS(0.003)S(0.914)DS(0.083)WEVWGSASTNR 337.43 8.71E-72 451830000 208250 244480 207160 217020 247160 176640 257990 219740 355330 TRUE FALSE 195216.0042 262581.5536 212073.933 222589.1006 227749.0506 227633.1005 219306.7946 247175.0227 296023.1275 0.659462002 0.887030536 0.716410014 0.751931454 0.769362355 0.768970663 0.740843448 0.834985512 1 18.17535037 0.902408467 3.721358562 0.999909983 0.765352694 0.645522196 0.057068213 0.262765 8.002739086 0.050681293 0.013025321 7.987455782 -0.902408467 -0.234557288 RSS(ph)DTEEESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSDTEEESR 10 1 Q96IZ7-2;Q96IZ7;C9J713;C9J8Q2;C9JVB3;F8WDM0;C9J367 Q96IZ7-2 RSRC1 Serine/Arginine-related protein 53 1 RS(0.039)S(0.836)DT(0.125)EEESR 169.66 2.80E-06 539760000 140530 148390 143740 173220 144700 121820 141380 123710 169100 TRUE FALSE 131734.4782 159376.95 147149.5807 177665.1185 133335.8457 156987.4564 120181.3815 139155.4658 140876.1176 0.935108664 1.131326961 1.044531772 1.261144341 0.946475868 1.114365296 0.853099756 0.987786065 1 17.10406753 1.750417159 25 0.935945025 1.078233078 0.254285441 0.10011951 3.749981393 7920.428453 0.041347123 0.022929168 56.28817381 -1.750417159 0.142288053 RSS(ph)GREEDDEELLR ddPTM_SK-BR-3_Pertuzumab_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(0.339)S(0.661)GREEDDEELLR 195.97 2.01E-08 1070800000 332960 376580 327740 343300 425510 293130 407520 336920 510150 TRUE FALSE 312120.628 404462.375 335514.1476 352109.6592 392092.161 377751.8724 346416.1592 378985.2037 425002.6693 0.734396865 0.951670199 0.789440095 0.828488112 0.922563996 0.888822353 0.815091726 0.89172429 1 18.69711238 -4.999999999 0.279032196 2.051822101 0.846089785 0.363887644 0.063343231 256.5100406 2.460986168 156.1139878 0.067720045 1.00E-05 4.999999999 -1.205732316 RSS(ph)LDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSLDEK 7 1 Q9NWB6;Q9NWB6-2;Q9NWB6-3 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 RS(0.356)S(0.644)LDEK 53.028 0.087071 339810000 156600 199620 180240 216230 173150 152400 178170 159460 195820 TRUE FALSE 146798.6855 214400.0725 184515.3779 221778.8279 159551.4975 196395.406 151455.0625 179368.932 163136.377 0.899852555 1.314238286 1.13104987 1.359468881 0.97802526 1.203872549 0.928395404 1.099502976 1 17.31571899 2.205928906 1.502046172 1.016098747 1.183657748 0.114281765 0.146920834 0.627286148 2.76331909 0.076885264 0.044482652 160.6678219 -2.205928906 0.167559001 RSS(ph)LGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RSSLGEK 7 1 A0A1B0GTL5;Q9BXF6 A0A1B0GTL5 RAB11FIP5 Rab11 family-interacting protein 5 1 RS(0.013)S(0.987)LGEK;RS(0.001)S(0.999)LGEK;RS(0.296)S(0.704)LGEK;RS(0.225)S(0.775)LGEK 123.96 0.0025684 1799770000 1840090 1427640 1528410 1472800 1630290 1096370 1840520 1375540 2107540 TRUE FALSE 1724922.052 1533343.951 1564664.607 1510594.541 1502253.6 1412874.221 1564551.113 1547279.197 1755777.959 0.982426077 0.873313134 0.891151754 0.860356251 0.855605683 0.804699828 0.891087113 0.881249926 1 20.74367898 0.476359478 2.296380377 0.999995087 0.876182708 0.420660238 0.044119117 7.372120913 31.07410641 0.039758087 0.010719859 2.994742443 -0.476359478 -0.123812379 RSS(ph)LLNAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSLLNAK 8 1 E9PCH4;Q8TEU7-2;Q8TEU7-5;Q8TEU7-3;Q8TEU7;Q8TEU7-4;D6RE77;B7Z7Y1;A0A5F9ZHG7 E9PCH4 RAPGEF6 Rap guanine nucleotide exchange factor 6 1 RS(0.066)S(0.934)LLNAK;RS(0.232)S(0.768)LLNAK 106.29 0.0025873 1158460000 782360 739600 738170 758760 923840 560200 940350 715930 1103580 TRUE FALSE 733393.4842 794360.7536 755679.741 778231.0662 851285.333 721920.6459 799353.2473 805315.4365 919385.3686 0.797699756 0.864012829 0.821940143 0.84646884 0.925928737 0.785220943 0.869443081 0.875928054 1 19.81031018 -5 0.237762756 1.865122489 0.831973374 0.620672974 0.038500285 106.7818527 1.06649186 44.54242795 0.056256066 1.00E-05 5 -1.033149115 RSS(ph)LLSLMTGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSLLSLMTGKK 12 2 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 RS(0.016)S(0.984)LLSLMTGKK 117.4 0.00038492 97398000 156490 187990 139810 139150 250160 89157 216670 181090 497280 TRUE FALSE 146695.5702 201908.9752 143126.3592 142720.8246 230513.4427 114895.1786 184182.345 203699.4851 414280.7554 0.354096994 0.487372326 0.345481554 0.344502666 0.556418418 0.277336509 0.444583396 0.491694298 1 18.66024928 0.605609243 1.777644083 0.99987514 0.402218858 0.847250133 0.079354452 0.650821576 2.524099758 0.06773405 0.019028994 4.032823762 -0.605609243 -0.597656282 RSS(ph)LPLDHGSPAQENPESEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSLPLDHGSPAQENPESEK 20 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5;A0A0A0MRX3 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 RS(0.033)S(0.957)LPLDHGS(0.005)PAQENPES(0.005)EK;RS(0.171)S(0.828)LPLDHGSPAQENPESEK 53.865 0.052456 946810000 835430 757350 773140 813130 799040 679310 838880 668290 874980 TRUE FALSE 783141.9276 813424.982 791479.2459 833996.2924 736286.6216 875415.7693 713097.7318 751727.4776 728940.1854 1.074356913 1.115900863 1.085794502 1.144121711 1.010078243 1.200943214 0.978266456 1.031260853 1 19.47544091 1.64433208 11.53712819 1.003851322 1.101740138 0.476474002 0.050250253 0.087170533 20.86016379 0.020379269 0.011024743 44.08918597 -1.64433208 0.097888816 RSS(ph)LPLDHGSPAQENPESEKS(ph)SPAVSR ddPTM_SK-BR-3_Pertuzumab_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(0.44)S(0.56)LPLDHGSPAQENPES(0.15)EKS(0.573)S(0.272)PAVS(0.004)R 148.88 6.21E-08 239640000 65470 99929 112090 133020 127780 92887 174120 134130 145970 TRUE FALSE 61372.34957 107327.8471 114748.8277 136433.5184 117744.6742 119701.969 148012.3225 150876.4258 121606.664 0.504679164 0.882581954 0.943606411 1.121924687 0.968241956 0.984337248 1.217139897 1.240692087 1 16.89186276 5.082399047 0.604492625 1.111421586 5.13E-19 0.751213101 0.102683681 2.647405895 0.543436048 0.046384978 2.241056419 120892.4134 -5.082399047 -1.111421586 RSS(ph)LPNGEGLQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RSSLPNGEGLQLK 13 1 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 RS(0.247)S(0.753)LPNGEGLQLK;RS(0.053)S(0.947)LPNGEGLQLK;RS(0.063)S(0.937)LPNGEGLQLK 215.67 1.76E-11 3079040000 2905330 2765410 2924350 2558260 3421870 2396550 3536370 2908600 5464560 TRUE FALSE 2723490.581 2970163.834 2993716.963 2623909.283 3153130.133 3088395.08 3006124.149 3271745.113 4552489.634 0.598242017 0.652426271 0.657599952 0.576367986 0.692616653 0.67839695 0.660325314 0.718671623 1 22.1182243 -1.200745517 0.363883465 1.190250244 0.62851224 0.926928346 0.031430035 4.246271075 0.37328207 0.818807595 0.0225416 0.062987516 1.200745517 -0.561738005 RSS(ph)LS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSLSPGR 8 1 Q9BUQ8;F8VVA2;F8W1J5 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 2 RS(0.24)S(0.778)LS(0.982)PGR 70.524 0.034157 245930000 335100 367990 360840 384180 408130 324190 412370 324930 407020 TRUE FALSE 314126.6892 395236.3625 369399.2952 394038.7092 376077.1161 417778.3902 350538.9468 365498.2258 339085.7326 0.926393118 1.165594198 1.08939793 1.162062191 1.109091536 1.232073043 1.033776751 1.07789326 1 18.37129056 1.605613549 25 1.041866527 1.119852224 0.166020023 0.080314766 0.373759599 4084.978096 0.03665478 0.018238922 40.32863746 -1.605613549 0.077985697 RSS(ph)LSSHSHQSQIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSLSSHSHQSQIYR 15 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 RS(0.021)S(0.978)LSSHSHQSQIYR;RS(0.029)S(0.97)LS(0.001)SHSHQSQIYR 235.21 5.31E-18 563110000 16127.8 109392 56051 69171 91250 43896 59674 73972 116801 TRUE FALSE 15118.38979 117491.4975 57380.55619 70946.04497 84083.59308 56568.06261 50726.43769 83207.56703 97306.15854 0.155369301 1.207441536 0.5896909 0.729101282 0.864113786 0.581341032 0.521307577 0.855111005 1 16.5702435 1.000651382 24.8935636 1.000000025 0.704708811 0.14266673 0.267208568 33.44020306 1277900.404 0.240356594 0.060089148 10.01500987 -1.000651382 -0.295291214 RSS(ph)LSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSLSSR 7 1 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 1 RS(0.015)S(0.985)LSSR;RS(0.015)S(0.983)LS(0.001)SR 94.804 0.0085334 1014850000 425630 469340 500810 486440 517970 397980 569480 506850 561900 TRUE FALSE 398990.5781 504090.4219 512689.4497 498922.8739 477290.7256 512870.3653 484091.7608 570131.3382 468115.26 0.852334056 1.076851077 1.095220544 1.065812027 1.019600868 1.095607021 1.034129417 1.217929401 1 18.83650427 4.738772156 23.74374608 1.075557706 0.852333961 0.582952097 0.059358975 5.506724882 617221.9064 0.012391159 0.071940482 54798.93981 -4.738772156 -0.223223745 RSS(ph)MIETGQGAEGGLSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSMIETGQGAEGGLSLR 18 1 P49796-1;P49796-4;P49796-6;P49796 P49796-1 RGS3 Regulator of G-protein signaling 3 1 RS(0.22)S(0.78)MIETGQGAEGGLSLR 222.78 3.37E-19 397530000 222420 127060 139040 148710 177690 110600 188930 142390 223170 TRUE FALSE 208499.1292 136467.6546 142338.0945 152526.1504 163734.9442 142528.4246 160601.7004 160167.7049 185921.4853 1.121436444 0.734006908 0.765581741 0.820379367 0.880667148 0.766605454 0.863814638 0.861480343 1 17.50433397 0.643131697 1.285573267 0.999795479 0.826113546 0.130067805 0.108977753 1.998446875 5.002987372 0.095730511 0.028750416 4.396749236 -0.643131697 -0.173681933 RSS(ph)NPPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSNPPAR 8 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 RS(0.143)S(0.857)NPPAR;RS(0.038)S(0.962)NPPAR 118.9 0.0011005 437740000 143362 185514 172156 171562 186075 138771 169161 154147 194315 TRUE FALSE 134389.2283 199249.6496 176239.6216 175964.5714 171461.4201 178831.9349 143796.8785 173392.5923 161882.5712 0.830164899 1.230828298 1.088688055 1.086988983 1.059171589 1.104701597 0.888278938 1.071101052 1 17.30458814 1.764969856 25 0.976293512 1.088705456 0.084182354 0.108253936 27.31378092 25872.83113 0.046193799 0.02561938 58.20628159 -1.764969856 0.112411944 RSS(ph)NVSYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSNVSYK 8 1 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 1 RS(0.098)S(0.892)NVS(0.01)YK 63.944 0.03848 0 137260 134740 134840 118280 145090 91250 158990 141040 178080 TRUE FALSE 128669.1416 144716.2898 138038.4685 121315.265 133695.2167 117592.3937 135150.9255 158649.1545 148357.2976 0.867292299 0.975457845 0.930446097 0.817723611 0.901170477 0.792629656 0.91098266 1.069372097 1 17.17871637 1.297510707 6.836977818 1.034051537 0.892454172 0.559568591 0.054980067 0.155881608 14.01583028 0.040145552 0.014306157 19.83858567 -1.297510707 -0.141597365 RSS(ph)PESDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSPESDR 8 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 RS(0.338)S(0.662)PESDR 96.009 0.0056628 100480000 50577 51423 50463 49696 54900 41190 45094 41536 51745 TRUE FALSE 47411.47585 55230.41243 51660.00619 50971.2835 50588.37546 53080.88434 38332.57333 46721.86103 43108.42521 1.099819249 1.281197635 1.198373773 1.182397252 1.173514811 1.231334341 0.889213028 1.083822032 1 15.39568224 1.750189938 25 0.986849871 1.203636196 0.683555546 0.065026916 1.560785089 3361.110701 0.027084693 0.015019886 56.25873183 -1.750189938 0.216786325 RSS(ph)PPGHYYQK ddPTM_SK-BR-3_Pertuzumab_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(0.203)S(0.797)PPGHYYQK 116.78 0.00057761 273190000 194730 199000 211220 186730 263710 201500 231790 260200 485600 TRUE FALSE 182542.1969 213734.1671 216230.2381 191521.8079 242999.2804 259669.7789 197035.2413 292686.5428 404550.2229 0.451222584 0.528325422 0.534495412 0.473419114 0.600665298 0.641872787 0.487047665 0.723486297 1 18.62595929 -4.999998171 0.194074317 3.045142253 0.465662286 0.852600214 0.062323439 47.74459373 0.469711274 37.5879678 0.150709002 1.00E-05 4.999998171 -2.579479967 RSS(ph)PVPPVPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSPVPPVPER 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RS(0.164)S(0.836)PVPPVPER;RS(0.275)S(0.725)PVPPVPER 102.65 0.0017396 4740700000 2750100 2947400 3246100 2802500 3254700 3072800 3460200 2956400 3422400 TRUE FALSE 2577976.15 3165628.563 3323099.025 2874416.895 2999088.991 3959867.477 2941375.133 3325513.048 2851179.33 0.904178886 1.110287427 1.165517367 1.008150159 1.05187666 1.388852478 1.03163456 1.166364042 1 21.44312735 4.738048955 4.588058024 1.124644386 0.890342872 0.251876506 0.113661441 0.248336684 13.85619856 0.024813648 0.187736305 54707.76283 -4.738048955 -0.234301514 RSS(ph)RS(ph)SPELTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSRSSPELTR 11 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RS(0.49)S(0.51)RS(0.501)S(0.449)PELT(0.051)R;RS(0.437)S(0.562)RS(0.801)S(0.199)PELTR 140.03 0.0010186 3872150000 2840310 3086520 2911050 3124790 3370300 2559450 3160270 2662460 3078640 TRUE FALSE 2662540.067 3315049.152 2980101.481 3204977.402 3105610.233 3298321.666 2686416.852 2994873.992 2564795.095 1.038110246 1.292520076 1.161925756 1.249603685 1.210860953 1.285998118 1.047419678 1.16768548 1 21.29041214 1.218256525 1.08619755 1.016681071 1.210157624 0.31726376 0.085880341 0.470629936 1.151628763 0.071617487 0.023832313 16.5293785 -1.218256525 0.193476553 RSS(ph)SEGLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RSSSEGLSK 9 1 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 RS(0.125)S(0.825)S(0.049)EGLSK;RS(0.094)S(0.904)S(0.001)EGLSK;RS(0.034)S(0.964)S(0.001)EGLSK;RS(0.064)S(0.934)S(0.002)EGLSK 152.32 4.95E-05 3822040000 2074230 1755770 1805490 1622820 1807600 1612080 2284120 1746030 2831130 TRUE FALSE 1944407.647 1885769.038 1848317.075 1664464.309 1665638.388 2077461.326 1941637.411 1964025.689 2358596.113 0.824391949 0.799530291 0.78365137 0.705701285 0.706199072 0.880804185 0.823217422 0.832709627 1 21.16949696 0.667399507 0.713410894 1.000494049 0.77620162 0.648931279 0.049957259 0.783417032 0.751215083 0.052544032 0.018771356 4.649427789 -0.667399507 -0.224292429 RSS(ph)SSGDQSSDSLNSPTLLAL ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSSSGDQSSDSLNSPTLLAL 21 1 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 1 RS(0.171)S(0.789)S(0.037)S(0.002)GDQSSDSLNSPTLLAL 197.85 9.40E-22 109030000 155220 184930 176660 172660 196020 143330 175170 154790 282440 TRUE FALSE 145505.0573 198622.4096 180850.4586 177090.7479 180625.3799 184707.0442 148904.8847 174115.8722 235298.9394 0.618383821 0.844127943 0.768598699 0.752620256 0.767642134 0.784988852 0.632832792 0.739977293 1 17.84413529 -0.799417045 8.930680135 1 0.745708969 0.593762019 0.06771472 0 0 0.065860874 0.015523557 0.158702203 0.799417045 -0.254291031 RSS(ph)TSGDT(ph)EEEEEEEVVPFSSDEQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.387)S(0.465)T(0.133)S(0.026)GDT(0.99)EEEEEEEVVPFSSDEQKR;RS(0.388)S(0.481)T(0.129)S(0.002)GDT(1)EEEEEEEVVPFSSDEQKR 193.03 6.59E-18 118717000 201093 170079 167946 186257 184895 115386 208910 156356 209679 TRUE FALSE 188506.9481 182671.8261 171929.7584 191036.67 170374.0925 148696.0651 177585.8849 175877.3908 174682.2203 1.079142157 1.045737945 0.984243034 1.093624008 0.975337342 0.851237549 1.016622554 1.00684197 1 17.41437325 2.556552284 9.638590818 0.963682535 1.038497407 0.344084682 0.054074143 0.573589204 66.75298313 0.017081152 0.016088474 360.2071129 -2.556552284 0.074814871 RSS(ph)TSSEPTPTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RSSTSSEPTPTVK 13 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 RS(0.067)S(0.899)T(0.032)S(0.001)S(0.001)EPTPTVK;RSS(0.792)T(0.128)S(0.011)S(0.069)EPTPTVK 245.93 4.07E-17 650830000 1473160 1322320 1370110 1303690 1591390 1183550 1785090 1378110 2071270 TRUE FALSE 1380957.545 1420225.949 1402609.656 1337144.893 1466408.649 1525221.672 1517432.326 1550170.067 1725561.656 0.800294525 0.823051407 0.812842387 0.774904152 0.849815272 0.883898681 0.879384588 0.898356811 1 20.71863459 1.163324971 0.508540065 1.002012395 0.802520299 0.898013375 0.020332762 0.271905777 0.184791252 0.022995143 0.011946742 14.5654857 -1.163324971 -0.199492096 RSS(ph)WECTGSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSWECTGSGR 11 1 Q8NEV8-2;Q8NEV8;E9PPH6 Q8NEV8-2 EXPH5 Exophilin-5 1 RS(0.116)S(0.884)WECTGSGR 105.31 0.0015205 536440000 106830 154930 88991 129950 149840 99138 139590 118420 145920 TRUE FALSE 100143.701 166401.1784 91101.90854 133284.737 138072.1708 127757.5312 118659.7754 133204.9977 121565.0093 0.823787219 1.368824626 0.749408971 1.096407081 1.135788757 1.050940003 0.976101397 1.095751141 1 16.8913685 -4.999999999 0.166072153 0.851390978 1.051490257 0 0.170075042 1445.225976 13.51321323 71.73825757 0.611341608 1.00E-05 4.999999999 0.200099279 RSSKDEEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSKDEEPR 9 2 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 0 49.418 0.094455 21308000 52127 53907 53965 54674 71505 44524 59710 51779 92096 FALSE TRUE 48864.46412 57898.33037 55245.07528 56077.0274 65889.28574 57377.35601 50757.03982 58243.72213 76724.58264 0.636881459 0.75462555 0.720043999 0.730887357 0.858776724 0.747835362 0.661548595 0.759127259 1 16.22740127 -2.018794574 1.801485957 1.288336736 0.733290816 0.66532821 0.059351915 382735.3987 109295.2271 456402.8746 0.015433753 0.009576469 2.018794574 -0.555045919 RSSLDAEIDSLT(ph)SILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 49 3 Q93052;A0A087WZF1;C9JUT4 Q93052 LPP Lipoma-preferred partner 1 RS(0.099)S(0.099)LDAEIDS(0.265)LT(0.442)S(0.095)ILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 120.53 2.88E-10 2539400000 401550 333390 404760 390540 350990 275930 401510 306450 341580 TRUE FALSE 376417.7023 358074.5425 414361.0983 400561.9176 323424.6612 355586.5117 341307.3029 344710.9571 284568.0913 1.322768482 1.258308832 1.456105273 1.407613607 1.136545773 1.249565649 1.199387118 1.21134789 1 18.11841438 2.737978148 24.99988259 1.181297528 1.359868386 0.579277937 0.084323588 41.36975754 1775581.975 0.025514505 0.025422319 546.9884397 -2.737978148 0.178570858 RSSLDAEIDSLTS(ph)ILADLECS(ph)SPYKPRPPQSSTGSTASPPVSTPVTGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 49 3 Q93052;A0A087WZF1;C9JUT4 Q93052 LPP Lipoma-preferred partner 2 RS(0.181)S(0.182)LDAEIDS(0.198)LT(0.198)S(0.216)ILADLECS(0.115)S(0.115)PY(0.11)KPRPPQS(0.115)S(0.115)T(0.115)GS(0.115)T(0.115)AS(0.106)PPVS(0.001)TPVTGHK 50.214 0.0053664 296130000 83098 70641 61701 67171 72303 55617 101920 67442 67616 TRUE FALSE 77897.04451 75871.33314 63164.57686 68894.72158 66624.61404 71672.72503 86638.04218 75862.28216 56330.45278 1.382858484 1.346897271 1.121322016 1.223045763 1.182745935 1.272361955 1.538032057 1.346736595 1 15.78162745 1.978651451 24.5065709 1.367327427 1.243892481 0 0.154060606 1232.00285 1414247.404 0.058432277 0.038154442 95.20317922 -1.978651451 -0.123434946 RSSLDAEIDSLTS(ph)ILADLECSSPYKPRPPQS(ph)STGSTASPPVSTPVTGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 49 3 Q93052;A0A087WZF1;C9JUT4 Q93052 LPP Lipoma-preferred partner 2 RS(0.2)S(0.22)LDAEIDS(0.129)LT(0.191)S(0.259)ILADLECS(0.014)S(0.004)PYKPRPPQS(0.237)S(0.215)T(0.195)GS(0.16)T(0.145)AS(0.028)PPVSTPVTGHK 107.94 3.15E-08 329440000 166690 121980 139400 132070 141110 122740 204720 141070 141680 TRUE FALSE 156257.1705 131011.5261 142706.6338 135459.1398 130027.7898 158173.0455 174024.1365 158682.9 118032.6927 1.323846528 1.109959649 1.209043279 1.14764085 1.101625209 1.34007826 1.474372333 1.344397865 1 16.84882699 2.221676519 23.95625747 1.3451798 1.171863479 0.081217584 0.137315481 182.9127541 259525.8508 0.046201188 0.03422621 166.6005839 -2.221676519 -0.17331632 RSSPES(ph)DR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSPESDR 8 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 RS(0.001)S(0.014)PES(0.986)DR 120.54 0.0015693 84305000 152970 153350 165260 156140 168020 130500 151930 140500 143290 TRUE FALSE 143395.8808 164704.1936 169180.0452 160146.8167 154824.387 168173.2315 129149.5069 158041.7343 119373.9733 1.201232369 1.37973286 1.417227228 1.341555553 1.29696937 1.408793113 1.081889991 1.323921202 1 16.8651288 1.011131298 0.610652917 1.006802604 1.361082064 0.48615025 0.099871769 0.625613574 0.560038971 0.095584576 0.041272945 10.25962053 -1.011131298 0.354279459 RSSS(ph)LKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.013)S(0.156)S(0.831)LKER;RS(0.001)S(0.024)S(0.976)LKER 84.507 0.0090803 2762350000 745070 666720 612860 656410 785620 518829 709150 635390 1285590 TRUE FALSE 698437.3987 716084.6425 627397.3286 673254.5919 723920.5742 668606.5098 602819.5409 714719.8402 1071016.724 0.652125577 0.668602671 0.585796015 0.628612586 0.67591902 0.624272707 0.562847925 0.667328366 1 20.03054958 0.961221121 23.27074633 1.000000001 0.62567983 0.919278131 0.034342834 814.874197 488997.0593 0.03437442 0.008593605 9.145787797 -0.961221121 -0.374320171 RSSS(ph)SGDQSSDSLNSPTLLAL ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSSSGDQSSDSLNSPTLLAL 21 1 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 1 RS(0.062)S(0.297)S(0.613)S(0.027)GDQS(0.001)S(0.001)DSLNSPTLLAL 206.21 4.59E-22 126720000 179010 207680 200870 206850 225050 169770 209190 187450 292630 TRUE FALSE 167806.0836 223056.8433 205634.7313 212158.1212 207375.4808 218779.843 177823.9015 210853.5451 243788.1625 0.688327447 0.914961748 0.843497605 0.870256041 0.850638024 0.897417827 0.729419754 0.864904772 1 17.89526855 -1.964803194 2.238038428 1.135678204 0.83733938 0.352252902 0.07113679 7899071.868 3246668.366 5558600.689 0.016029208 0.010844182 1.964803194 -0.298338824 RSSSS(ph)GDQSSDSLNS(ph)PTLLAL ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSSSGDQSSDSLNSPTLLAL 21 1 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 2 RS(0.21)S(0.229)S(0.262)S(0.285)GDQS(0.018)S(0.018)DS(0.174)LNS(0.795)PT(0.01)LLAL 61.136 0.034289 43903000 58990 76121 76561 113750 127620 55974 54813 37578 60806 TRUE FALSE 55297.9212 81757.07804 78377.06307 116669.0176 117597.24 72132.78514 46594.29951 42269.69602 50657.08578 1.09161276 1.613931729 1.54720829 2.303113489 2.321437133 1.423942653 0.919798263 0.834428104 1 15.62847646 1.869773203 3.664387564 0.914754698 1.753235119 0.539090847 0.358898501 0.19970056 4.426520764 0.188110616 0.102803033 74.0923216 -1.869773203 0.838480421 RSSTSGDT(ph)EEEEEEEVVPFSSDEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSSTSGDTEEEEEEEVVPFSSDEQK 25 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;O15231-2;H7BZT5;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 1 RS(0.231)S(0.231)T(0.146)S(0.146)GDT(0.245)EEEEEEEVVPFSSDEQK 99.135 0.0041839 152260000 265900 185940 213910 216020 237440 173210 271710 195130 243000 TRUE FALSE 249257.7936 199707.1911 218984.0462 221563.4389 218792.4202 223212.9152 230969.6079 219492.41 202441.7302 1.231256982 0.986492216 1.081713963 1.094455371 1.080767389 1.102603277 1.140918959 1.084225124 1 17.62714718 3.370220089 4.684760814 1.0951805 1.071911378 0 0.070110648 1.060514918 39.02215078 0.01832935 0.025217043 2345.417108 -3.370220089 -0.023269122 RST(ph)SPIIGS(ph)PPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RSTSPIIGSPPVR 13 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 2 RS(0.49)T(0.612)S(0.298)PIIGS(0.6)PPVR;RS(0.135)T(0.657)S(0.21)PIIGS(0.997)PPVR;RS(0.301)T(0.376)S(0.323)PIIGS(1)PPVR;RS(0.132)T(0.693)S(0.18)PIIGS(0.994)PPVR;RS(0.44)T(0.552)S(0.036)PIIGS(0.973)PPVR 110.74 0.002293 1108212000 701734 825982 815693 971515 1159443 865792 1147077 954680 1174506 TRUE FALSE 657813.7216 887138.5667 835041.6232 996445.7197 1068385.024 1115732.095 975083.4528 1073873.9 978473.361 0.672285775 0.906655819 0.853412731 1.018367755 1.09188974 1.140278458 0.996535513 1.097499372 1 19.90017305 4.28885036 0.582967172 1.072792945 0.607656333 0.732167434 0.071136626 1.258598434 0.464874731 0.037818801 0.369003213 19446.89905 -4.28885036 -0.465136612 RST(ph)SPIIGSPPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSTSPIIGSPPVR 13 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 RS(0.256)T(0.644)S(0.099)PIIGSPPVR 101.5 0.0011207 755700000 454460 533090 541460 495810 444970 274870 439180 408820 586140 TRUE FALSE 426016.1598 572560.5383 554303.6869 508533.324 410023.8511 354220.5069 373329.0361 459862.0769 488309.4474 0.872430714 1.17253627 1.135148398 1.041416108 0.839680357 0.725401707 0.764533716 0.94174315 1 18.89743616 2.783862339 3.649794259 0.820927854 1.09372996 0.411289944 0.113631063 0.16737971 4.65179318 0.034835513 0.03600842 607.9422679 -2.783862339 0.272802106 RSTAPSAAASASASAAASS(ph)PAGGGAEALELLEHCGVCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSTAPSAAASASASAAASSPAGGGAEALELLEHCGVCR 38 1 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 RSTAPSAAASASASAAAS(0.007)S(0.993)PAGGGAEALELLEHCGVCR 89.007 0.00026342 179150000 31704 53183 40400 45092 60537 31284 56848 40338 104460 TRUE FALSE 29719.70323 57120.72466 41358.30708 46249.13706 55782.66821 40315.18295 48324.17015 45374.28809 87024.95116 0.341507842 0.656371809 0.475246542 0.53144686 0.64099626 0.463260047 0.555290977 0.521394008 1 16.40914148 -1.669476242 2.320783529 1.079747982 0.533526604 0.735220757 0.089734827 1859213.055 1348299.961 874181.649 0.020542057 0.02140542 1.669476242 -0.546221378 RSTS(ph)PIIGSPPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSTSPIIGSPPVR 13 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 RS(0.096)T(0.147)S(0.756)PIIGSPPVR 88.149 0.0049252 765090000 361280 458930 407830 361780 359320 275670 385080 314630 471770 TRUE FALSE 338668.1297 492909.6547 417503.9202 371063.8873 331100.4566 355251.4539 327340.8289 353912.2481 393028.5392 0.861688391 1.254131966 1.062273801 0.944114359 0.842433624 0.903882081 0.832867836 0.90047468 1 18.58427455 3.203264329 2.792260134 0.882632014 1.107696564 0.302622774 0.106000093 0.209648791 3.3342698 0.029437244 0.03848588 1596.850758 -3.203264329 0.225064549 RSVSDNDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RSVSDNDIR 9 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;; 120.36 0.0010865 3415180000 3561170 4462340 3719110 3915300 4866830 3014830 4273110 4279230 5294520 FALSE TRUE 3338282.727 4792736.297 3807329.045 4015773.227 4484608.804 3885162.479 3632396.825 4813501.285 4410830.408 0.756837697 1.086583671 0.863177382 0.910434738 1.016726645 0.880823364 0.82351768 1.091291399 1 22.07261886 1.224938625 24.98404907 1.045645729 0.917101857 0.266530723 0.095176626 378.6631047 694484.1214 0.08491807 0.021693294 16.78566783 -1.224938625 -0.128543872 RSYS(ph)PDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RSYSPDGK 8 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RS(0.1)Y(0.001)S(0.899)PDGK;RS(0.075)Y(0.013)S(0.912)PDGK;RS(0.004)YS(0.996)PDGK;RS(0.001)YS(0.999)PDGK;RS(0.028)Y(0.001)S(0.971)PDGK 144.35 0.00062153 2119930000 1964730 1324950 1503440 1491510 1582120 1233250 1905830 1457800 1798610 TRUE FALSE 1841761.056 1423050.677 1539102.307 1529784.672 1457866.677 1589269.255 1620068.484 1639809.539 1498410.372 1.229143292 0.949706905 1.027156736 1.02093839 0.972942196 1.060636849 1.081191451 1.094366116 1 20.51500136 2.027330505 24.52857135 1.068383926 1.024365441 0 0.078660466 484.1194481 434484.5753 0.027038405 0.019968691 106.4953157 -2.027330505 -0.044018486 RSYS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.017)YS(0.983)PR 79.893 0.06986 291390000 336410 397950 355990 367860 433000 310190 383410 383570 494870 TRUE FALSE 315354.6986 427414.6321 364434.2509 377299.9104 398993.9266 399736.8175 325921.2299 431459.5588 412273 0.764917175 1.036727198 0.88396342 0.91517007 0.967790582 0.969592521 0.790547113 1.04653848 1 18.65324046 1.181107202 24.99998552 1.023270147 0.914729023 0.260058946 0.082059333 135.2891644 58865.23195 0.073631001 0.018407771 15.17424885 -1.181107202 -0.108541124 RSYS(ph)SPDITQAIQEEEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSYSSPDITQAIQEEEKR 18 2 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 RS(0.008)YS(0.817)S(0.175)PDITQAIQEEEKR 234.99 4.60E-24 273660000 191970 165770 146870 157670 195840 110130 221970 166790 298340 TRUE FALSE 179954.9404 178043.7833 150353.8258 161716.0791 180459.5164 141922.7432 188687.6592 187614.0987 248545.1266 0.724033268 0.716343892 0.604935722 0.650650774 0.726063387 0.571013985 0.759168613 0.754849235 1 17.92314829 0.75541106 1.198163295 0.998914158 0.667656158 0.772342501 0.055410572 0.367549476 0.932252273 0.049028591 0.01507097 5.693916053 -0.75541106 -0.331258 RSYSS(ph)PDITQAIQEEEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RSYSSPDITQAIQEEEKR 18 2 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 RSYS(0.091)S(0.909)PDITQAIQEEEKR 307.48 2.91E-51 369610000 233370 219480 226060 224380 275540 154280 257070 202890 406720 TRUE FALSE 218763.7883 235730.5276 231422.25 230137.9707 253900.1999 198818.1315 218524.74 228221.2631 338835.8045 0.645633624 0.695707255 0.682992313 0.679202043 0.749331082 0.586768366 0.644928125 0.673545299 1 18.37022681 -1.9489379 2.417830119 1.248101934 0.670317469 0.863125564 0.041328174 6025265.646 2852340.645 8405565.074 0.00988872 0.011247658 1.9489379 -0.577784465 RT(ph)ASPPPPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.609)AS(0.391)PPPPPK;RT(0.5)AS(0.5)PPPPPK;RT(0.591)AS(0.409)PPPPPK;RT(0.5)AS(0.5)PPPPPK 73.466 0.026314 1226770000 2745360 2362760 2502300 2330290 2650160 2060770 2935630 2341450 3050500 TRUE FALSE 2573532.818 2537701.209 2561655.738 2390089.187 2442027.124 2655680.845 2495459.535 2633785.187 2541351.843 1.012662936 0.998563507 1.007989407 0.940479451 0.960916581 1.044987475 0.981941773 1.036371722 1 21.2771647 2.248114886 24.99907987 1.011946509 0.987362454 0.237213033 0.027527264 382.0173547 999560.2357 0.009656287 0.007991 177.0577277 -2.248114886 -0.024584055 RT(ph)ETSLPETEVDHNMDVNTEEDDDGELALWSPEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTETSLPETEVDHNMDVNTEEDDDGELALWSPEVK 35 1 A0A2R8Y549;Q8NI35-3;Q8NI35;A0A0X1KG69;A0A087WUZ6;Q8NI35-4;Q8NI35-2;Q8NI35-5 A0A2R8Y549 INADL InaD-like protein 1 RT(0.246)ET(0.246)S(0.246)LPET(0.246)EVDHNMDVNT(0.015)EEDDDGELALWSPEVK 44.317 0.048543 21808000 22072 17387 20381 20926 21368 14168 19052 14630 26239 TRUE FALSE 20690.55292 18674.35157 20864.44694 21462.99659 19689.84347 18258.0716 16195.32947 16456.5877 21859.54139 0.946522736 0.854288351 0.954477799 0.981859418 0.900743667 0.835244952 0.740881484 0.752833164 1 14.41597551 2.208799754 3.458384949 0.800109179 0.925222663 0.238590625 0.078653152 0.246441151 6.169320219 0.028824602 0.021145778 161.7334141 -2.208799754 0.125113484 RT(ph)GTPSDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.498)GT(0.498)PS(0.003)DPR;RT(0.499)GT(0.499)PS(0.003)DPR 62.408 0.048532 761190000 746190 795870 768230 770200 843250 708240 884800 785600 1158770 TRUE FALSE 699487.2999 854797.0429 786452.7784 789964.6359 777024.5465 912697.3907 752132.4541 883683.8893 965363.8011 0.72458414 0.885466227 0.814669845 0.818307704 0.804903339 0.945443976 0.779118145 0.915389502 1 19.8807132 -5 0.173800903 1.664497644 0.798841052 0.483374048 0.059668454 116.7816745 1.111593061 26.61830224 0.184018479 1.00E-05 5 -0.865656592 RT(ph)NSDSALHQSTMTPTQPESFSSGSQDVHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTNSDSALHQSTMTPTQPESFSSGSQDVHQK 31 1 M0QXN6;M0QX46;Q6UUV9;Q6UUV9-2;Q6UUV9-3 M0QXN6 CRTC1 CREB-regulated transcription coactivator 1 1 RT(0.544)NS(0.328)DS(0.124)ALHQS(0.003)T(0.001)MTPTQPESFSSGSQDVHQK 92.372 0.00036862 166010000 27904 19541 23394 22402 23694 18153 36040 19751 34487 TRUE FALSE 26157.53845 20987.83597 23948.91673 22976.87325 21833.16882 23393.47641 30636.13658 22216.95583 28730.89691 0.910432366 0.730497069 0.833559662 0.799726974 0.7599195 0.814227154 1.066313268 0.773277489 1 14.81031541 1.89542772 9.352128101 0.951413178 0.798743155 0.361317675 0.086379472 0.337380262 27.97137828 0.032144614 0.020347818 78.60093646 -1.89542772 -0.152670023 RT(ph)PDPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RTPDPAK 7 1 Q8N6N3;Q8N6N3-3;Q8N6N3-2 Q8N6N3 C1orf52 UPF0690 protein C1orf52 1 RT(1)PDPAK;RT(1)PDPAK 55.567 0.074337 402590000 1729590 987710 1272680 1021990 1111600 872310 1536550 1280950 1370840 TRUE FALSE 1621338.049 1060841.076 1302868.571 1048215.994 1024299.42 1124131.736 1306158.592 1440879.427 1142037.948 1.419688419 0.928901774 1.140827739 0.917846903 0.89690489 0.984320826 1.143708573 1.261673861 1 20.12317916 -0.287152653 7.279828328 1.000021837 1.067814221 0.015035594 0.166818581 0 0 0.149124551 0.035148994 0.516234882 0.287152653 0.067792384 RT(ph)PDSTFSETFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RTPDSTFSETFK 12 1 Q9NZI5-3;Q9NZI5;B7Z1S6 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 RT(0.998)PDS(0.002)TFSETFK;RT(0.988)PDS(0.012)TFSETFK;RT(0.998)PDS(0.002)TFSETFK;RT(0.997)PDS(0.003)TFSETFK;RT(0.996)PDS(0.004)TFSETFK 243.83 1.34E-16 3832470000 5195870 4026760 4393070 4258470 4636880 3295340 5340280 4069480 4618870 TRUE FALSE 4870669.772 4324905.5 4497275.695 4367749.55 4272718.149 4246651.163 4539554.591 4577563.536 3847950.758 1.265782771 1.123950324 1.168745646 1.135084575 1.110387949 1.103613697 1.179733026 1.189610737 1 21.87565891 -1.542576959 2.839864827 0.992256798 1.15441777 0.524816417 0.04750272 6872008.143 7609085.253 410435.3144 0.010868197 0.028669693 1.542576959 0.162160972 RT(ph)PSDDEEDNLFAPPK ddPTM_SK-BR-3_Pertuzumab_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 1 RT(0.57)PS(0.43)DDEEDNLFAPPK 87.772 0.0062656 0 138980 112850 114910 126910 135100 98339 161380 112090 163430 TRUE FALSE 130281.4899 121205.5314 117635.7195 130166.7255 124489.791 126727.8729 137182.5672 126084.6832 136152.4772 0.956879321 0.890219068 0.863999847 0.95603641 0.914340991 0.930779046 1.007565709 0.926055007 1 17.05486371 2.199479681 1.131146892 0.98090587 0.90078726 0.331816374 0.036431317 0.458027131 1.116824371 0.024443755 0.013371723 158.2995504 -2.199479681 -0.080118611 RT(ph)PSTKPTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RTPSTKPTVR 10 2 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 RT(0.496)PS(0.477)T(0.027)KPTVR;RT(0.506)PS(0.465)T(0.028)KPTVR 95.631 0.011722 785540000 731920 781400 655480 662410 941280 407680 950840 778030 1178700 TRUE FALSE 686110.4337 839255.669 671028.2951 679408.5621 867355.6657 525370.5979 808270.3692 875168.7582 981967.3553 0.698710023 0.854667586 0.683350919 0.69188508 0.883283605 0.535018394 0.823113278 0.891240176 1 19.90531554 1.169723728 2.44824147 0.989203952 0.737410607 0.466938312 0.098080316 0.228311744 2.438652759 0.083031369 0.023217926 14.78167767 -1.169723728 -0.251793346 RT(ph)PTAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RTPTAEER 8 1 A0A1B0GTY1;A0A1B0GV98;A0A1B0GTC5;A0A1B0GU26;A0A1B0GTC3;A0A1B0GVH5;Q9C0B1;F8WCB8 A0A1B0GTY1 FTO Alpha-ketoglutarate-dependent dioxygenase FTO 1 RT(1)PTAEER;RT(1)PTAEER 97.734 0.0047008 90247000 42491 48088 48396 42804 50160 45123 53922 47821 42394 TRUE FALSE 39831.56416 51648.48556 49543.97597 43902.42311 46220.63594 58149.27759 45836.89669 53791.55712 35318.16752 1.127792492 1.462377274 1.402790106 1.243054954 1.308692924 1.646440958 1.297827716 1.523056288 1 15.10812287 -1.590844408 6.423497212 0.999091287 1.386043858 0.392879666 0.146663308 0.001708444 0.000108822 0.127112042 0.029895653 0.02565403 1.590844408 0.386952571 RT(ph)PTMPQEEAAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RTPTMPQEEAAEK 13 1 Q9NYV4-2 Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 RT(0.918)PT(0.082)MPQEEAAEK;RT(0.991)PT(0.009)MPQEEAAEK;RT(0.995)PT(0.005)MPQEEAAEK;RT(0.964)PT(0.036)MPQEEAAEK 177.6 7.43E-06 1372060000 1773000 1306230 1535830 1497840 1542650 1159500 1893080 1367540 2007190 TRUE FALSE 1662031.095 1402944.628 1572260.613 1536277.11 1421496.492 1494228.827 1609230.228 1538280.379 1672177.022 0.993932504 0.838992888 0.940247708 0.918728753 0.850087325 0.893582921 0.962356382 0.919926754 1 20.67329615 0.995920102 0.953056379 0.996636442 0.902337494 0.246744043 0.046702406 0.742546914 1.44749612 0.04087076 0.013858274 9.906496773 -0.995920102 -0.094298948 RT(ph)SDPALCTLIVSAAADSAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTSDPALCTLIVSAAADSAVR 21 1 Q6IA86-4;Q6IA86-7;Q6IA86-2;Q6IA86-3;Q6IA86-5;Q6IA86;Q6IA86-6 Q6IA86-4 ELP2 Elongator complex protein 2 1 RT(0.491)S(0.491)DPALCT(0.017)LIVSAAADSAVR 84.249 0.0018015 34727000 22567 25201 22103 22795 23270 18601 26917 23375 31691 TRUE FALSE 21154.57175 27066.90826 22627.2936 23379.95829 21442.46807 23970.80674 22881.04574 26293.4202 26401.56737 0.801261965 1.02520081 0.857043572 0.885551906 0.812166481 0.9079312 0.866654825 0.99590376 1 14.68833596 1.230262385 24.8451895 0.997951993 0.889805088 0.381853676 0.061611623 211.4286345 632998.0244 0.054053964 0.014425467 16.99269981 -1.230262385 -0.108146905 RT(ph)SDPSAAVNHVSSTTSLGENYEDDDLVNSDEVMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTSDPSAAVNHVSSTTSLGENYEDDDLVNSDEVMK 35 1 H7C3A2;Q8NHH9-2;Q8NHH9 H7C3A2 ATL2 Atlastin-2 1 RT(0.495)S(0.495)DPS(0.009)AAVNHVSSTTSLGENYEDDDLVNSDEVMK 215.82 1.51E-36 288550000 52953 84285 87103 88789 85418 68918 110820 106560 102770 TRUE FALSE 49638.76625 90525.5491 89169.12429 91067.47606 78709.61484 88813.50781 94203.5698 119864.2506 85617.02308 0.57977683 1.057331192 1.041488259 1.063660856 0.919322023 1.037334687 1.100290181 1.400004885 1 16.38561005 1.630145405 2.948368792 1.209348422 0.973969226 0.265689975 0.171194167 0.288495614 5.881066983 0.101920616 0.042271229 42.67223651 -1.630145405 -0.235379196 RT(ph)SFDDRLEDDDFDLIEENLGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RTSFDDRLEDDDFDLIEENLGVK 23 2 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 1 RT(0.5)S(0.5)FDDRLEDDDFDLIEENLGVK;RT(0.5)S(0.5)FDDRLEDDDFDLIEENLGVK 125.82 0.0025017 91726000 203275 160848 162532 154526 149880 114352 159620 120828 215375 TRUE FALSE 190552.3806 172757.3533 166387.3358 158491.3988 138109.0294 147363.5661 135686.4628 135913.6418 179427.5211 1.062001968 0.96282528 0.927323382 0.883317106 0.769720434 0.821298567 0.75621879 0.757484922 1 17.45304167 3.532033713 0.935203261 0.800362315 1.024048639 0.497038292 0.075695461 0.440109586 0.774604327 0.027714319 0.068104578 3404.346152 -3.532033713 0.223686324 RT(ph)SFSTSDVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RTSFSTSDVSK 11 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 RT(0.607)S(0.106)FS(0.286)T(0.001)SDVSK;RT(0.648)S(0.349)FS(0.003)TSDVSK 94.339 0.0050263 830070000 1255430 1440740 1281810 1302190 1691620 1028100 1476520 1477010 1883750 TRUE FALSE 1176854.877 1547413.889 1312215.139 1335606.4 1558766.989 1324895.78 1255129.533 1661417.95 1569339.956 0.749904361 0.986028479 0.83615735 0.851062509 0.993262794 0.844237589 0.799781799 1.058673071 1 20.58172648 1.228323707 24.9997723 1.029336626 0.873694264 0.440904626 0.076167075 219.472122 535959.2462 0.066234879 0.017303766 16.91701395 -1.228323707 -0.155642362 RT(ph)SNERPGSGQGQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RTSNERPGSGQGQGR 15 2 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 RT(0.726)S(0.274)NERPGSGQGQGR;RT(0.828)S(0.172)NERPGSGQGQGR;RT(0.774)S(0.226)NERPGSGQGQGR;RT(0.945)S(0.055)NERPGSGQGQGR 154.46 3.98E-06 6789960000 1300008 1399666 1267538 1263278 1320872 1076103 1404859 1108746 1108339 TRUE FALSE 1218642.82 1503298.727 1297604.6 1295695.852 1217136.041 1386756.467 1194213.435 1247175.379 923350.0608 1.319805859 1.62809187 1.405322483 1.403255285 1.318173998 1.501875102 1.293348521 1.350706987 1 19.81651818 -3.386628977 0.170973292 0.071037246 1.53967211 0.656160432 0.094425083 38.00649535 0.595605074 12.73177809 0.331911406 0.000410555 3.386628977 1.468634864 RT(ph)SPQVLGSILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RTSPQVLGSILK 12 1 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 RT(0.663)S(0.337)PQVLGSILK;RT(0.5)S(0.5)PQVLGSILK;RT(0.5)S(0.5)PQVLGSILK 188.27 5.52E-06 2406110000 3218870 3611810 2976890 3026320 4176350 2317230 3245140 3367980 3794640 TRUE FALSE 3017406.673 3879232.17 3047503.237 3103980.495 3848356.318 2986176.684 2758561.383 3788479.717 3161290.07 0.954485861 1.227104152 0.964006203 0.98187146 1.2173373 0.944606986 0.872606222 1.198396741 1 21.59208199 RT(ph)SPSDGAMANYESTEVMGDGESAHDSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.479)S(0.39)PS(0.13)DGAMANY(0.001)ESTEVMGDGESAHDSPR 52.642 0.057428 50550000 22118 22409 18763 26575 26903 16617 23092 15946 23769 TRUE FALSE 20733.67386 24068.18568 19208.06722 27256.95949 24790.1469 21414.05815 19629.56898 17936.8932 19801.80035 1.04706004 1.215454416 0.970016205 1.376488956 1.251913789 1.081419758 0.991302237 0.905821334 1 14.27334398 1.804630171 2.82932333 0.955851932 1.159510801 0.407921593 0.112390929 0.270828143 4.077011685 0.064104503 0.031284663 63.77201964 -1.804630171 0.20365887 RT(ph)SPSSLPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTSPSSLPGR 10 1 H0Y4R5;Q5SNT2 H0Y4R5 TMEM201 Transmembrane protein 201 1 RT(0.654)S(0.345)PS(0.001)SLPGR 97.463 0.0035403 328180000 105970 122190 73270 67429 83106 75786 94428 86690 64806 TRUE FALSE 99337.52686 131237.0747 75007.999 69159.3423 76579.18999 97664.18792 80269.39803 97513.43733 53989.45994 1.839942963 2.430790656 1.389308193 1.280978591 1.418410002 1.808949155 1.486760529 1.806156932 1 15.72039016 3.893482384 4.346768755 1.490698323 2.144839495 0.509880966 0.274682896 0.154748618 5.316152739 0.065081205 0.124417801 7824.96464 -3.893482384 0.654141172 RT(ph)SSEDNLYLAVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTSSEDNLYLAVLR 14 1 Q15149-4 Q15149-4 PLEC Plectin 1 RT(0.333)S(0.333)S(0.333)EDNLYLAVLR 177.67 1.21E-06 54510000 31897 52631 38281 48619 60189 30396 41746 38189 55476 TRUE FALSE 29900.62371 56527.854 39189.0434 49866.64585 55461.99873 39170.83176 35486.57485 42956.98071 46216.69721 0.646965826 1.223104579 0.847941237 1.078974675 1.200042454 0.847547188 0.767830178 0.929468857 1 15.49612654 RT(ph)SSEELRDATSLLAAGEGGLLDEVEPLRPDELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 RTSSEELRDATSLLAAGEGGLLDEVEPLRPDELER 35 3 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RT(0.426)S(0.426)S(0.084)EELRDAT(0.032)S(0.032)LLAAGEGGLLDEVEPLRPDELER;RT(0.333)S(0.333)S(0.333)EELRDATSLLAAGEGGLLDEVEPLRPDELER;RT(0.2)S(0.2)S(0.2)EELRDAT(0.2)S(0.2)LLAAGEGGLLDEVEPLRPDELER;RT(0.333)S(0.333)S(0.333)EELRDAT(0.001)S(0.001)LLAAGEGGLLDEVEPLRPDELER;RT(0.2)S(0.2)S(0.2)EELRDAT(0.2)S(0.2)LLAAGEGGLLDEVEPLRPDELER;RT(0.2)S(0.2)S(0.2)EELRDAT(0.2)S(0.2)LLAAGEGGLLDEVEPLRPDELER;RT(0.339)S(0.339)S(0.309)EELRDAT(0.007)S(0.007)LLAAGEGGLLDEVEPLRPDELER;RT(0.345)S(0.277)S(0.277)EELRDAT(0.05)S(0.05)LLAAGEGGLLDEVEPLRPDELER 197.79 2.12E-27 320774000 34664 50970 44724.2 50709.7 59886.1 35064.8 50040.3 41908.4 113959.1 TRUE FALSE 32494.44212 54743.87183 45785.07914 52010.99675 55182.88727 45187.43853 42537.22157 47140.75599 94938.59001 0.342268008 0.576624024 0.482259944 0.547838311 0.581248229 0.475964921 0.448049856 0.496539458 1 16.534707 -1.313852351 3.169480469 1.003326869 0.499783019 0.840309119 0.069300161 14299796.08 19507629.43 452165.6884 0.01649184 0.048545351 1.313852351 -0.50354385 RT(ph)SSLDTITGPYLTGQWPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RTSSLDTITGPYLTGQWPR 19 1 Q86VQ1;H7C2L5;H7C0Q2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 RT(0.333)S(0.333)S(0.333)LDTITGPYLTGQWPR;RT(0.333)S(0.333)S(0.333)LDT(0.001)ITGPYLTGQWPR;RT(0.333)S(0.333)S(0.333)LDTITGPYLTGQWPR 230.63 3.08E-20 479350000 87865 104216 94123 94836 125423 79858 108574 95376 165342 TRUE FALSE 82365.68649 111932.2611 96355.64201 97269.65232 115572.7835 102911.7082 92294.33665 107283.9035 137745.352 0.597956194 0.812602817 0.699520097 0.706155604 0.839032184 0.74711565 0.670035942 0.778856796 1 17.07164411 0.968401094 21.20081362 1.000000003 0.731571509 0.614286088 0.068042821 335.0141469 224773.8559 0.060229783 0.015057446 9.298247336 -0.968401094 -0.268428494 RT(ph)SSTLDSEGTFNSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RTSSTLDSEGTFNSYR 16 1 Q92609;Q92609-2;C9J397;C9JWX0;C9JW04;C9JDR8;C9JNM0;C9JED7;F2Z3C3;C9K0P2 Q92609 TBC1D5 TBC1 domain family member 5 1 RT(0.489)S(0.489)S(0.017)T(0.005)LDSEGTFNSYR;RT(0.497)S(0.497)S(0.004)TLDS(0.001)EGTFNSYR;RT(0.496)S(0.496)S(0.007)TLDSEGTFNSYR 189.57 5.84E-10 708260000 205693 294368 268479 254844 310271 200359 303524 289551 393544 TRUE FALSE 192819.0423 316163.313 274847.4487 261383.7285 285903.5672 258199.3907 258013.394 325702.0797 327858.964 0.588115816 0.964327189 0.838310002 0.797244417 0.87203218 0.787531894 0.786964586 0.993421305 1 18.32271581 1.230349387 24.5294801 0.996710867 0.823203472 0.40363789 0.094912707 164.4119949 491125.0006 0.079300889 0.021211155 16.99610428 -1.230349387 -0.173507395 RTAQEVETYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RTAQEVETYR 10 1 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;; 203.03 3.41E-07 2158040000 669600 789810 691610 703170 748000 642720 696940 715740 845540 FALSE TRUE 627690.9313 848288.3542 708015.3158 721214.5327 689255.0973 828262.8303 592440.3171 805101.7145 704413.9116 0.891082531 1.20424702 1.005112625 1.023850496 0.978480246 1.175818388 0.841040058 1.142938408 1 19.42606388 3.718621805 23.76464998 1.014245345 1.080427515 0 0.118090529 494.0959605 1381510.912 0.028279174 0.044688785 5231.446702 -3.718621805 0.066182171 RTAQEVETYRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RTAQEVETYRR 11 2 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;; 174.23 6.33E-06 968810000 337933 421012 345516 369276 486118 279890 400518 409862 704650 FALSE TRUE 316782.3768 452184.1665 353711.8027 378752.2473 447940.2532 360689.6994 340464.0441 461034.1729 587039.3628 0.539627147 0.770279125 0.602535069 0.645190547 0.763049774 0.614421659 0.579967998 0.785354786 1 19.16309772 0.958179172 4.819243942 0.999821002 0.652764078 0.709397898 0.073245961 0.117705458 8.926914648 0.067054113 0.016980908 9.081951358 -0.958179172 -0.347056923 RTAS(ph)PPPPPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RTASPPPPPKR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RT(0.109)AS(0.891)PPPPPKR;RT(0.011)AS(0.989)PPPPPKR;RT(0.06)AS(0.94)PPPPPKR 93.348 0.0048613 1707520000 720100 641930 586190 621250 705570 553900 690630 599960 783110 TRUE FALSE 675030.2264 689459.1651 600094.7036 637192.3268 650157.3783 713801.9382 587076.443 674866.3267 652403.8819 1.034681499 1.056798073 0.919820866 0.976683837 0.996556575 1.094110501 0.899866569 1.034430275 1 19.31540584 4.203066138 9.587521427 0.983740413 1.045740621 0.154641517 0.054362764 0.510836073 197.8111091 0.012745907 0.028254031 15961.222 -4.203066138 0.062000207 RTDALTS(ph)SPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RTDALTSSPGR 11 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RTDALT(0.162)S(0.419)S(0.419)PGR;RTDALT(0.004)S(0.498)S(0.498)PGR;RTDALT(0.045)S(0.477)S(0.477)PGR;RTDALT(0.019)S(0.491)S(0.491)PGR 167.73 2.00E-05 7090710000 3259170 3171350 3479700 3428250 3122330 3333660 3599250 3221840 2414770 TRUE FALSE 3055184.367 3406160.054 3562240.127 3516224.699 2877114.797 4296033.525 3059575.876 3624093.816 2011729.287 1.518685634 1.693150304 1.770735332 1.747861763 1.430169961 2.135492858 1.520868586 1.801481859 1 20.94000475 -0.330055372 7.444513028 1.000000017 1.706401063 0.559441369 0.195833433 0 0 0.16294658 0.038406877 0.467675509 0.330055372 0.706401046 RTDALTSS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RTDALTSSPGR 11 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RTDALT(0.067)S(0.279)S(0.654)PGR;RTDALT(0.023)S(0.078)S(0.9)PGR 203.74 3.77E-08 3878300000 3464800 3865200 3824500 3818300 3709000 3872700 4148100 3728900 2746000 TRUE FALSE 3247944.353 4151383.43 3915218.946 3916284.042 3417710.101 4990685.622 3526130.914 4194461.373 2287674.86 1.419757855 1.814673712 1.711440299 1.711905879 1.493966717 2.181553729 1.541360171 1.83350416 1 21.12545059 -1.308112766 6.263433939 0.999966453 1.7231787 0.525117684 0.213066473 8.61E-05 9.51E-06 0.177865677 0.041921407 0.049191179 1.308112766 0.723212248 RTDDIPVWDQEFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RTDDIPVWDQEFLK 14 1 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2;E5RGM3 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ;; 203.04 2.50E-08 588220000 673336 661155 592611 550444 748595 474152 685909 622287 660154 FALSE TRUE 631193.1017 710107.6041 606668.0128 564569.3249 689803.3684 611031.9852 583063.3131 699980.9018 549970.0326 1.147686354 1.291175086 1.103092854 1.026545614 1.254256282 1.111027781 1.060172879 1.272761897 1 19.06899348 -4.999999993 0.053816919 0.486466297 1.404909728 0.174737334 0.093153335 762.440391 3.021880234 56.30677077 11.27053682 1.00E-05 4.999999993 0.918443431 RTDEAAFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RTDEAAFQK 9 1 P26447 P26447 S100A4 Protein S100-A4 0 ;;;;; 185.61 6.84E-05 22133300000 13710340 15596300 12427620 12897010 16872200 9161200 14322820 13967160 25349100 FALSE TRUE 12852234.29 16751066.28 12722409.02 13227969.11 15547125.47 11805889.72 12175246.11 15710990.67 21118171.45 0.608586512 0.793206283 0.602438949 0.626378526 0.736196574 0.559039392 0.576529371 0.743956015 1 24.33198159 0.929501565 6.099410579 0.999984764 0.649136971 0.711965156 0.071562819 0.354963073 29.87615673 0.070835177 0.017806622 8.501617574 -0.929501565 -0.350847792 RTDLCDHALHISHDEL ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RTDLCDHALHISHDEL 16 1 Q9Y2B0;H0YI18 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;;;; 155.56 1.01E-07 3000230000 660647 1723890 1326516 1435450 1714920 1315820 1605790 1414360 1498870 FALSE TRUE 619298.2836 1851528.609 1357981.586 1472286.077 1580237.101 1695675.873 1365016.697 1590945.959 1248698.914 0.495954851 1.482766253 1.087517232 1.179056105 1.265506907 1.357954151 1.093151185 1.274082921 1 20.25199423 4.751450613 24.8469406 1.225369428 0.495954344 0.722862482 0.140331793 989.3379254 1907024.89 0.030925423 0.572038233 56422.27762 -4.751450613 -0.729415084 RTEEGPTLSYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RTEEGPTLSYGR 12 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;; 246.25 2.53E-16 3775970000 1157820 2111860 1632250 1688880 2150770 1397670 1887390 1850190 2429900 FALSE TRUE 1085354.113 2268224.312 1670967.741 1732219.52 1981857.2 1801154.64 1604393.391 2081190.294 2024333.992 0.536153677 1.120479289 0.825440736 0.85569848 0.979016905 0.889751714 0.792553698 1.028086424 1 20.94901591 -4.999998972 0.014249344 2.048830076 6.14E-08 0.113069017 0.151279585 22902.26496 24.75955942 2203.333986 1433.376875 1.00E-05 4.999998972 -2.048830015 RTEEPDRDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RTEEPDRDER 10 2 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 ;;; 194.17 2.77E-07 527887000 154292 163319 160982 148096 180143 158066 184356 153676 203229 FALSE TRUE 144635.1391 175411.3087 164800.5691 151896.3941 165995.2954 203697.0882 156713.5293 172862.7869 169308.767 0.854268457 1.036043861 0.973372921 0.897156106 0.980429415 1.203110104 0.925607882 1.020991352 1 17.36929715 2.46077737 24.99965182 1.034265121 0.959417954 0.217804581 0.083442955 445.1852839 680952.7139 0.027598092 0.023095649 288.9198428 -2.46077737 -0.074847167 RTEGYAAFQEDS(ph)S(ph)GDEAESPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RTEGYAAFQEDSSGDEAESPSK 22 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 2 RTEGYAAFQEDS(1)S(1)GDEAESPSK;RTEGYAAFQEDS(1)S(1)GDEAESPSK 132.51 3.67E-05 218160000 298520 247090 250530 264550 301930 204684 361790 244750 385640 TRUE FALSE 279836.1661 265384.8007 256472.6899 271338.8009 278217.6357 263772.948 307542.9482 275307.5763 321274.1927 0.871019747 0.82603834 0.79829845 0.844570797 0.8659819 0.821021277 0.957260045 0.856924031 1 18.29344557 1.156800316 0.547685013 0.997367516 0.823261458 0.604512596 0.039109742 0.501697944 0.384438955 0.038622313 0.018956332 14.34829563 -1.156800316 -0.174106058 RTELFIAAEGIHTGQFVYCGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RTELFIAAEGIHTGQFVYCGK 21 1 P62917;E9PKZ0;G3V1A1;E9PKU4 P62917 RPL8 60S ribosomal protein L8 0 ;; 167.73 7.61E-12 475825000 534312 592464 554761 568556 674546 477486 708174 537452 759844 FALSE TRUE 500870.3657 636330.651 567920.1929 583146.1095 621569.8781 615328.4569 601989.8831 604554.0653 633021.1276 0.791237992 1.005228141 0.897158354 0.921211132 0.981910162 0.972050426 0.950979133 0.955029838 1 19.27189413 4.749485697 24.76025723 0.955625813 0.791237884 0.716124477 0.033358088 794.8018943 1801274.571 0.007693324 0.115619042 56167.57795 -4.749485697 -0.16438793 RTES(ph)FHSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RTESFHSYR 9 1 Q9Y597-3;Q9Y597-2;Q9Y597 Q9Y597-3 KCTD3 BTB/POZ domain-containing protein KCTD3 1 RTES(1)FHSYR;RT(0.003)ES(0.991)FHS(0.006)YR;RT(0.024)ES(0.941)FHS(0.036)YR 144.92 6.03E-05 854260000 416244 468230 406620 430900 488820 366217 508810 426340 538230 TRUE FALSE 390192.0311 502898.2364 416265.2184 441957.6235 450430.049 471937.9029 432518.6641 479569.4875 448395.9359 0.870195289 1.121549497 0.928342978 0.985641457 1.004536422 1.052502632 0.964590955 1.069522378 1 18.77441368 2.477586326 24.87624185 1.015913473 0.992852145 0.063423886 0.069057995 78.93281299 4222494.465 0.022348641 0.018902314 300.3214322 -2.477586326 -0.023061328 RTETTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RTETTVK 7 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;E9PKL1 O60716-13 CTNND1 Catenin delta-1 0 ; 96.027 0.020898 151148000 148712 254140 166229 165342 238840 136524 206871 216716 241850 FALSE TRUE 139404.3814 272956.79 170172.0304 169584.9556 220082.4698 175936.2625 175852.614 243773.4697 201483.6726 0.691889222 1.354734041 0.844594642 0.841680884 1.092309203 0.873203572 0.872788409 1.209891931 1 17.62030341 3.752887556 24.6414628 0.947275847 1.079359737 0 0.197617739 850.915488 813762.3495 0.045819756 0.082562743 5660.927023 -3.752887556 0.13208389 RTETVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RTETVQK 7 1 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ; 107.9 0.011825 165436000 167963 263082 126761 127845 221982 90361 174983 181562 545250 FALSE TRUE 157450.4957 282560.865 129767.8308 131125.7191 204548.4292 116446.7538 148745.9236 204230.4154 454244.2526 0.346620777 0.622046098 0.285678531 0.288667866 0.450304936 0.256352729 0.32745802 0.449604842 1 18.79310873 0.840130913 5.514414887 0.99999717 0.377574433 0.777837991 0.105192495 1.46220002 50.2200465 0.104377147 0.026301218 6.920395462 -0.840130913 -0.622422737 RTGCTFPEKPDFH ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RTGCTFPEKPDFH 13 2 P55263-3;P55263-2;P55263;P55263-4;A0A5F9ZHJ1 P55263-3 ADK Adenosine kinase 0 ;;; 75.669 0.017301 995250000 1565230 1524230 1517740 1523470 1648020 1197670 1765040 1380720 2030270 FALSE TRUE 1467265.048 1637085.575 1553741.51 1562564.819 1518591.157 1543417.886 1500388.638 1553105.931 1691404.821 0.867483071 0.96788513 0.918610075 0.923826632 0.897828325 0.912506496 0.887066549 0.918234306 1 20.68979057 0.936599205 22.21433862 1 0.915041763 0.523847081 0.026309061 8431.214323 2954128.05 0.025734016 0.006433504 8.641700396 -0.936599205 -0.084958237 RTGGPAYGPSSDVSTAS(ph)ETESEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTGGPAYGPSSDVSTASETESEKR 24 2 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 RTGGPAYGPSSDVS(0.001)T(0.028)AS(0.954)ET(0.013)ES(0.004)EKR 135.84 1.31E-05 129170000 95878 68551 73079 87211 84428 69492 109170 88188 109380 TRUE FALSE 89877.16713 73626.58737 74812.46839 89448.98191 77797.36545 89553.21229 92800.97198 99198.46593 91123.77138 0.986319659 0.807984418 0.820998377 0.981620718 0.85375489 0.982764551 1.018405742 1.088612383 1 16.47553984 2.061750289 1.409794741 1.048835503 0.867277917 0.491182235 0.065483551 0.300776776 1.12281949 0.042332483 0.021106918 115.2790236 -2.061750289 -0.181557585 RTHEHVSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RTHEHVSEK 9 1 P20810-6;P20810-10;P20810-7;P20810-9;H0YA91;P20810-5;F8W7E0;E9PSG1 P20810-6;P20810-5 CAST Calpastatin 0 ;;;;; 114.5 0.0010573 172987900 306209 618582 491882 502271 696256 377487 583028 583023 754088 FALSE TRUE 287043.9253 664382.4549 503549.6733 515160.1242 641574.8623 486461.3689 495608.364 655814.7049 628225.8412 0.456912 1.057553528 0.80154244 0.820023772 1.021248762 0.774341546 0.788901588 1.043915519 1 19.26092376 4.752220586 24.86203382 0.894628076 0.456911685 0.611615913 0.113453457 1535.60879 2794855.526 0.025869739 0.519446233 56522.39889 -4.752220586 -0.437716391 RTHS(ph)DAS(ph)DDEAFTTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RTHSDASDDEAFTTSK 16 1 Q13017-2;Q13017;H0YK04 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 2 RT(0.012)HS(0.99)DAS(0.998)DDEAFTTSK;RT(0.234)HS(0.766)DAS(1)DDEAFTTSK 145.83 4.14E-06 801880000 752420 778610 786880 945240 943490 575180 882290 618250 1033000 TRUE FALSE 705327.3753 836259.0945 805545.1652 969496.4587 869392.1013 741225.1287 749998.8053 695439.8734 860585.6266 0.819590002 0.971732584 0.936043016 1.126554324 1.010233118 0.861303171 0.871498178 0.80810073 1 19.71495922 2.230439828 24.99130796 0.873721643 0.974651831 0.190185013 0.088377491 262.5312582 807919.9916 0.031511682 0.023677176 169.9964406 -2.230439828 0.100930188 RTHS(ph)EGSLLQEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RTHSEGSLLQEPR 13 1 P49796-1;P49796-4;P49796-6;P49796;C9J582 P49796-1 RGS3 Regulator of G-protein signaling 3 1 RT(0.036)HS(0.963)EGSLLQEPR;RT(0.01)HS(0.99)EGSLLQEPR;RT(0.375)HS(0.625)EGSLLQEPR 166.56 2.05E-05 1624170000 986380 1419540 1267420 1232270 1646260 1051580 1429160 1245850 2304430 TRUE FALSE 924644.2365 1524644.219 1297483.801 1263892.134 1516969.38 1355154.075 1214870.726 1401397.115 1919805.746 0.481634269 0.79416588 0.675841191 0.658343761 0.790168163 0.705880831 0.632809193 0.729968185 1 20.87252891 0.961189924 21.26234284 1.000000002 0.689584553 0.567107469 0.087528735 661.610716 362468.9547 0.076001935 0.019000484 9.145130847 -0.961189924 -0.310415448 RTIQEVLEEQS(ph)EDEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTIQEVLEEQSEDEDR 16 1 P18858;P18858-3;P18858-2;M0R0Q7 P18858 LIG1 DNA ligase 1;DNA ligase 1 RTIQEVLEEQS(1)EDEDR 104.18 0.00084601 86256000 57987 61950 67894 63227 63312 65179 86036 62131 60096 TRUE FALSE 54357.69718 66536.84246 69504.47774 64849.51186 58339.73091 83995.11921 73135.70052 69888.19212 50065.58937 1.085729697 1.328993492 1.388268442 1.295291091 1.165266037 1.677701596 1.460797754 1.395932676 1 15.61153174 2.278516154 24.99999936 1.435297588 1.283532967 0.06670697 0.187596369 291.5499715 182420.3598 0.059399734 0.049696738 189.8961476 -2.278516154 -0.151764622 RTIQEVLEEQS(ph)EDEDREAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RTIQEVLEEQSEDEDREAK 19 2 P18858;P18858-3;P18858-2;M0R0Q7 P18858 LIG1 DNA ligase 1;DNA ligase 1 RTIQEVLEEQS(1)EDEDREAK;RTIQEVLEEQS(1)EDEDREAK;RTIQEVLEEQS(1)EDEDREAK;RTIQEVLEEQS(1)EDEDREAK 234.21 2.06E-24 995070000 536812 384558 413993 429341 516832 324210 531701 433295 720372 TRUE FALSE 503213.8952 413031.0745 423813.1095 440358.6169 476242.0995 417804.1639 451977.3711 487392.8345 600137.2594 0.838498006 0.688227681 0.70619363 0.733763168 0.793555294 0.696181011 0.75312333 0.812135602 1 19.19493298 0.810071904 1.793480898 0.999789146 0.733050076 0.7522965 0.045973447 0.303157198 1.747037944 0.041138603 0.011611924 6.45761136 -0.810071904 -0.26673907 RTLEGELHDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 177.1 5.28E-06 2854720000 1930730 2554050 2222280 2301230 2541440 1927470 2475190 2245800 3215370 FALSE TRUE 1809889.056 2743154.519 2274993.531 2360283.458 2341845.554 2483899.299 2104058.238 2526193.074 2678703.975 0.67565848 1.024060346 0.849288892 0.881128889 0.874245746 0.92727652 0.785476207 0.943065414 1 21.35310373 1.003373372 24.39864743 1.000000024 0.87424994 0.211183419 0.090212523 88.99245843 643648.0791 0.078912234 0.019728058 10.07797721 -1.003373372 -0.125750085 RTNPPGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RTNPPGGK 8 1 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BTV5;Q9H910-2;H3BU16;H3BMT0 A6NGP5;Q9H910-2 HN1L Hematological and neurological expressed 1-like protein 0 ;; 83.783 0.028728 441050000 887000 855670 866780 1002480 1037330 796380 1161690 932870 1074130 FALSE TRUE 831484.2533 919024.6971 887340.4309 1028205.334 955862.2862 1026281.978 987505.3691 1049340.873 894850.7639 0.929187622 1.027014486 0.991607167 1.149024369 1.068180667 1.146875009 1.103541964 1.172643434 1 19.77128758 3.249123245 24.99875163 1.112188382 0.993406081 0.537324271 0.053819983 145.0661285 343328.5858 0.01310424 0.017563695 1774.693034 -3.249123245 -0.118782301 RTNS(ph)TGGSSGSSVGGGSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTNSTGGSSGSSVGGGSGK 19 1 G8JLD3;X6RLX0;Q8IUD2-3;Q8IUD2;Q8IUD2-2;X6RM00;Q8IUD2-4;Q8IUD2-5;K7EKH8;K7EIZ7 G8JLD3 ERC1 ELKS/Rab6-interacting/CAST family member 1 1 RT(0.122)NS(0.857)T(0.022)GGSSGSSVGGGSGK 212.01 6.26E-17 457650000 405470 426460 411740 463560 470600 288310 519690 350510 581410 TRUE FALSE 380092.3565 458035.5421 421506.6672 475455.7344 433640.9743 371540.4167 441767.3091 394271.9451 484368.9149 0.784716659 0.945633644 0.870218245 0.981598364 0.895270033 0.767060819 0.912047193 0.813991016 1 18.88574676 2.453392136 24.99859838 0.862829787 0.903546292 0.007173549 0.078803308 681.8838603 718359.3267 0.024212781 0.020258867 284.0482621 -2.453392136 0.040716505 RTPAPPEPGS(ph)PAPGEGPSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RTPAPPEPGSPAPGEGPSGR 20 1 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 RTPAPPEPGS(1)PAPGEGPSGR;RTPAPPEPGS(1)PAPGEGPSGR 161.2 1.40E-11 1605380000 316730 342260 319130 331830 383270 306140 362840 302880 451630 TRUE FALSE 296906.4347 367601.2865 326699.9143 340345.3196 353169.5202 394517.6482 308435.5104 340695.2347 376250.0354 0.789120018 0.977013294 0.868305338 0.904572193 0.938656444 1.04855179 0.819762077 0.9055022 1 18.52133219 4.753534887 24.18828032 0.923867473 0.789119866 0.312195436 0.065845114 2281.387752 3685079.648 0.014836182 0.331671891 56693.71114 -4.753534887 -0.134747607 RTPDGTENGDFLALDLGGTNFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTPDGTENGDFLALDLGGTNFR 22 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 158.69 3.28E-11 144540000 82359 111180 99533 105860 132960 69638 104130 78784 183180 FALSE TRUE 77204.29721 119411.8829 101893.9698 108576.5468 122517.8579 89741.36012 88516.6732 88620.35582 152606.0746 0.505905793 0.782484467 0.667692751 0.711482469 0.802837359 0.588058898 0.580033746 0.58071316 1 17.21945287 -0.997192152 4.634305946 1.000006539 0.66262917 0.570911896 0.094334565 11996299.97 2588585.554 927.4057893 0.022047842 0.100648625 0.997192152 -0.337377368 RTPDS(ph)TFSETFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTPDSTFSETFK 12 1 Q9NZI5-3;Q9NZI5;B7Z1S6 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 RTPDS(0.824)T(0.101)FS(0.074)ET(0.001)FK 155.37 7.66E-05 152560000 483100 348380 412610 403070 421420 299200 514880 399140 439980 TRUE FALSE 452863.6334 374174.4177 422397.304 413413.4586 388323.3731 385574.1829 437678.5239 448973.5076 366544.4956 1.235494295 1.020815814 1.152376612 1.127867049 1.059416736 1.051916445 1.194066557 1.224881325 1 18.48362882 1.730029041 24.99999957 1.157399396 1.10194302 0.01326504 0.083411414 1.816031187 5292.101924 0.03478387 0.019289369 53.70677082 -1.730029041 -0.055456376 RTPDSTFS(ph)ETFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTPDSTFSETFK 12 1 Q9NZI5-3;Q9NZI5;B7Z1S6 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 RTPDS(0.036)T(0.309)FS(0.491)ET(0.163)FK 186.67 1.21E-05 552550000 1173900 943420 1010200 974230 1100800 796710 1194500 877430 1077600 TRUE FALSE 1100427.694 1013271.798 1034162.421 999230.3912 1014347.608 1026707.243 1015395.814 986979.067 897741.5984 1.225773314 1.128689815 1.15196001 1.113049003 1.129888166 1.143655641 1.131055769 1.099402176 1 19.77594072 -5 0.149063728 0.496755112 1.18446538 0.772304382 0.026485524 63.85324226 0.567369625 9.487963005 0.128523834 1.00E-05 5 0.687710268 RTPIGTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTPIGTDR 8 1 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 0 71.614 0.080969 0 58832 60904 59999 58284 60751 48403 64271 54255 60205 FALSE TRUE 55149.81014 65413.39553 61422.20461 59779.66611 55979.86152 62376.16034 54634.16021 61028.85618 50156.39656 1.099556865 1.304188499 1.224613585 1.19186525 1.116106127 1.243633208 1.089276024 1.216771147 1 15.61414608 -0.860915196 0.227626406 0.869352434 1.244431951 0.393118711 0.069748228 13.07804933 0.736830136 1.25537493 0.141967006 0.137747842 0.860915196 0.375079518 RTPS(ph)DDEEDNLFAPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.017)PS(0.983)DDEEDNLFAPPK;RT(0.088)PS(0.912)DDEEDNLFAPPK;RT(0.017)PS(0.983)DDEEDNLFAPPK;RT(0.005)PS(0.995)DDEEDNLFAPPK 220.86 6.80E-15 1908410000 3662880 2900210 3211520 3207470 3366820 2655410 3944670 2818260 4210470 TRUE FALSE 3433626.879 3114944.566 3287698.771 3289779.11 3102403.538 3421983.76 3353203.354 3170125.965 3507715.356 0.978878424 0.888026607 0.937276386 0.937869461 0.884451337 0.975559135 0.955950815 0.903758043 1 21.74210025 2.217185451 24.99921962 0.955961465 0.922422031 0.176265293 0.035465292 397.0049883 464312.2141 0.01209927 0.008943867 164.8866334 -2.217185451 -0.033539433 RTPS(ph)EADR ddPTM_SK-BR-3_Pertuzumab_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(0.005)PS(0.995)EADR;RT(0.054)PS(0.946)EADR;RT(0.029)PS(0.971)EADR;RT(0.064)PS(0.936)EADR 124.6 0.00079497 883165000 729140 964010 810740 942050 874040 614407 724760 577516 672794 TRUE FALSE 683504.429 1035386.303 829971.1357 966224.5979 805396.4241 791776.3268 616088.9663 649620.1439 560500.335 1.219454095 1.847253675 1.480768313 1.723860875 1.436924073 1.412624181 1.099176803 1.159000456 1 19.09635571 1.928500776 1.34226032 1.050048084 1.59945869 0.597223121 0.170387793 0.252893943 0.845804007 0.113284481 0.050344414 84.82048983 -1.928500776 0.549410606 RTPS(ph)EAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTPSEAER 8 1 A0A0C4DGH3;Q9Y6R0 A0A0C4DGH3 NUMBL Numb-like protein 1 RT(0.005)PS(0.995)EAER 79.036 0.012229 0 95025 171490 140350 144670 150610 136800 115540 115950 99649 TRUE FALSE 89077.55487 184187.298 143679.1683 148382.4771 138781.6981 176291.9392 98215.84962 130426.6127 83016.93814 1.07300458 2.2186713 1.730721121 1.787375931 1.671727496 2.123565903 1.183082053 1.571084355 1 16.3411181 1.298665495 1.105192488 1.06208368 1.809221951 0.283263494 0.348654046 0.47584996 1.177049646 0.291101967 0.097814751 19.89140658 -1.298665495 0.747138271 RTPS(ph)LALTPPQAEQEVDVLDVNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTPSLALTPPQAEQEVDVLDVNVR 24 1 Q04721 Q04721 NOTCH2 Neurogenic locus notch homolog protein 2;Notch 2 extracellular truncation;Notch 2 intracellular domain 1 RT(0.419)PS(0.574)LALT(0.007)PPQAEQEVDVLDVNVR 85.881 3.14E-05 0 19324 20313 18254 23325 25961 14198 22770 25120 30664 TRUE FALSE 18114.54533 21816.99566 18686.9935 23923.55899 23922.12778 18296.73211 19355.84989 28256.2873 25545.9803 0.709095721 0.854028516 0.731504263 0.936490152 0.936434128 0.716227442 0.757686715 1.106095243 1 14.64080868 1.239343436 25 1.053047694 0.805149822 0.585272559 0.086482578 13.94655573 445526.4425 0.064932677 0.020533329 17.35175614 -1.239343436 -0.247897872 RTPS(ph)TKPTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RTPSTKPTVR 10 2 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 RT(0.017)PS(0.862)T(0.121)KPTVR;RT(0.005)PS(0.992)T(0.003)KPTVR 125.61 0.00021649 474920000 581110 601350 543690 564020 736650 336190 694540 565400 896470 TRUE FALSE 544739.3624 645874.5797 556586.5835 578493.7081 678796.4805 433242.5954 590400.1748 635991.4346 746843.3656 0.729389036 0.864805941 0.745252096 0.774585053 0.908887341 0.580098338 0.790527441 0.851572718 1 19.51044617 0.923168563 2.913123553 0.999334656 0.773950188 0.419518185 0.086335036 0.325485859 6.381262451 0.076581366 0.020181544 8.378544169 -0.923168563 -0.225384468 RTQAPT(ph)KASE ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTQAPTKASE 10 2 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 1 RTQAPT(0.517)KAS(0.483)E 83.617 0.054308 31431000 185390 157380 172160 207850 200500 123880 174540 118460 170640 TRUE FALSE 173786.7708 169032.579 176243.7165 213183.7829 184753.5388 159642.145 148369.3473 133249.9918 142159.0816 1.222480962 1.189038203 1.239764034 1.499614238 1.299625298 1.122982388 1.043685325 0.937330139 1 17.11714674 1.903526564 2.165109157 0.984206569 1.277533253 0.706045841 0.087528915 0.195405853 1.68749678 0.056306037 0.02754875 80.08046084 -1.903526564 0.293326684 RTQAPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTQAPTK 7 1 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 0 84.498 0.034476 45895000 40262 154450 33966 33607 177050 26393 28677 137970 137420 FALSE TRUE 37742.07329 165885.6387 34771.68956 34469.41252 163145.2072 34012.23065 24377.15007 155195.8582 114483.7142 0.329671985 1.448988966 0.303726078 0.301085729 1.425051662 0.297092306 0.21293116 1.355615157 1 16.80478286 1.22025388 24.98975525 1.177807764 0.647029979 0.197640796 0.466766304 490.0684429 668953.9881 0.434973727 0.109582427 16.60557353 -1.22025388 -0.530777785 RTQAPTKAS(ph)E ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RTQAPTKASE 10 2 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 1 RTQAPTKAS(1)E;RTQAPTKAS(1)E;RTQAPTKAS(1)E;RTQAPT(0.002)KAS(0.998)E;RTQAPTKAS(1)E 170.95 3.28E-06 1769464000 1615640 1368900 1512030 1770570 1664430 965204 1436170 992951 1435040 TRUE FALSE 1514519.976 1470254.78 1547896.066 1816005.824 1533712.382 1243842.726 1220829.641 1116923.118 1195522.553 1.266826771 1.229800957 1.294744345 1.51900591 1.282880342 1.040417617 1.021168223 0.934255163 1 20.18920992 2.222662922 4.035362574 0.998027007 1.314867518 0.802935846 0.07914688 0.101032847 3.679105606 0.032205996 0.024285123 166.9794101 -2.222662922 0.316840511 RTS(ph)EEDTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RTSEEDTPK 9 1 A0A1B0GW41;Q8WYH8-2;Q8WYH8 A0A1B0GW41 ING5 Inhibitor of growth protein 5 1 RT(0.025)S(0.755)EEDT(0.221)PK;RT(0.275)S(0.713)EEDT(0.011)PK 127.52 0.00046939 930220000 1074800 816720 932930 905520 966000 688390 1108940 790630 1031610 TRUE FALSE 1007530.187 877190.7986 955059.5402 928757.1762 890134.2567 887117.0179 942664.7419 889341.8959 859427.6265 1.172326971 1.020668607 1.111273958 1.080669445 1.035729163 1.03221841 1.096851803 1.0348072 1 19.71301663 2.761613321 0.010196033 3.13E-07 2.137299175 0.351828232 0.041534603 3200.466514 12.54913775 1277.548549 1351.883852 577.5815618 -2.761613321 2.137298862 RTS(ph)FSFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RTSFSFQK 8 1 H0Y7F8;Q9BPZ7-4;Q9BPZ7-3;Q9BPZ7-2;Q9BPZ7 H0Y7F8 MAPKAP1 Target of rapamycin complex 2 subunit MAPKAP1 1 RT(0.114)S(0.885)FSFQK;RT(0.183)S(0.817)FSFQK 143 0.00037273 633760000 792770 829750 715590 715580 935170 536260 943220 761660 1179800 TRUE FALSE 743151.9408 891185.5534 732564.1327 733942.9943 861725.5205 691069.5565 801792.9174 856754.9276 982883.7582 0.756093419 0.906704934 0.745321231 0.746724105 0.876731875 0.703104056 0.815755587 0.871674723 1 19.90666128 0.929473039 2.433141577 0.999305787 0.796801816 0.538571865 0.061729243 0.275017975 3.612513945 0.055476121 0.014990454 8.501059165 -0.929473039 -0.202503971 RTS(ph)FSTSDVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTSFSTSDVSK 11 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 RT(0.039)S(0.943)FS(0.012)T(0.006)SDVSK 115.04 0.00072093 1203000000 1954100 1902200 1720200 1578500 2293800 1283100 2111600 2246700 2718100 TRUE FALSE 1831796.369 2043040.867 1761003.956 1619006.982 2113654.201 1653510.141 1794985.183 2527205.441 2264431.55 0.80894314 0.902231232 0.777680366 0.714972807 0.933414923 0.730209814 0.792686881 1.116044086 1 21.1107175 1.244191215 24.99995617 1.058022082 0.811027637 0.671891844 0.072449764 68.56661517 304447.4911 0.048295162 0.0165443 17.54652887 -1.244191215 -0.246994445 RTS(ph)NERPGSGQGQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RTSNERPGSGQGQGR 15 2 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 RT(0.346)S(0.654)NERPGSGQGQGR;RT(0.478)S(0.522)NERPGSGQGQGR 127.53 6.11E-05 4173940000 380131 410455 396347 397960 358327 319020 342999 313288 351054 TRUE FALSE 356339.2793 440845.5153 405748.538 408172.3273 330185.4428 411115.8951 291569.4842 352402.6964 292460.8195 1.218417154 1.507366067 1.387360326 1.395647896 1.12899035 1.405712724 0.996952292 1.204956948 1 18.15788384 2.031590601 0.724380924 1.028324017 1.411596235 0.471301236 0.127046853 0.482746982 0.482304886 0.099835629 0.055813418 107.5450933 -2.031590601 0.383272218 RTS(ph)PQVLGSILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTSPQVLGSILK 12 1 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 RT(0.31)S(0.69)PQVLGSILK 175.26 1.73E-05 1580600000 3347000 3652500 3504000 3138400 4520500 2498900 3465800 3805200 4572700 TRUE FALSE 3137517.245 3922934.9 3587116.535 3218936.657 4165478.165 3220291.864 2946135.465 4280287.596 3809486.829 0.823606272 1.029780408 0.941627231 0.844979075 1.093448633 0.84533482 0.773368067 1.123586401 1 21.86116524 3.471776119 24.94811343 0.921817853 0.956198591 0 0.121594187 806.1031813 3762441.281 0.032301707 0.044192305 2963.303396 -3.471776119 0.034380738 RTS(ph)PSSLPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RTSPSSLPGR 10 1 H0Y4R5;Q5SNT2 H0Y4R5 TMEM201 Transmembrane protein 201 1 RT(0.175)S(0.825)PSSLPGR;RT(0.202)S(0.797)PSS(0.001)LPGR;RT(0.248)S(0.739)PS(0.004)S(0.009)LPGR 110.92 0.0011158 576740000 173510 181190 138885 161934 197930 132053 195902 182021 149072 TRUE FALSE 162650.3188 194605.4961 142179.4178 166089.5006 182385.3762 170174.5574 166528.3138 204746.7225 124190.9202 1.309679634 1.566986507 1.144845514 1.337372333 1.468588653 1.370265694 1.340905708 1.648644863 1 16.92220017 -1.275872533 4.672634344 0.999840238 1.386416294 0.441396096 0.140279104 0.000218191 3.38E-05 0.126936035 0.029906836 0.052981892 1.275872533 0.386576055 RTS(ph)SEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RTSSEELR 8 1 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RT(0.001)S(0.998)S(0.001)EELR;RT(0.004)S(0.996)SEELR 150.04 0.00030351 521780000 444050 501600 493450 483530 486520 504190 540340 489060 587910 TRUE FALSE 416257.7032 538738.9859 505154.867 495938.1984 448310.6817 649741.4682 459321.0333 550120.2176 489784.023 0.849880118 1.099952144 1.031382902 1.01256508 0.915323205 1.326587716 0.937803219 1.123189389 1 18.90178619 RTS(ph)SEELRDATSLLAAGEGGLLDEVEPLRPDELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTSSEELRDATSLLAAGEGGLLDEVEPLRPDELER 35 3 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RT(0.419)S(0.553)S(0.027)EELRDAT(0.001)S(0.001)LLAAGEGGLLDEVEPLRPDELER 146.98 5.06E-10 19477000 5241.2 8250.5 5821 7832.4 5749.1 3715.7 10004 5265.7 14590 TRUE FALSE 4913.162648 8861.375605 5959.076869 8033.392644 5297.588877 4788.362271 8503.993073 5923.134236 12154.83474 0.404214681 0.729041224 0.490263915 0.660921585 0.435842115 0.393947131 0.699638724 0.48730685 1 13.56924266 -1.308982711 3.020806803 1.003626762 0.555506255 0.582763749 0.122119555 15300806.14 19851523.76 501569.808 0.029101687 0.049092742 1.308982711 -0.448120506 RTS(ph)SPPRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTSSPPRK 8 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RT(0.004)S(0.498)S(0.498)PPRK 81.865 0.011351 379210000 11498 11790 11830 8725.9 10095 11719 11734 7787.1 11420 TRUE FALSE 10778.3607 12662.94387 12110.61319 8949.821367 9302.179421 15102.08506 9974.595633 8759.336577 9513.928224 1.132903302 1.330990057 1.272935101 0.940707262 0.977743284 1.587365881 1.048420316 0.920685585 1 13.21582543 1.510413489 10.21066808 0.968529094 1.217019585 0.249800581 0.181730733 0.141291588 29.22446956 0.096280247 0.044675742 32.3901895 -1.510413489 0.24849049 RTSS(ph)EELRDATSLLAAGEGGLLDEVEPLRPDELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTSSEELRDATSLLAAGEGGLLDEVEPLRPDELER 35 3 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RT(0.301)S(0.301)S(0.397)EELRDATSLLAAGEGGLLDEVEPLRPDELER 175.75 5.60E-15 124910000 5402.4 6722.6 5674.6 8695.9 8336.7 3799.9 6998.8 6761.4 15477 TRUE FALSE 5064.273428 7220.348299 5809.204192 8919.051516 7681.969211 4896.869444 5949.394914 7605.575674 12893.78871 0.392768452 0.559986553 0.45054284 0.691732408 0.595788358 0.379785147 0.461415573 0.589863526 1 13.65438863 0.853356047 4.677094226 0.999982234 0.506175413 0.730595124 0.09389496 0.703108907 21.90849209 0.088300966 0.022380741 7.134376875 -0.853356047 -0.493806821 RTSS(ph)PPRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTSSPPRK 8 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RT(0.01)S(0.207)S(0.784)PPRK 54.784 0.066824 113340000 172210 116830 163760 159740 156690 172830 182080 125780 143910 TRUE FALSE 161431.6835 125480.2148 167644.4645 163839.1988 144384.1995 222723.2153 154778.7943 141483.9099 119890.4913 1.346492801 1.046623576 1.398313267 1.366573755 1.204300674 1.857722101 1.291001419 1.180109518 1 16.87135772 3.823141009 5.119616132 1.364317434 1.183304882 0.03428819 0.232808334 0.472960765 19.7149752 0.055714985 0.102431658 6654.89196 -3.823141009 -0.181012552 RTSS(ph)TLDSEGTFNSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTSSTLDSEGTFNSYR 16 1 Q92609;Q92609-2;C9J397;C9JWX0;C9JW04;C9JDR8;C9JNM0;C9JED7;F2Z3C3;C9K0P2 Q92609 TBC1D5 TBC1 domain family member 5 1 RT(0.293)S(0.293)S(0.385)T(0.029)LDSEGTFNSYR 122.64 5.65E-05 262910000 92980 116640 98774 120510 132690 84084 124680 106320 170510 TRUE FALSE 87160.54777 125276.147 101116.9659 123602.4906 122269.0626 108357.6858 105985.3915 119594.286 142050.7795 0.613587255 0.881911014 0.711836755 0.870128915 0.860741934 0.762809512 0.746109186 0.841912213 1 17.11604722 -4.999999984 0.32208748 3.0309074 0.779428012 0.412701983 0.081984598 328.105452 2.893168731 454.6071362 0.066120819 1.00E-05 4.999999984 -2.251479387 RTSSTENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RTSSTENK 8 1 Q9Y2K7-5 Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 0 105.39 0.090147 759780000 831360 1038700 625900 639070 1150700 413360 676650 972510 1235400 FALSE TRUE 779326.6616 1115606.429 640746.6436 655469.6181 1060328.664 532690.3217 575192.6142 1093930.014 1029203.759 0.75721319 1.083950985 0.622565394 0.636870603 1.030241732 0.517575181 0.558871467 1.062889641 1 19.9730972 7.747625286 12.23380622 0.78344046 0.765219291 0 0.22245456 0 0 0.047672399 0 55927484.54 -7.747625286 -0.01822117 RTVQSLEIDLDSMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RTVQSLEIDLDSMR 14 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 199.84 3.22E-08 1987910000 1062181 1392800 1198828 1289920 1623230 1013086 1378510 1271550 2448550 FALSE TRUE 995700.9873 1495924.361 1227264.766 1323021.531 1495748.064 1305547.482 1171815.223 1430305.817 2039871.187 0.488119541 0.733342561 0.601638365 0.64858092 0.733256136 0.640014669 0.5744555 0.701174577 1 20.96004662 0.963124065 18.57996423 1.000000003 0.639480381 0.720015297 0.071691828 85.70202319 43181.75738 0.063292886 0.015823484 9.185949734 -0.963124065 -0.360519622 RVATPVDWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVATPVDWK 9 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ; 106.62 0.0046603 803390000 1199630 1291360 1104060 1124670 1429970 911400 1420460 1341830 1798840 FALSE TRUE 1124547.3 1386973.638 1130248.825 1153530.936 1317665.924 1174506.385 1207475.21 1509360.429 1498601.983 0.750397579 0.925511679 0.754202141 0.769738029 0.879263433 0.783734706 0.805734427 1.007178988 1 20.51518583 1.2375259 24.99975933 1.003589601 0.814940383 0.68046429 0.055122031 15.50192327 374452.2431 0.041744213 0.012694754 17.27929025 -1.2375259 -0.188649218 RVCEEIAIIPSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVCEEIAIIPSKK 13 2 H3BNC9;P08708;H0YN88;A0A075B716;H0YN73 H3BNC9 RPS17 40S ribosomal protein S17 0 68.044 0.028965 146830000 235240 237850 251920 269710 331700 227060 288510 243860 347090 FALSE TRUE 220516.7483 255460.6615 257895.6614 276631.2152 305649.62 292608.536 245250.6039 274306.4578 289158.4367 0.762615647 0.88346259 0.891883579 0.956676964 1.057031652 1.011931519 0.848153029 0.948637228 1 18.14150067 5.321596426 0.695779234 0.957788856 0.459382442 0.546746257 0.058145944 5.554658004 1.137717867 0.024160408 2.621352609 209699.0321 -5.321596426 -0.498406414 RVDAENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 151.56 0.0030031 2398202000 1024907 1759885 1135651 1203890 1964338 1044131 1261497 1587673 1947184 FALSE TRUE 960759.9004 1890188.717 1162589.178 1234783.856 1810066.817 1345554.67 1072347.236 1785897.469 1622186.411 0.592262328 1.165210548 0.716680383 0.761184934 1.115819245 0.82946982 0.66105056 1.100920003 1 20.62950818 1.207516174 24.99986421 1.05046029 0.852608986 0.187724568 0.183768369 417.3326479 336065.3975 0.167617696 0.041921928 16.12561083 -1.207516174 -0.197851304 RVDAYDRPELSLGSYEFLATVDYCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVDAYDRPELSLGSYEFLATVDYCK 25 2 P53992;G5EA31 P53992 SEC24C Protein transport protein Sec24C 0 108.59 0.0018694 106220000 158250 165440 144290 151140 230150 138080 230280 152920 223820 FALSE TRUE 148345.415 177689.3497 147712.6269 155018.5083 212074.9474 177941.4545 195751.6518 172012.3986 186462.9961 0.795575627 0.952946984 0.792181988 0.831363389 1.137356751 0.95429902 1.049815009 0.922501527 1 17.50852983 2.764804913 24.78146358 1.013772398 0.852866141 0.580142686 0.071548446 471.3665282 445092.1224 0.020130268 0.021345239 581.8417935 -2.764804913 -0.160906257 RVDIIPGFEFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RVDIIPGFEFDR 12 1 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ;;; 136.21 0.00018272 2483870000 963220 1322540 1128830 1161390 1348200 1017810 1344060 1212320 1337240 FALSE TRUE 902933.7796 1420462.238 1155606.381 1191193.234 1242317.81 1311635.224 1142530.681 1363680.821 1114046.005 0.810499544 1.275048096 1.037305798 1.069249589 1.115140492 1.177361813 1.025568671 1.22407945 1 20.08737738 2.72419703 21.4028022 1.108689759 1.084076152 0.018962384 0.129321547 997.0388863 1485648.04 0.038565889 0.036601144 529.9037948 -2.72419703 -0.024613606 RVEDAYILTCNVSLEYEKTEVNSGFFYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVEDAYILTCNVSLEYEKTEVNSGFFYK 28 2 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 257.96 7.43E-54 46080000 48291 52392 39599 47765 71374 29917 49080 46175 76608 FALSE TRUE 45268.55251 56271.15819 40538.30698 48990.73077 65768.57395 38553.55224 41720.90964 51940.05039 63821.62989 0.70929797 0.881694157 0.635181318 0.767619549 1.030506022 0.604082853 0.653711127 0.813831462 1 15.96175783 0.978483934 22.06757057 1.000000012 0.751448941 0.273597548 0.12546025 474.6388348 486807.2961 0.117597886 0.029399471 9.516646418 -0.978483934 -0.248551071 RVEEELEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVEEELEK 8 1 Q9NWB6;Q9NWB6-2;Q9NWB6-3 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 85.29 0.027013 228600000 775470 701500 768840 759610 796510 699820 773540 649370 1096700 FALSE TRUE 726934.717 753439.7899 787077.2479 779102.8786 733955.3176 901846.6734 657554.8582 730445.2739 913653.685 0.795634855 0.824644832 0.861461253 0.852733253 0.803318949 0.987077148 0.719698141 0.799477183 1 19.8012879 -2.416167998 2.374442369 2.641872249 0.83128801 0.382585853 0.067661211 7373599.171 633619.3089 66182490.35 0.015545394 0.003835588 2.416167998 -1.810584239 RVEHHDHAVVSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RVEHHDHAVVSGR 13 1 O95831-3;O95831;E9PMA0;O95831-5;O95831-2 O95831-3 AIFM1 "Apoptosis-inducing factor 1, mitochondrial" 0 ;; 111.12 0.00065242 177443000 51917 64998 56747 57812 93753 53170 52011 70713 89267 FALSE TRUE 48667.60764 69810.51955 58093.06564 59295.5538 86390.01756 68519.31586 44212.4334 79541.67371 74367.76101 0.654418084 0.938720201 0.781159266 0.797328748 1.16165952 0.921357789 0.59451075 1.069571984 1 16.18238972 0.20671257 0.020859152 1.830537099 7.34E-06 0.113877696 0.167166639 2064.214786 15.02893327 701.1019381 615.9810062 1.609580012 -0.20671257 -1.830529757 RVEHNQSYSQAGITETEWTSGSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVEHNQSYSQAGITETEWTSGSSK 24 1 P42167 P42167 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 0 ; 119.02 0.00027272 310180000 99106 84469 73012 64773 84234 58667 110012 76777 100044 FALSE TRUE 92903.13237 90723.17265 74743.87912 66435.18484 77618.60142 75603.21052 93516.7219 86362.77746 83346.01009 1.114668024 1.088512486 0.896790129 0.797100962 0.93128155 0.907100537 1.122029978 1.036195702 1 16.34682552 1.742151149 25 1.061134291 0.957332549 0.183278962 0.095784312 1.103963435 7726.980955 0.047342988 0.026254138 55.22696144 -1.742151149 -0.103801741 RVELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVELLK 6 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31;A0A3B3IRR8 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ; 100.74 0.059833 1461190000 1518070 1438990 1428130 1468980 1742300 1133170 1709610 1337200 1692500 FALSE TRUE 1423056.709 1545534.317 1462005.918 1506676.514 1605466.786 1460297.784 1453269.852 1504152.364 1410010.816 1.009252335 1.096115221 1.036875676 1.068556707 1.138620192 1.035664242 1.030679932 1.066766543 1 20.4272748 0.716562464 0.75249826 1.001151656 1.065942385 0.197436025 0.037057061 1.664394975 1.8180057 0.035250058 0.012587783 5.206698912 -0.716562464 0.064790729 RVELSGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVELSGPK 8 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 0 ; 118.67 0.0029536 878540000 1376230 1287030 1071130 982780 1348920 779770 1183920 1193600 1633200 FALSE TRUE 1290094.221 1382323.04 1096537.709 1007999.799 1242981.264 1004876.94 1006402.187 1342623.587 1360608.369 0.948174545 1.015959531 0.805917216 0.74084492 0.913548154 0.738549728 0.739670731 0.986781809 1 20.37582044 3.936924583 3.718829607 0.823078659 0.980571402 0.214253595 0.099986458 0.251656815 7.27462633 0.024032809 0.0492236 8648.177258 -3.936924583 0.157492742 RVEPPELPADLQHWISYNEASSQLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVEPPELPADLQHWISYNEASSQLLR 26 1 Q8WUY1;H0YAR9 Q8WUY1 THEM6 Protein THEM6 0 47.919 0.090209 37262000 23236 25452 25463 24972 30362 21630 28460 16456 45772 FALSE TRUE 21781.70024 27336.49256 26066.99438 25612.8238 27977.49099 27874.22987 24192.68721 18510.56782 38132.3575 0.57121305 0.716884409 0.683592521 0.671682148 0.733694238 0.730986272 0.634439851 0.485429411 1 15.21872811 -1.008340666 4.794987642 1.000002839 0.665920886 0.660152776 0.077679751 9488301.089 1995300.241 588.4572789 0.017255515 0.098097815 1.008340666 -0.334081953 RVES(ph)EES(ph)GDEEGKK ddPTM_SK-BR-3_Pertuzumab_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 106 0.0047581 2375790000 6790200 2512170 3403290 3507590 3500810 2421850 4405500 2705310 3131320 TRUE FALSE 6365213.503 2698173.681 3484017.646 3597600.698 3225870.504 3120998.78 3744936.174 3043073.909 2608682.463 2.440010846 1.03430514 1.33554685 1.37908724 1.236589945 1.196388914 1.435566125 1.166517563 1 21.31488991 4.744851553 24.99957535 1.247836231 2.440011375 0.881353669 0.140066235 226.5020271 900073.0583 0.031635549 0.298595295 55571.42746 -4.744851553 1.192175144 RVES(ph)EES(ph)GDEEGKKHSSGIVADLSEQSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVESEESGDEEGKKHSSGIVADLSEQSLK 29 3 Q15435;B5MBZ8;C9JD73;Q15435-3;H7C118;C9JRC4 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 2 RVES(0.783)EES(0.785)GDEEGKKHS(0.207)S(0.206)GIVADLS(0.019)EQSLK 54.926 0.03013 76787000 99465 74239 84618 85344 89335 57544 102900 70852 102450 TRUE FALSE 93239.6632 79735.73281 86625.17892 87534.07153 82318.98946 74156.01865 87471.10028 79698.02816 85350.43315 1.092433392 0.934215913 1.014935434 1.025584385 0.964482387 0.868841738 1.024846589 0.93377415 1 16.38111085 2.617864576 6.941554488 0.95731491 1.002570569 0.194319085 0.055983728 0.511145101 27.06942479 0.017150796 0.016137654 414.8246693 -2.617864576 0.045255659 RVES(ph)GGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVESGGAK 8 1 O15234 O15234 CASC3 Protein CASC3 1 RVES(1)GGAK;RVES(1)GGAK 73.848 0.026035 820220000 1351670 972260 1271220 1116060 1042950 995970 1263840 1137870 949650 TRUE FALSE 1267071.387 1044247.142 1301373.939 1144699.989 961040.9141 1283490.371 1074338.925 1279935.574 791147.28 1.601561959 1.319914975 1.644919943 1.446886083 1.214743371 1.622315343 1.357950602 1.617822126 1 19.59358677 -1.143335678 4.193524954 0.999880275 1.468411859 0.510828605 0.146802149 9258030.275 2524143.701 10106.67088 0.030554009 0.071889311 1.143335678 0.468531584 RVGDPPQPLPEEPMEVQGAERAS(ph)PEPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 RVGDPPQPLPEEPMEVQGAERASPEPQR 28 2 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR 171.69 1.58E-12 6054170000 2158444 2659188 2576227 2525100 2879071 2120157 2703894 2347912 3216948 TRUE FALSE 2023350.843 2856077.046 2637336.321 2589898.341 2652960.377 2732211.908 2298470.196 2641053.982 2680018.597 0.754976419 1.065692996 0.984073888 0.966373272 0.98990372 1.019474981 0.857632182 0.985461065 1 21.35381158 -0.207635726 8.363806272 0.999999999 0.962489893 0.017469699 0.088012186 0 0 0.078964606 0.018612136 0.619960862 0.207635726 -0.037510106 RVGDPPQPLPEEPMEVQGAERAS(ph)PEPQRENAS(ph)PAPGTTAEEAMSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVGDPPQPLPEEPMEVQGAERASPEPQRENASPAPGTTAEEAMSR 45 3 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 2 RVGDPPQPLPEEPMEVQGAERAS(1)PEPQRENAS(0.996)PAPGT(0.002)T(0.002)AEEAMSR 95.765 1.25E-05 149220000 18262 32171 25595 26071 31644 19538 25329 21489 62774 TRUE FALSE 17119.01402 34552.97431 26202.12549 26740.026 29158.80789 25178.30343 21531.15159 24171.94895 52296.61386 0.327344598 0.660711502 0.501029102 0.511314673 0.557565887 0.481451887 0.411712155 0.462208682 1 15.67442992 -1.28143266 3.874692829 1.000816005 0.501266001 0.770142486 0.087483456 6670801.19 2206330.311 45790.8838 0.020283724 0.052307907 1.28143266 -0.499550003 RVGDPPQPLPEEPMEVQGAERAS(ph)PEPQRENASPAPGTTAEEAMSR ddPTM_SK-BR-3_Pertuzumab_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(0.953)PEPQRENAS(0.041)PAPGT(0.004)T(0.002)AEEAMSR 116.77 2.17E-07 429550000 50224.1 78842 58934 67051 85924 47746.2 55703.2 49259 142578 TRUE FALSE 47080.66323 84679.54372 60331.94231 68771.64218 79175.87564 61529.75285 47351.02228 55409.09458 118780.8107 0.396365902 0.712905925 0.507926676 0.578979397 0.666571268 0.518010885 0.39864202 0.466481869 1 16.85794226 -1.845962831 5.993503774 1.054963887 0.539425602 0.672838802 0.102677273 0.054887408 0.001410644 0.072360031 0.024002246 0.014257296 1.845962831 -0.515538285 RVGMADANS(ph)PPKPLSKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVGMADANSPPKPLSKPR 18 3 P26358;P26358-2;K7EJL0 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 RVGMADANS(0.997)PPKPLS(0.003)KPR 75.112 0.096325 892140000 658760 409450 533560 522370 528090 414810 629000 447970 669830 TRUE FALSE 617529.3875 439766.104 546216.2952 535774.8986 486615.9416 534558.9131 534687.2893 503900.0406 558031.0457 1.10662192 0.788067451 0.97882779 0.960116651 0.872023063 0.957937586 0.958167639 0.902996427 1 19.08998586 -4.999948852 0.341119544 1.745073929 0.92920014 0.032214095 0.082002798 1209.449082 10.16072563 656.5200653 0.05931761 1.00E-05 4.999948852 -0.815873789 RVHNNS(ph)PDTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RVHNNSPDTSR 11 1 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 1 RVHNNS(1)PDTSR;RVHNNS(0.996)PDT(0.003)SR;RVHNNS(1)PDTSR 140.03 2.38E-05 510369000 365039 454644 401461 442727 455561 379250 432106 395155 448133 TRUE FALSE 342191.8606 488306.3148 410983.8445 454088.1244 419783.0767 488733.3184 367315.7168 444490.9716 373336.7073 0.916577058 1.307951523 1.100839635 1.216296484 1.124408794 1.309095272 0.983872493 1.190590057 1 18.51011784 0.857590555 0.816408553 1.005706656 1.165379253 0.087280058 0.127181925 1.591760546 2.212697771 0.108813852 0.038722924 7.20427952 -0.857590555 0.159672597 RVIISAPSADAPMFVMGVNHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RVIISAPSADAPMFVMGVNHEK 22 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;; 335.92 3.97E-81 12040340000 6455941 6665562 6272561 7118885 7182360 4646880 6952540 5496520 6683450 FALSE TRUE 6051875.177 7159087.146 6421349.109 7301567.641 6618286.418 5988358.82 5910071.171 6182772.621 5567939.018 1.086914774 1.285769676 1.153272169 1.311359125 1.188642044 1.075507257 1.061446821 1.110423911 1 22.40871198 2.267710167 4.210466863 1.065091341 1.215817728 0.527738953 0.067472111 0.14943267 5.896597809 0.022553341 0.017740252 185.2295053 -2.267710167 0.150726387 RVIISAPSADAPMFVMGVNHEKYDNSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVIISAPSADAPMFVMGVNHEKYDNSLK 28 2 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 201.1 2.54E-25 742380000 286040 284730 330320 387640 378000 213220 297990 288740 371460 FALSE TRUE 268137.267 305811.7055 338155.3464 397587.4987 348313.4048 274773.1527 253309.1659 324789.8246 309460.9263 0.866465664 0.988207814 1.092723887 1.284774474 1.125548899 0.887909036 0.818549757 1.049534196 1 18.23939774 2.232164657 24.99913329 0.91130768 1.072760539 0.21165106 0.122004665 205.4570284 803037.586 0.046496246 0.035169647 170.6729352 -2.232164657 0.16145286 RVLVDVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVLVDVER 8 1 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ; 134.05 0.0014321 492870000 473670 476610 501110 513850 578380 400630 562620 552250 661800 FALSE TRUE 444023.8402 511898.7003 512996.5658 527036.2609 532956.3679 516285.3773 478260.3541 621199.6282 551341.3046 0.805352032 0.92846064 0.930451903 0.955916519 0.966654164 0.936417012 0.867448802 1.126706131 1 19.07258616 5.777446368 0.957832648 0.956331291 1.76E-19 0.356832962 0.066931689 14.80121303 2.362897383 0.018917289 23.33864974 599026.9588 -5.777446368 -0.956331291 RVNALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVNALK 6 1 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W543;F8W118;F8VUX1;H0YHC3;H0YH88;F8W020;P55209-3;F8VXI6;F8VRJ2;F8VVB5 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 ; 138.53 0.019664 2146000000 1934520 2005280 1896400 1833780 2161220 1540300 2229300 2034280 2375000 FALSE TRUE 1813441.846 2153753.018 1941383.504 1880837.899 1991486.499 1984959.605 1895037.161 2288264.336 1978597.157 0.916529087 1.088525277 0.9811919 0.950591631 1.006514384 1.003215636 0.95776806 1.156508452 1 20.91604648 1.25747742 24.99993661 1.078254346 0.994398157 0.291556174 0.058528921 268.13973 354368.4783 0.036299653 0.013207133 18.09161844 -1.25747742 -0.083856189 RVNDAEPGS(ph)PEAPQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RVNDAEPGSPEAPQGK 16 1 Q8N8A6 Q8N8A6 DDX51 ATP-dependent RNA helicase DDX51 1 RVNDAEPGS(1)PEAPQGK;RVNDAEPGS(1)PEAPQGK;RVNDAEPGS(1)PEAPQGK 168.75 3.59E-09 2220240000 1631040 1441070 1540310 1524040 1667530 1192330 1898510 1368990 2191490 TRUE FALSE 1528956.118 1547768.322 1576846.881 1563149.447 1536568.92 1536536.315 1613846.05 1539911.415 1825716.161 0.837455542 0.847759556 0.863686762 0.856184263 0.841625304 0.841607446 0.883952328 0.84345609 1 20.80003106 -5 0.345813754 2.641558282 0.849204975 0.919133446 0.013792661 105.7720295 0.877209249 128.4814368 0.010327442 1.00E-05 5 -1.792353307 RVNNGNTAPEDS(ph)SPAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVNNGNTAPEDSSPAKK 17 2 G3V167;Q9UGN5-2;Q9UGN5;E9PJ27 G3V167 PARP2 Poly [ADP-ribose] polymerase 2 1 RVNNGNTAPEDS(0.725)S(0.275)PAKK;RVNNGNTAPEDS(0.607)S(0.393)PAKK 122.53 2.95E-05 404010000 1003020 482250 651960 626760 738490 503740 1048060 651110 1095500 TRUE FALSE 940242.7686 517956.2918 667424.7991 642843.7227 680491.9743 649161.5605 890913.1327 732402.5168 912653.9728 1.030229196 0.56752757 0.73130104 0.704367418 0.745618816 0.711289908 0.976178441 0.802497484 1 19.79970845 1.755312281 13.02059694 0.916085269 0.723742369 0.293140544 0.126036641 0.231604312 173.9102165 0.053585944 0.029490559 56.9262114 -1.755312281 -0.1923429 RVNS(ph)GDTEVGSSLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RVNSGDTEVGSSLLR 15 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 RVNS(0.967)GDT(0.033)EVGSSLLR;RVNS(0.996)GDT(0.004)EVGSSLLR;RVNS(0.876)GDT(0.124)EVGSSLLR;RVNS(0.995)GDT(0.005)EVGSSLLR 142.74 2.78E-06 873430000 194725 277743 252299 308524 370123 217495 261531 239420 352019 TRUE FALSE 182537.5098 298307.3807 258283.6514 316441.2482 341055.0326 280282.2758 222316.8545 269312.114 293264.7548 0.622432484 1.01719479 0.880718352 1.079029249 1.1629595 0.955731199 0.758075598 0.918324175 1 18.16184417 -4.363488262 7.040642302 0.999598139 0.932839727 0 0.155026622 0 0 0 0.033310628 4.33E-05 4.363488262 -0.066758412 RVNS(ph)NGKES(ph)PGSSEFFQEAVSHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVNSNGKESPGSSEFFQEAVSHGK 24 2 Q8N108-17;Q8N108;Q8N108-13;Q8N108-12 Q8N108-17 MIER1 Mesoderm induction early response protein 1 2 RVNS(0.921)NGKES(0.85)PGS(0.189)S(0.04)EFFQEAVSHGK 64.633 0.021051 185180000 107110 75221 84691 83733 109740 70564 100630 73262 119840 TRUE FALSE 100406.1763 80790.44111 86699.91051 85881.73054 101121.4631 90934.68129 85541.4657 82408.92197 99837.9298 1.005691689 0.809215909 0.868406533 0.860211452 1.012856169 0.910822985 0.85680328 0.825426991 1 16.6073004 4.764824608 23.27881755 0.883417406 1.005692102 0.203163372 0.067854312 4921.247271 4361714.709 0.015698057 1.078791527 58186.81798 -4.764824608 0.122274696 RVNTTQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RVNTTQK 7 1 P36578;H3BM89;H3BTP7 P36578 RPL4 60S ribosomal protein L4 0 ;;; 110.12 0.011025 1984901000 1040106 1232870 949170 879016 1356840 630774 1016611 1280000 1138870 FALSE TRUE 975007.6221 1324152.978 971684.7606 901573.0387 1250279.26 812868.214 864179.6183 1439810.818 948785.2396 1.027637848 1.395629825 1.024135621 0.950239318 1.317768455 0.856746269 0.910827427 1.517530794 1 19.85572204 3.781977824 6.496345125 1.060159771 1.231611875 0.048253092 0.217272864 0.469537806 42.8392485 0.052196767 0.094229097 6053.099662 -3.781977824 0.171452105 RVPDHHPC ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVPDHHPC 8 1 P78371;P78371-2 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 91.9 0.019497 55511000 197729 265830 187126 178451 290480 168653 231030 244690 242400 FALSE TRUE 185353.4948 285512.3298 191564.7171 183030.3548 267666.8725 217340.3832 196389.1963 275240.0851 201941.874 0.917855674 1.413834209 0.948613149 0.90635167 1.325464933 1.076252185 0.972503584 1.362966876 1 17.62358057 3.945534935 24.36832642 1.077990964 1.198766015 0.023011117 0.191784442 662.021659 510738.6942 0.045204027 0.081504416 8821.347596 -3.945534935 0.120775051 RVPGSS(ph)GR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RVPGSSGR 8 1 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 RVPGS(0.028)S(0.972)GR;RVPGS(0.053)S(0.947)GR;RVPGS(0.066)S(0.934)GR;RVPGS(0.028)S(0.972)GR 107.11 0.0024901 2482280000 777040 752140 742380 755730 890930 603460 830030 692350 1157270 TRUE FALSE 728406.4535 807829.2282 759989.6042 775123.3112 820959.9516 777669.1056 705574.7071 778791.4216 964114.1608 0.755518883 0.837897897 0.788277608 0.803974615 0.851517367 0.806615168 0.731837303 0.807779258 1 19.87884446 -2.133957291 2.1955027 1.397881672 0.797883017 0.768428751 0.034861866 5236711.557 1241989.198 10380633.42 0.008602917 0.007345861 2.133957291 -0.599998655 RVPLS(ph)PLSLLAGPADAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVPLSPLSLLAGPADAR 17 1 Q53ET0;H0YDQ8;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 RVPLS(0.967)PLS(0.033)LLAGPADAR;RVPLS(0.998)PLS(0.002)LLAGPADAR 146.6 2.64E-07 161647000 162980 212771 177538 240300 276820 123873 146028 137586 250738 TRUE FALSE 152779.3727 228524.7862 181749.2852 246466.5048 255079.6738 159633.1242 124132.4571 154763.915 208888.208 0.731392998 1.094005202 0.870079202 1.179896688 1.221130079 0.764203618 0.594253061 0.740893497 1 17.67237153 2.093603513 8.330039292 0.719989887 1.015952469 0.310630465 0.173863173 0.242944827 19.12812021 0.061467819 0.045349462 124.0519265 -2.093603513 0.295962582 RVPPPALS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RVPPPALSR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 RVPPPALS(1)R;RVPPPALS(1)R;RVPPPALS(1)R;RVPPPALS(1)R;RVPPPALS(1)R 92.925 0.0059697 1271890000 459078 604384 494748 487664 648445 486122 599797 570428 676245 TRUE FALSE 430345.1275 649133.2202 506483.6562 500178.2839 597518.7454 626457.5299 509863.0081 641647.1915 563375.3408 0.7638693 1.152221571 0.899016374 0.88782424 1.060605075 1.111971868 0.905014776 1.138933753 1 19.10373689 2.715108605 24.81881288 1.032226177 0.959028227 0.176397641 0.115400087 1856.053225 1964222.951 0.035903985 0.033867495 518.9297924 -2.715108605 -0.07319795 RVPRS(ph)TQQCPSANDSMGDERTAVSLVT(ph)ALPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVPRSTQQCPSANDSMGDERTAVSLVTALPGR 32 3 A0A1B0GUQ4;Q6IN97;Q68DX3-4;Q68DX3-2;Q68DX3 A0A1B0GUQ4 FRMPD2B;FRMPD2 Putative protein FRMPD2-like;FERM and PDZ domain-containing protein 2 2 RVPRS(0.449)T(0.449)QQCPS(0.102)ANDS(0.129)MGDERT(0.129)AVS(0.129)LVT(0.612)ALPGR 43.068 0.068869 38520000 1127.8 1112 2555.1 2511.1 2148.5 1752.7 2171.3 1187.5 2369.6 TRUE FALSE 1057.213011 1194.333637 2615.708179 2575.539077 1979.765477 2258.676037 1845.733722 1335.761989 1974.098452 0.535542192 0.605002064 1.325014047 1.304665973 1.00287069 1.144155721 0.934975518 0.676644059 1 10.94697823 4.201508005 3.765344457 1.063412724 0.554033803 0.543980975 0.184951852 0.164477788 5.00780636 0.047601019 0.125420702 15904.05997 -4.201508005 -0.509378921 RVPS(ph)PTPAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 RVPSPTPAPK 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RVPS(0.5)PT(0.5)PAPK;RVPS(0.989)PT(0.011)PAPK;RVPS(0.971)PT(0.029)PAPK;RVPS(0.787)PT(0.213)PAPK;RVPS(0.99)PT(0.01)PAPK;RVPS(0.807)PT(0.193)PAPK;RVPS(0.953)PT(0.047)PAPK;RVPS(0.998)PT(0.002)PAPK;RVPS(0.991)PT(0.009)PAPK;RVPS(0.754)PT(0.246)PAPK;RVPS(0.679)PT(0.321)PAPK 142.97 3.69E-05 32201330000 28363546 23994970 25614910 24775910 26029040 20152200 30130020 22242950 28724130 TRUE FALSE 26588322.29 25771582.55 26222507.76 25411701.8 23984824.19 25969813 25612303.21 25020031.27 23929887.14 1.111092674 1.076962143 1.095805743 1.061923178 1.002295751 1.085245946 1.07030606 1.045555757 1 24.51231026 1.924189216 0.010286272 1.40E-07 2.115137181 0.518048054 0.025409253 967.5894723 8.119529721 826.863665 841.3890048 83.98258067 -1.924189216 2.115137041 RVPSPT(ph)PAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVPSPTPAPK 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RVPS(0.341)PT(0.659)PAPK 113.24 0.00088746 2669300000 4241900 3737100 3718700 3769000 4041200 3171000 4698800 3507600 4336800 TRUE FALSE 3976407.051 4013798.772 3806909.32 3865718.921 3723820.453 4086416.223 3994258.562 3945531.581 3612960.063 1.100595352 1.110944683 1.053681539 1.06995894 1.03068409 1.13104384 1.105536317 1.092049597 1 21.78474988 4.143824511 5.298296256 1.076752293 1.105644549 0.116943011 0.037507141 0.493406052 23.01215826 0.009102853 0.020542924 13925.93972 -4.143824511 0.028892256 RVPVLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVPVLGK 7 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ; 117.93 0.008209 618070000 1053960 1338820 1016950 1029000 1557690 855910 1365760 1291790 1661110 FALSE TRUE 987994.525 1437947.626 1041072.534 1055405.882 1435355.311 1102997.322 1160976.967 1453072.825 1383860.01 0.713941091 1.039084601 0.752296133 0.762653646 1.037211351 0.797044003 0.838941048 1.050014318 1 20.40026658 1.239826822 24.99970743 1.025007216 0.857859378 0.300337216 0.111174068 40.34818644 796769.5384 0.078577304 0.025068274 17.37108005 -1.239826822 -0.167147838 RVQT(ph)PLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RVQTPLLR 8 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 1 RVQT(1)PLLR;RVQT(1)PLLR;RVQT(1)PLLR;RVQT(1)PLLR;RVQT(1)PLLR;RVQT(1)PLLR 124.67 0.00075882 5211880000 690676 960760 877710 961290 1005440 874267 1040150 903060 1207700 TRUE FALSE 647447.8221 1031895.67 898529.6957 985958.3289 926476.7981 1126653.69 884189.1638 1015809.029 1006127.068 0.643505023 1.025611678 0.893057869 0.979954084 0.920834781 1.119792645 0.878804668 1.009623 1 19.94038109 4.744501614 24.97464426 0.970321256 0.643504879 0.689313138 0.070483102 354.5456569 1490389.585 0.014973324 0.135846231 55526.66805 -4.744501614 -0.326816377 RVS(ph)EVEEEKEPVPQPLPSDDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RVSEVEEEKEPVPQPLPSDDTR 22 2 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 1 RVS(1)EVEEEKEPVPQPLPSDDTR;RVS(1)EVEEEKEPVPQPLPSDDTR;RVS(1)EVEEEKEPVPQPLPSDDTR;RVS(1)EVEEEKEPVPQPLPSDDTR;RVS(0.999)EVEEEKEPVPQPLPS(0.001)DDTR 166.49 6.07E-12 2937660000 3085500 2152130 2459390 2798150 3332520 2091460 2821910 2128450 2812720 TRUE FALSE 2892384.063 2311475.944 2517727.892 2869955.266 3070797.322 2695230.55 2398790.793 2394191.668 2343258.861 1.234342526 0.986436447 1.074455722 1.224770901 1.310481472 1.150206063 1.02369859 1.021735886 1 21.16008491 1.693037228 5.112091614 1.015202749 1.140770823 0.358221929 0.090228261 0.234602489 14.26691449 0.05455091 0.026856844 49.32160814 -1.693037228 0.125568073 RVS(ph)GPDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVSGPDPK 8 1 P22314;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 RVS(1)GPDPK;RVS(1)GPDPK 87.184 0.0094963 1577460000 4808300 2960900 3607400 3734000 3438200 2716740 3714400 3135300 2580600 TRUE FALSE 4507357.086 3180128.117 3692969.232 3829820.762 3168177.641 3501018.735 3157460.203 3526749.107 2149881.189 2.096561015 1.479211099 1.717755033 1.781410425 1.473652431 1.628470798 1.468667301 1.640439074 1 21.0358255 -2.632821384 0.178101809 2.32E-13 1.817980337 0.634696091 0.168819649 32.46223136 0.676260359 13.38923098 0.555187149 0.002329049 2.632821384 1.817980337 RVS(ph)GPDPKPGSNCSPAQSVLSEVPSVPTNGMAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 RVSGPDPKPGSNCSPAQSVLSEVPSVPTNGMAK 33 2 P22314;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 RVS(0.93)GPDPKPGS(0.023)NCS(0.023)PAQS(0.023)VLSEVPSVPTNGMAK;RVS(0.996)GPDPKPGS(0.004)NCSPAQSVLSEVPSVPTNGMAK;RVS(0.938)GPDPKPGS(0.007)NCS(0.026)PAQS(0.026)VLS(0.002)EVPSVPTNGMAK;RVS(0.987)GPDPKPGS(0.004)NCS(0.004)PAQS(0.004)VLSEVPSVPTNGMAK;RVS(0.998)GPDPKPGS(0.001)NCS(0.001)PAQSVLSEVPSVPTNGMAK;RVS(0.984)GPDPKPGS(0.006)NCS(0.008)PAQS(0.001)VLSEVPSVPTNGMAK;RVS(1)GPDPKPGSNCSPAQSVLSEVPSVPTNGMAK;RVS(0.834)GPDPKPGS(0.03)NCS(0.03)PAQS(0.099)VLS(0.007)EVPSVPTNGMAK;RVS(0.951)GPDPKPGS(0.008)NCS(0.008)PAQS(0.031)VLS(0.002)EVPSVPTNGMAK;RVS(0.47)GPDPKPGS(0.175)NCS(0.175)PAQS(0.175)VLS(0.003)EVPSVPTNGMAK 219.3 2.73E-36 14428170000 15561850 10873067 12546270 12961250 14097140 8812166 15447210 11034310 15833720 TRUE FALSE 14587861.59 11678120.19 12843873.45 13293857.62 12990007.49 11356095.27 13131044.27 12411967.89 13190969.84 1.105897577 0.88531172 0.973686818 1.007799864 0.984765157 0.860899191 0.995457076 0.940944301 1 23.6530473 RVS(ph)HS(ph)PPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVSHSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RVS(1)HS(1)PPPK 88.163 0.04539 5266500000 1588400 1276000 1423500 1339500 1399100 1220900 1563400 1177400 1342600 TRUE FALSE 1488984.879 1370476.368 1457266.092 1373873.838 1289220.33 1573354.01 1328982.684 1324400.982 1118511.386 1.331220135 1.225268141 1.302862099 1.228305634 1.152621552 1.406649972 1.188170903 1.184074653 1 20.09314851 0.866540467 1.540489603 1.001500868 1.265068766 0.583942133 0.071064802 0.370773443 1.699453771 0.060363634 0.017589387 7.354285193 -0.866540467 0.263567897 RVS(ph)HS(ph)PPPKQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 88.73 0.006844 755770000 224776 274680 192996 267192 327573 183863 261167 210581 611670 TRUE FALSE 210707.6714 295017.593 197573.9563 274048.5991 301846.7379 236941.2633 222007.4329 236872.5014 509578.3255 0.413494179 0.578944547 0.387720487 0.53779485 0.592346108 0.46497516 0.435668909 0.464840221 1 18.95894439 -1.462972881 2.907856305 1.014140572 0.48455901 0.852262575 0.067454721 19183938.93 21856485.48 2199028.805 0.015908735 0.034437143 1.462972881 -0.529581562 RVS(ph)HSPPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVSHSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RVS(0.5)HS(0.5)PPPK 45.997 0.089511 107560000 125480 150020 169710 186420 188830 153360 190000 155950 216640 TRUE FALSE 117626.4308 161127.6369 173735.6013 191203.8528 174000.0535 197632.5424 161511.2639 175420.7008 180481.3845 0.651737192 0.892765962 0.962623386 1.059410384 0.964088646 1.095030066 0.894891539 0.97196008 1 17.46149051 5.267642127 1.072143149 0.989584687 7.26E-12 0.79067858 0.055250491 2.088091065 0.893554258 0.015520502 3.085527866 185200.4881 -5.267642127 -0.989584687 RVS(ph)ISEGDDKIEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVSISEGDDKIEYR 14 2 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 1 RVS(1)ISEGDDKIEYR;RVS(1)ISEGDDKIEYR 237.09 1.45E-17 260990000 348480 263053 321120 324320 352270 244184 407750 284018 477660 TRUE FALSE 326669.2589 282529.7178 328737.118 332642.6003 324604.1352 314675.9568 346611.6729 319478.2725 397935.4602 0.820910151 0.709988795 0.82610662 0.835920981 0.815720557 0.790771339 0.871024846 0.802839416 1 18.60217494 -5 0.146124382 1.69523135 0.740363427 0.7052694 0.03948072 68.6369013 0.603446031 13.81276795 0.202800217 1.00E-05 5 -0.954867923 RVS(ph)LHCLLDQFDKDLPVYLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVSLHCLLDQFDKDLPVYLK 20 2 Q8IWF6 Q8IWF6 DENND6A Protein DENND6A 1 RVS(1)LHCLLDQFDKDLPVYLK 68.231 0.01113 89586000 212920 203700 212280 188500 208960 150880 255480 204560 185500 TRUE FALSE 199593.7173 218782.1599 217315.3818 193337.2291 192549.1245 194436.6067 217173.1458 230099.7663 154538.8516 1.29154394 1.415709756 1.406218434 1.251059051 1.245959333 1.258172975 1.405298043 1.488944456 1 17.23761006 -1.979144948 2.896152686 0.694243015 1.351445152 0.62874455 0.083285804 857288.0436 4631201.927 1816176.359 0.020185242 0.010491922 1.979144948 0.657202138 RVS(ph)LSEIGFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RVSLSEIGFGK 11 1 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;H0YBX5 E5RJM2 CDK16 Cyclin-dependent kinase 16 1 RVS(0.988)LS(0.012)EIGFGK;RVS(0.974)LS(0.026)EIGFGK;RVS(0.975)LS(0.025)EIGFGK;RVS(0.947)LS(0.053)EIGFGK 176.42 5.31E-06 1916813000 4628210 4553710 4763040 4834780 5162470 3954350 5939350 4360490 4951590 TRUE FALSE 4338538.598 4890871.427 4876021.558 4958848.64 4757030.431 5095906.651 5048799.606 4904906.775 4125137.641 1.051731839 1.185626239 1.182026391 1.202105014 1.15318102 1.23533009 1.223910581 1.189028634 1 21.97601083 4.738672436 20.98316717 1.185265112 1.051731509 0.220082859 0.066383475 1.155668985 213698.5349 0.013539016 0.078138727 54786.35867 -4.738672436 -0.133533604 RVS(ph)LVGADDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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;RVS(1)LVGADDLR 149.97 2.09E-05 1678340000 2084560 2243280 2021350 1941820 2691640 1690150 1797250 1978710 2319720 TRUE FALSE 1954091.111 2409374.785 2069297.377 1991650.389 2480249.452 2178068.868 1527769.047 2225756.299 1932543.746 1.011149742 1.246737514 1.070763537 1.030584892 1.283411802 1.12704764 0.790548235 1.15172363 1 20.88206964 1.941695956 20.1242229 0.957810711 1.138395213 0.238322509 0.121342159 36.63973843 12645.69917 0.045830822 0.029563477 87.43714248 -1.941695956 0.180584502 RVS(ph)PLNLSSVTP ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RVSPLNLSSVTP 12 1 Q9UJX2-3;Q9UJX2 Q9UJX2-3 CDC23 Cell division cycle protein 23 homolog 1 RVS(0.997)PLNLS(0.002)S(0.002)VTP;RVS(1)PLNLSSVTP;RVS(0.981)PLNLS(0.018)S(0.001)VTP;RVS(1)PLNLSSVTP;RVS(1)PLNLSSVTP;RVS(1)PLNLSSVTP 131.66 0.00020625 1550116000 1547362 2413270 1706017 1775839 2390690 1442650 1917698 2047191 1871851 TRUE FALSE 1450515.375 2591951.022 1746484.529 1821410.035 2202934.851 1859119.636 1630156.988 2302787.303 1559426.975 0.930159217 1.6621176 1.11995275 1.167999569 1.412656627 1.192181272 1.045356412 1.476688129 1 20.57258457 -4.999999999 0.153042076 0.065387715 1.338759005 0.069219936 0.221590809 286.0275991 2.575964764 81.35073 0.98837999 1.00E-05 4.999999999 1.27337129 RVS(ph)QDLEVEKPDASPTSLQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RVSQDLEVEKPDASPTSLQLR 21 2 O94885 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 RVS(1)QDLEVEKPDASPTSLQLR;RVS(1)QDLEVEKPDASPTSLQLR;RVS(1)QDLEVEKPDASPTSLQLR;RVS(1)QDLEVEKPDASPTSLQLR 179.67 2.96E-17 2051160000 1562930 1323709 1352898 1367420 1623190 1021927 1645590 1260600 1842940 TRUE FALSE 1465109.001 1421717.792 1384989.379 1402510.312 1495711.205 1316940.735 1398849.056 1417988.685 1535341.408 0.954256163 0.92599456 0.902072576 0.913484327 0.974188019 0.85775107 0.911099674 0.923565715 1 20.55012807 0.859456373 7.5563235 0.999999983 0.916944675 0.39653212 0.030771685 8.503002939 457.4817869 0.027556048 0.006904573 7.235297158 -0.859456373 -0.083055308 RVS(ph)RT(ph)PEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RVSRTPEPK 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RVS(1)RT(1)PEPK;RVS(1)RT(1)PEPK;RVS(1)RT(1)PEPK;RVS(1)RT(1)PEPK 108.72 0.0048507 17517670000 12553520 9286650 10033540 10140500 10388980 8114270 12020270 8597590 10976220 TRUE FALSE 11767817.59 9974243.229 10271540.31 10400722.4 9573071.418 10456728.02 10217942.1 9671018.037 9144217.973 1.286913504 1.090770502 1.123282531 1.137409719 1.046898865 1.143534423 1.1174211 1.057610182 1 23.12442836 8 0.063368846 0.87288342 1.635848373 0.512461572 0.053369881 301.1748746 1.419629578 3.290455837 20.92395556 100000000 -8 0.762964953 RVS(ph)S(ph)SSELDLPSGDHCEAGLLQLDVPLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 2 RVS(0.481)S(0.518)S(0.518)S(0.481)ELDLPS(0.001)GDHCEAGLLQLDVPLLR 110.59 0.00035018 46215000 11220 13910 14923 15519 16243 11258 13276 11648 17450 TRUE FALSE 10517.76023 14939.91087 15276.98061 15917.24381 14967.3403 14508.00184 11285.38705 13102.27844 14537.48227 0.723492558 1.027682139 1.050868391 1.094910626 1.029568946 0.997972109 0.776295843 0.901275627 1 13.82748981 1.771729789 25 0.869617583 1.005139114 0.110318829 0.11418406 45.11361669 34019.05389 0.049665042 0.027552867 59.11936889 -1.771729789 0.135521531 RVS(ph)SDLQHATAQLSLEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVSSDLQHATAQLSLEHR 18 1 P50548;P50548-2 P50548 ERF ETS domain-containing transcription factor ERF 1 RVS(0.906)S(0.094)DLQHATAQLSLEHR 143.35 4.99E-08 194470000 544160 281440 324780 311670 335510 200490 378550 263140 482090 TRUE FALSE 510101.997 302278.1104 332483.935 319667.9799 309160.398 258368.2083 321789.9418 295993.6082 401626.0646 1.270091864 0.752635691 0.827844516 0.795934348 0.769771749 0.643305381 0.801217775 0.736988045 1 18.61549337 4.740479859 24.88194277 0.779576642 1.270092042 0.735906542 0.089973923 71.74898933 930113.9353 0.018709202 0.121248409 55014.84063 -4.740479859 0.4905154 RVS(ph)SS(ph)SELDLPSGDHCEAGLLQLDVPLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 2 RVS(0.778)S(0.281)S(0.496)S(0.444)ELDLPS(0.001)GDHCEAGLLQLDVPLLR 99.663 0.0028226 84862000 65935 85805 85353 90814 98184 71790 89538 74260 117910 TRUE FALSE 61808.24605 92158.09148 87377.61347 93144.44099 90473.0247 92514.60759 76112.60813 83531.52447 98230.05927 0.629219269 0.938186255 0.889520113 0.948227474 0.921031967 0.941815655 0.774840295 0.850366223 1 16.58387695 7.999999369 0.016715294 1.593657112 2.82E-07 0.181609872 0.096676671 11994.47633 15.46835141 574.3085777 942.5819627 99999854.69 -7.999999369 -1.59365683 RVS(ph)SSSELDLPSGDHCEAGLLQLDVPLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 RVS(0.379)S(0.204)S(0.204)S(0.204)ELDLPS(0.008)GDHCEAGLLQLDVPLLR;RVS(0.761)S(0.08)S(0.08)S(0.08)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.595)S(0.135)S(0.135)S(0.135)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.852)S(0.108)S(0.039)S(0.001)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.838)S(0.151)S(0.005)S(0.005)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.812)S(0.088)S(0.088)S(0.01)ELDLPS(0.002)GDHCEAGLLQLDVPLLR;RVS(0.814)S(0.134)S(0.04)S(0.012)ELDLPSGDHCEAGLLQLDVPLLR 345.3 5.16E-120 3058250000 631520 804923 739446 793977 847960 704516 806395 723380 889956 TRUE FALSE 591994.2905 864520.3364 756986.0083 814351.794 781364.6421 907898.3323 685483.556 813695.5854 741416.5943 0.798463772 1.166038558 1.020999549 1.098372764 1.053880704 1.224545471 0.924559231 1.09748769 1 19.49992488 RVS(ph)TDLPEGQDVYTAACNSVIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RVSTDLPEGQDVYTAACNSVIHR 23 1 Q15751;H0YNB1 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 RVS(0.966)T(0.034)DLPEGQDVYTAACNSVIHR;RVS(0.937)T(0.063)DLPEGQDVYTAACNSVIHR;RVS(0.801)T(0.199)DLPEGQDVYTAACNSVIHR;RVS(0.783)T(0.217)DLPEGQDVYTAACNSVIHR 344.88 1.45E-88 2180390000 492527 658090 646430 693220 785950 666290 785490 674450 804630 TRUE FALSE 461700.6143 706815.6683 661763.6249 711009.1988 724224.6574 858637.1067 667713.0666 758656.5671 670332.0549 0.68876404 1.054426181 0.987217633 1.060682081 1.080396875 1.280913094 0.996092999 1.131762328 1 19.3545164 5.15647221 1.604360175 1.077577922 5.92E-14 0.654267258 0.087147229 2.218026274 2.218146132 0.021888405 5.1899846 143374.597 -5.15647221 -1.077577922 RVS(ph)VCAETYNPDEEEEDTDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 RVSVCAETYNPDEEEEDTDPR 21 1 P13861-2;P13861 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 1 RVS(1)VCAETYNPDEEEEDTDPR;RVS(1)VCAETYNPDEEEEDTDPR;RVS(1)VCAETYNPDEEEEDTDPR;RVS(1)VCAETYNPDEEEEDTDPR;RVS(1)VCAETYNPDEEEEDTDPR;RVS(1)VCAETYNPDEEEEDTDPR;RVS(1)VCAETYNPDEEEEDTDPR;RVS(1)VCAETYNPDEEEEDTDPR 242.9 2.77E-30 12275440000 5128780 6728670 5547260 5041740 6509390 2936912 7191420 4566730 8370200 TRUE FALSE 4807778.815 7226867.728 5678843.627 5171119.584 5998168.767 3784750.818 6113133.333 5136896.293 6973159.546 0.689469212 1.036383533 0.814386017 0.741574827 0.860179482 0.54275982 0.876666207 0.736666967 1 22.73338106 3.575153149 4.70243879 0.778938063 0.897977457 0.019289846 0.14401279 0.426582556 15.66532854 0.034659121 0.054460912 3759.699625 -3.575153149 0.119039394 RVSEVEEEKEPVPQPLPS(ph)DDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVSEVEEEKEPVPQPLPSDDTR 22 2 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 1 RVS(0.035)EVEEEKEPVPQPLPS(0.965)DDTR 232.2 4.40E-27 814270000 440610 315290 348050 454250 475370 294160 411070 308930 383970 TRUE FALSE 413033.0066 338634.3997 356305.9104 465906.824 438036.3578 379079.2167 349433.8697 347500.5905 319882.9265 1.291200538 1.0586198 1.113863482 1.45649169 1.369364607 1.185056111 1.092380495 1.086336787 1 18.28718447 1.697525587 2.916347718 1.05525853 1.223391657 0.356067893 0.117368021 0.351904554 6.696254939 0.081895866 0.036412538 49.83398153 -1.697525587 0.168133127 RVSHS(ph)PPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVSHSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RVS(0.094)HS(0.906)PPPK;RVS(0.013)HS(0.987)PPPK 55.04 0.080298 284090000 179719 152618 163445 152829 181107 144918 186701 152952 234630 TRUE FALSE 168470.7086 163917.9955 167321.9926 156750.8509 166883.5868 186753.4741 158706.9183 172048.3939 195468.7372 0.86188058 0.83858932 0.856003855 0.801922871 0.853761011 0.955413519 0.811929931 0.880183687 1 17.57657836 -4.999999996 0.255068363 1.915508288 0.842171 0.554884146 0.040837521 137.5233726 1.358108348 65.73592429 0.052898624 1.00E-05 4.999999996 -1.073337287 RVSLEPHQGPGT(ph)PESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVSLEPHQGPGTPESK 16 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 RVSLEPHQGPGT(1)PESK 129.02 4.39E-05 197440000 185230 239770 173020 178180 309700 149350 238030 245690 319550 TRUE FALSE 173636.7849 257522.8203 177124.1161 182752.4005 285377.4113 192464.9205 202339.6113 276364.9373 266215.0406 0.65224258 0.967348876 0.665342257 0.68648413 1.071980796 0.722967869 0.760060779 1.038126684 1 18.02223256 1.23598714 24.98919297 1.019063462 0.795636341 0.334509699 0.134402857 78.04062572 757719.2671 0.10267306 0.030227961 17.21817591 -1.23598714 -0.223427121 RVSS(ph)S(ph)SELDLPSGDHCEAGLLQLDVPLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 2 RVS(0.427)S(0.533)S(0.538)S(0.502)ELDLPSGDHCEAGLLQLDVPLLR 112.72 0.00096894 69563000 15714 17938 16497 17344 19297 14448 19328 17001 22820 TRUE FALSE 14730.48879 19266.14818 16888.31663 17789.0764 17781.49146 18618.90306 16429.94583 19123.61227 19011.19458 0.774832362 1.013410709 0.888335373 0.935715866 0.935316894 0.979365236 0.8642248 1.005913237 1 14.21456157 -3.798723661 0.010530224 2.020646534 1.14E-07 0.207555192 0.06646757 20120.24865 19.6874824 2148.819676 1657.518485 0.000158956 3.798723661 -2.02064642 RVSS(ph)SS(ph)ELDLPSGDHCEAGLLQLDVPLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 2 RVS(0.333)S(0.554)S(0.273)S(0.84)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.46)S(0.532)S(0.295)S(0.708)ELDLPS(0.005)GDHCEAGLLQLDVPLLR 157.42 3.05E-09 246045000 49791 62642 60168 70101 75656 55589 74024 60724 86090 TRUE FALSE 46674.67019 67280.07886 61595.21337 71899.91034 69714.28294 71636.64189 62924.78841 68305.52507 71721.02284 0.650780878 0.938080303 0.858816717 1.002494213 0.9720202 0.998823484 0.877354866 0.952378011 1 16.13010844 4.738616153 9.526508611 0.938838721 0.64984864 0.774667162 0.050397347 0.037856288 89.10840235 0.012024053 0.070024832 54779.25903 -4.738616153 -0.288990081 RVSSS(ph)S(ph)ELDLPSGDHCEAGLLQLDVPLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 2 RVS(0.35)S(0.387)S(0.418)S(0.845)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.448)S(0.496)S(0.504)S(0.552)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.319)S(0.482)S(0.519)S(0.681)ELDLPSGDHCEAGLLQLDVPLLR 187.35 6.10E-18 205540000 146193.7 184449 161182 160202 213607 132055 191691 176680 207590 TRUE FALSE 137043.6973 198105.7959 165005.3132 164313.0545 196831.1679 170177.1348 162948.7141 198738.8869 172941.8879 0.792426282 1.145504992 0.95410843 0.95010559 1.138134724 0.984013398 0.94221658 1.149165707 1 17.39992782 4.758795177 24.48589715 1.025378979 0.792425987 0.449167876 0.083322693 3675.671134 4447844.976 0.018866197 0.778184617 57384.57601 -4.758795177 -0.232952992 RVT(ph)QEQGVSLLEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVTQEQGVSLLEDK 14 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 RVT(0.5)QEQGVS(0.5)LLEDK 59.898 0.05698 7609200 27893 20835 26543 23897 25483 17201 28194 19947 16387 TRUE FALSE 26147.22692 22377.64508 27172.61249 24510.23748 23481.66797 22166.64947 23966.57144 22437.42686 13651.90384 1.915280626 1.639159296 1.990389972 1.795371384 1.720028815 1.623703897 1.755547924 1.643538303 1 13.73681454 -2.039211838 0.290307375 0.136543736 1.842159044 0.851957958 0.102662104 11.89232734 0.51290721 6.944631949 0.112615915 0.009136675 2.039211838 1.705615308 RVT(ph)QHESDNENEIQIQNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVTQHESDNENEIQIQNK 18 1 Q5VZL5-2;Q5VZL5-4;Q5VZL5 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 RVT(0.62)QHES(0.38)DNENEIQIQNK 118.47 7.76E-05 422960000 208300 238430 173520 190740 253220 155480 282880 183600 288690 TRUE FALSE 195262.8748 256083.6053 177635.9763 195634.7113 233333.1226 200364.552 240464.7701 206522.8642 240505.774 0.811884353 1.064771132 0.738593396 0.813430414 0.970176802 0.833096639 0.99982951 0.858702312 1 17.875712 1.740278964 25 0.949192802 0.880367349 0.12673688 0.098267956 0.666790178 9757.392172 0.044148427 0.024482524 54.98939779 -1.740278964 -0.068825453 RVTNVGS(ph)LLLTPQENESLFTFLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVTNVGSLLLTPQENESLFTFLGK 24 1 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 1 RVT(0.419)NVGS(0.571)LLLT(0.01)PQENESLFTFLGK 76.826 0.013707 35003000 24843 23274 26406 20715 28120 17928 27976 22850 31804 TRUE FALSE 23288.12098 24997.23118 27032.36279 21246.58197 25911.56863 23103.52256 23781.25852 25702.8728 26495.70694 0.878939408 0.943444583 1.020254445 0.801887718 0.977953473 0.871972302 0.897551387 0.970076883 1 14.693471 1.044143564 5.228090334 0.999679151 0.922147914 0.194717603 0.060246357 0.297050703 17.89978153 0.05643378 0.01425638 11.06989658 -1.044143564 -0.077531238 RVTQHES(ph)DNENEIQIQNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVTQHESDNENEIQIQNK 18 1 Q5VZL5-2;Q5VZL5-4;Q5VZL5 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 RVT(0.285)QHES(0.715)DNENEIQIQNK 116.43 7.56E-05 354140000 282470 261620 266560 275080 317280 211600 378910 250720 400360 TRUE FALSE 264790.7069 280990.617 272882.9291 282139.0185 292362.1086 272685.485 322095.9631 282022.9439 333537.3296 0.793886271 0.842456277 0.81814809 0.845899375 0.876549887 0.81755612 0.965696894 0.845551364 1 18.34748871 0.68480153 0.223930962 1.051786841 0.785710083 0.639599668 0.039622487 2.512511142 0.362756358 0.220850656 0.107171539 4.839511538 -0.68480153 -0.266076758 RVVFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVVFLK 6 1 Q02878;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ; 116 0.038405 540360000 730930 984350 703150 700720 1071360 522970 997000 934360 1230160 FALSE TRUE 685182.396 1057232.298 719829.0501 718701.6615 987219.7073 673942.9493 847509.1057 1051016.903 1024838.349 0.66857607 1.031608838 0.702383016 0.701282951 0.963293097 0.657609027 0.826968572 1.025544081 1 19.96696494 1.264122415 6.575528766 1.013909276 0.803981801 0.349595007 0.124042545 0.170749304 25.3336997 0.085340251 0.028787282 18.37056085 -1.264122415 -0.209927475 RVVLGDGVQLPPGDYST(ph)TPGGTLFSTT(ph)PGGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.008)S(0.162)T(0.631)T(0.196)PGGT(0.335)LFS(0.174)T(0.134)T(0.359)PGGT(0.002)R 75.905 0.0012724 612240000 134440 156400 155580 172190 247410 156800 206430 173040 380630 TRUE FALSE 126025.6404 167980.0187 159270.4311 176608.6869 227979.4166 202065.6146 175477.7379 194644.4249 317100.394 0.397431358 0.529737654 0.502271312 0.556948809 0.718950278 0.63722915 0.553382276 0.613825869 1 18.27458014 -5 0.144614691 2.529449766 0.411842784 0.824887237 0.067466146 57.50542408 0.502724498 25.33567207 0.387710397 1.00E-05 5 -2.117606982 RVVLGDGVQLPPGDYSTT(ph)PGGTLFS(ph)TTPGGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.009)S(0.088)T(0.43)T(0.467)PGGT(0.016)LFS(0.428)T(0.334)T(0.223)PGGT(0.007)R 78.172 0.0012809 227290000 176080 197210 193220 207450 285990 208550 243870 214880 396650 TRUE FALSE 165059.4671 211811.6336 197803.2696 212773.5182 263529.499 268754.9995 207303.9575 241708.241 330446.5525 0.499504279 0.64098606 0.598593837 0.643896922 0.797495077 0.813308529 0.627344894 0.731459412 1 18.33405742 -5 0.077613607 2.092907489 0.316768461 0.73156847 0.072332192 147.3028718 0.813356975 28.00084658 2.807118196 1.00E-05 5 -1.776139029 RVVLGDGVQLPPGDYSTT(ph)PGGTLFSTT(ph)PGGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.004)S(0.096)T(0.425)T(0.475)PGGT(0.007)LFS(0.23)T(0.166)T(0.593)PGGT(0.005)R;RVVLGDGVQLPPGDY(0.001)S(0.017)T(0.088)T(0.891)PGGT(0.02)LFS(0.087)T(0.077)T(0.809)PGGT(0.008)R;RVVLGDGVQLPPGDY(0.025)S(0.054)T(0.168)T(0.752)PGGT(0.002)LFS(0.012)T(0.106)T(0.855)PGGT(0.027)R;RVVLGDGVQLPPGDY(0.001)S(0.064)T(0.364)T(0.568)PGGT(0.003)LFS(0.081)T(0.07)T(0.843)PGGT(0.006)R;RVVLGDGVQLPPGDYS(0.044)T(0.182)T(0.773)PGGTLFS(0.013)T(0.027)T(0.96)PGGTR;RVVLGDGVQLPPGDY(0.032)S(0.083)T(0.27)T(0.567)PGGT(0.048)LFS(0.048)T(0.084)T(0.816)PGGT(0.052)R;RVVLGDGVQLPPGDYS(0.02)T(0.075)T(0.905)PGGTLFS(0.001)T(0.009)T(0.989)PGGT(0.002)R 169.83 1.99E-14 4173000000 1680080 2074470 1957940 2083390 2899310 1939250 2349000 2218330 4552160 TRUE FALSE 1574926.792 2228065.917 2004383.261 2136853.315 2671609.888 2499079.994 1996789.257 2495293.384 3792375.088 0.415287717 0.587512012 0.528529804 0.563460434 0.70446879 0.6589749 0.526527364 0.65797642 1 21.85467023 -5 0.192760866 2.843538173 0.502369777 0.796041145 0.070178166 62.15944853 0.610559689 44.00849439 0.182759449 1.00E-05 5 -2.341168397 RVVNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVVNGK 6 1 Q13185;S4R2Y4;C9JMM0;B8ZZ43 Q13185 CBX3 Chromobox protein homolog 3 0 ; 89.457 0.080404 933040000 1366140 1351400 1246080 1101400 1394590 864100 1304720 1356780 1477050 FALSE TRUE 1280635.736 1451459.062 1275637.606 1129663.789 1285064.527 1113551.643 1109089.348 1526176.97 1230520.813 1.040726595 1.179548568 1.036664795 0.918037124 1.044325714 0.904943363 0.901317017 1.240269123 1 20.23083763 3.597376271 3.553497366 0.985042994 1.116800766 0.139139704 0.103768538 0.325916955 7.639989026 0.026712898 0.04329847 3957.093128 -3.597376271 0.131757772 RVVYPLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVVYPLEK 8 1 O60832;O60832-2;C9IYT0;H7C2Q2 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ; 91.265 0.020219 495320000 429060 483310 467710 419790 580700 361220 565300 454570 714600 FALSE TRUE 402205.9005 519094.7753 478804.3021 430562.5221 535094.1644 465498.3501 480538.513 511324.0651 595328.6435 0.675603139 0.871946581 0.804268881 0.723235018 0.898821467 0.781918282 0.807181912 0.858893774 1 19.18332678 0.827318367 2.208275867 0.999901028 0.803397596 0.504008859 0.06416392 0.519479155 4.587374028 0.054965963 0.014998311 6.719212351 -0.827318367 -0.196503432 RVYATILNAGTNTDGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RVYATILNAGTNTDGFK 17 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 305.43 1.22E-46 4486500000 3899000 3917600 4014400 4124700 4801600 2999800 5250200 4022300 5210900 FALSE TRUE 3654968.55 4207663.18 4109623.464 4230546.785 4424501.705 3865793.562 4462981.25 4524493.009 4341167.126 0.841932237 0.969246992 0.946663269 0.974518295 1.019196353 0.890496369 1.028060225 1.04222963 1 22.04965153 5.856217544 0.935487495 0.985587094 1.47E-37 0.497553397 0.044305485 12.33264637 1.697558582 0.012931982 20.00691446 718153.9342 -5.856217544 -0.985587094 RWDDSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 RWDDSQK 7 1 Q16543;K7EKQ2 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;; 172.11 0.0014635 1932600000 2701980 2683820 2364440 2250940 3008440 1873420 2730240 2484140 3555090 FALSE TRUE 2532867.895 2882532.825 2420525.633 2308702.931 2772169.258 2414245.942 2320865.858 2794290.347 2961722.512 0.855200946 0.973262287 0.817269553 0.779513584 0.935998982 0.815149269 0.783620291 0.943467977 1 21.49800505 1.027777198 7.067933753 0.999914035 0.855376607 0.410944174 0.061811079 0.156631944 26.40534297 0.061403173 0.015398656 10.66049076 -1.027777198 -0.144537428 RWDNDDMTDDIPESSLFS(ph)PMPSEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RWDNDDMTDDIPESSLFSPMPSEEK 25 1 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 RWDNDDMTDDIPESSLFS(1)PMPSEEK;RWDNDDMTDDIPES(0.035)S(0.035)LFS(0.929)PMPS(0.001)EEK 201.01 3.91E-25 64438000 138072 104338 119970 121456 120871 95760 147283 102663 167037 TRUE FALSE 129430.32 112063.2941 122815.7451 124572.7666 111378.2792 123404.3575 125199.2815 115480.7015 139157.4456 0.930099855 0.805298585 0.882566826 0.895192967 0.800375997 0.886796656 0.899695168 0.829856434 1 17.08635858 -4.999999973 0.422441244 3.541313673 0.862447861 0.485992932 0.042753762 783.8903466 5.048751409 1850.129121 0.022796812 1.00E-05 4.999999973 -2.678865812 RWDQTADQT(ph)PGAT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RWDQTADQTPGATPK 15 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 RWDQT(0.034)ADQT(0.966)PGAT(1)PK 60.765 0.020505 0 314600 255070 243750 241200 280730 156510 365280 247100 379760 TRUE FALSE 294909.7476 273955.6482 249531.8651 247389.6004 258682.5982 201691.8963 310509.6551 277950.9789 316375.6027 0.932150726 0.865919009 0.788720315 0.781949045 0.817643952 0.637507743 0.981458913 0.87854745 1 18.27127882 1.616677068 25 0.947503406 0.809067399 0.434588562 0.080072284 0.661414579 1871.432525 0.035961985 0.019562911 41.36919479 -1.616677068 -0.138436007 RWDQTADQTPGAT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RWDQTADQTPGATPK 15 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 RWDQTADQT(0.001)PGAT(0.999)PK;RWDQTADQTPGAT(1)PK;RWDQTADQTPGAT(1)PK;RWDQTADQTPGAT(1)PK;RWDQTADQT(0.001)PGAT(0.999)PK 188.27 1.79E-07 2661130000 3284630 2213440 2643550 2474610 2695470 1962510 3338640 2026330 3126780 TRUE FALSE 3079050.872 2377325.401 2706256.254 2538112.682 2483778.659 2529054.778 2838041.926 2279321.761 2604900.218 1.182022578 0.912635879 1.038909758 0.974360808 0.953502419 0.970883553 1.089501205 0.875013079 1 21.31279668 4.752107138 24.77010781 0.985128316 1.182022726 0.529917613 0.060283482 1668.634469 3051073.895 0.013543501 0.266905219 56507.63583 -4.752107138 0.19689441 RWLLLCNPGLADTIVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RWLLLCNPGLADTIVEK 17 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 138.08 7.74E-06 44533000 89967 122330 93596 98856 147460 71549 114070 102240 188510 FALSE TRUE 84336.12607 131387.4405 95816.14132 101392.8123 135879.0864 92204.0348 96966.26247 115004.8891 157046.4632 0.537013852 0.836615087 0.610113334 0.645623023 0.865215833 0.587113093 0.61743678 0.732298498 1 17.26083193 0.963494121 19.32500754 1.000000005 0.679558073 0.491097894 0.104261345 214.2452972 113415.6899 0.093633457 0.023408364 9.193780294 -0.963494121 -0.320441932 RWQS(ph)PVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RWQSPVTK 8 1 A9Z1X7 A9Z1X7 SRRM1 1 RWQS(1)PVTK;RWQS(0.999)PVT(0.001)K;RWQS(1)PVTK;RWQS(0.999)PVT(0.001)K;RWQS(1)PVTK;RWQS(0.999)PVT(0.001)K 115.91 0.0014529 5180800000 6446430 5525460 5855660 5983760 6722290 5068740 7326630 5277210 7284040 TRUE FALSE 6042959.454 5934570.808 5994559.02 6137313.412 6194348.46 6532002.954 6228069.849 5936081.285 6068286.667 0.995826299 0.977964808 0.987850336 1.011374997 1.020773869 1.076416345 1.026330856 0.978213722 1 22.53285781 3.09066189 2.453689882 1.026698909 0.984692634 0.244965534 0.025247251 0.312758847 3.823079199 0.007844788 0.00969593 1232.145201 -3.09066189 -0.042006275 RWS(ph)AEVTSSTYSDEDRPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RWSAEVTSSTYSDEDRPPK 19 2 Q9UJM3 Q9UJM3 ERRFI1 ERBB receptor feedback inhibitor 1 1 RWS(0.363)AEVT(0.263)S(0.074)S(0.263)T(0.036)YSDEDRPPK 89.201 0.0019173 124120000 50017 44466 47070 51987 42784 30218 45496 36162 34967 TRUE FALSE 46886.52525 47758.30891 48186.52263 53321.07443 39423.91722 38941.44605 38674.29716 40676.9053 29130.7818 1.60951826 1.639444805 1.654144504 1.830403138 1.35334223 1.336779985 1.327609311 1.396354742 1 14.8302568 2.625870042 5.873219541 1.303977101 1.670264855 0.726290781 0.121971015 0.121476172 5.515621319 0.035687712 0.033551584 422.5421542 -2.625870042 0.366287754 RWS(ph)APESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RWSAPESR 8 1 P54253 P54253 ATXN1 Ataxin-1 1 RWS(1)APESR;RWS(1)APESR 116.74 0.001356 514220000 358560 446210 407300 434510 445700 332820 458640 343930 345230 TRUE FALSE 336118.3696 479247.8527 416961.3483 445660.2622 410696.5199 428899.7311 389871.1898 386870.4176 287608.8827 1.168664773 1.666317981 1.449751289 1.549535807 1.42796883 1.491260378 1.355560322 1.345126805 1 18.13374871 0.65688252 0.746859092 0.996473802 1.491317931 0.542349732 0.127763267 0.796940352 0.818806172 0.116245202 0.040864 4.538188386 -0.65688252 0.49484413 RWS(ph)GNEPTDEFSDLPLR ddPTM_SK-BR-3_Pertuzumab_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(1)GNEPTDEFSDLPLR;RWS(1)GNEPTDEFSDLPLR 242.71 1.24E-20 496068000 264335 295129 277569 269275 303534 228650 300385 281114 261765 TRUE FALSE 247790.7442 316980.6582 284153.0678 276185.0524 279695.664 294657.5432 255345.0579 316211.7017 218074.7304 1.136265278 1.453541442 1.303007768 1.266469764 1.282567969 1.351176923 1.170906218 1.450015328 1 17.73446308 -1.870471593 2.630196341 0.860375535 1.305960233 0.462933761 0.102050104 20441567.42 13021821.13 17826418.9 0.023381389 0.013474989 1.870471593 0.445584697 RWS(ph)GNESTDEFSELSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RWSGNESTDEFSELSFR 17 1 O75427 O75427 LRCH4 Leucine-rich repeat and calponin homology domain-containing protein 4 1 RWS(0.999)GNES(0.001)TDEFSELSFR 133.15 1.30E-05 31113000 21539 23576 23875 25667 27292 22100 22829 22708 28749 TRUE FALSE 20190.91244 25321.59157 24441.32627 26325.65867 25148.59641 28479.91124 19406.00338 25543.14379 23950.60617 0.843023024 1.0572422 1.020488838 1.099164609 1.050019203 1.189110248 0.810251033 1.066492581 1 14.54777455 -0.926779755 5.871774668 0.999999992 1.016640141 0.002222831 0.11282157 1.06E-08 2.07E-09 0.101762529 0.023985646 0.118364167 0.926779755 0.01664015 RY(ph)GCVFQGT(ph)NQQIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RYGCVFQGTNQQIK 14 1 H0YL25;Q13114 H0YL25 TRAF3 TNF receptor-associated factor 3 2 RY(1)GCVFQGT(1)NQQIK 76.82 0.037558 299660000 220140 401060 382200 382280 397520 327570 408860 350550 358730 TRUE FALSE 206361.8304 430754.8997 391265.9645 392089.952 366300.3827 422134.1413 347555.2387 394316.9392 298855.6455 0.690506716 1.441347708 1.309213898 1.31197104 1.225676638 1.412501814 1.162953566 1.319422755 1 18.18908927 -1.553030627 5.416458037 0.999005734 1.262118098 0.095948592 0.210983629 0.002244356 0.000185205 0.180989943 0.042505095 0.027987839 1.553030627 0.263112364 RYDDPEVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RYDDPEVQK 9 1 P38646;D6RJI2;A0A3B3ITI4 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ; 147.75 0.00014695 2165590000 2483400 2081900 1620790 1309460 2684700 1224140 1944270 2250000 3612000 FALSE TRUE 2327968.427 2236046.042 1659235.904 1343062.961 2473854.492 1577529.346 1652744.763 2530917.453 3009133.866 0.773634053 0.743086264 0.551399831 0.446328751 0.822115134 0.524246981 0.549242685 0.841078385 1 21.52091686 1.037618803 4.414805548 0.998187317 0.625800606 0.526332009 0.119619346 0.132519483 5.872512404 0.111490979 0.028395285 10.90482758 -1.037618803 -0.37238671 RYDEIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RYDEIVK 7 1 A0A2U3TZH3;Q05639;A0A2R8Y488 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ; 114.5 0.0094467 773970000 721140 666900 633790 642110 814080 467750 697690 648830 465360 FALSE TRUE 676005.1347 716277.9699 648823.7981 658587.6297 750145.4406 602781.8317 593077.8615 729837.8538 387688.4097 1.74368157 1.847560959 1.673570274 1.698755014 1.934918409 1.55481004 1.529779706 1.882537201 1 18.56453808 -2.39481303 0.30389156 9.97E-13 1.777953437 0.737377454 0.135798757 22.7572512 0.862284662 15.47998426 0.13177473 0.004028904 2.39481303 1.777953437 RYDFQNPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RYDFQNPSR 9 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 0 121.93 0.0027428 0 164380 389620 274720 318210 386630 247860 310330 350490 352850 FALSE TRUE 154091.7492 418467.8702 281236.4881 326375.8073 356265.6394 319413.1583 263798.8975 394249.448 293957.0555 0.524198165 1.423568043 0.956726443 1.110283973 1.21196492 1.086598033 0.897406245 1.341180423 1 18.16524588 4.75872743 24.57501118 1.117534146 0.524197454 0.572417543 0.163887126 2979.127096 3630251.652 0.037660322 1.532814698 57375.62502 -4.75872743 -0.593336692 RYDSNSGGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RYDSNSGGER 10 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 163.12 1.05E-05 237190000 116437 158588 140515 147707 165274 131338 158347 125946 176713 FALSE TRUE 109149.416 170330.0205 143848.0822 151497.4117 152294.0467 169253.1485 134604.3374 141670.6353 147218.4587 0.741411213 1.156988207 0.977106291 1.029065329 1.034476574 1.149673417 0.914316986 0.962315708 1 17.16759905 1.626027357 25 0.953738767 1.028435246 0.040396674 0.115493034 2.104582608 2890.033395 0.048385058 0.026763713 42.26952401 -1.626027357 0.07469648 RYEDDGIS(ph)DDEIEGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RYEDDGISDDEIEGKR 16 2 I3VM54;Q9Y2K7;Q9Y2K7-3 I3VM54 KDM2A Lysine-specific demethylase 2A 1 RYEDDGIS(1)DDEIEGKR 161.04 6.75E-09 356110000 212040 174850 186820 195700 220200 134970 271890 177900 282940 TRUE FALSE 198768.7949 187796.0759 191251.4586 200721.9933 202906.3802 173933.6479 231122.6186 200111.2066 235715.4861 0.84325726 0.796706568 0.811365692 0.851543514 0.860810563 0.737896567 0.980515207 0.848952311 1 17.84668702 1.151345368 0.663058845 0.996779779 0.813295146 0.464590812 0.057651629 0.552571463 0.582802981 0.051297941 0.021893546 14.16920124 -1.151345368 -0.183484632 RYEEELEINDFPQTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RYEEELEINDFPQTAR 16 1 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 133.78 5.11E-05 74282000 63515 77402 63899 78170 81712 77013 65200 56281 95773 FALSE TRUE 59539.70953 83132.92462 65414.71446 80175.97454 75294.66913 99245.4029 55423.86529 63307.80674 79787.86758 0.746225101 1.041924382 0.819857911 1.004864235 0.943685693 1.24386584 0.694640263 0.793451544 1 16.28388177 3.228463873 24.98912702 0.935800332 0.899250785 0.035619398 0.160677444 1501.513649 3716194.175 0.045768834 0.055303384 1692.247468 -3.228463873 -0.036549548 RYEEIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 RYEEIVK 7 1 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;;;; 155.88 0.0025357 3611260000 4145970 4847990 4252930 4696920 5407990 3438060 4641380 4139400 2787230 FALSE TRUE 3886481.138 5206940.224 4353811.508 4817450.919 4983268.28 4430572.11 3945448.157 4656213.202 2322023.307 1.673747687 2.242415142 1.875007669 2.074678107 2.146088829 1.908065305 1.699142358 2.00523965 1 21.14695102 -0.727121333 0.421769847 0.704933469 2.023859794 0.729190628 0.18164017 5.466169686 0.786845802 2.295437396 0.102864375 0.187447075 0.727121333 1.318926326 RYEPS(ph)DKDRQSPPPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RYEPSDKDRQSPPPAK 16 3 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RYEPS(0.502)DKDRQS(0.498)PPPAK 81.016 0.077115 682490000 159220 97620 118970 115570 123840 91091 139330 95345 151960 TRUE FALSE 149254.7044 104847.8864 121792.0246 118535.7219 114114.1059 117387.493 118438.76 107249.0331 126596.8943 1.178976034 0.828202674 0.962045912 0.93632409 0.901397357 0.927254129 0.93555818 0.847169543 1 16.94988249 4.750514041 24.98234303 0.915408731 1.178976195 0.727726322 0.050301628 920.391756 1923558.92 0.010908819 0.184356866 56300.7319 -4.750514041 0.263567464 RYEPSDKDRQS(ph)PPPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RYEPSDKDRQSPPPAK 16 3 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RYEPS(0.001)DKDRQS(0.999)PPPAK;RYEPS(0.122)DKDRQS(0.878)PPPAK 112.55 0.0040355 1146930000 621790 393720 449950 425040 499740 344700 582830 413350 670850 TRUE FALSE 582873.2738 422871.4385 460623.0265 435947.246 460492.4363 444209.2943 495440.0522 464957.6574 558880.8011 1.042929499 0.756639766 0.824188316 0.780036181 0.823954652 0.794819384 0.886486083 0.831944229 1 19.09218109 0.219127487 0.829687366 1.002101712 0.826937443 0.25945013 0.080348684 3.916787439 3.194348756 0.092615497 0.023868451 1.656256084 -0.219127487 -0.175164268 RYESQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RYESQLR 7 1 O15212 O15212 PFDN6 Prefoldin subunit 6 0 ; 86.794 0.031772 100275000 63850 162139 76669 96922 162198 85919 67205 128299 122864 FALSE TRUE 59853.74248 174143.9403 78487.62489 99409.18261 149459.6234 110722.4205 57128.23415 144317.4126 102357.2047 0.584753586 1.701335444 0.766801176 0.971198685 1.460176876 1.081725716 0.558126165 1.409938978 1 16.64325313 1.98112415 24.67287799 0.910174946 1.140429526 0 0.37648045 1743.302416 2278691.758 0.142973795 0.094008045 95.746774 -1.98112415 0.230254579 TSPVVAPTSEPS(ph)SPLHTQLLKDPEPAFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSPVVAPTSEPSSPLHTQLLKDPEPAFQR 29 1 B7ZM87;O75044 B7ZM87 SRGAP2 SLIT-ROBO Rho GTPase-activating protein 2 1 T(0.004)S(0.004)PVVAPT(0.194)S(0.182)EPS(0.308)S(0.308)PLHT(0.002)QLLKDPEPAFQR 44.596 0.075782 76115000 72386 70859 74494 96022 89508 40161 46618 30464 38589 TRUE FALSE 67855.48947 76105.47409 76261.03286 98486.08708 82478.40274 51754.82874 39628.06368 34267.49746 32148.24661 2.110705766 2.367328925 2.37216772 3.063497935 2.565564578 1.609880295 1.232666408 1.065921196 1 14.97245243 2.054603106 2.737035794 1.139567599 2.488925194 0.867873186 0.251497583 0.100792253 1.474462925 0.127259397 0.077006862 113.3974023 -2.054603106 1.349357596 up RYNEDLELEDAIHTAILTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RYNEDLELEDAIHTAILTLK 20 1 A0A024RA52;P25787;C9JCK5 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 0 ; 149.44 6.42E-08 129085000 283480 348090 304720 292970 446870 230280 408620 318290 519650 FALSE TRUE 265737.4928 373862.9458 311948.1023 300488.1062 411774.6328 296758.0977 347351.2244 358029.2071 432917.0579 0.613830035 0.86359024 0.720572444 0.694100869 0.951162873 0.68548488 0.802350515 0.827015708 1 18.72373112 -5 0.199321804 2.034977219 0.736746494 0.407143768 0.093505904 142.9097195 1.413819668 58.71635336 0.204648679 1.00E-05 5 -1.298230725 RYPS(ph)SISS(ph)SPQK ddPTM_SK-BR-3_Pertuzumab_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 RY(0.001)PS(0.551)S(0.398)IS(0.05)S(0.725)S(0.275)PQK 111.11 0.0049606 720050000 2865400 1936100 2215100 2069100 2286400 1790000 2833100 2318100 2421800 TRUE FALSE 2686059.729 2079450.859 2267643.218 2122196.609 2106835.367 2306743.942 2408302.956 2607519.888 2017585.935 1.33132358 1.030662845 1.123938851 1.051849427 1.044235753 1.143318806 1.193655703 1.292395949 1 20.94419869 2.00219529 24.51940835 1.179772712 1.10205168 0.018087369 0.110150869 122.7960127 1371500.948 0.037539042 0.027545119 100.5067639 -2.00219529 -0.077721032 RYPSS(ph)IS(ph)SSPQK ddPTM_SK-BR-3_Pertuzumab_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(0.074)S(0.926)IS(0.749)S(0.24)S(0.011)PQK 136.83 6.89E-05 326000000 1290500 896230 1064600 942060 1155900 790260 1337300 1100500 1137000 TRUE FALSE 1209729.909 962587.8017 1089852.815 966234.8545 1065120.277 1018395.233 1136784.28 1237899.847 947227.3547 1.277127294 1.01621622 1.150571517 1.02006646 1.124461061 1.075132837 1.200117664 1.306866658 1 19.85335122 1.707834461 7.436352154 1.189282873 1.101447338 0.048564607 0.104470755 0.232464066 29.57683719 0.045328025 0.023718946 51.03104489 -1.707834461 -0.087835536 RYPSS(ph)ISS(ph)SPQK ddPTM_SK-BR-3_Pertuzumab_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(0.06)S(0.929)IS(0.034)S(0.58)S(0.398)PQK 145.86 4.29E-05 381450000 1304200 873900 1069100 954230 1120100 796820 1358600 1050600 1112200 TRUE FALSE 1222572.45 938604.4653 1094459.557 978717.1573 1032131.864 1026848.999 1154890.543 1181769.723 926566.6349 1.319465221 1.012991867 1.181198972 1.056283618 1.113931611 1.108230061 1.246419307 1.275428748 1 19.82153521 1.755420699 25 1.198929566 1.120349604 0.007688548 0.108958839 13.90764144 20645.21616 0.044630783 0.024750502 56.94042431 -1.755420699 -0.078579962 RYPSS(ph)ISS(ph)SPQKDLTQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RYPSSISSSPQKDLTQAK 18 2 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 2 RY(0.003)PS(0.167)S(0.766)IS(0.141)S(0.533)S(0.379)PQKDLT(0.011)QAK 79.143 0.052878 643640000 850190 560590 683420 635120 828020 419270 867530 587540 1295400 TRUE FALSE 796978.1255 602096.6669 699631.0451 651418.2545 762990.6493 540306.4427 737451.9303 660895.6623 1079189.371 0.738497011 0.557915675 0.64829312 0.603618115 0.707003488 0.500659529 0.683338763 0.612400085 1 20.04151661 -0.974134032 1.070735343 1.029830665 0.625796626 0.73202079 0.069990674 81.01525101 37.77039586 8.61279381 0.018020019 0.106136795 0.974134032 -0.404034039 RYPSS(ph)ISSS(ph)PQK ddPTM_SK-BR-3_Pertuzumab_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(0.254)S(0.694)IS(0.051)S(0.041)S(0.959)PQK 123.14 0.0012108 799120000 2439000 1611400 2230800 1786900 2070800 1525100 2477600 1992100 2071600 TRUE FALSE 2286347.344 1730709.733 2283715.629 1832754.879 1908167.721 1965371.612 2106106.881 2240818.07 1725836.577 1.32477627 1.002823648 1.323251378 1.06195158 1.105647978 1.138793579 1.220339694 1.298395283 1 20.71886443 1.74630594 25 1.19561289 1.154521385 0 0.12521711 8.508017276 27536.03834 0.052586445 0.029161845 55.75783979 -1.74630594 -0.041091505 RYPSS(ph)ISSS(ph)PQKDLTQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RYPSSISSSPQKDLTQAK 18 2 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 2 RY(0.02)PS(0.441)S(0.538)IS(0.003)S(0.058)S(0.941)PQKDLTQAK;RYPS(0.205)S(0.789)IS(0.006)S(0.018)S(0.982)PQKDLTQAK 163.74 1.74E-11 1439480000 1624500 1142720 1405940 1348840 1647970 915910 1808360 1229860 2671900 TRUE FALSE 1522825.445 1227328.178 1439289.561 1383453.518 1518545.084 1180318.348 1537213.206 1383410.728 2225942.629 0.684126098 0.551374578 0.646597779 0.621513556 0.682203155 0.530255512 0.690589769 0.621494332 1 21.08598498 -4.999998879 0.378020362 6.232139213 0.615679253 0.823238349 0.054009604 207.1976937 1.559347977 887.974776 0.03222262 1.00E-05 4.999998879 -5.61645996 RYPSSISSS(ph)PQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RYPSSISSSPQK 12 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 RYPS(0.001)S(0.011)IS(0.001)S(0.094)S(0.893)PQK;RYPS(0.006)S(0.03)IS(0.008)S(0.081)S(0.876)PQK;RYPSSIS(0.018)S(0.366)S(0.616)PQK;RYPSSISS(0.101)S(0.899)PQK;RYPSSIS(0.001)S(0.294)S(0.705)PQK 197.06 2.11E-07 4268600000 2936720 4372540 1761538 1766504 4662410 1326374 2423510 4398200 4601380 TRUE FALSE 2752915.937 4696287.411 1803322.513 1811835.483 4296243.126 1709276.642 2060127.174 4947324.952 3833379.952 0.71814325 1.225103556 0.470426239 0.472646987 1.120745447 0.445892832 0.537417945 1.290590814 1 21.87018557 1.2352642 24.99999292 1.145295483 0.722689894 0.295963375 0.276929777 117.478474 890883.6987 0.230489831 0.066822222 17.18953782 -1.2352642 -0.422605589 RYPSSISSS(ph)PQKDLTQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RYPSSISSSPQKDLTQAK 18 2 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 RYPSSISS(0.016)S(0.984)PQKDLTQAK;RYPSSISS(0.021)S(0.979)PQKDLTQAK;RYPSSISS(0.003)S(0.997)PQKDLTQAK;RYPS(0.33)S(0.067)IS(0.067)S(0.069)S(0.468)PQKDLTQAK;RYPSSISS(0.016)S(0.984)PQKDLTQAK 273.96 2.63E-39 8236690000 8268150 5479110 6604980 6343230 7422590 4773700 8812730 5718560 11966370 TRUE FALSE 7750661.251 5884789.005 6761653.245 6506008.021 6839649.723 6151789.695 7491342.95 6432534.804 9969105.541 0.777468071 0.590302608 0.678260774 0.652617027 0.686084593 0.617085422 0.751455877 0.645246936 1 23.24903264 -2.773795384 0.385224755 1.675334445 0.659896533 0.757026797 0.057481434 39.40803331 1.456245017 21.92615401 0.034007871 0.001683467 2.773795384 -1.015437913 RYS(ph)DFEWLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 RYSDFEWLK 9 1 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 1 RY(0.001)S(0.999)DFEWLK;RYS(1)DFEWLK;RY(0.002)S(0.998)DFEWLK;RYS(1)DFEWLK;RYS(1)DFEWLK 190.35 2.28E-05 816778000 2320097 1828616 2071436 2007335 2229198 1697766 2372373 2111330 2495276 TRUE FALSE 2174886.27 1964008.631 2120571.44 2058846.615 2054125.781 2187883.483 2016657.693 2374934.198 2078798.316 1.046222837 0.94478075 1.020094842 0.990402291 0.988131348 1.052475109 0.970107431 1.142455322 1 20.98731836 1.262127727 24.99999988 1.071227843 0.998239936 0.273895342 0.046763191 220.3436363 233741.476 0.027107063 0.009886569 18.28637946 -1.262127727 -0.072987907 RYS(ph)DFEWLKNELER ddPTM_SK-BR-3_Pertuzumab_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 176.46 1.16E-06 161959000 176031 216430 176536 229228 286513 157690 215822 203359 394554 TRUE FALSE 165013.5339 232454.7024 180723.5173 235110.3786 264011.4247 203212.5431 183461.4947 228748.8188 328700.3885 0.502018068 0.707193269 0.549812302 0.715272591 0.803197787 0.61823031 0.558142007 0.695918918 1 18.32641364 0.967627402 22.0950229 1.000000002 0.637344262 0.619948457 0.088864731 607.3146265 414507.0958 0.082615764 0.020653941 9.281697332 -0.967627402 -0.36265574 RYS(ph)DFEWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 RYSDFEWLR 9 1 O60493-4;O60493;O60493-3 O60493-4 SNX3 Sorting nexin-3 1 RYS(1)DFEWLR;RYS(1)DFEWLR;RYS(1)DFEWLR;RYS(1)DFEWLR;RYS(1)DFEWLR;RYS(1)DFEWLR;RYS(1)DFEWLR;RYS(1)DFEWLR 237.53 1.79E-10 1259096000 502049 641991 592277 569592 697085 555094 605103 645374 839372 TRUE FALSE 470626.6493 689524.6816 606326.0901 584208.695 642338.756 715340.6266 514373.4227 725950.3645 699275.3906 0.673020466 0.986055981 0.86707769 0.83544867 0.918577666 1.022974119 0.735580616 1.038146593 1 19.41550121 -1.919660622 0.017115551 1.961143879 2.03E-06 0.192530693 0.110340763 5332.313602 13.00679482 852.4634994 648.354838 0.012032043 1.919660622 -1.961141847 RYS(ph)DHAGPAIPSVVAYPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RYSDHAGPAIPSVVAYPK 18 1 H0YIY6;P27448-6;P27448-7;J3KNR0;P27448-8;P27448-3;P27448-4;P27448-2;P27448 H0YIY6;J3KNR0 MARK3 MAP/microtubule affinity-regulating kinase 3 1 RYS(1)DHAGPAIPSVVAYPK;RY(0.003)S(0.997)DHAGPAIPSVVAYPK 178.69 5.36E-14 492050000 328503 317716 316090 321185 355170 239578 379110 284805 393370 TRUE FALSE 307942.5836 341240.0232 323587.8041 329427.1509 327276.3809 308740.2794 322265.975 320363.5312 327714.0057 0.939668669 1.041273846 0.987409138 1.005227562 0.998664614 0.942102791 0.983375655 0.97757046 1 18.32207781 2.432112194 24.99976684 0.973712755 1.000534004 0.072784249 0.028591137 215.7943161 119859.3792 0.009045044 0.007567633 270.4656986 -2.432112194 0.026821249 RYS(ph)FRVPEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 RY(0.001)S(0.999)FRVPEEER;RYS(1)FRVPEEER;RYS(1)FRVPEEER;RYS(1)FRVPEEER 126.16 0.00024669 1384950000 825320 1048330 954030 1018690 1365430 885290 984600 943910 1533070 TRUE FALSE 773664.6944 1125949.444 976660.0421 1044831.31 1258194.636 1140858.852 836968.3706 1061759.241 1277190.713 0.605755027 0.881582862 0.764693974 0.818069924 0.985126671 0.893256457 0.655319806 0.83132396 1 20.28454254 -2.660737884 1.962125004 4.834707526 0.806266578 0.23485455 0.110913377 4154041.608 119887.2536 71348573.47 0.027014079 0.002184048 2.660737884 -4.028440948 RYS(ph)GNMEYVISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RYSGNMEYVISR 12 1 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 RYS(1)GNMEYVISR;RYS(1)GNMEYVISR 149.73 6.78E-05 294690000 182836 254380 208380 237430 257000 187571 223750 225330 249300 TRUE FALSE 171392.6211 273214.5599 213322.872 243522.8558 236816.2567 241719.7027 190200.7647 253462.9465 207690.2195 0.825232029 1.315490737 1.027120452 1.172529243 1.140237886 1.163847308 0.915790667 1.22038942 1 17.66407375 RYS(ph)PPIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 RYSPPIQR 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RY(0.001)S(0.999)PPIQR;RYS(1)PPIQR;RYS(1)PPIQR;RYS(1)PPIQR;RYS(1)PPIQR;RY(0.002)S(0.998)PPIQR;RYS(1)PPIQR;RYS(1)PPIQR;RY(0.001)S(0.999)PPIQR 120.36 0.000929 93904490000 2298720 2786340 2660530 2804530 2991160 2574740 2744670 2463660 2918000 TRUE FALSE 2154847.219 2992643.513 2723639.028 2876498.988 2756246.359 3318025.641 2333132.214 2771253.374 2430966.949 0.886415679 1.231050679 1.120393278 1.18327359 1.133806595 1.364899528 0.959754807 1.139979865 1 21.21309885 1.632578912 25 1.037404068 1.159146399 0.166946945 0.125859434 1.311606787 1322.704743 0.052220543 0.028941135 42.91201542 -1.632578912 0.121742331 RYS(ph)PS(ph)PPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RYSPSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RY(0.097)S(0.912)PS(0.991)PPPK;RY(0.009)S(0.993)PS(0.998)PPPK;RY(0.019)S(0.982)PS(0.999)PPPK;RY(0.023)S(0.978)PS(0.999)PPPK 88.021 0.0087331 7874550000 3806740 3173270 3446410 3350250 3506610 2803040 4040300 2998670 3894730 TRUE FALSE 3568482.939 3408222.213 3528160.473 3436223.087 3231214.996 3612232.144 3434494.523 3373060.55 3244674.402 1.099796928 1.050404999 1.087369651 1.059034794 0.995851847 1.113280316 1.058502055 1.039568269 1 21.62964228 1.251376142 0.007249846 1.39E-07 2.096337025 0.295103784 0.032219002 3155.786079 19.82671953 2879.938921 2850.751059 17.83923151 -1.251376142 2.096336886 RYS(ph)PSPPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RYSPSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RY(0.029)S(0.834)PS(0.137)PPPK 67.385 0.037393 206890000 218770 195240 220510 222350 238830 160380 238620 202740 291190 TRUE FALSE 205077.5762 209695.7727 225740.6013 228055.8774 220073.2552 206679.1024 202841.1462 228052.5353 242588.5078 0.845372182 0.864409343 0.930549445 0.940093492 0.907187472 0.851974004 0.836153155 0.940079715 1 17.88815168 0.995992592 7.351667454 0.999985073 0.884231439 0.554474889 0.035041505 0.088094945 37.84807623 0.037179713 0.009319004 9.908150432 -0.995992592 -0.115753633 RYSPPIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 RYSPPIQR 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 0 88.177 0.023731 197570000 123190 113060 114350 137330 134910 109630 129940 125460 157030 FALSE TRUE 115479.7578 121431.08 117062.436 140854.1203 124314.7128 141278.4013 110456.7033 141123.9572 130820.6785 0.882733212 0.928225426 0.894831286 1.076696145 0.950268063 1.079939371 0.844336725 1.078758792 1 16.99723108 3.291163883 24.99999594 0.989592132 0.906550426 0.293206571 0.072746679 138.1099602 65636.38716 0.01875885 0.025399579 1955.077074 -3.291163883 -0.083041705 RYTCGEAPDYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 RYTCGEAPDYDR 12 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;; 183.96 2.39E-05 5034330000 1907170 2355930 2486080 2361400 3013960 2346860 2345700 2227960 4543640 FALSE TRUE 1787803.634 2530365.509 2545050.992 2421997.522 2777255.739 3024360.384 1993984.061 2506125.71 3785277.131 0.472304556 0.668475628 0.672355261 0.639846817 0.733699447 0.798979911 0.5267736 0.662071923 1 21.8519675 -2.363362587 2.164267282 3.134692065 0.650971221 0.589524351 0.092561102 3206839.654 337773.9314 33533669.56 0.021944261 0.004331491 2.363362587 -2.483720844 RYWEEETVPTTAGAS(ph)PGPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RYWEEETVPTTAGASPGPPR 20 1 O15213 O15213 WDR46 WD repeat-containing protein 46 1 RYWEEETVPTTAGAS(1)PGPPR;RYWEEETVPTTAGAS(1)PGPPR 169.01 6.99E-12 309060000 125212 153096 158972 136583 161581 137105 153130 128079 170000 TRUE FALSE 117375.2044 164431.3871 162742.8909 140087.951 148891.08 176684.9878 130169.5781 144069.9451 141625.9018 0.828769335 1.161026232 1.149104005 0.989140752 1.051298373 1.247547134 0.919108556 1.017257036 1 17.11172562 1.629158082 24.99999999 0.976149437 1.086377762 0.117030022 0.114525387 1.448719388 1696.476914 0.049951032 0.027664901 42.57533584 -1.629158082 0.110228325 S(ph)AEEGELAESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SAEEGELAESK 11 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 S(1)AEEGELAESK;S(1)AEEGELAESK;S(1)AEEGELAESK;S(1)AEEGELAESK 270.93 5.25E-27 1130390000 2782560 1485230 1796010 1924520 1713680 1126749 1867980 1145960 1208630 TRUE FALSE 2608404.537 1595197.975 1838612.205 1973906.441 1579094.485 1452023.145 1587893.74 1289035.629 1006901.845 2.590525134 1.584263633 1.826009372 1.960376229 1.568270525 1.4420702 1.577009466 1.280199887 1 19.94149162 8 0.09066303 0.527760826 5.049912924 0.688790009 0.237458624 96.04193583 0.624976325 4.038070959 54.02389773 99999999.99 -8 4.522152098 S(ph)AESPSWTPAEHVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAESPSWTPAEHVAK 15 0 Q13415 Q13415 ORC1 Origin recognition complex subunit 1 1 S(0.42)AES(0.42)PS(0.12)WT(0.039)PAEHVAK 75.548 0.020291 413520000 144680 116530 139110 142050 136300 107410 154050 115320 133490 TRUE FALSE 135624.7371 125158.0024 142409.7549 145695.2435 125595.5478 138417.5233 130951.6326 129717.9559 111209.6566 1.219541011 1.125423873 1.28055206 1.310095255 1.129358292 1.244653815 1.17752034 1.166427087 1 16.76292254 0.530632104 0.950168134 0.999364882 1.215953375 0.575027396 0.057814547 1.160264709 1.572961844 0.054934774 0.01762704 3.393376939 -0.530632104 0.216588493 S(ph)AGEEEDGPVLTDEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SAGEEEDGPVLTDEQK 16 0 H7BZV4;A0A0C4DG62;Q66PJ3-4;Q66PJ3-3;F5H7X4;Q66PJ3-7;F5GYV5;F8WCT1;Q66PJ3-2;Q66PJ3 H7BZV4;F5GYV5;Q66PJ3 ARL6IP4 ADP-ribosylation factor-like protein 6-interacting protein 4 1 S(1)AGEEEDGPVLTDEQK;S(1)AGEEEDGPVLTDEQK;S(1)AGEEEDGPVLTDEQK;S(1)AGEEEDGPVLTDEQK;S(1)AGEEEDGPVLTDEQK;S(1)AGEEEDGPVLTDEQK 482 4.84E-231 3463370000 7140500 4391940 4948440 5222350 5173070 3376080 6546150 4039730 4632610 TRUE FALSE 6693588.851 4717123.807 5065819.334 5356364.342 4766797.949 4350699.49 5564615.579 4544099.183 3859397.463 1.734361106 1.222243589 1.312593321 1.3878758 1.235114547 1.127300189 1.441835321 1.177411559 1 21.8799442 8 0.0309206 3.17E-10 3.202481952 0.451341511 0.148422505 1468.080293 3.477880131 113.1768391 282.3434607 99999999.95 -8 3.202481952 S(ph)ALSSSLRDLSEAGVHH ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SALSSSLRDLSEAGVHH 17 1 A0A0C4DGT3 A0A0C4DGT3 IQSEC1 1 S(0.273)ALS(0.27)S(0.226)S(0.226)LRDLS(0.005)EAGVHH 57.227 0.063169 452110000 160330 274730 226670 238780 284060 189890 268440 216360 294370 TRUE FALSE 150295.2315 295071.2951 232046.7194 244907.4991 261751.0734 244708.1604 228189.9141 243373.0223 245237.7453 0.612855217 1.203205056 0.946211274 0.998653363 1.067335997 0.997840524 0.930484473 0.992396264 1 17.90382152 -1.905789315 7.739328867 1.002155261 0.988448801 0 0.148610517 0.005796175 7.06E-05 0.150911668 0.030000643 0.012422548 1.905789315 -0.01370646 S(ph)APAS(ph)PTHPGLMSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 S(1)APAS(0.646)PT(0.354)HPGLMSPR;S(1)APAS(0.933)PT(0.067)HPGLMSPR 150.68 1.66E-06 575470000 351921 455260 336904 317401 394105 192627 433990 329087 609400 TRUE FALSE 329894.8928 488967.9241 344895.522 325546.047 363153.583 248235.2879 368917.2285 370174.2364 507687.2031 0.649799504 0.963128322 0.679346495 0.64123351 0.715309704 0.48895321 0.726662453 0.729138403 1 18.95358037 0.653633137 3.192567886 0.999991906 0.710076788 0.394558848 0.116685089 6.184792173 55.66743271 0.11737128 0.030499221 4.504360452 -0.653633137 -0.289915118 S(ph)APASPT(ph)HPGLMSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 S(1)APAS(0.056)PT(0.935)HPGLMS(0.01)PR;S(1)APAS(0.02)PT(0.97)HPGLMS(0.011)PR;S(1)APAS(0.031)PT(0.969)HPGLMS(0.001)PR;S(0.999)APAS(0.45)PT(0.551)HPGLMS(0.001)PR;S(1)APAS(0.083)PT(0.917)HPGLMSPR;S(1)APAS(0.17)PT(0.83)HPGLMSPR 220.93 8.51E-12 2187170000 2012470 2243860 1802310 1731450 2088600 1066670 2476690 1791980 3320230 TRUE FALSE 1886513.095 2409997.729 1845061.644 1775881.938 1924569.781 1374600.313 2105333.327 2015712.648 2766062.163 0.682021221 0.871273886 0.667035495 0.642025317 0.695779656 0.496952068 0.761130156 0.72873006 1 21.39940215 0.602752232 1.877470481 0.999810363 0.696652499 0.52056222 0.093254197 1.905669851 7.929724611 0.09096692 0.02531895 4.006380855 -0.602752232 -0.303157864 S(ph)APASPTHPGLMSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 S(1)APASPTHPGLMSPR 182.31 3.55E-07 2120400000 1154400 1097800 1074900 1116600 1108500 1020000 1330700 1035200 1195200 TRUE FALSE 1082148.165 1179082.254 1100397.136 1145253.846 1021442.881 1314457.442 1131173.889 1164446.999 995713.3987 1.086806872 1.184158269 1.105134406 1.150184228 1.02584025 1.320116254 1.136043655 1.169460008 1 19.92537102 -0.847134739 6.283271894 0.999999991 1.149928273 0.269353941 0.076083739 8.84E-09 1.41E-09 0.065919456 0.015537364 0.142188758 0.847134739 0.149928282 S(ph)APELPEGILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 133.32 0.00017215 71350000 112056 108998 104179 112455 126360 81979 114408 97898 122004 TRUE FALSE 105042.615 117068.3253 106650.1751 115340.7857 116436.1953 105645.0065 97253.58251 110120.7808 101640.7442 1.033469558 1.151785401 1.049285657 1.134788874 1.145566143 1.039396231 0.956836584 1.083431469 1 16.63311932 2.047227533 6.626007399 1.005987374 1.10329811 0.422638369 0.048748311 0.158646575 16.58725834 0.017097626 0.012469948 111.4878482 -2.047227533 0.097310736 S(ph)APPNLWAAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SAPPNLWAAQR 11 0 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 S(1)APPNLWAAQR;S(1)APPNLWAAQR;S(1)APPNLWAAQR;S(1)APPNLWAAQR;S(1)APPNLWAAQR 140.53 4.04E-05 882230000 242811 273113 237793 236420 327654 207961 285744 224519 380304 TRUE FALSE 227613.8929 293334.5707 243433.5623 242486.9375 301921.3765 267995.9647 242899.3399 252550.6914 316828.8055 0.718412875 0.925845648 0.768344159 0.765356348 0.952948 0.845869946 0.766658005 0.79712036 1 18.27334398 -1.160434019 4.649940653 1.000022151 0.822444159 0.374782953 0.073811783 1.59E-05 2.87E-06 0.067100625 0.015813797 0.069113992 1.160434019 -0.177577993 S(ph)APTTLYLVHTDHAYQATPPVTIPGSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAPTTLYLVHTDHAYQATPPVTIPGSAK 28 0 Q6ZNC4 Q6ZNC4 ZNF704 Zinc finger protein 704 1 S(0.172)APT(0.172)T(0.172)LY(0.154)LVHT(0.172)DHAY(0.154)QAT(0.005)PPVTIPGSAK 85.982 0.006231 228320000 275230 262770 229500 256860 380000 219010 442010 283020 362580 TRUE FALSE 258003.8456 282225.7642 234943.8484 263451.4625 350156.3328 282234.6317 375734.7039 318355.67 302063.0556 0.854139031 0.934327317 0.777797364 0.872173732 1.159216019 0.934356673 1.243894932 1.053937792 1 18.20449022 2.752707235 21.54963366 1.093638232 0.858426875 0.583308972 0.09132466 79.40973141 120964.5155 0.026072338 0.027469612 565.8577063 -2.752707235 -0.235211358 S(ph)ARHT(ph)PAR ddPTM_SK-BR-3_Pertuzumab_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 79.744 0.062432 701900000 91868 115799 103100 109739 98630 65006 125136 108520 121406 TRUE FALSE 86118.14587 124372.8784 105545.5807 112555.0885 90883.99765 83772.17692 106373.0185 122068.9609 101142.5543 0.851453144 1.229679034 1.043532877 1.112836128 0.898573289 0.828258467 1.051713784 1.20690012 1 16.62603059 4.807170077 21.69855618 1.046691713 0.851441142 0.199741667 0.12265292 48414.85704 15307824.46 0.030347753 117.7507837 64146.07344 -4.807170077 -0.195250571 S(ph)AS(ph)APTLAETEKETAEHLDLAGASSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SASAPTLAETEKETAEHLDLAGASSR 26 1 Q86W92-2 Q86W92-2 PPFIBP1 Liprin-beta-1 2 S(0.397)AS(0.436)APT(0.434)LAET(0.402)EKET(0.331)AEHLDLAGASSR 47.104 0.081897 41439000 0 2721.7 1408.3 1274.1 1886.2 2218.9 2085.4 1374.2 1872 TRUE FALSE 0 2923.2175 1441.705541 1306.795563 1738.065461 2859.460409 1772.71363 1545.771895 1559.551106 0 1.874396734 0.924436227 0.83793058 1.114465216 1.83351504 1.136681974 0.99116463 1 10.60691512 2.456127239 24.9947662 1.286907878 1.062959033 0.047620949 0.510910607 892.5142147 1062591.15 0.168533194 0.141017605 285.8427881 -2.456127239 -0.223948846 S(ph)AS(ph)PERMD ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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;S(1)AS(1)PERMD;S(1)AS(1)PERMD 117.45 0.0013957 2804985000 6384450 4995050 5699280 5197340 5232100 4822620 6738620 4586200 4491220 TRUE FALSE 5984858.671 5364888.699 5834469.613 5330712.543 4821191.971 6214832.105 5728226.489 5158797.165 3741606.368 1.599542572 1.433846368 1.559348857 1.424712281 1.288535323 1.661006395 1.530953801 1.378765337 1 21.83522636 0.868870808 3.719871853 1.000133497 1.498171564 0.69901905 0.10289828 0.357983269 9.04174872 0.094082434 0.024170542 7.393852926 -0.868870808 0.498038068 S(ph)AS(ph)PHDVDLCLVSPCEFEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SASPHDVDLCLVSPCEFEHR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 2 S(1)AS(1)PHDVDLCLVSPCEFEHR 75.646 0.0057822 15616000 8985.4 9477.5 8924.5 10886 9850.4 6974.1 10156 6689.7 7272.9 TRUE FALSE 8423.019853 10179.22396 9136.193354 11165.35319 9076.789319 8987.409455 8633.202084 7524.923771 6059.006005 1.390165292 1.680015493 1.507869995 1.842769784 1.498065741 1.483314169 1.424854518 1.241940306 1 12.56486542 1.164086781 0.971557424 1.001382571 1.597823087 0.722086045 0.119687475 0.245379198 0.499887651 0.101962672 0.03514839 14.59105791 -1.164086781 0.596440515 S(ph)AS(ph)PPPATSSSSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SASPPPATSSSSSSR 15 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 S(1)AS(0.999)PPPAT(0.001)SSSSSSR;S(1)AS(0.993)PPPAT(0.006)S(0.001)SSSSSR 117.97 0.00047931 130505000 216944 178857 186019 199963 188634 155295 219620 149739 167742 TRUE FALSE 203365.8623 192099.7584 190431.4585 205094.3891 173819.4466 200126.1455 186690.0199 168434.2438 139744.7765 1.455266288 1.374647147 1.362708956 1.467635458 1.243835017 1.432083191 1.335935585 1.205299031 1 17.09243483 0.98293996 1.777431442 1.000637052 1.3835472 0.804331751 0.062396267 0.14428368 0.948733447 0.05214132 0.014893875 9.614793476 -0.98293996 0.382910148 S(ph)ASASHQADIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SASASHQADIK 11 0 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 S(0.895)AS(0.102)AS(0.003)HQADIK;S(0.633)AS(0.361)AS(0.005)HQADIK 147.39 2.28E-05 977490000 2417300 1956090 1753020 1875500 2229320 1458900 2660690 2172340 1809220 TRUE FALSE 2266005.508 2100920.939 1794602.462 1923628.505 2054238.2 1880060.747 2261744.235 2443561.431 1507249.494 1.503404391 1.393877356 1.190647248 1.276250888 1.362905218 1.247345416 1.500577206 1.621205673 1 20.52348681 1.73994053 24.99999986 1.423994989 1.319846509 0 0.179321623 0.593086466 10786.47446 0.075301602 0.041758728 54.94656278 -1.73994053 -0.10414848 S(ph)ASDNTLVAMDFSGHAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 28 SASDNTLVAMDFSGHAGR 18 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 1 S(0.499)AS(0.499)DNT(0.001)LVAMDFSGHAGR;S(0.582)AS(0.418)DNTLVAMDFSGHAGR;S(0.602)AS(0.398)DNTLVAMDFSGHAGR;S(0.487)AS(0.487)DNT(0.027)LVAMDFSGHAGR;S(0.498)AS(0.498)DNT(0.003)LVAMDFSGHAGR;S(0.5)AS(0.5)DNTLVAMDFSGHAGR;S(0.496)AS(0.496)DNT(0.009)LVAMDFSGHAGR;S(0.481)AS(0.481)DNT(0.039)LVAMDFSGHAGR;S(0.478)AS(0.478)DNT(0.043)LVAMDFSGHAGR;S(0.495)AS(0.495)DNT(0.01)LVAMDFSGHAGR;S(0.467)AS(0.467)DNT(0.066)LVAMDFSGHAGR;S(0.467)AS(0.467)DNT(0.066)LVAMDFSGHAGR;S(0.498)AS(0.498)DNT(0.004)LVAMDFSGHAGR;S(0.48)AS(0.48)DNT(0.04)LVAMDFSGHAGR;S(0.496)AS(0.496)DNT(0.008)LVAMDFSGHAGR;S(0.497)AS(0.497)DNT(0.007)LVAMDFSGHAGR;S(0.457)AS(0.457)DNT(0.086)LVAMDFSGHAGR;S(0.333)AS(0.333)DNT(0.333)LVAMDFSGHAGR;S(0.402)AS(0.402)DNT(0.197)LVAMDFSGHAGR;S(0.357)AS(0.357)DNT(0.285)LVAMDFSGHAGR;S(0.595)AS(0.405)DNTLVAMDFSGHAGR;S(0.495)AS(0.495)DNT(0.009)LVAMDFSGHAGR;S(0.456)AS(0.456)DNT(0.088)LVAMDFSGHAGR;S(0.488)AS(0.488)DNT(0.023)LVAMDFSGHAGR;S(0.604)AS(0.395)DNTLVAMDFSGHAGR;S(0.493)AS(0.493)DNT(0.015)LVAMDFSGHAGR;S(0.499)AS(0.499)DNT(0.001)LVAMDFSGHAGR;S(0.45)AS(0.361)DNT(0.19)LVAMDFSGHAGR 284.71 9.31E-40 6595213900 1514103.9 2105841.3 1828470.7 2098861.2 2170844.8 1763695.7 2152718.2 1725990.2 1734665.1 TRUE FALSE 1419338.84 2261759.981 1871842.888 2152721.532 2000355.406 2272846.017 1829938.091 1941483.876 1445138.288 0.982147419 1.56508204 1.295269043 1.489630127 1.384196531 1.572753304 1.266271958 1.343458887 1 20.46277612 -0.357411382 7.285734448 1.000011467 1.379892158 0.302725374 0.170994004 0 0 0.144412839 0.034038433 0.43912546 0.357411382 0.379880691 S(ph)ASDSGCDPASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SASDSGCDPASK 12 0 Q7LBC6;H0Y9V5 Q7LBC6 KDM3B Lysine-specific demethylase 3B 1 S(0.998)AS(0.002)DSGCDPASK 121.56 0.00039244 56869000 271650 203190 230980 280830 309390 185270 255040 157830 250270 TRUE FALSE 254647.9114 218234.399 236458.9547 288036.5732 285091.7574 238754.4414 216799.1197 177535.4229 208498.3202 1.221342748 1.046696198 1.134104843 1.381481505 1.367357575 1.14511446 1.039812309 0.851495699 1 17.66967623 1.616240831 2.797623083 0.929612706 1.200844877 0.564863646 0.107197065 0.201127029 3.655853305 0.080381332 0.032312678 41.32766147 -1.616240831 0.271232171 S(ph)ASPHDVDLCLVSPCEFEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SASPHDVDLCLVSPCEFEHR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 S(0.563)AS(0.437)PHDVDLCLVSPCEFEHR;S(0.577)AS(0.423)PHDVDLCLVSPCEFEHR 206.49 1.27E-21 1750400000 263930 308860 311190 294940 300590 296720 406490 276670 260090 TRUE FALSE 247411.0924 331728.3158 318571.5738 302508.6597 276982.8739 382378.2472 345540.5982 311212.8585 216679.2988 1.141830779 1.530964507 1.470244622 1.396112418 1.278307967 1.764719793 1.594709786 1.436283301 1 17.7252018 S(ph)ASPHKDLPNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SASPHKDLPNDR 12 1 H9KV62;H9KV63;Q9BXT4-2;Q9BXT4;Q9BXT4-3;Q9BXT4-4 H9KV62 TDRD1 Tudor domain-containing protein 1 1 S(0.545)AS(0.455)PHKDLPNDR 58.079 0.06581 261280000 156230 141490 153630 141810 143900 133790 176910 138380 220740 TRUE FALSE 146451.8432 151966.0668 157274.1761 145449.0847 132598.6745 172413.0011 150383.9879 155657.0476 183897.068 0.796379436 0.826364816 0.855229384 0.790926611 0.721048334 0.937551659 0.817761749 0.846435723 1 17.48853895 -0.453576968 0.465808109 1.034671135 0.816398432 0.530466884 0.053282787 6.547945352 1.310226899 0.416411329 0.026964443 0.351903051 0.453576968 -0.218272702 S(ph)ASSPSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SASSPSPR 8 0 Q14669-3;Q14669;Q14669-2;G5E9G6;H7C1L9 Q14669-3;H7C1L9 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 S(0.978)AS(0.011)S(0.011)PSPR 74.464 0.042912 112900000 43414 42758 40781 43569 43455 36409 40627 39852 41040 TRUE FALSE 40696.79524 45923.84681 41748.34458 44687.0543 40042.21959 46919.68725 34535.35851 44827.60993 34190.15887 1.190307287 1.343189044 1.221063194 1.307015111 1.171162139 1.372315567 1.010096462 1.311126108 1 15.06129351 0.337239864 0.336636995 0.957580806 1.287740323 0.331021917 0.105471345 3.468549667 0.719571923 0.343623076 0.096399662 2.173901508 -0.337239864 0.330159517 S(ph)AVDLSCSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAVDLSCSR 9 0 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 S(1)AVDLSCSR 137.78 0.0013279 0 150470 255160 109250 114960 290080 61497 230230 153250 773250 TRUE FALSE 141052.3513 274052.3119 111841.4616 117910.0682 267298.2869 79250.18558 195709.1489 172383.5998 644189.5796 0.218960933 0.425421833 0.173615757 0.183036286 0.414937303 0.123023079 0.30380676 0.267597622 1 19.2971258 -0.118551659 1.940900488 1.000163046 0.268188282 0.846666995 0.09844394 46.93830837 79.71535064 0.125537855 0.023978223 0.7611116 0.118551659 -0.731974764 S(ph)AVFPGEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 108.35 0.0027545 1334117000 3735680 3467540 3325030 3352470 4209630 2156526 4482170 3339630 4816470 TRUE FALSE 3501870.457 3724280.27 3403901.282 3438500.056 3879022.641 2779080.048 3810110.219 3756590.157 4012570.041 0.872725067 0.928153336 0.848309499 0.856932096 0.96671774 0.69259353 0.949543604 0.936205504 1 21.93609514 1.55588334 13.42201682 0.959100895 0.867668553 0.301268338 0.072140128 0.166608034 36.98103788 0.035312058 0.016390642 35.96527124 -1.55588334 -0.091432342 S(ph)AVLLVDETATTPIFANR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SAVLLVDETATTPIFANR 18 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;A0A087WY36;A0A087WX73 Q12802-2 AKAP13 A-kinase anchor protein 13 1 S(1)AVLLVDETATTPIFANR;S(1)AVLLVDETATTPIFANR;S(1)AVLLVDETATTPIFANR;S(1)AVLLVDETATTPIFANR;S(1)AVLLVDETATTPIFANR;S(1)AVLLVDETATTPIFANR 355.43 1.49E-90 927371000 253214.3 282230.5 259314.8 252450.2 305686.1 188676.2 322949.1 249663.4 355645.3 TRUE FALSE 237366.069 303127.1399 265465.8695 258928.4995 281678.7468 243143.956 274525.8806 280834.4251 296285.8019 0.801138858 1.023090334 0.895979044 0.873914639 0.950699443 0.820639918 0.926557664 0.947849756 1 18.17662997 0.99905173 2.571736712 0.999004743 0.908543478 0.210740985 0.063036253 0.46510905 6.997038431 0.056677978 0.01526769 9.978189101 -0.99905173 -0.090461266 S(ph)AVSPDLHITPIYEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAVSPDLHITPIYEGR 16 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 S(0.542)AVS(0.458)PDLHITPIYEGR 103.1 0.00094372 47456000 50298 53268 62677 58519 68959 51617 61933 54997 74662 TRUE FALSE 47149.93796 57212.01815 64163.72804 60020.69661 63543.23831 66517.98997 52646.72161 61863.49651 62200.42987 0.758032349 0.919801009 1.031564061 0.964956299 1.021588411 1.06941367 0.846404466 0.994583103 1 15.92463693 4.728719928 2.132880831 0.98171779 0.699841346 0.608106767 0.058610784 0.482385683 2.520814852 0.015027304 0.259014225 53545.12392 -4.728719928 -0.281876444 IRDSAGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 IRDSAGQK 8 1 P52209-2;P52209;K7EPF6;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ; 120.33 0.0013881 400540000 306880 388540 319700 419290 677160 377120 626180 569270 913860 FALSE TRUE 287672.9286 417307.9059 327283.435 430049.6913 623978.5851 485988.422 532290.1222 640344.6126 761330.8622 0.377855336 0.548129501 0.429883315 0.564865701 0.819589243 0.63834063 0.699157421 0.841085846 1 19.53816404 2.06426664 0.237931847 1.073960339 0.295660217 0.811577651 0.083111582 1.078624988 0.214419753 0.215332908 0.316132105 115.948902 -2.06426664 -0.778300122 down S(ph)CSPLAFSAFGDLTIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SCSPLAFSAFGDLTIK 16 0 E9PLZ8;Q96EY5;Q96EY5-2 E9PLZ8 MVB12A Multivesicular body subunit 12A 1 S(0.5)CS(0.5)PLAFSAFGDLTIK 62.378 0.06093 0 25260 23575 25198 27271 29446 18436 27293 18925 23870 TRUE FALSE 23679.02169 25320.51753 25795.70846 27970.82003 27133.42994 23758.17392 23200.66803 21287.82791 19885.94279 1.190741718 1.273287256 1.297183077 1.406562431 1.364452781 1.194722029 1.166686853 1.070496286 1 14.27946134 1.511302791 1.367515323 1.014067176 1.302256902 0.755309444 0.061591464 0.200638226 0.71903562 0.055979383 0.018997823 32.45658262 -1.511302791 0.288189726 S(ph)CTPSPDQISHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SCTPSPDQISHR 12 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 S(0.582)CT(0.417)PS(0.001)PDQISHR 119.65 0.00031864 484320000 222570 176950 183540 162660 224460 198380 245920 181340 229620 TRUE FALSE 208639.741 190051.5621 187893.6555 166834.131 206831.817 255649.0856 209046.579 203980.6982 191294.9386 1.090670472 0.993500212 0.982219691 0.872130398 1.081219496 1.336413224 1.09279723 1.066315187 1 17.54543918 2.484571935 24.98404567 1.144025577 0.984803587 0.294866705 0.100224733 359.301633 1204835.851 0.03177611 0.027636865 305.1911496 -2.484571935 -0.15922199 S(ph)DDELLDDFFHDQSTATSQAGTLSSIPTALTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDDELLDDFFHDQSTATSQAGTLSSIPTALTR 32 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 S(1)DDELLDDFFHDQSTATSQAGTLSSIPTALTR 98.114 3.17E-05 26345000 7012.8 5556.6 6258.8 6739.8 5426.6 4757.8 9042.7 5853.1 5486.1 TRUE FALSE 6573.881366 5968.016446 6407.261692 6912.754678 5000.416726 6131.299624 7686.831083 6583.872419 4570.434468 1.438349332 1.305787554 1.401893351 1.512493993 1.094079077 1.341513518 1.681860037 1.440535351 1 12.1581156 S(ph)DEDRYQNGAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDEDRYQNGAER 12 1 Q9HCG8 Q9HCG8 CWC22 Pre-mRNA-splicing factor CWC22 homolog 1 S(1)DEDRYQNGAER;S(1)DEDRYQNGAER 211.57 1.84E-08 237370000 196398 160602 163142 164663 149900 137936 217220 159330 144283 TRUE FALSE 184105.7998 172493.1392 167011.8053 168888.5314 138127.4587 177755.884 184649.8776 179222.7012 120201.2352 1.531646488 1.435036328 1.389435017 1.405048218 1.149135102 1.478819113 1.536172879 1.491022126 1 16.8750922 4.920994732 1.198724575 1.383619132 1.648799152 0.08967883 0.165537664 6.364628282 5.86560684 0.044164499 2.323394054 83367.10726 -4.920994732 0.26518002 S(ph)DPEQNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDPEQNEK 8 0 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 S(1)DPEQNEK;S(1)DPEQNEK 67.93 0.065794 154480000 843810 498540 682690 629540 629700 486070 782110 574690 708710 TRUE FALSE 790997.4383 535452.4203 698883.7292 645695.0622 580245.9021 626390.5183 664839.8663 646441.3115 590421.7226 1.339716017 0.906898239 1.183702602 1.093616711 0.982765166 1.060920516 1.126042354 1.094880637 1 19.17138628 7.999978557 0.009024671 4.06E-09 2.291389939 0.091832631 0.112934162 57594.32718 40.18712351 4459.820527 5828.661094 99995062.79 -7.999978557 2.291389935 S(ph)DRLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDRLLK 6 1 F5H385;Q9BRY0 F5H385 SLC39A3 Zinc transporter ZIP3 1 S(1)DRLLK 90.657 0.029542 186940000 204490 155090 169110 153820 174540 111720 210290 158220 255810 TRUE FALSE 191691.3359 166573.025 173121.3691 157767.2816 160832.3325 143971.7504 178758.9667 177974.1153 213113.6584 0.899479355 0.781615905 0.812342908 0.740296435 0.754678671 0.675563225 0.838796387 0.835113604 1 17.70126353 0.806484861 1.655146564 0.999009845 0.781130116 0.569603039 0.05872547 0.487257233 2.395514042 0.053206656 0.015239788 6.404494557 -0.806484861 -0.217879729 S(ph)DSASSEPVGIYQGFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.628)DS(0.367)AS(0.004)SEPVGIYQGFEK;S(0.976)DS(0.024)ASSEPVGIYQGFEK;S(0.881)DS(0.119)ASSEPVGIYQGFEK;S(0.634)DS(0.365)AS(0.001)SEPVGIYQGFEK 437.56 1.40E-161 1149910000 2387260 1705530 2034860 2213700 2255170 1492050 1965870 1269890 1777960 TRUE FALSE 2237845.658 1831809.216 2083127.84 2270507.29 2078058.045 1922780.614 1671106.044 1428438.562 1481206.99 1.510825748 1.236700359 1.406371867 1.532876435 1.402949121 1.298117432 1.128205615 0.96437471 1 20.49834183 1.661339115 1.892602157 0.980755404 1.395780689 0.827092833 0.082165241 0.13515444 1.006860355 0.06454816 0.024538844 45.84997623 -1.661339115 0.415025286 S(ph)DSELEVKPAESLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SDSELEVKPAESLLR 15 1 Q92539 Q92539 LPIN2 Phosphatidate phosphatase LPIN2 1 S(0.995)DS(0.005)ELEVKPAESLLR;S(0.984)DS(0.016)ELEVKPAESLLR;S(0.972)DS(0.028)ELEVKPAESLLR;S(0.996)DS(0.004)ELEVKPAESLLR;S(1)DSELEVKPAESLLR 184.32 2.84E-07 905214000 1231760 699990 848700 811120 743681 563616 1095140 704109 862783 TRUE FALSE 1154666.34 751817.9879 868831.5648 831934.7124 685275.2941 726322.7897 930933.9238 792018.5586 718778.9435 1.60642761 1.045965515 1.208760458 1.157427774 0.953388104 1.010495363 1.295160261 1.101894492 1 19.45518862 4.743511695 24.71015526 1.114763169 1.60642785 0.699348645 0.104446626 264.7899211 1321479.154 0.024849661 0.205199084 55400.24621 -4.743511695 0.491664681 S(ph)DSLLSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SDSLLSFR 8 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 S(0.998)DS(0.002)LLSFR;S(0.997)DS(0.003)LLSFR;S(0.996)DS(0.004)LLSFR;S(0.996)DS(0.004)LLSFR 141.25 0.00066773 100671000 107236 117280 119080 114846 148194 111539 121095 110705 119591 TRUE FALSE 100524.2902 125963.5332 121904.6338 117793.1428 136555.441 143738.4986 102937.9289 124526.7629 99630.48951 1.008971156 1.26430708 1.223567549 1.182300151 1.370618991 1.442715973 1.033197061 1.24988609 1 16.60429969 -0.588507098 7.472690012 0.99999635 1.224730596 0.218881022 0.131672604 0 0 0.120113583 0.028311043 0.257924681 0.588507098 0.224734246 S(ph)DSPEIPFQAAAGPSDGLDAS(ph)SPGNSFVGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 31 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 S(0.496)DS(0.504)PEIPFQAAAGPS(0.073)DGLDAS(0.447)S(0.447)PGNS(0.034)FVGLR 131.81 1.88E-06 34862000 57632 42619 51127 44824 46823 42726 64407 52654 54134 TRUE FALSE 54024.916 45774.55511 52339.75658 45974.25973 43145.71045 55060.3026 54749.76828 59227.96781 45098.68568 1.197926618 1.014986455 1.160560575 1.019414624 0.956695518 1.220884861 1.213999199 1.313296982 1 15.46079777 2.204225218 24.99913273 1.206427512 1.072491169 0.229271986 0.103988567 222.7827868 162203.8326 0.035392594 0.026140374 160.038775 -2.204225218 -0.133936343 S(ph)DSPEIPFQAAAGPSDGLDASSPGNSFVGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 31 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 S(0.537)DS(0.463)PEIPFQAAAGPSDGLDASSPGNSFVGLR;S(0.5)DS(0.5)PEIPFQAAAGPSDGLDASSPGNSFVGLR 144.92 1.22E-08 131821000 144849 123840 133514 128951 125342 111446 147019 113729 132436 TRUE FALSE 135783.1597 133009.2425 136681.0151 132260.101 115498.1449 143618.651 124974.8658 127928.316 110331.576 1.23068268 1.205541036 1.238820472 1.198751126 1.046827654 1.301700349 1.132720752 1.159489609 1 16.75148621 -4.999999999 0.161982565 0.257486874 1.245267945 0.485478485 0.064777479 106.9472084 0.989310392 25.37240107 0.241614436 1.00E-05 4.999999999 0.987781071 S(ph)EAEDEDDEDYVPYVPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SEAEDEDDEDYVPYVPLR 18 0 Q9UJV9;D6RGI7;A0A499FJW5;D6RD33 Q9UJV9 DDX41 Probable ATP-dependent RNA helicase DDX41 1 S(1)EAEDEDDEDYVPYVPLR;S(1)EAEDEDDEDYVPYVPLR;S(1)EAEDEDDEDYVPYVPLR;S(1)EAEDEDDEDYVPYVPLR 306.77 2.18E-50 763850000 649160 507620 588790 540170 519100 454495 789840 469411 454820 TRUE FALSE 608530.2344 545204.713 602756.3768 554031.6767 478331.9799 585700.3284 671410.8245 528017.9967 378907.6038 1.6060122 1.438885648 1.590774033 1.462181469 1.262397416 1.545760292 1.771964505 1.393527054 1 18.53148657 0.981253651 24.68641109 0.999999992 1.529104812 0.616352896 0.130267733 788.0942872 1037815.344 0.130168507 0.032542127 9.577532867 -0.981253651 0.52910482 S(ph)EAEEGEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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;S(1)EAEEGEVR 163.9 6.57E-05 406240000 464280 302470 376420 282380 278200 443140 548010 376350 350100 TRUE FALSE 435221.5436 324865.1935 385348.8602 289626.3489 256351.2942 571067.3242 465840.988 423338.1259 291666.0483 1.492191313 1.113825882 1.321198893 0.99300673 0.878920586 1.957949263 1.597172488 1.451448081 1 18.15395793 2.247191065 24.99966788 1.570829694 1.167977829 0.245935361 0.286035569 208.8405747 604945.3134 0.092401262 0.076184757 176.6814947 -2.247191065 -0.402851865 S(ph)EEENVVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEEENVVLK 9 0 Q9H1A4 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 S(1)EEENVVLK 69.198 0.058657 375030000 302110 269160 285880 318560 363090 229540 246500 218910 264330 TRUE FALSE 283201.4744 289088.8865 292661.2086 326734.7889 334574.376 295804.4717 209539.6134 246241.3954 220211.6154 1.2860424 1.312777648 1.328999872 1.483730948 1.519331192 1.343273702 0.951537516 1.118203483 1 17.74853104 1.783796577 6.784363875 1.026707208 1.376086248 0.803151999 0.083046385 0.092389971 9.609001307 0.040498238 0.022985304 60.78502182 -1.783796577 0.34937904 S(ph)EEKEAGEI ddPTM_SK-BR-3_Pertuzumab_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 96.334 0.019568 498410000 1418890 702270 877550 885360 1003400 674700 1196680 866250 1426960 TRUE FALSE 1330084.208 754266.8015 898365.9004 908079.8365 924597.0115 869474.9372 1017248.943 974403.2194 1188791.157 1.118854392 0.634482177 0.755696991 0.763868263 0.777762356 0.731394183 0.855700294 0.819658872 1 20.18106386 0.685327592 0.934415806 0.99922404 0.773233034 0.163437984 0.127050947 1.530310218 2.353017148 0.110947577 0.036580242 4.845377211 -0.685327592 -0.225991005 S(ph)EEKET(ph)EENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEEKETEENK 10 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 2 S(1)EEKET(1)EENK 121.99 0.01255 254000000 37540 179160 129920 137700 151940 188720 94897 130510 94930 TRUE FALSE 35190.43841 192425.1928 133001.7638 141233.6151 140007.2453 243200.4004 80668.07583 146804.4608 79085.56973 0.444966617 2.433126466 1.681745029 1.785832935 1.770326063 3.075155192 1.020010049 1.85627367 1 16.27112686 0.894347125 1.285190157 1.031325051 1.861715838 0.08593118 0.711690781 1.200110835 3.915467097 0.602524772 0.183340544 7.840560773 -0.894347125 0.830390787 S(ph)EETQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SEETQER 7 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.979)EET(0.021)QER;S(1)EETQER 145.25 0.002412 316460000 325120 182507 248590 232570 166040 218920 297010 176645 150431 TRUE FALSE 304771.3196 196020.0082 254486.6722 238538.1399 152999.8882 282118.6501 252476.1078 198699.5171 125323.0943 2.431884732 1.564117207 2.03064466 1.903385336 1.220843525 2.251130582 2.014601612 1.585498014 1 16.93529277 0.936579901 4.286738365 1.000539856 1.890121602 0.431747921 0.335756336 0.27400255 13.60506348 0.295740625 0.075319146 8.641316288 -0.936579901 0.889581745 S(ph)EIQTQASISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEIQTQASISR 11 0 F8VXH2 F8VXH2 WIBG 1 S(0.943)EIQT(0.057)QASISR 64.224 0.044865 1047600000 397670 1009200 818680 750250 1072900 1047800 823600 1045500 706110 TRUE FALSE 372780.5446 1083922.218 838099.4762 769502.6852 988638.7619 1350282.85 700108.8259 1176032.976 588255.6794 0.633704965 1.842603915 1.424719736 1.308109232 1.680627653 2.295401299 1.19014376 1.999186778 1 19.16608382 2.724953337 22.94826353 1.661918925 1.412743588 0.08768296 0.468909006 783.150156 1320753.527 0.139086543 0.131966538 530.8274067 -2.724953337 -0.249175337 S(ph)EPDDELLFDFLNSSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEPDDELLFDFLNSSQK 17 0 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 1 S(1)EPDDELLFDFLNSSQK 70.529 0.034031 7614600 17224 10190 11648 14026 10840 9967.4 17771 9766.8 10553 TRUE FALSE 16145.98059 10944.4782 11924.29606 14385.93091 9988.670126 12844.82657 15106.40353 10986.20648 8791.636125 1.83651602 1.244873883 1.356322747 1.6363201 1.136155999 1.461028003 1.718269878 1.249620244 1 13.10191596 0.996618898 24.84872444 0.999999976 1.455334221 0.359442422 0.211658686 112.8192569 829149.5705 0.195481734 0.048870434 9.922449524 -0.996618898 0.455334245 S(ph)ESELIDELSEDFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SESELIDELSEDFDR 15 0 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;D6RC54;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 1 S(0.922)ES(0.078)ELIDELSEDFDR;S(1)ESELIDELSEDFDR;S(0.998)ES(0.002)ELIDELSEDFDR;S(1)ESELIDELSEDFDR;S(0.998)ES(0.002)ELIDELSEDFDR 260.12 7.21E-25 192151000 271139 254447 291394 325502 316669 234464 284582 234378 257975 TRUE FALSE 254168.894 273286.5206 298306.0033 333854.9324 291799.0941 302149.9506 241911.571 263640.6092 214917.3059 1.182635772 1.271589179 1.388003642 1.553411118 1.357727303 1.405889346 1.125603031 1.226707212 1 17.71342213 1.699038904 6.096881495 1.131709832 1.360154286 0.522227135 0.108786005 0.120775086 10.26571775 0.055696624 0.028243626 50.00793297 -1.699038904 0.228444453 S(ph)ESELIDELSEDFDRSECK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.998)ES(0.002)ELIDELSEDFDRSECK;S(1)ESELIDELSEDFDRSECK;S(0.529)ES(0.471)ELIDELSEDFDRSECK 169.84 8.09E-12 104215000 86452 78439 73117 116501 109361 63462 82527 74072 91979 TRUE FALSE 81041.12364 84246.70518 74851.36977 119490.6129 100772.2282 81782.44918 70152.84249 83320.05225 76627.11069 1.057603802 1.099437319 0.976826205 1.559377769 1.31509889 1.067278258 0.915509431 1.087344303 1 16.22556729 2.006237328 24.3824024 0.991520994 1.174815749 0.236631192 0.163713663 195.2833838 763378.9969 0.065777579 0.048439309 101.4465608 -2.006237328 0.183294754 S(ph)ESNEDLFGLVPFDEITGSQQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SESNEDLFGLVPFDEITGSQQQK 23 0 H0Y9P1;Q9NSY1 H0Y9P1 BMP2K BMP-2-inducible protein kinase 1 S(0.5)ES(0.5)NEDLFGLVPFDEITGSQQQK;S(0.5)ES(0.5)NEDLFGLVPFDEITGSQQQK;S(0.5)ES(0.5)NEDLFGLVPFDEITGSQQQK;S(0.5)ES(0.5)NEDLFGLVPFDEITGSQQQK 166.49 7.67E-12 158198000 381602 278700 317201 296634 334783 242421.1 412004 283350 460212 TRUE FALSE 357718.212 299335.238 324725.1575 304246.1306 308490.4936 312404.1362 350227.8251 318726.8712 383399.6441 0.933016547 0.780739478 0.846962595 0.793548287 0.804618623 0.814826359 0.913479787 0.831317598 1 18.54848947 0.439841236 0.660432515 1.002707743 0.825074746 0.500425969 0.049721844 1.433526238 0.996414393 0.056974621 0.017664786 2.753222028 -0.439841236 -0.177632997 S(ph)ETEDSILHQLFIVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SETEDSILHQLFIVR 15 0 Q9UKG1 Q9UKG1 APPL1 DCC-interacting protein 13-alpha 1 S(0.5)ET(0.5)EDS(0.001)ILHQLFIVR;S(0.495)ET(0.495)EDS(0.011)ILHQLFIVR;S(0.976)ET(0.024)EDSILHQLFIVR 158.45 1.17E-06 47944000 37569.3 35662.5 43759.6 35242.5 33118.6 33351 44213.6 34577.2 34065.1 TRUE FALSE 35217.90458 38302.98861 44797.59838 36146.88222 30517.59875 42978.89229 37584.18114 38894.23953 28379.41474 1.240966556 1.349675071 1.578524391 1.273700763 1.07534278 1.514438993 1.32434659 1.370508867 1 14.79255722 -1.347766853 4.341607207 0.99947216 1.358296637 0.36542035 0.139539907 0.000703395 0.00010567 0.133300133 0.031373816 0.044898636 1.347766853 0.358824477 S(ph)ETPPVPPPPPYLASYPGFPENGAPGPPISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SETPPVPPPPPYLASYPGFPENGAPGPPISR 31 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 S(0.5)ET(0.5)PPVPPPPPYLASYPGFPENGAPGPPISR 67.367 0.0036261 72490000 74204 62550 69425 70922 68913 53584 84606 56086 84358 TRUE FALSE 69559.7041 67181.26708 71071.79378 72741.97859 63500.85096 69052.83094 71920.11574 63088.46056 70278.10483 0.989777745 0.95593453 1.011293545 1.03505891 0.903565216 0.982565354 1.023364473 0.897697238 1 16.10078767 S(ph)EVLAEESIVCLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SEVLAEESIVCLQK 14 0 O43663-2;O43663-4;O43663;O43663-3;H0YLA0;H0YM42 O43663-2 PRC1 Protein regulator of cytokinesis 1 1 S(1)EVLAEESIVCLQK;S(1)EVLAEESIVCLQK 352.62 5.92E-82 119723000 220192 162477 191886 174550 207308 141226 266259 179633 192918 TRUE FALSE 206410.5758 174506.9661 196437.6265 179029.2485 191026.8659 181995.6536 226335.9348 202060.5755 160718.7395 1.28429688 1.085791033 1.222244694 1.113928899 1.188578672 1.132386019 1.408273456 1.257230962 1 17.29417863 S(ph)FDDPIVQTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFDDPIVQTER 11 0 O95757;E9PDE8;D6RJ96 O95757 HSPA4L Heat shock 70 kDa protein 4L 1 S(1)FDDPIVQTER 93.766 0.0094461 168770000 489510 396660 469930 486750 450520 369070 606890 436350 705100 TRUE FALSE 458872.4429 426029.1191 481076.9615 499240.8291 415137.9765 475614.5176 515892.4786 490829.258 587414.2549 0.781173489 0.725261799 0.818973931 0.849895665 0.706720978 0.809674797 0.878243036 0.835576008 1 19.16401875 0.052624638 0.289223325 1.063681594 0.75159959 0.689139435 0.045629335 3.115393185 0.416030739 0.280237892 0.061887687 1.12881985 -0.052624638 -0.312082003 S(ph)FDGNTLLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SFDGNTLLNR 10 0 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 S(1)FDGNTLLNR;S(1)FDGNTLLNR;S(1)FDGNTLLNR;S(1)FDGNTLLNR;S(0.999)FDGNT(0.001)LLNR;S(1)FDGNTLLNR 221.75 5.49E-09 1975000000 1795030 1548440 1497380 1533440 1152430 1082110 1763950 1238930 1225680 TRUE FALSE 1682682.277 1663088.109 1532898.561 1572790.667 1061922.796 1394497.59 1499462.073 1393613.138 1021106.09 1.647901519 1.628712359 1.501213807 1.54028135 1.039973032 1.365673562 1.468468446 1.36480739 1 19.96170133 8 0.044028024 0.055424149 3.786568853 0.600912772 0.139714328 454.2372665 1.517247274 33.12038519 121.1224286 99999999.91 -8 3.731144704 S(ph)FDYNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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(0.995)FDY(0.005)NYR;S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR;S(1)FDYNYR 186.67 0.0006246 28307460000 8357370 7125000 7563880 7352490 7271990 6940660 9153370 7030550 6554460 TRUE FALSE 7834297.13 7652542.414 7743298.806 7541167.341 6700877.239 8944315.87 7780907.144 7908329.644 5460478.283 1.434727276 1.401441782 1.418062376 1.381045204 1.227159397 1.638009604 1.424949746 1.448285156 1 22.38059589 -0.966621326 4.902725982 0.999996374 1.422420763 0.64342302 0.098659579 5879404.986 1199211.632 230.3225055 0.021508963 0.10798879 0.966621326 0.422424389 S(ph)FDYNYRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 125.74 0.00076514 506040000 426410 664970 487820 511470 731410 387130 666780 515900 1276790 TRUE FALSE 399721.7593 714205.0707 499391.3208 524595.1861 673968.009 498888.1465 566802.5291 580311.2506 1063685.501 0.375789422 0.671443834 0.469491518 0.493186366 0.633615865 0.46901847 0.53286665 0.54556657 1 20.02064022 0.534700901 3.176934458 0.999999502 0.531143682 0.760408534 0.083947166 7.233914375 48.73186328 0.072249155 0.018776621 3.425318033 -0.534700901 -0.46885582 S(ph)FEDRVGTIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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;S(1)FEDRVGTIK 185.32 8.85E-07 1206060000 778360 1189330 815530 1088380 1153020 498103 1642200 863160 2738150 TRUE FALSE 729643.837 1277389.231 834874.7567 1116309.673 1062466.46 641897.2501 1395967.355 970927.426 2281135.076 0.319859988 0.559979654 0.365990934 0.48936588 0.465762186 0.281393792 0.611961725 0.425633465 1 21.12132045 -0.76326782 0.56501637 1.11252812 0.43661089 0.752379743 0.101045849 7.314309088 1.591563987 1.589261977 0.038468 0.172477393 0.76326782 -0.67591723 S(ph)FEEKVENLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 SFEEKVENLK 10 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 1 S(1)FEEKVENLK;S(1)FEEKVENLK;S(1)FEEKVENLK;S(1)FEEKVENLK;S(1)FEEKVENLK;S(1)FEEKVENLK;S(1)FEEKVENLK;S(1)FEEKVENLK;S(1)FEEKVENLK;S(1)FEEKVENLK;S(1)FEEKVENLK 187.11 1.44E-06 72146560000 97317130 42911155 51445300 52567660 36589067 30662887 82219560 40193808 42548142 TRUE FALSE 91226224.55 46088341.57 52665606.81 53916635.15 33715509.27 39514764.71 69891500.27 45212093.41 35446582.23 2.573625405 1.300219617 1.485773903 1.521067244 0.951163897 1.114769386 1.971741586 1.275499373 1 25.07914319 4.740960344 24.92013328 1.382123666 2.573625842 0.629300686 0.29795566 145.8918659 1514927.861 0.07032037 0.474505154 55075.74032 -4.740960344 1.191502176 S(ph)FEERVETTVTSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SFEERVETTVTSLK 14 1 Q16890-5;E9PPQ1;J3KNE7;Q16890;E9PNK6 Q16890-5 TPD52L1 Tumor protein D53 1 S(1)FEERVETTVTSLK;S(1)FEERVETTVTSLK;S(1)FEERVETTVTSLK;S(1)FEERVETTVTSLK 247.3 4.97E-18 532225000 449245 437302 390566 473936 412854 231944 550519 375087 860780 TRUE FALSE 421127.5574 469680.2951 399830.41 486098.0001 380430.1122 298902.4675 467973.7867 421917.4376 717110.2571 0.587256357 0.654962456 0.55755779 0.677856711 0.530504352 0.416815217 0.652582754 0.588357834 1 19.45183543 0.179996529 1.58807783 1.000124516 0.584098896 0.755373269 0.074551016 6.281869516 11.49091615 0.069930099 0.019660948 1.513549151 -0.179996529 -0.41602562 S(ph)FEMTEFNQALEEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SFEMTEFNQALEEIK 15 0 Q9BVS4-2;Q9BVS4;H0Y919 Q9BVS4-2 RIOK2 Serine/threonine-protein kinase RIO2 1 S(1)FEMTEFNQALEEIK;S(1)FEMTEFNQALEEIK;S(1)FEMTEFNQALEEIK;S(1)FEMTEFNQALEEIK;S(1)FEMTEFNQALEEIK;S(0.999)FEMT(0.001)EFNQALEEIK 284.07 6.31E-34 280101000 451504 243260 320220 293970 263740 260611 412995 264831 194785 TRUE FALSE 423245.1706 261271.2235 327815.7696 301513.7679 243026.9243 335845.165 351070.2338 297895.7333 162274.1251 2.608211076 1.610060897 2.0201358 1.858052032 1.49763201 2.069616242 2.163439387 1.835756212 1 17.30807345 -1.897534614 1.700218268 0.372338152 1.937446466 0.490832742 0.305971015 158935.9228 54549.3782 398618.4927 0.076318766 0.012660924 1.897534614 1.565108314 S(ph)FEVEEVETPNSTPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 SFEVEEVETPNSTPPR 16 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 1 S(0.928)FEVEEVET(0.072)PNSTPPR;S(1)FEVEEVETPNSTPPR;S(1)FEVEEVETPNSTPPR;S(1)FEVEEVETPNSTPPR;S(1)FEVEEVETPNSTPPR;S(1)FEVEEVETPNSTPPR;S(1)FEVEEVETPNSTPPR;S(1)FEVEEVETPNSTPPR;S(1)FEVEEVETPNSTPPR 376.67 1.34E-104 7377937000 1291819 1210346 1136674 1286318 841773 799243 1730377 987214 1026210 TRUE FALSE 1210966.355 1299961.277 1163636.444 1319327.098 775663.5441 1029971.479 1470923.033 1110469.841 854928.9214 1.416452672 1.520548954 1.361091449 1.543200919 0.907284249 1.204745159 1.720520848 1.298903117 1 19.70544495 -1.619849625 2.047249168 0.934656115 1.392279849 0.218146309 0.217980196 790421.8197 515265.518 272999.4858 0.056574762 0.023996637 1.619849625 0.457623734 S(ph)FEVEEVETPNSTPPRR ddPTM_SK-BR-3_Pertuzumab_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(0.876)FEVEEVET(0.085)PNS(0.02)T(0.02)PPRR;S(1)FEVEEVETPNSTPPRR;S(1)FEVEEVETPNSTPPRR;S(1)FEVEEVETPNSTPPRR;S(1)FEVEEVETPNSTPPRR 276.08 5.91E-36 4370690000 586614 816930 573816 621655 659142 494185 759276 637740 793971 TRUE FALSE 549898.8769 877416.3472 587427.1865 637607.7198 607375.6462 636848.1871 645429.6126 717363.2428 661452.1109 0.831351005 1.326500185 0.888087251 0.963951448 0.918245835 0.962803167 0.975776783 1.084527861 1 19.33527718 3.754918437 20.64672527 0.967154754 1.112194305 0.097328661 0.128410175 73.53250358 54614.28503 0.029322263 0.052817843 5687.461067 -3.754918437 0.145039551 S(ph)FGNPFEGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 89.43 0.012082 117080000 46798 50843 57274 46452 48414 38955 65367 48973 65193 TRUE FALSE 43868.99672 54607.46862 58632.56633 47644.03696 44611.75973 50200.67612 55565.82519 55087.38685 54311.86714 0.807723966 1.005442668 1.079553501 0.877230695 0.821399854 0.924304001 1.023088104 1.01427901 1 15.72897984 1.716715038 7.546415491 1.013256229 0.942373281 0.189370741 0.081952565 0.280391431 40.38490388 0.044831933 0.023563824 52.08528416 -1.716715038 -0.070882948 S(ph)FGNPFEPQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SFGNPFEPQAR 11 0 J3KPJ3;Q8N5S9;Q8N5S9-2 J3KPJ3 CAMKK1 Calcium/calmodulin-dependent protein kinase kinase 1 1 S(1)FGNPFEPQAR;S(1)FGNPFEPQAR;S(1)FGNPFEPQAR 133.98 0.00015785 630930000 557679 434768 721947 774255 413545 631478 773461 428364 887759 TRUE FALSE 522774.8669 466958.6751 739071.9238 794123.6941 381066.8439 813775.4474 657487.7035 481846.1883 739586.2878 0.706847701 0.631378222 0.999304525 1.073740424 0.515243252 1.100311702 0.888993907 0.651507737 1 19.49635895 4.062668695 4.552080909 0.891499895 0.672405693 0.199535809 0.183360565 0.322623676 11.82455469 0.042669254 0.096109502 11552.3063 -4.062668695 -0.219094202 S(ph)FHIENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFHIENK 7 0 Q96L93-5;Q96L93-6;Q96L93-4;Q96L93;Q96L93-2;A0A1B0GTU3;H0Y534 Q96L93-5 KIF16B Kinesin-like protein KIF16B 1 S(1)FHIENK;S(1)FHIENK 123.86 0.002707 124240000 511750 455020 506650 438080 557620 379270 503790 442570 646560 TRUE FALSE 479720.481 488710.1542 518667.9773 449321.8745 513826.7745 488759.0921 428251.3665 497825.8387 538644.9591 0.89060609 0.907295513 0.962912524 0.834170759 0.953924781 0.907386366 0.795053141 0.924218876 1 19.03897513 3.254426413 24.99827213 0.888495391 0.923582404 0 0.060488297 688.7119798 1085134.07 0.016093739 0.021721061 1796.496657 -3.254426413 0.035087013 S(ph)FILDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFILDK 6 0 Q9BVP2-2;Q9BVP2 Q9BVP2-2 GNL3 Guanine nucleotide-binding protein-like 3 1 S(1)FILDK;S(1)FILDK 101.64 0.038067 83660000 209691 199039 230215 226368 234227 164572 317570 201425 319810 TRUE FALSE 196566.8146 213776.0547 235675.8085 232176.9861 215831.7562 212081.2648 269953.3267 226573.3546 266431.6449 0.73777578 0.802367357 0.884563876 0.871431718 0.810083038 0.796006288 1.013217956 0.850399564 1 18.02340592 7.999999999 0.077522749 1.132944586 0.172103959 0.518724496 0.060600298 169.3718113 0.959629969 1.858492628 17.49725649 99999999.77 -7.999999999 -0.960840628 S(ph)FKPWLEIFKQNQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFKPWLEIFKQNQQK 15 2 Q96JM4-2;Q96JM4 Q96JM4-2 LRRIQ1 Leucine-rich repeat and IQ domain-containing protein 1 1 S(1)FKPWLEIFKQNQQK 59.185 0.051184 418400000 319340 561850 462790 526520 634240 419990 566960 556190 919400 TRUE FALSE 299353.0794 603449.9586 473767.5973 540031.3946 584429.3488 541234.295 481949.6114 625631.5458 765946.2004 0.390827814 0.787849014 0.618539001 0.705051339 0.763016186 0.706621816 0.629221231 0.816808733 1 19.54688354 -5 0.150136364 2.144428163 0.580762152 0.541497366 0.10612896 111.4617413 0.994096222 37.99830669 0.499833993 1.00E-05 5 -1.563666012 S(ph)FLESNYFTKPNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFLESNYFTKPNLK 14 1 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 S(1)FLESNYFTKPNLK 155.24 3.57E-06 253790000 395950 411830 391800 459050 541080 375520 542830 426430 533790 TRUE FALSE 371168.1963 442322.3217 401093.681 470830.0002 498585.7594 483926.5279 461437.6809 479670.7242 444697.0006 0.834654148 0.994660007 0.901948249 1.058765855 1.121180846 1.088216308 1.037645139 1.078646187 1 18.76246315 3.220786437 12.42410159 1.068254519 0.927261541 0.670331656 0.050279948 0.437409382 304.132928 0.01349076 0.016359171 1662.594872 -3.220786437 -0.140992979 S(ph)FNDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFNDFR 6 0 P42356 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 S(1)FNDFR;S(1)FNDFR 141.2 0.012256 610490000 1590750 1788610 1806990 1793370 2093000 1759310 2215200 1865630 2086700 TRUE FALSE 1491187.797 1921040.545 1849852.656 1839390.91 1928624.223 2267194.237 1883051.325 2098558.012 1738416.289 0.857785219 1.105052085 1.064102233 1.058084258 1.109414491 1.304172223 1.08319931 1.20716656 1 20.72934217 2.647062106 3.653352348 1.157752576 1.041658855 0.244746442 0.101971954 0.34691081 8.686002248 0.031368817 0.029626738 443.6720866 -2.647062106 -0.116093721 S(ph)FQDYTGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFQDYTGQK 9 0 A0A087WYV3;A0A0D9SEW3;A0A087WXF8;Q9NP64-2;Q9NP64-3;Q9NP64;A0A087WXU5 A0A087WYV3 ZCCHC17 Nucleolar protein of 40 kDa 1 S(1)FQDYTGQK;S(1)FQDYTGQK 145.08 0.00010283 464870000 493860 350390 408770 356420 431140 298890 524640 393410 745300 TRUE FALSE 462950.1842 376333.2402 418466.2174 365566.3406 397280.0035 385174.6909 445975.1025 442528.1045 620904.6152 0.745605964 0.606104756 0.673962163 0.58876409 0.639840635 0.620344384 0.71826669 0.712715115 1 19.24401213 0.5035263 0.927454358 1.001058642 0.642940822 0.846281577 0.04609547 0.550820565 0.699240158 0.040709644 0.013052815 3.188058634 -0.5035263 -0.35811782 S(ph)FS(ph)KEVEER ddPTM_SK-BR-3_Pertuzumab_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 2 S(1)FS(1)KEVEER 113.69 0.021029 353110000 1112400 545380 741030 618090 789820 454970 913670 632600 1175800 TRUE FALSE 1042776.87 585760.5027 758607.5815 633951.2358 727790.7232 586312.4532 776673.6656 711581.5025 979551.384 1.064545349 0.597988541 0.774443887 0.647185279 0.742983712 0.598552013 0.79288711 0.726436116 1 19.90176165 0.140541777 1.313448589 1.000378737 0.726155404 0.259860351 0.133547043 10.63816727 14.90187143 0.120424881 0.033055859 1.382107351 -0.140541777 -0.274223333 S(ph)FSELPSCDGNESWAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SFSELPSCDGNESWAYR 17 0 Q8NEV8-2;Q8NEV8 Q8NEV8-2 EXPH5 Exophilin-5 1 S(0.998)FS(0.002)ELPSCDGNESWAYR;S(0.993)FS(0.007)ELPSCDGNESWAYR;S(0.649)FS(0.351)ELPSCDGNESWAYR;S(0.998)FS(0.002)ELPSCDGNESWAYR;S(0.998)FS(0.002)ELPSCDGNESWAYR;S(0.999)FS(0.001)ELPSCDGNESWAYR 331.34 5.38E-72 741392000 501632 554619 490064 524938 588259 375365 632315 459817 421612 TRUE FALSE 470235.7486 595683.5678 501688.5495 538408.7978 542059.5111 483726.782 537505.2359 517226.1646 351242.2335 1.338779064 1.695933777 1.428326385 1.532870328 1.543264048 1.377188549 1.530297853 1.472562566 1 18.4221068 -2.786715546 0.359412148 5.42E-17 1.52367193 0.700443798 0.100216528 39.84200964 1.395732634 30.61784543 0.067143406 0.001634122 2.786715546 1.52367193 S(ph)FSIS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFSISPVR 8 0 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(0.998)FS(0.021)IS(0.98)PVR 92.611 0.017039 38091000 169840 169230 166860 150610 168770 141880 163160 158950 212680 TRUE FALSE 159210.0176 181759.9653 170817.998 154474.9076 155515.485 182838.4528 138695.6727 178795.2574 177182.334 0.89856598 1.025835709 0.964080301 0.871841476 0.877714394 1.031922588 0.782784996 1.009103184 1 17.43487524 3.408272974 7.940312267 0.91386669 0.978590833 0.006861113 0.081186247 0.491075209 49.50179591 0.020521751 0.027864861 2560.194582 -3.408272974 0.064724143 S(ph)FSKEVEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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(0.999)FS(0.001)KEVEER;S(0.998)FS(0.002)KEVEER;S(0.999)FS(0.001)KEVEER;S(0.951)FS(0.049)KEVEER;S(0.996)FS(0.004)KEVEER;S(1)FSKEVEER;S(0.999)FS(0.001)KEVEER;S(0.999)FS(0.001)KEVEER;S(0.735)FS(0.265)KEVEER 158.04 4.06E-05 18758620000 15591990 13452450 14991560 13731060 15066060 8353250 16521980 11822760 26024690 TRUE FALSE 14616115.18 14448483.4 15347166.88 14083422.25 13882832.42 10764697.67 14044662.48 13298857.61 21681001.11 0.674143925 0.666412188 0.707862465 0.649574352 0.640322481 0.496503718 0.647786622 0.613387617 1 24.36992804 -1.290244466 5.798341319 1.000027546 0.640692306 0.807158376 0.055735093 2.08E-05 2.55E-06 0.05654483 0.013326724 0.051257277 1.290244466 -0.35933524 S(ph)FSLDEPPLFIPDNIATIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFSLDEPPLFIPDNIATIR 19 0 Q92576-2;Q92576;E7EVH3;D6R9X2;E9PE34;A0A1B0GX99 Q92576-2 PHF3 PHD finger protein 3 1 S(0.5)FS(0.5)LDEPPLFIPDNIATIR 195.45 9.60E-16 19939000 30121 29168 28394 32198 42096 20967 40868 25861 30539 TRUE FALSE 28235.78038 31327.62907 29067.51909 33024.25519 38789.94997 27019.83253 34740.2228 29089.80278 25441.84361 1.1098166 1.231342726 1.142508363 1.298029172 1.524651694 1.062023372 1.365475841 1.14338423 1 14.6349156 0.993492115 23.63448058 0.999999985 1.243996675 0.269738013 0.132506819 154.8185193 562254.2601 0.117835025 0.029458756 9.851267577 -0.993492115 0.24399669 S(ph)FSMHDLTTIQGDEPVGQRPYQPLPEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SFSMHDLTTIQGDEPVGQRPYQPLPEAK 28 1 Q6NUK4 Q6NUK4 REEP3 Receptor expression-enhancing protein 3 1 S(0.531)FS(0.452)MHDLT(0.015)T(0.003)IQGDEPVGQRPYQPLPEAK;S(0.499)FS(0.499)MHDLT(0.001)TIQGDEPVGQRPYQPLPEAK;S(0.498)FS(0.498)MHDLT(0.002)T(0.002)IQGDEPVGQRPYQPLPEAK 171.03 4.32E-12 340890000 308458 286843 226385 234772 296698 142750 444393 262191 478568 TRUE FALSE 289152.1644 308081.1542 231754.9591 240796.647 273396.5359 183959.6076 377760.3952 294926.1235 398691.9091 0.72525215 0.772729888 0.581288343 0.603966726 0.685733845 0.461407928 0.947499527 0.739734408 1 18.6049148 1.677647209 9.530333632 0.880809916 0.648161379 0.558922836 0.107076189 0.09087826 12.72114688 0.048353948 0.025912053 47.60441236 -1.677647209 -0.232648537 S(ph)FSSQRPVDR ddPTM_SK-BR-3_Pertuzumab_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 S(0.7)FS(0.288)S(0.012)QRPVDR 121.56 0.00030997 3499700000 4274900 4024800 3788000 3734500 4954500 3114900 5878700 3820200 5814600 TRUE FALSE 4007341.64 4322800.38 3877853.149 3830333.592 4565393.555 4014121.064 4997243.51 4297160.379 4844105.696 0.827261396 0.892383579 0.800530251 0.790720482 0.942463654 0.828660916 1.031613227 0.887090549 1 22.20779891 2.026812194 1.518556239 0.972987072 0.839679468 0.445937809 0.061014394 0.336723234 1.45360048 0.036418476 0.017906734 106.3682941 -2.026812194 -0.133307604 SSSSESSHSSSSHSHGKT(ph)TPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSSESSHSSSSHSHGKTTPTK 22 1 O75582-3;O75582 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 1 SSSSESSHSSSSHSHGKT(0.466)T(0.466)PT(0.068)K;SSSSESSHSS(0.001)S(0.001)S(0.001)HS(0.01)HGKT(0.694)T(0.236)PT(0.058)K 90.316 0.0013282 53766000 3317.7 17708.3 13689.5 13015.5 25319 15454.6 34070 25184.8 40820 TRUE FALSE 3110.051079 19019.44096 14014.2214 13349.49977 23330.54787 19916.09214 28961.51979 28329.17772 34006.87829 0.091453589 0.559282178 0.412099614 0.392552932 0.686053794 0.585648937 0.851637117 0.833042583 1 15.05353896 2.064438307 0.475430641 1.021083897 0.321620813 0.774609404 0.124992711 0.451981828 0.227896592 0.118931024 0.101975016 115.994743 -2.064438307 -0.699463084 down S(ph)FTLDDESLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SFTLDDESLK 10 0 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 S(0.995)FT(0.005)LDDESLK;S(0.995)FT(0.005)LDDESLK;S(0.999)FT(0.001)LDDESLK;S(1)FTLDDESLK 342.26 9.11E-54 306915000 1425080 918200 1094190 1198260 1297060 745510 1154100 794130 913730 TRUE FALSE 1335886.787 986184.4834 1120144.704 1229009.38 1195194.14 960726.6347 981053.4191 893278.8786 761222.5601 1.754922748 1.295527136 1.471507496 1.614520437 1.570098158 1.262083765 1.288786579 1.17347925 1 19.53795879 1.478296988 0.99330682 1.023039141 1.498654434 0.658910377 0.13152902 0.328713205 0.64347472 0.11922286 0.043847605 30.08132685 -1.478296988 0.475615293 S(ph)GAQASSTPLSPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGAQASSTPLSPTR 14 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 S(0.999)GAQASSTPLSPTR 196.52 2.59E-08 330710000 180880 128940 152090 162010 156810 107020 181510 128040 147310 TRUE FALSE 169559.0437 138486.8518 155697.6466 166167.4509 144494.7751 137914.9367 154294.2606 144026.0759 122723.0093 1.381640204 1.128450586 1.268691564 1.354004044 1.177405736 1.123790375 1.257256169 1.173586572 1 16.90504624 -4.96684249 0.1932954 2.31E-16 1.268303502 0.481857422 0.081852982 126.8348521 1.261298703 48.68561909 0.205225578 1.08E-05 4.96684249 1.268303502 S(ph)GASEANLIVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGASEANLIVAK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 S(1)GASEANLIVAK 159.22 7.48E-05 109320000 116900 101390 91562 90956 114010 48893 165180 86055 200220 TRUE FALSE 109583.4377 108897.0211 93733.89388 93290.08495 105056.1145 63007.61539 140412.7925 96799.15618 166801.9885 0.656967214 0.652852056 0.561947101 0.559286408 0.629825312 0.377738994 0.841793277 0.580323754 1 17.34777696 0.335428429 0.782551517 1.003983309 0.595236149 0.53365824 0.114879947 1.781510135 1.478865662 0.12319243 0.035806384 2.164853087 -0.335428429 -0.408747161 S(ph)GCCDDSALAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGCCDDSALAR 11 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 S(1)GCCDDSALAR 103.46 0.0028648 107410000 34292 40532 32779 35572 45938 24150 49625 29089 52800 TRUE FALSE 32145.72493 43533.03145 33556.53336 36484.83774 42330.21478 31121.71296 42184.19195 32720.82568 43987.3389 0.730794945 0.989671859 0.762868002 0.829439531 0.962327248 0.707515247 0.959007592 0.743869179 1 15.4248007 -1.914624256 2.553680743 1.091347676 0.849018306 0.187894525 0.104126741 21848396.85 11818544.95 11949481.05 0.022791656 0.012172387 1.914624256 -0.24232937 S(ph)GDEEFKGEDELCDSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGDEEFKGEDELCDSGR 17 1 O43823;M0QYL4 O43823 AKAP8 A-kinase anchor protein 8 1 S(1)GDEEFKGEDELCDSGR 168.75 1.25E-09 319660000 415690 132040 234180 195770 159710 183900 319560 148940 152690 TRUE FALSE 389672.7049 141816.379 239734.8602 200793.7896 147167.0208 236988.9446 271644.9446 167535.4869 127205.0526 3.063342981 1.114864356 1.88463316 1.578504828 1.156927479 1.863046631 2.135488639 1.317050569 1 16.95679645 4.750230345 24.55031228 1.5854088 3.06334412 0.620206464 0.378444429 992.7814988 2088524.215 0.08857481 1.416984483 56263.96634 -4.750230345 1.47793532 S(ph)GDETPGSEVPGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGDETPGSEVPGDK 14 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.925)GDET(0.075)PGSEVPGDK;S(0.98)GDET(0.02)PGSEVPGDK 263.98 1.24E-24 1335320000 2383800 1028250 1603870 1398050 1238380 1352600 2126230 1144940 997550 TRUE FALSE 2234602.213 1104382.7 1641914.554 1433926.33 1141122.63 1743073.662 1807421.55 1287888.279 831052.4606 2.688882254 1.328896492 1.975705063 1.725434191 1.373105411 2.097429158 2.174858551 1.549707558 1 19.66458003 0.987122072 19.28034405 0.999999975 1.859949956 0.352972068 0.393449373 36.27681186 54314.55485 0.353350569 0.08833827 9.707827986 -0.987122072 0.859949981 S(ph)GEGEVSGLMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SGEGEVSGLMR 11 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 S(1)GEGEVSGLMR;S(1)GEGEVSGLMR;S(1)GEGEVSGLMR;S(1)GEGEVSGLMR 261.72 1.11E-20 3480460000 638383 543271 572909 553412 531287 385256 495167 409836 584325 TRUE FALSE 598427.7476 583495.3501 586498.672 567613.4888 489561.8621 496473.1531 420921.3053 461004.9268 486797.3826 1.229315869 1.1986411 1.204810652 1.166015901 1.005678912 1.019876381 0.864674545 0.947016034 1 18.89296189 2.628485565 1.488658947 0.931333852 1.211879099 0.889102116 0.041259052 0.105658962 0.473088444 0.017025568 0.014886301 425.0945775 -2.628485565 0.280545247 S(ph)GGDGGDEVEGSGVGAGEGETVQHFPLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SGGDGGDEVEGSGVGAGEGETVQHFPLAR 29 0 Q96DT7-3;Q96DT7-2;Q96DT7 Q96DT7-3 ZBTB10 Zinc finger and BTB domain-containing protein 10 1 S(1)GGDGGDEVEGSGVGAGEGETVQHFPLAR;S(1)GGDGGDEVEGSGVGAGEGETVQHFPLAR;S(1)GGDGGDEVEGSGVGAGEGETVQHFPLAR 313.49 2.58E-92 994270000 236286 186669 178965 181470 158049 133454 223677 157488 123325 TRUE FALSE 221497.281 200490.167 183210.1343 186126.8274 145636.4691 171980.0034 190138.7104 177150.7235 102741.2608 2.155874664 1.951408475 1.783218669 1.811607391 1.417507124 1.673913694 1.850655802 1.724241284 1 16.64865616 -2.119089287 0.143971797 1.80E-20 2.148810322 0.73499454 0.161305048 28.86081638 0.576837497 11.54011476 1.166527602 0.0076017 2.119089287 2.148810322 S(ph)GGGAGSNGSVLDPAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGGGAGSNGSVLDPAER 17 0 Q15149-3;Q15149-2;H0YDN1;E9PMV1 Q15149-3 PLEC Plectin 1 S(1)GGGAGSNGSVLDPAER;S(1)GGGAGSNGSVLDPAER 255.08 4.91E-27 279490000 354526 335204 365215 330466 375094 297181 418510 312968 343350 TRUE FALSE 332336.8505 360022.8529 373878.0723 338946.317 345635.6303 382972.3304 355758.3108 352042.7437 286042.6669 1.16184363 1.258633395 1.307070992 1.184950206 1.208335924 1.338864354 1.243724633 1.230735077 1 18.12587083 0.63779249 2.755857115 1.000010122 1.251984173 0.671704584 0.052926676 2.202447282 16.08132028 0.048702981 0.01284861 4.343026607 -0.63779249 0.25197405 S(ph)GGGDLTLGLEPSEEEAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SGGGDLTLGLEPSEEEAPR 19 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 S(1)GGGDLTLGLEPSEEEAPR;S(0.997)GGGDLT(0.003)LGLEPSEEEAPR;S(1)GGGDLTLGLEPSEEEAPR;S(1)GGGDLTLGLEPSEEEAPR;S(1)GGGDLTLGLEPSEEEAPR;S(0.998)GGGDLT(0.002)LGLEPSEEEAPR;S(1)GGGDLTLGLEPSEEEAPR 454.58 1.07E-191 3789493000 1840084 1790324 1307393 1253836 1960296 1384709 2017607 1818229 1451988 TRUE FALSE 1724916.427 1922881.452 1338404.979 1286011.554 1806342.26 1784452.009 1715085.561 2045238.893 1209641.823 1.425972875 1.589628778 1.106447342 1.06313417 1.493286877 1.475190404 1.417845786 1.690780572 1 20.2061485 S(ph)GGNEVSIEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGGNEVSIEER 11 0 Q15061 Q15061 WDR43 WD repeat-containing protein 43 1 S(1)GGNEVSIEER 134.02 0.0001568 166930000 77330 124990 123630 110860 152880 121770 127120 107700 113170 TRUE FALSE 72490.05334 134244.3897 126562.562 113704.8553 140873.4215 156923.0222 108059.5361 121146.5821 94281.19589 0.768870745 1.423872368 1.342394534 1.206018382 1.494183651 1.664414847 1.146140915 1.28494957 1 16.52468244 0.769582261 1.563452841 1.00297566 1.326514885 0.119853484 0.237613067 1.500924379 6.283536539 0.208572775 0.060313685 5.882775316 -0.769582261 0.323539225 S(ph)GHHPGETPPLITPGSAQS ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGHHPGETPPLITPGSAQS 19 0 S4R445;Q14802;Q14802-2;Q14802-3 S4R445 FXYD3 FXYD domain-containing ion transport regulator 3 1 S(0.5)GHHPGET(0.5)PPLITPGSAQS 102.08 0.00025712 441520000 260340 291810 269590 255330 310760 214020 274710 301410 345180 TRUE FALSE 244045.7841 313415.916 275984.8021 261882.2001 286354.1631 275804.0997 233519.7858 339041.702 287567.2281 0.848656454 1.089887461 0.959722719 0.910681658 0.99578163 0.959094336 0.812052845 1.178999792 1 18.13353975 1.225491968 24.99998427 1.089499817 0.951238921 0.330813779 0.087497625 334.8538432 640547.6346 0.081217621 0.020808356 16.80706842 -1.225491968 -0.138260895 S(ph)GLLSSFSLSMTDLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGLLSSFSLSMTDLSK 16 0 Q96L93-5;Q96L93-6;Q96L93-4;Q96L93;Q96L93-2;A0A1B0GTU3 Q96L93-5 KIF16B Kinesin-like protein KIF16B 1 S(0.995)GLLS(0.003)S(0.003)FSLSMTDLSK 281.99 1.90E-28 0 88854 79452 79374 77689 97536 64290 82767 69748 96486 TRUE FALSE 83292.78675 85334.70875 81256.78876 79682.63127 89875.916 82849.47934 70356.85672 78456.19133 80381.86328 1.036213685 1.061616455 1.010884613 0.991301122 1.118111877 1.030698667 0.87528273 0.976043452 1 16.2945824 1.870014255 8.052996545 0.939097144 1.041976261 0.462811728 0.045842426 0.210419502 12.74258887 0.018177715 0.011364131 74.13345741 -1.870014255 0.102879117 S(ph)GMSPEQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGMSPEQSR 9 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.886)GMS(0.114)PEQSR 146.9 0.00036622 3436100000 1761800 1730400 1713600 1642900 1783900 1442600 2052300 1441900 1711600 TRUE FALSE 1651532.083 1858520.616 1754247.401 1685059.595 1643799.69 1859055.201 1744576.668 1621924.389 1425922.903 1.158219761 1.303380858 1.230254033 1.181732611 1.152797032 1.303755763 1.223471945 1.137455879 1 20.44346455 0.954716615 2.677201747 1.000686471 1.231072566 0.649602958 0.052137269 0.176140314 2.950621465 0.048571584 0.012964583 9.009830377 -0.954716615 0.230386094 S(ph)GNSDSIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.999)GNS(0.001)DSIER;S(0.999)GNS(0.001)DSIER;S(0.985)GNS(0.015)DSIER 169.57 6.12E-05 954900000 1095270 852810 968710 829470 827360 678530 948680 701450 752540 TRUE FALSE 1026719.006 915952.9397 991688.2587 850755.6045 762382.483 874410.596 806434.2411 789027.5766 626936.2124 1.637676985 1.460998618 1.58180089 1.357005047 1.216044739 1.394736145 1.286309875 1.258545225 1 19.25795914 7.999998878 0.048273012 0.15813685 3.59422309 0.815350728 0.078912395 209.0688454 0.762736247 13.11470466 54.22443934 99999741.74 -7.999998878 3.43608624 S(ph)GS(ph)IKGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSIKGSR 8 1 Q16629;Q16629-4;C9JAB2;H7BZZ6;H7C1N1 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 2 S(1)GS(1)IKGSR 93.614 0.006227 941340000 2464900 1112300 1500300 1552900 1781500 1009900 1878900 1155900 2242700 TRUE FALSE 2310626.309 1194655.849 1535887.824 1592750.043 1641588.176 1301441.736 1597176.388 1300216.659 1868378.882 1.236701149 0.639407703 0.822043023 0.85247701 0.878616319 0.696562003 0.854846093 0.695906313 1 20.83335561 S(ph)GSDAGEARPPTPASPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSDAGEARPPTPASPR 17 1 Q96FS4;F6RY50;E9PIB3 Q96FS4 SIPA1 Signal-induced proliferation-associated protein 1 1 S(0.595)GS(0.405)DAGEARPPTPASPR 73.21 0.016202 388360000 217080 177630 179110 182830 186720 144280 191530 189370 269820 TRUE FALSE 203493.3503 190781.91 183358.5738 187521.7273 172055.7644 185931.2938 162811.8546 213013.2614 224785.2989 0.905278732 0.848729481 0.815705363 0.83422594 0.765422673 0.827150595 0.724299389 0.94762986 1 17.77818816 -1.447760409 4.763287496 1.000413059 0.823604267 0.397541488 0.063349724 0.000258216 2.99E-05 0.056996559 0.01340311 0.035664783 1.447760409 -0.176808792 S(ph)GSFRDPTDDVHGSVLSLASSASSTYSSAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSFRDPTDDVHGSVLSLASSASSTYSSAEER 32 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1 Q8NEY1-5 NAV1 Neuron navigator 1 1 S(0.332)GS(0.332)FRDPT(0.332)DDVHGS(0.001)VLS(0.002)LASSASSTYSSAEER 125.47 8.12E-08 121920000 60177 118570 121500 121420 115430 98828 147730 111420 117540 TRUE FALSE 56410.62899 127349.0462 124382.0374 124535.8428 106364.5934 127358.0393 125579.258 125331.0323 97921.81466 0.576078264 1.300517628 1.270217855 1.271788551 1.08621959 1.300609468 1.282444146 1.279909208 1 16.57934267 4.741498717 24.99245061 1.244171797 0.576078022 0.795440916 0.102800706 106.3336709 904463.359 0.021728041 0.153056115 55144.05733 -4.741498717 -0.668093776 S(ph)GSGCQVSGSPLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGSGCQVSGSPLAK 14 0 Q3C1V9 Q3C1V9 Putative uncharacterized protein ENSP00000334305 1 S(0.25)GS(0.25)GCQVS(0.25)GS(0.25)PLAK;S(0.25)GS(0.25)GCQVS(0.25)GS(0.25)PLAK 61.375 0.055065 464410000 140850 902980 641960 714450 762370 889890 442720 619580 344030 TRUE FALSE 132034.4499 969837.5787 657187.5944 732783.9966 702496.5355 1146786.797 376338.246 696935.9269 286609.1705 0.460677688 3.383833033 2.292974762 2.556736043 2.451060914 4.001221576 1.313071195 2.431659551 1 18.12872525 1.618616526 25 1.654273887 2.599776083 0.170234386 0.967335499 1.220768672 2831.753976 0.406114871 0.222338244 41.55435307 -1.618616526 0.945502197 S(ph)GSMDPSGAHPSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SGSMDPSGAHPSVR 14 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 1 S(0.404)GS(0.313)MDPS(0.28)GAHPS(0.003)VR;S(0.5)GS(0.5)MDPSGAHPSVR;S(0.5)GS(0.5)MDPSGAHPSVR;S(0.5)GS(0.5)MDPSGAHPSVR 130.87 0.00019948 2784450000 2056900 2531890 2516680 2764660 3173080 2161330 3288680 2617260 3354920 TRUE FALSE 1928162.301 2719353.77 2576376.838 2835605.856 2923879.096 2785270.885 2795572.965 2944030.672 2794962.178 0.689870624 0.972948325 0.921793095 1.014541763 1.046124745 0.996532585 1.000218531 1.053334709 1 21.41439733 5.278272386 1.298864006 1.002513929 2.02E-18 0.861833404 0.038770322 1.813454188 1.007770085 0.010951224 3.400516585 189789.5894 -5.278272386 -1.002513929 S(ph)GSPRPTEPTDFLMLFEGSPSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGSPRPTEPTDFLMLFEGSPSGK 23 1 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 S(0.492)GS(0.492)PRPT(0.008)EPT(0.008)DFLMLFEGSPSGK;S(0.5)GS(0.5)PRPTEPTDFLMLFEGSPSGK 170.11 4.67E-12 88044000 141133 97410 119176 104752 118235 83477 147246 101983 160499 TRUE FALSE 132299.7375 104622.3378 122002.911 107440.1137 108949.3 107575.4548 125167.8293 114715.802 133710.68 0.989447794 0.782453112 0.912439537 0.803526791 0.814813746 0.804538985 0.936109436 0.857940458 1 17.02875518 0.618907483 0.916328882 0.998948525 0.851836451 0.289780269 0.066674725 1.455954886 2.033949266 0.058692318 0.019292043 4.158220189 -0.618907483 -0.147112074 S(ph)GSRDSTPSRPAQQPLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSRDSTPSRPAQQPLSR 18 2 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 S(0.385)GS(0.385)RDS(0.164)T(0.053)PS(0.012)RPAQQPLSR 52.202 0.070028 25641000 31727 68184 63277 69891 60926 52618 71021 63200 48382 TRUE FALSE 29741.2637 73232.41431 64777.96032 71684.52139 56141.11772 67807.96242 60372.06038 71090.65912 40306.73164 0.737873365 1.816878008 1.607125105 1.778475169 1.392847186 1.682298704 1.497815822 1.763741594 1 15.29873318 -0.86016376 6.394549099 0.999999971 1.57062456 0.21585663 0.313638272 1.19E-07 1.98E-08 0.265547406 0.062590121 0.137986386 0.86016376 0.570624589 S(ph)GSSS(ph)PDSEITELKFPSINHD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 2 S(0.766)GS(0.093)S(0.151)S(0.99)PDS(0.001)EITELKFPSINHD 184.4 2.26E-17 767910000 303700 212720 256800 246690 231960 218690 324830 232290 323050 TRUE FALSE 284691.9591 228470.0101 262891.4173 253020.483 213742.7973 281822.2529 276124.7571 261291.9178 269130.868 1.057819793 0.848917896 0.976816295 0.940139215 0.794196514 1.047156928 1.025986945 0.970873091 1 18.03794835 S(ph)GSTESLNPRPQTTISPADLHGMWYPTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SGSTESLNPRPQTTISPADLHGMWYPTVR 29 1 Q96JB2 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 1 S(0.489)GS(0.489)T(0.018)ES(0.001)LNPRPQT(0.002)T(0.002)ISPADLHGMWYPTVR;S(0.53)GS(0.451)T(0.016)ES(0.001)LNPRPQT(0.001)T(0.001)ISPADLHGMWYPTVR;S(0.488)GS(0.488)T(0.023)ESLNPRPQTTISPADLHGMWYPTVR 152.87 1.52E-08 329280000 142631 153948 151214 151054 167383 117386 189309 111742 167830 TRUE FALSE 133703.9803 165346.4701 154800.8675 154930.3014 154237.4144 151273.4326 160923.8729 125693.2347 139818.0888 0.956270977 1.182582823 1.107159087 1.108084817 1.103129185 1.081930342 1.150951742 0.898976919 1 17.09319149 1.240504765 24.99999981 0.94948843 1.109377811 0.481014141 0.063622965 34.93837951 449327.0489 0.042597 0.0137879 17.39821787 -1.240504765 0.159889381 S(ph)GTFDLLEMDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGTFDLLEMDR 11 0 H0YA26;E9PHT6;Q9NVE7;H0YA31 H0YA26 PANK4 Pantothenate kinase 4 1 S(0.682)GT(0.318)FDLLEMDR 100.19 0.0025958 0 20800 20152 17899 19801 23923 21660 31321 18452 24629 TRUE FALSE 19498.16513 21644.07505 18323.57273 20309.12718 22044.18408 27912.89038 26624.70682 20755.77282 20518.26079 0.950283522 1.054868893 0.893037325 0.98980744 1.074369037 1.360392611 1.297610314 1.011575641 1 14.32462083 2.461256453 6.196525333 1.211318691 0.977743928 0.347534732 0.11943767 0.137057599 20.05018462 0.0394184 0.033734773 289.2387346 -2.461256453 -0.233574763 S(ph)GTPTQDEMMDKPTSSSVDTMSLLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGTPTQDEMMDKPTSSSVDTMSLLSK 26 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 S(0.5)GT(0.5)PTQDEMMDKPTSSSVDTMSLLSK;S(0.492)GT(0.492)PT(0.016)QDEMMDKPTSSSVDTMSLLSK 147.5 1.15E-07 680100000 742940 305356 464730 399330 443910 311158 676270 432510 773410 TRUE FALSE 696440.7116 327964.876 475753.6151 409577.4839 409047.0992 400984.2634 574869.5917 486509.8256 644322.8746 1.080887765 0.509007035 0.738377658 0.635671183 0.634848017 0.622334359 0.89220733 0.755071479 1 19.29742429 1.11911093 1.018856654 0.983603036 0.683752022 0.208876385 0.160079236 0.644064957 1.431597144 0.135532742 0.045481884 13.15560817 -1.11911093 -0.299851013 S(ph)HDRLPYQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SHDRLPYQR 9 1 H3BUL5;H3BVF8;P49761-3;P49761-1;P49761;H3BRT8;H3BQR7;H3BV35;H3BRK0;P49761-2 H3BUL5 CLK3 Dual specificity protein kinase CLK3 1 S(1)HDRLPYQR;S(1)HDRLPYQR 117.98 0.0018745 112770000 86428 87583 98238 92785 97728 93396 130740 90406 83716 TRUE FALSE 81018.62576 94067.73645 100568.2518 95166.02018 90052.8371 120357.909 111136.7507 101693.3881 69743.25877 1.161669632 1.348771739 1.4419781 1.364519265 1.291204895 1.725728209 1.593512444 1.458110646 1 16.08976616 5.915516671 0.657141306 1.467453357 3.50E-09 0.094795779 0.19449117 22.07343409 2.205485581 0.072191736 34.49810944 823221.4362 -5.915516671 -1.467453354 S(ph)HGLESVPVLPGSGEAGVSFDLPAQADTLHSANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHGLESVPVLPGSGEAGVSFDLPAQADTLHSANK 34 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 S(0.613)HGLES(0.387)VPVLPGSGEAGVSFDLPAQADTLHSANK 218.01 6.18E-36 107610000 115510 91042 104300 94464 117790 102510 150390 102000 231840 TRUE FALSE 108280.4353 97782.84441 106774.0453 96888.10617 108539.2485 132102.9729 127840.4157 114734.9245 193144.4063 0.560619059 0.506268063 0.552819765 0.50163558 0.561959058 0.683959611 0.661890334 0.594037005 1 17.55932037 -2.641783762 0.203009626 1.694813269 0.482333382 0.899768329 0.045886768 13.28720565 0.312012415 4.164851313 0.115223895 0.002281478 2.641783762 -1.212479887 S(ph)HHAASTTTAPTPAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SHHAASTTTAPTPAAR 16 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 S(0.999)HHAAS(0.001)TTTAPTPAAR;S(1)HHAASTTTAPTPAAR;S(1)HHAASTTTAPTPAAR;S(0.998)HHAAS(0.002)TTTAPTPAAR 131.37 2.89E-05 714688000 221608 284043 256053 266510 296958 215032 304846 234809 331059 TRUE FALSE 207737.9509 305073.8393 262126.6981 273349.0978 273636.1166 277108.2476 259137.1724 264125.4205 275803.1142 0.753211041 1.106129059 0.950412394 0.991102289 0.992142954 1.00473212 0.939573047 0.957659312 1 18.07327922 4.756722441 24.88425042 0.992000729 0.753210825 0.72945798 0.0458376 2146.137276 2940459.238 0.011173302 0.375492252 57111.35199 -4.756722441 -0.238789904 S(ph)HHAPMSPGSSGGGGQPLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHHAPMSPGSSGGGGQPLAR 20 0 O14497;O14497-2 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 S(0.521)HHAPMS(0.411)PGS(0.068)SGGGGQPLAR 111.77 0.00018593 498790000 163370 139110 165040 179860 163460 138200 202010 147220 167820 TRUE FALSE 153144.9633 149409.8491 168954.8267 184475.5121 150622.511 178096.0965 171720.4759 165600.7411 139809.7578 1.095381078 1.068665388 1.208462337 1.319475228 1.077339045 1.273845969 1.228243855 1.184471983 1 17.09310553 3.953165733 3.352998231 1.201685299 1.083469896 0.155764044 0.092350926 0.321364074 7.477221689 0.021429499 0.045883522 8977.713311 -3.953165733 -0.118215402 S(ph)HS(ph)GTSPDNTAPPPPPPRPQPSHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHSGTSPDNTAPPPPPPRPQPSHSR 25 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 2 S(0.467)HS(0.533)GT(0.533)S(0.467)PDNTAPPPPPPRPQPSHSR 76.765 0.038571 215810000 26152 22850 27941 34455 40018 21243 22025 17725 28101 TRUE FALSE 24515.193 24541.83778 28603.77371 35339.17363 36875.1477 27375.50925 18722.55572 19938.00527 23410.76156 1.047176229 1.048314371 1.221821582 1.50952687 1.575136614 1.169355776 0.799741421 0.851659832 1 14.51488425 1.84267482 4.989787832 0.870900802 1.259322833 0.511919313 0.175637635 0.20437876 7.380116235 0.090720734 0.052262085 69.61051065 -1.84267482 0.388422031 S(ph)HSDNDRFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHSDNDRFK 9 1 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.989)HS(0.011)DNDRFK 77.593 0.019478 236180000 187530 164880 175630 167730 196320 124140 207870 140470 276490 TRUE FALSE 175792.8321 177087.8868 179796.0265 172034.2358 180901.8191 159977.2028 176701.8233 158007.9887 230342.0328 0.763181734 0.768804046 0.780561083 0.746864277 0.785361738 0.694520235 0.767128001 0.685971148 1 17.81341817 -1.076595186 5.823095212 1.000001036 0.753252738 0.843922 0.033873648 4.18E-07 6.62E-08 0.030078369 0.00708951 0.083831032 1.076595186 -0.246748298 S(ph)HSDNDRPNCSWNTQYSSAYYTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SHSDNDRPNCSWNTQYSSAYYTSR 24 1 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.813)HS(0.187)DNDRPNCSWNTQYSSAYYTSR;S(0.405)HS(0.405)DNDRPNCS(0.189)WNTQYSSAYYTSR;S(0.825)HS(0.175)DNDRPNCSWNTQYSSAYYTSR;S(0.599)HS(0.397)DNDRPNCS(0.004)WNTQYSSAYYTSR;S(0.33)HS(0.33)DNDRPNCS(0.33)WNT(0.011)QYSSAYYTSR;S(0.331)HS(0.331)DNDRPNCS(0.331)WNT(0.007)QYSSAYYTSR 310.9 1.12E-73 6265500000 719900 716472 778067 695594 792784 677291 921187 717899 902789 TRUE FALSE 674842.7441 769520.3324 796523.1167 713444.1197 730521.9426 872813.9168 783063.5612 807530.2704 752107.6837 0.89726878 1.023151803 1.059054619 0.948593047 0.971299667 1.160490626 1.041158837 1.073689696 1 19.52057971 2.280873945 24.99999194 1.072083318 0.9951507 0.344549284 0.058836815 177.5110646 104878.1384 0.019815802 0.016578963 190.9298998 -2.280873945 -0.076932618 S(ph)HSGTSPDNTAPPPPPPRPQPSHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SHSGTSPDNTAPPPPPPRPQPSHSR 25 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.308)HS(0.258)GT(0.217)S(0.217)PDNTAPPPPPPRPQPSHSR;S(0.249)HS(0.249)GT(0.249)S(0.249)PDNT(0.005)APPPPPPRPQPSHSR 139.16 1.25E-06 1315160000 52127.9 51282.1 49481 49507.1 54951.8 56094.1 81435.6 70814.6 91181.4 TRUE FALSE 48865.30779 55079.08004 50654.71269 50777.536 50636.10729 72287.55606 69225.08779 79655.95869 75962.63529 0.643280839 0.725081217 0.666837222 0.668454113 0.666592294 0.951619909 0.911304453 1.048620264 1 16.21300234 2.229528083 9.04551887 0.963861901 0.679655348 0.930545893 0.041152807 0.035894431 24.87236974 0.01454158 0.011181751 169.6399295 -2.229528083 -0.284206552 S(ph)HSLAQPPEFDSGVETFSIHAEKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHSLAQPPEFDSGVETFSIHAEKPK 25 1 A0A087X0K9;G5E9E7;Q07157-2;H0Y3R8;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 S(0.5)HS(0.5)LAQPPEFDS(0.001)GVETFSIHAEKPK 49.902 0.084881 104590000 43601 53019 44336 51856 55781 32689 65403 47686 72406 TRUE FALSE 40872.09124 56944.58193 45387.67086 53186.71275 51400.18527 42125.78364 55596.42732 53639.70207 60320.97084 0.677576814 0.944026284 0.752436014 0.881728394 0.852111373 0.698360505 0.9216766 0.889238043 1 15.88037203 1.144899197 1.553961788 0.991078301 0.819055276 0.339016434 0.08619105 0.415640884 1.94131009 0.072691391 0.021663585 13.96044292 -1.144899197 -0.172023025 S(ph)HSQASLAGPGPVDPSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SHSQASLAGPGPVDPSNR 18 0 Q9P2M7;Q9P2M7-2;A6PVU7;A2A3M4 Q9P2M7 CGN Cingulin 1 S(0.558)HS(0.438)QAS(0.004)LAGPGPVDPSNR;S(0.453)HS(0.355)QAS(0.192)LAGPGPVDPSNR;S(0.559)HS(0.434)QAS(0.007)LAGPGPVDPSNR;S(0.522)HS(0.418)QAS(0.059)LAGPGPVDPSNR 132.36 9.63E-06 2281530000 606673 657973 614554 625740 713023 539434 909670 636955 1546120 TRUE FALSE 568702.4199 706690.0055 629131.5111 641797.5478 657025.0498 695159.8388 773273.4285 716480.2339 1288062.584 0.441517693 0.548645706 0.488432409 0.498265811 0.510087831 0.539694148 0.600338398 0.556246446 1 20.29677126 -3.131392826 0.274230808 2.054858984 0.483416841 0.959677977 0.03132115 11.96105198 0.292249279 7.242462207 0.036853561 0.000738937 3.131392826 -1.571442143 S(ph)HSSPASLQLGTGAGAAGSPAQQHAHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SHSSPASLQLGTGAGAAGSPAQQHAHLR 28 0 C9JR84;C9J038;Q9GZV5 C9JR84 WWTR1 WW domain-containing transcription regulator protein 1 1 S(0.801)HS(0.148)S(0.051)PASLQLGTGAGAAGSPAQQHAHLR;S(0.518)HS(0.404)S(0.078)PASLQLGTGAGAAGSPAQQHAHLR 206.11 4.36E-25 1271910000 149762 199996 192990 201556 242142 165945 255730 198129 242090 TRUE FALSE 140388.6638 214803.9119 197567.8139 206728.2682 223125.1441 213850.6276 217385.6606 222865.8418 201683.615 0.696083634 1.065053856 0.979592784 1.025012707 1.106312697 1.060327224 1.07785484 1.105027008 1 17.62173436 4.739911662 24.97878062 1.051261262 0.696083518 0.88022998 0.041303939 39.01067136 721173.0272 0.010172894 0.063923213 54942.91051 -4.739911662 -0.355177745 S(ph)HSVGGPLQNIDFTQRPFHGISTVSLPNSLQEVVDPLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SHSVGGPLQNIDFTQRPFHGISTVSLPNSLQEVVDPLGK 39 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.545)HS(0.455)VGGPLQNIDFTQRPFHGISTVSLPNSLQEVVDPLGK;S(0.499)HS(0.499)VGGPLQNIDFT(0.001)QRPFHGISTVSLPNSLQEVVDPLGK 192.27 2.13E-24 772820000 463290 469620 389020 419250 561980 293994 766100 474120 560060 TRUE FALSE 434293.5059 504391.1534 398247.7381 430008.6648 517844.3577 378865.2952 651230.4171 533314.9257 466582.3679 0.930797081 1.081033464 0.853542194 0.921613619 1.109866967 0.812000884 1.395745879 1.143024174 1 18.83177226 1.743596122 25 1.211602932 0.960067198 0.391840676 0.131684369 0.799790213 3986.873129 0.054474902 0.030209168 55.41101713 -1.743596122 -0.251535735 S(ph)HTSEGAHLDITPNSGAAGNSAGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SHTSEGAHLDITPNSGAAGNSAGPK 25 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 S(0.359)HT(0.359)S(0.281)EGAHLDIT(0.002)PNSGAAGNSAGPK;S(0.333)HT(0.333)S(0.333)EGAHLDITPNSGAAGNSAGPK 200.52 1.11E-24 1467200000 551080 820740 626030 908180 1027580 542590 1277470 774200 698100 TRUE FALSE 516588.8865 881508.4436 640879.7272 931485.4363 946878.0119 699226.9248 1085925.233 870860.5742 581582.6001 0.888246805 1.515706356 1.101958221 1.601639107 1.628105813 1.202283089 1.867190031 1.497397917 1 19.14962458 3.232217833 24.99547732 1.522243352 1.23348354 0.166449553 0.284481185 229.786947 905538.0613 0.074468245 0.091061757 1706.938339 -3.232217833 -0.288759812 S(ph)HWIFEARK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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;S(1)HWIFEARK;S(1)HWIFEARK 80.787 0.024493 3254480000 2637590 6528420 5575260 5478380 5576310 6165040 5558990 5639840 5030710 TRUE FALSE 2472507.95 7011791.01 5707507.8 5618964.506 5138369.106 7944786.967 4725471.057 6343986.439 4191052.001 0.589949242 1.673038418 1.361831778 1.340705032 1.22603325 1.895654591 1.127514298 1.513697858 1 21.99888099 -1.380736157 5.358138787 0.999819475 1.37552472 0.079943466 0.346494654 0.000651102 7.53E-05 0.292335923 0.068871475 0.041616336 1.380736157 0.375705244 S(ph)IDQDYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SIDQDYER 8 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 S(1)IDQDYER;S(1)IDQDYER;S(1)IDQDYER;S(1)IDQDYER 156.58 0.00040977 3993740000 3794480 3789300 3709910 3491250 4090740 3105460 4426940 3774720 3757550 TRUE FALSE 3556990.27 4069863.715 3797910.817 3580841.386 3769469.782 4001955.889 3763161.445 4246002.101 3130390.63 1.136276807 1.30011369 1.213238623 1.143896021 1.204153164 1.278420607 1.202137972 1.356380913 1 21.57791127 -1.268521917 4.183775872 0.999798991 1.230970427 0.531582031 0.067637783 4762789.494 1444087.073 8733.894723 0.014399335 0.053886265 1.268521917 0.231171436 S(ph)IEALLEAGQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SIEALLEAGQAR 12 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 S(1)IEALLEAGQAR;S(1)IEALLEAGQAR;S(1)IEALLEAGQAR;S(1)IEALLEAGQAR;S(1)IEALLEAGQAR 140.33 6.25E-05 85281000 90527.8 76835 73221 76987 77885 67173.6 95084.8 74722 65612 TRUE FALSE 84861.82659 82523.94335 74957.8367 78962.61676 71768.22627 86565.52785 80827.71696 84051.20618 54660.93333 1.552513311 1.509742668 1.371323761 1.444589617 1.312971109 1.583681847 1.478710883 1.537683334 1 15.73822247 -1.768606697 2.819971012 0.89584401 1.467964156 0.765199726 0.082441511 6913000.264 6199529.024 5010641.289 0.019570219 0.017037007 1.768606697 0.572120146 S(ph)IEEGDGAFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SIEEGDGAFGR 11 0 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 S(1)IEEGDGAFGR 69.864 0.055949 168110000 62672 63903 55633 56532 47515 38032 50050 47763 51763 TRUE FALSE 58749.47139 68634.44461 56952.64103 57982.70683 43783.36357 49011.221 42545.46714 53726.31569 43123.4209 1.362356468 1.591581632 1.320689311 1.344575769 1.015303579 1.136533697 0.986597683 1.24587323 1 15.39618401 3.062708368 1.432883026 1.068484693 1.475267553 0.708200813 0.104427521 0.181340899 0.769981521 0.034832858 0.044283666 1155.336164 -3.062708368 0.40678286 S(ph)IEVENDFLPVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SIEVENDFLPVEK 13 0 Q5JPT1;Q5VSN0;Q5JPT2;Q96B97-2;Q96B97 Q5JPT1 SH3KBP1 SH3 domain-containing kinase-binding protein 1 1 S(1)IEVENDFLPVEK;S(1)IEVENDFLPVEK;S(1)IEVENDFLPVEK;S(1)IEVENDFLPVEK 250.17 1.01E-17 100112000 260095 221022 202927 278541 288771 215712 277437 237623 223205 TRUE FALSE 243816.1182 237386.6989 207740.5243 285688.8336 266092.0905 277984.5526 235837.8974 267290.7546 185950.6435 1.311187278 1.276611333 1.117180991 1.536369158 1.430982359 1.494937298 1.268282233 1.4374285 1 17.50456022 3.249642937 24.99343211 1.379458767 1.227081087 0.118258513 0.157029981 347.1393562 782882.2778 0.039368628 0.052818984 1776.817966 -3.249642937 -0.152377679 S(ph)IGSAVDQGNESIVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SIGSAVDQGNESIVAK 16 0 Q9H0H5;F8VRD2;F8W1E5 Q9H0H5 RACGAP1 Rac GTPase-activating protein 1 1 S(0.918)IGS(0.082)AVDQGNESIVAK;S(1)IGSAVDQGNESIVAK;S(0.999)IGS(0.001)AVDQGNESIVAK 336.32 9.86E-72 401450000 1026500 822990 929460 853820 1086990 710280 1180940 820580 1134530 TRUE FALSE 962253.1974 883925.0359 951507.2301 875730.4667 1001622.19 915326.3056 1003869.01 923031.2193 945169.6137 1.018074622 0.935202553 1.006705269 0.926532608 1.059727456 0.968425447 1.062104617 0.976577332 1 19.85021372 2.736828756 24.99641123 1.017133569 0.971403813 0.203260323 0.040682782 206.3733601 2978632.818 0.011309101 0.01118149 545.5427088 -2.736828756 -0.045729755 S(ph)IHEVDISNLEAALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SIHEVDISNLEAALR 15 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR 318.9 1.17E-56 2052987000 732776 864571 738926 775618 881522 554437 981640 770880 750823 TRUE FALSE 686912.8582 928584.7364 756453.6737 795521.671 812290.818 714493.9614 834452.1951 867126.0649 625505.7908 1.098171861 1.484534196 1.209347195 1.271805446 1.298614385 1.142265942 1.334043917 1.386279836 1 19.25466372 -1.273405126 4.134782284 0.999714632 1.288215585 0.372891419 0.112681161 0.000270734 4.76E-05 0.099648133 0.023464236 0.053283761 1.273405126 0.288500952 S(ph)INGSLYIFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SINGSLYIFR 10 0 Q8TCU6;Q8TCU6-3 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 1 S(1)INGSLYIFR;S(1)INGSLYIFR;S(1)INGSLYIFR 209.67 9.56E-08 190366000 145471 195468 205517 204400 189249 138334 179726 138538 266578 TRUE FALSE 136366.2298 209940.6541 210391.9603 209645.25 174386.1469 178268.7801 152777.7548 155834.7743 222084.4096 0.614028828 0.945319189 0.947351328 0.943989046 0.785224623 0.802707315 0.687926519 0.701691643 1 17.76074859 2.617282976 5.602021376 0.767716079 0.890235364 0.021555608 0.12973208 0.400894694 16.80459711 0.03984226 0.037420787 414.2695152 -2.617282976 0.122519285 S(ph)IPLSIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIPLSIK 7 0 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 S(1)IPLSIK;S(1)IPLSIK 111.06 0.0069899 156873000 630810 625890 561640 439110 684940 290530 977360 554200 1685030 TRUE FALSE 591328.7281 672231.5468 574962.366 450378.306 631147.5753 374401.2946 830813.9414 623393.0899 1403787.607 0.421238031 0.47886984 0.409579315 0.320830804 0.449603325 0.266707936 0.591837353 0.444079351 1 20.42089324 0.161179543 0.80829353 1.009786861 0.410522428 0.825119104 0.084092353 1.39668093 1.040886057 0.112593872 0.0259977 1.449370918 -0.161179543 -0.599264433 S(ph)IQDLTVTGTEPGQVSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SIQDLTVTGTEPGQVSSR 18 0 O43318;O43318-3;Q9UG54;O43318-2;O43318-4 O43318 MAP3K7;DKFZp586F0420 Mitogen-activated protein kinase kinase kinase 7 1 S(1)IQDLTVTGTEPGQVSSR;S(0.727)IQDLT(0.271)VT(0.001)GTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR;S(0.998)IQDLT(0.002)VTGTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR 381.49 1.23E-108 3547607000 1104172 1018724 1070258 1054709 1082200 892816 1211086 963083 1091566 TRUE FALSE 1035063.846 1094151.385 1095645.025 1081774.619 997208.3774 1150557.486 1029494.897 1083326.033 909376.5828 1.138212557 1.203188432 1.20483092 1.189578266 1.096584623 1.265215651 1.132088638 1.191284285 1 19.79451833 -3.879948313 0.389849247 2.10E-10 1.185078186 0.582077082 0.04703114 162.5107733 2.810440975 133.9194673 0.027048838 0.000131841 3.879948313 1.185078186 S(ph)IQEDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIQEDTK 7 0 Q8NDI1-3;Q8NDI1-2;Q8NDI1;H7BZ98 Q8NDI1-3 EHBP1 EH domain-binding protein 1 1 S(1)IQEDTK;S(1)IQEDTK 96.113 0.013605 434390000 845330 551390 636890 668420 639620 451730 826210 522930 669780 TRUE FALSE 792422.3043 592215.4893 651997.3316 685572.7888 589386.8253 582137.1178 702327.4807 588218.9616 557989.3911 1.420138657 1.06133826 1.168476215 1.228648429 1.056268873 1.043276319 1.25867533 1.054175888 1 19.08987817 S(ph)IQFVDWCPTGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIQFVDWCPTGFK 13 0 P68363;P68363-2;P68366-2;P68366 P68363;P68366-2 TUBA1B;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain 1 S(1)IQFVDWCPTGFK;S(1)IQFVDWCPTGFK 147.37 4.48E-05 459940000 3490800 3592800 2558580 2487580 3740800 1977660 4324000 3150000 7300400 TRUE FALSE 3272317.059 3858814.65 2619270.726 2551415.514 3447012.658 2548578.337 3675656.342 3543284.434 6081916.078 0.538040482 0.634473511 0.430665384 0.419508504 0.566764259 0.41904201 0.60435828 0.582593444 1 22.53609448 0.447959761 1.078955417 1.000630348 0.51066345 0.811183872 0.073257195 0.890222039 1.340977647 0.069786893 0.021524166 2.805173718 -0.447959761 -0.489966898 S(ph)IQGVGHMMSTMVLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SIQGVGHMMSTMVLSR 16 0 Q14573 Q14573 ITPR3 "Inositol 1,4,5-trisphosphate receptor type 3" 1 S(1)IQGVGHMMSTMVLSR 72.819 0.023699 10843000 9380.8 12003 10412 8355 13501 10530 14338 14348 17261 TRUE FALSE 8793.672473 12891.71461 10658.97756 8569.403445 12440.68592 13569.84006 12188.15001 16139.37938 14380.02759 0.611519861 0.896501382 0.741234847 0.595923992 0.865136443 0.943658833 0.847574869 1.1223469 1 13.81177882 1.856643545 1.077940564 1.031732143 0.751508575 0.557326704 0.10888055 0.420702049 0.901446277 0.087751932 0.03737705 71.8858719 -1.856643545 -0.280223568 S(ph)IS(ph)AAGRSQASPPKQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SISAAGRSQASPPKQAK 17 2 Q5VTL7 Q5VTL7 FNDC7 Fibronectin type III domain-containing protein 7 2 S(0.5)IS(0.5)AAGRS(0.5)QAS(0.5)PPKQAK;S(0.5)IS(0.5)AAGRS(0.5)QAS(0.5)PPKQAK 63.037 0.030557 2584200000 698160 2028780 1596160 1585050 1911090 1559080 1628400 1594840 2033420 TRUE FALSE 654463.4119 2178992.982 1634021.669 1625725.066 1761000.7 2009161.086 1384236.537 1793959.285 1694029.066 0.386335409 1.286278392 0.964577115 0.959679559 1.039533935 1.186025156 0.817126793 1.058989672 1 20.6920272 4.75272846 24.90314209 1.03599965 0.386334937 0.72194577 0.127285949 1323.287244 2325930.198 0.030430104 0.643989762 56588.53626 -4.75272846 -0.649664712 S(ph)ISEIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SISEIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE 35 1 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 1 S(0.5)IS(0.5)EIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE 105.31 1.30E-05 20737000 11295 12359 11774 15475 13589 7681.9 20928 11970 16061 TRUE FALSE 10588.06611 13274.07322 12053.28484 15872.1147 12521.77476 9899.539825 17790.04069 13464.48085 13380.31534 0.791316635 0.992059819 0.90082218 1.186228747 0.935835549 0.739858484 1.329568118 1.006290248 1 13.7078245 1.737235488 25 1.137193251 0.939962234 0.250962938 0.14907607 0.227618097 4115.182184 0.063564436 0.035249738 54.60538686 -1.737235488 -0.197231017 S(ph)ISESFLTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SISESFLTVK 10 0 F5H527;Q76I76;J3KSQ9;K7EP00;Q76I76-3;Q76I76-4 F5H527 SSH2 Protein phosphatase Slingshot homolog 2 1 S(0.994)IS(0.006)ESFLTVK;S(1)ISESFLTVK;S(0.996)IS(0.004)ESFLTVK;S(0.993)IS(0.007)ESFLTVK 240.8 2.86E-12 185942000 341117 343908 325961 323725 382215 196825 368661 277376 344446 TRUE FALSE 319767.0959 369371.3062 333692.9488 332032.3316 352197.3757 253645.1823 313383.7055 312007.0042 286955.7374 1.114342925 1.287206555 1.162872546 1.15708553 1.227357846 0.883917445 1.092097716 1.087300108 1 18.13046869 2.265733333 24.99984813 1.025867694 1.197905462 0.582333941 0.072799442 145.6891059 134038.608 0.023713493 0.019835547 184.3882886 -2.265733333 0.172037768 S(ph)ISESSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SISESSR 7 0 Q9H307 Q9H307 PNN Pinin 1 S(0.993)IS(0.007)ESSR;S(0.709)IS(0.291)ESSR;S(0.996)IS(0.004)ESSR;S(0.999)IS(0.001)ESSR 173.48 0.00090415 2083430000 1404720 1277460 1384010 1414730 1366020 1217310 1468050 1106190 1367840 TRUE FALSE 1316801.083 1372044.468 1416839.371 1451034.367 1258738.299 1568727.636 1247929.531 1244300.257 1139538.667 1.155556297 1.204035025 1.243344707 1.273352461 1.104603411 1.376633966 1.095118197 1.091933334 1 20.12001845 1.564702575 7.794576165 1.062485552 1.22386275 0.521201294 0.074732531 0.090955175 10.3313662 0.035780316 0.016730347 36.70308544 -1.564702575 0.161377197 S(ph)ISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 43 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 S(0.5)IS(0.5)LLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.485)IS(0.485)LLEPS(0.02)LELES(0.005)T(0.005)S(0.001)ETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.495)IS(0.495)LLEPS(0.009)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 156.02 3.74E-14 131668000 26059 94558.7 58607.8 72799.3 69920 46923.1 86399 62021.8 91959 TRUE FALSE 24428.01371 101559.9245 59998.00469 74667.45329 64428.76524 60469.03724 73444.27204 69765.35826 76610.44882 0.318860078 1.325666748 0.78315694 0.974637983 0.840991878 0.789305352 0.958671737 0.910650692 1 16.22525355 0.81020434 1.521778941 0.998649157 0.896726243 0.014100901 0.24835718 4.145210334 17.43313842 0.213035235 0.062054491 6.459580872 -0.81020434 -0.101922914 S(ph)ISQDSLDELSMEDYWIELENIKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SISQDSLDELSMEDYWIELENIKK 24 1 Q8N392;Q8N392-2 Q8N392 ARHGAP18 Rho GTPase-activating protein 18 1 S(0.5)IS(0.5)QDS(0.001)LDELSMEDYWIELENIKK 86.732 0.0071488 19100000 18560 16472 16341 17236 16378 10066 24002 14320 32743 TRUE FALSE 17398.36273 17691.60402 16728.61624 17678.30494 15091.73795 12971.89079 20403.12292 16107.88352 27277.98177 0.637817082 0.648567191 0.613264441 0.648079652 0.553257131 0.475544375 0.747970399 0.590508625 1 14.73544929 -0.254395379 0.865973099 1.011733345 0.614890285 0.745144145 0.070689663 5.818238219 3.399295164 0.306491626 0.021732836 0.556678722 0.254395379 -0.396843061 S(ph)ISTVNLSENSSVVIPPPDYLECLSMGAAADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SISTVNLSENSSVVIPPPDYLECLSMGAAADR 32 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 S(0.298)IS(0.298)T(0.298)VNLS(0.1)ENS(0.004)S(0.002)VVIPPPDYLECLSMGAAADR 50.891 0.046951 46231000 14844 17689 16991 17831 26415 15379 25585 24624 34341 TRUE FALSE 13914.94054 18998.71197 17394.03454 18288.57365 24340.47245 19818.66764 21748.76677 27698.3606 28609.26525 0.486378815 0.664075494 0.607986063 0.639253525 0.850789849 0.692735989 0.760200116 0.968160502 1 14.80419483 1.903447754 0.283922676 1.050423883 0.502843048 0.773386525 0.076468036 0.838667397 0.228357124 0.137005072 0.170200411 80.06593036 -1.903447754 -0.547580835 S(ph)ISTVNLSENSSVVIPPPDYLECLSMGAAADRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SISTVNLSENSSVVIPPPDYLECLSMGAAADRR 33 1 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 S(0.46)IS(0.46)T(0.075)VNLS(0.002)ENS(0.001)S(0.001)VVIPPPDYLECLSMGAAADRR 44.861 0.045547 68643000 57022 53085 52276 53109 52154 36526 62603 50060 76843 TRUE FALSE 53453.09481 57015.46863 53516.01141 54471.86685 48058.03522 47070.46325 53216.26133 56310.1012 64017.40688 0.834977507 0.890624463 0.835960312 0.850891492 0.750702622 0.735276006 0.83127799 0.879606094 1 15.96617662 -1.928788651 4.558167707 1.081689714 0.827511302 0.551960737 0.04920706 0.03699636 0.000577987 0.043150478 0.011942587 0.011781792 1.928788651 -0.254178411 S(ph)IVVIHPDTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SIVVIHPDTGR 11 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 1 S(1)IVVIHPDTGR;S(1)IVVIHPDTGR;S(1)IVVIHPDTGR 121.45 0.00026498 325460000 230981 326555 294389 272148 328774 343277 317686 274148 418144 TRUE FALSE 216524.3115 350733.472 301372.0461 279131.7784 302953.4163 442375.4973 270051.9336 308375.9813 348353.0651 0.621565685 1.006833317 0.865133901 0.801289859 0.869673462 1.269905569 0.775224795 0.885239753 1 18.41019073 2.439085583 24.99999867 0.968981385 0.85856579 0.174178556 0.155473391 376.6742822 247577.7576 0.051490076 0.043079756 274.8435711 -2.439085583 -0.110415596 S(ph)KDAS(ph)PINRWS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKDASPINRWSPTR 14 2 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 3 S(1)KDAS(1)PINRWS(0.967)PT(0.033)R;S(1)KDAS(1)PINRWS(0.951)PT(0.049)R 94.271 0.0027942 425990000 975200 550250 674160 711380 850790 498490 839130 607930 1003060 TRUE FALSE 914163.9728 590991.0825 690151.3936 729635.2152 783972.3853 642395.9707 713310.2466 683831.3987 835642.806 1.093964989 0.707229307 0.82589282 0.87314246 0.938166858 0.768744691 0.853606638 0.818329786 1 19.67252687 -1.236115728 4.161135994 1.000094974 0.842640055 0.133285129 0.104354263 9.645526437 52622308.34 9652.832873 0.022208126 0.058060968 1.236115728 -0.157454919 S(ph)KDEYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SKDEYEK 7 1 Q13247;Q13247-3;A0A590UJP7 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 S(1)KDEYEK;S(1)KDEYEK;S(1)KDEYEK;S(1)KDEYEK;S(1)KDEYEK;S(1)KDEYEK 158.31 0.00086329 3945500000 19857360 4486150 9620770 7270750 5423950 9098670 14536520 6509730 4555560 TRUE FALSE 18614523.28 4818309.214 9848979.208 7457329.754 4997974.846 11725308.32 12356903.78 7322484.12 3795207.606 4.904744408 1.269577244 2.595109472 1.964933287 1.316917377 3.089503801 3.255923011 1.929402784 1 21.85574738 5.739436775 12.24748838 2.384955509 2.417519026 0 1.17072135 201855247.8 0 0.240460684 0 548828.6507 -5.739436775 0.032563518 S(ph)KDEYEKS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKDEYEKSR 9 2 Q13247;Q13247-3;A0A590UJP7 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 2 S(1)KDEYEKS(1)R 107.82 0.0014538 558530000 1502700 293270 665420 464280 347400 608530 1017900 396100 273400 TRUE FALSE 1408648.689 314984.0159 681204.0766 476194.2108 320116.6053 784202.7323 865275.3447 445553.9569 227767.7738 6.184582946 1.382917393 2.990783399 2.090700554 1.405451702 3.44299248 3.798936656 1.956176458 1 17.79720411 4.748742588 24.88492492 2.44411893 6.18458514 0.632953428 0.930087992 958.6633223 2342941.14 0.223389231 3.081267039 56071.55343 -4.748742588 3.740466209 S(ph)KDRDPNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SKDRDPNR 8 2 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 S(1)KDRDPNR;S(1)KDRDPNR;S(1)KDRDPNR;S(1)KDRDPNR;S(1)KDRDPNR 79.693 0.02156 2037211000 4853480 2991026 3702050 3498590 3527280 2766988 4093020 3106280 3898120 TRUE FALSE 4549709.351 3212484.677 3789864.374 3588369.742 3250261.657 3565772.517 3479309.649 3494105.896 3247498.589 1.400988861 0.98921819 1.167010322 1.104964219 1.00085083 1.098005871 1.07138142 1.075937618 1 21.63089747 4.747444513 24.96503307 1.071554416 1.400989034 0.783485179 0.055622999 509.7477647 1432433.674 0.012438779 0.149263081 55904.20973 -4.747444513 0.329434618 S(ph)KDVEFQDGWPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKDVEFQDGWPR 12 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 S(1)KDVEFQDGWPR;S(1)KDVEFQDGWPR 60.307 0.083916 122450000 494770 370420 374470 384530 377610 322310 503960 332600 477310 TRUE FALSE 463803.2289 397846.2822 383352.6052 394397.6908 347954.0338 415355.6647 428395.8765 374125.8421 397643.8775 1.166378398 1.00050901 0.964060123 0.991836448 0.875039334 1.044541833 1.077335528 0.940856539 1 18.60111743 4.738368693 4.807121919 0.990643104 1.176082414 0.514290674 0.054832306 0.159298833 10.66874486 0.013547482 0.099050489 54748.05471 -4.738368693 0.185439311 S(ph)KEYHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKEYHR 6 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 S(0.986)KEY(0.014)HR;S(1)KEYHR 68.735 0.057748 659650000 1071910 649060 838820 851340 832880 639740 980020 760860 813740 TRUE FALSE 1004821.067 697117.0777 858717.2065 873186.8257 767468.9645 824422.5527 833075.0991 855855.0459 677921.537 1.482208503 1.028315284 1.266691143 1.288035234 1.132091138 1.216103203 1.228866548 1.262469178 1 19.37075878 -1.368534977 3.073054394 0.997515619 1.219883542 0.281302063 0.116411348 15464378.27 18247314.21 342551.8869 0.025185773 0.042802095 1.368534977 0.222367924 S(ph)KGDS(ph)DPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKGDSDPK 8 1 Q9BVI0 Q9BVI0 PHF20 PHD finger protein 20 2 S(1)KGDS(1)DPK 56.404 0.067038 600880000 25263 168630 115830 159940 147390 202490 88444 113510 45008 TRUE FALSE 23681.83393 181115.5407 118577.5423 164044.3312 135814.5839 260945.5758 75182.64327 127681.9734 37495.87404 0.631585062 4.830279206 3.162415742 4.37499686 3.622120765 6.959314393 2.005091099 3.405227286 1 15.19444423 3.340504983 20.48470429 3.738205081 3.334880919 0.003816613 1.855347826 24.93228095 4938.510674 0.475780891 0.644210523 2190.306961 -3.340504983 -0.403324163 S(ph)KPAGSDGERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKPAGSDGERR 11 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.635)KPAGS(0.365)DGERR 70.332 0.059171 0 49676 33788 40770 38628 40554 27630 46102 36754 53694 TRUE FALSE 46566.86783 36289.69868 41737.08365 39619.25988 37369.05243 35606.33246 39189.43309 41342.81781 44732.12452 1.041016235 0.811267049 0.933044967 0.885700384 0.835396325 0.795990194 0.876091478 0.924231036 1 15.44902366 -1.048213714 7.667770155 1.000000012 0.879068326 0.191391767 0.070426756 7.01E-09 7.18E-10 0.061620044 0.014523983 0.089492427 1.048213714 -0.120931685 S(ph)KPLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SKPLTR 6 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 1 S(0.996)KPLT(0.004)R;S(0.997)KPLT(0.003)R;S(1)KPLTR;S(0.977)KPLT(0.023)R;S(0.99)KPLT(0.01)R;S(1)KPLTR;S(1)KPLTR 113.62 0.015735 11693640000 11186690 7948790 9273280 8859780 9846910 6800870 11245410 8507460 12972160 TRUE FALSE 10486535.04 8537326.682 9493246.581 9087136.954 9073573.409 8764170.766 9559265.168 9569635.108 10807022.69 0.970344501 0.789979528 0.878433113 0.840854805 0.839599737 0.81096996 0.884541972 0.885501528 1 23.36546578 0.733793728 1.368697299 0.999566485 0.850224243 0.446279025 0.048735812 0.725202755 2.274513623 0.040950241 0.012165023 5.417435231 -0.733793728 -0.149342241 S(ph)KS(ph)EMLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKSEMLSR 8 1 E9PR23;E9PRA4;E9PNU3;E9PQC8;Q71H61 E9PR23 ILDR2 Immunoglobulin-like domain-containing receptor 2 2 S(1)KS(1)EMLSR;S(1)KS(1)EMLSR 80.037 0.0063487 148860000 42124 54319 49005 56902 50303 51205 50389 47077 56029 TRUE FALSE 39487.53403 58340.83528 50167.42174 58362.20165 46352.40529 65987.05226 42833.63724 52954.66708 46677.39794 0.845966909 1.24987334 1.074769031 1.250331086 0.993037473 1.413683178 0.917652636 1.134481985 1 15.51043652 1.634156859 25 1.019505573 1.143999675 0.109033443 0.161805049 1.55730688 1475.783569 0.065181695 0.036130563 43.06821366 -1.634156859 0.124494102 S(ph)KS(ph)PTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKSPTLR 7 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(0.998)KS(0.95)PT(0.052)LR;S(1)KS(0.692)PT(0.308)LR 90.142 0.0098755 534350000 1384160 833380 1041860 1064090 1070220 825190 1285220 854290 1171660 TRUE FALSE 1297527.896 895084.3223 1066573.411 1091396.351 986169.2383 1063408.957 1092513.192 960949.987 976102.3768 1.329294885 0.916998405 1.09268601 1.118116682 1.010313325 1.089444081 1.119260867 0.984476639 1 19.89667294 3.581864369 0.009350664 8.50E-06 2.156926777 0.112831438 0.105049783 16671.89842 37.42871399 4129.853556 4506.018093 3818.250074 -3.581864369 2.156918274 S(ph)KS(ph)SGS(ph)SRSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSSGSSRSK 10 2 P46100;P46100-4;A0A096LNL9;P46100-6;A0A096LNW1;A0A096LNN3;A0A087WWG0;A0A096LNL6;A0A096LNL7;A0A096LPG6 P46100 ATRX Transcriptional regulator ATRX 3 S(0.995)KS(0.995)S(0.011)GS(0.333)S(0.333)RS(0.333)K 58.699 0.072244 154490000 341400 255720 273150 303910 334910 313850 349090 230800 390480 TRUE FALSE 320032.3834 274653.7749 279629.247 311708.8451 308607.5196 404453.4001 296747.1953 259615.8881 325306.3654 0.983787646 0.844292655 0.859587382 0.958200879 0.948667325 1.243299988 0.912208388 0.79806581 1 18.31143953 3.057179591 3.101901314 0.99015003 0.879861636 0.089597843 0.11624969 0.473741795 9.301862245 0.035276412 0.042249929 1140.721405 -3.057179591 -0.110288394 S(ph)KSDATASISLSSNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSDATASISLSSNLK 16 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 S(0.498)KS(0.498)DAT(0.003)ASISLSSNLK 184.29 1.12E-09 442540000 405480 327600 348880 306100 315750 201580 446080 287170 457820 TRUE FALSE 380101.7306 351855.8449 357155.5984 313955.0442 290952.2687 259772.8736 379194.4452 323023.8066 381406.8844 0.996578054 0.922520959 0.936416234 0.823149914 0.762839583 0.681091203 0.994199268 0.846927048 1 18.54097136 3.265146342 10.25900749 0.845214465 0.943465414 0.190971408 0.096422503 0.67719567 252.3865184 0.026322632 0.035298561 1841.392383 -3.265146342 0.098250949 S(ph)KSDSYTLDPDTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKSDSYTLDPDTLR 14 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.78)KS(0.216)DS(0.004)YTLDPDTLR;S(0.483)KS(0.483)DS(0.034)YTLDPDTLR 173.21 1.66E-06 784140000 1654290 1570960 1588020 1864670 2139100 1100950 2290900 1584790 2480100 TRUE FALSE 1550750.942 1687275.513 1625688.584 1912520.589 1971103.715 1418776.393 1947400.813 1782654.52 2066155.288 0.750549076 0.816625702 0.7868182 0.92564223 0.95399592 0.686674618 0.942523935 0.862788257 1 20.97851726 -4.807783906 0.024209247 2.134147176 2.74E-06 0.345445714 0.0803621 2370.275021 4.468397275 279.2951985 137.5928981 1.56E-05 4.807783906 -2.13414444 S(ph)KSEDMDNVQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKSEDMDNVQSK 12 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 S(0.5)KS(0.5)EDMDNVQSK;S(0.604)KS(0.396)EDMDNVQSK 228.84 5.82E-12 884320000 2584300 1346960 1841730 1956250 1983390 1090160 1744580 1142090 2101930 TRUE FALSE 2422553.276 1446690.32 1885416.705 2006450.687 1827622.55 1404871.495 1482996.425 1284682.451 1751104.304 1.383443162 0.826158851 1.076701543 1.145820202 1.043697138 0.802277449 0.846892113 0.733641307 1 20.73983359 2.255584058 10.74193575 0.833327017 1.05836914 0.387804607 0.151532049 0.403753515 247.4659652 0.050149929 0.04112993 180.129174 -2.255584058 0.225042123 S(ph)KSEEAHAEDSVMDHHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 SKSEEAHAEDSVMDHHFR 18 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 S(0.631)KS(0.369)EEAHAEDSVMDHHFR;S(0.636)KS(0.364)EEAHAEDSVMDHHFR;S(0.579)KS(0.421)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.684)KS(0.316)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR 280.21 1.48E-39 18990060000 12633980 7849440 8696030 8248090 7690250 6541290 9887640 5940250 13417670 TRUE FALSE 11843241.74 8430620.705 8902303.938 8459749.953 7086288.786 8429654.234 8405080.174 6681903.289 11178174.2 1.059496975 0.754203733 0.796400538 0.756809637 0.633939735 0.754117272 0.751918876 0.597763389 1 23.41418123 4.739159501 6.137641123 0.747618225 1.067327679 0.445394488 0.106250218 0.106409245 20.61826148 0.022060461 0.141627909 54847.83652 -4.739159501 0.319709454 S(ph)KSKDQAEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSKDQAEEK 10 2 Q08170;A0A0D9SEM4 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 S(0.5)KS(0.5)KDQAEEK 70.332 0.042763 90573000 212690 43926 98546 91727 89841 54733 104030 74161 123550 TRUE FALSE 199378.1126 47178.32674 100883.5577 94080.87011 82785.25026 70533.52858 88431.66727 83420.1641 102928.7068 1.937050592 0.458359268 0.98013043 0.914039173 0.804297001 0.685265858 0.859154554 0.810465483 1 16.65128588 4.749444475 24.99760415 0.802540192 1.937051241 0.836807665 0.155793907 599.1105838 1375986.463 0.035523499 0.531982612 56162.24703 -4.749444475 1.134511048 S(ph)KSKPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKSKPPK 7 2 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BV80;H3BTY0 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 1 S(0.952)KS(0.048)KPPK;S(0.997)KS(0.003)KPPK 69.382 0.03125 362420000 900360 317670 610610 565480 449000 407960 545240 432180 426350 TRUE FALSE 844008.0748 341190.6173 625093.9576 579991.1742 413737.3512 525731.4293 463486.3238 486138.6243 355189.4307 2.376219566 0.960587754 1.759888959 1.632906624 1.164835762 1.480143788 1.304898974 1.368674241 1 18.43822913 8 0.064112173 0.489859652 3.498460717 0.282957164 0.35019606 468.8622316 2.234038804 19.95970184 129.6051851 100000000 -8 3.008601066 S(ph)KSLCHDEIENLLDSDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SKSLCHDEIENLLDSDHR 18 1 P30305;G8JLH2;B4DIG0;P30305-3;P30305-2;P30305-4 P30305 CDC25B M-phase inducer phosphatase 2 1 S(0.5)KS(0.5)LCHDEIENLLDSDHR;S(0.5)KS(0.5)LCHDEIENLLDSDHR;S(0.5)KS(0.5)LCHDEIENLLDSDHR;S(0.5)KS(0.5)LCHDEIENLLDSDHR 264.36 3.53E-31 1454640000 1429940 1417800 1532290 1378310 1776410 1084370 2327720 1595130 2207670 TRUE FALSE 1340442.608 1522775.387 1568636.642 1413679.768 1636897.924 1397410.016 1978699.995 1794285.492 1839195.615 0.728820033 0.827957274 0.85289277 0.768640245 0.890007518 0.759794121 1.075850758 0.97558165 1 20.8106435 1.738672256 10.29017598 1.016855838 0.814847436 0.779078703 0.053121744 0.038461596 19.68382234 0.022605177 0.012274016 54.78633593 -1.738672256 -0.202008403 S(ph)KSLGDLTSEDIACNFESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSLGDLTSEDIACNFESK 19 1 A0A2U3TZV8;Q4KWH8-2;Q4KWH8 A0A2U3TZV8 PLCH1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1" 1 S(0.488)KS(0.488)LGDLT(0.022)S(0.002)EDIACNFESK 147.39 6.42E-08 175990000 114230 95748 88227 96070 112800 58061 172490 80547 208090 TRUE FALSE 107080.5482 102837.2815 90319.7861 98535.31885 103941.143 74822.26816 146626.7258 90603.47026 173358.4347 0.617682943 0.593206103 0.52100024 0.568390682 0.599573613 0.431604429 0.845800933 0.522636643 1 17.40339851 -0.087905287 0.48106425 1.050402102 0.561226585 0.587349277 0.107568664 3.173188317 0.863518279 0.405930659 0.051725899 0.816760474 0.087905287 -0.489175517 S(ph)KSLTNLVAAGDDVLEDQEILMHHPPQVDELDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKSLTNLVAAGDDVLEDQEILMHHPPQVDELDR 33 1 Q7Z5Y7-2;Q7Z5Y7-3;Q7Z5Y7 Q7Z5Y7-2 KCTD20 BTB/POZ domain-containing protein KCTD20 1 S(0.333)KS(0.333)LT(0.333)NLVAAGDDVLEDQEILMHHPPQVDELDR;S(0.427)KS(0.427)LT(0.147)NLVAAGDDVLEDQEILMHHPPQVDELDR 177.58 7.60E-20 51729000 29972 22222 27729.9 27230 26055.2 16236.8 31826 17603.5 25798 TRUE FALSE 28096.10602 23867.34 28387.66632 27928.7679 24008.92969 20924.10058 27053.98676 19801.33573 21492.14714 1.30727311 1.110514452 1.320839009 1.299487097 1.117102425 0.973569576 1.258784736 0.921328874 1 14.391522 2.592966811 5.27565554 1.074624526 1.244095517 0.469482528 0.10761683 0.244268848 9.671912663 0.033990089 0.0318255 391.7119415 -2.592966811 0.169470991 S(ph)KSNPDFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSNPDFLK 9 1 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;H7C3G6;J3QL44;J3QRL2;K7EL39;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 S(0.69)KS(0.31)NPDFLK 69.714 0.032981 189020000 873320 547260 659110 574970 689510 513190 888660 640990 898040 TRUE FALSE 818660.4601 587779.6998 674744.4005 589724.7036 635358.6659 661339.6221 755413.6829 721019.0125 748151.3224 1.094244487 0.7856428 0.901882253 0.788242547 0.849238178 0.883965051 1.009707074 0.963734195 1 19.51297058 1.797407582 5.315714762 0.989909952 0.868747107 0.244892603 0.086299049 0.245331287 12.80505641 0.037418109 0.020987532 62.7202213 -1.797407582 -0.121162845 S(ph)KSPASVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSPASVDR 9 1 Q13243;Q13243-3 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 1 S(0.736)KS(0.254)PAS(0.01)VDR 80.69 0.01417 1891400000 976270 813140 934690 804520 939240 654710 1016800 719600 909280 TRUE FALSE 915167.0034 873345.7317 956861.2882 825165.3452 865475.8791 843714.1487 864340.2795 809443.644 757515.2938 1.208116867 1.152908382 1.263157716 1.089305196 1.142519347 1.11379157 1.141020236 1.068550893 1 19.53091549 1.203065932 0.302059514 0.977551382 1.217441343 0.647429819 0.043010066 1.036395544 0.327749538 0.095343277 0.06681232 15.96121441 -1.203065932 0.239889961 S(ph)KSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 SKSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 36 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.577)KS(0.423)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.599)KS(0.401)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.464)KS(0.464)PLPPEEEAKDEEEDQT(0.071)LVNLDTYTSDLHFQVSK;S(0.564)KS(0.436)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.475)KS(0.475)PLPPEEEAKDEEEDQT(0.047)LVNLDT(0.001)Y(0.001)T(0.001)S(0.001)DLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.489)KS(0.489)PLPPEEEAKDEEEDQT(0.022)LVNLDTYTSDLHFQVSK;S(0.578)KS(0.422)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.559)KS(0.441)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 288.41 8.99E-78 22705882000 7095976 2717618.9 3863955 4018712 4195258.4 2751141.6 5527587 3206794 6556064 TRUE FALSE 6651851.529 2918834.231 3955609.837 4121838.954 3865779.728 3545351.519 4698776.645 3607169.29 5461814.565 1.217883077 0.53440742 0.724229977 0.754664756 0.707783042 0.649116054 0.860295894 0.660434229 1 22.3809489 -1.58181216 2.923075371 1.015425173 0.741367143 0.131976807 0.18278786 42552694.58 44597070.26 5101301.348 0.03903989 0.026193157 1.58181216 -0.274058029 S(ph)KSPPKVPIVIQDDSLPAGPPPQIR ddPTM_SK-BR-3_Pertuzumab_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(0.616)KS(0.384)PPKVPIVIQDDSLPAGPPPQIR 179.97 1.38E-17 1247800000 799990 418300 588490 567060 559440 431340 766520 480460 616550 TRUE FALSE 749920.0539 449271.3672 602449.2607 581611.7196 515503.8391 555860.8558 651587.442 540446.4886 513643.8219 1.460000144 0.874674917 1.172893034 1.132324959 1.00362122 1.082191262 1.268558901 1.052181425 1 18.97040877 S(ph)KSPRDPDANWDSPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSPRDPDANWDSPSR 16 2 Q9UHB7;Q9UHB7-2;Q9UHB7-3 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 S(0.5)KS(0.5)PRDPDANWDSPS(0.001)R 73.315 0.027888 318140000 327060 250480 289430 309560 306590 195580 331260 199400 330200 TRUE FALSE 306589.8984 269025.7998 296295.4163 317503.8337 282511.6581 252040.771 281590.6383 224295.5289 275087.4868 1.114517792 0.977964512 1.077095217 1.154192208 1.026988401 0.916220414 1.023640303 0.815360711 1 18.06953099 2.40486017 5.498594399 0.949721011 1.065699709 0.463750073 0.070943142 0.209808085 11.44770103 0.023888595 0.019927856 254.0154721 -2.40486017 0.115978697 S(ph)KSQEEPKDTFEHDPSESIDEFNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSQEEPKDTFEHDPSESIDEFNK 24 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 S(0.5)KS(0.5)QEEPKDTFEHDPSESIDEFNK 143.01 1.32E-07 170600000 190950 50526 90837 76601 97837 61685 114590 72426 161820 TRUE FALSE 178998.7804 54266.99761 92991.69654 78566.71135 90153.27668 79492.45813 97408.2933 81468.54553 134811.1966 1.327773841 0.402540731 0.689792086 0.582790698 0.668737308 0.589657685 0.722553436 0.60431587 1 17.0405808 -1.273714451 4.675862019 1.000134107 0.666218932 0.120737344 0.242113515 0.000294905 4.58E-05 0.204245912 0.048121991 0.053245824 1.273714451 -0.333915175 S(ph)KTLAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKTLAFR 7 1 Q53EV4-2 Q53EV4-2 1 S(0.917)KT(0.083)LAFR 53.554 0.084168 536130000 128540 284830 267890 262240 292500 267610 251260 253770 300910 TRUE FALSE 120494.9109 305919.1096 274244.4773 268969.5224 269528.2299 344864.6627 213585.8956 285453.7431 250686.177 0.480660371 1.220326997 1.093975266 1.072933201 1.075161914 1.375682803 0.852005077 1.138689602 1 17.93552292 4.745114009 24.91598609 1.104427543 0.480660076 0.676735436 0.135304534 411.7352211 1565373.377 0.03012844 0.288522615 55605.02105 -4.745114009 -0.623767467 S(ph)KTPPPPPQTAQTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKTPPPPPQTAQTK 14 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 S(0.5)KT(0.5)PPPPPQTAQTK;S(0.5)KT(0.5)PPPPPQTAQTK 120.11 9.00E-05 528850000 623250 360435 469000 431190 458660 351456 602590 397499 670660 TRUE FALSE 584241.895 387121.9824 480124.9015 442255.0654 422638.6937 452915.6418 512237.2237 447127.6252 558722.5134 1.045674518 0.692869847 0.859326213 0.791546886 0.756437558 0.810627156 0.916800758 0.80026778 1 19.09177243 0.234456892 0.633286555 1.005660323 0.815047099 0.201859952 0.097028514 3.89492615 2.12343757 0.149217334 0.034840621 1.715761395 -0.234456892 -0.190613224 S(ph)LAIPDDDRFEDLEEANPFSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLAIPDDDRFEDLEEANPFSFR 22 1 Q96C92-4 Q96C92-4 SDCCAG3 Serologically defined colon cancer antigen 3 1 S(1)LAIPDDDRFEDLEEANPFSFR;S(1)LAIPDDDRFEDLEEANPFSFR 136.67 2.52E-06 63752000 79003 76087 80251 87799 72694 47496 95685 54616 77567 TRUE FALSE 74058.34325 81720.56065 82154.59162 90052.07098 66984.90647 61207.32417 81337.92255 61434.92782 64620.5666 1.146049116 1.264621543 1.27133815 1.393551244 1.03658804 0.947180246 1.258700238 0.950702401 1 15.97970578 2.720473177 24.96055789 1.063724083 1.268586627 0.534605307 0.105316505 683.447024 943151.6691 0.032886425 0.031060634 525.3795652 -2.720473177 0.204862544 S(ph)LALVAHTGYLPHQQDPHHVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLALVAHTGYLPHQQDPHHVHR 22 0 Q9Y485;F5H269;E7EMZ0 Q9Y485 DMXL1 DmX-like protein 1 1 S(0.999)LALVAHT(0.001)GYLPHQQDPHHVHR 125.6 9.51E-06 431920000 103220 120760 108940 124310 155600 100260 153810 146620 210430 TRUE FALSE 96759.64445 129701.1961 111524.1082 127500.0051 143379.8037 129203.4344 130747.6184 164925.8298 175307.8736 0.551941236 0.739848094 0.636161434 0.727291949 0.817874296 0.737008737 0.745817149 0.940778223 1 17.41953127 0.848270653 0.160352447 1.176408134 0.515608806 0.747883691 0.065702898 3.422491909 0.36361091 0.783678094 0.493806481 7.05132371 -0.848270653 -0.660799329 S(ph)LCHDEIENLLDSDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLCHDEIENLLDSDHR 16 0 P30305;G8JLH2;B4DIG0;P30305-3;P30305-2;P30305-4 P30305 CDC25B M-phase inducer phosphatase 2 1 S(1)LCHDEIENLLDSDHR;S(1)LCHDEIENLLDSDHR 207.22 3.01E-11 85463000 65646 76038 73756 69469 82495 69024 114509 82136 67271 TRUE FALSE 61537.33404 81667.93264 75505.52715 71251.69215 76016.17547 88950.10829 97339.4385 92390.8604 56043.03551 1.098037133 1.457236067 1.347277614 1.271374605 1.356389331 1.587175061 1.73686949 1.648569881 1 15.77424748 2.268063451 5.880006903 1.575794811 1.329233651 0.099290779 0.220300088 0.246928735 24.44655692 0.070913439 0.057402518 185.3802447 -2.268063451 -0.24656116 S(ph)LDADEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLDADEFR 8 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 1 S(1)LDADEFR;S(1)LDADEFR 103.26 0.0050433 380730000 855620 773500 792790 767580 937560 638800 892440 672910 1077780 TRUE FALSE 802068.2715 830770.7448 811595.3532 787277.4023 863927.8195 823211.1899 758626.907 756924.2948 897891.5553 0.893279669 0.925246195 0.903890173 0.876806779 0.9621739 0.916826965 0.844898142 0.843001909 1 19.77618169 1.788119716 25 0.878947752 0.913886968 0 0.048846663 257.208979 129787.2243 0.01990518 0.01120817 61.39312158 -1.788119716 0.034939216 S(ph)LDEIAMDLTETGTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLDEIAMDLTETGTQR 16 0 E9PGA7;Q9Y2L6-2;Q9Y2L6;C9JYK2 E9PGA7 FRMD4B FERM domain-containing protein 4B 1 S(1)LDEIAMDLTETGTQR;S(1)LDEIAMDLTETGTQR 180.74 1.75E-12 9397100 31051 25128 22884 23117 23849.8 18407 30224 19122.9 26389 TRUE FALSE 29107.57334 26988.50327 23426.81929 23710.22136 21976.73291 23720.80209 25692.19179 21510.43616 21984.50542 1.32400401 1.227614756 1.065605927 1.078496919 0.999646455 1.0789782 1.168649978 0.97843621 1 14.42419946 4.350344348 1.313956707 1.064550314 1.351679832 0.745686196 0.055258372 0.391843213 0.949518658 0.016037546 0.125318313 22404.96903 -4.350344348 0.287129518 S(ph)LDTITLSGDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLDTITLSGDER 12 0 Q8N9U0;Q8N9U0-2;H0YJ73 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 S(1)LDTITLSGDER 139.19 6.40E-05 113750000 153580 101420 124470 106370 121030 111780 173280 112000 155340 TRUE FALSE 143967.7019 108929.2423 127422.4872 109099.6343 111524.792 144049.0714 147298.2727 125983.4465 129412.7505 1.112469223 0.841719552 0.98462081 0.843036207 0.861775919 1.113097982 1.138205255 0.973501035 1 16.98162024 2.233500539 24.99986943 1.076891084 0.92058738 0.303227748 0.09326436 120.6326046 595992.139 0.031862933 0.024258085 171.1987303 -2.233500539 -0.156303705 S(ph)LEDLRAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLEDLRAPK 9 1 Q8TEH3;Q8TEH3-7;Q8TEH3-6 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 S(1)LEDLRAPK;S(1)LEDLRAPK 116.54 0.00078575 494490000 1218350 1090380 1111550 1212540 1362660 765680 1591850 1053700 1805290 TRUE FALSE 1142095.648 1171112.87 1137916.491 1243655.829 1255642.18 986719.3862 1353166.871 1185256.764 1503975.436 0.759384509 0.778678189 0.756605769 0.826912328 0.834882106 0.656074137 0.899726709 0.788082528 1 20.52034957 -1.849287456 0.280096661 1.214816972 0.763326687 0.548426191 0.061593851 20.38409893 0.926148807 2.956180135 0.068590661 0.01414857 1.849287456 -0.451490285 S(ph)LEGGGCPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLEGGGCPAR 10 0 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 S(1)LEGGGCPAR;S(1)LEGGGCPAR;S(1)LEGGGCPAR;S(1)LEGGGCPAR 136.5 0.00012171 1756940000 411475 400114 458233 485411 470922 392856 468807 413739 487933 TRUE FALSE 385721.5143 429738.8569 469102.5032 497867.4681 433937.6857 506267.1497 398513.7425 465395.2249 406493.8301 0.948898816 1.057184206 1.154021214 1.224784809 1.067513585 1.245448546 0.98036849 1.144901079 1 18.63287393 -1.073820108 6.142098962 0.999999789 1.10317697 0.103359609 0.095234558 2.55E-07 3.86E-08 0.085596657 0.020175284 0.084368415 1.073820108 0.103177182 S(ph)LELHQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLELHQGR 8 0 Q9NX05 Q9NX05 FAM120C Constitutive coactivator of PPAR-gamma-like protein 2 1 S(1)LELHQGR 60.799 0.094417 381010000 223800 339360 351590 335790 367550 161710 198960 319190 186810 TRUE FALSE 209792.7575 364486.5675 359929.8808 344406.9399 338684.1056 208393.0519 169127.7951 359041.5741 155630.2042 1.348020833 2.342004044 2.312725109 2.212982639 2.176210636 1.339027042 1.086728608 2.307017305 1 17.24776256 2.24022541 24.99854833 1.398903766 2.152409165 0.331867431 0.44693484 42.03297926 631179.2836 0.148837501 0.118488366 173.8703025 -2.24022541 0.753505399 S(ph)LELSSLAGPGEDPLSADSLGKPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLELSSLAGPGEDPLSADSLGKPTR 25 1 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 S(1)LELSSLAGPGEDPLSADSLGKPTR;S(1)LELSSLAGPGEDPLSADSLGKPTR;S(0.991)LELS(0.008)SLAGPGEDPLSADSLGKPTR;S(0.957)LELS(0.043)SLAGPGEDPLSADSLGKPTR;S(0.999)LELS(0.001)SLAGPGEDPLSADSLGKPTR;S(1)LELSSLAGPGEDPLSADSLGKPTR 282.21 1.46E-53 2483441000 1492121 1128463 1222852 1182204 1286177 944349 1526055 1096776 1430563 TRUE FALSE 1398731.81 1212015.575 1251858.627 1212541.356 1185165.847 1216967.226 1297237.22 1233710.898 1191792.794 1.173636741 1.01696837 1.050399561 1.017409539 0.994439514 1.021123162 1.088475469 1.035172309 1 20.184702 4.742543702 24.9579542 1.032994754 1.173636797 0.738608698 0.027083449 221.9278613 1390541.069 0.006742867 0.051476848 55276.90295 -4.742543702 0.140642043 S(ph)LENETLNKEEDCHSPTSKPPKPDQPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLENETLNKEEDCHSPTSKPPKPDQPLK 28 3 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.341)LENET(0.302)LNKEEDCHS(0.341)PT(0.008)S(0.009)KPPKPDQPLK;S(0.981)LENET(0.017)LNKEEDCHS(0.002)PTSKPPKPDQPLK 148.76 5.01E-08 2833200000 2088730 728632 1253210 1183930 1102510 911550 1707450 850260 1467130 TRUE FALSE 1958000.118 782580.6714 1282936.733 1214311.648 1015923.312 1174699.687 1451433.724 956416.8327 1222256.525 1.601955136 0.640275307 1.04964605 0.993499829 0.831186654 0.961090952 1.187503355 0.782500901 1 20.22111568 -0.431604502 8.443249555 1 0.984661664 0 0.260358334 0 0 0.223911282 0.052776395 0.370165124 0.431604502 -0.015338336 S(ph)LEPAENVHGAGGGAFPASQTPSKPASADGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLEPAENVHGAGGGAFPASQTPSKPASADGHR 32 1 P12931;P12931-2 P12931 SRC Proto-oncogene tyrosine-protein kinase Src 1 S(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;S(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;S(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;S(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;S(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR;S(1)LEPAENVHGAGGGAFPASQTPSKPASADGHR 220.48 3.95E-36 7308460000 1869440 1881090 2096930 2014030 1932230 1669420 2618560 1923420 1656070 TRUE FALSE 1752435.087 2020367.861 2146670.17 2065713.42 1780480.45 2151354.453 2225931.238 2163563.221 1379661.218 1.270192323 1.464394182 1.555940068 1.497261351 1.29052004 1.55933531 1.613389728 1.568184415 1 20.39588262 S(ph)LEPIDALTEQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLEPIDALTEQLR 13 0 A0A2U3TZV8;Q4KWH8-2;Q4KWH8 A0A2U3TZV8 PLCH1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1" 1 S(1)LEPIDALTEQLR 74.46 0.035715 6145500 9817.3 4536.6 5958.8 5949.5 7904.5 6062.5 8513.5 5118.8 9630.1 TRUE FALSE 9202.852717 4872.494584 6100.14555 6102.174242 7283.712455 7812.645334 7236.97971 5757.893448 8022.774097 1.147091094 0.607332891 0.760353648 0.760606514 0.90787954 0.973808466 0.902054529 0.717693578 1 12.96988546 2.736705306 23.814782 0.901119859 0.773845112 0.029784221 0.154972703 168.6525719 2164805.831 0.046023684 0.045459645 545.3876583 -2.736705306 -0.127274747 S(ph)LESCLLDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLESCLLDLR 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(1)LESCLLDLR;S(1)LESCLLDLR;S(1)LESCLLDLR;S(0.998)LES(0.002)CLLDLR;S(0.994)LES(0.006)CLLDLR;S(1)LESCLLDLR 203.03 2.23E-07 603143000 418424 440874 402990 405929 492029 355293 492298 406948 547538 TRUE FALSE 392235.5887 473516.7697 412549.1131 416345.8254 453387.0271 457860.3214 418482.4852 457756.3536 456150.3706 0.85988221 1.038071654 0.904414728 0.912738106 0.993942034 1.003748656 0.917422219 1.003520732 1 18.79914996 2.725447285 24.69650065 0.97528219 0.942932178 0.186240041 0.05191744 1788.431575 3368171.897 0.016394232 0.015541635 531.43149 -2.725447285 -0.032350012 S(ph)LESINSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLESINSR 8 0 E5RI99;P62888;E5RJH3;A0A0C4DH44 E5RI99 RPL30 60S ribosomal protein L30 1 S(1)LESINSR;S(1)LESINSR;S(1)LESINSR 133.44 0.00096426 930410000 512879 478271 533470 523060 561600 376190 597760 474337 601427 TRUE FALSE 480778.8189 513682.6825 546124.1603 536482.6051 517494.2014 484789.9461 508131.4373 533559.0186 501044.9483 0.959552273 1.025222755 1.089970395 1.0707275 1.032829895 0.967557796 1.01414342 1.064892522 1 18.93458051 2.464975099 24.7479489 1.009956644 1.044277786 0.063202355 0.041178724 418.6577696 853012.8454 0.014388179 0.012048569 291.7259742 -2.464975099 0.034321142 S(ph)LESLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLESLR 6 0 Q5VT97-2;Q5VT97 Q5VT97-2 SYDE2 Rho GTPase-activating protein SYDE2 1 S(0.999)LES(0.001)LR 74.127 0.085117 166700000 1316700 259260 340260 283100 346130 262900 346640 221790 394780 TRUE FALSE 1234290.097 278455.8802 348331.1279 290364.8253 318946.346 338794.9622 294664.55 249480.9697 328888.6676 3.752911605 0.846656962 1.059115628 0.882866617 0.969769948 1.03012051 0.895940113 0.758557513 1 18.32723977 4.739667985 24.99998481 0.93639438 3.752912501 0.989770582 0.090175975 7.958383225 179646.227 0.020171223 0.124356877 54912.09143 -4.739667985 2.816518121 S(ph)LESVLSLGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLESVLSLGPR 11 0 Q13470-2;Q13470 Q13470-2 TNK1 Non-receptor tyrosine-protein kinase TNK1 1 S(1)LESVLSLGPR;S(1)LESVLSLGPR;S(1)LESVLSLGPR 229 3.00E-12 137273000 47075.9 39205.8 49852.2 46032.9 49999 37691 51470 42543 37030.5 TRUE FALSE 44129.50345 42108.63823 51034.71773 47214.18215 46072.28023 48571.77984 43752.55132 47854.5872 30849.87032 1.430459933 1.364953492 1.65429278 1.530449939 1.493435134 1.574456532 1.418241013 1.551208699 1 14.9129768 -1.578129547 2.806449259 0.967196645 1.501150107 0.781507274 0.083447198 13231159.83 13061663.09 3221365.189 0.020958363 0.026416207 1.578129547 0.533953462 S(ph)LESVLSLGPRPT(ph)GGGSSPPEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLESVLSLGPRPTGGGSSPPEIR 23 1 Q13470-2;Q13470 Q13470-2 TNK1 Non-receptor tyrosine-protein kinase TNK1 2 S(0.998)LES(0.027)VLS(0.067)LGPRPT(0.365)GGGS(0.287)S(0.256)PPEIR;S(0.999)LES(0.053)VLS(0.019)LGPRPT(0.643)GGGS(0.24)S(0.047)PPEIR;S(1)LES(0.023)VLS(0.039)LGPRPT(0.569)GGGS(0.2)S(0.169)PPEIR 126.36 0.00011548 419355000 311758 349044 332602 345516 359428 267698 444582 310641 392730 TRUE FALSE 292245.6233 374887.5809 340491.4765 354382.5255 331199.9747 344978.0669 377921.0564 349425.2127 327180.8259 0.893223564 1.145811586 1.040682857 1.083139651 1.012284182 1.054395734 1.155083142 1.067988051 1 18.31972868 1.954222987 24.84763744 1.094876268 1.051446965 0.006132237 0.074492872 1114.296617 604834.6461 0.028198964 0.018202704 89.99595438 -1.954222987 -0.043429303 S(ph)LESVLSLGPRPTGGGS(ph)SPPEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLESVLSLGPRPTGGGSSPPEIR 23 1 Q13470-2;Q13470 Q13470-2 TNK1 Non-receptor tyrosine-protein kinase TNK1 2 S(1)LES(0.001)VLS(0.009)LGPRPT(0.016)GGGS(0.653)S(0.321)PPEIR;S(1)LESVLSLGPRPT(0.003)GGGS(0.63)S(0.366)PPEIR;S(1)LESVLSLGPRPT(0.024)GGGS(0.54)S(0.436)PPEIR;S(1)LES(0.014)VLSLGPRPT(0.181)GGGS(0.475)S(0.329)PPEIR 164.35 8.19E-12 1319070000 920800 1066740 944880 1002190 1056560 801725 1319120 905440 1129470 TRUE FALSE 863168.7717 1145722.54 967292.9998 1027907.892 973582.0396 1033169.993 1121330.202 1018486.177 940954.1603 0.917333498 1.217617805 1.027991629 1.092410168 1.034675312 1.09800247 1.191694824 1.08239723 1 19.84376492 1.999186924 24.99599032 1.120709744 1.076333394 0 0.088600607 97.81835698 3007214.732 0.03107741 0.0226539 99.81295741 -1.999186924 -0.04437635 S(ph)LGDEGLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLGDEGLNR 9 0 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 S(1)LGDEGLNR;S(1)LGDEGLNR;S(1)LGDEGLNR;S(1)LGDEGLNR 119.34 0.00088511 744670000 932150 616030 801540 641400 632450 602480 646370 455294 599480 TRUE FALSE 873808.3954 661641.5022 820552.9073 657859.4099 582779.9282 776406.1956 549452.8191 512138.4581 499422.9152 1.749636168 1.324812062 1.643002118 1.317239137 1.166906665 1.554606671 1.100175427 1.025460472 1 18.92990249 1.981555637 0.480180343 0.957930481 1.56467041 0.579647229 0.168084745 0.676473706 0.353149862 0.159482855 0.129060327 95.8419491 -1.981555637 0.606739929 S(ph)LGDLTSEDIACNFESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLGDLTSEDIACNFESK 17 0 A0A2U3TZV8;Q4KWH8-2;Q4KWH8 A0A2U3TZV8 PLCH1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1" 1 S(1)LGDLTSEDIACNFESK 230.45 8.22E-16 35326000 137160 108950 112490 100420 113870 86482 180700 101180 134870 TRUE FALSE 128575.4004 117016.7714 115158.3159 102996.9472 104927.1095 111447.9495 153605.7125 113812.5457 112359.3257 1.144323354 1.041451349 1.024911063 0.916674665 0.933853144 0.991888735 1.367093577 1.012933684 1 16.77776035 S(ph)LHGPCPVTTFGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLHGPCPVTTFGPK 14 0 O95544;O95544-2 O95544 NADK NAD kinase 1 S(1)LHGPCPVTTFGPK;S(1)LHGPCPVTTFGPK 136.26 1.81E-05 518700000 1050810 963860 828960 785240 863320 564370 1136370 683860 1144470 TRUE FALSE 985041.6778 1035225.197 848623.3227 805390.5878 795518.3297 727294.4572 965981.868 769241.4264 953450.5634 1.033133458 1.085767041 0.890054876 0.844711429 0.834357187 0.762802483 1.013143109 0.80679739 1 19.86279861 3.87095867 2.762870383 0.876395754 1.058334005 0.474139679 0.078983795 0.218076147 3.265622061 0.020094046 0.042245406 7429.48431 -3.87095867 0.181938251 S(ph)LHSAHSLASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLHSAHSLASR 11 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 S(1)LHSAHSLASR;S(1)LHSAHSLASR 211.77 5.28E-09 877110000 127558 263780 187750 190292 234670 148518 173332 167441 177981 TRUE FALSE 119574.3725 283310.5457 192203.5187 195175.2149 216239.9648 191392.7356 147342.4757 188346.3774 148274.8213 0.806437475 1.91071244 1.296265387 1.3163072 1.45837279 1.290797277 0.993712044 1.270251927 1 17.17791411 1.96636535 4.434808618 1.094540661 1.420912897 0.143496254 0.278078299 0.309089011 13.74766348 0.11744316 0.071888316 92.54764026 -1.96636535 0.326372236 S(ph)LIVEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLIVEGK 7 0 H0Y993;A0A494C028;P35659;B4DFG0;H0Y8X0;A0A494C198;D6R9L5 H0Y993 DEK Protein DEK 1 S(1)LIVEGK;S(1)LIVEGK;S(1)LIVEGK;S(1)LIVEGK;S(1)LIVEGK;S(1)LIVEGK 116.3 0.0057542 1238612000 4585100 3564810 4105670 3813790 3837760 3449200 5933280 3987530 4293970 TRUE FALSE 4298126.776 3828752.242 4203058.431 3911658.308 3536357.81 4444928.047 5043639.746 4485381.898 3577278.667 1.201507396 1.070297452 1.174931791 1.093473188 0.988560898 1.242544532 1.409909659 1.253853087 1 21.77043108 2.051053497 10.47681559 1.281630081 1.110113059 0.147459723 0.118197478 0.514159493 102.7721281 0.040268602 0.029719813 112.4743513 -2.051053497 -0.171517023 S(ph)LLDASEEAIKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLLDASEEAIKK 12 1 P18206;P18206-2 P18206 VCL Vinculin 1 S(1)LLDASEEAIKK 77.746 0.016901 45945000 82238 44170 55195 43114 48888 34955 75867 51267 86690 TRUE FALSE 77090.87038 47440.39276 56504.25146 44220.37823 45048.53368 45045.94105 64491.44766 57667.7978 72220.87896 1.067431905 0.656879194 0.78238111 0.612293548 0.623760529 0.623724631 0.892975115 0.798492051 1 16.14012836 1.65500413 7.488441823 0.884993155 0.717810708 0.237660884 0.141412293 0.175803666 18.71174071 0.066169904 0.033942694 45.18602413 -1.65500413 -0.167182447 S(ph)LLDRAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLLDRAEER 9 1 P02549-2;P02549 P02549-2 SPTA1 "Spectrin alpha chain, erythrocytic 1" 1 S(1)LLDRAEER 50.95 0.095624 103740000 35562 94841 70627 78780 73589 76472 73058 81830 57590 TRUE FALSE 33336.2379 101863.1263 72302.30579 80801.62817 67809.61678 98548.22498 62103.63114 92046.65563 47977.85695 0.694825489 2.123127892 1.506993234 1.684144172 1.413352348 2.054035575 1.294422783 1.9185237 1 15.5500811 -1.329077546 5.498821432 0.999872901 1.62147905 0.159840318 0.415397467 0.000557332 6.80E-05 0.346325968 0.081613337 0.046872968 1.329077546 0.621606149 S(ph)LLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR 40 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2;J3QLU9 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 S(1)LLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR;S(1)LLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR;S(1)LLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR;S(1)LLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR;S(1)LLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR;S(1)LLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR 136.32 3.15E-09 140072000 32206.2 44867.6 25049.4 34098 46535.3 21829.4 35651.3 33713.5 38603.7 TRUE FALSE 30190.47143 48189.64379 25643.5836 34973.01241 42880.60525 28131.19341 30305.71854 37922.70469 32160.49308 0.938744047 1.498411224 0.797362887 1.087452618 1.333331711 0.874712752 0.942327546 1.179170499 1 14.97300191 3.972845986 24.88025067 1.024178434 1.244720518 0.128130763 0.200735296 275.395801 1602702.896 0.047334114 0.089358889 9393.901162 -3.972845986 0.220542084 S(ph)LLGIDTEDAIQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLLGIDTEDAIQGR 14 0 P49454 P49454 CENPF Centromere protein F 1 S(1)LLGIDTEDAIQGR;S(1)LLGIDTEDAIQGR;S(1)LLGIDTEDAIQGR;S(1)LLGIDTEDAIQGR 260.96 1.83E-24 340068000 330745 314866 304942 307328 342589 246684 405852 291622 315118 TRUE FALSE 310044.2608 338179.0063 312175.3682 315214.5568 315683.4419 317897.6662 344998.2603 328031.6486 262522.7701 1.181018549 1.288189235 1.189136349 1.200713206 1.20249928 1.210933688 1.314165092 1.249535987 1 18.00208304 -1.201251543 4.285527912 0.999911434 1.234599351 0.731619986 0.043591821 3.76E-05 7.01E-06 0.043006158 0.010132831 0.062914168 1.201251543 0.234687918 S(ph)LLQSEQQPSWTDDLPLCHLSGVGSASNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLLQSEQQPSWTDDLPLCHLSGVGSASNR 29 0 Q15750;Q15750-2 Q15750 TAB1 TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 1 S(1)LLQSEQQPSWTDDLPLCHLSGVGSASNR;S(0.989)LLQS(0.008)EQQPS(0.002)WTDDLPLCHLSGVGSASNR;S(0.954)LLQS(0.046)EQQPSWTDDLPLCHLSGVGSASNR;S(0.995)LLQS(0.005)EQQPSWTDDLPLCHLSGVGSASNR 251.03 6.85E-47 663432000 84238.2 103278.4 105756.2 101419.5 117010.6 109419.5 146106.9 119246.8 173685.8 TRUE FALSE 78965.88143 110925.2402 108264.787 104022.0961 107821.0595 141007.1334 124199.5267 134135.0255 144696.5179 0.545734497 0.766606148 0.748219712 0.718898406 0.745153104 0.974502603 0.858344959 0.927009353 1 17.14267068 6.042073496 0.144148035 1.080481266 2.73E-08 0.744500185 0.068901239 21.34533861 0.34580351 0.309649489 4.427080842 1101725.74 -6.042073496 -1.080481239 S(ph)LNLVDSPQPLLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLNLVDSPQPLLEK 14 0 P46019 P46019 PHKA2 "Phosphorylase b kinase regulatory subunit alpha, liver isoform" 1 S(1)LNLVDSPQPLLEK 172.37 3.01E-06 55116000 156190 138040 143020 122360 152780 123710 190480 147870 285570 TRUE FALSE 146414.3467 148260.6252 146412.5019 125499.9648 140781.2751 159423.0687 161919.2923 166331.895 237906.5221 0.615428049 0.62318857 0.615420295 0.527517966 0.591750381 0.670108021 0.680600476 0.699148109 1 17.8600353 0.438885687 0.656865429 1.008902629 0.599586129 0.931396003 0.033180359 0.476718428 0.328154655 0.04378078 0.013548659 2.747170961 -0.438885687 -0.4093165 S(ph)LPAGDALYLSFNPPQPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SLPAGDALYLSFNPPQPSR 19 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GYF0 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR 303.34 4.23E-50 2077159000 367871.6 406286 391799.9 374085.7 478204.8 333179.1 452894 400051 562707 TRUE FALSE 344847.1732 436367.8382 401093.5786 383685.3724 440648.524 429362.4975 384986.7492 449998.248 468787.5665 0.735615016 0.930843455 0.855597732 0.818463201 0.939974853 0.915899926 0.821239249 0.959919333 1 18.83857478 -5 0.118395511 1.417345121 0.809032428 0.391735858 0.061833758 186.6756586 1.439934987 18.62887359 0.588778715 1.00E-05 5 -0.608312693 S(ph)LPAPQDNDFLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLPAPQDNDFLSR 13 0 O43353-2;O43353 O43353-2 RIPK2 Receptor-interacting serine/threonine-protein kinase 2 1 S(1)LPAPQDNDFLSR;S(1)LPAPQDNDFLSR 175.43 1.92E-05 195930000 68980 81135 71137 72949 87701 55924 69220 63592 92371 TRUE FALSE 64662.66493 87142.31982 72824.40323 74820.99484 80813.31723 72068.35095 58841.10361 71531.60118 76953.68336 0.84028031 1.132399594 0.946340709 0.972286076 1.050155284 0.936515938 0.764630113 0.929540966 1 16.23170276 1.998145683 19.69666699 0.866571791 1.000815429 0.126478107 0.095138535 5.325486772 56568.16022 0.033264807 0.024016046 99.57393788 -1.998145683 0.134243638 S(ph)LPEEDVAEIQHAEEFLIKPESK ddPTM_SK-BR-3_Pertuzumab_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 275.19 6.13E-52 611537000 287357 168273 225195 193653 231519 163185 302581 183260 305395 TRUE FALSE 269371.8383 180732.108 230536.7317 198622.4638 213336.4316 210293.8604 257211.7881 206140.4144 254422.6016 1.058757503 0.710361842 0.906117343 0.780679321 0.838512107 0.826553377 1.010962809 0.810228388 1 17.95686731 1.761977667 25 0.939328061 0.839675825 0.124341786 0.104491815 21.37046822 22832.07249 0.042922157 0.02380334 57.80663201 -1.761977667 -0.099652236 S(ph)LPGSALELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLPGSALELR 10 0 O75145-2;O75145;R4GN36 O75145-2 PPFIA3 Liprin-alpha-3 1 S(1)LPGSALELR;S(1)LPGSALELR;S(1)LPGSALELR;S(1)LPGSALELR 127.7 0.00036634 339325000 134085 263213 202215 216320 225384 208365 213571 200446 186546 TRUE FALSE 125692.8592 282701.5644 207011.6353 221871.1374 207683.2498 268516.593 181548.0112 225472.1243 155410.2675 0.808780921 1.819066198 1.332033196 1.427647871 1.336354754 1.727791846 1.168185437 1.450818714 1 17.2457223 0.237269709 0.772764669 0.993339145 1.432337669 0.135899719 0.281821037 4.993002539 3.72167435 0.337050624 0.086310371 1.726910019 -0.237269709 0.438998524 S(ph)LPGSPEFLHQEACPFVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLPGSPEFLHQEACPFVGR 19 0 Q96S53-3;Q96S53-2;Q96S53 Q96S53-3 TESK2 Dual specificity testis-specific protein kinase 2 1 S(1)LPGSPEFLHQEACPFVGR;S(0.997)LPGS(0.003)PEFLHQEACPFVGR;S(0.981)LPGS(0.019)PEFLHQEACPFVGR;S(0.999)LPGS(0.001)PEFLHQEACPFVGR 286.8 2.05E-40 801579000 176427 217517 219463 194786 271955 177406 226294 211333 378999 TRUE FALSE 165384.749 233622.185 224668.766 199784.5385 250596.7513 228620.2323 192363.3155 237718.3903 315741.6185 0.523797749 0.739915714 0.711558923 0.632746926 0.793676654 0.724073796 0.609242825 0.752888996 1 18.26838491 -4.999999195 0.435328446 7.350054885 0.685844527 0.618449272 0.078068986 732.4355178 4.490890028 4467.048754 0.040367948 1.00E-05 4.999999195 -6.664210358 S(ph)LPNLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SLPNLSR 7 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 S(0.993)LPNLS(0.007)R;S(0.994)LPNLS(0.006)R;S(0.999)LPNLS(0.001)R;S(1)LPNLSR;S(1)LPNLSR 103.42 0.0087905 1315418000 993374 1280428 1021435 928484 1383871 851041 1115555 1321347 1746040 TRUE FALSE 931200.4946 1375232.221 1045663.921 952310.4714 1275187.354 1096722.721 948287.8841 1486320.082 1454614.644 0.640169889 0.94542718 0.718859751 0.654682307 0.876649605 0.753961007 0.65191691 1.021796451 1 20.47220557 1.224085428 24.99012912 1.010898517 0.7611878 0.547894042 0.098480643 213.1012963 367889.8977 0.091160549 0.023205674 16.75272377 -1.224085428 -0.249710717 S(ph)LPRPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLPRPAK 7 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6 Q8NEY1-5 NAV1 Neuron navigator 1 1 S(1)LPRPAK;S(1)LPRPAK;S(1)LPRPAK;S(1)LPRPAK;S(1)LPRPAK;S(1)LPRPAK 98.033 0.0070009 2528354000 1866490 2445890 1722830 1708050 3124600 939138 3597730 2082250 6311490 TRUE FALSE 1749669.723 2626986.241 1763696.341 1751881.455 2879206.52 1210251.895 3058283.786 2342223.496 5258061.545 0.33275946 0.499611162 0.335427101 0.333180097 0.547579464 0.230170736 0.581637122 0.4454538 1 22.3260996 -0.017293356 0.646664339 1.031078996 0.394170206 0.758574396 0.105307202 2.049384583 0.940645821 0.252510916 0.035702951 0.96096295 0.017293356 -0.63690879 S(ph)LPS(ph)SPERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLPSSPERR 9 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 2 S(0.999)LPS(0.589)S(0.412)PERR 79.23 0.0184 329380000 392000 405200 396600 395380 436840 350150 527190 393780 479800 TRUE FALSE 367465.4197 435201.4296 406007.5393 405526.1202 402532.3485 451232.6208 448142.7537 442944.2998 399718.2804 0.919311019 1.088770394 1.015734229 1.014529833 1.007040129 1.128876619 1.121146507 1.108141212 1 18.60862403 2.243616075 24.99910479 1.102985545 1.021100016 0.32529916 0.054612471 131.5814104 650669.9483 0.017756511 0.014424381 175.2330723 -2.243616075 -0.081885529 S(ph)LPS(ph)SPLLTHQSISVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLPSSPLLTHQSISVR 16 0 J3QQY7;J3KTM5 J3QQY7 TANC2 2 S(1)LPS(0.5)S(0.5)PLLTHQSISVR 159.75 4.77E-09 171930000 39313 115330 102170 87489 119970 67101 115750 115800 140740 TRUE FALSE 36852.46951 123869.1532 104593.5206 89734.11586 110548.0401 86471.96941 98394.36207 130257.8849 117249.5848 0.314307889 1.056457073 0.892058772 0.76532566 0.942843766 0.737503417 0.839187296 1.110945383 1 16.83922329 4.747775504 24.94528189 0.903954335 0.314307572 0.715653709 0.119303376 672.5065509 1820478.232 0.027769991 0.348184203 55946.83262 -4.747775504 -0.589646762 S(ph)LPSHMEEAPNVFQLYQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLPSHMEEAPNVFQLYQR 18 0 Q5THJ4-2;Q5THJ4;H3BLS7 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 S(1)LPSHMEEAPNVFQLYQR;S(1)LPSHMEEAPNVFQLYQR 300 1.07E-49 194174000 142261 161595 164394 161268 160296 127717 178250 142884 90570 TRUE FALSE 133357.138 173559.6619 168293.5033 165406.4099 147706.9988 164586.8246 151523.0673 160723.3819 75453.2819 1.767413353 2.30022681 2.230433178 2.192169853 1.957595416 2.181307697 2.008170665 2.130104588 1 16.20329603 -1.870255939 0.454774732 4.95E-11 2.14837048 0.824009442 0.158202779 18.90149192 1.462880265 20.31120734 0.078438161 0.013481681 1.870255939 2.14837048 S(ph)LPSHMEEAPNVFQLYQRPTSASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLPSHMEEAPNVFQLYQRPTSASR 24 1 Q5THJ4-2;Q5THJ4;H3BLS7 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 S(1)LPSHMEEAPNVFQLYQRPTSASR;S(0.999)LPS(0.001)HMEEAPNVFQLYQRPTSASR 241.69 8.17E-38 627550000 30787 44653 36914 41191 49291 33957 52238 41160 44628 TRUE FALSE 28860.09663 47959.15458 37789.61751 42248.0308 45419.88369 43759.83465 44405.39685 46298.9166 37179.29849 0.776241021 1.289942428 1.01641556 1.136332112 1.221644451 1.17699463 1.194358115 1.245287525 1 15.18221193 3.003701665 23.58874854 1.181210906 1.081450169 0.133090149 0.14127194 122.6329593 781449.4357 0.037389003 0.044461853 1008.559827 -3.003701665 -0.099760737 S(ph)LPSS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLPSSPER 8 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 2 S(1)LPS(0.067)S(0.933)PER 103.87 0.0068552 230670000 383840 323010 343240 336860 358800 306570 448230 303840 358600 TRUE FALSE 359816.1396 346925.9965 351381.8149 345504.3979 330621.2953 395071.7823 381022.0727 341775.0928 298747.3434 1.204416198 1.161268892 1.176183898 1.156510361 1.106692001 1.322427767 1.275399032 1.14402722 1 18.18856636 0.98207134 22.88830773 0.999999994 1.200012413 0.519161684 0.060880613 345.9896003 441703.2547 0.063304413 0.015826103 9.595582414 -0.98207134 0.200012419 S(ph)LPSS(ph)PERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLPSSPERR 9 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 2 S(0.998)LPS(0.235)S(0.766)PERR;S(1)LPS(0.098)S(0.902)PERR 117.63 0.0039211 3233000000 1660950 1560270 1708080 1632710 1637700 1347840 1996850 1587970 1926260 TRUE FALSE 1556994.104 1675794.014 1748596.464 1674608.103 1509081.648 1736939.528 1697440.88 1786231.55 1604754.762 0.970238033 1.04426798 1.089634694 1.043528982 0.940381474 1.082370695 1.057757185 1.113086929 1 20.61392141 S(ph)LPSS(ph)PLLTHQSISVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLPSSPLLTHQSISVR 16 0 J3QQY7;J3KTM5 J3QQY7 TANC2 2 S(0.993)LPS(0.306)S(0.7)PLLTHQSISVR 68.401 0.025934 164480000 70476 162630 170320 156090 164280 153810 185380 177200 135910 TRUE FALSE 66065.03296 174671.2944 174360.0708 160095.5337 151378.1115 198212.4501 157583.99 199323.8101 113225.743 0.583480675 1.542681813 1.539933113 1.41394995 1.336958429 1.75059527 1.391768213 1.760410705 1 16.78884248 4.740464367 24.81657799 1.493243461 0.583480334 0.617449755 0.217697854 86.98791055 1133846.659 0.043933312 0.285453904 55012.87812 -4.740464367 -0.909763128 S(ph)LPSSPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLPSSPER 8 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 S(0.991)LPS(0.003)S(0.006)PER 83.869 0.020452 0 96732 112340 103250 92232 122150 91118 108580 98826 122230 TRUE FALSE 90677.71679 120657.7705 105699.1388 94598.82927 112556.8317 117422.2874 92299.43701 111164.6436 101829.0234 0.8904899 1.184905506 1.038006015 0.928996726 1.105351186 1.153131824 0.906415813 1.091679366 1 16.63578929 1.736223168 24.99999942 0.993047907 1.061760043 0.044772409 0.100121722 0.730249246 7651.975407 0.043644799 0.024203364 54.47825247 -1.736223168 0.068712136 S(ph)LPTTVPES(ph)PNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLPTTVPESPNYR 13 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 2 S(1)LPTTVPES(1)PNYR;S(1)LPTTVPES(1)PNYR;S(1)LPTTVPES(1)PNYR;S(1)LPTTVPES(1)PNYR;S(0.985)LPT(0.015)TVPES(1)PNYR;S(1)LPTTVPES(1)PNYR 356.37 5.00E-76 19231510000 4466350 5159270 4677430 5778540 6843470 4618180 6769400 4900410 6595600 TRUE FALSE 4186809.126 5541267.719 4788380.848 5926827.119 6306011.471 5951373.596 5754391.314 5512236.976 5494751.751 0.761965111 1.008465527 0.871446257 1.078634193 1.147642652 1.083101451 1.047252283 1.003182168 1 22.38962287 3.233436975 24.99926436 1.066812009 0.906708548 0.561707143 0.073320056 93.81894977 457761.3445 0.019935796 0.024520641 1711.736751 -3.233436975 -0.160103461 S(ph)LPTTVPESPNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLPTTVPESPNYR 13 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 1 S(1)LPTTVPESPNYR;S(0.371)LPT(0.371)T(0.257)VPESPNYR;S(1)LPTTVPESPNYR;S(1)LPTTVPESPNYR 268.93 7.53E-25 5603530000 652869 735024 775170 754693 818600 551997 903379 602266 885219 TRUE FALSE 612007.0947 789445.9418 793557.3985 774059.7001 754310.4581 711349.573 767925.7055 677460.2359 737470.2302 0.829873627 1.070478386 1.076053468 1.049614843 1.022835129 0.96458073 1.041297227 0.918627231 1 19.49222529 2.384733277 7.827448223 0.990057898 1.029483496 0 0.076431943 0.773425989 57.29468398 0.025380554 0.02119512 242.5120246 -2.384733277 0.039425598 S(ph)LPVSICR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLPVSICR 8 0 O94885;A0A087WW74 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 S(1)LPVSICR;S(1)LPVSICR;S(1)LPVSICR;S(1)LPVSICR 169.41 0.00031595 291210000 601866 656042 576812 572253 687780 458218 687827 550206 685459 TRUE FALSE 564196.2814 704616.0323 590494.253 586937.9808 633764.5332 590498.0981 584693.7268 618900.4303 571051.4647 0.987995507 1.233892348 1.034047349 1.027819763 1.109820344 1.034054082 1.023889724 1.083790987 1 19.12326125 3.730425069 24.51219718 1.045719701 1.13014656 0.132598957 0.066406161 152.1374172 1128743.192 0.015433098 0.02644088 5375.576779 -3.730425069 0.084426859 S(ph)LPVSVPVWGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLPVSVPVWGFK 12 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 S(1)LPVSVPVWGFK;S(1)LPVSVPVWGFK 247.88 1.15E-16 4594400000 2384400 3279900 2323300 2726500 4816400 1397560 5626200 3034200 6705700 TRUE FALSE 2235164.66 3522747.209 2378409.773 2796466.606 4438139.372 1801012.885 4782603.541 3413026.549 5586475.35 0.400102841 0.630584937 0.425744253 0.500577991 0.794443561 0.322388048 0.856103937 0.610944529 1 22.41350691 0.645351427 0.398445489 1.04264342 0.488388351 0.478655476 0.155890516 1.598948233 0.553602603 0.280623904 0.107546438 4.419279068 -0.645351427 -0.554255069 S(ph)LQEEHVAVAQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLQEEHVAVAQLR 13 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 S(1)LQEEHVAVAQLR;S(1)LQEEHVAVAQLR 169.25 1.86E-05 640360000 823700 789370 683960 683350 543260 501150 775320 574050 702810 TRUE FALSE 772146.0873 847815.7761 700183.8542 700885.9179 500594.551 645823.8695 659067.9637 645721.4061 585506.4707 1.318766104 1.44800411 1.195860147 1.197059218 0.854976975 1.103017476 1.12563737 1.102842477 1 19.15932559 3.483994185 1.601535832 1.060357225 1.383282157 0.683183809 0.091178578 0.207703834 1.075432979 0.027992866 0.050384993 3047.854182 -3.483994185 0.322924931 S(ph)LQLMDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLQLMDNR 8 0 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 S(1)LQLMDNR;S(1)LQLMDNR;S(1)LQLMDNR;S(1)LQLMDNR 129.84 0.0011261 524488000 1149185 1158720 1089775 1094578 1407350 804481 1278730 1030550 1280690 TRUE FALSE 1077259.562 1244512.834 1115624.978 1122666.725 1296822.408 1036721.605 1086996.308 1159216.436 1066934.565 1.009677254 1.166437826 1.0456358 1.05223578 1.215465737 0.971682462 1.018803161 1.086492531 1 20.02504027 2.189675277 24.99998959 1.018841732 1.098038277 0.264210356 0.065213361 148.2007249 75788.88981 0.022589 0.016683116 154.7658999 -2.189675277 0.079196545 S(ph)LQLPASPAPDPSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 254.59 1.11E-24 1563284000 1244907 1205970 1105356 1152140 1305330 880810 1198837 1135597 929038 TRUE FALSE 1166990.493 1295261.274 1131575.566 1181705.863 1202814.647 1135085.548 1019082.521 1277378.785 773975.556 1.507787273 1.67351703 1.462030109 1.526799979 1.554073172 1.466565112 1.316685667 1.65041231 1 19.56192848 -3.087470908 0.22195601 1.77E-13 1.595260221 0.704423353 0.104040544 30.74199516 0.657801341 14.60269195 0.192472206 0.000817578 3.087470908 1.595260221 S(ph)LQLPASPAPDPSPRPAYK ddPTM_SK-BR-3_Pertuzumab_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 192.58 4.33E-15 1919110000 1299760 1509790 1208460 1308730 1861120 888410 1732510 1376840 2247970 TRUE FALSE 1218410.342 1621576.423 1237125.242 1342314.227 1714955.143 1144879.545 1472736.209 1548741.505 1872769.285 0.650592869 0.865870898 0.660586038 0.716753654 0.915732203 0.611329732 0.786394897 0.826979339 1 20.83674175 0.878548101 2.075412451 0.999200738 0.746875342 0.43001479 0.094120763 0.442748886 3.824144538 0.080698191 0.022290581 7.560457924 -0.878548101 -0.252325396 S(ph)LQQLAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLQQLAEER 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 S(1)LQQLAEER;S(1)LQQLAEER 150.49 8.93E-05 627200000 341470 357780 317920 335060 333390 299700 416660 373600 429290 TRUE FALSE 320098.0022 384270.4035 325461.2125 343658.2069 307206.8942 386218.5248 354185.7011 420244.7824 357638.7257 0.895031716 1.074465308 0.910027883 0.960908823 0.858986659 1.079912484 0.990344937 1.175053908 1 18.44814344 2.207788925 24.99989967 1.05369665 0.955120356 0.378745314 0.075626309 253.4173315 205882.8099 0.026904976 0.019872801 161.3574142 -2.207788925 -0.098576294 S(ph)LQTLPTDSSTFDTDTFCPPRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLQTLPTDSSTFDTDTFCPPRPK 23 1 B0QY95;Q9NQG6 B0QY95 MIEF1 Mitochondrial dynamics protein MID51 1 S(1)LQTLPTDSSTFDTDTFCPPRPK 137.9 3.46E-06 206970000 173230 105560 128660 127630 136660 106350 191370 112860 157450 TRUE FALSE 162387.8435 113375.7722 131711.876 130905.2019 125927.2749 137051.5186 162675.8451 126950.8194 131170.5778 1.237989847 0.864338437 1.004126673 0.997976864 0.960026836 1.044834298 1.240185473 0.967829993 1 17.00108463 1.996945614 23.84561635 1.10764678 0.991733695 0 0.1186838 112.3566577 877174.6161 0.041594137 0.030092119 99.29916906 -1.996945614 -0.115913086 S(ph)LQTLPTDSSTFDTDTFCPPRPKPVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLQTLPTDSSTFDTDTFCPPRPKPVAR 27 2 B0QY95;Q9NQG6 B0QY95 MIEF1 Mitochondrial dynamics protein MID51 1 S(0.997)LQT(0.003)LPTDSSTFDTDTFCPPRPKPVAR;S(0.999)LQT(0.001)LPTDSSTFDTDTFCPPRPKPVAR 221.72 1.30E-34 371410000 266150 270950 261680 256400 281270 179217 428070 244920 447570 TRUE FALSE 249492.1466 291011.4199 267887.1732 262979.6581 259180.1888 230954.0386 363884.8775 275498.8011 372867.6756 0.669117124 0.780468351 0.71845105 0.705289504 0.695099645 0.619399464 0.975908885 0.738864802 1 18.50830421 1.736290636 15.18508382 0.892214376 0.710026957 0.595283378 0.079798768 0.048450387 124.0267479 0.033536629 0.018507349 54.4867164 -1.736290636 -0.182187418 S(ph)LRLS(ph)AQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLRLSAQK 8 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 2 S(1)LRLS(1)AQK 95.631 0.0033292 0 240370 244500 219590 212080 320880 159290 276470 248060 419160 TRUE FALSE 225325.6708 262603.0344 224798.7785 217522.3319 295679.3792 205274.4371 235015.8901 279030.837 349199.4881 0.645263462 0.752014374 0.643754605 0.622917098 0.846734859 0.587842892 0.673013272 0.799058551 1 18.41369192 0.932849423 3.150828345 0.999499892 0.683691966 0.663683615 0.072670449 0.174373736 4.182801672 0.063594027 0.016612263 8.567407476 -0.932849423 -0.315807926 S(ph)LS(ph)GSSPCPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.997)LS(0.897)GS(0.037)S(0.069)PCPK 82.505 0.026041 181270000 850810 567040 701120 691410 708440 479780 776300 499600 779970 TRUE FALSE 797559.3208 609024.2316 717750.8975 709152.7512 652801.9801 618284.6974 659901.0218 561976.1598 649787.9682 1.227414726 0.937266095 1.104592471 1.091360237 1.004638454 0.951517614 1.015563621 0.864860827 1 19.3096095 2.527768213 3.974517965 0.965636496 1.066667694 0.357863683 0.080796075 0.302695573 9.866517196 0.026048006 0.023541945 337.1073436 -2.527768213 0.101031198 S(ph)LS(ph)PGVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SLSPGVSR 8 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 2 S(1)LS(1)PGVSR;S(1)LS(1)PGVSR;S(1)LS(1)PGVSR;S(1)LS(1)PGVSR;S(1)LS(1)PGVSR 121.36 0.0021002 790550000 1956110 1483170 1872380 1724480 1531770 1674740 2181140 1539310 1375640 TRUE FALSE 1833680.567 1592985.45 1916793.738 1768733.076 1411470.963 2158210.251 1854098.306 1731496.242 1146036.797 1.600018928 1.389995028 1.672541181 1.543347544 1.231610509 1.883194551 1.617834882 1.510855713 1 20.12822194 0.933049436 14.74055428 0.999999997 1.563484226 0.517024203 0.169653582 74.6195671 16430.18182 0.154781946 0.038697046 8.571354079 -0.933049436 0.563484229 S(ph)LS(ph)PKPR ddPTM_SK-BR-3_Pertuzumab_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 114.97 0.0032922 1165940000 4032320 2118910 2790780 2717420 2813080 1997130 3406550 2119470 2992320 TRUE FALSE 3779944.289 2275796.301 2856978.62 2787153.598 2592152.044 2573669.01 2895769.452 2384090.495 2492882.461 1.51629463 0.912917611 1.146054282 1.118044529 1.039821205 1.032406883 1.161614917 0.956358967 1 21.24938343 4.749998535 24.92508341 1.058122548 1.516294911 0.771655489 0.0801721 793.9198018 1730046.649 0.018264958 0.289507211 56233.94285 -4.749998535 0.458172363 S(ph)LS(ph)RS(ph)PLPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSRSPLPSR 10 1 Q9NYV4;Q9NYV4-2 Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 3 S(1)LS(0.995)RS(0.731)PLPS(0.274)R 75.589 0.015773 0 300680 236650 270940 244320 267720 198500 272670 219990 268790 TRUE FALSE 281860.9755 254171.8122 277366.8247 250589.6648 246694.3511 255803.7276 231785.6648 247456.2358 223927.2126 1.258716939 1.135064423 1.238647244 1.119067495 1.101672049 1.142352127 1.03509378 1.105074425 1 17.77267034 2.30240204 0.345405436 0.996996602 1.237019222 0.671006517 0.04519208 0.876852603 0.253825043 0.052857881 0.075146657 200.6328489 -2.30240204 0.24002262 S(ph)LSDPIPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSDPIPQR 9 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.617)LS(0.383)DPIPQR 74.162 0.043922 167360000 172070 176800 181070 176840 207050 153520 203490 177880 347490 TRUE FALSE 161300.4459 189890.456 185365.0659 181378.0138 190789.1282 197838.7318 172978.5636 200088.7096 289491.6741 0.557185095 0.655944447 0.640312252 0.626539656 0.659048758 0.68340042 0.597525176 0.691172588 1 18.14316233 0.860246777 5.362302654 0.999996561 0.636376323 0.915180002 0.034984224 0.450858061 17.142685 0.030500436 0.007691972 7.248477194 -0.860246777 -0.363620238 S(ph)LSDSESDDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 S(0.956)LS(0.041)DS(0.003)ESDDSK;S(0.98)LS(0.019)DS(0.001)ESDDSK;S(0.997)LS(0.003)DSESDDSK;S(0.999)LS(0.001)DSESDDSK;S(0.995)LS(0.005)DSESDDSK;S(0.976)LS(0.022)DS(0.002)ESDDSK 324.67 1.56E-46 6627040000 10730540 6381140 8138650 8036530 7825230 5928580 8278900 5627290 7688540 TRUE FALSE 10058934.66 6853606.245 8331702.621 8242760.966 7210668.001 7640064.804 7037555.803 6329869.544 6405273.004 1.570414665 1.0699944 1.300756832 1.286871139 1.125739371 1.192777388 1.098712857 0.988227908 1 22.61082863 1.833788522 0.664585869 0.977837664 1.277493799 0.466872686 0.126326047 0.689347596 0.609433118 0.108627023 0.058626277 68.20065127 -1.833788522 0.299656135 S(ph)LSGS(ph)SPCPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)LS(0.004)GS(0.961)S(0.036)PCPK 203.78 2.91E-07 479720000 2806400 1867400 2082900 2167200 2257900 1400900 2418100 1543000 2378900 TRUE FALSE 2630752.434 2005664.239 2132307.372 2222814.021 2080573.642 1805317.088 2055528.354 1735646.947 1981846.222 1.327425107 1.012018096 1.07591969 1.121587536 1.049815883 0.910926927 1.037178531 0.875772766 1 20.91841359 2.442937915 5.115634885 0.966087689 1.102868296 0.433609064 0.092647233 0.211610921 13.94930578 0.030387007 0.025726628 277.2923673 -2.442937915 0.136780607 S(ph)LSGSS(ph)PCPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.999)LS(0.001)GS(0.015)S(0.985)PCPK;S(1)LSGS(0.004)S(0.996)PCPK;S(1)LSGSS(1)PCPK;S(0.982)LS(0.319)GS(0.216)S(0.483)PCPK 248.91 9.91E-13 1341010000 6011340 4025660 4795120 4952040 5120560 3754590 6115520 3810340 5311630 TRUE FALSE 5635100.96 4323724.055 4908862.511 5079117.73 4718411.873 4838479.182 5198554.55 4286069.337 4425084.639 1.273444786 0.977094092 1.109326242 1.147801261 1.066287373 1.093420709 1.174792117 0.968584713 1 22.07727362 1.222478657 24.99985148 0.984292235 1.106317771 0.339551241 0.076963996 335.4544731 521458.9106 0.068544279 0.017356963 16.69085781 -1.222478657 0.122025535 S(ph)LSGSSPCPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.999)LS(0.001)GSSPCPK;S(0.5)LS(0.5)GSSPCPK 206.36 1.59E-07 1028790000 940600 856206 844436 920130 977400 587660 907590 647771 1011530 TRUE FALSE 881729.525 919600.3831 864466.4207 943742.0936 900638.9466 757307.9021 771505.3052 728646.6353 842699.1083 1.046315958 1.091255911 1.025830468 1.11990399 1.068755073 0.8986694 0.915516936 0.86465813 1 19.68465807 2.24177452 24.99853207 0.912475731 1.069424898 0.763037173 0.041642081 34.14761557 265610.9783 0.01330202 0.010695835 174.4915979 -2.24177452 0.156949167 S(ph)LSLSLADSGHLPDVHGFNSYGSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLSLSLADSGHLPDVHGFNSYGSHR 25 0 Q9Y446;Q9Y446-2;E9PKC4;E9PRW6 Q9Y446 PKP3 Plakophilin-3 1 S(0.41)LS(0.317)LS(0.273)LADSGHLPDVHGFNSYGSHR;S(0.993)LS(0.007)LSLADSGHLPDVHGFNSYGSHR;S(0.995)LS(0.005)LSLADSGHLPDVHGFNSYGSHR 326.55 1.62E-87 2807920000 371380 715230 508730 462242 690870 341532 700870 534130 914090 TRUE FALSE 348135.9887 768186.3734 520797.3158 474103.9123 636611.857 440126.7441 595781.0501 600817.3063 761522.4738 0.457157866 1.008750759 0.683889621 0.622573763 0.835972514 0.577956343 0.782355177 0.788968582 1 19.53852709 0.756621918 1.926131122 0.99955219 0.73330367 0.2611907 0.150348769 1.33520797 7.906635819 0.13315289 0.037046679 5.709813429 -0.756621918 -0.266248521 S(ph)LSPILPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.513)LS(0.487)PILPGR;S(0.871)LS(0.129)PILPGR;S(0.81)LS(0.19)PILPGR;S(0.8)LS(0.2)PILPGR;S(0.868)LS(0.132)PILPGR 133.99 0.00027417 847459000 645245 810090 769900 777170 822390 723010 863440 747040 844050 TRUE FALSE 604860.2672 870069.9065 788162.3916 797113.4979 757802.8068 931731.2499 733975.1878 840309.5884 703172.6022 0.860187478 1.237348986 1.120866184 1.133595785 1.077691031 1.325039182 1.043805156 1.195026066 1 19.42351933 4.749700462 24.87257094 1.148405063 0.860187298 0.466197381 0.094414889 1266.428291 2827569.894 0.019700539 0.302392041 56195.36052 -4.749700462 -0.288217766 S(ph)LSPNHNTLQTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSPNHNTLQTLK 13 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.608)LS(0.392)PNHNTLQTLK 210.39 1.95E-08 1661300000 2153000 2627400 2524200 2383200 3367700 1961000 2948800 2822600 3830400 TRUE FALSE 2018247.573 2821935.43 2584075.216 2444356.947 3103214.427 2527108.866 2506654.815 3175007.823 3191081.495 0.632465068 0.884319449 0.80978039 0.765996403 0.9724648 0.791928652 0.785518897 0.994962939 1 21.60561402 -4.999999986 0.047700653 1.738772696 0.448496619 0.406632121 0.090124417 719.589615 2.545333342 69.04686451 16.54653778 1.00E-05 4.999999986 -1.290276076 S(ph)LSQSFENLLDEPAYGLIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSQSFENLLDEPAYGLIQK 20 0 Q8TC07-2;Q8TC07-3;C9JA93 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 S(0.386)LS(0.386)QS(0.228)FENLLDEPAYGLIQK 159.8 1.61E-11 10298000 51792 48748 52975 45088 45157 42204 64067 45919 67038 TRUE FALSE 48550.43117 52357.35264 54231.59202 46245.03441 41610.55137 54387.60968 54460.74812 51652.08823 55848.92472 0.869317206 0.937481839 0.971040934 0.828038045 0.745055551 0.9738345 0.975144077 0.924853764 1 15.76924188 S(ph)LSS(ph)SPVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSSSPVKK 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 2 S(0.817)LS(0.188)S(0.915)S(0.079)PVKK 100.09 0.0032738 268230000 1206300 646000 829130 765630 971790 551240 1151300 766450 1346600 TRUE FALSE 1130799.836 693830.5122 848797.3551 785277.362 895469.5334 710374.0394 978673.2531 862142.9697 1121843.761 1.007983354 0.618473389 0.75660924 0.699988171 0.79821234 0.633220119 0.872379281 0.768505384 1 20.09744033 0.573308938 0.829062997 1.000149621 0.740868849 0.274286472 0.114265351 1.564556538 1.77629129 0.101572603 0.033918582 3.743768088 -0.573308938 -0.259280772 S(ph)LSSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLSSLR 6 0 O94915;H0Y9X0;A0A286YEZ9;A0A2C9F2R7;C9J1G1;Q70YC5-2;Q70YC5;Q70YC5-4;Q70YC5-3;Q8TF61 O94915;Q8TF61 FRYL;ZNF365;FBXO41 Protein furry homolog-like;Protein ZNF365;F-box only protein 41 1 S(0.998)LS(0.002)SLR;S(0.997)LS(0.002)S(0.001)LR;S(0.999)LS(0.001)S(0.001)LR 160.54 0.0092092 558810000 364888 446260 386258 404954 440750 312047 519710 412485 380598 TRUE FALSE 342050.3114 479301.5547 395420.2222 415345.8052 406135.2729 402129.9032 441784.3103 463984.6602 317073.735 1.078772139 1.511640675 1.247092327 1.309934439 1.280885889 1.268253592 1.393317268 1.463333632 1 18.27445885 -0.444875412 7.018770468 0.999999996 1.330899521 0.404700848 0.12090373 0 0 0.105283075 0.024815459 0.359024915 0.444875412 0.330899526 S(ph)LSSS(ph)PVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLSSSPVKK 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 2 S(1)LS(0.002)S(0.158)S(0.84)PVKK;S(1)LS(0.181)S(0.103)S(0.716)PVKK;S(0.981)LS(0.019)S(0.366)S(0.633)PVKK 147.39 6.18E-05 1340770000 5138300 2501680 3490040 3085610 3730520 2328660 4760400 3119020 6038300 TRUE FALSE 4816702.975 2686906.99 3572825.397 3164791.977 3437540.007 3000906.339 4046622.213 3508436.513 5030468.721 0.9575058 0.534126567 0.710237076 0.62912467 0.683343879 0.596546069 0.804422498 0.697437298 1 22.2622614 0.357668996 0.769645926 1.003802861 0.672775017 0.379895845 0.117381147 2.073618989 1.711943757 0.121911647 0.036061148 2.27860474 -0.357668996 -0.331027844 S(ph)LSSSPDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSSSPDKR 9 1 Q9BVI0;Q5JWZ0;Q5JXL1;B0QYY0;Q9BVI0-2 Q9BVI0 PHF20 PHD finger protein 20 1 S(0.283)LS(0.283)S(0.217)S(0.217)PDKR 74.944 0.024291 101500000 122530 73572 75050 78105 92355 53595 90693 68695 98476 TRUE FALSE 114861.066 79019.34743 76830.22144 80109.30653 85101.81084 69067.00646 77094.4266 77271.72197 82039.71942 1.400066539 0.963184028 0.936500295 0.976469777 1.037324499 0.841872778 0.939720749 0.941881841 1 16.32403494 4.738849087 5.58571439 0.948239754 1.415790745 0.884681442 0.050527579 0.042749854 5.380931592 0.011443454 0.07638427 54808.64767 -4.738849087 0.46755099 S(ph)LSTSGESLYHVLGLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSTSGESLYHVLGLDK 17 0 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 S(0.486)LS(0.486)T(0.013)S(0.013)GES(0.002)LYHVLGLDK 164.02 1.70E-09 85121000 73520 90517 81235 79198 98220 68996 109380 109440 110490 TRUE FALSE 68918.51444 97218.97286 83161.93256 81230.35476 90506.1974 88914.02514 92979.48443 123103.8249 92048.50521 0.74871954 1.05617112 0.903457719 0.882473372 0.983244619 0.965947518 1.010114007 1.337379946 1 16.49010667 1.44798534 5.022962378 1.174138662 0.940709258 0.43178096 0.113319153 0.15986498 7.968507873 0.065821358 0.025466735 28.05338941 -1.44798534 -0.233429404 S(ph)LSVEHLETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSVEHLETK 10 0 J3KN34;P26045-2;P26045 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 S(0.61)LS(0.39)VEHLETK;S(0.62)LS(0.38)VEHLETK 167.71 3.32E-06 539550000 2504500 2287300 2207000 2150700 2528900 1658470 3135200 2290600 2467900 TRUE FALSE 2347747.816 2456654.072 2259351.082 2205890.603 2330290.395 2137243.366 2665105.866 2576586.452 2055991.547 1.141905383 1.19487557 1.098910687 1.072908401 1.133414385 1.03951953 1.296263046 1.25320868 1 20.9714029 1.74014359 24.99999952 1.211259529 1.120471722 0.092344188 0.087597044 0.386542581 6136.957467 0.036914492 0.020470848 54.97225972 -1.74014359 -0.090787807 S(ph)LT(ph)RS(ph)PPAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLTRSPPAIR 10 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(1)LT(1)RS(1)PPAIR;S(1)LT(1)RS(1)PPAIR 91.712 0.032944 1246170000 655660 545020 617110 607240 641370 436440 638450 470410 639440 TRUE FALSE 614623.411 585373.8479 631748.1406 622822.8065 590999.3874 562433.143 542720.3496 529141.724 532713.3331 1.153760142 1.098853382 1.18590638 1.169151902 1.109413545 1.055789499 1.018784994 0.993295439 1 19.02299986 2.126223659 1.666248311 1.002252885 1.148675425 0.889031404 0.023187843 0.124462335 0.664883689 0.014360477 0.007924179 133.7284032 -2.126223659 0.14642254 S(ph)LTAHSLLPLAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLTAHSLLPLAEK 13 0 F2Z2E2;Q86VI3 F2Z2E2 IQGAP3 Ras GTPase-activating-like protein IQGAP3 1 S(0.495)LT(0.495)AHS(0.011)LLPLAEK 150.37 2.85E-05 80952000 319310 328610 317920 295290 410710 219830 427910 330660 413570 TRUE FALSE 299324.9571 352940.6263 325461.2125 302867.6413 378454.4933 283291.3524 363748.868 371943.6289 344542.4952 0.868760635 1.024374732 0.944618493 0.879042921 1.09842617 0.822224707 1.055744569 1.079529039 1 18.39432241 1.604749056 25 1.05074238 0.95266801 0.262638305 0.081211497 0.401906538 3194.996647 0.036651087 0.01808469 40.24844036 -1.604749056 -0.09807437 S(ph)LTNDWEDHLAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLTNDWEDHLAVK 13 0 P08238;P07900;P07900-2 P08238;P07900 HSP90AB1;HSP90AA1 Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha 1 S(0.873)LT(0.127)NDWEDHLAVK;S(0.967)LT(0.033)NDWEDHLAVK 151.04 7.44E-07 84690000 301540 222835 231462 211763 232187 182837 308370 196642 225507 TRUE FALSE 282667.1497 239333.9353 236952.3879 217197.1971 213951.9696 235619.0738 262132.7813 221193.1866 187868.4249 1.504601691 1.27394444 1.261267763 1.156113366 1.138839429 1.254170699 1.39529983 1.177383516 1 17.51936309 -4.973323051 0.176027958 2.56E-31 1.327797495 0.43196774 0.105013952 152.2213015 1.468066772 54.0051061 0.359165733 1.06E-05 4.973323051 1.327797495 S(ph)LTNSHLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLTNSHLEK 9 0 F8VX12;F8VX04;Q9H2H9 F8VX12 SLC38A1 Sodium-coupled neutral amino acid transporter 1 1 S(0.995)LT(0.005)NSHLEK;S(0.995)LT(0.005)NSHLEK;S(0.996)LT(0.004)NSHLEK 153.81 4.97E-05 2095330000 2521800 1828790 1949490 1835730 2855150 1888560 2372610 2376210 3171310 TRUE FALSE 2363965.04 1964195.514 1995732.823 1882837.94 2630918.036 2433756.614 2016859.157 2672885.049 2641997.874 0.894764172 0.743450831 0.755387748 0.712656872 0.995806266 0.921180383 0.763384095 1.01169084 1 21.33319787 2.746491719 24.91755779 0.90924531 0.767516366 0.442487342 0.086647481 594.7514612 1868561.902 0.026197295 0.027331733 557.8169662 -2.746491719 -0.141728944 S(ph)LTRS(ph)PPAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLTRSPPAIR 10 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.966)LT(0.034)RS(1)PPAIR 86.498 0.0076914 193980000 174220 138610 163250 177340 158060 140250 151940 130690 144900 TRUE FALSE 163315.8812 148872.8286 167122.3671 181890.8446 145646.6052 180737.8982 129158.0075 147006.9342 120715.2539 1.352901774 1.233256145 1.384434541 1.506775977 1.206530248 1.497225018 1.06993941 1.217799155 1 16.88124846 1.675219957 8.239658832 1.10918609 1.34993357 0.567280352 0.109311135 0.090526241 10.66300834 0.049079519 0.025810211 47.33909569 -1.675219957 0.24074748 S(ph)LVGTPYWMAPELISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 16 SLVGTPYWMAPELISR 16 0 O96013;O96013-4;O96013-2;O96013-3;M0R1R1 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(0.99)LVGT(0.01)PYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR 346.92 4.44E-87 8762255000 2683229 2639120 2569010 2485906 2903784 2033032 3466850 2302666.1 2998059 TRUE FALSE 2515290.487 2834523.191 2629948.13 2549698.557 2675732.518 2619935.335 2947028.027 2590159.031 2497663.585 1.007057356 1.134869887 1.052963316 1.020833459 1.071294202 1.048954451 1.179913918 1.037032788 1 21.25214774 S(ph)LVGTPYWMAPEVISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLVGTPYWMAPEVISR 16 0 Q9NQU5-2;Q9NQU5 Q9NQU5-2 PAK6 Serine/threonine-protein kinase PAK 6 1 S(1)LVGTPYWMAPEVISR;S(1)LVGTPYWMAPEVISR;S(1)LVGTPYWMAPEVISR;S(1)LVGTPYWMAPEVISR 239.51 8.29E-20 168919000 89040 75802 86238 71077 121890 74169 101287 104049 280420 TRUE FALSE 83467.14534 81414.45895 88283.60608 72900.95615 112317.2511 95580.38627 86099.95465 117039.7467 233616.0904 0.357283375 0.348496796 0.377900366 0.312054517 0.480777034 0.409134431 0.368553187 0.500991804 1 17.83378012 -4.999999992 0.274440951 5.36806665 0.343977751 0.948498862 0.04515059 41.67380725 0.402486276 103.2695523 0.050399184 1.00E-05 4.999999992 -5.024088899 S(ph)LY(ph)S(ph)FIKGDT(ph)SGDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLYSFIKGDTSGDYR 15 1 P09525;Q6P452;P09525-2 P09525 ANXA4 Annexin A4;Annexin 4 S(0.886)LY(0.9)S(0.907)FIKGDT(0.669)S(0.637)GDYR 42.711 0.095013 2358500000 494420 709320 561830 691910 752670 595540 668390 533150 769410 TRUE FALSE 463475.1348 761838.7908 575156.8729 709665.582 693558.3343 767462.7302 568171.1245 599714.9511 640990.5004 0.723060848 1.188533668 0.897293911 1.107139001 1.082010317 1.197307495 0.886395546 0.935606613 1 19.28994345 1.623465866 25 0.933254708 1.039880292 0.083267073 0.14163478 1.802355485 2881.654556 0.059834753 0.033033063 42.02094997 -1.623465866 0.106625584 S(ph)LYESFVSSSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLYESFVSSSDR 12 0 P18615;P18615-3;A0A0A0MT02;A2ABK4 P18615 NELFE Negative elongation factor E 1 S(1)LYESFVSSSDR 156.14 7.65E-05 51029000 13318 19445 14564 14049 25417 8095.2 17944 13263 36737 TRUE FALSE 12484.45015 20884.72803 14909.46496 14409.52112 23420.85135 10432.15283 15253.46378 14918.91475 30605.35737 0.40791715 0.682387981 0.487152128 0.470816954 0.76525332 0.34086035 0.498391951 0.48746089 1 14.90149659 -1.291045539 3.208086891 1.002510772 0.525630087 0.601608644 0.123230751 26515552.18 36085080.69 642459.0404 0.027078521 0.051162818 1.291045539 -0.476880685 S(ph)MDELNHDFQALALEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 SMDELNHDFQALALEGR 17 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38 Q5T1Z4 PUM1 Pumilio homolog 1 1 S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR 266.74 7.07E-28 601198000 283671.9 309300 295370 296977 312061 267479.4 391798 276030 351007 TRUE FALSE 265917.3821 332200.8938 302376.3159 304597.9326 287552.9879 344696.3606 333051.5272 310492.9531 292421.6641 0.909362796 1.136033798 1.034042115 1.04163942 0.983350494 1.178764787 1.138942726 1.061798735 1 18.15769067 2.24346874 24.99987354 1.112518423 1.039325145 0.156418787 0.074333281 198.1457408 1009274.156 0.024753025 0.02009888 175.1736344 -2.24346874 -0.073193279 S(ph)MDLGIADETK ddPTM_SK-BR-3_Pertuzumab_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 202.61 1.54E-07 357345000 955270 690861 713850 706640 733530 483198 966230 664778 835170 TRUE FALSE 895481.3559 742013.0673 730782.8591 724773.5787 675921.5127 622689.4185 821352.7815 747776.9967 695774.7316 1.287027705 1.0664559 1.050315319 1.0416785 0.971466025 0.894958368 1.180486649 1.074740089 1 19.40826076 4.780542869 2.787918751 1.039342384 1.348520581 0.540232879 0.07335826 0.44962532 4.378926309 0.018283336 0.332487274 60331.32572 -4.780542869 0.309178197 S(ph)MDSSDLSDGAVTLQEYLELKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SMDSSDLSDGAVTLQEYLELKK 22 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 S(0.45)MDS(0.45)S(0.101)DLSDGAVTLQEYLELKK;S(1)MDSSDLSDGAVTLQEYLELKK;S(0.893)MDS(0.09)S(0.017)DLSDGAVTLQEYLELKK;S(0.988)MDS(0.01)S(0.002)DLSDGAVTLQEYLELKK 158.97 8.65E-12 690977000 1341350 769470 901940 866500 1045460 662160 1262490 898070 1125370 TRUE FALSE 1257397.298 826442.3594 923334.4427 888735.857 963353.7888 853314.8427 1073191.345 1010196.016 937538.4768 1.34116874 0.881502338 0.984849652 0.947946009 1.027535203 0.910165144 1.144690454 1.077498195 1 19.83851837 1.729262348 24.99999756 1.083883818 0.99438582 0.024550957 0.130900895 1.861568013 4979.158493 0.055195206 0.030608592 53.61204192 -1.729262348 -0.089497998 S(ph)MGYDDLDYGMMSDYGTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SMGYDDLDYGMMSDYGTAR 19 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 S(1)MGYDDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR 335.98 1.95E-75 172527000 74008 117591 83275 99640 135387 87954 120027 108762 124593 TRUE FALSE 69375.97139 126297.56 85250.32233 102196.9311 124754.2511 113344.892 102030.0656 122341.1751 103797.6234 0.668377263 1.216767358 0.821312854 0.984578719 1.201898917 1.091979645 0.982971115 1.178651024 1 16.66341389 2.98048905 23.89552002 1.082418868 0.95113699 0.225583431 0.151905345 805.0793253 986001.3308 0.043196882 0.046488593 956.0685893 -2.98048905 -0.131281879 S(ph)MPSMGYMTHTVSAPSLHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SMPSMGYMTHTVSAPSLHGK 20 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3;A0A1B0GUN0 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 S(0.989)MPS(0.011)MGYMTHTVSAPSLHGK 157.63 7.87E-09 229140000 237950 300940 243370 238690 393020 204100 340440 284110 424860 TRUE FALSE 223057.1343 323221.9107 249142.8513 244815.1895 362153.7946 263020.3567 289394.1825 319581.7589 353948.1213 0.630197254 0.913190073 0.703896521 0.691669696 1.023183265 0.74310426 0.817617512 0.902905651 1 18.43317839 -4.999999729 0.116943005 1.677037145 0.697622284 0.315502773 0.11062258 205.3333348 1.570283758 32.53395436 1.07079099 1.00E-05 4.999999729 -0.979414861 S(ph)MPVLGSVSSVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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(0.999)MPVLGS(0.001)VSSVTK;S(1)MPVLGSVSSVTK;S(1)MPVLGSVSSVTK;S(1)MPVLGSVSSVTK;S(1)MPVLGSVSSVTK 255.34 8.18E-24 1281183000 2396830 2659760 2022850 2144320 2385610 1286390 3844770 2071100 3294810 TRUE FALSE 2246816.689 2856691.398 2070832.957 2199346.882 2198253.814 1657749.91 3268282.432 2329681.394 2744884.926 0.81854677 1.040732663 0.754433433 0.801252854 0.800854634 0.603941497 1.190681038 0.848735542 1 21.38831424 -0.956807813 5.287217216 1.000000386 0.873548775 0.065117703 0.159705259 7.06E-07 1.39E-07 0.150414155 0.035452848 0.110456731 0.956807813 -0.126451611 S(ph)MSIDDTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SMSIDDTPR 9 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GUE9;Q96N67-7;A0A0C4DGY6;A0A1B0GVW2 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 S(0.987)MS(0.013)IDDTPR;S(0.999)MS(0.001)IDDTPR;S(1)MSIDDTPR;S(0.807)MS(0.192)IDDT(0.001)PR;S(0.998)MS(0.002)IDDTPR;S(0.985)MS(0.015)IDDTPR;S(1)MSIDDTPR 265.67 1.94E-15 3181690000 2707446 3565200 3216720 3340930 3792330 2949088 3504490 3204960 3250780 TRUE FALSE 2537991.788 3829171.118 3293022.117 3426663.92 3494495.699 3800441.831 2979024.259 3605106.311 2708203.817 0.937149476 1.413915413 1.215943238 1.265290263 1.290337041 1.403307169 1.100000022 1.331179835 1 21.36890489 -1.107003508 6.051178123 0.999998995 1.254764762 0.224487493 0.141793245 1.70E-06 2.50E-07 0.121097036 0.028542732 0.078162149 1.107003508 0.254765767 S(ph)MSVDLSHIPLKDPLLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SMSVDLSHIPLKDPLLFK 18 1 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 S(0.5)MS(0.5)VDLSHIPLKDPLLFK 128.67 2.88E-05 167080000 570210 500910 496010 495200 560420 297390 761290 592810 1223300 TRUE FALSE 534521.574 537997.8976 507775.5914 507907.6704 516406.8738 383241.6653 647141.632 666823.6334 1019123.327 0.52449155 0.527902643 0.498247443 0.498377043 0.506716763 0.376050332 0.634998351 0.65431103 1 19.95889722 0.846118011 1.294014043 0.997334913 0.49801071 0.892712611 0.054706194 0.179957531 0.574395338 0.048177302 0.014589314 7.016459307 -0.846118011 -0.499324204 S(ph)MVWPGDGLVPDTAEPHVAPSPTLPSTEDVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.986)MVWPGDGLVPDT(0.014)AEPHVAPSPTLPSTEDVIR 90.246 8.86E-05 129187000 13367.8 14881.3 11991.1 13081.6 17065.2 14739.9 14943.6 11818.5 17851.6 TRUE FALSE 12531.13326 15983.12694 12275.53455 13417.296 15724.96803 18995.06985 12702.94591 13294.06574 14872.05263 0.842596081 1.074708874 0.825409569 0.902181853 1.057350214 1.277232559 0.8541488 0.893895824 1 13.86031616 2.745911301 24.29667197 1.016616835 0.924169133 0.137102824 0.129471346 938.6379182 3102538.2 0.040212052 0.041876987 557.0719627 -2.745911301 -0.092447702 S(ph)NDSGEEAEKEFIFV ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNDSGEEAEKEFIFV 15 1 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 S(0.5)NDS(0.5)GEEAEKEFIFV 57.679 0.072753 13009000 159070 102090 126910 117740 151210 107460 168320 127080 217670 TRUE FALSE 149114.0926 109648.8498 129920.3651 120761.4077 139334.5766 138481.9575 143081.9786 142946.2177 181339.4708 0.822292532 0.604660692 0.716448353 0.665941106 0.768363203 0.763661419 0.789028323 0.788279667 1 17.46833345 0.513631477 0.399373726 1.029112939 0.679971402 0.684944152 0.058389557 1.161611416 0.365639889 0.122521733 0.040404554 3.263108217 -0.513631477 -0.349141537 S(ph)NENLDKIDMSLDDIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNENLDKIDMSLDDIIK 17 1 H9KVD1;Q96QD9-4;Q96QD9 H9KVD1 FYTTD1 UAP56-interacting factor 1 S(1)NENLDKIDMSLDDIIK 194.97 2.70E-11 38736000 145110 57382 87201 85880 98909 56922 106630 65122 126650 TRUE FALSE 136027.8241 61630.62299 89269.4489 88083.82619 91141.08612 73354.45735 90641.8214 73252.62505 105511.2968 1.289225213 0.584113975 0.846065318 0.834828391 0.863804056 0.695228469 0.859072196 0.694263337 1 16.68703795 4.753388532 24.92040479 0.786109026 1.289225585 0.639871309 0.115746254 1560.870516 2623217.1 0.025204834 0.575990298 56674.60886 -4.753388532 0.503116559 S(ph)NGDLSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SNGDLSPK 8 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 S(0.999)NGDLS(0.001)PK;S(1)NGDLSPK;S(1)NGDLSPK;S(1)NGDLSPK 130.36 0.0011027 1643670000 4134720 2442200 3102770 2799680 2913960 2528600 3816800 2768570 4255950 TRUE FALSE 3875935.256 2623023.029 3176369.17 2871524.529 2685109.336 3258565.772 3244506.273 3114232.059 3545604.451 1.093166288 0.739795729 0.895861119 0.809882932 0.757306511 0.919043796 0.915078464 0.878336008 1 21.75760017 0.95398469 0.824655615 0.9949926 0.851119807 0.113703852 0.100029829 1.221057079 1.813527624 0.087221861 0.031386101 8.994658716 -0.95398469 -0.143872793 S(ph)NGSLHTLACHPPLSPGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNGSLHTLACHPPLSPGPR 19 0 O15049 O15049 N4BP3 NEDD4-binding protein 3 1 S(0.962)NGS(0.037)LHT(0.001)LACHPPLSPGPR 92.993 0.0030549 77432000 28337 34197 31767 31601 31915 22167 37396 28514 41909 TRUE FALSE 26563.43775 36728.98146 32520.52824 32411.93516 29408.52464 28566.25305 31788.81697 32074.03567 34914.11716 0.760822267 1.051980816 0.931443522 0.92833323 0.842310419 0.81818632 0.91048606 0.918655211 1 15.09152287 4.778589666 23.66270389 0.922841677 0.760821332 0.372679131 0.066951633 16227.93869 9592545.275 0.01721988 5.393195783 60060.59998 -4.778589666 -0.162020345 S(ph)NIDISSGLEDEEPKRPLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNIDISSGLEDEEPKRPLPR 20 2 Q9BZ71;Q9BZ71-3 Q9BZ71 PITPNM3 Membrane-associated phosphatidylinositol transfer protein 3 1 S(1)NIDISSGLEDEEPKRPLPR 145.14 7.74E-08 127830000 125280 103410 117200 110770 112700 71616 155500 95314 132330 TRUE FALSE 117438.9484 111066.584 119980.0393 113612.5457 103848.9966 92290.37661 132184.2186 107214.1627 110243.2681 1.065270927 1.007468174 1.088320778 1.030562207 0.941998531 0.837152038 1.199023041 0.972523443 1 16.75033104 S(ph)NSAPLIHGLSDTSPVFQAEAPSAR ddPTM_SK-BR-3_Pertuzumab_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 273.97 3.43E-53 2505230000 985558 955611 1026777 923794 1032263 815946 1397472 928437 1435265 TRUE FALSE 923873.6841 1026365.433 1051132.635 947500.118 951193.2279 1051496.364 1187934.047 1044354.403 1195709.999 0.772656986 0.858373212 0.879086598 0.79241632 0.795504954 0.879390793 0.993496791 0.873417805 1 20.1894361 1.964313223 5.517027844 0.951724786 0.831955337 0.634157659 0.046629905 0.134825183 11.06769865 0.019641409 0.012304625 92.11136613 -1.964313223 -0.119769449 S(ph)NSDNNLNASAPDWAVCSTATSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNSDNNLNASAPDWAVCSTATSHR 24 0 Q9UPX8;Q9UPX8-3;A0A2R8Y2H5;A0A087X158 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 S(0.579)NS(0.421)DNNLNASAPDWAVCSTATSHR 108.57 0.0014852 178990000 21231 20392 20617 20756 23606 17954 23401 18681 22279 TRUE FALSE 19902.18961 21901.8449 21106.04498 21288.6341 21752.07998 23137.02834 19892.23729 21013.36397 18560.49097 1.072287885 1.180025083 1.137149066 1.146986582 1.171956066 1.246574155 1.071751675 1.13215561 1 14.17994725 0.777487575 1.173620389 1.001800132 1.155092299 0.460099577 0.050079203 0.66563397 1.663228652 0.043566911 0.013485981 5.990837994 -0.777487575 0.153292167 S(ph)NSEDSSVGKGDWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNSEDSSVGKGDWK 14 1 O94885 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 S(0.564)NS(0.436)EDSSVGKGDWK 62.765 0.045076 155940000 142110 89092 108040 114040 95261 64733 149620 83619 171720 TRUE FALSE 133215.5888 95688.46438 110602.7598 116966.4595 87779.58532 83420.36625 127185.87 94059.01622 143058.8226 0.9311945 0.668874961 0.773127849 0.817610947 0.613590855 0.58311934 0.889045972 0.657484904 1 17.12624895 -1.360441577 4.614562484 1.000290347 0.74046256 0.333699345 0.114667632 0.00031345 4.34E-05 0.101602423 0.023921391 0.043607222 1.360441577 -0.259827787 S(ph)NSELEDEILCLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SNSELEDEILCLEK 14 0 Q96PC5;Q96PC5-11;Q96PC5-10;Q96PC5-9;Q96PC5-13;Q96PC5-6;G3V599;Q96PC5-14;Q96PC5-7;Q96PC5-12;Q96PC5-8;Q96PC5-5;Q86UF2;A4D2H0;A0A5F9ZHA4;G3V5K6;A0A2R8YE69;Q8IX94;P0CG41;A4FU28 Q96PC5 MIA2;CTAGE6;CTAGE15;CTAGE5;CTAGE4;CTAGE8;CTAGE9 Melanoma inhibitory activity protein 2;cTAGE family member 6;cTAGE family member 15;cTAGE family member 4;cTAGE family member 8;cTAGE family member 9 1 S(0.976)NS(0.024)ELEDEILCLEK;S(0.857)NS(0.143)ELEDEILCLEK;S(0.838)NS(0.162)ELEDEILCLEK;S(0.872)NS(0.128)ELEDEILCLEK 237.86 2.75E-17 136389000 271472 174162 178661 180457 229989 175786 293492 214195 250320 TRUE FALSE 254481.0521 187057.1357 182898.9233 185087.8321 211926.5917 226532.5646 249485.5992 240937.7173 208539.9749 1.220298661 0.896984551 0.877044909 0.88754126 1.016239653 1.086278852 1.196344247 1.15535507 1 17.66996443 2.297092713 2.658856772 1.137822074 0.943479082 0.23513046 0.110913624 0.275520117 3.996700942 0.043424236 0.032495906 198.1950085 -2.297092713 -0.194342992 S(ph)NSFIGVPNGEVEMPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNSFIGVPNGEVEMPLK 17 0 Q9H7E2-2;Q9H7E2;Q9H7E2-3 Q9H7E2-2 TDRD3 Tudor domain-containing protein 3 1 S(0.5)NS(0.5)FIGVPNGEVEMPLK 79.311 0.014487 34424000 83137 63154 67681 70931 73025 47886 92309 66670 99611 TRUE FALSE 77933.60357 67829.98787 69286.42528 72751.20955 67289.91107 61709.91084 78468.1224 74993.89626 82985.28059 0.939125626 0.817373724 0.834924276 0.876676069 0.810865621 0.743624778 0.945566754 0.903701183 1 16.34056784 1.618034361 10.44663354 0.944187507 0.835315003 0.486999867 0.054359733 0.076982092 26.08165458 0.025122221 0.012931798 41.49868752 -1.618034361 -0.108872504 S(ph)NSGRELTDEEILASVMIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 SNSGRELTDEEILASVMIK 19 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 S(0.495)NS(0.495)GRELT(0.01)DEEILASVMIK;S(0.49)NS(0.49)GRELT(0.021)DEEILASVMIK;S(0.498)NS(0.498)GRELT(0.004)DEEILASVMIK;S(0.454)NS(0.454)GRELT(0.092)DEEILASVMIK;S(0.646)NS(0.352)GRELT(0.002)DEEILASVMIK;S(0.768)NS(0.232)GRELTDEEILASVMIK;S(0.333)NS(0.333)GRELT(0.333)DEEILASVMIK;S(0.369)NS(0.369)GRELT(0.263)DEEILASVMIK;S(0.497)NS(0.497)GRELT(0.006)DEEILASVMIK;S(0.496)NS(0.496)GRELT(0.008)DEEILASVMIK;S(0.5)NS(0.5)GRELT(0.001)DEEILASVMIK;S(0.453)NS(0.453)GRELT(0.095)DEEILASVMIK;S(0.5)NS(0.5)GRELTDEEILASVMIK;S(0.484)NS(0.484)GRELT(0.033)DEEILASVMIK 233.91 2.43E-24 1855219000 2000479 2062254 1923505 2143517 2651296 1287145 2258992 1898809 3704198 TRUE FALSE 1875272.59 2214945.432 1969131.447 2198523.275 2443073.907 1658722.866 1920277.121 2135879.483 3085943.424 0.607682103 0.717753091 0.638097067 0.712431491 0.791678126 0.537509163 0.622265822 0.69213177 1 21.55728018 0.950288524 20.30210863 1.000000001 0.661999117 0.700289781 0.069175064 628.8566142 256825.519 0.065008154 0.016252039 8.918432389 -0.950288524 -0.338000883 S(ph)NSIPTHEAAFELYSGSQMGSTLSLAERPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNSIPTHEAAFELYSGSQMGSTLSLAERPK 30 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;H0Y6F6;Q8NEY1-6 Q8NEY1-5 NAV1 Neuron navigator 1 1 S(0.485)NS(0.485)IPT(0.029)HEAAFELYSGSQMGSTLSLAERPK;S(0.486)NS(0.486)IPT(0.028)HEAAFELYSGSQMGSTLSLAERPK 157.47 1.07E-09 191090000 69447 53642 67760 62024 61999 56679 88541 66661 83729 TRUE FALSE 65100.43624 57613.70949 69367.2992 63615.64085 57129.84863 73041.30719 75265.09902 74983.77259 69754.08899 0.933284875 0.825954583 0.994454952 0.911998734 0.819017917 1.047125814 1.079006265 1.074973147 1 16.08999017 2.156034304 7.983225706 1.060197181 0.901432032 0.661218806 0.054320453 0.144914119 12.25708839 0.019841176 0.014649605 143.2301029 -2.156034304 -0.158765149 S(ph)NSLDKHQQSSTLGNSVVR ddPTM_SK-BR-3_Pertuzumab_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(0.916)NS(0.084)LDKHQQSSTLGNSVVR;S(0.584)NS(0.416)LDKHQQSSTLGNSVVR 258.05 3.11E-31 1584940000 1703620 1486390 1543710 1702080 1877710 1123540 2074340 1530650 1967430 TRUE FALSE 1596993.465 1596443.862 1580327.53 1745758.254 1730242.231 1447887.759 1763311.974 1721755.022 1639053.223 0.974338992 0.974003675 0.964170967 1.065101627 1.055635172 0.883368361 1.075811297 1.050457055 1 20.64443127 3.272440023 24.86718896 1.020969869 0.970563805 0.163576484 0.054229186 312.0786448 229060.8728 0.014404787 0.019503059 1872.578458 -3.272440023 -0.050406064 S(ph)NTPILVDGKDVMPEVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNTPILVDGKDVMPEVNK 18 1 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41 P06744 GPI Glucose-6-phosphate isomerase 1 S(0.587)NT(0.413)PILVDGKDVMPEVNK 106.69 0.00026749 86552000 319880 181970 185750 226010 227600 113100 287430 155060 296340 TRUE FALSE 299859.2818 195443.2481 190156.0777 231809.7992 209725.2141 145750.134 244332.5399 174419.5823 246878.9396 1.214600493 0.79165622 0.770240175 0.938961418 0.849506298 0.590370869 0.989685634 0.706498426 1 17.91344424 4.741293062 24.74734018 0.822147883 1.214600656 0.475528085 0.126847983 178.3423742 1615116.707 0.026844372 0.185568717 55117.95069 -4.741293062 0.392452773 S(ph)NTQGPAYSHLTEFAPPPTPMVDHLVASNPFEDDFGAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNTQGPAYSHLTEFAPPPTPMVDHLVASNPFEDDFGAPK 39 0 Q9BRQ0;Q5T171 Q9BRQ0 PYGO2 Pygopus homolog 2 1 S(0.772)NT(0.219)QGPAY(0.002)S(0.006)HLT(0.001)EFAPPPTPMVDHLVASNPFEDDFGAPK;S(0.294)NT(0.294)QGPAY(0.067)S(0.294)HLT(0.049)EFAPPPTPMVDHLVASNPFEDDFGAPK 209.05 8.02E-31 74673000 68366 55296 63255 67831 80110 42043 73091 53980 61002 TRUE FALSE 64087.0941 59390.17338 64755.43847 69571.6583 73818.48375 54180.13159 62131.68309 60719.52182 50820.37211 1.261051256 1.168629251 1.274202368 1.36897184 1.452537254 1.066110486 1.222574344 1.194787037 1 15.63311932 0.816762761 0.782637405 1.003465857 1.269153474 0.412149876 0.100994312 0.954098112 1.200116328 0.099393618 0.035769801 6.557869367 -0.816762761 0.265687616 S(ph)NVCINGNHVYLEQPEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNVCINGNHVYLEQPEAK 18 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 S(1)NVCINGNHVYLEQPEAK 144.27 6.42E-07 0 124210 190770 81290 66503 197600 25831 298440 100230 683330 TRUE FALSE 116435.9178 204894.8093 83218.23719 68209.57957 182081.2931 33287.99037 253691.6926 112743.9361 569277.8085 0.204532683 0.359920598 0.14618212 0.119817738 0.319846111 0.05847407 0.445637769 0.198047306 1 19.11877334 -0.742035871 0.589752958 1.140219364 0.224252605 0.810799009 0.116587464 6.443620966 1.516646346 1.852552235 0.043635109 0.181119049 0.742035871 -0.915966759 S(ph)PAFALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPAFALK 7 0 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 S(1)PAFALK 85.676 0.021647 101380000 119200 279600 122700 125230 358310 70072 396990 161770 933890 TRUE FALSE 111739.4848 300301.8749 125610.5019 128443.6138 330169.778 90300.64888 337465.035 181967.3406 778017.7258 0.143620744 0.385983333 0.161449409 0.165090858 0.424373079 0.116065028 0.433749803 0.233885854 1 19.5694435 -4.999997133 0.330036673 8.43085059 0.239501061 0.798020754 0.117583302 141.6492076 1.224936086 738.1798422 0.087957822 1.00E-05 4.999997133 -8.191349529 S(ph)PAFTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPAFTSR 7 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 S(1)PAFTSR 74.269 0.052316 0 70908 74868 76586 82297 86668 62374 79678 69745 94669 TRUE FALSE 66469.99485 80411.30462 78402.65609 84408.88035 79861.44488 80380.36124 67731.02359 78452.81678 78868.13231 0.84279915 1.019566487 0.994098044 1.070253319 1.0125946 1.019174144 0.858788228 0.994734051 1 16.26715486 1.020259794 24.99631404 1.000000592 0.977827352 0.01635333 0.071391485 1332.635239 1644186.089 0.068042478 0.01701062 10.47755126 -1.020259794 -0.02217324 S(ph)PAGGESATVAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPAGGESATVAAK 13 0 Q147X3 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 S(1)PAGGESATVAAK;S(1)PAGGESATVAAK 198.29 1.33E-07 182620000 412860 271550 366910 327150 272620 299600 440330 300050 254270 TRUE FALSE 387019.8296 291655.8445 375613.2785 335545.2229 251209.5249 386089.6564 374306.6043 337511.903 211830.6944 1.827024317 1.376834672 1.773176827 1.584025506 1.185897661 1.8226332 1.767008343 1.593309714 1 17.69255213 -1.662290079 2.405909389 0.905208842 1.615587772 0.471430534 0.205064987 5861055.146 4496277.656 3409273.281 0.050615412 0.021762557 1.662290079 0.710378931 S(ph)PAGS(ph)PELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPAGSPELR 9 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 S(1)PAGS(1)PELR;S(1)PAGS(1)PELR 122.33 0.00086102 733340000 714250 566120 677910 637180 550710 681870 818400 585580 411180 TRUE FALSE 669546.3675 608036.1138 693990.3453 653531.1175 507459.4581 878714.7998 695688.5177 658690.952 342551.4017 1.954586565 1.775021532 2.025945134 1.907833728 1.481411127 2.565205676 2.030902557 1.922896677 1 18.38596096 S(ph)PAKSPNPSTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SPAKSPNPSTPR 12 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 S(1)PAKSPNPSTPR;S(0.999)PAKS(0.001)PNPSTPR;S(0.999)PAKS(0.001)PNPSTPR;S(0.999)PAKS(0.001)PNPSTPR;S(1)PAKSPNPSTPR 114.63 0.00062816 2164340000 2052830 1590220 1894430 1761010 1816440 1521620 2400020 1365510 1617000 TRUE FALSE 1924347.035 1707961.543 1939366.774 1806200.498 1673784.13 1960886.993 2040159.282 1535996.929 1347112.254 1.428497907 1.26786876 1.439647489 1.340794349 1.242497888 1.455622564 1.514468654 1.140214503 1 20.36143864 1.047978869 5.387135272 1.001432512 1.381131275 0.720304785 0.083786828 0.089917254 5.527435691 0.083560745 0.021087334 11.16808908 -1.047978869 0.379698764 S(ph)PALSDANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPALSDANK 9 0 P52701;P52701-3;P52701-2;A0A087WWJ1;F8WAX8;F8W7G9 P52701 MSH6 DNA mismatch repair protein Msh6 1 S(1)PALSDANK;S(1)PALSDANK;S(1)PALSDANK 133.42 0.00029107 678450000 1352800 1014430 1150040 1121520 1208550 925300 1560090 1161180 1366110 TRUE FALSE 1268130.663 1089539.453 1177319.492 1150300.102 1113635.358 1192419.089 1326168.988 1306155.879 1138097.416 1.114254936 0.957334089 1.034462846 1.010722005 0.978506183 1.047730249 1.165250856 1.14766615 1 20.11819262 1.947005199 6.153944481 1.119758032 1.012319052 0.282092176 0.059868732 0.201157263 17.29394814 0.023252125 0.014414847 88.5126205 -1.947005199 -0.10743898 S(ph)PAMSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPAMSR 6 0 Q9BQI6 Q9BQI6 ANKRD32 Ankyrin repeat domain-containing protein 32 1 S(1)PAMSR;S(1)PAMSR 88.643 0.053571 670410000 371790 410160 382240 393950 461030 356200 485310 418330 484360 TRUE FALSE 348520.3276 440528.6732 391306.9133 404059.424 424822.5635 459029.1576 412542.2709 470559.4214 403517.1869 0.863706278 1.091722205 0.969740388 1.001343777 1.05279918 1.137570276 1.022366046 1.166144681 1 18.6222706 2.636191558 3.78860757 1.080185035 0.997841367 0.284317842 0.073188689 0.345636444 9.015161293 0.022395589 0.021062367 432.7046459 -2.636191558 -0.082343668 S(ph)PAPGLASGDRPPSVSSVHSEGDCNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPAPGLASGDRPPSVSSVHSEGDCNR 26 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(1)PAPGLASGDRPPSVSSVHSEGDCNR 124.98 6.96E-05 85821000 49996 40737 48895 49044 45338 45640 59044 43334 36850 TRUE FALSE 46866.83961 43753.20987 50054.81249 50302.55207 41777.33636 58815.5271 50190.90034 48744.34529 30699.49694 1.526632169 1.425209343 1.630476636 1.638546461 1.360847588 1.915846609 1.634909537 1.587789708 1 14.90592739 0.879632835 18.20891347 1 1.591549654 0.612374168 0.147527559 9948.052612 1504930.562 0.13814319 0.034535797 7.579365221 -0.879632835 0.591549654 S(ph)PAPGLASGDRPPSVSSVHSEGDCNRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPAPGLASGDRPPSVSSVHSEGDCNRR 27 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.977)PAPGLAS(0.021)GDRPPSVSSVHS(0.001)EGDCNRR 49.942 0.058298 258720000 6991.5 11316 13576 9258.3 9379 8328.6 10792 8709.6 11391 TRUE FALSE 6553.914495 12153.84841 13898.02913 9495.883652 8642.411173 10732.93162 9173.839788 9797.012732 9489.768511 0.690629544 1.280731811 1.464527729 1.000644393 0.910708324 1.131000361 0.96670849 1.032376366 1 13.21215718 3.113824604 19.16189289 1.006621488 1.221602567 0.053064884 0.203159883 2.935960494 480.8237566 0.057997155 0.069320248 1299.644591 -3.113824604 0.214981078 S(ph)PAVKPAAAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPAVKPAAAPK 11 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 S(1)PAVKPAAAPK;S(1)PAVKPAAAPK 84.173 0.009786 508380000 809870 491290 659680 534580 580210 514030 864040 580250 906780 TRUE FALSE 759181.6824 527665.6228 675327.9211 548298.2278 534642.6471 662422.1164 734485.2234 652695.4898 755432.56 1.004962882 0.698494678 0.893961893 0.725806984 0.707730478 0.8768779 0.97227107 0.864002327 1 19.52694344 2.00432047 24.24784591 0.937901242 0.799193975 0.297150211 0.097588684 94.329472 529402.1448 0.033588393 0.024697858 100.9997897 -2.00432047 -0.138707267 S(ph)PCPQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPCPQEK 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PCPQEK 76.228 0.043352 978080000 1524500 1549500 1580300 1498100 1444400 1779100 1690800 1370700 1041500 TRUE FALSE 1429084.266 1664226.592 1617785.462 1536543.782 1330962.65 2292697.289 1437280.237 1541834.912 867666.9217 1.647042466 1.918047756 1.864523611 1.770891276 1.533955735 2.642370282 1.656488453 1.776989388 1 19.7267818 0.641637359 1.905145997 1.000825987 1.880520108 0.444371749 0.300940184 1.528471383 7.005175043 0.259878119 0.072213372 4.381646725 -0.641637359 0.879694121 S(ph)PDKPGGSPSASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPDKPGGSPSASR 13 1 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 S(0.999)PDKPGGS(0.001)PSASR;S(1)PDKPGGSPSASR 99.813 0.001628 610230000 1047590 522710 710920 672330 520060 577990 1030910 612350 557370 TRUE FALSE 982023.2119 561411.9923 727783.3581 689583.1261 479216.5854 744846.3301 876334.616 688803.2454 464341.3463 2.114873508 1.209050189 1.567345583 1.485078018 1.032035138 1.604092197 1.887263805 1.483398476 1 18.82482622 S(ph)PDLEASLDTLENNCHVGSDIDFRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPDLEASLDTLENNCHVGSDIDFRPK 26 1 Q13111;Q13111-2;Q13111-3;K7EJF1 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 S(1)PDLEASLDTLENNCHVGSDIDFRPK;S(1)PDLEASLDTLENNCHVGSDIDFRPK;S(1)PDLEASLDTLENNCHVGSDIDFRPK 332.59 3.07E-95 1170020000 389667 274937 313348 315022 297154 262891 402150 276308 328196 TRUE FALSE 365278.438 295293.6216 320780.7625 323105.9979 273816.7235 338783.364 341851.3409 310805.662 273417.9674 1.335970864 1.080008108 1.173224882 1.181729207 1.001458412 1.239067671 1.250288502 1.136741908 1 18.06074853 4.75211173 24.32645245 1.148081099 1.335971045 0.336444765 0.087354993 1984.03272 3561568.456 0.020129914 0.385758743 56508.23338 -4.75211173 0.187889946 S(ph)PDNSIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPDNSIK 7 0 Q9UKL0 Q9UKL0 RCOR1 REST corepressor 1 1 S(1)PDNSIK;S(1)PDNSIK;S(1)PDNSIK;S(1)PDNSIK 151.22 0.0019887 3018760000 8616200 5421620 6753980 6113780 5831360 4749600 7687400 5356920 5713870 TRUE FALSE 8076927.422 5823042.386 6914187.595 6270669.945 5373388.508 6120732.417 6534745.736 6025743.254 4760188.184 1.696766411 1.223279871 1.452502995 1.317315556 1.128818505 1.285817321 1.37279147 1.265862403 1 22.18258718 -0.095702074 0.041533011 7.16E-18 2.331864955 0.484399904 0.133828644 193.1144384 2.351749278 76.18032389 55.66816887 0.802228203 0.095702074 2.331864955 AGS(ph)PFS(ph)PPPSSSSLTGEAAISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 AGSPFSPPPSSSSLTGEAAISR 22 0 Q96JY6;Q96JY6-5;Q96JY6-3;Q96JY6-4;C9JS55;C9JSR2;C9K0F0;C9J0X3;Q96JY6-2;C9J760;A0A087WXJ0 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 2 AGS(1)PFS(0.879)PPPS(0.093)S(0.022)S(0.005)S(0.001)LTGEAAISR;AGS(1)PFS(0.997)PPPS(0.002)S(0.001)SSLTGEAAISR;AGS(1)PFS(0.991)PPPS(0.003)S(0.005)S(0.001)SLTGEAAISR 152.04 6.46E-08 274289000 602580 553680 587230 762250 731350 317818 382700 261959 309074 TRUE FALSE 564865.5934 594675.0433 601159.3729 781810.6255 673912.7211 409566.8973 325317.6878 294665.1578 257487.5527 2.193758834 2.309529284 2.334712364 3.036304541 2.617263297 1.590627947 1.263430734 1.144386028 1 17.97414317 2.083233634 3.304204164 1.199808186 2.474587454 0.870640555 0.243158774 0.092635825 2.003275962 0.113917235 0.075381162 121.1249565 -2.083233634 1.274779268 up S(ph)PDPGIVPQEAPVGNSLSELSEENFDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPDPGIVPQEAPVGNSLSELSEENFDGK 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 1 S(1)PDPGIVPQEAPVGNSLSELSEENFDGK;S(1)PDPGIVPQEAPVGNSLSELSEENFDGK;S(1)PDPGIVPQEAPVGNSLSELSEENFDGK 219.65 1.77E-34 203886000 621650 428588 502347 509266 432790 349194 646590 345493 307016 TRUE FALSE 582742.0362 460321.1015 514262.9081 522334.6277 398800.4192 450000.6391 549639.8321 388628.5616 255773.0462 2.278355929 1.799724828 2.010621978 2.04218011 1.559196425 1.75937475 2.148935708 1.519427349 1 17.96450471 -2.020172233 0.275143265 5.23E-14 2.006994621 0.652985943 0.217879674 20.57140225 0.845714123 13.39667028 0.266228166 0.009546139 2.020172233 2.006994621 S(ph)PDPYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 75.131 0.082342 413570000 478140 423080 452090 404820 441870 463440 571240 434480 345830 TRUE FALSE 448214.0709 454405.2834 462813.7883 415208.3666 407167.3126 597227.6047 485587.8651 488725.7844 288108.7389 1.555711474 1.577200626 1.606385805 1.441151588 1.4132418 2.072924296 1.685432615 1.696324056 1 18.1362539 S(ph)PDREASGSGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPDREASGSGGR 12 1 Q8N5F7;A0A494C050 Q8N5F7 NKAP NF-kappa-B-activating protein 1 S(0.912)PDREAS(0.005)GS(0.083)GGR;S(0.962)PDREAS(0.007)GS(0.031)GGR 90.229 0.023618 253216000 461900 498310 515480 483620 508390 434990 567850 434910 517430 TRUE FALSE 432990.5035 535205.3909 527707.429 496030.508 468463.1001 560564.5515 482706.1642 489209.4709 431067.5903 1.004460816 1.241581142 1.224187206 1.150702394 1.08675092 1.300409876 1.11979229 1.134878803 1 18.71755457 0.805092112 1.526646116 1.000897373 1.178514601 0.253153659 0.083734137 0.835285025 3.5117699 0.073414508 0.021365535 6.383988739 -0.805092112 0.177617227 S(ph)PDSCRPQALPCLPSTQDVPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPDSCRPQALPCLPSTQDVPSR 22 1 Q9Y283-2;Q9Y283 Q9Y283-2 INVS Inversin 1 S(0.999)PDS(0.001)CRPQALPCLPSTQDVPSR 170.1 4.57E-12 209210000 32713 37823 32095 35939 38673 24428 29360 37782 30633 TRUE FALSE 30665.55172 40623.45427 32856.30856 36861.25558 35635.77858 31479.96704 24957.74056 42499.16587 25520.1544 1.201620932 1.591818515 1.287465116 1.444397828 1.396377859 1.233533565 0.977961974 1.665317741 1 14.63934944 2.194562918 4.806948887 1.188316226 1.402795645 0.124216129 0.210565595 0.31669692 16.19612993 0.073233698 0.054501264 156.5175058 -2.194562918 0.214479419 S(ph)PDSGHVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPDSGHVAK 9 0 O15169-2;O15169 O15169-2 AXIN1 Axin-1 1 S(0.999)PDS(0.001)GHVAK;S(0.998)PDS(0.002)GHVAK 93.839 0.0058792 328950000 1178710 912720 1127360 1127350 1064470 981510 1356390 1140670 1085300 TRUE FALSE 1104936.645 980298.7385 1154101.512 1156279.71 980870.8201 1264856.004 1153011.912 1283085.16 904156.4187 1.222063597 1.084213658 1.276440102 1.278849197 1.084846383 1.398934938 1.275235001 1.419096446 1 19.78621285 3.839873964 4.443109317 1.263337222 1.148887099 0.072402412 0.13082891 0.422190639 13.89510584 0.030611434 0.057208307 6916.30225 -3.839873964 -0.114450123 S(ph)PEASQTDS(ph)PVESPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPEASQTDSPVESPR 15 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 S(1)PEAS(0.008)QT(0.028)DS(0.964)PVESPR;S(1)PEASQT(0.056)DS(0.944)PVESPR 291.39 9.34E-44 284560000 217300 211900 197790 207406 241930 181172 226379 183766 241450 TRUE FALSE 203699.5809 227589.2965 202481.6722 212728.3891 222929.7937 233473.4153 192435.5705 206709.5896 201150.4352 1.012672832 1.131438251 1.006618117 1.057558682 1.108273982 1.16069058 0.956674891 1.0276368 1 17.61791533 1.687516995 11.32599321 0.994822102 1.077310019 0.383633132 0.050547274 0.124526948 22.87053615 0.022989388 0.012518998 48.6986582 -1.687516995 0.082487916 S(ph)PEAVGPELEAEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPEAVGPELEAEEK 14 0 Q96N64-3;Q96N64-2;Q96N64 Q96N64-3 PWWP2A PWWP domain-containing protein 2A 1 S(1)PEAVGPELEAEEK;S(1)PEAVGPELEAEEK 256.52 2.70E-24 324980000 841530 534180 632490 613460 570450 456780 806860 475630 521680 TRUE FALSE 788860.1395 573731.243 647492.9615 629202.4222 525649.1581 588644.9708 685878.8335 535013.4525 434608.2378 1.815106275 1.320111294 1.489831313 1.447746194 1.209478128 1.35442663 1.578154241 1.231024647 1 18.72935599 -3.836973988 0.149918698 1.41E-20 1.575420899 0.486320316 0.159382411 88.84740623 1.09635518 28.38989894 0.828378376 0.000145555 3.836973988 1.575420899 S(ph)PEDQLGK ddPTM_SK-BR-3_Pertuzumab_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 0.0006703 358870000 1192740 828950 949580 929910 900820 703780 1215040 873310 1022470 TRUE FALSE 1118088.533 890326.3205 972104.486 953773.0649 830073.2309 906949.8611 1032856.032 982344.6759 851813.1516 1.312598344 1.045213165 1.141217982 1.11969751 0.974478064 1.064728643 1.212538254 1.153239621 1 19.70017748 4.74771829 24.47843028 1.099118652 1.312598495 0.479199798 0.072600269 880.426595 2353308.615 0.017456134 0.213633807 55939.46268 -4.74771829 0.213479842 S(ph)PEGTPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPEGTPQK 8 0 C9J0I9;Q86WB0;Q86WB0-3;F8WAU5;F8WBD7;F8WDK5;F8WF13 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 S(1)PEGTPQK;S(0.991)PEGT(0.009)PQK;S(0.998)PEGT(0.002)PQK 74.486 0.042853 1955730000 4116200 3173070 3751840 3410500 3741230 2745080 3977440 3132980 3905900 TRUE FALSE 3858574.39 3408007.404 3840835.417 3498019.204 3447408.887 3537540.033 3381059.797 3524139.45 3253980.057 1.185801487 1.047335062 1.180350017 1.074997124 1.059443766 1.087142506 1.039053632 1.083024293 1 21.63377398 2.51361468 0.12479797 0.938507167 1.229666718 0.448004036 0.043436489 11.56636361 0.730459077 0.589147915 0.988808517 326.2982015 -2.51361468 0.291159551 S(ph)PEIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 82.452 0.062103 4242600000 584300 511800 584280 460340 435820 515770 637550 495710 368130 TRUE FALSE 547729.706 549694.2045 598139.3975 472153.1038 401592.4552 664664.4262 541955.2962 557600.4847 306686.7248 1.785958314 1.792363869 1.950326992 1.53952899 1.309454967 2.167242246 1.767129949 1.818143531 1 18.22640619 -1.728153875 2.473632945 0.833848802 1.781560883 0.530434354 0.22617057 9644344.466 7070987.907 9862338.389 0.058192509 0.018700195 1.728153875 0.947712081 S(ph)PEIHRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPEIHRR 7 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;Q9NYF8;Q9NYF8-2;Q9NYF8-4;Q9Y2W1;A0A3B3ITZ9 E9PK91;Q9NYF8;Q9NYF8-4;Q9Y2W1 BCLAF1;THRAP3 Bcl-2-associated transcription factor 1;Thyroid hormone receptor-associated protein 3 1 S(1)PEIHRR;S(1)PEIHRR;S(1)PEIHRR;S(1)PEIHRR 115.13 0.0035212 3739080000 1258470 1395280 1454110 1337570 1290140 1191530 1646320 1303380 1656950 TRUE FALSE 1179704.609 1498587.983 1488602.176 1371894.311 1188817.609 1535505.368 1399469.6 1466109.862 1380394.341 0.854614203 1.0856231 1.078389075 0.993842318 0.861215939 1.112367186 1.013818703 1.062094953 1 20.39664903 S(ph)PEPDGPAPAFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 131.13 0.00014057 261832000 243240 200193 226193 209150 194852 209364 262919 194023 164236 TRUE FALSE 228016.0426 215015.498 231558.4048 214517.1431 179549.1099 269803.9881 223496.7368 218247.1986 136823.9506 1.666492172 1.571475587 1.6923821 1.567833279 1.312263746 1.971906138 1.633462093 1.595094994 1 17.06196127 0.701733548 3.906039667 1.000004347 1.634413004 0.602796374 0.160024514 4.103948592 53.14084575 0.142828875 0.036540474 5.031917918 -0.701733548 0.634408656 S(ph)PEPEATLTFPFLDK ddPTM_SK-BR-3_Pertuzumab_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(1)PEPEATLTFPFLDK;S(0.999)PEPEAT(0.001)LTFPFLDK;S(1)PEPEATLTFPFLDK;S(0.97)PEPEAT(0.03)LTFPFLDK;S(0.994)PEPEAT(0.004)LT(0.002)FPFLDK;S(0.886)PEPEAT(0.114)LTFPFLDK 202.92 5.94E-09 1781133000 1746216 1163594 1453424 1350069 1336962 1077671 1499599 1117220 1056631 TRUE FALSE 1636923.458 1249747.71 1487899.904 1384714.056 1231962.398 1388777.123 1274748.052 1256707.376 880272.46 1.859564546 1.419728286 1.690272014 1.573051662 1.399523958 1.577667354 1.448128971 1.427634549 1 19.74759061 -2.930730078 0.176092064 8.13E-15 1.699681642 0.719514967 0.118438968 29.80460692 0.555592097 11.56992691 0.391627425 0.001172924 2.930730078 1.699681642 S(ph)PEPEVLSTQEDLFDQSNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPEPEVLSTQEDLFDQSNK 19 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 S(1)PEPEVLSTQEDLFDQSNK 225.54 1.10E-19 226360000 118970 70047 88500 87612 77064 73851 112080 72875 68997 TRUE FALSE 111523.8801 75233.35276 90599.26179 89860.27225 71011.7043 95170.58483 95274.6445 81973.60417 57480.95496 1.940188366 1.308839646 1.576161389 1.563305138 1.235395347 1.655689 1.657499333 1.426100249 1 15.81079641 0.967605377 17.83176548 0.999999987 1.538774576 0.451797057 0.193162606 73.26802313 40331.9392 0.17065851 0.042664611 9.281226628 -0.967605377 0.538774589 S(ph)PEPGQTWTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPEPGQTWTR 10 0 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 S(1)PEPGQTWTR;S(1)PEPGQTWTR;S(1)PEPGQTWTR;S(1)PEPGQTWTR;S(1)PEPGQTWTR;S(1)PEPGQTWTR 155.47 1.33E-05 5617750000 957477 814323 861230 884950 819036 758483 876916 566733 642849 TRUE FALSE 897550.2237 874616.3222 881658.7823 907659.3152 754712.2164 977444.7292 745430.5867 637490.8626 535553.3489 1.675930559 1.633107745 1.646257621 1.694806534 1.409219488 1.825111786 1.391888573 1.19034054 1 19.03067077 1.291208506 2.008350067 1.020566251 1.638866476 0.817173558 0.108489677 0.111077323 0.768582863 0.086107971 0.02547119 19.55277967 -1.291208506 0.618300225 S(ph)PERPTGDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SPERPTGDLR 10 1 Q5T200;Q5T200-2;Q5T9K0 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 S(0.997)PERPT(0.003)GDLR;S(0.968)PERPT(0.032)GDLR;S(1)PERPTGDLR;S(1)PERPTGDLR;S(1)PERPTGDLR 89.959 0.006757 2169920000 1789282 1875150 1833920 1886060 1964860 1556072 2079808 1722988 1957540 TRUE FALSE 1677294.034 2013988.057 1877421.448 1934459.493 1810547.821 2005284.726 1767960.098 1938106.845 1630813.928 1.02850117 1.234958828 1.151217448 1.186192649 1.110211159 1.229622026 1.084096762 1.188429171 1 20.63716075 -1.837778317 0.439879774 0.863170021 1.161450187 0.338431959 0.064987933 46.96244667 3.575153765 6.717387575 0.031805166 0.01452853 1.837778317 0.298280165 S(ph)PESCSKPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPESCSKPEK 10 1 Q03111 Q03111 MLLT1 Protein ENL 1 S(0.997)PES(0.002)CSKPEK;S(1)PESCSKPEK;S(0.982)PES(0.014)CS(0.003)KPEK;S(0.998)PES(0.001)CS(0.001)KPEK;S(0.976)PES(0.009)CS(0.015)KPEK;S(0.996)PES(0.002)CS(0.002)KPEK 129.34 0.000804 6032480000 8962910 5240293 6177820 5984060 6837830 4957670 9163860 5824170 9567750 TRUE FALSE 8401937.462 5628289.746 6324360.808 6137621.111 6300814.414 6388868.848 7789824.266 6551330.445 7970830.715 1.054085548 0.706110812 0.793438104 0.77001022 0.790484034 0.801531117 0.977291395 0.821913133 1 22.92629866 1.753835895 25 0.926435901 0.800235347 0.20184774 0.101805287 6.865173481 11249.9351 0.042785595 0.02372685 56.733019 -1.753835895 -0.126200554 S(ph)PESDRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPESDRPR 8 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 S(1)PESDRPR;S(1)PESDRPR;S(0.996)PES(0.004)DRPR;S(0.992)PES(0.008)DRPR 140.78 0.00039006 1377520000 332269 264685 312329 287933 247749 319688 374390 269954 227697 TRUE FALSE 311472.8764 284282.5528 319737.5914 295321.8482 228291.7929 411976.7359 318253.6952 303658.3511 189692.8997 1.641984897 1.49864625 1.685553818 1.556841867 1.203480959 2.171808942 1.677731194 1.600789231 1 17.53330615 S(ph)PETALEAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPETALEAFK 10 0 Q68DA7-5;Q68DA7-3 Q68DA7-5 FMN1 Formin-1 1 S(1)PETALEAFK 99.752 0.0047005 38865000 132930 93096 114600 118830 108420 83781 127350 88330 83319 TRUE FALSE 124610.1486 99988.92471 117318.3661 121879.379 99905.13055 107967.2146 108255.0498 99358.19494 69412.52064 1.795211403 1.440502719 1.690161444 1.755870236 1.439295528 1.555442932 1.559589664 1.431416033 1 16.0829083 0.087393788 0.521596563 0.948908836 1.624675855 0.745213112 0.113396362 1.819266192 0.643942576 0.297322325 0.051388369 1.222908007 -0.087393788 0.675767019 S(ph)PFEGAVTESQSLFSDNFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SPFEGAVTESQSLFSDNFR 19 0 O95628-3;O95628-2;O95628;O95628-8;O95628-4;O95628-7;O95628-9;O95628-10;O95628-6;O95628-5 O95628-3 CNOT4 CCR4-NOT transcription complex subunit 4 1 S(1)PFEGAVTESQSLFSDNFR;S(1)PFEGAVTESQSLFSDNFR;S(1)PFEGAVTESQSLFSDNFR;S(1)PFEGAVTESQSLFSDNFR;S(1)PFEGAVTESQSLFSDNFR 317 1.02E-61 952021000 132990 123210.5 142411.1 134996 155234 111811.7 157906 128290.6 158315 TRUE FALSE 124666.3933 132333.1336 145789.1585 138460.2259 143042.5478 144089.9227 134229.4612 144307.9638 131891.2037 0.945221438 1.003350715 1.105374387 1.049806371 1.084549566 1.09249077 1.017728684 1.094143959 1 17.00898882 4.47825544 2.207265178 1.064368698 0.941613428 0.573733666 0.033956654 0.262899861 2.121134474 0.007941883 0.050866405 30078.4491 -4.47825544 -0.12275527 S(ph)PFLKPDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPFLKPDER 9 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 S(1)PFLKPDER;S(1)PFLKPDER 114.86 0.0009504 1008330000 1401140 1082430 1102300 1039420 1124440 890160 1406970 1092190 1060480 TRUE FALSE 1313445.149 1162574.243 1128447.077 1066093.277 1036131.018 1147134.741 1196007.91 1228552.326 883479.037 1.486673813 1.31590473 1.277276573 1.206699007 1.172785063 1.298428931 1.353747922 1.39058458 1 19.75283638 -2.05779771 2.599905756 0.568177571 1.305481751 0.550252239 0.088646009 3264521.061 1559932.081 8418524.169 0.021453644 0.008753914 2.05779771 0.73730418 S(ph)PGAFDMSGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPGAFDMSGVR 11 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR 157.99 3.18E-05 1174360000 728206 837595 861991 984817 926167 571562 597690 551464 486914 TRUE FALSE 682628.8863 899611.4053 882437.8336 1010089.072 853429.5798 736562.6709 508071.9332 620315.4943 405644.9078 1.682823753 2.217731292 2.175394826 2.490081971 2.10388338 1.815781874 1.252504157 1.529208138 1 18.62985785 1.93510239 2.268576257 1.269874509 2.170102481 0.743398757 0.233391713 0.143362945 1.353773499 0.125116432 0.063719972 86.11967655 -1.93510239 0.900227972 S(ph)PGAPGPLTLK ddPTM_SK-BR-3_Pertuzumab_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 152.4 3.46E-05 5141957000 7835710 6466670 7748300 8682000 8889140 5087120 6579550 5176850 8299200 TRUE FALSE 7345286.898 6945468.975 7932093.335 8904794.819 8191022.801 6555688.962 5593007.559 5823191.118 6914009.905 1.06237726 1.004550047 1.147249345 1.287934924 1.184699315 0.948174656 0.80893832 0.842230659 1 22.72109124 2.084535593 4.642095506 0.865687086 1.126540973 0.639488437 0.088967066 0.136375154 5.312743094 0.037248773 0.026637213 121.4886184 -2.084535593 0.260853887 S(ph)PGASNFSTLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPGASNFSTLPK 12 0 Q9Y4E8 Q9Y4E8 USP15 Ubiquitin carboxyl-terminal hydrolase 15 1 S(0.941)PGAS(0.059)NFSTLPK;S(1)PGASNFSTLPK;S(1)PGASNFSTLPK;S(1)PGASNFSTLPK;S(1)PGASNFSTLPK;S(0.999)PGAS(0.001)NFSTLPK 162.32 6.61E-05 2474060000 1780380 1456440 1711140 1745100 1530930 1195650 1607350 1138150 1286150 TRUE FALSE 1668949.194 1564276.333 1751729.049 1789882.22 1410696.933 1540814.745 1366342.789 1280250.533 1071483.256 1.557606415 1.459916731 1.63486367 1.67047148 1.316583274 1.438020367 1.275188186 1.194839514 1 20.03117787 1.491716284 0.735494719 1.008247309 1.563927963 0.824807397 0.086289729 0.238941757 0.276887778 0.079352941 0.034660451 31.02532106 -1.491716284 0.555680654 S(ph)PGDFTSAAQLASTPFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPGDFTSAAQLASTPFHK 18 0 A0A590UJ99;O43683-2;O43683-3;O43683 A0A590UJ99 BUB1 Mitotic checkpoint serine/threonine-protein kinase BUB1 1 S(0.999)PGDFT(0.001)SAAQLASTPFHK 144.43 6.33E-08 228900000 199510 165540 200350 196120 220520 135690 235900 165860 175900 TRUE FALSE 187023.0252 177796.7538 205102.3966 201152.7712 203201.2487 174861.5003 200528.985 186567.9861 146541.1536 1.276249167 1.213288891 1.399623188 1.372670859 1.386649714 1.193258657 1.368414128 1.27314397 1 17.16094635 0.961564725 21.16788285 0.999999999 1.315076135 0.658992503 0.070821175 522.873354 287968.9163 0.066229996 0.016557499 9.153026619 -0.961564725 0.315076136 S(ph)PGEPGGAAPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPGEPGGAAPER 12 0 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 S(1)PGEPGGAAPER;S(1)PGEPGGAAPER;S(1)PGEPGGAAPER;S(1)PGEPGGAAPER 147.42 6.88E-05 969620000 106416.6 113968.7 95155.1 109486 123439.6 90496.7 114641.1 103063.6 135341 TRUE FALSE 99756.17497 122407.0611 97412.22391 112295.5961 113745.1517 116621.6282 97451.73133 115931.3173 112751.7128 0.884741992 1.085633718 0.863953385 0.995954681 1.008810855 1.034322454 0.864303778 1.028200056 1 16.78278982 S(ph)PGETSKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPGETSKPR 9 1 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 S(1)PGETSKPR;S(1)PGETSKPR;S(0.999)PGETSKPR;S(1)PGETSKPR 94.465 0.0052709 1137890000 1905600 1126690 1478080 1344110 1217110 1217510 1576000 1218570 941810 TRUE FALSE 1786331.898 1210111.3 1513140.756 1378602.138 1121523.09 1568985.372 1339693.431 1370711.147 784615.8267 2.276696234 1.542297847 1.928511641 1.757040951 1.429391368 1.999686113 1.70745145 1.746983811 1 19.58162691 -2.260682875 0.370756747 2.20E-13 1.812649829 0.542798427 0.232856551 39.31983058 1.929102248 32.80334145 0.148189494 0.005486775 2.260682875 1.812649829 S(ph)PGETSKPRPFAGGGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPGETSKPRPFAGGGYR 17 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 S(1)PGETSKPRPFAGGGYR;S(0.999)PGET(0.001)SKPRPFAGGGYR;S(1)PGETSKPRPFAGGGYR;S(0.95)PGET(0.041)S(0.009)KPRPFAGGGYR 165.17 1.31E-09 6038200000 2421740 1861380 2129930 2015040 1968540 1784910 2607240 1707440 2313770 TRUE FALSE 2270167.616 1999198.512 2180452.945 2066749.338 1813938.809 2300184.541 2216308.566 1920617.643 1927586.839 1.177725211 1.037150945 1.131182731 1.07219519 0.941041292 1.193297492 1.149784031 0.996384497 1 20.87836443 4.755770621 23.42805035 1.07966475 1.1777254 0.148686367 0.078063345 3026.823574 4120264.795 0.017915675 0.4683008 56986.32108 -4.755770621 0.09806065 S(ph)PGGGSEANGLALVSGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 380.17 2.72E-108 1983503000 1696640 1411794 1519097 1528698 1742039 1242005 1743836 1348407 1696598 TRUE FALSE 1590450.331 1516324.697 1555130.698 1567926.979 1605226.284 1600551.681 1482363.981 1516758.582 1413424.833 1.125245781 1.072801794 1.100257093 1.109310479 1.135699788 1.1323925 1.048774541 1.073108768 1 20.43076373 1.073107475 1.209107692 1.003975116 1.105693566 0.670138486 0.024193015 0.295618762 0.894377653 0.023351049 0.007342114 11.83334361 -1.073107475 0.10171845 S(ph)PGGPGSHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPGGPGSHVR 10 0 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 S(1)PGGPGSHVR;S(1)PGGPGSHVR;S(1)PGGPGSHVR 182.23 1.16E-06 2488080000 652000 650170 687630 627480 692640 649470 721430 627430 820560 TRUE FALSE 611192.4839 698309.2633 703940.9083 643582.1991 638242.8484 836961.4457 613258.2689 705766.0166 683603.235 0.894074885 1.02151252 1.029750698 0.941455754 0.933645155 1.224338041 0.897096792 1.032420534 1 19.3827997 S(ph)PGHMVILDQTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 235.71 3.02E-16 4883370000 5326330 5260900 4464760 3977250 6106910 2955360 5416830 5526230 7310900 TRUE FALSE 4992964.513 5650422.51 4570666.216 4079312.968 5627297.923 3808524.456 4604626.629 6216191.98 6090663.56 0.819773488 0.927718705 0.750438137 0.669764949 0.923921978 0.625305341 0.756013952 1.020609974 1 22.53816798 1.235678712 24.99962305 1.010305124 0.784967055 0.497595453 0.095396431 65.8100679 570829.6487 0.078012762 0.022822793 17.2059522 -1.235678712 -0.225338069 S(ph)PGKAEAESDALPDDTVIESEALPSDIAAEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPGKAEAESDALPDDTVIESEALPSDIAAEAR 32 1 G3V529;Q9GZR7;Q9GZR7-2;A0A1W2PRR2;F5GYL3 G3V529 DDX24 ATP-dependent RNA helicase DDX24 1 S(0.964)PGKAEAES(0.036)DALPDDTVIESEALPSDIAAEAR;S(1)PGKAEAESDALPDDTVIESEALPSDIAAEAR;S(0.998)PGKAEAES(0.002)DALPDDTVIESEALPSDIAAEAR 244.5 3.69E-47 715970000 490160 321310 391256 363961 375632 273309 468119 293109 434284 TRUE FALSE 459481.7606 345100.1267 400536.7771 373300.8554 346131.3779 352208.8715 397928.9018 329704.3039 361799.1948 1.269991109 0.953844375 1.107069288 1.031790178 0.956694716 0.97349269 1.099861214 0.911290872 1 18.46482967 4.747215472 24.84400412 1.015570693 1.26999125 0.63231727 0.063160965 691.4244926 1984706.154 0.014249181 0.168759162 55874.73447 -4.747215472 0.254420557 S(ph)PGLCSDSLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPGLCSDSLEK 11 0 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 S(0.998)PGLCS(0.002)DSLEK;S(1)PGLCSDSLEK;S(1)PGLCSDSLEK;S(1)PGLCSDSLEK 210.31 1.38E-08 841990000 1681950 1138290 1457510 1260520 1225470 1166380 1791890 1151220 1432540 TRUE FALSE 1576679.752 1222570.176 1492082.825 1292867.077 1129226.53 1503094.971 1523212.73 1294952.351 1193439.819 1.321122126 1.024408735 1.250237173 1.083311497 0.946194782 1.259464404 1.276321357 1.085058777 1 20.18669439 S(ph)PGLLDTTPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPGLLDTTPIR 11 0 Q8IY92-2;Q8IY92 Q8IY92-2 SLX4 Structure-specific endonuclease subunit SLX4 1 S(1)PGLLDTTPIR;S(1)PGLLDTTPIR;S(1)PGLLDTTPIR;S(1)PGLLDTTPIR 160.52 2.87E-05 294776000 188510 196025 198729 183764 199465 175599 218857 165725 182625 TRUE FALSE 176711.4956 210538.895 203442.9457 188479.6954 183799.8235 226291.5807 186041.4246 186416.1311 152143.7077 1.161477515 1.383815987 1.337176205 1.238826753 1.208067204 1.487354187 1.22280065 1.225263495 1 17.21507514 0.831400517 1.617472237 1.00149072 1.309194308 0.481296881 0.09463463 0.487893194 2.372689337 0.083074886 0.023928443 6.782667334 -0.831400517 0.307703588 S(ph)PGLLSSDNPQLSALLMGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPGLLSSDNPQLSALLMGK 19 0 H0Y6I7;F5H5V6;F5H6S1;F8W8R6;A0A087X0R0;O15550 H0Y6I7 KDM6A Lysine-specific demethylase 6A 1 S(1)PGLLSSDNPQLSALLMGK;S(0.997)PGLLS(0.003)SDNPQLSALLMGK 264.69 2.47E-31 169164000 261510 203195 234946 236687 214420 224904 319880 214815 184515 TRUE FALSE 245142.5559 218239.7692 240519.0301 242760.7891 197580.3181 289830.1338 271916.9636 241635.1256 153718.2545 1.594752404 1.419738794 1.564674481 1.579258039 1.28534063 1.885463342 1.768930857 1.571935138 1 17.22992897 2.245735668 24.99948356 1.646003348 1.493808729 0 0.25093543 414.4922628 1444185.233 0.07881026 0.064660383 176.090395 -2.245735668 -0.152194619 S(ph)PGLVPPS(ph)PEFAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPGLVPPSPEFAPR 14 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 2 S(1)PGLVPPS(1)PEFAPR 90.706 0.0082542 126800000 168800 148320 167010 158480 165000 158440 199210 148850 153440 TRUE FALSE 158235.1093 159301.7671 170971.5561 162546.8651 152041.5656 204179.0559 169340.3099 167434.2502 127829.8727 1.237857051 1.246201406 1.337492969 1.271587475 1.189405593 1.597271839 1.324731898 1.309820988 1 16.9638655 0.76261671 6.445239108 1.000000022 1.318938051 0.446510085 0.109915689 25.97528383 705.5952878 0.102341263 0.025698107 5.789175427 -0.76261671 0.318938029 S(ph)PGLVPPSPEFAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPGLVPPSPEFAPR 14 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 S(0.993)PGLVPPS(0.007)PEFAPR 75.102 0.032718 223930000 44842 44137 47502 47328 39965 42319 53040 39199 49490 TRUE FALSE 42035.41927 47404.9494 48628.76987 48542.51661 36826.31011 54535.80831 45087.1444 44093.08144 41229.79928 1.01953975 1.149773955 1.179456867 1.177364854 0.893196444 1.32272796 1.093557213 1.06944691 1 15.33139982 1.050764644 2.686082565 1.002941816 1.131238585 0.103169091 0.111426606 0.489714548 7.511294224 0.095254478 0.025639592 11.23995685 -1.050764644 0.128296769 S(ph)PGMLEPLGSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 SPGMLEPLGSSR 12 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR;S(1)PGMLEPLGSSR 214.58 4.56E-11 9564600000 2412173 2292689 2409140 2275152 2172977 2334131 2894204 2199799 1774214 TRUE FALSE 2261199.398 2462442.079 2466285.938 2333536.252 2002320.152 3007956.728 2460244.979 2474448.748 1478086.222 1.529815626 1.665966466 1.668567031 1.578755162 1.354670737 2.035034685 1.664480017 1.674089584 1 20.495299 -1.498531626 7.219289199 0.9998424 1.657358788 0.590201281 0.169061224 0.000398591 2.77E-05 0.152146272 0.035852872 0.031729876 1.498531626 0.657516389 S(ph)PGNLTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPGNLTER 8 0 Q9H0F6-2;Q9H0F6 Q9H0F6-2 SHARPIN Sharpin 1 S(1)PGNLTER 76.332 0.037842 286390000 125110 164680 187890 160170 138260 147910 170240 102080 123040 TRUE FALSE 117279.5884 176873.0785 192346.8395 164280.2334 127401.6173 190609.2159 144714.0924 114824.9127 102503.8291 1.144148364 1.725526549 1.876484431 1.602674112 1.242896177 1.859532639 1.411792063 1.120201203 1 16.64531828 1.307091614 2.712100736 1.019199538 1.616923993 0.433086955 0.237768375 0.230497763 2.794575872 0.203640186 0.060612683 20.28110501 -1.307091614 0.597724456 S(ph)PGNLTEREELAGSLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPGNLTEREELAGSLAR 17 1 Q9H0F6-2;Q9H0F6 Q9H0F6-2 SHARPIN Sharpin 1 S(1)PGNLTEREELAGSLAR;S(1)PGNLTEREELAGSLAR;S(0.999)PGNLT(0.001)EREELAGSLAR;S(1)PGNLTEREELAGSLAR 254.36 2.97E-27 1530700000 92694 127043 114671 153543 149188 79488 81444 90207 128703 TRUE FALSE 86892.448 136449.3959 117391.0503 157483.1733 137471.3763 102434.8952 69232.22829 101469.5425 107221.6378 0.810400305 1.272591975 1.094844778 1.468762989 1.28212345 0.955356561 0.645692695 0.946353223 1 16.71023655 2.066190659 5.073792291 0.818604133 1.196038758 0.376258525 0.190529934 0.169852334 8.47756985 0.069980901 0.050234168 116.4637203 -2.066190659 0.377434625 S(ph)PGNTSQPPAFFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPGNTSQPPAFFSK 14 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(1)PGNTSQPPAFFSK;S(1)PGNTSQPPAFFSK;S(1)PGNTSQPPAFFSK;S(1)PGNTSQPPAFFSK;S(1)PGNTSQPPAFFSK;S(1)PGNTSQPPAFFSK 297.73 1.12E-43 3859930000 3545730 3056810 3354010 3182320 3360680 2888860 4115230 3160640 2725040 TRUE FALSE 3323809.089 3283139.393 3433568.701 3263983.719 3096745.749 3722826.985 3498189.465 3555252.861 2270213.22 1.464095557 1.446181074 1.512443268 1.437743244 1.364077049 1.639857857 1.540907892 1.56604359 1 21.11439637 -1.518843912 6.584508671 0.99966235 1.497327734 0.807580386 0.076151041 0.00037825 2.76E-05 0.073887968 0.017404204 0.030280015 1.518843912 0.497665384 S(ph)PGPGPGPGAGAEPGATGGSSHFISSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPGPGPGPGAGAEPGATGGSSHFISSR 27 0 Q9ULI0-2;Q9ULI0;C9JG15 Q9ULI0-2 ATAD2B ATPase family AAA domain-containing protein 2B 1 S(1)PGPGPGPGAGAEPGATGGSSHFISSR 170.44 3.47E-12 324980000 20784 42075 50222 42265 45186 32386 46696 42197 46912 TRUE FALSE 19483.16654 45190.27678 51413.28956 43349.59145 41637.27383 41735.31246 39694.3683 47465.38834 39082.08414 0.498519129 1.156291374 1.315520671 1.109193443 1.065380078 1.067888609 1.01566662 1.214505045 1 15.25421978 4.74003101 24.95193795 1.129648693 0.498518916 0.808372332 0.094647129 57.80985597 980911.5071 0.024865422 0.157021677 54958.01146 -4.74003101 -0.631129777 S(ph)PGPPALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 102.07 0.005283 1870590000 4572200 3380690 4032720 3648550 3830670 3505330 5447760 4093960 3943620 TRUE FALSE 4286034.164 3630999.805 4128378.023 3742177.97 3529824.63 4517261.867 4630918.963 4605099.918 3285404.345 1.30456824 1.10519115 1.256581409 1.139031174 1.0743958 1.374948527 1.409543081 1.401684369 1 21.64763951 2.223596577 24.98791957 1.340704311 1.175620546 0.129056698 0.1355799 301.6250524 503669.7721 0.045227646 0.033537629 167.3387719 -2.223596577 -0.165083765 S(ph)PGPPALKHPATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPGPPALKHPATK 13 1 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 S(1)PGPPALKHPATK;S(1)PGPPALKHPATK 136.26 4.49E-05 468700000 657700 632660 659710 664840 790720 548850 1048640 672980 1299180 TRUE FALSE 616535.731 679502.8047 675358.6327 681900.92 728620.0408 707294.0852 891406.1671 757003.0344 1082338.465 0.569633022 0.627809901 0.623980995 0.630025581 0.673190563 0.653486971 0.8235928 0.699414332 1 20.04572029 0.337349989 0.280683973 1.092934677 0.569147905 0.879301125 0.043491189 1.290648655 0.200636378 0.20411252 0.063044608 2.174452818 -0.337349989 -0.523786772 S(ph)PGREEVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPGREEVAR 9 1 A0A494BZV2;A0A1W2PPU9 A0A494BZV2 1 S(1)PGREEVAR 116.03 0.00083613 273280000 38851 41618 49640 43094 36945 37730 46853 40777 36204 TRUE FALSE 36419.38526 44699.44002 50817.48424 44199.865 34043.48873 48622.0385 39827.82761 45868.09821 30161.31851 1.207486511 1.482012134 1.684856192 1.4654487 1.128713545 1.61206608 1.320493585 1.520759054 1 14.88041188 -2.892884747 0.378629576 6.28E-12 1.46159233 0.361580443 0.173663183 102.6032349 3.477085348 82.70213835 0.114647418 0.001279721 2.892884747 1.46159233 S(ph)PGSGSQSSGWHEVEPGMPSPTTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SPGSGSQSSGWHEVEPGMPSPTTLK 25 0 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;A0A590UJA3;S4R3W2 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 1 S(0.951)PGS(0.007)GS(0.011)QS(0.016)S(0.016)GWHEVEPGMPSPTTLK;S(0.988)PGS(0.009)GS(0.002)QS(0.001)S(0.001)GWHEVEPGMPSPTTLK;S(0.997)PGS(0.002)GSQSSGWHEVEPGMPSPTTLK;S(0.982)PGS(0.008)GS(0.002)QS(0.004)S(0.004)GWHEVEPGMPSPTTLK;S(0.989)PGS(0.009)GS(0.002)QSSGWHEVEPGMPSPTTLK;S(0.843)PGS(0.144)GS(0.007)QS(0.003)S(0.003)GWHEVEPGMPSPTTLK;S(0.994)PGS(0.006)GSQSSGWHEVEPGMPSPTTLK 217.74 9.66E-34 3542700000 2249990 2667220 2770860 2816600 2984480 2272930 3415420 2700140 3120310 TRUE FALSE 2109167.142 2864703.744 2836586.108 2888878.724 2750090.98 2929087.993 2903309.478 3037258.423 2599510.103 0.811371012 1.102016776 1.091200263 1.111316598 1.057926636 1.126784616 1.116867934 1.168396468 1 21.30980833 4.738619283 23.72021383 1.101551544 0.81137086 0.802694161 0.044419858 0.869696472 349819.2744 0.009271974 0.053513081 54779.65372 -4.738619283 -0.290180684 S(ph)PGSGSQSSGWHEVEPGMPSPTTLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPGSGSQSSGWHEVEPGMPSPTTLKK 26 1 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;A0A590UJA3;S4R3W2 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 1 S(0.977)PGS(0.022)GS(0.001)QSSGWHEVEPGMPSPTTLKK;S(0.48)PGS(0.13)GS(0.13)QS(0.13)S(0.13)GWHEVEPGMPSPTTLKK 212.39 3.27E-26 786510000 905600 1050000 1101380 1136560 1195430 811080 1474280 1079550 1557940 TRUE FALSE 848920.1125 1127743.093 1127505.254 1165726.054 1101545.75 1045225.629 1253225.401 1214334.194 1297909.749 0.654067136 0.868891765 0.868708517 0.898156482 0.848707509 0.805314568 0.965572068 0.935607576 1 20.30775864 7.923358854 0.184413329 0.980543694 1.60E-37 0.59920556 0.06056664 44.14597622 0.517874022 0.129010221 12.1572254 83822161.17 -7.923358854 -0.980543694 S(ph)PGSISYLPSFFTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPGSISYLPSFFTK 14 0 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 S(0.998)PGS(0.002)ISYLPSFFTK;S(1)PGSISYLPSFFTK 201.76 1.82E-08 1302760000 985080 990840 968250 1000870 1181470 836780 1280500 1029410 1165100 TRUE FALSE 923425.6012 1064202.825 991217.3472 1026554.019 1088682.112 1078344.802 1088500.913 1157934.105 970637.2832 0.951360119 1.09639599 1.021202631 1.057608271 1.121615799 1.110965775 1.121429118 1.192962731 1 19.88857275 2.834234226 3.719267988 1.117473245 1.038522907 0.299681577 0.058581805 0.2870556 7.350883275 0.016734458 0.017742677 682.7067957 -2.834234226 -0.078950338 S(ph)PGTLPNHPNFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPGTLPNHPNFR 12 0 H9KV62;H9KV63;Q9BXT4-2;Q9BXT4;Q9BXT4-3 H9KV62 TDRD1 Tudor domain-containing protein 1 1 S(0.794)PGT(0.206)LPNHPNFR;S(0.977)PGT(0.023)LPNHPNFR 73.758 0.024694 450310000 156376 139022 167299 161562 164561 139213 174500 128749 143616 TRUE FALSE 146588.7053 149315.3335 171267.4113 165707.9544 151637.0429 179401.5332 148335.345 144823.5961 119645.5618 1.225191333 1.247980546 1.431456451 1.3849904 1.267385439 1.499441605 1.239789782 1.210438514 1 16.86840736 0.967255098 1.681081126 1.003571285 1.339654675 0.597613156 0.087473721 0.269897815 1.572853227 0.078982636 0.022766858 9.273743893 -0.967255098 0.33608339 S(ph)PGVAAAVAEDGGLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPGVAAAVAEDGGLKK 16 1 E9PM04;Q9BTE7;E9PLH8;E9PM78;H0YD80;E9PLS2;E9PQV9 E9PM04 DCUN1D5 DCN1-like protein;DCN1-like protein 5 1 S(1)PGVAAAVAEDGGLKK;S(1)PGVAAAVAEDGGLKK 159.34 5.61E-09 269000000 513180 301350 399550 382760 412380 277870 550590 358960 477100 TRUE FALSE 481060.9799 323662.2676 409027.5147 392582.2696 379993.3383 358086.5582 468034.1409 403776.9462 397468.9278 1.21031091 0.814308352 1.029080479 0.987705559 0.956032816 0.900917111 1.177536427 1.015870469 1 18.60048256 1.748396794 25 1.079698616 0.968036947 0.091624846 0.111100377 3.966112019 10101.55518 0.046484608 0.025778241 56.02692588 -1.748396794 -0.111661669 S(ph)PGVVISDDEPGYDLDLFCIPNHYAEDLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPGVVISDDEPGYDLDLFCIPNHYAEDLER 30 0 P00492 P00492 HPRT1 Hypoxanthine-guanine phosphoribosyltransferase 1 S(0.998)PGVVIS(0.002)DDEPGYDLDLFCIPNHYAEDLER;S(1)PGVVISDDEPGYDLDLFCIPNHYAEDLER;S(1)PGVVISDDEPGYDLDLFCIPNHYAEDLER 163.48 2.31E-12 57392000 26511.9 27198.9 26267.2 27836.8 31407.8 26749.3 36479.7 23044.4 28794.9 TRUE FALSE 24852.5675 29212.73486 26890.27039 28551.13942 28941.15808 34471.38867 31009.90765 25921.54407 23988.84517 1.036005165 1.217763283 1.120948933 1.190183988 1.206442323 1.436975746 1.292680303 1.080566567 1 14.55007609 2.837481088 2.84657849 1.247284261 1.14565077 0.005962731 0.127553227 0.585204873 9.21366647 0.039589275 0.041977314 687.8299595 -2.837481088 -0.101633491 S(ph)PGYEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPGYEPR 7 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 S(1)PGYEPR;S(1)PGYEPR;S(1)PGYEPR 96.034 0.013666 449550000 665030 700520 695570 673290 680070 609250 709360 583270 691240 TRUE FALSE 623406.9594 752387.2297 712069.2489 690567.7613 626660.0455 785130.5847 602998.0534 656092.5434 575867.5784 1.082552626 1.306528198 1.236515608 1.199178053 1.088201644 1.363387373 1.04711235 1.139311481 1 19.13537757 1.262433888 1.08536925 1.009021039 1.221185885 0.298534407 0.096747944 0.482931307 1.168160172 0.081884211 0.027486428 18.29927519 -1.262433888 0.212164847 S(ph)PHEAGFCVYLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPHEAGFCVYLK 12 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(1)PHEAGFCVYLK;S(1)PHEAGFCVYLK;S(1)PHEAGFCVYLK 131.96 0.00012205 1148260000 1758490 1370070 1482370 1421040 1470750 1447390 1941390 1403480 1482300 TRUE FALSE 1648429.25 1471511.408 1517532.516 1457506.292 1355243.228 1865227.997 1650296.592 1578707.567 1234894.554 1.3348745 1.191608954 1.228876192 1.180267811 1.09745664 1.510435033 1.336386647 1.278414875 1 20.23595643 2.270533815 24.99977096 1.319421625 1.206408056 0.037245461 0.137544748 358.0494074 279956.8216 0.042863566 0.035859567 186.4377337 -2.270533815 -0.11301357 S(ph)PHGQTRPPASLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPHGQTRPPASLK 13 1 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C103 Q9H8V3-2 ECT2 Protein ECT2 1 S(1)PHGQTRPPASLK 93.226 0.0034589 279170000 319370 274800 301860 306460 321460 247660 376390 284280 405460 TRUE FALSE 299381.2018 295146.4779 309020.2617 314324.2824 296213.8283 319155.4216 319953.8137 319772.9838 337786.1066 0.886304072 0.87376737 0.914840059 0.930542365 0.876927211 0.944844727 0.947208329 0.946672991 1 18.36575046 1.623680233 0.198255381 1.029617194 0.847688344 0.782106867 0.018110252 1.211019765 0.24971161 0.086606055 0.09162269 42.0416965 -1.623680233 -0.18192885 S(ph)PHKDLGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SPHKDLGHR 9 1 O94888;C9JAT7 O94888 UBXN7 UBX domain-containing protein 7 1 S(1)PHKDLGHR;S(1)PHKDLGHR;S(1)PHKDLGHR;S(1)PHKDLGHR;S(1)PHKDLGHR;S(1)PHKDLGHR;S(1)PHKDLGHR 121.56 0.00036869 2571879000 1790598 1659431 1651862 1700085 1776698 1434849 1898796 1745615 1823155 TRUE FALSE 1678527.667 1782296.998 1691044.947 1743712.059 1637163.306 1849066.613 1614089.167 1963558.875 1518858.652 1.105124341 1.173444938 1.113365581 1.148041035 1.077890496 1.217405326 1.062698734 1.292785785 1 20.53455619 -1.08314284 4.474619764 0.999988723 1.142819073 0.316290186 0.068265598 6.46E-06 1.32E-06 0.055629707 0.013111012 0.082576631 1.08314284 0.14283035 S(ph)PHLES(ph)LK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPHLESLK 8 0 Q5VXH5;Q5VWM4 Q5VXH5 PRAMEF7;PRAMEF8 PRAME family member 7;PRAME family member 8 2 S(1)PHLES(1)LK 65.246 0.034209 312390000 87194 313830 239870 243040 235870 208520 199400 199930 160030 TRUE FALSE 81736.68319 337066.2997 245559.8297 249276.8179 217345.7217 268716.339 169501.8211 224891.7006 133319.9592 0.61308662 2.528250847 1.841883475 1.869763683 1.630256437 2.015574717 1.271391187 1.686856957 1 17.02453326 1.056143243 0.68061901 1.019139282 1.870455456 0.121930616 0.505170627 1.10853213 1.211002734 0.455108023 0.186138395 11.38002571 -1.056143243 0.851316174 S(ph)PHQLLSPSSFSPSATPSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPHQLLSPSSFSPSATPSQK 20 0 A0A3B3ITS5;Q14181;E9PIQ6 A0A3B3ITS5 POLA2 DNA polymerase alpha subunit B 1 S(1)PHQLLSPSSFSPSATPSQK 193.81 3.87E-18 159520000 255640 247760 245290 277380 284770 205880 309150 265480 302150 TRUE FALSE 239639.9487 266104.4082 251108.3946 284498.0404 262405.3129 265314.2138 262795.8275 298625.7624 251719.213 0.952012943 1.057147784 0.997573414 1.130219807 1.04245246 1.054008594 1.04400385 1.186344732 1 17.94145581 6.7285837 0.569481481 1.069892088 1.52E-12 0.254436242 0.057574199 45.45625503 1.734668075 0.023753713 51.71930729 5352833.069 -6.7285837 -1.069892088 S(ph)PHS(ph)KSPAEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPHSKSPAEQR 11 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 2 S(0.997)PHS(0.592)KS(0.411)PAEQR;S(0.993)PHS(0.608)KS(0.399)PAEQR 58.885 0.058886 444310000 572190 457840 479220 499670 573090 408690 741160 565520 838850 TRUE FALSE 536377.6493 491738.95 490587.3247 512492.3781 528081.8231 526672.1685 630029.9386 636126.4169 698840.5158 0.767525118 0.703649744 0.702001835 0.733346689 0.755654275 0.753637141 0.901536079 0.910259784 1 19.41460373 1.581764208 1.087248843 0.990359487 0.717476416 0.931456132 0.026308921 0.099057987 0.224267531 0.021850304 0.008071428 38.17369581 -1.581764208 -0.272883072 AEAPLPS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AEAPLPSPK 9 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 AEAPLPS(1)PK;AEAPLPS(1)PK;AEAPLPS(1)PK;AEAPLPS(1)PK 148.28 9.48E-05 1037200000 4145800 2766160 3405620 4919300 4795170 1672570 1901250 1127950 1600150 TRUE FALSE 3886321.778 2970969.365 3486402.915 5045537.566 4418576.691 2155413.807 1616175.213 1268777.04 1333074.628 2.915306989 2.228659449 2.615309633 3.784887554 3.314575643 1.616874076 1.212366644 0.951767451 1 20.34632612 2.08872361 4.443133827 1.147435658 2.854624313 0.814363069 0.42482497 0.109030737 3.917142184 0.192456215 0.136984709 122.6658324 -2.08872361 1.707188655 up S(ph)PIEPSALEPAYYQGVYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPIEPSALEPAYYQGVYSR 19 0 P55317-2;P55317 P55317-2 FOXA1 Hepatocyte nuclear factor 3-alpha 1 S(0.896)PIEPS(0.104)ALEPAYYQGVYSR;S(1)PIEPSALEPAYYQGVYSR;S(0.818)PIEPS(0.182)ALEPAYYQGVYSR 220.64 2.99E-19 224880000 92703 62437.2 82537 81788 74660 82985 104122 75608 51108 TRUE FALSE 86900.88471 67060.11525 84494.81662 83886.81855 68796.50476 106941.4224 88509.87272 85047.82523 42577.74463 2.04099314 1.575003933 1.984483146 1.970203431 1.615785556 2.511674192 2.078782554 1.997471354 1 15.37781191 S(ph)PIKASDLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPIKASDLTK 10 1 Q5QJE6;J3KP30 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 S(0.998)PIKAS(0.002)DLTK 51.009 0.096537 250270000 298380 297680 274090 244240 383190 212930 393370 298040 530040 TRUE FALSE 279704.9284 319720.5369 280591.5442 250507.6119 353095.8031 274399.4344 334387.8204 335250.9501 441572.8998 0.633428656 0.724049273 0.635436514 0.567307486 0.799631959 0.621413666 0.757265268 0.759219939 1 18.75229211 0.548743859 0.684876837 1.005569901 0.662022485 0.725605173 0.064233673 0.751315793 0.609046797 0.064876958 0.021989994 3.537886195 -0.548743859 -0.343547416 S(ph)PILEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPILEEK 7 0 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2;A0A0A0MR81 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 S(1)PILEEK;S(1)PILEEK;S(1)PILEEK;S(1)PILEEK 116.3 0.0057542 3733040000 8655500 5771500 7026800 6622300 6713300 5166140 9054900 5969800 7307700 TRUE FALSE 8113767.706 6198827.865 7193479.014 6792239.43 6186064.498 6657520.753 7697201.807 6715142.671 6087997.66 1.332748164 1.018204706 1.181583735 1.115677076 1.016108225 1.093548507 1.264324041 1.103013346 1 22.53753637 4.755708846 23.97690675 1.114454641 1.332748476 0.439155487 0.081358301 2095.806496 2930302.543 0.019478809 0.53972228 56978.2158 -4.755708846 0.218293835 S(ph)PILEEKDIPPLEFPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPILEEKDIPPLEFPK 16 1 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2;A0A0A0MR81 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 S(1)PILEEKDIPPLEFPK;S(1)PILEEKDIPPLEFPK;S(1)PILEEKDIPPLEFPK 126.22 4.41E-05 152314000 321699 279845 298258 327156 444335 151598 371017 248311 789090 TRUE FALSE 301564.4338 300565.015 305332.8206 335551.3768 409438.7215 195361.8816 315386.4452 279313.1749 657385.7813 0.458732821 0.457212528 0.464465203 0.51043297 0.622828685 0.297179962 0.479758544 0.424884722 1 19.32638073 -1.429374776 3.024016916 1.010069019 0.46360965 0.817102291 0.079629568 19808756.3 24119059.42 1711374.189 0.018935279 0.037207049 1.429374776 -0.546459369 S(ph)PIRQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPIRQDR 7 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PIRQDR;S(1)PIRQDR;S(1)PIRQDR;S(1)PIRQDR;S(1)PIRQDR;S(1)PIRQDR 100.58 0.005866 2881561000 799695 765054 770832 759896 712324 776403 892719 678064 571482 TRUE FALSE 749643.5174 821699.3942 789116.4991 779396.2179 656380.9464 1000537.942 758864.0735 762721.783 476097.9623 1.57455729 1.725904035 1.657466659 1.637050102 1.378667834 2.101537964 1.593924221 1.602026985 1 18.86089893 0.642483504 2.266065219 1.000176212 1.677426389 0.572890722 0.179626443 1.584326531 9.202978951 0.155034547 0.041946312 4.390191897 -0.642483504 0.677250177 S(ph)PISVPGGSALISNLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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;S(1)PISVPGGSALISNLGK;S(0.998)PIS(0.002)VPGGSALISNLGK 192.24 2.07E-10 226628000 856409 570835 678120 640588 595648 664760 952481 631026 681277 TRUE FALSE 802807.8894 613100.2174 694205.3266 657026.5726 548868.2088 856665.4205 809665.3165 709810.9852 567567.4675 1.414471293 1.080224383 1.223123886 1.157618451 0.967053681 1.50936315 1.426553428 1.250619575 1 19.11443237 2.231794729 24.99991318 1.348619501 1.163415378 0.084956442 0.174851794 236.3597069 873339.8223 0.058854386 0.044455744 170.5276194 -2.231794729 -0.185204123 S(ph)PLAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPLAIR 6 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PLAIR 95.352 0.088359 0 43720 53299 52407 47723 43960 54197 55246 47924 36757 TRUE FALSE 40983.64324 57245.31342 53650.11879 48947.65297 40507.55893 69842.79409 46962.37518 53907.41689 30622.01924 1.338371677 1.869416676 1.752011138 1.598446288 1.322824553 2.280803024 1.53361458 1.760413527 1 14.9022818 -1.299404152 5.401869755 0.999884083 1.705791657 0.373674586 0.275954953 0.000342263 4.44E-05 0.237382914 0.05594262 0.050187533 1.299404152 0.705907575 S(ph)PLAQMEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPLAQMEEER 10 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2 E7EPK1 7-Sep Septin-7 1 S(1)PLAQMEEER;S(1)PLAQMEEER 127.79 0.00036367 370720000 149289 125571 131239 119024 150229 118120 139894 125204 158035 TRUE FALSE 139945.268 134868.4075 134352.0511 122078.3573 138430.6203 152219.3265 118918.1934 140835.995 131657.9376 1.062945923 1.024384933 1.020462978 0.927238871 1.051441507 1.156172801 0.903236034 1.069711387 1 17.00643498 1.675804264 0.003765452 6.03E-05 2.030947517 0.006383198 0.071545123 44920.63095 166.8301922 44938.15383 45031.18618 47.40282928 -1.675804264 2.030887187 S(ph)PLAQMEEERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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;S(1)PLAQMEEERR;S(1)PLAQMEEERR;S(1)PLAQMEEERR;S(1)PLAQMEEERR 177.39 4.90E-06 5203310000 1224024 1300626 1284416 1234073 1300315 1086101 1278084 1137928 1439688 TRUE FALSE 1147414.523 1396925.702 1314882.954 1265741.402 1198193.505 1399640.727 1086447.169 1280000.816 1199394.772 0.956661267 1.164692172 1.096288716 1.055316758 0.998998439 1.166955835 0.905829502 1.067205599 1 20.19387516 1.737215907 25 0.986126618 1.082846782 0.201743468 0.075187783 0.238070253 4245.027123 0.032191272 0.017851701 54.6029249 -1.737215907 0.096720165 S(ph)PLDPDSGLLSCTLPNGFGGQSGPEGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPLDPDSGLLSCTLPNGFGGQSGPEGER 28 0 A0A087X0R7;Q9H4L4 A0A087X0R7 SENP3-EIF4A1;SENP3 Sentrin-specific protease 3 1 S(1)PLDPDSGLLSCTLPNGFGGQSGPEGER 167 3.76E-12 52659000 30608 28449 32840 34531 33331 32640 40223 26186 22541 TRUE FALSE 28692.29992 30555.39356 33618.98031 35417.12392 30713.31771 42062.63813 34191.93456 29455.37974 18778.76148 1.527912261 1.627125069 1.790266112 1.886020223 1.63553479 2.239904808 1.820776871 1.56854752 1 14.1968143 0.890355145 3.466357296 1.000567701 1.793150225 0.62678995 0.192172371 0.309892578 7.779664201 0.183520866 0.047435833 7.768821543 -0.890355145 0.792582524 S(ph)PLHIKDDVLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPLHIKDDVLPK 12 1 Q5UIP0-2;Q5UIP0 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 S(1)PLHIKDDVLPK 90.444 0.0053638 84952000 82742 60966 78115 74072 71362 59201 106140 63281 77248 TRUE FALSE 77563.32592 65479.98608 79967.92469 75972.81292 65757.51638 76291.36765 90225.29236 71181.77215 64354.80976 1.205245206 1.017483951 1.242609915 1.180530456 1.021796454 1.185480432 1.401997655 1.106083173 1 15.97376036 2.001665453 24.99978513 1.233954775 1.132128617 0 0.126726244 110.380799 1656885.404 0.044485393 0.032624536 100.384221 -2.001665453 -0.101826158 S(ph)PLIESTANMDNNQSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPLIESTANMDNNQSQK 17 0 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 S(1)PLIESTANMDNNQSQK 82.362 0.0050891 0 28713 24243 24306 24384 21963 19516 29243 18598 23161 TRUE FALSE 26915.90458 26037.97694 24882.5498 25009.73472 20238.11457 25149.95238 24858.28363 20920.00124 19295.27947 1.394947641 1.349448034 1.289566696 1.296158201 1.048863511 1.303425142 1.288309074 1.08420307 1 14.23596032 2.785412924 0.035387058 1.96E-13 2.518875896 0.620085347 0.083491009 139.886162 1.884996452 60.1232075 73.39294869 610.116716 -2.785412924 2.518875896 S(ph)PLLAGGS(ph)PPQPVVPAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPLLAGGSPPQPVVPAHK 18 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4;C9JIY9 Q8NFH5-2 NUP35 Nucleoporin NUP53 2 S(1)PLLAGGS(1)PPQPVVPAHK 122.41 1.91E-05 157890000 182030 141890 170470 162160 148970 141240 212200 155940 171470 TRUE FALSE 170637.0672 152395.6832 174513.6289 166321.3001 137270.4971 182013.6952 180382.58 175409.4523 142850.5493 1.194514604 1.066819022 1.221651788 1.16430284 0.960937832 1.274154675 1.262736342 1.227922841 1 17.12414706 S(ph)PLLLGAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPLLLGAQR 9 0 Q96DR7;Q96DR7-4;Q96DR7-3 Q96DR7 ARHGEF26 Rho guanine nucleotide exchange factor 26 1 S(1)PLLLGAQR 102 0.0038343 72211000 35644 34553 35651 38879 46935 32693 39011 35205 33776 TRUE FALSE 33413.10567 37111.34007 36496.65856 39876.70096 43248.91443 42130.93837 33161.66271 39600.42175 28138.5674 1.187448714 1.318878092 1.297033287 1.417154626 1.536997737 1.497266644 1.17851283 1.407336102 1 14.78026126 -0.356260486 0.935272569 0.989920823 1.350499489 0.469565555 0.117917915 17.69333413 10.62417524 0.803600805 0.037159405 0.440290702 0.356260486 0.360578667 S(ph)PLPTKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPLPTKR 7 1 D6R9T3;Q96FZ2;E7EMP6 D6R9T3 HMCES Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein 1 S(1)PLPTKR;S(1)PLPTKR;S(1)PLPTKR 89.247 0.011033 1123940000 1011820 1039810 983680 985030 1179340 759330 1199090 1029210 1338510 TRUE FALSE 948491.9924 1116798.614 1007013.354 1010307.537 1086719.394 978536.2443 1019297.586 1157709.134 1115104.034 0.850586101 1.001519661 0.903066731 0.906020879 0.974545299 0.877529105 0.914082951 1.038207287 1 20.08874688 1.241970926 24.99996156 1.019103667 0.923868607 0.468809362 0.044337608 72.01964133 527987.6005 0.030348655 0.010078592 17.4570528 -1.241970926 -0.09523506 S(ph)PLQDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPLQDLR 7 0 Q8NG31-2;Q8NG31;H0YN41;E9PPJ1;Q8NG31-3;Q8NG31-4 Q8NG31-2 CASC5 Protein CASC5 1 S(1)PLQDLR 79.974 0.032697 63268000 185080 201610 216700 201390 174790 194880 226910 179270 154020 TRUE FALSE 173496.1732 216537.4142 221840.2263 206558.0084 161062.6985 251138.6924 192886.952 201652.2541 128313.067 1.352131761 1.687571026 1.728898167 1.609797141 1.25523224 1.957233961 1.503252604 1.571564447 1 16.96930857 0.430077501 1.646177148 1.000063403 1.612133847 0.464097515 0.195603399 3.472264169 9.122672337 0.170126117 0.048295043 2.692015158 -0.430077501 0.612070444 S(ph)PLS(ph)PTETFSWPDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPLSPTETFSWPDVR 15 0 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 2 S(1)PLS(0.986)PT(0.007)ET(0.007)FS(0.001)WPDVR;S(1)PLS(0.968)PT(0.031)ETFSWPDVR 212.39 1.31E-09 73139000 63515 63348 64701 71991 73244 43106 47340 33521 45887 TRUE FALSE 59539.70953 68038.35183 66235.73827 73838.41094 67491.71169 55550.00243 40241.80648 37706.17064 38228.16326 1.557482873 1.779796517 1.732642445 1.931518667 1.765497108 1.453117223 1.052674339 0.986345339 1 15.22234826 1.89921255 2.216860719 0.992381176 1.763309575 0.931441564 0.091626199 0.069464677 0.627833297 0.053125405 0.026081374 79.28892873 -1.89921255 0.770928399 S(ph)PLSGIPVR ddPTM_SK-BR-3_Pertuzumab_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 92.47 0.0073262 0 184470 275962 234493 254234 289353 198334 235858 223775 262969 TRUE FALSE 172924.352 296394.5136 240055.2847 260758.0749 266628.3826 255589.8061 200493.2825 251713.8013 219077.7751 0.789328593 1.352919134 1.09575371 1.190253438 1.21704898 1.166662415 0.91516943 1.148970046 1 17.74108361 1.765140873 24.99984531 1.014852666 1.161123922 0.093650712 0.153276103 29.4919267 27756.0084 0.063852542 0.035412794 58.22920664 -1.765140873 0.146271257 S(ph)PLSPTETFSWPDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SPLSPTETFSWPDVR 15 0 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 S(1)PLSPTETFSWPDVR;S(1)PLSPTETFSWPDVR;S(0.999)PLS(0.001)PTETFSWPDVR;S(1)PLSPTETFSWPDVR;S(0.994)PLS(0.006)PTETFSWPDVR 197.06 9.04E-09 417551000 138293 125011.9 118768 103920.7 135395.5 128790.4 155060 118741.2 150003 TRUE FALSE 129637.488 134267.9112 121585.233 106587.4811 124762.0836 165970.0977 131810.1925 133566.3002 124966.5302 1.03737767 1.074430977 0.972942378 0.852928227 0.998363989 1.328116396 1.054763962 1.068816586 1 16.93118222 2.42941182 24.99986058 1.123908818 0.990321461 0.270754296 0.101837521 148.3033118 77710.47925 0.034143218 0.028566271 268.7892031 -2.42941182 -0.133587357 S(ph)PLTGYVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPLTGYVR 8 0 Q9NP66;H0YNS8;H0YKM5 Q9NP66 HMG20A High mobility group protein 20A 1 S(0.973)PLT(0.027)GYVR;S(1)PLTGYVR;S(1)PLTGYVR;S(1)PLTGYVR 106.88 0.0043116 1113620000 228908 276821 240597 248062 266574 206455 255597 232573 230422 TRUE FALSE 214581.0569 297317.1149 246304.0745 254427.6909 245638.3533 266055.207 217272.6027 261610.251 191963.0796 1.117824622 1.548824469 1.283080449 1.325399089 1.279612485 1.385970716 1.131845786 1.362815451 1 17.55046934 -0.613489832 0.274354788 0.847267633 1.376793038 0.342477462 0.126281962 10.26875965 0.84682295 1.511918462 0.164192323 0.243506281 0.613489832 0.529525405 S(ph)PLTILQDDNS(ph)PGTLTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPLTILQDDNSPGTLTLR 18 0 Q99618;J3KMY0 Q99618 CDCA3 Cell division cycle-associated protein 3 2 S(0.997)PLT(0.003)ILQDDNS(0.977)PGT(0.019)LT(0.004)LR;S(0.998)PLT(0.002)ILQDDNS(0.984)PGT(0.016)LTLR;S(1)PLTILQDDNS(0.999)PGT(0.001)LTLR 201.61 2.02E-15 60003000 85494 84144 88172 81190 81192 76466 105164 81096 97398 TRUE FALSE 80143.08315 90374.10931 90263.48148 83273.47285 74815.50783 98540.49288 89395.63449 91221.01411 81141.64458 0.987693601 1.113782075 1.112418684 1.026272924 0.922035882 1.21442563 1.101723227 1.124219439 1 16.30815492 2.21587294 24.9999907 1.120187472 1.054158287 0.16636238 0.076944314 466.8677259 514447.1798 0.028258732 0.020885598 164.3890705 -2.21587294 -0.066029185 S(ph)PMCNQPSINK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPMCNQPSINK 11 0 Q08499-10;A0A087WSZ7;A0A1B0GW84;Q08499-2;Q08499-9;Q08499-6;Q08499-11;Q08499;Q08499-3;A0A1W2PQN6;Q08499-7;Q08499-12 Q08499-10 PDE4D "cAMP-specific 3,5-cyclic phosphodiesterase 4D" 1 S(1)PMCNQPSINK 86.624 0.00906 0 132440 110760 122560 120910 127570 96676 142160 114390 139060 TRUE FALSE 124150.8168 118960.7856 125467.1811 124012.7553 117551.1668 124584.7918 120844.4277 128671.8433 115849.9876 1.071651533 1.026851949 1.083014195 1.070459806 1.014684327 1.075397541 1.04311127 1.110676366 1 16.82189836 -1.693564529 2.738739978 0.991463352 1.058976612 0.321373107 0.02800465 4395835.852 3904587.381 258710.0404 0.006040431 0.020250487 1.693564529 0.067513259 S(ph)PNELVDDLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPNELVDDLFK 11 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 S(1)PNELVDDLFK;S(1)PNELVDDLFK;S(1)PNELVDDLFK;S(1)PNELVDDLFK;S(1)PNELVDDLFK;S(1)PNELVDDLFK 188.25 3.39E-06 410321000 713093 431573 515895 465897 469289 448172 685146 440345 581506 TRUE FALSE 668461.782 463527.114 528132.273 477852.7058 432432.935 577551.9809 582414.7179 495323.0426 484448.8919 1.379839635 0.95681324 1.090171289 0.986384144 0.892628597 1.192183511 1.202221179 1.022446435 1 18.88598495 S(ph)PNRDFLTHVSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPNRDFLTHVSAR 13 1 O15067 O15067 PFAS Phosphoribosylformylglycinamidine synthase 1 S(1)PNRDFLTHVSAR 161.14 2.58E-05 58920000 40599 53812 54893 52151 63132 43172 60935 54015 51323 TRUE FALSE 38057.98106 57796.29647 56195.08788 53489.28295 58173.86738 55635.05556 51798.36244 60758.89165 42756.85974 0.890102344 1.351743248 1.314294086 1.251010558 1.360573899 1.301196016 1.211463207 1.421032602 1 15.38386828 -1.162218408 5.058770223 0.999984117 1.274844344 0.240935603 0.145103918 2.30E-05 3.81E-06 0.124213801 0.029275783 0.068830606 1.162218408 0.274860227 S(ph)PNREWEVLQPAPHQVITNLPEGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPNREWEVLQPAPHQVITNLPEGVR 25 1 O75376;O75376-2;A0A088AWL3 O75376 NCOR1 Nuclear receptor corepressor 1 1 S(1)PNREWEVLQPAPHQVITNLPEGVR;S(1)PNREWEVLQPAPHQVITNLPEGVR 190.56 5.06E-18 473530000 153334 134525 125224 137028 150819 138084 158602 128322 96615 TRUE FALSE 143737.0986 144485.371 128194.3724 140544.3705 138974.2841 177946.6092 134821.1025 144343.2842 80489.33234 1.785790669 1.795087209 1.592687735 1.746124193 1.72661743 2.210809855 1.675018273 1.793321922 1 16.29650997 -0.987211043 5.031216275 0.999993733 1.781005522 0.701651277 0.161924642 1.10E-05 2.21E-06 0.151180013 0.035633185 0.102988553 0.987211043 0.781011789 S(ph)PNSHDSEPWTLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPNSHDSEPWTLLR 14 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 S(0.994)PNS(0.006)HDSEPWTLLR;S(0.999)PNS(0.001)HDSEPWTLLR;S(0.989)PNS(0.011)HDSEPWTLLR;S(0.999)PNS(0.001)HDSEPWTLLR;S(0.999)PNS(0.001)HDSEPWTLLR;S(0.991)PNS(0.009)HDSEPWTLLR 183.22 9.23E-07 483229000 138730 257879 249741 264841 261064 235674 239748 210801 205147 TRUE FALSE 130047.1369 276972.6295 255664.9745 271637.2684 240561.0865 303709.258 203800.0131 237119.9689 170906.6404 0.760925009 1.620607771 1.495933533 1.589389785 1.407558454 1.777047733 1.192463983 1.387423966 1 17.38284893 0.838140104 1.212588776 1.007523089 1.461447378 0.160293003 0.278699841 1.027552889 2.880062142 0.237435972 0.073107825 6.888744931 -0.838140104 0.453924289 S(ph)PPADAIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPPADAIPK 9 0 P18754-2;C9JW69;P18754;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4;M0R1Q8 P18754-2 RCC1 Regulator of chromosome condensation 1 S(1)PPADAIPK;S(1)PPADAIPK;S(1)PPADAIPK;S(1)PPADAIPK;S(1)PPADAIPK;S(1)PPADAIPK 104.82 0.0033541 3852140000 4112910 2944380 3493790 3215670 3241350 2787020 4342460 3141050 4664150 TRUE FALSE 3855490.305 3162384.959 3576664.349 3298189.536 2986787.446 3591587.431 3691348.436 3533217.007 3885673.233 0.992232252 0.813857669 0.920474814 0.848807745 0.768666655 0.924315354 0.949989414 0.909293395 1 21.88973315 2.018149501 24.98987314 0.944941281 0.86570435 0.275427057 0.063005044 300.2594053 413422.5299 0.02181426 0.016108351 104.2676296 -2.018149501 -0.07923693 S(ph)PPAPGLQPMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SPPAPGLQPMR 11 0 P15408;P15408-3;P15408-2;C9JCN8 P15408 FOSL2 Fos-related antigen 2 1 S(1)PPAPGLQPMR;S(1)PPAPGLQPMR;S(1)PPAPGLQPMR;S(1)PPAPGLQPMR;S(1)PPAPGLQPMR 98.156 0.0060113 2615950000 575839 585107 518320 542068 602653 437691 554175 530446 617276 TRUE FALSE 539798.2649 628428.9311 530614.7952 555978.3826 555323.0644 564045.2864 471081.6035 596673.3508 514248.6478 1.049683392 1.22203322 1.031825358 1.081146999 1.079872678 1.096833776 0.91605803 1.160281808 1 18.97210657 3.262854517 0.707333879 1.026355322 1.143993692 0.109760698 0.078732827 1.20891402 1.304239126 0.043960534 0.083248797 1831.700723 -3.262854517 0.117638371 S(ph)PPAS(ph)PESWK ddPTM_SK-BR-3_Pertuzumab_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(0.994)PES(0.006)WK 134.56 0.00024469 886190000 2230600 1259950 1692080 1446250 1305540 1326170 2021860 1340440 1196340 TRUE FALSE 2090990.728 1353238.009 1732216.937 1483363.223 1203008.155 1709013.75 1718700.863 1507796.885 996663.1253 2.097991462 1.357768713 1.73801648 1.488329593 1.207035882 1.714735608 1.724455154 1.512845059 1 19.92674643 0.963792179 21.39559797 0.999999994 1.598935502 0.389406984 0.240727052 852.1073639 503521.507 0.212375296 0.053093824 9.200092191 -0.963792179 0.598935508 S(ph)PPDGQSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPPDGQSFR 9 0 P78314;P78314-3;P78314-4;H0YAD9 P78314 SH3BP2 SH3 domain-binding protein 2 1 S(1)PPDGQSFR 63.694 0.07803 271770000 128940 177770 172340 176380 208350 164990 152310 138760 133870 TRUE FALSE 120869.8756 190932.2758 176427.9862 180906.2094 191987.0314 212619.9346 129472.5295 156084.4914 111526.2322 1.083779782 1.711994318 1.5819416 1.62209559 1.721451785 1.906456719 1.160915481 1.399531648 1 16.76702356 1.654185436 8.564150683 1.210438729 1.618584224 0.421205677 0.229404547 0.10872758 14.18009492 0.1035998 0.054296539 45.10092365 -1.654185436 0.408145495 S(ph)PPEGDTTLFLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPPEGDTTLFLSR 13 0 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(1)PPEGDTTLFLSR;S(1)PPEGDTTLFLSR;S(0.998)PPEGDT(0.002)T(0.001)LFLSR 190.57 4.51E-06 685970000 112229 83902 104032 83113 106256 88744 119160 82055 98337 TRUE FALSE 105204.7872 90114.19138 106499.6882 85245.82029 97911.08238 114362.9522 101293.0642 92299.74738 81923.91942 1.284176685 1.099974123 1.299982825 1.040548608 1.195146461 1.395965342 1.236428444 1.126651997 1 16.32199712 0.972519002 3.804597194 1.000560278 1.219301519 0.344810976 0.09950741 0.243288779 9.908485827 0.092234188 0.023695178 9.386831057 -0.972519002 0.218741242 S(ph)PPEHYVQETPLMFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPPEHYVQETPLMFSR 16 0 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 S(1)PPEHYVQETPLMFSR;S(1)PPEHYVQETPLMFSR 94.057 0.001851 112790000 57857 60571 73959 73604 70526 70379 75117 66660 68631 TRUE FALSE 54235.83365 65055.73986 75713.34241 75492.80325 64987.17245 90696.27479 63853.9032 74982.64774 57176.04273 0.948576205 1.137814664 1.324214458 1.320357262 1.136615431 1.58626359 1.11679473 1.311434723 1 15.80312315 4.635130192 1.721446102 1.269838296 0.878588078 0.281498588 0.157012834 0.85303503 2.973467826 0.036157809 0.513896089 43164.84567 -4.635130192 -0.391250218 S(ph)PPGGPDKDFAWLS ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPPGGPDKDFAWLS 14 1 Q86UZ6 Q86UZ6 ZBTB46 Zinc finger and BTB domain-containing protein 46 1 S(1)PPGGPDKDFAWLS;S(1)PPGGPDKDFAWLS 110.84 0.0018048 156818000 308390 268930 253840 249043 260062 190657 301370 220880 263050 TRUE FALSE 289088.4204 288841.857 259861.2047 255433.865 239637.7796 245696.5808 256182.3663 248457.3542 219145.2556 1.319163491 1.318038377 1.185794344 1.165591581 1.093511146 1.121158567 1.16900713 1.133756483 1 17.74152792 8 0.18267667 1.029689349 2.410582698 0.848674615 0.037316779 21.73712935 0.247138465 0.086314325 8.376846768 100000000 -8 1.380893349 S(ph)PPGS(ph)GASTPVGPWDQAVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPPGSGASTPVGPWDQAVQR 20 0 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 2 S(1)PPGS(1)GASTPVGPWDQAVQR 131.31 2.13E-05 59433000 56033 58178 54137 61472 50570 48744 65046 45945 52197 TRUE FALSE 52525.99455 62485.55965 55421.15521 63049.47559 46598.43619 62815.60151 55292.95616 51681.33439 43484.98349 1.207911107 1.436945691 1.274489508 1.449913752 1.071598341 1.44453548 1.271541385 1.188486927 1 15.40822967 0.958743369 1.957404548 1.001361515 1.321767362 0.418254929 0.117252332 0.316792133 2.576878374 0.097382234 0.027301479 9.093757498 -0.958743369 0.320405847 S(ph)PPGSGASTPVGPWDQAVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 SPPGSGASTPVGPWDQAVQR 20 0 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 S(0.993)PPGS(0.007)GASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR;S(0.323)PPGS(0.323)GAS(0.301)T(0.053)PVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR;S(0.978)PPGS(0.022)GASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR;S(0.891)PPGS(0.109)GASTPVGPWDQAVQR;S(0.976)PPGS(0.024)GASTPVGPWDQAVQR 310.19 3.15E-66 6027387000 309527 278166 311933 311857 315998 285606 351297 287644 326986 TRUE FALSE 290154.2576 298761.7001 319332.1981 319859.7786 291180.7918 368055.8158 298623.2761 323556.9866 272409.9242 1.065138352 1.096735741 1.172248768 1.174185484 1.068906695 1.351110158 1.096227595 1.187757706 1 18.05541974 4.279055483 1.893021974 1.160074932 1.065587623 0.085949204 0.091730058 0.833506737 5.296550178 0.021669652 0.100122062 19013.21165 -4.279055483 -0.094487309 S(ph)PPHHSGFQQYQQADASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPPHHSGFQQYQQADASK 18 0 E9PD50;B1ALB4;Q92540-2;Q92540;Q92540-5;Q92540-4 E9PD50 SMG7 Protein SMG7 1 S(0.499)PPHHS(0.499)GFQQY(0.001)QQADASK;S(0.494)PPHHS(0.494)GFQQY(0.012)QQADASK 136.35 1.08E-05 454750000 427360 619100 689550 712170 665670 745520 920490 671420 501260 TRUE FALSE 400612.3005 664938.8082 705906.4516 730445.4879 613390.9634 960739.5215 782471.0699 755248.265 417596.4677 0.959328757 1.592299886 1.690403311 1.749165868 1.468860517 2.300640919 1.873749254 1.808559994 1 18.67174998 5.079877924 1.230260018 1.768779558 3.90E-12 0.306699001 0.331583105 3.26226684 2.427525553 0.084343019 8.949088944 120192.6536 -5.079877924 -1.768779558 S(ph)PPKVPIVIQDDSLPAGPPPQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPPKVPIVIQDDSLPAGPPPQIR 23 1 Q7Z422-5;Q7Z422;Q7Z422-4;Q7Z422-2;Q7Z422-3 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 S(1)PPKVPIVIQDDSLPAGPPPQIR;S(1)PPKVPIVIQDDSLPAGPPPQIR;S(1)PPKVPIVIQDDSLPAGPPPQIR;S(1)PPKVPIVIQDDSLPAGPPPQIR 211.03 3.37E-25 417862000 447888 286997 325463 328318 298460 284929 426927 270423 283697 TRUE FALSE 419855.4896 308246.5565 333183.1361 336743.1957 275020.1555 367183.3769 362913.2597 304185.9068 236346.1379 1.7764432 1.3042166 1.409725325 1.424788231 1.163632958 1.553583147 1.53551593 1.287035657 1 17.85054176 0.948971688 5.719599282 1.000063272 1.432674012 0.445187116 0.160876534 0.296578992 29.68808648 0.144269943 0.036322569 8.891431519 -0.948971688 0.43261074 S(ph)PPLMAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPPLMAK 7 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(1)PPLMAK 70.268 0.060304 565660000 1218300 1016100 1049400 1015400 1108000 905710 1365500 1103500 946600 TRUE FALSE 1142048.778 1091333.101 1074292.264 1041456.883 1020982.149 1167173.774 1160755.952 1241274.404 788606.3447 1.448186139 1.383875629 1.362266828 1.320629602 1.294666415 1.480046137 1.471907954 1.574010167 1 19.58894579 4.738390338 8.026418779 1.383260118 1.448701711 0.01289168 0.153735713 0.543078125 438.6076223 0.032757594 0.193515835 54750.78344 -4.738390338 0.065441593 S(ph)PPLPAVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 95.523 0.0083784 1807064000 59373 60322 56981 52787 72634 43976.8 60933 62830 54958 TRUE FALSE 55656.94991 64788.30364 58332.61623 54141.60379 66929.61863 56672.18826 51796.66232 70674.46381 45785.15476 1.215611265 1.415050446 1.274050869 1.182514378 1.461819207 1.237785229 1.131298182 1.543610897 1 15.48259228 -1.984289824 2.94244165 0.730762097 1.299493951 0.353771875 0.130282401 5410263.641 15696294.58 9716542.779 0.028312129 0.010368363 1.984289824 0.568731854 S(ph)PPPETIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPPPETIK 8 0 A0A1W2PNZ9;Q15652-3;Q15652;Q15652-2 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 S(1)PPPETIK;S(1)PPPETIK 100.45 0.0063931 369300000 767370 634300 690460 699590 708590 570140 884250 623170 873690 TRUE FALSE 719341.6815 681264.232 706838.0373 717542.6638 652940.1997 734730.1626 751664.9215 700974.1463 727865.4947 0.988289302 0.935975447 0.971110792 0.985817667 0.89706162 1.009431231 1.032697561 0.963054508 1 19.47331235 S(ph)PPPGPDGHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPPPGPDGHAK 11 0 P57081;P57081-2;P57081-3 P57081 WDR4 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 1 S(1)PPPGPDGHAK;S(1)PPPGPDGHAK;S(1)PPPGPDGHAK;S(1)PPPGPDGHAK;S(1)PPPGPDGHAK;S(1)PPPGPDGHAK 159.58 1.84E-05 2326460000 3602160 2840420 3170230 3064130 3061720 2799160 4036020 2942700 3237030 TRUE FALSE 3376707.236 3050727.652 3245429.353 3142760.763 2821264.862 3607232.051 3430856.27 3310102.573 2696748.781 1.25214008 1.131261345 1.203460024 1.165388777 1.046172666 1.337622576 1.272219457 1.227441946 1 21.3627897 2.230246862 24.99996165 1.240086524 1.162037339 0.017630668 0.101414786 370.2905413 1113476.666 0.033746315 0.025333945 169.9209244 -2.230246862 -0.078049185 S(ph)PPPGRDESYPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPPPGRDESYPR 12 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 S(1)PPPGRDESYPR 73.834 0.023093 528960000 118450 92075 101100 101390 134470 128230 129770 87558 146830 TRUE FALSE 111036.4259 98892.3288 103498.1397 103991.8391 123909.2686 165247.9194 110312.1932 98489.80904 122323.1244 0.907730459 0.808451626 0.846104448 0.850140474 1.012966838 1.350913166 0.901809807 0.805160999 1 16.90033764 2.731299165 6.116000449 1.028019105 0.844021782 0.242972404 0.139872098 0.205716797 35.571854 0.044281002 0.043783581 538.6406989 -2.731299165 -0.183997322 S(ph)PPPKATEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPPPKATEEK 10 1 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 1 S(1)PPPKATEEK;S(1)PPPKATEEK 69.716 0.034002 468530000 1289750 673370 936700 886620 838370 777840 1464060 760050 1025600 TRUE FALSE 1209026.85 723227.0154 958918.9663 909372.1702 772527.802 1002389.781 1244537.795 854943.9156 854420.7344 1.415025176 0.846453025 1.122303015 1.064314258 0.904153856 1.173180543 1.456586603 1.000612323 1 19.70458713 2.014173623 24.10942097 1.231069512 1.046027645 0 0.199897558 260.7328204 443505.4881 0.068726038 0.050731098 103.3174368 -2.014173623 -0.185041867 S(ph)PPPPTHSTQLGAPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPPPPTHSTQLGAPSR 16 0 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 S(0.999)PPPPT(0.001)HSTQLGAPSR 171.83 1.57E-12 0 32889 37733 39571 39693 26592 27320 36188 25633 31344 TRUE FALSE 30830.5362 40526.79058 40509.64281 40711.58958 24503.57159 35206.8405 30761.94535 28833.33648 26112.48391 1.180681865 1.552008255 1.551351566 1.559085291 0.938385321 1.348276197 1.178055119 1.104197386 1 14.67245208 2.753915745 24.98999256 1.148571893 1.491081148 0.542683388 0.155380942 585.225614 952435.4507 0.044498055 0.047042366 567.4345096 -2.753915745 0.342509255 S(ph)PPPVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPPPVSK 7 0 Q01130;Q01130-2 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 S(1)PPPVSK;S(1)PPPVSK;S(1)PPPVSK;S(1)PPPVSK 85.862 0.021503 4342720000 7461980 5141600 6284270 5734630 4841330 5984550 8252950 5300520 4444600 TRUE FALSE 6994947.992 5522289.414 6433335.852 5881790.315 4461111.471 7712192.434 7015496.764 5962301.59 3702767.547 1.889113455 1.49139511 1.737439839 1.588484894 1.204804626 2.082818415 1.894663026 1.610228434 1 21.82017255 0.961618348 22.38525311 0.999999994 1.694619596 0.449353785 0.241030335 1682.949862 981545.6605 0.229930061 0.057482515 9.154156817 -0.961618348 0.694619602 S(ph)PPREGSQGELTPANSQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPPREGSQGELTPANSQSR 19 1 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;J3QQX0 Q13098-7 GPS1 COP9 signalosome complex subunit 1 1 S(0.998)PPREGS(0.002)QGELTPANSQSR 51.664 0.080961 342590000 127990 172120 144340 146210 156340 129680 182520 127090 179220 TRUE FALSE 119979.3344 184863.9439 147763.813 149961.9961 144061.687 167116.5108 155152.8204 142957.4663 149307.0242 0.803574614 1.238146329 0.989664175 1.004386746 0.964868785 1.11928097 1.039152855 0.957473147 1 17.18792251 3.716651943 24.3756802 1.018097662 1.070502496 0 0.114440163 960.3178994 2235912.601 0.027935057 0.04382362 5207.771767 -3.716651943 0.052404834 S(ph)PPRPPR ddPTM_SK-BR-3_Pertuzumab_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 88.819 0.011099 12041630000 440804 758291 618537 599784 676902 637983 580627 508100 540039 TRUE FALSE 413214.8645 814435.6546 633208.9897 615175.4729 623740.8474 822158.3353 493567.3716 571537.4035 449903.0021 0.918453228 1.810247211 1.407434462 1.36735134 1.386389609 1.827412423 1.097052852 1.270356945 1 18.77925447 1.613997348 24.99999985 1.137764597 1.481562328 0.258358169 0.260461707 0.649117161 2636.705029 0.113410774 0.060877091 41.11472107 -1.613997348 0.343797731 S(ph)PPSSSEIFTPAHEENVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPPSSSEIFTPAHEENVR 18 0 I3L3A7;I3L2L5;I3L317;I3L4Q0;C9JLW8 I3L3A7 FAM195B Protein FAM195B 1 S(0.998)PPS(0.002)SSEIFTPAHEENVR;S(0.986)PPS(0.005)S(0.005)S(0.005)EIFTPAHEENVR 192.94 9.61E-15 339030000 70971 78114 74914 91069 77336 63164 60771 51409 63996 TRUE FALSE 66529.0518 83897.64184 76690.99546 93405.98472 71262.34252 81398.42142 51658.95272 57827.52682 53314.65417 1.247856763 1.573631924 1.438459963 1.751975816 1.336637058 1.526755124 0.968944721 1.084646008 1 15.70224451 1.737660112 6.891792031 1.024201102 1.490691903 0.712770323 0.137680325 0.063985968 8.841314204 0.061205692 0.032212454 54.65880241 -1.737660112 0.466490801 S(ph)PPSTGSTYGSSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPPSTGSTYGSSQK 14 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(1)PPSTGSTYGSSQK;S(0.998)PPS(0.002)TGSTYGSSQK;S(1)PPSTGSTYGSSQK;S(0.735)PPS(0.261)T(0.003)GSTYGSSQK;S(0.944)PPS(0.051)T(0.005)GSTYGSSQK;S(1)PPSTGSTYGSSQK 205.37 1.29E-08 4132910000 1825110 1146480 1511190 1311950 1173766 1425760 1900420 1311490 928277 TRUE FALSE 1710879.623 1231366.572 1547036.14 1345616.858 1081583.153 1837353.767 1615469.664 1475232.413 773341.5718 2.212320772 1.592267398 2.000456457 1.740003263 1.398584005 2.375863181 2.088947139 1.907607799 1 19.56074624 2.242408954 24.99949342 1.966253792 1.788594202 0 0.413301428 353.2564098 2294832.206 0.131519428 0.106201293 174.7466884 -2.242408954 -0.17765959 S(ph)PPSTGSTYGSSQKEESAASGGAAYTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPPSTGSTYGSSQKEESAASGGAAYTK 27 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.994)PPS(0.005)T(0.001)GSTYGSSQKEESAASGGAAYTK;S(0.302)PPS(0.237)T(0.211)GS(0.188)T(0.026)Y(0.024)GS(0.007)S(0.006)QKEESAASGGAAYTK;S(0.763)PPS(0.115)T(0.115)GS(0.004)T(0.004)YGSSQKEESAASGGAAYTK 216.71 2.19E-34 2753480000 1342420 798680 1054120 910720 882170 855420 1329970 892370 900400 TRUE FALSE 1258400.328 857815.0982 1079124.224 934090.617 812887.9267 1102365.867 1130553.345 1003784.359 750117.4232 1.677604452 1.143574421 1.438607064 1.245259193 1.083680903 1.469591071 1.507168492 1.338169636 1 19.51675693 S(ph)PPSTGSTYGSSQKEESAASGGAAYTKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPPSTGSTYGSSQKEESAASGGAAYTKR 28 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.999)PPSTGSTYGSSQKEESAASGGAAYTKR 136.33 4.33E-06 398510000 225250 204980 209750 223010 281610 192230 331360 218600 483610 TRUE FALSE 211152.0046 220156.9325 214725.3691 228732.8142 259493.4866 247723.6804 281675.6442 245892.6912 402892.3668 0.524090358 0.546441061 0.532959636 0.56772685 0.644076453 0.614863176 0.699133733 0.610318565 1 18.62003495 -5 0.152708676 2.526346794 0.463278489 0.937669049 0.034659083 27.4677521 0.24710491 12.62224058 0.15475857 1.00E-05 5 -2.063068305 S(ph)PPTQVAISSDSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPPTQVAISSDSAR 14 0 Q6ZUT6;Q6ZUT6-4;H0YM82;Q6ZUT6-3 Q6ZUT6 C15orf52 Uncharacterized protein C15orf52 1 S(1)PPTQVAISSDSAR 81.448 0.010236 0 598820 135360 236450 264050 264570 333490 464320 215190 285840 TRUE FALSE 561340.9251 145382.1952 242058.7057 270825.97 243791.7394 429763.1492 394699.5265 242056.9452 238131.4574 2.357273295 0.610512348 1.016491934 1.137296067 1.023769569 1.804730689 1.657485873 1.016484541 1 17.86139869 2.270294545 24.98440916 1.463013574 1.111560745 0 0.51517173 450.5176927 354695.0456 0.167846311 0.140418653 186.3350461 -2.270294545 -0.351452829 S(ph)PPVQPHTPVTISLGTAPSLQNNQPVEFNHAINYVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPPVQPHTPVTISLGTAPSLQNNQPVEFNHAINYVNK 37 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 S(1)PPVQPHTPVTISLGTAPSLQNNQPVEFNHAINYVNK 342.95 1.21E-129 1382500000 775590 690440 810080 740540 778950 570280 881030 703990 524220 TRUE FALSE 727047.2064 741560.896 829295.4801 759543.5101 717774.4091 734910.5783 748927.7306 791884.7012 436724.2954 1.664773895 1.698006966 1.898899349 1.739183091 1.643541284 1.682779241 1.714875354 1.813237114 1 18.73636327 -1.412288089 3.200727408 0.990316792 1.737519152 0.903256614 0.075257833 29177616.56 38538906.92 2590943.845 0.019121872 0.038700084 1.412288089 0.747202361 S(ph)PPVTLGPNLAPTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPPVTLGPNLAPTSR 15 0 B4DF95;Q15735;C9K0M5 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 S(1)PPVTLGPNLAPTSR;S(1)PPVTLGPNLAPTSR;S(1)PPVTLGPNLAPTSR;S(1)PPVTLGPNLAPTSR 160.81 1.77E-06 828250000 118954 112836 109457 121522 170693 122464 118928 99319 148375 TRUE FALSE 111508.8815 121190.4948 112053.3717 124640.4603 157287.4603 157817.3688 101095.8505 111719.1958 123610.254 0.902100577 0.980424285 0.906505473 1.008334311 1.272446705 1.276733634 0.817859742 0.903802008 1 16.9154389 3.012175016 15.63091331 1.052650814 0.939757122 0.135902927 0.142499815 6.355994883 8151.00744 0.044218568 0.052605834 1028.430662 -3.012175016 -0.112893692 S(ph)PPWEP ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPPWEP 6 0 F5H8F7;Q9UBL3-2;Q9UBL3-3;Q9UBL3;H0YAQ0 F5H8F7 ASH2L Set1/Ash2 histone methyltransferase complex subunit ASH2 1 S(1)PPWEP 77.674 0.032016 104720000 171320 189940 168110 176990 178180 152090 224060 163580 185140 TRUE FALSE 160597.387 204003.3552 172097.6486 181531.863 164186.4615 195995.914 190464.2831 184003.3231 154238.9379 1.041224668 1.322644969 1.115786006 1.176952237 1.064494243 1.270729147 1.23486511 1.192975817 1 17.2348075 -2.338827229 2.052274902 0.062094049 1.189139246 0.278966132 0.08789551 1446890.873 207497.7052 6270077.573 0.020846985 0.004583242 2.338827229 1.127045197 S(ph)PPYTAFLGNLPYDVTEESIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPPYTAFLGNLPYDVTEESIK 21 0 E7EX17;P23588-2;P23588;F8VX11;F8VP89;F8W0K0;F8VSC7;F8VYE9;F8VRU1 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.609)PPY(0.276)T(0.115)AFLGNLPYDVTEESIK 190.87 1.06E-17 47814000 81595 46020 62788 56374 51827 48690 72766 51922 45354 TRUE FALSE 76488.1146 49427.36868 64277.36101 57820.65228 47756.71648 62746.01258 61855.41383 58404.57599 37784.1244 2.024345299 1.308151756 1.701173761 1.530289591 1.263936038 1.660644876 1.637074163 1.545743799 1 15.20549257 0.931189459 20.04392772 0.999999999 1.568483671 0.429581955 0.210975403 2994.897657 872391.583 0.182042507 0.045510627 8.534723561 -0.931189459 0.568483671 S(ph)PQALSNGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPQALSNGTK 10 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 S(0.999)PQALS(0.001)NGTK;S(1)PQALSNGTK;S(1)PQALSNGTK 164.92 6.31E-06 1157750000 1487380 1217900 1301550 1250300 1303650 989970 1625900 1130830 1243950 TRUE FALSE 1394287.541 1308074.583 1332423.381 1282384.815 1201266.588 1275758.268 1382111.389 1272016.615 1036326.709 1.345413111 1.262222205 1.285717496 1.237432948 1.159158186 1.231038684 1.333663774 1.227428188 1 19.98304746 0.966172675 23.0914867 0.999999999 1.265073389 0.71297959 0.052423283 1023.0683 698376.4846 0.050524347 0.012631087 9.250659053 -0.966172675 0.265073391 S(ph)PQGQLDTSESKPDSFFLEPLMPAVLKPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPQGQLDTSESKPDSFFLEPLMPAVLKPAK 30 2 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 S(1)PQGQLDTSESKPDSFFLEPLMPAVLKPAK 273.54 1.46E-71 225970000 445070 253630 335470 312260 370820 222850 438850 278990 468500 TRUE FALSE 417213.8632 272409.0291 343427.5068 320273.1203 341697.293 287183.1773 373048.5166 313822.5156 390304.3234 1.068945021 0.697940076 0.879896753 0.820572822 0.875463766 0.73579297 0.95578884 0.804045707 1 18.57423992 -0.426756177 0.558946547 1.020805949 0.839439842 0.137210244 0.106524172 15.05640437 4.068458334 0.731966744 0.040941092 0.374320681 0.426756177 -0.181366107 S(ph)PQHFHRPDQGINIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 223.89 5.01E-15 822460000 297330 283350 319040 284340 303410 273790 398440 274390 229440 TRUE FALSE 278720.646 304329.5288 326607.7795 291636.6458 279581.4025 352828.7284 338697.6209 308648.1955 191144.9818 1.458163555 1.592139778 1.708691363 1.525735298 1.462666715 1.845869691 1.771940952 1.614733448 1 17.5443078 S(ph)PQKPIVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPQKPIVR 8 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y467;A0A2R8YES9;H7C5K3 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(1)PQKPIVR;S(1)PQKPIVR;S(1)PQKPIVR;S(1)PQKPIVR 96.015 0.0055964 1128830000 1487450 1115080 1375850 1389710 1366110 1116320 1353950 1066530 940840 TRUE FALSE 1394353.16 1197641.683 1408485.812 1425372.311 1258821.231 1438583.462 1150937.767 1199688.618 783807.7259 1.778947966 1.527978921 1.79697873 1.818522916 1.606033201 1.835378007 1.468392986 1.530590448 1 19.58014027 0.719790267 0.91009248 1.001363258 1.710630708 0.794157913 0.113292003 0.417938279 0.633768044 0.102279469 0.034169791 5.245540767 -0.719790267 0.70926745 S(ph)PQPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPQPNK 6 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 S(1)PQPNK;S(1)PQPNK 77.748 0.075107 460600000 1187460 744370 1421160 1058120 984100 929660 1539390 901320 976250 TRUE FALSE 1113138.998 799483.9293 1454870.586 1085273.151 906812.7557 1198037.75 1308572.76 1013851.786 813307.5682 1.368656879 0.983003184 1.788831978 1.334394506 1.114969036 1.473043898 1.608951904 1.246578571 1 19.63344151 0.990305205 24.28209832 0.999999976 1.389969053 0.225795394 0.225766723 446.6823468 1118788.404 0.217603029 0.054400757 9.779242253 -0.990305205 0.389969077 S(ph)PQPNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPQPNKR 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 S(1)PQPNKR 56.729 0.073411 93661000 187470 177340 198720 195900 182320 152190 179200 168680 150370 TRUE FALSE 175736.5873 190470.4381 203433.7322 200927.1257 168001.3226 196124.7824 152330.6236 189740.0693 125272.2756 1.402837033 1.52045165 1.623932601 1.603923332 1.341089414 1.565588088 1.2159963 1.514621399 1 16.93470764 0.382608623 0.417084517 0.952046551 1.549301781 0.595810297 0.123603341 1.657781695 0.507984694 0.284254189 0.078988591 2.413285051 -0.382608623 0.597255231 S(ph)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK ddPTM_SK-BR-3_Pertuzumab_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(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK 189.45 4.78E-18 58951000 210624 157753 156725 126118 182854 130937 197544 168834 265747 TRUE FALSE 197441.4198 169433.1963 160442.591 129354.4014 168493.3844 168736.3863 167924.1111 189913.2965 221392.1089 0.891817783 0.7653082 0.724698779 0.58427738 0.761063189 0.762160798 0.758491854 0.857814208 1 17.75624428 0.947485306 1.663713384 1.000109483 0.740913349 0.549799428 0.073794608 0.319033086 1.810621724 0.068063427 0.019630313 8.861052426 -0.947485306 -0.259196134 S(ph)PQPPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPQPPSR 7 0 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 S(1)PQPPSR 90.696 0.017779 1738100000 726030 666010 769900 784280 832010 633200 786490 613650 825450 TRUE FALSE 680589.0783 715322.0734 788162.3916 804405.9526 766667.2908 815994.5609 668563.1259 690265.5533 687677.0624 0.98969286 1.040200572 1.146122846 1.16974376 1.114865295 1.186595577 0.972205069 1.003764108 1 19.3913717 1.666085565 8.601358438 0.991477196 1.10688294 0.464335931 0.058517736 0.111774222 13.87974959 0.029507213 0.015562251 46.3538237 -1.666085565 0.115405744 S(ph)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 SPQPPVEEEDEHFDDTVVCLDTYNCDLHFK 30 0 Q00839;Q5RI18;A0A1W2PRI6;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;S(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK 361.83 9.92E-121 5046526500 1910432.6 1241703.5 1433350.7 1246595.3 1434622.4 1575294.4 2240648.2 1374803.3 1368220.9 TRUE FALSE 1790862.034 1333640.519 1467350.455 1278585.046 1321952.944 2030056.321 1904683.804 1546450.518 1139855.993 1.571130077 1.170007902 1.287312138 1.121707526 1.159754348 1.780976135 1.670986349 1.356706925 1 20.12042014 2.260064095 24.99940688 1.535283126 1.246518315 0.088157568 0.243400591 309.5275984 359848.0455 0.077359937 0.064667976 181.9969436 -2.260064095 -0.288764811 S(ph)PQQSAALPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPQQSAALPR 10 0 A0A0A6YYG7;Q6IBW4-2;Q6IBW4;Q6IBW4-4;E5RJN3 A0A0A6YYG7 NCAPH2 Condensin-2 complex subunit H2 1 S(1)PQQSAALPR;S(1)PQQSAALPR 121.66 0.00053421 965500000 204480 173528 229230 188696 217890 204290 235930 190359 215184 TRUE FALSE 191681.9618 186376.1937 234667.4439 193538.2588 200777.7983 263265.2066 200554.4868 214125.7402 179268.4003 1.069245676 1.039648892 1.309028493 1.079600524 1.119984325 1.468553333 1.118738643 1.194442188 1 17.45176168 4.170796612 5.294783906 1.197740408 1.054226056 0.140904231 0.129800965 0.306806393 18.06674691 0.029764279 0.068229891 14818.23956 -4.170796612 -0.143514351 S(ph)PQQTVPYVVPLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPQQTVPYVVPLSPK 15 0 Q9UQR0;H0Y6S1;B4DRC2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 2 S(1)PQQTVPY(0.001)VVPLS(0.999)PK;S(1)PQQTVPYVVPLS(1)PK;S(0.991)PQQT(0.009)VPYVVPLS(1)PK;S(1)PQQTVPYVVPLS(1)PK 213.48 5.14E-10 297970000 1010960 583140 739250 743850 764480 582590 964700 619380 890480 TRUE FALSE 947685.8182 626316.2924 756785.3591 762938.4503 704440.8246 750774.2754 820052.1908 696710.9564 741853.1353 1.277457455 0.844259143 1.020128275 1.028422492 0.949569114 1.01202548 1.105410427 0.93914944 1 19.50077408 1.991969492 24.2499949 1.034603652 0.997612034 0 0.115910634 1313.386672 3966088.422 0.041574394 0.029290463 98.16789811 -1.991969492 -0.036991618 S(ph)PQQTVPYVVPLSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPQQTVPYVVPLSPK 15 0 Q9UQR0;H0Y6S1;B4DRC2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 1 S(1)PQQTVPYVVPLSPK 180.93 1.69E-11 0 76392 74889 79422 70183 67576 67453 99695 70209 88889 TRUE FALSE 71610.76108 80433.85948 81305.92735 71984.0146 62268.85355 86925.58609 84746.66027 78974.7482 74052.85166 0.967022329 1.086168293 1.097944583 0.972062696 0.840870435 1.173831718 1.14440779 1.066464646 1 16.17626767 S(ph)PQREPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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;S(1)PQREPQR 125.24 0.00076936 2497425000 340128.7 387004.3 298273.5 313769.7 423169.7 224294.4 322934 309341.5 411140.3 TRUE FALSE 318840.6518 415658.501 305348.6883 321821.5617 389935.6587 289044.5522 274513.0447 347963.4672 342518.3279 0.930871798 1.213536524 0.891481312 0.939574719 1.138437354 0.843880542 0.801455053 1.015897366 1 18.38582166 2.219975724 24.99956452 0.886376893 1.027106083 0.154993167 0.116032222 336.8875713 453163.2901 0.042222362 0.031237865 165.9494144 -2.219975724 0.14072919 S(ph)PQRPGWSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPQRPGWSR 9 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PQRPGWSR;S(1)PQRPGWSR;S(1)PQRPGWSR;S(1)PQRPGWSR;S(1)PQRPGWSR;S(1)PQRPGWSR 95.498 0.0048474 6159980000 343275 355784 389591 326262 331715 361368 465394 295705 332025 TRUE FALSE 321790.0305 382126.6176 398832.2825 334634.4353 305663.442 465689.0753 395612.4902 332624.4202 276607.8825 1.163343675 1.381474071 1.441868825 1.2097791 1.105042413 1.683571238 1.430228548 1.202512442 1 18.07748274 S(ph)PQTLAPVGEDAMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPQTLAPVGEDAMK 14 0 Q92797 Q92797 SYMPK Symplekin 1 S(0.999)PQT(0.001)LAPVGEDAMK;S(1)PQTLAPVGEDAMK 199.65 2.13E-08 190542000 499330 365950 407220 400310 385600 345240 595220 394410 348420 TRUE FALSE 468077.8266 393045.3188 416879.4507 410582.6323 355316.5314 444905.1835 505972.2868 443652.9567 290266.4511 1.612579838 1.354084557 1.436195775 1.41450254 1.224104715 1.532747521 1.74313044 1.528433462 1 18.14701831 2.051859873 24.99598589 1.539305035 1.402774766 0 0.213978011 237.3214354 114385.5369 0.072231377 0.0533464 112.6833819 -2.051859873 -0.136530269 S(ph)PQVKPASTMGMGPLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPQVKPASTMGMGPLGK 17 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 S(1)PQVKPASTMGMGPLGK;S(0.999)PQVKPAS(0.001)TMGMGPLGK;S(1)PQVKPASTMGMGPLGK 121.5 9.10E-05 1065980000 1582470 1043080 1298560 1280780 1338490 976390 1673420 1230050 1395620 TRUE FALSE 1483426.027 1120310.729 1329362.456 1313646.983 1233370.395 1258257.943 1422506.206 1383624.45 1162682.006 1.275865645 0.963557295 1.143358588 1.129842017 1.060797697 1.082202989 1.223469701 1.190028265 1 20.14902514 1.771135525 25 1.161677387 1.095317663 0 0.097515524 72.03911991 55314.5119 0.04092249 0.02270221 59.03852855 -1.771135525 -0.066359724 S(ph)PRPDHPGTPPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPRPDHPGTPPHK 13 1 P30291 P30291 WEE1 Wee1-like protein kinase 1 S(1)PRPDHPGTPPHK;S(1)PRPDHPGTPPHK;S(1)PRPDHPGTPPHK 149.57 2.38E-05 619190000 621220 593970 646400 626960 693590 466012 674870 530980 608350 TRUE FALSE 582338.9491 637948.1568 661732.9133 643048.855 639118.2392 600542.0993 573679.5087 597274.0218 506812.4549 1.149022569 1.258746013 1.305676107 1.268810284 1.261054722 1.184939505 1.131936485 1.178491207 1 18.95109245 1.141055052 0.677601301 1.007372232 1.261164695 0.695532495 0.048865507 0.365885548 0.400348901 0.047487266 0.01991464 13.83741774 -1.141055052 0.253792463 S(ph)PRPTGSDLLPGAPILSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPRPTGSDLLPGAPILSLR 19 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 S(0.998)PRPT(0.001)GS(0.001)DLLPGAPILSLR;S(0.985)PRPT(0.007)GS(0.008)DLLPGAPILSLR;S(1)PRPTGSDLLPGAPILSLR;S(0.998)PRPTGS(0.002)DLLPGAPILSLR 163.74 1.52E-11 1134680000 510251 587983 654320 673409 640724 651734 754780 561393 619171 TRUE FALSE 478315.3007 631517.8731 669840.7794 690689.815 590404.1216 839879.0258 641607.746 631484.1518 515827.3601 0.92727788 1.224281459 1.298575514 1.338994145 1.144576979 1.628217289 1.243842021 1.224216086 1 18.97652877 4.926474214 1.720935868 1.293503184 0.650106752 0.295810283 0.15997368 1.792296883 3.567529481 0.037018048 2.19761324 84425.61123 -4.926474214 -0.643396432 S(ph)PS(ph)PAPAPAPAAAAGPPTR ddPTM_SK-BR-3_Pertuzumab_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 167.93 2.49E-11 812390000 428630 359725 385774 384087 373509 338723 499870 337616 399194 TRUE FALSE 401802.8134 386359.4133 394924.7415 393943.3227 344175.1098 436506.8314 424919.1341 379768.1008 332565.9425 1.208189902 1.161752795 1.187508073 1.184557023 1.034907866 1.312542193 1.277698885 1.14193323 1 18.34328091 2.215683888 24.99997746 1.217645711 1.161958369 0 0.097271968 650.5196679 710890.9035 0.033379275 0.024667734 164.3175263 -2.215683888 -0.055687342 S(ph)PS(ph)PAPPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPSPAPPPR 9 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 S(1)PS(1)PAPPPR;S(1)PS(1)PAPPPR;S(1)PS(1)PAPPPR;S(1)PS(1)PAPPPR 86.18 0.020924 2160490000 1870680 1640710 1684280 1588700 1723800 1429450 1895430 1442790 1718030 TRUE FALSE 1753597.478 1762189.876 1724231.917 1629468.732 1588419.701 1842109.01 1611227.868 1622925.507 1431279.694 1.225195526 1.231198824 1.204678529 1.138469817 1.109789867 1.287036362 1.125725373 1.133898227 1 20.44887419 -4.999999997 0.134278541 0.347479126 1.262075621 0.604392954 0.050434057 94.14202402 0.788360761 16.36324384 0.332827927 1.00E-05 4.999999997 0.914596495 S(ph)PS(ph)PAPPPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSPAPPPRR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 S(1)PS(1)PAPPPRR;S(1)PS(1)PAPPPRR 88.552 0.042402 1887600000 811570 765650 732450 735770 767700 615460 846000 597750 802400 TRUE FALSE 760775.2824 822339.5227 749824.0599 754651.1039 707407.9388 793133.3108 719150.1539 672380.4033 668474.2563 1.138077159 1.23017381 1.121694744 1.128915731 1.058242606 1.186482955 1.075808301 1.005843377 1 19.35051248 1.89128325 0.317410883 0.981463479 1.204566177 0.582604753 0.047254414 1.018077961 0.319117237 0.069978105 0.081073087 77.85441574 -1.89128325 0.223102698 S(ph)PS(ph)PASGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSPASGR 8 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)PS(0.999)PAS(0.001)GR;S(1)PS(0.999)PAS(0.001)GR 88.056 0.021762 188296000 417190 302700 389870 347850 312430 366180 409650 311340 214090 TRUE FALSE 391078.8226 325112.223 399117.9005 356776.4199 287893.0081 471890.2216 348226.7855 350211.4843 178356.9959 2.19267442 1.822817329 2.237747381 2.000350017 1.61413914 2.645762333 1.952414503 1.963542179 1 17.44440828 0.606668716 2.278339232 1.000159648 2.063574673 0.601346667 0.271029233 1.995588815 10.77050942 0.234993887 0.063501295 4.042673946 -0.606668716 1.063415025 S(ph)PS(ph)PEPIYNSEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSPEPIYNSEGK 13 0 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 2 S(1)PS(1)PEPIYNSEGK;S(1)PS(1)PEPIYNSEGK 186.69 1.11E-05 841080000 2951760 1392280 2109790 1758350 1532630 2088640 2819580 1566110 1170670 TRUE FALSE 2767014.611 1495365.86 2159835.215 1803472.238 1412263.422 2691596.462 2396810.155 1761642.281 975277.6142 2.837155873 1.533272002 2.214585041 1.849188592 1.448062994 2.759825944 2.457567076 1.806298284 1 19.89545342 0.980282207 21.0975794 0.999999972 2.115581095 0.384300724 0.461652472 190.9912281 204358.0633 0.431982516 0.107995629 9.556133482 -0.980282207 1.115581123 S(ph)PS(ph)PKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSPKPR 7 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)PS(1)PKPR 65.347 0.040304 559040000 1227700 513840 774440 685330 602870 558600 879090 547230 495330 TRUE FALSE 1150860.449 551885.2483 792810.0825 702916.7281 555523.0221 719858.7519 747278.6156 615552.8701 412656.223 2.788908501 1.33739713 1.921236221 1.703395439 1.346212637 1.744451463 1.810898694 1.491684448 1 18.65458087 8 0.048719662 4.99E-12 4.767702681 0.401215545 0.368073536 661.0880846 2.433110444 57.12924112 239.2694823 100000000 -8 4.767702681 S(ph)PS(ph)PKPTK ddPTM_SK-BR-3_Pertuzumab_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(0.792)PS(0.617)PKPT(0.591)K;S(0.83)PS(0.716)PKPT(0.454)K;S(0.995)PS(0.603)PKPT(0.402)K 66.56 0.034919 5107620000 8145000 3171330 4511100 4235900 3952000 3176510 5677100 3476010 4424400 TRUE FALSE 7635218.989 3406138.573 4618105.422 4344600.365 3641625.862 4093516.871 4825871.559 3909997.5 3685939.057 2.071444718 0.924089769 1.252897932 1.178695659 0.987977773 1.110576384 1.309265152 1.060787343 1 21.81360079 4.745968765 24.97579658 1.123101299 2.071445173 0.863153257 0.120946609 317.4497072 1070222.561 0.028459482 0.298563298 55714.56765 -4.745968765 0.948343874 S(ph)PS(ph)PLRGNVVPS(ph)PLPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPSPLRGNVVPSPLPTR 17 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 3 S(1)PS(1)PLRGNVVPS(1)PLPTR;S(1)PS(1)PLRGNVVPS(1)PLPTR;S(1)PS(1)PLRGNVVPS(1)PLPTR;S(1)PS(1)PLRGNVVPS(0.997)PLPT(0.003)R 139.47 1.17E-06 1193590000 600650 601520 618080 647790 695220 551650 771550 550490 803600 TRUE FALSE 563056.3887 646057.1667 632741.1495 664413.3881 640620.2256 710902.3997 655863.2402 619219.8883 669473.9685 0.841042991 0.965022088 0.945131819 0.99244096 0.956900874 1.061882064 0.979669518 0.924934975 1 19.35266843 5.833163 0.954886035 0.983855788 1.39E-14 0.563523004 0.037485739 10.20147125 1.475870522 0.010951682 16.82799222 681024.914 -5.833163 -0.983855788 S(ph)PS(ph)PLRGNVVPS(ph)PLPTRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSPLRGNVVPSPLPTRR 18 2 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 3 S(1)PS(1)PLRGNVVPS(0.998)PLPT(0.002)RR;S(1)PS(0.994)PLRGNVVPS(0.961)PLPT(0.045)RR 99.838 0.00063521 443920000 181575 199401 208279 215630 273898 166492 279232 192327 414920 TRUE FALSE 170210.5449 214164.8575 213219.4762 221163.4309 252387.1559 214555.5376 237363.7539 216339.4493 345667.1715 0.492411658 0.61956956 0.616834614 0.639816127 0.730144997 0.620699781 0.686682952 0.625860559 1 18.39902407 -5 0.191879956 2.586828241 0.566874045 0.83407311 0.05345552 50.96052168 0.500008153 30.93713815 0.131540487 1.00E-05 5 -2.019954197 S(ph)PS(ph)PLRGNVVPSPLPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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;S(1)PS(1)PLRGNVVPSPLPTR 97.776 0.001133 1044590000 524552 392684 417318 451306 372508 359934 444262 306372 412491 TRUE FALSE 491721.2267 421758.7319 427216.98 462887.276 343252.7243 463841.1028 377649.0374 344623.2186 343643.5873 1.430904707 1.227314426 1.243197882 1.346998149 0.998862592 1.349773777 1.098955579 1.002850719 1 18.39055351 7.999998043 0.087851626 0.806757026 2.333010223 0.498248598 0.112833978 136.8410776 0.866303934 2.028116545 25.19862607 99999549.47 -7.999998043 1.526253197 S(ph)PS(ph)PSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSPSFR 7 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 S(1)PS(0.607)PS(0.393)FR 82.645 0.034982 416050000 488560 450970 464450 490400 469410 436060 565120 421580 644050 TRUE FALSE 457981.9017 484360.288 475466.9733 502984.4942 432544.4321 561943.4432 480385.5023 474215.191 536553.8943 0.853561789 0.902724392 0.886149515 0.937435176 0.806152815 1.047319662 0.895316402 0.883816511 1 19.03336356 2.252313228 24.99985276 0.945807788 0.884642207 0.30753975 0.057616255 339.417939 617002.1267 0.018345572 0.015273094 178.7776516 -2.252313228 -0.061165582 S(ph)PS(ph)PSPTPEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPSPSPTPEAK 11 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 S(0.97)PS(0.595)PS(0.434)PT(0.001)PEAK;S(1)PS(0.821)PS(0.177)PT(0.002)PEAK;S(1)PS(0.732)PS(0.267)PT(0.001)PEAK 141.58 5.56E-05 1028670000 2520030 1469290 1743240 1681260 1777990 1272080 2294590 1491650 1978710 TRUE FALSE 2362305.821 1578077.76 1784590.476 1724403.978 1638353.837 1639308.846 1950537.531 1677885.786 1648450.518 1.433046242 0.957309754 1.082586621 1.046075669 0.993875048 0.994454385 1.18325513 1.017856325 1 20.65267915 4.746381157 24.98079271 1.043482007 1.433046433 0.796539592 0.063166458 451.2920751 1441507.432 0.015389202 0.167710425 55767.49757 -4.746381157 0.389564425 S(ph)PS(ph)PYYSR ddPTM_SK-BR-3_Pertuzumab_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(1)PS(0.998)PY(0.002)YSR;S(0.996)PS(0.687)PY(0.316)Y(0.001)SR;S(1)PS(0.993)PY(0.008)YSR;S(0.998)PS(0.988)PY(0.014)YSR;S(0.999)PS(0.98)PY(0.022)YSR;S(0.999)PS(0.97)PY(0.031)YSR 109.42 0.005295 4560290000 4531240 3960830 3969440 3702420 3803070 3498830 4813030 3321770 4178410 TRUE FALSE 4247637.777 4254093.974 4063596.991 3797430.365 3504392.223 4508885.422 4091360.833 3736500.297 3481006.377 1.22023269 1.222087383 1.167362697 1.090900146 1.006718128 1.295282149 1.175338506 1.073396567 1 21.73107303 -5 0.130999154 0.462372109 1.231537822 0.323687936 0.079207233 189.5019615 1.56285273 26.8937261 0.598919127 1.00E-05 5 0.769165713 S(ph)PSAIPEQNHSLNDQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSAIPEQNHSLNDQAK 17 0 Q13129 Q13129 RLF Zinc finger protein Rlf 1 S(0.943)PS(0.057)AIPEQNHSLNDQAK 135.76 9.51E-06 0 449920 339720 352900 371660 374210 241000 472830 293360 362490 TRUE FALSE 421760.3103 364873.2223 361270.9547 381197.4248 344821.0561 310572.7877 401933.531 329986.6418 301988.0772 1.396612456 1.208237178 1.196308669 1.262292963 1.141836655 1.028427316 1.330958277 1.092714139 1 18.20413207 7.999999876 0.023098094 1.06E-11 2.785370047 0.455450802 0.092639281 2485.549011 4.417729889 188.4156075 373.3999856 99999971.56 -7.999999876 2.785370047 S(ph)PSDSSTASTPVAEQIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSDSSTASTPVAEQIER 18 0 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 S(0.994)PS(0.006)DSSTASTPVAEQIER;S(0.795)PS(0.205)DSSTASTPVAEQIER 360.81 5.41E-91 398680000 172176 149314 182498 156205 129139 163318 203834 143907 106040 TRUE FALSE 161399.8115 160369.3639 186826.9387 160213.4848 118996.9439 210465.2554 173270.984 161874.1057 88341.23896 1.827004165 1.815339765 2.114832676 1.813575253 1.347014659 2.382412312 1.96138277 1.832373053 1 16.43079945 3.062014487 24.99965269 1.810355929 1.929726634 0.023430517 0.377094851 338.866056 136601.992 0.102225363 0.122182671 1153.491734 -3.062014487 0.119370706 S(ph)PSELFAQHIVTIVHHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSELFAQHIVTIVHHVK 18 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.991)PS(0.009)ELFAQHIVTIVHHVK;S(0.982)PS(0.018)ELFAQHIVTIVHHVK 244.16 6.60E-24 740330000 832370 763380 757700 758880 854370 642850 935440 764540 853040 TRUE FALSE 780273.4475 819901.4495 775673.0018 778354.1456 787271.2266 828430.3592 795179.4562 859994.502 710662.1132 1.097952787 1.153714873 1.091479323 1.095252063 1.107799631 1.16571623 1.118927605 1.210131349 1 19.43880426 S(ph)PSGHPHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSGHPHVR 9 0 Q8WX93-8;Q8WX93-3;Q8WX93-2;Q8WX93-9;Q8WX93-5;Q8WX93;Q8WX93-4;Q8WX93-7 Q8WX93-8 PALLD Palladin 1 S(0.995)PS(0.005)GHPHVR;S(0.998)PS(0.002)GHPHVR 118.28 0.00065394 384870000 101873 176724 137795 151821 228254 103792 175693 180591 192152 TRUE FALSE 95496.95078 189808.8288 141063.5625 155716.9839 210327.8516 133755.0655 149349.4657 203138.1839 160080.5899 0.596555465 1.185707955 0.881203415 0.972741193 1.313887285 0.835548305 0.932964239 1.268974484 1 17.28843886 4.751782354 24.42105584 1.031190242 0.596555072 0.432710115 0.161638829 1560.424386 2882093.355 0.036145664 0.669659899 56465.39288 -4.751782354 -0.43463517 S(ph)PSGPSGSLENGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSGPSGSLENGTK 14 0 Q14134-2;Q14134;E9PM74;E9PI31;E9PLI4;E9PJ94;E9PJD4 Q14134-2 TRIM29 Tripartite motif-containing protein 29 1 S(0.998)PS(0.002)GPSGSLENGTK 297.51 1.15E-43 160650000 287550 186350 222360 194970 267220 187230 264840 213860 392990 TRUE FALSE 269552.7588 200147.5479 227634.4842 199973.2603 246233.6191 241280.2616 225129.7007 240560.8918 327397.4302 0.823319715 0.611329013 0.695284884 0.61079667 0.752093927 0.736964433 0.687634294 0.734767196 1 18.32068347 -1.024742393 0.442834407 1.117501606 0.681977344 0.676188466 0.063680335 9.088406228 1.16524663 1.408425171 0.032509835 0.094462102 1.024742393 -0.435524262 S(ph)PSLAK ddPTM_SK-BR-3_Pertuzumab_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(0.966)PS(0.034)LAK;S(0.866)PS(0.134)LAK 77.923 0.074626 1152180000 1732740 1397770 1579970 1528950 1581380 1193980 2158000 1560630 1911870 TRUE FALSE 1624290.896 1501262.345 1617447.635 1568185.446 1457184.794 1538662.643 1834427.934 1755478.091 1592766.546 1.019792198 0.942550149 1.015495735 0.984567041 0.91487657 0.966031492 1.151724299 1.102156556 1 20.60310339 1.752527876 25 1.097228806 0.973212266 0.534677768 0.048222609 2.829756857 5072.093415 0.020439005 0.011334364 56.5624062 -1.752527876 -0.12401654 S(ph)PSLDNPTPFPNLGPSENPLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSLDNPTPFPNLGPSENPLKR 22 1 M0R0R8;M0R0X9;M0QXC8;M0QX56;M0R3C2;M0QYT9;M0R205;M0QZB8;M0QZB7;Q14653-3;Q14653-2;Q14653;Q14653-4 M0R0R8 IRF3 Interferon regulatory factor 3 1 S(0.5)PS(0.5)LDNPTPFPNLGPSENPLKR 175.46 8.96E-13 270410000 277360 166780 225650 191310 145170 181820 298990 189800 149420 TRUE FALSE 260000.5327 179128.5647 231002.5246 196219.3385 133768.9338 234308.4824 254159.2252 213496.9478 124480.8367 2.088679186 1.439005147 1.855727602 1.576301571 1.074614674 1.882285568 2.041753831 1.715098914 1 16.92556414 S(ph)PSLDVTVPEAELNLETPEISVGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPSLDVTVPEAELNLETPEISVGGK 25 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 S(0.494)PS(0.494)LDVT(0.012)VPEAELNLETPEISVGGK;S(0.49)PS(0.49)LDVT(0.021)VPEAELNLETPEISVGGK;S(0.481)PS(0.481)LDVT(0.037)VPEAELNLETPEISVGGK 154.8 4.65E-08 182239000 481033 375114 360035 400309 317571 209959 614120 354584 392826 TRUE FALSE 450926.0032 402887.8309 368575.2002 410581.6067 292630.2547 270570.7549 522038.4072 398854.5929 327260.8028 1.377879658 1.231091006 1.126243036 1.254600622 0.894180581 0.826774097 1.595175477 1.218766774 1 18.32008129 -0.625921387 11.93987979 0.999992817 1.195083796 0.069545725 0.218535826 0 0 0.209591945 0.049401295 0.2366348 0.625921387 0.195090978 S(ph)PSLESLSRPPSLGFGDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSLESLSRPPSLGFGDTR 19 1 Q5M775-4;Q5M775;J3KSG2 Q5M775-4 SPECC1 Cytospin-B 1 S(0.94)PS(0.057)LES(0.001)LS(0.001)RPPSLGFGDTR 57.238 0.053625 65046000 32361 42871 38615 43450 50910 38342 38891 41758 49985 TRUE FALSE 30335.58278 46045.21345 39530.96604 44565.00056 46911.73396 49410.71297 33059.6556 46971.57822 41642.18058 0.728482091 1.105734926 0.949301057 1.070188927 1.126543646 1.186554409 0.793898281 1.127980753 1 15.345758 4.747205024 24.7374623 1.032390851 0.728481912 0.436333328 0.112253891 992.1106803 2839023.111 0.026092359 0.308252006 55873.39019 -4.747205024 -0.303908939 S(ph)PSLGSDLTFATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSLGSDLTFATR 13 0 Q13425 Q13425 SNTB2 Beta-2-syntrophin 1 S(0.954)PS(0.045)LGS(0.001)DLTFATR;S(0.966)PS(0.032)LGS(0.002)DLTFATR 106.03 0.0014751 200854000 252350 139648 162588 161355 168761 123807 172164 136627 179161 TRUE FALSE 236555.864 149987.6832 166444.6641 165495.6425 155507.1918 159548.0711 146349.6065 153685.1817 149257.8717 1.584880324 1.004889602 1.115148315 1.108790046 1.041869283 1.068942423 0.980515164 1.029662154 1 17.18744749 4.741311148 24.99960567 1.047353994 1.584880516 0.936333417 0.04433793 62.18251499 565147.3195 0.010995321 0.076261814 55120.24613 -4.741311148 0.537526522 S(ph)PSLLQSGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSLLQSGAK 10 0 Q9BQG0;Q9BQG0-2;I3L1L3;I3L2H8 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 S(0.989)PS(0.011)LLQSGAK;S(0.993)PS(0.007)LLQSGAK 69.352 0.060038 263720000 550460 423050 587920 431040 429400 440060 571430 424360 502070 TRUE FALSE 516007.6912 454373.0622 601865.74 442101.2161 395676.6561 567098.1782 485749.3764 477342.2801 418271.2735 1.233667536 1.086311901 1.438936351 1.056972458 0.945980949 1.35581431 1.161326171 1.141226545 1 18.67407939 -4.999999678 0.214532725 0.060512264 1.214931579 0.136109262 0.14175203 300.0885829 2.998736905 121.2755955 0.28220847 1.00E-05 4.999999678 1.154419315 S(ph)PSLSLAPLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPSLSLAPLSPR 12 0 G3V160;Q969H4-2;Q969H4 G3V160 CNKSR1 Connector enhancer of kinase suppressor of ras 1 2 S(1)PSLSLAPLS(1)PR;S(0.998)PS(0.002)LSLAPLS(1)PR;S(0.999)PS(0.001)LSLAPLS(1)PR;S(0.997)PS(0.003)LSLAPLS(1)PR 189.47 1.15E-05 890110000 541054 608302 628010 731530 805950 422643 410555 357577 428491 TRUE FALSE 507190.3959 653341.313 642906.6938 750302.2983 742653.938 544653.1731 348996.0892 402221.2756 356973.0839 1.420808511 1.830225702 1.800994872 2.101845579 2.080419985 1.525754175 0.977653792 1.126755192 1 18.44545577 1.920703124 3.57039385 1.045430761 1.849249194 0.790016745 0.190356952 0.106218441 2.413623211 0.092976419 0.052334003 83.31114888 -1.920703124 0.803818432 S(ph)PSLSLAPLSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSLSLAPLSPR 12 0 G3V160;Q969H4-2;Q969H4 G3V160 CNKSR1 Connector enhancer of kinase suppressor of ras 1 1 S(0.998)PS(0.002)LSLAPLSPR 149.69 7.08E-05 56510000 40619 43396 35083 28707 36493 24799 52769 43197 66195 TRUE FALSE 38076.7293 46609.08499 35915.18533 29443.67022 33626.98699 31958.06872 44856.77833 48590.24054 55146.62686 0.690463433 0.845184695 0.651267129 0.533916069 0.60977414 0.579510852 0.813409285 0.88110993 1 15.75098502 1.319435687 2.040706027 0.977022241 0.669171227 0.657302766 0.087078469 0.226015137 1.614045777 0.087897873 0.026240491 20.86583106 -1.319435687 -0.307851014 S(ph)PSLSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPSLSSK 7 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3;Q9UPU5 A9Z1X7;Q8IYB3;Q9UPU5 SRRM1;USP24 Serine/arginine repetitive matrix protein 1;Ubiquitin carboxyl-terminal hydrolase 24 1 S(0.975)PS(0.025)LSSK;S(0.874)PS(0.126)LSSK;S(0.957)PS(0.043)LSSK;S(0.987)PS(0.013)LSSK;S(0.954)PS(0.046)LSSK;S(0.954)PS(0.046)LSSK 118.41 0.0052584 3943820000 10397150 8274060 8514140 7777770 8252660 6971110 10300150 8384360 8304590 TRUE FALSE 9746410.941 8886680.012 8716099.421 7977360.746 7604529.373 8983556.29 8755738.129 9431165.802 6918500.279 1.408746195 1.28448069 1.259824972 1.153047687 1.099158642 1.298483187 1.265554351 1.363180664 1 22.72202791 -2.2441176 2.330525706 0.032870156 1.260948977 0.465957533 0.089504298 2581560.102 417163.0025 13293009.29 0.021223833 0.005700099 2.2441176 1.228078821 S(ph)PSMSISEPISVTLPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSMSISEPISVTLPPR 17 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.933)PS(0.067)MSISEPISVTLPPR 182.7 7.69E-10 50140000 15259 19587 16128 24144 18776 18958 18533 17135 18428 TRUE FALSE 14303.96643 21037.24186 16510.56378 24763.57592 17301.4087 24430.86684 15754.1487 19274.34247 15352.24775 0.931718056 1.370303698 1.075449279 1.613026074 1.126962578 1.591354389 1.026178639 1.255473647 1 13.90616228 0.907891491 1.249984099 1.009643152 1.266017743 0.105221661 0.226240594 1.196793369 3.729079821 0.187967765 0.057671536 8.088937701 -0.907891491 0.256374591 S(ph)PSPAHLPDDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSPAHLPDDPK 12 0 Q92615;H0Y4V9;A0A087X183;H0Y641 Q92615 LARP4B La-related protein 4B 1 S(0.5)PS(0.5)PAHLPDDPK;S(0.5)PS(0.5)PAHLPDDPK 125.22 0.00019914 1136260000 2404720 2147790 2358700 2152910 2415070 2062720 2566080 1901530 2451420 TRUE FALSE 2254212.868 2306814.606 2414649.478 2208157.315 2225400.144 2658193.779 2181320.126 2138940.206 2042262.165 1.103782319 1.129538923 1.182340602 1.081231075 1.089674079 1.301592824 1.068090162 1.047338702 1 20.96173665 1.520981797 9.191704917 1.035047598 1.147611166 0.408304166 0.063516533 0.1096701 16.33317594 0.032310307 0.014992116 33.18805469 -1.520981797 0.112563568 S(ph)PSPAHLPDDPKVAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSPAHLPDDPKVAEK 16 1 Q92615;H0Y4V9;A0A087X183;H0Y641 Q92615 LARP4B La-related protein 4B 1 S(0.5)PS(0.5)PAHLPDDPKVAEK;S(0.536)PS(0.464)PAHLPDDPKVAEK 118.91 0.00014229 553870000 785760 865600 755230 952020 1450330 476160 1106360 726340 3817900 TRUE FALSE 736580.6842 929689.9247 773144.4122 976450.445 1336426.932 613619.6622 940471.5889 817025.1479 3180667.825 0.231580512 0.292293938 0.243076126 0.306995417 0.420171802 0.192921643 0.295683687 0.256872202 1 21.60089828 -1.828001035 2.608792466 1.256194793 0.280018194 0.933937686 0.060184328 7891434.423 5111127.42 12663657.63 0.013581627 0.014859321 1.828001035 -0.976176599 S(ph)PSPAVPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPSPAVPLR 9 0 Q6P4R8-3;Q6P4R8;E9PQ59;Q6P4R8-2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 S(0.931)PS(0.069)PAVPLR;S(0.987)PS(0.013)PAVPLR;S(0.942)PS(0.058)PAVPLR 116.3 0.0014008 1254080000 1355780 1452550 1426460 1445710 1524190 1247700 1707500 1361940 1656240 TRUE FALSE 1270924.15 1560098.313 1460296.305 1482809.366 1404486.266 1607890.735 1451476.227 1531981.207 1379802.844 0.921091122 1.130667559 1.058336929 1.074653073 1.017889093 1.165304697 1.051944655 1.110289933 1 20.39603071 4.750050237 24.6889579 1.080410722 0.92109101 0.487263492 0.049811941 1148.887628 2468681.163 0.010380586 0.165051089 56240.63775 -4.750050237 -0.159319712 S(ph)PSPGLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSPGLFR 8 0 E7ESG2;Q9HAW4-2;Q9HAW4-3;Q9HAW4 E7ESG2 CLSPN Claspin 1 S(0.947)PS(0.053)PGLFR 104.2 0.0048525 210610000 1065900 1130100 1208200 1089700 1330800 1076300 1325100 1190200 1496500 TRUE FALSE 999187.2217 1213773.78 1236859.075 1117663.547 1226284.336 1387010.338 1126413.557 1338799.09 1246724.482 0.801449908 0.973570181 0.992086938 0.896479986 0.983604921 1.112523543 0.903498385 1.073853212 1 20.24971124 4.742425605 4.051690998 0.987427802 0.784547416 0.455239077 0.065516681 0.212855015 7.463980983 0.014345191 0.127334378 55261.87359 -4.742425605 -0.202880386 S(ph)PSPQGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSPQGTK 8 0 Q9ULL5;Q9ULL5-2;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 S(0.799)PS(0.2)PQGT(0.001)K 65.278 0.067853 231990000 314700 380630 397410 355470 395540 349920 436230 377560 442460 TRUE FALSE 295003.4888 408812.2412 406836.7529 364591.962 364475.8839 450936.2235 370821.3613 424699.1971 368610.5676 0.800312076 1.109062727 1.103703444 0.989097964 0.988783057 1.223340466 1.00599764 1.152162294 1 18.49173791 S(ph)PSPS(ph)FR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSPSFR 7 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 S(1)PS(0.321)PS(0.679)FR 83.948 0.032025 428190000 421490 394570 391810 375750 416260 392590 475180 338590 576900 TRUE FALSE 395109.6933 423784.3733 401103.9182 385392.3811 383568.6187 505924.3598 403931.1704 380863.7068 480611.6631 0.822097597 0.881760485 0.834569672 0.801878961 0.798084292 1.052667671 0.840452285 0.79245623 1 18.87451213 S(ph)PSPSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSPSFR 7 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 S(0.991)PS(0.009)PSFR;S(0.999)PS(0.001)PSFR 132.76 0.0035012 589650000 342720 356170 340290 355420 382290 329370 402560 357770 486710 TRUE FALSE 321269.767 382541.1974 348361.8395 364540.6789 352266.4855 424453.7721 342199.8652 402438.372 405474.9567 0.792329493 0.943439764 0.859145143 0.899046101 0.868774951 1.046806381 0.843948213 0.992511043 1 18.62925329 7.999999743 0.049931354 1.18845309 0.398813251 0.321688566 0.065548678 630.7549939 2.376458716 8.853705842 38.3979795 99999940.88 -7.999999743 -0.789639839 HS(ph)DENDGGQPHKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HSDENDGGQPHKR 13 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 HS(1)DENDGGQPHKR;HS(1)DENDGGQPHKR 127.88 8.08E-05 445410000 404780 310120 326890 344920 269880 197921 320140 187266 210989 TRUE FALSE 379445.5424 333081.6075 334643.9852 353771.2311 248684.7134 255057.5797 272137.979 210646.5723 175773.5729 2.158717811 1.894947017 1.903835598 2.012653128 1.414801494 1.451057605 1.548230343 1.198397284 1 17.42335866 2.101548973 0.378625199 0.971490897 2.138083688 0.858228879 0.139675561 0.456555929 0.16424201 0.161708283 0.183773172 126.3423566 -2.101548973 1.166592792 up S(ph)PSPVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSPVLR 7 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-2 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 S(0.553)PS(0.447)PVLR 97.596 0.012463 254230000 144170 160680 176820 153280 186440 123050 178280 142650 195140 TRUE FALSE 135146.6571 172576.9144 181014.2539 157213.4243 171797.7545 158572.5375 151548.5691 160460.1665 162569.8733 0.831314279 1.061555323 1.113455096 0.967051404 1.056762553 0.975411583 0.93220574 0.987022769 1 17.3107004 2.103644591 6.517573098 0.962750157 1.02628518 0 0.077617648 0.448515318 24.69872276 0.028789018 0.021167986 126.9534743 -2.103644591 0.063535023 S(ph)PSPVQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSPVQGK 8 0 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 S(0.745)PS(0.255)PVQGK 105.52 0.0045854 737480000 1556800 1454000 1426400 1428200 1510900 1034100 1685600 1198000 1676300 TRUE FALSE 1459362.667 1561655.673 1460234.882 1464850.03 1392240.009 1332627.883 1432859.928 1347572.937 1396514.701 1.045003441 1.118252226 1.045628006 1.048932768 0.996939028 0.954252671 1.026025668 0.964954351 1 20.41339933 3.057007784 1.430419837 0.989095955 1.083169288 0.65827156 0.027590909 0.21533889 0.910986442 0.009580832 0.012121725 1140.270224 -3.057007784 0.094073333 S(ph)PSPYYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSPYYSR 8 0 P62995;P62995-3;H7BXF3;H7C2L4;Q13595;Q13595-3;Q13595-4 P62995;Q13595 TRA2B;TRA2A Transformer-2 protein homolog beta;Transformer-2 protein homolog alpha 1 S(0.996)PS(0.004)PYYSR;S(0.78)PS(0.22)PYYSR 108.15 0.004056 695010000 288960 249500 299980 260500 271080 328300 289720 300390 764640 TRUE FALSE 270874.5094 267973.2396 307095.6673 267184.871 249790.4703 423074.8805 246279.1756 337894.3527 637016.6442 0.425223598 0.420669133 0.482084212 0.419431538 0.3921255 0.664150434 0.386613408 0.530432534 1 19.28097154 -5 0.294744732 5.346451924 0.431276723 0.824871315 0.078371702 93.91353932 0.877582918 251.415303 0.073007337 1.00E-05 5 -4.915175201 S(ph)PSQDFSFIEDTEILDSAMYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SPSQDFSFIEDTEILDSAMYR 21 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 S(0.443)PS(0.443)QDFS(0.114)FIEDTEILDSAMYR;S(0.484)PS(0.484)QDFS(0.031)FIEDTEILDSAMYR;S(0.475)PS(0.475)QDFS(0.05)FIEDTEILDSAMYR;S(0.493)PS(0.493)QDFS(0.014)FIEDTEILDSAMYR;S(0.498)PS(0.498)QDFS(0.005)FIEDTEILDSAMYR 246.63 1.66E-30 416808200 192309.8 234128 206290.3 208179.3 213728 180145.8 261346.5 182722.5 237375.7 TRUE FALSE 180273.4729 251463.0807 211183.6033 213521.5333 196942.665 232150.968 222160.0185 205535.8063 197756.1622 0.911594718 1.271581517 1.067898977 1.079721264 0.995886363 1.173925331 1.123403772 1.039339579 1 17.59336312 1.068085462 4.341712807 1.001070808 1.106339855 0.067697837 0.096924149 0.381030106 13.35328069 0.085998334 0.021954682 11.69729551 -1.068085462 0.105269047 S(ph)PSQESIGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSQESIGAR 10 0 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 S(0.978)PS(0.021)QESIGAR 75.618 0.040336 131440000 142280 107560 156040 132830 132230 100740 149130 112530 127410 TRUE FALSE 133374.9488 115523.8543 159741.3425 136238.6427 121845.1892 129822.0026 126769.341 126579.6182 106144.4479 1.256541924 1.08836455 1.504942987 1.283521139 1.14791863 1.223069178 1.194309674 1.192522272 1 16.69566938 0.665349824 0.567852763 0.995002468 1.271804508 0.352371335 0.106639395 1.626452368 1.052671821 0.134882712 0.050402069 4.627536195 -0.665349824 0.27680204 S(ph)PSSDLDTDAEGDDFELLDQSELSQLDPASSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSSDLDTDAEGDDFELLDQSELSQLDPASSR 32 0 K7EQI9;Q86VR2-2;Q86VR2 K7EQI9 FAM134C Protein FAM134C 1 S(0.32)PS(0.32)S(0.32)DLDT(0.041)DAEGDDFELLDQSELSQLDPASSR 188.97 4.84E-20 23035000 9821.6 8922.4 7674.4 8752.6 11295 8176 9546.7 9950 12530 TRUE FALSE 9206.883588 9583.02378 7856.440392 8977.206534 10407.93626 10536.27847 8115.260962 11192.2794 10438.66205 0.881998434 0.918031806 0.752629058 0.859995897 0.997056539 1.00935143 0.777423478 1.072194822 1 13.34964919 2.857054655 6.740978795 0.945591215 0.846035141 0.285238443 0.087706457 0.379336712 19.61700175 0.026810263 0.02849738 719.5395255 -2.857054655 -0.099556074 S(ph)PSSDSWTCADTSTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSSDSWTCADTSTER 16 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;H0YIQ0 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 S(0.985)PS(0.015)SDSWTCADTSTER;S(0.818)PS(0.182)SDSWTCADTSTER 298.79 8.86E-46 893790000 379810 389660 433340 412920 382500 323540 417430 296705 242759 TRUE FALSE 356038.3701 418510.8318 443619.0294 423516.2263 352459.9929 416940.7458 354840.2467 333749.2724 202240.9546 1.760466226 2.069367367 2.193517284 2.094117025 1.742772593 2.061603925 1.754541989 1.650255622 1 17.62571565 0.732198365 0.691668406 0.987769132 2.045574076 0.815999171 0.146508548 0.419606439 0.401279837 0.145919891 0.053903284 5.397571011 -0.732198365 1.057804944 S(ph)PSSESSPQHPTPPARPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSSESSPQHPTPPARPR 18 1 O14733;O14733-4;O14733-2;O14733-3 O14733 MAP2K7 Dual specificity mitogen-activated protein kinase kinase 7 1 S(0.767)PS(0.146)S(0.034)ES(0.012)S(0.042)PQHPTPPARPR;S(0.384)PS(0.041)S(0.065)ES(0.28)S(0.231)PQHPTPPARPR 101.6 0.00038466 372730000 87980 103165 94536 110134 131900 77712 115363 101778 124515 TRUE FALSE 82473.48885 110803.4439 96778.43856 112960.2249 121541.1061 100146.1929 98065.38913 114485.2073 103732.6421 0.795058211 1.068163711 0.932960316 1.08895544 1.171676568 0.96542603 0.945366735 1.103656525 1 16.66251042 4.745382889 24.46693401 1.024588596 0.795058067 0.48774357 0.07652534 553.5700713 1985215.901 0.018293103 0.177208624 55639.4578 -4.745382889 -0.229530529 S(ph)PSSKPSLAVAVDSAPEVAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSSKPSLAVAVDSAPEVAVK 21 1 O60508;Q5SRN1 O60508 CDC40 Pre-mRNA-processing factor 17 1 S(0.975)PS(0.02)S(0.004)KPSLAVAVDSAPEVAVK;S(0.758)PS(0.097)S(0.113)KPS(0.032)LAVAVDSAPEVAVK 189.86 1.22E-17 527650000 627710 349980 478460 421650 454000 384500 631200 451920 428320 TRUE FALSE 588422.7516 375892.8834 489809.2971 432470.2529 418344.6713 495498.9082 536557.4198 508343.2068 356830.6249 1.649025365 1.053421027 1.372666086 1.211976278 1.172390042 1.388610936 1.503675364 1.424606441 1 18.44487991 2.201821379 24.08858782 1.386012508 1.2667579 0 0.205239795 309.8925216 203182.6357 0.069238667 0.051137975 159.1554003 -2.201821379 -0.119254608 S(ph)PSSKPSLAVAVDSAPEVAVKEDLETGVHLDPAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPSSKPSLAVAVDSAPEVAVKEDLETGVHLDPAVK 35 2 O60508;Q5SRN1 O60508 CDC40 Pre-mRNA-processing factor 17 1 S(0.641)PS(0.157)S(0.157)KPS(0.043)LAVAVDS(0.001)APEVAVKEDLETGVHLDPAVK;S(0.942)PS(0.046)S(0.011)KPS(0.001)LAVAVDSAPEVAVKEDLETGVHLDPAVK;S(0.25)PS(0.25)S(0.25)KPS(0.25)LAVAVDS(0.001)APEVAVKEDLETGVHLDPAVK 176.79 2.26E-20 215676000 459717 260980 330315 326409 407323 232340 477997 305934 551698 TRUE FALSE 430944.1336 280303.2307 338150.2278 334785.2075 375333.4946 299412.7863 406325.7874 344130.5333 459616.0397 0.937617699 0.609863901 0.735723296 0.728401924 0.816624013 0.651441117 0.884054846 0.748734821 1 18.81006962 0.298686948 0.492186262 1.018322586 0.726090268 0.339337825 0.099746123 2.570253586 0.975328622 0.193973567 0.047445908 1.989238921 -0.298686948 -0.292232317 S(ph)PSSNDKHVMSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSSNDKHVMSR 12 1 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C103 Q9H8V3-2 ECT2 Protein ECT2 1 S(0.944)PS(0.045)S(0.011)NDKHVMSR 90.561 0.005324 111150000 157740 171740 163980 166790 194560 140160 228300 185000 339610 TRUE FALSE 147867.335 184455.8083 167869.683 171070.1138 179280.0424 180621.9167 194068.5344 208097.6572 282926.897 0.522634421 0.651955718 0.593332358 0.604644223 0.633662067 0.638404897 0.685931725 0.735517405 1 18.11006981 0.44108484 0.55844355 1.01758563 0.597330031 0.940162368 0.03134878 0.411824141 0.216734497 0.043443 0.013096928 2.761117189 -0.44108484 -0.420255598 S(ph)PSSQTPNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPSSQTPNSR 10 0 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 1 S(0.887)PS(0.112)S(0.001)QTPNSR;S(0.998)PS(0.002)SQTPNSR;S(0.978)PS(0.022)SQTPNSR 131.49 0.00026097 1215500000 261715 272431 275874 302850 285432 205874 236530 218882 279861 TRUE FALSE 245334.7253 292602.0747 282417.8616 310621.6437 263015.3221 265306.4817 201064.5223 246209.8995 233150.3911 1.052259549 1.254992854 1.211311978 1.332280174 1.128092991 1.137919951 0.862381235 1.056013238 1 17.83090132 1.991951451 3.116664351 0.961904107 1.211679406 0.557482399 0.089038603 0.156063432 2.957391382 0.039560888 0.023225705 98.16382003 -1.991951451 0.2497753 S(ph)PSSVTGNALWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSSVTGNALWK 12 0 Q9NYB0;A0A590UJT3 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 S(0.999)PS(0.001)SVTGNALWK;S(0.999)PS(0.001)SVTGNALWK 221.86 2.35E-05 0 179173 165368 184551 166804 188551 157635 225490 178464 213730 TRUE FALSE 167958.8818 177612.0188 188928.6369 171084.473 173742.965 203141.6655 191679.8678 200745.6232 178057.0823 0.943286724 0.997500445 1.06105657 0.960840596 0.975771156 1.140879447 1.076507968 1.127422851 1 17.44198029 2.248445149 24.99932914 1.092581463 0.997812633 0.49630021 0.048536403 167.7228204 424193.9731 0.016099707 0.013317629 177.1924238 -2.248445149 -0.09476883 S(ph)PSTLLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPSTLLPK 8 0 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;B5MEG9;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 S(0.686)PS(0.309)T(0.004)LLPK;S(0.575)PS(0.42)T(0.004)LLPK;S(0.511)PS(0.485)T(0.003)LLPK 112.75 0.0031273 1853030000 1525480 1140850 1373220 1261440 1293760 1145330 1679130 1138260 1174810 TRUE FALSE 1430002.93 1225319.721 1405793.427 1293810.686 1192153.308 1475968.178 1427360.045 1280374.267 978726.6214 1.461085147 1.251952991 1.436349432 1.32193266 1.218065681 1.508049486 1.458384817 1.30820419 1 19.90054642 0.969799758 21.74118852 0.999999997 1.376135518 0.617291254 0.093305782 427.6413114 307860.6584 0.088687483 0.022171871 9.328241 -0.969799758 0.376135521 S(ph)PSTTYLHTPTPSEDAAIPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPSTTYLHTPTPSEDAAIPSK 21 0 Q13111 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 S(0.982)PS(0.016)T(0.001)T(0.002)YLHTPTPSEDAAIPSK;S(0.96)PS(0.029)T(0.004)T(0.007)YLHTPTPSEDAAIPSK;S(0.925)PS(0.032)T(0.032)T(0.008)Y(0.002)LHT(0.001)PTPSEDAAIPSK 244.78 2.28E-30 2811800000 1247660 987000 1134700 1045040 1164870 967960 1361670 1037350 1429990 TRUE FALSE 1169571.188 1060078.507 1161615.62 1071857.496 1073385.809 1247394.338 1157500.225 1166865.431 1191315.431 0.981747703 0.889838643 0.975069734 0.899726024 0.901008903 1.047073098 0.971615237 0.979476468 1 20.18412402 2.250891801 24.99998874 0.996219225 0.928937462 0.484342077 0.035847264 188.9366974 383046.0791 0.011628338 0.009665157 178.1934765 -2.250891801 -0.067281764 S(ph)PSVPKSPTPKS(ph)PPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSVPKSPTPKSPPSR 16 2 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 2 S(0.646)PS(0.133)VPKS(0.22)PT(0.201)PKS(0.799)PPS(0.001)R 59.814 0.052895 157350000 134820 94083 110190 139240 158080 61374 117400 84042 194550 TRUE FALSE 126381.8569 101049.0032 112803.7588 142813.1341 145665.0345 79091.67748 99796.95989 94534.8287 162078.3482 0.779757804 0.623457756 0.6959829 0.881136412 0.898732225 0.487984227 0.615732829 0.58326624 1 17.30633185 2.236767605 24.99999719 0.631733895 0.748939063 0.060475475 0.155743005 104.032908 1450495.326 0.053746081 0.041752242 172.4914626 -2.236767605 0.117205167 S(ph)PSVS(ph)PSKQPVSTSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPSVSPSKQPVSTSSK 16 1 Q96JG6;Q96JG6-3;H0Y7Q2 Q96JG6 CCDC132 Coiled-coil domain-containing protein 132 2 S(0.999)PS(0.006)VS(0.965)PS(0.029)KQPVSTSSK;S(0.892)PS(0.422)VS(0.579)PS(0.107)KQPVSTSSK;S(0.962)PS(0.046)VS(0.881)PS(0.111)KQPVSTSSK 150.69 4.07E-07 632300000 1925430 893280 1339560 1258260 1041890 1025770 1952200 1081490 923290 TRUE FALSE 1804920.773 959419.3807 1371334.996 1290549.082 960064.1622 1321893.147 1659485.733 1216516.407 769186.9343 2.346530723 1.247316274 1.78283709 1.677809417 1.248154537 1.718559024 2.157454397 1.581561455 1 19.55297473 4.758757656 24.02453302 1.617107626 2.346531912 0.347911122 0.331390245 3615.981608 4301119.537 0.078050044 3.040075419 57379.61848 -4.758757656 0.729424285 S(ph)PSWQRPNQGVPSTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SPSWQRPNQGVPSTGR 16 1 Q96HC4;Q96HC4-4;Q96HC4-7;H0Y8Y3;A0A0A0MSP3;Q96HC4-6 Q96HC4;Q96HC4-6 PDLIM5 PDZ and LIM domain protein 5 1 S(0.958)PS(0.042)WQRPNQGVPSTGR;S(0.996)PS(0.004)WQRPNQGVPSTGR;S(0.705)PS(0.295)WQRPNQGVPSTGR;S(1)PSWQRPNQGVPSTGR;S(0.966)PS(0.034)WQRPNQGVPSTGR 223.54 5.23E-15 3247110000 401545 357738 428525 476904 417411 373157 423122 300771 243291 TRUE FALSE 376413.0152 384225.2937 438689.8154 489142.164 384629.2238 480881.3682 359678.7842 338322.9214 202684.1604 1.857140758 1.895684858 2.164401079 2.413322102 1.897677762 2.372565115 1.774577666 1.669212438 1 17.62887382 0.950816888 1.40378838 1.008895557 2.084726148 0.745017841 0.201789277 0.230010144 0.918112984 0.18067461 0.054013351 8.929289182 -0.950816888 1.075830591 S(ph)PSYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPSYGR 6 0 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 1 S(1)PSYGR;S(1)PSYGR;S(1)PSYGR;S(0.999)PS(0.001)YGR;S(0.999)PS(0.001)YGR;S(1)PSYGR 187.63 0.0018233 24228660000 2973520 3061901 2724470 2952338 3014453 2650524 3175460 3104920 3382945 TRUE FALSE 2787412.691 3288607.336 2789095.715 3028099.991 2777710.021 3415687.251 2699329.253 3492576.097 2818309.625 0.989037069 1.166872265 0.989634244 1.074438367 0.985594342 1.211963093 0.957783073 1.239244995 1 21.42639869 S(ph)PTAALNESLVECPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPTAALNESLVECPK 15 0 Q53EZ4 Q53EZ4 CEP55 Centrosomal protein of 55 kDa 1 S(0.98)PT(0.02)AALNESLVECPK 129.37 6.96E-05 80783000 69147 43343 55835 53791 65574 39538 73538 46300 72111 TRUE FALSE 64819.2127 46552.16082 57159.43257 55171.36813 60424.08255 50951.97875 62511.65959 52080.65692 60075.20825 1.078967757 0.774898035 0.951464576 0.91837165 1.005807293 0.848136532 1.040556686 0.866924284 1 15.87448212 3.707569104 23.47380372 0.949675344 0.892603938 0 0.094674841 524.8153644 630079.7866 0.022459659 0.034867052 5099.987411 -3.707569104 -0.057071405 S(ph)PTESVNTPVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPTESVNTPVGK 12 0 A0A0A0MRB5;Q8WXG6-6;Q8WXG6-8;Q8WXG6-5;Q8WXG6-4;Q8WXG6-7;Q8WXG6-3;Q8WXG6-2;Q8WXG6 A0A0A0MRB5 MADD MAP kinase-activating death domain protein 1 S(0.977)PT(0.023)ESVNTPVGK;S(0.999)PT(0.001)ESVNTPVGK 198.48 0.00012117 0 283770 230780 251640 244080 232160 204722 291760 219667 252670 TRUE FALSE 266009.3422 247867.1913 257609.0196 250343.506 213927.0901 263821.918 248013.2966 247092.9085 210497.7447 1.263715878 1.177528964 1.22380893 1.189293056 1.016291602 1.253324203 1.178223059 1.173850622 1 17.68344525 -5 0.21638582 0.088888719 1.210055809 0.446484115 0.06623618 141.5649099 1.415528039 56.22671739 0.124581756 1.00E-05 5 1.12116709 S(ph)PTFSEELPVLGDGQQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SPTFSEELPVLGDGQQLR 18 0 Q8N0Z3 Q8N0Z3 SPICE1 Spindle and centriole-associated protein 1 1 S(0.992)PT(0.008)FSEELPVLGDGQQLR;S(0.937)PT(0.063)FSEELPVLGDGQQLR;S(0.919)PT(0.081)FSEELPVLGDGQQLR;S(0.644)PT(0.355)FSEELPVLGDGQQLR;S(0.887)PT(0.111)FS(0.002)EELPVLGDGQQLR 259.48 1.12E-30 236998000 97043 108230 108068 116664 105195 81961.8 101201 77749.9 80652 TRUE FALSE 90969.25186 116243.4618 110631.424 119657.7958 96933.40904 105622.8411 86026.84955 87457.14616 67190.66017 1.353897277 1.730053872 1.646529796 1.780869476 1.442661953 1.571986953 1.2803394 1.301626535 1 16.03597308 1.399204693 0.821798118 1.019412217 1.643985197 0.692198255 0.131240542 0.272140907 0.392337231 0.111076243 0.043934359 25.07290718 -1.399204693 0.62457298 S(ph)PTGPSNSFLANMGGTVAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 SPTGPSNSFLANMGGTVAHK 20 0 H0Y6J6;Q5W012;Q96I25 H0Y6J6 RBM17 Splicing factor 45 1 S(0.822)PT(0.178)GPSNSFLANMGGTVAHK;S(0.824)PT(0.176)GPSNSFLANMGGTVAHK;S(0.918)PT(0.082)GPSNSFLANMGGTVAHK;S(0.82)PT(0.18)GPSNSFLANMGGTVAHK;S(0.974)PT(0.026)GPSNSFLANMGGTVAHK;S(0.71)PT(0.29)GPSNSFLANMGGTVAHK;S(0.949)PT(0.051)GPSNSFLANMGGTVAHK;S(0.706)PT(0.294)GPSNSFLANMGGTVAHK;S(0.838)PT(0.162)GPSNSFLANMGGTVAHK;S(0.983)PT(0.017)GPSNSFLANMGGTVAHK;S(0.84)PT(0.16)GPSNSFLANMGGTVAHK;S(0.955)PT(0.045)GPSNSFLANMGGTVAHK 369.77 2.73E-112 24592440000 9778649 7804031 8985909 8597453 8080628 7680195 11464820 7912277 7228814 TRUE FALSE 9166620.814 8381849.575 9199059.005 8818078.199 7446008.073 9897342.619 9745776.675 8900142.201 6022278.243 1.522118448 1.391807093 1.527504813 1.464242907 1.236410503 1.643454888 1.618287346 1.477869643 1 22.52187793 3.000368422 24.0174936 1.456981085 1.47165434 0 0.191703793 168.4903922 10981650.13 0.05266135 0.062393028 1000.848683 -3.000368422 0.014673255 S(ph)PTGSPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPTGSPSR 8 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 S(0.99)PT(0.01)GSPSR 92.445 0.012349 80337000 64147 60745 71768 68919 66669 48889 53892 59290 57652 TRUE FALSE 60132.15378 65242.62301 73470.37085 70687.57822 61433.08567 63002.46065 45811.39491 66692.48701 48029.50875 1.251983527 1.358386223 1.529692324 1.471753096 1.279069623 1.311744848 0.953817686 1.388573166 1 15.55163343 2.146699568 2.146401334 1.114759182 1.409751342 0.406052477 0.141540262 0.270380797 2.461737504 0.066255055 0.040553371 140.1843615 -2.146699568 0.29499216 S(ph)PTGSTTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPTGSTTSR 9 0 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 S(0.893)PT(0.104)GS(0.003)TTSR 66.55 0.066518 108650000 63014 57137 62106 68105 67982 68656 75618 62294 72524 TRUE FALSE 59070.06622 61367.48293 63579.18365 69852.6896 62642.96795 88475.87266 64279.7829 70071.54303 60419.27588 0.977669218 1.015693784 1.052299663 1.156132519 1.036804348 1.464364996 1.063895288 1.159754764 1 15.88272127 3.3542944 1.363140821 1.168123323 1.000556682 0.191434724 0.12683027 0.592234809 2.276359055 0.040182616 0.067740525 2260.96792 -3.3542944 -0.167566641 S(ph)PTKTDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SPTKTDPK 8 1 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 S(0.974)PT(0.026)KTDPK;S(0.974)PT(0.026)KTDPK;S(0.699)PT(0.301)KTDPK;S(0.871)PT(0.129)KTDPK;S(0.887)PT(0.108)KT(0.004)DPK 113.44 0.0074902 4279050000 14984100 5174860 9057440 7383050 6434030 6928040 10841880 7015490 7301560 TRUE FALSE 14046271.93 5558012.019 9272286.754 7572511.562 5928727.237 8928052.681 9216240.745 7891389.369 6082882.466 2.30914735 0.913713531 1.524324497 1.244888686 0.974657536 1.46773388 1.515110771 1.297310841 1 22.5363237 4.751372254 24.94202472 1.277133644 2.309148026 0.687321258 0.22506317 1242.47515 2418838.166 0.052797735 0.968485159 56412.09825 -4.751372254 1.032014382 S(ph)PTKTDPKNEEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPTKTDPKNEEEEK 14 2 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 S(0.983)PT(0.017)KTDPKNEEEEK;S(0.998)PT(0.002)KTDPKNEEEEK 187.39 4.97E-07 1093020000 4832700 1234600 2290320 2204180 2439990 1489310 3246030 1683190 3901800 TRUE FALSE 4530229.934 1326011.069 2344647.472 2260742.99 2248363.028 1919249.62 2759317.936 1893339.977 3250564.373 1.393674886 0.407932567 0.721304734 0.695492453 0.691683895 0.590435813 0.848873494 0.582465 1 21.63225879 -1.503130309 3.486581483 1.005360553 0.710508729 0.078301771 0.26011157 26281213.69 22703536.8 991891.7586 0.053575126 0.031395665 1.503130309 -0.294851825 S(ph)PTKTDPKNEEEEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPTKTDPKNEEEEKR 15 3 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 S(0.998)PT(0.001)KTDPKNEEEEKR 101.96 0.0087822 93911000 328900 114240 175910 183070 224270 109040 261960 138780 372420 TRUE FALSE 308314.7361 122698.4485 180082.6683 187767.8861 206656.7389 140518.0779 222681.5299 156106.9885 310260.6961 0.993727984 0.395468875 0.580423723 0.605193918 0.666074503 0.452903251 0.717723942 0.503147806 1 18.24312142 -1.333890194 3.167454134 1.003142165 0.594905637 0.342617746 0.165959629 56428832.21 76818543.94 1665053.99 0.035300737 0.046356411 1.333890194 -0.408236529 S(ph)PTLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPTLLR 6 0 P55197-1;P55197;Q5JT35;H0Y5P4 P55197-1 MLLT10 Protein AF-10 1 S(0.994)PT(0.006)LLR;S(0.989)PT(0.011)LLR;S(0.989)PT(0.011)LLR 107.32 0.032906 497430000 293844 691920 732160 372800 405550 349985 389280 355600 449990 TRUE FALSE 275452.8286 743150.4767 749527.181 382366.6791 373699.7389 451019.988 330911.0779 399997.4428 374883.762 0.734768631 1.98234907 1.999358887 1.019960633 0.996841626 1.203092888 0.882703151 1.06699058 1 18.51608381 3.223987943 24.81508959 1.02350007 1.721085303 0.309035857 0.361134011 183.0125583 311642.4105 0.101043455 0.121281016 1674.896375 -3.223987943 0.697585233 S(ph)PTMEQAVQTASAHLPAPAAVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 SPTMEQAVQTASAHLPAPAAVGR 23 0 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.998)PT(0.002)MEQAVQTASAHLPAPAAVGR;S(0.883)PT(0.117)MEQAVQTASAHLPAPAAVGR;S(0.962)PT(0.038)MEQAVQTASAHLPAPAAVGR;S(0.979)PT(0.021)MEQAVQTASAHLPAPAAVGR;S(0.992)PT(0.008)MEQAVQTASAHLPAPAAVGR;S(0.978)PT(0.022)MEQAVQTASAHLPAPAAVGR;S(0.779)PT(0.221)MEQAVQTASAHLPAPAAVGR;S(0.967)PT(0.033)MEQAVQTASAHLPAPAAVGR;S(0.952)PT(0.048)MEQAVQTASAHLPAPAAVGR 252.77 1.15E-43 7047135000 596936 652805 703590 675619 641966 599388 781722 615609 593940 TRUE FALSE 559574.8413 701139.3614 720279.4871 692956.5274 591548.5799 772421.5853 664510.0433 692469.1388 494807.577 1.130893841 1.416993987 1.455675945 1.400456581 1.195512372 1.561054481 1.342966588 1.399471574 1 18.91650807 -0.929705987 7.813088966 0.999999998 1.378390362 0.455326932 0.123699703 3.21E-09 4.10E-10 0.107595628 0.025360533 0.117569322 0.929705987 0.378390364 S(ph)PTPALCDPPACSLPVASQPPQHLSEAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPTPALCDPPACSLPVASQPPQHLSEAGR 29 0 Q9P2R6;A0A590UJ84;A0A590UK57;H7BYW9 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 S(0.801)PT(0.199)PALCDPPACSLPVASQPPQHLSEAGR;S(0.962)PT(0.038)PALCDPPACSLPVASQPPQHLSEAGR 210.81 5.42E-26 618950000 171558 417720 365380 391490 395720 426980 515430 369360 333480 TRUE FALSE 160820.491 448648.4234 374046.9861 401536.2962 364641.7475 550242.1946 438146.0565 415475.4091 277820.0336 0.57886571 1.614888666 1.34636434 1.445310804 1.31251063 1.980570614 1.577085895 1.495483978 1 18.08379111 4.742600018 24.96354141 1.507556103 0.578865341 0.552293596 0.250722595 279.2156543 1725488.321 0.055103801 0.423794286 55284.07119 -4.742600018 -0.928690761 S(ph)PTPPLFSLPEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPTPPLFSLPEAR 13 0 A0A087WWS1;Q96FV9;Q96FV9-2;J3KRD7;J3QQZ3;J3KT14 A0A087WWS1 THOC1 THO complex subunit 1 1 S(0.991)PT(0.009)PPLFSLPEAR;S(1)PTPPLFSLPEAR;S(0.995)PT(0.005)PPLFSLPEAR;S(0.997)PT(0.003)PPLFSLPEAR 167.59 3.32E-05 238465000 60204 68435 63184 67216 70725 60993 71088 65861 64428 TRUE FALSE 56435.93911 73501.99861 64682.75432 68940.87636 65170.54379 78600.68896 60429.01435 74083.89083 53674.55058 1.051446887 1.369401286 1.20509168 1.284423914 1.21417959 1.464393984 1.125841087 1.380242406 1 15.71195059 -0.558710056 7.564542192 1 1.264398294 0.310223257 0.122669557 0 0 0.101155413 0.023842559 0.276242149 0.558710056 0.264398294 S(ph)PTVEPSTLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPTVEPSTLPR 11 0 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 S(0.996)PT(0.004)VEPSTLPR 85.522 0.011111 0 75609 79335 84380 70314 81599 78705 84783 76250 97195 TRUE FALSE 70876.76766 85209.04595 86381.53345 72118.37628 75190.54369 101425.8558 72070.57624 85769.98035 80972.5266 0.875318712 1.052320454 1.06680052 0.890652414 0.928593275 1.252595912 0.89006209 1.05924792 1 16.30514487 S(ph)PTVLCQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPTVLCQK 8 0 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 S(0.979)PT(0.021)VLCQK 73.931 0.04436 67863000 149840 106210 131630 118320 138630 109500 158890 123180 140050 TRUE FALSE 140461.7819 114073.8989 134752.3258 121356.2915 127742.559 141110.8724 135065.9196 138559.2942 116674.7502 1.203874717 0.977708533 1.154939912 1.040124716 1.09486036 1.209437964 1.157627672 1.187568809 1 16.83213285 2.406939361 10.1484411 1.154361697 1.083151784 0.045630274 0.08210568 0.710628679 97.84820212 0.025364225 0.02121101 255.2344902 -2.406939361 -0.071209914 S(ph)PVGKS(ph)PPSTGSTYGSSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPVGKSPPSTGSTYGSSQK 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 S(0.998)PVGKS(0.84)PPS(0.117)T(0.029)GS(0.007)T(0.004)Y(0.002)GS(0.001)S(0.001)QK 61.276 0.031779 219620000 620090 239080 393670 337930 237810 302100 466700 299650 209360 TRUE FALSE 581279.6738 256781.732 403008.0383 346601.8559 219133.3619 389311.3658 396722.6676 337061.9621 174416.4635 3.332711042 1.472233336 2.310607785 1.987208369 1.256380031 2.232079232 2.274571217 1.932512306 1 17.4121767 4.749317929 24.74961343 1.898564773 3.332711981 0.521858389 0.451292085 1127.556205 2594138.478 0.099696658 1.453444408 56145.88465 -4.749317929 1.434147209 S(ph)PVIGSEVFLPNSNHVASGAGEAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPVIGSEVFLPNSNHVASGAGEAEER 26 0 P29590-2;P29590-5;P29590-9;P29590-3;P29590-8;P29590;H3BVD2;P29590-12;P29590-13;P29590-11 P29590-2;P29590-12 PML Protein PML 1 S(1)PVIGSEVFLPNSNHVASGAGEAEER;S(1)PVIGSEVFLPNSNHVASGAGEAEER;S(1)PVIGSEVFLPNSNHVASGAGEAEER 256.29 8.10E-53 1020640000 92706 107721 117265 110519 105034 125527 151162 121148 96869 TRUE FALSE 86903.69694 115696.7749 120046.5812 113355.1046 96785.05333 161764.6071 128496.6614 136273.5945 80700.9381 1.07686105 1.433648451 1.48754877 1.404631809 1.199305183 2.004494755 1.592257345 1.688624664 1 16.30029782 2.274949478 24.99985478 1.631360252 1.362464119 0.147698856 0.273523434 263.0730049 180735.3155 0.084899464 0.071030006 188.3429977 -2.274949478 -0.268896133 S(ph)PVISRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPVISRPK 8 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2 A0A0U1RRM6 ENAH Protein enabled homolog 1 S(1)PVISRPK 120.06 0.00095332 894360000 309250 207750 263760 250430 237800 225230 303430 231720 216460 TRUE FALSE 289894.5945 223132.0262 270016.5118 256856.4578 219124.1472 290250.2447 257933.4884 260650.7521 180331.4276 1.607565572 1.23734409 1.497334743 1.424357702 1.215119018 1.609537775 1.430330208 1.445398373 1 17.46029132 -1.576364236 4.876033527 0.996361967 1.423183551 0.521206858 0.13021185 0.004688281 0.000407324 0.114779599 0.026868252 0.026523801 1.576364236 0.426821584 S(ph)PVLEEAPFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPVLEEAPFSR 11 0 K7EL81;Q9BZL4-3 K7EL81 PPP1R12C Protein phosphatase 1 regulatory subunit 12C 1 S(1)PVLEEAPFSR 93.203 0.0098861 171250000 176130 126550 149640 154450 169640 110300 176570 139210 164150 TRUE FALSE 165106.3377 135919.8937 153189.5315 158413.4485 156317.1587 142141.8194 150094.9677 156590.6749 136752.3046 1.207338613 0.993913003 1.120197074 1.158396921 1.14306782 1.039410779 1.097568105 1.145067905 1 17.06120562 -0.820506232 7.904766078 1.000000004 1.101714223 0.234033815 0.061301378 0 0 0.056309271 0.013272222 0.1511798 0.820506232 0.10171422 S(ph)PVLQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPVLQEK 7 0 A6NFI3 A6NFI3 ZNF316 Zinc finger protein 316 1 S(1)PVLQEK 65.5 0.073863 61681000 160290 103320 126080 118290 113660 118480 159230 111960 112860 TRUE FALSE 150257.735 110969.9203 129070.6771 121325.5217 104733.6021 152683.2526 135354.9397 125938.4525 94022.9369 1.598096592 1.180243077 1.372757344 1.290382173 1.11391545 1.623893676 1.439594892 1.339443934 1 16.52072512 -1.381392236 2.515312027 0.98998522 1.360364141 0.343539067 0.160177441 2591360.909 2632679.074 187895.9355 0.03861282 0.041553515 1.381392236 0.370378921 S(ph)PVPAQIAITVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPVPAQIAITVPK 13 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 S(1)PVPAQIAITVPK;S(1)PVPAQIAITVPK;S(1)PVPAQIAITVPK;S(1)PVPAQIAITVPK 190.44 4.63E-06 426100000 538908 453490 485103 484997 552123 429035 633595 493608 714514 TRUE FALSE 505178.7103 487066.8715 496609.8722 497442.8441 508761.4867 552890.4397 538593.3118 555236.0454 595256.9975 0.848673283 0.81824636 0.834278092 0.835677441 0.854692156 0.928826443 0.904808031 0.932766936 1 19.18315315 1.646516156 0.547454564 0.996371971 0.821579274 0.9042778 0.017717356 0.206349932 0.143345037 0.016758721 0.009999059 44.31146984 -1.646516156 -0.174792698 S(ph)PVPSAFSDQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPVPSAFSDQSR 12 0 Q9UQ35;Q9UQ35-2;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PVPSAFSDQSR;S(1)PVPSAFSDQSR;S(1)PVPSAFSDQSR 164.56 5.98E-05 10058300000 2462420 1682140 2084850 1905390 1584370 1824020 2762780 1572070 1491870 TRUE FALSE 2308301.528 1806687.396 2134303.627 1954285.533 1459939.971 2350584.964 2348526.787 1768346.4 1242867.259 1.857238986 1.453644693 1.717241814 1.572400849 1.174654784 1.891259864 1.889603874 1.422795867 1 20.24524079 0.987570543 22.5606891 0.999999985 1.644457284 0.473049631 0.219569773 154.6328102 280675.8137 0.209750423 0.052437606 9.717857873 -0.987570543 0.644457299 S(ph)PVREPIDNLTPEER ddPTM_SK-BR-3_Pertuzumab_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 206.28 2.41E-09 178100000 79672 66398 63662 68622 76692 67996 99225 81259 81510 TRUE FALSE 74685.47174 71314.17701 65172.0927 70382.9567 70668.91968 87625.34138 84347.13241 91404.36502 67905.45443 1.099844959 1.050198067 0.959747538 1.036484584 1.040695777 1.290402106 1.242126028 1.346053359 1 16.05123984 2.249207414 23.87273376 1.241875749 1.028510561 0.464952498 0.095574921 82.37737143 184710.1493 0.029734167 0.024611901 177.5037015 -2.249207414 -0.213365189 S(ph)PVS(ph)PLAAQGIPLPAQLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPVSPLAAQGIPLPAQLTK 19 0 K7EIF1;K7EPF0;K7EQS3;K7EM48;K7EN63;Q96SI1-2;Q96SI1 K7EIF1 KCTD15 BTB/POZ domain-containing protein KCTD15 2 S(1)PVS(1)PLAAQGIPLPAQLTK;S(1)PVS(1)PLAAQGIPLPAQLTK;S(1)PVS(1)PLAAQGIPLPAQLTK 257.75 7.71E-31 396199000 956010 718380 813500 770150 830880 744540 1107590 794420 1094420 TRUE FALSE 896175.0406 771569.6027 832796.6042 789913.3529 765626.0364 959476.6114 941517.1619 893605.0857 911754.2318 0.982912949 0.84624735 0.913400317 0.866366533 0.839728525 1.052341276 1.032643589 0.980094256 1 19.79828547 2.234563315 24.99999991 1.021644084 0.885967113 0.669046245 0.044107329 53.18055296 332598.5625 0.014955177 0.011455485 171.6181892 -2.234563315 -0.135676971 S(ph)PVSPLAAQGIPLPAQLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPVSPLAAQGIPLPAQLTK 19 0 K7EIF1;K7EPF0;K7EQS3;K7EM48;K7EN63;Q96SI1-2;Q96SI1 K7EIF1 KCTD15 BTB/POZ domain-containing protein KCTD15 1 S(0.999)PVS(0.001)PLAAQGIPLPAQLTK;S(0.942)PVS(0.058)PLAAQGIPLPAQLTK;S(0.928)PVS(0.072)PLAAQGIPLPAQLTK;S(0.997)PVS(0.003)PLAAQGIPLPAQLTK 379.21 1.62E-108 964525000 1920671 1546350 1715506 1613823 1733568 1508822 2138985 1637322 2237126 TRUE FALSE 1800459.631 1660843.363 1756198.612 1655236.43 1597420.562 1944394.418 1818264.057 1841745.256 1863735.218 0.966049047 0.891136974 0.942300492 0.888128536 0.857107032 1.04327825 0.975602134 0.988201134 1 20.82976548 2.235240646 24.99999368 0.998706357 0.910118508 0.646395268 0.03407588 54.2582611 408568.4193 0.011786304 0.009061599 171.8860557 -2.235240646 -0.088587849 S(ph)PVSSLQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPVSSLQIR 9 0 P55197-1;P55197;Q5JT35 P55197-1 MLLT10 Protein AF-10 1 S(1)PVSSLQIR;S(1)PVSSLQIR 101.3 0.0042794 371970000 72809 65126 76587 62589 70912 67348 76815 63891 59554 TRUE FALSE 68252.01466 69947.9968 78403.67981 64195.1397 65342.85757 86790.2743 65297.30387 71867.93199 49614.05267 1.375658931 1.409842435 1.580271629 1.293890264 1.317023183 1.749308303 1.316105022 1.448539842 1 15.59846119 0.156084434 1.307923649 0.999403572 1.447434813 0.492882807 0.138698991 6.661178106 9.432269736 0.130921704 0.036343763 1.432466368 -0.156084434 0.448031241 S(ph)PVSTRPLPSASQK ddPTM_SK-BR-3_Pertuzumab_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(0.995)PVS(0.004)T(0.001)RPLPSASQK;S(0.997)PVS(0.002)T(0.001)RPLPSASQK;S(0.999)PVS(0.001)TRPLPSASQK;S(0.992)PVS(0.008)TRPLPSASQK;S(0.999)PVS(0.001)TRPLPSASQK;S(0.996)PVS(0.003)T(0.001)RPLPSASQK;S(0.689)PVS(0.251)T(0.055)RPLPS(0.004)AS(0.001)QK;S(0.998)PVS(0.002)T(0.001)RPLPSASQK 157.84 3.14E-06 50557370000 22345820 20511670 20441190 20029360 23209320 16502140 24345890 18810900 24068900 TRUE FALSE 20947235.01 22030375.39 20926064.68 20543347.29 21386553.63 21266039.93 20695449.81 21159482.27 20051645.1 1.044664162 1.098681693 1.043608371 1.024521788 1.066573517 1.060563351 1.032107326 1.055249191 1 24.25721727 -4.999999986 0.102863974 0.82229275 1.091257879 0.4137332 0.020190647 163.3258858 1.136621315 6.178812325 0.301857553 1.00E-05 4.999999986 0.268965129 S(ph)PVTTLLECMHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPVTTLLECMHK 12 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 S(1)PVTTLLECMHK 151.1 4.42E-05 60751000 178340 168010 189910 172040 166490 157560 218480 161450 146790 TRUE FALSE 167178.0177 180449.6352 194414.7549 176454.8377 153414.547 203045.0142 185720.9523 181607.3879 122289.8007 1.367064275 1.475590231 1.589787159 1.442923585 1.254516289 1.660359352 1.518695355 1.485057518 1 16.89994456 0.874905731 17.68991431 1 1.488020998 0.638489496 0.11172439 7618.732234 1077392.434 0.103412199 0.02585305 7.497314529 -0.874905731 0.488020998 S(ph)PVVELSK ddPTM_SK-BR-3_Pertuzumab_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 1214410000 3267470 2335060 2661720 2508340 2262090 2418070 3616380 2408480 2405730 TRUE FALSE 3062964.885 2507950.272 2724857.255 2572708.251 2084434.576 3116127.555 3074137.392 2709184.03 2004198.121 1.528274502 1.25134848 1.359574798 1.283659646 1.040034193 1.554800158 1.533849054 1.3517546 1 20.9345937 S(ph)PYCKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPYCKR 6 1 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 S(1)PYCKR;S(1)PYCKR;S(0.929)PY(0.071)CKR 104.75 0.02056 2655940000 2886110 2368350 2688400 2373480 2578230 2354220 3347760 2417960 2520430 TRUE FALSE 2705473.527 2543705.098 2752170.118 2434387.515 2375746.216 3033845.096 2845794.467 2719847.629 2099753.95 1.288471693 1.211430081 1.31071077 1.159367989 1.131440289 1.44485743 1.355299018 1.295317305 1 21.00178885 2.252991852 24.99953631 1.314078442 1.228638805 0 0.125900092 536.7276859 929783.9404 0.039871857 0.033221659 179.0572258 -2.252991852 -0.085439636 S(ph)PYKFPS(ph)SPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPYKFPSSPLR 11 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 2 S(1)PYKFPS(0.704)S(0.296)PLR 137.61 4.25E-05 498830000 892990 759430 749750 708340 912170 583100 1096400 926300 983120 TRUE FALSE 837099.3499 815658.9874 767534.4241 726517.2036 840531.8477 751431.5042 932004.9985 1041950.594 819030.9208 1.022060741 0.995883021 0.937125088 0.887044903 1.026251667 0.917464146 1.137936279 1.272174917 1 19.64355839 1.657882596 5.539667614 1.157719912 0.964558451 0.513043683 0.078384519 0.096576533 6.394112699 0.037230509 0.018156129 45.48650786 -1.657882596 -0.193161461 S(ph)PYKFPSS(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPYKFPSSPLR 11 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 2 S(0.995)PY(0.005)KFPS(0.005)S(0.995)PLR 113.4 0.016708 168440000 523200 430040 443300 371740 492950 285370 604130 497740 503340 TRUE FALSE 490453.8459 461880.6091 453815.2853 381279.4778 454235.6955 367751.6864 513546.315 559883.9347 419329.3023 1.16961501 1.10147468 1.082240814 0.909260277 1.083243391 0.876999734 1.22468502 1.33518915 1 18.67772412 1.611847875 25 1.209964294 1.046913952 0.248599327 0.119445312 0.444460637 2772.532126 0.053192203 0.028121313 40.91173284 -1.611847875 -0.163050342 S(ph)PYQEFTDHLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPYQEFTDHLVK 12 0 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 1 S(0.999)PY(0.001)QEFTDHLVK;S(1)PYQEFTDHLVK;S(1)PYQEFTDHLVK 174.59 1.93E-05 264652000 538425 403073 503328 456038 446978 412110 588761 386353 392511 TRUE FALSE 504725.9404 432916.9443 515267.1778 467740.7072 411874.1509 531079.467 500481.7538 434590.0225 326998.3784 1.543512059 1.323911594 1.575748419 1.43040681 1.259560225 1.624104283 1.530532831 1.329028066 1 18.31892396 0.916651094 4.417161157 1.000143396 1.46722131 0.640731608 0.111275762 0.257758079 11.75592943 0.102769021 0.026126057 8.253745895 -0.916651094 0.467077914 S(ph)PYSGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPYSGPK 7 0 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23 Q14498-2 RBM39 RNA-binding protein 39 1 S(1)PYSGPK;S(1)PYSGPK;S(1)PYSGPK;S(1)PYSGPK 122.19 0.0045789 1718980000 3361130 2442000 2788970 2535720 2782320 2573470 4032410 2721830 3376110 TRUE FALSE 3150762.873 2622808.221 2855125.685 2600790.868 2563807.811 3316389.012 3427787.556 3061656.467 2812615.43 1.120225268 0.932515762 1.015114137 0.924687691 0.911538699 1.179112145 1.21871889 1.08854429 1 21.42348088 2.231366993 24.99984501 1.149677117 0.976355545 0.393868278 0.083511227 128.2930874 445850.5617 0.028614577 0.021572546 170.3597494 -2.231366993 -0.173321572 S(ph)QDDAMVDYFFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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;S(1)QDDAMVDYFFQR 162.59 4.22E-05 52749000 89184 90726 85352 104115 104496 81416 110641 78948 100105 TRUE FALSE 83602.13264 97443.44744 87376.58975 106786.7672 96289.30568 104919.4775 94051.40919 88804.83159 83396.8288 1.00246177 1.168431088 1.047720771 1.280465561 1.154591932 1.258075145 1.12775762 1.064846624 1 16.34770491 1.088879053 2.865769572 1.002826945 1.150049891 0.273833303 0.082732534 0.311369607 5.045968156 0.074293083 0.019930447 12.27097447 -1.088879053 0.147222947 S(ph)QDVELWEGEVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SQDVELWEGEVVK 13 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 S(1)QDVELWEGEVVK;S(1)QDVELWEGEVVK;S(1)QDVELWEGEVVK;S(1)QDVELWEGEVVK;S(1)QDVELWEGEVVK;S(1)QDVELWEGEVVK 233.49 1.29E-16 635475000 1323118 748849 958303 878760 702491 665022 1260144 769219 1335140 TRUE FALSE 1240306.406 804294.5591 981034.3997 901310.4693 647320.1906 857003.0557 1071197.106 865257.6854 1112296.509 1.115086127 0.723093665 0.881990002 0.810314932 0.581967295 0.770480757 0.963049958 0.777902006 1 20.08510999 -0.737004227 5.513229971 1.000000009 0.823403708 0.125918579 0.141973499 3.15E-08 7.09E-09 0.128028634 0.030176635 0.183229659 0.737004227 -0.1765963 S(ph)QEADVQDWEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SQEADVQDWEFR 12 0 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 S(1)QEADVQDWEFR;S(1)QEADVQDWEFR;S(1)QEADVQDWEFR;S(1)QEADVQDWEFR;S(1)QEADVQDWEFR;S(1)QEADVQDWEFR;S(1)QEADVQDWEFR;S(1)QEADVQDWEFR 289.09 4.71E-36 5462453000 4927195 4089057 4060442 4225535 3332525 2898123 4700593 2892774 3950485 TRUE FALSE 4618810.66 4391815.035 4156757.602 4333969.382 3070801.929 3734764.063 3995782.718 3253943.202 3291123.532 1.403414553 1.334442476 1.263020838 1.316866213 0.933055809 1.134799112 1.214109005 0.988702846 1 21.65014875 4.283992379 0.276376499 1.001849661 1.654978568 0.628962556 0.097895921 4.586116056 0.356395972 0.126633882 1.003842311 19230.57982 -4.283992379 0.653128907 S(ph)QEELREDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 190.03 2.27E-05 1554350000 2450490 1426106 1737265 1772936 1919130 1508222 2615880 1750850 2088220 TRUE FALSE 2297118.205 1531696.372 1778473.746 1818432.539 1768409.271 1943621.207 2223653.079 1969447.477 1739682.592 1.320423746 0.880445881 1.022297835 1.045266848 1.016512598 1.117227486 1.278194706 1.132072877 1 20.73039268 2.082960764 4.668742157 1.174385514 1.028368202 0.026378079 0.129499874 0.308489571 12.20145929 0.047301278 0.033830615 121.0488769 -2.082960764 -0.146017313 S(ph)QEEPKDTFEHDPSESIDEFNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SQEEPKDTFEHDPSESIDEFNK 22 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 S(0.979)QEEPKDT(0.006)FEHDPS(0.013)ES(0.002)IDEFNK;S(0.923)QEEPKDT(0.077)FEHDPSESIDEFNK;S(1)QEEPKDTFEHDPSESIDEFNK 302.66 4.01E-56 1005010000 2533740 836406 1448920 1198540 1282520 1054926 1989990 1146903 2058240 TRUE FALSE 2375157.736 898334.3705 1483289.067 1229296.566 1181796.053 1359466.011 1691609.474 1290096.364 1714706.447 1.385168721 0.523899803 0.865039651 0.716913713 0.689211879 0.792827258 0.986530071 0.75237156 1 20.70953018 -0.716900186 5.546867501 1.000000014 0.815677722 0.038144006 0.228852022 3.55E-08 8.54E-09 0.198575546 0.046804702 0.191910976 0.716900186 -0.184322292 S(ph)QESDGVEYIFISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SQESDGVEYIFISK 14 0 S4R337;Q5T2T1-2;Q5T2T1;U5GXS2 S4R337 MPP7 MAGUK p55 subfamily member 7 1 S(1)QESDGVEYIFISK;S(1)QESDGVEYIFISK;S(0.999)QES(0.001)DGVEYIFISK;S(1)QESDGVEYIFISK;S(0.998)QES(0.002)DGVEYIFISK 227.88 1.96E-12 342933000 646263 440820 512988 483091 580233 396131 621965 483098 768327 TRUE FALSE 605814.5524 473458.7715 525156.3176 495487.9329 534663.8407 510487.5891 528707.1223 543413.8487 640088.2601 0.946454716 0.739677324 0.820443602 0.774093143 0.835297058 0.797526874 0.825990969 0.848967061 1 19.28791132 0.541825228 1.176468462 1.000151449 0.808389982 0.51579863 0.053768176 1.170537493 2.240498378 0.045479778 0.013886537 3.481971625 -0.541825228 -0.191761466 S(ph)QESGYYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQESGYYDR 9 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 S(1)QESGYYDR 123.95 0.00057 270320000 123760 154060 140090 145020 156600 128080 165970 136930 166600 TRUE FALSE 116014.0825 165466.7627 143413.001 148741.4587 144301.2677 165054.6168 141084.3393 154026.0119 138793.3837 0.835876174 1.192180479 1.033284131 1.071675427 1.039684053 1.189210987 1.01650623 1.109750391 1 17.08257927 4.754724176 24.86813119 1.084633233 0.83587597 0.57395219 0.066468816 2066.652817 3179552.022 0.014356448 0.383058205 56849.17628 -4.754724176 -0.248757263 S(ph)QGGEEEGPLSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 210.91 2.74E-08 402530000 758838 543079 660900 713243 914630 653737 983840 734916 897682 TRUE FALSE 711343.6841 583289.1342 676576.8601 731546.0229 842798.6492 842460.2594 836322.3255 826671.8803 747853.075 0.951181065 0.779951509 0.904692222 0.978194845 1.126957523 1.126505042 1.118297636 1.105393436 1 19.51239534 3.065500533 2.043855976 1.1070262 0.853882245 0.750974077 0.056815817 0.121702468 1.031758486 0.016936778 0.020878199 1162.787978 -3.065500533 -0.253143955 S(ph)QGLSGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 150.51 0.00051189 2320070000 3185220 2868880 2431090 2154220 3635030 1178347 3482040 2117490 5100830 TRUE FALSE 2985862.766 3081294.86 2488756.603 2209500.932 3349549.407 1518516.65 2959940.428 2381863.288 4249468.52 0.702643813 0.725101232 0.585663028 0.519947594 0.788227843 0.357342722 0.696543677 0.560508514 1 22.01885098 -1.155275266 5.053411992 1.000020458 0.620160466 0.489759766 0.122819343 2.52E-05 4.20E-06 0.105664828 0.024904099 0.069939856 1.155275266 -0.379859992 S(ph)QGLSGDKTSGFRPIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQGLSGDKTSGFRPIAK 17 2 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 S(0.995)QGLS(0.005)GDKTSGFRPIAK;S(1)QGLSGDKTSGFRPIAK 92.792 0.0025369 1690110000 662720 693590 574770 518720 1040100 284070 986990 489590 2148160 TRUE FALSE 621241.5382 744944.1253 588403.8158 532031.2334 958414.7416 366076.3975 839000.0123 550716.3892 1789618.218 0.347136351 0.416258684 0.328787341 0.29728756 0.535541453 0.204555583 0.468815082 0.307728421 1 20.77122042 -1.645819238 2.754191011 1.066811922 0.368476931 0.822134843 0.093047538 11710375.46 10880063.08 5554922.09 0.020358647 0.022603764 1.645819238 -0.698334991 S(ph)QLDLFDDVGTFASGPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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;S(1)QLDLFDDVGTFASGPPK 133.09 1.41E-05 31745000 78136 64412 67240 66404 69727 52940 89783 63977 83602 TRUE FALSE 73245.60724 69181.1315 68834.96455 68108.03906 64250.92269 68222.91859 76320.87265 71964.66928 69648.28611 1.051649815 0.993292662 0.988322447 0.977885356 0.922505438 0.97953478 1.095804031 1.033258294 1 16.08780023 1.761429263 25 1.052065576 0.984031013 0.319975526 0.038726204 11.86191964 12977.40375 0.017189855 0.0095334 57.73368292 -1.761429263 -0.068034563 S(ph)QPKAPPVDDAEVDELVLQTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQPKAPPVDDAEVDELVLQTK 21 1 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 S(1)QPKAPPVDDAEVDELVLQTK;S(1)QPKAPPVDDAEVDELVLQTK 203.73 3.44E-22 113319000 117124 74062 98796 77345 102870 51855 149726 82114 244616 TRUE FALSE 109793.4179 79545.62754 101139.4878 79329.80364 94791.00516 66824.6967 127275.9763 92366.11366 203788.0093 0.538762895 0.390335171 0.49629754 0.389276111 0.465145155 0.3279128 0.624550859 0.453246067 1 17.63670964 -0.198127436 0.628207628 1.040626739 0.441751227 0.808587814 0.082562227 2.459591723 0.939361131 0.317527717 0.028846231 0.63368374 0.198127436 -0.598875512 S(ph)QPLLIPTTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SQPLLIPTTGR 11 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 S(1)QPLLIPTTGR;S(1)QPLLIPTTGR;S(1)QPLLIPTTGR 131.36 0.00021503 412327000 224858 259921 231005 246314 289200 201075 311325 238516 292556 TRUE FALSE 210784.5392 279165.8213 236484.5477 252634.8342 266487.3986 259122.0883 264644.7064 268295.2476 243726.5136 0.864840415 1.145406042 0.970286508 1.036550478 1.093386988 1.063167419 1.085826497 1.100804519 1 17.89490368 2.917189129 5.896387199 1.073969101 1.020506087 0.143628235 0.07393411 0.510993078 28.70227265 0.02090187 0.022355025 826.3977556 -2.917189129 -0.053463014 S(ph)QS(ph)T(ph)PHQEKVITESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQSTPHQEKVITESK 15 1 Q9ULI3-2;Q9ULI3 Q9ULI3-2 HEG1 Protein HEG homolog 1 3 S(0.999)QS(1)T(1)PHQEKVIT(0.001)ESK;S(0.999)QS(0.999)T(0.999)PHQEKVIT(0.002)ESK 89.468 0.0053469 191890000 349170 258260 357140 358850 350710 166197 232689 296300 184658 TRUE FALSE 327316.073 277381.8391 365611.5295 368058.6985 323166.6513 214175.3759 197799.4446 333293.7072 153837.3869 2.127675721 1.803084704 2.376610374 2.392517879 2.100702943 1.39221928 1.28576966 2.166532558 1 17.23104664 2.260094821 7.767491226 1.459847185 2.15302544 0.525972817 0.329745114 0.137343336 36.33631593 0.11077884 0.090317579 182.0098205 -2.260094821 0.693178255 S(ph)QSLPHSATVTLGGTSDPSTLSSSALSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQSLPHSATVTLGGTSDPSTLSSSALSER 29 0 A0A0A0MRY0;Q8WUA7-3;Q8WUA7-4;Q8WUA7;F8WDP1 A0A0A0MRY0 TBC1D22A TBC1 domain family member 22A 1 S(0.467)QS(0.467)LPHS(0.031)AT(0.031)VT(0.003)LGGTSDPSTLSSSALSER 75.718 1.64E-06 0 30445 31970 32618 34280 30722 25840 36857 23721 35534 TRUE FALSE 28539.5018 34337.09206 33391.71436 35159.68284 28309.21805 33299.58852 31330.63501 26682.61907 29603.14584 0.964069898 1.15991362 1.127978578 1.187700896 0.956290868 1.12486655 1.058354919 0.90134404 1 14.85346287 1.39968306 4.817200273 0.952821817 1.098129911 0.32167094 0.079311145 0.214475337 7.862417245 0.052269584 0.018738141 25.10053971 -1.39968306 0.145308093 S(ph)QSSDTEQQSPTSGGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.333)QS(0.333)S(0.333)DTEQQSPTSGGGK 68.919 0.037613 29544000 58614 47394 45295 44766 43824 33311 53129 41587 51780 TRUE FALSE 54945.45437 50903.10107 46369.41879 45914.77135 40382.23982 42927.34494 45162.79968 46779.22849 43137.58349 1.273725831 1.180017446 1.074919248 1.064379774 0.936126611 0.995126325 1.046947836 1.084419309 1 15.39665774 4.292119564 0.891102656 1.017835151 1.318710399 0.815712707 0.041165348 0.533200533 0.5147849 0.014805461 0.136789232 19593.8403 -4.292119564 0.300875248 S(ph)RADLTAEMISAPLGDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 SRADLTAEMISAPLGDFR 18 1 Q9H3Q1;Q9H3Q1-2;J3KRZ9;J3QQS6;J3QR93 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 S(0.794)RADLT(0.206)AEMISAPLGDFR;S(0.86)RADLT(0.14)AEMISAPLGDFR;S(0.838)RADLT(0.162)AEMISAPLGDFR;S(0.489)RADLT(0.489)AEMIS(0.022)APLGDFR;S(0.919)RADLT(0.081)AEMISAPLGDFR;S(1)RADLTAEMISAPLGDFR;S(0.5)RADLT(0.5)AEMISAPLGDFR;S(0.934)RADLT(0.066)AEMISAPLGDFR;S(0.902)RADLT(0.098)AEMISAPLGDFR;S(0.935)RADLT(0.065)AEMISAPLGDFR;S(0.8)RADLT(0.2)AEMISAPLGDFR 245.62 1.92E-24 1389508700 843071.6 934748.9 766455.8 808957.5 1122438.4 588692.6 1058788.1 888339.4 1118198 TRUE FALSE 790305.2535 1003958.681 784636.4935 829716.719 1034286.616 758638.597 900032.6537 999250.5296 931563.53 0.848364312 1.077713595 0.842279102 0.890671105 1.110269544 0.814371294 0.966152737 1.072659564 1 19.82929463 1.462516982 25 1.030689011 0.938294728 0.159316703 0.098119999 7.916632197 13557.09691 0.048934178 0.022652042 29.00794627 -1.462516982 -0.092394282 S(ph)RAPGPRDTDDDEEEPDPYGFIVQTAEIAEIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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)DDDEEEPDPY(0.001)GFIVQTAEIAEIAR 135.32 1.59E-08 12104000 10042 12260 7823.6 9553.1 11216 6084.7 9100.8 10507 15616 TRUE FALSE 9413.489145 13167.74316 8009.179487 9798.248719 10335.1406 7841.254113 7736.219528 11818.82208 13009.58872 0.723580841 1.012156759 0.61563664 0.753155917 0.794424853 0.602728824 0.594655196 0.908470078 1 13.66728773 3.970822424 24.68615669 0.720537842 0.879158289 0.060817298 0.1500235 348.4768689 1365747.512 0.034853389 0.064880544 9350.232797 -3.970822424 0.158620447 S(ph)RAS(ph)PATHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRASPATHR 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)RAS(0.999)PAT(0.001)HR;S(1)RAS(1)PATHR 122.1 0.00033879 254870000 40255 39113 43886 46157 47290 30314 46963 42283 34372 TRUE FALSE 37735.51141 42008.96722 44926.99664 47341.46676 43576.03416 39065.15969 39921.33413 47562.12563 28635.09115 1.317806576 1.467044997 1.568948966 1.653267542 1.521770402 1.364240801 1.394140285 1.660973432 1 14.80549658 -0.974868808 4.84999937 0.999994767 1.49053641 0.646612569 0.114641725 0.026653109 36914607.02 456.0530853 0.026732551 0.105957375 0.974868808 0.490541643 S(ph)RAS(ph)PVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.99)PVS(0.01)R;S(1)RAS(0.998)PVS(0.002)R;S(1)RAS(0.999)PVS(0.001)R;S(1)RAS(0.999)PVS(0.001)R 90.412 0.0075193 2337790000 114815 123068 150346 156336 114700 122498 112632 119688.8 135810 TRUE FALSE 107628.9341 132180.0828 153912.2781 160347.8464 105691.9247 157861.184 95743.87722 134632.2101 113142.4336 0.951269392 1.16826268 1.360340883 1.417221119 0.934149296 1.39524296 0.846224305 1.189935604 1 16.78778058 1.735588847 24.99999987 1.007525892 1.216026028 0.193612113 0.183970119 0.532100518 4407.837713 0.079123435 0.043877933 54.39874076 -1.735588847 0.208500137 S(ph)RASPVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRASPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.787)RAS(0.209)PVS(0.004)R;S(0.713)RAS(0.287)PVSR 64.439 0.040564 1900820000 390969 353844 382646 418609 372667 409322 401170 329437 437409 TRUE FALSE 366498.9482 380042.9779 391722.5438 429351.2156 343399.2371 527486.6166 341018.2828 370567.9346 364402.6121 1.005752802 1.042920564 1.074971833 1.17823309 0.942362172 1.447537968 0.935828316 1.016918985 1 18.47517378 1.595982549 25 0.982275681 1.104751732 0.167339765 0.136409036 1.549566876 3251.25134 0.065802604 0.030839711 39.44414517 -1.595982549 0.122476051 S(ph)RDKEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SRDKEER 7 2 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 1 S(1)RDKEER;S(1)RDKEER;S(1)RDKEER;S(1)RDKEER;S(1)RDKEER;S(1)RDKEER 90.05 0.013722 9014167000 14793366 7121357 10480818 9808631 8865014 6969491 10175655 8405228 10863442 TRUE FALSE 13867475.63 7648629.682 10729427.95 10060337.08 8168791.56 8981469.911 8649909.999 9454639.218 9050263.35 1.532273161 0.845127858 1.185537651 1.111607109 0.902602636 0.992398736 0.955763348 1.044681116 1 23.10952834 2.776226191 14.54239671 0.975800678 1.117544764 0.209135397 0.170695949 8.372299188 3230.644651 0.048372533 0.051269876 597.346318 -2.776226191 0.141744086 S(ph)RDREQDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRDREQDRK 9 3 O95232;J3KPP4;H0YA81;H0YBV7;H0YAR4;H0YAX1;H0YAY6 O95232 LUC7L3 Luc7-like protein 3 1 S(1)RDREQDRK;S(1)RDREQDRK 106.49 0.016174 898070000 305640 254170 260010 295910 293370 155444 311160 222010 393290 TRUE FALSE 286510.538 272989.0113 266177.56 303503.5516 270329.9036 200318.1594 264504.4467 249728.4372 327647.3582 0.874447881 0.833179345 0.812390374 0.926311609 0.825063584 0.611383411 0.807283929 0.762186634 1 18.32178437 2.463944698 24.99919706 0.768931915 0.851353624 0.060385484 0.098731313 431.8383112 819298.8009 0.030486351 0.025519684 291.0346497 -2.463944698 0.082421709 S(ph)RDRHDDYYR ddPTM_SK-BR-3_Pertuzumab_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 131.08 0.00013542 972830000 88843 299750 213712 275040 257370 243130 173017 232370 218150 TRUE FALSE 83282.47522 321943.8019 218781.3496 282097.992 237157.1984 313317.6841 147074.7071 261381.906 181739.3557 0.458252286 1.771458915 1.203819331 1.552211908 1.304930335 1.72399469 0.809261739 1.438224016 1 17.47151134 1.72979776 24.99999999 1.081802379 1.377965759 0.077788409 0.393626325 1.600480718 4541.364075 0.16154488 0.089584856 53.67817722 -1.72979776 0.29616338 S(ph)RECDITK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRECDITK 8 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 S(1)RECDITK 77.124 0.020607 324270000 640730 441070 466030 454160 549460 333900 717870 425640 634890 TRUE FALSE 600627.853 473727.2817 477084.4517 465814.5145 506307.628 430291.5096 610232.0579 478782.0909 528922.7575 1.13556818 0.895645489 0.901992673 0.880685332 0.95724304 0.813524288 1.153726228 0.905202289 1 19.01269752 1.742880427 24.99999963 1.031412554 0.922492135 0.138308303 0.101788575 1.180482459 6863.22382 0.042312318 0.023464176 55.31977774 -1.742880427 -0.108920419 S(ph)REDLSALTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SREDLSALTR 10 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 S(0.994)REDLS(0.006)ALTR;S(0.999)REDLS(0.001)ALTR;S(1)REDLSALTR 126.63 0.00022862 1131010000 827700 776823 804038 762800 855630 639206 834737 686430 945630 TRUE FALSE 775895.7345 834339.7832 823110.1611 782374.7394 788432.2712 823734.3956 709575.9362 772132.2965 787798.244 0.984891424 1.059077993 1.044823554 0.993115617 1.000804809 1.045615933 0.90070769 0.980114265 1 19.58746668 1.754359339 25 0.951633143 1.026562141 0.391418083 0.034986184 4.446113158 7044.080671 0.015433545 0.008558719 56.80143904 -1.754359339 0.074928998 S(ph)REDLSAQPVQTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SREDLSAQPVQTK 13 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 S(0.944)REDLS(0.056)AQPVQTK;S(1)REDLSAQPVQTK;S(1)REDLSAQPVQTK 204.78 4.55E-08 1917600000 3836650 2502320 3048650 2778760 2939270 2319400 3632690 2481600 4180960 TRUE FALSE 3596520.925 2687594.376 3120965.418 2850067.686 2708431.591 2988973.128 3088001.859 2791433.223 3483130.766 1.032554092 0.771603065 0.89602304 0.818248833 0.777585389 0.858128313 0.886559267 0.801414994 1 21.73195321 -1.915609759 7.807131954 1.03272916 0.850795949 0.263711894 0.075677226 0.03435539 0.00037136 0.058391918 0.01518122 0.012144796 1.915609759 -0.181933212 S(ph)REDLTAVVSVSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.598)REDLT(0.402)AVVSVSTK;S(0.997)REDLT(0.002)AVVSVSTK;S(1)REDLTAVVSVSTK;S(0.999)REDLT(0.001)AVVSVSTK;S(0.87)REDLT(0.125)AVVS(0.005)VSTK 241.64 5.00E-17 861607000 2992740 2023360 2482120 2214990 2471580 2006670 3025440 2128470 3448570 TRUE FALSE 2805429.746 2173171.68 2540997.059 2271830.393 2277472.077 2585963.053 2571803.359 2394214.165 2872981.388 0.976487268 0.756416901 0.884446056 0.790757087 0.79272079 0.900097391 0.89516882 0.833355265 1 21.45411722 -0.065962133 0.484025727 1.017636856 0.837461022 0.314043762 0.065612378 5.074250869 1.417199518 0.237356923 0.031419786 0.859088423 0.065962133 -0.180175833 S(ph)RENLSAVMLYNPGLEFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SRENLSAVMLYNPGLEFER 19 1 Q96L93-5;Q96L93-6;Q96L93-4;Q96L93;Q96L93-2;A0A1B0GTU3 Q96L93-5 KIF16B Kinesin-like protein KIF16B 1 S(0.5)RENLS(0.5)AVMLYNPGLEFER;S(0.711)RENLS(0.289)AVMLYNPGLEFER;S(0.859)RENLS(0.141)AVMLYNPGLEFER;S(0.731)RENLS(0.269)AVMLYNPGLEFER;S(0.764)RENLS(0.236)AVMLYNPGLEFER 197.54 4.74E-16 1839041000 479240 489710 453055 478592 536581 343374 608262 418689 521189 TRUE FALSE 449245.2239 525968.6379 463801.6785 490873.481 494440.0927 442500.4996 517058.7599 470963.2433 434199.1889 1.034652379 1.211353341 1.068177211 1.13052602 1.13874025 1.019118669 1.190833086 1.084670942 1 18.72799751 0.984343964 24.28116813 0.999999995 1.119955662 0.246660144 0.061434242 786.8825125 1220390.13 0.052511469 0.013127867 9.645926843 -0.984343964 0.119955667 S(ph)RERPSAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRERPSAPR 9 2 Q8N5F7;A0A494C050 Q8N5F7 NKAP NF-kappa-B-activating protein 1 S(1)RERPSAPR 79.152 0.021855 253430000 72196 77967 61186 68028 77655 53183 67306 53940 70506 TRUE FALSE 67677.38123 83739.7578 62637.36081 69773.71365 71556.28955 68536.06875 57214.09014 60674.52774 58738.09311 1.15218894 1.425646516 1.066383968 1.187878427 1.218226295 1.16680786 0.974054265 1.032967271 1 15.84200881 2.272396037 0.527486215 0.970307915 1.276074257 0.467019653 0.095728314 0.73721164 0.425135675 0.088256349 0.076398865 187.2388809 -2.272396037 0.305766342 S(ph)RERPSQPEGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SRERPSQPEGLR 12 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 S(0.975)RERPS(0.025)QPEGLR;S(1)RERPSQPEGLR;S(0.999)RERPS(0.001)QPEGLR 126.04 0.00023196 7787600000 1319800 1286226 1242469 1443633 1691634 1269580 1734420 1366500 1733870 TRUE FALSE 1237196.074 1381459.511 1271940.951 1480679.067 1558779.889 1636087.136 1474359.823 1537110.533 1444475.896 0.856501709 0.956374222 0.880555332 1.025063188 1.079131811 1.132651047 1.020688422 1.064130276 1 20.4621147 3.123576163 4.479683922 1.06238568 0.908208725 0.743602311 0.043284148 0.100876722 3.48777643 0.011984109 0.014562462 1329.156634 -3.123576163 -0.154176955 S(ph)RERPSQPEGLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.966)RERPS(0.034)QPEGLRK;S(1)RERPSQPEGLRK 160.64 0.0002405 3602880000 1065100 1047030 979260 1118560 1379280 860480 1459080 1029400 1842420 TRUE FALSE 998437.2923 1124553.191 1002488.51 1147264.143 1270956.913 1108886.607 1240304.499 1157922.856 1534908.2 0.65048665 0.732651758 0.653126037 0.747448052 0.82803448 0.722444904 0.808064287 0.754392254 1 20.54972094 -4.999999996 0.125061851 1.89964708 0.611974094 0.794152873 0.045356471 61.33325247 0.49095654 13.79793762 0.362248454 1.00E-05 4.999999996 -1.287672986 S(ph)RESASPTIPNLDLLEAHTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRESASPTIPNLDLLEAHTK 20 1 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 S(0.468)RES(0.468)AS(0.063)PT(0.001)IPNLDLLEAHTK;S(0.332)RES(0.332)AS(0.332)PT(0.005)IPNLDLLEAHTK 205.38 5.25E-22 132338000 250182 235567 222058 226509 268774 144249 272020 204274 358220 TRUE FALSE 234523.5552 253008.6258 227325.3206 232321.6044 247665.5742 185891.3446 231233.1263 229778.0586 298430.7678 0.785855818 0.847796719 0.761735535 0.778477387 0.829892896 0.622896044 0.774830049 0.769954319 1 18.18703676 -1.166497428 3.417432473 1.000319248 0.772852848 0.594277678 0.05934252 12004363.13 19301718.04 42325.35105 0.013952604 0.068155761 1.166497428 -0.2274664 S(ph)RESLNVDVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SRESLNVDVVK 11 1 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;H0YG16;G5E9S8;H0YJU9;H0YJT3;H0YJL0;H0YGB8 Q07866-6 KLC1 Kinesin light chain 1 1 S(0.857)RES(0.143)LNVDVVK;S(0.784)RES(0.216)LNVDVVK;S(1)RESLNVDVVK;S(1)RESLNVDVVK;S(0.858)RES(0.142)LNVDVVK;S(0.989)RES(0.011)LNVDVVK 170.77 9.28E-06 1880920000 6094410 4339050 4918520 4839210 4968100 3934960 6333340 4287530 4810050 TRUE FALSE 5712971.757 4660317.777 5035189.617 4963392.321 4577925.466 5070919.073 5383714.463 4822837.559 4007221.581 1.425669043 1.162979806 1.256528873 1.238611896 1.142418849 1.26544514 1.343503062 1.203536531 1 21.93417086 0.973516644 23.16356052 0.999999996 1.253102613 0.506142771 0.080759236 862.6936877 754553.0832 0.073745106 0.018436276 9.408418857 -0.973516644 0.253102617 S(ph)REYEHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SREYEHVR 8 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 S(1)REYEHVR 126.19 0.002749 0 142270 122510 95734 110740 122060 85157 111990 102390 105330 TRUE FALSE 133365.5747 131580.7679 98004.85569 113581.7759 112473.9 109740.4435 95198.13916 115173.6169 87749.74254 1.519840068 1.49950033 1.116867729 1.29438301 1.281757606 1.250607014 1.084882262 1.312523702 1 16.42110727 8 0.308802528 1.133445724 4.973843707 0.6164932 0.102817521 36.17995197 0.517929871 0.095085625 77.50225512 100000000 -8 3.840397983 S(ph)RGPKSDDDGFEIVPIEDPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRGPKSDDDGFEIVPIEDPAK 21 2 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 1 S(0.5)RGPKS(0.5)DDDGFEIVPIEDPAK 78.236 0.0046857 45118000 240330 103670 163770 137520 147550 103070 213420 131350 257660 TRUE FALSE 225288.1743 111345.8347 167654.7017 141048.996 135962.0182 132824.6358 181419.6523 147749.3366 214654.8815 1.049536692 0.518720254 0.781043043 0.657096615 0.633398212 0.618782275 0.845169004 0.688311096 1 17.71165946 0.204295011 0.789353308 1.004457085 0.70043254 0.243441481 0.147493071 4.137797343 3.092632517 0.181930856 0.044710311 1.600644958 -0.204295011 -0.304024545 S(ph)RGQNRPTNVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SRGQNRPTNVK 11 2 Q9BX40;Q9BX40-2;Q5TBQ1;Q5TBQ0;Q5TBP9;Q9BX40-3 Q9BX40 LSM14B Protein LSM14 homolog B 1 S(1)RGQNRPTNVK;S(1)RGQNRPTNVK;S(1)RGQNRPTNVK;S(1)RGQNRPTNVK 117.08 0.00071087 771260000 636600 558390 558930 579280 703150 387662 811640 589160 761450 TRUE FALSE 596756.3424 599733.7766 572188.0835 594145.3055 647927.4354 499573.7262 689942.1169 662717.9229 634359.0758 0.940723267 0.945416877 0.901994005 0.936607244 1.021389084 0.78752515 1.087620786 1.044704723 1 19.27494018 1.634541339 14.77268882 1.04944791 0.92744314 0.466613623 0.061103719 0.104875652 51.35986966 0.025367816 0.013895889 43.10635878 -1.634541339 -0.12200477 S(ph)RGSDSPAADVEIEYVTEEPEIYEPNFIFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRGSDSPAADVEIEYVTEEPEIYEPNFIFFK 31 1 Q13435;E9PPJ0;H0YCG1 Q13435 SF3B2 Splicing factor 3B subunit 2 1 S(0.369)RGS(0.369)DS(0.262)PAADVEIEY(0.001)VTEEPEIYEPNFIFFK;S(0.314)RGS(0.314)DS(0.314)PAADVEIEY(0.052)VT(0.006)EEPEIYEPNFIFFK 169.7 5.33E-13 16853600 38339 40773 31769 43256 51465 22755.4 49138 45271 72590 TRUE FALSE 35939.43043 43791.87534 32522.57568 44366.02219 47423.1465 29324.51458 41770.21307 50923.184 60474.26005 0.594293017 0.724140739 0.53779204 0.733634809 0.784187297 0.484909027 0.69071061 0.84206378 1 15.88403359 1.07428727 2.612171011 0.995714514 0.645085923 0.632513532 0.090792705 0.152794402 2.121634394 0.080488352 0.021830062 11.86553351 -1.07428727 -0.35062859 S(ph)RKSPHKDLGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRKSPHKDLGHR 12 3 O94888;C9JAT7 O94888 UBXN7 UBX domain-containing protein 7 1 S(0.561)RKS(0.439)PHKDLGHR;S(0.5)RKS(0.5)PHKDLGHR 87.566 0.0042633 77090000 150438 105879 122535 108547 165176 77997 128153 100057 261596 TRUE FALSE 141022.3541 113718.3913 125441.5881 111332.4998 152203.7432 100513.4677 108937.6474 112549.3367 217933.9376 0.647087625 0.521802123 0.575594556 0.510854349 0.698393949 0.461210717 0.499865457 0.516437862 1 17.73353135 -1.407251615 3.361806895 1.004584755 0.548240499 0.793069411 0.071560002 67023345.32 94701558.25 2977022.145 0.016010447 0.039151498 1.407251615 -0.456344256 S(ph)RLTPVSPESSSTEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRLTPVSPESSSTEEK 16 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.621)RLT(0.374)PVS(0.005)PESSSTEEK;S(0.742)RLT(0.257)PVS(0.001)PESSSTEEK 174.2 2.39E-09 1997510000 799460 527730 657020 584760 684920 530580 816450 582300 854490 TRUE FALSE 749423.2257 566803.6783 672604.8247 599765.9316 631129.146 683749.8328 694030.9021 655001.4368 711870.0988 1.05275278 0.796217848 0.94484208 0.842521596 0.886579092 0.960498037 0.974940376 0.920113709 1 19.44125448 2.233588856 21.25077205 0.963161293 0.892474594 0.139758956 0.06958839 29.20520927 124822.6998 0.023066558 0.017642118 171.2335481 -2.233588856 -0.070686699 S(ph)RPTS(ph)FADELAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRPTSFADELAAR 13 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;A0A0A0MT65 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 2 S(0.997)RPT(0.044)S(0.959)FADELAAR;S(1)RPT(0.246)S(0.754)FADELAAR 103.13 0.019545 208940000 621100 716130 691910 1014490 1113450 445580 538770 453330 715330 TRUE FALSE 582226.4597 769153.0103 708322.4319 1040523.531 1026004.128 574211.7126 457986.4402 509929.2484 595936.8018 0.976993631 1.290662043 1.188586491 1.746029995 1.721665998 0.963544642 0.768515116 0.855676721 1 19.18479982 2.062515024 8.927479412 0.853174427 1.361159101 0.520258555 0.233149863 0.24949988 32.91395355 0.090899809 0.067048538 115.4821935 -2.062515024 0.507984673 S(ph)RPTSEGSDIES(ph)TEPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 2 S(0.996)RPT(0.004)SEGS(0.15)DIES(0.824)T(0.026)EPQK 231.37 5.84E-15 769470000 3205900 2511900 2783600 2692000 2818400 2052800 3422200 2398900 3156600 TRUE FALSE 3005248.442 2697883.69 2849628.307 2761081.278 2597054.233 2645410.036 2909072.88 2698407.946 2629743.068 1.142791659 1.025911513 1.083614723 1.049943362 0.987569571 1.005957604 1.106219431 1.026110869 1 21.32649042 4.744768226 24.63079928 1.043254303 1.142791713 0.436076054 0.037410267 599.3384025 2377996.475 0.008862437 0.081765176 55560.76617 -4.744768226 0.09953741 S(ph)RS(ph)HS(ph)PMSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSHSPMSNR 10 1 Q13595 Q13595 TRA2A Transformer-2 protein homolog alpha 3 S(1)RS(0.998)HS(0.959)PMS(0.043)NR 49.794 0.072303 107360000 57741 52704 60106 51282 63978 36593 49140 41653 65911 TRUE FALSE 54127.09388 56606.259 61531.7427 52597.98294 58953.42595 47156.80506 41771.91319 46853.46874 54910.0283 0.985741504 1.030891091 1.120592078 0.957893932 1.07363678 0.858801325 0.760733776 0.853277082 1 15.74478203 2.19850348 6.699045847 0.837720416 1.041771608 0.530899264 0.074796167 0.115931795 13.80004826 0.026115161 0.019469607 157.9441265 -2.19850348 0.204051192 S(ph)RS(ph)HSDNDRPNCSWNTQYSSAYYTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSHSDNDRPNCSWNTQYSSAYYTSR 26 2 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 2 S(0.606)RS(0.741)HS(0.55)DNDRPNCS(0.099)WNT(0.004)QYSSAYYTSR 121.39 7.72E-05 172200000 28534 36605 30652 23774 34865 22501 28489 20654 37705 TRUE FALSE 26748.10787 39315.27229 31379.07991 24384.08109 32126.84354 28996.67343 24217.33893 23232.69737 31411.79192 0.851530786 1.251608708 0.998958608 0.776271572 1.022763796 0.923114272 0.770963306 0.739617066 1 14.93901862 3.449538167 5.09306373 0.865515043 1.090286248 0.238578672 0.134217894 0.185511282 12.47490553 0.035316908 0.050022354 2815.387425 -3.449538167 0.224771205 S(ph)RS(ph)HTSEGAHLDITPNSGAAGNSAGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSHTSEGAHLDITPNSGAAGNSAGPK 27 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 S(0.47)RS(0.376)HT(0.376)S(0.376)EGAHLDIT(0.376)PNS(0.025)GAAGNSAGPK 70.316 0.028013 538670000 76293 117040 94917 128140 141980 64924 155930 111160 110300 TRUE FALSE 71517.95732 125705.7634 97168.47606 131428.2893 130829.4635 83666.50485 132549.7441 125038.5707 91890.21743 0.778297835 1.367999412 1.05744092 1.430275094 1.423758341 0.910505026 1.442479382 1.360738653 1 16.48762366 4.746956089 24.63393203 1.256291221 0.778297539 0.365658217 0.194697597 910.477716 2671443.014 0.042154554 0.479726022 55841.37308 -4.746956089 -0.477993682 S(ph)RS(ph)PATAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SRSPATAK 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)RS(0.996)PAT(0.004)AK;S(0.995)RS(0.768)PAT(0.237)AK;S(0.999)RS(0.992)PAT(0.009)AK 105.2 0.0042928 1602680000 5602000 2595040 3603670 3492080 3105620 2625580 4162490 2842230 2743740 TRUE FALSE 5251380.82 2787179.462 3689150.754 3581692.685 2861717.133 3383542.323 3538363.267 3197088.672 2285792.069 2.297400928 1.21934952 1.613948532 1.566937227 1.251958641 1.480249393 1.547981251 1.398678697 1 21.12426274 8 0.040336076 1.72E-09 3.925923596 0.387629517 0.267907284 986.1299638 3.026991322 80.2566125 263.6542549 100000000 -8 3.925923594 S(ph)RS(ph)PESQVIGENTKQP ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSPESQVIGENTKQP 16 2 O95218-2 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 2 S(0.985)RS(0.989)PES(0.026)QVIGENTKQP;S(1)RS(1)PESQVIGENTKQP 158.02 5.61E-08 1648080000 737360 723970 707820 759430 828220 445240 876340 590050 1146220 TRUE FALSE 691209.9538 777573.4921 724609.8247 778918.2595 763174.9421 573773.5601 744940.9525 663719.0414 954908.4771 0.723849427 0.814291119 0.758826466 0.815699387 0.799212658 0.600867595 0.780117645 0.695060372 1 19.86500294 -0.986472722 5.104953297 1.000001647 0.754156509 0.595382386 0.06501103 0.003128639 42044240.83 161.6305926 0.014463344 0.103163787 0.986472722 -0.245845138 S(ph)RS(ph)PHEAGFCVYLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SRSPHEAGFCVYLK 14 1 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 2 S(1)RS(1)PHEAGFCVYLK;S(1)RS(1)PHEAGFCVYLK;S(1)RS(1)PHEAGFCVYLK;S(1)RS(1)PHEAGFCVYLK;S(1)RS(1)PHEAGFCVYLK 168.79 1.95E-06 1753316000 2638666 1924363 2215021 2121654 2216651 1577537 2574282 1727642 2550614 TRUE FALSE 2473516.605 2066844.839 2267562.344 2176099.234 2042564.172 2032946.323 2188292.313 1943341.907 2124900.046 1.164062569 0.972678617 1.067138357 1.024094869 0.961251884 0.956725624 1.029833058 0.914556857 1 21.01896355 4.743882216 24.69665167 0.997665526 1.164062652 0.606103419 0.04358722 344.1242657 1596964.588 0.010078701 0.085796068 55447.53142 -4.743882216 0.166397126 S(ph)RS(ph)PLAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 93.766 0.0061659 6310500000 573492 437503 463285 445765 478249 473020 625495 357241 559931 TRUE FALSE 537598.1594 469896.1773 474274.339 457204.0846 440689.2527 609573.1952 531707.8316 401843.3252 466474.8988 1.152469642 1.007334325 1.016719957 0.980125803 0.944722329 1.306765266 1.139842321 0.861446835 1 18.83143993 S(ph)RS(ph)PLDKDTYPPSASVVGASVGGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSPLDKDTYPPSASVVGASVGGHR 25 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 2 S(0.999)RS(0.999)PLDKDT(0.001)Y(0.001)PPSASVVGASVGGHR;S(0.983)RS(0.994)PLDKDT(0.006)Y(0.016)PPSASVVGASVGGHR 169.06 5.59E-12 2549400000 551970 573150 645720 617740 604820 442520 801070 506090 695240 TRUE FALSE 517423.183 615586.6224 661036.7833 633592.2542 557319.8769 570268.3403 680956.9903 569276.4505 579199.9526 0.893341204 1.062822294 1.141292882 1.093909368 0.962223623 0.984579397 1.175685508 0.98286688 1 19.14370196 S(ph)RS(ph)PLGFYVHLK ddPTM_SK-BR-3_Pertuzumab_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 98.227 0.0025478 180186000 355370 287426 289670 317020 339400 231266 273940 271268 331320 TRUE FALSE 333128.0261 308707.3201 296541.1092 325155.2699 312744.8931 298028.7399 232865.2401 305136.4069 276020.5516 1.206895733 1.118421503 1.074344311 1.178011087 1.133049301 1.079733876 0.843651818 1.105484375 1 18.07441616 1.967238635 11.11770166 0.964605079 1.129243261 0.491021265 0.072482445 0.681265461 229.3020231 0.027645444 0.017888594 92.73392358 -1.967238635 0.164638182 S(ph)RS(ph)PLLNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSPLLNDR 9 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(1)RS(1)PLLNDR;S(1)RS(1)PLLNDR 92.265 0.0058 449870000 483400 368560 408240 432170 374680 303690 431340 341600 317610 TRUE FALSE 453144.8569 395848.5659 417923.6456 443260.2139 345254.1442 391360.373 366664.5714 384249.512 264598.8392 1.71257311 1.496032889 1.579461372 1.675216019 1.304821084 1.479070635 1.385737642 1.452196514 1 18.01344721 -3.059801613 0.146038995 2.10E-13 1.718501826 0.764950942 0.097897306 31.71140276 0.479491145 10.39577029 0.551280588 0.000871362 3.059801613 1.718501826 S(ph)RS(ph)PPPVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SRSPPPVSK 9 1 Q01130;Q01130-2 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 2 S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK 88.282 0.0073344 23824830000 17705020 8802260 12363160 11121010 9223110 9717050 15928220 9551320 8532800 TRUE FALSE 16596894.4 9453988.489 12656419.99 11406393.94 8498764.145 12522204.59 13539931.28 10743823.33 7108620.556 2.334755987 1.329932919 1.78043263 1.60458613 1.195557433 1.761551977 1.904719935 1.511379492 1 22.7611382 4.750398554 24.20875072 1.572644611 2.334756709 0.442051283 0.283418653 1161.739336 2375704.121 0.06377678 1.021757201 56285.76251 -4.750398554 0.762112098 S(ph)RS(ph)PQWR ddPTM_SK-BR-3_Pertuzumab_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 89.9 0.0099767 1883530000 266005 274482 269802 271683 313431 223976 306517 221923 282551 TRUE FALSE 249356.2219 294804.9329 276201.8308 278654.8457 288815.3936 288634.2353 260557.6214 249630.5751 235391.4128 1.059325907 1.252403091 1.173372587 1.183793591 1.22695807 1.226188466 1.106912178 1.060491426 1 17.84470217 1.361993274 1.968330412 1.012113292 1.194043233 0.596447394 0.053605049 0.194384954 1.32211743 0.043642182 0.013287009 23.01406177 -1.361993274 0.181929941 S(ph)RS(ph)PT(ph)PPSSAGLGSNSAPPIPDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSPTPPSSAGLGSNSAPPIPDSR 24 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 3 S(1)RS(0.997)PT(0.956)PPS(0.022)S(0.025)AGLGSNSAPPIPDSR;S(0.98)RS(0.983)PT(0.774)PPS(0.205)S(0.057)AGLGSNSAPPIPDSR 136.08 1.95E-05 450360000 334042 281629 320256 314340 298413 225704 320184 235991 327201 TRUE FALSE 313134.9075 302481.1042 327852.6236 322406.4966 274976.8467 290861.0808 272175.3816 265454.9958 272589.0393 1.148743575 1.10965982 1.2027359 1.182756641 1.008759734 1.067031461 0.998482486 0.973828575 1 18.05636803 2.734073483 24.98869109 1.013392226 1.159381945 0.837287893 0.03312765 153.5817008 855288.2632 0.010918606 0.010618273 542.0926049 -2.734073483 0.145989719 S(ph)RS(ph)PTPPS(ph)SAGLGSNSAPPIPDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSPTPPSSAGLGSNSAPPIPDSR 24 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 3 S(0.95)RS(0.929)PT(0.268)PPS(0.666)S(0.187)AGLGSNSAPPIPDSR 101.39 0.0063654 359540000 113470 102000 110750 98786 106960 71834 116860 85369 124050 TRUE FALSE 106368.1152 109552.1861 113377.0423 101321.016 98559.79306 92571.30967 99337.92788 96027.50757 103345.2536 1.029250126 1.060060161 1.097070628 0.980412863 0.953694433 0.895748053 0.961223902 0.929191271 1 16.65711261 3.079282241 4.141727183 0.94423369 1.066299112 0.738135343 0.030907205 0.093432817 3.084663144 0.008708265 0.010479871 1200.279093 -3.079282241 0.122065422 S(ph)RS(ph)PTPPSS(ph)AGLGSNSAPPIPDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSPTPPSSAGLGSNSAPPIPDSR 24 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 3 S(0.987)RS(0.856)PT(0.187)PPS(0.443)S(0.526)AGLGSNSAPPIPDSR 134.96 5.26E-05 245450000 198520 171900 163310 185190 192960 137000 200540 135820 203510 TRUE FALSE 186094.9876 184627.6549 167183.7903 189942.2889 177805.7 176549.676 170470.8887 152777.426 169542.8663 1.097627943 1.088973302 0.986085667 1.120320147 1.048735956 1.041327659 1.005473674 0.901113856 1 17.37129056 1.574330263 2.754066039 0.950475683 1.060080426 0.535010822 0.043536882 0.179806236 3.080660349 0.02918431 0.011128985 37.52582623 -1.574330263 0.109604743 S(ph)RS(ph)PVDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSPVDLR 8 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(1)RS(1)PVDLR 57.836 0.061884 123780000 117990 87421 97457 97612 102750 76925 111580 81978 123100 TRUE FALSE 110605.2165 93893.7418 99768.72606 100116.8892 94680.42947 99131.99873 94849.61486 92213.13376 102553.8147 1.078509042 0.915555819 0.972842661 0.976237592 0.923226793 0.966633947 0.924876516 0.899168246 1 16.64602163 4.746537449 24.93736856 0.945496204 1.078509109 0.62729058 0.031752753 596.0406312 1863312.652 0.006944849 0.076434479 55787.57052 -4.746537449 0.133012906 S(ph)RS(ph)RS(ph)PPPVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SRSRSPPPVSK 11 2 Q01130;Q01130-2 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 3 S(1)RS(1)RS(1)PPPVSK;S(1)RS(0.999)RS(1)PPPVS(0.001)K;S(1)RS(1)RS(1)PPPVSK;S(1)RS(1)RS(1)PPPVSK 100.23 0.0027643 5966380000 9444100 5302360 7262410 6417380 5734320 4765230 7687270 4893960 5299580 TRUE FALSE 8853010.639 5694952.252 7434677.795 6582060.835 5283969.638 6140874.544 6534635.229 5504981.679 4415045.861 2.005191094 1.289896511 1.683941238 1.49082502 1.196809683 1.390897113 1.480083205 1.246868515 1 22.07399699 8 0.04377685 1.55E-10 3.901840765 0.528595075 0.190754328 561.3384874 1.864699225 42.97466486 156.0192811 99999999.99 -8 3.901840764 S(ph)RS(ph)RSPHEAGFCVYLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSRSPHEAGFCVYLK 16 2 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 2 S(0.667)RS(0.667)RS(0.667)PHEAGFCVYLK;S(0.667)RS(0.667)RS(0.667)PHEAGFCVYLK 87.02 0.003546 343220000 277780 316780 269350 302660 406630 162739 310400 266940 675410 TRUE FALSE 260394.2457 340234.7208 275739.1092 310426.768 374694.9201 209719.1075 263858.4016 300268.0466 562679.7077 0.462775256 0.604668546 0.490046301 0.551693555 0.665911557 0.372714894 0.468931788 0.533639373 1 19.10195441 0.930068243 21.14328977 1 0.518147546 0.780728608 0.080190079 3251.88406 983182.519 0.075573565 0.018893391 8.512717927 -0.930068243 -0.481852454 S(ph)RS(ph)RT(ph)PLISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSRTPLISR 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(1)RS(1)RT(0.997)PLIS(0.003)R 93.301 0.014212 1090800000 1119000 871800 935980 944620 1020000 605520 904590 722920 960000 TRUE FALSE 1048963.787 936348.9791 958181.8876 968860.5484 939893.3145 780323.7942 768955.1273 813178.1533 799769.7982 1.311582145 1.170773117 1.198072108 1.211424276 1.175204811 0.975685498 0.961470574 1.016765268 1 19.60922528 2.283351068 4.555230601 0.981259192 1.20823209 0.885992549 0.040174417 0.060241791 2.706011715 0.013874548 0.011125231 192.0220349 -2.283351068 0.226972898 S(ph)RS(ph)RT(ph)PLLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSRTPLLPR 10 2 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(1)RS(1)RT(1)PLLPR 80.632 0.037496 427510000 625050 555670 576930 544130 579590 355220 590330 391240 528780 TRUE FALSE 585929.2362 596812.385 590615.052 558093.297 534071.3394 457766.2475 501815.4969 440087.1752 440523.202 1.330075768 1.35478082 1.340712701 1.266887407 1.212356891 1.039142196 1.139135225 0.999010207 1 18.74885848 2.485884335 0.931293133 1.029058125 1.355524082 0.909777243 0.041733163 0.144961285 0.253421289 0.025901659 0.018615866 306.1148057 -2.485884335 0.326465957 S(ph)RS(ph)RTS(ph)PVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSRTSPVSR 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(0.999)RS(0.965)RT(0.234)S(0.789)PVS(0.014)R 53.631 0.094003 122900000 157400 138260 146780 157410 171150 88802 141460 113480 193270 TRUE FALSE 147548.615 148496.9143 150261.6909 161449.4071 157708.5694 114437.6958 120249.3863 127648.2278 161011.9884 0.916382789 0.922272408 0.933232937 1.002716684 0.979483397 0.710740218 0.746834987 0.792787103 1 17.29680859 2.247371414 24.99985848 0.783824603 0.946886259 0.396686839 0.081256828 146.1724245 414751.4363 0.025876333 0.021346019 176.7548804 -2.247371414 0.163061656 S(ph)RSDIDVNAAAGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SRSDIDVNAAAGAK 14 1 E3W994;J3KR49;O75122;A0A0U1RQI6;B3KR06;E7ENG2;O75122-2;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 S(0.5)RS(0.5)DIDVNAAAGAK;S(0.5)RS(0.5)DIDVNAAAGAK;S(0.5)RS(0.5)DIDVNAAAGAK;S(0.5)RS(0.5)DIDVNAAAGAK 199.81 1.22E-08 2865590000 3742580 3604220 3536800 3646880 4000610 2589710 4990210 3546530 5352350 TRUE FALSE 3508338.598 3871080.199 3620694.566 3740465.115 3686418.228 3337317.237 4241974.337 3989322.077 4459008.207 0.786797968 0.868148256 0.811995493 0.838855849 0.826735017 0.748443843 0.951326874 0.894665785 1 22.08829142 1.656041506 7.813951825 0.942480605 0.821391361 0.706215398 0.040742151 0.067849696 7.664358732 0.01869696 0.009666673 45.29408663 -1.656041506 -0.121089243 S(ph)RSDIDVNAAASAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SRSDIDVNAAASAK 14 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 S(0.5)RS(0.5)DIDVNAAASAK;S(0.5)RS(0.5)DIDVNAAASAK;S(0.5)RS(0.5)DIDVNAAASAK 187.73 5.54E-07 1632570000 2820950 2791450 2902170 2947740 3391840 2050380 3690020 2958100 4464680 TRUE FALSE 2644391.775 2998131.863 2971010.843 3023383.999 3125458.568 2642291.421 3136735.757 3327425.297 3719496.065 0.710954314 0.806058619 0.798767035 0.812847748 0.840290866 0.710389627 0.843322779 0.894590353 1 21.82667574 1.069093658 1.858473504 0.997271682 0.788579823 0.729738726 0.043621735 0.160509431 1.1117395 0.037551348 0.010730204 11.72448184 -1.069093658 -0.208691859 S(ph)RSESETSTMAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSESETSTMAAK 13 1 Q96B23-2;Q96B23;A0A087WVF1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 S(0.386)RS(0.386)ES(0.227)ETSTMAAK;S(0.429)RS(0.429)ES(0.141)ET(0.001)STMAAK 149.47 6.64E-05 873840000 879810 745990 792270 873700 1098410 676910 1008690 753100 1094250 TRUE FALSE 824744.2626 801223.8758 811063.0185 896120.6212 1012145.309 872322.9283 857446.2987 847126.1928 911612.6059 0.904709147 0.878908289 0.889701407 0.983005956 1.110280072 0.956900906 0.94058188 0.929261166 1 19.79806135 3.238669952 8.23095537 0.984511351 0.888139636 0.451119533 0.049623764 0.107402158 63.41217847 0.014720458 0.018751406 1732.486871 -3.238669952 -0.096371715 S(ph)RSGEGEVSGLMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SRSGEGEVSGLMR 13 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 S(0.657)RS(0.343)GEGEVSGLMR;S(0.5)RS(0.5)GEGEVSGLMR;S(0.5)RS(0.5)GEGEVSGLMR;S(0.5)RS(0.5)GEGEVSGLMR 186.97 4.45E-06 1953450000 1165590 1450120 1171450 1266810 1351420 746340 1022390 1028810 1512010 TRUE FALSE 1092637.803 1557488.394 1199237.347 1299318.489 1245284.925 961796.2422 869092.1109 1157259.193 1259645.763 0.867416725 1.236449516 0.95204333 1.031495145 0.988599304 0.763545014 0.689949616 0.918717966 1 20.26458665 2.346877882 4.425196273 0.802123496 1.042814803 0.285996559 0.126506251 0.191230973 6.537080528 0.043108528 0.035366956 222.2684814 -2.346877882 0.240691307 S(ph)RSGQAGYVPCNILGEARPEDAGAPFEQAGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSGQAGYVPCNILGEARPEDAGAPFEQAGQK 32 2 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 S(0.34)RS(0.34)GQAGY(0.32)VPCNILGEARPEDAGAPFEQAGQK 51.025 0.037684 68014000 15903 17437 15582 16090 17093 15020 17038 13067 17546 TRUE FALSE 14907.65962 18728.05362 15951.6124 16502.89664 15750.58473 19356.03017 14483.31007 14698.44371 14617.45925 1.019852997 1.281211277 1.091271207 1.128985302 1.077518635 1.324171995 0.990822675 1.005540256 1 13.83540495 1.609540935 25 0.998619645 1.157434843 0.394297976 0.090514616 0.154756385 2247.821015 0.040465769 0.020955737 40.69498894 -1.609540935 0.158815198 S(ph)RSGSSQELDVKPSASPQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSGSSQELDVKPSASPQER 20 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.312)RS(0.312)GS(0.312)S(0.063)QELDVKPSASPQER 116.44 4.95E-05 145680000 86928 74946 79097 90121 90807 64584 93262 76903 121810 TRUE FALSE 81487.33165 80495.07982 80973.21819 92433.65743 83675.38452 83228.35237 79278.2289 86504.50883 101479.1241 0.802996009 0.793218118 0.79792981 0.910863769 0.824557615 0.820152451 0.781226973 0.852436495 1 16.63082345 0.92991892 8.62994088 0.999999826 0.815782886 0.71786142 0.035468642 1.32382813 163.1034944 0.034581164 0.008655718 8.509791511 -0.92991892 -0.184216939 S(ph)RSHSDNDRPNCSWNTQYSSAYYTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SRSHSDNDRPNCSWNTQYSSAYYTSR 26 2 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.887)RS(0.07)HS(0.043)DNDRPNCSWNTQYSSAYYTSR;S(0.485)RS(0.485)HS(0.03)DNDRPNCSWNTQYSSAYYTSR;S(0.267)RS(0.267)HS(0.267)DNDRPNCS(0.19)WNT(0.009)QYSSAYYTSR;S(0.459)RS(0.459)HS(0.081)DNDRPNCS(0.001)WNTQYSSAYYTSR 318.55 2.53E-82 2795620000 306264 446278 386434 422720 472164 309047 471457 431032 659757 TRUE FALSE 287095.4829 479320.8875 395600.397 433567.7109 435082.1441 398263.8519 400766.3996 484847.294 549639.2945 0.522334349 0.872064447 0.719745478 0.788822261 0.791577583 0.724591302 0.729144375 0.882119053 1 19.06812562 -5 0.203398008 2.134464675 0.720689903 0.457058269 0.092939543 137.3580015 1.363748743 63.18103522 0.197554663 1.00E-05 5 -1.413774771 S(ph)RSHTSEGAHLDITPNSGAAGNSAGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SRSHTSEGAHLDITPNSGAAGNSAGPK 27 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 S(0.346)RS(0.218)HT(0.218)S(0.218)EGAHLDITPNSGAAGNSAGPK;S(0.249)RS(0.249)HT(0.249)S(0.249)EGAHLDIT(0.003)PNSGAAGNSAGPK;S(0.31)RS(0.229)HT(0.229)S(0.229)EGAHLDIT(0.003)PNSGAAGNSAGPK;S(0.245)RS(0.245)HT(0.245)S(0.245)EGAHLDIT(0.02)PNSGAAGNSAGPK 184.82 7.76E-18 4340990000 679410 1776340 1412250 1870560 2047480 896600 1845400 1620920 1043440 TRUE FALSE 636886.9409 1907862.062 1445749.237 1918561.736 1886679.18 1155433.865 1568699.402 1823295.43 869283.1231 0.732657662 2.194753368 1.663151163 2.207061986 2.170385148 1.329180142 1.804589736 2.097470182 1 19.72946661 -1.123074806 4.497927064 0.999936053 1.807059817 0.213999124 0.463090617 21.8036545 123886714 22948.5563 0.096737785 0.075322581 1.123074806 0.807123764 S(ph)RSIDKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSIDKDR 8 2 Q8TF01 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 S(0.5)RS(0.5)IDKDR 74.76 0.020947 51810000 78144 80796 81949 86493 95637 90202 81548 77426 106680 TRUE FALSE 73253.10653 86778.21991 83892.86898 88712.55681 88126.0558 116241.8531 69320.63445 87092.80654 88874.41882 0.824231624 0.976413923 0.94394844 0.998178756 0.991579545 1.307933764 0.77998411 0.979953598 1 16.4394806 5.679087365 1.037158824 0.995560768 1.02E-09 0.150334333 0.128149934 22.74702226 4.558438523 0.036000656 39.76347594 477625.3457 -5.679087365 -0.995560767 S(ph)RSKDSVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSKDSVPK 9 2 O15014 O15014 ZNF609 Zinc finger protein 609 1 S(0.623)RS(0.371)KDS(0.006)VPK 56.729 0.062628 616780000 1723700 737300 948290 895680 1030900 646220 1112600 840230 1341100 TRUE FALSE 1615816.694 791890.4592 970783.8866 918664.6652 949937.2725 832773.2235 945775.9589 945134.5651 1117261.746 1.446229319 0.708777922 0.868895664 0.822246594 0.850236997 0.745369853 0.846512433 0.845938356 1 20.09153578 4.745027455 24.99876888 0.823382225 1.446229598 0.858714394 0.07763996 230.5477188 891201.5173 0.016282404 0.155870806 55593.94014 -4.745027455 0.622847373 S(ph)RSPAPPADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSPAPPADK 10 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.614)RS(0.386)PAPPADK 82.651 0.010521 516730000 573420 396920 477690 437770 438630 385590 553930 425250 384630 TRUE FALSE 537530.6658 426308.3698 489021.0324 449003.9193 404181.7691 496903.5735 470873.3389 478343.3986 320432.7682 1.677514659 1.330414402 1.526126791 1.401242207 1.261362162 1.550726464 1.469491843 1.492804251 1 18.28966216 -1.151780229 4.790614683 0.999960736 1.454474877 0.610798263 0.116121105 4.38E-05 7.75E-06 0.101106196 0.023828905 0.070504976 1.151780229 0.454514141 S(ph)RSPAPPADKEAEKPVFFPAFAAEAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSPAPPADKEAEKPVFFPAFAAEAQK 27 3 C9J0Q5;C9JE98 C9J0Q5 NCOR2 1 S(0.557)RS(0.443)PAPPADKEAEKPVFFPAFAAEAQK 86.195 0.045567 260650000 643830 372220 426740 471370 495460 302060 592250 393880 599220 TRUE FALSE 603533.8296 399779.5561 436862.4743 483466.1522 456548.5702 389259.8185 503447.6107 443056.785 499206.3109 1.208986778 0.800830333 0.875114086 0.968469632 0.914548875 0.779757407 1.008496086 0.887522404 1 18.92927665 0.207408722 0.943956993 1.000387131 0.91269754 0.010821397 0.121396246 13.90147616 13.50442281 0.12875556 0.034535736 1.612162155 -0.207408722 -0.087689591 S(ph)RSPATAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SRSPATAK 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.594)RS(0.406)PATAK;S(0.816)RS(0.184)PATAK;S(0.5)RS(0.5)PATAK;S(0.619)RS(0.381)PATAK;S(0.641)RS(0.359)PATAK 103.08 0.0029317 2551560000 2520230 1665560 2130950 1896050 1840360 1493050 1976490 1780850 2903060 TRUE FALSE 2362493.303 1788879.795 2181497.14 1944705.853 1695825.549 1924069.297 1680133.673 2003193.043 2418520.532 0.97683409 0.739658718 0.901996535 0.80408904 0.701183028 0.795556321 0.694694815 0.828272085 1 21.20569335 4.749705382 24.2607406 0.794617714 0.976834252 0.236973467 0.09229808 1447.770809 3151522.197 0.020255544 0.303210567 56195.99711 -4.749705382 0.182216537 S(ph)RSPES(ph)QVIGENTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSPESQVIGENTK 14 1 O95218-2 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 2 S(0.987)RS(0.013)PES(0.996)QVIGENT(0.004)K;S(0.933)RS(0.067)PES(0.999)QVIGENT(0.001)K 259.55 2.40E-23 423750000 3593300 1975190 2389400 2348500 2236600 1526600 2824200 1811130 1805520 TRUE FALSE 3368401.767 2121435.123 2446077.696 2408766.486 2060946.458 1967304.638 2400737.429 2037253.567 1504167.048 2.239380109 1.410372023 1.626200826 1.601395596 1.370157963 1.307903029 1.59605772 1.35440646 1 20.52053337 8 0.079146195 0.658706524 3.73845579 0.575614024 0.207727821 167.0672356 0.964313279 5.72681458 56.35039047 100000000 -8 3.079749266 S(ph)RSPIIHS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSPIIHSPK 10 1 E9PQ01;E9PKN0;O94913 E9PQ01 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 2 S(0.611)RS(0.478)PIIHS(0.91)PK 65.477 0.039177 552520000 1595100 917440 1124700 1079400 1336100 959140 1436900 1085900 1450400 TRUE FALSE 1495265.538 985368.2122 1151378.415 1107099.231 1231168.096 1236028.148 1221450.185 1221477.005 1208318.87 1.237475947 0.815486902 0.952876301 0.916231021 1.01890993 1.02293209 1.010867425 1.010889622 1 20.2045698 2.722081888 23.31885548 1.014020227 0.948405564 0 0.106772805 870.7231101 1232146.588 0.032054249 0.030323492 527.3292817 -2.722081888 -0.065614663 S(ph)RSPITTNHRPS(ph)PDPEQRPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSPITTNHRPSPDPEQRPLR 21 3 P41212 P41212 ETV6 Transcription factor ETV6 2 S(0.5)RS(0.5)PIT(0.01)T(0.162)NHRPS(0.827)PDPEQRPLR 87.739 0.0036752 282380000 47187 43804 44431 44396 52406 44898 56612 42189 59389 TRUE FALSE 44233.6499 47047.29374 45484.9243 45535.27652 48290.24416 57859.32374 48123.55616 47456.38952 49476.59223 0.894031862 0.950900044 0.919322093 0.92033979 0.976022033 1.169428231 0.972653006 0.959168515 1 15.59445852 2.475368725 24.99700459 1.02909663 0.92804047 0.413567443 0.058147181 55.1833315 787076.9919 0.019185598 0.016156295 298.7918346 -2.475368725 -0.10105616 S(ph)RSPITTNHRPSPDPEQRPLR ddPTM_SK-BR-3_Pertuzumab_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(0.499)RS(0.499)PIT(0.001)T(0.001)NHRPSPDPEQRPLR 108.44 0.00022807 767980000 246238 270420 271624 265709 261406 229051 276549 231457 254782 TRUE FALSE 230826.4031 290442.1782 278067.0496 272527.5428 240876.2272 295174.3054 235083.0448 260354.9159 212257.2382 1.087484248 1.368349935 1.31004743 1.283949349 1.134831628 1.390644238 1.107538413 1.226600883 1 17.69545423 0.711976975 0.573964312 0.994678997 1.283475125 0.337474478 0.104617058 1.241892386 0.847483837 0.112473108 0.043335652 5.15201329 -0.711976975 0.288796129 S(ph)RSPLDKDTYPPSASVVGASVGGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSPLDKDTYPPSASVVGASVGGHR 25 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 S(0.639)RS(0.361)PLDKDTYPPSASVVGASVGGHR;S(0.5)RS(0.5)PLDKDT(0.001)YPPSASVVGASVGGHR 250.25 9.02E-40 518940000 390890 562300 626230 660830 615630 483470 781930 572220 733800 TRUE FALSE 366424.8927 603933.2771 641084.4713 677788.0166 567280.9031 623039.9405 664686.8556 643662.9266 611324.0395 0.599395523 0.987910238 1.048681926 1.108721354 0.927954516 1.019164797 1.087290557 1.052899747 1 19.22157777 4.756250368 3.144036063 1.03662049 0.523724288 0.884043231 0.049171531 0.119766861 1.774603752 0.011739264 0.154974125 57049.30636 -4.756250368 -0.512896202 S(ph)RSPLHPMSEIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSPLHPMSEIPR 13 1 Q9NVW2-2;Q9NVW2 Q9NVW2-2 RLIM E3 ubiquitin-protein ligase RLIM 1 S(0.628)RS(0.372)PLHPMSEIPR;S(0.5)RS(0.5)PLHPMSEIPR 105.06 0.00089789 430190000 179970 234489 235354 229360 254690 192120 253390 205890 235018 TRUE FALSE 168705.999 251850.8095 240936.708 235245.7659 234687.6748 247581.9252 215396.5219 231595.8197 195791.9775 0.861659405 1.28631833 1.230574976 1.201508708 1.198658279 1.264515167 1.100129457 1.182866748 1 17.57896213 0.462320492 0.929495136 0.999961663 1.190375101 0.132369856 0.121191864 3.098673389 3.785302527 0.109916986 0.03485033 2.899482502 -0.462320492 0.190413438 S(ph)RSPLLVTVVESDPRPQGQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSPLLVTVVESDPRPQGQPR 21 2 A0A2R8YH03;Q5VWN6;Q5VWN6-2 A0A2R8YH03 FAM208B Protein FAM208B 1 S(0.5)RS(0.5)PLLVTVVESDPRPQGQPR;S(0.599)RS(0.401)PLLVTVVESDPRPQGQPR 100.28 0.00037172 1028540000 494830 480630 492780 491620 509580 408760 576080 435400 530290 TRUE FALSE 463859.4736 516216.3453 504468.9743 504235.8015 469559.6423 526762.3763 489702.1521 489760.6484 441781.1732 1.049975648 1.168488783 1.141897856 1.141370054 1.062878345 1.1923604 1.108472207 1.108604617 1 18.75297241 0.650590926 1.628051596 1.000112235 1.131232015 0.434670393 0.043486023 1.165141201 4.300550407 0.037272189 0.010650454 4.472917891 -0.650590926 0.13111978 S(ph)RSPNRFDAHDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SRSPNRFDAHDPR 13 2 Q96T58;A0A669KB49;F6WRY4 Q96T58 SPEN Msx2-interacting protein 1 S(0.5)RS(0.5)PNRFDAHDPR;S(0.5)RS(0.5)PNRFDAHDPR;S(0.5)RS(0.5)PNRFDAHDPR;S(0.5)RS(0.5)PNRFDAHDPR 74.12 0.018249 6619330000 3059570 3672640 3482530 3458660 3850950 2694720 3702660 3293640 5182170 TRUE FALSE 2868076.975 3944566.087 3565137.256 3547415.071 3548511.921 3472641.919 3147480.507 3704858.204 4317232.349 0.664332318 0.913679359 0.825792306 0.821687318 0.821941381 0.804367622 0.729050524 0.858155852 1 22.04167531 0.980723361 23.68587447 1.000000004 0.808586165 0.482318318 0.065695864 632.8910408 777656.9755 0.061913491 0.015478373 9.565845469 -0.980723361 -0.19141384 S(ph)RSPPPVS(ph)K ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSPPPVSK 9 1 Q01130;Q01130-2 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 2 S(0.996)RS(0.062)PPPVS(0.942)K 112.44 0.023466 4834700000 4038200 2235500 2938300 2435600 2161400 2287400 3829000 2094200 1932300 TRUE FALSE 3785456.27 2401018.746 3007997.864 2498101.619 1991652.363 2947735.247 3254876.997 2355665.48 1609786.647 2.351526693 1.491513643 1.868569272 1.551821556 1.23721511 1.831134115 2.021930672 1.463340179 1 20.61843806 4.745725599 24.5208272 1.634584505 2.351527135 0.373346185 0.309239435 752.6084763 2575578.538 0.069831083 0.704655707 55683.3813 -4.745725599 0.71694263 S(ph)RSPPPVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSPPPVSK 9 1 Q01130;Q01130-2 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 S(0.5)RS(0.5)PPPVSK;S(0.5)RS(0.5)PPPVSK 55.776 0.076472 514890000 581780 414670 532220 418510 468740 560410 557560 580030 1890310 TRUE FALSE 545367.4283 445372.5983 544844.5097 429249.6751 431927.0512 722191.2695 473959.0541 652448.0223 1574805.049 0.346307899 0.282811259 0.345975846 0.272573215 0.274273347 0.458590903 0.300963636 0.414303994 1 20.58674181 -1.274658805 0.451544636 1.325716616 0.307544615 0.937901298 0.054088594 4.914762016 0.553371391 1.975320945 0.026360359 0.053130169 1.274658805 -1.018172002 S(ph)RSPQWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSPQWR 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.65)RS(0.35)PQWR 93.598 0.0089738 511590000 99686 104730 122830 104160 111210 129100 146930 96763 165650 TRUE FALSE 93446.8312 112484.3182 125743.5856 106832.9219 102476.0152 166369.0742 124899.2105 108844.0736 138001.9449 0.677141408 0.815092268 0.911172562 0.774140698 0.742569355 1.205556012 0.905053988 0.788714055 1 17.07432907 S(ph)RSPSDSAAYFCIYTYPR ddPTM_SK-BR-3_Pertuzumab_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(0.498)RS(0.498)PS(0.003)DSAAYFCIYTYPR 94.542 0.0011776 93854000 70713 53855 59488 65900 79846 46664 83638 70346 134750 TRUE FALSE 66287.19956 57842.48024 60899.08345 67591.10557 73575.21724 60135.13927 71097.25836 79128.85295 112259.3545 0.590482636 0.515257553 0.542485602 0.602097757 0.655403887 0.53568043 0.633330369 0.70487536 1 16.77647614 -0.042723868 0.43260723 1.065680128 0.544099545 0.913625858 0.040851338 1.198601062 0.283935478 0.171217227 0.024904246 0.906308666 0.042723868 -0.521580583 S(ph)RT(ph)PDRER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRTPDRER 8 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 2 S(1)RT(1)PDRER 59.57 0.033512 0 99800 59804 67360 83541 89383 55014 74267 59409 69379 TRUE FALSE 93553.69615 64231.95039 68957.81101 85684.80349 82363.21973 70895.64872 63131.35281 66826.34443 57799.19669 1.618598553 1.111294863 1.193058294 1.48245665 1.424989004 1.226585364 1.092253118 1.156181197 1 15.81876182 1.879565808 3.448738763 1.093718546 1.313804212 0.401365979 0.150249569 0.324820021 6.540848272 0.079127541 0.042925327 75.78195556 -1.879565808 0.220085666 S(ph)RT(ph)SVQTEDDQLIAGQSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 2 S(0.848)RT(0.848)S(0.304)VQTEDDQLIAGQSAR 181.11 7.37E-14 276070000 71877 67620 80622 71348 72313 60525 66065 62697 74093 TRUE FALSE 67378.34687 72626.65516 82534.39191 73178.91047 66633.82868 77997.58496 56159.16657 70524.85846 61726.39964 1.091564505 1.176589848 1.337100372 1.185536673 1.07950292 1.263601723 0.909807909 1.142539641 1 15.91360002 1.746647138 25 1.015347183 1.20030022 0.428419481 0.092777489 1.595591959 4945.629933 0.04168892 0.023118679 55.80166247 -1.746647138 0.184953037 S(ph)RTASGSSVTSLDGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRTASGSSVTSLDGTR 16 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 S(0.492)RT(0.492)AS(0.015)GSSVTSLDGTR;S(0.478)RT(0.478)AS(0.043)GS(0.001)SVTSLDGTR 185.06 1.04E-09 462115000 265328 341362 222232 230547 368804 101846 328242 273091 271160 TRUE FALSE 248721.5941 366636.7977 227503.448 236463.2263 339839.6215 131247.2869 279025.1593 307187.0125 225901.6442 1.101017192 1.622993046 1.007090713 1.046753011 1.504369845 0.580993057 1.235162145 1.359826368 1 17.78533525 3.871567323 5.691077691 1.105362241 1.386654209 0.129980725 0.274422921 0.350397476 15.93042744 0.064591789 0.11868129 7439.903859 -3.871567323 0.281291968 S(ph)RTGS(ph)ESSQTGTSTTSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 S(0.5)RT(0.5)GS(0.911)ES(0.087)S(0.002)QTGTSTTSSR 153.57 1.84E-08 175800000 67208 78040 73494 88851 88157 61747 62478 50610 51542 TRUE FALSE 63001.57125 83818.1628 75237.31239 91131.06708 81233.50483 79572.35652 53110.00392 56928.76991 42939.30723 1.467223747 1.952014791 1.752178068 2.122322715 1.891821505 1.853135546 1.236862151 1.32579619 1 15.39001129 1.714084449 4.216117321 1.196360061 1.858088908 0.73855453 0.182720961 0.086605568 3.564003073 0.091582286 0.044681584 51.77074906 -1.714084449 0.661728846 S(ph)RTGSESSQTGTSTTSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.49)RT(0.49)GS(0.02)ESSQTGTSTTSSR;S(0.498)RT(0.498)GS(0.004)ESSQTGTSTTSSR;S(0.499)RT(0.499)GS(0.002)ESSQTGTSTTSSR 191.5 1.35E-14 1536290000 64929 81195 76729 85449 94763 63840.8 77133 66276.8 80555 TRUE FALSE 60865.20979 87206.76228 78549.04811 87641.766 87320.69624 82270.60259 65567.62272 74551.60437 67109.85009 0.906948976 1.299462928 1.170454829 1.305944893 1.301160651 1.225909497 0.977019359 1.110889151 1 16.03423691 1.75633392 13.02443074 1.033769705 1.217180423 0.307256052 0.120425459 0.253453039 180.8645825 0.051540039 0.028372191 57.06028285 -1.75633392 0.183410718 S(ph)RTHS(ph)TSSSLGSGESPFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRTHSTSSSLGSGESPFSR 19 1 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 2 S(0.582)RT(0.419)HS(0.964)T(0.031)S(0.004)SSLGSGESPFSR;S(0.579)RT(0.421)HS(0.803)T(0.193)S(0.004)SSLGSGESPFSR 131.13 9.22E-06 523560000 299500 389120 356810 430100 534860 292150 427010 410630 538800 TRUE FALSE 280754.8296 417930.8497 365273.7017 441137.0942 492854.2531 376488.9623 362983.8147 461898.0594 448870.7992 0.625469133 0.931071592 0.813761337 0.982770755 1.097986891 0.838746835 0.808659898 1.029022294 1 18.77594072 4.740289772 24.69031358 0.916765112 0.625469016 0.493606333 0.09736292 120.5406157 1721008.009 0.023274056 0.1491936 54990.76634 -4.740289772 -0.291296095 S(ph)RTPPSAPSQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SRTPPSAPSQSR 12 1 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.5)RT(0.5)PPSAPSQSR;S(0.5)RT(0.5)PPSAPSQSR;S(0.5)RT(0.5)PPSAPSQSR 69.431 0.030277 4989460000 830881 846640 925433 915833 902391 687439 943221 732967 1004521 TRUE FALSE 778877.6414 909326.1065 947384.7078 939334.8253 831520.8509 885891.4797 801793.7675 824479.5434 836859.9556 0.930714436 1.086592924 1.132070786 1.122451635 0.993620074 1.05858988 0.958097902 0.985206112 1 19.67462669 2.244829798 1.597539787 0.982851343 1.078426527 0.19464229 0.061482093 0.474447934 2.401242829 0.032992344 0.020206964 175.723481 -2.244829798 0.095575184 S(ph)RTPS(ph)ASNDDQQE ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRTPSASNDDQQE 13 1 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 2 S(0.953)RT(0.047)PS(1)ASNDDQQE;S(0.994)RT(0.006)PS(0.963)AS(0.037)NDDQQE 175.7 0.0002131 174285000 246880 280640 307150 416090 478030 158339 154237 126647 212820 TRUE FALSE 231428.2215 301418.8776 314435.743 426767.5738 440487.4521 204048.8989 131110.5937 142459.1567 177298.9671 1.305299321 1.700059975 1.773477579 2.407050536 2.484433267 1.150874718 0.739488762 0.803496823 1 17.43582461 2.058137955 6.723375443 0.848563065 1.899979051 0.690018448 0.341091083 0.123565882 11.19141198 0.13647024 0.099945833 114.3241432 -2.058137955 1.051415986 S(ph)RTPSASNDDQQE ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRTPSASNDDQQE 13 1 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 S(0.642)RT(0.356)PS(0.001)ASNDDQQE 91.789 0.016759 120840000 59027 66393 65376 56733 66674 54460 79403 52148 78791 TRUE FALSE 55332.60544 71308.8068 66926.74959 58188.86483 61437.69299 70181.71792 67497.25729 58658.79259 65640.27309 0.842967325 1.086357558 1.01959889 0.886481151 0.935975585 1.069186867 1.028290318 0.893640289 1 16.00229362 1.254645842 24.99024865 0.946820073 0.996659837 0.003105387 0.081603413 657.975957 1022249.481 0.053480806 0.0193978 17.9740457 -1.254645842 0.049839765 S(ph)RTS(ph)PAPWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SRTSPAPWK 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.954)RT(0.431)S(0.615)PAPWK;S(0.978)RT(0.069)S(0.952)PAPWK;S(0.973)RT(0.105)S(0.922)PAPWK;S(0.99)RT(0.032)S(0.978)PAPWK;S(0.995)RT(0.006)S(1)PAPWK;S(1)RTS(1)PAPWK 153.75 0.00092461 7055400000 17743400 12570400 15280400 14212100 14363500 10290190 17561000 12313600 13444500 TRUE FALSE 16632872.27 13501125.5 15642858.3 14576806.55 13235448.65 13260800.81 14927891.08 13850980.07 11200526.1 1.485008126 1.205401012 1.396618174 1.301439452 1.18168098 1.183944459 1.332784813 1.23663656 1 23.41706316 -4.999999993 0.143749131 1.13E-09 1.387892927 0.565418036 0.087710968 106.5928239 0.928772378 30.55164296 0.478772681 1.00E-05 4.999999993 1.387892926 S(ph)RTS(ph)PITR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRTSPITR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.611)RT(0.555)S(0.833)PIT(0.001)R;S(0.649)RT(0.361)S(0.99)PITR 66.023 0.03571 1361110000 90078 70018 64353 86260 73216 49006 78684 64620 75028 TRUE FALSE 84440.17877 75202.20557 65879.48355 88473.57764 67465.9107 63153.23665 66886.06467 72687.94925 62505.3421 1.350927392 1.203132453 1.053981649 1.415456258 1.079362314 1.010365427 1.070085571 1.16290779 1 15.93169188 2.513724953 24.90429902 1.062512467 1.216832729 0.428044416 0.105884923 629.6347995 428387.9626 0.033636207 0.031702782 326.3810634 -2.513724953 0.154320262 S(ph)RTS(ph)PVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SRTSPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.922)RT(0.09)S(0.989)PVSR;S(0.559)RT(0.442)S(0.998)PVS(0.001)R;S(0.879)RT(0.132)S(0.964)PVS(0.025)R 77.358 0.019016 577990000 132609 114097 137840 143328 127426 115922 128990 106277 127433 TRUE FALSE 124309.2394 122544.8606 141109.6299 147006.0391 117418.476 149386.7996 109649.147 119545.9174 106163.6091 1.170921378 1.154301947 1.329171372 1.384712148 1.106014359 1.407137539 1.032831758 1.12605363 1 16.6959298 1.646876002 9.31270985 1.059701961 1.253255641 0.472035851 0.102189624 0.099513515 15.83341938 0.046538517 0.024581814 44.34820044 -1.646876002 0.19355368 S(ph)RTS(ph)PVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SRTSPVTR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.887)RT(0.116)S(0.994)PVT(0.002)R;S(0.96)RT(0.046)S(0.995)PVTR;S(0.731)RT(0.271)S(0.998)PVTR 92.295 0.0067593 6946900000 516040 543750 447653 501110 490177 498728 496600 511524 562920 TRUE FALSE 483741.9776 584009.8158 458271.5406 513969.331 451680.4757 642702.6774 422139.4402 575388.8974 468965.0154 1.031509732 1.245316381 0.977197713 1.095965187 0.963143221 1.370470411 0.90015124 1.226933521 1 18.83912078 3.976782294 24.99957331 1.073401098 1.148381472 0.029056203 0.146136171 51.57845908 3804765.684 0.032540637 0.063751399 9479.43152 -3.976782294 0.074980374 S(ph)RTSPITR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRTSPITR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.648)RT(0.219)S(0.133)PITR 83.397 0.011016 1541900000 134980 167520 144820 200750 143410 159560 188230 127420 162750 TRUE FALSE 126531.8427 179923.3551 148255.1988 205901.5849 132147.1571 205622.3818 160006.6589 143328.6675 135585.9736 0.933222216 1.327005665 1.09344053 1.51860535 0.974637373 1.516546117 1.18011218 1.057105419 1 17.04884841 1.240343729 4.070866221 1.015465682 1.234104786 0.144122067 0.19686914 0.34724891 11.67044255 0.147184911 0.042846966 17.39176783 -1.240343729 0.218639104 S(ph)RTSPVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRTSPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.482)RT(0.259)S(0.259)PVSR;S(0.572)RT(0.283)S(0.146)PVSR 87.568 0.0092245 2258400000 273830 312830 311200 360070 285910 296510 332450 254640 297540 TRUE FALSE 256691.4691 335992.2587 318581.811 369310.0058 263455.7819 382107.6236 282602.2088 286432.3645 247878.6518 1.03555295 1.355470736 1.28523295 1.489882259 1.062841757 1.541510819 1.140082886 1.155534623 1 17.9192745 1.21196726 1.9053654 1.01999248 1.298620366 0.240797752 0.163177902 0.390011387 2.519337543 0.131761435 0.038364084 16.29173212 -1.21196726 0.278627886 S(ph)RTSVQTEDDQLIAGQSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 1 S(0.502)RT(0.249)S(0.249)VQTEDDQLIAGQSAR;S(0.364)RT(0.364)S(0.272)VQTEDDQLIAGQSAR 247.73 4.73E-25 250610000 214862 222002 234770 206584 256160 206039 201328 180791 222740 TRUE FALSE 201414.171 238439.2591 240338.8553 211885.2952 236042.2269 265519.1145 171140.7354 203363.1543 185563.255 1.085420553 1.284948677 1.295185597 1.14184942 1.272031076 1.430881962 0.922277071 1.095923621 1 17.50155153 1.702766546 9.994537646 1.009602739 1.256944278 0.569316153 0.100497454 0.076812021 15.01389809 0.044513704 0.024037565 50.43900906 -1.702766546 0.247341538 S(ph)RVFDLQFSTDSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRVFDLQFSTDSPR 14 1 C9J470;E9PHA2;Q15003;C9JZP1 C9J470 NCAPH Condensin complex subunit 2 1 S(1)RVFDLQFSTDSPR 73.448 0.021685 156160000 70374 72982 83440 78363 102530 81123 82492 81095 106140 TRUE FALSE 65969.41696 78385.66322 85419.2362 80373.92725 94477.70739 104541.8932 70123.09042 91219.88926 88424.54831 0.746053197 0.886469478 0.966012695 0.908954909 1.06845564 1.18227229 0.793027409 1.031612725 1 16.43215932 5.602928339 0.728211769 0.989560671 0.085124016 0.395537509 0.100114829 9.734694351 1.548467901 0.036084012 9.661067387 400800.5779 -5.602928339 -0.904436655 S(ph)RYMELYDLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRYMELYDLNR 11 1 J3QKP7;J3QLW0;H3BRL0;Q9BXC9 J3QKP7 BBS2 Bardet-Biedl syndrome 2 protein 1 S(0.389)RY(0.306)MELY(0.306)DLNR 79.693 0.040117 1334700000 411790 392540 443370 402390 459810 406130 480440 423500 549240 TRUE FALSE 386016.799 421604.07 453886.9458 412716.0086 423698.3774 523373.138 408402.4822 476374.9072 457568.2958 0.843626629 0.921401404 0.991954534 0.901976847 0.925978441 1.143814252 0.892549781 1.041101212 1 18.80362757 S(ph)S(ph)PLAS(ph)LSKTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPLASLSKTR 11 1 X6RDY0;Q5T130;X6RIY5;Q5T124-7;Q5T124-6;Q5T124-3;Q5T124-2;Q5T124 X6RDY0 UBXN11 UBX domain-containing protein 11 3 S(1)S(1)PLAS(0.333)LS(0.333)KT(0.333)R 59.8 0.079652 185370000 33864 31193 32464 27699 47433 26467 45714 18552 69645 TRUE FALSE 31744.51269 33502.56218 33234.06141 28409.80323 43707.80352 34107.59324 38859.61009 20868.25804 58020.79958 0.547122979 0.577423311 0.572795647 0.489648599 0.753312671 0.587851141 0.669753095 0.35966857 1 15.82428256 -1.675046872 2.943051229 1.046307696 0.581180712 0.629596554 0.103391967 32128328.27 33622676.23 11245018.07 0.022287548 0.021132609 1.675046872 -0.465126984 S(ph)S(ph)SSQTLTQFDSNIAPADPDTAIVHPVPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSSQTLTQFDSNIAPADPDTAIVHPVPIR 30 0 Q96D71;Q96D71-3;H0YE73 Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 2 S(0.383)S(0.383)S(0.383)S(0.383)QT(0.383)LT(0.071)QFDS(0.015)NIAPADPDTAIVHPVPIR 51.844 0.03995 42698000 3537.1 2540.8 3017.7 4158.4 6801.5 1397.5 4225.7 3958.1 2518.2 TRUE FALSE 3315.719225 2728.923476 3089.281269 4265.111584 6267.337626 1800.935563 3592.095514 4452.277498 2097.896152 1.58049731 1.300790544 1.472561579 2.033042284 2.987439402 0.858448385 1.712237048 2.122258289 1 11.03472755 3.368698818 7.242683363 1.803559654 1.413924491 0.065511706 0.591046875 0.567497275 34.3687079 0.157055063 0.213180684 2337.215825 -3.368698818 -0.389635162 S(ph)SAIGIENIQEVQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSAIGIENIQEVQEK 15 0 J3KPC5;P47736-3;P47736;P47736-4;F2Z357;X6R8W7;P47736-2;A0A0A0MQY8 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 S(0.5)S(0.5)AIGIENIQEVQEK 123.14 0.0001097 117450000 155810 106220 134280 118570 153730 86839 147680 121470 193600 TRUE FALSE 146058.1302 114084.6393 137465.185 121612.7069 141656.6659 111908.0096 125536.755 136635.7969 161286.9093 0.905579572 0.707339733 0.852302184 0.75401474 0.878289915 0.693844343 0.778344353 0.847159869 1 17.29926982 0.887003565 3.534250543 0.999882286 0.788902901 0.462699489 0.068869986 0.390436916 9.983665168 0.058212654 0.0150204 7.709097966 -0.887003565 -0.210979385 S(ph)SDEDAAGEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSDEDAAGEPK 11 0 E9PHH9;Q9BUI4 E9PHH9 POLR3C DNA-directed RNA polymerase III subunit RPC3 1 S(0.993)S(0.007)DEDAAGEPK;S(0.99)S(0.01)DEDAAGEPK 196.15 6.45E-08 520010000 850170 408050 505400 539170 611330 442970 740030 500260 692350 TRUE FALSE 796959.3773 438262.4466 517388.3267 553006.015 563318.6078 570848.248 629069.3716 562718.5622 576792.3122 1.381709431 0.759827129 0.897009748 0.958761071 0.976640284 0.989694619 1.090634113 0.975599969 1 19.13769241 2.274823566 2.177315533 1.032034979 0.943745595 0 0.162109053 1.02138499 9.892781648 0.06973895 0.048596093 188.2884005 -2.274823566 -0.088289384 S(ph)SDGGSEEPPDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSDGGSEEPPDRR 13 1 Q9HCD6;Q9HCD6-2;Q9HCD6-3;Q9HCD6-4 Q9HCD6 TANC2 Protein TANC2 1 S(0.499)S(0.499)DGGS(0.002)EEPPDRR 101.75 0.0011013 55254000 67251 115790 106740 113440 114630 111690 94171 90177 59885 TRUE FALSE 63041.87996 124363.2121 109271.9232 116351.0625 105627.4222 143933.0899 80050.93279 101435.797 49889.80663 1.263622456 2.49275795 2.190265519 2.332161023 2.117214504 2.885019999 1.604554882 2.033196835 1 15.60645746 0.740107925 1.109059074 1.010666276 2.218182633 0.384923569 0.444060133 0.820975944 1.787383819 0.376528422 0.118190916 5.496774552 -0.740107925 1.207516356 S(ph)SDIVSSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSDIVSSVR 9 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 S(0.991)S(0.009)DIVSSVR 121.41 0.00064471 182360000 285600 274460 248040 259800 212720 194260 311170 249900 300500 TRUE FALSE 267724.8058 294781.304 253923.6259 266466.9078 196013.8293 250339.7085 264512.9473 281100.5651 250344.6087 1.06942509 1.177502106 1.014296362 1.064400425 0.782976036 0.999980426 1.056595341 1.122854479 1 17.93355586 3.755329309 2.714010127 1.002207713 1.126891987 0.221770225 0.091515939 0.385908011 5.667890474 0.025072322 0.048060394 5692.844344 -3.755329309 0.124684274 S(ph)SDPLGDTASNLGSAVDELMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 SSDPLGDTASNLGSAVDELMR 21 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 S(0.5)S(0.5)DPLGDTASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR;S(0.5)S(0.5)DPLGDTASNLGSAVDELMR 231.93 2.29E-35 496115000 140844.9 139438.8 144944.2 135670.9 150256.9 123860.2 160414.4 133669 204139.2 TRUE FALSE 132029.6691 149762.9938 148382.3449 139152.445 138456.3292 159616.629 136361.7499 150357.8689 170067.0487 0.776338921 0.88061147 0.872493208 0.818221084 0.8141279 0.938551179 0.801811703 0.884109356 1 17.37574411 0.977042091 23.04863778 1.000000002 0.849841017 0.528113109 0.046325006 536.4061979 538527.5403 0.040354869 0.010088717 9.485103859 -0.977042091 -0.150158985 S(ph)SDSEEAFETPESTTPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SSDSEEAFETPESTTPVK 18 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;E9PGB3 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 S(0.5)S(0.5)DSEEAFETPESTTPVK;S(0.491)S(0.491)DS(0.017)EEAFETPESTTPVK;S(0.5)S(0.5)DSEEAFETPESTTPVK;S(0.496)S(0.496)DS(0.007)EEAFETPESTTPVK;S(0.5)S(0.5)DSEEAFETPESTTPVK 491.25 3.45E-240 2685210000 6159010 4568140 5147680 5073840 5414080 3828080 6428570 4706610 3843380 TRUE FALSE 5773528.558 4906369.839 5269785.401 5204043.324 4988879.996 4933184.552 5464665.608 5294240.619 3201895.049 1.803159838 1.532333123 1.645833271 1.625301031 1.558102286 1.540707761 1.706697292 1.653471003 1 21.61049459 -1.381747238 3.321410147 0.994488102 1.624792339 0.856007508 0.081551155 37686029.59 53477878.28 2012504.047 0.018110948 0.041519562 1.381747238 0.630304237 S(ph)SEDLAGPLPSSVSSSSTTSSKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSEDLAGPLPSSVSSSSTTSSKPK 24 1 Q9NRF2-2;Q9NRF2-3;Q9NRF2 Q9NRF2-2 SH2B1 SH2B adapter protein 1 1 S(0.834)S(0.166)EDLAGPLPSSVSSSSTTSSKPK;S(0.566)S(0.434)EDLAGPLPSSVSSSSTTSSKPK 221.29 5.68E-33 1354160000 560170 297741 395260 361930 349550 320661 520940 320587 529330 TRUE FALSE 525109.9596 319786.0534 404635.7539 371217.7365 322097.753 413230.6252 442829.8832 360612.9926 440981.4034 1.190775746 0.725169023 0.917580086 0.841799073 0.730411193 0.937070412 1.004191741 0.81775102 1 18.75035829 2.033026075 24.99756961 0.948492993 0.860613873 0.030377495 0.137740835 452.8092086 342731.2929 0.047085031 0.034774437 107.9011505 -2.033026075 -0.087879121 S(ph)SEHLLRPSQVCPQRPLSQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSEHLLRPSQVCPQRPLSQER 21 2 Q0VF96 Q0VF96 CGNL1 Cingulin-like protein 1 1 S(0.983)S(0.017)EHLLRPSQVCPQRPLSQER;S(0.752)S(0.248)EHLLRPSQVCPQRPLSQER 158.2 1.26E-11 276900000 48520 92227 70416 78157 85851 57456 81859 66765 86287 TRUE FALSE 45483.21981 99055.58304 72086.30077 80162.64094 79108.60877 74042.61448 69585.00289 75100.75722 71885.14226 0.632720732 1.377970189 1.002798332 1.11514895 1.100486224 1.03001277 0.968002576 1.044732678 1 16.13340599 2.091326639 4.451995409 1.000238809 1.088121754 0 0.183383063 0.737605393 26.37744472 0.066877735 0.047671626 123.4032616 -2.091326639 0.087882945 S(ph)SFSHYSGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSFSHYSGLK 10 0 Q8NC51;Q8NC51-3 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 S(0.493)S(0.493)FS(0.013)HYSGLK;S(0.449)S(0.449)FS(0.102)HYSGLK;S(0.5)S(0.5)FSHYSGLK;S(0.648)S(0.35)FS(0.002)HYSGLK 228.12 1.44E-09 1375770000 1662050 2825340 2517110 2248510 3045220 1935000 2924220 2796930 2829910 TRUE FALSE 1558025.257 3034531.113 2576817.038 2306210.573 2806060.705 2493603.088 2485760.358 3146132.867 2357579.739 0.660857926 1.287138273 1.092992528 0.978211059 1.190229394 1.057696182 1.054369579 1.334475698 1 21.16887514 4.751378805 24.84711736 1.124397085 0.660857605 0.609943759 0.116493076 1277.456552 2476207.966 0.026112622 0.470838477 56412.94925 -4.751378805 -0.463539479 S(ph)SFSQHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSFSQHAR 8 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 S(0.811)S(0.189)FSQHAR;S(0.5)S(0.5)FSQHAR;S(0.472)S(0.472)FS(0.055)QHAR 127.93 0.00074416 1785220000 1190610 1962920 1534790 1684520 1845110 1225640 1745630 1606390 1720830 TRUE FALSE 1116091.845 2108256.639 1571195.944 1727747.635 1700202.503 1579462.371 1483888.987 1806951.328 1433612.356 0.778517178 1.47059045 1.095969867 1.20517072 1.185956926 1.10173602 1.035069892 1.260418355 1 20.45122355 2.227343905 6.082663715 1.094423598 1.187205702 0 0.181349432 0.500373919 67.36176391 0.061784289 0.047487837 168.7889086 -2.227343905 0.092782103 S(ph)SGPYGGGGQYFAKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSGPYGGGGQYFAKPR 16 1 F8W6I7;P09651-2;P09651;P09651-3;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 S(0.825)S(0.175)GPYGGGGQYFAKPR;S(0.604)S(0.396)GPYGGGGQYFAKPR;S(0.853)S(0.147)GPYGGGGQYFAKPR 310.28 7.39E-58 2064970000 1167660 1091120 1142290 1086310 1357590 841937 1415660 1141350 1963460 TRUE FALSE 1094578.245 1171907.66 1169385.658 1114186.554 1250970.358 1084990.544 1203394.925 1283850.06 1635745.842 0.669161564 0.716436277 0.714894471 0.681148945 0.764770618 0.6633002 0.735685762 0.784871358 1 20.64151717 0.746487798 1.550017432 0.999803896 0.705975699 0.908623192 0.029419554 0.213449053 0.849946515 0.024465768 0.007080556 5.578119291 -0.746487798 -0.293828197 S(ph)SGREEDDEELLR ddPTM_SK-BR-3_Pertuzumab_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(0.98)S(0.02)GREEDDEELLR;S(0.973)S(0.027)GREEDDEELLR 163 2.39E-05 503960000 641220 518880 546740 571410 593460 437170 670380 486470 778580 TRUE FALSE 601087.1848 557298.4151 559708.931 586073.348 546852.0455 563373.8821 569862.7425 547206.8504 648629.9682 0.926702765 0.859193134 0.862909453 0.903555766 0.84308785 0.868559749 0.878563696 0.843634857 1 19.30703616 -1.997906111 2.616091201 1.126974093 0.871411723 0.70557436 0.02570128 3274900.423 1777355.128 2505822.432 0.005570812 0.01004833 1.997906111 -0.255562369 S(ph)SGRNSPSAASTSSNDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSGRNSPSAASTSSNDSK 18 1 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 S(0.368)S(0.368)GRNS(0.255)PS(0.009)AASTSSNDSK;S(0.366)S(0.366)GRNS(0.256)PS(0.013)AASTSSNDSK;S(0.353)S(0.353)GRNS(0.293)PS(0.001)AASTSSNDSK;S(0.333)S(0.333)GRNS(0.333)PS(0.001)AASTSSNDSK 109.85 0.00021226 978791000 486260 330046 381279 388693 417618 277513 474931 305250 470807 TRUE FALSE 455825.8546 354482.9493 390323.1179 398667.5204 384819.9669 357626.4981 403719.5056 343361.1344 392226.2702 1.162150241 0.903771563 0.995147821 1.016422282 0.981117269 0.911786194 1.029302564 0.875415954 1 18.58132664 2.471992102 24.76156226 0.960722947 0.996338676 0.106532494 0.07629246 435.6894506 2103311.066 0.024524824 0.020583445 296.477747 -2.471992102 0.035615728 S(ph)SLGSHQLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 159.44 4.95E-06 298688000 181039 213188 193835 206556 245460 197141 237720 218310 242860 TRUE FALSE 169708.0922 228972.6613 198432.8577 211856.5767 226182.5617 254052.4064 202076.0929 245566.4841 202325.0971 0.83878913 1.131706667 0.980762449 1.047109725 1.117916487 1.255664325 0.998769287 1.213722309 1 17.62631576 2.856581447 3.80826149 1.118669215 1.01507893 0.230695792 0.106591597 0.404100591 10.40581299 0.030838615 0.032948956 718.7559398 -2.856581447 -0.103590286 S(ph)SLPNGEGLQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSLPNGEGLQLK 12 0 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 S(0.597)S(0.403)LPNGEGLQLK;S(0.729)S(0.271)LPNGEGLQLK 201.1 1.60E-07 243036000 904120 599800 756430 661300 647700 626909 889030 650910 760910 TRUE FALSE 847532.7431 644209.8161 774372.8768 678270.0776 596832.2547 807887.4513 755728.2048 732177.5463 633909.2053 1.336993904 1.016249347 1.221583265 1.069979852 0.941510629 1.274452941 1.192171053 1.155019584 1 19.27391669 S(ph)SLQVDWHEEEWEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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;S(0.5)S(0.5)LQVDWHEEEWEK 194.92 5.71E-08 134288000 264719 210335 222795 249693 286850 183018 293040 233814 216245 TRUE FALSE 248150.7103 225908.4223 228079.8026 256100.5451 264321.9581 235852.3256 249101.3725 263006.1926 180152.3125 1.377449486 1.253985692 1.266038717 1.421577895 1.467213795 1.309182892 1.382726477 1.459910167 1 17.45885765 -1.066208429 4.556558688 0.999980408 1.3523253 0.702145798 0.07461201 1.61E-05 3.30E-06 0.078237913 0.018439828 0.085860136 1.066208429 0.352344892 FKAEAPLPS(ph)PK ddPTM_SK-BR-3_Pertuzumab_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 131.72 0.00011961 6985350000 24391000 14599900 19884200 28171900 30147600 8626930 10595770 6153810 9704210 TRUE FALSE 22864410.85 15680891.79 20355862.61 28894838.65 27779929.11 11117384.64 9007032.655 6922126.725 8084514.659 2.82817359 1.939620676 2.517883073 3.574096884 3.436190084 1.375145585 1.114109261 0.856220443 1 22.94672974 2.110722512 5.980061522 1.062603281 2.715465814 0.778962618 0.468469 0.119818909 5.86585362 0.20367665 0.149440345 129.0394525 -2.110722512 1.652862532 up S(ph)SLVTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSLVTSK 7 0 A6NMQ3;Q5T5H1;O43768-2;O43768;O43768-9;O43768-3;O43768-4;A0A1W2PRU0;O43768-6;O43768-5;O43768-7 A6NMQ3 ENSA Alpha-endosulfine 1 S(0.781)S(0.219)LVTSK 208.72 0.00017447 1762500000 4143300 2900300 3326300 2820000 2891200 2398400 4294100 3403200 4682800 TRUE FALSE 3883978.249 3115041.23 3405201.407 2892365.974 2664136.815 3090779.145 3650239.569 3828097.011 3901210.428 0.995582864 0.798480699 0.87285766 0.741402195 0.682900055 0.792261582 0.935668464 0.981258787 1 21.89549039 1.606747583 3.68922199 0.982761864 0.811277621 0.461933296 0.081819552 0.170925559 5.423429127 0.049817815 0.021527339 40.43408155 -1.606747583 -0.171484243 S(ph)SPAPHSGPCPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 102.38 0.0010913 641550000 222680 272680 263310 294470 310740 225312 317010 251050 387730 TRUE FALSE 208742.8563 292869.5109 269555.8375 302026.5987 286335.7339 290355.9168 269477.2935 282394.1451 323015.3582 0.646231986 0.906673641 0.834498518 0.93502241 0.886446191 0.898891986 0.834255359 0.87424371 1 18.30124324 4.741762653 24.97141593 0.88477598 0.646231896 0.715510396 0.049073556 155.9112195 1215832.671 0.01043016 0.074786552 55177.58046 -4.741762653 -0.238544084 S(ph)SPATSLFVELDEEEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSPATSLFVELDEEEVK 17 0 A0A087WTL4;A0A087WX97;Q9BXK5-4;Q9BXK5 A0A087WTL4 BCL2L13 Bcl-2-like protein 13 1 S(0.468)S(0.468)PAT(0.055)S(0.009)LFVELDEEEVK;S(0.5)S(0.5)PATSLFVELDEEEVK;S(0.5)S(0.5)PATSLFVELDEEEVK 207.4 6.41E-12 25095000 167156 97244 101991 95591 125320 104936 138071 125822 118506 TRUE FALSE 156694.0043 104444.0469 104410.2747 98044.0269 115477.8727 135229.3197 117368.5353 141531.1537 98726.58302 1.587151095 1.057912102 1.057570023 0.9930864 1.169673549 1.369735643 1.188824041 1.43356682 1 16.59115098 2.462183041 24.03418045 1.260794843 1.129818252 0.011376557 0.198088429 366.7798955 590108.0165 0.063442623 0.053102981 289.8564979 -2.462183041 -0.130976591 S(ph)SPELTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSPELTR 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.894)S(0.106)PELTR;S(0.896)S(0.104)PELTR;S(0.5)S(0.5)PELTR;S(0.755)S(0.245)PELTR 221.16 2.80E-05 3776920000 2511500 2351530 2577540 2274180 2333340 2492570 3504460 2593660 2233630 TRUE FALSE 2354309.698 2525639.728 2638680.466 2332539.309 2150088.889 3212134.496 2978998.757 2917484.16 1860822.723 1.265198274 1.357270468 1.418018188 1.253498939 1.155450684 1.726190494 1.600904116 1.567846375 1 20.82750919 2.242831657 24.99999082 1.539298457 1.314894315 0.127637609 0.2039808 152.4994049 892640.3032 0.06532742 0.05287991 174.9168538 -2.242831657 -0.224404142 S(ph)SPEQPRPSTSK ddPTM_SK-BR-3_Pertuzumab_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(0.754)S(0.246)PEQPRPSTSK;S(0.997)S(0.003)PEQPRPSTSK 225.86 4.39E-11 775600000 785300 614130 676730 649990 708930 520140 800420 613470 915420 TRUE FALSE 736149.4748 659600.8242 692782.3552 666669.8438 653253.4975 670295.9742 680404.4517 690063.0799 762630.4882 0.965276744 0.864902249 0.908411565 0.874171508 0.85657931 0.878926275 0.892181026 0.904845912 1 19.54062468 0.642940873 2.018917377 0.999981282 0.88826615 0.555738986 0.030151299 1.304104089 6.499397835 0.025985079 0.00715352 4.394817785 -0.642940873 -0.111715133 S(ph)SPGAGPSDHHSASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSPGAGPSDHHSASR 15 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 S(0.5)S(0.5)PGAGPSDHHSASR;S(0.5)S(0.5)PGAGPSDHHSASR;S(0.5)S(0.5)PGAGPSDHHSASR;S(0.5)S(0.5)PGAGPSDHHSASR 188.27 1.97E-07 217125500 52273.6 78486.8 79861.3 87100.5 80773.3 70122.9 87351.6 73243.4 83042.2 TRUE FALSE 49001.88869 84298.04434 81755.64775 89335.64629 74429.69084 90366.24288 74254.03851 82387.99972 69181.92035 0.708304835 1.218498184 1.181748748 1.291314925 1.075854652 1.306211831 1.07331566 1.19088917 1 16.07810744 4.74167621 24.98850832 1.176632905 0.708304662 0.689582687 0.096583114 147.4202355 1182321.432 0.019770693 0.141236517 55166.5989 -4.74167621 -0.468328243 S(ph)SPGGQDEGGFMAQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSPGGQDEGGFMAQGK 16 0 F5GZ78;A0A1B0GTU4;P49023;A0A1B0GV30 F5GZ78 PXN Paxillin 1 S(0.5)S(0.5)PGGQDEGGFMAQGK;S(0.5)S(0.5)PGGQDEGGFMAQGK;S(0.607)S(0.393)PGGQDEGGFMAQGK 240.41 2.86E-19 436890000 1831020 1416640 1584760 1497690 1684710 1246760 1985920 1458820 1670720 TRUE FALSE 1716419.727 1521529.5 1622351.256 1536123.261 1552399.672 1606679.373 1688149.732 1640956.888 1391866.039 1.233178825 1.093158003 1.165594397 1.103643036 1.115336986 1.154334776 1.212867967 1.178961798 1 20.40858893 2.016420875 23.36854093 1.161596782 1.136762728 0 0.068822215 469.0680938 667526.0031 0.023076535 0.017036678 103.8534372 -2.016420875 -0.024834054 S(ph)SPGPAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPGPAPR 8 0 Q9H330-4;Q9H330 Q9H330-4 TMEM245 Transmembrane protein 245 1 S(0.986)S(0.014)PGPAPR 69.716 0.055804 1952500000 737500 840740 923560 858640 866210 717130 776280 783980 972470 TRUE FALSE 691341.1915 902989.2644 945467.2793 880674.1561 798181.3607 924153.7894 659884.0206 881861.6288 810158.4746 0.85334069 1.114583495 1.167015231 1.087039368 0.985216332 1.140707427 0.814512273 1.088505097 1 19.62784461 1.760648203 25 0.9501227 1.075414002 0.108203958 0.111456634 16.75506184 18979.53753 0.048424066 0.026854564 57.62994473 -1.760648203 0.125291301 S(ph)SPGPDTLVVLEFNPASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSPGPDTLVVLEFNPASK 18 0 O60303 O60303 KIAA0556 Uncharacterized protein KIAA0556 1 S(0.5)S(0.5)PGPDTLVVLEFNPASK;S(0.5)S(0.5)PGPDTLVVLEFNPASK;S(0.5)S(0.5)PGPDTLVVLEFNPASK;S(0.5)S(0.5)PGPDTLVVLEFNPASK 234.57 9.49E-24 220276300 362961 281746 329757 331195 312166 265220 435823 270908 251692 TRUE FALSE 340243.9189 302606.767 337578.9918 339694.0244 287649.7416 341784.7085 370475.3871 304731.4601 209682.9792 1.62265874 1.443163237 1.609949425 1.620036236 1.371831623 1.630006927 1.766835766 1.45329612 1 17.67785023 0.976150001 23.46604738 0.999999994 1.578236711 0.741377527 0.107405708 505.5028528 497366.0158 0.106697437 0.026674359 9.465640383 -0.976150001 0.578236717 S(ph)SPGQPEAGPEGAQERPSQAAPAVEAEGPGSSQAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPGQPEAGPEGAQERPSQAAPAVEAEGPGSSQAPR 36 1 P40222 P40222 TXLNA Alpha-taxilin 1 S(0.5)S(0.5)PGQPEAGPEGAQERPSQAAPAVEAEGPGSSQAPR 190.71 1.23E-23 274200000 33058 29239 29278 35368 37082 27136 38714 22773 33602 TRUE FALSE 30988.95879 31403.88598 29972.48799 36275.60276 34169.7293 34969.72268 32909.1951 25616.25918 27993.60912 1.107001196 1.121823408 1.07069038 1.295853014 1.220626078 1.249203793 1.175596721 0.915075261 1 14.77280988 1.24471065 24.99731265 0.957537599 1.170425177 0.627301548 0.070255861 95.60723728 388615.5545 0.054103523 0.018639993 17.56752784 -1.24471065 0.212887577 S(ph)SPGQTPEEGAQALAEFAALHGPALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 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)PGQTPEEGAQALAEFAALHGPALR;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)PGQTPEEGAQALAEFAALHGPALR;S(0.5)S(0.5)PGQTPEEGAQALAEFAALHGPALR;S(0.499)S(0.499)PGQT(0.003)PEEGAQALAEFAALHGPALR;S(0.5)S(0.5)PGQTPEEGAQALAEFAALHGPALR;S(0.482)S(0.482)PGQT(0.036)PEEGAQALAEFAALHGPALR 336.8 2.18E-95 12620370500 2372272.6 2497012.7 2577416.2 2438617.4 2866576.4 2215207.9 3057589.5 2615556.8 3189115.4 TRUE FALSE 2223796.293 2681894.118 2638553.729 2501196.451 2641447.053 2854702.46 2599132.34 2942114.824 2656831.437 0.837010682 1.009433297 0.993120486 0.941420828 0.994209499 1.074476318 0.978282741 1.1073773 1 21.34127527 4.738773588 24.07286168 1.008418859 0.837010636 0.57542979 0.047212446 7.288447269 822911.4 0.010369243 0.060168604 54799.12051 -4.738773588 -0.171408223 S(ph)SPHGSLGSVVNSLSGLKLDNILSGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPHGSLGSVVNSLSGLKLDNILSGPK 27 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5;A0A0A0MRX3 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.347)S(0.347)PHGS(0.299)LGS(0.007)VVNSLSGLKLDNILSGPK 118.01 0.00026244 38671000 73353 88261 85639 89670 99922 76947 124860 87471 189440 TRUE FALSE 68761.96667 94795.93628 87670.39752 91971.08401 92074.52919 99160.34977 106138.4021 98391.9469 157821.2402 0.435695263 0.600653855 0.555504427 0.582754792 0.58341025 0.628308013 0.672522925 0.623439195 1 17.26793186 -5 0.16856268 2.621155427 0.488054431 0.911021873 0.043032368 33.87608878 0.318684781 18.27711522 0.145587723 1.00E-05 5 -2.133100996 S(ph)SPIAQPASSFQVETASQGHSISHHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPIAQPASSFQVETASQGHSISHHK 26 0 Q8IZH2-2;Q8IZH2;H7C5E4 Q8IZH2-2 XRN1 5-3 exoribonuclease 1 1 S(0.5)S(0.5)PIAQPASSFQVETASQGHSISHHK 128.52 0.00014515 154470000 15739 31722 32577 31693 31856 29577 49958 33181 32053 TRUE FALSE 14753.92408 34070.72989 33349.74182 32506.29604 29354.15826 38115.39976 42467.26169 37323.72089 26703.14723 0.552516299 1.275906903 1.248906788 1.217320781 1.099277101 1.427374812 1.590346685 1.397727413 1 14.70472217 4.740823087 4.771414314 1.311519027 0.508319484 0.648366345 0.16783736 0.119324162 7.732150531 0.042293812 0.319831844 55058.33668 -4.740823087 -0.803199542 S(ph)SPIMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSPIMR 6 0 A0A087WZV0;O43314-2;O43314;A0A087WWN8;K7ENU7;H0Y9S9 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 S(0.753)S(0.247)PIMR;S(0.753)S(0.247)PIMR;S(0.745)S(0.255)PIMR 122.78 0.020008 656550000 635820 650930 649110 651540 758110 529460 714150 611800 795530 TRUE FALSE 596025.1612 699125.5345 664507.1957 668259.6195 698571.0987 682306.5069 607069.8373 688184.5767 662750.9037 0.899320028 1.054884317 1.002650003 1.008311895 1.05404775 1.029506717 0.915984926 1.038375916 1 19.33810721 -0.583655902 7.211592233 0.999998629 1.002178603 0 0.053304626 0 0 0.048933136 0.011533651 0.260821926 0.583655902 0.002179974 S(ph)SPINPAQSGSPNHVDSAYFPGSSTSSSSDNDEGSGGATNHISGNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSPINPAQSGSPNHVDSAYFPGSSTSSSSDNDEGSGGATNHISGNK 46 0 Q9NZB2;Q9NZB2-4;Q9NZB2-2;Q9NZB2-5;A0A0C4DH52 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 1 S(0.499)S(0.499)PINPAQS(0.001)GS(0.001)PNHVDSAYFPGSSTSSSSDNDEGSGGATNHISGNK;S(0.5)S(0.5)PINPAQSGSPNHVDSAYFPGSSTSSSSDNDEGSGGATNHISGNK 235.98 2.60E-60 612580000 25201 83084 63392 78688 82077 58518 99609 84636 70519 TRUE FALSE 23623.7144 89235.62581 64895.68818 80707.2673 75631.0035 75411.19664 84673.55517 95202.99091 58748.92333 0.402113146 1.518932105 1.104627702 1.373765896 1.287359822 1.28361836 1.441278416 1.620506139 1 15.84227479 4.745478717 24.8775845 1.336228296 0.402112686 0.718758109 0.182112139 383.4571412 1378879.8 0.039615016 0.394422593 55651.73615 -4.745478717 -0.93411561 S(ph)SPKEELHPAAPSQLAPSFSSSSSSSSGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPKEELHPAAPSQLAPSFSSSSSSSSGPR 30 1 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 S(0.5)S(0.5)PKEELHPAAPSQLAPSFSSSSSSSSGPR 170.47 1.02E-12 388240000 332290 234710 244380 264400 257300 183730 328490 204710 257800 TRUE FALSE 311492.5621 252088.1726 250176.809 271184.9516 237092.6959 236769.8684 279235.9741 230268.4941 214771.5145 1.450343928 1.1737505 1.164850979 1.262667222 1.103929897 1.102426776 1.300153676 1.072155656 1 17.71244313 8 0.022759336 1.01E-07 2.761507351 0.452706589 0.095649389 2740.54455 4.800258165 207.0541593 406.2593399 100000000 -8 2.76150725 S(ph)SPLPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPLPAK 7 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 S(0.529)S(0.471)PLPAK 125.98 0.0041922 547520000 2913000 1786200 2225500 1858900 1718200 2088500 3701300 2167100 2239700 TRUE FALSE 2730680.53 1918452.107 2278289.911 1906602.521 1583259.503 2691416.046 3146324.426 2437667.205 1865879.601 1.463481635 1.028175722 1.221027289 1.021825052 0.848532511 1.442438218 1.686241934 1.306443998 1 20.83142447 2.174200365 15.36247309 1.445972671 1.114491018 0.167635971 0.23476154 2.372335784 564.594324 0.081592293 0.060261309 149.348328 -2.174200365 -0.331481653 S(ph)SPNPFITGLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSPNPFITGLTR 12 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 S(0.521)S(0.479)PNPFITGLTR;S(0.913)S(0.087)PNPFITGLTR 198.85 1.87E-07 179263000 192569 215982 205371 203757 217310 193852 293646 226950 300640 TRUE FALSE 180516.45 231973.532 210242.4971 208985.7496 200243.3492 249813.9255 249616.5084 255285.2071 250461.2418 0.720736066 0.926185346 0.839421284 0.834403551 0.799498349 0.997415503 0.996627289 1.019260326 1 17.93422784 2.228372876 24.83356865 1.00215615 0.840543512 0.746722496 0.051383375 101.2974773 246920.1391 0.018437102 0.013773728 169.1892931 -2.228372876 -0.161612638 S(ph)SPPAPPLPPGSGSPGTPQALPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPPAPPLPPGSGSPGTPQALPR 23 0 Q9Y3L3;A0A2R8Y5V0 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 S(0.497)S(0.497)PPAPPLPPGS(0.004)GS(0.001)PGTPQALPR 136.26 1.26E-05 104840000 38550 43523 39896 42823 37011 34882 43609 36149 34415 TRUE FALSE 36137.22431 46745.48821 40842.35196 43921.91068 34104.30536 44951.86714 37070.2353 40662.28222 28670.91417 1.260414094 1.630414989 1.424522138 1.53193269 1.189508823 1.567856081 1.292956167 1.418241566 1 14.80730029 -3.393277473 0.217367478 3.35E-08 1.49986826 0.461966542 0.139577494 53.22935708 0.996431915 24.00119769 0.253901255 0.000404317 3.393277473 1.499868227 S(ph)SPPLPPPAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPPLPPPAEER 12 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 S(0.528)S(0.472)PPLPPPAEER 100.02 0.0036374 288980000 134350 135100 127030 144700 147600 117850 168060 117160 178160 TRUE FALSE 125941.2733 145102.9446 130043.2116 148413.247 136008.0914 151871.3819 142860.9632 131787.6839 148423.945 0.848523958 0.977624901 0.876160592 0.999927922 0.916348716 1.023226959 0.962519647 0.8879139 1 17.17936433 3.236853186 24.99965218 0.964877257 0.913723163 0.244773929 0.051527881 71.75100844 1050563.581 0.013489786 0.016938064 1725.254568 -3.236853186 -0.051154094 S(ph)SPPLRTPDVLESSGPAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSPPLRTPDVLESSGPAVR 19 1 E9PJN1;O75676-2;O75676;A0A0A6YYC0 E9PJN1 RPS6KA4 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-4 1 S(0.576)S(0.424)PPLRTPDVLESSGPAVR;S(0.987)S(0.013)PPLRTPDVLESSGPAVR;S(0.868)S(0.132)PPLRTPDVLESSGPAVR;S(0.74)S(0.26)PPLRTPDVLESSGPAVR 243.24 1.15E-24 2047090000 216151 314093 250456 288951 324901 197700 291018 243167 401825 TRUE FALSE 202622.4948 337348.7725 256396.9346 296365.9719 299384.586 254772.7806 247382.5526 273526.9352 334757.8116 0.605280856 1.007739807 0.765917704 0.885314581 0.894331889 0.761065976 0.738989634 0.817089029 1 18.3527582 2.233248505 24.99231374 0.798531507 0.84918371 0 0.12507265 507.0358728 2385464.137 0.041716729 0.031706892 171.0994072 -2.233248505 0.050652202 S(ph)SPPVLQGPAPAGFSQHPGLLVPHTHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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;S(0.5)S(0.5)PPVLQGPAPAGFSQHPGLLVPHTHAR 179.08 2.71E-17 2128980000 193497 289330 267794 258109 257587 223859 330886 209328 220414 TRUE FALSE 181386.3682 310752.2942 274146.2001 264732.5139 237357.1561 288483.4593 281272.7161 235463.0616 183625.4795 0.987806097 1.692315768 1.492963836 1.441698149 1.292615582 1.571042647 1.531773896 1.282300595 1 17.48640673 0.958288769 4.031953615 1.000536507 1.466792327 0.327724235 0.190774664 0.224434289 10.56708506 0.167526676 0.042841536 9.084243545 -0.958288769 0.46625582 S(ph)SPQLDPLR ddPTM_SK-BR-3_Pertuzumab_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 67.704 0.063091 513840000 552430 667630 482730 533010 691690 431790 593900 645620 570130 TRUE FALSE 517854.3924 717062.0199 494180.5836 546687.939 637367.4575 556440.7635 504850.2085 726227.0782 474971.6198 1.090284916 1.509694453 1.04044234 1.150990746 1.341906402 1.171524235 1.06290605 1.528990466 1 18.85748179 -1.982649313 3.179678202 0.798218822 1.229113273 0.15323982 0.174256809 0.137450261 0.000750031 0.093039218 0.036885886 0.010407602 1.982649313 0.430894451 S(ph)SPQLDPLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SSPQLDPLRK 10 1 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.5)S(0.5)PQLDPLRK;S(0.5)S(0.5)PQLDPLRK;S(0.5)S(0.5)PQLDPLRK;S(0.984)S(0.016)PQLDPLRK;S(0.98)S(0.02)PQLDPLRK;S(0.641)S(0.359)PQLDPLRK 169.09 2.90E-06 7702781000 9524040 6707090 7741980 7040510 7464010 6699260 9746000 7187340 6106430 TRUE FALSE 8927947.337 7203689.922 7925623.422 7221181.406 6877816.763 8633227.609 8284677.777 8084695.22 5087227.384 1.754973125 1.416034586 1.557945581 1.4194729 1.351977461 1.697039852 1.628525158 1.58921444 1 22.27844815 -2.03986695 2.539568104 0.314125643 1.543217024 0.648891203 0.127441853 2750460.612 1384629.461 10957580.02 0.030137083 0.009122903 2.03986695 1.229091382 S(ph)SPSARPPDVPGQQPQAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSPSARPPDVPGQQPQAAK 19 1 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 S(0.592)S(0.408)PSARPPDVPGQQPQAAK;S(0.493)S(0.493)PS(0.014)ARPPDVPGQQPQAAK 233.1 2.54E-24 1419100000 862210 586976 705710 672590 676531 613143 877710 603996 646450 TRUE FALSE 808245.8152 630436.3138 722449.7745 689849.7981 623398.9843 790147.4306 746105.5338 679406.2302 538553.3188 1.500772137 1.170610767 1.341463787 1.280931291 1.157543668 1.467166579 1.385388424 1.261539399 1 19.03872966 0.968151851 20.89659771 0.999999997 1.31800265 0.463129131 0.110348725 407.9031643 267640.0033 0.101447074 0.025361769 9.292912564 -0.968151851 0.318002653 S(ph)SPSIICMPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSPSIICMPK 10 0 Q9NZN8;Q9NZN8-5;F8VP97;F8VV52;F8VUB4;Q9NZN8-4;F8VX63;F8VVY1;F8VQD8;A0A087X050 Q9NZN8 CNOT2 CCR4-NOT transcription complex subunit 2 1 S(0.708)S(0.292)PSIICMPK;S(0.627)S(0.373)PSIICMPK 215.72 8.45E-09 290410000 710400 591810 598710 556410 590040 497740 797420 655170 480800 TRUE FALSE 665937.3321 635628.2282 612911.6839 570688.4226 543700.6385 641429.4579 677854.2739 736969.4167 400551.3739 1.662551611 1.586883156 1.53016997 1.424757122 1.357380536 1.601366266 1.692302955 1.839887377 1 18.61162777 4.577307671 1.633580418 1.530423758 1.684636002 0.042165134 0.223515197 3.048687343 10.07278688 0.055571161 0.674677187 37783.97725 -4.577307671 0.154212244 S(ph)SPSPQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSPSPQKR 8 1 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 S(0.629)S(0.371)PSPQKR;S(0.593)S(0.407)PSPQKR 128.36 0.0006963 647270000 534110 508240 482500 542370 505840 382680 580790 525900 515260 TRUE FALSE 500681.0085 545870.6184 493945.1279 556288.1324 466113.3669 493153.5037 493705.9313 591559.7726 429259.7773 1.166382305 1.271655644 1.150690454 1.295924198 1.085853815 1.148846293 1.150133223 1.378092717 1 18.71149147 2.736419137 24.99932641 1.16041004 1.217833114 0.096043076 0.102775647 537.9174889 6279532.214 0.029623298 0.029195085 545.0284054 -2.736419137 0.057423074 S(ph)SPVEFECINEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSPVEFECINEK 12 0 O75131;H0YB26 O75131 CPNE3 Copine-3 1 S(0.962)S(0.038)PVEFECINEK;S(0.62)S(0.38)PVEFECINEK 217.91 3.73E-11 289140000 753550 603400 556920 464820 988000 421880 825050 720650 1138170 TRUE FALSE 706386.6506 648076.3638 570130.4054 476748.0681 910406.4654 543669.9074 701341.4119 810624.7388 948202.0741 0.7449748 0.683479167 0.601275214 0.502791632 0.960139711 0.573369245 0.739653952 0.854907156 1 19.85483502 1.085845159 1.855667757 0.998433885 0.671566844 0.435502435 0.121603868 0.282687405 1.924598934 0.104984175 0.030065497 12.18555064 -1.085845159 -0.32686704 S(ph)SPVESLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPVESLKK 9 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 S(0.811)S(0.189)PVESLKK 81.799 0.01241 770130000 3520800 2031300 2625500 2636500 2668000 2115800 3655400 2288500 2689100 TRUE FALSE 3300439.413 2181699.566 2687778.1 2704157.054 2458466.042 2726597.113 3107306.705 2574224.263 2240271.838 1.473231666 0.973854837 1.19975534 1.207066485 1.097396307 1.217083153 1.38702217 1.149067814 1 21.09524237 2.015342931 22.51488377 1.241787507 1.162345381 0 0.159146361 232.6704918 341426.4401 0.054986445 0.040585762 103.5959866 -2.015342931 -0.079442126 S(ph)SPVKVGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPVKVGEK 9 1 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 1 S(0.882)S(0.118)PVKVGEK 139.78 6.70E-05 395470000 1578200 876100 1119300 1113100 1373700 775050 1588900 1080100 1825000 TRUE FALSE 1479423.279 940967.3556 1145850.325 1141664.03 1265815.143 998794.3531 1350659.196 1214952.863 1520395.71 0.973051469 0.61889635 0.753652695 0.750899271 0.832556377 0.656930526 0.888360304 0.799103059 1 20.53601543 0.731606323 0.680612534 1.001468783 0.746025406 0.293012615 0.103376324 1.165373025 1.083451575 0.097443986 0.036183194 5.390217918 -0.731606323 -0.255443377 S(ph)SPVNRPSSATNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPVNRPSSATNK 13 1 Q96L91-4;Q96L91-3;Q96L91-5;Q96L91-2;Q96L91;A0A0A0MR80;A0A0A0MR72 Q96L91-4 EP400 E1A-binding protein p400 1 S(0.567)S(0.433)PVNRPSSATNK 104.21 0.00093867 124090000 233320 194370 195480 186290 228130 182900 303720 237890 255990 TRUE FALSE 218716.9177 208761.357 200116.8779 191070.5168 210213.59 235700.2609 258180.0056 267591.0902 213263.6152 1.025570712 0.978888765 0.938354523 0.895935842 0.985698333 1.105206158 1.210614409 1.25474329 1 17.70227832 2.15400542 2.997876718 1.175282155 0.957981999 0.596253028 0.073039194 0.146015045 2.636286597 0.028685643 0.019619416 142.5625385 -2.15400542 -0.217300156 S(ph)SPVPEMLEESQELLEPVVDDVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSPVPEMLEESQELLEPVVDDVPK 24 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.475)S(0.475)PVPEMLEES(0.051)QELLEPVVDDVPK;S(0.5)S(0.5)PVPEMLEES(0.001)QELLEPVVDDVPK;S(0.5)S(0.5)PVPEMLEESQELLEPVVDDVPK;S(0.5)S(0.5)PVPEMLEES(0.001)QELLEPVVDDVPK 152.13 3.32E-07 76639000 267062 173195 198639 194957 216250 156408 276176 195113 253991 TRUE FALSE 250347.0661 186018.538 203350.8109 199959.9267 199266.5973 201560.4505 234765.9727 219473.2875 211598.2613 1.183124401 0.879111846 0.961023071 0.944997967 0.941721336 0.952561941 1.109489139 1.037216876 1 17.69096825 1.755018744 24.99988531 1.058064979 0.961336294 0.119561338 0.083752434 8.535161524 12979.84937 0.035347133 0.019601805 56.88774829 -1.755018744 -0.096728685 S(ph)SPVPPVPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPVPPVPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(0.617)S(0.383)PVPPVPER 158.05 8.51E-06 1332800000 692540 620330 672860 632300 630250 542650 730270 605490 718280 TRUE FALSE 649195.1576 666259.8787 688820.5569 648525.8885 580752.7073 699304.2458 620772.793 681086.7593 598394.4277 1.084895058 1.113412572 1.151114591 1.083776617 0.970518241 1.168634288 1.037397349 1.138190344 1 19.19073722 3.017550232 19.6547816 1.067248098 1.120351901 0.139342154 0.059938567 35.62499333 39893.01413 0.015651349 0.01869283 1041.238534 -3.017550232 0.053103803 S(ph)SREKEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSREKEQR 8 2 H7C1L9 H7C1L9 TRIP12 1 S(0.563)S(0.437)REKEQR 81.865 0.011351 149400000 82896 133780 115170 112430 137550 82080 126500 122180 170290 TRUE FALSE 77707.68733 143685.2104 117901.8868 115315.1441 126747.3779 105775.1635 107532.4994 137434.442 141867.4989 0.547748342 1.012812741 0.831070455 0.812836943 0.893420825 0.745591234 0.757978397 0.968752132 1 17.11418459 1.13898853 6.253390248 0.995529643 0.822093054 0.281000567 0.118829991 0.299575105 15.2623423 0.107375335 0.02705492 13.77173097 -1.13898853 -0.173436589 S(ph)SRLSTNGTHEILDPDLVVSDLVDTDPLQDTLSSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSRLSTNGTHEILDPDLVVSDLVDTDPLQDTLSSTK 36 1 Q9BVI0;Q5JWZ0;Q5JXL1 Q9BVI0 PHF20 PHD finger protein 20 1 S(0.2)S(0.2)RLS(0.2)T(0.2)NGT(0.2)HEILDPDLVVSDLVDTDPLQDTLSSTK 162.2 9.95E-18 19285000 11135 11252 10906 15052 20907 8805.7 12705 9247.4 21197 TRUE FALSE 10438.08023 12085.10979 11164.69547 15438.2598 19265.04855 11347.76264 10800.0032 10401.95825 17659.08376 0.591088437 0.684356558 0.632235263 0.874239004 1.090942702 0.642602006 0.61158344 0.589042919 1 14.10812287 -2.512186125 2.279280153 5.265597677 0.709891383 0.245772954 0.156986752 8704998.205 607345.4512 193166588.4 0.038894893 0.003074779 2.512186125 -4.555706294 S(ph)SRS(ph)SPELTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSRSSPELTR 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.787)S(0.213)RS(0.77)S(0.23)PELTR 128.35 0.060785 0 693310 695100 678170 689120 748300 539100 731130 568700 822350 TRUE FALSE 649916.9647 746565.9273 694256.5127 706803.9859 689531.5365 694729.4184 621503.844 639703.4469 685094.4724 0.948653056 1.089726975 1.013373397 1.03168835 1.006476573 1.014063675 0.907179767 0.933744867 1 19.38594342 1.849748912 5.847611878 0.939231719 1.026241226 0.377404533 0.041401597 0.184286332 8.075526856 0.017299859 0.010316356 70.75366029 -1.849748912 0.087009507 S(ph)SRSS(ph)PELTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSRSSPELTR 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.943)S(0.058)RS(0.328)S(0.57)PELT(0.101)R 120.21 0.04991 0 293010 296160 294460 297070 294690 237060 306000 245570 318720 TRUE FALSE 274671.0271 318087.9946 301444.7303 304693.3191 271546.2361 305495.3737 260118.1408 276229.9551 265523.573 1.034450629 1.197965179 1.135284249 1.147518903 1.022682216 1.150539556 0.979642364 1.040321776 1 18.01848042 2.087056619 0.890200459 1.000080154 1.141823417 0.363434124 0.059407547 0.504362118 0.743526236 0.043825916 0.022747264 122.1958958 -2.087056619 0.141743263 S(ph)SS(ph)PFLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSPFLSK 8 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 S(0.999)S(0.004)S(0.997)PFLSK;S(1)S(0.011)S(0.989)PFLSK 144.17 0.00086207 790360000 3292000 1899610 2502800 2232300 2104210 1660060 2955600 1796790 1927350 TRUE FALSE 3085959.596 2040259.101 2562167.598 2289584.597 1938953.835 2139292.373 2512435.218 2021123.187 1605662.834 1.921922543 1.270664711 1.595707109 1.425943572 1.207572221 1.332342213 1.564733994 1.258746945 1 20.61473755 -3.05989286 0.077918945 5.70E-15 1.936210413 0.459606816 0.186091138 178.6952473 1.484882456 39.5462796 7.809720887 0.000871178 3.05989286 1.936210413 S(ph)SS(ph)PVTELAS(ph)RSPIRQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSPVTELASRSPIRQDR 18 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(0.987)S(0.044)S(0.935)PVT(0.122)ELAS(0.514)RS(0.398)PIRQDR 51.577 0.091956 158960000 85716 90172 88329 100920 126360 59425 98652 71548 152940 TRUE FALSE 80351.18857 96848.4287 90424.20559 103509.7781 116436.1953 76580.03282 83860.04844 80480.9253 127413.326 0.630634103 0.760112241 0.709691902 0.812393659 0.913846291 0.601036291 0.658173294 0.631652338 1 16.95915665 4.745319187 22.91605771 0.740683702 0.63063394 0.076874248 0.125568799 717.5898083 2432886.621 0.028054375 0.260835635 55631.29725 -4.745319187 -0.110049762 S(ph)SSAPNVHINTIEPVNIDDLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.366)S(0.366)S(0.269)APNVHINTIEPVNIDDLIR;S(0.365)S(0.365)S(0.269)APNVHINTIEPVNIDDLIR 252.91 3.33E-37 2053292500 885869.5 924964 876514.4 750246 1019326.7 823991.1 1196899 1107533 1167946.7 TRUE FALSE 830424.5093 993449.297 897305.7355 769498.5825 939272.8927 1061863.954 1017435.106 1245810.933 973008.8505 0.853460386 1.021007462 0.92219689 0.790844381 0.965328211 1.091319934 1.045658635 1.28036958 1 19.8920934 2.290388913 3.658930859 1.103342644 0.91822684 0.52618801 0.092307477 0.197731438 5.434646493 0.033597855 0.026407678 195.159148 -2.290388913 -0.185115804 S(ph)SSDALSASFNGEMLGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSDALSASFNGEMLGNR 18 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.621)S(0.303)S(0.075)DALSASFNGEMLGNR;S(0.726)S(0.212)S(0.063)DALSASFNGEMLGNR;S(0.333)S(0.333)S(0.333)DALSASFNGEMLGNR 168.08 2.27E-11 273456000 174254 135977 139300 144171 163593 114524 171266 120943 162439 TRUE FALSE 163347.7532 146044.8786 142604.2618 147870.6719 150745.0657 147585.2197 145586.2533 136042.9998 135326.8815 1.207060647 1.079200798 1.05377631 1.092692526 1.113932901 1.090583172 1.07581178 1.005291767 1 17.04608892 S(ph)SSEDAESLAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SSSEDAESLAPR 12 0 Q4G0J3;Q4G0J3-3;H0YA82 Q4G0J3 LARP7 La-related protein 7 1 S(0.909)S(0.045)S(0.045)EDAESLAPR;S(0.781)S(0.109)S(0.109)EDAESLAPR;S(0.856)S(0.122)S(0.022)EDAESLAPR;S(0.842)S(0.133)S(0.025)EDAESLAPR;S(0.758)S(0.121)S(0.121)EDAESLAPR;S(0.727)S(0.136)S(0.136)EDAESLAPR 279.38 5.91E-28 4162220000 1874070 1857540 1910510 2060410 2167110 1550240 1960660 1525310 2082790 TRUE FALSE 1756775.304 1995074.194 1955828.199 2113283.609 1996913.922 1997769.122 1666677.235 1715748.311 1735158.894 1.012457885 1.149793371 1.127175273 1.21791936 1.150853636 1.151346502 0.960532918 0.988813369 1 20.72663635 1.741480586 7.296978752 0.98262734 1.139628592 0.658281112 0.051410241 0.072188156 11.96343501 0.023856166 0.012651618 55.14175521 -1.741480586 0.157001251 S(ph)SSETILSSLAGSDIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSETILSSLAGSDIVK 17 0 Q01850 Q01850 CDR2 Cerebellar degeneration-related protein 2 1 S(0.331)S(0.331)S(0.331)ET(0.006)ILSSLAGSDIVK 202.63 1.09E-11 20784000 78105 66000 71486 69717 79022 45191 76689 62689 100250 TRUE FALSE 73216.54747 70886.70867 73181.68168 71506.05625 72815.93088 58236.90809 65190.1964 70515.85965 83517.62736 0.876659812 0.84876344 0.876242345 0.85617921 0.871863021 0.697300797 0.780556135 0.844323071 1 16.34979311 S(ph)SSFSDTLEESSPIAAIFDTENLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSFSDTLEESSPIAAIFDTENLEK 25 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 S(0.2)S(0.2)S(0.2)FS(0.2)DT(0.2)LEESSPIAAIFDTENLEK;S(0.193)S(0.193)S(0.193)FS(0.193)DT(0.173)LEES(0.025)S(0.029)PIAAIFDTENLEK 154.79 4.66E-08 536550000 26588 22351.1 26932.7 31931 29941.5 18520.7 28763 18910.3 20270.3 TRUE FALSE 24923.90454 24005.9987 27571.55636 32750.40352 27590.01537 23867.32543 24450.25517 21271.29258 16887.05598 1.475917683 1.421562096 1.632703557 1.939379106 1.633796643 1.413350288 1.447869611 1.259621133 1 14.04363022 1.156117745 1.086351195 1.007613306 1.598193514 0.656880009 0.144125866 0.320580731 0.794044851 0.143994418 0.047422385 14.32576245 -1.156117745 0.590580208 S(ph)SSLESLQTAVAEVTLNGDIPFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSLESLQTAVAEVTLNGDIPFHR 24 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 S(0.367)S(0.367)S(0.265)LESLQTAVAEVTLNGDIPFHR;S(0.319)S(0.319)S(0.319)LES(0.043)LQTAVAEVTLNGDIPFHR 204.29 7.10E-25 46068000 30240.8 27729.4 29450 24294.8 25110 22661.3 28987 21943.5 20836 TRUE FALSE 28348.08231 29782.51363 30148.56791 24918.2457 23137.96189 29203.24943 24640.66845 24683.19428 17358.33699 1.633110494 1.715746943 1.736835039 1.435520333 1.332959597 1.682375993 1.419529328 1.421979207 1 14.08334112 -2.448062215 0.128591692 2.15E-12 1.898141947 0.727935674 0.116189772 32.53209315 0.522163076 10.46504632 1.096148401 0.003564001 2.448062215 1.898141947 S(ph)SSLESLQTAVAEVTLNGDIPFHRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSLESLQTAVAEVTLNGDIPFHRPR 26 1 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 S(0.319)S(0.319)S(0.319)LES(0.043)LQTAVAEVTLNGDIPFHRPR 106.99 0.0017485 86275000 22376 15316 24314 19612 19639 15566 22950 21181 11334 TRUE FALSE 20975.5261 16450.01258 24890.73956 20115.27712 18096.63216 20059.65151 19508.86056 23825.49448 9442.28218 2.221446649 1.742164899 2.636093594 2.130340604 1.91655278 2.124449484 2.066117088 2.523277108 1 13.20491988 -0.980592726 5.410607721 0.999996474 2.155971178 0.666544076 0.259914372 1.05E-05 1.98E-06 0.239119812 0.056360909 0.10457004 0.980592726 1.155974705 S(ph)SSLESLQTAVAEVTLNGDIPFHRPRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSLESLQTAVAEVTLNGDIPFHRPRPR 28 2 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 S(0.326)S(0.326)S(0.326)LES(0.021)LQTAVAEVTLNGDIPFHRPRPR;S(0.333)S(0.333)S(0.333)LESLQTAVAEVTLNGDIPFHRPRPR;S(0.333)S(0.333)S(0.333)LES(0.001)LQTAVAEVTLNGDIPFHRPRPR 221.23 1.26E-34 229916000 53076.5 62938 58384.5 61061 76347 58170 67581.7 58176.7 70661.4 TRUE FALSE 49754.53661 67597.99501 59769.40791 62627.92864 70351.01459 74962.73469 57448.45148 65440.18906 58867.55585 0.845194537 1.148306466 1.015320019 1.063878528 1.195072796 1.273413404 0.975893268 1.111651199 1 15.84518511 4.745810806 24.68680009 1.097117196 0.845194395 0.429459784 0.091548296 726.6143199 2474039.649 0.021144374 0.2161471 55694.30717 -4.745810806 -0.251922801 S(ph)SSLKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSLKER 7 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 S(0.333)S(0.333)S(0.333)LKER;S(0.475)S(0.475)S(0.051)LKER 93.649 0.008951 3148700000 2635290 1768190 2059110 1796290 2072500 1438520 2155850 1661450 3328600 TRUE FALSE 2470351.903 1899108.627 2107953.062 1842385.843 1909734.21 1853797.372 1832600.306 1868885.69 2773035.156 0.890847668 0.684848377 0.760160958 0.664393251 0.688680129 0.668508427 0.660864433 0.673949512 1 21.40303448 -1.646845954 8.440154897 1.000307268 0.706105094 0.626050993 0.069953491 0.000374885 1.57E-05 0.062779037 0.014782234 0.022550389 1.646845954 -0.294202174 S(ph)SSLSDLTHR ddPTM_SK-BR-3_Pertuzumab_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)LSDLTHR 77.74 0.020672 167380000 117520 182280 163340 168290 152620 172830 178580 149560 158750 TRUE FALSE 110164.633 195776.2009 167214.5019 172608.6063 140633.8408 222723.2153 151803.5869 168232.8952 132253.5994 0.832980225 1.480309055 1.264347456 1.305133524 1.06336494 1.684061653 1.147821969 1.272047762 1 17.01294746 0.574860759 1.656119572 1.000469062 1.286766595 0.098722967 0.228727287 4.09466611 13.61911175 0.192287088 0.054670823 3.757169246 -0.574860759 0.286297533 S(ph)SSMADGDNSYCLEAIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSMADGDNSYCLEAIIR 18 0 Q9ULV0;A0A0A0MR36;Q9ULV0-2;Q9ULV0-3 Q9ULV0 MYO5B Unconventional myosin-Vb 1 S(0.333)S(0.333)S(0.333)MADGDNSYCLEAIIR 108.89 0.0014783 29602000 51923 59264 58955 70520 65335 48918 65499 49217 55377 TRUE FALSE 48673.23212 63651.96822 60353.44044 72329.66259 60203.85265 63039.83248 55678.03301 55361.85079 46134.22095 1.05503531 1.37971265 1.308214146 1.567809342 1.304971698 1.366444067 1.206870559 1.20001703 1 15.49354967 1.074630214 1.157573871 1.007417579 1.341536332 0.399555954 0.126674579 0.438299548 1.225209881 0.109800364 0.034997613 11.87490693 -1.074630214 0.334118753 S(ph)SSMELHREENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSMELHREENR 12 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.333)S(0.333)S(0.333)MELHREENR;S(0.43)S(0.285)S(0.285)MELHREENR;S(0.355)S(0.355)S(0.291)MELHREENR 94.728 0.0025758 119210000 219222 285937 256903 251933 292821 230404 298629 260481 380015 TRUE FALSE 205501.2863 307108.073 262996.8605 258398.0273 269824.0198 296917.8945 253852.3538 293002.6262 316588.0415 0.649112599 0.970055822 0.830722662 0.816196424 0.852287467 0.93786832 0.8018381 0.925501244 1 18.27224724 -4.999999992 0.166997907 1.558214192 0.819720335 0.290369851 0.085423141 195.3259347 1.830555712 36.04303078 0.299539267 1.00E-05 4.999999992 -0.738493857 S(ph)SSMSYVDGFIGTWPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSMSYVDGFIGTWPK 16 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 S(0.331)S(0.331)S(0.331)MS(0.007)YVDGFIGTWPK;S(0.372)S(0.372)S(0.255)MSYVDGFIGTWPK 177.88 1.13E-08 81576000 267161 254496 222928 227336 232484 172665 305640 222579 291345 TRUE FALSE 250439.8699 273339.1486 228215.9574 233169.8266 214225.6444 222510.5825 259812.1194 250368.4781 242717.6373 1.031815704 1.126161047 0.94025288 0.960662889 0.882612598 0.916746657 1.070429501 1.031521569 1 17.88891942 3.952088552 5.502156167 0.973592548 1.079765612 0.367469579 0.058404493 0.187524328 17.04102492 0.015914726 0.030733796 8955.473479 -3.952088552 0.106173064 S(ph)SSPAGETEGDREPQARPGEGTAPLPPPGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSPAGETEGDREPQARPGEGTAPLPPPGQK 31 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(0.687)S(0.156)S(0.156)PAGET(0.001)EGDREPQARPGEGTAPLPPPGQK;S(0.332)S(0.332)S(0.332)PAGET(0.005)EGDREPQARPGEGTAPLPPPGQK 200.03 5.68E-26 1184950000 905690 764710 812630 815080 934190 665790 1086770 819740 1543220 TRUE FALSE 849004.4796 821329.9241 831905.9674 835996.3327 860822.4857 857992.7648 923818.9276 922086.3435 1285646.612 0.660371576 0.638845789 0.647072033 0.650253596 0.669563842 0.667362832 0.718563654 0.717216018 1 20.29406271 -0.30626085 0.433836609 1.065907144 0.640818681 0.990127106 0.010613452 0.519689123 0.102841829 0.062902785 0.005797386 0.494013879 0.30626085 -0.425088463 S(ph)SSPALKPKPNPPSPENTASSAPVDWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSPALKPKPNPPSPENTASSAPVDWR 27 2 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 S(0.328)S(0.328)S(0.328)PALKPKPNPPS(0.013)PENT(0.002)ASSAPVDWR 46.259 0.069579 55652000 170010 103880 125850 106860 113490 74750 130750 92696 152510 TRUE FALSE 159369.3776 111571.3833 128835.2214 109602.2085 104576.9532 96329.11154 111145.2513 104269.2996 127055.0957 1.254332828 0.878133873 1.014010659 0.862635283 0.823083502 0.758168029 0.874779958 0.820662084 1 16.95509471 7.682399209 1.017576334 0.866002705 199.9999999 0.652602227 0.083250475 562.0305626 1.449832585 0.024275006 260059.3952 48128154.56 -7.682399209 199.1339972 S(ph)SSPAPADIAQTVQEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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(0.391)S(0.391)S(0.218)PAPADIAQTVQEDLR;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;S(0.333)S(0.333)S(0.333)PAPADIAQTVQEDLR;S(0.333)S(0.333)S(0.333)PAPADIAQTVQEDLR 162.41 3.74E-11 151576000 250046.2 231257.7 240079.5 233915.1 267331.9 206603.6 269514.6 219664.8 304809 TRUE FALSE 234396.2547 248380.2607 245774.2991 239917.7575 246336.7309 266246.7054 229103.3878 247090.4338 253934.4088 0.923058265 0.978127627 0.967865286 0.94480208 0.970080156 1.04848613 0.902214824 0.973048257 1 17.95409637 2.499470516 23.95467232 0.973099615 0.959721035 0.076778012 0.038590844 2177.233512 2333634.953 0.012241265 0.011438858 315.8424615 -2.499470516 -0.013378579 S(ph)SSPAPPSQQSLYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSPAPPSQQSLYK 14 0 I3L3F1;A0A494BZY0;A0A494C199;A0A494C0J4;A0A494C1N2;Q9BXL6-3;Q9BXL6-2;Q9BXL6 I3L3F1 CARD14 Caspase recruitment domain-containing protein 14 1 S(0.333)S(0.333)S(0.333)PAPPSQQSLYK 73.927 0.019718 0 84944 96128 77453 85503 100870 53209 97072 75348 61917 TRUE FALSE 79627.50667 103245.4171 79290.22174 87697.15174 92948.07709 68569.57452 82516.95477 84755.36366 51582.6527 1.543687703 2.001553075 1.537148975 1.700128767 1.801925109 1.329314623 1.599703591 1.643098197 1 15.65459835 -2.513423917 0.187718066 9.26E-13 1.831290831 0.591738137 0.171410782 29.21124079 0.667308816 12.67557258 0.49802416 0.003066028 2.513423917 1.831290831 S(ph)SSPATEQSWMENDFDELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSPATEQSWMENDFDELR 19 0 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.333)S(0.333)S(0.333)PATEQSWMENDFDELR 173.28 7.06E-12 22372000 33325 33172 35202 29365 31908 35701 43590 30451 26693 TRUE FALSE 31239.24774 35628.0894 36037.00806 30118.55561 29402.07439 46007.29914 37054.08417 34252.87438 22237.76586 1.404783553 1.602143382 1.62053186 1.354387658 1.322168539 2.068881354 1.666268294 1.540301962 1 14.44072423 4.745099656 21.73739251 1.574572955 1.404783081 0 0.278711186 497.3710382 1653073.686 0.061405155 0.544402428 55603.18333 -4.745099656 -0.169789873 S(ph)SSPATEQSWMENDFDELREEGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSPATEQSWMENDFDELREEGFR 24 1 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.457)S(0.457)S(0.086)PATEQSWMENDFDELREEGFR 131.42 3.42E-05 67684000 4198.7 1668.8 4427.5 3513.6 2782.2 2099.3 4011.7 2100.8 0 TRUE FALSE 3935.910862 1792.359688 4532.522391 3603.764925 2563.697235 2705.333831 3410.182828 2363.089504 0 0 S(ph)SSPATEQSWMENDFDELREEGFRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSPATEQSWMENDFDELREEGFRR 25 2 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.333)S(0.333)S(0.333)PAT(0.001)EQSWMENDFDELREEGFRR;S(0.333)S(0.333)S(0.333)PAT(0.002)EQSWMENDFDELREEGFRR;S(0.333)S(0.333)S(0.333)PAT(0.002)EQSWMENDFDELREEGFRR 146.53 2.27E-07 285954000 35631.1 39890.1 38368.3 40628.9 47999 33187.3 41103.3 36913.7 49743 TRUE FALSE 33401.01305 42843.60451 39278.41419 41671.50636 44229.35216 42767.93476 34940.24175 41522.4567 41440.57195 0.805997878 1.033856496 0.947825099 1.005572665 1.067295891 1.032030514 0.843140915 1.001975956 1 15.33875629 1.080500022 19.4363412 1.001403783 0.96714829 0.03378942 0.082926002 20.53684702 4943.575332 0.076241153 0.019060328 12.03649452 -1.080500022 -0.034255493 S(ph)SSPELVTHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSPELVTHLK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.396)S(0.396)S(0.207)PELVTHLK;S(0.434)S(0.434)S(0.131)PELVTHLK;S(0.397)S(0.397)S(0.205)PELVTHLK 228.78 1.94E-12 2999930000 5216240 4776290 4987780 5036890 4708830 3450820 5614180 3902940 5382790 TRUE FALSE 4889764.85 5129931.481 5106092.497 5166145.125 4339017.486 4447015.715 4772385.828 4390230.65 4484367.575 1.090402329 1.14395874 1.138642721 1.15203427 0.967587383 0.991670652 1.064227173 0.979007759 1 22.09647311 2.74515544 24.99996521 1.008641822 1.134606591 0.817869628 0.030509699 218.7237562 829148.4516 0.009420742 0.009783807 556.1032586 -2.74515544 0.125964769 S(ph)SSPELVTHLKWDDPYYDIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSPELVTHLKWDDPYYDIAR 21 1 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.333)S(0.333)S(0.333)PELVTHLKWDDPYYDIAR;S(0.333)S(0.333)S(0.333)PELVTHLKWDDPYYDIAR 174.4 1.84E-12 138104000 35595 79923 46905 61686 122226 37624 54142 58216 243570 TRUE FALSE 33367.17249 85840.58208 48017.60875 63268.96719 112626.863 48485.43803 46023.90973 65484.39575 202916.5935 0.16443787 0.423033822 0.236637172 0.311797897 0.555040182 0.238942697 0.226811957 0.322715824 1 17.63052732 -1.506765976 2.521610481 1.03928067 0.311376287 0.791436734 0.111326767 2075819.217 1947155.094 560349.5333 0.027003803 0.031133936 1.506765976 -0.727904383 S(ph)SSPGKPQAVSSLNSSHSR ddPTM_SK-BR-3_Pertuzumab_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 230.55 3.29E-20 5002650000 3147040 3591370 3898850 3921790 3918230 2977690 5099400 3441640 4489910 TRUE FALSE 2950072.384 3857278.772 3991332.563 4022429.771 3610508.021 3837300.764 4334792.311 3871336.33 3740515.015 0.788680803 1.031215957 1.067054282 1.075367898 0.965243558 1.025874979 1.158875795 1.034974145 1 21.83480549 4.744901242 3.693673307 1.055247403 0.75804382 0.70977011 0.051340915 0.153867992 3.908719155 0.012661951 0.126727225 55577.78593 -4.744901242 -0.297203583 S(ph)SSPHDKNLPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSPHDKNLPQK 12 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.333)S(0.333)S(0.333)PHDKNLPQK;S(0.333)S(0.333)S(0.333)PHDKNLPQK 165.64 3.26E-05 495820000 797670 755130 744590 739430 993870 494620 1044150 669690 1918500 TRUE FALSE 747745.2586 811040.6109 762252.0264 758405.0257 915815.4593 637408.7645 887589.4009 753302.2707 1598289.956 0.467840804 0.507442725 0.476917235 0.474510287 0.572997068 0.398806713 0.555336907 0.471317653 1 20.60809773 -4.265895148 0.550450242 9.999999253 0.490627536 0.91573921 0.04853796 420.9776917 3.778114993 4625.883411 0.017775033 5.42E-05 4.265895148 -9.509371717 S(ph)SSPPPRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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;S(0.333)S(0.333)S(0.333)PPPRK;S(0.333)S(0.333)S(0.333)PPPRK;S(0.333)S(0.333)S(0.333)PPPRK;S(0.333)S(0.333)S(0.333)PPPRK 78.934 0.017971 9132620000 6730260 5286360 6192770 5851510 5773630 4504270 6527030 5320150 6928710 TRUE FALSE 6309025.04 5677767.595 6339665.429 6001669.653 5320192.39 5804579.628 5548362.445 5984382.439 5772263.54 1.092989777 0.983629309 1.098297987 1.039742834 0.921682171 1.005598512 0.961210868 1.036747958 1 22.46070574 2.96976408 23.84034695 0.982428404 1.050642246 0.389254612 0.042806586 380.7519855 300214.4786 0.012053178 0.012805451 932.7474695 -2.96976408 0.068213843 S(ph)SSPTLTPSQEGSPVFAGFEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSPTLTPSQEGSPVFAGFEGR 22 0 P0C860 P0C860 MSL3P1 Putative male-specific lethal-3 protein-like 2 1 S(0.333)S(0.333)S(0.333)PTLTPSQEGSPVFAGFEGR 103.73 0.00060242 25901000 13507 11708 12414 13993 15528 13247 18045 14833 15717 TRUE FALSE 12661.62098 12574.8725 12708.46594 14352.08407 14308.49352 17071.19385 15339.31977 16684.9327 13093.73116 0.966998697 0.960373506 0.970576361 1.096103463 1.092774347 1.30376847 1.171501047 1.27426877 1 13.67658864 2.921069212 1.571576876 1.198250048 0.961344632 0.541030228 0.084663486 0.229355073 1.146857322 0.027938375 0.031389398 833.8140556 -2.921069212 -0.236905416 S(ph)SSQRSPSPGPNHTSNSSNASNATVVPQNSSAR ddPTM_SK-BR-3_Pertuzumab_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(0.261)S(0.261)S(0.261)QRS(0.153)PS(0.062)PGPNHTSNS(0.001)S(0.001)NASNATVVPQNSSAR;S(0.234)S(0.234)S(0.234)QRS(0.234)PS(0.012)PGPNHT(0.012)S(0.012)NS(0.012)S(0.012)NAS(0.003)NATVVPQNSSAR 131.99 3.34E-08 176775000 25315.5 100724 64273 91366 109147 53612 75830 80481 118251 TRUE FALSE 23731.04804 108181.7098 65797.58591 93710.60624 100575.0349 69088.91408 64459.99547 90529.23001 98514.14417 0.240889755 1.098133782 0.667899889 0.951240119 1.020919745 0.70130959 0.65432224 0.918946521 1 16.58804325 7.999999902 0.039622819 1.306033658 3.88E-06 0.119223124 0.237300979 2778.002291 8.381247569 76.07353909 244.7755107 99999977.5 -7.999999902 -1.306029777 S(ph)SSSELLLTGPGAEEDPLPLIVQDQYVQEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSSELLLTGPGAEEDPLPLIVQDQYVQEAR 31 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.25)S(0.25)S(0.25)S(0.25)ELLLTGPGAEEDPLPLIVQDQYVQEAR;S(0.25)S(0.25)S(0.25)S(0.25)ELLLTGPGAEEDPLPLIVQDQYVQEAR;S(0.25)S(0.25)S(0.25)S(0.25)ELLLTGPGAEEDPLPLIVQDQYVQEAR 166.27 8.46E-13 87663000 66009 75166 56642 54845 70564 38885 80157 57166 74601 TRUE FALSE 61877.61452 80731.36885 57985.57499 56252.41555 65022.18808 50110.46825 68138.20199 64303.30094 62149.61116 0.995623518 1.298984295 0.932999803 0.905112912 1.046220352 0.80628772 1.096357656 1.034653311 1 15.92345774 3.844125091 5.182851777 0.976099014 1.160414151 0.30254223 0.108371101 0.214215107 8.484607596 0.025615192 0.047222112 6984.335465 -3.844125091 0.184315137 S(ph)SSSGSDDYAYTQALLLHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSSGSDDYAYTQALLLHQR 20 0 F6SS63;Q8N5C8-2;Q8N5C8 F6SS63 TAB3 TGF-beta-activated kinase 1 and MAP3K7-binding protein 3 1 S(0.354)S(0.354)S(0.27)S(0.008)GS(0.013)DDYAYTQALLLHQR 187.79 1.79E-17 132190000 49284 58332 61352 56526 69979 57961 61945 61322 91669 TRUE FALSE 46199.40241 62650.96197 62807.29841 57976.55286 64483.13162 74693.39978 52656.92232 68978.18669 76368.8517 0.604950859 0.820373236 0.822420359 0.759164916 0.844364295 0.978061057 0.689507844 0.903224091 1 16.22069671 -5 0.027939258 2.148007758 1.18E-16 0.430103669 0.091316534 1905.55569 4.013743288 233.4928025 100.688986 1.00E-05 5 -2.148007758 S(ph)SSSLLASPGHISVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSSLLASPGHISVK 15 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5 A0A499FIX8 ESYT2 Extended synaptotagmin-2 1 S(0.25)S(0.25)S(0.25)S(0.25)LLASPGHISVK;S(0.25)S(0.25)S(0.25)S(0.25)LLASPGHISVK 171.71 6.88E-07 347330000 196349 500550 397120 379000 536440 393390 611670 547600 621160 TRUE FALSE 184059.8666 537611.2428 406539.8739 388725.7816 494310.1663 506955.3068 519955.762 615969.0654 517484.3832 0.355681973 1.038893656 0.785608005 0.7511836 0.955217553 0.979653345 1.004775755 1.190314308 1 18.9811558 2.308544485 1.05644269 1.079826098 0.78458348 0.396943992 0.176571635 0.620331734 1.345606027 0.113245682 0.068277702 203.490662 -2.308544485 -0.295242618 S(ph)SSSQTLTQFDSNIAPADPDTAIVHPVPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSSQTLTQFDSNIAPADPDTAIVHPVPIR 30 0 Q96D71;Q96D71-3;H0YE73 Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.33)S(0.33)S(0.311)S(0.029)QTLTQFDSNIAPADPDTAIVHPVPIR;S(0.311)S(0.311)S(0.311)S(0.031)QT(0.031)LT(0.003)QFDSNIAPADPDTAIVHPVPIR;S(0.313)S(0.313)S(0.313)S(0.061)QT(0.001)LTQFDSNIAPADPDTAIVHPVPIR 263.09 1.28E-58 638930000 5645.7 12533.5 10885.9 4630.2 14492.8 13949.4 12960.8 9427 19756.3 TRUE FALSE 5292.345715 13461.49338 11144.11869 4749.018771 13354.59395 17976.36533 11017.44836 10603.9817 16458.8459 0.321550232 0.81788805 0.677089922 0.28853899 0.811393097 1.092200841 0.669393737 0.644272494 1 14.00657556 2.516580954 24.95775839 0.833798895 0.59500334 0.348637361 0.206143555 748.7200781 473554.9074 0.065887037 0.062109516 328.5344783 -2.516580954 -0.238795555 S(ph)SSTGNLLDKDDLAIPPPDYGAASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSTGNLLDKDDLAIPPPDYGAASR 25 1 Q9UQB8;Q9UQB8-2;Q9UQB8-4;Q9UQB8-5;Q9UQB8-3;I3L4C2;Q9UQB8-6;B4DWA1;I3L3C6 Q9UQB8 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 1 S(0.33)S(0.33)S(0.33)T(0.011)GNLLDKDDLAIPPPDYGAASR;S(0.351)S(0.351)S(0.294)T(0.005)GNLLDKDDLAIPPPDYGAASR;S(0.755)S(0.134)S(0.11)T(0.002)GNLLDKDDLAIPPPDYGAASR 158.2 1.52E-11 846620000 1321870 931800 1125880 950950 1159130 762920 1697290 1108890 2179290 TRUE FALSE 1239136.516 1000791.442 1152586.405 975352.987 1068096.606 983162.619 1442797.121 1247337.357 1815552.42 0.682512112 0.551232468 0.63484061 0.537221055 0.58830392 0.541522574 0.794687669 0.687029107 1 20.79197715 0.874756623 0.810342958 0.995673812 0.587708091 0.766702339 0.068502682 0.339771929 0.470861028 0.060714358 0.021741896 7.49474089 -0.874756623 -0.407965721 S(ph)SSVPHPFQVTLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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;S(0.5)S(0.5)SVPHPFQVTLLR 225.68 1.73E-12 1004540000 1055300 1321040 1005800 1074950 1428880 724070 1417530 1118630 1351570 TRUE FALSE 989250.6568 1418851.176 1029658.051 1102535.037 1316661.529 933097.2547 1204984.536 1258293.418 1125984.236 0.878565281 1.260098615 0.914451569 0.979174488 1.169342773 0.828694777 1.070161107 1.117505359 1 20.1027552 3.938013156 24.84387343 1.0109528 1.095420815 0.023947523 0.132393293 645.046723 409773.3586 0.030682689 0.055315129 8669.881387 -3.938013156 0.084468015 S(ph)STDFSELEQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSTDFSELEQPR 12 0 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 S(0.531)S(0.469)TDFSELEQPR 167.83 5.05E-05 170110000 195970 197600 217530 197680 229320 189980 234600 176710 204200 TRUE FALSE 183704.5875 212230.5096 222689.9143 202752.8035 211310.1322 244824.1419 199423.9079 198772.6325 170117.7008 1.079867566 1.247551011 1.309034352 1.191838371 1.242140772 1.439145608 1.172270181 1.1684418 1 17.37617374 0.943062428 1.86997179 1.002874433 1.254628939 0.405169401 0.092371012 0.367241858 2.68524285 0.081839912 0.023099032 8.771268963 -0.943062428 0.251754506 S(ph)STPLHS(ph)PSPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSTPLHSPSPIR 12 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 2 S(0.996)S(0.002)T(0.002)PLHS(0.906)PS(0.094)PIR;S(0.997)S(0.001)T(0.001)PLHS(0.7)PS(0.3)PIR;S(0.996)S(0.002)T(0.002)PLHS(0.687)PS(0.312)PIR 99.927 0.0018597 319648000 138579 423770 290511 295087 356116 277876 332844 377740 263085 TRUE FALSE 129905.5878 455146.3717 297402.0581 302659.432 328148.0859 358094.2903 282937.1322 424901.6705 219174.4139 0.592704164 2.076640077 1.3569196 1.38090677 1.4972007 1.633832544 1.290922271 1.938646318 1 17.74171986 -1.550697015 5.69973866 0.998613539 1.504448842 0.115120811 0.400918724 0.006198217 0.000488598 0.340634406 0.080094893 0.028138632 1.550697015 0.505835303 S(ph)STPLHSPSPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSTPLHSPSPIR 12 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 S(0.333)S(0.333)T(0.333)PLHSPSPIR 150.22 4.38E-05 189940000 122820 171110 143230 144830 178910 140670 158510 174950 154630 TRUE FALSE 115132.9154 183779.1624 146627.4832 148546.583 164859.1303 181279.1454 134742.897 196792.8926 128821.2541 0.893741613 1.426621436 1.138224312 1.153121696 1.279751012 1.407214568 1.045967904 1.527643044 1 16.97501112 4.75923084 23.81587376 1.245945935 0.893740954 0.299522536 0.169917686 3161.925194 3643003.58 0.035867013 1.431624192 57442.17026 -4.75923084 -0.352204981 S(ph)STPLPTISSSAENTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSTPLPTISSSAENTR 16 0 P42166;P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 S(0.91)S(0.09)TPLPTISSSAENTR 231.03 1.80E-15 137090000 190600 186570 164900 143050 194530 149530 217920 192920 229550 TRUE FALSE 178670.6862 200383.8369 168811.5059 146720.9052 179252.3985 192696.8836 185244.9191 217006.4867 191236.6221 0.934291164 1.04783192 0.882736288 0.767221799 0.93733301 1.007635889 0.968668642 1.134753816 1 17.5449993 1.728979449 1.662027409 1.055137124 0.924654604 0.331172489 0.080094071 0.472400822 2.577927987 0.063041599 0.024805891 53.57713043 -1.728979449 -0.130482521 S(ph)STPPGESYFGVSSLQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSTPPGESYFGVSSLQLK 18 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.378)S(0.378)T(0.244)PPGESYFGVSSLQLK 178.15 9.46E-14 628700000 409310 338470 363760 346890 345940 285470 464330 320990 418310 TRUE FALSE 383692.0177 363530.671 372388.559 355791.7847 318771.2679 367880.5548 394708.0271 361066.3081 348491.3586 1.1010087 1.043155481 1.068573294 1.020948657 0.914717854 1.055637524 1.132619267 1.036083964 1 18.41076336 0.984167043 24.34316448 0.99999999 1.050938925 0.064436531 0.056791907 2127.588524 3271173.173 0.056437326 0.014109331 9.641998123 -0.984167043 0.050938935 S(ph)STPPRQS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSTPPRQSPSR 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.568)S(0.216)T(0.216)PPRQS(0.985)PS(0.015)R 100.98 0.0020622 365760000 296060 308390 272000 278190 333080 208600 307590 271950 378570 TRUE FALSE 277530.1331 331223.5165 278451.9684 285328.8264 306921.2404 268819.4337 261469.735 305903.5561 315384.2213 0.879974692 1.050222218 0.882897588 0.904702287 0.973166124 0.852355367 0.829051415 0.969939317 1 18.26675096 3.78534935 6.899213489 0.902559535 0.974820594 0.051218503 0.0683437 0.378272804 36.62615232 0.016610119 0.030000828 6100.274105 -3.78534935 0.072261058 S(ph)STPVPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSTPVPSK 8 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C3G1 Q9H8V3-2 ECT2 Protein ECT2 1 S(0.449)S(0.275)T(0.275)PVPSK 99.688 0.006961 263870000 1182900 872770 1043300 1009000 991350 792580 1290900 864060 1392000 TRUE FALSE 1108864.401 937390.7989 1068047.569 1034892.648 913493.3699 1021384.98 1097341.529 971939.793 1159666.207 0.956192733 0.808328115 0.920995681 0.892405626 0.787720953 0.880757733 0.946256364 0.838120303 1 20.14527818 -1.59447373 0.421613867 1.084425141 0.874453666 0.306362413 0.05585061 39.25400909 3.311493301 3.502352669 0.031204272 0.025440537 1.59447373 -0.209971475 S(ph)STSPSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSTSPSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR 39 0 Q9BPZ3;D6RA77;D6R9Y1 Q9BPZ3 PAIP2 Polyadenylate-binding protein-interacting protein 2 1 S(0.23)S(0.23)T(0.23)S(0.23)PS(0.032)IINEDVIINGHS(0.047)HEDDNPFAEYMWMENEEEFNR;S(0.24)S(0.24)T(0.24)S(0.24)PS(0.041)IINEDVIINGHS(0.001)HEDDNPFAEYMWMENEEEFNR;S(0.248)S(0.248)T(0.248)S(0.248)PS(0.007)IINEDVIINGHSHEDDNPFAEYMWMENEEEFNR;S(0.242)S(0.242)T(0.242)S(0.242)PS(0.025)IINEDVIINGHS(0.006)HEDDNPFAEYMWMENEEEFNR 174.04 1.63E-18 122664000 36038 42195.8 42946.3 41698.7 43450.2 36125 44194.7 38944.2 48868.7 TRUE FALSE 33782.44591 45320.02094 43965.00652 42768.75924 40037.79656 46553.70106 37568.11502 43806.4691 40712.19827 0.829786829 1.113180395 1.079897632 1.050514614 0.983434898 1.143482864 0.922772943 1.076003531 1 15.3131735 -1.109921432 6.85748723 0.999999976 1.034237816 0 0.093728982 3.53E-08 4.64E-09 0.082171386 0.019367966 0.077638756 1.109921432 0.03423784 S(ph)SVKTPEPVVPTAPEPHPTTSTDQPVTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSVKTPEPVVPTAPEPHPTTSTDQPVTPK 29 1 Q14676;Q14676-3;Q14676-2 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 S(0.362)S(0.362)VKT(0.276)PEPVVPTAPEPHPTTSTDQPVTPK;S(0.374)S(0.374)VKT(0.251)PEPVVPTAPEPHPTTSTDQPVTPK 156.84 3.52E-09 1170530000 1295060 774860 941050 957940 1038480 609810 1280590 793930 1065870 TRUE FALSE 1214004.506 832231.4406 963372.1504 982522.3622 956921.9698 785852.2476 1088577.418 893053.9082 887969.4112 1.367169286 0.937229853 1.08491592 1.106482216 1.077651953 0.884999233 1.2259177 1.005725982 1 19.76015045 4.751572381 24.57318596 1.049247158 1.367169546 0.539752956 0.094523407 1341.826033 2534029.486 0.021306021 0.391016195 56438.09951 -4.751572381 0.317922389 S(ph)SVSHSVLSEMQVIEQETPVSAK ddPTM_SK-BR-3_Pertuzumab_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(0.213)S(0.213)VS(0.181)HS(0.181)VLS(0.213)EMQVIEQETPVSAK 148 7.15E-08 59518000 64596 59545 55938 58442 65208 34996 69789 51980 109810 TRUE FALSE 60553.05167 63953.77376 57264.87578 59941.72066 60086.82672 45098.77709 59324.78734 58469.81742 91482.0016 0.661912186 0.69908586 0.625968767 0.655229658 0.656815829 0.492979781 0.648485891 0.639140119 1 16.48120031 0.409413848 3.180882426 0.999999872 0.635419395 0.819161798 0.0539061 21.02214685 112.22315 0.051694817 0.013431445 2.566928952 -0.409413848 -0.364580477 S(ph)SVTVEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSVTVEER 8 0 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 S(0.991)S(0.009)VTVEER 182.92 0.0001948 0 373380 306120 313360 346730 339680 265900 450330 303070 385470 TRUE FALSE 350010.8123 328785.4433 320793.0472 355627.6788 313002.903 342661.0135 382807.1972 340908.9566 321132.5668 1.089926244 1.023830895 0.998942743 1.107417047 0.9746844 1.067039126 1.192053491 1.061583258 1 18.29280945 1.995028512 24.98174949 1.111800225 1.033411058 0.044435968 0.062237125 272.2649374 1368135.516 0.021615414 0.015539496 98.86179969 -1.995028512 -0.078389167 S(ph)SWPNSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSWPNSEK 8 0 Q9ULV0;A0A0A0MR36;Q9ULV0-2 Q9ULV0 MYO5B Unconventional myosin-Vb 1 S(0.654)S(0.346)WPNSEK;S(0.756)S(0.244)WPNSEK 155.06 0.0004354 175621000 603680 476840 495510 496800 563180 405940 715720 517200 901080 TRUE FALSE 565896.7464 512145.7298 507263.7312 509548.7291 518950.1146 523128.2881 608404.4304 581773.5585 750683.9268 0.753841565 0.682238838 0.675735437 0.678779325 0.691303085 0.696868908 0.810466841 0.774991362 1 19.51784607 0.78561691 0.712303129 1.000478033 0.686765441 0.888095356 0.03311979 0.281097579 0.293872278 0.031657043 0.011767912 6.104033526 -0.78561691 -0.313712592 S(ph)T(ph)S(ph)S(ph)SRSRK ddPTM_SK-BR-3_Pertuzumab_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(0.633)T(0.695)S(0.711)S(0.711)S(0.689)RS(0.56)RK 43.297 0.087694 10119000000 2715700 2236800 2186500 2347100 2585400 2822100 2911600 1865100 3104100 TRUE FALSE 2545729.185 2402414.999 2238364.813 2407330.56 2382353.113 3636794.457 2475032.61 2097961.841 2586005.657 0.984425219 0.929006088 0.865568413 0.930906919 0.921248222 1.406336621 0.957087083 0.811275039 1 21.302294 S(ph)TAALEEDAQILK ddPTM_SK-BR-3_Pertuzumab_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(0.99)T(0.01)AALEEDAQILK;S(0.979)T(0.021)AALEEDAQILK;S(0.995)T(0.005)AALEEDAQILK;S(0.989)T(0.011)AALEEDAQILK;S(0.986)T(0.014)AALEEDAQILK;S(0.995)T(0.005)AALEEDAQILK 297.52 9.90E-41 747996000 1444390 1391860 1213910 1232990 1792240 632872 1606570 1188840 2378870 TRUE FALSE 1353988.208 1494914.763 1242704.518 1264630.611 1651484.7 815571.8726 1365679.743 1337269.291 1981821.229 0.683204009 0.754313629 0.627051775 0.638115382 0.833316687 0.411526459 0.689103398 0.674767871 1 20.9183954 0.549064735 2.960451231 0.999996141 0.6625535 0.492600924 0.107273022 8.71615044 56.11276013 0.094421316 0.024707471 3.540501111 -0.549064735 -0.33744264 S(ph)TDSSSVSGSLQQETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 STDSSSVSGSLQQETK 16 0 Q9H8G2;A0A3B3ISJ3 Q9H8G2 CAAP1 Caspase activity and apoptosis inhibitor 1 1 S(0.82)T(0.173)DS(0.006)S(0.001)SVSGSLQQETK;S(0.714)T(0.181)DS(0.104)S(0.001)SVSGSLQQETK;S(0.869)T(0.124)DS(0.006)SSVSGSLQQETK 471.04 3.99E-206 532230000 877161 672349 711082 710199 652889 458410 722837 492460 683753 TRUE FALSE 822261.0588 722130.4195 727949.2008 728423.9087 601613.7316 590745.5253 614454.3023 553944.715 569630.2071 1.443499745 1.267717917 1.277932932 1.278766294 1.056147873 1.037068466 1.078689814 0.972463728 1 19.11966613 2.749207118 3.260426285 1.034089309 1.307156899 0.868519435 0.055806521 0.089014449 1.97526572 0.017889619 0.018015821 561.315608 -2.749207118 0.273067589 S(ph)TDSVPISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 STDSVPISK 9 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 S(0.99)T(0.009)DSVPISK;S(0.994)T(0.006)DSVPISK;S(0.992)T(0.008)DSVPISK;S(0.965)T(0.025)DS(0.011)VPISK 222.18 4.12E-07 4524730000 13324400 8951500 10405300 9445000 10174800 8305400 14149300 10282800 9752600 TRUE FALSE 12490449.59 9614278.374 10652118.63 9687374.69 9375712.251 10703034.15 12027743.82 11566630.22 8124828.056 1.537318637 1.183320842 1.31105773 1.192317502 1.153958236 1.317324389 1.480369029 1.423615384 1 22.95390585 2.002419727 24.93158255 1.36573854 1.261693943 0 0.167073746 185.8522065 1914899.726 0.056642623 0.041573874 100.5587177 -2.002419727 -0.104044597 S(ph)TECLLLSLLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STECLLLSLLHR 12 0 H0YES2;Q5TB30 H0YES2 DEPDC1 DEP domain-containing protein 1A 1 S(0.5)T(0.5)ECLLLSLLHR 115.33 0.00061946 9765800 6887.9 8023.7 5822.3 7989.4 9140 5814.4 8170.6 9041.7 7598.4 TRUE FALSE 6456.798634 8617.783097 5960.407705 8194.42153 8422.181269 7492.922891 6945.494382 10170.57615 6330.177952 1.020002705 1.361380859 0.941586121 1.294500975 1.330480965 1.18368282 1.097203654 1.606680922 1 12.62803034 S(ph)TENVNKLPELSSFGKPSSSVQGTGLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STENVNKLPELSSFGKPSSSVQGTGLIR 28 2 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 S(0.8)T(0.2)ENVNKLPELSSFGKPSSSVQGTGLIR;S(0.849)T(0.151)ENVNKLPELSSFGKPSSSVQGTGLIR 194.99 2.43E-19 863700000 827350 563420 673180 656660 679590 458410 940340 602860 990450 TRUE FALSE 775567.6404 605136.203 689148.1475 673511.0073 626217.7427 590745.5253 799344.7467 678128.3981 825137.4964 0.939925338 0.733376202 0.835191893 0.816240942 0.758925325 0.715935863 0.968741271 0.821836847 1 19.65427502 1.716231508 10.78744527 0.920078626 0.79541662 0.387639817 0.076632188 0.105290165 32.44252818 0.03261279 0.017728178 52.02732632 -1.716231508 -0.124662006 VTPTEEHVEGPLPS(ph)PVTNGTSPAQLNGGSACSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTPTEEHVEGPLPSPVTNGTSPAQLNGGSACSSR 34 0 H3BN50;Q15599-3;H3BQS0;H3BUQ9;Q15599;Q15599-2 H3BN50;Q15599 SLC9A3R2 Na(+)/H(+) exchange regulatory cofactor NHE-RF2 1 VTPTEEHVEGPLPS(1)PVTNGTSPAQLNGGSACSSR 381.99 7.13E-150 383570000 140520 162120 175930 232520 157930 91226 105420 72790 74428 TRUE FALSE 131725.104 174123.5335 180103.1427 238486.8569 145526.8149 117561.4653 89613.24967 81877.99173 62005.48598 2.124410477 2.80819561 2.904632386 3.84622188 2.346999021 1.895984902 1.445247114 1.320495928 1 15.92010824 2.128280124 1.892826555 1.292166182 2.902703118 0.732339036 0.438929505 0.178324156 1.241254811 0.233774076 0.134621138 134.3631338 -2.128280124 1.610536936 up VIHDNFGIVEGLMTTVHAITATQKTVDGPSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIHDNFGIVEGLMTTVHAITATQKTVDGPSGK 32 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 195.2 1.96E-21 123520000 194060 296170 178190 256560 246800 74258 93258 72768 84656 FALSE TRUE 181914.131 318098.735 182416.7509 263143.764 227417.3235 95695.07912 79274.82866 81853.24498 70526.3667 2.579377607 4.510351941 2.586504303 3.731140228 3.224571663 1.356869545 1.124045267 1.160604875 1 16.1058751 2.235292623 4.169886142 1.13706222 3.4253354 0.794234124 0.548788515 0.083454887 3.345058013 0.195353245 0.149310674 171.9066285 -2.235292623 2.28827318 up S(ph)TNTAVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STNTAVSR 8 0 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 S(0.976)T(0.024)NTAVSR;S(0.98)T(0.019)NTAVSR 98.898 0.0075482 1785870000 546600 542220 573320 578500 566140 502160 638170 529200 741350 TRUE FALSE 512389.2817 582366.533 586919.4211 593345.2894 521677.6481 647125.4401 542482.333 595271.7849 617613.8957 0.829627191 0.942929777 0.950301516 0.960705861 0.844666306 1.047783161 0.878351891 0.963825116 1 19.23634569 8 0.044550757 1.122891985 0.609409444 0.198167547 0.060589404 1238.195658 4.183035898 12.32112909 45.7465117 100000000 -8 -0.513482541 IKEEYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKEEYK 6 1 Q5VWI1 Q5VWI1 TCERG1L Transcription elongation regulator 1-like protein 0 105.95 0.029678 1915500000 2265600 1847100 1883000 2522600 3883400 2501100 5807400 3196100 6391300 FALSE TRUE 2123800.14 1983861.206 1927665.649 2587334.187 3578413.429 3223126.968 4936634.283 3595140.12 5324550.741 0.398869359 0.372587529 0.362033483 0.485925351 0.672059222 0.60533313 0.927145692 0.67520065 1 22.34422837 2.290930956 0.678478776 0.929001279 0.344934922 0.825095861 0.092325686 0.249864337 0.225444322 0.070668458 0.049066441 195.402878 -2.290930956 -0.584066357 down S(ph)TPLEENVVDREQIDFLAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STPLEENVVDREQIDFLAAR 20 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 S(0.577)T(0.423)PLEENVVDREQIDFLAAR;S(0.5)T(0.5)PLEENVVDREQIDFLAAR 98.019 0.00052028 124987000 33550 41559 37468 34678 41064 24890 35911 38049 53998 TRUE FALSE 31450.16539 44636.0716 38356.75865 35567.89619 37838.99908 32075.33894 30526.47893 42799.50141 44985.38496 0.699119623 0.992234959 0.852649337 0.790654481 0.841139831 0.713016883 0.678586589 0.951409029 1 15.45716875 5.030493567 15.90200234 0.835851526 0.28150707 0.148811796 0.108999262 21409374.53 312286524.9 0.027245481 318218369.3 107273.7757 -5.030493567 -0.554344456 S(ph)TPLSQPSANGVQTEGLDYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STPLSQPSANGVQTEGLDYDR 21 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 S(0.499)T(0.499)PLS(0.003)QPSANGVQTEGLDYDR 212.65 8.77E-23 153410000 36386 44379 39428 38010 45711 34530 42496 38832 59311 TRUE FALSE 34108.66521 47664.86734 40363.25078 38985.40095 42121.04245 44498.25045 36124.11931 43680.26068 49411.61094 0.690296563 0.964649127 0.816877856 0.788992713 0.852452321 0.900562633 0.731085642 0.884008027 1 15.59256247 0.985742109 24.35207467 1.000000008 0.831863016 0.343089876 0.078198654 664.6444098 1135196.614 0.070901796 0.017725449 9.677030485 -0.985742109 -0.168136992 S(ph)TPPPNNLVNPVQELETER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STPPPNNLVNPVQELETER 19 0 Q8NDI1-3;Q8NDI1-2;Q8NDI1 Q8NDI1-3 EHBP1 EH domain-binding protein 1 1 S(0.5)T(0.5)PPPNNLVNPVQELETER;S(0.5)T(0.5)PPPNNLVNPVQELETER 124.25 3.11E-05 44473000 28990 30228 27230 30040 36401 25714 34197 26614 34030 TRUE FALSE 27175.56765 32466.11257 27875.90846 30810.87726 33542.21229 33137.21437 29069.47732 29936.81648 28350.17316 0.95856796 1.145182161 0.983271189 1.086796793 1.183139592 1.168854038 1.025372126 1.055965913 1 14.79106993 1.604538974 25 1.030494019 1.086678075 0.13133065 0.073174794 0.749564726 5587.331844 0.036886568 0.018165019 40.22897561 -1.604538974 0.056184056 S(ph)TPPPNNLVNPVQELETERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STPPPNNLVNPVQELETERR 20 1 Q8NDI1-3;Q8NDI1-2;Q8NDI1 Q8NDI1-3 EHBP1 EH domain-binding protein 1 1 S(0.5)T(0.5)PPPNNLVNPVQELETERR 61.703 0.02958 68384000 36885 24042 38489 49143 32034 26945 41383 23159 36414 TRUE FALSE 34576.43369 25822.0947 39401.97726 50404.09258 29518.17886 34723.58408 35178.00333 26050.45213 30336.26816 1.139772154 0.851195492 1.298840617 1.661512626 0.973032632 1.144622796 1.159602201 0.858723031 1 14.888756 1.250432967 24.08927509 0.929361558 1.163335262 0.184835856 0.213720389 228.9682239 464591.8763 0.146723626 0.05256018 17.80053137 -1.250432967 0.233973704 S(ph)TPPYLFPEYPEASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STPPYLFPEYPEASK 15 0 Q8TE76-2;Q8TE76-3;Q8TE76 Q8TE76-2 MORC4 MORC family CW-type zinc finger protein 4 1 S(0.499)T(0.499)PPY(0.001)LFPEYPEASK;S(0.499)T(0.499)PPY(0.002)LFPEYPEASK 117.79 0.00035876 111307000 118441 77227 100191 91757 81808 83238 149839 87055 90447 TRUE FALSE 111027.9892 82944.96743 102567.5778 94111.63996 75383.12968 107267.4593 127372.033 97924.00838 75350.81139 1.473481004 1.100783998 1.361200708 1.248979782 1.000428904 1.423574045 1.690387013 1.299574704 1 16.20133543 2.038496004 24.99242337 1.444268144 1.233898199 0 0.217292808 254.5499004 165258.187 0.074626485 0.055115213 109.2687572 -2.038496004 -0.210369945 S(ph)TPQPPSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STPQPPSGK 9 0 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 S(0.5)T(0.5)PQPPSGK 77.192 0.023467 0 231650 144710 182910 159510 166030 149520 236370 176940 212130 TRUE FALSE 217151.44 155424.479 187248.7116 163603.2966 152990.6735 192683.9967 200928.5129 199031.3485 176724.1326 1.228759405 0.879475127 1.059553717 0.925755268 0.86570335 1.090309478 1.136961375 1.126226201 1 17.43113954 2.034574633 24.53322718 1.105619253 0.982358041 0.153250028 0.108848667 200.5609238 142311.6322 0.037280697 0.027533506 108.2865787 -2.034574633 -0.123261212 S(ph)TPVRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STPVRDR 7 1 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 S(0.5)T(0.5)PVRDR;S(0.5)T(0.5)PVRDR 111.46 0.0039819 147036000 319760 309750 327120 310850 312830 267640 342190 269570 305960 TRUE FALSE 299746.7924 332684.2123 334879.4409 318826.9373 288261.5937 344903.3232 290881.7862 303226.4079 254893.2994 1.175969682 1.305190105 1.313802448 1.250825102 1.130910833 1.353128246 1.1411904 1.189620946 1 17.95953392 0.61363097 0.518397113 0.988484468 1.274715167 0.53440989 0.071403907 1.119518361 0.595156951 0.093605822 0.033757475 4.108005063 -0.61363097 0.286230699 S(ph)TSATDTHHVEMAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 STSATDTHHVEMAR 14 0 H3BTL2;H3BS02;O14874-2;O14874-3;O14874;H3BQP2;H3BNP3 H3BTL2 BCKDK "[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial" 1 S(0.855)T(0.126)S(0.019)ATDTHHVEMAR;S(0.979)T(0.02)S(0.001)ATDTHHVEMAR;S(0.964)T(0.034)S(0.001)ATDTHHVEMAR;S(0.499)T(0.499)S(0.002)ATDTHHVEMAR;S(0.359)T(0.359)S(0.282)ATDTHHVEMAR 260.56 1.17E-24 4800100000 1243980 1266456 1014984 1035815 1517670 921924 1043782 1243896 1427668 TRUE FALSE 1166121.512 1360225.72 1039059.9 1062395.767 1398478.32 1188068.493 887276.5791 1399199.154 1189380.988 0.98044405 1.143641721 0.873614015 0.893234193 1.175803493 0.998896489 0.745998623 1.176409551 1 20.18177949 1.972207207 24.97075356 0.92754716 1.013329767 0 0.140848856 1977.154798 1776395.634 0.05545025 0.035864279 93.80094347 -1.972207207 0.085782607 S(ph)TSEGAWPQLPSGLSMMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STSEGAWPQLPSGLSMMR 18 0 G3V1A6;P57764 G3V1A6 GSDMD Gasdermin-D 1 S(0.333)T(0.333)S(0.333)EGAWPQLPSGLSMMR 81.346 0.0042502 0 70512 88738 69836 91842 70618 45588 80316 57438 62499 TRUE FALSE 66098.77979 95308.25385 71492.5429 94198.82121 65071.94714 58748.51554 68273.36142 64609.26074 52067.51314 1.269482174 1.830474476 1.373073892 1.809166897 1.249760997 1.128314221 1.311246827 1.240874719 1 15.66809588 2.609137643 6.992685316 1.204268217 1.580150498 0.510184099 0.187123118 0.196288221 10.30472248 0.054578637 0.051346718 406.5721657 -2.609137643 0.37588228 S(ph)TSFRGGMGSGGLATGIAGGLAGMGGIQNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 STSFRGGMGSGGLATGIAGGLAGMGGIQNEK 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.324)T(0.324)S(0.324)FRGGMGS(0.028)GGLATGIAGGLAGMGGIQNEK;S(0.333)T(0.333)S(0.333)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.333)T(0.333)S(0.333)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.329)T(0.329)S(0.329)FRGGMGS(0.006)GGLAT(0.006)GIAGGLAGMGGIQNEK 190.89 1.55E-18 1298341000 1727011 2227072 1711945 1829490 2052617 861957 2287402 1433296 5811870 TRUE FALSE 1618920.464 2391966.728 1752553.144 1876437.811 1891412.741 1110789.993 1944427.305 1612246.161 4841831.351 0.334361184 0.494021075 0.361960799 0.387547123 0.390639947 0.229415259 0.401589226 0.332982717 1 22.2071214 -1.223435044 3.893160595 1.000591796 0.374771684 0.898960055 0.066688785 37769878.14 68405319.19 272576.0188 0.015875345 0.059781245 1.223435044 -0.625820112 S(ph)TSFRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STSFRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR 40 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.333)T(0.333)S(0.333)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR 306.62 2.21E-94 448890000 58084 188290 71592 121070 209000 36495 118510 65584 963280 TRUE FALSE 54448.62612 202231.1875 73290.19605 124176.8612 192585.9831 47030.51405 100740.5257 73772.30677 802502.345 0.067848557 0.252000743 0.09132708 0.15473707 0.239981832 0.058604831 0.125532999 0.09192784 1 19.61414608 -1.205548665 4.345322812 1.000296315 0.140897916 0.94381783 0.066292919 17031536.07 7087826.817 47754.76673 0.014553247 0.062294734 1.205548665 -0.859398399 S(ph)TSGPRPGCQPSSPCVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STSGPRPGCQPSSPCVPK 18 1 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 S(0.38)T(0.38)S(0.24)GPRPGCQPSSPCVPK 103.95 0.00031547 303160000 128960 104550 100920 98004 109730 75339 116020 99634 181150 TRUE FALSE 120888.6238 112290.9908 103313.8701 100518.9486 101112.2484 97088.14627 98623.87808 112073.5242 150914.8947 0.801038387 0.744068311 0.684583654 0.666063802 0.669995156 0.643330444 0.653506589 0.742627323 1 17.20337568 0.884010379 6.121245218 0.999997803 0.692549828 0.805981722 0.046726346 0.828123155 43.50655929 0.047463395 0.011930111 7.656149039 -0.884010379 -0.307447975 S(ph)TSGSPRPAGAKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STSGSPRPAGAKPK 14 2 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3-2 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 S(0.307)T(0.307)S(0.223)GS(0.164)PRPAGAKPK 76.85 0.013728 183830000 797860 546830 664270 651240 757530 517770 1032800 677100 861390 TRUE FALSE 747923.3668 587317.8622 680026.7981 667951.9209 698036.6495 667241.7937 877941.228 761637.4255 717618.4442 1.042229855 0.818426375 0.947616109 0.93078979 0.972712805 0.929800229 1.223409508 1.061340371 1 19.45285745 1.76190342 25 1.115425989 0.927936637 0.451966035 0.078434752 8.757932433 9386.703562 0.033342791 0.018491259 57.7967502 -1.76190342 -0.187489351 S(ph)TSPSAAGGQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STSPSAAGGQQK 12 0 Q2TB10 Q2TB10 ZNF800 Zinc finger protein 800 1 S(0.479)T(0.26)S(0.26)PSAAGGQQK 102.87 0.0024201 314330000 1211000 752680 974500 736040 769670 728370 1068600 711450 801060 TRUE FALSE 1135205.672 808409.2104 997615.6002 754928.0325 709223.2229 938638.5949 908373.3504 800276.0986 667357.911 1.701044751 1.211357799 1.494873416 1.131219126 1.062732922 1.40649954 1.361148696 1.199170768 1 19.34810118 8 0.03109974 6.39E-11 3.212473297 0.364778413 0.169022027 1653.298316 3.938917198 127.492763 319.7333016 100000000 -8 3.212473297 S(ph)TSQSIVSLLTGTAGEDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 STSQSIVSLLTGTAGEDEK 19 0 V9GZ20;V9GXZ5;Q70EL4-2;Q70EL4-3;Q70EL4-4;Q70EL4 V9GZ20 USP43 Ubiquitin carboxyl-terminal hydrolase 43 1 S(0.319)T(0.319)S(0.319)QS(0.043)IVSLLTGTAGEDEK;S(0.331)T(0.331)S(0.331)QS(0.006)IVSLLTGTAGEDEK;S(0.331)T(0.331)S(0.331)QS(0.006)IVSLLTGTAGEDEK;S(0.319)T(0.319)S(0.319)QS(0.044)IVSLLTGTAGEDEK;S(0.333)T(0.333)S(0.333)QSIVSLLTGTAGEDEK 216.32 4.05E-19 151307000 469973 394260 399555 416271 546053 256625 555191 369250 542970 TRUE FALSE 440558.2289 423451.4206 409032.6333 426953.2186 503168.2001 330708.4715 471945.2637 415351.6753 452344.7993 0.973943394 0.936125321 0.904249665 0.943866757 1.112355444 0.731098207 1.043330805 0.91821919 1 18.78706336 0.199585863 0.880411157 1.000444077 0.942036612 0.026633639 0.098316233 15.53734414 13.57133575 0.107990587 0.0278067 1.58338258 -0.199585863 -0.058407465 S(ph)TSQSSESSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STSQSSESSVK 11 0 Q9NXV6 Q9NXV6 CDKN2AIP CDKN2A-interacting protein 1 S(0.223)T(0.223)S(0.223)QS(0.11)S(0.11)ES(0.11)SVK 66.486 0.065641 206680000 85707 409580 318130 325880 351360 520300 243490 346010 196780 TRUE FALSE 80342.75186 439905.7294 325676.1938 334242.6325 323765.6029 670502.1636 206980.935 389210.1102 163936.1468 0.490085643 2.683396786 1.986603933 2.03885866 1.97494945 4.090020273 1.262570452 2.374156755 1 17.32277447 S(ph)TSTPNVHMVSTTLPVDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 STSTPNVHMVSTTLPVDSR 19 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 S(0.361)T(0.361)S(0.278)T(0.001)PNVHMVSTTLPVDSR;S(0.355)T(0.355)S(0.284)T(0.006)PNVHMVSTTLPVDSR;S(0.363)T(0.363)S(0.268)T(0.006)PNVHMVSTTLPVDSR;S(0.36)T(0.36)S(0.28)T(0.001)PNVHMVSTTLPVDSR;S(0.33)T(0.33)S(0.33)T(0.009)PNVHMVSTTLPVDSR;S(0.327)T(0.327)S(0.327)T(0.019)PNVHMVSTTLPVDSR 213.47 2.17E-17 4022720000 973607 1198447 1145790 1164840 1322685 998621 1427761 1121589 1635033 TRUE FALSE 912670.6758 1287181.263 1172968.68 1194731.766 1218806.656 1286906.671 1213681.493 1261621.856 1362135.43 0.67002932 0.944973044 0.861124859 0.877102042 0.894776414 0.944771455 0.89101382 0.926208825 1 20.37743872 4.743827204 24.92606886 0.909111832 0.670029215 0.782537299 0.040785378 236.1151514 1117466.347 0.008734436 0.074795365 55440.50836 -4.743827204 -0.239082616 S(ph)TSTSSPVRPAATFPPATHCPLGGTLDGVYPTLMEPVLLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STSTSSPVRPAATFPPATHCPLGGTLDGVYPTLMEPVLLPK 41 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.164)T(0.164)S(0.164)T(0.164)S(0.164)S(0.164)PVRPAAT(0.009)FPPAT(0.004)HCPLGGT(0.004)LDGVYPTLMEPVLLPK 74.031 0.0011426 47985000 68073 53412 64238 56956 63856 51504 91684 59790 49742 TRUE FALSE 63812.43244 57366.68006 65761.7557 58417.58739 58841.00734 66372.3687 77936.83535 67254.91311 41439.73885 1.539885004 1.384339806 1.586924954 1.409699699 1.419917426 1.601659917 1.880726991 1.622956973 1 15.33872729 2.14178006 6.321075422 1.632919574 1.470690455 0 0.234389676 0.486451566 26.8173093 0.079849441 0.058799047 138.6053712 -2.14178006 -0.162229119 S(ph)TTLPRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STTLPRPR 8 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 S(0.333)T(0.333)T(0.333)LPRPR 54.549 0.078458 738970000 1046200 1289600 1218300 1156600 1397100 1094400 1316600 1126300 1486400 TRUE FALSE 980720.2095 1385083.326 1247198.651 1186280.314 1287377.402 1410335.514 1119188.053 1266921.034 1238310.237 0.791982639 1.118526912 1.007177857 0.957983127 1.03962429 1.138919369 0.903802633 1.023104708 1 20.23994137 S(ph)TTPAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 STTPAPK 7 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.986)T(0.013)T(0.001)PAPK;S(0.985)T(0.014)T(0.001)PAPK;S(0.984)T(0.015)T(0.001)PAPK 93.162 0.015879 542190000 2273120 1525540 1917270 1957810 1603270 1636430 1730780 1482910 1229400 TRUE FALSE 2130849.477 1638492.569 1962748.55 2008050.719 1477355.641 2108840.776 1471265.607 1668054.578 1024205.198 2.080490786 1.599769824 1.916362614 1.96059415 1.44244107 2.05900222 1.436494962 1.628633189 1 19.96607336 0.501396699 0.522888091 0.96053215 1.840345041 0.589856599 0.216215163 1.248291424 0.616853624 0.296892429 0.095308583 3.172463976 -0.501396699 0.879812891 S(ph)TTPPPAEPVSLPQEPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STTPPPAEPVSLPQEPPK 18 0 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.378)T(0.378)T(0.244)PPPAEPVSLPQEPPK;S(0.333)T(0.333)T(0.333)PPPAEPVSLPQEPPK 188.9 3.72E-14 140470000 269623 209092 233287 220174 226956 174760 277879 197981 225147 TRUE FALSE 252747.7777 224573.3892 238820.6778 225824.0376 209131.7913 225210.375 236213.6237 222699.3637 187568.5112 1.347495782 1.197287262 1.273245047 1.20395495 1.114962154 1.200683279 1.259345837 1.18729611 1 17.51705812 -5 0.189323461 0.05470722 1.264938478 0.627236199 0.056849677 94.820497 0.927206951 33.86943593 0.154212642 1.00E-05 5 1.210231258 S(ph)VAS(ph)SQPAKPTK ddPTM_SK-BR-3_Pertuzumab_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(0.887)S(0.113)QPAKPTK;S(1)VAS(0.548)S(0.452)QPAKPTK 121.27 0.00021583 327080000 1433660 1067540 1011910 1034720 1246050 647090 1526430 972770 1794470 TRUE FALSE 1343929.78 1146581.772 1035912.983 1061272.667 1148190.259 833894.3784 1297555.992 1094222.476 1494961.364 0.898972918 0.76696415 0.692936291 0.709899729 0.768040089 0.557803297 0.86795286 0.731940304 1 20.51167677 0.262415666 1.055706506 1.000667349 0.740391846 0.408244785 0.094111722 3.550670925 4.251104365 0.089266012 0.025924742 1.829850738 -0.262415666 -0.260275503 S(ph)VASSQPAKPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVASSQPAKPTK 12 1 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 S(0.999)VAS(0.001)SQPAKPTK;S(0.998)VAS(0.002)SQPAKPTK 143.28 3.76E-05 791920000 1500860 1115840 1309140 1263080 1452800 983100 1585840 1072030 1466790 TRUE FALSE 1406923.852 1198457.955 1340193.419 1295492.771 1338702.948 1266905.011 1348058.014 1205875.305 1221973.273 1.151354029 0.980756274 1.096745279 1.060164571 1.095525555 1.03676982 1.103181259 0.986826252 1 20.2207813 1.224419409 24.99869846 0.993413051 1.067862868 0.350354622 0.045360237 304.1626208 537680.8569 0.038752768 0.009878428 16.76561193 -1.224419409 0.074449817 S(ph)VDEVNYWDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SVDEVNYWDK 10 0 F5H5P2;P12694;P12694-2;F5GXU9 F5H5P2 BCKDHA "2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial" 1 S(1)VDEVNYWDK;S(1)VDEVNYWDK;S(1)VDEVNYWDK;S(1)VDEVNYWDK;S(1)VDEVNYWDK;S(1)VDEVNYWDK 245.15 1.71E-12 1525780000 2468550 1466480 1557010 1351050 1816870 1333260 1864090 1690510 1317950 TRUE FALSE 2314047.862 1575059.705 1593943.012 1385720.23 1674180.359 1718150.518 1584587.01 1901573.895 1097975.631 2.10755849 1.434512444 1.451710737 1.262068293 1.524788267 1.564834838 1.443189599 1.731890801 1 20.0664146 -2.137196898 2.029326856 4.42E-05 1.526733721 0.365618263 0.229022852 3092372.125 694435.3478 14230465.12 0.05069985 0.007291269 2.137196898 1.526689511 S(ph)VDEVNYWDKQDHPISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SVDEVNYWDKQDHPISR 17 1 F5H5P2;P12694;P12694-2 F5H5P2 BCKDHA "2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial" 1 S(1)VDEVNYWDKQDHPISR;S(1)VDEVNYWDKQDHPISR;S(1)VDEVNYWDKQDHPISR;S(1)VDEVNYWDKQDHPISR 261.54 1.63E-27 1098710000 950620 886640 792350 777750 1227860 582450 887830 765910 1402970 TRUE FALSE 891122.3911 952287.7481 811144.9162 797708.3817 1131428.829 750593.8597 754708.1337 861535.5495 1168805.243 0.762421623 0.814753145 0.693994933 0.682498976 0.968021691 0.642188991 0.645709059 0.737107875 1 20.15660312 -0.676623844 4.130522654 1.000000868 0.738733609 0.415739379 0.095483607 30066870.47 75251229.49 459.9766651 0.023080441 0.210560138 0.676623844 -0.261267259 S(ph)VDFDSLTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 229.86 1.50E-09 880980000 1335840 1332260 1074370 1009000 1507470 870123 1142740 1121990 1912040 TRUE FALSE 1252232.159 1430901.917 1099854.564 1034892.648 1389079.387 1121313.385 971396.7457 1262072.921 1592908.172 0.786129534 0.898295295 0.690469534 0.649687576 0.87203984 0.703941008 0.609825954 0.792307393 1 20.60323167 3.961217812 6.755086029 0.73340182 0.843574014 0.043618346 0.117878688 0.271462265 57.55398807 0.027589236 0.052839885 9145.718117 -3.961217812 0.110172194 S(ph)VDIHDSIQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 220.25 9.73E-12 3104020000 1242791 3030040 2567980 2901700 3000350 2269603 3500380 2796670 2499580 TRUE FALSE 1165006.93 3254387.314 2628893.698 2976162.535 2764714.614 2924800.542 2975530.515 3145840.406 2082383.95 0.559458274 1.562818093 1.262444276 1.429209313 1.327668038 1.404544317 1.428905805 1.510691823 1 20.98980467 4.746121887 24.94031692 1.386110954 0.559457868 0.724445363 0.155836528 407.9720688 1345634.099 0.031840959 0.336735587 55734.21484 -4.746121887 -0.826653086 S(ph)VEDDAEGHLIYHVGDWLQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVEDDAEGHLIYHVGDWLQER 21 0 B1AVT0;P49760-3;P49760 B1AVT0 CLK2 Dual specificity protein kinase CLK2 1 S(1)VEDDAEGHLIYHVGDWLQER;S(1)VEDDAEGHLIYHVGDWLQER 252.04 4.18E-36 50395000 30044 25962.9 34934 40841 26355.5 32184.4 41828 23226 37392.2 TRUE FALSE 28163.59967 27885.22013 35762.65098 41889.0492 24285.64534 41475.51381 35556.27971 26125.81723 31151.20026 0.904093564 0.895157166 1.148034448 1.34470097 0.779605445 1.331425867 1.141409622 0.838677708 1 14.92700013 4.058124288 3.361039936 1.104304853 0.899631146 0.140745012 0.182551721 0.397077331 8.692347334 0.043253264 0.103097781 11432.05454 -4.058124288 -0.204673707 S(ph)VEDVRPHHTDANNQSACFEAPDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SVEDVRPHHTDANNQSACFEAPDQK 25 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.655)VEDVRPHHT(0.281)DANNQS(0.064)ACFEAPDQK;S(0.713)VEDVRPHHT(0.112)DANNQS(0.175)ACFEAPDQK;S(0.997)VEDVRPHHT(0.003)DANNQSACFEAPDQK;S(0.913)VEDVRPHHT(0.085)DANNQS(0.002)ACFEAPDQK;S(0.625)VEDVRPHHT(0.375)DANNQSACFEAPDQK;S(0.987)VEDVRPHHT(0.013)DANNQSACFEAPDQK 233.71 1.38E-38 7357260000 4177500 3119930 3782510 3724470 3787630 2918380 4923540 3153680 4214320 TRUE FALSE 3916037.732 3350932.863 3872232.923 3820046.206 3490164.818 3760868.93 4185300.885 3547423.89 3510922.766 1.115387034 0.954430811 1.102910312 1.088046209 0.994087609 1.071191017 1.192080021 1.010396447 1 21.74341883 1.998350457 24.98899068 1.099534665 1.04541392 0 0.072532992 138.3328902 2095635.412 0.025778015 0.018778821 99.62089907 -1.998350457 -0.054120745 S(ph)VELDLNQAHMEETPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVELDLNQAHMEETPK 16 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 S(1)VELDLNQAHMEETPK 214.14 6.85E-14 94978000 112830 81346 88533 97277 106500 70030 125350 92921 109910 TRUE FALSE 105768.1717 87368.94248 90633.04457 99773.29251 98135.9196 90246.52416 106554.9312 104522.3914 91565.31095 1.155111806 0.954170762 0.989818564 1.089640733 1.071758711 0.98559731 1.163704137 1.141506432 1 16.48251352 1.740861017 25 1.11540577 1.028140689 0.110396582 0.07217956 0.527807648 5772.376847 0.032024686 0.017759457 55.06314548 -1.740861017 -0.087265081 S(ph)VENLFLSLATHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVENLFLSLATHVK 14 0 Q4VX76 Q4VX76 SYTL3 Synaptotagmin-like protein 3 1 S(1)VENLFLSLATHVK 134.29 2.55E-05 128800000 68531 76012 63687 63445 74500 58168 86371 61274 122680 TRUE FALSE 64241.76704 81640.00757 65197.68572 65073.10611 68649.07052 74960.15732 73420.47038 68924.19378 102203.9155 0.628564637 0.798795303 0.637917691 0.636698759 0.671687285 0.733437237 0.718372384 0.674379191 1 16.64109094 S(ph)VENLPECGITHEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 306.43 3.30E-45 9537160000 4506933 4674151 4779043 4561152 4784837 4043629 5916340 4246612 5396510 TRUE FALSE 4224852.109 5020230.003 4892404.157 4678198.882 4409055.203 5210959.049 5029239.742 4776810.856 4495797.618 0.939733606 1.116649465 1.088217169 1.040571502 0.98070589 1.159073315 1.1186535 1.062505758 1 22.10014566 2.229252844 24.99960465 1.09977627 1.052400191 0.078037658 0.06549086 457.5089267 1228808.471 0.023646572 0.017702733 169.5324523 -2.229252844 -0.047376079 S(ph)VGGSGGGSFGDNLVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVGGSGGGSFGDNLVTR 17 0 P02545;P02545-3;P02545-5;P02545-4;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 S(0.603)VGGS(0.012)GGGS(0.385)FGDNLVTR;S(0.829)VGGS(0.005)GGGS(0.166)FGDNLVTR 208.59 5.29E-12 689320000 824770 765310 745210 796340 898410 591030 885370 737150 1343250 TRUE FALSE 773149.118 821974.3487 762886.7331 816775.4326 827852.5026 761650.7664 752616.9879 829184.8002 1119052.897 0.690895953 0.734526805 0.681725355 0.729880986 0.739779598 0.680620879 0.672548179 0.740970156 1 20.0938468 0.880262714 7.099168031 0.999999699 0.704407564 0.937671134 0.023772555 0.879580326 52.15536712 0.023342691 0.005853017 7.590365938 -0.880262714 -0.295592136 S(ph)VPSIAAATGTHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SVPSIAAATGTHSR 14 0 Q8IY63-2;Q8IY63 Q8IY63-2 AMOTL1 Angiomotin-like protein 1 1 S(0.521)VPS(0.479)IAAATGTHSR;S(0.764)VPS(0.236)IAAATGTHSR;S(0.995)VPS(0.005)IAAATGTHSR 218.12 3.54E-12 426997000 254060 303595 302800 272052 310270 250961 357288 300830 540390 TRUE FALSE 238158.8381 326073.4897 309982.559 279033.3149 285902.6458 323409.3667 303715.9813 338389.2877 450195.4179 0.529012133 0.724293222 0.688551119 0.619804875 0.635063429 0.718375518 0.674631436 0.751649782 1 18.78019185 0.473704847 0.90225802 1.002084805 0.659495306 0.796983734 0.054992249 0.781244911 0.921957688 0.052170386 0.016664015 2.97649287 -0.473704847 -0.342589499 S(ph)VS(ph)FY(ph)T(ph)RK ddPTM_SK-BR-3_Pertuzumab_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 47.706 0.053689 501440000 1079100 969230 833130 846020 1009500 355280 376750 734170 1068100 TRUE FALSE 1011561.057 1040992.798 852892.237 867730.3055 930217.9421 457843.5685 320259.8351 825832.7406 889827.2098 1.136806164 1.169881957 0.958491972 0.975167196 1.045391658 0.51453087 0.359912387 0.928082139 1 19.76316569 2.247250411 24.63797549 0.611758754 1.055341271 0.411098999 0.19981503 115.3177536 326958.0214 0.066939194 0.055179503 176.7056399 -2.247250411 0.443582517 S(ph)VS(ph)PCSNVESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SVSPCSNVESR 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)VS(0.989)PCS(0.011)NVESR;S(1)VS(0.982)PCS(0.018)NVESR;S(1)VS(1)PCSNVESR;S(1)VS(1)PCSNVESR;S(1)VS(0.978)PCS(0.022)NVESR;S(1)VS(1)PCSNVESR;S(1)VS(0.999)PCS(0.001)NVESR 162.32 3.69E-05 8298210000 5353930 4838040 5093320 5077120 5090700 4450820 6153190 4233890 4753100 TRUE FALSE 5018837.078 5196253.516 5214135.956 5207407.495 4690896.957 5735699.481 5230576.283 4762500.486 3959776.904 1.267454506 1.312259161 1.316775183 1.315075981 1.184636678 1.448490564 1.320927014 1.202719396 1 21.91698772 0.927378306 3.207731575 1.000498205 1.313059036 0.702131708 0.064257078 0.165018691 4.070971188 0.05728851 0.014933355 8.460154736 -0.927378306 0.312560831 S(ph)VS(ph)PPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SVSPPPK 7 0 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 2 S(1)VS(1)PPPK;S(1)VS(1)PPPK;S(1)VS(1)PPPK;S(1)VS(1)PPPK 87.913 0.027766 2810650000 8929900 6052500 7151700 6734100 7445300 5526040 9122300 5943900 8200400 TRUE FALSE 8370993.499 6500633.398 7321341.701 6906908.407 6860576.171 7121318.04 7754495.802 6686008.999 6831700.263 1.225316272 0.951539609 1.071671973 1.011008701 1.004226753 1.042393221 1.135075531 0.978674231 1 22.70381325 1.97247927 24.51174482 1.061877313 1.038273034 0 0.08275491 3268.361703 2911009.597 0.031033132 0.020091997 93.8597234 -1.97247927 -0.023604279 S(ph)VS(ph)PPPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SVSPPPKR 8 1 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 2 S(1)VS(1)PPPKR;S(1)VS(1)PPPKR;S(1)VS(1)PPPKR 83.397 0.063657 12303860000 3930300 2824160 3350800 3059360 3250320 2622070 4253300 2802100 3750500 TRUE FALSE 3684309.539 3033263.745 3430282.558 3137868.357 2995052.978 3379019.043 3615557.151 3151948.353 3124517.321 1.179161182 0.970794345 1.097859991 1.004272992 0.95856501 1.081453132 1.15715702 1.008779286 1 21.57520191 2.047162263 24.99993606 1.084407456 1.036758928 0 0.077222212 301.6586722 159903.072 0.026839188 0.019822049 111.4710938 -2.047162263 -0.047648528 S(ph)VS(ph)PYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SVSPYSR 7 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 S(1)VS(1)PYSR;S(1)VS(0.924)PY(0.073)S(0.003)R;S(1)VS(0.867)PY(0.133)SR;S(1)VS(0.919)PY(0.006)S(0.075)R;S(1)VS(0.913)PY(0.082)S(0.005)R 125.97 0.0058443 2931740000 5016500 4584190 5070300 4653170 4861450 3995130 5500850 4129920 4900760 TRUE FALSE 4702526.22 4923608.197 5190569.91 4772578.22 4479651.327 5148459.175 4676048.61 4645549.603 4082791.496 1.151791911 1.205941622 1.271328677 1.16894978 1.097203061 1.261014475 1.145306738 1.137836602 1 21.96112446 0.318508634 0.518154734 0.986722602 1.207335192 0.55970669 0.051922032 1.803574872 0.757827461 0.099611304 0.025194183 2.0821338 -0.318508634 0.22061259 S(ph)VS(ph)RS(ph)PVPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSRSPVPEK 10 1 Q13243;Q13243-3 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 3 S(1)VS(1)RS(1)PVPEK 101.3 0.002739 0 871060 405620 647610 520620 416910 572810 826380 407170 356590 TRUE FALSE 816541.9095 435652.5268 662971.615 533979.9906 384167.5703 738170.9482 702471.9907 458006.0708 297072.8253 2.748625387 1.466483938 2.231680445 1.797471681 1.293176412 2.484814784 2.364645739 1.541729945 1 18.18045712 4.757756984 23.36639959 1.879338335 2.748627327 0.261478612 0.486965913 2572.540138 3131248.796 0.110087061 3.608759897 57247.56038 -4.757756984 0.869288992 S(ph)VSGFLHFDTATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSGFLHFDTATK 13 0 Q92621 Q92621 NUP205 Nuclear pore complex protein Nup205 1 S(0.996)VS(0.004)GFLHFDTATK 148.7 2.80E-05 41314000 153040 148380 137120 139260 141030 96665 244130 166230 126260 TRUE FALSE 143461.4996 159366.2096 140372.5512 142833.6474 129954.0727 124570.6163 207524.9729 186984.1814 105186.3903 1.363878912 1.515083929 1.334512485 1.357909963 1.235464705 1.184284544 1.972926081 1.777646146 1 16.68258853 1.752609536 25 1.680321196 1.350597968 0.133441137 0.263815347 5.785457479 10309.55448 0.109933796 0.060964343 56.5730425 -1.752609536 -0.329723228 S(ph)VSGS(ph)PEPAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SVSGSPEPAAK 11 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 S(0.989)VS(0.015)GS(0.997)PEPAAK;S(0.945)VS(0.056)GS(1)PEPAAK;S(0.951)VS(0.049)GS(1)PEPAAK;S(0.993)VS(0.007)GS(1)PEPAAK 203.29 5.43E-08 1990640000 7488900 5571380 6451080 5960140 7028250 5520150 8392900 6256390 10826100 TRUE FALSE 7020183.117 5983890.772 6604102.664 6113087.283 6476279.596 7113727.693 7134462.561 7037514.064 9019153.971 0.778363818 0.663464754 0.732230837 0.677789436 0.718058436 0.788735586 0.791034568 0.780285389 1 23.10456068 0.361234298 0.440891035 1.025456715 0.700301701 0.841106997 0.037072326 0.88585329 0.293258583 0.080353504 0.021543118 2.297387733 -0.361234298 -0.325155014 S(ph)VSHGSNHTQKPDEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 SVSHGSNHTQKPDEQR 16 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.964)VS(0.036)HGSNHTQKPDEQR;S(0.997)VS(0.003)HGSNHTQKPDEQR;S(0.965)VS(0.035)HGSNHTQKPDEQR;S(0.9)VS(0.1)HGSNHTQKPDEQR;S(0.967)VS(0.033)HGSNHTQKPDEQR;S(0.995)VS(0.005)HGSNHTQKPDEQR;S(0.488)VS(0.488)HGS(0.012)NHT(0.012)QKPDEQR;S(0.998)VS(0.002)HGSNHTQKPDEQR;S(0.977)VS(0.023)HGSNHTQKPDEQR;S(0.968)VS(0.032)HGSNHTQKPDEQR;S(0.752)VS(0.248)HGSNHTQKPDEQR 325.11 6.11E-59 8126546000 1199480 2798123 2713555 2877764 3161849 2376532 3512548 2885569 3114676 TRUE FALSE 1124406.688 3005298.938 2777921.806 2951612.296 2913530.134 3062598.209 2985874.036 3245838.642 2594816.454 0.433328024 1.158193264 1.07056582 1.137503307 1.122827061 1.18027547 1.150707223 1.250893348 1 21.30720106 4.739622057 24.98944688 1.136720366 0.4333278 0.918209902 0.065702834 21.07144138 496019.3747 0.014146742 0.086490322 54906.28456 -4.739622057 -0.703392567 S(ph)VSPESNDSISEELNHFKPIVCSPCTPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSPESNDSISEELNHFKPIVCSPCTPPK 29 1 Q8NCN4 Q8NCN4 RNF169 E3 ubiquitin-protein ligase RNF169 1 S(0.506)VS(0.44)PES(0.023)NDS(0.023)IS(0.007)EELNHFKPIVCSPCTPPK 96.158 0.00066793 98741000 57571 48111 55331 55432 49860 34006 57537 43827 66362 TRUE FALSE 53967.73388 51673.1885 56643.47745 56854.47897 45944.19673 43822.98016 48909.861 49298.89743 55285.75349 0.976159869 0.934656494 1.024558297 1.028374859 0.831031393 0.792663162 0.884673861 0.891710691 1 15.75462014 2.736962582 24.96372647 0.866717594 0.987160719 0.456402367 0.05910795 112.527405 1757833.623 0.017713927 0.017532425 545.7108414 -2.736962582 0.120443126 S(ph)VSPLLSTHVLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSPLLSTHVLGK 13 0 Q96H12;X6RL08;X6R907;Q96H12-2 Q96H12 MSANTD3 Myb/SANT-like DNA-binding domain-containing protein 3 1 S(0.582)VS(0.418)PLLSTHVLGK 100.68 0.001475 174580000 782090 1076900 1017900 947350 1160400 913020 1276800 1010800 1189000 TRUE FALSE 733140.383 1156634.797 1042045.069 971660.6049 1069266.865 1176594.052 1085355.693 1137000.605 990548.2188 0.740135986 1.167671371 1.051988231 0.980932161 1.079469777 1.187821077 1.095712125 1.147849831 1 19.91786768 2.482453734 24.15677392 1.118414431 1.027078192 0.158682215 0.117885696 325.8506251 1476161.102 0.037667743 0.032416288 303.706253 -2.482453734 -0.091336239 S(ph)VSPSPVPLLFQPDQNAPPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSPSPVPLLFQPDQNAPPIR 21 0 Q02241-2;Q02241-3 Q02241-2 KIF23 Kinesin-like protein KIF23 1 S(0.49)VS(0.49)PS(0.021)PVPLLFQPDQNAPPIR 157.42 6.08E-09 47362000 3306.5 4365.6 4092.6 3204.7 5621 2915.8 3765 4130.5 5846.1 TRUE FALSE 3099.552067 4688.833566 4189.678405 3286.938028 5179.549334 3757.544126 3200.473203 4646.202017 4870.348143 0.636412835 0.962730677 0.860242078 0.674887694 1.063486466 0.771514482 0.657134379 0.953977392 1 12.24980919 S(ph)VSQDLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SVSQDLIK 8 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 S(0.983)VS(0.017)QDLIK;S(0.979)VS(0.021)QDLIK;S(0.995)VS(0.005)QDLIK 147.62 0.00056048 608210000 1403010 1279110 1105170 1026480 1342670 727760 1409930 1290160 2132660 TRUE FALSE 1315198.109 1373816.635 1131385.154 1052821.215 1237222.114 937852.4978 1198524.086 1451239.316 1776705.268 0.740245516 0.773238342 0.636788315 0.592569422 0.696357542 0.527860481 0.674576761 0.816814889 1 20.76077295 0.99197163 2.871278416 0.998377924 0.66381891 0.717678737 0.069429283 0.140515518 2.751347668 0.06871251 0.018211915 9.816838133 -0.99197163 -0.334559014 S(ph)VSS(ph)QRS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSSQRSR 8 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 3 S(0.995)VS(0.016)S(0.99)QRS(0.999)R 73.219 0.035983 53575000 159510 139830 140920 143580 144530 109500 155720 132450 145870 TRUE FALSE 149526.5538 150183.1587 144262.6889 147264.5059 133179.1968 141110.8724 132371.2316 148986.6741 121523.3546 1.230434712 1.235837828 1.187119047 1.211820611 1.095914421 1.161183156 1.08926578 1.225992111 1 16.89087408 -5 0.045210741 0.225470314 1.59401106 0.623184746 0.047194966 382.6075393 1.286002224 37.699988 9.723977462 1.00E-05 5 1.368540746 S(ph)VSSSPWLPQDGFDPSDYAEPMDAVVKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVSSSPWLPQDGFDPSDYAEPMDAVVKPR 29 1 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 S(0.876)VS(0.121)S(0.002)SPWLPQDGFDPSDYAEPMDAVVKPR;S(0.966)VS(0.028)S(0.005)S(0.001)PWLPQDGFDPSDYAEPMDAVVKPR 194.83 2.83E-19 276550000 298960 326880 311490 394250 526550 182258 378580 272825 504900 TRUE FALSE 280248.6273 351082.5353 318878.6899 404367.1225 485196.887 234872.9259 321815.4436 306887.8018 420628.9282 0.666260945 0.834660937 0.758099761 0.961339307 1.153503372 0.558385099 0.765081577 0.729592715 1 18.68218855 -0.446592535 7.232866673 1.000006945 0.803449375 0.12697697 0.162036292 0 0 0.150942725 0.035577541 0.357608197 0.446592535 -0.19655757 S(ph)VSTLKPCAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVSTLKPCAK 10 1 A0A286YFF8;Q7Z3U7-2;Q7Z3U7-6;Q7Z3U7-5;Q7Z3U7;F8VZV1 A0A286YFF8 MON2 Protein MON2 homolog 1 S(0.986)VS(0.012)T(0.001)LKPCAK;S(0.959)VS(0.018)T(0.023)LKPCAK 72.958 0.028117 522940000 693970 637020 704860 759440 866130 626510 1029740 649450 1258590 TRUE FALSE 650535.6565 684185.6236 721579.6121 778928.5161 798107.6436 807373.2665 875340.0466 730535.2621 1048523.198 0.62043039 0.652523115 0.688186597 0.742881528 0.761173091 0.770009922 0.834831359 0.696727801 1 19.99992735 -5 0.054364524 2.099696877 0.21179159 0.828296573 0.044369732 166.3989256 0.665785558 25.43491995 5.009966287 1.00E-05 5 -1.887905287 S(ph)VVDMDLDDTDDGDDNAPLFYQPGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVVDMDLDDTDDGDDNAPLFYQPGKR 26 1 E7EMW7;O95071-2;O95071;E7ET84 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 S(1)VVDMDLDDTDDGDDNAPLFYQPGKR 110.08 0.00097551 28828000 28166 28572 26287 25968 34029 18316 37120 24652 48942 TRUE FALSE 26403.14034 30687.50061 26910.54005 26634.38284 31356.49961 23603.53186 31554.20061 27729.85647 40773.26402 0.647560135 0.752637821 0.660004557 0.65323156 0.769045608 0.578897286 0.773894398 0.680099009 1 15.31533583 -0.745555187 0.673236988 1.044266052 0.690223779 0.717064404 0.061277858 10.37007071 2.962604049 1.0925134 0.019757407 0.179657277 0.745555187 -0.354042273 S(ph)VVS(ph)DLEADDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVVSDLEADDVK 12 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 2 S(1)VVS(1)DLEADDVK;S(1)VVS(1)DLEADDVK 155.56 0.00010036 56651000 1168500 550180 726220 614590 556220 335249 885150 437700 758890 TRUE FALSE 1095365.671 590915.8997 743446.2813 630361.4199 512536.7249 432029.944 752429.9748 492347.8085 632226.3564 1.732553001 0.934658756 1.175917887 0.997050208 0.810685476 0.683346937 1.190127503 0.778752425 1 19.27008165 4.740092991 24.84035825 0.968140095 1.732553275 0.697022905 0.162340066 71.51697991 1159198.648 0.037893122 0.240527251 54965.85536 -4.740092991 0.76441318 S(ph)VVSDLEADDVKGSVPLSSSPPATHFPDETEITNPVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVVSDLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 38 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 S(0.46)VVS(0.46)DLEADDVKGS(0.079)VPLSSSPPATHFPDETEITNPVPK;S(0.64)VVS(0.36)DLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 213.17 9.72E-32 278250000 115515 94858 108176 121022 125915 76690 160765 89633 177483 TRUE FALSE 108285.1224 101881.385 110741.9858 124127.6294 116026.1438 98829.15804 136659.7807 100823.8774 147859.9407 0.732349288 0.689039807 0.748965442 0.839494652 0.784703032 0.668397117 0.924251559 0.681887717 1 17.17387171 -5 0.144999125 1.833162404 0.681404526 0.471428589 0.078935123 109.7957643 0.961256617 26.39701421 0.39971269 1.00E-05 5 -1.151757878 S(ph)WASPVYTEADGTFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SWASPVYTEADGTFSR 16 0 E9PMS6;E9PJ10;E9PK58;E9PLU6;Q8WWI1-3;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(1)WASPVYTEADGTFSR;S(1)WASPVYTEADGTFSR;S(0.991)WAS(0.009)PVYTEADGTFSR;S(1)WASPVYTEADGTFSR;S(0.999)WAS(0.001)PVYTEADGTFSR 367.68 3.39E-104 628724000 282123 364624 275253 334471 383908 215557 383346 289018 393882 TRUE FALSE 264465.425 391621.1404 281782.1311 343054.0921 353757.4143 277784.8066 325866.8261 325102.5335 328140.5496 0.805951673 1.19345549 0.858723896 1.045448642 1.078066745 0.846542151 0.993070885 0.990741723 1 18.32395436 2.275204858 24.99999644 0.956928736 1.006678378 0.022755222 0.115545484 616.0999053 420322.9534 0.037027961 0.030978981 188.4537823 -2.275204858 0.049749642 S(ph)WDQQIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SWDQQIK 7 0 F8W8D3;Q14493;E7EUV9;H0YAE8;Q14493-2 F8W8D3 SLBP Histone RNA hairpin-binding protein 1 S(1)WDQQIK 74.841 0.047296 54190000 69904 58704 59536 63335 66718 38630 65739 56401 90315 TRUE FALSE 65528.83342 63050.50524 60948.22203 64960.28333 61478.23741 49781.85389 55882.04724 63442.789 75240.84304 0.870921042 0.83798244 0.810041722 0.863364639 0.817085972 0.661633388 0.742708946 0.843196148 1 16.19922839 2.465672525 24.995074 0.77555775 0.838572647 0 0.089120707 495.6185193 1082035.934 0.027984693 0.023430999 292.1948287 -2.465672525 0.063014898 S(ph)WEDSPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 S(0.997)WEDS(0.003)PER 72.325 0.043794 0 42958 45607 38191 42522 48529 36594 46725 34353 48522 TRUE FALSE 40269.33546 48983.78973 39096.90856 43613.18651 44717.7281 47158.09375 39719.02002 38642.04767 40423.36474 0.996189598 1.211769234 0.967185904 1.078910348 1.106234684 1.16660486 0.982575802 0.955933479 1 15.30290179 1.61562872 7.977670604 0.974935376 1.088385443 0.337840961 0.071448961 0.122902872 18.2823828 0.035323208 0.017519901 41.26945366 -1.61562872 0.113450068 S(ph)WGQQAQEYQEQK ddPTM_SK-BR-3_Pertuzumab_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 347.52 7.82E-76 1657670000 936733 706020 807702 816284 1052215 697714 1013788 732270 1181927 TRUE FALSE 878104.5536 758294.4554 826861.0729 837231.2294 969578.2783 899132.7054 861779.9009 823695.5214 984655.7482 0.891788379 0.770111236 0.839746352 0.850278111 0.984687572 0.91314422 0.875209333 0.836531471 1 19.9092599 2.969040522 11.6818179 0.911084873 0.824029654 0.349185576 0.055695856 1.228453444 462.1425311 0.016171229 0.017347187 931.1947569 -2.969040522 -0.087055219 S(ph)WHDVQVSSAYVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SWHDVQVSSAYVK 13 0 O43399;O43399-7;O43399-5;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 1 S(1)WHDVQVSSAYVK;S(0.963)WHDVQVS(0.037)SAYVK;S(1)WHDVQVSSAYVK 267.07 1.77E-24 616940000 769030 763820 699680 751480 979900 532211 798840 751900 805100 TRUE FALSE 720897.7851 820374.0276 716276.74 770764.2491 902942.6067 685851.676 679061.3581 845776.3701 670723.6089 1.074806039 1.223117864 1.067916397 1.149153301 1.346221595 1.022554845 1.012430976 1.260990904 1 19.35535886 -3.218950779 0.224580515 0.708402893 1.157544859 0.122758182 0.109091783 133.9221322 2.745600487 18.43172476 0.203051011 0.000604017 3.218950779 0.449141966 S(ph)WTSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SWTSPK 6 0 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.989)WT(0.006)S(0.006)PK;S(0.998)WT(0.001)S(0.001)PK 72.485 0.089658 1892130000 900820 725990 788710 710830 776290 644240 1013850 740210 721250 TRUE FALSE 844439.2842 779743.055 807418.5737 729071.1012 715323.3148 830221.6296 861832.6046 832626.8479 600868.7155 1.405364038 1.297692882 1.343752059 1.213361725 1.190481874 1.381702206 1.434310994 1.385705107 1 19.19669028 S(ph)Y(ph)KCKECGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYKCKECGK 9 2 A0A0A0MR41;A6NNF4-3;A6NNF4;F5H2M4;A0A087X0A2;A0A087WZJ7;A0A494C0U8;O75437-2;O75437;Q8N7M2;A0A087WTN2;Q96JC4 A0A0A0MR41;A0A087WTN2 ZNF726;ZNF254;ZNF283;ZNF479 Zinc finger protein 726;Zinc finger protein 254;Zinc finger protein 283;Zinc finger protein 479 2 S(1)Y(1)KCKECGK 77.677 0.075481 56653000 89429 72056 73710 81100 96870 61951 98446 67132 111160 TRUE FALSE 83831.79853 77391.10121 75458.43601 83181.1633 89262.22095 79835.24801 83684.93623 75513.57798 92606.67788 0.905245717 0.835696766 0.814827156 0.898219925 0.963885359 0.862089537 0.903659846 0.815422599 1 16.49882861 3.175840304 9.006450189 0.902241739 0.843206001 0.174112256 0.055006973 0.45646188 60.7701046 0.014666892 0.017571511 1499.133483 -3.175840304 -0.059035738 S(ph)Y(ph)YGGLT(ph)LMNCIVKVLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYYGGLTLMNCIVKVLPK 18 1 F8VPF1 F8VPF1 POC1B 3 S(0.768)Y(0.732)Y(0.732)GGLT(0.768)LMNCIVKVLPK 52.522 0.043221 941810000 163180 864610 645940 631320 1045700 1232100 525500 618470 856190 TRUE FALSE 152966.8551 928626.624 661262.0018 647520.74 963574.9402 1587787.269 446706.1535 695687.3409 713286.3578 0.214453639 1.301898759 0.927063857 0.907799137 1.350894952 2.226016594 0.626264821 0.975326856 1 19.44412186 2.748342066 23.50709338 1.246677583 0.930029637 0.129080144 0.487647173 786.5535617 1890267.903 0.146601647 0.153520427 560.1986607 -2.748342066 -0.316647946 S(ph)YDNLTTACDNTVPLASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SYDNLTTACDNTVPLASR 18 0 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 S(0.999)YDNLT(0.001)TACDNTVPLASR;S(1)YDNLTTACDNTVPLASR 354.04 1.74E-90 898970000 448130 386960 413380 396300 351780 342560 502090 366990 381240 TRUE FALSE 420082.3432 415610.921 423185.5688 406469.7289 324152.6178 441451.511 426806.2657 412809.5093 317608.5811 1.322641667 1.308563262 1.332412265 1.279781949 1.020604093 1.389923123 1.343812136 1.299742935 1 18.27689037 -2.12674377 2.289279677 0.427736708 1.293338112 0.450362044 0.099499985 1751469.122 441896.3498 5219374.771 0.024608758 0.007468893 2.12674377 0.865601405 S(ph)YDVPPPPMEPDHPFYSNISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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(0.999)Y(0.001)DVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK 230.93 4.73E-26 4056960000 5262010 4569150 4781500 4880750 5131490 3453610 6159840 4347960 5073130 TRUE FALSE 4932670.187 4907454.62 4894919.438 5005998.308 4728483.475 4450611.142 5236229.177 4890812.377 4226391.829 1.167111424 1.161145208 1.158179278 1.184461477 1.118799124 1.053052183 1.238936045 1.157207513 1 22.0109951 -1.378886265 3.248895023 0.998498488 1.157078589 0.517289851 0.046970085 1201088.182 1029444.627 11323.3497 0.010530495 0.04179398 1.378886265 0.158580101 S(ph)YEDMIGEEVPSDQYYWAPLAQHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SYEDMIGEEVPSDQYYWAPLAQHER 25 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(0.999)Y(0.001)EDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER 197.13 5.32E-25 394113000 225048 211954 237056 308518 323099 198939 209910 151114 161904 TRUE FALSE 210962.6474 227647.2947 242679.0803 316435.0942 297724.1079 256369.4598 178435.9442 169980.9155 134881.1765 1.564062925 1.687761782 1.799206432 2.346028575 2.207306577 1.900705988 1.322912128 1.260227113 1 17.0413295 1.654776464 3.278655474 1.167377 1.907536411 0.681153118 0.235395976 0.137968455 3.493564986 0.15814203 0.069327614 45.16234295 -1.654776464 0.740159411 S(ph)YELPDGQVITIGNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SYELPDGQVITIGNER 16 0 P60709;A0A2R8Y793;P63267-2;A0A2R8YEA7;Q562R1;Q9BYX7;P63261;P68133;P68032;P63267;P62736;Q6S8J3;A5A3E0 P60709;P63261;P68133;Q6S8J3 ACTB;ACTG2;ACTBL2;POTEKP;ACTG1;ACTA1;ACTC1;ACTA2;POTEE;POTEF "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Beta-actin-like protein 2;Putative beta-actin-like protein 3;Putative beta-actin-like protein 3, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F" 1 S(1)YELPDGQVITIGNER;S(1)YELPDGQVITIGNER;S(1)YELPDGQVITIGNER 244.08 5.16E-20 209113000 489813 379351 427016 410785 393962 390590 542892 381440 437624 TRUE FALSE 459156.4787 407438.5428 437145.0212 421326.4386 363021.8137 503346.9923 461490.3846 429063.6237 364581.7272 1.259406175 1.11755064 1.199031626 1.155643322 0.995721361 1.380614975 1.265807774 1.176865409 1 18.47588273 2.234369255 24.99965071 1.23747791 1.149429532 0.032159372 0.115756832 221.7390707 1322560.033 0.038663877 0.029570383 171.5415205 -2.234369255 -0.088048377 S(ph)YENLAAEIMPVEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SYENLAAEIMPVEYR 15 0 Q9UJC3;Q9UJC3-2 Q9UJC3 HOOK1 Protein Hook homolog 1 1 S(1)YENLAAEIMPVEYR;S(1)YENLAAEIMPVEYR;S(0.997)Y(0.003)ENLAAEIMPVEYR;S(1)YENLAAEIMPVEYR 196.01 9.59E-09 93767000 70393 64183 62075 61444 62353 57985 79622 55454.1 62763 TRUE FALSE 65987.22779 68935.1761 63547.44831 63020.75706 57456.0469 74724.32819 67683.42027 62377.66645 52287.44984 1.262008914 1.318388568 1.215348014 1.205275018 1.098849668 1.429106381 1.294448677 1.19297588 1 15.67417709 0.904425577 4.464204195 1.000065151 1.263785825 0.484184368 0.084509607 0.444815603 18.77093878 0.079827577 0.020281302 8.024640339 -0.904425577 0.263720674 S(ph)YS(ph)PAHNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SYSPAHNR 8 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 S(0.999)Y(0.002)S(0.999)PAHNR;S(1)YS(1)PAHNR 120.09 0.0022933 1501220000 2300360 1808050 2060130 1901790 1672370 2072100 2564000 1631080 1315830 TRUE FALSE 2156384.574 1941919.903 2108997.256 1950593.151 1541028.806 2670281.632 2179552.003 1834723.928 1096209.472 1.967128207 1.771486155 1.923899865 1.77939819 1.405779502 2.435922786 1.988262333 1.673698298 1 20.06409208 4.755032767 21.03252182 1.825286224 1.96712916 0 0.379213396 2153.79338 2749644.165 0.08133848 1.68463936 56889.58517 -4.755032767 0.141842936 S(ph)YSHDVLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SYSHDVLPK 9 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 S(0.499)Y(0.002)S(0.499)HDVLPK;S(0.496)Y(0.007)S(0.496)HDVLPK;S(0.591)Y(0.001)S(0.408)HDVLPK;S(0.499)Y(0.001)S(0.499)HDVLPK 86.344 0.0091474 1362340000 4811200 4536450 4933990 4875510 5675710 3744330 5843600 4415510 6523130 TRUE FALSE 4510075.58 4872333.478 5051026.573 5000623.841 5229962.631 4825257.287 4967406.429 4966796.143 5434377.462 0.829915774 0.896576197 0.929458178 0.920183384 0.962384867 0.887913532 0.914070924 0.913958623 1 22.37368335 -3.05576738 0.01223269 1.987839012 3.07E-07 0.546276726 0.030105887 5578.855335 7.354453507 679.5975569 524.1683926 0.000879493 3.05576738 -1.987838705 S(ph)YSPAHNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SYSPAHNR 8 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.556)YS(0.444)PAHNR;S(0.565)Y(0.006)S(0.429)PAHNR;S(0.737)Y(0.001)S(0.262)PAHNR 86.898 0.010117 919600000 714120 885290 889820 890870 860120 877450 883200 763360 969340 TRUE FALSE 669424.5039 950837.7927 910926.9506 913731.2324 792569.6448 1130755.571 750772.3592 858667.1764 807550.8918 0.82895643 1.177433896 1.128011819 1.131484395 0.981448541 1.400228248 0.929690459 1.063297911 1 19.62319366 1.613825211 25 0.997368553 1.117925169 0.108612537 0.147041521 1.000605094 4181.36805 0.062706095 0.033623766 41.09842807 -1.613825211 0.120556616 S(ph)YSPDGKESPSDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYSPDGKESPSDKK 14 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 S(0.534)Y(0.001)S(0.464)PDGKESPSDKK 65.716 0.029945 131050000 196510 101920 133290 140170 184770 75890 179080 111800 370670 TRUE FALSE 184210.7899 109466.2628 136451.7017 143766.9995 170258.9095 97798.21103 152228.6165 125758.4761 308802.7824 0.596532157 0.354485999 0.441873291 0.465562513 0.551351604 0.316701198 0.492963876 0.407245282 1 18.23632623 -1.287182904 3.202353154 1.00289284 0.444266699 0.807452493 0.083789896 14993395.28 20850417.52 419613.8976 0.020001415 0.051619892 1.287182904 -0.55862614 S(ph)YSPDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYSPDHR 7 0 A0A024RAC6;Q14241 A0A024RAC6 TCEB3 Transcription elongation factor B polypeptide 3 1 S(0.924)YS(0.076)PDHR 138.54 0.0029112 1186100000 2144400 2493600 2335200 2327700 2370400 2187800 2554800 1944700 2382100 TRUE FALSE 2010185.832 2678228.739 2390592.047 2387432.723 2184238.346 2819382.344 2171731.458 2187500.076 1984512.121 1.012937039 1.349565321 1.204624563 1.203032573 1.100642482 1.420692932 1.094340233 1.102286075 1 20.92035294 1.564424232 9.600612447 1.068174642 1.226872109 0.269101386 0.116063929 0.139107629 21.93318988 0.05650965 0.026397289 36.67956967 -1.564424232 0.158697467 S(ph)YSPYDYQPCLAGPNQDFHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYSPYDYQPCLAGPNQDFHSK 21 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7 E9PGF5 TNS1 Tensin-1 1 S(0.495)Y(0.009)S(0.495)PY(0.002)DYQPCLAGPNQDFHSK 78.758 0.0016577 0 40997 45483 44362 37712 46239 32828 54477 37687 70609 TRUE FALSE 38431.07095 48850.60865 45414.28759 38679.75377 42607.57546 42304.91068 46308.67959 42392.30491 58823.90175 0.653324071 0.83045509 0.772038002 0.657551652 0.724324198 0.719178929 0.78724257 0.720664622 1 15.84411486 -1.342773397 3.175120863 1.002084904 0.745293537 0.692318257 0.055390301 14513092.93 19334291.84 282258.3833 0.013485203 0.045417853 1.342773397 -0.256791367 SAAAGALGS(ph)PGLPLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAAAGALGSPGLPLRK 16 1 O75145-2;O75145;A0A0C4DGR8;A0A0C4DGR7 O75145-2 PPFIA3 Liprin-alpha-3 1 SAAAGALGS(1)PGLPLRK 166.21 4.14E-09 525200000 592160 554510 550980 616870 596410 416910 756880 522050 746740 TRUE FALSE 555097.7626 595566.4974 564049.5058 632699.9286 549570.3644 537265.149 643392.8705 587229.0917 622104.2699 0.892290552 0.957341922 0.90668001 1.017031966 0.88340555 0.863625561 1.034220309 0.943939979 1 19.24679688 1.727652918 23.4510178 0.99178311 0.925139635 0.335675461 0.047823904 0.699821571 1492.569186 0.020703555 0.011479333 53.41373141 -1.727652918 -0.066643475 SAADS(ph)ISESVPVGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SAADSISESVPVGPK 15 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 1 S(0.006)AADS(0.965)IS(0.008)ES(0.02)VPVGPK;SAADS(1)ISESVPVGPK;SAADS(0.999)IS(0.001)ESVPVGPK;SAADS(0.981)IS(0.019)ESVPVGPK 245.19 4.63E-18 214674000 690655 548473 622786 612054 691960 467000 809998 536630 789990 TRUE FALSE 647428.1364 589082.5116 637558.778 627760.3418 637616.2528 601815.3189 688546.3196 603629.4368 658135.5655 0.983730663 0.895077766 0.968734728 0.953846555 0.968822058 0.914424551 1.046207432 0.917181001 1 19.32802526 2.381657444 0.572395572 0.990578307 0.935629361 0.060996272 0.043221696 1.567275252 1.044837048 0.035406143 0.030397923 240.8005333 -2.381657444 -0.054948946 SAAEMYGSSFDLDYDFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SAAEMYGSSFDLDYDFQR 18 0 B4DY08;G3V4W0;G3V5X6;G3V3K6;G3V251;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ;;;; 367 3.89E-107 661950000 484198 508402 514360 471695 611856 446753 576471 484845 639109 FALSE TRUE 453892.9115 546044.6131 526560.8621 483799.4923 563803.2979 575723.3387 490034.5252 545378.9655 532437.5791 0.852480984 1.025556111 0.988962618 0.908650162 1.058909664 1.081297341 0.920360516 1.024305922 1 19.02225287 4.745390004 24.3608214 0.998015713 0.852480887 0.427196098 0.053950575 556.1409925 1983712.491 0.012333627 0.119664579 55640.3693 -4.745390004 -0.145534825 SAAEMYGSVTEHPS(ph)PSPLLSSSFDLDYDFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SAAEMYGSVTEHPSPSPLLSSSFDLDYDFQR 31 0 P07910;G3V2Q1;G3V576;G3V555;G3V575 P07910 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 SAAEMYGSVTEHPS(0.826)PS(0.174)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.566)PS(0.431)PLLS(0.002)S(0.001)SFDLDYDFQR;SAAEMYGSVTEHPS(0.898)PS(0.102)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.986)PS(0.014)PLLSSSFDLDYDFQR;SAAEMY(0.001)GS(0.002)VT(0.011)EHPS(0.778)PS(0.202)PLLS(0.001)S(0.001)S(0.001)FDLDY(0.001)DFQR 372.6 2.58E-137 448525000 147592 185281 196310 194787 252238 175226 214402 185322 289829 TRUE FALSE 138354.4802 198999.398 200966.5659 199785.5642 232428.245 225810.9016 182254.4105 208459.8596 241454.6675 0.573003958 0.824168777 0.832315929 0.827424735 0.962616492 0.93521034 0.754818337 0.863349886 1 17.88139283 5.221548963 1.33221484 0.867993209 1.44E-16 0.631118803 0.072780604 2.908409899 1.886408222 0.019345129 4.679246924 166551.6589 -5.221548963 -0.867993209 SAAEMYGSVTEHPSPS(ph)PLLSSSFDLDYDFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SAAEMYGSVTEHPSPSPLLSSSFDLDYDFQR 31 0 P07910;G3V2Q1;G3V576;G3V555;G3V575 P07910 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 SAAEMYGS(0.003)VT(0.003)EHPS(0.186)PS(0.808)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.001)PS(0.999)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.02)PS(0.98)PLLSSSFDLDYDFQR;SAAEMYGS(0.001)VT(0.004)EHPS(0.435)PS(0.558)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.053)PS(0.947)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.401)PS(0.599)PLLSSSFDLDYDFQR;SAAEMYGSVT(0.001)EHPS(0.094)PS(0.9)PLLS(0.002)S(0.002)S(0.002)FDLDYDFQR 248.49 1.22E-46 636062000 186440 220063 219144 269499 338596 209990 245170 204344 285030 TRUE FALSE 174771.0532 236356.6935 224342.1992 276414.8006 312004.036 270610.7041 208409.0345 229856.7982 237456.6516 0.736012455 0.995367752 0.944771172 1.164064256 1.313941024 1.139621494 0.877671917 0.967994776 1 17.85730464 5.385219858 0.993343526 1.057877911 1.14E-11 0.385535505 0.12573559 7.429961945 2.355515066 0.041435494 11.41938173 242783.886 -5.385219858 -1.057877911 SAALPIFSSFVSNWDEATKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SAALPIFSSFVSNWDEATKR 20 1 O76021;J3QSV6;O76021-2;I3L3U9 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 ; 312.46 4.14E-66 245990000 498210 446590 477920 461330 543930 341890 521400 426120 535290 FALSE TRUE 467027.9254 479655.9883 489256.4881 473168.5088 501211.9319 440588.0929 443220.9104 479322.02 445946.6409 1.04727311 1.07559054 1.0971189 1.061042881 1.123928035 0.987983881 0.993887765 1.074841643 1 18.76651157 2.228631127 24.99999632 1.010632224 1.081546893 0.531493635 0.031088514 144.2410466 363160.7515 0.010796484 0.008069096 169.2899306 -2.228631127 0.070914669 SAAMLGNSEDHTALSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SAAMLGNSEDHTALSR 16 0 O60749;O60749-2 O60749 SNX2 Sorting nexin-2 0 ;; 261.17 8.06E-27 1186410000 872290 963750 1024870 918270 1029500 1003150 1143360 920760 1702600 FALSE TRUE 817694.926 1035107.053 1049180.4 941834.3628 948647.2228 1292743.12 971923.7824 1035718.913 1418425.061 0.576480879 0.729758012 0.739679825 0.664000086 0.668803202 0.911393316 0.685213346 0.730189378 1 20.4358585 -5 0.178619945 2.134126174 0.659787259 0.585750236 0.079563042 97.59584612 0.937922218 39.28434048 0.23847207 1.00E-05 5 -1.474338915 SAAS(ph)PVVSSMPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SAASPVVSSMPER 13 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;H7C1M2 P18583-7 SON Protein SON 1 SAAS(1)PVVSSMPER;SAAS(1)PVVSSMPER;SAAS(1)PVVSSMPER;SAAS(1)PVVSSMPER 228.17 8.27E-12 888840000 1282130 1025940 1137290 1094370 1161230 978710 1374240 1073630 1202600 TRUE FALSE 1201883.772 1101901.665 1164267.056 1122453.387 1070031.68 1261247.689 1168185.47 1207675.069 1001878.291 1.199630517 1.099835853 1.162084323 1.120349046 1.068025617 1.25888314 1.165995391 1.205410956 1 19.93427583 2.258793061 24.99999748 1.173949973 1.129813014 0.012396793 0.073972312 595.5626569 735898.5121 0.022564848 0.018857552 181.4650784 -2.258793061 -0.044136959 SAAVETASLS(ph)PSLVPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SAAVETASLSPSLVPAR 17 0 Q2KHT3;Q2KHT3-3 Q2KHT3 CLEC16A Protein CLEC16A 1 SAAVETAS(0.004)LS(0.977)PS(0.019)LVPAR;SAAVETAS(0.001)LS(0.999)PSLVPAR 286.84 1.71E-36 170449000 212747 237730 244100 286610 285910 173388 201529 155123 191973 TRUE FALSE 199431.545 255331.7766 249890.1673 293964.8978 263455.7819 223442.3009 171311.5974 174490.448 159931.4661 1.246981284 1.596507446 1.562482814 1.838067924 1.647304238 1.397112815 1.071156299 1.09103263 1 17.28709429 1.869943296 2.6813027 1.050908828 1.589161579 0.729241245 0.145388802 0.138534584 1.792717402 0.079487288 0.040229031 74.12134582 -1.869943296 0.538252752 SACGVCPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SACGVCPGR 9 0 P49207 P49207 RPL34 60S ribosomal protein L34 0 ;;;;; 126.67 0.0010866 536319000 489443 539884 540643 553700 508853 461694 586372 460568 519665 FALSE TRUE 458809.6363 579857.5731 553467.3073 567908.8794 468889.738 594977.5628 498450.9622 518070.9286 432929.5543 1.059778968 1.339380893 1.27842348 1.311781267 1.083062437 1.37430572 1.151344271 1.196663345 1 18.72377277 0.575000537 0.75290002 0.997583226 1.255718451 0.308480951 0.105247823 1.4888021 1.444867523 0.098234302 0.033427126 3.758378691 -0.575000537 0.258135225 SACMLS(ph)SPESSLT(ph)PPLSTNLHLESELDALASLENHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SACMLSSPESSLTPPLSTNLHLESELDALASLENHVK 37 0 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 2 S(0.078)ACMLS(0.426)S(0.391)PES(0.123)S(0.183)LT(0.79)PPLS(0.007)T(0.002)NLHLESELDALASLENHVK 68.708 0.0049434 46787000 31096 36244 34033 29303 45604 27737 47303 34067 51626 TRUE FALSE 29149.75687 38927.54347 34840.27883 30054.96459 42022.4458 35744.22163 40210.35429 38320.33994 43009.28708 0.677754942 0.905096227 0.810064086 0.698801739 0.977055158 0.831081472 0.934922595 0.890978264 1 15.3923606 6.906073224 0.041454899 1.430184736 1.62E-07 0.411943106 0.082597706 613.5009792 2.348552659 24.07074219 66.38961006 8055142.437 -6.906073224 -1.430184574 SACMLSS(ph)PESSLT(ph)PPLSTNLHLESELDALASLENHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SACMLSSPESSLTPPLSTNLHLESELDALASLENHVK 37 0 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 2 S(0.185)ACMLS(0.375)S(0.423)PES(0.025)S(0.025)LT(0.957)PPLS(0.007)T(0.002)NLHLESELDALASLENHVK 121.43 2.48E-08 54400000 61285 60934 65433 62532 81603 60902 90674 74441 101950 TRUE FALSE 57449.28125 65445.61676 66985.10166 64136.67699 75194.22955 78483.41874 77078.27548 83735.12271 84933.88638 0.676400006 0.77054777 0.788673456 0.755136492 0.885326608 0.924053073 0.907509108 0.98588592 1 16.37405265 2.467408574 0.503758766 1.006721249 0.711751636 0.899517248 0.033414228 0.295697615 0.156162094 0.030767133 0.032118803 293.3651861 -2.467408574 -0.294969613 SACMLSS(ph)PESSLTPPLSTNLHLESELDALASLENHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SACMLSSPESSLTPPLSTNLHLESELDALASLENHVK 37 0 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 1 S(0.006)ACMLS(0.102)S(0.564)PES(0.149)S(0.149)LT(0.03)PPLSTNLHLESELDALASLENHVK 129.9 1.44E-08 114470000 34115 37405 36286 39742 37578 26280 38994 33899 40377 TRUE FALSE 31979.80305 40174.50512 37146.72106 40761.847 34626.77546 33866.60938 33147.2117 38131.36477 33637.81785 0.950709799 1.194325544 1.104314234 1.211786305 1.029400171 1.006801616 0.985415042 1.13358616 1 15.0377965 2.608525132 9.672063701 1.02382086 1.126568636 0.206764226 0.08004037 0.44752195 32.79883552 0.023712286 0.022343743 405.9991573 -2.608525132 0.102747776 SACMLSSPESSLT(ph)PPLSTNLHLESELDALASLENHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SACMLSSPESSLTPPLSTNLHLESELDALASLENHVK 37 0 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 1 SACMLSSPESSLT(1)PPLSTNLHLESELDALASLENHVK;SACMLSSPESSLT(1)PPLSTNLHLESELDALASLENHVK;SACMLSSPES(0.006)S(0.033)LT(0.955)PPLS(0.005)T(0.001)NLHLESELDALASLENHVK;SACMLSSPESSLT(0.986)PPLS(0.014)T(0.001)NLHLESELDALASLENHVK 341.97 1.96E-129 560219000 302516 290835 327624 304815 382351 313660 467947 357660 470830 TRUE FALSE 283582.0636 312368.726 335395.396 312637.069 352322.6948 404208.5502 397782.6916 402314.6383 392245.4313 0.722970979 0.796360393 0.855065143 0.797044513 0.898220009 1.030499065 1.014116825 1.02567068 1 18.58139712 2.451869919 2.582047023 1.020128162 0.803334729 0.905616462 0.034021578 0.082330788 1.118601816 0.013261356 0.01103416 283.0544056 -2.451869919 -0.216793432 SADGVIVSGVKDVDDFFEHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SADGVIVSGVKDVDDFFEHER 21 1 G3V5X9;Q9UNH7;A0A0A0MRI2;Q9UNH7-2 G3V5X9;Q9UNH7-2 SNX6 "Sorting nexin-6;Sorting nexin-6, N-terminally processed" 0 227.2 1.29E-25 33681000 52581 88213 72215 89324 129150 46287 83792 63102 249580 FALSE TRUE 49290.04907 94744.38231 73927.9739 91616.20507 119007.08 59649.30549 71228.16749 70980.4236 207923.4857 0.237058594 0.455669459 0.355553745 0.440624611 0.57235997 0.286881039 0.34256913 0.341377615 1 17.6656932 -1.365053604 3.167935603 1.005972687 0.384157806 0.812216011 0.09380913 36283491.82 48304935.14 2010915.676 0.021128863 0.043146582 1.365053604 -0.621814881 SADTLWDIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SADTLWDIQK 10 0 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 ;;; 218.04 1.62E-08 248389000 712062 925660 632476 680657 1094150 483799 668246 878550 1395950 FALSE TRUE 667495.3105 994196.8295 647478.6294 698123.811 1008219.873 623463.9175 568048.716 988238.9014 1162956.927 0.573963915 0.854887061 0.55675203 0.60030066 0.866945154 0.536102329 0.488452068 0.849763975 1 20.14936623 1.020384637 6.647356354 0.999767161 0.646572889 0.487010977 0.126819668 0.117708517 19.8402865 0.12268036 0.030793784 10.48056357 -1.020384637 -0.353194271 SADTLWGIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SADTLWGIQK 10 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 194.84 9.75E-07 566760000 1165970 1783850 1029190 1089040 1985430 621940 1011500 1530020 1365950 FALSE TRUE 1092994.019 1915928.11 1053602.873 1116986.61 1829502.337 801483.9816 859834.9653 1721046.365 1137964.121 0.960481969 1.683645447 0.925866513 0.981565754 1.607697733 0.70431393 0.755590576 1.512390711 1 20.11802364 2.222215195 24.99999182 0.939858599 1.240358004 0.103471901 0.332749095 446.1751425 682411.5532 0.119660889 0.088632042 166.8073548 -2.222215195 0.300499404 SAEEVEEIKAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAEEVEEIKAEK 12 1 Q8WUA2 Q8WUA2 PPIL4 Peptidyl-prolyl cis-trans isomerase-like 4 0 116.19 0.00021051 0 128760 91339 99043 94765 102680 70264 107700 68588 137310 FALSE TRUE 120701.1414 98101.8346 101392.3467 97196.83034 94615.92699 90548.07616 91551.38484 77151.36278 114392.0739 1.055153013 0.857592936 0.886358147 0.849681512 0.827119605 0.791559004 0.800329793 0.674446752 1 16.80362757 7.999999999 0.634296703 0.813456145 18.52504811 0.392502921 0.083076101 190.1687906 1.292420444 0.02987693 4712.69606 99999999.86 -7.999999999 17.71159196 SAEHYTETALDEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SAEHYTETALDEIR 14 0 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;D6RBM8 H3BLV9 SRPK1 SRSF protein kinase 1 0 ; 219.35 5.05E-12 168818000 234375 359390 330330 341900 393920 391260 398800 334370 321620 FALSE TRUE 219705.8871 385999.6095 338165.5836 350673.7328 362983.1122 504210.4104 339003.6423 376116.8305 267939.5443 0.819983059 1.440622028 1.262096584 1.308779314 1.354720197 1.881806629 1.265224374 1.403737666 1 18.03154799 4.742134944 24.31235795 1.384346025 0.819982738 0.37490018 0.219710637 237.2785719 1613849.519 0.047804636 0.351417624 55224.9007 -4.742134944 -0.564363286 SAEKEISLWFKPEELVDYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAEKEISLWFKPEELVDYK 19 2 Q32Q12;P22392-2;P22392 Q32Q12 NME1-NME2;NME2 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B 0 121.46 1.97E-05 143450000 125840 170420 139530 197830 255110 114730 158540 126020 481150 FALSE TRUE 117963.899 183038.0741 142839.7175 202906.6527 235074.6897 147850.6885 134768.3988 141753.8744 400842.9567 0.294289564 0.456632881 0.356348328 0.50619987 0.586450843 0.368849411 0.336212466 0.353639429 1 18.6126776 -2.002362651 3.569819515 1.603233548 0.408368556 0.818794289 0.087621264 0.033296038 2.20E-05 0.006714986 0.019911196 0.009945746 2.002362651 -1.194864992 SAEPS(ph)PTVMSTSLGSNLSELDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SAEPSPTVMSTSLGSNLSELDR 22 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 S(0.159)AEPS(0.836)PT(0.005)VMSTSLGSNLSELDR;S(0.196)AEPS(0.8)PT(0.004)VMSTSLGSNLSELDR 85.087 0.0033488 52993000 38586 38358 36929 42598 44325 32090 42253 30435 38306 TRUE FALSE 36170.97114 41198.06623 37804.97332 43691.1368 40843.8933 41353.86206 35917.55491 34234.87675 31912.48113 1.133442774 1.290970328 1.184645379 1.369092444 1.27987207 1.2958523 1.125501798 1.072773897 1 14.96183316 1.463887884 2.21863708 1.025966137 1.259095176 0.667897012 0.066149402 0.169965597 1.594830122 0.052216042 0.016970237 29.09965795 -1.463887884 0.233129039 SAEPSANTTLVS(ph)ETEEEGSVPAFGAAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SAEPSANTTLVSETEEEGSVPAFGAAAK 28 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 SAEPSANT(0.005)T(0.021)LVS(0.753)ET(0.221)EEEGS(0.001)VPAFGAAAK;SAEPSANT(0.003)T(0.009)LVS(0.89)ET(0.099)EEEGSVPAFGAAAK;SAEPSANT(0.001)T(0.005)LVS(0.855)ET(0.139)EEEGSVPAFGAAAK;SAEPS(0.001)ANT(0.027)T(0.118)LVS(0.766)ET(0.087)EEEGSVPAFGAAAK 225.86 9.37E-35 911670000 2245180 1444820 1806180 1589570 1456560 1451250 2082260 1754930 1140210 TRUE FALSE 2104658.192 1551795.976 1849023.443 1630361.057 1342167.653 1870202.316 1770044.444 1974036.874 949901.585 2.215659206 1.633638685 1.946542117 1.716347339 1.412954431 1.968837978 1.863397716 2.078148836 1 19.85741852 4.74858419 23.6633564 1.756104649 2.215659749 0.189509355 0.316714219 1116.650959 2636040.025 0.066288748 0.863285601 56051.10643 -4.74858419 0.4595551 SAEPSPTVMSTS(ph)LGSNLSELDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SAEPSPTVMSTSLGSNLSELDR 22 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 SAEPSPTVMS(0.034)T(0.339)S(0.627)LGSNLSELDR;SAEPSPTVMS(0.122)T(0.085)S(0.793)LGSNLSELDR 224.57 7.12E-26 141793000 253420 280960 257570 282460 363500 267940 383560 284570 342270 TRUE FALSE 237558.8946 301762.5707 263679.682 289708.4018 334952.1763 345289.9284 326048.7388 320099.1909 285142.9259 0.833122175 1.058285314 0.924728121 1.016011184 1.174681698 1.210936331 1.143457225 1.122592082 1 18.12132572 2.883338601 4.055899323 1.145585986 0.962906211 0.551582828 0.077893336 0.16312262 4.600539234 0.022278605 0.023958018 764.4315459 -2.883338601 -0.182679775 SAESPS(ph)WTPAEHVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAESPSWTPAEHVAK 15 0 Q13415 Q13415 ORC1 Origin recognition complex subunit 1 1 S(0.036)AES(0.407)PS(0.555)WT(0.001)PAEHVAK 120.82 7.65E-05 459220000 362530 303810 334970 317520 315140 272860 423780 260710 278450 TRUE FALSE 339839.8944 326304.4085 342915.6466 325668.1008 290390.1756 351630.2525 360238.1232 293260.2174 231974.8961 1.464985652 1.406636726 1.478244639 1.403893724 1.251817246 1.51581166 1.552918566 1.264189454 1 17.82360916 0.968156668 5.318739198 1.000183221 1.440846004 0.755733971 0.080708792 0.093993279 10.02880246 0.079563695 0.020075322 9.293015636 -0.968156668 0.440662783 SAEVGPSSEPEVQTLPYLPHYIPGVDPET(ph)SHGGHPHGNMPGLDRPLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SAEVGPSSEPEVQTLPYLPHYIPGVDPETSHGGHPHGNMPGLDRPLSR 48 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 SAEVGPSSEPEVQTLPYLPHYIPGVDPET(0.428)S(0.428)HGGHPHGNMPGLDRPLS(0.145)R;SAEVGPSSEPEVQT(0.001)LPY(0.001)LPHY(0.002)IPGVDPET(0.624)S(0.168)HGGHPHGNMPGLDRPLS(0.204)R 180.49 2.58E-29 650290000 102889 186808 144844 169119 179006 152040 209051 149657 141432 TRUE FALSE 96449.36115 200639.4587 148279.7681 173458.8799 164947.5908 195931.4798 177705.7433 168342.0059 117826.0855 0.818573924 1.702844135 1.258462992 1.472160253 1.39992422 1.662887119 1.508203744 1.428732909 1 16.84629945 3.200693135 24.8231127 1.45820411 1.354649924 0.0095246 0.274200782 618.3030536 405311.635 0.072472352 0.086622862 1587.424704 -3.200693135 -0.103554186 SAEVGPSSEPEVQTLPYLPHYIPGVDPETSHGGHPHGNMPGLDRPLS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SAEVGPSSEPEVQTLPYLPHYIPGVDPETSHGGHPHGNMPGLDRPLSR 48 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 SAEVGPSSEPEVQTLPY(0.001)LPHY(0.001)IPGVDPET(0.317)S(0.317)HGGHPHGNMPGLDRPLS(0.365)R;SAEVGPSSEPEVQT(0.007)LPY(0.015)LPHY(0.015)IPGVDPET(0.173)S(0.173)HGGHPHGNMPGLDRPLS(0.617)R;SAEVGPSSEPEVQTLPYLPHYIPGVDPET(0.11)S(0.11)HGGHPHGNMPGLDRPLS(0.781)R;SAEVGPSSEPEVQTLPYLPHYIPGVDPET(0.093)S(0.112)HGGHPHGNMPGLDRPLS(0.795)R;SAEVGPSSEPEVQTLPYLPHYIPGVDPET(0.142)S(0.142)HGGHPHGNMPGLDRPLS(0.716)R 175.33 1.31E-22 2599896000 230617 378260 329953 355865 358726 274811 444607 314536 297449 TRUE FALSE 216183.0936 406266.764 337779.641 364997.0984 330553.107 354144.4745 377942.3079 353806.512 247802.8403 0.872399579 1.639475817 1.363098343 1.472933474 1.333935909 1.429138076 1.52517343 1.42777424 1 17.9188332 -0.844848841 6.268021487 0.999999976 1.415639421 0.247618721 0.202829447 5.89E-08 1.06E-08 0.171936924 0.04052592 0.142939138 0.844848841 0.415639445 SAFSS(ph)LQNIPESLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SAFSSLQNIPESLRR 15 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 SAFS(0.18)S(0.82)LQNIPESLRR;SAFS(0.393)S(0.607)LQNIPESLRR 173.87 5.79E-07 307110000 114311 168191 128333 122364 187804 89813 150299 138326 292820 TRUE FALSE 107156.4786 180644.0366 131377.1194 125504.0674 173054.6314 115740.5551 127763.0603 155596.3056 243946.4503 0.439262299 0.740506929 0.53854901 0.514473841 0.709395981 0.474450663 0.523734041 0.637829759 1 17.89620497 0.881346013 6.382116452 0.999998208 0.574594952 0.671329334 0.09518954 1.376067107 73.84469651 0.086889509 0.021822368 7.609322892 -0.881346013 -0.425403256 SAFVVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAFVVER 7 0 P40763;P40763-2;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 100.45 0.022762 524230000 137460 168850 140080 164580 189040 151860 176900 163760 227990 FALSE TRUE 128856.624 181351.8297 143402.7638 168803.4014 174193.561 195699.5168 150375.4873 184205.7965 189936.9961 0.678417721 0.954799925 0.755001746 0.888733658 0.917112329 1.030339116 0.791712464 0.969825786 1 17.53516142 3.029105226 9.34202482 0.922921887 0.823803573 0.308838596 0.094257872 0.478489421 143.9462787 0.025632858 0.030521788 1069.313935 -3.029105226 -0.099118314 SAGAENPRPFS(ph)PPRAPPPPPPPPPPPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAGAENPRPFSPPRAPPPPPPPPPPPPR 28 2 Q8N3V7-2 Q8N3V7-2 SYNPO Synaptopodin 1 S(0.003)AGAENPRPFS(0.997)PPRAPPPPPPPPPPPPR 125.71 1.94E-05 244810000 39090 40416 40666 46689 51593 35424 44843 44058 52785 TRUE FALSE 36643.42668 43408.44269 41630.61672 47887.11878 47541.0939 45650.33374 38119.20845 49558.73828 43974.8425 0.83328159 0.987119913 0.946691662 1.088966238 1.081097537 1.038101131 0.866841273 1.126979324 1 15.42439079 5.677034075 1.01814842 1.010846136 4.46E-19 0.365606029 0.075325603 13.26251649 2.632791163 0.022521996 22.96706675 475372.5221 -5.677034075 -1.010846136 SAGGRPGS(ph)GPQLGTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SAGGRPGSGPQLGTGR 16 1 O14908;O14908-2;K7EM11;K7ESN1 O14908 GIPC1 PDZ domain-containing protein GIPC1 1 SAGGRPGS(1)GPQLGTGR;SAGGRPGS(1)GPQLGTGR;SAGGRPGS(1)GPQLGTGR;SAGGRPGS(1)GPQLGTGR;SAGGRPGS(1)GPQLGTGR;SAGGRPGS(1)GPQLGTGR 177.09 1.82E-09 2790630000 562396 612833 616477 522550 645870 508191 622325 535683 687301 TRUE FALSE 527196.6383 658207.793 631100.1256 535959.5177 595145.9755 654897.4919 529013.1436 602564.2017 572586.023 0.920729143 1.149535208 1.102192684 0.936033183 1.03940011 1.143753891 0.923901602 1.052355764 1 19.12713293 2.245632774 0.678938263 0.997376642 1.069587108 0 0.08686863 2.055667377 1.84670039 0.072682232 0.048832174 176.0486804 -2.245632774 0.072210466 SAGGRPGSGPQLGTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SAGGRPGSGPQLGTGR 16 1 O14908;O14908-2;K7EM11;K7ESN1 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ;; 185.02 1.58E-09 215677000 106203 126721 107730 105017 143241 92305 129626 118668 155159 FALSE TRUE 99555.94381 136103.5547 110285.4065 107711.914 131991.4297 118951.9551 110189.7847 133483.961 129261.9605 0.770187481 1.052928132 0.853193051 0.833283926 1.021115796 0.920239447 0.852453299 1.032662358 1 16.97993825 1.223968008 24.97935288 1.016331268 0.910687679 0.235290097 0.085296804 410.8841725 703323.811 0.074802954 0.019031085 16.74819499 -1.223968008 -0.105643589 SAGGSS(ph)PEGGEDS(ph)DREDGNYCPPVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAGGSSPEGGEDSDREDGNYCPPVKR 26 2 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EID7;K7ENB9 Q9H6Z4 RANBP3 Ran-binding protein 3 2 SAGGS(0.15)S(0.85)PEGGEDS(1)DREDGNYCPPVKR 160.78 9.59E-12 266410000 133560 125920 120160 129270 148580 113730 167940 134060 208360 TRUE FALSE 125200.718 135243.2478 123010.2519 132587.2871 136911.1261 146562.0047 142758.9561 150797.6861 173583.3699 0.721271387 0.779125603 0.708652286 0.763824824 0.788734118 0.844332062 0.822423001 0.868733486 1 17.40526921 1.011120843 0.418255346 1.012975128 0.729754111 0.912945398 0.024599075 0.335670137 0.158923051 0.03521487 0.018654824 10.25937355 -1.011120843 -0.283221017 SAGGSSPEGGEDS(ph)DREDGNYCPPVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 331.7 2.84E-95 2180260000 926230 753750 806900 765670 899630 762100 1150110 720430 1250840 TRUE FALSE 868258.9177 809558.4343 826040.049 785318.3885 828976.6887 982105.8983 977661.6826 810377.2714 1042066.723 0.833208564 0.776877734 0.79269401 0.753616223 0.795512101 0.942459707 0.938194897 0.777663515 1 19.99101623 2.250975666 21.12225403 0.913690746 0.78718419 0.526069407 0.058529944 24.9681562 42479.12211 0.018643232 0.01544314 178.2278902 -2.250975666 -0.126506556 SAHATAPVNIAGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SAHATAPVNIAGSR 14 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ; 160.65 4.72E-06 600110000 104384 147671 142703 158478 157777 143562 179931 143160 169444 FALSE TRUE 97850.79177 158604.7145 146087.9825 162544.8138 145385.8309 185006.0189 152952.0169 161033.8411 141162.7017 0.69317738 1.123559641 1.034890809 1.1514714 1.029916749 1.310587121 1.083515795 1.140767633 1 17.10699942 4.739466697 24.80274039 1.112705226 0.693177236 0.693404826 0.086941159 35.75207373 978496.8794 0.018755762 0.113555199 54886.64652 -4.739466697 -0.419527991 SAHTLVGPTPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAHTLVGPTPSR 12 0 Q13428-3;Q13428-8;A0A6I8PRA0 Q13428-3 TCOF1 Treacle protein 0 74.46 0.036444 109070000 38973 55910 67041 49537 61202 47692 63013 50992 72489 FALSE TRUE 36533.7495 60049.63457 68631.24418 50808.20329 56395.4418 61459.90619 53564.78563 57358.46345 60390.1176 0.604962384 0.994361941 1.136464821 0.841333074 0.933852161 1.01771463 0.886979323 0.949798837 1 15.88202486 4.74027048 24.53235051 0.976436424 0.60496222 0.674711308 0.079559913 73.91865139 1060434.251 0.020255126 0.129089197 54988.32358 -4.74027048 -0.371474204 SAKSEESLT(ph)SLHAVDGDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAKSEESLTSLHAVDGDSK 19 1 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.131)AKS(0.159)EES(0.313)LT(0.392)S(0.006)LHAVDGDSK 226.14 2.54E-19 315260000 669260 453450 526400 559990 629000 377860 796530 490830 888870 TRUE FALSE 627372.2113 487023.9098 538886.4566 574360.2915 579600.8773 486942.048 677097.7211 552111.206 740511.8547 0.847214271 0.657685501 0.72772158 0.775626059 0.782703037 0.657574953 0.914364459 0.74558051 1 19.49816331 0.391722694 0.431336598 1.023299149 0.722953902 0.470260481 0.07823764 1.950702048 0.637130026 0.166317866 0.04655581 2.464465222 -0.391722694 -0.300345247 SALPVS(ph)PSISSAPVPVEIENLPQS(ph)PGTDQHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SALPVSPSISSAPVPVEIENLPQSPGTDQHDR 32 0 Q9HCM4-2;Q9HCM4-4;Q9HCM4-3;Q9HCM4 Q9HCM4-2 EPB41L5 Band 4.1-like protein 5 2 S(0.016)ALPVS(0.956)PS(0.008)IS(0.01)S(0.011)APVPVEIENLPQS(0.927)PGT(0.073)DQHDR 71.575 0.0016597 22861000 14286 10954 16141 14809 15904 14043 17178 13214 20660 TRUE FALSE 13391.86476 11765.04556 16523.87214 15189.02401 14654.96399 18096.98613 14602.31837 14863.79699 17211.71253 0.778066955 0.683548806 0.960036493 0.882481856 0.851452984 1.051434371 0.848394275 0.863586175 1 14.07110303 3.970647494 4.416921907 0.914969622 0.732813562 0.55826579 0.070501127 0.132420184 6.46581094 0.016624814 0.034218442 9346.467366 -3.970647494 -0.18215606 SALS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SALSPSK 7 0 P49792;Q7Z3J3 P49792 RANBP2;RGPD4 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 4 1 SALS(0.999)PS(0.001)K;S(0.002)ALS(0.998)PSK 107.08 0.0079283 345290000 687150 457950 556790 534060 568880 391620 665160 464460 590250 TRUE FALSE 644142.5081 491857.0945 569997.3217 547764.8838 524202.4596 504674.3366 565425.433 522448.8534 491733.4618 1.309942394 1.000251422 1.159159109 1.113946734 1.066029669 1.026316848 1.149861616 1.062463497 1 18.90751701 SALS(ph)PSKS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SALSPSKSPAK 11 1 P49792;Q7Z3J3 P49792 RANBP2;RGPD4 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 4 2 SALS(0.996)PS(0.034)KS(0.97)PAK 130.21 0.00013019 445330000 3422000 1192600 1942200 1790800 1792100 1219200 2581700 1423400 1787700 TRUE FALSE 3207823.128 1280901.345 1988269.901 1836754.96 1651355.695 1571163.248 2194598.052 1601114.623 1489321.321 2.153882499 0.860057079 1.335017416 1.233283197 1.108797458 1.054952498 1.473555788 1.075063252 1 20.50622362 4.749868797 24.96752921 1.16928663 2.153883085 0.767257879 0.174493625 825.9789808 1823658.83 0.040743518 0.635572243 56217.14646 -4.749868797 0.984596455 SALSGHLETVILGLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 89.541 0.0057553 91148000 164110 244050 184580 168390 289060 106240 182490 257190 392130 FALSE TRUE 153838.648 262119.7159 188958.3248 172711.1725 266358.3936 136909.7633 155127.3187 289300.7376 326680.9697 0.470914018 0.802372162 0.578418525 0.528684522 0.815347138 0.41909317 0.474858755 0.885575728 1 18.31752289 1.089249837 5.241167799 0.99554482 0.597826101 0.563021918 0.132706233 0.144103547 5.941186337 0.127049125 0.03212624 12.28145545 -1.089249837 -0.397718719 SALSS(ph)SLRDLSEAGVHH ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SALSSSLRDLSEAGVHH 17 1 A0A0C4DGT3 A0A0C4DGT3 IQSEC1 1 SALS(0.015)S(0.806)S(0.179)LRDLSEAGVHH 186.11 3.27E-10 135140000 87242 129050 114520 125550 144350 87350 132250 106910 156950 TRUE FALSE 81781.67895 138604.9963 117236.4685 128771.8256 133013.3333 112566.527 112420.3402 120257.9488 130754.0311 0.625462009 1.060043772 0.896618387 0.984840196 1.017279025 0.860902919 0.85978489 0.919726511 1 16.9964959 SALSSS(ph)LR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SALSSSLR 8 0 A0A0C4DGT3;A0A3B3IU98;Q6DN90-2;A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90 A0A0C4DGT3;A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 SALSS(0.001)S(0.999)LR;SALS(0.001)S(0.012)S(0.987)LR 114.4 0.0027937 474210000 1733640 1823890 1899650 1801680 1679460 1695580 2371600 1766200 1283710 TRUE FALSE 1625134.567 1958932.713 1944710.595 1847914.159 1547561.986 2185066.421 2016000.597 1986713.958 1069450.508 1.519597733 1.831718905 1.818420376 1.727909936 1.447062744 2.043167406 1.885080779 1.857696025 1 20.02843829 -0.805438108 5.849098861 0.999999919 1.785966814 0.654902771 0.174306992 1.78E-07 3.61E-08 0.161184684 0.037991591 0.156517136 0.805438108 0.785966895 SALSSS(ph)LRDLSEAGVHH ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SALSSSLRDLSEAGVHH 17 1 A0A0C4DGT3 A0A0C4DGT3 IQSEC1 1 SALSS(0.082)S(0.917)LRDLSEAGVHH 232.6 5.52E-17 378210000 173860 315170 263520 259030 333780 209080 267490 261850 364370 TRUE FALSE 162978.4129 338505.5147 269770.8188 265677.1483 307566.2652 269438.0019 227382.3578 294542.5489 303554.2931 0.536900372 1.115139935 0.888706979 0.875221186 1.013216654 0.887610579 0.749066519 0.970312579 1 18.21159505 2.005046432 24.92553395 0.863518281 0.919797685 0 0.163156787 614.1356551 3033342.083 0.056543655 0.041622619 101.1687612 -2.005046432 0.056279404 SALVTSSSS(ph)LPSFPSTLSWSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SALVTSSSSLPSFPSTLSWSR 21 0 Q14161-3;Q14161;F8VXI9;Q14161-6;Q14161-4 Q14161-3 GIT2 ARF GTPase-activating protein GIT2 1 SALVTSSS(0.004)S(0.996)LPSFPSTLSWSR 242.45 4.99E-30 64561000 113870 120210 121500 102300 146430 99540 135800 124980 180790 TRUE FALSE 106743.08 129110.4735 124382.0374 104925.1912 134929.9785 128275.5821 115438.0507 140584.0281 150614.9811 0.708714892 0.857221988 0.825827793 0.696645118 0.895860276 0.851678772 0.766444678 0.933400032 1 17.20050575 1.071241404 4.466484293 0.998600738 0.80900337 0.547666417 0.06388685 0.13775943 4.965285195 0.056536355 0.014408047 11.78260731 -1.071241404 -0.189597369 SAMDSPVPASMFAPEPS(ph)SPGAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAMDSPVPASMFAPEPSSPGAAR 23 0 O00178;F8WAZ4 O00178 GTPBP1 GTP-binding protein 1 1 SAMDSPVPASMFAPEPS(0.5)S(0.5)PGAAR 57.679 0.014338 0 26857 25690 26783 24980 27507 21658 31551 24359 29604 TRUE FALSE 25176.06831 27592.11433 27418.30541 25621.02909 25346.71118 27910.31301 26820.22046 27400.27477 24662.90115 1.02080725 1.118770017 1.111722633 1.038848955 1.027726261 1.131671933 1.087472244 1.11099155 1 14.5900549 3.290245598 24.99999138 1.07427427 1.095261034 0 0.04728426 379.4376019 183531.0894 0.012587062 0.017042952 1950.94757 -3.290245598 0.020986764 SAMDSPVPASMFAPEPSS(ph)PGAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 SAMDSPVPASMFAPEPSSPGAAR 23 0 O00178;F8WAZ4 O00178 GTPBP1 GTP-binding protein 1 1 SAMDSPVPASMFAPEPS(0.061)S(0.939)PGAAR;SAMDSPVPASMFAPEPS(0.004)S(0.996)PGAAR;SAMDSPVPASMFAPEPS(0.001)S(0.999)PGAAR;SAMDSPVPASMFAPEPS(0.01)S(0.99)PGAAR;SAMDSPVPASMFAPEPS(0.335)S(0.665)PGAAR;SAMDSPVPASMFAPEPS(0.168)S(0.832)PGAAR;SAMDSPVPASMFAPEPS(0.251)S(0.749)PGAAR;SAMDSPVPASMFAPEPS(0.205)S(0.795)PGAAR;SAMDSPVPASMFAPEPS(0.048)S(0.952)PGAAR;SAMDSPVPASMFAPEPS(0.137)S(0.863)PGAAR 360.78 3.13E-102 2006429000 1765679 2021793 1964459 2001483 2118864 1564823 2040726 1613151 1823604 TRUE FALSE 1655168.303 2171488.657 2011056.895 2052844.442 1952456.969 2016561.997 1734738.081 1814556.453 1519232.711 1.089476478 1.429332479 1.32373196 1.351237652 1.285159906 1.327355567 1.141851455 1.194390063 1 20.53491144 1.227723211 0.85548483 1.009869977 1.327351738 0.49199537 0.094089135 0.390548756 0.632289761 0.080382019 0.029822248 16.89363906 -1.227723211 0.317481762 SAMPFT(ph)ASPASSTTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAMPFTASPASSTTAR 16 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 SAMPFT(0.816)AS(0.184)PASSTTAR 166.35 6.99E-08 208620000 242580 241950 265240 255980 294530 229990 304870 236450 343870 TRUE FALSE 227397.3508 259864.2297 271531.6181 262548.8802 271398.8019 296384.3794 259157.5738 265971.303 286475.8755 0.79377487 0.907106852 0.94783415 0.916478149 0.94737053 1.034587568 0.904640132 0.928424785 1 18.12805413 5.779543291 0.904178731 0.952443889 1.94E-16 0.635947768 0.038348829 7.72247834 1.183660859 0.011375546 11.2672224 601926.2601 -5.779543291 -0.952443889 SAMPFTAS(ph)PASSTTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SAMPFTASPASSTTAR 16 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 SAMPFT(0.072)AS(0.926)PAS(0.002)STTAR;SAMPFT(0.462)AS(0.537)PASSTTAR;SAMPFTAS(1)PASSTTAR;SAMPFTAS(0.992)PAS(0.008)STTAR;SAMPFT(0.002)AS(0.998)PASSTTAR;SAMPFT(0.003)AS(0.974)PAS(0.019)S(0.002)T(0.001)T(0.001)AR;SAMPFT(0.016)AS(0.98)PASS(0.004)TTAR;SAMPFT(0.055)AS(0.866)PAS(0.004)S(0.055)T(0.016)T(0.004)AR 247.34 2.92E-20 2074160000 1975997 1945260 2008479 2129860 2332690 1891962 2484350 1867020 2847290 TRUE FALSE 1852322.875 2089289.074 2056121.07 2184515.813 2149489.937 2438140.716 2111844.781 2100121.557 2372058.905 0.780892444 0.880791396 0.866808605 0.920936579 0.906170556 1.027858419 0.890300311 0.885358097 1 21.17770841 7.478288724 0.297571992 0.953607817 1.42E-12 0.523492126 0.047381077 32.91889144 0.624986903 0.046178615 15.72851538 30080754.4 -7.478288724 -0.953607817 SAMQSVVDDWIESYKHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAMQSVVDDWIESYKHDR 18 1 Q8N3U4;Q8N3U4-2;B1AMT4;B1AMT1;B1AMT2;B1AMT3;B1AMT0 Q8N3U4 STAG2 Cohesin subunit SA-2 0 135.28 5.25E-06 50226000 119910 110920 114260 118300 124980 99364 133040 108200 81470 FALSE TRUE 112405.0471 119132.6322 116970.3012 121335.7783 115164.5749 128048.7738 113091.8871 121709.0082 67872.13068 1.656129637 1.755251103 1.723392208 1.787711349 1.696787382 1.886617857 1.666249253 1.793210364 1 16.05053168 -0.889062838 6.263256313 0.999999918 1.744778501 0.923048182 0.067661689 6.68E-08 1.17E-08 0.056005459 0.013200612 0.129103246 0.889062838 0.744778583 SANAEDAQEFSDVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SANAEDAQEFSDVER 15 0 Q9HCY8 Q9HCY8 S100A14 Protein S100-A14 0 ; 310.22 9.05E-56 423270000 376710 379130 380040 341270 520950 348950 432810 441360 561320 FALSE TRUE 353132.3935 407201.1797 389054.7283 350027.566 480036.6884 449686.2003 367914.1585 496464.7676 467632.0657 0.755150084 0.870772579 0.831967602 0.748510617 1.026526459 0.961623963 0.786759903 1.061656811 1 18.83501433 2.743414715 24.99898597 0.939946506 0.818190178 0.476838586 0.082755321 478.1421832 2462472.238 0.02553685 0.026314507 553.8787653 -2.743414715 -0.121756327 SANMDHWQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SANMDHWQQR 10 0 Q9NZL9;Q9NZL9-2;Q9NZL9-3;Q9NZL9-4;H7C0X7 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 0 ;; 96.171 0.0069221 447860000 343910 419410 351720 301252 466910 236064 374290 364020 493760 FALSE TRUE 322385.287 450463.5528 360062.9645 308982.6363 430240.772 304211.8446 318168.6892 409468.6983 411348.2662 0.783728323 1.095090438 0.87532389 0.751146077 1.04592825 0.739548139 0.773477648 0.995430714 1 18.65000084 3.677550235 6.286316785 0.860339336 0.968647572 0 0.131878909 0.403815748 37.52653013 0.032445876 0.051256725 4759.378401 -3.677550235 0.108308236 SANPPHTIQASEEQSST(ph)PAPVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SANPPHTIQASEEQSSTPAPVKK 23 1 Q9Y450;Q9Y450-4;J3QT46;B7Z524;H0YDX7;E9PHZ9;E9PS53 Q9Y450 HBS1L HBS1-like protein 1 SANPPHTIQAS(0.072)EEQS(0.072)S(0.343)T(0.514)PAPVKK 60.95 0.042839 137720000 64543 58245 56615 74929 76625 34785 98309 62773 107600 TRUE FALSE 60503.36884 62557.5204 57957.93454 76851.80499 70607.18159 44826.86481 83568.47811 70610.34723 89640.86488 0.67495298 0.697868327 0.646557065 0.857330026 0.78766734 0.500071757 0.932258722 0.787702655 1 16.45186895 1.160235979 1.097940484 0.987684984 0.702089078 0.395603646 0.112834529 0.446239692 1.125162238 0.098047233 0.032187698 14.4622538 -1.160235979 -0.285595906 SANPTRPS(ph)SPVTSHISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SANPTRPSSPVTSHISK 17 1 Q92560;F8W6N3;H0Y8E8 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 SANPT(0.001)RPS(0.499)S(0.499)PVT(0.001)SHISK;S(0.009)ANPT(0.006)RPS(0.492)S(0.492)PVT(0.001)SHISK 131.82 1.55E-05 542490000 231765 278050 299427 279841 328440 234364 353950 268189 377900 TRUE FALSE 217259.2424 298637.1113 306529.5498 287022.1938 302645.6473 302021.0822 300878.4834 301672.987 314826.0487 0.690092968 0.948578152 0.973647356 0.911685024 0.961310694 0.959326852 0.95569755 0.958221177 1 18.26419539 4.738657976 5.68608353 0.957141846 0.68136966 0.938513327 0.021605039 0.028168568 3.841399157 0.004574679 0.030179441 54784.53456 -4.738657976 -0.275772186 SANTS(ph)PESSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SANTSPESSSR 11 0 P20749;H7C0A2 P20749 BCL3 B-cell lymphoma 3 protein 1 SANT(0.051)S(0.949)PESSSR;SANT(0.059)S(0.931)PES(0.01)SSR;SANT(0.078)S(0.922)PES(0.001)SSR;SANT(0.223)S(0.776)PES(0.001)SSR 152.02 3.48E-05 389313000 770840 781180 824650 783640 813060 747110 881450 733390 834850 TRUE FALSE 722594.5004 839019.38 844211.0874 803749.5291 749205.5473 962788.5287 749284.7555 824955.3559 695508.1417 1.038944704 1.206340127 1.213804752 1.155629217 1.077206006 1.384295123 1.077319891 1.186118906 1 19.40770788 0.259437792 1.206823875 0.99982747 1.177081457 0.220814954 0.097089012 6.506776246 9.286289289 0.085926673 0.025058097 1.817346724 -0.259437792 0.177253987 SAPAS(ph)PNHAGVLSAHSSGAQTPESLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAPASPNHAGVLSAHSSGAQTPESLSR 27 0 Q01167;Q01167-2 Q01167 FOXK2 Forkhead box protein K2 1 S(0.133)APAS(0.867)PNHAGVLSAHSSGAQTPESLSR 194.63 1.67E-18 205690000 20181 59921 49104 61726 67539 57993 65291 55232 47140 TRUE FALSE 18917.90723 64357.61319 50268.77007 63309.99366 62234.75938 74734.63766 55501.22068 62127.83678 39272.02946 0.48171453 1.638764639 1.280014574 1.612088668 1.584709531 1.902999124 1.413250638 1.581986916 1 15.26121453 4.742500082 24.88400098 1.521865855 0.4817141 0.640499094 0.239737184 213.9425798 1351331.347 0.051042968 0.388990196 55271.35129 -4.742500082 -1.040151755 SAPAS(ph)PTHPGLMSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 S(0.111)APAS(0.859)PT(0.03)HPGLMSPR;S(0.181)APAS(0.771)PT(0.049)HPGLMSPR;SAPAS(0.994)PT(0.006)HPGLMSPR;S(0.024)APAS(0.825)PT(0.151)HPGLMSPR;S(0.006)APAS(0.917)PT(0.077)HPGLMSPR;SAPAS(0.958)PT(0.042)HPGLMSPR;SAPAS(0.948)PT(0.052)HPGLMSPR;SAPAS(0.965)PT(0.035)HPGLMSPR 219.12 1.94E-12 6713530000 2378080 2350950 2606040 2760560 2945560 2877770 2652430 2659090 2021720 TRUE FALSE 2229240.218 2525016.784 2667856.499 2831400.643 2714227.599 3708535.482 2254722.745 2991083.24 1684281.871 1.323555312 1.499165209 1.583972698 1.68107292 1.611504372 2.20184967 1.338684922 1.775880446 1 20.68370217 -1.086729598 4.926237634 0.99998042 1.617737069 0.388081644 0.24717503 4.89E-05 9.06E-06 0.220036793 0.051861528 0.081897454 1.086729598 0.617756649 SAPS(ph)SPAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SAPSSPAPR 9 0 E9PAK5;O75064 E9PAK5 DENND4B DENN domain-containing protein 4B 1 S(0.001)APS(0.499)S(0.499)PAPR;S(0.001)APS(0.5)S(0.5)PAPR 78.655 0.021921 162570000 416080 500930 465050 489330 521960 453240 592720 456350 533730 TRUE FALSE 390038.2955 538019.3784 476081.2056 501887.0362 480967.3671 584083.0303 503847.1385 513326.3021 444647.015 0.877186358 1.209992107 1.070694707 1.128731374 1.081683562 1.313588106 1.133139595 1.154457996 1 18.76230097 SAPTTLYLVHT(ph)DHAYQATPPVTIPGSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SAPTTLYLVHTDHAYQATPPVTIPGSAK 28 0 Q6ZNC4 Q6ZNC4 ZNF704 Zinc finger protein 704 1 S(0.06)APT(0.06)T(0.06)LY(0.324)LVHT(0.493)DHAY(0.001)QATPPVTIPGSAK;S(0.162)APT(0.162)T(0.162)LY(0.162)LVHT(0.19)DHAY(0.162)QAT(0.002)PPVTIPGSAK 142.37 2.21E-07 1239890000 1963070 1728920 1654950 1741870 2527000 1537750 3133300 2095570 2491210 TRUE FALSE 1840204.953 1856931.036 1694206.196 1786569.333 2328539.613 1981673.462 2663490.753 2357206.527 2075410.957 0.886670154 0.894729321 0.816323239 0.860826781 1.121965558 0.954834249 1.283355831 1.135778203 1 20.98496561 2.738969354 24.3509769 1.118246812 0.861600333 0.625631516 0.08947053 15.08742443 898871.6555 0.027441152 0.027505468 548.2382766 -2.738969354 -0.256646479 SAQGSSS(ph)PVPSMVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SAQGSSSPVPSMVQK 15 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 SAQGSS(0.002)S(0.998)PVPSMVQK;SAQGSSS(1)PVPSMVQK;SAQGSS(0.002)S(0.998)PVPSMVQK;SAQGSSS(1)PVPSMVQK;SAQGSS(0.008)S(0.987)PVPS(0.005)MVQK;SAQGSS(0.001)S(0.999)PVPS(0.001)MVQK 351.81 2.27E-82 1195890000 3213320 2444510 2848290 2857910 2913080 2508006 3982250 2756330 3227250 TRUE FALSE 3012204.037 2625504.064 2915852.784 2931248.809 2684298.448 3232026.618 3385148.582 3100463.868 2688601.126 1.120361071 0.976531639 1.084524125 1.090250532 0.998399659 1.202122021 1.2590743 1.153188488 1 21.35842431 2.229701972 24.96574071 1.185135826 1.049255403 0.239739889 0.079517227 174.5130976 491815.2881 0.027041898 0.020267214 169.7078658 -2.229701972 -0.135880423 SAQNLPGGGPASHSNPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAQNLPGGGPASHSNPR 17 0 Q9BYV8-5;Q9BYV8-2;Q9BYV8 Q9BYV8-5 CEP41 Centrosomal protein of 41 kDa 0 149.34 3.29E-07 42234000 33315 33836 34106 35987 46327 28399 37797 32992 38325 FALSE TRUE 31229.87362 36341.25265 34915.01043 36910.48735 42688.66429 36597.33028 32129.69074 37111.12382 31928.30991 0.978124859 1.138214104 1.093543959 1.15604263 1.337016097 1.146234498 1.006307281 1.162326598 1 14.96254857 0.850396884 0.9724571 1.007101845 1.13348454 0.124086933 0.098124235 1.574885468 2.971893088 0.092805934 0.030707136 7.085930423 -0.850396884 0.126382695 SAQSLEYCAELLGLDQDDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAQSLEYCAELLGLDQDDLR 20 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 157.91 3.52E-09 33509000 26536 31463 33839 27646 34540 28043 37121 30984 33828 FALSE TRUE 24875.15913 33792.55326 34641.67706 28355.44316 31827.36773 36138.55886 31555.05066 34852.4206 28181.88826 0.882664742 1.199087618 1.229217742 1.006158384 1.129355401 1.282332771 1.119692562 1.23669572 1 14.78248066 4.743094814 24.57444979 1.163285103 0.882664597 0.439194229 0.094040635 317.2179315 1719180.274 0.020629572 0.163453495 55347.09281 -4.743094814 -0.280620506 SAS(ph)ADNLTLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SASADNLTLPR 11 0 Q8ND76-3;Q8ND76-2;Q8ND76 Q8ND76-3 CCNY Cyclin-Y 1 S(0.01)AS(0.99)ADNLTLPR;S(0.056)AS(0.944)ADNLTLPR 107.53 0.002292 780630000 845380 963070 857820 855020 1097540 700230 1065780 948120 1025460 TRUE FALSE 792469.1748 1034376.705 878167.8955 876961.2607 1011343.636 902375.0337 905976.1832 1066494.869 854304.1013 0.927619537 1.210782792 1.027933606 1.026521188 1.183821585 1.056269111 1.060484413 1.248378496 1 19.70439018 2.829325187 21.81107601 1.104673141 1.071930153 0.065477379 0.097906763 99.53621858 23907.25057 0.028035444 0.029736086 675.033283 -2.829325187 -0.032742989 SAS(ph)ASHQADIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SASASHQADIK 11 0 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 S(0.154)AS(0.522)AS(0.324)HQADIK;SAS(0.5)AS(0.5)HQADIK 177.41 2.01E-05 453030000 2050690 1599916 1474032 1595773 1911880 1228126 2570968 1809319 1601060 TRUE FALSE 1922340.973 1718375.445 1508996.735 1636723.237 1761728.657 1582666.039 2185475.216 2035216.46 1333832.743 1.441215913 1.288299043 1.131323806 1.227082815 1.320801777 1.186555097 1.638492703 1.52584083 1 20.34714634 1.761767497 25 1.454395748 1.253560887 0.048984704 0.184555584 18.61133806 20064.47609 0.076945609 0.042671868 57.77866414 -1.761767497 -0.200834861 SAS(ph)ASPLTPCSVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SASASPLTPCSVTR 14 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 S(0.001)AS(0.92)AS(0.079)PLTPCSVTR;S(0.001)AS(0.898)AS(0.101)PLTPCSVTR;SAS(1)ASPLTPCSVTR 148.57 8.10E-06 426186000 243800 224874 240910 196300 259358 171199 311869 224145 459227 TRUE FALSE 228540.9932 241523.9049 246624.499 201337.3903 238989.0689 220621.3721 265107.1387 252129.9967 382579.047 0.597369341 0.631304581 0.644636712 0.526263505 0.624678928 0.576668727 0.692947355 0.659027196 1 18.54539834 0.241128097 0.792604263 1.006114317 0.608163261 0.902679561 0.039967868 0.848386639 0.659296412 0.050148017 0.013065028 1.742320704 -0.241128097 -0.397951056 SAS(ph)DNTLVAMDFSGHAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SASDNTLVAMDFSGHAGR 18 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 1 S(0.262)AS(0.738)DNTLVAMDFSGHAGR;S(0.108)AS(0.892)DNTLVAMDFSGHAGR;S(0.152)AS(0.848)DNTLVAMDFSGHAGR;S(0.232)AS(0.768)DNTLVAMDFSGHAGR;S(0.145)AS(0.855)DNTLVAMDFSGHAGR;S(0.032)AS(0.968)DNTLVAMDFSGHAGR;SAS(0.771)DNT(0.229)LVAMDFSGHAGR 379.78 3.16E-108 6158110000 2371939 2589703 2394250 2536428 2743760 2153487 3244547 2396546 2797547 TRUE FALSE 2223483.572 2781447.305 2451042.741 2601517.037 2528276.157 2775163.738 2758057.298 2695760.044 2330618.333 0.954031615 1.193437495 1.051670583 1.116234692 1.084809178 1.190741401 1.183401529 1.156671603 1 21.15228133 2.25685317 24.98693011 1.153308441 1.093277698 0.058682636 0.079981222 487.9322169 666495.6598 0.025027953 0.020901779 180.6563245 -2.25685317 -0.060030744 SAS(ph)DTNLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SASDTNLQK 9 0 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 S(0.021)AS(0.951)DT(0.028)NLQK 71.085 0.053056 407050000 725820 233880 385430 327070 281160 233500 483310 250330 344810 TRUE FALSE 680392.2218 251196.7186 394572.5816 335463.1699 259078.8277 300907.6594 410842.1523 281584.2515 287258.9834 2.368567255 0.874460793 1.373577867 1.167807412 0.901899828 1.047513487 1.430215158 0.980245241 1 18.13199249 4.745833102 24.97671919 1.129803817 2.368567845 0.819702226 0.186858812 359.8797796 1235945.435 0.043680016 0.448093691 55697.16649 -4.745833102 1.238764027 SAS(ph)EPSLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SASEPSLHR 9 0 Q96II5;P10398;P04049;P04049-2;H7C155 Q96II5;P04049 ARAF;RAF1 Serine/threonine-protein kinase A-Raf;RAF proto-oncogene serine/threonine-protein kinase 1 S(0.083)AS(0.917)EPSLHR;S(0.025)AS(0.975)EPSLHR;S(0.065)AS(0.935)EPSLHR;S(0.121)AS(0.879)EPSLHR;S(0.111)AS(0.888)EPS(0.002)LHR;S(0.111)AS(0.889)EPSLHR 121.29 0.00039814 3824730000 3657070 4933790 5141630 4968580 5365880 4235900 5956800 4968290 6160690 TRUE FALSE 3428180.517 5299092.945 5263591.892 5096082.175 4944465.43 5458735.566 5063633.14 5588591.943 5132431.039 0.667944779 1.032472313 1.025555307 0.992917807 0.963376885 1.063576992 0.986595456 1.088878136 1 22.29121091 4.739974142 24.99547732 1.018231712 0.667944665 0.899234645 0.036948369 32.31295032 571336.3522 0.007887919 0.049401704 54950.81547 -4.739974142 -0.350287048 SAS(ph)LETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SASLETK 7 0 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 SAS(1)LETK;SAS(1)LETK 108.43 0.0076091 271920000 585850 356450 402520 394380 337610 270010 507070 312290 430440 TRUE FALSE 549182.6943 382841.9289 412067.9645 404500.4585 311095.4725 347957.5038 431039.5609 351280.0939 358596.7833 1.531476912 1.067611163 1.149112272 1.128009166 0.867535591 0.970330801 1.202017366 0.979596333 1 18.45200302 SAS(ph)MKLPDNTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 SASMKLPDNTVK 12 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 SAS(1)MKLPDNTVK;S(0.001)AS(0.999)MKLPDNTVK;S(0.124)AS(0.876)MKLPDNTVK;S(0.029)AS(0.971)MKLPDNTVK;SAS(0.979)MKLPDNT(0.021)VK;S(0.002)AS(0.998)MKLPDNTVK;SAS(0.999)MKLPDNT(0.001)VK;S(0.391)AS(0.609)MKLPDNTVK;S(0.003)AS(0.997)MKLPDNTVK;S(0.01)AS(0.99)MKLPDNTVK;SAS(1)MKLPDNTVK 188.44 5.57E-06 10546490000 24899720 17917760 16076890 14898920 21581740 6171555 28710690 14499780 40905630 TRUE FALSE 23341290.97 19244409.59 16458241.42 15281251.51 19886797.2 7953182.742 24405788.57 16310109.45 34078216.09 0.684932888 0.56471294 0.482954899 0.448417003 0.583563328 0.233380254 0.716169781 0.478608076 1 25.02234648 -0.236094764 0.959139688 1.009644787 0.520290397 0.550646025 0.134676061 10.03677228 6.822575506 0.499968509 0.037539104 0.580637708 0.236094764 -0.48935439 SAS(ph)PCIADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SASPCIADK 9 0 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 S(0.008)AS(0.992)PCIADK;SAS(1)PCIADK 142.71 0.00010877 237225000 440200 348020 368780 405120 450170 317985 474630 360620 529820 TRUE FALSE 412648.6678 373787.7629 377527.6358 415516.0651 414815.4641 409782.1074 403463.6377 405644.2008 441389.6192 0.934885303 0.846843121 0.855316073 0.941381598 0.939794336 0.928390904 0.914075955 0.919016178 1 18.75169317 3.235391642 24.99994114 0.933888528 0.868735353 0.407416023 0.033567288 67.64820976 533675.8961 0.008942652 0.011119639 1719.458277 -3.235391642 -0.065153176 SAS(ph)PDDDLGSSNWEAADLGNEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SASPDDDLGSSNWEAADLGNEER 23 0 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 S(0.142)AS(0.858)PDDDLGSSNWEAADLGNEER;S(0.148)AS(0.852)PDDDLGSSNWEAADLGNEER;S(0.101)AS(0.899)PDDDLGSSNWEAADLGNEER;S(0.101)AS(0.899)PDDDLGSSNWEAADLGNEER;S(0.147)AS(0.853)PDDDLGSSNWEAADLGNEER;S(0.129)AS(0.871)PDDDLGSSNWEAADLGNEER 383.27 4.90E-137 2388360000 1017400 1104060 1047520 1120340 1158870 912622 1163640 929130 1136140 TRUE FALSE 953722.7501 1185805.751 1072367.669 1149089.821 1067857.025 1176081.156 989162.9847 1045133.926 946510.8943 1.007619411 1.252817858 1.132969177 1.214027042 1.128203628 1.242543708 1.04506244 1.104196404 1 19.85225959 1.657406556 8.047569661 1.055930477 1.170282532 0.337518312 0.073992966 0.123503411 14.4746058 0.0323092 0.016799211 45.43667643 -1.657406556 0.114352055 SAS(ph)PDDDLGSSNWEAADLGNEERK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SASPDDDLGSSNWEAADLGNEERK 24 1 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 S(0.001)AS(0.999)PDDDLGSSNWEAADLGNEERK;S(0.005)AS(0.995)PDDDLGSSNWEAADLGNEERK;S(0.118)AS(0.882)PDDDLGSSNWEAADLGNEERK;SAS(0.999)PDDDLGS(0.001)SNWEAADLGNEERK;S(0.065)AS(0.804)PDDDLGS(0.106)S(0.025)NWEAADLGNEERK 256.46 4.42E-44 4005210000 2241800 2031110 1919440 2079320 2514770 1244558 2476940 1796930 4316010 TRUE FALSE 2101489.74 2181495.498 1964970.023 2132678.871 2317270.108 1603841.691 2105545.842 2021280.666 3595640.049 0.584454982 0.606705752 0.546486855 0.593129135 0.644466653 0.446051793 0.585583043 0.562147667 1 21.77781717 -1.31762218 3.17854308 1.002904265 0.570480181 0.872691053 0.051478357 7904902.966 10770163.68 217623.1642 0.011287053 0.048125784 1.31762218 -0.432424085 SAS(ph)PDGGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SASPDGGPR 9 0 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 S(0.014)AS(0.986)PDGGPR;S(0.001)AS(0.999)PDGGPR;S(0.002)AS(0.998)PDGGPR 152.67 8.38E-05 737770000 1352660 1398620 1356210 1409780 1530140 1093930 1397480 1266940 1358690 TRUE FALSE 1267999.425 1502175.28 1388379.942 1445957.342 1409968.977 1409729.833 1187940.848 1425120.248 1131915.862 1.120224098 1.327108605 1.226575215 1.277442424 1.245648219 1.245436945 1.049495716 1.259033729 1 20.11033529 0.977075178 0.527058739 1.002875366 1.259856638 0.410705624 0.080610692 0.849061403 0.582923733 0.084822646 0.039321084 9.485826529 -0.977075178 0.256981272 SAS(ph)PDYNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SASPDYNR 8 0 Q14669-3;Q14669;Q14669-2;G5E9G6;C9JLD7;C9JLJ5;C9JSX9;F8W9P3 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 SAS(1)PDYNR;SAS(1)PDYNR;S(0.004)AS(0.994)PDY(0.002)NR;S(0.006)AS(0.994)PDYNR;S(0.067)AS(0.933)PDYNR;S(0.021)AS(0.979)PDYNR 196.79 0.00015654 1615380000 2497780 2587890 2520010 2469380 2313580 2082210 2903200 2018120 2391610 TRUE FALSE 2341448.408 2779500.068 2579785.827 2532748.471 2131880.759 2683310.225 2467892.112 2270086.724 1992434.841 1.175169376 1.395026834 1.294790562 1.271182585 1.069987693 1.346749299 1.238631278 1.139353056 1 20.92610111 -0.564714981 0.245132203 0.854868865 1.325923581 0.437661324 0.091641651 9.799244981 0.709932784 1.227311933 0.16654556 0.272448875 0.564714981 0.471054716 SAS(ph)PHDVDLCLVS(ph)PCEFEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SASPHDVDLCLVSPCEFEHR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 2 S(0.024)AS(0.976)PHDVDLCLVS(1)PCEFEHR 174.61 1.67E-12 41218000 22362 26987 30028 29216 35816 32139 35027 27151 38235 TRUE FALSE 20962.40234 28985.14556 30740.27834 29965.73202 33003.15583 41417.00757 29775.02652 30540.86212 31853.33149 0.658091363 0.909956485 0.965056931 0.940740909 1.036097459 1.300240999 0.934753921 0.95879648 1 14.95915665 5.410086057 0.711848255 1.037221 6.86E-18 0.540876388 0.105308938 5.440543879 1.047497824 0.038982441 5.645753585 257090.5167 -5.410086057 -1.037221 SAS(ph)PHDVDLCLVSPCEFEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SASPHDVDLCLVSPCEFEHR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 S(0.002)AS(0.998)PHDVDLCLVSPCEFEHR;S(0.031)AS(0.969)PHDVDLCLVSPCEFEHR;S(0.152)AS(0.848)PHDVDLCLVSPCEFEHR 269.53 1.25E-37 1871140000 320318 345604 347320 331291 357860 344279 417388 311296 308943 TRUE FALSE 300269.8682 371192.8798 355558.5944 339792.4879 329755.1191 443666.7584 354804.5442 350161.9908 257378.4175 1.166647426 1.442206707 1.381462354 1.320205833 1.281207346 1.723791617 1.37853262 1.36049477 1 17.97353156 0.710680083 3.215860026 1.000026954 1.399217603 0.413979595 0.142271913 2.79889761 30.05997872 0.12722935 0.033047769 5.136651274 -0.710680083 0.399190649 SAS(ph)PHKDLPNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SASPHKDLPNDR 12 1 H9KV62;H9KV63;Q9BXT4-2;Q9BXT4;Q9BXT4-3;Q9BXT4-4 H9KV62 TDRD1 Tudor domain-containing protein 1 1 S(0.023)AS(0.977)PHKDLPNDR 97.904 0.0028216 277920000 421710 333540 369370 336480 383620 286960 432700 353390 490880 TRUE FALSE 395315.9239 358235.6486 378131.6308 345114.6465 353492.0326 369800.6936 367820.652 397511.5194 408948.9568 0.966663241 0.875991105 0.92464261 0.843906411 0.864391574 0.904271028 0.899429246 0.972032115 1 18.64156126 1.159806543 2.944499014 0.999693407 0.894389917 0.557200663 0.033422721 0.169482886 2.630699134 0.029146861 0.007951379 14.4479604 -1.159806543 -0.10530349 SAS(ph)PPKAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SASPPKAK 8 1 P52701;P52701-3;P52701-2;A0A087WWJ1;F8WAX8;F8W7G9 P52701 MSH6 DNA mismatch repair protein Msh6 1 S(0.007)AS(0.993)PPKAK 68.355 0.03435 396780000 783080 594400 692140 749240 895860 391540 926810 621730 1406100 TRUE FALSE 734068.4206 638409.9945 708557.8877 768466.7669 825502.7693 504571.2419 787843.4446 699354.3591 1171412.826 0.626652197 0.544991467 0.60487462 0.656017033 0.704706958 0.430737337 0.672558322 0.597017843 1 20.15981817 -0.181715691 1.156063595 1.003156123 0.599243517 0.727880112 0.075896237 9.678333064 8.697333316 0.207805979 0.020272099 0.658088512 0.181715691 -0.403912606 SAS(ph)PPQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SASPPQKR 8 1 U3KQ90;P55199 U3KQ90 ELL RNA polymerase II elongation factor ELL 1 S(0.004)AS(0.996)PPQKR;S(0.03)AS(0.97)PPQKR 90.827 0.0079139 1772050000 271340 263580 290450 285680 260970 241870 338250 244120 334810 TRUE FALSE 254357.3138 283095.7375 297339.6112 293011.0325 240474.4689 311693.9426 287532.5527 274598.9194 278928.048 0.911910134 1.014941808 1.066008289 1.050489668 0.862137998 1.117470777 1.030848474 0.984479407 1 18.08953349 SAS(ph)PTVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SASPTVPR 8 0 Q92817;K7EKI0;K7EQ87 Q92817 EVPL Envoplakin 1 S(0.003)AS(0.625)PT(0.371)VPR;S(0.236)AS(0.693)PT(0.071)VPR;S(0.126)AS(0.825)PT(0.049)VPR;S(0.001)AS(0.978)PT(0.021)VPR 129.42 0.0011448 5912500000 4012160 4332680 4075200 4033120 4632130 3659740 4509650 4039120 6311230 TRUE FALSE 3761046.068 4653476.135 4171865.668 4136616.687 4268341.195 4716247.527 3833469.848 4543413.023 5257844.941 0.715320841 0.885053893 0.79345544 0.786751366 0.811804312 0.896992509 0.729095265 0.864120771 1 22.32604017 0.983640438 24.17709247 1.000000004 0.809466237 0.542567286 0.057227585 485.1495086 716983.1469 0.04994795 0.012486987 9.630313782 -0.983640438 -0.190533766 SAS(ph)QS(ph)SLDKLDQELK ddPTM_SK-BR-3_Pertuzumab_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 2 S(0.001)AS(0.997)QS(0.676)S(0.326)LDKLDQELK;S(0.044)AS(0.919)QS(0.642)S(0.395)LDKLDQELK;S(0.114)AS(0.864)QS(0.549)S(0.472)LDKLDQELK 119.62 0.00011276 620969000 1353870 492270 744850 806020 723720 485570 976310 509930 615340 TRUE FALSE 1269133.693 528718.183 762518.1937 826703.8378 666881.9505 625746.1764 829921.3791 573595.883 512635.7788 2.475702528 1.031371989 1.487446303 1.612653412 1.300888424 1.220644759 1.618929879 1.11891504 1 18.96757465 4.748179086 24.94676771 1.33792547 2.475703153 0.731208209 0.223123348 668.7040789 1734335.861 0.049925186 0.650926827 55998.84705 -4.748179086 1.137777683 SAS(ph)QS(ph)SLDKLDQELKEQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SASQSSLDKLDQELKEQQK 19 2 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 2 S(0.166)AS(0.796)QS(0.555)S(0.484)LDKLDQELKEQQK 65.854 0.015022 131580000 600280 199920 335810 349850 388510 197330 451600 194660 475340 TRUE FALSE 562709.5463 214722.2848 343775.5718 358827.7433 357997.9918 254295.9676 383886.7724 218963.7295 396002.6832 1.420974075 0.542224318 0.868114249 0.906124525 0.904029207 0.642157183 0.969404473 0.552934964 1 18.59515068 SAS(ph)QSS(ph)LDKLDQELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SASQSSLDKLDQELK 15 1 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 2 S(0.016)AS(0.947)QS(0.23)S(0.806)LDKLDQELK;SAS(1)QS(0.077)S(0.923)LDKLDQELK 215.08 1.36E-12 382549000 3545450 1173550 1874930 1990510 1859880 1221970 2558880 1269790 1497500 TRUE FALSE 3323546.613 1260440.863 1919404.225 2041589.857 1713812.527 1574732.902 2175199.699 1428326.077 1247557.576 2.664042669 1.010326808 1.538529574 1.636469447 1.373734215 1.262252687 1.743566583 1.144897922 1 20.25067497 4.749035693 24.85612435 1.383178625 2.664043445 0.72866424 0.252873291 735.4771526 1745163.667 0.057096808 0.810992334 56109.40885 -4.749035693 1.28086482 SAS(ph)QSSLDKLDQELK ddPTM_SK-BR-3_Pertuzumab_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 S(0.017)AS(0.954)QS(0.023)S(0.006)LDKLDQELK;S(0.009)AS(0.986)QS(0.005)SLDKLDQELK;SAS(0.688)QS(0.292)S(0.02)LDKLDQELK 252.66 7.22E-25 971040000 1813360 770596 1123760 1112240 1217830 758970 1343450 920050 1498050 TRUE FALSE 1699865.035 827651.7296 1150416.118 1140781.961 1122186.544 978072.3182 1142012.144 1034920.268 1248015.777 1.362054123 0.663174092 0.921796133 0.914076554 0.899176569 0.783701886 0.915062265 0.829252552 1 20.25120474 4.752676851 24.93990502 0.857262307 1.362054478 0.739961707 0.092333999 1186.995168 2097090.939 0.020911971 0.439857798 56581.812 -4.752676851 0.504792171 SAS(ph)QSSLDKLDQELKEQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SASQSSLDKLDQELKEQQK 19 2 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 S(0.112)AS(0.637)QS(0.125)S(0.125)LDKLDQELKEQQK 66.871 0.013861 102460000 88032 42867 60499 64371 74823 40926 75430 41027 143400 TRUE FALSE 82522.23426 46040.91728 61934.06485 66022.86884 68946.7034 52740.67182 64119.97176 46149.31126 119465.6136 0.690761398 0.38539054 0.518425872 0.552651653 0.57712593 0.441471569 0.536723245 0.386297863 1 16.86623589 -1.664253309 2.79188932 1.057391662 0.503105179 0.736541365 0.091780578 11402802.13 10613558.28 4677598.188 0.019606508 0.021664401 1.664253309 -0.554286483 SAS(ph)SDTSEELNSQDSPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SASSDTSEELNSQDSPPK 18 0 O14745;O14745-2;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 S(0.001)AS(0.377)S(0.306)DT(0.316)SEELNSQDSPPK;S(0.038)AS(0.944)S(0.017)DTSEELNSQDSPPK;SAS(0.952)S(0.048)DTSEELNSQDSPPK;SAS(0.631)S(0.365)DT(0.003)SEELNSQDSPPK 479.83 1.44E-239 1474990000 2450690 1464650 1683850 1718200 1534030 1378900 2105660 1625430 1565650 TRUE FALSE 2297305.688 1573094.21 1723791.717 1762291.921 1413553.472 1776966.045 1789935.831 1828368.514 1304332.901 1.761287848 1.206052695 1.321588773 1.351105933 1.083736729 1.362356224 1.37229984 1.401765234 1 20.3148807 -2.224235393 2.11570827 0.000170846 1.335350869 0.290117033 0.172688876 1769293.159 340286.4305 8451066.356 0.039113666 0.005967118 2.224235393 1.335180023 SAS(ph)SSWLEGTSTQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SASSSWLEGTSTQAK 15 0 K7EL81;Q9BZL4-3;Q9BZL4-5;Q9BZL4-2;Q9BZL4-4;Q9BZL4 K7EL81;Q9BZL4-5 PPP1R12C Protein phosphatase 1 regulatory subunit 12C 1 S(0.005)AS(0.482)S(0.482)S(0.03)WLEGTSTQAK 226.93 8.38E-13 216870000 242330 258110 189970 173200 288220 71243 359610 266860 483580 TRUE FALSE 227162.9979 277220.733 194476.1781 177644.6052 265584.3638 91809.69757 305689.819 300178.0584 402867.374 0.563865462 0.688119095 0.482730027 0.440950587 0.659235225 0.227890625 0.758785245 0.745103917 1 18.61994545 1.152029982 1.766454198 0.978552383 0.533968791 0.549518245 0.140302503 0.240500979 1.411515038 0.120985954 0.035249929 14.19155491 -1.152029982 -0.444583591 SAS(ph)TDLGTADVVLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SASTDLGTADVVLGR 15 0 A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5;H7C0E9;Q9Y2K5-3;Q9Y2K5-2 A0A0U1RRA6 R3HDM2 R3H domain-containing protein 2 1 SAS(0.985)T(0.015)DLGTADVVLGR 246.86 3.42E-18 102410000 147420 179540 154120 178580 122070 99447 235060 144560 142420 TRUE FALSE 138193.2454 192833.3284 157775.7992 183162.6651 112483.1146 128155.7345 199814.9352 162608.6342 118649.1819 1.164721434 1.625239427 1.329767274 1.543733064 0.948031101 1.080123204 1.684081862 1.370499413 1 16.85634263 -1.715352966 2.479086756 0.926620201 1.372937895 0.163153817 0.235972596 15555743.61 11698690.87 7083588.118 0.05933412 0.01925959 1.715352966 0.446317694 SAS(ph)TLCLPSVGAARPQVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SASTLCLPSVGAARPQVK 18 1 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 SAS(0.81)T(0.189)LCLPSVGAARPQVK;SAS(0.733)T(0.267)LCLPSVGAARPQVK;SAS(0.808)T(0.192)LCLPSVGAARPQVK;SAS(0.833)T(0.167)LCLPSVGAARPQVK 277.07 2.42E-39 7028960000 3322620 3492270 2665190 2522050 3631180 1611560 5101550 3170800 4131840 TRUE FALSE 3114663.145 3750841.305 2728409.565 2586770.073 3346001.77 2076791.211 4336619.938 3566681.36 3442209.211 0.904844231 1.08966105 0.792633276 0.751485431 0.97205067 0.603330908 1.259836248 1.036160541 1 21.71490335 1.704339297 14.44273718 1.109852404 0.873585095 0.381229116 0.146020307 0.149104734 54.8531532 0.065144264 0.035894571 50.62199966 -1.704339297 -0.236267309 SAS(ph)VNKEPVSLPGIMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.023)AS(0.977)VNKEPVSLPGIMR 73.21 0.016199 0 109330 83565 80754 99356 81730 66944 112660 68860 96215 TRUE FALSE 102487.2305 89752.23955 82669.52301 101905.6432 75311.25548 86269.64605 95767.67888 77457.32258 80156.09493 1.278595602 1.119718215 1.031356668 1.271339918 0.939557442 1.076270571 1.194764777 0.96633104 1 16.2905246 4.734707074 2.849626359 1.083885423 1.312554026 0.28976224 0.101073366 0.541388221 6.246265591 0.022560488 0.286316675 54288.40394 -4.734707074 0.228668603 SAS(ph)VSSISLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SASVSSISLTK 11 0 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 SAS(0.764)VS(0.066)S(0.17)ISLTK;S(0.002)AS(0.995)VS(0.002)S(0.001)ISLTK;S(0.001)AS(0.998)VS(0.001)SISLTK 122.34 0.00041196 356225000 679710 582070 630650 856050 726190 351589 537720 355867 413750 TRUE FALSE 637168.1644 625167.0684 645609.3158 878017.6923 669157.9667 453087.0367 457093.8779 400297.7783 344692.4521 1.848512088 1.813695266 1.873001024 2.547249547 1.941318885 1.314467532 1.326091927 1.161318665 1 18.39495018 2.222210358 4.541894156 1.229657318 1.98959803 0.765143802 0.221763026 0.10620744 5.30226939 0.087076422 0.06612182 166.8054969 -2.222210358 0.759940712 SAS(ph)WGSADQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SASWGSADQLK 11 0 Q86VQ1;H7C0Q2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 SAS(1)WGSADQLK;S(0.001)AS(0.999)WGSADQLK;SAS(0.869)WGS(0.131)ADQLK 251.14 4.78E-17 876570000 818053 681665 674984 658884 820730 480411 756821 691530 1094250 TRUE FALSE 766852.523 732136.1859 690994.9392 675792.0789 756273.1765 619097.8569 643342.717 777869.0427 911612.6059 0.841204387 0.803122051 0.757991865 0.741314978 0.829599296 0.679123844 0.705719417 0.853289037 1 19.79806135 0.961438725 5.358690368 0.999918847 0.763166949 0.689483165 0.050568699 0.127051628 12.9802873 0.050078673 0.01263235 9.150371466 -0.961438725 -0.236751898 SAS(ph)WGSTDQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SASWGSTDQLK 11 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 SAS(0.999)WGSTDQLK;SAS(0.987)WGS(0.006)T(0.006)DQLK;SAS(0.984)WGS(0.016)TDQLK;SAS(0.969)WGS(0.029)T(0.002)DQLK 243.75 8.13E-16 868545000 2262970 1929080 1893000 1972830 2182550 1366050 2258410 1737440 2105490 TRUE FALSE 2121334.747 2071911.09 1937902.854 2023456.158 2011141.327 1760406.459 1919782.387 1954363.209 1754070.117 1.209378534 1.181201977 1.104803528 1.153577692 1.146556975 1.003612365 1.094473002 1.11418762 1 20.74227499 8 0.116994954 0.965887849 1.71835421 0.652622381 0.040190881 60.10318399 0.485283996 0.285460738 7.353429584 100000000 -8 0.752466362 SASAS(ph)PLTPCSVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SASASPLTPCSVTR 14 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 SAS(0.087)AS(0.913)PLTPCSVTR 179.27 1.98E-06 81453000 118850 76224 96329 82550 100360 58570 112410 77882 151940 TRUE FALSE 111411.3907 81867.70427 98613.96937 84668.37276 92478.13043 75478.2082 95555.16406 87605.73914 126580.2324 0.880164213 0.646765318 0.779062951 0.668890957 0.73058904 0.596287483 0.754897998 0.692096526 1 16.9496926 -0.980152026 4.957790427 1.000002513 0.714025124 0.562216721 0.077946606 1.87E-06 3.85E-07 0.0651912 0.015365578 0.104676206 0.980152026 -0.285977388 SASDNT(ph)LVAMDFSGHAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SASDNTLVAMDFSGHAGR 18 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 1 S(0.311)AS(0.311)DNT(0.377)LVAMDFSGHAGR 82.406 0.019649 2848500 3376.6 4433.5 3393.7 3285.7 4938.8 3555.1 5003.6 4045.4 3822.3 TRUE FALSE 3165.264633 4761.760953 3474.200167 3370.016625 4550.92657 4581.399658 4253.356631 4550.477095 3184.333437 0.994011681 1.495371338 1.091029013 1.058311478 1.429161443 1.438731134 1.335713334 1.429020291 1 11.6367757 2.720161721 24.47656498 1.355292143 1.204187292 0.13936991 0.184847364 1221.710921 1625273.335 0.056083617 0.052975957 525.0029223 -2.720161721 -0.151104851 SASDNTLVAMDFSGHAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SASDNTLVAMDFSGHAGR 18 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ; 165.3 4.80E-10 459650000 268360 370580 321070 339250 344890 234320 370470 294320 303890 FALSE TRUE 251563.8266 398018.1288 328685.932 347955.7293 317803.7306 301964.3801 314921.4628 331066.4999 253168.7958 0.993660478 1.572145286 1.298287694 1.374402119 1.255303718 1.192739331 1.243918951 1.307690779 1 17.94974007 -0.148537115 0.312352213 0.911724283 1.35789642 0.224512258 0.148651382 7.525142136 0.990687217 0.960766873 0.155431587 0.710334462 0.148537115 0.446172137 SASQS(ph)SLDKLDQELKEQQK ddPTM_SK-BR-3_Pertuzumab_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 SAS(0.001)QS(0.741)S(0.257)LDKLDQELKEQQK;SASQS(0.739)S(0.261)LDKLDQELKEQQK;SAS(0.001)QS(0.613)S(0.386)LDKLDQELKEQQK 215.48 2.12E-19 771540000 2052670 861850 1160330 1135320 1285060 742510 1684760 852810 2170230 TRUE FALSE 1924197.049 925662.2708 1187853.576 1164454.233 1184136.571 956860.5834 1432145.879 959285.2058 1808004.593 1.064265576 0.511980044 0.65699699 0.644054909 0.65494113 0.529235704 0.792114071 0.530576753 1 20.78596691 -1.772518507 5.368441096 1.020475306 0.659237817 0.282857261 0.162308574 0.034591362 0.001465769 0.136670038 0.03233479 0.016884239 1.772518507 -0.361237489 SASQSS(ph)LDKLDQELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SASQSSLDKLDQELK 15 1 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 SASQS(0.019)S(0.981)LDKLDQELK;SASQS(0.247)S(0.752)LDKLDQELK;SASQS(0.064)S(0.936)LDKLDQELK;SASQS(0.027)S(0.973)LDKLDQELK 301.59 1.45E-44 2396800000 4849690 1975020 2729400 2444020 2463600 1888370 3891850 2361190 3037590 TRUE FALSE 4546156.56 2121252.536 2794142.657 2506737.691 2270118.794 2433511.764 3308303.223 2655989.769 2530596.605 1.796476195 0.83824207 1.104143841 0.990571822 0.897068616 0.961635592 1.30732145 1.049550831 1 21.27104612 4.747495272 24.91331027 1.030379875 1.796476608 0.787985677 0.126678754 566.1803991 1578696.806 0.032327577 0.395198243 55910.7441 -4.747495272 0.766096733 SASQSS(ph)LDKLDQELKEQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SASQSSLDKLDQELKEQQK 19 2 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 SAS(0.004)QS(0.248)S(0.748)LDKLDQELKEQQK 177.22 2.12E-14 417130000 641830 234380 358250 342150 413880 246570 557500 261570 697420 TRUE FALSE 601659.006 251733.7391 366747.8592 350930.1483 381375.5343 317750.7563 473908.0506 294227.5903 581016.0965 1.03552898 0.433264656 0.63121807 0.603993849 0.656394094 0.546888044 0.815653909 0.506401788 1 19.14821861 -4.821917813 0.493727425 9.999924622 0.635780025 0.282150448 0.170231975 2195.874381 12.80348062 21724.67885 0.073398009 1.51E-05 4.821917813 -9.364144597 SASS(ph)GAEGDVSS(ph)EREP ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SASSGAEGDVSSEREP 16 1 Q8TEA8 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1 2 SAS(0.003)S(0.997)GAEGDVS(0.001)S(0.999)EREP;SAS(0.057)S(0.942)GAEGDVS(0.007)S(0.993)EREP 199.41 4.57E-10 375460000 541370 600350 555930 587530 571260 480310 701540 486270 522320 TRUE FALSE 507486.6181 644800.5387 569116.9221 602607.0145 526395.544 618967.6998 596350.5898 546981.8799 435141.4177 1.166256756 1.481818353 1.307889571 1.384853268 1.209711424 1.422451816 1.370475357 1.257020954 1 18.73112482 0.875775408 3.472112261 1.000134047 1.348834146 0.551704543 0.093913978 0.369109222 8.651029527 0.080714114 0.020854724 7.51234299 -0.875775408 0.348700099 SASS(ph)GAEGDVSSEREP ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SASSGAEGDVSSEREP 16 1 Q8TEA8 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1 1 SAS(0.031)S(0.969)GAEGDVSSEREP;SAS(0.001)S(0.999)GAEGDVSSEREP;SAS(0.002)S(0.998)GAEGDVSSEREP;SAS(0.014)S(0.986)GAEGDVSSEREP 359.54 2.85E-87 3576090000 3347650 3655190 3584490 3747510 3612060 2845930 4082570 2787110 3177050 TRUE FALSE 3138126.562 3925824.071 3669515.796 3843677.451 3328383.378 3667503.791 3470426.529 3135086.819 2646779.83 1.185639442 1.483245424 1.386407646 1.452208985 1.257521816 1.385647476 1.311188218 1.184490974 1 21.33580676 0.982184367 1.123921289 0.998130599 1.382093674 0.637060069 0.087436114 0.302229178 0.792600688 0.075470382 0.02404461 9.598080026 -0.982184367 0.383963075 SASS(ph)SWLEGTSTQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SASSSWLEGTSTQAK 15 0 K7EL81;Q9BZL4-3;Q9BZL4-5;Q9BZL4-2;Q9BZL4-4;Q9BZL4 K7EL81;Q9BZL4-5 PPP1R12C Protein phosphatase 1 regulatory subunit 12C 1 SAS(0.253)S(0.742)S(0.005)WLEGTSTQAK 397.04 7.00E-115 131860000 208370 221630 156600 149690 258060 63960 331160 242590 444610 TRUE FALSE 195328.4937 238039.7158 160314.626 153531.2988 237793.0086 82424.2137 281505.6323 272877.8955 370401.7187 0.527342298 0.642652838 0.432812857 0.414499423 0.641986785 0.222526542 0.76000088 0.736707963 1 18.49873127 1.210384846 1.686800433 0.971351267 0.500619268 0.595735094 0.137016448 0.221833166 1.158074385 0.115856283 0.034354069 16.23247886 -1.210384846 -0.470732 SASSGAEGDVSS(ph)EREP ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SASSGAEGDVSSEREP 16 1 Q8TEA8 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1 1 SASSGAEGDVS(0.017)S(0.983)EREP;SASSGAEGDVS(0.003)S(0.997)EREP 281.09 4.46E-35 815880000 1444480 1629080 1482880 1460350 1561060 1257460 1760410 1344940 1472340 TRUE FALSE 1354072.575 1749698.778 1518054.614 1497825.053 1438460.645 1620468.289 1496452.863 1512858.72 1226596.942 1.10392626 1.426465955 1.237614869 1.221122442 1.172724792 1.321109024 1.220003745 1.233378845 1 20.22622983 -4.208214543 0.249878567 5.85E-10 1.282386307 0.418313061 0.087047789 103.4930452 1.478053536 52.55256099 0.119543188 6.19E-05 4.208214543 1.282386307 SASVVSSDSISTSADNFS(ph)PDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SASVVSSDSISTSADNFSPDLR 22 0 Q13614 Q13614 MTMR2 Myotubularin-related protein 2 1 SASVVSSDSISTSADNFS(1)PDLR;SASVVSSDSISTSADNFS(1)PDLR 344.52 4.44E-82 315390000 252126 296290 288442 301070 282590 245680 344430 246811 286230 TRUE FALSE 236345.8837 318227.6199 295283.9805 308795.9659 260396.5213 316603.8277 292785.919 277625.8966 238456.3639 0.991149407 1.334531881 1.238314531 1.294978926 1.092009108 1.327722282 1.227838562 1.164262895 1 17.86336576 0.876875581 2.787929559 1.000266208 1.232818177 0.276784428 0.106209589 0.536892487 8.449262946 0.090280781 0.023881167 7.5313977 -0.876875581 0.232551969 SASYKPVFVTEITDDLHFYVQDVETGTQLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SASYKPVFVTEITDDLHFYVQDVETGTQLEK 31 1 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;;;; 413.43 9.83E-176 5433547700 892061 720653.7 780466 789890.3 882438 584725.5 996934 724394.9 1019264 FALSE TRUE 836228.4944 774011.6498 798979.0221 810160.2224 813134.8791 753526.2596 847453.0018 814837.1979 849142.2537 0.984791995 0.91152177 0.94092482 0.954092461 0.957595592 0.887396966 0.998010637 0.959600343 1 19.69564674 1.64253397 12.56864628 0.983977691 0.937761437 0.374133731 0.028217389 0.114002615 32.98928082 0.012101224 0.00658827 43.90702081 -1.64253397 -0.046216254 SAT(ph)FPNAGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SATFPNAGPR 10 0 Q86X27;Q86X27-3 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 S(0.096)AT(0.904)FPNAGPR;S(0.001)AT(0.999)FPNAGPR;S(0.003)AT(0.997)FPNAGPR 208.63 1.23E-06 657750000 753320 826820 615200 632320 780860 455630 817030 687700 1175090 TRUE FALSE 706171.0459 888038.6131 629792.8345 648546.4017 719534.4054 587162.9845 694523.9364 773560.8588 978959.8876 0.721348295 0.907124617 0.643328539 0.662485164 0.734998864 0.599782475 0.709450862 0.790186471 1 19.90089022 0.86782417 3.327991116 0.999855386 0.71775302 0.557930259 0.080843218 0.484321249 10.17192322 0.081441457 0.021121266 7.376055403 -0.86782417 -0.282102367 SATDGNT(ph)STTPPTSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SATDGNTSTTPPTSAK 16 0 A0A669KAX4;Q13620-1;K4DI93;Q13620;A0A669KAU9 A0A669KAX4 CUL4B Cullin-4B 1 SATDGNT(0.536)S(0.284)T(0.153)T(0.027)PPTSAK 163.23 1.82E-08 0 156950 117520 143460 129800 136390 104850 174250 135190 165810 TRUE FALSE 147126.7797 126221.3031 146862.9389 133130.8878 125678.4796 135118.4929 148122.8302 152068.7691 138135.2398 1.065092295 0.913751648 1.063182278 0.963772082 0.909821996 0.978160917 1.072302986 1.100868752 1 17.07572189 1.741823311 6.603492208 1.064233281 0.980136759 0.276292879 0.057062707 0.163069841 20.25399221 0.026584187 0.013996455 55.18528766 -1.741823311 -0.084096523 SATDGNTS(ph)TTPPTSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SATDGNTSTTPPTSAK 16 0 A0A669KAX4;Q13620-1;K4DI93;Q13620;A0A669KAU9 A0A669KAX4 CUL4B Cullin-4B 1 SATDGNT(0.01)S(0.455)T(0.19)T(0.345)PPTSAK 205.98 2.23E-11 421910000 1130700 807850 900010 847300 945230 765700 1170300 882090 1167300 TRUE FALSE 1059931.505 867664.0546 921358.6622 869043.1525 870995.4487 986745.1599 994824.3795 992220.8782 972470.089 1.089937385 0.892226984 0.947441646 0.893645123 0.895652687 1.014679188 1.022987124 1.02030992 1 19.89129435 2.217806331 23.43328758 1.017052679 0.934971039 0.265511612 0.057342208 130.5872425 147441.6704 0.019895 0.014714558 165.1225286 -2.217806331 -0.08208164 SATDGNTSTT(ph)PPTSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SATDGNTSTTPPTSAK 16 0 A0A669KAX4;Q13620-1;K4DI93;Q13620;A0A669KAU9 A0A669KAX4 CUL4B Cullin-4B 1 SATDGNT(0.002)S(0.043)T(0.181)T(0.774)PPTSAK 202.18 4.74E-12 0 1113900 835750 1005000 845860 938680 789380 1253400 865810 1130300 TRUE FALSE 1044182.987 897629.7996 1028839.075 867566.1996 864959.8593 1017261.191 1065464.306 973908.2844 941645.628 1.108891664 0.953256483 1.092596879 0.921329823 0.918561966 1.080301508 1.131491799 1.034261994 1 19.8448247 2.114262696 19.58652463 1.079135626 1.001713915 0.137673905 0.071872271 3.06086055 510.1900176 0.025851067 0.019092313 130.0956262 -2.114262696 -0.077421711 SATLSGS(ph)ATNLASLTAALAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SATLSGSATNLASLTAALAK 20 0 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 SATLSGS(0.998)AT(0.001)NLASLTAALAK;SATLS(0.004)GS(0.986)AT(0.01)NLASLTAALAK;SATLS(0.004)GS(0.994)AT(0.002)NLASLTAALAK 349.31 4.88E-95 106847000 309541 282046 290814 288505 326038 232226 357832 279039 446518 TRUE FALSE 290167.3814 302928.9793 297712.2454 295908.5267 300432.2907 299265.8763 304178.4135 313877.6334 371991.2612 0.780038167 0.814344343 0.800320536 0.795471716 0.807632657 0.804497061 0.817703116 0.843776901 1 18.5049092 0.420719211 0.961686789 1.00093067 0.800984704 0.980587917 0.008713589 0.242789208 0.299313675 0.007948079 0.002478477 2.634627442 -0.420719211 -0.199945965 SATREPPYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SATREPPYR 9 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 103.7 0.0030824 172116000 111889 135617 159294 139786 154253 132611 179765 123714 188344 FALSE TRUE 104886.0672 145658.2238 163072.5289 143373.1454 142138.5916 170893.6429 152810.9071 139159.9652 156908.1697 0.668455106 0.928302357 1.039286414 0.9137392 0.905871198 1.089131581 0.973887513 0.886887952 1 17.25956094 4.742383473 2.985243205 0.97642658 0.616007854 0.703195298 0.061600945 0.209368274 2.731643993 0.014376008 0.181331709 55256.51271 -4.742383473 -0.360418726 SATRPS(ph)PS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SATRPSPSPER 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.004)AT(0.004)RPS(0.993)PS(1)PER;SAT(0.003)RPS(0.996)PS(1)PER;S(0.127)AT(0.032)RPS(0.841)PS(1)PER;SAT(0.026)RPS(0.976)PS(0.998)PER;S(0.001)AT(0.001)RPS(0.998)PS(1)PER;S(0.001)AT(0.005)RPS(0.994)PS(1)PER 160.46 0.00032821 17375300000 5697940 5109300 5057790 5275490 5233070 4136560 5915520 4455700 5112020 TRUE FALSE 5341316.107 5487597.888 5177763.167 5410868.005 4822085.791 5330717.721 5028542.693 5012003.953 4258790.837 1.254186061 1.288534257 1.215782452 1.270517434 1.132266405 1.251697471 1.180744227 1.176860791 1 22.02201245 -5 0.13696641 0.203959836 1.313142515 0.798156611 0.037905527 53.58509646 0.454111834 11.56896454 0.218492882 1.00E-05 5 1.10918268 SATRPS(ph)PS(ph)PERS(ph)STGPEPPAPTPLLAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SATRPSPSPERSSTGPEPPAPTPLLAER 28 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(0.001)AT(0.003)RPS(0.992)PS(0.997)PERS(0.747)S(0.252)T(0.008)GPEPPAPTPLLAER 93.966 0.0016088 407970000 153850 154820 156920 143230 159380 119940 176190 124190 152210 TRUE FALSE 144220.8031 166283.0339 160642.2165 146905.5243 146862.9377 154564.7309 149771.9452 139695.3949 126805.1677 1.137341685 1.311326951 1.266842822 1.158513702 1.15817786 1.218915079 1.181118624 1.1016538 1 16.95225402 0.749613586 0.382288766 0.976744231 1.255260737 0.60078832 0.054423986 1.184167726 0.412362642 0.109464157 0.047184859 5.618412036 -0.749613586 0.278516506 SATRPSPS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SATRPSPSPER 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SATRPS(0.014)PS(0.986)PER;SATRPS(0.023)PS(0.977)PER 101.2 0.0020946 1793460000 380590 688640 363430 360430 779580 224783 355700 648200 824900 TRUE FALSE 356769.5513 739627.6221 372050.7312 369679.244 718354.9315 289674.2031 302366.0872 729129.1969 687218.8609 0.519149825 1.076262111 0.541386089 0.537935242 1.045307357 0.421516666 0.439985141 1.060985427 1 19.39041011 1.216675089 24.99655452 1.030493278 0.671033342 0.31258685 0.230792139 360.2265404 411421.9896 0.22101426 0.055441809 16.46929805 -1.216675089 -0.359459936 SATSPEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SATSPEGK 8 0 P13639 P13639 EEF2 Elongation factor 2 0 ;; 94.114 0.024634 115806000 294939 248018 279677 265743 288896 202175 293185 230281 337856 FALSE TRUE 276479.2945 266381.5108 286311.0705 272562.4153 266207.2735 260539.6405 249224.631 259032.0898 281465.651 0.982284316 0.946408593 1.017214959 0.968368305 0.945789558 0.925653413 0.885453092 0.92029734 1 18.10259935 2.556998901 2.365295769 0.919612431 0.98007407 0.261416609 0.033747984 0.289719331 3.22005651 0.011934924 0.010563011 360.5777305 -2.556998901 0.06046164 SATTT(ph)PSGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SATTTPSGSPR 11 0 A0A096LNZ0;A0A096LP60;A0A096LP25;Q2M2I8;Q2M2I8-2 A0A096LNZ0;A0A096LP25;Q2M2I8 AAK1 AP2-associated protein kinase 1 2 S(0.001)AT(0.043)T(0.184)T(0.75)PS(0.022)GS(1)PR;SATT(0.016)T(0.979)PS(0.004)GS(1)PR 142.12 0.00020057 233120000 464380 483760 430220 482960 448020 410240 540360 397350 475910 TRUE FALSE 435315.2847 519578.0938 440425.0216 495353.5712 412834.3164 528669.6283 459338.0345 446960.0222 396477.5465 1.097956968 1.310485545 1.110844802 1.24938619 1.041255224 1.333416313 1.15854741 1.127327452 1 18.59687964 0.918587649 2.22653894 1.000977094 1.194243486 0.290085049 0.092183555 0.441110077 4.685362472 0.076827917 0.021031157 8.290632201 -0.918587649 0.193266392 SATTTGS(ph)PGTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SATTTGSPGTEK 12 0 Q6GYQ0-2;A0A1B0GUI1;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5;Q6GYQ0-6;Q6GYQ0-3 Q6GYQ0-2 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 1 SATTT(0.003)GS(0.997)PGTEK;SATTT(0.034)GS(0.966)PGTEK;SATTT(0.008)GS(0.992)PGTEK 356.23 9.78E-72 1472450000 2832010 2156840 2336520 2424730 2504260 1829690 3161140 2212270 2394250 TRUE FALSE 2654759.549 2316534.678 2391943.358 2486952.677 2307585.521 2357891.8 2687156.404 2488476.779 1994634.208 1.330950577 1.16138321 1.199188978 1.246821431 1.156896594 1.182117399 1.34719258 1.247585532 1 20.92769277 4.753772161 23.15690177 1.208493123 1.330950828 0.173615813 0.089049296 1899.18533 2891037.728 0.020026802 0.430277684 56724.69388 -4.753772161 0.122457705 SATTTPSGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_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(0.006)GS(0.994)PR 215.77 1.32E-11 482950000 314277 316002 302763 347912 374760 300497 351446 271698 314457 TRUE FALSE 294606.9636 339399.1169 309944.6813 356840.0109 345327.8613 387245.6057 298749.935 305620.0934 261972.0952 1.124573834 1.295554462 1.183120977 1.362129851 1.318185668 1.478194101 1.140388386 1.166613158 1 17.99905362 1.124891599 1.785039177 1.013710601 1.281505402 0.438732073 0.102780701 0.305212886 1.864883611 0.092169703 0.026702324 13.33188624 -1.124891599 0.267794801 SAVADKHELLSLASSNHLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SAVADKHELLSLASSNHLGK 20 1 A0A087WZK9;B3KS98;O15372;E5RJT0 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ; 245.61 3.66E-30 880370000 942640 1432150 1471690 1534600 1600640 1228360 1935960 1427470 1849450 FALSE TRUE 883641.8451 1538187.876 1506599.182 1573980.434 1474932.191 1582967.591 1645680.771 1605692.772 1540764.847 0.573508571 0.998327473 0.977825516 1.021557856 0.957272743 1.027390776 1.068093404 1.042140061 1 20.55521526 4.739454184 5.457469971 1.012704632 0.556848898 0.951616824 0.031060255 0.033552233 3.806991579 0.008396563 0.057208586 54885.06513 -4.739454184 -0.455855733 SAVAVYSYSCEGPEEES(ph)EDDSHLEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAVAVYSYSCEGPEEESEDDSHLEGR 26 0 A0A1B0GTY1;A0A1B0GV98;A0A1B0GTC5;A0A1B0GU26;A0A1B0GTC3;A0A1B0GVH5;Q9C0B1;A0A1B0GUC3;A0A1B0GTI3 A0A1B0GTY1 FTO Alpha-ketoglutarate-dependent dioxygenase FTO 1 SAVAVYSYSCEGPEEES(1)EDDSHLEGR 308.43 7.12E-82 315080000 119830 120330 109370 120040 143310 134610 146980 115980 71022 TRUE FALSE 112330.0542 129239.3584 111964.308 123120.4296 132055.0107 173469.7218 124941.7135 130460.3583 59167.96938 1.898494327 2.184279091 1.892312838 2.080862854 2.231866533 2.93181807 2.111644439 2.204915255 1 15.85252876 2.854876319 4.398162689 2.227775096 2.016304568 0 0.480212149 0.831955337 26.31795468 0.134135753 0.143063895 715.9394923 -2.854876319 -0.211470529 SAVAVYSYSCEGPEEES(ph)EDDSHLEGRDPDIWHVGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SAVAVYSYSCEGPEEESEDDSHLEGRDPDIWHVGFK 36 1 A0A1B0GTY1;A0A1B0GV98;A0A1B0GTC5;A0A1B0GU26;A0A1B0GTC3;A0A1B0GVH5;Q9C0B1;A0A1B0GUC3;A0A1B0GTI3 A0A1B0GTY1 FTO Alpha-ketoglutarate-dependent dioxygenase FTO 1 SAVAVYSYS(0.001)CEGPEEES(0.986)EDDS(0.013)HLEGRDPDIWHVGFK;SAVAVYSYS(0.001)CEGPEEES(0.97)EDDS(0.029)HLEGRDPDIWHVGFK;SAVAVYSYSCEGPEEES(0.96)EDDS(0.04)HLEGRDPDIWHVGFK;SAVAVYSYSCEGPEEES(0.989)EDDS(0.011)HLEGRDPDIWHVGFK 232.25 1.24E-40 855670000 385355.2 350989 367219.1 378314 438239 298315.4 515137 340676 554334 TRUE FALSE 361236.5059 376976.5908 375929.7105 388022.1777 403821.4767 384434.2132 437896.9891 383210.1485 461812.0743 0.782215377 0.816298689 0.814031792 0.840216615 0.874428148 0.832447298 0.948214682 0.829796729 1 18.81694637 -4.999999775 0.053269636 1.664683919 0.533714894 0.721229773 0.03507814 226.837884 0.890490974 20.48644172 4.167059644 1.00E-05 4.999999775 -1.130969025 SAVENCQDSWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SAVENCQDSWR 11 0 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;; 336.9 2.36E-57 2668260000 983890 1251730 1076220 1115980 1243100 886970 1247720 1046870 1230580 FALSE TRUE 922310.0812 1344409.392 1101748.447 1144617.936 1145471.94 1143023.84 1060635.969 1177574.024 1025188.248 0.899649487 1.311378075 1.074679161 1.116495374 1.117328396 1.114940444 1.034576792 1.14864175 1 19.96745742 0.605467106 0.36507834 0.98938028 1.138661401 0.036873533 0.104554352 4.96964006 1.441461015 0.23540069 0.087930294 4.031504105 -0.605467106 0.149281122 SAVGHEYQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SAVGHEYQSK 10 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;; 183.03 1.71E-06 4285520000 7682720 8384340 7911880 7882580 8711660 6094890 8884540 7617360 9552420 FALSE TRUE 7201872.269 9005125.257 8099553.53 8084860.348 8027481.365 7854385.801 7552385.707 8568404.164 7958059.391 0.904978452 1.131573015 1.01777998 1.015933653 1.00872348 0.986972504 0.949023542 1.076695177 1 22.92398524 3.172936751 1.91098103 0.995826737 1.044762143 0 0.063551842 0.767172394 5.736020887 0.019426511 0.025998697 1489.144189 -3.172936751 0.048935406 SAVHYDEES(ph)GS(ph)EEETLQYFSTVDPNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SAVHYDEESGSEEETLQYFSTVDPNYR 27 0 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 2 S(0.222)AVHY(0.328)DEES(0.695)GS(0.689)EEET(0.06)LQY(0.007)FSTVDPNYR 63.776 0.016125 36613000 17821 22295 29257 23191 22581 19124 27312 19569 25122 TRUE FALSE 16705.61542 23945.745 29950.98986 23786.12032 20807.57935 24644.78835 23216.81915 22012.23273 20928.97591 0.798205106 1.144143178 1.43107766 1.136516207 0.994199594 1.177543921 1.109314629 1.051758711 1 14.3532141 2.9989227 24.99674614 1.08343843 1.186403507 0 0.162550485 114.2418376 2650883.509 0.047908539 0.056574051 997.522499 -2.9989227 0.102965077 SAVRPAS(ph)LNLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SAVRPASLNLNR 12 1 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A0U1RRC1;A0A0U1RQJ5 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 SAVRPAS(1)LNLNR;SAVRPAS(1)LNLNR;SAVRPAS(1)LNLNR 129.29 0.00014341 1366120000 594020 600250 497300 600550 734550 458200 642490 550360 703790 TRUE FALSE 556841.3486 644693.1346 509096.1908 615961.1297 676861.406 590474.9017 546154.5891 619073.6575 586322.9023 0.949717888 1.099553048 0.868286381 1.050549326 1.154417478 1.007081421 0.931491141 1.055857881 1 19.16133589 SAVSDKQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SAVSDKQDR 9 1 O95757;E9PDE8;D6RJ96 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 ;;;; 137.46 0.00014963 827968000 1451200 1438570 1359710 1363130 1771920 1026753 1595440 1390510 2122780 FALSE TRUE 1360371.982 1545083.22 1391962.963 1398110.224 1632760.551 1323159.923 1356218.583 1564118.234 1768474.304 0.769234803 0.873681464 0.787098212 0.790574237 0.923259415 0.748192903 0.766886225 0.884444988 1 20.75407383 0.962975596 5.186246416 0.999918305 0.811215063 0.577435827 0.052914441 0.148111875 14.1224431 0.048912305 0.012351697 9.182809956 -0.962975596 -0.188703243 SAYQEYDS(ph)DSDVPEELKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SAYQEYDSDSDVPEELKR 18 1 Q96JG6;Q96JG6-3;H0Y7Q2 Q96JG6 CCDC132 Coiled-coil domain-containing protein 132 1 SAYQEYDS(0.999)DS(0.001)DVPEELKR;SAYQEYDS(0.999)DS(0.001)DVPEELKR;SAYQEYDS(0.998)DS(0.002)DVPEELKR 255.99 8.61E-31 1491690000 1896480 1213330 1336100 1403220 1418490 950150 1918730 1251680 1415110 TRUE FALSE 1777782.702 1303166.216 1367792.923 1439229.001 1307087.517 1224442.881 1631034.249 1407955.003 1178918.999 1.507976972 1.1053908 1.160209416 1.220803976 1.108716984 1.038614936 1.383499842 1.194276286 1 20.16903317 4.745041282 24.40279915 1.166827631 1.50797719 0.521159732 0.106499254 457.9464331 1724321.763 0.024920258 0.234894522 55595.7101 -4.745041282 0.341149558 SCAHDWVYE ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 142.36 0.00024313 20278700000 7082850 13229200 8799450 9164710 13715300 6151080 9847900 11151400 15300100 FALSE TRUE 6639547.062 14208703.73 9008177.109 9399891.974 12638155.66 7926796.942 8371298.818 12543676.84 12746414.47 0.520895274 1.114721616 0.706722438 0.737453815 0.991506725 0.621884449 0.656757148 0.984094536 1 23.60358814 3.74539001 24.13438354 0.784574503 0.875373838 0 0.200849966 1072.600698 1416972.384 0.047448364 0.085302019 5564.037003 -3.74539001 0.090799334 SCATFSSSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SCATFSSSHR 10 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-5;D6RCQ9;D6RE64;D6RBT0;D6RHE8 D6REX3 SEC31A Protein transport protein Sec31A 0 ;;; 142.83 3.51E-05 325920000 176585 424686 225663 250683 430980 202275 261679 374247 391906 FALSE TRUE 165532.8601 456130.1933 231015.8329 257115.9502 397132.5693 260668.5088 222442.6633 420972.5618 326494.3568 0.507000677 1.397053835 0.707564551 0.787505036 1.216353548 0.798385955 0.681306303 1.289371632 1 18.31669853 SCCTSVNEVICHGIPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SCCTSVNEVICHGIPDR 17 0 P53582;H0Y955 P53582 METAP1 Methionine aminopeptidase 1 0 ;;; 221.47 3.67E-15 1606430000 970730 1088430 1009300 1028770 1128830 819718 1198350 945940 1250780 FALSE TRUE 909973.7421 1169018.49 1033241.073 1055169.98 1040176.245 1056357.28 1018668.542 1064042.691 1042016.738 0.87328131 1.121880722 0.991578192 1.01262287 0.998233721 1.013762295 0.977593263 1.021137812 1 19.99094702 3.694543047 24.93033376 1.000779523 1.027755561 0 0.061530909 1186.583264 908027.152 0.014886514 0.023064531 4949.291651 -3.694543047 0.026976038 SCDEPLT(ph)PPPHS(ph)PTSMLQLIHDPVS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 3 S(0.007)CDEPLT(0.993)PPPHS(0.334)PT(0.334)S(0.334)MLQLIHDPVS(0.998)PR;S(0.003)CDEPLT(0.997)PPPHS(0.92)PT(0.04)S(0.04)MLQLIHDPVS(1)PR;SCDEPLT(0.999)PPPHS(0.84)PT(0.08)S(0.08)MLQLIHDPVS(1)PR;S(0.004)CDEPLT(0.996)PPPHS(0.888)PT(0.057)S(0.057)MLQLIHDPVS(0.999)PR;S(0.099)CDEPLT(0.901)PPPHS(0.643)PT(0.188)S(0.188)MLQLIHDPVS(0.981)PR 125.42 9.99E-05 336217000 311674 369812 359682 395335 423730 326032 403923 320962 459662 TRUE FALSE 292166.8807 397193.2653 368213.8269 405479.9654 390451.955 420152.1457 343358.496 361034.8122 382941.4427 0.762954458 1.037216715 0.961540815 1.058856316 1.019612691 1.097170739 0.896634466 0.942793785 1 18.54676427 4.744270223 24.84082448 0.999010111 0.762954346 0.626734516 0.057876562 395.4156312 1720282.205 0.01371653 0.121726848 55497.09142 -4.744270223 -0.236055765 SCDEPLT(ph)PPPHS(ph)PTSMLQLIHDPVSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 2 SCDEPLT(0.999)PPPHS(0.872)PT(0.108)S(0.021)MLQLIHDPVSPR;SCDEPLT(0.997)PPPHS(0.72)PT(0.134)S(0.145)MLQLIHDPVS(0.004)PR 180.96 3.11E-17 441060000 478750 612900 611440 714750 724180 492390 588280 513200 778380 TRUE FALSE 448785.8921 658279.7537 625943.6455 733091.6951 667305.824 634534.9997 500072.8753 577274.1497 648463.3495 0.692075955 1.015137948 0.965272202 1.130505981 1.029057116 0.978520992 0.771165981 0.890218622 1 19.30666551 1.776899158 24.99975791 0.863020218 0.982019435 0.070038916 0.123674293 85.85358029 56005.90077 0.053457068 0.029682638 59.82726614 -1.776899158 0.118999217 SCDEPLT(ph)PPPHSPTSMLQLIHDPVSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 S(0.001)CDEPLT(0.998)PPPHS(0.001)PTSMLQLIHDPVSPR;S(0.001)CDEPLT(0.996)PPPHS(0.003)PTSMLQLIHDPVSPR 132.73 6.59E-05 336550000 355040 446120 421310 495270 516790 360290 456960 379100 513710 TRUE FALSE 332818.6802 479151.189 431303.6722 507979.4667 476203.398 464299.8742 388443.0902 426431.4695 427968.4823 0.777671006 1.11959457 1.007793074 1.18695532 1.112706701 1.084892681 0.907644152 0.996408584 1 18.70714503 -0.871666894 6.095329648 0.999999996 1.032202017 7.90E-05 0.116914507 6.37E-09 1.04E-09 0.106839601 0.025182332 0.134379526 0.871666894 0.032202021 SCDEPLTPPPHS(ph)PTSMLQLIHDPVS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 2 SCDEPLTPPPHS(0.989)PT(0.005)S(0.006)MLQLIHDPVS(1)PR;S(0.002)CDEPLT(0.09)PPPHS(0.843)PT(0.082)S(0.082)MLQLIHDPVS(0.9)PR 143.72 8.57E-08 205637000 88113 112676 109299 102708 115915 100293 133243 105703 124602 TRUE FALSE 82598.16462 121018.6483 111891.6239 105343.6612 106811.5035 129245.961 113264.4491 118900.2522 103805.1212 0.795704139 1.165825412 1.077900806 1.014821426 1.028961791 1.245082703 1.09112583 1.145417979 1 16.6635181 SCDEPLTPPPHS(ph)PTSMLQLIHDPVSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 SCDEPLTPPPHS(0.897)PT(0.052)S(0.052)MLQLIHDPVSPR;SCDEPLTPPPHS(0.976)PT(0.012)S(0.012)MLQLIHDPVSPR;SCDEPLTPPPHS(0.67)PT(0.165)S(0.165)MLQLIHDPVSPR;SCDEPLTPPPHS(0.848)PT(0.076)S(0.076)MLQLIHDPVSPR;SCDEPLTPPPHS(0.892)PT(0.091)S(0.017)MLQLIHDPVSPR;SCDEPLTPPPHS(0.91)PT(0.045)S(0.045)MLQLIHDPVSPR;SCDEPLTPPPHS(0.986)PT(0.012)S(0.002)MLQLIHDPVSPR;SCDEPLTPPPHS(0.723)PT(0.139)S(0.139)MLQLIHDPVSPR;SCDEPLTPPPHS(0.916)PT(0.042)S(0.042)MLQLIHDPVSPR 146.88 2.36E-07 2859275000 1273309 1568702 1552988 1539216 1583825 1456527 1906310 1502655 1837950 TRUE FALSE 1193614.863 1684850.328 1589825.609 1578714.888 1459437.773 1877002.7 1620476.513 1690264.785 1531184.271 0.779537045 1.100357651 1.038298028 1.031041735 0.953143133 1.225850301 1.058315804 1.103893774 1 20.54621648 2.271843946 24.99999776 1.10163567 1.007006448 0.223081065 0.101409929 314.6851634 236367.4428 0.032695088 0.027353082 187.0010072 -2.271843946 -0.094629222 SCFES(ph)S(ph)PDPELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SCFESSPDPELK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 SCFES(1)S(1)PDPELK;SCFES(1)S(1)PDPELK 203.87 1.76E-07 467120000 2310200 1361400 1680600 1596000 1622260 1321920 2278100 1318370 1758900 TRUE FALSE 2165608.706 1462199.473 1720464.626 1636956.062 1494854.243 1703536.844 1936520.054 1482971.397 1465328.227 1.477900081 0.99786481 1.174115528 1.117125864 1.020149763 1.162563317 1.321560602 1.012040422 1 20.48279243 4.751232764 24.70623155 1.121157626 1.477900346 0.560151417 0.103647927 1463.969948 2854166.037 0.025086096 0.449163316 56393.98239 -4.751232764 0.35674272 SCFES(ph)SPDPELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SCFESSPDPELK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SCFES(0.806)S(0.194)PDPELK 148.28 0.00031786 0 457440 304520 376230 342000 370470 275750 461660 297400 438490 TRUE FALSE 428809.647 327066.9777 385154.3533 350776.299 341374.7806 355354.5486 392438.3688 334531.0447 365303.1862 1.173845899 0.895330208 1.05434162 0.960233341 0.934497134 0.97276608 1.074281264 0.915762734 1 18.47873481 4.756176124 24.38288325 0.982791331 1.17384612 0.544052452 0.056637222 2161.556902 2991897.405 0.013087076 0.393666902 57039.55441 -4.756176124 0.191054789 SCFESS(ph)PDPELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SCFESSPDPELK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SCFES(0.377)S(0.623)PDPELK;SCFES(0.001)S(0.999)PDPELK;SCFES(0.001)S(0.999)PDPELK;SCFESS(1)PDPELK;SCFES(0.001)S(0.999)PDPELK;SCFES(0.004)S(0.996)PDPELK 322.75 6.87E-47 28250900000 82987800 54100400 62936700 61150300 63350800 50513200 85036900 53825900 73592800 TRUE FALSE 77793741.74 58106049.91 64429588.24 62719520.23 58375483.71 65095540.83 72286406.29 60546182.1 61309686.25 1.268865435 0.947746652 1.050887587 1.022995289 0.952141289 1.061749697 1.179037289 0.987546761 1 25.86961169 2.003264341 24.94718477 1.086664165 1.031695742 0 0.103245974 288.239705 2202807.109 0.03571818 0.026244612 100.7544743 -2.003264341 -0.054968423 SCFGFEGLLGAEDLSGVS(ph)PVVCSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SCFGFEGLLGAEDLSGVSPVVCSK 24 0 Q96FF9;B5MBX0 Q96FF9 CDCA5 Sororin 1 SCFGFEGLLGAEDLSGVS(1)PVVCSK 172 3.86E-12 13330000 22833 16807 19893 19608 22826 21341 26905 21718 30070 TRUE FALSE 21403.92329 18051.40777 20364.87135 20111.17448 21033.33804 27501.80026 22870.84502 24429.54011 25051.12274 0.854409741 0.720582784 0.812932481 0.802805315 0.839616581 1.097827053 0.912966866 0.975187434 1 14.61258764 2.409231293 6.773724389 0.984538542 0.79055736 0.743569655 0.055759512 0.101528453 8.132384261 0.018295164 0.015282374 256.5850171 -2.409231293 -0.193981182 SCGTDSQSENEAS(ph)PVKRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SCGTDSQSENEASPVKRPR 19 2 H0Y398;C9JQ48;Q9H8U3 H0Y398 ZFAND3 AN1-type zinc finger protein 3 1 SCGTDSQSENEAS(1)PVKRPR 190.3 6.32E-15 615400000 551370 418030 482900 445720 519260 365220 597720 438670 604940 TRUE FALSE 516860.7359 448981.3762 494354.616 457157.9298 478479.4142 470653.0851 508097.435 493438.9151 503971.6059 1.025575111 0.890886254 0.980917596 0.907110489 0.949417405 0.933888099 1.00818663 0.979100627 1 18.94298293 1.743477815 9.948267137 0.994628656 0.943667007 0.257794973 0.037722856 0.115469297 54.92225944 0.015907112 0.008628626 55.3959245 -1.743477815 -0.050961649 SCGYSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SCGYSVR 7 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 100.74 0.046513 0 94705 151990 94915 100550 137600 68996 108200 133510 151100 FALSE TRUE 88777.5831 163243.4977 97166.42862 103130.2832 126793.4511 88914.02514 91976.41448 150179.0174 125880.4339 0.705253234 1.296813911 0.771894612 0.819271749 1.007253051 0.706337136 0.730664899 1.193029074 1 16.94169453 3.751621215 21.1567771 0.861463329 1.040608473 0.026949231 0.205335053 128.1274871 110639.1153 0.04821685 0.086805177 5644.444597 -3.751621215 0.179145144 SCLLLQFTDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SCLLLQFTDKR 11 1 P61019;E9PKL7;A0A3B3ITL1;Q8WUD1;E9PE37;H0YD31;H0YDL5 P61019 RAB2A;RAB2B Ras-related protein Rab-2A;Ras-related protein Rab-2B 0 162.49 0.0018126 0 162020 233970 144330 157430 268320 115350 201870 248780 211170 FALSE TRUE 151879.4574 251293.3822 147753.5758 161469.9203 247247.2296 148649.6724 171601.4676 279840.7306 175924.3628 0.863322481 1.42841718 0.839869893 0.917837176 1.405417792 0.844963541 0.975427535 1.59068776 1 17.42459576 1.289416268 24.99980417 1.295358446 1.052639569 0.146137644 0.255710923 172.474636 84785.24681 0.157068236 0.057355965 19.47225587 -1.289416268 -0.242718877 SCLLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SCLLLR 6 0 Q9H0U4;E9PLD0;Q92928;P62820;E7END7;P62820-2;P62820-3 Q9H0U4;P62820 RAB1B;RAB1C;RAB1A Ras-related protein Rab-1B;Putative Ras-related protein Rab-1C;Ras-related protein Rab-1A 0 123.34 0.043811 188450000 216000 450690 398530 294430 393260 196280 258840 273290 374150 FALSE TRUE 202480.9456 484059.5565 407983.3198 301985.5723 362374.9459 252942.8497 220029.345 307410.8581 311701.9479 0.649597947 1.552956469 1.308889221 0.968827992 1.162568756 0.811489474 0.705896599 0.986233356 1 18.24980765 2.649311084 1.43341709 0.840215241 1.255603538 0.107626614 0.257974175 0.474726062 1.975176874 0.111109797 0.098343565 445.9755848 -2.649311084 0.415388298 SCMLTGT(ph)PESVQSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SCMLTGTPESVQSAK 15 0 Q96AE4;E9PEB5;Q96AE4-2;C9JSZ1 Q96AE4;C9JSZ1 FUBP1 Far upstream element-binding protein 1 1 SCMLTGT(0.996)PES(0.004)VQSAK;SCMLTGT(0.614)PES(0.386)VQSAK 259.58 8.10E-24 578280000 796320 605290 689480 658680 725590 583210 803100 654680 984280 TRUE FALSE 746479.7527 650106.3014 705834.7912 675582.8439 668605.0883 751573.2594 682682.6106 736418.2391 819997.3093 0.910344149 0.792815164 0.86077696 0.82388422 0.815374734 0.916555763 0.832542501 0.89807397 1 19.64525965 0.337744823 0.608922297 1.006095938 0.838554921 0.579791054 0.039838999 1.47708415 0.823995305 0.054501709 0.014680655 2.176430599 -0.337744823 -0.167541017 SCQGACGPS(ph)PPDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SCQGACGPSPPDQK 14 0 P18754-2 P18754-2 RCC1 Regulator of chromosome condensation 1 SCQGACGPS(1)PPDQK 93.51 0.0047553 72735000 193390 131160 151850 143870 149590 109080 194000 125460 234180 TRUE FALSE 181286.0651 140871.2229 155451.9537 147561.9478 137841.8048 140569.6252 164911.501 141123.9572 195093.8451 0.929224933 0.722069027 0.796806038 0.756363932 0.706541022 0.720523116 0.845293202 0.723364477 1 17.57380874 -1.146665036 4.50732004 1.000028281 0.77261403 0.51269818 0.068894426 2.02E-05 3.82E-06 0.059961073 0.014130949 0.071340305 1.146665036 -0.227414252 SCQHECGGISASIGHDPHLLYTLSAVQILTLYDSINVIDVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SCQHECGGISASIGHDPHLLYTLSAVQILTLYDSINVIDVNK 42 0 P53611;Q5T4U8 P53611 RABGGTB Geranylgeranyl transferase type-2 subunit beta 0 ; 103.62 2.66E-06 100127000 44416 55847 53995 53381 62474 63568 59180 55826 32063.5 FALSE TRUE 41636.08184 59981.96999 55275.7869 54750.84683 57567.54405 81919.04966 50306.5084 62795.99899 26711.89471 1.558709417 2.245515364 2.069332314 2.049680392 2.155127694 3.066762974 1.883299891 2.350862777 1 14.70519469 2.69313451 5.658420756 2.205640004 2.039457835 0 0.537105531 1.041248405 84.19496405 0.156776074 0.149459284 493.3265742 -2.69313451 -0.166182169 SCS(ph)FSSESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SCSFSSESR 9 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 SCS(0.998)FS(0.002)SESR;S(0.001)CS(0.983)FS(0.017)SESR;S(0.007)CS(0.992)FS(0.001)SESR;S(0.001)CS(0.932)FS(0.066)S(0.001)ESR 252.82 7.29E-15 1441090000 1823980 2057570 1773940 2034610 1691340 1415390 2364660 1581490 1838500 TRUE FALSE 1709820.348 2209914.624 1816018.695 2086821.537 1558508.979 1823990.116 2010101.185 1778942.508 1531642.473 1.116331244 1.442839738 1.185667495 1.362473015 1.017540977 1.190871988 1.312382766 1.16146068 1 20.54664814 -4.999999964 0.152374903 0.116438604 1.317229403 0.251679903 0.12235498 169.0085533 1.518761808 45.07896802 0.557766724 1.00E-05 4.999999964 1.200790799 SCS(ph)PLAFSAFGDLTIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SCSPLAFSAFGDLTIK 16 0 E9PLZ8;Q96EY5;Q96EY5-2 E9PLZ8 MVB12A Multivesicular body subunit 12A 1 S(0.039)CS(0.961)PLAFSAFGDLTIK;S(0.01)CS(0.99)PLAFSAFGDLTIK 232.74 4.62E-14 72282000 474470 442490 464870 491910 528250 341020 522220 346200 486180 TRUE FALSE 444773.7697 475252.42 475896.9359 504533.2434 486763.3759 439466.938 443917.9591 389423.8321 405033.4172 1.098116231 1.173365949 1.174957215 1.245658314 1.201785718 1.085014024 1.096003293 0.961460995 1 18.62768142 1.614820881 1.492707691 0.982825079 1.177942665 0.734326708 0.045440511 0.186104834 0.811053637 0.036618291 0.013079679 41.19275901 -1.614820881 0.195117586 SCS(ph)PSPVSPQVQPQAADTISDSVAVPASLLGMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SCSPSPVSPQVQPQAADTISDSVAVPASLLGMR 33 0 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 S(0.09)CS(0.447)PS(0.447)PVS(0.016)PQVQPQAADTISDSVAVPASLLGMR 138.15 5.95E-09 102890000 98849 93611 100150 90877 103350 86689 111100 81138 109270 TRUE FALSE 92662.21754 100542.0558 102525.6053 93209.05767 95233.30789 111714.707 94441.5864 91268.25791 91032.13109 1.017906715 1.104467781 1.126257334 1.023913826 1.046150483 1.227200832 1.037453318 1.002593884 1 16.47408823 1.505011758 10.45586331 1.007523992 1.094969506 0.284912873 0.059634398 0.124126245 30.17114477 0.030598574 0.014194783 31.98981714 -1.505011758 0.087445515 SCSDT(ph)ALNAIVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SCSDTALNAIVAK 13 0 Q86X02 Q86X02 CDR2L Cerebellar degeneration-related protein 2-like 1 S(0.002)CS(0.135)DT(0.862)ALNAIVAK 118.03 0.0051361 38571000 94605 76357 79305 76967 95650 66805 86325 73848 118390 TRUE FALSE 88683.84192 82010.55173 81186.15205 78942.10352 88138.03483 86090.51901 73381.36765 83068.08536 98629.94417 0.899157377 0.831497497 0.823138984 0.800386781 0.893623489 0.872863913 0.744006988 0.842219734 1 16.5897381 -1.541303225 3.223965411 1.005581331 0.831886593 0.547532809 0.045843275 14441532.59 19451276.26 707959.1206 0.010902429 0.028753901 1.541303225 -0.173694738 SCSPS(ph)PVSPQVQPQAADTISDSVAVPASLLGMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SCSPSPVSPQVQPQAADTISDSVAVPASLLGMR 33 0 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 S(0.013)CS(0.148)PS(0.807)PVS(0.031)PQVQPQAADTISDSVAVPASLLGMR 149.62 1.49E-10 109790000 76020 85195 90533 79630 86313 76492 101540 79985 88919 TRUE FALSE 71262.0439 91502.92645 92680.48551 81673.44061 79534.32515 98573.99866 86315.01965 89971.30332 74077.84446 0.961988627 1.235226634 1.251122872 1.102535329 1.07365874 1.33068125 1.165193457 1.214550774 1 16.1767545 -1.197812332 5.17055961 0.999987054 1.181920032 0.190468862 0.104081876 1.43E-05 2.23E-06 0.09309939 0.021942175 0.063414368 1.197812332 0.181932978 SCSSISTALPQVNEDLVSLPHQLPEASEPPQS(ph)PSEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SCSSISTALPQVNEDLVSLPHQLPEASEPPQSPSEKR 37 1 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 SCSSISTALPQVNEDLVSLPHQLPEAS(0.454)EPPQS(0.536)PS(0.01)EKR 306.64 1.60E-93 247730000 73052 60029 76379 83671 76402 45087 85722 66635 75688 TRUE FALSE 68479.80572 64473.60962 78190.74595 85818.13951 70401.69511 58102.88497 72868.7819 74954.52643 63055.18384 1.086029753 1.022494991 1.240036761 1.361000544 1.116509236 0.921460877 1.155635072 1.188713154 1 15.94432736 2.481043653 24.99626907 1.074075977 1.169689559 0.169078331 0.11488449 366.2719745 2334166.825 0.040785863 0.034876635 302.7217691 -2.481043653 0.095613582 SCSSSCAVHDLIFWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SCSSSCAVHDLIFWR 15 0 O95197-3;B7Z4M1;O95197-6;O95197-5 O95197-3 RTN3 Reticulon-3;Reticulon 0 ; 157.38 1.96E-06 706360000 381450 462770 434300 396900 540780 356330 463190 449560 510920 FALSE TRUE 357575.7254 497033.9723 444601.8011 407085.126 498309.3202 459196.6865 393738.9595 505688.5556 425644.1513 0.840081379 1.167721842 1.04453873 0.956397791 1.170718119 1.078827666 0.92504257 1.18805475 1 18.69928828 -1.414775652 5.240557504 0.999956927 1.050247058 0.015164751 0.113923687 5.17E-05 5.78E-06 0.099527287 0.02343872 0.038479051 1.414775652 0.050290131 SCT(ph)PSPDQISHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SCTPSPDQISHR 12 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 S(0.149)CT(0.851)PS(0.001)PDQISHR 133.25 0.00061286 544180000 259340 241670 273640 226080 280020 265260 344740 276780 304590 TRUE FALSE 243108.3723 259563.4983 280130.87 231881.5956 258028.3587 341836.2559 293049.4374 311336.5923 253751.9613 0.958055146 1.022902432 1.103955487 0.913812033 1.016852668 1.347127542 1.154865704 1.226932752 1 17.95305945 2.303913403 16.35717629 1.196244703 1.015480998 0.449399323 0.097439736 2.350753994 587.3590833 0.030772882 0.025745553 201.332276 -2.303913403 -0.180763705 SCTKPS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SCTKPSPSK 9 1 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 SCT(0.001)KPS(0.99)PS(0.009)K;S(0.002)CT(0.002)KPS(0.952)PS(0.044)K;SCTKPS(0.967)PS(0.032)K;SCT(0.004)KPS(0.932)PS(0.064)K;SCTKPS(0.998)PS(0.002)K;SCT(0.001)KPS(0.982)PS(0.018)K 110.38 0.0013908 17022700000 21615980 11123540 14364280 13287280 14419050 9385680 18570260 11951480 19926550 TRUE FALSE 20263074.4 11947138.48 14705007.5 13628254.1 13286635.98 12095173.45 15785821.91 13443648.59 16600680.07 1.220617126 0.719677653 0.885807536 0.82094553 0.800366968 0.728595057 0.95091417 0.809825171 1 23.98473901 -1.66893434 5.974784887 1.001543241 0.853283159 0.07129446 0.143238685 0.002607774 0.000144498 0.122828195 0.028662401 0.021432146 1.66893434 -0.148260083 SCTKPS(ph)PSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SCTKPSPSKK 10 2 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 S(0.002)CT(0.039)KPS(0.91)PS(0.049)KK;SCT(0.002)KPS(0.824)PS(0.173)KK 66.004 0.0351 1002020000 3143600 1215830 1944110 1717220 1874780 1299530 2572900 1417370 2516800 TRUE FALSE 2946847.687 1305851.318 1990225.207 1761286.772 1727542.341 1674683.215 2187117.531 1594331.765 2096729.821 1.405449409 0.622803809 0.949204417 0.840016084 0.823922245 0.798711974 1.043108897 0.760389702 1 20.99970954 -0.855379403 7.851205628 0.999999998 0.886572857 0.01267276 0.210017879 0 1.69E-10 0.178161743 0.041993126 0.139514902 0.855379403 -0.113427141 SCTPS(ph)PDQISHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SCTPSPDQISHR 12 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 SCT(0.002)PS(0.996)PDQIS(0.002)HR;S(0.015)CT(0.011)PS(0.975)PDQISHR 161.49 0.00022038 438130000 613070 664650 677900 689440 698190 603690 748330 585069 729320 TRUE FALSE 574699.0431 713861.3776 693980.1081 707132.1976 643356.9738 777965.5029 636124.8637 658116.1525 607591.7804 0.945863755 1.174902954 1.142181528 1.163827788 1.058863853 1.280408208 1.046960943 1.083155128 1 19.21274283 1.597018303 25 1.048771812 1.135694759 0.166433757 0.087442752 1.323513792 3042.006383 0.04148562 0.019501774 39.5383283 -1.597018303 0.086922948 SCTPSPDQISHRAS(ph)LEDAPVDDLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SCTPSPDQISHRASLEDAPVDDLTR 25 1 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 SCTPSPDQISHRAS(1)LEDAPVDDLTR;SCTPSPDQISHRAS(1)LEDAPVDDLTR;SCTPSPDQISHRAS(1)LEDAPVDDLTR;SCTPSPDQIS(0.022)HRAS(0.978)LEDAPVDDLTR 276.95 2.58E-53 992990000 168482 234283 197751 207713 270518 164312 228601 197066 375654 TRUE FALSE 157937.0124 251629.5571 202441.7471 213043.2672 249272.6075 211746.207 194324.4023 221670.1239 312954.9206 0.504663777 0.804044099 0.64687191 0.68074746 0.796512824 0.676602901 0.620934165 0.708313272 1 18.25559533 0.950986625 22.45343556 1.000000001 0.685196847 0.585199036 0.084852979 2777.135566 1272231.128 0.074805409 0.018701352 8.932779724 -0.950986625 -0.314803153 SCVEEPEPEPEAAEGDGDKKGNAEGS(ph)S(ph)DEEGKLVIDEPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SCVEEPEPEPEAAEGDGDKKGNAEGSSDEEGKLVIDEPAK 40 3 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 2 SCVEEPEPEPEAAEGDGDKKGNAEGS(1)S(1)DEEGKLVIDEPAK 92.967 0.00011511 389290000 571820 122340 212070 226010 270390 144440 333780 151010 502020 TRUE FALSE 536030.8069 131398.1809 217100.4005 231809.7992 249154.6601 186137.4832 283732.7877 169863.9309 418229.6188 1.281666297 0.314177129 0.519093796 0.554264425 0.595736526 0.4450605 0.678413902 0.406149931 1 18.67393571 -1.272245417 3.720072473 1.000799584 0.566586855 0.17523462 0.264852237 13508556.78 9240258.142 85219.22181 0.054740573 0.053426237 1.272245417 -0.434212729 SCVEEPEPEPEAAEGDGDKKGNAEGS(ph)SDEEGKLVIDEPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SCVEEPEPEPEAAEGDGDKKGNAEGSSDEEGKLVIDEPAK 40 3 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 SCVEEPEPEPEAAEGDGDKKGNAEGS(0.5)S(0.5)DEEGKLVIDEPAK 86.959 0.00027981 153920000 300130 75140 128750 143480 175900 86150 213110 93667 267180 TRUE FALSE 281345.399 80703.44378 131804.0108 147161.9397 162085.5235 111020.1065 181156.1339 105361.5311 222585.932 1.263985538 0.362572078 0.592148882 0.661146634 0.728193027 0.498774139 0.813870546 0.473352158 1 17.76400289 -1.59863889 3.052225199 1.021135581 0.644957475 0.136704929 0.2477153 171026665.6 178987136.4 28910789.34 0.054801635 0.025197712 1.59863889 -0.376178106 SCYDLSCHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SCYDLSCHAR 10 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;;;;; 225.91 3.28E-09 4670890000 2163090 3993100 2881340 3075260 3835750 2385980 2941260 3380370 3206010 FALSE TRUE 2027706.058 4288753.279 2949686.745 3154176.378 3534505.668 3074773.693 2500245.368 3802416.636 2670906.219 0.759182798 1.605729639 1.104376756 1.180938647 1.323335744 1.151209904 0.936103765 1.423642885 1 21.34889789 2.00842768 22.71027145 1.095526206 1.23777066 0 0.243809277 171.2664076 461509.5344 0.084531528 0.062282545 101.9594959 -2.00842768 0.142244454 SCYLSSLDLLLEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SCYLSSLDLLLEHR 14 0 Q9BQ69 Q9BQ69 MACROD1 O-acetyl-ADP-ribose deacetylase MACROD1 0 ; 196.84 2.43E-08 540230000 763520 1023130 851540 864850 1113020 718650 927040 901000 1093520 FALSE TRUE 715732.6461 1098883.61 871738.9309 887043.5152 1025607.899 926112.5887 788038.9582 1013491.833 911004.4476 0.785652197 1.20623298 0.956898655 0.973698337 1.125799003 1.016584048 0.865022076 1.112499325 1 19.79709857 1.978887572 24.47532157 0.968332957 1.03126333 0 0.125246386 1926.879423 2233797.241 0.047178094 0.030817712 95.25495417 -1.978887572 0.062930373 SDAEEDGGTVS(ph)QEEEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDAEEDGGTVSQEEEDR 17 0 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 SDAEEDGGT(0.001)VS(0.999)QEEEDR 180.08 9.23E-10 115870000 159050 148410 156940 163430 172050 201430 224230 202900 121780 TRUE FALSE 149095.3444 159398.4308 160662.6909 167623.8905 158537.887 259579.5711 190608.7931 228232.5116 101454.1313 1.469583767 1.571137901 1.583599297 1.652213551 1.562655803 2.558590447 1.878768176 2.249612793 1 16.63046809 SDAEEDGGTVS(ph)QEEEDRKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDAEEDGGTVSQEEEDRKPK 20 2 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 SDAEEDGGTVS(1)QEEEDRKPK;SDAEEDGGTVS(1)QEEEDRKPK 228.31 1.64E-25 1296720000 1710630 596180 775930 688900 906490 618720 1314260 843800 1098900 TRUE FALSE 1603564.722 640321.7875 794335.426 706578.3403 835297.932 797334.4199 1117198.914 949150.2874 915486.4908 1.751598454 0.699433355 0.867664825 0.771806408 0.912408802 0.870940672 1.220333588 1.036771484 1 19.80417907 1.751505786 25 1.103731674 0.923348466 0.004063975 0.297005029 10.56264357 20430.13037 0.126999018 0.070427205 56.42944592 -1.751505786 -0.180383209 SDAGLES(ph)DTAMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDAGLESDTAMK 12 0 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 SDAGLES(1)DTAMK;SDAGLES(0.995)DT(0.005)AMK 282.12 4.23E-28 416780000 1425830 949530 1081060 1058740 1105230 758590 1343890 806250 1058480 TRUE FALSE 1336589.845 1019834.189 1106703.254 1085909.061 1018429.694 977582.6183 1142386.171 906912.0873 881812.85 1.515729608 1.156519991 1.255031897 1.231450711 1.154927255 1.108605549 1.295497305 1.028463225 1 19.75011297 8 0.094685989 0.90478971 2.13527943 0.519302661 0.101845186 137.0871452 0.926272246 1.474628977 21.90425776 100000000 -8 1.23048972 SDALETLGFLNHYQMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SDALETLGFLNHYQMK 16 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0;M0R076 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;; 270.21 9.37E-29 2388400000 2897840 3060650 2895890 2796740 3580960 2184110 3288520 3063030 3686210 FALSE TRUE 2716469.367 3287263.711 2964581.878 2868509.083 3299725.846 2814627.101 2795436.955 3445456.038 3070957.737 0.884567487 1.070435998 0.965360689 0.934076379 1.07449406 0.916530718 0.910281806 1.121948373 1 21.55025723 1.238029463 24.99999513 1.060974166 0.972606899 0.241336507 0.069685209 21.54020704 1013386.532 0.052685392 0.016209455 17.29933715 -1.238029463 -0.088367267 SDAPDSTGDQPGLHQDNSSNGKSEWLDPS(ph)QKSPLHVGETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDAPDSTGDQPGLHQDNSSNGKSEWLDPSQKSPLHVGETR 40 2 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 SDAPDSTGDQPGLHQDNS(0.004)S(0.004)NGKS(0.02)EWLDPS(0.529)QKS(0.441)PLHVGET(0.001)R 105.68 5.32E-06 107530000 93758 69560 66425 80324 112150 48665 98475 73615 205600 TRUE FALSE 87889.85414 74710.29478 68000.63237 82385.24983 103342.1914 62713.79549 83709.58795 82805.9948 171284.0318 0.513123455 0.436177815 0.39700509 0.480986167 0.603338153 0.366139183 0.488717991 0.483442583 1 17.38603113 -4.796767715 0.435441744 9.999999438 0.454854805 0.866852805 0.065067307 296.6500798 2.193414996 2550.996461 0.034544105 1.60E-05 4.796767715 -9.545144633 SDATADDLIDVVEGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDATADDLIDVVEGNR 16 0 Q9Y295 Q9Y295 DRG1 Developmentally-regulated GTP-binding protein 1 0 96.64 0.0077801 25649000 18221 19328 20264 20826 22128 16634 24895 16300 19292 FALSE TRUE 17080.58014 20759.06523 20744.67165 21360.43042 20390.15614 21435.96577 21162.22586 18335.09088 16072.04057 1.062751183 1.291625985 1.290730418 1.329042839 1.268672516 1.333742637 1.31671058 1.140806658 1 13.97226549 1.007154846 3.83635971 1.000932924 1.280628431 0.565348742 0.077931762 0.123444177 4.715399145 0.069019323 0.017738124 10.16611096 -1.007154846 0.279695506 SDDNRESLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDDNRESLEK 10 1 P30085;P30085-3;A0A494BXC7;P30085-2 P30085 CMPK1 UMP-CMP kinase 0 ; 126.71 0.00034237 670240000 575580 611130 568190 601750 769140 440400 662250 510320 1411550 FALSE TRUE 539555.4752 656378.7011 581667.7351 617191.9238 708734.847 567536.3307 562951.7605 574034.5754 1175953.186 0.458823941 0.558167373 0.494635111 0.524843957 0.602689678 0.482618133 0.478719533 0.488144071 1 20.1653992 -1.799048201 2.635402883 1.143816095 0.513127568 0.929079887 0.042448661 6093164.821 4413585.903 5611074.428 0.010478119 0.015883704 1.799048201 -0.630688527 SDDNSYDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDDNSYDEK 9 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 151.83 0.00019061 173480000 412040 324030 351390 320670 370530 255700 408440 337850 395290 FALSE TRUE 386251.1519 348021.5184 359725.1367 328898.9351 341430.0684 329516.4391 347198.2138 380031.3162 329313.5453 1.172897858 1.056808999 1.092348438 0.998740986 1.036793273 1.000616111 1.054308937 1.154010582 1 18.32910233 7.975626152 1.039809568 1.046973863 153.9431975 0.387337071 0.048118066 1738.450329 2.104475448 0.013043253 633834.1612 94542297.54 -7.975626152 152.8962236 SDEAVKPFGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SDEAVKPFGLK 11 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 156.71 2.82E-05 22099020000 45091400 32980000 41583600 39869700 44835900 31066900 59007200 40106900 55223600 FALSE TRUE 42269209.76 35421873.52 42569982.63 40892824 41314669.27 40035409.7 50159618.16 45114334.75 46006424.4 0.918767549 0.769933199 0.925305176 0.888850297 0.898019566 0.870213459 1.090274213 0.980609455 1 25.455332 1.752576904 25 1.02832298 0.872532732 0.642406101 0.050867151 2.51470904 4491.604311 0.022671864 0.012572846 56.56879195 -1.752576904 -0.155790248 SDEDDWSKPLPPSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDEDDWSKPLPPSER 15 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y650;A0A2R8YCU0;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 0 ; 144.97 3.78E-06 244839000 428690 307150 359410 317910 317610 328500 446590 328060 337890 FALSE TRUE 401859.0581 329891.7056 367935.3749 326068.1088 292666.1918 423332.6172 379627.9754 369019.0131 281493.9761 1.427593811 1.17193167 1.307080812 1.158348442 1.039689004 1.503878069 1.34861847 1.310930409 1 18.10274452 2.235569495 24.9999997 1.329554666 1.223150793 0.020744083 0.159522715 184.895473 1545344.282 0.053033258 0.040848658 172.0162577 -2.235569495 -0.106403873 SDEDYLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDEDYLYR 8 0 E7EMD0;P16435;H0Y4R2 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 ; 147.34 0.0012538 630380000 1647340 1495850 1420730 1322870 1615340 1415020 1773070 1709900 1420600 FALSE TRUE 1544235.93 1606604.29 1454430.387 1356817.084 1488477.712 1823513.303 1507214.614 1923384.779 1183492.683 1.304812402 1.357510962 1.228930612 1.146451604 1.257699126 1.540789673 1.273530995 1.625176739 1 20.17461936 SDEDYLYREELAQFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDEDYLYREELAQFHR 16 1 E7EMD0;P16435;H0Y4R2 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 169.09 3.45E-09 40219000 30840 49526 39643 40292 73023 26842 41625 43225 100820 FALSE TRUE 28909.77945 53192.95657 40583.35068 41325.96093 67288.06814 34590.84966 35383.71768 48621.7364 83992.49068 0.344194811 0.633306098 0.483178322 0.49201971 0.801120048 0.411832646 0.421272395 0.578881945 1 16.35797273 0.962141364 22.41538749 1.000000002 0.519211077 0.586782201 0.127488944 1197.132958 708801.489 0.115584265 0.028896066 9.165187704 -0.962141364 -0.480788924 SDEGHPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDEGHPFR 8 0 Q9NQC3-5;Q9NQC3;Q9NQC3-4;Q9NQC3-2;F8W914;A0A0U1RQR6;H7C106;Q9NQC3-3;Q9NQC3-6 Q9NQC3-5;Q9NQC3-2 RTN4 Reticulon-4;Reticulon 0 ; 117.4 0.0020865 748050000 1930710 2053350 1967850 1996370 2205770 1903800 2362420 2067110 2152130 FALSE TRUE 1809870.308 2205382.171 2014528.331 2047600.234 2032537.722 2453396.154 2008197.053 2325193.234 1792925.6 1.009450871 1.230046674 1.123598398 1.142044173 1.133643093 1.368375885 1.120067142 1.29687101 1 20.77388419 SDEGQLS(ph)PATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SDEGQLSPATR 11 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 SDEGQLS(1)PATR;SDEGQLS(0.997)PAT(0.003)R;SDEGQLS(1)PATR;SDEGQLS(1)PATR 181.9 6.32E-06 1904190000 2187040 2443230 2202290 2234690 2427540 1904270 2497690 2035120 2418080 TRUE FALSE 2050157.07 2624129.291 2254529.359 2292035.929 2236890.801 2454001.836 2123184.572 2289209.212 2014486.827 1.017706864 1.302629164 1.119158154 1.137776578 1.110402298 1.218177157 1.053958032 1.136373384 1 20.94198094 0.575439878 0.370327124 0.981667449 1.177818016 0.209359722 0.080007176 2.934309117 0.85221609 0.180425063 0.064938357 3.762182668 -0.575439878 0.196150567 SDEHVDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDEHVDVR 8 0 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 0 76.827 0.03114 0 107420 136300 124650 122670 143350 101620 136590 125850 167370 FALSE TRUE 100696.774 146391.7938 127606.7569 125817.9199 132091.8692 130956.0443 116109.5975 141562.6495 139434.8657 0.722177867 1.049893748 0.915171081 0.902341887 0.947337443 0.939191526 0.832715669 1.015260055 1 17.08923183 1.196512615 24.97653144 1.007630491 0.916538136 0.198749937 0.084569149 291.231793 172985.3009 0.075577311 0.018894936 15.72217459 -1.196512615 -0.091092356 SDES(ph)GEEKNGDEDCQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDESGEEKNGDEDCQR 16 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 1 SDES(1)GEEKNGDEDCQR;SDES(1)GEEKNGDEDCQR 217.17 8.78E-15 307290000 604890 327370 417510 413450 445350 321460 583750 344070 513510 TRUE FALSE 567031.0147 351608.8154 427413.5344 424059.827 410374.0075 414260.2835 496222.1068 387027.8969 427801.8636 1.325452418 0.821896409 0.999092268 0.991252874 0.959261851 0.968346141 1.159934421 0.9046896 1 18.70658324 SDES(ph)PKPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SDESPKPGK 9 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 SDES(1)PKPGK;S(0.001)DES(0.999)PKPGK;SDES(1)PKPGK;SDES(1)PKPGK;SDES(1)PKPGK;SDES(1)PKPGK 112.13 0.0021867 4082068000 13899590 5254312 8165900 6955280 7122300 5166678 10798240 5914866 9756420 TRUE FALSE 13029639.47 5643346.728 8359599.004 7133764.26 6562943.288 6658214.065 9179144.158 6653350.04 8128010.473 1.603053972 0.694308496 1.028492647 0.877676559 0.807447691 0.819168982 1.129322383 0.818570555 1 22.95447083 4.749394028 24.81441641 0.904007076 1.603054415 0.754676097 0.12647606 723.415142 1656979.519 0.029541279 0.437697352 56155.72365 -4.749394028 0.699047339 SDESDQQESLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDESDQQESLHK 12 0 P49770;G3V5E5;H0YJJ8 P49770 EIF2B2 Translation initiation factor eIF-2B subunit beta 0 143.76 0.00032381 0 220060 215820 203770 227920 247250 165750 273330 218080 311410 FALSE TRUE 206286.8374 231799.5374 208603.5206 233768.8131 227831.9824 213599.3343 232346.704 245307.7681 259433.6592 0.79514292 0.893482897 0.804072691 0.901073568 0.878189758 0.823329305 0.895591978 0.945551047 1 17.98500614 1.187626331 1.775441671 0.998187766 0.85196623 0.676135534 0.035850443 0.181575615 1.049840232 0.030468834 0.008921797 15.40374538 -1.187626331 -0.146221536 SDESPKPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDESPKPGK 9 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 0 94.692 0.0077978 74680000 139290 115600 144000 193260 214730 149420 255730 179090 294360 FALSE TRUE 130572.0875 124159.1443 147415.748 198219.3788 197865.972 192555.1284 217385.6606 201449.7807 245229.4144 0.532448719 0.506297928 0.601134038 0.808301807 0.80686068 0.785204046 0.886458344 0.821474786 1 17.90377251 3.376525011 0.388245972 0.957357033 0.372562822 0.887471428 0.052801241 0.626585568 0.153996046 0.051656125 0.155386207 2379.715343 -3.376525011 -0.584794211 SDFFELLSNHHLDSQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDFFELLSNHHLDSQSR 17 0 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 146.58 2.50E-07 238350000 156760 259420 243820 240010 251410 204820 261500 238080 233470 FALSE TRUE 146948.6714 278627.7267 249603.5255 246169.0629 231665.2727 263948.209 222290.5026 267804.8121 194502.3487 0.755511038 1.432516001 1.283293118 1.265635426 1.191066711 1.357043813 1.142867961 1.376871867 1 17.56942805 -0.775064876 5.614460365 0.999999992 1.247535636 0.114288247 0.188790332 6.71E-08 1.49E-08 0.160881053 0.037920023 0.167855325 0.775064876 0.247535645 SDGSLEDGDDVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDGSLEDGDDVHR 13 0 Q9NRX5 Q9NRX5 SERINC1 Serine incorporator 1 0 ; 136.3 1.12E-05 155080000 217810 386970 342990 334260 362010 330060 364930 317680 338460 FALSE TRUE 204177.6609 415621.6614 351125.8848 342837.6775 333579.1949 425342.9639 310212.1343 357343.0473 281968.8395 0.724114272 1.473998553 1.245264851 1.215870797 1.18303567 1.508475067 1.100164596 1.267313963 1 18.10517621 -1.370032003 7.786964266 0.999996996 1.242348169 0.077088827 0.215540352 9.94E-06 8.04E-07 0.184033672 0.043376614 0.042654809 1.370032003 0.242351172 SDGTETSTNLHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDGTETSTNLHQK 13 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ; 203.82 8.28E-08 639340000 407690 444910 454720 437070 469490 364060 570980 412850 532790 FALSE TRUE 382173.4106 477851.5993 465506.1731 448285.9562 432618.1492 469158.212 485366.8497 464395.2313 443863.907 0.861014839 1.076572327 1.048758788 1.009962624 0.974663951 1.056986623 1.093503756 1.046255899 1 18.75975787 2.09861322 10.11119791 1.061522755 1.013621687 0.107992811 0.062413349 0.709508765 66.80978539 0.022595213 0.01668437 125.4911849 -2.09861322 -0.047901068 SDHPGISITDLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SDHPGISITDLSK 13 0 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 0 ;;; 154.47 4.19E-05 1035150000 2271530 2546820 2729850 2596970 2895700 2201410 3331690 2585580 3097490 FALSE TRUE 2129358.992 2735389.203 2794603.331 2663612.647 2668283.403 2836921.33 2832134.014 2908395.355 2580498.908 0.825173374 1.060023391 1.082970166 1.032208399 1.034018419 1.09936932 1.09751413 1.127067074 1 21.29921859 4.739333923 4.887247088 1.072206484 0.812007224 0.801939406 0.037677512 0.071177959 5.087734657 0.008628191 0.062998401 54869.86895 -4.739333923 -0.260199259 SDHTLTS(ph)PGGGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SDHTLTSPGGGGK 13 0 C9J0Q5;Q9Y618;Q9Y618-4 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 SDHTLT(0.066)S(0.934)PGGGGK;SDHTLT(0.059)S(0.941)PGGGGK;SDHTLT(0.044)S(0.955)PGGGGK 156.17 2.70E-05 903260000 1426710 1583810 1695860 1623090 1714770 1455100 2275900 1621780 1519000 TRUE FALSE 1337414.768 1701076.94 1736086.6 1664741.237 1580098.881 1875163.748 1934649.923 1824262.803 1265469.087 1.056852974 1.344226388 1.37189175 1.31551316 1.248627009 1.481793406 1.528800619 1.44157042 1 20.27124083 2.242164814 24.99642651 1.422813687 1.294327334 0.009129299 0.170382798 192.1879473 1332901.995 0.055141658 0.044457155 174.6484816 -2.242164814 -0.128486353 SDIYVCMISFAHNVAAQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDIYVCMISFAHNVAAQGK 19 0 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 290.16 1.61E-49 552230000 987340 1004020 1036640 1122240 1275410 995700 1169350 1109820 1087540 FALSE TRUE 925544.1519 1078358.685 1061229.59 1151038.578 1175244.443 1283142.426 994016.8232 1248383.47 906022.5482 1.021546488 1.190211753 1.171305938 1.270430389 1.297147014 1.416236747 1.097121507 1.377872408 1 19.78918743 5.854704249 0.799196355 1.243874519 4.03E-11 0.216162641 0.123789839 18.23552605 2.289432958 0.037452312 30.44086069 715655.8883 -5.854704249 -1.243874519 SDKGS(ph)PGEDGFVPSALGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDKGSPGEDGFVPSALGTR 19 1 G3V238;A0A494BZY7;Q5JPI9 G3V238 METTL10 Protein-lysine N-methyltransferase METTL10 1 S(0.01)DKGS(0.99)PGEDGFVPSALGTR;S(0.074)DKGS(0.926)PGEDGFVPSALGTR 81.839 0.0032146 375750000 311450 258655 301380 292770 257440 189322 316530 204894 257971 TRUE FALSE 291956.9005 277806.0853 308528.8759 300282.9739 237221.7009 243976.188 269069.265 230475.4669 214913.9735 1.358482632 1.292638542 1.435592441 1.397224056 1.103798403 1.135227198 1.251985902 1.072408011 1 17.71339976 2.73975344 24.99981614 1.140170223 1.368694782 0.745694657 0.073987658 59.57346586 1248584.228 0.02281115 0.022983568 549.2289743 -2.73975344 0.228524559 SDKLHELEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDKLHELEK 9 1 Q3V6T2;A0A2U3TZV9;A0A2R8Y4X4;A0A2R8YG73;A0A2R8Y7B1;A0A2R8Y4W8;Q3V6T2-5;Q3V6T2-4;Q3V6T2-2;Q3V6T2-3;A0A2R8YGU1;A0A2R8Y7D9;A0A2R8Y6B2;A0A087WXD9;A0A2R8YG52 Q3V6T2 CCDC88A Girdin 0 ; 66.435 0.05813 197159000 175720 884760 602710 632220 910730 544850 524420 629930 900240 FALSE TRUE 164721.9989 950268.551 617006.5658 648443.8355 839204.9395 702139.3501 445788.0895 708578.1471 749984.1282 0.21963398 1.267051548 0.822692831 0.864610078 1.118963599 0.936205612 0.594396698 0.944790857 1 19.51650054 1.005423098 24.97954319 1.000000225 0.869369453 0.029981146 0.283800188 525.6284844 2421101.078 0.252353461 0.063088365 10.12565434 -1.005423098 -0.130630773 SDKNNEFIVIHNGIITNYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDKNNEFIVIHNGIITNYK 19 1 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 208.17 1.70E-16 799200000 1278550 986700 1158200 1190510 1129840 883580 1563660 1012690 1273680 FALSE TRUE 1198527.838 1059756.295 1185673.051 1221060.502 1041106.924 1138655.202 1329203.699 1139126.576 1061094.58 1.129520272 0.998738769 1.117405624 1.150755574 0.981163172 1.073094919 1.252672217 1.073539152 1 20.01712182 1.944275521 24.9997181 1.143329792 1.070257923 0 0.083425013 548.0270114 245860.4352 0.031783122 0.020515591 87.95803543 -1.944275521 -0.073071869 SDKQYAENYTRPSS(ph)R ddPTM_SK-BR-3_Pertuzumab_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 SDKQYAENYTRPS(0.055)S(0.945)R;SDKQYAENYTRPS(0.043)S(0.957)R 140.95 3.82E-06 467690000 293560 279990 269140 273090 363920 228144 379040 280190 545580 TRUE FALSE 275186.6036 300720.7509 275524.1279 280097.9517 335339.1912 294005.4692 322206.4708 315172.3383 454519.1734 0.605445534 0.661623906 0.60618813 0.616251125 0.737788878 0.646849432 0.708895223 0.693419237 1 18.79398163 -5 0.209292731 2.662245162 0.607331231 0.907953062 0.035111712 37.48509356 0.373661586 26.06284733 0.069680274 1.00E-05 5 -2.054913931 SDKS(ph)PDLAPTPAPQSTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SDKSPDLAPTPAPQSTPR 18 1 F8WAE5;Q9BY44-4;Q9BY44-3;Q9BY44;Q9BY44-2 F8WAE5 EIF2A "Eukaryotic translation initiation factor 2A;Eukaryotic translation initiation factor 2A, N-terminally processed" 1 SDKS(1)PDLAPTPAPQSTPR;SDKS(1)PDLAPTPAPQSTPR;SDKS(1)PDLAPTPAPQSTPR;SDKS(1)PDLAPTPAPQSTPR;SDKS(1)PDLAPTPAPQSTPR;SDKS(1)PDLAPTPAPQSTPR;S(0.006)DKS(0.994)PDLAPTPAPQSTPR;SDKS(1)PDLAPTPAPQSTPR 267.18 1.86E-31 21432870000 19583310 11063760 14209510 13488750 14017140 10373200 18099210 11318470 17967130 TRUE FALSE 18357625.58 11882932.3 14546566.29 13834894.16 12916290.37 13367774.45 15385401.49 12731605.89 14968299.93 1.226433574 0.793873209 0.97182488 0.924279593 0.862909644 0.893072327 1.02786566 0.850571271 1 23.83540704 -0.316118158 8.70356404 1 0.934612406 0.016149798 0.11976115 0 0 0.102010903 0.0240442 0.482927395 0.316118158 -0.065387594 SDKTEEIAEEEETVFPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SDKTEEIAEEEETVFPK 17 1 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;;; 236.16 3.21E-20 838060000 3670320 1949500 2712090 2411330 2484340 1874990 3439000 1971280 3293250 FALSE TRUE 3440601.223 2093843.008 2776422.056 2473208.81 2289229.958 2416269.175 2923353.876 2217398.647 2743585.3 1.254052944 0.76317766 1.011968557 0.9014514 0.834393579 0.880697668 1.065523232 0.808212031 1 21.387631 -0.578575226 7.276440768 1 0.933460262 0.015310377 0.143251837 0 0 0.122187279 0.028799818 0.263891119 0.578575226 -0.066539738 SDKVPENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDKVPENK 8 1 Q9UBF2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 58.978 0.092598 99644000 191390 160170 195870 225350 246970 165300 311400 216790 357410 FALSE TRUE 179411.2415 172029.1535 200516.1289 231132.8625 227573.9724 213019.4266 264708.4609 243856.7087 297755.962 0.602544582 0.577752171 0.673424396 0.776249318 0.764296946 0.715416159 0.889011454 0.818981783 1 18.18377087 3.272689271 0.173796982 1.079675848 0.314792938 0.885559465 0.043004097 2.822167943 0.164657537 0.171410351 0.54771269 1873.653466 -3.272689271 -0.764882909 SDLDYIRS(ph)PLPFQNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDLDYIRSPLPFQNR 15 1 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;H7BYL6 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 1 SDLDYIRS(1)PLPFQNR;SDLDYIRS(1)PLPFQNR 128.38 4.38E-05 339310000 302270 346450 342600 411050 461190 275660 351550 314920 386830 TRUE FALSE 283351.4603 372101.5185 350726.6338 421598.2389 424969.9978 355238.567 298838.3411 354238.4552 322265.574 0.879248307 1.15464247 1.088315545 1.308232318 1.31869499 1.102316213 0.927304575 1.099212835 1 18.29789056 1.98885366 24.64679338 1.004273975 1.154396596 0.203092648 0.127230622 664.0725788 1468397.996 0.049473109 0.034078788 97.46611614 -1.98885366 0.150122621 SDLPGSDKDTEDGSAWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDLPGSDKDTEDGSAWK 17 1 H3BN50;Q15599-3;H3BQS0;Q15599 H3BN50;Q15599 SLC9A3R2 Na(+)/H(+) exchange regulatory cofactor NHE-RF2 0 161.91 2.65E-09 241560000 719820 372750 493420 462940 517410 348800 589680 429850 494040 FALSE TRUE 674767.7511 400348.7978 505124.1554 474819.8242 476774.7057 449492.8977 501262.9583 483517.7187 411581.5324 1.639450991 0.972708361 1.227276045 1.153647058 1.158396741 1.092111434 1.217894679 1.174779918 1 18.65081872 4.750229646 24.97415629 1.135665743 1.639451295 0.784691985 0.084578231 800.357486 1712899.929 0.018980136 0.310037778 56263.87583 -4.750229646 0.503785552 SDLYSSGR ddPTM_SK-BR-3_Pertuzumab_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 ; 219.74 1.47E-05 1116490000 418250 481820 415600 444570 490290 374900 479150 422920 548720 FALSE TRUE 392072.4791 517494.4541 425458.2283 455978.4189 451784.6011 483127.544 407305.9057 475722.493 457135.0871 0.857673126 1.13203836 0.930705693 0.997469745 0.988295613 1.056859466 0.890996813 1.040660641 1 18.80226103 3.821589812 22.49897365 0.981251216 1.019529822 0 0.081286009 45.71507396 10871.07366 0.018796033 0.033885016 6631.164657 -3.821589812 0.038278606 SDNKDDDIDIDAI ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDNKDDDIDIDAI 13 1 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 140.09 0.00031959 180470000 1562400 968090 1224700 1173400 1257300 849790 1609500 994470 1418100 FALSE TRUE 1464612.173 1039768.391 1253750.462 1203511.431 1158556.73 1095110.578 1368170.417 1118631.769 1181409.949 1.239715456 0.880108037 1.061232355 1.018707716 0.980655979 0.926952223 1.158082695 0.946861646 1 20.17207824 SDNSDIRPSGS(ph)PPPPTLPASPSNHVSSLPPFIAPPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDNSDIRPSGSPPPPTLPASPSNHVSSLPPFIAPPGR 37 1 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 S(0.009)DNS(0.203)DIRPS(0.167)GS(0.612)PPPPT(0.007)LPAS(0.001)PSNHVSSLPPFIAPPGR;SDNS(0.003)DIRPS(0.198)GS(0.798)PPPPT(0.001)LPASPSNHVSSLPPFIAPPGR 176.95 3.65E-23 263230000 33356 118003 89847 92459 81724 77872 98874 76069 67585 TRUE FALSE 31268.3075 126740.0649 91978.21327 94831.65447 75305.7267 100352.3823 84048.7616 85566.3821 56304.62688 0.555341705 2.250970691 1.633581792 1.684260419 1.337469598 1.782311469 1.49275053 1.519704274 1 15.78096586 0.160488638 0.640711096 0.974037793 1.641081711 0.10014355 0.431021886 5.769388711 3.013281208 0.746979279 0.153673891 1.447066995 -0.160488638 0.667043917 SDPDGGDS(ph)PLPASGGPLTCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDPDGGDSPLPASGGPLTCK 20 0 Q8N1G0 Q8N1G0 ZNF687 Zinc finger protein 687 1 SDPDGGDS(1)PLPASGGPLTCK;SDPDGGDS(1)PLPASGGPLTCK 266.39 1.02E-36 175804000 305730 223170 242200 220540 267930 211320 331840 256730 353050 TRUE FALSE 286594.905 239693.739 247945.0984 226199.4298 246887.8586 272324.6535 282083.6727 288783.3056 294123.6742 0.974402709 0.814942013 0.84299606 0.769062301 0.839401518 0.925884848 0.959064834 0.981843119 1 18.16606339 2.010633872 2.200882754 0.978767368 0.839057002 0.568475962 0.052592289 0.215749837 1.959108819 0.027466278 0.01483155 102.4787624 -2.010633872 -0.139710367 SDPES(ph)PIKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SDPESPIKK 9 1 Q8NDI1-3;Q8NDI1-2;Q8NDI1;H7C0Q4 Q8NDI1-3 EHBP1 EH domain-binding protein 1 1 SDPES(1)PIKK;S(0.002)DPES(0.998)PIKK;SDPES(1)PIKK;S(0.015)DPES(0.985)PIKK 107.85 0.0016582 1786960000 6117600 3175900 4566940 4979900 4947680 2659950 4961140 3020680 4371400 TRUE FALSE 5734710.336 3411046.941 4675269.973 5107692.665 4559109.171 3427834.384 4217263.114 3397818.547 3641785.1 1.574697622 0.936641468 1.283785244 1.402524456 1.251888578 0.941251142 1.15802086 0.933009075 1 21.79621436 2.253494585 24.87389928 1.033037222 1.246018991 0.382989107 0.171542514 298.170194 496629.2381 0.058438431 0.048704875 179.2646199 -2.253494585 0.212981769 SDPFLEFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDPFLEFFR 9 0 Q99829;B0QZ18;F2Z2V0;A6PVH9;E7ENH5;Q5JX45;Q5JX60;Q5JX52;Q5JX44;Q5JX61;Q5JX59;Q5JX58;Q5JX56 Q99829 CPNE1 Copine-1 0 75.213 0.058258 0 9708 34059 10474 8823.9 37810 7045.5 7574.7 29601 22248 FALSE TRUE 9100.393609 36580.7638 10722.44823 9050.336213 34840.55512 9079.421476 6438.944055 33296.75001 18534.66507 0.490993151 1.973640401 0.578507795 0.488292407 1.879750995 0.489861643 0.347400076 1.796458144 1 14.17793842 3.8512452 7.977805345 0.874240886 1.328128973 0.022438165 0.637428773 0.608237057 38.00458165 0.153039277 0.276976979 7099.785047 -3.8512452 0.453888087 SDPMVQCIIEESGEHIIAGAGELHLEICLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 SDPMVQCIIEESGEHIIAGAGELHLEICLK 30 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;;;;;; 365.18 8.87E-137 2958042000 2757931.2 2634482.3 2930619 2954241.2 3105928.6 2903619 3970690.4 2520389 3325593.8 FALSE TRUE 2585317.209 2829542.111 3000134.667 3030052.031 2862001.496 3741846.669 3375322.237 2835065.115 2770530.711 0.933148728 1.021299674 1.082873637 1.09367206 1.033015619 1.350588411 1.218294467 1.023293156 1 21.40173093 3.997084134 0.715401083 1.159811051 0.921411339 0.216144181 0.10608991 1.663914553 1.222021428 0.047742135 0.276221724 9933.0846 -3.997084134 -0.238399713 SDPPQEAAQFTSQVIILNHPGQISAGYSPVIDCHTAHIACK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDPPQEAAQFTSQVIILNHPGQISAGYSPVIDCHTAHIACK 41 0 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 392.4 1.03E-194 336020000 231490 255130 257170 255350 276030 170270 313670 230240 313090 FALSE TRUE 217001.4541 274020.0907 263270.1938 261902.7133 254351.7173 219424.1849 266638.0955 258985.9708 260833.2564 0.831954702 1.050556568 1.009342894 1.004100156 0.975150641 0.84124313 1.022254981 0.992917753 1 17.9927683 SDPVVSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDPVVSYR 8 0 P13639 P13639 EEF2 Elongation factor 2 0 147.34 0.0012538 761210000 720400 912790 860790 833780 889080 654590 895590 786400 979810 FALSE TRUE 675311.45 980373.9214 881208.3453 855176.2064 819255.2432 843559.5066 761304.5938 884583.7711 816273.3812 0.827310391 1.201036251 1.07955051 1.047659064 1.003653019 1.03342768 0.932658851 1.083685676 1 19.63869289 2.893530333 2.54059928 1.001478077 1.077172484 0 0.100175741 0.658183016 8.325025934 0.031231728 0.034193363 782.5828629 -2.893530333 0.075694407 SDPYLEFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SDPYLEFHK 9 0 O75131;A0A087WYQ3 O75131 CPNE3 Copine-3 0 ;; 136.63 0.00018722 1201150000 2127210 2990620 1670540 1426550 4542640 1177650 1827350 3269540 5366160 FALSE TRUE 1994071.723 3212048.617 1710165.998 1463157.688 4185879.379 1517618.437 1553355.832 3677749.266 4470513.229 0.446049843 0.718496614 0.382543549 0.327290764 0.936330834 0.339472978 0.347467003 0.822668244 1 22.09200904 1.055397888 5.168395708 0.997431157 0.504228306 0.45367505 0.192907479 0.151674637 7.922209739 0.177047432 0.044754248 11.36051156 -1.055397888 -0.493202851 SDQDYILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SDQDYILK 8 0 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7;F8VZ69 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;;; 164.57 0.0007662 1062330000 1482430 1337980 1448990 1494620 1578600 1189450 1706830 1339980 1641260 FALSE TRUE 1389647.353 1437045.431 1483360.727 1532974.48 1454623.124 1532824.906 1450906.687 1507279.453 1367323.103 1.016326975 1.050991845 1.084864816 1.121150134 1.063847397 1.121040742 1.061129358 1.102357921 1 20.38292277 4.494530977 0.001098464 1.053694536 1.093349404 0 0.040699443 8820668.551 9577.941272 172932.5755 172822.2774 31227.05135 -4.494530977 0.039654868 SDQWKPLNLEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDQWKPLNLEEK 12 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 207.39 7.21E-08 2037540000 2524770 1579160 1961500 1908270 2168220 1329550 2442030 1839090 2918860 FALSE TRUE 2366749.153 1696082.65 2008027.706 1957239.439 1997936.747 1713369.502 2075870.272 2068704.435 2431683.409 0.973296583 0.697493203 0.825776784 0.804890732 0.821627001 0.704602209 0.853676208 0.850729345 1 21.21352398 0.815414245 1.495119875 0.99900483 0.79662326 0.364664122 0.077003772 0.627520014 2.567001865 0.065051871 0.019023549 6.537538278 -0.815414245 -0.20238157 SDRPELTGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SDRPELTGAK 10 1 H0YL12;P13804-2;P13804;H0YK49;H0YNX6;H0YKF0;H0YLU7 H0YL12 ETFA "Electron transfer flavoprotein subunit alpha, mitochondrial" 0 ;; 81.625 0.01865 365545000 481620 449640 399630 404450 537430 384860 472590 461100 738330 FALSE TRUE 451476.2639 482931.8135 409109.4123 414828.8717 495222.4157 495962.8343 401729.5168 518669.35 615097.9532 0.733990841 0.785129931 0.665112622 0.674411075 0.805111467 0.806315208 0.653114703 0.843230492 1 19.23045665 0.974724018 5.649475845 0.999914327 0.731371672 0.710697447 0.055548889 0.09042456 12.17519394 0.052631876 0.013256264 9.434611417 -0.974724018 -0.268542654 SDS(ph)DAEAQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDSDAEAQGK 10 0 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 1 S(0.007)DS(0.993)DAEAQGK 88.275 0.012908 65362000 159090 109740 134950 125570 104880 80970 134170 88285 110220 TRUE FALSE 149132.8409 117865.2638 138151.0777 128792.3388 96643.14787 104344.7246 114052.4541 99307.57659 91823.56995 1.624123751 1.283605765 1.504527408 1.40260653 1.052487372 1.136361009 1.242082552 1.0815042 1 16.4865769 2.800210442 6.243089407 1.130659096 1.435975765 0.725037167 0.106519287 0.132033767 10.51262468 0.030990253 0.03277785 631.2631556 -2.800210442 0.305316669 SDS(ph)DSSTLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDSDSSTLAK 10 0 Q6AWC2-7;Q6AWC2-3;Q6AWC2-2;Q6AWC2-4;Q6AWC2;Q6AWC2-6 Q6AWC2-7 WWC2 Protein WWC2 1 SDS(0.983)DS(0.017)STLAK 212.27 4.57E-08 502300000 916830 594640 660480 677050 695240 465230 866540 594970 622880 TRUE FALSE 859447.2469 638667.7643 676146.8975 694424.2492 640638.6549 599534.3486 736610.3716 669253.3142 518917.304 1.65623162 1.230769834 1.302995472 1.338217562 1.234567916 1.155356246 1.419513988 1.289710921 1 18.98514512 -4.808710588 0.158141051 4.68E-24 1.399413876 0.4210539 0.129864095 140.6573509 1.360355188 45.22611369 0.548657306 1.55E-05 4.808710588 1.399413876 SDS(ph)DSSTLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDSDSSTLSK 10 0 H0YAU4;H3BLZ3;Q8IX03-2;H0YBE8;Q8IX03 H0YAU4;H0YBE8 WWC1 Protein KIBRA 1 SDS(0.391)DS(0.143)S(0.143)T(0.324)LSK;S(0.001)DS(0.866)DS(0.031)S(0.031)T(0.071)LSK 185.18 0.0022873 0 916740 634130 751500 661640 762400 589920 887270 662960 938080 TRUE FALSE 859362.8798 681081.645 769325.9349 678618.8026 702524.1794 760220.3274 754232.1005 745732.0154 781508.3878 1.099620802 0.87149627 0.984411616 0.868344874 0.89893364 0.972760292 0.965097896 0.954221384 1 19.57590183 SDS(ph)DYDLSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDSDYDLSPK 10 0 Q08499-10;A0A087WSZ7;A0A1B0GW84;Q08499-2;Q08499-9;Q08499-6;Q08499-11;Q08499;A0A1W2PQN6;Q08499-7;Q08499-12 Q08499-10 PDE4D "cAMP-specific 3,5-cyclic phosphodiesterase 4D" 1 SDS(1)DYDLSPK;SDS(1)DYDLSPK 244.71 1.82E-12 917760000 2049780 1359160 1472060 1534940 1401680 922740 1948050 1156050 1332520 TRUE FALSE 1921487.929 1459793.621 1506977.958 1574329.159 1291597.707 1189120.059 1655957.987 1300385.387 1110113.804 1.730892745 1.314994567 1.357498622 1.418169159 1.163482251 1.07116951 1.491701105 1.171398268 1 20.08227615 7.821375575 0.937398021 1.26270418 200 0.486448048 0.154330755 713.2628253 1.901034845 0.044238867 302955.708 66278943.15 -7.821375575 198.7372958 SDS(ph)ENVYEVIQDLHVPPREESAEQVDDPPEPVYANIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDSENVYEVIQDLHVPPREESAEQVDDPPEPVYANIER 38 1 A0A0G2JRG8;A0A0G2JNY3 A0A0G2JRG8 1 S(0.117)DS(0.845)ENVY(0.038)EVIQDLHVPPREESAEQVDDPPEPVYANIER 88.06 0.00036217 14202000 6205.7 5280.9 6512.7 6887.1 9633.8 5965.9 7420.8 6225.3 6994.2 TRUE FALSE 5817.296314 5671.903331 6667.18432 7063.834646 8877.200209 7688.158482 6308.119931 7002.542409 5826.822836 0.998365057 0.973412697 1.144222934 1.212296108 1.523506113 1.319442636 1.082600262 1.201777127 1 12.50849373 3.668770669 2.013485777 1.235804512 0.990457006 0.326047554 0.138129459 0.370557303 2.963951664 0.040542035 0.079073989 4664.130239 -3.668770669 -0.245347506 SDS(ph)FENPVLQQHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SDSFENPVLQQHFR 14 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 1 S(0.003)DS(0.997)FENPVLQQHFR;S(0.003)DS(0.997)FENPVLQQHFR;S(0.008)DS(0.992)FENPVLQQHFR;SDS(1)FENPVLQQHFR;S(0.011)DS(0.989)FENPVLQQHFR;SDS(1)FENPVLQQHFR 268.6 2.06E-25 1450165000 2335440 2165450 1982950 2118830 1038096 1385550 1930710 1040690 1654560 TRUE FALSE 2189268.979 2325782.171 2029986.51 2173202.765 956568.1276 1785535.792 1641217.959 1170622.437 1378403.247 1.588264526 1.687301721 1.472708741 1.576608855 0.693968278 1.295365341 1.190666057 0.849259779 1 20.39456657 2.770987583 23.11310432 1.05597181 1.58081602 0.724143651 0.174947826 141.9278624 101162.0189 0.051177371 0.054275371 590.1842055 -2.770987583 0.52484421 SDS(ph)IKFQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SDSIKFQHR 9 1 Q8TDM6-4;Q8TDM6;Q8TDM6-3;A0A0J9YYG8 Q8TDM6-4 DLG5 Disks large homolog 5 1 S(0.001)DS(0.999)IKFQHR;S(0.032)DS(0.968)IKFQHR;S(0.007)DS(0.993)IKFQHR 101.53 0.0023734 328770000 498780 435090 378515 408708 576890 205306 617120 410453 810540 TRUE FALSE 467562.2501 467304.5163 387493.5545 419196.1392 531583.3865 264574.5093 524588.5851 461698.9606 675255.6377 0.692422579 0.692040896 0.573847196 0.620796208 0.7872328 0.391813847 0.776874054 0.683739513 1 19.36507425 0.59705328 1.247361619 0.999172804 0.63834316 0.500327163 0.110602756 1.09317403 2.455741506 0.093478999 0.028222848 3.954151273 -0.59705328 -0.360829644 SDS(ph)LLSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SDSLLSFR 8 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 S(0.014)DS(0.986)LLSFR;SDS(1)LLSFR;SDS(0.998)LLS(0.002)FR;SDS(1)LLSFR;SDS(0.998)LLS(0.002)FR 218.94 7.02E-06 1088380000 1606740 1632150 1500130 1434610 1709280 953888 1971580 1575690 2190480 TRUE FALSE 1506177.012 1752996.084 1535713.792 1471424.521 1575040.044 1229259.981 1675959.882 1772418.365 1824874.737 0.825359122 0.960611733 0.841544771 0.806315355 0.863094881 0.673613348 0.918397218 0.97125481 1 20.79936601 1.492925146 9.132533929 0.972363588 0.842366881 0.455388833 0.07090293 0.105161071 24.49222615 0.039551556 0.01826679 31.11180055 -1.492925146 -0.129996707 SDS(ph)PEIPFQAAAGPSDGLDAS(ph)SPGNSFVGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 31 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 S(0.312)DS(0.688)PEIPFQAAAGPS(0.001)DGLDAS(0.496)S(0.496)PGNS(0.007)FVGLR 185.44 1.18E-18 24124000 47895 37467 43722 35507 42965 34554 57015 40632 43588 TRUE FALSE 44897.33745 40241.09566 44759.10649 36418.16973 39590.70221 44529.17886 48466.13005 45704.99464 36312.88121 1.236402509 1.108176887 1.232595845 1.002899481 1.090266068 1.226263997 1.33468148 1.258644126 1 15.14819378 2.118375762 6.610753229 1.2458389 1.138340822 0.041232719 0.109860151 0.358100616 19.32796543 0.038544305 0.028370539 131.3335739 -2.118375762 -0.107498078 SDS(ph)PEIPFQAAAGPSDGLDASSPGNSFVGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 31 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 S(0.133)DS(0.867)PEIPFQAAAGPSDGLDASSPGNSFVGLR;S(0.122)DS(0.878)PEIPFQAAAGPSDGLDASSPGNSFVGLR;S(0.135)DS(0.865)PEIPFQAAAGPSDGLDASSPGNSFVGLR;S(0.141)DS(0.859)PEIPFQAAAGPSDGLDASSPGNSFVGLR 206.65 3.73E-26 1163660000 1188170 994450 1067570 1040300 993040 855930 1333900 921250 1043650 TRUE FALSE 1113804.561 1068080.113 1092893.265 1066995.859 915050.6441 1103023.096 1133894.078 1036270.09 869458.0728 1.281033089 1.228443494 1.256982135 1.227196449 1.052437918 1.268632877 1.304138881 1.19185746 1 19.72975693 SDS(ph)PENKYSDSTGHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SDSPENKYSDSTGHSK 16 1 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5;Q9BTA9-3;A0A494C0B7;A0A494C0C1;A0A494C0S5;C9JVK6;C9JD58;J3QTA0;E9PMZ7;C9JMU2 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 S(0.001)DS(0.999)PENKYSDSTGHSK;S(0.004)DS(0.996)PENKYSDSTGHSK;S(0.001)DS(0.999)PENKYSDSTGHSK 258.16 6.47E-27 1121420000 1636040 1268130 1448770 1498590 1845250 1020530 2099670 1357040 3033510 TRUE FALSE 1533643.177 1362023.665 1483135.509 1537046.357 1700331.508 1315140.444 1784843.976 1526469.431 2527197.584 0.606855272 0.538946252 0.586869629 0.608201894 0.672813048 0.520394785 0.706254227 0.604016655 1 21.26910703 -5 0.236377755 3.242013751 0.560279688 0.850115474 0.052423484 53.71464486 0.53675916 57.68817866 0.075547677 1.00E-05 5 -2.681734063 SDS(ph)PVPTAPTSGGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDSPVPTAPTSGGPK 15 0 Q86U44;F5H6D8;B4DTN4;B4E349 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 1 SDS(1)PVPTAPTSGGPK 167.37 1.14E-09 0 154730 87486 112890 98837 101690 87067 159990 111270 127890 TRUE FALSE 145045.7255 93963.55447 115567.8041 101373.3248 93703.6776 112201.8295 136000.9848 125162.3044 106544.3328 1.361364999 0.881919779 1.084692175 0.951466137 0.879480636 1.053099931 1.276473194 1.174743894 1 16.70109433 1.953786984 10.30963351 1.177239473 1.010880476 0.098101953 0.151651177 1.053113097 231.31104 0.057478882 0.036764834 89.90564967 -1.953786984 -0.166358997 SDS(ph)PVPTAPTSGGPKPSTASAVPELATDPELEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDSPVPTAPTSGGPKPSTASAVPELATDPELEKK 34 2 Q86U44;F5H6D8;B4DTN4;B4E349 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 1 S(0.173)DS(0.739)PVPT(0.023)APT(0.023)S(0.021)GGPKPS(0.007)T(0.007)AS(0.007)AVPELATDPELEKK;S(0.003)DS(0.996)PVPTAPTSGGPKPSTASAVPELATDPELEKK 216.7 2.10E-36 408190000 626010 240090 329750 331950 369120 227390 561710 287870 606180 TRUE FALSE 586829.1516 257866.5134 337571.8257 340468.399 340130.8042 293033.8016 477486.8002 323811.2032 505004.6419 1.162027243 0.510622066 0.668452916 0.674188652 0.673520154 0.58025962 0.945509725 0.641204409 1 18.94593712 0.500947306 0.664427768 1.001323718 0.690794285 0.125346591 0.193542875 2.81582698 2.083426246 0.209060362 0.068463909 3.169182917 -0.500947306 -0.310529433 SDS(ph)QASLTVPLSPQVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDSQASLTVPLSPQVVR 17 0 Q8TEV9;Q8TEV9-2 Q8TEV9 SMCR8 Smith-Magenis syndrome chromosomal region candidate gene 8 protein 1 S(0.001)DS(0.999)QASLTVPLSPQVVR 135.27 1.49E-05 31449000 64010 70563 60927 61569 54896 41001 73506 50325 53205 TRUE FALSE 60003.72836 75787.55794 62372.21721 63148.96478 50584.6896 52837.3231 62484.4577 56608.18703 44324.74178 1.353729902 1.709825143 1.407164818 1.424688836 1.1412292 1.192050331 1.409697049 1.277123899 1 15.43582461 3.206229853 1.743087764 1.245821752 1.549795198 0.451700761 0.142247097 0.298599922 1.86428811 0.044410862 0.061800095 1607.791961 -3.206229853 0.303973446 SDS(ph)VSASER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDSVSASER 9 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 SDS(0.962)VS(0.038)ASER;SDS(1)VSASER 220.82 4.64E-07 451400000 611300 591460 598960 533560 548900 415410 749420 463110 852430 TRUE FALSE 573039.8242 635252.3138 613167.614 547252.0529 505791.6082 535332.1234 637051.4283 520930.3029 710153.9261 0.806923405 0.894527638 0.863429169 0.770610473 0.712228138 0.753825479 0.897061052 0.733545621 1 19.43777224 -0.750515842 11.96733556 1 0.817404244 0.457096545 0.065699285 0 0 0.066502122 0.0156747 0.177616848 0.750515842 -0.182595756 SDS(ph)YSQSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SDSYSQSLK 9 0 Q9H8W4 Q9H8W4 PLEKHF2 Pleckstrin homology domain-containing family F member 2 1 SDS(0.999)YS(0.001)QSLK;SDS(0.995)YS(0.004)QSLK;SDS(0.756)YS(0.225)QS(0.019)LK 181.49 4.98E-05 247900000 490770 443957 422151 500194 555790 417662 635770 403213 623690 TRUE FALSE 460053.5817 476828.0382 432164.6211 513029.8249 512140.4953 538234.2392 540442.1907 453555.0306 519592.1098 0.885412948 0.917696842 0.831738229 0.987370314 0.985658723 1.035878392 1.040127786 0.872905924 1 18.98702 3.17767281 8.296540753 0.996092647 0.880214864 0.505201567 0.050182381 0.191731575 23.41935099 0.014065871 0.016874731 1505.472442 -3.17767281 -0.115877783 SDSAFFWEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SDSAFFWEER 10 0 O75116;C9JFJ0;D6REE7;Q13464;A0A0U1RQV4 O75116;Q13464 ROCK2;ROCK1 Rho-associated protein kinase 2;Rho-associated protein kinase 1 0 ;;; 191.45 1.84E-06 334979000 331570 364335 373863 356800 379361 308847 340414 351221 299937 FALSE TRUE 310817.6256 391310.7425 382731.2069 365956.0921 349567.5173 398006.1152 289372.0809 395071.715 249875.577 1.243889576 1.566022367 1.531687136 1.464553264 1.398966323 1.592817193 1.158064683 1.581073747 1 17.93085037 -1.066295515 0.344823758 0.770831026 1.48775128 0.442839862 0.149597526 12.94355932 1.141344046 3.003892567 0.116057643 0.085842921 1.066295515 0.716920254 SDSDYDLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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;SDSDYDLS(1)PK 256.31 3.83E-17 1328890000 5581140 3157420 4332950 3940620 4761770 3072000 4555860 3354300 5065810 TRUE FALSE 5231826.41 3391198.662 4435729.62 4041742.981 4387799.792 3958836.53 3872751.088 3773091.739 4220293.585 1.239683047 0.803545676 1.051047642 0.957692374 1.039690653 0.938047662 0.917649687 0.894035371 1 22.00891193 2.072751517 9.929012361 0.928020344 0.990707998 0.08651206 0.110851608 1.033478607 133.1095956 0.038347741 0.028310386 118.2364869 -2.072751517 0.062687653 SDSFENPVLQQHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SDSFENPVLQQHFR 14 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;;;; 273.08 5.33E-33 4775800000 4012440 5153970 4370910 4524290 5491820 3563770 4801640 4508970 5398110 FALSE TRUE 3761308.543 5535575.302 4474590.049 4640390.941 5060514.61 4592572.546 4081678.658 5071924.83 4497130.568 0.836379662 1.230912738 0.9949878 1.031855951 1.125276336 1.021222861 0.907618446 1.127813559 1 22.10057334 2.006604509 24.24624302 0.992264697 1.063095601 0 0.112862777 290.2491987 1065544.273 0.03913454 0.028825994 101.5323666 -2.006604509 0.070830903 SDSHPSDALTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SDSHPSDALTR 11 0 P49748;P49748-3;K7EQP4;J3QKU9;K7EJW8 P49748 ACADVL "Very long-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 ;;; 140.39 3.86E-05 1495200000 462692 870735 704453 709125 983189 682315 771590 881529 975671 FALSE TRUE 433732.9336 935205.1254 721162.9578 727322.348 905973.3019 879288.264 655897.2426 991589.8361 812825.207 0.533611569 1.150561175 0.887230061 0.894807816 1.114597941 1.081767958 0.806935165 1.219929977 1 19.63258562 4.750083226 24.68204866 1.00234407 0.533611237 0.578421603 0.129626157 1072.295273 2296862.471 0.028999952 0.45459194 56244.90992 -4.750083226 -0.468732832 SDSILLTHDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDSILLTHDGR 11 0 O96013;O96013-4;O96013-2;O96013-3 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ; 222.74 7.45E-12 633270000 524270 716500 546560 571960 751990 417280 578040 629090 604410 FALSE TRUE 491456.8765 769550.4055 559524.6613 586637.4619 692931.7388 537741.962 491368.2683 707633.2713 503530.0664 0.976022902 1.528310734 1.111204074 1.16504952 1.376147692 1.067944097 0.975846928 1.405344623 1 18.9417184 2.213502798 24.87340272 1.09435681 1.252445431 0.081428158 0.187308242 411.7087871 408675.834 0.065654232 0.048508501 163.4943683 -2.213502798 0.158088621 SDSKS(ph)SPQAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDSKSSPQAGR 11 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 S(0.006)DS(0.252)KS(0.371)S(0.371)PQAGR;SDS(0.051)KS(0.475)S(0.475)PQAGR 89.613 0.031836 138450000 786130 572760 699800 678270 753010 548850 769440 605320 827690 TRUE FALSE 736927.5266 615167.7464 716399.5865 695675.5565 693871.6321 707294.0852 654069.6151 680895.5345 689543.1919 1.068718443 0.89213809 1.038948096 1.008893373 1.006277258 1.025742975 0.94855496 0.98745886 1 19.3952814 SDSKSS(ph)PQAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDSKSSPQAGR 11 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SDS(0.005)KS(0.022)S(0.973)PQAGR;SDS(0.019)KS(0.031)S(0.951)PQAGR 158.52 1.80E-05 1537740000 1241260 852010 1140360 1033250 1171930 811090 1184470 1027650 1405170 TRUE FALSE 1163571.752 915093.7069 1167409.878 1059764.944 1079891.345 1045238.516 1006869.72 1155954.365 1170638.049 0.993963722 0.781705077 0.997242383 0.905288313 0.922480989 0.892879329 0.86010336 0.987456683 1 20.15886365 1.159074636 7.423003918 0.996939304 0.901815817 0.24765171 0.061770055 0.317914989 24.707018 0.054790379 0.013770935 14.42363209 -1.159074636 -0.095123487 SDSQASLTVPLS(ph)PQVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SDSQASLTVPLSPQVVR 17 0 Q8TEV9;Q8TEV9-2 Q8TEV9 SMCR8 Smith-Magenis syndrome chromosomal region candidate gene 8 protein 1 SDSQASLT(0.052)VPLS(0.948)PQVVR;SDSQASLTVPLS(1)PQVVR;SDSQASLTVPLS(1)PQVVR;SDSQASLTVPLS(1)PQVVR 311.54 4.12E-58 832160000 904258 1039022 1050138 1083976 1157232 866752 1202307 938435 1036959 TRUE FALSE 847662.1059 1115952.27 1075047.769 1111792.659 1066347.667 1116969.232 1022032.227 1055600.676 863883.8439 0.981222316 1.291785091 1.244435553 1.28697008 1.234364636 1.292962289 1.183066722 1.221924317 1 19.72047782 0.22058828 1.131505003 0.999390339 1.232484485 0.347554369 0.091691181 4.817463193 6.066012375 0.085011505 0.024218773 1.661836448 -0.22058828 0.233094146 SDSVLPASHGHLPQAGS(ph)LER ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 SDSVLPASHGHLPQAGSLER 20 0 Q8N4C8;Q8N4C8-4;Q8N4C8-2;Q8N4C8-3;Q8N4C8-5 Q8N4C8 MINK1 Misshapen-like kinase 1 1 SDSVLPASHGHLPQAGS(1)LER;SDSVLPASHGHLPQAGS(1)LER;SDSVLPASHGHLPQAGS(1)LER;SDSVLPASHGHLPQAGS(1)LER;SDSVLPASHGHLPQAGS(1)LER;SDSVLPASHGHLPQAGS(1)LER;SDSVLPASHGHLPQAGS(1)LER;SDSVLPASHGHLPQAGS(1)LER;SDSVLPASHGHLPQAGS(1)LER 205.12 1.50E-21 5203590000 2166300 2947750 2881500 2735010 3204930 2605240 3583730 3098400 4135870 TRUE FALSE 2030715.15 3166004.477 2949850.541 2805194.987 2953227.726 3357330.495 3046382.956 3485242.06 3445566.578 0.589370457 0.918863242 0.856129311 0.814146215 0.857109465 0.974391416 0.884145724 1.011514937 1 21.7163098 4.740341124 24.87667329 0.9028889 0.589370345 0.703751656 0.065918098 81.83615716 1143290.585 0.014764736 0.095316295 54997.26895 -4.740341124 -0.313518555 SDT(ph)SSPEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDTSSPEVR 9 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SDT(0.454)S(0.273)S(0.273)PEVR 125.97 0.0039579 0 479450 475720 459740 503130 495010 432530 555460 456160 465530 TRUE FALSE 449442.0803 510942.8038 470645.2499 516041.1676 456133.9114 557394.3895 472173.9296 513112.5801 387830.0356 1.15886352 1.317440004 1.213534814 1.330585876 1.176118066 1.437213053 1.217476436 1.323034662 1 18.56506501 -0.641716956 6.069174166 1.000000002 1.272831621 0.507186404 0.084188684 1.03E-09 3.38E-10 0.068802584 0.016216924 0.228182873 0.641716956 0.27283162 SDTALEEAVAEVLDHRPIEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDTALEEAVAEVLDHRPIEPK 21 1 A0A3B3ITN0;Q86TP1 A0A3B3ITN0 PRUNE Protein prune homolog 0 131.71 7.66E-06 21989000 32679 28029 33057 31945 31533 23461 37426 23758 34625 FALSE TRUE 30633.67972 30104.29632 33841.12765 32764.76278 29056.52538 30233.80984 31814.31875 26724.2386 28845.86381 1.061978241 1.043626099 1.173170887 1.13585653 1.007303008 1.048115946 1.102907472 0.926449586 1 14.81607685 1.244133908 24.99687876 0.963224777 1.085592514 0.485934779 0.050611428 104.8358905 470218.1744 0.036904375 0.012632825 17.54421369 -1.244133908 0.122367737 SDTDTGVCS(ph)GTDEDPDDKNAPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDTDTGVCSGTDEDPDDKNAPFR 23 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 SDTDT(0.003)GVCS(0.961)GT(0.036)DEDPDDKNAPFR 146.57 7.67E-08 89678000 116030 80065 93270 104780 107850 69838 128450 78627 82797 TRUE FALSE 108767.8894 85993.09591 95482.40845 107468.8322 99379.89605 89999.09687 109190.115 88443.75403 68977.64581 1.576857084 1.246680644 1.384251482 1.558024066 1.440755115 1.304757444 1.582978278 1.282208939 1 16.07384127 -0.67638995 7.207930485 1 1.41488046 0.539859326 0.122297913 0 0 0.112422381 0.026498209 0.210673567 0.67638995 0.414880461 SDTFINLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDTFINLR 8 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 103.74 0.016506 0 147460 174570 159750 148660 204570 112710 156600 174840 229560 FALSE TRUE 138230.7418 187495.3444 163539.3454 152474.8673 188503.8974 145247.5473 133119.2838 196669.1589 191244.953 0.722794195 0.980393686 0.855130255 0.797275248 0.985667305 0.759484342 0.696066912 1.028362609 1 17.54506215 2.203046953 24.99996968 0.826546612 0.878528981 0 0.127190219 701.5975801 493888.2306 0.044716995 0.033026988 159.6051693 -2.203046953 0.051982369 SDTS(ph)SPEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDTSSPEVR 9 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SDT(0.052)S(0.474)S(0.474)PEVR 135.55 0.00022836 326350000 484140 475020 501690 451950 509550 406660 511890 426680 525480 TRUE FALSE 453838.5416 510190.9751 513590.3237 463547.8021 469531.9984 524056.1404 435136.8467 479951.9372 437773.9933 1.036695986 1.165420932 1.173186008 1.058874692 1.072544294 1.197092903 0.993976009 1.09634639 1 18.73982673 1.425276275 0.673816528 1.003641235 1.130787868 0.201054174 0.063571384 0.818407606 0.841441256 0.057813892 0.026394454 26.62418208 -1.425276275 0.127146633 SDTSGHFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SDTSGHFER 9 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;;;; 175.93 5.35E-05 7520760000 4139160 6694730 5513290 4594840 6240290 1765538 6845320 5787410 8948380 FALSE TRUE 3880097.364 7190414.775 5644067.842 4712751.373 5750202.796 2275220.159 5818927.815 6509980.878 7454837.569 0.52048047 0.964530039 0.757101384 0.632173583 0.771338442 0.305200501 0.780557291 0.873255898 1 22.82974549 1.13814301 3.003295027 0.986660041 0.697943032 0.289366295 0.174855035 0.344426203 5.662528058 0.16535504 0.044630779 13.74494512 -1.13814301 -0.288717009 SDTSS(ph)PEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDTSSPEVR 9 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SDT(0.033)S(0.289)S(0.678)PEVR 160.53 6.84E-05 261080000 707290 692870 697970 665120 722890 574140 805600 607400 737500 TRUE FALSE 663021.9814 744170.8157 714526.178 682188.1052 666117.1354 739884.8976 684807.7588 683235.2271 614406.4856 1.079125948 1.211202735 1.162953508 1.110320482 1.084163581 1.20422703 1.114584196 1.112024764 1 19.22883392 -1.594615135 0.287582772 0.877167405 1.160547189 0.456907029 0.045824317 19.72490313 1.044769402 1.764598017 0.052218784 0.025432255 1.594615135 0.283379784 SDVEDHSVHLLFSANR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDVEDHSVHLLFSANR 16 0 P23919-2;P23919;H7C312;G5E9E9;H7C3A4;H7BZ20 P23919-2 DTYMK Thymidylate kinase 0 119 0.00013217 89626000 57154 81055 68905 69671 90426 60470 75697 75955 65785 FALSE TRUE 53576.83316 87056.39654 70539.45914 71458.87581 83324.30672 77926.70735 64346.93759 85438.14895 54805.05851 0.977589197 1.588473745 1.287097597 1.303873725 1.520376202 1.421888955 1.174105809 1.558946405 1 15.74202144 -1.168679726 4.004487494 0.999837806 1.361558801 0.263127813 0.18581899 11921918.6 3490231.789 17499.93153 0.038828717 0.067814142 1.168679726 0.361720995 SDVLELTDDNFESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SDVLELTDDNFESR 14 0 H7BZJ3 H7BZJ3 PDIA3 0 ;;; 422.87 2.33E-152 3947510000 3576650 4127080 3926780 4170320 3966780 3026890 4409050 3220170 3347500 FALSE TRUE 3352793.861 4432653.297 4019925.076 4277337.472 3655245.1 3900704.006 3747953.884 3622215.313 2788780.624 1.202243673 1.589459299 1.441463355 1.533766204 1.310696535 1.398713105 1.343940019 1.298852725 1 21.41120302 0.545460035 0.523252658 0.9803031 1.461144377 0.581945998 0.107820626 1.090896418 0.558909267 0.145736386 0.04909005 3.511236115 -0.545460035 0.480841277 SDVLQPGAEVTTDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDVLQPGAEVTTDDR 15 0 P53992;G5EA31;P53992-2 P53992 SEC24C Protein transport protein Sec24C 0 145.58 1.72E-05 0 95429 96552 82956 96711 81077 63339 81107 86404 83957 FALSE TRUE 89456.26924 103700.8105 84923.75549 99192.76799 74709.53947 81623.94108 68945.75831 97191.7296 69944.03432 1.278969252 1.482625524 1.214167246 1.418173386 1.068133118 1.16698932 0.985727503 1.38956425 1 16.09391339 2.734965827 24.97479856 1.113669179 1.348454698 0.421185229 0.131676491 273.0487922 1896997.35 0.038172242 0.037277722 543.2075866 -2.734965827 0.23478552 SDVS(ph)PIIQPVPSIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDVSPIIQPVPSIK 14 0 P40818;P40818-2;A0A075B720 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 SDVS(1)PIIQPVPSIK;SDVS(1)PIIQPVPSIK 222.57 4.03E-12 144875000 485170 387520 427120 422680 510840 352150 523260 392210 670080 TRUE FALSE 454804.0758 416212.384 437251.4881 433526.6844 470720.687 453809.9883 444802.0207 441178.2819 558239.3191 0.814711648 0.74558056 0.783268883 0.77659647 0.843223813 0.812930893 0.796794503 0.790303131 1 19.09052422 -5 0.266643294 2.403420408 0.775751706 0.856897077 0.026202109 71.49675309 0.697532809 55.13769398 0.032890946 1.00E-05 5 -1.627668702 SDWEVKEEMDFPQLMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SDWEVKEEMDFPQLMK 16 1 O15371-2;O15371;O15371-3;B0QYA5 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 112.34 0.00068102 135970000 182030 135460 164570 159470 189420 105500 227480 160800 234120 FALSE TRUE 170637.0672 145489.5993 168473.6781 163562.2702 174543.7173 135956.1374 193371.4858 180876.234 195043.8595 0.874865108 0.745932734 0.8637733 0.838592256 0.894894706 0.697054179 0.991425653 0.927361848 1 17.57343905 1.645265727 9.580124808 0.969432724 0.819942744 0.574443641 0.062231613 0.075385813 12.85232115 0.027472255 0.014552414 44.18407087 -1.645265727 -0.14948998 SDYAQLLEDMQNAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SDYAQLLEDMQNAFR 15 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ;; 276.47 3.55E-33 420050000 667944 706627 703348 683854 710215 636083 812362 666404 742196 FALSE TRUE 626138.5774 758946.3983 720031.7467 701402.8514 654437.5788 819709.8362 690555.8597 749606.0063 618318.6928 1.012647013 1.227435637 1.1644994 1.134371093 1.058414676 1.325707674 1.116828373 1.212329524 1 19.2379911 -1.014359324 4.832231195 0.999997168 1.16405343 0.234350158 0.087986663 2.36E-06 4.81E-07 0.074851097 0.017642268 0.096747706 1.014359324 0.164056263 SDYDGIGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 113.26 0.0042572 1182370000 1315370 1405900 1468340 1445570 1548950 1271990 1653540 1334980 1665130 FALSE TRUE 1233043.34 1509994.299 1503169.718 1482665.774 1427301.715 1639192.864 1405607.028 1501655.192 1387209.046 0.888866277 1.088512437 1.083592788 1.068812071 1.028901678 1.18164805 1.013262588 1.082501009 1 20.40375378 4.741576762 24.77835022 1.072730514 0.8888662 0.552474878 0.050649158 171.552408 1409263.367 0.010566295 0.074813684 55153.96792 -4.741576762 -0.183864313 SDYDMVDYLNELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SDYDMVDYLNELR 13 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;;; 288.11 5.25E-33 590031000 860840 973880 950960 987219 952336 811906 1093529 877063 707288 FALSE TRUE 806961.561 1045987.089 973517.2203 1012552.711 877543.3721 1046290.082 929564.4783 986566.2462 589237.0635 1.36950238 1.775154947 1.652165623 1.718413137 1.489287464 1.775669161 1.577572994 1.674311253 1 19.16848865 -1.225540643 3.28135947 0.998157422 1.644259152 0.707226208 0.126851316 14508557.35 21504474.86 274097.0218 0.027557198 0.059492108 1.225540643 0.64610173 SDYLNTFEFMDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SDYLNTFEFMDK 12 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 182.08 4.03E-05 131731000 304430 265540 264290 263940 330100 196994 273920 252670 361890 FALSE TRUE 285376.2697 285200.8579 270559.0836 270713.1472 304175.2776 253862.9699 232848.2389 284216.4057 301488.2211 0.946558604 0.945976784 0.897411788 0.897922799 1.008912642 0.842032796 0.772329473 0.942711475 1 18.20174211 2.199858668 24.99997436 0.858790038 0.932656333 0.036324803 0.069421138 243.6362709 157378.2953 0.024335473 0.017973234 158.4377507 -2.199858668 0.073866294 SEAAAPHTDAGGGLS(ph)S(ph)DEEEGTSSQAEAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEAAAPHTDAGGGLSSDEEEGTSSQAEAAR 30 0 Q01831-2;Q01831 Q01831-2 XPC DNA repair protein complementing XP-C cells 2 SEAAAPHTDAGGGLS(1)S(1)DEEEGTSSQAEAAR 188.49 1.75E-18 247430000 308650 310300 273100 276270 257330 226510 310280 204610 276860 TRUE FALSE 289332.1475 333274.9349 279578.061 283359.5559 237120.3398 291899.7599 263756.3945 230156.0089 230650.2774 1.254419248 1.444936198 1.212129741 1.22852467 1.028051397 1.265551306 1.143533827 0.997857065 1 17.8153475 3.093152091 0.299298378 0.990221145 1.464153063 0.587315566 0.089886913 1.982881942 0.309134029 0.115302842 0.327352366 1239.230491 -3.093152091 0.473931918 SEAEDLAEPLSSTEGVAPLSQAPS(ph)PLAIPAIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SEAEDLAEPLSSTEGVAPLSQAPSPLAIPAIK 32 0 Q6P4R8-3;Q6P4R8;E9PQ59;Q6P4R8-2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 SEAEDLAEPLS(0.029)S(0.029)T(0.029)EGVAPLS(0.152)QAPS(0.762)PLAIPAIK;SEAEDLAEPLSSTEGVAPLS(0.023)QAPS(0.977)PLAIPAIK;SEAEDLAEPLSSTEGVAPLS(0.17)QAPS(0.83)PLAIPAIK 126.36 8.11E-08 140748100 197192 154833 176821 156333 172212 142028 214248 155670 162598 TRUE FALSE 184850.1047 166296.9964 181015.2776 160344.7695 158687.1642 183029.178 182123.5014 175105.7422 135459.3434 1.364616867 1.227652462 1.336307065 1.183711403 1.171474483 1.351174259 1.344488293 1.292681168 1 17.04750038 -1.053926313 4.146097499 0.999971174 1.284760128 0.623027866 0.069427009 0.459467043 19070093.18 1413.977202 0.016154634 0.088322975 1.053926313 0.284788953 SEAEEAITSFNGHKPPGSSEPITVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEAEEAITSFNGHKPPGSSEPITVK 25 1 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 0 140.81 2.31E-07 156200000 183660 175810 174340 187030 202220 180060 247490 190320 261930 FALSE TRUE 172165.0484 188827.1553 178475.4271 191829.5064 186338.4569 232040.399 210381.1721 214081.8709 218212.1909 0.788979973 0.865337333 0.817898516 0.879096194 0.853932387 1.063370465 0.964112826 0.981072002 1 17.73537218 2.300560324 8.263353697 0.997500642 0.842405512 0.837644561 0.035219479 0.09523284 11.35004978 0.011291596 0.009412586 199.7838252 -2.300560324 -0.15509513 SEAEEGEVRT(ph)PTK ddPTM_SK-BR-3_Pertuzumab_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(0.996)PT(0.004)K;SEAEEGEVRT(0.995)PT(0.005)K;SEAEEGEVRT(0.997)PT(0.003)K;SEAEEGEVRT(1)PTK 193.64 2.74E-06 3665450000 3712700 2561130 3251560 3659290 4660210 2339220 2536560 2352400 5018760 TRUE FALSE 3480328.734 2750758.73 3328688.539 3753193.577 4294215.905 3014514.84 2156226.376 2646102.318 4181096.534 0.832396168 0.657903664 0.796128124 0.897657719 1.027054953 0.720986664 0.515708346 0.632872811 1 21.99544992 -0.962317339 6.750992513 1.000000025 0.747213451 0.211382954 0.143730443 5.84E-08 8.98E-09 0.150736082 0.035528832 0.109064311 0.962317339 -0.252786574 SEAESASPEETPDGSAS(ph)PVEMQDEGAEEPHEAGEQLPPFLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEAESASPEETPDGSASPVEMQDEGAEEPHEAGEQLPPFLLK 42 0 Q9C0C9 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 S(0.001)EAES(0.001)AS(0.002)PEET(0.031)PDGS(0.238)AS(0.727)PVEMQDEGAEEPHEAGEQLPPFLLK 47.936 0.055401 41759000 26757 20415 22717 22040 18816 17624 23419 20401 22174 TRUE FALSE 25082.32713 21926.54784 23255.85797 22605.58371 17338.26726 22711.7627 19907.53836 22948.10976 18473.01615 1.357781909 1.186950072 1.258909632 1.223708328 0.938572625 1.229456117 1.077655008 1.242250295 1 14.17313182 8 0.162655227 1.030328802 2.112017261 0.360077468 0.101906616 68.19934397 0.713117583 0.263976636 17.76887336 100000000 -8 1.081688458 SEAGHAS(ph)SPDSEVTSLCQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEAGHASSPDSEVTSLCQK 19 0 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 S(0.048)EAGHAS(0.521)S(0.43)PDS(0.001)EVTSLCQK 101.6 0.0002901 128320000 54936 133200 100910 107840 113040 113650 135140 106000 114160 TRUE FALSE 51497.65382 143062.2666 103303.6329 110607.357 104162.2944 146458.91 114877.0116 119234.3333 95105.9585 0.541476629 1.504240837 1.086195171 1.162990823 1.095223643 1.539955144 1.207884484 1.253699928 1 16.53724811 SEAHLTELLEEICDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 SEAHLTELLEEICDR 15 0 Q9Y2B0;F8VXJ7;F8W031;F8W1K5 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;;;;;;;;; 280.87 9.92E-34 1790655600 689801.6 1091319 965901 1030040 1145704 993745 1281548 942449 1144508 FALSE TRUE 646628.1492 1172121.394 988812.6279 1056472.57 1055725.029 1280623.049 1089391.775 1060115.832 953482.221 0.678175361 1.229305978 1.03705408 1.108014966 1.107230954 1.343101131 1.142540208 1.111835972 1 19.86284651 4.745051465 24.81377202 1.143919773 0.678175128 0.690624691 0.095895609 373.613076 1428238.075 0.021716262 0.207701214 55597.01376 -4.745051465 -0.465744645 SEALKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SEALKDR 7 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 106.91 0.0091254 561910000 1443600 1803470 1539390 1694570 2120400 1324030 1787620 1854590 1857740 FALSE TRUE 1353247.653 1937000.795 1575905.058 1738055.535 1953872.337 1706255.967 1519582.976 2086139.644 1547671.193 0.874376715 1.251558344 1.018242806 1.12301343 1.262459589 1.10246671 0.981851303 1.347921738 1 20.56166757 4.758087238 24.06287525 1.126887884 0.874376328 0.312528597 0.12125716 3456.142605 4258928.743 0.026750199 0.983462643 57291.11012 -4.758087238 -0.252511557 SEALS(ph)SVLDQEEAMEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SEALSSVLDQEEAMEIK 17 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 S(0.002)EALS(0.982)S(0.017)VLDQEEAMEIK;S(0.005)EALS(0.969)S(0.026)VLDQEEAMEIK 138.39 4.00E-06 31096000 72272 48434 53598 46254 57293 46395 68657 56100 93203 TRUE FALSE 67748.62453 52020.10376 54869.36987 47440.95595 52793.43889 59788.48334 58362.52023 63104.20849 77646.81719 0.87252288 0.669957967 0.706653175 0.61098391 0.679917617 0.770005591 0.751640857 0.812708245 1 16.24463917 0.804411024 0.926310704 0.99957441 0.702519827 0.626843188 0.068342542 0.49413079 0.82782337 0.060931466 0.020431297 6.373984814 -0.804411024 -0.297054584 SEANDAVNS(ph)STK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEANDAVNSSTK 12 0 O15234;J3KSY7;K7EQ38 O15234 CASC3 Protein CASC3 1 SEANDAVNS(0.499)S(0.499)T(0.002)K 199.03 1.85E-07 195020000 811850 542310 643300 591120 588810 581740 800960 618170 590910 TRUE FALSE 761037.7577 582463.1967 658559.3798 606289.14 542567.2377 749678.8942 680863.4837 695349.8853 492283.3036 1.54593453 1.183186983 1.337765013 1.231585828 1.102144301 1.522860696 1.383072468 1.412499429 1 18.90912928 2.232354055 24.99998881 1.369600607 1.27255872 0 0.17632309 418.2542341 1684710.018 0.058114767 0.044004543 170.7473824 -2.232354055 -0.097041887 SEAPAEVTHFS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SEAPAEVTHFSPK 13 0 Q6PID6 Q6PID6 TTC33 Tetratricopeptide repeat protein 33 1 SEAPAEVTHFS(1)PK;SEAPAEVTHFS(1)PK 153.95 2.81E-05 863180000 2311100 1494550 1807210 1802320 2028980 1299360 2147100 1668080 2751200 TRUE FALSE 2166452.376 1605208.037 1850077.875 1848570.583 1869632.095 1674464.139 1825162.288 1876343.46 2292006.947 0.945220685 0.700350424 0.807186853 0.806529223 0.815718337 0.730566782 0.796316211 0.818646498 1 21.12817999 0.698090429 2.481007483 0.999967097 0.78895264 0.478763403 0.064187308 1.414337183 10.61789261 0.054954071 0.014696612 4.989883764 -0.698090429 -0.211014457 SEASLHPVLMSEAPWNTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SEASLHPVLMSEAPWNTR 18 0 O96019-2;O96019;H7C5S0 O96019-2 ACTL6A Actin-like protein 6A 0 ; 132.51 1.47E-05 408970000 287090 388890 374580 383320 417510 323040 434650 373350 462980 FALSE TRUE 269121.5494 417683.8202 383465.2145 393156.6402 384720.4488 416296.4039 369478.2676 419963.5693 385705.647 0.697738162 1.082908232 0.994191341 1.019317822 0.997445725 1.079311146 0.957928074 1.088818825 1 18.55714074 4.744825655 24.96438506 1.024667779 0.697738014 0.848440016 0.043785304 236.945764 944135.0781 0.009343718 0.08748976 55568.11373 -4.744825655 -0.326929765 SEAVVEYVFSGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SEAVVEYVFSGSR 13 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;; 209.95 7.86E-08 536740000 595980 631910 668540 713680 725040 546290 714290 571240 831950 FALSE TRUE 558678.6757 678697.2739 684398.0845 731994.2371 668098.2831 703995.0547 607188.8456 642560.5715 693092.1704 0.806066927 0.979230906 0.98745609 1.056128273 0.963938581 1.015730786 0.876057863 0.927092527 1 19.4026877 -0.126092156 7.304049959 0.999999993 0.957471517 0.038556341 0.070723313 8896807.068 1218064.887 0.065626274 0.01591671 0.748010758 0.126092156 -0.042528477 SECDS(ph)SPEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SECDSSPEPK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SECDS(0.662)S(0.338)PEPK 169.21 4.93E-06 90909000 441030 252430 320680 301920 326690 262890 435330 282060 368980 TRUE FALSE 413426.7196 271120.1799 328286.681 309667.7783 301033.0852 338782.0753 370056.3079 317275.8119 307394.8543 1.344937021 0.881993228 1.067964139 1.007394151 0.979304243 1.102107178 1.203846788 1.032144187 1 18.22973349 2.103874181 8.038912433 1.114043265 1.032093831 0 0.130330144 0.612810245 42.5554378 0.044984061 0.033183997 127.0206062 -2.103874181 -0.081949434 SECDSS(ph)PEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SECDSSPEPK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SECDS(0.037)S(0.963)PEPK;SECDS(0.382)S(0.618)PEPK;SECDS(0.157)S(0.843)PEPK;SECDS(0.32)S(0.68)PEPK 205.12 1.83E-07 1119780000 3815850 2164130 2878870 2582480 2845380 2238940 3700100 2447030 3291540 TRUE FALSE 3577022.76 2324364.437 2947158.156 2648750.809 2621915.333 2885285.632 3145304.355 2752547.082 2742160.71 1.304454092 0.847639757 1.074757634 0.965935658 0.956149406 1.052194214 1.147016783 1.00378766 1 21.38688169 2.012431853 23.45737822 1.074853887 1.007845021 0 0.124011556 312.8592269 590321.4334 0.042368539 0.03126375 102.9039044 -2.012431853 -0.067008866 SEDDSAKFDS(ph)NEEDSASVFSPSFGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SEDDSAKFDSNEEDSASVFSPSFGLK 26 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 SEDDS(0.011)AKFDS(0.989)NEEDSASVFSPSFGLK;SEDDS(0.025)AKFDS(0.975)NEEDSASVFSPSFGLK;SEDDSAKFDS(1)NEEDSASVFSPSFGLK;S(0.001)EDDS(0.196)AKFDS(0.803)NEEDSASVFSPSFGLK;SEDDS(0.035)AKFDS(0.965)NEEDSASVFSPSFGLK;SEDDSAKFDS(1)NEEDSASVFSPSFGLK;SEDDSAKFDS(1)NEEDSASVFSPSFGLK 420.99 5.18E-187 2648355000 2521683 1409203 1731293 1780536 1750453 1099874 2349546 1336576 2093334 TRUE FALSE 2363855.362 1513541.856 1772360.088 1826227.568 1612979.482 1417389.769 1997253.389 1503450.456 1743943.032 1.355465929 0.867884919 1.016294716 1.047183041 0.924903769 0.81275004 1.145251509 0.862098376 1 20.73392148 4.747701916 24.69553592 0.966708639 1.35546617 0.611988419 0.098928216 697.8900956 1885326.642 0.022122601 0.274023308 55937.35354 -4.747701916 0.388757531 SEDES(ph)ET(ph)EDEEEKSQEDQEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEDESETEDEEEKSQEDQEQK 21 1 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 2 SEDES(1)ET(1)EDEEEKSQEDQEQK 214.16 3.67E-24 512470000 2516500 913100 1350900 1294800 1448600 986920 1775000 1058000 1698300 TRUE FALSE 2358996.757 980706.8741 1382943.986 1328026.76 1334832.799 1271827.783 1508855.228 1190093.629 1414842.759 1.667320798 0.69315609 0.977454192 0.938639119 0.943449575 0.898918113 1.066447292 0.841149041 1 20.43221029 4.749476264 24.99765404 0.920379387 1.667321225 0.846322844 0.10009272 619.6006959 1418905.199 0.024124909 0.361758864 56166.35808 -4.749476264 0.746941838 SEDES(ph)ET(ph)EDEEEKSQEDQEQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SEDESETEDEEEKSQEDQEQKR 22 2 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 2 S(0.01)EDES(0.978)ET(0.762)EDEEEKS(0.25)QEDQEQKR;S(0.051)EDES(0.975)ET(0.975)EDEEEKSQEDQEQKR 112.86 0.00030785 1556970000 2148240 824520 1127010 1149610 1273420 686530 1566850 924480 1810590 TRUE FALSE 2013785.493 885568.3187 1153743.209 1179110.939 1173410.73 884720.0661 1331915.388 1039903.363 1508390.832 1.335055511 0.587094737 0.764883467 0.78170121 0.77792221 0.586532381 0.883004166 0.689412413 1 20.52457886 -1.440676678 2.714361263 1.006758895 0.775546812 0.069743837 0.211716288 22883863.83 24419023.62 1187253.703 0.046592064 0.036251278 1.440676678 -0.231212082 SEDHLTESHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SEDHLTESHQR 11 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 ; 233.54 1.03E-15 464330000 351950 482760 520830 525810 530060 503250 549900 469870 512730 FALSE TRUE 329922.0777 518504.0527 533184.3336 539303.1748 488431.2258 648530.1054 467447.6 528534.3038 427152.0506 0.7723762 1.21386296 1.248230771 1.262555509 1.143459864 1.518265228 1.094335376 1.237344648 1 18.70439018 4.738756288 5.630842679 1.228758365 0.756940793 0.514185578 0.134612755 0.102229589 13.34045035 0.02797227 0.185701072 54796.93761 -4.738756288 -0.471817572 SEDKVIAVYDLGGGTFDISILEIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SEDKVIAVYDLGGGTFDISILEIQK 25 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;; 266.04 1.90E-45 202943000 415379 324157 287402 267707 468767 239399 321771 364566 521201 FALSE TRUE 389381.1699 348157.9216 294219.3112 274576.8148 431951.9307 308509.605 273524.4257 410082.8676 434209.186 0.896759402 0.801820719 0.677598081 0.632360677 0.994801457 0.710509162 0.629936986 0.944436186 1 18.72803072 1.088531457 6.507148387 0.998413986 0.753859458 0.365934284 0.114879982 0.197726632 10.95502343 0.106891843 0.026850321 12.26115711 -1.088531457 -0.244554528 SEDLLDYGPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SEDLLDYGPFR 11 0 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ;;;; 208.25 4.70E-08 245962000 616317 817811 553362 598740 913990 476782 703934 787773 608321 FALSE TRUE 577742.8191 878362.5774 566488.008 614104.6821 842208.9123 614421.2235 598385.6317 886128.1932 506788.2952 1.140008214 1.733194286 1.117800102 1.211757824 1.661855493 1.212382427 1.180740829 1.748517481 1 18.95102368 -1.420022984 3.01892591 0.993493502 1.367105338 0.181615795 0.250089755 52948006.38 67856223.18 2987761.071 0.055963502 0.038016928 1.420022984 0.373611836 SEDMPFS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 179.72 5.19E-05 2308740000 6556360 4359850 4870230 4904160 5278350 3624440 6698900 4302070 5761510 TRUE FALSE 6146009.131 4682657.83 4985754.155 5030009.048 4863809.683 4670756.99 5694462.135 4839192.91 4799876.76 1.280451444 0.975578763 1.038725452 1.047945458 1.013319701 0.973099357 1.186376738 1.008191075 1 22.19456593 -1.637074177 9.913452043 0.999985269 1.058356462 0.038572881 0.097111011 2.89E-05 1.06E-06 0.085999394 0.020265138 0.023063532 1.637074177 0.058371193 SEDPDQQYLILNTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEDPDQQYLILNTAR 15 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 107.99 0.0049672 0 28480 34117 35114 34121 33809 37659 34697 29270 43345 FALSE TRUE 26697.48764 36643.05818 35946.92066 34996.60263 31153.77752 48530.54196 29494.50696 32924.42393 36110.43948 0.739328793 1.014749715 0.995471702 0.969154713 0.862736039 1.343947696 0.816786153 0.911770236 1 15.14012836 4.742200001 23.95772908 0.989692385 0.739328622 0.237078496 0.140938318 283.3137154 1864878.377 0.03052202 0.223354313 55233.17407 -4.742200001 -0.250363763 SEDPPTT(ph)PIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SEDPPTTPIR 10 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0;H7C151 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SEDPPT(0.072)T(0.928)PIR;SEDPPT(0.064)T(0.936)PIR;SEDPPT(0.042)T(0.958)PIR 125.54 0.0045425 2807820000 2829710 2888250 3022520 3361950 3847700 2799180 3260830 2624230 3267810 TRUE FALSE 2652603.502 3102099.035 3094215.602 3448223.329 3545517.163 3607257.825 2771898.814 2951870.892 2722391.4 0.974365222 1.139475769 1.136579994 1.266615568 1.302353939 1.325032773 1.018185267 1.08429335 1 21.37644307 1.626497829 12.55795433 1.038332103 1.185233412 0.344052167 0.101587635 0.127249059 60.56144657 0.050384572 0.027000221 42.31533948 -1.626497829 0.146901309 SEDRRS(ph)S(ph)EER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 82.515 0.087457 1511500000 2069100 1685100 1920000 1854400 1588500 2055400 2287700 1629100 1220100 TRUE FALSE 1939598.724 1809866.557 1965543.307 1901987.043 1463745.618 2648760.613 1944680.623 1832496.721 1016457.428 1.908194747 1.780563069 1.933719261 1.871192036 1.440046162 2.60587462 1.913194365 1.802826829 1 19.95511836 SEDRRS(ph)S(ph)EEREAGEI ddPTM_SK-BR-3_Pertuzumab_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(0.248)EDRRS(0.929)S(0.823)EEREAGEI;SEDRRS(1)S(1)EEREAGEI;S(0.008)EDRRS(0.993)S(0.999)EEREAGEI 120.29 0.00016674 33525140000 2567130 2758120 2542370 2762590 3051620 2049410 2810360 2618200 3700080 TRUE FALSE 2406457.916 2962334.075 2602676.217 2833482.736 2811958.075 2641041.398 2388972.608 2945088.033 3082512.745 0.780680605 0.961012758 0.844335914 0.91921201 0.91222918 0.856781988 0.775008185 0.955417958 1 21.55567543 1.01165871 24.30563762 1.000000028 0.869805289 0.407234201 0.058030269 125.5433658 261726.54 0.05548269 0.013870672 10.2720875 -1.01165871 -0.13019474 SEDSGIGLSASS(ph)PELSEHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SEDSGIGLSASSPELSEHLR 20 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 SEDSGIGLSAS(0.037)S(0.963)PELSEHLR;SEDSGIGLSAS(0.033)S(0.967)PELSEHLR;SEDSGIGLSAS(0.028)S(0.972)PELSEHLR;SEDSGIGLSAS(0.067)S(0.933)PELSEHLR 217.09 6.97E-25 1470750000 735800 943620 1009000 1121470 1096520 892570 1111220 957560 796360 TRUE FALSE 689747.5914 1013486.607 1032933.956 1150248.819 1010403.742 1150240.469 944602.8771 1077113.474 663442.3713 1.039649593 1.527618148 1.556930943 1.733758452 1.522971378 1.733745867 1.423790397 1.623522284 1 19.33961163 -1.072753175 4.348378118 0.999953434 1.532123141 0.409955564 0.195689091 11977884.48 2954968.209 5616.47322 0.041602843 0.084575938 1.072753175 0.532169707 SEDSTKDDIDLDALAAEIEGAGAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SEDSTKDDIDLDALAAEIEGAGAAK 25 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ;; 230.9 1.79E-34 115680400 333916 165248 242692 208559 207452 154422.5 305984 201747 288654 FALSE TRUE 313016.7936 177483.1339 248448.7688 213910.977 191159.5567 199001.7689 260104.5398 226935.557 240475.7826 1.301656201 0.738049927 1.033155048 0.889532304 0.794922277 0.827533512 1.081624673 0.943694016 1 17.87553209 -0.910938401 6.085590342 1.000000015 0.93816487 0.003098961 0.162251253 2.95E-08 5.20E-09 0.14161913 0.033379941 0.122761334 0.910938401 -0.061835144 SEEAHAEDSVMDHHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SEEAHAEDSVMDHHFR 16 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;;;;; 201.3 3.36E-11 5643870000 3738440 4730860 4677990 4963600 4686000 4771830 5316500 4592350 4485520 FALSE TRUE 3504457.714 5081137.797 4788954.132 5090974.379 4317980.462 6149379.857 4519340.181 5165715.007 3736857.734 0.937808705 1.359735414 1.281545746 1.362367727 1.155511066 1.645601811 1.209395835 1.382368657 1 21.83339421 4.742595641 24.63724374 1.316572296 0.937808523 0.308615209 0.168464391 351.6708054 2147145.097 0.034118439 0.261370195 55283.51404 -4.742595641 -0.378763773 SEEDNEIES(ph)EEEVQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEEDNEIESEEEVQPK 16 0 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;C9J7Y7 P52701 MSH6 DNA mismatch repair protein Msh6 1 SEEDNEIES(1)EEEVQPK 312.21 1.13E-57 141010000 90070 48567 68266 58148 46796 54307 87015 60756 47495 TRUE FALSE 84432.67948 52162.95121 69885.30176 59640.17612 43120.83093 69984.5493 73967.90856 68341.52034 39567.77767 2.133874694 1.318318953 1.76621751 1.50729153 1.089796634 1.768725802 1.869397599 1.727201384 1 15.27203842 SEEEIDFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SEEEIDFLR 9 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ; 187 9.55E-05 31758000 199734 235100 229630 238840 243020 197456 266060 213700 232470 FALSE TRUE 187233.0055 252507.0486 235076.932 244969.0388 223934.1895 254458.3418 226166.773 240380.9154 193669.2552 0.966766797 1.303805544 1.213806145 1.264883466 1.156271238 1.313880933 1.167799054 1.241192956 1 17.56323542 -1.311682601 6.044292844 0.999985121 1.215264645 0.288350531 0.0989868 1.72E-05 1.96E-06 0.082937912 0.019547303 0.048788492 1.311682601 0.215279524 SEEHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEEHLK 6 0 E9PD50;D6R9J3;D6RAD0 E9PD50 SMG7 0 88.591 0.05113 208070000 432140 219320 494070 544810 371510 527580 448550 242720 812020 FALSE TRUE 405093.1288 235558.681 505789.5737 558790.747 342333.1032 679883.7815 381294.0916 273024.1263 676488.6162 0.598817362 0.348207901 0.74766901 0.826016482 0.506044145 1.005018806 0.563637115 0.403590127 1 19.36770613 3.883342347 4.527177362 0.707053188 0.467696388 0.200009532 0.20421879 0.313031726 11.04175178 0.048425907 0.091534426 7644.381406 -3.883342347 -0.239356799 SEEHNDKEHSSDKGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEEHNDKEHSSDKGR 15 2 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 0 90.367 0.0019437 54082000 14149 32826 24659 27290 37344 21196 36420 27301 55865 FALSE TRUE 13263.43935 35256.4712 25243.92312 27990.3076 34411.15288 27314.94111 30959.15911 30709.58995 46540.7706 0.284985383 0.757539481 0.542404494 0.601414786 0.739376517 0.586903499 0.665205125 0.659842748 1 15.50620748 -4.999999999 0.168664064 2.477767926 0.524894466 0.547795628 0.121440536 103.6235656 0.975059715 51.22442362 0.40691306 1.00E-05 4.999999999 -1.95287346 SEEHS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEEHSPPR 8 0 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 SEEHS(1)PPR 84.658 0.01114 26215000 62157 73754 72908 68909 71933 63273 74533 67392 70061 TRUE FALSE 58266.70432 79214.8229 74637.41219 70677.3216 66283.67234 81538.88795 63357.46858 75806.03955 58367.36649 0.998275369 1.357176581 1.278752438 1.210904755 1.135628971 1.396994465 1.085494727 1.298774368 1 15.83287436 -2.260976401 0.395410013 0.695908481 1.240115975 0.221027348 0.123904563 79.65155019 4.15099033 21.39239843 0.072328101 0.005483068 2.260976401 0.544207494 SEEIKDTILQTVDLVSQETGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEEIKDTILQTVDLVSQETGEK 22 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 152.13 3.97E-08 39762000 64946 41415 53225 48948 59981 45453 61145 50625 60279 FALSE TRUE 60881.14579 44481.40969 54487.52213 50204.08855 55270.33421 58574.54323 51976.87489 56945.64269 50218.04548 1.212336028 0.885765451 1.085018774 0.999722073 1.100607036 1.166404281 1.035023852 1.133967723 1 15.61591826 2.729233357 24.11660648 1.0913986 1.025604425 0.026569806 0.092902689 917.0787185 2371198.958 0.027324605 0.026122257 536.084632 -2.729233357 -0.065794174 SEEITTGSAWFSFLESHNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEEITTGSAWFSFLESHNK 19 0 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 227 1.37E-19 145140000 288210 235660 270640 241470 299690 207630 314640 259310 277100 FALSE TRUE 270171.4506 253108.5116 277059.7086 247666.529 276153.5563 267569.4104 267462.653 291685.4243 230850.2199 1.170332221 1.096418759 1.200170867 1.072845108 1.196245585 1.15906067 1.158598216 1.263526734 1 17.81659758 3.989300672 24.10098474 1.15728516 1.130620812 0.001075101 0.07398556 1179.559538 2334117.081 0.016062226 0.034300041 9756.648784 -3.989300672 -0.026664348 SEEITTGSAWFSFLESHNKLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEEITTGSAWFSFLESHNKLDK 22 1 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 264.72 9.98E-38 299620000 297390 179010 232790 212440 234840 181610 296140 212930 281700 FALSE TRUE 278776.8908 192264.0867 238311.8887 217891.5701 216396.6137 234037.8588 251736.5562 239514.7792 234682.4501 1.187889808 0.819252085 1.015465317 0.928452766 0.922082642 0.997253347 1.07266886 1.020590926 1 17.84035043 1.998981643 7.698576872 1.038258788 0.957040591 0.050322303 0.094687478 0.228899214 108.4746898 0.033998355 0.023601936 99.76578936 -1.998981643 -0.081218197 SEEITTGSAWFSFLESHNKLDKDNLSYIEHIFEISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SEEITTGSAWFSFLESHNKLDKDNLSYIEHIFEISR 36 2 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ; 213.73 4.25E-32 908057000 668678.8 729033 597180.9 548724 1006456 450489.6 814957 738791.2 1075330 FALSE TRUE 626827.3875 783011.3619 611346.313 562805.1868 927413.0056 580538.6344 692761.7635 831030.9076 895850.4761 0.699700904 0.874042469 0.682420035 0.628235628 1.035231917 0.648030726 0.773300659 0.927644657 1 19.77289843 1.138448147 3.593304321 0.994770009 0.764611935 0.336410949 0.119532237 0.241591337 5.488775184 0.102759031 0.02709468 13.75460577 -1.138448147 -0.230158073 SEEKT(ph)PIKKPGDGR ddPTM_SK-BR-3_Pertuzumab_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(0.001)EEKT(0.999)PIKKPGDGR 81.157 0.014698 279790000 783370 295990 458780 432930 432580 284610 700030 404870 707550 TRUE FALSE 734340.2701 317905.4076 469662.4783 444039.7167 398606.9117 366772.2867 595067.0003 455418.9107 589455.3341 1.245794597 0.539320605 0.79677365 0.753305113 0.676229205 0.622222356 1.009520087 0.772609703 1 19.16902297 1.728941879 15.70788674 0.917625788 0.743801772 0.10867886 0.197854855 0.213907349 289.3102579 0.083178486 0.045934758 53.57249572 -1.728941879 -0.173824015 SEENTKEEKPDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SEENTKEEKPDSK 13 2 P50502;Q3KNR6;Q8NFI4;F6VDH7;Q8IZP2 P50502 ST13;ST13P5;ST13P4 Hsc70-interacting protein;Putative protein FAM10A5;Putative protein FAM10A4 0 ;;;; 152.07 2.53E-05 2790670000 5294270 2072869 3129010 3049530 3424900 1939786 4043210 2457410 4137810 FALSE TRUE 4962911.091 2226346.378 3203231.595 3127786.103 3155922.169 2499770.728 3436968.196 2764223.048 3447182.78 1.439700593 0.645845178 0.929231723 0.907345593 0.915507639 0.725163384 0.997036831 0.801878875 1 21.71698637 4.752056845 24.99976085 0.860253049 1.439700973 0.716652361 0.113478034 1212.161432 2245310.021 0.025466455 0.50571671 56501.09249 -4.752056845 0.579447924 SEEPAGQILSHLS(ph)SELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SEEPAGQILSHLSSELK 17 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SEEPAGQILSHLS(0.904)S(0.096)ELK;SEEPAGQILSHLS(0.997)S(0.003)ELK 239.22 1.82E-20 145008000 260080 202614 214630 205610 215325 153156 255140 183943 243992 TRUE FALSE 243802.0571 217615.7514 219721.125 210886.3007 198414.2431 197369.6509 216884.1256 206908.6885 203268.159 1.199410957 1.070584554 1.080942171 1.037478284 0.976120629 0.970981643 1.066985241 1.017909984 1 17.63302472 8 0.518954689 1.014040181 7.362858057 0.738936022 0.03375698 64.82078553 0.649873911 0.017412814 452.7967473 100000000 -8 6.348817877 SEEQLKEEGIEYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SEEQLKEEGIEYK 13 1 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 ;;; 230.97 2.92E-12 3211450000 4398960 2278880 2779510 2409300 3565970 2191610 3030980 2559610 5365590 FALSE TRUE 4123636.946 2447610.646 2845441.29 2471126.717 3285913.101 2824292.229 2576512.687 2879182.943 4470038.366 0.92250594 0.547559203 0.636558583 0.552820024 0.735097293 0.63182729 0.576396101 0.644106987 1 22.09185578 -1.550841607 2.544307003 1.026049525 0.638044883 0.483683589 0.110386385 5987531.251 5484721.984 1061623.133 0.024790561 0.028129266 1.550841607 -0.388004642 SEETQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SEETQER 7 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 180.18 0.0016059 206710000 328090 330880 356560 348090 350560 280620 336820 306690 346850 FALSE TRUE 307555.4326 355378.6995 365017.7716 357022.5787 323028.4317 361630.4385 286316.9679 344980.9216 288958.4943 1.064358511 1.229860712 1.263218693 1.235549692 1.11790599 1.251496134 0.990858457 1.193877074 1 18.14050275 1.74594738 24.99999987 1.066617154 1.204610309 0.359656612 0.082184467 1.574988944 5345.564159 0.03500092 0.019409656 55.71182436 -1.74594738 0.137993155 SEEVPAFGVAS(ph)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SEEVPAFGVASPPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK 44 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 1 SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK;SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK;SEEVPAFGVAS(0.999)PPPLT(0.001)DTPDTTANAEGDLPTTMGGPLPPHLALK;SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK;SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK 266.79 1.76E-67 269103000 475482 384395 449425 429804 455753 320788 519562 413520 615275 TRUE FALSE 445722.4304 412856.0058 460085.5732 440833.4983 419959.9978 413394.288 441658.5015 465148.8823 512581.6277 0.869563805 0.805444408 0.897584986 0.860025944 0.819303649 0.806494548 0.86163545 0.90746304 1 18.96742224 0.951988211 2.132579621 0.999368809 0.844318222 0.7523398 0.028733951 0.175793254 1.73361111 0.027305609 0.007543445 8.953404603 -0.951988211 -0.155050588 SEEWADNHLPLTDAELAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SEEWADNHLPLTDAELAR 18 0 O60664-4;O60664;O60664-3;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 0 ;;; 153.36 3.38E-08 1623780000 2235370 2490910 2425820 2363320 2630130 2033120 2723560 2210060 2924420 FALSE TRUE 2095462.182 2675339.568 2483361.596 2423966.792 2423570.199 2620048.739 2315187.462 2485990.856 2436315.41 0.860094786 1.098108873 1.019310384 0.994931437 0.994768653 1.075414427 0.950282321 1.020389579 1 21.21626949 1.711563836 25 0.987505859 1.018076484 0 0.065281057 2.891534407 2664.890472 0.027874197 0.015457607 51.47114583 -1.711563836 0.030570625 SEFVVPDLELPSWLTTGNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEFVVPDLELPSWLTTGNYR 20 0 P17900 P17900 GM2A Ganglioside GM2 activator;Ganglioside GM2 activator isoform short 0 190.24 4.42E-17 22682000 35951 36562 32376 32598 38672 27276 31894 31728 60028 FALSE TRUE 33700.89108 39269.08852 33143.97401 33434.51987 35634.85712 35150.13841 27111.79079 35689.31064 50008.939 0.673897342 0.785241385 0.662760992 0.66857087 0.712569749 0.702877108 0.542138892 0.713658625 1 15.60989838 0.961877351 24.12019754 1.000000001 0.679195246 0.738233295 0.059736408 2738.970789 1732948.574 0.062666638 0.01566666 9.159617776 -0.961877351 -0.320804755 SEGEGKPQGEGKPASQAKPESQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEGEGKPQGEGKPASQAKPESQPR 24 3 Q969E4 Q969E4 TCEAL3 Transcription elongation factor A protein-like 3 0 110.14 0.00088566 82378000 147870 78039 95728 102850 111530 72282 127490 88581 132170 FALSE TRUE 138615.0807 83817.08876 97998.71337 105489.3051 102770.8837 93148.64 108374.0581 99640.53284 110109.9731 1.258878526 0.761212507 0.890007604 0.958035881 0.933347641 0.845960065 0.984234715 0.904918328 1 16.74858562 0.206328427 0.785026211 1.001117492 0.91880581 0 0.13038648 13.71658352 10.18624759 0.165026024 0.040577534 1.60815693 -0.206328427 -0.082311682 SEGEIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SEGEIAR 7 0 P50395;P50395-2;Q5SX91 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;; 113.85 0.014047 806140000 974800 1297690 1147130 1186820 1328210 957830 1224250 1161730 1164160 FALSE TRUE 913789.0081 1393772.318 1174340.465 1217275.81 1223897.744 1234339.972 1040685.078 1306774.548 969854.1752 0.942192168 1.437094724 1.210842305 1.255112203 1.261939965 1.272706767 1.073032528 1.347392815 1 19.88740832 -2.201352936 0.330612324 0.710004977 1.250316432 0.178881093 0.139337984 63.53168091 2.883727342 13.80204531 0.1105769 0.006289948 2.201352936 0.540311456 SEGFDTYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SEGFDTYR 8 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ;;;; 219.16 1.53E-05 8273780000 10791900 11308500 11381500 11070700 12164600 10085910 12295400 10701900 10544300 FALSE TRUE 10116454.24 12145793.11 11651474.55 11354792.9 11209241.39 12997548.49 10451818.91 12038055.77 8784388.211 1.15164016 1.382656688 1.326384294 1.292610553 1.276041213 1.479619089 1.189817511 1.37039205 1 23.06651038 -1.639541934 2.479980278 0.959941804 1.313812001 0.516265387 0.093773622 7761431.737 6374650.759 1987506.201 0.020343219 0.022932852 1.639541934 0.353870197 SEGSMSTDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SEGSMSTDKR 10 1 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 0 ; 109.66 0.0048173 172070000 204915 229450 209919 202160 256950 180933 221945 200880 295360 FALSE TRUE 192089.7359 246438.7167 214898.3778 207347.7679 236770.1835 233165.4199 188666.4077 225960.3102 246062.5079 0.780654223 1.001528916 0.873348726 0.842662987 0.962235919 0.947586131 0.76674179 0.918304508 1 17.90866533 SEGTYLNSVIESHTEFIFTTIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SEGTYLNSVIESHTEFIFTTIK 22 0 A0A0A0MSX9;P41252;J3KR24;Q5TCC6 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;; 338.3 4.54E-81 340916000 587615 510118 574560 574108 609372 496984 673357 530907 469761 FALSE TRUE 550837.2261 547887.6675 588188.8345 588840.5832 561514.3812 640455.2129 572393.369 597191.9076 391354.8543 1.407513462 1.399976674 1.502955254 1.504620619 1.434796004 1.63650765 1.462594274 1.525960138 1 18.57811781 -0.702749048 6.305609761 0.999999997 1.482895328 0.833652022 0.067994541 2.84E-09 4.51E-10 0.06359582 0.014989679 0.198267236 0.702749048 0.482895331 SEHPGLSIGDTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SEHPGLSIGDTAK 13 0 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ;;; 184.98 9.05E-06 1560550000 3096550 3398470 3484760 3495740 3474020 2744100 4386720 3105330 3366780 FALSE TRUE 2902742.463 3650096.255 3567420.153 3585446.607 3201184.483 3536277.123 3728972.06 3493037.286 2804842.668 1.034903846 1.30135508 1.271878881 1.278305784 1.141306256 1.260775574 1.329476374 1.245359437 1 21.41948842 -1.462234938 3.383892209 0.996237412 1.248451442 0.404873119 0.086953418 6633496.719 2869580.268 181110.9763 0.018911846 0.034495708 1.462234938 0.25221403 SEHPPLCGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SEHPPLCGR 9 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 69.954 0.053781 428150000 437610 736100 644460 658340 798670 546820 678150 645330 713760 FALSE TRUE 410220.7713 790601.6099 659746.8955 675234.119 735945.6799 704678.0571 576467.7031 725900.871 594628.8449 0.689877013 1.329571575 1.109510413 1.135555607 1.237655533 1.185072105 0.969458021 1.220762964 1 19.18162992 -0.745522861 5.995827699 0.999999996 1.125669445 0.029823033 0.176812619 9.13E-09 1.52E-09 0.153211597 0.036112319 0.17967065 0.745522861 0.125669448 SEHQNSS(ph)PTCQEDEEDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEHQNSSPTCQEDEEDVR 18 0 Q9NP74-3;Q9NP74-2;Q9NP74;S4R313 Q9NP74-3 PALMD Palmdelphin 1 SEHQNS(0.077)S(0.921)PT(0.002)CQEDEEDVR 123.64 2.16E-05 152840000 36806 41522 48594 41247 40584 42699 54130 35541 23574 TRUE FALSE 34502.37816 44596.33208 49746.67263 42305.46785 37396.69635 55025.50814 46013.70902 39978.37209 19639.34711 1.756798634 2.270764493 2.53301051 2.154117834 1.904172076 2.801799257 2.342934761 2.035626331 1 14.26145935 SEIDLFNIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SEIDLFNIR 9 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;;;; 180.45 0.00011314 303399000 637618 1024735 565006 553255 743030 425664 704941 745251 1077304 FALSE TRUE 597710.6276 1100607.446 578408.2091 567452.46 684675.421 548546.2867 599241.6414 838297.2278 897495.0028 0.665976552 1.226310389 0.64446956 0.632262529 0.762873798 0.611197037 0.667682427 0.934041109 1 19.77554438 3.813918138 6.079779018 0.721115135 0.97639621 0.141253219 0.186412593 0.262301143 14.72106624 0.042736787 0.07779717 6515.055773 -3.813918138 0.255281075 SEIDLLDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEIDLLDIR 9 0 P12429;D6RA82 P12429 ANXA3 Annexin A3;Annexin 0 96.253 0.017433 11441000 51538 67428 53665 49627 74572 42812 60293 59426 61593 FALSE TRUE 48312.32858 72420.43928 54937.95914 50900.51284 68715.41593 55171.12941 51252.62438 66845.46691 51312.73039 0.941527146 1.411354234 1.070649695 0.991966564 1.339149474 1.075193797 0.998828634 1.30270727 1 15.64702917 -5 0.118033329 0.529383681 1.221223031 0.026801352 0.163684132 430.5484067 3.314008126 48.69578648 1.554693605 1.00E-05 5 0.69183935 IKELEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 IKELEQK 7 1 O60925 O60925 PFDN1 Prefoldin subunit 1 0 66.435 0.061909 407460000 558710 552730 649960 714540 1078800 637780 1190600 931360 1390100 FALSE TRUE 523741.3384 593654.7043 665377.3581 732876.3061 994075.3997 821896.7325 1012080.583 1047642.346 1158083.33 0.452248405 0.512618297 0.574550502 0.632835555 0.858379854 0.709704312 0.873927253 0.904634683 1 20.14330764 2.803921115 0.380795754 1.005980205 0.379131728 0.915928316 0.052824697 0.398161663 0.114159679 0.052345593 0.096288482 636.6798645 -2.803921115 -0.626848478 down SELDMLDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SELDMLDIR 9 0 P08133;P08133-2 P08133 ANXA6 Annexin A6 0 ;;;; 133.23 0.00065763 265942000 831601 898739 832427 666970 1228015 483869 893510 1080371 1444170 FALSE TRUE 779552.5779 965282.5707 852172.5615 684085.5794 1131571.655 623554.1253 759536.4704 1215257.698 1203128.697 0.647937814 0.80231032 0.708297095 0.568588864 0.9405242 0.518277161 0.6313011 1.010081216 1 20.19835954 1.231979679 24.89967157 1.005040874 0.694281631 0.554160556 0.118059979 116.8418498 442062.0805 0.098111497 0.026815212 17.06002562 -1.231979679 -0.310759242 SELHLMDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SELHLMDR 8 0 P42704;B8ZZ38;A0A0C4DG06;C9JCA9 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 ;; 115.7 0.0024136 354211000 456547 575130 485931 461527 688190 514887 455796 602072 647520 FALSE TRUE 427972.5382 617713.2236 497457.5128 473370.5642 634142.3334 663526.5184 387453.6212 677242.0145 539444.7289 0.793357531 1.145090851 0.922165861 0.877514486 1.175546445 1.230017614 0.718245263 1.255442825 1 19.04111562 2.760502272 24.95305374 1.043244255 0.967564256 0.111343003 0.175418378 3040.032113 3457260.255 0.052590415 0.055738715 576.1058321 -2.760502272 -0.07568 SELISS(ph)TFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SELISSTFK 9 0 H0YHG7;Q92730 H0YHG7 RND1 Rho-related GTP-binding protein Rho6 1 SELIS(0.046)S(0.477)T(0.477)FK;SELIS(0.047)S(0.477)T(0.477)FK;SELIS(0.047)S(0.477)T(0.477)FK 62.2 0.0883 2781390000 755160 2509510 1936820 2022940 2041360 2267720 1638390 1852890 1532700 TRUE FALSE 707895.8836 2695316.732 1982762.285 2074852.065 1881039.82 2922373.951 1392728.63 2084227.395 1276882.468 0.554393925 2.110857341 1.552815027 1.624935823 1.473150322 2.28867889 1.090725783 1.632278183 1 20.28419431 -0.625039437 8.586682979 0.999969466 1.589790053 0.103019103 0.482940008 0 0 0.413782675 0.097529512 0.237115838 0.625039437 0.589820587 SELKDFFQSYGNVVELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SELKDFFQSYGNVVELR 17 1 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ; 178.71 8.73E-10 389180000 760890 770050 776280 772940 864570 576070 826810 707430 763310 FALSE TRUE 713267.2531 827065.3032 794693.7282 792774.949 796670.1597 742372.0573 702837.5162 795754.1927 635908.6298 1.121650532 1.300603993 1.249697977 1.246680595 1.25280602 1.167419378 1.105249219 1.251365614 1 19.27845996 0.465196495 0.392411626 0.978276193 1.253884154 0.500788848 0.06456793 1.860266191 0.547814188 0.153438397 0.04788404 2.918747293 -0.465196495 0.275607961 SELKELLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SELKELLTR 9 1 P26447 P26447 S100A4 Protein S100-A4 0 ; 119.34 0.00076955 2632700000 1749280 2692200 2335100 2919400 4032200 2211400 3358900 1691710 9838200 FALSE TRUE 1639795.687 2891533.289 2390489.675 2994316.747 3715527.277 2849795.281 2855264.127 1902923.717 8196140.863 0.200069242 0.352792044 0.291660394 0.365332514 0.45332643 0.347699647 0.348366893 0.232173135 1 22.96651335 -2.023321805 2.875676998 1.780627554 0.331076218 0.898871741 0.071230258 20300475.82 10339350.1 104518960.2 0.016479713 0.00947716 2.023321805 -1.449551336 SELLSQLQQHEEESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SELLSQLQQHEEESR 15 0 Q92665 Q92665 MRPS31 "28S ribosomal protein S31, mitochondrial" 0 ;; 179.17 6.82E-07 484580000 354084 355073 319615 300647 393680 319825 308699 333020 493660 FALSE TRUE 331922.5145 381362.9744 327196.4187 308362.111 362761.9608 412153.2856 262412.4508 374598.2801 411264.9568 0.807077065 0.927292657 0.795585457 0.749789414 0.882063873 1.002159991 0.638061781 0.91084415 1 18.64970862 SELNEIKENQRS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SELNEIKENQRSPVR 15 2 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 SELNEIKENQRS(1)PVR;SELNEIKENQRS(1)PVR;SELNEIKENQRS(1)PVR;SELNEIKENQRS(1)PVR;SELNEIKENQRS(1)PVR 183.22 2.68E-07 4889030000 4017433 4309154 4204228 4760890 5651530 3016086 5014680 3927728 7533440 TRUE FALSE 3765989.04 4628208.246 4303954.274 4883062.498 5207681.631 3886781.066 4262775.288 4418113.487 6276060.196 0.600056233 0.737438473 0.685773262 0.778045835 0.829769229 0.619302707 0.679211982 0.703962892 1 22.58142776 -0.946108469 4.253559805 1.000009156 0.70569767 0.652781277 0.067791489 17631557.57 36893046.04 2521.407066 0.015673196 0.113211757 0.946108469 -0.294311486 SELNLR ddPTM_SK-BR-3_Pertuzumab_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 ; 177.57 0.0084773 907950000 952920 1292740 1018520 1104670 1235930 782730 1120010 1123440 1037450 FALSE TRUE 893278.4382 1388455.815 1042679.775 1133017.702 1138865.043 1008691.444 952074.8982 1263703.957 864292.8928 1.033536716 1.606464459 1.206396332 1.310918685 1.317684147 1.167071317 1.101565113 1.462124666 1 19.72116077 2.584476996 0.900238543 1.17297203 1.350485413 0.045820033 0.184279328 1.205935819 2.015734008 0.11112515 0.088537461 384.1289122 -2.584476996 0.177513383 SELPVVDETTTLLNERNS(ph)LLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SELPVVDETTTLLNERNSLLHK 22 1 Q6P4Q7 Q6P4Q7 CNNM4 Metal transporter CNNM4 1 SELPVVDETT(0.007)T(0.006)LLNERNS(0.987)LLHK 71.052 0.010152 19887000 22053 16346 18150 17675 30845 16244 26355 22472 29441 TRUE FALSE 20672.7421 17556.27485 18580.52657 18128.57042 28422.55812 20933.3791 22403.31242 25277.67867 24527.1069 0.842852856 0.715790693 0.757550682 0.73912388 1.158822287 0.853479344 0.913410314 1.030601724 1 14.58208945 2.778493421 24.99156814 0.968482589 0.754776523 0.626202555 0.086197509 334.9651349 209634.1779 0.02468871 0.026186045 600.4729129 -2.778493421 -0.213706066 SELVAMLEEEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SELVAMLEEEELR 13 0 B4DZG7;F8VYN9;P40616-2;P40616 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ;; 186.02 1.90E-05 35066800 61403 72234 72060 70808 67098 64868 77232 62123 59021 FALSE TRUE 57559.89584 77582.28052 73769.29723 72625.05316 61828.39374 83594.33856 65651.77859 69879.1933 49170.01381 1.170630052 1.577837273 1.50029035 1.477019173 1.257441049 1.700108096 1.335199515 1.421174978 1 15.58549114 0.359448013 1.15014011 0.999418245 1.45904158 0.431665163 0.153352142 2.585990377 3.863711387 0.13348313 0.040146923 2.287957818 -0.359448013 0.459623335 SELVAMLEEEELRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SELVAMLEEEELRK 14 1 B4DZG7;F8VYN9;P40616-2;P40616 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ;;;;; 294.31 2.30E-43 715142000 833700 724093 762382 762120 786594 583538 933687 676119 861872 FALSE TRUE 781520.2052 777705.5991 780466.0611 781677.2895 724818.0802 751995.9477 793689.3023 760533.9455 718019.9953 1.088437941 1.083125267 1.086969814 1.088656715 1.009467821 1.04731895 1.105386072 1.059209981 1 19.45366449 2.878340496 19.91305308 1.054832588 1.086225139 0.309477934 0.029282925 6.294794768 1004.148337 0.009016539 0.009563504 755.6844685 -2.878340496 0.031392551 SENFEELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SENFEELLK 9 0 P29373;Q5SYZ4 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 ; 138.66 0.00030332 156509000 201895 173387 187143 165075 219961 151926 207980 175850 364460 FALSE TRUE 189258.7523 186224.7539 191582.1203 169311.104 202686.1503 195784.5699 176795.3298 197805.2596 303629.2715 0.623321827 0.613329383 0.630973817 0.557624445 0.66754483 0.644814543 0.582273669 0.651469664 1 18.21195136 0.945364401 18.48650141 1 0.617414683 0.939234807 0.030384538 102.6648875 34738.07735 0.026922332 0.006730583 8.817884404 -0.945364401 -0.382585317 SENLGQGDKPDYFSSVATVVYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SENLGQGDKPDYFSSVATVVYLR 23 1 P27694 P27694 RPA1 "Replication protein A 70 kDa DNA-binding subunit;Replication protein A 70 kDa DNA-binding subunit, N-terminally processed" 0 129.66 3.43E-05 193800000 244350 210070 244500 232800 226220 204600 276350 208720 237920 FALSE TRUE 229056.5697 225623.8014 250299.6555 238774.0421 208453.5937 263664.6986 234913.883 234779.1514 198209.615 1.155627943 1.138309064 1.262802793 1.204654185 1.051682552 1.330231627 1.185179049 1.184499306 1 17.59666742 0.626282136 3.338480161 1.000002075 1.193944559 0.396212779 0.073262453 7.859147036 69.07327971 0.06500573 0.016823519 4.229432867 -0.626282136 0.193942485 SENPAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SENPAKR 7 1 O43709;O43709-3;O43709-2;H7C170;F2Z3D9 O43709 WBSCR22 Probable 18S rRNA (guanine-N(7))-methyltransferase 0 69.998 0.09335 29287000 69584 82169 78248 81070 82626 65086 78563 69110 69489 FALSE TRUE 65228.86165 88252.87826 80104.07951 83150.39345 76136.88726 83875.27162 66783.20749 77738.53563 57890.83698 1.126756237 1.524470587 1.383709127 1.436330822 1.315180281 1.448852288 1.153605838 1.34284698 1 15.82104739 0.768815151 0.596101067 0.997735811 1.399265532 0.42432368 0.124296565 0.931845559 0.706696574 0.125076435 0.049334166 5.872393518 -0.768815151 0.401529721 SENSEDGAAWMQEPGRYS(ph)PPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SENSEDGAAWMQEPGRYSPPPR 22 1 P35548 P35548 MSX2 Homeobox protein MSX-2 1 SENSEDGAAWMQEPGRYS(1)PPPR;SENSEDGAAWMQEPGRY(0.015)S(0.985)PPPR 109.45 0.00059024 353350000 368190 400140 384910 381790 449970 360010 456120 370420 444680 TRUE FALSE 345145.6451 429766.7819 394040.247 391587.3778 414631.1713 463939.0427 387729.0404 416667.7524 370460.0353 0.93166769 1.160089459 1.063651162 1.057030018 1.119233202 1.252332232 1.046615029 1.12473064 1 18.49895839 4.749341461 24.88605657 1.107455199 0.931667584 0.371199907 0.069846279 1532.834637 3538260.312 0.015300397 0.225035904 56148.927 -4.749341461 -0.175787615 SEPDKADPFSFEGPEIVDCDGCTIDWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEPDKADPFSFEGPEIVDCDGCTIDWK 27 1 Q99733;Q99733-2;C9JZI7;E9PP22;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 226.89 1.22E-34 101090000 183510 95131 126510 116640 126390 105080 186750 105410 166660 FALSE TRUE 172024.4367 102174.5982 129510.8769 119633.1799 116463.8392 135414.8902 158748.5712 118570.6705 138843.3693 1.238982009 0.735898291 0.932784025 0.86164129 0.838814556 0.975306857 1.14336444 0.853988715 1 17.08309876 2.019199128 10.37024168 1.026106636 0.896019047 0.031760931 0.146486302 0.637840831 332.99711 0.050651472 0.037069249 104.5199342 -2.019199128 -0.130087589 SEPFS(ph)PSLRPEPPKHPESIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SEPFSPSLRPEPPKHPESIK 20 2 O60885 O60885 BRD4 Bromodomain-containing protein 4 1 S(0.003)EPFS(0.965)PS(0.032)LRPEPPKHPESIK;SEPFS(0.96)PS(0.039)LRPEPPKHPESIK 128.97 8.91E-06 341170000 977480 564180 676550 730340 736530 524490 921150 609230 790620 TRUE FALSE 916301.2717 605952.4742 692598.0855 749081.7609 678685.9048 675901.7486 783032.109 685293.7066 658660.4144 1.391158861 0.919977064 1.051525293 1.137280675 1.030403361 1.026176363 1.188825215 1.040435544 1 19.32917532 SEPTQALELTEDDIKEDGIVPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SEPTQALELTEDDIKEDGIVPLR 23 1 O43396;K7ER96 O43396 TXNL1 Thioredoxin-like protein 1 0 ; 197.28 2.73E-24 104393000 171769 106561 128281 122019 130805 96627 157945 105332 149080 FALSE TRUE 161018.2849 114450.8873 131323.8859 125150.2141 120532.1029 124521.6463 134262.6135 118482.9321 124197.5849 1.296468728 0.921522648 1.05737874 1.007670272 0.970486689 1.002609241 1.081040454 0.953987408 1 16.92227759 4.748921476 24.86666419 1.005409995 1.296468903 0.801490008 0.046384807 611.7805643 1468277.704 0.010878867 0.152919342 56094.65433 -4.748921476 0.291058907 SEPVKEES(ph)SELEQPFAQDTSSVGPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SEPVKEESSELEQPFAQDTSSVGPDR 26 1 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 SEPVKEES(0.965)S(0.035)ELEQPFAQDTSSVGPDR;S(0.003)EPVKEES(0.583)S(0.414)ELEQPFAQDTSSVGPDR 213.35 1.95E-26 545690000 342310 172437 236027 235702 276064 201101 306200 235257 352230 TRUE FALSE 320885.4281 185204.4149 241625.6719 241750.5124 254383.047 259155.5941 260288.1526 264629.3543 293440.5375 1.093527946 0.631148022 0.823422946 0.823848383 0.866898109 0.883162212 0.887021796 0.901815941 1 18.16270866 1.417519431 0.554617453 0.993813574 0.80149967 0.099326082 0.113608811 1.172727044 0.891617886 0.107300072 0.057657369 26.15287456 -1.417519431 -0.192313903 SEPVKEESS(ph)ELEQPFAQDTSSVGPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEPVKEESSELEQPFAQDTSSVGPDR 26 1 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 SEPVKEES(0.366)S(0.634)ELEQPFAQDTSSVGPDR 288.02 5.77E-62 391260000 341930 186480 232870 231200 268250 183200 335310 243450 381380 TRUE FALSE 320529.2117 200287.1732 238393.7864 237132.9834 247182.7271 236086.866 285033.3784 273845.2684 317725.2142 1.008825228 0.630378592 0.750314346 0.746346128 0.777976428 0.743053606 0.897106574 0.86189341 1 18.27742006 1.296876041 0.952962452 0.990371544 0.750434186 0.315842931 0.099232143 0.485027321 0.929836584 0.084492169 0.030151465 19.80961529 -1.296876041 -0.239937358 SEPVKEESSELEQPFAQDT(ph)SSVGPDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEPVKEESSELEQPFAQDTSSVGPDRK 27 2 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 SEPVKEESSELEQPFAQDT(0.48)S(0.48)S(0.04)VGPDRK 234.25 2.70E-43 332580000 362410 204050 262020 240910 288540 179650 357420 233520 438860 TRUE FALSE 339727.405 219158.0743 268235.2381 247092.1585 265879.2323 231512.0386 303828.1891 262675.486 365611.4309 0.929203456 0.599428945 0.733662067 0.675832695 0.727218051 0.633218819 0.831013922 0.718455343 1 18.47995165 0.201783235 0.696539503 1.007666179 0.707709619 0.430622424 0.095347254 2.574920216 1.58691284 0.135264907 0.031104625 1.591414222 -0.201783235 -0.299956559 SEPVKEESSELEQPFAQDTS(ph)SVGPDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SEPVKEESSELEQPFAQDTSSVGPDRK 27 2 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 SEPVKEES(0.001)S(0.009)ELEQPFAQDT(0.181)S(0.688)S(0.122)VGPDRK;SEPVKEESSELEQPFAQDT(0.075)S(0.462)S(0.462)VGPDRK 242.23 1.60E-45 478080000 240363 124914 160354 163079 180907 113996 249510 169416 311180 TRUE FALSE 225319.1089 134162.7625 164157.6726 167263.8832 166699.294 146904.7946 212098.2918 190567.9605 259242.0477 0.869145692 0.517519298 0.633221632 0.645203526 0.64302568 0.566670399 0.818147726 0.735096649 1 17.98394021 0.947097454 0.860822202 0.995123504 0.628585989 0.513253268 0.102368526 0.477562478 0.763255307 0.088720205 0.031249845 8.853142489 -0.947097454 -0.366537516 SEPVKEESSELEQPFAQDTSSVGPDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEPVKEESSELEQPFAQDTSSVGPDRK 27 2 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 285.55 1.03E-61 252870000 275730 179630 195660 197440 230680 154910 268500 171970 345140 FALSE TRUE 258472.5515 192929.9921 200301.1476 202506.6447 212563.3233 199630.0022 228240.9176 193440.8331 287533.9043 0.898928953 0.670981715 0.696617493 0.704287883 0.73926351 0.69428335 0.793787843 0.672758343 1 18.13337255 -1.561969519 2.927026951 1.014210467 0.727360303 0.594448639 0.068897322 17829348.87 17850696.54 1966667.735 0.015152421 0.027417666 1.561969519 -0.286850164 SEPVS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SEPVSPSR 8 0 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 SEPVS(0.999)PS(0.001)R;SEPVS(0.976)PS(0.024)R;SEPVS(0.999)PS(0.001)R;SEPVS(0.903)PS(0.097)R 178.94 0.00025908 3078250000 3069770 3015900 3156580 3098620 2871460 2861690 3491300 2714170 2585740 TRUE FALSE 2877638.575 3239200.374 3231455.568 3178135.835 2645947.115 3687813.447 2967811.977 3053040.099 2154163.289 1.335849789 1.503693053 1.50009778 1.475345834 1.22829459 1.711947031 1.377709847 1.417274222 1 21.03869618 0.512683561 1.654362059 1.000141498 1.461318845 0.551461229 0.125866075 1.930438554 5.790353172 0.106830372 0.030342841 3.255993737 -0.512683561 0.461177347 SEPVS(ph)PSRER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SEPVSPSRER 10 1 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 SEPVS(0.998)PS(0.002)RER;SEPVS(0.965)PS(0.035)RER;SEPVS(1)PSRER;SEPVS(1)PSRER 153.75 9.51E-06 1557616000 850480 1116545 1050509 1197535 1342442 831116 1098135 1036332 1543615 TRUE FALSE 797249.975 1199215.154 1075427.57 1228265.776 1237012.02 1071045.697 933479.8513 1165720.331 1285975.684 0.61995727 0.932533304 0.836273642 0.955123639 0.961924891 0.832866212 0.725892303 0.906487071 1 20.29443193 4.746330154 24.69823045 0.876713804 0.619957123 0.522006286 0.08090868 751.5436009 2388981.797 0.020027607 0.215949225 55760.94871 -4.746330154 -0.256756682 SEPVSPS(ph)RER ddPTM_SK-BR-3_Pertuzumab_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 S(0.001)EPVS(0.259)PS(0.74)RER 79.089 0.073795 577260000 311910 394050 343960 367110 430230 251490 348740 308790 498460 TRUE FALSE 292388.1099 423225.872 352118.8936 376530.6641 396441.4713 324091.0804 296449.6745 347343.1112 415263.8058 0.704102081 1.019173513 0.847940246 0.90672642 0.95467379 0.780446251 0.713882767 0.836439647 1 18.66366861 2.22535143 24.96795334 0.797659695 0.900268904 0.00538779 0.109605344 382.7251017 723420.5927 0.037230886 0.027658332 168.0163051 -2.22535143 0.102609209 SERDDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SERDDLR 7 1 Q32MZ4-4 Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 65.235 0.064876 112840000 258290 435650 402460 369290 448400 410290 392880 406660 326150 FALSE TRUE 242124.09 467905.9793 412006.5413 378766.6066 413184.4728 528734.0625 333971.2913 457432.3962 271713.458 0.891100837 1.722056694 1.516327326 1.393992809 1.520662524 1.94592519 1.229130474 1.683510267 1 18.0517265 -1.287970482 3.47170962 0.998287654 1.509156659 0.219252932 0.286811308 29666635.76 46075329.8 535407.8732 0.06043892 0.051526366 1.287970482 0.510869005 SES(ph)ELIDELSEDFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SESELIDELSEDFDR 15 0 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;D6RC54;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 1 SES(1)ELIDELSEDFDR;S(0.001)ES(0.999)ELIDELSEDFDR;S(0.011)ES(0.989)ELIDELSEDFDR;S(0.053)ES(0.947)ELIDELSEDFDR;SES(1)ELIDELSEDFDR;SES(1)ELIDELSEDFDR 344.38 4.18E-70 248749000 388607 413988 426213 519047 504908 369494 402859 310978 353394 TRUE FALSE 364284.7816 444640.1023 436322.9736 532366.6248 465254.5624 476160.9196 342454.0329 349804.2878 294410.2584 1.237337257 1.510273809 1.482023677 1.808247538 1.580293312 1.617338072 1.163186483 1.188152511 1 18.16746842 1.665011532 4.910576827 1.120258445 1.540940476 0.645404763 0.14756666 0.100060845 5.448398135 0.078870992 0.037858307 46.23932996 -1.665011532 0.42068203 SES(ph)ENWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SESENWR 7 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;C9IYH5;C9JH78;Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 SES(1)ENWR;SES(1)ENWR 112.8 0.0065797 558590000 774360 821230 707340 753760 581780 451700 949070 610330 1048920 TRUE FALSE 725894.1899 882034.7237 724118.4388 773102.7577 536089.3456 582098.4573 806765.7642 686531.044 873848.4757 0.830686566 1.009368041 0.828654462 0.884710312 0.613480896 0.666132028 0.923233017 0.785640833 1 19.73702361 3.517889591 2.012133142 0.796206064 0.929105842 0.109978928 0.120932846 0.552949342 4.466662597 0.034718397 0.059581774 3295.259273 -3.517889591 0.132899778 SES(ph)FSSEDLIPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SESFSSEDLIPSR 13 0 Q9P219;Q9P219-2;A0A0A0MR69;Q9P219-3 Q9P219 CCDC88C Protein Daple 1 SES(1)FSSEDLIPSR;SES(0.999)FS(0.001)SEDLIPSR 242.94 6.16E-17 208769000 424720 449420 443070 466070 393410 354030 563030 347030 330690 TRUE FALSE 398137.5333 482695.5244 453579.8296 478030.1453 362513.1655 456232.7138 478608.8784 390357.4594 275495.7027 1.445167854 1.752098199 1.646413448 1.735163709 1.315857787 1.656042941 1.737264407 1.41692758 1 18.07167029 0.937072447 4.50833029 1.000248272 1.629945317 0.663267033 0.138147519 0.168347871 9.352168698 0.125628952 0.031908711 8.6511222 -0.937072447 0.629697045 SES(ph)LESPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SESLESPR 8 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;Q5VY93 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 S(0.003)ES(0.992)LES(0.006)PR;SES(0.997)LES(0.003)PR 180.74 0.00024914 340190000 863870 797230 792690 764990 691870 615930 805880 626640 829730 TRUE FALSE 809801.9188 856257.7387 811492.9811 784620.9385 637533.3211 793738.9922 685045.7754 704877.3834 691242.7027 1.171516047 1.238722283 1.173962456 1.135087481 0.922300255 1.148278295 0.991035092 1.019724882 1 19.39883282 2.981056561 4.206797734 1.024041954 1.198405206 0.665153112 0.05856519 0.114484609 4.744895877 0.016274591 0.018361526 957.3187411 -2.981056561 0.174363252 SES(ph)LSNCSIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SESLSNCSIGK 11 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 SES(0.993)LS(0.007)NCSIGK;SES(0.5)LS(0.5)NCSIGK;SES(1)LSNCSIGK;SES(0.999)LSNCSIGK;SES(1)LSNCSIGK;SES(0.999)LSNCSIGK 278.84 2.95E-27 2217610000 3034870 2395430 2578800 2602220 2734060 1932670 3481360 2476940 3236620 TRUE FALSE 2844922.904 2572790.13 2639970.354 2668997.371 2519337.956 2490600.455 2959362.387 2786191.411 2696407.213 1.055079103 0.954154891 0.979069608 0.98983468 0.934331411 0.92367371 1.097520572 1.033297715 1 21.36260696 1.738855387 25 1.050064405 0.970471754 0.376371822 0.042699635 0.047566025 3210.517502 0.018232536 0.010110869 54.80944286 -1.738855387 -0.079592651 SES(ph)NEDLFGLVPFDEITGSQQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SESNEDLFGLVPFDEITGSQQQK 23 0 H0Y9P1;Q9NSY1 H0Y9P1 BMP2K BMP-2-inducible protein kinase 1 S(0.147)ES(0.853)NEDLFGLVPFDEITGSQQQK 172.75 2.99E-12 37722000 112750 82664 83628 87819 95557 63239 115990 83220 127870 TRUE FALSE 105693.1788 88784.52857 85611.69565 90072.58422 88052.33868 81495.0727 98598.3763 93610.20019 106527.6709 0.992166428 0.833441 0.80365688 0.845532278 0.826567763 0.765013184 0.925565869 0.878740701 1 16.7008687 0.931464354 1.220916905 0.99659746 0.840994107 0.336501365 0.063124259 0.564271526 1.69990896 0.055604444 0.017201665 8.540127491 -0.931464354 -0.155603353 SES(ph)PDHMVSQYQQALEEIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SESPDHMVSQYQQALEEIER 20 0 Q14149;H0YHQ4;H0YIR5 Q14149 MORC3 MORC family CW-type zinc finger protein 3 1 S(0.1)ES(0.9)PDHMVSQYQQALEEIER;S(0.135)ES(0.865)PDHMVSQYQQALEEIER;S(0.112)ES(0.888)PDHMVSQYQQALEEIER;S(0.456)ES(0.544)PDHMVSQYQQALEEIER;S(0.194)ES(0.806)PDHMVSQYQQALEEIER 282.86 4.78E-45 247004000 59090.8 60563.8 66530 68128.7 66757.9 56717.1 70047.4 56571.7 76615.7 TRUE FALSE 55392.41231 65048.00677 68108.12302 69876.99778 61515.00382 73090.40604 59544.44266 63634.80127 63828.04471 0.867838151 1.019113261 1.067056391 1.094769519 0.96376137 1.145114289 0.932888402 0.996972437 1 15.96190283 1.630354426 25 0.973689674 1.031005638 0.083193099 0.076429253 1.80242974 1998.127643 0.032732675 0.01813399 42.69277908 -1.630354426 0.057315964 SES(ph)PIPVAEQGTLMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SESPIPVAEQGTLMR 15 0 P86452 P86452 ZBED6 Zinc finger BED domain-containing protein 6 1 SES(1)PIPVAEQGTLMR;S(0.001)ES(0.999)PIPVAEQGTLMR;SES(1)PIPVAEQGTLMR 187.35 3.61E-07 465900000 403668 459632 403186 422447 470641 344870 468563 388445 388729 TRUE FALSE 378403.1404 493663.6315 412749.7623 433287.7052 433678.7543 444428.3705 398306.3281 436943.2133 323847.6186 1.168460469 1.524370115 1.274518442 1.337936981 1.339144491 1.37233793 1.229918966 1.349224722 1 18.30495561 -3.107533974 0.265578969 0.278534544 1.367190846 0.522661229 0.095686073 46.74098328 1.130403363 18.78417643 0.114030063 0.000780667 3.107533974 1.088656302 SES(ph)PKEPEQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 SESPKEPEQLR 11 1 F8W6I7;P09651-2;P09651;P09651-3;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 SES(1)PKEPEQLR;S(0.006)ES(0.994)PKEPEQLR;S(0.009)ES(0.991)PKEPEQLR;S(0.038)ES(0.962)PKEPEQLR;S(0.001)ES(0.999)PKEPEQLR;S(0.002)ES(0.998)PKEPEQLR;S(0.015)ES(0.985)PKEPEQLR;S(0.007)ES(0.993)PKEPEQLR;SES(1)PKEPEQLR;S(0.021)ES(0.979)PKEPEQLR 193.15 2.84E-06 27978040000 24621690 13165440 16179370 16827180 15616070 11477180 19564430 12092160 16550160 TRUE FALSE 23080662.37 14140222.88 16563152.3 17258993.93 14389646.85 14790455.55 16630925.35 13601892.79 13787831.38 1.673987862 1.025558153 1.201287704 1.251755512 1.043648306 1.072718047 1.206203129 0.986514298 1 23.71689222 4.744257454 24.87567663 1.115824219 1.67398812 0.786432223 0.093868387 255.8467845 1117139.892 0.020812548 0.182873331 55495.45979 -4.744257454 0.558163901 SES(ph)PKEPEQLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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(0.001)ES(0.999)PKEPEQLRK;SES(1)PKEPEQLRK;S(0.115)ES(0.885)PKEPEQLRK;S(0.021)ES(0.979)PKEPEQLRK;S(0.286)ES(0.714)PKEPEQLRK;S(0.423)ES(0.577)PKEPEQLRK;SES(1)PKEPEQLRK;S(0.001)ES(0.999)PKEPEQLRK 150.19 5.35E-05 34603270000 18102780 8644000 11458900 11741650 12023290 7596120 14327520 8871040 15114210 TRUE FALSE 16969759.31 9284010.754 11730710.52 12042960.62 11079029.3 9788996.531 12179241.39 9978608.872 12591550.71 1.34771004 0.737320682 0.931633505 0.956431888 0.879878067 0.777425812 0.96725508 0.792484508 1 23.58595263 4.7492493 24.85757246 0.87698285 1.347710328 0.737337487 0.087652495 699.9662952 1627805.739 0.019330055 0.280484078 56137.01288 -4.7492493 0.470727478 SES(ph)PPAELPSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SESPPAELPSLR 12 0 Q14669-3;Q14669;Q14669-2;G5E9G6;H7C1L9 Q14669-3;H7C1L9 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 SES(1)PPAELPSLR;SES(1)PPAELPSLR;SES(1)PPAELPSLR;SES(1)PPAELPSLR;S(0.001)ES(0.999)PPAELPSLR;SES(1)PPAELPSLR 296.56 2.82E-36 2329070000 1994040 1836710 1900200 1882690 1676450 1583370 2293480 1567780 1579690 TRUE FALSE 1869236.596 1972701.919 1945273.641 1931003.013 1544788.379 2040463.215 1949593.966 1763520.784 1316029.534 1.420360674 1.498979976 1.478138287 1.467294588 1.173825009 1.550469167 1.481421135 1.340031313 1 20.32776044 0.870570796 3.790381064 1.000102047 1.447011475 0.649347256 0.100817599 0.394580739 10.35343022 0.092596252 0.023756054 7.422851908 -0.870570796 0.446909428 SES(ph)PPPLSDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 209.19 1.78E-08 2699350000 5171730 3499290 3884150 3741010 4262340 2716370 4804700 3315780 5010830 TRUE FALSE 4848040.651 3758381.073 3976283.872 3837010.65 3927593.01 3500541.922 4084279.84 3729762.432 4174490.102 1.161349179 0.900320993 0.952519655 0.919156725 0.940855749 0.838555569 0.978390112 0.893465391 1 21.99316856 4.742412336 24.95067227 0.92622984 1.161349272 0.723005581 0.045398714 174.5642553 1130746.374 0.009362144 0.070990199 55260.18514 -4.742412336 0.235119431 SES(ph)QERPGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SESQERPGSR 10 1 A0A3B3ISF0;Q659C4;Q659C4-9;H0Y9K3;D6R9W6;A0A3B3IT29;A0A3B3ISF8;G3V0E9;Q659C4-3 A0A3B3ISF0 LARP1B La-related protein 1B 1 SES(0.904)QERPGS(0.096)R;S(0.013)ES(0.987)QERPGSR 110.38 0.0011469 94367000 106919 98469 100148 115300 117297 85546 116986 99264 99765 TRUE FALSE 100227.1306 105759.7472 102523.5579 118258.7932 108084.9668 110241.7415 99445.03534 111657.3289 83113.57699 1.205905633 1.272472574 1.233535622 1.422857702 1.300448984 1.326398712 1.196495674 1.343430676 1 16.34279655 -1.192522133 5.173553922 0.999981309 1.281300146 0.638131824 0.067933636 1.39E-05 2.18E-06 0.062639864 0.014763377 0.064191551 1.192522133 0.281318837 SES(ph)VEGFLSPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SESVEGFLSPSR 12 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 S(0.062)ES(0.938)VEGFLSPSR 211.22 3.61E-08 78879000 200670 188220 175720 153460 172310 122060 209820 171290 228600 TRUE FALSE 188110.4229 202156.0046 179888.1614 157398.0434 158777.4677 157296.7405 178359.4389 192675.9336 190445.1832 0.987740513 1.061491823 0.944566612 0.826474268 0.833717425 0.825942341 0.936539512 1.011713346 1 17.53901627 3.641431949 3.196717978 0.895845081 1.02418206 0.320151709 0.068927994 0.248151764 4.927255802 0.018782392 0.031724792 4379.574804 -3.641431949 0.128336979 SES(ph)WER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SESWER 6 0 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 1 SES(1)WER;SES(1)WER 146.27 0.011581 1205820000 1065510 1094320 1052550 1020290 1005340 704360 993370 770540 1296070 TRUE FALSE 998821.6311 1175344.591 1077516.983 1046472.369 926384.6517 907697.2977 844423.3905 866743.6152 1079747.544 0.925051079 1.08853648 0.997934183 0.969182449 0.85796412 0.840656969 0.78205632 0.802728026 1 20.0422626 2.829736767 1.948186229 0.831688702 1.022643467 0.46778063 0.071404745 0.213328831 1.602512974 0.023305677 0.024520175 675.6733154 -2.829736767 0.190954765 SESAPTLHPYSPLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SESAPTLHPYSPLSPK 16 0 Q8WUF5;K7EN03 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 SESAPTLHPYSPLS(1)PK 202.94 1.87E-11 547280000 1331300 1050200 1221100 1660400 1820800 635850 1088500 733190 1073500 TRUE FALSE 1247976.309 1127957.901 1250065.069 1703008.675 1677801.713 819409.5728 925289.5301 824730.3855 894325.9149 1.395437937 1.261238081 1.397773505 1.904237199 1.876051767 0.916231498 1.034622295 0.922181021 1 19.77044116 2.216989079 24.99868712 0.975983773 1.517522186 0.671536486 0.206424187 177.3133513 205482.5022 0.087207652 0.064464605 164.8120946 -2.216989079 0.541538413 SESELIDELS(ph)EDFDRSECK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SESELIDELSEDFDRSECK 19 1 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;D6RC54;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 1 SESELIDELS(1)EDFDRSECK;SESELIDELS(1)EDFDRSECK 266.09 1.07E-31 70980000 158687 120630 125902 127158 164520 112096 172567 138256 226220 TRUE FALSE 148755.0639 129561.5707 128888.4549 130421.0896 151599.2628 144456.2955 146692.1804 155517.5659 188462.4206 0.78930889 0.687466341 0.683894723 0.692027032 0.804400487 0.766499205 0.778363028 0.825191385 1 17.52391735 0.57584875 0.457027185 1.018504113 0.703567287 0.819874318 0.039216111 0.721785233 0.29997304 0.067489088 0.023556004 3.765726284 -0.57584875 -0.314936826 SESELIDELSEDFDR ddPTM_SK-BR-3_Pertuzumab_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 ;;;; 316.11 5.77E-56 402492000 491276 502510 517508 503543 517905 523399 617875 490824 467655 FALSE TRUE 460527.9121 539716.3633 529783.5341 516464.7659 477230.8304 674495.7946 525230.3798 552104.4568 389600.3593 1.182052072 1.385307663 1.359812745 1.325627027 1.224924 1.731250443 1.348126015 1.417104588 1 18.57163548 -0.7177503 6.252675515 0.999999996 1.379881017 0.388717253 0.146203092 7.75E-09 1.24E-09 0.12999684 0.030640549 0.191535686 0.7177503 0.379881021 SESELIDELSEDFDRSECK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 331.8 2.46E-75 328370000 290926 260561 268175 268156 344732 217215 369799 247428 526971 FALSE TRUE 272717.461 279853.2076 274536.2376 275037.3369 317658.1393 279921.4443 314351.073 278319.9305 439016.1357 0.621201452 0.637455403 0.625344299 0.626485713 0.723568255 0.637610834 0.716035351 0.633962872 1 18.74391444 -5 0.257101743 3.204266243 0.624281507 0.903806023 0.035735974 48.88708795 0.481876666 56.79582754 0.043357653 1.00E-05 5 -2.579984736 SESGGLGVSMVEYVLS(ph)SSPADKLDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SESGGLGVSMVEYVLSSSPADKLDSR 26 1 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;C9JW01 Q8TB72-3 PUM2 Pumilio homolog 2 1 SESGGLGVSMVEYVLS(0.331)S(0.331)S(0.331)PADKLDS(0.007)R 61.499 0.034069 27182000 35606 33005 31293 34897 41960 29013 43137 33494 47737 TRUE FALSE 33377.48402 35448.72454 32035.28474 35792.5161 38664.63086 37388.58211 36669.00731 37675.79963 39769.38631 0.839275813 0.891357092 0.805526253 0.900001721 0.972220958 0.940134752 0.922041065 0.947356827 1 15.27937068 3.001439776 5.741412904 0.947017068 0.849481216 0.741808565 0.029675804 0.082474994 10.05251822 0.008465318 0.009706363 1003.320708 -3.001439776 -0.097535853 SESGGLGVSMVEYVLSSS(ph)PGDSCLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SESGGLGVSMVEYVLSSSPGDSCLR 25 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2 Q5T1Z4 PUM1 Pumilio homolog 1 1 SESGGLGVSMVEYVLS(0.004)S(0.141)S(0.854)PGDS(0.001)CLR;SESGGLGVSMVEYVLSS(0.036)S(0.963)PGDSCLR;SESGGLGVSMVEYVLS(0.001)S(0.159)S(0.795)PGDS(0.044)CLR;SESGGLGVSMVEYVLS(0.001)S(0.166)S(0.833)PGDSCLR 184.38 1.22E-17 69420100 92952.8 96549.3 102213 92548.2 118668 110074.7 131233 92690.6 110178 TRUE FALSE 87135.05017 103697.9106 104637.5406 94923.1435 109348.294 141851.479 111555.83 104263.2254 91788.58002 0.949301647 1.129747411 1.139984305 1.03414982 1.191306086 1.545415333 1.21535631 1.135906291 1 16.48602705 2.482731488 24.99721337 1.264865834 1.089710014 0.185413103 0.147149067 346.0121837 1541718.262 0.046790044 0.040303143 303.9005514 -2.482731488 -0.17515582 SESHTDLTFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SESHTDLTFSR 11 0 O15226;O15226-2 O15226 NKRF NF-kappa-B-repressing factor 0 ; 123.62 0.00036619 366770000 176944 379450 327910 336200 337650 362290 291580 317840 286490 FALSE TRUE 165869.3909 407544.8728 335688.1801 344827.4612 311132.331 466877.2417 247860.2859 357523.0237 238672.9682 0.694965132 1.707545165 1.406477586 1.444769652 1.303592666 1.956137912 1.038493332 1.497961945 1 17.86467565 -0.785046786 8.8864636 1.00000049 1.410297248 0.103857642 0.342622313 0 0 0.291421283 0.068688654 0.164041304 0.785046786 0.410296759 SESIRPDEFSLEIFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SESIRPDEFSLEIFER 16 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 0 ;;; 204.13 2.37E-11 350246000 283898 322053 288133 281225 357061 220233 305012 284761 336322 FALSE TRUE 266129.331 345898.1392 294967.6508 288441.7096 329018.8694 283810.6919 259278.2822 320314.0377 280187.6855 0.949825223 1.23452299 1.052750232 1.029458911 1.174280264 1.012930641 0.925373582 1.143212405 1 18.09603402 2.107456648 9.26563607 1.003309812 1.100518666 0.09568995 0.093749908 0.437143411 34.68873705 0.032996724 0.024360469 128.0727243 -2.107456648 0.097208854 SESLIDASEDS(ph)QLEAAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SESLIDASEDSQLEAAIR 18 0 O94888;C9JAT7 O94888 UBXN7 UBX domain-containing protein 7 1 SESLIDASEDS(1)QLEAAIR;SESLIDAS(0.001)EDS(0.999)QLEAAIR;SESLIDAS(0.004)EDS(0.996)QLEAAIR;SESLIDAS(0.049)EDS(0.951)QLEAAIR 378.05 5.11E-108 371535000 413035 524920 524420 516239 590510 428416 617570 568010 876760 TRUE FALSE 387183.8766 563785.623 536859.49 529486.5667 544133.7266 552092.7444 524971.1117 638927.2988 730423.0919 0.530081648 0.771861719 0.73499797 0.724903926 0.744956906 0.755853355 0.718721954 0.874735897 1 19.47837285 -5 0.1292783 1.919550133 0.617501028 0.695755418 0.065662618 87.81601377 0.7182072 20.76870365 0.485082434 1.00E-05 5 -1.302049105 SESPKEPEQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SESPKEPEQLR 11 1 F8W6I7;P09651-2;P09651;P09651-3;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 ;;;;;;; 182.35 5.31E-06 27677050000 11249260 9449470 10309300 10216330 10665890 8132710 12760070 9007670 12863370 FALSE TRUE 10545188.9 10149118.59 10553841.46 10478498.32 9828234.024 10480491.35 10846815.96 10132297.43 10716390.45 0.984024327 0.947065025 0.984831741 0.977801096 0.917121681 0.977987076 1.012170657 0.945495359 1 23.35331572 2.005558905 24.987315 0.989200448 0.962547159 0.149594832 0.02592322 229.4655887 1031443.363 0.009102829 0.006701983 101.2882121 -2.005558905 -0.026653289 SESPKEPEQLRK ddPTM_SK-BR-3_Pertuzumab_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" 0 116.19 0.00048856 987910000 2684500 2036300 2299700 2406300 2830000 1826500 3442100 2176800 4192200 FALSE TRUE 2516481.937 2187069.771 2354249.97 2468049.732 2607743.216 2353780.899 2925989.06 2448578.272 3492494.737 0.720539937 0.626219919 0.674088337 0.706672427 0.746670621 0.673954029 0.837793406 0.701097197 1 21.73582651 -2.235866694 0.185849727 1.414198873 0.622417771 0.771491808 0.05083527 16.34079056 0.408461669 2.989010401 0.152198956 0.005809427 2.235866694 -0.791781103 SESQESLVTS(ph)PSKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SESQESLVTSPSKPK 15 1 E7EWD6;Q76L83;Q76L83-2;A0A5F9ZHN2 E7EWD6 ASXL2 Putative Polycomb group protein ASXL2 1 SESQESLVT(0.162)S(0.837)PS(0.001)KPK 130.27 3.68E-05 445570000 398670 149340 231400 216890 217180 160120 301050 184380 257240 TRUE FALSE 373717.9563 160397.289 236888.9173 222455.7646 200123.5589 206344.0447 255910.3473 207400.2489 214304.9822 1.743860327 0.748453383 1.105382222 1.038033565 0.933825975 0.962852299 1.194140914 0.967780808 1 17.70930586 4.750956873 24.94264015 1.001939744 1.743860801 0.805608697 0.115728466 874.8117781 1760185.591 0.028247957 0.495478789 56358.1687 -4.750956873 0.741921057 SESSEKPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SESSEKPAR 9 1 A0A087WVI0;E9PBL8;Q8WTW3 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 0 ; 75.294 0.035266 115792000 102819 122389 131078 139110 153070 95304 158015 135744 206289 FALSE TRUE 96383.74233 131450.8089 134187.2321 142679.7981 141048.4997 122816.7177 134322.1177 152691.9372 171858.0332 0.5608335 0.764880212 0.780802791 0.830218963 0.820726835 0.71464054 0.781587658 0.88847716 1 17.39085776 -4.999327756 0.033633737 2.195054112 1.58E-06 0.6586911 0.066104345 844.2122689 2.132566608 114.3335952 41.59455807 1.00E-05 4.999327756 -2.195052529 SESVEGFLS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SESVEGFLSPSR 12 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 SESVEGFLS(0.978)PS(0.022)R;SESVEGFLS(0.95)PS(0.05)R;SESVEGFLS(0.982)PS(0.018)R 239.31 3.81E-16 237344000 319544 348031 342622 333196 424099 308932 362396 332371 525230 TRUE FALSE 299544.3114 373799.5774 350749.1556 341746.3735 390791.9753 398115.6533 308058.0841 373868.251 437565.7199 0.684569878 0.854270708 0.801591943 0.781017246 0.893104641 0.909841963 0.704027007 0.854427653 1 18.73914019 -2.718490298 1.447560229 3.066824828 0.811529355 0.396257439 0.073554001 487205.3634 19011.59794 3291432.03 0.019029185 0.001912096 2.718490298 -2.255295472 SESVEGFLSPS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SESVEGFLSPSR 12 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 SESVEGFLS(0.373)PS(0.627)R 225.72 1.78E-11 199200000 179530 182090 213180 175250 231550 192550 212430 181730 272530 TRUE FALSE 168293.5378 195572.1331 218236.7303 179747.2117 213364.997 248136.0592 180578.0936 204419.3905 227042.9824 0.74124087 0.861388143 0.961213282 0.791688031 0.939755965 1.092903452 0.795347611 0.900355467 1 17.79260592 4.718998496 1.964177025 0.91688319 0.692731119 0.301709749 0.088912257 0.960187348 4.109283496 0.021552801 0.38454949 52359.86229 -4.718998496 -0.224152071 SET(ph)PPVPPPPPYLASYPGFPENGAPGPPISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SETPPVPPPPPYLASYPGFPENGAPGPPISR 31 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 S(0.15)ET(0.85)PPVPPPPPYLASYPGFPENGAPGPPISR 119.22 8.03E-05 55247000 85290 73456 86682 70985 80409 68799 93943 66355 104640 TRUE FALSE 79951.85115 78894.75867 88738.13797 72806.59528 74094.00149 88660.15444 79857.11927 74639.56782 87174.908 0.917142937 0.905016827 1.017932109 0.835178344 0.849946426 1.017037545 0.91605625 0.856204721 1 16.41162532 SETAPAETATPAPVEKS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SETAPAETATPAPVEKSPAK 20 1 P16401 P16401 HIST1H1B Histone H1.5 1 SETAPAETATPAPVEKS(1)PAK;SETAPAETATPAPVEKS(1)PAK;SETAPAETATPAPVEKS(1)PAK;SETAPAETATPAPVEKS(1)PAK 313.01 1.50E-66 2974590000 5682850 2182120 3351210 2772930 3519630 2227900 4558160 2180760 4055940 TRUE FALSE 5327170.563 2343686.435 3430702.284 2844088.078 3243212.457 2871058.563 3874706.224 2453032.686 3378977.412 1.57656294 0.693608199 1.015307848 0.841700826 0.959820698 0.849682674 1.146709715 0.725968951 1 21.68815528 4.75059294 24.95396815 0.913951664 1.576563353 0.705836691 0.136299158 1013.044223 2100924.118 0.030546644 0.515714787 56310.96118 -4.75059294 0.66261169 SETAPAETATPAPVEKS(ph)PAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SETAPAETATPAPVEKSPAKK 21 2 P16401 P16401 HIST1H1B Histone H1.5 1 SETAPAETATPAPVEKS(1)PAKK;SETAPAETATPAPVEKS(1)PAKK 182.03 2.51E-17 274970000 830500 250184 442230 393930 450800 311921 606230 275791 512180 TRUE FALSE 778520.4875 268707.8837 452719.9044 404038.9107 415395.9864 401967.5291 515331.4395 310224.1134 426693.8492 1.824541153 0.629743982 1.060994681 0.946905871 0.973522321 0.942051379 1.207731118 0.727041447 1 18.70284179 4.751828338 24.99971472 0.948802282 1.82454172 0.749680597 0.161206864 1166.957187 2198801.192 0.03795759 0.740557277 56471.37189 -4.751828338 0.875739439 FPSLSESLMNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 FPSLSESLMNR 11 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 0 81.296 0.03409 0 10653 13044 10967 50143 109820 70772 143530 87520 169750 FALSE TRUE 9986.247746 14009.79133 11227.14242 51429.75427 101195.1802 91202.72751 122009.009 98447.06466 141417.6284 0.070615296 0.099066796 0.079389978 0.363672866 0.715576844 0.644917671 0.862756718 0.69614422 1 17.10960244 2.868744107 1.572591838 0.801913619 0.071030307 0.923394353 0.093543671 0.08300734 0.413844501 0.031795928 0.034258138 739.1696164 -2.868744107 -0.730883312 down SETEDSILHQLFIVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SETEDSILHQLFIVR 15 0 Q9UKG1 Q9UKG1 APPL1 DCC-interacting protein 13-alpha 0 ; 245.03 4.52E-18 148244000 209180 267700 248620 247040 290880 202553 274520 253170 308560 FALSE TRUE 196087.7972 287520.7865 254517.3838 253379.4646 268035.4582 261026.7629 233358.2745 284778.8318 257059.3426 0.762811401 1.118499657 0.990111393 0.985684714 1.042698761 1.015433869 0.907799235 1.107833035 1 17.97174192 4.753558026 25 1.015663171 0.76281122 0.639798312 0.06076656 1924.714314 3208357.341 0.01447158 0.341719879 56696.73183 -4.753558026 -0.25285195 SETELKDTYAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SETELKDTYAR 11 1 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 140.14 3.53E-05 1303720000 2839200 2561800 2580100 2540700 2611500 2028400 3328300 2308000 3632800 FALSE TRUE 2661499.54 2751478.338 2641301.19 2605898.663 2406403.324 2613966.152 2829252.313 2596158.881 3026462.211 0.879409474 0.90914016 0.872735559 0.861037899 0.795120889 0.863703549 0.934838143 0.857819692 1 21.52920091 0.038445264 0.753784186 1.003331217 0.872573906 0.54425667 0.036500119 3.992146941 2.417378111 0.077771175 0.013225858 1.092559919 -0.038445264 -0.130757311 SETSWES(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SETSWESPK 9 0 E5RJU9;Q86UE4 E5RJU9 MTDH Protein LYRIC 1 SETSWES(1)PK;SETSWES(1)PK 192.14 3.68E-05 705630000 1265740 760570 849910 812820 933200 658230 1129580 742890 965570 TRUE FALSE 1186519.593 816883.3942 870070.2666 833678.3373 859910.2363 848250.3155 960209.9655 835641.4518 804410.1292 1.475018215 1.015506101 1.0816252 1.036384684 1.068994789 1.054499794 1.193682092 1.038825124 1 19.61757172 4.743368668 24.9986584 1.071052219 1.475018379 0.85442979 0.05354366 194.6460836 1011996.043 0.013071239 0.1081192 55382.00416 -4.743368668 0.40396616 SEVELAAALSDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEVELAAALSDKR 13 1 Q03252 Q03252 LMNB2 Lamin-B2 0 157.56 7.65E-05 99434000 156690 142110 148660 152640 172780 108220 203160 164330 226260 FALSE TRUE 146883.0526 152631.9723 152186.2854 156557.0008 159210.5558 139461.3572 172698.044 184846.9622 188495.7443 0.779238031 0.809736967 0.807372527 0.83055987 0.844637402 0.739864752 0.916190679 0.980642629 1 17.52417243 1.523345626 3.794168387 0.983264591 0.806346181 0.877952103 0.029587242 0.059681311 1.869186577 0.018061564 0.007215924 33.36918702 -1.523345626 -0.17691841 SEVLSESSELLQQELEELRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEVLSESSELLQQELEELRK 20 1 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 151.87 1.14E-07 23138000 17393 17495 15612 16598 19671 14335 21705 17188 21761 FALSE TRUE 16304.40318 18790.348 15982.32401 17023.93278 18126.11901 18473.28179 18450.53675 19333.95964 18128.94852 0.899357354 1.036483058 0.88159134 0.939046893 0.999843923 1.01899356 1.017738935 1.066468892 1 14.14600763 2.562384492 3.135618229 1.025349629 0.945929063 0.468918799 0.043520118 0.251325565 4.782109592 0.015066311 0.013664638 365.0770157 -2.562384492 -0.079420567 SEVQQPVHPKPLS(ph)PDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SEVQQPVHPKPLSPDSR 17 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 SEVQQPVHPKPLS(0.947)PDS(0.053)R;SEVQQPVHPKPLS(0.983)PDS(0.017)R;SEVQQPVHPKPLS(0.795)PDS(0.205)R;SEVQQPVHPKPLS(0.994)PDS(0.006)R;SEVQQPVHPKPLS(1)PDSR;SEVQQPVHPKPLS(1)PDSR;SEVQQPVHPKPLS(0.999)PDS(0.001)R 199.6 7.96E-12 15785350000 10085230 7093200 8920570 8089260 9414510 6910810 10117040 7730690 12842760 TRUE FALSE 9454013.457 7618387.908 9132170.133 8296844.107 8675132.361 8905848.659 8600083.774 8695883.664 10699220.39 0.883617041 0.712050751 0.853536034 0.775462492 0.810819111 0.832382953 0.803804713 0.812758626 1 23.35100234 -4.99999999 0.328837819 2.959906504 0.797484356 0.622723662 0.046032526 208.1178555 1.805154106 284.8995989 0.034981595 1.00E-05 4.99999999 -2.162422148 SEVQQPVHPKPLSPDS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEVQQPVHPKPLSPDSR 17 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 SEVQQPVHPKPLS(0.003)PDS(0.997)R 154.65 7.87E-08 3864200000 947550 604250 816470 778840 830380 654680 959490 750110 1238400 TRUE FALSE 888244.5369 648989.2987 835837.054 798826.353 765165.3044 843675.4882 815623.382 843762.8847 1031703.04 0.860949811 0.629046609 0.810152749 0.774279344 0.741652661 0.817750317 0.79056022 0.817835028 1 19.97659634 -1.420166549 0.250717529 1.193139943 0.729124855 0.572984445 0.06069098 13.50303316 0.658774767 1.747548951 0.090754218 0.038004362 1.420166549 -0.464015088 SEVQQPVHPKPLSPDSR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 147.56 2.37E-07 1965200000 1843500 1805050 1801820 1809330 2257540 1477140 2194290 1804060 3271890 FALSE TRUE 1728118.626 1938697.78 1844560.021 1855760.471 2080241.915 1903566.339 1865276.585 2029300.862 2725790.422 0.633988076 0.711242422 0.676706473 0.680815537 0.763170161 0.698353888 0.684306677 0.744481618 1 21.37824321 -5 0.291608852 3.389771093 0.680462901 0.902767359 0.031538649 69.24959658 0.650802752 100.6846674 0.031668023 1.00E-05 5 -2.709308192 SEWETLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SEWETLSR 8 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ; 190.52 0.00043276 332430000 184642 234410 215940 201259 229833 177838 236696 210859 254425 FALSE TRUE 173085.5868 251765.9603 221062.1988 206423.6467 211782.8433 229176.9436 201205.6322 237185.2103 211959.8239 0.8165962 1.187800385 1.042943869 0.973881007 0.999165028 1.081228223 0.949263066 1.119010226 1 17.69343131 3.467485343 24.30016151 1.015776352 1.058785212 0 0.103787003 554.3356372 1397940.205 0.0264072 0.035904848 2934.170477 -3.467485343 0.04300886 SEWLDPSQKS(ph)PLHVGETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SEWLDPSQKSPLHVGETR 18 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 SEWLDPS(0.172)QKS(0.828)PLHVGETR;SEWLDPS(0.124)QKS(0.876)PLHVGETR;SEWLDPS(0.206)QKS(0.794)PLHVGETR;SEWLDPS(0.03)QKS(0.97)PLHVGETR 175.48 1.96E-12 1326880000 1285230 1075500 1185600 1152470 1287980 979700 1406780 1101400 1625960 TRUE FALSE 1204789.749 1155131.139 1213722.992 1182044.331 1186827.246 1262523.486 1195846.399 1238912.214 1354576.772 0.889421533 0.852761662 0.896016392 0.872630002 0.876160932 0.932042769 0.882819212 0.914612032 1 20.36941073 -5 0.169976906 1.454436593 0.859132645 0.79556686 0.018570275 52.04095262 0.491192386 7.922045558 0.06073288 1.00E-05 5 -0.595303948 SEWNTVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEWNTVER 8 0 B5MCF9;O00541-2;O00541 B5MCF9 PES1 Pescadillo homolog 0 111.39 0.007543 109430000 80673 102930 90096 101310 108070 76137 102210 88090 88132 FALSE TRUE 75623.82094 110551.0443 92233.11967 103909.7861 99582.61813 98116.51592 86884.55937 99088.23041 73422.19985 1.029985769 1.505689622 1.256202073 1.415236622 1.356301205 1.3363331 1.183355437 1.349567714 1 16.16392872 -0.063615782 0.545314761 0.97221532 1.333724579 0.328042456 0.131902136 4.860308321 1.64649711 0.417191291 0.053463103 0.863742359 0.063615782 0.361509259 SEYPDLFEWFCVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SEYPDLFEWFCVK 13 0 A6PWM2;Q6UXH1-3;Q6UXH1-2;Q6UXH1-4;Q6UXH1;Q6UXH1-6;Q6UXH1-5 A6PWM2 CRELD2 Cysteine-rich with EGF-like domain protein 2 0 126.67 0.00020086 0 47364 55627 46020 48784 64350 41719 53652 45291 45402 FALSE TRUE 44399.57179 59745.68096 47111.61613 50035.88003 59296.21058 53762.59805 45607.38068 50945.68105 37824.11289 1.173843043 1.579565954 1.245544509 1.32285667 1.567682783 1.421384242 1.20577529 1.346910136 1 15.20701863 0.600695552 0.801139725 1.000178839 1.389013435 0.406112682 0.136426181 1.251828755 1.377510636 0.129345981 0.043880091 3.987452766 -0.600695552 0.388834595 SFAGAVSPQEEEEFRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SFAGAVSPQEEEEFRR 16 1 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ;;;; 227.67 7.72E-15 2374510000 785947 852076 855018 809462 876319 728145 989131 823744 973378 FALSE TRUE 736755.9802 915164.5936 875299.4307 830234.1653 807496.4406 938348.6411 840819.9892 926590.2517 810914.9235 0.908549046 1.128558086 1.079397364 1.023824006 0.995784412 1.157148073 1.036878179 1.142647921 1 19.62919104 2.260880111 24.99688448 1.084342378 1.048001352 0.094613842 0.073257464 754.0174166 844465.0638 0.024080993 0.020133533 182.3392277 -2.260880111 -0.036341025 SFAIASLVETGHLAAFSLTSHLNDTFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFAIASLVETGHLAAFSLTSHLNDTFR 27 0 A0A3B3IUD7;Q14690 A0A3B3IUD7 PDCD11 Protein RRP5 homolog 0 184.59 7.59E-18 19525000 10131 13863 12746 11691 15169 10159 15695 14397 10671 FALSE TRUE 9496.918794 14889.43094 13048.34114 11991.01085 13977.68793 13091.73838 13341.68046 16194.49714 8889.941163 1.068276901 1.67486271 1.467764623 1.348829045 1.572303761 1.472646235 1.50076139 1.821665278 1 13.11795816 2.712775521 24.23874792 1.503500122 1.45039336 0 0.251097902 3779.582953 3552911.949 0.073601685 0.069416055 516.1495121 -2.712775521 -0.053106763 SFCEEDHAALVNQESEQS(ph)DDELLTLSSPHGNANGDKPHGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFCEEDHAALVNQESEQSDDELLTLSSPHGNANGDKPHGVK 41 1 O75061-4;O75061;O75061-2;S4R305 O75061-4 DNAJC6 Putative tyrosine-protein phosphatase auxilin 1 SFCEEDHAALVNQES(0.015)EQS(0.98)DDELLT(0.005)LSSPHGNANGDKPHGVK 122.88 6.29E-09 103520000 33544 30625 32134 28859 41721 26334 39529 38321 47194 TRUE FALSE 31444.54092 32892.50687 32896.23365 29599.5708 38444.40095 33936.1983 33601.99342 43105.4612 39317.01652 0.799769253 0.836597224 0.836692012 0.752843766 0.977805652 0.863142764 0.854642503 1.096356362 1 15.26286623 1.248565711 24.86691377 1.048178172 0.8466148 0.65592017 0.060898151 94.66866714 235296.1496 0.038921438 0.013840334 17.72416199 -1.248565711 -0.201563372 SFDFIHLDPFGTSVNYLDSAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFDFIHLDPFGTSVNYLDSAFR 22 0 Q7Z2T5-2;Q7Z2T5 Q7Z2T5-2 TRMT1L TRMT1-like protein 0 148.38 7.11E-08 80863000 87096 128100 98459 96211 143990 85513 114620 126250 84297 FALSE TRUE 81644.81683 137584.6573 100794.494 98679.93714 132681.6062 110199.2149 97433.79508 142012.5904 70227.28612 1.162579694 1.959133905 1.435261129 1.405150941 1.88931701 1.56917946 1.387406526 2.022185368 1 16.09974406 -1.166337518 4.408000168 0.999872008 1.605293907 0.318469788 0.277571562 0.00031152 5.89E-05 0.239797447 0.05650895 0.068180861 1.166337518 0.605421899 SFDVNKPGCEVDDLK ddPTM_SK-BR-3_Pertuzumab_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 0 147.12 3.43E-06 205820000 130510 77278 95594 91135 85517 74399 124650 69182 75903 FALSE TRUE 122341.6121 82999.74353 97861.53482 93473.67839 78800.83978 95876.78353 105959.8897 77819.52499 63234.29895 1.934735011 1.31257474 1.547602115 1.478211666 1.246172427 1.516214857 1.675671138 1.230653716 1 15.94841968 -3.011792079 0.277289899 4.39E-11 1.532805643 0.406458123 0.200628465 68.98279688 1.796726708 40.52998554 0.227563007 0.000973213 3.011792079 1.532805643 SFDVNKPGCEVDDLKGGVAGGSILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFDVNKPGCEVDDLKGGVAGGSILK 25 2 P41091;Q2VIR3;Q2VIR3-2 P41091 EIF2S3;EIF2S3L Eukaryotic translation initiation factor 2 subunit 3;Putative eukaryotic translation initiation factor 2 subunit 3-like protein 0 89.434 0.0081089 336200000 985130 621580 745640 719140 811690 617740 1001100 685180 999270 FALSE TRUE 923472.4718 667602.43 763326.9329 737594.3499 747943.1416 796071.5098 850994.3488 770726.2313 832485.3815 1.109295721 0.801938923 0.91692533 0.886014777 0.898445977 0.956258846 1.022233384 0.925813532 1 19.66706541 2.096473857 4.193913971 0.986090134 0.903844742 0.079422482 0.080505952 0.355804178 11.49777047 0.029688743 0.021008194 124.8745271 -2.096473857 -0.082245393 SFDWGYEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SFDWGYEER 9 0 P18615;P18615-3;A0A0A0MT02;E9PD43;A0A0A0MSN9;A0A0G2JI50 P18615 NELFE Negative elongation factor E 0 ;;;;; 173.48 0.00012889 459466000 816680 921432 901257 845840 943700 772554 956772 828075 990834 FALSE TRUE 765565.4566 989655.784 922635.2416 867545.6864 869585.6087 995577.7984 813312.9208 931461.9866 825457.4044 0.927443927 1.198918053 1.117726047 1.05098783 1.053459093 1.206092275 0.985287571 1.128419203 1 19.65483424 0.284604563 0.495778867 0.993829918 1.102248037 0.04581349 0.08839635 6.399146076 2.430831499 0.177720393 0.042581107 1.925770648 -0.284604563 0.108418119 SFDYNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFDYNYR 7 0 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 0 87.323 0.045195 102370000 94100 107360 93495 96419 115310 86370 85383 90250 119460 FALSE TRUE 88210.44897 115309.0461 95712.74555 98893.27478 106254.0177 111303.6169 72580.61181 101517.9112 99521.35426 0.886346952 1.158636224 0.961730739 0.993688998 1.067650441 1.118389292 0.729296866 1.020061593 1 16.6027185 1.75974931 25 0.890127697 1.037760545 0.18209916 0.109278219 12.2138615 14422.98734 0.045664694 0.025324221 57.51078694 -1.75974931 0.147632848 SFEAPATINSASLHPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFEAPATINSASLHPEK 17 0 Q9Y3F4;Q9Y3F4-2 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 195.17 3.33E-11 215260000 142900 165040 188040 164770 202790 159590 205740 185400 184110 FALSE TRUE 133956.1441 177259.7333 192500.3976 168998.2772 186863.6914 205661.0423 174891.197 208547.5981 153380.8516 0.873356372 1.155683591 1.255048434 1.101821221 1.218298695 1.340852135 1.1402414 1.359671667 1 17.22675886 4.75836781 2.700473483 1.209694835 0.797952383 0.479462442 0.106624669 0.383472181 3.608326979 0.022773121 0.361675756 57328.13447 -4.75836781 -0.411742451 SFEEEFGTASDKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFEEEFGTASDKER 14 1 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 ; 230.23 9.02E-13 397220000 288380 296730 285580 287150 292590 204817 336620 282560 349700 FALSE TRUE 270330.8106 318700.1979 292354.0925 294518.7551 269611.1617 263944.343 286146.956 317838.238 291332.8109 0.927910625 1.093938568 1.00350555 1.010935755 0.92544043 0.905989072 0.982199551 1.09097989 1 18.15230867 5.04586581 16.18998656 1.0002799 0.527860045 0.131008817 0.05957355 6993799.113 64308564.77 0.015027763 101584550.8 111138.8274 -5.04586581 -0.472419855 SFEEKVENLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SFEEKVENLK 10 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 0 ;;; 190.15 8.51E-07 4802530000 8154710 6700990 7460030 7478990 10246640 5491220 8779510 6824470 13482720 FALSE TRUE 7644321.258 7197138.272 7636985.434 7670913.545 9441910.227 7076446.071 7463103.98 7676520.102 11232366.93 0.680561925 0.640749925 0.679908828 0.682929394 0.84059845 0.630004888 0.664428435 0.683428537 1 23.42115863 -2.197782397 2.174944497 1.852779188 0.683317037 0.743888156 0.057511097 4362416.906 894892.518 18283329.11 0.013448577 0.006341874 2.197782397 -1.169462151 SFELPPYT(ph)PPPILS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFELPPYTPPPILSPVR 17 0 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 2 SFELPPY(0.004)T(0.996)PPPILS(1)PVR 127.32 0.00021568 42268000 51247 52672 55157 75497 80363 57571 57692 61211 83844 TRUE FALSE 48039.54175 56571.88969 56465.35009 77434.38084 74051.61415 74190.81311 49041.62019 68853.32809 69849.89475 0.68775396 0.809906585 0.80838132 1.108582642 1.060153554 1.062146384 0.70210013 0.985732739 1 16.09197032 3.407316726 10.23885099 0.962018695 0.778946146 0.433510085 0.115459375 0.475105447 66.52095359 0.034629023 0.046914744 2554.56364 -3.407316726 -0.183072549 SFELPPYTPPPILS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SFELPPYTPPPILSPVR 17 0 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 SFELPPY(0.017)T(0.131)PPPILS(0.853)PVR;SFELPPYT(0.032)PPPILS(0.967)PVR;SFELPPYTPPPILS(1)PVR;SFELPPYT(0.001)PPPILS(0.999)PVR 162.41 2.98E-09 109631000 487595 507604 456334 514789 592874 430671 493705 431544 509459 TRUE FALSE 457077.2993 545187.5283 467158.458 527999.3573 546312.0676 554998.7263 419678.5186 485423.2183 424427.0017 1.076927946 1.284526023 1.100680343 1.244028667 1.287175569 1.307642361 0.988812015 1.14371427 1 18.69515692 1.722306649 10.98353475 1.051511213 1.214947657 0.470707465 0.086124632 0.089462866 34.68891453 0.038398089 0.020903706 52.76022624 -1.722306649 0.163436445 SFEVNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SFEVNLR 7 0 Q7Z4W1;J3KS22;J3QS36;J3QL34;J3QS45;J3KRZ4;J3KSZ5 Q7Z4W1 DCXR L-xylulose reductase 0 ;;; 189.31 0.0012958 880990000 1504650 1684780 1616790 1623020 1809110 1445400 1688880 1464380 1516770 FALSE TRUE 1410476.642 1809522.864 1655141.022 1664669.441 1667029.798 1862663.516 1435648.123 1647211.066 1263611.288 1.116226687 1.432024928 1.309849823 1.317390448 1.319258393 1.474079516 1.136146959 1.303574194 1 20.2691213 0.626187457 0.823807066 1.000877598 1.330625643 0.417314296 0.110822849 1.075003839 1.267753014 0.098970132 0.03357102 4.228510928 -0.626187457 0.329748045 SFFDNISCDDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SFFDNISCDDNR 12 0 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;A0A0G2JQ95;A0A096LP11 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;;; 214.67 1.01E-10 447168000 1014623 844130 847719 922496 978710 738059 1033140 806592 1054283 FALSE TRUE 951119.5576 906630.2635 867827.295 946168.8091 901846.0645 951124.6519 878230.2482 907296.7867 878316.3564 1.082889497 1.032236571 0.988057764 1.077252863 1.026789559 1.082895297 0.999901962 1.032995435 1 19.74438114 1.622471921 25 1.012336957 1.03993392 0.212925857 0.031163522 1.660390385 2835.350114 0.014444755 0.007965824 41.92488895 -1.622471921 0.027596963 SFFQAATEHLLPMGTALPLLEAQAATHTLVDPITGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFFQAATEHLLPMGTALPLLEAQAATHTLVDPITGQR 37 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 219.92 2.51E-39 191090000 179620 233330 166990 157200 231240 169340 231590 205370 140040 FALSE TRUE 168377.9048 250605.996 170951.0817 161234.0181 213079.3432 218225.709 196865.2295 231010.8966 116666.4193 1.443242244 2.148055948 1.465298092 1.3820088 1.826398242 1.870510043 1.68741983 1.980097597 1 16.83202984 -1.245922389 3.445515054 0.998209711 1.735607672 0.462661928 0.245454122 23740958.22 36623038.57 467069.4392 0.055409693 0.056764604 1.245922389 0.737397961 SFGEKS(ph)YLNVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFGEKSYLNVHR 12 1 Q6ZN11-3;Q6ZN11-2;Q6ZN11 Q6ZN11-3 ZNF793 Zinc finger protein 793 1 S(0.006)FGEKS(0.552)Y(0.442)LNVHR 76.655 0.018438 348430000 1110700 296800 495260 348350 447100 330960 426100 308620 394210 TRUE FALSE 1041183.27 318775.3808 507007.8011 357289.2508 411986.5695 426502.7793 362210.2607 347151.8864 328413.8043 3.170339541 0.970651588 1.543807825 1.087923973 1.254473972 1.298674945 1.102908148 1.057056317 1 18.32515524 4.742487665 24.99539665 1.193144033 3.170340306 0.931529686 0.170751471 89.60150095 570285.0171 0.038343903 0.292034678 55269.77098 -4.742487665 1.977196273 SFGS(ph)PNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SFGSPNR 7 0 D6RAD4;P50613;D6REC6;D6R9G1 D6RAD4 CDK7 Cyclin-dependent kinase 7 1 S(0.001)FGS(0.999)PNR;S(0.002)FGS(0.998)PNR;S(0.001)FGS(0.999)PNR 86.136 0.021292 3062370000 1446480 2141850 1387930 1520580 2247100 1111240 1596980 1876410 1924160 TRUE FALSE 1355947.399 2300434.803 1420852.355 1559600.657 2070621.83 1432036.949 1357527.675 2110683.919 1603005.265 0.845878319 1.435076261 0.886367865 0.972922978 1.291712432 0.893345131 0.846864139 1.316704296 1 20.61234773 3.874662574 9.208753561 1.013508157 1.179466144 0.033787436 0.212434566 0.661886478 53.96077626 0.05059593 0.091397847 7493.118033 -3.874662574 0.165957987 SFGSAQEFAWAHDSSEYAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFGSAQEFAWAHDSSEYAIR 20 0 P35606;P35606-2;H0Y938 P35606 COPB2 Coatomer subunit beta 0 ; 213.72 4.58E-23 203125000 173393 270860 243130 290290 260930 203280 266580 226390 223640 FALSE TRUE 162540.6416 290914.7562 248897.1584 297739.3329 240437.6103 261963.636 226608.8038 254655.2898 186313.0392 0.872406152 1.561429932 1.335908423 1.598059557 1.290503399 1.40604027 1.216279895 1.366814104 1 17.50736912 0.259344231 0.677976156 0.99121126 1.371885797 0.191495825 0.201910017 3.809089514 2.363674216 0.271298019 0.067758327 1.81695525 -0.259344231 0.380674537 SFGTEDRPTDRPAPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SFGTEDRPTDRPAPPR 16 2 Q9BX40;Q9BX40-2;Q5TBQ1;Q5TBQ0;A0A0C4DFV2 Q9BX40 LSM14B Protein LSM14 homolog B 0 ;;; 213.94 3.50E-13 748630000 305618 317636 329167 311966 312277 341368 376984 290654 246105 FALSE TRUE 286489.9149 341154.0999 336974.9967 319971.5757 287752.0241 439915.4 320458.7489 326942.7917 205028.4856 1.397317617 1.66393513 1.643552093 1.5606201 1.403473392 2.145630636 1.562996225 1.594621307 1 17.64546484 0.604754927 2.535666072 1.000063102 1.641374512 0.472011845 0.206377296 3.373992493 20.63878421 0.181379862 0.048319361 4.024898444 -0.604754927 0.641311411 SFGTEDRPTDRPIPPRDEVFEYIIFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFGTEDRPTDRPIPPRDEVFEYIIFR 26 3 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9;I3L4Q1 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ; 237.32 2.51E-45 88678000 39303 40654 39224 40328 45516 35680 43952 41326 46550 FALSE TRUE 36843.09539 43664.06446 40154.4118 41362.88476 41941.35696 45980.23678 37361.80563 46485.64207 38780.50428 0.950041679 1.125928228 1.035427789 1.066589657 1.08150623 1.185653401 0.96341722 1.198685859 1 15.24304394 4.75257373 24.1106991 1.07837894 0.950041536 0.236937539 0.07423351 2117.288558 3642860.962 0.015545738 0.310794723 56568.37851 -4.75257373 -0.128337405 SFGTRPLS(ph)SGFSPEEAQQQDEEFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFGTRPLSSGFSPEEAQQQDEEFEK 25 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 SFGTRPLS(0.926)S(0.046)GFS(0.028)PEEAQQQDEEFEK;SFGTRPLS(0.965)S(0.034)GFS(0.001)PEEAQQQDEEFEK 308.5 1.21E-74 1189590000 722360 537680 618910 634810 730220 491610 775340 563610 823300 TRUE FALSE 677148.777 577490.3867 633590.8375 651100.2993 672871.4668 633529.8264 659084.9649 633977.9492 685885.9113 0.987261534 0.841962748 0.923755434 0.949283676 0.981025351 0.923666481 0.960925066 0.92431983 1 19.3876091 3.406224655 3.252556536 0.953982308 0.898186716 0.135876783 0.041932544 0.304487797 6.440901938 0.010896593 0.015769353 2548.148036 -3.406224655 -0.055795592 SFGTRPLSS(ph)GFSPEEAQQQDEEFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SFGTRPLSSGFSPEEAQQQDEEFEK 25 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 SFGTRPLS(0.399)S(0.516)GFS(0.084)PEEAQQQDEEFEK;SFGTRPLS(0.274)S(0.589)GFS(0.137)PEEAQQQDEEFEK;SFGT(0.003)RPLS(0.394)S(0.584)GFS(0.019)PEEAQQQDEEFEK 200.58 3.99E-25 8938900000 2238768 1800991 1824859 1870904 2002359 1481375 2275782 1606223 2178644 TRUE FALSE 2098647.507 1934338.248 1868145.517 1918914.564 1845101.801 1909023.914 1934549.616 1806763.477 1815014.242 1.156270545 1.065742738 1.0292732 1.057244907 1.016577038 1.051795556 1.065859194 0.99545416 1 20.79154944 4.942814379 1.545111638 1.03710276 1.254601877 0.729861705 0.023789492 0.958656631 1.459112318 0.005804727 0.365911981 87662.60639 -4.942814379 0.217499117 SFGTRPLSSGFS(ph)PEEAQQQDEEFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFGTRPLSSGFSPEEAQQQDEEFEK 25 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 SFGTRPLS(0.136)S(0.226)GFS(0.637)PEEAQQQDEEFEK;SFGTRPLS(0.018)S(0.033)GFS(0.948)PEEAQQQDEEFEK 280.17 1.89E-53 517130000 302900 237471 235661 253144 323030 199444 335150 224310 343040 TRUE FALSE 283942.0297 255053.5999 241250.9902 259640.1036 297660.5268 257020.2451 284897.3689 252315.5973 285784.4079 0.993553259 0.892468563 0.844171283 0.908517387 1.041556217 0.899350133 0.996896125 0.882887905 1 18.12456768 2.976222686 24.44358381 0.962670519 0.894313507 0.156229234 0.059187787 785.3961665 807404.6365 0.016643839 0.017759248 946.7224729 -2.976222686 -0.068357012 SFGTRPLSSGFSPEEAQQQDEEFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFGTRPLSSGFSPEEAQQQDEEFEK 25 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 100.27 0.0057369 169320000 100250 90056 88176 101850 90556 66724 114590 72079 119370 FALSE TRUE 93975.53145 96723.83994 90267.57636 104463.6434 83444.09705 85986.13563 97408.2933 81078.22182 99446.37584 0.944986991 0.972623076 0.907701016 1.05045199 0.839086355 0.864648258 0.979505713 0.815295893 1 16.60163117 2.719980869 24.99361606 0.902296971 0.959347874 0.204636939 0.066532447 1504.255097 2023531.667 0.019812129 0.018707426 524.7843421 -2.719980869 0.057050903 SFGWETLDSFMQHDVQELCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFGWETLDSFMQHDVQELCR 20 0 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 184.8 3.88E-17 10088000 17313 26256 20662 19022 27064 16399 28852 21789 27452 FALSE TRUE 16229.41023 28200.02156 21152.1124 19510.13672 24938.50261 21133.12508 24525.91045 24509.40461 22870.08385 0.709634925 1.233052827 0.924881279 0.853085491 1.090442115 0.924051054 1.072401422 1.0716797 1 14.48117403 1.662300498 10.08830988 1.05363163 0.985632745 0.061193357 0.140246186 0.40062521 61.27536119 0.063331094 0.034027352 45.95158525 -1.662300498 -0.067998885 SFIKDYPVVSIEDPFDQDDWGAWQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFIKDYPVVSIEDPFDQDDWGAWQK 25 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 353.09 4.57E-103 2787900000 3301900 4150700 3038600 3241200 5991100 2659300 4536000 3604000 8498600 FALSE TRUE 3095239.973 4458022.147 3110677.027 3324374.679 5520583.173 3426996.74 3855868.91 4053967.333 7080128.757 0.437172837 0.629652694 0.439353172 0.469535907 0.779729206 0.484030285 0.544604349 0.572583843 1 22.75534417 -4.999999999 0.341498241 5.976603961 0.528549715 0.668135203 0.101534836 231.4960503 1.942760684 840.3796866 0.07520933 1.00E-05 4.999999999 -5.448054245 SFKLS(ph)GFSFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFKLSGFSFK 10 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 SFKLS(1)GFSFK;SFKLS(1)GFSFK 147.35 1.64E-05 1677930000 7072000 4354600 5327100 5176100 5356400 3638500 7647500 4579900 5733400 TRUE FALSE 6629376.144 4677019.115 5453461.328 5308927.489 4935729.951 4688875.884 6500828.371 5151710.597 4776458.501 1.387927089 0.979181357 1.141737404 1.11147778 1.033345092 0.981663691 1.36101431 1.07856283 1 22.1875099 SFKPDFGAESIYGGFLLGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFKPDFGAESIYGGFLLGVR 20 1 P35606;P35606-2;H0Y938 P35606 COPB2 Coatomer subunit beta 0 ; 173.09 4.91E-12 316130000 542710 688730 535630 516940 733060 369640 656360 638170 529000 FALSE TRUE 508742.7499 739724.2858 548335.3965 530205.5556 675488.4246 476349.0674 557944.9113 717846.9293 440706.4825 1.154380001 1.678496494 1.24421904 1.203080909 1.532739933 1.080876017 1.266023836 1.628854936 1 18.74945859 -2.221841399 2.04650694 4.34E-05 1.351565412 0.226011217 0.202660332 2622478.477 461196.8104 12125140.46 0.046508781 0.006000102 2.221841399 1.351522018 SFLDDFESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFLDDFESK 9 0 Q8TF74;Q8TF74-2;A8MWR2;J3KSA3 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 0 ; 141.88 0.00024582 22864000 213710 177081 215710 203169 224700 153683 237480 185991 277180 FALSE TRUE 200334.2726 190192.2615 220826.7431 208382.6605 207052.9684 198048.7873 201872.0787 209212.3858 230916.8673 0.867560152 0.823639536 0.956304083 0.902414202 0.896655886 0.857662714 0.874219718 0.906007379 1 17.81701403 0.85224585 4.176567581 0.999990502 0.883688816 0.537178454 0.034043272 0.866610538 23.37081973 0.033759733 0.008605731 7.116162392 -0.85224585 -0.116301686 SFLDDPIWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFLDDPIWR 9 0 Q7L576;Q7L576-2;Q7L576-3;H0YL50 Q7L576 CYFIP1 Cytoplasmic FMR1-interacting protein 1 0 ; 136.8 0.00042496 103776000 263790 357170 325750 338680 373780 286430 367430 333710 296700 FALSE TRUE 247279.8548 383615.2384 333476.9438 347371.1022 344424.8266 369117.6912 312337.2826 375374.4281 247178.8532 1.000408617 1.551974343 1.349132175 1.405343126 1.393423515 1.49332229 1.263608429 1.51863488 1 17.9151958 -1.254208715 4.74202757 0.999901221 1.38412869 0.354597803 0.156955319 0.000160439 2.52E-05 0.131591983 0.031007562 0.055691804 1.254208715 0.384227469 SFLEDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SFLEDIR 7 0 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;;; 111.04 0.015516 604586000 2315470 3366160 2457080 2476250 3330750 1780660 2556020 3146340 2720550 FALSE TRUE 2170548.866 3615393.989 2515363.098 2539794.767 3069166.331 2294707.635 2172768.53 3539167.475 2266472.63 0.957677069 1.595163313 1.109814019 1.120593619 1.354159892 1.012457687 0.958656417 1.56153109 1 21.11201731 3.729498979 24.86081762 1.143912276 1.331115064 0.026239204 0.236127129 220.7845245 2308418.862 0.056623764 0.096252416 5364.1261 -3.729498979 0.187202788 SFLEDIRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFLEDIRK 8 1 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ; 111.74 0.0050917 2552500000 2388000 3914400 2003590 2027070 4284000 1196980 2243600 3553600 4529600 FALSE TRUE 2238539.343 4204226.249 2051116.101 2079088.048 3947551.921 1542528.695 1907193.009 3997274.782 3773580.498 0.593213619 1.114121257 0.543546402 0.550958976 1.046102481 0.408770582 0.505406738 1.059279055 1 21.84750262 1.220532083 24.96473941 1.02963995 0.694615329 0.285051072 0.229137015 385.8638658 534304.6528 0.218720599 0.055133242 16.61621425 -1.220532083 -0.335024622 SFLEEVLASGLHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFLEEVLASGLHSR 14 0 A0A2R8YE10;Q9NRW7;A0A087WU65 A0A2R8YE10 VPS45 Vacuolar protein sorting-associated protein 45 0 230.36 9.43E-13 73011000 131750 210930 179100 180140 219170 136700 200040 191590 211090 FALSE TRUE 123504.0027 226547.4767 183348.3366 184762.6974 201957.2723 176163.0709 170045.8591 215510.4332 175857.7153 0.702295048 1.288243034 1.042594783 1.050637426 1.14841292 1.001736378 0.966951372 1.225481821 1 17.42404911 SFLIWVNEEDHTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SFLIWVNEEDHTR 13 0 P12532;P12532-2;F8WCN3 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ;;;;;;; 255.78 7.57E-24 4611446000 3843807 4459726 4036149 4088423 5391990 3639251 4504240 4307362 4606764 FALSE TRUE 3603229.981 4789928.753 4131888.36 4193338.856 4968524.856 4689843.685 3828871.027 4845145.627 3837865.328 0.938863059 1.248071088 1.076611087 1.092622721 1.294606358 1.221992771 0.997656432 1.26245848 1 21.87187266 -1.113157549 5.265363275 0.99999698 1.141306995 0.125448721 0.117502668 3.79E-06 6.38E-07 0.103273811 0.02434135 0.077062386 1.113157549 0.141310015 SFLSEPSS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_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(0.003)S(0.997)PGR 181.44 6.53E-06 4158110000 5616460 6712870 6330820 6636310 6391770 5338150 7346960 5773400 6423950 TRUE FALSE 5264935.794 7209897.88 6480990.04 6806608.95 5889786.167 6879187.247 6245351.554 6494221.699 5351751.245 0.983778123 1.347203476 1.211003603 1.271847034 1.100534367 1.285408632 1.166973439 1.213476001 1 22.35157963 -0.994056643 0.517019358 0.934218297 1.218159111 0.251137823 0.102715253 24.1893174 3.953078184 2.5081079 0.042436016 0.101377916 0.994056643 0.283940814 SFLVIVDGS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFLVIVDGSPK 11 0 Q9H116;Q9H116-4 Q9H116 GZF1 GDNF-inducible zinc finger protein 1 1 SFLVIVDGS(1)PK 130.2 0.00024036 77102000 355120 235450 272740 248570 264150 199660 321650 224290 322400 TRUE FALSE 332893.6731 252882.963 279209.5216 254948.727 243404.7245 257298.6008 273421.5686 252293.1002 268589.3572 1.239414981 0.941522649 1.039540526 0.94921381 0.906233691 0.957962756 1.017991075 0.939326498 1 18.03504261 4.742741442 24.9850143 0.973364975 1.239415086 0.816461986 0.040248932 178.6689656 1067703.235 0.009576708 0.07409671 55302.07699 -4.742741442 0.266050112 SFPIKPVPS(ph)PSWSGSCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFPIKPVPSPSWSGSCR 17 1 Q9P0U3-2;Q9P0U3 Q9P0U3-2 SENP1 Sentrin-specific protease 1 1 SFPIKPVPS(0.985)PS(0.015)WSGSCR;SFPIKPVPS(0.642)PS(0.352)WS(0.005)GSCR 144.4 3.11E-07 1146660000 1480110 1493600 1481090 1587660 1599040 942800 1428450 1089160 1449550 TRUE FALSE 1387472.557 1604187.698 1516222.154 1628402.044 1473457.849 1214971.055 1214267.184 1225144.024 1207610.741 1.148940226 1.328398005 1.255555373 1.348449454 1.220143047 1.006094939 1.005512077 1.014518986 1 20.20372406 2.301234328 3.961783113 1.004901536 1.277986031 0.851320132 0.052940668 0.069261951 2.181277196 0.017749681 0.014174688 200.0941209 -2.301234328 0.273084496 SFQSLACS(ph)PGLPAADR ddPTM_SK-BR-3_Pertuzumab_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;SFQSLACS(1)PGLPAADR;SFQSLACS(1)PGLPAADR;SFQSLACS(1)PGLPAADR;SFQSLACS(1)PGLPAADR;SFQSLACS(1)PGLPAADR 293.08 1.45E-45 3377100000 2972890 3615240 3633220 4200170 4269850 2725450 3397440 2500540 2353800 TRUE FALSE 2786822.122 3882916.131 3719401.694 4307953.473 3934513.205 3512243.171 2888025.412 2812737.923 1960935.574 1.421169649 1.980134474 1.896748544 2.196886798 2.006446952 1.791105847 1.472779346 1.434385689 1 20.90311071 1.347561024 1.155678471 1.050659707 1.924931901 0.669879735 0.205837529 0.242012887 0.639782782 0.180928897 0.060561271 22.2618383 -1.347561024 0.874272194 SFREPAPAEALPQQYPEPAPAALCGPPPRAPS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFREPAPAEALPQQYPEPAPAALCGPPPRAPSR 33 2 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 SFREPAPAEALPQQYPEPAPAALCGPPPRAPS(1)R;SFREPAPAEALPQQYPEPAPAALCGPPPRAPS(1)R 184.46 4.86E-20 385140000 106581 176238 140431 140219 204610 103690 184071 130696 361629 TRUE FALSE 99910.28546 189286.8449 143762.0896 143817.2569 188540.756 133623.6197 156471.2624 147013.6833 301270.7837 0.33162952 0.628294727 0.477185633 0.477368748 0.625818254 0.443533283 0.519370848 0.48797856 1 18.20070125 -1.625361209 2.63287776 1.050548134 0.509913714 0.770108587 0.085855457 8669062.523 7683249.232 2992707.993 0.018950801 0.023694022 1.625361209 -0.54063442 SFS(ph)ADNFIGIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFSADNFIGIQR 12 0 Q8N7R7-3;Q8N7R7;Q8N7R7-2 Q8N7R7-3 CCNYL1 Cyclin-Y-like protein 1 1 S(0.003)FS(0.997)ADNFIGIQR 132.44 0.00018981 55597000 68153 75970 68905 68141 99208 50946 79166 72501 84871 TRUE FALSE 63887.42539 81594.89785 70539.45914 69889.61342 91416.60387 65653.28316 67295.79324 81552.90944 70705.48181 0.903571035 1.154010916 0.997651912 0.988461031 1.292921023 0.928545871 0.951776178 1.153417067 1 16.10953445 -1.96291867 7.579127628 0.976444812 1.044991525 0.014043375 0.12147041 0.058223139 0.00028486 0.141636141 0.025531228 0.01089134 1.96291867 0.068546713 SFS(ph)ASQSTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SFSASQSTDR 10 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 SFS(0.993)AS(0.006)QSTDR;SFS(0.699)AS(0.301)QSTDR;S(0.001)FS(0.942)AS(0.057)QSTDR;SFS(0.997)AS(0.003)QSTDR 240.73 2.88E-12 1660120000 1107360 1267940 1103660 1368470 1432530 1146220 1512960 1143520 1058180 TRUE FALSE 1038052.314 1361819.597 1129839.336 1403587.257 1320024.872 1477115.107 1286105.694 1286290.989 881562.9219 1.177513582 1.544778669 1.281632097 1.592157771 1.497368866 1.675564012 1.45889268 1.45910287 1 19.74970402 0.555800334 3.90910654 1.000000151 1.466931043 0.5056544 0.143123048 27.29476983 239.0542036 0.128154415 0.032779981 3.595839794 -0.555800334 0.466930892 SFS(ph)EDTLMDGPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SFSEDTLMDGPAR 13 0 Q9BRG2;M0QZQ6 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 SFS(0.632)EDT(0.367)LMDGPAR;SFS(1)EDTLMDGPAR;S(0.007)FS(0.99)EDT(0.003)LMDGPAR;S(0.108)FS(0.892)EDTLMDGPAR;S(0.002)FS(0.991)EDT(0.006)LMDGPAR 191.84 3.38E-06 438858000 1038215 972819 1039085 975464 1003197 908577 1295597 932581 1346294 TRUE FALSE 973234.9764 1044847.531 1063732.587 1000496.058 924409.9543 1170868.43 1101334.258 1049015.791 1121588.834 0.867728839 0.931578043 0.948415814 0.89203461 0.824196824 1.04393731 0.981941175 0.935294431 1 20.09711246 2.22680155 24.99998839 0.990024298 0.905630835 0.54683932 0.043235246 200.2235577 425676.0295 0.016412856 0.012219312 168.5782536 -2.22680155 -0.084393462 SFS(ph)FEKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFSFEKPR 8 1 P78314;P78314-3;P78314-4;H0YAD9 P78314 SH3BP2 SH3 domain-binding protein 2 1 S(0.451)FS(0.549)FEKPR 83.862 0.021411 0 262670 199440 227830 220210 182260 166620 348270 205980 223280 TRUE FALSE 246229.9536 214206.7451 233234.2352 225860.9614 167946.0348 214720.4892 296050.1467 231697.0564 186013.1256 1.323723543 1.151567904 1.253859019 1.21422056 0.902871958 1.154329774 1.591555143 1.2455952 1 17.5050449 SFS(ph)LDEPPLFIPDNIATIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFSLDEPPLFIPDNIATIR 19 0 Q92576-2;Q92576;E7EVH3;D6R9X2;E9PE34;A0A1B0GX99 Q92576-2 PHF3 PHD finger protein 3 1 S(0.083)FS(0.917)LDEPPLFIPDNIATIR 197.15 8.41E-16 18415000 25204 30376 28658 33203 33442 21316 34906 24578 31038 TRUE FALSE 23626.52663 32625.07065 29337.78129 34055.04519 30815.60022 27469.58316 29672.16935 27646.6174 25857.55729 0.913718429 1.261722841 1.134592141 1.317024838 1.191744443 1.062342543 1.147524069 1.069189061 1 14.65829837 1.184997941 0.959493278 1.003323846 1.17280138 0.159428736 0.109271621 0.792833055 1.575987764 0.093809955 0.032634503 15.31080201 -1.184997941 0.169477533 SFS(ph)LEGLTGGAGVGNKPSSSLEVSSANAEELRHPFSGEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFSLEGLTGGAGVGNKPSSSLEVSSANAEELRHPFSGEER 40 2 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36;H0YLH1 Q12802-2 AKAP13 A-kinase anchor protein 13 1 SFS(1)LEGLTGGAGVGNKPSSSLEVSSANAEELRHPFSGEER 169.2 4.53E-19 97905000 53046 51049 54008 55785 68586 45700 76963 57207 97555 TRUE FALSE 49725.94555 54828.72108 55289.09526 57216.53754 63199.53222 58892.84812 65423.11264 64349.41988 81272.44027 0.611842654 0.674628704 0.680293284 0.7040091 0.777625626 0.724634918 0.804985213 0.791774182 1 16.31047859 -5 0.080865401 1.999223445 0.423335451 0.951383672 0.02328522 42.67703051 0.244126957 7.468285808 0.681945197 1.00E-05 5 -1.575887994 SFS(ph)MQDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SFSMQDLR 8 0 Q9H6H4;E5RGS2 Q9H6H4 REEP4 Receptor expression-enhancing protein 4;Receptor expression-enhancing protein 1 S(0.009)FS(0.991)MQDLR;S(0.002)FS(0.998)MQDLR;SFS(1)MQDLR;S(0.001)FS(0.999)MQDLR 150.09 0.00051891 526065000 1614390 1912740 1417790 1426650 1665230 1130500 2363120 1471200 1748110 TRUE FALSE 1513348.212 2054361.26 1451420.648 1463260.254 1534449.553 1456856.998 2008792.094 1654882.559 1456339.148 1.039145459 1.410633823 0.996622696 1.0047524 1.053634763 1.000355583 1.379343608 1.136330477 1 20.47391493 3.961577 24.16052867 1.104308876 1.245449979 0.125070597 0.146165448 513.4488413 798058.7484 0.038014091 0.068863514 9153.285311 -3.961577 0.141141103 SFS(ph)PEER ddPTM_SK-BR-3_Pertuzumab_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 SFS(1)PEER;S(0.004)FS(0.996)PEER;S(0.001)FS(0.999)PEER;S(0.065)FS(0.935)PEER 181.69 0.00070089 2027570000 2318220 2410920 2514130 2425810 2828240 2372870 2716800 2347190 3341660 TRUE FALSE 2173126.748 2589427.025 2573766.351 2488060.391 2606121.439 3057879.049 2309441.062 2640241.838 2783915.358 0.780600869 0.930138561 0.924513148 0.893727025 0.9361353 1.09840949 0.829565832 0.948391563 1 21.40868392 4.741185542 4.674616915 0.937864762 0.770856554 0.352061468 0.069607176 0.21769096 13.00799538 0.015473728 0.119362783 55104.30665 -4.741185542 -0.167008208 SFS(ph)PLQPGQAPTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFSPLQPGQAPTGR 14 0 Q7Z3C6;H7C152;Q7Z3C6-2;H7C1G6 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 S(0.071)FS(0.929)PLQPGQAPTGR 95.755 0.0038206 186640000 217410 312610 273010 284980 308430 203450 328120 251930 395050 TRUE FALSE 203802.6962 335755.9697 279485.9261 292293.0693 284207.1519 262182.7123 278921.4521 283384.0151 329113.6029 0.619247258 1.020182596 0.849208066 0.888122116 0.863553343 0.796632865 0.847492932 0.861052271 1 18.32822613 0.896635756 16.74028126 1 0.858467627 0.18462564 0.099058395 3777.429761 611779.7827 0.087184026 0.021796007 7.881987758 -0.896635756 -0.141532373 SFS(ph)PTMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFSPTMK 7 0 A3KN83-3;A3KN83-2;A3KN83;A3KN83-4 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 1 SFS(0.973)PT(0.027)MK;SFS(0.999)PT(0.001)MK 117.89 0.0053818 360870000 1303230 992370 1124260 1100060 1231140 969170 1622060 1117100 1609810 TRUE FALSE 1221663.161 1065846.107 1150927.978 1128289.402 1134451.231 1248953.646 1378847.161 1256572.394 1341122.311 0.910925984 0.79474191 0.858182709 0.841302387 0.845896919 0.931274974 1.028129314 0.936955849 1 20.35500939 2.091753473 3.311201183 0.990080515 0.842971615 0.753995071 0.036158125 0.100836059 2.181701549 0.014232239 0.009495962 123.5246047 -2.091753473 -0.147108899 SFS(ph)SQRPVDR ddPTM_SK-BR-3_Pertuzumab_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(0.5)S(0.5)QRPVDR 124.6 0.0011346 595930000 459780 588010 425330 465900 662350 304590 738840 467120 808580 TRUE FALSE 431003.1905 631546.8722 435419.0285 477855.7828 610331.7028 392520.1884 628057.8011 525440.9603 673622.7744 0.63982871 0.937537887 0.646384067 0.709381869 0.906043747 0.582700294 0.932358324 0.780022559 1 19.36158139 0.730290713 0.8161781 0.998297252 0.7589195 0.270745635 0.124821317 1.346048604 1.708412085 0.110255727 0.038365485 5.373914011 -0.730290713 -0.239377752 SFSEDT(ph)LMDGPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFSEDTLMDGPAR 13 0 Q9BRG2;M0QZQ6 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 SFS(0.318)EDT(0.682)LMDGPAR 249.04 1.94E-16 226790000 449090 425050 424940 379760 406340 363690 525960 359000 509520 TRUE FALSE 420982.2585 456521.1443 435019.7775 389505.2845 374427.6955 468681.399 447097.1808 403821.9403 424477.8204 0.991765031 1.075488806 1.024835119 0.917610452 0.882090129 1.104136368 1.053287497 0.95133814 1 18.69532965 3.466441058 24.97425728 0.993306117 1.041894459 0.085754139 0.066187947 522.1388579 1220951.102 0.019351415 0.026284234 2927.123581 -3.466441058 0.048588342 SFSEFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFSEFGK 7 0 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 91.065 0.0388 154020000 248560 259420 259560 261980 257050 222300 296390 237880 311200 FALSE TRUE 233003.0733 278627.7267 265716.8858 268702.8503 236862.3299 286474.4013 251949.071 267579.8416 259258.7096 0.898728045 1.074709225 1.024910161 1.036427477 0.913613781 1.104975033 0.97180562 1.032095863 1 17.98403293 -1.283084704 4.330588206 0.999988918 1.01410199 0 0.065036896 6.10E-06 1.01E-06 0.055177536 0.012995258 0.052109307 1.283084704 0.014113072 SFSERFPEDGPELEEILTQLATADAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SFSERFPEDGPELEEILTQLATADAR 26 1 G3V1D3;G3V180;Q9NY33-4;Q9NY33;Q9NY33-2 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ;; 174.86 1.93E-12 143034000 58161 81003 76173 86059 80459 65032 87388 74170 107428 FALSE TRUE 54520.80683 87000.5464 77979.85953 88267.41964 74140.0747 83805.68269 74284.98067 83430.28777 89497.57279 0.609187547 0.972099507 0.871306976 0.986254899 0.828403189 0.936401738 0.830022294 0.932207267 1 16.44956094 4.745927653 24.94904081 0.909486 0.609187401 0.716315654 0.061095517 451.3456972 1528479.273 0.01302441 0.136673143 55709.29377 -4.745927653 -0.3002986 SFSKEELMS(ph)SDLEETAGSTSIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFSKEELMSSDLEETAGSTSIPK 23 1 O00567 O00567 NOP56 Nucleolar protein 56 1 S(0.007)FS(0.006)KEELMS(0.523)S(0.464)DLEETAGSTSIPK;S(0.002)FS(0.002)KEELMS(0.498)S(0.498)DLEETAGSTSIPK 183.49 2.20E-17 1016480000 453599 435219 446718 418792 555500 279691 474079 372082 778990 TRUE FALSE 425209.0483 467443.0676 457314.3619 429538.9117 511873.2708 360433.2513 402995.2551 418537.2568 648971.5365 0.655204465 0.72028285 0.704675531 0.66187635 0.788745333 0.555391463 0.620975239 0.644923904 1 19.30779568 -0.939481678 6.021375833 1.000000135 0.671312431 0.739338731 0.061750438 1.14E-07 2.01E-08 0.0608811 0.014349807 0.114952474 0.939481678 -0.328687704 SFSKEELMSS(ph)DLEETAGSTSIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SFSKEELMSSDLEETAGSTSIPK 23 1 O00567 O00567 NOP56 Nucleolar protein 56 1 S(0.007)FS(0.006)KEELMS(0.103)S(0.885)DLEETAGSTSIPK;S(0.008)FS(0.006)KEELMS(0.224)S(0.763)DLEETAGSTSIPK;SFSKEELMS(0.245)S(0.755)DLEETAGSTSIPK 230.85 1.91E-33 1029140000 868150 773960 727200 794600 993030 466073 919660 683580 1336240 TRUE FALSE 813814.0412 831264.8037 744449.5274 814990.7813 915041.4295 600620.709 781765.5207 768926.4677 1113212.912 0.731049768 0.746725802 0.668739573 0.732106835 0.821982408 0.539538037 0.702260558 0.690727227 1 20.08629812 -0.79741845 5.918216544 1.000000023 0.701800957 0.629435361 0.071321581 1.97E-08 4.22E-09 0.06445636 0.015192509 0.159434223 0.79741845 -0.298199066 SFSLASSSNS(ph)PISQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SFSLASSSNSPISQR 15 0 Q9BXB4 Q9BXB4 OSBPL11 Oxysterol-binding protein-related protein 11 1 SFSLASSS(0.001)NS(0.999)PISQR;SFSLASSSNS(1)PISQR;SFSLASSSNS(1)PISQR;SFSLASSSNS(1)PISQR 436.54 5.17E-154 2338630000 1863880 2110070 2255040 2229110 2371430 2029210 2611250 2158890 2235570 TRUE FALSE 1747223.078 2266301.778 2308530.614 2286312.736 2185187.454 2615009.986 2219717.304 2428432.169 1862438.925 0.938137114 1.216846227 1.239520171 1.227590718 1.173293483 1.40407825 1.191833608 1.303898956 1 20.82876169 4.740272869 4.55996699 1.233829547 0.918740412 0.42350621 0.102237818 0.160701554 8.736455187 0.020912347 0.162906769 54988.62609 -4.740272869 -0.315089135 SFSQPEAGGS(ph)HHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFSQPEAGGSHHK 13 0 C9IYN3;V9GYK2;Q8WVV9-4;Q8WVV9;B7WPG3;Q8WVV9-5;Q8WVV9-3;Q8WVV9-2 C9IYN3 HNRNPLL Heterogeneous nuclear ribonucleoprotein L-like 1 SFSQPEAGGS(1)HHK 122.16 0.00015347 110060000 189630 130240 170290 160180 177940 131580 187840 150980 230060 TRUE FALSE 177761.3968 139883.1051 174329.3592 164290.49 163965.3102 169565.01 159675.1358 169830.1853 191661.4998 0.927475769 0.729844571 0.909569003 0.857190882 0.855494246 0.884710858 0.833110124 0.886094419 1 17.54820104 -5 0.214690381 1.733863731 0.831750065 0.394094401 0.053994964 139.0131138 1.389217533 43.94581668 0.101836424 1.00E-05 5 -0.902113666 SFSS(ph)QRPGMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFSSQRPGMER 11 1 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 SFS(0.257)S(0.743)QRPGMER 83.573 0.016457 0 148970 211740 140610 153220 254710 107850 297130 204370 335510 TRUE FALSE 139646.2336 227417.4499 143945.3356 157151.8846 234706.1041 138984.5442 252578.1149 229886.0444 279511.2135 0.499608699 0.813625497 0.514989484 0.562238211 0.839701925 0.49724139 0.903642154 0.822457323 1 18.09254664 1.650764176 7.228239351 0.899195757 0.637897837 0.523911524 0.128211854 0.10173916 10.38644166 0.059562469 0.030276465 44.74702599 -1.650764176 -0.26129792 SFSS(ph)QRPVDR ddPTM_SK-BR-3_Pertuzumab_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(0.397)S(0.603)QRPVDR 101.56 0.0085541 469260000 580180 693350 573760 578530 841520 368730 958150 634810 953690 TRUE FALSE 543867.5695 744686.3554 587369.8581 593376.0592 775430.4137 475176.3652 814484.3025 714067.4259 794512.9779 0.684529497 0.937286585 0.7392829 0.746842501 0.975982061 0.598072503 1.025136562 0.898748599 1 19.59971126 1.621723036 24.99982615 0.971444225 0.800758669 0.378891011 0.115281123 0.879096028 1582.286341 0.04792306 0.026401754 41.85265719 -1.621723036 -0.170685556 SFSSPPS(ph)PSNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFSSPPSPSNK 11 0 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 SFSS(0.001)PPS(0.922)PS(0.077)NK 165.02 0.00092312 0 276050 176350 230820 213100 232850 205850 215440 186130 180710 TRUE FALSE 258772.5233 189407.1375 236295.1594 218568.5068 214562.9003 265275.5533 183136.772 209368.7402 150548.3336 1.71886674 1.258115138 1.569563434 1.451816182 1.425209401 1.762062369 1.216464957 1.39070779 1 17.19986721 0.85478638 1.09483864 1.006985142 1.487894286 0.468325037 0.16744421 0.595332708 1.39733333 0.143876629 0.045715281 7.157912414 -0.85478638 0.480909144 SFSSPPS(ph)PSNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFSSPPSPSNKR 12 1 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 SFSSPPS(0.975)PS(0.025)NKR 94.717 0.0039524 218180000 292660 189220 254780 226330 228220 221570 266590 182540 216580 TRUE FALSE 274342.933 203230.0457 260823.5019 232138.011 210296.5218 285533.6621 226617.3044 205330.5208 180431.3988 1.520483324 1.126356316 1.445554951 1.28657214 1.165520653 1.582505395 1.255974879 1.137997722 1 17.46109089 1.128099246 2.645522901 1.00916375 1.333674397 0.404323185 0.143850458 0.248033991 3.240406058 0.123106183 0.033697966 13.43071847 -1.128099246 0.324510648 SFSSQRPGMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFSSQRPGMER 11 1 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 0 66.617 0.056745 79241000 42368 45915 49970 45429 59552 52251 46905 45329 59533 FALSE TRUE 39716.26251 49314.59437 51155.312 46594.78505 54875.02614 67335.01548 39872.03069 50988.42543 49596.5577 0.800786675 0.994314861 1.031428679 0.93947619 1.106428121 1.357655019 0.80392738 1.028063797 1 15.59795237 5.423077139 1.255179188 1.034970535 5.59E-10 0.220435854 0.138799758 11.24714511 4.422054344 0.037281687 22.87647766 264897.0605 -5.423077139 -1.034970535 SFSSQRPVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SFSSQRPVDR 10 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;H7C5N8 E7EPN9 PRRC2C Protein PRRC2C 0 ; 102.4 0.0026923 345100000 349260 453820 415620 402170 489320 376880 326500 410970 516470 FALSE TRUE 327400.44 487421.305 425478.7027 412490.3631 450890.781 485679.1379 277544.3561 462280.5092 430267.8205 0.760922441 1.132832347 0.988869449 0.95868281 1.04793052 1.128783318 0.645050229 1.074401773 1 18.71487542 SFTDLEELDETELYMCHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SFTDLEELDETELYMCHK 18 0 H0YLB7;H0YKU8;Q6JHV3;H0YMI4;Q9Y6I4-2;Q9Y6I4 H0YLB7 USP3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase 3 0 203.37 1.19E-15 32321000 87101 88127 94773 87522 91853 79848 109690 87306 118400 FALSE TRUE 81649.50389 94652.01478 97021.06032 89767.96269 84639.2359 102898.8214 93243.00281 98206.34628 98638.27511 0.827766947 0.959587084 0.983604592 0.910072308 0.858077007 1.043193641 0.945302447 0.995621083 1 16.58985995 2.231627794 24.99967527 0.988371732 0.92531687 0.39389223 0.051520957 231.3438086 834214.8289 0.019262155 0.014534336 170.4620843 -2.231627794 -0.063054862 SGAGSS(ph)PETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SGAGSSPETK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SGAGS(0.063)S(0.937)PETK;SGAGS(0.024)S(0.976)PETK;SGAGSS(1)PETK;SGAGS(0.002)S(0.998)PETK;SGAGS(0.021)S(0.979)PETK;SGAGS(0.026)S(0.974)PETK;SGAGS(0.359)S(0.641)PETK 303.79 6.58E-29 3640689100 14665810 7906172 12121814 10879383 9958255 7573032 12851877 9041711 10279109 TRUE FALSE 13747903.13 8491553.201 12409349.15 11158566.39 9176173.822 9759243.4 10924857.35 10170588.52 8563459.302 1.605414663 0.991603148 1.449104703 1.303044248 1.071549884 1.139637973 1.27575282 1.187672897 1 23.02976228 2.766246896 23.43109853 1.162371097 1.298312482 0.238061552 0.169891571 676.3702575 572414.9304 0.049192698 0.052162423 583.7768859 -2.766246896 0.135941385 SGAHSSAS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SGAHSSASPPR 11 0 P18615;P18615-3;A0A0A0MT02;E9PD43;A0A0A0MSN9;P18615-4;A0A0G2JI50 P18615 NELFE Negative elongation factor E 1 SGAHS(0.001)S(0.049)AS(0.95)PPR;SGAHS(0.002)S(0.052)AS(0.946)PPR;SGAHSS(0.002)AS(0.998)PPR;SGAHS(0.005)S(0.015)AS(0.98)PPR;SGAHS(0.002)S(0.028)AS(0.971)PPR;SGAHS(0.002)S(0.016)AS(0.982)PPR;SGAHS(0.003)S(0.041)AS(0.956)PPR 121.21 0.00043679 4358761000 247949.3 333571 303152 330370 349386 277127 355493 295014 414536 TRUE FALSE 232430.5959 358268.9439 310342.9086 338847.8535 321946.6329 357129.0661 302190.1249 331847.1473 345347.2636 0.673034422 1.037416484 0.898640126 0.981180074 0.932240289 1.034115813 0.875032632 0.960908576 1 18.39768827 4.748532107 24.81668407 0.958280323 0.67303425 0.747608224 0.053177495 607.0955218 1510883.799 0.011660424 0.156154289 56044.38487 -4.748532107 -0.285246073 SGAHSSAS(ph)PPRS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGAHSSASPPRSR 13 1 P18615;P18615-3;A0A0A0MT02;E9PD43;A0A0A0MSN9;P18615-4;A0A0G2JI50 P18615 NELFE Negative elongation factor E 2 S(0.005)GAHS(0.033)S(0.038)AS(0.924)PPRS(1)R;SGAHSS(0.001)AS(0.998)PPRS(1)R 73.597 0.020711 416870000 100248 220492 198392 202392 234409 189308 220712 203283 243412 TRUE FALSE 93973.65663 236817.4571 203097.9519 207585.7214 215999.4627 243958.1464 187618.2846 228663.33 202784.9647 0.463415307 1.167825521 1.001543444 1.023674125 1.065165078 1.203038632 0.925208064 1.127614813 1 17.62959116 4.744818167 24.95908173 1.061438465 0.463415035 0.835630358 0.083738351 253.7629883 1012139.499 0.018465396 0.172333344 55567.15573 -4.744818167 -0.59802343 SGAHVDFYDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SGAHVDFYDK 10 0 P35270 P35270 SPR Sepiapterin reductase 0 ;;; 129.7 0.0002961 1738690000 1716460 1996000 1747550 1726050 2454030 1248020 2024310 2022820 2571130 FALSE TRUE 1609029.833 2143785.917 1789002.711 1770343.365 2261300.383 1608303.114 1720783.508 2275373.53 2141991.793 0.751183939 1.000837596 0.835205213 0.826494 1.055699835 0.750844667 0.803356723 1.062269957 1 21.03052152 1.231182486 24.99973574 1.03113506 0.868515319 0.334451964 0.09956576 219.3512217 743208.6984 0.084355084 0.02278092 17.02873888 -1.231182486 -0.162619741 SGAQASS(ph)TPLS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_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(0.011)S(0.6)T(0.389)PLS(0.99)PT(0.01)R;SGAQAS(0.02)S(0.759)T(0.22)PLS(0.999)PT(0.001)R 223.29 5.23E-12 1706010000 2092070 2145330 2195140 2220690 2315000 1729410 2629600 2107870 3178900 TRUE FALSE 1961131.073 2304172.465 2247209.757 2277676.665 2133189.238 2228662.592 2235315.892 2371042.209 2648321.054 0.740518628 0.870050277 0.848541288 0.860045523 0.805487399 0.841537921 0.844050191 0.89530014 1 21.3366466 0.873494274 1.770711684 0.999902687 0.835293283 0.692682114 0.036393795 0.287688542 1.76890603 0.031780278 0.009018794 7.472987817 -0.873494274 -0.164609404 SGAQASS(ph)TPLSPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGAQASSTPLSPTR 14 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 SGAQAS(0.212)S(0.527)T(0.26)PLS(0.001)PTR 128.74 0.00076205 0 108830 134630 132830 116680 133870 98443 133410 100310 132770 TRUE FALSE 102018.5246 144598.1453 135980.7903 119674.2063 123356.3902 126861.896 113406.409 112833.9243 110609.8293 0.922327837 1.307281154 1.229373476 1.08194911 1.115238953 1.146931487 1.025283284 1.020107571 1 16.75512007 1.944178678 0.845615124 0.994767216 1.183802394 0.162819321 0.103742818 0.742804417 0.987209108 0.086542935 0.04199894 87.93842398 -1.944178678 0.189035178 SGAQASST(ph)PLS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SGAQASSTPLSPTR 14 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 2 SGAQAS(0.009)S(0.303)T(0.687)PLS(0.899)PT(0.101)R;SGAQAS(0.017)S(0.15)T(0.833)PLS(0.999)PT(0.001)R;SGAQAS(0.001)S(0.438)T(0.561)PLS(0.997)PT(0.003)R 221.69 2.21E-11 2949320000 3608410 3387720 3551300 3627460 3904820 3093420 4423130 3490160 5089570 TRUE FALSE 3382566.059 3638550.314 3635538.513 3720546.765 3598151.188 3986440.137 3759922.719 3925914.159 4240087.887 0.797758478 0.858130871 0.857420556 0.877469256 0.848602973 0.940178657 0.886755845 0.925903958 1 22.01566274 -4.999999359 0.029045956 1.851184393 0.29855462 0.824559414 0.023503559 560.5325658 1.226578273 50.41406496 21.03185678 1.00E-05 4.999999359 -1.552629773 SGAQASST(ph)PLSPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SGAQASSTPLSPTR 14 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 SGAQAS(0.003)S(0.025)T(0.972)PLSPTR;SGAQASS(0.03)T(0.97)PLSPTR;SGAQASS(0.01)T(0.989)PLS(0.001)PTR 263.59 1.40E-23 1353670000 1653030 1784840 1816030 1809280 2019330 1379840 1952330 1646430 2006200 TRUE FALSE 1549569.803 1916991.411 1859107.089 1855709.188 1860739.967 1778177.408 1659596.241 1851990.41 1671352.259 0.927135375 1.146970305 1.112337078 1.110304053 1.113314059 1.0639154 0.992966164 1.108079042 1 20.6725844 2.001568867 7.606753249 1.031715407 1.095763241 0.078444246 0.06682638 0.210218597 92.58884334 0.024354149 0.017001664 100.3618984 -2.001568867 0.064047834 SGAQASSTPLS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_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(0.908)PT(0.092)R;SGAQASSTPLS(1)PTR;SGAQASSTPLS(0.999)PT(0.001)R;SGAQASSTPLS(0.995)PT(0.005)R;SGAQASSTPLS(0.961)PT(0.039)R;SGAQASSTPLS(0.999)PT(0.001)R;SGAQASSTPLS(0.958)PT(0.042)R;SGAQAS(0.001)STPLS(0.887)PT(0.112)R;SGAQASSTPLS(0.889)PT(0.111)R 243.47 1.63E-17 39122071000 8487120 8587895 8567133 8682183 9550034 6818841 9153670 7421313 9616014 TRUE FALSE 7955926.309 9223751.681 8770349.44 8904982.515 8800012.853 8787329.702 7781162.162 8347880.264 8011039.142 0.993120389 1.151380179 1.094782997 1.111588941 1.098485814 1.096902605 0.971304974 1.04204712 1 22.93355796 1.752359034 24.99999998 1.004542259 1.099513369 0.465613206 0.043098936 3.196334885 5799.372412 0.018071203 0.010021289 56.54042051 -1.752359034 0.094971111 SGAQASSTPLSPT(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGAQASSTPLSPTR 14 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 SGAQASSTPLS(0.444)PT(0.556)R 147.64 8.92E-05 243880000 148560 156520 138030 157670 162290 121130 163420 142760 172340 TRUE FALSE 139261.8948 168108.9037 141304.1368 161716.0791 149544.398 156098.2646 138916.6881 160583.9003 143575.3406 0.969956917 1.170875882 0.984181101 1.12634996 1.041574391 1.087221969 0.967552558 1.118464351 1 17.13144846 SGAVQGAGSLGPGS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SGAVQGAGSLGPGSPVR 17 0 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 SGAVQGAGSLGPGS(1)PVR;SGAVQGAGSLGPGS(1)PVR;SGAVQGAGSLGPGS(1)PVR;SGAVQGAGSLGPGS(1)PVR 361.27 2.38E-88 1101410000 940470 864000 917360 906490 970000 790810 1028460 848180 1104780 TRUE FALSE 881607.6615 927971.459 939120.2124 929752.0681 893820.1128 1019104.009 874251.9708 954077.1401 920385.0808 0.957868266 1.008242613 1.020355753 1.010177248 0.971137116 1.107258288 0.949876295 1.036606481 1 19.81187807 4.738761667 4.339924221 1.012179912 0.95387634 0.14937565 0.041395138 0.387574316 17.51451213 0.008721496 0.069845556 54797.61635 -4.738761667 -0.058303572 SGCSEAQPPES(ph)PETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SGCSEAQPPESPETR 15 0 Q9Y6A5;A0A494BZT8;A0A494C117;H0Y8F2 Q9Y6A5 TACC3 Transforming acidic coiled-coil-containing protein 3 1 SGCSEAQPPES(1)PETR;SGCSEAQPPES(0.903)PET(0.097)R;SGCSEAQPPES(0.998)PET(0.002)R;SGCSEAQPPES(1)PETR;SGCSEAQPPES(0.997)PET(0.003)R 206.95 1.16E-09 421755000 399637 429386 427340 415554 490028 342818 407367 380966 570705 TRUE FALSE 374624.4335 461178.1862 437476.7066 426217.8192 451543.1776 441783.9914 346286.1002 428530.4437 475450.6486 0.787935477 0.969981191 0.920130634 0.896450179 0.949716188 0.929190007 0.728332375 0.901314248 1 18.85893607 SGDAAIVDMVPGKPMCVESFSDYPPLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SGDAAIVDMVPGKPMCVESFSDYPPLGR 28 1 P68104;A0A087WVQ9;Q5VTE0 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3 0 ;;;;; 208.72 1.61E-25 4012570000 4203304 3970456 4062056 4115463 4500340 3389490 5071972 3794548 5249565 FALSE TRUE 3940226.706 4264432.693 4158409.887 4221072.748 4146901.45 4367980.739 4311476.884 4268305.671 4373378.688 0.900957129 0.975088827 0.950846058 0.965174308 0.948214583 0.998765726 0.985845771 0.975974407 1 22.06031685 8 0.205385396 0.997975238 0.65319016 0.571451488 0.018995135 40.64907734 0.49948376 0.03163276 4.551121464 100000000 -8 -0.344785078 SGDET(ph)PGSEVPGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SGDETPGSEVPGDK 14 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.024)GDET(0.976)PGSEVPGDK;S(0.341)GDET(0.659)PGSEVPGDK;S(0.06)GDET(0.94)PGSEVPGDK 328.49 2.64E-67 4235900000 5514500 2293470 3531700 2988400 2603760 2933850 4598200 2465380 2135190 TRUE FALSE 5169357.289 2463280.905 3615473.592 3065087.403 2399271.193 3780804.868 3908742.598 2773188.12 1778812.995 2.906071241 1.384789133 2.032520339 1.723108282 1.348804624 2.125465059 2.197388151 1.55901049 1 20.76248342 4.750437299 24.56371066 1.756881721 2.90607213 0.494766222 0.383553535 1301.155475 2691025.461 0.086702722 1.421401891 56290.78416 -4.750437299 1.149190408 SGDGEGTPVEHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGDGEGTPVEHVR 13 0 Q7L576;Q7L576-2;Q7L576-3 Q7L576 CYFIP1 Cytoplasmic FMR1-interacting protein 1 0 112.44 0.0009008 340530000 231950 265820 247360 264280 311440 221000 292160 281080 313810 FALSE TRUE 217432.6635 285501.5894 253227.496 271061.8722 286980.7587 284799.1124 248353.3203 316173.4567 261433.0837 0.831695287 1.092063733 0.968613048 1.036830796 1.09772166 1.089376709 0.949968982 1.209385791 1 17.9960822 4.746249747 24.63821243 1.046040846 0.83169516 0.463144458 0.075113275 699.1452142 2240198.967 0.016276495 0.174522512 55750.62583 -4.746249747 -0.214345686 SGDGVVTVDDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SGDGVVTVDDLR 12 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ;;;; 226.2 3.69E-11 1453720000 2374470 2470940 2300710 2365460 2540350 1836980 2699410 2163010 2382800 FALSE TRUE 2225856.161 2653890.969 2355283.928 2426161.708 2340841.158 2367286.305 2294658.531 2433066.56 1985095.287 1.121284291 1.336908604 1.186484066 1.222189043 1.179208461 1.192530314 1.155943771 1.225667391 1 20.92077683 -5 0.179085689 0.134698991 1.254578133 0.534924703 0.058005572 91.3253196 0.878422321 28.01928207 0.167968057 1.00E-05 5 1.119879141 SGDVYSFSVLEPHGCGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGDVYSFSVLEPHGCGR 17 0 P57081;P57081-2 P57081 WDR4 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 0 158.17 3.37E-09 165460000 221760 402620 335200 407350 437070 518530 324290 306710 315710 FALSE TRUE 207880.4375 432430.4037 343151.1023 417803.2906 402744.2853 668221.1934 275665.7251 345003.4187 263015.9614 0.790371947 1.644122286 1.304677862 1.588509261 1.531254161 2.540610804 1.048095042 1.311720463 1 18.00479083 1.595610652 25 1.134865888 1.562629403 0.19115393 0.432658461 1.473216797 2997.268841 0.215939815 0.101109468 39.41038272 -1.595610652 0.427763515 SGDWMIDYVSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGDWMIDYVSNR 12 0 P35573-2;P35573-3;P35573 P35573-2 AGL "Glycogen debranching enzyme;4-alpha-glucanotransferase;Amylo-alpha-1,6-glucosidase" 0 77.062 0.068476 64814000 52251 66495 60864 63362 68503 45796 61709 57220 73638 FALSE TRUE 48980.70318 71418.35899 62307.72282 64987.97619 63123.05071 59016.56176 52456.30833 64364.04296 61347.34208 0.79841606 1.164163867 1.015654806 1.05934461 1.02894516 0.962006825 0.855070596 1.049174109 1 15.90471322 2.207637843 4.535187577 0.942383999 1.036787931 0.000952863 0.103528055 0.363864513 17.2322071 0.036652567 0.027485678 161.3012909 -2.207637843 0.094403933 SGDYYVTVVEDVTLGQIVATATLIIEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGDYYVTVVEDVTLGQIVATATLIIEHK 28 0 Q96EK6;G3V5E4;G3V4W4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 0 148.87 6.93E-08 141980000 38358 24434 33499 33742 31283 30486 37890 23077 33090 FALSE TRUE 35957.24125 26243.11878 34293.6121 34607.87685 28826.15937 39286.8133 32208.74625 25958.21425 27567.06523 1.304355068 0.951973616 1.244006637 1.255406644 1.045673855 1.425135863 1.168377772 0.941638656 1 14.75065807 1.259095733 9.737996156 0.970734334 1.186504133 0.339537317 0.131546132 0.295578215 135.4498012 0.088644754 0.031028648 18.15915908 -1.259095733 0.215769799 SGEDGEKDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGEDGEKDTK 10 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 79.659 0.024024 244880000 953050 307290 576030 506590 452340 356280 628160 433250 457770 FALSE TRUE 893400.3017 330042.0713 589693.7036 519589.9571 416815.0411 459132.2523 533973.2396 487342.2162 381365.2297 2.342637011 0.865422555 1.546270236 1.362447115 1.092955017 1.203917443 1.400162359 1.277888434 1 18.54081379 4.751188788 24.94535347 1.246427342 2.342637719 0.75662244 0.199789516 987.191565 1950035.947 0.045549397 0.820913232 56388.27229 -4.751188788 1.096210377 SGEHDFGAAFDGDGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGEHDFGAAFDGDGDR 16 0 A0A3B3ITK7;P36871;P36871-2;P36871-3 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 0 113.47 0.00065841 78310000 54575 59055 59164 63618 68461 48158 67747 59566 106720 FALSE TRUE 51159.24817 63427.49365 60567.39802 65250.54559 63084.34922 62060.43282 57588.96628 67002.94622 88907.74256 0.575419493 0.713407987 0.681238734 0.733912972 0.709548431 0.698031814 0.647738483 0.753623299 1 16.44002144 0.878515268 4.561768448 0.999978065 0.685550655 0.838054292 0.044056203 0.29738321 10.65266268 0.038905539 0.009872913 7.559886368 -0.878515268 -0.31442741 SGEIWAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGEIWAR 7 0 Q12996;E9PLP8 Q12996 CSTF3 Cleavage stimulation factor subunit 3 0 100.74 0.046513 0 130250 68768 83500 86644 92037 61278 94503 66006 94395 FALSE TRUE 122097.885 73859.65427 85480.65943 88867.43173 84808.78528 78967.96383 80333.15247 74246.9944 78639.86468 1.552620741 0.939213903 1.086988893 1.130055756 1.078445209 1.004172173 1.021532181 0.944139397 1 16.26297322 4.744664498 24.98868827 1.030047841 1.552620972 0.882475888 0.060426443 224.7892071 920239.4142 0.014568008 0.1341169 55547.49749 -4.744664498 0.522573131 SGES(ph)S(ph)SQLSQEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGESSSQLSQEQK 13 0 Q6ZMI0-4;Q6ZMI0-3;Q6ZMI0-5;Q6ZMI0-2;Q6ZMI0 Q6ZMI0-4 PPP1R21 Protein phosphatase 1 regulatory subunit 21 2 S(0.285)GES(0.559)S(0.6)S(0.508)QLS(0.048)QEQK;S(0.272)GES(0.581)S(0.63)S(0.516)QLS(0.001)QEQK 112.5 0.0013099 590900000 300000 1056410 807900 854200 964760 847070 862460 840720 674940 TRUE FALSE 281223.5355 1134627.696 827063.7695 876120.2182 888991.6413 1091605.358 733142.1297 945685.7427 562288.1537 0.500141313 2.017875867 1.47088955 1.558133872 1.581025023 1.941362895 1.303854838 1.68185251 1 19.10095013 -1.307806965 3.441087257 0.997758752 1.55395956 0.118815945 0.416652287 55804138.02 83752880.81 1320999.534 0.087962941 0.049225829 1.307806965 0.556200808 SGEWTEDEVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SGEWTEDEVLR 11 0 Q13938-4;Q13938 Q13938-4 CAPS Calcyphosin 0 ;;;; 240.13 2.63E-15 2168850000 2577590 2976760 2509470 2578640 3285430 1831170 2765550 2832160 3164770 FALSE TRUE 2416263.243 3197162.408 2568995.813 2644812.268 3027405.581 2359799.052 2350881.452 3185761.41 2636549.442 0.916449054 1.212631312 0.974378016 1.003133955 1.148245329 0.895033112 0.891650812 1.2083071 1 21.33021962 2.235655495 24.99856233 0.975829779 1.060394309 0.026217784 0.120432475 177.3451245 1526024.668 0.041788473 0.032232129 172.050324 -2.235655495 0.08456453 SGEWTEDEVLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SGEWTEDEVLRR 12 1 Q13938-4;Q13938 Q13938-4 CAPS Calcyphosin 0 ;;;;; 270.02 1.23E-22 4855720000 2720220 3436410 2903350 3133400 3642050 2421710 3351230 2982940 3839540 FALSE TRUE 2549966.286 3690845.372 2972218.833 3213808.349 3356018.084 3120818.364 2848744.173 3355366.625 3198695.97 0.797189327 1.153859387 0.929197042 1.004724544 1.049183203 0.975653327 0.89059548 1.04897954 1 21.60905244 2.009067076 24.58015676 0.959057808 1.003382956 0 0.098438505 568.0772151 1540005.599 0.033971496 0.025051115 102.1097179 -2.009067076 0.044325148 SGFEPASLKEEVGEEAIVELVENGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGFEPASLKEEVGEEAIVELVENGKK 26 2 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ; 262.74 3.82E-53 574140000 1046630 584580 745340 762750 861830 514080 1064390 654200 1138620 FALSE TRUE 981123.2966 627862.9115 763019.8168 782323.4563 794145.3483 662486.5506 904794.6008 735878.3101 948576.9662 1.03431069 0.661899808 0.804383665 0.824733769 0.837196534 0.698400419 0.953844161 0.775770798 1 19.85540531 0.218945753 0.522624627 1.012293243 0.796138563 0.167963668 0.111143256 4.291246578 1.689369509 0.225541691 0.048946743 1.655563156 -0.218945753 -0.21615468 SGFEPPGDFPFEDYSQHIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SGFEPPGDFPFEDYSQHIYR 20 0 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 0 ;; 254.82 3.86E-36 395360000 463810 623340 596870 589980 671510 585780 675810 567270 658000 FALSE TRUE 434780.96 669492.7422 611028.0383 605119.8856 618772.3133 754885.1767 574478.5644 638094.9082 548175.5492 0.793141833 1.221310843 1.114657593 1.103879745 1.128784956 1.377086552 1.047982832 1.164033874 1 19.06427845 4.745374414 24.80411232 1.152295744 0.793141648 0.538358259 0.102100419 517.5676743 1884035.913 0.021938427 0.215641902 55638.37203 -4.745374414 -0.359154097 SGFGEISS(ph)PVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SGFGEISSPVIR 12 0 P57740;G3V1T4 P57740 NUP107 Nuclear pore complex protein Nup107 1 SGFGEIS(0.005)S(0.995)PVIR;SGFGEIS(0.097)S(0.903)PVIR;SGFGEIS(0.007)S(0.993)PVIR;SGFGEIS(0.003)S(0.997)PVIR;SGFGEIS(0.036)S(0.964)PVIR;SGFGEIS(0.005)S(0.995)PVIR 252.2 4.94E-21 1560012000 3238100 3247040 3536220 3433980 3635280 3205080 4183440 3072480 4213660 TRUE FALSE 3035433.101 3487454.22 3620100.808 3522101.741 3349779.773 4130334.566 3556172.009 3456085.891 3510372.925 0.864703884 0.993471148 1.031258184 1.003341188 0.954251826 1.176608484 1.013046786 0.984535252 1 21.74319287 5.650194114 1.102712479 1.029626871 4.97E-15 0.40924128 0.058970461 10.2078786 2.254063498 0.016075074 19.71763149 446883.2879 -5.650194114 -1.029626871 SGGASHSELIHNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SGGASHSELIHNLR 14 0 F6S8N6;A0A0A0MRJ6;P22061;P22061-2;A0A3F2YNX8;F8WDT3;F8WAV5;F8WAX2;H7C4X2 F6S8N6 PCMT1 Protein-L-isoaspartate O-methyltransferase;Protein-L-isoaspartate(D-aspartate) O-methyltransferase 0 ;;;;; 279.77 1.79E-33 5187340000 2209070 2672580 2296340 2179530 2487220 1780270 2885860 2198040 3442770 FALSE TRUE 2070808.252 2870460.604 2350810.269 2235460.43 2291883.774 2294205.049 2453152.084 2472470.132 2868149.446 0.722001517 1.000805801 0.819626143 0.77940863 0.799081016 0.799890345 0.85530832 0.86204369 1 21.45168877 0.627813682 1.85074908 0.999930361 0.838833968 0.353073284 0.072335485 2.325474825 9.954230444 0.069666897 0.019446685 4.244374353 -0.627813682 -0.161096393 SGGGGGGGGSSWGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGGGGGGGGSSWGGR 15 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 192.68 2.89E-07 43857000 29561 31868 27360 32683 28800 23440 33372 26479 46567 FALSE TRUE 27710.82978 34227.53988 28008.99212 33521.70111 26538.16417 30206.74748 28368.17841 29784.96144 38794.66687 0.714294825 0.88227436 0.721980478 0.864080138 0.68406733 0.778631444 0.731239129 0.767759175 1 15.24357072 -1.048029669 5.327565333 1.000001934 0.771942711 0.570442534 0.063177868 1.32E-06 2.35E-07 0.055549038 0.013092923 0.08953036 1.048029669 -0.228059222 SGGGGYSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SGGGGYSSR 9 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;; 97.635 0.015256 122693000 125737 132397 129492 123094 153704 97377 132375 126303 148525 FALSE TRUE 117867.3456 142199.8116 132563.6114 126252.8004 141632.7079 125488.1591 112526.5977 142072.2076 123735.218 0.952577185 1.149226663 1.071349075 1.020346531 1.144643458 1.014166873 0.90941447 1.148195396 1 16.91689666 2.023975292 23.9085937 0.997301333 1.077304746 0.057428758 0.080996803 221.4112901 220793.7801 0.028057701 0.020720584 105.6757386 -2.023975292 0.080003413 SGGGLHSVAEGVRLS(ph)PEPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SGGGLHSVAEGVRLSPEPGR 20 1 Q9NWK9-2;Q9NWK9 Q9NWK9-2 ZNHIT6 Box C/D snoRNA protein 1 1 SGGGLHSVAEGVRLS(1)PEPGR;SGGGLHSVAEGVRLS(1)PEPGR;SGGGLHSVAEGVRLS(1)PEPGR;SGGGLHSVAEGVRLS(1)PEPGR 269.08 1.85E-37 1038120000 632540 787140 800300 820390 923850 614213 867590 732980 1370730 TRUE FALSE 592950.4505 845420.6646 819283.4939 841442.5963 851294.5476 791526.3222 737502.9338 824494.1665 1141946.308 0.519245473 0.740333113 0.717444847 0.736849527 0.74547686 0.693137949 0.645829781 0.722007822 1 20.12306339 0.953517713 21.75146315 1.000000001 0.69490888 0.681550909 0.066797285 1247.428959 583737.849 0.059919876 0.014979969 8.984992371 -0.953517713 -0.305091121 SGGGYGGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SGGGYGGDR 9 0 Q92804-2;Q92804;A0A075B7F4;A0A075B7C1 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;;; 114.89 0.0036388 579308000 627582 638742 624726 617513 673286 517711 680519 599365 665819 FALSE TRUE 588302.7629 686035.1223 639544.7957 633359.429 620408.8335 667165.7614 578481.4936 674197.0396 554689.5075 1.060598326 1.236791237 1.152977994 1.141826951 1.118479483 1.202773358 1.042892439 1.215449419 1 19.08132091 -5 0.207808895 0.2871584 1.171568869 0.305800443 0.064601941 155.7990267 1.551674126 46.16819252 0.128389655 1.00E-05 5 0.884410469 SGGIETIANEYSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGGIETIANEYSDR 14 0 O95757;D6RJ96 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 99.161 0.0053296 104040000 68940 99903 111110 86780 103670 112470 97753 107950 94872 FALSE TRUE 64625.16846 107299.9221 113745.5817 89006.92172 95528.17638 144938.2632 83095.84514 121427.7951 79037.2503 0.817654564 1.357586728 1.439138903 1.126138895 1.208647518 1.833796882 1.051350405 1.53633628 1 16.27024514 4.740095549 24.18395616 1.335453972 0.817654312 0.285868126 0.247897083 99.89139689 1573619.657 0.052136087 0.32870083 54966.17913 -4.740095549 -0.51779966 SGGIVIS(ph)PFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 135.26 0.0001561 676286000 865591 746551 849506 810940 747667 837980 968440 790021 714996 TRUE FALSE 811415.2044 801826.4128 869656.6835 831750.0933 688948.2498 1079891.223 823231.4126 888656.8609 595658.5485 1.362215327 1.346117528 1.459991946 1.396353826 1.15661607 1.812936665 1.382052544 1.491889713 1 19.18412604 SGGIVIS(ph)PFRLEELTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SGGIVISPFRLEELTNR 17 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 SGGIVIS(1)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR;S(0.007)GGIVIS(0.993)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR 295.69 2.40E-46 3549135000 1480112 1709712 1584555 1650811 2101766 1329773 1776624 1570614 2486611 TRUE FALSE 1387474.432 1836300.855 1622141.393 1693173.605 1936701.776 1713656.878 1510235.725 1766708.615 2071579.56 0.669766423 0.886425456 0.783045664 0.817334578 0.934891333 0.827222334 0.729026176 0.85283165 1 20.9822998 -2.744074673 1.525316463 3.529839815 0.81460137 0.381598348 0.074946263 1071582.75 35979.37611 9365445.006 0.018619409 0.001802708 2.744074673 -2.715238445 SGGLQT(ph)PECLS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SGGLQTPECLSR 12 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 SGGLQT(1)PECLS(1)R;SGGLQT(1)PECLS(1)R;SGGLQT(1)PECLS(1)R;SGGLQT(1)PECLS(1)R 210.31 2.39E-07 979370000 3035700 2492570 2716150 2308510 2171030 2136000 3501900 2238380 2689250 TRUE FALSE 2845700.956 2677122.476 2780578.361 2367750.275 2000526.061 2752628.525 2976822.605 2517846.67 2240396.802 1.270177209 1.194932288 1.241109771 1.056844159 0.892933814 1.228634375 1.328703292 1.123839611 1 21.09532284 -2.429242241 1.741937145 0.000201263 1.178726159 0.147761854 0.123399332 3135668.015 275539.9282 12302518.94 0.032473855 0.003721841 2.429242241 1.178524896 SGGLQT(ph)PECLS(ph)REGS(ph)PIPHDPEFGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGGLQTPECLSREGSPIPHDPEFGSK 26 1 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 3 S(0.196)GGLQT(0.842)PECLS(0.985)REGS(0.977)PIPHDPEFGSK 62.183 0.051278 111090000 118830 129270 98813 120320 181490 43651 98861 85926 399380 TRUE FALSE 111392.6424 138841.2853 101156.891 123407.6149 167236.5075 56252.33509 84037.71083 96654.05025 332720.8979 0.334793045 0.417290546 0.304029268 0.37090431 0.502633013 0.169067634 0.252577194 0.290495881 1 18.34395296 -1.299671558 3.352405662 1.003006496 0.329108718 0.844797066 0.090219518 39802337.94 57650441.62 1205391.674 0.023704208 0.050156641 1.299671558 -0.673897778 SGGLQT(ph)PECLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SGGLQTPECLSR 12 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 SGGLQT(1)PECLSR;SGGLQT(1)PECLSR;SGGLQT(1)PECLSR;SGGLQT(1)PECLSR;SGGLQT(0.999)PECLS(0.001)R 206.88 9.50E-07 1027000000 1680480 1272010 1588300 1339670 1332210 1245450 1463350 1176680 1631210 TRUE FALSE 1575301.757 1366190.944 1625975.226 1374048.2 1227583.6 1604991.197 1243934.253 1323591.088 1358950.513 1.159204652 1.005327958 1.196493331 1.011109814 0.903332085 1.181051982 0.915363908 0.973980344 1 20.37406149 3.069900686 11.03737435 0.994791684 1.106421364 0.296034664 0.088785856 0.644093481 98.51916199 0.023866592 0.02853517 1174.628911 -3.069900686 0.11162968 SGGLQTPECLS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGGLQTPECLSR 12 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 SGGLQTPECLS(1)R 85.909 0.011967 624680000 762390 660900 706740 701340 728400 626800 912580 679000 854000 TRUE FALSE 714673.3708 709833.7237 723504.2065 719337.5718 671194.4022 807746.9848 775747.101 763774.6447 711461.8829 1.004513928 0.99771153 1.016926168 1.011069727 0.943401774 1.135334168 1.090356517 1.073528552 1 19.44042694 2.236440265 25 1.08508686 0.998902374 0.50419227 0.038747151 39.39466895 464470.3867 0.012761221 0.009888735 172.3615002 -2.236440265 -0.086184486 SGGLQTPECLS(ph)REGS(ph)PIPHDPEFGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SGGLQTPECLSREGSPIPHDPEFGSK 26 1 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 S(0.041)GGLQT(0.243)PECLS(0.719)REGS(0.996)PIPHDPEFGSK;SGGLQT(0.101)PECLS(0.899)REGS(1)PIPHDPEFGSK;S(0.01)GGLQT(0.092)PECLS(0.899)REGS(1)PIPHDPEFGSK 177.98 3.33E-17 301037000 334357 484345 338700 570620 939780 221490 447356 439678 1382790 TRUE FALSE 313430.1922 520206.4078 346734.1239 585263.0753 865973.4697 285430.5674 380279.1208 494572.7662 1151993.416 0.272076375 0.451570643 0.300986203 0.508043768 0.751717378 0.247771006 0.33010529 0.429319091 1 20.13570104 0.934394263 20.57863855 1.000000001 0.403837722 0.616204523 0.146017642 2499.947713 784164.3227 0.137050337 0.034262584 8.597937087 -0.934394263 -0.596162278 SGGMERPFVLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SGGMERPFVLAR 12 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 155.88 6.63E-05 1783372000 1133175 1595820 1215480 1181290 1533010 847420 1348260 1335270 1267000 FALSE TRUE 1062251.6 1713976.173 1244311.76 1211603.901 1412613.578 1092056.397 1146100.93 1501981.399 1055529.515 1.006368448 1.62380696 1.178850749 1.147863593 1.338298511 1.034605269 1.085806615 1.422964851 1 20.00953549 3.719017459 21.33469476 1.168375075 1.371832005 0.067698083 0.195600905 73.76757686 194210.4383 0.047005543 0.074607002 5236.214858 -3.719017459 0.20345693 SGGPPPKR ddPTM_SK-BR-3_Pertuzumab_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 ;; 92.439 0.018883 236412000 368114 324656 354186 349259 371667 275026 407862 313418 443900 FALSE TRUE 345074.4018 348693.868 362587.4592 358221.5772 342477.7731 354421.5415 346706.8795 352548.9272 369810.2223 0.933112124 0.942899485 0.980469001 0.968663265 0.926090606 0.958387627 0.93752649 0.95332391 1 18.49642558 0.935352024 20.77744629 1 0.951206671 0.476708489 0.016421425 3792.254951 1218809.955 0.01604866 0.004012165 8.616919274 -0.935352024 -0.04879333 SGGPS(ph)PKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SGGPSPKR 8 1 Q96E39 Q96E39 RBMXL1 "RNA binding motif protein, X-linked-like-1" 1 SGGPS(1)PKR;SGGPS(1)PKR;SGGPS(1)PKR;SGGPS(1)PKR;SGGPS(1)PKR;SGGPS(1)PKR 110.39 0.0021043 4558360000 5564950 4610750 4424870 4771000 5473360 2865490 5067860 3904330 8056680 TRUE FALSE 5216649.713 4952134.727 4529830.006 4893431.937 5043504.384 3692710.446 4307981.441 4391794.195 6711968.06 0.777216111 0.737806659 0.674888493 0.729060671 0.751419604 0.55016806 0.641835808 0.654322869 1 22.67830442 -0.647374036 12.40301236 1 0.686071171 0.688740851 0.065542103 0 0 0.065315036 0.015394902 0.225229858 0.647374036 -0.313928829 SGGPS(ph)SPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGGPSSPKR 9 1 Q93075 Q93075 TATDN2 Putative deoxyribonuclease TATDN2 1 SGGPS(0.567)S(0.432)PKR 60.598 0.057992 79985000 67880 50030 56710 56837 52901 44065 64441 54282 75254 TRUE FALSE 63631.51197 53734.27326 58055.18798 58295.53364 48746.36885 56785.85016 54778.67029 61059.22719 62693.62124 1.014959907 0.857093149 0.926014271 0.929847925 0.777533151 0.905767589 0.873751894 0.973930457 1 15.93603104 1.129752392 4.755573908 0.997955104 0.893252872 0.276254935 0.060159237 0.238547802 8.224226334 0.051899749 0.013252195 13.48194006 -1.129752392 -0.104702232 SGGSGHAVAEPAS(ph)PEQELDQNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGGSGHAVAEPASPEQELDQNK 22 0 P46013 P46013 MKI67 Antigen KI-67 1 SGGSGHAVAEPAS(1)PEQELDQNK 203.99 7.87E-23 266880000 246850 228360 285350 244440 257890 229130 266670 192480 182290 TRUE FALSE 231400.0991 245268.012 292118.6368 250712.7442 237636.3597 295276.1114 226685.3091 216511.5517 151864.6214 1.523726178 1.615043779 1.923546341 1.650896318 1.564790782 1.944337718 1.492680172 1.425687891 1 17.21242629 0.977689237 1.442086308 1.006515329 1.709700073 0.693141698 0.146276391 0.237914444 1.008713859 0.13164358 0.039193132 9.499248232 -0.977689237 0.703184745 SGILPILVHCLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGILPILVHCLER 13 0 O00629 O00629 KPNA4 Importin subunit alpha-3 0 ; 161.63 4.18E-05 311310000 538200 790350 570430 541430 837350 437640 670660 671140 662730 FALSE TRUE 504515.0227 848868.3364 583960.869 555324.0104 771587.9087 563979.5635 570100.7591 754933.3064 552116.0816 0.913784328 1.537481636 1.057677703 1.005810243 1.397510296 1.021487296 1.032574087 1.367345259 1 19.0746121 -4.999996149 0.078509132 0.439176478 1.352718878 0.013287028 0.208502679 740.1900026 4.127861954 73.11200324 7.143290636 1.00E-05 4.999996149 0.9135424 SGIYETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGIYETR 7 0 A0A087WY71;Q96CW1-2;Q96CW1;E9PFW3 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 103.91 0.019241 260230000 192170 243600 246630 243940 266620 199510 286420 234730 311460 FALSE TRUE 180142.4227 261636.3975 252480.1801 250199.9134 245680.7407 257105.2982 243473.98 264036.5572 259475.3139 0.694256498 1.008328667 0.973041236 0.964253245 0.946836664 0.990866123 0.938331961 1.017578718 1 17.98523776 4.742513137 24.99874099 0.976373822 0.694256389 0.923912063 0.025744092 95.95117513 606844.1772 0.005790294 0.044354984 55273.01276 -4.742513137 -0.282117433 SGKNS(ph)QEDS(ph)EDS(ph)EDKDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGKNSQEDSEDSEDKDVK 18 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 S(0.036)GKNS(0.976)QEDS(0.988)EDS(1)EDKDVK 100.93 0.00050185 303750000 2138400 324610 620500 696590 846470 419740 940490 380220 822610 TRUE FALSE 2004561.361 348644.4622 635218.553 714465.6787 779991.6607 540912.1241 799472.2556 427691.304 685311.0767 2.925038613 0.508738986 0.926905422 1.042542143 1.13815709 0.789294296 1.166583005 0.624083454 1 19.38639948 4.745401793 24.99958004 0.90200604 2.925039535 0.901078357 0.210909583 237.8823679 869266.8959 0.050203604 0.49967983 55641.87975 -4.745401793 2.023033496 SGKNS(ph)QEDSEDSEDKDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGKNSQEDSEDSEDKDVK 18 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 S(0.025)GKNS(0.975)QEDSEDSEDKDVK 178.53 4.61E-14 193650000 541760 126780 214140 232960 213370 123010 283810 145280 312580 TRUE FALSE 507852.2087 136166.9231 219219.5019 238938.148 196612.7809 158520.9901 241255.3253 163418.5278 260408.3787 1.950214549 0.522897626 0.841829679 0.91755169 0.755017108 0.608739976 0.926449934 0.627547119 1 17.99041634 4.745828102 24.99804534 0.766858446 1.950215104 0.852558609 0.153557761 299.1691456 1029029.995 0.03401317 0.351692024 55696.52535 -4.745828102 1.183356658 SGKPAELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGKPAELLK 9 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 77.305 0.024231 0 3430700 3726300 2657800 2188250 5355000 1840780 3154500 4220400 4981000 FALSE TRUE 3215978.611 4002199.129 2720844.271 2244404.2 4934439.901 2372183.303 2681512.01 4747326.23 4149638.922 0.775002036 0.964469248 0.655682174 0.540867348 1.189125125 0.571660173 0.646203696 1.14403357 1 21.98455438 1.233365421 24.99998503 1.072016901 0.763945994 0.301306461 0.195449421 167.1471546 804290.4512 0.159741503 0.044646565 17.11454751 -1.233365421 -0.308070908 SGKPAELLKMFGIDRDAIAQAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGKPAELLKMFGIDRDAIAQAVR 23 3 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 194.33 1.50E-18 616180000 1692600 1103800 898280 1010700 777980 518970 1086600 1011900 1079400 FALSE TRUE 1586663.187 1185526.501 919587.6258 1036636.273 716880.589 668788.2142 923674.4175 1138237.942 899241.1668 1.764446787 1.318363243 1.022626254 1.152790054 0.797206151 0.743725086 1.027170965 1.265776062 1 19.77834856 5.357820183 0.787619474 0.97215399 3.26861656 0.730726655 0.150321072 3.143053788 0.744281983 0.052003269 7.943263286 227939.8107 -5.357820183 2.29646257 SGKYDLDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SGKYDLDFK 9 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;; 107.06 0.0025861 42234640000 63821600 49800400 48828500 47083000 64597400 31485200 65375100 51079300 79815000 FALSE TRUE 59827119.98 53487673.43 49986735.08 48291229.49 59524180.78 40574466.12 55572710.67 57456663.04 66493360.88 0.899745767 0.804406225 0.751755279 0.726256409 0.895189835 0.610203268 0.835763299 0.864096239 1 25.98670696 0.964194012 2.137726534 0.997919826 0.780856165 0.397001128 0.083595894 0.314786147 3.1296197 0.071344088 0.01971993 9.208608559 -0.964194012 -0.217063661 SGKYDLDFKSPDDPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGKYDLDFKSPDDPSR 16 2 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 120.29 7.21E-05 5504100000 9685500 7264100 7682500 8506700 11676700 7035900 11550500 6553600 25383000 FALSE TRUE 9079301.844 7801941.522 7864732.528 8724996.324 10759659.08 9067050.112 9818609.755 7371831.386 21146413.32 0.429354222 0.368948691 0.371918037 0.412599347 0.508817213 0.428774846 0.464315608 0.348609066 1 24.33390965 -4.866063288 0.41189613 10 0.404566845 0.930779164 0.049801138 179.9910441 1.353429867 1457.058717 0.029853624 1.36E-05 4.866063288 -9.595433155 SGLCS(ph)PSYVAVTPFSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGLCSPSYVAVTPFSLR 17 0 H0YBT0;A0A087WUS5;P01106;P01106-2;H0YBG3;A0A0B4J1R1 H0YBT0 MYC Myc proto-oncogene protein 1 SGLCS(0.713)PS(0.287)YVAVTPFSLR;S(0.001)GLCS(0.868)PS(0.126)Y(0.005)VAVTPFSLR 129.36 3.55E-05 121361000 202910 201950 192895 227650 398210 208097 227210 226700 317840 TRUE FALSE 190210.2253 216902.5881 197470.5605 233491.8844 366936.1929 268171.2257 193141.9698 255003.994 264790.4507 0.718342466 0.819148076 0.745761639 0.881798735 1.385760672 1.012767738 0.729414408 0.963040749 1 18.01449157 2.998806675 24.11325063 0.994159865 0.776642692 0.345206448 0.160190641 39.57141096 799659.6526 0.04993014 0.058893492 997.256039 -2.998806675 -0.217517173 SGLEPAS(ph)SPSKGSEPRPLVPPVSGHATIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SGLEPASSPSKGSEPRPLVPPVSGHATIAR 30 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.019)GLEPAS(0.475)S(0.475)PS(0.013)KGS(0.019)EPRPLVPPVSGHATIAR;S(0.004)GLEPAS(0.516)S(0.464)PS(0.013)KGS(0.003)EPRPLVPPVSGHATIAR;S(0.001)GLEPAS(0.495)S(0.495)PS(0.01)KGSEPRPLVPPVSGHATIAR 163.55 1.86E-12 717460000 497516 603987 638278 658660 681291 462433 929636 561416 657295 TRUE FALSE 466377.3617 648706.8259 653418.2556 675562.3307 627785.1531 595929.9001 790245.7121 631510.0234 547588.2182 0.851693565 1.184661767 1.193265731 1.233705015 1.146454822 1.088281085 1.443138632 1.153257142 1 19.06273188 4.741057092 4.52788023 1.204301658 0.82789249 0.435083185 0.115079599 0.172696854 9.127903373 0.026329163 0.208100073 55088.01104 -4.741057092 -0.376409168 SGLFTNTEPHS(ph)ITEDVTISAVMLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGLFTNTEPHSITEDVTISAVMLR 24 0 P57740;P57740-2;F5GY77 P57740 NUP107 Nuclear pore complex protein Nup107 1 SGLFTNTEPHS(1)ITEDVTISAVMLR 174.53 1.80E-12 69061000 49881 64658 53501 60533 55785 45986 68354 55663 46370 TRUE FALSE 46759.03725 69445.3456 54770.06899 62086.37926 51403.87113 59261.41168 58104.95227 62612.64808 38630.54744 1.210416118 1.797679562 1.417791686 1.607183521 1.330653447 1.534055705 1.504119308 1.620806647 1 15.2374545 -1.176297729 3.780836094 0.999604813 1.519826403 0.48372471 0.162416493 4078437.808 2537811.596 12263.10965 0.03378521 0.06663498 1.176297729 0.52022159 SGLIFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGLIFYR 7 0 P34897-3;P34897-2;P34897;H0YIZ0;G3V2Y4 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial;Serine hydroxymethyltransferase" 0 ; 114.02 0.013954 190948000 484860 646170 479200 443950 796850 450560 420790 602690 725960 FALSE TRUE 454513.4781 694013.0991 490566.8503 455342.5086 734268.6153 580629.3578 357696.4459 677937.1732 604792.5861 0.751519593 1.147522498 0.811132381 0.752890361 1.21408336 0.960047082 0.591436559 1.120941607 1 19.20608093 SGLLSSFSLS(ph)MTDLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SGLLSSFSLSMTDLSK 16 0 Q96L93-5;Q96L93-6;Q96L93-4;Q96L93;Q96L93-2;A0A1B0GTU3 Q96L93-5 KIF16B Kinesin-like protein KIF16B 1 SGLLSSFS(0.001)LS(0.998)MT(0.001)DLSK;SGLLSSFS(0.185)LS(0.814)MT(0.001)DLSK;SGLLSS(0.001)FS(0.164)LS(0.822)MT(0.014)DLSK 230.97 1.85E-15 205776000 383151 353203 326980 354460 419563 233683 486313 333474 412098 TRUE FALSE 359170.2629 379354.5176 334736.12 363556.0437 386612.2144 301143.4886 413394.8804 375108.963 343316.1815 1.046179243 1.104971271 0.975008281 1.058954 1.12611125 0.877160777 1.204122912 1.09260496 1 18.38917833 1.689585769 25 1.113595525 1.037974198 0.113480636 0.084412814 0.785507737 390.8931143 0.035058505 0.019441667 48.93118897 -1.689585769 -0.075621327 SGLS(ph)LEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SGLSLEELR 9 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 S(0.006)GLS(0.994)LEELR;SGLS(1)LEELR;S(0.002)GLS(0.998)LEELR 150.09 9.03E-05 639630000 1034350 1108280 1100630 1091780 1138810 982780 1382300 994920 1136220 TRUE FALSE 969611.8799 1190338.204 1126737.463 1119796.923 1049372.456 1266492.632 1175036.948 1119137.952 946577.5417 1.024334338 1.257517902 1.190327695 1.182995448 1.108596401 1.337970294 1.241353081 1.182299286 1 19.85236117 0.956037397 20.73899219 0.999999998 1.204619172 0.327035661 0.084541248 1060.372751 500224.19 0.075359832 0.018839958 9.037272908 -0.956037397 0.204619173 SGLSLEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SGLSLEELR 9 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 0 ;; 79.474 0.02684 2163000000 367950 1623680 1119840 1231790 1426170 1281390 895750 1168200 863740 FALSE TRUE 344920.6663 1743898.957 1146403.134 1263399.817 1314164.361 1651306.491 761440.6032 1314052.342 719576.214 0.479338616 2.423508341 1.593164298 1.755755391 1.826303226 2.294831957 1.058179229 1.826147552 1 19.45678797 -1.325230719 5.632926893 0.999888014 1.708096066 0.113655174 0.56092189 0.000709139 8.49E-05 0.48822056 0.115056739 0.047289996 1.325230719 0.708208052 SGMNVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SGMNVAR 7 0 P14618;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34;H3BU13 P14618;P14618-2;H3BU13 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;; 111.65 0.015195 568820000 784790 971320 781710 792200 999780 617840 807500 803640 988780 FALSE TRUE 735671.3948 1043237.543 800252.5304 812529.1932 921261.3117 796200.3782 686422.8715 903976.223 823746.2302 0.893080135 1.266455014 0.971479445 0.986382897 1.118380003 0.966560269 0.833294097 1.097396492 1 19.65184043 3.060025206 0.889022001 0.960606275 1.09667329 0.002398919 0.121815217 1.10941069 1.93166275 0.061114519 0.083070321 1148.220261 -3.060025206 0.136067015 SGMS(ph)PEQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SGMSPEQSR 9 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.398)GMS(0.602)PEQSR;S(0.033)GMS(0.967)PEQSR;SGMS(1)PEQSR;SGMS(1)PEQSR;SGMS(1)PEQSR;S(0.003)GMS(0.997)PEQSR;SGMS(1)PEQSR;SGMS(1)PEQSR 151.13 8.77E-05 15957450000 7959550 8068690 8120120 8187850 8265040 6708700 9159650 6989540 8189850 TRUE FALSE 7461375.974 8666104.203 8312733.081 8397964.093 7615937.098 8645392.783 7786245.517 7862199.455 6822911.127 1.093576603 1.270147602 1.218355761 1.230847645 1.116229855 1.267112032 1.141191109 1.152323299 1 22.70195599 0.568015376 0.708803171 0.997011278 1.211195462 0.50090641 0.05961883 1.05995669 0.924989186 0.058124384 0.019872224 3.69841274 -0.568015376 0.214184185 SGMS(ph)PPPCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SGMSPPPCK 9 0 Q9H6T0-2;Q9H6T0 Q9H6T0-2 ESRP2 Epithelial splicing regulatory protein 2 1 SGMS(1)PPPCK;SGMS(1)PPPCK;SGMS(1)PPPCK;SGMS(1)PPPCK;SGMS(1)PPPCK;SGMS(1)PPPCK 113.44 0.0018873 1053838000 2723800 2041590 2479980 2269500 2517460 2220710 3558390 2469670 2213910 TRUE FALSE 2553322.22 2192751.448 2538806.297 2327739.212 2319748.847 2861792.927 3024842.454 2778013.736 1844394.119 1.384369097 1.188873585 1.376498803 1.262061719 1.257729475 1.551616814 1.640019573 1.506193122 1 20.81471554 2.242265234 24.9981792 1.49781043 1.289398933 0.051470947 0.182411452 127.6589948 861428.8078 0.057857985 0.046671588 174.6888693 -2.242265234 -0.208411497 SGNFGGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SGNFGGSR 8 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;; 142.04 0.0014512 3937550000 2358220 2997980 2258120 2298710 3367970 1806040 2431240 2709260 3135650 FALSE TRUE 2210623.22 3219953.559 2311683.673 2357698.79 3103463.222 2327414.429 2066698.133 3047517.075 2612289.758 0.846239669 1.232617304 0.884926209 0.902541069 1.188024113 0.890948036 0.791144293 1.166607596 1 21.3168835 SGNLTEDDKHNNAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SGNLTEDDKHNNAK 14 1 P13797;A0A0A0MSQ0;P13797-3;P13797-2 P13797 PLS3 Plastin-3 0 ;;;; 250.31 1.48E-18 2958683000 2605339 1572408 1864232 1773374 2131236 1306505 2328186 1815239 2870952 FALSE TRUE 2442275.483 1688830.724 1908452.463 1818881.779 1963857.322 1683671.784 1979096.123 2041875.585 2391771.564 1.021115695 0.706100344 0.797924222 0.760474707 0.821089 0.703943391 0.827460345 0.853708446 1 21.18964817 0.858848128 1.836390014 0.999261208 0.789306344 0.313372204 0.088699244 0.556432308 3.621755492 0.074599614 0.021016654 7.22517097 -0.858848128 -0.209954864 SGNQVSEFISNTFLDKQHEVEIPS(ph)PTQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGNQVSEFISNTFLDKQHEVEIPSPTQK 28 1 Q08499-10;A0A087WSZ7;A0A1B0GW84;Q08499-2;Q08499-9;Q08499-6;Q08499-11;Q08499;Q08499-3;Q08499-4;D6RHE0;Q08499-5;Q08499-8 Q08499-10 PDE4D "cAMP-specific 3,5-cyclic phosphodiesterase 4D" 1 SGNQVSEFISNTFLDKQHEVEIPS(0.997)PT(0.003)QK 119.35 7.58E-05 71120000 86898 86109 81416 101040 134840 40080 106030 70742 210220 TRUE FALSE 81459.2093 92484.59996 83347.22597 103632.8575 124250.2103 51650.44536 90131.78583 79574.29442 175132.9239 0.465127901 0.528082315 0.475908379 0.591738293 0.709462319 0.29492139 0.514647868 0.454365134 1 17.4180908 -1.741819468 2.645440423 1.102876483 0.504025977 0.687940897 0.104925193 19774402.15 15133050.55 13320486.64 0.023465826 0.018120932 1.741819468 -0.598850506 SGPASTFNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGPASTFNDR 10 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 116.52 0.0025118 175320000 107440 119800 104620 108050 145510 92087 124960 111920 149160 FALSE TRUE 100715.5222 128670.1167 107101.6358 110822.7459 134082.2316 118671.022 106223.4081 125893.4584 124264.2324 0.810494864 1.035455772 0.86188627 0.891831413 1.079009052 0.954989378 0.854818849 1.013110981 1 16.92305157 SGPFGQIFRPDNFVFGQS(ph)GAGNNWAK ddPTM_SK-BR-3_Pertuzumab_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 146.88 1.21E-07 71435000 46937 45633 43874 36371 51671 29243 56614 43353 60028 TRUE FALSE 43999.29695 49011.7148 44914.712 37304.34144 47612.96809 37684.97938 48125.25628 48765.71748 50008.939 0.879828643 0.980059081 0.898133672 0.745953467 0.952089147 0.753564865 0.96233308 0.975140014 1 15.60989838 1.555610125 9.561422116 0.980620871 0.88146876 0.322495964 0.074632145 0.15671516 22.58581558 0.039462417 0.018390135 35.94265255 -1.555610125 -0.099152111 SGPFGQIFRPDNFVFGQSGAGNNWAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGPFGQIFRPDNFVFGQSGAGNNWAK 26 1 Q5JP53;P07437;Q5ST81;P68371;M0QY85;M0QZL7;Q13885;Q9BVA1;P04350;M0R278;M0R1I1 Q5JP53;P68371;Q13885;Q9BVA1;P04350 TUBB;TUBB4B;TUBB4A;TUBB2A;TUBB2B Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-2B chain;Tubulin beta-4A chain 0 ; 307.77 1.05E-81 8815600000 5284600 5708600 4928300 4257500 6558900 2995100 5992800 5953900 6100400 FALSE TRUE 4953846.319 6131270.684 5045201.603 4366754.658 6043790.451 3859736.749 5094235.274 6697257.521 5082203.83 0.97474373 1.206419673 0.992719256 0.859224621 1.189206622 0.759461225 1.002367368 1.317786091 1 22.27702281 5.057235179 21.15524834 1.034646013 0.00047641 0.014446041 0.164675749 214.6808694 1333618.181 0.035925743 161036.0301 114086.7423 -5.057235179 -1.034169604 SGPKPFSAPKPQTS(ph)PS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGPKPFSAPKPQTSPSPK 18 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 2 SGPKPFS(0.002)APKPQT(0.557)S(0.745)PS(0.695)PK;SGPKPFS(0.028)APKPQT(0.114)S(0.858)PS(1)PK 109.41 0.0017867 3772100000 8618300 2720820 4658300 4179000 4524100 3559890 7716300 3411710 6029900 TRUE FALSE 8078895.987 2922272.344 4768797.076 4286240.215 4168795.435 4587572.453 6559312.45 3837669.504 5023470.735 1.60822993 0.581723772 0.949303246 0.853242796 0.829863585 0.913227666 1.305733186 0.763947817 1 22.26025304 1.953400361 24.88062371 1.070268179 0.902354141 0 0.291575993 1102.354819 588570.5998 0.109642574 0.070775182 89.82564843 -1.953400361 -0.167914039 SGPKPFSAPKPQTS(ph)PS(ph)PKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGPKPFSAPKPQTSPSPKR 19 3 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 2 SGPKPFS(0.003)APKPQT(0.466)S(0.53)PS(1)PKR 63.726 0.017264 791700000 2213000 935060 1362000 1328700 1465200 1027500 2062900 1040600 2009100 TRUE FALSE 2074492.28 1004292.815 1394307.283 1362796.691 1350129.102 1324122.57 1753587.296 1170521.201 1673768.231 1.2394143 0.600019045 0.83303486 0.814208722 0.806640416 0.791102702 1.047688243 0.699332906 1 20.67466834 SGPKPFSAPKPQTSPS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGPKPFSAPKPQTSPSPK 18 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 SGPKPFSAPKPQT(0.226)S(0.17)PS(0.604)PK;SGPKPFSAPKPQT(0.057)S(0.239)PS(0.705)PK 101.41 0.00052764 40387900000 4603900 1753480 2659800 2345200 2703400 2100940 4216000 2253400 3950800 TRUE FALSE 4315750.117 1883309.484 2722891.712 2405381.802 2491085.869 2707447.272 3583849.939 2534741.95 3291385.957 1.31122578 0.572193449 0.827278158 0.730811225 0.756850124 0.822585776 1.088857395 0.770113862 1 21.65026378 1.933689937 10.85314811 0.961299735 0.795989967 0.04436338 0.204568156 1.572222033 253.3391175 0.077653389 0.049564549 85.84004512 -1.933689937 -0.165309768 SGPKPFSAPKPQTSPS(ph)PKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGPKPFSAPKPQTSPSPKR 19 3 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 SGPKPFSAPKPQT(0.006)S(0.038)PS(0.957)PKR 111.4 0.00015479 2632700000 627170 382070 488580 475570 632430 322490 599000 420100 1038300 TRUE FALSE 587916.5492 410358.8603 500169.3483 487773.9313 582761.4989 415587.6278 509185.5108 472550.4098 865001.0223 0.679671508 0.474402746 0.578229777 0.563899832 0.673711919 0.480447557 0.588653074 0.546300406 1 19.72234231 -1.514575822 2.99157749 1.01532877 0.565104549 0.795896975 0.067820535 16421015.28 19097590.5 2064062.403 0.014502659 0.030579063 1.514575822 -0.450224221 SGPKPFSAPKPQTSPSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGPKPFSAPKPQTSPSPK 18 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 0 208.17 3.72E-16 418330000 789420 459380 573150 593080 613620 415340 820740 534490 882640 FALSE TRUE 740011.6114 493392.9732 586745.3887 608299.4369 565428.7604 535241.9155 697677.6564 601222.2531 735321.6819 1.006378065 0.67098929 0.797943816 0.827256222 0.768954288 0.727901718 0.948806044 0.817631613 1 19.488016 1.055328392 0.827162043 0.992284678 0.786265715 0.230516752 0.098607196 0.747735481 1.148045522 0.086146425 0.031485372 11.35869378 -1.055328392 -0.206018963 SGPLFNFDVHDDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SGPLFNFDVHDDVR 14 0 Q14320;B0S8I6 Q14320 FAM50A Protein FAM50A 0 ;;;;;; 193.96 1.99E-07 1941299000 2780661 3099539 3082661 2992176 3384876 2497092 3480292 2924688 3373871 FALSE TRUE 2606624.392 3329032.093 3155783.175 3068960.302 3119041.493 3217961.923 2958454.524 3289841.735 2810750.134 0.927376774 1.184392754 1.122754789 1.091865216 1.109682947 1.144876553 1.052549812 1.17044973 1 21.42252378 -1.766237097 2.844026349 0.976663734 1.107875719 0.15305659 0.072465501 23250876.27 16822812.83 3754031.388 0.015581531 0.017130219 1.766237097 0.131211985 SGPPS(ph)PPSTATSFGGPRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SGPPSPPSTATSFGGPRPR 19 1 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2;A0A087X0E3 A0A0A0MS59 SRCAP Helicase SRCAP 1 SGPPS(1)PPSTATSFGGPRPR;SGPPS(1)PPSTATSFGGPRPR;SGPPS(1)PPSTATSFGGPRPR;SGPPS(1)PPSTATSFGGPRPR;SGPPS(1)PPSTATSFGGPRPR 253.95 4.16E-31 3410100000 517408 549179 531049 539668 568898 424335 614351 483518 680871 TRUE FALSE 485024.3569 589840.7846 543645.7331 553516.7945 524219.0459 546833.626 522234.7709 543886.2867 567229.2315 0.855076449 1.039863166 0.958423337 0.975825581 0.924174949 0.964043451 0.92067676 0.958847423 1 19.11357236 2.774944916 24.51984965 0.947276923 0.971245844 0 0.050359863 1522.900812 1026300.566 0.014118901 0.014974746 595.5865967 -2.774944916 0.023968921 SGPS(ph)PLS(ph)SPNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SGPSPLSSPNGK 12 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 2 SGPS(1)PLS(0.556)S(0.444)PNGK;S(0.001)GPS(0.999)PLS(0.759)S(0.241)PNGK;SGPS(1)PLS(0.742)S(0.258)PNGK;SGPS(1)PLS(0.879)S(0.121)PNGK 159.75 9.88E-05 694240000 3944210 2632080 3310780 2924120 3329680 2520150 3999030 2796440 3936550 TRUE FALSE 3697348.937 2826961.942 3389313.265 2999157.87 3068180.364 3247676.394 3399412.577 3145581.69 3279514.374 1.12740745 0.862006267 1.033480229 0.914512799 0.935559359 0.990291861 1.036559743 0.959160818 1 21.64505077 2.010251866 22.9858703 1.005333239 0.96440506 0.009480401 0.073244957 222.6486908 499198.843 0.024939711 0.018391862 102.3886616 -2.010251866 -0.040928179 SGPS(ph)PLSS(ph)PNGK ddPTM_SK-BR-3_Pertuzumab_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 2 SGPS(1)PLS(0.135)S(0.865)PNGK;SGPS(1)PLS(0.135)S(0.865)PNGK 222.56 3.58E-11 795880000 6092700 3881300 5059000 4642000 5080800 3945400 6336200 4380100 6217500 TRUE FALSE 5711368.783 4168675.49 5179001.869 4761121.579 4681774.463 5084372.932 5386145.632 4926965.127 5179759.083 1.102632128 0.804801039 0.999853813 0.91917819 0.903859501 0.981584829 1.039844816 0.951195808 1 22.30445357 2.061503212 6.273414886 1.003721757 0.933244645 0.070199828 0.078016807 0.358290605 27.37582113 0.027248423 0.019901044 115.2134581 -2.061503212 -0.070477112 SGPS(ph)PLSSPNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SGPSPLSSPNGK 12 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 SGPS(1)PLSSPNGK;SGPS(1)PLSSPNGK;SGPS(1)PLSSPNGK;SGPS(1)PLSSPNGK 212.69 1.82E-08 495700000 1550610 1177640 1328340 1281700 1278780 987030 1695940 1105670 1500920 TRUE FALSE 1453560.088 1264833.691 1359848.852 1314590.592 1178349.777 1271969.538 1441649.541 1243715.333 1250406.756 1.162469797 1.011537794 1.087525196 1.051330366 0.942373169 1.017244614 1.15294446 0.994648604 1 20.25396605 4.748417045 23.71992656 1.042952806 1.162469933 0.319940961 0.057828641 914.4154984 2200485.864 0.013885807 0.179731083 56029.53844 -4.748417045 0.119517127 SGQGAFGNMCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGQGAFGNMCR 11 0 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 ; 178.84 1.71E-05 157611000 91044 128437 88115 85872 126742 59600 106655 114310 124689 FALSE TRUE 85345.71856 137946.6091 90205.12941 88075.6209 116788.1946 76805.55247 90663.07289 128581.8551 103877.6004 0.821598865 1.32797262 0.868379026 0.847878855 1.124286604 0.739385124 0.872787517 1.237820807 1 16.66452507 3.747939713 20.0644595 0.935954953 1.107122452 0.051573509 0.187363551 73.163909 70508.93852 0.04403188 0.079114968 5596.799037 -3.747939713 0.171167499 SGQGFHGNSEVNAILS(ph)PR ddPTM_SK-BR-3_Pertuzumab_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 223.82 3.18E-19 1232300000 613460 709450 649420 807020 911770 641900 833830 662990 756860 TRUE FALSE 575064.6337 761978.4162 664824.5491 827729.4995 840163.2621 827206.1096 708804.9324 745765.7609 630535.1765 0.912026252 1.208462977 1.054381379 1.312741192 1.332460572 1.31191112 1.124132259 1.182750446 1 19.26621733 5.31642058 1.609753287 1.197847926 3.67E-20 0.365869738 0.11216205 6.826806353 4.506651545 0.028810858 20.35637822 207214.7091 -5.31642058 -1.197847926 SGQKPVLDVHAELDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGQKPVLDVHAELDR 15 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 ; 130.29 3.64E-05 649120000 1360990 1270570 1390730 1329170 1540170 1121520 1715500 1336570 1759970 FALSE TRUE 1275808.065 1364644.325 1423718.772 1363278.752 1419211.261 1445284.618 1458276.701 1503443.707 1466219.637 0.870134346 0.93072299 0.971013303 0.929791634 0.967939062 0.985721771 0.994582711 1.025387785 1 20.4836698 8 0.246654559 1.012032468 0.205375758 0.817361792 0.018911846 21.7393722 0.294674855 0.025172257 7.245384007 100000000 -8 -0.80665671 SGQVYSFGCNDEGALGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGQVYSFGCNDEGALGR 17 0 P18754-2;C9JW69;P18754;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4 P18754-2 RCC1 Regulator of chromosome condensation 0 307.97 1.13E-57 138950000 134740 153200 134900 144380 154130 112410 172360 129330 173600 FALSE TRUE 126306.8639 164543.0874 138099.8917 148085.0352 142025.2515 144860.9422 146516.2181 145477.1352 144625.0385 0.873340227 1.137721996 0.954882316 1.023923912 0.98202395 1.00163114 1.013076433 1.005891765 1 17.14195782 3.783824932 24.99951398 0.999437013 1.030981513 0 0.066135449 516.0616613 227517.8698 0.015093414 0.02721002 6078.899058 -3.783824932 0.0315445 SGS(ph)AAQAEGLCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SGSAAQAEGLCK 12 0 F8WF93;H7BZZ2;F8WE30;H7C0X4;Q92685 F8WF93 ALG3 "Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase" 1 SGS(1)AAQAEGLCK;SGS(1)AAQAEGLCK;SGS(1)AAQAEGLCK;SGS(1)AAQAEGLCK 206.49 9.39E-08 1463200000 2729920 1748670 1725920 1561490 2229260 1444100 2883890 2170420 3092760 TRUE FALSE 2559059.18 1878143.346 1766859.637 1601560.477 2054182.912 1860988.227 2451477.467 2441401.715 2576558.376 0.993208306 0.728934909 0.685744074 0.621589051 0.79725844 0.722276757 0.951454269 0.947543722 1 21.29701385 1.692332337 4.761220954 0.966478828 0.742455497 0.496792847 0.097833271 0.126793991 6.723842283 0.050655969 0.0246676 49.24162055 -1.692332337 -0.224023331 SGS(ph)FGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSFGK 6 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 SGS(1)FGK 87.251 0.05523 497090000 1885400 1036700 1527600 1336600 1218000 988290 1622800 1208600 1819700 TRUE FALSE 1767396.18 1113458.347 1563835.393 1370899.419 1122343.193 1273593.279 1379476.205 1359496.37 1515980.314 1.165843753 0.734480742 1.031567085 0.904298958 0.740341535 0.840112017 0.909956543 0.896777061 1 20.53181959 4.758487129 24.43864132 0.879881311 1.165844118 0.467488329 0.095112543 3211.801846 3938990.812 0.021633136 0.854498044 57343.88721 -4.758487129 0.285962807 SGS(ph)FSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SGSFSK 6 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;G3V3H3;Q07866-5;Q07866-10;H0YG16 Q07866-6 KLC1 Kinesin light chain 1 1 S(0.001)GS(0.937)FS(0.062)K;S(0.043)GS(0.943)FS(0.015)K;S(0.001)GS(0.991)FS(0.008)K;SGS(0.989)FS(0.011)K 93.143 0.048204 2140280000 5204010 3347090 3807070 3707670 3769380 2315840 4759560 3162960 3896220 TRUE FALSE 4878300.304 3594912.026 3897375.498 3802815.089 3473348.1 2984385.413 4045908.164 3557862.519 3245915.711 1.502904184 1.107518601 1.200701387 1.171569267 1.07006725 0.919427884 1.246461253 1.096104408 1 21.63019411 4.739463936 24.49461142 1.117341845 1.50290434 0.631854789 0.095616542 38.15593559 1034425.418 0.021749869 0.132375867 54886.29753 -4.739463936 0.385562495 SGS(ph)GGGSAKEPQEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGSGGGSAKEPQEER 15 1 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;F6UYG0 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 S(0.041)GS(0.942)GGGS(0.017)AKEPQEER;S(0.022)GS(0.977)GGGS(0.001)AKEPQEER 145.52 2.45E-06 764860000 690530 505750 549570 568350 620220 364690 605290 405270 997250 TRUE FALSE 647310.9599 543196.2562 562606.0599 582934.8232 571510.423 469970.0828 514532.3837 455868.8516 830802.5325 0.779139368 0.653821137 0.677183853 0.70165268 0.687901638 0.565682054 0.61931971 0.54870903 1 19.66414609 -1.65117693 7.77927741 1.000672548 0.652211668 0.727850741 0.066447206 0.000754762 3.38E-05 0.062651465 0.014740732 0.022326625 1.65117693 -0.34846088 SGS(ph)GSESTGAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGSGSESTGAEER 13 0 Q14669-3;Q14669;Q14669-2;G5E9G6;H7C1L9 Q14669-3;H7C1L9 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 S(0.027)GS(0.79)GS(0.181)ES(0.001)TGAEER;S(0.012)GS(0.909)GS(0.079)ESTGAEER 147.31 4.15E-05 112000000 169955 155324 170207 154419 151270 139057 173305 122403 144189 TRUE FALSE 159317.8199 166824.3506 174244.3904 158381.653 139389.8644 179200.4985 147319.5241 137685.284 120122.9244 1.326289888 1.388780297 1.450550686 1.31849648 1.160393531 1.491809323 1.226406407 1.14620323 1 16.87415198 1.192921385 1.617422625 1.005456513 1.363210719 0.628857895 0.091466623 0.215460949 1.054225476 0.082490472 0.024569138 15.59270224 -1.192921385 0.357754206 SGS(ph)IKGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSIKGSR 8 1 Q16629;Q16629-4;C9JAB2;H7BZZ6;H7C1N1 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 1 S(0.021)GS(0.978)IKGS(0.002)R 69.451 0.06089 0 589040 535340 529330 547680 818010 345520 719470 462640 2437500 TRUE FALSE 552173.0379 574977.1306 541885.9576 561734.396 753766.7943 445266.015 611592.1527 520401.6224 2030665.503 0.271917279 0.283147141 0.266851412 0.276625764 0.371192002 0.21927098 0.301178186 0.256271464 1 20.95352118 -1.610701461 2.695764227 1.064135387 0.281084107 0.971946274 0.038399178 3284182.901 3049892.826 1483120.908 0.008849339 0.024507473 1.610701461 -0.78305128 SGS(ph)MDPSGAHPSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSMDPSGAHPSVR 14 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 1 S(0.047)GS(0.953)MDPSGAHPSVR 103.83 0.0024163 0 80808 106470 105690 108340 129570 81808 131000 97325 137990 TRUE FALSE 75750.37153 114353.1496 108197.0167 111120.1878 119394.0949 105424.6416 111357.7661 109476.2405 114958.5776 0.658936229 0.994733512 0.941182633 0.966610671 1.038583613 0.917066336 0.968677314 0.952310326 1 16.81075459 4.741427222 24.98660325 0.969205745 0.658936116 0.895251936 0.033680735 75.03126766 653972.1479 0.00734452 0.051414254 55134.98003 -4.741427222 -0.310269629 SGS(ph)PAPETTNESVPFAQHSSLDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGSPAPETTNESVPFAQHSSLDSR 24 0 O15047 O15047 SETD1A Histone-lysine N-methyltransferase SETD1A 1 S(0.13)GS(0.774)PAPET(0.095)T(0.001)NESVPFAQHSSLDSR;S(0.125)GS(0.662)PAPET(0.207)T(0.006)NESVPFAQHSSLDSR 208.41 4.14E-25 578490000 107633 248580 252920 226480 257060 216540 287020 223660 290610 TRUE FALSE 100896.4427 266985.1218 258919.3818 232291.8602 236871.5445 279051.5828 243984.0156 251584.4433 242105.3136 0.416746089 1.102764404 1.069449398 0.959466179 0.978382263 1.152604124 1.007759854 1.039152919 1 17.88527522 4.741767369 24.99223495 1.044963791 0.416745857 0.917941346 0.058413752 78.63694907 612838.5211 0.013657181 0.098096604 55178.17965 -4.741767369 -0.628217934 SGS(ph)PKLDPSEVYLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGSPKLDPSEVYLK 14 1 Q5TCQ9;Q5TCQ9-1;Q5TCQ9-3;Q5TCQ9-2 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 S(0.15)GS(0.85)PKLDPSEVYLK;S(0.033)GS(0.967)PKLDPSEVYLK 124.84 5.73E-05 511070000 3048200 1515120 1918510 1969670 2590600 1171870 2527600 1691420 4192900 TRUE FALSE 2857418.603 1627301.061 1964017.963 2020215.067 2387144.726 1510169.845 2148609.845 1902597.51 3493077.903 0.818023154 0.46586452 0.562259995 0.578348128 0.683392925 0.43233214 0.615105046 0.544676518 1 21.73606739 -1.382251809 3.2220701 1.004337554 0.573121742 0.584872507 0.108617208 57174652.69 74889824.63 2315699.436 0.02336644 0.041471352 1.382251809 -0.431215812 SGS(ph)PRPTEPTDFLMLFEGS(ph)PSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SGSPRPTEPTDFLMLFEGSPSGK 23 1 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 2 S(0.427)GS(0.572)PRPTEPTDFLMLFEGS(0.974)PS(0.026)GK;S(0.103)GS(0.894)PRPTEPT(0.003)DFLMLFEGS(0.981)PS(0.019)GK;S(0.427)GS(0.572)PRPTEPTDFLMLFEGS(0.862)PS(0.138)GK 180.61 2.56E-17 85056000 167365 96840 123149 113861 121319 97233 160594 103338 151092 TRUE FALSE 156889.9234 104010.1344 126070.1524 116782.866 111791.0951 125302.5887 136514.4206 116239.9768 125873.7691 1.246406813 0.826305076 1.001560161 0.927777621 0.888120662 0.995462276 1.084534304 0.923464655 1 16.94161814 2.008662113 24.66166195 1.019043847 0.956894466 0 0.116538353 487.8375426 1388901.027 0.0399253 0.029439641 102.0145487 -2.008662113 -0.06214938 SGS(ph)PRPTEPTDFLMLFEGSPSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SGSPRPTEPTDFLMLFEGSPSGK 23 1 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 S(0.032)GS(0.967)PRPT(0.001)EPTDFLMLFEGSPSGK;S(0.143)GS(0.857)PRPTEPTDFLMLFEGSPSGK;S(0.152)GS(0.845)PRPT(0.002)EPT(0.001)DFLMLFEGSPSGK;S(0.026)GS(0.973)PRPT(0.001)EPTDFLMLFEGSPSGK;S(0.118)GS(0.875)PRPT(0.007)EPT(0.001)DFLMLFEGSPSGK;S(0.126)GS(0.874)PRPTEPTDFLMLFEGSPSGK 270.45 8.25E-52 1303825000 2278793 1529640 1854286 1776367 1835107 1329597 2281923 1504165 2296678 TRUE FALSE 2136167.414 1642896.137 1898270.54 1821951.585 1690985.099 1713430.07 1939769.83 1691963.311 1913347.605 1.116455478 0.858650113 0.99212006 0.952232402 0.883783529 0.895514263 1.013809423 0.884294786 1 20.86766757 -1.249488416 3.73366241 1.000077674 0.946019488 0.038586372 0.077226365 10223042.85 3421194.114 6977.609824 0.015977331 0.056300413 1.249488416 -0.054058187 SGS(ph)PSDNSGAEEMEVSLAKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 1 S(0.157)GS(0.533)PS(0.157)DNS(0.153)GAEEMEVSLAKPK;S(0.107)GS(0.835)PS(0.058)DNSGAEEMEVSLAKPK;S(0.013)GS(0.693)PS(0.222)DNS(0.072)GAEEMEVSLAKPK 196.32 5.88E-22 1760830000 1500380 994450 1197110 1204880 1258010 884870 1530290 983950 1321200 TRUE FALSE 1406473.894 1068080.113 1225506.015 1235799.261 1159210.969 1140317.604 1300837.221 1106798.323 1100683.185 1.277819007 0.97037924 1.113404867 1.122756555 1.053174052 1.036008926 1.181845275 1.005555766 1 20.06996784 1.060188038 0.009142084 1.72E-06 2.133681822 0.150370901 0.086291109 5022.205477 32.87610743 3874.258229 3794.041885 11.4865085 -1.060188038 2.133680102 SGS(ph)SPGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSSPGLR 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.118)GS(0.441)S(0.441)PGLR 99.136 0.0073717 264560000 173050 151740 159460 155530 166780 197060 241030 171280 175640 TRUE FALSE 162219.1094 162974.9875 163242.4665 159521.1631 153681.7716 253948.023 204889.7891 192664.685 146324.5493 1.108625382 1.113791146 1.115619131 1.090187285 1.050280163 1.73551208 1.400242065 1.316694197 1 17.15881231 2.28891194 24.99997311 1.40898154 1.100632698 0.344918978 0.178134829 92.50650208 45930.01851 0.055262195 0.0462356 194.4965668 -2.28891194 -0.308348842 SGS(ph)SQELDVKPSASPQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSSQELDVKPSASPQER 18 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.067)GS(0.467)S(0.467)QELDVKPSASPQER 192.63 9.97E-15 334020000 582980 377120 487850 461530 489630 361170 678480 468120 505550 TRUE FALSE 546492.3224 405042.3572 499422.0324 473373.6412 451176.4349 465433.9159 576748.2227 526565.8125 421170.439 1.297556219 0.96170652 1.18579555 1.123947925 1.071244307 1.105096352 1.369393883 1.250243995 1 18.68404465 1.78399695 25 1.246549366 1.110528375 0.051513835 0.124916131 127.3449382 70090.83441 0.051583415 0.028787347 60.81307298 -1.78399695 -0.136020992 SGS(ph)SS(ph)PDSEITELKFPSINHD ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 2 S(0.278)GS(0.637)S(0.199)S(0.865)PDS(0.021)EITELKFPSINHD;S(0.101)GS(0.732)S(0.176)S(0.99)PDS(0.001)EITELKFPSINHD 111.65 3.01E-05 286240000 357410 317350 341100 290980 353950 263090 410270 265910 479990 TRUE FALSE 335040.3461 340846.9242 349191.0531 298447.0394 326152.1948 339039.8121 348753.8223 299109.4488 399876.5681 0.837859412 0.852380338 0.873247099 0.746347906 0.815632174 0.847861163 0.872153685 0.748004441 1 18.60919522 -1.387459036 5.559869919 1.000065805 0.832541583 0.589496343 0.045636741 3.59E-05 3.96E-06 0.04265125 0.010049054 0.040977076 1.387459036 -0.167524222 SGS(ph)TGSSLSVSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSTGSSLSVSVR 13 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 S(0.001)GS(0.985)T(0.013)GSSLSVSVR 158.11 5.02E-05 105710000 88873 93662 99009 98110 110890 92185 97370 105310 134550 TRUE FALSE 83310.59757 100596.8319 101357.5402 100627.6687 102181.1467 118797.313 82770.27244 118458.1853 112092.7358 0.743229229 0.897442918 0.904229338 0.897718019 0.911576883 1.059812772 0.738408889 1.056787351 1 16.77433326 5.486869005 1.276104487 0.920879522 2.52E-10 0.283205062 0.093450145 11.160388 3.880521858 0.023354792 21.39873276 306809.6427 -5.486869005 -0.920879522 SGS(ph)VSNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSVSNYR 8 0 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 1 S(0.021)GS(0.971)VS(0.008)NYR 125.97 0.0026651 0 261120 262110 273030 306330 302700 242380 310660 196900 278440 TRUE FALSE 244776.9653 281516.8971 279506.4005 314190.9464 278927.163 312351.1713 264079.417 221483.3984 231966.5652 1.055225201 1.213609801 1.204942619 1.35446652 1.202445545 1.346535312 1.138437416 0.954807423 1 17.82355735 1.395857002 4.05222764 0.980862416 1.229375139 0.602075306 0.083673995 0.142665863 3.80806267 0.058150284 0.020129107 24.88037961 -1.395857002 0.248512723 SGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFK 39 0 P28072;A0A087X2I4 P28072 PSMB6 Proteasome subunit beta type-6;Proteasome subunit beta type 0 315.7 1.89E-110 193380000 93426 98571 87430 88698 104750 73140 102770 96605 88375 FALSE TRUE 87578.63343 105869.2994 89503.88089 90974.14085 96523.35754 94254.33067 87360.59257 108666.3469 73624.64158 1.189528826 1.437960133 1.215678324 1.235647996 1.311019728 1.280200876 1.186567305 1.475950777 1 16.16790109 -1.210833837 3.943842139 0.999794398 1.288665682 0.466547942 0.09793769 0.000175641 3.51E-05 0.086789622 0.020440815 0.061541229 1.210833837 0.288871284 SGSGSVGNGSSRYS(ph)PS(ph)QNSPIHHIPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSGSVGNGSSRYSPSQNSPIHHIPSR 27 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 S(0.01)GS(0.012)GS(0.015)VGNGS(0.018)S(0.021)RY(0.007)S(0.916)PS(0.673)QNS(0.329)PIHHIPSR 113.37 0.00058749 339360000 84602 123190 108900 116060 147440 97694 148040 116220 234540 TRUE FALSE 79306.91184 132311.1158 111483.1594 119038.2961 135860.6571 125896.6719 125842.7763 130730.3228 195393.7588 0.405882523 0.677151187 0.570556399 0.609222612 0.695317281 0.644322893 0.644047062 0.669060893 1 17.57602486 -5 0.177883976 2.5465046 0.537537974 0.773290802 0.069691526 60.85513851 0.584021222 33.19544608 0.205546581 1.00E-05 5 -2.008966626 SGSGSVGNGSSRYS(ph)PS(ph)QNSPIHHIPSRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSGSVGNGSSRYSPSQNSPIHHIPSRR 28 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 S(0.006)GS(0.007)GS(0.008)VGNGS(0.038)S(0.041)RY(0.05)S(0.831)PS(0.539)QNS(0.433)PIHHIPS(0.046)RR 61.941 0.015809 133190000 18603 31082 28268 27581 45168 19891 37706 27928 108580 TRUE FALSE 17438.67144 33383.34362 28938.53031 28288.77515 41620.68748 25633.2088 32052.33535 31414.87228 90457.29655 0.192783469 0.369050866 0.319913721 0.312730716 0.460114209 0.283373589 0.354336649 0.347289533 1 16.46494926 -4.746283082 0.409272734 10 0.322689158 0.91129974 0.06583914 162.7900236 1.367200253 1303.841279 0.035608072 1.79E-05 4.746283082 -9.677310842 SGSGSVGNGSSRYS(ph)PSQNS(ph)PIHHIPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SGSGSVGNGSSRYSPSQNSPIHHIPSR 27 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 S(0.001)GS(0.001)GS(0.006)VGNGS(0.006)S(0.006)RYS(0.979)PS(0.002)QNS(1)PIHHIPSR;SGSGSVGNGS(0.001)S(0.012)RYS(0.986)PS(0.001)QNS(0.999)PIHHIPSR;SGSGSVGNGS(0.001)S(0.001)RY(0.001)S(0.991)PS(0.006)QNS(1)PIHHIPSR;S(0.005)GS(0.006)GS(0.009)VGNGS(0.08)S(0.089)RY(0.279)S(0.527)PS(0.007)QNS(0.997)PIHHIPSR;SGSGSVGNGS(0.003)S(0.003)RY(0.001)S(0.991)PS(0.001)QNS(1)PIHHIPSR;S(0.001)GS(0.002)GS(0.002)VGNGS(0.027)S(0.042)RY(0.009)S(0.878)PS(0.048)QNS(0.992)PIHHIPSR 172.4 4.94E-12 7056960000 432089 638153 521594 552057 673921 452810 749094 578216 1133548 TRUE FALSE 405045.3208 685402.5121 533966.456 566223.7173 620993.9631 583528.8962 636774.3089 650407.5404 944351.5158 0.428913719 0.725791721 0.565431883 0.599589991 0.657587723 0.617914925 0.674297969 0.688734576 1 19.84896445 -5 0.210115935 2.822228219 0.572287928 0.751805654 0.072135885 70.03944651 0.698489205 53.60776372 0.140227545 1.00E-05 5 -2.249940292 SGSGSVGNGSSRYS(ph)PSQNS(ph)PIHHIPSRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SGSGSVGNGSSRYSPSQNSPIHHIPSRR 28 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 S(0.023)GS(0.025)GS(0.031)VGNGS(0.122)S(0.15)RY(0.071)S(0.589)PS(0.301)QNS(0.653)PIHHIPS(0.035)RR;SGSGSVGNGS(0.005)S(0.097)RY(0.199)S(0.696)PS(0.204)QNS(0.775)PIHHIPS(0.024)RR;SGSGSVGNGS(0.006)S(0.125)RY(0.054)S(0.81)PS(0.244)QNS(0.731)PIHHIPS(0.029)RR;SGSGSVGNGS(0.001)S(0.344)RY(0.17)S(0.48)PS(0.209)QNS(0.775)PIHHIPS(0.021)RR 107.94 0.0014045 1481330000 157471 132418 123897 129686 169142 102867 167828 113572 371983 TRUE FALSE 147615.1712 142222.3665 126835.8953 133013.9623 155858.2696 132563.033 142663.7494 127751.7142 309896.6342 0.4763368 0.458934854 0.409284521 0.429220416 0.50293631 0.42776532 0.460359145 0.41223976 1 18.24142756 -1.404518363 3.316060972 1.005859313 0.446127557 0.972665481 0.02912657 13761764.57 18822755.48 768379.7883 0.006503005 0.039398677 1.404518363 -0.559731755 SGSGSVGNGSSRYS(ph)PSQNSPIHHIPSR ddPTM_SK-BR-3_Pertuzumab_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(0.01)S(0.038)RYS(0.942)PS(0.01)QNSPIHHIPSR;SGSGSVGNGS(0.01)S(0.01)RYS(0.85)PS(0.13)QNSPIHHIPSR 198.73 3.32E-25 1683100000 71327 150579 138764 149798 146390 78758 123157 105319 194097 TRUE FALSE 66862.77039 161728.0258 142055.5476 153642.0703 134893.1199 101494.1561 104690.7512 118468.309 161700.9568 0.413496443 1.000167402 0.878507774 0.950161788 0.834213493 0.627665773 0.647434334 0.732638268 1 17.30296869 2.368954483 7.319823387 0.711663184 0.857186605 0 0.188920695 0.470007099 28.89920405 0.060603883 0.050564186 233.8592126 -2.368954483 0.145523421 SGSGSVGNGSSRYSPS(ph)QNSPIHHIPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 SGSGSVGNGSSRYS(0.054)PS(0.946)QNSPIHHIPSR 199.79 3.09E-25 353230000 43242 88845 69990 82342 76365 45748 65366 51385 103250 TRUE FALSE 40535.56041 95423.17624 71650.19585 84455.03512 70367.60094 58954.70494 55564.97513 57800.53036 86016.90798 0.471251076 1.109353713 0.832978045 0.981842258 0.818067082 0.685385075 0.64597736 0.671967079 1 16.39233265 2.422562911 4.619682024 0.713407544 0.890807288 0.019923735 0.189991942 0.353599828 15.88251967 0.061071251 0.05121964 264.5835937 -2.422562911 0.177399744 SGSIVELIAGGGS(ph)SCSPVLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSIVELIAGGGSSCSPVLSR 21 0 P42858 P42858 HTT Huntingtin 1 SGSIVELIAGGGS(0.52)S(0.325)CS(0.154)PVLS(0.001)R 93.684 0.0017669 46898000 46908 55024 60101 69878 65440 62379 73731 55500 60798 TRUE FALSE 43972.11201 59098.03421 61526.6241 71671.18778 60300.60637 80386.80466 62675.72104 62429.29717 50650.42103 0.868148993 1.166782684 1.214730753 1.415016624 1.190525274 1.587090552 1.237417572 1.232552384 1 15.62828664 5.349288691 0.917693215 1.296708973 5.05E-16 0.388913191 0.153863251 5.153247969 1.543401224 0.043140076 8.711502267 223505.7452 -5.349288691 -1.296708973 SGSLDSELSVS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGSLDSELSVSPK 13 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7 Q12802-2 AKAP13 A-kinase anchor protein 13 1 SGSLDSELSVS(1)PK;SGSLDSELSVS(1)PK 174.24 2.13E-05 204958000 734940 415830 519900 506730 612110 387540 682090 508210 674420 TRUE FALSE 688941.4173 446618.4859 532232.2735 519733.5497 564037.3497 499416.5068 579816.9367 571661.1372 561854.9451 1.226190894 0.794899982 0.947277012 0.925031548 1.003884285 0.888870893 1.031969091 1.017453245 1 19.09983819 1.665990382 8.793846125 1.018179419 0.94299882 0.023410514 0.110396493 0.28669852 36.57749563 0.049470526 0.026170323 46.34366563 -1.665990382 -0.0751806 SGSLGQPSPS(ph)AQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSLGQPSPSAQR 13 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 SGSLGQPS(0.183)PS(0.817)AQR 144.41 4.33E-05 150400000 97376 93373 105890 110350 132350 79409 93089 78454 148300 TRUE FALSE 91281.40998 100286.4341 108401.7608 113181.7678 121955.7649 102333.0892 79131.16865 88249.1546 123547.7719 0.738834934 0.811721915 0.877407655 0.916097199 0.987114239 0.828287614 0.640490455 0.714291753 1 16.91470947 1.985727344 24.78607557 0.742333667 0.866350648 0.057880204 0.112534294 900.5591203 1563921.445 0.042239157 0.028439613 96.76701484 -1.985727344 0.124016981 SGSMDPSGAHPSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SGSMDPSGAHPSVR 14 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ;;;;; 178.84 1.47E-06 1236900000 697684 1584990 1417859 1455056 1503590 1266706 1612450 1308255 1530430 FALSE TRUE 654017.2038 1702344.309 1451491.285 1492395.2 1385504.107 1632383.459 1370678.092 1471593.517 1274991.346 0.512958151 1.335181069 1.138432264 1.170513984 1.086677263 1.280309442 1.075048937 1.154198827 1 20.28205602 4.747713575 24.99663335 1.166824178 0.51295781 0.811479702 0.097113124 477.2363808 1303300.095 0.021484645 0.267402929 55938.85534 -4.747713575 -0.653866368 SGSS(ph)PEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SGSSPEVK 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SGS(0.005)S(0.995)PEVK;SGS(0.008)S(0.992)PEVK;S(0.005)GS(0.084)S(0.911)PEVK;S(0.002)GS(0.04)S(0.958)PEVK 160.16 0.00037232 2475610000 9274430 4768230 6861390 6211070 6469560 4790320 7703980 5590720 7569720 TRUE FALSE 8693959.982 5121274.711 7024145.411 6370456.572 5961466.855 6173207.62 6548839.719 6288733.699 6306284.83 1.378618349 0.812090613 1.113832566 1.010175839 0.945321535 0.978897685 1.038462406 0.997216883 1 22.5883589 4.755858757 24.92754522 0.990402104 1.378618676 0.723614243 0.076036574 1905.663256 2746115.728 0.017553317 0.531971431 56997.88715 -4.755858757 0.388216573 SGSS(ph)PGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SGSSPGLR 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.002)GS(0.097)S(0.901)PGLR;S(0.016)GS(0.087)S(0.897)PGLR;SGS(0.054)S(0.946)PGLR;S(0.339)GS(0.1)S(0.56)PGLR 162.59 0.00035755 3408360000 3000140 2864590 3028220 2924110 2894200 3119080 4198830 3110420 2989700 TRUE FALSE 2812366.593 3076687.224 3100050.808 2999147.613 2666901.207 4019507.762 3569254.422 3498762.784 2490699.756 1.129147175 1.235270216 1.244650545 1.204138558 1.070743754 1.613806623 1.433032791 1.40473085 1 21.24811969 2.251947982 24.99999958 1.410299765 1.195261451 0.220475615 0.161349673 261.6963484 488699.7082 0.050138057 0.041727243 178.6273611 -2.251947982 -0.215038314 SGSS(ph)PSQSPCSDLEEPWLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGSSPSQSPCSDLEEPWLPR 20 0 Q5SYE7-2;Q5SYE7 Q5SYE7-2 NHSL1 NHS-like protein 1 1 S(0.002)GS(0.014)S(0.985)PSQSPCSDLEEPWLPR;S(0.123)GS(0.123)S(0.754)PSQSPCSDLEEPWLPR 291 1.93E-54 82196000 67195 66504 73315 63256 78634 64479 80572 62814 97366 TRUE FALSE 62989.3849 71428.02536 75054.06642 64879.25605 72458.40283 83093.04057 68490.97659 70656.46617 81114.98559 0.776544364 0.880577428 0.925279908 0.799843032 0.893280105 1.024385814 0.844368967 0.871065508 1 16.30768085 2.477805155 24.99994495 0.922515126 0.862871463 0.257965191 0.067304197 48.92431016 1788544.798 0.022553162 0.019076631 300.4727939 -2.477805155 -0.059643663 SGSS(ph)QELDVKPSAS(ph)PQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSSQELDVKPSASPQER 18 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.034)GS(0.232)S(0.735)QELDVKPS(0.349)AS(0.651)PQER 131.5 9.55E-06 245380000 388940 218880 290040 258660 258100 289190 426690 266260 255570 TRUE FALSE 364596.9397 235086.1029 296919.8858 265297.6535 237829.8671 372674.4584 362711.7957 299503.1471 212913.716 1.712416403 1.104137899 1.394554993 1.246033645 1.117024641 1.750354395 1.703562375 1.406687896 1 17.69990937 2.241592892 24.99854962 1.551135498 1.293846155 0.02789737 0.267170817 127.750703 1053206.677 0.086336908 0.069360843 174.4186383 -2.241592892 -0.257289343 SGSS(ph)S(ph)PDSEITELKFPSINHD ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 2 S(0.085)GS(0.515)S(0.546)S(0.848)PDS(0.007)EITELKFPSINHD;S(0.019)GS(0.172)S(0.813)S(0.992)PDS(0.003)EITELKFPSINHD 130.83 8.08E-06 991810000 200160 160970 202126 180866 194423 151074 253300 166439 245850 TRUE FALSE 187632.3429 172888.3863 206920.5242 185507.3278 179153.8018 194686.6113 215320.0165 187219.2755 204816.0467 0.91610177 0.844115434 1.010274964 0.905726532 0.874705887 0.950543741 1.051284897 0.914084997 1 17.64396923 1.995950398 24.38125523 0.995844801 0.914455039 0.307285303 0.053295348 138.6872827 834991.5782 0.019851543 0.014310188 99.07187862 -1.995950398 -0.081389762 SGSS(ph)SPDSEITELKFPSINHD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 1 S(0.11)GS(0.097)S(0.388)S(0.388)PDS(0.016)EITELKFPSINHD 61.612 0.02871 121180000 42737 49106 53175 50776 64829 50222 38087 35186 50076 TRUE FALSE 40062.16746 52741.85933 54436.33611 52078.99812 59737.59185 64720.27611 32376.20793 39579.04955 41717.9921 0.9603091 1.264247311 1.304864721 1.248358214 1.431938328 1.551375626 0.776073016 0.948728536 1 15.3483821 1.702280193 9.593019696 0.901312337 1.294710302 0.564269681 0.15928677 0.079952832 14.50353122 0.073645135 0.03962261 50.38255561 -1.702280193 0.393397965 SGSSQELDVKPSAS(ph)PQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGSSQELDVKPSASPQER 18 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SGSSQELDVKPS(0.106)AS(0.894)PQER;SGSSQELDVKPS(0.025)AS(0.975)PQER 126.32 1.69E-05 167740000 584470 368730 499900 464760 500640 449840 729770 439880 449830 TRUE FALSE 547889.066 396031.1529 511757.8641 476686.5284 461321.7539 579701.5055 620347.7634 494799.9863 374750.467 1.462010362 1.056786282 1.365596335 1.272010499 1.231010484 1.546900022 1.655362216 1.320345216 1 18.51557075 2.248443934 24.7643099 1.462834139 1.259154528 0 0.203590912 282.3678236 707520.0173 0.065408448 0.054097619 177.191928 -2.248443934 -0.203679612 SGSSS(ph)PDSEITELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGSSSPDSEITELK 14 0 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 1 SGSSS(0.998)PDS(0.001)EITELK;SGSS(0.002)S(0.997)PDS(0.001)EITELK 206.88 1.07E-08 825870000 3899700 2568200 3117800 2890500 2813200 2381000 3481500 2568100 2679700 TRUE FALSE 3655624.738 2758352.2 3191755.688 2964675.124 2592262.62 3068356.048 2959481.396 2888732.938 2232440.758 1.637501342 1.235576886 1.429715739 1.327997221 1.161178683 1.374440077 1.325670742 1.293979662 1 21.09019046 -4.587315222 0.142052575 1.12E-12 1.461239118 0.517961655 0.115796518 103.8116883 1.002541988 30.14751498 0.645977751 2.59E-05 4.587315222 1.461239118 SGSSS(ph)PDSEITELKFPSINHD ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 1 SGS(0.001)S(0.023)S(0.974)PDS(0.003)EITELKFPSINHD;SGSS(0.004)S(0.676)PDS(0.32)EITELKFPSINHD;SGS(0.003)S(0.016)S(0.969)PDS(0.012)EITELKFPSINHD;SGS(0.001)S(0.014)S(0.897)PDS(0.087)EITELKFPSINHD;SGS(0.009)S(0.09)S(0.888)PDS(0.013)EITELKFPSINHD;SGSS(0.089)S(0.904)PDS(0.007)EITELKFPSINHD;SGS(0.001)S(0.019)S(0.646)PDS(0.334)EITELKFPSINHD;S(0.024)GS(0.024)S(0.138)S(0.814)PDSEITELKFPSINHD 281.4 3.05E-45 19965879000 6849780 6659708 7035860 7376460 7867090 5635626 8699240 6174041 9883150 TRUE FALSE 6421064.497 7152799.71 7202753.922 7565752.452 7249240.486 7262539.739 7394869.722 6944883.61 8233588.417 0.779862215 0.868734183 0.874801309 0.918888833 0.880447275 0.882062519 0.898134488 0.843481998 1 22.9730899 -5 0.128168814 1.388177586 0.821488963 0.588134162 0.035593031 108.6602472 0.883798193 11.07151385 0.26666351 1.00E-05 5 -0.566688623 SGST(ph)SPLGFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGSTSPLGFAR 11 0 O75385 O75385 ULK1 Serine/threonine-protein kinase ULK1 1 S(0.001)GS(0.011)T(0.906)S(0.082)PLGFAR 105.94 0.0048578 0 230060 226930 250580 259310 241720 217250 297190 202190 262680 TRUE FALSE 215660.9553 243732.1333 256523.8759 265964.3336 222736.2863 279966.5482 252629.1185 227433.8666 218837.011 0.985486661 1.113761023 1.17221431 1.215353529 1.017818171 1.279338202 1.154416784 1.039284285 1 17.73949723 1.132716883 4.54221763 1.004163227 1.142227102 0.236235333 0.085785008 0.267161903 8.693591995 0.075567281 0.019381538 13.57428248 -1.132716883 0.138063874 SGSTGS(ph)SLSVSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SGSTGSSLSVSVR 13 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 SGST(0.007)GS(0.977)S(0.016)LSVSVR;SGSTGS(0.941)S(0.058)LSVSVR;SGST(0.005)GS(0.846)S(0.15)LSVSVR;SGSTGS(0.999)S(0.001)LSVSVR 283.42 1.45E-32 1154720000 732690 766040 758550 816310 792850 707580 912650 808470 743790 TRUE FALSE 686832.2408 822758.3987 776543.1642 837257.8966 730582.7592 911846.8594 775806.6051 909409.2592 619646.6439 1.108425661 1.327786419 1.253203212 1.351186043 1.179031253 1.471559426 1.252014536 1.46762557 1 19.24108622 4.743887155 24.11219678 1.299705726 1.108425525 0.139100219 0.137433743 588.9516255 2665927.878 0.027410439 0.232631718 55448.162 -4.743887155 -0.191280201 SGSYS(ph)GRSPS(ph)PYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGSYSGRSPSPYGR 14 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 S(0.006)GS(0.013)Y(0.002)S(0.977)GRS(0.009)PS(0.993)PYGR;S(0.012)GS(0.057)Y(0.001)S(0.885)GRS(0.047)PS(0.998)PYGR 156.17 6.75E-05 1786260000 2822150 3045900 3024850 3234000 3390110 2261090 3117130 2538470 3701400 TRUE FALSE 2645516.669 3271421.605 3096600.87 3316989.915 3123864.436 2913829.977 2649745.295 2855403.567 3083612.428 0.857927749 1.060905571 1.004212087 1.075683145 1.013053524 0.944940405 0.859299071 0.925993014 1 21.55619002 2.129549529 4.089538824 0.910715175 1.013931929 0.182785923 0.067863684 0.241985967 7.396256402 0.024801094 0.017739951 134.75644 -2.129549529 0.103216754 SGSYSGRS(ph)PS(ph)PYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGSYSGRSPSPYGR 14 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 SGS(0.003)YS(0.184)GRS(0.813)PS(0.997)PY(0.002)GR;S(0.008)GS(0.218)Y(0.001)S(0.117)GRS(0.655)PS(1)PYGR 183.75 1.64E-05 1470160000 1815000 2093420 2034530 2074230 2190120 1526320 2074420 1675360 2396600 TRUE FALSE 1701402.39 2248418.995 2082790.012 2127458.253 2018116.81 1966943.806 1763379.979 1884532.384 1996591.977 0.852153274 1.126128433 1.043172584 1.065544827 1.010780787 0.985150611 0.883194964 0.943874565 1 20.9291081 2.143700126 2.658936154 0.930534111 1.041238389 0.138799308 0.075870841 0.328643052 4.65276643 0.031977413 0.020944891 139.219518 -2.143700126 0.110704278 SGSYSGRS(ph)PSPYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGSYSGRSPSPYGR 14 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 SGSYS(0.065)GRS(0.832)PS(0.103)PYGR;SGSYS(0.257)GRS(0.606)PS(0.136)PYGR 97.203 0.00807 149272000 256730 308450 282310 295070 293130 221093 266700 233788 322680 TRUE FALSE 240661.7276 331287.9589 289006.5265 302641.9958 270108.7522 284918.96 226710.8109 262976.9464 268822.6234 0.895243579 1.232366364 1.075082606 1.125805529 1.004784303 1.059877165 0.843347216 0.97825452 1 18.03629503 2.231991789 1.665105937 0.931158701 1.103993928 0.211716352 0.098124148 0.381728455 2.100248243 0.048882853 0.029939552 170.6050134 -2.231991789 0.172835227 SGT(ph)PPRQGSITSPQANEQSVTPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGTPPRQGSITSPQANEQSVTPQR 24 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.077)GT(0.918)PPRQGS(0.004)ITSPQANEQSVTPQR 79.054 0.031196 237980000 167840 206900 201190 191620 197500 192860 227900 196540 232060 TRUE FALSE 157335.194 222219.0913 205962.3218 196537.2936 181989.1467 248535.5512 193728.5107 221078.4516 193327.6868 0.813826496 1.149442663 1.065353469 1.016601899 0.941350666 1.285566259 1.002073288 1.143542631 1 17.56068874 SGT(ph)PTQDEMMDKPTSSSVDTMSLLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGTPTQDEMMDKPTSSSVDTMSLLSK 26 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 S(0.029)GT(0.946)PT(0.024)QDEMMDKPTSSSVDTMSLLSK;S(0.068)GT(0.917)PT(0.015)QDEMMDKPTSSSVDTMSLLSK 235.86 1.02E-44 573690000 979640 390920 594960 510120 626070 423460 878560 526600 955990 TRUE FALSE 918326.0811 419864.1236 609072.7322 523210.5428 576900.9876 545706.0277 746828.0842 592347.1692 796429.0931 1.153054414 0.527183308 0.764754499 0.656945543 0.72435951 0.685190976 0.937720747 0.743753806 1 19.6031864 1.069280325 0.800015344 0.985922869 0.724387852 0.113452303 0.172423825 1.031027106 1.495951968 0.14882831 0.055508505 11.72952228 -1.069280325 -0.261535017 SGTHNMYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SGTHNMYR 8 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ;;;; 155.07 0.00041492 891226000 442126 1662930 610704 620905 1601700 461265 584368 1364090 1046140 FALSE TRUE 414454.1229 1786055.067 625190.1873 636838.4735 1475908.943 594424.7175 496747.4434 1534399.639 871532.4757 0.47554639 2.049327039 0.71734583 0.730711122 1.693464081 0.682045402 0.56997009 1.76057655 1 19.7331949 3.754040613 23.5564377 0.974404165 1.377396095 0.016868377 0.555287646 468.6701665 410116.05 0.131429276 0.236825732 5675.976815 -3.754040613 0.40299193 SGTICSSELPGAFEAAGFHLNEHLYNMIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGTICSSELPGAFEAAGFHLNEHLYNMIIR 30 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;U3KQE2;A0A075B7C0 A0A0C4DGQ5 CAPNS1 Calpain small subunit 1 0 ; 241.69 7.08E-46 885090000 792310 1136770 870370 689550 1254750 709800 983870 1098840 862930 FALSE TRUE 742720.7314 1220937.634 891015.5874 707245.0204 1156206.996 914707.7374 836347.8273 1236032.593 718901.4083 1.033132948 1.698338075 1.239412772 0.983785832 1.608297025 1.272368821 1.163369299 1.719335334 1 19.4554344 -2.142795402 2.603722391 0.190719398 1.343789783 0.143558204 0.260631843 47218939.95 38035508.18 219055071.5 0.059436194 0.00719788 2.142795402 1.153070385 SGTIFDNFLITNDEAYAEEFGNETWGVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGTIFDNFLITNDEAYAEEFGNETWGVTK 29 0 P27797;K7EL50 P27797 CALR Calreticulin 0 77.791 0.0046133 35273000 42378 32928 36682 36318 41361 28835 42689 35672 35450 FALSE TRUE 39725.63663 35366.02338 37552.11436 37249.98137 38112.6739 37159.1964 36288.18076 40125.72772 29533.16598 1.345119472 1.197501934 1.271523493 1.261293198 1.290504172 1.258219197 1.228726401 1.358666651 1 14.8500484 -1.843423197 2.887491652 0.906308189 1.265352278 0.754749851 0.049163628 8503659.265 8576973.627 5572362.84 0.010735172 0.014340913 1.843423197 0.359044088 SGTLKS(ph)PPKGFDTTAINK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGTLKSPPKGFDTTAINK 18 2 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E7EUY6;E7EU80 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 1 S(0.144)GT(0.107)LKS(0.749)PPKGFDTTAINK 115.55 9.70E-05 715110000 837020 351450 540540 469960 539390 319880 667480 361890 725340 TRUE FALSE 784632.4123 377471.7237 553361.8641 482019.9692 497028.4852 412224.1632 567397.5706 407072.7631 604276.0681 1.2984668 0.62466767 0.915743471 0.797681713 0.822518897 0.682178535 0.938970779 0.673653624 1 19.20484828 4.751872736 24.9001137 0.804520743 1.298467139 0.616672227 0.121779001 1306.450602 2443650.666 0.025661791 0.493061837 56477.14515 -4.751872736 0.493946396 SGTSEFLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGTSEFLNK 9 0 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 117.89 0.004092 0 54555 60374 52478 54771 72382 39082 67749 48053 48200 FALSE TRUE 51140.49993 64844.15378 53722.80294 56176.51659 66697.40969 50364.33896 57590.6664 54052.52283 40155.10862 1.273573941 1.614841947 1.337882147 1.398988037 1.660994379 1.254244869 1.43420522 1.346093304 1 15.29329592 0.117055619 0.611511859 0.977450998 1.451423238 0.507753021 0.130375513 2.629021832 1.230859938 0.255578743 0.047625892 1.309349596 -0.117055619 0.47397224 SGTSSPQS(ph)PVFR ddPTM_SK-BR-3_Pertuzumab_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;SGTSS(0.001)PQS(0.999)PVFR 260.97 2.55E-21 2128930000 2363890 2422630 2551530 2595770 2558710 1958400 2844290 2095640 2098260 TRUE FALSE 2215938.345 2602004.046 2612053.497 2662381.853 2357759.238 2523758.288 2417815.12 2357285.267 1748046.851 1.267665305 1.488520771 1.49426973 1.523060925 1.348796365 1.443758951 1.383152356 1.348525222 1 20.73731242 0.270758679 0.689856008 0.98811001 1.449861378 0.751219365 0.075588538 1.20408149 0.77549786 0.102530999 0.026243766 1.865342902 -0.270758679 0.461751367 SGTT(ph)PKPVINSTPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGTTPKPVINSTPGR 15 1 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 1 S(0.132)GT(0.116)T(0.752)PKPVINSTPGR 75.55 0.050922 375800000 697200 440340 525910 507370 558770 363530 617150 427680 665400 TRUE FALSE 653563.4965 472943.2318 538384.8336 520389.9732 514886.4582 468475.2096 524614.0868 481076.7894 554340.4414 1.178992994 0.853163862 0.971216952 0.938755202 0.928827161 0.845103793 0.946375274 0.867836358 1 19.08041274 4.747188217 24.98886439 0.916911488 1.178993127 0.723483836 0.050517884 543.2258079 1573357.062 0.010795523 0.126916197 55871.22805 -4.747188217 0.262081639 SGTYSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGTYSSR 7 0 Q9UK58 Q9UK58 CCNL1 Cyclin-L1 0 ; 82.263 0.058079 306080000 319710 320620 308010 339910 355240 292630 321640 246040 364190 FALSE TRUE 299699.9218 344359.0384 315316.1427 348632.6661 327340.8834 377107.5305 273413.068 276758.6356 303404.3362 0.987790503 1.134983905 1.039260502 1.149069491 1.078893227 1.242920702 0.901150825 0.912177588 1 18.21088218 1.649660836 9.57786666 0.93035415 1.101453244 0.542591747 0.072255198 0.076881628 12.38364508 0.031561947 0.01676569 44.63348889 -1.649660836 0.171099094 SGVRGT(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SGVRGTPVR 9 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RFR3 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 1 SGVRGT(1)PVR;SGVRGT(1)PVR;SGVRGT(1)PVR;S(0.001)GVRGT(0.999)PVR 97.779 0.010444 2077980000 715110 851550 773210 822160 948790 588929 880240 809230 1213950 TRUE FALSE 670352.5416 914599.648 791550.9063 843258.0175 874275.8606 758943.2418 748256.1837 910264.1468 1011333.903 0.662839978 0.904349835 0.782680086 0.833807722 0.864477952 0.750437852 0.739870563 0.900062921 1 19.94782797 1.001121112 5.379739852 0.999788027 0.800806641 0.511600777 0.067942515 0.11345711 12.47157843 0.062286789 0.015712839 10.0258479 -1.001121112 -0.198981386 SGVSS(ph)DNEDDDDEEDGNYLHPSLFASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SGVSSDNEDDDDEEDGNYLHPSLFASK 27 0 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 S(0.029)GVS(0.139)S(0.832)DNEDDDDEEDGNYLHPSLFASK;S(0.003)GVS(0.127)S(0.87)DNEDDDDEEDGNYLHPSLFASK;S(0.019)GVS(0.154)S(0.826)DNEDDDDEEDGNYLHPSLFASK;S(0.017)GVS(0.16)S(0.823)DNEDDDDEEDGNYLHPSLFASK;S(0.006)GVS(0.157)S(0.838)DNEDDDDEEDGNYLHPSLFASK 298.75 5.88E-71 2186400000 867010 1389000 1349900 1375240 1398490 1178370 1760460 1335760 1564420 TRUE FALSE 812745.3918 1491843.005 1381920.265 1410530.987 1288658.237 1518546.29 1496495.366 1502532.576 1303308.195 0.623601842 1.144658654 1.06031733 1.082269713 0.988759406 1.165147503 1.14822831 1.15286053 1 20.31374685 4.741861574 24.98502722 1.099597498 0.623601664 0.845902919 0.062873025 113.7738928 861118.1309 0.01451451 0.105129358 55190.1499 -4.741861574 -0.475995834 SGVTNMSS(ph)PHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SGVTNMSSPHK 11 0 Q9NVG8 Q9NVG8 TBC1D13 TBC1 domain family member 13 1 SGVTNMS(0.006)S(0.994)PHK;SGVTNMS(0.002)S(0.998)PHK;SGVT(0.007)NMS(0.193)S(0.8)PHK 98.942 0.0033139 1073730000 1114176 801468 906991 880025 1107750 695664 1072943 919311 1178992 TRUE FALSE 1044441.713 860809.5246 928505.2548 902607.9314 1020751.783 896490.9036 912065.1579 1034089.002 982210.6186 1.063358198 0.876400141 0.945321947 0.918955583 1.039239206 0.912727766 0.928584094 1.052817983 1 19.90567289 1.242858404 24.9967331 1.026409003 0.944971547 0.189612629 0.058674117 132.8233463 772562.8657 0.038931906 0.013094488 17.49276266 -1.242858404 -0.081437455 SGWSSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SGWSSGR 7 0 Q9BQ39;A0A087WVC1 Q9BQ39 DDX50 ATP-dependent RNA helicase DDX50 0 112.37 0.014818 40026000 56796 55899 55544 57167 62903 42503 64023 54766 63353 FALSE TRUE 53241.23974 60037.82012 56861.52991 58634.002 57962.85212 54772.92612 54423.34551 61603.65565 52778.97502 1.008758501 1.137532893 1.077351917 1.110934837 1.098218601 1.037779269 1.031155787 1.167200682 1 15.68767571 2.253976703 24.88424055 1.057513307 1.093362711 0.052350646 0.053873139 525.3846197 848059.596 0.017105212 0.014260346 179.4637353 -2.253976703 0.035849404 SGYFDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SGYFDER 7 0 P12532;P12532-2;F8WCN3;C9JSQ1;C9J6W7;C9JT96 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ;; 100.45 0.022762 5289000000 10141000 11526700 9898500 10066500 14108300 8548300 11380600 11270200 12800100 FALSE TRUE 9506292.912 12380148.86 10133297.09 10324823.43 13000291.03 11016055.44 9674184.682 12677309.28 10663680.62 0.891464519 1.160963958 0.950262621 0.968223243 1.219118566 1.03304439 0.90720878 1.188830549 1 23.34620214 4.777968368 22.98149843 1.042958888 0.891463323 0.182131795 0.105822621 16013.29315 9337947.228 0.024110153 6.726914512 59974.73922 -4.777968368 -0.151495565 SGYHDDS(ph)DEDLLE ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SGYHDDSDEDLLE 13 0 Q99523;Q99523-2 Q99523 SORT1 Sortilin 1 SGYHDDS(1)DEDLLE;SGYHDDS(1)DEDLLE;SGYHDDS(1)DEDLLE;SGYHDDS(1)DEDLLE;SGYHDDS(1)DEDLLE 220.53 2.17E-11 14116690000 7045870 7750170 7538220 6762300 7893090 5910950 11078150 7848620 11383770 TRUE FALSE 6604881.574 8324000.651 7717030.138 6935832.067 7273198.551 7617345.309 9417084.252 8828537.484 9483745.245 0.696442324 0.877712384 0.813711244 0.731338926 0.766912055 0.803200119 0.992971027 0.930912552 1 23.17702548 1.76397296 6.092422849 0.970619948 0.793350056 0.749750664 0.052247834 0.093479403 8.746259591 0.025765748 0.013926683 58.07282587 -1.76397296 -0.177269893 SGYHDDSDEDLLE ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SGYHDDSDEDLLE 13 0 Q99523;Q99523-2 Q99523 SORT1 Sortilin 0 ; 93.096 0.013426 357960000 416260 429620 511640 495080 548520 599740 536240 490780 813950 FALSE TRUE 390207.0296 461429.5118 523776.3424 507784.591 505441.4518 772875.202 455835.7902 552054.9633 678096.4867 0.5754447 0.680477662 0.772421555 0.748838257 0.745382791 1.139771725 0.672228509 0.8141245 1 19.37113104 6.316790925 0.205397616 0.94487858 3.92E-11 0.408962737 0.126259784 28.41933176 0.63177233 0.222316451 7.598044268 2073914.867 -6.316790925 -0.94487858 SGYLSSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SGYLSSER 8 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 122.19 0.0032597 761011000 549038 1194790 406533 406999 1365660 304251 452667 1017990 1083750 FALSE TRUE 514674.6916 1283253.495 416176.1547 417443.2834 1258406.572 392083.3246 384793.7857 1145088.292 902865.1237 0.570046044 1.42131251 0.460950527 0.46235398 1.393792427 0.434265666 0.426191881 1.268282784 1 19.78415096 3.963594856 24.38000958 0.725450626 1.042064957 0.032390924 0.407823499 635.3201093 1145105.43 0.097418148 0.176944254 9195.913038 -3.963594856 0.316614331 SHDDGNIDLESDS(ph)FLKFDSEPSAVALELPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHDDGNIDLESDSFLKFDSEPSAVALELPTR 31 1 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;P18583-8 P18583-7 SON Protein SON 1 SHDDGNIDLES(0.217)DS(0.783)FLKFDSEPSAVALELPTR 164.76 9.08E-13 49722000 108180 65102 79917 76567 78701 50215 122180 72956 122090 TRUE FALSE 101409.2069 69922.21982 81812.66898 78531.83885 72520.14092 64711.25533 103860.2433 82064.7172 101712.3903 0.997019209 0.687450365 0.804353027 0.772097073 0.7129922 0.636218018 1.021116926 0.806831075 1 16.63413591 1.72381178 13.53824338 0.934334653 0.761202031 0.355668419 0.110099374 0.111539264 77.32177248 0.046426124 0.025531916 52.94339418 -1.72381178 -0.173132622 SHDDGNIDLESDSFLKFDSEPSAVALELPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHDDGNIDLESDSFLKFDSEPSAVALELPTR 31 1 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;P18583-8 P18583-7 SON Protein SON 0 87.339 0.0003859 46036000 31402 26361 29706 31529 36347 17180 33063 24775 40826 FALSE TRUE 29436.60487 28312.79587 30410.64035 32338.08752 33492.45324 22139.58711 28105.51009 27868.21329 34011.87685 0.865480167 0.832438503 0.894118266 0.950788093 0.98472817 0.650936942 0.826343992 0.819367111 1 15.053751 2.271076796 24.99984781 0.805804629 0.896050753 0.141782434 0.093182283 310.3077091 238576.9364 0.030119544 0.025198047 186.6709749 -2.271076796 0.090246124 SHDPEEAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHDPEEAIR 9 0 Q9NTI5-2;Q9NTI5;Q9NTI5-3;Q29RF7;Q29RF7-3 Q9NTI5-2;Q29RF7 PDS5B;PDS5A Sister chromatid cohesion protein PDS5 homolog B;Sister chromatid cohesion protein PDS5 homolog A 0 121.73 0.0006056 189280000 245540 276320 262530 270800 261230 237090 287710 240350 217020 FALSE TRUE 230172.0897 296779.0203 268757.3356 277749.1865 240714.0496 305534.0342 244570.5565 270358.2266 180797.96 1.273090082 1.641495404 1.48650646 1.53624071 1.33139804 1.689919699 1.352728518 1.495361046 1 17.46401887 -0.767009086 0.54315364 0.892464273 1.50336247 0.555491619 0.132564669 10.03438492 2.053247758 1.988136896 0.051433215 0.170997954 0.767009086 0.610898196 SHEAEVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SHEAEVLK 8 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 0 ;;;; 103.83 0.0046967 3925100000 6026140 6212220 5028010 5023420 7459120 3441080 5327380 5985640 7552630 FALSE TRUE 5648974.654 6672179.233 5147276.772 5152329.462 6873310.804 4434463.935 4528588.826 6732960.33 6292047.261 0.897795967 1.060414672 0.818060729 0.818863757 1.09238067 0.704772827 0.71973217 1.070074659 1 22.58509808 2.226657237 24.99662481 0.831104049 0.932583539 0.009208143 0.142645598 520.0059037 1091984.155 0.051162671 0.038082797 168.5222453 -2.226657237 0.10147949 SHEGETAYIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SHEGETAYIR 10 0 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;; 196.27 3.36E-07 3717980000 732980 851080 704870 739160 894420 557360 855170 729280 901190 FALSE TRUE 687104.0902 914094.8487 721589.8493 758128.097 824175.8611 718260.784 726945.1975 820332.2133 750775.5671 0.915192396 1.217534092 0.961125909 1.009793246 1.09776596 0.956691741 0.968258997 1.09264639 1 19.51802217 3.751501257 23.70279005 1.008541968 1.088370425 0.048365243 0.087141225 407.2032104 395887.5223 0.020317443 0.036596546 5642.885748 -3.751501257 0.079828458 SHEGETSYIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHEGETSYIR 10 0 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 95.483 0.0073913 432070000 33627 59213 60661 65992 67716 49566 62794 61382 82813 FALSE TRUE 31522.3461 63597.19213 62099.90757 67685.46644 62397.85851 63874.89956 53378.62265 69045.67782 68990.97531 0.456905355 0.921819004 0.900116389 0.981077107 0.904435084 0.925844276 0.773704422 1.000792894 1 16.07412004 4.739385372 24.96475052 0.911055723 0.456905211 0.828096142 0.066858285 26.99273159 816911.3004 0.015325544 0.092825235 54876.36957 -4.739385372 -0.454150512 SHEHAGHDSSVNSVCWAPHDYGLILACGSSDGAISLLTYTGEGQWEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHEHAGHDSSVNSVCWAPHDYGLILACGSSDGAISLLTYTGEGQWEVK 48 0 P55735;P55735-4;P55735-3;P55735-2;A8MXL6 P55735 SEC13 Protein SEC13 homolog 0 30.669 0.054354 29024000 16225 15721 7807 6533.8 23379 6819.5 9944.8 13298 6802 FALSE TRUE 15209.50621 16884.9992 7992.185727 6701.46837 21542.90765 8788.178945 8453.669563 14958.28457 5666.702257 2.684013651 2.979687026 1.410376858 1.182604638 3.801665707 1.550845367 1.491814671 2.639680698 1 12.46829369 8 0.061624469 6.60E-14 6.5124751 0.181107745 0.825953305 588.9150738 2.704930906 56.48270518 341.9333714 100000000 -8 6.5124751 SHELDIDENPAS(ph)DFDDSGSLLGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SHELDIDENPASDFDDSGSLLGFK 24 0 Q96RS0 Q96RS0 TGS1 Trimethylguanosine synthase 1 SHELDIDENPAS(1)DFDDSGSLLGFK;SHELDIDENPAS(0.905)DFDDS(0.042)GS(0.052)LLGFK;S(0.001)HELDIDENPAS(0.738)DFDDS(0.113)GS(0.148)LLGFK;SHELDIDENPAS(1)DFDDSGSLLGFK 232.2 3.58E-34 108367000 80661 67085 70863.7 70142 79530 62524.4 106084 78753 91973 TRUE FALSE 75612.57199 72052.0432 72544.62043 71941.96247 73284.03461 80574.17928 90177.68904 88585.48541 76622.11213 0.986824428 0.940355743 0.9467844 0.938919073 0.95643454 1.051578677 1.176914686 1.156134736 1 16.22547317 2.079242058 3.327631088 1.128538586 0.950103674 0.682132064 0.04896923 0.109986326 2.416548353 0.019024349 0.012568537 120.0168042 -2.079242058 -0.178434912 SHESNAPGS(ph)AGGQASEKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SHESNAPGSAGGQASEKPR 19 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 SHESNAPGS(1)AGGQASEKPR;SHESNAPGS(1)AGGQASEKPR;SHESNAPGS(0.987)AGGQAS(0.013)EKPR 152.88 3.10E-08 426381000 265040 411351 429647 386929 470453 397620 619293 512305 598508 TRUE FALSE 248451.6195 441807.8561 439838.4297 396858.2532 433505.5191 512406.4392 526435.7639 576267.407 498613.1483 0.498285335 0.886073417 0.882123609 0.795924164 0.869422559 1.027663312 1.055800004 1.155740495 1 18.9275614 2.259335631 1.856271133 1.079550145 0.802404866 0.588808856 0.114921541 0.265276723 1.843176415 0.055077945 0.035930337 181.6919271 -2.259335631 -0.277145279 SHFEQWGTLTDCVVMR ddPTM_SK-BR-3_Pertuzumab_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 ;;;; 304.71 2.86E-46 2130220000 1478271 1569970 1369928 1412306 1481960 1276160 1662770 1481494 1290449 FALSE TRUE 1385748.657 1686212.212 1402423.339 1448548.163 1365572.84 1644566.675 1413453.075 1666461.787 1075064.725 1.288990908 1.568475063 1.304501307 1.347405537 1.270223836 1.529737361 1.314760908 1.55010368 1 20.03599209 -1.151786507 4.510785513 0.99994055 1.398351739 0.546729645 0.113529328 6.09E-05 1.15E-05 0.098632148 0.02324436 0.070503957 1.151786507 0.398411189 SHFEQWGTLTDCVVMRDPNTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 299.25 3.07E-55 770373000 637160 590650 621370 609170 690180 487780 787850 554000 739280 FALSE TRUE 597281.293 634382.3406 636109.1898 624802.3335 635976.0469 628594.1676 669719.2065 623168.1195 615889.3921 0.969786622 1.030026412 1.032830242 1.014471659 1.032614062 1.02062834 1.087401756 1.011818238 1 19.23231175 SHFEQWGTLTDCVVMRDPNTKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SHFEQWGTLTDCVVMRDPNTKR 22 2 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8W646 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ;; 255.37 2.67E-37 2191905000 1564099 2013280 1785427 1771522 2674100 1416734 2425100 1694640 3764460 FALSE TRUE 1466204.836 2162345.346 1827778.172 1816982.254 2464086.973 1825722.107 2061478.769 1906219.534 3136147.307 0.467517847 0.689491001 0.582810051 0.579367637 0.785705113 0.582154449 0.657328425 0.607822066 1 21.58056189 -5 0.313207981 4.380938886 0.608890308 0.683404917 0.081872802 167.2373857 1.505093483 373.621493 0.06795651 1.00E-05 5 -3.772048578 SHFGGPDYEEGPNSLINEEEFFDAVEAALDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 258.19 1.69E-58 32905000 19351 22097 23963 20550 20658 18070 21502 21162 19934 FALSE TRUE 18139.85545 23733.08487 24531.41368 21077.34779 19035.60401 23286.51566 18277.97471 23804.12228 16606.88662 1.092309225 1.429111032 1.477183185 1.269193213 1.146247605 1.402220428 1.100626212 1.433388619 1 14.01949401 3.019679266 19.49378038 1.225889281 1.373993871 0.076672828 0.16338109 33.41180884 33093.41159 0.043189475 0.051593154 1046.35551 -3.019679266 0.14810459 SHGLES(ph)VPVLPGSGEAGVSFDLPAQADTLHSANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHGLESVPVLPGSGEAGVSFDLPAQADTLHSANK 34 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 S(0.419)HGLES(0.581)VPVLPGSGEAGVSFDLPAQADTLHSANK 133.23 5.51E-08 138330000 59670 46187 49587 47540 57068 40168 62784 47644 103720 TRUE FALSE 55935.36121 49606.73354 50763.22706 48759.95689 52586.10948 51763.84953 53370.12206 53592.45828 86408.46194 0.647336614 0.574095782 0.587479813 0.564296086 0.608575923 0.599059957 0.617649254 0.620222338 1 16.39888498 -0.814614166 0.597142744 1.080229871 0.590413715 0.968308198 0.022647442 2.72699181 0.621924565 0.438112647 0.008316288 0.153244831 0.814614166 -0.489816155 SHHAASTTTAPTPAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SHHAASTTTAPTPAAR 16 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ; 68.034 0.028986 52443000 13773.6 33041 28024.1 28302 31991 23167 27114 30615 29481 FALSE TRUE 12911.53496 35487.39002 28688.84489 29028.27724 29478.55591 29854.93682 23048.50741 34437.35014 24560.43065 0.525704746 1.444900968 1.168092095 1.181912388 1.200245889 1.215570576 0.938440687 1.402147651 1 14.58404824 -0.176956601 7.618821394 0.999992466 1.156156668 0.020417465 0.257128241 15020429.62 1971489.94 0.221263004 0.053664161 0.66533964 0.176956601 0.156164202 SHHAPMS(ph)PGSSGGGGQPLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 SHHAPMSPGSSGGGGQPLAR 20 0 O14497;O14497-2 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 SHHAPMS(1)PGSSGGGGQPLAR;SHHAPMS(1)PGSSGGGGQPLAR;S(0.035)HHAPMS(0.93)PGS(0.035)SGGGGQPLAR;SHHAPMS(1)PGSSGGGGQPLAR;SHHAPMS(1)PGSSGGGGQPLAR;SHHAPMS(0.998)PGS(0.002)SGGGGQPLAR;SHHAPMS(1)PGSSGGGGQPLAR;SHHAPMS(1)PGSSGGGGQPLAR;SHHAPMS(1)PGSSGGGGQPLAR;SHHAPMS(1)PGSSGGGGQPLAR 298.66 3.33E-54 4852760000 1438062 2486211 2416897 2382275 2487176 2328962 3095323 2356515 2548015 TRUE FALSE 1348056.266 2670292.649 2474226.938 2443408.21 2291843.23 3001295.522 2631208.052 2650731.085 2122734.836 0.635056364 1.257949229 1.165584555 1.151066148 1.079665341 1.413881504 1.23953685 1.248733964 1 21.01749274 4.741483721 24.9666438 1.209773558 0.635056152 0.710326348 0.111911201 137.6827862 1175907.145 0.02474528 0.173928833 55142.15327 -4.741483721 -0.574717406 SHHCTLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SHHCTLAR 8 0 Q9HCN6-3 Q9HCN6-3 0 ;;; 100.82 0.013568 1829710000 3042160 3910900 3584580 3413480 4155870 3168290 3850220 3549600 4793480 FALSE TRUE 2851756.636 4200467.105 3669607.93 3501075.676 3829484.734 4082923.89 3272915.255 3992775.374 3993417.221 0.714114373 1.051847797 0.918914235 0.876711719 0.958949321 1.022413553 0.819577588 0.999839274 1 21.92919238 3.92587835 0.009362241 1.838781793 5.96E-05 0.103717199 0.097653986 21165.74118 40.97231181 3820.507554 4231.225907 8430.985639 -3.92587835 -1.838722215 SHHGEHERPEFIAYPHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SHHGEHERPEFIAYPHLR 18 1 P12074;H0YIV9 P12074 COX6A1 "Cytochrome c oxidase subunit 6A1, mitochondrial" 0 ;;; 204.07 3.74E-16 4962290000 710811 1009937 914246 756945 1153520 872788 811694 914962 1632330 FALSE TRUE 666322.6083 1084713.786 935932.3469 776369.4902 1062927.192 1124747.727 689988.0201 1029197.02 1359883.578 0.489985039 0.797651949 0.688244466 0.570908792 0.781631023 0.82709119 0.507387567 0.756827302 1 20.37505171 0.979833756 24.36384965 1.000000008 0.678378296 0.44422757 0.117084841 1027.933083 1241899.582 0.105638942 0.026409735 9.546270936 -0.979833756 -0.321621712 SHILEDDENS(ph)VDISMLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SHILEDDENSVDISMLK 17 0 O75717;O75717-2 O75717 WDHD1 WD repeat and HMG-box DNA-binding protein 1 1 SHILEDDENS(1)VDISMLK;SHILEDDENS(1)VDISMLK;SHILEDDENS(1)VDISMLK 269.01 2.57E-28 765650000 763600 826120 796980 843960 1107740 522224 1368600 1105690 1864240 TRUE FALSE 715807.6391 887286.7844 815884.742 865617.4424 1020742.569 672981.5912 1163391.135 1243737.83 1553086.301 0.460893666 0.571305525 0.525331233 0.557353086 0.657234932 0.433318864 0.74908338 0.800816948 1 20.56670657 1.229669785 1.359760179 0.990178614 0.541046657 0.825770566 0.071914664 0.139074105 0.498442729 0.05908047 0.018388033 16.96952886 -1.229669785 -0.449131957 SHISDQS(ph)PLSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SHISDQSPLSSK 12 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 SHISDQS(1)PLSSK;SHISDQS(1)PLSSK;SHISDQS(0.99)PLS(0.01)SK;SHISDQS(0.996)PLS(0.002)S(0.002)K 264.29 1.64E-21 1011370000 2609890 3568100 3778760 3514590 3724740 3647820 4896920 3905980 5735080 TRUE FALSE 2446541.644 3832285.837 3868393.972 3604780.33 3432213.945 4700886.417 4162672.307 4393650.201 4777858.098 0.512058247 0.802092854 0.809650243 0.754476223 0.718358284 0.983889919 0.871242348 0.919585746 1 22.18793258 6.404890967 0.175770692 1.019540938 1.61E-12 0.647674142 0.084333204 23.53497318 0.425487018 0.214403786 5.73943066 2540334.857 -6.404890967 -1.019540938 SHKDEVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SHKDEVVK 8 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 102.53 0.0029725 326560000 928950 938190 782960 857600 1113490 546840 979800 923320 1165320 FALSE TRUE 870808.6777 1007654.564 801532.1809 879607.4679 1026040.987 704703.8308 832888.086 1038598.534 970820.5637 0.89698211 1.0379411 0.825623407 0.906045361 1.056880154 0.725884738 0.857921759 1.069815137 1 19.88884514 1.236271748 24.99998687 1.034907607 0.901598893 0.249748341 0.096456716 88.68325147 968526.1667 0.077505924 0.022947807 17.22946324 -1.236271748 -0.133308714 SHLEPSGNPLPAT(ph)PTTSAPSAPPAS(ph)SQGPDTAPRPSPPQEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHLEPSGNPLPATPTTSAPSAPPASSQGPDTAPRPSPPQEEAR 43 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 2 SHLEPSGNPLPAT(0.987)PT(0.014)T(0.004)S(0.015)APS(0.064)APPAS(0.321)S(0.301)QGPDT(0.196)APRPS(0.099)PPQEEAR 105.18 7.63E-05 55378000 15542 14134 16737 23544 25080 27051 29254 26372 25981 TRUE FALSE 14569.25396 15180.49607 17134.00954 24148.1789 23110.31797 34860.18456 24867.63428 29664.60225 21644.60326 0.673112544 0.701352475 0.791606542 1.115667431 1.067717329 1.610571658 1.148906912 1.370531116 1 14.40171974 3.132205337 1.495258568 1.281422787 0.694263318 0.671124423 0.167103884 0.193590335 0.895424377 0.053168608 0.071404567 1355.830307 -3.132205337 -0.587159468 SHLEPSGNPLPATPTTSAPSAPPASSQGPDT(ph)APRPSPPQEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHLEPSGNPLPATPTTSAPSAPPASSQGPDTAPRPSPPQEEAR 43 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 SHLEPSGNPLPATPTTSAPSAPPAS(0.186)S(0.186)QGPDT(0.489)APRPS(0.139)PPQEEAR 209.56 8.09E-36 950050000 179220 199570 163310 185890 161960 164100 224490 131810 154180 TRUE FALSE 168002.9401 214346.3705 167183.7903 190660.2521 149240.3149 211473.0061 190829.8086 148266.7686 128446.362 1.307961841 1.668761709 1.301584473 1.484356966 1.16188822 1.646391559 1.485677022 1.154308821 1 16.9708065 1.095341377 3.949720024 1.006576395 1.450368396 0.493558906 0.154790552 0.154899789 4.243042201 0.136534718 0.035224569 12.45493247 -1.095341377 0.443792001 SHLEPSGNPLPATPTTSAPSAPPASSQGPDTAPRPS(ph)PPQEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SHLEPSGNPLPATPTTSAPSAPPASSQGPDTAPRPSPPQEEAR 43 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 SHLEPSGNPLPATPTTSAPSAPPAS(0.006)S(0.006)QGPDT(0.02)APRPS(0.969)PPQEEAR;SHLEPSGNPLPATPTTSAPSAPPAS(0.006)S(0.006)QGPDT(0.183)APRPS(0.804)PPQEEAR 231.98 1.17E-45 1152660000 267827 277251 255117 274761 232444 231827 308065 224104 253014 TRUE FALSE 251064.1862 297778.9525 261168.4957 281811.8324 214188.7859 298751.6915 261873.5132 252083.8777 210784.3289 1.191095123 1.41271865 1.239031844 1.336967667 1.016151376 1.417333504 1.242376578 1.195932729 1 17.68540809 -4.472131188 0.204970195 4.11E-11 1.314395146 0.333423928 0.115918216 119.5104969 1.445946639 49.09088098 0.241109925 3.37E-05 4.472131188 1.314395146 SHLEVPLEENVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHLEVPLEENVNR 13 0 Q96CT7;M0R2F5 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 103.83 0.0015793 126650000 80240 76571 86204 93341 94141 78841 91930 69688 69319 FALSE TRUE 75217.92163 82240.39651 88248.79959 95736.28809 86747.54561 101601.1168 78145.94994 78388.7002 57749.21108 1.302492627 1.424095585 1.528138618 1.657793869 1.502142522 1.759350733 1.353195108 1.357398633 1 15.81751362 -0.463671401 7.265338109 1 1.491457665 0.540100895 0.14072348 0 0 0.131235621 0.030932533 0.343817991 0.463671401 0.491457665 SHLGNVHDQDN ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SHLGNVHDQDN 11 0 Q8WW12;Q8WW12-3 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 0 ;; 224.31 1.18E-11 400983000 374619 459253 452246 474279 482577 366329 514126 342822 496244 FALSE TRUE 351172.2655 493256.57 462973.4887 486449.8021 444677.349 472082.2354 437037.5792 385624.0813 413417.6705 0.849436999 1.193119223 1.11986865 1.176654596 1.075612826 1.141901445 1.057133283 0.932771163 1 18.65724053 1.433505648 4.087054789 0.968608601 1.10956535 0.207915096 0.09658327 0.268258278 8.048169649 0.062490663 0.022579138 27.13348941 -1.433505648 0.140956748 SHLLDCCPHDILAGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHLLDCCPHDILAGTR 16 0 Q9NQ29-3;Q9NQ29;Q9NQ29-2 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 0 101.96 0.00089887 82183000 56513 124010 99044 104870 117630 116300 90565 104480 88443 FALSE TRUE 52975.95221 133191.8294 101393.3705 107561.1417 108391.8143 149873.922 76985.61901 117524.558 73681.29194 0.71898783 1.807675 1.376107392 1.459816175 1.471090034 2.034083796 1.044846215 1.595039323 1 16.16901074 -0.643631504 9.850451855 1.000021423 1.463011998 0.121702324 0.364906268 0 0 0.311211327 0.073353213 0.227179164 0.643631504 0.462990575 SHLLNCCPHDVLSGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SHLLNCCPHDVLSGTR 16 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ;; 192.85 2.71E-10 1784060000 924020 1064530 1049100 1098230 1197030 955060 1337930 1014910 1273370 FALSE TRUE 866187.2376 1143348.909 1073985.147 1126412.441 1103020.092 1230770.318 1137319.817 1141623.748 1060836.321 0.816513557 1.077780697 1.012394774 1.061815493 1.039764637 1.160188706 1.072097358 1.076154469 1 20.01677065 4.740333708 24.88497324 1.065160024 0.816513468 0.75920617 0.043518642 70.31216242 986732.1114 0.010106119 0.064971583 54996.32988 -4.740333708 -0.248646556 SHNVAAGSYEAPLPPGSFHGDFAYGT(ph)YR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SHNVAAGSYEAPLPPGSFHGDFAYGTYR 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 SHNVAAGSYEAPLPPGS(0.238)FHGDFAY(0.034)GT(0.681)Y(0.047)R;SHNVAAGSYEAPLPPGS(0.285)FHGDFAY(0.004)GT(0.706)Y(0.005)R 149.67 1.18E-07 665120000 240040 289940 240630 288070 299690 175638 359190 222720 264120 TRUE FALSE 225016.3249 311407.4593 246337.8572 295462.3639 276153.5563 226341.8394 305332.7941 250527.0823 220036.6657 1.022631043 1.415252582 1.119530949 1.342786953 1.255034271 1.028655104 1.387645068 1.138569708 1 17.74738442 0.994032787 24.6867582 0.999999982 1.237277795 0.213531739 0.137110576 241.4705429 998985.361 0.115849283 0.028962321 9.863539477 -0.994032787 0.237277813 SHPFIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SHPFIK 6 0 O14579;M0QXB4;O14579-3;O14579-2 O14579 COPE Coatomer subunit epsilon 0 ; 94.669 0.044219 827120000 2667130 2768200 2731900 2597720 2951200 2166990 3426500 2516550 3373700 FALSE TRUE 2500199.094 2973160.408 2796701.958 2664381.893 2719424.657 2792564.835 2912728.135 2830746.807 2810607.675 0.889558196 1.057835441 0.995052416 0.947973606 0.967557543 0.993580449 1.036333943 1.007165401 1 21.42245066 1.942794971 8.222161098 1.017775573 0.985074762 0.130228955 0.043427685 0.828119824 110.5349876 0.018278934 0.011533589 87.65868898 -1.942794971 -0.032700811 SHPLDPIDTVDFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SHPLDPIDTVDFER 14 0 P47897;A0A1B0GVU9;P47897-2;A0A0U1RQT0;C9J165;A0A0U1RQE9;A0A0U1RQL2;A0A0U1RRI9;A0A0U1RQM8;A0A0U1RQU2 P47897 QARS Glutamine--tRNA ligase 0 ;;;;; 227.42 2.04E-12 4058570000 2000430 2287370 2307750 2252060 2358520 1953790 2649680 2022230 2436850 FALSE TRUE 1875226.657 2456729.255 2362490.92 2309851.672 2173291.353 2517817.456 2252385.082 2274709.867 2030123.992 0.923700554 1.21013754 1.163717551 1.137788471 1.070521486 1.240228412 1.109481535 1.120478294 1 20.95313641 0.645998177 1.934469325 1.000102658 1.138084325 0.146071282 0.08663147 2.78376386 13.15332175 0.074526823 0.020659105 4.425865143 -0.645998177 0.137981667 SHPS(ph)GSGAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SHPSGSGAKK 10 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 1 SHPS(0.991)GS(0.009)GAKK;SHPS(0.975)GS(0.025)GAKK 86.288 0.0083671 74813000 153623 116855 129671 161716 195870 76551 137253 112135 180108 TRUE FALSE 144008.0107 125507.0658 132746.8574 165865.9063 180487.1603 98650.031 116673.1868 126135.3016 150046.8113 0.959753889 0.836452736 0.884702955 1.105427733 1.202872349 0.657461696 0.777578583 0.840639668 1 17.19505313 2.214878868 24.99992685 0.792837018 0.96529671 0.279193281 0.134563841 324.419482 342475.2304 0.052180572 0.038559028 164.0132249 -2.214878868 0.172459692 SHQGLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 129.56 0.0084873 979583000 676190 821609 799132 823251 776740 697507 866865 744985 782933 FALSE TRUE 633868.4749 882441.7852 818087.7884 844377.0144 715737.9736 898865.9478 736886.6408 837998.0172 652256.4244 0.971808711 1.352906238 1.254242592 1.294547639 1.097326062 1.378086768 1.129749916 1.284767748 1 19.31507972 -1.127264982 3.512952917 0.999809639 1.233198115 0.230698256 0.124577501 17727872.92 30787489.27 41092.83556 0.026442065 0.074599346 1.127264982 0.233388476 SHS(ph)ANDSEEFFREDDGGADLHNATNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHSANDSEEFFREDDGGADLHNATNLR 27 1 B0QY16;Q6ICG6-3;Q6ICG6;Q6ICG6-2 B0QY16 KIAA0930 Uncharacterized protein KIAA0930 1 S(0.053)HS(0.946)ANDS(0.001)EEFFREDDGGADLHNATNLR 129.13 3.29E-05 152730000 69795 64728 65640 79008 73121 59271 77749 62426 104070 TRUE FALSE 65426.65554 69520.52847 67197.0118 81035.47904 67378.37162 76381.57552 66091.25924 70220.02352 86700.04468 0.754632316 0.801851126 0.77505164 0.93466479 0.777143447 0.880986576 0.762297868 0.809919116 1 16.40374512 -1.451978225 2.781264261 1.00567939 0.809982823 0.525732766 0.056064844 8506567.913 9211289.861 375631.4798 0.012440663 0.035320088 1.451978225 -0.195696566 SHS(ph)DTSIASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.008)HS(0.935)DT(0.053)S(0.004)IASR;S(0.065)HS(0.921)DT(0.014)S(0.001)IASR 140.78 0.0047408 318430000 147839 156434 147040 171204 180341 130491 167105 136842 149531 TRUE FALSE 138586.0209 168016.5361 150527.8582 175597.3845 166177.7453 168161.6334 142049.1566 153927.0249 124573.3101 1.112485658 1.348736226 1.208347584 1.409590741 1.333975514 1.34990098 1.14028564 1.23563406 1 16.92663548 0.871776575 0.997002317 1.005522978 1.291057768 0.463645446 0.093364244 0.583660792 1.167908457 0.082172049 0.02699769 7.443489412 -0.871776575 0.28553479 SHS(ph)GPAGSFNKPAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SHSGPAGSFNKPAIR 15 1 Q9UJM3 Q9UJM3 ERRFI1 ERBB receptor feedback inhibitor 1 1 SHS(1)GPAGSFNKPAIR;S(0.001)HS(0.999)GPAGSFNKPAIR;S(0.032)HS(0.968)GPAGSFNKPAIR 215.81 1.38E-12 908380000 570560 597410 566980 624240 637270 353733 584750 391635 455380 TRUE FALSE 534849.6681 641642.858 580429.0333 640259.0552 587221.3848 455849.9747 497072.1661 440531.4918 379374.1361 1.409821116 1.691319457 1.529964692 1.687671863 1.547868789 1.201584218 1.31024263 1.161205918 1 18.5332618 1.839139061 0.897988954 1.053698658 1.603254149 0.769349177 0.109810639 0.244155503 0.366262491 0.088675722 0.039563035 69.04608534 -1.839139061 0.549555491 SHS(ph)GT(ph)SPDNTAPPPPPPRPQPSHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHSGTSPDNTAPPPPPPRPQPSHSR 25 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 2 S(0.423)HS(0.571)GT(0.54)S(0.466)PDNTAPPPPPPRPQPSHSR 111.89 0.037591 466300000 67806 52596 66587 55981 75191 51152 67791 39272 59303 TRUE FALSE 63562.1435 56490.26257 68166.47508 57417.56724 69285.80217 65918.75202 57626.36889 44175.19565 49404.94619 1.28655425 1.143413098 1.379750012 1.162182568 1.402406186 1.3342541 1.166408899 0.894145203 1 15.59236786 1.410424123 3.733248269 0.950667175 1.277915592 0.715719492 0.086703578 0.116830415 2.767283281 0.061462453 0.021188708 25.72907202 -1.410424123 0.327248417 SHS(ph)GTS(ph)PDNTAPPPPPPRPQPSHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHSGTSPDNTAPPPPPPRPQPSHSR 25 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 2 S(0.41)HS(0.484)GT(0.325)S(0.782)PDNTAPPPPPPRPQPSHSR 108.73 0.0043645 490080000 73379 48396 60486 68135 68342 38571 64193 37403 47743 TRUE FALSE 68786.33938 51979.2902 61920.75648 69883.45945 62974.695 49705.82155 54567.85559 42072.84688 39774.38487 1.729413028 1.306853402 1.556799852 1.756996612 1.583297773 1.249694287 1.37193462 1.057787494 1 15.279552 1.491833821 1.132905777 0.997395173 1.543976448 0.678715863 0.146752917 0.289612558 0.720197238 0.133566961 0.04703568 31.0337188 -1.491833821 0.546581275 SHS(ph)GTSPDNTAPPPPPPRPQPSHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SHSGTSPDNTAPPPPPPRPQPSHSR 25 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.056)HS(0.338)GT(0.303)S(0.303)PDNTAPPPPPPRPQPSHSR;S(0.068)HS(0.338)GT(0.297)S(0.297)PDNTAPPPPPPRPQPSHSR;S(0.055)HS(0.347)GT(0.299)S(0.299)PDNTAPPPPPPRPQPSHSR 91.599 0.0077258 1007810000 140723 136918 139886 122315 137962 154309 216686 175488 243712 TRUE FALSE 131915.3986 147055.5512 143204.162 125453.81 127127.021 198855.5033 184195.9459 197398.0631 203034.8928 0.649717873 0.724287088 0.705317988 0.617892857 0.62613386 0.979415413 0.907213255 0.972237138 1 17.63136816 2.235645922 24.99999316 0.952452775 0.676216217 0.928989257 0.041090068 20.76257117 178082.3329 0.015901251 0.01226032 172.0465315 -2.235645922 -0.276236558 SHS(ph)LAQPPEFDSGVETFSIHAEKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHSLAQPPEFDSGVETFSIHAEKPK 25 1 A0A087X0K9;G5E9E7;Q07157-2;H0Y3R8;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 S(0.144)HS(0.856)LAQPPEFDSGVETFSIHAEKPK 138.16 7.41E-06 76372000 230170 246190 205040 223350 209200 128970 390680 208790 360030 TRUE FALSE 215764.0706 264418.1638 209903.6456 229081.5391 192770.2759 166201.5453 332101.1609 234857.8911 299938.6671 0.719360637 0.881574111 0.699821892 0.763761276 0.642698982 0.554118437 1.107230235 0.78301972 1 18.194308 1.734395689 25 0.960894182 0.728255384 0.51712836 0.114446168 0.401290957 2383.274413 0.051124373 0.028351054 54.24949371 -1.734395689 -0.232638798 SHS(ph)LSRPGPTEGDAEGEAEGPVGSTLGSYATLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHSLSRPGPTEGDAEGEAEGPVGSTLGSYATLTR 34 1 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 SHS(0.89)LS(0.11)RPGPTEGDAEGEAEGPVGSTLGSYATLTR 328.15 1.91E-117 161640000 21281 24019 19887 22742 31814 20598 35674 20552 49626 TRUE FALSE 19949.0602 25797.39175 20358.72903 23325.59822 29315.45677 26544.30822 30325.01488 23117.96244 41343.1 0.482524537 0.623983004 0.492433539 0.564195675 0.709077374 0.642049295 0.733496397 0.559173416 1 15.33535895 -4.999999999 0.144384368 2.408576327 0.467916094 0.755965923 0.074005032 63.10200943 0.551167252 25.42806142 0.391592047 1.00E-05 4.999999999 -1.940660233 SHS(ph)PERK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 SHS(1)PERK;S(0.005)HS(0.995)PERK;S(0.012)HS(0.988)PERK 98.044 0.0070758 736410000 1043190 589400 843970 761570 721440 589110 779150 651960 883600 TRUE FALSE 977898.6 633039.7893 863989.367 781113.1755 664781.0125 759176.4936 662323.6908 733358.6411 736121.4517 1.328447361 0.859966501 1.173704916 1.061119974 0.903086048 1.031319617 0.899747846 0.996246801 1 19.48958429 2.853706037 6.575761245 0.960732674 1.07755262 0.230411355 0.122218488 0.412834123 21.06629773 0.034686085 0.036870968 714.0128653 -2.853706037 0.116819946 SHS(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SHSPLR 6 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 S(0.196)HS(0.804)PLR;S(0.08)HS(0.92)PLR 92.491 0.048981 238320000 505040 394720 476760 438700 430890 462150 496270 378090 368290 TRUE FALSE 473430.4479 423945.4795 488068.9723 449957.7847 397049.6375 595565.2026 421858.9206 425295.3688 306820.0198 1.543023328 1.381739952 1.590733788 1.466520291 1.294079956 1.941089773 1.374939357 1.386139565 1 18.2270331 0.832185684 1.935338744 1.002215497 1.515099053 0.464838253 0.174230601 0.519016094 3.598285905 0.150594607 0.041989125 6.794940902 -0.832185684 0.512883556 SHS(ph)SPASLQLGTGAGAAGSPAQQHAHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SHSSPASLQLGTGAGAAGSPAQQHAHLR 28 0 C9JR84;C9J038;Q9GZV5 C9JR84 WWTR1 WW domain-containing transcription regulator protein 1 1 S(0.112)HS(0.867)S(0.021)PASLQLGTGAGAAGSPAQQHAHLR;S(0.149)HS(0.758)S(0.093)PASLQLGTGAGAAGSPAQQHAHLR 313.69 1.56E-82 1478970000 137011 314460 274270 269630 369600 239280 339930 257650 312120 TRUE FALSE 128435.7261 337742.9456 280775.8139 276549.1623 340573.1069 308356.2516 288960.6523 289818.1697 260025.1556 0.493935772 1.298885659 1.079802503 1.063547723 1.309769842 1.185870847 1.111279605 1.11457743 1 17.98829168 4.746268437 24.9989807 1.154667722 0.493935456 0.812097817 0.098403179 376.7176418 1221789.767 0.021959781 0.237459716 55753.02516 -4.746268437 -0.660732266 SHS(ph)VGGPLQNIDFTQRPFHGIS(ph)TVSLPNSLQEVVDPLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHSVGGPLQNIDFTQRPFHGISTVSLPNSLQEVVDPLGK 39 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 2 S(0.339)HS(0.38)VGGPLQNIDFT(0.185)QRPFHGIS(0.398)T(0.384)VS(0.314)LPNSLQEVVDPLGK 84.014 0.00081717 69238000 24460 24641 18961 21190 28339 16414 34854 21892 52048 TRUE FALSE 22929.09226 26465.44528 19410.76387 21733.77127 26113.36925 21152.45534 29627.96627 24625.26439 43360.85256 0.528797081 0.610353434 0.447656417 0.501230257 0.60223376 0.487823788 0.68328837 0.567914673 1 15.4041055 -0.155931021 0.506597037 1.054132917 0.525991283 0.831979079 0.06388312 1.993021826 0.560629178 0.270552108 0.029490594 0.698343312 0.155931021 -0.528141634 SHS(ph)VGGPLQNIDFTQRPFHGISTVS(ph)LPNSLQEVVDPLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHSVGGPLQNIDFTQRPFHGISTVSLPNSLQEVVDPLGK 39 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 2 S(0.427)HS(0.572)VGGPLQNIDFT(0.001)QRPFHGIS(0.009)T(0.008)VS(0.982)LPNSLQEVVDPLGK 128.4 1.53E-08 60564000 31730 36116 27232 32179 42895 20196 60600 34910 69323 TRUE FALSE 29744.07594 38790.06622 27877.9559 33004.76762 39526.19973 26026.25735 51513.59258 39268.59035 57752.54346 0.515026251 0.671659877 0.482713907 0.571485958 0.684406216 0.450651275 0.891970977 0.679945644 1 15.81759686 1.183022421 0.762257264 0.987192888 0.563192489 0.592709867 0.111484515 0.392114436 0.52408319 0.095801277 0.037615176 15.24131437 -1.183022421 -0.424000399 SHS(ph)VGGPLQNIDFTQRPFHGISTVSLPNSLQEVVDPLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHSVGGPLQNIDFTQRPFHGISTVSLPNSLQEVVDPLGK 39 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.137)HS(0.862)VGGPLQNIDFT(0.001)QRPFHGISTVSLPNSLQEVVDPLGK 243.94 1.30E-50 282480000 244630 322070 263010 258420 323860 191140 437560 310890 367100 TRUE FALSE 229319.045 345916.3979 269248.7214 265051.4947 298425.342 246319.0151 371951.9401 349705.3009 305828.6384 0.749828552 1.131079155 0.880390806 0.866666693 0.975792665 0.805415138 1.2162103 1.143468129 1 18.22236398 1.723005984 11.41316684 1.132746034 0.927136599 0.429144103 0.115876811 0.095012751 41.66624145 0.051516816 0.028110704 52.84525327 -1.723005984 -0.205609435 SHSAGRT(ph)PGRT(ph)PGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHSAGRTPGRTPGK 14 2 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 2 S(0.001)HS(0.006)AGRT(0.993)PGRT(1)PGK 73.918 0.039962 131220000 317530 262630 248060 262170 324980 139660 314410 198650 500080 TRUE FALSE 297656.3641 282075.3985 253944.1003 268897.7261 299457.3817 179977.5748 267267.1393 223451.8898 416613.4174 0.714466581 0.677067484 0.609543739 0.645437028 0.718789576 0.432001389 0.64152312 0.536353081 1 18.66834978 -1.052848384 4.851585419 1.000009594 0.62226156 0.659969336 0.085291765 0.115158611 51350026.09 1074.391984 0.018587069 0.088542466 1.052848384 -0.377748034 SHSAHFFEFLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SHSAHFFEFLTK 12 0 P30046;J3KQ18;B5MC82;P30046-2;A6NHG4 P30046 DDT;DDTL D-dopachrome decarboxylase;D-dopachrome decarboxylase-like protein 0 ; 99.752 0.0020931 866930000 779360 1399620 1078540 1067950 1426360 831620 1425030 1308290 1432390 FALSE TRUE 730581.2488 1503249.321 1104123.478 1095355.405 1314339.439 1071695.194 1211359.981 1471632.886 1193314.855 0.612228403 1.259725641 0.925257465 0.917909804 1.101418819 0.898082504 1.015121848 1.233231012 1 20.18654332 1.454354687 24.79459264 1.119136006 0.986767812 0.110593819 0.173695675 22.51152608 24522.76378 0.085352128 0.039491853 28.46785118 -1.454354687 -0.132368195 SHSGTS(ph)PDNTAPPPPPPRPQPSHS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHSGTSPDNTAPPPPPPRPQPSHSR 25 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 2 S(0.211)HS(0.228)GT(0.269)S(0.292)PDNTAPPPPPPRPQPS(0.205)HS(0.795)R 66.097 0.060527 305470000 118050 87628 101700 83995 103810 93318 132210 104060 120100 TRUE FALSE 110661.4612 94116.0683 104112.372 86150.4539 95657.18135 120257.3917 112386.3379 117052.1201 100054.5341 1.106011459 0.940647709 1.040556262 0.861034981 0.95605044 1.201918461 1.123250824 1.169883215 1 16.61042702 2.248692558 25 1.13530313 0.97807041 0.42776798 0.081609932 165.5514667 408488.9585 0.02604133 0.021552439 177.2933958 -2.248692558 -0.157232721 SHSGTS(ph)PDNTAPPPPPPRPQPSHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SHSGTSPDNTAPPPPPPRPQPSHSR 25 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.006)HS(0.176)GT(0.147)S(0.67)PDNTAPPPPPPRPQPSHSR;S(0.021)HS(0.146)GT(0.128)S(0.705)PDNTAPPPPPPRPQPSHSR 134.51 2.99E-05 1680400000 98792 106207 98898 80975 109152 120920 159460 136090 182596 TRUE FALSE 92608.78507 114070.6768 101243.9073 83052.95559 100579.6422 155827.641 135550.4534 153081.1361 152119.548 0.60878951 0.749875202 0.665554878 0.545971617 0.661188148 1.024376177 0.891078465 1.006321266 1 17.21484603 2.245749365 24.98785552 0.964658007 0.658472674 0.874067704 0.062806559 58.67670463 203958.6191 0.022494937 0.018456508 176.0959487 -2.245749365 -0.306185333 SHSLS(ph)RPGPTEGDAEGEAEGPVGSTLGSYATLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHSLSRPGPTEGDAEGEAEGPVGSTLGSYATLTR 34 1 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 SHS(0.154)LS(0.843)RPGPT(0.003)EGDAEGEAEGPVGSTLGSYATLTR 193.97 4.92E-21 99793000 28332 32115 27873 24523 33548 24823 34337 24591 60116 TRUE FALSE 26558.75069 34492.82802 28534.16072 25152.3017 30913.27541 31988.99713 29188.48562 27661.24048 50082.25124 0.530302653 0.688723593 0.569745968 0.50221987 0.617250116 0.638729217 0.582810974 0.552316236 1 15.61201179 -1.61162382 2.987427192 1.028120311 0.593230439 0.852610889 0.054101668 25644220.12 26653026.52 5631027.923 0.012836599 0.024455479 1.61162382 -0.434889872 SHSTEPGLVLTLGQGDVGQLGLGENVMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHSTEPGLVLTLGQGDVGQLGLGENVMER 29 0 P18754-2;C9JW69;P18754;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4 P18754-2 RCC1 Regulator of chromosome condensation 0 209.68 1.12E-25 60152000 9819 11685 10748 12471 11832 10127 12919 10148 18613 FALSE TRUE 9204.446317 12550.16956 11002.94764 12791.02697 10902.76245 13050.5005 10981.91588 11415.00014 15506.37006 0.593591297 0.809355737 0.709575974 0.824888541 0.703115069 0.841621892 0.708219644 0.736149086 1 13.92057338 -2.335356587 2.210880285 2.394298412 0.747148119 0.556118837 0.072575888 4570346.478 442423.652 31982860.09 0.015368501 0.004620015 2.335356587 -1.647150293 SHTEEDCT(ph)EELFDFLHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHTEEDCTEELFDFLHAR 18 0 P07919 P07919 UQCRH "Cytochrome b-c1 complex subunit 6, mitochondrial" 1 S(0.315)HT(0.315)EEDCT(0.37)EELFDFLHAR 76.85 0.053535 9951600 13389 13313 11849 9903.3 13802 10011 14927 9746.5 9129.6 TRUE FALSE 12551.00639 14298.70837 12130.06388 10157.43544 12718.04659 12901.01318 12688.83493 10963.37198 7605.810781 1.650186516 1.879971614 1.594841658 1.335483585 1.672148698 1.696204857 1.668307994 1.441446848 1 12.89288633 -2.599058721 0.256965734 1.01E-14 1.716165134 0.675355523 0.138464373 28.76048008 0.850884715 16.28007378 0.206565381 0.002517337 2.599058721 1.716165134 SHTEEDCTEELFDFLHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SHTEEDCTEELFDFLHAR 18 0 P07919 P07919 UQCRH "Cytochrome b-c1 complex subunit 6, mitochondrial" 0 ;;;;; 403.89 2.23E-147 1557170000 333297 353277 325281 343272 477170 397043 407689 362922 517581 FALSE TRUE 312436.5357 379433.9967 332996.8189 352080.9407 439694.993 511662.8686 346559.8192 408233.6106 431193.3874 0.724585638 0.879962466 0.772267917 0.816526763 1.019716456 1.186620397 0.803722481 0.946752948 1 18.71797553 2.749798932 21.73908208 0.981092975 0.807595445 0.476011541 0.100103125 125.6971431 243143.6374 0.030712945 0.032210479 562.0810354 -2.749798932 -0.17349753 SHTPS(ph)PTSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SHTPSPTSPK 10 0 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 1 SHTPS(0.999)PTSPK;SHT(0.004)PS(0.987)PT(0.008)S(0.001)PK;SHT(0.001)PS(0.972)PT(0.026)SPK;SHTPS(0.997)PT(0.002)SPK;SHT(0.001)PS(0.996)PT(0.003)SPK 165.78 6.03E-06 767893000 2248980 1822590 1751910 1612870 1897420 1337136 2217420 1743900 2472690 TRUE FALSE 2108220.356 1957536.46 1793466.133 1654258.975 1748404.287 1723145.457 1884938.457 1961629.754 2059982.065 1.02341685 0.950268691 0.870622207 0.803045329 0.848747335 0.83648566 0.915026635 0.952255744 1 20.97420035 -0.281544357 6.534872595 1 0.896010161 0.188379577 0.064777906 8572500.092 1311808.307 0.063524071 0.01540685 0.522944552 0.281544357 -0.10398984 SHTPSPTS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SHTPSPTSPK 10 0 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 1 SHTPSPT(0.002)S(0.998)PK;SHTPSPT(0.047)S(0.953)PK;SHTPSPT(0.407)S(0.593)PK;SHTPS(0.01)PT(0.004)S(0.986)PK;SHTPSPT(0.01)S(0.99)PK;SHTPSPT(0.007)S(0.993)PK 145.01 3.27E-05 4069520000 8422380 5121250 6945010 6727280 6716370 4686850 7694320 4985670 7245380 TRUE FALSE 7895238.27 5500432.679 7109748.917 6899913.394 6188893.393 6039867.51 6540628.147 5608141.874 6036079.271 1.308007718 0.911259185 1.177875339 1.143111792 1.025316785 1.000627599 1.083588842 0.929103417 1 22.52518032 2.659630739 7.117822542 1.017583315 1.104780288 0.244849411 0.104554151 0.528258852 41.31720509 0.03231235 0.030451335 456.699713 -2.659630739 0.087196973 SHTSEGAHLDITPNSGAAGNSAGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SHTSEGAHLDITPNSGAAGNSAGPK 25 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 0 ;; 200.23 3.91E-25 1379720000 259176 760740 548458 717285 750394 418219 801650 626632 394943 FALSE TRUE 242954.6368 817065.9811 561467.6828 735691.7475 691461.0822 538952.0361 681450.0247 704868.3846 329024.4619 0.738409039 2.483298587 1.706461822 2.235978879 2.101549162 1.638030294 2.071122678 2.142297811 1 18.32783532 -0.942425212 6.866388364 0.999999948 1.941475173 0.248937268 0.478161424 3.28E-07 5.13E-08 0.400506698 0.09440033 0.114175991 0.942425212 0.941475224 SHVATCSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SHVATCSK 8 0 Q9Y508;A0A096LNV3;A0A096LP02;Q9Y508-2 Q9Y508 RNF114 E3 ubiquitin-protein ligase RNF114 0 ; 101.64 0.0052489 276240000 228895 296620 186846 142740 322150 118903 176025 290490 310730 FALSE TRUE 214568.8705 318582.0534 191278.0754 146402.9501 296849.6385 153228.3659 149631.6854 326758.3159 258867.1556 0.828876379 1.230677769 0.738904381 0.565552434 1.146725771 0.591918915 0.578024991 1.26226255 1 17.98185241 3.847485808 5.175933859 0.796674561 1.046690839 0.063555677 0.260094148 0.386255298 15.213836 0.062679024 0.115623759 7038.592272 -3.847485808 0.250016279 SHVEDGDIAGAPAS(ph)SPEAPPAEQDPVQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHVEDGDIAGAPASSPEAPPAEQDPVQLK 29 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 SHVEDGDIAGAPAS(0.539)S(0.461)PEAPPAEQDPVQLK 166.88 2.66E-12 298700000 128660 105160 107530 114870 126140 78200 137630 100320 129570 TRUE FALSE 120607.4003 112946.1558 110080.6624 117817.7587 116233.4732 100775.0705 116993.6592 112845.1728 107943.9299 1.117315261 1.046340965 1.019794836 1.091471829 1.0767949 0.933587193 1.083837315 1.045405452 1 16.71992259 SHVEDGDIAGAPASS(ph)PEAPPAEQDPVQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SHVEDGDIAGAPASSPEAPPAEQDPVQLK 29 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 SHVEDGDIAGAPAS(0.098)S(0.902)PEAPPAEQDPVQLK;SHVEDGDIAGAPAS(0.099)S(0.901)PEAPPAEQDPVQLK;SHVEDGDIAGAPAS(0.205)S(0.795)PEAPPAEQDPVQLK;SHVEDGDIAGAPAS(0.057)S(0.943)PEAPPAEQDPVQLK 249.04 3.10E-46 3128570000 3339480 2662600 2963850 2934130 3382410 2214720 3731590 2607490 3532110 TRUE FALSE 3130467.908 2859741.674 3034153.922 3009424.743 3116769.163 2854073.711 3172072.722 2933040.866 2942578.023 1.063852134 0.971849056 1.031120976 1.02271706 1.059196779 0.969922867 1.077991033 0.996758911 1 21.48864924 3.721716817 24.5396044 1.027111485 1.008340768 0 0.037996473 574.6280159 2609200.426 0.008948175 0.014309393 5268.861923 -3.721716817 -0.018770717 SHVLPEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SHVLPEGR 8 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 0 70.919 0.050085 57020000 82625 106500 97549 84950 104180 86823 92082 88905 112340 FALSE TRUE 77453.64874 114385.3708 99862.90835 87129.96082 95998.12304 111887.3906 78275.15895 100004.985 93589.72826 0.827587067 1.222200053 1.067028511 0.930977816 1.025733538 1.195509301 0.836364849 1.06854659 1 16.51406258 1.734528663 25 0.956700839 1.062752243 0.060418065 0.127352933 0.933149858 5722.652738 0.055535183 0.030797113 54.26610649 -1.734528663 0.106051404 SHVSSEPYEPIS(ph)PPQVPVVHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SHVSSEPYEPISPPQVPVVHEK 22 0 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 SHVSSEPYEPIS(1)PPQVPVVHEK;SHVSSEPYEPIS(1)PPQVPVVHEK;SHVSSEPYEPIS(1)PPQVPVVHEK;SHVSSEPYEPIS(1)PPQVPVVHEK;SHVSSEPYEPIS(1)PPQVPVVHEK 254.48 7.87E-37 1417660000 499962 794820 759850 802150 918180 649688 979280 775340 994420 TRUE FALSE 468670.2709 853669.2998 777874.0008 822734.527 846069.8466 837242.3788 832446.0552 872142.9057 828444.8778 0.565722939 1.030447918 0.93895686 0.993107145 1.021274763 1.010619296 1.004829745 1.052747055 1 19.66004618 4.74080911 24.99951948 1.00223824 0.565722788 0.956330895 0.029588285 39.12228069 434947.1036 0.007107132 0.047287567 55056.56479 -4.74080911 -0.436515452 SIAADHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIAADHK 7 0 K7ELV2;Q96EE3;Q96EE3-1;K7EP88;K7ENI5 K7ELV2 SEH1L Nucleoporin SEH1 0 ; 77.058 0.039078 346380000 542910 545160 602250 585700 598150 459840 632990 512350 640180 FALSE TRUE 508930.2322 585524.2136 616535.6544 600730.0536 551173.7118 592588.3431 538079.0259 576318.0253 533329.8223 0.954250467 1.097865128 1.156011962 1.126376266 1.033457513 1.111110458 1.008904815 1.080603411 1 19.02466848 1.812725959 1.25429218 1.026183603 1.093756974 0.074709978 0.060923353 0.845539575 2.48198879 0.047521587 0.01939498 64.97195861 -1.812725959 0.067573372 SICEVLDLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SICEVLDLER 10 0 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;H0Y8X0;D6RDA2 H0Y993 DEK Protein DEK 0 ;; 186.78 3.03E-06 85085000 241605 382727 234882 241842 422966 152225 219911 317238 389499 FALSE TRUE 226483.3743 411064.5053 240453.512 248048.0752 389747.9565 196169.8863 186937.3871 356845.8626 324489.1006 0.697969127 1.266805278 0.741021845 0.764426524 1.201112628 0.604550002 0.576097585 1.099716021 1 18.30781049 2.217105495 24.99774816 0.75597221 0.945541694 0.021642065 0.244368398 507.2332561 590982.9382 0.087266952 0.064510493 164.8562799 -2.217105495 0.189569484 SIEAVHEDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SIEAVHEDIR 10 0 P23919-2;P23919;H7C312;H7BZ20 P23919-2 DTYMK Thymidylate kinase 0 ;;; 160.18 7.46E-06 3073170000 2820310 3295320 3151690 3173760 3622910 2635960 3392180 3138960 3736230 FALSE TRUE 2643791.831 3539308.922 3226449.575 3255204.055 3338381.263 3396918.861 2883554.1 3530866.066 3112629.076 0.849375806 1.137080209 1.036567319 1.045805323 1.072527815 1.091334296 0.926404666 1.134367758 1 21.56970223 -2.868449714 9.342632012 0.999286694 1.038754695 0 0.089912499 15432519.29 0 0 0.018392167 0.001353787 2.868449714 0.039468001 SIEEIVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SIEEIVR 7 0 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 ;;; 158.38 0.0033101 644460000 794520 957340 954310 933800 1022320 873050 1033110 883050 1169840 FALSE TRUE 744792.4115 1028222.45 976946.6839 957762.8889 942031.111 1125085.362 878204.7464 993300.7363 974586.1465 0.764214035 1.055034953 1.002422092 0.98273805 0.966596041 1.154423717 0.901105305 1.019202602 1 19.89443019 4.745251642 24.90648907 1.008695218 0.764213917 0.588257089 0.064662577 506.4562399 1885167.344 0.01413661 0.137726465 55622.64561 -4.745251642 -0.244481301 SIEHLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SIEHLDK 7 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 ;;; 113.7 0.0060716 1778200000 4706370 4905480 5119760 4838370 5176940 4037300 6338800 4657040 5772500 FALSE TRUE 4411806.703 5268686.843 5241203.125 4962530.766 4770364.015 5202802.97 5388355.787 5238481.695 4809032.458 0.917400068 1.095581469 1.089866448 1.031918751 0.991959205 1.081881442 1.120465672 1.089300549 1 22.19731523 2.032641109 24.95533114 1.087773806 1.043428356 0.072981944 0.059922587 414.5962769 316972.1371 0.021938728 0.016202749 107.8055473 -2.032641109 -0.04434545 SIEIPRPVDGVEVPGCGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIEIPRPVDGVEVPGCGK 18 1 P26368-2;P26368;K7ENG2 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 166.76 2.27E-11 339720000 555550 460420 469480 455960 518650 392620 582700 476300 672380 FALSE TRUE 520779.1172 494509.9759 480616.2873 467660.7055 477917.3211 505963.0203 495329.5445 535767.1035 560155.4343 0.929704659 0.882808495 0.858005221 0.834876673 0.853186976 0.903254685 0.884271604 0.956461494 1 19.09546768 1.120317457 1.678588639 1.001152023 0.872274825 0.721769888 0.026560136 0.179264857 0.97882443 0.024693485 0.007227347 13.192207 -1.120317457 -0.128877199 SIESTLDDLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIESTLDDLFR 11 0 A0A087X208;A0A494C0G5;A0A494C1I6;O00468-2;O00468-6;O00468-3;O00468-5;O00468-4;O00468-7;O00468 A0A087X208 AGRN Agrin;Agrin N-terminal 110 kDa subunit;Agrin C-terminal 110 kDa subunit;Agrin C-terminal 90 kDa fragment;Agrin C-terminal 22 kDa fragment 0 ; 121.5 0.00095446 13211200 34598 40258 33939 37900 42566 26450 37322 39857 40301 FALSE TRUE 32432.57294 43238.74421 34744.04911 38872.57816 39223.03806 34085.68562 31725.91258 44833.23419 33574.50275 0.965988184 1.287844664 1.034834361 1.157800563 1.168238838 1.01522533 0.944940654 1.335335761 1 15.03507841 2.240954148 24.99195501 1.054033538 1.134998067 0.018806012 0.132933569 163.6512943 1708777.028 0.044081689 0.035267084 174.1622985 -2.240954148 0.080964529 SIEVIENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SIEVIENR 8 0 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 ;; 137.42 0.0017419 730040000 901720 1180130 1112890 1127390 1236190 1028060 1141930 1025480 1165500 FALSE TRUE 845282.9548 1267508.053 1139288.276 1156320.736 1139104.624 1324844.233 970708.1977 1153513.435 970970.5206 0.870554705 1.305403229 1.173350016 1.190891702 1.173160873 1.364453611 0.999729834 1.188000471 1 19.88906797 1.00386307 1.096780053 1.01079804 1.1852686 0.085029001 0.141417422 1.041939884 2.625160454 0.119701734 0.038531711 10.08934726 -1.00386307 0.174470561 SIFAS(ph)PESVTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIFASPESVTGK 12 0 O75940 O75940 SMNDC1 Survival of motor neuron-related-splicing factor 30 1 SIFAS(0.998)PES(0.002)VTGK;SIFAS(0.999)PES(0.001)VTGK 184.98 1.43E-05 216790000 591730 474630 568700 503900 522390 435210 635960 442680 766960 TRUE FALSE 554694.6756 509772.0991 582189.8326 516830.9271 481363.5966 560848.062 540603.702 497949.5725 638949.4212 0.8681355 0.797828564 0.911167321 0.808876117 0.753367294 0.877765975 0.846082153 0.779325493 1 19.28534221 -1.587905517 3.074821886 1.008935997 0.834686963 0.551889422 0.047907578 17637395.01 16660707.93 1252533.377 0.01097671 0.02582822 1.587905517 -0.174249034 SIFEMYEPSELESSHLTDQDNEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIFEMYEPSELESSHLTDQDNEIR 24 0 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ; 231.37 1.23E-33 87903000 104059 144776 129015 131373 148779 129193 151062 135921 151517 FALSE TRUE 97546.13294 155495.3657 132075.2967 134744.2536 137094.4975 166488.9218 128411.6555 152891.036 126227.8339 0.772778316 1.231862743 1.046324671 1.067468636 1.086087698 1.318955707 1.017300635 1.211230767 1 16.94567054 4.749750433 24.63705951 1.123989221 0.772778065 0.534324936 0.102566182 1012.224005 2228601.757 0.021945428 0.334187533 56201.82693 -4.749750433 -0.351211156 SIFGEDALANVSIEKPIHQGPDAAVTGHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIFGEDALANVSIEKPIHQGPDAAVTGHIR 30 1 P53618 P53618 COPB1 Coatomer subunit beta 0 ; 286.96 2.40E-72 953240000 594650 612520 663030 690480 695950 499200 814060 597450 730310 FALSE TRUE 557431.918 657871.6181 678757.3847 708198.8858 641292.8943 643310.9362 691999.2604 672042.9476 608416.543 0.91620112 1.081284895 1.115612967 1.164003336 1.054035926 1.057352801 1.137377457 1.104577046 1 19.21469986 4.742486907 3.745109786 1.098285794 0.896360082 0.574127565 0.046527299 0.174932831 4.674013535 0.010217974 0.098543921 55269.67455 -4.742486907 -0.201925712 SIFKPFIFVDDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SIFKPFIFVDDVK 13 1 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 141.85 3.65E-05 150160000 505230 399960 427740 421960 535070 323010 546350 411950 766490 FALSE TRUE 473608.5562 429573.4546 437886.1948 432788.208 493047.7606 416257.7434 464429.8896 463382.8643 638557.8673 0.741684631 0.672724394 0.685742385 0.677758791 0.772126985 0.651871607 0.727310575 0.725670903 1 19.28445784 -0.714405314 0.57764287 1.05524471 0.694615031 0.8711327 0.035518941 4.504792292 1.047675831 0.504322043 0.013251243 0.193016611 0.714405314 -0.360629679 SIFQHIQSAQSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SIFQHIQSAQSQR 13 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 103.21 0.0016283 323160000 260500 508990 217600 239290 473870 145110 252150 394150 493810 FALSE TRUE 244195.77 546676.1492 222761.5748 245430.5865 436654.1617 187000.9013 214342.4483 443360.4951 411389.9209 0.593587148 1.328851587 0.541485251 0.596588721 1.06141191 0.454558782 0.521020174 1.077713557 1 18.65014692 3.900179733 7.524522117 0.708787202 1.002948667 0.065756062 0.290514021 0.407380532 34.53510261 0.068592721 0.124557125 7946.570355 -3.900179733 0.294161464 SIFYVPDMKPSMFDVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIFYVPDMKPSMFDVSR 17 1 Q12931-2;Q12931;I3L0K7;I3L239 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ; 179.1 8.53E-10 440390000 1254140 1246510 998140 951560 1723390 713750 981250 1448220 1698930 FALSE TRUE 1175645.616 1338802.897 1021816.352 975978.6406 1588041.901 919798.0382 834120.672 1629033.455 1415367.607 0.830629167 0.945904718 0.721944141 0.689558413 1.121999608 0.649865119 0.589331469 1.15096138 1 20.43274538 1.221933602 24.99991797 1.075480853 0.7912999 0.358829792 0.157113962 313.0493379 470679.4657 0.148421119 0.037524278 16.6699233 -1.221933602 -0.284180953 SIGGSAS(ph)S(ph)HAQRPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SIGGSASSHAQRPSR 15 1 REV__Q08AD1-2 2 SIGGS(0.572)AS(0.752)S(0.675)HAQRPS(0.001)R 96.464 0.044113 508270000 361560 243760 575360 660980 190830 302400 468750 200360 954730 TRUE FALSE 338930.605 261808.244 589007.8109 677941.8658 175842.9816 389697.9709 398465.2892 225375.387 795379.3952 0.426124447 0.329161461 0.740536924 0.8523503 0.221080635 0.489952309 0.500975122 0.283355828 1 19.60128366 -1.331997786 3.315583414 1.003073904 0.494458428 0.412149061 0.194364017 94723687.07 131898918.1 2854517.562 0.04507011 0.046558847 1.331997786 -0.508615476 SIGS(ph)PESTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 S(0.002)IGS(0.998)PESTPK;SIGS(1)PESTPK;SIGS(1)PESTPK;SIGS(1)PESTPK 171.49 4.20E-06 1439510000 2896530 2205720 2607880 2416530 2868280 2070760 3091240 2318730 3625850 TRUE FALSE 2715241.358 2369033.804 2669740.145 2478542.251 2643016.859 2668554.796 2627737.26 2608228.545 3020672.211 0.898886462 0.784273711 0.883823189 0.820526716 0.874976387 0.883430776 0.869918043 0.863459642 1 21.52643821 -5 0.199400194 1.660682981 0.832104633 0.635711463 0.033484339 79.89326397 0.790450607 20.961482 0.07290607 1.00E-05 5 -0.828578348 SIGTANRPMGAGEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 124.46 7.51E-05 335750000 145580 225430 128200 118360 213210 92623 160190 202800 219320 FALSE TRUE 136468.4077 242121.0718 131240.9645 121397.318 196465.3466 119361.7565 136170.9966 228120.0264 182714.0751 0.746895977 1.3251364 0.718286013 0.664411419 1.075261151 0.653270726 0.745268237 1.248508229 1 17.47922825 3.885237104 7.124919135 0.842960357 1.069295789 0.062184393 0.236998923 0.40686871 26.84258604 0.055663122 0.101162454 7677.805464 -3.885237104 0.226335431 SIIECVDDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIIECVDDFR 10 0 Q9Y6Y8;Q9Y6Y8-2;H7C0V8 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 ; 163.16 1.52E-05 146286000 126344 145473 139712 135747 153455 146696 171180 134556 125415 FALSE TRUE 118436.3546 156243.9723 143026.0346 139230.4978 141403.2633 189044.7538 145513.1482 151355.6128 104482.4263 1.133552874 1.495409112 1.368900395 1.33257336 1.353368871 1.809344983 1.392704528 1.448622684 1 16.67290078 SIIPLPHPVRPEDIE ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SIIPLPHPVRPEDIE 15 1 P61599;A8MZB2 P61599 NAA20 N-alpha-acetyltransferase 20 0 87.02 0.0066873 96888000 90024 108110 105800 103860 108970 87238 122670 91739 133610 FALSE TRUE 84389.55854 116114.5769 108309.626 106525.2234 100411.9358 112422.1944 104276.7723 103192.8161 111309.6278 0.758151475 1.043167416 0.973048137 0.957017156 0.902095692 1.009995241 0.936817186 0.927078979 1 16.76421886 SIITVEELTEIERLEDLDTCMMT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIITVEELTEIERLEDLDTCMMTPK 25 1 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SIITVEELTEIERLEDLDT(0.182)CMMT(0.818)PK;SIITVEELTEIERLEDLDT(0.161)CMMT(0.839)PK 79.875 0.039183 39754000 42616 51749 46256 56648 87848 25127 43283 44767 156915 TRUE FALSE 39948.74063 55580.5498 47353.21416 58101.68358 80948.77244 32380.757 36793.11597 50356.25849 130724.8728 0.305594029 0.425171956 0.362235687 0.444457756 0.619230072 0.247701576 0.281454594 0.385207936 1 16.99617414 -1.252927492 4.295248804 1.000382703 0.380951678 0.777633787 0.103530718 296.7863934 119108614.5 78411.27937 0.024348861 0.055856344 1.252927492 -0.619431025 SIKPSDS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIKPSDSPR 9 1 Q92610;H0YM74 Q92610 ZNF592 Zinc finger protein 592 1 SIKPS(0.001)DS(0.999)PR;SIKPS(0.015)DS(0.985)PR 103.44 0.0020724 755160000 2875600 2143400 2316600 2074830 2368600 2122600 3079700 2272600 2950800 TRUE FALSE 2695621.329 2302099.566 2371550.846 2128073.65 2182579.71 2735360.162 2617927.576 2556339.113 2458292.417 1.096542181 0.936462868 0.964714706 0.865671486 0.887843812 1.112707399 1.064937416 1.039884065 1 21.22922511 2.236101225 24.99999946 1.062234565 0.94649588 0.373753312 0.066538755 62.03863821 630617.4036 0.023328811 0.018040913 172.2269955 -2.236101225 -0.115738685 SILDADPEAQALLEISGHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SILDADPEAQALLEISGHSR 20 0 Q6P9B6 Q6P9B6 TLDC1 TLD domain-containing protein 1 0 ; 189.11 2.31E-17 69034200 99420 151737 131746 141930 151704 114924 145835 117953 153672 FALSE TRUE 93197.47967 162971.7654 134871.0773 145572.1641 139789.7798 148100.6932 123968.3956 132679.6917 128023.1504 0.727973647 1.272986681 1.053489755 1.137076877 1.091910169 1.156827438 0.968327956 1.03637265 1 16.96604519 1.712974906 10.33148169 1.002858453 1.097232383 0.037365631 0.140111966 0.260590351 67.24770017 0.060056282 0.032540303 51.63865309 -1.712974906 0.09437393 SILKPSTPIPPQEGEEVGES(ph)SEEQDNAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.788)S(0.212)EEQDNAPK;SILKPSTPIPPQEGEEVGES(0.5)S(0.5)EEQDNAPK;SILKPSTPIPPQEGEEVGES(0.5)S(0.5)EEQDNAPK 192.02 1.54E-18 589250000 1441370 824000 1063500 990080 1154160 751238 1373910 980730 1608550 TRUE FALSE 1351157.225 885009.8174 1088726.722 1015487.129 1063516.929 968108.2153 1167904.95 1103176.299 1340072.613 1.00827165 0.6604193 0.812438603 0.757785152 0.793626344 0.72242967 0.871523631 0.823221285 1 20.35387975 0.700183769 0.920711984 0.999124941 0.780309611 0.295182844 0.092636877 1.0948868 1.664306654 0.079334166 0.026333621 5.013993522 -0.700183769 -0.21881533 SILPYPVS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SILPYPVSPK 10 0 Q8IWI9-3;Q8IWI9;H3BP52;H3BTF4 Q8IWI9-3 MGA MAX gene-associated protein 1 SILPYPVS(1)PK;SILPYPVS(1)PK;SILPYPVS(1)PK;SILPYPVS(1)PK 148.18 2.68E-05 674616000 1946590 1328840 1489590 1488280 1680030 1087940 1793070 1247330 1707150 TRUE FALSE 1824756.407 1427228.696 1524923.778 1526471.784 1548087.221 1402010.617 1524215.8 1403061.896 1422215.636 1.28303779 1.003524824 1.072216997 1.073305444 1.088503868 0.98579328 1.071719197 0.986532464 1 20.43970879 4.743955455 24.99861871 1.040831942 1.283037892 0.791648323 0.039864973 248.4914502 1151425.244 0.008643222 0.075020575 55456.88283 -4.743955455 0.24220595 SILS(ph)PGGSCGPIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SILSPGGSCGPIK 13 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;P78347-5 A0A494C1K3 GTF2I General transcription factor II-I 1 SILS(1)PGGSCGPIK;SILS(1)PGGSCGPIK;SILS(1)PGGSCGPIK;SILS(1)PGGSCGPIK;SILS(1)PGGSCGPIK 348.08 7.55E-76 1356421000 3842770 3515370 3322130 3110140 4486980 2504049 3670100 3728240 6071810 TRUE FALSE 3602257.885 3775651.653 3400932.492 3189951.458 4134590.69 3226927.296 3119802.577 4193718.971 5058385.686 0.712135869 0.746414348 0.672335544 0.630626381 0.817373555 0.637936191 0.616758541 0.829062715 1 22.27024561 0.983107594 4.88275258 0.999699934 0.690999402 0.743014862 0.059619222 0.080236637 6.871258871 0.056707278 0.014355301 9.618505411 -0.983107594 -0.308700532 SILVS(ph)PTGPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SILVSPTGPSR 11 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 SILVS(0.988)PT(0.012)GPSR;SILVS(0.998)PT(0.002)GPSR 142.77 3.93E-05 308940000 276100 269950 333270 299070 317370 286920 352260 257100 391130 TRUE FALSE 258819.3939 289937.3789 341175.3218 306744.6425 292445.0404 369749.1462 299441.8832 289199.5009 325847.8762 0.794295169 0.889793674 1.047038654 0.941373766 0.897489478 1.134729342 0.918962206 0.887529188 1 18.31383907 4.520259723 2.282204111 0.975953152 0.786105714 0.393340019 0.074092176 0.395402432 3.329863125 0.017757421 0.124375956 33132.92081 -4.520259723 -0.189847438 SILYDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SILYDER 7 0 A0A024RA52;P25787 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 0 ;;; 143.94 0.0055544 3245160000 6601100 9420500 7070900 6979900 9679400 5005400 7551100 8274900 9653500 FALSE TRUE 6187948.934 10118003.62 7238625.087 7159016.051 8919218.969 6450377.724 6418882.656 9308039.48 8042268.486 0.769428296 1.258103188 0.900072548 0.890173719 1.109042677 0.802059485 0.798143293 1.157389796 1 22.93917107 3.729349263 24.91077265 0.929550322 1.057796134 0 0.166102912 221.2964328 2474212.651 0.040276864 0.068393962 5362.277221 -3.729349263 0.128245812 SINHQIES(ph)PSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.986)PS(0.014)ER;SINHQIES(0.972)PS(0.028)ER 301.45 1.59E-36 1602480000 519210 834070 817830 730590 899410 682140 901600 772870 958810 TRUE FALSE 486713.5729 895825.4106 837229.3138 749338.1763 828773.9666 879062.7444 766413.45 869364.5208 798778.4169 0.609322389 1.121494261 1.048137126 0.938105187 1.037551778 1.100508884 0.959481921 1.088367565 1 19.60743583 4.745411804 24.99687908 1.038043095 0.609322192 0.839200055 0.058791052 309.550579 1129381.152 0.0138417 0.137477982 55643.16238 -4.745411804 -0.428720903 SINKLDS(ph)PDPFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SINKLDSPDPFK 12 1 P42566;B1AUU8;P42566-2 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 SINKLDS(1)PDPFK 99.055 0.0024293 156770000 1050600 466940 588170 655620 658810 512490 888510 589100 946610 TRUE FALSE 984844.8214 501512.7235 602121.6702 672444.3192 607069.7201 660437.5434 755286.174 662650.4318 788614.6757 1.24882893 0.635941403 0.763518216 0.852690598 0.769792573 0.837465449 0.957737913 0.840271494 1 19.58896103 1.875716395 5.145314428 0.924681952 0.811421642 0.016393015 0.163923439 0.562105104 20.50091683 0.07020466 0.041294231 75.11322256 -1.875716395 -0.11326031 SINNAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SINNAEK 7 0 P62244;I3L3P7;I3L246;H3BN98;H3BV27;H3BT37;I3L303 P62244 RPS15A 40S ribosomal protein S15a 0 ;; 114.89 0.013499 211815000 291609 253746 280682 263282 306454 223537 305514 268657 299422 FALSE TRUE 273357.7132 272533.6179 287339.9096 270038.2619 282386.339 288068.5031 259705.012 302199.4178 249446.5339 1.095856932 1.092553236 1.151909811 1.082549666 1.132051565 1.154830651 1.041124957 1.211479723 1 17.9283711 -1.183813897 4.843087518 0.999987088 1.115836621 0.390080923 0.046979304 5.80E-06 9.77E-07 0.040255454 0.009487244 0.065491676 1.183813897 0.115849533 SINNAEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SINNAEKR 8 1 P62244;I3L3P7;I3L246;H3BN98;H3BV27;H3BT37;I3L303 P62244 RPS15A 40S ribosomal protein S15a 0 ;; 136.57 0.0012594 850660000 383896 668230 334920 401250 759670 241274 423530 520290 948130 FALSE TRUE 359868.6346 717706.4445 342864.4606 411546.7543 700008.5826 310925.887 360025.6084 585249.3518 789880.9778 0.455598558 0.908626065 0.434071044 0.521023757 0.886220332 0.393636378 0.455797289 0.740933594 1 19.59127575 0.969365497 7.655436926 0.999988254 0.590111737 0.359721395 0.180432982 0.377760369 90.47556709 0.168777998 0.042285068 9.318918146 -0.969365497 -0.409876517 SINNPDMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SINNPDMR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;; 138.98 0.0015873 932130000 1039040 1459140 1076850 1082620 1503830 831520 1192120 1280900 1538650 FALSE TRUE 974008.3411 1567176.244 1102393.391 1110401.862 1385725.258 1071566.325 1013372.673 1440823.185 1281839.375 0.7598521 1.222599551 0.860008993 0.866256634 1.081044384 0.835959908 0.790561355 1.124027872 1 20.28978406 3.742434116 24.40112508 0.917354681 1.029386764 0 0.154531439 750.6688198 1196185.106 0.036610664 0.065670111 5526.295653 -3.742434116 0.112032083 SINPLGGFVHYGEVTNDFVMLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SINPLGGFVHYGEVTNDFVMLK 22 0 P39023;G5E9G0 P39023 RPL3 60S ribosomal protein L3 0 ;; 246.77 5.45E-31 1556060000 2391880 2609890 2309480 2048970 2842870 1837050 2884950 2627640 1884370 FALSE TRUE 2242176.5 2803128.971 2364261.956 2101550.039 2619602.458 2367376.513 2452378.53 2955706.638 1569856.474 1.428268468 1.785595702 1.506037014 1.338689284 1.668689146 1.50802099 1.562167352 1.882787814 1 20.58220123 -1.257874739 3.875790972 0.999264183 1.585847049 0.565406573 0.161190499 11314564 3672367.665 73752.94541 0.034920417 0.055223669 1.257874739 0.586582866 SIPLDEGEDEAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIPLDEGEDEAQR 13 0 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 157.68 3.00E-06 57228000 193295 170740 172521 174065 191034 138338 188635 150532 171098 FALSE TRUE 181197.011 183381.7673 176613.2796 178531.8026 176030.9602 178273.9349 160350.933 169326.2516 142540.6385 1.27119545 1.286522701 1.239038084 1.252497565 1.234952798 1.250688483 1.12494889 1.187915625 1 17.12101377 0.735307027 0.384482714 0.975922643 1.283416368 0.894297817 0.02787338 0.511770021 0.17811266 0.051903162 0.022021653 5.436345207 -0.735307027 0.307493724 SIPLDEGEDEAQRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIPLDEGEDEAQRR 14 1 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 187.11 1.58E-06 964370000 241510 320970 296310 305080 360310 264300 392310 310710 367050 FALSE TRUE 226394.3202 344734.9528 303338.6131 312908.8693 332012.706 340599.1194 333486.7575 349502.8275 305786.9838 0.740366112 1.12736961 0.991993215 1.023290349 1.085764678 1.1138444 1.090585196 1.142961754 1 18.22216747 4.744364148 24.96311352 1.072483269 0.740365965 0.800584664 0.052011719 274.7143815 1181612.468 0.012216852 0.10960162 55509.09514 -4.744364148 -0.332117304 SIQEIQELDKDDESLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SIQEIQELDKDDESLR 16 1 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;;;;;; 274.52 2.83E-35 18433700000 9509240 6781737 7762315 7410800 7807062 5954299 9502546 6497817 7986944 FALSE TRUE 8914073.643 7283863.864 7946440.777 7600973.674 7193926.843 7673208.461 8077727.445 7309083.756 6653871.449 1.339682275 1.094680581 1.194258236 1.142338522 1.081164086 1.153194576 1.213989105 1.098470839 1 22.66576256 -5 0.173367245 0.374467468 1.198123169 0.396626925 0.070880876 152.3101902 1.448441282 32.92332759 0.230289094 1.00E-05 5 0.823655701 SIQEIQELDKDDESLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SIQEIQELDKDDESLRK 17 2 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;; 328.83 3.41E-72 5119200000 9429900 5145400 6548700 6509100 6921200 4228580 8292600 5203900 8060400 FALSE TRUE 8839699.392 5526370.77 6704038.257 6676134.526 6377636.871 5449302.401 7049201.615 5853618.37 6715067.168 1.316397762 0.822980714 0.998357587 0.994202196 0.949750272 0.811503782 1.049758914 0.871714046 1 22.6789704 4.749649735 24.84417836 0.938865946 1.316398 0.69177546 0.079522427 845.4512729 1894118.219 0.017572397 0.269148706 56188.79715 -4.749649735 0.377532054 SIQFVDWCPTGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIQFVDWCPTGFK 13 0 P68363;P68363-2;P68366-2;P68366 P68363;P68366-2 TUBA1B;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 ; 256.52 1.67E-23 673650000 2570060 2380580 2462990 2303320 2858600 2099780 3029100 2633530 2930400 FALSE TRUE 2409204.532 2556840.62 2521413.286 2362427.091 2634097.087 2705952.399 2574914.576 2962332.018 2441297.309 0.986854212 1.047328652 1.032816969 0.967693317 1.078974313 1.108407562 1.054732075 1.21342534 1 21.21921657 2.555376404 7.615753978 1.094283131 1.019260529 0.334342706 0.057283143 0.347184911 30.1799877 0.01683589 0.015821038 359.2331482 -2.555376404 -0.075022603 SIRDT(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SIRDTPAK 8 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 S(0.015)IRDT(0.985)PAK 67.08 0.097037 7430700000 7570700 5456200 6267900 5110000 5581500 4317400 7567400 4465800 8364800 TRUE FALSE 7096863.401 5860182.725 6416577.548 5241131.251 5143151.505 5563763.293 6432738.622 5023364.96 6968660.841 1.018397015 0.840933841 0.920776272 0.752100206 0.738040152 0.798397772 0.923095379 0.720850831 1 22.73245001 7.999988625 1.002145646 0.832040018 183.0964241 0.270626178 0.091060614 2407.71984 3.206141349 0.025820705 1007804.372 99997380.89 -7.999988625 182.2643841 SIRPDNMSEYSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 79.614 0.023675 1598390000 770890 758640 741280 743150 786800 599224 952100 717090 1029200 FALSE TRUE 722641.371 814810.495 758863.5117 762220.4871 725007.9018 772210.2412 809341.4439 806620.265 857419.8711 0.842809218 0.950305122 0.885054729 0.888969935 0.845569279 0.900620883 0.943926624 0.940752941 1 19.70964233 1.259212821 1.245884007 0.993602845 0.89176353 0.582729951 0.031669502 0.324435844 0.994516248 0.029441079 0.009436092 18.16405552 -1.259212821 -0.101839315 SIS(ph)ADDDLQESSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SISADDDLQESSR 13 0 P18615;P18615-3;A0A0A0MT02;E9PD43;A0A0A0MSN9;P18615-4;A0A0G2JI50;A2ABK4 P18615 NELFE Negative elongation factor E 1 SIS(1)ADDDLQESSR;SIS(1)ADDDLQESSR 336.95 1.21E-62 1818750000 1278240 1302530 1239950 1197760 1217430 1126400 1682670 1222750 2049470 TRUE FALSE 1198237.24 1398970.676 1269362.2 1228496.549 1121817.959 1451573.394 1430369.255 1375413.029 1707400.217 0.701790493 0.819357209 0.743447369 0.71951294 0.657032808 0.850165872 0.837746909 0.80555983 1 20.70336984 0.799693224 0.666111804 0.999140583 0.746924892 0.667235146 0.055607911 0.644729345 0.605536001 0.058133937 0.022311614 6.305118072 -0.799693224 -0.25221569 SIS(ph)LGDSEGPIVATLAQPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SISLGDSEGPIVATLAQPLR 20 0 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 SIS(1)LGDSEGPIVATLAQPLR;S(0.178)IS(0.822)LGDSEGPIVATLAQPLR;S(0.105)IS(0.895)LGDSEGPIVATLAQPLR;S(0.002)IS(0.998)LGDSEGPIVATLAQPLR;S(0.116)IS(0.442)LGDS(0.442)EGPIVATLAQPLR;S(0.001)IS(0.999)LGDSEGPIVATLAQPLR;SIS(1)LGDSEGPIVATLAQPLR;SIS(1)LGDSEGPIVATLAQPLR 284.5 5.72E-45 1258701000 451919.5 456630.4 465786.2 441674.4 466970.2 395525.4 516564 454275.4 498377.4 TRUE FALSE 423634.6652 490439.7899 476834.8686 453008.5129 430296.2442 509707.1622 439110.0237 510992.6837 415194.9923 1.02032701 1.181227614 1.148460067 1.091074125 1.036371469 1.227633212 1.057599518 1.2307294 1 18.66342952 -2.439938532 2.03487768 2.92E-05 1.127284017 0.214197617 0.074536527 1226784.097 178381.5912 5586422.779 0.016687549 0.003631294 2.439938532 1.127254819 SIS(ph)LLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 43 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 S(0.118)IS(0.873)LLEPS(0.009)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 217.81 5.35E-44 82576000 13075 62074 40579 43489 42967 31950 49005 33297 59742 TRUE FALSE 12256.65909 66670.02355 41541.55304 44605.00137 39592.54514 41173.44634 41657.15519 37454.20375 49770.67425 0.246262669 1.339544311 0.834659238 0.89621051 0.795499473 0.827263182 0.836981934 0.752535591 1 15.60300831 SIS(ph)NEGLTLNNSHVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SISNEGLTLNNSHVSK 16 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 S(0.002)IS(0.998)NEGLTLNNSHVSK;S(0.004)IS(0.996)NEGLTLNNSHVSK;SIS(1)NEGLTLNNSHVSK;SIS(1)NEGLTLNNSHVSK 266.16 2.36E-27 3648120000 1067500 1535960 1460100 1454790 1480440 1124290 1942930 1364880 2042020 TRUE FALSE 1000687.081 1649684.077 1494734.262 1492122.374 1364172.214 1448854.272 1651605.684 1535288.272 1701193.67 0.588226431 0.969721499 0.878638504 0.877103178 0.801891189 0.851669212 0.970851063 0.902477066 1 20.69811596 4.746003347 24.92383499 0.903412927 0.588226275 0.734282399 0.060152331 461.2402796 1544539.007 0.014155379 0.148121197 55719.00426 -4.746003347 -0.315186652 SIS(ph)PEWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SISPEWK 7 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 1 SIS(1)PEWK 98.048 0.012114 90251000 347740 257510 313240 268550 311670 237330 352800 235310 380350 TRUE FALSE 325975.5741 276576.3083 320670.2007 275441.4477 287192.6954 305843.3183 299900.9152 264688.9715 316867.1278 1.028745318 0.872846326 1.012002106 0.869264823 0.906350549 0.965209993 0.946456381 0.835331116 1 18.27351848 4.762111368 23.69058615 0.929225125 1.02874555 0.239463708 0.057315965 4768.97947 4797138.589 0.012425704 0.665231694 57824.43102 -4.762111368 0.099520425 SIS(ph)PSALQDLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SISPSALQDLLR 12 0 Q92793-2;Q92793 Q92793-2 CREBBP CREB-binding protein 1 S(0.001)IS(0.999)PSALQDLLR;SIS(0.999)PS(0.001)ALQDLLR 170.79 4.22E-05 104717000 105734 137603 114177 114202 129785 92336 116711 108822 120034 TRUE FALSE 99116.29768 147791.2693 116885.3324 117132.6167 119592.2096 118991.9043 99211.26904 122408.6662 99999.54995 0.991167438 1.477919344 1.168858584 1.171331438 1.195927479 1.189924398 0.992117155 1.224092171 1 16.60963398 2.29949787 0.622793428 1.045671191 1.271263715 0.116104836 0.13651946 1.092511253 0.843328283 0.111304202 0.08330809 199.2956732 -2.29949787 0.225592524 SIS(ph)REPS(ph)PALGPNLDGSGLLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SISREPSPALGPNLDGSGLLPR 22 1 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 2 S(0.454)IS(0.546)REPS(1)PALGPNLDGSGLLPR;S(0.466)IS(0.535)REPS(1)PALGPNLDGSGLLPR 200.43 9.37E-23 498090000 340148 316503 326264 296933 286788 249670 344397 289805 251040 TRUE FALSE 318858.7439 339937.2114 334003.1362 304552.8035 264264.8273 321745.6759 292757.8671 325987.7922 209139.8022 1.524620089 1.625406584 1.597032858 1.456216369 1.26357979 1.538423928 1.399818992 1.558707567 1 17.67410813 -3.259369617 0.187061871 1.50E-15 1.619276173 0.685138877 0.105238833 36.66872917 0.644078086 14.8152787 0.314095746 0.000550339 3.259369617 1.619276173 SIS(ph)SPNVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SISSPNVNR 9 0 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 S(0.001)IS(0.899)S(0.101)PNVNR;S(0.042)IS(0.936)S(0.022)PNVNR 140.61 0.00011402 1411740000 1255340 1467970 1318780 1238030 1593490 1000350 1791200 1248890 2078340 TRUE FALSE 1176770.51 1576660.026 1350062.084 1269799.946 1468343.723 1289134.806 1522626.189 1404816.666 1731451.627 0.679643885 0.910600101 0.779728445 0.733373041 0.848042013 0.744539891 0.879392854 0.811351957 1 20.72355065 0.180718345 0.67909042 1.006129546 0.799402801 0.468425633 0.068529505 2.898284228 1.686687521 0.107930695 0.023621477 1.516066826 -0.180718345 -0.206726745 SIS(ph)TVNLSENSSVVIPPPDYLECLSMGAAADRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SISTVNLSENSSVVIPPPDYLECLSMGAAADRR 33 1 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 S(0.064)IS(0.872)T(0.064)VNLSENSSVVIPPPDYLECLSMGAAADRR;S(0.001)IS(0.95)T(0.049)VNLSENSSVVIPPPDYLECLSMGAAADRR 207.86 1.62E-27 216680000 32796.6 47625 40552 42967 48677 34337.1 55835 48263 91483 TRUE FALSE 30743.91935 51151.20455 41513.91259 44069.60596 44854.10477 44249.66335 47463.0601 54288.74179 76213.8963 0.403389944 0.671153255 0.544702667 0.578235835 0.588529218 0.580598362 0.622761234 0.712320776 1 16.21776645 0.710562792 1.060897 1.00064877 0.570311853 0.815043498 0.065815312 0.374550797 0.732858394 0.056091956 0.017806454 5.135264203 -0.710562792 -0.430336917 SISASKAS(ph)PPGDLQNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SISASKASPPGDLQNPK 17 1 O00273 O00273 DFFA DNA fragmentation factor subunit alpha 1 SISASKAS(1)PPGDLQNPK;SISASKAS(1)PPGDLQNPK;SIS(0.004)AS(0.002)KAS(0.995)PPGDLQNPK;SISAS(0.001)KAS(0.999)PPGDLQNPK;SISASKAS(1)PPGDLQNPK;SISASKAS(1)PPGDLQNPK 208.27 3.23E-12 3387780000 5857930 3823640 4514830 4575310 5253300 3099770 5833090 4206590 6620690 TRUE FALSE 5491292.618 4106746.284 4621923.9 4692720.201 4840727.009 3994623.278 4958472.306 4731792.021 5515654.068 0.995583217 0.744561975 0.837964789 0.850800312 0.877634266 0.724233831 0.898981743 0.857884117 1 22.39510055 0.664717141 1.237236982 0.999376758 0.831808538 0.27193185 0.076262606 1.290890794 3.117928297 0.065162152 0.01977249 4.62079968 -0.664717141 -0.167568221 SISEPQHS(ph)DAEGDAASPLPSEWTSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SISEPQHSDAEGDAASPLPSEWTSVR 26 0 A0A2R8YFA9 A0A2R8YFA9 1 SIS(0.001)EPQHS(0.999)DAEGDAASPLPSEWTSVR 157.42 7.09E-09 96507000 52658 70840 63132 65703 57815 55115 81768 56670 68286 TRUE FALSE 49362.22978 76085.06731 64629.52085 67389.05021 53274.44311 71025.80578 69507.6475 63745.37425 56888.62546 0.867699463 1.337439017 1.136071057 1.184578634 0.936469157 1.248506274 1.221819774 1.120529345 1 15.7958526 SISLLEPS(ph)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 43 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 S(0.01)IS(0.046)LLEPS(0.854)LELES(0.047)T(0.041)S(0.002)ETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.002)IS(0.014)LLEPS(0.984)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.005)IS(0.02)LLEPS(0.502)LELES(0.236)T(0.214)S(0.022)ET(0.001)SDMPEVFSSHESSHEEPLQPFPQLAR 220.25 4.49E-44 278038000 33790.4 150153 91875.6 105709 101341 66987.6 135083 99226.7 133093 TRUE FALSE 31675.51918 161270.4844 94054.93262 108421.6719 93382.08665 86325.83267 114828.5582 111615.3719 110878.9185 0.285676661 1.454473822 0.848267046 0.977838469 0.842198751 0.778559476 1.035621196 1.006641961 1 16.75862557 1.605589874 24.99999537 1.015855371 0.932266121 0.022931365 0.285263691 1.314821194 14224.72629 0.136866236 0.068086414 40.32643902 -1.605589874 -0.08358925 SISPS(ph)ALQDLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SISPSALQDLLR 12 0 Q92793-2;Q92793 Q92793-2 CREBBP CREB-binding protein 1 S(0.007)IS(0.369)PS(0.624)ALQDLLR 89.231 0.010007 16064000 20962 23971 21617 22411 23647 15760 20598 19726 22657 TRUE FALSE 19650.02584 25745.83778 22129.76545 22986.1042 21789.86001 20309.65616 17509.52112 22188.83452 18875.40033 1.041038892 1.363988966 1.172413038 1.217781017 1.154405185 1.075985452 0.927637073 1.175542459 1 14.20421962 2.319147244 2.309342089 1.022165806 1.221287209 0.342010723 0.099500993 0.259522742 2.840142408 0.03962367 0.029200304 208.5197731 -2.319147244 0.199121403 SISS(ph)PNVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SISSPNVNR 9 0 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 S(0.008)IS(0.266)S(0.725)PNVNR 123.38 0.0015354 0 249310 335990 289950 247930 311630 219340 351260 263440 438670 TRUE FALSE 233706.1321 360867.0492 296827.7509 254292.3035 287155.8369 282659.8973 298591.8239 296331.0639 365453.1431 0.639496845 0.987450939 0.812218356 0.695827381 0.785752818 0.773450448 0.81704544 0.810859257 1 18.47932692 0.246973576 1.931899685 1.000007383 0.806350779 0.332182422 0.090983407 23.54955309 58.20261244 0.086693031 0.023917905 1.765930374 -0.246973576 -0.193656604 SISS(ph)PSVSSETMDKPVDLSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SISSPSVSSETMDKPVDLSTR 21 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 S(0.027)IS(0.213)S(0.755)PS(0.004)VSSETMDKPVDLSTR 130.3 9.13E-06 281270000 161810 130720 156890 169480 163990 115970 161960 125550 159660 TRUE FALSE 151682.6009 140398.6448 160611.5049 173829.1437 151110.8869 149448.6564 137675.6016 141225.1939 133011.7146 1.140370241 1.055535937 1.207498944 1.306870935 1.136072017 1.123575144 1.035063731 1.061750045 1 17.02119379 1.881984449 2.201073293 1.031557541 1.165099841 0.486841478 0.064252826 0.309567181 2.771037047 0.041545664 0.020068333 76.20517232 -1.881984449 0.1335423 SITFLCGDAGPLAVAAVLYHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SITFLCGDAGPLAVAAVLYHK 21 0 O43813;E9PHS0 O43813 LANCL1 LanC-like protein 1 0 189.9 2.00E-17 119110000 351510 395670 372800 343980 454310 346390 463430 400810 455200 FALSE TRUE 329509.6166 424965.8185 381642.992 352807.1092 418630.3252 446387.1698 393942.9738 450852.0108 379224.1793 0.868904554 1.120618995 1.006378319 0.930339172 1.103912535 1.177106298 1.038812911 1.188879917 1 18.53269143 2.661426475 13.36527118 1.104972036 1.008878874 0.306041083 0.085566367 2.284162259 393.5398541 0.025930933 0.024446242 458.5920009 -2.661426475 -0.096093162 SITHDIEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 186.78 4.13E-05 3636260000 4659900 5000140 5810720 5643290 5795060 4873290 7090140 5235460 6678760 FALSE TRUE 4368245.177 5370355.568 5948553.022 5788106.375 5339939.364 6280129.712 6027039.329 5889118.706 5564031.81 0.785086306 0.965191385 1.069108378 1.040271978 0.959724809 1.12870126 1.083214391 1.058426498 1 22.40769924 5.467468463 0.974272412 1.057050373 2.61E-05 0.763632952 0.046244174 3.212441774 0.871782134 0.013702663 5.013027869 293405.6434 -5.467468463 -1.057024294 SITS(ph)PTTLYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SITSPTTLYDR 11 0 Q08999;F5H837 Q08999 RBL2 Retinoblastoma-like protein 2 1 SIT(0.161)S(0.838)PT(0.001)TLYDR;SIT(0.149)S(0.663)PT(0.171)T(0.017)LYDR 168.98 1.83E-05 236650000 452859 550850 496480 533360 571800 431520 603430 488010 549600 TRUE FALSE 424515.3636 591635.5072 508256.7401 547046.9206 526893.1345 556092.8189 512951.2735 548939.1227 457868.2094 0.927156231 1.292152403 1.110050293 1.194769388 1.150752823 1.214525943 1.120303316 1.198902023 1 18.80457287 -1.426576848 5.736875875 0.9999173 1.16112541 0.192524731 0.095279097 8.67E-05 8.66E-06 0.079331547 0.018689055 0.037447528 1.426576848 0.16120811 SITS(ph)TPLSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SITSTPLSGK 10 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 1 SITS(0.5)T(0.5)PLSGK 196.24 3.54E-07 119830000 239070 203800 254790 235240 318410 195700 216140 152610 258960 TRUE FALSE 224107.0355 218889.5641 260833.7391 241276.6567 293403.363 252195.4131 183731.8135 171663.6944 215737.9031 1.038793055 1.01460875 1.209030659 1.118378612 1.359999142 1.168989823 0.851643642 0.795704844 1 17.71892014 1.72806012 6.336701268 0.869432985 1.149327178 0.582756618 0.106974349 0.097647544 10.36650881 0.05433777 0.0281669 53.46383656 -1.72806012 0.279894193 SITSPT(ph)TLYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SITSPTTLYDR 11 0 Q08999;F5H837 Q08999 RBL2 Retinoblastoma-like protein 2 1 SIT(0.022)S(0.319)PT(0.609)T(0.049)LYDR 182.41 6.48E-05 147520000 310750 418590 361370 369370 427300 308120 447270 371440 394150 TRUE FALSE 291300.7122 449582.8391 369941.8671 378848.6595 393741.5816 397069.2421 380206.0158 417815.1016 328363.8187 0.887127922 1.36916071 1.126621893 1.153746661 1.199101604 1.209235669 1.157880357 1.272415162 1 18.32493564 -1.637544566 2.94786637 0.98421025 1.185406123 0.154030993 0.123052472 39784528.61 51311207.95 4950585.403 0.025997107 0.023038565 1.637544566 0.201195872 SITST(ph)PLSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SITSTPLSGK 10 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 1 SITS(0.022)T(0.978)PLSGK 179.94 2.29E-05 131480000 270310 223660 263510 242650 345280 208820 204360 154930 272650 TRUE FALSE 253391.7796 240220.0191 269760.5816 248876.8098 318163.1016 269102.9441 173718.1152 174273.3515 227142.9536 1.11556082 1.057571962 1.187624698 1.095683603 1.400717462 1.184729439 0.764796409 0.767240844 1 17.79324103 1.750637726 8.164155162 0.828240709 1.167757905 0.657269904 0.11186787 0.074253083 17.80678143 0.052651303 0.028348113 56.31676843 -1.750637726 0.339517195 SIVDYKPNLDLLEQQHQLIQEALIFDNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SIVDYKPNLDLLEQQHQLIQEALIFDNK 28 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;; 344.15 2.93E-97 803096000 2746853 1248599 1523035 1307470 1235227 1002027 1879172 1495674 1480731 FALSE TRUE 2574932.374 1341046.569 1559162.109 1341021.894 1138217.254 1291295.928 1597407.604 1682412.191 1233587.43 2.08735296 1.087111085 1.263925095 1.087091082 0.922688758 1.046781036 1.294928568 1.363837009 1 20.23442854 4.740762231 24.95390173 1.146539934 2.087353294 0.82475553 0.138089184 81.25510426 920913.3988 0.033329717 0.221965005 55050.62204 -4.740762231 0.940813359 SIVECQPDASATPGVGTADS(ph)PAAPTDSRDDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SIVECQPDASATPGVGTADSPAAPTDSRDDQK 32 1 Q7Z2Z1;Q7Z2Z1-2 Q7Z2Z1 TICRR Treslin 1 SIVECQPDASATPGVGT(0.001)ADS(0.991)PAAPT(0.007)DS(0.001)RDDQK 104.31 3.58E-06 61198000 31450 22359 27862 25736 31854 21071 43929 21363 39078 TRUE FALSE 29481.60064 24014.48362 28522.8998 26396.42933 29352.31533 27153.85564 37342.25427 24030.21758 32555.62935 0.905576124 0.737644583 0.876128042 0.810809985 0.901604912 0.834075586 1.147029101 0.738127877 1 14.99061941 1.881720161 19.62064019 0.981212205 0.83653596 0.194483839 0.109522957 4.75931015 773.4250428 0.040675603 0.026234495 76.15881208 -1.881720161 -0.144676244 SIVEGIIEEEEEDEEGSESISKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SIVEGIIEEEEEDEEGSESISKR 23 1 Q9Y570;Q9Y570-4;Q9Y570-2 Q9Y570 PPME1 Protein phosphatase methylesterase 1 0 228.15 1.18E-32 52799000 38958 35704 34175 36379 39447 29960 48444 35068 54523 FALSE TRUE 36519.68832 38347.56131 34985.64714 37312.54673 36348.99174 38608.96564 41180.27193 39446.31699 45422.75907 0.803995377 0.844236724 0.770222854 0.821450469 0.800237425 0.849991644 0.906599968 0.868426265 1 15.47112772 1.119279809 0.6400773 0.99684678 0.804174221 0.828668599 0.026833358 0.282583077 0.280231594 0.026294861 0.011394038 13.16072485 -1.119279809 -0.192672559 SIVIRPLEPQPAPHLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIVIRPLEPQPAPHLAR 17 1 Q15029;Q15029-3;Q15029-2;K7EP67 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ; 133.45 1.22E-05 697700000 1142500 1297610 1198370 1178390 1320930 955460 1406770 1150170 1395880 FALSE TRUE 1070992.964 1393686.395 1226795.902 1208629.482 1217189.486 1231285.791 1195837.898 1293771.256 1162898.61 0.920968479 1.198459077 1.054946572 1.0393249 1.046685821 1.058807518 1.028325159 1.112540031 1 20.14929389 3.569288355 8.34701733 1.04821193 1.093564399 0 0.072910777 0.746021345 60.66158024 0.01760612 0.027311299 3709.269214 -3.569288355 0.04535247 SIVTDLVSQMDPHGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SIVTDLVSQMDPHGR 15 0 O60313-10;O60313-9;O60313-2;E5KLJ9;O60313-13;O60313;O60313-11;A0A2R8YDM2;A0A2R8Y3X5;C9JMB8;A0A2R8YE78;A0A2R8YFD1;A0A2R8YGE5;A0A2R8YD53;A0A2R8Y4Q3;A0A2R8Y4G4 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 167.55 1.10E-09 0 165710 175220 149910 158690 220790 139760 165320 171770 191010 FALSE TRUE 155338.5069 188193.4711 153465.936 162762.2541 203450.044 180106.4432 140531.8008 193215.8626 159129.197 0.976178538 1.182645766 0.964410924 1.022830864 1.27852115 1.13182525 0.883130207 1.214207488 1 17.27983904 -1.999488934 2.557257213 0.927772731 1.072481556 0.036808183 0.123589392 42549612.36 20137233.52 18102379.54 0.028459092 0.010011775 1.999488934 0.144708825 SIYDDISS(ph)PGLGS(ph)TPLTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SIYDDISSPGLGSTPLTSR 19 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4 Q8NFH5-2 NUP35 Nucleoporin NUP53 2 SIYDDIS(0.095)S(0.905)PGLGS(0.639)T(0.356)PLT(0.003)S(0.002)R 128.99 2.98E-05 56133000 124460 144240 139700 139820 147170 125610 176830 130520 190190 TRUE FALSE 116670.2708 154919.6797 143013.75 143408.0179 135611.8619 161871.5679 150315.9831 146815.7093 158446.0603 0.736340623 0.977743968 0.90260212 0.905090462 0.855886613 1.021619392 0.948688676 0.926597411 1 17.27363226 2.24487402 24.99992625 0.969517703 0.89450546 0.333222072 0.066276818 213.3384522 844783.6677 0.02202297 0.018008407 175.7413748 -2.24487402 -0.075012243 SIYDDISS(ph)PGLGST(ph)PLTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SIYDDISSPGLGSTPLTSR 19 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4 Q8NFH5-2 NUP35 Nucleoporin NUP53 2 SIYDDIS(0.397)S(0.603)PGLGS(0.018)T(0.972)PLT(0.006)S(0.004)R 181.86 1.62E-13 66963000 77320 82180 86678 85505 91139 67109 104510 79895 117790 TRUE FALSE 72480.67922 88264.69271 88734.04309 87699.20306 83981.31058 86482.27888 88839.69572 89870.06662 98130.08805 0.738618304 0.899466152 0.904249093 0.893703499 0.855816114 0.881302367 0.905325752 0.915825802 1 16.58240793 -4.999996818 0.017218133 2.089378155 2.62E-05 0.573077751 0.042143392 3813.322004 4.976482306 390.532337 232.3396415 1.00E-05 4.999996818 -2.089351929 SIYGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 119.22 0.049314 6007990000 13163200 9526900 10920450 9546010 9364850 10044920 14623000 10634650 17065700 FALSE TRUE 12339338.81 10232281.59 11179488.23 9790976.778 8629372.457 12944725.34 12430416.9 11962409.46 14217324.42 0.867908647 0.719705149 0.786328559 0.688665215 0.606961774 0.910489552 0.874314782 0.841396673 1 23.76114665 2.206704593 24.99994103 0.894259744 0.737066969 0.549531042 0.07728341 157.4429605 123557.0462 0.02742651 0.020257523 160.9550447 -2.206704593 -0.157192776 SIYGEKFEDENFILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 262.23 4.98E-25 36888604900 29637576.1 25192721.9 26049763.5 28561313.6 36035740.4 20949561.7 38260786.7 29288979.6 58613391 FALSE TRUE 27782613.12 27058017.24 26667676.19 29294245.26 33205638.71 26997360.08 32523936.93 32945773.18 48830437.39 0.568960972 0.554121951 0.546128145 0.599917732 0.680019277 0.552879751 0.666058685 0.674697483 1 25.54127736 -4.999999999 0.18842221 2.760781014 0.520819105 0.924156373 0.037034194 31.39871971 0.306646894 20.62513695 0.096205336 1.00E-05 4.999999999 -2.239961909 SIYVGNVDYGATAEELEAHFHGCGSVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIYVGNVDYGATAEELEAHFHGCGSVNR 28 0 Q92843-2;Q86U42-2;Q86U42;B4DEH8;G3V4T2 Q92843-2 PABPN1 Polyadenylate-binding protein 2 0 ; 175.9 2.93E-13 191283000 37973 52499 40870 44568 51008 35501 48058 35731 47415 FALSE TRUE 35596.33771 56386.08059 41839.4557 45711.69033 47002.03744 45749.56239 40852.14905 40192.094 39501.13019 0.901147323 1.427454868 1.059196421 1.157224872 1.189890953 1.158183631 1.034202031 1.017492254 1 15.26960631 1.715588808 3.142932885 1.011875673 1.174175903 0.170814139 0.130232053 0.317253029 6.894732484 0.071533008 0.033032456 51.95038947 -1.715588808 0.16230023 SIYYITGESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SIYYITGESK 10 0 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 0 ; 185.81 3.28E-06 1278350000 1977710 1730830 1793740 1904130 2030850 1416600 2042840 1636860 1764150 FALSE TRUE 1853928.661 1858982.454 1836288.36 1952993.199 1871355.233 1825549.423 1736535.107 1841225.574 1469701.968 1.261431706 1.264870358 1.249429068 1.328836214 1.273288921 1.242122187 1.181555951 1.252788398 1 20.4870922 -0.172771297 0.46051849 0.961443359 1.274281368 0.863708494 0.032583832 1.922513843 0.458868823 0.163348851 0.018238532 0.671782526 0.172771297 0.31283801 SKAEELGLPILGVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKAEELGLPILGVLR 15 1 P09110;C9JDE9;H7C131 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 ; 143.67 3.99E-06 378720000 1078550 1382960 1038910 1167050 1736440 838090 1237220 1373650 1608630 FALSE TRUE 1011045.481 1485355.797 1063553.436 1196998.479 1600067.007 1080032.978 1051710.347 1545153.226 1340139.261 0.754433148 1.108359288 0.793614117 0.893189621 1.193955773 0.805911004 0.784776909 1.152979598 1 20.3539515 SKAELMEISEDKTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKAELMEISEDKTK 14 2 P05455;E7ERC4;E9PGX9;E9PFL9 P05455 SSB Lupus La protein 0 ; 168.69 1.94E-06 911790000 2943000 1582500 1986500 1907750 2234400 1258910 2614300 1781560 3158900 FALSE TRUE 2758802.883 1699669.947 2033620.718 1956706.095 2058919.237 1622336.88 2222309.985 2003991.688 2631659.183 1.048313133 0.645854888 0.772752312 0.743525646 0.782365456 0.616469219 0.844452047 0.761493624 1 21.32754123 0.269420794 1.176743639 1.000337634 0.759008244 0.250566008 0.11784649 5.310825625 7.412051948 0.103616433 0.030343668 1.859605381 -0.269420794 -0.24132939 SKAEVACIAVYETDVFVVGTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 176.84 6.02E-17 232203000 509018 580990 484273 426911 735982 459949 614222 622345 676276 FALSE TRUE 477159.472 624007.1041 495760.1843 437866.259 678180.9425 592728.8097 522125.1133 700046.1432 563401.1667 0.846926666 1.107571551 0.879941707 0.777183799 1.20372655 1.052054637 0.926737721 1.242535842 1 19.10380303 2.733978014 24.99677407 1.06500502 0.933189499 0.3281127 0.12440774 623.4867917 3400929.781 0.03933681 0.038230688 541.9734521 -2.733978014 -0.131815521 SKCEELSGLHGQLQEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SKCEELSGLHGQLQEAR 17 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;; 169.43 1.19E-09 1093390000 1764990 1691930 1631840 1711840 2026260 1219840 2261550 1603570 2188790 FALSE TRUE 1654522.426 1817202.258 1670548.015 1755768.713 1867125.713 1571988.006 1922451.573 1803779.244 1823466.809 0.9073499 0.996564483 0.916138428 0.962873963 1.023942802 0.862087535 1.054283831 0.989203223 1 20.79825251 1.667116607 14.05970545 1.016018267 0.9512892 0.309731445 0.048346506 0.15123734 32.43329243 0.020144103 0.011080517 46.46400133 -1.667116607 -0.064729068 SKDAS(ph)PINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKDASPINR 9 1 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 SKDAS(1)PINR;S(0.008)KDAS(0.992)PINR 119.25 0.00051907 1098010000 1285950 797270 1014510 929020 818250 809470 1055870 812990 824170 TRUE FALSE 1205464.685 856300.7004 1038574.656 952860.226 753987.9457 1043150.848 897552.0957 914493.5911 686610.7027 1.755674184 1.247141498 1.512610643 1.387773628 1.098130196 1.519275543 1.307221242 1.331895334 1 19.38913282 -4.289385878 0.107779844 3.52E-14 1.620248192 0.426320049 0.163574013 147.3564854 1.244411564 34.75561656 2.092803362 5.14E-05 4.289385878 1.620248192 SKDAS(ph)PINRWS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKDASPINRWSPTR 14 2 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(0.003)KDAS(0.997)PINRWS(0.999)PT(0.001)R 105.5 0.00053417 91478000 197430 156960 185090 198830 211090 145180 213290 164510 337280 TRUE FALSE 185073.2087 168581.4817 189480.4222 203932.3144 194511.8429 187091.1092 181309.1446 185049.4356 280985.7891 0.658656829 0.59996444 0.674341656 0.725774478 0.692247973 0.665838332 0.645260905 0.658572223 1 18.10013764 -1.274432149 3.12334835 1.001832082 0.661522804 0.914385899 0.032190512 5564359.971 7550455.059 96501.5835 0.008461098 0.053157904 1.274432149 -0.340309278 SKDDQVTVIGAGVTLHEALAAAELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SKDDQVTVIGAGVTLHEALAAAELLK 26 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;; 244.74 1.65E-45 1359163000 3005490 2433310 2242270 1820799 3851440 1786751 2712170 3270910 3494590 FALSE TRUE 2817381.746 2613474.804 2295457.703 1867523.785 3548963.438 2302557.008 2305505.287 3679290.314 2911320.353 0.967733332 0.897693997 0.788459333 0.641469697 1.219021958 0.79089785 0.791910545 1.263787515 1 21.47324217 1.246658742 24.9974903 1.131893784 0.862022624 0.306069997 0.162862367 177.8418837 548978.7338 0.104233468 0.036605756 17.64650657 -1.246658742 -0.26987116 GGGPLILLDLNDENS(ph)NQSFHSEGSLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GGGPLILLDLNDENSNQSFHSEGSLQK 27 0 I3L1Q2;Q8WUZ0;Q8WUZ0-2 I3L1Q2 BCL7C B-cell CLL/lymphoma 7 protein family member C 1 GGGPLILLDLNDENS(0.708)NQS(0.241)FHS(0.051)EGSLQK 115.92 0.00045387 39682000 55687 69281 77207 78114 91043 62101 114500 93988 146310 TRUE FALSE 52201.65007 74410.63733 79038.3865 80118.53749 83892.85003 80028.55057 97331.78797 105722.6087 121889.9158 0.428268817 0.610474106 0.648440734 0.657302427 0.688267356 0.656564163 0.798522071 0.867361406 1 16.89521925 2.974887564 0.097760423 1.332569728 1.53E-21 0.898023673 0.049441324 8.66861649 0.298966355 1.396106343 2.584199324 943.8164975 -2.974887564 -1.332569728 down SKDEEEDEES(ph)DDADDTPILKPVSLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKDEEEDEESDDADDTPILKPVSLLR 26 2 A0A3B3IS53;A0A3F2YNX6;Q92794;A0A3B3ITI3 A0A3B3IS53 KAT6A Histone acetyltransferase KAT6A 1 SKDEEEDEES(1)DDADDTPILKPVSLLR;S(0.002)KDEEEDEES(0.997)DDADDT(0.001)PILKPVSLLR 145.79 1.15E-07 200653000 347142 167821 236523 210625 222134 161384 299642 183486 239921 TRUE FALSE 325415.0019 180246.6415 242133.4373 216029.9941 204688.4917 207972.9409 254713.4638 206394.631 199876.6352 1.628079248 0.901789453 1.211414416 1.080816644 1.024074132 1.040506514 1.274353371 1.032610094 1 17.60875031 4.751124572 24.82016241 1.087825002 1.628079623 0.728991979 0.106348839 1011.979398 1999131.238 0.024999091 0.443862183 56379.93518 -4.751124572 0.540254621 SKDESQSLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKDESQSLLR 10 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 ; 107.09 0.0021248 568450000 320070 386270 324430 332390 447270 255440 346790 370630 494870 FALSE TRUE 300037.39 414869.8327 332125.6328 340919.6901 412143.2184 329181.3813 294792.0589 416903.9714 412273 0.72776386 1.006298818 0.805596371 0.826927037 0.999685205 0.798454862 0.715040905 1.011232779 1 18.65324046 1.198253807 24.98513844 1.005617191 0.849120051 0.330971593 0.097237674 221.1584224 137085.439 0.092799666 0.023201051 15.78533513 -1.198253807 -0.15649714 SKDEYEKS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SKDEYEKSR 9 2 Q13247;Q13247-3;A0A590UJP7 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 SKDEYEKS(1)R;SKDEYEKS(1)R;SKDEYEKS(1)R;SKDEYEKS(1)R;SKDEYEKS(1)R;SKDEYEKS(1)R 134.61 0.00019211 6694130000 9995430 4374190 6330110 5896800 4999240 5304120 8589200 4831770 5998250 TRUE FALSE 9369833.879 4698059.579 6480263.198 6048121.871 4606619.856 6835333.339 7301329.198 5435027.121 4997103.325 1.87505306 0.940156581 1.296803924 1.210325558 0.921858036 1.367859116 1.461112313 1.087635529 1 22.25266062 4.75210636 24.53484235 1.190139156 1.875053647 0.599876036 0.18194068 1362.147149 2467144.37 0.044227137 0.8606679 56507.5346 -4.75210636 0.684914491 SKDEYEKS(ph)RS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKDEYEKSRSR 11 3 Q13247;Q13247-3 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 2 SKDEY(0.002)EKS(0.999)RS(1)R 72.433 0.066479 520330000 700240 309370 444460 464300 433920 350700 536970 370600 570140 TRUE FALSE 656413.2284 332276.0767 455002.8011 476214.7241 399841.6735 451941.3969 456456.3335 416870.2258 474979.9508 1.381980918 0.69955811 0.957941068 1.002599632 0.841807476 0.951495734 0.961001265 0.877658573 1 18.85750709 -1.186819182 5.018231065 1.000005377 0.935243881 0 0.174211786 9.24E-06 1.50E-06 0.148690883 0.035043867 0.065040043 1.186819182 -0.064761496 SKDHFGLEGDEESTMLEDSVS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKDHFGLEGDEESTMLEDSVSPK 23 1 Q9Y490 Q9Y490 TLN1 Talin-1 1 SKDHFGLEGDEESTMLEDSVS(1)PK;SKDHFGLEGDEESTMLEDS(0.015)VS(0.985)PK 126.04 3.12E-05 427120000 892700 502700 726750 686270 783820 474060 881630 631420 970860 TRUE FALSE 836827.5005 539920.4311 743988.8532 703880.8501 722261.939 610913.4263 749437.7662 710254.1769 808817.194 1.034631196 0.667543216 0.919847969 0.870259504 0.892985392 0.755317062 0.92658486 0.878139315 1 19.62545414 0.736969229 0.892942721 0.999742582 0.845200659 0.135630575 0.099434728 1.5923738 2.371637691 0.087638096 0.029542878 5.457191935 -0.736969229 -0.154541923 SKDQDDQKPGPSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SKDQDDQKPGPSER 14 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 ;; 136.34 1.55E-05 1174060000 1994910 1223700 1524240 1459270 1707730 1147960 2053860 1438140 2470660 FALSE TRUE 1870052.144 1314304.021 1560395.693 1496717.339 1573611.774 1479357.416 1745902.76 1617694.945 2058290.885 0.908546094 0.638541438 0.75810261 0.72716512 0.764523511 0.718730976 0.84822936 0.785940878 1 20.97301545 0.538514607 0.606424817 1.005957771 0.735468261 0.502084276 0.072503671 1.16492155 0.763288399 0.081863097 0.027540861 3.455529516 -0.538514607 -0.27048951 SKDRDPNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKDRDPNR 8 2 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 0 ; 57.598 0.062015 11766600 17461.6 15284.5 15497.2 13241.8 16810.9 12097.3 16320.5 13968.1 18734.8 FALSE TRUE 16368.70963 16416.18028 15864.8009 13581.60701 15490.63973 15589.59413 13873.39254 15712.04803 15607.84085 1.048749137 1.0517906 1.016463523 0.870178466 0.992490882 0.998830926 0.88887327 1.006676592 1 13.92998335 3.46132597 24.84031792 0.952946353 1.042198484 0.395816795 0.046976295 184.8305519 290671.524 0.012084578 0.016378175 2892.850364 -3.46132597 0.089252131 SKDVVDYSEENFAIVFAAMGVNMETAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKDVVDYSEENFAIVFAAMGVNMETAR 27 1 P21281 P21281 ATP6V1B2 "V-type proton ATPase subunit B, brain isoform" 0 ; 221.45 2.33E-34 143988000 466410 412760 459070 454960 492540 372320 533320 412490 501270 FALSE TRUE 437218.2307 443321.1799 469959.3572 466635.0438 453857.8952 479802.7399 453353.6171 463990.2845 417604.7987 1.046966491 1.061580665 1.125368671 1.117408242 1.086811973 1.148939719 1.085604424 1.111075079 1 18.67177876 4.253759605 3.040107808 1.102963033 1.050166663 0.153370128 0.039555501 0.354173768 6.531757475 0.008620823 0.026912114 17937.40465 -4.253759605 -0.05279637 SKDVVEPLLRPQWYVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKDVVEPLLRPQWYVR 16 2 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ; 172.56 2.55E-09 1444490000 1197380 1157280 1124420 1145810 1334630 908810 1402800 1122550 1741270 FALSE TRUE 1122438.123 1242966.215 1151091.773 1175213.424 1229813.543 1171168.694 1192463.163 1262702.839 1450640.788 0.773753318 0.856839423 0.793505727 0.810134 0.847772621 0.807345763 0.822025117 0.870444874 1 20.46825889 0.823065844 2.078973896 0.999912871 0.817707985 0.855753307 0.023903389 0.212107211 1.65736364 0.020609824 0.005676587 6.653740273 -0.823065844 -0.182204886 SKDYEFMWNPHLGYILTCPSNLGTGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKDYEFMWNPHLGYILTCPSNLGTGLR 27 1 P12277;H0YJG0;H0YJK0 P12277 CKB Creatine kinase B-type 0 158.8 9.22E-12 171720000 328990 432360 284330 271930 401430 182040 385780 274570 154900 FALSE TRUE 308399.1032 464372.3843 291074.4419 278908.1842 369903.3071 234591.9928 327935.8704 308850.6689 129046.1893 2.389835026 3.598497459 2.255583396 2.161305077 2.866441149 1.817891672 2.541228626 2.393334283 1 16.97752801 -0.618388474 0.178188994 1.02E-13 3.184901902 0.534843904 0.455471069 13.04721151 0.605635827 9.527088352 1.921614855 0.240775075 0.618388474 3.184901902 SKEEACK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKEEACK 7 1 P22102;P22102-2;F8WD69;C9JBJ1;C9JTV6;H7C366 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 76.827 0.036211 141370000 228440 138570 184960 167800 175870 128810 200370 146750 216430 FALSE TRUE 214142.3482 148829.867 189347.3385 172106.0321 162057.8796 165995.3559 170326.3786 165072.0605 180306.4348 1.187657825 0.825427374 1.050141881 0.954519634 0.898791437 0.920629129 0.944649473 0.915508427 1 17.46009136 4.75590793 24.69594417 0.939004735 1.187658064 0.634372131 0.059396161 1960.402144 2790809.316 0.013417782 0.395058448 57004.3411 -4.75590793 0.248653329 SKEESSGTPAHQMNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKEESSGTPAHQMNLR 16 1 A0A0U1RRM8;H0YJ34;Q96AC1-2;Q96AC1;Q96AC1-3 A0A0U1RRM8 FERMT2 Fermitin family homolog 2 0 96.096 0.0047465 36452000 40017 49044 47465 45532 67741 44243 52762 54828 107950 FALSE TRUE 37512.4074 52675.26879 48590.89221 46700.42821 62420.89511 57015.23587 44850.82792 61673.39649 89932.44762 0.417117608 0.585720396 0.540304345 0.519283412 0.69408647 0.633978474 0.49871686 0.685774691 1 16.45655411 -5 0.218482932 3.185784512 0.511914439 0.786466194 0.073541218 68.9761562 0.690094324 66.21329919 0.138802002 1.00E-05 5 -2.673870073 SKEEVNDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKEEVNDKR 9 2 R4GMX3;P35226;Q5T8Z2 R4GMX3 COMMD3-BMI1;BMI1 Polycomb complex protein BMI-1 0 ; 77.662 0.017979 268679000 227333 144222 200762 212475 249333 138314 241557 184116 355360 FALSE TRUE 213104.6333 154900.3469 205524.1694 217927.4682 229751.3919 178243.0065 205337.7704 207103.2879 296048.1203 0.719831064 0.523226923 0.694225551 0.736121776 0.776060972 0.602074441 0.693595927 0.699559544 1 18.17547217 -5 0.236095725 2.843225907 0.634557537 0.664906462 0.071177454 100.2235338 1.001611938 88.50267782 0.116760745 1.00E-05 5 -2.20866837 SKEGHSLEMENENLVENGADS(ph)DEDDNSFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 SKEGHSLEMENENLVENGADSDEDDNSFLK 30 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(0.999)DEDDNS(0.001)FLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(1)DEDDNSFLK;SKEGHSLEMENENLVENGADS(0.987)DEDDNS(0.013)FLK 478.92 2.89E-272 16452841000 4286281 3199873 3763101 3761517 4494543 2784194 4788334 3650490 7751984 TRUE FALSE 4018010.323 3436794.926 3852363.533 3858043.894 4141559.723 3587945.61 4070367.769 4106261.712 6458127.791 0.622163335 0.532165829 0.596513983 0.597393551 0.641294173 0.55557055 0.630270552 0.635828501 1 22.62268456 -5 0.290010266 4.174124781 0.57169232 0.940363311 0.03175761 49.72037444 0.468588551 95.39091666 0.031251103 1.00E-05 5 -3.602432461 SKEGHSLEMENENLVENGADSDEDDNS(ph)FLKQQS(ph)PQEPK ddPTM_SK-BR-3_Pertuzumab_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(0.457)DEDDNS(0.543)FLKQQS(1)PQEPK 109.91 2.26E-05 156810000 54497 39637 42880 54149 69552 31163 52341 33179 142690 TRUE FALSE 51086.13005 42571.76472 43897.13385 55538.55501 64089.66648 40159.25221 44492.95296 37321.47119 118874.1172 0.429749817 0.35812476 0.36927411 0.467204774 0.539138948 0.337830077 0.374286296 0.313957925 1 16.8590751 -1.303205184 3.379915808 1.002667516 0.394436147 0.890456039 0.066265362 20342864.06 29344925.02 549012.7906 0.015782654 0.049750198 1.303205184 -0.608231369 SKEGLTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SKEGLTER 8 1 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 ;;; 121.6 0.0013007 1131300000 1800900 1753280 1810530 1807210 2002780 1392910 2073910 1727820 2073270 FALSE TRUE 1688184.884 1883094.675 1853476.627 1853586.068 1845489.738 1795020.505 1762946.449 1943542.13 1727227.843 0.977395594 1.090241037 1.0730933 1.073156663 1.068469192 1.039249403 1.02067973 1.125237842 1 20.72002697 SKEIEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKEIEAK 7 1 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 90.629 0.015502 227590000 310250 282760 279070 272160 339940 212030 398290 312100 471880 FALSE TRUE 290832.0063 303695.8446 285689.6722 279144.0864 313242.4837 273239.619 338570.112 351066.372 393120.1795 0.739804318 0.772526724 0.726723498 0.710073155 0.796811001 0.695053658 0.86123819 0.893025569 1 18.5846109 1.266880499 1.394864106 0.992763168 0.742199861 0.860454697 0.035495589 0.119503674 0.443216215 0.02915727 0.009083787 18.48759841 -1.266880499 -0.250563306 SKEIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKEIKR 6 2 Q15172;Q15172-2 Q15172 PPP2R5A Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform 0 54.525 0.091258 301530000 420660 365020 416420 357340 431180 319550 469050 367160 548210 FALSE TRUE 394331.6415 392046.4606 426297.679 366509.9494 397316.8621 411798.8975 398720.3069 413000.7342 456710.2094 0.863417619 0.85841405 0.933409567 0.802500014 0.869953975 0.901663438 0.873026919 0.904294946 1 18.80091951 0.476874466 1.038058348 1.00036581 0.873535691 0.599354324 0.03293992 1.357159478 1.992460726 0.030963985 0.009663994 2.998295729 -0.476874466 -0.126830119 SKEINQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKEINQTR 8 1 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7;E7EN38;A0A494BZX5;A0A494C122;H7C0P8 Q92878-2 RAD50 DNA repair protein RAD50 0 ; 85.533 0.015208 129628000 190678 178882 189086 185276 234700 127092 220270 183971 288880 FALSE TRUE 178743.8043 192126.6094 193571.2092 190030.4958 216267.6087 163781.3972 187242.5584 206940.1843 240664.0618 0.742710827 0.798318652 0.804321209 0.789608945 0.898628599 0.680539487 0.778024592 0.859871569 1 17.8766612 0.924832823 3.395689243 0.999714923 0.786787766 0.61775096 0.054099298 0.208223343 5.801961549 0.048572918 0.012587967 8.410713175 -0.924832823 -0.212927157 SKEITVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SKEITVR 7 1 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;; 119.27 0.0043945 1159220000 1954490 2113360 2240880 2262810 2682110 1957220 2859370 2177000 3517570 FALSE TRUE 1832161.96 2269835.373 2294034.732 2320877.536 2471467.9 2522237.641 2430634.014 2448803.242 2930464.843 0.62521206 0.774564956 0.782822813 0.791982726 0.843370602 0.860695411 0.829436333 0.835636451 1 21.4826981 7.315105497 0.069930174 1.194151051 6.86E-13 0.832254109 0.037874492 90.11377495 0.529109302 1.757357814 10.81713534 20658819.29 -7.315105497 -1.194151051 SKENMAQESSIQEQGVTSNTS(ph)DSESSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKENMAQESSIQEQGVTSNTSDSESSSK 28 1 Q92796-2;Q92796-3 Q92796-2 DLG3 Disks large homolog 3 1 SKENMAQESSIQEQGVT(0.096)S(0.061)NT(0.161)S(0.682)DS(0.001)ESSSK;SKENMAQESSIQEQGVTS(0.011)NT(0.243)S(0.732)DS(0.014)ESSSK 262.47 5.08E-54 737890000 682820 400050 503310 511480 525230 382960 614210 440230 582310 TRUE FALSE 640083.5151 429670.1183 515248.7509 524605.4427 483980.5545 493514.3352 522114.9125 495193.6846 485118.6991 1.319436905 0.885701003 1.062108618 1.081396045 0.997653884 1.017306354 1.076262188 1.020768083 1 18.88797826 4.755343585 24.96061222 1.019911217 1.319437145 0.745326698 0.055425819 1814.887569 2699161.938 0.013599411 0.384417479 56930.3148 -4.755343585 0.299525928 SKENPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKENPR 6 1 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 69.432 0.085289 15846000 53780 58203 63592 53388 65784 44844 53817 49098 73804 FALSE TRUE 50414.0058 62512.41068 65100.43227 54758.02647 60617.59 57789.73482 45747.64046 55227.99338 61485.63561 0.819931441 1.01669943 1.058790913 0.890582425 0.98588214 0.939890012 0.744037856 0.898225949 1 15.90796178 1.980694583 22.34886931 0.849726693 0.973270228 0.069278427 0.091780762 242.7731407 281044.3267 0.035499035 0.023370875 95.65211636 -1.980694583 0.123543535 SKEQAELEAAR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 194.39 4.85E-07 3013440000 4204500 4561360 4161070 4605990 5236490 3285690 5364440 4363460 5059600 FALSE TRUE 3941347.85 4899087.84 4259772.545 4724187.501 4825237.198 4234215.364 4560092.023 4908247.586 4215120.074 0.935049959 1.16226531 1.010593404 1.12077175 1.144744898 1.004530189 1.081841547 1.164438379 1 22.0071423 4.758989601 24.04492857 1.085317146 0.935049714 0.358075628 0.063570735 3109.350804 3659608.757 0.013803116 0.533078566 57410.27158 -4.758989601 -0.150267433 SKESDEPHHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKESDEPHHSK 11 1 Q8IVM0-2;Q8IVM0 Q8IVM0-2 CCDC50 Coiled-coil domain-containing protein 50 0 87.001 0.0090646 20461000 25034 51054 49391 48532 63682 39385 59549 51524 76562 FALSE TRUE 23467.16663 54834.09128 50562.57784 49777.41328 58680.6726 50754.81014 50620.18028 57956.88482 63783.30759 0.36792019 0.859693443 0.7927243 0.780414424 0.920000464 0.795738134 0.793627395 0.908652859 1 15.96089129 4.740085861 24.94969211 0.839064813 0.36792003 0.816097621 0.072455218 49.35729314 807301.3359 0.015230215 0.096664981 54964.95299 -4.740085861 -0.471144783 SKESSQVTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKESSQVTSR 10 1 A0A2R8YE10;Q9NRW7;A0A087WU65 A0A2R8YE10 VPS45 Vacuolar protein sorting-associated protein 45 0 96.64 0.0060214 48713000 56824 64213 57201 57919 81066 43358 71707 59069 91477 FALSE TRUE 53267.48727 68967.39733 58557.83473 59405.2996 74699.40336 55874.75074 60955.20105 66443.89468 76208.89774 0.698966772 0.904978282 0.768385798 0.779506086 0.980192675 0.733178833 0.799843625 0.871865316 1 16.21767183 0.911126768 3.810532996 0.999885252 0.815296627 0.35664226 0.081155002 0.420710282 14.06443599 0.070385175 0.018059071 8.149421267 -0.911126768 -0.184588624 SKESVPEFPLS(ph)PPK ddPTM_SK-BR-3_Pertuzumab_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 156.73 3.33E-06 9419000000 9625920 4910200 6325520 6525240 7407850 4904780 8610950 5592460 8100900 TRUE FALSE 9023450.85 5273756.317 6475564.322 6692688.706 6826067.343 6320710.364 7319817.988 6290690.942 6748807.456 1.337043753 0.781435291 0.959512383 0.991684642 1.011447932 0.936567002 1.084609101 0.932118894 1 22.68620116 3.133288522 4.835157871 1.000598351 0.964248361 0 0.144682813 1.393271375 53.70297835 0.039809024 0.048304997 1359.216137 -3.133288522 -0.03634999 SKESVPEFPLS(ph)PPKKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKESVPEFPLSPPKKK 16 3 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 SKESVPEFPLS(1)PPKKK 97.457 0.0021886 880970000 994520 640460 763370 924050 1353000 487580 1077100 696850 2624900 TRUE FALSE 932274.7685 687880.3248 781477.4969 947762.6874 1246740.838 628336.4308 915598.8543 783853.2565 2186787.232 0.426321662 0.314562073 0.357363298 0.433404162 0.570124436 0.287333135 0.418695903 0.358449713 1 21.06038143 -2.146468847 2.382765375 2.365323675 0.388772421 0.85517838 0.078094682 7215564.821 1806414.518 53221525.41 0.018270137 0.007137254 2.146468847 -1.976551253 SKETSSPGTDDVFTPAPSDS(ph)PSSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKETSSPGTDDVFTPAPSDSPSSQR 25 1 P19634 P19634 SLC9A1 Sodium/hydrogen exchanger 1 1 SKETSSPGTDDVFTPAPS(0.033)DS(0.961)PS(0.005)S(0.001)QR 163.75 1.07E-11 437180000 516420 466510 399830 420040 652020 396020 579140 551390 777160 TRUE FALSE 484098.194 501050.8858 409314.1564 430818.9375 600812.9793 510344.5452 492303.3335 620232.2553 647446.9754 0.747703229 0.773887137 0.632197187 0.665411924 0.927972486 0.788241454 0.760376297 0.957966102 1 19.30440252 1.23762884 0.597463548 1.007856992 0.71578864 0.562025699 0.080270683 0.573663623 0.506810323 0.081458573 0.038536138 17.28338644 -1.23762884 -0.292068353 SKEYFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SKEYFSK 7 1 Q06830;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ;;; 117.89 0.0046782 28432530000 26586190 23969350 25048980 23868770 26363780 18211050 31804510 23769630 36628110 FALSE TRUE 24922207.83 25744065.61 25643153.63 24481283.05 24293275.07 23468284.5 27035718.98 26737320.63 30514641.81 0.816729489 0.843662717 0.840355715 0.802279876 0.796118638 0.769082745 0.885991687 0.876212829 1 24.86299832 0.919240796 1.285903538 0.997760279 0.819533804 0.808283401 0.028228732 0.241132985 0.798523114 0.027514734 0.008385723 8.303110081 -0.919240796 -0.178226475 SKFDEMAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKFDEMAK 8 1 O15347;E7ES08;E7EQU1;E9PES6 O15347 HMGB3 High mobility group protein B3 0 82.287 0.018845 397790000 1364000 1908000 984370 979870 2362600 641300 1303500 1729500 3155900 FALSE TRUE 1278629.675 2049270.305 1007719.721 1005015.123 2177050.926 826432.8994 1108052.276 1945431.882 2629159.902 0.486326326 0.779439206 0.383285825 0.382257132 0.828040518 0.314333449 0.421447275 0.7399443 1 21.32617046 0.987633597 4.575881562 0.999258663 0.51975225 0.476240752 0.167846803 0.145805312 10.00919023 0.156169735 0.039655518 9.719268878 -0.987633597 -0.479506414 SKFDNLYGCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKFDNLYGCR 10 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 180.97 1.77E-06 2871400000 3136000 5118400 3064700 2860600 5854800 2063240 3304400 4944400 5545500 FALSE TRUE 2939723.358 5497371.662 3137396.131 2934007.839 5394987.625 2658863.894 2808935.897 5561719.224 4619920.225 0.636314745 1.189927833 0.679101798 0.635077598 1.167766403 0.575521603 0.608005281 1.203856117 1 22.13943651 3.878961306 9.86910712 0.799936824 0.950170407 0 0.263195589 1.040233294 96.36241539 0.062784239 0.113341978 7567.654675 -3.878961306 0.150233583 SKFDS(ph)DEEEEDTENVEAASSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKFDSDEEEEDTENVEAASSGK 22 1 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 S(0.364)KFDS(0.636)DEEEEDTENVEAASSGK;S(0.02)KFDS(0.98)DEEEEDTENVEAASSGK 330.51 5.87E-81 502120000 908500 431940 570000 636390 744070 531590 876200 537560 688950 TRUE FALSE 851638.6067 463921.287 583520.6692 652720.8448 685633.7436 685051.4034 744821.9442 604675.5493 573959.7942 1.483794885 0.808281855 1.016657743 1.137223986 1.194567547 1.193552946 1.297690103 1.053515517 1 19.13059015 3.121776455 3.973092745 1.17954482 1.02759727 0 0.188274954 0.46678514 13.62011161 0.052561338 0.064205547 1323.660031 -3.121776455 -0.15194755 SKFENEEFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKFENEEFFR 10 1 Q13951-2;A0A494C0A9;Q13951;H3BSC0;J3KRT0 Q13951-2 CBFB Core-binding factor subunit beta 0 ; 138.99 4.56E-05 332510000 484490 497990 529700 519150 628490 410050 637830 550710 710100 FALSE TRUE 454166.6357 534861.6978 542264.7341 532472.2679 579130.9306 528424.7784 542193.3128 619467.3558 591579.7226 0.767718396 0.904124461 0.916638474 0.900085394 0.978956696 0.893243562 0.916517744 1.047140955 1 19.17421308 6.011791172 0.679159666 0.947454096 1.78E-49 0.584282195 0.048249109 11.36020587 1.039880489 0.017257028 12.28571759 1027522.101 -6.011791172 -0.947454096 SKFS(ph)PQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SKFSPQK 7 1 Q9NS91;F8WE49 Q9NS91 RAD18 E3 ubiquitin-protein ligase RAD18 1 S(0.004)KFS(0.996)PQK;S(0.001)KFS(0.999)PQK;S(0.011)KFS(0.989)PQK 72.434 0.031259 1317810000 3648200 2447490 2545930 2244530 3279370 1603260 3247430 2928150 3522450 TRUE FALSE 3419865.674 2628704.706 2606320.662 2302128.44 3021821.509 2066095.135 2760508.019 3293735.973 2934530.339 1.165387738 0.895783789 0.888155978 0.784496384 1.029746215 0.704063307 0.940698408 1.122406516 1 21.48469819 1.389800102 7.039027888 1.056228801 0.899466234 0.182220742 0.127768479 0.325168303 21.03591987 0.077822959 0.028544328 24.53579315 -1.389800102 -0.156762567 SKGESDDFHMDFDSAVAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SKGESDDFHMDFDSAVAPR 19 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 ;;; 197.09 4.83E-16 1580470000 2093820 2070590 2194760 2135980 2413180 1581810 2773240 2129720 2869050 FALSE TRUE 1962771.544 2223898.638 2246820.744 2190792.863 2223658.577 2038452.868 2357418.407 2395620.23 2390187.02 0.821179066 0.930428715 0.940018804 0.91657801 0.930328279 0.852842414 0.986290356 1.002273132 1 21.18869208 1.603336012 6.89134284 0.99858702 0.909025284 0.590525266 0.037771178 0.092242729 9.497339158 0.019313135 0.009282663 40.11769867 -1.603336012 -0.089561736 SKGGVVGIKVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKGGVVGIKVDK 12 2 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 124.16 0.00018441 1542200000 6564400 4149400 6362000 7500100 5674800 4202300 8827200 3443200 9823600 FALSE TRUE 6153545.922 4456625.893 6512909.644 7692565.264 5229124.099 5415435.791 7503643.308 3873091.099 8183977.697 0.7519016 0.54455499 0.795812243 0.939954329 0.638946524 0.661711944 0.91686996 0.47325289 1 22.96437078 -2.493092558 2.303861904 4.779466142 0.723715525 0.267241424 0.147543034 4881385.935 817308.979 95194699.51 0.033943404 0.003212976 2.493092558 -4.055750616 SKGHYEVTGS(ph)DDETGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SKGHYEVTGSDDETGK 16 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 SKGHYEVTGS(1)DDETGK;SKGHYEVTGS(1)DDETGK;SKGHYEVTGS(1)DDETGK;SKGHYEVT(0.029)GS(0.971)DDETGK;SKGHYEVT(0.007)GS(0.993)DDETGK 220.36 6.98E-15 4081770000 4933990 3290864 3998480 3936700 4320400 2858902 5294700 3435755 4646960 TRUE FALSE 4625180.373 3534522.995 4093325.834 4037722.387 3981093.212 3684220.597 4500808.889 3864716.575 3871352.355 1.194719558 0.912994393 1.057337452 1.042974655 1.028346905 0.951662432 1.162593449 0.998285927 1 21.88440619 SKGHYEVTGS(ph)DDETGKLQGSGVSLASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKGHYEVTGSDDETGKLQGSGVSLASK 27 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 SKGHYEVTGS(1)DDETGKLQGSGVSLASK 332.76 1.44E-95 1208500000 2180900 1554100 1840900 2074100 2700100 1219900 2592900 1663000 3539900 TRUE FALSE 2044401.362 1669167.181 1884567.017 2127324.917 2488045.038 1572065.327 2204118.716 1870629.211 2949067.821 0.693236469 0.565998235 0.639038209 0.721355034 0.843671692 0.533071947 0.747395058 0.634312035 1 21.49182757 -5 0.253578608 3.066207952 0.636505337 0.559361949 0.090304953 133.1457726 1.31659589 142.8954276 0.119521697 1.00E-05 5 -2.429702616 SKGQENDHVHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SKGQENDHVHEK 12 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 0 ;; 158.58 4.61E-05 279411000 228294 174149 195754 195007 211898 142341 239129 172787 245039 FALSE TRUE 214005.4861 187043.1732 200397.3773 200011.2098 195256.3858 183432.536 203273.8264 194359.8373 204140.4079 1.048324966 0.91624767 0.981664431 0.979772755 0.956480825 0.898560642 0.995754973 0.952089002 1 17.63920225 -1.13736331 3.357827374 1.000045335 0.962608447 0.056167517 0.041504226 8241796.435 12066749.7 4138.717386 0.009194027 0.072884754 1.13736331 -0.037436887 SKGQESFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SKGQESFK 8 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 0 ;; 97.456 0.0074955 12185900000 12955900 13032500 10240200 9641200 15561800 6502500 13409700 12372500 19691000 FALSE TRUE 12145013.35 13997439.86 10483102.38 9888609.515 14339639 8379666.191 11399039.97 13917233.86 16404444.89 0.740348938 0.853271168 0.639040361 0.602800618 0.874131316 0.510816809 0.694875081 0.848381884 1 23.96758344 1.00871753 3.455919504 0.99838112 0.7040188 0.456282751 0.107854749 0.18547845 5.451726279 0.098995815 0.02569197 10.2027567 -1.00871753 -0.29436232 SKGYAFIEFASFEDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKGYAFIEFASFEDAK 16 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 209.31 1.15E-11 319272000 1058090 939190 906090 983830 1316880 621348 1228530 870850 2011660 FALSE TRUE 991866.0356 1008728.605 927582.8827 1009076.743 1213457.557 800721.0809 1044323.332 979577.5395 1675900.95 0.591840488 0.601902281 0.553483118 0.602110013 0.724062813 0.477785445 0.62314144 0.584508016 1 20.67650545 -1.060165013 4.020769488 1.000052391 0.592871157 0.814776011 0.060701091 10388075.26 24127667.77 9985.802731 0.013065993 0.087063272 1.060165013 -0.407181234 SKHDSSAPDPAPDS(ph)ADEVMPEAVPEVASEPGLESASHPNVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKHDSSAPDPAPDSADEVMPEAVPEVASEPGLESASHPNVDR 42 1 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(0.003)KHDS(0.003)S(0.003)APDPAPDS(0.991)ADEVMPEAVPEVASEPGLESASHPNVDR 99.619 2.22E-05 110360000 15032 28677 25083 32631 28912 22621 34782 26457 32985 TRUE FALSE 14091.17395 30800.27492 25677.98061 33468.3667 26641.36815 29151.31548 29566.762 29760.21469 27479.59041 0.512786899 1.120841849 0.934438258 1.217935428 0.969496552 1.060835152 1.075953519 1.082993387 1 14.74607288 4.742734764 24.99567347 1.055913222 0.512786685 0.822500014 0.079565772 155.7674395 932733.2642 0.016856441 0.131601697 55301.22663 -4.742734764 -0.543126538 SKHEEEEWT(ph)DDDLVESL ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SKHEEEEWTDDDLVESL 17 1 D6RHI7;P51946 D6RHI7 CCNH Cyclin-H 1 S(0.001)KHEEEEWT(0.999)DDDLVESL;S(0.003)KHEEEEWT(0.997)DDDLVESL;S(0.02)KHEEEEWT(0.98)DDDLVESL;SKHEEEEWT(1)DDDLVESL;S(0.009)KHEEEEWT(0.991)DDDLVESL 210.38 5.55E-12 2819242000 3891250 3827461 4061740 4118240 4554170 3149269 5008620 3892444 5433260 TRUE FALSE 3647703.609 4110850.195 4158086.391 4223921.011 4196503.859 4058411.836 4257623.929 4378424.202 4526413.806 0.805870556 0.908191423 0.918627101 0.933171644 0.927114497 0.896606455 0.940617476 0.96730533 1 22.10993705 5.898057944 0.900674508 0.936118104 9.82E-23 0.687189851 0.02825347 8.396535416 1.058397892 0.008049842 12.49372068 790784.1284 -5.898057944 -0.936118104 SKIEDYFPEFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKIEDYFPEFAR 12 1 P63092-4;P63092;P63092-3;A0A590UJ58;B0AZR9;A0A590UJF0;A0A590UJY2;A0A0A0MR13;P63092-2;A0A590UJB0;Q5JWF2 P63092-4;P63092-2;Q5JWF2 GNAS Guanine nucleotide-binding protein G(s) subunit alpha isoforms short;Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas 0 ; 164.88 5.12E-05 549500000 1230500 1070610 1058540 1036480 1496100 751150 1313240 1161190 1730830 FALSE TRUE 1153485.202 1149879.078 1083649.069 1063077.832 1378602.341 967994.8111 1116331.854 1306167.128 1441943.291 0.799951849 0.797450971 0.751519893 0.737253565 0.956072509 0.671312677 0.774185684 0.90583807 1 20.459583 1.055587016 3.482113258 0.997948156 0.780540472 0.511323932 0.071789616 0.153403558 3.87522004 0.062599038 0.016289427 11.36545996 -1.055587016 -0.217407684 SKIETEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SKIETEIK 8 1 Q9HB71;B2ZWH1;Q9HB71-2 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;;;; 134.68 0.00079016 3469390000 5391040 3780700 4225280 4271560 4873650 3112800 5338010 3917160 5196620 FALSE TRUE 5053624.43 4060626.962 4325505.637 4381175.461 4490893.188 4011414.828 4537624.956 4406226.049 4329270.551 1.167315457 0.937947147 0.999130358 1.011989297 1.037332533 0.926579843 1.048126908 1.017775627 1 22.04569253 SKLEVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKLEVGR 7 1 P41223;C9JCD9 P41223 BUD31 Protein BUD31 homolog 0 90.657 0.028749 0 349730 413140 368420 370330 461680 284790 420240 381370 451710 FALSE TRUE 327841.0236 443729.3155 377159.0964 379833.2948 425421.5151 367004.2498 357228.9133 428984.884 376316.6828 0.871183869 1.179138039 1.002238576 1.009344821 1.130488056 0.975253733 0.949277376 1.139957125 1 18.52158772 2.148317053 19.89449795 1.003879081 1.05157382 0 0.09521553 13.67864215 3001.915579 0.033155437 0.024486986 140.707437 -2.148317053 0.04769474 SKLNLAQFLNEDLS(ph) ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKLNLAQFLNEDLS 14 1 Q9BPX3 Q9BPX3 NCAPG Condensin complex subunit 3 1 SKLNLAQFLNEDLS(1) 100.04 0.0051072 264580000 357130 396770 363190 374220 387540 309440 462030 313170 372800 TRUE FALSE 334777.8708 426147.2636 371805.0383 383823.1188 357104.1717 398770.3047 392752.8908 352269.9639 310577.2716 1.077921346 1.372113489 1.197141814 1.235837757 1.149807807 1.283964865 1.264589932 1.134242574 1 18.24459273 0.977385115 3.675473827 1.000503073 1.238872501 0.454491855 0.07904852 0.168003657 6.20877026 0.069365954 0.01787388 9.49259856 -0.977385115 0.238369429 SKLPKPVQDLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKLPKPVQDLIK 12 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 125.53 0.00017076 143740000 709260 1086500 640720 600310 1301100 408780 759450 1066700 1460400 FALSE TRUE 664868.6827 1166945.591 655918.181 615714.9709 1198916.854 526788.15 645577.5229 1199879.843 1216649.805 0.546474984 0.959146654 0.539118305 0.506074113 0.98542477 0.432982562 0.530619016 0.986216278 1 20.21448254 1.224195303 24.51321987 0.993108726 0.654100553 0.377105253 0.186720456 233.8561194 399041.4863 0.170780699 0.043542186 16.75696269 -1.224195303 -0.339008173 SKLPNTVLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKLPNTVLGK 10 1 A0A024R571;Q9H4M9 A0A024R571 EHD1 EH domain-containing protein 1 0 96.103 0.0058137 0 328180 262510 294470 304180 369150 232440 368880 293630 479890 FALSE TRUE 307639.7996 281946.5135 301454.9675 311985.7738 340158.4481 299541.6547 313569.8685 330290.3519 399793.2588 0.769497216 0.705230785 0.75402714 0.78036777 0.850835877 0.749241384 0.784330055 0.826152879 1 18.60889462 -5 0.170134423 1.916204913 0.713884153 0.824812776 0.033732692 52.1333772 0.492243261 16.04785119 0.12250451 1.00E-05 5 -1.20232076 SKLS(ph)PSPSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SKLSPSPSLR 10 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 S(0.001)KLS(0.949)PS(0.051)PSLR;S(0.002)KLS(0.943)PS(0.055)PSLR;SKLS(0.941)PS(0.059)PSLR;SKLS(1)PSPSLR 177.38 1.41E-06 2604580000 5157300 4447000 4472300 4396100 4679500 3279490 5058400 3873080 4389990 TRUE FALSE 4834513.799 4776260.507 4578385.068 4508911.369 4311990.946 4226225.525 4299939.88 4356642.564 3657272.309 1.321890576 1.305962505 1.251857855 1.232861813 1.179018291 1.155567638 1.175723194 1.191227285 1 21.80233662 7.999999999 0.027483633 3.43E-13 2.919694963 0.937173323 0.022560763 357.6012862 0.754541925 26.53111325 59.82947678 99999999.82 -7.999999999 2.919694963 SKLTFSCLGGSDNFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKLTFSCLGGSDNFK 15 1 A0A087WYT3;Q15185-4;Q15185;Q15185-3;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 129.11 6.19E-05 485740000 577700 529840 500630 540670 764190 400870 725410 543480 945180 FALSE TRUE 541542.7882 569069.9049 512505.18 554544.5076 704173.6 516594.6614 616641.5049 611334.6743 787423.3519 0.68774032 0.722698792 0.650863578 0.704252047 0.894275739 0.656057075 0.783113053 0.776373564 1 19.58677997 -5 0.167631165 2.073702411 0.660344628 0.63975105 0.065970902 79.66110636 0.747725239 28.27204782 0.230959344 1.00E-05 5 -1.413357783 SKPAGS(ph)DGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SKPAGSDGER 10 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 SKPAGS(1)DGER;SKPAGS(1)DGER;S(0.002)KPAGS(0.998)DGER;SKPAGS(1)DGER;SKPAGS(1)DGER;SKPAGS(1)DGER 125.36 0.00024905 4955770000 8080700 5698770 6714650 6478860 6668850 5227910 7547410 5996140 7622690 TRUE FALSE 7574943.411 6120712.86 6873924.669 6645118.516 6145105.422 6737122.749 6415745.937 6744771.278 6350413.795 1.192826744 0.963828982 1.082437285 1.046407168 0.96767008 1.06089508 1.010287856 1.062099494 1 22.59841917 4.752300052 24.8044257 1.026087859 1.192826868 0.638146421 0.039882518 1343.75844 2425900.053 0.008726 0.178763991 56532.74223 -4.752300052 0.16673901 SKPAGS(ph)DGERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SKPAGSDGERR 11 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.013)KPAGS(0.987)DGERR;S(0.002)KPAGS(0.998)DGERR;S(0.004)KPAGS(0.996)DGERR;S(0.029)KPAGS(0.971)DGERR;S(0.004)KPAGS(0.996)DGERR;S(0.149)KPAGS(0.851)DGERR;S(0.008)KPAGS(0.992)DGERR 94.717 0.0065334 6128893000 3542449 3120649 3294593 3096065 3409751 2438780 3855696 2976344 3991823 TRUE FALSE 3320733.441 3351705.099 3372742.302 3175515.27 3141962.911 3142816.196 3277570.179 3347947.1 3325561.953 0.998548061 1.007861272 1.014187181 0.954880803 0.944791574 0.945048157 0.985568823 1.006731237 1 21.66516672 3.246831487 24.9999289 0.969879438 1.008124843 0.354601013 0.021372231 178.6126185 539879.6583 0.006035848 0.00804084 1765.352704 -3.246831487 0.038245405 SKPAGSDGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SKPAGSDGER 10 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;;; 128.36 0.00030242 1639736000 2935030 2414490 2649310 2447320 2762640 2012123 2852530 2482590 3077820 FALSE TRUE 2751331.711 2593261.352 2712152.884 2510122.375 2545673.398 2592990.246 2424819.608 2792546.826 2564111.959 1.073015436 1.011368222 1.05773575 0.978944139 0.992808988 1.011262491 0.945676182 1.089089272 1 21.29002783 3.239460456 24.9998593 0.996692563 1.041138172 0.205685031 0.039258441 33.5477688 932010.0955 0.010189028 0.013037337 1735.643221 -3.239460456 0.044445609 SKPAGSDGERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKPAGSDGERR 11 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 140.14 2.18E-05 254700000 670700 688130 656560 663930 797820 520380 768270 630660 1106110 FALSE TRUE 628722.0842 739079.8612 672133.9133 680967.5678 735162.4355 670605.2583 653075.0458 709399.2893 921493.0953 0.682286267 0.802046011 0.729396581 0.738982822 0.797794839 0.727737692 0.708713987 0.769836793 1 19.81361383 SKPCGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SKPCGSPR 8 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 SKPCGS(1)PR;SKPCGS(1)PR;SKPCGS(1)PR;SKPCGS(1)PR;SKPCGS(1)PR 84.658 0.010474 2560570000 4605230 4162510 4208820 4264190 5275240 3029370 4455140 4705390 5437590 TRUE FALSE 4316996.875 4470706.571 4308655.198 4373616.335 4860943.93 3903899.941 3787133.116 5292868.299 4530021.101 0.952975004 0.986906346 0.951133582 0.965473722 1.073051057 0.861784052 0.836007831 1.168398156 1 22.11108634 2.223796021 24.99976697 0.937105886 0.980373328 0 0.096497248 878.3891346 1487299.641 0.03446321 0.025562691 167.4156374 -2.223796021 0.043267441 SKPDLESS(ph)LESLVFDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SKPDLESSLESLVFDLR 17 1 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 SKPDLES(0.04)S(0.956)LES(0.004)LVFDLR;SKPDLES(0.106)S(0.894)LESLVFDLR;SKPDLES(0.031)S(0.969)LESLVFDLR;SKPDLES(0.116)S(0.884)LESLVFDLR 236.04 2.15E-20 231400000 449161 312709 368793 324013 372125 325608 465003 339434 630200 TRUE FALSE 421048.8148 335862.2997 377540.9441 332327.7221 342899.8036 419605.7438 395280.117 381813.0821 525015.5488 0.801973991 0.639718767 0.71910431 0.632986438 0.65312314 0.799225365 0.75289221 0.727241475 1 19.00200062 -0.135929222 0.463973061 1.041360929 0.687745724 0.698945636 0.059061678 2.70259912 0.670219212 0.256903463 0.030538714 0.731258249 0.135929222 -0.353615204 SKPDPEVGPLLGVQPLPGS(ph)PTADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKPDPEVGPLLGVQPLPGSPTADR 24 1 A0A6E1W9L1;Q9H5J0 A0A6E1W9L1 ZBTB3 Zinc finger and BTB domain-containing protein 3 1 SKPDPEVGPLLGVQPLPGS(0.819)PT(0.181)ADR;SKPDPEVGPLLGVQPLPGS(0.84)PT(0.16)ADR 112.06 0.0010144 260440000 219790 194529 216940 208750 237490 202450 271130 209650 386310 TRUE FALSE 206033.7362 208932.1296 222085.9192 214106.8784 218838.4934 260894.0285 230476.5735 235825.264 321832.3653 0.640189609 0.649195519 0.690067076 0.665274539 0.679976649 0.810651931 0.716138581 0.732758073 1 18.29594989 -5 0.153833426 2.130402563 0.603812873 0.890282159 0.035342889 38.79998109 0.350329024 13.31652795 0.15833167 1.00E-05 5 -1.52658969 SKPGAAMVEMADGYAVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKPGAAMVEMADGYAVDR 18 1 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 255.82 1.30E-30 1461130000 2515000 2732200 2732400 2638100 2817800 1988700 3177100 2611200 3126000 FALSE TRUE 2357590.639 2934494.931 2797213.818 2705798.112 2596501.354 2562805.406 2700723.35 2937214.068 2604250.405 0.905285696 1.12680982 1.074095568 1.038993066 0.99702446 0.984085632 1.037044419 1.127853935 1 21.31243674 3.038080978 7.481931975 1.027155067 1.060172379 0 0.068607979 0.734769576 117.1312936 0.019138724 0.022797926 1091.643865 -3.038080978 0.033017312 SKPIPIMPAS(ph)PQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SKPIPIMPASPQK 13 1 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;O00429-7;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 1 SKPIPIMPAS(1)PQK;SKPIPIMPAS(1)PQK;SKPIPIMPAS(1)PQK 184.03 5.97E-06 4276990000 14717500 8566600 10854300 10852400 11213800 7598290 12871600 9758800 9844900 TRUE FALSE 13796357.95 9200879.978 11111769.12 11130890.96 10333113.38 9791792.975 10941623.07 10977207.66 8201722.59 1.682129308 1.12182287 1.354809188 1.357140629 1.259871115 1.193870296 1.334064028 1.3384027 1 22.96749552 -3.911897266 0.255462731 3.33E-20 1.337632804 0.343812492 0.145202318 124.7539862 2.050511165 65.58438861 0.186040441 0.000122491 3.911897266 1.337632804 SKPIPIMPAS(ph)PQKGHAVNLLDVPVPVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKPIPIMPASPQKGHAVNLLDVPVPVAR 28 2 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;O00429-7;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 1 S(0.212)KPIPIMPAS(0.788)PQKGHAVNLLDVPVPVAR;SKPIPIMPAS(1)PQKGHAVNLLDVPVPVAR 139.73 6.57E-08 5241500000 460361 398318 427553 448030 533624 286088 501375 368363 627980 TRUE FALSE 431547.8268 427809.8792 437694.7591 459527.2083 491715.3236 368676.9613 426198.4733 414353.9314 523166.0811 0.824877304 0.817732446 0.83662679 0.878358183 0.939883799 0.704703486 0.814652342 0.792012224 1 18.99690948 -2.472600566 2.196712633 2.910478087 0.825042929 0.457214638 0.059534467 1640758.945 216544.2092 15557714.38 0.014099935 0.003368212 2.472600566 -2.085435158 SKPLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKPLTR 6 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 84.244 0.051138 2272530000 2490300 2466800 2633000 2525000 2839600 1972280 2950100 2573400 3369600 FALSE TRUE 2334436.568 2649444.439 2695456.003 2589795.775 2616589.27 2541645.219 2507759.892 2894694.655 2807191.992 0.831591347 0.943805927 0.960196528 0.922557411 0.932102 0.905404841 0.893333944 1.031170887 1 21.42069631 -5 0.115397585 1.247647673 0.887667153 0.31745317 0.045793788 249.7573282 1.892200258 14.32904502 0.492416355 1.00E-05 5 -0.359980519 SKPNLPSES(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKPNLPSESR 10 1 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 SKPNLPS(0.005)ES(0.995)R 85.163 0.0087373 995930000 1112500 742860 915290 769520 668230 941580 1327200 720890 509250 TRUE FALSE 1042870.611 797862.1273 937001.111 789267.186 615749.9113 1213398.861 1128198.681 810894.7034 424252.8851 2.458134399 1.880628642 2.208591017 1.860369637 1.451374718 2.860083934 2.659259891 1.911347528 1 18.69456495 2.239915669 24.9998333 2.312161739 1.986605717 0 0.566507112 99.1345267 1829007.958 0.18640846 0.148074223 173.7463417 -2.239915669 -0.325556022 SKPNLPSES(ph)RS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKPNLPSESRSR 12 2 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 2 SKPNLPS(0.159)ES(0.841)RS(1)R 81.854 0.081288 382780000 1442300 989290 1268300 1187700 986950 1151800 1659000 1058300 830850 TRUE FALSE 1352029.018 1062538.061 1298384.675 1218178.393 909438.9282 1484305.962 1410248.351 1190431.085 692175.7675 1.953303021 1.535069719 1.87580198 1.75992638 1.313884379 2.144406135 2.037413642 1.719839296 1 19.40077891 2.216524301 24.99905907 1.84790788 1.695749585 0 0.354915283 864.0021724 980159.7861 0.120025535 0.088713002 164.6358086 -2.216524301 -0.152158296 SKPPPTYES(ph)EEEDKCKPMSYEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKPPPTYESEEEDKCKPMSYEEK 23 3 O60885;O60885-2;O60885-3 O60885 BRD4 Bromodomain-containing protein 4 1 SKPPPT(0.012)YES(0.988)EEEDKCKPMSYEEK 88.595 0.004356 213640000 108060 26396 52939 44542 49222 35172 76484 34470 58951 TRUE FALSE 101296.7175 28350.38731 54194.73808 45685.02313 45356.30267 45325.58543 65015.93424 38773.65538 49111.69726 2.062578228 0.57726344 1.103499596 0.930226925 0.923533602 0.922908145 1.323838064 0.789499397 1 15.58377906 4.75131503 24.90208443 0.962501507 2.062578961 0.767797097 0.192733757 998.0021846 1948491.596 0.046653049 0.849331693 56404.66576 -4.75131503 1.100077454 SKQEALKNDLVEALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKQEALKNDLVEALK 15 2 P47756-2;B1AK88 P47756-2 CAPZB F-actin-capping protein subunit beta 0 141.85 2.64E-06 195710000 987240 605520 775310 728290 863810 499150 1033900 673270 1378300 FALSE TRUE 925450.4107 650353.3308 793700.7193 746979.1544 795969.847 643246.502 878876.2933 757329.2416 1148252.826 0.805963974 0.566385134 0.691224704 0.650535437 0.693200861 0.56019588 0.765403118 0.659549208 1 20.1310089 -0.341435455 0.649414851 1.028396 0.658630046 0.637390618 0.076738484 5.049456065 1.82378884 0.421363116 0.025757624 0.45557989 0.341435455 -0.369765954 SKRPPKS(ph)PEEEGQMS(ph)S ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SKRPPKSPEEEGQMSS 16 3 Q9BRL6-2;Q9BRL6 Q9BRL6-2 SRSF8 Serine/arginine-rich splicing factor 8 2 S(0.017)KRPPKS(0.983)PEEEGQMS(0.528)S(0.472);S(0.041)KRPPKS(0.959)PEEEGQMS(0.8)S(0.2);S(0.003)KRPPKS(0.997)PEEEGQMS(0.541)S(0.459) 97.253 0.0045024 490350000 951990 530030 657720 641970 730150 441360 835530 568250 1241410 TRUE FALSE 892406.6453 569273.9727 673321.429 658444.0371 672806.9643 568773.4671 710250.0332 639197.2634 1034210.651 0.862886728 0.550442961 0.651048631 0.636663369 0.650551185 0.549959011 0.686755674 0.618053259 1 19.98009864 -1.23523564 3.230410643 1.001214675 0.640349984 0.610292107 0.087342972 97472021.38 142731062.9 1188463.712 0.018953639 0.058178746 1.23523564 -0.36086469 SKRPPKS(ph)PEEEGQMSS(ph) ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKRPPKSPEEEGQMSS 16 3 Q9BRL6-2;Q9BRL6 Q9BRL6-2 SRSF8 Serine/arginine-rich splicing factor 8 2 S(0.001)KRPPKS(0.999)PEEEGQMS(0.019)S(0.981) 182.77 3.00E-09 247520000 514630 290140 349240 340340 399560 265710 427610 296720 671730 TRUE FALSE 482420.2269 311622.2675 357524.1377 349073.7006 368180.1693 342416.1636 363493.8502 333766.1452 559613.9235 0.862059014 0.556852241 0.638876416 0.623775939 0.657918172 0.611879278 0.649543971 0.59642216 1 19.09407233 -1.535655326 2.844099241 1.017243911 0.638959457 0.644159158 0.081486044 9942374.898 10295337.78 1313175.76 0.01764232 0.029130281 1.535655326 -0.378284454 SKS(ph)ATT(ph)TPSGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKSATTTPSGSPR 13 1 A0A096LNZ0;A0A096LP60;A0A096LP25;Q2M2I8;Q2M2I8-2 A0A096LNZ0;A0A096LP25;Q2M2I8 AAK1 AP2-associated protein kinase 1 3 S(0.001)KS(0.788)AT(0.258)T(0.549)T(0.395)PS(0.01)GS(0.998)PR;S(0.001)KS(0.994)AT(0.294)T(0.615)T(0.096)PS(0.002)GS(0.999)PR 181.29 8.76E-05 354930000 729160 629200 648810 617830 721630 485640 713760 598210 976700 TRUE FALSE 683523.1772 675786.6227 664200.0796 633684.5638 664956.0907 625836.3843 606738.3142 672897.8353 813682.4603 0.840036759 0.830528684 0.816289046 0.778786068 0.817218169 0.769140807 0.745669649 0.82697842 1 19.63410637 -0.83779116 7.628172408 1 0.80078571 0.808676434 0.030083016 2.39E-10 3.14E-11 0.03213332 0.007573896 0.145281007 0.83779116 -0.19921429 SKS(ph)DATASISLSSNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSDATASISLSSNLK 16 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 S(0.355)KS(0.638)DAT(0.007)ASISLSSNLK 197.68 1.52E-12 0 258820 191270 205030 199300 205590 124910 292580 184010 290210 TRUE FALSE 242620.9182 205431.8298 209893.4084 204414.3754 189443.7907 160969.4893 248710.3452 206984.0536 241772.0762 1.003510918 0.849692128 0.868145783 0.845483807 0.783563568 0.665790243 1.028697561 0.856112322 1 17.8832881 1.655479915 16.1325519 0.956512122 0.839819655 0.285698281 0.093322758 0.202372743 61.26345001 0.041311872 0.022808205 45.23555418 -1.655479915 -0.116692467 SKS(ph)DGEAKPEPSPSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKSDGEAKPEPSPSPR 16 2 P26358;K7EJL0;K7ENQ6;K7ERQ1 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 S(0.052)KS(0.948)DGEAKPEPSPSPR;S(0.478)KS(0.522)DGEAKPEPSPSPR 96.016 0.0018555 326960000 572150 305930 355850 407930 431380 206650 347640 196700 355500 TRUE FALSE 536340.1528 328581.3755 364290.93 418398.1744 397501.1549 266306.5003 295514.6093 221258.428 296164.7534 1.810952001 1.109454693 1.230027969 1.412721027 1.342162261 0.899183638 0.997804789 0.747078866 1 18.17604043 2.238840158 24.99999999 0.919736064 1.324869258 0.581012368 0.195067421 5.973776066 534311.6564 0.067483669 0.053201352 173.316599 -2.238840158 0.405133194 SKS(ph)DLSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SKSDLSER 8 1 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 S(0.029)KS(0.969)DLS(0.002)ER;S(0.069)KS(0.931)DLSER;S(0.348)KS(0.652)DLSER;S(0.016)KS(0.983)DLS(0.001)ER 153.38 0.00026766 5814000000 5457700 4268400 4635880 4440790 4675400 3677510 5693690 4067400 5543080 TRUE FALSE 5116112.299 4584436.777 4745845.263 4554748.19 4308212.944 4739147.438 4839974.042 4575223.843 4617904.138 1.107886207 0.992752695 1.027705453 0.986323677 0.932936851 1.026255049 1.048088894 0.990757648 1 22.13880679 4.742743032 24.29722803 1.004763172 1.107886268 0.536263034 0.031140359 245.6004436 1426706.349 0.007731013 0.057874795 55302.27935 -4.742743032 0.103123096 SKS(ph)DSYTLDPDTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SKSDSYTLDPDTLR 14 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.412)KS(0.538)DS(0.049)YTLDPDTLR;S(0.117)KS(0.614)DS(0.07)YT(0.199)LDPDTLR;S(0.017)KS(0.85)DS(0.118)YT(0.015)LDPDTLR 180.81 2.45E-06 1095010000 2336070 2148700 2227670 2563540 2862930 1816900 3261950 2221970 3474740 TRUE FALSE 2189859.549 2307791.984 2280511.384 2629324.776 2638087.026 2341409.535 2772850.88 2499387.846 2894783.446 0.756484756 0.797224396 0.78780034 0.908297572 0.911324483 0.808837545 0.957878519 0.863410992 1 21.465024 8 0.101574192 1.074247497 0.125337326 0.657265668 0.046325204 67.90760179 0.48725947 0.507847444 8.991025818 100000000 -8 -0.948910171 SKS(ph)EDMDNVQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SKSEDMDNVQSK 12 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 S(0.02)KS(0.98)EDMDNVQSK;S(0.015)KS(0.985)EDMDNVQSK;S(0.064)KS(0.936)EDMDNVQSK;SKS(1)EDMDNVQSK 229.23 2.28E-11 827200000 1869131 951323 1294009 1437870 1549661 767957 1321368 886002 1695255 TRUE FALSE 1752145.427 1021759.945 1324703.505 1474768.179 1427956.876 989653.7192 1123241.135 996621.3 1412305.989 1.240627344 0.723469243 0.937972022 1.044227094 1.011081796 0.700736049 0.795324203 0.705669528 1 20.42962126 2.242691284 24.99924405 0.781704845 0.950031068 0.25415037 0.152278104 155.7582818 942670.9989 0.051640986 0.04176134 174.8603259 -2.242691284 0.168326223 SKS(ph)EEAHAEDSVMDHHFR ddPTM_SK-BR-3_Pertuzumab_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(0.197)KS(0.803)EEAHAEDSVMDHHFR 242.09 2.53E-24 2479900000 3965700 2438200 2510800 2559500 2196500 2107300 3021500 1719900 4245100 TRUE FALSE 3717493.916 2618726.865 2570357.362 2625181.103 2023995.75 2715643.301 2568454.125 1934633.301 3536565.386 1.051159391 0.74047178 0.726794808 0.742296781 0.57230548 0.767875892 0.726256649 0.547037334 1 21.7539175 4.744525323 3.969460146 0.71611436 1.083821255 0.408983094 0.121776615 0.21789 7.083570373 0.0252228 0.233310955 55529.69946 -4.744525323 0.367706895 SKS(ph)HESQLGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SKSHESQLGNR 11 1 A8MY87;A0A2R8Y4X0;A0A0A0MQW1;A0A2R8Y5H9;Q8IVT5-4;Q8IVT5-3;Q8IVT5-2;Q8IVT5;J3QLI1 A8MY87 KSR1 Kinase suppressor of Ras 1 1 S(0.01)KS(0.985)HES(0.005)QLGNR;S(0.167)KS(0.828)HES(0.004)QLGNR;S(0.003)KS(0.994)HES(0.003)QLGNR 123.76 0.00022 378515000 203318 267395 240805 258058 327856 184406 321069 280397 327608 TRUE FALSE 190592.6893 287193.204 246517.0083 264680.2052 302107.5123 237641.0186 272927.6841 315405.1827 272928.1084 0.698325616 1.052266862 0.903230561 0.969779942 1.106912418 0.870709214 0.999998446 1.155634664 1 18.05816146 4.745302202 24.5154279 0.996252178 0.698325435 0.559935248 0.085588834 447.9398068 1628853.373 0.018963514 0.18311536 55629.12161 -4.745302202 -0.297926743 SKS(ph)KDQAEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSKDQAEEK 10 2 Q08170;A0A0D9SEM4 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 S(0.316)KS(0.684)KDQAEEK 61.167 0.073517 103050000 126110 33904 64244 58123 62995 32280 70919 47112 89818 TRUE FALSE 118217.0002 36414.28744 65767.89802 59614.53458 58047.62681 41598.71198 60285.35433 52994.03691 74826.79555 1.579875222 0.486647693 0.878935113 0.796700355 0.775759892 0.555933361 0.805665322 0.708222723 1 16.19126737 4.749227866 24.92146004 0.736888757 1.579875719 0.75711616 0.147350888 674.2855923 1575274.194 0.031929806 0.467531259 56134.24247 -4.749227866 0.842986962 SKS(ph)LDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SKSLDSR 7 1 Q9P2M7;Q9P2M7-2;A6PVU7 Q9P2M7 CGN Cingulin 1 S(0.007)KS(0.993)LDSR;S(0.216)KS(0.784)LDSR;S(0.004)KS(0.996)LDSR;S(0.309)KS(0.691)LDSR;S(0.235)KS(0.765)LDSR;S(0.033)KS(0.967)LDSR 145.89 0.0013664 3994350000 15148800 9829970 13005100 11828800 12127100 9897640 13702700 10451200 21949000 TRUE FALSE 14200663.65 10557791.21 13313587.11 12132347.03 11174686.48 12754927.99 11648107.34 11756055.33 18285570.1 0.776604917 0.577383759 0.728092536 0.66349296 0.611120486 0.697540625 0.637010893 0.642914345 1 24.12420227 -1.697788162 2.827494776 1.047246319 0.662010057 0.769545679 0.057256208 14988362.72 14080854.15 5072937.065 0.011984459 0.0200545 1.697788162 -0.385236262 SKS(ph)LENFFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSLENFFLR 10 1 Q6ZMT1;J3QKZ0 Q6ZMT1 STAC2 SH3 and cysteine-rich domain-containing protein 2 1 S(0.002)KS(0.998)LENFFLR 153.94 0.0053084 0 104780 111540 94811 97424 134400 63943 114690 114940 167440 TRUE FALSE 98222.00684 119798.5377 97059.96169 99924.06478 123844.7661 82402.30607 97493.29923 129290.512 139493.1823 0.70413482 0.858812852 0.69580434 0.716336549 0.887819491 0.590726405 0.698910854 0.926859004 1 17.08983509 1.11504944 4.632857363 0.994774246 0.739838741 0.561568938 0.084539244 0.147762164 4.878409133 0.078549784 0.020045238 13.03315138 -1.11504944 -0.254935505 SKS(ph)LKEGLTVQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSLKEGLTVQER 13 2 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;H7C3G6;J3QL44 A0A494BZV2 MPRIP Myosin phosphatase Rho-interacting protein 1 S(0.19)KS(0.81)LKEGLTVQER 69.979 0.036414 134590000 88050 75699 76625 95690 122900 44370 125990 77606 278730 TRUE FALSE 82539.10767 81303.83272 78442.58118 98145.5674 113247.9298 57178.89871 107098.9691 87295.27993 232208.1623 0.355453085 0.350133397 0.337811472 0.422662005 0.487700039 0.246239831 0.461219658 0.37593545 1 17.82505916 -5 0.367778689 9.101043202 0.360773088 0.893442667 0.067363983 144.0206043 1.119654251 926.2824499 0.043234799 1.00E-05 5 -8.740270114 SKS(ph)NPDFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSNPDFLK 9 1 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;H7C3G6;J3QL44;J3QRL2;K7EL39;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 S(0.272)KS(0.728)NPDFLK 68.033 0.035861 154520000 923950 562210 686340 640410 729320 510400 921830 676550 953470 TRUE FALSE 866121.6188 603836.6134 702620.3089 656844.0048 672042.1491 657744.1943 783610.1494 761018.7568 794329.6973 1.090380508 0.760183857 0.884544933 0.826916087 0.846049381 0.828049356 0.986504913 0.958064088 1 19.59937842 1.700626815 6.653341142 0.978814969 0.85839915 0.24885582 0.086471915 0.155169689 15.42067002 0.039331181 0.020216727 50.19111163 -1.700626815 -0.120415819 SKS(ph)NPDFLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKSNPDFLKK 10 2 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;H7C3G6;J3QL44;J3QRL2;K7EL39;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 S(0.066)KS(0.934)NPDFLKK;S(0.042)KS(0.958)NPDFLKK 103.14 0.0022479 2157600000 2242130 1197560 1471680 1461160 1724260 1028870 2129900 1441130 3014400 TRUE FALSE 2101799.086 1286228.588 1506588.945 1498655.839 1588843.575 1325888.067 1810541.268 1621058.253 2511277.166 0.83694429 0.512181055 0.599929377 0.596770384 0.632683479 0.527973608 0.720964333 0.645511485 1 21.25998984 0.239224497 0.781484766 1.006396566 0.606140655 0.597540886 0.093740489 1.835534955 1.394005575 0.111279605 0.028726738 1.734700472 -0.239224497 -0.400255911 SKS(ph)PASVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SKSPASVDR 9 1 Q13243;Q13243-3 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 1 S(0.056)KS(0.944)PASVDR;S(0.034)KS(0.966)PASVDR;S(0.066)KS(0.932)PAS(0.001)VDR 120.87 0.00038139 5804300000 4280000 3309390 3810800 3498200 3863320 2886760 4194200 3342160 3918000 TRUE FALSE 4012122.44 3554420.679 3901193.976 3587969.734 3559910.431 3720120.749 3565318.647 3759436.033 3264060.489 1.2291814 1.088956743 1.195196593 1.099235062 1.090638621 1.139721755 1.092295519 1.151766656 1 21.63823636 -4.999999999 0.136023004 0.558893229 1.182434652 0.497217514 0.045089268 116.378927 0.9822056 14.00726644 0.271515592 1.00E-05 4.999999999 0.623541424 SKS(ph)PCQTLGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSPCQTLGGR 11 1 B4DFJ1;Q9BSI4-2;Q9BSI4 B4DFJ1 TINF2 TERF1-interacting nuclear factor 2 1 S(0.001)KS(0.998)PCQTLGGR 86.43 0.0087669 159220000 101420 105760 103990 128400 118600 90933 131450 102140 107270 TRUE FALSE 95072.30324 113590.5804 106456.6919 131694.9614 109285.6344 117183.8809 111740.2928 114892.4038 89365.94401 1.063853846 1.27107235 1.191244529 1.473659377 1.22290024 1.311281185 1.250367733 1.285639682 1 16.44743753 -1.611825891 8.946845686 0.999912247 1.260733561 0.388186343 0.102061435 0.000161207 6.99E-06 0.089172764 0.021011219 0.024444103 1.611825891 0.260821314 SKS(ph)PIPGQGYLGTERPSSVSSVHSEGDYHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKSPIPGQGYLGTERPSSVSSVHSEGDYHR 30 2 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KRE4 O75376 NCOR1 Nuclear receptor corepressor 1 1 S(0.077)KS(0.923)PIPGQGYLGTERPSSVSSVHSEGDYHR;S(0.281)KS(0.719)PIPGQGYLGTERPSSVSSVHSEGDYHR 128.26 5.38E-06 781430000 205093 210260 222050 220610 273750 175731 307510 211081 287880 TRUE FALSE 192256.5952 225827.8692 227317.1309 226271.2261 252250.7793 226461.6869 261401.7303 237434.9275 239830.9682 0.801633737 0.941612632 0.947822262 0.943461254 1.051785685 0.9442554 1.089941521 0.990009461 1 17.87165843 6.592776333 0.397552708 1.025306616 6.90E-15 0.639413171 0.046230739 14.04389384 0.536486513 0.030869259 9.312692658 3915401.775 -6.592776333 -1.025306616 SKS(ph)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 36 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.087)KS(0.913)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.13)KS(0.87)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 236.31 7.23E-50 2042600000 2202200 842120 1282210 1254950 1276220 844330 1785520 1126620 2022070 TRUE FALSE 2064368.233 904471.441 1312624.627 1287154.142 1175990.829 1088074.364 1517797.852 1267280.987 1684573.454 1.225454567 0.536914219 0.779202963 0.764083121 0.698094124 0.645904969 0.90099832 0.752285977 1 20.68395191 0.516385503 0.891897013 0.999367664 0.753302626 0.091542821 0.184539579 3.096566079 3.744077942 0.164955499 0.053442378 3.283866573 -0.516385503 -0.246065038 SKS(ph)PS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKSPSPPR 8 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 2 S(0.417)KS(0.583)PS(1)PPR;S(0.318)KS(0.682)PS(1)PPR 59.542 0.055742 897460000 1149690 715290 882640 786110 781630 675110 1058650 743590 834110 TRUE FALSE 1077732.955 768250.8159 903576.6376 806282.9135 720243.9327 870003.2975 899915.2605 836428.8483 694891.6524 1.550936684 1.105569211 1.300312983 1.160300186 1.036483789 1.251998487 1.295043993 1.203682395 1 19.40642852 -4.999990396 0.030228108 3.20E-14 1.932494038 0.287336593 0.132284424 2463.117883 5.604923839 280.2730684 112.8645587 1.00E-05 4.999990396 1.932494038 SKS(ph)PSGQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SKSPSGQKR 9 2 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(0.043)KS(0.941)PS(0.016)GQKR;S(0.266)KS(0.659)PS(0.075)GQKR;S(0.014)KS(0.959)PS(0.027)GQKR 106.26 0.0015471 1215470000 1516990 983910 1292440 1199140 1256190 739110 1267210 1088390 1691610 TRUE FALSE 1422044.304 1056759.72 1323097.287 1229911.963 1157533.905 952479.0586 1077203.625 1224277.887 1409269.363 1.009064939 0.749863545 0.938853368 0.872730221 0.821371652 0.675867285 0.764370285 0.868732351 1 20.42651596 2.648967893 4.402789263 0.793454786 0.876529593 0.03827827 0.105813045 0.475297168 16.30727014 0.032469661 0.030632156 445.6233029 -2.648967893 0.083074806 SKS(ph)PSPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKSPSPPR 8 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 S(0.057)KS(0.473)PS(0.47)PPR;S(0.01)KS(0.675)PS(0.315)PPR 72.096 0.028488 521000000 504040 358700 428840 373570 459830 340645 483050 368170 443320 TRUE FALSE 472493.0361 385258.5212 439012.2873 383156.4387 423716.8067 438983.6816 410621.1369 414136.8349 369327.028 1.279335116 1.043136548 1.188681721 1.037444892 1.147267258 1.188604267 1.111809063 1.121328263 1 18.49453932 0.511062764 1.570725324 1.000048762 1.135310125 0.278989348 0.070811192 3.397227154 9.479387808 0.05967473 0.017111625 3.243864938 -0.511062764 0.135261363 SKS(ph)PTISDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKSPTISDK 9 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 S(0.003)KS(0.744)PT(0.253)ISDK;S(0.01)KS(0.987)PT(0.003)ISDK 125.03 0.00064883 494810000 1590900 874260 1188500 1082410 1266390 930670 1613830 1056420 1585780 TRUE FALSE 1491328.409 938991.1201 1216691.781 1110186.473 1166932.838 1199339.321 1371851.174 1188316.362 1321103.073 1.128850912 0.710762952 0.920966581 0.840348112 0.883301887 0.907831754 1.03841343 0.899488001 1 20.3333116 1.950325029 5.948115409 0.98199777 0.87381271 0.089838335 0.108218133 0.356677132 29.78979199 0.043048674 0.0266879 89.19182068 -1.950325029 -0.10818506 SKS(ph)PVGNPQLIQFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKSPVGNPQLIQFSR 15 1 G8JLP4;Q9Y4F3-3;Q9Y4F3-4;Q9Y4F3-5;Q9Y4F3 G8JLP4 KIAA0430 Meiosis arrest female protein 1 1 S(0.061)KS(0.939)PVGNPQLIQFSR;S(0.062)KS(0.938)PVGNPQLIQFSR 163.95 9.14E-07 1101780000 250460 241526 231050 244080 263650 198149 316440 226020 293400 TRUE FALSE 234784.1557 259408.8363 236530.6151 250343.506 242943.9925 255351.3996 268992.7597 254239.0945 244429.6446 0.960538793 1.061282222 0.967683832 1.024194534 0.993921965 1.044682612 1.100491555 1.040131998 1 17.89905974 2.098478924 5.245457532 1.061384 1.006326401 0.222716734 0.037805835 0.232099456 10.12431546 0.013350264 0.009711623 125.4523854 -2.098478924 -0.055057599 SKSEEAHAEDSVMDHHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 SKSEEAHAEDSVMDHHFR 18 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;;;;;;; 212.76 5.91E-17 11111690000 9164100 11655930 11040920 11577000 13189120 8172770 12907020 9936330 16926660 FALSE TRUE 8590535.339 12518947.19 11302815.84 11874085.42 12153299.72 10532116.03 10971732.17 11176902.67 14101491.1 0.609193402 0.887774711 0.801533381 0.84204467 0.861845009 0.7468796 0.778054753 0.792604314 1 23.74934439 -1.877463562 2.365265084 1.102645821 0.799918323 0.419989127 0.076776378 23073904.46 12349681.24 13257372.69 0.017004496 0.013259784 1.877463562 -0.302727497 SKSERPPTILMTEEPSS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SKSERPPTILMTEEPSSPK 19 2 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SKSERPPTILMTEEPS(0.012)S(0.988)PK;SKSERPPTILMTEEPS(0.028)S(0.972)PK 155.76 1.18E-08 601410000 1368660 738230 1053060 1206790 1328790 584000 826140 556680 897620 TRUE FALSE 1282998.014 792889.3173 1078039.08 1237758.274 1224432.193 752591.3196 702267.9765 626182.7234 747801.4232 1.715693464 1.06029394 1.441611432 1.655196468 1.637376121 1.006405305 0.939110243 0.83736498 1 19.51229569 2.139356194 6.247968105 0.933431458 1.439449379 0.676317937 0.188918735 0.147882413 7.932888944 0.075942925 0.055900953 137.8339475 -2.139356194 0.506017921 SKSHES(ph)QLGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSHESQLGNR 11 1 A8MY87;A0A2R8Y4X0;A0A0A0MQW1;A0A2R8Y5H9;Q8IVT5-4;Q8IVT5-3;Q8IVT5-2;Q8IVT5;J3QLI1 A8MY87 KSR1 Kinase suppressor of Ras 1 1 SKS(0.318)HES(0.682)QLGNR 145.86 2.18E-05 222970000 151080 201800 197660 192210 242540 149900 234180 212980 278190 TRUE FALSE 141624.1725 216741.482 202348.5885 197142.434 223491.8868 193173.6966 199066.883 239571.0218 231758.2918 0.611085676 0.935204865 0.873101829 0.850638104 0.964331783 0.833513636 0.858941794 1.033710682 1 17.82226143 4.742228094 24.93685894 0.904430536 0.611085561 0.666036789 0.06778696 205.1288248 1394704.733 0.014651486 0.109192 55236.74692 -4.742228094 -0.293344975 SKSPS(ph)GQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSPSGQKR 9 2 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(0.038)KS(0.174)PS(0.788)GQKR 88.275 0.010155 1173900000 1423900 847810 1317300 1144000 1230900 779330 1227400 1013100 1607700 TRUE FALSE 1334780.641 910582.7345 1348546.978 1173356.977 1134230.079 1004309.92 1043362.765 1139587.765 1339364.484 0.996577598 0.679861789 1.006855859 0.876055018 0.846841986 0.749840638 0.778998381 0.850842156 1 20.35311719 2.474366228 24.94729105 0.816133901 0.873055043 0 0.111194705 271.7965816 2461115.045 0.036191561 0.030435666 298.1029185 -2.474366228 0.056921141 SKSPS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKSPSPPR 8 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 S(0.002)KS(0.255)PS(0.743)PPR 69.01 0.033324 278530000 345320 261370 344650 288180 322920 241010 384200 265460 358290 TRUE FALSE 323707.0376 280722.1068 352825.2608 295575.1867 297559.1658 310585.6745 326592.7767 298603.2653 298489.0844 1.084485345 0.94047696 1.182037399 0.990237842 0.996884581 1.040526072 1.094153166 1.00038253 1 18.18731865 SKT(ph)FDWAEFRPIQQALAQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SKTFDWAEFRPIQQALAQER 20 2 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 S(0.044)KT(0.956)FDWAEFRPIQQALAQER;S(0.067)KT(0.933)FDWAEFRPIQQALAQER;S(0.162)KT(0.838)FDWAEFRPIQQALAQER 173.07 2.59E-10 1001150000 408850 427260 302783 302429 488920 153495 636940 348701 983910 TRUE FALSE 383260.8083 458894.775 309965.1557 310189.8402 450522.1954 197806.5147 541436.7601 392237.0874 819689.0647 0.467568527 0.55984006 0.378149678 0.378423787 0.549625724 0.241318963 0.660539201 0.478519361 1 19.64471723 0.259274087 0.826102401 1.006400607 0.449498946 0.69058138 0.113512491 1.580107664 1.328063229 0.125360216 0.034056984 1.816661812 -0.259274087 -0.55690166 SKTDLLVNDNPDPAPLS(ph)PELQDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKTDLLVNDNPDPAPLSPELQDFK 24 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 SKTDLLVNDNPDPAPLS(1)PELQDFK 204.53 6.51E-25 356770000 693420 392230 517750 499420 463680 370140 622550 362550 436920 TRUE FALSE 650020.08 421271.1173 530031.2745 512235.9627 427264.4432 476993.4093 529204.407 407815.1656 363995.2294 1.785792855 1.157353403 1.456148959 1.407260099 1.1738188 1.310438629 1.453877316 1.120386018 1 18.47356002 -4.481541049 0.102805718 5.26E-13 1.590747505 0.398601159 0.173632585 189.14334 1.471283799 41.9097001 2.612063638 3.30E-05 4.481541049 1.590747505 SKTIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKTIPR 6 1 Q9UKL3;A0A087WTW5 Q9UKL3 CASP8AP2 CASP8-associated protein 2 0 72.234 0.078556 66328000 267720 189510 185520 181800 202050 149890 191950 167390 224310 FALSE TRUE 250963.8831 203541.5176 189920.622 186465.2958 186181.808 193160.8097 163168.8795 188289.01 186871.2119 1.342977768 1.089207457 1.016318244 0.99782783 0.996310808 1.033657393 0.873162205 1.007587033 1 17.51168481 8 0.696296309 0.97267432 45.64979541 0.862685637 0.044362315 94.84356316 0.506441324 0.016243077 6593.484743 99999999.94 -8 44.67712109 SKTPSS(ph)PCPASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SKTPSSPCPASK 12 1 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 S(0.004)KT(0.004)PS(0.2)S(0.792)PCPASK;SKTPS(0.045)S(0.955)PCPASK;S(0.008)KT(0.008)PS(0.049)S(0.936)PCPASK 107.73 0.0010791 781320000 1145940 783790 940880 926740 1018660 674870 1140880 814340 1376130 TRUE FALSE 1074217.661 841822.6271 963198.1179 950521.7174 938658.5527 869694.0134 969815.6354 916012.1416 1146445.013 0.936998852 0.73428958 0.840160764 0.829103626 0.818755843 0.758600721 0.845932971 0.799002247 1 20.12873573 -1.34777671 3.345966341 1.001219672 0.814235495 0.51523627 0.054475087 27768020.83 44762017.59 343052.4418 0.011587964 0.044897617 1.34777671 -0.186984177 SKVDDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SKVDDLR 7 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ;;; 81.958 0.023521 2446750000 8419900 8082000 8044000 8088600 8615800 6172400 9805400 7579800 10269600 FALSE TRUE 7892913.489 8680399.689 8234807.479 8296167.17 7939149.822 7954271.679 8335171.299 8526154.715 8555537.416 0.922550286 1.014594323 0.962512006 0.969683933 0.927954544 0.929722038 0.974242867 0.996565651 1 23.02842705 1.330592075 3.963209046 0.99877448 0.961343796 0.286639314 0.026996825 0.345169638 8.742210078 0.022045752 0.007193139 21.40878765 -1.330592075 -0.037430684 SKVGS(ph)TENIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SKVGSTENIK 10 1 E7EVA0;H0Y2V1;F8W9U4;H7C4C5;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 SKVGS(0.846)T(0.154)ENIK;SKVGS(0.5)T(0.5)ENIK;S(0.002)KVGS(0.96)T(0.038)ENIK;S(0.004)KVGS(0.978)T(0.019)ENIK 147.56 1.62E-05 7440340000 9368780 5395680 6766440 6534730 8266070 5139960 9057560 6685870 11652970 TRUE FALSE 8782404.784 5795181.761 6926943.152 6702422.235 7616886.206 6623783.012 7699462.964 7520615.587 9708014.026 0.90465514 0.596948227 0.713528342 0.690400963 0.784597775 0.682300519 0.793103815 0.774681162 1 23.21074476 0.344356908 0.581261374 1.012141469 0.70564239 0.493569227 0.081813571 1.693760241 0.880078718 0.119645645 0.032112533 2.209820043 -0.344356908 -0.306499079 SKVGST(ph)ENIK ddPTM_SK-BR-3_Pertuzumab_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(0.326)T(0.674)ENIK;SKVGS(0.296)T(0.704)ENIK;SKVGS(0.376)T(0.624)ENIK 150.78 3.39E-05 7435900000 9360550 5519340 7074260 6626440 8517840 5219690 9129850 6820040 12354090 TRUE FALSE 8774689.885 5927997.676 7242064.788 6796485.669 7848883.206 6726529.768 7760913.75 7671537.007 10292112.57 0.852564508 0.575974819 0.703651922 0.66035866 0.762611481 0.65356162 0.754064212 0.745380208 1 23.29503581 0.042490129 0.556992765 1.022966859 0.681666783 0.595013433 0.074333049 2.390041773 0.908550261 0.186363669 0.029555922 1.102783167 -0.042490129 -0.341300076 SKYDEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SKYDEER 7 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ;; 97.635 0.010809 648000000 1480310 1298010 1287430 1236290 1428030 1009449 1528420 1239360 1460040 FALSE TRUE 1387660.04 1394116.011 1317968.448 1268015.294 1315878.284 1300860.539 1299247.61 1394096.824 1216349.892 1.140839531 1.14614719 1.083543852 1.042475774 1.081825462 1.069478896 1.068152855 1.146131416 1 20.21412686 SKYHPDEVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SKYHPDEVGK 10 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 101.93 0.0018113 87832000 192840 215360 242350 220920 262590 193680 299500 226140 350590 FALSE TRUE 180770.4886 231305.4785 248098.6564 226589.1812 241967.2406 249592.2719 254592.7554 254374.0768 292074.2641 0.618919607 0.791940636 0.849436896 0.77579304 0.828444236 0.854550717 0.871671307 0.870922598 1 18.15597572 8 0.093941746 1.088046836 0.016724249 0.779405307 0.044893846 75.20776187 0.504715008 0.712389201 10.38022826 99999999.96 -8 -1.071322587 SKYNDDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SKYNDDIR 8 1 Q9Y3D6 Q9Y3D6 FIS1 Mitochondrial fission 1 protein 0 ;; 70.919 0.045678 1058690000 2672630 2828380 2261280 2292600 2871480 1633390 2553790 2626160 3288200 FALSE TRUE 2505354.859 3037796.198 2314918.629 2351431.997 2645965.544 2104923.177 2170872.898 2954041.857 2739378.177 0.914570642 1.108936409 0.845052592 0.858381664 0.965900059 0.768394519 0.792469224 1.078362192 1 21.38541702 3.880553682 5.082381777 0.880664 1.018811154 0.134562522 0.106373825 0.282375342 11.58225389 0.025750969 0.047892339 7595.453024 -3.880553682 0.138147154 SLAAEWGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLAAEWGK 8 0 Q16698-2;Q16698 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 114.28 0.010619 0 295440 230280 232760 236270 348100 189250 230780 252650 444640 FALSE TRUE 276948.9378 247330.1708 238281.1771 242333.0882 320761.6302 243883.4028 196176.6815 284193.9087 370426.7115 0.747648399 0.667689891 0.643261325 0.654199821 0.865924676 0.658385033 0.529596477 0.767206845 1 18.49882861 0.984026192 24.1730257 1.000000007 0.671525597 0.581537416 0.084994115 443.6504483 671373.8748 0.082595098 0.020648775 9.638871533 -0.984026192 -0.32847441 SLAALDALNT(ph)DDENDEEEYEAWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLAALDALNTDDENDEEEYEAWK 23 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 SLAALDALNT(1)DDENDEEEYEAWK;SLAALDALNT(1)DDENDEEEYEAWK;SLAALDALNT(1)DDENDEEEYEAWK;SLAALDALNT(1)DDENDEEEYEAWK;SLAALDALNT(1)DDENDEEEYEAWK;SLAALDALNT(1)DDENDEEEYEAWK 273.63 4.16E-51 782631000 635751 495751 541793 525918 565922 425184 653790 471318 671742 TRUE FALSE 595960.4798 532456.9199 554644.5858 539413.9463 521476.7689 547927.7185 555760.259 530163.0898 559623.9206 1.064930318 0.951454897 0.991102355 0.963886507 0.931834308 0.979099889 0.993095968 0.947356019 1 19.0940981 4.745694731 24.88810749 0.970494625 1.064930365 0.651007498 0.021899547 503.2899152 1755732.384 0.004962447 0.050539867 55679.42359 -4.745694731 0.09443574 SLADELALVDVLEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLADELALVDVLEDK 15 0 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50;C9J7H8;F5H793 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 ;;; 232.42 1.47E-13 375251000 1035190 658600 829970 775670 776090 660930 984870 743640 751070 FALSE TRUE 970399.3058 707363.4293 849657.2803 795575.0054 715139.022 851729.7617 837197.8866 836485.091 625711.5649 1.550873214 1.130494415 1.357905668 1.271472432 1.142921215 1.361217867 1.337993308 1.336854132 1 19.25513824 -1.117132603 3.62471186 0.999813677 1.298211131 0.399444075 0.118979985 11721230.13 19542949.18 25800.05576 0.026780385 0.07636026 1.117132603 0.298397454 SLADELALVDVLEDKLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLADELALVDVLEDKLK 17 1 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50;C9J7H8;F5H793 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 213.99 1.54E-13 307690000 441610 359380 394840 353550 438710 340070 459680 327530 475110 FALSE TRUE 413970.4184 385988.8691 404205.7913 362622.6916 404255.4863 438242.6884 390755.2515 368422.8415 395811.0717 1.045878825 0.975184619 1.021208905 0.916150956 1.021334458 1.107201692 0.987226683 0.93080479 1 18.59445244 1.476635374 24.99999993 0.963272355 1.010548062 0.136998875 0.050973453 0.141368054 6400.819413 0.026625472 0.012326122 29.96645535 -1.476635374 0.047275707 SLAEDFAEQPIKDAVITVPVFFNQAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLAEDFAEQPIKDAVITVPVFFNQAER 27 1 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2;J3QL06;J3KTF1 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 269.57 3.32E-54 540780000 692050 696370 709110 720610 766240 528690 886650 619730 624880 FALSE TRUE 648735.8258 747929.9594 725930.4241 739102.0726 706062.6013 681314.2204 753705.0638 697104.6547 520583.4911 1.24617057 1.43671471 1.39445533 1.419757033 1.356290803 1.308751107 1.447808232 1.339083291 1 18.98977004 0.960812456 22.6572023 0.999999999 1.382974474 0.783203949 0.061021518 887.4816018 513119.3352 0.053441781 0.013360445 9.137185792 -0.960812456 0.382974475 SLAEGYFDAAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLAEGYFDAAGR 12 0 O43813;E9PHS0;F8WDS9 O43813 LANCL1 LanC-like protein 1 0 ;;; 215.06 9.85E-11 1123430000 986130 1080110 1105620 1143420 1252390 1053360 1215530 1013550 1565790 FALSE TRUE 924409.8836 1160082.468 1131845.829 1172762.093 1154032.341 1357447.932 1033272.561 1140093.949 1304449.534 0.708658986 0.889327213 0.86768081 0.899047501 0.884689144 1.040628937 0.792113864 0.874003876 1 20.3150097 4.740355926 5.165147888 0.896066817 0.700081733 0.435207471 0.069872539 0.156345384 13.99524439 0.015336815 0.109199648 54999.14341 -4.740355926 -0.195985084 SLAELTACSIELFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLAELTACSIELFHK 15 0 E7ESJ7;Q9NRY5 E7ESJ7 FAM114A2 Protein FAM114A2 0 175.01 8.80E-07 47460000 110120 129370 122210 129480 141990 101940 143720 120640 106940 FALSE TRUE 103227.7858 138948.6894 125108.8789 132802.676 130838.6782 131368.4231 122170.5202 135702.1696 89091.02314 1.158677745 1.55962615 1.404281537 1.490640373 1.468595528 1.474541637 1.371300002 1.523185668 1 16.44299245 -1.378768186 5.03602995 0.999672653 1.440099093 0.597601728 0.111034049 0.000354426 4.37E-05 0.093371073 0.021991737 0.041805345 1.378768186 0.44042644 SLAGSSGPGAS(ph)SGTSGDHGELVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLAGSSGPGASSGTSGDHGELVVR 24 0 P29692;P29692-2;E9PRY8;E9PK01;E9PQ49;A0A087X1X7;E9PI39;E9PPR1;E9PL12;E9PMW7;H0YCK7;E9PIZ1 P29692 EEF1D Elongation factor 1-delta 1 SLAGS(0.038)S(0.038)GPGAS(0.914)S(0.01)GTSGDHGELVVR 256.75 4.55E-44 154080000 67680 88242 73013 80939 77711 62878 89809 72550 106370 TRUE FALSE 63444.02961 94775.5295 74744.90284 83016.03177 71607.89153 81029.85786 76342.9742 81608.0272 88616.15982 0.715941988 1.069506168 0.843468087 0.936804663 0.808068096 0.914391439 0.861501721 0.920915862 1 16.43528219 -1.64825946 7.210610783 1.000305364 0.895025863 0.125434205 0.092285139 0.000407882 1.99E-05 0.080450394 0.018907822 0.022477114 1.64825946 -0.105279502 SLAGSSGPGASSGTSGDHGELVVR ddPTM_SK-BR-3_Pertuzumab_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 ;; 391.13 2.21E-137 1863650000 239557 451520 389872 400935 410134 393142 407587 358834 377902 FALSE TRUE 224563.555 484951.0106 399119.948 411223.6709 377923.73 506635.7133 346473.1132 403635.2148 314827.7149 0.713290299 1.540369503 1.267740828 1.306186373 1.200414424 1.609247501 1.100516558 1.282082853 1 18.26420302 -0.358227745 7.947372668 0.999994709 1.282101081 0.084523609 0.24442791 0 0 0.207868648 0.04899511 0.438300792 0.358227745 0.282106372 SLAPDRS(ph)DDEHDPLDNTSRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 SLAPDRSDDEHDPLDNTSRPR 21 2 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR 232 1.73E-26 53812190000 4569410 5170310 5031440 5072110 5633870 4430350 5709850 4642240 5892960 TRUE FALSE 4283418.785 5553125.132 5150788.133 5202268.93 5191408.576 5709320.124 4853711 5221833.883 4909386.906 0.872495663 1.131123955 1.049171359 1.059657556 1.057445395 1.162939535 0.988659296 1.063642769 1 22.22711144 -1.080019395 7.759594483 0.999999996 1.056373695 0.026643929 0.078497626 4.63E-09 5.80E-10 0.067069342 0.015808395 0.083172663 1.080019395 0.056373699 SLATMDS(ph)PPHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLATMDSPPHQK 12 0 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 SLATMDS(1)PPHQK 118.24 0.0021671 145550000 378840 324710 362310 352170 357810 276410 422960 289720 318550 TRUE FALSE 355129.0806 348751.8663 370904.1643 361207.2784 329709.0459 356205.0799 359541.0746 325892.1798 265381.9471 1.338181005 1.31415068 1.397623947 1.361084589 1.242394404 1.342235535 1.354806077 1.228011865 1 18.01771071 0.898845752 2.923262537 1.000235528 1.338499948 0.876541208 0.039987885 0.131447286 2.436767014 0.038387491 0.01010273 7.922199092 -0.898845752 0.33826442 SLAVPTIEELEDEEERNHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLAVPTIEELEDEEERNHR 19 1 Q9BVJ6-3;Q9BVJ6;Q9BVJ6-2 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 0 ; 147.92 6.05E-08 60652000 48506 58273 51047 58083 60517 42552 57820 50033 71594 FALSE TRUE 45470.09605 62587.59355 52257.85895 59573.50811 55764.23893 54836.07163 49150.42777 56279.73019 59644.49889 0.762351883 1.049343942 0.876155554 0.998809768 0.93494354 0.919381882 0.824056345 0.943586269 1 15.86410146 1.994235278 22.76370483 0.89517848 0.937268681 0 0.087606126 263.0585792 1038767.654 0.030474101 0.021744521 98.68139448 -1.994235278 0.042090201 SLAYLTAATHGLDEEAESLKETFDPEKETIPDIDPNAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLAYLTAATHGLDEEAESLKETFDPEKETIPDIDPNAK 38 2 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITI7 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 141.69 2.77E-13 106630000 247060 137830 168860 174650 207660 117190 250760 147820 277930 FALSE TRUE 231596.9556 148035.0766 172865.4389 179131.8147 191351.2213 151020.8506 213160.8659 166275.6524 231541.6875 1.000238696 0.639345244 0.746584517 0.773648221 0.826422332 0.652240433 0.920615498 0.718124041 1 17.82091244 -0.602316686 0.441083257 1.057144648 0.759594157 0.236158586 0.113794098 12.37792281 2.0643127 1.132092516 0.059346816 0.249852278 0.602316686 -0.29755049 SLCLS(ph)PSEASQMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLCLSPSEASQMK 13 0 Q9H1A4;H0Y564 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 SLCLS(0.854)PS(0.146)EASQMK 153.09 4.78E-05 56783000 106740 75553 106070 103520 89680 98782 125670 81780 62608 TRUE FALSE 100059.3339 81147.02273 108586.0305 106176.4985 82636.89455 127298.7598 106826.9502 91990.41302 52158.32034 1.918377227 1.555782897 2.081854435 2.035657931 1.584347311 2.440622301 2.048128649 1.763676676 1 15.67060979 SLDADEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLDADEFR 8 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ;;;;; 244.87 1.33E-08 7222600000 8872710 11510740 9776690 10264120 12172720 8068650 10465010 10127140 10123390 FALSE TRUE 8317382.919 12363007.17 10008597.7 10527514.7 11216723.67 10397938.27 8895878.903 11391535.72 8433730.809 0.986204458 1.465900139 1.186734309 1.248263068 1.329983601 1.232898999 1.054797586 1.350711326 1 23.00773954 -0.387360175 0.337648263 0.926873648 1.271992546 0.168392907 0.142690361 11.36092784 1.447678189 1.138945287 0.122882122 0.409864048 0.387360175 0.345118899 SLDEMEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLDEMEK 7 0 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 114.93 0.013479 203488000 265770 221976 236310 217990 247980 191655 276810 218810 300570 FALSE TRUE 249135.9301 238411.334 241915.3848 223583.9925 228504.6511 246982.6872 235304.9103 246128.9102 250402.9252 0.994940174 0.952110818 0.966104468 0.892896887 0.91254785 0.986341062 0.939705117 0.982931449 1 17.93389189 1.080819345 4.055099497 0.999738411 0.949489806 0.256376327 0.030541385 0.276389392 8.220947524 0.028320006 0.007275894 12.04534781 -1.080819345 -0.050248604 SLDFLIELLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLDFLIELLHK 11 0 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 ; 137.17 8.40E-05 138737000 761400 737180 772790 723770 892240 666160 936640 778510 845310 FALSE TRUE 713745.3331 791761.5742 791120.9437 742343.1635 822167.0695 858469.5778 796199.5273 875708.6872 704222.3001 1.013522766 1.124306308 1.123396609 1.054131861 1.167482298 1.219032084 1.130608229 1.243511725 1 19.42567139 2.718065878 23.88175698 1.163165106 1.09384341 0.181214495 0.072347874 723.953673 843594.548 0.020840449 0.019672336 522.4754369 -2.718065878 -0.069321696 SLDFYTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLDFYTR 7 0 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ;; 92.491 0.042407 387030000 707121 717290 672145 682320 769230 489195 784246 680240 1210630 FALSE TRUE 662863.5589 770398.8979 688088.5968 699829.4864 708817.7787 630417.6551 666655.5929 765169.4614 1008568.032 0.657232371 0.763854171 0.682243116 0.693884264 0.702796198 0.625062103 0.660992191 0.75866916 1 19.94387697 0.869392735 4.052510309 0.999953945 0.688753047 0.882329873 0.036193203 0.260357243 7.480252961 0.037361407 0.009542023 7.402744067 -0.869392735 -0.311200899 SLDGAAAVDSADRS(ph)PRPTSAPAITQGQVAEGGVLDASAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLDGAAAVDSADRSPRPTSAPAITQGQVAEGGVLDASAK 39 2 A0A2R8Y4N6;A0A2R8YD30;A0A2U3TZH6;A0A3B3IU06;A0A2R8Y5Z6;A0A2R8Y5G2;A0A2R8Y570;A0A2R8YCW8;A0A2R8Y6G5;A0A3B3ITP0;A0A2R8YFR9;Q4VB86;A0A3B3IUD6;A0A2R8Y7Y3;A0A2R8Y7N0;A0A2R8Y420;P11171-3;P11171-7;P11171-5;P11171-4;P11171-6;P11171-2;P11171 A0A2R8Y4N6 EPB41 Protein 4.1 1 SLDGAAAVDS(0.005)ADRS(0.991)PRPT(0.002)S(0.002)APAITQGQVAEGGVLDASAK 219.5 8.42E-40 142870000 55658 45933 51956 50932 51095 42853 49736 38614 52669 TRUE FALSE 52174.46513 49333.92711 53188.42086 52239.00135 47082.20481 55223.96544 42278.54853 43435.0429 43878.20365 1.189074775 1.124337895 1.21218319 1.190545579 1.073020336 1.258573981 0.963543286 0.989900208 1 15.42121684 1.679574648 7.508479572 0.983205515 1.169530728 0.757181294 0.050570614 0.055309343 5.876186161 0.02266939 0.01177563 47.81615476 -1.679574648 0.186325213 SLDGAEFSRPAS(ph)VSENHDAGPDGDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLDGAEFSRPASVSENHDAGPDGDKR 26 2 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 S(0.001)LDGAEFS(0.049)RPAS(0.928)VS(0.021)ENHDAGPDGDKR;S(0.002)LDGAEFS(0.034)RPAS(0.962)VS(0.002)ENHDAGPDGDKR;SLDGAEFS(0.018)RPAS(0.955)VS(0.027)ENHDAGPDGDKR;SLDGAEFS(0.029)RPAS(0.968)VS(0.002)ENHDAGPDGDKR 208.34 1.08E-25 2865870000 1383920 997360 1260360 1096690 1271970 1174900 1461240 1139440 1198960 TRUE FALSE 1297302.918 1071205.572 1290256.334 1124832.922 1172074.607 1514074.557 1242140.627 1281701.592 998845.8304 1.298801955 1.072443354 1.29174723 1.12613267 1.173428943 1.515824075 1.243575925 1.283182603 1 19.92990249 3.825850562 7.00376774 1.25310178 1.171815898 0.002357183 0.143009308 0.708190129 43.30795449 0.034225596 0.062087373 6696.541462 -3.825850562 -0.081285882 SLDGAEFSRPAS(ph)VSENHDAGPDGDKRDEDGESGGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLDGAEFSRPASVSENHDAGPDGDKRDEDGESGGQR 36 3 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 SLDGAEFS(0.062)RPAS(0.886)VS(0.052)ENHDAGPDGDKRDEDGESGGQR 169.7 5.69E-18 922110000 299860 227330 247380 241730 357370 165930 298500 234420 514860 TRUE FALSE 281092.2979 244161.7497 253247.9704 247933.201 329303.6018 213831.2974 253742.6961 263687.853 428926.5399 0.655339019 0.569239082 0.590422711 0.578031849 0.767738928 0.498526618 0.591576115 0.614762269 1 18.71037106 0.740873301 5.51830195 0.999999933 0.600507106 0.759851892 0.069151971 7.500257574 159.6394701 0.060662765 0.015285105 5.506470302 -0.740873301 -0.399492827 SLDLFNCEITNLEDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLDLFNCEITNLEDYR 16 0 Q9BTT0;Q9BTT0-3;Q9BTT0-2;E9PPH5 Q9BTT0 ANP32E Acidic leucine-rich nuclear phosphoprotein 32 family member E 0 ;; 143.05 3.37E-06 62825000 73361 71495 74876 70301 81371 67913 87174 71870 76589 FALSE TRUE 68769.46596 76788.56419 76652.09408 72105.04268 74980.44989 87518.38062 74103.06798 80843.12771 63805.80112 1.077793316 1.203473083 1.201334248 1.130070329 1.17513531 1.371636734 1.161384493 1.267018457 1 15.96139998 4.739553798 23.24001338 1.200212616 1.077793245 0.108856977 0.09486989 60.21414303 1408391.717 0.019854618 0.121201985 54897.65559 -4.739553798 -0.12241937 SLDLFNCEVTNLNDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLDLFNCEVTNLNDYR 16 0 Q92688;Q92688-2;P39687;H0YN26 Q92688;P39687 ANP32B;ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member B;Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;;;;; 455.84 1.40E-182 1535980000 549478 594301 589136 614252 632077 593683 730417 539088 618734 FALSE TRUE 515087.1528 638303.6644 603110.5841 630014.7462 582436.2221 765069.6445 620897.7517 606394.3235 515463.2982 0.999270277 1.238310597 1.170035939 1.222230076 1.129927628 1.484236893 1.204543086 1.176406401 1 18.97551018 4.741723361 23.87968561 1.21922564 0.999270125 0.210322341 0.12069564 223.4548223 1686992.18 0.025982953 0.184009371 55172.58868 -4.741723361 -0.219955515 SLDLFNCEVTNLNDYRENVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLDLFNCEVTNLNDYRENVFK 21 1 P39687;H0YN26 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ; 320.62 5.39E-67 450610000 193502 248119 223559 240100 293940 165868 290710 194673 482190 FALSE TRUE 181391.0552 266489.9889 228861.9251 246261.3725 270855.1381 213751.399 247120.7343 218978.3526 401709.3739 0.451547977 0.663390018 0.569720151 0.613033672 0.674256454 0.532104583 0.615172934 0.545116362 1 18.6157926 -1.370575471 3.082826715 1.004663781 0.592103785 0.798356997 0.065714636 13412967.66 16724172.17 558831.1274 0.013706497 0.042601464 1.370575471 -0.412559996 SLDLLAALPT(ph)PPHNQTEDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLDLLAALPTPPHNQTEDVR 20 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 SLDLLAALPT(1)PPHNQTEDVR;SLDLLAALPT(1)PPHNQTEDVR 158.94 9.66E-11 270370000 355650 363950 411060 402430 429290 394840 502760 407570 431320 TRUE FALSE 333390.5014 390897.2367 420810.5373 412757.0351 395575.2951 508823.8983 427375.8054 458456.0117 359329.9056 0.92781173 1.087850554 1.17109801 1.148685452 1.100869393 1.416035488 1.189368875 1.27586378 1 18.45494948 5.905222979 0.585444541 1.215702705 6.35E-17 0.358662981 0.108971335 12.41021976 1.131932902 0.044400121 13.85390591 803938.781 -5.905222979 -1.215702705 SLDPADERDDVLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLDPADERDDVLAK 14 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 0 70.26 0.040773 88783000 221040 182910 192090 211290 209490 165650 230540 175140 259890 FALSE TRUE 207205.501 196452.8467 196646.4655 216712.0591 193037.5004 213470.4659 195972.6672 197006.6145 216512.68 0.957013238 0.907350307 0.908244568 1.000920866 0.891575959 0.985949025 0.905132518 0.909907976 1 17.72409199 3.076438177 0.005838843 1.862005381 1.06E-05 0.081434032 0.040723146 22816.24572 41.72094997 6516.070461 6787.814321 1192.444506 -3.076438177 -1.861994742 SLDQEIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLDQEIAR 8 0 P48681 P48681 NES Nestin 0 ;; 125.25 0.0029544 2828630000 2120730 2658400 2333600 2348460 2638240 2001550 2594780 2176250 2475350 FALSE TRUE 1987997.295 2855230.702 2388954.094 2408725.46 2431043.273 2579364.993 2205716.828 2447959.603 2062198.094 0.964018588 1.38455695 1.158450345 1.168037866 1.178860207 1.250784297 1.069595028 1.187063265 1 20.97575149 0.580319535 0.48340525 0.990555605 1.210132478 0.15882216 0.110785763 2.533858579 1.16389926 0.162565872 0.056851984 3.804692264 -0.580319535 0.219576873 SLDS(ph)DES(ph)EDEEDDYQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLDSDESEDEEDDYQQK 17 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 S(0.042)LDS(0.975)DES(0.983)EDEEDDYQQK;S(0.005)LDS(0.996)DES(0.999)EDEEDDYQQK 294.65 2.27E-46 1346080000 1471220 870230 1000900 991580 985550 763280 1198380 797350 1095090 TRUE FALSE 1379138.966 934662.7347 1024641.821 1017025.622 908148.8785 983626.5452 1018694.044 896900.9027 912312.4044 1.511695949 1.024498549 1.123126043 1.114777807 0.995436294 1.078168553 1.116606591 0.98310721 1 19.79916841 4.741808092 24.98809263 1.066015342 1.511696115 0.875461918 0.054040545 98.09605158 754776.819 0.011968919 0.086093244 55183.35387 -4.741808092 0.445680773 SLDS(ph)DES(ph)EDEEDDYQQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SLDSDESEDEEDDYQQKR 18 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 S(0.001)LDS(0.999)DES(1)EDEEDDYQQKR;SLDS(1)DES(1)EDEEDDYQQKR;SLDS(1)DES(1)EDEEDDYQQKR;SLDS(1)DES(1)EDEEDDYQQKR;SLDS(1)DES(1)EDEEDDYQQKR;S(0.041)LDS(0.959)DES(1)EDEEDDYQQKR;SLDS(1)DES(1)EDEEDDYQQKR 252.11 6.26E-30 19943900000 19079040 14081470 15438710 15516330 16758180 10975140 18686890 12875930 21031700 TRUE FALSE 17884916.94 15124076.69 15804923.49 15914505.3 15442060.14 14143484.75 15884964.33 14483518.2 17521373.4 1.020748576 0.863178722 0.902036794 0.908290973 0.881327039 0.807213249 0.906604977 0.82662003 1 24.06261253 4.743389137 24.43121368 0.881918631 1.020748655 0.389515876 0.052327209 336.7979698 1704040.08 0.010765898 0.088473734 55384.6145 -4.743389137 0.138830024 SLDSEPSVPSAAKPPS(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLDSEPSVPSAAKPPSPEK 19 1 Q7Z3K3-5;Q7Z3K3-7;Q7Z3K3-2;Q7Z3K3-3;Q7Z3K3-6;Q7Z3K3 Q7Z3K3-5 POGZ Pogo transposable element with ZNF domain 1 SLDSEPSVPSAAKPPS(1)PEK;SLDSEPSVPSAAKPPS(1)PEK;SLDSEPSVPSAAKPPS(1)PEK 199.94 4.06E-16 2336170000 4872400 1838320 2688640 2503040 2432500 1778600 3702100 2030730 2967840 TRUE FALSE 4567445.181 1974431.126 2752415.81 2567272.244 2241461.262 2292052.947 3147004.474 2284271.111 2472488.331 1.847307073 0.798560341 1.113216906 1.038335434 0.906560906 0.927022756 1.272808625 0.923875386 1 21.23753228 4.747638892 24.94463677 1.011628367 1.847307519 0.809495802 0.129391636 518.9588728 1425927.138 0.031149265 0.384329593 55929.23667 -4.747638892 0.835679152 SLDSESIS(ph)PGDFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLDSESISPGDFHR 14 0 Q52LW3;F8VWZ8 Q52LW3 ARHGAP29 Rho GTPase-activating protein 29 1 SLDSESIS(1)PGDFHR;SLDSESIS(1)PGDFHR 190.24 4.03E-07 195325000 134312 159921 171074 179114 206510 152074 163043 150354 200971 TRUE FALSE 125905.6517 171761.7172 175131.9561 183710.3685 190291.5376 195975.2951 138596.2158 169126.0279 167427.6418 0.752000389 1.02588626 1.046015785 1.097252321 1.136559863 1.170507408 0.827797694 1.010144001 1 17.35317821 -1.93586206 3.395933586 0.992038524 1.013146245 0 0.129473404 0.012128109 0.00022906 0.194816021 0.028596954 0.011591455 1.93586206 0.021107721 SLDTITLS(ph)GDERDFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLDTITLSGDERDFGR 16 1 Q8N9U0;Q8N9U0-2;H0YJ73 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 SLDT(0.012)IT(0.039)LS(0.948)GDERDFGR 77.871 0.013758 105120000 30960 40244 37825 44232 52679 39046 44427 40900 62130 TRUE FALSE 29022.26887 43223.70763 38722.22686 45367.068 48541.80384 50317.94634 37765.58379 46006.45503 51760.10162 0.560707339 0.83507772 0.74810956 0.876487228 0.937822808 0.972137704 0.729627311 0.888840122 1 15.65955283 5.421133637 0.826073456 0.871234187 1.29E-30 0.53470352 0.089514073 5.84452526 1.368188589 0.029322184 6.064645111 263714.2736 -5.421133637 -0.871234187 SLDWENPTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLDWENPTER 10 0 P35573-2;P35573-3;P35573 P35573-2 AGL "Glycogen debranching enzyme;4-alpha-glucanotransferase;Amylo-alpha-1,6-glucosidase" 0 91.584 0.019468 0 112080 137040 115530 118400 140660 112160 140410 113760 123050 FALSE TRUE 105065.1129 147186.5842 118270.4262 121438.3445 129613.131 144538.7712 119356.824 127963.1864 102512.1601 1.024903902 1.43579634 1.153720945 1.184623799 1.264368353 1.409967082 1.164318691 1.248273242 1 16.64543553 0.284285857 1.273201524 0.999829088 1.25063414 0.265558568 0.121079053 5.883733618 9.250753074 0.107469527 0.031467802 1.924357945 -0.284285857 0.250805052 SLEAQVAHADQQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SLEAQVAHADQQLR 14 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;;; 169.92 3.26E-06 1178730000 1259340 2042930 1760700 1831380 2007180 1647600 1842830 1715910 1893850 FALSE TRUE 1180520.157 2194190.663 1802464.635 1878376.311 1849544.179 2123235.373 1566514.749 1930145.141 1577754.2 0.748228182 1.390705005 1.142424235 1.190537988 1.172263829 1.345732671 0.992876298 1.223349708 1 20.58944103 0.451356346 0.785044902 1.000313937 1.178311684 0.039769145 0.181903875 4.867440559 4.518338761 0.175398908 0.055904086 2.827198789 -0.451356346 0.177997747 SLEDALSSDTSGHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLEDALSSDTSGHFR 15 0 E5RK69;P08133;P08133-2;E7EMC6 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ;; 246.86 3.26E-18 3244140000 2140370 2619890 2527180 2042080 3340010 1751890 2991060 3082100 4906210 FALSE TRUE 2006408.062 2813869.382 2587125.903 2094483.23 3077699.088 2257632.203 2542578.321 3466906.97 4087331.856 0.490884551 0.688436731 0.632962038 0.512432879 0.75298488 0.552348643 0.622063099 0.848207851 1 21.96272795 1.08227157 3.033850283 0.996769061 0.615781255 0.751143258 0.078305356 0.104211679 1.90324094 0.067105413 0.017836033 12.08569333 -1.08227157 -0.380987806 SLEEIYLFSLPIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLEEIYLFSLPIK 13 0 P15880;H0YEN5;E9PQD7;E9PPT0;E9PMM9;H3BNG3;H0YE27 P15880 RPS2 40S ribosomal protein S2 0 ; 216.54 6.35E-11 90138000 334826 400884 357160 344821 447740 342654 364767 378657 333283 FALSE TRUE 313869.8383 430565.8685 365632.0039 353669.6906 412576.3065 441572.6473 310073.5747 425933.16 277655.9142 1.130427347 1.55071744 1.316852929 1.2737697 1.485926593 1.590359235 1.116754799 1.534032369 1 18.0829386 -1.194007334 3.562884805 0.999513262 1.376009847 0.328759809 0.168324339 28520116.73 49258203.45 164223.6033 0.037014869 0.063972403 1.194007334 0.376496585 SLEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLEELR 6 0 P41229-4;P41229-3;P41229-2;P41229-5;P41229;J3KSH6;Q9BYE0;Q9BYE0-2;P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3 P41229-4;P52948-6;REV__O94964-2 KDM5C;HES7;NUP98 Lysine-specific demethylase 5C;Transcription factor HES-7;Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 0 107.22 0.07317 124590000 305230 370360 337130 329580 354420 299270 365260 305490 318120 FALSE TRUE 286126.1992 397781.8398 345126.8828 338037.5808 326585.2829 385664.3908 310492.6539 343631.099 265023.7169 1.079624882 1.500929217 1.302249047 1.275499358 1.232287007 1.455207086 1.17156554 1.296605085 1 18.01576195 -0.076835404 0.481348178 0.961508665 1.329445044 0.334188852 0.124096512 4.772749789 1.310619967 0.458225113 0.059586043 0.837846762 0.076835404 0.367936379 SLENETLNKEEDCHS(ph)PTSKPPKPDQPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLENETLNKEEDCHSPTSKPPKPDQPLK 28 3 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SLENETLNKEEDCHS(0.986)PT(0.013)S(0.001)KPPKPDQPLK;SLENETLNKEEDCHS(0.991)PT(0.008)S(0.002)KPPKPDQPLK 226.07 1.01E-34 2510000000 2515180 832020 1474370 1378010 1434930 1059790 2089890 1073070 1839580 TRUE FALSE 2357759.374 893623.6265 1509342.753 1413372.07 1322236.386 1365734.169 1776530.396 1207045.152 1532542.214 1.538462923 0.583098866 0.984862106 0.922240221 0.862773224 0.891155987 1.159204869 0.787609725 1 20.54749538 SLENYHFVDEHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLENYHFVDEHGK 13 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 151.56 2.33E-05 220050000 682210 581630 600440 572650 529140 454310 754220 523420 635860 FALSE TRUE 639511.6939 624694.4904 614682.7203 587345.1685 487583.4788 585461.9219 641131.7128 588770.1392 529730.8582 1.207238891 1.179267699 1.16036797 1.108761477 0.920436239 1.105206376 1.210297084 1.111451467 1 19.01490003 3.271160236 3.625467912 1.088924799 1.18138888 0.296507358 0.076511434 0.364467024 10.01087892 0.023783378 0.031795325 1867.068431 -3.271160236 0.092464081 SLENYHFVDEHGKDQGINIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLENYHFVDEHGKDQGINIR 20 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 177.08 4.31E-17 514010000 245971 280095 252738 258033 304460 200237 321740 215661 415860 FALSE TRUE 230576.1142 300833.5252 258733.0647 264654.5636 280548.9397 258042.1713 273498.0739 242586.7506 346450.2794 0.665538832 0.868331022 0.746811534 0.76390345 0.809781248 0.744817328 0.789429509 0.700206537 1 18.40228879 -2.094945801 2.642579835 1.407086344 0.771565847 0.633328932 0.056631242 11790642.11 6357099.669 28658631.06 0.012708638 0.008036264 2.094945801 -0.635520497 SLEPEPQQSLEDGS(ph)PAKGEPSQAWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLEPEPQQSLEDGSPAKGEPSQAWR 25 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 SLEPEPQQSLEDGS(1)PAKGEPSQAWR;SLEPEPQQSLEDGS(1)PAKGEPSQAWR;SLEPEPQQSLEDGS(1)PAKGEPSQAWR;SLEPEPQQSLEDGS(1)PAKGEPSQAWR;SLEPEPQQSLEDGS(1)PAKGEPSQAWR;SLEPEPQQSLEDGS(1)PAKGEPSQAWR 260.53 2.89E-45 3700190000 2181100 1604470 1823660 1866610 1883010 1494940 2567060 1551040 1657960 TRUE FALSE 2044588.844 1723266.628 1866918.076 1914510.373 1735125.99 1926504.91 2182153.184 1744690.758 1381235.765 1.480260572 1.247626706 1.351628826 1.386085143 1.256212758 1.39476906 1.579855691 1.263137548 1 20.39752817 0.985163135 24.39689357 0.999999987 1.377479746 0.614800664 0.096683136 457.1833735 751767.7446 0.099386902 0.024846725 9.664138268 -0.985163135 0.37747976 SLEQYDQVLDGAHGAS(ph)LTDLANLSEGVSLAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.93)LT(0.07)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.919)LT(0.081)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.982)LT(0.018)DLANLSEGVSLAER 201.13 4.82E-27 817710000 105396 119553 130823 127999 137839 117393 154423 119147 160243 TRUE FALSE 98799.4525 128404.8285 133926.1833 131283.671 127013.681 151282.4534 131268.7047 134022.7652 133497.4081 0.740085174 0.961852596 1.003211862 0.983417378 0.951431813 1.1332239 0.983305269 1.003935336 1 17.02645221 5.339917513 1.278663591 1.010466747 1.61E-12 0.750898245 0.048022919 2.671174739 1.278690967 0.012422544 5.156904398 218734.6134 -5.339917513 -1.010466747 SLESINSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SLESINSR 8 0 E5RI99;P62888;E5RJH3;A0A0C4DH44 E5RI99 RPL30 60S ribosomal protein L30 0 ;;;; 180.45 0.00055607 1570090000 1209890 1397160 1329640 1335520 1400610 1149180 1400970 1202590 1204960 FALSE TRUE 1134165.145 1500607.18 1361179.689 1369791.704 1290611.74 1480929.611 1190907.554 1352736.009 1003844.392 1.129821668 1.494860351 1.355966821 1.364545856 1.285669125 1.475258141 1.186346773 1.347555478 1 19.93710422 0.101429018 0.543257558 0.974828403 1.36701738 0.441681244 0.114118604 2.892262232 1.105756147 0.264465843 0.046913473 1.263074647 -0.101429018 0.392188977 SLETCMYDHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLETCMYDHK 10 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 152.54 1.79E-05 993320000 732020 735940 716210 799400 962920 541130 936440 894370 945730 FALSE TRUE 686204.1749 790429.7633 733198.8394 819913.9574 887296.1474 697345.4465 796029.5155 1006034.063 787881.5534 0.870948396 1.003234255 0.930595261 1.04065637 1.126179619 0.885089191 1.010341608 1.276884906 1 19.58761923 6.139289011 0.289220582 1.068209237 0.565378568 0.217967368 0.10493795 31.58603067 1.146167462 0.11123572 6.5302665 1378126.267 -6.139289011 -0.502830669 SLETEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLETEHK 7 0 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 ;;; 105.12 0.0079989 1330790000 1910510 1628860 1472340 1509340 1946030 1281310 2145920 1636410 2017750 FALSE TRUE 1790934.589 1749462.489 1507264.6 1548072.22 1793196.654 1651203.397 1824159.218 1840719.391 1680974.49 1.065414496 1.040743033 0.896661198 0.920937366 1.066760183 0.982289384 1.085179596 1.095031127 1 20.6808664 2.141777808 1.656008978 1.063020536 0.981769117 0.156955244 0.062216729 0.576796576 3.056717644 0.036535783 0.020426728 138.6046523 -2.141777808 -0.081251418 SLETENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLETENR 7 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 171.08 0.0022125 43876600000 16382200 18824700 18030600 17210400 18723400 16886500 20424000 16096300 23158600 FALSE TRUE 15356867.35 20218500.38 18458294.35 17652048 17252939.69 21761358.42 17361610.81 18105958.49 19293280.05 0.795969752 1.047955574 0.956721423 0.914932451 0.894246061 1.12792425 0.89987865 0.938459321 1 24.2015951 SLETENRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLETENRR 8 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 138.4 0.0011338 14473870000 8319794 10148907 9277672 9117271 10437963 7910163 9549959 9088138 13215207 FALSE TRUE 7799072.945 10900342.63 9497742.761 9351235.609 9618207.491 10193698.65 8118031.305 10222812.03 11009503.58 0.708394606 0.990084844 0.862685833 0.849378498 0.873627718 0.925899935 0.73736579 0.928544322 1 23.39224608 0.998942378 24.9882959 1.000000028 0.861307015 0.269339481 0.081510461 41.60054342 982918.071 0.074728933 0.018682233 9.975676993 -0.998942378 -0.138693013 SLFFGSILAPVRS(ph)PQGPSPVLAEDS(ph)EGEG ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLFFGSILAPVRSPQGPSPVLAEDSEGEG 29 1 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 2 SLFFGSILAPVRS(1)PQGPSPVLAEDS(1)EGEG 148.98 2.51E-08 30733000 68287 81171 67716 84325 111720 57987 74837 79218 124390 TRUE FALSE 64013.03857 87180.9853 69322.2555 86488.92226 102945.9619 74726.90556 63615.8866 89108.54168 103628.5054 0.617716509 0.841283824 0.66894968 0.834605516 0.993413554 0.721103766 0.61388405 0.859884463 1 16.66106138 0.994668478 24.45985562 1.000000016 0.756112945 0.325690145 0.114470982 169.1861558 776194.2213 0.109264942 0.027316235 9.877987625 -0.994668478 -0.243887071 SLFS(ph)PQNTLAAPTGHPPTSGVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLFSPQNTLAAPTGHPPTSGVEK 23 0 Q5VT52-2;Q5VT52-3;Q5VT52 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 SLFS(0.672)PQNT(0.328)LAAPTGHPPTSGVEK 190.6 9.49E-18 146950000 154960 123910 149790 141650 140870 108700 176780 129390 155670 TRUE FALSE 145261.3302 133084.4253 153343.0895 145284.9788 129806.6384 140079.9254 150273.4801 145544.6263 129687.6713 1.120085886 1.026191803 1.182402984 1.120268236 1.000917336 1.080132938 1.158733738 1.122270335 1 16.98468181 -1.434515736 3.454553364 0.998858057 1.102694818 0.251065573 0.054983465 0.000487441 7.98E-05 0.053612499 0.012498506 0.036769207 1.434515736 0.103836761 SLGGES(ph)SGGTTPVGSFHTEAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLGGESSGGTTPVGSFHTEAAR 22 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 SLGGES(0.574)S(0.425)GGT(0.001)TPVGSFHTEAAR 185.84 2.19E-17 222310000 80501 127260 110900 106280 116720 88120 121860 113960 151240 TRUE FALSE 75462.58611 136682.4628 113530.6004 109007.3247 107553.282 113558.8135 103588.2243 128188.1569 125997.067 0.598923355 1.084806703 0.901057486 0.865157637 0.853617347 0.901281405 0.822147902 1.017390007 1 16.94303062 1.221828934 24.90485491 1.00869516 0.88570272 0.188125973 0.119259414 493.5906945 734681.3118 0.106008743 0.02679747 16.66590623 -1.221828934 -0.12299244 SLGGESS(ph)GGTTPVGSFHTEAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLGGESSGGTTPVGSFHTEAAR 22 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 S(0.004)LGGES(0.153)S(0.843)GGTTPVGSFHTEAAR;SLGGES(0.175)S(0.825)GGTTPVGSFHTEAAR 186.65 2.01E-17 360470000 207875 319970 258140 277040 301250 276770 293770 260070 285600 TRUE FALSE 194864.4748 343660.9117 264263.2027 284149.3154 277591.0402 356669.006 249721.9157 292540.312 237931.515 0.818993965 1.444369031 1.110669189 1.194248334 1.166684625 1.499040621 1.049553758 1.22951477 1 17.86018685 -0.748219636 8.417557508 1.000021687 1.206603217 0.082048123 0.191029985 0 0 0.162005146 0.038184979 0.178558432 0.748219636 0.20658153 SLGGQQGS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLGGQQGSPK 10 0 A0A0C4DGT3;A0A3B3IU98;Q6DN90-2;A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90;A0A2R8Y695 A0A0C4DGT3;A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 SLGGQQGS(1)PK;SLGGQQGS(1)PK;SLGGQQGS(1)PK;SLGGQQGS(1)PK 132.9 0.00022169 855620000 1865310 1163530 1421510 1386480 1457690 979562 1713680 1178600 1345080 TRUE FALSE 1748563.577 1249678.972 1455228.888 1422059.424 1343208.907 1262345.648 1456729.593 1325750.804 1120577.458 1.560412949 1.115209808 1.298641944 1.269041612 1.198675645 1.126513511 1.299981168 1.183096085 1 20.09581095 -5 0.088582995 0.263539261 1.442202215 0.407991041 0.114766118 254.6738894 1.57297137 36.30828625 2.658909136 1.00E-05 5 1.178662954 SLGLALTHSFGPSLADTDLS(ph)PMDGISTCGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLGLALTHSFGPSLADTDLSPMDGISTCGPK 31 0 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4 Q8NEY1-5 NAV1 Neuron navigator 1 1 SLGLALTHSFGPSLADTDLS(1)PMDGISTCGPK;SLGLALTHSFGPSLADT(0.001)DLS(0.999)PMDGISTCGPK 457.84 1.02E-245 307220000 489560 440570 480090 410010 671600 413540 607830 582120 799670 TRUE FALSE 458919.3135 473190.2612 491477.9615 420531.5507 618855.2451 532922.2847 516691.5343 654798.9634 666199.9109 0.688861265 0.710282685 0.737733454 0.631239278 0.928933245 0.799943494 0.775580311 0.982886597 1 19.34559564 1.529619113 0.440841808 1.014669466 0.687393507 0.643454384 0.075289098 0.613456024 0.327035289 0.081603436 0.057266503 33.8547112 -1.529619113 -0.32727596 SLGLSLS(ph)GGDQEDAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SLGLSLSGGDQEDAGR 16 0 C9JEV6;Q9UJ70;Q9UJ70-2;H7C3G9;H0YEB7;H0YE82;H7C1L7 C9JEV6 NAGK N-acetyl-D-glucosamine kinase 1 SLGLSLS(1)GGDQEDAGR;SLGLSLS(1)GGDQEDAGR;SLGLSLS(1)GGDQEDAGR;SLGLS(0.002)LS(0.998)GGDQEDAGR;SLGLS(0.075)LS(0.925)GGDQEDAGR 260.58 8.99E-27 643543000 1138819 1189515 1117364 1094252 1206516 992248 1306580 996732 1439486 TRUE FALSE 1067542.352 1277587.928 1143868.402 1122332.359 1111761.1 1278693.89 1110670.459 1121176.184 1199226.487 0.890192439 1.065343321 0.953838507 0.935880229 0.927065164 1.06626555 0.92615571 0.934916128 1 20.19367272 3.721516067 24.85161844 0.961926801 0.996072335 0 0.059919845 653.2832561 2896455.644 0.014638681 0.023366466 5266.42698 -3.721516067 0.034145533 SLGNILQAKPTSS(ph)PAKGPPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLGNILQAKPTSSPAKGPPQK 21 2 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 SLGNILQAKPT(0.005)S(0.109)S(0.886)PAKGPPQK 183.49 3.38E-17 1421000000 1837300 980100 1228800 1174700 1439300 888610 1804500 1139800 2078100 TRUE FALSE 1722306.673 1052667.624 1257947.716 1204844.791 1326263.184 1145137.282 1533931.977 1282106.539 1731251.685 0.994833211 0.608038469 0.726611692 0.695938552 0.766071852 0.661450494 0.886024828 0.740566233 1 20.72338404 0.543902949 0.64764666 1.003112449 0.7252247 0.289665724 0.11261756 1.685862421 1.239595977 0.119314415 0.04036235 3.498669741 -0.543902949 -0.277887749 SLGS(ph)VQAPSYGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLGSVQAPSYGAR 13 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.002)LGS(0.998)VQAPSYGAR;SLGS(0.991)VQAPS(0.009)YGAR;SLGS(1)VQAPSYGAR;SLGS(1)VQAPSYGAR;SLGS(1)VQAPSYGAR;SLGS(1)VQAPSYGAR 229.15 6.55E-12 2504990000 620923 931278 567542 544503 972630 441079 940369 693883 2160250 TRUE FALSE 582060.5378 1000230.792 581004.3643 558475.8688 896243.5632 568411.347 799369.3984 780515.82 1799690.319 0.323422609 0.555779392 0.322835745 0.31031776 0.497998769 0.31583842 0.444170527 0.433694515 1 20.77931725 0.128294204 1.286830643 1.001070471 0.401602541 0.836972348 0.083332075 3.237876068 4.36930282 0.082076218 0.022188439 1.343674897 -0.128294204 -0.59946793 SLGSVQAPS(ph)YGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLGSVQAPSYGAR 13 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 SLGS(0.173)VQAPS(0.827)YGAR 144.8 4.35E-05 797310000 125150 137910 126140 112910 140690 111710 153340 130550 201960 TRUE FALSE 117317.0849 148120.9999 129132.1004 115807.4618 129640.7749 143958.8635 130348.0905 146849.4549 168251.5713 0.697271853 0.880354333 0.767494172 0.688299437 0.770517469 0.855616756 0.774721386 0.87279693 1 17.36026045 0.800137669 1.207407818 1.000734248 0.78113727 0.59825787 0.059447591 0.549677923 1.478218475 0.055388571 0.017034379 6.311573858 -0.800137669 -0.219596977 SLGSVQAPSYGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLGSVQAPSYGAR 13 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 198.81 2.86E-07 863370000 269619 413200 291700 295740 411568 224061 324836 394160 446453 FALSE TRUE 252744.0281 443793.7579 298619.2618 303329.1891 379245.1095 288743.7734 276129.8574 443371.7437 371937.1101 0.679534312 1.193195693 0.802875684 0.81553892 1.019648481 0.776324184 0.742410074 1.192061054 1 18.50469917 1.23160424 24.99993267 1.096030526 0.880940153 0.277305621 0.155011877 254.8139064 915713.7549 0.13524539 0.036730757 17.04528392 -1.23160424 -0.215090374 SLGSVQAPSYGARPVSS(ph)AASVYAGAGGSGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLGSVQAPSYGARPVSSAASVYAGAGGSGSR 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 SLGSVQAPSYGARPVS(0.22)S(0.639)AAS(0.14)VYAGAGGSGSR 160.91 1.20E-12 484620000 36849 92376 48596 48258 108050 38758 111100 66618 358960 TRUE FALSE 34542.68687 99215.61516 49748.72007 49496.38198 99564.18885 49946.80542 94441.5864 74935.40394 299047.257 0.115509125 0.331772363 0.166357386 0.16551358 0.332937977 0.167019774 0.315808235 0.250580476 1 18.19001396 -4.917232099 0.363324693 10 0.215826685 0.913484299 0.074675539 114.493363 0.959581282 804.8725693 0.048143257 1.21E-05 4.917232099 -9.784173315 SLGSVQAPSYGARPVSSAASVYAGAGGS(ph)GSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLGSVQAPSYGARPVSSAASVYAGAGGSGSR 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 SLGSVQAPSYGARPVSSAASVYAGAGGS(0.912)GS(0.088)R;SLGSVQAPSYGARPVSSAASVYAGAGGS(0.744)GS(0.256)R 246.59 1.85E-46 648610000 66370 136301 82468 91808 156232 69588 155024 93648 562870 TRUE FALSE 62216.02017 146392.8679 84424.1799 94163.94871 143962.1689 89676.92593 131779.5904 105340.1589 468923.3607 0.13267844 0.312189326 0.180038332 0.200808824 0.307005752 0.191240048 0.281025859 0.224642591 1 18.83899263 -4.207102254 0.483179103 9.999999999 0.227429113 0.947416085 0.057119887 154.8798837 1.760714488 1470.976167 0.024795054 6.21E-05 4.207102254 -9.772570886 SLGTADVHFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SLGTADVHFER 11 0 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 ;;;;;;; 248.98 2.58E-16 14267030000 10030070 11905300 11161740 10670430 12007310 10070910 11940120 9487960 11548030 FALSE TRUE 9402305.823 12786780.8 11426501.74 10944251.3 11064304.31 12978218.23 10149809.85 10672552.69 9620589.19 0.977310811 1.32910579 1.187713301 1.137586387 1.150065146 1.349004512 1.055009174 1.109345018 1 23.19769382 1.609300487 25 1.061617936 1.201237402 0.254710312 0.106092598 0.181015127 3042.869717 0.048063206 0.02483153 40.67246437 -1.609300487 0.139619467 SLGTIQQCCDAIDHLCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLGTIQQCCDAIDHLCR 17 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 247.4 9.57E-21 1483420000 1936360 2084810 1956220 2038890 2168520 1917450 2711620 1812570 2280370 FALSE TRUE 1815166.684 2239171.502 2002622.462 2091211.369 1998213.187 2470986.688 2305037.754 2038873.354 1899761.515 0.955470815 1.17865926 1.054144137 1.10077573 1.051823174 1.300682569 1.213330061 1.073225949 1 20.85738689 2.330698201 20.71844501 1.175001177 1.082806825 0.099596106 0.097616246 8.316281366 1861.000703 0.031283735 0.026173807 214.1401985 -2.330698201 -0.092194352 SLGYHGSSYS(ph)PEGVEPVS(ph)PVSS(ph)PSLTHDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLGYHGSSYSPEGVEPVSPVSSPSLTHDK 29 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 3 SLGYHGS(0.004)S(0.023)YS(0.972)PEGVEPVS(1)PVS(0.333)S(0.662)PS(0.004)LT(0.001)HDK 184.86 3.80E-18 71414000 35310 63219 63106 62222 69718 64989 90513 77434 60407 TRUE FALSE 33100.01013 67899.80054 64602.90412 63818.72186 64242.62951 83750.26929 76941.41593 87101.80535 50324.68146 0.657729153 1.349234582 1.283722067 1.268139609 1.276563063 1.664198697 1.528900208 1.730796954 1 15.61897851 4.968095847 1.847893404 1.41636422 5.64E-19 0.529559338 0.214106651 1.43167881 2.993231427 0.053328964 4.274873673 92917.14275 -4.968095847 -1.41636422 SLGYHGSSYS(ph)PEGVEPVS(ph)PVSSPSLTHDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLGYHGSSYSPEGVEPVSPVSSPSLTHDK 29 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 2 SLGYHGSSYS(0.999)PEGVEPVS(1)PVSSPSLTHDK;SLGYHGSSYS(1)PEGVEPVS(1)PVSSPSLTHDK 241.01 9.42E-46 680720000 154426 440170 425840 447890 468700 371170 563480 441260 446820 TRUE FALSE 144760.7523 472760.6448 435941.1259 459383.6157 431890.1926 478320.7536 478991.4051 496352.2823 372242.8554 0.388887927 1.270032824 1.171120196 1.234096529 1.160237695 1.284969601 1.286771252 1.333409829 1 18.50588463 4.740224761 24.97486505 1.22982521 0.388887644 0.88424001 0.094137471 40.27088153 604318.5016 0.019986574 0.127652992 54982.5352 -4.740224761 -0.840937567 SLGYHGSSYSPEGVEPVS(ph)PVSSPSLTHDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLGYHGSSYSPEGVEPVSPVSSPSLTHDK 29 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 SLGYHGSSYSPEGVEPVS(0.985)PVS(0.011)S(0.003)PS(0.001)LTHDK;SLGYHGSSYSPEGVEPVS(0.597)PVS(0.299)S(0.078)PS(0.021)LT(0.005)HDK 172.06 3.28E-12 460740000 68777 220636 173992 210987 196005 145105 226384 191027 163439 TRUE FALSE 64472.37034 236972.119 178119.1724 216401.2836 180611.5579 186994.4579 192439.8208 214877.1415 136159.975 0.473504569 1.740394848 1.308161024 1.589316417 1.326465857 1.373343803 1.413336194 1.578122656 1 17.05494315 4.749913552 24.78978499 1.438289222 0.473503929 0.685836228 0.200001758 788.449429 1721588.021 0.041852339 0.653327961 56222.94003 -4.749913552 -0.964785293 SLHDAIMIVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLHDAIMIVR 10 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;; 175.93 2.65E-06 1695365000 142134 299699 194276 166403 333071 141687 179571 274993 229433 FALSE TRUE 133238.0867 321889.0258 198884.3185 170673.1827 306912.9472 182589.7368 152645.9956 309326.4814 191139.1501 0.697073763 1.684055965 1.040521099 0.892926345 1.605704258 0.95527126 0.798611878 1.618331363 1 17.54426378 SLHDALCVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLHDALCVIR 10 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;; 202.2 2.28E-07 1613850000 321133 759896 435490 411520 761837 392337 406653 668625 531474 FALSE TRUE 301033.8588 816159.4905 445820.0285 422080.2999 702005.3951 505598.3228 345679.1578 752104.3031 442767.5559 0.679891412 1.843313675 1.006894074 0.95327739 1.585494207 1.141904632 0.780723775 1.698643663 1 18.75618999 3.740042171 24.58617205 1.142471196 1.368824076 0 0.395909758 995.0666945 1893418.085 0.093686024 0.167486228 5495.942384 -3.740042171 0.22635288 SLHDALCVLAQTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLHDALCVLAQTVK 14 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 155.43 5.85E-06 369130000 574020 1075560 610720 600190 1235700 428350 719000 1044650 1087900 FALSE TRUE 538093.1129 1155195.582 625206.5668 615591.8915 1138653.107 552007.6913 611192.6249 1175076.852 906322.4619 0.593710446 1.274596659 0.689827951 0.679219502 1.256344353 0.609063236 0.674365527 1.296532858 1 19.78966491 1.235816891 24.99723303 1.148266413 0.846417621 0.210282328 0.257686022 122.406196 1115098.228 0.20368449 0.05974719 17.21142748 -1.235816891 -0.301848792 SLHDALCVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLHDALCVVK 10 0 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 101.38 0.0033706 1262030000 1971100 3613500 2373000 2349800 4138100 1763110 2539700 3613100 3145100 FALSE TRUE 1847732.37 3881047.3 2429288.681 2410099.846 3813110.318 2272091.235 2158895.562 4064203.488 2620162.492 0.705197626 1.481223898 0.927151918 0.91982839 1.455295361 0.867156614 0.823954838 1.551126505 1 21.32122485 SLHDPDGLVATYISEVHEHDGHLYLGSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLHDPDGLVATYISEVHEHDGHLYLGSFR 29 0 Q9HDC9;H0Y512 Q9HDC9 APMAP Adipocyte plasma membrane-associated protein 0 88.517 0.00054107 38499000 3600.6 10330 6410.1 5342 7550.2 5736.3 7797.2 7861.2 9100 FALSE TRUE 3375.244873 11094.84395 6562.150599 5479.084764 6957.237748 7392.276689 6628.082246 8842.688125 7581.151212 0.445215348 1.463477464 0.865587615 0.722724638 0.917702016 0.975086301 0.874284401 1.166404399 1 12.88820123 1.242041652 24.96568453 1.083202189 0.943559731 0.061004546 0.25686491 292.3476231 2096822.51 0.181345013 0.060179179 17.45989598 -1.242041652 -0.139642458 SLHLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLHLLK 6 0 Q16236-3;Q16236-2;Q16236 Q16236-3 NFE2L2 Nuclear factor erythroid 2-related factor 2 0 80.377 0.064673 1202800000 1327900 1294300 1167000 1372900 1721900 1374900 1468100 1152500 1819600 FALSE TRUE 1244789.109 1390131.319 1194681.791 1408130.938 1586668.92 1771811.31 1247972.034 1296392.162 1515897.005 0.821156784 0.917035468 0.788102218 0.928909374 1.046686493 1.168820378 0.823256481 0.85519805 1 20.5317403 3.030452004 8.254790057 0.973453903 0.851129903 0.277956126 0.099998844 0.337994528 79.26355003 0.029960218 0.03563302 1072.6351 -3.030452004 -0.122324 SLHLS(ph)PQEQSASYQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLHLSPQEQSASYQDR 16 0 Q5JW53;Q9H410-4;Q9H410 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 SLHLS(1)PQEQSASYQDR;SLHLS(1)PQEQSASYQDR;SLHLS(1)PQEQSASYQDR 252.75 9.96E-27 1230480000 472869 589740 662950 601990 621960 587360 698330 563610 515160 TRUE FALSE 443272.9734 633404.9632 678675.4871 617438.0826 573113.7705 756921.297 593621.8995 633977.9492 429176.4679 1.032845476 1.475861354 1.581343661 1.438657822 1.33538023 1.763659831 1.38316507 1.477196437 1 18.71121145 -1.148630414 4.766495825 0.999959869 1.458705144 0.346201392 0.185995077 7.19E-05 1.28E-05 0.163217043 0.038467268 0.071018188 1.148630414 0.458745275 SLHLS(ph)PQEQSASYQDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLHLSPQEQSASYQDRR 17 1 Q5JW53;Q9H410-4;Q9H410 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 SLHLS(1)PQEQSASYQDRR;SLHLS(1)PQEQSASYQDRR;SLHLS(1)PQEQSASYQDRR 215.48 2.63E-15 613623000 87675 140867 127609 141697 157313 123217 166392 124021 187876 TRUE FALSE 82187.57825 151296.9393 130635.9457 145333.1849 144958.2716 158787.7476 141443.0643 139505.2949 156518.2819 0.525098904 0.966640685 0.834636978 0.92853808 0.926142747 1.014499685 0.903683983 0.891303515 1 17.25597165 4.742137288 24.99776548 0.925563816 0.525098753 0.854793566 0.052775223 124.8948557 872867.4006 0.012075315 0.089574597 55225.1988 -4.742137288 -0.400465064 SLHPWYGITPTSS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLHPWYGITPTSSPK 15 0 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 SLHPWYGITPTS(0.067)S(0.932)PK;SLHPWYGITPTS(0.053)S(0.947)PK 221.79 9.59E-13 1054010000 1309100 1198750 1359100 1371340 1544100 976440 1577740 1325010 1944850 TRUE FALSE 1227165.768 1287506.697 1391338.494 1406530.906 1422832.615 1258322.377 1341172.534 1490440.415 1620241.971 0.757396605 0.79463853 0.858722659 0.868099291 0.878160571 0.776626207 0.827760642 0.919887549 1 20.62777785 -5 0.149070849 1.607157039 0.777882488 0.66681759 0.041262447 91.60311518 0.813962218 16.41417732 0.222303015 1.00E-05 5 -0.829274551 SLHQAIEGDTSGDFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLHQAIEGDTSGDFLK 16 0 E5RK69;H0YC77;P08133;P08133-2;E7EMC6;E5RFF0 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ; 195.17 9.54E-11 612690000 385240 397980 403680 339330 536740 281580 522860 463970 891120 FALSE TRUE 361128.5161 427446.8533 413255.4802 348037.7823 494586.6055 362867.5749 444461.997 521897.6758 742386.3151 0.486442852 0.575774155 0.556658268 0.468809534 0.666211911 0.488785377 0.598693683 0.70300013 1 19.50181059 0.843265373 1.564071096 0.99957501 0.547113593 0.866472359 0.056821501 0.182120166 0.840361048 0.047246671 0.013707748 6.970523139 -0.843265373 -0.452461417 SLIEEGGDWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLIEEGGDWDR 11 0 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9;H7C531 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ;;; 214.71 3.11E-11 729200000 911970 1030430 979220 956360 1012570 846760 1108560 885440 884040 FALSE TRUE 854891.4256 1106724.109 1002447.561 980901.8167 933046.8367 1091205.866 942341.7194 995989.1331 736488.0129 1.160767603 1.502704851 1.361118638 1.331863927 1.266886657 1.481634252 1.279507206 1.352349415 1 19.49030252 -1.273557465 0.482639271 0.836516438 1.366616393 0.524650991 0.100786074 19.32829486 2.384918573 4.178995941 0.045815473 0.053265074 1.273557465 0.530099955 SLIEEGGDWDRR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 231.67 4.62E-12 3450130000 2156900 2775380 2567990 2640740 2776470 2285730 2759550 2371790 2726950 FALSE TRUE 2021903.479 2980872.023 2628903.935 2708505.859 2558417.246 2945583.145 2345781.096 2667913.202 2271804.428 0.889998916 1.312116477 1.157187609 1.192226684 1.126160868 1.296583064 1.032562956 1.174358659 1 21.11540721 0.722137324 0.82730822 1.002191212 1.173586554 0.098407747 0.123190368 1.856686244 2.395969602 0.10761026 0.037203392 5.273965976 -0.722137324 0.171395342 SLIGS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLIGSPGR 8 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.006)LIGS(0.994)PGR;SLIGS(1)PGR;SLIGS(1)PGR;S(0.02)LIGS(0.98)PGR;SLIGS(1)PGR;SLIGS(1)PGR 126.29 0.0012853 1958280000 2053400 2157710 2246340 2190030 2304810 2158460 2764830 2132640 2043990 TRUE FALSE 1924881.359 2317469.093 2299624.246 2246229.878 2123799.52 2781572.362 2350269.409 2398904.799 1702834.864 1.130398138 1.360947642 1.350468148 1.319111985 1.247214022 1.633495074 1.380209824 1.408771249 1 20.6995071 SLIPDIKPLAGQEAVVDLHADDS(ph)RISEDETER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLIPDIKPLAGQEAVVDLHADDSRISEDETER 32 2 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2 S4R3H4 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 SLIPDIKPLAGQEAVVDLHADDS(0.546)RIS(0.446)EDET(0.008)ER 66.376 0.0023232 1712800000 42657 40088 52629 50654 53487 44039 56516 45351 43554 TRUE FALSE 39987.17451 43056.15723 53877.38473 51953.8674 49286.34678 56752.34439 48041.95047 51013.17218 36284.55603 1.102043924 1.186624888 1.484857213 1.4318452 1.358328506 1.564090913 1.324033025 1.405919701 1 15.147068 4.265245249 2.67680307 1.391558745 1.116668943 0.274298388 0.149119474 0.29316254 4.075400613 0.032989209 0.112603952 18418.11793 -4.265245249 -0.274889802 SLIPDIKPLAGQEAVVDLHADDS(ph)RISEDETERNGDDGTHDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLIPDIKPLAGQEAVVDLHADDSRISEDETERNGDDGTHDK 41 3 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2 S4R3H4 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 SLIPDIKPLAGQEAVVDLHADDS(0.49)RIS(0.49)EDET(0.02)ERNGDDGTHDK;SLIPDIKPLAGQEAVVDLHADDS(0.333)RIS(0.333)EDET(0.333)ERNGDDGT(0.001)HDK;SLIPDIKPLAGQEAVVDLHADDS(0.495)RIS(0.495)EDET(0.009)ERNGDDGTHDK 155.37 3.76E-14 620054000 484934 352539 375918 396710 477005 274119 478456 370484 725454 TRUE FALSE 454582.8466 378641.3544 384834.9525 406890.2502 439542.9514 353252.7053 406715.9646 416739.7429 604371.0408 0.752158551 0.626504794 0.6367528 0.673245776 0.72727335 0.584496413 0.672957401 0.689542872 1 19.20507501 0.567732982 2.23770046 0.999982947 0.659430507 0.823117325 0.048019103 1.413306868 6.874060231 0.042351953 0.011468637 3.696008672 -0.567732982 -0.340552441 SLIPDIKPLAGQEAVVDLHADDSRIS(ph)EDETER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SLIPDIKPLAGQEAVVDLHADDSRISEDETER 32 2 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2 S4R3H4 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 SLIPDIKPLAGQEAVVDLHADDS(0.333)RIS(0.667)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.004)RIS(0.994)EDET(0.002)ER;SLIPDIKPLAGQEAVVDLHADDS(0.007)RIS(0.993)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.037)RIS(0.963)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.002)RIS(0.998)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.451)RIS(0.549)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.05)RIS(0.95)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.253)RIS(0.714)EDET(0.033)ER 302.1 4.09E-90 8268200000 3356700 2624419 2962762 2965506 3011755 2568075 3783784 2790063 2853352 TRUE FALSE 3146610.139 2818733.713 3033040.114 3041605.905 2775223.911 3309436.563 3216440.716 3138408.507 2377109.118 1.323712957 1.185782214 1.275936427 1.279539875 1.167478552 1.392210622 1.353089217 1.320262702 1 21.1807767 -0.895789991 4.645442638 0.999997898 1.283256973 0.631488334 0.068901644 4622470.63 995054.894 98.62335587 0.016987536 0.127118866 0.895789991 0.283259075 SLIPDIKPLAGQEAVVDLHADDSRIS(ph)EDETERNGDDGTHDK ddPTM_SK-BR-3_Pertuzumab_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(0.094)RIS(0.781)EDET(0.126)ERNGDDGTHDK 196.44 1.57E-35 1312400000 349030 225690 253610 297690 319060 201630 350460 253770 554190 TRUE FALSE 327184.8353 242400.3224 259625.749 305329.2294 294002.3146 259837.3078 297911.7765 285453.7431 461692.1088 0.70866456 0.525025916 0.562335253 0.661326506 0.636793025 0.562793478 0.645260707 0.618277284 1 18.81657155 -5 0.332102688 5.069888621 0.589376163 0.825552692 0.055275157 136.8901558 1.177587772 393.5293758 0.044527773 1.00E-05 5 -4.480512457 SLKDMEESIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLKDMEESIR 10 1 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 158.04 7.40E-06 483820000 559200 765580 635050 721420 951420 477640 774340 646230 1162630 FALSE TRUE 524200.6702 822264.3398 650113.6859 739932.8586 876699.311 615526.9142 658234.9056 726913.238 968579.5421 0.541205598 0.848938372 0.671203198 0.76393608 0.905139199 0.63549444 0.679587868 0.750494106 1 19.88551101 -2.075048664 1.897991199 1.375218788 0.729714026 0.409583905 0.103784112 1597242.637 415673.0305 2592194.539 0.024891718 0.008413009 2.075048664 -0.645504762 SLKES(ph)EQES(ph)EEEILAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLKESEQESEEEILAQK 17 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 S(0.144)LKES(0.856)EQES(1)EEEILAQK 162.77 1.59E-09 132780000 529800 222790 335680 315630 336960 259000 445520 294800 483840 TRUE FALSE 496640.7637 239285.6034 343642.4881 323729.6002 310496.5208 333769.0955 378718.412 331606.4289 403083.9783 1.232102466 0.593637099 0.852533235 0.803131897 0.770302313 0.828038606 0.939552134 0.822673306 1 18.62072091 0.938281574 0.72436011 0.993690247 0.814053513 0.033483381 0.16317381 1.81752539 2.133989238 0.145658379 0.055837658 8.675241507 -0.938281574 -0.179636734 SLKES(ph)EQES(ph)EEEILAQKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLKESEQESEEEILAQKK 18 2 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 SLKES(1)EQES(1)EEEILAQKK;SLKES(1)EQES(1)EEEILAQKK 185.06 2.95E-14 329120000 545590 214297 316030 324590 388220 236890 504950 274370 792120 TRUE FALSE 511442.4958 230163.7729 323526.3808 332919.5289 357730.7672 305276.2974 429237.4352 308625.6985 659910.0547 0.775018493 0.348780521 0.490258299 0.504492281 0.54209019 0.462602888 0.650448394 0.46767843 1 19.33190987 -2.290521781 0.36185146 1.643923435 0.493807949 0.600239904 0.118172885 32.15574179 1.515409103 16.70652286 0.079909742 0.005122456 2.290521781 -1.150115486 SLKQPLEQNQTIS(ph)PLSTYEESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLKQPLEQNQTISPLSTYEESK 22 1 Q9UQR1 Q9UQR1 ZNF148 Zinc finger protein 148 1 SLKQPLEQNQT(0.002)IS(0.998)PLSTYEESK 182.54 2.77E-17 130760000 175880 126570 154490 157430 165480 80018 154240 87528 213900 TRUE FALSE 164871.9848 135941.3745 158154.5758 161469.9203 152483.8683 103117.8976 131113.1439 98456.06347 178198.7082 0.925214254 0.762863973 0.887518082 0.906122845 0.8556957 0.578668042 0.735769329 0.552507167 1 17.44312735 2.273451736 22.96259094 0.694970888 0.857705483 0.248784814 0.12706908 86.54144398 56954.07063 0.038633249 0.03232038 187.694582 -2.273451736 0.162734595 SLLEAVSFLHANNIVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLLEAVSFLHANNIVHR 17 0 J3KNN3;P15735-2;P15735;H3BTI9;H3BP07;H3BTW6 J3KNN3 PHKG2 "Phosphorylase b kinase gamma catalytic chain, liver/testis isoform" 0 166.92 1.32E-09 44473000 34415 52787 46236 47165 56154 32850 43625 48262 55988 FALSE TRUE 32261.02658 56695.4044 47332.73975 48375.33375 51743.89135 42333.26172 37083.83624 54287.61694 46643.2411 0.691654907 1.215511681 1.014782391 1.037134912 1.109354542 0.907596915 0.795052731 1.163890323 1 15.50938042 2.224311361 24.94771591 0.931503567 1.042424206 0 0.161986226 541.8081541 948595.9186 0.056280096 0.0417589 167.6144134 -2.224311361 0.110920639 SLLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHR 40 0 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2;J3QLU9 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 0 ; 118.82 9.49E-07 61125000 10670.3 14802.6 11418.3 12637.6 17233.7 9995.8 14280.8 14967.9 12095 FALSE TRUE 10002.46497 15898.59991 11689.14747 12961.90221 15880.23472 12881.42519 12139.52662 16836.67526 10076.26636 0.99267572 1.577826482 1.160067335 1.286379473 1.576003864 1.278392683 1.204764362 1.670923997 1 13.29867354 -1.225133741 5.25629661 0.99997124 1.34018518 0.207603111 0.210747198 6.29E-05 9.27E-06 0.180667867 0.04258023 0.059547874 1.225133741 0.340213939 SLLENDQLLSHGGQDLSADAFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLLENDQLLSHGGQDLSADAFHR 23 0 Q9UBB9 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 0 115.36 0.00033559 151680000 22397 25782 29425 29648 28148 17567 27695 24546 33677 FALSE TRUE 20995.21175 27690.92611 30122.9749 30408.81787 25937.36962 22638.30772 23542.39186 27610.62213 28056.09114 0.748329896 0.986984465 1.073669698 1.083857966 0.924482655 0.806894575 0.83911874 0.9841222 1 14.7760264 2.486364375 23.52694075 0.882689234 0.99344147 0.042682303 0.10874372 341.5736005 869429.4324 0.035763319 0.031504623 306.4533514 -2.486364375 0.110752236 SLLGDSAPTLHLNKGT(ph)PS(ph)QSPVVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLLGDSAPTLHLNKGTPSQSPVVGR 25 1 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 2 SLLGDSAPTLHLNKGT(0.998)PS(0.532)QS(0.47)PVVGR 170.29 1.34E-10 176490000 166170 207460 175620 186470 222110 128750 259940 208350 306110 TRUE FALSE 155769.7163 222820.5543 179785.7893 191255.1359 204666.3765 165918.0349 220964.4102 234362.9561 255018.2635 0.610817885 0.873743516 0.704991819 0.749966427 0.802555761 0.650612363 0.866465041 0.919004596 1 17.96024105 1.364667558 2.297826937 0.978316539 0.749048129 0.600846633 0.076977625 0.199685476 1.807981059 0.061478167 0.018737635 23.1562142 -1.364667558 -0.22926841 SLLGDSAPTLHLNKGT(ph)PSQS(ph)PVVGR ddPTM_SK-BR-3_Pertuzumab_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(0.992)PS(0.433)QS(0.574)PVVGR;SLLGDSAPTLHLNKGT(0.998)PS(0.016)QS(0.986)PVVGR;SLLGDSAPTLHLNKGT(0.712)PS(0.29)QS(0.998)PVVGR;SLLGDSAPTLHLNKGT(0.986)PS(0.027)QS(0.986)PVVGR 233.78 3.47E-37 2722000000 2484370 2795150 2595930 2717020 3358070 1935000 3641220 2815420 4317880 TRUE FALSE 2328877.716 3002105.814 2657506.685 2786743.333 3094340.728 2493603.088 3095252.864 3166931.385 3597197.933 0.647414393 0.834567869 0.738771326 0.774698358 0.860208636 0.693207083 0.860462205 0.880388414 1 21.77844211 1.092627127 1.266367393 0.997712503 0.76833696 0.598182306 0.064478418 0.284409871 0.933741816 0.053706377 0.016700254 12.37733447 -1.092627127 -0.229375544 SLLGDSAPTLHLNKGT(ph)PSQSPVVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLLGDSAPTLHLNKGTPSQSPVVGR 25 1 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 1 SLLGDSAPTLHLNKGT(0.937)PS(0.055)QS(0.008)PVVGR 106.6 0.005634 151780000 90671 109170 102820 110350 128240 64150 141570 122900 173580 TRUE FALSE 84996.06396 117253.0604 105258.939 113181.7678 118168.5477 82669.06361 120342.8928 138244.3355 144608.3766 0.587767223 0.810831731 0.727889638 0.782677812 0.817162535 0.571675483 0.832198629 0.9559912 1 17.1417916 1.34338147 3.307401101 0.985375459 0.733449326 0.612220864 0.084830511 0.158711208 2.829436541 0.063460517 0.020041156 22.04862292 -1.34338147 -0.251926134 SLLGLDSGELQSGPESSSS(ph)PGVHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLLGLDSGELQSGPESSSSPGVHVR 25 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7 P49815 TSC2 Tuberin 1 SLLGLDSGELQSGPES(0.019)S(0.04)S(0.301)S(0.641)PGVHVR 167.48 8.09E-12 108280000 48359 65657 64028 63371 70825 53243 73920 55531 63383 TRUE FALSE 45332.29651 70518.3126 65546.7744 64997.20715 65262.69019 68613.38977 62836.38224 62464.16759 52803.96783 0.858501707 1.335473744 1.241322898 1.23091521 1.23594292 1.299398371 1.189993571 1.182944581 1 15.68835872 0.682044855 1.75937405 1.000217944 1.22276808 0.168219176 0.130244842 1.876879292 8.269637998 0.111280153 0.031377315 4.808890133 -0.682044855 0.222550136 SLLGLSNSEPNGS(ph)VETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLLGLSNSEPNGSVETK 17 0 Q13033-2;Q13033;G3V340;G3V3G7 Q13033-2 STRN3 Striatin-3 1 SLLGLS(0.001)NS(0.009)EPNGS(0.99)VETK 195.25 3.04E-11 40334000 155980 84531 124990 96702 108010 91019 126760 91580 172420 TRUE FALSE 146217.4902 90789.76319 127954.8218 99183.53704 99527.33029 117294.7077 107753.5148 103013.9646 143641.9881 1.017930009 0.63205588 0.890789828 0.690491258 0.692884661 0.816576749 0.750153323 0.717157747 1 17.132118 -1.585538202 6.049511898 1.000718991 0.768785551 0.281373481 0.111972485 0.000944476 6.47E-05 0.09430429 0.022161056 0.025969393 1.585538202 -0.23193344 SLLLTTIPQIGSTEWSETLHNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLLLTTIPQIGSTEWSETLHNLK 23 0 B4DUC8;Q13126-4;Q13126;Q13126-3;Q13126-2 B4DUC8 MTAP S-methyl-5-thioadenosine phosphorylase 0 199.04 2.68E-24 77214000 160150 163310 157780 157500 201180 145150 182310 165660 216100 FALSE TRUE 150126.4974 175401.6423 161522.6161 161541.7166 185380.1343 187052.4487 154974.308 186343.0157 180031.5139 0.833890101 0.974282993 0.897190789 0.897296885 1.029709356 1.038998365 0.860817668 1.035057761 1 17.45788994 2.760773587 24.62777999 0.978016181 0.912355754 0.334612968 0.061745106 1050.066024 1164218.707 0.018694175 0.019812399 576.4658528 -2.760773587 -0.065660427 SLLNEIESVYDEHQEQHSEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLLNEIESVYDEHQEQHSEGR 21 0 O75182-2;O75182;M0QYC5 O75182-2 SIN3B Paired amphipathic helix protein Sin3b 0 ; 120.41 2.06E-05 43714000 27466 48068 38769 41717 41378 30695 40429 35677 48174 FALSE TRUE 25746.95209 51627.00473 39688.61899 42787.52885 38128.33879 39556.14821 34367.04677 40131.35198 40133.44818 0.641533515 1.28638348 0.988916248 1.066131389 0.950038945 0.98561549 0.856319313 0.999947769 1 15.29251749 2.724985219 19.27300093 0.944165682 1.043043995 0 0.16315851 99.79909906 141681.1279 0.048802036 0.046459608 530.8663765 -2.724985219 0.098878313 SLLQDAAIEEVEMEDFDANIEEQKEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLLQDAAIEEVEMEDFDANIEEQKEEK 27 1 P49750;P49750-1;H0YIQ2;P49750-3;F8VU51;H0YI23;U3KQT9 P49750 YLPM1 YLP motif-containing protein 1 0 169.57 5.59E-12 10149000 26456 11363 13728 13824 16267 11849 23631 12491 23808 FALSE TRUE 24800.16619 12204.32834 14053.63464 14178.74724 14989.45544 15269.61395 20087.75093 14050.52885 19834.29099 1.250368173 0.615314575 0.708552408 0.714860302 0.755734371 0.769859329 1.012778875 0.708395821 1 14.27570921 1.775133759 24.99999999 0.906757945 0.764856217 0.039837284 0.189486018 93.91197594 64222.06494 0.08081462 0.044853881 59.58456301 -1.775133759 -0.141901728 SLLSHEFQDET(ph)DTEEETLYSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLLSHEFQDETDTEEETLYSSK 22 0 O75976-2;O75976 O75976-2 CPD Carboxypeptidase D 1 S(0.042)LLS(0.038)HEFQDET(0.64)DT(0.28)EEETLYSSK 92.632 0.00752 80893000 49508 34183 45069 43735 40982 32664 60471 52415 45254 TRUE FALSE 46409.38265 36713.94489 46138.05796 44857.31414 37763.43903 42093.56654 51403.93494 58959.12813 37700.81505 1.230991494 0.973823639 1.223794709 1.189823458 1.001661078 1.116516088 1.363470123 1.563868793 1 15.20230809 1.743865459 6.213914748 1.346136617 1.114797319 0.218598846 0.160353748 0.168879439 17.72895293 0.071523606 0.037568762 55.44539213 -1.743865459 -0.231339298 SLLSNVS(ph)IEDEEEELVAIVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLLSNVSIEDEEEELVAIVR 20 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 SLLSNVS(1)IEDEEEELVAIVR 121.74 3.33E-05 15852000 15307 15097 11573 15383 11986 11000 16294 13912 13168 TRUE FALSE 14348.96219 16214.79759 11847.51703 15777.75382 11044.66791 14175.52143 13850.86597 15648.94382 10970.17573 1.307997478 1.478080022 1.079975136 1.438240755 1.006790427 1.29218727 1.262592898 1.426498919 1 13.42129902 4.009344999 10.90702449 1.229212203 1.389617447 0.174298651 0.158627531 1.140970858 379.5274244 0.034830061 0.074735594 10217.50829 -4.009344999 0.160405245 SLLVNPEGPTLMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 140.14 9.12E-05 385530000 631100 640270 652480 660700 716710 539130 825830 618380 719050 FALSE TRUE 591600.5775 687676.257 667957.1337 677654.6806 660422.4877 694768.079 702004.4581 695586.1042 599035.9098 0.987587836 1.147971675 1.115053577 1.131242167 1.102475623 1.159810401 1.171890444 1.161175971 1 19.19228296 4.742276678 24.61972474 1.132738918 0.987587766 0.416497627 0.049617325 253.377865 1678594.847 0.010445791 0.078513682 55242.92656 -4.742276678 -0.145151152 SLNFQEDDDT(ph)SRETFASDTNEALASLDESQEGHAEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLNFQEDDDTSRETFASDTNEALASLDESQEGHAEAK 37 1 Q9H814 Q9H814 PHAX Phosphorylated adapter RNA export protein 1 S(0.001)LNFQEDDDT(0.246)S(0.246)RET(0.246)FAS(0.246)DT(0.014)NEALASLDESQEGHAEAK 71.255 0.0060535 30574000 18506 16051 17988 14242 21319 10570 19506 16729 31919 TRUE FALSE 17347.74249 17239.43274 18414.68385 14607.47383 19644.69174 13621.38741 16581.25638 18817.65248 26591.5127 0.652378926 0.648305831 0.692502306 0.549328427 0.738757962 0.512245677 0.623554462 0.707656337 1 14.69867823 0.82637466 3.344630277 0.999921427 0.633976138 0.763521239 0.06421603 0.420959971 7.366838699 0.056673256 0.01468232 6.704627591 -0.82637466 -0.365945289 SLNFQEDDDTS(ph)RETFASDTNEALASLDESQEGHAEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLNFQEDDDTSRETFASDTNEALASLDESQEGHAEAK 37 1 Q9H814 Q9H814 PHAX Phosphorylated adapter RNA export protein 1 SLNFQEDDDT(0.379)S(0.515)RET(0.106)FASDTNEALASLDESQEGHAEAK 182.43 2.57E-23 112860000 49327 38571 47062 43859 54464 35221 65406 53928 97494 TRUE FALSE 46239.71112 41426.83697 48178.33286 44984.49619 50186.61714 45388.73093 55598.9775 60661.02951 81221.62156 0.569302979 0.510046908 0.593171276 0.553848782 0.617897257 0.558825717 0.684534197 0.746858144 1 16.30957621 0.85679336 0.743048949 1.003783149 0.55265363 0.957131935 0.029359046 0.14372306 0.169280983 0.026343498 0.009787894 7.191067414 -0.85679336 -0.451129519 SLNS(ph)TPPPPPAPAPAPPPALARPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLNSTPPPPPAPAPAPPPALARPR 24 1 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 S(0.012)LNS(0.494)T(0.494)PPPPPAPAPAPPPALARPR;S(0.006)LNS(0.576)T(0.418)PPPPPAPAPAPPPALARPR 96.351 0.0039325 962030000 990040 1274360 1145080 1131470 1228050 1044700 1561660 1066690 1381130 TRUE FALSE 928075.1637 1368714.94 1172241.838 1160505.436 1131603.907 1346287.931 1327503.581 1199868.595 1150610.481 0.806593699 1.189555426 1.018799896 1.008599744 0.983481313 1.170064026 1.153738475 1.042810417 1 20.13396809 2.243530654 24.9989245 1.112086924 1.029761637 0.10989334 0.105676007 257.3831371 1294623.656 0.03556179 0.028899474 175.1986092 -2.243530654 -0.082325287 SLNST(ph)PPPPPAPAPAPPPALAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLNSTPPPPPAPAPAPPPALAR 22 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 SLNS(0.136)T(0.864)PPPPPAPAPAPPPALAR;SLNS(0.032)T(0.968)PPPPPAPAPAPPPALAR;SLNS(0.029)T(0.971)PPPPPAPAPAPPPALAR 261.92 2.49E-39 472200000 569110 557830 571670 555890 498080 529620 704720 511730 344907 TRUE FALSE 533490.421 599132.3136 585230.2824 570155.0785 458962.806 682512.6963 599053.7783 575620.617 287339.7935 1.856653457 2.085100383 2.036718532 1.984253805 1.597282438 2.375280806 2.084827065 2.003274973 1 18.13239828 0.906042396 18.13522882 0.999999999 2.023106057 0.722440975 0.195051803 1794.430152 346354.5855 0.176356218 0.044089055 8.054570655 -0.906042396 1.023106057 SLNST(ph)PPPPPAPAPAPPPALARPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLNSTPPPPPAPAPAPPPALARPR 24 1 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 S(0.008)LNS(0.156)T(0.835)PPPPPAPAPAPPPALARPR;S(0.005)LNS(0.428)T(0.566)PPPPPAPAPAPPPALARPR 99.536 0.0077269 1052250000 1078570 1324410 1216620 1199710 1217910 1101040 1595110 1010940 1341980 TRUE FALSE 1011064.229 1422470.694 1245478.801 1230496.59 1122260.261 1418892.374 1355938.064 1137158.084 1117994.868 0.904354982 1.272340987 1.114029086 1.10062812 1.003815217 1.269140328 1.212830311 1.017140701 1 20.09248214 1.155037462 7.748138334 1.004093704 1.144168541 0.138268427 0.113956698 0.416266548 32.8039682 0.102009585 0.025600054 14.29017219 -1.155037462 0.140074837 SLPAPVAQRPDS(ph)PGGGLQAPGQK ddPTM_SK-BR-3_Pertuzumab_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 253.21 1.05E-43 2482410000 2789760 2139100 2576080 2352210 2641730 2191240 3173820 2401840 3249410 TRUE FALSE 2615153.901 2297481.19 2637185.834 2412571.691 2434259.182 2823815.416 2697935.155 2701715.011 2707062.479 0.966048594 0.848698989 0.97418728 0.891213893 0.899225341 1.043129015 0.996628329 0.998024623 1 21.36829675 2.245861229 24.99998104 1.009034376 0.913545217 0.601681182 0.037803649 106.0531773 363165.7689 0.01243145 0.010207441 176.1413128 -2.245861229 -0.095489159 SLPDCTPHPNSIS(ph)IDAGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLPDCTPHPNSISIDAGPR 19 0 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49;A0A087X246;A0A087WWE6 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 SLPDCTPHPNS(0.114)IS(0.886)IDAGPR;SLPDCTPHPNS(0.293)IS(0.707)IDAGPR;SLPDCTPHPNS(0.427)IS(0.573)IDAGPR;SLPDCTPHPNS(0.152)IS(0.848)IDAGPR 283.19 5.37E-40 1588790000 1004480 1001020 1037990 974710 1064120 768530 1076150 801250 1232450 TRUE FALSE 941611.3898 1075136.562 1062611.613 999722.7088 980548.3077 990392.135 914791.298 901287.8263 1026746.133 0.917082967 1.047129887 1.034931205 0.97368052 0.955005601 0.964593002 0.890961523 0.877809808 1 19.96964808 2.553450184 1.370407294 0.917736279 1.013004359 0.226943843 0.049349614 0.409733052 1.561675863 0.022927431 0.018361706 357.6433747 -2.553450184 0.09526808 SLPEEDVAEIQHAEEFLIKPESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLPEEDVAEIQHAEEFLIKPESK 23 1 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ; 176.84 3.39E-17 51568000 78318 49903 61326 61044 57808 46647 73804 51988 79631 FALSE TRUE 73416.21618 53597.87004 62780.68168 62610.49239 53267.99287 60113.23165 62737.77536 58478.81624 66340.07166 1.10666471 0.80792602 0.946346305 0.943780898 0.802953502 0.906137575 0.945699542 0.881500649 1 16.01759295 -1.212267408 3.385626416 1.000192991 0.909889839 0.078555567 0.08507016 21374939 33965938.74 44188.93414 0.018208251 0.061338421 1.212267408 -0.090303153 SLPELDRDKSDS(ph)DTEGLLFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SLPELDRDKSDSDTEGLLFSR 21 2 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 SLPELDRDKS(0.176)DS(0.824)DTEGLLFSR;SLPELDRDKS(0.163)DS(0.827)DT(0.01)EGLLFSR;SLPELDRDKS(0.028)DS(0.945)DT(0.028)EGLLFSR;SLPELDRDKS(0.017)DS(0.983)DTEGLLFSR;SLPELDRDKS(0.397)DS(0.601)DT(0.002)EGLLFSR 198.68 4.40E-22 1299914000 901001 682910 765869 724148 1120310 491102 836594 806221 2651660 TRUE FALSE 844608.9557 733473.367 784035.7743 742730.8637 1032325.372 632875.175 711154.4963 906879.4666 2209080.816 0.382335019 0.332026498 0.354914935 0.336217153 0.467309917 0.286488014 0.321923259 0.410523445 1 21.07501477 0.77199336 4.352299599 0.999996082 0.35113231 0.947720524 0.047302802 0.713451594 13.46974121 0.042758111 0.010872628 5.915525895 -0.77199336 -0.648863772 SLPLSPELESS(ph)P ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLPLSPELESSP 12 0 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 SLPLSPELES(0.157)S(0.843)P;SLPLSPELES(0.067)S(0.933)P;SLPLSPELESS(1)P;SLPLSPELES(0.094)S(0.906)P 212.82 1.66E-08 122978000 187144 212683 215375 205088 246400 207343 242340 203387 269040 TRUE FALSE 175430.9911 228430.2706 220483.7967 210350.9053 227048.7379 267199.5582 206003.3668 228780.3147 224135.4859 0.782700653 1.019161556 0.98370767 0.938498892 1.012997728 1.192134111 0.91910197 1.020723308 1 17.77401155 4.740246939 24.55026953 1.008408078 0.782700558 0.492598968 0.072715049 98.49323669 1433750.771 0.016357226 0.104822276 54985.34311 -4.740246939 -0.22570752 SLPS(ph)RQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLPSRQK 7 1 Q96PB8 Q96PB8 LRRC3B Leucine-rich repeat-containing protein 3B 1 S(0.158)LPS(0.842)RQK 62.717 0.050734 3494200000 2883500 1701300 2791100 2998600 2139700 2454900 2768900 1509200 1942100 TRUE FALSE 2703026.882 1827266.022 2857306.21 3075549.153 1971656.593 3163589.778 2353729.15 1697626.942 1617950.964 1.670648211 1.129370459 1.766002972 1.90089145 1.218613319 1.955306341 1.454759262 1.04924499 1 20.62573645 1.274569888 4.18851302 1.006808111 1.575689301 0.44494747 0.263480137 0.190228223 6.438731268 0.204737556 0.063536344 18.81784504 -1.274569888 0.56888119 SLPS(ph)SPERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLPSSPERR 9 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 S(0.082)LPS(0.505)S(0.413)PERR;S(0.026)LPS(0.603)S(0.371)PERR 74.962 0.024261 998820000 219467 185404 226415 244890 201715 279440 215360 231670 224573 TRUE FALSE 205730.9522 199131.5051 231785.6707 251174.292 185873.1176 360109.7917 183068.7673 260594.5095 187090.3155 1.099634429 1.064360304 1.238897214 1.34252963 0.993494062 1.924791194 0.978504776 1.392880806 1 17.51337536 3.802557961 2.119652889 1.284060484 1.081430841 0.071447348 0.276009734 0.786575029 6.950425562 0.069641962 0.151184622 6346.846001 -3.802557961 -0.202629643 SLPSS(ph)PERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLPSSPERR 9 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 S(0.019)LPS(0.119)S(0.862)PERR;S(0.002)LPS(0.031)S(0.968)PERR 97.452 0.0040926 1109990000 183766 205665 236810 216550 215806 272920 155570 202396 180140 TRUE FALSE 172264.4141 220892.6506 242427.245 222107.0396 198857.4673 351707.5735 132243.7227 227665.5861 150073.4703 1.1478672 1.471896733 1.615390413 1.479988697 1.325067428 2.343569273 0.881193208 1.517027532 1 17.19530944 -0.549311076 9.076196473 0.999988988 1.475868221 0.136328599 0.373877924 0 0 0.325443333 0.076707729 0.28228573 0.549311076 0.475879232 SLPSSSQLKGS(ph)PQAISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLPSSSQLKGSPQAISR 17 1 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 SLPSSS(0.001)QLKGS(0.998)PQAISR 94.234 0.0017353 634460000 142710 154410 142110 145360 148180 105290 185260 126980 120430 TRUE FALSE 133778.0358 165842.6771 145480.9163 149090.1837 136542.5405 135685.5138 157481.9829 142833.7325 100329.455 1.333387447 1.652980942 1.45003196 1.486006116 1.360941715 1.35239959 1.569648543 1.423647049 1 16.61438569 -2.828030796 0.381020294 6.95E-13 1.487724379 0.661916673 0.100965955 54.66166049 1.937797271 44.52587345 0.0666994 0.00148583 2.828030796 1.487724379 SLPTTVPES(ph)PNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 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;SLPTTVPES(1)PNYR 371.62 2.84E-91 54551760000 9984910 9336110 10674760 9538310 8397420 8277470 10314060 8005740 9486190 TRUE FALSE 9359972.307 10027365.3 10927970.35 9783079.183 7737920.507 10667041.22 8767562.454 9005274.262 7902883.606 1.184374309 1.268823609 1.382782652 1.237912599 0.979126214 1.349765699 1.109413082 1.139492204 1 22.91394773 2.989745422 24.85070053 1.137430578 1.293792079 0.312390663 0.110723813 526.3332972 1275508.228 0.030343905 0.03424958 976.6645442 -2.989745422 0.156361501 SLPVPQLVPETEDEKKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLPVPQLVPETEDEKKR 17 2 O00154-6;O00154-4;O00154-7;O00154;O00154-5 O00154-6 ACOT7 Cytosolic acyl coenzyme A thioester hydrolase 0 83.418 0.0031132 165260000 553730 316140 420030 393600 442080 267090 477120 344850 560480 FALSE TRUE 519073.0277 339547.3345 429993.31 403700.4424 407360.8201 344194.5472 405580.2854 387905.2816 466932.2672 1.111666647 0.727187557 0.920890117 0.864580306 0.872419511 0.737140205 0.86860625 0.830752786 1 18.83285376 4.754840168 24.9587239 0.844000043 1.111666855 0.507237827 0.079808401 2431.346185 3727514.761 0.017019027 0.46298757 56864.36168 -4.754840168 0.267666812 SLQALGEVIEAELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLQALGEVIEAELR 14 0 K7ER00;Q9Y285;Q9Y285-2;K7ER16;K7EK06 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ; 148.91 1.77E-05 30650500 37078 45893 47575 45589 49179 40393 46347 42346 57351 FALSE TRUE 34757.35417 49290.96547 48703.50147 46758.89092 45316.67972 52053.80337 39397.69761 47632.99132 47778.7476 0.727464739 1.031650429 1.019354921 0.978654596 0.948469393 1.089476095 0.824586235 0.996949349 1 15.54408142 -2.156409363 8.761654094 1.89578477 0.961823251 0.012660365 0.105374649 0.129366192 0.002309392 0.007158391 0.022044596 0.006975746 2.156409363 -0.933961519 SLQAMKEILCGTNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLQAMKEILCGTNEK 15 1 Q9H9S4;B7ZBJ5;Q5TAW7;B7ZBJ6;B7ZBJ7 Q9H9S4 CAB39L Calcium-binding protein 39-like 0 67.275 0.07543 81673000 107660 202850 166250 184940 236340 129460 178580 193860 262370 FALSE TRUE 100921.7528 217869.2251 170193.5285 189685.8735 217778.8097 166833.0004 151803.5869 218063.8477 218578.752 0.461718039 0.996753907 0.778637113 0.867814789 0.996340256 0.763262663 0.694502944 0.997644308 1 17.73779364 4.750707586 24.64296884 0.863517454 0.461717738 0.570134541 0.114431655 1244.630223 2524967.364 0.026896605 0.452114247 56325.82823 -4.750707586 -0.401799716 SLQARPVS(ph)MPVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLQARPVSMPVDR 13 1 A0A2U3TZV8;Q4KWH8-2;Q4KWH8;Q4KWH8-3;Q4KWH8-4 A0A2U3TZV8 PLCH1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1" 1 SLQARPVS(1)MPVDR 111.77 0.00041817 0 160630 292710 192100 202010 273970 107960 328620 150340 405990 TRUE FALSE 150576.455 314382.553 196656.7027 207193.9186 252453.5013 139126.2994 279346.4818 169110.2799 338227.6462 0.445192629 0.929499869 0.581432964 0.612587176 0.746401142 0.41133923 0.825912621 0.499989524 1 18.36763506 -1.352447611 4.648726404 1.00033283 0.659184519 0.314891696 0.166418104 0.000512138 7.13E-05 0.14375125 0.033849875 0.044417324 1.352447611 -0.341148311 SLQDIIAILGMDELSEEDKLTVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLQDIIAILGMDELSEEDKLTVSR 24 1 P06576;F8W079 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 130.01 6.97E-05 116300000 167800 125520 133280 118590 180710 127710 127480 125120 235700 FALSE TRUE 157297.6975 134813.6314 136441.4645 121633.2202 166517.7655 164577.8038 108365.5575 140741.5074 196360.1473 0.801067323 0.6865631 0.694853138 0.619439442 0.848022207 0.838142597 0.551871441 0.716751894 1 17.58314263 0.930652478 22.05928144 1 0.708389216 0.469269346 0.093090174 10912.53485 3471256.701 0.087363929 0.021840982 8.524177382 -0.930652478 -0.291610784 SLQEEHVAVAQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 167.32 3.21E-05 3586270000 2685200 3908130 3160290 3393610 3871210 2806330 3564220 3418380 3333330 FALSE TRUE 2517138.125 4197492.012 3235253.571 3480695.778 3567180.782 3616471.914 3029798.3 3845172.268 2776975.689 0.906431459 1.511533583 1.16502769 1.253412405 1.284556 1.302305933 1.091042429 1.38466184 1 21.40508312 -1.938663538 2.735087782 0.831142231 1.248489756 0.169405706 0.163542565 23376308.79 19514154.67 25308403.95 0.036466086 0.011516923 1.938663538 0.417347525 SLQELFLAHILSPWGAEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLQELFLAHILSPWGAEVK 19 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 175.73 2.00E-12 348200000 911300 1206060 991220 885770 1397330 435790 910670 1149240 1191140 FALSE TRUE 854263.3597 1295357.937 1014732.206 908500.3578 1287589.338 561595.4985 774123.4877 1292725.144 992331.0389 0.860865302 1.305368759 1.022574289 0.915521456 1.297540123 0.565935637 0.780106091 1.302715619 1 19.92046195 2.2555154 24.99984725 0.869964498 1.095679955 0.101609813 0.231504147 397.9993423 586849.3632 0.076426485 0.063788557 180.1006995 -2.2555154 0.225715457 SLQQSWELLATHENHLNQDDTVPESSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLQQSWELLATHENHLNQDDTVPESSR 27 0 O60437;K7EKI8 O60437 PPL Periplakin 0 ; 239.25 2.33E-45 203035000 56776 64897 70054 67738 66299 56611 70505 57180 102752 FALSE TRUE 53222.49151 69702.04141 71715.71396 69476.27176 61092.14398 72953.6767 59933.42979 64319.04887 85602.0274 0.621743353 0.814256899 0.837780554 0.811619466 0.713676368 0.852242393 0.700140308 0.751372962 1 16.38535735 -2.224824216 2.292226231 1.744591595 0.772739428 0.517923978 0.071337888 6035151.298 860776.5406 23398894.26 0.016639929 0.005959033 2.224824216 -0.971852167 SLQSVAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLQSVAEER 9 0 P61313;A0A2R8YEM3;E7EQV9;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;;; 238.63 6.28E-10 2259290000 2784660 3486990 3271870 3334090 3545610 2799180 3581160 3116220 3452500 FALSE TRUE 2610373.101 3745170.368 3349480.301 3419648.394 3267152.093 3607257.825 3044198.304 3505286.927 2876255.446 0.907559551 1.302099357 1.164528104 1.188923744 1.135904705 1.254150715 1.05838941 1.218698058 1 21.45576038 -1.17876276 0.504889874 0.934993009 1.169497813 0.142782744 0.110717835 42.58248021 5.952211875 3.971972959 0.046997445 0.066257835 1.17876276 0.234504805 SLRDDYEVSCPELDQLVEAALAVPGVYGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLRDDYEVSCPELDQLVEAALAVPGVYGSR 30 1 P51570;P51570-2;K7EII7 P51570 GALK1 Galactokinase 0 ; 176.84 8.09E-18 479650000 297000 353790 334360 332420 367440 309800 374230 312070 363900 FALSE TRUE 278411.3002 379984.9797 342291.1771 340950.46 338582.7446 399234.2308 318117.6857 351032.6265 303162.7391 0.918355933 1.253402647 1.129067438 1.124645004 1.116834957 1.316897426 1.049329765 1.157901619 1 18.20973292 0.324589954 1.150440899 0.999975104 1.146920293 0.119392064 0.107519133 6.381874669 9.175923871 0.094042758 0.028059399 2.111494496 -0.324589954 0.146945189 SLRQS(ph)FR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SLRQSFR 7 1 J3QRV5;Q6P1M3;Q6P1M3-2;A0A087WW77;Q15334 J3QRV5;A0A087WW77 LLGL2;LLGL1 Lethal(2) giant larvae protein homolog 2;Lethal(2) giant larvae protein homolog 1 1 SLRQS(1)FR;SLRQS(1)FR;SLRQS(1)FR;SLRQS(1)FR;SLRQS(1)FR;SLRQS(1)FR;S(0.034)LRQS(0.966)FR 125.97 0.002421 4564220000 5597200 6622910 5473990 5589540 6459190 3681230 6371360 5367630 6418610 TRUE FALSE 5246881.243 7113277.148 5603835.628 5732977.059 5951911.273 4743941.341 5416033.717 6037790.421 5347302.525 0.981220198 1.330255229 1.047974301 1.072125064 1.11306799 0.887165317 1.012853432 1.129128265 1 22.35037987 3.691830719 5.062098435 1.031027154 1.183807407 0.164202603 0.106745318 0.223858814 14.40871249 0.026573057 0.043345449 4918.477844 -3.691830719 0.152780253 SLRVDIAEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLRVDIAEGR 10 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;; 181.31 1.73E-06 1059410000 351578 641140 440990 511768 766408 398366 604721 453579 1140560 FALSE TRUE 329573.3606 688610.6727 451450.4911 524900.8333 706217.4072 513367.7973 514048.7 510209.3366 950193.1677 0.346848801 0.724705982 0.475114436 0.552414868 0.743235619 0.540277298 0.540993892 0.536953278 1 19.85786131 -1.960848928 2.745507427 1.33745456 0.567767915 0.599951271 0.113267743 12132806.2 4649955.515 26001190.44 0.024559537 0.01094337 1.960848928 -0.769686646 SLS(ph)ASPALGSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSASPALGSTK 12 0 O95544;O95544-2 O95544 NADK NAD kinase 1 SLS(0.985)AS(0.014)PALGSTK;SLS(0.949)AS(0.051)PALGSTK 190.34 7.10E-06 184648000 342960 421730 274260 326170 553390 186386 529070 393550 647640 TRUE FALSE 321494.7458 452955.328 280765.5767 334540.0744 509928.9817 240192.6125 449740.8651 442685.5838 539544.7001 0.595863041 0.839513998 0.520375006 0.620041443 0.945109796 0.445176484 0.833556265 0.820479904 1 19.04138296 1.122482753 1.588754916 0.990276776 0.675409046 0.340018422 0.149539977 0.394868119 1.94361354 0.127078545 0.03759483 13.25814464 -1.122482753 -0.31486773 SLS(ph)CLSDLDGGVALEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSCLSDLDGGVALEPR 17 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 S(0.002)LS(0.998)CLSDLDGGVALEPR 170.91 1.88E-09 29730000 43121 34822 30628 23467 24516 17096 86083 28294 86691 TRUE FALSE 40422.13358 37400.25711 31354.51062 24069.20295 22590.61225 22031.33767 73175.65331 31826.56818 72221.71205 0.559695034 0.517853372 0.434142445 0.333268241 0.312795302 0.305051446 1.013208511 0.440678672 1 16.140145 1.747427971 25 0.803417105 0.418863678 0.545669577 0.175002439 1.566873341 4427.896506 0.074194904 0.041144916 55.90208042 -1.747427971 -0.384553428 SLS(ph)DPIPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLSDPIPQR 9 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 SLS(1)DPIPQR;SLS(1)DPIPQR;S(0.257)LS(0.743)DPIPQR 117.28 0.0012344 731570000 775740 874280 831040 795820 932800 727970 924590 794130 1033870 TRUE FALSE 727187.8181 939012.6009 850752.6612 816242.0885 859541.6507 938123.1214 785956.313 893278.8786 861310.4179 0.844280765 1.090213913 0.987742216 0.947674696 0.997946423 1.089181208 0.912512256 1.037116073 1 19.71617376 SLS(ph)DS(ph)ESDDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 SLS(1)DS(1)ESDDSK;SLS(1)DS(0.992)ES(0.008)DDSK 359.73 3.49E-71 964060000 4315600 2294100 2914700 2743000 2982400 2139550 3947700 2299980 3028900 TRUE FALSE 4045494.3 2463957.551 2983838.06 2813390.024 2748174.334 2757203.352 3355779.034 2587137.566 2523357.023 1.603219149 0.97646014 1.18248747 1.114939344 1.089094532 1.092672708 1.329886736 1.025276068 1 21.26691291 4.749304225 24.90635596 1.120605691 1.603219438 0.701857025 0.102113583 890.5697948 2064520.508 0.024170085 0.355991786 56144.11297 -4.749304225 0.482613747 SLS(ph)DSESDDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 SLS(0.862)DS(0.138)ESDDSK;SLS(0.978)DS(0.022)ESDDSK;SLS(0.944)DS(0.056)ESDDSK;S(0.001)LS(0.949)DS(0.05)ESDDSK 362 1.14E-71 1426250000 3312330 2022480 2321200 2273370 2436660 1708390 3076320 1943170 2653930 TRUE FALSE 3105017.178 2172226.524 2376259.96 2331708.523 2245294.553 2201574.46 2615054.375 2185779.052 2210971.938 1.40436752 0.982475845 1.074758082 1.054607923 1.015523768 0.995749617 1.182762355 0.988605515 1 21.07624928 4.744910904 24.90589816 1.046862859 1.404367688 0.785162751 0.060219273 322.5494038 1265005.875 0.014158056 0.1335975 55579.02247 -4.744910904 0.35750483 SLS(ph)DSESDDSKSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSDSESDDSKSK 13 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 S(0.018)LS(0.967)DS(0.014)ES(0.001)DDSKSK 91.858 0.0039779 0 77752 66739 67613 65128 92341 36529 82628 53486 198220 TRUE FALSE 72885.64111 71680.425 69216.81229 66799.29474 85088.91035 47074.3293 70238.69848 60163.84484 165135.8014 0.441367895 0.434069562 0.419150855 0.404511282 0.515266281 0.285064346 0.425339011 0.364329505 1 17.3332934 -1.672827051 2.821250974 1.070162593 0.412157751 0.909455948 0.058391517 12985664.14 12060703.21 6557410.697 0.012696215 0.021240902 1.672827051 -0.658004842 SLS(ph)ESSVIMDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SLSESSVIMDR 11 0 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2;H3BNX5 H3BSS6 ZNF106 Zinc finger protein 106 1 SLS(0.981)ES(0.013)S(0.006)VIMDR;SLS(0.973)ES(0.027)S(0.001)VIMDR;SLS(0.976)ES(0.012)S(0.012)VIMDR;SLS(0.487)ES(0.487)S(0.026)VIMDR;SLS(0.931)ES(0.065)S(0.005)VIMDR 218.3 1.12E-11 1953110000 1875210 2242010 2098690 2224720 2556670 1726490 2522050 1974600 2480690 TRUE FALSE 1757843.953 2408010.753 2148471.918 2281810.082 2355879.451 2224899.636 2143892.016 2221133.157 2066646.813 0.850577826 1.165177687 1.039593173 1.104112259 1.139952621 1.076574682 1.03737707 1.074752175 1 20.97886042 -1.112759299 6.651834246 0.999999912 1.070306518 0.038517963 0.085219557 9.84E-08 1.30E-08 0.072733189 0.017143356 0.077133085 1.112759299 0.070306606 SLS(ph)FEMQQDELIEKPMSPMQYAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSFEMQQDELIEKPMSPMQYAR 23 1 Q9Y6Y0 Q9Y6Y0 IVNS1ABP Influenza virus NS1A-binding protein 1 S(0.02)LS(0.98)FEMQQDELIEKPMSPMQYAR;SLS(1)FEMQQDELIEKPMSPMQYAR 232.47 3.93E-34 552820000 264230 238770 233410 239080 260070 197883 323810 233600 238970 TRUE FALSE 247692.316 256448.7792 238946.5954 245215.1976 239645.1513 255008.6097 275257.6966 262765.4742 199084.3632 1.244157562 1.288141244 1.200227841 1.231715006 1.203736684 1.280907278 1.382618364 1.319869979 1 17.60302039 2.094627469 8.025404931 1.290270439 1.236573679 0 0.104778024 0.740378189 55.17284936 0.035333751 0.026060667 124.3447543 -2.094627469 -0.05369676 SLS(ph)FSDEMSSCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLSFSDEMSSCR 12 0 Q14153-2;Q14153 Q14153-2 FAM53B Protein FAM53B 1 S(0.143)LS(0.81)FS(0.046)DEMSSCR;SLS(0.997)FS(0.003)DEMSSCR;SLS(0.984)FS(0.016)DEMSSCR;SLS(0.845)FS(0.155)DEMSSCR 221.96 1.01E-10 558918000 955300 1071222 1016885 1052177 1152989 898577 1213390 946204 1076995 TRUE FALSE 895509.4783 1150536.391 1041005.992 1079177.643 1062437.895 1157981.593 1031453.434 1064339.652 897237.5768 0.998073979 1.282309637 1.160234501 1.202778028 1.184121043 1.290607552 1.149587869 1.186240612 1 19.77513052 -1.091781405 6.699061783 0.999999842 1.191285337 0.329014555 0.080548568 1.65E-07 2.24E-08 0.067924058 0.016009841 0.080950325 1.091781405 0.191285495 SLS(ph)GSS(ph)PCPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 SLS(1)GS(0.001)S(0.999)PCPK 207.34 1.96E-07 349700000 1438600 850410 1071800 942850 1143900 963470 1549400 1070800 2780800 TRUE FALSE 1348560.594 913375.2413 1097223.602 967045.1272 1054062.708 1241608.148 1317081.854 1204491.737 2316666.515 0.582112525 0.39426272 0.47362173 0.417429579 0.454991127 0.535945998 0.568524578 0.519924525 1 21.14361895 -0.508974283 0.430303734 1.124692219 0.449256328 0.887519605 0.057185994 2.437101153 0.415960094 0.492925066 0.031840937 0.309760272 0.508974283 -0.675435891 SLS(ph)GSSPCPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.001)LS(0.988)GS(0.01)S(0.001)PCPK;SLS(0.961)GS(0.038)S(0.002)PCPK 133.42 0.00020731 587480000 674750 533850 582770 571020 648800 437050 673360 521150 1105210 TRUE FALSE 632518.602 573376.8095 596593.5796 585673.3399 597845.8651 563219.2401 572395.9192 586216.7247 920743.3111 0.686965188 0.622732528 0.647947775 0.636087532 0.649307856 0.611700605 0.621667203 0.63667769 1 19.81243949 -1.570400589 2.787196446 1.023077218 0.636344841 0.967604746 0.020745363 3573270.568 3605465.367 611651.4211 0.004717807 0.026890533 1.570400589 -0.386732377 SLS(ph)KSDSDLLTCSPTEDATMGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSKSDSDLLTCSPTEDATMGSR 23 1 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.096)LS(0.447)KS(0.447)DS(0.01)DLLTCSPTEDATMGSR;S(0.018)LS(0.519)KS(0.456)DS(0.007)DLLTCSPTEDATMGSR 174.53 1.56E-12 920960000 365860 292410 310020 304080 362630 242120 433080 273300 517060 TRUE FALSE 342961.4757 314060.3407 317373.8208 311883.2076 334150.5026 312016.1135 368143.6745 307422.1066 430759.3457 0.796178839 0.729085379 0.736777563 0.724031204 0.775724325 0.724339742 0.854638856 0.713674839 1 18.71652257 -3.620576444 0.280649223 1.74302332 0.738762652 0.743204738 0.044437964 44.80345916 0.875403677 19.23632702 0.047012142 0.000239565 3.620576444 -1.004260668 SLS(ph)LGDKEISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.006)LS(0.994)LGDKEISR;S(0.011)LS(0.989)LGDKEISR;S(0.064)LS(0.936)LGDKEISR;S(0.192)LS(0.808)LGDKEISR 170.74 9.30E-06 1176800000 1423140 1305680 1245920 1490850 1532580 958250 1643020 1247520 1787570 TRUE FALSE 1334068.208 1402353.906 1275473.811 1529107.735 1412217.349 1234881.219 1396664.404 1403275.618 1489213.019 0.895820941 0.941674487 0.856475061 1.026789127 0.948297746 0.829217314 0.937854012 0.942293413 1 20.5061187 0.905259417 2.269828533 0.99947765 0.916436573 0.184272509 0.053581226 0.687044338 7.488270644 0.048613245 0.013257096 8.040062365 -0.905259417 -0.083041078 SLS(ph)LSLADSGHLPDVHGFNSYGSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSLSLADSGHLPDVHGFNSYGSHR 25 0 Q9Y446;Q9Y446-2;E9PKC4;E9PRW6 Q9Y446 PKP3 Plakophilin-3 1 S(0.254)LS(0.745)LS(0.001)LADSGHLPDVHGFNSYGSHR 303.42 3.34E-63 829060000 66676 144220 73864 98241 135810 52053 121040 93515 162600 TRUE FALSE 62502.86818 154898.1989 75616.08896 100762.0304 125144.0304 67079.85609 102891.1757 105190.5536 135461.0096 0.461408551 1.143489181 0.558212944 0.743845264 0.923838017 0.495196782 0.759563036 0.776537499 1 17.04751813 0.748064262 3.415644035 0.99997742 0.74796869 0.144577637 0.202629335 4.931062361 64.52110019 0.179463744 0.046377466 5.598404343 -0.748064262 -0.25200873 SLS(ph)MDSQVPVYSPSIDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SLSMDSQVPVYSPSIDLK 18 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 S(0.088)LS(0.911)MDS(0.001)QVPVYSPSIDLK;S(0.028)LS(0.968)MDS(0.004)QVPVYSPSIDLK;S(0.141)LS(0.859)MDSQVPVYSPSIDLK;S(0.01)LS(0.99)MDSQVPVYSPSIDLK;S(0.031)LS(0.969)MDSQVPVYSPSIDLK;S(0.124)LS(0.876)MDSQVPVYSPSIDLK;SLS(0.998)MDS(0.001)QVPVYSPSIDLK;S(0.05)LS(0.95)MDSQVPVYSPSIDLK 308.24 1.72E-60 1224584000 3743530 2944900 3134450 3228010 3084790 2379490 4245610 2752680 3379410 TRUE FALSE 3509229.14 3162943.46 3208800.634 3310846.202 2842523.037 3066410.135 3609020.195 3096358.157 2815364.639 1.246456353 1.123457834 1.139746017 1.175991968 1.009646494 1.089169798 1.281901514 1.099807149 1 21.42489036 4.740901043 23.78205879 1.130866557 1.24645642 0.183195094 0.081312335 205.5814819 2088722.498 0.018876577 0.125592117 55068.2206 -4.740901043 0.115589863 SLS(ph)MVDLQDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLSMVDLQDAR 11 0 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 SLS(1)MVDLQDAR;SLS(1)MVDLQDAR;S(0.001)LS(0.999)MVDLQDAR;SLS(1)MVDLQDAR;S(0.013)LS(0.987)MVDLQDAR;S(0.003)LS(0.997)MVDLQDAR 297.53 1.22E-35 1044839000 1406722 1803100 1723090 1627920 2304980 1396890 1886880 1894060 3014930 TRUE FALSE 1318677.781 1936603.4 1763962.509 1669695.183 2123956.169 1800149.466 1603959.861 2130537.56 2511718.706 0.525010137 0.771027184 0.702293017 0.664762013 0.845618645 0.716700267 0.638590562 0.848238919 1 21.26024347 -5 0.207556772 2.365370842 0.671126685 0.553031798 0.087810688 115.4503875 1.149642901 65.42920868 0.183175686 1.00E-05 5 -1.694244157 SLS(ph)PDEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSPDEER 8 0 Q5UIP0-2;Q5UIP0;H7C2B5 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 S(0.006)LS(0.994)PDEER;S(0.029)LS(0.971)PDEER 115.7 0.0025317 510570000 1125080 1408730 1313970 1310040 1218300 936280 1389490 1081820 1167110 TRUE FALSE 1054663.251 1513033.835 1345137.989 1343657.844 1122619.632 1206568.837 1181148.874 1216887.608 972311.8012 1.084696545 1.556119995 1.383443035 1.381920741 1.154588097 1.240927895 1.214784056 1.251540511 1 19.89105951 2.748164895 22.42716909 1.193548542 1.390957282 0.274450373 0.135912661 182.8421644 426957.4947 0.038508935 0.040262976 559.9701739 -2.748164895 0.19740874 SLS(ph)PFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSPFR 6 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36;H0YLH1 Q12802-2 AKAP13 A-kinase anchor protein 13 1 S(0.028)LS(0.972)PFR 80.229 0.068249 42609000 33816 98071 44490 49815 104130 43397 51279 75921 128160 TRUE FALSE 31699.51692 105332.2789 45545.32381 51093.33724 95952.04984 55925.00941 43590.19 85399.90397 106769.2681 0.296897389 0.986541172 0.426577091 0.478539735 0.898686032 0.523793133 0.408265326 0.799854729 1 16.70413692 1.000918513 8.483546304 0.999981044 0.596258441 0.303620071 0.215162997 0.112693498 96.61899907 0.196487267 0.049186781 10.02117193 -1.000918513 -0.403722603 SLS(ph)PFRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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;SLS(1)PFRR 117.81 0.0031527 244050000 195252 206561 216887 201751 234900 195691 243190 227860 296760 TRUE FALSE 183031.5259 221854.9914 222031.6621 206928.2722 216451.9015 252183.8149 206725.9172 256308.8226 247228.8389 0.740332425 0.897366959 0.898081563 0.836990835 0.875512349 1.020042063 0.836172342 1.036727041 1 17.91548752 8 0.12232657 1.038167754 0.305826463 0.461638836 0.067895411 94.00933216 0.787167954 0.403905244 11.77278538 99999999.92 -8 -0.73234129 SLS(ph)PGGAALGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SLSPGGAALGYR 12 0 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 SLS(1)PGGAALGYR;SLS(1)PGGAALGYR;SLS(1)PGGAALGYR;S(0.005)LS(0.995)PGGAALGYR;SLS(1)PGGAALGYR;S(0.001)LS(0.999)PGGAALGYR;SLS(1)PGGAALGYR;SLS(1)PGGAALGYR 248.91 8.32E-17 20781100000 3610630 4419380 3808360 3827570 4776940 3559240 4333190 3985930 5191270 TRUE FALSE 3384647.113 4746595.494 3898696.098 3925791.926 4401778.402 4586734.809 3683468.387 4483582.135 4324813.5 0.782611115 1.097526054 0.901471496 0.907736698 1.01779612 1.060562452 0.851705718 1.036711094 1 22.04420649 2.736936994 24.91951413 0.978913003 0.948057155 0.084318736 0.09525102 744.0278497 11419361.67 0.029212073 0.0289154 545.6786896 -2.736936994 -0.030855848 SLS(ph)PGVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSPGVSR 8 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 S(0.053)LS(0.947)PGVSR;S(0.007)LS(0.993)PGVSR 130.53 0.0010948 1039830000 1311290 1298390 1427880 1309220 1444100 1313130 1598050 1291800 1658120 TRUE FALSE 1229218.7 1394524.147 1461749.988 1342816.802 1330686.211 1692209.314 1358437.238 1453084.074 1381369.06 0.889855387 1.009523224 1.058189321 0.972091268 0.963309697 1.225023321 0.983399207 1.051915897 1 20.39766739 SLS(ph)PIIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SLSPIIGK 8 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6;X6RC15 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 SLS(1)PIIGK;SLS(1)PIIGK;SLS(1)PIIGK;SLS(1)PIIGK;SLS(1)PIIGK;SLS(1)PIIGK;SLS(1)PIIGK;S(0.001)LS(0.999)PIIGK 175.93 0.00027613 7889604000 14742410 11138760 13464860 11848450 14643480 11453620 14956190 12624160 25531970 TRUE FALSE 13819708.87 11963485.38 13784252.84 12152501.29 13493440.15 14760094.16 12713648.16 14200314.17 21270519.26 0.649711871 0.562444444 0.648044962 0.571330729 0.63437286 0.693922606 0.597712167 0.66760543 1 24.34235192 -5 0.305625757 4.266031247 0.604088588 0.90246012 0.038696625 73.80896134 0.675152709 154.7742394 0.034097613 1.00E-05 5 -3.661942659 SLS(ph)PILPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSPILPGR 9 0 M0QZS0;A0A590UK10;A0A3B3IPE9;A0A087WZG4;Q6ZSZ5-2;Q6ZSZ5-1;Q6ZSZ5-6;Q6ZSZ5-5;Q6ZSZ5 M0QZS0 ARHGEF18 Rho guanine nucleotide exchange factor 18 1 S(0.281)LS(0.719)PILPGR 90.263 0.012114 200160000 202640 227070 228530 221910 256010 212800 277500 226750 269640 TRUE FALSE 189957.1241 243882.4991 233950.8395 227604.5863 235904.0073 274231.9055 235891.4512 255060.2366 224635.3421 0.84562439 1.085681785 1.041469421 1.013218064 1.050164258 1.220787001 1.050108362 1.135441264 1 17.7772254 2.465767108 24.97837035 1.1078516 1.020140832 0.236054922 0.084153485 335.0414879 737063.8895 0.026675306 0.022334712 292.2584711 -2.465767108 -0.087710768 SLS(ph)PNHNTLQTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSPNHNTLQTLK 13 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 SLS(1)PNHNTLQTLK;S(0.2)LS(0.8)PNHNTLQTLK 266.28 1.35E-24 1314000000 2257570 2649660 2488930 2414990 3179120 1922810 3084050 2856600 3647200 TRUE FALSE 2116272.724 2845843.583 2547968.595 2476962.732 2929444.739 2477894.033 2621625.333 3213252.798 3038458.758 0.696495458 0.936607606 0.83857271 0.81520367 0.964121936 0.815510175 0.86281419 1.057527205 1 21.53490828 1.245785485 24.78496235 1.028763618 0.8565728 0.508614889 0.073795768 102.115311 350317.2786 0.046005649 0.016026822 17.61105954 -1.245785485 -0.172190818 SLS(ph)PSHLTEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLSPSHLTEDR 11 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 SLS(1)PSHLTEDR;SLS(1)PSHLTEDR;S(0.108)LS(0.885)PS(0.008)HLTEDR;S(0.089)LS(0.897)PS(0.014)HLTEDR 310.68 1.39E-45 2925890000 1528290 1925080 1757380 1772800 1883210 1617940 1946090 1599810 1699910 TRUE FALSE 1432637.057 2067614.926 1799065.883 1818293.049 1735310.283 2085013.013 1654291.871 1799549.8 1416184.039 1.011617853 1.459990276 1.270361644 1.283938386 1.225342353 1.472275464 1.168133396 1.270703348 1 20.43357733 0.493086662 1.00727577 0.999985588 1.297601567 0.278002703 0.133234829 2.020910458 2.884204811 0.115558441 0.036381073 3.112337333 -0.493086662 0.297615979 SLS(ph)PSLLGYQQPALMAAPLSLADAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSPSLLGYQQPALMAAPLSLADAHR 26 0 Q13469-3;Q13469-4;Q13469-2;Q13469;Q13469-5 Q13469-3 NFATC2 "Nuclear factor of activated T-cells, cytoplasmic 2" 1 S(0.174)LS(0.786)PS(0.039)LLGYQQPALMAAPLSLADAHR 195.94 4.57E-25 105820000 61839 87844 70665 80933 84735 76712 81540 75563 52498 TRUE FALSE 57968.60738 94348.06116 72341.20717 83009.8778 78080.2549 98857.50908 69313.83398 84997.20688 43735.74465 1.325428613 2.157230017 1.654052257 1.897987069 1.785273248 2.260336708 1.584832602 1.94342654 1 15.41652524 -1.501232026 6.64242248 0.999590696 1.841538746 0.478420382 0.270638125 0.001419597 0.000106595 0.22676518 0.053425187 0.031533195 1.501232026 0.841948051 SLS(ph)PVAAPPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSPVAAPPLR 11 0 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 S(0.037)LS(0.963)PVAAPPLR;S(0.01)LS(0.99)PVAAPPLR 97.911 0.0029367 42708000 188379 189669 209047 196249 200561 188698 219864 182824 169912 TRUE FALSE 176588.6947 203712.2901 214005.6936 201285.0816 184809.7481 243172.0493 186897.4343 205649.9788 141552.5895 1.247512993 1.439127965 1.51184584 1.421980921 1.305590726 1.717891917 1.320339211 1.452816791 1 17.11097862 -0.095308685 1.329646667 0.998730401 1.438096241 0.514171302 0.13001864 17.17499039 19.58222225 0.210130948 0.032954347 0.8029552 0.095308685 0.43936584 SLS(ph)PVAAPPLREPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLSPVAAPPLREPR 14 1 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 S(0.023)LS(0.977)PVAAPPLREPR;S(0.023)LS(0.977)PVAAPPLREPR;S(0.204)LS(0.796)PVAAPPLREPR;S(0.056)LS(0.944)PVAAPPLREPR 119.04 0.00012732 2872320000 3419240 3802770 3755440 3510590 3990920 3485300 4087780 3390900 4259110 TRUE FALSE 3205235.872 4084331.048 3844520.81 3600677.683 3677489.242 4491449.531 3474855.338 3814261.329 3548237.026 0.90333195 1.151087432 1.083501689 1.014779356 1.036427165 1.265825676 0.979318831 1.074973656 1 21.75867096 -1.173676796 7.646814304 0.999999965 1.073048521 0.032691128 0.097577016 5.28E-08 5.63E-09 0.084932855 0.020018856 0.067038333 1.173676796 0.073048556 SLS(ph)QSFENLLDEPAYGLIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSQSFENLLDEPAYGLIQK 20 0 Q8TC07-2;Q8TC07-3;C9JA93 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 S(0.103)LS(0.566)QS(0.332)FENLLDEPAYGLIQK 165.47 1.07E-11 12240000 38087 35205 38083 34628 41287 30357 48287 36508 48326 TRUE FALSE 35703.20266 37811.61483 38986.34674 35516.61311 38044.48556 39120.5731 41046.81262 41066.10416 40260.0784 0.886814037 0.939183835 0.968362415 0.882179432 0.944967995 0.971696396 1.019541299 1.020020472 1 15.29706236 2.034870802 2.353421774 1.014903169 0.929830129 0.707623667 0.02613164 0.177840493 1.873385964 0.01379628 0.007789395 108.3604506 -2.034870802 -0.08507304 SLS(ph)RS(ph)PLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSRSPLPR 9 1 Q9NYV4-3;J3QSD7 Q9NYV4-3 CDK12 Cyclin-dependent kinase 12 2 S(0.399)LS(0.607)RS(0.994)PLPR 66.498 0.036167 139790000 259730 238910 269240 247380 262690 201930 269260 206780 354850 TRUE FALSE 243473.9629 256599.145 275626.4999 253728.1896 242059.387 260223.9129 228886.9627 232596.9382 295623.2426 0.823595468 0.867993811 0.932357339 0.858282276 0.818810405 0.880255256 0.774252257 0.786801931 1 18.17340018 3.001691537 24.93937629 0.835673284 0.883198474 0 0.068016684 125.2072461 1845947.007 0.018147734 0.021548228 1003.902504 -3.001691537 0.04752519 SLS(ph)S(ph)SPQAQPPRPAELSDEEVAELFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSSSPQAQPPRPAELSDEEVAELFQR 27 1 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 2 S(0.099)LS(0.892)S(0.554)S(0.455)PQAQPPRPAELSDEEVAELFQR 155.61 1.75E-08 56575000 30077 25082 28372 30875 31045 26353 36649 25671 35741 TRUE FALSE 28194.53426 26939.09738 29044.99724 31667.30477 28606.85093 33960.68329 31153.82268 28876.08086 29775.5962 0.946900746 0.904737463 0.975463162 1.063532181 0.960748216 1.140554267 1.046287116 0.969790182 1 14.86184278 3.50101141 2.562828472 1.037989782 0.926778578 0.398244923 0.052279152 0.234825506 3.079386168 0.014256247 0.022819695 3169.650736 -3.50101141 -0.111211203 SLS(ph)SPPSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLSSPPSSK 9 0 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A1B0GWJ4;Q5VW27;O00712-5;Q5VW26;A0A2R8Y7V8;Q5VW30;A0A1B0GWI9;Q5VW31;A0A1B0GVN4;A0A1B0GWB8;O00712-6 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 SLS(0.951)S(0.049)PPSSK;SLS(0.921)S(0.079)PPSSK;SLS(0.898)S(0.1)PPSS(0.001)K 173.24 5.83E-05 383901000 942150 886740 823910 837030 1014700 589930 1276420 955680 1322250 TRUE FALSE 883182.5133 952395.1523 843453.5343 858509.6069 935009.5551 760233.2143 1085032.671 1074998.752 1101557.933 0.801757662 0.864589255 0.765691489 0.77935947 0.84880652 0.690143652 0.984998281 0.975889438 1 20.07111394 1.638783037 7.381853096 0.987399173 0.799290304 0.785984705 0.04786591 0.052410829 5.826035149 0.022775843 0.011502091 43.52943566 -1.638783037 -0.188108869 SLS(ph)SPTVTLSAPLEGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.881)S(0.118)PTVTLSAPLEGAK;S(0.024)LS(0.974)S(0.002)PTVTLSAPLEGAK 325.68 2.14E-59 168525000 367670 321740 346890 313980 491610 258200 435660 393180 691170 TRUE FALSE 344658.191 345561.9644 355118.3946 322037.2584 453000.9337 332738.1485 370336.8275 442269.3885 575809.2619 0.598563125 0.600132695 0.616729216 0.559277663 0.786720471 0.577861751 0.643158858 0.768083145 1 19.13523147 0.915544235 2.038639952 0.999568411 0.621741289 0.792198735 0.061689322 0.167655914 1.458998949 0.053745609 0.014921124 8.232736876 -0.915544235 -0.377827123 SLS(ph)SS(ph)PQAQPPRPAELSDEEVAELFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSSSPQAQPPRPAELSDEEVAELFQR 27 1 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 2 S(0.408)LS(0.592)S(0.256)S(0.744)PQAQPPRPAELSDEEVAELFQR 116.97 0.00032336 51021000 19247 17167 16724 17779 19702 12732 23486 16199 25505 TRUE FALSE 18042.36463 18438.06254 17120.70118 18235.23924 18154.68439 16407.52171 19964.49233 18221.48081 21248.05073 0.849130344 0.867753131 0.805753967 0.858207629 0.854416465 0.772189502 0.939591711 0.857560114 1 14.37504288 0.726993278 0.791886124 0.999089359 0.838952677 0.575220077 0.041416302 0.691905011 0.831627357 0.037365542 0.01313728 5.333266409 -0.726993278 -0.160136682 SLS(ph)TEVEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSTEVEPK 9 0 A0A087WVA8;Q8IWB9;Q8IWB9-2 A0A087WVA8 TEX2 Testis-expressed sequence 2 protein 1 SLS(0.874)T(0.126)EVEPK 209.97 7.92E-06 172190000 748780 460440 435580 516700 434440 346080 767040 452230 610580 TRUE FALSE 701915.1964 494531.4567 445912.1633 529959.3968 400320.8348 445987.6779 652029.4729 508691.911 508670.2535 1.379902189 0.972204396 0.876623235 1.041852542 0.786994781 0.87677169 1.28183134 1.000042577 1 18.9563712 -0.493493616 7.859109379 1.000000057 1.015103732 0 0.181766186 0 0 0.171897588 0.04051665 0.321000999 0.493493616 0.015103675 SLS(ph)TNGENMGLAVQYLDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSTNGENMGLAVQYLDPR 19 0 J3KRN4;J3QRB6;Q99759;Q99759-2 J3KRN4 MAP3K3 Mitogen-activated protein kinase kinase kinase 3 1 S(0.153)LS(0.812)T(0.036)NGENMGLAVQYLDPR 102.45 0.00041122 57337000 26654 22224 16756 19767 23516 18690 28305 23521 35882 TRUE FALSE 24985.77372 23869.48808 17153.46023 20274.25469 21669.14822 24085.49959 24060.92802 26457.64863 29893.06239 0.835838543 0.798495911 0.573827466 0.678226085 0.72488887 0.805722053 0.80490007 0.885076553 1 14.86752308 1.259318709 0.93815467 0.995055265 0.711848096 0.609004413 0.071975365 0.354544788 0.668008406 0.071155557 0.025371435 18.16848475 -1.259318709 -0.283207169 SLS(ph)TSGESLYHVLGLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLSTSGESLYHVLGLDK 17 0 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 SLS(0.979)T(0.02)SGESLYHVLGLDK;S(0.025)LS(0.952)T(0.017)S(0.005)GES(0.001)LYHVLGLDK;S(0.057)LS(0.875)T(0.057)S(0.004)GES(0.006)LYHVLGLDK;S(0.096)LS(0.84)T(0.024)S(0.035)GES(0.006)LYHVLGLDK 347.9 8.97E-88 5355950000 5179533 5416367 4679755 4511667 6128932 3782791 6803296 6749690 6373019 TRUE FALSE 4855355.275 5817400.448 4790760.999 4627444.013 5647590.404 4874821.353 5783204.924 7592403.654 5309320.958 0.91449647 1.095695757 0.902330267 0.871569839 1.063712375 0.918162867 1.089255099 1.430014067 1 22.34009593 1.49547848 5.261891202 1.229927474 0.97221031 0.414658648 0.124178587 0.129323248 7.999550693 0.065990109 0.02813709 31.29525397 -1.49547848 -0.257717164 SLS(ph)VEHLETK ddPTM_SK-BR-3_Pertuzumab_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(0.112)LS(0.888)VEHLETK;S(0.048)LS(0.952)VEHLETK;S(0.24)LS(0.76)VEHLETK;S(0.141)LS(0.859)VEHLETK 195.77 2.23E-07 1457910000 6650900 5948220 5922710 5788520 6465700 4320460 8339700 5971990 6601400 TRUE FALSE 6234632.041 6388632.398 6063199.478 5937063.223 5957910.003 5567706.665 7089239.407 6717606.097 5499583.693 1.133655271 1.161657455 1.102483354 1.079547754 1.083338364 1.012386932 1.28905019 1.221475383 1 22.39089098 1.739124554 25 1.197137169 1.102865115 0.123374158 0.082609819 0.125791099 5302.076811 0.035114972 0.019473206 54.84342314 -1.739124554 -0.094272054 SLS(ph)VPDSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSVPDSGR 9 0 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 SLS(1)VPDSGR 156.57 7.41E-05 161000000 341230 375950 344320 378010 381440 262960 445280 315160 491860 TRUE FALSE 319873.0234 403785.7292 352487.433 387710.3766 351483.2411 338872.2832 378514.3978 354508.4198 409765.3885 0.780624798 0.985407115 0.860217683 0.946176489 0.857767032 0.826990987 0.923734431 0.865149741 1 18.6444386 -1.705865697 4.111930499 1.006810116 0.889690147 0.273806899 0.059467859 0.003521695 0.000251914 0.054617994 0.012174555 0.019684949 1.705865697 -0.117119969 SLS(ph)VPVDLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLSVPVDLSR 10 0 Q9NYF3;D6RHW3 Q9NYF3 FAM53C Protein FAM53C 1 SLS(1)VPVDLSR;SLS(1)VPVDLSR;SLS(1)VPVDLSR;SLS(1)VPVDLSR 211.37 6.30E-08 547486000 729070 963760 753100 764250 874330 514370 827000 727530 910170 TRUE FALSE 683438.8101 1035117.793 770963.8876 783861.9489 805663.6487 662860.2689 702999.0275 818363.722 758256.7471 0.901329019 1.365128365 1.016758361 1.033768512 1.06252091 0.87418974 0.927125318 1.079269951 1 19.5323269 3.650648372 4.328751974 0.98603876 1.173816328 0.145275068 0.126421937 0.248204886 8.713031109 0.031795015 0.051463277 4473.50958 -3.650648372 0.187777568 SLS(ph)YS(ph)PVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SLSYSPVER 9 0 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 SLS(0.959)Y(0.073)S(0.968)PVER;SLS(0.97)Y(0.097)S(0.933)PVER;S(0.043)LS(0.931)Y(0.043)S(0.983)PVER;S(0.018)LS(0.982)Y(0.448)S(0.553)PVER;SLS(0.997)Y(0.007)S(0.996)PVER 173.04 8.15E-05 4612740000 5149140 5217850 5326780 5106660 5673240 4861540 5839320 4893320 6645270 TRUE FALSE 4826864.519 5604185.043 5453133.737 5237705.541 5227686.615 6264987.677 4963768.176 5504261.774 5536131.507 0.871884007 1.012292616 0.985007984 0.946094856 0.944285122 1.131654418 0.896613126 0.994243321 1 22.40044678 SLSCLS(ph)DLDGGVALEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLSCLSDLDGGVALEPR 17 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 SLSCLS(1)DLDGGVALEPR;SLSCLS(0.999)DLDGGVALEPR;S(0.007)LS(0.007)CLS(0.985)DLDGGVALEPR;SLSCLS(1)DLDGGVALEPR 248.13 8.29E-21 136767000 306894 269183 232166 216051 199520 124732 346101 159795 362487 TRUE FALSE 287686.0524 289113.5894 237673.0872 221595.2344 183850.504 160740.1035 294206.3681 179745.7575 301985.5779 0.952648316 0.957375486 0.787034562 0.733794097 0.608805577 0.532277417 0.974239797 0.595213052 1 18.20412013 3.827748801 1.916615761 0.736307391 0.956966713 0.25035138 0.150731071 0.457833078 3.290392522 0.040566958 0.094743165 6725.875146 -3.827748801 0.220659322 SLSDSES(ph)DDSKSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSDSESDDSKSK 13 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 SLSDS(0.023)ES(0.977)DDSKSK 156.49 1.23E-06 0 273510 126820 163730 156100 187330 111190 234800 145430 322840 TRUE FALSE 256391.4973 136209.8848 167613.7529 160105.7903 172617.8575 143288.748 199593.9198 163587.2556 268955.9184 0.95328446 0.50643944 0.623201579 0.595286362 0.641807247 0.53275923 0.742106443 0.608230734 1 18.03701021 -0.489432985 0.731495134 1.028923251 0.630130458 0.421190516 0.126542598 12.69241389 4.909976208 1.12191604 0.039604844 0.324016417 0.489432985 -0.398792793 SLSDSESDDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 0 195.27 0.0019854 0 212520 151780 165160 150640 178630 135730 211000 154130 233510 FALSE TRUE 199218.7526 163017.9491 169077.6732 154505.6774 164601.1204 174913.0476 179362.5088 173373.4698 194535.6725 1.024073117 0.837984864 0.869134545 0.794227997 0.84612307 0.899130969 0.922003181 0.891216853 1 17.5696752 0.810836946 0.81233553 0.997798794 0.868642369 0.250197532 0.06110411 1.091089651 1.458788916 0.055675163 0.019697952 6.468996945 -0.810836946 -0.129156425 SLSEEIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSEEIKR 8 1 P15924 P15924 DSP Desmoplakin 0 ; 101.25 0.0088608 322580000 422320 412860 406330 439650 465510 317590 584070 396560 473440 FALSE TRUE 395887.7451 443428.584 415968.3395 450932.1633 428950.7224 409273.0774 496494.1257 446071.3889 394419.8055 1.003721769 1.124255369 1.054633499 1.143279716 1.087548638 1.037658535 1.258796133 1.130955857 1 18.58937247 SLSEGHPTAQHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLSEGHPTAQHEK 13 0 P49748;P49748-3;P49748-2;G3V1M7;J3QRJ8 P49748 ACADVL "Very long-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 ;;; 210.91 1.51E-08 1545950000 1905630 2629060 2081040 2025730 3173270 1887690 2171000 2725090 3984480 FALSE TRUE 1786360.02 2823718.338 2130403.252 2077713.661 2924054.175 2432635.459 1845478.705 3065323.485 3319444.547 0.538150282 0.850659891 0.641795102 0.625922088 0.880886586 0.732844132 0.555960095 0.923444703 1 21.66251042 1.078634524 6.301606278 0.998453397 0.700510565 0.509660334 0.111887113 0.151126907 8.740558793 0.102101234 0.025661772 11.984903 -1.078634524 -0.297942832 SLSEINKPNFYNNDFDDDFSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSEINKPNFYNNDFDDDFSHR 22 1 Q5QJE6;J3KP30 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 0 ; 287.93 9.44E-47 335656000 440408 431763 469042 434147 462082 360795 532447 414172 535917 FALSE TRUE 412843.6494 463731.1818 480167.8977 445287.947 425791.9437 464950.6595 452611.5153 465882.2859 446468.9905 0.924686055 1.038663808 1.075478718 0.997354702 0.953687608 1.041395191 1.01375801 1.043481845 1 18.76820045 SLSGS(ph)PLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLSGSPLK 8 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 SLS(0.009)GS(0.991)PLK;SLS(0.094)GS(0.906)PLK;SLS(0.025)GS(0.975)PLK;SLS(0.005)GS(0.995)PLK 101.38 0.0057013 2570790000 1952910 1667940 1573630 1484630 1800770 1128700 2021100 1552650 1989920 TRUE FALSE 1830680.849 1791436.013 1610957.247 1522728.119 1659344.788 1454537.367 1718054.818 1746501.77 1657789.497 1.104290293 1.080617302 0.971750183 0.918529236 1.000938172 0.877395695 1.036352819 1.053512387 1 20.6608294 4.099641791 2.282829175 0.977235656 1.099040542 0.452230928 0.051643147 0.276437328 2.788934117 0.013396346 0.039516521 12578.87469 -4.099641791 0.121804886 SLSGS(ph)SPCPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SLSGS(0.5)S(0.5)PCPK;SLSGS(0.5)S(0.5)PCPK;SLS(0.333)GS(0.663)S(0.004)PCPK 177.57 2.42E-06 1349040000 2955520 2365350 2646320 2510480 2562100 1980980 3272950 2258680 3405400 TRUE FALSE 2770539.279 2540482.975 2709091.96 2574903.167 2360883.001 2552856.767 2782201.532 2540681.17 2837016.74 0.976567829 0.895476907 0.954908697 0.907609437 0.83217098 0.899838458 0.980678574 0.895546767 1 21.43594323 -1.443764539 3.036548622 1.001628698 0.920021786 0.253279632 0.044189582 9237434.552 10984660.68 128220.4635 0.010569898 0.035994443 1.443764539 -0.081606912 SLSGSS(ph)PCPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SLSGS(0.066)S(0.934)PCPK;SLSGS(0.001)S(0.999)PCPK;SLSGS(0.374)S(0.626)PCPK;SLSGS(0.499)S(0.501)PCPK;SLSGS(0.026)S(0.974)PCPK;SLSGS(0.041)S(0.959)PCPK 229 1.92E-09 5882190000 9334060 6967860 8180470 7138090 7008990 6272400 10438960 6514890 8700740 TRUE FALSE 8749857.846 7483767.604 8374514.611 7321265.474 6458532.198 8083140.056 8873734.859 7328288.358 7248530.285 1.207121651 1.032453106 1.155339673 1.010034474 0.891012653 1.115141931 1.2242116 1.011003344 1 22.78925707 4.750018399 23.67466321 1.073023665 1.20712182 0.18468211 0.093884244 1669.823269 3450135.887 0.023202092 0.348704764 56236.51498 -4.750018399 0.134098155 SLSKS(ph)DSDLLTCSPTEDATMGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSKSDSDLLTCSPTEDATMGSR 23 1 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.012)LS(0.22)KS(0.763)DS(0.005)DLLTCSPTEDATMGSR;SLS(0.016)KS(0.983)DS(0.001)DLLTCSPTEDATMGSR 236.08 6.25E-37 486020000 731470 559930 627100 585740 745070 488410 822550 611530 1047480 TRUE FALSE 685688.5984 601387.7998 641975.1081 600771.0801 686555.2077 629406.0383 699216.2637 687880.8666 872648.821 0.785755486 0.689152137 0.735662609 0.688445415 0.786748565 0.721259255 0.801257329 0.788267686 1 19.73504166 0.228407854 0.508263032 1.020048793 0.720504759 0.84056066 0.035462879 0.946459599 0.358471775 0.070581085 0.015520481 1.6920292 -0.228407854 -0.299544033 SLSLS(ph)TNLQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSLSTNLQER 11 0 A0A087WWS6;P01562 A0A087WWS6 IFNA13;IFNA1 Interferon alpha-1/13 1 SLS(0.001)LS(0.499)T(0.499)NLQER;SLS(0.013)LS(0.493)T(0.493)NLQER 79.036 0.029629 234318000 449700 539610 470770 494460 569550 357080 484730 400990 456710 TRUE FALSE 421554.0797 579563.2859 481936.8867 507148.6807 524819.8405 460163.1993 412049.2365 451054.4842 380482.1505 1.107947059 1.523233836 1.26664782 1.332910571 1.379354694 1.209421253 1.08296601 1.185481326 1 18.53746925 2.015588528 3.253034035 1.102660924 1.342188857 0.465128713 0.112249296 0.19788743 4.209695728 0.04801296 0.029344164 103.6545875 -2.015588528 0.239527934 SLSLSLADSGHLPDVHGFNSYGSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSLSLADSGHLPDVHGFNSYGSHR 25 0 Q9Y446;Q9Y446-2;E9PKC4;E9PRW6 Q9Y446 PKP3 Plakophilin-3 0 ; 193.39 1.23E-18 522140000 125927 228108 204376 204010 240160 195884 201580 194029 183543 FALSE TRUE 118045.4539 244997.3537 209223.8952 209245.242 221298.8024 252432.5309 171354.9504 218253.9478 152908.4876 0.772000663 1.602248231 1.368294845 1.368434449 1.447263039 1.650873244 1.120637272 1.427350118 1 17.22230896 -1.019431465 6.970574718 0.999999946 1.368792648 0.152361063 0.249755367 1.86E-07 2.63E-08 0.215809934 0.050866882 0.095624359 1.019431465 0.368792702 SLSNS(ph)NPDISGTPTSPDDEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLSNSNPDISGTPTSPDDEVR 21 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A0U1RRC1;A0A0U1RQJ5 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 SLSNS(0.732)NPDIS(0.265)GT(0.003)PTSPDDEVR;SLSNS(1)NPDISGTPTSPDDEVR;SLSNS(1)NPDISGTPTSPDDEVR;SLSNS(0.994)NPDIS(0.006)GTPTSPDDEVR 427.07 6.51E-174 1607590000 843620 972790 1005680 939680 998000 905870 1110720 932100 977800 TRUE FALSE 790819.3301 1044816.384 1029535.205 963793.7797 919621.1057 1167379.963 944177.8474 1048474.737 814598.8632 0.970808291 1.282614586 1.26385544 1.183151393 1.128925103 1.433073401 1.159070912 1.287105573 1 19.63573028 -0.990947531 4.69351058 0.999995855 1.225683002 0.229684135 0.121129484 4.65E-06 9.99E-07 0.103781823 0.024461161 0.102106283 0.990947531 0.225687146 SLSNVIAHEISHSWTGNLVTNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSNVIAHEISHSWTGNLVTNK 22 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 152.48 2.37E-08 466880000 477860 529420 537880 550900 635420 429520 676430 540110 616470 FALSE TRUE 447951.5956 568618.8077 550638.7676 565037.0267 585516.6764 553515.4513 575005.6012 607543.9224 513577.1745 0.872218661 1.107173052 1.07216363 1.100198869 1.140075349 1.077764899 1.11960895 1.182965195 1 18.97022156 4.739283842 24.1168297 1.10254797 0.872218542 0.69467216 0.04743032 18.56643007 618916.8434 0.009989452 0.059509985 54863.54197 -4.739283842 -0.230329427 SLSQS(ph)FENLLDEPAYGLIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSQSFENLLDEPAYGLIQK 20 0 Q8TC07-2;Q8TC07-3;C9JA93 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 S(0.002)LS(0.009)QS(0.989)FENLLDEPAYGLIQK;S(0.008)LS(0.049)QS(0.943)FENLLDEPAYGLIQK 295.78 8.45E-55 185250000 255281 216636 229327 199337 204760 181469 317130 206664 275322 TRUE FALSE 239303.4179 232675.9548 234766.7447 204452.3249 188678.9756 233856.1544 269579.3006 232466.4553 229368.9796 1.04331204 1.014417709 1.023533109 0.891368682 0.822600231 1.019563129 1.175308453 1.013504336 1 17.80731077 1.995536785 24.99733567 1.086171193 0.968044994 0.241256935 0.080677218 237.0202374 1327493.924 0.031723698 0.022847364 98.97756954 -1.995536785 -0.118126199 SLSS(ph)PGGPSKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSSPGGPSKPK 12 1 Q9BZE9;Q9BZE9-2;J3KRY8;Q9BZE9-3;J3QL04;J3QR12;Q9BZE9-4 Q9BZE9 ASPSCR1 Tether containing UBX domain for GLUT4 1 SLS(0.019)S(0.981)PGGPSKPK;SLS(0.023)S(0.977)PGGPSKPK 120.77 0.00023501 685720000 1622510 1088080 1354820 1354410 1393150 1032180 1722060 1173760 1596220 TRUE FALSE 1520959.995 1168642.575 1386956.97 1389166.454 1283737.619 1330153.61 1463853.09 1320306.52 1329800.57 1.143750446 0.878810403 1.042981182 1.044642697 0.965361008 1.000265483 1.100806484 0.992860546 1 20.34277847 SLSS(ph)PPSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLSSPPSSK 9 0 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A1B0GWJ4;Q5VW27;O00712-5;Q5VW26;A0A2R8Y7V8;Q5VW30;A0A1B0GWI9;Q5VW31;A0A1B0GVN4;A0A1B0GWB8;O00712-6 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 SLS(0.077)S(0.923)PPSSK;SLS(0.198)S(0.802)PPSSK;SLS(0.128)S(0.865)PPS(0.007)SK 163.84 6.58E-05 814570000 1857250 1788860 1568260 1712270 2052650 1184730 2561750 1827870 2592660 TRUE FALSE 1741008.038 1921309.056 1605459.868 1756209.747 1891443.149 1526742.319 2177639.37 2056083.593 2159928.297 0.806048997 0.889524462 0.743293132 0.813087059 0.875697194 0.706848612 1.008199843 0.951922152 1 21.04255199 1.670373299 8.106166315 0.984402375 0.811527601 0.698591439 0.055804253 0.065708959 7.556608648 0.025584876 0.013399747 46.81373568 -1.670373299 -0.172874774 SLSS(ph)PTDNLELSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLSSPTDNLELSLR 14 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 SLS(0.002)S(0.998)PTDNLELSLR;SLSS(0.998)PT(0.002)DNLELSLR;SLSS(1)PTDNLELSLR;SLSS(1)PTDNLELSLR;SLSS(0.999)PTDNLELSLR;SLS(0.005)S(0.995)PTDNLELSLR 376.88 2.02E-97 2408210000 3544170 3760490 3665320 3664310 3903680 2832890 3458300 2882670 2936740 TRUE FALSE 3322346.726 4038920.592 3752263.121 3758342.398 3597100.719 3650699.355 2939760.02 3242577.695 2446579.122 1.357955971 1.650844052 1.533677406 1.536162213 1.470257261 1.492164844 1.201579787 1.325351658 1 21.22233451 1.350352815 0.693122886 1.015008021 1.556265531 0.748507762 0.094467227 0.269507683 0.296923849 0.082275235 0.035947323 22.40540583 -1.350352815 0.541257509 SLSS(ph)PTVTLSAPLEGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSSPTVTLSAPLEGAK 17 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-2;Q96PU5-4;Q96PU5-5;Q96PU5-6;Q96PU5-9 Q96PU5-7;Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 SLS(0.057)S(0.943)PTVTLSAPLEGAK 367.6 1.19E-104 135380000 187690 155430 162150 155220 214400 112560 213530 167870 286200 TRUE FALSE 175942.8179 166938.1989 165996.2746 159203.208 197561.8888 145054.2447 181513.1588 188828.939 238431.3711 0.737918073 0.70015199 0.696201485 0.667710827 0.828590164 0.608368958 0.761280523 0.791963483 1 17.86321454 0.801729192 1.539224676 0.999378467 0.707441337 0.719140092 0.056618329 0.32869534 1.397644578 0.046921973 0.013630462 6.334745802 -0.801729192 -0.291937129 SLSS(ph)SPDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLSSSPDKR 9 1 Q9BVI0;Q5JWZ0;Q5JXL1;B0QYY0;Q9BVI0-2 Q9BVI0 PHF20 PHD finger protein 20 1 S(0.096)LS(0.129)S(0.459)S(0.316)PDKR;S(0.026)LS(0.065)S(0.454)S(0.454)PDKR;SLS(0.018)S(0.785)S(0.196)PDKR 133.89 0.00016182 3135270000 1829830 1383180 1403410 1434680 1519960 1130420 1606210 1280370 1710630 TRUE FALSE 1715304.207 1485592.086 1436699.548 1471496.318 1400588.473 1456753.903 1365373.722 1440227.013 1425114.802 1.203625283 1.042436781 1.008128991 1.03254581 0.982789927 1.022201089 0.958079812 1.010604206 1 20.44264671 7.999996753 0.940272767 0.997776069 137.0348399 0.896587229 0.021307756 320.2737191 0.581113714 0.006207031 93672.20697 99999252.44 -7.999996753 136.0370639 SLSS(ph)SPQAQPPRPAELSDEEVAELFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSSSPQAQPPRPAELSDEEVAELFQR 27 1 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 SLS(0.092)S(0.454)S(0.454)PQAQPPRPAELSDEEVAELFQR 102.47 0.0014766 271330000 46673 68991 64464 62624 73368 93013 58520 54992 64460 TRUE FALSE 43751.82024 74099.16543 65993.11652 64231.03786 67605.97323 119864.3432 49745.46927 61857.87225 53701.20957 0.814726905 1.379841646 1.228894415 1.196081771 1.258928314 2.232060397 0.926337966 1.151889739 1 15.71266696 1.593293866 24.99999988 1.029308298 1.348982012 0.15694141 0.355697694 1.718374092 2940.099437 0.178854639 0.083368873 39.20070397 -1.593293866 0.319673714 SLSS(ph)SPVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSSSPVKK 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 SLS(0.003)S(0.73)S(0.268)PVKK 96.604 0.004444 492150000 1461900 744010 1130300 1054200 1296100 889040 1293300 1020700 1804700 TRUE FALSE 1370402.289 799097.2745 1157111.25 1081252.557 1194309.534 1145691.416 1099381.671 1148136.642 1503483.911 0.911484505 0.531497057 0.769619975 0.719164701 0.794361367 0.762024394 0.731222771 0.763650767 1 20.519878 -5 0.217109113 2.359970389 0.69463883 0.394011508 0.095084076 134.757732 1.347750647 79.868093 0.173613964 1.00E-05 5 -1.665331559 SLSSS(ph)LDDTEVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLSSSLDDTEVKK 13 1 O95292 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 1 SLS(0.015)S(0.113)S(0.872)LDDTEVKK;SLSS(0.002)S(0.997)LDDTEVKK;SLS(0.005)S(0.036)S(0.959)LDDTEVKK 198.87 7.50E-08 1256520000 1500900 768780 876400 833090 1083020 732560 1299480 994860 1569500 TRUE FALSE 1406961.348 825701.2711 897188.6219 854468.4998 997963.9779 944038.1799 1104635.038 1119070.461 1307540.311 1.07603669 0.631492019 0.686165172 0.653493046 0.763237638 0.721995469 0.844819107 0.855859243 1 20.31842399 1.166786889 1.070919977 0.993524485 0.726798654 0.254985052 0.125891735 0.538807414 1.299545858 0.108743906 0.036062054 14.68205642 -1.166786889 -0.266725831 SLSSS(ph)PDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLSSSPDKR 9 1 Q9BVI0;Q5JWZ0;Q5JXL1;B0QYY0;Q9BVI0-2 Q9BVI0 PHF20 PHD finger protein 20 1 SLS(0.001)S(0.375)S(0.623)PDKR;SLS(0.005)S(0.039)S(0.955)PDKR;SLSS(0.03)S(0.97)PDKR 143 6.31E-05 3991100000 2171990 1490930 1620490 1569280 1964310 1178390 2035120 1491270 2059590 TRUE FALSE 2036049.023 1601320.009 1658928.788 1609550.382 1810041.016 1518572.063 1729972.649 1677458.342 1715831.124 1.186625534 0.933262013 0.966836867 0.93805874 1.054906273 0.885035854 1.008241793 0.977636038 1 20.71047614 4.744067963 24.97413302 0.967649723 1.186625628 0.682433107 0.046298002 311.386001 1411997.431 0.009705333 0.085100961 55471.25134 -4.744067963 0.218975905 SLSSS(ph)PQAQPPRPAELSDEEVAELFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLSSSPQAQPPRPAELSDEEVAELFQR 27 1 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 SLS(0.006)S(0.038)S(0.956)PQAQPPRPAELSDEEVAELFQR;SLS(0.002)S(0.004)S(0.994)PQAQPPRPAELSDEEVAELFQR;SLS(0.011)S(0.099)S(0.89)PQAQPPRPAELSDEEVAELFQR 289.23 1.14E-70 1289030000 247333 295176 295095 304579 325891 284732 326566 256155 312457 TRUE FALSE 231852.869 317031.1382 302094.7928 312395.0128 300296.8354 366929.5062 277600.46 288136.5156 260305.9082 0.89069384 1.217917566 1.160537596 1.20010727 1.153630502 1.409608828 1.066439337 1.106915005 1 17.98984853 1.588391422 25 1.064958027 1.180805856 0.149300604 0.127102979 1.687658488 2159.894678 0.062421919 0.028964186 38.76068312 -1.588391422 0.115847829 SLSSS(ph)PVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLSSSPVKK 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 SLS(0.003)S(0.163)S(0.833)PVKK;SLS(0.001)S(0.428)S(0.572)PVKK 84.658 0.0093977 1342650000 4349000 2155400 2824220 2700960 3497300 2063880 3771900 2216450 5922700 TRUE FALSE 4076803.853 2314988.059 2891211.832 2770271.206 3222636.165 2659688.652 3206338.612 2493178.662 4934163.108 0.826240188 0.469175422 0.585957896 0.561447027 0.653127206 0.539035414 0.649824204 0.505289065 1 22.23437398 -1.765816548 2.934106275 1.084589028 0.588427141 0.615620749 0.099340728 26787673.17 27068371.25 16535271.15 0.021134946 0.017146815 1.765816548 -0.496161887 SLST(ph)EVEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLSTEVEPK 9 0 A0A087WVA8;Q8IWB9;Q8IWB9-2 A0A087WVA8 TEX2 Testis-expressed sequence 2 protein 1 SLS(0.261)T(0.739)EVEPK 230.84 8.44E-07 287340000 899790 535420 538820 569860 471670 371440 853050 503560 691850 TRUE FALSE 843473.7501 575063.0539 551601.0648 584483.5724 434626.9408 478668.6982 725143.0718 566430.5745 576375.7655 1.463409464 0.997722473 0.957016408 1.014066877 0.754068729 0.830480265 1.258108191 0.9827453 1 19.13665015 4.738733314 5.595314232 0.981580462 1.480051516 0.58130168 0.130409619 0.113381765 14.38508242 0.032491789 0.216352222 54794.03895 -4.738733314 0.498471055 SLSYS(ph)PVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLSYSPVER 9 0 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SLS(0.002)YS(0.998)PVER;SLS(0.006)YS(0.994)PVER;SLSYS(1)PVER;SLSYS(1)PVER;SLS(0.003)YS(0.997)PVER;SLSYS(1)PVER 206.85 1.33E-05 3218090000 3849360 4103620 4186390 3777710 4398390 3717420 4265290 3812210 4901680 TRUE FALSE 3608435.429 4407456.295 4285693.148 3874652.434 4052958.192 4790578.807 3625749.362 4288172.81 4083557.942 0.883649866 1.079317683 1.049499777 0.948842281 0.992506596 1.173138443 0.88788978 1.050107007 1 21.96139527 SLT(ph)AHSLLPLAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLTAHSLLPLAEK 13 0 F2Z2E2;Q86VI3 F2Z2E2 IQGAP3 Ras GTPase-activating-like protein IQGAP3 1 S(0.318)LT(0.538)AHS(0.145)LLPLAEK 159.08 0.00016987 112110000 358340 396150 373780 358450 533630 251740 519640 384150 547690 TRUE FALSE 335912.1391 425481.3582 382646.2381 367648.4339 491720.8524 324413.2513 441724.8061 432111.9731 456277.0008 0.736202216 0.932506695 0.838627056 0.805757102 1.077680557 0.711000666 0.968106666 0.94703869 1 18.79955041 0.720653775 0.022213042 1.867519459 7.62E-08 0.210192784 0.104277997 630.2005563 7.240962586 316.4083731 290.5290808 5.255980861 -0.720653775 -1.867519383 SLT(ph)PPPSSTESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLTPPPSSTESK 12 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 SLT(1)PPPSSTESK;SLT(1)PPPSSTESK;SLT(0.995)PPPS(0.004)STESK;SLT(1)PPPSSTESK 177.16 0.00026413 1084040000 2660910 1993140 2141780 2112390 2246640 1659530 2566990 1828630 2451910 TRUE FALSE 2494368.393 2140714.159 2192584.033 2166597.504 2070197.957 2138609.371 2182093.68 2056938.481 2042670.381 1.221131131 1.047997846 1.073391015 1.060669173 1.013476269 1.046967436 1.068255407 1.006985023 1 20.96202499 4.738693333 7.707728263 1.046506758 1.22282258 0.82300696 0.026273031 0.038112284 24.17943315 0.005833957 0.034896775 54788.99486 -4.738693333 0.176315822 SLT(ph)RS(ph)PPAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLTRSPPAIR 10 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.345)LT(0.655)RS(1)PPAIR 77.367 0.076104 247200000 178450 128190 174110 135980 176080 176780 190560 170500 830160 TRUE FALSE 167281.133 137681.321 178239.9714 139469.477 162251.3871 227813.5162 161987.2971 191787.3003 691600.933 0.241875228 0.199076251 0.257720837 0.201661783 0.234602615 0.329400244 0.234220761 0.277309198 1 19.39958029 -4.849126947 0.373878376 10 0.224908662 0.980282038 0.033640744 57.02457832 0.488322564 413.4027082 0.021523521 1.42E-05 4.849126947 -9.775091338 SLTAEIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLTAEIDR 8 0 P54136;E5RH09;E5RJM9 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 161.02 0.00081417 257020000 333260 473810 404980 393460 476160 326890 430300 408380 500440 FALSE TRUE 312401.8515 508891.3854 414586.3168 403556.8497 438764.3143 421257.8364 365780.5097 459367.142 416913.331 0.74932085 1.220616727 0.99441847 0.96796341 1.052411333 1.010420644 0.877353835 1.101828864 1 18.66938798 1.983124151 23.76448156 0.970546976 1.026253902 0 0.127519797 1469.193793 2068909.736 0.048316896 0.032040838 96.1887212 -1.983124151 0.055706926 SLTDPSQESHTEAIS(ph)DAETSSSDISFSGIATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLTDPSQESHTEAISDAETSSSDISFSGIATR 32 0 Q5QJE6;J3KP30 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 SLTDPSQESHTEAIS(1)DAETSSSDISFSGIATR;SLTDPSQESHTEAIS(1)DAETSSSDISFSGIATR 234.02 9.72E-47 1098540000 132708 132351 126251 165483 141634 132652 158944 99169 124788 TRUE FALSE 124402.0432 142150.4058 129245.7333 169729.5739 130510.637 170946.479 135111.8228 111550.4679 103960.0766 1.196632854 1.367355723 1.243224683 1.63264187 1.255391889 1.644347374 1.29965105 1.07301256 1 16.66567008 1.249528371 3.717300268 1.014526849 1.381082565 0.479021682 0.150476908 0.180107221 4.652086028 0.119793207 0.035021082 17.76349306 -1.249528371 0.366555716 SLTEISTDFDRSS(ph)PPLQPPPVNSLTTENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLTEISTDFDRSSPPLQPPPVNSLTTENR 29 1 J3KRR7;Q9NQC7-2;Q9NQC7 J3KRR7 CYLD Ubiquitin carboxyl-terminal hydrolase CYLD 1 SLTEISTDFDRS(0.229)S(0.771)PPLQPPPVNSLTTENR 161.55 3.85E-12 235910000 61240 58910 62697 71298 54089 52776 58016 50551 60169 TRUE FALSE 57407.09772 63271.7577 64184.20245 73127.62739 49841.06812 68011.57445 49317.03939 56862.40363 50126.40519 1.145246652 1.26224407 1.280446946 1.458864387 0.994307649 1.356801354 0.983853504 1.134380241 1 15.61328315 1.716961118 9.645235292 1.046932248 1.25278029 0.375095506 0.127607337 0.10721485 26.28509806 0.05494655 0.029617725 52.11480509 -1.716961118 0.205848042 SLTNDWEDHLAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 SLTNDWEDHLAVK 13 0 P08238;P07900;P07900-2 P08238;P07900 HSP90AB1;HSP90AA1 Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha 0 ;;;;;;;;;;;; 252.2 9.43E-24 59768900000 71638701 61830973 68320812 66502446 70353859 56576097 79376666 61240765 61563908 FALSE TRUE 67154962.58 66409002.58 69941413.92 68209011.35 64828550.71 72908697.77 67474871.83 68886809.32 51288494.04 1.309357271 1.294812878 1.363686247 1.32990864 1.263997938 1.421541013 1.315594718 1.34312404 1 25.61213187 -0.947963963 5.256699828 0.999999024 1.331021403 0.858952295 0.042056871 4.36E-07 8.73E-08 0.036915375 0.008701012 0.112729099 0.947963963 0.331022379 SLTSS(ph)LENIFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SLTSSLENIFSR 12 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 SLTS(0.013)S(0.987)LENIFSR;SLTS(0.013)S(0.987)LENIFSR;SLT(0.001)S(0.022)S(0.977)LENIFSR;SLT(0.068)S(0.21)S(0.721)LENIFSR;SLT(0.007)S(0.272)S(0.721)LENIFSR;SLT(0.001)S(0.025)S(0.975)LENIFSR;SLT(0.001)S(0.27)S(0.729)LENIFSR;SLTS(0.131)S(0.868)LENIFSR 314.16 2.28E-46 1811789000 3219176 3523304 3332190 3695752 4457968 3414988 4469120 3499960 4135351 TRUE FALSE 3017693.521 3784173.094 3411231.12 3790591.253 4107857.176 4400839.598 3799016.945 3936937.71 3445134.203 0.875929164 1.098410939 0.99015914 1.100273902 1.192364922 1.277407305 1.102719581 1.142753077 1 21.71612875 3.060296181 4.044806865 1.156174987 1.012655799 0.376176731 0.088311258 0.222873222 7.456491234 0.024546815 0.029320339 1148.936908 -3.060296181 -0.143519188 SLTTECHLLDS(ph)PGLNCSNPFTQLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLTTECHLLDSPGLNCSNPFTQLER 25 0 Q15398-1;Q15398 Q15398-1 DLGAP5 Disks large-associated protein 5 1 SLTTECHLLDS(1)PGLNCSNPFTQLER;SLTTECHLLDS(1)PGLNCSNPFTQLER;SLTTECHLLDS(0.999)PGLNCS(0.001)NPFTQLER;SLTTECHLLDS(1)PGLNCSNPFTQLER 298.39 2.79E-63 347463000 111119 118964 120913 127692 141290 113862 122649 106358 124566 TRUE FALSE 104164.2601 127772.2183 123781.1135 130968.7929 130193.6533 146732.111 104258.9211 119637.0304 103775.1299 1.003749745 1.231241228 1.192782063 1.262044124 1.254574709 1.413942928 1.004661918 1.152848766 1 16.66310121 1.640641433 13.47936561 1.059463313 1.224977668 0.368085286 0.107160265 0.13067438 44.88539241 0.047055436 0.025720783 43.71610223 -1.640641433 0.165514355 SLTVSDDAESS(ph)EPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLTVSDDAESSEPER 15 0 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 SLTVSDDAES(0.12)S(0.88)EPER 218.21 7.47E-12 0 70324 65872 68770 67704 71878 60791 82249 65194 81929 TRUE FALSE 65922.54637 70749.23142 70401.25688 69441.39926 66232.99182 78340.37484 69916.52601 73333.61441 68254.52062 0.965834142 1.036550118 1.031451928 1.017389012 0.970382492 1.147768296 1.024350115 1.074414028 1 16.05863698 2.283885915 24.99998959 1.062455261 1.013009972 0.280697675 0.044384847 175.1726963 96618.77981 0.013963069 0.011682304 192.2586616 -2.283885915 -0.04944529 SLVASLAEPDFVVTDFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLVASLAEPDFVVTDFAK 18 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 203.82 5.49E-18 0 70763 67291 62738 73750 80165 55860 90270 59381 84241 FALSE TRUE 66334.07015 72273.29566 64226.17499 75642.54986 73869.16427 71985.87519 76734.85153 66794.84856 70180.63288 0.945190538 1.029818237 0.915155255 1.077826556 1.052557682 1.025722799 1.093390703 0.951756144 1 16.09878534 3.228597649 24.99993248 1.042199102 0.97073266 0.300772769 0.048832736 219.9179031 551835.8512 0.013061243 0.015787807 1692.768811 -3.228597649 -0.071466442 SLVDTVYALKDEVQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLVDTVYALKDEVQELR 17 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 0 ; 196.06 1.49E-11 212356000 474280 477120 485520 473780 582400 404930 556920 437730 599930 FALSE TRUE 444595.6614 512446.4612 497036.7637 485937.9969 536660.6533 521826.7175 473415.0162 492381.5541 499797.8073 0.889551044 1.025307542 0.994475679 0.972269165 1.073755518 1.044075644 0.947213072 0.985161493 1 18.93098505 4.745126208 24.71179614 1.004146685 0.889550983 0.505931981 0.035926264 579.2652982 2180190.86 0.008709404 0.083168551 55606.58289 -4.745126208 -0.114595702 SLVEIIEHGLVDEQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SLVEIIEHGLVDEQQK 16 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;;;;; 270.75 3.91E-35 418699000 939633 893624 941502 944366 1027014 835541 1135280 849339 943136 FALSE TRUE 880823.0478 959788.8508 963834.872 968600.0304 946356.4632 1076748.123 965055.3034 955380.8438 785720.5087 1.121038637 1.221539772 1.226689212 1.232753911 1.204444141 1.370395848 1.228242476 1.215929625 1 19.58365669 0.689549662 3.398663356 1.000005372 1.23379976 0.586631104 0.060061349 3.028914795 32.42743806 0.054812205 0.014166789 4.892712107 -0.689549662 0.233794388 SLVESVSS(ph)SPNKESNEEEQVWHFLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLVESVSSSPNKESNEEEQVWHFLGK 26 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;Q9H2U2-4 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 1 S(0.048)LVES(0.225)VS(0.225)S(0.249)S(0.249)PNKES(0.005)NEEEQVWHFLGK;SLVES(0.004)VS(0.016)S(0.49)S(0.49)PNKESNEEEQVWHFLGK 156.57 1.59E-08 3067900000 1864112 1239864 1406537 1318104 1452509 991891 1784800 1207353 1832055 TRUE FALSE 1747440.557 1331664.821 1439900.722 1351928.78 1338434.802 1278233.83 1517185.809 1358093.68 1526273.185 1.144906806 0.872494409 0.943409565 0.885771167 0.876930038 0.837486921 0.994046036 0.889810352 1 20.54158178 -0.433907062 6.307093422 1.00001071 0.924620124 0.054709086 0.087561923 0 0 0.075431128 0.017779287 0.368207761 0.433907062 -0.075390586 SLVESVSSS(ph)PNKESNEEEQVWHFLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLVESVSSSPNKESNEEEQVWHFLGK 26 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;Q9H2U2-4 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 1 SLVESVS(0.016)S(0.116)S(0.868)PNKESNEEEQVWHFLGK 174.06 1.83E-12 132830000 221660 139790 145940 155040 166340 112440 206400 119600 190460 TRUE FALSE 207786.6963 150140.1971 149401.7657 159018.5889 153276.3274 144899.6027 175452.2361 134532.3233 158670.9956 1.30954429 0.94623593 0.941582078 1.002190654 0.966000918 0.913207875 1.105761236 0.847869661 1 17.27567891 4.741024821 24.97855087 0.970240279 1.309544411 0.724774431 0.066595911 114.8652734 1164270.155 0.014769078 0.099960603 55083.91769 -4.741024821 0.339304132 SLVESVSSSPNKESNEEEQVWHFLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLVESVSSSPNKESNEEEQVWHFLGK 26 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;Q9H2U2-4 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 101.3 0.0025638 105930000 220500 184320 171440 200890 262610 143670 229540 178710 365610 FALSE TRUE 206699.2986 197967.2446 175506.6378 206045.1775 241985.6699 185145.1967 195122.6079 201022.3369 304587.3291 0.678620806 0.649952331 0.576211224 0.67647324 0.794470573 0.607855873 0.640613017 0.659982598 1 18.2164964 -1.501128442 1.823374784 1.042679833 0.653201512 0.776610064 0.057099624 33734.92775 21224.72879 7088.061085 0.015427179 0.031540717 1.501128442 -0.389478321 SLVGS(ph)WLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLVGSWLK 8 0 B0QY16;Q6ICG6-3;Q6ICG6;Q6ICG6-2 B0QY16 KIAA0930 Uncharacterized protein KIAA0930 1 SLVGS(1)WLK;SLVGS(1)WLK 143.5 0.00062981 277670000 841190 763220 777790 796140 900350 583430 934320 742430 1318710 TRUE FALSE 788541.4195 819729.6029 796239.5461 816570.3003 829640.1428 751856.7698 794227.3898 835124.0198 1098608.782 0.717763623 0.746152422 0.724770782 0.743276691 0.755173413 0.684371709 0.722939233 0.760165068 1 20.0672463 0.737952208 3.310072821 0.999990894 0.728596359 0.950665808 0.019333498 0.480626204 5.846435172 0.018314126 0.004745398 5.469557704 -0.737952208 -0.271394535 SLVHEVGKPPQDVTDDS(ph)PPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SLVHEVGKPPQDVTDDSPPSK 21 1 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 SLVHEVGKPPQDVTDDS(0.994)PPS(0.006)K;SLVHEVGKPPQDVTDDS(1)PPSK;SLVHEVGKPPQDVTDDS(1)PPSK;SLVHEVGKPPQDVTDDS(1)PPSK 248.95 8.32E-31 1567240000 1632740 1231830 1505050 1378890 1537360 1142440 1970140 1297370 1994310 TRUE FALSE 1530549.718 1323035.975 1540750.497 1414274.652 1416621.947 1472243.882 1674735.797 1459349.5 1661446.777 0.921215015 0.796315593 0.927354711 0.851230789 0.852643591 0.886121603 1.007998462 0.878360668 1 20.66400865 1.905404219 6.538577659 0.960458246 0.866968165 0.417852266 0.050125525 0.217334648 12.62544021 0.01980553 0.01216117 80.42743508 -1.905404219 -0.093490081 SLVIELDKELYGPDNHLVEWHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLVIELDKELYGPDNHLVEWHR 22 1 J3KMX2;B9EGA3;Q92925-3;Q92925-2;Q92925 J3KMX2 SMARCD2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 0 ; 139.69 8.72E-08 256610000 541520 534860 513300 471130 686190 391960 591950 573200 711060 FALSE TRUE 507627.2298 574461.5909 525475.7184 483219.9934 632299.4054 505112.4891 503192.5929 644765.2818 592379.4924 0.856929108 0.969752664 0.887059267 0.81572708 1.067389087 0.852683956 0.849442966 1.088432821 1 19.17616217 1.236195678 24.99946393 1.04421644 0.903240458 0.388994414 0.075125193 63.98713713 676325.987 0.057269686 0.016940896 17.22644562 -1.236195678 -0.140975982 SLVLQRPQTWADCVTWACHHWHTQYSNNIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLVLQRPQTWADCVTWACHHWHTQYSNNIR 30 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 182.97 2.00E-18 438081000 46402 100535 35279 30539 108656 23922 51802 82929 34791 FALSE TRUE 43497.78165 107978.716 36115.83454 31322.68244 100122.5961 30827.89306 44034.77101 93282.8682 28984.15734 1.500743359 3.725439202 1.246054323 1.080682874 3.454390441 1.063611845 1.519270355 3.21840884 1 14.82297692 5.982183248 0.059196581 5.30E-10 5.21690969 0.049211434 1.045337654 621.7415572 4.12490079 97.63243886 320.8918769 959805.5311 -5.982183248 5.21690969 SLWEITVES(ph)LRYLT(ph)EKGLLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLWEITVESLRYLTEKGLLQK 21 2 E3W980;Q8TDG4 E3W980 HELQ Helicase POLQ-like 2 SLWEIT(0.015)VES(0.679)LRY(0.627)LT(0.679)EKGLLQK 79.97 0.013167 424030000 1750800 429380 703680 636000 652900 419300 838330 481490 792440 TRUE FALSE 1641220.553 461171.742 720371.6219 652320.8367 601623.8677 540345.1032 712630.1992 541605.0864 660176.6446 2.486032438 0.698558099 1.091180107 0.988100446 0.911307409 0.81848564 1.079453817 0.820394194 1 19.33249258 4.743843426 24.99995223 0.932907829 2.486033088 0.941168635 0.122570484 119.472736 565366.0583 0.027558943 0.235783728 55442.5792 -4.743843426 1.553125259 SLYDEVAAQGEVVRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLYDEVAAQGEVVRK 15 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 106.36 0.0040774 0 69384 83448 87686 98001 108930 60741 94231 90993 160760 FALSE TRUE 65041.37929 89626.57675 89765.95333 100515.8716 100375.0772 78275.94065 80101.93635 102353.6764 133928.1175 0.485643945 0.669214041 0.670254723 0.750521052 0.749469784 0.584462338 0.598096485 0.764243374 1 17.03109935 -5 0.334339657 4.563276948 0.645374293 0.631480801 0.08356783 251.3176544 2.149531593 637.5470416 0.068214993 1.00E-05 5 -3.917902655 SLYGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SLYGER 6 0 E9PEI0;Q69YH5 E9PEI0 CDCA2 Cell division cycle-associated protein 2 0 ;; 139.92 0.027558 1170550000 903910 1135160 827190 720560 822430 557740 1129530 852550 1404640 FALSE TRUE 847335.8866 1219208.428 846811.3374 739050.7895 757839.6653 718750.4838 960167.4625 958992.7442 1170196.51 0.724097089 1.041883493 0.723648832 0.631561266 0.647617438 0.614213491 0.820518139 0.819514275 1 20.15831939 -0.622410612 8.111703777 1.000000482 0.767154259 0.272063906 0.125112154 0 0 0.130430643 0.030742797 0.238555475 0.622410612 -0.232846222 SLYHDISGDTSGDYRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SLYHDISGDTSGDYRK 16 1 P50995;P50995-2 P50995 ANXA11 Annexin A11 0 ; 119.54 0.00012082 589150000 88341 143482 153744 131572 233511 92423 216371 167598 553990 FALSE TRUE 82811.8945 154105.5566 157390.8803 134948.3603 215171.988 119104.0197 183928.1772 188522.9792 461525.4901 0.179430814 0.333904757 0.341023158 0.292396332 0.466219077 0.258065962 0.398522251 0.408477935 1 18.8160508 -5 0.261116266 5.33301688 0.284006035 0.905410022 0.068924295 51.10116075 0.501672222 118.7235973 0.081687512 1.00E-05 5 -5.049010845 SLYQSAGVAPES(ph)FEYIEAHGTGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SLYQSAGVAPESFEYIEAHGTGTK 24 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 SLYQSAGVAPES(1)FEYIEAHGTGTK 290.67 5.44E-62 233860000 358980 343170 363560 360570 397500 303220 476960 334250 511600 TRUE FALSE 336512.0826 368578.6639 372183.8149 369822.8366 366281.9534 390754.6916 405444.2759 375981.8483 426210.6549 0.78954404 0.864780501 0.873239114 0.867699651 0.859391827 0.916811176 0.951276725 0.882150279 1 18.70120713 8 0.053301574 1.208946175 0.270627292 0.768747514 0.027332613 202.7722049 0.812818812 3.203710151 15.30579828 99999999.98 -8 -0.938318882 SLYQSAGVAPESFEYIEAHGTGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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 ;;;;;;;; 401.96 1.91E-157 11381371000 10996979 11611446 12615890 13146608 13964772 10745432 17005499 12655430 15873092 FALSE TRUE 10308697.71 12471169.54 12915144.87 13483972.22 12868035.14 13847463.78 14455682.3 14235488.29 13223770.4 0.779558129 0.943087271 0.976661306 1.019676825 0.973098802 1.047164565 1.093158899 1.076507521 1 23.65663025 6.124184687 0.45933657 1.055720178 6.05E-17 0.816625764 0.037582806 6.690524262 0.403695308 0.022928488 5.037233687 1331020.324 -6.124184687 -1.055720178 SMDFEEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SMDFEEAER 9 0 O43396;K7ER96 O43396 TXNL1 Thioredoxin-like protein 1 0 81.95 0.046137 316940000 378210 449080 423950 440180 491320 408790 460850 390410 543620 FALSE TRUE 354538.5112 482330.3505 434006.2942 451475.764 452733.7091 526801.0368 391749.8208 439153.5479 452886.3101 0.782842191 1.065014198 0.958311798 0.99688543 0.999663048 1.163208128 0.865006983 0.969677242 1 18.7887894 4.749898853 24.22398277 0.99888654 0.782841993 0.451780454 0.075867966 1045.803827 2234278.963 0.017246431 0.262813862 56221.03718 -4.749898853 -0.216044547 SMDIDDFIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SMDIDDFIR 9 0 A0A494C0G7;Q9UNQ2 A0A494C0G7 DIMT1 Probable dimethyladenosine transferase 0 ; 121.58 0.0014188 62874000 193123 297670 271200 278690 302980 335570 327780 246850 261460 FALSE TRUE 181035.7762 319709.7965 277632.9921 285841.6572 279185.173 432443.6115 278632.432 277669.7659 217820.6369 0.83112316 1.467766329 1.274594529 1.312279962 1.281720488 1.985319746 1.279182891 1.274763355 1 17.73278112 4.743800572 24.27552782 1.386945165 0.831122804 0.29890939 0.251170161 437.9252237 2028710.126 0.055068882 0.464716999 55437.10873 -4.743800572 -0.555822361 SMDS(ph)SDLSDGAVTLQEYLELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SMDSSDLSDGAVTLQEYLELK 21 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 S(0.233)MDS(0.295)S(0.295)DLS(0.176)DGAVT(0.001)LQEYLELK 142.98 9.10E-08 10560000 8894.7 5615.2 7455 6779.5 6902.3 4938.5 8885.7 6985.8 7587 TRUE FALSE 8337.996604 6030.955251 7631.836121 6953.473448 6360.221201 6364.16478 7553.371776 7857.992508 6320.680686 1.319161182 0.954162305 1.207438961 1.100114654 1.006255737 1.006879654 1.195025054 1.243219346 1 12.62586422 -1.532683238 7.559089619 0.999965882 1.116272972 0.099315099 0.116620841 6.21E-05 3.84E-06 0.10454647 0.024634619 0.029330317 1.532683238 0.11630709 SMDS(ph)SDLSDGAVTLQEYLELKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SMDSSDLSDGAVTLQEYLELKK 22 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 SMDS(0.996)S(0.003)DLSDGAVTLQEYLELKK 275.54 1.19E-45 197330000 407400 249380 279980 258100 317720 200070 391540 262540 349980 TRUE FALSE 381901.5612 267844.3547 286621.2578 264723.283 292767.5528 257826.9611 332832.2119 295318.6969 291566.077 1.309828513 0.918640321 0.983040485 0.907935812 1.004120767 0.884283123 1.141532702 1.012870564 1 18.15346335 -0.344251027 8.567780845 1.000001368 1.007892005 0 0.126015148 0 0 0.110991306 0.026160902 0.452635876 0.344251027 0.007890637 SMDSSDLS(ph)DGAVTLQEYLELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SMDSSDLSDGAVTLQEYLELK 21 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 S(0.24)MDS(0.24)S(0.24)DLS(0.28)DGAVT(0.001)LQEYLELK 87.16 0.0021931 0 10156 6007.7 7575.3 8089 6565.5 5995 9177.4 5585.9 8664.7 TRUE FALSE 9520.354089 6452.516359 7754.989693 8296.577435 6049.872114 7725.659179 7801.334069 6283.311911 7218.505594 1.318881584 0.893885344 1.07432066 1.149348342 0.838105898 1.070257421 1.080740877 0.870444974 1 12.81748448 4.75197376 24.59374149 1.006962819 1.31888184 0.491912513 0.102331115 1588.496021 2912530.939 0.022783948 0.44466587 56490.2843 -4.75197376 0.311919022 SMEAEMIQLQEELAAAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SMEAEMIQLQEELAAAER 18 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 240.46 1.38E-23 232608000 218339 253708 254460 249798 258653 213413 274214 217596 246099 FALSE TRUE 204673.5517 272492.8043 260495.9114 256208.2396 238339.4367 275021.8686 233098.1564 244763.3396 205023.487 0.998293194 1.329080918 1.270566193 1.249653117 1.16249821 1.341416404 1.136933918 1.193830732 1 17.64542967 0.667508452 0.931546178 1.000504288 1.239198601 0.290941857 0.100684655 1.199395276 1.80425879 0.088048816 0.028994768 4.650594265 -0.667508452 0.238694314 SMEIEVLVDADPVVDSSQKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SMEIEVLVDADPVVDSSQKR 20 1 O00154-6;O00154-4;O00154-7;O00154;O00154-5;K7EKP8 O00154-6 ACOT7 Cytosolic acyl coenzyme A thioester hydrolase 0 ; 173.98 6.53E-12 101976000 216959 191076 214217 204153 228041 180310 239457 183023 216587 FALSE TRUE 203379.9235 205223.4659 219298.3284 209391.9116 210131.5797 232362.5699 203552.6459 205873.8244 180437.2305 1.127150549 1.137367634 1.215371838 1.16046955 1.16456886 1.287775085 1.128107793 1.140971982 1 17.46113752 0.761689119 1.658859244 1.000625624 1.178317593 0.572404363 0.047407368 0.585283083 2.694626951 0.0426855 0.01219839 5.776823772 -0.761689119 0.177691968 SMEMLVEHQAHDILT ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SMEMLVEHQAHDILT 15 0 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2;H0YD73 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ;;; 125.97 8.72E-05 653040000 741150 910310 910370 920970 944530 806010 967890 804990 862270 FALSE TRUE 694762.7445 977710.2996 931964.4063 944603.6494 870350.4239 1038692.003 822763.88 905494.7735 718351.5665 0.967162566 1.361047077 1.297365315 1.314960102 1.211593967 1.445938244 1.145349879 1.260517573 1 19.45433056 0.466269316 1.039593833 1.000156403 1.274229906 0.255158394 0.130409585 2.366333806 3.4415905 0.113001815 0.035198882 2.925966272 -0.466269316 0.274073503 SMESS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SMESSPR 7 0 Q1ED39;H3BPL4 Q1ED39 KNOP1 Lysine-rich nucleolar protein 1 1 SMES(0.004)S(0.996)PR;SMES(0.104)S(0.895)PR;SMES(0.052)S(0.948)PR;SMES(0.004)S(0.996)PR;SMES(0.137)S(0.863)PR 96.311 0.013453 839707000 1981530 2333690 2142340 2062420 2512320 1913370 2451250 2055100 2215310 TRUE FALSE 1857509.574 2506478.836 2193157.316 2115345.189 2315012.521 2465728.858 2083707.819 2311683.759 1845560.45 1.006474524 1.358112565 1.188342174 1.146180386 1.254368299 1.336032563 1.129037967 1.252564639 1 20.81562756 -1.295566155 0.788957792 0.938922615 1.219629044 0.283849523 0.102834728 128.1445329 30.81603624 17.26469896 0.031314879 0.050633022 1.295566155 0.280706429 SMGFIGHYLDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SMGFIGHYLDQK 12 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;; 175.57 2.73E-05 4298200000 10143020 10983400 9712630 9434190 12913150 6447770 11491800 10970540 13574830 FALSE TRUE 9508186.484 11796622.36 9943018.17 9676287.287 11899003.29 8309136.528 9768711.275 12340236.07 11309103.18 0.840755128 1.043108563 0.879204833 0.85561933 1.052161529 0.734729925 0.863791861 1.091177247 1 23.43098119 1.240228101 24.99997489 1.045588649 0.902519284 0.295712233 0.095757727 55.55591131 833041.5428 0.07040396 0.022652223 17.38713801 -1.240228101 -0.143069366 SMGSQEDDSGNKPS(ph)SYS ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SMGSQEDDSGNKPSSYS 17 1 Q9UNS2-2;Q9UNS2;H7C3P9 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 1 SMGSQEDDS(0.001)GNKPS(0.333)S(0.333)YS(0.333) 115.26 0.00031876 0 189970 140600 163990 153000 172470 129160 206320 144040 215740 TRUE FALSE 178080.1168 151010.1703 167879.9202 156926.239 158924.9019 166446.3953 175384.2314 162023.7111 179731.6003 0.990811391 0.840198218 0.934059008 0.873114348 0.884234612 0.926083087 0.975811884 0.901475928 1 17.45548456 1.997842819 5.32196888 0.955491672 0.89860854 0.217352762 0.046364375 0.227467876 20.74057838 0.017255434 0.011478614 99.50452229 -1.997842819 -0.056883133 SMGTGDTPGLEVPS(ph)SPLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SMGTGDTPGLEVPSSPLRK 19 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SMGTGDTPGLEVPS(0.644)S(0.356)PLRK;SMGTGDTPGLEVPS(0.5)S(0.5)PLRK;SMGTGDTPGLEVPS(0.742)S(0.258)PLRK 229.15 5.33E-20 3835616000 4076810 3243290 3532250 3795520 4117820 3085530 4829260 3375510 5469840 TRUE FALSE 3821649.739 3483426.566 3616036.638 3892919.469 3794423.028 3976272.422 4105157.296 3796949.854 4556888.367 0.83865336 0.764430964 0.793531978 0.854293359 0.832678513 0.872584997 0.900868524 0.833233019 1 22.1196176 0.343078167 0.196828977 1.081596534 0.749645349 0.745289262 0.032209048 3.309376251 0.308299799 0.315794429 0.123532402 2.203322996 -0.343078167 -0.331951186 SMGTGDTPGLEVPSS(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 SMGTGDTPGLEVPSSPLR 18 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SMGTGDTPGLEVPS(0.007)S(0.993)PLR;SMGTGDTPGLEVPS(0.302)S(0.698)PLR;SMGTGDTPGLEVPS(0.003)S(0.997)PLR;SMGTGDTPGLEVPSS(1)PLR;SMGTGDTPGLEVPS(0.008)S(0.992)PLR;SMGTGDTPGLEVPS(0.016)S(0.984)PLR;SMGTGDTPGLEVPS(0.003)S(0.997)PLR;SMGTGDTPGLEVPSS(1)PLR;SMGTGDTPGLEVPSS(1)PLR;SMGTGDTPGLEVPS(0.001)S(0.999)PLR;SMGTGDTPGLEVPS(0.005)S(0.995)PLR 427.31 8.05E-169 3396219000 5336510 5809490 5876590 6165400 6584560 5499760 6554330 5334780 5687550 TRUE FALSE 5002507.365 6239630.684 6015985.49 6323614.602 6067435.218 7087451.431 5571569.064 6000839.026 4738261.162 1.055768602 1.316860863 1.269661018 1.334585492 1.280519374 1.495791639 1.175867871 1.266464389 1 22.17592629 -0.503534107 7.526144831 1.000006302 1.281794039 0.371557791 0.111805027 0 0 0.097279944 0.022929103 0.313664878 0.503534107 0.281787736 SMGTGDTPGLEVPSS(ph)PLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SMGTGDTPGLEVPSSPLRK 19 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SMGTGDTPGLEVPS(0.22)S(0.78)PLRK;SMGTGDTPGLEVPS(0.382)S(0.618)PLRK;SMGTGDTPGLEVPS(0.015)S(0.985)PLRK;SMGTGDTPGLEVPS(0.288)S(0.712)PLRK 258.11 3.14E-31 4988960000 2911110 2359550 2639360 2619470 2859580 2013090 3045620 2217560 3170980 TRUE FALSE 2728908.822 2534253.537 2701966.866 2686690.035 2635000.122 2594236.403 2588957.555 2494427.247 2641722.953 1.033003411 0.959318438 1.022804781 1.017021877 0.997455134 0.982024402 0.980026143 0.944242561 1 21.33304774 2.097859864 2.171773829 0.972749475 1.002683458 0.275367561 0.023629643 0.458468142 4.19696449 0.011779196 0.006893857 125.2736883 -2.097859864 0.029933983 SMIEISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SMIEISR 7 0 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;Q5SZW8;E9PM09;Q5SZX9 P49368 CCT3 T-complex protein 1 subunit gamma 0 126.2 0.009247 280340000 169900 210810 201850 196960 227560 176690 202910 185760 208550 FALSE TRUE 159266.2623 226418.5917 206637.9773 202014.3271 209688.3555 227697.5347 172485.5292 208952.5449 173741.6577 0.916684371 1.303191156 1.189340427 1.162728212 1.206897403 1.310552332 0.992770136 1.202662319 1 17.40658418 1.080342003 0.927766503 1.013657955 1.189789405 0.103836632 0.125489508 0.975987923 1.839249996 0.10795655 0.037474475 12.03211581 -1.080342003 0.176131451 SMIIDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SMIIDRR 7 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 113.5 0.0098063 471200000 293260 450310 411920 422700 485240 344150 468570 413010 486950 FALSE TRUE 274905.3801 483651.4209 421690.9369 433547.1976 447131.2078 443500.5182 398312.2785 464575.2076 405674.8992 0.677649469 1.192214312 1.039479982 1.068705997 1.102190963 1.093241211 0.981850934 1.145190912 1 18.62996451 4.748811296 24.99547158 1.077555224 0.677649249 0.801424143 0.062606739 635.3969179 1549334.702 0.014435588 0.204889934 56080.42493 -4.748811296 -0.399905975 SMMS(ph)PMADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SMMSPMADR 9 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 S(0.154)MMS(0.846)PMADR;S(0.166)MMS(0.834)PMADR 51.436 0.047007 184425000 341560 365580 383710 334940 360560 314800 413590 312660 431050 TRUE FALSE 320182.3693 392647.9236 392811.7824 343535.1275 332243.072 405677.6496 351576.0191 351696.2892 359104.9703 0.891612191 1.093407098 1.093863396 0.956642642 0.925197643 1.129690991 0.979034121 0.979369038 1 18.4540461 3.237736936 24.99997166 0.998960128 1.050328291 0.002445465 0.077492702 55.67263835 1689789.686 0.021313973 0.026930837 1728.76888 -3.237736936 0.051368163 SMMS(ph)PMAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SMMSPMAER 9 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 S(0.008)MMS(0.992)PMAER;S(0.009)MMS(0.991)PMAER 91.215 0.0033129 245730000 483890 526030 525040 471140 517970 436490 536600 432330 626630 TRUE FALSE 453604.1887 564977.8085 537494.1967 483230.25 477290.7256 562497.5772 456141.8116 486307.3522 522041.4048 0.86890462 1.082247123 1.029600702 0.925655026 0.914277529 1.077496099 0.873765581 0.93154939 1 18.99380471 3.244559802 24.9931817 0.94923484 1.017728589 0.023710571 0.076931878 263.6498328 1098382.888 0.020249825 0.026725025 1756.142698 -3.244559802 0.068493749 SMNLRPEEDDIPWEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SMNLRPEEDDIPWEDLR 17 1 Q14CX7;Q14CX7-2 Q14CX7 NAA25 "N-alpha-acetyltransferase 25, NatB auxiliary subunit" 0 ;;; 164.59 2.35E-09 340984000 250828 294660 289619 299183 324676 275149 358861 290030 288854 FALSE TRUE 235129.1232 316476.933 296488.8994 306860.5423 299177.2566 354580.0496 305053.1246 326240.8839 240642.4013 0.977089332 1.315133706 1.23207256 1.275172374 1.243244146 1.47347287 1.267661571 1.35570823 1 17.87653134 4.741971806 24.41242887 1.285637098 0.97708917 0.368495147 0.119140347 221.7786713 1587075.026 0.024585803 0.177467499 55204.15997 -4.741971806 -0.308547928 SMNLRPEEDDIPWEDLRDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SMNLRPEEDDIPWEDLRDNR 20 2 Q14CX7;Q14CX7-2 Q14CX7 NAA25 "N-alpha-acetyltransferase 25, NatB auxiliary subunit" 0 69.122 0.011382 82653000 43201 61234 56223 58992 70546 41539 62678 52838 92834 FALSE TRUE 40497.12653 65767.82907 57556.63611 60505.83459 65005.60173 53530.63497 53280.01577 59434.94061 77339.40567 0.523628623 0.850379292 0.74420841 0.782341603 0.840523678 0.692152138 0.688911627 0.768494923 1 16.23891606 -2.235390228 1.827916093 1.685353566 0.745529244 0.441886621 0.092614082 1648183.585 264280.5281 4656253.642 0.024269569 0.005815804 2.235390228 -0.939824322 SMQHS(ph)PNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 SMQHSPNLR 9 0 O76041-2;O76041 O76041-2 NEBL Nebulette 1 SMQHS(1)PNLR;SMQHS(1)PNLR;S(0.001)MQHS(0.999)PNLR;SMQHS(1)PNLR;SMQHS(1)PNLR;SMQHS(1)PNLR;S(0.001)MQHS(0.999)PNLR;S(0.001)MQHS(0.999)PNLR;S(0.001)MQHS(0.999)PNLR;SMQHS(1)PNLR;S(0.004)MQHS(0.996)PNLR;S(0.009)MQHS(0.991)PNLR 145.29 6.28E-05 9290410000 3020020 4911870 4559340 6436560 6202320 2651730 2730910 2192649 2514030 TRUE FALSE 2831002.339 5275549.966 4667489.698 6601733.027 5715214.806 3417241.404 2321435.398 2466406.054 2094422.152 1.351686591 2.518857032 2.22853339 3.152054623 2.728778819 1.631591511 1.108389441 1.177606937 1 20.99812083 2.038384997 3.811598845 1.146151507 2.421283163 0.63262235 0.455016966 0.142153937 4.372877179 0.190677585 0.125578365 109.2408315 -2.038384997 1.275131656 SMQHSPNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SMQHSPNLR 9 0 O76041-2;O76041 O76041-2 NEBL Nebulette 0 ; 63.816 0.055819 104216000 28422 60111 48365 50180 62406 41995 42071 53261 45518 FALSE TRUE 26643.11775 64561.68099 49512.24064 51467.70375 57504.88449 54118.27477 35762.84412 59910.75309 37920.75174 0.702599936 1.702542223 1.305676664 1.357243762 1.516448959 1.427141401 0.943094281 1.579893603 1 15.21069994 0.052198649 0.484289485 0.970717805 1.36241971 0.063457494 0.302255155 8.927720688 2.72541486 0.895866727 0.146804205 1.127713161 -0.052198649 0.391701905 SMS(ph)APSDLEMIGNEDLEFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SMSAPSDLEMIGNEDLEFTR 20 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;Q9Y4D8-2 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 1 S(0.136)MS(0.864)APSDLEMIGNEDLEFTR;S(0.164)MS(0.833)APS(0.003)DLEMIGNEDLEFTR;S(0.147)MS(0.849)APS(0.003)DLEMIGNEDLEFTR 167.99 5.05E-11 83413000 112309 108764 106546 113688 125062 82729.5 133132 108186 151961 TRUE FALSE 105279.7802 116816.9997 109073.3214 116605.4266 115240.135 106612.1636 113170.0925 121693.2602 126597.7274 0.831608768 0.922741681 0.861574087 0.921070456 0.910285969 0.842133313 0.89393463 0.961259438 1 16.94989198 1.130701022 3.140678959 0.998031978 0.884969237 0.641696631 0.030999395 0.137814619 2.479791245 0.026702579 0.007146428 13.51142086 -1.130701022 -0.11306274 SMS(ph)FQGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SMSFQGIR 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 SMS(1)FQGIR;SMS(1)FQGIR;SMS(1)FQGIR;S(0.048)MS(0.952)FQGIR;S(0.002)MS(0.998)FQGIR;S(0.154)MS(0.846)FQGIR 167.09 0.00033009 1859600000 2515020 2822060 2334390 2726280 2156580 1768300 3461160 2215350 3080120 TRUE FALSE 2357609.388 3031008.259 2389762.833 2796240.96 1987210.906 2278779.504 2942191.19 2491941.324 2566028.074 0.918777706 1.181206196 0.93130814 1.089715654 0.774430696 0.888057121 1.146593531 0.971127849 1 21.29110552 3.835329206 7.418351313 0.979611844 1.066512577 0.062437771 0.119399998 0.598635067 36.62369107 0.030012362 0.054384189 6844.302657 -3.835329206 0.086900733 SMS(ph)GGHGLR ddPTM_SK-BR-3_Pertuzumab_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(0.038)MS(0.962)GGHGLR;S(0.067)MS(0.933)GGHGLR 104.07 0.01112 497430000 144318 208450 163590 185945 218110 137534 211567 188767 216900 TRUE FALSE 135285.394 223883.8549 167470.4321 190716.6635 200980.5204 177237.8331 179844.4924 212334.9755 180697.9888 0.748682345 1.238994725 0.926797433 1.055444307 1.112245475 0.980851167 0.995276669 1.175082119 1 17.46322092 4.763497836 24.43530702 1.054106337 0.748681833 0.517966618 0.094376974 4883.036898 4784649.959 0.021307973 1.465272743 58009.32822 -4.763497836 -0.305424504 SMS(ph)PTSTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SMSPTSTPK 9 0 E9PQ01;E9PKN0;O94913 E9PQ01 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 1 S(0.297)MS(0.663)PT(0.039)S(0.001)TPK;SMS(0.919)PT(0.08)S(0.001)TPK;S(0.001)MS(0.939)PT(0.037)S(0.019)T(0.004)PK;SMS(0.425)PT(0.425)S(0.15)TPK 139.98 0.00011558 348486000 1299690 983810 1113950 1020400 1138830 862940 1329050 1019050 1541340 TRUE FALSE 1218344.723 1056652.316 1140373.42 1046585.192 1049390.886 1112056.769 1129771.291 1146280.636 1284080.397 0.948807198 0.822886417 0.888085686 0.815046468 0.817231451 0.866033601 0.879829093 0.892686033 1 20.2923041 0.685053105 1.137252635 0.9997304 0.856183672 0.542055843 0.03969306 0.739732193 1.587186421 0.034510643 0.010718417 4.842315747 -0.685053105 -0.143546728 SMS(ph)VDLSHIPLKDPLLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SMSVDLSHIPLKDPLLFK 18 1 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 S(0.134)MS(0.866)VDLSHIPLKDPLLFK;S(0.017)MS(0.965)VDLS(0.019)HIPLKDPLLFK 205.96 5.47E-16 462610000 1575370 1420460 1238320 1178280 1438090 796280 2077020 1595650 3207720 TRUE FALSE 1476770.404 1525632.336 1267693.535 1208516.66 1325148.212 1026153.109 1765590.133 1794870.415 2672330.809 0.552615117 0.570899505 0.474377473 0.45223318 0.49587731 0.383991797 0.660692953 0.671649786 1 21.34966718 0.922135964 1.267811922 0.995297518 0.498239685 0.856785728 0.064927704 0.189006627 0.609734507 0.059935457 0.018338624 8.358646594 -0.922135964 -0.497057833 SMSHQAAIASQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SMSHQAAIASQR 12 0 Q4G0F5 Q4G0F5 VPS26B Vacuolar protein sorting-associated protein 26B 0 93.494 0.0054167 21725000 10174 21358 8540.5 14270 18214 7462.3 10080 18270 18945 FALSE TRUE 9537.227501 22939.36854 8743.084693 14636.19236 16783.54591 9616.54487 8568.597578 20551.04972 15782.95711 0.604273802 1.453426527 0.553957324 0.927341578 1.063396789 0.60929931 0.542901911 1.302103882 1 13.94607992 3.960887562 24.66708537 0.814878327 1.07877744 0.030866718 0.315506207 702.2687568 1067098.736 0.074864578 0.135512442 9138.766098 -3.960887562 0.263899113 SMSPT(ph)STPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SMSPTSTPK 9 0 E9PQ01;E9PKN0;O94913 E9PQ01 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 1 SMS(0.421)PT(0.57)S(0.009)TPK 113.44 0.020113 149570000 515910 378980 428910 405120 441000 345440 491250 369790 593600 TRUE FALSE 483620.114 407040.0735 439083.9477 415516.0651 406365.6389 445162.9203 417591.623 415959.0955 494524.3252 0.977950102 0.823094139 0.887891506 0.840233824 0.821730334 0.900184071 0.844430904 0.841129696 1 18.91568196 -1.647679509 6.137889375 1.000942701 0.862950227 0.439475077 0.046970583 0.000530904 3.05E-05 0.03984804 0.009329758 0.022507149 1.647679509 -0.137992474 SMSSIPPYPASSLASS(ph)SPPGSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SMSSIPPYPASSLASSSPPGSGR 23 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 SMSSIPPYPASSLAS(0.017)S(0.706)S(0.277)PPGSGR 188.84 2.10E-17 141060000 30808 35874 30830 31976 33183 24668 35921 29596 40078 TRUE FALSE 28879.78227 38530.14829 31561.30216 32796.5583 30576.94103 31789.25115 30534.97952 33291.12575 33388.72289 0.864956182 1.153986884 0.945268325 0.982264533 0.915786481 0.95209545 0.914529724 0.997076943 1 15.02707329 3.723971194 24.92575427 0.951291645 1.035969894 0.044103601 0.075462131 201.2008402 1592074.561 0.017752019 0.028813914 5296.283137 -3.723971194 0.084678249 SMSSIPPYPASSLASSS(ph)PPGSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SMSSIPPYPASSLASSSPPGSGR 23 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 SMSSIPPYPASSLASSS(1)PPGSGR;SMSSIPPYPASSLASS(0.016)S(0.984)PPGSGR;SMSSIPPYPASSLAS(0.002)S(0.058)S(0.926)PPGS(0.014)GR 348.91 1.51E-101 306797000 181282 195035 180366 179863 220363 176350 191296 170049 227963 TRUE FALSE 169935.8832 209475.5943 184644.3667 184478.5891 203056.5789 227259.3822 162612.9407 191279.992 189914.5026 0.894802034 1.102999463 0.972249955 0.971377049 1.069199962 1.196640483 0.85624288 1.007190022 1 17.53499055 1.699099339 25 0.947221706 1.034183532 0.145744113 0.090811531 1.029255935 645.1721324 0.039115301 0.021691382 50.0148924 -1.699099339 0.086961826 SMTEAEQQQLIDDHFLFDKPVSPLLLASGMAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SMTEAEQQQLIDDHFLFDKPVSPLLLASGMAR 32 1 P12277;G3V4N7 P12277 CKB Creatine kinase B-type 0 ; 240.23 5.87E-47 410070000 377580 456420 406770 449860 381650 303900 499340 273380 248200 FALSE TRUE 353947.9418 490213.8117 416418.7765 461404.1692 351676.7485 391630.9966 424468.6026 307512.0948 206773.8166 1.711763838 2.370773146 2.01388543 2.231443888 1.700779888 1.894006713 2.052816017 1.487190689 1 17.65769399 0.650203088 0.611751449 0.966263356 2.096110603 0.677540969 0.222217622 0.726558614 0.528496825 0.240184636 0.087851397 4.468925223 -0.650203088 1.129847247 SMVNTKPEKTEEDSEEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SMVNTKPEKTEEDSEEVR 18 2 Q16543 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 135.04 5.20E-06 245590000 427850 274090 355530 316390 398200 193870 417100 304460 580390 FALSE TRUE 401071.6322 294383.9088 363963.3395 324509.103 366926.9783 249837.1218 354559.7272 342472.5012 483519.1595 0.829484467 0.608836078 0.752738195 0.671140112 0.758867505 0.516705733 0.733289923 0.70829148 1 18.88321353 0.498167963 1.98081525 0.99996058 0.688026206 0.547799143 0.086308926 3.07395479 11.31666598 0.072723769 0.020037857 3.148965941 -0.498167963 -0.311934374 SNAAAYLQHLCYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNAAAYLQHLCYR 13 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 0 ; 113.72 0.00079937 726060000 593810 786350 589290 586010 888490 462270 717850 683010 857580 FALSE TRUE 556644.4921 844572.1722 603268.2371 601048.0087 818711.5794 595719.8447 610215.0567 768285.302 714444.3578 0.779129244 1.182138487 0.844387993 0.841280363 1.145941696 0.83382259 0.85411138 1.075360584 1 19.44646213 3.836595989 24.53134085 0.929116794 1.010578536 0 0.143769612 37.27746273 8284.174962 0.033949454 0.061203232 6864.295789 -3.836595989 0.081461741 SNAEDTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNAEDTLR 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 88.496 0.033905 212330000 263930 275930 231190 280630 277990 188260 300830 261090 268220 FALSE TRUE 247411.0924 296360.1443 236673.936 287831.4409 256157.7868 242607.6059 255723.3343 293687.6612 223452.3492 1.107220816 1.326278937 1.059169603 1.288111053 1.146364259 1.085724123 1.144419986 1.314318969 1 17.76960769 -1.474191264 2.969555774 0.995071922 1.180424453 0.267041129 0.095617154 17771884.06 20838134.92 726402.6557 0.021047829 0.033558979 1.474191264 0.185352531 SNDLFPVHHLDNNEFCPGDFVVDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNDLFPVHHLDNNEFCPGDFVVDKR 25 1 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 0 102.07 0.002043 193410000 223970 197240 226960 216960 237870 170160 268630 208440 290290 FALSE TRUE 209952.1175 211843.8548 232343.5984 222527.5609 219188.6497 219282.4297 228351.4253 234464.1928 241838.7237 0.868149295 0.875971605 0.96073778 0.920148591 0.906342237 0.906730016 0.944230196 0.96950641 1 17.88368574 8 0.03544235 1.258007831 0.408294033 0.697633147 0.022830196 642.9003617 1.740460207 12.24210804 34.86613744 99999999.93 -8 -0.849713799 SNDRNS(ph)MDIQCEVDALLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SNDRNSMDIQCEVDALLER 19 1 Q02241;H7BYN4;A0A2U3TZL8;A0A2R8Y531;H0YME6;Q02241-2 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 SNDRNS(1)MDIQCEVDALLER;SNDRNS(1)MDIQCEVDALLER;SNDRNS(1)MDIQCEVDALLER;S(0.116)NDRNS(0.884)MDIQCEVDALLER;SNDRNS(1)MDIQCEVDALLER;SNDRNS(1)MDIQCEVDALLER;SNDRNS(1)MDIQCEVDALLER;SNDRNS(1)MDIQCEVDALLER 281.57 6.46E-40 1519273000 869885.4 902398.7 901078 908103.4 989023 891646.1 1106624 778617.9 1034747.6 TRUE FALSE 815440.8256 969213.2387 922451.9957 931406.8707 911349.1231 1149049.854 940696.0046 875830.0588 862041.5408 0.945941451 1.124323125 1.070078357 1.080466342 1.057198615 1.332940235 1.091242081 1.01599519 1 19.71739787 4.742437465 24.06308717 1.107082169 0.945941342 0.20247428 0.091826835 341.0977644 2116998.471 0.020680095 0.153876195 55263.38272 -4.742437465 -0.161140827 SNDS(ph)GEEAEKEFIFV ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SNDSGEEAEKEFIFV 15 1 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SNDS(1)GEEAEKEFIFV;SNDS(1)GEEAEKEFIFV;SNDS(1)GEEAEKEFIFV;SNDS(1)GEEAEKEFIFV;S(0.002)NDS(0.998)GEEAEKEFIFV 237.06 2.63E-17 1837554000 5229640 3472430 4136120 4008640 4810150 3383960 5402700 4036660 6751150 TRUE FALSE 4902326.168 3729532.33 4234230.72 4111508.489 4432380.222 4360854.318 4592615.291 4540645.887 5624339.451 0.871627008 0.663105839 0.752840535 0.731020687 0.78807125 0.77535404 0.81656083 0.80732074 1 22.42325224 0.298291189 0.449710268 1.023157115 0.736380073 0.645614332 0.053218263 1.525377221 0.497270825 0.119203699 0.029215236 1.987427016 -0.298291189 -0.286777042 SNEDQSMGNWQIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNEDQSMGNWQIKR 14 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 266.2 1.23E-24 1036200000 325620 352650 314440 341290 473980 280840 426700 315350 649980 FALSE TRUE 305240.0254 378760.5729 321898.6653 350048.0792 436755.5227 361913.9489 362720.2963 354722.1417 541494.139 0.563699592 0.69947308 0.594463803 0.64644851 0.806574792 0.66836171 0.669850826 0.655080298 1 19.0465862 -5 0.274531745 3.36692454 0.640819031 0.742244651 0.062836819 109.2313752 1.054825336 146.9406666 0.071545205 1.00E-05 5 -2.726105508 SNEDS(ph)LILEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNEDSLILEK 10 0 A0A0U1RRH6;O94880 A0A0U1RRH6 PHF14 PHD finger protein 14 1 SNEDS(1)LILEK;S(0.001)NEDS(0.999)LILEK 138.77 5.87E-05 162496000 598180 415110 495840 446160 457850 397550 676720 466260 638480 TRUE FALSE 560740.9816 445845.1763 507601.559 457609.2209 421892.3079 512316.2313 575252.1184 524473.5874 531913.5633 1.054195682 0.838191028 0.954293318 0.860307487 0.793159523 0.963156924 1.081476687 0.98601281 1 19.0208323 2.000381533 24.99885751 1.029241311 0.895604913 0.364474547 0.073850429 11.80877353 773694.8058 0.02579895 0.018871221 100.0878899 -2.000381533 -0.133636398 SNEEGSEEKGPEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNEEGSEEKGPEVR 14 1 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ; 244.56 1.23E-17 2005040000 3094600 2176350 2474620 2489590 2865800 1944420 3104300 2371040 4352600 FALSE TRUE 2900914.51 2337489.218 2533319.155 2553477.094 2640731.628 2505742.489 2638839.034 2667069.563 3626122.941 0.800004456 0.644624922 0.698630244 0.704189333 0.728252095 0.691025244 0.727730162 0.735515482 1 21.78999641 -0.381411521 0.631693346 1.028466073 0.700068182 0.83577707 0.039487698 3.198003712 1.076033844 0.250045991 0.013999489 0.415516696 0.381411521 -0.328397891 SNEHDHS(ph)KSKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNEHDHSKSKEK 12 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 SNEHDHS(0.5)KS(0.5)KEK;SNEHDHS(0.596)KS(0.404)KEK 92.063 0.0037734 89081000 148181 66047 94934 117469 119302 47128 91586 72689 182154 TRUE FALSE 138906.6157 70937.1886 97185.87931 120483.4534 109932.5022 60733.08854 77853.52954 81764.38166 151751.3206 0.915356882 0.467456812 0.640428557 0.793953245 0.724425341 0.400214563 0.513033621 0.538805075 1 17.21134955 -1.045672829 4.995909246 1.000006778 0.602943413 0.354581927 0.157021948 1.14E-05 2.18E-06 0.14630824 0.034484594 0.090017546 1.045672829 -0.397063365 SNELGDVGVHCVLQGLQTPSCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNELGDVGVHCVLQGLQTPSCK 22 0 P13489;E9PMJ3;E9PLZ3;E9PIM9;E9PMN0;E9PIK5 P13489 RNH1 Ribonuclease inhibitor 0 176.27 5.36E-13 339380000 385070 340300 366700 338710 409920 283730 444320 345320 514060 FALSE TRUE 360969.1561 365496.1661 375398.2972 347401.872 377726.5367 365638.245 377698.3409 388433.9621 428260.065 0.842873724 0.853444428 0.876566198 0.811193712 0.882002707 0.853776186 0.881936869 0.907004864 1 18.70812763 0.758601004 0.919212949 1.000355421 0.853607215 0.857002753 0.018966399 0.299959475 0.478261442 0.016566193 0.005541258 5.735892513 -0.758601004 -0.146748206 SNGELSES(ph)PGAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SNGELSESPGAGK 13 0 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2;A0A0A0MR81;F5H176 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 SNGELS(0.001)ES(0.999)PGAGK;SNGELSES(1)PGAGK;SNGELS(0.001)ES(0.999)PGAGK 282.93 1.58E-32 686970000 1793730 1242520 1507430 1396010 1506960 1173890 2062670 1364900 1815590 TRUE FALSE 1681463.641 1334517.474 1543186.951 1431833.98 1388609.44 1512772.986 1753391.782 1535310.77 1512556.3 1.111670119 0.882292761 1.020250917 0.946631858 0.918054713 1.000143259 1.159224144 1.015043717 1 20.52855741 1.984554518 23.60172019 1.076756597 0.967048408 0.183779779 0.074719947 365.8498756 559041.6147 0.02709827 0.018135701 96.50604502 -1.984554518 -0.109708189 SNKPIILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNKPIILR 8 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 88.948 0.012999 822740000 727590 763110 729010 736060 870990 613590 976400 750910 816830 FALSE TRUE 682051.4407 819611.4584 746302.4615 754948.5457 802585.9588 790723.4722 829997.8845 844662.7665 680495.7961 1.002286046 1.204432802 1.096704 1.109409566 1.179413544 1.161981421 1.219695829 1.24124612 1 19.37622672 2.733520599 23.31929374 1.177734587 1.118994869 0.075038671 0.08106539 357.3712315 1653485.325 0.02343311 0.022777497 541.4029269 -2.733520599 -0.058739718 SNLDEEVNVIPPHT(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNLDEEVNVIPPHTPVR 17 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 SNLDEEVNVIPPHT(1)PVR;SNLDEEVNVIPPHT(1)PVR 145.13 1.79E-06 468970000 343050 355860 355130 335000 344420 255710 459440 316570 314210 TRUE FALSE 321579.1129 382208.2447 363553.8513 343596.6672 317370.6425 329529.3259 390551.2372 356094.4614 261766.3211 1.228496896 1.460112374 1.388848839 1.312608382 1.212419692 1.258868308 1.491984284 1.360352469 1 17.99791997 -1.927534026 2.447802284 0.763109006 1.356423576 0.559266975 0.093531969 21020807.32 11022549.5 28503500.72 0.023048639 0.011815877 1.927534026 0.59331457 SNLES(ph)S(ph)QK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNLESSQK 8 0 Q13315;E9PIN0 Q13315 ATM Serine-protein kinase ATM 2 SNLES(1)S(1)QK 60.434 0.048763 70764000 149620 263490 144190 137530 279720 97799 179390 228910 307720 TRUE FALSE 140255.5513 282999.0738 147610.2549 141059.2526 257751.9195 126031.9837 152492.1349 257489.9174 256359.5441 0.547104855 1.103914718 0.575793874 0.550239911 1.005431339 0.491621968 0.594836972 1.004409328 1 17.96780908 1.223494479 24.64912985 1.002205116 0.713478644 0.277877539 0.203924527 326.3849003 533967.8425 0.188250337 0.04785263 16.72994367 -1.223494479 -0.288726472 SNMGHPEPASGLAALAK ddPTM_SK-BR-3_Pertuzumab_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 ;; 152.71 2.03E-07 1865480000 1750970 1924990 1996050 2020550 2187580 1571480 2611820 1930680 2460480 FALSE TRUE 1641379.913 2067518.263 2043397.249 2072400.734 2015776.291 2025140.765 2220201.838 2171729.648 2049809.993 0.800747347 1.008638981 0.996871542 1.011020895 0.983396655 0.987965115 1.083125678 1.059478515 1 20.96705875 4.740460569 4.945604744 1.017835547 0.789405706 0.823245539 0.031414733 0.077214243 5.779409609 0.008260742 0.0606091 55012.39709 -4.740460569 -0.228429841 SNNIAELS(ph)PGAINSCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNNIAELSPGAINSCR 16 0 Q9Y2I9;F8VZ81;Q9Y2I9-2;Q9Y2I9-3 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 SNNIAELS(1)PGAINSCR 125.23 8.20E-05 96671000 119670 146320 143150 155020 129590 95279 131230 92683 116240 TRUE FALSE 112180.0683 157153.685 146545.5856 158998.0756 119412.5241 122784.5006 111553.2798 104254.6766 96838.79306 1.158420761 1.622838122 1.513294218 1.641884111 1.233106283 1.267926796 1.151948266 1.076579677 1 16.56329748 2.14356548 1.150659006 1.059602395 1.508568083 0.575799031 0.146259867 0.313901105 0.783857024 0.096885824 0.050530926 139.176362 -2.14356548 0.448965688 SNNWS(ph)LEDVTASDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SNNWSLEDVTASDK 14 0 Q14680-3;Q14680-4;Q14680-5;Q14680-2;Q14680-8;Q14680-6;Q14680 Q14680-3 MELK Maternal embryonic leucine zipper kinase 1 SNNWS(1)LEDVTASDK;SNNWS(1)LEDVTASDK;SNNWS(1)LEDVTASDK;SNNWS(1)LEDVTASDK 425.62 8.67E-153 685651000 1357340 854412 1020090 938662 981390 844103 1395200 912713 878649 TRUE FALSE 1272386.512 917673.5535 1044287.017 962749.6561 904315.5881 1087781.833 1186002.712 1026667.227 731996.8056 1.738240526 1.253657866 1.426627833 1.31523751 1.2354092 1.486047241 1.620229355 1.402556977 1 19.48147783 -2.063020857 2.439177283 0.394288547 1.425143546 0.434391976 0.155561922 5585743.554 2133438.916 18822736.83 0.036825248 0.008649264 2.063020857 1.030854999 SNPKS(ph)PQKPIVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNPKSPQKPIVR 12 2 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y467;A0A2R8YES9;H7C5K3 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(0.022)NPKS(0.978)PQKPIVR;S(0.121)NPKS(0.879)PQKPIVR 72.315 0.022031 2337680000 2913200 1928680 2433370 2526530 2937800 1484690 2580770 1720390 2870000 TRUE FALSE 2730868.012 2071481.474 2491090.686 2591365.037 2707077.039 1913295.901 2193807.497 1935184.479 2390978.459 1.142155004 0.866373959 1.041870819 1.083809445 1.132204696 0.800214612 0.91753545 0.809369265 1 21.1891697 2.2320383 24.99994581 0.876807428 1.027626618 0.434476841 0.094671807 165.4089219 634004.0089 0.034412757 0.026020147 170.6232851 -2.2320383 0.15081919 SNQWHGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNQWHGR 7 0 Q9BTL3;A0A3B3IU46 Q9BTL3 FAM103A1 RNMT-activating mini protein 0 65.252 0.071089 43572000 82686 129610 106840 97148 123040 78702 102510 96681 103570 FALSE TRUE 77510.83086 139206.4593 109374.2953 99640.98215 113376.9347 101421.9898 87139.57716 108751.8357 86283.49791 0.898327406 1.613361334 1.267615453 1.154809257 1.31400485 1.175450605 1.009921703 1.260401332 1 16.39679704 2.323627761 0.85631575 1.070868686 1.328099685 0.065682196 0.193485253 0.964128815 1.371240684 0.138342362 0.087188084 210.6821594 -2.323627761 0.257230999 SNRDELELELAENRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNRDELELELAENRK 15 2 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 161.24 9.35E-07 298870000 121240 91778 109190 106360 109920 91599 145170 113010 170790 FALSE TRUE 113651.8048 98573.33861 111780.0384 109089.3777 101287.3266 118042.1443 123403.1062 127119.5473 142284.0457 0.798767032 0.692792633 0.785611892 0.766701405 0.711867069 0.829623193 0.867301078 0.89342095 1 17.11841438 1.392227979 0.830112555 0.994611709 0.744350745 0.834422342 0.036481532 0.193015938 0.28373092 0.031811253 0.012484744 24.67334201 -1.392227979 -0.250260964 SNRNS(ph)IER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SNRNSIER 8 1 Q8TF01 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 S(0.04)NRNS(0.96)IER;SNRNS(1)IER;S(0.001)NRNS(0.999)IER;S(0.004)NRNS(0.996)IER 98.353 0.0045919 430387000 350892 346159 367852 359893 382399 292304 390425 331957 383718 TRUE FALSE 328930.2961 371788.9725 376577.6232 369128.4637 352366.9251 376687.4196 331884.3958 373402.5622 319672.9869 1.028958685 1.163029057 1.178008898 1.154706462 1.102273071 1.178352363 1.03819969 1.168076683 1 18.28623731 -0.01292641 0.472235323 0.985206363 1.141402553 0.300009612 0.056684126 4.765477454 1.329944536 0.194755194 0.028654444 0.970674432 0.01292641 0.156196191 SNS(ph)APLIHGLSDTSPVFQAEAPSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SNSAPLIHGLSDTSPVFQAEAPSAR 25 0 Q96E09 Q96E09 FAM122A Protein FAM122A 1 S(0.101)NS(0.899)APLIHGLSDTSPVFQAEAPSAR;S(0.043)NS(0.957)APLIHGLSDTSPVFQAEAPSAR;S(0.138)NS(0.862)APLIHGLSDTSPVFQAEAPSAR 267.13 1.00E-45 1131581000 374386 371529 407462 397225 410294 349165 487306 354170 486469 TRUE FALSE 350953.8486 399037.3937 417127.1911 407418.466 378071.1643 449963.2673 414238.9892 398388.9041 405274.1812 0.865966461 0.984610943 1.029246891 1.005290948 0.932877498 1.110268772 1.022120353 0.983010817 1 18.62853874 4.822231032 1.984983762 1.015543448 0.798876149 0.51458285 0.04408567 0.7793835 2.763796112 0.010675015 0.330598746 66409.62564 -4.822231032 -0.216667299 SNS(ph)AWQIYLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNSAWQIYLQR 11 0 Q8N4C8;Q8N4C8-4 Q8N4C8 MINK1 Misshapen-like kinase 1 1 S(0.006)NS(0.994)AWQIYLQR 94.507 0.0088663 89609000 95089 181830 138330 126380 157340 104350 110730 124880 197950 TRUE FALSE 89137.54923 195292.8824 141611.2529 129623.1248 144983.1511 134474.151 94127.06447 140471.5429 164910.8662 0.540519562 1.184232955 0.858713899 0.786019307 0.879160691 0.815435357 0.570775393 0.851802832 1 17.33132694 3.454417493 4.087740304 0.784501936 0.942948629 0 0.190588389 0.434432438 16.26149171 0.050529105 0.073503472 2847.19684 -3.454417493 0.158446692 SNS(ph)DESNFSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNSDESNFSEK 11 0 A0A087WWW9;O95999 A0A087WWW9 BCL10 B-cell lymphoma/leukemia 10 1 SNS(1)DESNFSEK;SNS(0.996)DES(0.004)NFSEK 242.4 9.53E-16 851610000 2070860 1348580 1564100 1393540 1272870 1020570 1643380 1044910 1706390 TRUE FALSE 1941248.569 1448430.266 1601201.191 1429300.596 1172903.925 1315191.991 1396970.425 1175369.314 1421582.485 1.365554647 1.018885841 1.126351237 1.005429238 0.825069201 0.92516052 0.982686858 0.826803457 1 20.43906638 8 0.461338302 0.922807986 10.55228274 0.669429859 0.089037968 56.25491828 0.658613892 0.049964567 513.9055336 100000000 -8 9.629474754 SNS(ph)DNNLNASAPDWAVCSTATSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SNSDNNLNASAPDWAVCSTATSHR 24 0 Q9UPX8;Q9UPX8-3;A0A2R8Y2H5;A0A087X158 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 S(0.248)NS(0.752)DNNLNASAPDWAVCSTATSHR;S(0.016)NS(0.984)DNNLNASAPDWAVCSTATSHR;S(0.202)NS(0.798)DNNLNASAPDWAVCSTATSHR 300.2 2.40E-62 1453080000 272164 267210 302408 262863 337635 202968 325994 256292 318099 TRUE FALSE 255129.7411 286994.5064 309581.2606 269608.5096 311118.5091 261561.5667 277114.2261 288290.6204 265006.2219 0.962731136 1.08297271 1.168203744 1.017366716 1.174004545 0.987001606 1.045689509 1.087863592 1 18.01566671 2.211343637 24.99998849 1.033527798 1.090306124 0.113954391 0.067586894 425.4966783 390834.7381 0.023975043 0.017710918 162.6835487 -2.211343637 0.056778326 SNS(ph)EDKLNSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNSEDKLNSK 10 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 SNS(1)EDKLNSK 125.36 0.00024905 570980000 970700 424990 607050 517930 539620 463150 958820 556260 1002700 TRUE FALSE 909945.6197 456456.7018 621449.5127 531220.9607 497240.4219 596853.8864 815053.8422 625710.2855 835342.8923 1.08930791 0.546430341 0.743945413 0.635931622 0.595253071 0.714501664 0.97571171 0.74904604 1 19.67200899 1.756157295 25 0.899515112 0.695323848 0.221459771 0.160627323 8.748943074 12443.02578 0.066996059 0.037153008 57.03708146 -1.756157295 -0.204191264 SNS(ph)EDSSVGKGDWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNSEDSSVGKGDWK 14 1 O94885 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 S(0.003)NS(0.996)EDS(0.001)SVGKGDWK 98.175 0.0033256 0 139570 88495 77414 96542 85031 48495 133890 73967 158430 TRUE FALSE 130834.5628 95047.26188 79250.29664 99019.43117 78353.00826 62494.71925 113814.4375 83201.94277 131987.0095 0.991268484 0.720125884 0.600440126 0.750221037 0.593641818 0.47349144 0.86231545 0.630379786 1 17.01003642 -1.509531741 6.295829982 1.000248721 0.695478854 0.289382899 0.146002123 0.00047362 3.69E-05 0.131355571 0.030935942 0.030936292 1.509531741 -0.304769867 SNS(ph)ELEDEILCLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNSELEDEILCLEK 14 0 Q96PC5;Q96PC5-11;Q96PC5-10;Q96PC5-9;Q96PC5-13;Q96PC5-6;G3V599;Q96PC5-14;Q96PC5-7;Q96PC5-12;Q96PC5-8;Q96PC5-5;Q86UF2;A4D2H0;A0A5F9ZHA4;G3V5K6;A0A2R8YE69;Q8IX94;P0CG41;A4FU28 Q96PC5 MIA2;CTAGE6;CTAGE15;CTAGE5;CTAGE4;CTAGE8;CTAGE9 Melanoma inhibitory activity protein 2;cTAGE family member 6;cTAGE family member 15;cTAGE family member 4;cTAGE family member 8;cTAGE family member 9 1 S(0.1)NS(0.9)ELEDEILCLEK 152.68 6.92E-06 13813000 36076 25716 25991 24670 32911 20504 36229 24916 41344 TRUE FALSE 33818.06756 27620.0394 26607.51879 25303.07397 30326.30282 26423.17195 30796.79778 28026.81745 34443.41931 0.981844086 0.801895978 0.772499343 0.734627237 0.880467254 0.767147179 0.894127192 0.813706014 1 15.07194075 0.089158072 0.68415623 1.006253499 0.816249604 0.331575257 0.073414732 4.125440599 2.250399178 0.13753969 0.025158218 1.227886068 -0.089158072 -0.190003896 SNS(ph)FNNPLGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNSFNNPLGNR 11 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 SNS(1)FNNPLGNR;SNS(1)FNNPLGNR 190.24 0.00080561 0 336480 381370 337070 374430 388350 276500 389060 307580 431350 TRUE FALSE 315420.3174 409607.0316 345065.4596 384038.5077 357850.5575 356321.0614 330724.0649 345982.0401 359354.8984 0.877740414 1.139839845 0.960235859 1.068688668 0.995813774 0.991557547 0.920327137 0.962786487 1 18.45504983 2.164622737 2.52420311 0.953489615 1.024078305 0.058880568 0.070741939 0.48713934 6.244671065 0.029465071 0.019368931 146.0907563 -2.164622737 0.07058869 SNS(ph)FSDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 SNSFSDER 8 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 SNS(0.999)FS(0.001)DER;S(0.001)NS(0.997)FS(0.002)DER;S(0.253)NS(0.685)FS(0.061)DER;S(0.001)NS(0.967)FS(0.032)DER;S(0.328)NS(0.343)FS(0.328)DER;S(0.024)NS(0.936)FS(0.041)DER;S(0.426)NS(0.462)FS(0.113)DER;S(0.001)NS(0.998)FS(0.001)DER;SNS(0.977)FS(0.023)DER 204.56 9.08E-05 15686849000 19493230 15636326 16585790 12575453 14687940 15885315 22823510 18308666 17636320 TRUE FALSE 18273183.53 16794055.85 16979212.77 12898160.41 13534408.44 20471147.56 19401336.56 20594543.25 14692704.26 1.243690965 1.14302007 1.155622034 0.877861569 0.92116524 1.393286573 1.320474177 1.401685006 1 23.80859662 2.22628388 24.99988173 1.310297584 1.081721237 0.304090359 0.154350672 255.8194264 520937.4201 0.055894564 0.041580102 168.3774312 -2.22628388 -0.228576346 SNS(ph)GRELTDEEILASVMIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNSGRELTDEEILASVMIK 19 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 S(0.238)NS(0.715)GRELT(0.047)DEEILASVMIK;S(0.177)NS(0.823)GRELTDEEILASVMIK 252.84 4.44E-31 352920000 626320 616450 616480 687230 816290 403780 715030 582980 1163450 TRUE FALSE 587119.7492 662092.5994 631103.1967 704865.4853 752181.8762 520344.7312 607817.8895 655766.3363 969262.6788 0.605738529 0.683088923 0.651116782 0.727218225 0.776035117 0.536845937 0.62709305 0.676562041 1 19.88652818 0.938674895 20.29299311 1 0.658142452 0.731282195 0.06477732 1245.37699 412107.3071 0.06150509 0.015376272 8.68310185 -0.938674895 -0.341857548 SNS(ph)LDKHQQSSTLGNSVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNSLDKHQQSSTLGNSVVR 19 1 A0A0A0MSY4;Q9BZ29-5;X6RGR3;Q6ZSL5;A0A088AWN3;Q9BZ29-3;Q9BZ29;Q9BZ29-4 A0A0A0MSY4 DOCK9 Dedicator of cytokinesis protein 9 1 S(0.163)NS(0.837)LDKHQQSSTLGNSVVR 202.15 3.42E-16 836570000 481030 497110 497700 535010 543430 315530 588530 509330 550870 TRUE FALSE 450923.191 533916.5416 509505.679 548739.2624 500751.1999 406618.3888 500285.3901 572920.9717 458926.2382 0.982561365 1.163403826 1.110212571 1.195702526 1.091136567 0.886021227 1.090121567 1.248394456 1 18.80790277 2.473285761 24.99951549 1.051192772 1.123166468 0.05805064 0.103882636 274.6261713 1789966.549 0.034268418 0.028789133 297.3621997 -2.473285761 0.071973696 SNS(ph)LPHSAVSNAGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNSLPHSAVSNAGSK 15 0 A0A088AWN2;Q8TBZ3-4;Q8TBZ3-5;Q8TBZ3-6;Q8TBZ3;Q8TBZ3-2;Q8TBZ3-7 A0A088AWN2 WDR20 WD repeat-containing protein 20 1 S(0.195)NS(0.805)LPHSAVSNAGSK;S(0.021)NS(0.552)LPHS(0.391)AVS(0.035)NAGSK 228.01 4.21E-13 1241620000 880480 722120 823360 778940 869620 593490 1019590 715930 1163640 TRUE FALSE 825372.3285 775586.5162 842890.488 798928.9191 801323.5531 764820.9285 866711.9449 805315.4365 969420.9666 0.851407548 0.800051312 0.869478294 0.824130019 0.826600188 0.788946139 0.894051165 0.83071799 1 19.88676376 -0.306399944 0.58741962 1.016971849 0.830672577 0.739919047 0.030643157 3.625345384 1.152751201 0.164423159 0.011785335 0.493855683 0.306399944 -0.186299272 SNS(ph)LPIKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNSLPIKK 8 1 Q96JQ2 Q96JQ2 CLMN Calmin 1 S(0.095)NS(0.905)LPIKK 52.344 0.087899 158880000 167440 134420 147790 133070 165160 111530 198360 156510 221690 TRUE FALSE 156960.2293 144372.5967 151295.6486 136484.8015 152188.9998 143726.9005 168617.7595 176050.618 184688.5068 0.849864629 0.781708614 0.819193631 0.738999973 0.824030701 0.778212477 0.912984584 0.95322996 1 17.49473456 1.518135542 2.115573581 0.983478036 0.79681392 0.844054688 0.032478325 0.098478865 0.890452542 0.023643266 0.007996597 32.97125983 -1.518135542 -0.186664116 SNS(ph)LSTPRPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNSLSTPRPTR 11 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 SNS(0.57)LS(0.143)T(0.143)PRPT(0.143)R 86.288 0.038361 77308000 185780 185570 162250 179580 183630 136680 215500 147850 178780 TRUE FALSE 174152.3614 199309.7959 166098.6466 184188.3268 169208.4405 176137.2972 183187.7756 166309.398 148940.463 1.16927501 1.338184344 1.115201626 1.236657407 1.136081069 1.182602052 1.229939614 1.11661663 1 17.18437622 -4.999999992 0.156451389 0.255044472 1.257929854 0.509607012 0.062800564 105.1975548 0.95766579 24.23363791 0.268271479 1.00E-05 4.999999992 1.002885382 SNS(ph)LVSTFTMEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SNSLVSTFTMEK 12 0 Q9HB21 Q9HB21 PLEKHA1 Pleckstrin homology domain-containing family A member 1 1 S(0.023)NS(0.977)LVSTFTMEK;SNS(0.951)LVS(0.046)T(0.002)FTMEK;SNS(1)LVSTFTMEK 209.79 5.35E-08 236887000 667490 634420 563540 587550 826510 371193 758410 702010 838940 TRUE FALSE 625712.9924 681393.1169 576907.4349 602627.5277 761599.2386 478350.3933 644693.4612 789657.4938 698915.4942 0.895262729 0.97492919 0.825432316 0.862232319 1.089687158 0.684418069 0.922419758 1.129832577 1 19.4147585 1.340913835 6.840877027 1.062423361 0.890026755 0.310204254 0.107018518 0.233162348 13.07359463 0.066741432 0.024107307 21.9236992 -1.340913835 -0.172396606 SNS(ph)MLELAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNSMLELAPK 10 0 Q9P2M7;Q9P2M7-2;A6PVU7;A2A3M4 Q9P2M7 CGN Cingulin 1 SNS(1)MLELAPK;SNS(1)MLELAPK 143.56 3.54E-05 384470000 967750 789130 815820 720730 987540 547500 969700 785390 2294000 TRUE FALSE 907180.255 847558.0063 835171.6357 739225.152 909982.5919 705554.3621 824302.4873 883447.6704 1911116.58 0.474685984 0.443488385 0.437007163 0.386802752 0.476152319 0.369184366 0.431319835 0.462267807 1 20.86598436 0.576603434 2.850918006 0.999996748 0.430361512 0.966283309 0.033209966 1.093740727 7.175577963 0.029085851 0.007641836 3.772275766 -0.576603434 -0.569635236 SNS(ph)PDKFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SNSPDKFK 8 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 S(0.043)NS(0.957)PDKFK;S(0.005)NS(0.995)PDKFK;S(0.003)NS(0.997)PDKFK;S(0.131)NS(0.869)PDKFK;S(0.001)NS(0.999)PDKFK;S(0.001)NS(0.999)PDKFK 151.98 0.00028131 9816100000 37273980 14288770 21357660 18698880 18102830 13952980 26846610 15896390 21333000 TRUE FALSE 34941068.13 15346725.4 21864273.78 19178724.92 16681106.76 17980978.82 22821210.06 17881089.28 17772384.48 1.966031523 0.863515271 1.230238621 1.079130656 0.938597 1.011736992 1.284082622 1.006116501 1 24.08313392 4.746767077 24.9431404 1.070692325 1.966031978 0.837079169 0.126524655 400.7478501 1218025.422 0.029944631 0.338888756 55817.0753 -4.746767077 0.895339654 SNS(ph)PGTASSGSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SNSPGTASSGSSR 13 0 Q96GY0;H0YAP0 Q96GY0 ZC2HC1A Zinc finger C2HC domain-containing protein 1A 1 SNS(0.993)PGT(0.007)ASSGSSR;SNS(0.999)PGTASSGSSR;S(0.013)NS(0.985)PGT(0.002)ASSGSSR;S(0.001)NS(0.956)PGT(0.042)ASSGSSR 261.84 4.63E-24 839743000 809620 724324 749676 743653 788127 650685 850490 567200 684910 TRUE FALSE 758947.3294 777953.7026 767458.6687 762736.395 726230.6846 838527.1965 722966.9201 638016.1686 570594.0963 1.330100214 1.36341001 1.345016841 1.336740776 1.272762353 1.469568651 1.267042412 1.118161181 1 19.12210529 1.183892784 2.367406763 1.00727785 1.350419162 0.854070642 0.050555543 0.08671325 0.855571142 0.041942997 0.011821321 15.27188988 -1.183892784 0.343141312 SNS(ph)PLPVPPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SNSPLPVPPSK 11 0 Q13247;Q13247-3 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 SNS(1)PLPVPPSK;S(0.001)NS(0.999)PLPVPPSK;SNS(1)PLPVPPSK;SNS(1)PLPVPPSK;SNS(1)PLPVPPSK;SNS(1)PLPVPPSK;SNS(1)PLPVPPSK 182.72 5.94E-06 17061440000 23253740 13603100 17565190 16065750 16457610 14454960 22111790 14749050 17339260 TRUE FALSE 21798329.92 14610287.68 17981844.6 16478024.34 15165095.7 18627872.3 18796332.37 16590501.36 14445225.49 1.509033551 1.011426764 1.244829623 1.140724619 1.049834474 1.289552199 1.301214189 1.148511068 1 23.78408939 4.755949614 24.63833472 1.167457182 1.509033891 0.515231336 0.108566787 2705.268088 3832996.888 0.025833304 0.771830481 57009.81263 -4.755949614 0.341576709 SNS(ph)TTQVSQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SNSTTQVSQPR 11 0 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 SNS(0.967)T(0.03)T(0.003)QVSQPR;SNS(0.801)T(0.198)T(0.001)QVSQPR;S(0.003)NS(0.956)T(0.04)T(0.002)QVSQPR 208.88 1.90E-08 702160000 500028 510399 478881 481674 475365 369610 566596 408574 593835 TRUE FALSE 468732.1401 548189.473 490240.2835 494034.5703 438031.7504 476310.4069 481640.1898 459585.3633 494720.1022 0.947469363 1.108080045 0.990944741 0.998614304 0.885413284 0.962787655 0.973560985 0.928980572 1 18.916253 3.328730463 2.071421849 0.952593047 1.040181028 0.24787352 0.050197166 0.315368331 2.750077595 0.014200047 0.020968276 2131.72149 -3.328730463 0.087587981 SNS(ph)WVNTGGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNSWVNTGGPK 11 0 Q96N67-2;Q96N67-6;Q96N67;A0A1B0GWE0;A0A0U1RRC1 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 SNS(1)WVNTGGPK 202.58 4.15E-08 93824000 301400 221410 238570 229590 262490 153180 331390 244130 386180 TRUE FALSE 282535.912 237803.4268 244228.9931 235481.6681 241875.0942 197400.5793 281701.146 274610.1679 321724.0632 0.878193285 0.739153374 0.759125664 0.731936759 0.751809149 0.613571075 0.875598621 0.853558062 1 18.29546432 1.141353072 1.603667386 0.988578507 0.748909812 0.550279483 0.071315272 0.244101577 1.20927841 0.060924609 0.018035212 13.84691647 -1.141353072 -0.239668695 SNSGLATYS(ph)PPMGPVSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNSGLATYSPPMGPVSER 18 0 H0Y465;P21359-2;P21359-6;P21359;J3KSB5;P21359-4 H0Y465 NF1 Neurofibromin;Neurofibromin truncated 1 SNSGLAT(0.003)YS(0.997)PPMGPVSER;SNSGLATYS(1)PPMGPVSER 160.21 4.32E-11 89641000 142279 153020 159069 159197 171939 125587 186313 153513 165064 TRUE FALSE 133374.0114 164349.76 162842.1918 163282.2645 158435.6045 161841.9282 158377.0953 172679.436 137513.752 0.969895806 1.195151449 1.184188413 1.187388622 1.15214371 1.176914496 1.151718231 1.255724852 1 17.06921638 4.742653675 24.80888027 1.171669329 0.969895718 0.459040864 0.065232689 283.015675 1715345.35 0.013039454 0.100436144 55290.90202 -4.742653675 -0.201773611 SNSLSEQLAINTS(ph)PDAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SNSLSEQLAINTSPDAVK 18 0 Q5T1M5;Q5T1M5-2;Q5T1M5-3 Q5T1M5 FKBP15 FK506-binding protein 15 1 SNSLSEQLAINT(0.017)S(0.983)PDAVK;SNSLSEQLAINT(0.064)S(0.936)PDAVK;SNSLSEQLAINT(0.012)S(0.988)PDAVK;SNSLSEQLAINT(0.17)S(0.83)PDAVK 250.79 1.02E-22 256560000 981159 700288 869464 829629 871940 585718 898146 642176 825971 TRUE FALSE 919750.0096 752138.0522 890088.0967 850918.6847 803461.3496 754805.2783 763477.3453 722353.0872 688111.1041 1.336630094 1.093047398 1.293523809 1.236600717 1.16763317 1.096923555 1.109526268 1.049762288 1 19.392282 1.838956352 0.853061141 1.014010413 1.225989285 0.623582367 0.065749482 0.410134772 0.558940104 0.055357667 0.025297916 69.01704367 -1.838956352 0.211978872 SNSS(ph)SEAVLGQEELSAQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNSSSEAVLGQEELSAQAK 19 0 A0A1B0GTL5;Q9BXF6 A0A1B0GTL5 RAB11FIP5 Rab11 family-interacting protein 5 1 SNS(0.036)S(0.482)S(0.482)EAVLGQEELSAQAK 417.28 2.94E-148 70357000 110670 95551 106430 143850 153180 70653 102220 69443 134860 TRUE FALSE 103743.3623 102625.6955 108954.5699 147541.4345 141149.8607 91049.37414 86893.05996 78113.11141 112350.9948 0.923386237 0.913438245 0.969769516 1.313218764 1.256329425 0.810401139 0.773407126 0.695259633 1 16.77765337 2.121531688 10.38197138 0.796386607 1.049473734 0.404868659 0.151049071 0.3552342 30.6342614 0.060204161 0.044459097 132.2914229 -2.121531688 0.253087127 SNT(ph)ENLSQHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNTENLSQHFR 11 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 S(0.04)NT(0.96)ENLSQHFR 171.08 5.50E-05 207170000 118720 171330 124510 129700 170630 90588 163760 132710 278730 TRUE FALSE 111289.5271 184015.4515 127463.436 133028.3216 157229.4081 116739.285 139205.7083 149279.1356 232208.1623 0.479266215 0.792459014 0.548918844 0.572883917 0.677105432 0.502735493 0.599486714 0.642867736 1 17.82505916 0.738426913 3.830297061 0.999995189 0.608113811 0.665351198 0.088994993 2.249898243 32.37546421 0.081023283 0.020756806 5.475539465 -0.738426913 -0.391881379 SNT(ph)PILVDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SNTPILVDGK 10 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41 P06744 GPI Glucose-6-phosphate isomerase 1 SNT(1)PILVDGK;S(0.006)NT(0.994)PILVDGK;S(0.002)NT(0.998)PILVDGK;S(0.001)NT(0.999)PILVDGK 145.49 0.00033909 630627000 3494900 1929460 2288890 2303910 2136010 1467620 2939100 1867180 1676680 TRUE FALSE 3276160.448 2072319.226 2343183.552 2363032.231 1968256.391 1891298.069 2498409.24 2100301.533 1396831.276 2.345423176 1.483585929 1.677499346 1.691709136 1.409086712 1.353991782 1.788626359 1.503618632 1 20.41372634 8 0.044664852 2.12E-14 4.36612443 0.51072199 0.242653501 622.7256932 2.108948696 52.59371333 195.9193792 100000000 -8 4.36612443 SNTAGS(ph)QSQVETEA ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNTAGSQSQVETEA 14 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 1 SNTAGS(0.882)QS(0.118)QVETEA;S(0.009)NT(0.009)AGS(0.926)QS(0.055)QVETEA 151.7 7.20E-06 216470000 178859 243060 224850 220921 261590 177035 263090 240050 241540 TRUE FALSE 167664.5345 261056.4153 230183.5482 226590.2069 241045.7766 228142.1306 223642.0969 270020.7709 201225.4136 0.833217492 1.297333228 1.143908933 1.126051639 1.197889334 1.133764004 1.111400856 1.341882052 1 17.618453 4.751922732 24.90509074 1.173122719 0.833217258 0.546945639 0.095986495 1546.289764 2882012.258 0.020699542 0.399401186 56483.64722 -4.751922732 -0.339905461 SNTENLSQHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SNTENLSQHFR 11 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;; 253.79 2.03E-20 1809370000 827370 1601780 1235520 1151790 1753450 939660 1200550 1480530 1954320 FALSE TRUE 775586.3886 1720377.458 1264827.118 1181346.881 1615741.11 1210924.588 1020538.673 1665377.43 1628131.367 0.476365977 1.056657646 0.776858148 0.725584499 0.992389891 0.743751157 0.626815928 1.022876571 1 20.63478568 1.206079046 24.92750271 1.01143898 0.795926296 0.258229886 0.165190604 322.5186567 247504.6736 0.151183021 0.037807386 16.07233759 -1.206079046 -0.215512685 SNTGGQAFPQCVFDHWQILPGDPFDNSSRPSQVVAETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNTGGQAFPQCVFDHWQILPGDPFDNSSRPSQVVAETR 38 1 P13639 P13639 EEF2 Elongation factor 2 0 ; 259.25 1.36E-62 435760000 384700 464250 428430 433150 531430 375000 522120 445670 519630 FALSE TRUE 360622.3137 498623.5531 438592.5619 444265.3623 489693.6315 483256.4124 443832.9531 501312.8805 432900.3961 0.833037616 1.151820506 1.013148904 1.026253074 1.131192385 1.116322408 1.025254209 1.158032853 1 18.72367559 4.749819566 24.6319354 1.076594862 0.83303744 0.625147021 0.059546937 884.8537029 1935807.097 0.013064378 0.202068732 56210.77404 -4.749819566 -0.243557422 SNTHEFVNLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNTHEFVNLVK 11 0 O75436;S4R3Q6;O75436-2 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ; 95.401 0.0077857 522360000 1228970 1308230 1365130 1274140 1390580 962640 1665850 1304910 1276700 FALSE TRUE 1152050.961 1405092.71 1397511.528 1306836.59 1281369.456 1240538.541 1416071.257 1467830.886 1063610.522 1.083151151 1.32105943 1.31393165 1.228679636 1.204735596 1.166346623 1.331381392 1.380045473 1 20.02053852 SNTPILVDGKDVMPEVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNTPILVDGKDVMPEVNK 18 1 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41 P06744 GPI Glucose-6-phosphate isomerase 0 143.57 9.53E-08 291710000 637470 447690 508200 495740 669320 415890 752690 557730 1352100 FALSE TRUE 597571.8906 480837.4334 520254.744 508461.5277 616754.3071 535950.6916 639831.1221 627363.8182 1126425.775 0.530502678 0.426870056 0.461863316 0.451393726 0.547532133 0.47579761 0.568018893 0.556950872 1 20.10332082 -0.831809516 0.3776463 1.19747579 0.453528972 0.947313809 0.037552265 2.243672665 0.257558941 0.532853306 0.024520403 0.147295841 0.831809516 -0.743946818 SNVSDAVAQSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SNVSDAVAQSTR 12 0 P60174;P60174-3;P60174-4 P60174 TPI1 Triosephosphate isomerase 0 ;;;; 190.36 1.57E-05 1361860000 579774 706817 571548 575159 702871 471394 710518 582514 844750 FALSE TRUE 543486.9803 759150.4661 585105.3885 589918.5537 647670.3469 607477.7954 603982.422 655242.1552 703755.7677 0.772266467 1.078712958 0.83140404 0.838243295 0.920305561 0.863194056 0.858227314 0.931064703 1 19.42471532 0.966907124 7.614652699 0.999997113 0.892514509 0.177241954 0.080703788 0.704084584 156.3254349 0.075142062 0.018826819 9.266316375 -0.966907124 -0.107482604 SNVSSPATPTASSSSST(ph)TPTRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNVSSPATPTASSSSSTTPTRK 22 1 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SNVSSPATPTASS(0.001)S(0.002)S(0.061)S(0.216)T(0.534)T(0.186)PTRK;SNVSSPATPTASSSS(0.001)S(0.127)T(0.53)T(0.34)PT(0.002)RK 199.31 1.04E-22 737750000 210842 178184 190393 186292 207496 167066 245691 191434 225218 TRUE FALSE 197645.7756 191376.9288 194909.2119 191072.5681 191200.1012 215295.2421 208851.9154 215334.9563 187627.6608 1.053393592 1.01998249 1.038808516 1.018360338 1.019040051 1.147460034 1.113119007 1.147671699 1 17.51751301 2.248947333 24.9996054 1.112948555 1.029249458 0.407323284 0.042344024 154.8898787 372801.6549 0.01281896 0.010617043 177.3974339 -2.248947333 -0.083699097 SNVSSPATPTASSSSSTT(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SNVSSPATPTASSSSSTTPTR 21 0 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SNVSSPATPTASSSSS(0.001)T(0.026)T(0.971)PT(0.002)R 235.25 9.50E-29 235480000 127480 133070 134030 130610 142770 117750 150700 119960 120020 TRUE FALSE 119501.2544 142922.6413 137209.2549 133961.6737 131557.4201 151742.5135 128103.934 134937.2701 99987.88664 1.195157317 1.429399561 1.372258776 1.339779029 1.315733581 1.517608968 1.281194536 1.349536175 1 16.60946571 0.233898048 1.214277217 0.999407317 1.36439924 0.620997814 0.085556448 3.096546453 4.33431504 0.076538583 0.022087566 1.713554999 -0.233898048 0.364991924 SNYNFEKPFLWLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNYNFEKPFLWLAR 14 1 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 251.91 3.13E-24 3935100000 2871200 7718600 1880200 1704350 8062700 1126380 2708500 7184700 3972900 FALSE TRUE 2691496.717 8290093.175 1924799.232 1748086.506 7429488.065 1451547.621 2302385.569 8081725.61 3309797.324 0.813190795 2.504713239 0.581545951 0.528155151 2.244695774 0.438560878 0.695627358 2.441758458 1 21.65831145 3.962238107 23.82938691 1.074480844 1.750194292 0.063185358 0.801460721 449.2752664 719336.1197 0.189280228 0.343288912 9167.229563 -3.962238107 0.675713448 SNYNLPMHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SNYNLPMHK 9 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ; 101.65 0.003842 545770000 836950 877460 910420 943130 961580 718680 1050090 907630 1061450 FALSE TRUE 784566.7935 942428.0514 932015.5923 967332.3125 886061.3856 926151.2492 892638.7531 1020949.603 884287.1378 0.88723081 1.065748908 1.053973933 1.093912001 1.002006416 1.047342215 1.009444461 1.154545351 1 19.75415538 4.741546768 24.50480642 1.051908307 0.887230729 0.556965672 0.046551288 153.1663556 1256821.007 0.009895192 0.069887021 55150.15895 -4.741546768 -0.164677577 SPAAECLSEKETEELMAWMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPAAECLSEKETEELMAWMR 20 1 Q12931-2;Q12931;I3L0K7 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 200.99 1.19E-21 24643000 38396 33003 30538 33133 51928 21906 31897 32595 71340 FALSE TRUE 35992.8629 35446.57646 31262.37578 33983.24887 47849.78435 28229.90659 27114.34097 36664.5575 59432.89313 0.605605095 0.596413444 0.52601134 0.571791934 0.805106092 0.474987925 0.456217753 0.616906827 1 15.85897399 0.961503197 23.29250008 1.000000002 0.568309004 0.658077386 0.09506034 1872.668919 1133060.474 0.091729921 0.02293248 9.151729954 -0.961503197 -0.431690997 SPAAET(ph)PPLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.012)PAAET(0.988)PPLQR 77.204 0.052311 0 141370 148030 156240 168040 144400 125080 177660 137150 118450 TRUE FALSE 132521.9041 158990.2952 159946.0866 172352.1909 133059.4065 161188.5655 151021.5323 154273.4794 98679.92978 1.342946882 1.611171548 1.620857321 1.746577964 1.34839381 1.63344832 1.530417914 1.563372408 1 16.59046907 -2.180614464 0.568679841 0.281464803 1.56721519 0.654662049 0.124966514 82.58400008 6.39025767 75.84373339 0.047280559 0.006597593 2.180614464 1.285750386 SPAAPYFLGSSFS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPAAPYFLGSSFSPVR 16 0 P30291 P30291 WEE1 Wee1-like protein kinase 1 SPAAPYFLGS(0.001)S(0.06)FS(0.939)PVR 128.26 6.48E-05 80541000 70069 90782 54709 67081 110230 38649 67435 94890 82119 TRUE FALSE 65683.50637 97503.59374 56006.72332 68802.41203 101572.9804 49806.33889 57323.74779 106737.2254 68412.80839 0.960105394 1.425224253 0.818658445 1.005694893 1.484707072 0.728026521 0.837909584 1.560193594 1 16.06197883 2.20926559 24.9999968 0.988370095 1.128205848 0.022273002 0.292865973 725.2022339 618874.1144 0.105440838 0.077885848 161.9069865 -2.20926559 0.139835753 SPAGLQVLNDYLADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPAGLQVLNDYLADK 15 0 P24534;C9JZW3;F2Z2G2;F8WF65 P24534 EEF1B2 Elongation factor 1-beta 0 ; 205.88 9.72E-09 127933000 259510 211758 244630 222500 245390 216450 258200 209580 274590 FALSE TRUE 243267.7323 227436.7827 250432.7391 228209.7267 226118.0593 278935.6012 219485.307 235746.5243 228759.1551 1.063422936 0.994219368 1.094744117 0.997598223 0.988454688 1.219341806 0.95946021 1.030544654 1 17.80346996 1.608528408 25 0.996253675 1.053752552 0.153084738 0.068880577 0.148821021 4861.298991 0.031501139 0.016149375 40.60022197 -1.608528408 0.057498877 SPAGPAATPAQAQAAST(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.022)T(0.978)PR;SPAGPAATPAQAQAAS(0.005)T(0.995)PR;SPAGPAATPAQAQAAS(0.004)T(0.996)PR;SPAGPAATPAQAQAAS(0.002)T(0.998)PR;SPAGPAATPAQAQAAS(0.002)T(0.998)PR;SPAGPAATPAQAQAAS(0.002)T(0.998)PR 340.24 1.11E-74 5762910000 2870230 2648710 3064400 2419720 3101330 2675960 3066560 2986340 2436540 TRUE FALSE 2690587.428 2844823.244 3137089.015 2481814.112 2857764.052 3448466.211 2606757.797 3359191.123 2029865.733 1.325500196 1.401483457 1.545466266 1.222649395 1.40785866 1.698864193 1.28420208 1.654883408 1 20.95295287 -1.265915624 3.916868465 0.999417503 1.440357824 0.451577267 0.153273835 136.512667 26006974.44 25794.55709 0.032979926 0.05421062 1.265915624 0.440940322 SPAGSQQQFGYSPGQQQTHPQGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPAGSQQQFGYSPGQQQTHPQGSPR 25 0 Q8TAP9 Q8TAP9 MPLKIP M-phase-specific PLK1-interacting protein 1 SPAGSQQQFGYSPGQQQT(0.004)HPQGS(0.996)PR 154.4 5.22E-08 389550000 83217 101320 104480 91308 118520 87189 113470 99080 107310 TRUE FALSE 78008.59652 108821.8382 106958.3149 93651.11786 109211.9173 112359.0489 96456.2269 111450.3561 89399.26775 0.872586526 1.217256483 1.196411533 1.047560234 1.221619819 1.256822922 1.07893755 1.24665849 1 16.44797539 4.744606232 24.88206851 1.166803147 0.872586389 0.504286325 0.088612785 482.7623663 1986855.294 0.01889915 0.172726017 55540.04561 -4.744606232 -0.294216758 SPALKS(ph)PLQSVVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPALKSPLQSVVVR 14 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 SPALKS(0.999)PLQS(0.001)VVVR;S(0.001)PALKS(0.986)PLQS(0.013)VVVR 80.585 0.0096197 1333330000 1484860 1270150 1411430 1401750 1300460 1055500 1422680 1009190 1049060 TRUE FALSE 1391925.263 1364193.228 1444909.786 1437721.278 1198327.117 1360205.715 1209362.342 1135189.593 873965.1088 1.592655415 1.560924131 1.653280859 1.645055693 1.371138396 1.556361577 1.383765015 1.298895781 1 19.73721616 0.994858348 0.562317022 0.98770795 1.611576113 0.876376062 0.070248066 0.282086973 0.217883297 0.071463028 0.032219232 9.882307151 -0.994858348 0.623868163 SPALLLSQLLPYMENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPALLLSQLLPYMENR 16 0 Q13268;C9JZP6;Q13268-2;H0YJG9;H0YJP4 Q13268;H0YJP4 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 112.51 0.002607 40956000 57425 48422 50982 59175 62689 43442 44807 50321 56148 FALSE TRUE 53830.87176 52007.21526 52191.31712 60693.53068 57765.65882 55983.00018 38088.60632 56603.68762 46776.53607 1.150809279 1.111822714 1.115758487 1.297520847 1.2349281 1.196817996 0.814267355 1.210087201 1 15.51349741 1.779304683 24.99999999 0.989295534 1.174544863 0.362292327 0.108891914 60.07290067 36873.72173 0.047831836 0.026584404 60.15956445 -1.779304683 0.18524933 SPALLLSQLLPYMENRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPALLLSQLLPYMENRR 17 1 Q13268;C9JZP6;Q13268-2;H0YJG9;H0YJP4 Q13268;H0YJP4 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;; 199.08 2.18E-11 2043050000 224495 313479 235657 231603 408220 183281 238943 294757 477320 FALSE TRUE 210444.2587 336689.3113 241246.8953 237546.3251 376160.0479 236191.2494 203115.7154 331558.0603 397652.2084 0.529216874 0.846692925 0.606678123 0.597372076 0.945952367 0.593964385 0.510787344 0.833789058 1 18.60114766 0.999294916 10.69361395 0.999998758 0.670450142 0.406216679 0.13648777 0.07226793 263.5774115 0.127203098 0.031812571 9.983778012 -0.999294916 -0.329548616 SPAVATSTAAPPPPSS(ph)PLPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPAVATSTAAPPPPSSPLPSK 21 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 SPAVATSTAAPPPPS(0.001)S(0.999)PLPSK;SPAVATSTAAPPPPS(0.011)S(0.989)PLPSK;SPAVATSTAAPPPPS(0.008)S(0.992)PLPSK;SPAVATSTAAPPPPS(0.008)S(0.992)PLPSK;SPAVATSTAAPPPPS(0.002)S(0.998)PLPSK;SPAVATSTAAPPPPS(0.003)S(0.997)PLPSK 321.42 5.35E-67 5385200000 7076460 6572690 7281180 7823240 7057960 5066760 7222950 4720700 3983250 TRUE FALSE 6633557 7059338.806 7453893.028 8023997.583 6503656.292 6529451.36 6139935.702 5310089.787 3318419.842 1.999010769 2.127319369 2.246217592 2.4180176 1.959865418 1.967638717 1.850258856 1.600186245 1 21.662065 1.005875538 0.763510455 0.998844573 2.183802513 0.899028829 0.123508466 0.199487118 0.263208764 0.118188296 0.044671539 10.13620857 -1.005875538 1.18495794 SPDDPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPDDPSR 7 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;; 110.61 0.015737 4488160000 6786650 8327530 6963770 6796520 8295410 5042500 7330130 7448690 7599860 FALSE TRUE 6361885.691 8944108.986 7128953.913 6970930.21 7643921.961 6498187.892 6231045.056 8378675.343 6331394.269 1.00481591 1.412660246 1.125969038 1.101010285 1.207304685 1.026343901 0.984150535 1.323353907 1 22.59409181 3.637511559 4.679660935 1.098410219 1.246922445 0.064459352 0.140045204 0.341411056 12.87144018 0.034996494 0.055842986 4340.218157 -3.637511559 0.148512227 SPDKPGGS(ph)PSASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPDKPGGSPSASR 13 1 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 SPDKPGGS(0.998)PS(0.002)ASR;SPDKPGGS(0.999)PS(0.001)ASR 123.59 0.00013423 1004090000 1311580 962140 1042780 1089270 1026370 805270 1349660 924620 1214450 TRUE FALSE 1229490.549 1033377.847 1067515.234 1117222.512 945763.0404 1037738.377 1147291.013 1040060.842 1011750.449 1.215211271 1.021376217 1.055117134 1.104247113 0.934778967 1.025686104 1.133966398 1.027981597 1 19.94842206 4.743466914 24.73168903 1.045001047 1.215211352 0.505706986 0.054693215 394.7036885 1989544.956 0.012843051 0.106100417 55394.53403 -4.743466914 0.170210305 SPDLEAS(ph)LDTLENNCHVGSDIDFRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPDLEASLDTLENNCHVGSDIDFRPK 26 1 Q13111;Q13111-2;Q13111-3;K7EJF1 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 S(0.001)PDLEAS(0.858)LDT(0.142)LENNCHVGSDIDFRPK 144.55 1.47E-07 146890000 84462 53682 65238 62636 52221 52700 83569 43611 77285 TRUE FALSE 79175.67419 57656.67114 66785.47617 64243.3458 48119.77331 67913.63449 71038.60427 49055.92935 64385.63422 1.229710247 0.895489682 1.037272941 0.99779006 0.747368165 1.054794836 1.103330038 0.761907993 1 15.97445121 4.748028587 24.28695616 0.964186321 1.22971046 0.347002723 0.119243092 1035.593528 2656390.451 0.027083347 0.339112949 55979.44485 -4.748028587 0.265524139 SPDTNYLFMGDYVDR ddPTM_SK-BR-3_Pertuzumab_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 86.467 0.017554 64623000 31203 24892 24410 36974 32979 21165 30582 23077 25990 FALSE TRUE 29250.05993 26735.02958 24989.01673 37922.81544 30388.96237 27274.99191 25996.51301 25958.21425 21652.1011 1.350910925 1.234754515 1.154115096 1.751461221 1.403511014 1.259692618 1.200646205 1.198877381 1 14.40221941 1.185600812 1.139583968 1.01703014 1.338094103 0.345550333 0.15999176 0.608254315 1.628102375 0.157258627 0.051166749 15.33207067 -1.185600812 0.321063963 SPEDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPEDKR 6 1 A0A3B3ISG5;P14735;Q5T5N3 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 91.26 0.077118 165719000 431440 357790 407270 400970 406740 305450 418150 390910 452540 FALSE TRUE 404436.9405 384281.1439 416930.6367 411259.569 374796.2811 393628.4564 355452.2894 439715.974 377008.1505 1.072753838 1.019291343 1.1058929 1.090850605 0.994133099 1.044084739 0.942823886 1.166330153 1 18.52423619 2.741644931 24.96552109 1.020294581 1.068995488 0.09737064 0.060840461 545.1518748 4412682.97 0.017639957 0.018013418 551.6262588 -2.741644931 0.048700907 SPEDLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPEDLER 7 0 P06744;A0A2U3TZU2;P06744-2;Q8N196 P06744 GPI;SIX5 Glucose-6-phosphate isomerase;Homeobox protein SIX5 0 ;;;;; 167.24 0.0025446 12919900000 10442200 13784000 11385900 12248000 13214400 8933570 13805600 11477400 12936600 FALSE TRUE 9788641.342 14804581.7 11655978.92 12562304.42 12176594.33 11512546.63 11735578.44 12910378.65 10777397.89 0.908256468 1.373669401 1.081520702 1.165615722 1.129826926 1.068212082 1.088906485 1.197912408 1 23.36150556 2.910139523 1.220993702 1.095177368 1.175040073 0 0.12422294 1.304823553 4.059260029 0.049958007 0.055648149 813.0916916 -2.910139523 0.079862705 SPEEGAETPVYLALLPPDAEGPHGQFVSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPEEGAETPVYLALLPPDAEGPHGQFVSEK 30 0 P16152 P16152 CBR1 Carbonyl reductase [NADPH] 1 0 ;;; 211.78 3.87E-26 769073000 748730 671695 709066 683686 817540 581418 857970 688514 1048880 FALSE TRUE 701868.3258 721427.9967 725885.3804 701230.5402 753333.7062 749263.9381 729325.3635 774476.4885 873815.152 0.803222883 0.825607104 0.830708164 0.802492997 0.862120214 0.857462744 0.834644904 0.886316158 1 19.7369686 -4.999988036 0.181535975 1.697918355 0.801012793 0.913516588 0.01679733 34.48369595 0.333144938 8.628187232 0.048422123 1.00E-05 4.999988036 -0.896905563 SPFEGAVT(ph)ESQSLFSDNFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPFEGAVTESQSLFSDNFR 19 0 O95628-3;O95628-2;O95628;O95628-8;O95628-4;O95628-7;O95628-9;O95628-10;O95628-6;O95628-5 O95628-3 CNOT4 CCR4-NOT transcription complex subunit 4 1 S(0.24)PFEGAVT(0.76)ESQSLFSDNFR 240.53 2.81E-23 166680000 23969 26659 22556 23416 23959 23413 22076 21004 31856 TRUE FALSE 22468.82308 28632.8601 23091.03897 24016.8942 22077.35679 30171.95302 18765.90874 23626.39564 26539.0278 0.846633239 1.078896345 0.870078555 0.90496511 0.83188265 1.136889913 0.707106111 0.890250985 1 14.6958279 3.740197586 21.97725626 0.893594927 0.977894865 0.025000145 0.123479812 222.5832264 374082.5109 0.029164738 0.052014517 5497.90949 -3.740197586 0.084299938 SPFNSPS(ph)PQDSPR ddPTM_SK-BR-3_Pertuzumab_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(0.019)PS(0.981)PQDSPR 178.01 1.57E-05 100420000 261620 267660 287860 268900 287830 263110 325930 260190 222080 TRUE FALSE 245245.6712 287477.8249 294688.1751 275800.4292 265224.9929 339065.5858 277059.8223 292675.2942 185013.4133 1.325556168 1.55382153 1.59279357 1.490705048 1.433544672 1.832654075 1.497512085 1.581913922 1 17.49727034 -1.191950539 4.517130358 0.99988887 1.549509987 0.626891755 0.130331934 0.000146261 2.62E-05 0.114327439 0.026941251 0.064276092 1.191950539 0.549621117 SPGAPSAGEAEARPSPSTTPLPDS(ph)SPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPGAPSAGEAEARPSPSTTPLPDSSPSR 28 1 Q5SYE7-2;Q5SYE7 Q5SYE7-2 NHSL1 NHS-like protein 1 1 S(0.073)PGAPS(0.084)AGEAEARPS(0.001)PS(0.001)T(0.001)T(0.001)PLPDS(0.418)S(0.418)PS(0.005)R 100.55 0.00083029 196220000 23010 22226 20250 28454 25070 19629 23144 17745 27470 TRUE FALSE 21569.84517 23871.63617 20730.33956 29184.17781 23101.10333 25295.57365 19673.77206 19960.50231 22885.07954 0.94252874 1.043109163 0.905845205 1.275249132 1.009439504 1.10533038 0.859676805 0.87220594 1 14.48211969 1.717503978 9.64733632 0.901190095 1.037473079 0.264707165 0.105786011 0.142231073 35.32403457 0.048410803 0.026096607 52.1799884 -1.717503978 0.136282984 SPGAPSAGEAEARPSPSTTPLPDSS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPGAPSAGEAEARPSPSTTPLPDSSPSR 28 1 Q5SYE7-2;Q5SYE7 Q5SYE7-2 NHSL1 NHS-like protein 1 1 SPGAPSAGEAEARPSPSTTPLPDS(0.249)S(0.716)PS(0.034)R 133.71 9.35E-06 228110000 70689 75206 77088 76304 99480 73440 85372 72898 86366 TRUE FALSE 66264.70167 80774.33049 78916.56376 78262.08982 91667.24208 94640.9358 72571.26115 81999.47577 71950.95665 0.920970405 1.122630389 1.096810486 1.087714375 1.274023951 1.315353405 1.008621213 1.139657895 1 16.13472625 4.744927051 4.268248194 1.134106309 0.903444212 0.303348217 0.099860155 0.28668163 12.06755202 0.023397894 0.202973951 55581.08891 -4.744927051 -0.230662097 SPGGPGSHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPGGPGSHVR 10 0 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 0 ; 124.1 0.00044442 72713000 105262 155532 121022 136168 158219 101952 142786 142379 151467 FALSE TRUE 98673.83932 167047.7511 123892.699 139662.3014 145793.118 131383.8873 121376.5649 160155.3316 126186.1792 0.78197026 1.32381971 0.981824632 1.106795549 1.155381032 1.041190788 0.961884777 1.269198676 1 16.94519438 2.132208162 17.2099561 1.052995933 1.094609754 0 0.158057943 8.106394902 1271.552211 0.054456236 0.04021875 135.5839126 -2.132208162 0.041613821 SPGLVPPS(ph)PEFAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPGLVPPSPEFAPR 14 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 SPGLVPPS(1)PEFAPR 150.34 7.59E-06 230090000 309390 312090 322350 321810 267130 294780 327240 234880 195640 TRUE FALSE 290025.8322 335197.4683 329996.2942 330068.1894 246150.6874 379878.2006 278173.3999 264205.285 162986.4201 1.779447834 2.056597526 2.024685823 2.025126935 1.510252739 2.330735287 1.706727467 1.62102637 1 17.31439224 0.892804436 1.410156937 1.004170419 1.960819888 0.649356076 0.217252099 0.300840314 1.177798503 0.183447147 0.054571243 7.81275914 -0.892804436 0.956649469 SPGLYAIGYEECIERPLS(ph)PHMEQSSLDPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPGLYAIGYEECIERPLSPHMEQSSLDPGK 30 1 A0A6I8PS01;Q6P1R3-3;Q6P1R3;Q6P1R3-2 A0A6I8PS01 MSANTD2 Myb/SANT-like DNA-binding domain-containing protein 2 1 S(0.003)PGLYAIGYEECIERPLS(0.997)PHMEQS(0.001)SLDPGK 77.766 0.0021211 55146000 40228 49932 33719 35759 62372 30756 39600 53723 43061 TRUE FALSE 37710.20129 53629.01723 34518.8306 36676.63648 57473.55472 39634.75792 33662.34763 60430.43481 35873.84092 1.051189399 1.494933798 0.962228457 1.0223783 1.602102068 1.104837311 0.938353596 1.684526476 1 15.1306446 -1.561201967 3.311436768 0.992588509 1.210576536 0.062198549 0.272144887 22398687.68 11914631.66 1177749.807 0.058890913 0.027466166 1.561201967 0.217988027 SPGQLQRPTGVAVDTNGDIIVADYDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPGQLQRPTGVAVDTNGDIIVADYDNR 27 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 0 135.3 1.97E-05 186110000 59964 61974 60539 77498 67837 62136 80534 63114 69961 FALSE TRUE 56210.96028 66562.61944 61975.01367 79486.72988 62509.35566 80073.65451 68458.67434 70993.92183 58284.05713 0.964431151 1.142038196 1.063327035 1.363781689 1.072494928 1.373851761 1.174569474 1.218067604 1 15.83081369 5.641276544 0.642395407 1.204697409 0.410101152 0.214394607 0.122356458 12.35908971 1.624955917 0.044352059 9.384828618 437800.7928 -5.641276544 -0.794596257 SPGS(ph)GSQSSGWHEVEPGMPSPTTLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPGSGSQSSGWHEVEPGMPSPTTLKK 26 1 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;A0A590UJA3;S4R3W2 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 1 S(0.078)PGS(0.282)GS(0.078)QS(0.282)S(0.282)GWHEVEPGMPSPTTLKK 198.48 2.87E-25 581890000 469380 690450 645950 633940 686730 495090 859930 657230 993460 TRUE FALSE 440002.3437 741571.6364 661272.239 650207.9737 632796.9959 638014.4459 730991.4797 739286.6122 827645.108 0.531631661 0.896001957 0.798980424 0.785612054 0.764575287 0.770879257 0.883218511 0.893241083 1 19.65865275 -4.999999999 0.047016331 1.877182396 0.348481961 0.481560109 0.08898351 634.3981398 2.213384839 71.48478808 17.48026154 1.00E-05 4.999999999 -1.528700435 SPGS(ph)PPGPELPIETALDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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;SPGS(1)PPGPELPIETALDDR 146.76 1.18E-07 122897000 27849 27325.3 27325.6 27065.2 30578.3 24164.2 29388 21764.1 25716 TRUE FALSE 26105.9808 29348.49364 27973.77614 27759.73885 28176.80366 31140.01227 24981.54222 24481.39579 21423.83347 1.218548531 1.369899261 1.30573159 1.295740974 1.315208303 1.453521953 1.166063126 1.142717797 1 14.38692903 1.293911907 1.855284067 1.023816298 1.325939966 0.711908276 0.068656732 0.157933466 0.950832401 0.056904048 0.016976577 19.67487162 -1.293911907 0.302123668 SPGS(ph)PPGPELPIETALDDRER ddPTM_SK-BR-3_Pertuzumab_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 S(0.001)PGS(0.999)PPGPELPIETALDDRER;S(0.001)PGS(0.999)PPGPELPIETALDDRER 154.86 1.81E-08 114171000 61947 72431 63664 74657 96165 52536 66449 65152 96370 TRUE FALSE 58069.84785 77793.8666 65174.14014 76572.82501 88612.58881 67702.29035 56485.58933 73286.37062 80285.22443 0.723294333 0.968968663 0.811782499 0.953759868 1.103722253 0.843272107 0.703561455 0.912825132 1 16.29284688 0.98641442 24.56231039 1.00000002 0.872395773 0.105570336 0.117717554 1446.502795 2615238.532 0.114335082 0.028583771 9.692022634 -0.98641442 -0.127604247 SPGS(ph)PVGEGTGSPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPGSPVGEGTGSPPK 15 0 P35611;P35611-3;E7EV99;E7ENY0;P35611-2;P35611-6;P35611-4;H0Y9H2;P35611-5;A0A0A0MSR2 P35611 ADD1 Alpha-adducin 1 SPGS(1)PVGEGTGSPPK;SPGS(1)PVGEGTGSPPK;SPGS(1)PVGEGTGSPPK;SPGS(1)PVGEGTGSPPK 320.35 1.54E-56 781460000 1308640 989830 1061740 1078950 1212440 777370 1182070 1030490 1204720 TRUE FALSE 1226734.558 1063118.043 1086924.974 1106637.684 1117219.853 1001784.099 1004829.577 1159148.945 1003644.449 1.222280021 1.059257632 1.082978115 1.102619244 1.113162987 0.998146406 1.001180825 1.154939825 1 19.93681684 2.2516074 24.96832896 1.033201887 1.10319185 0.262753936 0.062180103 322.1652413 616544.8526 0.020481375 0.017033876 178.4873329 -2.2516074 0.069989964 SPGS(ph)TPTT(ph)PTSSQAPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658;P35658-5;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 2 SPGS(1)TPTT(0.952)PT(0.048)SSQAPQK;SPGS(1)TPTT(0.939)PT(0.061)SSQAPQK;SPGS(0.992)T(0.008)PTT(0.76)PT(0.239)SSQAPQK;SPGS(0.984)T(0.016)PTT(0.82)PT(0.172)S(0.007)SQAPQK 328.92 3.20E-71 2358130000 3316830 2805740 3166060 3735610 3420360 2051540 2885310 2023190 2246790 TRUE FALSE 3109235.531 3013479.909 3241160.438 3831472.077 3151738.723 2643786.294 2452684.551 2275789.725 1871786.234 1.6611061 1.609948751 1.731586855 2.046960282 1.683813389 1.412440291 1.310344369 1.215838477 1 20.83598425 1.80158194 1.332403255 1.10105718 1.741120372 0.806993637 0.130630896 0.195594274 0.652554789 0.108461764 0.043953204 63.32598301 -1.80158194 0.640063191 SPGS(ph)TPTTPTSSQAPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658;P35658-5;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 S(0.013)PGS(0.877)T(0.085)PT(0.023)T(0.001)PTSSQAPQK;S(0.008)PGS(0.988)T(0.004)PTTPTSSQAPQK;S(0.329)PGS(0.67)T(0.001)PTTPTSSQAPQK;S(0.003)PGS(0.987)T(0.01)PTTPTSSQAPQK 355.38 7.76E-88 1444910000 1044680 956930 949040 910947 943520 786670 1351720 1125390 1042590 TRUE FALSE 979295.3436 1027782.093 971551.677 934323.4422 869419.7452 1013768.858 1149042.135 1265897.419 868574.9936 1.127473564 1.183296895 1.118558195 1.075696916 1.000972572 1.167163303 1.322904923 1.457441704 1 19.72829089 1.888283685 4.684302543 1.290710732 1.11159738 0.247356812 0.121441691 0.258902237 8.554291396 0.051690764 0.030026601 77.31854718 -1.888283685 -0.179113352 SPGSNS(ph)KVPEIEVTVEGPNNNNPQTSAVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPGSNSKVPEIEVTVEGPNNNNPQTSAVR 29 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 S(0.061)PGS(0.41)NS(0.529)KVPEIEVTVEGPNNNNPQTSAVR;S(0.008)PGS(0.366)NS(0.626)KVPEIEVTVEGPNNNNPQTSAVR;S(0.053)PGS(0.343)NS(0.604)KVPEIEVTVEGPNNNNPQTSAVR 238.11 1.54E-45 1222590000 231162 297559 242755 283424 465670 192699 389554 242150 987300 TRUE FALSE 216693.9831 319590.578 248513.2632 290697.1397 429098.1566 248328.0731 331143.9941 272382.9605 822513.2518 0.263453485 0.388553713 0.302138917 0.353425479 0.521691481 0.301913766 0.402600193 0.331159358 1 19.6496794 -4.621325976 0.436086124 9.999999999 0.35168223 0.888320686 0.071492451 221.9541158 1.922224222 1902.60225 0.036092385 2.39E-05 4.621325976 -9.648317769 SPGTGPSPFSS(ph)SLGHLNHLGGSLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPGTGPSPFSSSLGHLNHLGGSLDR 25 0 O15049 O15049 N4BP3 NEDD4-binding protein 3 1 SPGTGPSPFS(0.005)S(0.498)S(0.498)LGHLNHLGGSLDR 124.31 0.00025636 274200000 54385 84819 60530 61777 65635 51822 96602 68714 93176 TRUE FALSE 50981.13993 91099.08701 61965.80018 63362.30241 60480.29186 66782.17014 82117.42691 77293.09416 77624.32366 0.656767589 1.173589446 0.798278133 0.816268657 0.779140983 0.860325308 1.057882672 0.995732916 1 16.24422117 1.751630024 10.58288067 1.018749795 0.875531444 0.252256363 0.132554269 0.202718537 111.3984707 0.062760712 0.034249149 56.44559095 -1.751630024 -0.143218351 SPGTGPSPFSSS(ph)LGHLNHLGGSLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPGTGPSPFSSSLGHLNHLGGSLDR 25 0 O15049 O15049 N4BP3 NEDD4-binding protein 3 1 SPGTGPSPFSS(0.059)S(0.941)LGHLNHLGGSLDR 236.29 3.27E-38 246840000 106860 166740 132630 124700 176400 110200 208810 143310 198320 TRUE FALSE 100171.8234 179085.6031 135776.0462 127900.0131 162546.2556 142012.9511 177500.879 161202.569 165219.1108 0.606296831 1.083927896 0.821793832 0.774123602 0.98382236 0.859543126 1.074336244 0.975689605 1 17.33402105 1.747547556 24.99999216 1.019143972 0.879370515 0.248426873 0.127979697 3.264948779 9103.486097 0.05506454 0.030536234 55.91747553 -1.747547556 -0.139773457 SPHS(ph)PSPIATPPSQSSSCSDAPMLSTVHSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPHSPSPIATPPSQSSSCSDAPMLSTVHSAK 31 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 S(0.048)PHS(0.913)PS(0.039)PIATPPSQSSSCSDAPMLSTVHSAK;S(0.102)PHS(0.439)PS(0.439)PIAT(0.02)PPSQSSSCSDAPMLSTVHSAK 186.05 3.51E-18 307130000 106196 117605 137000 124214 144984 111506 153933 111204 157653 TRUE FALSE 99549.38193 126312.5966 140249.7047 127401.5415 133597.5415 143695.9721 130852.1757 125088.0642 131339.6958 0.757953498 0.961724449 1.067839421 0.970015506 1.017190885 1.094078764 0.996288098 0.95240105 1 17.00294349 4.751298916 2.384580264 1.017327074 0.691739195 0.786024883 0.041739361 0.252888356 1.706775561 0.009932634 0.172495054 56402.57302 -4.751298916 -0.325587879 SPHSPS(ph)PIATPPSQSSSCSDAPMLSTVHSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPHSPSPIATPPSQSSSCSDAPMLSTVHSAK 31 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 S(0.001)PHS(0.454)PS(0.546)PIATPPSQSSSCSDAPMLSTVHSAK 161.38 3.22E-12 161910000 70831 94972 109630 99438 98569 74819 111560 89440 124600 TRUE FALSE 66397.81415 102003.8257 112230.4754 101989.7474 90827.78835 96418.03072 94832.61367 100606.7809 103803.4551 0.639649365 0.982663107 1.081182465 0.982527483 0.874997738 0.928851845 0.913578586 0.969204549 1 16.66349494 4.740018184 24.92191173 0.968901192 0.639649253 0.775929201 0.055208474 66.08681191 1129857.397 0.015316623 0.096369756 54956.38841 -4.740018184 -0.32925194 SPIIFIGTGEHIDDFEPFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPIIFIGTGEHIDDFEPFK 19 0 G3V4F7;P61011-2;P61011 G3V4F7 SRP54 Signal recognition particle 54 kDa protein 0 ; 211.29 1.36E-16 224240000 533880 482630 509630 503310 572390 441400 647150 487950 583290 FALSE TRUE 500465.4038 518364.4274 521718.6643 516225.7867 527436.7983 568825.0145 550115.8653 548871.6316 485935.1308 1.029901672 1.066735855 1.073638499 1.062334773 1.085405777 1.170578084 1.132076754 1.12951626 1 18.89040421 2.467780579 24.75982232 1.122998642 1.063334796 0.175092632 0.045648254 213.3657975 565575.0169 0.013962763 0.011696208 293.6165823 -2.467780579 -0.059663845 SPILLGSLAHQIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPILLGSLAHQIYR 14 0 P31937 P31937 HIBADH "3-hydroxyisobutyrate dehydrogenase, mitochondrial" 0 212.17 2.82E-09 174050000 107970 310970 98866 79946 388740 83278 92552 311540 286610 FALSE TRUE 101212.3504 333994.5424 101211.1482 81997.54971 358209.9285 107319.0067 78674.68681 350436.4548 238772.9394 0.423885348 1.398795622 0.423880313 0.343412239 1.500211579 0.449460508 0.329495826 1.467655655 1 17.86527982 1.227473535 24.99937928 1.233827801 0.72148468 0.205677442 0.437447423 408.6613971 921428.3372 0.390668869 0.101361199 16.88392971 -1.227473535 -0.51234312 SPITS(ph)SPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPITSSPPK 9 0 Q52LA3;G3V5T8 Q52LA3;G3V5T8 LIN52 Protein lin-52 homolog 1 SPIT(0.082)S(0.621)S(0.297)PPK;SPIT(0.06)S(0.585)S(0.355)PPK;SPIT(0.082)S(0.617)S(0.301)PPK 81.865 0.021056 417120000 1814750 1172930 1225620 1137570 1226070 875280 1702370 1272110 1659970 TRUE FALSE 1701168.037 1259774.958 1254692.285 1166761.972 1129779.408 1127959.127 1447115.423 1430935.734 1382910.283 1.230136226 0.910959281 0.907283936 0.843700409 0.816957847 0.815641579 1.046427552 1.034727814 1 20.39927613 1.644672071 9.447903653 1.030399718 0.911456666 0.148575388 0.118129778 0.191371321 32.09403769 0.055544522 0.029352474 44.123715 -1.644672071 -0.118943052 SPLAQMEEERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SPLAQMEEERR 11 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2 E7EPK1 7-Sep Septin-7 0 ;;;; 136.7 0.00015036 2365950000 756914 1006029 831130 922317 1071830 643050 875132 852294 1155340 FALSE TRUE 709540.1039 1080516.434 850844.7961 945985.2157 987652.7954 828688.096 743914.0809 958704.782 962506.2902 0.737179706 1.12260714 0.883988816 0.982835359 1.026126068 0.860969018 0.772892695 0.996050407 1 19.87643644 2.219464916 24.92093646 0.875175159 0.966401574 0 0.11945589 489.2783445 638530.7019 0.04124992 0.030512561 165.754343 -2.219464916 0.091226415 SPLLAGGS(ph)PPQPVVPAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPLLAGGSPPQPVVPAHK 18 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4;C9JIY9 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 SPLLAGGS(1)PPQPVVPAHK;SPLLAGGS(1)PPQPVVPAHK;SPLLAGGS(1)PPQPVVPAHK 165.66 1.78E-11 880160000 1920080 1642110 1881350 1689540 1879550 1522880 2321730 1614070 1557810 TRUE FALSE 1799905.62 1763693.533 1925976.51 1732896.457 1731937.725 1962510.734 1973608.14 1815590.193 1297801.447 1.386888283 1.358985642 1.484030176 1.335255451 1.334516716 1.512181034 1.520731962 1.398973777 1 20.30763825 0.949247271 23.20844105 1 1.425460664 0.784574533 0.068590548 3514.084923 1606939.08 0.070093961 0.01752349 8.897075408 -0.949247271 0.425460664 SPLPAGPSSCTSPRS(ph)PLPAPPRPFLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPLPAGPSSCTSPRSPLPAPPRPFLYR 27 2 Q8N3V7-2 Q8N3V7-2 SYNPO Synaptopodin 1 S(0.001)PLPAGPS(0.137)S(0.137)CT(0.123)S(0.123)PRS(0.48)PLPAPPRPFLYR 68.733 0.011766 91427000 26400 41443 35180 33716 45917 30764 43612 35433 48111 TRUE FALSE 24747.67113 44511.48284 36014.48621 34581.20964 42310.86404 39645.06739 37072.78547 39856.88805 40080.96329 0.617442025 1.110539248 0.898543429 0.862783895 1.055634909 0.989124615 0.924947467 0.994409435 1 15.29062956 4.752492876 24.96312958 0.974680356 0.61744178 0.712065886 0.072296656 1357.295754 2431892.652 0.016876894 0.353066007 56557.84793 -4.752492876 -0.357238576 SPLS(ph)PTETFSWPDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPLSPTETFSWPDVR 15 0 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 S(0.001)PLS(0.998)PT(0.001)ETFSWPDVR;SPLS(0.999)PT(0.001)ETFSWPDVR;SPLS(0.998)PT(0.002)ETFSWPDVR;SPLS(0.991)PT(0.009)ETFSWPDVR 290.34 7.13E-44 265206000 116381 126385 107587 77547 98705 119776 145930 146414 259868 TRUE FALSE 109096.921 135742.6769 110139.0144 79536.98731 90953.10746 154353.3868 124049.1512 164694.1102 216494.352 0.503925021 0.627003317 0.508738512 0.367385969 0.420117692 0.712967269 0.572990243 0.760731671 1 17.72396986 0.975596456 0.97066782 0.999328371 0.514012097 0.750716614 0.091682565 0.316422634 0.633596787 0.088407115 0.029678385 9.453583307 -0.975596456 -0.485316274 SPLVAAMQHFLPVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPLVAAMQHFLPVLK 15 0 O95373;E9PLB2 O95373 IPO7 Importin-7 0 80.706 0.016176 53117000 158040 249400 199670 167020 294240 92383 182720 263250 397470 FALSE TRUE 148148.5585 267865.8355 204406.2667 171306.016 271131.5773 119052.4724 155322.8323 296117.342 331129.6892 0.447403429 0.80894539 0.617299727 0.517338135 0.818807815 0.359534274 0.469069483 0.894263944 1 18.33703684 1.10073474 5.361917844 0.9943117 0.593936216 0.523464345 0.147695533 0.163449342 6.618420792 0.14308152 0.036163064 12.61057066 -1.10073474 -0.400375485 SPMFPALGEAS(ph)SDDDLFQSAKPKPAKK ddPTM_SK-BR-3_Pertuzumab_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(0.5)S(0.5)DDDLFQSAKPKPAKK 150.04 7.22E-08 266080000 446240 212800 312910 301490 353990 207260 460900 265660 669140 TRUE FALSE 418310.635 228555.9334 320332.373 309226.7438 326189.0533 267092.5974 391792.3238 298828.2358 557456.2112 0.750391917 0.409998003 0.574632351 0.554710375 0.585138432 0.479127494 0.702821703 0.536056877 1 19.08849896 -1.455346608 0.38356523 1.283317406 0.540601036 0.63566553 0.099948562 14.06850515 1.144941338 3.967762732 0.061835998 0.035047205 1.455346608 -0.742716371 SPMFPALGEASS(ph)DDDLFQSAKPKPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPMFPALGEASSDDDLFQSAKPKPAK 26 2 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;Q5SRD0 Q641Q2;A0A0A0MR88 FAM21A;FAM21C;FAM21D WASH complex subunit FAM21A;WASH complex subunit FAM21C;Putative WASH complex subunit FAM21 1 SPMFPALGEAS(0.212)S(0.788)DDDLFQSAKPKPAK 165.34 6.66E-12 634040000 617140 366060 462800 428160 478060 329490 607030 401060 666700 TRUE FALSE 578514.309 393163.4633 473777.8345 439147.3105 440515.096 424608.4142 516011.4869 451133.2238 555423.463 1.041573408 0.70786254 0.853002918 0.79065315 0.793115749 0.764476913 0.929041572 0.812232925 1 19.0832286 0.454205903 0.745602003 1.001007039 0.817469235 0.209657515 0.094160148 2.437280411 2.089106263 0.094013571 0.029949582 2.845810011 -0.454205903 -0.183537804 SPPAS(ph)PESWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPPASPESWK 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 S(0.011)PPAS(0.989)PESWK 72.187 0.051125 102280000 212720 195100 225200 258270 332980 259010 338510 244930 326540 TRUE FALSE 199406.2349 209545.407 230541.8503 264897.6455 306829.094 333781.9823 287753.5681 275510.0497 272038.3645 0.73300777 0.770278881 0.847460801 0.973751059 1.127889056 1.226966582 1.057768336 1.012761748 1 18.0534506 3.189940824 1.903878918 1.097336267 0.771616669 0.813890254 0.066278664 0.129036822 0.958059152 0.021599716 0.029280517 1548.605595 -3.189940824 -0.325719598 SPPLS(ph)PVGTTPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPPLSPVGTTPVK 13 0 C9J4K0;Q9BVC5-2;Q9BVC5 C9J4K0 C2orf49 Ashwin 1 SPPLS(0.998)PVGT(0.002)TPVK 126.56 0.00019625 74602000 186030 157130 172400 217920 295120 206770 241870 185990 222480 TRUE FALSE 174386.7144 168764.0687 176489.4094 223512.1961 271942.4657 266461.1424 205603.8389 209211.2609 185346.6507 0.940867902 0.910532065 0.952212563 1.205914406 1.467210034 1.437636673 1.109293522 1.12875663 1 17.49986652 3.224009701 4.502756592 1.25039565 0.9285415 0.48045094 0.141523596 0.153953346 7.508154664 0.04104433 0.052357325 1674.98029 -3.224009701 -0.32185415 SPPMELQPPVS(ph)PQQSECNPVGALQELVVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPPMELQPPVSPQQSECNPVGALQELVVQK 30 0 H3BV98;F8VSA1;Q15633-2;Q15633;F8VW32;F8VZ57 H3BV98 TARBP2 RISC-loading complex subunit TARBP2 1 S(0.003)PPMELQPPVS(0.798)PQQS(0.2)ECNPVGALQELVVQK 44.365 0.079464 8021500 32622 30052 34825 33803 37034 27321 41557 29436 48657 TRUE FALSE 30580.24725 32277.08135 35651.06545 34670.44221 34125.49903 35208.12918 35325.91365 33111.1494 40535.83236 0.754400378 0.79626048 0.879495088 0.855303572 0.841860079 0.868568058 0.871473745 0.816836548 1 15.30691015 -5 0.101982892 1.473328535 0.739890246 0.715690509 0.034311412 106.3581164 0.735288289 10.87331353 0.544564807 1.00E-05 5 -0.733438289 SPPSTGS(ph)TYGSSQKEESAASGGAAYTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPPSTGSTYGSSQKEESAASGGAAYTK 27 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.122)PPS(0.096)T(0.096)GS(0.537)T(0.096)Y(0.016)GS(0.018)S(0.018)QKEES(0.001)AASGGAAYTK 75.326 0.010008 1076800000 420770 249470 326240 270360 256770 267200 409750 262190 233700 TRUE FALSE 394434.7568 267941.0184 333978.5669 277297.8953 236604.32 344336.3024 348311.7914 294924.9987 194693.9602 2.025921895 1.376216386 1.715402812 1.424275797 1.215262762 1.768602898 1.789022068 1.514813291 1 17.5708486 4.750381176 23.90583564 1.531600807 2.025922452 0.298094121 0.252725783 1323.014619 2675563.998 0.056898344 0.888974464 56283.51028 -4.750381176 0.494321645 SPPVRPNESLSGS(ph)WK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPPVRPNESLSGSWK 15 1 Q6ZNC4;E5RGL7 Q6ZNC4 ZNF704 Zinc finger protein 704 1 SPPVRPNESLS(0.005)GS(0.995)WK;SPPVRPNESLS(0.003)GS(0.997)WK 152 1.76E-06 633190000 431500 351250 374930 388840 483450 375500 625800 459050 494420 TRUE FALSE 404493.1852 377256.9155 383823.5167 398818.2927 445481.7871 483900.7543 531967.0996 516363.403 411898.1079 0.982022441 0.915898637 0.931840932 0.968245022 1.081533949 1.174806936 1.291501683 1.253619264 1 18.65192797 2.501001385 1.941010847 1.21680433 0.936940845 0.641648721 0.079722326 0.163119004 1.242176715 0.030031544 0.024775601 316.9577568 -2.501001385 -0.279863485 SPPYT(ph)AFLGNLPYDVTEESIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPPYTAFLGNLPYDVTEESIK 21 0 E7EX17;P23588-2;P23588;F8VX11;F8VP89;F8W0K0;F8VSC7;F8VYE9;F8VRU1 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.326)PPY(0.256)T(0.417)AFLGNLPYDVTEESIK 153.11 1.70E-07 50457000 94826 59780 64993 62262 62412 56176 81825 61930 49948 TRUE FALSE 88891.00993 64206.1734 66534.66465 63859.74833 57510.41328 72393.09926 69556.10088 69662.09682 41611.35612 2.13621997 1.542996417 1.598954489 1.534671164 1.382084571 1.73974381 1.671565346 1.67411263 1 15.34468969 -1.907734554 2.477733105 0.623158076 1.638116191 0.524429299 0.196549293 15602428.01 7508967.777 34151310.03 0.045221898 0.012367031 1.907734554 1.014958114 SPQLSLSPRPAS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPQLSLSPRPASPK 14 1 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 SPQLS(0.004)LS(0.012)PRPAS(0.983)PK 77.221 0.013024 0 173150 134900 151580 147690 154020 105870 174020 119920 235040 TRUE FALSE 162312.8506 144888.1364 155175.5492 151479.9754 141923.8905 136432.9503 147927.3165 134892.276 195810.3056 0.82892905 0.739941322 0.792478969 0.773605735 0.724802967 0.696760826 0.755462365 0.688892628 1 17.57909717 -1.359606557 5.533447803 1.000071253 0.750891342 0.776983347 0.042072308 3.50E-05 4.05E-06 0.038560395 0.009086181 0.043691147 1.359606557 -0.249179911 SPQNDDHS(ph)DTDSEENRDNQQFLTTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPQNDDHSDTDSEENRDNQQFLTTVK 26 1 Q86W56-3;Q86W56-2;Q86W56 Q86W56-3 PARG Poly(ADP-ribose) glycohydrolase 1 S(0.011)PQNDDHS(0.982)DT(0.007)DSEENRDNQQFLTTVK 127.4 5.79E-05 127140000 95574 79919 89829 85969 84403 72012 113100 78197 90146 TRUE FALSE 89592.19394 85836.28592 91959.7863 88175.11009 77774.32885 92800.69538 96141.70497 87960.06758 75100.05023 1.192971159 1.142959101 1.224497001 1.174101879 1.035609545 1.235694185 1.280181633 1.171238465 1 16.19652625 SPQNSHSHST(ph)PSSSVRPNSPSPTALAFGDHPIVQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPQNSHSHSTPSSSVRPNSPSPTALAFGDHPIVQPK 36 1 B3KRP1;Q9UKI8;Q9UKI8-4;Q9UKI8-5;Q9UKI8-2;C9JWT6 B3KRP1 TLK1 Serine/threonine-protein kinase tousled-like 1 1 S(0.001)PQNS(0.001)HS(0.001)HS(0.134)T(0.521)PS(0.134)S(0.035)S(0.035)VRPNS(0.134)PS(0.002)PT(0.002)ALAFGDHPIVQPK 95.371 0.00023082 195940000 23953 56332 51787 52727 52626 41521 66129 50251 47696 TRUE FALSE 22453.82449 60502.87989 53015.4121 54080.06409 48492.96624 53507.43866 56213.57036 56524.94797 39735.22947 0.565086066 1.522650824 1.334216835 1.361010489 1.22040232 1.346599463 1.414703554 1.422539865 1 15.27813106 4.746081795 24.98508847 1.354482152 0.565085684 0.738898358 0.141692021 410.3311152 1363072.616 0.030093746 0.317107634 55729.06997 -4.746081795 -0.789396468 SPQPVCS(ph)PAGSEGTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPQPVCSPAGSEGTPK 16 0 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 SPQPVCS(0.977)PAGS(0.023)EGTPK 174.65 3.98E-09 117540000 331260 137800 187770 182830 201000 127980 253270 151980 266910 TRUE FALSE 310527.0279 148002.8554 192223.9931 187521.7273 185214.2708 164925.7484 215294.5147 170955.0375 222360.9967 1.396499532 0.665597194 0.864468121 0.843321131 0.832944057 0.741702686 0.968220677 0.768817554 1 17.76254423 -1.845143528 7.724278304 1.008762939 0.862341103 0.020518129 0.199937387 0.027417412 0.000549665 0.175915034 0.039925418 0.014284218 1.845143528 -0.146421836 SPQPVPS(ph)PRPQSQPPHSSPSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPQPVPSPRPQSQPPHSSPSPR 22 1 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 SPQPVPS(1)PRPQSQPPHSSPSPR 168.11 5.91E-12 191240000 36536 100100 84127 84563 85386 82934 90260 82867 76628 TRUE FALSE 34249.27698 107511.5082 86122.53217 86733.02974 78680.12799 106875.6995 76726.35093 93213.12736 63838.29176 0.536500524 1.684122573 1.349073257 1.358636444 1.232491124 1.674162897 1.201886028 1.460144449 1 15.96213443 -1.078125213 4.277221271 0.999959788 1.352714621 0.073304143 0.321136545 18988722.65 4786337.865 7111.487685 0.065790369 0.083536214 1.078125213 0.352754833 SPQPVPSPRPQSQPPHSS(ph)PSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPQPVPSPRPQSQPPHSSPSPR 22 1 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 SPQPVPS(0.002)PRPQS(0.002)QPPHS(0.167)S(0.713)PS(0.116)PR 65.581 0.013782 67710000 15841 34573 36356 34247 36354 37679 39479 33340 30131 TRUE FALSE 14849.54009 37132.82089 37218.38149 35125.836 33498.90348 48556.31563 33559.49046 37502.57239 25101.94145 0.591569386 1.479280835 1.48268936 1.399327461 1.334514446 1.934364947 1.336928083 1.494010831 1 14.61551133 4.739185461 24.73884948 1.46375552 0.591569086 0.566628622 0.229733363 28.84376725 1141688.564 0.047753795 0.285082207 54851.11509 -4.739185461 -0.872186433 SPQQTVPYVVPLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPQQTVPYVVPLSPK 15 0 Q9UQR0;H0Y6S1;B4DRC2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 1 SPQQTVPYVVPLS(1)PK 82.865 0.010237 55817000 240930 151140 179310 179650 189120 137080 217250 148140 202010 TRUE FALSE 225850.6214 162330.5629 183563.3179 184260.1231 174267.2781 176652.7707 184675.3794 166635.6051 168293.226 1.342006608 0.964569797 1.090735036 1.09487546 1.035497876 1.049672497 1.097342916 0.990150401 1 17.36061758 4.748673585 24.8942193 1.047591648 1.342006779 0.807515076 0.046163943 580.3228825 1428500.251 0.010578899 0.14675896 56062.64521 -4.748673585 0.294415131 SPQYCQVIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPQYCQVIHR 10 0 Q13228;Q13228-4;A6PVX1;F2Z2W8;F8WCR4;C9JVL0 Q13228 SELENBP1 Selenium-binding protein 1 0 ;;;;; 164.64 6.10E-06 8494590000 2221480 4667440 2147490 2161420 5116590 1373333 2365090 4057920 4632040 FALSE TRUE 2082441.532 5013022.114 2198429.477 2216885.696 4714753.661 1769791.943 2010466.711 4564560.245 3858922.6 0.53964325 1.299072988 0.56970033 0.574483069 1.221779794 0.458623333 0.520991717 1.182858719 1 21.87976668 5.008639587 18.40565525 0.817088254 0.139530719 0.078806798 0.316150033 101620137 2887163222 0.073325587 1700211194 102009.2576 -5.008639587 -0.677557535 SPRPASPAS(ph)NVVVLPSGSTVYVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPRPASPASNVVVLPSGSTVYVK 23 1 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 1 S(0.023)PRPAS(0.357)PAS(0.62)NVVVLPSGSTVYVK 99.446 0.0016111 201130000 334350 340820 351180 369980 382560 278370 444000 325260 397370 TRUE FALSE 313423.6303 366054.6674 359510.1554 379474.3132 352515.2808 358730.9 377426.3219 365869.427 331046.3799 0.946766524 1.105750401 1.085981232 1.146287458 1.064851641 1.083627316 1.14010104 1.105190841 1 18.33667383 4.740209098 24.91312191 1.098577854 0.946766471 0.542884952 0.041275232 89.98607429 1359815.927 0.008626512 0.05415975 54980.5523 -4.740209098 -0.151811383 SPRPDHPGT(ph)PPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPRPDHPGTPPHK 13 1 P30291 P30291 WEE1 Wee1-like protein kinase 1 SPRPDHPGT(1)PPHK 94.922 0.0072316 78154000 106340 96056 104210 99105 113930 82016 138590 100390 128980 TRUE FALSE 99684.36922 103168.0862 106681.9104 101648.2021 104982.3974 105692.6878 117809.7161 112923.9125 107452.4048 0.927707197 0.960128221 0.992829436 0.945983501 0.97701301 0.983623289 1.096389759 1.050920291 1 16.71333824 1.891658639 5.706499598 1.057166553 0.965586646 0.654519241 0.029054055 0.123874563 5.43745688 0.012043643 0.007242176 77.92173952 -1.891658639 -0.091579907 SPS(ph)FASEWDEIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPSFASEWDEIEK 13 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.358)PS(0.642)FASEWDEIEK;S(0.089)PS(0.911)FASEWDEIEK;S(0.004)PS(0.996)FASEWDEIEK;SPS(1)FASEWDEIEK;SPS(1)FASEWDEIEK;SPS(1)FASEWDEIEK 383.96 6.33E-108 1570198000 1795840 1300040 1462810 1445980 1516630 1156840 1794460 1334890 1817640 TRUE FALSE 1683441.58 1396296.314 1497508.544 1483086.295 1397519.998 1490800.928 1525397.382 1501553.955 1514264.142 1.111722542 0.922095608 0.988934825 0.979410563 0.922903712 0.984505204 1.007352245 0.991606361 1 20.53018545 1.992590419 24.82306298 0.999334525 0.97479636 0 0.052243696 1078.913605 3614500.197 0.018490669 0.013126988 98.30835268 -1.992590419 -0.024538165 SPS(ph)GSAFGS(ph)QENLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSGSAFGSQENLR 14 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 2 S(0.001)PS(0.999)GS(0.001)AFGS(0.999)QENLR 226.08 3.71E-12 149440000 335140 377120 344950 394010 358270 280600 483340 330740 361940 TRUE FALSE 314164.1856 405042.3572 353132.3769 404120.9637 330132.9194 361604.6648 410867.6541 372033.617 301529.8758 1.04190069 1.343290963 1.171135616 1.340235234 1.094859733 1.19923329 1.3626101 1.233820085 1 18.20194143 -0.792132741 4.935303969 0.99999974 1.237361306 0.295847347 0.106382474 6.76E-05 31770599.01 22.92627925 0.022609729 0.161386521 0.792132741 0.237361566 SPS(ph)GSAFGSQENLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSGSAFGSQENLR 14 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 S(0.018)PS(0.982)GSAFGSQENLR 236.65 2.99E-17 139130000 139330 135110 124280 143810 136850 90631 139880 111060 148270 TRUE FALSE 130609.584 145113.685 127227.9803 147500.4081 126102.353 116794.6984 118906.2926 124926.0855 123522.7791 1.057372453 1.174792909 1.029996096 1.194115038 1.020883386 0.94553166 0.962626435 1.011360709 1 16.91441759 2.515450705 7.433500037 0.975086654 1.110194183 0.608986852 0.051000856 0.147911752 24.66889116 0.015266659 0.014143718 327.6805808 -2.515450705 0.135107528 SPS(ph)LDNPTPFPNLGPSENPLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPSLDNPTPFPNLGPSENPLKR 22 1 M0R0R8;M0R0X9;M0QXC8;M0QX56;M0R3C2;M0QYT9;M0R205;M0QZB8;M0QZB7;Q14653-3;Q14653-2;Q14653;Q14653-4 M0R0R8 IRF3 Interferon regulatory factor 3 1 S(0.437)PS(0.563)LDNPTPFPNLGPSENPLKR;S(0.197)PS(0.803)LDNPTPFPNLGPSENPLKR;S(0.378)PS(0.622)LDNPTPFPNLGPSENPLKR 274.34 1.29E-45 1397510000 1912240 1203300 1468500 1213120 949800 1235590 2044660 1313610 1205430 TRUE FALSE 1792556.312 1292393.584 1503333.513 1244250.713 875206.5393 1592284.775 1738082.215 1477617.1 1004235.946 1.784995169 1.286942167 1.496992335 1.239002366 0.87151485 1.585568393 1.730750848 1.471384396 1 19.93766684 4.747177412 23.64367307 1.38020807 1.784995613 0.209079992 0.262248688 952.9904084 2614787.442 0.063849778 0.716797899 55869.83793 -4.747177412 0.404787543 SPS(ph)LNLLQNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSLNLLQNK 10 0 O43353-2;O43353 O43353-2 RIPK2 Receptor-interacting serine/threonine-protein kinase 2 1 S(0.217)PS(0.783)LNLLQNK;S(0.029)PS(0.971)LNLLQNK 103.97 0.0028775 90097000 260310 230420 225550 228900 271870 160846 228480 209000 317140 TRUE FALSE 244017.6618 247480.5366 230900.1525 234773.9615 250518.4269 207279.6291 194221.5451 235094.1101 264207.2852 0.923584153 0.936690812 0.873935601 0.888597608 0.948188944 0.784534117 0.735110483 0.88980934 1 18.01131072 2.237182543 24.99999596 0.818457502 0.910612193 0.070911835 0.074711662 47.76383091 866469.4833 0.025138503 0.019580158 172.6563452 -2.237182543 0.09215469 SPS(ph)MPENLNRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSMPENLNRPR 12 1 P30307-4;P30307-3;P30307-2;P30307;D6RJC2;H0Y999 P30307-4 CDC25C M-phase inducer phosphatase 3 1 S(0.289)PS(0.711)MPENLNRPR;S(0.161)PS(0.839)MPENLNRPR 133.66 9.65E-05 756000000 339200 384990 340750 359530 391800 229631 472640 313703 400970 TRUE FALSE 317970.0775 413495.0602 348832.7509 368756.1485 361029.6084 295921.742 401772.0198 352869.5101 334045.5166 0.951876501 1.237840473 1.044267124 1.103909887 1.080779686 0.885872515 1.202746332 1.056351582 1 18.34968517 3.727617429 24.95717671 1.063159444 1.123015279 0.004207674 0.105278422 68.09088807 3424726.282 0.025446634 0.042519592 5340.936678 -3.727617429 0.059855835 SPS(ph)MPSLNQTWPELNQSSEDTAIVHPVPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPSMPSLNQTWPELNQSSEDTAIVHPVPIR 30 0 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2 E9PMG1 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.061)PS(0.912)MPS(0.027)LNQTWPELNQSSEDTAIVHPVPIR;S(0.051)PS(0.928)MPS(0.021)LNQTWPELNQSSEDTAIVHPVPIR;S(0.262)PS(0.288)MPS(0.182)LNQT(0.268)WPELNQSSEDTAIVHPVPIR 241.09 4.16E-36 274184000 108966 103024 112202 109044 114107 109726 141431 107618 101222 TRUE FALSE 102146.0126 110652.0042 114863.4844 111842.2537 105145.4965 141402.1149 120224.7345 121054.3442 84327.39428 1.211302845 1.312171508 1.362113527 1.326286133 1.246872353 1.676823008 1.42569014 1.435528101 1 16.36371376 5.025733955 0.643025999 1.397755587 1.04317522 0.025527676 0.171536832 10.97493394 2.640775236 0.067443406 3.102560183 106104.5371 -5.025733955 -0.354580367 SPS(ph)MSISEPISVTLPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSMSISEPISVTLPPR 17 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.061)PS(0.939)MSISEPISVTLPPR 199.65 1.37E-11 31658000 12974 20078 17703 17080 18110 22815 19574 14791 16102 TRUE FALSE 12161.9805 21564.59601 18122.92352 17518.30172 16687.71365 29401.32013 16639.06042 16637.68891 13414.47218 0.906631311 1.607562022 1.350997884 1.305925532 1.24400822 2.191761237 1.240381298 1.240279058 1 13.71150267 SPS(ph)PAHLPDDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SPSPAHLPDDPK 12 0 Q92615;H0Y4V9;A0A087X183;H0Y641 Q92615 LARP4B La-related protein 4B 1 S(0.012)PS(0.988)PAHLPDDPK;S(0.118)PS(0.882)PAHLPDDPK;S(0.003)PS(0.997)PAHLPDDPK;S(0.017)PS(0.983)PAHLPDDPK;S(0.136)PS(0.864)PAHLPDDPK 218.56 3.57E-11 4493700000 2687360 2007970 2358890 2357770 2381550 1980950 2861320 2012890 2546850 TRUE FALSE 2519162.935 2156642.188 2414843.985 2418274.37 2194512.67 2552818.107 2432291.629 2264203.747 2121764.282 1.187296325 1.016438163 1.13813019 1.139746951 1.034286744 1.203158206 1.146353367 1.067132559 1 21.01683296 0.977028904 5.220608963 1.000081654 1.117145034 0.318537352 0.058829626 0.20907165 22.20671027 0.054543861 0.013771592 9.484815853 -0.977028904 0.11706338 SPS(ph)PAVPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSPAVPLR 9 0 Q6P4R8-3;Q6P4R8;E9PQ59;Q6P4R8-2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 S(0.351)PS(0.649)PAVPLR 142.83 0.00010846 371800000 183790 191400 206120 178970 190920 159030 219850 185490 201930 TRUE FALSE 172286.912 205571.4552 211009.2637 183562.6732 175925.9133 204939.3794 186885.5335 208648.8348 168226.5785 1.0241361 1.221991537 1.25431585 1.091163328 1.045767648 1.218234248 1.110915619 1.240284601 1 17.36004613 3.222251502 24.89006681 1.125886568 1.191138364 0.03273547 0.093181062 521.4832358 795857.3269 0.025401891 0.030447826 1668.213001 -3.222251502 0.065251796 SPS(ph)PEPIYNSEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSPEPIYNSEGK 13 0 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 1 SPS(1)PEPIYNSEGK;S(0.017)PS(0.983)PEPIYNSEGK 204.23 5.08E-07 139490000 549940 446380 473980 505620 432490 320190 504770 349570 433610 TRUE FALSE 515520.2371 479430.4397 485223.0294 518595.0652 398523.98 412623.6551 429084.4246 393214.584 361237.6898 1.42709427 1.327188312 1.343223709 1.435606195 1.103218162 1.142249734 1.187817431 1.088520371 1 18.4625889 2.7317863 24.99984067 1.124907505 1.367254086 0.841002762 0.059712592 216.1967538 797847.7189 0.018129424 0.017455377 539.2452148 -2.7317863 0.242346581 SPS(ph)PGLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPSPGLFR 8 0 E7ESG2;Q9HAW4-2;Q9HAW4-3;Q9HAW4 E7ESG2 CLSPN Claspin 1 S(0.028)PS(0.972)PGLFR;S(0.01)PS(0.99)PGLFR;S(0.082)PS(0.918)PGLFR;S(0.205)PS(0.795)PGLFR 136.63 0.00082084 607227000 2544250 2663100 2862190 2586010 3280260 2583950 3190900 3031590 3605200 TRUE FALSE 2385009.934 2860278.695 2930082.498 2652371.395 3022641.612 3329894.418 2712454.168 3410090.685 3003468.83 0.794085129 0.952325081 0.975566142 0.883102687 1.006383546 1.108682862 0.903107148 1.135384077 1 21.51819826 6.415525959 0.468951219 1.013196743 9.20E-26 0.425205355 0.076666595 22.49956853 1.09206872 0.041768179 17.68347531 2603310.432 -6.415525959 -1.013196743 SPS(ph)PGPNHTSNSSNASNATVVPQNSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPSPGPNHTSNSSNASNATVVPQNSSAR 28 0 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 S(0.351)PS(0.649)PGPNHTSNSSNASNATVVPQNSSAR;S(0.201)PS(0.799)PGPNHTSNSSNASNATVVPQNSSAR;S(0.008)PS(0.992)PGPNHTSNSSNASNATVVPQNSSAR 250.78 1.34E-46 2097940000 113638 341324 324837 332754 362140 314904 360769 347517 287898 TRUE FALSE 106525.6004 366595.9841 332542.287 341293.031 333698.9852 405811.6728 306675.0377 390905.2624 239845.9639 0.444141726 1.528464262 1.386482731 1.422967581 1.391305402 1.691967904 1.278633306 1.629817972 1 17.87174864 4.741898234 24.92752142 1.433944195 0.444141341 0.717015175 0.191629573 141.9084194 1059815.605 0.038383932 0.278725894 55194.80888 -4.741898234 -0.989802854 SPS(ph)PISISSSETSSIMQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSPISISSSETSSIMQK 18 0 Q5VT06 Q5VT06 CEP350 Centrosome-associated protein 350 1 SPS(1)PISISSSETSSIMQK;S(0.004)PS(0.995)PISISSSETSSIMQK 294.05 3.08E-49 62484000 111798 92037 108507 105208 103229 83777 126524 93883 120751 TRUE FALSE 104800.7627 98851.51524 111080.8373 107907.8154 95121.81075 107962.0599 107552.9008 105604.4992 100596.878 1.041789415 0.982649931 1.104217541 1.072675589 0.945574183 1.073214816 1.069147501 1.049779091 1 16.61822601 SPS(ph)PLVSLQAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSPLVSLQAVK 12 0 Q9UPZ3-2;Q9UPZ3 Q9UPZ3-2 HPS5 Hermansky-Pudlak syndrome 5 protein 1 S(0.001)PS(0.999)PLVSLQAVK;S(0.001)PS(0.999)PLVSLQAVK 194.59 1.39E-06 196735000 700520 662980 571500 601650 807230 456290 750590 714300 894210 TRUE FALSE 656675.7037 712067.729 585056.2499 617089.3576 743833.412 588013.5158 638045.9976 803481.9274 744960.5742 0.881490547 0.955846193 0.785351964 0.828351699 0.998486951 0.789321658 0.856482906 1.078556309 1 19.50680455 1.244082386 24.99998198 1.039278182 0.868910477 0.508305367 0.068886031 94.89814667 429669.4471 0.04684461 0.016026883 17.54213245 -1.244082386 -0.170367705 SPS(ph)PPTQHTGQPPGQPSAPSQLSAPR ddPTM_SK-BR-3_Pertuzumab_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(0.013)PS(0.873)PPT(0.114)QHTGQPPGQPSAPSQLSAPR;S(0.001)PS(0.998)PPT(0.001)QHTGQPPGQPSAPSQLSAPR;S(0.002)PS(0.99)PPT(0.008)QHTGQPPGQPSAPSQLSAPR;S(0.003)PS(0.996)PPT(0.001)QHTGQPPGQPSAPSQLSAPR;S(0.001)PS(0.952)PPT(0.039)QHT(0.008)GQPPGQPSAPSQLSAPR;S(0.065)PS(0.82)PPT(0.115)QHTGQPPGQPSAPSQLSAPR 211.5 6.71E-26 20077200000 422356 457126 431160 433243 544800 393098 477412 441911 654394 TRUE FALSE 395921.4919 490972.0847 441387.3188 444360.7489 502013.6056 506579.0112 405828.5027 497084.5611 545171.4139 0.726233038 0.900582958 0.809630343 0.815084463 0.92083626 0.929210517 0.744405323 0.911794985 1 19.05635039 -5 0.256018437 1.977841426 0.830835361 0.34991705 0.070184703 226.6859482 2.236697912 116.3951535 0.091385605 1.00E-05 5 -1.147006066 SPS(ph)PQGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSPQGTK 8 0 Q9ULL5;Q9ULL5-2;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 S(0.129)PS(0.871)PQGTK;S(0.029)PS(0.97)PQGT(0.001)K 95.362 0.010179 594210000 1331680 1245010 1332690 1168690 1362630 1075370 1535160 1276400 1543070 TRUE FALSE 1248332.526 1337191.836 1364302.036 1198680.564 1255614.536 1385811.862 1304977.01 1435761.35 1285521.648 0.971070793 1.040193946 1.061282817 0.932446813 0.976735427 1.078015188 1.015134215 1.116870612 1 20.29392247 2.235243769 24.99997306 1.050493081 1.00827575 0.23089631 0.048213412 171.4843878 1292504.861 0.017847884 0.013709205 171.8872918 -2.235243769 -0.04221733 SPS(ph)PSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSPSFR 7 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 S(0.02)PS(0.976)PS(0.003)FR 87.639 0.020134 176320000 245620 349730 312680 300950 382890 265860 370640 338900 505640 TRUE FALSE 230247.0826 375624.3731 320096.9173 308672.8865 352819.3639 342609.4661 315065.9729 381212.411 421245.4174 0.546586558 0.891699607 0.759882254 0.732762598 0.837562498 0.813325088 0.747939229 0.904965123 1 18.68430147 -4.999999998 0.141781123 1.763552754 0.707913102 0.451700682 0.090332242 141.502445 1.223457682 30.32829349 0.501678816 1.00E-05 4.999999998 -1.055639652 SPS(ph)PTVHASSTPAVNIQPDVSGGWDWHAKPGGFGMGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSPTVHASSTPAVNIQPDVSGGWDWHAKPGGFGMGSK 38 1 O75061-4;O75061;O75061-2 O75061-4 DNAJC6 Putative tyrosine-protein phosphatase auxilin 1 S(0.034)PS(0.604)PT(0.36)VHAS(0.001)STPAVNIQPDVSGGWDWHAKPGGFGMGSK 166.64 3.73E-18 206000000 111160 265220 237250 255730 323110 216860 342670 306860 402940 TRUE FALSE 104202.694 284857.1648 242877.682 262292.4647 297734.244 279463.9616 291289.8147 345172.1465 335686.7109 0.3104165 0.848580404 0.723524865 0.781360883 0.886940812 0.832514224 0.867743063 1.02825681 1 18.3567559 4.738568294 12.19485779 0.848871388 0.310067621 0.780755691 0.09271305 0.027999212 422.0469327 0.021480755 0.123729699 54773.2226 -4.738568294 -0.538803768 SPS(ph)PVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSPVLR 7 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-2 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 S(0.302)PS(0.698)PVLR;S(0.23)PS(0.77)PVLR 100.98 0.0098527 759370000 515710 545110 523380 537680 581620 479670 647550 506610 627430 TRUE FALSE 483432.6317 585470.5116 535794.8208 551477.7791 535941.9113 618142.9422 550455.8891 569861.3737 522707.8796 0.924861955 1.120072098 1.025036816 1.05504011 1.025318217 1.182578198 1.053085118 1.090210031 1 18.99564538 SPS(ph)PVQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPSPVQGK 8 0 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 S(0.108)PS(0.892)PVQGK;S(0.379)PS(0.621)PVQGK;S(0.014)PS(0.986)PVQGK;S(0.032)PS(0.968)PVQGK 122.57 0.0014526 4693880000 9481680 8124620 8514280 8609120 8692850 6444180 10330390 7490880 9874140 TRUE FALSE 8888238.574 8726175.318 8716242.742 8830044.594 8010148.626 8304510.153 8781443.922 8426132.857 8226082.245 1.080494737 1.06079359 1.059586141 1.073420412 0.973750126 1.009534054 1.067512293 1.024319063 1 22.97177407 2.805390487 24.99990287 1.022689925 1.065779144 0.526766671 0.024569331 187.6139995 70182.28677 0.007805428 0.008278906 638.8376251 -2.805390487 0.043089219 SPS(ph)PYYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSPYYSR 8 0 P62995;P62995-3;H7BXF3;H7C2L4;Q13595;Q13595-3;Q13595-4 P62995;Q13595 TRA2B;TRA2A Transformer-2 protein homolog beta;Transformer-2 protein homolog alpha 1 S(0.263)PS(0.737)PYYSR 124.81 0.0013521 561210000 137980 120500 136430 119050 114820 128540 121550 133560 201780 TRUE FALSE 129344.0781 129421.9454 139666.184 122105.0246 105802.5004 165647.4113 103324.7059 150235.26 168101.6145 0.769439833 0.769903048 0.830843799 0.726376275 0.629396099 0.985400479 0.614656238 0.893716937 1 17.35897405 1.003230198 24.68170999 1.000000025 0.766015232 0.382972472 0.103012972 58.82948604 449506.6087 0.087140249 0.021785062 10.07465535 -1.003230198 -0.233984793 SPS(ph)QDFSFIEDTEILDSAMYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSQDFSFIEDTEILDSAMYR 21 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 S(0.401)PS(0.522)QDFS(0.077)FIEDTEILDSAMYR 255.7 1.29E-36 94650000 50414 47650 56833 57482 50538 43475 59285 47030 50899 TRUE FALSE 47258.67773 51178.05558 58181.1056 58957.08544 46568.94934 56025.52674 50395.76462 52901.79903 42403.62808 1.114496091 1.206926339 1.372078481 1.390378326 1.098230304 1.321243707 1.188477659 1.247577187 1 15.37190009 -0.124717221 0.649568527 0.984665343 1.259269087 0.369733757 0.09848679 6.067936216 2.579100643 0.332815753 0.036199929 0.750382641 0.124717221 0.274603744 SPS(ph)SLLIANLHLQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SPSSLLIANLHLQ 13 0 Q658Y4 Q658Y4 FAM91A1 Protein FAM91A1 1 S(0.013)PS(0.67)S(0.317)LLIANLHLQ;S(0.005)PS(0.969)S(0.026)LLIANLHLQ;S(0.105)PS(0.857)S(0.037)LLIANLHLQ;S(0.053)PS(0.932)S(0.015)LLIANLHLQ;S(0.007)PS(0.805)S(0.187)LLIANLHLQ;S(0.036)PS(0.963)S(0.001)LLIANLHLQ;S(0.002)PS(0.582)S(0.415)LLIANLHLQ 208.23 4.99E-08 342127000 662818 741538 719791 757768 893214 617605 925540 664500 1162181 TRUE FALSE 621333.4045 796442.2451 736864.7824 777213.6098 823064.5755 795897.5375 786763.8693 747464.2877 968205.4831 0.641737126 0.822596297 0.761062394 0.80273622 0.850092868 0.822033702 0.812600097 0.772009972 1 19.88495374 -5 0.146849151 1.709190432 0.725119083 0.641456149 0.052890081 87.67848403 0.772914191 18.29683319 0.263350282 1.00E-05 5 -0.984071349 SPS(ph)TLLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSTLLPK 8 0 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;B5MEG9;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 S(0.368)PS(0.632)T(0.001)LLPK 113.66 0.0029436 610200000 421490 336470 372750 377910 357170 318490 449270 318320 314040 TRUE FALSE 395109.6933 361382.5889 381591.806 387607.8104 329119.309 410432.8927 381906.1343 358062.9527 261624.6952 1.510215589 1.381301519 1.458546586 1.481541374 1.257982579 1.568784982 1.459748033 1.368612976 1 17.9971392 0.810305793 3.641491395 1.000038439 1.441660498 0.741790545 0.081998732 0.630922237 11.50037792 0.071702042 0.018441488 6.461090034 -0.810305793 0.44162206 SPS(ph)WQRPNQGVPSTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSWQRPNQGVPSTGR 16 1 Q96HC4;Q96HC4-4;Q96HC4-7;H0Y8Y3;A0A0A0MSP3;Q96HC4-6 Q96HC4;Q96HC4-6 PDLIM5 PDZ and LIM domain protein 5 1 S(0.104)PS(0.416)WQRPNQGVPS(0.352)T(0.128)GR 143.46 3.71E-06 235690000 112620 107700 121070 132360 112770 105040 113500 76013 66735 TRUE FALSE 105571.3152 115674.2201 123941.8376 135756.5817 103913.4991 135363.3428 96481.72868 85503.39038 55596.49738 1.898884286 2.080602655 2.22931018 2.441818965 1.869065571 2.434745878 1.735392214 1.537927647 1 15.76270637 1.150625594 1.479035253 1.020440774 2.158711128 0.775778328 0.205065939 0.154753254 0.659798616 0.172479337 0.051981426 14.14573747 -1.150625594 1.138270354 SPSDEYKDNLHQVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSDEYKDNLHQVSK 15 1 Q9UKD2 Q9UKD2 MRTO4 mRNA turnover protein 4 homolog 0 ; 143.38 2.66E-06 701520000 921640 712080 838330 824200 908510 555620 1008270 744800 1072510 FALSE TRUE 863956.1976 764803.1441 858215.5835 845350.3674 837159.2894 716018.4743 857089.2738 837789.9195 893501.1523 0.966933501 0.855962124 0.960508648 0.946109991 0.936942596 0.801362676 0.95924809 0.937648393 1 19.76911006 0.959542165 1.858333593 0.998141274 0.913275317 0.198615876 0.0520643 0.586474295 4.248967631 0.045984453 0.013008486 9.110499013 -0.959542165 -0.084865957 SPSELFAQHIVTIVHHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSELFAQHIVTIVHHVK 18 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ; 182.07 2.44E-14 364370000 492130 526890 562740 505040 573480 422201 612520 530900 690310 FALSE TRUE 461328.4618 565901.4838 576088.4585 518000.1814 528441.1941 544083.5748 520678.3124 597184.0337 575092.8014 0.802180901 0.984017679 1.001731298 0.900724509 0.918879862 0.946079613 0.905381377 1.038413335 1 19.13343525 1.234078383 24.99331039 1.019206697 0.93534464 0.325257508 0.055507071 157.5065425 878215.1494 0.046665571 0.013224715 17.14266678 -1.234078383 -0.083862058 SPSGSAFGS(ph)QENLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPSGSAFGSQENLR 14 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 SPSGS(0.001)AFGS(0.999)QENLR;SPSGS(0.002)AFGS(0.998)QENLR;SPSGS(0.001)AFGS(0.999)QENLR;SPSGSAFGS(1)QENLR 231.06 7.14E-13 2170230000 777660 835200 848370 904420 848610 724089 1039480 814120 989320 TRUE FALSE 728987.6488 897039.077 868493.737 927628.9484 781963.5937 933121.7397 883619.6241 915764.6741 824196.1007 0.884483254 1.088380637 1.053746476 1.125495434 0.948759152 1.132159857 1.072098768 1.111100469 1 19.65262811 4.74199892 24.84687748 1.070175425 0.884483177 0.504123 0.056616424 231.1285356 1670168.621 0.011747586 0.086456167 55207.60659 -4.74199892 -0.185692247 SPSHSSSNRPFT(ph)PPTSTGGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPSHSSSNRPFTPPTSTGGSK 21 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 SPSHSSSNRPFT(1)PPTSTGGSK;SPSHSSSNRPFT(1)PPTSTGGSK 224.93 4.39E-25 381820000 268540 726940 707870 704530 759570 741060 967930 802180 796510 TRUE FALSE 251732.5608 780763.394 724661.0107 722609.4326 699916.4362 954991.9919 822797.8823 902333.9388 663567.3353 0.379362496 1.176615171 1.092068539 1.088976799 1.054778315 1.439178725 1.2399614 1.35982272 1 19.33988334 4.738810274 6.803986043 1.188628963 0.365831396 0.773389302 0.136410663 0.052680022 17.02464809 0.032308157 0.19925557 54803.74971 -4.738810274 -0.822797567 SPSPFHAVAECR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSPFHAVAECR 12 0 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;C9JBE1;E7EPX3;B9ZVU2;F8WAN0;E5RJ35 E5RIA4 DNPEP Aspartyl aminopeptidase 0 90.731 0.004926 0 137280 202450 167770 181390 215750 148030 186850 170960 196730 FALSE TRUE 128687.8899 217439.6086 171749.5836 186044.7745 198805.8653 190763.8579 158833.5771 192304.7323 163894.4921 0.785187398 1.326704796 1.047927734 1.135149645 1.213011266 1.163943068 0.969120897 1.173344692 1 17.32240785 1.759555777 25 1.046307034 1.134147423 0.026450603 0.148186887 27.2682986 32497.46256 0.061896015 0.034324505 57.48516436 -1.759555777 0.087840389 SPSPGGPQLS(ph)PQLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPSPGGPQLSPQLPR 15 0 H7C1V4;Q9HCH0-2;Q9HCH0 H7C1V4 NCKAP5L Nck-associated protein 5-like 1 SPSPGGPQLS(1)PQLPR;SPSPGGPQLS(1)PQLPR;SPSPGGPQLS(1)PQLPR;SPSPGGPQLS(1)PQLPR 211.45 1.44E-09 1166180000 651390 756630 808510 731630 858170 683980 758440 772860 1009020 TRUE FALSE 610620.6627 812651.6725 827688.239 750404.8644 790772.7899 881433.9225 644718.963 869353.2723 840608.0435 0.726403545 0.96674268 0.984630406 0.892692938 0.940715231 1.048567081 0.766967397 1.034195757 1 19.68107374 4.742163418 24.61262509 0.944546718 0.726403442 0.437976084 0.080463607 278.3682216 1901577.217 0.018178625 0.134078824 55228.52156 -4.742163418 -0.218143276 SPSSESS(ph)PQHPTPPARPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSSESSPQHPTPPARPR 18 1 O14733;O14733-4;O14733-2;O14733-3 O14733 MAP2K7 Dual specificity mitogen-activated protein kinase kinase 7 1 S(0.01)PS(0.002)S(0.01)ES(0.054)S(0.925)PQHPTPPARPR 100.9 0.00046168 210990000 91035 83209 81932 94116 109810 60381 101410 85841 117910 TRUE FALSE 85337.28185 89369.88094 83875.46573 96531.1759 101185.9656 77812.0145 86204.51194 96558.43781 98230.05927 0.868749164 0.909801761 0.853867608 0.982705056 1.030091667 0.792140563 0.877577725 0.982982587 1 16.58387695 -4.999999984 0.24765903 1.574194716 0.895819359 0.144734944 0.070048929 363.1403176 3.607355125 105.2835361 0.102709591 1.00E-05 4.999999984 -0.678375357 SPSVPKS(ph)PTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPSVPKSPTPK 11 1 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 1 SPS(0.003)VPKS(0.944)PT(0.053)PK;SPSVPKS(0.936)PT(0.064)PK;SPSVPKS(0.997)PT(0.003)PK;SPSVPKS(0.936)PT(0.064)PK 155.39 1.91E-05 2077780000 6740560 3497640 4831920 5021590 4710600 3260730 6081980 3634830 4342410 TRUE FALSE 6318680.382 3756608.905 4946535.424 5150452.501 4340648.478 4202049.817 5170043.561 4088646.527 3617633.718 1.746633539 1.038416047 1.367340038 1.423707568 1.199858475 1.161546509 1.429123003 1.130199143 1 21.78661491 -4.722141391 0.160859796 4.91E-13 1.378929967 0.26300301 0.191506583 195.3686554 1.955155424 62.85410369 0.756205256 1.90E-05 4.722141391 1.378929967 SPSVPKS(ph)PTPKS(ph)PPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSVPKSPTPKSPPSR 16 2 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 2 S(0.068)PS(0.351)VPKS(0.577)PT(0.117)PKS(0.871)PPS(0.015)R 68.42 0.026306 148990000 371900 243020 252930 337330 377580 152550 330110 191620 496720 TRUE FALSE 348623.4429 261013.4537 258929.619 345986.4589 347926.3899 196588.7086 280613.0701 215544.1788 413814.2231 0.842463655 0.63075032 0.625714643 0.836091269 0.840779196 0.475065132 0.678113642 0.520871847 1 18.65862371 -0.974209119 4.550847502 1.000007024 0.672324897 0.374301318 0.129068192 0.090565105 73943828.32 1228.540696 0.028534063 0.106118446 0.974209119 -0.327682127 SPSWQRPNQGVPSTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPSWQRPNQGVPSTGR 16 1 Q96HC4;Q96HC4-4;Q96HC4-7;H0Y8Y3;A0A0A0MSP3;Q96HC4-6 Q96HC4;Q96HC4-6 PDLIM5 PDZ and LIM domain protein 5 0 71.601 0.03665 162320000 48492 57687 52924 50299 62365 48305 61752 50194 82212 FALSE TRUE 45456.97228 61958.2055 54179.38227 51589.7575 57467.10447 62249.86933 52492.86088 56460.83139 68490.28609 0.663699553 0.904627635 0.791052065 0.753241962 0.839054817 0.908886105 0.766427823 0.824362616 1 16.06361177 -5 0.344064108 3.059038553 0.807815465 0.422874923 0.071567343 408.9449405 3.407989093 619.6705106 0.052025727 1.00E-05 5 -2.251223088 SPT(ph)GPSNSFLANMGGTVAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPTGPSNSFLANMGGTVAHK 20 0 H0Y6J6;Q5W012;Q96I25 H0Y6J6 RBM17 Splicing factor 45 1 S(0.459)PT(0.541)GPSNSFLANMGGTVAHK 223.9 1.75E-24 832590000 602660 473740 529920 514860 521620 453130 692480 507020 457530 TRUE FALSE 564940.5864 508816.2025 542489.9526 528072.1793 480654.0693 583941.275 588649.0527 570322.5631 381165.2872 1.482140702 1.334896486 1.423240706 1.385415191 1.261012179 1.53198965 1.544340664 1.4962605 1 18.54005721 2.218940293 24.99794798 1.453187014 1.378179148 0 0.16674834 825.412467 1051638.177 0.055265883 0.040872192 165.5542342 -2.218940293 -0.075007866 SPT(ph)PPPSSKPSSIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPTPPPSSKPSSIPR 15 1 B4E2D5;R4GND2;F6S7C4;Q8NEM7-2;Q8NEM7;Q8NEM7-3;H7C5F9 B4E2D5 SUPT20H Transcription factor SPT20 homolog 1 S(0.002)PT(0.998)PPPSSKPSSIPR;S(0.063)PT(0.937)PPPSSKPSSIPR 98.796 0.0045103 651340000 1090100 1006680 1040850 1042480 1169610 869050 1248470 907930 1157220 TRUE FALSE 1021872.587 1081215.635 1065539.454 1069231.802 1077753.549 1119930.627 1061273.514 1021287.059 964072.5061 1.059954081 1.121508629 1.105248253 1.109078202 1.117917524 1.161666389 1.100823338 1.059346732 1 19.87878213 1.018155903 2.490060785 1.000895221 1.113964478 0.687903122 0.024628635 0.142579671 1.952777479 0.021936819 0.005949053 10.42691667 -1.018155903 0.113069257 SPTDWALFTYEGNSNDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPTDWALFTYEGNSNDIR 18 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;F8WBG8;F8WC20;F8WBB2;F8WFE1;Q9UJU6 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 151.74 1.06E-07 54937000 11965 13603 10551 11703 13352 8440 13865 9658.7 12981 FALSE TRUE 11216.13201 14610.18027 10801.2747 12003.31879 12303.38778 10876.49099 11786.07197 10864.60996 10814.38724 1.037149101 1.35099474 0.998787491 1.109939798 1.137687 1.005742697 1.089851113 1.004644065 1 13.4006643 3.868858877 5.989964009 1.05899876 1.210140796 0.30133386 0.089748519 0.20839687 9.946587577 0.020441499 0.037417699 7393.64981 -3.868858877 0.151142035 SPTEYHEPVYANPFYRPT(ph)TPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPTEYHEPVYANPFYRPTTPQR 22 1 Q9NP74-3;Q9NP74-2;Q9NP74;S4R313 Q9NP74-3 PALMD Palmdelphin 1 SPTEYHEPVYANPFY(0.001)RPT(0.5)T(0.5)PQR;SPTEYHEPVYANPFYRPT(0.5)T(0.5)PQR 114.62 0.0003255 750220000 178078 213061 208927 197550 255580 184351 250780 216390 221294 TRUE FALSE 166932.4159 228836.2581 213882.8471 202619.4675 235507.7778 237570.141 213177.8671 243406.7678 184358.6018 0.905476686 1.241256203 1.160145743 1.099050793 1.277443935 1.288630629 1.156321783 1.320289726 1 17.49215521 4.743521122 24.83886412 1.199782684 0.905476554 0.466064383 0.096429136 393.827858 1971953.666 0.020269968 0.169565537 55401.44883 -4.743521122 -0.29430613 SPTEYHEPVYANPFYRPTT(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPTEYHEPVYANPFYRPTTPQR 22 1 Q9NP74-3;Q9NP74-2;Q9NP74;S4R313 Q9NP74-3 PALMD Palmdelphin 1 SPTEYHEPVYANPFY(0.074)RPT(0.151)T(0.775)PQR 116.35 0.00024355 145750000 94752 92550 83346 88028 113060 78192 109940 92679 103140 TRUE FALSE 88821.64146 99402.4983 85323.00648 90286.94751 104180.7237 100764.7611 93455.51763 104250.1772 85925.26769 1.033708056 1.156848282 0.992990872 1.050761318 1.212457365 1.172702323 1.087637201 1.213265666 1 16.39079482 2.773309828 24.79010545 1.140907476 1.064024601 0.217319536 0.073647573 837.1268206 597204.701 0.020938109 0.022207265 593.3484722 -2.773309828 -0.076882875 SPTLSQVHSPLVTS(ph)PSANLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPTLSQVHSPLVTSPSANLK 20 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 SPTLSQVHSPLVT(0.161)S(0.754)PS(0.085)ANLK 101.92 0.00019813 239800000 170760 177230 199550 174050 176940 134050 194550 132860 170340 TRUE FALSE 160072.4364 190352.2936 204283.4202 178516.4177 163043.8461 172748.0589 165379.0336 149447.8635 141909.1536 1.127992327 1.341367268 1.439536599 1.25796267 1.148931144 1.217314419 1.165386654 1.053123493 1 17.11460812 1.726373053 0.685809644 1.004099439 1.323565299 0.542548522 0.087701631 0.480345051 0.459196397 0.08439848 0.042345269 53.25655297 -1.726373053 0.31946586 SPTLYGISHDDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPTLYGISHDDLK 13 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 225.23 1.28E-11 410450000 484860 410680 429960 469920 475370 334760 567770 436710 422480 FALSE TRUE 454513.4781 441087.1745 440158.8542 481978.9428 438036.3578 431399.7776 482638.1594 491234.2048 351965.3587 1.291358558 1.253211896 1.250574363 1.369393126 1.24454395 1.225688174 1.371266085 1.395689072 1 18.42507392 -0.879778873 4.992958752 0.999999249 1.294365805 0.709891814 0.060211081 5.09E-07 1.14E-07 0.058901416 0.013883162 0.131892812 0.879778873 0.294366557 SPTPKS(ph)PPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPTPKSPPSR 10 1 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 1 SPT(0.01)PKS(0.983)PPS(0.007)R;S(0.035)PT(0.004)PKS(0.961)PPSR 87.083 0.0079445 726570000 294170 472790 406520 472330 623390 300880 407700 406770 957470 TRUE FALSE 275758.4248 507795.8635 416162.8464 484450.7875 574431.464 387739.1716 346569.1699 457556.1299 797662.0715 0.345708333 0.636605251 0.521728262 0.607338376 0.720143886 0.486094532 0.434481195 0.57362152 1 19.60541815 0.949974977 22.74580698 1.000000001 0.542580844 0.656419488 0.104686099 3232.24532 1469667.225 0.097668777 0.024417194 8.911995879 -0.949974977 -0.457419156 SPVGKS(ph)PPSTGSTYGSSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPVGKSPPSTGSTYGSSQK 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 SPVGKS(0.997)PPS(0.003)TGSTYGSSQK;S(0.003)PVGKS(0.985)PPS(0.007)T(0.003)GS(0.001)T(0.001)YGSSQK 204.53 2.75E-16 432580000 571060 359965 449180 434840 475430 326261 573890 437280 554820 TRUE FALSE 535318.374 386617.1831 459834.7617 445998.7306 438091.6456 420447.2543 487840.5222 491875.3706 462216.9577 1.158153904 0.836440933 0.994846152 0.96491209 0.947805221 0.909631824 1.055436228 1.064165566 1 18.81821066 1.67857881 7.759739851 1.04444552 0.955620738 0.127326107 0.082726697 0.188359521 20.79509301 0.037133099 0.019378922 47.70663778 -1.67857881 -0.088824782 SPVPSPGSS(ph)SPQLQVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPVPSPGSSSPQLQVK 16 0 Q8N3F8 Q8N3F8 MICALL1 MICAL-like protein 1 1 SPVPSPGS(0.001)S(0.582)S(0.417)PQLQVK;SPVPSPGS(0.398)S(0.43)S(0.171)PQLQVK 228.49 4.26E-15 718460000 837690 745340 809330 820630 887650 661060 891390 790700 996420 TRUE FALSE 785260.4782 800525.7491 828527.6898 841688.7551 817937.5496 851897.2906 757734.3448 889420.6355 830111.0649 0.945970378 0.96435981 0.998092574 1.013947158 0.985335076 1.026244953 0.912810799 1.071447753 1 19.66294485 4.318231106 1.847723413 0.993869404 0.945996425 0.177086077 0.039720227 0.827893569 4.856474056 0.009980532 0.051344955 20808.03676 -4.318231106 -0.047872979 SPVPSPGSSS(ph)PQLQVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPVPSPGSSSPQLQVK 16 0 Q8N3F8 Q8N3F8 MICALL1 MICAL-like protein 1 1 SPVPSPGS(0.017)S(0.263)S(0.721)PQLQVK 319.86 5.22E-58 429850000 1081400 830980 957840 970640 1043700 838700 1113900 893450 1146500 TRUE FALSE 1013717.104 892506.6238 980560.4171 995548.2657 961732.0121 1080819.075 946881.0359 1004999.199 955141.7433 1.061326354 0.934423221 1.026612462 1.042304216 1.006899781 1.131579771 0.991351328 1.052199013 1 19.86535532 3.622559062 4.265416481 1.038558925 0.98645612 0.086329917 0.049316593 0.34674697 10.91572721 0.012049085 0.019316891 4193.330202 -3.622559062 -0.052102804 SPVSFS(ph)PTDHSLSTSSGSSIFTPEYDDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPVSFSPTDHSLSTSSGSSIFTPEYDDSR 29 0 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 1 SPVS(0.023)FS(0.428)PT(0.428)DHS(0.119)LSTSSGSSIFTPEYDDSR 139.94 5.68E-08 135170000 41176 61743 61148 63228 70946 58955 68850 62197 61740 TRUE FALSE 38598.86766 66314.51596 62598.45944 64850.53752 65374.18734 75974.35145 58526.58167 69962.43236 51435.19514 0.750436886 1.289282869 1.217035519 1.260820287 1.271001056 1.477088815 1.137870314 1.360205442 1 15.65046826 4.740520553 24.90611007 1.260638699 0.750436703 0.609606181 0.125873809 99.52685382 1264651.618 0.025864088 0.169126382 55019.99577 -4.740520553 -0.510201996 SPWSNKYDPPLEDGAMPSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SPWSNKYDPPLEDGAMPSAR 20 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;; 102.48 0.000273 1392770000 2157250 2222220 2212160 2144330 2529090 1729420 2549340 2090090 2859720 FALSE TRUE 2022231.573 2386755.481 2264633.48 2199357.138 2330465.473 2228675.479 2167090.134 2351042.337 2382414.258 0.848816098 1.001822195 0.950562427 0.923163187 0.978194899 0.935469334 0.909619361 0.986831879 1 21.18399286 1.075886875 7.146574697 0.9998261 0.942876003 0.245024084 0.041073297 0.298939181 21.65810247 0.037036778 0.009287821 11.90931755 -1.075886875 -0.056950097 SPYAIDNNELLDFLS(ph)RVPSDVQVVQYQELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SPYAIDNNELLDFLSRVPSDVQVVQYQELK 30 1 Q6DN14-5;Q6DN14-3;Q6DN14-2;Q6DN14 Q6DN14-5 MCTP1 Multiple C2 and transmembrane domain-containing protein 1 1 S(0.011)PY(0.01)AIDNNELLDFLS(0.332)RVPS(0.332)DVQVVQY(0.314)QELK 44.05 0.076606 65314000 7601.2 28609 24178 20571 29770 31050 21340 24290 19846 TRUE FALSE 7125.454461 30727.24013 24751.51358 21098.88669 27431.98429 40013.63095 18140.26511 27322.65997 16533.57439 0.430968785 1.85847533 1.497045527 1.276123734 1.659168407 2.420144005 1.097177457 1.652556146 1 14.01311103 -1.039485437 4.028211084 0.999934271 1.529166455 0.07564294 0.515549959 12661863.48 6534826.462 7365.895631 0.108355514 0.091309205 1.039485437 0.529232184 SPYGSRS(ph)PFEHSVEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPYGSRSPFEHSVEHK 16 1 O14646 O14646 CHD1 Chromodomain-helicase-DNA-binding protein 1 1 SPYGS(0.162)RS(0.837)PFEHSVEHK;S(0.018)PYGS(0.154)RS(0.828)PFEHSVEHK;S(0.003)PYGS(0.026)RS(0.97)PFEHSVEHK 194.18 1.54E-10 640630000 439860 556890 501680 591020 727710 366090 650450 587310 976920 TRUE FALSE 412329.9478 598122.715 513580.0865 606186.5738 670558.592 471774.24 552921.061 660636.9463 813865.7409 0.50663141 0.734915705 0.631037849 0.7448238 0.823917949 0.579670843 0.679376257 0.811727184 1 19.63443129 -5 0.196068407 2.407748158 0.632740627 0.579167739 0.089971897 103.4552546 1.020091924 56.8291523 0.21603393 1.00E-05 5 -1.775007531 SPYLYPLYGLGELPQGFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SPYLYPLYGLGELPQGFAR 19 0 P50395;P50395-2;Q5SX87;Q5SX91;P31150 P50395;P31150 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 ; 234.69 8.93E-24 209279000 254231 315360 254957 267642 327190 197324 281010 284710 270266 FALSE TRUE 238319.1355 338709.5825 261004.7004 274510.1468 301493.8172 254288.2355 238875.1593 320256.6702 225156.8586 1.058458254 1.504327182 1.159212746 1.219195136 1.339039011 1.129382587 1.060927749 1.422371373 1 17.7805709 -5 0.119111404 0.218733773 1.359177755 0.139020082 0.153664963 242.2196912 1.876183658 45.62774091 1.413597127 1.00E-05 5 1.140443981 SPYQEFTDHLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SPYQEFTDHLVK 12 0 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 0 ;;;;; 211.52 3.09E-08 6674280000 5782270 5597280 5628730 5627370 6163030 4348320 6352100 5321110 6631950 FALSE TRUE 5420368.042 6011708.435 5762246.134 5771777.841 5679010.484 5603609.395 5399661.575 5985462.297 5525034.701 0.981055927 1.088085191 1.042933926 1.044659111 1.027868745 1.014221575 0.977308174 1.083334788 1 22.39755209 2.577136176 2.380698021 1.012767043 1.048430041 0.02823546 0.037341017 0.539707602 6.050589224 0.013022419 0.011685522 377.6905996 -2.577136176 0.035662998 SQAFLEMASEEAAVTMVNYYTPITPHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQAFLEMASEEAAVTMVNYYTPITPHLR 28 0 O95758-1;O95758-6;O95758;O95758-5;O95758-4;O95758-2;X6R242 O95758-1 PTBP3 Polypyrimidine tract-binding protein 3 0 97.691 0.0018335 10660000 6396.7 8449.9 9070.3 8951.1 10053 6020.4 8074.1 6488.7 11728 FALSE TRUE 5996.341965 9075.539388 9285.451799 9180.80038 9263.477932 7758.391747 6863.463661 7298.828478 9770.521034 0.613717727 0.928869541 0.950353801 0.939642865 0.948104804 0.794061209 0.702466495 0.747025512 1 13.25421978 2.132545683 6.608422176 0.775199986 0.896040551 0.01795744 0.126953132 0.370807539 20.55125873 0.04472021 0.032937325 135.6893254 -2.132545683 0.120840565 SQALGNQNSENEILLEGDDDTLSS(ph)VDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQALGNQNSENEILLEGDDDTLSSVDEK 28 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 SQALGNQNSENEILLEGDDDT(0.115)LS(0.401)S(0.484)VDEK 53.895 0.048306 76279000 34922 44579 42560 40254 47243 35766 42530 36603 43884 TRUE FALSE 32736.29436 47879.67554 43569.5433 41286.98579 43532.72535 46091.06359 36153.02133 41172.96512 36559.4769 0.895425677 1.309637872 1.191744166 1.12931008 1.190737096 1.260714526 0.988882347 1.126191308 1 15.15795781 1.725320841 11.52025229 1.044568567 1.182931805 0.192391338 0.115260025 0.132532719 65.03679752 0.049894673 0.027242305 53.12767873 -1.725320841 0.138363239 SQANGAGALSYVS(ph)PNTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SQANGAGALSYVSPNTSK 18 0 A0A494C0Q6;A0A494C0K5;A0A494C0W0;O95453-2;O95453-3;O95453;F5H1Z4;A0A494C002;A0A494C156;A0A494C1G3;A0A494BZU6;A0A494BZW7;A0A494C0P9;A0A494C1K5;A0A494C1N1;A0A494C0Q2 A0A494C0Q6;A0A494C0Q2 PARN Poly(A)-specific ribonuclease PARN 1 SQANGAGALSYVS(1)PNTSK;SQANGAGALSYVS(1)PNTSK;SQANGAGALSYVS(1)PNTSK;SQANGAGALSYVS(1)PNTSK 431.71 4.94E-169 1041260000 1944790 1419200 1770920 1668000 1652330 1318580 2139930 1442120 1684390 TRUE FALSE 1823069.065 1524279.045 1812927.059 1710803.704 1522562.667 1699232.641 1819067.363 1622171.856 1403254.427 1.299172146 1.086245669 1.291944656 1.219168577 1.085022529 1.2109227 1.296320416 1.15600694 1 20.42034518 0.980246849 23.58872433 0.999999995 1.20936307 0.431232668 0.076857743 661.0486626 789410.0578 0.071035403 0.017758851 9.555355496 -0.980246849 0.209363075 SQAPGQPGASQWGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQAPGQPGASQWGSR 15 0 K7EQ55;K7EK33;Q96EP5;Q96EP5-2;K7EQ02 K7EQ55 DAZAP1 DAZ-associated protein 1 0 185.95 9.35E-07 68095000 34040 34921 35287 32217 35663 26299 39909 31086 42012 FALSE TRUE 31909.49716 37506.58718 36124.0243 33043.74276 32862.17184 33891.09437 33925.01595 34967.15553 34999.92579 0.911701852 1.071619049 1.032117168 0.944108938 0.938921186 0.968319035 0.969288225 0.999063705 1 15.09506424 3.247395743 24.99925213 0.966987434 1.023243273 0.07306568 0.045089266 251.9078515 712776.4306 0.011898274 0.015873851 1767.647823 -3.247395743 0.056255839 SQAPLESSLDSLGDVFLDS(ph)GRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SQAPLESSLDSLGDVFLDSGRK 22 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 SQAPLESSLDSLGDVFLDS(1)GRK;SQAPLESSLDSLGDVFLDS(1)GRK;SQAPLESSLDSLGDVFLDS(1)GRK 170.77 4.15E-12 123013000 113019 74942 98805 98061 98206 67698 117313 84712 150472 TRUE FALSE 105945.3425 80490.78366 101148.7013 100577.4113 90493.2969 87241.31361 99723.00473 95288.47967 125357.2511 0.845147302 0.642091167 0.80688353 0.802326235 0.721883227 0.695941502 0.795510462 0.760135364 1 16.93568592 0.006134866 0.954078015 1.003003441 0.74917804 0.613659755 0.059936289 4.407626614 3.623381921 0.097556757 0.017420672 1.014226296 -0.006134866 -0.253825401 SQATS(ph)PGQTNGDSSLEVLATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SQATSPGQTNGDSSLEVLATR 21 0 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;Q96JY6-4;C9JS55;C9JSR2;C9K0F0;C9J0X3;Q96JY6-2;C9J760 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 SQATS(1)PGQTNGDSSLEVLATR;SQATS(1)PGQTNGDSSLEVLATR;SQATS(1)PGQTNGDSSLEVLATR;SQAT(0.001)S(0.999)PGQTNGDSSLEVLATR;S(0.009)QAT(0.132)S(0.855)PGQT(0.005)NGDSSLEVLATR 376.92 1.08E-112 1794756000 1668240 1846240 1888880 1909210 1963560 1477461 2039950 1511373 1182943 TRUE FALSE 1563827.836 1982937.531 1933685.126 1958203.561 1809349.918 1903980.006 1734078.435 1700071.246 985502.1712 1.586833476 2.012108739 1.962131776 1.987010905 1.83596746 1.931989661 1.75958865 1.725081178 1 19.91049952 0.376057744 0.789745253 0.988636775 1.917203454 0.828371383 0.123509755 0.77089612 0.673740407 0.127341668 0.038494901 2.377156336 -0.376057744 0.92856668 SQDADS(ph)PGSSGAPENLTFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SQDADSPGSSGAPENLTFK 19 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;H0Y8L4;H0Y8U8 P55196-5 MLLT4 Afadin 1 SQDADS(1)PGSSGAPENLTFK;SQDADS(1)PGSSGAPENLTFK;SQDADS(1)PGSSGAPENLTFK 270.5 2.78E-39 479630000 1686220 1440600 1497890 1435230 1627490 1154980 1743350 1332290 1455680 TRUE FALSE 1580682.5 1547263.523 1533420.658 1472060.432 1499673.5 1488403.976 1481950.852 1498629.339 1212717.604 1.303421749 1.275864651 1.264449904 1.213852612 1.236622191 1.227329406 1.222008196 1.235761182 1 20.20981221 -4.806789892 0.193531649 6.56E-12 1.292842333 0.940965706 0.020015497 27.60765056 0.290541329 10.66506507 0.051451943 1.56E-05 4.806789892 1.292842333 SQDATFS(ph)PGSEQAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SQDATFSPGSEQAEK 15 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SQDATFS(1)PGSEQAEK;SQDATFS(0.998)PGS(0.002)EQAEK;SQDATFS(1)PGSEQAEK 376.94 7.15E-98 736630000 1735300 1138660 1312760 1239790 1377690 1115700 1775560 1266290 1593790 TRUE FALSE 1626690.671 1222967.571 1343899.287 1271605.11 1269491.785 1437784.478 1509331.261 1424389.094 1327776.153 1.22512418 0.92106457 1.012142961 0.957695397 0.95610377 1.08285156 1.136736233 1.072762974 1 20.34058052 2.164833666 7.981143045 1.090687125 0.998903062 0.06798909 0.089221456 0.394040382 37.34034128 0.030807904 0.022755796 146.161727 -2.164833666 -0.091784063 SQDATFS(ph)PGSEQAEKS(ph)PGPIVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SQDATFSPGSEQAEKSPGPIVSR 23 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 2 SQDAT(0.04)FS(0.958)PGS(0.001)EQAEKS(1)PGPIVSR;SQDAT(0.004)FS(0.996)PGSEQAEKS(1)PGPIVSR;SQDAT(0.017)FS(0.982)PGS(0.001)EQAEKS(1)PGPIVSR 193.89 2.71E-18 1172110000 3605420 2580310 3169070 3139560 3277950 1908920 3224200 2227400 3870310 TRUE FALSE 3379763.198 2771358.837 3244241.837 3220126.425 3020513.03 2459994.215 2740761.142 2505495.793 3224330.258 1.048206272 0.859514571 1.006175416 0.998696215 0.936787732 0.762947347 0.850024942 0.777059294 1 21.62056809 2.388398764 6.874100292 0.834556617 0.963484106 0.366613166 0.079677298 0.214303102 13.94218929 0.0251687 0.020998127 244.567511 -2.388398764 0.128927488 SQDATFSPGSEQAEKS(ph)PGPIVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SQDATFSPGSEQAEKSPGPIVSR 23 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SQDATFSPGSEQAEKS(1)PGPIVSR;SQDATFSPGSEQAEKS(0.998)PGPIVS(0.002)R;SQDATFSPGSEQAEKS(1)PGPIVSR;SQDATFSPGSEQAEKS(1)PGPIVSR 272.99 7.12E-52 3941170000 3434021 2721323 3025995 3422959 3327474 1753045 2789383 2005906 3336191 TRUE FALSE 3219091.756 2922812.586 3097773.03 3510797.923 3066147.614 2259120.633 2371140.915 2256347.78 2779359.169 1.15821366 1.051613846 1.114563769 1.263168129 1.103185097 0.812820688 0.853125044 0.811823029 1 21.40632085 2.274640216 7.05673801 0.8551443 1.129881302 0.7607575 0.074641767 0.087359885 12.70337287 0.025364519 0.020862597 188.2089257 -2.274640216 0.274737002 SQDIYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SQDIYLR 7 0 J3QQ67;Q07020;F8VYV2;G3V203;A0A075B7A0;F8VXR6 J3QQ67 RPL18 60S ribosomal protein L18 0 ;;;;;;; 198.64 0.00091886 6649320000 3759260 4862670 4152940 4380320 4792100 3474610 4503830 4159240 4112800 FALSE TRUE 3523974.627 5222707.146 4251449.698 4492726.427 4415747.796 4477673.501 3828522.503 4678530.27 3426347.11 1.028493178 1.524278475 1.24081115 1.311229214 1.288762538 1.306835927 1.117377306 1.365457182 1 21.70823988 -0.970344659 0.293508166 0.841880673 1.32493969 0.246531351 0.137485904 16.7558562 1.250589891 2.378911028 0.148424708 0.107066928 0.970344659 0.483059017 SQDLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQDLAK 6 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 106.76 0.074087 804870000 1082000 856310 823460 801310 966770 657070 1019200 917720 1365600 FALSE TRUE 1014279.551 919712.0834 842992.8601 821872.9712 890843.784 846755.4424 866380.4218 1032299.362 1137672.538 0.891539101 0.808415473 0.740980231 0.722416112 0.783040598 0.744287494 0.761537607 0.90737829 1 20.11765393 1.062701503 3.432049575 0.998284499 0.773975585 0.717722385 0.047363306 0.107446792 2.580939715 0.04468742 0.011656601 11.55317902 -1.062701503 -0.224308914 SQDLHCGACR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQDLHCGACR 10 0 Q9Y2B0;F8VXJ7;F8W031;F8W1U5;F8VP03;Q9Y2B0-2 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 63.212 0.080057 211950000 238960 674630 292260 373970 705910 224190 293140 572720 553870 FALSE TRUE 224003.9202 724580.3072 299192.5452 383566.7033 650470.6761 288910.0136 249186.3784 644225.3527 461425.5189 0.485460624 1.570308268 0.648409186 0.831264609 1.409698098 0.626124915 0.540035972 1.396163251 1 18.81573827 SQDQDS(ph)EVNELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQDQDSEVNELSR 13 0 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 SQDQDS(1)EVNELSR 179.9 1.40E-05 161390000 294700 264110 279380 276590 281590 243720 324820 256810 260940 TRUE FALSE 276255.2531 283664.9792 286007.0255 283687.7677 259475.0573 314078.0075 276116.2565 288873.2938 217387.4283 1.270796822 1.30488217 1.315655776 1.304986999 1.193606545 1.444784595 1.270157427 1.328840845 1 17.72990898 -1.178418594 3.332288744 0.999443468 1.305664206 0.701328204 0.06238405 13676552.03 22245535.77 82194.12325 0.013164381 0.066310363 1.178418594 0.306220738 SQDVAVS(ph)PQQQQCSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 376.94 7.15E-98 5206750000 4722640 4186240 4331430 4566180 5327830 3953420 5877320 4292850 6188970 TRUE FALSE 4427058.393 4496193.565 4434173.565 4683355.909 4909403.723 5094708.176 4996070.428 4828821.772 5155990.925 0.858624163 0.87203287 0.860004145 0.908332846 0.952174625 0.988114264 0.968983557 0.936545825 1 22.29781829 2.877718504 2.069740977 0.971252621 0.86442701 0.890774817 0.017096618 0.089399018 0.757768435 0.005516163 0.005997225 754.6029599 -2.877718504 -0.106825611 SQEADVQDWEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SQEADVQDWEFR 12 0 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ;; 304.56 1.78E-36 1141200000 1844780 1905030 2050520 1944490 2022220 1771260 2017220 1692160 1649210 FALSE TRUE 1729318.513 2046080.403 2099159.303 1994388.905 1863402.998 2282594.008 1714756.588 1903429.901 1373946.197 1.258650824 1.489199801 1.527832245 1.451577151 1.356241608 1.661341626 1.248052211 1.385374409 1 20.38989408 0.647537472 0.913368967 1.000997246 1.459954436 0.551070266 0.121303229 0.78913113 1.127057042 0.106159313 0.035078707 4.441579829 -0.647537472 0.45895719 SQEDEISS(ph)PVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQEDEISSPVNK 12 0 Q5UIP0-2;Q5UIP0;H7C2B5 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 SQEDEIS(0.082)S(0.918)PVNK 227.34 2.86E-06 0 1217300 879830 1068400 970220 933760 770330 1522900 890570 1019300 TRUE FALSE 1141111.366 944973.5287 1093742.953 995117.4878 860426.2562 992711.7657 1294555.283 1001759.625 849172.2451 1.343792585 1.112817257 1.288010717 1.171867655 1.013252919 1.169034635 1.524490809 1.179689551 1 19.69569769 SQEEPKDTFEHDPSESIDEFNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQEEPKDTFEHDPSESIDEFNK 22 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 ; 217.84 7.38E-26 489850000 746370 413640 519880 498340 599850 367730 646330 447380 904060 FALSE TRUE 699656.034 444266.336 532211.7991 511128.2481 552740.2007 473887.6814 549418.8167 503236.3778 753166.5455 0.928952618 0.58986467 0.706632288 0.678639075 0.733888413 0.629193748 0.72947852 0.668160822 1 19.52260939 -1.538498162 3.070411416 1.011624262 0.696220437 0.503068655 0.090491389 29047134.57 32141591.18 2784232.342 0.019662159 0.028940221 1.538498162 -0.315403826 SQEPIPDDQKVS(ph)DDDKEKGEGALPTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQEPIPDDQKVSDDDKEKGEGALPTGK 27 3 E5RJU9;Q86UE4;H0YBJ8 E5RJU9 MTDH Protein LYRIC 1 SQEPIPDDQKVS(1)DDDKEKGEGALPTGK;SQEPIPDDQKVS(1)DDDKEKGEGALPTGK 190.23 4.51E-18 689560000 2226580 323760 685900 626550 809220 415230 1065060 539400 1065600 TRUE FALSE 2087222.332 347731.5273 702169.8719 642628.3337 745667.1254 535100.1603 905364.1405 606745.2774 887744.476 2.351152149 0.391702271 0.790959438 0.723888857 0.839956931 0.602763717 1.019847676 0.683468378 1 19.75978495 4.746331812 24.99846595 0.745048679 2.351152923 0.882437145 0.18286875 303.3932854 975936.0739 0.042753726 0.46211629 55761.16162 -4.746331812 1.606104244 SQEPLDLVLVPDDCRPGT(ph)PPSDLIEIQVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQEPLDLVLVPDDCRPGTPPSDLIEIQVVK 30 1 Q8NCA9 Q8NCA9 ZNF784 Zinc finger protein 784 1 SQEPLDLVLVPDDCRPGT(0.895)PPS(0.105)DLIEIQVVK;SQEPLDLVLVPDDCRPGT(0.97)PPS(0.03)DLIEIQVVK 98.342 0.00097367 73567000 259000 212975 236560 224201 261130 239210 360710 216899 356500 TRUE FALSE 242789.6523 228743.8906 242171.3149 229954.3772 240621.9031 308266.0438 306624.8842 243979.3176 296997.8469 0.817479503 0.770187033 0.815397544 0.774262775 0.810180631 1.037940332 1.032414502 0.821485139 1 18.18009295 2.282081069 8.289547687 0.983854567 0.794685878 0.665827729 0.06154454 0.135277284 23.0327511 0.020321091 0.016879271 191.4613288 -2.282081069 -0.189168689 SQEQILEILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQEQILEILR 10 0 P12270 P12270 TPR Nucleoprotein TPR 0 97.452 0.014073 16523000 17275 23846 21394 19805 21888 14042 21755 21162 22939 FALSE TRUE 16193.78859 25611.58265 21901.47578 20313.22983 20169.00477 18095.69745 18493.03971 23804.12228 19110.33271 0.847383917 1.340195539 1.146054133 1.062944855 1.055397888 0.946906458 0.967698469 1.245615272 1 14.22206528 3.171449345 2.856960713 1.028895786 1.167558252 0 0.145777205 0.474978647 7.865424563 0.041815203 0.053541755 1484.052773 -3.171449345 0.138662467 SQEQLAAELAEYTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQEQLAAELAEYTAK 15 0 P15311;E7EQR4 P15311 EZR Ezrin 0 179.33 1.57E-06 28399000 85534 78743 89535 78578 102500 71480 100300 87198 117020 FALSE TRUE 80180.57962 84573.21365 91658.81248 80594.44451 94450.06347 92115.11562 85260.94614 98084.86225 97488.60602 0.822461033 0.867518955 0.940200257 0.826706297 0.968831819 0.944880837 0.874573446 1.006116163 1 16.57294599 7.999999995 0.093916326 1.056993718 0.456596433 0.512290861 0.046657122 131.0517745 0.879275266 0.695960103 10.13417195 99999998.76 -7.999999995 -0.600397285 SQESGYYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SQESGYYDR 9 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 187.22 9.49E-05 3556350000 2552870 2902250 2647630 2616690 2893980 2280850 2906960 2562750 3173210 FALSE TRUE 2393090.424 3117135.61 2710433.034 2683838.695 2666698.485 2939294.368 2471088.335 2882714.979 2643580.751 0.90524582 1.179133873 1.025288534 1.015228566 1.008744856 1.111861012 0.934750464 1.090458454 1 21.33406197 3.657241695 9.117466165 1.022506092 1.073828467 0 0.08203235 0.90867787 111.5643983 0.019793466 0.030722589 4541.943163 -3.657241695 0.051322375 SQET(ph)PEKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQETPEKPR 9 1 J3QQY0;Q68DK7;J3KSZ8;Q68DK7-2;Q68DK7-3;J3KTC2 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 S(0.001)QET(0.999)PEKPR;SQET(1)PEKPR 97.86 0.010355 1550300000 1369080 888100 1100500 973700 1152930 899540 1397080 996820 1379050 TRUE FALSE 1283391.727 953855.8481 1126604.38 998686.7905 1062383.528 1159222.595 1187600.824 1121275.171 1148877.646 1.117083034 0.830250159 0.980613021 0.86927167 0.924714248 1.009004396 1.033705224 0.9759744 1 20.13179373 2.235384457 23.87402112 1.010344122 0.930348067 0.116079081 0.076749221 70.64981668 531035.3739 0.025416896 0.019584491 171.942983 -2.235384457 -0.079996055 SQFSDKPVQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQFSDKPVQDR 11 1 Q9BWS9-3;Q9BWS9;E9PKF1;E9PI70;E9PIP0;E9PRL3;E9PPH0;E9PPA0 Q9BWS9-3 CHID1 Chitinase domain-containing protein 1 0 ; 107.93 0.001944 1298870000 2372400 2146710 2288390 2399500 2668600 1724500 3087700 2243630 2712500 FALSE TRUE 2223915.719 2305654.642 2342671.691 2461075.232 2459018.921 2222335.155 2624728.05 2523752.144 2259766.227 0.984135302 1.020306709 1.036687629 1.089083996 1.08817403 0.983435866 1.161504238 1.116820012 1 21.1077421 4.017550679 0.678636309 1.085702209 0.972122169 0.220424056 0.052738369 1.916528294 1.228038224 0.024231821 0.147172559 10412.39606 -4.017550679 -0.113580039 SQGDEAGGHGEDRPEPLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 217.02 6.58E-25 9866010000 5680120 3562060 4468490 4786100 4520340 2886870 4731840 3275330 4337900 TRUE FALSE 5324611.429 3825798.629 4574484.693 4908919.429 4165330.731 3720262.505 4022344.52 3684262.16 3613876.466 1.47337948 1.05864123 1.26581103 1.358352859 1.152593557 1.029438206 1.113027675 1.019476508 1 21.78511576 2.464931859 5.159788316 1.058226147 1.248035491 0.516790706 0.109560224 0.176743048 13.93346379 0.03686975 0.031784775 291.6969306 -2.464931859 0.189809343 SQGS(ph)SQFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQGSSQFR 8 0 Q15172 Q15172 PPP2R5A Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform 1 S(0.017)QGS(0.742)S(0.242)QFR;S(0.002)QGS(0.958)S(0.04)QFR 94.465 0.010846 886610000 339550 355420 353850 363400 356680 310070 423010 321330 385810 TRUE FALSE 318298.1716 381735.6666 362243.4891 372725.4592 328667.7916 399582.1754 359583.5775 361448.7578 321415.8186 0.990300269 1.187669195 1.127024459 1.159636327 1.022562589 1.24319387 1.11874885 1.124551864 1 18.29408141 -1.033386963 5.3895616 0.999999195 1.130805697 0.20549022 0.073297632 6.20E-07 1.11E-07 0.061847575 0.014577523 0.092600437 1.033386963 0.130806502 SQHCKPEEGLEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQHCKPEEGLEAR 13 1 B9A060;E7ENJ0;A0A087WZT8;E7EP80;E7EQY6;E7ER35;E9PC03;E7EMU0;E7EUF2;E7ETG4;P43360;P43357;P43356 B9A060 MAGEA2B;MAGEA2;MAGEA3;MAGEA6 Melanoma-associated antigen 6;Melanoma-associated antigen 3;Melanoma-associated antigen 2 0 82.908 0.0066522 98471000 63063 88970 98229 95002 102020 69875 114010 96208 95496 FALSE TRUE 59115.9994 95557.43137 100559.0383 97439.91216 94007.76073 90046.77817 96915.25892 108219.7806 79557.10067 0.743063773 1.201117569 1.263985709 1.224779578 1.181638847 1.131850927 1.218184902 1.360278085 1 16.27970308 4.738456118 6.861332896 1.208961039 0.735589169 0.704661188 0.092266024 0.054124862 18.33118147 0.019471562 0.119117344 54759.0768 -4.738456118 -0.47337187 SQHFFDTSVPLMDDGDDNTLYHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQHFFDTSVPLMDDGDDNTLYHR 23 0 H3BU86;O14662;F8W9Z6;B7ZBM8;O14662-6;O14662-2;O14662-5;Q96NX8;O14662-4 H3BU86;Q96NX8 STX16-NPEPL1;STX16 Syntaxin-16 0 111.58 0.0005471 31455000 8457.5 19189 17202 15767 17550 14590 21712 17816 18211 FALSE TRUE 7928.160172 20609.77353 17610.03956 16171.60791 16171.69379 18801.89615 18456.48716 20040.36682 15171.46645 0.522570458 1.358456257 1.160734173 1.065922531 1.065928191 1.239293262 1.216526248 1.320924835 1 13.88907292 2.236791222 24.96188272 1.213656814 1.097469481 0.070931727 0.226675639 145.989531 2059504.711 0.077569128 0.060254894 172.5008431 -2.236791222 -0.116187333 SQHSGNAQVTQTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SQHSGNAQVTQTK 13 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;;; 204.17 8.00E-08 449240000 512521 735022 735603 705467 803651 590074 903095 725317 979329 FALSE TRUE 480443.2255 789443.7937 753051.8505 723570.4776 740535.4922 760418.7847 767684.2887 815874.4241 815872.6632 0.588870356 0.967606625 0.923001694 0.886866922 0.907660626 0.932031209 0.940936403 1.000002158 1 19.63798448 4.741413784 24.99963201 0.938925022 0.58887023 0.901469769 0.03693213 76.11559881 666895.2778 0.008392136 0.058759671 55133.27405 -4.741413784 -0.350054792 SQHSS(ph)GNGNDFEMITK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQHSSGNGNDFEMITK 16 0 Q99442 Q99442 SEC62 Translocation protein SEC62 1 S(0.118)QHS(0.353)S(0.529)GNGNDFEMITK 105.06 0.00084545 200730000 227410 281350 266940 296410 361350 271810 382030 314260 276070 TRUE FALSE 213176.814 302181.4467 273271.9429 304016.3824 332971.0286 350277.1345 324748.1481 353496.0528 229992.1335 0.926887415 1.313877314 1.18817952 1.321855569 1.44774964 1.522996153 1.411996763 1.536991928 1 17.81122499 5.680263998 0.586017842 1.401610195 2.81E-12 0.344228963 0.166956193 10.26955094 1.165691286 0.068788137 12.46397186 478921.1296 -5.680263998 -1.401610195 SQIDVALS(ph)QDSTYQGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SQIDVALSQDSTYQGER 17 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 1 SQIDVALS(0.999)QDS(0.001)TYQGER;SQIDVALS(1)QDSTYQGER;SQIDVALS(0.998)QDS(0.002)TYQGER 356.5 6.74E-88 787020000 485307 562740 524113 525593 571686 439530 603029 476278 546094 TRUE FALSE 454932.5012 604405.8551 536545.2079 539080.6062 526788.0876 566415.1758 512610.3997 535742.3567 454947.3835 0.999967288 1.328518147 1.179356619 1.184929567 1.157909918 1.245012492 1.126746561 1.177591907 1 18.79534018 0.007315618 0.54495765 0.984262817 1.200047001 0.276711391 0.084607855 4.658368078 1.663957322 0.235595924 0.034872771 1.016987508 -0.007315618 0.215784183 SQIHDIVLVGGSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SQIHDIVLVGGSTR 14 0 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;; 190.26 1.75E-07 21757040000 11338830 15368290 11986080 11181900 15415270 8860330 15818080 14987680 16396590 FALSE TRUE 10629152.87 16506174.18 12270395.48 11468846.48 14204616.88 11418163.44 13446305.75 16858924.84 13659893.2 0.778128548 1.208367733 0.89827902 0.839600011 1.039877594 0.835889656 0.9843639 1.234191555 1 23.70344287 1.449927648 24.99730766 1.114490133 0.957152327 0.226432501 0.133926942 25.05716515 23037.59421 0.068932787 0.031866578 28.17913436 -1.449927648 -0.157337806 SQIYGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQIYGSR 7 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 85.161 0.048888 530700000 207390 363720 235580 255830 356710 180637 261210 303470 425180 FALSE TRUE 194409.8301 390650.2073 241168.0688 262395.0309 328695.4355 232783.9695 222043.9855 341358.8975 354214.7112 0.548847419 1.102862741 0.680852774 0.740779597 0.927955348 0.657183234 0.626862686 0.963706155 1 18.43426461 3.756184317 24.75330198 0.769757127 0.873356689 0 0.187222198 1027.522761 875144.9056 0.043966316 0.079243298 5704.063048 -3.756184317 0.103599561 SQKPVMVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQKPVMVK 8 1 P46779 P46779 RPL28 60S ribosomal protein L28 0 ; 99.653 0.0060746 1077080000 2266350 2099200 2009470 2066980 2553100 1492930 2631100 2219780 2909400 FALSE TRUE 2124503.199 2254626.952 2057135.577 2120022.206 2352589.825 1923914.655 2236590.981 2496924.419 2423802.345 0.876516686 0.93020248 0.848722497 0.874667941 0.970619502 0.793758889 0.922761291 1.030168332 1 21.20884062 1.354419937 4.721872298 1.013586618 0.88529425 0.568046913 0.047015528 0.140881124 4.629425085 0.031093075 0.010755034 22.61621567 -1.354419937 -0.128292368 SQLDDHPES(ph)DDEENFIDANDDEDMEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SQLDDHPESDDEENFIDANDDEDMEK 26 0 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 SQLDDHPES(1)DDEENFIDANDDEDMEK;SQLDDHPES(1)DDEENFIDANDDEDMEK;SQLDDHPES(1)DDEENFIDANDDEDMEK 369.46 4.90E-126 956343000 991130 558686 707530 655750 610650 538645 932640 596316 607598 TRUE FALSE 929096.9425 600051.6928 724312.9457 672577.6552 562692.0122 694143.0673 792799.2902 670767.3653 506185.9686 1.835485375 1.185437231 1.430922607 1.328716513 1.111630996 1.371320247 1.566221388 1.32514018 1 18.94930799 -1.86888945 2.073603247 0.796118083 1.38129407 0.275444437 0.20001278 2773242.242 1282118.689 2778571.783 0.049023133 0.013524168 1.86888945 0.585175986 SQLDDHPES(ph)DDEENFIDANDDEDMEKFTDADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQLDDHPESDDEENFIDANDDEDMEKFTDADK 32 1 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 S(0.002)QLDDHPES(0.998)DDEENFIDANDDEDMEKFTDADK;SQLDDHPES(1)DDEENFIDANDDEDMEKFTDADK 202.52 8.42E-27 103283000 219550 86330 115241 113168 106626 79885 166058 95795 124059 TRUE FALSE 205808.7574 92721.96303 117974.5709 116072.0825 98252.02407 102946.5027 141159.1445 107755.2166 103352.7514 1.991323448 0.897140731 1.141474893 1.123067174 0.950647396 0.996069299 1.36579958 1.042596497 1 16.65721727 4.745689361 24.93916203 1.08092383 1.991323888 0.833050076 0.130197658 344.0153306 1203470.751 0.032261731 0.326029937 55678.7352 -4.745689361 0.910400058 SQLDDHPES(ph)DDEENFIDANDDEDMEKFTDADKETEIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQLDDHPESDDEENFIDANDDEDMEKFTDADKETEIVK 38 2 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 SQLDDHPES(1)DDEENFIDANDDEDMEKFTDADKETEIVK 217.44 1.52E-39 330890000 851910 331910 466190 461510 501590 225190 611900 365870 879900 TRUE FALSE 798590.4738 356484.9618 477248.247 473353.1279 462197.1447 290198.6973 520151.2756 411549.6749 733039.0056 1.089424257 0.486311041 0.651054369 0.64574071 0.630521897 0.395884387 0.709581989 0.561429435 1 19.48353044 -1.371280527 5.162239443 1.000211984 0.626832907 0.265658961 0.182317546 0.000389335 4.74E-05 0.154513706 0.036398787 0.042532359 1.371280527 -0.373379077 SQLDIIIHSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQLDIIIHSLK 11 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 122.33 0.00039312 502920000 728290 878000 811460 786450 953200 693500 876370 829680 729510 FALSE TRUE 682707.6289 943008.0336 830708.2144 806631.6385 878339.517 893702.192 744966.4543 933267.3744 607750.0682 1.123336162 1.55163789 1.366858283 1.327242366 1.445231458 1.470509406 1.225777657 1.535610481 1 19.21311862 -1.306514585 3.520687387 0.998609489 1.387132825 0.44697725 0.132939724 32380915.08 61322931.09 503705.7212 0.028838527 0.049372534 1.306514585 0.388523336 SQLDIIIHSLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQLDIIIHSLKK 12 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 166.38 3.38E-05 540380000 2413900 2334000 2340000 2319500 2814300 1788050 3061600 2404700 2869100 FALSE TRUE 2262818.308 2506811.789 2395505.905 2379022.297 2593276.23 2304231.008 2602541.503 2704932.088 2390228.675 0.946695323 1.048774879 1.002207835 0.995311587 1.084949008 0.964021155 1.08882532 1.131662471 1 21.18871722 1.644216538 8.785396553 1.082800343 1.013996717 0.263442857 0.050636158 0.132598822 19.63695245 0.022021798 0.011507012 44.07745775 -1.644216538 -0.068803625 SQLIDELADKFNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQLIDELADKFNR 13 1 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 0 134.88 5.69E-06 0 107670 120730 112910 117060 127290 88186 142290 116060 127730 FALSE TRUE 100931.1269 129668.9748 115588.2785 120063.9578 117293.1569 113643.8666 120954.9355 130550.3465 106411.0378 0.94850242 1.218566959 1.086243315 1.128303607 1.102264946 1.067970663 1.136676588 1.226849668 1 16.69928828 1.602197084 25 1.13632792 1.107328294 0 0.08617716 2.522994327 11082.06428 0.040389863 0.019502384 40.01262867 -1.602197084 -0.028999626 SQLLGSAHEVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQLLGSAHEVQR 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 192.14 4.46E-06 907490000 305430 493280 369720 307270 526240 295040 390330 427810 531000 FALSE TRUE 286313.6815 529802.9645 378489.933 315155.0684 484911.2332 380213.2584 331803.6401 481223.0202 442372.6696 0.647222808 1.197639458 0.85559068 0.712419844 1.096160017 0.859486321 0.750054565 1.087822674 1 18.75490273 3.72180616 24.71080029 0.886828772 0.981207145 0 0.184470239 638.9103223 2970420.306 0.044849422 0.071786708 5269.945939 -3.72180616 0.094378374 SQLQALHIGLDSS(ph)SIGSGPGDAEADDGFPESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQLQALHIGLDSSSIGSGPGDAEADDGFPESR 32 0 O75116;E9PF63;Q14DU5 O75116 ROCK2 Rho-associated protein kinase 2 1 SQLQALHIGLDS(0.091)S(0.496)S(0.413)IGSGPGDAEADDGFPESR 186.89 6.39E-20 413190000 82162 111620 99811 96388 111500 79842 104450 94190 115590 TRUE FALSE 77019.62708 119884.4609 102178.5641 98861.47926 102743.2398 102891.0893 88788.69217 105949.8288 96297.28226 0.799811015 1.244941271 1.061074224 1.026627927 1.066938104 1.068473449 0.922026978 1.100236957 1 16.55520746 1.932315383 24.89596196 0.997880625 1.069927844 0 0.116328125 460.5221157 169388.9017 0.045013144 0.029052359 85.56878849 -1.932315383 0.072047219 SQLQALHIGLDSSS(ph)IGS(ph)GPGDAEADDGFPESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SQLQALHIGLDSSSIGSGPGDAEADDGFPESR 32 0 O75116;E9PF63;Q14DU5 O75116 ROCK2 Rho-associated protein kinase 2 2 SQLQALHIGLDS(0.015)S(0.111)S(0.875)IGS(1)GPGDAEADDGFPESR;SQLQALHIGLDS(0.025)S(0.142)S(0.835)IGS(0.998)GPGDAEADDGFPESR;S(0.008)QLQALHIGLDS(0.184)S(0.499)S(0.523)IGS(0.785)GPGDAEADDGFPES(0.002)R 215.64 4.80E-36 528137000 200692 240972 245649 242085 223828 192623 257657 203760 257449 TRUE FALSE 188131.046 258813.8176 251475.9103 248297.3109 206249.4518 248230.1331 219023.7248 229199.8845 214479.0987 0.877153285 1.206708808 1.172496116 1.157676027 0.961629609 1.157362814 1.021189133 1.06863506 1 17.71047754 2.775366932 24.89939594 1.050859215 1.132206534 0.047298071 0.103259435 1109.353355 750473.0478 0.029418027 0.031201451 596.1656271 -2.775366932 0.08134732 SQLQALHIGLDSSS(ph)IGSGPGDAEADDGFPESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SQLQALHIGLDSSSIGSGPGDAEADDGFPESR 32 0 O75116;E9PF63;Q14DU5 O75116 ROCK2 Rho-associated protein kinase 2 1 SQLQALHIGLDS(0.022)S(0.134)S(0.822)IGS(0.022)GPGDAEADDGFPESR;SQLQALHIGLDS(0.04)S(0.277)S(0.683)IGSGPGDAEADDGFPESR;SQLQALHIGLDS(0.032)S(0.156)S(0.78)IGS(0.032)GPGDAEADDGFPESR 288.09 8.26E-75 745992000 154448 183359 193423 193642 207087 143268 219019 173315 215100 TRUE FALSE 144781.3754 196935.0911 198011.0849 198611.1816 190823.2224 184627.1458 186179.1342 194953.7593 179198.4204 0.807938904 1.09897783 1.104982312 1.108331095 1.064871119 1.030294494 1.03895522 1.087921193 1 17.45119839 4.742192839 24.99447707 1.071527484 0.807938804 0.83872967 0.035617739 141.1932824 971555.3885 0.00886772 0.065629201 55232.26323 -4.742192839 -0.26358868 SQLQALHIGLDSSSIGS(ph)GPGDAEADDGFPESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQLQALHIGLDSSSIGSGPGDAEADDGFPESR 32 0 O75116;E9PF63;Q14DU5 O75116 ROCK2 Rho-associated protein kinase 2 1 SQLQALHIGLDS(0.041)S(0.152)S(0.121)IGS(0.685)GPGDAEADDGFPESR 132.59 4.23E-08 252400000 48498 61357 60112 60959 66889 51502 67212 63835 77376 TRUE FALSE 45462.59675 65899.93612 61537.88503 62523.31114 61635.80776 66369.79133 57134.18457 71804.94027 64461.44573 0.705268029 1.022315515 0.954646368 0.96993343 0.956165458 1.029604449 0.886331107 1.113920724 1 15.97614892 4.74365172 24.91340081 0.982166314 0.705267908 0.690773036 0.059913852 279.4287406 1367343.308 0.012646574 0.106596672 55418.11125 -4.74365172 -0.276898406 SQLQDLVEFPYVNLHNEVVGIIESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQLQDLVEFPYVNLHNEVVGIIESR 25 0 Q12769;G3V198;E9PR16 Q12769 NUP160 Nuclear pore complex protein Nup160 0 ; 190.93 7.74E-18 121876000 290420 318990 331600 352730 381870 315690 352510 287460 308640 FALSE TRUE 272243.1306 342608.3515 339465.7086 361781.649 351879.4706 406824.5782 299654.398 323350.0138 257125.9901 1.058792736 1.332453212 1.320231022 1.407020927 1.368509929 1.582199365 1.165399102 1.257554764 1 17.97211592 0.908295518 1.468010605 1.006087009 1.337117381 0.353913216 0.136762387 0.535646649 2.297197363 0.120757066 0.03563604 8.096466409 -0.908295518 0.331030372 SQNHS(ph)RS(ph)PS(ph)EERGHSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQNHSRSPSEERGHSTR 17 2 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 3 S(0.017)QNHS(0.984)RS(1)PS(1)EERGHSTR 83.602 0.0040574 177500000 44132 53387 59895 57239 65180 33277 51950 44339 90792 TRUE FALSE 41369.8569 57339.82903 61315.73768 58707.84965 60061.02572 42883.52969 44160.57978 49874.82175 75638.22866 0.546943756 0.758080009 0.810644812 0.776166374 0.794056482 0.566955764 0.583839423 0.659386432 1 16.20682796 -1.209310228 5.473863567 1.000014256 0.696518019 0.50130223 0.097699354 1.87E-05 2.70E-06 0.104176898 0.024553578 0.061757509 1.209310228 -0.303496237 SQNHS(ph)RS(ph)PSEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQNHSRSPSEER 12 1 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 2 S(0.17)QNHS(0.828)RS(0.951)PS(0.052)EER 70.335 0.027061 107750000 133430 185970 179890 162720 157150 123930 182080 142210 175320 TRUE FALSE 125078.8545 199739.4123 184157.0758 166895.6707 144808.0729 159706.5792 154778.7943 159965.2315 146057.9594 0.856364521 1.367535279 1.260849299 1.142667414 0.991442531 1.0934466 1.059708043 1.095217489 1 17.15618145 2.991919643 5.220881232 1.05639828 1.218801424 0.089875529 0.135657006 0.24772719 20.95417904 0.038765717 0.04393604 981.5663092 -2.991919643 0.162403144 SQPAPVS(ph)PQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQPAPVSPQQK 11 0 Q13118-2;Q13118 Q13118-2 KLF10 Krueppel-like factor 10 1 SQPAPVS(1)PQQK 126.71 0.0010141 0 262020 202250 222520 244470 206260 131110 215030 156990 237100 TRUE FALSE 245620.6359 217224.8004 227798.2795 250743.5141 190061.1716 168959.3286 182788.2477 176590.5471 197526.4783 1.243482079 1.09972497 1.153254396 1.269417226 0.962206046 0.855375594 0.925386051 0.894009495 1 17.59168653 2.604672184 5.402831285 0.911661943 1.168923155 0.825093676 0.060189574 0.089263419 3.562819544 0.01874867 0.01758306 402.4131689 -2.604672184 0.257261213 SQPDPVDT(ph)PTSSKPQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQPDPVDTPTSSKPQSK 17 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 SQPDPVDT(0.895)PT(0.065)S(0.015)S(0.025)KPQSK 162.81 4.52E-09 306020000 599470 344240 458530 450790 465680 328320 609490 382100 763850 TRUE FALSE 561950.2428 369727.8878 469406.5481 462358.0346 429107.3713 423100.6542 518102.6327 429806.0261 636358.5003 0.883071794 0.581005656 0.737644815 0.72656849 0.674317026 0.664877823 0.814167851 0.675414921 1 19.27948023 -1.467881868 0.423570104 1.177505944 0.701131126 0.508340276 0.084955439 21.03605437 1.929524962 4.089248317 0.045592416 0.03405008 1.467881868 -0.476374818 SQPERDWVLNEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQPERDWVLNEFR 13 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2;A0A0U1RQJ0 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ; 202.25 8.70E-08 335460000 248010 507850 351310 341200 620910 203645 335830 370300 981930 FALSE TRUE 232487.4968 545451.7424 359643.2391 349955.7697 572146.2332 262434.0056 285475.4092 416532.7701 818039.5395 0.284200806 0.666779191 0.439640411 0.427798111 0.699411466 0.320808461 0.348975074 0.509184153 1 19.64181105 -1.234308334 3.879488906 1.00056766 0.469180883 0.606051304 0.136185367 87400485.04 136422040.1 578770.9216 0.031772088 0.058303103 1.234308334 -0.531386777 SQPFVDHVFTFTILDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQPFVDHVFTFTILDNR 17 0 Q8TDN6 Q8TDN6 BRIX1 Ribosome biogenesis protein BRX1 homolog 0 ; 250.55 2.39E-21 579140000 458953 542650 466447 467630 536820 402988 492200 471457 478270 FALSE TRUE 430227.951 582828.3706 477511.3431 479630.1775 494660.3226 519324.0936 418399.1794 530319.4443 398443.6473 1.079771139 1.462762362 1.198441351 1.203759128 1.241481263 1.303381538 1.0500837 1.330977286 1 18.60401617 -3.214386456 0.156120165 0.502688841 1.327116337 0.229180915 0.122425836 84.13074773 1.28889404 14.2266142 0.56157589 0.000610399 3.214386456 0.824427496 SQPPGEDS(ph)DT(ph)DVDDDSRPPGRPAEVHLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SQPPGEDSDTDVDDDSRPPGRPAEVHLER 29 2 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 2 S(0.002)QPPGEDS(0.998)DT(1)DVDDDSRPPGRPAEVHLER;SQPPGEDS(1)DT(1)DVDDDSRPPGRPAEVHLER;SQPPGEDS(1)DT(1)DVDDDSRPPGRPAEVHLER;SQPPGEDS(1)DT(1)DVDDDSRPPGRPAEVHLER;S(0.001)QPPGEDS(0.999)DT(1)DVDDDSRPPGRPAEVHLER;S(0.002)QPPGEDS(0.998)DT(1)DVDDDSRPPGRPAEVHLER;SQPPGEDS(1)DT(1)DVDDDSRPPGRPAEVHLER 204.54 4.55E-25 6376800000 616168 596789 562303 540936 554188 412075.1 649369 471838 536373 TRUE FALSE 577603.1448 640975.8785 575641.0927 554817.3336 510664.31 531034.4919 552002.1469 530748.0129 446848.8812 1.292614056 1.434435456 1.288223193 1.241621848 1.142812104 1.188398392 1.235321761 1.187757283 1 18.76942749 7.999999703 0.048351049 0.481603158 2.633684272 0.747257873 0.05630733 249.6793959 0.912300039 9.797213175 40.59908293 99999931.64 -7.999999703 2.152081114 SQPPGEDS(ph)DTDVDDDSRPPGRPAEVHLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQPPGEDSDTDVDDDSRPPGRPAEVHLER 29 2 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 SQPPGEDS(0.991)DT(0.009)DVDDDSRPPGRPAEVHLER;SQPPGEDS(0.997)DT(0.003)DVDDDSRPPGRPAEVHLER 256.17 3.06E-58 1762290000 158233 168908 157254 155455 186719 115640 184389 150656 252686 TRUE FALSE 148329.479 181414.1241 160984.1391 159444.2385 172054.8429 149023.3907 156741.5812 169465.7332 210511.0742 0.704616038 0.86177948 0.764730026 0.757414968 0.817319676 0.707912357 0.744576416 0.805020514 1 17.6835366 0.88646886 6.815478615 0.999999443 0.7722273 0.707505019 0.046906509 1.5573289 93.41264358 0.044772291 0.011232583 7.699612334 -0.88646886 -0.227772143 SQPVT(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SQPVTPEK 8 0 P54274-2;P54274 P54274-2 TERF1 Telomeric repeat-binding factor 1 1 SQPVT(1)PEK;SQPVT(1)PEK;SQPVT(1)PEK;SQPVT(1)PEK 109.24 0.040881 1682350000 6458000 4212100 5066610 4486580 4695140 3728920 6542800 3974760 3683290 TRUE FALSE 6053805.308 4523968.267 5186792.382 4601713.239 4326402.644 4805398.67 5561767.88 4471017.536 3068525.104 1.972871364 1.474313591 1.690320987 1.499649859 1.409929037 1.566028795 1.812521551 1.457057506 1 21.54911396 0.980175815 22.84269484 0.999999992 1.618170415 0.58823044 0.166538604 315.5964416 363651.7455 0.150010675 0.037502669 9.553792721 -0.980175815 0.618170422 SQQALADALEEGSQHEEACQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQQALADALEEGSQHEEACQR 21 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 ; 248.7 1.51E-30 767320000 590360 775960 681310 707040 858000 624140 878950 737560 738980 FALSE TRUE 553410.4214 833412.8858 697470.9949 725183.8434 790616.141 804319.0859 747159.6073 829645.9896 615639.464 0.898919666 1.353735318 1.132921191 1.177935928 1.284219397 1.306477464 1.213631762 1.347616646 1 19.23172619 4.751436816 24.70699607 1.235641124 0.898919413 0.47831222 0.107369989 1432.344857 2748342.187 0.022607867 0.412745531 56420.4851 -4.751436816 -0.336721711 SQQPLKPQVHT(ph)PVATVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQQPLKPQVHTPVATVK 17 1 Q6P3W7;A0A0U1RQQ9 Q6P3W7 SCYL2 SCY1-like protein 2 1 SQQPLKPQVHT(0.997)PVAT(0.002)VK 70.352 0.048109 179220000 163790 119480 141450 140350 161450 106440 204410 141870 265760 TRUE FALSE 153538.6763 128326.4235 144805.2608 143951.6186 148770.3683 137167.5001 173760.6181 159582.7818 221402.9391 0.69348075 0.579605781 0.654034953 0.650179348 0.671943963 0.619537846 0.784816222 0.720779871 1 17.75631485 0.459457492 0.485499617 1.02278797 0.624481278 0.857986246 0.044127487 0.655336243 0.275968544 0.071693442 0.021809674 2.880431103 -0.459457492 -0.398306692 SQQQPTPVT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SQQQPTPVTPK 11 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 SQQQPT(0.011)PVT(0.989)PK;SQQQPTPVT(1)PK;SQQQPTPVT(1)PK;SQQQPTPVT(1)PK;SQQQPTPVT(1)PK;SQQQPTPVT(1)PK 211.52 1.01E-07 2530700000 4429120 3064210 3334960 3120580 3883040 2116540 4951260 3034430 4988110 TRUE FALSE 4151909.285 3291087.297 3414066.826 3200659.366 3578081.702 2727550.739 4208864.528 3413285.265 4155562.217 0.999120954 0.791971609 0.821565566 0.770210912 0.861034323 0.656361425 1.012826739 0.821377491 1 21.98661225 1.684593642 13.59120775 0.937141119 0.814390123 0.27248794 0.098257605 0.161696028 35.57598616 0.040706857 0.022375976 48.37195521 -1.684593642 -0.122750996 SQQSEVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQQSEVTR 8 0 Q5T123;Q9H299 Q5T123 SH3BGRL3 SH3 domain-binding glutamic acid-rich-like protein 3 0 ; 172.94 0.00065293 141320000 194219 207480 200244 200926 217180 168158 212240 186169 260900 FALSE TRUE 182063.1795 222842.0351 204993.8822 206082.1013 200123.5589 216702.4848 180416.5823 209412.6095 217354.1045 0.837633961 1.025248801 0.943133247 0.948139911 0.920725925 0.997002036 0.830058318 0.963462871 1 17.72968781 SQRPEESEPLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQRPEESEPLEK 12 1 Q5TFE4;Q5TFE4-2 Q5TFE4 NT5DC1 5-nucleotidase domain-containing protein 1 0 ; 138.31 7.00E-05 569190000 529460 430260 500620 456550 521300 388780 585910 429660 523190 FALSE TRUE 496322.0437 462116.8981 512494.9428 468265.8459 480359.2008 501014.4747 498058.2348 483303.9968 435866.2091 1.138702734 1.060226483 1.175807925 1.074333904 1.10207947 1.149468493 1.142686046 1.108835663 1 18.73352584 -1.696034296 1.742867188 0.964556375 1.120051869 0.534641113 0.034884268 81202.70959 39114.17936 12521.06666 0.008977198 0.020135652 1.696034296 0.155495494 SQRPFS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQRPFSPR 8 1 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 S(0.002)QRPFS(0.998)PR 61.213 0.052925 220530000 379770 441990 392870 404630 464540 343490 457310 418900 455970 TRUE FALSE 356000.8736 474715.3995 402189.0619 415013.4908 428056.9023 442649.9869 388740.611 471200.5871 379865.6613 0.937175717 1.249692846 1.058766566 1.092526999 1.126863904 1.16528034 1.02336339 1.240440069 1 18.53512978 -1.951633538 2.611615685 0.914171711 1.114817434 0.120859457 0.094412235 14373228.87 8213973.373 7492750.866 0.019941392 0.011178061 1.951633538 0.200645723 SQRRPRLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQRRPRLR 8 3 Q86V40-2;Q86V40 Q86V40-2 TRABD2A Metalloprotease TIKI1 0 0 0.096582 11380000 18365 61890 46736 49505 45201 14058 9410.3 29612 27516 FALSE TRUE 17215.56743 66472.4 47844.59999 50775.38211 41651.09579 18116.31639 7999.312876 33309.12338 22923.40184 0.751004042 2.899761583 2.087150953 2.215002052 1.816968358 0.790297902 0.348958367 1.453061968 1 14.48453354 2.322294895 3.657229849 0.781083738 2.145971271 0.420880354 0.597891039 0.170837838 4.480455375 0.209103608 0.167299028 210.0365589 -2.322294895 1.364887533 SQS(ph)DLSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQSDLSSR 8 0 Q1W6H9 Q1W6H9 FAM110C Protein FAM110C 1 S(0.015)QS(0.985)DLS(0.001)SR 107.51 0.0062613 0 677010 594770 598920 551960 681210 455180 634550 525670 661770 TRUE FALSE 634637.1526 638807.3897 613126.6652 566124.2281 627710.5145 586583.0768 539405.1184 591301.0566 551316.3118 1.151130737 1.158694883 1.112114139 1.026859202 1.138566919 1.063968296 0.978394992 1.07252596 1 19.07252076 3.206361187 0.378148641 0.998383154 1.195952591 0.580531009 0.04069893 1.31921151 0.325177072 0.040746714 0.10627718 1608.278244 -3.206361187 0.197569437 SQS(ph)DRTEYNQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SQSDRTEYNQK 11 1 Q9NXL2-1;Q9NXL2 Q9NXL2-1 ARHGEF38 Rho guanine nucleotide exchange factor 38 1 S(0.083)QS(0.917)DRTEYNQK;S(0.009)QS(0.991)DRTEYNQK;S(0.001)QS(0.999)DRTEYNQK;SQS(0.976)DRT(0.024)EYNQK;S(0.299)QS(0.701)DRTEYNQK;S(0.015)QS(0.985)DRTEYNQK 206.49 1.59E-08 3075020000 1851299 1538478 1650232 1570004 1789798 1319567 2052020 1513253 2139470 TRUE FALSE 1735429.5 1652388.512 1689376.282 1610292.961 1649234.485 1700504.572 1744338.651 1702185.968 1782378.635 0.973659281 0.927069299 0.947821214 0.903451673 0.925299738 0.954064719 0.978657742 0.955008063 1 20.76537241 1.972270496 3.595709028 0.974681023 0.934640796 0.461825083 0.020756571 0.212183757 5.524044555 0.009147679 0.005430962 93.81461407 -1.972270496 -0.040040227 SQS(ph)FSEAEPQLPPAPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQSFSEAEPQLPPAPVR 17 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;E7ERH1 E9PGF5 TNS1 Tensin-1 1 S(0.029)QS(0.965)FS(0.006)EAEPQLPPAPVR 137.73 6.31E-06 41300000 49554 45911 44761 51514 54184 43761 60691 52337 91848 TRUE FALSE 46452.5036 49310.29821 45822.75206 52835.93645 49928.60721 56394.0903 51590.94798 58871.38966 76517.97544 0.607079622 0.644427638 0.598849509 0.690503586 0.65250821 0.737004475 0.67423305 0.769379866 1 16.22351108 -1.393381807 0.232340057 1.294808651 0.592268584 0.928710989 0.030899564 4.643592928 0.209148601 0.860328593 0.054838802 0.040422037 1.393381807 -0.702540066 SQS(ph)FSHQQPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SQSFSHQQPSR 11 0 B3KNS5;Q8WVR3-2;Q8WVR3-3;Q8WVR3 B3KNS5 C7orf43 Uncharacterized protein C7orf43 1 S(0.016)QS(0.951)FS(0.032)HQQPSR;S(0.001)QS(0.957)FS(0.041)HQQPSR;S(0.251)QS(0.742)FS(0.007)HQQPSR 144.29 2.37E-05 704360000 616178 864910 692968 687505 852470 466009 881310 730314 958610 TRUE FALSE 577612.5189 928948.8363 709405.5282 705147.5422 785520.4449 600538.2333 749165.7472 821495.3105 798611.7981 0.723270706 1.163204499 0.888298332 0.882966598 0.983607363 0.751977663 0.938084998 1.028654113 1 19.60713486 1.283040919 7.340142767 1.014202249 0.923176676 0.109012294 0.121991778 0.491373329 65.81188184 0.082176791 0.029198367 19.18849527 -1.283040919 -0.091025573 SQS(ph)GEDESMNQPGPIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SQSGEDESMNQPGPIK 16 0 A0A0C4DG33;O43933-2;O43933 A0A0C4DG33 PEX1 Peroxisome biogenesis factor 1 1 SQS(1)GEDESMNQPGPIK;SQS(1)GEDESMNQPGPIK;S(0.002)QS(0.998)GEDESMNQPGPIK;S(0.083)QS(0.917)GEDESMNQPGPIK;S(0.004)QS(0.992)GEDES(0.004)MNQPGPIK 464.79 8.87E-206 943800000 1800390 1546969 1604630 1783570 1865950 1104079 1824980 1370723 1589700 TRUE FALSE 1687706.804 1661508.194 1642692.581 1829339.426 1719405.814 1422808.684 1551341.191 1541860.784 1324368.8 1.274348054 1.254566095 1.240358865 1.381291545 1.298283238 1.074329661 1.17138156 1.164223126 1 20.3368735 2.245295655 24.99996269 1.12110155 1.282391375 0.692468291 0.061355279 99.13100317 367967.5022 0.020952562 0.017160373 175.9120765 -2.245295655 0.161289825 SQS(ph)IEQESQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SQSIEQESQEK 11 0 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 SQS(1)IEQESQEK;SQS(1)IEQESQEK;SQS(1)IEQESQEK 288.55 1.38E-28 1190260000 1836820 1257830 1532900 1472960 1646340 1155530 2089930 1507080 1985800 TRUE FALSE 1721856.715 1350961.042 1569261.112 1510758.647 1517043.097 1489112.753 1776564.398 1695242.255 1654357.151 1.040801083 0.816607853 0.948562474 0.913199817 0.916998543 0.900115644 1.07386993 1.02471359 1 20.65783929 1.753017142 12.11485687 1.036129201 0.912863092 0.441118257 0.057691517 0.117125452 86.72854926 0.02466694 0.013537846 56.6261639 -1.753017142 -0.123266109 SQS(ph)LNIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 156.18 0.0016375 1181920000 1306990 1734530 1411520 1514500 1712090 969690 1851450 1411610 1854390 TRUE FALSE 1225187.829 1862956.406 1445001.921 1553364.634 1577629.358 1249623.761 1573842.261 1587852.616 1544880.329 0.793063259 1.205890431 0.935348773 1.005491885 1.021198424 0.808880622 1.018747039 1.027815932 1 20.55906366 3.730198624 24.95002625 0.970743341 1.04146103 0 0.118491239 393.1188874 3187190.504 0.028089712 0.048009385 5372.774632 -3.730198624 0.070717689 SQS(ph)LPHSATVTLGGTSDPSTLSSSALSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQSLPHSATVTLGGTSDPSTLSSSALSER 29 0 A0A0A0MRY0;Q8WUA7-3;Q8WUA7-4;Q8WUA7;F8WDP1 A0A0A0MRY0 TBC1D22A TBC1 domain family member 22A 1 S(0.23)QS(0.77)LPHSATVTLGGTSDPSTLSSSALSER 186.95 4.04E-18 116440000 50172 50737 42383 54826 41148 28468 55351 37582 58466 TRUE FALSE 47031.82408 54493.62027 43388.34477 56232.92798 37916.40206 36686.24946 47051.6314 42274.19543 48707.6469 0.965594256 1.118789836 0.890791232 1.154498966 0.778448652 0.753192811 0.966000914 0.867917014 1 15.57186067 2.729146571 24.97976446 0.868970541 1.023209228 0.369739546 0.10296175 713.7958385 1894022.952 0.031205653 0.029788604 535.9775149 -2.729146571 0.154238688 SQS(ph)LPNSLDYTQTSDPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SQSLPNSLDYTQTSDPGR 18 0 Q96TC7;H0YLG5;H0YNE5 Q96TC7 RMDN3 Regulator of microtubule dynamics protein 3 1 S(0.122)QS(0.865)LPNS(0.012)LDYTQTSDPGR;S(0.001)QS(0.999)LPNSLDYTQTSDPGR;SQS(1)LPNSLDYTQTSDPGR;SQS(1)LPNSLDYTQTSDPGR;S(0.161)QS(0.839)LPNSLDYTQTSDPGR 378.86 4.19E-108 3634670000 1569982 1532130 1440410 1289540 1710890 1274060 1785910 1672640 2552640 TRUE FALSE 1471719.629 1645570.499 1474577.205 1322631.78 1576523.601 1641860.439 1518129.375 1881472.786 2126587.893 0.692056808 0.773807894 0.693400546 0.621950207 0.741339498 0.772063287 0.713880381 0.884737843 1 21.02010905 1.06540102 2.597876665 0.999965324 0.717331679 0.830260488 0.044238136 0.099356464 1.385673948 0.041807641 0.011332635 11.6252157 -1.06540102 -0.282633645 SQS(ph)LPTTLLS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQSLPTTLLSPVR 13 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7 E9PHV5 SSFA2 Sperm-specific antigen 2 2 S(0.03)QS(0.969)LPT(0.001)T(0.001)LLS(0.998)PVR 100.97 0.0031569 38755000 130790 172930 121160 132660 178550 83565 136070 139120 195180 TRUE FALSE 122604.0874 185733.9171 124033.9724 136064.2802 164527.4032 107688.8589 115667.5667 156489.4382 162603.1971 0.754007852 1.142252554 0.76280156 0.836787238 1.011833753 0.662280083 0.711348662 0.962400746 1 17.3109961 2.24835148 24.99489816 0.794114284 0.912499909 0.014797074 0.153063152 421.9652719 1077226.879 0.051101889 0.042263698 177.154211 -2.24835148 0.118385625 SQS(ph)LQDQPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQSLQDQPTR 10 0 Q8N4C8;Q8N4C8-2;Q8N4C8-3 Q8N4C8 MINK1 Misshapen-like kinase 1 1 S(0.001)QS(0.999)LQDQPTR 139.28 4.46E-05 192280000 226840 378840 306450 303260 373640 309380 328180 335400 451890 TRUE FALSE 212642.4893 406889.7078 313719.1387 311042.165 344295.8216 398692.9836 278972.4557 377275.4283 376466.6397 0.564837536 1.080812122 0.833325202 0.826214416 0.914545368 1.059039345 0.741028358 1.002148367 1 18.5221625 4.75600966 24.79771795 0.918083205 0.564837215 0.524902195 0.109092921 2762.077667 3925257.311 0.024675138 0.749595365 57017.69547 -4.75600966 -0.35324599 SQS(ph)MDAMGLSNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SQSMDAMGLSNK 12 0 J3KPC5;P47736-3;P47736;P47736-4;F2Z357;X6R8W7;P47736-2;A0A0A0MQY8 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 S(0.001)QS(0.999)MDAMGLSNK;SQS(1)MDAMGLSNK;SQS(0.991)MDAMGLS(0.009)NK;SQS(1)MDAMGLSNK 226.1 1.69E-11 956080000 2479740 1830570 1958440 1802670 2521320 1379750 2353300 2273060 3344940 TRUE FALSE 2324537.5 1966107.308 2004895.122 1848929.564 2323305.698 1778061.427 2000444.512 2556856.545 2786647.905 0.834169791 0.70554565 0.719464816 0.663495937 0.833727754 0.638064616 0.717867696 0.91753843 1 21.4100993 1.131701716 3.777521601 0.994729505 0.722786723 0.697980604 0.063435383 0.104051184 2.567423264 0.053797621 0.014062938 13.54258956 -1.131701716 -0.271942782 SQS(ph)MDIDGVSCEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQSMDIDGVSCEK 13 0 O95155-2;O95155;O95155-4 O95155-2 UBE4B Ubiquitin conjugation factor E4 B 1 SQS(1)MDIDGVSCEK;S(0.002)QS(0.998)MDIDGVSCEK 297.96 9.48E-41 241800000 1413920 1073560 1113620 1238150 1002330 854140 1725070 969650 1366160 TRUE FALSE 1325425.271 1153047.499 1140035.592 1269923.025 923611.045 1100716.352 1466411.768 1090712.937 1138139.07 1.164554759 1.013098952 1.001666336 1.115788974 0.811509831 0.96711938 1.288429337 0.958330107 1 20.11824542 SQS(ph)PAASDCSSSSSSASLPSSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SQSPAASDCSSSSSSASLPSSGR 23 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 S(0.001)QS(0.988)PAAS(0.011)DCSSSSSSASLPSSGR;S(0.032)QS(0.932)PAAS(0.035)DCSSSSSSASLPSSGR;S(0.016)QS(0.984)PAASDCSSSSSSASLPSSGR;S(0.005)QS(0.984)PAAS(0.011)DCSSSSSSASLPSSGR;S(0.078)QS(0.922)PAASDCSSSSSSASLPSSGR 347.27 1.68E-101 2887590000 663053 745637 687710 686227 728900 710821 891028 698726 805089 TRUE FALSE 621553.6963 800844.7393 704022.806 703836.7466 671655.1342 916023.4835 757426.6233 785963.4792 670714.4448 0.926703907 1.194017432 1.049661017 1.049383612 1.001402518 1.365742889 1.129283303 1.171830255 1 19.35533915 SQS(ph)PHYFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQSPHYFR 8 0 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 S(0.011)QS(0.989)PHYFR;S(0.003)QS(0.997)PHYFR 84.507 0.011209 1298440000 1077180 1287600 1193810 1206340 1285920 1056780 1309260 1115880 1423790 TRUE FALSE 1009761.227 1382935.244 1222127.737 1237296.727 1184929.03 1361855.231 1112948.618 1255200.074 1186150.251 0.851292849 1.165902248 1.030331306 1.043119728 0.998970433 1.148130458 0.938286374 1.058213387 1 20.17785534 1.709499101 24.99999666 0.997076239 1.05170116 0.032381096 0.090072433 2.095307271 1793.04885 0.037719809 0.02091753 51.22702098 -1.709499101 0.054624921 SQS(ph)PINCIRPSVLGPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQSPINCIRPSVLGPLK 17 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 S(0.076)QS(0.924)PINCIRPSVLGPLK;S(0.076)QS(0.924)PINCIRPSVLGPLK 138.93 1.22E-06 588410000 547420 577300 440860 410070 651870 371150 648620 624620 716880 TRUE FALSE 513157.9594 620043.8927 451317.4074 420593.0904 600674.7597 478294.9799 551365.4525 702605.182 597228.0968 0.859232782 1.038202817 0.75568683 0.704241968 1.0057711 0.800858135 0.923207491 1.176443616 1 19.18792251 1.39395116 5.6039793 1.08472422 0.868640531 0.416619149 0.10948014 0.202755391 9.398077784 0.072995816 0.026509629 24.77143465 -1.39395116 -0.21608369 SQS(ph)PINCIRPSVLGPLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQSPINCIRPSVLGPLKR 18 2 Q96E09 Q96E09 FAM122A Protein FAM122A 1 SQS(1)PINCIRPSVLGPLKR 83.606 0.0020731 386830000 274020 264370 268300 221950 301140 220080 361000 325900 406890 TRUE FALSE 256869.5773 283944.2299 274664.2027 227645.6128 277489.6791 283613.5233 306871.4014 366589.3324 338977.4304 0.757777817 0.837649367 0.810272833 0.671565692 0.818608126 0.836673766 0.905285644 1.081456461 1 18.37082969 1.54181358 2.03793123 1.041112265 0.789787954 0.796092677 0.05253843 0.131525769 1.119706809 0.041536283 0.014279651 34.81878242 -1.54181358 -0.251324311 SQS(ph)SDLLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQSSDLLER 9 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 S(0.038)QS(0.905)S(0.057)DLLER 78.744 0.03032 120570000 282890 228170 228730 216560 187550 149270 264940 160370 303170 TRUE FALSE 265184.4199 245063.9442 234155.5836 222117.2962 172820.5795 192361.8258 225214.7066 180392.5475 252568.9684 1.049948541 0.970285248 0.927095617 0.87943225 0.684251041 0.761620982 0.891695872 0.714230844 1 17.94631787 3.347711632 1.802938935 0.807127707 0.991013465 0.425318433 0.092296404 0.312094559 2.068353867 0.027169307 0.041947232 2226.955976 -3.347711632 0.183885758 SQS(ph)SDTEQQSPTSGGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.002)QS(0.499)S(0.499)DTEQQSPTSGGGK 205.78 2.04E-17 0 62536 58388 55292 55484 54277 42093 67131 44611 62813 TRUE FALSE 58621.98339 62711.10827 56603.55235 56907.81337 50014.30336 54244.56578 57065.32976 50180.78155 52329.10451 1.120255811 1.198398269 1.081683948 1.087498322 0.955764556 1.036604128 1.090508433 0.958945925 1 15.67532595 3.43301992 1.536504805 1.024148703 1.161040142 0.606581494 0.046823153 0.258400744 1.241791404 0.014747385 0.02570905 2710.315943 -3.43301992 0.136891439 SQS(ph)SLSGKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQSSLSGKPK 10 1 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 SQS(0.76)S(0.24)LSGKPK 88.092 0.0075277 236200000 291090 205040 245060 242570 287080 178690 381390 276060 421960 TRUE FALSE 272871.1965 220221.3749 250872.9389 248794.7569 264533.8948 230274.9022 324204.1102 310526.6987 351532.15 0.77623397 0.626461548 0.713655746 0.707743963 0.752516931 0.655060717 0.922260198 0.883352202 1 18.42329711 1.68478189 5.523707569 0.929783466 0.699210166 0.815152522 0.051445629 0.055874592 3.83619889 0.02506776 0.012421592 48.39292688 -1.68478189 -0.2305733 SQS(ph)SSQFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQSSSQFR 8 0 Q16537-2;Q16537 Q16537-2 PPP2R5E Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform 1 S(0.088)QS(0.806)S(0.101)S(0.005)QFR;S(0.065)QS(0.853)S(0.073)S(0.009)QFR 95.483 0.0093849 177980000 274757 326200 251362 295210 357920 217066 357770 268512 401650 TRUE FALSE 257560.4498 350352.1874 257324.4253 302785.5884 329810.407 279729.4304 304125.7099 302036.3143 334612.0202 0.769728624 1.047040053 0.769023256 0.904885569 0.985650207 0.835981416 0.90889057 0.902646337 1 18.35212975 0.493368984 1.85352647 0.99998736 0.894438888 0.137559968 0.086025829 8.212130048 27.63088778 0.074727355 0.020807876 3.114361231 -0.493368984 -0.105548472 SQS(ph)TSEQEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQSTSEQEKR 10 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 S(0.206)QS(0.635)T(0.131)S(0.028)EQEKR;S(0.012)QS(0.711)T(0.231)S(0.046)EQEKR 85.837 0.0085552 455440000 637200 492990 522850 565420 510290 383200 699830 485860 771920 TRUE FALSE 597318.7894 529491.4926 535252.2489 579929.6345 470213.8818 493823.6193 594896.9884 546520.6905 643081.5652 0.928838303 0.823365995 0.832324044 0.901797946 0.731188557 0.767901999 0.925072371 0.849846614 1 19.29464221 0.710933768 1.098656929 0.998220876 0.834842246 0.371867076 0.063381726 1.004217321 2.087889075 0.057397367 0.018032158 5.139652633 -0.710933768 -0.163378629 SQS(ph)TTFNPDDMSEPEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQSTTFNPDDMSEPEFK 17 0 F5GZP6;Q86W92-3;Q86W92-4;Q86W92;Q86W92-2 F5GZP6;Q86W92-2 PPFIBP1 Liprin-beta-1 1 S(0.003)QS(0.96)T(0.036)T(0.001)FNPDDMSEPEFK;S(0.001)QS(0.998)T(0.001)TFNPDDMSEPEFK 346.14 1.62E-87 258130000 594170 470240 423910 448000 500370 262562 628870 382290 689810 TRUE FALSE 556981.9603 505057.0589 433965.3454 459496.4385 461072.9586 338359.3871 534576.7816 430019.748 574676.2547 0.969209978 0.878854929 0.755147515 0.799574429 0.802317748 0.588782613 0.930222499 0.74828174 1 19.13238991 -1.125042679 5.037702845 1.000007463 0.809161223 0.243931253 0.105650321 8.19E-06 1.42E-06 0.094654952 0.022309514 0.074982052 1.125042679 -0.19084624 SQS(ph)VPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SQSVPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR 36 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 S(0.218)QS(0.762)VPAS(0.018)T(0.002)GLGWGSGLVAPLQEGSIDSTLAGTQDTR;S(0.202)QS(0.797)VPAS(0.001)TGLGWGSGLVAPLQEGSIDSTLAGTQDTR;S(0.194)QS(0.698)VPAS(0.054)T(0.054)GLGWGSGLVAPLQEGSIDSTLAGTQDTR;S(0.179)QS(0.821)VPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR;S(0.221)QS(0.778)VPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR 275.92 2.35E-76 1052693000 183869.8 169681.3 159371.7 174644.3 162432.2 106320.6 220500.9 140110.4 204537.9 TRUE FALSE 172361.7174 182244.68 163152.072 179125.9684 149675.4302 137013.6312 187438.8371 157603.4919 170399.2031 1.011517157 1.069516034 0.957469689 1.051213651 0.878381046 0.804074366 1.099998319 0.924907447 1 17.37855906 3.648302176 1.351140382 0.956999936 1.041798161 0.139062435 0.083929734 0.931606001 3.354442282 0.026736977 0.062014481 4449.407428 -3.648302176 0.084798225 SQS(ph)WEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SQSWEER 7 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;Q6Y7W6-4;Q6Y7W6-5;E7ESB6 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 SQS(1)WEER;SQS(1)WEER;SQS(1)WEER;SQS(1)WEER;S(0.005)QS(0.995)WEER 140.78 0.0027286 3149010000 4668800 4786510 4550330 5120900 4537530 3754940 5733710 4146940 5345980 TRUE FALSE 4376588.142 5140908.181 4658265.976 5252310.964 4181170.697 4838930.222 4873993.415 4664694.588 4453701.402 0.982685579 1.154300147 1.045931363 1.179313674 0.938808043 1.086496329 1.094369149 1.047374794 1 22.08657341 2.758664179 24.99445898 1.048156216 1.093743696 0.123528722 0.069515379 1927.640933 2396604.969 0.019563952 0.020722515 573.672694 -2.758664179 0.04558748 SQS(ph)WEERGDR ddPTM_SK-BR-3_Pertuzumab_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(0.103)QS(0.897)WEERGDR;S(0.001)QS(0.999)WEERGDR;S(0.008)QS(0.992)WEERGDR 174.95 1.79E-06 1264970000 1112030 1768890 1396230 1579900 1715670 1153020 1495260 1313220 1831050 TRUE FALSE 1042430.027 1899860.456 1429349.235 1620442.909 1580928.199 1485878.156 1271059.644 1477178.408 1525435.926 0.683365332 1.245454118 0.93701034 1.062281857 1.036377977 0.974067892 0.833243549 0.968364769 1 20.54079015 1.988481197 9.153392145 0.912358461 1.021473912 0.005588201 0.145519666 0.434268599 291.1799447 0.053112566 0.036097969 97.38256218 -1.988481197 0.109115451 SQSAAVT(ph)PSSTTSSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQSAAVTPSSTTSSTR 16 0 Q16186;A0A087WX59 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 1 SQSAAVT(0.941)PS(0.051)S(0.006)T(0.001)TSSTR 180.62 4.95E-12 0 219810 217700 226820 236760 215570 211310 266830 189690 239080 TRUE FALSE 206052.4845 233818.7345 232200.2775 242835.6624 198640.0018 272311.7667 226821.3186 213373.2141 199176.0035 1.034524646 1.173930245 1.165804482 1.219201401 0.997308904 1.367191639 1.138798423 1.071279724 1 17.60368432 -0.654348731 6.95917531 1.000000162 1.156600455 0.157543436 0.103561791 0 0 0.088537555 0.020868502 0.221641596 0.654348731 0.156600293 SQSASVES(ph)IPEVLEECTSPADHSDSASVHDMDYVNPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQSASVESIPEVLEECTSPADHSDSASVHDMDYVNPR 37 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 SQSAS(0.001)VES(0.999)IPEVLEECTSPADHSDSASVHDMDYVNPR;S(0.025)QS(0.025)AS(0.023)VES(0.927)IPEVLEECTSPADHSDSASVHDMDYVNPR 274.11 5.30E-76 69659000 69399 93080 95685 107926 102765 88351 116570 87677 96213 TRUE FALSE 65055.44047 99971.74005 97954.69339 110695.5639 94694.25143 113856.4994 99091.41068 98623.66645 80154.42874 0.811626276 1.247239131 1.222074624 1.381028667 1.181397621 1.420464237 1.236256215 1.230420677 1 16.29049461 4.738896429 6.26342594 1.256530506 0.80131514 0.58080561 0.113581944 0.076231715 16.30163136 0.023228871 0.147395356 54814.62272 -4.738896429 -0.455215366 SQSDLDDQHDYDS(ph)VAS(ph)DEDTDQEPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQSDLDDQHDYDSVASDEDTDQEPLR 26 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 2 SQSDLDDQHDYDS(1)VAS(0.997)DEDT(0.003)DQEPLR;SQSDLDDQHDYDS(1)VAS(1)DEDTDQEPLR 217.93 1.90E-34 999410000 406908 458412 416452 439253 469993 352180 475150 391338 403883 TRUE FALSE 381440.3546 492353.3015 426330.4381 450524.9756 433081.6456 453848.6488 403905.6686 440197.4107 336472.3181 1.133645575 1.463280261 1.267059473 1.338965946 1.287124148 1.348843945 1.200412773 1.308272292 1 18.36012829 -0.545029928 0.406696779 0.91703752 1.327532691 0.507478591 0.089286752 6.410519165 0.980711186 0.795659944 0.052210829 0.28508218 0.545029928 0.410495171 SQSDLDDQHDYDSVAS(ph)DEDTDQEPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SQSDLDDQHDYDSVASDEDTDQEPLR 26 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 SQSDLDDQHDYDSVAS(1)DEDTDQEPLR;SQSDLDDQHDYDSVAS(1)DEDTDQEPLR;SQSDLDDQHDYDS(0.001)VAS(0.999)DEDTDQEPLR 229.51 5.24E-35 1389560000 823330 722440 759230 743380 785120 626532 767150 637211 846320 TRUE FALSE 771799.245 775930.2093 777239.2941 762456.3893 723459.8422 807401.6175 652122.9794 716768.196 705063.7246 1.094651757 1.100510751 1.102367441 1.081400677 1.026091426 1.145147012 0.924913531 1.016600587 1 19.42739413 1.738233013 17.59920777 0.978331617 1.091023969 0.668405083 0.036905454 0.028510578 201.2105114 0.015370915 0.008505047 54.73095336 -1.738233013 0.112692351 SQSGS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQSGSPVR 8 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 S(0.001)QS(0.032)GS(0.967)PVR 80.758 0.023773 0 98566 107320 109830 93944 128290 91385 89333 107170 123000 TRUE FALSE 92396.93001 115266.0845 112435.2195 96354.76209 118214.6209 117766.366 75938.34598 120550.4104 102470.5054 0.901692928 1.12487085 1.097244705 0.940317038 1.153645339 1.149270861 0.741075158 1.176440088 1 16.64484919 SQSQNLFSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQSQNLFSVK 10 0 Q86W26 Q86W26 NLRP10 "NACHT, LRR and PYD domains-containing protein 10" 0 63.283 0.079591 505740000 2016100 1656300 1721400 1744400 2238600 1727100 2039800 1470400 2600200 FALSE TRUE 1889915.9 1778934.175 1762232.421 1789164.257 2062789.386 2225685.733 1733950.927 1653982.677 2166209.822 0.872452835 0.821219698 0.81350957 0.82594227 0.952257424 1.02745621 0.80045382 0.763537613 1 21.04674156 2.773527173 23.21851697 0.898524117 0.827975567 0.1671575 0.081571045 511.9592072 339949.8321 0.025022317 0.02653833 593.6454909 -2.773527173 -0.07054855 SQSS(ph)DTEQQS(ph)PTSGGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 SQS(0.016)S(0.984)DTEQQS(0.722)PT(0.257)S(0.021)GGGK;SQS(0.001)S(0.999)DTEQQS(1)PTSGGGK;SQS(0.018)S(0.982)DTEQQS(0.956)PT(0.044)SGGGK;SQS(0.07)S(0.93)DT(0.009)EQQS(0.991)PTSGGGK;SQS(0.022)S(0.978)DTEQQS(0.998)PT(0.002)SGGGK;SQS(0.044)S(0.956)DTEQQS(0.986)PT(0.013)S(0.001)GGGK;SQS(0.042)S(0.958)DTEQQS(0.989)PT(0.011)SGGGK;S(0.026)QS(0.167)S(0.807)DT(0.001)EQQS(0.998)PT(0.001)SGGGK;SQSS(1)DTEQQS(1)PTSGGGK 361.79 2.65E-88 4726605000 9068220 6327723 7530370 7102980 7263820 5708641 8968230 6322561 7623510 TRUE FALSE 8500656.297 6796234.195 7708993.932 7285254.492 6693348.878 7356632.985 7623527.168 7111946.659 6351096.931 1.33845482 1.070088249 1.213805114 1.147086019 1.053888635 1.158324785 1.200348105 1.11979816 1 22.59857436 -5 0.209657767 0.255141059 1.181191809 0.331191248 0.077572644 186.2465314 1.856933852 58.49694806 0.154887128 1.00E-05 5 0.92605075 SQSS(ph)DTEQQSPTSGGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SQSS(1)DTEQQSPTSGGGK;SQSS(1)DTEQQSPTSGGGK;SQSS(1)DTEQQSPTSGGGK;SQS(0.036)S(0.964)DTEQQSPTSGGGK;SQSS(1)DTEQQSPTSGGGK;SQS(0.006)S(0.994)DTEQQSPTSGGGK;SQS(0.026)S(0.974)DTEQQSPTSGGGK;SQS(0.053)S(0.947)DTEQQSPTSGGGK 423.03 1.88E-160 7803726000 7463680 5773140 6194160 6026030 6297160 5019788 7763650 5372690 7152940 TRUE FALSE 6996541.592 6200589.293 6341088.4 6180668.132 5802606.455 6468919.306 6599562.757 6043482.173 5959068.104 1.174099955 1.040530027 1.064107389 1.037187027 0.97374394 1.085558882 1.107482351 1.014165649 1 22.5066553 4.740840522 24.27004319 1.048520091 1.174100022 0.516088464 0.040013281 121.9947418 1298528.332 0.009585642 0.062905838 55060.54708 -4.740840522 0.12557993 SQSSDTEQQS(ph)PTSGGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SQSSDTEQQS(0.499)PT(0.499)S(0.002)GGGK;SQSSDTEQQS(0.974)PT(0.025)S(0.001)GGGK;SQSSDTEQQS(0.998)PT(0.002)SGGGK;SQSSDTEQQS(0.499)PT(0.499)S(0.003)GGGK;SQSSDTEQQS(0.969)PT(0.03)S(0.001)GGGK;SQSSDT(0.002)EQQS(0.997)PT(0.001)SGGGK;SQSSDTEQQS(0.975)PT(0.024)S(0.001)GGGK;SQSSDTEQQS(0.558)PT(0.221)S(0.221)GGGK;SQSSDTEQQS(0.882)PT(0.088)S(0.03)GGGK 404.8 3.06E-140 7983749000 8861030 6531058 7756414 7322495 7980266 5886654 8837130 6763936 8323782 TRUE FALSE 8306433.95 7014624.33 7940399.803 7510402.619 7353528.099 7586035.448 7512084.396 7608428.299 6934489.011 1.197843696 1.011556053 1.145059108 1.083050619 1.060428258 1.093957383 1.083293143 1.097186583 1 22.72535815 -5 0.267015827 0.387700286 1.098077197 0.284885201 0.04865458 275.1551403 2.683256612 92.79157872 0.054823754 1.00E-05 5 0.71037691 SQSSDTEQQSPT(ph)SGGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SQSSDTEQQS(0.223)PT(0.774)S(0.002)GGGK;SQSSDTEQQS(0.245)PT(0.753)S(0.002)GGGK 322.83 1.07E-57 2025020000 2375100 1770360 2120300 1942130 2166760 1658630 2388300 1900230 2250300 TRUE FALSE 2226446.731 1901439.296 2170594.517 1991968.344 1996591.41 2137449.555 2030196.587 2137477.898 1874710.393 1.187621693 1.014257618 1.157829244 1.062547235 1.065013251 1.140149201 1.082938781 1.140164319 1 20.83823631 SQSSHS(ph)YDDSTLPLIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQSSHSYDDSTLPLIDR 17 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;H0YC95 O60716-13 CTNND1 Catenin delta-1 1 S(0.002)QS(0.015)S(0.135)HS(0.849)YDDSTLPLIDR;SQSSHS(1)YDDSTLPLIDR 205.39 5.10E-12 494300000 210807 320740 314690 317370 319260 268170 352790 282330 415730 TRUE FALSE 197612.9662 344487.9233 322154.5954 325514.2515 294186.6074 345586.3256 299892.4146 317579.522 346341.9773 0.570571802 0.994646754 0.930163297 0.939863698 0.849410775 0.997818192 0.865885265 0.916953597 1 18.40183773 4.744559587 24.97272346 0.932785974 0.570571642 0.830514712 0.051970553 249.2404906 1037517.394 0.011522973 0.105340826 55534.08072 -4.744559587 -0.362214332 SQSSHSYDDSTLPLIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SQSSHSYDDSTLPLIDR 17 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;H0YC95 O60716-13 CTNND1 Catenin delta-1 0 ;;; 251.35 5.70E-22 1700700000 422872 783461 701984 734401 843859 632796 766841 721968 847593 FALSE TRUE 396405.1964 841469.2676 718635.392 753246.973 777585.7181 815473.9326 651860.3111 812107.294 706124.2526 0.561381648 1.191673087 1.017718042 1.066734318 1.101202395 1.154858978 0.923152418 1.150091207 1 19.42956254 4.746826852 24.99135113 1.07237935 0.561381393 0.800886994 0.080575003 444.6909784 1344406.269 0.018281967 0.207825239 55824.75838 -4.746826852 -0.510997957 SQSSNDTFPTAMHIAAAIEVHEVLLPGLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQSSNDTFPTAMHIAAAIEVHEVLLPGLQK 30 0 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 ; 120.33 1.43E-05 148875000 520920 468870 470120 430630 582750 397370 509440 485890 694200 FALSE TRUE 488316.5471 503585.6227 481271.4684 441680.6949 536983.1657 512084.2682 433054.2014 546554.4361 578333.5353 0.844351083 0.870752934 0.832169395 0.76371275 0.928500827 0.885447993 0.748796629 0.945050568 1 19.14154224 1.036376766 7.808641848 0.999932137 0.839966278 0.537900291 0.052780336 0.133777697 23.07337892 0.04901557 0.012278343 10.87368546 -1.036376766 -0.159965859 SQT(ph)PERPAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQTPERPAKK 10 2 A8CG34-2;A8CG34;A6NF01;C9JFL1;Q96HA1-2;Q96HA1-3;Q96HA1 A8CG34-2;Q96HA1-2 POM121C;POM121B;POM121 Nuclear envelope pore membrane protein POM 121C;Putative nuclear envelope pore membrane protein POM 121B;Nuclear envelope pore membrane protein POM 121 1 S(0.001)QT(0.999)PERPAKK;SQT(1)PERPAKK 128.31 0.00053528 480970000 767380 407590 533740 475720 524210 399110 720230 437610 689490 TRUE FALSE 719351.0556 437768.3877 546400.5649 487927.7806 483040.6612 514326.578 612238.1978 492246.5718 574409.6647 1.252331045 0.762118771 0.95123846 0.84944215 0.840934077 0.895400286 1.065856366 0.85696081 1 19.1317205 SQT(ph)PPGVAT(ph)PPIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQTPPGVATPPIPK 14 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 2 S(0.4)QT(0.6)PPGVAT(1)PPIPK 100.45 0.010916 0 120270 68470 96906 93367 92884 87028 127960 91652 153900 TRUE FALSE 112742.5154 73539.59004 99204.65608 95762.95529 85589.26532 112151.5708 108773.5859 103094.954 128213.0958 0.879336972 0.573573156 0.773748231 0.746904633 0.667554783 0.874727891 0.848381246 0.804090669 1 16.9681841 1.270035309 0.466303488 0.999363982 0.697130657 0.429836263 0.08950084 0.759890838 0.454033713 0.095842823 0.056015994 18.62238536 -1.270035309 -0.302233325 SQT(ph)PPGVATPPIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SQTPPGVATPPIPK 14 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 S(0.001)QT(0.999)PPGVATPPIPK;S(0.001)QT(0.999)PPGVATPPIPK;S(0.001)QT(0.999)PPGVATPPIPK 163.99 4.69E-05 2457280000 2297860 1635310 1808910 1692700 1828800 1451330 2327140 1570600 2296200 TRUE FALSE 2154041.044 1756390.054 1851818.199 1736137.548 1685173.425 1870305.411 1978206.961 1766692.867 1912949.386 1.126031384 0.918158142 0.96804349 0.907571084 0.880929437 0.977707735 1.034113592 0.923543968 1 20.86736727 2.008793752 24.98419733 0.993734868 0.951125577 0.015318651 0.071013345 522.7793887 1485278.129 0.024939609 0.01839511 102.045475 -2.008793752 -0.042609291 SQT(ph)PPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SQTPPRR 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.191)QT(0.809)PPRR;S(0.009)QT(0.991)PPRR;S(0.007)QT(0.993)PPRR;S(0.011)QT(0.989)PPRR;S(0.003)QT(0.997)PPRR;S(0.199)QT(0.801)PPRR 78.113 0.021223 4704614000 777161 706086 740191 748777 738203 611340 843372 625372 753006 TRUE FALSE 728519.8803 758365.3421 757748.6801 767991.8855 680227.5141 787823.9337 716916.1981 703451.0708 627324.434 1.161312777 1.208888577 1.207905573 1.224233975 1.084331292 1.255847678 1.142815678 1.121351302 1 19.25885223 0.868111877 1.20367264 1.000219848 1.192996429 0.621387012 0.046315175 0.372359833 1.052872889 0.039212423 0.012122643 7.380943431 -0.868111877 0.192776581 SQTEAVTFLANHDDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SQTEAVTFLANHDDSR 16 0 B4DEM9;Q9Y2S7 B4DEM9 POLDIP2 Polymerase delta-interacting protein 2 0 ;;;; 214.54 1.69E-14 2126468000 1551500 1584670 1570620 1518410 2018440 1523630 1595910 1615270 2569770 FALSE TRUE 1454394.385 1702000.616 1607875.848 1557374.971 1859919.864 1963477.247 1356618.111 1816940.015 2140858.786 0.679350919 0.795008352 0.75104246 0.727453385 0.868772792 0.91714468 0.6336794 0.848696807 1 21.02975821 -5 0.288973652 2.746468447 0.760143068 0.419469176 0.084493165 247.334612 2.335196621 260.3480532 0.087578263 1.00E-05 5 -1.986325378 SQTGDVS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 SQT(0.001)GDVS(0.999)PK;SQT(0.004)GDVS(0.996)PK;SQTGDVS(1)PK 115.05 0.001614 200450000 583070 399953 438503 444889 461931 304712 474050 371271 555900 TRUE FALSE 546576.6895 429565.9363 448904.4982 456305.6049 425652.8026 392677.4078 402970.6034 417625.0016 463116.6987 1.180213737 0.92755441 0.969311837 0.985292921 0.919104847 0.847901639 0.870127561 0.901770553 1 18.82101625 7.23437919 1.288840981 0.917560272 199.9999978 0.701315877 0.050686379 651.7047042 1.89548641 0.0146809 382674.5285 17154544.48 -7.23437919 199.0824375 SQTTTERDS(ph)DT(ph)DVEEEELPVENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SQTTTERDSDTDVEEEELPVENR 23 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 2 SQTTT(0.001)ERDS(0.999)DT(1)DVEEEELPVENR;S(0.001)QT(0.003)T(0.002)T(0.012)ERDS(0.983)DT(1)DVEEEELPVENR;S(0.002)QT(0.016)T(0.02)T(0.016)ERDS(0.946)DT(1)DVEEEELPVENR;SQTTT(0.001)ERDS(0.999)DT(1)DVEEEELPVENR;SQTTTERDS(1)DT(1)DVEEEELPVENR 234.35 1.05E-36 2825100000 744917 787005 758930 772147 783988 605666 842612 618907 648781 TRUE FALSE 698293.9747 845275.6691 776932.178 791961.5993 722416.7449 780511.942 716270.153 696178.9013 540495.2598 1.291952079 1.563890994 1.437444943 1.465251702 1.336582943 1.444068061 1.325210795 1.288038866 1 19.04392244 0.580814776 0.528504868 0.980401375 1.462126478 0.755913316 0.074750891 0.70611835 0.378382069 0.096478744 0.033688988 3.809033358 -0.580814776 0.481725103 SQTTTERDS(ph)DTDVEEEELPVENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQTTTERDSDTDVEEEELPVENR 23 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 SQTTTERDS(1)DTDVEEEELPVENR;SQT(0.002)T(0.001)T(0.002)ERDS(0.93)DT(0.064)DVEEEELPVENR 339.78 3.54E-87 986800000 383920 319840 382140 335180 426750 344400 321240 299409 277086 TRUE FALSE 359891.1325 343521.2864 391204.5413 343781.2863 393234.7764 443822.6891 273073.0442 336790.8727 230838.5566 1.559059881 1.488145185 1.694710568 1.489271512 1.703505611 1.922654065 1.18296115 1.458988818 1 17.81652469 1.15262026 1.255453802 1.040030815 1.614860205 0.530727954 0.178912528 0.319067398 1.018165325 0.156978222 0.049311307 14.21085671 -1.15262026 0.574829391 SQVDHVIWPDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQVDHVIWPDGK 12 0 O43865-2;O43865;H0Y8B3;Q96HN2-4;Q96HN2-3;Q96HN2-2;Q96HN2 O43865-2 AHCYL1;AHCYL2 Putative adenosylhomocysteinase 2;Adenosylhomocysteinase;Putative adenosylhomocysteinase 3 0 ; 93.348 0.0072229 313100000 753360 693380 744230 705770 824250 630660 888750 796790 865910 FALSE TRUE 706208.5424 744718.5767 761883.4871 723881.2531 759516.7299 812721.3041 755490.1883 896270.9855 721384.027 0.978963376 1.032346918 1.056141332 1.003461715 1.052860476 1.126613944 1.047278786 1.242432535 1 19.46040795 2.419043543 5.127340273 1.101763792 1.026597766 0.280436754 0.064524943 0.271922134 14.72516466 0.020410177 0.017086558 262.4481666 -2.419043543 -0.075166026 SQVDHVIWPDGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQVDHVIWPDGKR 13 1 O43865-2;O43865;H0Y8B3;Q96HN2-4;Q96HN2-3;Q96HN2-2;Q96HN2 O43865-2 AHCYL1;AHCYL2 Putative adenosylhomocysteinase 2;Adenosylhomocysteinase;Putative adenosylhomocysteinase 3 0 ; 110.44 0.00068712 163379000 301100 341330 341630 326670 414800 262190 404620 338220 500900 FALSE TRUE 282254.6885 366602.4284 349733.6249 335052.9053 382223.2812 337879.9967 343950.9873 380447.5115 417296.5541 0.676388735 0.878517747 0.838093729 0.802913185 0.915951204 0.809687963 0.824236347 0.91169579 1 18.67071348 -5 0.136221953 1.561009667 0.772528923 0.511530619 0.059964689 128.4995566 1.085449672 19.59178099 0.377686964 1.00E-05 5 -0.788480743 SQVEEELFSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SQVEEELFSVR 11 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 240.8 2.48E-15 398453000 431363 581820 513788 552984 595880 438718 611910 488949 520119 FALSE TRUE 404364.7598 624898.5582 525975.294 567174.5056 549081.9885 565368.7646 520159.7762 549995.359 433307.7788 0.933204479 1.442158643 1.213860724 1.308941435 1.26718701 1.304774094 1.200439507 1.269294912 1 18.72503261 -1.026181642 3.991733133 0.999966936 1.258945246 0.250481295 0.129058418 16929532.45 41391837.73 8227.579564 0.027314819 0.094149574 1.026181642 0.25897831 SQWLDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SQWLDVK 7 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 157.86 0.0033674 1086780000 2246720 2234940 2100230 2052020 2880760 1495810 2466530 2434690 4250300 FALSE TRUE 2106101.806 2400417.283 2150048.447 2104678.307 2654516.73 1927626.065 2096696.725 2738666.406 3540897.472 0.594793219 0.677912112 0.607204378 0.594391203 0.749673423 0.544389122 0.59213709 0.773438493 1 21.75568364 0.954558517 3.551752795 0.999421008 0.625331239 0.824050308 0.056271103 0.094540851 3.16909124 0.051311348 0.013252794 9.006551088 -0.954558517 -0.37408977 SQWVAPSSVVLHDEGQNEEDVEKEEETER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SQWVAPSSVVLHDEGQNEEDVEKEEETER 29 1 Q9Y2L1;G3V1J5;Q9Y2L1-2;F2Z2C0 Q9Y2L1 DIS3 Exosome complex exonuclease RRP44 0 150.4 2.24E-08 65719000 45318 34849 38173 41563 41595 29132 50431 35436 52452 FALSE TRUE 42481.62727 37429.25622 39078.48159 42629.57695 38328.29649 37541.93548 42869.33973 39860.2626 43697.42235 0.972176961 0.856555243 0.89429718 0.975562737 0.87712946 0.859133868 0.981049623 0.912187961 1 15.41526056 0.924745322 0.772636496 0.998274962 0.901894042 0.224399193 0.047307177 0.989873952 1.294087294 0.043605382 0.016121552 8.409018778 -0.924745322 -0.09638092 SRADLES(ph)PQRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRADLESPQRK 11 2 A0A087X1K6;Q9Y2Y9 A0A087X1K6 KLF13 Krueppel-like factor 13 1 SRADLES(1)PQRK;SRADLES(1)PQRK 100.54 0.0031121 385440000 371190 298190 292040 279200 406120 231495 422410 344560 494180 TRUE FALSE 347957.8805 320268.2979 298967.3267 286364.7447 374224.9734 298323.8485 359073.542 387579.0745 411698.1655 0.845177146 0.777920148 0.726180857 0.69556964 0.908978968 0.724617872 0.872176687 0.941415598 1 18.65122749 1.329599136 1.621703156 0.998630511 0.773000436 0.611995699 0.063037831 0.218046586 1.041466241 0.053744708 0.016503422 21.3598961 -1.329599136 -0.225630075 SRAS(ph)PVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SRASPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.255)RAS(0.742)PVS(0.003)R;S(0.105)RAS(0.894)PVS(0.001)R;S(0.114)RAS(0.885)PVS(0.001)R 65.241 0.039232 5814470000 824616 826675 825487 813728 786295 766374 942441 684806 790029 TRUE FALSE 773004.7565 887882.8772 845067.9415 834609.6381 724542.5625 987613.7328 801130.7212 770305.5365 658168.0561 1.174479298 1.349021529 1.283969852 1.268079832 1.100847353 1.500549478 1.217213011 1.170378187 1 19.32809648 0.977730435 2.190709646 1.002737957 1.283745057 0.405102544 0.105411661 0.289703984 3.044919419 0.09021305 0.024864251 9.500149391 -0.977730435 0.2810071 SRDEIVEMIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRDEIVEMIR 10 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 194.17 4.50E-07 224656000 126409 154681 138978 132268 186633 105200 138842 143601 168610 FALSE TRUE 118497.2863 166133.7422 142274.6238 135662.2208 171975.597 135569.5322 118023.931 161529.901 140467.9017 0.84358978 1.182716764 1.01286217 0.965788049 1.224305303 0.965128193 0.840219933 1.149941723 1 17.09988097 2.050198023 24.99965376 0.959891847 1.059572733 0.01914166 0.129947142 215.8755433 107509.4701 0.044954551 0.033201129 112.2530172 -2.050198023 0.099680886 SRDPFWNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRDPFWNR 8 1 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ; 121.05 0.0013223 267940000 94851 178997 125878 135414 191300 97252 145802 194118 155588 FALSE TRUE 88914.44522 192250.1241 128863.8856 138888.9525 176276.0697 125327.0736 123940.3437 218354.0596 129619.3577 0.685965791 1.483189915 0.994171611 1.07151397 1.35995173 0.966885471 0.956186992 1.68457909 1 16.98392166 1.27839027 24.99986725 1.342297192 1.103179904 0.136298266 0.27321149 272.1270746 170805.6917 0.165257581 0.060343782 18.98411126 -1.27839027 -0.239117288 SRDPQLCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SRDPQLCR 8 1 Q8TAT6;Q8TAT6-2;I3L4S2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ;;; 116.05 0.0021395 551887000 283552 496478 344188 356596 499508 299388 330303 377811 481000 FALSE TRUE 265804.9865 533237.7477 352352.3019 365746.8571 460278.6566 385816.4554 280777.1315 424981.535 400717.9926 0.663321816 1.330705777 0.879302423 0.912728811 1.148634863 0.962812907 0.700685112 1.06055017 1 18.61222776 1.991803587 24.58086756 0.87330316 1.019095097 0 0.197827842 691.884175 2074947.095 0.071460215 0.050329008 98.13040395 -1.991803587 0.145791937 SRDS(ph)DESGDKTTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRDSDESGDKTTR 13 2 A0A0A0MSK5;J3KN66;Q5JTV8;Q5JTV8-3;H0YD16;Q5JTV8-2;H0YDU3 A0A0A0MSK5 TOR1AIP1 Torsin-1A-interacting protein 1 1 S(0.005)RDS(0.995)DESGDKTTR;SRDS(0.712)DES(0.266)GDKT(0.02)T(0.001)R 123.19 0.00011808 505850000 684800 481900 415050 432960 482380 308860 626470 406290 544570 TRUE FALSE 641939.5904 517580.3774 424895.182 444070.4866 444495.8206 398022.8681 532536.6394 457016.2009 453677.7489 1.414968206 1.140854667 0.936557244 0.978823598 0.979761123 0.877325082 1.173821376 1.007358642 1 18.79130838 4.725645292 1.765979096 1.002463214 1.547250721 0.760968331 0.075283974 0.44786675 1.436631874 0.020085018 0.406519245 53167.384 -4.725645292 0.544787508 SRDSFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRDSFLK 7 1 P46778;M0R181 P46778 RPL21 60S ribosomal protein L21 0 81.548 0.024536 206050000 288750 291520 230000 304500 380430 219470 383050 354490 584550 FALSE TRUE 270677.6529 313104.4441 235455.7086 312313.9855 350552.5624 282827.4262 325615.2086 398748.8568 486984.8287 0.555823584 0.642944966 0.48349701 0.641321797 0.719842882 0.580772561 0.668635221 0.818811662 1 18.8935173 1.031346972 1.272958501 1.002494911 0.594937322 0.820210109 0.061628562 0.184717167 0.615804227 0.058140954 0.017935465 10.74847801 -1.031346972 -0.407557589 SRDYNGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRDYNGR 7 1 P98179 P98179 RBM3 RNA-binding protein 3 0 ; 113.7 0.0055374 43709000 39554 45595 35216 47600 45961 34500 61170 43500 83599 FALSE TRUE 37078.38575 48970.90124 36051.34015 48821.49659 42351.40846 44459.58994 51998.12637 48931.07076 69645.78683 0.532385194 0.703142336 0.517638493 0.700997129 0.608097207 0.638367258 0.746608356 0.702570435 1 16.08774846 0.26581233 0.433800342 1.040733996 0.598321933 0.783076478 0.062733078 1.26055628 0.377307584 0.15386505 0.036167826 1.84421831 -0.26581233 -0.442412064 SREDAGDNDDTEGAIGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SREDAGDNDDTEGAIGVR 18 1 Q9H0S4;Q9H0S4-2 Q9H0S4 DDX47 Probable ATP-dependent RNA helicase DDX47 0 106.34 0.00041216 222850000 26295 33806 45834 44047 37825 32835 41062 34807 46090 FALSE TRUE 24649.24289 36309.03142 46921.20412 45177.32059 34854.37708 42313.93147 34905.1343 39152.73057 38397.28125 0.641952818 0.945614643 1.221992876 1.176576026 0.907730338 1.102003321 0.909052234 1.019674552 1 15.22871654 4.695965509 2.75418035 1.04903725 0.585699879 0.614298828 0.101112226 0.27433883 3.036410001 0.025842587 0.275205052 49655.28841 -4.695965509 -0.463337371 SREDLS(ph)AQPVQTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SREDLSAQPVQTK 13 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 S(0.001)REDLS(0.999)AQPVQTK 220.32 5.52E-11 400280000 870360 561310 719120 641040 727860 548570 857480 611890 929550 TRUE FALSE 815885.7212 602869.9764 736177.866 657490.1717 670696.8116 706933.2537 728908.8345 688285.8134 774402.0999 1.053568581 0.778497342 0.950640328 0.849029428 0.86608341 0.91287621 0.941253691 0.888796419 1 19.56272334 0.313578765 0.565397187 1.004219005 0.889903571 0.121682673 0.072896712 4.289804792 2.075979183 0.114200622 0.029132456 2.058632215 -0.313578765 -0.114315435 SREDMIDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SREDMIDIK 9 1 P20340-2;P20340;P20340-4;P20340-3;F5H3K7 P20340-2 RAB6A Ras-related protein Rab-6A 0 110.84 0.0020266 156340000 254950 256000 232870 237080 295990 174000 310500 298450 370840 FALSE TRUE 238993.1346 274954.5064 238393.7864 243163.8742 272744.1394 224230.9753 263943.4075 335712.1395 308944.4083 0.773579739 0.889980524 0.771639751 0.787079706 0.882825946 0.725797164 0.854339488 1.08664255 1 18.23698774 1.324114281 5.225876539 1.041771964 0.812297339 0.7602435 0.054356115 0.085383086 3.604558006 0.035546646 0.012323035 21.09183091 -1.324114281 -0.229474625 SREDMTEAEQIIFDHFSDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SREDMTEAEQIIFDHFSDPK 20 1 Q14997;Q14997-3;Q14997-2 Q14997 PSME4 Proteasome activator complex subunit 4 0 ;; 180.32 3.31E-17 54094000 67685 92935 93754 94591 90108 76044 115645 83063 114501 FALSE TRUE 63448.71667 99816.0041 95977.88915 97018.3652 83031.28116 97996.66833 98305.10585 93433.59839 95390.0434 0.665150307 1.046398561 1.006162548 1.017070144 0.870439704 1.027325964 1.0305594 0.97949005 1 16.54155107 4.743235692 24.99639028 1.001427096 0.665150172 0.820202269 0.048819371 195.1936705 1043613.418 0.011414268 0.092776171 55365.04946 -4.743235692 -0.336276924 SREDVSNFDPDFIKEEPVLT(ph)PIDEGHLPMINQDEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SREDVSNFDPDFIKEEPVLTPIDEGHLPMINQDEFR 36 2 P24723-2;P24723 P24723-2 PRKCH Protein kinase C eta type 1 SREDVSNFDPDFIKEEPVLT(1)PIDEGHLPMINQDEFR 104.92 2.64E-05 24889000 16235 15186 17835 19692 22782 13612 24204 15918 21854 TRUE FALSE 15218.88033 16310.38724 18258.05462 20197.33006 20992.79362 17541.56343 20574.8349 17905.39734 18206.42622 0.835907066 0.895858805 1.002835724 1.10935171 1.153043072 0.963481972 1.130086413 0.98346579 1 14.15216014 3.942009023 1.509598262 1.064424099 0.850643824 0.589602423 0.06444564 0.269705571 1.151025672 0.017360233 0.054607133 8750.019538 -3.942009023 -0.213780275 SRENLS(ph)AVMLYNPGLEFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRENLSAVMLYNPGLEFER 19 1 Q96L93-5;Q96L93-6;Q96L93-4;Q96L93;Q96L93-2;A0A1B0GTU3 Q96L93-5 KIF16B Kinesin-like protein KIF16B 1 S(0.262)RENLS(0.738)AVMLYNPGLEFER 183.25 1.66E-14 647550000 112100 104930 97165 109920 115240 76492 128590 94461 109160 TRUE FALSE 105083.8611 112699.1264 99469.79968 112740.7333 106189.5153 98573.99866 109309.1233 106254.6638 90940.4908 1.155523356 1.23926235 1.093790003 1.239719868 1.167681352 1.083939594 1.201985192 1.168397738 1 16.47263517 -4.139532576 0.355428303 4.12E-12 1.174749475 0.513339384 0.051696996 186.5623706 2.753581724 139.5146807 0.035979212 7.25E-05 4.139532576 1.174749475 SREPQAKPQLDLS(ph)IDSLDLSCEEGTPLSITSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SREPQAKPQLDLSIDSLDLSCEEGTPLSITSK 32 2 Q14980;Q14980-2;A0A087WY61;Q14980-5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 SREPQAKPQLDLS(0.998)IDS(0.002)LDLSCEEGTPLSITSK 232.25 1.76E-37 74671000 171000 110080 119110 120540 145310 82228 207060 132790 188080 TRUE FALSE 160297.4152 118230.4377 121935.3454 123633.2605 133897.9388 105965.8887 176013.2753 149369.1238 156688.233 1.023034163 0.754558498 0.77820359 0.789039854 0.854550059 0.676284918 1.123334356 0.953288712 1 17.25753731 1.728621377 12.45485402 1.026802034 0.802673364 0.511954755 0.097650376 0.064416529 45.87119205 0.041233553 0.022603088 53.53297468 -1.728621377 -0.22412867 SRFS(ph)GGFGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SRFSGGFGAR 10 1 A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7 A0A2R8YFS5 1 S(0.087)RFS(0.913)GGFGAR;S(0.004)RFS(0.996)GGFGAR;S(0.001)RFS(0.999)GGFGAR;SRFS(1)GGFGAR;SRFS(1)GGFGAR 145.83 1.80E-05 1779930000 659452 795183 746379 678715 860613 593942 709865 667616 950135 TRUE FALSE 618178.0765 854059.1767 764083.4623 696131.976 793023.9265 765403.4136 603427.3333 750969.3272 791551.3304 0.780970296 1.078968784 0.96529869 0.879452727 1.001860392 0.96696624 0.762335063 0.948731053 1 19.59432338 SRGEVEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRGEVEEK 8 1 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 0 72.643 0.043799 0 148310 126090 141040 131190 151860 119540 176820 133220 179360 FALSE TRUE 139027.5418 135425.8348 144385.5354 134556.5575 139933.5282 154049.2574 150307.4825 149852.8103 149423.6573 0.930425238 0.906321243 0.96628297 0.900503708 0.936488443 1.030956277 1.005914895 1.002872055 1 17.18904905 2.285411235 7.417276105 1.01062142 0.928699085 0.815861669 0.019346329 0.085195367 11.12339479 0.006489252 0.005377354 192.9350959 -2.285411235 -0.081922335 DKVVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 DKVVGK 6 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85 P47756-2 CAPZB F-actin-capping protein subunit beta 0 80.18 0.059458 1435000000 2405300 2431700 2917100 3746500 4717000 3152700 5556900 4285400 5833500 FALSE TRUE 2254756.567 2611745.598 2986294.99 3842641.533 4346545.847 4062833.31 4723694.433 4820441.623 4859851.164 0.463955889 0.537412672 0.614482808 0.790691197 0.894378387 0.835999534 0.971983354 0.991890793 1 22.2124807 3.190439012 0.608451232 0.999169964 0.436668603 0.962327744 0.037272401 0.153601159 0.120700736 0.025404191 0.046719822 1550.383052 -3.190439012 -0.562501361 down SRIPS(ph)PLQPEMQGTPDDEPSEPEPSPSTLIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SRIPSPLQPEMQGTPDDEPSEPEPSPSTLIYR 32 1 Q96GY3;K7EMY4 Q96GY3 LIN37 Protein lin-37 homolog 1 SRIPS(1)PLQPEMQGTPDDEPSEPEPSPSTLIYR;SRIPS(1)PLQPEMQGTPDDEPSEPEPSPSTLIYR;SRIPS(1)PLQPEMQGTPDDEPSEPEPSPSTLIYR;SRIPS(1)PLQPEMQGTPDDEPSEPEPSPSTLIYR;S(0.02)RIPS(0.978)PLQPEMQGT(0.003)PDDEPSEPEPSPSTLIYR;SRIPS(0.998)PLQPEMQGT(0.002)PDDEPSEPEPSPSTLIYR;S(0.001)RIPS(0.999)PLQPEMQGT(0.001)PDDEPSEPEPSPSTLIYR 262.95 1.13E-59 1816662000 629464 710436 643723 675447 774140 499205 730367 673472 989819 TRUE FALSE 590066.9719 763037.4206 658992.4135 692780.1135 713342.1671 643317.3796 620855.2487 757556.4617 824611.8144 0.715569389 0.925329236 0.799154708 0.840128775 0.865064209 0.780145722 0.75290608 0.918682522 1 19.65335561 1.01620164 5.814207824 0.999792614 0.819566914 0.543829342 0.058650718 0.106900245 12.652854 0.055361828 0.013935408 10.38010245 -1.01620164 -0.1802257 SRKS(ph)PHKDLGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRKSPHKDLGHR 12 3 O94888;C9JAT7 O94888 UBXN7 UBX domain-containing protein 7 1 S(0.136)RKS(0.864)PHKDLGHR 117.4 0.0003002 615850000 291640 207500 226340 232740 315160 153560 263900 224660 543490 TRUE FALSE 273386.773 222863.5159 231708.8917 238712.5024 290408.6049 197890.2792 224330.6449 252709.2955 452778.0079 0.603798701 0.49221365 0.511749439 0.527217529 0.641392912 0.437058063 0.495453933 0.558130676 1 18.78844436 0.815233745 5.89580461 0.99999961 0.522240382 0.866506933 0.057602358 2.027974635 64.65648501 0.052160325 0.013121077 6.534821733 -0.815233745 -0.477759228 SRLDQELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRLDQELK 8 1 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 ; 99.013 0.0064886 1512890000 1639520 2296000 1622020 1534950 2510100 1324290 1691390 2102000 2330800 FALSE TRUE 1536905.37 2465998.229 1660495.08 1574339.416 2312966.871 1706591.025 1437781.772 2364439.327 1941774.422 0.791495321 1.269971527 0.855143142 0.810773588 1.191161468 0.878882225 0.740447374 1.217669416 1 20.88894418 3.754791801 21.94821032 0.932831128 1.064204766 0.007591471 0.191469449 232.8586193 184697.7201 0.045791715 0.082501598 5685.802905 -3.754791801 0.131373638 SRLEEEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRLEEEKR 8 2 Q9Y6D9;Q9Y6D9-3 Q9Y6D9 MAD1L1 Mitotic spindle assembly checkpoint protein MAD1 0 52.255 0.08103 150120000 297230 243890 293400 334060 227700 209590 319590 222240 283750 FALSE TRUE 278626.9049 261947.8694 300359.5866 342632.5452 209817.3605 270095.2306 271670.4464 249987.1532 236390.2919 1.178673213 1.10811602 1.270608806 1.449435772 0.887588736 1.142581738 1.149245361 1.057518696 1 17.85081126 2.731006093 24.99806549 1.072099437 1.230926441 0.428180571 0.114264912 714.9072287 2365634.955 0.036857875 0.03535029 538.277334 -2.731006093 0.158827004 SRLNS(ph)HGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SRLNSHGGR 9 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IU26;B1AN86 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 SRLNS(1)HGGR;S(0.001)RLNS(0.999)HGGR;S(0.016)RLNS(0.984)HGGR 88.338 0.0077832 341090000 111620 136612 107959 176662 235752 97462 120012 115653 259694 TRUE FALSE 104633.9034 146726.8946 110519.8385 181195.446 217236.9889 125597.6972 102017.3147 130092.5316 216349.3937 0.483633911 0.678194157 0.510839603 0.837513075 1.004102601 0.580531774 0.471539638 0.601307586 1 17.72300355 5.578079309 0.792944028 0.684844502 1.44E-11 0.100943565 0.189299936 25.14903506 4.557967804 0.066328011 20.76057026 378511.7008 -5.578079309 -0.684844502 SRLT(ph)PVSPESSSTEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SRLTPVSPESSSTEEK 16 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.345)RLT(0.655)PVSPESSSTEEK;S(0.203)RLT(0.796)PVS(0.001)PESSSTEEK;S(0.128)RLT(0.872)PVSPESSSTEEK 217.86 2.24E-14 2607650000 2049670 1340470 1713350 1528950 1875260 1423110 2110280 1621950 2395390 TRUE FALSE 1921384.813 1439719.794 1753991.471 1568185.446 1727984.644 1833938.755 1793863.105 1824454.028 1995583.934 0.962818341 0.721452888 0.878936456 0.785827857 0.865904267 0.918998556 0.898916389 0.914245699 1 20.92837953 1.512943484 0.563407519 0.993937866 0.819112999 0.352316587 0.064847544 0.697065376 0.527664549 0.058679199 0.032241837 32.5794302 -1.512943484 -0.174824866 SRLTPVS(ph)PESSSTEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRLTPVSPESSSTEEK 16 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.008)RLT(0.026)PVS(0.966)PESSSTEEK 170.11 3.26E-09 235340000 119320 74469 66225 80217 95014 54212 137380 95734 225690 TRUE FALSE 111851.9742 79982.76224 67795.88827 82275.50403 87551.98371 69862.12434 116781.1444 107686.6006 188020.881 0.594891236 0.425392977 0.360576378 0.437587057 0.465650322 0.371565775 0.621107314 0.572737454 1 17.52053337 0.67412594 0.816834646 1.001017195 0.429905144 0.826361652 0.077580836 0.410054712 0.497323283 0.071918246 0.02473045 4.721999531 -0.67412594 -0.571112051 SRNDQVVTDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRNDQVVTDLR 11 1 A0A5F9ZHC6;A0A5F9ZHM8;P04424-3;P04424-2;P04424;F8W943 A0A5F9ZHC6 ASL Argininosuccinate lyase 0 ; 89.403 0.01118 1532650000 969990 1231210 1029550 1176250 1200710 972410 1302830 1079650 1309890 FALSE TRUE 909280.0574 1322370.069 1053971.412 1206434.566 1106411.08 1253128.981 1107482.736 1214446.679 1091260.897 0.833238009 1.211781778 0.965828992 1.105541828 1.013883191 1.148331242 1.014865226 1.112883897 1 20.05756463 SRNPS(ph)KSHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRNPSKSHLR 10 2 Q92615 Q92615 LARP4B La-related protein 4B 1 SRNPS(0.965)KS(0.035)HLR;SRNPS(0.961)KS(0.039)HLR 96.464 0.0035077 157095000 145206 187724 119093 151355 253660 64029 169758 129694 255820 TRUE FALSE 136117.8157 201623.2803 121917.9422 155239.0255 233738.5668 82513.13288 144304.3639 145886.5814 213121.9893 0.63868499 0.946046351 0.572057077 0.728404544 1.096736041 0.387163864 0.677097489 0.684521489 1 17.70131993 2.225047177 24.9999336 0.652334037 0.783113791 0.051001509 0.20713387 587.2048835 1086324.915 0.071059478 0.05276963 167.8986394 -2.225047177 0.130779754 SRNS(ph)PLLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.011)RNS(0.989)PLLER;S(0.002)RNS(0.998)PLLER;SRNS(1)PLLER;SRNS(1)PLLER;S(0.035)RNS(0.965)PLLER;S(0.143)RNS(0.857)PLLER 158.11 4.06E-05 20902820000 2101630 2423110 2248150 2358200 2477220 1969520 2800460 1945170 2672540 TRUE FALSE 1970092.73 2602519.586 2301477.18 2418715.404 2282669.134 2538088.452 2380557.021 2188028.756 2226475.809 0.884848028 1.168896413 1.033686138 1.086342549 1.025238687 1.139957794 1.069204081 0.98273188 1 21.08633051 1.243086071 24.30578654 0.99136592 1.070549785 0.100881792 0.07658475 126.3293022 678546.4139 0.048897379 0.016477404 17.50193519 -1.243086071 0.079183865 LEAMCFDGVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 LEAMCFDGVKR 11 1 P47813;X6RAC9 P47813 EIF1AX "Eukaryotic translation initiation factor 1A, X-chromosomal" 0 121.68 0.00065191 445390000 718280 938560 870460 1057400 1352900 906770 1452100 1197300 1924100 FALSE TRUE 673324.137 1008051.959 891107.7223 1084534.674 1246648.691 1168539.779 1234371.086 1346785.541 1602955.28 0.420051729 0.628870918 0.555915523 0.676584486 0.777718946 0.728990879 0.77005959 0.840189092 1 20.61230275 4.03042091 0.129658207 1.159902984 4.49E-12 0.892567885 0.051836893 7.665122186 0.215198906 0.437603938 1.708521067 10725.58304 -4.03042091 -1.159902984 down SRPALS(ph)PLGDIDFCPPNPGPDGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SRPALSPLGDIDFCPPNPGPDGPR 24 1 Q9ULL5;Q9ULL5-2;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 S(0.074)RPALS(0.926)PLGDIDFCPPNPGPDGPR;S(0.017)RPALS(0.983)PLGDIDFCPPNPGPDGPR;S(0.035)RPALS(0.965)PLGDIDFCPPNPGPDGPR;S(0.001)RPALS(0.999)PLGDIDFCPPNPGPDGPR 177.1 2.62E-17 684330000 259922 269557 266574 260956 288870 291106 346774 259175 347705 TRUE FALSE 243653.946 289515.2808 272897.2612 267652.5728 266183.3154 375143.5765 294778.458 291533.5693 289670.7892 0.841140892 0.999463154 0.942094513 0.923988827 0.918916664 1.295068714 1.017632668 1.00643068 1 18.14405468 SRPFTVAASFQSTSVKS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRPFTVAASFQSTSVKSPK 19 2 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 SRPFTVAASFQSTS(0.001)VKS(0.999)PK;SRPFTVAASFQSTS(0.001)VKS(0.999)PK 182.4 1.53E-14 2477600000 2613800 1527100 1914720 2540900 2782900 1148150 1622280 1137090 2947300 TRUE FALSE 2450206.924 1640168.073 1960138.063 2606103.796 2564342.26 1479602.266 1379034.175 1279058.19 2455376.59 0.997894553 0.667990434 0.798304452 1.061386594 1.044378394 0.602596878 0.561638561 0.520921391 1 21.22751288 2.213920965 24.9944062 0.62577597 0.871369771 0.285273221 0.177775655 283.6698728 287752.2442 0.066120121 0.048854241 163.6518674 -2.213920965 0.245593802 SRPQGLTEAEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRPQGLTEAEQR 12 1 Q00653;Q00653-4;Q00653-3 Q00653 NFKB2 Nuclear factor NF-kappa-B p100 subunit;Nuclear factor NF-kappa-B p52 subunit 0 ; 89.663 0.0054639 0 195439 229749 189062 195526 245970 139962 230512 207291 240570 FALSE TRUE 183206.8219 246759.855 193546.6399 200543.5282 226652.5084 180366.7573 195948.8656 233171.7377 200417.3129 0.914126725 1.231230234 0.965718167 1.000629763 1.13090284 0.899955971 0.977704285 1.163431114 1 17.61264761 3.749246765 23.89490763 1.013105914 1.096272426 0.027293472 0.107751594 548.3014203 592143.5723 0.025354523 0.045648204 5613.668523 -3.749246765 0.083166511 SRPT(ph)S(ph)EGSDIESTEPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 2 S(0.032)RPT(0.932)S(0.938)EGS(0.098)DIESTEPQK 136.14 2.59E-05 939400000 1694900 1400700 1615000 1645300 1645500 1309200 1764700 1314300 1596600 TRUE FALSE 1588819.234 1504409.285 1653308.563 1687521.183 1516269.068 1687144.787 1500099.618 1478393.248 1330117.146 1.194495718 1.13103518 1.242979664 1.268701174 1.139951524 1.268418193 1.127795114 1.111475973 1 20.34312188 1.065300061 1.420197624 1.003212116 1.202157928 0.642442802 0.04949213 0.250917208 1.024812916 0.044107466 0.013281281 11.62251353 -1.065300061 0.198945812 SRPT(ph)SEGS(ph)DIESTEPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 2 SRPT(0.576)S(0.424)EGS(0.996)DIES(0.004)T(0.001)EPQK;SRPT(0.657)S(0.572)EGS(0.771)DIESTEPQK 190.83 6.93E-09 402030000 921080 688230 746590 791350 775570 539400 941130 626480 847950 TRUE FALSE 863431.247 739187.2653 764299.4674 811657.3808 714659.8607 695116.0236 800016.2935 704697.4071 706421.667 1.222260425 1.046382493 1.081930953 1.14897011 1.011661864 0.983995899 1.132491161 0.997559163 1 19.43017007 4.741359283 24.60109495 1.059276072 1.222260499 0.466221551 0.057098167 190.0958753 1670882.812 0.01262965 0.086808262 55126.35574 -4.741359283 0.162984427 SRPT(ph)SFADELAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRPTSFADELAAR 13 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;A0A0A0MT65 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 S(0.315)RPT(0.343)S(0.343)FADELAAR 99.711 0.017421 60415000 115300 132800 124790 180190 194820 89625 110560 76058 116330 TRUE FALSE 108083.5788 142632.6502 127750.0777 184813.9805 179519.6231 115498.2826 93982.55439 85554.00872 96913.77148 1.115255109 1.471748009 1.318182914 1.906993997 1.85236443 1.191763367 0.96975438 0.882784845 1 16.56441407 2.021929626 6.879118827 0.978800313 1.514245327 0.574006313 0.230485345 0.128849602 24.3291499 0.092671132 0.06651831 105.1791427 -2.021929626 0.535445014 SRPTS(ph)EGSDIES(ph)TEPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 2 S(0.002)RPT(0.169)S(0.825)EGS(0.353)DIES(0.522)T(0.128)EPQK;SRPT(0.077)S(0.92)EGS(0.268)DIES(0.635)T(0.1)EPQK 203.06 1.20E-10 278301000 776440 614700 658410 667410 675660 485400 795860 546890 709790 TRUE FALSE 727844.0064 660213.0276 674027.7961 684536.8705 622596.3891 625527.1002 676528.1814 615170.4204 591321.4636 1.230877029 1.11650442 1.139866955 1.15763914 1.052889887 1.057846093 1.144095425 1.040331627 1 19.17358312 7.999999992 0.071856626 0.885498879 1.651714636 0.628508803 0.041455834 171.9202292 0.909507953 1.646311499 13.26673813 99999998.22 -7.999999992 0.766215757 SRPTSEGS(ph)DIESTEPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 1 SRPTSEGS(0.999)DIESTEPQK;S(0.024)RPT(0.153)S(0.153)EGS(0.67)DIESTEPQK;S(0.002)RPT(0.052)S(0.098)EGS(0.848)DIESTEPQK;S(0.001)RPT(0.061)S(0.109)EGS(0.828)DIESTEPQK 325.38 7.43E-59 4655970000 5016380 4025240 4206490 4221020 4527930 3657540 5555480 4034600 5421600 TRUE FALSE 4702413.73 4323272.958 4306269.929 4329338.519 4172324.643 4713412.423 4722487.349 4538328.691 4516699.935 1.041117143 0.957175154 0.953410674 0.958518073 0.923755109 1.04355226 1.045561453 1.004788619 1 22.10683764 2.224343041 24.9854915 1.029813353 0.963281998 0.415506436 0.032880181 189.6693725 333316.398 0.011622135 0.008624272 167.6266404 -2.224343041 -0.066531354 SRPVS(ph)MDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SRPVSMDAR 9 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 S(0.146)RPVS(0.854)MDAR;SRPVS(1)MDAR;S(0.024)RPVS(0.976)MDAR 101.72 0.005753 1324630000 1349360 1541440 1501420 1363680 2003650 1084530 1564670 1540040 2493920 TRUE FALSE 1264905.966 1655569.821 1537034.391 1398674.338 1846291.411 1397616.205 1330062.259 1732317.384 2077668.641 0.608810251 0.796840165 0.73978803 0.673194132 0.888636126 0.672684844 0.640170542 0.833779434 1 20.98653415 0.971246129 6.398557001 0.999961955 0.725412298 0.563635633 0.080517044 0.149782112 27.01247327 0.073948577 0.018572588 9.359359503 -0.971246129 -0.274549657 SRQELASGLPS(ph)PAATQELPVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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;SRQELASGLPS(1)PAATQELPVER;SRQELASGLPS(1)PAATQELPVER;SRQELASGLPS(1)PAATQELPVER;SRQELASGLPS(1)PAATQELPVER 243.49 5.55E-31 7192790000 4450540 5568898 5576099 8099850 8509520 2775683 2901525 2849401 3713833 TRUE FALSE 4171988.646 5981225.002 5708366.702 8307705.864 7841216.625 3576977.623 2466468.263 3205154.987 3093970.28 1.348425572 1.933187607 1.844997264 2.685127882 2.534354217 1.15611247 0.797185506 1.035935932 1 21.56102791 2.107208106 6.088794191 0.936138636 2.044955752 0.67751545 0.369197775 0.127277147 6.412872482 0.144903027 0.106354179 127.9994508 -2.107208106 1.108817116 SRQELASGLPSPAATQELPVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRQELASGLPSPAATQELPVER 22 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 135.54 1.18E-08 0 63904 53668 50535 52196 61564 50632 60559 48468 56373 FALSE TRUE 59904.36271 57641.63456 51733.71406 53535.43773 56729.01178 65248.63646 51478.74015 54519.33649 46963.98212 1.275538402 1.227358328 1.101561489 1.139925435 1.20792593 1.38933356 1.096132351 1.160875506 1 15.51926712 0.862718293 1.514055893 1.002803334 1.202432524 0.372788789 0.084920041 0.656634429 2.895953698 0.079348635 0.023199718 7.289844982 -0.862718293 0.19962919 SRQELEQHSVDTASTSDAVTFITYVQSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRQELEQHSVDTASTSDAVTFITYVQSLK 29 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 86.982 0.0011354 78617000 49867 54144 56933 61652 57207 39919 62845 53419 73079 FALSE TRUE 46745.91349 58152.8781 58283.47765 63234.0947 52714.19298 51442.96727 53421.97567 60088.47974 60881.64279 0.767816231 0.955179188 0.957324326 1.038639757 0.865847086 0.844966806 0.877472637 0.986972049 1 15.89371967 SRQPS(ph)PLLLLPPPAGLTSDPGPSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SRQPSPLLLLPPPAGLTSDPGPSVR 25 1 I3L2J0 I3L2J0 CIC 1 S(0.008)RQPS(0.992)PLLLLPPPAGLTSDPGPSVR;S(0.058)RQPS(0.942)PLLLLPPPAGLTSDPGPSVR;S(0.012)RQPS(0.988)PLLLLPPPAGLTSDPGPSVR;S(0.027)RQPS(0.973)PLLLLPPPAGLTSDPGPSVR 117.49 0.00060797 352291000 218715 223546 223123 247493 255948 203192 263846 212077 293830 TRUE FALSE 205026.0186 240097.5784 228415.5829 253844.0894 235846.8765 261850.2319 224284.7417 238555.2803 244787.8748 0.837566071 0.980839344 0.93311641 1.036996173 0.963474505 1.069702623 0.916241223 0.974538794 1 17.90117257 4.73905483 24.55892131 0.978864203 0.837566019 0.507534785 0.045156048 26.30136363 1306523.002 0.009979043 0.05888117 54834.61899 -4.73905483 -0.141298184 SRS(ph)APPNLWAAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSAPPNLWAAQR 13 1 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 S(0.016)RS(0.984)APPNLWAAQR;S(0.003)RS(0.997)APPNLWAAQR 192.16 1.79E-06 1445510000 325750 483080 328620 320200 568760 179193 305370 393120 533220 TRUE FALSE 305361.889 518847.7458 336415.0216 328416.8741 524091.8839 230923.1101 259582.6034 442201.8974 444222.1373 0.687408086 1.167991647 0.7573126 0.739307762 1.179796863 0.519837016 0.584353146 0.995452185 1 18.76092176 2.225790849 24.99999806 0.71569497 0.914121468 0.050113649 0.225163148 423.218715 828550.4474 0.0791532 0.058838363 168.1863903 -2.225790849 0.198426498 SRS(ph)DIDVNAAAGAK ddPTM_SK-BR-3_Pertuzumab_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(0.443)RS(0.557)DIDVNAAAGAK;S(0.442)RS(0.558)DIDVNAAAGAK;SRS(1)DIDVNAAAGAK 240.82 1.25E-17 5281760000 7585060 6948800 6581920 6828880 7616810 4822940 9780950 6475450 10190270 TRUE FALSE 7110324.634 7463296.382 6738046.251 7004120.622 7018616.467 6215244.484 8314387.349 7283924.187 8489448.105 0.837548513 0.879126215 0.793696618 0.825038393 0.826745906 0.732114079 0.979379018 0.857997375 1 23.01723934 1.696168084 10.01795409 0.937785708 0.821372956 0.577481125 0.052089824 0.085200152 14.99042801 0.022885468 0.012353664 49.67845539 -1.696168084 -0.116412753 SRS(ph)FDYNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SRSFDYNYR 9 1 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.026)RS(0.974)FDYNYR;S(0.011)RS(0.989)FDYNYR;S(0.021)RS(0.979)FDYNYR;S(0.001)RS(0.999)FDYNYR 177.16 3.18E-05 3135260000 1709470 1669210 1890080 1422890 1845060 1471560 1585910 1592850 3291200 TRUE FALSE 1602477.324 1792800.045 1934913.59 1459403.766 1700156.43 1896375.483 1348117.518 1791720.829 2741877.458 0.584445275 0.65385856 0.705689302 0.532264402 0.620070173 0.69163393 0.491676794 0.653464955 1 21.38673266 0.959161308 24.04816246 1.000000001 0.617352981 0.772847063 0.065640852 2806.550619 1652659.587 0.064488786 0.016122196 9.102513005 -0.959161308 -0.38264702 SRS(ph)FTLDDESLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSFTLDDESLK 12 1 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 S(0.055)RS(0.944)FT(0.001)LDDESLK;S(0.017)RS(0.977)FT(0.007)LDDESLK 202.61 8.16E-08 899810000 1952210 1479400 1587090 1907860 2274900 1035660 1649180 1257320 1990200 TRUE FALSE 1830024.661 1588936.315 1624736.524 1956818.918 2096238.531 1334638.229 1401900.769 1414299.17 1658022.763 1.103739166 0.958332027 0.979924137 1.180212336 1.264300212 0.804957724 0.845525647 0.85300347 1 20.66103238 2.208707712 24.99999944 0.859053743 1.066113982 0.518099245 0.103155494 188.1715092 157581.1303 0.041045718 0.030318353 161.6991406 -2.208707712 0.207060239 SRS(ph)GEGEVSGLMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SRSGEGEVSGLMR 13 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 S(0.115)RS(0.885)GEGEVSGLMR;S(0.005)RS(0.995)GEGEVSGLMR;S(0.263)RS(0.737)GEGEVSGLMR;S(0.206)RS(0.777)GEGEVS(0.018)GLMR;S(0.025)RS(0.975)GEGEVSGLMR;S(0.061)RS(0.939)GEGEVSGLMR 221.79 1.12E-11 14691400000 4190700 5429620 4331470 4298300 4821850 2522460 3479400 3675440 5603960 TRUE FALSE 3928411.568 5831634.714 4434214.514 4408601.655 4443161.351 3250653.253 2957696.271 4134326.775 4668622.873 0.841449754 1.249112398 0.949790684 0.944304514 0.951707061 0.696276684 0.633526492 0.885555952 1 22.15456562 2.762355278 1.379697192 0.762703426 1.059454063 0.218926068 0.14871804 0.389598255 1.509146655 0.061115223 0.059633924 578.5691571 -2.762355278 0.296750636 SRS(ph)GSSQELDVKPSASPQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSGSSQELDVKPSASPQER 20 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.224)RS(0.688)GS(0.069)S(0.019)QELDVKPSASPQER 119.2 2.84E-05 176280000 87141 80357 78050 74483 97367 62978 89013 85959 129200 TRUE FALSE 81687.00036 86306.71589 79901.38286 76394.35988 89720.18858 81158.72624 75666.32701 96691.17037 107635.6853 0.758921171 0.801841096 0.742331715 0.70974937 0.833554302 0.754013188 0.702985509 0.898318899 1 16.71579694 1.036447852 4.532642983 0.999015628 0.759116127 0.820512384 0.038798344 0.06690117 3.171043902 0.036988354 0.009405466 10.87546543 -1.036447852 -0.239899501 SRS(ph)HSDNDRFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSHSDNDRFK 11 2 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.139)RS(0.845)HS(0.016)DNDRFK 89.466 0.0063717 50752000 41235 57385 55011 49960 79384 28315 67145 48416 113890 TRUE FALSE 38654.17496 61633.84511 56315.8869 51242.05818 73149.50086 36489.08084 57077.23059 54460.84418 94881.02324 0.40739627 0.649590856 0.593542154 0.540066458 0.770960286 0.384577227 0.601566347 0.573990903 1 16.53383195 0.137002172 2.686060614 1.00000075 0.574469753 0.602284583 0.110809172 115.055067 354.4220153 0.094479397 0.024963401 1.370888622 -0.137002172 -0.425530997 SRS(ph)HSDNDRPNCSWNTQYSSAYYTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSHSDNDRPNCSWNTQYSSAYYTSR 26 2 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.153)RS(0.819)HS(0.029)DNDRPNCSWNTQYSSAYYTSR;S(0.366)RS(0.618)HS(0.015)DNDRPNCSWNTQYSSAYYTSR 327.98 3.62E-95 1430370000 163520 213390 207451 218750 280720 160822 248626 213532 345060 TRUE FALSE 153285.5751 229189.6176 212371.8357 224363.4953 258673.3836 207248.7007 211346.8394 240191.9402 287467.2568 0.533227947 0.797272079 0.738768784 0.780483655 0.89983599 0.720947154 0.735203173 0.835545387 1 18.13303811 -5 0.108356013 1.728740188 0.621185386 0.525844809 0.084079552 156.0253813 1.12929249 25.69533571 1.07557012 1.00E-05 5 -1.107554802 SRS(ph)HTSEGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSHTSEGTR 10 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 S(0.024)RS(0.976)HTSEGTR;S(0.153)RS(0.847)HTSEGTR 88.552 0.0073378 90683000 47979 33888 33378 37303 38711 20076.6 35952 30365 19220.8 TRUE FALSE 44976.08003 36397.10278 34169.74192 38260.25813 35670.79421 25872.3885 30561.33136 34156.13709 16012.72431 2.808771273 2.273011268 2.133911836 2.389365944 2.227653054 1.615739334 1.908565387 2.133062209 1 13.96693116 -0.237257453 0.13330203 4.57E-14 2.991062188 0.770502778 0.231244505 10.85134489 0.429968151 7.037110151 2.520721889 0.579085308 0.237257453 2.991062188 SRS(ph)LSNS(ph)NPDISGTPTSPDDEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSLSNSNPDISGTPTSPDDEVR 23 1 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A0U1RRC1;A0A0U1RQJ5 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 2 S(0.334)RS(0.662)LS(0.068)NS(0.937)NPDISGTPTSPDDEVR 172.25 2.97E-12 209710000 68119 83988 70791 84199 66901 51996 105500 68310 89961 TRUE FALSE 63855.55339 90206.55891 72470.19595 86359.68889 61646.86533 67006.40112 89681.25441 76838.65387 74945.92793 0.852021653 1.203621883 0.966966424 1.152293277 0.822551232 0.894063266 1.19661277 1.025254553 1 16.19356247 -0.350193178 6.305308613 1 1.032205318 0 0.13769661 0 6.53E-18 0.124731001 0.029399379 0.446484948 0.350193178 0.032205318 SRS(ph)PAPPADKEAFAAEAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSPAPPADKEAFAAEAQK 19 2 Q9Y618;Q9Y618-4;Q9Y618-5 Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.16)RS(0.84)PAPPADKEAFAAEAQK 120.08 2.46E-05 330170000 584260 412610 458380 478250 538820 345440 645780 463650 403240 TRUE FALSE 547692.2095 443160.0737 469252.9901 490522.7047 496503.2507 445162.9203 548951.2841 521537.7231 335936.639 1.630343779 1.319177554 1.39684969 1.460164352 1.477966953 1.325139531 1.634091732 1.552488364 1 18.35782963 3.231917146 23.91354841 1.450020832 1.413596084 0 0.188430513 733.0604213 2638699.907 0.049179212 0.0601544 1705.756935 -3.231917146 -0.036424748 SRS(ph)PAYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SRSPAYSR 8 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 S(0.213)RS(0.787)PAYSR;S(0.034)RS(0.966)PAYSR;S(0.131)RS(0.869)PAYSR 93.839 0.006531 1874930000 229754 202751 233434 230000 255669 206901 219777 219009 268221 TRUE FALSE 215374.1073 217762.895 238971.1647 235902.1894 235589.7881 266629.9599 186823.4792 246352.7557 223453.1823 0.963844439 0.974534767 1.069446236 1.055711926 1.054313864 1.193225163 0.836074372 1.102480409 1 17.76961307 -1.181174045 6.474896654 0.999999879 1.024191278 0.005855773 0.094366929 1.54E-07 1.95E-08 0.085450217 0.020140709 0.065890978 1.181174045 0.024191399 SRS(ph)PES(ph)QVIGENTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSPESQVIGENTK 14 1 O95218-2 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 2 S(0.365)RS(0.637)PES(0.998)QVIGENTK 158.64 4.43E-06 0 604170 342530 423180 417850 378700 269210 514740 330420 339510 TRUE FALSE 566356.0782 367891.2776 433218.0294 428572.7384 348958.4296 346926.5567 437559.5156 371673.6643 282843.5877 2.002364921 1.300688061 1.531652292 1.515228759 1.233750542 1.226566809 1.547001716 1.314060776 1 18.10964494 7.999999994 0.039866311 1.07E-10 3.73406974 0.485923043 0.192606284 784.1124655 2.379745929 61.15342746 198.1689506 99999998.71 -7.999999994 3.73406974 SRS(ph)PGRPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSPGRPPK 9 2 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 S(0.191)RS(0.809)PGRPPK 65.842 0.051519 167020000 274070 214560 174480 151900 229670 155250 261240 197460 203460 TRUE FALSE 256916.4479 230446.2456 178618.748 155798.0112 211632.6446 200068.1547 222069.4872 222113.3157 169501.2116 1.515720422 1.359555153 1.053790391 0.919155738 1.24856125 1.180334659 1.310135103 1.310393675 1 17.37093606 4.414833331 2.311349052 1.163245766 1.512689304 0.485253908 0.12909594 0.334315307 3.160918063 0.034428136 0.177608003 25991.61891 -4.414833331 0.349443537 SRS(ph)PHEAGFCVYLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SRSPHEAGFCVYLK 14 1 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(0.428)RS(0.572)PHEAGFCVYLK;S(0.025)RS(0.975)PHEAGFCVYLK;S(0.083)RS(0.917)PHEAGFCVYLK 177.4 1.27E-06 929960000 785110 879070 772770 870630 1002550 641110 923320 897740 1338150 TRUE FALSE 735971.3666 944157.2575 791100.4693 892971.8398 923813.7671 826188.0494 784876.7377 1009824.815 1114804.12 0.660179984 0.846926595 0.709631813 0.801012325 0.828678106 0.741106024 0.70404901 0.905831614 1 20.08835881 1.047843132 4.606552184 0.998766548 0.761317137 0.679382755 0.058057074 0.096631916 4.316318022 0.052404316 0.013317526 11.16459907 -1.047843132 -0.237449411 SRS(ph)PIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSPIER 7 1 Q14135-4;G5E9M7;Q14135;Q14135-2;A0A0A6YYI5;A0A075B6E4;Q14135-6;E7ERW0;G5E9M9;E7EWF5;F8W708;E7EQU6;Q14135-5;F8WBN7;E7EUJ2;C9JX59;C9JBN2 Q14135-4 VGLL4 Transcription cofactor vestigial-like protein 4 1 S(0.012)RS(0.988)PIER;S(0.012)RS(0.988)PIER 93.325 0.0090952 1577230000 418520 506180 451830 482510 495220 429030 503830 448620 473750 TRUE FALSE 392325.5803 543658.0939 462547.621 494892.0235 456327.4188 552883.9963 428285.3688 504631.1945 394678.0645 0.994039486 1.377472281 1.171961816 1.253913171 1.156201623 1.400848048 1.085151184 1.278589412 1 18.59031681 -1.314260176 3.497281896 0.999109159 1.22297495 0.226699481 0.123839619 6022980.863 4527059.851 36859.06813 0.025188691 0.048499786 1.314260176 0.22386579 SRS(ph)PIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSPIQR 7 1 Q9Y252 Q9Y252 RNF6 E3 ubiquitin-protein ligase RNF6 1 S(0.008)RS(0.992)PIQR;S(0.116)RS(0.884)PIQR 91.584 0.01155 126250000 52960 59300 65369 46399 57666 54811 64450 49191 65662 TRUE FALSE 49645.32814 63690.6337 66919.58355 47589.67689 53137.14497 70634.04592 54786.32082 55332.60463 54702.58801 0.907549897 1.164307504 1.223334873 0.869971214 0.971382651 1.291237736 1.001530692 1.011517126 1 15.73932147 1.584658552 25 1.004851837 1.092156812 0.038144031 0.133399727 2.477699744 2659.675943 0.07155085 0.033156721 38.42895296 -1.584658552 0.087304975 SRS(ph)PITTNHRPSPDPEQRPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSPITTNHRPSPDPEQRPLR 21 3 P41212 P41212 ETV6 Transcription factor ETV6 1 S(0.463)RS(0.534)PIT(0.001)T(0.001)NHRPSPDPEQRPLR;S(0.468)RS(0.531)PITT(0.001)NHRPSPDPEQRPLR 91.722 0.0014082 1311460000 418450 453660 465390 464460 422440 383790 510200 371830 404750 TRUE FALSE 392259.9615 487249.4584 476429.2706 476378.8299 389263.2664 494583.9427 433700.2465 418253.794 337194.6102 1.163304364 1.445009628 1.412920777 1.412771188 1.154417226 1.466761116 1.286201598 1.240392881 1 18.36322195 0.791824433 1.215143562 1.000034954 1.36043689 0.478711748 0.109332013 0.591987701 1.598090484 0.095838576 0.029409086 6.191907115 -0.791824433 0.360401936 SRS(ph)PLDKDTYPPSASVVGASVGGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSPLDKDTYPPSASVVGASVGGHR 25 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 S(0.132)RS(0.868)PLDKDTYPPSASVVGASVGGHR 224.79 4.18E-34 117300000 144230 176740 189800 203480 197190 147850 252620 181670 241170 TRUE FALSE 135202.9018 189826.0135 194302.1456 208701.6413 181703.4928 190531.8949 214741.9762 204351.8994 200917.169 0.672928563 0.944797373 0.967075868 1.038744684 0.904370163 0.948310669 1.068808491 1.017095256 1 17.61624133 5.231015616 1.386714425 0.993449982 2.95E-12 0.815217681 0.047121547 1.865326763 1.258313504 0.013073939 3.618819128 170221.9715 -5.231015616 -0.993449982 SRS(ph)PLLVTVVESDPRPQGQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSPLLVTVVESDPRPQGQPR 21 2 A0A2R8YH03;Q5VWN6;Q5VWN6-2 A0A2R8YH03 FAM208B Protein FAM208B 1 S(0.013)RS(0.801)PLLVT(0.093)VVES(0.093)DPRPQGQPR;S(0.184)RS(0.63)PLLVT(0.07)VVES(0.116)DPRPQGQPR 78.991 0.0063815 1420010000 45991 55960 46194 52376 43304.6 46635 60984.1 38534.6 70635 TRUE FALSE 43112.50541 60103.33663 47289.74349 53720.05683 39903.6314 60097.76744 51840.10035 43345.72964 58845.56218 0.732638177 1.02137416 0.803624636 0.912899033 0.678107744 1.021279519 0.880951739 0.736601504 1 15.844646 SRS(ph)PPPVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSPPPVSK 9 1 Q01130;Q01130-2 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 S(0.088)RS(0.912)PPPVSK 89.44 0.0073311 487790000 476840 332750 413440 365310 400930 484620 478520 477540 1630700 TRUE FALSE 446995.4356 357387.1562 423246.992 374684.4731 369442.5751 624521.9269 406770.3684 537161.9202 1358525.635 0.329029813 0.263069866 0.311548771 0.275802284 0.271943764 0.459705662 0.299420458 0.395400651 1 20.37361036 -4.999998936 0.288816509 6.305038486 0.278214369 0.942712013 0.052749315 47.46707196 0.448279471 151.4858643 0.051163133 1.00E-05 4.999998936 -6.026824117 SRS(ph)PPRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSPPRPK 8 2 Q8WUQ7-2;Q8WUQ7 Q8WUQ7-2 CACTIN Cactin 1 S(0.386)RS(0.614)PPRPK 58.37 0.054985 246160000 258340 237030 261600 248500 237670 207990 315020 240770 256880 TRUE FALSE 242170.9606 254579.9478 267805.2755 254876.9307 219004.3569 268033.3366 267785.6755 270830.6645 214005.0685 1.131613201 1.189597749 1.251396882 1.190985487 1.023360608 1.252462563 1.251305296 1.265533879 1 17.70728544 4.730733288 4.808206811 1.19520809 1.128450059 0 0.09556077 0.648790979 43.32728819 0.021274618 0.143558881 53793.93179 -4.730733288 -0.066758032 SRS(ph)PQAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSPQAFR 8 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 S(0.009)RS(0.991)PQAFR;S(0.231)RS(0.769)PQAFR 87.789 0.0091296 1454170000 470740 489410 473730 483640 496600 392000 467960 432090 522020 TRUE FALSE 441277.2237 525646.4256 484967.0993 496051.0212 457599.0392 505164.0364 397793.7423 486037.3876 434891.4896 1.014683511 1.208684093 1.115145067 1.140631705 1.052214288 1.161586392 0.914696543 1.117606114 1 18.73029595 1.755253894 25 1.00497509 1.124737431 0.312147121 0.072250894 6.042420433 9059.435141 0.030136305 0.016712364 56.91855865 -1.755253894 0.119762341 SRS(ph)PQWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSPQWR 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.082)RS(0.918)PQWR 90.696 0.010265 440120000 115300 97200 109480 113560 110740 127720 133280 95945 165810 TRUE FALSE 108083.5788 104396.7891 112076.9173 116474.1419 102042.9271 164590.6906 113295.9013 107923.9445 138135.2398 0.782447542 0.75575783 0.811356446 0.843189196 0.738717558 1.191518477 0.820181016 0.781291903 1 17.07572189 SRS(ph)PVDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSPVDLR 8 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 S(0.102)RS(0.898)PVDLR;S(0.247)RS(0.753)PVDLR 85.288 0.010204 690710000 713970 807410 847640 800580 888370 864780 816170 818370 1390510 TRUE FALSE 669283.8922 867191.4765 867746.4211 821124.2382 818601.0037 1114427.947 693792.8855 920545.296 1158424.898 0.577753373 0.748595337 0.749074388 0.708828203 0.706650043 0.962020023 0.598910544 0.794652547 1 20.14373308 -5 0.219299982 2.337954801 0.698169563 0.431547048 0.101927312 149.4777072 1.495766152 88.45282001 0.181465546 1.00E-05 5 -1.639785238 SRS(ph)SDIVSSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.228)RS(0.698)S(0.074)DIVSSVR;S(0.033)RS(0.927)S(0.04)DIVSSVR;S(0.005)RS(0.702)S(0.293)DIVSSVR;S(0.001)RS(0.968)S(0.031)DIVSSVR;S(0.002)RS(0.753)S(0.245)DIVSSVR;SRS(0.775)S(0.225)DIVSSVR 238.65 7.74E-16 5171260000 1962120 2176720 1781980 2078990 1584550 1157140 2478990 1822400 2099650 TRUE FALSE 1839314.412 2337886.614 1824249.407 2132340.403 1460105.835 1491187.533 2107288.463 2049930.652 1749204.851 1.051514584 1.336542494 1.042902097 1.219034124 0.834725466 0.852494511 1.204712222 1.171921431 1 20.73826782 SRS(ph)TSSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSTSSLR 8 1 Q08499-10 Q08499-10 PDE4D "cAMP-specific 3,5-cyclic phosphodiesterase 4D" 1 S(0.035)RS(0.955)T(0.01)SSLR 93.442 0.0067016 114690000 57265 73786 63056 82872 89624 37766 57137 53734 84977 TRUE FALSE 53680.88587 79249.19221 64551.7181 84998.63582 82585.29257 48668.43112 48569.83728 60442.80818 70793.78973 0.758271115 1.119437065 0.911827412 1.20065102 1.16656126 0.687467521 0.68607483 0.853786871 1 16.11133519 2.231712556 24.99975913 0.767207729 1.034758553 0.326242082 0.155723916 151.7797005 554087.1132 0.054017086 0.040781449 170.4953568 -2.231712556 0.267550824 SRS(ph)VEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSVEK 6 1 Q8TF01 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 S(0.027)RS(0.973)VEK 76.064 0.046051 198470000 333730 194610 310020 304040 291980 175610 284010 271910 339400 TRUE FALSE 312842.435 209019.1269 317373.8208 311842.1811 269049.0686 226305.7562 241425.3371 305858.562 282751.9474 1.10642009 0.739231432 1.122446101 1.102882523 0.951537456 0.800368515 0.853841465 1.081720444 1 18.10917743 2.475294994 24.97309744 0.905905324 0.992619654 0.052648636 0.133242621 158.8899682 2172663.823 0.046161214 0.038872247 298.7411128 -2.475294994 0.08671433 SRS(ph)VS(ph)PCSNVESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSVSPCSNVESR 13 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.162)RS(0.838)VS(0.996)PCS(0.004)NVESR;S(0.003)RS(0.991)VS(0.742)PCS(0.264)NVESR 149.99 0.00052637 526030000 813440 777340 732130 771490 918100 666320 861830 741460 1101540 TRUE FALSE 762528.2424 834895.0624 749496.4693 791287.7395 845996.1294 858675.7672 732606.5923 834032.9132 917685.8578 0.830925132 0.909783076 0.816724441 0.862264284 0.921879881 0.935696851 0.798319584 0.908843594 1 19.80764085 0.986092766 24.77154521 1.000000004 0.867606889 0.46554514 0.04487573 595.1042543 1060000.845 0.041490144 0.010372536 9.684847045 -0.986092766 -0.132393115 SRS(ph)WEDS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.375)RS(0.625)WEDS(1)PER;S(0.3)RS(0.7)WEDS(1)PER;S(0.001)RS(0.999)WEDS(1)PER;S(0.035)RS(0.965)WEDS(1)PER;S(0.003)RS(0.997)WEDS(1)PER 155.43 0.0001521 8465350000 5147540 5152630 4835110 4633370 5412900 4341830 5537680 4650390 6377250 TRUE FALSE 4825364.66 5534136.087 4949801.093 4752270.118 4987792.669 5595245.837 4707356.293 5231001.428 5312845.776 0.908244821 1.041651936 0.931666625 0.894486744 0.938817515 1.053154199 0.886032927 0.984595008 1 22.3410534 SRS(ph)WEDSPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRSWEDSPER 10 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IU26;B1AN86 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 S(0.052)RS(0.948)WEDSPER;S(0.007)RS(0.976)WEDS(0.017)PER 138.24 0.00085052 430740000 481330 469220 510160 494980 523580 376640 451390 406820 542190 TRUE FALSE 451204.4145 503961.537 522261.2361 507682.0248 482460.1388 485369.8538 383708.26 457612.3725 451694.9863 0.998913931 1.115712045 1.156225444 1.123948771 1.068110458 1.074552228 0.84948532 1.013100403 1 18.78498937 1.902464948 6.842923035 0.941369255 1.103069359 0.524094697 0.060141122 0.163800498 9.854173051 0.024895966 0.015358593 79.88494634 -1.902464948 0.161700104 SRS(ph)WPASPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SRSWPASPR 9 1 Q86YD1 Q86YD1 PTOV1 Prostate tumor-overexpressed gene 1 protein 1 SRS(1)WPASPR;S(0.043)RS(0.843)WPAS(0.114)PR;S(0.005)RS(0.995)WPASPR 134.18 0.0012945 429270000 178071 263974 188724 197046 282952 151337 199453 225478 349049 TRUE FALSE 166925.854 283518.9096 193200.6224 202102.534 260730.0913 195025.5351 169546.8743 253629.4246 290790.467 0.5740417 0.974993825 0.664398061 0.695010865 0.896625306 0.670673758 0.583055133 0.872206807 1 18.14962045 1.001119184 24.89113882 1.000000015 0.735943015 0.351352391 0.126317513 31.21171389 694140.2544 0.120095228 0.030023807 10.0258034 -1.001119184 -0.264057 SRSES(ph)ETSTMAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSESETSTMAAK 13 1 Q96B23-2;Q96B23;A0A087WVF1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 S(0.209)RS(0.209)ES(0.581)ET(0.001)STMAAK 121.28 0.00015049 145020000 189660 172570 170330 181040 224890 148130 215330 153550 243680 TRUE FALSE 177789.5192 185347.2624 174370.308 185685.7929 207228.0466 190892.7263 183043.2655 172721.0555 203008.2338 0.875774917 0.913003669 0.858932196 0.91467124 1.020786412 0.940320118 0.901654392 0.850808129 1 17.63117872 3.004493663 24.48942852 0.937039045 0.885850686 0.237504543 0.048579516 163.1421322 889070.9536 0.013961787 0.016621511 1010.400757 -3.004493663 -0.05118836 SRSHS(ph)DNDRPNCSWNTQYSSAYYTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSHSDNDRPNCSWNTQYSSAYYTSR 26 2 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.202)RS(0.236)HS(0.325)DNDRPNCS(0.237)WNTQYSSAYYTSR 135.32 1.69E-05 191500000 57823 82200 87289 77805 92709 77330 89029 81490 98261 TRUE FALSE 54203.96165 88286.17353 89359.5363 79801.60802 85428.00911 99653.91565 75679.92795 91664.20588 81860.60431 0.662149542 1.078494036 1.091606116 0.974847531 1.043579019 1.217361104 0.924497548 1.119759702 1 16.3208817 4.740471137 24.77474667 1.056998643 0.66214939 0.700434017 0.081000055 78.90053344 1023057.169 0.017630765 0.114733052 55013.73573 -4.740471137 -0.394849253 SRSHT(ph)SEGAHLDITPNSGAAGNSAGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRSHTSEGAHLDITPNSGAAGNSAGPK 27 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 S(0.216)RS(0.216)HT(0.28)S(0.28)EGAHLDIT(0.008)PNSGAAGNSAGPK 93.397 0.0082323 187020000 46063 86294 71375 87435 103860 42670 93876 82673 50558 TRUE FALSE 43179.99905 92683.29755 73068.04871 89678.73013 95703.25455 54988.13631 79800.1653 92994.90604 42119.54318 1.025177288 2.200482022 1.734777806 2.129147739 2.272181684 1.305525468 1.894611367 2.207880214 1 15.36220217 -0.966025261 5.533476001 0.999998354 1.866979897 0.296449686 0.40858302 7.40E-06 1.38E-06 0.352679546 0.083127209 0.108137105 0.966025261 0.866981543 SRSS(ph)SS(ph)PPPKQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SRSSSSPPPKQK 12 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.229)RS(0.345)S(0.426)S(0.056)S(0.944)PPPKQK;S(0.252)RS(0.338)S(0.407)S(0.024)S(0.98)PPPKQK;S(0.233)RS(0.345)S(0.422)S(0.036)S(0.964)PPPKQK;S(0.03)RS(0.176)S(0.789)S(0.469)S(0.535)PPPKQK 88.311 0.011816 793400000 849340 888160 765450 838140 1163360 555116 1109610 729590 2135770 TRUE FALSE 796181.3255 953920.2905 783606.8355 859648.0914 1071994.398 715368.9776 943234.2816 820680.9175 1779296.189 0.447469809 0.536122258 0.440402694 0.483139399 0.602482265 0.402051655 0.530116507 0.461239069 1 20.76287526 -1.620163114 2.765792695 1.045349322 0.490351004 0.888398432 0.057037651 11756412.89 11278371.94 3843772.284 0.012568186 0.023979321 1.620163114 -0.554998317 SRSWEDS(ph)PER ddPTM_SK-BR-3_Pertuzumab_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(0.001)RS(0.001)WEDS(0.999)PER 71.279 0.031164 136170000 70759 103290 67202 92175 110480 61683 87299 96404 174250 TRUE FALSE 66330.3205 110937.6991 68796.06318 94540.36655 101803.3465 79489.88076 74209.32539 108440.2516 145166.5493 0.456925654 0.764209796 0.473911266 0.651254487 0.701286536 0.547577118 0.511201277 0.747005782 1 17.14734953 0.955910843 4.766603993 0.999792513 0.593856737 0.649096332 0.097860869 0.137631323 9.991006875 0.088526644 0.022429023 9.034639814 -0.955910843 -0.405935776 SRT(ph)ASGS(ph)SVTSLDGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRTASGSSVTSLDGTR 16 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 S(0.08)RT(0.92)AS(0.005)GS(0.605)S(0.362)VT(0.004)S(0.024)LDGTR 260.11 2.25E-25 528810000 754400 739300 635580 766380 891160 453650 675790 567280 424190 TRUE FALSE 707183.4506 794038.5412 650656.2577 786046.6083 821171.8884 584611.3906 574461.5632 638106.1567 353389.9486 2.001141949 2.246918862 1.841184958 2.224303808 2.323699051 1.654295468 1.625574144 1.805671495 1 18.43090148 0.91886856 0.531336448 0.987349018 2.126108345 0.736973204 0.199181628 0.538408985 0.365059874 0.228889124 0.102442421 8.295996499 -0.91886856 1.138759327 SRT(ph)ASGSSVT(ph)SLDGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRTASGSSVTSLDGTR 16 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 S(0.018)RT(0.972)AS(0.153)GS(0.203)S(0.129)VT(0.322)S(0.203)LDGTR 206.6 6.34E-11 764520000 736250 705230 593970 777440 893570 444360 678810 567710 393930 TRUE FALSE 690169.4267 757445.963 608059.2489 797390.4266 823392.6167 572639.5184 577028.7423 638589.8432 328180.5381 2.103017536 2.308016092 1.852819343 2.429730999 2.508962358 1.744891765 1.758266184 1.945849217 1 18.32413016 0.644594259 0.56157809 0.97435656 2.197961026 0.693263812 0.239556928 0.845789012 0.528623989 0.304520475 0.112149711 4.411581016 -0.644594259 1.223604466 SRT(ph)ASGSSVTSLDGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRTASGSSVTSLDGTR 16 1 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 S(0.039)RT(0.958)AS(0.003)GSSVTSLDGTR;S(0.003)RT(0.936)AS(0.046)GS(0.001)S(0.005)VT(0.009)SLDGTR 182.77 3.38E-09 513870000 315990 441440 254720 269800 447620 123440 396730 317740 338240 TRUE FALSE 296212.75 474124.6769 260762.0787 276723.5248 412465.7308 159075.1241 337244.0196 357410.5384 281785.5589 1.051199185 1.682572658 0.925391918 0.982035864 1.46375752 0.564525467 1.196810869 1.268377769 1 18.10423815 3.889827015 5.990006145 1.058613697 1.396678694 0.173548667 0.278860019 0.290844335 15.83180996 0.064954553 0.119222798 7759.379891 -3.889827015 0.338064997 SRT(ph)GS(ph)ESSQTGTSTTSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 S(0.14)RT(0.86)GS(0.629)ES(0.368)S(0.003)QTGTSTTSSR 145.81 2.02E-07 610410000 102040 104810 109650 119360 115490 83584 104980 74633 65119 TRUE FALSE 95653.49855 112570.2415 112250.9498 122422.9797 106419.8813 107713.3439 89239.22359 83951.09434 54250.21822 1.763191038 2.075019146 2.069133609 2.25663571 1.961648907 1.985491441 1.64495603 1.547479385 1 15.72734132 1.127391722 0.948666894 1.013850006 2.056991715 0.865873575 0.130633892 0.166016344 0.325462085 0.115294857 0.039918953 13.40885586 -1.127391722 1.043141709 SRT(ph)GSES(ph)SQTGTSTTSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 S(0.357)RT(0.643)GS(0.085)ES(0.915)S(0.001)QTGTSTTSSR 164.04 7.25E-11 194610000 77205 85722 80161 102640 91935 60110 70714 48965 75273 TRUE FALSE 72372.87686 92068.94607 82062.45677 105273.9162 84714.79595 77462.7812 60111.09218 55078.38804 62709.45002 1.154098415 1.468182962 1.308613881 1.678756808 1.350909567 1.235264879 0.958565131 0.878310813 1 15.93639525 1.891840067 2.269762934 0.927681573 1.403999221 0.698189307 0.133920045 0.1546211 1.46308373 0.073971755 0.036347518 77.95429833 -1.891840067 0.476317648 SRT(ph)PSASNDDQQE ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRTPSASNDDQQE 13 1 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 S(0.048)RT(0.948)PS(0.004)ASNDDQQE;S(0.312)RT(0.682)PS(0.006)ASNDDQQE 126.46 0.001199 462510000 746020 715490 741280 717060 734120 640810 852580 703070 864350 TRUE FALSE 699327.9399 768465.6241 758863.5117 735460.9736 676465.1765 825801.4443 724743.544 790849.8371 720084.4011 0.971174961 1.067188267 1.053853563 1.021353848 0.939424844 1.146812017 1.006470273 1.098273808 1 19.45780649 2.239761701 24.99999591 1.060303552 1.024703006 0.151710162 0.056039266 82.05233108 1707929.31 0.018865549 0.01498238 173.6847553 -2.239761701 -0.035600547 SRT(ph)S(ph)VQTEDDQLIAGQSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 2 S(0.429)RT(0.781)S(0.749)VQT(0.041)EDDQLIAGQSAR;S(0.162)RT(0.93)S(0.908)VQTEDDQLIAGQSAR;S(0.511)RT(0.766)S(0.72)VQT(0.002)EDDQLIAGQSAR 235.69 8.28E-24 871510000 332782 298391 298431 310826 322292 240104 359474 279108 338175 TRUE FALSE 311953.7687 320484.1801 305509.9242 318802.3214 296980.4864 309418.127 305574.2109 313955.2482 281731.4078 1.107273666 1.137552191 1.084401369 1.131582467 1.0541263 1.098273456 1.084629553 1.114377877 1 18.10396088 -5 0.18386786 0.580881919 1.121741243 0.64348759 0.023881793 79.14829931 0.767642976 12.1477853 0.064030521 1.00E-05 5 0.540859324 SRT(ph)SPAPWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRTSPAPWK 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.205)RT(0.739)S(0.056)PAPWK 88.803 0.020268 1959800000 2949700 2102200 2440400 2294700 2153800 2230700 2680500 2018600 2101100 TRUE FALSE 2765083.542 2257849.075 2498287.44 2353585.887 1984649.236 2874666.878 2278583.91 2270626.653 1750412.836 1.579675083 1.289895177 1.427256124 1.344589024 1.133817803 1.642279363 1.301740859 1.297194928 1 20.73926379 0.77614581 1.893020952 1.000824528 1.382361708 0.420616043 0.143563658 0.75877874 4.537799783 0.12208287 0.034089848 5.972357694 -0.77614581 0.38153718 SRT(ph)SPITR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRTSPITR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.133)RT(0.534)S(0.333)PITR 70.488 0.082774 1390400000 115280 106230 106100 105610 109730 96213 120210 84759 137670 TRUE FALSE 108064.8306 114095.3797 108616.7421 108320.1314 101112.2484 123988.1312 102185.6265 95341.34773 114691.9876 0.942217785 0.994798173 0.947029905 0.944443755 0.881598188 1.081053121 0.890956976 0.831281676 1 16.80740508 1.59902461 25 0.895825997 0.964177362 0.142780178 0.064657276 1.104227009 3113.353685 0.030368187 0.01438757 39.72140573 -1.59902461 0.068351365 SRT(ph)SPVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRTSPVTR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.121)RT(0.588)S(0.291)PVTR;S(0.16)RT(0.753)S(0.087)PVTR 87.568 0.024625 21006000000 1931340 2027080 2084200 1917760 1697500 1837750 2067370 1900220 2173140 TRUE FALSE 1810460.877 2177167.112 2133638.208 1966972.968 1564185.197 2368278.592 1757387.061 2137466.65 1810428.895 1.000017665 1.202569799 1.178526378 1.086467949 0.863985988 1.308131238 0.970702062 1.180641038 1 20.78790009 3.113263531 6.402534977 1.066025573 1.149977696 0.035658308 0.130026962 0.521924819 27.40794727 0.034232897 0.041112096 1297.966643 -3.113263531 0.083952122 SRTGS(ph)ESS(ph)QTGTSTTSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 S(0.244)RT(0.322)GS(0.427)ES(0.121)S(0.882)QT(0.001)GT(0.001)S(0.001)TTSSR;S(0.118)RT(0.171)GS(0.71)ES(0.005)S(0.994)QT(0.002)GTSTTSSR 83.247 0.0022987 195169000 99662 141083 108102 157081 179643 73832 116414 97556 178750 TRUE FALSE 93424.33332 151528.9321 110666.2305 161111.9644 165534.5634 95146.09984 98958.80143 109736.0813 148915.4702 0.627364861 1.017549969 0.743147977 1.08190213 1.111600851 0.638926901 0.664530027 0.736901822 1 17.18413411 2.214629807 24.99629064 0.721561765 0.914031621 0.148333015 0.175484622 340.8508036 356024.3749 0.061542354 0.045475547 163.919193 -2.214629807 0.192469856 SRTPS(ph)ASNDDQQE ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SRTPSASNDDQQE 13 1 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 S(0.002)RT(0.001)PS(0.997)ASNDDQQE;SRTPS(1)ASNDDQQE;S(0.002)RT(0.007)PS(0.968)AS(0.023)NDDQQE;S(0.001)RT(0.008)PS(0.976)AS(0.016)NDDQQE 222.33 4.64E-11 1275090000 1066527 1181840 1250200 1866500 1932910 730045 608667 527166 678625 TRUE FALSE 999774.9789 1269344.663 1279855.334 1914397.55 1781107.046 940797.1402 517403.0339 592983.8355 565358.1034 1.76839241 2.245204686 2.263795861 3.386168056 3.150405088 1.664072973 0.915177532 1.04886413 1 19.10880545 2.014950461 4.808888874 1.036665218 2.515781578 0.713611911 0.457860664 0.112398392 6.949387926 0.202803215 0.136799165 103.5024097 -2.014950461 1.47911636 SRTPS(ph)NDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRTPSNDGK 9 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 S(0.003)RT(0.007)PS(0.989)NDGK 59.294 0.062512 241640000 593720 371910 411340 481570 598450 343640 377710 327360 621960 TRUE FALSE 556560.125 399446.6034 421097.179 493927.9015 551450.151 442843.2895 321075.892 368231.6166 518150.858 1.074127576 0.770907926 0.812692235 0.95325115 1.064265633 0.854660921 0.619657166 0.710664879 1 18.98301267 1.983297384 24.05743656 0.735174996 0.902029649 0.179534759 0.136550085 636.0859726 916178.4464 0.054115403 0.035954774 96.22709694 -1.983297384 0.166854654 SRTS(ph)PAPWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SRTSPAPWK 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.041)RT(0.279)S(0.68)PAPWK;S(0.07)RT(0.222)S(0.709)PAPWK;S(0.144)RT(0.144)S(0.713)PAPWK 82.437 0.011176 5768700000 9666500 7674800 8569200 8234400 7494200 7997400 9739600 7700100 7774500 TRUE FALSE 9061491.02 8243050.178 8772465.471 8445708.645 6905635.762 10306119.55 8279237.398 8661474.435 6476885.725 1.399050625 1.272687296 1.35442647 1.303976788 1.066196943 1.591215283 1.278274428 1.337289988 1 22.62686886 -1.337937991 5.425337117 0.999917231 1.323427153 0.385864533 0.128988168 0.000114532 1.40E-05 0.110769314 0.026101926 0.045926358 1.337937991 0.323509921 SRTS(ph)PITR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRTSPITR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.142)RT(0.086)S(0.772)PITR;S(0.084)RT(0.053)S(0.863)PITR 80.014 0.016076 5142300000 383840 428930 466810 404830 421790 479550 588750 401300 507140 TRUE FALSE 359816.1396 460688.4235 477882.9536 415218.6232 388664.3148 617988.3002 500472.4032 451403.1884 422495.0578 0.851645796 1.090399556 1.131097145 0.982777468 0.919926299 1.462711312 1.184563923 1.068422411 1 18.68857494 2.284761685 24.99999416 1.202850352 1.026127623 0.267756797 0.143694578 162.716027 88047.03569 0.047823795 0.040012124 192.6467493 -2.284761685 -0.176722729 QDVEALWENMAVIDCFASDHAPHTLEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 QDVEALWENMAVIDCFASDHAPHTLEEK 28 0 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 ; 279.27 6.40E-62 62668000 51140 56845 61515 61406 76635 61014 93099 65848 116567 FALSE TRUE 47939.23869 61053.86295 62974.16485 62981.78192 70616.39623 78627.75132 79139.66924 74069.26775 97111.21465 0.493652961 0.628700436 0.64847469 0.648553127 0.727170353 0.809667057 0.814938517 0.7627262 1 16.56735029 4.184178636 0.106353722 1.209878502 2.06E-12 0.918288378 0.038914793 10.70680397 0.225021795 0.641627793 2.183146888 15281.94512 -4.184178636 -1.209878502 down SRTS(ph)PVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SRTSPVTR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.117)RT(0.112)S(0.772)PVTR;S(0.242)RT(0.094)S(0.664)PVTR;S(0.325)RT(0.141)S(0.533)PVTR;S(0.238)RT(0.164)S(0.597)PVTR;S(0.271)RT(0.075)S(0.655)PVTR;S(0.215)RT(0.215)S(0.57)PVTR 92.707 0.0070172 23871365000 1457430 1550760 1538156 1605658 1785690 1624223 1617123 1307478 1747986 TRUE FALSE 1366212.058 1665579.884 1574641.787 1646861.903 1645449.111 2093109.813 1374650.419 1470719.506 1456235.844 0.93818049 1.143756961 1.081309592 1.130903287 1.12993312 1.437342599 0.943975129 1.009945959 1 20.47381259 1.60504635 25 0.982708115 1.139345848 0.271277333 0.122640375 0.367879054 3227.735209 0.05877344 0.029082922 40.27600162 -1.60504635 0.156637732 SRTS(ph)VQTEDDQLIAGQSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 1 S(0.006)RT(0.005)S(0.974)VQT(0.015)EDDQLIAGQSAR 271.38 1.31E-33 0 157140 148250 163010 163650 193010 161630 149830 135560 173190 TRUE FALSE 147304.8879 159226.5843 166876.6742 167849.5361 177851.7732 208289.9572 127364.3825 152484.9644 144283.4701 1.020940845 1.103567748 1.156588998 1.16333171 1.232655224 1.443616216 0.882737172 1.056842923 1 17.1385465 1.636868551 18.49250112 0.977522621 1.173948807 0.411909129 0.115839257 0.233995606 144.2849974 0.052976176 0.029278794 43.33796863 -1.636868551 0.196426186 SRWDETPASQMGGS(ph)TPVLTPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SRWDETPASQMGGSTPVLTPGK 22 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 SRWDETPASQMGGS(0.596)T(0.404)PVLTPGK 158.8 1.23E-11 245150000 247620 215660 217500 227710 230990 160740 286630 192890 223660 TRUE FALSE 232121.9062 231627.6908 222659.2027 233553.4241 212848.9772 207143.0286 243652.4924 216972.7411 186329.7011 1.245759022 1.243106651 1.194974292 1.253441737 1.142324471 1.111701609 1.307641729 1.164456014 1 17.50749813 0.978716269 24.09784092 0.999999996 1.214940307 0.590461531 0.055925526 724.9579451 820812.2645 0.051543713 0.012885928 9.521738926 -0.978716269 0.214940311 SRWDETPASQMGGST(ph)PVLTPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SRWDETPASQMGGSTPVLTPGK 22 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 SRWDETPASQMGGS(0.375)T(0.625)PVLTPGK;SRWDETPASQMGGS(0.214)T(0.783)PVLT(0.003)PGK;SRWDETPAS(0.001)QMGGS(0.228)T(0.77)PVLTPGK 141.38 1.98E-07 263669000 423870 367022 348821 340608 418613 250225 449600 356587 423708 TRUE FALSE 397340.7333 394196.6908 357095.1988 349348.5779 385736.8236 322460.8954 382186.6539 401107.6719 352988.3975 1.125648141 1.116741212 1.01163438 0.989688557 1.092774794 0.913516982 1.082717326 1.136319705 1 18.42926124 4.115911253 2.971418284 1.032425627 1.123578777 0.262231127 0.06188898 0.341420707 5.818780344 0.015059906 0.03952569 13059.04001 -4.115911253 0.09115315 SS(ph)AIGIENIQEVQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSAIGIENIQEVQEK 15 0 J3KPC5;P47736-3;P47736;P47736-4;F2Z357;X6R8W7;P47736-2;A0A0A0MQY8 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 S(0.494)S(0.506)AIGIENIQEVQEK;S(0.206)S(0.794)AIGIENIQEVQEK;S(0.028)S(0.972)AIGIENIQEVQEK 389.31 1.97E-114 346780000 978310 657900 864650 673460 845400 532760 894110 754700 1202750 TRUE FALSE 917079.3234 706611.6005 885159.9063 690742.1238 779005.6942 686559.1634 760046.506 848925.9563 1002003.255 0.915245853 0.705198907 0.88339025 0.689361158 0.777448267 0.68518656 0.758526983 0.847228741 1 19.93445576 0.919163121 3.40553778 0.999750057 0.770550004 0.472011933 0.076087487 0.279819326 7.689632289 0.066394986 0.017199523 8.301625185 -0.919163121 -0.229200054 SS(ph)DEENGPPSS(ph)PDLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSDEENGPPSSPDLDR 16 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 2 S(0.228)S(0.772)DEENGPPSS(1)PDLDR;S(0.071)S(0.929)DEENGPPS(0.007)S(0.993)PDLDR 388.54 3.27E-121 855760000 1558840 1314850 1435430 1352060 1376700 1275670 1757000 1253660 1346460 TRUE FALSE 1461274.987 1412202.862 1469479.077 1386756.149 1268579.535 1643935.22 1493554.161 1410182.211 1121727.128 1.302700943 1.258954007 1.310014745 1.23626871 1.130916338 1.465539328 1.331477259 1.257152632 1 20.09729034 0.952180184 17.8615237 0.999999998 1.293113656 0.542921214 0.083190638 174.7070636 65257.29888 0.078180297 0.019545074 8.957363191 -0.952180184 0.293113658 SS(ph)DSWEVWGSASTNR ddPTM_SK-BR-3_Pertuzumab_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(0.425)S(0.557)DS(0.019)WEVWGSASTNR;S(0.212)S(0.787)DSWEVWGSASTNR;S(0.187)S(0.812)DS(0.001)WEVWGSASTNR 216.07 2.37E-12 441270000 298377 261580 280568 265734 256957 241642 324611 249048 298736 TRUE FALSE 279702.1162 280947.6554 287223.2055 272553.1843 236776.6337 311400.1227 275938.5941 280142.191 248875.0317 1.123865718 1.128870395 1.154086063 1.095140732 0.951387659 1.251230871 1.108743582 1.125633974 1 17.92506197 -2.088507304 2.17005399 0.811487438 1.121138338 0.202618611 0.07283303 4511164.15 1319735.065 4198948.408 0.016792153 0.008156291 2.088507304 0.3096509 SS(ph)DTEEESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSDTEEESR 9 0 Q96IZ7-2;Q96IZ7;C9J713;C9J8Q2;C9JVB3;F8WDM0;C9J367 Q96IZ7-2 RSRC1 Serine/Arginine-related protein 53 1 S(0.157)S(0.843)DTEEESR;S(0.306)S(0.694)DTEEESR 206.85 1.33E-05 145108000 134959 116086 135259 122517 114709 100248 134747 104473 124054 TRUE FALSE 126512.1571 124681.1282 138467.4074 125660.9936 105700.2179 129187.9702 114542.9383 117516.684 103348.586 1.224130508 1.206413489 1.339809404 1.215894658 1.022754369 1.250021652 1.108316453 1.137090391 1 16.65715912 2.986433365 23.94987916 1.121951046 1.260351479 0.463244006 0.076058492 322.0628653 568556.02 0.020911261 0.023094781 969.2445446 -2.986433365 0.138400433 SS(ph)DTEENVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSDTEENVK 9 0 H0YBT0;A0A087WUS5;P01106;P01106-2;A0A494C1T8 H0YBT0 MYC Myc proto-oncogene protein 1 S(0.358)S(0.642)DTEENVK 169.65 0.00062774 0 221720 135730 171910 155950 192400 158530 195690 160060 189840 TRUE FALSE 207842.941 145779.5904 175987.7864 159951.941 177289.6801 204295.0375 166348.1012 180043.8433 158154.4776 1.314176773 0.921754431 1.112758798 1.011365239 1.120990583 1.291743621 1.051807725 1.13840497 1 17.27097488 3.599039565 21.13354371 1.110804244 1.067598783 0 0.125311375 17.38018636 2960.493036 0.031045844 0.048096115 3972.277362 -3.599039565 -0.043205461 SS(ph)FSQHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSFSQHAR 8 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 S(0.377)S(0.622)FS(0.001)QHAR;S(0.372)S(0.624)FS(0.004)QHAR 132.25 0.00062499 1517870000 1194200 2243120 1542430 1931860 2047810 1276700 1816050 1720010 1862410 TRUE FALSE 1119457.154 2409202.939 1579017.168 1981434.798 1886983.263 1645262.565 1543750.162 1934757.035 1551561.739 0.721503454 1.552759956 1.01769535 1.277058301 1.216183163 1.060391297 0.994965345 1.246973927 1 20.56528967 2.235034631 24.57353139 1.066042882 1.197455682 0.014117269 0.219584049 194.4233037 1354964.63 0.073430139 0.056431009 171.8045379 -2.235034631 0.1314128 SS(ph)GFISELPSEEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SSGFISELPSEEGK 14 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 S(0.105)S(0.895)GFISELPSEEGK;S(0.009)S(0.991)GFISELPSEEGK;S(0.005)S(0.995)GFISELPSEEGK;S(0.28)S(0.72)GFISELPSEEGK;S(0.07)S(0.93)GFISELPSEEGK;S(0.25)S(0.75)GFISELPSEEGK 425.39 2.19E-132 1067650000 3597500 2630670 2938900 2869850 3397390 2220190 3884990 2873060 4456600 TRUE FALSE 3372338.897 2825447.544 3008612.096 2943495.21 3130572.694 2861122.811 3302471.816 3231767.865 3712764.669 0.908309359 0.761009058 0.810342794 0.792804142 0.843191792 0.770617873 0.889491285 0.870447807 1 21.82406244 0.90686839 0.89240432 0.998714143 0.806952591 0.607894677 0.045245017 0.409578538 0.685146727 0.038410887 0.013239859 8.0699044 -0.90686839 -0.191761551 SS(ph)GGREDLESSGLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSGGREDLESSGLQR 15 1 Q9UK76;J3KT51;Q9UK76-2;Q9UK76-3;J3KSH8 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 S(0.042)S(0.954)GGREDLES(0.004)SGLQR 161.8 4.29E-06 252730000 391080 315700 322780 331280 350430 278140 399200 286840 421160 TRUE FALSE 366603.0009 339074.7565 330436.494 339781.2057 322908.6414 358434.5028 339343.666 322652.6054 350865.6752 1.044852851 0.966394779 0.941774922 0.968408225 0.920319838 1.021571867 0.967161196 0.919590112 1 18.42055929 SS(ph)GPTSLFAVTVAPPGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSGPTSLFAVTVAPPGAR 18 0 Q00839;A0A1X7SBS1;A0A1W2PP22;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(0.235)S(0.765)GPTSLFAVTVAPPGAR 148.41 7.30E-08 29024000 30957 33231 32844 36485 38805 28369 38365 31331 37772 TRUE FALSE 29019.45663 35691.45782 33623.07519 37421.26687 35757.41183 36558.66977 32612.52441 35242.74432 31467.60918 0.922200872 1.134228457 1.068497927 1.189199556 1.136324391 1.161787334 1.036383928 1.119968921 1 14.94157995 -0.5257176 7.104165041 1.000008283 1.09925328 0.136769841 0.07547885 0 0 0.066181888 0.015599221 0.298045384 0.5257176 0.099244997 SS(ph)GSETEQVVDFSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSGSETEQVVDFSDR 15 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 S(0.061)S(0.643)GS(0.291)ET(0.005)EQVVDFSDR 159.44 1.85E-06 145940000 80067 112870 97070 104490 109000 90215 108230 90134 103490 TRUE FALSE 75055.74939 121227.0122 99372.54624 107171.3903 100439.5797 116258.606 92001.91626 101387.4283 86216.85043 0.870546175 1.40607099 1.152588453 1.243044599 1.164964612 1.348444131 1.067099016 1.175958386 1 16.39568224 0.933576877 1.055626057 1.005279206 1.212384115 0.108818678 0.148028509 1.047282378 2.404030732 0.124321426 0.040261625 8.581770131 -0.933576877 0.207104909 SS(ph)IEDAQCPGLPDLIEENHVVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSIEDAQCPGLPDLIEENHVVNK 23 0 Q15398-1;Q15398;Q15398-3 Q15398-1 DLGAP5 Disks large-associated protein 5 1 S(0.212)S(0.788)IEDAQCPGLPDLIEENHVVNK 351.12 7.93E-102 117180000 113560 77307 85003 81378 78414 71741 118050 75624 107610 TRUE FALSE 106452.4823 83030.89072 87019.3113 83466.29725 72255.68075 92451.46208 100349.4984 85065.82287 89649.19581 1.187433767 0.926175522 0.970664717 0.931032303 0.805982475 1.031258131 1.119357486 0.948874355 1 16.45200302 2.028721569 24.99999156 1.045831549 0.955110827 0.061414375 0.102620908 376.2053693 327457.3615 0.036211277 0.026743495 106.8369716 -2.028721569 -0.090720721 SS(ph)ITEPEGPNGPNIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSITEPEGPNGPNIQK 16 0 Q13625-2;Q13625;Q13625-3 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 S(0.005)S(0.994)IT(0.001)EPEGPNGPNIQK;S(0.158)S(0.842)ITEPEGPNGPNIQK 379.19 7.73E-105 278330000 1138980 714820 818340 666050 772970 483990 1044140 674570 705820 TRUE FALSE 1067693.275 767746.0166 837751.4112 683141.9706 712264.0542 623710.0561 887580.9003 758791.5494 588014.0822 1.815761403 1.305659235 1.424713177 1.161778249 1.211304416 1.060705985 1.509455177 1.290430914 1 19.16549118 7.368303826 1.081861416 1.262507321 199.9996597 0.56182657 0.155879404 459.9487211 1.951552436 0.043074168 225084.9224 23350910.84 -7.368303826 198.7371523 SS(ph)LETLEDIEENAPLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSLETLEDIEENAPLRR 17 1 Q8TDN4-2;Q8TDN4;V9GYB4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 S(0.19)S(0.81)LETLEDIEENAPLRR;S(0.114)S(0.886)LETLEDIEENAPLRR;S(0.165)S(0.834)LETLEDIEENAPLRR 287.65 6.29E-37 257623000 45877.6 34875.6 39457.9 46534.5 45258.3 35577.3 55436.3 41529.6 42115.6 TRUE FALSE 43006.20291 37457.82571 40393.86002 47728.65405 41703.89568 45847.88896 47124.14146 46714.66198 35086.23428 1.225728659 1.067593216 1.151273736 1.360324213 1.188611332 1.30672014 1.343094875 1.331424216 1 15.09861749 3.366800731 7.026998597 1.276815221 1.12817554 0.145596314 0.112004604 0.258284373 15.04634446 0.02767673 0.037579872 2327.023298 -3.366800731 -0.148639681 SS(ph)LGSHQLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSLGSHQLPR 10 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 S(0.184)S(0.815)LGS(0.001)HQLPR 158.01 5.25E-06 201220000 152790 194020 203550 180320 206890 163110 222320 192300 229200 TRUE FALSE 143227.1466 208385.4427 208378.3021 184947.3165 190641.694 210197.2091 188985.1799 216309.0783 190945.0393 0.750096191 1.091337295 1.091299899 0.968589271 0.998411347 1.100825713 0.989736003 1.132834239 1 17.54279791 4.743512886 24.96582057 1.049066319 0.750096065 0.734494829 0.056012585 259.3109753 1307218.484 0.01281549 0.106233636 55400.39814 -4.743512886 -0.298970254 SS(ph)LGSLQTPEAVTTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSLGSLQTPEAVTTR 15 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 S(0.007)S(0.993)LGSLQTPEAVTTR;S(0.248)S(0.752)LGSLQTPEAVTTR;S(0.271)S(0.729)LGSLQTPEAVTTR 311.7 3.71E-56 941290000 1539940 1569340 1539600 1534160 1727340 1356090 1991260 1553080 1881520 TRUE FALSE 1443557.904 1685535.566 1576120.039 1573529.143 1591681.684 1747571.169 1692689.049 1746985.457 1567482.157 0.920940566 1.075314037 1.005510673 1.00385777 1.015438471 1.11489063 1.079877714 1.114516965 1 20.58001759 2.255860366 24.21066544 1.084642528 1.014068899 0.341034087 0.048987223 177.6105505 248561.8109 0.015450982 0.012895069 180.2438129 -2.255860366 -0.070573629 SS(ph)LLCLQGNYAGHDWFVS(ph)S(ph)LFMIMLGDKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSLLCLQGNYAGHDWFVSSLFMIMLGDKEK 30 1 Q96NH3;Q96NH3-4 Q96NH3 TBC1D32 Protein broad-minded 3 S(0.47)S(0.494)LLCLQGNY(0.036)AGHDWFVS(1)S(1)LFMIMLGDKEK 48.08 0.088297 276290000 273140 65536 120880 127290 116500 71003 160240 74266 138690 TRUE FALSE 256044.655 70388.35363 123747.3307 130556.4769 107350.5599 91500.41346 136213.4996 83538.27358 115541.743 2.216035939 0.609202802 1.071018382 1.12995073 0.929106288 0.791925161 1.178911587 0.72301379 1 16.81805464 4.747741155 24.9971451 0.938972667 2.216036605 0.834255784 0.180219179 473.3814628 1288915.402 0.041409432 0.517721265 55942.40782 -4.747741155 1.277063938 SS(ph)LPNGEGLQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSLPNGEGLQLK 12 0 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 S(0.025)S(0.975)LPNGEGLQLK;S(0.011)S(0.989)LPNGEGLQLK;S(0.039)S(0.961)LPNGEGLQLK;S(0.035)S(0.965)LPNGEGLQLK 243.92 2.38E-16 1177250000 3821300 2306550 3096840 2672430 2595050 2616890 3614160 2682330 3081650 TRUE FALSE 3582131.654 2477329.362 3170298.507 2741009.078 2391245.241 3372343.661 3072250.26 3017224.805 2567302.707 1.395289946 0.964954135 1.234875225 1.06766104 0.931423176 1.313574614 1.196684073 1.175250895 1 21.29182198 SS(ph)LS(ph)GDEEDELFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSLSGDEEDELFK 13 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 2 S(0.105)S(0.895)LS(1)GDEEDELFK;S(0.136)S(0.864)LS(1)GDEEDELFK;S(0.151)S(0.849)LS(1)GDEEDELFK;S(0.18)S(0.82)LS(1)GDEEDELFK 287.48 5.57E-33 726310000 3658150 1949350 2367260 2394800 2405980 1623200 3002590 1814220 2517410 TRUE FALSE 3429192.921 2093681.902 2423412.525 2456254.622 2217024.036 2091791.49 2552379.504 2040729.361 2097238.008 1.635099549 0.998304386 1.155525751 1.171185442 1.057116087 0.997403004 1.217019477 0.973055682 1 21.00005917 4.744196616 24.9731858 1.086440298 1.635099787 0.809943625 0.08556282 250.8699058 1111574.931 0.018893256 0.168392696 55487.68629 -4.744196616 0.548659489 SS(ph)LTTAALPFTQSILTQVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSLTTAALPFTQSILTQVGR 20 0 Q3MII6;C9JMI8 Q3MII6 TBC1D25 TBC1 domain family member 25 1 S(0.143)S(0.857)LTTAALPFTQSILTQVGR 252.76 4.59E-36 74095000 108370 101010 101730 100430 124870 88753 147740 133030 155600 TRUE FALSE 101587.3151 108488.8855 104143.0836 103007.2038 115063.2139 114374.5503 125587.7586 149639.0883 129629.3548 0.783675236 0.836916034 0.803391206 0.794628686 0.887632389 0.88231983 0.968821906 1.154361129 1 16.98403293 1.712233525 1.576203351 1.075672449 0.818162846 0.818483425 0.048749659 0.133764996 0.652445643 0.034509066 0.013286787 51.55057634 -1.712233525 -0.257509603 SS(ph)LVTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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(0.071)S(0.929)LVTSK;S(0.367)S(0.633)LVTSK;S(0.152)S(0.848)LVTSK;S(0.005)S(0.995)LVTSK;S(0.007)S(0.993)LVTSK;S(0.138)S(0.862)LVTSK;S(0.008)S(0.992)LVTSK;S(0.061)S(0.939)LVTSK 191.17 0.00055565 7288347000 21770190 15675590 17512470 14369270 15127340 12795420 22608260 17761580 25558780 TRUE FALSE 20407632.67 16836226.99 17927874.06 14738009.8 13939299.74 16489250.04 19218361.3 19979152.36 21292854.5 0.958426343 0.790698447 0.841966682 0.69215754 0.654646832 0.774402983 0.902573269 0.938303146 1 24.34386603 1.563199028 2.81894422 0.964238519 0.784013395 0.472583278 0.082501878 0.220377964 3.925354479 0.059560333 0.022584232 36.57623748 -1.563199028 -0.180225124 SS(ph)LYGIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSLYGIAK 8 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.382)S(0.618)LYGIAK;S(0.039)S(0.961)LYGIAK 162.64 0.00035724 390050000 1686880 1480820 1408310 1447300 1847030 951560 1704030 1250400 2216760 TRUE FALSE 1581301.192 1590461.454 1441715.778 1484440.168 1701971.714 1226259.925 1448526.521 1406515.192 1846768.435 0.856253097 0.861213254 0.780669493 0.803804169 0.921594544 0.664003078 0.784357418 0.761608855 1 20.81657155 2.260111308 24.99972999 0.78020009 0.836366139 0.021307569 0.091053008 578.5629466 671156.3211 0.028154775 0.023536683 182.01673 -2.260111308 0.056166048 SS(ph)MIETGQGAEGGLSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSMIETGQGAEGGLSLR 17 0 P49796-1;P49796-4;P49796-6;P49796 P49796-1 RGS3 Regulator of G-protein signaling 3 1 S(0.198)S(0.802)MIETGQGAEGGLSLR 177.12 1.10E-09 96572000 113950 95530 115690 95367 107000 92389 114070 94951 102940 TRUE FALSE 106818.0729 102603.1406 118434.2214 97814.27868 98596.65162 119060.2045 96966.26247 106805.8414 85758.64898 1.245566181 1.196417409 1.381017808 1.140576255 1.149699217 1.388317166 1.13068785 1.245423554 1 16.38799456 -1.535276458 0.340513703 0.822043253 1.256580923 0.397377284 0.090595675 23.63503449 1.584090303 3.651480407 0.0717986 0.029155705 1.535276458 0.434537669 SS(ph)PAFTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSPAFTK 7 0 Q5VVQ6-2;Q5VVQ6 Q5VVQ6-2 YOD1 Ubiquitin thioesterase OTU1 1 S(0.015)S(0.985)PAFTK;S(0.114)S(0.886)PAFTK 75.571 0.048021 0 745980 645400 683400 649750 707140 587730 848280 660960 729870 TRUE FALSE 699290.4434 693186.0875 699610.5707 666423.685 651604.0769 757398.11 721088.289 743482.311 608049.9819 1.150054213 1.140014979 1.150580695 1.096001488 1.071629136 1.245618177 1.185902986 1.222732231 1 19.21383039 2.243720994 24.99999733 1.182166193 1.126937739 0.051127561 0.070040247 246.1856235 1192676.472 0.022076575 0.017952825 175.2754108 -2.243720994 -0.055228454 SS(ph)PELTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSPELTR 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.062)S(0.938)PELTR;S(0.108)S(0.892)PELTR 202.28 0.00032773 973710000 958520 930040 908930 824230 927970 823960 1220940 925050 850760 TRUE FALSE 898527.9442 998901.1293 930490.2488 845381.1372 855090.9795 1061823.876 1037871.382 1040544.529 708762.6599 1.26774165 1.409359135 1.312837571 1.192756313 1.206456022 1.498137439 1.464342636 1.468114205 1 19.43494307 2.238766694 24.99999997 1.407264857 1.296672667 0.011718767 0.154134591 12.18743183 1478774.506 0.051072937 0.040233376 173.2872838 -2.238766694 -0.110592191 SS(ph)PEQPRPSTSK ddPTM_SK-BR-3_Pertuzumab_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(0.049)S(0.951)PEQPRPSTSK;S(0.138)S(0.862)PEQPRPSTSK 186.51 3.07E-05 3061880000 1391620 1158060 1202440 1181210 1248820 936620 1453990 1047430 1532740 TRUE FALSE 1304520.988 1243803.967 1230962.445 1211521.848 1150742.715 1207006.989 1235977.698 1178203.941 1276915.792 1.02161865 0.974068905 0.964012233 0.948787583 0.901189195 0.94525183 0.967939864 0.922695097 1 20.28423196 5.282733359 0.819747303 0.946998946 1.14389487 0.427862499 0.026280011 4.920407446 1.357476989 0.008321291 1.082382737 191749.1112 -5.282733359 0.196895924 SS(ph)PGAGPSDHHSASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSPGAGPSDHHSASR 15 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 S(0.408)S(0.592)PGAGPSDHHSASR;S(0.022)S(0.978)PGAGPSDHHSASR;S(0.188)S(0.812)PGAGPSDHHSASR;S(0.226)S(0.774)PGAGPSDHHSASR 258.13 5.30E-25 4994230000 470841 1600530 1414090 1502590 1554860 1433260 1690590 1478710 1504340 TRUE FALSE 441371.9023 1719034.907 1447632.883 1541149.003 1432747.568 1847018.895 1437101.724 1663330.199 1253255.936 0.352180181 1.371655109 1.155097567 1.229716101 1.143220253 1.473776299 1.146694529 1.327207118 1 20.25724964 4.74369579 24.99947083 1.241207093 0.352179813 0.808131158 0.134479646 202.09748 983836.6606 0.027760197 0.233954724 55423.73501 -4.74369579 -0.88902728 SS(ph)PGPDTLVVLEFNPASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPGPDTLVVLEFNPASK 18 0 O60303 O60303 KIAA0556 Uncharacterized protein KIAA0556 1 S(0.017)S(0.983)PGPDTLVVLEFNPASK 440.29 1.50E-190 87602000 146080 107730 123180 109260 103760 102280 155600 107210 87508 TRUE FALSE 136937.1136 115706.4413 126101.8878 112063.7966 95611.10815 131806.5756 132269.2245 120595.4045 72902.34948 1.878363517 1.58714283 1.729736952 1.537176749 1.311495567 1.807988036 1.814334181 1.654204636 1 16.15367769 4.741911662 23.57314545 1.6113595 1.878363749 0.10680665 0.250661077 347.1330104 2441660.476 0.054328677 0.389830408 55196.51549 -4.741911662 0.267004249 SS(ph)PGQTPEEGAQALAEFAALHGPALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSPGQTPEEGAQALAEFAALHGPALR 26 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 1 S(0.054)S(0.946)PGQTPEEGAQALAEFAALHGPALR;S(0.419)S(0.581)PGQTPEEGAQALAEFAALHGPALR 315.47 4.34E-82 23688000000 429080 473320 470890 440750 499400 401940 549100 437200 565950 TRUE FALSE 402224.6487 508365.1053 482059.7332 452060.3912 460179.1385 517973.553 466767.5526 491785.3824 471489.2888 0.853093927 1.078211356 1.022419267 0.958792494 0.976011862 1.098590287 0.989985486 1.043046776 1 18.84686547 SS(ph)PIMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSPIMR 6 0 A0A087WZV0;O43314-2;O43314;A0A087WWN8;K7ENU7;H0Y9S9 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 S(0.159)S(0.841)PIMR;S(0.063)S(0.937)PIMR 139.31 0.046618 1340880000 886850 977520 966200 1009770 1029760 769200 1096220 901300 1061690 TRUE FALSE 831343.6416 1049896.598 989118.7203 1035682.408 948886.8035 991255.5531 931851.9878 1013829.289 884487.0802 0.939916094 1.187011796 1.118296403 1.17094125 1.072810248 1.120712303 1.053550706 1.146234141 1 19.75448154 1.751613855 25 1.074002361 1.114951588 0.02298489 0.075936565 11.88976295 22806.28768 0.031982485 0.017736796 56.44348941 -1.751613855 0.040949227 SS(ph)PINPAQS(ph)GSPNHVDSAYFPGSSTSSSSDNDEGSGGATNHISGNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPINPAQSGSPNHVDSAYFPGSSTSSSSDNDEGSGGATNHISGNK 46 0 Q9NZB2;Q9NZB2-4;Q9NZB2-2;Q9NZB2-5;A0A0C4DH52 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 2 S(0.47)S(0.53)PINPAQS(0.814)GS(0.185)PNHVDSAYFPGSSTSSSSDNDEGSGGATNHISGNK 160.76 3.19E-21 124760000 22805 47292 46432 48105 51658 38411 63037 46671 47014 TRUE FALSE 21377.67576 50793.54889 47533.38897 49339.45574 47600.98906 49499.63215 53585.18706 52497.97709 39167.05968 0.545807521 1.296843554 1.213606264 1.259718144 1.215332206 1.263807714 1.368118707 1.340360433 1 15.25735321 4.740270148 24.93764155 1.261733117 0.545807274 0.824840686 0.100948134 51.51176813 751359.3127 0.021637288 0.138232427 54988.28157 -4.740270148 -0.715925843 SS(ph)PLKITLFLEEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPLKITLFLEEDK 14 1 Q9NQW6 Q9NQW6 ANLN Actin-binding protein anillin 1 S(0.12)S(0.88)PLKITLFLEEDK 172.66 1.71E-06 153830000 571380 406750 509080 535480 625470 413840 746880 423850 1029100 TRUE FALSE 535618.3457 436866.1932 521155.618 549221.3234 576348.1092 533308.8899 634892.2777 476768.6055 857336.5618 0.624746884 0.50956207 0.607877514 0.640613439 0.672254206 0.622053128 0.740540304 0.556104366 1 19.70950214 -5 0.180539604 2.560364111 0.540690931 0.77905425 0.062929502 55.84848542 0.538603422 31.23657542 0.180064763 1.00E-05 5 -2.019673181 SS(ph)PLPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SSPLPAK 7 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 S(0.09)S(0.91)PLPAK;S(0.064)S(0.936)PLPAK;S(0.02)S(0.98)PLPAK;S(0.127)S(0.873)PLPAK;S(0.179)S(0.821)PLPAK 120.87 0.0047134 2187670000 9729950 6356320 7595350 6740320 5948380 7253100 12482790 7328740 7573070 TRUE FALSE 9120969.798 6826948.547 7775515.289 6913288.023 5481218.229 9346952.226 10611111.52 8243749.322 6309075.693 1.445690342 1.082083791 1.23243335 1.095768756 0.868783083 1.481508969 1.681880523 1.306649297 1 22.58899723 2.199277111 24.99218533 1.453969814 1.14607242 0.148066362 0.226381514 184.5567808 117414.0303 0.078529489 0.057998791 158.2257311 -2.199277111 -0.307897393 SS(ph)PNPFITGLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SSPNPFITGLTR 12 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 S(0.316)S(0.684)PNPFITGLTR;S(0.131)S(0.869)PNPFITGLTR;S(0.18)S(0.82)PNPFITGLTR;S(0.133)S(0.867)PNPFITGLTR;S(0.142)S(0.858)PNPFITGLTR 247.79 1.18E-16 1445300000 1063718 1134578 1122311 1115544 1261183 1027990 1533990 1231586 1558650 TRUE FALSE 997141.7892 1218583.336 1148932.747 1144170.748 1162134.775 1324754.025 1303982.44 1385352.223 1298501.246 0.767917468 0.938453729 0.884814513 0.881147208 0.89498164 1.020217754 1.00422117 1.066885556 1 20.30841597 2.254542085 5.049549747 1.021964328 0.883239819 0.719345258 0.046187366 0.100048589 6.862210448 0.015799777 0.012480767 179.6975207 -2.254542085 -0.13872451 SS(ph)PNVANQPPS(ph)PGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.263)S(0.737)PNVANQPPS(1)PGGK;S(0.28)S(0.72)PNVANQPPS(1)PGGK;S(0.436)S(0.564)PNVANQPPS(1)PGGK 291.25 9.42E-44 826852000 1750240 1206500 1406750 1394460 1488780 903730 1349650 1026530 993690 TRUE FALSE 1640695.603 1295830.515 1440118.774 1430244.204 1371857.224 1164622.18 1147282.512 1154694.53 827836.7195 1.981907258 1.565321379 1.739616932 1.727688771 1.657159186 1.406825951 1.385880192 1.394833671 1 19.65898672 1.32732803 0.407940757 0.971888488 1.790917374 0.82645106 0.110994393 0.43343427 0.213305081 0.140836852 0.093937561 21.24848792 -1.32732803 0.819028886 SS(ph)PPLPPPAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPPLPPPAEER 12 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 S(0.104)S(0.896)PPLPPPAEER 96.551 0.0056858 241960000 145790 124930 128200 131680 101790 102560 155680 105360 145840 TRUE FALSE 136665.2641 134179.9472 131240.9645 135059.1317 93795.824 132167.4071 132337.2293 118514.4279 121498.3618 1.124832155 1.104376595 1.080187112 1.11161278 0.771992499 1.087812256 1.089209988 0.975440542 1 16.89057734 SS(ph)PQKEVK ddPTM_SK-BR-3_Pertuzumab_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(0.145)S(0.855)PQKEVK;S(0.13)S(0.87)PQKEVK 86.014 0.0098919 533850000 1646950 1447910 1577900 1710200 1973110 1220790 2164100 1439040 3013800 TRUE FALSE 1543870.339 1555114.763 1615328.533 1754086.627 1818149.9 1573212.255 1839613.296 1618707.312 2510777.31 0.61489736 0.619375823 0.643357946 0.698622941 0.724138255 0.626583747 0.732686761 0.644703656 1 21.25970265 -5 0.225769808 2.770580443 0.622507063 0.87318598 0.04061133 48.8665862 0.489286126 39.43742682 0.068224813 1.00E-05 5 -2.14807338 SS(ph)PQLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SSPQLAK 7 0 Q13370-2;Q13370 Q13370-2 PDE3B "cGMP-inhibited 3,5-cyclic phosphodiesterase B" 1 S(0.447)S(0.553)PQLAK;S(0.118)S(0.882)PQLAK;S(0.13)S(0.87)PQLAK;S(0.071)S(0.929)PQLAK;S(0.014)S(0.986)PQLAK;S(0.017)S(0.983)PQLAK;S(0.114)S(0.886)PQLAK 110.22 0.0071884 16092290000 61820300 30918960 55741500 50289000 36169750 38946140 58086700 30098530 38307340 TRUE FALSE 57951077.78 33208231.97 57063714.7 51579500.88 33329123.74 50189258.38 49377138.59 33856397.73 31913597.48 1.815874184 1.040566862 1.788069012 1.616223333 1.044354957 1.572660632 1.547213178 1.06087688 1 24.92766791 1.218686654 10.97204878 1.029368376 1.471914721 0.342156966 0.26365377 0.581284069 306.3943136 0.222173049 0.058968372 16.54575745 -1.218686654 0.442546344 SS(ph)PQLDPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSPQLDPLR 9 0 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.015)S(0.985)PQLDPLR;S(0.191)S(0.809)PQLDPLR 154.66 7.88E-05 566330000 966220 1113220 786930 780330 1099820 639940 887010 1082820 900580 TRUE FALSE 905746.015 1195643.967 805596.3512 800354.5889 1013444.574 824680.2894 754011.0851 1218012.461 750267.38 1.207230967 1.593623819 1.073745671 1.066759145 1.35077787 1.099181854 1.004989828 1.623437848 1 19.51704531 3.909931936 5.850850662 1.164123293 1.415565455 0.165404851 0.209555027 0.284400184 18.18980048 0.049175047 0.090902518 8127.031363 -3.909931936 0.251442162 SS(ph)PQLDPLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSPQLDPLRK 10 1 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.479)S(0.521)PQLDPLRK;S(0.135)S(0.865)PQLDPLRK;S(0.041)S(0.959)PQLDPLRK 135.04 9.47E-05 6673640000 6729800 5014770 5661600 5064440 5133520 4611840 6858900 5076290 4452410 TRUE FALSE 6308593.831 5386068.789 5795895.826 5194402.104 4730354.047 5943203.341 5830471.62 5710075.981 3709274.007 1.700762418 1.452054709 1.562541838 1.400382418 1.275277598 1.602255139 1.571863283 1.539405277 1 21.82270541 -1.966316713 2.460441572 0.578467378 1.510169965 0.655729524 0.116816028 7998925.375 3878167.456 19229054.66 0.027087098 0.010806456 1.966316713 0.931702586 SS(ph)PQLDPLRKS(ph)PTMEQAVQTASAHLPAPAAVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SSPQLDPLRKSPTMEQAVQTASAHLPAPAAVGR 33 2 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 2 S(0.456)S(0.544)PQLDPLRKS(0.5)PT(0.5)MEQAVQTASAHLPAPAAVGR;S(0.45)S(0.55)PQLDPLRKS(0.845)PT(0.155)MEQAVQTASAHLPAPAAVGR;S(0.468)S(0.532)PQLDPLRKS(0.5)PT(0.5)MEQAVQT(0.001)ASAHLPAPAAVGR;S(0.471)S(0.529)PQLDPLRKS(0.799)PT(0.196)MEQAVQT(0.004)AS(0.002)AHLPAPAAVGR;S(0.463)S(0.535)PQLDPLRKS(0.5)PT(0.5)MEQAVQT(0.002)ASAHLPAPAAVGR;S(0.479)S(0.521)PQLDPLRKS(0.96)PT(0.034)MEQAVQT(0.005)AS(0.001)AHLPAPAAVGR;S(0.48)S(0.52)PQLDPLRKS(0.942)PT(0.044)MEQAVQT(0.007)AS(0.007)AHLPAPAAVGR;S(0.478)S(0.522)PQLDPLRKS(0.73)PT(0.164)MEQAVQT(0.08)AS(0.027)AHLPAPAAVGR 180.81 6.66E-20 2949472000 1275331 1605319 1491827 1654752 2163386 984418 1815123 1469988 2819404 TRUE FALSE 1195510.309 1724178.489 1527213.841 1697215.738 1993482.39 1268603.496 1542962.157 1653519.238 2348827.258 0.508981793 0.734059298 0.650202707 0.722580059 0.84871392 0.540100806 0.656907464 0.703976519 1 21.16350919 0.796081788 4.739775037 0.999997627 0.672319017 0.541797235 0.095653778 2.675657783 61.69994952 0.08484821 0.021491285 6.252904381 -0.796081788 -0.32767861 SS(ph)PSARPPDVPGQQPQAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSPSARPPDVPGQQPQAAK 19 1 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 S(0.162)S(0.838)PSARPPDVPGQQPQAAK;S(0.007)S(0.993)PSARPPDVPGQQPQAAK 237.73 1.91E-24 1475150000 1369150 956920 1124710 1080310 1036520 867590 1390240 977180 1026900 TRUE FALSE 1283457.346 1027771.352 1151388.652 1108032.584 955115.9003 1118049.149 1181786.418 1099183.074 855503.756 1.500235781 1.201363928 1.345860429 1.295181436 1.116436829 1.306889819 1.381392437 1.284837228 1 19.70641466 -2.280048748 1.872309105 1.53E-05 1.29899177 0.469463199 0.101445353 1369791.985 182414.7857 5788008.378 0.023262662 0.005247486 2.280048748 1.298976477 SS(ph)PSIICMPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSPSIICMPK 10 0 Q9NZN8;Q9NZN8-5;F8VP97;F8VV52;F8VUB4;Q9NZN8-4;F8VX63;F8VVY1;F8VQD8;A0A087X050 Q9NZN8 CNOT2 CCR4-NOT transcription complex subunit 2 1 S(0.181)S(0.817)PS(0.002)IICMPK;S(0.04)S(0.96)PSIICMPK 180.66 2.07E-06 248080000 1039100 839730 875120 806820 884290 702510 1087530 908250 723300 TRUE FALSE 974064.5858 901904.4829 895878.2597 827524.3671 814841.4305 905313.2327 924464.9726 1021647.012 602576.5573 1.616499305 1.496746715 1.486745956 1.373309926 1.352262083 1.502403673 1.534186754 1.695464252 1 19.20078502 5.300277454 1.003787295 1.449600317 1.946023956 0.093272155 0.179348289 13.84478524 5.089845148 0.048347853 9.692073399 199653.742 -5.300277454 0.496423638 SS(ph)PSPQKR ddPTM_SK-BR-3_Pertuzumab_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(0.111)S(0.889)PSPQKR;S(0.41)S(0.59)PSPQKR;S(0.127)S(0.87)PS(0.002)PQKR 105.2 0.0027162 324020000 299895 299298 295292 322628 316586 244477 340498 304112 319787 TRUE FALSE 281125.1073 321458.3353 302296.4657 330907.1807 291722.6126 315053.5411 289443.4859 342081.0526 266412.4838 1.055224978 1.206618889 1.13469332 1.242085866 1.095003539 1.182577996 1.08644866 1.284027864 1 18.02330216 SS(ph)PVESLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSPVESLKK 9 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 S(0.016)S(0.984)PVESLKK;S(0.071)S(0.929)PVESLKK 143.97 6.17E-05 1412590000 3466870 2003590 2502700 2443460 2647500 1806180 3112480 2263830 2896750 TRUE FALSE 3249884.795 2151937.888 2562065.226 2506163.32 2439576.03 2327594.845 2645792.519 2546474.159 2413263.711 1.346676196 0.891712695 1.061659865 1.038495424 1.010903209 0.964500827 1.096354496 1.055199292 1 21.20255415 4.752399356 24.96723414 1.016527017 1.34667642 0.771519313 0.056742768 1178.187707 2125596.044 0.013734554 0.282703688 56545.67024 -4.752399356 0.330149403 SS(ph)PVKKPSLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPVKKPSLLK 11 2 O60318 O60318 MCM3AP Germinal-center associated nuclear protein 1 S(0.459)S(0.54)PVKKPS(0.001)LLK 46.318 0.095551 521670000 1156900 784160 890070 869110 984780 716220 1312800 1002600 1139800 TRUE FALSE 1084491.694 842220.0223 911182.8807 891412.834 907439.3512 922981.0871 1115957.827 1127776.817 949560.0166 1.142099157 0.886958178 0.959584297 0.938764079 0.955641913 0.972009216 1.17523675 1.187683556 1 19.85689966 1.772233118 7.952350292 1.135469713 0.96127471 0.395142238 0.082697271 0.151406693 26.872456 0.03506886 0.019538322 59.1879255 -1.772233118 -0.174195003 SS(ph)PVKVGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSPVKVGEK 9 1 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 1 S(0.002)S(0.998)PVKVGEK;S(0.156)S(0.844)PVKVGEK 167.84 3.61E-05 2127530000 5805600 3342100 4281500 4088200 4970900 2878100 5971100 3936400 6727500 TRUE FALSE 5442237.859 3589552.561 4383059.202 4193110.133 4580505.566 3708960.748 5075788.988 4427868.205 5604636.789 0.971024183 0.640461228 0.782041614 0.7481502 0.817270724 0.661766478 0.905641022 0.790036602 1 22.41818945 0.691034666 0.727292319 1.000121657 0.758824985 0.296028248 0.099618974 1.21003147 1.221992475 0.090882366 0.032563781 4.909470626 -0.691034666 -0.241296672 SS(ph)PVNRPSSATNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSPVNRPSSATNK 13 1 Q96L91-4;Q96L91-3;Q96L91-5;Q96L91-2;Q96L91;A0A0A0MR80;A0A0A0MR72 Q96L91-4 EP400 E1A-binding protein p400 1 S(0.117)S(0.883)PVNRPSSATNK;S(0.131)S(0.869)PVNRPSSATNK 106.36 0.00083598 248310000 299328 243994 247032 222932 258687 196016 372346 260838 309928 TRUE FALSE 280593.5948 262059.5696 252891.7157 228652.8125 238370.7665 252602.6371 316516.174 293404.1985 258199.0146 1.086733794 1.014951858 0.97944493 0.885568107 0.923205563 0.978325334 1.225861278 1.136349025 1 17.97812397 1.758685518 25 1.141460162 0.976794234 0.431687419 0.075943462 7.254252118 9019.647199 0.033860623 0.018777922 57.37008832 -1.758685518 -0.164665928 SS(ph)PVPPVPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SSPVPPVPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(0.007)S(0.993)PVPPVPER;S(0.253)S(0.747)PVPPVPER;S(0.189)S(0.811)PVPPVPER;S(0.117)S(0.883)PVPPVPER;S(0.364)S(0.636)PVPPVPER 177.57 2.42E-06 3061040000 2842280 2667600 2827620 2556960 2797250 2476250 3445310 2680240 3084160 TRUE FALSE 2664386.768 2865111.88 2894692.482 2622575.923 2577565.269 3191103.176 2928717.75 3014873.864 2569393.772 1.036970977 1.11509256 1.126605238 1.020698326 1.003180321 1.241967351 1.139847766 1.173379455 1 21.29299658 2.246506864 24.99987536 1.152584776 1.075156105 0.205001646 0.071268068 263.1822918 828005.2694 0.023676637 0.019489184 176.4033644 -2.246506864 -0.077428671 SS(ph)REKEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSREKEQR 8 2 H7C1L9 H7C1L9 TRIP12 1 S(0.124)S(0.876)REKEQR;S(0.443)S(0.557)REKEQR;S(0.114)S(0.886)REKEQR 82.417 0.010606 322077000 176648 274325 261450 263914 304732 187811 270748 265674 409802 TRUE FALSE 165591.917 294636.3084 267651.7175 270686.48 280799.5779 242028.9868 230151.8509 298843.9837 341403.3988 0.485033007 0.863015159 0.783974965 0.792864046 0.822486182 0.708923777 0.674134621 0.875339803 1 18.3811179 1.001199334 5.408340294 0.999746377 0.751287173 0.415766322 0.104929507 0.137473226 15.39084634 0.0947461 0.023897137 10.02765385 -1.001199334 -0.248459203 SS(ph)RSS(ph)PELTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSRSSPELTR 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.425)S(0.568)RS(0.509)S(0.498)PELTR;S(0.445)S(0.555)RS(0.39)S(0.611)PELTR;S(0.435)S(0.563)RS(0.067)S(0.935)PELTR 95.6 0.0041604 2287370000 1289600 1243630 1318390 1368580 1341850 1060250 1361020 1118940 1335240 TRUE FALSE 1208886.238 1335709.659 1349662.833 1403700.08 1236466.514 1366326.963 1156947.686 1258642.122 1112379.818 1.086756716 1.200767613 1.213311147 1.261889201 1.111550654 1.228291759 1.040065333 1.131485938 1 20.08521804 1.459704654 0.977551609 1.018507803 1.193520764 0.435494689 0.063851811 0.401182648 0.767092066 0.052905756 0.019477806 28.8207086 -1.459704654 0.175012961 SS(ph)S(ph)AS(ph)T(ph)AAT(ph)WLWQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSASTAATWLWQAR 15 0 J3QKM6 J3QKM6 LLGL2 5 S(0.635)S(0.683)S(0.683)AS(1)T(1)AAT(1)WLWQAR 43.184 0.074649 247140000 7344.9 15506 11247 11143 12768 18641 10532 14094 11199 TRUE FALSE 6885.19582 16654.08037 11513.78415 11428.94825 11765.25278 24022.35409 8952.824374 15853.66692 9329.814552 0.737977779 1.785038736 1.234084996 1.224992006 1.261038225 2.574794382 0.959592961 1.699247808 1 13.18763269 4.754725373 23.78275049 1.477526578 0.737976666 0.18988424 0.473041267 2556.259001 3760828.101 0.101739876 2.491132543 56849.33296 -4.754725373 -0.739549912 SS(ph)SESLIFSGNQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSSESLIFSGNQGR 14 0 Q8IZW8 Q8IZW8 TNS4 Tensin-4 1 S(0.01)S(0.99)S(0.001)ESLIFSGNQGR;S(0.006)S(0.993)S(0.001)ESLIFSGNQGR;SS(0.999)SESLIFSGNQGR;S(0.001)S(0.998)S(0.001)ESLIFSGNQGR 317.77 5.94E-56 589720000 704890 904150 824490 883410 973740 548833 680400 670576 729610 TRUE FALSE 660772.1932 971094.2068 844047.2922 906079.7962 897266.3883 707272.1775 578380.3365 754298.8897 607833.3775 1.087094289 1.59763225 1.388616228 1.490671341 1.476171631 1.163595491 0.951544219 1.24096326 1 19.21331637 2.123587071 4.324724887 1.058670858 1.434608883 0.528184117 0.150563339 0.142534903 4.703643867 0.05393885 0.038768537 132.9190018 -2.123587071 0.375938025 SS(ph)SKESLVR ddPTM_SK-BR-3_Pertuzumab_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(0.092)S(0.453)S(0.453)KES(0.002)LVR 91.123 0.0066412 411700000 559550 403220 438760 476420 465790 308130 548200 384990 476130 TRUE FALSE 524528.7643 433074.8284 449167.5944 488645.7438 429208.7323 397082.1289 466002.4992 433056.849 396660.8271 1.32236089 1.091801355 1.13237195 1.231898162 1.082054751 1.001062121 1.174813512 1.091756028 1 18.5975464 2.700931796 23.00786396 1.082649168 1.167100939 0.349117741 0.079753335 340.5580879 208230.6998 0.025001245 0.023572219 502.2637047 -2.700931796 0.084451771 SS(ph)SPELVTHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSPELVTHLK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.139)S(0.431)S(0.431)PELVTHLK;S(0.1)S(0.45)S(0.45)PELVTHLK 235.31 1.04E-15 1294500000 1542980 1472710 1454350 1515460 1436980 1040100 1619280 1174050 1589820 TRUE FALSE 1446407.636 1581750.981 1488847.869 1554349.269 1324125.387 1340359.985 1376483.997 1320632.727 1324468.771 1.092066244 1.194253134 1.124109455 1.173564302 0.999740738 1.011998179 1.039272519 0.997103711 1 20.3369824 2.736400704 24.9999415 1.014473552 1.150392623 0.838840741 0.029632588 67.35569021 779605.9578 0.00862752 0.008519646 545.0052724 -2.736400704 0.135919071 SS(ph)SQPSSCCSDPSKPGGNVEGATQSLAEQMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSQPSSCCSDPSKPGGNVEGATQSLAEQMR 31 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.018)S(0.43)S(0.43)QPS(0.104)S(0.018)CCSDPSKPGGNVEGATQSLAEQMR 160.52 1.23E-12 538800000 192550 137780 150300 147980 163400 107000 201900 132750 181630 TRUE FALSE 180498.6392 147981.3746 153865.187 151777.4173 150567.2231 137889.163 171626.9693 149324.1297 151314.7796 1.192868533 0.977970393 1.016854978 1.003057452 0.995059594 0.911273594 1.134237976 0.986844313 1 17.20719338 4.744370159 24.81707095 1.008324205 1.192868622 0.540618649 0.054773875 473.2747634 2021659.709 0.012671777 0.113720447 55509.86339 -4.744370159 0.184544417 SS(ph)SS(ph)PPPKQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSSPPPKQK 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.446)S(0.553)S(0.22)S(0.781)PPPKQK 66.989 0.036599 117470000 211540 136870 165520 169300 201510 107600 206590 135620 362860 TRUE FALSE 198300.089 147003.9972 169446.2126 173644.5246 185684.2175 138662.3733 175613.7474 152552.4555 302296.3218 0.655979166 0.486291055 0.560530183 0.574418252 0.614245705 0.458696859 0.580932465 0.504645424 1 18.2056039 -1.437450566 3.063278522 1.008506465 0.549353373 0.84826317 0.05918403 21519302.55 26700191.68 1588318.832 0.012507391 0.03652157 1.437450566 -0.459153092 SS(ph)SVPHPFQVTLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSVPHPFQVTLLR 14 0 Q5VV41;Q5VV41-2 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 S(0.174)S(0.825)S(0.001)VPHPFQVTLLR;S(0.013)S(0.983)S(0.004)VPHPFQVTLLR;S(0.023)S(0.976)S(0.001)VPHPFQVTLLR 236.12 3.10E-17 4590290000 1554720 2000140 1551100 1690120 2064520 1127480 2115810 1708890 1960840 TRUE FALSE 1457412.85 2148232.447 1587892.824 1733491.341 1902380.927 1452965.173 1798563.933 1922248.678 1633563.136 0.892168058 1.315059332 0.972042518 1.061171926 1.164559168 0.889445373 1.101006684 1.176721386 1 20.63959078 3.780462235 24.97525125 1.054125131 1.136739594 0.011891244 0.132444005 453.7833395 212466.9177 0.030706599 0.055357042 6032.012523 -3.780462235 0.082614463 SS(ph)TDFSELEQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSTDFSELEQPR 12 0 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 S(0.014)S(0.986)TDFSELEQPR 225.97 1.72E-11 170630000 272910 292960 289000 291780 299990 248270 329930 263320 345930 TRUE FALSE 255829.0503 314651.0632 295855.2165 299267.5688 276429.9955 319941.5187 280460.0594 296196.0816 288192.0482 0.887703363 1.091810358 1.026590492 1.038431042 0.959186755 1.110167753 0.973170707 1.027773263 1 18.136671 SS(ph)TDSLPGPISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSTDSLPGPISR 12 0 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 S(0.04)S(0.955)T(0.005)DSLPGPISR 144.51 6.62E-05 105760000 95948 85986 74626 77504 97841 84472 105320 86603 109080 TRUE FALSE 89942.78595 92352.49291 76396.16396 79492.88385 90156.96253 108857.6951 89528.24374 97415.57519 90873.84332 0.989754397 1.016271454 0.840683756 0.874760888 0.992111253 1.1978991 0.985192664 1.071986962 1 16.47157748 2.474654799 24.99814485 1.063573615 0.930107455 0.414329986 0.074789431 75.42106148 764394.1418 0.025446327 0.021410622 298.3010616 -2.474654799 -0.13346616 SS(ph)TPLPTISSSAENTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSTPLPTISSSAENTR 16 0 P42166;P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 S(0.016)S(0.982)T(0.002)PLPTISSSAENTR 154.46 3.71E-07 169410000 278970 241670 205280 194620 265690 213580 329050 273630 316410 TRUE FALSE 261509.7657 259563.4983 210149.3385 199614.2787 244823.7791 275237.0788 279712.0073 307793.3078 263599.1269 0.992073717 0.984690281 0.797230784 0.757264567 0.928773103 1.044150191 1.061126456 1.16765678 1 18.00798607 2.25025192 3.241461924 1.076159406 0.882256084 0.540842612 0.081838027 0.195020014 4.281208356 0.033827393 0.02538026 177.9311229 -2.25025192 -0.193903322 SS(ph)TPPRQS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSTPPRQSPSR 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.286)S(0.357)T(0.357)PPRQS(0.997)PS(0.002)R 75.764 0.021165 468060000 75708 73576 65270 73595 80382 55401 76773 69222 78122 TRUE FALSE 70969.57142 79023.6436 66818.23522 75483.5723 74069.12197 71394.36934 65261.60138 77864.51908 65082.93351 1.090448257 1.214199166 1.02666293 1.159805931 1.138072886 1.096975282 1.002745234 1.196389205 1 15.98999166 -4.999999999 0.091531933 0.649291789 1.19807883 0.190835381 0.068522815 311.2423739 1.97474695 21.33035366 1.436266606 1.00E-05 4.999999999 0.548787041 SS(ph)TSSEPTPTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSTSSEPTPTVK 12 0 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 S(0.183)S(0.817)TSSEPTPTVK 244.18 2.30E-16 116140000 574120 401730 465610 444460 459040 387660 619010 452790 484600 TRUE FALSE 538186.854 431474.5072 476654.4891 455865.5961 422988.8501 499571.1489 526195.1971 509321.8282 403717.1294 1.333079067 1.068754521 1.180664516 1.129170805 1.047735702 1.237428666 1.30337595 1.261580922 1 18.62298527 2.12904955 21.61072793 1.234613411 1.14333517 0.002468323 0.111955425 6.785573492 1308.41893 0.037738899 0.027872054 134.6013917 -2.12904955 -0.09127824 SS(ph)VEKENQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSVEKENQK 9 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 S(0.262)S(0.738)VEKENQK;S(0.214)S(0.786)VEKENQK 126.83 0.00028006 396150000 1244950 533230 788320 821450 688690 547620 963410 599360 769880 TRUE FALSE 1167030.802 572710.904 807019.3227 842529.7977 634603.0654 705709.0041 818955.6144 674191.4154 641382.0544 1.819556369 0.892932535 1.25825055 1.313616108 0.989430654 1.100294278 1.276860818 1.051154161 1 19.29082446 4.750926795 24.87262011 1.128055127 1.81955683 0.722099877 0.137884342 1011.781928 2035000.535 0.031908441 0.554934256 56354.26573 -4.750926795 0.691501703 SSAQLLEDWGMEDIDHVFSEEDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 ;;;;;; 257.34 6.76E-44 479502000 369938.7 449440 428368 414949 426166 356754 509076 395309.1 457370 FALSE TRUE 346784.8971 482717.0052 438529.0913 425597.2938 392696.6414 459743.0884 432744.7798 444664.3113 381031.9923 0.910120158 1.266867389 1.15089835 1.116959474 1.030613306 1.206573458 1.135717705 1.166999938 1 18.53955261 3.240746397 22.50570522 1.120470879 1.149004052 0 0.107171664 99.36916334 1023092.166 0.028214571 0.036361503 1740.790056 -3.240746397 0.028533174 SSATS(ph)GDIWPGLSAYDNS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSATSGDIWPGLSAYDNSPR 20 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 S(0.001)S(0.002)AT(0.108)S(0.889)GDIWPGLS(0.001)AYDNS(0.999)PR 171.47 1.14E-11 27409000 65854 51044 59904 55961 53389 62208 70333 52987 47659 TRUE FALSE 61732.31569 54823.35087 61324.95117 57397.054 49196.0433 80166.43974 59787.21959 59602.54359 39704.40501 1.554797652 1.380787619 1.544537719 1.445609221 1.239057563 2.019081755 1.505808224 1.501156952 1 15.27701146 SSATSGDIWPGLSAYDNS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 SSATSGDIWPGLSAYDNSPR 20 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR 372.31 3.56E-112 15430367000 7026537 5854108 6764190 6074852 5412064 7652900 8699040 5980032 5067603 TRUE FALSE 6586758.592 6287552.248 6924639.781 6230742.987 4987022.325 9862167.996 7394699.71 6726652.159 4221787.321 1.560182475 1.489310514 1.640215211 1.475854304 1.181258539 2.336017247 1.751556662 1.593318575 1 22.00942247 SSDEENGPPSS(ph)PDLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSDEENGPPSSPDLDR 16 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 SSDEENGPPSS(1)PDLDR;SSDEENGPPSS(1)PDLDR 356.81 1.85E-87 900610000 1077840 1192500 1190320 1159180 1262760 1118500 1359050 1073830 1288490 TRUE FALSE 1010379.918 1280793.941 1218554.953 1188926.521 1163587.923 1441392.793 1155273.069 1207900.039 1073432.695 0.941260615 1.193175824 1.135194557 1.107592984 1.083987779 1.342788234 1.076241738 1.125268538 1 20.03380031 0.674823679 1.893414201 1.000308816 1.1386082 0.124787977 0.10073276 2.645725057 12.85471325 0.086617727 0.024111834 4.729592009 -0.674823679 0.138299384 SSDITSDLGNVLTST(ph)PNAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSDITSDLGNVLTSTPNAK 19 0 B7Z2R7;Q5T8D3-4;Q5T8D3-2;Q5T8D3-3 B7Z2R7 ACBD5 Acyl-CoA-binding domain-containing protein 5 1 SSDITSDLGNVLT(0.006)S(0.034)T(0.96)PNAK;SSDITSDLGNVLTS(0.083)T(0.917)PNAK 209.45 2.49E-15 47767000 220127 213950 200437 168134 215000 146344 303490 208666 294010 TRUE FALSE 206349.644 229791.0806 205191.4603 172448.6031 198114.7673 188591.1371 257984.492 234718.4094 244937.8316 0.842457217 0.938160835 0.837728737 0.704050501 0.808836944 0.769955118 1.053265191 0.958277486 1 17.9020561 1.7327349 10.03252168 1.00212961 0.828653777 0.655477745 0.063475463 0.067634958 27.58775921 0.032987455 0.01786548 54.04243394 -1.7327349 -0.173475833 SSDQPLTVPVS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SSDQPLTVPVSPK 13 0 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 SSDQPLTVPVS(1)PK;SSDQPLTVPVS(1)PK;SSDQPLTVPVS(1)PK;SSDQPLTVPVS(1)PK;SSDQPLTVPVS(1)PK;SSDQPLTVPVS(1)PK 265.43 2.67E-24 3109710000 9014750 5332510 6643620 6419650 6634570 4768810 8326610 5250140 8550680 TRUE FALSE 8450532.889 5727334.589 6801209.804 6584389.087 6113517.635 6145488.032 7078112.131 5905631.536 7123516.268 1.18628674 0.804003862 0.954754583 0.924317267 0.85821628 0.862704288 0.993626162 0.829033207 1 22.76415812 4.751510729 24.58621723 0.903320407 1.186286969 0.642176353 0.066378411 1049.80311 1993041.338 0.014649413 0.269563121 56430.0882 -4.751510729 0.282966561 SSDS(ph)EEAFETPESTTPVK ddPTM_SK-BR-3_Pertuzumab_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(0.258)S(0.258)DS(0.483)EEAFETPESTTPVK 500.53 9.09E-267 641210000 746220 517960 579870 569710 567100 413560 681240 551100 395500 TRUE FALSE 699515.4222 556310.2973 593624.7902 584329.7231 522562.2536 532948.0584 579094.3863 619906.0481 329488.495 2.123034439 1.688405835 1.801655594 1.773444997 1.585980274 1.617501268 1.757555712 1.881419405 1 18.32986856 -2.048299159 2.473363946 7.40E-05 1.759353983 0.723934915 0.150690614 2958638.333 1012419.912 16743513.75 0.033708313 0.008947482 2.048299159 1.759280007 SSDSFLKLT(ph)T(ph)RAQLGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSDSFLKLTTRAQLGAK 17 2 D6REZ4;A0A1B0GWD8;Q9C093-2;Q9C093 D6REZ4 SPEF2 Sperm flagellar protein 2 2 S(0.413)S(0.413)DS(0.375)FLKLT(0.4)T(0.4)RAQLGAK 67.274 0.063129 238800000 234130 145870 186680 162120 156130 139010 204160 194480 198280 TRUE FALSE 219476.2212 156670.3666 191108.1378 166280.2737 143868.1796 179139.9304 173548.1033 218761.2561 165185.7871 1.328662866 0.948449436 1.156928457 1.006625792 0.87094769 1.084475448 1.050623703 1.324334617 1 17.33373003 -0.613953874 6.964658347 0.999995789 1.076670101 0.025637783 0.147455177 0 0 0.128627906 0.030317888 0.243246235 0.613953874 0.076674312 SSDVSWSDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSDVSWSDTR 10 0 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 90.919 0.024434 111110000 206230 218290 224060 224370 235080 177940 233490 216290 285640 FALSE TRUE 193322.4324 234452.4187 229374.809 230127.7141 216617.7651 229308.3894 198480.3421 243294.2826 237964.8387 0.812399149 0.985239752 0.963902105 0.967066039 0.91029316 0.96362299 0.834074241 1.02239593 1 17.86038889 SSDYQFPS(ph)SPFTDTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSDYQFPSSPFTDTLK 16 0 Q9UK61-3;Q9UK61 Q9UK61-3 FAM208A Protein FAM208A 1 SSDYQFPS(0.498)S(0.498)PFT(0.004)DTLK;SSDYQFPS(0.689)S(0.31)PFT(0.001)DTLK;SSDYQFPS(0.848)S(0.152)PFTDTLK 246.38 3.58E-20 199414000 523379 392222 467871 407783 467476 391400 639605 451729 506820 TRUE FALSE 490621.6426 421262.525 478969.1211 418247.4022 430762.3207 504390.8262 543702.1681 508128.36 422228.4678 1.161981439 0.997712275 1.13438377 0.9905713 1.020211458 1.194592181 1.287696613 1.203444104 1 18.68766433 2.205644227 9.711103249 1.205514654 1.059176459 0.22962404 0.091492676 0.358849541 101.0030168 0.031096309 0.023118629 160.5625388 -2.205644227 -0.146338195 SSECMKDDPITLFVALSPQGTAQGELFLDDGHTFNYQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSECMKDDPITLFVALSPQGTAQGELFLDDGHTFNYQTR 39 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 141.49 2.56E-13 188083000 244331 210972 219958 213681 234194 153057 259688 199307 196121 FALSE TRUE 229038.7589 226592.5864 225175.5076 219164.4162 215801.3479 197242.0712 220750.1952 224190.9177 163387.1381 1.401816333 1.386844699 1.378171564 1.341381083 1.320797649 1.207206843 1.351086737 1.372145447 1 17.31793489 -3.93226158 0.216048268 2.98E-16 1.397211465 0.809570775 0.052887899 38.07118038 0.577435082 16.83740091 0.107706345 0.00011688 3.93226158 1.397211465 SSEELDMDKVTAAMVLTSLST(ph)SPLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSEELDMDKVTAAMVLTSLSTSPLVR 26 1 Q6ZNC4;E5RGL7 Q6ZNC4 ZNF704 Zinc finger protein 704 1 SSEELDMDKVTAAMVLTSLS(0.031)T(0.855)S(0.114)PLVR;SSEELDMDKVTAAMVLTS(0.001)LS(0.016)T(0.552)S(0.431)PLVR 168.87 1.43E-11 132964000 237187 181002 210776 209616 249368 216770 344307 278488 209486 TRUE FALSE 222341.8891 194403.5764 215775.7063 214995.1014 229783.6432 279347.98 292681.3617 313257.8398 174521.4333 1.274009071 1.11392379 1.236385137 1.231912307 1.316649989 1.60065142 1.677051101 1.794953399 1 17.4130447 2.369945971 3.12984352 1.58824292 1.204188913 0.286626414 0.214178162 0.225314082 4.433184378 0.071834568 0.057911867 234.3937198 -2.369945971 -0.384054007 SSEIEQAVQSLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSEIEQAVQSLDR 13 0 Q9BPX5 Q9BPX5 ARPC5L Actin-related protein 2/3 complex subunit 5-like protein 0 ;; 122.42 0.00054719 97245000 138122 161572 150448 142726 166254 126560 152037 140003 168006 FALSE TRUE 129477.1906 173534.959 154016.6976 146388.5908 153197.0815 163095.8175 129240.4633 157482.6827 139964.7132 0.925070238 1.239847923 1.100396622 1.045896408 1.094540745 1.165263828 0.923378902 1.1251599 1 17.09470363 1.750693059 25 1.011332256 1.11054713 0.121478476 0.093970561 5.457808911 11264.92695 0.040356899 0.022379672 56.32394408 -1.750693059 0.099214873 SSELEGDTITLKPRPSADLTNSSAPS(ph)PSHK ddPTM_SK-BR-3_Pertuzumab_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(0.928)PS(0.07)HK 107.6 0.00013352 393090000 80274 61370 81310 70943 82462 45857 103860 70674 156760 TRUE FALSE 75249.79363 65913.89866 83238.7116 72763.51749 75985.76716 59095.17147 88287.15719 79497.80447 130595.7433 0.57620403 0.504717053 0.637376912 0.557166073 0.58183954 0.452504576 0.676033958 0.608731973 1 16.99474835 0.277715894 0.873598604 1.004069216 0.56095014 0.838416626 0.059413146 1.04712701 0.972500459 0.062516918 0.0176853 1.895465541 -0.277715894 -0.443119076 SSEPVKETVQTTQS(ph)PTPVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSEPVKETVQTTQSPTPVEK 20 1 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 SSEPVKETVQT(0.006)T(0.031)QS(0.96)PT(0.003)PVEK;SSEPVKETVQTTQS(1)PTPVEK;SSEPVKETVQT(0.001)T(0.001)QS(0.994)PT(0.004)PVEK;SSEPVKETVQT(0.008)T(0.008)QS(0.983)PT(0.001)PVEK 320.06 7.14E-67 3392150000 1986892 1402500 1614439 1576841 1692215 1153275 2154750 1340450 1665698 TRUE FALSE 1862535.976 1506342.559 1652734.255 1617305.41 1559315.26 1486206.771 1831665.241 1507808.133 1387682.243 1.342191979 1.085509717 1.19100339 1.16547244 1.123683226 1.070999343 1.319945723 1.086565848 1 20.40424582 -2.75831392 1.003071701 0.010260989 1.171727994 0.253364151 0.093428034 16687.06315 775.3953636 36808.65237 0.025950407 0.001744561 2.75831392 1.161467005 SSEPVQADESQS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSEPVQADESQSPR 14 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 SSEPVQADESQS(1)PR 281.49 2.64E-33 164740000 183780 157440 170930 182950 205120 134850 192790 149820 194620 TRUE FALSE 172277.5379 169097.0214 174984.5403 187644.8067 189010.7026 173779.0059 163882.9293 168525.3568 162136.6647 1.062545219 1.04292895 1.079241026 1.157324946 1.165749295 1.071805728 1.010770325 1.03940313 1 17.30685085 1.857867709 4.519537193 1.019480366 1.094752232 0.485638821 0.039292985 0.245790722 7.489187101 0.021065652 0.011978506 72.08878558 -1.857867709 0.075271867 SSEPVQHEESIRKPS(ph)PEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSEPVQHEESIRKPSPEPR 19 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 SSEPVQHEES(0.015)IRKPS(0.985)PEPR;SSEPVQHEES(0.099)IRKPS(0.901)PEPR;SSEPVQHEES(0.276)IRKPS(0.724)PEPR;SSEPVQHEES(0.01)IRKPS(0.99)PEPR 160.67 1.47E-11 7097860000 1097490 1222110 1094180 1182030 1474210 931310 1406890 1131070 1966840 TRUE FALSE 1028800.06 1312596.296 1120134.466 1212362.891 1358431.493 1200164.078 1195939.905 1272286.579 1638561.698 0.627867758 0.801066141 0.683608355 0.739894563 0.829038965 0.732449733 0.729871757 0.77646547 1 20.64399857 -5 0.275650757 2.844770902 0.723660357 0.704661026 0.054034352 118.6058622 1.14355059 124.8483067 0.059065962 1.00E-05 5 -2.121110545 SSESPSS(ph)SPS(ph)SPARK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSESPSSSPSSPARK 15 1 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 2 SSESPS(0.005)S(0.949)S(0.046)PS(0.604)S(0.396)PARK 91.317 0.019859 259160000 375690 345940 359300 430320 436110 214920 374780 296950 441450 TRUE FALSE 352176.2335 371553.7576 367822.7657 441362.7397 401859.6798 276963.9151 318585.2183 334024.8612 367769.1431 0.957601365 1.010290734 1.000145805 1.200108133 1.092695478 0.75309177 0.866264134 0.908246022 1 18.48844091 2.252003769 24.99989764 0.866072272 1.046088302 0.476065294 0.087937103 189.4998555 352407.8319 0.030320863 0.025236216 178.6503079 -2.252003769 0.18001603 SSESPSS(ph)SPSS(ph)PARK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSESPSSSPSSPARK 15 1 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 2 SSESPS(0.01)S(0.986)S(0.004)PS(0.474)S(0.526)PARK 118.72 0.00094134 263150000 405700 365700 358370 462010 477040 245950 416130 315840 439910 TRUE FALSE 380307.9612 392776.8085 366870.7056 473865.9588 439575.2027 316951.7723 353735.1697 355273.3192 366486.1791 1.037714334 1.071737028 1.001049225 1.29299817 1.199431869 0.864839632 0.965207394 0.969404413 1 18.48339927 2.235760546 24.99998622 0.945985189 1.105461309 0.472203146 0.088850448 74.85242253 668297.1698 0.034299194 0.026459039 172.0919463 -2.235760546 0.159476119 SSESPSSSPSS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSESPSSSPSSPAR 14 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 SSESPSSSPS(0.12)S(0.88)PAR 172.82 1.39E-07 0 114060 128260 132680 154030 149930 101990 107770 95341 94907 TRUE FALSE 106921.1882 137756.5039 135827.2323 157982.6706 138155.1026 131432.8573 91610.88899 107244.5337 79066.40858 1.352296002 1.74228862 1.717887972 1.998101007 1.747329935 1.662309693 1.158657521 1.356385545 1 16.27077727 1.781281753 4.246053399 1.189701663 1.727696553 0.666358354 0.17694821 0.120259112 4.206279733 0.085429179 0.0450169 60.43405741 -1.781281753 0.53799489 SSETGAFRVPS(ph)PGMEEAGCSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSETGAFRVPSPGMEEAGCSR 21 1 Q96RL1-2;Q96RL1-3;Q96RL1;Q96RL1-4 Q96RL1-2 UIMC1 BRCA1-A complex subunit RAP80 1 S(0.001)S(0.001)ET(0.001)GAFRVPS(0.997)PGMEEAGCSR 63.085 0.054479 80245000 50067 95953 81322 88001 128600 46297 94356 80331 285150 TRUE FALSE 46933.39584 103057.46 83250.99624 90259.25465 118500.2747 59662.19233 80208.19376 90360.50218 237556.6229 0.197567196 0.433822719 0.35044696 0.379948383 0.498829598 0.251149354 0.337638214 0.380374586 1 17.8579119 0.826219247 8.32755551 0.999999996 0.358250142 0.853622187 0.084142763 12.3050869 590.0131568 0.074215037 0.018580385 6.702228763 -0.826219247 -0.641749854 SSFASSSASDASKPSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSFASSSASDASKPSSPR 18 1 Q96IF1 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 SSFASSSASDASKPS(0.24)S(0.76)PR 72.585 0.013093 319150000 263430 193550 190950 217610 243960 163190 241520 174430 238980 TRUE FALSE 246942.3865 207880.6434 195479.4242 223194.241 224800.3657 210300.3038 205306.3182 196207.9695 199092.6941 1.240338766 1.044139989 0.981851318 1.121056913 1.129124133 1.056293425 1.031209704 0.985510645 1 17.60308076 1.7367206 0.014451118 4.51E-07 2.087150887 0.276735591 0.067743393 830.4670912 11.48414747 822.9976343 832.9128834 54.54068647 -1.7367206 2.087150436 AEDTAVYYCAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 AEDTAVYYCAR 11 0 A0A0C4DH42;P0DP02;A0A0J9YVY3;A0A0B4J1X5;A0A0B4J1V1;P01767;P01780;P01772;P01763;P01762 A0A0C4DH42 IGHV3-66;IGHV3-74;IGHV3-21 Ig heavy chain V-III region BUT;Ig heavy chain V-III region JON;Ig heavy chain V-III region KOL;Ig heavy chain V-III region WEA;Ig heavy chain V-III region TRO 0 ;;; 232.46 7.35E-13 771270000 2591490 1581770 160410 112308 160619 48434.9 69352.8 53252.7 87788.6 FALSE TRUE 2429293.267 1698885.897 164215.001 115190.0134 148004.6316 62417.26936 58953.99148 59901.41682 73136.11552 33.21605543 23.22909666 2.24533392 1.575008634 2.023687348 0.853439766 0.8060859 0.819040174 1 16.15829638 4.261681182 1.260075345 0.880593277 36.13889883 0.99521495 0.791049369 0.044470213 0.104573936 0.247486524 1.637453979 18267.5869 -4.261681182 35.25830555 up SSFDEMLPGTHFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSFDEMLPGTHFQR 14 0 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;E9PFG7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 ; 120.53 0.00012423 212206000 271647 281080 247305 246350 378510 244161 254565 289555 537650 FALSE TRUE 254645.0992 301891.4557 253171.1914 252671.7581 348783.3514 314646.3171 216395.3415 325706.5791 447912.7416 0.568514971 0.673996133 0.565224357 0.564109333 0.778685934 0.702472352 0.483119415 0.727165246 1 18.77285818 0.983062507 23.80343772 1.000000005 0.619338118 0.67553874 0.083271691 331.1016784 465321.4505 0.078237974 0.019559494 9.617506918 -0.983062507 -0.380661887 SSFDWLTGSSTDPLVDHT(ph)SPSSDSLLFAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSFDWLTGSSTDPLVDHTSPSSDSLLFAHK 30 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 1 SSFDWLTGSSTDPLVDHT(0.644)S(0.353)PS(0.001)S(0.001)DSLLFAHK;SSFDWLT(0.001)GS(0.001)S(0.001)T(0.001)DPLVDHT(0.451)S(0.451)PS(0.035)S(0.035)DS(0.024)LLFAHK 286.29 1.81E-71 339850000 392311 368028 405030 431278 415447 326745 511999 406486 439397 TRUE FALSE 367756.9548 395277.1761 414637.5029 442345.3236 382819.4685 421070.9772 435229.5031 457236.6719 366058.8021 1.004639016 1.079818799 1.13270737 1.208399637 1.045786814 1.150282345 1.188960628 1.249079845 1 18.48171589 5.003744039 0.828345192 1.151179507 0.859542392 0.252938636 0.073507083 4.384377097 1.718644627 0.02299041 1.294327261 100865.8237 -5.003744039 -0.291637115 SSFDWLTGSSTDPLVDHT(ph)SPSSDSLLFAHKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSFDWLTGSSTDPLVDHTSPSSDSLLFAHKR 31 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 1 SSFDWLTGSSTDPLVDHT(0.542)S(0.456)PS(0.002)SDSLLFAHKR 169.23 7.19E-13 162860000 91611 130640 104570 103220 152820 88081 180900 121640 260350 TRUE FALSE 85877.23104 140312.7215 107050.4498 105868.8 140818.1336 113508.5548 153775.7244 136827.0218 216895.9031 0.395937543 0.646912733 0.493556809 0.488108805 0.649242939 0.523331945 0.708983997 0.630841892 1 17.72664328 -0.140117993 0.350154269 1.108300964 0.511069367 0.772522394 0.078971161 2.549632985 0.402830238 0.437518335 0.06414754 0.724239166 0.140117993 -0.597231596 SSFDWLTGSSTDPLVDHTS(ph)PSSDSLLFAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSFDWLTGSSTDPLVDHTSPSSDSLLFAHK 30 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 1 SSFDWLTGSSTDPLVDHT(0.004)S(0.634)PS(0.108)S(0.194)DS(0.059)LLFAHK;SSFDWLTGSSTDPLVDHT(0.03)S(0.97)PSSDSLLFAHK 419.46 5.05E-176 767045000 936350 980440 928250 1068450 1018560 782480 1282180 973370 1023770 TRUE FALSE 877745.5249 1053032.798 950268.5284 1095868.236 938566.4063 1008369.273 1089929.012 1094897.387 852896.1732 1.02913526 1.23465532 1.114166716 1.284878829 1.100446263 1.182288425 1.277915233 1.283740532 1 19.7020106 4.747588056 24.14024632 1.194106781 1.02913512 0.210931234 0.09304816 1055.545558 2822531.647 0.020012223 0.241014441 55922.6903 -4.747588056 -0.164971661 SSFFSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SSFFSDR 7 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y650;A0A2R8YCU0;A0A2R8YF89;A0A087WX09;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 0 ;;;;; 147.34 0.005021 2994980000 3015350 3736200 3043890 2987440 4212530 2468250 3513020 3539800 4542630 FALSE TRUE 2826624.626 4012832.136 3116092.508 3064102.768 3881694.886 3180793.706 2986275.264 3981751.822 3784435.706 0.746907821 1.060351515 0.823396868 0.809659089 1.025699784 0.840493525 0.789093935 1.052138847 1 21.85164677 1.221195271 24.99851929 1.026069551 0.88180602 0.287002179 0.100587031 381.952174 549829.7765 0.09175872 0.023158039 16.64160734 -1.221195271 -0.144263531 SSFFSDRGS(ph)GSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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(0.958)GS(0.042)R;SSFFSDRGS(0.981)GS(0.019)R;SSFFSDRGS(0.999)GS(0.001)R;SSFFSDRGS(0.987)GS(0.013)R;SSFFSDRGS(0.997)GS(0.003)R;SSFFSDRGS(0.986)GS(0.014)R;SS(0.002)FFS(0.035)DRGS(0.726)GS(0.237)R 194.55 8.39E-07 4583140000 4426740 3894770 3800540 3485610 2897170 2675780 3254510 1636761 4586420 TRUE FALSE 4149678.245 4183142.823 3890690.604 3575056.654 2669637.955 3448234.248 2766526.439 1841114.214 3820916.873 1.086042535 1.094800793 1.018260992 0.93565413 0.698690404 0.902462514 0.724047796 0.481851418 1 21.86548744 3.043929249 1.41330651 0.745543724 1.085552123 0.512993155 0.135913286 0.29275764 1.209379335 0.047108337 0.058989333 1106.443519 -3.043929249 0.340008399 SSFSQHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSFSQHAR 8 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;; 138.06 0.0007214 842606000 615165 3020260 1379568 1330937 3136520 1146628 1178763 2783160 2284410 FALSE TRUE 576662.9208 3243883.193 1412292.004 1365091.097 2890190.371 1477640.89 1002018.431 3130643.652 1903127.213 0.303008079 1.704501502 0.742090174 0.717288412 1.518653273 0.776427808 0.526511536 1.644999678 1 20.85994057 SSFTPS(ph)SPENVIGDFLLQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSFTPSSPENVIGDFLLQDR 20 0 F5H212;P15822 F5H212 HIVEP1 Zinc finger protein 40 1 S(0.002)S(0.002)FT(0.002)PS(0.497)S(0.497)PENVIGDFLLQDR 71.558 0.01809 14789000 19697 19681 15623 14560 17095 12767 21904 15965 14013 TRUE FALSE 18464.19993 21138.20172 15993.58494 14933.63425 15752.42766 16452.62565 18619.69855 17958.26539 11674.13977 1.58163259 1.810686023 1.370001152 1.279206395 1.34934376 1.409322311 1.594952511 1.538294533 1 13.51102863 -3.523991799 0.182362262 3.17E-34 1.611442368 0.491924052 0.154817712 72.73723776 1.145942358 29.0347858 0.540945092 0.000299232 3.523991799 1.611442368 SSFTPSS(ph)PENVIGDFLLQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSFTPSSPENVIGDFLLQDR 20 0 F5H212;P15822 F5H212 HIVEP1 Zinc finger protein 40 1 SSFTPS(0.051)S(0.949)PENVIGDFLLQDR;SSFTPS(0.083)S(0.917)PENVIGDFLLQDR;SSFT(0.007)PS(0.229)S(0.764)PENVIGDFLLQDR;SSFTPS(0.008)S(0.992)PENVIGDFLLQDR 246.48 5.09E-30 321603000 368856 383124 400038 400692 425500 315067 426278 333552 305830 TRUE FALSE 345769.9614 411490.8996 409527.0903 410974.4351 392082.9464 406021.7282 362361.5713 375196.7014 254784.9973 1.357104873 1.61505153 1.607343818 1.61302447 1.538877684 1.5935857 1.422224916 1.472601234 1 17.9589208 0.357793808 0.719095212 0.989808695 1.570954818 0.801552834 0.083512345 0.86706039 0.643450619 0.095878679 0.027862591 2.279259681 -0.357793808 0.581146123 SSFVSDNSLNRS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSFVSDNSLNRSPR 14 1 Q6UB98-2;Q6UB98 Q6UB98-2 ANKRD12 Ankyrin repeat domain-containing protein 12 1 SSFVSDNS(0.007)LNRS(0.993)PR;SSFVSDNS(0.001)LNRS(0.999)PR 87.287 0.0042408 411120000 440350 464240 454790 475530 505060 363200 493700 406800 608850 TRUE FALSE 412789.2795 498612.8126 465577.8336 487732.9049 465394.6249 468049.9439 419674.2683 457589.8755 507229.0017 0.813812456 0.983013217 0.917884884 0.961563521 0.917523689 0.92275864 0.827386184 0.902136656 1 18.95227771 1.967908854 24.65294598 0.886764323 0.928580577 0 0.061502982 1299.459553 998264.0831 0.022823061 0.014747162 92.87714432 -1.967908854 0.041816254 SSGEIVYCGQVFEKS(ph)PLR ddPTM_SK-BR-3_Pertuzumab_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 238.17 4.32E-24 3792540000 3545760 2851330 3108460 3364320 3362450 2417560 3999780 3006330 3135490 TRUE FALSE 3323837.211 3062445.44 3182194.139 3450654.147 3098376.74 3115470.326 3400050.121 3381676.918 2612156.463 1.27244951 1.172382085 1.218224936 1.320998262 1.186137501 1.192681361 1.301625752 1.294592022 1 21.31680988 -1.055357252 4.882832805 0.999994171 1.238869932 0.682381604 0.052362877 3.36E-06 6.49E-07 0.051220592 0.012072515 0.088032442 1.055357252 0.238875761 SSGFGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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;S(0.002)S(0.007)GFGS(0.992)PR 85.807 0.018383 525810000 1167930 1243800 1264220 1233260 1397800 1060310 1488950 1249100 1601350 TRUE FALSE 1094831.346 1335892.246 1294207.895 1264907.54 1288022.426 1366404.284 1265695.77 1405052.885 1334074.34 0.82066742 1.001362672 0.970116774 0.948153714 0.965480249 1.02423399 0.948744558 1.05320434 1 20.34740763 4.742226816 24.67058832 0.984376793 0.820667344 0.714244821 0.033334381 154.3890164 1038861.997 0.007128462 0.052894746 55236.58448 -4.742226816 -0.163709449 SSGGGYGGGPAGGHGGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSGGGYGGGPAGGHGGNR 18 0 Q9H2U1-2;Q9H2U1;Q9H2U1-3 Q9H2U1-2 DHX36 ATP-dependent RNA helicase DHX36 0 ;;; 216.99 8.66E-19 159890000 69698 86088 81237 79943 81690 61029 91794 75079 80670 FALSE TRUE 65335.72659 92462.04509 83163.98 81994.47272 75274.39692 78647.08158 78030.34187 84452.77842 67205.65585 0.972176014 1.375807496 1.237455076 1.220053159 1.120060447 1.170244983 1.161068081 1.25663201 1 16.03629503 2.893185493 5.083004963 1.154824108 1.238746465 0.013983201 0.118186488 0.519559774 20.24187041 0.03369524 0.036062192 781.96172 -2.893185493 0.083922357 SSGGGYSGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSGGGYSGDR 10 0 Q92804-2;Q92804;A0A075B7F4 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;;; 152.11 4.33E-05 256327000 376064 430903 406132 427435 459948 349825 424826 404602 446028 FALSE TRUE 352526.8255 462807.5065 415765.6428 438403.7057 423825.5394 450813.7986 361127.2852 455117.4503 371583.0453 0.948716121 1.245502216 1.118903696 1.17982699 1.140594397 1.213224888 0.971861579 1.224806826 1 18.50332515 1.752267338 25 1.065443595 1.152075053 0.101968494 0.102340506 8.013089144 14636.22552 0.041821748 0.023192473 56.52848393 -1.752267338 0.086631458 SSGHCHPDVATMLNILALVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSGHCHPDVATMLNILALVYR 21 0 Q6P597;Q6P597-3;Q6P597-2;K7ENJ3;K7EL76 Q6P597 KLC3 Kinesin light chain 3 0 105.38 0.00022672 19543000 21147 33002 25626 24157 34145 21018 23491 29112 21478 FALSE TRUE 19823.44702 35445.50242 26233.86082 24776.90952 31463.38943 27085.5554 19968.74263 32746.69728 17893.18305 1.107877059 1.980950082 1.466137174 1.384712237 1.758400915 1.513736004 1.115997225 1.830121404 1 14.12712243 -3.004523437 0.207324029 2.65E-09 1.632600434 0.197165045 0.292621832 78.31486483 1.637455997 34.94925681 0.644222709 0.000989638 3.004523437 1.632600431 SSGHS(ph)SSELS(ph)PDAVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSGHSSSELSPDAVEK 16 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.001)S(0.001)GHS(0.99)S(0.008)S(0.004)ELS(0.996)PDAVEK 148.89 1.30E-06 148510000 414910 462670 528920 549660 501750 390260 648830 444390 463080 TRUE FALSE 388941.5237 496926.5682 541466.2322 563765.2062 462344.579 502921.7267 551543.9649 499873.0697 385788.9564 1.008171741 1.28807878 1.403529632 1.461330598 1.198439124 1.303618775 1.429652031 1.295716379 1 18.55745232 SSGHSSSELS(ph)PDAVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSGHSSSELSPDAVEK 16 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SSGHSSSELS(1)PDAVEK;SSGHSSSELS(1)PDAVEK;SSGHSSSELS(0.999)PDAVEK;SSGHSSSELS(1)PDAVEK 320 6.40E-47 1374540000 1089410 2097270 1939600 2141610 2176090 1702710 2638580 1863180 2164870 TRUE FALSE 1021225.773 2252554.053 1985608.228 2196567.338 2005188.669 2194254.736 2242949.424 2095802.124 1803539.211 0.566234305 1.248963171 1.100950961 1.217920478 1.111807637 1.21663822 1.243637738 1.162049658 1 20.78239936 4.74276572 24.98849755 1.175601846 0.566234064 0.853304008 0.077565573 134.9767979 802059.1052 0.016440026 0.12803678 55305.16851 -4.74276572 -0.609367782 SSGNS(ph)PTPVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSGNSPTPVSR 11 0 H0YBT1;O95429-2;O95429 H0YBT1 BAG4 BAG family molecular chaperone regulator 4 1 SSGNS(0.982)PT(0.018)PVSR;S(0.007)S(0.021)GNS(0.846)PT(0.126)PVS(0.001)R 139.74 4.08E-05 335740000 502030 424850 452330 409610 537220 435920 554570 425800 554040 TRUE FALSE 470608.8384 456306.3361 463059.4812 420121.2861 495028.9082 561763.0274 471417.3769 478962.0673 461567.1448 1.019589119 0.988602289 1.003233195 0.91020622 1.072495982 1.217077588 1.021340843 1.037686657 1 18.81618101 2.599520604 9.347808331 1.079868442 0.985695075 0.313370524 0.064616202 0.39211056 28.2513472 0.019924349 0.01877196 397.6679628 -2.599520604 -0.094173367 SSGNSSSSGSGSGSTSAGS(ph)SSPGARR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSGNSSSSGSGSGSTSAGSSSPGARR 26 1 Q12797;E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2 Q12797 ASPH Aspartyl/asparaginyl beta-hydroxylase 1 SSGNSSSSGSGSGSTS(0.001)AGS(0.359)S(0.359)S(0.279)PGARR 62.582 0.0026976 0 3616.1 4583.6 2878.8 4272 4884.1 4188.8 4844.8 3649.9 8902.3 TRUE FALSE 3389.774756 4922.974513 2947.086495 4381.626752 4500.522488 5398.038561 4118.367217 4105.598049 7416.448619 0.457061719 0.66379136 0.39737166 0.590798504 0.606829861 0.727846822 0.555301793 0.553580057 1 12.8565128 -5 0.246662509 3.562982234 0.528426096 0.688402758 0.091836449 102.0301828 1.014228335 131.5817927 0.131739048 1.00E-05 5 -3.034556138 SSGNSSSSGSGSGSTSAGSSS(ph)PGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSGNSSSSGSGSGSTSAGSSSPGAR 25 0 Q12797;E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2 Q12797 ASPH Aspartyl/asparaginyl beta-hydroxylase 1 SSGNSSSSGSGSGSTSAGS(0.015)S(0.084)S(0.9)PGAR;SSGNSSSSGSGSGSTSAGSSS(0.999)PGAR;SSGNSSSSGSGSGSTSAGS(0.021)S(0.117)S(0.862)PGAR 293.04 7.14E-63 604460000 449589 444632 397006 412231 448950 359523 490381 396191 382511 TRUE FALSE 421450.027 477553.0159 406423.1698 422809.5454 413691.278 463311.4537 416852.9215 445656.3185 318667.443 1.322538704 1.49859368 1.275383409 1.326804964 1.298191224 1.453902694 1.308112676 1.398499684 1 18.28169211 -1.990595379 2.693112889 0.658217713 1.362337342 0.716107556 0.071274294 17041439.42 16321509.03 36239893.01 0.016164012 0.010218911 1.990595379 0.704119628 SSGPYGGGGQYFAKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSGPYGGGGQYFAKPR 16 1 F8W6I7;P09651-2;P09651;P09651-3;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 ;; 336.06 8.83E-72 7881410000 2855339 3514003 2901930 3156384 4305975 2505821 4178298 3723877 5051230 FALSE TRUE 2676628.429 3774183.438 2970765.15 3237382.157 3967801.093 3229210.844 3551801.004 4188811.241 4208147.081 0.636058668 0.896875362 0.705955636 0.769312977 0.942885554 0.767371193 0.844029673 0.995405142 1 22.0047537 1.307979872 3.092750461 1.006036944 0.795530594 0.496780586 0.086370443 0.205021641 3.237718158 0.067973444 0.020565651 20.3226282 -1.307979872 -0.210506349 SSGQPS(ph)PESQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSGQPSPESQTR 12 0 C9J6N8 C9J6N8 TFAP2A 1 SSGQPS(0.995)PES(0.005)QTR;SSGQPS(1)PESQTR 204.33 1.20E-07 304910000 391880 375390 360150 350970 399500 292700 422070 319520 395800 TRUE FALSE 367352.9303 403184.2662 368692.9281 359976.4844 368124.8815 377197.7384 358784.5218 359412.7754 329738.423 1.114073777 1.222739717 1.118137597 1.091703178 1.116414879 1.143930195 1.088088305 1.089993614 1 18.33096248 -4.999999991 0.073991272 0.528110307 1.286241582 0.618969595 0.033995657 169.1805834 0.895982782 13.1664675 1.465120477 1.00E-05 4.999999991 0.758131275 SSGRNS(ph)PSAASTSSNDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSGRNSPSAASTSSNDSK 18 1 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 S(0.002)S(0.002)GRNS(0.866)PS(0.113)AAS(0.006)T(0.008)S(0.002)S(0.002)NDSK;S(0.041)S(0.041)GRNS(0.897)PS(0.02)AASTSSNDSK 140.66 7.60E-08 108250000 231028 152144 185257 183942 180160 138687 232332 161567 235201 TRUE FALSE 216568.3699 163408.9001 189651.3835 188662.2631 166010.9603 178723.6855 197495.9735 181738.9956 195944.4336 1.105254004 0.833955306 0.967883496 0.962835533 0.847234888 0.912114124 1.007918264 0.927502722 1 17.58008506 1.749666656 25 0.977421156 0.927054496 0.044184972 0.077384988 7.527883042 16976.50778 0.032753077 0.018163376 56.19098644 -1.749666656 -0.05036666 SSGS(ph)PYGGGYGSGGGSGGYGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 15 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(0.866)PYGGGYGS(0.134)GGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;S(0.051)S(0.051)GS(0.896)PY(0.003)GGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;S(0.112)S(0.112)GS(0.777)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;S(0.001)S(0.003)GS(0.996)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;S(0.001)S(0.001)GS(0.998)PYGGGYGSGGGSGGYGSR 608 0 20972468600 2412301 2446848 2412737 2317300 2605737 2276666 3035283 2434344 2936998 TRUE FALSE 2261319.386 2628015.172 2469968.261 2376765.841 2401092.927 2933902.516 2580170.492 2738277.207 2446794.06 0.92419686 1.074064718 1.009471251 0.971379602 0.981322035 1.199080284 1.05451069 1.119128598 1 21.22246125 2.283277817 24.99999911 1.096713149 1.004694985 0.383927783 0.062438553 137.4902077 76865.92642 0.019954632 0.016695176 191.9896499 -2.283277817 -0.092018164 SSGSEGSS(ph)PNWLQALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSGSEGSSPNWLQALK 16 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 SSGSEGS(0.012)S(0.988)PNWLQALK;SSGSEGS(0.002)S(0.998)PNWLQALK 287.57 3.26E-36 142237000 601890 483030 549750 573410 546220 391792 623520 427960 551250 TRUE FALSE 564218.7793 518794.0438 562790.3296 588124.6714 503322.0845 504895.9902 530028.9645 481391.7481 459242.8138 1.228584884 1.129672644 1.225474439 1.280639901 1.095982494 1.09940967 1.154136654 1.048229245 1 18.80889762 1.375900889 0.64513292 1.000229568 1.198316976 0.611496662 0.053717148 0.490522278 0.477491302 0.05186794 0.024130425 23.76297927 -1.375900889 0.198087409 SSGSPYGGGYGSGGGSGGYGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSGSPYGGGYGSGGGSGGYGSR 22 0 P51991;H7C1J8;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 223.07 1.86E-25 253719000 29644.5 33851.3 28882.8 28003.9 31061.7 27030.1 34530.3 23063.1 31811.6 FALSE TRUE 27789.10366 36357.68547 29567.91366 28722.52748 28622.23938 34833.25107 29352.80208 25942.5788 26502.03845 1.048564763 1.371882602 1.115684505 1.083785594 1.080001428 1.314361201 1.107567712 0.978889939 1 14.69381571 1.395586509 4.319655702 0.993177077 1.181474294 0.328398358 0.103543324 0.236419898 7.061867076 0.073844706 0.025887114 24.86488809 -1.395586509 0.188297217 SSGSSSSGLGTVSNS(ph)PASQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSGSSSSGLGTVSNSPASQR 20 0 Q9UPP1-4;Q9UPP1-3;Q9UPP1-2;Q9UPP1;H0Y3N9;Q9UPP1-5;H0Y589 Q9UPP1-4 PHF8 Histone lysine demethylase PHF8 1 SSGSSSSGLGTVS(0.002)NS(0.998)PASQR;SSGSSSSGLGTVSNS(0.999)PAS(0.001)QR 331.5 7.95E-80 702880000 383740 360860 412590 396280 464650 393290 529930 401340 430470 TRUE FALSE 359722.3984 387578.4499 422376.8296 406449.2157 428158.2633 506826.4385 450471.9161 451448.1825 358621.7761 1.003069034 1.080744327 1.177777976 1.133364572 1.193899233 1.413261749 1.256119807 1.25884208 1 18.45210357 3.916430314 0.757712854 1.250158171 0.993160564 0.291348185 0.105431882 1.167399482 1.039334958 0.043124986 0.2129572 8249.551038 -3.916430314 -0.256997607 SSHKDS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SSHKDSPR 8 1 O15042-2;O15042;E7ET15;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 S(0.022)S(0.022)HKDS(0.956)PR;S(0.001)S(0.001)HKDS(0.999)PR;SSHKDS(1)PR;S(0.002)S(0.002)HKDS(0.997)PR;SSHKDS(1)PR 112.13 0.0018776 1135390000 1886320 1623420 2093610 1759180 2094920 1314010 2086930 2126650 2192510 TRUE FALSE 1768258.598 1743619.706 2143271.418 1804323.537 1930393.434 1693343.356 1774014.221 2392166.934 1826565.917 0.968078174 0.954588986 1.173388487 0.987822843 1.056843017 0.927063918 0.971229236 1.309652672 1 20.80070239 4.229892401 24.8067185 1.050223003 0.961333562 0.116883209 0.110771336 272.7485204 2441506.906 0.025933215 0.064831537 16978.22953 -4.229892401 -0.088889442 SSHPEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSHPEDLR 8 0 B0QYR6;Q9UJY5-4;Q9UJY5-3;Q9UJY5;Q9UJY5-6;Q9UJY5-2 B0QYR6 GGA1 ADP-ribosylation factor-binding protein GGA1 0 ; 89.698 0.013721 956530000 960710 1456380 1339430 1378730 1476020 1095370 1439870 1316350 1451410 FALSE TRUE 900580.876 1564211.891 1371201.912 1414110.546 1360099.343 1411585.537 1223974.861 1480699.195 1209160.295 0.744798585 1.293634845 1.134011693 1.169498 1.124829644 1.167409767 1.012251946 1.224568158 1 20.20557408 1.76703216 24.99999998 1.081257712 1.133839078 0 0.15321352 99.00983691 86988.15031 0.064524031 0.035787687 58.48333899 -1.76703216 0.052581366 SSHSSDSGGS(ph)DVDLDPTDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSHSSDSGGSDVDLDPTDGK 20 0 P78545-2;P78545;Q5SR36 P78545-2 ELF3 ETS-related transcription factor Elf-3 1 S(0.013)S(0.013)HS(0.11)S(0.094)DS(0.094)GGS(0.677)DVDLDPTDGK 118.35 1.69E-05 0 98724 165020 163130 144940 161470 120180 171430 151630 237270 TRUE FALSE 92545.04107 177238.2525 166999.5206 148659.4058 148788.7975 154874.015 145725.663 170561.3393 197668.1042 0.468183987 0.896645684 0.844848092 0.752065724 0.752720314 0.783505339 0.737223962 0.862867279 1 17.59272057 0.958330746 4.060841088 0.999785708 0.772867758 0.331274319 0.113376313 0.278798313 13.38243201 0.10163448 0.025978439 9.085121639 -0.958330746 -0.22691795 SSHYDELLAAEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SSHYDELLAAEAR 13 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;;;; 206.64 6.02E-08 11809610000 6129610 9669320 8688390 9061290 9678740 7030370 9299570 8197920 9814440 FALSE TRUE 5745968.652 10385246.51 8894482.714 9293818.042 8918610.803 9059923.69 7905185.811 9221448.358 8176346.56 0.702755027 1.27015733 1.087830934 1.136671247 1.090781896 1.108065029 0.966835952 1.127820144 1 22.96302492 1.77181383 24.99999999 1.028828124 1.095777043 0 0.149539934 117.1096504 88086.18772 0.063217037 0.035072098 59.13081018 -1.77181383 0.066948919 SSHYGGS(ph)LPNVNQIGSGLAEFQSPLHSPLDSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSHYGGSLPNVNQIGSGLAEFQSPLHSPLDSSR 33 0 Q53ET0 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 SSHYGGS(1)LPNVNQIGSGLAEFQSPLHSPLDSSR;S(0.002)S(0.002)HYGGS(0.996)LPNVNQIGSGLAEFQSPLHSPLDSSR;SSHYGGS(1)LPNVNQIGSGLAEFQSPLHSPLDSSR;S(0.012)S(0.012)HYGGS(0.975)LPNVNQIGSGLAEFQSPLHSPLDSSR 345.4 2.17E-131 2418440000 428818 721432 588250 667910 699540 537481 746170 618130 707690 TRUE FALSE 401979.0468 774847.5759 602203.5678 685049.7014 644600.9502 692643.0394 634288.7356 695304.8912 589571.9671 0.681815061 1.314254441 1.021425036 1.161944155 1.093337177 1.174823564 1.075846158 1.179338452 1 19.1693084 4.753726432 24.75333972 1.131259497 0.68181469 0.709071258 0.089715315 1282.131892 2092629.769 0.019337881 0.46054673 56718.72138 -4.753726432 -0.449444807 SSILLDVKPWDDETDMAQLEACVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 78.717 0.020739 68107000 66503 52837 58049 61603 60082 45411 82074 52249 68170 FALSE TRUE 62340.69594 56749.10646 59425.94969 63183.83727 55363.40208 58520.41851 69767.76564 58772.40266 56791.9866 1.097702329 0.999244961 1.046379133 1.112548461 0.974845315 1.030434433 1.228479048 1.0348714 1 15.79339976 SSISSVLKDPDSNPYSLLDNTES(ph)DQTADTDASESHHSTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSISSVLKDPDSNPYSLLDNTESDQTADTDASESHHSTNR 40 1 B4DXZ6;P51114;P51114-3;H7C4S4;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 1 SSISSVLKDPDS(0.003)NPY(0.012)S(0.063)LLDNT(0.094)ES(0.411)DQT(0.411)ADT(0.004)DAS(0.001)ES(0.001)HHSTNR 69.755 0.001832 105050000 18721 43077 34676 42973 47741 35203 54480 45452 44520 TRUE FALSE 17549.28603 46266.4659 35498.5311 44075.75993 43991.61444 45365.53463 46311.22977 51126.78225 37089.32439 0.473162731 1.247433504 0.957109133 1.18836783 1.186099104 1.223142653 1.248640425 1.378477044 1 15.17871637 4.742104242 24.98974139 1.176023108 0.473162465 0.769187839 0.121445906 166.9867911 1177544.629 0.028729746 0.212582304 55220.99685 -4.742104242 -0.702860643 SSISSVLKDPDSNPYSLLDNTES(ph)DQTADTDASESHHSTNRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSISSVLKDPDSNPYSLLDNTESDQTADTDASESHHSTNRR 41 2 B4DXZ6;P51114;P51114-3;H7C4S4;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 1 SSISSVLKDPDSNPYSLLDNT(0.007)ES(0.95)DQT(0.041)ADT(0.001)DASESHHSTNRR 147.05 1.03E-13 119530000 20208 67108 49328 60134 77302 46045 82264 68390 100260 TRUE FALSE 18943.21735 72076.74615 50498.08345 61677.14025 71231.01274 59337.44402 69929.2769 76928.64204 83525.9583 0.226794373 0.8629263 0.604579516 0.738418828 0.852800904 0.710407222 0.837216098 0.921014779 1 16.34993701 5.375633556 0.209755064 0.98080978 1.05E-21 0.530911518 0.147825711 16.230426 0.517303985 0.262243474 4.334962624 237483.5627 -5.375633556 -0.98080978 SSKAS(ph)LGS(ph)LEGEAEAEASSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSKASLGSLEGEAEAEASSPK 21 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 S(0.002)S(0.008)KAS(0.99)LGS(1)LEGEAEAEASSPK;S(0.022)S(0.1)KAS(0.913)LGS(0.965)LEGEAEAEASSPK;S(0.077)S(0.266)KAS(0.752)LGS(0.906)LEGEAEAEASSPK 182.91 2.56E-17 432057000 1264440 618900 787050 633590 766130 601280 1229840 748870 1652840 TRUE FALSE 1185300.957 664724 805719.1977 649848.9921 705961.2402 774859.775 1045436.909 842368.068 1376970.326 0.860803559 0.482743881 0.585139115 0.471941174 0.512691688 0.562728013 0.759229803 0.611754699 1 20.39306604 0.580016251 0.737566532 1.000969685 0.565875407 0.506771063 0.121797143 1.051486191 0.990590984 0.118398042 0.040508135 3.802036226 -0.580016251 -0.435094278 SSKDEEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSKDEEPR 8 1 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 0 79.906 0.024464 163710000 544490 432100 456150 489520 552030 336490 539510 432980 620800 FALSE TRUE 510411.3428 464093.1336 466970.0934 502081.912 508675.7906 433629.2005 458615.4841 487038.5061 517184.4695 0.986903848 0.897345456 0.90290819 0.970798509 0.983548077 0.838442038 0.886754168 0.941711391 1 18.98031943 2.257711256 24.99866758 0.902630607 0.936185054 0.027800192 0.051650491 610.6060286 797064.8811 0.017514217 0.014632453 181.0136212 -2.257711256 0.033554447 SSLDVLPSQVYSLVGS(ph)SPLR ddPTM_SK-BR-3_Pertuzumab_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(0.5)S(0.5)PLR 133.16 2.07E-07 0 26493 29400 35164 39695 35827 34647 47249 35107 36041 TRUE FALSE 24834.85042 31576.80659 35998.10669 40713.6409 33013.29194 44649.02645 40164.45109 39490.18623 30025.52427 0.827124622 1.051665453 1.19891684 1.355967694 1.099507594 1.487035699 1.337676929 1.31522054 1 14.87390182 4.868188439 0.730016411 1.300214901 0.472293112 0.499503731 0.139172564 2.394299754 0.849373359 0.047889775 1.701882799 73822.44734 -4.868188439 -0.827921789 SSLDVLPSQVYSLVGSS(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSLDVLPSQVYSLVGSSPLR 20 0 Q5SQL3;J3KP92;Q86Z02;H3BLW0;Q86Z02-4;Q86Z02-3;Q86Z02-2 Q5SQL3 HIPK1 Homeodomain-interacting protein kinase 1 1 SSLDVLPSQVYSLVGS(0.086)S(0.914)PLR;SSLDVLPSQVYSLVGS(0.458)S(0.542)PLR 294.52 1.52E-54 122464000 259226 290800 280781 293380 334160 252969 344430 290013 330320 TRUE FALSE 243001.5074 312331.1346 287441.2579 300908.6275 307916.4215 325997.0437 292785.919 326221.7614 275187.4581 0.883039907 1.134975906 1.044528918 1.093467811 1.11893334 1.184636269 1.06395081 1.185452868 1 18.07005519 4.743581632 24.55651952 1.103841441 0.883039789 0.586506184 0.05810455 277.1465695 1355395.92 0.012327039 0.103487272 55409.16842 -4.743581632 -0.220801652 SSLFPFEDAFLDDSHGDQALSSGLS(ph)SPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSLFPFEDAFLDDSHGDQALSSGLSSPTR 29 0 Q8NE35-2 Q8NE35-2 1 SSLFPFEDAFLDDSHGDQALS(0.065)S(0.054)GLS(0.418)S(0.418)PT(0.045)R;SSLFPFEDAFLDDSHGDQALS(0.027)S(0.107)GLS(0.288)S(0.288)PT(0.288)R;SSLFPFEDAFLDDSHGDQALSSGLS(0.619)S(0.379)PT(0.002)R;SSLFPFEDAFLDDSHGDQALSS(0.001)GLS(0.882)S(0.116)PT(0.001)R 253.21 4.57E-58 438704000 210735 235655 241286 261658 269703 178817 199154 158935.9 230781 TRUE FALSE 197545.4725 253103.1414 247009.4179 268372.5873 248521.6143 230438.565 169292.7066 178779.397 192262.1602 1.02747973 1.316448027 1.28475316 1.395867949 1.292618444 1.198564319 0.880530555 0.929873027 1 17.55271532 1.852455547 3.969774233 0.92887451 1.277511944 0.697484463 0.098309291 0.114861597 2.899156846 0.045959359 0.025307744 71.19599227 -1.852455547 0.348637434 SSLFPFEDAFLDDSHGDQALSSGLSS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSLFPFEDAFLDDSHGDQALSSGLSSPTR 29 0 Q8NE35-2 Q8NE35-2 1 SSLFPFEDAFLDDSHGDQALSSGLS(0.206)S(0.632)PT(0.162)R;SSLFPFEDAFLDDSHGDQALSSGLS(0.156)S(0.688)PT(0.156)R 298.86 3.96E-81 346310000 99283 107432 107534 125657 119571 76582 89050 73588 100169 TRUE FALSE 93069.05426 115386.3771 110084.7573 128881.5714 110180.376 98689.9802 75697.7792 82775.62379 83450.14678 1.115265315 1.382698312 1.319167928 1.544413956 1.320313747 1.182622008 0.90710181 0.991917054 1 16.34862697 1.987203675 2.888815779 0.960956657 1.349498078 0.712926629 0.10672565 0.131021562 2.083229161 0.050647065 0.028975066 97.09652227 -1.987203675 0.388541421 SSLFS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSLFSPR 7 0 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 SSLFS(1)PR;SSLFS(1)PR;SSLFS(1)PR 82.426 0.025723 110167000 323812 455769 334716 338437 474347 237202 336574 377967 408659 TRUE FALSE 303545.1849 489514.611 342655.6216 347121.8664 437093.7 305678.3667 286107.8533 425157.012 340451.1729 0.891596825 1.437840871 1.00647508 1.019593686 1.283866043 0.897862575 0.840378522 1.248804662 1 18.37708838 2.225051456 24.99813519 0.965072481 1.148666335 0.094553552 0.184587657 386.3801457 714975.6205 0.065825629 0.048880621 167.9002938 -2.225051456 0.183593854 SSLGQS(ph)AS(ph)ETEEDTVSVSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSLGQSASETEEDTVSVSKK 20 1 Q13435;E9PPJ0;H0YCG1;E9PJ04 Q13435 SF3B2 Splicing factor 3B subunit 2 2 SSLGQS(0.999)AS(0.98)ET(0.021)EEDTVSVSKK;SSLGQS(0.999)AS(0.947)ET(0.053)EEDTVSVSKK 120.57 0.00011991 444810000 1259690 860680 937090 980650 1231310 632440 1277860 847030 1642520 TRUE FALSE 1180848.252 924405.6427 959318.2173 1005815.139 1134607.879 815015.1612 1086256.756 952783.56 1368372.801 0.862957997 0.675551021 0.701064956 0.735044674 0.829165764 0.595609004 0.793831005 0.696289461 1 20.3840299 -1.853194652 2.295067196 1.124775049 0.728905298 0.528880583 0.077980618 5836516.369 3138067.319 3981223.713 0.019432649 0.014021851 1.853194652 -0.395869751 SSLGQSAS(ph)ETEEDTVSVSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SSLGQSASETEEDTVSVSKK 20 1 Q13435;E9PPJ0;H0YCG1;E9PJ04 Q13435 SF3B2 Splicing factor 3B subunit 2 1 SSLGQS(0.01)AS(0.986)ET(0.004)EEDTVSVSKK;SSLGQSAS(0.967)ET(0.033)EEDTVSVSKK;SSLGQS(0.002)AS(0.987)ET(0.012)EEDTVSVSKK;SSLGQSAS(0.919)ET(0.08)EEDTVSVSKK;S(0.001)S(0.001)LGQS(0.336)AS(0.595)ET(0.067)EEDTVSVSKK 270.01 4.57E-38 1914310000 1100902 1154580 994910 1121120 1392050 727737 1484670 1075390 2097620 TRUE FALSE 1031998.509 1240066.305 1018509.735 1149889.837 1282724.008 937822.8581 1262057.517 1209654.809 1747513.671 0.590552467 0.709617513 0.582833629 0.658014788 0.734028025 0.536661243 0.722201799 0.69221479 1 20.73687231 0.343296816 0.954603847 1.001857585 0.643353731 0.758082261 0.062505032 1.173539067 1.322561973 0.057414488 0.017340219 2.204432557 -0.343296816 -0.358503854 SSLGSLQT(ph)PEAVTTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSLGSLQTPEAVTTR 15 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 SSLGSLQT(1)PEAVTTR 137.73 0.000167 170210000 109060 119250 117500 142200 150150 116410 150250 125160 165810 TRUE FALSE 102234.1293 128079.3941 120287.1555 145849.0927 138357.8247 150015.6772 127721.4074 140786.5015 138135.2398 0.740101725 0.927202894 0.870792679 1.055842759 1.001611355 1.086005841 0.924611327 1.019193232 1 17.07572189 5.947204932 0.531344424 1.007454563 2.67E-16 0.642481016 0.059964068 8.846641557 0.707830326 0.02941758 7.329577569 885533.3702 -5.947204932 -1.007454563 SSLLDDLLTESEDMAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 154.47 3.18E-07 17924500 33846 31546 32370 37753 39862 33450 39400 31526 44203 FALSE TRUE 31727.63928 33881.69866 33137.83169 38721.8059 36731.39932 43106.47198 33492.33577 35462.0905 36825.23374 0.86157333 0.920067444 0.899867518 1.051501972 0.997451899 1.170568863 0.90949418 0.962983446 1 15.16840706 3.250480396 24.86355305 1.013774622 0.900318693 0.412721963 0.068157936 211.4207232 441001.0846 0.018398688 0.024719688 1780.247548 -3.250480396 -0.113455929 SSLS(ph)GDEEDELFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSLSGDEEDELFK 13 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 SSLS(1)GDEEDELFK;SSLS(1)GDEEDELFK;SSLS(1)GDEEDELFK;SSLS(1)GDEEDELFK 302.53 5.05E-41 493019000 1429580 822160 958940 871620 1071740 835620 1547230 1048180 1824100 TRUE FALSE 1340105.14 883033.5819 981686.5096 893987.2448 987569.8636 1076849.929 1315237.225 1179047.58 1519645.926 0.88185354 0.581078504 0.645996869 0.588286541 0.649868398 0.708618969 0.865489258 0.775869931 1 20.53530379 1.391394846 0.896524234 0.973337566 0.647131086 0.529896374 0.094459917 0.354782821 0.595278643 0.081182817 0.030542961 24.62605508 -1.391394846 -0.326206481 SSLS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SSLSPGR 7 0 Q9BUQ8;F8VVA2;F8W1J5 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 SSLS(1)PGR;S(0.012)S(0.012)LS(0.977)PGR;SS(0.003)LS(0.996)PGR;S(0.001)S(0.011)LS(0.988)PGR;S(0.001)S(0.003)LS(0.997)PGR 166.82 0.0011635 3795400000 2181190 2693690 2322590 2409290 2843970 2031140 2624060 2368870 2689150 TRUE FALSE 2044673.211 2893133.61 2377682.932 2471116.46 2620616.068 2617497.145 2230606.564 2664628.634 2240313.492 0.91267281 1.291396771 1.061317061 1.103022621 1.169754178 1.168361997 0.995667156 1.189399896 1 21.0952692 -0.659617754 0.38143095 0.961725679 1.12859917 0.069001697 0.107463324 23.12784122 2.990476059 1.188555323 0.071145964 0.218968804 0.659617754 0.16687349 SSMIT(ph)SLEGLGTDNVFSLHEDNHYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSMITSLEGLGTDNVFSLHEDNHYR 25 0 Q8IZQ1-2;Q8IZQ1 Q8IZQ1-2 WDFY3 WD repeat and FYVE domain-containing protein 3 1 S(0.022)S(0.022)MIT(0.512)S(0.445)LEGLGTDNVFSLHEDNHYR;S(0.014)S(0.014)MIT(0.529)S(0.443)LEGLGTDNVFSLHEDNHYR 130.01 0.00017788 70426000 14265.1 19826.2 17762.7 18672.1 25164.5 19978.6 18364.5 19806.9 26280.9 TRUE FALSE 13372.27285 21294.15248 18184.03963 19151.2577 23188.18168 25746.09749 15610.91371 22279.83507 21894.44801 0.610760904 0.972582294 0.830531997 0.874708405 1.059089577 1.175919004 0.713007869 1.017602045 1 14.41827746 4.742462363 24.61906942 0.936684719 0.610760746 0.407900816 0.128755527 339.998337 2145198.417 0.029784646 0.226333133 55266.55111 -4.742462363 -0.325923972 SSMITS(ph)LEGLGTDNVFSLHEDNHYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.09)S(0.909)LEGLGTDNVFSLHEDNHYR 158.1 4.22E-11 69886000 12383 18340 15202 16914 15085 15472 22172 17748 18006 TRUE FALSE 11607.97013 19697.91268 15562.59862 17348.04188 13900.28495 19938.51523 18847.51443 19963.87687 15000.68228 0.773829478 1.313134451 1.037459386 1.156483522 0.926643515 1.329173891 1.256443813 1.33086459 1 13.8727405 2.220545174 24.99498037 1.25393881 1.083223419 0.207155933 0.168862711 377.9475549 524368.6108 0.057531532 0.042574028 166.1671509 -2.220545174 -0.170715391 SSPAFGDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSPAFGDRR 9 1 P13716;P13716-2 P13716 ALAD Delta-aminolevulinic acid dehydratase 0 ; 74.267 0.066662 192658000 126662 283440 152974 146918 304670 115336 164045 240030 313190 FALSE TRUE 118734.4515 304426.1925 156602.6155 150688.1646 280742.4472 148631.6309 139447.9752 269998.2739 260916.5657 0.455066742 1.166756858 0.600201889 0.577533911 1.075985522 0.569651952 0.53445428 1.034806943 1 17.99322902 1.211185211 24.81449135 1.017404166 0.735922127 0.22314438 0.233925237 381.7989162 346072.1575 0.217658136 0.054470295 16.26242142 -1.211185211 -0.281482039 SSPCIHYFTGTPDPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPCIHYFTGTPDPSR 16 0 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 131.24 4.56E-05 248630000 536070 596770 626860 620590 691480 480940 800810 610210 920090 FALSE TRUE 502518.3356 640955.4717 641729.4152 636515.3901 637173.9501 619779.5706 680735.9749 686396.0617 766521.035 0.65558323 0.836187714 0.837197397 0.830395202 0.831254357 0.808561725 0.888085185 0.895469309 1 19.54796586 0.519989247 0.031347668 1.816080766 1.82E-11 0.722582291 0.045145489 130.6261954 1.796112601 55.61544124 47.91724379 3.311229229 -0.519989247 -1.816080766 SSPDLTGVVTIYEDLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSPDLTGVVTIYEDLRR 17 1 O60784;O60784-4;O60784-2;V9GYF4;B0QY02;V9GZ68;Q6UW50;B0QY01 O60784 TOM1 Target of Myb protein 1 0 ; 127.57 6.39E-05 60966000 31438 38810 39607 36589 35174 27752.7 39046 33020 42133 FALSE TRUE 29470.3517 41683.53278 40546.49674 37527.93569 32411.57593 35764.45396 33191.41479 37142.61969 35100.73011 0.839593695 1.187540335 1.155146819 1.069149718 0.923387514 1.018909118 0.945604683 1.058172282 1 15.09921342 2.936201167 6.622523697 0.985549658 1.102776943 0.068604359 0.100701405 0.341775482 29.19609528 0.029214397 0.031261057 863.3783765 -2.936201167 0.117227285 SSPNVANQPPS(ph)PGGK ddPTM_SK-BR-3_Pertuzumab_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 280.26 1.12E-33 2827880000 3453470 2527470 2866320 3034800 3120130 1972780 2681980 1922870 2369850 TRUE FALSE 3237323.477 2714606.509 2934310.464 3112678.106 2875087.576 2542289.561 2279841.997 2162944.552 1974306.725 1.639726713 1.374966956 1.486248528 1.576592971 1.456251726 1.287687231 1.154755727 1.095546363 1 20.91291471 1.849131121 1.373666222 1.040689638 1.494937913 0.878740055 0.072890115 0.141886695 0.501032149 0.055430316 0.023281443 70.65308352 -1.849131121 0.454248275 SSPS(ph)PEVVKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSPSPEVVKPK 11 1 A0A1W2PNZ9;Q15652-3;Q15652;Q15652-2 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 S(0.006)S(0.006)PS(0.989)PEVVKPK 53.3 0.084106 234450000 819190 662120 662750 822840 929530 591070 1063200 652160 1365800 TRUE FALSE 767918.3602 711144.0537 678470.743 843955.4675 856528.4633 761702.3138 903783.0303 733583.6116 1137839.157 0.674891838 0.624995237 0.596280009 0.741717722 0.752767611 0.669428811 0.794297705 0.644716441 1 20.1178652 -5 0.154694778 2.169011656 0.588762815 0.730012496 0.06000295 64.51590548 0.584122126 23.08386924 0.268085931 1.00E-05 5 -1.58024884 SSPS(ph)PQKR ddPTM_SK-BR-3_Pertuzumab_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(0.002)S(0.013)PS(0.985)PQKR 76.143 0.022397 22023000 54964 41422 44121 49087 51248 33573 53745 40960 48800 TRUE FALSE 51523.90135 44488.92798 45167.57096 50346.65552 47223.1888 43264.98009 45686.43619 46073.94616 40654.96474 1.267345863 1.094304921 1.110997666 1.238388862 1.161560196 1.064199179 1.12376032 1.133291997 1 15.31114392 -4.999999995 0.154850636 0.480530501 1.181420609 0.428914395 0.058785021 147.9028612 1.339760887 23.50167208 0.271779911 1.00E-05 4.999999995 0.700890108 SSPSGASS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSPSGASSPR 10 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 SSPSGASS(1)PR;SSPSGASS(1)PR;SSPSGAS(0.053)S(0.947)PR 166.11 5.92E-06 1127676000 2345330 2408380 2363830 2270980 2547560 2067590 2709700 2258050 2686350 TRUE FALSE 2198539.982 2586698.961 2419901.164 2329257.192 2347484.914 2664469.668 2303405.641 2539972.513 2237980.831 0.982376592 1.155818194 1.081287708 1.04078514 1.048929858 1.190568584 1.029233856 1.134939352 1 21.09376625 -1.780047153 2.63192388 0.976935303 1.087549669 0.142989907 0.062980601 20721204.95 16006193.47 3084781.88 0.013545084 0.016594067 1.780047153 0.110614366 SSPSTGS(ph)LDSGNESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSPSTGSLDSGNESK 15 0 Q15057;A0A0U1RQT1;A0A087X1H5 Q15057 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 1 SSPST(0.001)GS(0.999)LDSGNESK;SSPST(0.002)GS(0.997)LDSGNESK;SSPS(0.001)T(0.058)GS(0.941)LDSGNESK 294.98 5.23E-44 242060000 1109780 814360 935750 1016150 1040980 656382 1178490 794890 1073860 TRUE FALSE 1040320.851 874656.0617 957946.4319 1042226.129 959225.6299 845868.8279 1001786.365 894133.7663 894625.8286 1.162855819 0.977678079 1.070778868 1.164985512 1.072208737 0.94550012 1.11978252 0.99944998 1 19.77092489 2.433312085 24.9999895 1.030257066 1.075573356 0.194841589 0.06854224 347.2049023 198132.8956 0.023579948 0.019728427 271.213988 -2.433312085 0.04531629 SSQCHTGS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSQCHTGSSPR 11 0 O15226;O15226-2 O15226 NKRF NF-kappa-B-repressing factor 1 SSQCHT(0.023)GS(0.488)S(0.488)PR 59.248 0.06518 271070000 138610 176700 199230 189650 220530 193600 214920 218900 265060 TRUE FALSE 129934.6475 189783.0519 203955.8297 194516.7401 203210.4634 249489.1772 182694.7412 246230.1469 220819.7736 0.58841944 0.859447724 0.923630281 0.880884609 0.920254831 1.129831686 0.827347742 1.115072907 1 17.75250984 5.293592831 0.840008987 0.967761306 1.03E-30 0.617480092 0.094942684 3.592847195 1.015730921 0.028499526 4.007804204 196604.2181 -5.293592831 -0.967761306 SSQDPSVPQNPPTPLGHS(ph)NPLDHQIPLDPPAPEVVPTPSDWTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSQDPSVPQNPPTPLGHSNPLDHQIPLDPPAPEVVPTPSDWTK 43 0 Q9UEG4 Q9UEG4 ZNF629 Zinc finger protein 629 1 S(0.001)S(0.001)QDPS(0.002)VPQNPPT(0.103)PLGHS(0.893)NPLDHQIPLDPPAPEVVPTPSDWTK 69.914 0.0030112 34271000 28979 27071 28339 24507 27368 22348 32729 26661 41921 TRUE FALSE 27165.25612 29075.36501 29011.21446 25135.89111 25218.62768 28799.50481 27821.59029 29989.68454 34924.11428 0.777836652 0.832529775 0.83069292 0.719728807 0.722097845 0.824630929 0.796629803 0.858709953 1 15.09193591 0.805344486 1.60718862 0.999963521 0.790772212 0.742984635 0.040033492 0.394338056 1.829738389 0.041082337 0.011833462 6.38769963 -0.805344486 -0.209191308 SSQEEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSQEEVR 7 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 120.45 0.010595 389420000 770340 856800 854790 793500 939120 666920 853250 835570 1009620 FALSE TRUE 722125.7945 920238.3635 875066.0225 813862.5534 865365.3034 859448.9775 725313.0837 939892.7538 841107.8996 0.858541211 1.09407885 1.040373088 0.967607787 1.028839824 1.021805856 0.862330605 1.117446114 1 19.68193136 SSQQPST(ph)PQQAPPGQPQQGTFVAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSQQPSTPQQAPPGQPQQGTFVAHK 25 0 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 S(0.009)S(0.009)QQPS(0.243)T(0.738)PQQAPPGQPQQGTFVAHK;SSQQPS(0.084)T(0.916)PQQAPPGQPQQGTFVAHK;SSQQPS(0.018)T(0.982)PQQAPPGQPQQGTFVAHK;SSQQPS(0.042)T(0.958)PQQAPPGQPQQGTFVAHK 244.49 3.34E-38 1969290000 1550890 1285370 1433320 1327710 1775020 1295040 1895700 1640000 2546200 TRUE FALSE 1453822.563 1380540.132 1467319.027 1361781.286 1635617.089 1668897.025 1611457.384 1844757.61 2121222.771 0.685370053 0.650822795 0.69173264 0.641979383 0.771072757 0.78676179 0.759683238 0.869667079 1 21.01646471 1.114881017 0.444841439 1.014157308 0.653618168 0.910986957 0.032456721 0.278132185 0.151108767 0.039265291 0.021681088 13.028098 -1.114881017 -0.36053914 SSQRHS(ph)PPFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSQRHSPPFSK 11 1 Q8WV28-3;Q8WV28;Q8WV28-2 Q8WV28-3 BLNK B-cell linker protein 1 S(0.003)S(0.029)QRHS(0.967)PPFSK 62.377 0.049271 141900000 143750 184230 156420 183200 230770 128310 186130 168880 191580 TRUE FALSE 134752.9441 197870.5809 160130.3563 187901.2222 212646.2551 165351.0141 158221.5344 189965.0398 159604.0603 0.844295213 1.239759067 1.00329751 1.177296002 1.332336124 1.036007566 0.991337777 1.190226861 1 17.28413783 -1.101245292 7.608706652 0.999999985 1.103189611 0.049079732 0.140734416 3.41E-08 3.82E-09 0.125966709 0.029690634 0.079205385 1.101245292 0.103189626 SSRFS(ph)GGFGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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;SSRFS(1)GGFGAR;SSRFS(1)GGFGAR;SSRFS(1)GGFGAR 158.93 1.77E-05 2459100000 549146 691306 580521 593150 784497 468122 627311 566026 1052372 TRUE FALSE 514775.9321 742491.0155 594291.2323 608371.2332 722885.7701 603261.2221 533251.5392 636695.5921 876724.3146 0.58715827 0.846892236 0.67785417 0.693913951 0.824530309 0.688085424 0.608231722 0.726220981 1 19.74176373 -1.338228056 3.434119378 1.001540314 0.71122367 0.562335853 0.081252259 32917277.56 48746019.29 515242.4532 0.01917222 0.045895694 1.338228056 -0.290316644 SSRPS(ph)MDS(ph)EGGSLLLDEDSEVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSRPSMDSEGGSLLLDEDSEVFK 23 1 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;Q96JY6-4;C9JS55;C9JSR2;H0YBP7 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 2 S(0.001)S(0.001)RPS(0.972)MDS(0.675)EGGS(0.351)LLLDEDSEVFK;SSRPS(0.998)MDS(0.985)EGGS(0.016)LLLDEDSEVFK 171.95 3.65E-12 130734000 215930 148390 179420 192329 188427 123461 190926 138123 206383 TRUE FALSE 202415.3267 159376.95 183675.9271 197264.4878 173628.7035 159102.1865 162298.4188 155367.9606 171936.344 1.177268994 0.926953233 1.06827866 1.147311168 1.009842942 0.925355179 0.943944805 0.903636526 1 17.39151501 2.403134609 4.742751851 0.939602861 1.054831445 0.432817817 0.071026579 0.224278664 9.492399879 0.024850162 0.02070225 253.0082072 -2.403134609 0.115228584 SSRPS(ph)MDSEGGSLLLDEDSEVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SSRPSMDSEGGSLLLDEDSEVFK 23 1 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;Q96JY6-4;C9JS55;C9JSR2;H0YBP7 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 SSRPS(0.998)MDS(0.001)EGGS(0.001)LLLDEDSEVFK;SSRPS(0.997)MDS(0.003)EGGSLLLDEDSEVFK;S(0.107)S(0.107)RPS(0.759)MDS(0.01)EGGS(0.016)LLLDEDSEVFK;S(0.012)S(0.012)RPS(0.973)MDS(0.003)EGGS(0.001)LLLDEDSEVFK;SSRPS(0.994)MDS(0.005)EGGSLLLDEDSEVFK;S(0.025)S(0.025)RPS(0.949)MDS(0.002)EGGSLLLDEDSEVFK 267.64 1.64E-44 472971000 917670 604987 719847 750383 762648 589134 950710 697684 865998 TRUE FALSE 860234.6728 649780.867 736922.1108 769639.0982 702752.7025 759207.422 808159.8615 784791.3832 721457.3392 1.19235695 0.900650436 1.021435462 1.066783933 0.974073815 1.052324761 1.120176922 1.087786263 1 19.46055456 2.004332257 21.62779526 1.083568268 1.013555868 0.011114156 0.079939735 42.40662962 211698.8392 0.028110943 0.020629755 101.002531 -2.004332257 -0.0700124 SSS(ph)APLIHGLSDLSQVFQPYTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSAPLIHGLSDLSQVFQPYTLR 23 0 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 S(0.01)S(0.025)S(0.965)APLIHGLSDLSQVFQPYTLR;S(0.107)S(0.107)S(0.785)APLIHGLSDLSQVFQPYTLR 271.82 8.13E-52 2566600000 925150 1084530 897410 890810 1049390 765670 1117270 1033730 1037770 TRUE FALSE 867246.5129 1164829.73 918696.989 913669.6927 966975.1424 986706.4994 949745.7357 1162793.466 864559.4827 1.003107976 1.347310108 1.062618602 1.056803738 1.118459934 1.141282375 1.098531396 1.344954846 1 19.7216057 -2.410818799 2.008940525 6.13E-05 1.149514129 0.138436847 0.114761859 1091751.879 153945.6949 4932341.821 0.026452719 0.003883123 2.410818799 1.149452788 SSS(ph)APNVHINTIEPVNIDDLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SSSAPNVHINTIEPVNIDDLIR 22 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(0.131)S(0.131)S(0.738)APNVHINTIEPVNIDDLIR;S(0.018)S(0.088)S(0.894)APNVHINTIEPVNIDDLIR;SS(0.001)S(0.999)APNVHINTIEPVNIDDLIR;S(0.027)S(0.108)S(0.865)APNVHINTIEPVNIDDLIR;S(0.004)S(0.004)S(0.993)APNVHINTIEPVNIDDLIR;S(0.088)S(0.088)S(0.823)APNVHINTIEPVNIDDLIR 346.02 4.39E-96 4326410000 879637 977538 896491 838662 973569 959593 1370726 1034110 1201475 TRUE FALSE 824582.0904 1049915.931 917756.1899 860183.4868 897108.8179 1236611.921 1165198.361 1163220.91 1000941.061 0.823806838 1.048928825 0.916893338 0.859374763 0.896265378 1.235449289 1.16410287 1.162127278 1 19.93292559 2.245678911 24.99999282 1.158072873 0.926938551 0.65134731 0.083100597 96.60571847 339287.3401 0.027968282 0.022941339 176.0673838 -2.245678911 -0.231134322 SSS(ph)ASSPEMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSASSPEMK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SS(0.001)S(0.999)ASSPEMK;SS(0.046)S(0.953)AS(0.001)SPEMK;S(0.005)S(0.005)S(0.99)ASSPEMK 178.1 0.00010415 621720000 1309650 1047260 1139470 1340170 1339760 795660 1153860 825130 1240810 TRUE FALSE 1227681.344 1124800.22 1166498.766 1374561.031 1234540.654 1025354.126 980849.4049 928149.2968 1033710.795 1.187644891 1.088118868 1.128457565 1.32973462 1.194280508 0.991915853 0.948862496 0.897881014 1 19.97940118 2.159475323 4.611344274 0.950118937 1.171103664 0.737442054 0.066963658 0.124084045 4.85219832 0.028127335 0.020566928 144.369457 -2.159475323 0.220984727 SSS(ph)DALSASFNGEMLGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSDALSASFNGEMLGNR 18 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.119)S(0.119)S(0.763)DALSASFNGEMLGNR 124.43 3.34E-05 66848000 27050 31137 29582 35849 33105 22478 35036 25804 43422 TRUE FALSE 25356.98879 33442.41588 30283.69901 36768.94603 30505.06684 28967.0337 29782.67706 29025.6862 36174.58768 0.700961377 0.924472621 0.837153951 1.016430273 0.84327338 0.80075643 0.823303843 0.802377803 1 15.14268895 2.505755833 24.97246243 0.836373812 0.879081889 0 0.096481689 2425.225454 2115057.566 0.028268416 0.026606517 320.4467221 -2.505755833 0.042708077 SSS(ph)EITLSECDAEDAGEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSEITLSECDAEDAGEPR 19 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 SS(0.04)S(0.96)EITLSECDAEDAGEPR;S(0.021)S(0.021)S(0.957)EITLSECDAEDAGEPR 380.73 8.96E-109 347950000 130079 143103 128521 134926 151389 120233 199322 123966 181958 TRUE FALSE 121937.5876 153698.495 131569.5788 138388.4296 139499.5186 154942.3153 169435.5165 139443.428 151588.0343 0.80440114 1.013922344 0.867941717 0.912924494 0.920254156 1.02212761 1.117736748 0.919884136 1 17.20979635 2.226367082 5.096133859 1.035912634 0.913829414 0.357328037 0.071167769 0.174642077 12.51408949 0.024913606 0.019075704 168.4096924 -2.226367082 -0.12208322 SSS(ph)ENDVELLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSENDVELLTK 12 0 Q9C0D6 Q9C0D6 FHDC1 FH2 domain-containing protein 1 1 S(0.03)S(0.03)S(0.941)ENDVELLTK;SS(0.006)S(0.994)ENDVELLTK 250.46 3.53E-17 115046000 413620 323650 382290 346990 453630 307660 445640 354970 583900 TRUE FALSE 387732.2625 347613.3828 391358.0993 355894.3509 418003.7297 396476.4476 378820.4191 399288.7859 486443.3179 0.797075935 0.714602031 0.804529706 0.731625531 0.85930614 0.815051688 0.77875552 0.820833119 1 18.89191218 -5 0.19267509 1.949388785 0.746020363 0.755407887 0.03865409 62.73072533 0.61610601 22.81465626 0.094962892 1.00E-05 5 -1.203368422 SSS(ph)ETILSSLAGSDIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSSETILSSLAGSDIVK 17 0 Q01850 Q01850 CDR2 Cerebellar degeneration-related protein 2 1 S(0.266)S(0.266)S(0.468)ETILSSLAGSDIVK;S(0.252)S(0.252)S(0.496)ETILSSLAGSDIVK;S(0.013)S(0.013)S(0.973)ETILSSLAGSDIVK;S(0.24)S(0.24)S(0.521)ETILSSLAGSDIVK 408.89 2.24E-140 433372000 1351050 1086330 1228690 1223290 1280050 799362 1337130 1109700 1609040 TRUE FALSE 1266490.192 1166763.004 1257835.107 1254681.692 1179520.036 1030124.833 1136639.77 1248248.488 1340480.829 0.944802913 0.870406333 0.938346211 0.935993761 0.879923092 0.768474125 0.847934372 0.931194584 1 20.35431916 2.489525547 24.44769408 0.862204977 0.915541114 0.011750494 0.063742487 863.5453854 1701969.413 0.019764778 0.017771037 308.6921224 -2.489525547 0.053336137 SSS(ph)FSELCHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSFSELCHR 10 0 Q5T8I3-2;Q5T8I3 Q5T8I3-2 FAM102B Protein FAM102B 1 S(0.27)S(0.27)S(0.459)FSELCHR 180.97 1.25E-06 127790000 103710 129830 126990 92562 163130 139180 144380 153630 385180 TRUE FALSE 97218.97623 139442.7483 130002.2628 94937.29763 150318.4278 179359.0066 122731.5594 172811.0437 320890.9696 0.302965759 0.434548683 0.405129078 0.295855311 0.468440817 0.558940648 0.382471216 0.538535079 1 18.29172367 -4.999999882 0.232103732 4.192739156 0.356458679 0.8758351 0.070682086 52.14683285 0.521735757 78.1060072 0.114407255 1.00E-05 4.999999882 -3.836280477 SSS(ph)FSLPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SSSFSLPSR 9 0 Q14153-2;Q14153 Q14153-2 FAM53B Protein FAM53B 1 SS(0.011)S(0.989)FSLPSR;SS(0.002)S(0.998)FSLPSR;SS(0.005)S(0.995)FSLPSR;SS(0.02)S(0.979)FSLPSR;SS(0.01)S(0.99)FSLPSR;SS(0.006)S(0.994)FSLPSR 235.01 3.62E-10 3101270000 4519950 5063000 4628630 4818240 4922270 3808760 5694170 4254260 4733460 TRUE FALSE 4237054.398 5437869.788 4738423.289 4941884.196 4535694.77 4908287.182 4840382.071 4785413.726 3943414.947 1.074463239 1.378974787 1.201604029 1.253199134 1.150194649 1.244679357 1.227459483 1.213520208 1 21.9110141 -4.007401613 0.305926629 1.87E-13 1.244022209 0.417593807 0.078691216 125.9959537 2.050275133 79.65311091 0.070025517 9.83E-05 4.007401613 1.244022209 SSS(ph)FSSWDDSSDSYWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSFSSWDDSSDSYWK 16 0 Q9NP61;Q9NP61-2 Q9NP61 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 1 S(0.146)S(0.146)S(0.707)FS(0.001)SWDDSSDSYWK 153.94 1.75E-08 0 119960 101770 99012 110070 113450 75147 145260 85814 115340 TRUE FALSE 112451.9177 109305.1567 101360.6114 112894.5825 104540.0946 96840.71899 123479.6115 96528.0668 96089.00888 1.170289079 1.137540682 1.05486166 1.1748959 1.087950598 1.00782306 1.285054482 1.004569284 1 16.5520838 1.057038466 24.99999976 0.999986379 1.127183685 0.339123589 0.074670875 79.15202366 34691.92033 0.068123834 0.017030958 11.40350786 -1.057038466 0.127197305 SSS(ph)FTLLQSLAIEDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSSFTLLQSLAIEDSR 16 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;Q9Y4D8-2 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 1 S(0.143)S(0.143)S(0.707)FT(0.006)LLQSLAIEDSR;S(0.141)S(0.141)S(0.713)FT(0.005)LLQSLAIEDSR;S(0.077)S(0.077)S(0.846)FTLLQSLAIEDSR;S(0.094)S(0.094)S(0.812)FTLLQSLAIEDSR 136.01 2.07E-05 96559000 136816 169156 152300 166347 189358 112485 163981 162814 206993 TRUE FALSE 128252.9308 181680.4862 155912.6279 170615.7456 174486.5865 144957.5935 139393.5714 183141.6863 172444.5311 0.743734405 1.053558991 0.904132053 0.989394935 1.01184181 0.840604179 0.808338603 1.062032441 1 17.39577285 2.237869311 24.99999848 0.898148172 0.953202479 0 0.110410148 59.56140784 2153801.067 0.037157227 0.029076881 172.9295897 -2.237869311 0.055054307 SSS(ph)FVLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSSFVLPK 8 0 Q8WYP3-2;Q8WYP3 Q8WYP3-2 RIN2 Ras and Rab interactor 2 1 SS(0.009)S(0.99)FVLPK;SS(0.001)S(0.999)FVLPK;S(0.005)S(0.041)S(0.954)FVLPK;S(0.002)S(0.014)S(0.984)FVLPK 115.71 0.0025286 602260000 3703630 3551010 3409590 3435790 3937050 2142330 4277530 2946210 3943640 TRUE FALSE 3471826.409 3813930.475 3490467.085 3523958.188 3627849.974 2760785.893 3636154.087 3314050.804 3285421.007 1.056737143 1.160865066 1.062410899 1.072604753 1.104226815 0.84031419 1.106754379 1.008714194 1 21.64764682 SSS(ph)KESLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SSSKESLVR 9 1 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 S(0.098)S(0.02)S(0.857)KES(0.025)LVR;S(0.082)S(0.357)S(0.561)KESLVR;S(0.022)S(0.084)S(0.895)KESLVR;S(0.032)S(0.189)S(0.78)KESLVR;S(0.214)S(0.116)S(0.656)KES(0.014)LVR 137.01 0.00010707 5297890000 6275300 4171770 4582630 4360500 4595730 3221600 5541110 3698040 4709230 TRUE FALSE 5882540.175 4480652.192 4691332.148 4472397.812 4234799.904 4151623.622 4710271.997 4159748.434 3923229.09 1.499412866 1.14208273 1.195783381 1.139978755 1.079416931 1.058215956 1.200610999 1.060286906 1 21.90361015 7.242288135 1.211991916 1.117593189 199.9999989 0.772500182 0.065705482 376.5542715 1.399027915 0.017158917 207228.5449 17469808.14 -7.242288135 198.8824057 SSS(ph)LDALGPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSLDALGPTR 11 0 Q9H425;Q9H425-3;Q9H425-2;E5RI90 Q9H425 C1orf198 Uncharacterized protein C1orf198 1 S(0.004)S(0.073)S(0.923)LDALGPTR 110.58 0.0018621 81208000 224800 194590 203570 195200 212730 142900 224840 177060 248630 TRUE FALSE 210730.1693 208997.6461 208398.7765 200209.1625 196023.0439 184152.9102 191127.3293 199166.3308 207132.0468 1.017371153 1.009006811 1.006115566 0.966577435 0.946367532 0.889060448 0.922731814 0.961542812 1 17.66019125 3.034198173 2.075491099 0.932994444 1.011183313 0.511303616 0.028901502 0.20587899 1.792685841 0.008977268 0.010823393 1081.927532 -3.034198173 0.078188869 SSS(ph)LDGEHHDGYHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSLDGEHHDGYHR 14 0 Q9C0J8 Q9C0J8 WDR33 pre-mRNA 3 end processing protein WDR33 1 S(0.311)S(0.311)S(0.378)LDGEHHDGYHR 73.279 0.060636 49299000 28115 31071 27947 33671 32257 22441 38475 26724 27940 TRUE FALSE 26355.33234 33371.52917 28609.91604 34535.05486 29723.66534 28919.3524 32706.03093 30060.55023 23276.6335 1.13226564 1.433692255 1.229126026 1.48367911 1.27697441 1.242419889 1.405101426 1.291447504 1 14.5065948 0.957344782 22.21872147 0.999999998 1.324315164 0.466211134 0.104763549 1730.830308 901576.0657 0.088089053 0.022022263 9.064519382 -0.957344782 0.324315166 SSS(ph)LDMNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SSSLDMNR 8 0 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.001)S(0.046)S(0.953)LDMNR;S(0.006)S(0.076)S(0.917)LDMNR;SSS(1)LDMNR;SS(0.034)S(0.966)LDMNR;S(0.002)S(0.008)S(0.99)LDMNR;S(0.001)S(0.008)S(0.991)LDMNR 167.73 0.00069826 2211310000 3904380 4391540 3991980 4359630 4514440 3176120 4706040 3792750 4689690 TRUE FALSE 3660011.825 4716694.191 4086671.651 4471505.487 4159894.093 4093014.284 4000412.991 4266283.186 3906950.442 0.936795048 1.207257236 1.046000381 1.144500181 1.064741965 1.047623804 1.023922123 1.091972691 1 21.89761153 2.496414376 6.529391993 1.042622242 1.098703797 0.054459645 0.072652866 0.345056428 61.3829788 0.02205428 0.019865233 313.6276731 -2.496414376 0.056081555 SSS(ph)LEGFHNHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSLEGFHNHFK 12 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 S(0.09)S(0.09)S(0.819)LEGFHNHFK;S(0.187)S(0.187)S(0.626)LEGFHNHFK 147.1 4.21E-05 793950000 1055230 849990 922250 971270 1069120 732900 1191140 867940 1467960 TRUE FALSE 989185.0379 912924.144 944126.2055 996194.4326 985155.6278 944476.3324 1012539.615 976304.2196 1222947.993 0.808852906 0.746494658 0.772008467 0.814584462 0.805558073 0.772294765 0.827949857 0.798320309 1 20.22193162 -5 0.23392181 2.171668979 0.766309488 0.888955206 0.023073596 47.66083295 0.476635844 26.43693103 0.036921514 1.00E-05 5 -1.405359491 SSS(ph)LESLQTAVAEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSLESLQTAVAEVR 15 0 R4GN62;A0A087WZG6;A0A087X1S9;Q8TEW8-5;Q8TEW8-2;Q8TEW8 R4GN62 PARD3B Partitioning defective 3 homolog B 1 SSS(1)LESLQTAVAEVR;SSS(0.978)LES(0.022)LQTAVAEVR 268.93 9.82E-26 91962000 228659 213246 222987 227146 235652 157586 264825 191236 200645 TRUE FALSE 214347.6414 229034.9557 228276.3569 232974.9509 217144.8425 203078.52 225116.9498 215112.2356 167156.0533 1.282320545 1.370186429 1.365648162 1.393757189 1.299054615 1.214903774 1.346747218 1.286894679 1 17.35083608 -3.763043544 0.250757087 3.57E-10 1.362049271 0.805569411 0.050004883 37.68555845 0.65738654 19.30784625 0.071628307 0.000172566 3.763043544 1.36204927 SSS(ph)LESQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSLESQGK 9 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 SS(0.003)S(0.997)LESQGK;SS(0.004)S(0.996)LESQGK;SSS(1)LESQGK 206.27 1.43E-05 1486810000 3698670 2765920 3070500 3120260 3395740 2431200 4058180 2882240 3696240 TRUE FALSE 3467176.847 2970711.595 3143333.71 3200331.154 3129052.278 3133047.973 3449693.583 3242094.009 3079313.665 1.125957672 0.964731728 1.020790362 1.03930015 1.0161525 1.017450092 1.120280023 1.05286254 1 21.5541774 SSS(ph)LGNLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSLGNLKK 9 1 F5GZP6;Q86W92-3;Q86W92-4;Q86W92;H0YGH8;Q86W92-2 F5GZP6;Q86W92-2 PPFIBP1 Liprin-beta-1 1 S(0.001)S(0.016)S(0.984)LGNLKK;SS(0.004)S(0.996)LGNLKK;SS(0.001)S(0.999)LGNLKK 154.67 4.60E-05 1350440000 2187720 1500060 1759840 1671300 1968440 1215720 2123320 1630570 2781050 TRUE FALSE 2050794.51 1611126.003 1801584.236 1714188.388 1813846.663 1566678.628 1804947.878 1834150.254 2316874.789 0.885155521 0.695387602 0.777592404 0.739870966 0.782885062 0.676203408 0.779044205 0.791648415 1 21.14374865 0.647689435 1.887062939 0.999894729 0.753824416 0.630372978 0.056548372 0.947056981 4.334054367 0.047296697 0.013165057 4.443134238 -0.647689435 -0.246070313 SSS(ph)LIQLTSQNSSPNQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSLIQLTSQNSSPNQQR 18 0 O95639;H7C419 O95639 CPSF4 Cleavage and polyadenylation specificity factor subunit 4 1 SSS(1)LIQLTSQNSSPNQQR;S(0.001)S(0.033)S(0.967)LIQLTSQNSSPNQQR;SS(0.043)S(0.956)LIQLTSQNSSPNQQR 396.71 5.50E-127 380247000 246520 265695 224073 259678 266459 199508 312050 238487 323198 TRUE FALSE 231090.7533 285367.3343 229388.1174 266341.7771 245532.385 257102.7209 265260.9994 268262.6269 269254.1659 0.858262499 1.059843711 0.851938972 0.989183496 0.911898184 0.954869983 0.985169528 0.996317461 1 18.03860914 1.721102099 2.797225164 0.99633527 0.942107021 0.165856919 0.059830598 0.475760416 8.01229356 0.033864177 0.015253562 52.61409437 -1.721102099 -0.054228249 SSS(ph)LKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSLKER 7 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 S(0.004)S(0.019)S(0.976)LKER;S(0.016)S(0.026)S(0.958)LKER 112.3 0.0168 3280100000 4126900 2741100 2901500 2840900 3031300 2108580 3267700 2488000 4973900 TRUE FALSE 3868604.696 2944053.896 2970324.95 2913802.304 2793233.926 2717292.816 2777738.721 2798632.277 4143723.957 0.933605794 0.710485044 0.716825006 0.703184462 0.674087838 0.65576106 0.670348399 0.675390616 1 21.98249647 -1.082164115 9.049855368 1.000000001 0.709382769 0.551976716 0.079701634 1.98E-09 2.37E-10 0.071940878 0.016956628 0.082762935 1.082164115 -0.290617232 SSS(ph)LSDLTHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSLSDLTHR 10 0 Q5T9C2-3;Q5T9C2;Q5T9C2-2 Q5T9C2-3 FAM102A Protein FAM102A 1 S(0.289)S(0.289)S(0.421)LSDLTHR 100.04 0.0027612 142170000 126940 160250 142100 141000 161400 160650 153110 132960 142460 TRUE FALSE 118995.052 172115.0767 145470.6791 144618.2987 148724.2951 207027.0471 130152.5769 149560.3487 118682.5057 1.002633466 1.450214383 1.225712908 1.218530885 1.25312736 1.744377117 1.096645004 1.260171816 1 16.85674777 0.87626991 1.598996786 1.005930182 1.308311182 0.161056332 0.20099601 0.882231978 4.40305577 0.173148255 0.050102675 7.520901655 -0.87626991 0.302381 SSS(ph)MAAGLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSMAAGLER 10 0 Q9UQB8;Q9UQB8-2;Q9UQB8-4;Q9UQB8-5;Q9UQB8-3;I3L4C2;Q9UQB8-6;B4DWA1;I3L3C6;I3L0Y9 Q9UQB8 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 1 SS(0.004)S(0.996)MAAGLER;SS(0.002)S(0.998)MAAGLER;S(0.029)S(0.075)S(0.896)MAAGLER 182.92 1.81E-06 1309440000 1498930 2225760 1562720 1522460 2481190 975230 2081890 1992860 3041380 TRUE FALSE 1405114.647 2390557.586 1599788.456 1561528.901 2286327.346 1256763.069 1769729.922 2241672.958 2533754.03 0.554558426 0.943484473 0.631390592 0.616290643 0.902347789 0.496008316 0.698461611 0.884723983 1 21.27284505 1.077575808 3.672330688 0.99591843 0.705394927 0.368271598 0.139828693 0.223606283 5.752984469 0.125345282 0.032505551 11.95572199 -1.077575808 -0.290523503 SSS(ph)MELHREENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSMELHREENR 12 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.137)S(0.137)S(0.726)MELHREENR;S(0.165)S(0.165)S(0.67)MELHREENR 160.47 4.12E-05 828430000 394040 516630 442930 444070 525740 353500 546920 446780 702760 TRUE FALSE 369377.7398 554881.8228 453436.5088 455465.588 484450.5011 455549.7114 464914.4234 502561.4665 585464.816 0.630913643 0.947762884 0.774489767 0.777955525 0.827463048 0.778099211 0.794094556 0.858397384 1 19.15922295 0.875779215 3.207716997 0.999906046 0.804118566 0.419331869 0.077153823 0.515291661 10.51638401 0.067688941 0.01762072 7.512408832 -0.875779215 -0.19578748 SSS(ph)MSSIDLVSASDDVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSMSSIDLVSASDDVHR 18 0 Q9Y5P4-3;Q9Y5P4;A0A2U3TZL3;A0A2R8YFA1;A0A0A0MRE4 Q9Y5P4-3 COL4A3BP Collagen type IV alpha-3-binding protein 1 S(0.127)S(0.127)S(0.745)MSSIDLVSASDDVHR;S(0.087)S(0.087)S(0.819)MS(0.006)SIDLVSASDDVHR 241.13 1.86E-23 562490000 251500 278480 250010 272270 232740 216280 327280 234750 285700 TRUE FALSE 235759.0639 299098.949 255940.3553 279256.9092 214461.5392 278716.525 278207.4023 264059.0542 238014.8243 0.990522606 1.256640001 1.075312666 1.173275278 0.901042781 1.171004898 1.16886586 1.109422722 1 17.86069191 -2.102897471 2.190306788 0.799910842 1.119086351 0.083849682 0.101714271 7122613.03 1957715.741 7095669.257 0.023982639 0.007890464 2.102897471 0.319175509 SSS(ph)MSYVDGFIGTWPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSMSYVDGFIGTWPK 16 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 S(0.047)S(0.047)S(0.907)MSYVDGFIGTWPK;S(0.017)S(0.017)S(0.967)MSYVDGFIGTWPK 383.79 3.22E-121 342910000 1364090 1217830 1259840 1231840 1193320 894770 1719730 1202330 1628480 TRUE FALSE 1278714.042 1307999.4 1289724 1263451.1 1099601.461 1153075.574 1461872.452 1352443.547 1356676.168 0.942534462 0.96412057 0.950649853 0.931284215 0.810511371 0.849926903 1.077539716 0.996880154 1 20.37164497 1.728272805 13.07062038 1.0270764 0.916670083 0.524864595 0.051870005 0.086009346 69.35183209 0.026348095 0.014472163 53.49002547 -1.728272805 -0.110406317 SSS(ph)PAGETEGDREPQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSPAGETEGDREPQAR 17 1 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 SS(0.002)S(0.998)PAGETEGDREPQAR;SSS(0.999)PAGETEGDREPQAR;S(0.001)S(0.019)S(0.98)PAGETEGDREPQAR 261.94 1.56E-27 1609530000 864100 719540 795540 769590 787360 785710 846040 744670 749230 TRUE FALSE 810017.5235 772815.4903 814410.5845 789338.9823 725523.9217 1012531.722 719184.1563 837643.6887 624178.6728 1.29773342 1.238131843 1.304771566 1.264604218 1.162365767 1.622182504 1.152208795 1.341993447 1 19.25159954 -0.74191363 6.427029248 0.999999998 1.292262517 0.341517602 0.129824708 4.92E-09 5.11E-10 0.110140161 0.025960285 0.181170036 0.74191363 0.29226252 SSS(ph)PAGETEGDREPQARPGEGTAPLPPPGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSPAGETEGDREPQARPGEGTAPLPPPGQK 31 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(0.012)S(0.012)S(0.977)PAGETEGDREPQARPGEGTAPLPPPGQK;S(0.007)S(0.321)S(0.671)PAGET(0.002)EGDREPQARPGEGTAPLPPPGQK 220.12 3.38E-35 985440000 576790 491330 531430 523480 600540 442220 685430 508480 1002340 TRUE FALSE 540689.7435 527708.5844 544035.7706 536913.383 553376.0109 569881.7352 582656.1347 571964.8473 835042.9786 0.647499299 0.631953801 0.651506311 0.642976945 0.662691652 0.682457969 0.697755864 0.684952586 1 19.67149093 -5 0.247721272 3.049443038 0.629197296 0.991211339 0.010122097 14.08172196 0.139878648 14.57080383 0.014191569 1.00E-05 5 -2.420245741 SSS(ph)PAPADIAQTVQEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 SSSPAPADIAQTVQEDLR 18 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 1 SS(0.004)S(0.996)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;S(0.241)S(0.241)S(0.519)PAPADIAQTVQEDLR;SS(0.001)S(0.999)PAPADIAQTVQEDLR;S(0.133)S(0.133)S(0.733)PAPADIAQTVQEDLR;S(0.011)S(0.067)S(0.922)PAPADIAQTVQEDLR;SS(0.016)S(0.984)PAPADIAQTVQEDLR;S(0.086)S(0.086)S(0.828)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;SS(0.002)S(0.998)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;SS(0.004)S(0.996)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR 481.29 1.30E-239 1.75061E+11 15814296 15576343 17291307 16448845 17605667 15365080 18798511 15869239 20206569 TRUE FALSE 14824507.44 16729631.64 17701464.97 16870950.21 16222988.93 19800729.16 15979848.79 17850548.42 16833962.09 0.880630915 0.993802383 1.051532899 1.002197232 0.96370592 1.176237006 0.949262491 1.060389011 1 24.00487144 4.772384445 2.122023331 1.027860548 0.832037688 0.355097321 0.062705959 0.806502048 3.800967745 0.014140358 0.311105455 59208.55264 -4.772384445 -0.19582286 SSS(ph)PATEQSWMENDFDELREEGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSSPATEQSWMENDFDELREEGFR 24 1 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 SS(0.005)S(0.989)PAT(0.006)EQSWMENDFDELREEGFR;S(0.104)S(0.104)S(0.791)PATEQSWMENDFDELREEGFR;SS(0.004)S(0.996)PATEQSWMENDFDELREEGFR;S(0.162)S(0.162)S(0.676)PATEQSWMENDFDELREEGFR 285.77 7.44E-53 414178000 48658.3 44498.3 51876.7 54095.9 53355.1 52415.3 59972.6 42704 49426.5 TRUE FALSE 45612.86386 47793.00043 53107.23982 55484.09238 49164.80567 67546.74622 50980.26539 48035.6884 41176.89784 1.107729485 1.16067511 1.28973387 1.347456833 1.193990034 1.640403958 1.238079313 1.1665689 1 15.32954752 4.15433995 1.676017681 1.297752851 1.110589695 0.086503037 0.163452005 0.810747951 4.096688457 0.041745062 0.169581809 14267.23944 -4.15433995 -0.187163156 SSS(ph)PATEQSWMENDFDELREEGFRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSSPATEQSWMENDFDELREEGFRR 25 2 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.074)S(0.395)S(0.531)PATEQSWMENDFDELREEGFRR;S(0.31)S(0.31)S(0.38)PATEQSWMENDFDELREEGFRR;S(0.076)S(0.397)S(0.527)PATEQSWMENDFDELREEGFRR;S(0.302)S(0.302)S(0.396)PATEQSWMENDFDELREEGFRR 283.75 9.72E-54 827000000 95437 104537 81859 94816 104050 86365 114984 89628 122595 TRUE FALSE 89463.76853 112277.0283 83800.73414 97249.13908 95878.33272 111297.1735 97743.21666 100818.2531 102133.1025 0.875952716 1.099320646 0.820505126 0.952180407 0.938758643 1.089726746 0.957017992 0.987126119 1 16.64009101 SSS(ph)PELVTHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSPELVTHLK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.098)S(0.086)S(0.816)PELVTHLK;S(0.002)S(0.257)S(0.741)PELVTHLK;S(0.277)S(0.277)S(0.447)PELVTHLK 262.35 1.03E-20 6024370000 7606300 7070800 7295000 7366300 7396300 5156380 8078100 5993000 8028000 TRUE FALSE 7130235.261 7594329.389 7468040.845 7555331.729 6815424.433 6644943.199 6866863.898 6741239.242 6688074.937 1.066111748 1.135503035 1.11662039 1.12967211 1.019041278 0.993550949 1.0267325 1.007949119 1 22.67315958 2.711564114 7.173718224 1.010765866 1.116706196 0.859037517 0.020596212 0.064791597 13.39195478 0.006133882 0.005884433 514.7117877 -2.711564114 0.10594033 SSS(ph)PHDKNLPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSPHDKNLPQK 12 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.002)S(0.094)S(0.903)PHDKNLPQK 129.77 0.00013826 180050000 284730 284630 283430 307000 395710 173130 359930 241560 704110 TRUE FALSE 266909.2576 305704.3014 290153.0934 314878.1397 364632.5328 223109.8205 305961.8379 271719.2977 586589.4923 0.455018818 0.521155434 0.494644206 0.536794716 0.621614498 0.380350864 0.521594474 0.463218829 1 19.1619917 -1.702213058 2.792756909 1.073410222 0.50176378 0.864827318 0.06220329 10329912.96 9349355.569 5346670.507 0.013439215 0.019851208 1.702213058 -0.571646442 SSS(ph)PPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SSSPPPR 7 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.001)S(0.001)S(0.998)PPPR;S(0.001)S(0.006)S(0.992)PPPR;S(0.001)S(0.014)S(0.985)PPPR;S(0.002)S(0.002)S(0.996)PPPR;S(0.001)S(0.007)S(0.991)PPPR;S(0.003)S(0.003)S(0.994)PPPR 129.68 0.0038147 1555854000 5040670 5143659 5450539 5407921 5491634 4711815 5047751 4685097 5243755 TRUE FALSE 4725183.463 5524500.864 5579828.359 5546697.408 5060343.218 6072039.501 4290887.599 5270041.674 4368538.415 1.081639444 1.264610801 1.277275791 1.269691801 1.1583607 1.389947604 0.98222499 1.206362672 1 22.05871925 1.715950954 12.96007648 1.071984891 1.245293135 0.41366085 0.099212192 0.10579555 47.48165173 0.04103366 0.022526335 51.99372748 -1.715950954 0.173308243 SSS(ph)PPPRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSPPPRK 8 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.052)S(0.052)S(0.896)PPPRK;S(0.291)S(0.291)S(0.418)PPPRK;S(0.298)S(0.298)S(0.404)PPPRK 87.308 0.0094428 3588450000 2479390 2013480 2310320 2203000 2141390 1591890 2353640 2006900 2642440 TRUE FALSE 2324209.406 2162560.154 2365121.881 2259532.71 1973213.867 2051442.801 2000733.532 2257465.883 2201399.693 1.055787104 0.982356889 1.074371859 1.026407297 0.896345118 0.931881115 0.908846103 1.025468428 1 21.06998968 2.8157561 7.900731578 0.942179361 1.03298451 0.440256632 0.04524521 0.251924296 23.39249655 0.013000373 0.013794546 654.2686339 -2.8157561 0.090805148 SSS(ph)PQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSPQPK 7 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.005)S(0.256)S(0.739)PQPK;SS(0.036)S(0.964)PQPK 85.744 0.021594 391520000 2095500 1330530 2452300 1896360 1850350 1450060 2773000 1494880 2181900 TRUE FALSE 1964346.396 1429043.826 2510469.714 1945023.808 1705030.975 1868668.782 2357214.393 1681519.059 1817726.794 1.080660967 0.786170854 1.381103982 1.070030884 0.938001783 1.028025107 1.296792456 0.925066992 1 20.79370395 4.008276325 22.55293101 1.113351987 0.933787439 0.129879926 0.162244338 190.6321808 137993.4598 0.038333255 0.082783577 10192.39685 -4.008276325 -0.179564548 SSS(ph)PTLTPSQEGSPVFAGFEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSPTLTPSQEGSPVFAGFEGR 22 0 P0C860 P0C860 MSL3P1 Putative male-specific lethal-3 protein-like 2 1 S(0.105)S(0.105)S(0.79)PTLTPSQEGSPVFAGFEGR;S(0.107)S(0.107)S(0.785)PTLTPSQEGSPVFAGFEGR 263.09 2.25E-37 178214000 115330 123224 116050 119293 134603 109857 145519 110647 140745 TRUE FALSE 108111.7012 132347.6332 118802.7608 122354.2603 124031.8233 141570.9325 123699.7769 124461.5215 117253.7503 0.922031926 1.12872836 1.013210755 1.043499761 1.057806877 1.207389377 1.054975015 1.061471563 1 16.83927454 2.463001225 24.9987492 1.092364756 1.042476796 0.085209673 0.072201985 547.7598644 969773.6616 0.023062441 0.01930356 290.4030843 -2.463001225 -0.049887961 SSS(ph)PTQYGLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSPTQYGLTK 11 0 Q9NYL2 Q9NYL2 ZAK Mitogen-activated protein kinase kinase kinase MLT 1 S(0.008)S(0.204)S(0.786)PT(0.001)QYGLTK 86.756 0.01493 72086000 269320 265130 286960 284560 273160 201790 329470 220800 302110 TRUE FALSE 252463.7419 284760.5011 293766.8267 291862.2914 251707.1155 260043.4972 280069.0321 248367.366 251685.8893 1.003090569 1.131412261 1.167196252 1.15962914 1.000084336 1.033206502 1.112772086 0.986814822 1 17.94126481 2.74160365 24.99582112 1.040576289 1.126656123 0.352106788 0.057217585 301.36206 2475434.279 0.017681283 0.018018758 551.5738273 -2.74160365 0.086079834 SSS(ph)PTSYWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SSSPTSYWK 9 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 S(0.001)S(0.021)S(0.978)PTSYWK;SSS(0.999)PTSYWK;SS(0.011)S(0.989)PTSYWK;SS(0.001)S(0.999)PTSYWK;SS(0.002)S(0.997)PTSYWK 179.57 5.21E-05 3964060000 12253200 8956900 10305900 9374700 9747400 8602200 12080900 9386800 9202000 TRUE FALSE 11486294.08 9620078.196 10550360.81 9615270.673 8981878.523 11085515.49 10269481.2 10558762.64 7666126.753 1.498317789 1.254881181 1.376230938 1.254254069 1.171631883 1.446038639 1.339591886 1.377326906 1 22.87006642 -1.106932109 4.333002839 0.99995503 1.33311333 0.554048929 0.095635819 3.80E-05 7.83E-06 0.084716333 0.01996514 0.078175 1.106932109 0.3331583 SSS(ph)PVGLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSSPVGLAK 9 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 SSS(1)PVGLAK;SS(0.013)S(0.987)PVGLAK;SS(0.017)S(0.983)PVGLAK;SS(0.101)S(0.898)PVGLAK 200.68 2.38E-05 4673150000 14978300 12181200 13599800 13206600 14484700 10195400 16568200 12534900 16277200 TRUE FALSE 14040834.94 13083108.72 13922393.68 13545503.71 13347130.09 13138646.47 14083952.22 14099909.86 13560430.17 1.035426957 0.96480042 1.026692628 0.998899264 0.984270405 0.968895995 1.038606597 1.039783376 1 23.69289961 1.675600884 9.606769738 1.029131361 0.996000053 0.241010027 0.024521326 0.144147491 20.24613719 0.01093537 0.005862812 47.38063579 -1.675600884 -0.033131308 SSS(ph)PVQVEEEPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSPVQVEEEPVR 13 0 Q8IZ21-3;Q8IZ21;Q8IZ21-2;A0A0J9YVR0 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 S(0.022)S(0.092)S(0.886)PVQVEEEPVR 152.88 1.31E-06 0 235690 288990 306260 251400 271510 230330 313060 229210 310730 TRUE FALSE 220938.5836 310387.1203 313524.6318 257851.3496 250186.6998 296822.5319 266119.5593 257827.3731 258867.1556 0.853482486 1.199020863 1.211141024 0.996075956 0.966467527 1.146621058 1.028015928 0.995983335 1 17.98185241 3.220233171 24.99631903 1.02981501 1.129305582 0.028076097 0.109781248 438.4565922 597998.139 0.030942609 0.037051087 1660.478173 -3.220233171 0.099490572 SSS(ph)PVTELASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSSPVTELASR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SSS(1)PVTELASR;SSS(1)PVTELASR;S(0.003)S(0.001)S(0.996)PVTELASR;SS(0.001)S(0.999)PVTELASR 308.91 1.54E-45 7921300000 4844070 4607260 4788120 4505890 4178880 4487430 5466680 4170980 3776800 TRUE FALSE 4540888.306 4948386.324 4901696.468 4621518.766 3850687.622 5782878.194 4647002.084 4691736.034 3146427.681 1.443188519 1.572699844 1.557860839 1.468814552 1.223828421 1.837918675 1.47691368 1.491131057 1 21.58528335 0.568611414 2.522715536 1.000025946 1.523884529 0.529923633 0.15048732 3.929968897 22.06423672 0.132101699 0.03520472 3.703492023 -0.568611414 0.523858584 SSS(ph)PVTELASRS(ph)PIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSPVTELASRSPIR 15 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.094)S(0.409)S(0.496)PVT(0.018)ELAS(0.071)RS(0.912)PIR 83.251 0.0027919 0 184200 235890 227150 236140 243220 167380 241300 209070 230730 TRUE FALSE 172671.2508 253355.541 232538.1053 242199.7522 224118.4823 215699.8888 205119.3051 235172.8497 192219.6724 0.89830166 1.31805209 1.209751855 1.260015425 1.165949767 1.122153035 1.067108806 1.2234588 1 17.55239647 2.313029536 3.193022575 1.103160508 1.202921407 0.042937754 0.122994711 0.510987242 10.53997904 0.043737591 0.034211702 205.6030419 -2.313029536 0.099760899 SSS(ph)PVTELASRS(ph)PIRQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSPVTELASRSPIRQDR 18 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.279)S(0.33)S(0.391)PVTELAS(0.254)RS(0.746)PIRQDR;S(0.01)S(0.041)S(0.949)PVTELAS(0.119)RS(0.881)PIRQDR 122.6 0.0006785 1093291000 495951 678996 587028 648168 832470 409356 634362 535819 1022880 TRUE FALSE 464910.3122 729269.5703 600952.5814 664801.0882 767091.1642 527530.4319 539245.3072 602717.1816 852154.7199 0.545570307 0.855794791 0.705215341 0.780141297 0.900178273 0.619054756 0.632802113 0.707286092 1 19.70075587 -2.165652189 2.24782594 1.647424171 0.725335171 0.404010549 0.107236714 7224811.224 1562175.481 23827100.77 0.025657875 0.006828854 2.165652189 -0.922089 SSS(ph)QIPEGFGLTSGGSNYSLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSQIPEGFGLTSGGSNYSLAR 22 0 Q9Y4E6-2;Q9Y4E6;A2RRE0 Q9Y4E6-2 WDR7 WD repeat-containing protein 7 1 S(0.127)S(0.127)S(0.747)QIPEGFGLTSGGSNYSLAR 130.83 1.37E-05 71849000 37281 45111 38401 51442 54836 33148 58570 43674 63783 TRUE FALSE 34947.64876 48451.06538 39311.88985 52762.08881 50529.40176 42717.28949 49787.97224 49126.79504 53137.20525 0.657686993 0.91181057 0.739818545 0.992940607 0.95092321 0.803905461 0.936970095 0.924527265 1 15.69743473 7.117775651 0.263411753 0.954158432 3.85E-34 0.418835686 0.085531064 34.78511507 0.729433783 0.097915816 13.63514093 13115222.15 -7.117775651 -0.954158432 SSS(ph)QPSSCCSDPSKPGGNVEGATQSLAEQMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSQPSSCCSDPSKPGGNVEGATQSLAEQMR 31 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.002)S(0.037)S(0.961)QPSSCCSDPSKPGGNVEGATQSLAEQMR;S(0.127)S(0.127)S(0.744)QPS(0.001)SCCSDPSKPGGNVEGATQSLAEQMR 174.66 1.58E-13 373730000 424270 318070 326490 298910 340720 259060 421470 292510 344840 TRUE FALSE 397715.698 341620.2338 334234.497 306580.5367 313961.2256 333846.4165 358274.4862 329030.5174 287283.9762 1.384399169 1.189137794 1.163428957 1.067168941 1.092860206 1.162078097 1.247109188 1.145314548 1 18.132118 SSS(ph)RPCS(ph)PVHHHEGHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSRPCSPVHHHEGHAK 17 1 Q9Y2K6 Q9Y2K6 USP20 Ubiquitin carboxyl-terminal hydrolase 20 2 S(0.136)S(0.163)S(0.759)RPCS(0.941)PVHHHEGHAK 115.36 0.00016002 90604000 43884 38461 41726 32619 39472 27198 53758 35427 56418 TRUE FALSE 41137.37878 41308.69246 42715.76042 33456.05876 36372.02834 35049.62108 45697.48696 39850.13893 47001.47133 0.875235979 0.878880837 0.908817516 0.711808754 0.773848718 0.745713274 0.97225652 0.847848755 1 15.5204183 1.112432372 1.231962906 0.985521288 0.834504744 0.308015767 0.077288688 0.607743299 1.892107655 0.075103807 0.023595011 12.95484949 -1.112432372 -0.151016544 SSS(ph)SPELQTLQDILGDPGDKADVGR ddPTM_SK-BR-3_Pertuzumab_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(0.009)S(0.009)S(0.974)S(0.007)PELQTLQDILGDPGDKADVGR 205.93 2.42E-25 146450000 93677 75018 68064 83443 94039 61604 137390 87535 131550 TRUE FALSE 87813.92379 80572.41078 69678.51022 85584.28865 86653.55628 79388.07474 116789.645 98463.93744 109593.4552 0.801269781 0.735193636 0.635790797 0.78092518 0.790681854 0.724387005 1.065662587 0.898447241 1 16.74180212 1.756259607 14.01216726 0.985737666 0.734198098 0.776578303 0.06134742 0.128076141 100.8857213 0.028252884 0.015579676 57.05051997 -1.756259607 -0.251539568 SSS(ph)SQTLTQFDSNIAPADPDTAIVHPVPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSSQTLTQFDSNIAPADPDTAIVHPVPIR 30 0 Q96D71;Q96D71-3;H0YE73 Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.161)S(0.161)S(0.669)S(0.009)QTLTQFDSNIAPADPDTAIVHPVPIR 299.43 2.37E-81 311120000 14722 17840 17226 14163 12660 11514 16459 16520 21886 TRUE FALSE 13800.5763 19160.89216 17634.60885 14526.44656 11665.73467 14837.90489 13991.12575 18582.55837 18233.08521 0.756897483 1.0508859 0.967176353 0.796708094 0.639811339 0.813790136 0.767348235 1.019166979 1 14.15427108 3.240305299 24.97289319 0.813151876 0.957992138 0.043351071 0.132883756 67.81288963 970641.0574 0.035092297 0.045158229 1739.022892 -3.240305299 0.144840262 SSS(ph)T(ph)LS(ph)Y(ph)HKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSTLSYHKK 10 1 O43345 O43345 ZNF208 Zinc finger protein 208 4 S(0.001)S(0.006)S(0.994)T(1)LS(1)Y(1)HKK 45.661 0.060295 174960000 293100 323720 282260 315160 289900 251500 454470 269750 334960 TRUE FALSE 274755.3942 347688.5656 288955.3405 323247.5392 267132.4234 324103.9672 386326.4426 303428.8813 279053.0121 0.984599278 1.245958834 1.035485474 1.158373231 0.957281992 1.161442282 1.38441954 1.087352109 1 18.09017969 2.002879823 24.99820434 1.218210609 1.094438616 0.01384252 0.130708892 149.4932756 1297661.806 0.045418275 0.033363178 100.6653072 -2.002879823 -0.123771993 SSS(ph)TEPPPPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSTEPPPPVR 11 0 Q8N684-2;Q8N684;Q8N684-3;F5H669;F5H6M0;F5H047;J3QT54;F5H5B7;F5H1W4;F5H2K8;F5H6P5;F5H6A8;F5GXA3;C9JM38;C9J286;C9J323 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 1 SS(0.001)S(0.99)T(0.009)EPPPPVR 127.7 0.00029503 162010000 335840 262560 305690 292750 297420 257400 378290 302970 341380 TRUE FALSE 314820.3739 282000.2156 312941.1112 300262.4606 274061.8329 331707.2015 321568.9264 340796.4714 284401.4726 1.106957608 0.991556805 1.100349827 1.055769711 0.963644212 1.166334332 1.130686573 1.198293625 1 18.11756941 2.216827683 24.99942551 1.135416239 1.044832886 0.256816056 0.06646688 270.2606784 310879.2968 0.022258975 0.016453118 164.7508574 -2.216827683 -0.090583353 SSS(ph)TGNLLDKDDLAIPPPDYGAASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.095)S(0.095)S(0.795)T(0.015)GNLLDKDDLAIPPPDYGAASR;S(0.095)S(0.095)S(0.667)T(0.142)GNLLDKDDLAIPPPDYGAASR 198.7 4.55E-25 581240000 1038040 718930 839410 722890 882130 585120 1272080 826250 1675320 TRUE FALSE 973070.9294 772160.3252 859321.2016 741440.5812 812851.0681 754034.6454 1081343.413 929409.1313 1395698.269 0.697192904 0.55324302 0.615692676 0.531232715 0.582397418 0.540256202 0.774768757 0.665909783 1 20.41255565 0.729045407 0.773483098 0.998908099 0.584469592 0.766697084 0.068392836 0.447512194 0.517453914 0.062375696 0.022129019 5.358526794 -0.729045407 -0.414438507 SSS(ph)TSDILEPFTVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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(0.991)T(0.008)S(0.001)DILEPFTVER;SSS(0.892)T(0.107)S(0.001)DILEPFTVER;SSS(0.999)T(0.001)SDILEPFTVER;SSS(0.997)T(0.003)SDILEPFTVER;S(0.009)S(0.19)S(0.657)T(0.139)S(0.005)DILEPFTVER;S(0.014)S(0.346)S(0.638)T(0.002)SDILEPFTVER 323.02 8.62E-57 2593203000 3734580 4067110 4070200 4174640 4355780 3710510 5380880 3767670 4424480 TRUE FALSE 3500839.304 4368243.056 4166747.066 4281768.33 4013694.609 4781674.002 4574066.998 4238071.893 3686005.705 0.949765026 1.185088523 1.13042339 1.161628243 1.088900813 1.297250841 1.240927813 1.149773558 1 21.81362687 4.740773579 24.56923882 1.171239756 0.949764929 0.380573511 0.081137003 155.0127732 1720869.292 0.018322034 0.122288816 55052.06054 -4.740773579 -0.221474827 SSS(ph)VEEKPLSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSVEEKPLSHR 12 1 Q06190 Q06190 PPP2R3A Serine/threonine-protein phosphatase 2A regulatory subunit B subunit alpha 1 S(0.046)S(0.218)S(0.736)VEEKPLSHR 69.331 0.03044 181040000 81743 91545 77682 102440 83830 56159 111300 76117 136630 TRUE FALSE 76626.85155 98323.08705 79524.65372 105068.7838 77246.32995 72371.19163 94611.59826 85620.375 113825.5703 0.67319541 0.863804915 0.698653681 0.923068371 0.678637759 0.635807854 0.831198104 0.752206861 1 16.79646516 -0.082237659 1.313743295 1.000705134 0.762607855 0.406455503 0.091959199 20.90381138 23.76672533 0.145221214 0.023856963 0.827489213 0.082237659 -0.238097279 SSS(ph)VGS(ph)SSSYPISPAVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SSSVGSSSSYPISPAVSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 2 SSS(0.999)VGS(0.999)S(0.001)SSYPISPAVSR;SS(0.001)S(0.999)VGS(0.952)S(0.041)S(0.007)SYPISPAVSR;SSS(1)VGS(0.819)S(0.18)SSYPISPAVSR;SS(0.028)S(0.972)VGS(0.99)S(0.01)SSYPISPAVSR;SSS(1)VGS(0.999)S(0.001)SSYPISPAVSR 406.71 4.66E-147 1870620000 1323200 1386420 1216970 1400430 1333840 1053230 1990630 1129130 1307320 TRUE FALSE 1240383.274 1489071.979 1245837.103 1436367.405 1229085.587 1357280.403 1692153.512 1270104.366 1089119.846 1.138885934 1.367225089 1.143893491 1.318833193 1.128512708 1.246217675 1.553688988 1.166175027 1 20.05473129 1.972013218 24.69908734 1.326095064 1.229957056 0 0.162085275 1678.231189 1481081.3 0.060593475 0.039221309 93.75905431 -1.972013218 -0.096138007 SSS(ph)VGSSSSYPIS(ph)PAVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSVGSSSSYPISPAVSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 2 S(0.083)S(0.112)S(0.805)VGSS(0.001)SSYPIS(0.999)PAVSR;S(0.082)S(0.127)S(0.791)VGSSSSYPIS(1)PAVSR 188.88 5.20E-14 599090000 948450 991580 1032980 1263090 1297280 973740 1377090 981610 1119320 TRUE FALSE 889088.2075 1064997.615 1057482.773 1295503.028 1195396.862 1254842.931 1170608.139 1104166.169 932498.2609 0.953447577 1.142090725 1.134031899 1.389281977 1.28192932 1.345678575 1.25534619 1.184094615 1 19.83074151 4.74284367 0.883351492 1.255387364 0.808317533 0.35528558 0.111684644 2.172952052 1.305678053 0.034207113 0.946205703 55315.096 -4.74284367 -0.447069831 SSS(ph)VGSSSSYPISPAVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 SSSVGSSSSYPISPAVSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 SSS(0.993)VGS(0.007)SSSYPISPAVSR;SSS(0.998)VGS(0.002)SSSYPISPAVSR;SSS(0.996)VGS(0.004)SSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(0.998)VGS(0.002)SSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(0.998)VGS(0.001)SSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR 456.95 4.25E-192 43989790000 5496990 6373420 5694240 6745590 7465570 5718040 8465870 6010090 6883450 TRUE FALSE 5152943.208 6845314.648 5829310.062 6918693.26 6879254.247 7368745.323 7196491.387 6760462.966 5734557.726 0.898577267 1.193695307 1.016523042 1.20649117 1.199613741 1.284971863 1.254933986 1.178898755 1 22.45125079 3.224093225 24.2297365 1.210869829 1.067179934 0.283464389 0.105444031 184.3095176 308677.5927 0.027761136 0.03333593 1675.302455 -3.224093225 -0.143689895 SSSALDS(ph)PAGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSALDSPAGPR 12 0 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 SSS(0.002)ALDS(0.998)PAGPR 90.861 0.0090447 247770000 281750 234670 250790 240290 242710 214060 274610 212880 226360 TRUE FALSE 264115.7704 252045.211 256738.8572 246456.2482 223648.5356 275855.647 233434.7799 239458.5366 188579.0537 1.400557301 1.336549347 1.361438889 1.306912106 1.185967006 1.462811705 1.237861657 1.26980453 1 17.52480991 -4.099635281 0.202666635 2.78E-18 1.378923838 0.674403705 0.073033003 52.51573244 0.724612293 21.49157069 0.157322743 7.95E-05 4.099635281 1.378923838 SSSASS(ph)PEMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSASSPEMK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SSSAS(0.001)S(0.999)PEMK;SSSAS(0.262)S(0.738)PEMK 168.05 2.42E-05 218570000 893350 555220 694490 589320 732630 700400 1217140 837850 932040 TRUE FALSE 837436.8182 596329.0665 710963.6308 604442.9489 675092.1951 902594.11 1034641.156 942457.4168 776476.5028 1.078508899 0.767993705 0.915628004 0.778443323 0.869430295 1.162422954 1.332482249 1.21376167 1 19.56658274 2.195979712 4.52448434 1.224238947 0.865037554 0.59329857 0.119175988 0.109037713 4.877098512 0.041268598 0.030685917 157.0289446 -2.195979712 -0.359201393 SSSGLLEWESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSGLLEWESK 11 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0;M0R076 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 188.99 6.77E-06 182460000 401360 361580 377260 377870 382020 281810 433430 324250 448910 FALSE TRUE 376239.594 388351.7594 386208.7854 387566.7839 352017.6902 363163.9722 368441.1953 364733.3263 373984.0209 1.006031202 1.038418054 1.032687932 1.0363191 0.941263986 0.971068152 0.985178977 0.975264465 1 18.5126171 2.75715266 24.88194033 0.974326467 1.030760384 0.712545512 0.016951957 370.4141167 495728.6388 0.004856634 0.005142975 571.6795545 -2.75715266 0.056433917 KGATLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 KGATLK 6 1 P14618;P14618-3;B4DNK4;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 85.265 0.088045 687600000 833890 1347500 1486700 2168500 2124100 1628600 2464900 2068300 2151000 FALSE TRUE 781698.3134 1447270.302 1521965.226 2224147.381 1957281.754 2098750.382 2095311.128 2326531.808 1791984.204 0.436219422 0.807635636 0.849318439 1.241164613 1.09224275 1.171187992 1.169268749 1.298299283 1 20.77312649 4.731555271 0.56657372 1.189470545 0.006732773 0.803631007 0.113526107 1.503353748 0.368576117 0.054034752 1.176508069 53895.84323 -4.731555271 -1.182737773 down SSSISEEKGDS(ph)DDEKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SSSISEEKGDSDDEKPR 17 2 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 S(0.065)S(0.065)S(0.065)IS(0.012)EEKGDS(0.792)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSIS(0.001)EEKGDS(0.999)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSS(0.001)IS(0.046)EEKGDS(0.953)DDEKPR 281.58 2.89E-36 10272060000 13001870 4177060 6504650 6000580 6357140 4397110 8747210 5018620 9510430 TRUE FALSE 12188106.17 4486333.869 6658943.37 6154565.042 5857875.868 5666484.276 7435647.066 5645205.754 7923077.793 1.538304493 0.566236251 0.840449071 0.776789677 0.739343475 0.715187257 0.938479624 0.712501619 1 22.91762954 4.748511666 24.98934786 0.778114522 1.538304908 0.790063521 0.121791272 593.8538298 1491272.102 0.027320228 0.370554342 56041.74704 -4.748511666 0.760190386 SSSPELVTHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSPELVTHLK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 113.47 0.0013871 317260000 296600 293220 306820 324210 347290 250050 427230 279050 366400 FALSE TRUE 278036.3354 314930.3139 314097.9153 332529.7775 320015.2443 322235.3758 363170.8277 313890.0068 305245.473 0.910861454 1.031728041 1.02900106 1.089384797 1.048386537 1.055659803 1.189766466 1.028319941 1 18.21961037 6.341834467 0.569410191 1.084880643 9.86E-18 0.409122724 0.053580354 18.40833422 1.059897003 0.02384045 19.65842027 2197022.31 -6.341834467 -1.084880643 SSSQPSS(ph)CCSDPSKPGGNVEGATQSLAEQMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSQPSSCCSDPSKPGGNVEGATQSLAEQMR 31 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.011)S(0.011)S(0.039)QPS(0.352)S(0.455)CCS(0.132)DPSKPGGNVEGATQSLAEQMR 98.74 0.00042917 190550000 260410 186100 194030 173360 199690 152880 256900 178950 204380 TRUE FALSE 244111.4029 199879.0376 198632.4832 177808.7111 184007.1529 197013.9742 218380.2299 201292.3014 170267.6577 1.433692143 1.173910773 1.166589627 1.044289406 1.080693512 1.157083952 1.282570236 1.182211021 1 17.3774449 4.751246404 3.557198911 1.150222722 1.47104119 0.574566439 0.079948888 0.25192286 5.577064163 0.019898458 0.219861582 56395.75361 -4.751246404 0.320818468 SSSQRS(ph)PS(ph)PGPNHTSNSSNASNATVVPQNSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSQRSPSPGPNHTSNSSNASNATVVPQNSSAR 33 1 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 2 S(0.387)S(0.398)S(0.41)QRS(0.423)PS(0.378)PGPNHT(0.002)S(0.002)NSSNASNATVVPQNSSAR 120.15 6.21E-07 532910000 36169 129660 105050 129010 143180 75061 112830 107350 165430 TRUE FALSE 33905.24685 139260.1613 107541.8356 132320.615 131935.2204 96729.89219 95912.18896 120752.8838 137818.6643 0.246013463 1.010459375 0.780314017 0.960106642 0.957310253 0.701863515 0.695930333 0.876172211 1 17.07241175 4.7478191 24.80551375 0.853481407 0.246013106 0.739525685 0.11639867 625.2917512 1675254.926 0.028762732 0.359171583 55952.44894 -4.7478191 -0.607468301 SSSQSGS(ph)GPSSPDSVLRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSQSGSGPSSPDSVLRPR 19 1 O75427;H7C5D9 O75427 LRCH4 Leucine-rich repeat and calponin homology domain-containing protein 4 1 SS(0.001)S(0.004)QS(0.132)GS(0.355)GPS(0.172)S(0.336)PDSVLRPR 175.8 4.91E-12 69712000 84603 79514 87266 95762 120450 72466 81176 75854 120780 TRUE FALSE 79307.84925 85401.29929 89335.99073 98219.41504 110990.3429 93385.75781 69004.4124 85324.53888 100621.0377 0.788183575 0.848741985 0.887846048 0.976132002 1.103053053 0.928093766 0.68578514 0.847979118 1 16.61857245 -3.331654153 8.20014795 0.998548993 0.88402623 0 0.116853371 0 0 0 0.027180168 0.000465957 3.331654153 -0.114522763 SSSQSGSGPSS(ph)PDSVLRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSQSGSGPSSPDSVLRPR 19 1 O75427;H7C5D9 O75427 LRCH4 Leucine-rich repeat and calponin homology domain-containing protein 4 1 SSSQSGSGPS(0.023)S(0.977)PDSVLRPR 169.9 8.02E-12 192760000 70729 78338 69195 83711 97496 50077 79504 60958 97290 TRUE FALSE 66302.19814 84138.22703 70836.33808 85859.16598 89839.05744 64533.41697 67583.11328 68568.74049 81051.67048 0.818023833 1.038081344 0.873965184 1.059313959 1.108417099 0.796200949 0.833827519 0.845987998 1 16.3065543 2.213832102 24.99999927 0.850765616 0.97676634 0.22423246 0.099571762 292.4346436 295643.3022 0.034939409 0.025815592 163.618385 -2.213832102 0.126000725 SSSRPCS(ph)PVHHHEGHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSRPCSPVHHHEGHAK 17 1 Q9Y2K6 Q9Y2K6 USP20 Ubiquitin carboxyl-terminal hydrolase 20 1 S(0.035)S(0.035)S(0.035)RPCS(0.896)PVHHHEGHAK 53.779 0.047343 54951000 11724 15610 12731 12812 15306 11608 10872 13561 13695 TRUE FALSE 10990.21577 16765.78064 13032.98533 13140.77761 14103.9285 14959.04116 9241.844531 15254.1207 11409.21603 0.96327528 1.469494539 1.142320848 1.151768674 1.236187348 1.311136639 0.810033267 1.336999901 1 13.47791204 1.769289533 25 1.0311818 1.232536742 0.145744198 0.180403295 37.29329667 30356.63544 0.075745676 0.042014617 58.78811471 -1.769289533 0.201354942 SSSS(ph)ELLLTGPGAEEDPLPLIVQDQYVQEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSSELLLTGPGAEEDPLPLIVQDQYVQEAR 31 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.117)S(0.117)S(0.117)S(0.649)ELLLTGPGAEEDPLPLIVQDQYVQEAR 196.99 8.52E-26 57137000 50653 62802 46470 47971 59453 33071 68335 53928 71831 TRUE FALSE 47482.71915 67451.92543 47572.29034 49202.01707 54783.8012 42618.06084 58088.80114 60661.02951 59841.94205 0.793468887 1.127168055 0.794965683 0.822199537 0.915474988 0.712177101 0.97070381 1.013687515 1 15.86886938 1.529088801 9.565437911 1.001690884 0.881835858 0.237678927 0.110135002 0.193332304 28.02371877 0.059976398 0.027858419 33.81339679 -1.529088801 -0.119855026 SSSSESSHS(ph)SSSHSHGKTTPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSSSESSHSSSSHSHGKTTPTK 22 1 O75582-3;O75582 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 1 SSSSES(0.014)S(0.049)HS(0.17)S(0.17)S(0.17)S(0.17)HS(0.17)HGKT(0.043)T(0.043)PT(0.002)K;SSSSESSHS(0.125)S(0.125)S(0.125)S(0.125)HS(0.125)HGKT(0.125)T(0.125)PT(0.125)K 93.633 0.00067639 89235000 8820.5 81226 46609.2 54099 98740 61151 79222 89037 117995 TRUE FALSE 8268.44065 87240.05756 47714.79223 55487.27193 90985.3587 78804.301 67343.39656 100153.4654 98300.87222 0.084113604 0.887479995 0.485395411 0.564463678 0.92558038 0.801664311 0.685074253 1.018846152 1 16.5849166 4.562670754 0.201863358 1.031476221 1.43E-13 0.460202897 0.209160569 14.40154957 0.587118819 0.442964078 3.803877913 36531.77327 -4.562670754 -1.031476221 GDVAEGDLIEHFSQFGTVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 GDVAEGDLIEHFSQFGTVEK 20 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ; 350.27 4.35E-95 228630000 314990 549660 552350 546720 632670 510880 694960 586870 755520 FALSE TRUE 295275.3382 590357.3983 565452.0028 560749.7608 582982.6503 658362.7626 590757.1997 660142.0114 629418.8312 0.469123775 0.937940476 0.898371601 0.890900833 0.926223718 1.045985169 0.938575668 1.048811981 1 19.26366082 4.73956149 5.50670622 0.952942289 0.451276214 0.88528026 0.05559318 0.047443629 5.596827611 0.01321455 0.089721711 54898.62794 -4.73956149 -0.501666075 down SSSSPELQT(ph)LQDILGDPGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSSPELQTLQDILGDPGDK 20 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;H3BQK4;A0A2R8Y670 P49815 TSC2 Tuberin 1 S(0.163)S(0.163)S(0.163)S(0.163)PELQT(0.346)LQDILGDPGDK 92.307 0.0061484 9724900 66752 41401 57582 51902 47275 47515 74578 52873 45150 TRUE FALSE 62574.11148 44466.37312 58947.87223 53233.89319 43562.2122 61231.80916 63395.72125 59474.31044 37614.17332 1.663578007 1.182170687 1.567171814 1.415261549 1.158132915 1.627891929 1.685421097 1.581167554 1 15.19898876 SSSSS(ph)QESLNRPFSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSSSQESLNRPFSSK 16 1 E3W994;J3KR49;O75122;A0A0U1RQI6;B3KR06;E7ENG2;O75122-2;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 S(0.022)S(0.015)S(0.013)S(0.109)S(0.841)QESLNRPFSSK;SS(0.006)S(0.033)S(0.241)S(0.719)QESLNRPFSSK;SSSS(0.022)S(0.978)QESLNRPFSSK 209.85 6.79E-12 857490000 411590 350570 379820 425880 358590 292894 483400 297968 373630 TRUE FALSE 385829.3166 376526.5676 388829.5098 436808.8018 330427.7879 377447.7431 410918.6577 335169.9607 311268.7393 1.239537634 1.209651083 1.249176229 1.403317284 1.061551471 1.212610505 1.320141106 1.07678645 1 18.24780117 1.071109359 5.203865939 1.001594705 1.240905212 0.501159774 0.086268716 0.141151596 6.484392065 0.077279822 0.019536092 11.77902541 -1.071109359 0.239310507 SSSSSASPSS(ph)PSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 SSSSSASPSSPSSR 14 0 E9PK91;Q9NYF8-3;H0YF63;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 SSSSSASPS(0.031)S(0.964)PS(0.005)SR;SSSSSASPS(0.002)S(0.993)PS(0.005)SR;SSSSSASPS(0.077)S(0.923)PSSR;SSSSSASPS(0.002)S(0.997)PSSR;SSSSSASPS(0.077)S(0.846)PS(0.077)SR;SSSSSASPS(0.002)S(0.998)PSSR;SSSSSAS(0.001)PS(0.115)S(0.879)PS(0.003)S(0.001)R;SSSSSAS(0.002)PS(0.008)S(0.989)PS(0.001)S(0.001)R;SSSSSAS(0.003)PS(0.132)S(0.835)PS(0.022)S(0.009)R 338.04 1.06E-68 5186057000 2738972 2696805 2958959 2703467 2840545 2690805 3235038 2621788 3836179 TRUE FALSE 2567544.632 2896479.248 3029146.905 2772842.54 2617460.054 3467596.722 2749974.085 2949124.003 3195895.942 0.803388057 0.906312127 0.947824009 0.86762604 0.819006658 1.085015528 0.86047047 0.922784739 1 21.607789 SSSSSGVPYS(ph)PAIPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSSSSGVPYSPAIPNK 16 0 A0A0A0MRE1;B4DJ07;A0A0A0MSB8;Q9UPT5-2;Q9UPT5-5;Q9UPT5-1;Q9UPT5-6;Q9UPT5;Q9UPT5-4 A0A0A0MRE1 EXOC7 Exocyst complex component 7 1 SSSSSGVPYS(1)PAIPNK;SSSSS(0.001)GVPY(0.001)S(0.998)PAIPNK;SSSSS(0.001)GVPY(0.001)S(0.999)PAIPNK;SSSSSGVPYS(1)PAIPNK 211.09 8.40E-12 629510000 1513030 1389126 1487837 1526920 1801480 1140701 2023480 1463280 2046340 TRUE FALSE 1418332.153 1491978.334 1523129.196 1566103.352 1659999.028 1470002.861 1720077.959 1645973.729 1704792.634 0.831967551 0.875167046 0.893439569 0.918647418 0.973724894 0.862276638 1.00896609 0.965497912 1 20.70116483 5.030561269 0.201181403 1.017811396 0.663560737 0.647454473 0.035842406 9.20751496 0.313460375 0.069530394 0.840520261 107290.5 -5.030561269 -0.354250659 SSSSSGVPYS(ph)PAIPNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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;SSSSS(0.001)GVPYS(0.999)PAIPNKR 163.62 1.65E-09 407390000 492780 438080 501910 491460 552080 367940 613240 500190 648190 TRUE FALSE 461937.7794 470515.899 513815.5422 504071.6956 508721.8638 474158.305 521290.355 562639.8226 540002.9015 0.855435736 0.871321057 0.951505151 0.933461087 0.942072464 0.878066217 0.965347322 1.041919999 1 19.04260763 7.999999996 0.140740182 1.028558962 0.426688863 0.604157339 0.036604958 55.07248136 0.515650659 0.153313499 6.682277845 99999999.1 -7.999999996 -0.601870099 SSSSSNASGNGGDGKEERPEGS(ph)PTLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSSSNASGNGGDGKEERPEGSPTLFK 27 2 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 S(0.001)S(0.001)S(0.001)S(0.001)S(0.001)NAS(0.001)GNGGDGKEERPEGS(0.818)PT(0.175)LFK 52.155 0.051519 95933000 108280 62723 83034 89407 83002 49584 108320 72532 94464 TRUE FALSE 101502.9481 67367.07618 85003.60569 91701.33499 76483.35773 63898.09587 92078.42159 81587.77986 78697.34814 1.289788671 0.856027271 1.080133038 1.165240471 0.971867027 0.811947256 1.170032076 1.036728451 1 16.2640274 -2.994660006 0.005327746 3.10E-07 1.995853202 0.020866222 0.143262106 297138.6541 173.0187033 34259.50868 30642.0637 0.001012372 2.994660006 1.995852891 SSSSSSQPEHSAMLVSTAAS(ph)PSLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSSSSSQPEHSAMLVSTAASPSLIK 25 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 SSSSSSQPEHSAMLVST(0.002)AAS(0.997)PS(0.001)LIK;SSSSSSQPEHSAMLVSTAAS(1)PSLIK;SSSSSSQPEHSAMLVSTAAS(1)PSLIK 250.21 1.14E-39 1176640000 1036700 1017670 1174980 1155140 1279850 1020640 1554780 1099990 2009150 TRUE FALSE 971814.7976 1093019.346 1202851.08 1184782.848 1179335.744 1315282.199 1321655.173 1237326.173 1673809.885 0.580600465 0.653012839 0.718630647 0.707835973 0.704581658 0.785801429 0.789608894 0.739227426 1 20.67470424 -5 0.072599202 2.002641896 0.367938367 0.909975402 0.032843281 78.33486488 0.407976864 12.93404628 1.49827067 1.00E-05 5 -1.634703528 SSSSVGS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSSVGSPTR 10 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 SSSSVGS(0.925)PT(0.075)R 106.29 0.0025556 58184000 57293 60179 60882 64527 83498 53176 51758 51456 74915 TRUE FALSE 53707.1334 64634.71578 62326.14979 66182.87206 76940.40389 68527.04796 43997.3684 57880.39487 62411.20253 0.86053675 1.035626829 0.99863722 1.060432573 1.232797972 1.097992751 0.704959472 0.927403936 1 15.92951739 1.756901455 25 0.850353769 1.048234664 0.310108077 0.117382512 7.672662134 10468.99748 0.052336203 0.029023513 57.13489783 -1.756901455 0.197880895 SSST(ph)SDILEPFTVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.291)T(0.7)S(0.009)DILEPFTVER 308.93 4.70E-55 959050000 571790 600890 613630 616170 610310 568480 790920 530660 620350 TRUE FALSE 536002.6846 645380.5208 628185.5934 631981.9654 562378.7145 732590.9475 672328.8885 596914.0691 516809.5774 1.037137677 1.248778175 1.215506873 1.222852658 1.088173941 1.417525873 1.300921883 1.154998079 1 18.97927328 4.742323261 24.11201484 1.228822636 1.037137556 0.151456583 0.114992903 350.3108131 2244724.372 0.025206079 0.188305862 55248.85228 -4.742323261 -0.191685079 SSSTGSSSSTGGGGQESQPS(ph)PLALLAATCSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSTGSSSSTGGGGQESQPSPLALLAATCSR 31 0 P08047;H3BVI2;P08047-2 P08047 SP1 Transcription factor Sp1 1 SSSTGSSSSTGGGGQES(0.006)QPS(0.992)PLALLAATCSR 80.011 0.0011256 75153000 27626 26365 21934 24605 23627 24705 32318 26877 31329 TRUE FALSE 25896.93797 28317.09203 22454.28484 25236.40596 21771.43073 31836.93245 27472.21593 30232.65261 26099.98751 0.992220321 1.084946574 0.860317839 0.966912568 0.834154833 1.219806425 1.052575827 1.158339735 1 14.6717615 2.236087437 24.99999001 1.109536323 0.955380106 0.440654296 0.08931475 62.22366434 628972.6895 0.031037928 0.024004222 172.2215275 -2.236087437 -0.154156218 SSSVGSSSSYPIS(ph)PAVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SSSVGSSSSYPISPAVSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 SSSVGSSSSYPIS(1)PAVSR;SSSVGSSSSYPIS(1)PAVSR;SSSVGSSSSYPIS(1)PAVSR;SSSVGSSSSYPIS(1)PAVSR;SSSVGSSSSYPIS(1)PAVSR;SSSVGSSSSYPIS(1)PAVSR 494.24 5.99E-241 5198180000 2046480 2169410 2250620 2369520 2272800 1786870 2541360 2021140 2422780 TRUE FALSE 1918394.47 2330035.374 2304005.769 2430325.895 2094303.456 2302710.362 2160306.661 2273483.778 2018402.366 0.950451952 1.154395879 1.141499737 1.20408395 1.037604539 1.140857938 1.070305256 1.12637788 1 20.94478237 -0.451239864 0.575721116 0.985506594 1.114812482 0.153271625 0.07154281 15.59659296 4.334404587 0.5378136 0.027481433 0.35380188 0.451239864 0.129305888 SSSVS(ph)PSSWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSSVSPSSWK 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 SSSVS(0.957)PS(0.016)S(0.026)WK 95.401 0.0057459 0 284810 186600 242680 221230 233350 207400 300190 209360 238550 TRUE FALSE 266984.2505 200416.0582 248436.4842 226907.1363 215023.6323 267273.0131 255179.2963 235499.0569 198734.4639 1.343421998 1.008461513 1.250092608 1.141760377 1.081964487 1.344875005 1.284021358 1.184993545 1 17.60048256 2.254207485 24.99921488 1.237440088 1.154296643 0 0.126685438 559.193247 893428.7389 0.040008587 0.033366687 179.5591269 -2.254207485 -0.083143445 SST(ph)PLHSPSPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSTPLHSPSPIR 12 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 S(0.293)S(0.293)T(0.414)PLHSPSPIR 139.3 0.00021788 235010000 148220 251810 195080 208100 267450 185150 217980 234160 216940 TRUE FALSE 138943.1748 270454.2744 199707.3897 213440.1983 246445.5558 238599.7993 185295.9226 263395.3914 180731.3125 0.768783078 1.496443924 1.104996068 1.180980735 1.363601871 1.320190708 1.025256332 1.457386591 1 17.46348696 -0.809539529 7.466370648 1 1.223479094 0.087652979 0.216049149 0 0 0.183789757 0.043319661 0.155045966 0.809539529 0.223479095 SST(ph)PLPTISSSAENTR ddPTM_SK-BR-3_Pertuzumab_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 SS(0.002)T(0.998)PLPTISSSAENTR;S(0.005)S(0.002)T(0.993)PLPTISSSAENTR;SS(0.006)T(0.994)PLPTISSSAENTR;S(0.078)S(0.003)T(0.919)PLPTISSSAENTR;S(0.001)S(0.097)T(0.903)PLPTISSSAENTR;SS(0.023)T(0.977)PLPTISSSAENTR;SS(0.021)T(0.979)PLPTISSSAENTR;SS(0.067)T(0.933)PLPTISSSAENTR 457.17 1.14E-182 25822460000 5829160 5088260 4531520 4718230 5515590 4149260 7502250 5681850 6715600 TRUE FALSE 5464323.281 5465000.065 4639009.794 4839307.77 5082417.81 5347084.004 6377357.26 6391241.48 5594722.976 0.976692377 0.976813345 0.82917596 0.864977192 0.908430647 0.955737045 1.139887942 1.142369606 1 22.41563527 1.869855051 4.037143832 1.105670082 0.908354682 0.66404321 0.059224319 0.130293315 3.361856408 0.029060512 0.016228762 74.10628651 -1.869855051 -0.1973154 SST(ph)PPGESYFGVSSLQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SSTPPGESYFGVSSLQLK 18 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.038)S(0.038)T(0.923)PPGESYFGVSSLQLK;S(0.031)S(0.031)T(0.938)PPGESYFGVSSLQLK;S(0.018)S(0.018)T(0.964)PPGESYFGVSSLQLK;S(0.147)S(0.147)T(0.706)PPGESYFGVSSLQLK;S(0.171)S(0.171)T(0.658)PPGESYFGVSSLQLK;S(0.227)S(0.227)T(0.547)PPGESYFGVSSLQLK 247.5 2.43E-23 6319100000 3463064 2606516 2767938 2635016 2927076 2204581 3604191 2430478 3114709 TRUE FALSE 3246317.006 2799505.157 2833594.796 2702634.972 2697195.258 2841007.746 3063776.019 2733928.528 2594843.946 1.251064447 1.078872262 1.092009714 1.041540466 1.039444111 1.094866514 1.180716869 1.053600365 1 21.30721635 4.739620102 24.56818842 1.083882382 1.251064513 0.561510339 0.048659334 57.95556725 1343693.826 0.01181243 0.071759738 54906.03743 -4.739620102 0.167182131 SST(ph)PPRQS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSTPPRQSPSR 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.003)S(0.057)T(0.94)PPRQS(0.888)PS(0.112)R;S(0.265)S(0.325)T(0.41)PPRQS(0.998)PS(0.002)R;S(0.269)S(0.311)T(0.42)PPRQS(0.999)PSR;S(0.244)S(0.324)T(0.432)PPRQS(0.831)PS(0.169)R 120.9 0.0057429 2788499000 541890 583825 487696 515211 574975 365460 537451 473788 592771 TRUE FALSE 507974.0722 627052.0105 499264.3794 528432.1865 529818.7828 470962.3693 456865.212 532941.4747 493833.6907 1.028633894 1.26976353 1.010996999 1.070061028 1.072868848 0.953686187 0.925139821 1.079192216 1 18.91366574 3.315375066 0.960697936 0.985367755 1.159455914 0.289651323 0.079085177 0.543378874 1.071749277 0.032839036 0.05993188 2067.164632 -3.315375066 0.174088159 SST(ph)PVPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSTPVPSK 8 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C3G1 Q9H8V3-2 ECT2 Protein ECT2 1 S(0.003)S(0.066)T(0.931)PVPSK 145.46 0.0063605 333110000 1232100 879370 1093000 1007000 1054400 804700 1316200 939610 1445400 TRUE FALSE 1154985.06 944479.4698 1118926.476 1032841.325 971591.6772 1037003.827 1118848.029 1056922.377 1204153.402 0.959167709 0.784351452 0.929222534 0.857732348 0.806867028 0.861189135 0.929157387 0.877730673 1 20.19958776 0.619006968 0.773350634 0.999852075 0.863784461 0.342030895 0.054109339 1.35909361 1.433436683 0.050985719 0.017542631 4.159172836 -0.619006968 -0.136067614 SSTAISSIAADGEFLHELEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSTAISSIAADGEFLHELEEK 21 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ; 261.69 1.18E-36 295880000 319670 256050 303640 323590 321630 225870 390760 265840 324220 FALSE TRUE 299662.4253 275008.2084 310842.4842 331893.8672 296370.4772 291075.0023 332169.1656 299030.7092 270105.5875 1.109426977 1.018150757 1.150818416 1.228756022 1.097239343 1.077634139 1.229775247 1.107088202 1 18.04316396 3.848522259 4.5025385 1.141772294 1.061315697 0.091986081 0.072276578 0.337990915 11.22780575 0.01728307 0.03233008 7055.410042 -3.848522259 -0.080456597 SSTAKPEVEHPEPDHSKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSTAKPEVEHPEPDHSKR 18 2 Q9NZI5-3;Q9NZI5;B7Z1S6;F8WFB0 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 0 38.824 0.07491 59464000 70255 41138 45680 52033 53398 34961 59076 40002 51566 FALSE TRUE 65857.86496 44183.90032 46763.55117 53368.25487 49204.33648 45053.67316 50218.10223 44996.33776 42959.30147 1.533029232 1.028506023 1.088554738 1.242298013 1.145370963 1.048752461 1.168969246 1.047417817 1 15.39068291 4.744711627 24.86916688 1.103397199 1.533029437 0.77900529 0.073025602 302.0605577 1221225.784 0.016815854 0.156787589 55553.52573 -4.744711627 0.429632238 SSTFPQTDVLSSS(ph)LEAEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSTFPQTDVLSSSLEAEHR 19 0 D4PHA4;Q86WP2-3;Q86WP2;Q86WP2-2;Q86WP2-4 D4PHA4 GPBP1 Vasculin 1 SSTFPQTDVLSS(0.066)S(0.933)LEAEHR;SSTFPQTDVLSS(0.106)S(0.894)LEAEHR;SSTFPQTDVLSS(0.146)S(0.854)LEAEHR;SSTFPQTDVLSS(0.056)S(0.944)LEAEHR 178.76 2.40E-14 1052050000 1203920 1415190 1380070 1553570 1891930 1533840 1822160 1488990 1764400 TRUE FALSE 1128568.796 1519972.14 1412805.912 1593437.236 1743345.449 1976634.708 1548944.024 1674893.679 1469910.242 0.767780756 1.034057793 0.961151145 1.084037101 1.186021704 1.344731571 1.053767761 1.13945303 1 20.48729663 3.134696726 2.69052209 1.156236391 0.946855403 0.450301068 0.111407963 0.252416382 3.702683768 0.032752116 0.041271876 1363.630562 -3.134696726 -0.209380988 SSTPLHS(ph)PSPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSTPLHSPSPIR 12 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 SSTPLHS(0.499)PS(0.499)PIR 80.69 0.012326 0 69499 71412 73440 71383 81179 57558 78083 56871 94629 TRUE FALSE 65149.18165 76699.41878 75182.03148 73214.80863 74803.5288 74174.06022 66375.17904 63971.46954 78834.80857 0.826401216 0.97291311 0.953665428 0.928711694 0.948864216 0.940879563 0.841952689 0.81146223 1 16.26654515 1.751314773 25 0.869358405 0.937369921 0.072161828 0.062567816 5.59445887 10983.07851 0.026024788 0.01443214 56.40463235 -1.751314773 0.068011516 SSTS(ph)PCGTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSTSPCGTSK 10 0 H0Y459;O75376;O75376-2;A0A088AWL3;O75376-3 H0Y459;O75376 NCOR1 Nuclear receptor corepressor 1 1 S(0.001)S(0.008)T(0.066)S(0.912)PCGT(0.012)S(0.001)K;SST(0.008)S(0.991)PCGT(0.001)SK 126.34 0.00040392 301149000 1305880 801540 1044840 965000 962550 927130 1295430 960670 899230 TRUE FALSE 1224147.302 860886.8556 1069624.098 989763.5337 886955.2057 1194777.38 1101192.298 1080611.764 749142.7038 1.634064239 1.149162705 1.427797525 1.321194919 1.183960281 1.59485953 1.469936625 1.442464511 1 19.51488104 2.24676219 24.99770649 1.428146675 1.327300703 0 0.20264216 554.4272388 1689848.823 0.063344874 0.052156958 176.5071041 -2.24676219 -0.100845972 SSTSPCGTSKS(ph)PNREWEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSTSPCGTSKSPNREWEGK 19 2 H0Y459 H0Y459 NCOR1 1 SSTSPCGT(0.004)S(0.045)KS(0.951)PNREWEGK 130.83 8.76E-06 113810000 83773 56059 64794 67218 82418 32268 64996 47085 143550 TRUE FALSE 78529.79747 60209.66669 66330.94428 68942.92768 75945.22274 41583.24777 55250.45319 52963.6659 119590.5776 0.656655391 0.503464971 0.554650254 0.576491301 0.635043531 0.347713412 0.461996708 0.442874907 1 16.8677442 -1.053038014 4.937296423 1.000010206 0.516642051 0.727692609 0.091765055 1.02E-05 1.95E-06 0.087606459 0.020648605 0.088503814 1.053038014 -0.483368155 SSTSPSIINEDVIINGHS(ph)HEDDNPFAEYMWMENEEEFNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSTSPSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR 39 0 Q9BPZ3;D6RA77;D6R9Y1 Q9BPZ3 PAIP2 Polyadenylate-binding protein-interacting protein 2 1 S(0.165)S(0.165)T(0.151)S(0.151)PS(0.151)IINEDVIINGHS(0.216)HEDDNPFAEYMWMENEEEFNR 112.98 1.24E-05 65875000 18449 20102 21799 18150 23135 18581 23686 21195 26178 TRUE FALSE 17294.31002 21590.373 22316.08257 18615.75973 21318.07042 23945.03306 20134.50419 23841.24241 21808.72268 0.792999676 0.989987965 1.023264081 0.85359239 0.977502017 1.097956694 0.923231703 1.093197559 1 14.41261765 2.474910132 24.97786103 1.017229638 0.942519142 0.269466595 0.081960374 129.4976357 1462829.324 0.02740256 0.023065064 298.4764921 -2.474910132 -0.074710497 SSTVATLQGTPDHGDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSTVATLQGTPDHGDPR 17 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 ; 77.191 0.018307 618100000 915170 960900 978820 1019200 1023020 957380 1102080 877170 953970 FALSE TRUE 857891.1433 1032046.036 1002038.073 1045354.398 942676.1359 1233760.064 936833.3352 986686.6054 794746.2441 1.079452907 1.298585609 1.260827692 1.315331032 1.186134748 1.55239496 1.178782966 1.241511505 1 19.60013477 -0.399113146 7.4331602 1.000006694 1.272064443 0.312361508 0.122658001 7122246.573 958172.1252 0.105006289 0.025467766 0.398920959 0.399113146 0.272057748 SSVKT(ph)PEPVVPTAPEPHPTTSTDQPVTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSVKTPEPVVPTAPEPHPTTSTDQPVTPK 29 1 Q14676;Q14676-3;Q14676-2 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 S(0.156)S(0.156)VKT(0.688)PEPVVPTAPEPHPTTSTDQPVTPK 118.23 0.00015286 289360000 130350 79581 85690 93165 99642 67121 128220 82731 117840 TRUE FALSE 122191.6262 85473.26004 87722.60727 95555.77163 91816.51926 86497.74308 108994.6013 93060.14746 98171.74272 1.244672069 0.870650328 0.893562698 0.973353115 0.935264229 0.881085949 1.110244132 0.947932112 1 16.58302021 1.746011374 25 1.028043353 0.946038855 0.024173675 0.113852356 3.753275862 12629.01818 0.048957212 0.027149349 55.72003416 -1.746011374 -0.082004498 SSVKT(ph)PESIVPIAPELQPSTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SSVKTPESIVPIAPELQPSTSR 22 1 Q14676;Q14676-3;Q14676-2 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 S(0.004)S(0.004)VKT(0.946)PES(0.046)IVPIAPELQPSTSR;S(0.208)S(0.208)VKT(0.58)PES(0.005)IVPIAPELQPSTSR;S(0.016)S(0.016)VKT(0.968)PESIVPIAPELQPSTSR 179.86 8.93E-17 522750000 859160 582140 686600 631700 710080 463410 899430 573600 723470 TRUE FALSE 805386.7092 625242.2513 702886.4762 647910.4915 654313.1811 597188.9442 764568.8214 645215.2226 602718.1832 1.336257527 1.037370812 1.166194244 1.074980828 1.085603852 0.990826162 1.26853452 1.070508972 1 19.20112406 7.639151312 0.012401323 1.21E-06 2.409038143 0.185549269 0.101686063 18500.77781 18.77524912 1531.139363 2166.634445 43566363.62 -7.639151312 2.409036936 SSVKT(ph)PETVVPTALELQPSTSTDRPVTSEPTSQATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSVKTPETVVPTALELQPSTSTDRPVTSEPTSQATR 36 2 Q14676;Q14676-2;H0Y6Z8 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 S(0.021)S(0.021)VKT(0.952)PET(0.006)VVPTALELQPSTSTDRPVTSEPTSQATR 82.363 0.065527 158710000 9273.2 7392.9 8203.6 7778.8 8668.1 5086.4 7699.1 4520 6218.1 TRUE FALSE 8692.806965 7940.278008 8398.193266 7978.417177 7987.342391 6554.761109 6544.69143 5084.33195 5180.25894 1.678064179 1.53279558 1.621191791 1.540157986 1.541880915 1.265334646 1.263390789 0.981482202 1 12.3388085 1.803253397 0.959448902 0.977673937 1.600469688 0.931026468 0.065051859 0.114822248 0.196336005 0.050021702 0.021344375 63.57017356 -1.803253397 0.622795751 SSVKTPET(ph)VVPTALELQPSTSTDRPVTSEPTSQATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSVKTPETVVPTALELQPSTSTDRPVTSEPTSQATR 36 2 Q14676;Q14676-2;H0Y6Z8 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 SSVKT(0.393)PET(0.607)VVPTALELQPSTSTDRPVTSEPTSQATR 260.69 1.76E-60 383700000 44500 42311 35157 38623 44767 27692 51096 40578 45999 TRUE FALSE 41714.82443 45443.75046 35990.94064 39614.13157 41251.1804 35686.23086 43434.62915 45644.25262 38321.46974 1.088549701 1.185856147 0.939184767 1.033732053 1.076450895 0.931233356 1.133428061 1.191088258 1 15.22586527 -0.591596367 6.898955327 0.999995327 1.068174878 0.06041837 0.088365354 0 0 0.083299743 0.019633938 0.256096494 0.591596367 0.068179551 SSVLPS(ph)PSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSVLPSPSGR 10 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 SSVLPS(0.823)PS(0.177)GR;SSVLPS(0.847)PS(0.153)GR 121.58 0.00053644 343510000 331340 407120 406650 429240 480970 313810 410580 356420 479970 TRUE FALSE 310602.0209 437263.5884 416295.93 440255.0251 443196.5563 404401.8527 349017.3406 400919.8216 399859.9063 0.776777106 1.093541967 1.041104456 1.101023179 1.108379583 1.011358844 0.872849053 1.002650717 1 18.6091351 1.984997377 23.70952741 0.943804995 1.04113249 0.062139363 0.101321837 599.6595178 947675.9268 0.037789505 0.02535457 96.60450449 -1.984997377 0.097327495 SSVNSHMTQSTDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSVNSHMTQSTDSR 14 0 Q9NXV6 Q9NXV6 CDKN2AIP CDKN2A-interacting protein 0 ; 130.61 4.63E-05 70154000 32161 54200 42308 49166 55285 36608 49771 51208 62730 FALSE TRUE 30148.10042 58213.0244 43311.56574 50427.6828 50943.13911 47176.13532 42308.3006 57601.43152 52259.95775 0.576887195 1.113912581 0.828771541 0.964939219 0.974802531 0.902720502 0.809573953 1.102209684 1 15.67341834 4.756138239 24.55627963 0.944784914 0.576886808 0.586645425 0.100693828 2170.581489 3032281.268 0.023003816 0.695590202 57034.57886 -4.756138239 -0.367898106 SSVQGASS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSVQGASSR 9 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 SSVQGAS(0.013)S(0.987)R 87.442 0.014117 1260000000 4700500 3950600 4595800 4143400 3958400 3982800 4774100 3774400 3402300 TRUE FALSE 4406304.096 4243106.535 4704814.546 4249726.659 3647523.231 5132569.705 4058268.026 4245642.148 2834434.15 1.554562167 1.496985398 1.659877879 1.499321005 1.286861165 1.810791655 1.431773613 1.497879973 1 21.43462932 0.377686227 1.303312292 0.999760403 1.544101145 0.602262237 0.135849695 2.193156183 3.967888491 0.118203841 0.034945531 2.386086739 -0.377686227 0.544340742 SSVQGASS(ph)REGS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSVQGASSREGSPAR 15 1 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 2 SSVQGAS(0.347)S(0.653)REGS(1)PAR;S(0.105)S(0.139)VQGAS(0.347)S(0.409)REGS(1)PAR 96.55 0.0020806 1856230000 773400 1111850 818040 980170 1348390 532690 803650 847900 1724020 TRUE FALSE 724994.2746 1194172.531 837444.2951 1005322.822 1242492.889 686468.9555 683150.1432 953762.1815 1436269.924 0.504775782 0.831440184 0.583068879 0.69995396 0.865083135 0.477952608 0.475641891 0.66405497 1 20.45389548 0.951545961 22.91998256 1.000000002 0.638011841 0.414734262 0.135632779 5552.394366 2626426.158 0.133515782 0.033378945 8.944291845 -0.951545961 -0.361988161 SSVTDSFSSLVNRPTLGQFTEEEIHAEVCYAECLLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSVTDSFSSLVNRPTLGQFTEEEIHAEVCYAECLLQR 37 1 F6WE04;Q5SRH9-5;Q5SRH9-6;Q5SRH9-4;Q5SRH9;A0A0A0MRQ0;A0A0A0MSH8;E9PAZ4;A0A0A0MSW9;Q5SRH9-3;E9PQ33;F8W961;E9PQX3;U5GXS1 F6WE04 TTC39A Tetratricopeptide repeat protein 39A 0 197.04 2.37E-30 96741000 36705 45992 45595 38887 45858 36886 50168 37589 28735 FALSE TRUE 34407.69957 49397.29553 46676.53493 39884.90626 42256.49766 47534.38941 42645.77414 42282.06939 23938.94286 1.437310735 2.063470213 1.949816046 1.666109756 1.765178099 1.985651149 1.781439322 1.766246306 1 14.54707182 0.358122225 1.386549167 0.999623645 1.848699164 0.661395449 0.178834296 2.349549595 4.500918201 0.163527312 0.047756468 2.280983928 -0.358122225 0.849075519 SSWSSSDEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SSWSSSDEKR 10 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;Q9ULU4-2 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 0 117.99 0.001419 82516000 48498 54234 52976 46773 58239 40819 56649 48348 78770 FALSE TRUE 45462.59675 58249.54179 54232.61574 47973.27437 53665.14386 52602.78266 48155.00835 54384.35423 65622.77813 0.692786835 0.887642118 0.826429744 0.731046075 0.817782261 0.801593352 0.733815448 0.828742028 1 16.00190905 0.96851999 22.40972924 1.000000003 0.795000056 0.585550021 0.056188263 785.038269 558848.055 0.054310954 0.013577739 9.300793242 -0.96851999 -0.204999946 SSYLNIVGLVGSIDNDFCGTDMTIGTDSALHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SSYLNIVGLVGSIDNDFCGTDMTIGTDSALHR 32 0 A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 ; 223.61 4.88E-36 200900000 160624 196886 181009 182862 205193 165386 237855 173047 176760 FALSE TRUE 150570.8306 211463.6443 185302.619 187554.5485 189077.9695 213130.2534 202190.8509 194652.2989 147257.6141 1.022499458 1.436011616 1.258356793 1.273649242 1.28399452 1.447329258 1.373041741 1.321848789 1 17.16798271 -0.515933378 6.331068182 0.999999999 1.319292819 0.380826107 0.119276006 0 1.23E-10 0.104351546 0.024595895 0.304836258 0.515933378 0.319292819 SSYSS(ph)PTSLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 SSYSS(1)PTS(0.009)LS(0.991)PR;SSYS(0.001)S(0.999)PTS(0.023)LS(0.977)PR;SSYSS(0.964)PT(0.036)S(0.003)LS(0.997)PR;SSYS(0.014)S(0.986)PTS(0.006)LS(0.994)PR;SSYS(0.001)S(0.995)PT(0.004)S(0.048)LS(0.952)PR;SSYS(0.002)S(0.997)PT(0.002)SLS(1)PR 330.24 5.66E-58 4187530000 4672040 4952400 4799140 4738840 4844110 3709940 5053590 4215050 3602370 TRUE FALSE 4379625.356 5319080.849 4912977.867 4860446.657 4463673.141 4780939.452 4295851.095 4741308.271 3001111.175 1.459334593 1.772370479 1.637052938 1.619549018 1.487340149 1.593056429 1.431420179 1.579850927 1 21.51706533 -2.745724108 0.219304298 3.36E-18 1.691302977 0.777308341 0.09672438 20.05894058 0.485541149 9.60182728 0.185841773 0.001795874 2.745724108 1.691302977 SSYSS(ph)PTSLSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 SSYS(0.124)S(0.872)PT(0.003)S(0.001)LSPR 117.2 0.0007965 284560000 73711 83628 71701 89284 90507 55892 83081 66801 61527 TRUE FALSE 69097.56009 89819.90413 73401.78158 91575.1786 83398.94531 72027.11307 70623.77534 75141.2519 51257.74622 1.348041324 1.75231864 1.432013442 1.786562722 1.627050572 1.405194695 1.377816633 1.465949197 1 15.64548242 0.671269135 0.564294284 0.989081631 1.597428485 0.584647432 0.144808608 0.904740362 0.5818108 0.165951122 0.062340597 4.691039986 -0.671269135 0.608346854 SSYSSPTSLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SSYSSPTSLSPR 12 0 Q96JY6;Q96JY6-5;Q96JY6-3;Q96JY6-4;C9JS55;C9JSR2;C9K0F0;C9J0X3;Q96JY6-2;C9J760;A0A087WXJ0 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 SSYSSPTSLS(1)PR;SSYSSPTSLS(1)PR;SSYSSPTSLS(1)PR;SSYSSPTSLS(1)PR;SSYSSPTSLS(1)PR;SSYSSPTSLS(1)PR;SSYSSPTSLS(1)PR;SSYSSPTSLS(1)PR 286.53 1.53E-28 8076630000 4352687 5375440 4348101 4678410 5343600 3164990 5040250 4402464 3480668 TRUE FALSE 4080260.09 5773443.171 4451240.009 4798465.921 4923935.211 4078671.234 4284511.304 4952121.321 2899722.025 1.407121116 1.99103332 1.535057489 1.65480204 1.69807146 1.406573181 1.47755932 1.70779174 1 21.46748318 -2.66792805 0.199324038 1.50E-15 1.762957652 0.526710463 0.177733902 34.08502785 0.779385477 15.28112381 0.437744029 0.002148186 2.66792805 1.762957652 ST(ph)FSTNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STFSTNYR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.198)T(0.69)FS(0.107)T(0.005)NYR;S(0.022)T(0.674)FS(0.301)T(0.003)NYR 148.73 0.0057751 467760000 541570 678690 535990 577160 753270 456920 710310 575220 1101160 TRUE FALSE 507674.1004 728940.9138 548703.9359 591970.9027 694111.2127 588825.3865 603805.6097 647037.4832 917369.2822 0.553402114 0.794599217 0.598127653 0.64529183 0.756632281 0.641862986 0.658192531 0.705318453 1 19.80714307 0.759987442 3.882380522 0.999995882 0.671369651 0.693527229 0.069502451 1.602199486 25.40299337 0.060606119 0.015513327 5.754232984 -0.759987442 -0.328626231 ST(ph)PDSTYSESFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STPDSTYSESFK 12 0 Q6ISB3;Q6ISB3-2 Q6ISB3 GRHL2 Grainyhead-like protein 2 homolog 1 S(0.211)T(0.789)PDSTYSESFK;S(0.113)T(0.872)PDS(0.007)T(0.007)Y(0.001)SESFK 278.38 6.95E-27 448310000 1297540 853700 1043450 952900 1102800 951270 1573190 1125890 1189440 TRUE FALSE 1216329.288 916908.8363 1068201.127 977353.0273 1016190.536 1225886.206 1337304.764 1266459.845 990914.7799 1.227481225 0.925315532 1.077994948 0.986313906 1.025507498 1.237125766 1.349565867 1.278071405 1 19.91840146 2.217415247 6.175267146 1.257831003 1.032546815 0.296404282 0.119851706 0.139881181 17.89245743 0.040098302 0.030428482 164.9739023 -2.217415247 -0.225284189 ST(ph)SATDTHHVEMAR ddPTM_SK-BR-3_Pertuzumab_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(0.365)T(0.534)S(0.101)ATDTHHVEMAR;S(0.238)T(0.611)S(0.151)ATDTHHVEMAR 148.33 1.45E-05 922320000 99433 85727 76489 78074 96574 73829 73462 88606 99481 TRUE FALSE 93209.66602 92074.31628 78303.3552 80077.51102 88989.4676 95142.23379 62447.05509 99668.65415 82876.97843 1.124675004 1.110975786 0.94481431 0.966221411 1.073753765 1.147993515 0.753490973 1.202609652 1 16.33868379 4.170675178 3.455554478 0.996117705 1.121421843 0.102320541 0.12211348 0.440070997 10.46193549 0.029416693 0.076852808 14814.0968 -4.170675178 0.125304138 ST(ph)TPGGTGIKPFLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STTPGGTGIKPFLER 15 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 S(0.018)T(0.491)T(0.491)PGGTGIKPFLER 107.65 0.0018438 199080000 486660 388560 442750 428360 412510 368850 580470 404460 685390 TRUE FALSE 456200.8193 417329.3867 453252.2391 439352.4428 380113.1286 475331.0072 493433.9123 454957.7213 570993.9812 0.798959068 0.730882287 0.793795126 0.769451968 0.665704265 0.832462378 0.864166574 0.796781991 1 19.12311601 0.675902671 0.57283686 1.003871421 0.755755389 0.669452538 0.05021812 0.788778228 0.522405152 0.059194415 0.022260204 4.741357156 -0.675902671 -0.248116032 ST(ph)TPTSSPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 STTPTSSPFR 10 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;H7C5N8;A0A2R8YET2;A0A2R8Y7F4;A0A2R8Y424 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.077)T(0.673)T(0.237)PT(0.01)S(0.002)SPFR;S(0.008)T(0.489)T(0.489)PT(0.013)SSPFR;S(0.161)T(0.419)T(0.419)PTSSPFR 195.4 4.00E-06 1796330000 2402910 3221180 2300690 2282110 3370970 1755390 2400400 2849540 2548200 TRUE FALSE 2252516.152 3459679.519 2355263.453 2340672.806 3106227.614 2262142.597 2040482.304 3205311.342 2122888.958 1.061061693 1.629703478 1.109461446 1.102588431 1.463207768 1.065596289 0.961181835 1.509881772 1 21.01759748 3.739141804 21.58085983 1.161649942 1.381075018 0.085219349 0.225630866 123.8324319 222311.6742 0.053794187 0.095670183 5484.560156 -3.739141804 0.219425075 STAGDTHLGGEDFDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 15 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 ;;;;;;;;;;;;;; 215 1.65E-14 1.3231E+11 22678050 27473500 22273880 19596770 27749930 17100020 28229290 25332930 30666610 FALSE TRUE 21258671.33 29507666.53 22802226.95 20099656.3 25570562.44 22036518.18 23996570.03 28495802.08 25548154.68 0.832102029 1.154982303 0.892519528 0.786736128 1.000877079 0.862548331 0.93926823 1.115376137 1 24.60671575 -0.960423311 6.603970829 1.000000006 0.953481696 0.017173262 0.117276037 1.05E-08 1.58E-09 0.108055926 0.025469023 0.109540997 0.960423311 -0.04651831 STAPSAAASASASAAAS(ph)SPAGGGAEALELLEHCGVCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 STAPSAAASASASAAASSPAGGGAEALELLEHCGVCR 37 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 STAPSAAAS(0.001)AS(0.003)AS(0.01)AAAS(0.493)S(0.493)PAGGGAEALELLEHCGVCR;STAPS(0.001)AAAS(0.001)AS(0.006)AS(0.002)AAAS(0.525)S(0.465)PAGGGAEALELLEHCGVCR;STAPSAAASAS(0.001)AS(0.001)AAAS(0.528)S(0.47)PAGGGAEALELLEHCGVCR;S(0.001)T(0.001)APS(0.005)AAAS(0.005)AS(0.005)AS(0.02)AAAS(0.482)S(0.482)PAGGGAEALELLEHCGVCR;STAPSAAASAS(0.001)AS(0.005)AAAS(0.497)S(0.497)PAGGGAEALELLEHCGVCR 83.054 0.00064511 75915100 23712.4 29906.9 25299.87 29363.8 29044.9 25184.8 38225.1 24781.9 31825.7 TRUE FALSE 22228.28321 32121.23799 25899.99486 30117.32482 26763.83072 32455.24292 32493.60112 27875.97477 26513.78507 0.838367029 1.211491981 0.976850148 1.135911932 1.009430779 1.224089387 1.225536114 1.051376659 1 14.69445502 2.246511432 24.99880988 1.155635108 1.055322452 0.086913497 0.120591812 331.0957942 1041025.414 0.038643744 0.031790656 176.4052201 -2.246511432 -0.100312656 STAPSAAASASASAAASS(ph)PAGGGAEALELLEHCGVCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 STAPSAAASASASAAASSPAGGGAEALELLEHCGVCR 37 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 STAPSAAASASASAAAS(0.107)S(0.893)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAASS(1)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.002)S(0.998)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.03)S(0.97)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.052)S(0.948)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.004)S(0.996)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.028)S(0.972)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.025)S(0.975)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.003)S(0.997)PAGGGAEALELLEHCGVCR;STAPSAAAS(0.001)AS(0.001)AS(0.002)AAAS(0.215)S(0.781)PAGGGAEALELLEHCGVCR;STAPSAAASAS(0.002)AS(0.006)AAAS(0.413)S(0.579)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.006)S(0.994)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.005)S(0.995)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.097)S(0.903)PAGGGAEALELLEHCGVCR 405.01 4.65E-199 33417858000 2137515.8 2277034.8 2370571.7 2101819.5 2554751.8 2222358 3075286.4 1955878.9 2825637.6 TRUE FALSE 2003732.502 2445628.826 2426802.78 2155755.747 2354111.899 2863916.678 2614175.754 2200074.686 2354020.43 0.851195884 1.038915718 1.030918317 0.915776142 1.000038856 1.216606551 1.110515321 0.934603055 1 21.16669541 2.450054174 24.98373205 1.086650772 0.981786709 0.200583471 0.091392853 313.7165361 289568.133 0.030654829 0.025648165 281.873452 -2.450054174 -0.104864062 STAQQELDGKPAS(ph)PTPVIVASHTANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 STAQQELDGKPASPTPVIVASHTANK 26 1 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 1 STAQQELDGKPAS(0.999)PT(0.001)PVIVASHTANK;STAQQELDGKPAS(0.891)PT(0.109)PVIVASHTANK;STAQQELDGKPAS(0.937)PT(0.063)PVIVASHTANK;STAQQELDGKPAS(0.941)PT(0.059)PVIVASHTANK 270.93 1.04E-60 9177630000 7750560 3983060 5148590 5346340 4403190 3894570 7532590 4563720 4446690 TRUE FALSE 7265466.285 4277969.907 5270716.986 5483536.136 4057381.219 5018869.136 6403148.059 5133510.488 3704508.712 1.961249615 1.154800876 1.422784341 1.480233025 1.095254873 1.354800198 1.728474288 1.385746637 1 21.8208508 4.751485995 24.56396495 1.363915044 1.961250104 0.464741682 0.210502002 1645.586433 3127274.985 0.049995759 0.906457999 56426.87441 -4.751485995 0.59733506 STAQQELDGKPAS(ph)PTPVIVASHTANKEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 STAQQELDGKPASPTPVIVASHTANKEEK 29 2 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 1 STAQQELDGKPAS(0.997)PT(0.003)PVIVASHTANKEEK;STAQQELDGKPAS(0.964)PT(0.036)PVIVASHTANKEEK;STAQQELDGKPAS(0.831)PT(0.169)PVIVASHTANKEEK;STAQQELDGKPAS(0.989)PT(0.011)PVIVASHTANKEEK;STAQQELDGKPAS(0.96)PT(0.04)PVIVASHTANKEEK;STAQQELDGKPAS(0.884)PT(0.116)PVIVASHTANKEEK;STAQQELDGKPAS(0.816)PT(0.184)PVIVASHTANKEEK;STAQQELDGKPAS(0.955)PT(0.045)PVIVASHTANKEEK;STAQQELDGKPAS(0.995)PT(0.005)PVIVASHTANKEEK 294.1 4.49E-81 27093900000 4932830 2115755 3017228 3163160 3248237 2012152 4352830 2518072 4414040 TRUE FALSE 4624092.976 2272407.702 3088798.073 3244332.041 2993133.569 2593027.618 3700163.551 2832458.832 3677308.208 1.257466797 0.617954105 0.839961705 0.882257308 0.813946887 0.705142857 1.006215237 0.770253314 1 21.81021867 -0.076479837 0.617252163 1.009672477 0.83523015 0.03343891 0.17647577 14.30404457 5.832653159 0.522088503 0.064055549 0.838533007 0.076479837 -0.174442327 STAS(ph)PASTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.993)PAS(0.006)TK;STAS(1)PASTK;STAS(0.99)PAS(0.01)TK;STAS(0.992)PAS(0.008)TK 184.27 4.64E-05 1044810000 2899790 2021570 2534040 2183060 2507120 2072410 2964070 2536080 2976630 TRUE FALSE 2718297.32 2171249.146 2594148.625 2239081.016 2310220.908 2670681.124 2519635.221 2852715.171 2479811.223 1.096171069 0.875570336 1.046107301 0.902923978 0.931611603 1.076969529 1.016059286 1.150375941 1 21.24179887 2.233298526 24.98758182 1.057774815 0.964777714 0.261148984 0.075117743 164.2283319 779846.7126 0.0251074 0.019091761 171.1191153 -2.233298526 -0.092997101 STAYEDYYYHPPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 STAYEDYYYHPPPR 14 0 O43390;O43390-3;B4DT28;A0A286YEZ8;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;;;; 198.74 2.16E-08 6661250000 1824280 2117130 2028090 2038690 2172020 1748320 2254280 1819690 2540290 FALSE TRUE 1710101.571 2273884.508 2076197.253 2091006.237 2001438.311 2253031.602 1916271.642 2046882.302 2116299.188 0.808062291 1.074462685 0.981050914 0.988048499 0.945725596 1.064609208 0.905482388 0.967198926 1 21.01311217 -0.375459778 6.093697355 0.999999995 0.976801563 0.003497622 0.076018799 0 0 0.066239661 0.015612838 0.421250299 0.375459778 -0.023198432 STCAPS(ph)PQREVLTVPEANSEPWTLDTLGGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 STCAPSPQREVLTVPEANSEPWTLDTLGGER 31 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 S(0.176)T(0.176)CAPS(0.649)PQREVLTVPEANSEPWTLDTLGGER;S(0.08)T(0.08)CAPS(0.841)PQREVLTVPEANSEPWTLDTLGGER;S(0.039)T(0.039)CAPS(0.921)PQREVLTVPEANSEPWTLDTLGGER 195.07 5.22E-20 309675000 41678.6 76284 60848 75791 123471 40335 60606 63358 169751 TRUE FALSE 39070.01082 81932.14673 62291.34329 77735.92537 113774.0857 51979.05972 51518.69294 71268.38577 141418.4615 0.276272351 0.579359625 0.440475329 0.549687251 0.804520743 0.36755498 0.364299628 0.503953904 1 17.10961094 0.930239909 20.68369498 1.000000001 0.486066441 0.554470601 0.144963061 3973.312126 1178080.548 0.135393531 0.033848383 8.516083469 -0.930239909 -0.51393356 STDSEVSQS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STDSEVSQSPAK 12 0 O75175;H7C3F5;A0A2H2FJL5;B7Z6J7;A0A0G2JNJ7;H7C148 O75175 CNOT3 CCR4-NOT transcription complex subunit 3 1 STDSEVS(0.001)QS(0.999)PAK;STDSEVS(0.001)QS(0.999)PAK 183.23 1.66E-05 2113200000 3449800 2352700 2594800 2520200 2941300 2376000 3294500 2348100 3346700 TRUE FALSE 3233883.176 2526896.356 2656349.881 2584872.599 2710302.163 3061912.629 2800520.31 2641265.454 2788114.149 1.159881914 0.906310223 0.95274072 0.927104293 0.972091535 1.098202034 1.00444966 0.947330458 1 21.4108582 2.442965644 24.98150817 1.017529087 0.965722903 0.003433332 0.078032639 440.9875129 322537.2814 0.02540347 0.021254161 277.3100722 -2.442965644 -0.051806183 STEDGAELEEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 STEDGAELEEQK 12 0 Q8IVF2;Q8IVF2-3;Q8IVF2-2 Q8IVF2 AHNAK2 Protein AHNAK2 0 ;; 69.672 0.049345 1615650000 1875380 2992760 2767670 2780500 2794760 2571550 3304420 2935140 2619370 FALSE TRUE 1758003.313 3214347.064 2833320.439 2851852.337 2575270.823 3313914.739 2808952.898 3301598.69 2182180.225 0.805617837 1.47299798 1.298389751 1.306882128 1.180136633 1.518625593 1.287223147 1.512981674 1 21.05733883 4.747553914 24.58220332 1.339879146 0.805617487 0.509109889 0.158553799 687.6939454 1879685.762 0.032580333 0.398347486 55918.2941 -4.747553914 -0.534261659 STELDSNWNWFQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STELDSNWNWFQLR 14 0 Q8N6H7;G5E9L0;A0A0D9SF70;E9PQP3;E9PIY6;H0YF45;E9PJT7;E9PK28;E9PN48;H0YDX1;E9PMR9;E9PM63 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 0 168.83 7.98E-06 80303000 211220 161280 169840 181250 195940 108560 192280 143060 165920 FALSE TRUE 198000.1172 173221.339 173868.685 185901.1819 180551.6628 139899.5097 163449.399 160921.3559 138226.8801 1.432428462 1.253166814 1.257850028 1.344898921 1.306197916 1.01210061 1.182471882 1.164182797 1 17.07667867 2.257154387 24.99984305 1.109892573 1.302798958 0.682610335 0.076685775 153.9368061 206971.8782 0.025257011 0.021097036 180.7816673 -2.257154387 0.192906384 STELLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STELLIR 7 0 K7EK07;Q71DI3;Q16695;P84243;P68431;Q6NXT2;K7EMV3;A0A590UJJ6;B4DEB1;K7ES00;K7EP01;Q5TEC6 K7EK07;Q5TEC6 H3F3B;HIST2H3A;HIST3H3;H3F3A;HIST1H3A;H3F3C;HIST2H3PS2 Histone H3;Histone H3.2;Histone H3.1t;Histone H3.3;Histone H3.1;Histone H3.3C 0 94.662 0.032653 118460000 377670 643800 466130 563410 812410 470520 526980 343280 1081700 FALSE TRUE 354032.3089 691467.6219 477186.8237 577868.0545 748606.5957 606351.4857 447964.2412 386139.2637 901157.282 0.39286406 0.767310697 0.52952668 0.641251051 0.830716913 0.672858665 0.497098842 0.428492641 1 19.7814194 4.758230036 23.19876833 0.645557963 0.392863426 0.197630487 0.169352145 2863.933428 3377670.879 0.037432808 1.273934828 57309.95088 -4.758230036 -0.252694536 STETSDFENIES(ph)PLNER ddPTM_SK-BR-3_Pertuzumab_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 165.16 2.45E-09 127613000 236264 250068 273333 284668 255292 220639 261312 206811 279675 TRUE FALSE 221476.658 268583.2949 279816.5878 291973.0628 235242.3961 284333.8975 222130.6915 232631.8086 232995.4357 0.950562217 1.152740585 1.200953087 1.253127822 1.009643796 1.220341062 0.953369283 0.998439338 1 17.82994217 1.695713124 8.190195185 0.983412609 1.141570837 0.353239697 0.092994281 0.119076728 15.66046003 0.04259136 0.022499119 49.6264403 -1.695713124 0.158158228 STFDAHIYEGR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 111.26 0.0016845 1133660000 1943590 2870500 2134120 2219830 3036450 1674660 2242330 2605390 2328350 FALSE TRUE 1821944.171 3083034.807 2184742.334 2276794.596 2797979.465 2158107.156 1906113.433 2930678.677 1939733.343 0.939275585 1.589411667 1.126310656 1.173766798 1.442455725 1.112579295 0.982667767 1.510866783 1 20.88742691 2.159326072 24.99999996 1.130805535 1.27886187 0.039331501 0.225258867 77.82231723 24549.73533 0.078429715 0.057924195 144.319851 -2.159326072 0.148056335 STFETEHAGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STFETEHAGQR 11 0 P49750;P49750-1;H0YIQ2;P49750-3;F8VU51;H0YI23 P49750 YLPM1 YLP motif-containing protein 1 0 158.05 3.03E-05 276970000 138680 164020 137210 153960 174210 128480 182110 131280 183330 FALSE TRUE 130000.2664 176164.2115 140464.686 157910.8743 160528.2493 165570.0903 154804.2961 147670.597 152731.0386 0.851171232 1.153427706 0.919686576 1.033914754 1.051051906 1.084063146 1.013574565 0.966866973 1 17.22063376 4.76999018 24.06483911 1.028784402 0.851170712 0.435743949 0.063166309 8224.097175 6296803.333 0.014319004 1.964168361 58883.03406 -4.76999018 -0.17761369 STFREES(ph)PLR ddPTM_SK-BR-3_Pertuzumab_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 STFREES(1)PLR;STFREES(1)PLR;STFREES(1)PLR;STFREES(1)PLR;STFREES(1)PLR;STFREES(1)PLR;STFREES(1)PLR;STFREES(1)PLR 179.8 1.25E-06 17540910000 6655690 9851740 7335840 8159360 11668030 5020090 6834210 8167020 15699530 TRUE FALSE 6239122.244 10581173.08 7509849.589 8368742.991 10751669.99 6469308.489 5809483.656 9186690.425 13079177.02 0.477027127 0.809009089 0.574183649 0.639852414 0.822044841 0.494626572 0.444178074 0.702390556 1 23.64076843 -1.857528304 2.898998996 1.146445862 0.620938819 0.455818008 0.130342256 114246108.4 128171883.1 117831444.4 0.03169734 0.013882628 1.857528304 -0.525507044 STFS(ph)PAPRPEMPGTVEVESTFLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STFSPAPRPEMPGTVEVESTFLAR 24 1 Q92576-2;Q92576;E7EVH3;E7ER40 Q92576-2 PHF3 PHD finger protein 3 1 S(0.3)T(0.3)FS(0.401)PAPRPEMPGTVEVESTFLAR 57.427 0.052994 80919000 46687 35030 43973 38454 40865 41654 50898 46496 44042 TRUE FALSE 43764.94401 37623.65765 45016.06033 39440.79474 37655.62774 53678.8336 43266.31741 52301.12795 36691.10568 1.192794363 1.025416295 1.226892989 1.07494157 1.026287626 1.462993077 1.179204513 1.425444314 1 15.16314276 2.262855972 24.9999277 1.277316865 1.11231219 0.234309982 0.140989377 289.4818338 297875.9193 0.04290091 0.035877285 183.170686 -2.262855972 -0.165004674 STFS(ph)PISDIGLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STFSPISDIGLAK 13 0 Q8TEK3;Q8TEK3-1;H7C2S2 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 STFS(0.998)PIS(0.002)DIGLAK 188.09 6.72E-06 21837000 99256 77736 89823 85253 98470 62429 106740 84537 108290 TRUE FALSE 93043.74414 83491.65432 91953.64398 87440.73631 90736.56341 80451.23885 90735.32793 95091.63054 90215.69942 1.03134759 0.925467018 1.019264325 0.969240796 1.00577354 0.891765395 1.005759846 1.054047479 1 16.46109089 1.492756159 11.35047612 1.027983795 0.972807049 0.211520923 0.04340517 0.122449176 51.22123544 0.021113116 0.009789198 31.0996971 -1.492756159 -0.055176746 STFS(ph)TNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 STFSTNYR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.01)T(0.319)FS(0.435)T(0.236)NYR;S(0.005)T(0.102)FS(0.839)T(0.054)NYR;S(0.003)T(0.126)FS(0.871)TNYR 179.09 0.00025823 1272760000 1019470 1298020 1027650 1067670 1395350 832050 1348580 1102010 2070820 TRUE FALSE 955663.1925 1394126.751 1052026.343 1095068.22 1285764.84 1072249.328 1146372.949 1239598.374 1725186.764 0.553947672 0.808101929 0.609804321 0.634753432 0.74529023 0.621526521 0.664492084 0.718529959 1 20.71832112 0.75675691 3.133099291 0.999978109 0.671511441 0.684799534 0.071229533 0.977749041 11.88558125 0.062745026 0.016344296 5.711588489 -0.75675691 -0.328466668 STFSTNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STFSTNYR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 155.38 0.00095373 3588700000 2053060 3586400 1858090 1788600 3716200 1283470 2277300 3415300 5072300 FALSE TRUE 1924562.639 3851940.788 1902164.772 1834498.504 3424344.642 1653986.954 1935840.006 3841707.723 4225700.362 0.455442288 0.911550857 0.450141896 0.434128866 0.810361443 0.391411319 0.458111044 0.909129232 1 22.01075904 1.132871007 5.536974246 0.989628699 0.573803258 0.47814432 0.172261101 0.18574374 7.865546308 0.163247329 0.041311797 13.57910063 -1.132871007 -0.415825441 STFVLDEFKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 STFVLDEFKR 10 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;; 178.54 3.54E-06 4395723000 6818721 8250141 4370217 4174833 6826993 2387693 5953679 6318979 10908405 FALSE TRUE 6391949.424 8860990.024 4473880.611 4281966.283 6290828.509 3076981.208 5060980.105 7107917.438 9087721.735 0.703361042 0.975050764 0.492299472 0.471181492 0.692233839 0.338586644 0.556903067 0.782145145 1 23.11548723 -0.60330075 6.331902694 1.000000001 0.625024669 0.3025733 0.178210165 1.33E-09 2.10E-10 0.178724197 0.042125697 0.249286781 0.60330075 -0.374975332 STGDIAGTVVPETNKEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STGDIAGTVVPETNKEPR 18 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 0 160.55 3.68E-11 127260000 154490 122910 132810 131440 133800 95515 150370 126270 187790 FALSE TRUE 144820.7467 132010.3843 135960.3159 134812.9729 123291.8877 123088.6299 127823.4145 142035.0875 156446.6358 0.925687829 0.843804557 0.869052346 0.86171858 0.788076312 0.786777097 0.817041631 0.907882018 1 17.25531111 0.972045487 4.087173878 0.999748897 0.840144666 0.616087547 0.040543233 0.136817915 6.812461523 0.03987384 0.010190014 9.376602105 -0.972045487 -0.159604231 STGEPLGHVPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STGEPLGHVPAR 12 0 Q93052;C9JUT4;C9JE51;C9J2R5;C9JIY7;C9JT42;C9J3U9;C9J1K7;C9J5C8;C9J4E3 Q93052 LPP Lipoma-preferred partner 0 ; 95.401 0.0020397 261210000 397190 445390 397220 425920 485270 348860 476340 357000 437710 FALSE TRUE 372330.5869 478367.139 406642.246 436849.8283 447158.8517 449570.2187 404917.2391 401572.2359 364653.3733 1.021053456 1.311840707 1.115147358 1.197986527 1.226257275 1.23287004 1.11041682 1.101243716 1 18.47616621 1.153541545 1.446626977 1.00624942 1.191830801 0.351607506 0.078411068 0.369969711 1.514689301 0.066118058 0.020033254 14.2410347 -1.153541545 0.18558138 STGNFLTLTQAIDKFSADGMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STGNFLTLTQAIDKFSADGMR 21 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;Q9P2J5-3 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 98.684 0.00086444 77600000 208320 161950 172970 177940 228220 167930 242980 175670 257610 FALSE TRUE 195281.6231 173940.9465 177072.9301 182506.2417 210296.5218 216408.6649 206547.4047 197602.7862 214613.2268 0.909923521 0.810485678 0.825079296 0.850396056 0.979886119 1.008365925 0.962416939 0.920739086 1 17.71137947 2.764828154 5.518818173 0.97431169 0.837703968 0.756911247 0.035066478 0.080560929 7.743983109 0.010618094 0.010968344 581.8729307 -2.764828154 -0.136607722 STGS(ph)PTQETQAPFIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 STGSPTQETQAPFIAK 16 0 O15231-3;H0Y704;O15231-2 O15231-3 ZNF185 Zinc finger protein 185 1 ST(0.003)GS(0.997)PTQETQAPFIAK;STGS(1)PTQETQAPFIAK;STGS(1)PTQETQAPFIAK;STGS(0.999)PT(0.001)QETQAPFIAK;STGS(1)PTQETQAPFIAK;STGS(1)PTQETQAPFIAK 396.72 8.41E-122 2439200000 2348320 2204790 2113180 2073560 2202510 1647480 2548860 1923060 2217000 TRUE FALSE 2201342.843 2368034.946 2163305.628 2126771.06 2029533.749 2123080.731 2166682.105 2163158.274 1846968.378 1.191868182 1.282119918 1.171273777 1.151492947 1.098845965 1.1494949 1.173101896 1.171193996 1 20.81672774 -5 0.07236144 0.421421871 1.382560412 0.658951426 0.041564816 184.1291469 0.956190331 17.82556434 2.079136083 1.00E-05 5 0.961138541 STGSSQLTHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STGSSQLTHK 10 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 0 64.439 0.072078 36989000 60888 72261 52522 57331 75381 32850 65327 59651 62915 FALSE TRUE 57077.12877 77611.27963 53767.84664 58802.21052 69460.88033 42333.26172 55531.82282 67098.55866 52414.08005 1.088965574 1.480733413 1.0258283 1.121878138 1.325233225 0.807669651 1.059482924 1.280162861 1 15.6776668 3.842062138 5.35676405 1.083909723 1.30304644 0.182523214 0.171020507 0.290195465 11.98582087 0.041272116 0.075877576 6951.237677 -3.842062138 0.219136717 STHALSEVEVESDSFMNAVLWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STHALSEVEVESDSFMNAVLWLR 23 0 C9JIF9;P13798 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 ; 235.56 4.26E-37 134673000 51544 190996 88370 68369 177388 54781 97578 177824 104677 FALSE TRUE 48317.95305 205137.5426 90466.17813 70123.46429 163456.662 70595.3854 82947.08477 200025.7178 87205.73246 0.554068542 2.352340113 1.037387974 0.804115307 1.874379785 0.80952689 0.951165507 2.293722123 1 16.41213535 3.735942887 24.57386947 1.214676611 1.615615872 0 0.645398687 742.0513717 2067068.318 0.151632456 0.268122805 5444.310516 -3.735942887 0.400939261 STHDHWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 STHDHWK 7 0 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ;; 110.63 0.0067597 396916000 759440 1199540 990820 995150 1246270 773790 1204680 1152890 1284970 FALSE TRUE 711908.006 1288355.19 1014322.718 1020687.234 1148392.981 997170.6116 1024049.418 1296830.854 1070500.206 0.665023698 1.203507653 0.947522208 0.953467574 1.072762971 0.931499692 0.956608333 1.211425133 1 20.02985364 1.265044029 24.98463236 1.105712822 0.984458061 0.133482437 0.143787648 401.8222571 379082.9488 0.086991045 0.031745774 18.4095863 -1.265044029 -0.121254761 STHHLASHGFYEFLNWFDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STHHLASHGFYEFLNWFDER 20 0 Q8TCJ2 Q8TCJ2 STT3B Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B 0 ; 101.5 0.00012645 100441000 43461.2 112074 67531 66720 109634 42012 61467 97208 68978 FALSE TRUE 40741.04107 120372.0756 69132.86721 68432.14816 101023.7879 54140.18239 52250.59398 109344.6328 57465.12619 0.708969836 2.094697838 1.203040379 1.190846566 1.758001671 0.942139798 0.909257448 1.902799838 1 15.81039907 2.226326712 24.99508248 1.143343252 1.45230595 0.033032223 0.457257657 540.7701688 1104839.287 0.160307671 0.119254331 168.3940382 -2.226326712 0.308962698 STHSELLEDYYQSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 STHSELLEDYYQSGR 15 0 A0A3B3ITW3;P28288 A0A3B3ITW3 ABCD3 ATP-binding cassette sub-family D member 3 0 ;;; 230.86 2.72E-13 1170390000 512883 822520 723740 728120 933700 650916 945980 884050 906180 FALSE TRUE 480782.5686 883420.2366 740907.4546 746804.7919 860370.9684 838824.8825 804139.081 994425.5885 754932.7039 0.636854869 1.170197333 0.981421855 0.989233594 1.139665779 1.111125373 1.065179819 1.317237395 1 19.52598852 4.744848119 24.65052745 1.090158257 0.636854622 0.671934481 0.100897995 343.4308726 1346396.138 0.022359291 0.208619376 55570.9881 -4.744848119 -0.453303635 STIGGQIMYLTGMVDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STIGGQIMYLTGMVDKR 17 1 P15170-2;P15170-3;P15170;H3BR35;H3BSV8 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ; 184.21 5.60E-11 229350000 327720 383340 358270 366570 418990 313440 446490 320320 517470 FALSE TRUE 307208.5902 411722.8925 366768.3336 375976.8068 386084.2155 403925.0397 379542.9695 360312.6571 431100.914 0.712614101 0.955049918 0.850771413 0.872131778 0.895577353 0.936961687 0.880404001 0.835796551 1 18.7176661 -5 0.17807553 1.465819572 0.852873655 0.293048924 0.065349162 186.8713237 1.794041446 31.14541172 0.191859734 1.00E-05 5 -0.612945916 STIGVMVTAS(ph)HNPEEDNGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 15 STIGVMVTASHNPEEDNGVK 20 0 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A494C099;A0A494C163;D6RCQ8;D6RF77;D6RC77 O95394-4 PGM3 Phosphoacetylglucosamine mutase 1 STIGVMVT(0.001)AS(0.999)HNPEEDNGVK;STIGVMVT(0.059)AS(0.941)HNPEEDNGVK;STIGVMVT(0.004)AS(0.996)HNPEEDNGVK;STIGVMVT(0.004)AS(0.996)HNPEEDNGVK;STIGVMVT(0.001)AS(0.999)HNPEEDNGVK;STIGVMVT(0.003)AS(0.997)HNPEEDNGVK;STIGVMVT(0.003)AS(0.997)HNPEEDNGVK;STIGVMVT(0.009)AS(0.991)HNPEEDNGVK;STIGVMVT(0.007)AS(0.993)HNPEEDNGVK;STIGVMVT(0.002)AS(0.998)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVT(0.002)AS(0.998)HNPEEDNGVK;STIGVMVT(0.004)AS(0.996)HNPEEDNGVK;STIGVMVT(0.001)AS(0.999)HNPEEDNGVK 299.94 5.51E-55 18014870000 20172090 15964320 16510470 16792980 17130570 11531790 23526370 15025740 21756830 TRUE FALSE 18909554.9 17146334.86 16902106.15 17223916.3 15785204.13 14860830.57 19998809.23 16901736.71 18125474.52 1.043258474 0.945979916 0.932505581 0.950260159 0.870885014 0.819886429 1.103353692 0.932485199 1 24.11151543 -1.195920962 5.100418882 1.000003872 0.951129415 0.038168557 0.078913178 3.37E-06 5.32E-07 0.074165666 0.01747963 0.063691142 1.195920962 -0.048874457 STKPGAAPTEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 STKPGAAPTEHK 12 1 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ;; 126.1 0.00017633 241041000 506694 367819 427875 430028 434322 318894 558500 398539 568710 FALSE TRUE 474980.927 395052.7015 438024.3971 441063.2465 400212.1021 410953.521 474758.1099 448297.4714 473788.627 1.002516523 0.833816345 0.924514376 0.930928311 0.844706013 0.867377344 1.002046235 0.946197198 1 18.85388404 1.73051259 9.455155682 0.979472948 0.894721872 0.366419125 0.050380488 0.098161632 31.39388113 0.022203524 0.01196848 53.76660201 -1.73051259 -0.084751077 STLESEKPGS(ph)PEAAET(ph)SPPSNIIDHCEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STLESEKPGSPEAAETSPPSNIIDHCEK 28 1 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 2 STLES(0.002)EKPGS(0.998)PEAAET(0.593)S(0.4)PPS(0.007)NIIDHCEK 95.205 0.034106 199560000 460280 223020 282140 385710 366130 275670 430870 304070 386960 TRUE FALSE 431471.8964 239532.6329 288832.494 395607.9716 337375.6267 355251.4539 366265.0435 342033.8088 322373.8761 1.338420785 0.743027431 0.895955024 1.227171309 1.046535255 1.101985862 1.136149889 1.060984882 1 18.29837531 3.259398127 24.99647739 1.102653216 0.92522866 0.030086936 0.162218099 353.7390092 424339.2751 0.041907433 0.05668168 1817.180749 -3.259398127 -0.177424556 STLINSLFLTDLYS(ph)PEYPGPSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STLINSLFLTDLYSPEYPGPSHR 23 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1;A0A5F9ZGZ7 E7EPK1 7-Sep Septin-7 1 STLINSLFLTDLY(0.001)S(0.998)PEY(0.001)PGPSHR 133.44 1.48E-05 38714000 68642 71093 65254 65050 72320 59342 70991 54905 65169 TRUE FALSE 64345.81975 76356.79969 66801.8557 66719.29313 66640.27892 76473.07206 60346.5586 61760.01011 54291.87289 1.185183276 1.406413071 1.230420911 1.228900194 1.227444834 1.408554688 1.111521032 1.137555343 1 15.72844863 1.607521711 6.822122872 1.087390185 1.285471535 0.56905769 0.081437679 0.088721558 8.945773331 0.040762365 0.019662164 40.50621947 -1.607521711 0.198081349 STLINSLFLTDLYSPEYPGPSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STLINSLFLTDLYSPEYPGPSHR 23 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1;A0A5F9ZGZ7 E7EPK1 7-Sep Septin-7 0 ; 229.15 5.79E-33 771080000 459080 543520 564550 538720 570420 484320 644850 481330 557820 FALSE TRUE 430347.0023 583762.7863 577941.3926 552544.4673 525621.5142 624135.3217 548160.729 541425.11 464716.2383 0.926042533 1.256170407 1.243643637 1.188993243 1.131059065 1.343046079 1.179560092 1.165066045 1 18.82599053 -0.46641586 7.585932334 0.999996507 1.196769628 0.197275075 0.108574205 0 0 0.094667073 0.022313243 0.341652135 0.46641586 0.19677312 STLPDADRER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 STLPDADRER 10 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;; 138.65 5.38E-05 4443800000 4361330 4435890 3777400 3430260 3731210 2655190 3940220 4141600 4269360 FALSE TRUE 4088362.14 4764327.911 3867001.712 3518286.279 3438175.818 3421700.25 3349420.59 4658687.877 3556776.235 1.149457225 1.339507351 1.087220971 0.989178415 0.96665508 0.962022917 0.94170124 1.309806288 1 21.76213878 3.646778923 2.752649882 1.013229081 1.250617099 0.367308685 0.114194784 0.231410335 3.44829445 0.029812516 0.052113272 4433.828833 -3.646778923 0.237388018 STLS(ph)PPEASPGPPAAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STLSPPEASPGPPAAPR 17 0 Q6NUJ5-2;Q6NUJ5 Q6NUJ5-2 PWWP2B PWWP domain-containing protein 2B 1 STLS(1)PPEASPGPPAAPR;STLS(1)PPEASPGPPAAPR 287.78 9.72E-37 187095000 233582 224139 217831 213533 224449 187314 245083 200303 218266 TRUE FALSE 218962.5196 240734.4848 222998.0542 219012.6183 206821.6809 241388.511 208335.0794 225311.2705 181835.9945 1.204175885 1.323909963 1.226369151 1.2044514 1.137407813 1.327506755 1.145730689 1.239090594 1 17.47227828 -5 0.189065958 0.00517352 1.274085103 0.562104458 0.062671961 92.09537934 0.90023741 34.42782813 0.157840264 1.00E-05 5 1.268911582 STLTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 STLTSR 6 0 H0YDZ5;M0R104;Q9Y2N7-4;Q9Y2N7-6;Q9Y2N7-7;Q9Y2N7-5;Q9Y2N7-3;Q9Y2N7-2;Q9Y2N7 H0YDZ5 HIF3A Hypoxia-inducible factor 3-alpha 0 ;;;;;;; 144.9 0.026088 11624690000 5237780 5627820 5499540 5195740 5327220 4175970 5928410 4665320 5270290 FALSE TRUE 4909956.7 6044509.649 5629991.686 5329071.485 4908841.63 5381504.748 5039499.957 5247795.472 4390644.552 1.118276973 1.376679341 1.282269976 1.213733296 1.118023008 1.225675339 1.147781356 1.195222116 1 22.06600131 0.760498117 0.262899905 0.94967185 1.308964512 0.434426689 0.076578042 2.496663096 0.483223728 0.306360254 0.149225457 5.76100321 -0.760498117 0.359292662 STMGKPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STMGKPQR 8 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ; 105.57 0.003979 245220000 339640 328590 318920 331080 340290 248890 369130 317820 358780 FALSE TRUE 318382.5387 352919.1455 326484.933 339576.0733 313564.9961 320740.5026 313782.3833 357500.5266 298897.3002 1.065190413 1.180737147 1.092298033 1.136096154 1.049072694 1.07307929 1.049799992 1.196064757 1 18.18929034 2.748484346 24.55953928 1.074342728 1.124559489 0.128727799 0.057193749 955.0636799 2363620.888 0.015979394 0.016733588 560.3822186 -2.748484346 0.050216761 STMKPVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STMKPVQK 8 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 60.019 0.086589 394310000 522810 331830 343370 308760 363070 231170 368270 325060 309700 FALSE TRUE 490088.2553 356399.0385 351514.8986 316683.3043 334555.9468 297905.0263 313051.3324 365644.4565 258009.0693 1.89950011 1.381343065 1.362412955 1.227411522 1.296682895 1.154630057 1.213334606 1.417176759 1 17.97706225 7.999999989 0.770660105 1.233280213 133.3067215 0.763814243 0.114604091 189.5232057 0.740925926 0.0350022 43569.85884 99999997.47 -7.999999989 132.0734413 STNGDTFLGGEDFDQALLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 STNGDTFLGGEDFDQALLR 19 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;; 302.15 1.19E-49 485104000 277951 306820 243299 210333 391645 222705 267489 299467 454086 FALSE TRUE 260554.5431 329537.272 249070.1672 215730.5009 360886.7815 286996.3182 227381.5077 336856.1142 378296.1131 0.688758182 0.871109326 0.658400017 0.57026888 0.953979618 0.758655213 0.601067523 0.890456186 1 18.52915643 1.021728143 7.306296945 0.999902055 0.733423612 0.395781035 0.115486113 0.141001635 30.62532477 0.107222524 0.026877643 10.51303579 -1.021728143 -0.266478442 STPDGTEHGEFLALDLGGTNFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STPDGTEHGEFLALDLGGTNFR 22 0 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 ; 246.22 6.07E-31 480490000 285170 401750 365050 404710 388010 279480 440770 306570 315940 FALSE TRUE 267321.7187 431495.988 373709.1584 415095.5438 357537.2598 360161.339 374680.6304 344845.9393 263207.5729 1.015630803 1.639375278 1.419826771 1.577065352 1.358385155 1.368354774 1.423517668 1.31016724 1 18.00584147 0.451293375 0.81446867 0.995454288 1.4407658 0.346043681 0.166541869 1.793264127 1.76430371 0.157900524 0.050340027 2.826788883 -0.451293375 0.445311512 STPEYFAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STPEYFAER 9 0 P08133;P08133-2 P08133 ANXA6 Annexin A6 0 ; 93.467 0.02182 290700000 296620 377030 314860 289200 441020 264301 314470 397410 460930 FALSE TRUE 278055.0837 404945.6935 322328.6279 296621.3616 406384.0682 340600.4081 267318.1429 447027.5133 383997.8053 0.724105919 1.054552104 0.839402266 0.772455877 1.058297893 0.886985299 0.696144976 1.164140803 1 18.55073854 1.221120264 24.99998698 1.082070434 0.874473265 0.337718191 0.127321337 338.1279088 484678.6194 0.116685885 0.029444031 16.63873345 -1.221120264 -0.207597169 STPFIVPS(ph)SPTEQEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STPFIVPSSPTEQEGR 16 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 STPFIVPS(0.47)S(0.47)PT(0.061)EQEGR 105.14 0.0013709 42458000 95830 106660 97164 118940 118870 91950 120100 92740 127020 TRUE FALSE 89832.17136 114557.2174 99468.77596 121992.2018 109534.4297 118494.4723 102092.12 104318.7931 105819.5414 0.848918547 1.082571478 0.939984946 1.152832455 1.035105881 1.119778736 0.964775679 0.985817853 1 16.69124655 4.748487861 24.44009586 1.032566015 0.84891841 0.428736616 0.067486457 1005.334195 2474984.099 0.015149793 0.203744442 56038.67542 -4.748487861 -0.183647605 STPFIVPSS(ph)PTEQEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 STPFIVPSSPTEQEGR 16 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 STPFIVPS(0.208)S(0.791)PTEQEGR;STPFIVPS(0.024)S(0.976)PTEQEGR;STPFIVPS(0.183)S(0.817)PTEQEGR;STPFIVPS(0.047)S(0.953)PTEQEGR;STPFIVPS(0.08)S(0.92)PT(0.001)EQEGR;STPFIVPS(0.003)S(0.771)PT(0.226)EQEGR;STPFIVPS(0.038)S(0.959)PT(0.004)EQEGR 379.99 5.91E-105 16631990000 8485080 9501390 9277550 9600990 9794140 7819600 10378900 8192130 10159700 TRUE FALSE 7954013.989 10204882.8 9497617.867 9847367.658 9024947.752 10076991.58 8822680.298 9214935.464 8463980.436 0.939748626 1.205683647 1.122121907 1.163444048 1.06627701 1.190573591 1.042379571 1.088723625 1 23.01290486 1.093550051 1.056901067 1.004149363 1.125213105 0.136344235 0.078013547 0.763683902 1.81293751 0.065437754 0.021574245 12.40366564 -1.093550051 0.121063741 STPKEDDSSASTSQSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STPKEDDSSASTSQSTR 17 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 154.48 1.24E-07 363810000 241090 163810 192010 180220 208540 130290 255010 167570 301600 FALSE TRUE 226000.6073 175938.6628 196564.5679 184844.7503 192162.1096 167902.6079 216773.6179 188491.4834 251261.0116 0.899465483 0.700222696 0.782312252 0.735668256 0.764790798 0.668239799 0.862742757 0.750181981 1 17.9388273 -0.024545177 0.760472899 1.007228858 0.759935809 0.513905435 0.069399115 3.983555062 2.320721229 0.146215029 0.021230557 0.945050079 0.024545177 -0.247293049 STPLASPSPSPGRS(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STPLASPSPSPGRSPQR 17 1 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 STPLASPSPS(0.003)PGRS(0.997)PQR;STPLASPSPS(0.076)PGRS(0.924)PQR 175.65 7.29E-10 1058570000 374936 486428 358775 413917 396867 247750 462351 326231 357125 TRUE FALSE 351469.425 522443.6352 367285.3124 424538.811 365698.6667 319271.4031 393025.7598 366961.6585 297518.5304 1.18133625 1.756003683 1.234495586 1.426932334 1.229162655 1.073114346 1.321012709 1.233407741 1 18.18262 3.164794363 1.067155693 1.188586856 1.491949177 0.273395392 0.176793982 0.569157652 1.392070645 0.069569779 0.10283614 1461.485001 -3.164794363 0.303362321 STPLEENVVDREQIDFLAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STPLEENVVDREQIDFLAAR 20 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 ; 230.29 1.62E-25 287990000 143431 174941 153295 158926 203757 119571 174417 147700 255461 FALSE TRUE 134453.9097 187893.8137 156931.2298 163004.3102 187754.7471 154089.2066 148264.7901 166140.6701 212822.9088 0.631764271 0.882864607 0.737379405 0.765915245 0.882211169 0.72402547 0.696658038 0.780652192 1 17.69929393 -1.490613368 2.728372982 1.009462922 0.767804245 0.485131151 0.076672013 10384002.35 10812062.01 737332.5961 0.017839915 0.032313696 1.490613368 -0.241658676 STPSHGSVSSLNSTGSLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 359.74 1.39E-95 1343509000 257983 509156 480496 521056 536144 396748 646459 492943 627607 TRUE FALSE 241836.3045 546854.44 491893.592 534427.1791 494037.4129 511282.7069 549528.4744 554488.0187 522855.3372 0.462530049 1.045900082 0.940783343 1.022132014 0.944883561 0.977866478 1.051014373 1.060499873 1 18.99605231 4.741318664 24.9995793 1.003080611 0.462529855 0.943430711 0.041772107 55.58229309 503784.1077 0.009946253 0.068626677 55121.20004 -4.741318664 -0.540550756 STPST(ph)KQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STPSTKQR 8 1 Q9NQ75-2;Q9NQ75 Q9NQ75-2 CASS4 Cas scaffolding protein family member 4 1 S(0.129)T(0.129)PS(0.01)T(0.732)KQR 71.349 0.079172 157080000 153620 236290 286180 284620 263300 231340 276210 259190 245300 TRUE FALSE 144005.1984 253785.1575 292968.3247 291923.8311 242621.4801 298124.1025 234794.8747 291550.442 204357.8453 0.70467174 1.241866477 1.433604491 1.428493389 1.187238394 1.458833656 1.148939863 1.426666256 1 17.6407381 4.739088731 3.559733678 1.311851161 0.633155451 0.602182276 0.150015422 0.172796283 3.920719855 0.031718741 0.314734505 54838.89955 -4.739088731 -0.67869571 STPTDLILCVPHLYSCLEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STPTDLILCVPHLYSCLEDR 20 0 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 ; 124.35 2.71E-05 218998000 239340 293000 296680 311310 335680 238350 355990 270140 323620 FALSE TRUE 224360.1366 314694.0249 303717.3897 319298.7416 309317.0469 307157.7757 302612.6043 303867.5737 269605.7313 0.832178661 1.16723789 1.126524233 1.184317337 1.147294033 1.139285037 1.122426452 1.127081283 1 18.04049164 4.742250119 24.82203647 1.135386836 0.832178533 0.775100622 0.049677584 128.9137195 867259.2023 0.01008578 0.075121731 55239.54831 -4.742250119 -0.303208303 STQIENQHQGAQDTSDLMS(ph)PSKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 STQIENQHQGAQDTSDLMSPSKR 23 1 Q9NVR2;H0YBW3 Q9NVR2 INTS10 Integrator complex subunit 10 1 STQIENQHQGAQDT(0.003)S(0.003)DLMS(0.787)PS(0.207)KR;STQIENQHQGAQDTS(0.002)DLMS(0.777)PS(0.221)KR;STQIENQHQGAQDTSDLMS(0.771)PS(0.229)KR 170.77 2.97E-12 1136990000 658970 462160 520390 540100 521600 348452 661630 454420 511920 TRUE FALSE 617726.244 496378.8073 532733.8965 553959.8804 480635.64 449044.4358 562424.7238 511155.3373 426477.2449 1.448438929 1.163904554 1.249149639 1.298920135 1.126990117 1.052915346 1.318768423 1.198552428 1 18.70210924 -5 0.09724094 0.348967513 1.376603964 0.393792734 0.102483183 234.7492801 1.563622987 32.0096719 1.833030452 1.00E-05 5 1.027636451 STS(ph)FRGGMGSGGLATGIAGGLAGMGGIQNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 STSFRGGMGSGGLATGIAGGLAGMGGIQNEK 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.115)T(0.115)S(0.771)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.135)T(0.135)S(0.73)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.024)T(0.12)S(0.857)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.026)T(0.026)S(0.948)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.053)T(0.167)S(0.78)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.021)T(0.113)S(0.866)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.123)T(0.123)S(0.754)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.024)T(0.12)S(0.856)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.137)T(0.137)S(0.725)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.004)T(0.025)S(0.971)FRGGMGSGGLATGIAGGLAGMGGIQNEK 308.91 9.58E-93 10439300000 6674213 9348540 6864621 7667506 8728789 3677755 9663800 5817666 23377750 TRUE FALSE 6256485.922 10040715.63 7027453.052 7864267.185 8043265.122 4739463.165 8214802.904 6544014.406 19475852.5 0.321243238 0.515546913 0.360829034 0.403795787 0.41298655 0.243350742 0.421794266 0.336006571 1 24.21518314 -1.610492216 5.345863347 1.00507688 0.386446702 0.880237962 0.072149602 0.004158052 0.000302962 0.066536425 0.01561512 0.024519284 1.610492216 -0.618630178 STS(ph)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 STSFRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR 40 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.125)T(0.125)S(0.751)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.044)T(0.184)S(0.771)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.136)T(0.136)S(0.652)FRGGMGS(0.075)GGLATGIAGGLAGMGGIQNEKETMQSLNDR 287.51 2.05E-78 855304000 185190 388426 226668 337259 471406 116679 329392 191641 2314650 TRUE FALSE 173599.2885 417185.4652 232044.672 345913.6369 434383.6743 150362.3332 280002.7275 215567.8007 1928319.962 0.090026184 0.216346599 0.12033515 0.179386017 0.225265352 0.077975822 0.145205533 0.111790473 1 20.87891302 -1.130267223 4.077890662 1.000239081 0.149824099 0.9670919 0.049515412 495423758.7 940188754.7 1577825.171 0.011066738 0.074085425 1.130267223 -0.850414982 STS(ph)GPRPGCQPSSPCVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STSGPRPGCQPSSPCVPK 18 1 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 S(0.111)T(0.111)S(0.777)GPRPGCQPSSPCVPK 128.67 1.38E-05 392190000 134170 103640 106400 117520 120870 83088 129360 97461 183640 TRUE FALSE 125772.5392 111313.6134 108923.8582 120535.7622 111377.3578 107074.1568 109963.6689 109629.2204 152989.2976 0.822100246 0.727590852 0.711970445 0.787870551 0.728007511 0.699880047 0.718767068 0.716580977 1 17.22307121 -0.768749558 5.668134261 1.000000028 0.733877855 0.823344058 0.037911728 1.26E-08 2.71E-09 0.034383351 0.008104233 0.170314037 0.768749558 -0.266122173 STS(ph)LNERPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.032)T(0.138)S(0.83)LNERPK 76.24 0.021797 514760000 208290 190090 192990 262730 282730 197000 334990 204900 282010 TRUE FALSE 195253.5007 204164.4614 197567.8139 269472.0966 260525.5263 253870.702 284761.3594 230482.216 234940.7091 0.831075642 0.869004193 0.840926269 1.146979157 1.108899038 1.08057349 1.212056269 0.981022901 1 17.84193719 3.242694945 24.99922393 1.106749671 0.850848768 0.734028244 0.067839265 44.44264767 268731.2274 0.017494599 0.022864349 1748.618 -3.242694945 -0.255900903 STS(ph)LSALVR ddPTM_SK-BR-3_Pertuzumab_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(0.008)T(0.022)S(0.953)LS(0.017)ALVR;S(0.008)T(0.001)S(0.99)LSALVR;ST(0.016)S(0.984)LSALVR;S(0.009)T(0.026)S(0.965)LSALVR;S(0.095)T(0.234)S(0.672)LSALVR 213.25 2.30E-06 1180760000 2725178 3361326 2893024 3822207 4152877 2178537 3389582 2739989 3745005 TRUE FALSE 2554613.974 3610202.074 2961647.895 3920291.303 3826726.792 2807445.266 2881345.646 3082082.658 3119939.472 0.818802415 1.157138498 0.949264536 1.256527999 1.226538792 0.899839658 0.923526136 0.98786617 1 21.57308661 2.206101163 24.99997756 0.942316456 1.081843515 0.193994353 0.129721131 296.8995141 228667.6099 0.046640347 0.034448587 160.731561 -2.206101163 0.13952706 STS(ph)PIIGS(ph)PPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.01)S(0.989)PIIGS(1)PPVR 218.34 5.05E-11 426600000 543730 583920 576910 630820 774880 660780 778180 655170 657050 TRUE FALSE 509698.9099 627154.0444 590594.5776 647007.9092 714024.0505 851536.4591 661499.1333 736969.4167 547384.1103 0.931154011 1.145729356 1.078939937 1.181999801 1.304429626 1.555647018 1.208473393 1.346347844 1 19.06219403 2.976828937 2.71072326 1.310312702 1.075538468 0.327492961 0.14691011 0.285661907 4.216258061 0.042852843 0.049141406 948.0449671 -2.976828937 -0.234774234 STS(ph)PIIGSPPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 STSPIIGSPPVR 12 0 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 ST(0.001)S(0.999)PIIGSPPVR;ST(0.001)S(0.999)PIIGSPPVR;S(0.001)T(0.024)S(0.975)PIIGSPPVR;ST(0.002)S(0.998)PIIGSPPVR 255.24 4.11E-21 2486300000 3459570 3297330 3502810 2984800 2375660 2294840 3008340 2443200 2507360 TRUE FALSE 3243041.689 3541467.744 3585898.307 3061395.021 2189085.247 2957323.054 2557267.345 2748238.898 2088865.418 1.552537402 1.695402544 1.716672734 1.465577914 1.047978117 1.415755668 1.224237485 1.315661064 1 20.99428811 3.000434039 4.423178261 1.232971567 1.668291252 0.725492052 0.127648338 0.094133098 4.624431546 0.034843122 0.039945603 1000.99991 -3.000434039 0.435319685 STS(ph)PSAAGGQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STSPSAAGGQQK 12 0 Q2TB10 Q2TB10 ZNF800 Zinc finger protein 800 1 S(0.002)T(0.022)S(0.976)PSAAGGQQK 152.32 7.31E-05 383730000 927740 587690 750490 571360 653670 617520 886700 601570 601350 TRUE FALSE 869674.4095 631203.1791 768291.9772 586022.0649 602333.395 795787.9994 753747.5667 676677.3387 500980.8001 1.735943592 1.25993487 1.533575692 1.169749549 1.202308342 1.588460075 1.50454382 1.350705134 1 18.93439579 4.749080612 24.54417536 1.366604024 1.735943862 0.306653591 0.184962879 1554.130785 3625846.095 0.041582722 0.583829093 56115.21252 -4.749080612 0.369339837 STS(ph)QGSINSPVYSR ddPTM_SK-BR-3_Pertuzumab_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(0.032)T(0.146)S(0.822)QGSINSPVYSR;S(0.001)T(0.002)S(0.997)QGSINSPVYSR;ST(0.015)S(0.985)QGSINSPVYSR;STS(0.999)QGSINSPVYSR 313.04 9.18E-56 1327660000 2265730 2607530 2288020 2410550 2522670 1800220 2853450 2251090 2667090 TRUE FALSE 2123922.004 2800594.234 2342292.915 2472408.794 2324549.674 2319914.29 2425601.663 2532143.542 2221935.449 0.955888257 1.260430061 1.05416785 1.112727553 1.046182361 1.044096169 1.091661625 1.139611658 1 21.08338547 3.727386139 24.99902388 1.073828841 1.138128191 0.006115526 0.082874236 26.24452932 2476592.818 0.019470196 0.032524657 5338.093042 -3.727386139 0.06429935 STS(ph)QSIVSLLTGTAGEDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STSQSIVSLLTGTAGEDEK 19 0 V9GZ20;V9GXZ5;Q70EL4-2;Q70EL4-3;Q70EL4-4;Q70EL4 V9GZ20 USP43 Ubiquitin carboxyl-terminal hydrolase 43 1 S(0.104)T(0.104)S(0.792)QSIVSLLTGTAGEDEK 277.07 1.79E-39 42373000 93885 77334 78546 82620 108300 47958 115590 71102 102420 TRUE FALSE 88008.90544 83059.88983 80409.14821 84740.16908 99794.55486 61802.69607 98258.35258 79979.24121 85325.44034 1.031449766 0.973448124 0.942381872 0.993140718 1.169575621 0.724317341 1.151571585 0.937343434 1 16.38068833 3.010445901 24.43281333 1.003827259 0.97390437 0 0.123002617 1057.817254 2474193.143 0.032142907 0.038377315 1024.344172 -3.010445901 -0.029922889 STS(ph)TPNVHMVSTTLPVDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 STSTPNVHMVSTTLPVDSR 19 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 S(0.168)T(0.168)S(0.652)T(0.012)PNVHMVSTTLPVDSR;S(0.116)T(0.116)S(0.765)T(0.003)PNVHMVSTTLPVDSR;S(0.13)T(0.13)S(0.711)T(0.029)PNVHMVSTTLPVDSR 189.09 4.94E-14 1043470000 279307 342355 305011 299378 341155 256568 405570 313032 496150 TRUE FALSE 261825.6734 367703.3204 312246.005 307060.5463 314362.0625 330635.0166 344758.5436 352114.7343 413339.3597 0.633439974 0.889591837 0.755422869 0.742877587 0.760542288 0.799911764 0.83408109 0.851878066 1 18.65696722 0.810051931 0.843578389 0.999739982 0.773772505 0.587069922 0.062785776 0.630667554 0.90021091 0.057232852 0.019930116 6.457314387 -0.810051931 -0.225967478 STS(ph)TPT(ph)SPGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STSTPTSPGPR 11 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;H3BRB0;A0A0C4DGL7 Q8WWM7 ATXN2L Ataxin-2-like protein 2 S(0.194)T(0.253)S(0.543)T(0.077)PT(0.751)S(0.182)PGPR 97.463 0.033145 126260000 241120 249110 296510 250940 236370 216000 232150 183480 257670 TRUE FALSE 226028.7296 267554.3636 303543.3572 257379.5452 217806.4537 278355.6935 197341.2627 206387.8819 214663.2124 1.052945808 1.246391315 1.414044604 1.19899233 1.014642664 1.296708879 0.919306389 0.961449703 1 17.71171545 1.973396698 1.085127582 0.946250387 1.251857297 0.374861905 0.127829299 0.455423943 0.987771594 0.099635683 0.045709419 94.05820739 -1.973396698 0.30560691 STS(ph)TPTS(ph)PGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 STSTPTSPGPR 11 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;H3BRB0;A0A0C4DGL7 Q8WWM7 ATXN2L Ataxin-2-like protein 2 STS(1)TPT(0.029)S(0.971)PGPR;S(0.001)T(0.004)S(0.994)T(0.009)PT(0.297)S(0.694)PGPR;ST(0.001)S(0.999)T(0.001)PT(0.112)S(0.888)PGPR;ST(0.002)S(0.998)T(0.011)PT(0.026)S(0.964)PGPR;ST(0.001)S(0.999)T(0.001)PT(0.112)S(0.887)PGPR 225.44 7.99E-12 949107000 1618900 1722480 1791900 1729670 1738140 1270570 1572770 1301370 1607900 TRUE FALSE 1517575.939 1850014.211 1834404.714 1774056.261 1601633.496 1637362.933 1336947.739 1463848.909 1339531.103 1.132915791 1.381090897 1.36943794 1.324386016 1.195667269 1.222340362 0.998071442 1.092806958 1 20.35329665 2.082739581 1.300218343 1.019763158 1.324999962 0.65897421 0.081078751 0.232953031 0.739605232 0.052887366 0.026483566 120.9872431 -2.082739581 0.305236804 STS(ph)YGYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STSYGYSR 8 0 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 S(0.002)T(0.062)S(0.935)YGYSR 111.61 0.0033577 565630000 615550 742210 772720 758600 881260 575020 839970 722610 1009300 TRUE FALSE 577023.8243 797164.0007 791049.2833 778066.9603 812049.3944 741018.9393 714024.2964 812829.4492 840841.3097 0.686245808 0.948055229 0.940783087 0.925343405 0.965758206 0.881282747 0.849178422 0.966685913 1 19.68147402 4.741758504 24.99495475 0.926049783 0.68624572 0.75809475 0.043858096 161.2418135 1260220.803 0.010710874 0.076613974 55177.05337 -4.741758504 -0.239804063 STSAPQMS(ph)PGSSDNQSSSPQPAQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 STSAPQMSPGSSDNQSSSPQPAQQK 25 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 STSAPQMS(0.998)PGS(0.001)S(0.001)DNQSSSPQPAQQK;STSAPQMS(0.994)PGS(0.005)S(0.002)DNQSSSPQPAQQK;S(0.001)T(0.001)S(0.001)APQMS(0.515)PGS(0.405)S(0.077)DNQSSSPQPAQQK 283.77 6.22E-53 984200000 813545 671463 764909 748610 784726 638337 916283 668800 939767 TRUE FALSE 762626.6707 721178.8192 783053.0027 767820.6 723096.7854 822614.5294 778894.8705 752301.1522 782913.8166 0.974087638 0.921147135 1.00017778 0.980721739 0.923596915 1.050708918 0.994866681 0.960899062 1 19.57849398 2.248011936 24.99931851 1.002281801 0.961085922 0.295036116 0.03197435 254.0486874 671975.1427 0.010851078 0.008965121 177.0157607 -2.248011936 -0.041195879 STSESFIQHIVSLVHHVK ddPTM_SK-BR-3_Pertuzumab_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 ; 258.34 4.09E-31 157399000 139314 238380 215310 205936 265890 138678 222440 229450 307990 FALSE TRUE 130594.5854 256029.9032 220417.2549 211220.6664 245008.0719 178712.0874 189087.187 258097.3376 256584.4793 0.508973052 0.997838622 0.8590436 0.823201259 0.954882667 0.696503888 0.736939302 1.005896141 1 17.96907438 1.222243644 24.85315224 1.00294834 0.819720085 0.268429813 0.137505395 379.0395042 577316.0223 0.12433506 0.031467595 16.68182819 -1.222243644 -0.183228255 STSGPRPGCQPSS(ph)PCVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STSGPRPGCQPSSPCVPK 18 1 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 STSGPRPGCQPS(0.009)S(0.991)PCVPK;STSGPRPGCQPS(0.022)S(0.978)PCVPK 225.5 2.44E-19 1067090000 780100 560730 684730 702730 795660 558500 815430 558090 1337110 TRUE FALSE 731274.9335 602247.0326 700972.119 720763.2415 733172.0731 719729.8835 693163.8416 627768.765 1113937.703 0.656477406 0.54064696 0.629274076 0.647040889 0.658180499 0.646113227 0.622264459 0.563558234 1 20.08723712 -1.960664344 2.947750721 1.29286249 0.617513409 0.902401353 0.039217803 42443660.95 48749378.08 85658232.69 0.00962159 0.010948022 1.960664344 -0.675349081 STSGS(ph)PRPAGAKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STSGSPRPAGAKPK 14 2 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3-2 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 S(0.007)T(0.035)S(0.178)GS(0.779)PRPAGAKPK 88.992 0.0033008 328990000 991840 685220 809870 793210 975830 644370 1202500 865490 1102000 TRUE FALSE 929762.5049 735954.4018 829080.4988 813565.1115 899192.2481 830389.1585 1022196.288 973548.3317 918069.0808 1.012736976 0.801632924 0.903069841 0.886169819 0.979438549 0.904495289 1.113419796 1.060430366 1 19.80824319 1.760934367 12.68217243 1.064774842 0.901616844 0.531371174 0.062568916 0.200784267 112.4128117 0.028206786 0.015544796 57.66793062 -1.760934367 -0.163157998 STSHTSDFNPNSGSDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STSHTSDFNPNSGSDQR 17 0 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB06;F8VRK6 Q99700;F8WB06 ATXN2 Ataxin-2 0 97.933 0.0019525 44020000 17205 31557 29252 36199 36388 29030 38736 31297 29132 FALSE TRUE 16128.16976 33893.51312 29945.87125 37127.92762 33530.23326 37410.48974 32927.89641 35204.49934 24269.681 0.664539833 1.396537232 1.233879887 1.529806989 1.381568767 1.541449586 1.356750276 1.450554679 1 14.56686753 4.739572063 24.87530227 1.375934782 0.664539593 0.662507982 0.155981034 43.1111713 1060110.876 0.032526225 0.199387292 54899.9644 -4.739572063 -0.711395189 STSQGSINS(ph)PVYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STSQGSINSPVYSR 14 0 O14639-3;F8W8M4;O14639-5;O14639-2;O14639;J3QSX6;A0A0A0MRL6;A0A3B3IS55;O14639-4;O14639-6;A0A494C1P1;A0A494C1G0;H0Y7N6;F6XFR5 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 STSQGS(0.096)INS(0.904)PVYSR 285.9 1.10E-33 96249000 153980 153930 164770 151230 162690 135320 188400 147430 153070 TRUE FALSE 144342.6667 165327.1374 168678.4222 155110.8178 149912.9837 174384.6873 160151.169 165836.96 127521.6281 1.131907338 1.296463508 1.322743637 1.216349102 1.175588689 1.367491067 1.255874563 1.300461439 1 16.96038243 -1.501811074 2.824180238 0.989530702 1.267808898 0.56787583 0.070400424 10120378.75 11106776.5 823994.0179 0.016112683 0.031491179 1.501811074 0.278278196 STSSFPCPAGHFNGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STSSFPCPAGHFNGFR 16 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ; 182.1 2.20E-09 2183560000 944420 5298700 967460 949500 5352300 809170 1326720 4922400 1392150 FALSE TRUE 885310.438 5691021.261 990408.6081 973865.7775 4931951.948 1042764.243 1127790.653 5536972.476 1159791.171 0.763336073 4.906936181 0.853954257 0.839690628 4.25244826 0.899096552 0.972408379 4.774111592 1 20.14543363 STSTPTS(ph)PGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 STSTPTSPGPR 11 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;H3BRB0;A0A0C4DGL7 Q8WWM7 ATXN2L Ataxin-2-like protein 1 ST(0.005)S(0.027)T(0.051)PT(0.004)S(0.913)PGPR;STS(0.001)T(0.209)PT(0.008)S(0.783)PGPR;STST(0.015)PT(0.2)S(0.785)PGPR;STS(0.001)T(0.055)PT(0.004)S(0.94)PGPR;STST(0.006)PT(0.004)S(0.99)PGPR;STST(0.009)PT(0.005)S(0.985)PGPR;ST(0.001)ST(0.004)PT(0.152)S(0.843)PGPR 215.71 1.32E-11 16274750000 13065019 14053055 14336466 14972742 15996725 11787364 12553040 11212900 13644283 TRUE FALSE 12247302.78 15093557.81 14676533.74 15356967.91 14740406.75 15190184.63 10670828.19 12612855.25 11366964.02 1.077447132 1.32784425 1.291156875 1.351017552 1.296776054 1.336344921 0.93875798 1.109606331 1 23.43834364 1.748147192 11.37412505 1.020616404 1.290255849 0.671943443 0.086715078 0.055104486 41.37894261 0.036971058 0.020217387 55.99473485 -1.748147192 0.269639445 STSTSSPVRPAATFPPAT(ph)HCPLGGTLDGVYPTLMEPVLLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STSTSSPVRPAATFPPATHCPLGGTLDGVYPTLMEPVLLPK 41 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.104)T(0.104)S(0.104)T(0.104)S(0.093)S(0.093)PVRPAAT(0.026)FPPAT(0.186)HCPLGGT(0.186)LDGVYPTLMEPVLLPK 112.64 6.80E-06 47746000 83978 82828 82645 76604 86443 74063 125520 80748 69232 TRUE FALSE 78721.96689 88960.6713 84605.37843 78569.78833 79654.11547 95443.78579 106699.4413 90829.56555 57676.73194 1.364882583 1.542401386 1.466889256 1.362244109 1.381044189 1.654805717 1.849956433 1.574804301 1 15.8157018 2.233081594 24.94832877 1.620785257 1.442840934 0 0.228046836 264.388375 1203860.431 0.076476862 0.058106377 171.0336617 -2.233081594 -0.177944324 STT(ph)PGGTGIKPFLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STTPGGTGIKPFLER 15 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 S(0.004)T(0.004)T(0.991)PGGTGIKPFLER 104.88 0.0021969 161240000 762990 625160 723190 696200 772180 568740 960430 671720 1142300 TRUE FALSE 715235.8179 671447.4969 740344.4083 714065.6707 711536.0976 732926.0053 816422.4377 755585.7206 951642.7505 0.751580168 0.705566765 0.777964638 0.75035056 0.747692448 0.770169273 0.857908535 0.79398043 1 19.86006056 -0.041712315 0.297091114 1.072684366 0.718926967 0.883652703 0.028082852 1.762042608 0.23031468 0.17848313 0.034506829 0.908422088 0.041712315 -0.353757398 STT(ph)PPPAEPVSLPQEPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STTPPPAEPVSLPQEPPK 18 0 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.075)T(0.075)T(0.849)PPPAEPVSLPQEPPK 198.95 1.87E-14 142310000 266100 181810 198510 222310 232570 182140 295620 183050 259190 TRUE FALSE 249445.276 195271.4016 203218.7509 228014.851 214304.8903 234720.8612 251294.5254 205904.1954 215929.5146 1.155216213 0.904329369 0.941134663 1.055968895 0.992476136 1.087025373 1.163780347 0.953571335 1 17.72020093 2.721118898 1.664216646 1.071243088 0.976163414 0 0.089860412 0.646274789 3.576141788 0.034741423 0.033403712 526.1612952 -2.721118898 -0.095079674 STT(ph)PPPAEPVSLPQEPPKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 STTPPPAEPVSLPQEPPKPR 20 1 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.141)T(0.141)T(0.719)PPPAEPVSLPQEPPKPR;STT(1)PPPAEPVSLPQEPPKPR;S(0.004)T(0.005)T(0.992)PPPAEPVSLPQEPPKPR;ST(0.002)T(0.997)PPPAEPVSLPQEPPKPR;S(0.216)T(0.114)T(0.67)PPPAEPVSLPQEPPKPR;S(0.046)T(0.359)T(0.595)PPPAEPVSLPQEPPKPR;S(0.001)T(0.006)T(0.993)PPPAEPVSLPQEPPKPR 244.78 1.04E-29 31905900000 11643780 8100640 9676160 8917090 9185880 7928430 12103790 8176690 11545890 TRUE FALSE 10915016.59 8700419.814 9905683.085 9145917.626 8464458.039 10217239.03 10288939.06 9197567.746 9618806.37 1.134757908 0.904521775 1.029824565 0.950837066 0.87999048 1.062214857 1.069669007 0.956206767 1 23.19742645 STT(ph)PTSSPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STTPTSSPFR 10 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;H7C5N8;A0A2R8YET2;A0A2R8Y7F4;A0A2R8Y424 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.054)T(0.022)T(0.923)PT(0.001)SSPFR;S(0.001)T(0.004)T(0.977)PT(0.018)SSPFR 191.55 8.71E-06 1816290000 1933880 2577280 1860050 1743540 2847290 1494280 1914720 2313580 2113920 TRUE FALSE 1812841.903 2768104.493 1904171.264 1788282.188 2623675.329 1925654.378 1627625.511 2602435.556 1761093.096 1.029384481 1.571810428 1.081243955 1.015438759 1.489799339 1.093442694 0.924213215 1.477738776 1 20.74803974 4.225857498 0.08735427 0.832237077 1.691285851 0.026144366 0.233189529 156.6592584 2.612515474 7.220831382 20.44563643 16821.22027 -4.225857498 0.859048773 STTS(ph)VSEEDVSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 STTSVSEEDVSSR 13 0 Q96IZ0 Q96IZ0 PAWR PRKC apoptosis WT1 regulator protein 1 STT(0.008)S(0.991)VSEEDVSSR;STT(0.029)S(0.971)VSEEDVSSR;S(0.004)T(0.003)T(0.018)S(0.972)VS(0.003)EEDVSSR;STT(0.025)S(0.975)VSEEDVSSR 265.34 2.72E-24 1214316000 1282822 1399710 1301280 1415470 1413350 1022280 1545920 1339850 1361410 TRUE FALSE 1202532.461 1503345.985 1332146.976 1451793.357 1302351.192 1317395.641 1314123.648 1507133.222 1134181.876 1.060264219 1.325489339 1.174544405 1.280035757 1.148273676 1.161538258 1.158653365 1.328828518 1 20.11322058 2.710495584 24.75772137 1.168379014 1.223394596 0.045048758 0.103960766 1854.362682 1635834.827 0.030163917 0.028443955 513.4469564 -2.710495584 0.055015582 STTSVS(ph)EEDVSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STTSVSEEDVSSR 13 0 Q96IZ0 Q96IZ0 PAWR PRKC apoptosis WT1 regulator protein 1 STTS(0.001)VS(0.999)EEDVSSR 284.45 1.62E-23 0 111200 113070 117780 113890 118800 91055 125120 100640 106430 TRUE FALSE 104240.1905 121441.8204 120573.7972 116812.6102 109469.9272 117341.1003 106359.4176 113205.1255 88666.14544 1.175648157 1.369652643 1.35986285 1.317443198 1.234630497 1.323403648 1.199549355 1.276757042 1 16.43609574 -0.009881237 0.4213043 0.954648722 1.324587114 0.651833138 0.064590632 2.474116794 0.574906959 0.252684354 0.039330124 0.977504496 0.009881237 0.369938392 STTTGHLIYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 STTTGHLIYK 10 0 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5;P68104;A0A087WVQ9;Q5VTE0;A0A087WV01;A6PW80;Q5JR01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;;;; 87.258 0.012999 23351480000 20820600 24517000 24384600 23913300 26645900 19124500 29212000 22797300 26677100 FALSE TRUE 19517475.81 26332264.19 24963014.23 24526955.76 24553238.5 24645432.69 24831931.79 25643593.09 22224519.67 0.878195619 1.184829395 1.123219516 1.103598914 1.104781514 1.108929824 1.117321416 1.153842399 1 24.4056489 4.74805716 24.92461673 1.120410735 0.878195485 0.701584726 0.047658909 618.8556806 1624212.903 0.01022914 0.130996399 55983.12789 -4.74805716 -0.242215249 STVDAEAVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 STVDAEAVHK 10 0 P52701;P52701-3;A0A494C0M1;P52701-4;A0A087WYT6 P52701 MSH6 DNA mismatch repair protein Msh6 0 84.17 0.018575 0 112010 109050 120120 116790 140030 97338 147550 124320 151150 FALSE TRUE 104999.494 117124.1755 122969.3031 119787.0291 129032.6087 125437.9004 125426.2473 139841.6257 125922.0885 0.833844922 0.930132091 0.976550695 0.951278926 1.024701942 0.99615486 0.996062317 1.110540869 1 16.94217185 6.895468033 0.358567467 1.030376323 6.11E-18 0.725261212 0.036916072 14.94308439 0.438075641 0.028053122 9.130488203 7860823.29 -6.895468033 -1.030376323 STVDGLQVTQLNVDHTTENEDELFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STVDGLQVTQLNVDHTTENEDELFR 25 0 Q15750;Q15750-2 Q15750 TAB1 TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 0 ; 301.12 3.06E-63 148149000 98122 111097 110608 109717 115622 91373 123051 113322 115063 FALSE TRUE 91980.71917 119322.7375 113231.674 112532.524 106541.5145 117750.9018 104600.6449 127470.5012 95858.24196 0.959549406 1.244783287 1.181240879 1.173947296 1.111448659 1.228385785 1.091201369 1.329781337 1 16.54861486 STVLSLDWHPNNVLLAAGSCDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 STVLSLDWHPNNVLLAAGSCDFK 23 0 A0A1W2PNV4;E9PF58;Q92747;Q92747-2;C9JEY1;C9K057;O15143 A0A1W2PNV4;Q92747;C9JEY1 ARPC1A;ARPC1B Actin-related protein 2/3 complex subunit 1A;Actin-related protein 2/3 complex subunit 1B 0 ; 259.93 1.05E-43 398810000 1324880 1156310 1213430 1183940 1394950 904890 1586630 1183240 1255080 FALSE TRUE 1241958.126 1241924.396 1242213.133 1214321.905 1285396.254 1166117.053 1348729.561 1330970.119 1045599.04 1.187795779 1.187763519 1.188039665 1.161364786 1.229339551 1.115262169 1.289910864 1.272925919 1 19.99589829 STVPGHAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 STVPGHAGR 9 0 P00491;G3V5M2;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 ;;;;; 144.09 0.00010039 1824106000 2378671 4149250 2221332 2227614 4486130 2144375 2520187 3967780 2241124 FALSE TRUE 2229794.228 4456464.787 2274023.044 2284778.347 4133807.446 2763421.251 2142308.356 4463166.067 1867065.926 1.194277179 2.386881323 1.217966121 1.223726658 2.214066139 1.480087667 1.14741977 2.390470526 1 20.83234144 -1.37550648 3.939899828 0.997777039 1.641825061 0.144038291 0.502039847 38950454.55 14170438.66 740275.7054 0.109488895 0.0421205 1.37550648 0.644048023 STVTGERQS(ph)GDGQESTEPVENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 STVTGERQSGDGQESTEPVENK 22 1 O15234;J3KSY7 O15234 CASC3 Protein CASC3 1 STVTGERQS(1)GDGQESTEPVENK;STVTGERQS(0.999)GDGQES(0.001)TEPVENK;STVTGERQS(1)GDGQESTEPVENK 309.83 2.22E-67 2475410000 2072190 1499250 1814720 1725750 2090570 1320960 2034630 1541940 2801040 TRUE FALSE 1942495.327 1610256.03 1857766.015 1770035.667 1926385.065 1702299.708 1729556.12 1734454.603 2333528.329 0.832428432 0.69005206 0.796118904 0.758523325 0.825524611 0.729496054 0.741176398 0.743275572 1 21.15408155 -0.935546491 4.465626462 1.000003971 0.759431444 0.738752754 0.043903362 5104010.632 1142955.485 210.8430247 0.009412719 0.115998803 0.935546491 -0.240572527 SVAAEGALLPQT(ph)PPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVAAEGALLPQTPPSPR 17 0 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 2 SVAAEGALLPQT(1)PPS(1)PR;SVAAEGALLPQT(1)PPS(1)PR 171.79 8.93E-09 198821000 267240 265640 260020 270960 291520 233569 307170 220340 277120 TRUE FALSE 250513.9254 285308.262 266187.7972 277913.2923 268625.1951 300996.5786 261112.7101 247849.934 230866.8817 1.085101178 1.235812863 1.152992561 1.203781548 1.163550151 1.303766813 1.131009819 1.073562098 1 17.81670171 1.191976421 2.393800202 1.007650368 1.191793141 0.55194636 0.057757461 0.182896622 1.830010388 0.047777139 0.013483369 15.55881155 -1.191976421 0.184142774 SVAAEGALLPQTPPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SVAAEGALLPQTPPSPR 17 0 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 SVAAEGALLPQT(0.002)PPS(0.998)PR;SVAAEGALLPQT(0.026)PPS(0.974)PR;SVAAEGALLPQTPPS(1)PR;SVAAEGALLPQTPPS(1)PR;SVAAEGALLPQTPPS(1)PR;SVAAEGALLPQTPPS(1)PR 399.04 1.45E-122 1272022000 1770270 1892150 1931210 1908280 2029040 1761694 2091780 1690738 2188170 TRUE FALSE 1659471.961 2032246.755 1977019.213 1957249.696 1869687.383 2270266.459 1778137.008 1901830.361 1822950.291 0.910322113 1.114811942 1.08451625 1.073671457 1.025638161 1.245380343 0.975417167 1.043270555 1 20.79784379 1.609078909 25 1.007006249 1.081468928 0.130836596 0.083547407 0.224994539 4415.591774 0.037140864 0.019146415 40.65171841 -1.609078909 0.074462679 SVAHVTEADLFHTIETLMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVAHVTEADLFHTIETLMR 19 0 A5YKK6-3;A5YKK6-2;A5YKK6;H3BMZ2 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 264.38 1.44E-31 22386000 25851 47890 38971 47199 47178 39776 50985 46155 31288 FALSE TRUE 24233.03206 51435.82543 39895.41052 48410.20625 43472.83019 51258.68549 43340.27257 51917.55335 26065.83067 0.929685778 1.973304671 1.530563558 1.857228602 1.667809123 1.966508804 1.662723629 1.991785875 1 14.66987222 -1.644531294 7.656018318 0.998634761 1.718945689 0.326638954 0.31335901 0.006273601 0.000291283 0.260661631 0.061357678 0.022670897 1.644531294 0.720310928 SVAPLPPQRS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SVAPLPPQRSPR 12 1 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 1 SVAPLPPQRS(1)PR;SVAPLPPQRS(1)PR;SVAPLPPQRS(1)PR;SVAPLPPQRS(1)PR;SVAPLPPQRS(1)PR 135.47 7.70E-05 2055543000 1978863 2179796 2133617 2130915 2607527 1653578 2264740 2069310 2374690 TRUE FALSE 1855009.497 2341190.364 2184227.403 2185597.887 2402742.348 2130939.125 1925163.262 2327667.909 1978338.898 0.937660124 1.183412188 1.104071403 1.104764148 1.21452515 1.077135534 0.973121068 1.176576931 1 20.91585816 -0.931628809 4.649629661 0.999998939 1.098445713 0.106711702 0.087484724 9.23E-07 2.12E-07 0.081275962 0.019156722 0.117049939 0.931628809 0.098446774 SVASGGWQEPENPHTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVASGGWQEPENPHTQR 17 0 E5RGG1;H9KVE0;Q9UJW0-2;Q9UJW0;Q9UJW0-3 E5RGG1 DCTN4 Dynactin subunit 4 0 124.29 0.00042995 0 58607 68225 65501 60162 78586 63192 83260 55548 85199 FALSE TRUE 54938.89249 73276.44999 67054.71465 61705.85877 72414.17256 81434.50456 70775.93595 62483.29008 70978.73649 0.774019026 1.032371857 0.94471553 0.869356963 1.020223466 1.147308456 0.997142799 0.88030998 1 16.11509927 2.703600979 22.83320599 1.019376383 0.932925133 0.21142248 0.091831551 380.2035948 248321.2933 0.029063605 0.027403377 505.3601334 -2.703600979 -0.086451251 SVAVS(ph)DEEEVEEEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 391.59 1.79E-121 1745650000 475542 514589 496778 487505 507793 425374 594847 495549 673316 TRUE FALSE 445778.6751 552689.705 508561.8088 500015.2036 467912.9861 548172.5684 505655.2146 557419.3835 560935.2098 0.794706175 0.985300433 0.906631996 0.891395646 0.834165832 0.977247566 0.901450303 0.993732206 1 19.09747462 1.224009758 1.70731834 1.005372876 0.905482371 0.318064901 0.057597115 0.446133259 2.364209397 0.05000283 0.014835767 16.74980511 -1.224009758 -0.099890504 SVAVS(ph)DEEEVEEEAERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVAVSDEEEVEEEAERR 17 1 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 S(0.004)VAVS(0.996)DEEEVEEEAERR 74.776 0.0037708 0 25291 26179 27608 23857 31049 24664 26616 19086 28558 TRUE FALSE 23708.08146 28117.3204 28262.8748 24469.21101 28610.53679 31784.09641 22625.17789 21468.92911 23791.48531 0.996494382 1.181822826 1.187940746 1.028486061 1.20255362 1.335944183 0.950977949 0.90237868 1 14.53815772 1.6115825 9.693358756 0.942538507 1.159005671 0.501203275 0.09599648 0.072556508 20.11484709 0.046215027 0.023205164 40.88674147 -1.6115825 0.216467163 SVDEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVDEALR 7 0 P32119 P32119 PRDX2 Peroxiredoxin-2 0 ; 187.72 0.0013498 1892440000 3668400 4923800 3913300 3669000 5083800 3100700 4119700 4284000 4830400 FALSE TRUE 3438801.392 5288363.275 4006125.324 3763152.752 4684538.855 3995821.754 3501989.23 4818866.83 4024175.034 0.85453574 1.314148423 0.995514681 0.935136449 1.164099179 0.992954263 0.8702378 1.197479431 1 21.94026163 3.723282402 24.70833582 1.008866415 1.128469562 0.004440369 0.146951444 302.0290254 1943992.615 0.035758585 0.057765937 5287.88987 -3.723282402 0.119603147 SVDETLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SVDETLR 7 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5;Q13162;H7C3T4 Q06830;Q13162 PRDX1;PRDX4 Peroxiredoxin-1;Peroxiredoxin-4 0 ;;;;;;; 182.95 0.0015117 15857230000 12517180 14886610 13993970 14022000 14898770 12417680 15634440 12854040 16048360 FALSE TRUE 11733752.05 15988830.09 14325913.58 14381828.26 13728680.7 16002462.63 13290200.87 14458895.19 13369785.04 0.877632065 1.195892832 1.071514129 1.075696297 1.026843787 1.196912485 0.99404746 1.081460558 1 23.67247293 1.029224072 1.150824962 1.004747684 1.082851491 0.018125074 0.093605784 1.433425727 3.960257777 0.079288401 0.025190509 10.69606594 -1.029224072 0.078103807 SVDGPIRLPIVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVDGPIRLPIVDK 13 1 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 103.88 0.0014374 323000000 1139600 1104400 1077000 969080 1304100 851030 1311500 1124000 1512100 FALSE TRUE 1068274.47 1186170.925 1102546.949 993948.2334 1201681.246 1096708.546 1114852.75 1264333.874 1259720.741 0.848024832 0.94161419 0.875231242 0.789022678 0.953926697 0.870596561 0.884999916 1.003662028 1 20.26467252 1.239135723 24.79932565 1.001831074 0.884910264 0.547209977 0.045751559 10.00952596 431817.7008 0.033116836 0.010420882 17.3434592 -1.239135723 -0.11692081 SVDIS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVDISPTR 8 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 SVDIS(0.811)PT(0.188)R 64.82 0.069096 306010000 672460 779620 767320 728230 886450 696780 796990 731190 817310 TRUE FALSE 630371.929 837343.876 785521.1928 746917.6147 816831.7928 897929.0747 677488.7484 822480.681 680895.681 0.925798102 1.229768229 1.153658651 1.096963361 1.199643081 1.318746909 0.994996396 1.207939342 1 19.37707426 -0.969220144 6.057045868 0.999999916 1.147084463 0.128764114 0.114224002 1.17E-07 1.96E-08 0.099736202 0.023508035 0.107344514 0.969220144 0.147084546 SVDISLGDS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVDISLGDSPR 11 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 SVDISLGDS(1)PR;SVDIS(0.011)LGDS(0.989)PR 177.41 8.39E-06 438140000 484350 430810 465830 458070 514940 464340 558130 477890 507320 TRUE FALSE 454035.3981 462707.6207 476879.7076 469824.8517 474498.6896 598387.4201 474443.5879 537555.6185 422645.0146 1.074271274 1.094790201 1.128322093 1.111629939 1.122688481 1.415815636 1.122558108 1.271884442 1 18.68908691 2.446339522 24.99935793 1.217723859 1.106534595 0.165658902 0.105574318 285.6343544 231976.3611 0.031998205 0.026771838 279.4727846 -2.446339522 -0.111189264 SVDISLGDS(ph)PRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVDISLGDSPRR 12 1 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 SVDISLGDS(1)PRR 164.41 3.51E-05 305450000 210110 260850 241250 238330 250760 191610 260220 199690 335610 TRUE FALSE 196959.5902 280163.6054 246972.5639 244445.9513 231066.3211 246924.6965 221202.4268 224621.7361 279594.5229 0.704447241 1.002035385 0.883324041 0.874287339 0.826433647 0.883152838 0.791154363 0.803383892 1 18.09297657 3.042656904 2.84394787 0.845322552 0.896062245 0 0.093420683 0.818610869 13.49121689 0.026929003 0.032081589 1103.206733 -3.042656904 0.050739693 SVDLHPTEPWMLASLYNGSVCVWNHETQTLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVDLHPTEPWMLASLYNGSVCVWNHETQTLVK 32 0 P35606;D6R997 P35606 COPB2 Coatomer subunit beta 0 ; 307.94 3.54E-104 122904500 131473.8 171624 145846 143699 194027 146915 194214 167424 122230 FALSE TRUE 123245.0895 184331.2195 149305.536 147386.5596 178788.9021 189326.9755 165093.4137 188327.2549 101829.0234 1.21031397 1.810203157 1.466237533 1.44739245 1.755775477 1.859263393 1.621280537 1.849445755 1 16.63578929 2.737509892 24.82215814 1.672188435 1.535097971 0.018896677 0.283124323 274.215173 6477973.015 0.079722488 0.079161901 546.3989957 -2.737509892 -0.137090463 SVDVTNTTFLLMAASIYLHDQNPDAALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVDVTNTTFLLMAASIYLHDQNPDAALR 28 0 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 0 ; 281.66 8.36E-62 269320000 200595 224590 237090 236920 266490 217180 225050 213297 166940 FALSE TRUE 188040.117 241218.8773 242713.8868 242999.7683 245560.9504 279876.3404 191305.8418 239927.6 139076.6355 1.352061159 1.734431354 1.745180891 1.74723646 1.765652077 2.012389352 1.375542635 1.725146708 1 17.08552055 -0.921061107 11.56707081 1.000000027 1.688391327 0.554522807 0.192092187 0 0 0.173594382 0.040916588 0.119933054 0.921061107 0.688391301 SVEDEMDS(ph)PGEEPFYTGQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 SVEDEMDSPGEEPFYTGQGR 20 0 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;A0A590UJA3;S4R3W2;A0A590UK73;B1AKN7 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 1 SVEDEMDS(1)PGEEPFYTGQGR;SVEDEMDS(1)PGEEPFYTGQGR;SVEDEMDS(1)PGEEPFYTGQGR;SVEDEMDS(1)PGEEPFYTGQGR;SVEDEMDS(1)PGEEPFYTGQGR;SVEDEMDS(1)PGEEPFYTGQGR;SVEDEMDS(1)PGEEPFYTGQGR;SVEDEMDS(1)PGEEPFYTGQGR;SVEDEMDS(1)PGEEPFYTGQGR;SVEDEMDS(1)PGEEPFYTGQGR 425.24 1.37E-173 1403647000 2316970 2466550 2388400 2283888 2285530 2106276 2707398 2210010 2389962 TRUE FALSE 2171954.984 2649175.928 2445053.976 2342496.433 2106033.693 2714323.689 2301448.804 2485934.613 1991061.902 1.090852565 1.330534186 1.228015047 1.176506079 1.057743956 1.363254294 1.155890131 1.248547125 1 20.92510664 -1.493220154 2.9424196 0.993035284 1.216625963 0.311199087 0.095443124 28534459.92 34607803.14 1633491.546 0.021686225 0.032120319 1.493220154 0.223590679 SVEEEEQVWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SVEEEEQVWR 10 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;; 232.75 7.32E-10 2184120000 1478810 1701720 1528790 1647120 1652290 1335810 1816480 1479400 1405050 FALSE TRUE 1386253.922 1827717.119 1565053.621 1689387.888 1522525.808 1721436.662 1544115.687 1664106.347 1170538.078 1.184287763 1.561433288 1.337037769 1.443257524 1.300705921 1.470637047 1.319150326 1.421659302 1 20.15874044 -2.876290099 0.458911807 6.84E-10 1.396652649 0.558377078 0.105123143 108.2486828 4.091889081 106.3072714 0.048140322 0.001329566 2.876290099 1.396652648 SVEETLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SVEETLR 7 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 ;; 173.59 0.0019951 1007490000 1090710 1199620 1079300 1050180 1532440 1097910 1021820 1222970 1824060 FALSE TRUE 1022444.408 1288441.113 1104901.506 1077129.397 1412088.344 1414858.794 868607.5771 1375660.497 1519612.602 0.672832278 0.847874722 0.727094198 0.708818415 0.929242323 0.931065452 0.571598035 0.905270524 1 20.53527215 1.00588757 24.99371516 1.000000073 0.772335504 0.335506329 0.111454395 130.4047429 553586.4611 0.102755759 0.02568894 10.13648939 -1.00588757 -0.227664569 SVEGWILFVTGVHEEATEEDIHDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SVEGWILFVTGVHEEATEEDIHDK 24 0 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ;;; 302.42 1.52E-62 334973000 457351 339750 393233 387216 375740 340667 448959 343148 376808 FALSE TRUE 428726.2173 364905.4435 402560.6725 397152.6181 346230.8961 439012.0326 381641.7659 385990.7832 313916.3105 1.365734124 1.162429066 1.282382148 1.265154453 1.102940129 1.398500231 1.215743665 1.229597731 1 18.26002047 0.550982432 2.072224496 1.000039667 1.249698186 0.460179266 0.086365646 3.096799691 13.26430211 0.073103543 0.020015868 3.556169326 -0.550982432 0.249658518 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIK 32 1 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 236.34 8.45E-47 84479000 52444 42615 38416 43179 56636 30183 56679 43823 76801 FALSE TRUE 49161.62366 45770.25894 39327.24566 44287.04624 52188.03702 38896.34212 48180.51013 49294.39802 63982.41695 0.768361466 0.71535683 0.614657081 0.692175262 0.81566217 0.607922363 0.753027354 0.770436635 1 15.96538787 0.677292877 1.278848369 0.9997935 0.697262228 0.67445368 0.063252034 0.604466311 1.567886732 0.057087692 0.01719127 4.756558876 -0.677292877 -0.302531272 SVEMHHEALSEALPGDNVGFNVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 244.74 1.05E-37 573690000 667447 713830 765280 827560 672850 566207 944230 541254 547106 FALSE TRUE 625672.6837 766682.7159 783432.803 848796.5907 620007.0751 729661.7693 802651.4773 608830.7533 455790.4742 1.372719965 1.682094645 1.718844178 1.862251712 1.360289673 1.600871038 1.761009768 1.335768929 1 18.79801125 0.994302728 4.211517876 1.001187736 1.640429289 0.624723941 0.158052648 0.105439419 5.486039493 0.143139601 0.03652423 9.869672187 -0.994302728 0.639241553 SVESTS(ph)PEPSK ddPTM_SK-BR-3_Pertuzumab_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(0.017)S(0.983)PEPSK;SVEST(0.124)S(0.876)PEPSK;SVEST(0.257)S(0.742)PEPSK;SVES(0.001)T(0.021)S(0.978)PEPSK;SVEST(0.011)S(0.989)PEPSK;SVEST(0.032)S(0.968)PEPSK 336.8 1.08E-57 5848600000 10645940 8141410 9199130 8273560 8994400 7175990 11276000 8016780 11186770 TRUE FALSE 9979629.619 8744208.468 9417337.708 8485873.557 8288016.106 9247581.821 9585268.481 9017692.63 9319625.818 1.070818702 0.938257462 1.010484529 0.910538011 0.889307819 0.992269647 1.028503576 0.967602435 1 23.1518406 2.016263873 24.99952311 1.003998479 0.962356711 0.088357199 0.052306301 496.4238877 763060.0523 0.018909344 0.01396196 103.8159 -2.016263873 -0.041641768 SVFALTNGIYPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVFALTNGIYPHK 13 0 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ; 186.51 7.75E-06 3648000000 2825710 2982000 3115600 3060300 3341200 2121700 3447900 2925910 3940200 FALSE TRUE 2648853.855 3202790.383 3189503.503 3138832.479 3078795.63 2734200.347 2930919.404 3291216.304 3282555.165 0.806948771 0.975700398 0.971652674 0.956216216 0.937926546 0.832948788 0.892877425 1.002638536 1 21.64638783 1.226923127 24.85683756 1.001319361 0.920242306 0.298645786 0.056306093 342.8300708 732235.5585 0.054244573 0.014026766 16.86254521 -1.226923127 -0.081077055 SVFGT(ph)PTLETANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVFGTPTLETANK 13 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 SVFGT(1)PTLETANK;SVFGT(1)PTLETANK 194.13 1.00E-06 0 1156060 954510 1143150 1090620 1213130 956910 1519080 1017030 1471800 TRUE FALSE 1083704.268 1025182.914 1170266.058 1118607.156 1117855.663 1233154.383 1291308.056 1144008.434 1226147.072 0.883828941 0.836101098 0.954425521 0.912294439 0.91168155 1.005714903 1.053142878 0.933010779 1 20.2257006 2.98035677 0.659378142 1.011504629 0.859184549 0.565363789 0.041924024 0.533511318 0.510385575 0.029856669 0.040815406 955.777429 -2.98035677 -0.15232008 SVFKPIVQIAVIENSESLDCQLLAVTHAGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SVFKPIVQIAVIENSESLDCQLLAVTHAGVR 31 1 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ;; 295.11 1.53E-81 613002000 820305 877336 902287 880086 970331 729727 1109198 926648 821696 FALSE TRUE 768963.5743 942294.8703 923689.6737 902670.4967 894125.1174 940387.3388 942884.0572 1042342.043 684549.6292 1.123313112 1.376517976 1.349339236 1.318634118 1.306150904 1.373731427 1.377378669 1.522668333 1 19.38479561 -1.017366467 5.119021812 0.999996757 1.34860005 0.548932075 0.097748891 3.28E-06 6.30E-07 0.08556943 0.02016872 0.096080119 1.017366467 0.348603293 SVFPEQANNNEWAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SVFPEQANNNEWAR 14 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;; 227.48 4.68E-12 334443000 155733 153007 156800 153388 165237 135031 192216 131610 186420 FALSE TRUE 145985.9495 164335.7975 160519.37 157324.1958 152259.9526 174012.2577 163394.9952 148041.7982 155305.2977 0.939993366 1.05814676 1.033573049 1.012999544 0.980391235 1.120452813 1.052088999 0.953230833 1 17.24474752 SVGDES(ph)WEQTQEGDVGALYHEQLALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SVGDESWEQTQEGDVGALYHEQLALK 26 0 O75691 O75691 UTP20 Small subunit processome component 20 homolog 1 SVGDES(1)WEQTQEGDVGALYHEQLALK;SVGDES(1)WEQTQEGDVGALYHEQLALK;SVGDES(1)WEQTQEGDVGALYHEQLALK 316.67 3.86E-82 324899000 292284 250170 246975 252699 219242 167356 343918 227319 212090 TRUE FALSE 273990.4662 268692.8471 252833.3636 259183.6842 202023.6177 215668.9604 292350.6887 255700.2775 176690.8088 1.550677525 1.520695099 1.430936704 1.466877003 1.143373665 1.220600901 1.654589113 1.447162301 1 17.43086747 -1.855972043 2.659961472 0.819074131 1.437146033 0.447933501 0.149580209 13900785.76 8900733.117 15931409.46 0.037579991 0.013932465 1.855972043 0.618071902 SVGGDS(ph)DTEDMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVGGDSDTEDMR 12 0 Q9UK61-3;Q9UK61;Q9UK61-2;A0A087X0F1;Q9UK61-4 Q9UK61-3 FAM208A Protein FAM208A 1 SVGGDS(1)DTEDMR 209.19 0.00010982 0 75296 83125 84975 79697 82802 72028 104270 84673 98223 TRUE FALSE 70583.35777 89279.66149 86990.64713 81742.15995 76299.06493 92821.31432 88635.6815 95244.61044 81828.94676 0.862571994 1.091052311 1.06307915 0.998939412 0.932421447 1.134333485 1.08318248 1.163947652 1 16.32032366 2.216845056 24.99524709 1.101393849 1.013887549 0.288216926 0.07727381 350.12612 403002.9671 0.027950684 0.020660077 164.7574477 -2.216845056 -0.0875063 SVGGSGGGS(ph)FGDNLVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVGGSGGGSFGDNLVTR 17 0 P02545;P02545-3;P02545-5;P02545-4;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 S(0.001)VGGS(0.008)GGGS(0.992)FGDNLVTR;S(0.001)VGGS(0.052)GGGS(0.947)FGDNLVTR 204.6 9.06E-12 687940000 1041300 825890 883820 873520 1113470 716140 1040440 787730 1514280 TRUE FALSE 976126.8918 887039.7549 904784.6278 895936.0021 1026022.558 922877.9924 884435.681 886079.8245 1261536.885 0.773760088 0.703142148 0.717208223 0.71019406 0.81331158 0.731550542 0.70107794 0.702381226 1 20.26675096 -1.231357655 4.502341443 1.000094312 0.72756819 0.843670741 0.036275821 3.33E-05 5.69E-06 0.034088284 0.008031913 0.058700574 1.231357655 -0.272526122 SVGQYDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVGQYDNR 8 0 P13861-2;P13861;H7C1L0 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 0 103.74 0.010969 248560000 239900 375540 231620 259620 344600 226460 269440 290810 362830 FALSE TRUE 224885.0872 403345.3723 237114.1358 266282.2887 317536.506 291835.3257 229039.9734 327118.2687 302271.329 0.743984181 1.33438184 0.784441371 0.880937963 1.050501571 0.965474717 0.757729733 1.082200782 1 18.20548462 3.895494279 10.89096449 0.917030825 1.078486947 0.046377709 0.17510672 0.903960386 116.2387319 0.040767991 0.073556072 7861.298362 -3.895494279 0.161456121 SVGRPS(ph)PLASGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVGRPSPLASGR 12 1 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 SVGRPS(0.997)PLAS(0.003)GR;S(0.003)VGRPS(0.988)PLAS(0.009)GR 83.252 0.0078148 1013330000 272553 265167 266077 271670 318923 232235 351386 251578 391770 TRUE FALSE 255494.3943 284800.2406 272388.4721 278641.5121 293876.0741 299277.4745 298698.9314 282988.0671 326381.0561 0.782810122 0.872600402 0.834571943 0.853730653 0.900407878 0.916957246 0.915184646 0.867048077 1 18.3161978 -4.004268248 0.020788376 2.085198128 2.86E-13 0.751379545 0.028683001 1190.914999 2.211826099 144.1978011 84.75006029 9.90E-05 4.004268248 -2.085198128 SVHELEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SVHELEK 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;; 150.17 0.0019672 13817930000 14881890 21091130 19688480 20310460 21700610 15954490 24119400 18874580 22728330 FALSE TRUE 13950459.07 22652739.21 20155500.04 20831660.79 19996331.63 20560292.26 20502919.88 21231112.86 18934824.89 0.73676198 1.196353245 1.0644672 1.100177103 1.05606108 1.085845387 1.082815394 1.121273261 1 24.17453874 4.748790228 24.99754861 1.094092084 0.736761783 0.829053551 0.050117289 547.7178722 1338402.179 0.011168259 0.157968584 56077.70453 -4.748790228 -0.357330301 SVHIS(ph)TPEKEPCAPLTIPSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVHISTPEKEPCAPLTIPSIR 21 1 E9PHV5;P28290-3;P28290;P28290-2 E9PHV5 SSFA2 Sperm-specific antigen 2 1 SVHIS(0.587)T(0.413)PEKEPCAPLTIPSIR 115.88 8.65E-05 53940000 51869 91696 94664 87556 97956 83242 113470 83842 110650 TRUE FALSE 48622.61188 98485.26725 96909.47478 89802.83519 90262.9309 107272.6141 96456.2269 94309.85826 92181.80017 0.527464334 1.06838082 1.051286421 0.974192683 0.97918386 1.163707086 1.04636953 1.023085447 1 16.49219432 4.740144103 24.99075512 1.044826461 0.527464163 0.897283155 0.054274707 39.77147281 627622.0087 0.01263027 0.080512711 54972.32471 -4.740144103 -0.517362298 SVICDIS(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVICDISPLR 10 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 SVICDIS(1)PLR;SVICDIS(1)PLR 105.03 0.0027304 164816000 242390 247970 258830 234600 258270 229870 296330 214346 266780 TRUE FALSE 227219.2426 266329.9568 264969.5698 240620.2332 237986.516 296229.7374 251898.0675 241107.5699 222252.6945 1.022346402 1.198320485 1.192199583 1.082642591 1.070792489 1.33285105 1.133385888 1.084835306 1 17.76184138 1.023764218 2.823427512 1.002051747 1.160143536 0.231418066 0.085531974 0.314461306 5.642898775 0.076496117 0.0203783 10.5624391 -1.023764218 0.158091789 SVIDLRPEDVVHESGS(ph)LGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SVIDLRPEDVVHESGSLGDR 20 1 Q96C24-2;Q96C24 Q96C24-2 SYTL4 Synaptotagmin-like protein 4 1 SVIDLRPEDVVHES(0.349)GS(0.651)LGDR;SVIDLRPEDVVHES(0.101)GS(0.899)LGDR;SVIDLRPEDVVHES(0.313)GS(0.687)LGDR;SVIDLRPEDVVHES(0.121)GS(0.879)LGDR 138.78 7.14E-07 1383800000 1067355 1970300 1727050 1718490 2072310 1559180 2163520 1960990 2070590 TRUE FALSE 1000551.156 2116183.062 1768016.442 1762589.363 1909559.132 2009289.955 1839120.261 2205823.918 1724995.152 0.580031286 1.226776237 1.024939948 1.021793806 1.106993912 1.164809044 1.066159669 1.278742097 1 20.71816088 4.746344892 24.99343406 1.110012263 0.58003103 0.771820889 0.090775025 431.7584389 1386239.969 0.019849639 0.217335528 55762.84104 -4.746344892 -0.529981234 SVIDLRPEDVVHESGSLGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVIDLRPEDVVHESGSLGDR 20 1 Q96C24-2;Q96C24 Q96C24-2 SYTL4 Synaptotagmin-like protein 4 0 60.602 0.034355 53428000 49129 130860 104670 115010 132250 98599 136660 120510 134820 FALSE TRUE 46054.10359 140549.0106 107152.8218 117961.3513 121863.6185 127062.9307 116169.1017 135555.9388 112317.671 0.410034353 1.251352608 0.954015702 1.050247483 1.084990611 1.131281743 1.034290514 1.206897699 1 16.7772254 4.74724305 24.99023083 1.085937307 0.410034009 0.849201636 0.089926129 394.0461514 1134139.375 0.019841705 0.236341516 55878.28268 -4.74724305 -0.675903297 SVIEDVINDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVIEDVINDVR 11 0 J3KNC0;P52655 J3KNC0 GTF2A1 Transcription initiation factor IIA subunit 1;Transcription initiation factor IIA alpha chain;Transcription initiation factor IIA beta chain 0 ; 128.81 0.00060034 17887200 35089 55126 37295 37232 58076 31251 45479 52958 55965 FALSE TRUE 32892.84213 59207.5864 38179.65501 38187.43615 53514.94523 40272.65638 38659.84616 59569.92287 46624.07995 0.705490428 1.269892863 0.818882754 0.819049645 1.147796274 0.86377375 0.829181963 1.277664309 1 15.50878764 1.24322415 24.99998951 1.13883215 0.941712798 0.193543305 0.180552719 186.4063781 999319.0692 0.122915488 0.041615984 17.5075006 -1.24322415 -0.197119353 SVISHSVTSDMQTIEQES(ph)PIMAKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVISHSVTSDMQTIEQESPIMAKPR 25 1 Q9NP61;Q9NP61-2;H0Y6A0 Q9NP61;H0Y6A0 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 1 SVISHSVTSDMQT(0.007)IEQES(0.993)PIMAKPR 97.408 0.0050945 293990000 28610 78959 59382 63844 62648 79633 59227 62552 47984 TRUE FALSE 26819.35117 84805.20652 60790.56908 65482.34513 57727.87879 102621.7544 50346.46119 70361.75489 39975.16041 0.670900402 2.12144756 1.520708571 1.638075856 1.444093737 2.567138025 1.259443631 1.760136899 1 15.2868162 -0.268129817 1.289834665 0.996131367 1.667175864 0.126732416 0.500795684 73.09148205 69.93974308 1.974804172 0.125479094 0.539349379 0.268129817 0.671044498 SVKEDSVPTGAEENVVCES(ph)PVEIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SVKEDSVPTGAEENVVCESPVEIIK 25 1 O75363 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 SVKEDSVPTGAEENVVCES(1)PVEIIK;SVKEDSVPTGAEENVVCES(1)PVEIIK;SVKEDSVPTGAEENVVCES(1)PVEIIK;SVKEDSVPTGAEENVVCES(1)PVEIIK 210.68 1.03E-25 620630000 879360 712350 710160 909890 1230090 618390 1007400 640350 1732360 TRUE FALSE 824322.4273 765093.1352 727005.3306 933239.3178 1133483.693 796909.1543 856349.7222 720299.1071 1443217.925 0.571169754 0.530130012 0.503739122 0.646637838 0.785386374 0.552175206 0.59336134 0.499092407 1 20.46085773 -1.829846677 2.735541392 1.143702617 0.580288164 0.70969004 0.083320196 22299009.11 15899819.15 21077445.61 0.020901227 0.014796307 1.829846677 -0.563414453 SVLLLAYKPMEGNFEEIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVLLLAYKPMEGNFEEIAR 19 1 Q16531;F5GY55;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ; 207.07 3.05E-16 704120000 1170060 1150500 1180570 1051000 1266130 881890 1393460 1193620 1399860 FALSE TRUE 1096828.033 1235684.217 1208573.678 1077970.439 1166693.257 1136477.327 1184523.609 1342646.084 1166214.323 0.940502969 1.05956872 1.036322102 0.924333048 1.000410675 0.97450126 1.015699761 1.151285882 1 20.15340152 1.435125949 14.63490838 1.0782877 1.000655119 0.283534236 0.054086442 1.722962871 598.5247472 0.030194247 0.012834821 27.23491031 -1.435125949 -0.077632581 SVLNSITEEVLDHMGTFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVLNSITEEVLDHMGTFR 18 0 Q13416 Q13416 ORC2 Origin recognition complex subunit 2 0 184.8 5.64E-14 60806000 33117 36761 34745 42027 38210 36615 34463 30369 26137 FALSE TRUE 31044.26609 39482.82269 35569.16781 43105.48397 35209.14073 47185.15611 29295.59309 34160.6365 21774.56585 1.425712288 1.813254187 1.633519036 1.979625416 1.616984742 2.166984932 1.345404234 1.568832037 1 14.41035633 0.926921921 1.206949763 1.014671807 1.750279711 0.489048376 0.234200087 0.42653228 1.254418091 0.195309592 0.06059611 8.451268922 -0.926921921 0.735607903 SVLSEGHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVLSEGHQR 9 0 O76071 O76071 CIAO1 Probable cytosolic iron-sulfur protein assembly protein CIAO1 0 ; 110.88 0.0022149 217611000 676100 795180 913960 914340 1000410 891590 974240 836950 965220 FALSE TRUE 633784.1079 854055.9546 935639.5628 937803.5124 921841.8341 1148977.559 828161.7564 941445.0499 804118.5464 0.788172479 1.062102047 1.163559238 1.16625032 1.146400413 1.428865886 1.029900081 1.170778928 1 19.61704868 5.250373704 1.138657775 1.167494055 0.051711492 0.508512574 0.113760835 3.473501217 1.678576131 0.029724066 6.131847513 177981.0253 -5.250373704 -1.115782563 SVMEELKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVMEELKR 8 1 P61326;Q96A72;F5H6N1;F5H6P7;F5H3U9 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ; 128.36 0.0018228 1046870000 1126950 1066130 1021920 1047290 1299200 745333 1242220 1066030 1341880 FALSE TRUE 1056416.211 1145067.375 1046160.425 1074165.234 1197166.073 960498.5376 1055960.643 1199126.192 1117911.559 0.944990865 1.02429156 0.935816806 0.960867813 1.070895155 0.859190094 0.944583348 1.072648531 1 20.09237463 1.246944539 24.9775587 1.036324273 0.96373922 0.216886029 0.057950906 245.7177956 732063.3597 0.038272083 0.013444573 17.65812307 -1.246944539 -0.072585053 SVNEILGLAESS(ph)PNEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SVNEILGLAESSPNEPK 17 0 Q9H8G2;Q9H8G2-2 Q9H8G2 CAAP1 Caspase activity and apoptosis inhibitor 1 1 SVNEILGLAES(0.144)S(0.856)PNEPK;SVNEILGLAES(0.039)S(0.961)PNEPK;SVNEILGLAESS(1)PNEPK;SVNEILGLAESS(1)PNEPK;SVNEILGLAES(0.002)S(0.998)PNEPK 297.87 3.40E-46 448193000 1364085 944144 1067999 1046491 1156884 815011 1312175 882301 1277741 TRUE FALSE 1278709.355 1014049.404 1093332.441 1073345.731 1066026.997 1050291.445 1115426.54 992458.222 1064477.773 1.201255102 0.952626189 1.027106877 1.008330806 1.001455385 0.98667297 1.047862688 0.932342833 1 20.02171439 4.746668815 24.99082201 0.998977018 1.201255201 0.790635578 0.033359468 434.8928257 1340382.071 0.007334274 0.081364855 55804.44778 -4.746668815 0.202278183 SVNELIYKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVNELIYKR 9 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 121.9 0.00096357 777220000 968740 1382470 1113050 1221240 1608360 893930 1420670 1109610 2357000 FALSE TRUE 908108.2927 1484829.517 1139452.072 1252579.086 1482045.893 1151993.079 1207653.722 1248147.251 1963601.473 0.462470774 0.756176616 0.580286829 0.637898832 0.754759005 0.586673566 0.615019768 0.635641839 1 20.90507072 -1.747691348 2.404214949 1.089941369 0.636288593 0.65378614 0.084770432 5792969.269 3934497.236 3090986.621 0.019633486 0.017877577 1.747691348 -0.453652776 SVNESLNNLFITEEDYQALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVNESLNNLFITEEDYQALR 20 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 393.38 1.05E-130 70388000 53113 68778 65279 73949 79425 62343 84071 68826 79611 FALSE TRUE 49788.75214 73870.39468 66827.44871 75846.65654 73187.28089 80340.41205 71465.33403 77419.0776 66323.40979 0.750696508 1.113790665 1.007599714 1.143588015 1.103490926 1.211343209 1.077528044 1.167296402 1 16.01723056 4.73969631 24.73735602 1.102417807 0.750696377 0.743894993 0.064977633 40.74395578 887345.4797 0.01458594 0.089736046 54915.67295 -4.73969631 -0.35172143 SVPGTTSSPLVGDIS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SVPGTTSSPLVGDISPK 17 0 Q9UQR0;H0Y6S1;B4DRC2;Q9UQR0-2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 1 SVPGTTSSPLVGDIS(1)PK;SVPGTTSSPLVGDIS(1)PK;SVPGTTSSPLVGDIS(1)PK;SVPGTTSSPLVGDIS(1)PK 276.67 9.66E-36 382137000 449410 274894 333614 313353 325922 242500 365981 244258 377538 TRUE FALSE 421282.2303 295247.4378 341527.4816 321394.1685 300325.4008 312505.8133 311105.5467 274754.149 314524.4688 1.339425934 0.938710552 1.085853457 1.021841543 0.954855442 0.993581881 0.989129869 0.873554131 1 18.26281273 4.743679582 24.87770658 0.989631073 1.33942609 0.803143646 0.055473462 222.4744942 1081169.312 0.012862287 0.108148512 55421.66673 -4.743679582 0.349795016 SVPSIAAATGTHS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVPSIAAATGTHSR 14 0 Q8IY63-2;Q8IY63 Q8IY63-2 AMOTL1 Angiomotin-like protein 1 1 SVPSIAAATGT(0.014)HS(0.986)R 124.91 6.08E-05 137720000 75018 126250 96177 98992 123000 97451 117180 87381 116220 TRUE FALSE 70322.75729 135597.6814 98458.36386 101532.3023 113340.0762 125583.5217 99609.94685 98290.7102 96822.13119 0.726308711 1.400482304 1.016899366 1.04864767 1.170600923 1.297053888 1.028793166 1.015167803 1 16.56304923 1.573342991 11.2620074 1.013888501 1.134823807 0.048694539 0.178455609 0.28278609 67.4846881 0.087846312 0.04105354 37.44061651 -1.573342991 0.120935306 SVPTWLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVPTWLK 7 0 P62277;J3KMX5;E9PS50 P62277 RPS13 40S ribosomal protein S13 0 ; 116.54 0.012638 398420000 880820 1243230 917990 881310 1389540 739890 1025200 1112490 1259270 FALSE TRUE 825691.0485 1335280.043 939765.1563 903925.9067 1280411.134 953484.2319 871480.7775 1251386.825 1049089.702 0.787054765 1.272798733 0.895791041 0.861628806 1.220497286 0.908868165 0.83070187 1.192831102 1 20.00070661 3.753052982 24.37680322 0.97127452 1.07052443 0 0.174696425 899.9936742 846020.8297 0.041573213 0.074910691 5663.083718 -3.753052982 0.099249911 SVPVNNLPERS(ph)PTDS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVPVNNLPERSPTDSPR 17 1 P49454 P49454 CENPF Centromere protein F 2 SVPVNNLPERS(0.958)PT(0.05)DS(0.993)PR 83.245 0.0017415 0 116200 127130 132170 141650 142930 129280 147080 132370 151480 TRUE FALSE 108927.2494 136542.8375 135305.1348 145284.9788 131704.8544 166601.0373 125026.7194 148896.6859 126197.0094 0.863152383 1.081981563 1.072173861 1.151255323 1.043644814 1.320166287 0.990726484 1.179874916 1 16.9453182 5.411040753 1.321194517 1.110704683 3.22E-16 0.381330328 0.096503914 6.739968074 2.869583799 0.023067239 15.56572163 257656.2926 -5.411040753 -1.110704683 SVPVTVDDDDDDNDPENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVPVTVDDDDDDNDPENR 18 0 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;P46100-3;A0A096LP59 P46100;P46100-3;A0A096LP59 ATRX Transcriptional regulator ATRX 0 260.08 2.34E-30 126750000 36370 47616 46435 39436 51379 43626 51453 36867 62252 FALSE TRUE 34093.66662 51141.53818 47536.46013 40447.99452 47343.90059 56220.11799 43738.10032 41469.9261 51861.73904 0.65739536 0.98611306 0.91659981 0.77991975 0.912886869 1.084038427 0.843359693 0.799624673 1 15.66238296 2.496496316 24.71391391 0.92677575 0.871051458 0.103877072 0.116660341 2314.297485 2952009.211 0.037283524 0.034666914 313.6868519 -2.496496316 -0.055724292 SVPVTVDDDDDDNDPENRYDSICK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVPVTVDDDDDDNDPENRYDSICK 24 1 A0A096LP59 A0A096LP59 ATRX 0 99.407 0.0044222 75182000 20305 17801 20427 22740 18276 14832 29215 17213 28593 FALSE TRUE 19034.1463 19119.00456 20911.53809 23323.5469 16840.67668 19113.75762 24834.48197 19362.08094 23820.64358 0.799060959 0.802623342 0.877874605 0.979131685 0.70697824 0.802403073 1.042561335 0.812827784 1 14.53992477 -4.999997629 0.041890316 1.699840738 0.469645638 0.215649902 0.094574022 1133.89711 3.542597275 96.14678149 27.36075826 1.00E-05 4.999997629 -1.230195101 SVQNHNNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SVQNHNNK 8 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 82.529 0.020036 583240000 563350 555220 677370 613810 638440 452650 703550 612790 685200 FALSE TRUE 528090.9291 596329.0665 693437.5363 629561.4038 588299.4977 583322.7068 598059.2089 689298.1804 570835.6934 0.925118971 1.044659739 1.214776063 1.102876731 1.030593399 1.02187497 1.047690633 1.207524667 1 19.12271602 -0.922327496 4.661300066 0.999999252 1.079143391 0.066065846 0.086268276 6.64E-07 1.54E-07 0.08254808 0.019456585 0.119583842 0.922327496 0.079144139 SVRPIHSST(ph)S(ph)SPTISIHEVGHTGVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVRPIHSSTSSPTISIHEVGHTGVTK 26 1 P46019 P46019 PHKA2 "Phosphorylase b kinase regulatory subunit alpha, liver isoform" 2 S(0.192)VRPIHS(0.28)S(0.304)T(0.325)S(0.486)S(0.363)PT(0.05)ISIHEVGHTGVTK 87.25 0.01974 178720000 24681 54048 41387 51078 44181 39647 57258 41824 53596 TRUE FALSE 23136.26027 58049.77016 42368.71918 52388.74795 40711.20248 51092.44528 48672.69446 47045.81847 44650.48136 0.518163737 1.300092819 0.948897255 1.173307574 0.91177522 1.144275352 1.090082189 1.053646389 1 15.44638811 4.752584806 24.99989246 1.083523794 0.518163359 0.708908991 0.112638964 1273.259833 2269707.864 0.024287881 0.513867072 56569.82114 -4.752584806 -0.565360435 SVRPIHSSTS(ph)S(ph)PTISIHEVGHTGVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVRPIHSSTSSPTISIHEVGHTGVTK 26 1 P46019 P46019 PHKA2 "Phosphorylase b kinase regulatory subunit alpha, liver isoform" 2 S(0.025)VRPIHS(0.041)S(0.181)T(0.426)S(0.485)S(0.735)PT(0.107)ISIHEVGHTGVTK 127.64 4.72E-05 163240000 48808 104780 103290 100760 101930 99671 131700 108000 116920 TRUE FALSE 45753.1944 112538.0202 105740.0876 103345.6722 93924.82897 128444.3997 111952.8076 121484.0377 97405.29667 0.469719779 1.155358323 1.085568149 1.060986165 0.964268188 1.318659293 1.149350307 1.247201558 1 16.5717126 4.73995067 24.9301954 1.129065189 0.469719556 0.788858286 0.106117111 49.98696914 896407.3302 0.024042062 0.151469286 54947.84573 -4.73995067 -0.659345633 SVRPTDSNVS(ph)PAISIHEIGAVGATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVRPTDSNVSPAISIHEIGAVGATK 25 1 A6NIT2;A6NMN0;P46020-3;P46020-2;P46020 A6NIT2 PHKA1 "Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform" 1 S(0.235)VRPT(0.145)DS(0.036)NVS(0.584)PAISIHEIGAVGATK;S(0.001)VRPT(0.001)DS(0.002)NVS(0.996)PAISIHEIGAVGATK 229.25 2.17E-34 451970000 516430 703770 759050 788920 872340 675050 988500 868730 997670 TRUE FALSE 484107.5682 755877.8631 777055.0244 809165.0228 803829.9353 869925.9765 840283.6018 977192.8528 831152.4318 0.58245341 0.909433498 0.934912773 0.973545877 0.967126973 1.046650341 1.010986156 1.175708348 1 19.66475356 5.299567573 0.720266329 1.028873141 1.39E-37 0.800390457 0.067269128 2.558345135 0.565779304 0.023608855 2.569194662 199327.6622 -5.299567573 -1.028873141 SVS(ph)ANPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.004)VS(0.996)ANPK;S(0.001)VS(0.999)ANPK;S(0.003)VS(0.997)ANPK;S(0.001)VS(0.999)ANPK;S(0.001)VS(0.999)ANPK;SVS(1)ANPK 90.263 0.018113 2741380000 6118160 5902110 4814120 5218370 7470570 2372750 8502430 4638220 11156730 TRUE FALSE 5735235.287 6339108.366 4928313.2 5352282.209 6883861.567 3057724.407 7227569.554 5217311.977 9294599.688 0.617050274 0.68202059 0.530234046 0.575848599 0.740630237 0.328978601 0.777609558 0.561327239 1 23.1479613 -0.474594051 0.816756124 1.022505501 0.602183613 0.500966307 0.124539583 13.92365539 6.372723587 1.100749302 0.036147491 0.335278689 0.474594051 -0.420321888 SVS(ph)CDNVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSCDNVSK 9 0 Q96CB8;A0A087WXN4 Q96CB8 INTS12 Integrator complex subunit 12 1 SVS(1)CDNVSK 138.45 0.00014295 189930000 223170 169160 169520 177250 184770 134770 276280 169830 233690 TRUE FALSE 209202.1881 181684.7824 173541.0945 181798.5351 170258.9095 173675.9112 234854.3789 191033.6493 194685.6293 1.0745641 0.933221333 0.891391394 0.933805622 0.874532497 0.892083878 1.206326218 0.981241656 1 17.57078687 1.761648555 24.99999998 1.081820369 0.92619112 0.349790415 0.081293197 10.61771364 11505.75332 0.034427163 0.019091996 57.76284224 -1.761648555 -0.155629249 SVS(ph)HGSNHTQKPDEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SVSHGSNHTQKPDEQR 16 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.289)VS(0.709)HGS(0.001)NHTQKPDEQR;S(0.396)VS(0.603)HGS(0.001)NHT(0.001)QKPDEQR;S(0.376)VS(0.624)HGSNHTQKPDEQR;S(0.449)VS(0.549)HGS(0.001)NHT(0.001)QKPDEQR;S(0.311)VS(0.689)HGSNHTQKPDEQR 166.91 3.93E-09 1353022000 184252.1 260467.4 251070.9 267390.7 306201.1 221835.9 268741.4 263838 281118.9 TRUE FALSE 172720.09 279752.6773 257026.4203 274252.3981 282153.3008 285876.3231 228446.1219 296778.7551 234198.3395 0.737494938 1.194511788 1.097473282 1.171026228 1.204762175 1.220659052 0.975438692 1.267211184 1 17.83737132 4.743427829 24.92263526 1.138825425 0.737494767 0.64625275 0.093892904 296.163992 1516459.812 0.020509288 0.169058828 55389.54905 -4.743427829 -0.401330658 SVS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SVSPER 6 0 Q14966;Q14966-3;Q14966-4;A0A096LPI0;Q14966-2;Q14966-6;A0A096LPB4;A0A096LNR2;A0A096LNX0;A0A096LNQ0 Q14966 ZNF638 Zinc finger protein 638 1 S(0.034)VS(0.966)PER;S(0.004)VS(0.996)PER;S(0.003)VS(0.997)PER 96.027 0.044765 938770000 814050 844230 859100 827840 873760 744460 806960 694670 883620 TRUE FALSE 763100.0636 906737.6676 879478.2577 849083.7759 805138.4142 959373.5167 685963.8394 781401.0787 736138.1136 1.036626211 1.231749384 1.194719091 1.153429989 1.093732819 1.303252065 0.931841222 1.061487056 1 19.48961694 1.705789541 10.40919163 0.999444678 1.17555424 0.514566263 0.078084855 0.08082501 17.94861018 0.033545441 0.01817799 50.79132481 -1.705789541 0.176109562 SVS(ph)PLVWCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVSPLVWCR 9 0 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 SVS(1)PLVWCR;S(0.001)VS(0.999)PLVWCR 144.77 0.0001036 72705000 98305 103092 95385 101457 107250 95064 121721 86185 134939 TRUE FALSE 92152.26553 110725.0389 97647.57724 104060.5584 98827.01763 122507.4336 103470.0661 96945.38697 112416.8092 0.819737424 0.984950914 0.868620787 0.925667248 0.87911246 1.089760815 0.920414543 0.862374477 1 16.77849825 SVS(ph)PPPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SVSPPPKR 8 1 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 S(0.001)VS(0.999)PPPKR;S(0.008)VS(0.992)PPPKR;S(0.149)VS(0.851)PPPKR;S(0.128)VS(0.872)PPPKR 91.584 0.0075851 3303880000 2660660 2040690 2383280 2025220 2407660 2379110 2687030 2394660 7040900 TRUE FALSE 2494134.04 2191784.811 2439812.527 2077190.574 2218572.096 3065920.435 2284134.797 2693638.572 5865728.304 0.425204495 0.37365945 0.415943665 0.354123216 0.378226195 0.522683677 0.389403443 0.459216389 1 22.48387882 -4.999999975 0.332716815 7.088313105 0.388405378 0.944938471 0.044623526 70.73663123 0.607550936 304.8458903 0.033967556 1.00E-05 4.999999975 -6.699907727 SVS(ph)PSPVPLLFQPDQNAPPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SVSPSPVPLLFQPDQNAPPIR 21 0 Q02241-2;Q02241-3 Q02241-2 KIF23 Kinesin-like protein KIF23 1 S(0.137)VS(0.863)PSPVPLLFQPDQNAPPIR;S(0.072)VS(0.464)PS(0.464)PVPLLFQPDQNAPPIR;S(0.126)VS(0.871)PS(0.003)PVPLLFQPDQNAPPIR;S(0.126)VS(0.871)PS(0.003)PVPLLFQPDQNAPPIR;S(0.002)VS(0.998)PSPVPLLFQPDQNAPPIR;SVS(1)PSPVPLLFQPDQNAPPIR;S(0.002)VS(0.986)PS(0.012)PVPLLFQPDQNAPPIR 444.45 6.48E-198 2549779000 569396 552205 626980 605639 659432 497607 688590 466108 659390 TRUE FALSE 533758.5208 593090.8328 641852.2617 621180.7221 607642.8707 641258.0629 585342.3221 524302.6098 549333.5492 0.971647411 1.079655218 1.16841992 1.130789705 1.106145568 1.167338248 1.065549925 0.954433988 1 19.06732288 1.400463508 4.429778357 0.979673018 1.110070664 0.45529097 0.056198689 0.182277919 5.768953648 0.039547219 0.013992399 25.14568713 -1.400463508 0.130397646 SVS(ph)PYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSPYSR 7 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 S(0.006)VS(0.994)PYSR 106.6 0.017849 0 103870 85523 115920 87759 107020 112870 92209 102120 321200 TRUE FALSE 97368.96211 91855.21191 118669.6771 90011.04452 98615.0809 145453.7367 78383.11648 114869.9068 267589.645 0.363874178 0.343268933 0.443476343 0.336377159 0.368531005 0.543570125 0.292922831 0.429276353 1 18.02966276 -4.056377693 0.566844616 10 0.385287017 0.884614899 0.069262963 486.9413585 5.362140207 5492.97876 0.02635551 8.78E-05 4.056377693 -9.614712983 SVS(ph)SDS(ph)LGPPRPAPARTPTQPPPEPGDLPTIEEALQIIHSAEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSSDSLGPPRPAPARTPTQPPPEPGDLPTIEEALQIIHSAEPR 44 2 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 S(0.434)VS(0.523)S(0.046)DS(0.686)LGPPRPAPART(0.249)PT(0.061)QPPPEPGDLPTIEEALQIIHSAEPR 95.522 9.82E-05 27743000 6585.5 8553.4 8894.7 7628.6 10247 6122.3 5329.4 6088.3 15932 TRUE FALSE 6173.32531 9186.702636 9105.686484 7824.362791 9442.241954 7889.708623 4530.305946 6848.437657 13272.84628 0.465109381 0.692142623 0.686038721 0.5895015 0.711395413 0.594424772 0.34132136 0.515973553 1 13.69619016 -1.091356073 4.958999692 1.000013024 0.582447319 0.580553509 0.113487029 1.85E-05 3.38E-06 0.124131091 0.029257067 0.081029643 1.091356073 -0.417565705 SVS(ph)SDSLGPPRPAPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SVSSDSLGPPRPAPAR 16 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 S(0.001)VS(0.967)S(0.032)DSLGPPRPAPAR;SVS(0.804)S(0.195)DS(0.001)LGPPRPAPAR;S(0.006)VS(0.826)S(0.168)DS(0.001)LGPPRPAPAR 183.6 1.19E-09 4125900000 1533000 1654030 1672710 1692820 1476400 1336460 2087480 1459470 1813490 TRUE FALSE 1437052.266 1776496.102 1712387.471 1736260.627 1360449.5 1722274.306 1774481.753 1641688.042 1510806.803 0.95118202 1.175859215 1.133425841 1.149227435 0.900478801 1.139969917 1.174525922 1.08663003 1 20.52688775 4.754914557 23.63228347 1.109656567 0.951181756 0.197035514 0.086891172 2188.307847 3162104.618 0.020031662 0.493606714 56874.10258 -4.754914557 -0.158474811 SVS(ph)TMNLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSTMNLSK 9 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 S(0.002)VS(0.629)T(0.369)MNLSK 104.59 0.0033934 71759000 69501 124170 59515 69043 133150 32357 138270 74326 434260 TRUE FALSE 65151.05647 133363.676 60926.72391 70814.76027 122692.9361 41697.94063 117537.6971 83605.76471 361779.2006 0.180085136 0.36863279 0.168408587 0.195740275 0.339137617 0.115257982 0.324887934 0.231096107 1 18.46474994 -1.132921237 0.835724726 1.142362237 0.244825149 0.89488947 0.081788258 25.41138798 7.502627196 9.087979855 0.024019034 0.073634063 1.132921237 -0.897537087 SVS(ph)TTNIAGHFNDESPLGLR ddPTM_SK-BR-3_Pertuzumab_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(0.902)T(0.094)T(0.004)NIAGHFNDESPLGLR;SVS(0.806)T(0.188)T(0.007)NIAGHFNDESPLGLR;SVS(0.887)T(0.094)T(0.02)NIAGHFNDESPLGLR;S(0.004)VS(0.957)T(0.038)T(0.001)NIAGHFNDESPLGLR;S(0.004)VS(0.948)T(0.037)T(0.01)NIAGHFNDESPLGLR 370.59 2.55E-112 4716920000 1022180 1297383 1097805 954450 1561493 727899 1285018 1077408 2275080 TRUE FALSE 958203.5784 1393442.587 1123845.453 978942.8029 1438859.639 938031.6248 1092341.48 1211924.76 1895354.45 0.505553765 0.73518839 0.592947379 0.5164959 0.75915069 0.494910925 0.5763257 0.639418532 1 20.85403624 0.871071014 8.069834226 0.999999956 0.606573434 0.663501571 0.089262396 5.644158654 353.5375844 0.080010777 0.020036087 7.43140643 -0.871071014 -0.393426523 SVS(ph)VDESRPELIFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SVSVDESRPELIFR 14 1 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 S(0.005)VS(0.995)VDESRPELIFR;SVS(1)VDESRPELIFR;S(0.003)VS(0.997)VDESRPELIFR 254.05 1.84E-24 600700000 388283 416611 342085 419752 497327 280174 365918 371624 391502 TRUE FALSE 363981.0601 447457.3119 350199.4177 430523.547 458268.9435 361055.6856 311051.9929 418022.0744 326157.787 1.115966182 1.371904427 1.073711656 1.319985492 1.405052897 1.106996981 0.953685625 1.281655969 1 18.31521055 2.021157343 24.16076133 1.062561176 1.251197814 0.294079217 0.131880612 179.7376627 205251.3257 0.046495952 0.034335934 104.9922742 -2.021157343 0.188636637 SVS(ph)VDSGEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SVSVDSGEQR 10 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 S(0.005)VS(0.991)VDS(0.004)GEQR;SVS(1)VDSGEQR;SVS(1)VDSGEQR 170.68 4.46E-06 654560000 895920 1271060 1089040 1495570 1779570 971180 1194080 958830 1256840 TRUE FALSE 839845.9665 1365170.605 1114872.543 1533948.858 1639809.751 1251543.9 1015038.789 1078542.036 1047065.285 0.802095131 1.303806577 1.064759342 1.464998297 1.566100772 1.195287361 0.969413087 1.030061881 1 19.99791997 1.809413323 5.192891627 1.00088138 1.245539674 0.219987197 0.20725688 0.326409944 14.93515695 0.096850042 0.05483381 64.47826209 -1.809413323 0.244658294 SVSDNDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSDNDIR 8 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 158.61 0.00084673 1100800000 1863600 2316400 2107000 2069300 2240500 1941100 2277200 1919300 2338000 FALSE TRUE 1746960.603 2487908.666 2156979.035 2122401.741 2064540.168 2501464.059 1935755 2158928.83 1947772.696 0.89690168 1.27730955 1.107407984 1.089655762 1.059949229 1.284268983 0.993830032 1.108409022 1 20.89339389 1.622874478 25 1.038340761 1.133162509 0.103021068 0.113387109 1.622347128 2696.07296 0.048221886 0.026605353 41.9637681 -1.622874478 0.094821748 SVSDPVEDKKEQES(ph)DEEEEEEEEDEPSGATTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSDPVEDKKEQESDEEEEEEEEDEPSGATTR 32 2 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 S(0.002)VS(0.01)DPVEDKKEQES(0.988)DEEEEEEEEDEPSGATTR 72.292 0.0015453 52488000 46011 19214 22272 18228 23396 12257 30250 20059 39133 TRUE FALSE 43131.25364 20636.62455 22800.30236 18695.76134 21558.57253 15795.39692 25714.29333 22563.41031 32601.44949 1.322985766 0.632997148 0.699364682 0.573464114 0.661276504 0.484499836 0.788746934 0.692098378 1 14.99264849 -0.68581861 13.37658222 1 0.708242869 0.114162989 0.22627987 0 0 0.19619181 0.046242853 0.206149075 0.68581861 -0.291757131 SVSDQFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVSDQFYR 8 0 P55010;H0YLZ1;H0YN40;H0YMJ8;H0YM54;H0YK11;H0YK29 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 153.04 0.0010411 645690000 314370 447860 345940 319550 407100 282030 334750 361640 380420 FALSE TRUE 294694.1429 481020.0204 354145.8602 327750.194 375128.0082 363447.4826 284557.3452 406791.5501 316925.4444 0.929853213 1.51777028 1.117442182 1.034155508 1.183647494 1.146791743 0.897868411 1.283555982 1 18.27378397 3.640839803 5.138879536 1.081265204 1.280681927 0.065083686 0.175620626 0.307863173 13.57683834 0.043144361 0.068329124 4373.607478 -3.640839803 0.199416723 SVSDYDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SVSDYDGK 8 0 P07237;H7BZ94;I3L398;I3L312;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ;;; 179.21 0.00057125 2388700000 4633400 3796950 4061370 4075930 3547900 2761120 4833700 3497030 3518580 FALSE TRUE 4343403.765 4078080.129 4157707.614 4180525.264 3269262.246 3558210.521 4108931.559 3933641.893 2931306.267 1.481729771 1.391215983 1.418380488 1.426164612 1.115291937 1.21386515 1.401740789 1.341941624 1 21.48311228 -4.69692002 0.111007092 4.20E-12 1.550368247 0.580575296 0.09986892 119.9197601 0.945430252 28.13945212 1.273859553 2.01E-05 4.69692002 1.550368247 SVSDYDGKLSNFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSDYDGKLSNFK 13 1 P07237;H7BZ94;I3L398;I3L312;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 177.93 1.37E-05 216210000 715550 786220 762640 970150 1124400 665050 1314100 828220 1878300 FALSE TRUE 670765.0028 844432.5469 780730.1809 995045.6915 1036094.16 857039.1388 1117062.905 931625.0901 1564799.596 0.428658727 0.539642616 0.498933015 0.635893372 0.662125784 0.547698978 0.713869627 0.595363836 1 20.57754647 -5 0.118888564 2.40327315 0.362562455 0.842442026 0.061862197 52.7005709 0.40768016 17.72628574 0.552601413 1.00E-05 5 -2.040710694 SVSEINS(ph)DDELSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SVSEINSDDELSGK 14 0 A0A2R8Y7M0;P82094;P82094-2;F8WF45 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 SVS(0.001)EINS(0.999)DDELSGK;SVSEINS(1)DDELSGK;SVSEINS(1)DDELSGK;SVSEINS(1)DDELSGK 363.28 3.16E-83 2430740000 7324800 5428760 5891030 6000090 6015770 4767560 7359000 4990980 6182780 TRUE FALSE 6866353.843 5830711.039 6030768.014 6154062.468 5543315.691 6143877.177 6255586.268 5614114.84 5150834.076 1.333056694 1.131993567 1.170833291 1.194770085 1.076197682 1.192792679 1.214480252 1.089942863 1 22.29637464 -5 0.172628332 0.319183793 1.213246608 0.469455169 0.065819454 131.3899487 1.247509982 30.65597826 0.218754252 1.00E-05 5 0.894062816 SVSGS(ph)PEPAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SVSGSPEPAAK 11 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 SVS(0.001)GS(0.999)PEPAAK;SVS(0.001)GS(0.999)PEPAAK;SVSGS(1)PEPAAK;SVSGS(1)PEPAAK 207.34 2.44E-08 1252250000 2145260 1603990 1921540 1819090 1890270 1679670 2231290 1599340 2273860 TRUE FALSE 2010992.006 1722751.089 1967119.836 1865770.929 1741815.819 2164563.462 1896728.779 1799021.12 1894338.076 1.061580312 0.909421138 1.038420682 0.984919721 0.919485197 1.142648975 1.001262025 0.949683239 1 20.8532624 SVSLVGEDERK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVSLVGEDERK 11 1 B7Z6D5;Q96GQ7 B7Z6D5 DDX27 Probable ATP-dependent RNA helicase DDX27 0 ; 93.091 0.015246 394700000 660740 279050 362720 308580 406680 262820 498560 276040 585890 FALSE TRUE 619385.4629 299711.1524 371323.8897 316498.6852 374740.9933 338691.8675 423805.5564 310504.2016 488101.174 1.268969418 0.614034893 0.760751888 0.648428445 0.767752698 0.693896851 0.868273995 0.636147213 1 18.8968207 -0.171474652 8.562329253 0.999990859 0.764634388 0.109371903 0.18938983 0 0 0.160554053 0.037842953 0.673791221 0.171474652 -0.235356471 SVSMLSLNT(ph)PNSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SVSMLSLNTPNSNR 14 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C3G1 Q9H8V3-2 ECT2 Protein ECT2 1 SVSMLSLNT(1)PNSNR;SVSMLSLNT(1)PNSNR;SVSMLS(0.001)LNT(0.999)PNSNR;SVSMLSLNT(1)PNSNR 216.34 6.89E-11 634228000 1447120 1504710 1524680 1506250 1766290 1309090 1801070 1377720 2338770 TRUE FALSE 1356547.342 1616120.294 1560846.13 1544902.925 1627572.708 1687003.032 1531016.274 1549731.375 1948414.178 0.696231509 0.829454185 0.801085389 0.792902732 0.835331998 0.865833892 0.785775576 0.795380876 1 20.89386896 -5 0.274176266 2.363858598 0.791531419 0.682400958 0.043230508 127.0550266 1.227551243 98.40170099 0.048351286 1.00E-05 5 -1.572327179 SVSS(ph)DSLGPPRPAPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSSDSLGPPRPAPAR 16 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 S(0.005)VS(0.347)S(0.642)DS(0.006)LGPPRPAPAR 108.97 0.00061083 872930000 258790 247030 245600 237010 238550 182190 288410 227050 281500 TRUE FALSE 242592.7959 265320.3582 251425.748 243092.0779 219815.2453 234785.2954 245165.598 255397.6923 234515.8314 1.03444102 1.13135372 1.07210565 1.03657001 0.937315165 1.001149022 1.045411717 1.089042436 1 17.83932579 3.25801903 3.237479801 1.016264379 1.092012601 0.296144887 0.044647717 0.260364507 5.634901288 0.013153468 0.017559034 1811.419464 -3.25801903 0.075748222 SVSS(ph)YGNIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVSSYGNIR 9 0 Q8N122;Q8N122-3 Q8N122 RPTOR Regulatory-associated protein of mTOR 1 SVS(0.062)S(0.938)YGNIR;SVS(0.068)S(0.932)YGNIR 153.23 8.24E-05 422650000 483090 522010 487070 496690 492200 356640 604080 461550 582300 TRUE FALSE 452854.2592 560660.1636 498623.5304 509435.9063 453544.5974 459596.1784 513503.812 519175.5335 485110.3682 0.93350769 1.155737334 1.027855851 1.050144338 0.934930744 0.947405392 1.058529864 1.070221474 1 18.88795349 3.253630563 2.354741576 1.006268249 1.066819137 0.020960285 0.069017952 0.602747381 6.808535357 0.020553155 0.028255546 1793.207567 -3.253630563 0.060550888 SVSSDS(ph)LGPPRPAPARTPTQPPPEPGDLPTIEEALQIIHSAEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSSDSLGPPRPAPARTPTQPPPEPGDLPTIEEALQIIHSAEPR 44 2 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 S(0.014)VS(0.014)S(0.014)DS(0.526)LGPPRPAPART(0.419)PT(0.014)QPPPEPGDLPTIEEALQIIHSAEPR 169.25 1.37E-20 24652000 9404.6 9012.9 7983.8 9128.5 10752 7795.7 10850 8975.9 14982 TRUE FALSE 8815.982874 9680.224494 8173.179506 9362.752765 9907.581291 10046.19204 9223.143226 10096.56087 12481.40741 0.706329229 0.77557155 0.654828357 0.750135979 0.793787188 0.804892566 0.738950578 0.808928075 1 13.607493 -4.205401843 0.198329398 1.81362161 0.702369702 0.803100378 0.040159574 42.60324235 0.559917042 13.80860945 0.101304706 6.23E-05 4.205401843 -1.111251908 SVSSNVASVS(ph)PIPAGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SVSSNVASVSPIPAGSK 17 0 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 SVSSNVASVS(1)PIPAGSK;SVSSNVAS(0.031)VS(0.969)PIPAGSK;SVSSNVAS(0.004)VS(0.996)PIPAGSK;SVSSNVASVS(1)PIPAGSK 373.43 1.87E-77 1242790000 1833350 1439690 1676910 1620380 1593240 1412410 2020380 1476420 2269430 TRUE FALSE 1718603.896 1546286.146 1716687.097 1661961.694 1468113.357 1820149.838 1717442.775 1660754.287 1890647.472 0.909002827 0.817860637 0.907988995 0.879043671 0.776513538 0.962712439 0.908388687 0.87840505 1 20.85044895 0.165424176 0.366058831 1.021138578 0.85953541 0.362350112 0.050956148 4.002304851 0.839484764 0.186703734 0.040430048 1.463605982 -0.165424176 -0.161603168 SVSSNVASVS(ph)PIPAGSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSSNVASVSPIPAGSKK 18 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 S(0.005)VS(0.004)S(0.004)NVAS(0.032)VS(0.953)PIPAGS(0.001)KK 48.198 0.095748 0 311790 175860 246810 253170 265070 180630 315120 217370 385560 TRUE FALSE 292275.6205 188880.8574 252664.4498 259666.7708 244252.4714 232774.9487 267870.6814 244509.123 321207.5452 0.90992763 0.588033688 0.786608078 0.808408067 0.760419471 0.724687051 0.833948908 0.761218491 1 18.29314626 -4.231654886 0.213737983 1.827544675 0.72338187 0.403375472 0.084252449 91.24563927 1.2278263 32.47042951 0.16317803 5.87E-05 4.231654886 -1.104162805 SVSSVLSSLT(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSSVLSSLTPAK 13 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 SVSSVLS(0.001)S(0.022)LT(0.977)PAK 145.86 0.00046956 166150000 505700 313210 390770 379310 484150 357060 556360 332000 648760 TRUE FALSE 474049.1397 336400.3943 400039.2489 389043.7368 446126.812 460137.4256 472938.983 373450.9308 540477.7649 0.87709277 0.622413013 0.740158569 0.719814509 0.825430464 0.851353109 0.875038741 0.690964467 1 19.04387574 2.684953147 3.50182851 0.846844597 0.719348529 0.230246686 0.096240239 0.298663213 7.44041858 0.029373933 0.028289146 484.120136 -2.684953147 -0.127496068 SVST(ph)MNLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSTMNLSK 9 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 SVS(0.382)T(0.618)MNLSK 157.03 0.00077716 88002000 85313 170320 85146 78170 186830 42467 192270 92045 616090 TRUE FALSE 79973.41162 182930.67 87165.70333 80175.97454 172157.1254 54726.53351 163440.8984 103537.0209 513260.5989 0.155814438 0.356408948 0.169827381 0.156209097 0.335418549 0.106625238 0.31843648 0.201724078 1 18.96933199 SVST(ph)PSEAGSQDSGDGAVGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVSTPSEAGSQDSGDGAVGSR 21 0 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7;E7EQL5;E7EV09;E7EQU2;E7ETL8;E9PGG1;E7EMU4;E7ESD3;E7ET01;E7ERR6;E7EUM4;E7ERH4 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 1 SVS(0.099)T(0.9)PSEAGSQDSGDGAVGSR 144.68 2.20E-08 0 23891 25742 30173 29961 29305 22338 26074 22587 29629 TRUE FALSE 22395.70496 27647.96446 30888.71781 30729.84998 27003.50351 28786.61797 22164.44576 25407.03667 24683.72849 0.907306405 1.120088664 1.251379743 1.244943607 1.093979928 1.166218385 0.897937513 1.029303036 1 14.59127271 1.749493178 25 0.971165022 1.146349269 0.337220778 0.100716568 2.963031421 6788.335754 0.046012265 0.025516089 56.16854558 -1.749493178 0.175184248 SVSTTNIAGHFNDES(ph)PLGLR ddPTM_SK-BR-3_Pertuzumab_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 291.64 1.14E-54 727160000 685310 668170 819270 747060 803450 785460 861740 774150 732120 TRUE FALSE 642417.6704 717642.002 838703.4713 766230.8244 740350.278 1012209.551 732530.087 870804.3316 609924.4423 1.053274186 1.176608039 1.37509405 1.256271714 1.213839333 1.659565482 1.201017759 1.42772493 1 19.21827101 4.47979119 1.662695108 1.322625657 1.023792931 0.187865556 0.170957077 0.866902825 3.384841479 0.040574363 0.354375606 30185.0007 -4.47979119 -0.298832726 SVSTTNIAGHFNDES(ph)PLGLRR ddPTM_SK-BR-3_Pertuzumab_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 SVSTTNIAGHFNDES(1)PLGLRR 165.79 6.70E-12 217090000 84440 96694 107610 113750 130730 71670 113890 99637 161720 TRUE FALSE 79155.05113 103853.3244 110162.56 116669.0176 120462.9931 92359.96553 96813.2518 112076.8988 134727.8872 0.587517943 0.770837623 0.817667094 0.865960418 0.894120702 0.685529681 0.718583612 0.831876021 1 17.03968898 -3.282710828 0.953929286 4.781851042 0.774023496 0.385899655 0.090556304 27125.38885 461.8424957 220180.4064 0.027624905 0.000521542 3.282710828 -4.007827545 SVTEQGAELSNEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SVTEQGAELSNEER 14 0 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;E5RGE1 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;;; 432.2 9.58E-153 4964030000 1595760 1747380 1750130 1758720 1737590 1511870 1997750 1483300 1589900 FALSE TRUE 1495884.23 1876757.833 1791643.91 1803851.733 1601126.691 1948322.326 1698205.934 1668493.27 1324535.419 1.129365217 1.416917816 1.352658362 1.361875045 1.208821348 1.470947698 1.2821144 1.259681883 1 20.33705499 0.743143263 1.732421421 1.000472958 1.335274249 0.501938426 0.098017719 0.673254982 3.24008486 0.083280421 0.023592632 5.535326755 -0.743143263 0.334801291 SVTLLEVCGS(ph)WPEGFGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 207.79 7.38E-16 80808000 94181 106622 99666 118843 138943 111376 121724 110155 106332 TRUE FALSE 88286.37933 114516.4038 102030.1246 121892.7126 128030.9772 143528.4432 103472.6162 123908.0942 88584.50227 0.996634593 1.292736324 1.151783009 1.376004938 1.445297698 1.620243265 1.168066802 1.398755889 1 16.4347667 5.728016232 0.734662958 1.335655474 6.39E-10 0.212710895 0.175894939 15.44818926 2.132429567 0.059425267 23.8688574 534584.3396 -5.728016232 -1.335655474 SVTQATQTS(ph)PGVPWPSQSANFPEFSFDFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVTQATQTSPGVPWPSQSANFPEFSFDFTR 30 0 A0A0C4DGH6;A0JNW5;H0YHT7 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 SVTQATQT(0.031)S(0.969)PGVPWPSQSANFPEFSFDFTR;SVTQAT(0.001)QT(0.017)S(0.98)PGVPWPSQSANFPEFSFDFTR 153.65 8.83E-09 291220000 134185 150862 165765 159482 169902 121518 139113 131259 171348 TRUE FALSE 125786.6004 162031.9795 169697.0241 163574.5781 156558.5823 156598.2739 118254.2971 147646.9751 142748.9118 0.881173795 1.135083815 1.188779808 1.145890193 1.096740986 1.097019038 0.828407696 1.034312438 1 17.12312022 1.851696099 8.648973787 0.939019226 1.110249631 0.286500364 0.097633578 0.301870625 21.04989751 0.039471866 0.024783018 71.071601 -1.851696099 0.171230405 SVTVVEDDEDEDGDDLLHHHHGSHCSSSGDPAEYNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SVTVVEDDEDEDGDDLLHHHHGSHCSSSGDPAEYNLR 37 0 P02545;P02545-6;P02545-5;P02545-4 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;; 125.02 5.92E-09 5228154000 200131 728046 598407 763837 707732 771363 855020 752226 696593 FALSE TRUE 187605.158 781951.2834 612601.4966 783438.3506 652149.5836 994042.9761 726817.6886 846143.072 580327.1281 0.323274837 1.347431897 1.055614096 1.349994361 1.123762016 1.7129011 1.252427559 1.458045008 1 19.14650685 4.740545689 24.94637612 1.292247398 0.323274497 0.683739158 0.206073142 94.40718636 1186325.973 0.045202868 0.295034957 55023.18034 -4.740545689 -0.968972901 SVTVVEDDEDEDGDDLLHHHHVS(ph)GSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVTVVEDDEDEDGDDLLHHHHVSGSR 26 0 P02545-2;Q3BDU5;Q5TCI8 P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 SVTVVEDDEDEDGDDLLHHHHVS(0.5)GS(0.5)R;SVTVVEDDEDEDGDDLLHHHHVS(0.5)GS(0.5)R 118.22 0.00028639 407920000 184527 181916 194197 186645 231770 131056 205658 163798 255503 TRUE FALSE 172977.7845 195385.2499 198803.4445 191434.6267 213567.7191 168889.7397 174821.4921 184248.5409 212857.8987 0.812644424 0.917914022 0.933972598 0.899354113 1.003334715 0.793438913 0.821306107 0.865594098 1 17.6995311 2.22098503 24.99997184 0.849357317 0.916212465 0.05021624 0.071328476 407.5433879 579696.7721 0.02422633 0.017931519 166.3355313 -2.22098503 0.066855148 SVTVVEDDEDEDGDDLLHHHHVSGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 SVTVVEDDEDEDGDDLLHHHHVSGSR 26 0 P02545-2;Q3BDU5;Q5TCI8 P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;;;;;; 293.4 1.53E-70 10489430000 2562310.6 4266531.6 3582454.3 3819149.8 4338946.8 3247764.5 4208393.8 3664831.2 4461152.5 FALSE TRUE 2401940.153 4582430.039 3667431.808 3917155.65 3998183.421 4185341.388 3577384.219 4122393.443 3716557.328 0.646280937 1.23297709 0.986781982 1.053974231 1.075776066 1.126133951 0.962553219 1.109196786 1 21.82553543 4.753099774 24.81098966 1.067465126 0.646280613 0.742623917 0.078100142 1186.745165 2025135.529 0.017893934 0.391035866 56636.93913 -4.753099774 -0.421184514 SVVEFLQGYIGVPHGGFPEPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVVEFLQGYIGVPHGGFPEPFR 22 0 P11498 P11498 PC "Pyruvate carboxylase, mitochondrial" 0 121.46 2.73E-05 58045000 67877 80332 66235 61144 93913 69625 65486 60647 103110 FALSE TRUE 63628.69973 86279.86487 67806.12548 62713.05856 86537.45181 89724.60723 55666.98224 68218.91145 85900.27488 0.740727545 1.004418961 0.789358655 0.730068194 1.007417635 1.044520607 0.648041957 0.794164065 1 16.39037513 -1.11772504 5.014740854 1.000005665 0.849496037 0.116912777 0.133470929 8.27E-06 1.46E-06 0.12647586 0.029809525 0.076256165 1.11772504 -0.150509627 SVVLFGVETHVCIQQTALELVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SVVLFGVETHVCIQQTALELVGR 23 0 Q96CN7 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 ;;;;;; 191.79 1.11E-17 207431600 184094.4 214839.5 203149.9 209293 231504.1 192276.1 220848 196188.3 186984.2 FALSE TRUE 172572.2601 230746.4401 207968.7116 214663.8127 213322.7018 247783.0887 187733.8927 220682.8411 155775.3291 1.107827929 1.48127718 1.335055511 1.378034725 1.369425461 1.590643976 1.205158055 1.416673888 1 17.24910724 -1.018516984 4.712244134 0.999991273 1.367989154 0.418101788 0.133402058 1.08E-05 2.24E-06 0.113833043 0.02683007 0.095825924 1.018516984 0.36799788 SVVLMSHLGRPDGVPMPDKYSLEPVAVELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SVVLMSHLGRPDGVPMPDKYSLEPVAVELK 30 2 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;; 156.96 1.12E-07 2766170000 3186400 3034460 2559770 2556950 3289600 1463170 3855020 2687160 3605530 FALSE TRUE 2986968.912 3259134.576 2620488.953 2622565.666 3031248.086 1885563.426 3276995.539 3022657.841 3003743.75 0.994415356 1.085024172 0.872407626 0.873099 1.009156685 0.627737778 1.090970406 1.006296839 1 21.51833031 -0.796284611 5.73876748 1.000000007 0.947247426 0.016090326 0.134316595 1.08E-08 2.20E-09 0.121243882 0.028577454 0.159851012 0.796284611 -0.05275258 SVVNMEWDKIWAFNKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVVNMEWDKIWAFNKK 16 2 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 173.37 2.39E-09 288480000 563200 456770 479690 496080 658150 339400 666880 466480 1043340 FALSE TRUE 527950.3173 490589.7261 491068.4733 508810.2527 606461.5538 437379.2703 566887.535 524721.0548 869199.8138 0.607398102 0.56441536 0.564966151 0.585377775 0.69772398 0.503197612 0.652194727 0.603682889 1 19.72932834 -5 0.327622232 5.057744665 0.577520597 0.858092716 0.051538879 109.7978026 0.955240695 309.8453845 0.039221276 1.00E-05 5 -4.480224068 SVVS(ph)DLEADDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SVVSDLEADDVK 12 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 SVVS(1)DLEADDVK;SVVS(1)DLEADDVK;SVVS(1)DLEADDVK;SVVS(1)DLEADDVK;SVVS(1)DLEADDVK;SVVS(1)DLEADDVK 362.27 2.05E-72 5260250000 9630950 5564590 7430570 7103970 6619130 5211600 9372140 5963280 6234240 TRUE FALSE 9028166.031 5976598.034 7606826.629 7286269.897 6099290.23 6716104.317 7966874.614 6707808.635 5193705.069 1.738290086 1.150738818 1.464624296 1.402904054 1.174362069 1.293123931 1.533948214 1.291526674 1 22.30833266 0.9768909 23.41421029 0.999999992 1.375394506 0.340555319 0.171011331 992.8142571 1005924.716 0.1500163 0.037504075 9.481802394 -0.9768909 0.375394515 SVVS(ph)DLEADDVKGSVPLS(ph)SSPPATHFPDETEITNPVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVVSDLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 38 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 2 S(0.451)VVS(0.549)DLEADDVKGS(0.015)VPLS(0.361)S(0.327)S(0.297)PPATHFPDETEITNPVPK;S(0.033)VVS(0.967)DLEADDVKGS(0.01)VPLS(0.692)S(0.148)S(0.132)PPAT(0.017)HFPDETEITNPVPK 128.14 1.78E-08 176109000 162221 117609 139833 151032 178368 100281 207217 119318 282650 TRUE FALSE 152067.8772 126316.8927 143149.9048 154907.7368 164359.6968 129230.4968 176146.7346 134215.115 235473.889 0.645795072 0.536436941 0.607922625 0.657855261 0.697995423 0.548810305 0.748052089 0.569978759 1 17.84520757 -5 0.235087132 3.085700409 0.584239646 0.746379067 0.067745287 75.2414753 0.752197673 74.80278183 0.101327481 1.00E-05 5 -2.501460763 SVVS(ph)DLEADDVKGSVPLSSSPPATHFPDETEITNPVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVVSDLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 38 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 S(0.018)VVS(0.982)DLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 292.04 2.06E-92 94783000 55736 42457 51278 55861 60043 27261 70496 44403 77825 TRUE FALSE 52247.58325 45600.56046 52494.33838 57294.48783 55327.46498 35130.80815 59925.77925 49946.81229 64835.50473 0.805848331 0.703326991 0.809654195 0.88369001 0.853351342 0.541845217 0.924274123 0.770362049 1 15.98449645 -4.999992822 0.288631402 2.671557895 0.772188874 0.283449978 0.106081063 311.3760202 2.941584134 312.8952477 0.106179238 1.00E-05 4.999992822 -1.899369021 SVVS(ph)FDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SVVSFDK 7 0 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 SVVS(1)FDK;SVVS(1)FDK;SVVS(1)FDK;SVVS(1)FDK 129.85 0.0037975 887200000 2158260 1544040 1696640 1791510 1934050 1467550 2966870 2197500 2662030 TRUE FALSE 2023178.359 1658362.328 1736885.102 1837483.18 1782157.515 1891207.861 2522015.387 2471862.712 2217719.996 0.91227854 0.747778047 0.78318503 0.828546067 0.803598975 0.852771254 1.137210916 1.114596395 1 21.08064579 1.821828607 4.493127456 1.094349521 0.804388932 0.831400476 0.055631638 0.073330927 2.418466979 0.025478112 0.01413684 66.34811782 -1.821828607 -0.289960589 SVVS(ph)FDKVKEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVVSFDKVKEPR 12 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 S(0.039)VVS(0.961)FDKVKEPR 86.539 0.0057679 209770000 712860 645240 658470 839400 1105600 439070 1132700 768580 2963300 TRUE FALSE 668243.3651 693014.241 674089.2194 860940.4251 1018770.636 565822.3813 962862.1505 864538.9049 2468706.086 0.270685672 0.280719623 0.273053655 0.348741565 0.412673927 0.229197953 0.390027049 0.350199203 1 21.23532365 -5 0.300014469 6.712951063 0.279490354 0.944062427 0.052376806 53.16461425 0.491842228 190.9142561 0.0484892 1.00E-05 5 -6.433460709 SVVSDLEADDVKGSVPLS(ph)SSPPATHFPDETEITNPVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVVSDLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 38 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 SVVSDLEADDVKGS(0.006)VPLS(0.639)S(0.162)S(0.162)PPAT(0.03)HFPDETEITNPVPK;SVVSDLEADDVKGS(0.025)VPLS(0.564)S(0.201)S(0.201)PPAT(0.009)HFPDETEITNPVPK 164.9 4.37E-18 5560400000 265561 215613 241546 242067 322358 147519 370556 203614 617390 TRUE FALSE 248940.011 231577.2109 247275.5852 248278.849 297041.303 190105.3405 314994.5679 229035.6561 514343.6205 0.483995526 0.450238326 0.480759507 0.482710078 0.577515286 0.369607657 0.612420482 0.445296971 1 18.97237299 -5 0.339413302 6.50051913 0.471541815 0.84698342 0.06825803 126.2432899 1.065424851 502.9768772 0.047414541 1.00E-05 5 -6.028977316 SVVSDLEADDVKGSVPLSSS(ph)PPATHFPDETEITNPVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SVVSDLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 38 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 SVVSDLEADDVKGSVPLS(0.024)S(0.138)S(0.835)PPAT(0.001)HFPDET(0.001)EITNPVPK 151.79 8.83E-14 58783000 81700 71913 81461 78949 102970 48204 118700 69806 208450 TRUE FALSE 76586.54284 77237.51335 83393.29339 80974.965 94883.15156 62119.71227 100902.037 78521.43276 173658.3484 0.441018492 0.444767062 0.48021471 0.466288927 0.546378291 0.357712214 0.58103764 0.452160426 1 17.40589224 -5 0.344168118 6.852609035 0.456253826 0.884711271 0.060021521 113.0368148 0.94173539 486.86316 0.040769698 1.00E-05 5 -6.396355208 SVWGSLAVQNS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SVWGSLAVQNSPK 13 0 P18615;P18615-3;P18615-4 P18615 NELFE Negative elongation factor E 1 SVWGSLAVQNS(1)PK;SVWGSLAVQNS(1)PK 257.54 6.98E-24 384190000 791910 535070 607220 542720 647790 461510 826740 588520 865200 TRUE FALSE 742345.7667 574687.1395 621623.5452 556647.114 596915.1865 594740.445 702778.0121 661998.0175 720792.5306 1.029902136 0.797298966 0.862416741 0.772270925 0.828137309 0.825120156 0.975007346 0.91843074 1 19.45922454 1.730054485 7.417399209 0.958798208 0.843272869 0.343351091 0.071952414 0.125183733 20.01485389 0.032228577 0.016993949 53.70991752 -1.730054485 -0.115525339 SVWVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SVWVAR 6 0 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;; 107.65 0.07231 1678840000 1497600 1751560 1431020 1382040 2058700 1282240 1702820 1772290 2244610 FALSE TRUE 1403867.889 1881247.325 1464964.47 1417505.486 1897018.006 1652401.873 1447497.949 1993564.308 1869970.09 0.750743499 1.006030703 0.78341599 0.758036449 1.014464358 0.883651499 0.774075455 1.066094222 1 20.83458376 1.227423769 24.99886546 1.033047215 0.86058391 0.374623697 0.096361494 263.2376499 590870.0334 0.084641076 0.021947649 16.88199506 -1.227423769 -0.172463305 SVYAHFPINVVIQENGSLVEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SVYAHFPINVVIQENGSLVEIR 22 0 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ;;; 287.14 2.71E-46 1878269000 1920666 2437399 2336558 2334930 2429891 1971263 2643037 2074031 1987771 FALSE TRUE 1800454.944 2617866.558 2391982.259 2394848.257 2239057.163 2540334.627 2246738.139 2332978.336 1655999.179 1.087231785 1.580838078 1.444434448 1.446165124 1.352088329 1.534019256 1.356726602 1.408804042 1 20.65927053 -0.033101318 0.947043521 0.99418964 1.428576714 0.460875675 0.134047532 6.088373924 4.7928139 0.236659463 0.037362197 0.926613624 0.033101318 0.434387074 SVYATMGDHENRS(ph)PVKEPVEQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SVYATMGDHENRSPVKEPVEQPR 23 2 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 SVYATMGDHENRS(1)PVKEPVEQPR;SVYATMGDHENRS(1)PVKEPVEQPR;SVYATMGDHENRS(1)PVKEPVEQPR;SVYATMGDHENRS(1)PVKEPVEQPR 280.97 3.08E-52 1624143000 1437447 818716 1095164 968207 1088740 913928 1368768 909935 1565710 TRUE FALSE 1347479.758 879334.5845 1121141.807 993052.8308 1003234.752 1177764.177 1163533.945 1023542.388 1304382.886 1.033040047 0.674138394 0.859518949 0.76132004 0.76912597 0.902928266 0.892018715 0.784694739 1 20.31493599 2.231240659 24.9537751 0.887174017 0.80244192 0.099646906 0.104986465 319.7194198 1089916.097 0.035151575 0.026492404 170.3101999 -2.231240659 -0.084732097 SVYRGS(ph)LTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SVYRGSLTQR 10 1 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36-3;Q9BV36 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 SVYRGS(1)LTQR;SVYRGS(0.999)LT(0.001)QR;SVYRGS(0.999)LTQR;SVYRGS(0.987)LT(0.013)QR 146.67 1.71E-05 1831300000 636720 720450 595490 613898 925980 455497 834580 625180 1016660 TRUE FALSE 596868.8318 773792.8676 609615.304 629651.662 853257.266 586991.5895 709442.4769 703235.0992 846972.8781 0.704708317 0.913598165 0.719757763 0.743414197 1.007419822 0.693046501 0.837621245 0.830292347 1 19.69195625 -4.999994094 0.311189765 2.715222029 0.799969221 0.284209547 0.098295061 386.6397207 3.495146981 434.7064055 0.083200532 1.00E-05 4.999994094 -1.915252808 SWDIFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SWDIFFR 7 0 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;Q02218-3;C9J4G7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 ; 181.2 0.0015712 254530000 742680 1012520 801840 764480 1316130 709930 738330 1067510 1601380 FALSE TRUE 696196.9845 1087488.034 820860.0235 784097.8511 1212766.459 914875.2662 627624.2708 1200790.973 1334099.333 0.521847937 0.815147724 0.615291533 0.587735734 0.909052594 0.685762479 0.470447931 0.900076137 1 20.34743466 1.048477803 7.672540854 0.99973928 0.667220325 0.478084601 0.128946044 0.165768253 21.15682786 0.120507703 0.030192614 11.18092677 -1.048477803 -0.332518955 SWDSSSPVDRPEPEAAS(ph)PTTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SWDSSSPVDRPEPEAASPTTR 21 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SWDSSSPVDRPEPEAAS(0.867)PT(0.127)T(0.006)R;SWDSSSPVDRPEPEAAS(0.99)PT(0.009)T(0.001)R;SWDSSSPVDRPEPEAAS(0.993)PT(0.006)T(0.001)R 222.69 2.32E-25 1352470000 689390 765110 792710 745980 728170 679970 840880 654832 724020 TRUE FALSE 646242.3105 821759.5405 811513.4555 765123.1097 670982.4655 876266.3006 714797.8503 736589.2167 603176.3847 1.071398561 1.362386793 1.345399913 1.26848983 1.112415013 1.452752997 1.185056094 1.221183779 1 19.20222042 0.707964307 1.235486199 1.000777579 1.28129203 0.317408284 0.115415354 1.033768714 2.624896335 0.100946628 0.03070453 5.104630448 -0.707964307 0.280514451 SWEDS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 208.75 5.53E-05 4859400000 5755930 6151520 6124460 6411310 7100890 5001070 5803840 5246500 6843620 TRUE FALSE 5395676.616 6606984.941 6269735.083 6575835.069 6543214.743 6444797.723 4933608.072 5901537.074 5701375.611 0.946381537 1.158840496 1.09968813 1.153376925 1.147655441 1.130393464 0.86533644 1.035107574 1 22.44287862 1.756611619 25 0.95645188 1.114831915 0.433085403 0.074335628 5.481036634 7598.855826 0.030916278 0.017144879 57.09678034 -1.756611619 0.158380035 SWEEQMIEVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SWEEQMIEVGR 11 0 Q00059;Q00059-2 Q00059 TFAM "Transcription factor A, mitochondrial" 0 ;; 224.68 1.40E-11 504920000 388583 433123 381596 356864 505871 344968 367829 406079 549277 FALSE TRUE 364262.2837 465191.8776 390647.6373 366021.7344 466141.9322 444554.6615 312676.4562 456778.857 457599.1202 0.796029248 1.016592596 0.85368966 0.799874209 1.018668768 0.971493698 0.683297765 0.998207463 1 18.80372475 SWGHES(ph)PEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SWGHESPEER 10 0 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 SWGHES(1)PEER 142.29 2.32E-05 184340000 158310 197760 211630 208400 209360 186630 254260 185560 241810 TRUE FALSE 148401.6597 212402.3562 216649.9635 213747.8968 192917.7101 240507.0513 216136.0734 208727.5745 201450.3488 0.736666184 1.05436579 1.075450923 1.061045057 0.957643962 1.193877562 1.072899971 1.036124165 1 17.62006478 4.738787541 5.661924224 1.064811109 0.725768109 0.730519765 0.060881793 0.067845233 9.073502193 0.013438561 0.089001162 54800.88105 -4.738787541 -0.339043 SWHDIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SWHDIEK 7 0 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;; 124.08 0.0041813 1264680000 1193290 2071500 1887810 1936160 2070380 1736700 2562680 2045070 1870830 FALSE TRUE 1118604.109 2224876.015 1932589.745 1985845.144 1907780.706 2238057.097 2178429.925 2300401.491 1558576.387 0.717708877 1.427505276 1.239971143 1.274140402 1.224053388 1.435962405 1.397704946 1.475963264 1 20.57179743 4.744339886 24.76659278 1.327859598 0.717708577 0.635018769 0.140359203 329.2743751 1411031.809 0.030216252 0.269921992 55505.9942 -4.744339886 -0.610151021 SWHDIEKDNAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SWHDIEKDNAR 11 1 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 81.92 0.012231 127580000 37599 69357 58283 71809 79549 45083 75090 53086 102980 FALSE TRUE 35245.74571 74492.26445 59665.50028 73651.74051 73301.54243 58097.73024 63830.9516 59713.90396 85791.97272 0.410828013 0.868289446 0.695467168 0.858492213 0.854410268 0.67719308 0.744020094 0.696031366 1 16.38855505 -2.587947018 2.164095222 5.84023186 0.74150575 0.288358371 0.133410417 2969391.864 263678.1996 70402622.33 0.030142471 0.002582575 2.587947018 -5.09872611 SWHDVQVSSAYVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SWHDVQVSSAYVK 13 0 O43399;O43399-7;O43399-5;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 0 ; 128.9 0.00015992 521810000 626590 785590 533230 495990 833080 422730 672370 704670 1047810 FALSE TRUE 587372.8504 843755.901 545878.4674 508717.9431 767653.2573 544765.2886 571554.3605 792649.6007 872923.7419 0.672879912 0.966586038 0.625344966 0.582774782 0.879404718 0.624069735 0.654758638 0.908039915 1 19.7354961 1.072905457 4.838102673 0.99759924 0.724932009 0.412838101 0.120489838 0.189109008 7.647434205 0.115036388 0.029181395 11.82784043 -1.072905457 -0.272667231 SWHPEEFNCAHCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SWHPEEFNCAHCK 13 0 Q96HC4;Q96HC4-4;Q96HC4-7;H0Y8Y3;A0A0A0MSP3;Q96HC4-6 Q96HC4;Q96HC4-6 PDLIM5 PDZ and LIM domain protein 5 0 ; 102.87 0.00095715 479850000 211306 308030 286600 271680 367720 218600 363800 298320 344360 FALSE TRUE 198080.7347 330836.8617 293398.2873 278651.7688 338840.7545 281706.2713 309251.5674 335565.9087 286884.0913 0.690455625 1.153207416 1.022706717 0.97130436 1.181106812 0.981951526 1.077966944 1.169691589 1 18.13010844 4.74634586 24.98921717 1.069664616 0.690455441 0.703479063 0.077387644 501.7763945 1610573.635 0.016739677 0.181118834 55762.96532 -4.74634586 -0.379209174 SWLKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SWLKPR 6 1 P53396;P53396-2;P53396-3;K7ESG8 P53396 ACLY ATP-citrate synthase 0 91.26 0.043863 3047800000 3003700 5417500 4442400 4036900 5629300 3492000 4371200 5096400 4851800 FALSE TRUE 2815703.779 5818617.337 4547775.826 4140493.688 5187197.486 4500083.712 3715779.14 5732696.759 4042003.236 0.696610966 1.43953802 1.12512919 1.024366743 1.283323437 1.113330062 0.919291481 1.418281091 1 21.94663905 2.006525571 24.89493382 1.081745114 1.15924695 0 0.229413919 742.5680564 2832872.276 0.079969226 0.058899414 101.5139136 -2.006525571 0.077501835 SWPEGHFATITLTFIDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SWPEGHFATITLTFIDK 17 0 O95433;G3V438 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 202.82 1.02E-11 146460000 375510 421970 374670 330730 462440 271010 428790 454580 365480 FALSE TRUE 352007.4994 453213.0979 383557.3493 339217.0917 426121.8278 349246.1875 364496.9202 511335.3137 304479.0269 1.156097689 1.488487081 1.259716813 1.114090173 1.399511264 1.147028717 1.197116675 1.679377785 1 18.21598333 3.716323193 20.38705262 1.254517597 1.354454646 0.012657914 0.199503364 113.7331379 214735.9729 0.04787913 0.075415681 5203.831105 -3.716323193 0.099937048 SWPS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SWPSPK 6 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 SWPS(1)PK;SWPS(1)PK;S(0.001)WPS(0.999)PK;S(0.006)WPS(0.994)PK 101.43 0.038321 1434320000 6650780 3929550 5126420 4484470 5098080 3806480 6233860 4206620 7512630 TRUE FALSE 6234519.552 4220497.971 5248021.103 4599549.092 4697697.361 4905348.983 5299150.565 4731825.767 6258723.52 0.996132763 0.674338459 0.838513011 0.734902106 0.75058394 0.783761891 0.846682322 0.756036874 1 22.57743702 -2.075856203 0.569739466 1.233277649 0.788780916 0.344471796 0.086681956 130.7061992 11.06075537 39.5798723 0.032078622 0.00839738 2.075856203 -0.444496733 SWQGDGS(ph)PMANGAGAVVHHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SWQGDGSPMANGAGAVVHHQR 21 0 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 SWQGDGS(1)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR 175.46 2.80E-12 1371660000 317169 326447 320279 326534 337631 285046 373241 271954 386026 TRUE FALSE 297317.9585 350617.4755 327876.1691 334913.4153 311114.8232 367334.1529 317276.977 305908.0555 321595.7668 0.924508309 1.09024282 1.019528871 1.041411144 0.967409572 1.142223222 0.986570751 0.951219161 1 18.29488889 1.533730674 11.09164204 0.973570445 1.036392469 0.136962677 0.060447886 0.179970073 29.96194005 0.028978451 0.013460316 34.17674308 -1.533730674 0.062822024 SWS(ph)LATFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.006)WS(0.994)LATFR;S(0.003)WS(0.997)LATFR 128.86 0.0011702 74217000 140917 184894 160675 197521 195884 144072 186000 166566 131952 TRUE FALSE 132097.2565 198583.7441 164486.2869 202589.7233 180500.0608 185663.2476 158111.0267 187362.1318 109928.3588 1.201666776 1.806483299 1.4963044 1.842925025 1.641979038 1.68894769 1.438309718 1.704402157 1 16.74620409 -0.515095062 6.556336313 0.99999897 1.610708814 0.503146749 0.188046925 0 0 0.160468059 0.037822684 0.30542525 0.515095062 0.610709844 SWS(ph)PPPEVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 SWSPPPEVSR 10 0 Q9NR19;Q9NR19-2;F8WCJ4;C9IYL0;B4DEH9;C9JY31;C9JXD9 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 1 SWS(1)PPPEVSR;S(0.001)WS(0.999)PPPEVSR;SWS(1)PPPEVSR;SWS(1)PPPEVSR;SWS(1)PPPEVSR;S(0.007)WS(0.993)PPPEVSR;S(0.007)WS(0.993)PPPEVSR;S(0.108)WS(0.892)PPPEVSR 168.71 5.09E-06 28715600000 4497090 4926300 4974840 5056110 5251770 4620090 5879330 4644430 5951310 TRUE FALSE 4215625.164 5291048.378 5092845.554 5185858.343 4839317.169 5953834.982 4997779.048 5224297.309 4957997.914 0.850267636 1.067174386 1.027198003 1.045958153 0.976062768 1.200854677 1.008023629 1.053711074 1 22.24132623 4.741636969 24.50855648 1.049889793 0.850267538 0.508529274 0.060851668 168.6825539 1343764.811 0.012926409 0.091287214 55161.61448 -4.741636969 -0.199622255 SWSHYTVPAGMTVIQWVSDFSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SWSHYTVPAGMTVIQWVSDFSER 23 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 275.2 1.01E-51 384780000 186888 398050 290156 280002 443530 226473 303745 392120 261310 FALSE TRUE 175191.0137 427522.0362 297038.6373 287187.3254 408696.9429 291852.0786 258201.2571 441077.0452 217695.6729 0.804751934 1.963851787 1.364467348 1.319214671 1.87737743 1.340642534 1.186065178 2.02611765 1 17.73195321 -1.750257485 2.683008237 0.894366359 1.494587272 0.139077721 0.378844217 44481916.7 34064830.72 31116583.52 0.082641613 0.017772254 1.750257485 0.600220913 SWSTAT(ph)SPLGGERPFR ddPTM_SK-BR-3_Pertuzumab_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(0.001)WS(0.01)T(0.012)AT(0.546)S(0.431)PLGGERPFR 111.77 0.0012788 237660000 286550 266870 275160 299470 277770 192940 330220 217920 333640 TRUE FALSE 268615.347 286629.3325 281686.9251 307154.9072 255955.0647 248638.6459 280706.5766 245127.7917 277953.3286 0.966404498 1.031213887 1.013432458 1.105059287 0.920856267 0.894533795 1.009905433 0.881902703 1 18.08448313 2.710600555 24.9977324 0.943786598 1.026792762 0.411796363 0.051943713 716.2585134 640371.0306 0.015540929 0.01465445 513.5710747 -2.710600555 0.083006163 SWSYNGYYS(ph)DLSTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SWSYNGYYSDLSTAR 15 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 SWSYNGYYS(0.999)DLS(0.001)TAR;SWSYNGYYS(1)DLSTAR;SWSYNGYYS(1)DLSTAR;SWSYNGYYS(1)DLSTAR 182.09 5.89E-07 143618000 292438 339515 319680 316439 335033 222228 394518 243472 470570 TRUE FALSE 274134.8276 364653.0439 327262.9606 324559.3605 308720.8596 286381.616 335363.6884 273870.0151 392028.827 0.699272117 0.930168954 0.834793102 0.82789667 0.787495302 0.730511626 0.855456705 0.698596624 1 18.58060022 3.055797295 3.025471358 0.803087314 0.846751237 0 0.098222885 0.932814327 17.41502094 0.0271667 0.032538779 1137.096427 -3.055797295 0.043663923 SWTS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 SWTSPK 6 0 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 1 SWT(0.018)S(0.982)PK;SWTS(1)PK;S(0.003)WT(0.01)S(0.987)PK;SWT(0.202)S(0.798)PK;SWT(0.021)S(0.979)PK 129.77 0.016835 3691540000 14156400 9360300 10997800 10757600 10825800 8348430 14135500 8849500 11790900 TRUE FALSE 13270376.19 10053346.35 11258673.01 11033658.23 9975585.337 10758486.22 12016013 9954379.555 9822922.618 1.350960067 1.023457757 1.14616326 1.123256149 1.015541476 1.095242896 1.223262513 1.013382671 1 23.2277209 7.626620471 0.013677175 1.87E-06 2.416267165 0.231265128 0.097124 13289.30159 14.90044737 1085.706722 1590.858636 42327290.75 -7.626620471 2.416265291 SWVIGS(ph)PEILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SWVIGSPEILR 11 0 Q6P0Q8;Q6P0Q8-2;A0A669KBJ4;E7ERL6 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 SWVIGS(1)PEILR;SWVIGS(1)PEILR;SWVIGS(1)PEILR;SWVIGS(1)PEILR 158.11 3.17E-05 227419000 486330 494318 543342 505372 607552 561223 760260 627979 588688 TRUE FALSE 455891.4734 530917.8191 556230.3288 518340.7011 559837.3167 723238.9694 646266.0709 706383.5605 490432.1697 0.9295709 1.082550966 1.134163628 1.056905997 1.141518341 1.474697245 1.317748123 1.440328763 1 18.90369409 2.405544447 6.325034479 1.336952128 1.072653353 0.432601679 0.136775418 0.166947243 11.47027287 0.042234833 0.035257771 254.4160156 -2.405544447 -0.264298775 SYCAEIAHNVSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SYCAEIAHNVSSK 13 0 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ;;;;; 204.13 8.03E-08 8195690000 8851320 8737490 9351180 9206920 9279480 7244340 11403930 8506620 9822610 FALSE TRUE 8297331.681 9384422.851 9572994.406 9443185.154 8550707.072 9335663.356 9694016.565 9568690.232 8183152.935 1.013952904 1.146797931 1.169841806 1.153978818 1.044915956 1.140839409 1.18463099 1.169315826 1 22.96422538 4.741005273 23.98347742 1.138406321 1.013952827 0.237205633 0.059903541 156.6142471 1536304.738 0.013073318 0.088417587 55081.43846 -4.741005273 -0.124453494 SYDAAGTIHDYVVAMLCGLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYDAAGTIHDYVVAMLCGLPR 21 0 A0A0B4J2A0;Q9UHJ6 A0A0B4J2A0 TRPV1;SHPK Sedoheptulokinase 0 180.14 5.50E-17 55886000 114090 118250 105980 119440 145150 114750 99790 110610 47589 FALSE TRUE 106949.3106 127005.353 108493.8956 122505.0326 133750.5045 147876.4622 84827.4159 124419.902 39646.08846 2.697600563 3.203477517 2.736559894 3.089965173 3.373611614 3.729913036 2.13961627 3.138264248 1 15.27489091 0.019801575 0.761303068 0.943956769 3.048469709 0.682555585 0.430105989 2.798146415 1.693095969 0.863022813 0.140770027 1.046650235 -0.019801575 2.10451294 SYDNLT(ph)TACDNTVPLASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SYDNLTTACDNTVPLASR 18 0 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 S(0.15)YDNLT(0.847)T(0.003)ACDNTVPLASR;S(0.002)YDNLT(0.995)T(0.003)ACDNTVPLASR 335.4 5.16E-74 770610000 446660 461130 482340 504560 471950 442970 570950 439570 421220 TRUE FALSE 418704.3479 495272.545 493781.3326 517507.8638 434884.9508 570848.248 485341.3479 494451.2821 350915.6608 1.19317658 1.41137202 1.40712253 1.474735732 1.239286243 1.626739162 1.383071211 1.409031677 1 18.42076481 -1.546998549 9.293129187 0.999975152 1.402802718 0.519106054 0.118566845 5.38E-05 2.62E-06 0.101128437 0.023834738 0.028379285 1.546998549 0.402827566 SYDQVHSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SYDQVHSGK 9 0 Q15067-2;Q15067;Q15067-3 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ;;; 113.93 0.0017211 1334650000 2381640 2324350 2220410 2403930 2708380 1671460 2920650 2345390 1955470 FALSE TRUE 2232577.404 2496447.292 2273079.174 2465618.914 2495674.76 2153983.368 2482725.646 2638217.104 1629089.424 1.370444968 1.53241882 1.395306568 1.513495132 1.531944608 1.322200817 1.523995927 1.619442779 1 20.63563437 -0.775027368 7.261413993 1.000011587 1.47360155 0.736841438 0.089416445 0 3.22E-10 0.078403909 0.018479978 0.167869823 0.775027368 0.473589963 SYDSGSFTIMQEVYSAFLPDGCDHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYDSGSFTIMQEVYSAFLPDGCDHLR 26 0 Q8TEQ6 Q8TEQ6 GEMIN5 Gem-associated protein 5 0 159.73 1.91E-11 45066000 108540 116440 121820 118320 128100 103400 122460 107710 102970 FALSE TRUE 101746.6751 125061.3388 124709.6279 121356.2915 118039.5427 133249.9014 104098.2599 121157.8306 85783.64179 1.186084818 1.457869311 1.453769336 1.414678708 1.376014591 1.553325304 1.213497792 1.412365202 1 16.38841494 0.14720319 0.696720199 0.988160351 1.409362631 0.529783075 0.111917828 2.476925218 1.458223186 0.17929279 0.037262551 1.40347018 -0.14720319 0.42120228 SYDVPPPPMEPDHPFYSNISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SYDVPPPPMEPDHPFYSNISK 21 0 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 0 ; 273.44 1.03E-44 670430000 1285830 1240940 1293030 1259240 1339060 1039160 1525500 1204720 1428420 FALSE TRUE 1205352.196 1332820.489 1323701.282 1291554.23 1233895.629 1339148.623 1296765.437 1355131.944 1190007.474 1.012894643 1.120010183 1.112347032 1.085332873 1.036880571 1.125327909 1.08971201 1.138759187 1 20.1825392 -2.520618044 1.969607331 2.55E-05 1.094315289 0.336845922 0.03937338 466788.8399 43411.99741 2093971.725 0.008784256 0.003015657 2.520618044 1.094289814 SYEALVQHVIEDHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SYEALVQHVIEDHER 15 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 ;;;;; 261.64 3.39E-25 1103743000 1017779 1206962 1174425 1167296 1229440 1031579 1298175 1022134 1245167 FALSE TRUE 954078.0292 1296326.722 1202282.916 1197250.792 1132884.742 1329379.111 1103525.71 1149749.68 1037340.584 0.919734602 1.249663556 1.159004993 1.154154007 1.092104907 1.281526176 1.063802697 1.108362767 1 19.98445821 1.017520114 1.444194872 1.004550641 1.1531544 0.130579922 0.100171567 0.676097321 2.877241217 0.084678892 0.025285475 10.41166327 -1.017520114 0.148603759 SYEDMIGEEVPSDQYYWAPLAQHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 182.39 2.23E-17 715240000 521934 628813 618895 579730 672210 546414 705130 640670 767490 FALSE TRUE 489267.0826 675370.9688 633575.4817 594606.8533 619417.3382 704154.8515 599402.3026 720659.0598 639390.9608 0.765208007 1.056272313 0.990904658 0.929958179 0.968761487 1.101289969 0.937458205 1.127102358 1 19.28633882 2.43494202 24.81340589 1.028868434 0.963363906 0.205011627 0.090588304 293.4219312 172614.0095 0.029427934 0.024621191 272.2337838 -2.43494202 -0.065504528 SYELPDGQVITIGNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 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 ;;;;;;;;;;;; 344.54 1.54E-72 34499629000 4474890 4890420 4834970 4824860 5223000 4310820 5305850 4354530 4944770 FALSE TRUE 4194814.623 5252511.785 4949657.772 4948674.076 4812806.649 5555283.754 4510287.05 4898202.656 4119455.943 1.018293357 1.275049875 1.201531911 1.201293119 1.168311232 1.348547923 1.094874448 1.189041156 1 21.97402238 0.590267742 1.075391819 1.000824429 1.204002021 0.291374121 0.089919457 1.528017577 2.688480119 0.076677225 0.024028554 3.892850645 -0.590267742 0.203177592 SYENQKPPFDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYENQKPPFDAK 12 1 E7EMD0;P16435;H0Y4R2 E7EMD0;P16435 POR NADPH--cytochrome P450 reductase 0 121.04 0.00034958 124010000 158330 117500 117760 124770 177970 101100 188130 172080 204810 FALSE TRUE 148420.4079 126199.8223 120553.3228 127971.8094 163992.9541 130285.9288 159921.653 193564.5668 170625.8879 0.86985867 0.739628809 0.706535944 0.750014028 0.961125865 0.763576562 0.937264884 1.134438444 1 17.38047703 1.53502139 3.155004516 1.065674736 0.785245815 0.653160191 0.080697401 0.127261959 2.769530792 0.056300486 0.021424266 34.27846687 -1.53502139 -0.28042892 SYETLVDFDNHLDDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SYETLVDFDNHLDDIR 16 0 M0R1B0;O43402 M0R1B0 EMC8 ER membrane protein complex subunit 8 0 ; 153.74 4.22E-07 290640000 276770 322440 349420 345630 324580 301210 360270 306270 319740 FALSE TRUE 259447.4597 346313.7931 357708.4074 354499.451 299088.7961 388164.4373 306250.8581 344508.4837 266373.3284 0.973999391 1.300106866 1.342883725 1.330836886 1.122818106 1.457219608 1.149705415 1.2933295 1 18.02309011 -0.740353748 0.900018051 0.980825233 1.261035943 0.237766476 0.136110701 60.59750262 26.28579623 3.868902499 0.038689108 0.181821925 0.740353748 0.28021071 SYGPAPGAGHVQEESNLSLQALESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SYGPAPGAGHVQEESNLSLQALESR 25 0 Q13155 Q13155 AIMP2 Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 0 ; 332.25 6.74E-88 669130000 292984 376747 364502 352957 376098 339117 439630 365372 454591 FALSE TRUE 274646.6544 404641.7399 373148.1596 362014.4742 346560.7802 437014.5728 373711.5628 410989.4985 378716.8253 0.725203202 1.068454615 0.985295964 0.95589752 0.915092114 1.153934929 0.986783628 1.085215842 1 18.53075999 2.264744062 24.99991947 1.051552238 0.957589977 0.265997985 0.09851071 368.0027235 351367.216 0.032088924 0.026839773 183.9687517 -2.264744062 -0.093962261 SYHEEFNPPKEPMKDDITGEPLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYHEEFNPPKEPMKDDITGEPLIR 24 2 F8W1A4;P54819-2;P54819;P54819-6;P54819-3;P54819-5;F8VY04;A0A5K1VW67;P54819-4 F8W1A4 AK2 "Adenylate kinase 2, mitochondrial;Adenylate kinase 2, mitochondrial;Adenylate kinase 2, mitochondrial, N-terminally processed" 0 138.35 4.34E-06 90331000 101240 105480 116190 119180 154020 92995 161880 118730 150110 FALSE TRUE 94903.56912 113289.849 118946.0817 122238.3606 141923.8905 119841.1469 137607.5968 133553.7019 125055.6713 0.758890566 0.905915324 0.951145042 0.977471548 1.13488568 0.958302376 1.100370702 1.06795398 1 16.93221096 5.608826327 0.457621066 1.061263953 0.23549515 0.726172993 0.055753423 4.95673933 0.438714294 0.031922087 2.615893148 406280.8264 -5.608826327 -0.825768803 SYIEGYVPSQADVAVFEAVSS(ph)PPPADLCHALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYIEGYVPSQADVAVFEAVSSPPPADLCHALR 32 0 P24534;C9JZW3;F2Z2G2 P24534 EEF1B2 Elongation factor 1-beta 1 SYIEGYVPSQADVAVFEAVS(0.242)S(0.757)PPPADLCHALR 63.727 0.0055749 25942000 28389 35624 33626 31052 39489 23050 30171 28205 39874 TRUE FALSE 26612.18317 38261.63803 34423.6246 31848.84689 36387.69323 29704.16081 25647.13864 31726.45634 33218.7718 0.801118817 1.151807726 1.036270239 0.958760519 1.095395502 0.894198045 0.772067637 0.95507614 1 15.01971111 2.141798226 6.717194235 0.871893439 1.029354544 0.137016279 0.110521315 0.24988773 14.82201374 0.03895231 0.028709095 138.6111689 -2.141798226 0.157461104 SYIEGYVPSQADVAVFEAVSSPPPADLCHALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SYIEGYVPSQADVAVFEAVSSPPPADLCHALR 32 0 P24534;C9JZW3;F2Z2G2 P24534 EEF1B2 Elongation factor 1-beta 0 ; 145.86 4.58E-10 176160000 352349 424595 405907 387630 429997 380736 490576 364609 417362 FALSE TRUE 330296.1051 456032.4556 415535.3057 397577.2421 396226.7701 490648.3025 417018.6831 410131.2363 347701.5859 0.949941324 1.311562771 1.195091776 1.143443856 1.139559859 1.411118966 1.199358013 1.179549513 1 18.40749012 0.775598975 3.2120213 1.000045778 1.210865122 0.19150064 0.11940778 2.192644355 29.48027929 0.104389022 0.027131379 5.964842424 -0.775598975 0.210819345 SYIYSGSHDGHINYWDSETGENDSFAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYIYSGSHDGHINYWDSETGENDSFAGK 28 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 96.338 0.0011869 117920000 33440 49570 55553 48516 52013 42682 58072 47126 56017 FALSE TRUE 31347.05009 53240.21438 56870.74339 49761.0027 47928.10879 55003.60052 49364.64271 53009.78484 46667.40082 0.671711935 1.140843789 1.218639616 1.066290426 1.027014746 1.178630041 1.057797131 1.135906091 1 15.5101275 4.740574428 24.90964608 1.115256329 0.671711776 0.794250037 0.068763108 73.06417807 903692.475 0.01613464 0.105204136 55026.82162 -4.740574428 -0.443544554 SYLEGS(ph)SDNQLKDSESTPVDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYLEGSSDNQLKDSESTPVDDR 22 1 Q9UHI6;E9PJ60 Q9UHI6 DDX20 Probable ATP-dependent RNA helicase DDX20 1 SYLEGS(0.544)S(0.456)DNQLKDSESTPVDDR 129.24 9.35E-06 220960000 122380 88461 110380 91491 115050 102800 135230 97436 167500 TRUE FALSE 114720.4543 95010.74448 112998.2657 93838.81395 106014.4371 132476.6912 114953.5169 109601.0991 139543.1679 0.822114447 0.680869912 0.809772828 0.672471575 0.759725028 0.949359923 0.82378463 0.785427913 1 17.09035197 2.359112791 7.627883467 0.871744324 0.743150769 0.452038075 0.075875641 0.214886878 13.47822724 0.023969441 0.020003581 228.6192478 -2.359112791 -0.128593555 SYLTPVRDEESESQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SYLTPVRDEESESQR 15 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4;A0A3B3ISH4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 0 ; 134.14 3.37E-05 273670000 227090 225590 223740 216410 248770 189906 248630 199353 288360 FALSE TRUE 212876.8423 242292.9183 229047.2185 221963.447 229232.6077 244728.7793 211350.2397 224242.6609 240230.8531 0.886134481 1.008583682 0.953446302 0.923958951 0.954218015 1.018723349 0.879779749 0.933446549 1 17.87406192 1.728231828 24.99999994 0.926870431 0.961519426 0.016018659 0.047502295 1.832978843 4415.082961 0.020104751 0.011149137 53.48497881 -1.728231828 0.034648995 SYMNPGDQS(ph)PADSNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 SYMNPGDQSPADSNK 15 0 Q92754;Q92754-2 Q92754 TFAP2C Transcription factor AP-2 gamma 1 SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK;SYMNPGDQS(1)PADSNK 456.56 2.75E-176 6335130000 15068930 9423869 11299960 10220220 11024234 8502977 14489170 9688339 11480770 TRUE FALSE 14125792.57 10121622.07 11568000.39 10482488.15 10158435.13 10957648.43 12316653.47 10897949.45 9564555.318 1.476889631 1.058242828 1.209465574 1.095972348 1.062091733 1.145651634 1.287739269 1.139409945 1 23.18926646 4.747535218 24.82678114 1.142249766 1.476889821 0.636390941 0.082706899 766.2604189 2119684.944 0.01967815 0.243619734 55915.88689 -4.747535218 0.334640055 SYNPFDDDGEDEGARPAPWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SYNPFDDDGEDEGARPAPWR 20 1 O95721 O95721 SNAP29 Synaptosomal-associated protein 29 0 ;;; 192.98 8.22E-18 792720000 306347 344716 360971 337747 365963 266815 337133 292832 365386 FALSE TRUE 287173.2881 370239.1313 369533.4026 346414.1598 337221.7422 343840.1591 286583.0364 329392.7198 304400.7161 0.943405429 1.216288634 1.213970214 1.138020187 1.107821777 1.129564225 0.941466367 1.082102316 1 18.21561223 1.851998314 6.553758429 1.005468594 1.146691839 0.283821668 0.083236372 0.249036478 12.48495919 0.035604869 0.021648778 71.12107527 -1.851998314 0.141223245 SYQFGIIGNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYQFGIIGNDR 11 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 123.67 0.0021796 0 117480 139630 126550 135130 148200 116590 144860 107750 141210 FALSE TRUE 110127.1365 149968.3505 129551.8258 138597.6646 136560.9698 150247.6403 123139.5878 121202.8247 117641.1387 0.936127767 1.274795128 1.101245934 1.178139434 1.160826657 1.277169211 1.046739169 1.030275854 1 16.84403313 1.583617146 7.655140315 1.023701019 1.163873684 0.28922939 0.095328597 0.133160059 16.37684271 0.045977867 0.021771652 38.33691355 -1.583617146 0.140172665 SYQNS(ph)PS(ph)SDDGIRPLPEYSTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SYQNSPSSDDGIRPLPEYSTEK 22 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 2 SYQNS(1)PS(0.57)S(0.43)DDGIRPLPEYSTEK;SYQNS(1)PS(0.852)S(0.148)DDGIRPLPEYSTEK;SYQNS(0.998)PS(0.647)S(0.354)DDGIRPLPEYSTEK 255.95 8.00E-31 1422780000 2241840 1733410 1951830 1979330 2170340 1721290 2474250 1729010 2318700 TRUE FALSE 2101527.236 1861753.48 1998128.329 2030122.959 1999890.251 2218198.48 2103259.182 1944880.705 1931693.991 1.087919332 0.963793173 1.034391751 1.050954742 1.035303863 1.148317741 1.088815927 1.006826503 1 20.88143514 3.110052085 1.718886849 1.071148342 1.013156725 0.000590546 0.052415411 0.586676575 3.551144623 0.017058866 0.022083562 1288.40406 -3.110052085 -0.057991617 SYQNS(ph)PSS(ph)DDGIRPLPEYSTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYQNSPSSDDGIRPLPEYSTEK 22 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 2 SYQNS(1)PS(0.202)S(0.798)DDGIRPLPEYSTEK 247.51 2.63E-31 523480000 994380 780280 872260 859930 926060 753820 1103600 756360 1053600 TRUE FALSE 932143.5308 838052.7431 892950.4191 881997.2597 853330.9831 971435.5968 938125.4253 850793.211 877747.3535 1.061972477 0.954776724 1.017320549 1.004841833 0.972182918 1.106737141 1.068787529 0.969291685 1 19.74344622 2.267913578 24.99393862 1.047127712 0.997928056 0.093550996 0.046370875 308.5840046 262756.9894 0.015134276 0.012660554 185.3162821 -2.267913578 -0.049199655 SYQNSPS(ph)SDDGIRPLPEYSTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SYQNSPSSDDGIRPLPEYSTEK 22 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 SYQNS(0.075)PS(0.463)S(0.463)DDGIRPLPEYSTEK;SYQNSPS(0.5)S(0.5)DDGIRPLPEYSTEK 209.89 3.12E-23 995390000 925210 797070 819500 832340 842100 631590 1012110 692600 922610 TRUE FALSE 867302.7576 856085.8922 838938.927 853699.2535 775964.8629 813919.78 860353.5015 779072.6346 768620.4307 1.128388894 1.11379539 1.091486634 1.110690296 1.009555343 1.058935916 1.119347687 1.013598655 1 19.5519118 7.999999666 0.041855407 0.79117739 1.56345149 0.524719606 0.033859129 601.0885999 1.912210551 9.392410704 32.24924306 99999923.05 -7.999999666 0.7722741 SYQSELEALRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYQSELEALRR 11 1 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 134.08 0.00023795 116820000 58191 79110 65169 62853 90677 49215 58303 73689 122090 FALSE TRUE 54548.92918 84967.38671 66714.83946 64465.91439 83555.59419 63422.57156 49561.00641 82889.23386 101712.3903 0.536305646 0.835369088 0.655916543 0.633805913 0.821488847 0.623548138 0.487266166 0.814937429 1 16.63413591 0.996046359 24.60931142 1.000000015 0.667019916 0.522292055 0.10786616 89.2429476 555494.6549 0.106088442 0.02652211 9.909377169 -0.996046359 -0.332980099 SYS(ph)AGNASQLEQLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SYSAGNASQLEQLSR 15 0 Q14678;Q14678-2 Q14678 KANK1 KN motif and ankyrin repeat domain-containing protein 1 1 SYS(1)AGNASQLEQLSR;SYS(1)AGNASQLEQLSR;SYS(1)AGNASQLEQLSR 310.24 4.08E-56 672790000 307849 359530 304921 310545 422610 229705 402900 248857 616030 TRUE FALSE 288581.2806 386149.9753 312153.8701 318514.1105 389419.9153 296017.1046 342488.8853 279927.3443 513210.6133 0.562305754 0.752420089 0.608237363 0.620630404 0.758791625 0.576794589 0.667345679 0.545443405 1 18.96919148 -1.206537394 4.584270446 1.000081476 0.6464127 0.706176315 0.073441073 5.45E-05 9.44E-06 0.063398642 0.014939772 0.062153073 1.206537394 -0.353668777 SYS(ph)EPEKMNEVGIVEEAEPAPLGPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SYSEPEKMNEVGIVEEAEPAPLGPQR 26 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 S(0.019)YS(0.981)EPEKMNEVGIVEEAEPAPLGPQR;S(0.011)YS(0.989)EPEKMNEVGIVEEAEPAPLGPQR 281.55 4.30E-61 229200000 271990 230983 210655 210532 322490 100541 281840 220640 668760 TRUE FALSE 254966.6314 248085.2217 215651.8361 215934.6075 297162.9363 129565.5546 239580.7085 248187.3897 557139.6356 0.457635061 0.445283742 0.387069636 0.387577178 0.533372457 0.232554904 0.430019143 0.445467121 1 19.08767943 0.565963764 2.58628998 0.999986893 0.407934895 0.855364741 0.075749774 1.906525746 10.9517998 0.06588556 0.017504131 3.680982598 -0.565963764 -0.592051998 SYS(ph)HDVLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYSHDVLPK 9 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 S(0.312)Y(0.001)S(0.687)HDVLPK 79.659 0.027605 111850000 150560 127530 140170 137550 158980 118850 168820 110820 182960 TRUE FALSE 141136.7184 136972.4539 143494.8986 141079.7659 146494.3521 153160.0656 143507.0082 124656.1209 152422.794 0.92595546 0.898634976 0.94142677 0.925581812 0.96110528 1.004837017 0.941506217 0.817831229 1 17.21771914 3.73797694 2.172393157 0.944144818 0.911301517 0.051994147 0.051406798 0.932337133 8.678348837 0.013965626 0.028217482 5469.869187 -3.73797694 -0.032843301 SYS(ph)LSELSVLQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SYSLSELSVLQAK 13 0 Q9P0V3;Q9P0V3-2 Q9P0V3 SH3BP4 SH3 domain-binding protein 4 1 SYS(0.965)LS(0.035)ELSVLQAK;SYS(0.866)LS(0.134)ELSVLQAK;SYS(0.991)LS(0.009)ELSVLQAK;SYS(0.996)LS(0.004)ELSVLQAK;SYS(0.892)LS(0.108)ELSVLQAK;SYS(0.993)LS(0.007)ELSVLQAK 353.22 5.09E-76 2679890000 3890910 3362270 3602290 3334700 4719050 2933680 4631520 4049330 6766040 TRUE FALSE 3647384.889 3611215.969 3687738.02 3420274.048 4348434.849 3780585.792 3937066.573 4554897.764 5636744.214 0.647072982 0.640656349 0.654231925 0.606781844 0.771444416 0.670703805 0.69846465 0.80807246 1 22.42643067 0.473265665 0.513390104 1.020482298 0.641920365 0.874611615 0.040959861 0.614215736 0.287646198 0.062453279 0.019378976 2.973484403 -0.473265665 -0.378561934 SYS(ph)PAHNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYSPAHNR 8 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.084)YS(0.916)PAHNR 88.056 0.009588 769910000 406630 473190 406860 419420 436680 397580 398840 388040 510140 TRUE FALSE 381179.7542 508225.48 416510.9113 430183.0273 402384.9143 512354.8918 339037.6446 436487.6482 424994.3384 0.896905487 1.195840589 0.980038729 1.012208842 0.946800646 1.205556982 0.797746262 1.027043442 1 18.6970841 2.47438532 0.726522785 0.956431359 1.056819331 0 0.123253593 1.846105125 1.967239414 0.089779132 0.06915173 298.1160237 -2.47438532 0.100387972 SYS(ph)PDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 SYSPDGK 7 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK;S(0.006)YS(0.994)PDGK;S(0.007)YS(0.993)PDGK;SYS(1)PDGK;S(0.01)YS(0.99)PDGK;SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK;SYS(1)PDGK;S(0.001)YS(0.999)PDGK 154.35 0.0017667 50712061000 62546840 41469910 50118550 47375420 48029280 40005600 59373400 43191020 53550190 TRUE FALSE 58632144.93 44540385.29 51307385.67 48591153.48 44257254.09 51554567.28 50470909.87 48583513.92 44612317.34 1.31425912 0.998387619 1.150072194 1.089186942 0.992041139 1.155612852 1.131322309 1.089015698 1 25.41093875 4.752735432 24.57032966 1.085495919 1.314259319 0.588436095 0.062221612 1464.050543 2537699.446 0.014153797 0.299886799 56589.44464 -4.752735432 0.2287634 SYS(ph)PDGKES(ph)PSDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SYSPDGKESPSDKK 14 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 2 S(0.407)Y(0.005)S(0.588)PDGKES(0.987)PS(0.013)DKK;S(0.097)Y(0.008)S(0.895)PDGKES(0.615)PS(0.385)DKK;S(0.092)Y(0.006)S(0.902)PDGKES(0.851)PS(0.149)DKK 109.72 0.0005801 7655600000 6633960 1645370 2901440 2713710 2876640 1947180 4189030 2054430 3798180 TRUE FALSE 6218752.286 1767194.907 2970263.527 2783348.393 2650720.298 2509299.256 3560923.841 2310930.108 3164239.221 1.965323053 0.558489666 0.938697526 0.879626412 0.837711726 0.793018189 1.125364927 0.730327243 1 21.59342724 4.748288971 24.99764582 0.860089904 1.965323646 0.838917826 0.152500297 525.4719586 1350207.436 0.036325274 0.480612753 56013.0177 -4.748288971 1.105233742 SYS(ph)PDGKESPS(ph)DKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYSPDGKESPSDKK 14 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 2 S(0.002)YS(0.998)PDGKES(0.451)PS(0.549)DKK 133.48 0.00021813 740160000 2641200 705630 1221900 1158800 1325300 820220 1817700 909780 1779900 TRUE FALSE 2475892.007 757875.5794 1250884.045 1188536.77 1221216.284 1057004.199 1545152.76 1023368.036 1482823.191 1.66971492 0.511103133 0.843582736 0.801536405 0.823575117 0.712832255 1.04203439 0.690148388 1 20.49991515 -0.719738423 7.614034645 0.999999997 0.851307931 0.001492204 0.310976918 0 0 0.265082403 0.062480521 0.190660873 0.719738423 -0.148692066 SYS(ph)PDGKESPSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SYSPDGKESPSDK 13 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 S(0.012)YS(0.966)PDGKES(0.022)PSDK;S(0.001)YS(0.957)PDGKES(0.042)PS(0.001)DK 170.35 7.09E-05 217400000 320210 185595 228663 235420 296670 164195 302190 194633 528930 TRUE FALSE 300168.6277 199336.6469 234086.9943 241461.2758 273370.7349 211595.431 256879.4149 218933.3585 440648.166 0.681197951 0.452371443 0.531233334 0.547968412 0.620383235 0.480191335 0.582958094 0.496843912 1 18.74926767 -1.747419701 2.84536565 1.087720698 0.541008093 0.813275903 0.067792996 10325622.44 9168730.321 6398970.609 0.014601443 0.017888763 1.747419701 -0.546712605 SYS(ph)PDGKESPSDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 SYSPDGKESPSDKK 14 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 S(0.14)Y(0.025)S(0.834)PDGKES(0.001)PSDKK;S(0.107)Y(0.001)S(0.629)PDGKES(0.254)PS(0.009)DKK;S(0.072)Y(0.045)S(0.797)PDGKES(0.081)PS(0.005)DKK;S(0.015)YS(0.985)PDGKESPSDKK;S(0.001)YS(0.96)PDGKES(0.015)PS(0.024)DKK;S(0.009)YS(0.959)PDGKES(0.03)PS(0.001)DKK;S(0.012)YS(0.984)PDGKES(0.003)PSDKK 149.19 5.95E-06 10241890000 13865790 6512610 8778480 8716210 10857680 5452010 12291230 6954650 21415740 TRUE FALSE 12997954.96 6994810.421 8986709.691 8939882.705 10004961.61 7025916.781 10448274.17 7822953.362 17841314.64 0.728531233 0.392056895 0.503702214 0.501077577 0.56077491 0.393800397 0.585622437 0.438474043 1 24.08871859 -1.455437229 3.194260911 1.009022817 0.503222378 0.701463122 0.099662908 16843594.62 20048960.23 1347722.344 0.022409446 0.035039893 1.455437229 -0.505800439 SYS(ph)PDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 SYSPDHR 7 0 A0A024RAC6;Q14241 A0A024RAC6 TCEB3 Transcription elongation factor B polypeptide 3 1 S(0.027)YS(0.973)PDHR;S(0.281)Y(0.001)S(0.718)PDHR;S(0.009)YS(0.991)PDHR;S(0.181)Y(0.002)S(0.817)PDHR;SYS(1)PDHR;S(0.002)YS(0.998)PDHR 108.81 0.0075208 1441867000 2561494 3225196 2958075 2857216 3212208 2620069 3041944 2557461 3090377 TRUE FALSE 2401174.663 3463992.868 3028241.936 2930537 2959934.141 3376440.387 2585832.737 2876765.636 2574573.114 0.93264963 1.345463001 1.176211279 1.138261323 1.149679582 1.3114564 1.004373394 1.117375778 1 21.29590181 1.67707674 9.604417304 1.046845401 1.192625273 0.224033601 0.115126496 0.152594116 21.50631022 0.050896405 0.027294219 47.54192251 -1.67707674 0.145779872 SYS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SYSPER 6 0 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8W6A0;F8VWU8;Q8NEY8-6;F8WF16;B7Z8L1;Q8NEY8-3;Q8NEY8-5 F8W0Q9;Q8NEY8-6 PPHLN1 Periphilin-1 1 S(0.075)YS(0.925)PER;S(0.031)YS(0.969)PER 111.29 0.029347 1032760000 1236650 1384300 1232480 1308260 1447830 1087650 1332560 1186600 1382990 TRUE FALSE 1159250.284 1486795.012 1261715.008 1341832.166 1334123.272 1401636.898 1132754.999 1334749.622 1152160.035 1.006153876 1.290441404 1.095086594 1.164623079 1.157932259 1.216529698 0.983157691 1.158475891 1 20.13590969 1.743308092 25 1.050783434 1.16428638 0.252839459 0.08642872 1.08019919 5712.541282 0.035809548 0.019858186 55.37427991 -1.743308092 0.113502946 SYS(ph)PGRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SYSPGRR 7 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 1 SYS(1)PGRR;S(0.007)Y(0.001)S(0.993)PGRR 76.345 0.025119 225710000 236055 267315 274320 255470 255670 242293 316160 236453 262000 TRUE FALSE 221280.7389 287107.2807 280826.9999 262025.7927 235590.7095 312239.0558 268754.7431 265974.6775 218270.5074 1.013791288 1.315373681 1.286600756 1.200463571 1.079352004 1.430514179 1.231292062 1.218555272 1 17.73575768 0.713186358 3.285708936 1.000013651 1.241618205 0.250932615 0.116987219 3.883724814 43.10629987 0.103290135 0.026777458 5.166380134 -0.713186358 0.241604554 SYS(ph)PYDYQPCLAGPNQDFHSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYSPYDYQPCLAGPNQDFHSK 21 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7 E9PGF5 TNS1 Tensin-1 1 S(0.168)YS(0.832)PYDYQPCLAGPNQDFHSK 217.84 3.64E-25 346180000 302040 225040 270250 232820 300000 252230 333980 311470 575050 TRUE FALSE 283135.8556 241702.1958 276660.4576 238794.5554 276439.2101 325044.7064 283902.7995 350357.7151 479070.44 0.591010908 0.504523293 0.577494319 0.498453955 0.577032493 0.678490425 0.592611808 0.731328184 1 18.86987827 0.486025658 0.530274762 1.022388145 0.537138194 0.90606226 0.044569822 0.487607974 0.243777151 0.062925888 0.019870885 3.062144338 -0.486025658 -0.48524995 SYS(ph)SER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYSSER 6 0 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 S(0.089)YS(0.83)S(0.081)ER 76.478 0.07862 222830000 548130 689950 564170 533880 763070 430030 581680 595740 837220 TRUE FALSE 513823.5217 741034.6159 577552.3788 547580.2647 703141.5603 554172.68 494462.4841 670119.4504 697482.5734 0.736682953 1.062441764 0.828052773 0.785080926 1.008113446 0.794532654 0.708924499 0.960768736 1 19.41179765 3.728354094 24.96528149 0.84668168 0.929555776 0 0.126174237 150.316911 3043854.921 0.030942335 0.052119972 5350.00384 -3.728354094 0.082874096 SYS(ph)SERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SYSSERR 7 1 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 S(0.002)YS(0.499)S(0.499)ERR;S(0.003)YS(0.499)S(0.499)ERR 69.812 0.062207 377500000 790040 853800 838580 853380 960700 694810 868110 719060 1068690 TRUE FALSE 740592.8067 917016.2404 858471.5136 875279.1756 885250.4973 895390.3677 737944.9646 808836.2238 890318.735 0.831828847 1.029986458 0.964229416 0.983107668 0.99430739 1.005696424 0.828854809 0.908479393 1 19.76396239 1.756202963 25 0.895814379 0.976443636 0.109096129 0.067203953 9.258709547 13133.89884 0.027849621 0.015444033 57.04307943 -1.756202963 0.080629257 SYS(ph)SPDITQAIQEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SYSSPDITQAIQEEEK 16 0 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 SYS(0.931)S(0.069)PDITQAIQEEEK;SYS(0.927)S(0.073)PDITQAIQEEEK;SYS(0.994)S(0.006)PDITQAIQEEEK 338.14 7.83E-72 425170000 669450 483520 515720 519930 650040 434120 761850 512960 849550 TRUE FALSE 627550.3195 519320.3239 527953.1219 533272.284 598988.4805 559443.3967 647617.6652 577004.1852 707754.6167 0.886677818 0.733757593 0.745955038 0.753470584 0.846322251 0.790448248 0.915031354 0.815260221 1 19.43288973 1.080943969 0.51847059 0.998182253 0.765032099 0.534876328 0.057305032 0.623904263 0.431129581 0.059920053 0.029540931 12.0488048 -1.080943969 -0.233150154 SYS(ph)SPDITQAIQEEEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SYSSPDITQAIQEEEKR 17 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 SYS(0.5)S(0.5)PDITQAIQEEEKR;S(0.001)YS(0.941)S(0.058)PDITQAIQEEEKR;S(0.124)YS(0.701)S(0.175)PDITQAIQEEEKR;S(0.003)YS(0.88)S(0.118)PDITQAIQEEEKR 270.74 8.35E-36 6670300000 2747837 2228011 2276775 2449841 2691975 1546081 3142005 2202941 3566999 TRUE FALSE 2575854.787 2392975.253 2330781.178 2512708.068 2480558.142 1992409.486 2670890.519 2477983.033 2971643.823 0.866811415 0.805269876 0.784340694 0.845561654 0.834742752 0.670473854 0.898792277 0.833876191 1 21.50282978 0.70126151 1.224970116 0.998822395 0.806481117 0.483910407 0.060042936 0.791926348 1.965735744 0.051901618 0.015816181 5.026451654 -0.70126151 -0.192341279 SYSEDDIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYSEDDIHR 9 0 A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739;Q9Y5A9;Q9Y5A9-2 A0A024R7W5;Q9Y5A9 YTHDF3;YTHDF2 YTH domain-containing family protein 3;YTH domain-containing family protein 2 0 118.18 0.0010317 713670000 418830 333230 442560 370470 364850 353550 465770 394450 466110 FALSE TRUE 392616.1779 357902.6959 453057.7322 379976.8874 336196.1527 455614.1456 395932.1125 443697.9508 388313.2298 1.011081127 0.921685558 1.166732672 0.978531912 0.865785986 1.173316052 1.019620456 1.142628983 1 18.56686134 2.215160387 24.99966693 1.081600327 1.00341981 0.200948564 0.091657094 461.9865258 493560.645 0.033595737 0.024826105 164.1195763 -2.215160387 -0.078180516 SYSFDEIRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SYSFDEIRK 9 1 P43490 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;; 137.95 0.00024083 1807660000 2339800 2512220 2245720 2306560 2837210 1643450 2573500 2266730 3076780 FALSE TRUE 2193356.095 2698227.383 2298989.539 2365750.235 2614386.971 2117887.336 2187627.566 2549736.23 2563245.541 0.855694883 1.052660519 0.896905701 0.922951078 1.019951826 0.826252227 0.85346001 0.994729607 1 21.28954025 2.242780446 24.99999397 0.89786441 0.95527916 0.004666324 0.07813798 234.9576438 1391992.482 0.026015744 0.021057095 174.8962292 -2.242780446 0.05741475 SYSMIVNNLLKPISVEGSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SYSMIVNNLLKPISVEGSSK 20 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 246.16 4.70E-30 298900000 1107240 834380 957870 887630 971990 642000 1033930 939150 839500 FALSE TRUE 1037939.825 896158.3634 980591.1287 910408.0886 895653.8262 827334.978 878901.795 1056404.945 699382.0266 1.484081354 1.28135744 1.402082255 1.301732178 1.280636036 1.182951444 1.256683417 1.510483405 1 19.4157212 -3.961681841 0.24113925 3.58E-09 1.358526267 0.47882934 0.106240041 87.96444231 1.384736016 43.78368176 0.15879934 0.000109224 3.961681841 1.358526263 SYSS(ph)PDITQAIQEEEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYSSPDITQAIQEEEKR 17 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 SYS(0.067)S(0.933)PDITQAIQEEEKR 369.48 1.05E-104 132900000 221460 200090 211900 206670 233240 138360 267340 187720 287020 TRUE FALSE 207599.2139 214904.8718 216926.3681 211973.5021 214922.2712 178302.2859 227254.8489 211157.2552 239114.5078 0.868199993 0.898752961 0.907207054 0.886493689 0.898825727 0.745677406 0.950401759 0.883080066 1 17.86734214 0.54515106 1.35473561 0.999648041 0.880907847 0.343702965 0.052273783 2.134533314 5.074981132 0.04626761 0.0136816 3.508738964 -0.54515106 -0.118740194 SYSSGGEDGYVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SYSSGGEDGYVR 12 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ; 154.84 0.00016712 381250000 367430 469190 415920 417480 452890 343620 475310 383720 501710 FALSE TRUE 344433.2122 503929.3158 425785.8188 428193.2436 417321.8463 442817.5158 404041.6781 431628.2867 417971.3598 0.824059362 1.205655134 1.018696159 1.024455943 0.998446033 1.059444637 0.966673119 1.032674313 1 18.67304456 3.513849403 22.80526028 1.012188724 1.063516545 0 0.095890843 351.6850167 218364.6615 0.023289685 0.036073456 3264.746031 -3.513849403 0.051327821 SYSYVCGISSKDEPDWESLIFLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 SYSYVCGISSKDEPDWESLIFLAR 24 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 124.81 9.42E-05 33804000 21679 36484 22801 23384 51687 15880 28327 24440 50545 FALSE TRUE 20322.15009 39185.31332 23341.85049 23984.07303 47627.71152 20464.29821 24079.62932 27491.3878 42108.71297 0.482611523 0.930574947 0.554323532 0.569575067 1.131065477 0.485987264 0.571844344 0.652866969 1 15.36183116 SYVAWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SYVAWDR 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 105.04 0.018649 2385850000 1263410 2150180 1307540 1508580 2001940 939410 1492880 1834850 1859640 FALSE TRUE 1184335.423 2309381.564 1338555.466 1547292.717 1844715.708 1210602.417 1269036.503 2063935.062 1549254.07 0.76445526 1.490640953 0.863999967 0.998734001 1.190712191 0.781409867 0.819127429 1.332212128 1 20.56314233 3.751208525 22.66989542 0.975691039 1.178789412 0.032403718 0.239935112 274.3056117 258159.6979 0.056830243 0.10234387 5639.083494 -3.751208525 0.203098373 SYVS(ph)EPELATLSGDMAQPSLGLVGPESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.107)Y(0.017)VS(0.873)EPELAT(0.003)LSGDMAQPSLGLVGPESR;S(0.006)Y(0.001)VS(0.992)EPELAT(0.001)LSGDMAQPSLGLVGPESR;S(0.038)YVS(0.962)EPELATLSGDMAQPSLGLVGPESR;S(0.037)YVS(0.962)EPELATLSGDMAQPSLGLVGPESR;S(0.052)YVS(0.948)EPELATLSGDMAQPSLGLVGPESR 252.85 1.20E-53 458027000 232139 263313 229422 224821 311095 166204 290105 257412 383373 TRUE FALSE 217609.8344 282808.9685 234863.9982 230590.2875 286662.8536 214184.3967 246606.4485 289550.4548 319385.5696 0.681338968 0.885478229 0.735361959 0.72198092 0.897544789 0.670613882 0.77212771 0.906585902 1 18.28493961 1.069537132 3.367098497 0.997527142 0.773039329 0.53163772 0.07548248 0.161482603 3.671632599 0.066185801 0.017318313 11.73646025 -1.069537132 -0.224487813 T(ph)AMRVSPHHPAPTPNPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAMRVSPHHPAPTPNPR 17 1 A8MZI9;Q01196-7;Q01196-3;Q01196-4;Q01196;Q01196-9;Q01196-10;Q01196-2;Q01196-8;Q01196-11 A8MZI9 RUNX1 Runt-related transcription factor 1 1 T(0.5)AMRVS(0.5)PHHPAPTPNPR 85.932 0.0098066 28024000 17343 19665 20406 17796 19075 12403 21970 17275 20842 TRUE FALSE 16257.53259 21121.01706 20890.03996 18252.67549 17576.92644 15983.54475 18675.80246 19431.82178 17363.33556 0.936313909 1.216414726 1.203112149 1.051219418 1.012301259 0.920534232 1.075588409 1.119129543 1 14.0837565 3.10854092 5.902523985 1.025833172 1.15108384 0.146252104 0.092081702 0.264392471 12.84001533 0.026259044 0.031573639 1283.928739 -3.10854092 0.125250668 T(ph)ANSPGSGARPDPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TANSPGSGARPDPVR 15 1 A0A3B3ISR7;E9PIF2;Q13206 A0A3B3ISR7 DDX10 Probable ATP-dependent RNA helicase DDX10 1 T(0.545)ANS(0.454)PGS(0.001)GARPDPVR 97.284 0.0054532 297340000 348040 313910 333230 320610 350010 247570 364510 303330 284450 TRUE FALSE 326256.7977 337152.223 341134.373 328837.3954 322521.6265 319039.44 309855.1094 341201.4182 236973.4574 1.37676515 1.422742558 1.439546761 1.387654968 1.361003169 1.346308754 1.307551963 1.439829684 1 17.85436595 -3.41630613 0.270718848 7.48E-12 1.419749466 0.880377475 0.044266418 25.27651103 0.535987038 14.20503109 0.054065135 0.000383437 3.41630613 1.419749466 T(ph)AS(ph)PPPPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 119.27 0.0045293 2127410000 3606400 2755850 3014330 2974300 3044830 2183390 3778600 2516280 3047780 TRUE FALSE 3380681.862 2959896.001 3085831.331 3050625.573 2805701.334 2813699.249 3212034.009 2830443.097 2539085.829 1.331456315 1.165732945 1.215331635 1.20146611 1.105004527 1.108154446 1.265035617 1.114748885 1 21.27587773 -5 0.121097791 0.402149851 1.278645643 0.532062038 0.06372578 135.9140015 1.064749924 20.0522404 0.587793833 1.00E-05 5 0.876495792 T(ph)AS(ph)PPPPPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TASPPPPPKR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 T(1)AS(1)PPPPPKR 62.528 0.073144 615770000 986220 784090 932450 892330 899850 682920 1071900 718940 936700 TRUE FALSE 924494.2507 842144.8394 954568.1543 915228.6985 829179.4108 880067.9177 911178.546 808701.2416 780358.7187 1.184704199 1.079176562 1.223242762 1.172830746 1.062561859 1.127773544 1.16764063 1.036319864 1 19.57377794 1.130544046 4.57031366 1.002659225 1.144904684 0.554274639 0.047865325 0.152004386 4.971807224 0.044427905 0.0113827 13.50653804 -1.130544046 0.142245459 T(ph)ASGSSVTSLDGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 T(0.651)AS(0.349)GSSVTSLDGTR 91.845 0.058062 212050000 55058 80899 65936 78862 82831 44351 82652 70324 48357 TRUE FALSE 51612.01806 86888.84614 67500.03306 80885.73243 76325.78738 57154.41372 70259.0999 79104.1062 40285.9043 1.281143342 2.156805157 1.675524832 2.007792399 1.894602807 1.41871989 1.744011984 1.963567843 1 15.29798752 -1.83255241 2.613120282 0.71295852 1.786499995 0.451200243 0.265393581 18017630.42 11774793.08 32428927.51 0.058899193 0.01470441 1.83255241 1.073541474 T(ph)AY(ph)FS(ph)LDT(ph)RFKVGT(ph)DGVITVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAYFSLDTRFKVGTDGVITVK 21 2 A0A087WXI5;P12830-2;P12830;A0A087WX17;A0A087WU43;H3BVI7;H3BNC6 A0A087WXI5 CDH1 Cadherin-1;E-Cad/CTF1;E-Cad/CTF2;E-Cad/CTF3 5 T(1)AY(1)FS(1)LDT(1)RFKVGT(1)DGVITVK 52.298 0.037926 39857000 29951 27435 22082 24948 26824 13843 28615 24640 32252 TRUE FALSE 28076.42037 29466.31595 22605.79547 25588.20792 24717.35124 17839.24938 24324.4464 27716.35824 26868.93284 1.044939914 1.096668636 0.841335813 0.952334358 0.919923072 0.66393591 0.905300056 1.031539228 1 14.7136514 4.010804614 3.871422745 0.887768207 1.068542728 0.314650731 0.101481745 0.23250078 7.491152553 0.025187579 0.055801502 10251.90596 -4.010804614 0.180774521 T(ph)CNSPQNSTDSVSDIVPDSPFPGALGSDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TCNSPQNSTDSVSDIVPDSPFPGALGSDTR 30 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 T(0.505)CNS(0.3)PQNS(0.081)T(0.114)DS(0.001)VSDIVPDSPFPGALGSDTR;T(0.418)CNS(0.232)PQNS(0.343)T(0.008)DSVSDIVPDSPFPGALGSDTR 170.44 6.26E-12 291001000 135917 123571 121157 130169 128294 113512 154788 114406 126260 TRUE FALSE 127410.1976 132720.3254 124030.9013 133509.3569 118218.3068 146281.0717 131578.9764 128689.8409 105186.3903 1.211280254 1.261763285 1.179153509 1.269264555 1.123893561 1.390684396 1.250912556 1.223445738 1 16.68258853 0.789140246 5.147512799 1.000000699 1.241655832 0.547220895 0.068443221 4.024341204 97.91256726 0.060662061 0.015317629 6.153755626 -0.789140246 0.241655133 T(ph)DKSSASAPDVDDPEAFPALA ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TDKSSASAPDVDDPEAFPALA 21 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 T(0.25)DKS(0.25)S(0.25)AS(0.25)APDVDDPEAFPALA;T(0.25)DKS(0.25)S(0.25)AS(0.25)APDVDDPEAFPALA 129.12 2.75E-05 83603000 423080 354030 401800 616780 522380 167051 254590 158989 240030 TRUE FALSE 396600.178 380242.7496 411330.8857 632607.619 481354.382 215275.9119 216416.593 178839.1266 199967.4423 1.983323752 1.901523294 2.056989282 3.163553084 2.407163768 1.07655481 1.082259144 0.894341221 1 17.6094056 2.232643533 24.36350535 1.028813192 2.253488706 0.768075814 0.351403975 56.41015194 232264.9164 0.141253503 0.107153885 170.861232 -2.232643533 1.224675514 T(ph)ES(ph)KIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 72.138 0.057848 1865670000 1025570 1288270 1083390 1174710 1433640 901620 1301780 1081840 1724980 TRUE FALSE 961381.4044 1383654.851 1109088.522 1204855.047 1321047.697 1161903.057 1106590.174 1216910.105 1437069.694 0.668987321 0.962830722 0.771770866 0.838411006 0.919264878 0.808522413 0.770032364 0.846799644 1 20.4546986 0.958179333 22.00729352 1.000000002 0.828400106 0.32144193 0.080863011 2201.526198 1158512.196 0.071536181 0.017884045 9.081954736 -0.958179333 -0.171599896 T(ph)FSLDAVPPDHSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TFSLDAVPPDHSPR 14 0 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 1 T(0.557)FS(0.443)LDAVPPDHSPR;T(0.556)FS(0.444)LDAVPPDHSPR;T(0.573)FS(0.427)LDAVPPDHSPR;T(0.569)FS(0.431)LDAVPPDHSPR;T(0.549)FS(0.433)LDAVPPDHS(0.018)PR 143.67 3.33E-05 3543680000 737322 765300 714710 812020 930600 685211 1018610 779690 816710 TRUE FALSE 691174.3322 821963.6083 731663.2587 832857.8079 857514.4299 883020.2922 865878.8868 877036.0128 680395.8249 1.015841525 1.208066802 1.075349425 1.224078364 1.260317007 1.297803808 1.272610523 1.289008516 1 19.37601476 3.123838556 5.622410523 1.248508335 1.119974438 0.232850893 0.098471872 0.248668164 11.30767946 0.025425233 0.030643524 1329.959929 -3.123838556 -0.128533897 T(ph)GRYARLPKDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGRYARLPKDPK 12 3 Q01970 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 T(1)GRYARLPKDPK 85.42 0.012017 73239000 214660 331960 310260 339430 426470 279110 369730 353120 570990 TRUE FALSE 201224.8138 356538.6638 317619.5137 348140.3485 392976.7665 359684.526 314292.4189 397207.8093 475688.0803 0.423018407 0.749521963 0.667705429 0.731866874 0.826122795 0.756135251 0.660711151 0.835017369 1 18.85965635 -5 0.042892356 2.261569619 6.71E-14 0.615476304 0.091613139 563.6151888 1.801313049 89.02696365 24.59346293 1.00E-05 5 -2.261569619 T(ph)HDHQLESSLSPVEVFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THDHQLESSLSPVEVFAK 18 0 Q5JW53;Q9H410-4;Q9H410 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 T(0.316)HDHQLES(0.316)S(0.316)LS(0.053)PVEVFAK 69.922 0.048592 77706000 120360 106760 113940 113780 137320 81790 131690 92284 141440 TRUE FALSE 112826.8824 114664.6215 116642.7106 116699.7874 126535.4411 105401.4453 111944.3071 103805.8605 117832.7503 0.957517178 0.973113343 0.989900604 0.990384992 1.073856299 0.894500426 0.950027109 0.880959328 1 16.84638105 2.205422359 24.99999854 0.928484193 0.992443055 0.353614044 0.043747281 204.2665283 154100.6264 0.014980941 0.011064878 160.4805332 -2.205422359 0.063958862 T(ph)HSTSSSLGSGESPFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 1 T(0.773)HS(0.139)T(0.039)S(0.041)S(0.007)S(0.001)LGSGESPFSR;T(0.248)HS(0.248)T(0.166)S(0.112)S(0.112)S(0.112)LGSGESPFSR 153.95 5.75E-07 1073250000 560550 711060 680440 820760 1021610 622210 877260 688720 765260 TRUE FALSE 525466.1761 763707.6223 696580.3581 841822.0911 941376.8716 801831.9263 745723.0071 774708.2081 637533.1622 0.824217793 1.197910426 1.092618234 1.320436553 1.476592791 1.257710146 1.169700733 1.21516535 1 19.28214086 5.256042614 1.285753797 1.231818159 3.50E-15 0.464844509 0.12938409 4.226834516 2.423361456 0.035130202 9.485958239 180319.4665 -5.256042614 -1.231818159 T(ph)HTDSSEKELEPEAAEEALENGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THTDSSEKELEPEAAEEALENGPK 24 1 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 1 T(0.25)HT(0.25)DS(0.25)S(0.25)EKELEPEAAEEALENGPK 103.16 0.0048088 73069000 146830 66761 83090 101720 92111 62459 130170 65227 89188 TRUE FALSE 137640.1724 71704.0539 85060.93404 104330.3074 84876.97362 80489.89936 110652.2169 73370.73453 74301.94662 1.852443693 0.965036007 1.144800882 1.404139624 1.142325033 1.083281166 1.489223661 0.987467191 1 16.18111239 7.974479584 0.02203216 1.40E-05 2.821674418 0.157957724 0.256527447 7746.154947 13.19178009 608.0163399 1164.644553 94293028.3 -7.974479584 2.821660434 T(ph)ISAQDTLAYATALLNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TISAQDTLAYATALLNEK 18 0 Q9UPU5;A0A0U1RQI9 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 T(0.333)IS(0.333)AQDT(0.333)LAYATALLNEK 206.74 1.01E-17 0 173420 161940 158420 185650 208720 157330 248570 167430 243980 TRUE FALSE 162565.9518 173930.2061 162177.7972 190414.0933 192327.9731 202748.617 211299.2361 188334.0041 203258.1618 0.799800364 0.855710809 0.797890701 0.936809088 0.946225093 0.997493115 1.039560892 0.926575358 1 17.63295376 2.977249943 1.881809343 0.99449232 0.821869586 0.802260639 0.036657336 0.128956199 0.918604993 0.012054164 0.014053206 948.9644497 -2.977249943 -0.172622734 T(ph)KFASDDEHDEHDENGATGPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TKFASDDEHDEHDENGATGPVK 22 1 P05455 P05455 SSB Lupus La protein 1 T(0.601)KFAS(0.399)DDEHDEHDENGATGPVK;T(0.5)KFAS(0.5)DDEHDEHDENGATGPVK;T(0.604)KFAS(0.396)DDEHDEHDENGATGPVK 213.11 1.90E-23 2160800000 2681070 1529360 1834830 1905570 2039170 1252470 2350680 1548070 2331710 TRUE FALSE 2513266.615 1642595.406 1878353.034 1954470.152 1879021.814 1614037.757 1998217.357 1741349.947 1942532.538 1.293809275 0.845594796 0.966960912 1.006145387 0.967305194 0.83089355 1.028666093 0.896432834 1 20.88950733 4.748297359 24.89692854 0.941456611 1.293809476 0.732618469 0.066647421 636.3719537 1627172.973 0.014918585 0.195483857 56014.09963 -4.748297359 0.352352865 T(ph)KFASDDEHDEHDENGATGPVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKFASDDEHDEHDENGATGPVKR 23 2 P05455 P05455 SSB Lupus La protein 1 T(0.5)KFAS(0.5)DDEHDEHDENGATGPVKR 120.57 7.64E-05 2297100000 181130 149570 124380 153840 196600 78630 174110 120630 362390 TRUE FALSE 169793.3966 160644.3184 127330.3523 157787.7949 181159.829 101329.2045 148003.8219 135690.921 301904.7679 0.562407139 0.532102621 0.421756679 0.522640951 0.600056204 0.335633005 0.49023347 0.449449414 1 18.20373402 -1.382121432 3.193048654 1.00547969 0.484892963 0.821120537 0.074888194 62507153.42 82967304.98 3166702.084 0.017281563 0.041483803 1.382121432 -0.520586727 T(ph)KSPTDDEVTPSAVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKSPTDDEVTPSAVVR 16 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 T(0.577)KS(0.352)PT(0.072)DDEVTPSAVVR 139.11 4.78E-06 932010000 159500 110620 122990 129200 144520 112640 154740 115440 141110 TRUE FALSE 149517.1797 118810.4199 125907.3809 132515.4907 133169.9822 145157.3394 131538.1735 129852.9381 117557.8294 1.27186067 1.010655101 1.071025057 1.127236624 1.132804024 1.2347739 1.118923122 1.104587749 1 16.8430111 3.138498642 6.174150294 1.134069647 1.088350842 0 0.087713729 0.658903761 34.6811377 0.023842209 0.028697532 1375.620507 -3.138498642 -0.045718805 T(ph)KT(ph)WSVMPPMS(ph)THRHGLGVAVLEGPMYAVGGHDGWSYLNTVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKTWSVMPPMSTHRHGLGVAVLEGPMYAVGGHDGWSYLNTVER 43 2 H0Y9Y5;Q96PQ7-5;Q96PQ7-4;Q96PQ7-6;Q96PQ7;Q96PQ7-2;Q96PQ7-3 H0Y9Y5 KLHL5 Kelch-like protein 5 3 T(0.664)KT(0.664)WS(0.664)VMPPMS(0.503)T(0.503)HRHGLGVAVLEGPMYAVGGHDGWSYLNTVER 47.795 0.023814 43116000 7222.7 13871 12326 14040 14675 10200 17826 13482 11328 TRUE FALSE 6770.6441 14898.02327 12618.37854 14400.29017 13522.4847 13144.57442 15153.15679 15165.25738 9437.283618 0.717435692 1.578634687 1.337077389 1.525893546 1.432878913 1.392834522 1.605669322 1.606951533 1 13.20415595 4.744128805 24.91295619 1.460897617 0.717435359 0.606424854 0.180601715 346.0357936 1548170.708 0.037382531 0.328386191 55479.02313 -4.744128805 -0.743462258 T(ph)LDSDEERPRPAPPDWSHMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLDSDEERPRPAPPDWSHMR 20 2 Q9BW71;Q9BW71-2 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 T(0.5)LDS(0.5)DEERPRPAPPDWSHMR 70.533 0.016809 155400000 119420 179220 171760 216930 222490 441280 193580 148430 187570 TRUE FALSE 111945.7154 192489.6353 175834.2283 222496.7911 205016.5329 568670.3724 164554.4761 166961.8122 156263.3553 0.716391346 1.231828377 1.125242883 1.423857761 1.31199367 3.63917933 1.053058638 1.068464273 1 17.25361997 2.904074718 2.356325057 1.739322799 1.090064726 0.097656737 0.774538284 0.633448776 6.934789366 0.249154677 0.274934961 801.8159993 -2.904074718 -0.649258073 T(ph)LTPPLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TLTPPLRR 8 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 T(0.83)LT(0.17)PPLRR;T(0.885)LT(0.115)PPLRR;T(0.717)LT(0.283)PPLRR;T(0.582)LT(0.418)PPLRR;T(0.636)LT(0.364)PPLRR 95.523 0.0056196 2062727000 1367520 1238430 1288830 1274560 1415690 1008160 1518320 1104490 1482880 TRUE FALSE 1281929.364 1330124.646 1319401.656 1307267.367 1304507.418 1299199.426 1290662.011 1242388.008 1235377.748 1.03768209 1.076694677 1.068014749 1.058192419 1.055958325 1.05166167 1.044750898 1.005674588 1 20.23652082 1.334582757 1.55053105 0.997326856 1.062320815 0.815069634 0.010624305 0.138625785 0.612594773 0.009548679 0.002958782 21.60641715 -1.334582757 0.06499396 S(ph)PSPTVHASSTPAVNIQPDVSGGWDWHAKPGGFGMGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 SPSPTVHASSTPAVNIQPDVSGGWDWHAKPGGFGMGSK 38 1 O75061-4;O75061;O75061-2 O75061-4 DNAJC6 Putative tyrosine-protein phosphatase auxilin 1 S(0.438)PS(0.438)PT(0.121)VHAS(0.001)S(0.001)T(0.001)PAVNIQPDVSGGWDWHAKPGGFGMGSK;S(0.499)PS(0.499)PT(0.002)VHASSTPAVNIQPDVSGGWDWHAKPGGFGMGSK;S(0.448)PS(0.448)PT(0.101)VHAS(0.001)S(0.001)T(0.001)PAVNIQPDVSGGWDWHAKPGGFGMGSK 142.81 2.38E-13 344245000 85425 177359 181958 176693 214515 151666 215306 203397 276217 TRUE FALSE 80078.40174 190490.8449 186274.1297 181227.2415 197667.8572 195449.5121 183022.8641 228791.5632 230114.5983 0.347993575 0.827808606 0.809484192 0.787552128 0.858997468 0.849357292 0.795355295 0.994250538 1 17.81199298 4.73989147 5.136183237 0.847304311 0.324892296 0.817094857 0.076563456 0.062343036 5.456985787 0.016262866 0.115535132 54940.35606 -4.73989147 -0.522412015 down T(ph)NSDSALHQSTMTPTQPESFSSGSQDVHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TNSDSALHQSTMTPTQPESFSSGSQDVHQK 30 0 M0QXN6;M0QX46;Q6UUV9;Q6UUV9-2;Q6UUV9-3 M0QXN6 CRTC1 CREB-regulated transcription coactivator 1 1 T(0.609)NS(0.39)DS(0.001)ALHQSTMTPTQPESFSSGSQDVHQK 228.33 3.25E-35 181400000 120580 122540 119280 127150 141740 120520 152740 112660 162900 TRUE FALSE 113033.113 131612.9891 122109.3779 130412.8843 130608.3122 155312.1675 129838.055 126725.849 135710.9376 0.832896117 0.969803845 0.899775509 0.960960749 0.962400779 1.144433678 0.95672506 0.93379245 1 17.05017747 2.845216668 2.414912818 1.006939513 0.916582845 0.310182759 0.06560284 0.379373266 4.339847934 0.021263918 0.022643504 700.1912315 -2.845216668 -0.090356668 T(ph)PDRER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPDRER 6 1 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 T(1)PDRER;T(1)PDRER 97.431 0.066413 344090000 576130 564470 726800 660950 612990 510100 612240 595400 636350 TRUE FALSE 540071.0517 606263.9461 744040.0392 677911.096 564848.2381 657357.5892 520440.2958 669737.0006 530139.074 1.018734665 1.143594155 1.403480852 1.278741993 1.065471809 1.239971965 0.981705219 1.263323217 1 19.01601135 2.737690244 24.99865383 1.109202089 1.231937779 0.118531729 0.131582167 143.7600234 4129011.23 0.040808516 0.040527735 546.6259482 -2.737690244 0.12273569 T(ph)PDSTFSETFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TPDSTFSETFK 11 0 Q9NZI5-3;Q9NZI5;B7Z1S6 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 T(1)PDSTFSETFK;T(1)PDSTFSETFK;T(0.998)PDS(0.002)TFSETFK;T(0.994)PDS(0.006)TFSETFK;T(0.999)PDS(0.001)TFSETFK 278.01 3.41E-26 5170370000 7156710 5960010 6603310 6302400 6829480 5406680 8212700 6286410 6275130 TRUE FALSE 6708784.296 6401295.342 6759943.632 6464130.254 6293120.19 6967500.746 6981281.878 7071282.127 5227770.264 1.283297459 1.224479084 1.293083531 1.236498531 1.203786676 1.33278633 1.33542247 1.35263827 1 22.31776431 2.234600096 24.99959627 1.290535028 1.25057374 0 0.104357012 401.5503763 2534624.93 0.033707203 0.025789562 171.6327243 -2.234600096 -0.039961289 T(ph)PDVDNPEQPFDALNIEECSLTQQNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPDVDNPEQPFDALNIEECSLTQQNK 26 0 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 T(1)PDVDNPEQPFDALNIEECSLTQQNK 115.63 0.0042461 26673000 76310 42596 52467 51882 48832 45085 73203 47016 58937 TRUE FALSE 71533.89332 45749.85216 53711.54202 53213.37996 44996.9317 58100.30761 62226.88973 52886.05109 49100.03395 1.456901097 0.931768239 1.09392067 1.08377481 0.91643382 1.183304836 1.26734922 1.077108239 1 15.5834364 T(ph)PELPEPSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TPELPEPSVK 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(1)PELPEPSVK;T(1)PELPEPSVK;T(1)PELPEPSVK;T(1)PELPEPSVK;T(1)PELPEPSVK 154 0.00017063 717544000 1718678 1400457 1539891 1449285 1577453 1277686 1970135 1335432 1864426 TRUE FALSE 1611109.012 1504148.293 1576417.942 1486476.107 1453566.205 1646533.207 1674731.547 1502163.625 1553241.256 1.037256129 0.968393215 1.014921498 0.957015596 0.935827708 1.060062756 1.07821727 0.967115456 1 20.5668505 2.219976999 24.99961487 1.038697217 0.983963723 0.187097698 0.041798373 306.9428563 412912.4072 0.015020719 0.011113376 165.9499014 -2.219976999 -0.054733494 T(ph)PESFLGPNAALVDLDSLVSRPGPTPPGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPESFLGPNAALVDLDSLVSRPGPTPPGAK 30 1 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 T(0.991)PES(0.009)FLGPNAALVDLDSLVSRPGPTPPGAK;T(0.995)PES(0.005)FLGPNAALVDLDSLVSRPGPTPPGAK 101.58 0.00067023 30170000 19226.7 14419 20422.2 17637.1 17430.2 15412.8 27080.3 16877.2 22675.1 TRUE FALSE 18023.33517 15486.59776 20906.62423 18089.69785 16061.3024 19862.22515 23019.86042 18984.35557 18890.47932 0.954096233 0.819809678 1.106728097 0.957609256 0.850232656 1.051441036 1.218595887 1.004969501 1 14.20537169 2.020374733 13.35516747 1.107862273 0.945995717 0.289530853 0.097531776 1.279417113 836.6148401 0.035834288 0.0263811 104.8032457 -2.020374733 -0.161866556 T(ph)PLSEAEFEEIMNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPLSEAEFEEIMNR 14 0 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 1 T(1)PLSEAEFEEIMNR;T(1)PLSEAEFEEIMNR 193.51 2.80E-06 37202000 18484.2 13361.7 17487.6 18981.2 17007 17474.5 15268.8 16629.9 17728.3 TRUE FALSE 17327.30692 14351.01417 17902.41413 19468.28973 15671.33882 22519.10448 12979.38519 18706.17962 14769.3322 1.173195015 0.971676578 1.212134299 1.318156397 1.061072946 1.524720561 0.878806503 1.266555547 1 13.85031698 -0.150130872 0.832651263 0.995856165 1.159272015 0.073065004 0.182130654 24.84522514 14.90541735 0.534814377 0.05465299 0.707732482 0.150130872 0.16341585 T(ph)PNGPNIDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPNGPNIDKK 10 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;Q5TBM3 Q92598-2 HSPH1 Heat shock protein 105 kDa 1 T(1)PNGPNIDKK 64.65 0.041799 271530000 704080 397740 594180 526340 579470 441950 748380 480060 590000 TRUE FALSE 660012.8896 427189.0834 608274.2302 539846.7755 533960.7637 569533.7905 636167.3666 539996.5477 491525.1885 1.342785487 0.869109241 1.237524026 1.098309483 1.086334487 1.158707232 1.294272159 1.098614192 1 18.90690582 2.110909374 5.968393337 1.17857452 1.105826527 0 0.142088449 0.671213781 32.77728837 0.050229682 0.036852202 129.0949857 -2.110909374 -0.072747994 T(ph)PPAPSPFDLPELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPPAPSPFDLPELK 14 0 O95239 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 T(1)PPAPSPFDLPELK 136.33 0.00030992 37375000 76027 56280 68910 62870 60500 50425 77128 56078 75867 TRUE FALSE 71268.60578 60447.02976 70544.57774 64483.35064 55748.57405 64981.87892 65563.37242 63079.46174 63204.30758 1.127590959 0.95637516 1.1161356 1.020236644 0.882037573 1.028124212 1.037324431 0.998024726 1 15.94773527 4.757638416 24.01008343 1.01216776 1.127591136 0.287410659 0.059774249 3649.381463 4592746.008 0.014169325 0.488971485 57231.93325 -4.757638416 0.115423377 T(ph)PPFSESEEQLHLHDAGMKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TPPFSESEEQLHLHDAGMKPR 21 1 Q8IVM0-2 Q8IVM0-2 CCDC50 Coiled-coil domain-containing protein 50 1 T(0.969)PPFS(0.03)ES(0.001)EEQLHLHDAGMKPR;T(0.999)PPFS(0.001)ESEEQLHLHDAGMKPR;T(1)PPFSESEEQLHLHDAGMKPR 185.96 5.00E-17 1219270000 256057 232287 251915 245322 230816 220052 302657 239364 222949 TRUE FALSE 240030.8494 249485.7712 257890.5428 251617.3778 212688.6424 283577.4402 257276.3926 269249.1223 185737.3716 1.292313159 1.343217948 1.388468786 1.354694404 1.14510419 1.526765657 1.385162234 1.449622766 1 17.5029046 T(ph)PPPPSPLPFPTQAILPPAPSSYFSHPTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPPPPSPLPFPTQAILPPAPSSYFSHPTIR 30 0 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A1B0GWJ4;Q5VW27;O00712-5;Q5VW26;A0A2R8Y7V8;Q5VW30;A0A1B0GWI9;Q5VW31;A0A1B0GVN4;A0A1B0GWB8;O00712-6 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 T(0.864)PPPPS(0.136)PLPFPTQAILPPAPSSYFSHPTIR 119.3 0.00016727 222430000 30259 34759 34396 34113 40534 31560 48336 36209 24066 TRUE FALSE 28365.1432 37332.59253 35211.88936 34988.39733 37350.62315 40670.85967 41088.46553 40729.77336 20049.22913 1.414774754 1.862046281 1.756271482 1.745124319 1.862945598 2.028549796 2.04937882 2.031488248 1 14.29125915 2.710769855 3.955299551 1.895901029 1.731293971 0 0.330047946 0.708199109 25.05351071 0.096707684 0.094469218 513.7713168 -2.710769855 -0.164607058 T(ph)PPRDLPTIPGVT(ph)SPSSDEPPMEASQSHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TPPRDLPTIPGVTSPSSDEPPMEASQSHLR 30 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 T(0.995)PPRDLPT(0.008)IPGVT(0.795)S(0.155)PS(0.04)S(0.008)DEPPMEASQSHLR;T(0.999)PPRDLPT(0.027)IPGVT(0.79)S(0.171)PS(0.01)S(0.002)DEPPMEASQSHLR;T(0.955)PPRDLPT(0.142)IPGVT(0.658)S(0.183)PS(0.048)S(0.014)DEPPMEASQSHLR 102.26 0.00043297 397627000 65687.3 86848 83269 82312 92393 78321 97805 75623 104686 TRUE FALSE 61576.04915 93278.31629 85244.18 84424.26527 85136.82648 100931.0013 83140.04823 85064.69802 87213.2303 0.70604023 1.069543187 0.977422573 0.968021308 0.976191642 1.157290023 0.953296282 0.975364606 1 16.41225939 4.745359696 24.95259853 1.010768579 0.706040086 0.708346937 0.061219381 415.4005588 1524478.899 0.013773782 0.135547798 55636.48645 -4.745359696 -0.304728493 T(ph)PPRDLPTIPGVTSPSSDEPPMEAS(ph)QSHLRNSPEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPPRDLPTIPGVTSPSSDEPPMEASQSHLRNSPEDK 36 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 T(0.998)PPRDLPT(0.002)IPGVT(0.004)S(0.004)PS(0.003)S(0.003)DEPPMEAS(0.406)QS(0.346)HLRNS(0.234)PEDK 70.025 0.020108 119930000 44064 26607 26018 31843 43203 30107 38992 23040 53342 TRUE FALSE 41306.1129 28577.00996 26635.15925 32660.14529 39810.01065 38798.40215 33145.51158 25916.59472 44438.8756 0.929504006 0.643063299 0.599366183 0.734945357 0.895837487 0.873073444 0.745867467 0.583196455 1 15.43953469 2.9936326 24.5795453 0.804949318 0.686127136 0.074622041 0.138333566 458.5934754 1770282.726 0.03910538 0.045204311 985.4454764 -2.9936326 -0.118822181 T(ph)PPRDLPTIPGVTSPSSDEPPMEAS(ph)QSHLRNSPEDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TPPRDLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 37 3 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 T(0.997)PPRDLPT(0.003)IPGVTSPSSDEPPMEAS(0.578)QS(0.339)HLRNS(0.083)PEDKR;T(1)PPRDLPTIPGVTSPSSDEPPMEAS(0.574)QS(0.314)HLRNS(0.112)PEDKR;T(0.841)PPRDLPT(0.159)IPGVTSPSSDEPPMEAS(0.375)QS(0.294)HLRNS(0.331)PEDKR 193.7 3.57E-24 792080000 201728 186247 237805 230956 272026 185675 286851 216076 490020 TRUE FALSE 189102.2046 200036.9217 243445.8469 236882.722 250662.1753 239276.3583 243840.3555 243053.5642 408232.4963 0.463221831 0.490007345 0.596341176 0.580264247 0.614018182 0.586127661 0.597307558 0.595380246 1 18.6390315 -5 0.201940181 2.996914965 0.495786004 0.93622382 0.036688801 34.42692458 0.341395651 27.74056901 0.090171084 1.00E-05 5 -2.501128961 T(ph)PPRDLPTIPGVTSPSSDEPPMEASQSHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 19 TPPRDLPTIPGVTSPSSDEPPMEASQSHLR 30 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 T(1)PPRDLPTIPGVTSPSSDEPPMEASQSHLR;T(0.999)PPRDLPT(0.001)IPGVTSPSSDEPPMEASQSHLR;T(0.998)PPRDLPT(0.002)IPGVTSPSSDEPPMEASQSHLR;T(0.998)PPRDLPT(0.002)IPGVTSPSSDEPPMEASQSHLR;T(0.972)PPRDLPT(0.025)IPGVT(0.003)SPSSDEPPMEASQSHLR;T(0.999)PPRDLPT(0.001)IPGVTSPSSDEPPMEASQSHLR;T(1)PPRDLPTIPGVTSPSSDEPPMEASQSHLR;T(0.997)PPRDLPT(0.003)IPGVTSPSSDEPPMEASQSHLR;T(0.847)PPRDLPT(0.146)IPGVT(0.003)S(0.003)PS(0.001)S(0.001)DEPPMEASQSHLR;T(0.99)PPRDLPT(0.01)IPGVTSPSSDEPPMEASQSHLR;T(0.988)PPRDLPT(0.012)IPGVTSPSSDEPPMEASQSHLR;T(0.987)PPRDLPT(0.013)IPGVTSPSSDEPPMEASQSHLR;T(0.964)PPRDLPT(0.036)IPGVTSPSSDEPPMEASQSHLR;T(0.5)PPRDLPT(0.118)IPGVT(0.216)S(0.159)PS(0.004)S(0.002)DEPPMEASQSHLR;T(0.998)PPRDLPT(0.002)IPGVTSPSSDEPPMEASQSHLR;T(0.895)PPRDLPT(0.104)IPGVTSPSSDEPPMEASQSHLR;T(0.926)PPRDLPT(0.074)IPGVTSPSSDEPPMEASQSHLR;T(0.996)PPRDLPT(0.004)IPGVTSPSSDEPPMEASQSHLR;T(0.978)PPRDLPT(0.022)IPGVTSPSSDEPPMEASQSHLR 226.44 9.92E-35 32759902000 716653.5 807769 846071 790965.3 976265.7 867887.2 1007394.7 941348.6 1265551.7 TRUE FALSE 671799.4367 867577.0572 866140.2037 811262.8087 899593.73 1118432.146 856345.2169 1058878.045 1054322.945 0.637185636 0.822876009 0.821513188 0.769463296 0.853243054 1.060806037 0.812222878 1.004320402 1 20.00788541 7.018340364 0.172475165 1.026994204 2.17E-17 0.586713875 0.081201841 31.60743731 0.464161411 0.198516512 7.881859084 10431346.33 -7.018340364 -1.026994204 T(ph)PPRDLPTIPGVTSPSSDEPPMEASQSHLRNS(ph)PEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPPRDLPTIPGVTSPSSDEPPMEASQSHLRNSPEDK 36 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 T(0.779)PPRDLPT(0.216)IPGVT(0.003)S(0.001)PSSDEPPMEAS(0.035)QS(0.058)HLRNS(0.907)PEDK;T(0.987)PPRDLPT(0.013)IPGVTSPSSDEPPMEAS(0.323)QS(0.266)HLRNS(0.41)PEDK 95.108 0.0017465 221449000 107765 83950 97403 97047 126473 87906 129210 87578 192124 TRUE FALSE 101020.181 90165.74535 99713.44516 99537.39032 116540.3207 113283.0352 109836.16 98512.30608 160057.2632 0.631150246 0.563334294 0.622986069 0.621886119 0.728116415 0.707765664 0.686230402 0.615481635 1 17.28822862 -5 0.188564867 2.518693649 0.576797646 0.847816242 0.04723579 49.25227032 0.481105788 28.07626334 0.130461004 1.00E-05 5 -1.941896002 T(ph)PPRDLPTIPGVTSPSSDEPPMEASQSHLRNS(ph)PEDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TPPRDLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 37 3 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 T(0.947)PPRDLPT(0.053)IPGVTSPSSDEPPMEAS(0.036)QS(0.03)HLRNS(0.934)PEDKR;T(0.986)PPRDLPT(0.014)IPGVTSPSSDEPPMEAS(0.347)QS(0.271)HLRNS(0.382)PEDKR;T(0.996)PPRDLPT(0.004)IPGVTSPSSDEPPMEAS(0.26)QS(0.181)HLRNS(0.56)PEDKR;T(0.999)PPRDLPT(0.001)IPGVTSPSSDEPPMEAS(0.213)QS(0.165)HLRNS(0.622)PEDKR 146.2 2.25E-13 1683920000 379801 361037 397492 411798 516210 328780 528212 388651 896151 TRUE FALSE 356029.9334 387768.5551 406920.6979 422365.4339 475668.9489 423693.4487 449011.5143 437174.9329 746577.6087 0.476882683 0.519394837 0.545048088 0.565735469 0.637132621 0.567514273 0.601426441 0.585571986 1 19.50993271 -5 0.216751759 3.195927789 0.50246533 0.948683564 0.032689187 30.2771051 0.302778691 28.95714338 0.063543035 1.00E-05 5 -2.693462459 T(ph)PPRWAEDQNSLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 81.723 0.020547 121180000 231660 232990 259310 276820 251130 222530 364630 216120 369900 TRUE FALSE 217160.8141 250240.822 265460.9557 283923.6699 231407.2628 286770.7985 309957.1166 243103.0577 308161.3004 0.704698526 0.812044931 0.861435084 0.921347585 0.750929018 0.930586671 1.00582752 0.788882502 1 18.23332617 7.699768732 0.19033976 0.978812228 7.53E-15 0.41909354 0.077412137 46.36333272 0.599024392 0.149741788 13.04268459 50092041.51 -7.699768732 -0.978812228 T(ph)PPSEEDSAEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPPSEEDSAEAER 13 0 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 T(0.996)PPS(0.004)EEDSAEAER 97.297 0.042961 56202000 50022 58498 53763 51932 80338 32859 76773 59829 116500 TRUE FALSE 46891.21231 62829.25279 55038.28375 53264.66304 74028.57755 42344.85988 65261.60138 67298.78235 97055.39738 0.483138636 0.647354547 0.567081123 0.54880681 0.762745602 0.436295776 0.672415993 0.693405871 1 16.56652082 0.745161202 1.420367078 0.999271606 0.588046054 0.673267051 0.090992484 0.467288946 1.589110345 0.075561276 0.022271769 5.561106368 -0.745161202 -0.411225552 T(ph)PPTANHPVEPVTSVTQPSELLQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPPTANHPVEPVTSVTQPSELLQQK 25 0 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 1 T(1)PPTANHPVEPVTSVTQPSELLQQK;T(1)PPTANHPVEPVTSVTQPSELLQQK 267.78 4.54E-45 869150000 754640 635490 728850 708910 585320 612080 1042940 627700 360300 TRUE FALSE 707408.4295 682542.3408 746138.6662 727101.8308 539351.3283 788777.5597 886560.8292 706069.7267 300163.6024 2.356742869 2.273901084 2.485773293 2.422351761 1.79685786 2.627825471 2.953592048 2.352282959 1 18.19538952 4.20084928 21.5321093 2.369542086 2.315321758 0 0.540726387 1231.090985 1008989.251 0.124297482 0.268807579 15879.95547 -4.20084928 -0.054220329 T(ph)PRT(ph)PQLK ddPTM_SK-BR-3_Pertuzumab_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 134.13 0.0043811 572880000 1062060 1237670 1127850 1374070 2036690 659940 1102120 1129430 2724500 TRUE FALSE 995587.5604 1329308.375 1154603.135 1409330.962 1876736.583 850453.9648 936867.3376 1270441.822 2269763.349 0.438630556 0.585659459 0.508688774 0.620915376 0.826842404 0.374688386 0.41275992 0.559724353 1 21.11411046 -1.8165866 2.38029849 1.169668235 0.536346172 0.561303067 0.127470442 11562756.43 6997613.632 11254071.22 0.031556577 0.015255042 1.8165866 -0.633322063 T(ph)PRTPQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPRTPQLK 8 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 1 T(0.778)PRT(0.222)PQLK;T(0.913)PRT(0.087)PQLK 86.189 0.026206 862200000 1099300 1294890 1121980 1277270 1549540 734560 1314970 1121740 2190610 TRUE FALSE 1030496.775 1390765.003 1148593.895 1310046.911 1427845.379 946615.5474 1117802.456 1261791.708 1824983.039 0.564661015 0.762070098 0.629372367 0.717840595 0.782388301 0.518698271 0.612500189 0.691399142 1 20.79945163 -1.853262613 1.738141998 1.188042343 0.661684006 0.623792 0.083002466 135785.0107 51716.97222 105476.1053 0.021836748 0.014019657 1.853262613 -0.526358337 T(ph)PRTPRT(ph)PQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPRTPRTPQLK 11 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 2 T(0.97)PRT(0.06)PRT(0.97)PQLK 77.324 0.05283 554400000 424670 522320 407250 575020 823330 246880 449860 488420 1243700 TRUE FALSE 398090.6628 560993.1163 416910.1623 589775.9867 758668.983 318150.2482 382407.6693 549400.3121 1036118.435 0.384213473 0.54143725 0.402376937 0.569216768 0.732222261 0.307059731 0.369077179 0.530248564 1 19.98275749 0.96061091 22.54705686 1.000000002 0.469506564 0.648006569 0.121285714 1325.09318 758509.7966 0.115930591 0.028982648 9.132946416 -0.96061091 -0.530493437 T(ph)PS(ph)PES(ph)HRSPAEGSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPSPESHRSPAEGSER 16 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 3 T(0.999)PS(0.968)PES(0.889)HRS(0.139)PAEGS(0.005)ER;T(1)PS(0.996)PES(0.939)HRS(0.063)PAEGS(0.002)ER 90.972 0.0044104 213246000 123525 138824 132751 142795 149928 113692 125237 111439 120441 TRUE FALSE 115793.7907 149102.6734 135899.9164 146459.3615 138153.2597 146513.0348 106458.8745 125352.4045 100338.619 1.154030142 1.485994873 1.354412865 1.459650959 1.376870252 1.460185881 1.060996011 1.249293698 1 16.61451746 1.731697228 8.640052457 1.119940879 1.393448325 0.578521159 0.111303049 0.069021852 17.21320117 0.047305597 0.025316247 53.91346291 -1.731697228 0.273507446 T(ph)PS(ph)PESHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TPSPESHR 8 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 2 T(1)PS(1)PESHR;T(1)PS(1)PESHR;T(1)PS(1)PESHR 93.096 0.020072 650400000 228805 222889 227175 225409 214453 214260 244850 185143 206240 TRUE FALSE 214484.5035 239391.9335 232563.6983 231193.3766 197610.7264 276113.3838 208137.0156 208258.5111 171817.2116 1.248329556 1.393294253 1.353552977 1.345577514 1.150121833 1.607018186 1.211386296 1.212093417 1 17.39051504 1.014161709 1.745567247 1.006286178 1.346607936 0.442917994 0.120626739 0.300098089 1.884879102 0.100791208 0.028960436 10.33146025 -1.014161709 0.340321758 T(ph)PS(ph)PPPPIPEDIALGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPSPPPPIPEDIALGK 16 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 T(1)PS(1)PPPPIPEDIALGK 121.79 0.00051377 90800000 190660 136380 161780 149370 133240 129280 204100 139550 111930 TRUE FALSE 178726.9309 146477.7171 165617.498 153203.0871 122775.8679 166601.0373 173497.0998 156973.1247 93248.1599 1.916680513 1.570837615 1.776094007 1.642960968 1.316657272 1.786641554 1.860595426 1.683391124 1 16.50878764 -1.88597715 2.47061892 0.637183882 1.694262212 0.628768635 0.167642526 15218996.85 8479268.506 32225429.42 0.040266422 0.01300238 1.88597715 1.05707833 T(ph)PSEADRWLEEVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPSEADRWLEEVSK 14 1 P49757-3;P49757;G3V3Z8;P49757-8;P49757-7;P49757-6;P49757-5;P49757-4;P49757-2;P49757-9 P49757-3 NUMB Protein numb homolog 1 T(0.99)PS(0.01)EADRWLEEVSK 128.59 0.00011778 72757000 107370 93985 109280 88203 129440 82906 129580 98895 239300 TRUE FALSE 100649.9034 100943.7472 111872.1732 90466.43831 119274.3045 106839.6163 110150.682 111242.2584 199359.2841 0.504866898 0.506340839 0.561158582 0.453785931 0.598288187 0.535914928 0.552523463 0.557998886 1 17.60501127 -5 0.328504895 5.677873661 0.515777345 0.944095542 0.035856789 67.17102715 0.583106898 219.2053581 0.027140825 1.00E-05 5 -5.162096316 T(ph)PSNTPSAEADWS(ph)PGLELHPDYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPSNTPSAEADWSPGLELHPDYK 23 0 Q9Y3Z3-4;Q9Y3Z3;A0A2R8YCS7;Q9Y3Z3-3;A0A2R8YF51;A0A2R8Y5D2;A0A2R8Y586;A0A2R8Y7R5;A0A2R8Y755 Q9Y3Z3-4 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 2 T(0.976)PS(0.019)NT(0.009)PS(0.01)AEADWS(0.986)PGLELHPDYK;T(0.998)PS(0.002)NTPSAEADWS(1)PGLELHPDYK 200.4 4.33E-24 195688000 171729 108333 128277 128313 141830 145244 182024 142328 128153 TRUE FALSE 160980.7884 116354.088 131319.791 131605.7288 130691.2439 187173.585 154731.191 160097.9641 106763.4364 1.507826966 1.089830863 1.230007158 1.232685395 1.22411987 1.753161862 1.449290096 1.49955799 1 16.70405812 2.367122434 20.19138149 1.474012545 1.229220062 0.110703131 0.211077359 3.276639207 585.3803286 0.064862011 0.054267272 232.8747673 -2.367122434 -0.244792483 T(ph)PSPAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.987)PS(0.013)PAPK 114.28 0.066402 2860700000 2988200 2234600 2590300 2289900 2490600 1956200 3264500 2035800 2873300 TRUE FALSE 2801173.896 2400052.109 2651743.139 2348662.711 2294998.323 2520923.184 2775018.531 2289974.111 2393727.668 1.170214112 1.002642089 1.107788148 0.981173733 0.95875498 1.053137004 1.159287486 0.956656073 1 21.1908276 4.749685598 24.17080745 1.041318238 1.170214232 0.296803527 0.066063484 1497.795244 3254102.637 0.015869478 0.233040609 56193.43728 -4.749685598 0.128895994 T(ph)PSSEEISPTKFPGLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPSSEEISPTKFPGLYR 17 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 T(0.568)PS(0.416)S(0.016)EEISPTKFPGLYR 167.63 3.55E-09 153890000 75197 89856 84944 79458 100730 60537 108340 83574 124200 TRUE FALSE 70490.554 96509.03174 86958.91179 81497.0268 92819.07213 78013.04916 92095.42278 94008.39787 103470.2176 0.68126419 0.932722806 0.840424557 0.787637531 0.897060761 0.753966223 0.890066967 0.908555138 1 16.65885604 1.05201481 1.69355797 0.997245551 0.83432583 0.392556398 0.072591211 0.377899791 2.191321556 0.06245619 0.018109694 11.27235895 -1.05201481 -0.162919722 T(ph)PSSPSKSPASFEIPASAMEANGVDGDGLNKPAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPSSPSKSPASFEIPASAMEANGVDGDGLNKPAKK 35 3 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911;H0YA73 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 T(0.325)PS(0.325)S(0.325)PS(0.026)KSPASFEIPASAMEANGVDGDGLNKPAKK 130.45 1.56E-08 656080000 753510 311590 465230 471660 569160 272790 645570 397060 634140 TRUE FALSE 706349.1542 334660.4478 476265.4753 483763.5941 524460.4695 351540.0446 548772.7717 446633.815 528297.9373 1.337028037 0.633469155 0.901509246 0.91570222 0.992736167 0.665420059 1.038756226 0.845420327 1 19.01099225 0.16985308 0.769960094 1.001756978 0.887564742 0 0.198147059 15.94148039 11.13795134 0.268255286 0.06128343 1.478608096 -0.16985308 -0.114192236 T(ph)PTAPAVNLAGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TPTAPAVNLAGAR 13 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.998)PT(0.002)APAVNLAGAR;T(0.996)PT(0.004)APAVNLAGAR;T(0.995)PT(0.005)APAVNLAGAR 146.88 0.00047516 829220000 70777 63292 82321 77992 80871 86091 85488 76844 69481 TRUE FALSE 66347.19391 67978.20554 84273.69299 79993.40676 74519.71788 110944.0741 72669.86803 86438.14255 57884.17224 1.146206145 1.174383306 1.455902188 1.381956477 1.287393686 1.916656486 1.255435903 1.493294958 1 15.82088129 4.083684239 2.32956029 1.425588642 1.148055793 0.147885237 0.230557112 0.48524858 5.115548644 0.055026711 0.157055018 12125.06957 -4.083684239 -0.277532849 T(ph)QITTMESNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TQITTMESNLK 11 0 H7BYU4;A0A3B3ISI4;A0A3B3ITS6;A0A3B3IRF0;A0A3B3IUE2;A0A3B3ITL3;A0A3B3IRT9;A0A3B3ISW5;A0A3B3IRX5;A0A3B3ITJ8;A0A2R8YF72;Q9UL68-4;Q9UL68 H7BYU4 MYT1L Myelin transcription factor 1-like protein 1 T(0.25)QIT(0.25)T(0.25)MES(0.25)NLK 99.283 0.054672 173390000 1109600 687180 593870 588050 512140 380290 1219000 554710 907750 TRUE FALSE 1040152.117 738059.5222 607956.8768 603140.3586 471918.5903 490073.5495 1036222.267 623966.7646 756240.6607 1.375424743 0.975958528 0.803919848 0.797550819 0.624032289 0.648039143 1.370228183 0.825090209 1 19.5284859 -0.147528116 8.183517756 1 0.92832163 0.007564146 0.260733086 0 0 0.249491487 0.058805707 0.711986704 0.147528116 -0.07167837 T(ph)RSPDVISSASTALSQDIPEIASEALSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 TRSPDVISSASTALSQDIPEIASEALSR 28 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 T(0.603)RS(0.397)PDVISSASTALSQDIPEIASEALSR;T(0.422)RS(0.422)PDVIS(0.039)S(0.039)AS(0.039)T(0.039)ALSQDIPEIASEALSR;T(0.467)RS(0.467)PDVIS(0.016)S(0.016)AS(0.016)T(0.016)ALSQDIPEIASEALSR;T(0.588)RS(0.41)PDVIS(0.001)S(0.001)ASTALSQDIPEIASEALSR;T(0.5)RS(0.5)PDVISSASTALSQDIPEIASEALSR;T(0.485)RS(0.485)PDVIS(0.015)S(0.015)ASTALSQDIPEIASEALSR;T(0.476)RS(0.476)PDVIS(0.022)S(0.022)AS(0.002)T(0.001)ALSQDIPEIASEALSR;T(0.499)RS(0.499)PDVISSAS(0.001)T(0.001)ALSQDIPEIASEALSR;T(0.483)RS(0.483)PDVIS(0.008)S(0.008)AS(0.008)T(0.01)ALSQDIPEIASEALSR 233.72 7.38E-45 10648668000 389569.3 428887 438552 423857 470574 373411.6 535899 424005 499166 TRUE FALSE 365186.8529 460642.2397 448954.6605 434733.8882 433617.0162 481209.4671 455545.92 476942.9576 415851.9699 0.8781655 1.107707245 1.079602101 1.045405384 1.04271964 1.157165294 1.095452115 1.146905611 1 18.66571054 2.270291278 24.90787263 1.108270171 1.048551471 0.15082601 0.074018769 363.3054949 285185.5589 0.023769617 0.01988525 186.3336441 -2.270291278 -0.059718699 T(ph)RSWDSSSPVDRPEPEAASPTTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TRSWDSSSPVDRPEPEAASPTTR 23 2 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 T(0.5)RS(0.5)WDSSSPVDRPEPEAASPTTR 200.52 1.15E-22 709050000 58419 52003 43456 53059 72935 41639 56229 50122 73437 TRUE FALSE 54762.65907 55853.35623 44486.79684 54420.58377 67206.97931 53659.50335 47797.98345 56379.84203 61179.89028 0.895108815 0.912936522 0.727147379 0.889517512 1.098514218 0.877077469 0.781269519 0.921542059 1 15.9007699 T(ph)RSYDNLTTACDNTVPLASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.5)RS(0.5)YDNLTTACDNTVPLASR;T(0.625)RS(0.375)YDNLTTACDNTVPLASR;T(0.67)RS(0.33)YDNLTTACDNTVPLASR 266.67 1.47E-36 2406100000 864210 1026170 956970 1015030 929400 684680 1152680 834660 1329860 TRUE FALSE 810120.6388 1102148.695 979669.7803 1041077.388 856408.673 882336.0011 979846.335 938869.1383 1107897.775 0.731223275 0.994810821 0.884260085 0.939687227 0.773003333 0.796405608 0.884419445 0.847433003 1 20.07939334 -1.320559021 3.289556593 1.000756848 0.869702464 0.233979217 0.07843897 102638074.7 144043263.4 760393.2421 0.018449425 0.04780144 1.320559021 -0.131054384 T(ph)RTPASINATPANINLADLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TRTPASINATPANINLADLTR 21 1 Q7KZ85;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 1 T(0.616)RT(0.384)PASINATPANINLADLTR 186.71 5.07E-17 206450000 51187 53322 45601 43648 53633 29835 53817 48087 54349 TRUE FALSE 47983.29704 57270.01636 46682.67725 44768.08158 49420.88053 38447.88017 45747.64046 54090.7678 45277.80079 1.059753261 1.264858614 1.031027931 0.988742403 1.091503555 0.849155204 1.010376822 1.194642117 1 15.46651627 3.73551973 4.071785018 1.013299587 1.171729635 0.249411784 0.098884589 0.229571048 8.819101253 0.024712909 0.043501184 5439.008409 -3.73551973 0.158430048 T(ph)RTSQEELLAEVVQGQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TRTSQEELLAEVVQGQSR 18 1 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;A0A087WTC9;Q6PJT7-9;Q6PJT7-2;H0YJA2;Q6PJT7-3;Q6PJT7-11;G3V5I6 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 1 T(0.497)RT(0.252)S(0.252)QEELLAEVVQGQSR;T(0.436)RT(0.282)S(0.282)QEELLAEVVQGQSR 201.79 2.21E-15 327211000 258650 300100 250450 262404 192043 120525 176853 138246 182470 TRUE FALSE 242461.5582 322319.7163 256390.7923 269137.7309 176960.7174 155318.6109 150335.5345 155506.3174 152014.5782 1.594988856 2.120321091 1.686619766 1.770473162 1.164103598 1.021734973 0.988954719 1.022969766 1 17.21385016 2.709304822 2.144216179 0.999693678 1.856421251 0.882301388 0.137241153 0.088532333 0.803470703 0.04686861 0.045576061 512.0411005 -2.709304822 0.856727572 T(ph)S(ph)RT(ph)KRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSRTKRR 7 3 J3KN16 J3KN16 KIAA0368 3 T(1)S(1)RT(1)KRR;T(1)S(1)RT(1)KRR 65.347 0.079116 3736300000 2917500 2678700 2555100 2575200 3269400 1856060 2845100 2384800 3403800 TRUE FALSE 2734898.883 2877033.735 2615708.179 2641283.992 3012634.512 2391874.391 2418503.668 2682547.53 2835683.791 0.964458341 1.014582001 0.922425902 0.931445178 1.062401429 0.843491224 0.852882002 0.945996708 1 21.43526523 2.219970785 24.99952809 0.891504328 0.974018549 0.213400375 0.060148262 288.0318733 387341.6807 0.0211423 0.01564202 165.947527 -2.219970785 0.082514221 SSSHSSPGS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 SSSHSSPGSPK 11 0 Q6NZY4;Q6NZY4-2;F5GX80 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 SSSHSSPGS(1)PK;SSSHS(0.001)S(0.001)PGS(0.997)PK;SSSHSSPGS(1)PK;SSSHSSPGS(1)PK 107.74 0.0013896 661940000 414928 965830 971010 1015900 1065500 863440 1330780 1098230 1131590 TRUE FALSE 388958.3971 1037341.058 994042.8157 1041969.714 981819.928 1112701.111 1131241.893 1235346.433 942720.3186 0.412591507 1.100369895 1.054440852 1.105279788 1.041475301 1.180308825 1.199976145 1.310406075 1 19.8464703 4.740008418 5.170205905 1.127162006 0.380143592 0.863853743 0.088822398 0.057040313 5.131068269 0.021455027 0.152003927 54955.15262 -4.740008418 -0.747018413 down T(ph)SFGSLTDSSEEALEGMVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSFGSLTDSSEEALEGMVR 19 0 G3V160;Q969H4-2;Q969H4 G3V160 CNKSR1 Connector enhancer of kinase suppressor of ras 1 1 T(0.5)S(0.5)FGSLTDSSEEALEGMVR 99.569 0.0086672 30735000 22992 20348 17482 18685 23870 14941 22699 17919 24441 TRUE FALSE 21552.97176 21854.58709 17896.6813 19164.48873 21995.34649 19254.22415 19295.49568 20156.22659 20361.63921 1.058508676 1.073321596 0.878941087 0.941205595 1.080234566 0.945612677 0.947639602 0.989911784 1 14.31356609 4.19712671 6.153678106 0.965223722 1.066257264 0.376806453 0.051534615 0.161816297 19.6263077 0.012631672 0.029052742 15744.42159 -4.19712671 0.101033542 T(ph)SLASLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSLASLR 7 0 Q9HDC5 Q9HDC5 JPH1 Junctophilin-1 1 T(0.786)S(0.214)LASLR 197.5 0.0047043 240090000 565170 466470 460410 441590 537900 440840 696200 490760 539910 TRUE FALSE 529797.0186 501007.9242 471331.1426 452921.947 495655.5038 568103.3516 591811.2732 552032.4663 449795.533 1.177861894 1.113857047 1.047878665 1.006950745 1.101957373 1.263025775 1.315733994 1.227296462 1 18.77890981 2.287528255 6.242812177 1.238462364 1.082495499 0.215710034 0.094734905 0.190132705 16.85820372 0.030991347 0.025506587 193.8778769 -2.287528255 -0.155966864 T(ph)SLMAFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSLMAFLR 8 0 O75363;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 T(0.983)S(0.017)LMAFLR;T(0.977)S(0.023)LMAFLR 153.05 0.0050007 12908900 54582 76340 49266 53014 90938 36788 46136 66062 93886 TRUE FALSE 51165.81005 81992.29303 50434.61279 54374.42899 83796.09631 47408.0984 39218.33511 74309.98612 78215.82007 0.654161907 1.048282725 0.64481345 0.695184541 1.071344598 0.606119048 0.5014118 0.950063377 1 16.25517282 T(ph)SPADGKPR ddPTM_SK-BR-3_Pertuzumab_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(0.5)S(0.5)PADGKPR 81.017 0.036334 415660000 363890 266000 313070 297210 304710 201420 332500 252540 243910 TRUE FALSE 341114.7745 285694.9168 320496.1682 304836.9118 280779.3057 259566.6842 282644.7118 284070.1749 203199.8453 1.678715719 1.405979992 1.577246123 1.500182795 1.381788974 1.277396072 1.390969129 1.397984209 1 17.63253978 -3.348507085 0.117696171 5.77E-12 1.72028141 0.778682982 0.085115493 44.63931487 0.511744212 12.02901675 0.934541906 0.000448222 3.348507085 1.72028141 T(ph)SPADHGGSVGSESGGSAVDSVAGEHSVSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSPADHGGSVGSESGGSAVDSVAGEHSVSGR 31 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 T(0.5)S(0.5)PADHGGSVGSESGGSAVDSVAGEHSVSGR 214.99 1.70E-34 294030000 27657 28906 35280 38740 31336 32714 39688 33578 38054 TRUE FALSE 25925.99774 31046.23032 36116.85826 39734.13399 28874.99696 42158.00073 33737.15285 37770.28721 31702.54156 0.817789252 0.979297835 1.139241729 1.253342225 0.91081016 1.329798769 1.064178176 1.19139619 1 14.95231088 4.570104852 1.363105275 1.133416366 0.745011306 0.417927121 0.119933825 0.831155308 1.736130241 0.029262713 0.408758021 37162.49399 -4.570104852 -0.388405061 T(ph)SPAPWKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSPAPWKR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.586)S(0.414)PAPWKR 93.098 0.0066274 162600000 481790 441020 399590 418260 422720 299630 525270 351590 473870 TRUE FALSE 451635.6239 473673.5797 409068.4635 428993.2597 389521.2764 386128.3169 446510.6399 395486.7854 394778.0357 1.144024194 1.199847856 1.03619864 1.086669523 0.986684266 0.978089666 1.131042255 1.001795312 1 18.5906822 3.893254683 2.945850185 1.039096421 1.171777822 0.578733899 0.049311039 0.184695102 3.148340885 0.012843353 0.026983193 7820.86309 -3.893254683 0.132681402 T(ph)SPCQSPTISEGPVPSLPIRPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSPCQSPTISEGPVPSLPIRPSR 23 1 A0A0D9SGJ6;J3KQV8;O43426;J3KPK1;C9JFZ1;O43426-4;O43426-2 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 T(0.804)S(0.196)PCQSPTISEGPVPSLPIRPSR 93.176 0.0075179 147970000 13057 28134 28699 31400 33159 17956 21685 18767 45941 TRUE FALSE 12239.78568 30217.07063 29379.75383 32205.77716 30554.8259 23139.60571 18433.53556 21110.10126 38273.15031 0.319800842 0.789510934 0.767633539 0.841471812 0.798335795 0.604591091 0.481630998 0.551564245 1 15.22404504 2.214349416 22.41315211 0.601409122 0.730143768 0 0.201679471 178.6085254 165340.2771 0.069572822 0.05142731 163.813397 -2.214349416 0.128734646 T(ph)SPDSLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TSPDSLRR 8 1 Q9BRL6-2;Q9BRL6 Q9BRL6-2 SRSF8 Serine/arginine-rich splicing factor 8 1 T(0.988)S(0.012)PDSLRR;T(0.962)S(0.032)PDS(0.006)LRR;T(0.992)S(0.007)PDS(0.001)LRR;T(0.57)S(0.43)PDSLRR 96.143 0.0177 1073610000 1446090 1462450 1424190 1414360 1650870 1211540 1523160 1378740 2070300 TRUE FALSE 1355581.808 1570731.32 1457972.459 1450654.872 1521217.329 1561291.93 1294776.298 1550878.724 1724753.555 0.785956813 0.910698989 0.845322194 0.841079508 0.881991125 0.905226098 0.750702206 0.899188594 1 20.7179588 -2.227196141 1.434547899 1.312632825 0.852393955 0.444224381 0.051842681 86948.47368 12835.33199 87692.52106 0.013799596 0.005926576 2.227196141 -0.46023887 T(ph)SPDTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSPDTLR 7 0 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.652)S(0.348)PDTLR;T(0.563)S(0.437)PDTLR 196.95 0.0048439 1816820000 2371320 1905800 1976890 1898840 1924560 1522080 2279990 1785360 1932940 TRUE FALSE 2222903.314 2046907.415 2023782.764 1947567.449 1773412.821 1961479.787 1938126.666 2008266.126 1610319.827 1.380411069 1.271118557 1.256758273 1.20942897 1.101279877 1.218068457 1.203566294 1.247122524 1 20.61891582 7.999993478 0.024366496 1.38E-07 2.867949651 0.679290972 0.057370781 1296.88798 2.430121199 99.24141888 204.169261 99998498.24 -7.999993478 2.867949513 T(ph)SPDTLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 TSPDTLRR 8 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.947)S(0.053)PDTLRR;T(0.5)S(0.5)PDTLRR;T(0.995)S(0.005)PDTLRR;T(0.5)S(0.5)PDTLRR;T(0.982)S(0.015)PDT(0.003)LRR;T(0.942)S(0.058)PDTLRR;T(0.594)S(0.406)PDTLRR;T(0.5)S(0.5)PDTLRR;T(0.5)S(0.5)PDTLRR 140.17 0.00038316 15157312000 9231742 8448714 7970693 8349030 9388500 5864203 9040515 7743880 10153009 TRUE FALSE 8653943.747 9074265.575 8159761.602 8563280.245 8651165.081 7557103.209 7684973.704 8710720.464 8458406.207 1.02311754 1.072810333 0.964692568 1.012398794 1.02278903 0.893442928 0.908560492 1.02983 1 23.01195442 2.263781087 24.89073688 0.943830208 1.018742406 0.270879486 0.047439236 225.4420177 222493.7709 0.016182925 0.013534635 183.5612842 -2.263781087 0.074912198 T(ph)SPENVQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSPENVQDR 9 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 T(0.695)S(0.305)PENVQDR;T(0.662)S(0.338)PENVQDR 186.97 0.00045915 688950000 616790 527170 569840 612440 608110 433890 634910 480070 535560 TRUE FALSE 578186.2149 566202.2153 583356.8739 628156.2473 560351.4936 559146.9994 539711.1397 540007.7963 446171.5762 1.295883122 1.2690235 1.307472069 1.407880468 1.255910335 1.253210714 1.209649311 1.210314205 1 18.76723908 0.762186093 0.641466139 0.997487867 1.308274051 0.832505174 0.042325781 0.433520224 0.371804137 0.045368498 0.017404649 5.783438115 -0.762186093 0.310786183 T(ph)SPGGRT(ph)SPEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSPGGRTSPEAR 12 1 Q8TD16;Q8TD16-2 Q8TD16 BICD2 Protein bicaudal D homolog 2 2 T(0.744)S(0.256)PGGRT(0.593)S(0.407)PEAR 118.62 0.0029821 128440000 252160 222980 243670 245300 255380 178570 272940 199220 305150 TRUE FALSE 236377.7557 239489.6712 249449.9675 251594.8133 235323.485 230120.2602 232015.1809 224093.0555 254218.4937 0.929821243 0.942062349 0.98124241 0.989679428 0.925674138 0.905206607 0.912660513 0.88149785 1 17.95570946 2.560060989 7.170618984 0.916442592 0.960915876 0.189321144 0.034814275 0.332500575 24.97941027 0.010394555 0.009762674 363.1290463 -2.560060989 0.044473284 T(ph)SPGGRTS(ph)PEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSPGGRTSPEAR 12 1 Q8TD16;Q8TD16-2 Q8TD16 BICD2 Protein bicaudal D homolog 2 2 T(0.999)S(0.001)PGGRT(0.002)S(0.998)PEAR;T(0.999)S(0.001)PGGRT(0.258)S(0.742)PEAR 164.63 0.0014241 298740000 366430 319840 332020 343060 388750 246230 372920 280430 451550 TRUE FALSE 343495.8004 343521.2864 339895.6712 351863.5004 358219.1431 317312.6038 317004.108 315442.3028 376183.3879 0.913107307 0.913175056 0.903537163 0.93535098 0.952246045 0.843505094 0.842685026 0.838533314 1 18.52107662 2.231323912 24.99992714 0.864473956 0.919897151 0.114609421 0.048988538 228.0439606 787793.4633 0.016171001 0.012192612 170.3428511 -2.231323912 0.055423195 T(ph)SPHWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSPHWK 6 0 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 T(0.902)S(0.098)PHWK 124.34 0.067688 415820000 1169800 810020 907010 941320 899260 716680 1199500 800810 855330 TRUE FALSE 1096584.306 869994.7236 928524.7055 965475.8649 828635.747 923573.8817 1019646.111 900792.8913 712569.8974 1.538914723 1.220925451 1.303064736 1.354920926 1.162883459 1.296116893 1.430941883 1.26414671 1 19.44267201 -1.895761789 1.588095104 0.785095678 1.314641619 0.477086676 0.105559856 74998.23355 23806.82824 60166.47042 0.02699194 0.012712712 1.895761789 0.529545941 T(ph)SPINEDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TSPINEDIR 9 0 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 T(0.958)S(0.042)PINEDIR;T(0.958)S(0.042)PINEDIR;T(0.5)S(0.5)PINEDIR;T(0.603)S(0.397)PINEDIR 163.12 0.00070716 1313370000 2289780 1635800 1873080 1801890 1695980 1668580 2222690 1547070 1705400 TRUE FALSE 2146466.757 1756916.334 1917510.342 1848129.548 1562784.572 2150271.959 1889418.269 1740225.095 1420757.723 1.510790139 1.236605162 1.349639218 1.300805562 1.099965566 1.513468429 1.329866619 1.224857037 1 20.43822913 0.902093914 3.247485931 1.000375503 1.325694705 0.438497024 0.12006051 0.368166903 8.57393932 0.10502592 0.027322468 7.981672682 -0.902093914 0.325319203 T(ph)SPINLGLNVNDLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSPINLGLNVNDLLK 15 0 P50616 P50616 TOB1 Protein Tob1 1 T(0.5)S(0.5)PINLGLNVNDLLK 123.38 0.0011523 11770000 54445 34086 44285 37791 40373 26254 47894 36002 44566 TRUE FALSE 51037.38464 36609.76291 45335.46111 38760.78104 37202.26744 33833.1036 40712.73933 40496.92895 37127.64669 1.374646367 0.986051263 1.22107015 1.043987015 1.002009843 0.911264425 1.096561268 1.090748608 1 15.18020625 4.746103205 24.89511458 1.05425551 1.374646529 0.609143949 0.082882539 653.4578221 2156752.415 0.020078881 0.214944647 55731.81732 -4.746103205 0.320391019 T(ph)SPKPAVVETVTTAKPQQIQALMDEVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSPKPAVVETVTTAKPQQIQALMDEVTK 28 2 P56192;H0YIP0;H0YI94 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 1 T(0.5)S(0.5)PKPAVVETVTTAKPQQIQALMDEVTK;T(0.5)S(0.5)PKPAVVETVTTAKPQQIQALMDEVTK 187.32 3.84E-16 3014100000 716260 282708 459270 423980 461870 308309 615410 343140 713820 TRUE FALSE 671430.5652 303639.9945 470164.1013 434860.0446 425596.5933 397312.8033 523134.9837 385981.7843 594678.8305 1.129064178 0.510594928 0.790618527 0.731251933 0.715674699 0.668113245 0.879693301 0.649059231 1 19.18175119 -1.513950554 2.973601702 1.009168192 0.743727229 0.171741616 0.163007459 49889999.46 56043112.06 3715329.602 0.036733194 0.030623121 1.513950554 -0.265440963 T(ph)SPLKDNPS(ph)PEPQLDDIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSPLKDNPSPEPQLDDIKR 19 2 Q96JC9-2;Q96JC9 Q96JC9-2 EAF1 ELL-associated factor 1 2 T(0.864)S(0.136)PLKDNPS(1)PEPQLDDIKR;T(0.5)S(0.5)PLKDNPS(1)PEPQLDDIKR 164.96 4.30E-11 1056680000 1541890 557670 812800 772250 817090 513920 1062300 597470 1110340 TRUE FALSE 1445385.857 598960.4671 832079.9998 792067.2424 752919.0474 662280.3612 903017.9769 672065.4447 925017.0809 1.562550451 0.647512872 0.899529335 0.856273099 0.813951507 0.715965548 0.976217624 0.726543821 1 19.81912048 4.747155218 24.99967835 0.826068004 1.562550822 0.808434537 0.112132148 441.0375574 1282846.633 0.0245093 0.2883777 55866.98288 -4.747155218 0.736482819 T(ph)SPLKDNPSPEPQLDDIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSPLKDNPSPEPQLDDIKR 19 2 Q96JC9-2;Q96JC9 Q96JC9-2 EAF1 ELL-associated factor 1 1 T(0.78)S(0.22)PLKDNPSPEPQLDDIKR;T(0.5)S(0.5)PLKDNPSPEPQLDDIKR 166.34 9.57E-10 604540000 1274650 546570 791200 725300 762510 531660 990320 610170 1090990 TRUE FALSE 1194871.932 587038.6115 809967.6376 743912.4259 702625.5404 685141.6112 841830.7097 686351.0676 908896.7209 1.314639941 0.645880437 0.891154758 0.818478501 0.773053224 0.753816793 0.926211626 0.755147479 1 19.79375684 -0.524159356 12.66428719 0.999999994 0.841223326 0.047935192 0.180188709 0 0 0.151653106 0.03574498 0.299116688 0.524159356 -0.158776667 T(ph)SPLNSSGSSQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSPLNSSGSSQGR 13 0 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.679)S(0.321)PLNSSGSSQGR;T(0.663)S(0.337)PLNSSGSSQGR 230.22 4.98E-11 328300000 750870 510010 566060 544310 470140 488300 712080 520280 315630 TRUE FALSE 703874.387 547771.6711 579487.2105 558277.9161 433217.1009 629264.2831 605310.2146 585238.1033 262949.314 2.676844356 2.083183496 2.203798146 2.123138896 1.647530828 2.393101064 2.3020034 2.225668873 1 18.00442521 -1.026659929 5.405499917 1.000010505 2.192835609 0.682453836 0.258569795 1.90E-05 3.42E-06 0.233446948 0.055023672 0.094045944 1.026659929 1.192825103 T(ph)SPPCSPANLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TSPPCSPANLSR 12 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 T(0.944)S(0.056)PPCSPANLSR;T(0.614)S(0.386)PPCSPANLSR;T(0.621)S(0.379)PPCSPANLSR 147.33 0.00073208 4260920000 3286680 2740870 2752880 2929840 2656110 2246410 3217360 2153870 3131610 TRUE FALSE 3080972.566 2943806.867 2818179.614 3005024.655 2447509.835 2894912.1 2734946.737 2422785.411 2608924.06 1.180936085 1.128360504 1.080207606 1.151825268 0.938129964 1.109619151 1.048304463 0.928653098 1 21.31502352 4.48124872 0.261783294 0.977889036 1.303339641 0.499388948 0.060758113 6.965091035 0.449602369 0.078288893 0.729741203 30286.47434 -4.48124872 0.325450605 T(ph)SPPLLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TSPPLLDR 8 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.975)S(0.025)PPLLDR;T(0.681)S(0.319)PPLLDR;T(0.643)S(0.357)PPLLDR;T(0.665)S(0.335)PPLLDR;T(0.922)S(0.078)PPLLDR 183.72 0.0024793 31292500000 9865020 8476520 8987150 8707350 8317840 6921440 10246530 7494500 7915220 TRUE FALSE 9247586.008 9104130.361 9200329.442 8930795.343 7664590.399 8919547.368 8710157.951 8430204.822 6594118.648 1.402399093 1.380644002 1.395232621 1.354357697 1.162337351 1.352651938 1.320897972 1.278442999 1 22.65274841 -4.311933173 0.163375879 2.65E-15 1.432636066 0.769352597 0.060181468 48.91651409 0.557864034 16.18414821 0.247328767 4.88E-05 4.311933173 1.432636066 T(ph)SPQVLGSILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSPQVLGSILK 11 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 T(0.6)S(0.4)PQVLGSILK;T(0.792)S(0.208)PQVLGSILK 145.29 0.0004059 360590000 1884660 1343810 1463020 1420000 1670450 1122700 1709690 1394120 1629690 TRUE FALSE 1766702.495 1443307.091 1497723.525 1456439.604 1539259.595 1446805.264 1453337.856 1568178.951 1357684.211 1.301261723 1.063065387 1.103145719 1.072738117 1.133739041 1.065641961 1.07045353 1.155039543 1 20.37271653 4.742198461 24.95708282 1.085532697 1.301261807 0.724661418 0.04225928 164.2147316 1126532.294 0.008689617 0.064124399 55232.97822 -4.742198461 0.21572911 T(ph)SPSKSPFLHSGMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TSPSKSPFLHSGMK 14 1 O14497;H0Y488;A0A1B0GTU5;O14497-3;O14497-2;H0YEW5 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 T(0.499)S(0.499)PS(0.002)KSPFLHSGMK;T(0.566)S(0.434)PSKSPFLHSGMK;T(0.495)S(0.495)PS(0.009)KS(0.001)PFLHSGMK 147.92 1.28E-05 1932390000 2454070 1773070 2132350 2007090 2230840 1557720 2884370 1858390 2762400 TRUE FALSE 2300474.139 1904349.948 2182930.349 2058595.327 2055638.825 2007408.477 2451885.496 2090414.082 2301337.594 0.999624803 0.827496997 0.948548511 0.894521227 0.893236538 0.872279009 1.065417565 0.908347427 1 21.1340412 1.754806565 24.99999999 0.995555939 0.900885073 0.317526365 0.058528416 5.783847254 8910.868147 0.024042586 0.013332973 56.85996193 -1.754806565 -0.094670865 T(ph)SPTPPESATTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSPTPPESATTVK 13 0 Q5M775-4;Q5M775;J3KSG2 Q5M775-4 SPECC1 Cytospin-B 1 T(0.615)S(0.381)PT(0.004)PPESATTVK 160.18 0.0004951 285270000 1008300 711580 811440 775480 863800 569260 958400 696190 892560 TRUE FALSE 945192.3029 764266.1236 830687.74 795380.1297 795960.6324 733596.1208 814696.8173 783110.854 743585.9698 1.271127134 1.027811382 1.117137458 1.069654568 1.070435248 0.986565307 1.095632315 1.053154424 1 19.50414002 4.743844284 24.91588289 1.059624287 1.271127227 0.740156823 0.040508462 271.6900482 1281152.167 0.008924858 0.076147653 55442.68875 -4.743844284 0.21150294 T(ph)SPTVATQTGASATSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TSPTVATQTGASATSTR 17 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 T(0.66)S(0.339)PTVATQTGASATSTR;T(0.666)S(0.334)PTVATQTGASATSTR;T(0.677)S(0.323)PTVATQTGASATSTR 348.22 1.53E-86 842950000 640390 550720 584030 562360 588650 488780 673180 485570 565340 TRUE FALSE 600309.133 591495.8818 597883.4674 576791.1097 542419.8035 629882.8513 572242.9085 546194.4834 470981.1018 1.274592825 1.255880288 1.269442585 1.224658712 1.151680612 1.337384555 1.215001847 1.159695116 1 18.84530965 0.910206599 1.937611977 1.000828517 1.250828991 0.742895558 0.046689675 0.204156757 1.580829892 0.041242199 0.011544401 8.132172818 -0.910206599 0.250000473 T(ph)SPYILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TSPYILR 7 0 P49454 P49454 CENPF Centromere protein F 1 T(0.5)S(0.5)PYILR;T(0.758)S(0.242)PYILR;T(0.886)S(0.114)PYILR 164.77 0.013249 597620000 1462540 1254160 1361570 1292080 1319600 1117180 1581590 1192030 1369880 TRUE FALSE 1371002.232 1347019.311 1393867.083 1325236.96 1215963.939 1439691.73 1344445.262 1340857.569 1141238.178 1.201328748 1.180313923 1.221363875 1.161227328 1.065477796 1.261517322 1.178058435 1.174914751 1 20.12216849 0.591350917 3.034828873 1.000001846 1.184081799 0.564674299 0.049800864 5.700083619 41.44032901 0.045043303 0.011758828 3.902571936 -0.591350917 0.184079953 T(ph)SSDSALHTSVMNPSPQDTYPGPTPPSILPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSSDSALHTSVMNPSPQDTYPGPTPPSILPSR 32 0 Q53ET0;H0YDQ8 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 T(0.329)S(0.329)S(0.329)DS(0.013)ALHTSVMNPSPQDTYPGPTPPSILPSR;T(0.332)S(0.332)S(0.332)DS(0.004)ALHTSVMNPSPQDTYPGPTPPSILPSR 213.57 1.28E-27 1269900000 67045 190228 128016 164654 178486 133742 188195 171705 141670 TRUE FALSE 62848.77313 204312.6791 131052.6 168879.3004 164468.4295 172351.1443 159976.9069 193142.7472 118024.3618 0.532506782 1.731105985 1.110386008 1.430885097 1.393512552 1.46030143 1.355456657 1.636465085 1 16.84872516 4.752621739 24.99993797 1.398564698 0.532506198 0.610813725 0.214947283 1547.609339 2751521.202 0.045307837 0.955875954 56574.63219 -4.752621739 -0.8660585 T(ph)SSESIYSRPGSSIPGSPGHTIYAK ddPTM_SK-BR-3_Pertuzumab_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(0.483)S(0.483)S(0.008)ES(0.009)IYS(0.011)RPGS(0.003)S(0.003)IPGSPGHTIYAK 167.03 1.93E-11 360510000 376180 568240 526300 527420 555840 457260 701730 546990 537520 TRUE FALSE 352635.5653 610313.0809 538784.0845 540954.4901 512186.5686 589263.539 596512.101 615282.9056 447804.4395 0.787476707 1.362900916 1.203168252 1.208015023 1.143772869 1.315894813 1.332081705 1.37399912 1 18.77250931 2.234388825 24.9611742 1.28957705 1.182828354 0.052343758 0.177883764 276.2622975 1652945.623 0.059914231 0.045835441 171.5492507 -2.234388825 -0.106748697 T(ph)SSGTSLSAMHSSGSSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSSGTSLSAMHSSGSSGK 18 0 Q12888;Q12888-2;A6NNK5;Q12888-3;M0R142 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 T(0.28)S(0.28)S(0.241)GT(0.093)S(0.093)LS(0.014)AMHSSGSSGK;T(0.353)S(0.353)S(0.281)GT(0.006)S(0.006)LS(0.002)AMHSSGSSGK 146.89 2.96E-07 465859000 163513 384185 343065 374004 407817 317982 455487 377190 402780 TRUE FALSE 153279.0132 412630.4571 351202.6638 383601.5758 375788.6979 409778.2414 387190.9529 424283.0018 335553.4159 0.456794674 1.229701256 1.046637129 1.143190793 1.119907234 1.221201221 1.153887681 1.264427604 1 18.35618292 4.74254702 24.99826125 1.150464468 0.456794404 0.878371266 0.080751898 117.8874733 739229.8 0.017369465 0.13273466 55277.32521 -4.74254702 -0.693670064 T(ph)SSISGPLSPAYTGQVPYNYNQLEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSSISGPLSPAYTGQVPYNYNQLEGR 26 0 Q01082-3 Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 T(0.332)S(0.332)S(0.332)IS(0.003)GPLS(0.001)PAYTGQVPYNYNQLEGR 186.69 4.62E-17 137460000 94790 87930 62853 77288 87983 45052 120390 82847 143150 TRUE FALSE 88857.2631 94440.42869 64343.90284 79271.34093 81073.17009 58057.78104 102338.6371 93190.63032 119257.3402 0.745088419 0.791904536 0.539538302 0.664708275 0.679817024 0.486827737 0.858132816 0.781424692 1 16.86371854 1.139999236 1.400926983 0.983245216 0.660911804 0.515196708 0.103315303 0.309838416 1.204422166 0.092908222 0.028310307 13.80381837 -1.139999236 -0.322333412 T(ph)SSPPRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSSPPRK 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(0.382)S(0.382)S(0.235)PPRK 84.568 0.01257 3027100000 549030 414280 502110 457250 420400 338090 511730 383910 491950 TRUE FALSE 514667.1923 444953.7223 514020.2863 468983.8091 387383.4798 435691.0946 435000.8372 431842.0086 409840.3669 1.25577477 1.085675688 1.254196336 1.144308485 0.945205771 1.063075114 1.061390903 1.053683442 1 18.64470256 2.939461544 7.479932299 1.034889235 1.184436351 0.65365395 0.058530454 0.180889335 19.90540655 0.016888354 0.01802617 869.884403 -2.939461544 0.149547116 T(ph)SSPRSPPSSSEIFTPAHEENVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSSPRSPPSSSEIFTPAHEENVR 23 1 I3L3A7;I3L2L5;I3L317;I3L4Q0;C9JLW8 I3L3A7 FAM195B Protein FAM195B 1 T(0.265)S(0.265)S(0.265)PRS(0.197)PPS(0.002)S(0.002)S(0.002)EIFTPAHEENVR 74.838 0.026268 89865000 48279 45428 46194 46715 65428 28531 52187 34217 65793 TRUE FALSE 45257.30357 48791.53639 47289.74349 47913.78599 60289.5488 36767.43654 44362.04383 38489.06777 54811.72326 0.825686566 0.890166072 0.862766954 0.874152155 1.09993894 0.670795121 0.809353204 0.70220503 1 15.74219687 2.203623841 24.99999191 0.778988744 0.899595269 0.193823637 0.113069528 260.4723604 186386.8229 0.037885714 0.027981612 159.817319 -2.203623841 0.120606524 T(ph)SSRESLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSSRESLNR 9 1 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 T(0.333)S(0.333)S(0.333)RESLNR;T(0.477)S(0.262)S(0.262)RESLNR 93.258 0.015393 721420000 141961 147977 162664 157613 211454 100788 148807 137445 226130 TRUE FALSE 133075.9144 158933.371 166522.4669 161657.6164 194847.2558 129883.8594 126494.7718 154605.3108 188387.4421 0.706394826 0.843651622 0.883936132 0.858112487 1.034290044 0.68945073 0.671460743 0.820677371 1 17.52334327 T(ph)TFQDELIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TTFQDELIR 9 0 E7ETZ8;Q49MG5;A0A0C4DG83;A2VCS9;Q49MG5-2;C9JXH8 E7ETZ8 MAP9 Microtubule-associated protein 9 1 T(0.5)T(0.5)FQDELIR;T(0.5)T(0.5)FQDELIR 96.253 0.083763 80828000 18087.1 12468.6 13240.4 13544.5 16516 11794 16806.8 10185 13359.2 TRUE FALSE 16955.0607 13391.78812 13554.46854 13892.0748 15218.89998 15198.73634 14286.77637 11456.61967 11129.46322 1.523439214 1.203273496 1.217890592 1.248225052 1.367442408 1.365630673 1.283689616 1.029395529 1 13.44209639 1.229787782 5.174566254 1.005171973 1.297397575 0.639763608 0.093291014 0.115963158 8.515821696 0.078835212 0.0228451 16.97414007 -1.229787782 0.292225603 T(ph)TGTPPDSSLVTYELHSRPEQDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTGTPPDSSLVTYELHSRPEQDK 23 1 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18 Q13561 DCTN2 Dynactin subunit 2 1 T(0.355)T(0.355)GT(0.289)PPDSSLVTYELHSRPEQDK 153.24 7.77E-08 126400000 178380 100900 129820 123690 126040 114810 161660 121600 135380 TRUE FALSE 167215.5142 108370.741 132899.3917 126864.0948 116141.3268 147953.7832 137420.5838 136782.0277 112784.2034 1.482614667 0.96086808 1.178351114 1.124839215 1.029765901 1.311830724 1.218438218 1.212776466 1 16.78320549 2.239306438 24.99999876 1.209367635 1.130537001 0 0.15622175 61.71208866 2068701.099 0.050821137 0.040190445 173.50278 -2.239306438 -0.078830634 T(ph)TPDQELAPASEPVWERPWSVEEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTPDQELAPASEPVWERPWSVEEIR 25 1 Q641Q2;Q641Q2-2;E7ESD2;A0A087WYF6;Q5T1D7 Q641Q2 FAM21A WASH complex subunit FAM21A 1 T(0.5)T(0.5)PDQELAPASEPVWERPWSVEEIR 85 0.028686 61118000 2837.2 4015.6 3296 2658 4489 3190.5 4654 1757.4 2868.5 TRUE FALSE 2659.624717 4312.919202 3374.182676 2726.20878 4136.452048 4111.545557 3956.175906 1976.815259 2389.728819 1.112939969 1.804773482 1.411952122 1.140802571 1.730929474 1.720507166 1.655491566 0.827213215 1 11.2226312 1.237014597 24.99998709 0.913606333 1.541190524 0.510632306 0.241761029 30.79297611 497858.7642 0.185357262 0.055783339 17.25895901 -1.237014597 0.627584192 T(ph)TPDQELAPASEPVWERPWSVEEIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTPDQELAPASEPVWERPWSVEEIRR 26 2 Q641Q2;Q641Q2-2;E7ESD2;A0A087WYF6;Q5T1D7 Q641Q2 FAM21A WASH complex subunit FAM21A 1 T(0.594)T(0.406)PDQELAPASEPVWERPWSVEEIRR 176.11 3.41E-11 158750000 29227 26349 25820 27674 28812 22978 35538 23030 35645 TRUE FALSE 27397.73424 28299.90738 26432.46259 28384.16169 26549.22174 29611.37558 30209.40682 25905.3462 29695.61922 0.922618721 0.952999402 0.890113198 0.955836667 0.894045062 0.997163095 1.017301798 0.872362553 1 14.8579625 2.230984114 24.99909627 0.97873703 0.924182436 0.223691746 0.044093635 224.4141783 740460.5984 0.015206643 0.011446658 170.2096248 -2.230984114 -0.054554594 T(ph)TPDQELVPASEPVWERPWSVEEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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;T(0.5)T(0.5)PDQELVPASEPVWERPWSVEEIR;T(0.5)T(0.5)PDQELVPASEPVWERPWSVEEIR 172 1.04E-11 465579000 32675.5 22871.7 28007.5 25553.5 23074 24429.7 36382.8 23269.6 22797.4 TRUE FALSE 30630.39878 24565.14447 28671.85113 26209.24607 21261.86112 31482.15781 30927.5369 26174.86078 18992.36666 1.612774191 1.293421979 1.509651305 1.37998842 1.119495084 1.657621631 1.628419325 1.378177941 1 14.21313207 -2.084285483 1.920614031 0.346538108 1.450134389 0.41691525 0.166269404 1604265.399 411611.5235 4583947.521 0.044792764 0.008235965 2.084285483 1.103596281 T(ph)TPDQELVPASEPVWERPWSVEEIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTPDQELVPASEPVWERPWSVEEIRR 26 2 A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;A0A0A0MT65 A0A0A0MR88 FAM21C WASH complex subunit FAM21C 1 T(0.5)T(0.5)PDQELVPASEPVWERPWSVEEIRR 125.59 0.00526 92801000 26740 21784 26021 24868 28432 17856 28154 21838 27797 TRUE FALSE 25066.39113 23396.91003 26638.23041 25506.15498 26199.06541 23010.73733 23932.56907 24564.52237 23157.50112 1.082430742 1.010338287 1.150306774 1.101420868 1.131342508 0.993662365 1.033469412 1.060758768 1 14.49919196 2.233843128 24.99998695 1.024584025 1.091403345 0.444346074 0.040504113 128.2239303 679505.4092 0.01535503 0.011711788 171.3338317 -2.233843128 0.06681932 T(ph)TPPEAAQNGQSPMAALILVADNAGGSHASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 268.22 1.07E-58 332480000 271810 285200 333940 346040 322420 264240 467340 289140 195919 TRUE FALSE 254797.8973 306316.5048 341861.2145 354919.9722 297098.4338 340521.7984 397266.7056 325239.7655 163218.8532 1.561081286 1.876722564 2.094495873 2.174503529 1.820245811 2.086289615 2.433951089 1.992660523 1 17.31644819 2.20476928 24.74398342 2.047623315 1.939513691 0 0.407144278 990.8162932 725526.6831 0.139697206 0.103178909 160.2393888 -2.20476928 -0.108109624 T(ph)TPVDLCLLEESVGSLEGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 120.24 0.0004375 19744800 17098.1 13800.9 16030.4 16533.7 18009.2 10983.8 17692.7 14021.1 14068.7 TRUE FALSE 16027.96044 14822.733 16410.64866 16957.98273 16594.83008 14154.64475 15039.84389 15771.6652 11720.54308 1.367510049 1.264679707 1.400161114 1.44685981 1.415875524 1.207678232 1.283203669 1.345642867 1 13.5167518 -0.426941269 0.449381563 0.930931255 1.358954737 0.697094959 0.071432509 4.713696785 0.908296273 0.587470013 0.041795445 0.374161184 0.426941269 0.428023482 T(ph)VHRDSEEEDDYLFDDPLPIPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TVHRDSEEEDDYLFDDPLPIPLR 23 1 B3KSJ7;Q96SD1-2;Q96SD1-3;Q96SD1 B3KSJ7 DCLRE1C Protein artemis 1 T(0.466)VHRDS(0.466)EEEDDY(0.068)LFDDPLPIPLR;T(0.494)VHRDS(0.494)EEEDDY(0.013)LFDDPLPIPLR;T(0.469)VHRDS(0.469)EEEDDY(0.062)LFDDPLPIPLR;T(0.481)VHRDS(0.481)EEEDDY(0.039)LFDDPLPIPLR 125.73 7.74E-05 227872000 177943 192743 198963 198833 198038 164083 221282 178988 184233 TRUE FALSE 166805.8653 207013.8923 203682.4963 203935.3914 182484.8943 211451.0984 188102.8184 201335.0458 153483.3221 1.086801243 1.34877125 1.327065987 1.328713691 1.188955854 1.377681272 1.225558685 1.311771488 1 17.22772237 -1.545025373 2.795616835 0.984784858 1.285043287 0.48864544 0.087623931 10461084.35 10643322.51 1195850.333 0.019492293 0.028508517 1.545025373 0.300258429 T(ph)VLSLFDEEEDKMEDQNIIQAPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVLSLFDEEEDKMEDQNIIQAPQK 24 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;B1AP61;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 T(0.527)VLS(0.473)LFDEEEDKMEDQNIIQAPQK 74.748 0.040829 19664000 67017 42399 43836 65321 82750 28804 79247 53908 71999 TRUE FALSE 62822.5256 45538.26608 44875.81062 66997.24745 76251.1488 37119.24721 67364.64804 60638.53247 59981.90177 1.047358015 0.759200104 0.748155849 1.116957707 1.271235932 0.618840785 1.123082898 1.010947147 1 15.87223964 3.243489736 24.99990982 1.019563537 0.81700384 0.15352379 0.184306813 184.1876442 934171.0899 0.048978441 0.064303328 1751.82103 -3.243489736 -0.202559697 T(ph)WSEKDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TWSEKDLR 8 1 Q92879-4;G5EA30;Q92879-6;Q92879;Q92879-5;Q92879-3;Q92879-2;F5H0D8;E9PKU1;F5H4Y5;E9PQK4;E9PSH0;E9PKA1 Q92879-4 CELF1 CUGBP Elav-like family member 1 1 T(0.5)WS(0.5)EKDLR 88.596 0.023446 108540000 600070 447820 518960 555550 593900 345650 644460 467820 616740 TRUE FALSE 562512.6899 480977.0588 531269.9763 569806.3535 547257.4897 445433.5438 547829.2059 526228.3568 513802.1097 1.094804165 0.936113437 1.033997265 1.108999638 1.065113357 0.866935996 1.066226073 1.024184889 1 18.97085329 2.244227855 0.003444638 0.495623057 1.536354171 0.007462387 0.073313748 204472.791 416.771807 62609.40197 63300.07459 175.4800928 -2.244227855 1.040731114 T(ph)YSDTDSCSDIPLEDPDRPVHCSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TYSDTDSCSDIPLEDPDRPVHCSK 24 1 Q9HB20 Q9HB20 PLEKHA3 Pleckstrin homology domain-containing family A member 3 1 T(0.432)Y(0.068)S(0.376)DT(0.109)DS(0.015)CS(0.001)DIPLEDPDRPVHCSK 68.834 0.049018 230650000 59944 71226 70952 69501 84517 68585 96452 70442 89074 TRUE FALSE 56192.21204 76499.64715 72635.01495 71284.51332 77879.37575 88384.37612 81989.91802 79236.83876 74206.97396 0.757236268 1.030895657 0.97881656 0.96061744 1.049488634 1.191052153 1.104881572 1.067781565 1 16.17926716 2.614336157 3.52453429 1.104946023 0.955825132 0.42285639 0.085588049 0.238943983 5.435159837 0.027419017 0.025566894 411.4680869 -2.614336157 -0.149120891 T(ph)YTHEVVTLWYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TYTHEVVTLWYR 12 0 G3V5T9;P24941;Q00526;K7EJ83 G3V5T9 CDK2;CDK3 Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 1 T(0.608)YT(0.392)HEVVTLWYR;T(0.593)YT(0.407)HEVVTLWYR 184.21 5.38E-05 496450000 423520 473660 346860 374630 485530 233480 423810 436050 429430 TRUE FALSE 397012.6392 508730.2792 355087.683 384243.64 447398.4323 300881.8858 360263.625 490491.8024 357755.3588 1.109732194 1.422006035 0.992543296 1.074040208 1.250570876 0.841026915 1.007011121 1.371025731 1 18.44861385 3.912484877 5.79751219 1.066881775 1.277597785 0.185470784 0.163316185 0.269239494 17.42913752 0.039330384 0.072842466 8174.945708 -3.912484877 0.210716009 TAAAAAEHSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 TAAAAAEHSQR 11 0 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;;;;;; 178.53 7.50E-06 1890461000 1754497 1862512 1767413 1812881 1868639 1414872 2076533 1630688 1915488 FALSE TRUE 1644686.165 2000414.326 1809336.871 1859402.596 1721883.631 1823322.578 1765176.154 1834282.986 1595780.678 1.030646747 1.253564699 1.133825529 1.165199342 1.079022734 1.142589707 1.106152104 1.149458075 1 20.60583095 -4.999956583 0.180806007 0.407410851 1.171271992 0.300853557 0.059559462 138.9862389 1.341036884 29.45841579 0.168606974 1.00E-05 4.999956583 0.763861141 TAADKDRGEEDADGSK ddPTM_SK-BR-3_Pertuzumab_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 ;; 236.78 5.45E-20 1294300000 3948200 2006590 2733130 2566180 2825340 1819710 3526220 2281560 4072080 FALSE TRUE 3701089.21 2155160.011 2797961.134 2632032.523 2603449.193 2345030.736 2997496.047 2566417.788 3392423.541 1.090986772 0.635286245 0.824767633 0.775856107 0.76743047 0.691255295 0.88358544 0.756514556 1 21.69388487 -1.128759962 4.496183601 1.000025386 0.790176175 0.195524671 0.122945626 2.75E-05 5.32E-06 0.104513669 0.024631129 0.074342992 1.128759962 -0.209849211 TAADKDRGEEDADGSKTQDLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAADKDRGEEDADGSKTQDLFR 22 3 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 92.098 0.00093093 160490000 71213 68904 64794 62815 96023 49612 76726 44196 211750 FALSE TRUE 66755.90545 74005.72385 66330.94428 64426.93925 88481.74092 63934.17902 65221.64859 49713.96789 176407.557 0.378418627 0.41951561 0.376009653 0.365216436 0.501575683 0.36242313 0.369721398 0.281813142 1 17.42855284 -1.695322089 2.952105537 1.077415335 0.385705198 0.927029929 0.054494748 24085168.92 23637481.1 13960034.61 0.01247658 0.0201687 1.695322089 -0.691710137 TAAGSSWEDPSLLEWDADDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAAGSSWEDPSLLEWDADDFR 21 0 K7EP90;Q9BTD8-4;Q9BTD8-2;Q9BTD8-3;Q9BTD8;K7EQ03 K7EP90 RBM42 RNA-binding protein 42 0 208.15 7.63E-22 65206000 101120 105010 106310 102410 117430 96232 120520 94470 116840 FALSE TRUE 94791.0797 112785.0497 108831.7234 105038.014 108207.5215 124012.6162 102449.1449 106264.7875 97338.64918 0.97382777 1.158687229 1.118073081 1.079098743 1.111660398 1.27403264 1.052502225 1.091701892 1 16.57072513 -0.265216792 7.609501468 0.99999876 1.115058373 0.15629833 0.076662974 0 0 0.067352182 0.015875061 0.542979219 0.265216792 0.115059613 TAAKGEAAAERPGEAAVAS(ph)SPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAAKGEAAAERPGEAAVASSPSK 23 2 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 TAAKGEAAAERPGEAAVAS(0.541)S(0.452)PS(0.007)K 58.08 0.040277 131530000 118180 89746 102620 105710 132640 66581 143370 82533 168410 TRUE FALSE 110783.3248 96390.88722 105054.1949 108422.6976 122222.9894 85801.85385 121872.9995 92837.42673 140301.283 0.789610204 0.687027839 0.748775725 0.77278479 0.871146627 0.611554307 0.868652067 0.661700483 1 17.09816868 -1.968801106 2.448483347 1.207900034 0.752057217 0.470722944 0.082839541 8120619.782 3385141.893 9569682.279 0.017670679 0.010744814 1.968801106 -0.455842817 TAALESNLPGS(ph)PNTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.999)PNTSR;TAALESNLPGS(0.999)PNT(0.001)SR;TAALESNLPGS(1)PNTSR;TAALESNLPGS(1)PNTSR 436.99 5.95E-161 2515280000 2111690 2174430 2124270 2345700 2219870 1712120 2632310 1848680 1826570 TRUE FALSE 1979523.092 2335427.06 2174658.688 2405894.633 2045530.365 2206381.25 2237619.553 2079491.767 1521703.667 1.300859777 1.534744977 1.429094728 1.581053319 1.344236995 1.449941469 1.470469975 1.366555008 1 20.53725601 0.785619386 2.849839201 1.000049527 1.453812691 0.744278797 0.081123771 0.488301522 5.793576958 0.068616018 0.018062546 6.104068326 -0.785619386 0.453763164 TAAPS(ph)PSLLYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TAAPSPSLLYK 11 0 Q9BTC0;Q9BTC0-1;Q9BTC0-2;Q9BTC0-3 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 TAAPS(0.994)PS(0.005)LLYK;TAAPS(0.988)PS(0.012)LLYK;TAAPS(0.993)PS(0.007)LLYK 208.27 2.11E-08 245262000 797770 582910 732790 641020 779650 578570 905800 729800 1370940 TRUE FALSE 747838.9998 626069.2629 750172.1248 657469.6584 718419.434 745593.7667 769983.699 820917.1365 1142121.257 0.654780738 0.548163567 0.656823538 0.575656616 0.629022032 0.652814893 0.674169834 0.718765307 1 20.1232844 0.240456745 0.534384225 1.025213104 0.601115772 0.928867579 0.032870428 0.606137861 0.25184115 0.061573799 0.013874075 1.739629427 -0.240456745 -0.424097332 TAAYGHFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TAAYGHFGR 9 0 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ;;; 151.97 0.001698 701760000 2690540 3399870 2526340 2486110 3552480 1896440 3135330 2971290 3656660 FALSE TRUE 2522143.904 3651599.912 2586265.978 2549907.792 3273482.551 2443911.442 2665216.373 3342262.097 3046339.823 0.827925987 1.198684364 0.848974877 0.837039838 1.074562505 0.802245181 0.874891354 1.09714027 1 21.53864545 3.840611015 7.722982222 0.919669727 1.037019307 0.044323584 0.133100437 0.471090941 29.28632866 0.031117833 0.056344515 6928.050033 -3.840611015 0.11734958 TADEDRGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TADEDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 118.18 0.00094087 668875000 777793 1121285 1019894 1023355 1197729 832481 1072790 1014387 1348360 FALSE TRUE 729112.3245 1204306.108 1044086.367 1049616.022 1103664.196 1072804.751 911935.0988 1141035.45 1123310.005 0.649074896 1.072104853 0.929473042 0.934395685 0.982510786 0.955038899 0.81182852 1.015779655 1 20.0993247 4.753109115 24.59496118 0.953384094 0.649074629 0.673786733 0.068298577 1392.027211 2353241.241 0.017033409 0.371640896 56638.15721 -4.753109115 -0.304309465 TADGIVSHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TADGIVSHLK 10 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 121.9 0.00050283 1819700000 3413670 3326020 3065160 3290150 3345570 2145820 3663870 2863320 2395620 FALSE TRUE 3200014.488 3572281.982 3137867.043 3374580.819 3082822.428 2765283.4 3114506.707 3220811.805 1995775.546 1.603393976 1.789921712 1.57225448 1.690861894 1.544673916 1.385568335 1.560549589 1.613814646 1 20.92851805 -2.785341665 0.198130812 3.62E-17 1.733634123 0.794154565 0.096899921 21.48338175 0.468092805 9.505426855 0.25000289 0.0016393 2.785341665 1.733634123 TADGRVS(ph)PAGGTLDDKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TADGRVSPAGGTLDDKPK 18 2 C9JA69;Q8WY36-2;Q8WY36 C9JA69 BBX HMG box transcription factor BBX 1 T(0.004)ADGRVS(0.988)PAGGT(0.009)LDDKPK 71.527 0.012196 104750000 248500 133890 171260 154880 179190 85943 186790 126030 197020 TRUE FALSE 232946.8286 143803.3549 175322.3681 158854.483 165117.1402 110753.3489 158782.5736 141765.1229 164136.0892 1.419229797 0.876122708 1.068152464 0.967821786 1.005977059 0.67476537 0.967383677 0.863704768 1 17.32453296 4.742443026 24.93239302 0.930379184 1.419229993 0.671227996 0.108034219 223.2497141 1433625.414 0.024776399 0.188232294 55264.09039 -4.742443026 0.488850809 TAEEKIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TAEEKIQR 8 1 H3BTZ3;B4DEX3;Q8TE60-2;Q8TE60 H3BTZ3 ADAMTS18 A disintegrin and metalloproteinase with thrombospondin motifs 18 0 ; 84.476 0.015892 173471000 292270 272230 305290 317750 307670 275340 327510 204162 322170 FALSE TRUE 273977.3424 292386.1925 312531.623 325904.0029 283506.8393 354826.1882 278402.916 229652.0751 268397.7457 1.020788538 1.089376484 1.164434605 1.214257602 1.056293668 1.322016276 1.0372774 0.855640849 1 18.03401303 1.478602891 7.077141165 0.932590315 1.142129064 0.497976681 0.090325856 0.095459869 12.81429492 0.04689304 0.020882701 30.10252261 -1.478602891 0.20953875 TAELSLGRNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TAELSLGRNER 11 1 Q9H611-2;Q9H611;Q9H611-3 Q9H611-2 PIF1 ATP-dependent DNA helicase PIF1 0 ;;; 90.685 0.0067911 334781000 80974.5 332093 230473 248307 340531 209247 164604 232712 278703 FALSE TRUE 75906.45059 356681.5113 235939.9284 254678.978 313787.0689 269653.2121 139923.1583 261766.6055 232185.6688 0.326921343 1.536190899 1.016169213 1.096876389 1.351448909 1.161368888 0.602634775 1.127402078 1 17.8249194 1.788470103 24.99999999 0.867487684 1.13739751 0.032416485 0.338936378 240.645232 120576.2762 0.140483957 0.07921126 61.44267334 -1.788470103 0.269909827 TAENATSGETLEENEAGD ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TAENATSGETLEENEAGD 18 0 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 333.62 1.27E-74 839990000 2018740 2047040 2027170 2008690 2158230 1756910 2223610 1829530 2246400 FALSE TRUE 1892390.667 2198604.972 2075255.43 2060236.386 1988731.322 2264101.396 1890200.323 2057950.848 1871461.328 1.011183421 1.174806521 1.108895706 1.100870403 1.062662259 1.209803998 1.010013029 1.099649144 1 20.83573381 1.051630404 0.936916638 1.00417847 1.113925088 0.182518924 0.062826576 0.789885451 1.510383632 0.053322984 0.018351061 11.2623859 -1.051630404 0.109746618 TAENFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 129.2 0.037913 71833700000 26169670 25803880 25595080 24302660 26956660 21681940 29748130 24455220 37770100 FALSE TRUE 24531757.07 27714426.12 26202207.38 24926307.4 24839592.66 27941164.1 25287674.07 27508508.05 31466026.31 0.77962679 0.880772992 0.832714215 0.792165721 0.789409899 0.887978794 0.803650065 0.874228852 1 24.90729166 0.903539009 4.68358682 0.999983569 0.830175003 0.691799333 0.036955892 0.322493287 14.52305069 0.033595143 0.008515864 8.008275563 -0.903539009 -0.169808566 TAESQT(ph)PTPSATSFFSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TAESQTPTPSATSFFSGK 18 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 TAESQT(0.999)PT(0.001)PSATSFFSGK;TAES(0.001)QT(0.998)PTPSATSFFSGK;TAES(0.002)QT(0.818)PT(0.088)PS(0.088)AT(0.004)S(0.001)FFSGK 183.22 7.20E-13 398118000 1017510 842170 963780 1258180 1282090 618020 878190 641430 832070 TRUE FALSE 953825.8654 904525.1431 986641.3167 1290467.029 1181399.823 796432.3413 746513.5622 721513.9475 693192.1416 1.375990592 1.304869298 1.42333021 1.861629628 1.704289117 1.148934463 1.07692156 1.040857079 1 19.40289577 2.104755134 6.102496372 1.063817116 1.501437638 0.67224623 0.162308085 0.154773187 7.882231102 0.069594496 0.051074185 127.2785252 -2.104755134 0.437620522 TAESQTPTPSATSFFSGKS(ph)PVTTLLECMHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAESQTPTPSATSFFSGKSPVTTLLECMHK 30 1 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 TAESQTPTPSATSFFS(0.238)GKS(0.756)PVT(0.002)T(0.004)LLECMHK 282.16 7.48E-72 271780000 603180 415110 516830 539430 549180 346030 677440 436430 705480 TRUE FALSE 565428.0405 445845.1763 529089.4517 553272.6871 506049.6181 445923.2437 575864.161 490919.2462 587730.8304 0.962052714 0.758587355 0.900224089 0.941370877 0.861022754 0.758720184 0.979809347 0.835279044 1 19.16479605 -5 0.227316887 1.694120219 0.855256329 0.187010864 0.07745874 243.6339783 2.439276374 77.51657571 0.128752752 1.00E-05 5 -0.83886389 TAESQTPTPSATSFFSGKSPVT(ph)TLLECMHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAESQTPTPSATSFFSGKSPVTTLLECMHK 30 1 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 TAESQTPT(0.001)PS(0.004)AT(0.01)S(0.029)FFS(0.105)GKS(0.311)PVT(0.405)T(0.135)LLECMHK 64.583 0.012392 224400000 124110 91828 104000 103930 104480 79478 144660 84405 125900 TRUE FALSE 116342.1766 98627.04067 106466.9291 106597.0198 96274.56225 102422.0084 122969.576 94943.15005 104886.4767 1.109219991 0.940321801 1.01506822 1.016308519 0.917892996 0.97650347 1.172406395 0.905199155 1 16.67846915 TAFDDAIAELDTLNEDSYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TAFDDAIAELDTLNEDSYK 19 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;; 306 3.70E-50 125130000 374420 212620 269957 245733 244939 217250 334948 247699 271077 FALSE TRUE 350985.7206 228362.606 276360.5075 252038.9248 225702.479 279966.5482 284725.6569 278624.7654 225832.4975 1.554186065 1.011203474 1.223741094 1.11604365 0.99942427 1.239708861 1.260782483 1.233767365 1 17.78489358 4.751048033 24.70230146 1.149253862 1.554186364 0.611036826 0.104455248 1229.697682 2432506.448 0.024803957 0.430770771 56369.99972 -4.751048033 0.404932502 TAFDEAIAELDTLNEDSYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TAFDEAIAELDTLNEDSYK 19 0 P27348 P27348 YWHAQ 14-3-3 protein theta 0 ;;; 176.21 1.07E-12 40694900 145504 103017 120441 114082 112545 97070 149565 97977 103262 FALSE TRUE 136397.1644 110644.4859 123297.9174 117009.5373 103706.1697 125092.5332 127139.1167 110209.6441 86026.9051 1.58551751 1.286161414 1.433248322 1.360150492 1.205508551 1.454109421 1.477899462 1.281106696 1 16.39250032 0.935338265 6.280598414 1.000015928 1.391149407 0.596065999 0.104090596 0.393725233 37.18736512 0.094124535 0.023647267 8.616646274 -0.935338265 0.391133479 TAFDEAIAELDTLNEESYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 188.04 1.71E-14 40716800 220860 136139 166752 154164 160801 133219 210033 153882 147344 FALSE TRUE 207036.7668 146218.8732 170707.4362 158120.1092 148172.3381 171677.1627 178540.5015 173094.5064 122751.3345 1.686635568 1.191179499 1.390676825 1.288133525 1.207093501 1.398576751 1.454489291 1.410123215 1 16.90537918 -2.16970095 2.325487276 0.100120658 1.362655804 0.414608848 0.14019124 2455683.666 653018.23 11636215.78 0.0320228 0.006765487 2.16970095 1.262535146 TAFDEAIAELDTLS(ph)EESYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TAFDEAIAELDTLSEESYK 19 0 B7Z2E6;H0YB80;P63104-2;P63104;E7EX29;B0AZS6 B7Z2E6;P63104 YWHAZ 14-3-3 protein zeta/delta 1 TAFDEAIAELDT(0.059)LS(0.939)EES(0.002)YK;TAFDEAIAELDTLS(0.974)EES(0.024)Y(0.002)K 124.43 1.10E-05 8425500 29344 18598.9 22055.7 21775.8 19524.3 18401.8 24775.8 17664.6 16789.7 TRUE FALSE 27507.41142 19975.98191 22578.87162 22334.60389 17990.94024 23714.10093 21060.8988 19870.06419 13987.3906 1.966586349 1.428142137 1.614230435 1.596767012 1.286225626 1.695391342 1.50570606 1.420569766 1 13.77183923 -2.97200487 0.198510847 7.74E-15 1.670722054 0.570140862 0.167223311 42.17201416 0.860381972 18.31112068 0.405132933 0.001066584 2.97200487 1.670722054 TAFDEAIAELDTLSEESYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAFDEAIAELDTLSEESYK 19 0 B7Z2E6;H0YB80;P63104-2;P63104;E7EX29;B0AZS6 B7Z2E6;P63104 YWHAZ 14-3-3 protein zeta/delta 0 393.37 9.00E-127 177120000 647960 428090 588530 527820 513120 442890 688310 486570 478450 FALSE TRUE 607405.3402 459786.229 602490.2095 541364.7548 472821.625 570745.1533 585104.3055 547319.3356 398593.6041 1.523871266 1.153521342 1.511540083 1.358187259 1.186224817 1.43189742 1.467921962 1.373126237 1 18.60455904 -1.45313689 5.032482988 0.99934242 1.371558849 0.476424308 0.12373391 0.000866737 9.42E-05 0.113747385 0.026764721 0.035225982 1.45313689 0.372216428 TAFQEALDAAGDKLVVVDFSATWCGPCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TAFQEALDAAGDKLVVVDFSATWCGPCK 28 1 P10599;P10599-2 P10599 TXN Thioredoxin 0 ;;; 326.91 8.02E-96 762653000 2135700 1427133 1663931 1630729 1836705 1549456 2879800 1565233 2273280 FALSE TRUE 2002030.349 1532799.412 1703400.229 1672576.267 1692457.598 1996758.794 2448000.725 1760655.786 1893854.882 1.057119196 0.809354205 0.899435456 0.883159678 0.893657489 1.05433569 1.292602062 0.929667739 1 20.85289436 2.155461783 4.36165036 1.12073634 0.892304464 0.297207915 0.113362076 0.177728177 6.268643978 0.041019187 0.029839544 143.0414101 -2.155461783 -0.228431876 TAFVVEHDFIMATYLADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAFVVEHDFIMATYLADR 18 0 P61221 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 118.53 0.00010008 20125000 39976 48285 57498 49336 58458 40197 52878 47588 47431 FALSE TRUE 37473.97352 51860.07164 58861.87971 50602.04529 53866.94449 51801.22136 44949.4348 53529.46655 39514.45968 0.948361026 1.312432767 1.489628865 1.280595653 1.363221082 1.310943431 1.137543956 1.354680463 1 15.27009306 1.752440255 24.99993314 1.183840392 1.314059651 0.087396431 0.16098173 9.268352605 16717.72179 0.071095236 0.039426174 56.55099551 -1.752440255 0.13021926 TAFYNEDDS(ph)EEEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TAFYNEDDSEEEQR 14 0 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 TAFYNEDDS(1)EEEQR;TAFYNEDDS(1)EEEQR;TAFYNEDDS(1)EEEQR 363.3 3.01E-83 1875960000 1685060 1603440 1695440 1449460 1869050 1309620 1991960 1564530 2001230 TRUE FALSE 1579595.103 1722160.366 1735656.637 1486655.598 1722262.352 1687686.034 1693284.09 1759865.014 1667211.785 0.947447179 1.032958369 1.041053484 0.891701709 1.033019541 1.012280533 1.015638269 1.055573761 1 20.66900595 TAGAPDPAWDWQHVGPGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAGAPDPAWDWQHVGPGYR 19 0 H3BM67;H3BUP2;H3BUN4;O60936;O60936-3 H3BM67 NOL3 Nucleolar protein 3 0 98.035 0.0010208 68166000 26384 29282 34524 34370 41908 32161 40257 32090 39688 FALSE TRUE 24732.67254 31450.06975 35342.92558 35251.99239 38616.71473 41445.35861 34220.83658 36096.50714 33063.81641 0.748028365 0.951192971 1.068930614 1.066180381 1.167944869 1.253495909 1.034993546 1.091722344 1 15.01296564 5.194535418 0.7931122 1.112346951 0.240625885 0.720838695 0.070634717 2.46684931 0.717164511 0.023814291 2.240521087 156507.5949 -5.194535418 -0.871721066 TAHETDKSEGGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TAHETDKSEGGKR 13 2 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 0 ;; 174.39 1.20E-05 608620000 660770 495250 586530 589200 652600 380057 798140 554100 969480 FALSE TRUE 619413.5852 531918.8253 600442.7686 604319.8695 601347.4285 489773.2862 678466.3166 623280.6047 807667.5249 0.766916542 0.658586372 0.743428143 0.748228511 0.744548233 0.60640458 0.840031691 0.771704427 1 19.62340201 0.693936776 0.911618995 0.999381092 0.714049957 0.676120094 0.059549863 0.562898864 0.836590114 0.052344752 0.017418759 4.942387309 -0.693936776 -0.285331135 TAHLDEEVNKGDILVVATGQPEMVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAHLDEEVNKGDILVVATGQPEMVK 25 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" 0 157.83 2.80E-09 168290000 219150 143660 165000 170470 198230 122080 224980 146430 243830 FALSE TRUE 205433.7927 154296.7359 168913.8779 174844.5488 182661.8154 157322.5142 191246.3376 164712.1078 203133.1978 1.011325549 0.759584044 0.831542455 0.860738425 0.899221877 0.774479582 0.941482435 0.810857652 1 17.63206651 -1.916890989 0.37027571 1.143224945 0.845750461 0.21891247 0.077286241 50.25107419 3.00538614 6.272840655 0.05062632 0.01210902 1.916890989 -0.297474484 TAHNLENVLIHFWER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAHNLENVLIHFWER 15 0 H7BYG8;O94822;O94822-3 H7BYG8 LTN1 E3 ubiquitin-protein ligase listerin 0 212.69 4.35E-10 22742000 21909 23174 22495 23404 25226 18933 26139 21786 23886 FALSE TRUE 20537.7548 24889.82707 23028.59202 24004.58626 23244.85172 24398.64975 22219.69961 24506.03006 19899.27229 1.032085721 1.250790818 1.157257999 1.206304729 1.168125717 1.226107638 1.116608652 1.231503831 1 14.28042805 -1.390354215 3.091715267 0.997686869 1.177655981 0.419800381 0.063980023 20346316.28 27550757.52 424921.898 0.013386206 0.040704815 1.390354215 0.179969112 TAHNSEAADLEESFNEHELEPSS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAHNSEAADLEESFNEHELEPSSPK 25 0 A0A0D9SGE8;Q5JRC6;Q8IWS0-2 A0A0D9SGE8 PHF6 PHD finger protein 6 1 TAHNSEAADLEESFNEHELEPS(0.029)S(0.971)PK 277.04 7.08E-53 162820000 36522 56975 56026 56298 65825 47137 79523 50103 80280 TRUE FALSE 34236.15321 61193.48828 57354.96318 57742.70199 60655.37003 60744.68669 67599.26441 56358.46984 66880.74937 0.511898469 0.914964154 0.857570582 0.863368047 0.906918218 0.908253679 1.010743226 0.842671028 1 16.02930339 4.738905057 24.73542006 0.911047999 0.511898335 0.837741841 0.055478143 9.378808236 673214.4074 0.013114099 0.076909625 54815.71164 -4.738905057 -0.399149664 TAHNSEADLEESFNEHELEPS(ph)SPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAHNSEADLEESFNEHELEPSSPK 24 0 Q8IWS0-5;Q8IWS0 Q8IWS0-5 PHF6 PHD finger protein 6 1 TAHNSEADLEESFNEHELEPS(0.5)S(0.5)PK 200.06 1.01E-24 148000000 73990 93051 109050 112160 115020 74329 136600 93340 143730 TRUE FALSE 69359.09798 99940.59286 111636.7175 115038.2155 105986.7932 95786.57567 116118.0981 104993.7045 119740.5345 0.579244934 0.834642949 0.932321857 0.960729096 0.885137131 0.799951128 0.969747618 0.876843459 1 16.86955209 4.866963891 1.720973415 0.912314602 0.380935077 0.778939209 0.056491995 0.595456945 1.353939165 0.01366478 0.574294078 73614.5888 -4.866963891 -0.531379525 TAIGKAGYTDKVVIGMDVAASEFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAIGKAGYTDKVVIGMDVAASEFFR 25 2 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 100.88 0.0032799 12646000 67206 45831 80927 87857 84483 82178 63234 27823 41060 FALSE TRUE 62999.69643 49224.37493 82846.62666 90111.55936 77848.04597 105901.4546 53752.64874 31296.7628 34206.82074 1.841729078 1.439022214 2.421932961 2.634315537 2.275804775 3.095916319 1.57140148 0.914927553 1 15.0619964 1.483042148 5.243822466 1.023465988 2.224144145 0.609744337 0.441060584 0.124032296 7.580964807 0.288181271 0.12044705 30.41180158 -1.483042148 1.200678157 TAITT(ph)PNFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.109)T(0.891)PNFK;TAIT(0.015)T(0.985)PNFK;TAIT(0.019)T(0.981)PNFK;TAIT(0.002)T(0.998)PNFK 133.05 0.0032179 262960000 2053760 1732550 1878570 1707480 2034920 1079270 2582110 1550990 2916200 TRUE FALSE 1925218.828 1860829.805 1923130.568 1751296.828 1875105.592 1390837.729 2194946.577 1744634.516 2429467.381 0.792444814 0.765941465 0.79158526 0.720856284 0.771817562 0.572486686 0.903468223 0.718113991 1 21.21220863 -1.220297918 3.409696572 1.000523075 0.76091104 0.464528799 0.082557592 173926499.9 258156786.2 959881.9934 0.017960413 0.060214638 1.220297918 -0.239612035 TALAEAELEYNPEHVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TALAEAELEYNPEHVSR 17 0 Q9NSE4 Q9NSE4 IARS2 "Isoleucine--tRNA ligase, mitochondrial" 0 ; 208.43 5.18E-12 418710000 250730 376800 339120 346900 451490 327090 351180 364160 610380 FALSE TRUE 235037.2569 404698.6641 347164.0865 355802.0413 416031.7966 421515.5731 298523.8192 409626.1776 508503.6348 0.462213524 0.79586189 0.682717021 0.699704028 0.818149111 0.828933255 0.587063295 0.805552113 1 18.95589856 -5 0.205258463 2.317952351 0.67010627 0.443142843 0.109686524 145.2478152 1.44411485 78.84851482 0.234642379 1.00E-05 5 -1.647846082 TALIHDGLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 TALIHDGLAR 10 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 ;;;;;;; 189.72 9.80E-07 15958460000 8680520 9378280 8365890 8221090 9744290 6926810 9390140 8037490 9659630 FALSE TRUE 8137221.748 10072657.61 8564332.861 8432057.088 8979012.77 8926467.6 7982175.681 9040988.319 8047375.349 1.011164684 1.251669914 1.064239269 1.047802137 1.115769102 1.109239623 0.991898021 1.123470439 1 22.94008689 2.344613612 0.333662102 1.007101059 1.154688091 0.099584018 0.073281847 2.58278404 0.695251572 0.090289608 0.136458982 221.1126614 -2.344613612 0.147587032 TALINSTGEEVAMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TALINSTGEEVAMR 14 0 P02545;P02545-6;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 168.76 8.00E-06 75124000 29416 30598 33376 35371 33783 28221 32284 32670 42815 FALSE TRUE 27574.90507 32863.50776 34167.69448 36278.67974 31129.81945 36367.94457 27443.31391 36748.92142 35668.8999 0.773079774 0.92134907 0.957912764 1.017095561 0.87274403 1.019598156 0.769390533 1.030279081 1 15.1223791 4.741254205 3.755509985 0.937127688 0.75552599 0.312200489 0.08065051 0.339388007 9.170209198 0.018090532 0.172014526 55113.01942 -4.741254205 -0.181601698 TALKEDGVLCCQGECQWLHLDLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TALKEDGVLCCQGECQWLHLDLIK 24 1 P19623 P19623 SRM Spermidine synthase 0 ; 215.73 8.34E-33 449140000 1165660 726690 937470 897470 898290 724330 1268480 776170 922380 FALSE TRUE 1092703.421 780494.8837 959707.2311 920500.5996 827741.9269 933432.3125 1078283.2 873076.5331 768428.8192 1.421996929 1.015702254 1.248921445 1.197899632 1.077187511 1.214728403 1.403231078 1.136184005 1 19.5515521 2.004895447 24.93774688 1.245701299 1.173700416 0 0.148829478 427.9193313 2179840.17 0.051188915 0.037671115 101.1335955 -2.004895447 -0.072000883 TALPTSGSS(ph)AGELELLAGEVPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TALPTSGSSAGELELLAGEVPAR 23 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 TALPT(0.008)S(0.271)GS(0.127)S(0.594)AGELELLAGEVPAR 103.26 2.78E-05 0 29568 27036 27024 29906 28628 25770 36084 21785 30192 TRUE FALSE 27717.39166 29037.77357 27665.02204 30673.43859 26379.67236 33209.38066 30673.53919 24504.9052 25152.76015 1.10196223 1.154456743 1.099880167 1.219485989 1.048778432 1.320307611 1.219489988 0.974243187 1 14.6184291 1.230702958 24.99330671 0.987121458 1.166689221 0.488986693 0.076166031 165.0096713 524834.5901 0.067297464 0.018040718 17.0099469 -1.230702958 0.179567764 TALPTSGSSAGELELLAGEVPARS(ph)PGAFDMSGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TALPTSGSSAGELELLAGEVPARSPGAFDMSGVR 34 1 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(0.998)PGAFDMS(0.002)GVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR 279.02 3.94E-74 563980000 119811.2 195878.9 171667 243620 274184 85758.8 121935.5 108439.6 232670 TRUE FALSE 112312.4309 210381.9776 175739.0223 249871.7016 252650.6946 110515.9734 103652.4038 121978.5228 193835.8739 0.579420252 1.085361411 0.906638275 1.289089045 1.303425881 0.570152321 0.53474314 0.629287656 1 17.56447607 2.218684944 24.99867497 0.630320107 1.034404241 0.3362718 0.238650802 234.7775174 295290.1389 0.084940165 0.062813951 165.456923 -2.218684944 0.404084135 TAMPS(ph)PGVSQNK ddPTM_SK-BR-3_Pertuzumab_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(1)PGVSQNK 242.35 2.87E-16 671640000 1850470 1238590 1535410 1357720 1436800 1283830 1974410 1361930 1348890 TRUE FALSE 1734652.386 1330296.492 1571830.65 1392561.394 1323959.524 1654450.88 1678365.55 1531969.958 1123751.545 1.543626252 1.183799478 1.39873503 1.239207546 1.178160359 1.472256823 1.493537925 1.36326394 1 20.09989167 2.221656765 24.98902796 1.389796332 1.300790734 0 0.17361742 736.0141447 1088045.502 0.05859713 0.043386944 166.593006 -2.221656765 -0.089005597 TANKDHLVTAYNHLFETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TANKDHLVTAYNHLFETK 18 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 221.37 4.05E-19 650160000 1411000 1060600 1140800 1162800 1249400 827170 1377600 1025500 1477600 FALSE TRUE 1322688.029 1139127.928 1167860.315 1192639.417 1151277.164 1065960.551 1171041.669 1153535.932 1230979.014 1.074500876 0.92538371 0.948724796 0.968854386 0.935253282 0.865945348 0.951309206 0.937088219 1 20.23137474 4.741655448 24.94677915 0.93752698 1.074500927 0.597880002 0.034118059 185.7504774 1497220.03 0.007502435 0.053546075 55163.96172 -4.741655448 0.136973948 TANS(ph)PGSGARPDPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TANSPGSGARPDPVR 15 1 A0A3B3ISR7;E9PIF2;Q13206 A0A3B3ISR7 DDX10 Probable ATP-dependent RNA helicase DDX10 1 T(0.24)ANS(0.758)PGS(0.002)GARPDPVR 84.499 0.0050295 452100000 349010 369020 348630 352800 385670 315260 410200 317200 296380 TRUE FALSE 327166.0871 396342.6248 356899.6682 361853.4453 355381.0339 406270.4442 348694.3181 356803.1182 246912.2633 1.32502972 1.605196192 1.445451366 1.46551427 1.439300864 1.645404075 1.412219521 1.445060336 1 17.91363897 0.411745597 1.371295721 0.999931314 1.491283418 0.726256787 0.091341031 1.525400602 3.083038337 0.078145674 0.022935553 2.580747984 -0.411745597 0.491352104 TAPAAPAEDAVAAAAAAPS(ph)EPS(ph)EPS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAPAAPAEDAVAAAAAAPSEPSEPSR 26 0 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 3 TAPAAPAEDAVAAAAAAPS(1)EPS(1)EPS(1)R 51.234 0.023544 0 113940 105800 108100 119670 103100 63143 120630 77628 63626 TRUE FALSE 106808.6988 113633.5421 110664.183 122740.9348 95002.94189 81371.35906 102542.6514 87320.02668 53006.40956 2.015014782 2.143769839 2.087750971 2.315586659 1.792291586 1.535123011 1.934533054 1.647348451 1 15.6938792 0.473241284 0.320811713 0.81821705 2.195368791 0.783578035 0.173822628 1.3987728 0.296950426 0.598910553 0.200882614 2.97331748 -0.473241284 1.37715174 TAPAAPAEDAVAAAAAAPSEPSEPS(ph)RPSPQPKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPKPR 34 2 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 TAPAAPAEDAVAAAAAAPS(0.004)EPS(0.108)EPS(0.507)RPS(0.38)PQPKPR 138.69 1.93E-09 1501200000 1002700 892270 957030 1088000 862960 552900 1094400 597290 509790 TRUE FALSE 939942.7969 958334.5992 979731.2035 1115919.922 795186.6026 712513.2544 930304.8799 671862.9713 424702.7556 2.213178004 2.25648312 2.306863307 2.627531626 1.87233681 1.677675139 2.19048468 1.581960471 1 18.69609394 0.76485098 0.44853096 0.927308296 2.335432711 0.741822781 0.234815631 0.757066361 0.349540151 0.350831378 0.148364048 5.819035141 -0.76485098 1.408124415 TAPAAPAEDAVAAAAAAPSEPSEPSRPS(ph)PQPKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPKPR 34 2 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 TAPAAPAEDAVAAAAAAPS(0.098)EPS(0.098)EPS(0.187)RPS(0.616)PQPKPR;TAPAAPAEDAVAAAAAAPSEPS(0.047)EPS(0.125)RPS(0.827)PQPKPR;TAPAAPAEDAVAAAAAAPSEPS(0.003)EPS(0.192)RPS(0.805)PQPKPR;TAPAAPAEDAVAAAAAAPS(0.001)EPS(0.003)EPS(0.07)RPS(0.926)PQPKPR 171.41 6.10E-15 3415380000 3117950 2944070 2952780 3423650 2839970 1689540 3314410 2059720 1714060 TRUE FALSE 2922803.075 3162052.006 3022821.336 3511506.655 2616930.212 2177282.771 2817444.99 2316880.576 1427972.313 2.04682055 2.214365067 2.116862707 2.459085953 1.832619714 1.524737385 1.973038948 1.622496848 1 20.44553658 0.82347652 0.385111625 0.912227017 2.23724653 0.746482177 0.206035515 0.825710818 0.306286456 0.373720617 0.172956072 6.660035135 -0.82347652 1.325019513 TAPFDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TAPFDSR 7 0 P14854;A0A494C160;K7EQD3 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 ; 97.068 0.028543 402840000 1241050 1174710 1016330 1000450 1399630 821370 1137910 1161380 1424020 FALSE TRUE 1163374.896 1261686.751 1040437.828 1026123.241 1289708.706 1058486.185 967290.9593 1306380.85 1186341.862 0.980640516 1.063510267 0.877013499 0.864947342 1.087130739 0.892226953 0.815356003 1.101184145 1 20.17808837 3.982894128 20.43108764 0.93177356 1.020778317 0.072907554 0.096326469 44.48237295 157405.7591 0.023021448 0.047333085 9613.778856 -3.982894128 0.089004757 TAPPALPTGYDS(ph)EEEEESRPMSYDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 TAPPALPTGYDSEEEEESRPMSYDEK 26 1 H0Y6K2;A0A140T9E9;A0A0G2JK44;P25440-4;P25440-3;P25440;P25440-2;A0A0G2JHN8;A0A140T9I1 H0Y6K2 BRD2 Bromodomain-containing protein 2 1 TAPPALPTGYDS(1)EEEEESRPMSYDEK;TAPPALPTGYDS(1)EEEEESRPMSYDEK;TAPPALPTGYDS(1)EEEEESRPMSYDEK;TAPPALPTGYDS(1)EEEEESRPMSYDEK;TAPPALPT(0.033)GYDS(0.954)EEEEES(0.006)RPMS(0.008)YDEK;TAPPALPT(0.003)GYDS(0.997)EEEEESRPMSYDEK;TAPPALPTGYDS(0.999)EEEEESRPMSYDEK;TAPPALPT(0.001)GYDS(0.999)EEEEESRPMSYDEK 321.39 1.88E-82 3087320000 2746770 1890900 2237320 2284730 2143470 1729150 2626160 1841760 1833540 TRUE FALSE 2574854.569 2030904.203 2290390.287 2343360.04 1975130.513 2228327.535 2232391.688 2071707.79 1527510.329 1.685654441 1.329551863 1.499427037 1.534104219 1.293039055 1.458797032 1.461457671 1.356264341 1 20.5427507 -3.148133899 0.277705655 3.49E-16 1.483928727 0.663679735 0.104991136 42.20342509 1.031333354 24.5735341 0.115410709 0.000710994 3.148133899 1.483928727 TAPPALPTGYDS(ph)EEEEESRPMSYDEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 TAPPALPTGYDSEEEEESRPMSYDEKR 27 2 H0Y6K2;A0A140T9E9;A0A0G2JK44;P25440-4;P25440-3;P25440;P25440-2;A0A0G2JHN8;A0A140T9I1 H0Y6K2 BRD2 Bromodomain-containing protein 2 1 TAPPALPT(0.012)GYDS(0.972)EEEEES(0.012)RPMS(0.003)YDEKR;TAPPALPT(0.004)GYDS(0.995)EEEEESRPMSYDEKR;TAPPALPTGYDS(1)EEEEESRPMSYDEKR;TAPPALPT(0.008)GYDS(0.991)EEEEES(0.001)RPMSYDEKR;TAPPALPTGYDS(1)EEEEESRPMSYDEKR;TAPPALPTGYDS(1)EEEEESRPMSYDEKR;TAPPALPTGY(0.006)DS(0.994)EEEEESRPMSYDEKR;TAPPALPTGYDS(1)EEEEESRPMSYDEKR;TAPPALPTGYDS(1)EEEEESRPMSYDEKR;TAPPALPTGYDS(1)EEEEESRPMSYDEKR;TAPPALPTGYDS(1)EEEEESRPMSYDEKR;TAPPALPT(0.003)GY(0.003)DS(0.992)EEEEES(0.001)RPMSYDEKR 365.18 5.59E-127 4966070000 3227038 2995317 3030476 3292265 3423329 2126327 3851146 2620535 4494428 TRUE FALSE 3025063.452 3217093.387 3102360.322 3376750.094 3154474.549 2740163.087 3273702.41 2947714.563 3744278.932 0.807916159 0.859202385 0.828560152 0.901842559 0.842478514 0.731826645 0.87432119 0.787258272 1 21.83625648 -1.156560079 5.529676617 1.000003618 0.833093591 0.560944745 0.047382847 1.93E-06 2.94E-07 0.041856627 0.009865488 0.069733252 1.156560079 -0.166910028 TAPPALPTGYDSEEEEES(ph)RPMSYDEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAPPALPTGYDSEEEEESRPMSYDEKR 27 2 H0Y6K2;A0A140T9E9;A0A0G2JK44;P25440-4;P25440-3;P25440;P25440-2;A0A0G2JHN8;A0A140T9I1 H0Y6K2 BRD2 Bromodomain-containing protein 2 1 TAPPALPTGYDS(0.203)EEEEES(0.65)RPMS(0.148)YDEKR 268.22 8.14E-54 215350000 76080 71209 72290 75132 80118 52120 93501 67698 108110 TRUE FALSE 71318.28861 76481.38845 74004.75294 77060.01432 73825.85546 67166.1979 79481.39307 76150.24432 90065.74258 0.791847006 0.849172907 0.821674821 0.85559739 0.819688522 0.74574634 0.88248196 0.845496214 1 16.45869085 0.552945787 1.162695381 0.999742235 0.823385223 0.702681157 0.03608502 0.858383118 1.635433117 0.032080594 0.009829801 3.572282423 -0.552945787 -0.176357012 TAPPAS(ph)PEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TAPPASPEAR 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 TAPPAS(1)PEAR;TAPPAS(1)PEAR 154.94 1.43E-05 1040600000 634770 645760 635120 609590 647310 529300 687060 542610 651430 TRUE FALSE 595040.8788 693572.7423 650185.3463 625233.1114 596472.8837 682100.3175 584041.7314 610356.0529 542702.1246 1.096441034 1.277998944 1.198051964 1.152074192 1.099079692 1.256859494 1.076173659 1.124661256 1 19.04980103 0.909992456 0.411706491 0.987340045 1.209943512 0.408613587 0.06466957 1.203985034 0.526871346 0.09490246 0.046618774 8.128163963 -0.909992456 0.222603467 TAPRS(ph)PDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAPRSPDAR 9 1 Q86XP1-2;Q86XP1;A0A0D9SFR6;Q86XP1-5;Q86XP1-3 Q86XP1-2 DGKH Diacylglycerol kinase eta 1 T(0.11)APRS(0.89)PDAR 57.836 0.068297 129660000 167030 232470 186580 230780 247370 156080 186810 200640 272560 TRUE FALSE 156575.8905 249682.3207 191005.7657 236702.2055 227942.558 201137.7623 158799.5748 225690.3457 227067.9752 0.689555145 1.099592844 0.841183199 1.042428838 1.003851635 0.885804183 0.699348178 0.993932964 1 17.79276472 2.009398055 22.07485545 0.84641006 0.949343743 0 0.141570411 106.1403251 249305.9376 0.04856072 0.035784844 102.187566 -2.009398055 0.102933683 TAPSS(ph)PLTSPSDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAPSSPLTSPSDTR 14 0 A0A087WVA8;Q8IWB9;Q8IWB9-2 A0A087WVA8 TEX2 Testis-expressed sequence 2 protein 1 TAPS(0.257)S(0.733)PLT(0.01)SPSDTR 115.06 0.0010793 0 201540 145910 175800 167250 181680 148930 189540 162160 202980 TRUE FALSE 188925.9712 156713.3282 179970.059 171541.9182 167411.5857 191923.6733 161120.2366 182406.033 169101.3267 1.117235298 0.926742157 1.064273489 1.014432716 0.990007523 1.134962552 0.952802913 1.078678899 1 17.36752845 3.790244663 24.99991653 1.030553083 1.004519766 0 0.068305713 498.5604061 197450.0491 0.015622955 0.028164682 6169.424625 -3.790244663 -0.026033316 TAPTALGITLSS(ph)SPTSTPELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAPTALGITLSSSPTSTPELR 21 0 F5H1U9;O75970-5;O75970-3;O75970-2;O75970 F5H1U9 MPDZ Multiple PDZ domain protein 1 TAPTALGIT(0.002)LS(0.074)S(0.63)S(0.293)PT(0.001)STPELR 151.57 6.37E-08 60067000 89784 80462 77092 88897 99483 63771 90712 69695 94883 TRUE FALSE 84164.57971 86419.4902 78920.65865 91178.24752 91670.00648 82180.65246 77110.57773 78396.57417 79046.41433 1.064748862 1.093275273 0.998409091 1.153477337 1.159698479 1.039650605 0.975510128 0.991779005 1 16.2704124 1.998969851 24.99876402 0.991676542 1.08486278 0.522886165 0.045446627 35.17731728 853666.622 0.018446677 0.013449758 99.76308043 -1.998969851 0.093186238 TAPTALGITLSSS(ph)PTSTPELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAPTALGITLSSSPTSTPELR 21 0 F5H1U9;O75970-5;O75970-3;O75970-2;O75970 F5H1U9 MPDZ Multiple PDZ domain protein 1 TAPTALGITLSS(0.03)S(0.922)PT(0.022)S(0.022)T(0.005)PELR 236.27 8.36E-30 62858000 73860 81957 76016 78657 87812 61152 79749 65924 85478 TRUE FALSE 69237.23444 88025.18156 77819.13542 80675.47179 80915.59974 78805.58968 67791.3778 74154.75652 71211.16959 0.97228054 1.236114813 1.092793952 1.132904743 1.136276798 1.106646473 0.95197675 1.041336028 1 16.11981593 1.852144385 5.633061113 0.996270292 1.127895953 0.380901255 0.067800151 0.195082774 8.079570486 0.028058787 0.016635767 71.14500014 -1.852144385 0.13162566 TAPTLS(ph)PEHWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TAPTLSPEHWK 11 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 TAPTLS(1)PEHWK;TAPTLS(1)PEHWK;TAPT(0.001)LS(0.999)PEHWK;TAPTLS(1)PEHWK;TAPT(0.006)LS(0.994)PEHWK;TAPTLS(1)PEHWK 234.04 1.12E-15 3894420000 3520990 2850240 3188280 2941550 3373780 2379070 3898860 2828890 3680670 TRUE FALSE 3300617.521 3061274.735 3263907.507 3017035.153 3108816.928 3065868.888 3314262.138 3182083.144 3066342.399 1.07640214 0.998347326 1.064430218 0.98391985 1.013851855 0.999845578 1.080851942 1.037745538 1 21.54808737 1.753586993 25 1.047697879 1.022942031 0.032255179 0.034635066 11.63474745 19382.10995 0.014669265 0.008135067 56.70051364 -1.753586993 -0.024755848 TAQALS(ph)SGSGSQETKIPISLVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAQALSSGSGSQETKIPISLVLR 23 1 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 T(0.001)AQALS(0.3)S(0.255)GS(0.255)GS(0.187)QET(0.001)KIPISLVLR 49.793 0.083444 14809000 22544 18997 19862 20618 20625 16244 22211 16910 32618 TRUE FALSE 21133.01128 20403.55765 20333.13602 21147.09279 19005.1957 20933.3791 18880.66675 19021.25072 27173.84508 0.77769676 0.750852799 0.748261277 0.778214961 0.699392951 0.770350278 0.694810274 0.699983777 1 14.7299311 -1.138161513 6.355798239 1.000000867 0.739616403 0.86624718 0.032114005 3.77E-07 5.12E-08 0.02974586 0.007011143 0.07275092 1.138161513 -0.260384464 TAQALSSGSGS(ph)QETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TAQALSSGSGSQETK 15 0 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 TAQALSSGSGS(1)QETK;TAQALSSGSGS(1)QETK;TAQALSSGS(0.002)GS(0.998)QETK;TAQALSSGSGS(1)QETK;TAQALSS(0.015)GS(0.194)GS(0.783)QET(0.007)K;TAQALSSGS(0.006)GS(0.994)QETK 369.44 1.67E-97 2275840000 5883930 3164550 4266040 3746250 3816580 3157640 4978180 3540880 5097160 TRUE FALSE 5515665.324 3398856.575 4367232.483 3842385.117 3516841.202 4069199.408 4231748.124 3982966.662 4246411.067 1.298900468 0.800406866 1.028452595 0.904854725 0.828191418 0.958267898 0.99654698 0.937960692 1 22.01781261 -1.472189002 8.618271441 1.000001249 0.95580941 0 0.13662819 2.88E-06 1.76E-07 0.116056226 0.027353942 0.033714056 1.472189002 -0.044191839 TAQALSSGSGS(ph)QETKIPISLVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TAQALSSGSGSQETKIPISLVLR 23 1 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 TAQALSSGSGS(1)QETKIPISLVLR;TAQALSS(0.001)GS(0.004)GS(0.995)QETKIPISLVLR 220.78 1.14E-32 1150010000 591410 481840 490920 499570 637860 372850 613870 444620 1166170 TRUE FALSE 554394.7038 517515.935 502564.8542 512389.812 587765.0486 480485.7423 521825.8924 500131.7857 971528.6933 0.570641616 0.53268209 0.517292858 0.527405743 0.604989902 0.494566703 0.537118354 0.514788487 1 19.88989708 -1.504748852 3.247805893 1.011438902 0.535150658 0.956788987 0.030889866 12262321.34 14395829.39 1237300.377 0.006792791 0.031278877 1.504748852 -0.476288244 TAQEHDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TAQEHDKR 8 1 A0A087WY55;Q9NP79 A0A087WY55 VTA1 Vacuolar protein sorting-associated protein VTA1 homolog 0 ; 130.66 0.00067418 59249000 185755 120790 156974 146926 128789 107656 161263 150792 103044 FALSE TRUE 174128.9261 129733.4173 160697.4974 150696.3699 118674.4314 138734.5396 137083.1102 169618.7131 85845.29071 2.028403943 1.511246758 1.871943074 1.755441314 1.382422151 1.616099595 1.596862322 1.975865091 1 16.38945137 -1.588086154 3.270327537 0.968882468 1.692183081 0.547772865 0.203688145 6329210.982 4878465.119 1339449.394 0.043713562 0.02581748 1.588086154 0.723300613 TAQEHDKRDPVVAYYCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAQEHDKRDPVVAYYCR 17 2 A0A087WY55;Q9NP79 A0A087WY55 VTA1 Vacuolar protein sorting-associated protein VTA1 homolog 0 132.64 1.38E-05 116670000 170640 160540 145490 159300 187800 133150 214520 138090 225710 FALSE TRUE 159959.947 172426.5486 148941.0915 163387.9077 173050.9455 171588.2435 182354.7175 155330.8405 188037.5429 0.850680904 0.916979376 0.792081673 0.868911097 0.920299973 0.912521196 0.969778241 0.826062913 1 17.52066121 2.75675182 3.920145982 0.927368038 0.855334786 0.294179379 0.053160895 0.274036257 9.66194005 0.016077349 0.016326367 571.1521549 -2.75675182 -0.072033253 TAQSPAMVGS(ph)PIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAQSPAMVGSPIR 13 0 Q5VWG9 Q5VWG9 TAF3 Transcription initiation factor TFIID subunit 3 1 TAQSPAMVGS(1)PIR 106.19 0.0014615 105610000 53148 63145 58579 50492 61385 55200 62119 58772 70937 TRUE FALSE 49821.56155 67820.3215 59968.52154 51787.7102 56564.06972 71135.3439 52804.83263 66109.81357 59097.15643 0.843044988 1.147607188 1.01474462 0.876314756 0.95713691 1.203701636 0.893525777 1.118663191 1 15.85080109 TAQVPS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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;TAQVPS(1)PPR 127.78 0.00045727 16814280000 4087920 3521350 3835650 3751480 3832890 3082580 4352230 3395130 4122860 TRUE FALSE 3832064.384 3782074.418 3926633.429 3847749.328 3531870.281 3972470.804 3699653.516 3819019.454 3434728.031 1.115682042 1.10112777 1.14321524 1.120248617 1.02828237 1.15656051 1.07713143 1.111884091 1 21.71176444 -5 0.245482267 0.360188739 1.118147899 0.47902425 0.035111871 144.8824013 1.441294956 46.35818669 0.047862486 1.00E-05 5 0.75795916 TAQVPS(ph)PPRGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 102.5 0.0017317 4666120000 2579620 2831110 2535370 2925620 4261290 1720320 3379260 2280970 7840410 TRUE FALSE 2418166.189 3040728.33 2595510.174 3000696.362 3926625.473 2216948.457 2872571.335 2565754.126 6531794.92 0.370214653 0.46552722 0.397365534 0.459398435 0.601155658 0.339408767 0.439782842 0.392809964 1 22.63904806 -1.474926555 3.33728819 1.009991494 0.434855328 0.862071346 0.071246809 172139762.8 240595842.5 16130347.32 0.015783807 0.033502209 1.474926555 -0.575136166 TAS(ph)EINFDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TASEINFDK 9 0 Q9Y4K4 Q9Y4K4 MAP4K5 Mitogen-activated protein kinase kinase kinase kinase 5 1 T(0.002)AS(0.998)EINFDK;TAS(1)EINFDK 126.34 0.00049945 145455000 377210 278578 279990 290720 318050 194548 407480 302110 433630 TRUE FALSE 353601.0994 299204.205 286631.495 298180.3674 293071.636 250710.8494 346382.1569 339829.0985 361254.3516 0.978814782 0.828236957 0.793434027 0.825402839 0.811261192 0.694000912 0.958831791 0.940692055 1 18.46265544 1.609524042 10.54923753 0.963690335 0.819128166 0.488015928 0.069802608 0.072734629 27.78707474 0.033387748 0.016778491 40.69340603 -1.609524042 -0.144562169 TAS(ph)EINFDKLQFEPPLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TASEINFDKLQFEPPLRK 18 2 Q9Y4K4 Q9Y4K4 MAP4K5 Mitogen-activated protein kinase kinase kinase kinase 5 1 T(0.023)AS(0.977)EINFDKLQFEPPLRK 142.04 6.03E-08 198450000 352430 295850 311640 292260 408880 174080 436560 291400 726390 TRUE FALSE 330372.0354 317755.0418 319032.248 299759.8864 376768.2141 224334.07 371101.8808 327781.9315 605150.8163 0.545933388 0.525084051 0.527194609 0.495347405 0.622602174 0.370707705 0.613238668 0.541653291 1 19.20693521 0.033222654 1.03802478 1.003613989 0.524028689 0.824719281 0.068178309 2.618278046 2.464172466 0.086757391 0.01766472 1.079500019 -0.033222654 -0.479585299 TAS(ph)FGNILDVPEIVISGNGQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TASFGNILDVPEIVISGNGQPR 22 0 O43318;O43318-3 O43318 MAP3K7 Mitogen-activated protein kinase kinase kinase 7 1 T(0.146)AS(0.854)FGNILDVPEIVISGNGQPR;T(0.143)AS(0.857)FGNILDVPEIVISGNGQPR;T(0.118)AS(0.882)FGNILDVPEIVISGNGQPR;T(0.117)AS(0.883)FGNILDVPEIVISGNGQPR 271.66 2.62E-45 162885000 547270 550994 479843 460605 519079 293991 718242 509219 673079 TRUE FALSE 513017.3476 591790.1691 491225.1026 472424.9041 478312.6292 378861.4292 610548.2799 572796.1131 560737.7666 0.914897084 1.055377762 0.876033561 0.842505949 0.853005911 0.67564814 1.088830317 1.021504431 1 19.09696672 1.617274302 25 1.041376539 0.889513069 0.394707777 0.095441134 0.826824653 2191.184468 0.04742232 0.02585457 41.42612415 -1.617274302 -0.15186347 TAS(ph)FSESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 TASFSESR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 TAS(0.992)FS(0.008)ESR;TAS(1)FSESR;T(0.001)AS(0.997)FS(0.002)ESR;TAS(1)FSESR;T(0.001)AS(0.993)FS(0.007)ESR;TAS(0.994)FS(0.006)ESR;T(0.008)AS(0.99)FS(0.002)ESR;TAS(0.997)FS(0.003)ESR;TAS(1)FSESR 203.78 9.74E-05 55706430000 22846770 20083670 20078660 22081480 21596140 18700620 28108610 17988970 20757430 TRUE FALSE 21416831.45 21570685.82 20554935.3 22648128.16 19900066.28 24099185.41 23893984.88 20234932.5 17292880.83 1.238476784 1.247373762 1.188635687 1.309679305 1.150766403 1.393589978 1.381723792 1.170130801 1 24.04367489 0.990233833 23.24522255 0.999999995 1.271001097 0.57310118 0.075748177 133.1599817 316946.5561 0.07745318 0.019363295 9.77763527 -0.990233833 0.271001102 TAS(ph)FSESRADEVAPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TASFSESRADEVAPAK 16 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 T(0.001)AS(0.986)FS(0.013)ESRADEVAPAK;TAS(0.999)FS(0.001)ESRADEVAPAK;TAS(0.999)FS(0.001)ESRADEVAPAK;TAS(0.999)FS(0.001)ESRADEVAPAK 252.66 9.41E-27 5730600000 4188190 4101040 3839250 4586100 5984600 2969840 5782100 3522620 8533900 TRUE FALSE 3926058.664 4404685.269 3930318.823 4703787.09 5514593.657 3827184.597 4915127.783 3962426.861 7109536.959 0.552224243 0.619546012 0.55282346 0.661616518 0.775661437 0.538316999 0.691342884 0.557339653 1 22.76132417 -5 0.335894296 4.97977616 0.606268852 0.709572619 0.076222013 197.0768968 1.678790696 561.6081734 0.057800577 1.00E-05 5 -4.373507308 TAS(ph)FSESRADEVAPAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TASFSESRADEVAPAKK 17 2 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 T(0.001)AS(0.989)FS(0.01)ESRADEVAPAKK;T(0.001)AS(0.996)FS(0.003)ESRADEVAPAKK;T(0.003)AS(0.975)FS(0.022)ESRADEVAPAKK 215.98 2.84E-15 2247990000 1858670 1625910 1560950 2116280 2698960 1144480 2647360 1550090 5709700 TRUE FALSE 1742339.163 1746294.068 1597976.471 2170587.328 2486994.569 1474872.797 2250412.945 1743622.149 4756714.184 0.366290489 0.367121925 0.335941242 0.456320738 0.522838765 0.310061261 0.47310241 0.36656021 1 22.18153391 -5 0.35402115 8.14243829 0.379099341 0.887954092 0.066887736 133.0906709 1.078330961 722.6421767 0.047381544 1.00E-05 5 -7.763338949 TAS(ph)GSS(ph)VTS(ph)LDGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 3 TAS(0.999)GS(0.205)S(0.794)VT(0.29)S(0.712)LDGTR 122.58 7.22E-05 115050000 252460 232060 195060 268910 273900 145620 284110 197560 124840 TRUE FALSE 236658.9793 249241.9639 199686.9153 275810.6859 252388.9989 187658.1301 241510.343 222225.8009 104003.3975 2.275492772 2.396479056 1.92000377 2.651939191 2.426738019 1.804346152 2.322138977 2.136716744 1 16.66627113 -1.754126365 0.422540225 1.01E-12 2.274665943 0.728953747 0.239866936 20.15274994 1.544112223 20.60983324 0.134524237 0.017614634 1.754126365 2.274665943 TAS(ph)GSS(ph)VTSLDGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 TAS(1)GS(0.008)S(0.99)VT(0.002)SLDGTR;TAS(0.999)GS(0.061)S(0.938)VT(0.003)SLDGTR;TAS(1)GSS(0.999)VT(0.001)SLDGTR;T(0.001)AS(0.999)GS(0.001)S(0.999)VTSLDGTR;TAS(1)GS(0.023)S(0.964)VT(0.013)SLDGTR 255.64 4.00E-24 3654140000 5359680 5319720 4480770 6469010 6485750 3087040 6566300 4691810 1927940 TRUE FALSE 5024227.196 5713597.604 4587055.98 6635015.749 5976385.357 3978218.334 5581744.274 5277592.806 1606154.359 3.128109803 3.55731538 2.855924746 4.130995076 3.720928392 2.476859283 3.475222815 3.285856541 1 20.61517912 -1.358960154 0.574555602 7.20E-11 3.348503068 0.72258184 0.453891341 22.79307833 3.367903528 35.2960594 0.178338072 0.043756225 1.358960154 3.348503068 TAS(ph)GSSVT(ph)SLDGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 TAS(1)GS(0.001)S(0.028)VT(0.623)S(0.349)LDGTR;TAS(1)GSS(0.004)VT(0.915)S(0.081)LDGTR 224.97 1.57E-11 630130000 1432300 1343910 1150340 1556400 1604220 972680 1619570 1200270 668580 TRUE FALSE 1342654.9 1443414.495 1177626.608 1596339.859 1478231.032 1253476.926 1376730.514 1350126.352 556989.6788 2.410556157 2.591456448 2.114270071 2.866013357 2.653964855 2.250449108 2.471734336 2.423970143 1 19.08729107 -0.91249031 0.739728067 0.769256903 2.471103259 0.834649075 0.206183233 14.45576204 4.209536515 8.110984974 0.069496999 0.122323441 0.91249031 1.701846357 TAS(ph)GSSVTS(ph)LDGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 T(0.029)AS(0.971)GS(0.02)S(0.034)VT(0.371)S(0.575)LDGTR 171.26 4.45E-06 239360000 1073300 970410 933130 1220500 1186100 706140 1234100 919560 537150 TRUE FALSE 1006124.069 1042260.166 955264.2843 1251820.096 1092948.49 909991.1548 1049058.162 1034369.09 447496.1949 2.248341059 2.329092801 2.134686943 2.79738713 2.442363763 2.033517078 2.344283982 2.311458962 1 18.77151589 -1.787253779 0.582679862 1.55E-07 2.33057857 0.812619352 0.200821197 37.26586711 4.077006486 52.03296192 0.080368902 0.01632098 1.787253779 2.330578415 TAS(ph)GSSVTSLDGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 TAS(0.872)GS(0.128)SVTSLDGTR;TAS(1)GSSVTSLDGTR;TAS(0.922)GS(0.078)SVTSLDGTR;TAS(0.991)GS(0.009)SVTSLDGTR;TAS(0.961)GS(0.038)SVTSLDGTR;TAS(1)GSSVTSLDGTR;TAS(0.987)GS(0.013)SVTSLDGTR;TAS(0.997)GS(0.002)SVTSLDGTR;TAS(0.999)GS(0.001)SVTSLDGTR;TAS(0.984)GS(0.016)SVTSLDGTR 348.73 7.97E-82 57855250000 12282352 15517799 11606541 18444930 18885350 7836709 16126211 11909055 4731618 TRUE FALSE 11513621.51 16666752.98 11881853.63 18918258.13 17402170.79 10099039.67 13708235.37 13395926.73 3941880.388 2.920844972 4.228122455 3.014260318 4.799297865 4.414687681 2.561985315 3.477587856 3.398359517 1 21.91045257 -0.097153672 0.558294001 0.767431971 3.756042962 0.590028321 0.68999824 3.4553001 1.184721324 2.420871569 0.287496367 0.799551289 0.097153672 2.988610991 TAS(ph)LNQRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.024)AS(0.976)LNQRPR 85.813 0.015028 0 50323 56317 45667 53410 63806 26715 53494 49359 74823 TRUE FALSE 47173.37326 60486.76928 46750.24281 54780.59102 58794.93414 34427.18682 45473.07131 55521.5798 62334.55792 0.756777217 0.970356914 0.749989161 0.878815746 0.943215707 0.55229696 0.729500181 0.890703033 1 15.92774459 TAS(ph)LPGYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 194.12 3.44E-05 3093780000 2470710 2369530 2251800 2304560 2387790 1729650 2803490 1978920 2481680 TRUE FALSE 2316072.671 2544972.467 2305213.759 2363698.911 2200262.605 2228971.876 2383132.701 2225992.518 2067471.576 1.120244021 1.230958866 1.114991754 1.143280004 1.064228709 1.078114883 1.15267979 1.076673819 1 20.97943606 -4.999999997 0.040395393 0.356475665 1.501139875 0.535089937 0.041910819 600.1888791 1.810691662 46.42441684 13.81007692 1.00E-05 4.999999997 1.144664209 TAS(ph)NPKVENEDEPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TASNPKVENEDEPVR 15 1 Q9UBF8-2 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 T(0.026)AS(0.974)NPKVENEDEPVR;T(0.008)AS(0.992)NPKVENEDEPVR 214.59 1.49E-12 1323800000 2312300 1338980 1500050 1633550 1522130 1004730 1941440 1299850 2078620 TRUE FALSE 2167577.271 1438119.472 1535631.894 1675469.659 1402588.05 1294779.241 1650339.095 1462139.134 1731684.894 1.251715759 0.830474111 0.88678483 0.967537261 0.8099557 0.747699102 0.953025058 0.844344799 1 20.723745 4.742632161 24.81220363 0.874187336 1.251715923 0.694782225 0.077347359 194.9745715 1188133.852 0.016956083 0.129997817 55288.16314 -4.742632161 0.377528587 TAS(ph)PLPLRPDAPVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TASPLPLRPDAPVEK 15 1 Q9HCK8-2;Q9HCK8;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 T(0.016)AS(0.984)PLPLRPDAPVEK;T(0.002)AS(0.998)PLPLRPDAPVEK;T(0.231)AS(0.769)PLPLRPDAPVEK;TAS(1)PLPLRPDAPVEK 179.69 4.00E-07 2185990000 3941740 2826410 3255990 3093940 3565390 2730000 4851480 3521380 4749890 TRUE FALSE 3695033.53 3035680.337 3333223.62 3173335.738 3285378.651 3518106.682 4124045.613 3961032.045 3957102.674 0.933772468 0.767147226 0.842339433 0.801934142 0.830248523 0.889061258 1.042188175 1.000992992 1 21.91601307 1.918697019 3.185681722 1.016888913 0.82604082 0.77264439 0.0441404 0.101724936 1.84408753 0.020656308 0.011331764 82.92720326 -1.918697019 -0.190848094 TAS(ph)PPGPPPYGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TASPPGPPPYGK 12 0 P54259 P54259 ATN1 Atrophin-1 1 TAS(1)PPGPPPYGK;T(0.002)AS(0.998)PPGPPPYGK;TAS(1)PPGPPPYGK;TAS(1)PPGPPPYGK 194.24 1.87E-06 937890000 1400050 1059000 1203720 1148370 1225190 891910 1517160 1071930 1455360 TRUE FALSE 1312423.37 1137409.462 1232272.807 1177839.118 1128968.52 1149389.938 1289675.943 1205762.82 1212451.014 1.082454759 0.93810756 1.016348531 0.971452953 0.931145676 0.947988764 1.063693236 0.994483741 1 20.20949503 1.745612299 25 1.024407241 0.978017565 0.120939718 0.047311634 2.534730209 9012.949066 0.02022452 0.011215308 55.66885632 -1.745612299 -0.046389676 TAS(ph)PPPPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 TASPPPPPK 9 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 TAS(1)PPPPPK;TAS(1)PPPPPK;TAS(1)PPPPPK;TAS(1)PPPPPK;TAS(1)PPPPPK;T(0.001)AS(0.999)PPPPPK;TAS(1)PPPPPK 126.29 0.00050095 8236930000 4074890 2981480 3268630 3139500 3328770 2584390 4089530 2868270 4168500 TRUE FALSE 3819849.909 3202231.881 3346163.447 3220064.885 3067341.832 3330461.439 3476342.942 3226379.823 3472750.42 1.099949448 0.922102511 0.963548497 0.927237635 0.883260085 0.959027006 1.001034489 0.92905606 1 21.7276473 -0.586301706 8.050111045 0.999988489 0.957339574 0.040249118 0.058427282 0 0 0.051829857 0.012216414 0.25923778 0.586301706 -0.042648915 TAS(ph)PPPPPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 TASPPPPPKR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(0.028)AS(0.972)PPPPPKR;T(0.002)AS(0.998)PPPPPKR;T(0.144)AS(0.856)PPPPPKR;T(0.068)AS(0.932)PPPPPKR;T(0.005)AS(0.995)PPPPPKR;T(0.054)AS(0.946)PPPPPKR;TAS(1)PPPPPKR;T(0.038)AS(0.962)PPPPPKR 127.51 0.00026703 16111475000 4610260 3173085 3750160 3429287 3714240 2704370 4517950 3150617 4562330 TRUE FALSE 4321712.056 3408023.515 3839115.566 3517288.31 3422538.573 3485077.717 3840525.34 3543978.468 3800847.649 1.137039012 0.896648282 1.010068259 0.925395763 0.900467182 0.916921181 1.010439169 0.932417922 1 21.85788977 4.749024244 24.86675713 0.950821096 1.137039124 0.647512975 0.043573244 901.2152484 2141688.003 0.010023827 0.143426985 56107.92961 -4.749024244 0.186218028 TAS(ph)PWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 117.39 0.023878 2717980000 10186600 6641780 8159900 7598140 9122200 5573950 9523400 7159940 10660700 TRUE FALSE 9549038.89 7133544.302 8353456.681 7793121.136 8405779.209 7183058.879 8095454.581 8053874.27 8881360.299 1.075177514 0.803204021 0.9405605 0.877469315 0.946451774 0.808779133 0.911510659 0.906828909 1 23.08234923 0.639174382 2.561406837 0.999984443 0.897975921 0.109981363 0.076808532 5.850650567 39.29786188 0.064081065 0.017054796 4.356867793 -0.639174382 -0.102008522 TAS(ph)QGPQTDSVIQNSENIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TASQGPQTDSVIQNSENIK 19 0 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 T(0.15)AS(0.849)QGPQTDSVIQNSENIK 254.8 6.83E-31 100400000 327200 215430 261470 317920 373420 220570 420040 254170 386840 TRUE FALSE 306721.1361 231380.6614 267672.1919 326078.3654 344093.0995 284244.9783 357058.9015 285903.684 322273.9049 0.951740527 0.717962757 0.830573583 1.011805053 1.067703882 0.88199812 1.107936125 0.887145002 1 18.29792785 3.277076057 5.329180041 1.001698263 0.805637809 0.400095115 0.089746654 0.138180516 9.468270706 0.022908371 0.030584446 1892.67505 -3.277076057 -0.196060454 TAS(ph)TDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TASTDLK 7 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 TAS(0.979)T(0.021)DLK;T(0.012)AS(0.9)T(0.088)DLK 118.71 0.005187 694490000 2022310 1269540 1407290 1412480 1448830 811910 1761350 1073520 1841010 TRUE FALSE 1895737.227 1363538.063 1440671.583 1448726.628 1335044.736 1046295.237 1497251.919 1207551.335 1533733.538 1.236027759 0.889031914 0.939323258 0.944575177 0.870454159 0.682188406 0.976213848 0.787327985 1 20.54861643 4.738672304 7.896863981 0.886357422 1.239049043 0.579619381 0.093647294 0.065118837 47.47979898 0.020517807 0.12217406 54786.34199 -4.738672304 0.352691621 TAS(ph)TPTPPQTGGGLEPQANGETPQVAVIVRPDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TASTPTPPQTGGGLEPQANGETPQVAVIVRPDDR 34 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JWW9;C9JSU8;C9J556;C9JWH7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 T(0.013)AS(0.346)T(0.346)PT(0.295)PPQT(0.001)GGGLEPQANGETPQVAVIVRPDDR;T(0.079)AS(0.526)T(0.394)PT(0.001)PPQTGGGLEPQANGETPQVAVIVRPDDR 169.84 9.15E-15 1573080000 63639 37640 67916 57002 64698 38791 88105 53617 46920 TRUE FALSE 59655.94859 40426.90476 69526.99959 58464.76782 59616.88006 49989.33198 74894.47318 60311.20048 39088.74889 1.526166743 1.034233786 1.778695957 1.495692993 1.525167261 1.278867536 1.916011009 1.542929927 1 15.25446579 3.976301129 24.98292313 1.554515864 1.265237508 0.081765179 0.276949211 61.28792895 1867080.706 0.063103349 0.122890123 9468.934865 -3.976301129 -0.289278356 TASES(ph)ISNLSEAGS(ph)IK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TASESISNLSEAGSIK 16 0 J3KP58;P30622-2;P30622-1;P30622;F5H6A0;F5H1T5 J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 2 TAS(0.003)ES(0.997)ISNLSEAGS(1)IK;T(0.001)AS(0.005)ES(0.985)IS(0.009)NLSEAGS(1)IK 174.2 5.78E-09 185768000 608890 367390 471150 450300 502260 320431 653110 469240 679280 TRUE FALSE 570780.6618 394591.9379 482325.9005 461855.4604 462814.5256 412934.2279 555182.2187 527825.6469 565903.7797 1.008617865 0.697277438 0.852310795 0.81613779 0.81783254 0.729689821 0.981054092 0.932712708 1 19.11019725 1.67092556 7.477545294 0.967505799 0.809864992 0.413680257 0.083814942 0.108515222 11.28003942 0.037760679 0.019533492 46.87330325 -1.67092556 -0.157640807 TASESISNLS(ph)EAGSIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TASESISNLSEAGSIK 16 0 J3KP58;P30622-2;P30622-1;P30622;F5H6A0;F5H1T5 J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 1 TASESIS(0.268)NLS(0.731)EAGS(0.001)IK 133.62 3.43E-05 107130000 123410 87951 117230 107050 116020 81340 117210 89146 139170 TRUE FALSE 115685.9884 94462.98355 120010.751 109797.0842 106908.2572 104821.5376 99635.44862 100276.0743 115941.6279 0.997795101 0.814746051 1.035096308 0.947003127 0.922086908 0.904088889 0.859358717 0.864884133 1 16.82303912 2.310395631 2.933115316 0.890863177 0.940151233 0.050016555 0.068156647 0.629638045 11.05027579 0.025853325 0.01991465 204.3598762 -2.310395631 0.049288056 TASESISNLSEAGS(ph)IK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 354.8 2.38E-87 1171010000 2043380 1060030 1444590 1279200 1454730 1139560 1696960 1181740 2007410 TRUE FALSE 1915488.493 1138515.724 1478856.357 1312026.438 1340481.374 1468532.473 1442516.602 1329282.84 1672360.303 1.145380269 0.680783754 0.884292909 0.784535746 0.801550582 0.878119667 0.862563288 0.794854337 1 20.67345427 -1.509881562 8.451394722 1.000011511 0.840309603 0.119068288 0.119747481 2.27E-05 1.31E-06 0.101176962 0.023845921 0.030911383 1.509881562 -0.159701908 TASFSESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TASFSESR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;; 110.31 0.0080274 490020000 497490 873300 533020 540570 893790 448100 561800 776010 934290 FALSE TRUE 466352.9889 937960.0407 545663.4861 554441.9414 823595.3388 577459.1957 477563.3055 872896.5567 778350.9633 0.599155151 1.205060551 0.701050698 0.712328972 1.058128502 0.741900791 0.613557801 1.121469103 1 19.5700613 3.773535835 24.01160453 0.817788807 0.947687752 0 0.221890965 423.331463 218998.0803 0.05251922 0.094679805 5936.57331 -3.773535835 0.129898945 TASGS(ph)SVTSLDGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 TAS(0.308)GS(0.66)S(0.033)VTSLDGTR 341.16 5.94E-69 225730000 234000 275910 246070 362880 370430 158520 316370 244880 101140 TRUE FALSE 219354.3577 296338.6635 251906.8966 372192.1152 341337.922 204282.1506 268933.2555 275453.807 84259.08061 2.603331963 3.516993793 2.989670606 4.417234468 4.05105206 2.424452643 3.191742108 3.269129037 1 16.36254455 -0.372692215 0.609066679 0.759633863 3.380765979 0.597565908 0.596395586 6.128163254 1.963158756 3.93058927 0.232085477 0.423943309 0.372692215 2.621132116 TASGSS(ph)VTS(ph)LDGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 2 TAS(0.003)GS(0.196)S(0.695)VT(0.141)S(0.964)LDGTR;TASGS(0.011)S(0.988)VT(0.256)S(0.746)LDGTR 200.71 2.76E-08 412520000 1698380 1294130 1159670 1271500 1280240 853450 1491300 988090 1071310 TRUE FALSE 1592081.427 1389948.732 1187177.92 1304128.843 1179695.115 1099827.16 1267693.41 1111455.212 892501.4401 1.783841858 1.557363013 1.330169193 1.46120643 1.321785111 1.232297351 1.420382481 1.245325959 1 19.76749497 8 0.131062773 0.982868697 3.304505673 0.807268234 0.091678751 40.16658083 0.355518769 0.487341317 17.27243456 100000000 -8 2.321636976 TASGSSVT(ph)SLDGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 TASGS(0.003)S(0.017)VT(0.584)S(0.395)LDGTR;TASGS(0.001)S(0.007)VT(0.496)S(0.496)LDGTR 180.49 1.95E-05 2166900000 2959140 2829980 2791320 3090060 2703760 1971100 3682140 2636760 1714110 TRUE FALSE 2773932.71 3039514.664 2857531.429 3169356.171 2491417.596 2540124.572 3130037.29 2965965.29 1428013.967 1.942510909 2.12849085 2.001052856 2.219415386 1.744673128 1.778781321 2.191881425 2.076986191 1 20.44557866 -1.479268226 3.364200084 0.981928519 2.020888094 0.801315587 0.158052021 23507757.03 37572203.7 4099095.342 0.036982176 0.033168954 1.479268226 1.038959575 TASGSSVTS(ph)LDGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TASGSSVTSLDGTR 14 0 Q92597;Q92597-3;Q92597-2;E5RJY1;E7ESM1 Q92597 NDRG1 Protein NDRG1 1 TASGS(0.004)S(0.038)VT(0.027)S(0.931)LDGTR;TASGSS(0.003)VT(0.303)S(0.694)LDGTR 257.23 2.56E-24 2344780000 2923400 2866330 2498190 2845920 2498860 1869120 3481900 2508300 1315260 TRUE FALSE 2740429.612 3078556.056 2557448.247 2918951.125 2302609.616 2408704.601 2959821.419 2821466.776 1095734.609 2.500997586 2.809581837 2.334003348 2.663921629 2.101430033 2.198255473 2.701221076 2.574954513 1 20.06346698 -1.289055298 3.416126991 0.994445636 2.497212212 0.814774037 0.222535996 12181771.16 18341247.5 701550.9413 0.056024821 0.05139782 1.289055298 1.502766577 TASPLPLRPDAPVEKS(ph)PEETATQVPSLESLTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TASPLPLRPDAPVEKSPEETATQVPSLESLTLK 33 2 Q9HCK8-2;Q9HCK8;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 TASPLPLRPDAPVEKS(0.984)PEET(0.01)AT(0.005)QVPSLESLTLK 199.99 3.10E-27 77966000 207350 116290 134490 143120 147330 81579 161140 99212 136010 TRUE FALSE 194372.3336 124900.2326 137680.1663 146792.7015 135759.2961 105129.533 136978.553 111598.8366 113309.0523 1.715417521 1.102297036 1.215085322 1.295507274 1.198132835 0.927812305 1.208893289 0.984906627 1 16.7899036 4.740461598 24.9221098 1.133980754 1.715417726 0.715022569 0.118358861 86.45540385 1133351.905 0.026433662 0.171600016 55012.52743 -4.740461598 0.581436972 TAST(ph)PT(ph)PPQTGGGLEPQANGETPQVAVIVRPDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TASTPTPPQTGGGLEPQANGETPQVAVIVRPDDR 34 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JWW9;C9JSU8;C9J556;C9JWH7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 2 T(0.019)AS(0.132)T(0.849)PT(0.657)PPQT(0.343)GGGLEPQANGETPQVAVIVRPDDR 126.62 3.37E-07 270770000 112550 74842 101910 81246 91382 73803 134430 93369 123700 TRUE FALSE 105505.6964 80383.37955 104327.3533 83330.90991 84205.22634 95108.72801 114273.4695 105026.3252 103053.6709 1.023793675 0.780014713 1.012359409 0.808616609 0.817100697 0.922904805 1.108873352 1.019142009 1 16.65303637 1.888055932 5.638587392 1.049629823 0.885682179 0.41184889 0.0843108 0.200482482 8.519759354 0.03509785 0.021047231 77.27801034 -1.888055932 -0.163947645 TAST(ph)PTPPQT(ph)GGGLEPQANGETPQVAVIVRPDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TASTPTPPQTGGGLEPQANGETPQVAVIVRPDDR 34 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JWW9;C9JSU8;C9J556;C9JWH7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 2 T(0.003)AS(0.028)T(0.969)PT(0.247)PPQT(0.754)GGGLEPQANGETPQVAVIVRPDDR 155.46 2.26E-10 246600000 107060 78861 90806 75937 88518 80388 107380 86912 123100 TRUE FALSE 100359.3057 84699.95049 92959.9612 77885.67198 81566.15334 103594.7106 91279.36587 97763.15452 102553.8147 0.97860139 0.825907361 0.906450544 0.759461481 0.795349774 1.010149753 0.890063096 0.953286377 1 16.64602163 2.239893078 24.99999133 0.949337875 0.852447586 0.38857352 0.067688758 40.88996023 767204.6581 0.02315893 0.018397141 173.7373039 -2.239893078 -0.096890289 TAST(ph)PTPPQTGGGLEPQANGETPQVAVIVRPDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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(0.02)AS(0.134)T(0.817)PT(0.029)PPQTGGGLEPQANGETPQVAVIVRPDDR;TAS(0.015)T(0.967)PT(0.018)PPQTGGGLEPQANGETPQVAVIVRPDDR;T(0.023)AS(0.136)T(0.817)PT(0.023)PPQTGGGLEPQANGETPQVAVIVRPDDR;T(0.018)AS(0.112)T(0.864)PT(0.006)PPQTGGGLEPQANGETPQVAVIVRPDDR;T(0.001)AS(0.026)T(0.949)PT(0.024)PPQTGGGLEPQANGETPQVAVIVRPDDR 233.04 1.22E-46 2107420000 273826 280519 275552.2 234636.7 288016 253820.7 358670 280059 326016 TRUE FALSE 256687.7195 301288.9186 282088.4283 240657.875 265396.3852 327094.6157 304890.7632 315024.9826 271601.8235 0.945088351 1.10930374 1.038610215 0.886068701 0.977152442 1.204316714 1.122565229 1.15987801 1 18.05113364 2.249813304 24.99872337 1.133489384 1.00902185 0.394297609 0.078034328 231.1955694 513618.5739 0.027338227 0.02268131 177.751512 -2.249813304 -0.124467534 TASTPTPPQTGGGLEPQANGETPQVAVIVRPDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TASTPTPPQTGGGLEPQANGETPQVAVIVRPDDR 34 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JWW9;C9JSU8;C9J556;C9JWH7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 84.938 0.00059 280150000 44117 50003 49022 52367 51779 37386 51376 49526 63259 FALSE TRUE 41355.79572 53705.27415 50184.82499 53710.82588 47712.48621 48178.73129 43672.64575 55709.43012 52700.66423 0.784730066 1.019062567 0.952261717 1.019167911 0.905348859 0.914195902 0.828692511 1.057091612 1 15.68553353 TATAVAHCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TATAVAHCK 9 0 P62249;M0R210;M0R3H0;M0R1M5;Q6IPX4 P62249 RPS16 40S ribosomal protein S16 0 ; 91.867 0.0088667 0 1497250 1841830 1255470 1241570 2010640 842280 1477210 1498760 1953280 FALSE TRUE 1403539.795 1978201.01 1285250.341 1273430.788 1852732.445 1085432.563 1255716.074 1685883.485 1627264.949 0.862514611 1.215660062 0.789822421 0.782558973 1.138556106 0.667028785 0.771672784 1.036022736 1 20.63401774 3.886624253 5.869462193 0.862632133 1.055516465 0.120673011 0.165443358 0.310892105 16.04155153 0.039652191 0.072852186 7702.3678 -3.886624253 0.192884332 TATESFASDPILYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TATESFASDPILYR 14 0 P14618;P14618-3;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 74.841 0.034185 0 50270 45921 53236 49471 51957 41047 53199 42689 44211 FALSE TRUE 47123.69043 49321.03862 54498.78306 50740.50961 47876.5068 52896.60256 45222.30383 48018.81562 36831.89849 1.279426051 1.339084887 1.47966261 1.377624062 1.299865301 1.436162803 1.227802684 1.303729039 1 15.16866814 0.557849377 0.680020708 0.995114712 1.379109376 0.716263241 0.069635852 0.765669618 0.618137392 0.075006971 0.025580256 3.612845393 -0.557849377 0.383994664 TATESFASDPILYRPVAVALDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TATESFASDPILYRPVAVALDTK 23 1 P14618;P14618-3;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 279.16 6.60E-52 4791825000 4366080 3322320 3747520 3621680 3804380 2781410 4744700 3359790 4015410 FALSE TRUE 4092814.846 3568308.03 3836412.944 3714618.44 3505599.341 3584357.915 4033276.283 3779267.177 3345212.13 1.223484397 1.066691107 1.14683697 1.110428366 1.047945303 1.071488974 1.205686254 1.129754117 1 21.67366627 4.752241516 24.22123195 1.108535565 1.223484516 0.305075347 0.05767112 2131.953559 3774396.355 0.013361249 0.26521563 56525.12305 -4.752241516 0.114948951 TATESFASDPILYRPVAVALDTKGPEIR ddPTM_SK-BR-3_Pertuzumab_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 ; 214 3.08E-27 636590000 282721 380118 311852 376311 560740 225850 507609 312183 1209630 FALSE TRUE 265025.9973 408262.3322 319249.2767 385967.7774 516701.7423 291049.2286 431497.7429 351159.7347 1007734.938 0.262991772 0.405128687 0.316798857 0.383005255 0.512735763 0.28881526 0.428185752 0.348464384 1 19.94268479 -4.786255641 0.412501422 10 0.360852405 0.88425877 0.071831279 201.3519818 1.618454879 1628.941268 0.038281115 1.64E-05 4.786255641 -9.639147595 TATPPGYKPGS(ph)PPSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TATPPGYKPGSPPSFR 16 1 P54259 P54259 ATN1 Atrophin-1 1 TATPPGYKPGS(0.971)PPS(0.029)FR;TATPPGYKPGS(0.854)PPS(0.146)FR 112.56 0.00044175 743880000 773340 547350 637770 619430 631320 434570 741840 522790 672260 TRUE FALSE 724938.0299 587876.3635 652898.2056 635325.6225 581738.6738 560023.3043 630607.9789 588061.4823 560055.463 1.294403997 1.04967526 1.165774193 1.134397688 1.038716185 0.999942579 1.125974159 1.050005796 1 19.09521018 4.743903469 24.6717681 1.08170864 1.294404106 0.599879161 0.056807807 349.6762805 1614646.54 0.013213541 0.1118512 55450.24501 -4.743903469 0.212695465 TATPQQAQEVHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 TATPQQAQEVHEK 13 0 P60174;P60174-3;P60174-4;U3KPZ0 P60174 TPI1 Triosephosphate isomerase 0 ;;;;;; 234.9 1.13E-16 16831790000 12990040 11359590 11142670 10550920 12441500 7776326 15090940 9923320 17941120 FALSE TRUE 12177016.58 12200665.86 11406979.39 10821674.47 11464394.78 10021225.08 12828193.64 11162268.35 14946631.17 0.814699744 0.816281992 0.76318063 0.724020975 0.76702199 0.670467142 0.858266555 0.746808309 1 23.83331702 -0.548806382 0.890576509 1.011581193 0.772446669 0.652784455 0.052531498 16.78758933 8.211730147 0.718561819 0.015936284 0.282613965 0.548806382 -0.239134524 TAVAHRPGAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAVAHRPGAFK 11 1 Q969H8 Q969H8 MYDGF Myeloid-derived growth factor 0 71.153 0.029928 511640000 333370 442580 300810 295470 435280 245980 363410 375230 500590 FALSE TRUE 312504.9668 475349.0837 307945.3553 303052.2604 401094.8646 316990.4328 308920.0442 422078.2915 417038.2951 0.749343575 1.139821185 0.738410258 0.726677296 0.961769865 0.7600991 0.740747427 1.012085213 1 18.66982034 3.899772624 8.175874884 0.827351074 0.967935229 0.050646816 0.145070189 0.467569947 44.3402598 0.033678564 0.061003222 7939.124706 -3.899772624 0.140584155 TAVAPSAVNLADPRT(ph)PTAPAVNLAGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TAVAPSAVNLADPRTPTAPAVNLAGAR 27 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 TAVAPSAVNLADPRT(0.994)PT(0.006)APAVNLAGAR;TAVAPSAVNLADPRT(0.96)PT(0.04)APAVNLAGAR 124.9 0.00012437 737010000 271030 297910 339490 326500 343230 232270 348260 259830 461100 TRUE FALSE 254066.7161 319967.5664 347542.8631 334878.5428 316274.1003 299322.5784 296041.6461 292270.3475 384139.4312 0.66139192 0.832946426 0.90473103 0.871763 0.823331516 0.779202951 0.770661958 0.760844432 1 18.55127054 2.468307493 22.71119006 0.803182413 0.8360312 0 0.093492177 301.4596108 776776.4505 0.030269349 0.025379108 293.9730329 -2.468307493 0.032848788 TAVIPINGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 141.73 3.99E-05 2797830000 2407141 2232806 2200659 2058644 2140408 2008839 2996050 2227436 2403597 TRUE FALSE 2256482.342 2398125.279 2252859.671 2111472.29 1972308.99 2588758.209 2546820.116 2505536.288 2002421.133 1.126877011 1.19761285 1.125067866 1.054459652 0.984962133 1.292814067 1.271870375 1.251253419 1 20.93331399 2.215878473 24.99995691 1.233849747 1.113156316 0.188821518 0.098462126 317.4235272 349857.7505 0.035192171 0.026009302 164.3911651 -2.215878473 -0.120693432 TAVPS(ph)PVEAAAASDPAAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TAVPSPVEAAAASDPAAAR 19 0 Q147X3;Q147X3-2;J3KNC2 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 TAVPS(1)PVEAAAASDPAAAR;TAVPS(1)PVEAAAASDPAAAR 148.52 9.93E-08 187851000 77506 75055 62670 81197 77178 50146 69340 54458 83803 TRUE FALSE 72655.03781 80612.15029 64156.56199 83280.65249 71116.7512 64622.33615 58943.11072 61257.20118 69815.73791 1.040668479 1.154641528 0.918941258 1.1928636 1.018634957 0.925612735 0.844266816 0.877412501 1 16.09126467 2.258685511 3.397183438 0.889980064 1.066428605 0.463718629 0.082569029 0.188751601 4.575513676 0.030261034 0.023020669 181.4201457 -2.258685511 0.176448541 TAVTATNVSAHGSQANS(ph)PSTPNSAGGYPSPCYQPDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAVTATNVSAHGSQANSPSTPNSAGGYPSPCYQPDRR 37 1 A0A087X0P4;P40424-2 A0A087X0P4 PBX1 Pre-B-cell leukemia transcription factor 1 1 TAVTATNVSAHGS(0.003)QANS(0.91)PS(0.039)T(0.039)PNS(0.009)AGGYPSPCYQPDRR 101.44 2.34E-05 63664000 5719.2 9409.2 4765 7322.4 8421.8 7798.5 8315.6 7500.6 9393.6 TRUE FALSE 5361.245481 10105.86696 4878.02805 7510.305181 7760.3858 10049.80035 7068.752978 8437.066421 7825.747475 0.685077751 1.291361239 0.623330623 0.959691736 0.991647868 1.284196862 0.903268729 1.078116365 1 12.93401284 2.681845258 3.769837946 1.056800269 0.911315771 0.140039444 0.200360684 0.55217271 16.01512985 0.064100298 0.061512547 480.6680523 -2.681845258 -0.145484497 TAWLDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TAWLDGK 7 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 101.28 0.021339 152110000 716430 774010 635780 591450 713710 498020 794030 671100 919630 FALSE TRUE 671589.9252 831318.5058 650861.0018 606627.6083 657658.0956 641790.2893 674972.5729 754888.3123 766137.812 0.876591541 1.085076983 0.849535151 0.791799594 0.858407045 0.83769562 0.881006736 0.985316611 1 19.5472444 -0.451263204 6.396120463 1.000000731 0.900260865 0.132334443 0.083216941 0 0 0.08469883 0.019963706 0.353782866 0.451263204 -0.099739865 TAWVFDDKYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TAWVFDDKYK 10 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ; 145.55 2.76E-05 658620000 1985600 1888070 1475870 1650140 2693700 963720 1680270 2118550 2948000 FALSE TRUE 1861324.84 2027864.667 1510878.333 1692485.386 2482147.668 1241930.319 1428329.112 2383055.631 2455959.755 0.757880839 0.825691326 0.615188555 0.689134007 1.010663006 0.50568024 0.581576758 0.970315424 1 21.22785549 1.195299352 11.31430404 0.986129606 0.706618504 0.398732757 0.139189107 0.770048584 196.0611846 0.131297165 0.033025235 15.67831377 -1.195299352 -0.279511103 TCAYTNHTVLPEALER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TCAYTNHTVLPEALER 16 0 P11216;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 0 ;;; 173.03 4.36E-09 609680000 646230 845770 766820 785810 803690 698760 926500 812760 890030 FALSE TRUE 605783.6179 908391.6908 785009.3325 805975.215 740571.4293 900480.6686 787579.9262 914234.8751 741478.2432 0.816994461 1.225109029 1.058708519 1.086984308 0.998777019 1.214439772 1.062175369 1.232989482 1 19.50004484 2.248806292 24.99440813 1.12796231 1.068098063 0.091399905 0.121182635 648.5278764 1582087.384 0.038822302 0.032138526 177.3398319 -2.248806292 -0.059864247 TCDISFSDPDDLLNFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TCDISFSDPDDLLNFK 16 0 P61081 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 225.13 1.67E-14 50074000 138210 100180 123850 118900 128180 95758 156010 121950 165100 FALSE TRUE 129559.6828 107597.4314 126787.7805 121951.1753 118113.2599 123401.7801 132617.7488 137175.7259 137543.7434 0.941952572 0.782277905 0.921799693 0.88663557 0.858732334 0.897182068 0.964185978 0.997324361 1 17.06953099 1.690750496 2.036834169 0.999195838 0.871140202 0.591524569 0.042110987 0.192084275 1.673772884 0.028886366 0.011500444 49.0625928 -1.690750496 -0.128055636 TCDSITPSKSS(ph)PVPVSDTQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TCDSITPSKSSPVPVSDTQK 20 1 Q76FK4-2;Q76FK4-4;Q76FK4;F8WE42;F5H101;F5GWN9 Q76FK4-2 NOL8 Nucleolar protein 8 1 TCDSITPSKS(0.038)S(0.962)PVPVSDTQK 178.35 3.77E-17 206030000 556900 310280 379160 378920 398890 262210 546080 323040 437260 TRUE FALSE 522044.6231 333253.454 388153.8543 388643.7287 367562.7884 337905.7704 464200.3736 363372.2551 364278.4812 1.433092126 0.914831568 1.065541541 1.066886321 1.009015924 0.927602886 1.274300837 0.997512271 1 18.47468225 -2.948278539 9.875490584 1.004893167 1.070013351 0 0.160495911 0 0 0 0.032178772 0.001126475 2.948278539 0.065120184 TCEERPAEDGS(ph)DEEDPDSMEAPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 TCEERPAEDGSDEEDPDSMEAPTR 24 1 Q9H6Y2;D6RGJ8 Q9H6Y2 WDR55 WD repeat-containing protein 55 1 TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR;TCEERPAEDGS(1)DEEDPDSMEAPTR 292.37 4.61E-62 23006560000 6837310 6783350 6911880 6773240 6808530 5407350 7902300 6087950 7124630 TRUE FALSE 6409374.972 7285596.292 7075833.058 6947052.805 6273815.518 6968364.164 6717423.476 6848043.959 5935483.226 1.079840466 1.227464726 1.192124177 1.170427502 1.057001642 1.174018003 1.131739948 1.153746662 1 22.50093406 -5 0.191723333 0.307237644 1.185955236 0.434293584 0.051510496 117.5473606 1.153106301 31.00897174 0.132399472 1.00E-05 5 0.878717592 TCEESSFCKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TCEESSFCKR 10 1 Q14697;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 239.54 4.88E-12 2515820000 1488240 1825440 1570900 1620130 2139310 1123490 2005000 1580380 2488000 FALSE TRUE 1395093.715 1960597.477 1608162.49 1661705.279 1971297.222 1447823.325 1704368.864 1777693.922 2072736.727 0.673068459 0.945897977 0.775864329 0.801696258 0.951060111 0.698508067 0.822279473 0.857655436 1 20.98310545 0.830218869 3.182605909 0.999922205 0.819356459 0.305801785 0.089181961 1.031576095 17.07561003 0.07709193 0.020067997 6.764237824 -0.830218869 -0.180565746 TCFS(ph)PNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TCFSPNR 7 0 O00303 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 1 TCFS(1)PNR;T(0.008)CFS(0.992)PNR 80.455 0.031329 174910000 431790 612170 418980 439890 674170 307580 447630 579540 573570 TRUE FALSE 404765.0347 657495.7038 428918.4035 451178.3221 621223.4077 396373.3529 380512.0371 651896.8447 477837.4616 0.847076814 1.375981911 0.897624062 0.944208771 1.300072635 0.829515023 0.796321067 1.364264833 1 18.86616044 2.208827998 24.9974054 0.955418911 1.084542148 0.010702085 0.224281252 589.8098059 495873.3709 0.08006807 0.059142109 161.7439326 -2.208827998 0.129123237 TCFSLHLDGNVLDHFSELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TCFSLHLDGNVLDHFSELR 19 0 K7EIG1;A0A494C0R8;O75153;I3L2B0;I3L318 K7EIG1 CLUH Clustered mitochondria protein homolog 0 197.21 4.62E-16 19554000 13198 30659 25041 27777 33063 27109 33204 26932 26827 FALSE TRUE 12371.96074 32929.02426 25634.98435 28489.80485 30466.36535 34934.92822 28225.36845 30294.51948 22349.40039 0.553570142 1.473373947 1.147009937 1.274745825 1.36318491 1.563125973 1.262913902 1.35549585 1 14.44794851 4.745666153 24.98945234 1.319036273 0.553569783 0.691532522 0.157468486 446.7451165 1571118.187 0.034063195 0.347103529 55675.75987 -4.745666153 -0.765466489 TCFVDCLIEQTHPEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TCFVDCLIEQTHPEIR 16 0 Q15029;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;; 179.81 2.57E-09 909110000 272196 301272 290898 300090 357137 297870 368005 281691 291227 FALSE TRUE 255159.7382 323578.4924 297798.2379 307790.8175 329088.9006 383860.2335 312826.0666 316860.7414 242619.3323 1.051687579 1.333688001 1.227429962 1.268616208 1.356400158 1.582150234 1.28936991 1.305999561 1 17.88833499 4.741353553 23.90228089 1.313596902 1.051687399 0.215418262 0.142514076 196.5209948 1681674.073 0.031197621 0.213959169 55125.62838 -4.741353553 -0.261909503 TCLS(ph)PGSSEMSLQPDLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TCLSPGSSEMSLQPDLVR 18 0 Q6UB98-2;Q6UB98 Q6UB98-2 ANKRD12 Ankyrin repeat domain-containing protein 12 1 T(0.05)CLS(0.907)PGS(0.036)S(0.007)EMSLQPDLVR 122.01 9.17E-05 0 19227 23076 21944 21229 21873 22561 21485 13439 20935 TRUE FALSE 18023.61639 24784.57105 22464.52204 21773.77208 20155.18281 29073.99445 18263.52371 15116.88873 17440.81325 1.033416053 1.421067395 1.288043265 1.248437889 1.155633199 1.667009103 1.047171565 0.866753661 1 14.09017969 1.538607337 7.468838082 0.942000083 1.309906047 0.472308093 0.167867172 0.093520189 9.558675051 0.082686643 0.038286638 34.56267413 -1.538607337 0.367905964 TCNS(ph)PQNSTDSVSDIVPDSPFPGALGSDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TCNSPQNSTDSVSDIVPDSPFPGALGSDTR 30 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 T(0.2)CNS(0.595)PQNS(0.197)T(0.009)DSVSDIVPDSPFPGALGSDTR 156.96 2.18E-09 147060000 80035 73200 67435 79623 70854 61036 98851 71427 73061 TRUE FALSE 75025.75222 78619.80416 69034.59005 81666.26098 65289.41265 78656.10236 84029.21024 80344.81818 60866.64711 1.232625022 1.291672992 1.134194067 1.341724325 1.072663203 1.292269348 1.380546066 1.320013866 1 15.89336428 TCNSPQNS(ph)TDSVSDIVPDSPFPGALGSDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TCNSPQNSTDSVSDIVPDSPFPGALGSDTR 30 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 T(0.025)CNS(0.231)PQNS(0.705)T(0.039)DSVSDIVPDSPFPGALGSDTR;T(0.095)CNS(0.33)PQNS(0.546)T(0.023)DS(0.005)VSDIVPDSPFPGALGSDTR;T(0.047)CNS(0.216)PQNS(0.723)T(0.015)DSVSDIVPDSPFPGALGSDTR 194.64 2.51E-19 458660000 255424 257916 264169 244266 253154 208587 310943 214133 263002 TRUE FALSE 239437.4678 277012.369 270435.2134 250534.2791 233272.306 268802.6808 264319.9838 240867.9764 219105.2671 1.092796494 1.264288954 1.234270709 1.143442521 1.064658596 1.226819803 1.206360702 1.099325359 1 17.74126464 -2.222704098 0.255924603 0.763094383 1.207427817 0.373497232 0.067199679 36.57241568 1.272252992 5.064704434 0.100571036 0.005988195 2.222704098 0.444333435 TCNTNPHLNALSTDSACRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TCNTNPHLNALSTDSACRR 19 1 Q9NZB2;Q9NZB2-4;Q9NZB2-6;A0A0C4DG79 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 95.414 0.00093499 67676000 31078 93107 63242 62337 86442 94479 53704 67948 69750 FALSE TRUE 29132.88346 100000.7392 64742.13011 63936.67296 79653.19401 121753.5536 45651.58376 76431.45737 58108.2744 0.501355164 1.720938028 1.114163702 1.100302386 1.370771974 2.095287716 0.785629658 1.315328293 1 15.82645599 1.626952687 25 1.037781766 1.341643511 0.085915844 0.430869564 1.960696216 2561.776493 0.183700799 0.101659989 42.35968163 -1.626952687 0.303861745 TCNVLVALEQQS(ph)PDIAQGVHLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TCNVLVALEQQSPDIAQGVHLDR 23 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 1 TCNVLVALEQQS(1)PDIAQGVHLDR;TCNVLVALEQQS(1)PDIAQGVHLDR 114.06 0.0001253 87685000 81917 70736 81391 80905 77082 69211 88796 74362 88606 TRUE FALSE 76789.9612 75973.36704 83321.63296 82981.15927 71028.29065 89191.09215 75481.86414 83646.25939 73817.08618 1.040273535 1.029211135 1.128758087 1.12414569 0.962220189 1.208271645 1.022552746 1.133155801 1 16.17166717 4.184814285 5.930424961 1.085498511 1.034657673 0.069278284 0.072458059 0.433507159 39.30167454 0.015830149 0.03601914 15304.3287 -4.184814285 -0.050840838 TCNVLVALEQQSPDIAQGVHLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TCNVLVALEQQSPDIAQGVHLDR 23 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ; 244.98 1.76E-37 870690000 512150 512370 542220 510680 538870 475620 645610 499720 531930 FALSE TRUE 480095.4457 550306.4079 555081.7145 523784.9134 496549.3239 612923.773 548806.774 562111.142 443147.4466 1.083376311 1.241813334 1.25258922 1.18196532 1.12050589 1.383114757 1.238429282 1.268451723 1 18.75742727 -1.113150298 5.163337813 0.999993947 1.229643381 0.411721814 0.082589754 5.35E-06 9.18E-07 0.074292316 0.017510405 0.077063673 1.113150298 0.229649434 TCPSLSPTS(ph)PLNNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TCPSLSPTSPLNNK 14 0 O75925;O75925-2 O75925 PIAS1 E3 SUMO-protein ligase PIAS1 1 TCPSLSPT(0.014)S(0.986)PLNNK 218.68 4.13E-08 0 200940 144860 178500 159970 167870 130430 233960 149480 201040 TRUE FALSE 188363.5241 155585.5851 182734.1043 164075.101 154686.1674 168083.0236 198879.87 168142.907 167485.1252 1.124658228 0.92895166 1.091046766 0.979639838 0.923581525 1.00356986 1.187447958 1.003927404 1 17.35367345 1.888011758 22.64300469 1.087346301 1.004503569 0.067981537 0.081248145 18.51127058 3716.182208 0.030945356 0.019968676 77.27015043 -1.888011758 -0.082842732 TCS(ph)FGGFDLTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 TCSFGGFDLTNR 12 0 O94885;A0A1B0GWB9 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 T(0.005)CS(0.995)FGGFDLTNR;TCS(1)FGGFDLTNR;TCS(1)FGGFDLTNR;TCS(1)FGGFDLTNR;TCS(1)FGGFDLTNR;TCS(1)FGGFDLTNR;TCS(1)FGGFDLTNR 277.79 6.89E-28 2155382000 2793919 3182810 2404625 2670476 3088005 1507737 3469600 2552052 3875761 TRUE FALSE 2619052.597 3418468.564 2461663.841 2739004.935 2845485.544 1942996.196 2949365.69 2870681.31 3228871.451 0.811135605 1.058719313 0.762391405 0.848285532 0.881263187 0.601757061 0.913435464 0.88906646 1 21.62259857 5.090335367 13.25520631 0.862638077 0.000247064 0.018687502 0.124390146 8946616.177 26534482.07 0.028399622 216955319.2 123121.9166 -5.090335367 -0.862391013 TCS(ph)LPDLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TCSLPDLSK 9 0 Q96PY6-4;Q96PY6-2;Q96PY6-6;Q96PY6;Q96PY6-3 Q96PY6-4 NEK1 Serine/threonine-protein kinase Nek1 1 TCS(1)LPDLSK 96.24 0.005391 0 597720 465540 518380 501200 537750 328330 729980 450370 825010 TRUE FALSE 560309.7722 500009.066 530676.2184 514061.6405 495517.2842 423113.541 620526.2758 506599.6859 687310.5012 0.815220735 0.727486435 0.7721055 0.747932179 0.720951132 0.615607561 0.902832526 0.737075434 1 19.39060248 0.384798256 0.815185316 1.001454432 0.745925302 0.523196406 0.073109226 1.654513136 1.531199086 0.074063968 0.022650532 2.425483117 -0.384798256 -0.25552913 TCTDIKPEWLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TCTDIKPEWLVK 12 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 80.469 0.012973 0 253720 194720 220540 213840 216310 139270 265520 197890 313090 FALSE TRUE 237840.1181 209137.2714 225771.3129 219327.4964 199321.8852 179474.9881 225707.741 222597.0021 260833.2564 0.911847367 0.801804472 0.865577174 0.840872439 0.764173587 0.688083225 0.865333448 0.853407289 1 17.9927683 0.768600487 1.87331556 0.999450776 0.816718486 0.461971188 0.06108542 0.766511039 4.433548416 0.056950105 0.015926625 5.869491623 -0.768600487 -0.18273229 TCVQEITAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TCVQEITAHR 10 0 F5GYK2;Q9NRL3;Q9NRL3-3;M0R317;Q13033-2;Q13033 F5GYK2;Q13033-2 STRN4;STRN3 Striatin-4;Striatin-3 0 ; 103.43 0.0045612 310300000 208829 321380 338420 245600 291210 235594 263080 279020 298650 FALSE TRUE 195758.7657 345175.3096 346447.4822 251902.5118 268339.5413 303606.1633 223633.5963 313856.2612 248803.3856 0.786801052 1.38734169 1.392454855 1.012456125 1.078520457 1.220265401 0.898836629 1.261462984 1 17.92464659 3.224406096 24.99978889 1.071392484 1.260480562 0.023746217 0.198485927 395.8616766 699171.8095 0.054707111 0.0656826 1676.509797 -3.224406096 0.189088078 TDAGFTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDAGFTLR 8 0 P18206;P18206-2 P18206 VCL Vinculin 0 96.492 0.020795 0 149460 182680 162650 154440 205050 143820 180230 165320 178620 FALSE TRUE 140105.5654 196205.8173 166508.1348 158403.1919 188946.2001 185338.4993 153206.1847 185960.5659 148807.1681 0.941524304 1.318523965 1.11895238 1.064486301 1.269738566 1.245494432 1.02956186 1.249674786 1 17.1830845 -1.468573812 3.432857127 0.997586617 1.161185277 0.140493634 0.119344358 385085531.1 883142303.2 9962498.433 0.026242992 0.033995872 1.468573812 0.16359866 TDCEPVGLEPAVEQSSAASELAEASSEELAEAPTEAPS(ph)PEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TDCEPVGLEPAVEQSSAASELAEASSEELAEAPTEAPSPEAR 42 0 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 TDCEPVGLEPAVEQSSAASELAEASSEELAEAPTEAPS(1)PEAR;TDCEPVGLEPAVEQSSAASELAEASSEELAEAPT(0.001)EAPS(0.999)PEAR 272.25 1.97E-80 66336000 121187 117586 120916 118788 131697 109618 142582 100648 142296 TRUE FALSE 113602.122 126292.1898 123784.1846 121836.3012 121354.0489 141262.9371 121203.1528 113214.1244 118545.8783 0.958296683 1.065344418 1.044188009 1.027756535 1.02368847 1.191630946 1.022415578 0.955023709 1 16.85508598 1.473154237 25 0.981246652 1.05520932 0.210906626 0.058702318 0.885320941 5581.015535 0.029730483 0.013763506 29.7272159 -1.473154237 0.073962667 TDDEVVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TDDEVVQR 8 0 P14625;Q96GW1;A0A1W2PRR1;F8VPC7 P14625 HSP90B1 Endoplasmin 0 ; 201.49 0.00026301 308900000 872980 805480 800500 860390 722580 714470 975990 634660 496740 FALSE TRUE 818341.7401 865118.5773 819488.238 882469.064 665831.4815 920725.8905 829649.3601 713898.6981 413830.8849 1.977478651 2.090512354 1.980249101 2.132438869 1.608945842 2.224884425 2.004802905 1.725097676 1 18.65868179 0.857690736 2.636803429 1.000771196 2.010968372 0.795341888 0.160338834 0.21650391 2.886336519 0.137622008 0.036644233 7.205941571 -0.857690736 1.010197176 TDDEVVQREEEAIQLDGLNASQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TDDEVVQREEEAIQLDGLNASQIR 24 1 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 ;;;;; 397.8 6.92E-138 2078910000 1119887 1486273 1179364 1456850 1617120 739040 1277852 1046908 1331017 FALSE TRUE 1049795.272 1596318.199 1207339.071 1494235.237 1490117.918 952388.8507 1086249.956 1177616.768 1108861.664 0.946732407 1.439600855 1.088809461 1.347539811 1.343826707 0.858888788 0.979608179 1.062005123 1 20.08064796 2.240344392 24.99992191 0.969997928 1.246922666 0.431795813 0.146650089 39.59383036 554924.3772 0.048161597 0.038373926 173.9179435 -2.240344392 0.276924739 TDDIPVWDQEFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDDIPVWDQEFLK 13 0 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2;E5RGM3 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 147.26 9.93E-05 19108000 64299 58694 57611 51592 68703 48430 70787 58031 65678 FALSE TRUE 60274.64037 63039.76483 58977.56013 52915.93807 63307.34351 62410.9548 60173.1465 65276.29809 54715.9175 1.101592427 1.152128443 1.077886707 0.967103185 1.157018769 1.140636174 1.099737503 1.193003811 1 15.73967297 TDDVHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TDDVHAK 7 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;; 105.95 0.0078123 755720000 3136760 2002180 2597520 2437080 2446960 1783940 2764840 2205310 3015500 FALSE TRUE 2940435.791 2150423.49 2659134.401 2499619.599 2254785.632 2298934.518 2350277.91 2480647.808 2512193.569 1.170465456 0.855994346 1.058491047 0.994994824 0.897536583 0.915110422 0.935548096 0.987442942 1 21.2605162 2.856128409 8.47135129 0.939990681 0.999462714 0.13811563 0.082736338 0.688423837 45.77838584 0.023593349 0.025047911 718.0065548 -2.856128409 0.059472033 TDDYLDQPCYETINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TDDYLDQPCYETINR 15 0 P50395;P50395-2;Q5SX87;Q5SX91 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;; 398.14 1.15E-114 3416490000 2723810 2791040 2659080 2549560 2825260 2062260 3144500 2475910 3011260 FALSE TRUE 2553331.594 2997691.506 2722154.633 2614986.026 2603375.476 2657600.984 2673011.417 2785032.814 2508661.253 1.017806446 1.194936743 1.085102515 1.042383073 1.037754888 1.059370204 1.065513096 1.110166951 1 21.25848624 3.513880154 4.315990307 1.056436601 1.124655403 0.144550221 0.050638891 0.258419572 10.6296427 0.012701811 0.019435779 3264.977212 -3.513880154 0.068218802 TDEAAFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TDEAAFQK 8 0 P26447 P26447 S100A4 Protein S100-A4 0 ; 143.12 0.0014111 655370000 933280 836240 759970 843350 983310 627320 984950 810710 1312120 FALSE TRUE 874867.6708 898156.0797 777996.8473 864991.7888 906084.7991 808417.1003 837265.8913 911928.9281 1093118.695 0.800340964 0.821645521 0.711722204 0.791306372 0.828898822 0.73955107 0.76594234 0.834245112 1 20.06001863 0.864145415 3.281077951 0.999916363 0.777127898 0.791906585 0.035395298 0.261478873 5.27271423 0.033782861 0.008772681 7.313839318 -0.864145415 -0.222788465 TDEFPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TDEFPR 6 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ; 133.95 0.033135 536420000 711860 717320 714740 703130 784700 597370 735540 631740 933140 FALSE TRUE 667305.9533 770431.1192 731693.9703 721173.5062 723072.8273 769821.0215 625252.6054 710614.1296 777392.9057 0.858389559 0.9910447 0.941215137 0.927682129 0.930125323 0.990259901 0.8042942 0.914099067 1 19.56828442 1.763198365 25 0.885679104 0.945028435 0.025200943 0.060284222 23.52845475 23891.07973 0.024935503 0.013828429 57.96934125 -1.763198365 0.059349331 TDEGHPFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TDEGHPFK 8 0 A8MT72;Q2NKQ5;Q16799-3;Q16799-2;Q16799 A8MT72 RTN1 Reticulon;Reticulon-1 0 ;;; 95.099 0.0098907 2671040000 4764750 4181570 4559870 3935410 4760480 3952750 5720700 5088400 7538700 FALSE TRUE 4466532.803 4491177.794 4668032.27 4036399.283 4386611.104 5093844.757 4862934.143 5723697.941 6280442.268 0.711181253 0.715105338 0.743264896 0.642693478 0.698455764 0.811064658 0.774298041 0.911352688 1 22.58243473 1.218583519 1.022554755 1.001894564 0.709326474 0.879144686 0.037087807 0.153841544 0.339257543 0.033692841 0.011477608 16.54182871 -1.218583519 -0.29256809 TDEGIAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TDEGIAYR 8 0 P32119 P32119 PRDX2 Peroxiredoxin-2 0 ; 151.29 0.0011062 3818000000 4305690 5927270 5498440 5596860 5747180 5184060 6104830 5021020 5198090 FALSE TRUE 4036204.549 6366131.238 5628865.593 5740484.903 5295819.666 6680613.966 5189467.416 5647905.4 4330495.198 0.932042264 1.470070037 1.299820306 1.32559549 1.222913183 1.542690538 1.198354271 1.304216987 1 22.04610058 -0.810854977 6.541263577 1.000000002 1.307089178 0.224221891 0.16399302 1.04E-08 1.90E-09 0.138945355 0.032749734 0.154577053 0.810854977 0.307089177 TDEVPAGGS(ph)RS(ph)EAEDEDDEDYVPYVPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDEVPAGGSRSEAEDEDDEDYVPYVPLR 28 1 Q9UJV9;D6RGI7;A0A499FJW5;D6RD33 Q9UJV9 DDX41 Probable ATP-dependent RNA helicase DDX41 2 TDEVPAGGS(1)RS(1)EAEDEDDEDYVPYVPLR 135.82 5.51E-06 96536000 112120 100060 96620 83841 76176 49000 102910 81453 98848 TRUE FALSE 105102.6093 107468.5465 98911.87203 85992.502 70193.44424 63145.50455 87479.60087 91622.58635 82349.63022 1.276297283 1.305027676 1.201121022 1.04423665 0.852383235 0.76679767 1.062295005 1.112604709 1 16.32947455 3.24332559 2.470864804 0.95441356 1.276520017 0.66821477 0.098223359 0.167534789 2.084211333 0.031258655 0.04243516 1751.15904 -3.24332559 0.322106457 TDFEEFFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TDFEEFFLR 9 0 B1AKV2;B1AKV6;B1AKV3;Q9NVA1-5;Q9NVA1-2;Q9NVA1 B1AKV2 UQCC1 Ubiquinol-cytochrome-c reductase complex assembly factor 1 0 ;;;;; 218.63 1.22E-06 191344000 302447 314833 244243 245125 386247 219343 221448 307552 400562 FALSE TRUE 283517.3822 338143.5629 250036.5593 251415.3225 355912.7187 282663.7634 188243.9282 345950.5442 333705.6145 0.849603273 1.013298992 0.749272857 0.753404533 1.06654699 0.847045273 0.564101771 1.036693808 1 18.34821643 1.993201972 24.9557401 0.790267428 0.885462172 0 0.164070172 887.9989934 3259871.016 0.060097561 0.042730254 98.44688347 -1.993201972 0.095194744 TDFKEEPEPGFKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TDFKEEPEPGFKR 13 2 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RRC8 P47897 QARS Glutamine--tRNA ligase 0 ;; 123.02 0.0001284 966580000 2863540 1744790 2240750 2257380 2359750 1482820 3118800 1893900 3861900 FALSE TRUE 2684316.143 1873976.067 2293901.648 2315308.193 2174424.754 1910886.062 2651164.894 2130357.584 3217323.941 0.834331945 0.582464216 0.712984359 0.719637884 0.675848871 0.593936482 0.824027963 0.662152032 1 21.61742977 -0.741105499 0.491182805 1.075985901 0.682881228 0.549108921 0.083957905 8.99847785 1.611675663 1.142182608 0.0378142 0.181507469 0.741105499 -0.393104673 TDGCHAYLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TDGCHAYLSK 10 0 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 0 ;;; 160.33 7.41E-06 4072780000 14725600 14685000 13064300 12851000 16433100 9064200 15674400 13912900 16153600 FALSE TRUE 13803950.98 15772292.68 13374191.37 13180778.42 15142510.61 11680887.4 13324169.23 15649956.19 13457459.8 1.025747146 1.172011131 0.99381247 0.979440296 1.125213141 0.867986051 0.990095414 1.162920523 1 23.68190278 3.825744243 4.955301778 1.009381635 1.104866318 0.124383684 0.087823513 0.343968703 13.56826091 0.021298323 0.039266691 6694.90229 -3.825744243 0.095484683 TDGEPGPQGWSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDGEPGPQGWSPR 13 0 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 130.56 4.30E-05 0 47810 46793 48242 50546 59036 39551 60790 49178 54317 FALSE TRUE 44817.65744 50257.60241 49386.32302 51843.09593 54399.5507 50968.73164 51675.10385 55317.98155 45251.1418 0.990420477 1.110637222 1.091382915 1.145674869 1.202169681 1.126352388 1.14196243 1.222465983 1 15.46566657 6.146786261 0.735183369 1.1434792 9.63E-10 0.332872885 0.061039843 19.47630209 1.561176504 0.019342733 29.24381112 1402123.477 -6.146786261 -1.143479199 TDGFAEAIHS(ph)PQVAGVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 250.81 2.70E-25 8540743000 2795550 2655700 3532110 5150960 5856010 2526520 2061580 1444239 2062750 TRUE FALSE 2620581.516 2852330.791 3615893.317 5283142.354 5396102.597 3255885.309 1752465.218 1624555.418 1718463.699 1.524955992 1.659814399 2.104142973 3.074340387 3.14007366 1.894648872 1.019785998 0.945353352 1 20.71268795 1.801396145 3.740790154 0.978212789 2.238633496 0.569853179 0.517008804 0.192159053 4.867549531 0.298966875 0.1562802 63.29889733 -1.801396145 1.260420708 TDGS(ph)IS(ph)GDRQPVTVADYISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TDGSISGDRQPVTVADYISR 20 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 2 T(0.002)DGS(0.998)IS(1)GDRQPVTVADYISR;TDGS(1)IS(1)GDRQPVTVADYISR;T(0.003)DGS(0.997)IS(1)GDRQPVTVADYISR;TDGS(1)IS(1)GDRQPVTVADYISR;T(0.004)DGS(0.996)IS(1)GDRQPVTVADYISR 182.41 2.70E-17 2977350000 3076470 2255460 2672730 2635980 2731080 2244230 3328910 2428650 3658860 TRUE FALSE 2883919.234 2422456.605 2736128.418 2703623.71 2516591.993 2892102.769 2829770.85 2731872.299 3048172.629 0.946114143 0.794724217 0.897629088 0.886965418 0.825606781 0.948798878 0.928349931 0.896232803 1 21.53951318 1.121750684 0.426363995 1.002399562 0.856810725 0.35834158 0.047803604 1.052114315 0.535629851 0.059339406 0.033708986 13.23581487 -1.121750684 -0.145588838 TDGS(ph)ISGDRQPVT(ph)VADYISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDGSISGDRQPVTVADYISR 20 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 2 T(0.01)DGS(0.99)IS(0.152)GDRQPVT(0.847)VADYIS(0.001)R 169.85 2.55E-10 78304000 205190 176980 205480 189100 201700 164050 239850 165040 258420 TRUE FALSE 192347.5242 190083.7833 210354.0826 193952.6261 185859.2956 211408.5719 203886.7192 185645.6073 215288.0325 0.893442714 0.882927774 0.977082099 0.900898317 0.863305282 0.981980138 0.947041583 0.862312712 1 17.7159086 -5 0.234646093 1.430942819 0.911241376 0.255517666 0.043736208 250.8384303 2.508001935 51.67484334 0.070811886 1.00E-05 5 -0.519701443 TDGS(ph)ISGDRQPVTVADYISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TDGSISGDRQPVTVADYISR 20 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 TDGS(0.999)IS(0.001)GDRQPVTVADYISR;TDGS(0.999)IS(0.001)GDRQPVTVADYISR;TDGS(0.999)IS(0.001)GDRQPVTVADYISR;TDGS(0.991)IS(0.009)GDRQPVTVADYISR;TDGS(0.998)IS(0.002)GDRQPVTVADYISR;T(0.001)DGS(0.999)ISGDRQPVTVADYISR 296.55 7.43E-55 3341040000 1984600 1773710 1995400 1940710 2049610 1415540 2451850 1791370 2681500 TRUE FALSE 1860387.429 1905037.334 2042731.83 1990511.904 1888641.898 1824183.419 2084217.854 2015026.488 2233940.327 0.832782956 0.852770019 0.914407518 0.891031815 0.845430773 0.81657661 0.932978303 0.902005512 1 21.09115922 0.920854303 1.147684056 0.997786825 0.867374816 0.612111778 0.033904358 0.41656095 1.110422368 0.032259169 0.010153837 8.334015489 -0.920854303 -0.130412009 TDIELEIYGMEGIPEKDMDER ddPTM_SK-BR-3_Pertuzumab_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 0 155.87 1.85E-08 42026000 170250 118310 139340 127960 126760 96426 158530 124950 162020 FALSE TRUE 159594.3564 127069.7955 142645.2106 131243.6702 116804.7809 124262.6209 134759.8982 140550.2825 134977.8153 1.182374719 0.941412448 1.056804855 0.97233512 0.865362805 0.920615144 0.998385534 1.041284319 1 17.04236278 4.744320354 24.80453681 0.975188958 1.182374819 0.575072986 0.056147134 448.4961169 1931403.324 0.013767227 0.122264094 55503.49788 -4.744320354 0.20718586 TDKTLVLLMGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDKTLVLLMGK 11 1 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 126.1 0.0010405 0 582110 752660 639440 710760 1073800 435820 744210 660790 981490 FALSE TRUE 545676.7742 808387.7295 654607.8188 728999.3049 989468.0795 561634.1591 632622.6194 743291.0861 817672.9783 0.667353317 0.9886443 0.800574112 0.891553621 1.210102456 0.686868924 0.773686591 0.909032224 1 19.64116444 -4.707153745 14.95744391 0.998173471 0.874138942 0 0.162165071 0 0 0 0.03344083 1.96E-05 4.707153745 -0.12403453 TDKVDFDSAEDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TDKVDFDSAEDTR 13 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 0 ; 112.96 0.00078366 396300000 1070150 802730 904110 950620 970500 682980 1168450 827660 1219070 FALSE TRUE 1003171.222 862164.9644 925555.9162 975014.5186 894280.8448 880145.2387 993251.7699 930995.1729 1015599.342 0.987762773 0.848922335 0.911339618 0.960038549 0.880544924 0.866626437 0.977995681 0.916695329 1 19.95389993 0.953209092 0.843599093 0.997679655 0.905092316 0.217484658 0.046583735 0.896970966 1.38646375 0.04185055 0.014894585 8.978609668 -0.953209092 -0.092587339 TDKVFEVMLATDR ddPTM_SK-BR-3_Pertuzumab_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 ; 173.03 2.04E-05 431390000 917470 969790 781760 809690 1103370 553750 1121520 844670 1852000 FALSE TRUE 860047.1904 1041594.261 800303.7164 830468.0162 1016715.771 713608.6356 953358.4877 950128.9088 1542889.236 0.557426399 0.675093349 0.518704582 0.538255111 0.658968737 0.462514495 0.617904685 0.615811483 1 20.55720306 0.468593282 1.687180379 0.999968292 0.577209137 0.814008988 0.06334568 1.433738613 4.117289703 0.055972607 0.015830585 2.941665463 -0.468593282 -0.422759155 TDLCDHALHISHDEL ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TDLCDHALHISHDEL 15 0 Q9Y2B0;H0YI18 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;;; 255.16 5.92E-25 1017870000 451784 945680 813910 863310 897350 719450 970820 822320 845830 FALSE TRUE 423507.6459 1015699.131 833216.3296 885463.9962 826875.7507 927143.5357 825254.5537 924988.4621 704655.5087 0.601013745 1.441412319 1.182444924 1.25659132 1.173446798 1.315740137 1.171146104 1.312681801 1 19.4265586 4.749603623 24.81882347 1.244766564 0.601013331 0.741525005 0.116790547 680.929301 1530335.866 0.024800201 0.375034669 56182.83144 -4.749603623 -0.643753233 TDLEKDIISDTSGDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 195.92 4.31E-11 428828000 1317830 977374 1058309 946474 1431390 487015 1323600 1144585 2944650 FALSE TRUE 1235349.373 1049739.788 1083412.589 970762.1252 1318974.403 627608.3245 1125138.468 1287488.957 2453168.892 0.5035729 0.427911748 0.441637994 0.395717608 0.537661474 0.255835759 0.458646965 0.524826872 1 21.22621513 0.719109414 2.292486046 0.999817839 0.427530222 0.851705006 0.07403124 0.450547096 3.206782906 0.063424954 0.017155145 5.23732367 -0.719109414 -0.572287616 TDLEKDIISDTSGDFRK ddPTM_SK-BR-3_Pertuzumab_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 ; 146.76 2.39E-07 268426000 550970 401000 424490 387670 595580 228830 563230 436250 1332630 FALSE TRUE 516485.7712 430690.4572 434559.1033 397618.2685 548805.5493 294889.5063 478778.8903 490716.7728 1110205.444 0.465216392 0.38793762 0.391422241 0.358148369 0.494327921 0.26561706 0.431252515 0.442005374 1 20.08239524 0.466388465 1.863251455 0.99997828 0.394125819 0.902945507 0.061522299 1.160861339 3.760744525 0.051416822 0.014300188 2.926769124 -0.466388465 -0.605852461 TDLFYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDLFYER 7 0 Q7RTV0 Q7RTV0 PHF5A PHD finger-like domain-containing protein 5A 0 96.492 0.029528 100360000 117130 181580 114980 109490 200730 76030 102300 165440 179060 FALSE TRUE 109799.0424 195024.3721 117707.3799 112299.6988 184965.4755 97978.62676 86961.06471 186095.5482 149173.7292 0.736048116 1.307364059 0.789062394 0.752811499 1.239933308 0.656808858 0.582951604 1.247508855 1 17.18663396 2.211024644 24.99661381 0.8033995 0.978079817 0 0.26415891 541.6897957 491732.0325 0.094766885 0.070005841 162.5640999 -2.211024644 0.174680317 TDLLVNDNPDPAPLS(ph)PELQDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TDLLVNDNPDPAPLSPELQDFK 22 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 TDLLVNDNPDPAPLS(1)PELQDFK;TDLLVNDNPDPAPLS(1)PELQDFK;TDLLVNDNPDPAPLS(1)PELQDFK 171.07 4.15E-12 165628000 324979 172641 219050 215967 167033 161297 258967 147019 136038 TRUE FALSE 304639.1445 185423.5193 224245.9694 221509.0789 153914.902 207860.8255 220137.3025 165374.6458 113332.379 2.688015087 1.636103653 1.978657569 1.954508331 1.358084101 1.834081552 1.94240432 1.459200339 1 16.79020057 -0.721168454 0.103826058 4.91E-21 2.620667915 0.540375177 0.305755026 40.89748435 0.962871884 18.83008889 6.625689462 0.190034103 0.721168454 2.620667915 TDLQGS(ph)ASPSKVEGVHTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDLQGSASPSKVEGVHTPR 19 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 T(0.003)DLQGS(0.484)AS(0.484)PS(0.029)KVEGVHTPR 59.943 0.038022 0 33391 60880 63074 78518 83381 43237 69544 48936 76920 TRUE FALSE 31301.11691 65387.61855 64570.14507 80532.90481 76832.5926 55718.82001 59116.52281 55045.76732 64081.55508 0.488457511 1.02038127 1.007624503 1.256725195 1.1989814 0.869498562 0.922520103 0.858995498 1 15.96762154 -2.962427954 9.118267198 1.013085965 0.974205898 0 0.210056993 71419360.29 23203388.3 0 0.045557625 0.001090365 2.962427954 -0.038880066 TDLQGSAS(ph)PSKVEGVHTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TDLQGSASPSKVEGVHTPR 19 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 TDLQGSAS(0.999)PS(0.001)KVEGVHTPR;TDLQGSAS(0.998)PS(0.002)KVEGVHTPR 251.34 3.50E-26 1167580000 1114770 876750 936990 886430 937890 707720 1185670 782550 1074510 TRUE FALSE 1044998.536 941665.4823 959215.8453 909177.2945 864231.9027 912027.2751 1007889.791 880253.0901 895167.3394 1.167377863 1.05194352 1.071549199 1.015650655 0.965441728 1.018834396 1.125923329 0.983339149 1 19.77179787 7.999994135 0.961434778 1.034028785 101.2568542 0.466201859 0.046193952 1363.105367 2.179677433 0.014158001 300616.8319 99998649.5 -7.999994135 100.2228254 TDMDNQIVVSDYAQMDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TDMDNQIVVSDYAQMDR 17 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ; 329.11 1.39E-71 234150000 262080 237036 239320 261100 255100 197278 291380 235139 242960 FALSE TRUE 245676.8806 254586.3921 244996.7834 267800.268 235065.475 254228.9561 247690.274 264496.6218 202408.4064 1.213768168 1.257785665 1.210408143 1.323068902 1.161342452 1.25601975 1.223715351 1.306747217 1 17.62690968 -1.626170866 2.929442587 0.980612888 1.24141327 0.727005642 0.046984269 6005845.043 5559167.194 876759.0153 0.009603738 0.02364989 1.626170866 0.260800382 TDNAGDQHGGGGGGGGGAGAAGGGGGGENYDDPHKTPASPVVHIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TDNAGDQHGGGGGGGGGAGAAGGGGGGENYDDPHKTPASPVVHIR 45 1 P14866 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;; 236.43 1.55E-55 1559345000 229166 183040 201746 210597 221125 150394 277485 193741 259534 FALSE TRUE 214822.9091 196592.4721 206531.5104 216001.2756 203758.7345 193810.3064 235878.7003 217929.9903 216216.0987 0.993556495 0.909240677 0.955208755 0.999006442 0.942384659 0.896373154 1.090939582 1.007926753 1 17.72211442 1.739399879 25 1.038127537 0.947001762 0.496101349 0.039587557 0.091898717 2704.734571 0.017043594 0.009451498 54.87820267 -1.739399879 -0.091125775 TDNSECISSHCGTT(ph)SPSYTNTAFDVLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDNSECISSHCGTTSPSYTNTAFDVLLK 28 0 F5H212;P15822 F5H212 HIVEP1 Zinc finger protein 40 1 TDNSECISSHCGT(0.048)T(0.465)S(0.465)PS(0.018)Y(0.001)T(0.003)NTAFDVLLK 157.15 2.46E-08 94863000 42504 46128 49521 55081 58230 36772 51917 33585 30673 TRUE FALSE 39843.75051 49543.36512 50695.66151 56494.47171 53656.85069 47387.47946 44132.52782 37778.16118 25553.47814 1.559230031 1.938811024 1.983904548 2.210832959 2.099786588 1.854443422 1.727065395 1.478396051 1 14.64123205 1.06626371 1.226408217 1.00786338 1.966991229 0.769647566 0.168401767 0.208424642 0.647487462 0.155979723 0.048801196 11.64833119 -1.06626371 0.959127849 TDNSSLS(ph)SPLNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDNSSLSSPLNPK 13 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 TDNS(0.001)S(0.072)LS(0.63)S(0.296)PLNPK 135.14 9.17E-05 171210000 497380 308900 381550 353290 341860 292210 480910 298050 492740 TRUE FALSE 466249.8736 331771.2774 390600.5462 362356.0195 315011.6946 376566.2834 408802.01 335262.1986 410498.5108 1.135813801 0.808215545 0.951527316 0.882721886 0.767388154 0.917338976 0.995867218 0.816719646 1 18.64701746 -0.48480724 7.417179801 0.999999999 0.90616091 0.066949199 0.105604625 0 0 0.092221381 0.021736788 0.327486016 0.48480724 -0.093839088 TDNSSLSS(ph)PLNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TDNSSLSSPLNPK 13 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 TDNSS(0.001)LS(0.23)S(0.768)PLNPK;TDNSSLS(0.247)S(0.753)PLNPK;TDNSSLS(0.394)S(0.605)PLNPK 281.14 2.04E-32 522370000 1989710 1120800 1560360 1268440 1241650 1104090 1940920 1180610 1896050 TRUE FALSE 1865177.603 1203785.198 1597372.476 1300990.318 1144135.818 1422822.86 1649897.065 1328011.757 1579587.006 1.180800802 0.762088567 1.01125957 0.82362688 0.724325924 0.900756245 1.044511672 0.840733529 1 20.59111597 1.971759111 23.84506836 0.968179127 0.886460792 0.036132863 0.137839137 1115.347076 941735.6309 0.052483496 0.033975944 93.70421151 -1.971759111 -0.081718335 TDPTTLTDEEINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDPTTLTDEEINR 13 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" 0 177.44 3.59E-05 95152000 117830 86605 95227 86984 97978 65676 118410 70755 92152 FALSE TRUE 110455.2306 93017.32431 97485.82941 89216.1567 90283.2031 84635.59504 100655.5198 79588.9175 76771.23588 1.438758011 1.211616867 1.269822327 1.162103953 1.176002992 1.102438877 1.311109801 1.036702309 1 16.22827825 8 0.068387818 0.783926952 2.173996092 0.568751405 0.085237821 215.7285052 1.090863441 3.961715182 28.99497696 99999999.97 -8 1.39006914 TDPVPEEGEDVAATISATETLSEEEQEELRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 TDPVPEEGEDVAATISATETLSEEEQEELRR 31 1 H0YC42;P55327-8;H0YC44;P55327-2;P55327-4;P55327-3;E5RFR7 H0YC42;P55327-2 TPD52 0 ;;;;;;;; 329.14 2.04E-105 3643780000 223808.8 196892.6 178038.5 191206.6 187832.6 128756.9 197841.2 149231.6 225153.8 FALSE TRUE 209801.0067 211470.733 182261.6573 196113.2851 173080.9853 165926.9268 168176.7487 167863.4938 187574.1762 1.118496218 1.127397903 0.97167777 1.045523904 0.922733549 0.884593659 0.896587964 0.894917931 1 17.5171017 3.611617345 0.743414317 0.906216681 1.14788708 0.736701439 0.045912294 0.408435906 0.424688221 0.021359061 0.065309382 4089.002206 -3.611617345 0.241670399 TDQDEEHCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TDQDEEHCR 9 0 Q16186;A0A087WX59;A0A087WUX6 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 0 ;;; 197.21 2.84E-05 1093870000 948290 786248 841449 731100 807683 808056 1077451 640079 748887 FALSE TRUE 888938.2216 844462.62 861408.5676 749861.2637 744250.8352 1041328.65 915897.2251 719994.2721 623892.9217 1.424824983 1.353537748 1.380699376 1.20190699 1.192914376 1.669082327 1.468035929 1.154035007 1 19.25093892 1.047443178 4.609392238 1.002436595 1.385515166 0.494935281 0.133897133 0.150648753 6.759209775 0.131944578 0.033529573 11.15432201 -1.047443178 0.383078571 TDQVIQSLIALVNDPQPEHPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TDQVIQSLIALVNDPQPEHPLR 22 0 P68036-2;P68036;P68036-3;A0A1B0GUS4 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ; 243.52 9.13E-31 1612330000 478070 461730 461260 455050 449629 368161 490700 386833 470932 FALSE TRUE 448148.4521 495916.9696 472201.305 466727.3534 414316.9521 474443.1041 417124.0904 435129.9516 392330.4069 1.142273054 1.264028892 1.203580698 1.189628296 1.05604089 1.209294757 1.063195927 1.109090562 1 18.58170963 1.761524035 0.391073219 0.99852939 1.234413158 0.544126506 0.05519322 0.727058181 0.310129234 0.061583617 0.055166959 57.74628304 -1.761524035 0.235883768 TDRDKYNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TDRDKYNR 8 2 P61077-3;P61077-2;P61077;A0A087WY85;H9KV45;D6RAH7 P61077-3 UBE2D3 Ubiquitin-conjugating enzyme E2 D3 0 ; 166.16 0.00018002 306230000 286510 354580 318100 334880 469920 230460 399740 280890 718830 FALSE TRUE 268577.8505 380833.4721 325645.4822 343473.5878 433014.3788 296990.0608 339802.698 315959.7348 598852.6292 0.448487386 0.635938549 0.543782337 0.573552776 0.723073353 0.495931797 0.567422904 0.527608496 1 19.19184149 -1.232986564 4.615758613 1.000123709 0.570712126 0.768834132 0.074982545 8.57E-05 1.42E-05 0.065214022 0.015366691 0.058480818 1.232986564 -0.429411582 TDRPLPENPYHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDRPLPENPYHSR 13 1 P51970 P51970 NDUFA8 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 0 110.44 0.00063599 146650000 199490 162650 163400 157320 212760 149720 158640 214330 197330 FALSE TRUE 187004.277 174692.7752 167275.9252 161357.0975 196050.6878 192941.7335 134853.4047 241089.5723 164394.3482 1.137534709 1.062644654 1.017528443 0.981524604 1.19256343 1.173651866 0.820304385 1.466532 1 17.32680118 2.760987947 24.68172032 1.098355246 1.046567603 0.035640189 0.166897267 3499.727469 3851512.321 0.048060156 0.050946532 576.7504569 -2.760987947 -0.051787643 TDS(ph)IGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TDSIGEK 7 0 A0A286YFF8;Q7Z3U7-2;Q7Z3U7-6;Q7Z3U7-5;Q7Z3U7;Q7Z3U7-3 A0A286YFF8 MON2 Protein MON2 homolog 1 TDS(1)IGEK;TDS(1)IGEK 109.02 0.0074706 1282200000 3889100 2150600 2502200 2801200 2276300 1480730 4153800 2199300 2811100 TRUE FALSE 3645688.173 2309832.662 2561553.366 2873083.534 2097528.58 1908192.713 3530976.252 2473887.446 2341909.25 1.556716245 0.986303232 1.093788483 1.226812497 0.895648958 0.814802159 1.507734022 1.056354958 1 21.15925374 1.006217371 24.98055703 0.999999644 1.136942521 0.045549838 0.237656239 469.6490169 1886976.34 0.21638882 0.054097205 10.1441899 -1.006217371 0.136942878 TDS(ph)PDMHEDT ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TDSPDMHEDT 10 0 Q9BW61 Q9BW61 DDA1 DET1- and DDB1-associated protein 1 1 T(0.003)DS(0.997)PDMHEDT;TDS(1)PDMHEDT;TDS(1)PDMHEDT;TDS(1)PDMHEDT;TDS(1)PDMHEDT 210.08 8.79E-08 1716180000 2548990 1947670 2106340 1998630 2200660 1696810 2551300 1845290 2723550 TRUE FALSE 2389453.266 2091877.513 2156303.379 2049918.229 2027829.041 2186651.502 2168756.25 2075678.518 2268971.91 1.053099536 0.921949498 0.950343797 0.903456857 0.893721527 0.963719071 0.955832128 0.914810143 1 21.11360732 -0.463768202 7.352595957 0.999999999 0.942222636 0.129468072 0.044751838 0 0 0.039334303 0.009271184 0.343741366 0.463768202 -0.057777364 TDS(ph)TSDGRPAWMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 TDSTSDGRPAWMR 13 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 1 TDS(0.975)T(0.024)SDGRPAWMR;TDS(0.982)T(0.018)SDGRPAWMR;TDS(0.98)T(0.019)S(0.001)DGRPAWMR;TDS(0.925)T(0.045)S(0.03)DGRPAWMR;TDS(0.984)T(0.015)S(0.001)DGRPAWMR;TDS(0.597)T(0.393)S(0.01)DGRPAWMR;T(0.002)DS(0.864)T(0.133)S(0.001)DGRPAWMR;T(0.001)DS(0.985)T(0.014)SDGRPAWMR;TDS(0.46)T(0.46)S(0.08)DGRPAWMR;TDS(0.333)T(0.333)S(0.333)DGRPAWMR;T(0.004)DS(0.848)T(0.124)S(0.023)DGRPAWMR;T(0.001)DS(0.492)T(0.492)S(0.015)DGRPAWMR 218.2 1.49E-11 10639764000 6284570 6648690 6749880 8112150 6715680 3245385 5204390 3565049 4181070 TRUE FALSE 5891229.982 7140965.926 6909990.341 8320321.503 6188257.583 4182274.965 4424040.035 4010153.215 3483222.406 1.691316056 2.05010335 1.983792459 2.388685112 1.776589853 1.200691336 1.270099787 1.15127682 1 21.73199116 2.330019698 3.605691865 1.182410783 2.029530797 0.839786708 0.180966066 0.084066369 2.134571606 0.063259194 0.050723273 213.8059063 -2.330019698 0.847120014 TDSEEQDKS(ph)RDEDNDEDEERLEEEEQNEEEEVDN ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDSEEQDKSRDEDNDEDEERLEEEEQNEEEEVDN 34 3 Q9NRF9 Q9NRF9 POLE3 DNA polymerase epsilon subunit 3 1 TDS(0.001)EEQDKS(0.999)RDEDNDEDEERLEEEEQNEEEEVDN 148.47 9.41E-10 111020000 65707 33910 46076 49063 44331 28197 50418 40266 65513 TRUE FALSE 61594.51616 36420.73168 47168.94448 50322.03964 40849.42208 36337.01616 42858.28896 45293.29874 54578.45707 1.128549971 0.667309661 0.864241076 0.922012866 0.748453223 0.665775804 0.785260179 0.829875031 1 15.73604399 4.752781423 24.44881596 0.794364894 1.128550284 0.468942851 0.105194228 1521.650333 2616003.466 0.023484247 0.484672549 56595.43776 -4.752781423 0.33418539 TDSEKPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDSEKPFR 8 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 120.12 0.0014256 500030000 636710 547920 587100 550510 596710 473060 673040 545580 707350 FALSE TRUE 596859.4577 588488.5669 601026.2892 564637.0186 549846.8036 609624.7425 572123.9002 613696.864 589288.7153 1.012847255 0.998642179 1.019918206 0.958167031 0.933068612 1.034509446 0.970871977 1.041419678 1 19.16861511 1.238242971 24.99999986 1.020709832 0.991845721 0.140016517 0.031591511 17.69877675 1391770.224 0.023912524 0.007365333 17.30784396 -1.238242971 -0.028864111 TDSLFVLPSRDDAT(ph)PVRDEPMDAESITFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TDSLFVLPSRDDATPVRDEPMDAESITFK 29 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 TDSLFVLPSRDDAT(1)PVRDEPMDAESITFK;T(0.02)DS(0.019)LFVLPS(0.016)RDDAT(0.945)PVRDEPMDAESITFK 173.23 7.03E-11 85025000 117559 83245 100959 95632 92825 75284 128327 98189 109824 TRUE FALSE 110201.192 89408.54642 103353.7952 98086.07902 85534.89894 97017.26867 109085.5577 110448.1128 91493.66491 1.204468005 0.977210242 1.129627885 1.07205323 0.934872365 1.060371434 1.192274435 1.207166779 1 16.48138423 1.756208834 24.99999988 1.151694406 1.056278777 0.100216995 0.092094268 10.95279666 15531.86384 0.03896237 0.021606766 57.04385064 -1.756208834 -0.095415629 TDSREDEIS(ph)PPPPNPVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 TDSREDEISPPPPNPVVK 18 1 P10644;P10644-2;K7EPB2;K7EIE5;K7EID3;K7EJ40;K7EK41;K7EMU2;K7EMZ6 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 1 TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDS(0.004)REDEIS(0.996)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK 214.49 6.07E-19 15083300000 6939970 5135250 5860740 5215940 5794350 5154600 7988580 5550570 8959640 TRUE FALSE 6505609.666 5515469.253 5999759.52 5349789.851 5339285.124 6642649.342 6790766.591 6243570.883 7464218.203 0.871572814 0.738921224 0.803802804 0.71672474 0.715317396 0.889932363 0.909776002 0.836466823 1 22.83155973 2.167434723 7.262360917 0.9032373 0.767613229 0.573400609 0.059851439 0.161375356 13.78135024 0.020611809 0.01522625 147.0397391 -2.167434723 -0.135624071 TDSS(ph)PNQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TDSSPNQAR 9 0 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 1 TDS(0.037)S(0.963)PNQAR;TDS(0.263)S(0.737)PNQAR;TDS(0.001)S(0.999)PNQAR;TDS(0.002)S(0.998)PNQAR 207.67 1.19E-05 3854220000 3969610 3600730 4160280 3961330 4159230 3708920 4026630 3765860 4052650 TRUE FALSE 3721159.196 3867331.796 4258963.806 4062984.434 3832580.853 4779624.995 3422874.213 4236035.911 3376236.534 1.102161877 1.145456415 1.26145303 1.203406335 1.13516361 1.415666511 1.013813511 1.254662068 1 21.68698455 -1.22115613 5.280237311 0.999985394 1.189241164 0.238082147 0.107580816 1.65E-05 2.44E-06 0.093000607 0.021918762 0.060095765 1.22115613 0.18925577 TDSTSDGRPAWMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TDSTSDGRPAWMR 13 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 214 1.30E-09 1550190000 1032520 1117600 1044520 1022390 1327180 1075960 1637660 1403430 1530170 FALSE TRUE 967896.4163 1200348.267 1069296.508 1048626.258 1222948.636 1386572.185 1392108.086 1578651.325 1274774.742 0.759268587 0.941615979 0.838812123 0.822597298 0.959344892 1.087699764 1.092042414 1.23837669 1 20.28181091 2.362582743 2.370962033 1.115851708 0.857156699 0.742039291 0.073000808 0.1423507 1.640766265 0.027798932 0.021359304 230.4532 -2.362582743 -0.258695009 TDT(ph)SPVLETAGTVAAMAATPSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDTSPVLETAGTVAAMAATPSAR 23 0 Q8WWH5 Q8WWH5 TRUB1 Probable tRNA pseudouridine synthase 1 1 T(0.005)DT(0.498)S(0.498)PVLETAGTVAAMAATPSAR 113.49 0.0085115 44888000 71735 64392 69704 63353 72568 49296 70325 51087 86328 TRUE FALSE 67245.2344 69159.65068 71357.4118 64978.74524 66868.80201 63526.95495 59780.41912 57465.32441 71919.2991 0.935009591 0.961628541 0.992187253 0.903495252 0.929775496 0.883308872 0.831215263 0.79902509 1 16.13409134 2.529489062 1.432979832 0.859473436 0.962834945 0.236778866 0.056454263 0.398745367 1.659870115 0.024768764 0.01957613 338.4457479 -2.529489062 0.10336151 TDTESELDLISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TDTESELDLISR 12 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ;;; 279.64 1.28E-27 563826000 615140 597610 657440 619010 690680 537105 689830 571040 752300 FALSE TRUE 576639.4855 641857.6662 673034.7873 634894.8446 636436.7789 692158.4943 586396.3956 642335.601 626736.27 0.920067201 1.024127208 1.073872408 1.013017556 1.015477816 1.104385573 0.935635009 1.024889785 1 19.25749896 -1.3466803 14.67688996 1 1.01812716 0.001177519 0.054857004 0 0 0.050223806 0.011837865 0.045011108 1.3466803 0.01812716 TDTGEPMGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TDTGEPMGR 9 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;; 168.66 0.00013739 1786500000 1701930 1780350 1795710 1797370 1803840 1523980 1947670 1631350 1589070 FALSE TRUE 1595409.239 1912168.966 1838305.089 1843493.557 1662173.683 1963928.286 1655634.965 1835027.639 1323843.951 1.205133912 1.44440662 1.388611617 1.392530861 1.255566172 1.48350437 1.250626982 1.386135909 1 20.33630164 -1.758945754 0.43064044 0.708474525 1.37053142 0.592374987 0.090419393 25.23772585 1.971414522 7.64764553 0.045988232 0.017420244 1.758945754 0.662056895 TDVAVQIISNIYHNFPEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDVAVQIISNIYHNFPEQR 19 0 O60306 O60306 AQR Intron-binding protein aquarius 0 208.93 2.47E-16 52318000 122700 145000 147080 148890 149290 121940 172690 149620 139360 FALSE TRUE 115020.426 155735.9509 150568.8071 152710.7695 137565.3656 157142.0985 146796.7377 168300.3864 116099.9157 0.990702063 1.3413959 1.296889891 1.315339193 1.18488773 1.35350743 1.264400037 1.449616783 1 16.8250074 4.744658865 24.31488908 1.290678253 0.990701866 0.353552235 0.119630925 441.4528351 1760083.254 0.024029255 0.218825773 55546.77697 -4.744658865 -0.299976387 TDVLVLSCDLITDVALHEVVDLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TDVLVLSCDLITDVALHEVVDLFR 24 0 Q9NR50-3;Q9NR50-2;Q9NR50 Q9NR50-3 EIF2B3 Translation initiation factor eIF-2B subunit gamma 0 ;; 285.55 1.31E-52 780310000 436550 442039 449626 464440 494879 435681 507944 424842 368720 FALSE TRUE 409227.1148 474768.0275 460291.341 476358.3167 456013.1996 561455.032 431782.5127 477884.4589 307178.25 1.332213836 1.545578268 1.498450301 1.550755357 1.484523073 1.827782508 1.405641554 1.55572362 1 18.22871654 -0.614944836 6.278305385 0.999999999 1.528476315 0.624100917 0.128043497 1.64E-09 5.24E-10 0.110389175 0.026018978 0.242691834 0.614944836 0.528476316 TDVSNFDEEFTGEAPTLS(ph)PPRDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TDVSNFDEEFTGEAPTLSPPRDAR 24 1 Q16512;Q16512-2 Q16512 PKN1 Serine/threonine-protein kinase N1 1 TDVSNFDEEFTGEAPT(0.479)LS(0.521)PPRDAR;TDVSNFDEEFTGEAPT(0.124)LS(0.876)PPRDAR 221.86 5.40E-33 221380000 111484 188937 129433 193597 242638 106420 180436 145589 220725 TRUE FALSE 104506.4154 202926.0921 132503.2119 198565.0268 223582.1902 137141.7264 153381.2969 163766.1071 183884.5716 0.568326176 1.103551485 0.720578191 1.079835166 1.215883357 0.745803333 0.83411727 0.890591885 1 17.48844091 4.757236624 24.17207244 0.930577533 0.568325676 0.356405541 0.159011322 3238.115079 4190935.994 0.037420056 1.24715757 57179.00895 -4.757236624 -0.362251858 TDWDAGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDWDAGFK 8 0 P52298-2;P52298;C9JQX9;B3KSB0;P52298-3 P52298-2 NCBP2 Nuclear cap-binding protein subunit 2 0 112.94 0.0068495 85399000 187560 154830 170410 164870 189900 121500 210280 174180 210040 FALSE TRUE 175820.9544 166293.7743 174452.2057 169100.8433 174986.02 156575.0776 178750.4661 195926.7564 174982.9671 1.004788965 0.950342637 0.996966782 0.966384592 1.000017447 0.894801821 1.021530662 1.119690446 1 17.41685497 1.496209017 7.227717176 1.063509227 0.970414862 0.449560561 0.042298775 0.089425564 11.34063986 0.020472895 0.009308119 31.34794073 -1.496209017 -0.093094365 TDY(ph)NS(ph)LDRIMASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TDYNSLDRIMASK 13 1 Q9H0V1 Q9H0V1 TMEM168 Transmembrane protein 168 2 T(0.001)DY(0.93)NS(0.941)LDRIMAS(0.128)K 55.261 0.095553 80192000 127230 115720 111570 114020 127410 87474 146180 111010 179310 TRUE FALSE 119266.9014 124288.0292 114216.4931 116945.9462 117403.7325 112726.3238 124261.6661 124869.8429 149382.0026 0.798402079 0.832014748 0.764593399 0.782865032 0.785929566 0.754617838 0.831838266 0.835909552 1 17.18864682 0.650048392 1.216482181 0.999718106 0.790139169 0.888305596 0.023177149 0.365750896 0.843514177 0.022067655 0.006720075 4.467333671 -0.650048392 -0.209578937 TDYNASVSVPDSSGPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TDYNASVSVPDSSGPER 17 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ; 318.35 4.97E-58 493180000 388540 437830 438920 462490 489010 419750 549910 402910 505370 FALSE TRUE 364221.975 470247.3888 449331.3897 474358.2764 450605.1272 540925.0109 467456.1006 453214.2004 421020.4822 0.865093245 1.116922831 1.06724354 1.126686934 1.070268897 1.284795001 1.110293015 1.076465919 1 18.68353089 4.738896142 24.99999994 1.114514285 0.86509317 0.517200536 0.072969319 20.95429083 1560676.362 0.016223482 0.095007691 54814.58651 -4.738896142 -0.249421115 TDYYAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TDYYAR 6 0 P46777;A0A2R8Y4A2;R4GNJ2 P46777 RPL5 60S ribosomal protein L5 0 ;;;; 191.24 0.0024569 9320360000 5906680 6856300 6150370 6182580 6670910 4338090 6530790 5961400 6746280 FALSE TRUE 5536991.443 7363947.586 6296259.681 6341235.47 6147003.638 5590426.16 5551558.668 6705693.913 5620282.285 0.98518031 1.310245146 1.120274634 1.128277042 1.093717953 0.994687789 0.987772213 1.193124041 1 22.42221116 2.851759788 1.547661175 1.037091661 1.175412097 0.12579253 0.098634944 0.497876596 2.405380602 0.036143053 0.038392765 710.8202442 -2.851759788 0.138320436 TEAACLSAPHLAS(ph)PPATPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TEAACLSAPHLASPPATPK 19 0 Q5TGY3 Q5TGY3 AHDC1 AT-hook DNA-binding motif-containing protein 1 1 TEAACLSAPHLAS(1)PPATPK 133.41 7.57E-06 268690000 338780 239510 280240 268880 268040 200250 343260 224120 274360 TRUE FALSE 317576.3645 257243.5696 286887.4251 275779.916 246989.2196 258058.9242 291791.3497 252101.8753 228567.5436 1.389420211 1.125459746 1.255153819 1.20655764 1.080596203 1.129026983 1.276608853 1.102964452 1 17.80226103 -5 0.104017073 0.402425778 1.316626801 0.428858319 0.084683798 198.2513647 1.391483195 25.79454557 1.219863642 1.00E-05 5 0.914201023 TEAEIAHIALETLEGHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TEAEIAHIALETLEGHQR 18 0 O75955;A0A140T9R1;A0A140T9X0;A2AB09;A0A140T9C3;A0A140T959;A2AB13;A2AB11;A0A0G2JJQ6;A0A140T910;A2AB12;A0A140T957;A2AB10;A0A140T9B1 O75955 FLOT1 Flotillin-1 0 202.03 7.74E-16 17593000 13813 15473 12996 12743 14869 9881.5 13809 11761 12215 FALSE TRUE 12948.46899 16618.63702 13304.27126 13070.00695 13701.24872 12734.12864 11738.46865 13229.38674 10176.23759 1.27242204 1.633082647 1.307386069 1.28436535 1.346396308 1.251359211 1.15351755 1.300027306 1 13.31291664 2.025102595 0.236163609 0.953056527 1.572256503 0.535202513 0.107898982 1.658976037 0.335672634 0.273941832 0.390841263 105.9503985 -2.025102595 0.619199976 TEAQDLCRAS(ph)PEPPGPESSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 185.72 2.12E-17 5127310000 1067770 1748600 1249680 1513430 2325340 957010 1645330 1172300 3648660 TRUE FALSE 1000940.182 1878068.163 1279323 1552267.176 2142717.176 1233283.251 1398628.041 1318664.236 3039675.075 0.329291835 0.617851618 0.420874919 0.510668785 0.70491652 0.405728646 0.460124193 0.433817498 1 21.53548568 -1.486508367 5.922370817 1.000461422 0.4927914 0.691155406 0.108005043 0.00060409 5.24E-05 0.096004497 0.022608811 0.032620577 1.486508367 -0.507670022 TECAEPPRDEPPADGALKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TECAEPPRDEPPADGALKR 19 2 H0YDU8;P53041 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 94.281 0.00091201 141040000 246750 182900 193540 198940 205330 165440 259540 179030 260140 FALSE TRUE 231306.358 196442.1063 198130.8602 204045.1372 189204.2101 213199.8423 220624.3865 201382.2896 216720.9534 1.067300389 0.906428766 0.914221062 0.941510887 0.873031458 0.983752789 1.018011332 0.9292239 1 17.72547912 2.041420216 24.98224563 0.988530345 0.931988381 0.113216708 0.055139061 220.8207121 133185.1731 0.01921895 0.014194119 110.0069734 -2.041420216 -0.056541964 TEDEEFLIQHLLQAPS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 TEDEEFLIQHLLQAPSPPR 19 0 Q9ULL5;Q9ULL5-2 Q9ULL5 PRR12 Proline-rich protein 12 1 TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR 308.03 1.22E-61 2257786000 1621516 1651326 1701274 1713864 1761506 1358988 1919715 1481050 1872347 TRUE FALSE 1520028.208 1773591.895 1741629.023 1757844.652 1623164.424 1751305.774 1631871.558 1665962.353 1559840.19 0.974476884 1.137034362 1.116543242 1.126938941 1.040596617 1.122746923 1.046178684 1.068033997 1 20.5729668 0.946160038 0.770482479 1.000974502 1.097228364 0.18291815 0.050548038 0.996446495 1.308462583 0.044993063 0.016727172 8.834053754 -0.946160038 0.096253861 TEDFIIDTLELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TEDFIIDTLELR 12 0 Q01780;Q01780-2 Q01780 EXOSC10 Exosome component 10 0 ;; 132.91 0.00040137 26208900 58622 67229 63735 62353 70757 56811 71480 64312 66763 FALSE TRUE 54952.95366 72206.70511 65246.8243 63953.08354 65200.03064 73211.41345 60762.23759 72341.49477 55619.82399 0.988010204 1.298218871 1.173085774 1.149825349 1.172244462 1.316282724 1.092456488 1.300642281 1 15.76331156 -1.486623091 3.018240759 0.994590041 1.19205132 0.248445704 0.10142536 21858232.77 24659937.3 980457.0615 0.021502103 0.032611961 1.486623091 0.197461279 TEDGDWEWS(ph)DDEMDEKSEEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TEDGDWEWSDDEMDEKSEEGK 21 1 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 1 TEDGDWEWS(1)DDEMDEKSEEGK 140.41 1.00E-07 73573000 105240 44962 34496 90418 92050 63612 55654 68817 44391 TRUE FALSE 98653.21626 48291.03326 35314.26141 92738.27896 84820.76431 81975.75175 47309.19937 77408.95393 36981.85532 2.66761133 1.305803423 0.954907781 2.507669725 2.293577852 2.216647895 1.279254352 2.093160369 1 15.17452998 -1.441854567 6.65168208 0.999848917 1.779510753 0.164821688 0.579970615 0.001342183 0.000112621 0.580025044 0.136687459 0.036153091 1.441854567 0.779661836 TEDGGWEWS(ph)DDEFDEESEEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TEDGGWEWSDDEFDEESEEGK 21 0 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 TEDGGWEWS(1)DDEFDEESEEGK;TEDGGWEWS(1)DDEFDEESEEGK 321.38 3.31E-67 86097000 433470 219593 284910 271360 246160 213853 345350 235110 232000 TRUE FALSE 406339.8865 235851.8942 291668.1997 278323.557 226827.5866 275588.8895 293567.9736 264464.001 193277.7012 2.102362993 1.220274728 1.509062856 1.440018974 1.173583839 1.425870071 1.5188921 1.368310981 1 17.56031568 8 0.035090704 7.68E-12 3.606935465 0.369161548 0.231319962 1396.10912 3.742981158 113.4804127 319.8914812 100000000 -8 3.606935465 TEDGGWEWS(ph)DDEFDEESEEGKAAISQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TEDGGWEWSDDEFDEESEEGKAAISQLR 28 1 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 TEDGGWEWS(1)DDEFDEESEEGKAAISQLR;TEDGGWEWS(1)DDEFDEESEEGKAAISQLR;TEDGGWEWS(1)DDEFDEESEEGKAAISQLR;TEDGGWEWS(1)DDEFDEESEEGKAAISQLR 355.98 2.71E-111 870113000 257573 215781 215823 227260 277035 111702.7 249287 196355 438806 TRUE FALSE 241451.9657 231757.6498 220942.4235 233091.8764 255277.7886 143949.4561 211908.7286 220870.354 365566.4438 0.660487224 0.633968609 0.604383764 0.63761836 0.698307498 0.393770978 0.579672265 0.60418662 1 18.47977412 0.90260635 18.27730347 1 0.597636263 0.705300144 0.080920288 2620.927566 491857.6848 0.076391336 0.019100873 7.99109604 -0.90260635 -0.402363737 TEDGKVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TEDGKVEK 8 1 O75436;S4R3Q6;O75436-2;S4R2Y3 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ; 92.062 0.010984 1197420000 1959150 1136150 1362250 1321770 1386370 776660 1629940 1072430 1634690 FALSE TRUE 1836530.299 1220271.728 1394563.213 1355688.856 1277490.093 1000869.134 1385545.629 1206325.246 1361849.678 1.348555812 0.896039958 1.024021399 0.995476136 0.938055141 0.734933635 1.017399828 0.88579912 1 20.37713604 4.742209489 24.9232998 0.938786792 1.348555975 0.693810771 0.086021525 192.0025859 1311399.953 0.019411141 0.143663915 55234.38075 -4.742209489 0.409769183 TEDPDLPAFYFDPLINPISHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TEDPDLPAFYFDPLINPISHR 21 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;; 244.74 3.57E-30 374752000 366542 415787 407310 382325 421229 326108 490803 373453 379722 FALSE TRUE 343600.7905 446572.3021 416971.5855 392136.1068 388147.3735 420250.0857 417211.6465 420079.4291 316343.9451 1.086162058 1.411666982 1.318095674 1.239587837 1.226978988 1.328459394 1.318854535 1.327919929 1 18.27113446 -1.332093422 5.521452028 0.999938907 1.297746011 0.500062004 0.087463997 6.11E-05 7.39E-06 0.078605902 0.018523799 0.046548595 1.332093422 0.297807104 TEDSLMPEEEFLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TEDSLMPEEEFLRR 14 1 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 ; 148.08 1.26E-05 214130000 139024 140642 131653 137446 150423 118851 150197 130521 154111 FALSE TRUE 130322.736 151055.28 134775.8713 140973.0971 138609.3844 153161.3543 127676.3542 146816.8342 128388.8785 1.0150625 1.176544898 1.049747244 1.098016422 1.07960585 1.192948767 0.994450265 1.143532336 1 16.97016071 -4.803184099 0.310106547 0.270765912 1.09864443 0.159309887 0.064971414 444.1268789 4.535923818 210.4320518 0.054771592 1.57E-05 4.803184099 0.827878518 TEDTEHVIIPVCLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TEDTEHVIIPVCLR 14 0 Q9Y4E8;Q9Y4E8-2;Q9Y4E8-3 Q9Y4E8;Q9Y4E8-2 USP15 Ubiquitin carboxyl-terminal hydrolase 15 0 163.51 4.27E-06 109910000 281520 254580 287860 287530 284500 243410 337330 251540 346440 FALSE TRUE 263900.1657 273429.3681 294688.1751 294908.5066 262156.5176 313678.5156 286750.4981 282945.3227 288616.9259 0.914361363 0.947378146 1.021035666 1.02179907 0.90831997 1.086833402 0.9935332 0.980349028 1 18.13879638 4.331712188 2.056082328 1.003101834 0.915156374 0.321917995 0.043934055 0.423151492 3.179102506 0.010611852 0.050691155 21464.07553 -4.331712188 -0.08794546 TEDTPDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TEDTPDKK 8 1 Q9UKX7-2;Q9UKX7 Q9UKX7-2 NUP50 Nuclear pore complex protein Nup50 0 91.867 0.019535 91262000 223140 106190 177520 181850 126490 114690 206010 123860 193080 FALSE TRUE 209174.0657 114052.4181 181730.8582 186516.5789 116555.9856 147799.1412 175120.713 139324.1936 160853.7007 1.300399462 0.709044415 1.129789725 1.159541733 0.724608667 0.918842032 1.08869558 0.86615473 1 17.2953896 4.772555404 23.64895673 0.958283571 1.300400896 0.335541627 0.154716319 9842.974504 6847145.72 0.035702114 5.893725385 59231.86457 -4.772555404 0.342117324 TEEARPSPAPGPGT(ph)PTGTPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TEEARPSPAPGPGTPTGTPTR 21 1 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 TEEARPSPAPGPGT(0.748)PT(0.249)GT(0.003)PTR;TEEARPSPAPGPGT(0.962)PT(0.037)GTPTR;TEEARPSPAPGPGT(0.869)PT(0.131)GTPTR 257.98 2.73E-36 1936670000 304290 287007 279737 309524 339540 241664 315438 308383 313690 TRUE FALSE 285245.0321 308257.2969 286372.4937 317466.9099 312873.898 311428.4737 268141.0003 346885.2964 261333.1125 1.09149977 1.17955698 1.09581404 1.214797876 1.19722256 1.191691595 1.026050613 1.327368327 1 17.99553041 -1.589678847 7.408710408 0.999859058 1.154522297 0.276240015 0.0825052 0.000173264 9.60E-06 0.072062562 0.016969928 0.025722972 1.589678847 0.154663239 TEEARPSPAPGPGTPT(ph)GTPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TEEARPSPAPGPGTPTGTPTR 21 1 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 TEEARPSPAPGPGT(0.318)PT(0.682)GTPTR 249.25 1.98E-30 605580000 102940 116900 116910 104160 121360 105830 121410 106650 124440 TRUE FALSE 96497.16915 125555.3976 119683.1604 106832.9219 111828.8751 136381.403 103205.6976 119965.4873 103670.1601 0.930809493 1.211104502 1.154461036 1.030507929 1.078698779 1.315531903 0.995519806 1.157184354 1 16.66164117 -0.147882957 0.826945406 0.996587308 1.121335414 0.075275732 0.110938326 19.52932202 11.62432611 0.325178712 0.033443267 0.711405213 0.147882957 0.124748106 TEEDSEEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TEEDSEEVR 9 0 Q16543;K7EKQ2 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ; 180.34 0.00011342 584590000 889190 750640 801620 776430 714270 681250 918580 713080 587710 FALSE TRUE 833537.1851 806218.1666 820634.805 796354.5083 658174.1154 877915.8158 780847.4567 802109.6077 489617.4042 1.702425563 1.646628898 1.676073599 1.626483253 1.344262091 1.793064969 1.594811479 1.638237531 1 18.90129532 -1.082167329 4.104972234 0.999893447 1.630040032 0.749271409 0.114115442 16440504.86 39197957.51 25292.43933 0.025153495 0.082762323 1.082167329 0.630146584 TEEEEIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TEEEEIDR 8 0 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ; 190.52 0.00043276 361140000 840760 582950 677880 673710 608150 614780 872950 590330 540560 FALSE TRUE 788138.3324 626112.2246 693959.6337 690998.5392 560388.3522 792257.0059 742059.2516 664034 450337.0438 1.75010771 1.390319169 1.540978348 1.534403062 1.244375429 1.759253467 1.64778639 1.474526711 1 18.78064563 0.960940499 21.7890243 0.999999997 1.541388685 0.555070741 0.153997477 989.8208032 552165.0481 0.142291405 0.035572851 9.13988011 -0.960940499 0.541388687 TEEEFKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TEEEFKK 7 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 119.17 0.0077625 3284990000 6880400 3940770 4875210 7026600 8188700 6123600 14130100 7068600 7762800 FALSE TRUE 6449768.046 4232548.711 4990852.283 7206914.452 7545592.534 7891383.912 12011422.68 7951130.27 6467138.53 0.997314039 0.654470086 0.771724969 1.114389992 1.166759069 1.220228061 1.857300973 1.229466515 1 22.62469608 2.776451575 1.330251144 1.439889473 0.764957661 0.422283564 0.244960896 0.293730886 1.062831137 0.103232706 0.101669715 597.6564005 -2.776451575 -0.674931813 TEEGSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TEEGSVR 7 0 O43896 O43896 KIF1C Kinesin-like protein KIF1C 0 81.635 0.090843 0 681820 482080 538910 489080 447650 493560 664610 493420 451430 FALSE TRUE 639146.1033 517773.7048 551693.1997 501630.6208 412493.3747 636042.7597 564957.9004 555024.5732 376083.4167 1.699479623 1.376752289 1.466943703 1.333828078 1.096813517 1.691227881 1.502214337 1.475801773 1 18.52069317 -1.983537028 2.635079876 0.593236931 1.449535857 0.407378224 0.172483063 16852421.71 7105071.672 41699447.31 0.04050687 0.01038635 1.983537028 0.856298926 TEELIES(ph)PKLESSEGEIIQTVDR ddPTM_SK-BR-3_Pertuzumab_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(0.999)PKLES(0.001)SEGEIIQTVDR 209.58 4.93E-25 901680000 410685 227100 280928 275636 312149 197451 345738 243555 332498 TRUE FALSE 384980.9589 243914.7203 287591.7448 282709.2864 287634.0767 254451.8984 293897.7966 273963.3779 277001.9358 1.389813244 0.880552403 1.03823009 1.02060401 1.038382912 0.918592492 1.060995461 0.989030554 1 18.07953653 4.748840062 24.98997798 0.994244799 1.389813464 0.834361219 0.055520662 563.6850211 1370326.811 0.012773612 0.180062518 56084.13961 -4.748840062 0.395568665 TEEPDRDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TEEPDRDER 9 1 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 ;; 144.65 9.03E-05 1179510000 1605020 1495240 1586400 1572250 1542440 1378370 1715180 1405260 1520430 FALSE TRUE 1504564.663 1605949.125 1624030.157 1612596.597 1421302.984 1776283.043 1458004.682 1580709.804 1266660.411 1.187820074 1.267860835 1.282135404 1.273108864 1.122086845 1.402335644 1.151062013 1.247934956 1 20.27259836 -0.130623024 0.676085519 0.986355574 1.253470773 0.484971818 0.078082689 4.689916423 2.108706065 0.237317122 0.025363763 0.740247546 0.130623024 0.267115198 TEEPLGS(ph)PHPSGTVESPGEGPQDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TEEPLGSPHPSGTVESPGEGPQDTR 25 0 A0A0A0MR84;M0R202;A0A0B4J2G2;Q9NWS9-2;Q9NWS9 A0A0A0MR84 ZNF446 Zinc finger protein 446 1 TEEPLGS(1)PHPSGTVESPGEGPQDTR 206.4 2.43E-25 196000000 23621 22852 29911 33187 28464 24269 35275 27550 34259 TRUE FALSE 22142.60377 24543.98586 30620.50304 34038.63461 26228.55226 31275.06633 29985.84123 30989.67815 28540.95158 0.775818694 0.859956816 1.072862023 1.192624377 0.9189796 1.095796201 1.050625139 1.085796949 1 14.80074582 4.193518328 1.942771927 1.06220837 0.785156071 0.677016284 0.070282028 0.200524614 1.401111017 0.017451511 0.066914967 15614.14931 -4.193518328 -0.2770523 TEES(ph)PAS(ph)DEAGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TEESPASDEAGEK 13 0 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 2 TEES(1)PAS(1)DEAGEK;TEES(1)PAS(1)DEAGEK 261.17 7.04E-13 213020000 1045360 453750 614180 596110 514080 552680 844500 494470 386520 TRUE FALSE 979932.7836 487346.1221 628748.6396 611407.1918 473706.2305 712229.744 717875.065 556205.668 322007.315 3.043200381 1.513462892 1.952591169 1.898736965 1.471103942 2.211843368 2.229375022 1.727307555 1 18.29673394 4.747876114 24.71686595 1.828206046 3.043201133 0.534554754 0.372864511 872.4105388 2314715.025 0.083334109 1.047154166 55959.79492 -4.747876114 1.214995087 TEES(ph)PASDEAGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TEESPASDEAGEK 13 0 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 TEES(0.998)PAS(0.002)DEAGEK;TEES(1)PASDEAGEK 259.61 5.85E-24 338160000 1529780 830750 1118520 1017600 925870 955920 1403850 879100 774430 TRUE FALSE 1434033.801 892259.5944 1145051.823 1043713.339 853155.905 1231878.586 1193355.725 988857.5701 645172.63 2.222713323 1.382978063 1.77479913 1.617727241 1.32236841 1.909378248 1.849668863 1.532702294 1 19.29932571 4.752417033 24.13466856 1.608457519 2.222713996 0.353878579 0.27591043 1697.005179 2955706.381 0.060546207 1.181353619 56547.97189 -4.752417033 0.614256476 TEESPASDEAGEKEAKS(ph)D ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TEESPASDEAGEKEAKSD 18 2 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 TEESPASDEAGEKEAKS(1)D;TEESPASDEAGEKEAKS(1)D;TEESPASDEAGEKEAKS(1)D 234.64 7.09E-24 1404440000 1608470 594760 875810 878110 910670 544070 1116320 573520 1218970 TRUE FALSE 1507798.734 638796.6492 896584.6268 900643.7892 839149.6517 701134.1768 948938.1794 645125.2345 1015516.032 1.484761132 0.629036499 0.882885743 0.886882886 0.826328315 0.690421573 0.934439388 0.63526839 1 19.95378159 4.747978349 24.84935199 0.807278254 1.484761522 0.74155778 0.12505153 554.6333289 1463406.049 0.026805609 0.343924643 55972.96968 -4.747978349 0.677483268 TEFLDLDNSPLSPPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 TEFLDLDNSPLSPPSPR 17 0 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 TEFLDLDNSPLS(0.001)PPS(0.999)PR;TEFLDLDNSPLSPPS(1)PR;TEFLDLDNSPLS(0.004)PPS(0.996)PR;TEFLDLDNSPLS(0.001)PPS(0.999)PR;TEFLDLDNSPLS(0.015)PPS(0.985)PR;TEFLDLDNSPLS(0.004)PPS(0.996)PR;TEFLDLDNSPLS(0.002)PPS(0.998)PR 223.07 3.31E-15 752810000 1045217 892900 964233 869159 935070 876063 1109998 917583 943804 TRUE FALSE 979798.7337 959011.2451 987105.0621 891463.0914 861633.3741 1128968.166 943564.1046 1032145.257 786277.0152 1.246124095 1.219686226 1.255416403 1.133777376 1.095839453 1.435840225 1.200040299 1.312699262 1 19.58467816 TEFLHSQNSLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TEFLHSQNSLSPR 13 0 Q96FS4;F6RY50 Q96FS4 SIPA1 Signal-induced proliferation-associated protein 1 1 TEFLHS(0.022)QNS(0.046)LS(0.932)PR;TEFLHSQNS(0.009)LS(0.991)PR 246.86 3.37E-17 47863000 135183 156338 147690 155446 162474 109824 150151 126228 169900 TRUE FALSE 126722.1373 167913.4282 151193.2765 159435.0075 149713.9474 141528.406 127637.2515 141987.8437 141542.5924 0.895293319 1.18631025 1.068182191 1.126410113 1.057730715 0.999899773 0.901758611 1.003145705 1 17.11087672 2.20442579 2.9896668 0.956587817 1.088183134 0.227535537 0.079136195 0.260205463 4.777804117 0.030296062 0.021582918 160.1127034 -2.20442579 0.131595317 TEGPS(ph)PALLEETPLEPAVGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TEGPSPALLEETPLEPAVGPK 21 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 T(0.213)EGPS(0.786)PALLEET(0.001)PLEPAVGPK 73.76 0.0091335 13046000 39620 32750 36706 39618 38539 21934 24983 23045 26206 TRUE FALSE 37140.25492 35174.84408 37576.68365 40634.66495 35512.3024 28265.98973 21237.03108 25922.21898 21832.0493 1.701180426 1.611156314 1.721170703 1.861239153 1.626613329 1.294701626 0.972745654 1.187347034 1 14.41415994 2.126691768 2.696436714 1.058006232 1.707650383 0.927041277 0.08473345 0.065504645 0.948860014 0.037898498 0.02453465 133.8726216 -2.126691768 0.649644151 TEGT(ph)PPPPGQPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TEGTPPPPGQPAK 13 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;A0A494C150;Q9Y4D8-2 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 1 T(0.001)EGT(0.999)PPPPGQPAK;TEGT(1)PPPPGQPAK 154.1 0.00051461 267180000 981430 827090 884060 972070 1045300 598350 1101030 830120 1150760 TRUE FALSE 920004.0482 888328.6042 905030.3207 997014.9619 963206.3545 771083.9316 935940.773 933762.3093 958690.7218 0.959646346 0.92660603 0.944027412 1.039975603 1.004710208 0.804309371 0.976269773 0.973997441 1 19.87070594 1.503173736 24.9999998 0.983085048 0.944716266 0.076157581 0.060834756 2.172066408 2077.513016 0.032197379 0.014905624 31.85471591 -1.503173736 -0.038368782 TEHAEFLHCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TEHAEFLHCK 10 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 ; 146.11 1.69E-05 235800000 447800 476870 441900 409760 517300 314310 474450 437620 448310 FALSE TRUE 419772.9973 512177.951 452382.0767 420275.1353 476673.3447 405046.1946 403310.6271 492257.8203 373484.1648 1.123937872 1.371351182 1.211248345 1.125282341 1.276287965 1.084507009 1.079860045 1.318015238 1 18.51068755 -5 0.068305881 0.276370594 1.46982018 0.228928186 0.102862465 373.5816233 1.842882143 42.81264474 5.615432304 1.00E-05 5 1.193449586 YKEENIELAFDDLEPPTDDSVAAVDQASHQSLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YKEENIELAFDDLEPPTDDSVAAVDQASHQSLVR 34 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 142.64 1.65E-10 33328000 19218 39427 39396 41614 46651 33518 53431 43110 49909 FALSE TRUE 18015.17969 42346.2161 40330.49172 42681.88569 42987.21864 43194.10248 45419.51758 48492.3784 41578.86548 0.433277327 1.018455305 0.969975762 1.026528387 1.033871852 1.038847549 1.092370296 1.166274689 1 15.34356277 4.740103912 5.172900512 1.04090973 0.405692928 0.928911847 0.053069269 0.042610095 3.840523622 0.013622255 0.096594375 54967.23767 -4.740103912 -0.635216802 down TEIIILATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TEIIILATR 9 0 P23396;P23396-2;E9PPU1;E9PL09;F2Z2S8;H0YCJ7;H0YEU2;H0YF32;E9PQ96;E9PJH4;E9PK82 P23396 RPS3 40S ribosomal protein S3 0 ; 106.36 0.0068607 188569000 382650 509030 391790 397360 538190 269230 419260 432060 482980 FALSE TRUE 358700.6195 546719.1108 401083.4438 407556.9303 495922.7284 346952.3304 356395.8552 486003.6421 402367.5178 0.891475091 1.358755582 0.996808704 1.012897195 1.232511837 0.862277185 0.885747083 1.20786003 1 18.61815432 2.235483455 24.99997359 0.96522567 1.116224327 0.092183501 0.158039726 138.8165583 1127779.72 0.055101928 0.042437532 171.9821821 -2.235483455 0.150998657 TEIIPDRDGSDPYQEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TEIIPDRDGSDPYQEPK 17 1 Q99447-3;Q99447;Q99447-4;I3L1L9;Q99447-2;I3L3V9 Q99447-3 PCYT2 Ethanolamine-phosphate cytidylyltransferase 0 ; 127.83 3.55E-05 442460000 720310 495950 587920 602910 598130 414330 693200 453170 750800 FALSE TRUE 675227.0829 532670.654 601865.74 618381.6913 551155.2825 533940.3449 589261.0954 509749.2721 625486.6296 1.079522808 0.851609977 0.96223598 0.988640943 0.881162372 0.853639901 0.942084239 0.814964298 1 19.25461952 2.720447911 24.38268183 0.895067935 0.94930928 0.163286705 0.074358224 1290.341439 1737008.462 0.022209425 0.020978713 525.3490019 -2.720447911 0.054241345 TEIKEEEDQPSTSATQSS(ph)PAPGQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TEIKEEEDQPSTSATQSSPAPGQSK 25 1 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 TEIKEEEDQPSTSAT(0.002)QS(0.097)S(0.901)PAPGQSK 115.99 4.17E-07 0 197340 98087 130960 107760 121390 94835 167120 116100 148290 TRUE FALSE 184988.8417 105349.4635 134066.433 110525.304 111856.5191 122212.325 142061.9075 130595.3406 123539.441 1.497407145 0.852759756 1.085211589 0.894656015 0.905431643 0.989257552 1.149931603 1.05711455 1 16.91461218 4.748965126 24.93820728 0.99773663 1.497407433 0.752661228 0.091032397 780.1755282 1869937.905 0.022809405 0.322669671 56100.29251 -4.748965126 0.499670803 TEIMS(ph)PLYQDEAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TEIMSPLYQDEAPK 14 0 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 1 TEIMS(1)PLYQDEAPK;TEIMS(1)PLYQDEAPK;TEIMS(1)PLYQDEAPK;T(0.004)EIMS(0.996)PLYQDEAPK;TEIMS(1)PLYQDEAPK 276.63 4.35E-33 403069000 1441840 872970 1200100 1129500 1052240 827610 1265590 852880 1152650 TRUE FALSE 1351597.808 937605.6071 1228566.939 1158484.882 969601.3149 1066527.572 1075826.529 959363.9454 960265.2686 1.407525454 0.976402706 1.279403701 1.206421725 1.009722362 1.110659322 1.120343059 0.999061381 1 19.87307347 2.749811128 24.48415362 1.065900277 1.187593339 0.330753389 0.114837521 847.5170878 1844424.39 0.033385965 0.035120296 562.0968197 -2.749811128 0.121693062 TEKHESQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TEKHESQR 8 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 72.79 0.027184 43410000 38026 84930 53870 65179 93666 38729 57468 85788 91501 FALSE TRUE 35646.02054 91218.30557 55147.82184 66851.60349 86309.85019 49909.43359 48851.20691 96498.82064 76228.89198 0.467618243 1.196636908 0.723450393 0.876985114 1.132245897 0.654731196 0.64084897 1.265908741 1 16.21805029 1.230995817 24.99988157 1.132954368 0.837200412 0.246204182 0.229628238 283.7554004 937705.8359 0.19545346 0.052610136 17.02142114 -1.230995817 -0.295753956 TELDAHFENLLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TELDAHFENLLAR 13 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39;F8WFB9 B7ZC38 SH3GLB2 Endophilin-B2 0 ; 170.95 2.59E-05 295510000 661820 809470 759880 773820 861760 681840 817860 766890 811740 FALSE TRUE 620397.8676 869404.0011 777904.7124 793677.5313 794080.8458 878676.1393 695229.4856 862637.9046 676255.35 0.917401789 1.285614969 1.150312101 1.173635863 1.174232257 1.299325971 1.02805765 1.27560973 1 19.36720858 -0.867395025 4.807296188 0.999999393 1.16909315 0.156726601 0.118097433 6.72E-07 1.58E-07 0.099962866 0.023561389 0.135707852 0.867395025 0.169093757 TELEETTAEAEEEIQALTAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TELEETTAEAEEEIQALTAHR 21 0 O14578-4;H7BYJ3;O14578;O14578-3 O14578-4 CIT Citron Rho-interacting kinase 0 108.92 0.00027066 0 5847.8 6309.2 6793.4 8634.7 7184.1 6572.7 7980.4 5701.2 6366.2 FALSE TRUE 5481.796637 6776.339733 6954.542656 8856.281021 6619.889765 8470.131791 6783.813106 6413.00737 5303.640093 1.033591371 1.277677145 1.311277261 1.66984955 1.248178543 1.59704121 1.279086248 1.20917092 1 12.37276716 0.981484226 2.257204978 1.003317112 1.353387697 0.284926499 0.177688356 0.395127872 4.444567053 0.158810578 0.043576849 9.582619099 -0.981484226 0.350070585 TELHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TELHGK 6 0 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 111.69 0.027635 152660000 909180 798680 848980 802890 884850 607610 975890 806000 1042300 FALSE TRUE 852276.0467 857815.0982 869118.2065 823493.5167 815357.4503 783017.1433 829564.3542 906630.8742 868333.3965 0.981507852 0.987886798 1.000903812 0.948360987 0.938991237 0.901747124 0.955352354 1.044104578 1 19.72788955 1.247683278 24.99665322 1.022052292 0.961988237 0.434201891 0.029676727 192.3996297 527197.0776 0.023310576 0.008246797 17.68818527 -1.247683278 -0.060064055 TELNKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TELNKK 6 1 Q92901 Q92901 RPL3L 60S ribosomal protein L3-like 0 ;; 97.071 0.066524 4748560000 5031170 4404300 5667320 7252920 7346510 5179600 8942180 7042680 9239910 FALSE TRUE 4716278.051 4730398.955 5801751.507 7439042.206 6769544.739 6674866.436 7601383.124 7921974.101 7697709.329 0.612685911 0.61452034 0.753698439 0.966396871 0.879423274 0.867123731 0.987486381 1.029133962 1 22.87599776 3.583586096 0.68955958 0.983634822 0.546693207 0.879482932 0.052881613 0.309804995 0.276855906 0.028634873 0.08625362 3833.417278 -3.583586096 -0.436941616 TEMDKS(ph)PFNSPSPQDSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TEMDKSPFNSPSPQDSPR 18 1 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5;P08651-4 P08651-3 NFIC Nuclear factor 1 C-type 1 TEMDKS(1)PFNSPSPQDSPR;TEMDKS(1)PFNSPSPQDSPR 178.19 5.45E-14 387740000 347340 235970 270120 274310 281810 174711 333610 211078 271860 TRUE FALSE 325600.6094 253441.4643 276527.374 281349.259 259677.7794 225147.2295 283588.2776 237431.5529 226484.8097 1.437626699 1.11902191 1.220953292 1.242243395 1.146557156 0.994094173 1.25212935 1.048333234 1 17.78905477 8 0.119048312 0.964440949 2.004836279 0.459154955 0.09910745 102.5035339 0.839510715 0.654282036 17.68225338 100000000 -8 1.04039533 TEMDWVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TEMDWVLK 8 0 P52597;A0A1B0GW42 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 119.27 0.0040145 304090000 591340 517880 529770 508260 586290 368560 580170 468680 774560 FALSE TRUE 554329.085 556224.3741 542336.3946 521302.8121 540245.1484 474957.2889 493178.8945 527195.7297 645280.9322 0.859050775 0.861987929 0.840465552 0.807869543 0.837224721 0.736047302 0.764285554 0.817001872 1 19.29956787 3.382407034 1.613507824 0.804681984 0.859759483 0 0.071268421 0.861949111 4.582819801 0.020834068 0.034136101 2412.165125 -3.382407034 0.055077499 TEMEDLMSSKDDVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TEMEDLMSSKDDVGK 15 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 229.54 4.09E-13 704980000 1658530 1038520 1254830 1312330 1443990 820332 1705690 992213 2215590 FALSE TRUE 1554725.568 1115413.101 1284595.16 1346006.61 1330584.85 1057148.531 1449937.619 1116092.977 1845793.716 0.842307325 0.604299978 0.695958139 0.729229165 0.720874082 0.572733845 0.785536112 0.604668316 1 20.8158099 -1.715541551 2.524172661 1.059301887 0.690017762 0.567100998 0.083817523 10724871.98 8224218.654 4017791.075 0.018991646 0.019251228 1.715541551 -0.369284125 TENDHINLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TENDHINLK 9 0 A8MUA9;A8MU27;P55854;P55854-2 A8MUA9 SUMO3 Small ubiquitin-related modifier 3 0 ;;;; 140.16 0.00010975 3731510000 7395420 6011040 6573520 6271670 6854990 4917640 7705400 6071710 8507470 FALSE TRUE 6932553.863 6456103.656 6729446.999 6432611.67 6316626.737 6337282.837 6550046.803 6829776.359 7087518.297 0.978135586 0.910911745 0.949478607 0.907597187 0.891232512 0.894146946 0.924166475 0.963634388 1 22.75684912 1.047962182 2.929562891 0.999341498 0.92089827 0.507563482 0.025779548 0.186396149 3.437482133 0.023822269 0.00633062 11.16765997 -1.047962182 -0.078443228 TENNDHINLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TENNDHINLK 10 0 P61956;P61956-2 P61956 SUMO2 Small ubiquitin-related modifier 2 0 ;;;;; 167.11 5.34E-06 17187700000 46164400 35807700 41336100 38618000 42609400 31631200 49588900 35710800 49638400 FALSE TRUE 43275052.61 38458939.37 42316611.81 39609003.26 39263029.6 40762613.95 42153504.81 40169371.99 41353430.36 1.046468267 0.930006024 1.023291452 0.957816629 0.949450366 0.985713001 1.019347233 0.971367348 1 25.30150367 1.988877639 24.27765618 0.999923447 0.978082111 0.031272271 0.035676117 974.4483744 2127002.037 0.012913873 0.008911844 97.47149754 -1.988877639 -0.021841335 TENPLILIDEVDKIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TENPLILIDEVDKIGR 16 1 K7EKE6;K7EJE8;P36776-2;P36776;P36776-3 K7EKE6 LONP1 "Lon protease homolog, mitochondrial" 0 ; 87.287 0.0050338 13474000 17248.5 21201.6 18172.1 19107.1 25018 13787.7 21114.4 18941.1 34871 FALSE TRUE 16168.94717 22771.38852 18603.15079 19597.42053 23053.1872 17767.98517 17948.49174 21305.93803 29050.80482 0.556574844 0.78384708 0.640366107 0.674591312 0.793547282 0.611617656 0.617831136 0.733402677 1 14.82629051 0.953084592 14.15187498 1.000000002 0.675625082 0.665352061 0.073387829 14.03121467 4233.088336 0.066718334 0.01668051 8.976036138 -0.953084592 -0.32437492 TENSWGEPS(ph)SPSTLVDNGTAAWGKPPSSGSGWGDHPAEPPVAFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TENSWGEPSSPSTLVDNGTAAWGKPPSSGSGWGDHPAEPPVAFGR 45 1 A0A1B0GU24;Q9HCJ0-2;Q9HCJ0;K7ELY5 A0A1B0GU24 TNRC6C Trinucleotide repeat-containing gene 6C protein 1 TENSWGEPS(0.395)S(0.395)PS(0.105)T(0.105)LVDNGTAAWGKPPSSGSGWGDHPAEPPVAFGR 87.676 3.97E-05 98939000 33089 30048 40667 44934 37986 24578 30564 20673 21844 TRUE FALSE 31018.01856 32272.78518 41631.64044 46087.08251 35002.73279 31673.26961 25981.21194 23254.06956 18198.09528 1.704465114 1.773415552 2.28769219 2.532522322 1.923428372 1.740471688 1.427688532 1.277829861 1 14.15149984 1.689261468 1.351152633 1.093778753 2.064399287 0.713063264 0.241070125 0.239015833 0.835162869 0.213023573 0.080083264 48.89466419 -1.689261468 0.970620535 TENVFVDEPLIHATTYIPLMDNADS(ph)SPVVDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TENVFVDEPLIHATTYIPLMDNADSSPVVDKR 32 1 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 1 TENVFVDEPLIHATTYIPLMDNADS(0.5)S(0.5)PVVDKR;TENVFVDEPLIHATTYIPLMDNADS(0.5)S(0.5)PVVDKR 173.22 7.00E-15 106662000 77984 76219 74454 71749 97640 59882 114986 84265 106210 TRUE FALSE 73103.12065 81862.33407 76220.08404 73590.20081 89971.74826 77168.9613 97744.91678 94785.67074 88482.86486 0.826183926 0.925177255 0.861410672 0.831688722 1.016826799 0.872134525 1.104676221 1.071231937 1 16.43311048 1.999398394 1.460921182 1.066649684 0.879747792 0.56844785 0.06542171 0.265040876 1.054693915 0.040263188 0.019181942 99.86157093 -1.999398394 -0.186901892 TEPAAEAEAASGPSES(ph)PSPPAAEELPGSHAEPPVPAQGEAPGEQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TEPAAEAEAASGPSESPSPPAAEELPGSHAEPPVPAQGEAPGEQAR 46 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 1 TEPAAEAEAASGPSES(0.999)PS(0.001)PPAAEELPGSHAEPPVPAQGEAPGEQAR 351.58 5.78E-159 287120000 50526 52012 48392 37071 54974 49180 62415 42325 64945 TRUE FALSE 47363.66785 55863.0226 49539.88109 38022.30462 50656.56379 63377.46763 53056.45018 47609.36942 54105.25994 0.875398582 1.032487833 0.915620425 0.702746917 0.936259503 1.171373499 0.980615383 0.87993976 1 15.72348123 2.462086388 24.99951677 1.015040264 0.903104603 0.227264708 0.106411675 403.3093138 670606.2407 0.037751059 0.031595646 289.7919973 -2.462086388 -0.111935662 TEPS(ph)SPLSDPSDIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TEPSSPLSDPSDIIR 15 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 TEPS(0.727)S(0.273)PLSDPSDIIR 210.91 1.73E-09 85126000 202720 185790 191590 196220 171920 166970 220270 167360 136520 TRUE FALSE 190032.1171 199546.0849 196134.6053 201255.3374 158418.0967 215171.5285 187242.5584 188255.2644 113733.93 1.670848066 1.754499162 1.724503894 1.76952768 1.392883343 1.891885107 1.646321008 1.655225176 1 16.79530319 -2.332336907 0.44704804 2.03E-14 1.711277758 0.746842315 0.1260861 37.96419728 2.108700858 37.5663962 0.060997881 0.004652251 2.332336907 1.711277758 TEPSS(ph)PLSDPSDIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TEPSSPLSDPSDIIR 15 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 TEPS(0.001)S(0.999)PLSDPSDIIR;TEPS(0.009)S(0.991)PLSDPSDIIR;TEPS(0.064)S(0.936)PLSDPSDIIR;TEPS(0.095)S(0.903)PLS(0.002)DPSDIIR;TEPS(0.014)S(0.986)PLSDPSDIIR 248.99 1.88E-18 1635185000 2405880 2016690 2205530 2144860 1848850 1849620 2356910 1740140 1457870 TRUE FALSE 2255300.265 2166007.826 2257846.213 2199900.739 1703648.779 2383575.268 2003513.226 1957400.31 1214542.079 1.856914062 1.783394634 1.859010283 1.811300553 1.402708732 1.962530002 1.649603798 1.611636471 1 20.21198104 -2.295241043 0.264332056 1.36E-10 1.843510732 0.735752886 0.144612389 18.50031824 0.643425912 11.09071584 0.181146451 0.005067094 2.295241043 1.843510732 TEPTS(ph)PTPSAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TEPTSPTPSAFK 12 0 Q86XN7-2;Q86XN7 Q86XN7-2 PROSER1 Proline and serine-rich protein 1 1 TEPT(0.002)S(0.988)PT(0.008)PS(0.001)AFK;TEPT(0.018)S(0.922)PT(0.06)PSAFK;TEPT(0.023)S(0.488)PT(0.488)PSAFK 236.08 4.81E-16 523770000 2369090 1634340 2055940 2094770 2146180 1465780 2232220 1621070 1872620 TRUE FALSE 2220812.886 1755348.234 2104707.868 2148525.345 1977627.68 1888926.891 1897519.334 1823464.158 1560067.624 1.423536295 1.125174452 1.349113227 1.377200136 1.2676551 1.210798084 1.216305822 1.168836613 1 20.57317714 0.924121617 0.756601685 1.000762082 1.290563904 0.581728856 0.081348808 0.593340545 0.747355486 0.077478252 0.028946576 8.396950971 -0.924121617 0.289801822 TEQELPRPQS(ph)PSDLDS(ph)LDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TEQELPRPQSPSDLDSLDGR 20 1 P54259 P54259 ATN1 Atrophin-1 2 TEQELPRPQS(0.983)PS(0.017)DLDS(1)LDGR;TEQELPRPQS(0.996)PS(0.004)DLDS(1)LDGR 169.13 6.39E-12 220410000 247440 224132 260590 262610 269930 204813 268490 225330 258850 TRUE FALSE 231953.1721 240726.9665 266771.3179 269349.0172 248730.7866 263939.1882 228232.417 253462.9465 215646.2628 1.075618789 1.116304838 1.237078327 1.249031695 1.153420344 1.223945107 1.058364815 1.175364429 1 17.71830719 0.656429957 0.784803724 1.00175307 1.173710103 0.370254398 0.065152976 1.269086467 1.417071009 0.064502957 0.022356241 4.533461761 -0.656429957 0.171957032 TEQFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TEQFYR 6 0 O76021;J3QSV6;I3L3U9;I3L3C4;I3L234 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 ; 132.72 0.034376 383410000 459750 478580 460220 471180 463000 356960 485640 408300 383110 FALSE TRUE 430975.0682 514014.5612 471136.6357 483271.2765 426637.8477 460008.5572 412822.7905 459277.1538 319166.466 1.350314378 1.610490499 1.476147045 1.514166831 1.336725167 1.441280981 1.293440366 1.438989376 1 18.28394955 -1.246928267 0.223573907 0.631400735 1.551503321 0.712430746 0.08794518 9.428366594 0.432918065 2.212646475 0.17732672 0.056633282 1.246928267 0.920102586 TES(ph)PATAAETASEELDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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;T(0.007)ES(0.993)PATAAETASEELDNR;TES(1)PATAAETASEELDNR;TES(1)PATAAETASEELDNR;TES(1)PATAAETASEELDNR;TES(1)PATAAETASEELDNR 506.48 4.95E-267 4038790000 636534 565891 589225 586211 577917 493259 717528 501212 623939 TRUE FALSE 596694.4732 607790.1584 603201.6953 601254.1667 532529.73 635654.8659 609941.3376 563789.4215 519799.5501 1.147931877 1.169277962 1.160450591 1.1567039 1.024490556 1.222884602 1.17341644 1.084628529 1 18.98759586 0.984002702 3.978847643 1.000352366 1.153631793 0.493884287 0.049746478 0.153463936 6.992358616 0.04528567 0.011597677 9.63835021 -0.984002702 0.153279427 TESDDLHTFLLEIK ddPTM_SK-BR-3_Pertuzumab_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 ; 191.06 5.32E-07 79405000 240057 202490 232116 228634 250800 161164 295760 207360 315700 FALSE TRUE 225032.2609 217482.5703 237621.9011 234501.1355 231103.1797 207689.4305 251413.5337 233249.3525 263007.6305 0.855611149 0.826905934 0.903479115 0.89161343 0.878693821 0.789670741 0.955917261 0.886853937 1 18.00474513 -5 0.147989323 1.466463591 0.832068699 0.500240643 0.042118184 111.0102529 0.982635035 15.07902561 0.210359728 1.00E-05 5 -0.634394892 TESSTEGKEQEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TESSTEGKEQEEK 13 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 179.5 1.25E-05 953130000 1102330 513560 669790 649100 778170 435880 877900 553360 1062810 FALSE TRUE 1033337.133 551584.5168 685677.7351 665757.0049 717055.6672 561711.4801 746267.045 622448.2141 885420.145 1.16705853 0.622963595 0.774409459 0.75191084 0.809847925 0.634401062 0.842839469 0.702997574 1 19.75600267 -1.204724232 4.882959264 1.000030047 0.770329543 0.151092133 0.152496282 4.34E-05 7.06E-06 0.128344856 0.030247219 0.062413102 1.204724232 -0.229700504 TET(ph)PPPLASLNVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TETPPPLASLNVSK 14 0 K7ELG9;Q3MHD2;Q3MHD2-2 K7ELG9 LSM12 Protein LSM12 homolog 1 T(0.001)ET(0.999)PPPLASLNVSK;T(0.131)ET(0.869)PPPLASLNVSK;T(0.006)ET(0.994)PPPLASLNVSK 146.27 9.34E-05 446962000 1108120 603650 724350 649800 654910 606810 922720 623210 578850 TRUE FALSE 1038764.747 648344.8741 741531.9241 666474.9681 603476.0104 781986.1963 784366.7021 701019.1404 482236.1955 2.154058026 1.344455021 1.537694456 1.3820509 1.251411686 1.621583373 1.626519762 1.453684205 1 18.87938041 -2.223013072 1.20576201 0.025179611 1.524828669 0.322994539 0.246873655 19127.25906 2572.800465 50481.21162 0.065109157 0.005983936 2.223013072 1.499649058 TETGQELECLQDHLDDLVVECR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TETGQELECLQDHLDDLVVECR 22 0 Q92896;Q92896-3;Q92896-2;H3BM42 Q92896 GLG1 Golgi apparatus protein 1 0 ;;; 257.86 3.70E-37 96977000 89453.1 110953 84593 95471.1 132313 88781 138166 109449.9 98903 FALSE TRUE 83854.39015 119168.0756 86599.58591 97921.05006 121921.6707 114410.6335 117449.291 123114.9609 82395.45036 1.017706558 1.446294365 1.05102388 1.188427876 1.479713627 1.388555229 1.425434177 1.494196104 1 16.33027706 2.754397742 24.21658633 1.38945087 1.200128467 0.186142083 0.178988208 790.2288646 1208339.096 0.049558186 0.052386956 568.0646203 -2.754397742 -0.189322403 TETVVDDWDEEFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TETVVDDWDEEFDR 14 0 Q9P275;K7EKN3;K7EKL7;K7EIH0 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36 0 ;; 218.54 1.24E-11 195393000 327688 240909 280217 279599 331749 208522 305899 236061 460900 FALSE TRUE 307178.593 258746.153 286863.8796 286773.9837 305694.7718 268718.9163 260032.2848 265533.7355 383972.8125 0.800000893 0.673865817 0.747094248 0.746860128 0.796136502 0.699838394 0.677215356 0.691543065 1 18.55064464 -1.159737314 4.720765628 1.000029854 0.723509334 0.779218764 0.045236341 1.39E-05 2.48E-06 0.042927814 0.010117092 0.069224956 1.159737314 -0.27652052 TETVVDDWDEEFDRGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TETVVDDWDEEFDRGK 16 1 Q9P275;K7EKN3;K7EKL7;K7EIH0 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36 0 ;; 212.25 4.56E-12 145810000 149500 161758 176831 177341 182139 148328 218312 159985 245914 FALSE TRUE 140143.0619 173734.7306 181025.5148 181891.8703 167834.5377 191147.8857 185578.1423 179959.4794 204869.3647 0.684060606 0.848026892 0.883614371 0.88784319 0.81922711 0.933023275 0.905836471 0.878410882 1 17.64434474 5.503597229 1.026328855 0.897248367 5.33E-18 0.686446115 0.045854977 4.176762351 1.133719358 0.012185103 5.995785792 318857.9346 -5.503597229 -0.897248367 TEVHIRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TEVHIRPK 8 1 P28838-2;P28838;H0Y9Q1 P28838-2 LAP3 Cytosol aminopeptidase 0 71.223 0.029621 189160000 482550 460980 516240 524440 547410 450380 549830 467190 640170 FALSE TRUE 452348.0569 495111.4388 528485.4566 537898.0183 504418.6267 580397.3947 467388.0959 525519.6999 533321.4913 0.848171439 0.928354561 0.990932233 1.008581179 0.945805926 1.088269279 0.876372138 0.985371316 1 19.02464594 4.705808012 1.528742725 0.979036401 0.803461529 0.409249183 0.05288118 1.06064382 2.439076537 0.013290774 0.275738916 50793.48511 -4.705808012 -0.175574872 TEVLS(ph)PNSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TEVLSPNSK 9 0 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 T(0.001)EVLS(0.996)PNS(0.003)K;TEVLS(0.982)PNS(0.018)K;TEVLS(0.755)PNS(0.245)K;TEVLS(1)PNSK 175.57 5.64E-05 739060000 2111520 1430640 1632430 1636580 1545460 1230940 2124020 1373730 1406890 TRUE FALSE 1979363.732 1536566.074 1671152.01 1678577.414 1424085.806 1586292.395 1805542.919 1545243.214 1172070.97 1.688774641 1.310983817 1.42581128 1.432146565 1.215016703 1.35340985 1.540472348 1.318387072 1 20.1606285 -2.735289611 0.528957568 1.31E-22 1.40891144 0.496651947 0.130557109 194.4749433 8.812154044 222.2003617 0.054136503 0.001839545 2.735289611 1.40891144 TEVS(ph)PVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TEVSPVPR 8 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 1 TEVS(1)PVPR;TEVS(1)PVPR;T(0.001)EVS(0.999)PVPR 126.29 0.0012853 955310000 1428210 1243660 1377730 1259990 1322390 1165860 1633620 1211450 1311090 TRUE FALSE 1338820.886 1335741.88 1410410.406 1292323.477 1218534.824 1502424.856 1388673.847 1362702.199 1092260.609 1.225733927 1.222914998 1.291276454 1.183164042 1.115608137 1.375518666 1.271375929 1.247598044 1 20.05888569 -1.211103428 4.312182215 0.999902202 1.24673986 0.555181988 0.067840866 6.20E-05 1.13E-05 0.063802803 0.015032521 0.061503038 1.211103428 0.246837658 TEVSETARPS(ph)SPDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TEVSETARPSSPDTR 15 1 O75132 O75132 ZBED4 Zinc finger BED domain-containing protein 4 1 TEVSET(0.007)ARPS(0.497)S(0.497)PDTR 85.563 0.0047808 257720000 319720 286730 306160 273200 296920 210950 320480 262470 227680 TRUE FALSE 299709.2959 307959.7875 313422.2598 280210.7745 273601.1009 271847.8405 272426.9992 295239.9573 189678.7371 1.580089052 1.62358624 1.652384788 1.477291439 1.442444762 1.433201447 1.436254813 1.556526376 1 17.53319844 -3.071939402 0.172882827 1.66E-11 1.68475604 0.849298415 0.070943881 22.38943079 0.391972009 8.528855403 0.27364687 0.000847346 3.071939402 1.68475604 TEWLDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 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 ;;;;;;;;; 179.97 0.0016129 51279090000 54544910 39399440 42869560 39038940 42658030 32069600 53438070 37443680 67309700 FALSE TRUE 51131041.45 42316615.53 43886446.21 40040745.29 39307840.4 41327572.91 45425527.5 42118605.87 56075276.23 0.911828615 0.754639449 0.782634508 0.714053465 0.700983447 0.737001682 0.810081208 0.751108308 1 25.74086149 -1.294062737 3.16644576 1.001348691 0.767904343 0.597985964 0.059162135 11278145.14 15604451.96 145220.8855 0.013339518 0.050808604 1.294062737 -0.233444348 TEWLDGKHVVFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TEWLDGKHVVFGK 13 1 P62937;P62937-2 P62937;P62937-2 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed" 0 ; 155.08 2.79E-05 4542700000 11839300 11768700 12310900 12470500 16667100 8674900 14947900 10713800 7077800 FALSE TRUE 11098299.35 12640066.79 12602920.36 12790514.14 15358133.2 11179202.8 12706601.16 12051441.51 5896469.456 1.882193986 2.143666967 2.137367192 2.169181786 2.604632028 1.895914647 2.154950731 2.043840234 1 22.49141996 0.088102696 1.04007304 0.99232739 2.154300034 0.768612408 0.195344611 2.807918097 2.784115259 0.233970558 0.054255579 1.224905814 -0.088102696 1.161972645 TEYGDLELCIEVVDNVQDAIDHIHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TEYGDLELCIEVVDNVQDAIDHIHK 25 0 P54886-2;P54886 P54886-2 ALDH18A1 Delta-1-pyrroline-5-carboxylate synthase;Glutamate 5-kinase;Gamma-glutamyl phosphate reductase 0 140.59 2.25E-07 12080000 28572 19386 23467 21603 28814 24559 26630 24071 41017 FALSE TRUE 26783.72952 20821.35961 24023.64832 22157.36955 26551.06467 31648.78462 22637.07872 27076.31734 34170.99772 0.783814676 0.609328407 0.703042051 0.648426181 0.777005837 0.926188485 0.66246467 0.792377137 1 15.06048475 2.624429864 5.023457162 0.809380769 0.676578726 0.334066175 0.099795046 0.280227365 10.5359325 0.03057219 0.028705563 421.1432687 -2.624429864 -0.132802043 TEYLSNADER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TEYLSNADER 10 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0;H0YJ21 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 99.973 0.010958 0 195840 258320 213720 221820 278730 174210 248020 230240 260870 FALSE TRUE 183582.724 277446.2816 218789.5393 227512.2767 256839.6701 224501.5989 210831.7035 258985.9708 217329.1117 0.844722194 1.276618118 1.006719889 1.046855964 1.181800579 1.033002883 0.970103369 1.191676388 1 17.72952191 TEYNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TEYNLR 6 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 135.82 0.031258 397770000 422780 642480 518300 500340 613110 405770 537850 551520 490710 FALSE TRUE 396318.9545 690049.8877 530594.3208 513179.5715 564958.8138 522909.2119 457204.3857 620378.486 408807.3309 0.969451682 1.687958692 1.297908038 1.255309122 1.381968402 1.279109185 1.118385976 1.517532684 1 18.64106154 -4.257160549 0.178050358 1.40E-08 1.406690872 0.139283938 0.203992764 154.5688361 1.88622697 55.58481324 0.625341181 5.53E-05 4.257160549 1.406690858 TFCPAHK ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;; 101.69 0.0088735 21821610000 15130922 16011210 15627130 15682390 18052290 13033950 19812050 15706640 19160220 FALSE TRUE 14183904.6 17196696.65 15997812.9 16084826.68 16634535.96 16796639.78 16841417.03 17667648.58 15962255.5 0.88859025 1.077335007 1.002227593 1.007678813 1.042116884 1.052272329 1.055077525 1.106839104 1 23.92816119 2.562898018 2.327743487 1.057970106 1.008862848 0.204045985 0.052716987 0.556626673 5.989642078 0.018467184 0.016382053 365.5089519 -2.562898018 -0.049107258 TFCQLILDPIFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TFCQLILDPIFK 12 0 P13639 P13639 EEF2 Elongation factor 2 0 ; 173.72 7.52E-05 339760000 1141860 1088640 1184840 1115490 1231210 879060 1331210 977930 1159720 FALSE TRUE 1070393.021 1169244.038 1212944.964 1144115.362 1134515.733 1132830.352 1131607.419 1100026.713 966155.2399 1.107889267 1.210203071 1.255434856 1.184194128 1.174258221 1.1725138 1.171248027 1.138561038 1 19.88189549 0.419516707 0.627382456 0.994148987 1.200786795 0.69839583 0.037248308 1.072485244 0.673274418 0.050475602 0.015169256 2.627342598 -0.419516707 0.206637808 TFDHYCEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TFDHYCEYR 9 0 Q14204;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 187.5 4.05E-05 1713240000 1521660 3063280 1517860 1647120 3370240 943100 1651390 2983170 2795570 FALSE TRUE 1426422.017 3290088.439 1553864.356 1689387.888 3105554.945 1215357.66 1403779.4 3355625.341 2328971.307 0.612468695 1.41267882 0.667189137 0.725379434 1.333444915 0.521843123 0.602746541 1.44081867 1 21.15126143 5.011595682 18.42160722 0.925356653 0.100841015 0.085360028 0.341375234 72773876.13 1911701003 0.078720358 1553276437 102705.9684 -5.011595682 -0.824515638 TFDQLTPEESKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 ;;;;;; 206.45 5.63E-08 5289490000 5302960 5091850 4921510 5247440 6457390 3269086 5898700 4492940 8195020 FALSE TRUE 4971057.2 5468855.872 5038250.541 5382098.194 5950252.637 4212818.059 5014244.696 5053893.449 6827218.22 0.728123379 0.801037215 0.737965358 0.788329598 0.871548623 0.617062165 0.734449161 0.740256615 1 22.70286644 -0.824480054 6.863031781 1.000000002 0.752636623 0.592870085 0.064495733 2.22E-09 3.24E-10 0.05971588 0.014075168 0.149802805 0.824480054 -0.247363379 TFEHVTSEIGAEEAEEVGVEHLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 TFEHVTSEIGAEEAEEVGVEHLLR 24 0 P51665;H3BNT7;H3BTM8 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ;;;;;; 340.33 1.56E-87 754953000 146357.9 180639 164152.4 151865.1 168333 142548.3 183867.7 151146.1 181428.5 FALSE TRUE 137197.6203 194013.6995 168046.1724 155762.2156 155112.8052 183699.6801 156298.4453 170017.0233 151146.9113 0.90771038 1.283610084 1.111806857 1.030535221 1.02623867 1.215371711 1.034082959 1.124846164 1 17.20559197 3.477626676 24.71751576 1.077919575 1.146684355 0 0.110484646 37.1607736 1817339.023 0.027847718 0.03895868 3003.493361 -3.477626676 0.06876478 TFEINPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 TFEINPR 7 0 P14625;H0YIV0;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ;;;;;; 182.95 0.0015117 2355157000 2975349 3519110 3269840 3575690 3519870 2566336 3809360 2897610 2464720 FALSE TRUE 2789127.217 3779668.566 3347402.149 3667448.259 3243433.609 3307195.542 3238181.832 3259382.987 2053342.309 1.358335239 1.840739632 1.630221193 1.786087124 1.579587385 1.610640139 1.577029713 1.587354905 1 20.96954273 -0.544243344 0.48003371 0.865666799 1.674698071 0.692202752 0.129791376 4.748380323 0.936295428 1.148023679 0.059598687 0.285598983 0.544243344 0.809031272 TFEMSDFIVDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TFEMSDFIVDTR 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 83.862 0.029222 216020000 21635 30254 25261 27761 32258 22505 29989 26223 27047 FALSE TRUE 20280.90397 32494.03764 25860.20285 28473.39426 29724.5868 29001.82816 25492.42785 29496.99927 22532.68097 0.900066175 1.44208484 1.147675365 1.263648755 1.319176659 1.287100643 1.131353517 1.309076328 1 14.45973136 -1.153416088 5.468498436 0.999994452 1.236435768 0.188091194 0.145215134 8.63E-06 1.34E-06 0.123544559 0.029119049 0.070239904 1.153416088 0.236441316 TFFPEYTHQLFGDDETAFGYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TFFPEYTHQLFGDDETAFGYK 21 0 O14929 O14929 HAT1 Histone acetyltransferase type B catalytic subunit 0 211.03 1.72E-22 82896000 92593 69366 86114 86197 83344 62619 83469 81425 67214 FALSE TRUE 86797.76941 74501.93082 88156.66475 88408.96095 76798.49843 80696.08877 70953.59834 91591.09049 55995.54918 1.550083367 1.330497368 1.574351284 1.578856931 1.371510764 1.441116123 1.267129252 1.63568519 1 15.77302454 -2.958652009 0.347237371 8.86E-11 1.47113952 0.580253815 0.122731407 62.12051263 1.923223378 45.82676482 0.091363829 0.001099887 2.958652009 1.47113952 TFGETHPFTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TFGETHPFTK 10 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 121.83 0.00050465 1258200000 3531100 4007000 3874400 3818800 4334100 3014300 4634600 3704700 5225000 FALSE TRUE 3310094.754 4303682.449 3966302.598 3916796.873 3993717.269 3884479.477 3939684.756 4167239.95 4352913.745 0.760431965 0.988690036 0.911183366 0.899810357 0.917481371 0.892386044 0.905068418 0.95734494 1 22.05355 -5 0.200166782 1.409240946 0.896567667 0.256027341 0.056924866 228.9996001 2.267313973 37.37026505 0.127348555 1.00E-05 5 -0.512673279 TFHHVYSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TFHHVYSGK 9 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 147.4 5.35E-05 1468080000 1861680 2317580 1911200 1852840 2444790 1342790 2179350 2063270 2760100 FALSE TRUE 1745160.772 2489176.035 1956534.567 1900387.011 2252786.055 1730431.675 1852576.7 2320873.801 2299421.479 0.758956454 1.082522738 0.850881226 0.826463103 0.979718627 0.752550887 0.805670781 1.009329443 1 21.1328395 TFHIEEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TFHIEEPR 8 0 Q969N2;Q969N2-5;Q969N2-6;Q969N2-4;A0A1W2PP53;Q969N2-2;A0A1W2PNP0;A0A1W2PPR6;Q969N2-3;A0A1W2PR73 Q969N2 PIGT GPI transamidase component PIG-T 0 ; 128.36 0.0011368 323730000 530120 777760 605870 630230 836610 447660 783140 710250 664480 FALSE TRUE 496940.7355 835346.1597 620241.5225 646402.7688 770906.0253 576892.1748 665715.4273 798926.276 553573.9953 0.897695231 1.509005421 1.120431104 1.16768991 1.392597976 1.042122968 1.202577131 1.443214968 1 19.07841665 -1.876359899 2.481441723 0.885652106 1.231784135 0.120993757 0.186298181 26779915.6 14779779.05 17978269.98 0.040037772 0.013293523 1.876359899 0.346132029 TFHIFYYLLSGAGEHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TFHIFYYLLSGAGEHLK 17 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 174.95 7.46E-10 28674000 43490 109040 64416 64277 87600 24897 35843 71482 55029 FALSE TRUE 40768.03853 117113.4351 65943.97794 65926.45664 80720.24936 32084.35973 30468.6749 80406.68505 45844.3044 0.889271613 2.55459073 1.438433385 1.438051193 1.760747609 0.699854871 0.664612001 1.753907843 1 15.48445489 2.24826606 24.97940122 0.954755822 1.711836806 0.230254405 0.508679908 218.7058861 562894.6626 0.171267716 0.141611455 177.1193705 -2.24826606 0.757080984 TFIAIKPDGVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TFIAIKPDGVQR 12 1 Q32Q12;P22392-2;J3KPD9;P22392;E7ERL0;E5RHP0;F6XY72;C9K028;P15531;P15531-2 Q32Q12;P15531 NME1-NME2;NME2;NME1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Nucleoside diphosphate kinase A 0 ; 142.57 5.61E-05 23105000000 11308900 11009000 10906100 10830000 13077800 9079900 15349600 11035400 15869400 FALSE TRUE 10601096.14 11824117.81 11164797.84 11107916.14 12050722.34 11701119.73 13048069.98 12413193.98 13220694.62 0.801856214 0.89436434 0.844494042 0.840191567 0.911504477 0.885060889 0.986942846 0.938921467 1 23.65629464 1.977429893 1.086044488 0.985217865 0.853098394 0.739971242 0.032138707 0.244289324 0.530847118 0.02308041 0.010616961 94.9357734 -1.977429893 -0.13211947 TFLDKDAQRLS(ph)PIPEEVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TFLDKDAQRLSPIPEEVPK 19 2 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 T(0.012)FLDKDAQRLS(0.988)PIPEEVPK;TFLDKDAQRLS(1)PIPEEVPK 107.75 0.00015046 479081000 1036870 788260 858770 933540 1225450 514860 1006470 787210 1721660 TRUE FALSE 971974.1576 846623.5906 879140.4299 957496.2169 1129208.1 663491.7239 855559.1671 885494.9014 1434303.824 0.677662669 0.590267959 0.612938776 0.667568615 0.787286544 0.462587991 0.596497864 0.617369128 1 20.45191923 -1.362854865 3.152937292 1.00373071 0.619059462 0.673283965 0.081615251 17991012.6 23747751 617420.161 0.018702153 0.043365578 1.362854865 -0.384671248 TFLEGDWTS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TFLEGDWTSPSK 12 0 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 TFLEGDWT(0.263)S(0.736)PS(0.002)K;TFLEGDWTS(0.661)PS(0.339)K;TFLEGDWT(0.001)S(0.989)PS(0.01)K;TFLEGDWT(0.02)S(0.98)PSK;TFLEGDWT(0.002)S(0.983)PS(0.015)K 225.36 1.24E-11 841456000 3707770 2516110 3080910 2767590 3069890 2394780 4013600 2609550 3551220 TRUE FALSE 3475707.294 2702405.402 3153990.64 2838611.045 2828793.223 3086114.11 3411797.94 2935358.062 2958498.44 1.174821405 0.91343817 1.066078183 0.959476945 0.95615843 1.043135284 1.153219449 0.992178337 1 21.4964337 2.004148659 24.73893888 1.073662076 1.004468289 0.001616591 0.084232209 200.4016156 1195011.577 0.02887167 0.021231713 100.9598413 -2.004148659 -0.069193787 TFLEGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TFLEGFR 7 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 0 103.02 0.019706 55402000 125280 192960 145860 146040 224410 124190 160870 193040 194050 FALSE TRUE 117438.9484 207246.9592 149319.8681 149787.6336 206785.7438 160041.6369 136749.0369 217141.4689 161661.8014 0.726448347 1.281978534 0.923655847 0.926549329 1.27912557 0.989978063 0.845895788 1.343183529 1 17.3026193 4.769681 23.38109294 1.056217813 0.726446984 0.280180076 0.172940326 7555.350304 5676182.415 0.039169029 4.64490375 58841.12942 -4.769681 -0.329770829 TFLRPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TFLRPPK 7 1 O75937;S4R3J5 O75937 DNAJC8 DnaJ homolog subfamily C member 8 0 67.032 0.086761 0 538020 800410 699080 779330 846000 597120 714890 755890 843050 FALSE TRUE 504346.2886 859673.1892 715662.5077 799328.9272 779558.5726 769498.8506 607698.8812 850264.5304 702339.5087 0.718094714 1.224013712 1.018969457 1.138094778 1.109945494 1.095622332 0.865249461 1.210617543 1 19.42180907 -0.256687804 7.485151202 1.000000002 1.053482483 0.007995323 0.154561452 0 0 0.134562679 0.031716727 0.553748033 0.256687804 0.053482481 TFLVGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 TFLVGER 7 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;;;;;; 143.94 0.0055544 3320740000 2820170 3306820 3300510 3278040 3268900 2838720 3451380 2890870 2865020 FALSE TRUE 2643660.594 3551660.394 3378799.656 3362160.056 3012173.78 3658212.381 2933877.61 3251801.483 2386829.653 1.107603381 1.488024245 1.415601508 1.408630084 1.261997804 1.532665884 1.229194386 1.362393616 1 21.18666418 0.122030997 0.69310705 0.98776192 1.382273016 0.418680967 0.127268507 3.125420774 1.787305827 0.212590373 0.041905659 1.324436061 -0.122030997 0.394511096 TFLVWVNEEDHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 TFLVWVNEEDHLR 13 0 P12277;H0YJG0 P12277 CKB Creatine kinase B-type 0 ;;;;;; 209.21 3.97E-08 522581000 782095 1065711 941567 1077264 920707 777331 1014569 700481 483694 FALSE TRUE 733145.07 1144617.351 963901.4139 1104908.418 848398.3862 1001733.841 862443.7972 787937.5948 402962.3466 1.819388526 2.840506963 2.392038417 2.741964423 2.105403627 2.485924179 2.14025902 1.955362831 1 18.62028551 0.682258621 0.744547984 0.986149143 2.483064701 0.685303677 0.293793889 0.573930103 0.598980147 0.264398296 0.093793991 4.811257721 -0.682258621 1.496915559 TFNMDEYVGLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TFNMDEYVGLPR 12 0 D6RAY7;D6R9P4;D6RFF8;P46926;D6R917;D6RB13;Q8TDQ7-3;Q8TDQ7;Q8TDQ7-2 D6RAY7;Q8TDQ7-3 GNPDA1;GNPDA2 Glucosamine-6-phosphate isomerase;Glucosamine-6-phosphate isomerase 1;Glucosamine-6-phosphate isomerase 2 0 141.73 0.00014136 34127000 53051 77230 73898 73394 79767 35869 45986 53589 68357 FALSE TRUE 49730.63261 82948.18956 75650.89546 75277.4143 73502.42158 46223.79802 39090.82621 60279.70461 56947.7751 0.873267349 1.45656594 1.328425831 1.321867521 1.29069874 0.811687514 0.686432897 1.058508511 1 15.79735186 2.24124543 24.95889289 0.842272293 1.294969102 0.479613763 0.183383181 45.1249098 419500.2464 0.061524035 0.049314127 174.2791488 -2.24124543 0.452696809 TFNQVEIKPEMIGHYLGEFSITYKPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TFNQVEIKPEMIGHYLGEFSITYKPVK 27 2 K7EM56;A0A0B4J2B4;S4R417;K7ELC2;P62841 K7EM56 RPS15 40S ribosomal protein S15 0 ;; 264.85 1.62E-53 2127936000 3710350 2621095 2927430 2727833 3322640 2102749 3966680 2987330 3439900 FALSE TRUE 3478125.817 2815163.601 2996870.022 2797833.813 3061693.257 2709778.501 3371913.159 3360304.726 2865758.467 1.213684215 0.982345035 1.045751083 0.976297844 1.068371006 0.94557114 1.176621546 1.17257081 1 21.45048559 1.704680047 11.5868623 1.130044198 1.03177095 0.140657155 0.087238525 0.163770593 42.61036547 0.036529149 0.019937056 50.66173357 -1.704680047 -0.098273248 TFNTSTGGLLLPSDTKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TFNTSTGGLLLPSDTKR 17 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 143.22 8.93E-07 463880000 368120 294900 326770 311270 359170 224970 406210 289260 532710 FALSE TRUE 345080.0263 316734.7028 334521.1387 319257.7152 330962.237 289915.1869 345302.5816 325374.7477 443797.2596 0.777562319 0.713692336 0.753770177 0.719377392 0.74575097 0.653260426 0.778063799 0.733160786 1 18.75954123 -0.072171599 1.141150265 1.001673434 0.731787468 0.844693605 0.035795313 4.401668089 4.261521054 0.059922373 0.009288526 0.846892722 0.072171599 -0.269885966 TFNVDMYEEIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 135.58 0.00012512 366944000 422270 469160 465030 499080 514680 390891 526000 440860 431030 FALSE TRUE 395840.8745 503897.0946 476060.7312 511887.2377 474259.1089 503734.8861 447131.1831 495902.3415 359088.3084 1.102349659 1.403267895 1.325748347 1.425519087 1.320731134 1.402816172 1.245184465 1.381003864 1 18.45397916 -1.109220146 3.832690985 0.999874375 1.332509618 0.534921118 0.095298324 2331247.813 1350563.189 2281.509355 0.019705891 0.077764226 1.109220146 0.332635242 TFQARPLS(ph)ADLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TFQARPLSADLTK 13 1 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 TFQARPLS(1)ADLTK 103.9 0.00095323 216490000 175920 160230 153410 145750 167170 95981 173750 135130 231850 TRUE FALSE 164909.4812 172093.5959 157048.9576 149490.1918 154041.1425 123689.1566 147697.8005 152001.278 193152.7372 0.853777604 0.890971562 0.813081709 0.773948089 0.797509498 0.64036968 0.764668431 0.78694861 1 17.5593826 3.57749201 1.842130367 0.7700319 0.872905043 0.074386432 0.089157078 0.534836853 3.607407461 0.024051382 0.044690421 3780.001831 -3.57749201 0.102873144 TFQEDSSPVVHQS(ph)LQEVSEPLTATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TFQEDSSPVVHQSLQEVSEPLTATK 25 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 TFQEDSSPVVHQS(1)LQEVSEPLTATK;TFQEDSSPVVHQS(1)LQEVSEPLTATK;TFQEDSSPVVHQS(1)LQEVSEPLTATK;TFQEDSSPVVHQS(1)LQEVSEPLTATK 210.68 1.09E-25 896900000 567345 557796 566459 507131 748260 366803 734160 628307 1161030 TRUE FALSE 531835.8892 599095.7962 579895.675 520144.84 689494.6779 472693.0716 624079.5236 706752.512 967246.5925 0.549845193 0.61938269 0.599532404 0.537758255 0.712842706 0.48869965 0.645212429 0.730684933 1 19.88352422 0.872892363 1.806258979 0.9990811 0.592468779 0.826130339 0.059780485 0.180298741 1.154713015 0.049440286 0.013979885 7.462637784 -0.872892363 -0.406612321 TFQQIQEEEDDDYPGSYS(ph)PQDPSAGPLLTEELIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TFQQIQEEEDDDYPGSYSPQDPSAGPLLTEELIK 34 0 Q9NQG5;A2A2M0 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 1 TFQQIQEEEDDDYPGS(0.014)Y(0.02)S(0.844)PQDPS(0.107)AGPLLT(0.014)EELIK;TFQQIQEEEDDDYPGS(0.005)Y(0.022)S(0.946)PQDPS(0.026)AGPLLTEELIK;TFQQIQEEEDDDY(0.001)PGS(0.097)Y(0.082)S(0.618)PQDPS(0.096)AGPLLT(0.107)EELIK 154.42 1.07E-10 196959000 81059 63943 68947 55765.7 64407.9 50770.7 79002 62661.6 82116 TRUE FALSE 75985.66188 68677.40625 70582.4554 57196.74227 59349.56334 65427.3769 67156.38352 70485.0387 68410.30911 1.110734082 1.003904341 1.031751739 0.83608367 0.867552919 0.956396452 0.981670517 1.030327733 1 16.06192613 4.61268606 0.987773581 0.951171774 1.155330356 0.352349326 0.064151762 1.938970917 1.73806856 0.021078296 0.402602241 40990.76844 -4.61268606 0.204158582 TFS(ph)ATVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 TFSATVR 7 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 TFS(0.995)AT(0.005)VR;TFS(0.992)AT(0.008)VR;T(0.047)FS(0.905)AT(0.047)VR;TFS(0.988)AT(0.012)VR;TFS(0.988)AT(0.012)VR;TFS(1)ATVR;TFS(0.771)AT(0.229)VR;TFS(0.966)AT(0.034)VR;T(0.002)FS(0.972)AT(0.026)VR;T(0.416)FS(0.583)AT(0.002)VR;TFS(0.967)AT(0.033)VR;TFS(0.991)AT(0.009)VR 189.73 0.00057774 1.11453E+11 16201687 16816090 16910788 18444076 19863273 15624141 21563110 16778766 20247315 TRUE FALSE 15187652.33 18061170.8 17311919.88 18917382.22 18303291.66 20134576.87 18329921.84 18873631.87 16867907.32 0.900387466 1.070741643 1.026322919 1.121501432 1.085095579 1.193661815 1.086674327 1.118907729 1 24.00777766 5.948199452 0.737975058 1.103527632 6.50E-18 0.51800772 0.054929656 10.59470718 1.109322888 0.017933187 14.58418566 887563.5368 -5.948199452 -1.103527632 TFS(ph)LDAVPPDHS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TFSLDAVPPDHSPR 14 0 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 2 T(0.381)FS(0.619)LDAVPPDHS(1)PR;T(0.417)FS(0.583)LDAVPPDHS(1)PR 103.73 0.00058027 233470000 169781 198644 199805 232306 234424 151592 233250 176128 174196 TRUE FALSE 159154.7103 213351.8084 204544.469 238267.3653 216013.2847 195354.1495 198276.3279 198117.9685 145121.5623 1.096699262 1.470159259 1.409469866 1.641846749 1.488498892 1.346141445 1.366277518 1.365186299 1 17.14690237 0.339123113 0.867105173 0.996829697 1.425831847 0.456155792 0.13672782 2.15310889 2.096328785 0.139888007 0.041720954 2.183348754 -0.339123113 0.429002151 TFS(ph)LDAVPPDHSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TFSLDAVPPDHSPR 14 0 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 1 T(0.207)FS(0.785)LDAVPPDHS(0.007)PR 105.53 0.00064062 464870000 186190 202240 218530 198470 214740 150890 227820 184250 194110 TRUE FALSE 174536.7003 217214.06 223713.6348 203563.0762 197875.1866 194449.4935 193660.506 207254.0181 161711.787 1.079307226 1.343217239 1.383409577 1.258801724 1.223628718 1.202444776 1.197565803 1.281625922 1 17.30306531 2.700172754 2.295321274 1.18987368 1.301466444 0.110544373 0.107161161 0.511732982 5.3203599 0.036342063 0.0352352 501.3866355 -2.700172754 0.111592764 TFS(ph)LTEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TFSLTEVR 8 0 O95239;O95239-2 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 T(0.14)FS(0.859)LTEVR;T(0.114)FS(0.885)LT(0.002)EVR;T(0.078)FS(0.922)LTEVR;T(0.467)FS(0.533)LTEVR;T(0.006)FS(0.992)LT(0.002)EVR 208.59 5.67E-05 1202070000 1353343 1463775 1402172 1821406 2319020 1487065 1987730 1419732 1670840 TRUE FALSE 1268639.677 1572154.424 1435432.182 1868146.362 2136893.524 1916356.525 1689688.34 1596988.665 1391966.01 0.911401333 1.129448861 1.031226461 1.342091939 1.535162144 1.376726523 1.213886207 1.147289987 1 20.40869255 3.242962426 24.99272056 1.294565366 1.047644917 0.356069549 0.151799486 114.5790635 650555.2064 0.041306325 0.054065053 1749.695302 -3.242962426 -0.246920448 TFSAT(ph)VR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TFSATVR 7 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 TFS(0.399)AT(0.601)VR 167.04 0.012309 7724700000 2998300 3163400 3204700 3428200 3530700 3025200 4208800 3101600 3631400 TRUE FALSE 2810641.755 3397621.428 3280716.997 3516173.416 3253413.064 3898526.13 3577729.513 3488841.587 3025295.88 0.929046899 1.123070788 1.084428475 1.162257695 1.075403264 1.288642924 1.182604827 1.153223263 1 21.52864482 5.818291518 0.81123405 1.155609658 1.24E-19 0.370610814 0.078732896 11.87828735 1.587565412 0.024470645 18.54993543 658099.4351 -5.818291518 -1.155609658 TFSATVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TFSATVR 7 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 0 ;; 102.72 0.041389 254340000 334845 370117 316561 395770 441850 330774 436920 346193 468330 FALSE TRUE 313887.6492 397520.8478 324069.9764 405926.1282 407148.8833 426263.0841 371407.9022 389415.9581 390162.6975 0.804504509 1.018859185 0.830602153 1.040402199 1.043536161 1.092526494 0.951930834 0.998086082 1 18.57371633 3.220446531 24.99939443 1.020072669 0.905691374 0.470273642 0.067021689 229.2781673 316427.9046 0.018586033 0.022255818 1661.29413 -3.220446531 -0.114381296 TFSHELSDFGLESTAGEIPVVAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TFSHELSDFGLESTAGEIPVVAIR 24 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 261.46 4.61E-44 1949457000 1444042 1645075 1547435 1630020 1507333 1300149 1783843 1359574 1016717 FALSE TRUE 1353661.989 1766878.065 1584140.889 1671849.073 1388953.146 1675480.91 1516372.303 1529319.807 847020.3645 1.598145742 2.085992426 1.870251242 1.973800328 1.639810806 1.978088108 1.790243029 1.805528971 1 19.69203713 -2.118291959 0.384907596 4.84E-10 1.900939178 0.753937805 0.150808583 21.1225514 1.169696643 18.49900278 0.090652489 0.007615669 2.118291959 1.900939178 TFSVVAGDLVLPGSCQDPACSDKAPGMEGTAALHGDS(ph)PARPQQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TFSVVAGDLVLPGSCQDPACSDKAPGMEGTAALHGDSPARPQQAK 45 2 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 TFSVVAGDLVLPGSCQDPACS(0.005)DKAPGMEGT(0.065)AALHGDS(0.93)PARPQQAK 70.024 0.00069352 114680000 131090 83454 104750 99455 114690 72258 147920 96907 138520 TRUE FALSE 122885.3109 89633.02099 107234.7195 102007.1837 105682.71 93117.71159 125740.7692 109006.0523 115400.1171 1.064862965 0.776715165 0.929242726 0.883943502 0.915793785 0.80691176 1.089606946 0.944592215 1 16.81628516 1.737454928 24.99999999 1.014059362 0.886539024 0.289602514 0.08407549 0.164495838 3521.572449 0.034728791 0.019258845 54.63298476 -1.737454928 -0.127520338 TFTEMDSHEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TFTEMDSHEEK 11 0 B0YIW6;P48444;P48444-2;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 ;;; 145.09 0.00025324 1022410000 2918500 2222600 2484680 2439590 2482330 1804840 3115380 2234480 2931980 FALSE TRUE 2735836.295 2387163.617 2543617.783 2502194.01 2287377.815 2325868.009 2648257.691 2513459.747 2442613.597 1.120044652 0.977298915 1.041350865 1.024392075 0.936446853 0.952204643 1.084190186 1.02900424 1 21.21999423 -0.615104247 5.838682779 1 1.018065777 0.011445954 0.055911905 0 0 0.051296679 0.012090743 0.242602769 0.615104247 0.018065777 TFTTQETITNAETAKEWFLQAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TFTTQETITNAETAKEWFLQAAK 23 1 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90 P06744 GPI Glucose-6-phosphate isomerase 0 273.6 1.03E-51 151730000 51784 66903 55848 67205 99963 33531 77337 53984 158190 FALSE TRUE 48542.93188 71856.56773 57172.74093 68929.59408 92112.30921 43210.85537 65741.03481 60724.02123 131787.0671 0.36834367 0.545247492 0.433826643 0.523037621 0.698948017 0.327883884 0.49884284 0.460773751 1 17.00784927 -1.813957499 2.335563957 1.18926572 0.485245895 0.72028142 0.10140877 4304704.739 2563198.758 4589345.015 0.024192456 0.015347672 1.813957499 -0.704019825 TFVEESIYNEFLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TFVEESIYNEFLER 14 0 P30837 P30837 ALDH1B1 "Aldehyde dehydrogenase X, mitochondrial" 0 87.001 0.016717 0 19321 16547 17034 17140 22049 14084 19114 17042 26902 FALSE TRUE 18111.7331 17772.1571 17438.05452 17579.84142 20317.36048 18149.82217 16248.03315 19169.73121 22411.88241 0.808130829 0.792979223 0.778071837 0.784398254 0.906544132 0.809830332 0.72497405 0.855337846 1 14.45197621 0.983402955 23.80835423 1.000000002 0.797099992 0.663172654 0.044726698 333.3599008 478203.884 0.043429053 0.010857263 9.625049134 -0.983402955 -0.202900011 TFVLTPELS(ph)PGKLQVLPFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TFVLTPELSPGKLQVLPFEK 20 1 Q96DY7 Q96DY7 MTBP Mdm2-binding protein 1 TFVLT(0.007)PELS(0.993)PGKLQVLPFEK 128.29 1.21E-05 59864000 379390 240190 326910 275680 343780 207470 392330 258170 335830 TRUE FALSE 355644.6571 257973.9175 334664.4596 282754.4155 316780.9055 267363.221 333503.7587 290403.0928 279777.8035 1.271168237 0.922067134 1.196179452 1.0106392 1.132258891 0.955626993 1.192030799 1.037977599 1 18.09392198 1.939790214 0.007436767 8.39E-07 2.148224858 0.069853699 0.11076507 10015.21565 59.80347004 8577.314077 8690.597223 87.05429733 -1.939790214 2.148224019 TFVNITPAEVGVLVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TFVNITPAEVGVLVGK 16 0 P07737;I3L3D5 P07737 PFN1 Profilin-1 0 ; 180.97 5.54E-09 67429000 327530 308750 314200 318070 358030 269440 354820 285950 335930 FALSE TRUE 307030.482 331610.1713 321652.9724 326232.2147 329911.768 347222.954 301618.035 321651.487 279861.1128 1.097081616 1.184909786 1.149330713 1.165693266 1.17884105 1.240697396 1.077741855 1.149325405 1 18.09435151 0.642970438 0.979408263 1.000976482 1.164930212 0.549119338 0.044646262 0.826607606 1.320142659 0.039311977 0.012710644 4.395116968 -0.642970438 0.16395373 TFVQEDIYDEFVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TFVQEDIYDEFVER 14 0 P05091;P05091-2;S4R3S4 P05091 ALDH2 "Aldehyde dehydrogenase, mitochondrial" 0 ;;;;; 327.3 5.88E-68 1059866000 619324 670850 608478 558565 807677 592975 569450 645859 974440 FALSE TRUE 580561.6164 720520.432 622911.3855 572898.7235 744245.3064 764157.2564 484066.259 726495.9179 811799.6689 0.715153798 0.887559406 0.767321557 0.705714409 0.916784442 0.941312599 0.596287825 0.894920195 1 19.63076423 -2.858270161 1.298420647 3.615435012 0.799024281 0.239469701 0.11004695 314580.458 9353.05597 2411561.049 0.029473439 0.001385893 2.858270161 -2.816410732 TGADTTAAGPLFQQRPYPS(ph)PGAVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TGADTTAAGPLFQQRPYPSPGAVLR 25 1 O60828-2;O60828;O60828-5;O60828-4;H7C053 O60828-2 PQBP1 Polyglutamine-binding protein 1 1 TGADTTAAGPLFQQRPYPS(1)PGAVLR;TGADTTAAGPLFQQRPYPS(1)PGAVLR 168.26 6.97E-12 292610000 281810 254310 260540 239360 294760 219189 333940 216450 411470 TRUE FALSE 264172.0151 273139.377 266720.1318 245502.3828 271610.7386 282465.3061 283868.7971 243474.259 342792.9988 0.770645889 0.796805588 0.778079286 0.716182605 0.792346225 0.824011304 0.828105586 0.710266137 1 18.38697812 -1.742688272 2.891885192 1.039090239 0.783022006 0.75913321 0.039339126 229754006.6 215608861.5 64826366.77 0.009301428 0.018084717 1.742688272 -0.256068232 TGAIVDVPVGEELLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TGAIVDVPVGEELLGR 16 0 P25705;P25705-2;K7EK77;K7ERX7;K7EJP1;K7EQH4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ; 113.77 0.0014785 73698000 232560 216395 257760 245390 265590 242379 276500 260990 294940 FALSE TRUE 218004.4847 232417.111 263874.1889 251687.1228 244731.6327 312349.8826 235041.3919 293575.176 245712.6086 0.88723361 0.945890047 1.073913913 1.024315049 0.996007629 1.271200059 0.956570333 1.194790848 1 17.90661237 4.731224989 0.691368215 1.082395015 0.755817614 0.335633787 0.094700085 3.368734464 1.22249883 0.034766002 0.865899414 53854.87089 -4.731224989 -0.326577401 TGASSLLNKSS(ph)PVKKPSLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGASSLLNKSSPVKKPSLLK 20 3 O60318 O60318 MCM3AP Germinal-center associated nuclear protein 1 TGASSLLNKS(0.051)S(0.949)PVKKPSLLK 94.08 0.0010127 405850000 1355600 618880 927120 924450 1092500 560150 1453400 782640 1757500 TRUE FALSE 1270755.416 664702.5191 949111.7242 948172.9521 1006699.457 721856.2117 1235476.163 880354.3268 1464161.896 0.867906356 0.453981572 0.648228674 0.647587507 0.687560207 0.493016663 0.84381117 0.601268432 1 20.48164365 -0.328660855 0.420357755 1.075078618 0.61322144 0.38203324 0.132895229 6.212324969 1.152409142 0.825890175 0.07556695 0.469179626 0.328660855 -0.461857178 TGCTFPEKPDFH ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TGCTFPEKPDFH 12 1 P55263-3;P55263-2;P55263;P55263-4;A0A5F9ZHJ1 P55263-3 ADK Adenosine kinase 0 ;; 143.42 5.67E-05 1782860000 4824200 3914490 4657400 4587400 4322100 3668190 5297200 3755570 4478500 FALSE TRUE 4522261.933 4204322.913 4767875.727 4705120.45 3982659.701 4727136.905 4502934.037 4224461.182 3731009.418 1.21207465 1.126859367 1.277905037 1.261085118 1.067448311 1.266986055 1.20689431 1.132256907 1 21.83113457 0.920690685 3.020218252 1.000299852 1.203228916 0.501918528 0.064481082 0.275798377 5.832646907 0.057964861 0.015208027 8.330876283 -0.920690685 0.202929064 TGDLGIPPNPEDRS(ph)PS(ph)PEPIYNSEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 TGDLGIPPNPEDRSPSPEPIYNSEGK 26 1 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 2 TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(0.994)PS(0.977)PEPIY(0.029)NSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK 193.94 1.24E-18 10839030000 8890460 5871710 6952040 6637370 6816660 5014660 8539470 5956700 7462440 TRUE FALSE 8334021.979 6306457.518 7116945.672 6807696.151 6281307.021 6462310.936 7259055.75 6700407.107 6216910.555 1.340540757 1.014403772 1.144772087 1.095028808 1.010358274 1.039473044 1.16763072 1.077771193 1 22.56776639 4.747389497 24.94546289 1.079267969 1.340540895 0.689562639 0.056933073 669.9038856 1892730.628 0.013269167 0.157804189 55897.12829 -4.747389497 0.261272926 TGDLGIPPNPEDRS(ph)PS(ph)PEPIYNSEGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TGDLGIPPNPEDRSPSPEPIYNSEGKR 27 2 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 2 TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGKR;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGKR;TGDLGIPPNPEDRS(1)PS(0.999)PEPIYNS(0.001)EGKR;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGKR;TGDLGIPPNPEDRS(0.998)PS(0.901)PEPIY(0.006)NS(0.094)EGKR 133.47 1.68E-05 2141080000 1424580 1414530 1360680 1529150 1907990 987100 1806860 1219700 2849970 TRUE FALSE 1335418.081 1519263.273 1392955.972 1568390.578 1758144.162 1272059.746 1535938.117 1371982.23 2374291.595 0.562449062 0.63988066 0.586682771 0.660572013 0.740492097 0.535763909 0.646903742 0.577849087 1 21.1790657 -1.434877337 3.44913193 1.004259126 0.620928879 0.80839725 0.058311834 2578699.724 1432286.088 79327.49624 0.012385045 0.036738605 1.434877337 -0.383330247 TGEAIVDAALSALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGEAIVDAALSALR 14 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 87.667 0.01594 31074000 134470 140830 128750 133760 170840 98579 140380 108450 138850 FALSE TRUE 126053.7627 151257.1997 131804.0108 137192.5081 157422.9155 127037.157 119331.3222 121990.2212 115675.038 1.089723115 1.307604496 1.139433477 1.186016538 1.360906538 1.098224467 1.031608239 1.054594175 1 16.81971805 2.0127498 24.87562681 1.040413695 1.218221445 0.556939529 0.077471697 148.9278314 290565.8781 0.026874569 0.019836515 102.9792679 -2.0127498 0.17780775 TGEDEDEEDNDALLKENES(ph)PDVRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGEDEDEEDNDALLKENESPDVRR 24 2 A0A087WWS1;Q96FV9 A0A087WWS1 THOC1 THO complex subunit 1 1 TGEDEDEEDNDALLKENES(1)PDVRR 100.95 0.0020969 44430000 50429 27907 36382 37314 36138 21829 43542 27519 43473 TRUE FALSE 47272.73891 29973.26332 37244.99822 38271.54041 33299.86725 28130.67794 37013.28132 30954.80773 36217.07545 1.305261077 0.827600322 1.028382269 1.056726418 0.919452132 0.776724172 1.021984267 0.854702025 1 15.14438243 2.684814211 9.381785399 0.913118973 1.012291449 0.181869872 0.134836744 1.097967884 186.0615641 0.040978057 0.038664698 483.9652857 -2.684814211 0.099172477 TGEEDEEEFFCNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TGEEDEEEFFCNR 13 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 0 ; 214.82 7.02E-11 166343000 527350 449950 484320 484980 508950 410290 641800 428110 596800 FALSE TRUE 494344.1048 483264.7662 495808.2991 497425.4079 468979.12 528734.0625 545568.0482 481560.4759 497190.2245 0.994275592 0.971991689 0.99722053 1.000473025 0.943258932 1.063444204 1.097302443 0.968563846 1 18.92343841 2.225019687 24.99934314 1.047350702 0.983171315 0.263144145 0.038789545 229.3611369 423444.7228 0.013708774 0.010178765 167.8880122 -2.225019687 -0.064179387 TGENFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TGENFR 6 0 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ;;; 137.44 0.029627 3437460000 2309970 2320940 2376250 2279660 2359710 2010160 2552890 2005590 2176200 FALSE TRUE 2165393.101 2492784.813 2432615.772 2338159.935 2174387.895 2590460.56 2170107.844 2255992.326 1812978.161 1.194384548 1.374966818 1.341778861 1.28967904 1.199345884 1.428842672 1.196985099 1.244357144 1 20.78993012 0.516678134 0.73864125 0.996064269 1.314658067 0.577580428 0.077677369 1.033328626 0.922729462 0.076729786 0.025421991 3.286080016 -0.516678134 0.318593798 TGEPS(ph)PPHDILHEPPDVVS(ph)DDEKDHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGEPSPPHDILHEPPDVVSDDEKDHGK 27 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 2 T(0.153)GEPS(0.847)PPHDILHEPPDVVS(1)DDEKDHGK 72.792 0.02501 67208000 134930 67841 76312 74007 84517 55221 103840 62657 103090 TRUE FALSE 126484.9722 72864.01823 78122.15668 75906.14491 77879.37575 71162.40626 88270.156 70479.86438 85883.61301 1.472748615 0.848404203 0.909628204 0.883825706 0.906801344 0.828591203 1.027788107 0.820643915 1 16.39009526 4.74190803 24.99650153 0.903109559 1.472748828 0.876285941 0.067253043 97.63787649 729069.1195 0.014570773 0.10596013 55196.05387 -4.74190803 0.569639269 TGEPSPPHDILHEPPDVVS(ph)DDEKDHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TGEPSPPHDILHEPPDVVSDDEKDHGK 27 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TGEPSPPHDILHEPPDVVS(1)DDEKDHGK;TGEPSPPHDILHEPPDVVS(1)DDEKDHGK 300.65 3.61E-71 808370000 1834420 740200 1013190 1020660 1193530 684550 1454410 866120 1497310 TRUE FALSE 1719606.927 795005.1782 1037223.345 1046851.864 1099794.968 882168.4723 1236334.723 974256.9886 1247399.288 1.378553718 0.637330152 0.831508688 0.839227562 0.881670351 0.707206169 0.991129893 0.781030579 1 20.25049191 -1.694829991 6.484250434 1.001514078 0.855806104 0.020039811 0.202351957 0.00395407 0.000186092 0.17491243 0.040819628 0.020191566 1.694829991 -0.145707973 TGFINLDKPSNPSSHEVVAWIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGFINLDKPSNPSSHEVVAWIR 22 1 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 155.76 1.01E-08 277610000 252520 295600 299990 284630 317600 217440 373090 290320 351000 FALSE TRUE 236715.224 317486.5316 307105.9045 291934.0877 292656.9771 280211.3982 317148.6181 326567.0911 292415.8325 0.809515757 1.085736463 1.050236924 0.998352535 1.000824664 0.958263429 1.08458087 1.116790046 1 18.1576619 1.662516393 8.349364276 1.07533044 1.004617127 0.163461355 0.079202484 0.229475863 27.72684595 0.03710995 0.019458019 45.97443416 -1.662516393 -0.070713313 TGFSTSPESPYTHWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGFSTSPESPYTHWK 15 0 E9PKG1;Q99873-2;Q99873-3;Q99873;Q99873-5 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 182.02 5.64E-07 664910000 604040 627390 672350 651390 693520 516770 858090 663880 793670 FALSE TRUE 566234.2146 673842.6084 688298.4595 668105.7702 639053.7367 665953.1099 729427.3706 746766.8794 661201.3497 0.856371837 1.019118622 1.040981631 1.010442236 0.966503981 1.007186556 1.103184939 1.129409188 1 19.33473014 1.804353213 5.371511847 1.087034305 0.99387352 0.341694652 0.06009866 0.236419196 11.98528626 0.026945832 0.015273698 63.73136397 -1.804353213 -0.093160786 TGGGGGGGHLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGGGGGGGHLAR 12 0 Q12830-4;Q12830;F5GXF5;Q12830-2 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 0 129.82 0.00022747 28587000 22328 16028 18098 17579 18728 15209 20160 15558 20867 FALSE TRUE 20930.53034 17214.7298 18527.29311 18030.1069 17257.17843 19599.5914 17137.19516 17500.45055 17384.16289 1.203999897 0.990253595 1.065756989 1.037157038 0.992695394 1.12743947 0.985793521 1.006689287 1 14.08548598 4.746409382 24.78676931 1.028842043 1.203999993 0.621954671 0.04362051 541.4626039 1709919.932 0.009445478 0.100625936 55771.12209 -4.746409382 0.17515795 TGGIGDSRPPSFHPHAGGGS(ph)QENLDNDTETDSLVSAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TGGIGDSRPPSFHPHAGGGSQENLDNDTETDSLVSAQR 38 1 Q92997-2;Q92997 Q92997-2 DVL3 Segment polarity protein dishevelled homolog DVL-3 1 TGGIGDSRPPSFHPHAGGGS(1)QENLDNDTETDSLVSAQR;TGGIGDSRPPSFHPHAGGGS(1)QENLDNDTETDSLVSAQR 230.65 2.80E-40 507950000 63386 98130 108800 108399 112752 101345 145159 100390 125960 TRUE FALSE 59418.78341 105395.6473 111380.7874 111180.7019 103896.9127 130601.6563 123393.7555 112923.9125 104936.4623 0.566235817 1.004375839 1.061411686 1.059504956 0.990093534 1.244578419 1.17589018 1.076117014 1 16.67915653 5.024670202 1.463606806 1.100120061 4.14E-18 0.809744399 0.07810829 1.056582026 1.214719353 0.021706617 2.062749673 105844.9646 -5.024670202 -1.100120061 TGGMAFHSYFMEAIAPPLLQELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TGGMAFHSYFMEAIAPPLLQELK 23 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;; 211.17 5.32E-25 2120546000 3770780 3140680 3096790 2776618 3881310 2187462 4120860 3472880 2846559 FALSE TRUE 3534773.611 3373219.215 3170247.321 2847870.719 3576487.569 2818946.769 3502975.299 3906476.713 2371449.913 1.490553771 1.422429036 1.336839249 1.200898532 1.508143836 1.188701795 1.477144965 1.647294632 1 21.17733797 -2.007368576 2.893580851 0.583415674 1.396632772 0.455398702 0.139983075 950886.5675 11784882.16 2722583.482 0.030272792 0.009831764 2.007368576 0.813217098 TGGMAFHSYFMEAIAPPLLQELKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 162.65 1.15E-11 517960000 1420430 1289251 1164844 1095009 1814080 790667 1763970 1399670 1691500 FALSE TRUE 1331527.822 1384708.486 1192474.65 1123108.785 1671609.474 1018919.727 1499479.074 1574421.881 1409177.722 0.944897014 0.982635805 0.846220197 0.796995842 1.186230415 0.723059775 1.064080882 1.117262823 1 20.42642214 1.601234936 25 1.068037072 0.917750428 0.232783082 0.125476068 0.797870361 2997.694964 0.058627254 0.028119183 39.92408174 -1.601234936 -0.150286645 TGGS(ph)PSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGGSPSVR 8 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 T(0.092)GGS(0.905)PS(0.003)VR 95.608 0.0099963 208960000 133380 137650 136480 126780 152770 126390 179530 149720 199760 TRUE FALSE 125031.9839 147841.7492 139717.3701 130033.3894 140772.0604 162876.7412 152611.1432 168412.8716 166418.7655 0.751309406 0.888371866 0.839552977 0.781362541 0.845890546 0.978716197 0.917030857 1.011982459 1 17.3444586 2.279318855 5.845734839 0.964820678 0.830182719 0.744618305 0.044919714 0.105236785 8.928636399 0.01554454 0.012686765 190.2474545 -2.279318855 -0.134637959 TGGVPLIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGGVPLIK 8 0 A0A0C4DH79;A0A087WWP8;Q5VWQ0-4;Q5VWQ0;A0A0C4DGT8 A0A0C4DH79 RSBN1 Round spermatid basic protein 1 0 61.962 0.082648 344370000 343830 1643000 1221800 1431400 1365800 1435900 979720 1208200 573650 FALSE TRUE 322310.2941 1764649.43 1250781.673 1468132.147 1258535.577 1850421.02 832820.0813 1359046.43 477904.1091 0.674424613 3.692475951 2.617223098 3.07202244 2.63344791 3.871950429 1.742651016 2.843763851 1 18.86636165 1.619043061 25 1.969928871 2.854854644 0.153629375 0.966042251 1.316566434 2937.540067 0.402508459 0.220609188 41.59518511 -1.619043061 0.884925773 TGHSGTLDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TGHSGTLDPK 10 0 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ; 104.79 0.0026344 274770000 634740 463630 533390 483310 547180 333060 619540 467330 648230 FALSE TRUE 595012.7564 497957.6476 546042.2627 495712.5528 504206.69 429209.0152 526645.7285 525677.1792 540036.2253 1.101801562 0.922081935 1.011121545 0.917924631 0.93365346 0.794778193 0.975204447 0.973410958 1 19.04269666 4.742397473 24.42166938 0.939523837 1.101801649 0.410574235 0.060517721 278.9086609 1775155.949 0.013980591 0.105140735 55258.29405 -4.742397473 0.162277812 TGHSLLHTLYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGHSLLHTLYGR 12 0 P31040;D6RFM5;P31040-2;A0A494C1T6 P31040 SDHA "Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial" 0 100.04 0.0020003 230640000 217370 260450 251190 228760 287490 204670 302350 218510 334500 FALSE TRUE 203765.1997 279733.989 257148.3454 234630.3689 264911.6951 263754.9065 257015.4244 245791.4545 278669.789 0.731206639 1.003818857 0.922770804 0.841965574 0.950629403 0.946478294 0.92229382 0.882016868 1 18.08819708 -4.999999124 0.010529905 2.024060481 2.84E-07 0.176305703 0.072582471 27774.266 22.21066168 2500.14321 1819.398403 1.00E-05 4.999999124 -2.024060197 TGISDVFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TGISDVFAK 9 0 P19338 P19338 NCL Nucleolin 0 ; 82.287 0.043923 362250000 1892860 962300 1227660 1070210 1153170 948630 1369480 973500 1041000 FALSE TRUE 1774389.271 1033549.693 1256780.675 1097673.4 1062604.68 1222484.081 1164139.188 1095043.618 867250.3749 2.04599424 1.19175468 1.449155528 1.265693775 1.225257101 1.40960917 1.34233345 1.262661452 1 19.72608903 4.743532341 24.98090751 1.297987338 2.045994551 0.785429397 0.126903366 220.2778609 1106771.076 0.026712038 0.222503703 55402.88003 -4.743532341 0.748007213 TGISHGHTVYVVHDGFEGLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGISHGHTVYVVHDGFEGLAK 21 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 58.672 0.024593 445350000 176620 196880 189900 219830 220630 122380 260690 191130 203920 FALSE TRUE 165565.6695 211457.2001 194404.5177 225471.21 203302.6098 157709.1193 221601.9546 214993.0012 169884.4346 0.974578217 1.244712033 1.1443339 1.327203463 1.196711224 0.928331778 1.304427655 1.265525012 1 17.37419415 -1.24380266 4.19229678 0.999877949 1.180613587 0.144124289 0.131575542 0.000136882 2.47E-05 0.116180308 0.027365508 0.057042341 1.24380266 0.180735639 TGKPEEASLDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TGKPEEASLDSR 12 1 Q9BY42;A2A2L5;A0A0A0MQR2 Q9BY42 RTFDC1 Protein RTF2 homolog 0 ;;; 111.12 0.0012919 2099940000 5350360 3864010 4571710 4404120 4818900 3403740 5701100 4124770 5536030 FALSE TRUE 5015490.518 4150105.321 4680153.12 4517137.175 4440443.033 4386344.483 4846272.981 4639756.614 4612030.829 1.087479834 0.899843361 1.014770563 0.979424757 0.962795609 0.951065733 1.050789373 1.006011622 1 22.13697073 1.741414498 25 1.022215167 0.975853803 0.095773738 0.049579055 0.827676604 7293.662576 0.020824996 0.011548435 55.1333648 -1.741414498 -0.046361365 TGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPR 39 2 P38606;P38606-2;C9JVW8;C9JA17 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 236.89 2.33E-50 298660000 160493 159443 130492 108715 190222 108346 156306 150236 141315 FALSE TRUE 150448.0296 171248.3256 133587.3319 111504.811 175282.7314 139623.7313 132869.3664 168993.2953 117728.6136 1.277922376 1.454602415 1.134705725 0.947134325 1.488871109 1.185979577 1.128607246 1.435447936 1 16.84510548 -5 0.181804731 0.051439403 1.296908877 0.152737086 0.172517213 259.1057219 2.504359513 90.20432232 0.50258387 1.00E-05 5 1.245469474 TGMGSGS(ph)AGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TGMGSGSAGK 10 0 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 TGMGS(0.314)GS(0.686)AGK;TGMGS(0.085)GS(0.915)AGK 96.745 0.0068511 51607000 443120 279892 349760 349460 349960 244210 404560 312010 341570 TRUE FALSE 415385.9102 300615.4949 358056.4724 358427.7352 322475.5533 314709.4626 343899.9838 350965.1353 284559.7604 1.459749297 1.056423067 1.258282169 1.259586861 1.133243691 1.105952093 1.208533432 1.23336179 1 18.11837214 -5 0.173210152 0.241900984 1.243667785 0.297751454 0.107722525 186.5479284 1.773438358 48.98546654 0.344095253 1.00E-05 5 1.001766801 TGPFAEHSNQLWNISAVPSWSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TGPFAEHSNQLWNISAVPSWSK 22 0 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;A6PVN9;H0Y6E5;Q68CR8;B7ZBQ0;B4DDQ6;B7ZBP7;B7ZBP9 Q15257 PPP2R4;DKFZp781M17165 Serine/threonine-protein phosphatase 2A activator 0 ; 228.15 3.87E-26 234443000 834820 884400 699800 642340 973390 516310 949780 869010 979180 FALSE TRUE 782570.1064 949881.8962 716399.5865 658823.5319 896943.8759 665360.3154 807369.3063 977507.8114 815748.5323 0.95932763 1.164429795 0.878211309 0.807630668 1.099534771 0.815643901 0.989728175 1.19829552 1 19.63776496 1.4525213 24.99999902 1.097436185 0.963573409 0.190206434 0.121106559 21.16101256 21509.58098 0.063399101 0.029327208 28.34792662 -1.4525213 -0.133862776 TGPPPIS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TGPPPISPSK 10 0 Q14135-4;G5E9M7;Q14135;Q14135-2;A0A0A6YYI5;A0A075B6E4;E7ERW0;E7EWF5;F8W708;E7EQU6;F8WBN7;E7EUJ2;A0A096LP98 Q14135-4 VGLL4 Transcription cofactor vestigial-like protein 4 1 TGPPPIS(0.999)PS(0.001)K;TGPPPIS(0.999)PS(0.001)K;TGPPPIS(1)PSK;TGPPPIS(1)PSK;TGPPPIS(0.971)PS(0.029)K 210.95 7.10E-08 1712220000 2239800 1356500 1603500 1642970 1759680 1171020 2010230 1379060 1902640 TRUE FALSE 2099614.916 1456936.671 1641535.777 1685131.392 1621481.831 1509074.464 1708814.674 1551238.677 1585077.092 1.324613753 0.919158241 1.035618889 1.063122671 1.022967172 0.952051147 1.078064078 0.97865188 1 20.59612158 4.748788911 24.83110879 1.008923593 1.324613945 0.811526767 0.04820802 563.6438232 1368321.462 0.011307369 0.157056926 56077.53451 -4.748788911 0.315690352 TGQAGSLSGS(ph)PKPFSPQLSAPITTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGQAGSLSGSPKPFSPQLSAPITTK 25 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 TGQAGSLS(0.079)GS(0.918)PKPFS(0.004)PQLSAPITTK 227.77 3.07E-34 1232900000 2524500 1202400 1584700 1565900 1753900 1186400 2371400 1488300 2178900 TRUE FALSE 2366496.051 1291426.947 1622289.832 1606083.645 1616155.769 1528894.42 2015830.585 1674117.531 1815227.514 1.303691154 0.711440818 0.893711571 0.884783661 0.890332345 0.842260493 1.110511255 0.922263198 1 20.79171895 1.750822461 25 1.018523488 0.891124105 0.045449356 0.15741091 7.135447825 14571.8599 0.066538812 0.036898908 56.34072881 -1.750822461 -0.127399384 TGQIWPNDGEGAFHGDADGS(ph)FGTPPGYGCAADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGQIWPNDGEGAFHGDADGSFGTPPGYGCAADR 33 0 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 TGQIWPNDGEGAFHGDADGS(0.638)FGT(0.316)PPGY(0.046)GCAADR 47.337 0.056723 130170000 35370 35137 34397 39871 43779 36226 46646 38665 42191 TRUE FALSE 33156.25484 37738.58004 35212.91308 40894.15736 40340.77394 46683.85812 39651.86534 43492.41036 35149.04954 0.94330445 1.073672846 1.001816935 1.163449877 1.147705968 1.328168435 1.128106332 1.23737088 1 15.10119806 3.191965079 5.446145145 1.182080579 1.019857897 0.41479964 0.088777879 0.16341376 10.9593172 0.023020769 0.028241024 1555.840523 -3.191965079 -0.162222682 TGQLEGAPAPGPAAS(ph)PQTLDHSGATATGGASELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TGQLEGAPAPGPAASPQTLDHSGATATGGASELK 34 0 P55317-2;P55317 P55317-2 FOXA1 Hepatocyte nuclear factor 3-alpha 1 TGQLEGAPAPGPAAS(0.905)PQT(0.093)LDHS(0.002)GATATGGASELK;TGQLEGAPAPGPAAS(0.681)PQT(0.267)LDHS(0.052)GATATGGASELK;TGQLEGAPAPGPAAS(0.992)PQT(0.008)LDHSGATATGGASELK 310.14 1.64E-104 6974100000 3287710 2138340 2609320 2557800 2439120 1985630 3524520 2198120 2139180 TRUE FALSE 3081938.1 2296664.919 2671214.303 2623437.478 2247561.354 2558849.147 2996050.946 2472560.121 1782137.038 1.72934967 1.288713982 1.498882659 1.472073933 1.261160789 1.435831865 1.68115632 1.387413015 1 20.76517685 -2.112961798 1.848420091 0.249013017 1.464344916 0.497764894 0.148079788 938709.3271 216078.5006 2958258.624 0.03593757 0.007709713 2.112961798 1.215331899 TGQPAQPAPSAQQPPRPPAS(ph)PDEPSVAASSVGSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TGQPAQPAPSAQQPPRPPASPDEPSVAASSVGSSR 35 1 O94964-2 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 TGQPAQPAPSAQQPPRPPAS(0.999)PDEPS(0.001)VAASSVGSSR;TGQPAQPAPSAQQPPRPPAS(1)PDEPSVAASSVGSSR;TGQPAQPAPSAQQPPRPPAS(1)PDEPSVAASSVGSSR 287.88 2.11E-75 2115810000 627433 570581 579098 586558 570189 431167 724968 489748 480721 TRUE FALSE 588163.0885 612827.4109 592834.478 601610.0713 525408.656 555637.9135 616265.7787 550894.1159 400485.5595 1.468624959 1.530211006 1.480289274 1.502201657 1.311929091 1.387410608 1.538796503 1.375565492 1 18.6113907 -3.048541235 0.298113576 2.18E-14 1.493087495 0.814126012 0.068368919 30.24362813 0.811960901 19.03100911 0.072411222 0.00089425 3.048541235 1.493087495 TGQPMIHIYLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TGQPMIHIYLDK 12 0 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;A0A0D9SFL3;C9JGE3;Q01844-2;H7BY36 B0QYK0 EWSR1 RNA-binding protein EWS 0 ; 112.72 0.001243 658870000 2863370 2049090 2400280 2161980 2447850 1969130 2961570 2247390 2482800 FALSE TRUE 2684156.783 2200806.756 2457215.775 2217460.067 2255605.735 2537585.865 2517510.072 2527981.589 2068404.64 1.297694238 1.064011709 1.18797634 1.072062992 1.090505064 1.226832417 1.217126486 1.222189092 1 20.98008702 2.234073838 24.99861501 1.189619737 1.134762645 0 0.093945551 300.6322375 1674987.541 0.03090793 0.023594659 171.4248735 -2.234073838 -0.054857093 TGRDT(ph)PENGETAIGAENSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGRDTPENGETAIGAENSEK 20 1 Q8N3X1-2;Q8N3X1 Q8N3X1-2 FNBP4 Formin-binding protein 4 1 T(0.037)GRDT(0.963)PENGETAIGAENSEK 120.27 6.26E-05 225940000 264310 137310 181600 171250 191490 133090 224040 146540 172490 TRUE FALSE 247767.3089 147476.5753 185907.6378 175644.5649 176451.1478 171510.9225 190447.2819 164835.8416 143700.3047 1.724194736 1.026278793 1.29371777 1.222297791 1.227910743 1.193532073 1.325308825 1.147080669 1 17.1327036 -5 0.038025852 2.88E-10 1.871522389 0.269301573 0.170756824 1685.940956 4.797765604 206.5748874 65.93192566 1.00E-05 5 1.871522389 TGS(ph)CSELDACPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGSCSELDACPSK 13 0 A0A1B0GUA8;Q9H1H9-3;Q9H1H9-4;Q9H1H9-2;Q9H1H9;H0Y9Z7 A0A1B0GUA8 KIF13A Kinesin-like protein KIF13A 1 TGS(0.988)CS(0.012)ELDACPSK 273.81 3.94E-32 171420000 437530 237620 287470 300590 287510 181980 384050 219320 328890 TRUE FALSE 410145.7783 255213.632 294288.9242 308303.6483 264930.1244 234514.6718 326465.2678 246702.5848 273996.1343 1.496903522 0.931449755 1.074062322 1.125211672 0.966911906 0.855905038 1.19149589 0.9003871 1 18.06379601 4.744823011 24.97251074 1.01694348 1.496903737 0.691874293 0.102778786 398.8441251 1590424.587 0.02292615 0.215009361 55567.77543 -4.744823011 0.479960258 TGS(ph)EPALSPAVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TGSEPALSPAVVR 13 0 O75815;O75815-3;O75815-2 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 TGS(0.999)EPALS(0.001)PAVVR;T(0.001)GS(0.999)EPALSPAVVR 197.68 1.38E-07 230919000 296952 207365 222411 194326 252935 177870 286733 217634 366020 TRUE FALSE 278366.3044 222718.5204 227686.694 199312.7342 233070.5054 229218.1815 243740.0485 244806.084 304928.8974 0.912889224 0.730394929 0.746687821 0.653636752 0.764343778 0.751710262 0.799334043 0.802830057 1 18.21811335 0.536908307 0.94252338 1.000435968 0.751504415 0.564944994 0.064214497 1.046966002 1.410389976 0.058064786 0.018686803 3.442772353 -0.536908307 -0.248931553 TGS(ph)ESS(ph)QTGTSTTSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TGSESSQTGTSTTSSR 16 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 T(0.35)GS(0.649)ES(0.002)S(0.998)QTGTSTTSSR;TGS(1)ES(0.003)S(0.996)QT(0.001)GTSTTSSR;TGS(0.996)ES(0.004)S(0.998)QT(0.002)GTSTTSSR 191.41 1.02E-09 579470000 2049823 1364356 1442940 1696482 1656621 967277 1570696 959133 1155040 TRUE FALSE 1921528.237 1465374.338 1477167.218 1740016.6 1526516.669 1246514.167 1335184.716 1078882.866 962256.3622 1.996898449 1.522852324 1.53510777 1.808267182 1.586392909 1.295407561 1.387556133 1.121201074 1 19.87606178 1.620580523 0.746050207 0.997394847 1.674322969 0.734339228 0.152938158 0.343677673 0.389912262 0.139147414 0.062884236 41.74269871 -1.620580523 0.676928122 TGS(ph)ESSQTGTSTTSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TGSESSQTGTSTTSSR 16 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 TGS(0.579)ES(0.421)SQTGTSTTSSR;T(0.005)GS(0.554)ES(0.368)S(0.059)QT(0.014)GTSTTSSR;T(0.008)GS(0.968)ES(0.021)S(0.003)QTGTSTTSSR;T(0.038)GS(0.962)ESSQTGTSTTSSR;T(0.002)GS(0.99)ES(0.007)S(0.001)QTGTSTTSSR;TGS(0.909)ES(0.091)SQTGTSTTSSR 356.58 1.91E-87 4795063000 4589196 3076845 3428063 4153014 3855930 2339438 3181661 2137169 2572527 TRUE FALSE 4301966.414 3304657.805 3509378.273 4259587.37 3553100.812 3014795.773 2704600.47 2403999.254 2143155.625 2.007304726 1.541958861 1.637481774 1.987530593 1.657882783 1.406708752 1.261971104 1.121710074 1 21.03130518 1.830952854 1.353110967 1.057193776 1.733966684 0.79537751 0.150590064 0.203349657 0.697672319 0.118526923 0.049073587 67.75679486 -1.830952854 0.676772909 TGS(ph)NAAQYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TGSNAAQYK 9 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 T(0.003)GS(0.997)NAAQYK;TGS(1)NAAQYK;TGS(1)NAAQYK 189.52 4.00E-05 533650000 1156100 706510 737760 728810 825850 400723 869190 593190 736250 TRUE FALSE 1083741.765 758820.7355 755260.0156 747512.4985 760991.0723 516405.2249 738863.0287 667251.0773 613365.1186 1.766878702 1.237143607 1.231338387 1.21870722 1.240682017 0.841921409 1.204605554 1.087852988 1 19.2263866 8 0.744252884 1.108891385 107.4081705 0.721944009 0.125086339 193.1759309 0.84657647 0.041089262 34404.92303 100000000 -8 106.2992791 TGS(ph)PGDAPERPPLCDFSEGLSAPMDFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TGSPGDAPERPPLCDFSEGLSAPMDFYR 28 1 A0A2R8Y575;Q5VVD7;Q8IWE5 A0A2R8Y575 PLEKHM2 Pleckstrin homology domain-containing family M member 2 1 T(0.011)GS(0.989)PGDAPERPPLCDFSEGLSAPMDFYR;T(0.001)GS(0.999)PGDAPERPPLCDFSEGLSAPMDFYR;T(0.022)GS(0.978)PGDAPERPPLCDFSEGLSAPMDFYR;T(0.159)GS(0.841)PGDAPERPPLCDFSEGLSAPMDFYR 230.32 3.22E-35 375115000 158029 113504 120909 125322 133376 102004 164131 102436 134274 TRUE FALSE 148138.247 121907.9543 123777.0186 128537.9747 122901.187 131450.8989 139521.0803 115225.3601 111862.802 1.324285146 1.089798862 1.106507404 1.149068077 1.098677888 1.175108227 1.247251793 1.030059663 1 16.77137085 1.094229669 7.073830253 1.000918992 1.157308888 0.438221454 0.072256786 0.205968645 12.19229658 0.068557039 0.017196554 12.42309108 -1.094229669 0.156389896 TGS(ph)PGPELLFHEGQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TGSPGPELLFHEGQQK 16 0 A6NHN7;A6NHB5;Q14202-2;Q14202;A6NL54;Q14202-3 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 1 T(0.027)GS(0.973)PGPELLFHEGQQK;T(0.094)GS(0.906)PGPELLFHEGQQK;T(0.133)GS(0.867)PGPELLFHEGQQK 211.49 4.48E-12 411190000 1212730 714960 939560 971800 852640 614120 1021770 648350 883390 TRUE FALSE 1136827.394 767896.3823 961846.8069 996738.0333 785677.0938 791406.4746 868565.0741 729297.9247 735946.5021 1.544714719 1.043413319 1.306952074 1.354362077 1.06757365 1.075358701 1.180201376 0.99096595 1 19.48924137 2.72363488 24.06997551 1.083657788 1.266634597 0.441511144 0.134046658 590.3608182 952042.8459 0.041490257 0.039280551 529.2183323 -2.72363488 0.182976809 TGS(ph)QEGTSMEGSRPAAPAEPGTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TGSQEGTSMEGSRPAAPAEPGTLK 24 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 T(0.014)GS(0.85)QEGT(0.068)S(0.068)MEGSRPAAPAEPGTLK;T(0.024)GS(0.966)QEGT(0.005)S(0.005)MEGSRPAAPAEPGTLK;T(0.021)GS(0.978)QEGT(0.001)S(0.001)MEGSRPAAPAEPGTLK;T(0.021)GS(0.979)QEGTSMEGSRPAAPAEPGTLK 257.04 4.19E-44 2731580000 5100330 2914650 3280430 3540310 2812300 1934110 4295110 2347000 3312690 TRUE FALSE 4781109.45 3130453.719 3358243.349 3631160.348 2591433.302 2492456.159 3651098.129 2640028.116 2759780.638 1.732423724 1.134312516 1.216851551 1.315742381 0.93899974 0.903135606 1.322966789 0.956607956 1 21.39612217 6.852449842 1.351089326 1.112622618 199.9969992 0.616396236 0.15496785 330.1049208 2.45496987 0.040498358 201618.3042 7119505.692 -6.852449842 198.8843766 TGS(ph)QGQCTQVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGSQGQCTQVR 11 0 P62857 P62857 RPS28 40S ribosomal protein S28 1 T(0.002)GS(0.998)QGQCTQVR 137.93 7.14E-05 170630000 182820 127530 124230 139330 90912 93061 125420 68364 111050 TRUE FALSE 171377.6225 136972.4539 127176.7943 142905.4437 83772.13824 119926.2 106614.4353 76899.39589 92515.03759 1.852429908 1.480542596 1.374660786 1.5446726 0.905497532 1.296288723 1.152401146 0.831209692 1 16.49740026 8 0.206292797 0.906672716 5.28847002 0.702257334 0.170892009 27.87018266 0.343401167 0.272972274 39.88474967 100000000 -8 4.381797304 TGS(ph)TSSKEDDYESDAATIVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TGSTSSKEDDYESDAATIVQK 21 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 T(0.023)GS(0.968)T(0.009)SSKEDDYESDAATIVQK;T(0.027)GS(0.96)T(0.013)SSKEDDYESDAATIVQK 344.07 2.02E-81 407360000 1190430 506490 786520 1177960 1105840 285360 392340 210270 334300 TRUE FALSE 1115923.111 543991.0466 805176.6258 1208188.448 1018991.787 367738.7996 333512.2593 236522.6724 278503.1703 4.006859634 1.953266981 2.891086033 4.338149711 3.658815754 1.320411538 1.197516922 0.849263842 1 18.08733423 2.184192444 6.79062186 1.10730814 3.153919913 0.738050284 0.667833299 0.131115069 12.70519853 0.274881477 0.20368881 152.8243102 -2.184192444 2.046611773 TGS(ph)YGALAEITASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.001)GS(0.999)YGALAEITASK;T(0.077)GS(0.923)YGALAEITASK 170.74 3.28E-06 288370000 433510 462240 239638 205799 474050 69292 617640 341891 1024230 TRUE FALSE 406377.3829 496464.7306 245322.3265 211080.1508 436820.0252 89295.47554 525030.6159 384576.8439 853279.3962 0.476253598 0.581831382 0.287505274 0.247375188 0.511930825 0.10464975 0.615309145 0.450704477 1 19.70265869 0.488538904 1.09618448 0.999625897 0.394617686 0.594740383 0.154892483 1.291090929 2.084767758 0.139869797 0.04322324 3.079916229 -0.488538904 -0.60500821 TGSDHTNPT(ph)SPLLVKPSDLLEENKINSSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGSDHTNPTSPLLVKPSDLLEENKINSSVK 30 2 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;Q96D71;Q96D71-3;H0YE73 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 TGSDHT(0.02)NPT(0.49)S(0.49)PLLVKPSDLLEENKINSSVK 89.833 0.0011013 386250000 269270 202460 277470 351240 333970 163220 359300 211820 416000 TRUE FALSE 252416.8714 217450.3491 284051.7194 360253.413 307741.3434 210338.9643 305426.3006 238266.1933 346566.9125 0.728335171 0.62744117 0.819615806 1.039491654 0.887970929 0.606921656 0.881290999 0.687504158 1 18.4027744 -4.999999997 0.026746023 2.067727974 9.59E-15 0.172609124 0.134319174 3407.717953 6.876182325 395.3254534 176.676086 1.00E-05 4.999999997 -2.067727974 TGSDHTNPTS(ph)PLLVKPSDLLEENKINSSVK ddPTM_SK-BR-3_Pertuzumab_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(0.037)S(0.963)PLLVKPSDLLEENKINSSVK 168.48 1.06E-12 368090000 389480 304030 417000 502150 511970 259930 514400 309870 618090 TRUE FALSE 365103.142 326540.6975 426891.4369 515036.0191 471761.9414 334967.5714 437270.4955 348557.9516 514926.786 0.709038939 0.63414976 0.829033269 1.000212133 0.916172851 0.650514948 0.849189647 0.676907788 1 18.97400779 -5 0.026486819 2.060774172 4.73E-17 0.207115801 0.122252806 3243.958293 6.483303905 373.7076907 168.3168151 1.00E-05 5 -2.060774172 TGSEPALS(ph)PAVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TGSEPALSPAVVR 13 0 O75815;O75815-3;O75815-2 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 TGSEPALS(1)PAVVR;TGSEPALS(1)PAVVR 220.06 2.25E-11 411430000 588580 599370 583260 630820 708610 458260 654210 553940 687510 TRUE FALSE 551741.8284 643747.9784 597095.2026 647007.9092 652958.629 590552.2228 556117.2839 623100.6284 572760.1395 0.963303468 1.123939908 1.042487355 1.129631524 1.140021073 1.03106376 0.970942713 1.087891048 1 19.12757157 -1.202307497 5.479381723 0.999997386 1.061409149 0.087814145 0.061943784 1.98E-06 2.88E-07 0.060029456 0.014148476 0.062761383 1.202307497 0.061411763 TGSES(ph)SQTGTSTTSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TGSESSQTGTSTTSSR 16 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 T(0.036)GS(0.422)ES(0.533)S(0.008)QTGTSTTSSR;TGS(0.208)ES(0.791)S(0.001)QTGTSTTSSR;T(0.025)GS(0.234)ES(0.74)S(0.002)QTGTSTTSSR;TGS(0.24)ES(0.751)S(0.009)QTGTSTTSSR 344.41 8.41E-73 3881687000 2961144 1934548 2253054 2761263 2547885 1698754 2152425 1428069 1724146 TRUE FALSE 2775811.283 2077783.947 2306497.505 2832121.683 2347784.39 2189156.703 1829688.853 1606366.558 1436374.894 1.932511696 1.446547106 1.605776816 1.971714832 1.634520625 1.524084493 1.273824028 1.118347699 1 20.45400091 1.622978603 1.498212791 1.029601885 1.677886611 0.758541149 0.154446594 0.201893692 0.887313107 0.131977619 0.047402019 41.97383041 -1.622978603 0.648284726 TGSGS(ph)PFAGNS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TGSGSPFAGNSPAR 14 0 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 2 TGS(0.005)GS(0.995)PFAGNS(1)PAR;T(0.011)GS(0.078)GS(0.914)PFAGNS(0.998)PAR 150.92 1.04E-05 347010000 593420 508090 530860 486180 480560 481010 696390 535280 566460 TRUE FALSE 556278.9015 545709.5123 543452.2499 498656.2019 442818.7561 619869.7785 591972.7845 602110.8863 471914.1665 1.178771355 1.156374508 1.151591303 1.05666716 0.938345969 1.313522294 1.254407743 1.275890679 1 18.84816496 2.204477001 24.99972649 1.237445863 1.110263977 0.195025598 0.107955668 254.2808029 186508.9652 0.03809266 0.02813464 160.1315844 -2.204477001 -0.127181886 TGSGS(ph)PFAGNSPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TGSGSPFAGNSPAR 14 0 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 TGS(0.021)GS(0.979)PFAGNSPAR;TGS(0.013)GS(0.987)PFAGNSPAR;T(0.001)GS(0.013)GS(0.985)PFAGNSPAR 233.43 3.64E-17 859310000 897120 892210 808720 769420 895340 610170 871960 775210 1127430 TRUE FALSE 840970.8606 958270.1567 827903.2203 789164.6198 825023.608 786316.1737 741217.6929 871996.6749 939254.6495 0.895359806 1.020245316 0.881447029 0.840203048 0.878381181 0.837170382 0.789155202 0.928392184 1 19.84115683 3.69505694 3.587130234 0.860489229 0.963911564 0.162159604 0.065304193 0.24732035 6.659586491 0.01613262 0.027769182 4955.151531 -3.69505694 0.103422336 TGSGSPFAGNS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 318.02 5.77E-56 1344000000 1424700 1294763 1329335 1484615 1696456 1367762 1834153 1336669 1242159 TRUE FALSE 1335530.57 1390628.6 1360867.454 1522712.734 1563223.189 1762612.686 1559138.785 1503555.067 1034834.638 1.290573895 1.343817213 1.315057888 1.471455127 1.510601918 1.703279558 1.506655003 1.452942346 1 19.98096882 3.20585192 5.264440543 1.490771951 1.321529671 0.052607479 0.179427542 0.307345304 21.4547765 0.046426163 0.05763668 1606.393433 -3.20585192 -0.16924228 TGSQEGT(ph)SMEGSRPAAPAEPGTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGSQEGTSMEGSRPAAPAEPGTLK 24 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 T(0.062)GS(0.313)QEGT(0.461)S(0.164)MEGSRPAAPAEPGTLK 136.18 3.65E-05 1545800000 880300 484750 571870 563990 505800 326360 702900 382240 541740 TRUE FALSE 825203.5944 520641.3944 585435.0265 578462.9382 466076.5083 420574.834 597506.6704 429963.5054 451320.0942 1.828422011 1.153596751 1.297161447 1.281713236 1.032696116 0.931877041 1.323908858 0.95267973 1 18.78379149 6.848100095 1.330213613 1.138384524 200 0.681246229 0.149325446 257.2333853 2.058245375 0.038826824 154477.072 7048555.031 -6.848100095 198.8616155 TGSQGQCTQVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TGSQGQCTQVR 11 0 P62857 P62857 RPS28 40S ribosomal protein S28 0 ;; 192.44 3.23E-06 74746000 35288 73317 25960.9 27681.3 76434 16746.5 28921 58653 76979 FALSE TRUE 33079.38707 78745.46697 26576.70481 28391.64902 70431.18196 21580.94269 24584.56454 65975.95616 64130.7076 0.515811977 1.227890194 0.414414651 0.442715356 1.098244267 0.336514963 0.383350901 1.028773245 1 15.96872771 1.208438093 24.61312137 1.014387851 0.650140609 0.215684594 0.30206318 339.5453265 277433.1708 0.290905293 0.072767881 16.15987859 -1.208438093 -0.364247242 TGSS(ph)SPPGGPPKPGSQLDSMLGSLQSDLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGSSSPPGGPPKPGSQLDSMLGSLQSDLNK 30 1 F5GZ78;A0A1B0GTU4;P49023;P49023-2;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 1 TGS(0.015)S(0.492)S(0.492)PPGGPPKPGSQLDSMLGSLQSDLNK 295.35 3.32E-81 411700000 1071100 504360 728170 735750 760120 532340 986940 600110 901390 TRUE FALSE 1004061.763 541703.3392 745442.5363 754630.5906 700423.2414 686017.9162 838957.5093 675035.0545 750942.1858 1.337069327 0.721364906 0.992676334 1.004911703 0.93272592 0.913542919 1.117206524 0.898917476 1 19.51834231 TGSSS(ph)PPGGPPKPGSQLDSMLGSLQSDLNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGSSSPPGGPPKPGSQLDSMLGSLQSDLNK 30 1 F5GZ78;A0A1B0GTU4;P49023;P49023-2;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 1 TGSS(0.019)S(0.981)PPGGPPKPGSQLDSMLGSLQSDLNK 352.05 2.08E-120 537480000 1110200 533440 769860 777100 729870 533940 975040 556240 943430 TRUE FALSE 1040714.564 572936.4526 788121.4428 797041.7016 672548.9544 688079.8102 828841.8038 625687.7884 785965.4382 1.324122554 0.728958838 1.002743129 1.014092558 0.855697874 0.875458101 1.054552482 0.796075448 1 19.58410635 4.756379809 24.95538342 0.919654155 1.324122899 0.601221941 0.104432603 2711.728073 3797651.467 0.023931877 0.777214943 57066.31231 -4.756379809 0.404468744 TGTGDIATCYS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGTGDIATCYSPR 13 0 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 TGTGDIATCYS(1)PR 140.43 4.13E-05 128850000 286780 204750 252490 277910 259340 172460 293180 188480 256130 TRUE FALSE 268830.9517 219909.903 258479.182 285041.6411 238972.4825 222246.4023 249220.3807 212012.1429 213380.2483 1.259868023 1.030601027 1.211354772 1.335838923 1.119937222 1.041550959 1.167963683 0.993588416 1 17.70306711 1.236682813 24.96528552 0.996794111 1.156164362 0.366011743 0.092170103 57.16165807 759854.8648 0.073605475 0.021997694 17.24577886 -1.236682813 0.159370251 TGTITTFEHAHNMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 TGTITTFEHAHNMR 14 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;;;; 169.62 1.91E-06 14472300000 5371970 6267200 5996360 6625300 6642000 4999730 7019160 5705890 6639800 FALSE TRUE 5035747.987 6731230.009 6138596.491 6795316.415 6120364.113 6443070.887 5966702.121 6418282.927 5531574.485 0.91036431 1.216874152 1.109737654 1.228459715 1.106441598 1.164780643 1.078662528 1.160299467 1 22.39925875 -0.565802877 5.701926193 1 1.130150673 0.151137536 0.088962976 5025557.189 881378.8915 0.104382047 0.018193856 0.271767252 0.565802877 0.130150673 TGTIVVEGHELHDEDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TGTIVVEGHELHDEDIR 17 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;;;; 188.27 2.43E-10 1931350000 2129780 2229660 2134640 2206470 2294360 1780820 2471660 2097840 2324480 FALSE TRUE 1996480.872 2394746.346 2185274.669 2263091.756 2114170.221 2294913.825 2101057.529 2359759.942 1936509.271 1.03096892 1.236630458 1.128460732 1.168644937 1.091742886 1.185077634 1.084971583 1.21856372 1 20.88502698 -1.549326075 2.838942198 0.992310896 1.146691373 0.336153239 0.063036894 10651636.47 11028768.79 624536.8195 0.013627599 0.028227598 1.549326075 0.154380477 TGTLQDLIQHGS(ph)PINNECHPSLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TGTLQDLIQHGSPINNECHPSLER 24 0 A0A2R8YH03;Q5VWN6 A0A2R8YH03 FAM208B Protein FAM208B 1 TGTLQDLIQHGS(1)PINNECHPSLER;TGTLQDLIQHGS(1)PINNECHPSLER;TGTLQDLIQHGS(1)PINNECHPSLER;TGTLQDLIQHGS(1)PINNECHPSLER 265.97 3.79E-44 1117670000 424679 513210 504480 463140 567760 521820 794190 505630 643470 TRUE FALSE 398099.0995 551208.6024 516446.5038 475024.9565 523170.4198 672460.963 675108.5824 568759.0185 536070.7 0.742624246 1.02823863 0.963392522 0.886123708 0.975935487 1.254425886 1.259364823 1.060977626 1 19.03206376 2.336168112 5.825083457 1.177746804 0.935408831 0.499722704 0.109167145 0.155802141 7.740437465 0.036382114 0.030167476 216.8543368 -2.336168112 -0.242337973 TGTLQPWNS(ph)DSTLNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGTLQPWNSDSTLNSR 16 0 Q9H0H5;F8VRD2;H0YIK5 Q9H0H5 RACGAP1 Rac GTPase-activating protein 1 1 TGTLQPWNS(1)DSTLNSR 93.181 0.0035898 0 57226 57302 58057 56133 61490 46561 63019 49965 53874 TRUE FALSE 53644.32681 61544.6997 59434.13946 57573.46781 56660.82344 60002.40485 53569.88599 56203.24024 44882.08136 1.195228144 1.371253245 1.324228682 1.282771789 1.262437519 1.33688998 1.193569558 1.252242288 1 15.45385196 0.2477609 0.493447871 0.976482784 1.315105389 0.721202205 0.054977284 1.355967631 0.496426267 0.117179096 0.026535193 1.769134698 -0.2477609 0.338622605 TGTRFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TGTRFER 7 1 Q16401-2;Q16401;Q4VXH0 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ; 73.665 0.04403 95516000 53198 107424 94962 102456 116785 80600 82866 85618 118507 FALSE TRUE 49868.43214 115377.7847 97214.54348 105085.1944 107613.1772 103867.9116 70441.01259 96307.59577 98727.41612 0.505112299 1.168649898 0.984676266 1.064397293 1.090002974 1.052067558 0.713489883 0.975489885 1 16.59116315 1.773881359 25 0.866327935 1.008042273 0.013951073 0.19557751 86.05912132 60939.75388 0.0822498 0.045641542 59.41298309 -1.773881359 0.141714338 TGVHHYSGNNIELGTACGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGVHHYSGNNIELGTACGK 19 0 E5RI99;P62888;A0A0B4J213 E5RI99 RPL30 60S ribosomal protein L30 0 131.25 9.23E-06 138360000 66460 122450 128980 135070 135420 96174 157020 121120 104260 FALSE TRUE 62300.38723 131516.3254 132039.4665 138536.1249 124784.6595 123937.8725 133476.3087 136242.0986 86858.33245 0.717264371 1.514147482 1.520170406 1.594966435 1.436645811 1.426896753 1.53671277 1.56855531 1 16.40637664 4.740016291 24.88703036 1.482259728 0.717264104 0.640205289 0.171039001 62.54146774 1069134.159 0.034276754 0.215861276 54956.14882 -4.740016291 -0.764995625 TGVIHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGVIHEK 7 0 Q96M27;Q96M27-3;Q96M27-2;Q96M27-5 Q96M27 PRRC1 Protein PRRC1 0 73.248 0.049407 168550000 795460 634880 741440 707470 743420 519330 966350 668610 1115100 FALSE TRUE 745673.5785 681887.1758 759027.3069 725624.8779 685034.792 669252.1404 821454.7887 752087.4303 928982.6062 0.802677654 0.734015009 0.817052227 0.781096302 0.737403249 0.72041407 0.884252066 0.809581821 1 19.82529206 0.731494004 0.839503786 0.998800376 0.769899682 0.710936707 0.044487517 0.523892783 0.698551999 0.041465842 0.014283709 5.388824056 -0.731494004 -0.228900693 TGVNSGVMLMNMTRMRRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGVNSGVMLMNMTRMRRK 18 3 Q4G148-2;Q4G148 Q4G148-2 GXYLT1 Glucoside xylosyltransferase 1 0 42.338 0.064801 145580000 59918 361080 285270 351320 300040 335280 214870 282210 120260 FALSE TRUE 56167.83934 387814.7389 292036.7391 360335.466 276476.0687 432069.8932 182652.2383 317444.5397 100187.8291 0.560625376 3.870876756 2.914892375 3.5965992 2.759577398 4.312598617 1.823098074 3.168494044 1 16.61234773 0.262820168 0.870475882 0.985069418 3.031200613 0.218566939 1.073431015 4.081070566 3.718016302 1.104845136 0.307247143 1.831555857 -0.262820168 2.046131195 TGYES(ph)GEYEMLGEGLGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TGYESGEYEMLGEGLGVK 18 0 Q13561;Q13561-3;Q13561-2;F8W1I6;F8VW18;F8VX93;F8VRV7;H0YHL1 Q13561 DCTN2 Dynactin subunit 2 1 T(0.133)GYES(0.866)GEYEMLGEGLGVK 93.754 0.0021929 18410000 36050 22507 27359 28718 24023 24381 38839 22986 41866 TRUE FALSE 33793.69485 24173.4417 28007.9684 29454.9525 22136.33048 31419.39891 33015.45251 25855.8527 34878.29414 0.968903316 0.693079816 0.803020018 0.844506683 0.634673542 0.900829576 0.946590231 0.741316436 1 15.09004186 2.103857927 19.84704486 0.898932936 0.77918552 0.193871801 0.108762221 3.741550049 700.1193582 0.036849009 0.027214822 127.0158523 -2.103857927 -0.119747417 THASLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THASLFK 7 0 H0YNM6;O43868 H0YNM6 SLC28A2 Sodium/nucleoside cotransporter 2 0 94.887 0.013871 286350000 273270 286510 189870 199170 329670 152720 238740 297610 335870 FALSE TRUE 256166.5185 307723.4985 194373.8061 204281.0394 303779.048 196807.7848 202943.1534 334767.2636 279811.1272 0.915497968 1.099754329 0.694660745 0.730067605 1.085657497 0.703359394 0.725286215 1.1964044 1 18.09409381 1.234811849 24.99999649 1.098202226 0.850149686 0.305220776 0.155298659 127.8906658 852823.0488 0.130688669 0.037553294 17.17164294 -1.234811849 -0.24805254 THCAATPSSSEDTETVSNS(ph)SEGRASPHDVLETIFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THCAATPSSSEDTETVSNSSEGRASPHDVLETIFVR 36 1 H0YEM7;O75143-4;O75143-3;O75143-2;O75143;O75143-5 H0YEM7 ATG13 Autophagy-related protein 13 1 THCAATPSSSEDTETVS(0.073)NS(0.424)S(0.345)EGRAS(0.155)PHDVLET(0.002)IFVR 111.23 9.48E-06 51693000 19256 17172 16588 15724 19316 12602 20657 14118 21257 TRUE FALSE 18050.80133 18443.43275 16981.47519 16127.50446 17798.99928 16239.99282 17559.67462 15880.66338 17709.06937 1.019297003 1.041468208 0.958914036 0.910691811 1.005078183 0.917043831 0.991563941 0.896753129 1 14.11220078 3.879986935 3.022208026 0.954100825 1.029557174 0.409718121 0.03792538 0.219205081 3.90479418 0.008824188 0.018194545 7585.547551 -3.879986935 0.075456349 THDHQLESSLS(ph)PVEVFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THDHQLESSLSPVEVFAK 18 0 Q5JW53;Q9H410-4;Q9H410 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 T(0.36)HDHQLES(0.074)S(0.074)LS(0.493)PVEVFAK 85.932 0.0059196 121750000 39779 45854 46329 44936 47258 32211 49858 39492 55108 TRUE FALSE 37289.3034 49249.07787 47427.94576 46089.13384 43546.54731 41509.7928 42382.25576 44422.66313 45910.11879 0.812224067 1.072728173 1.033060837 1.00389925 0.948517417 0.904153461 0.923157179 0.967600701 1 15.48652454 2.701365817 4.636715311 0.937800128 1.004848448 0 0.073517705 0.380082022 19.82339597 0.022853953 0.022053943 502.7659039 -2.701365817 0.067048319 THEAQIQEMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 THEAQIQEMR 10 0 P35579 P35579 MYH9 Myosin-9 0 ;;;;; 174.77 3.01E-06 5808680000 1913286 2095790 1907190 1935150 2102150 1581000 2134210 1788974 2006370 FALSE TRUE 1793536.845 2250964.472 1952429.447 1984809.225 1937055.619 2037409.035 1814205.024 2012331.342 1671493.885 1.073014302 1.346678257 1.168074538 1.187446297 1.15887688 1.218915039 1.085379396 1.203911878 1 20.67270665 -0.312434962 0.241761819 0.909199302 1.241531936 0.334534226 0.076815399 8.954940822 0.732562667 0.797132416 0.142689272 0.487040456 0.312434962 0.332332633 THEDIEAQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THEDIEAQIR 10 0 O75533;B4DGZ4;A0A494C1M2;O75533-2;F8WC19 O75533 SF3B1 Splicing factor 3B subunit 1 0 170.89 4.19E-06 322800000 161550 171680 169740 194340 171530 143110 230920 161970 186340 FALSE TRUE 151438.8739 184391.3658 173766.313 199327.0934 158058.7257 184423.5338 196295.6898 182192.311 155238.6502 0.975523001 1.187792896 1.119349548 1.284004294 1.018166066 1.188000112 1.264476917 1.173627256 1 17.24412827 4.742402181 24.36710885 1.167213194 0.975522894 0.261978522 0.092173377 325.8932271 2067024.369 0.019942168 0.148898481 55258.89304 -4.742402181 -0.1916903 THETLSHAGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 THETLSHAGQK 11 0 Q16890-5;E9PPQ1;J3KNE7;Q16890;E9PNK6;E9PNQ9;Q16890-4;Q16890-3;Q16890-2 Q16890-5 TPD52L1 Tumor protein D53 0 ;;;; 282.95 9.72E-28 740997000 579112 648554 689627 700462 820741 538562 797397 674625 1218380 FALSE TRUE 542866.4137 696573.613 705985.2781 718437.0408 756283.3126 694036.1066 677834.7225 758853.4163 1015024.507 0.534830844 0.686262852 0.695535205 0.707802655 0.745088722 0.683762906 0.667801337 0.747620783 1 19.95308313 -5 0.220194332 2.599706445 0.645007145 0.807757502 0.050626089 67.01057653 0.670662638 47.53545925 0.09524667 1.00E-05 5 -1.9546993 THFGGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 THFGGGK 7 0 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4;A0A2R8Y8A0 E7ETK0 RPS24 40S ribosomal protein S24 0 ;;;;; 117.93 0.0051196 7105820000 32501610 27145790 31164270 30196460 30846580 24995910 37118760 25885250 31932730 FALSE TRUE 30467392.25 29155692.54 31903501.2 30971352.29 28424014.04 32211823.44 31553146.53 29117080.44 26602951.07 1.145263628 1.095957079 1.199246697 1.164207392 1.068453419 1.210836473 1.18607693 1.094505657 1 24.66508296 0.960037664 4.92662862 1.000082142 1.153500816 0.558833083 0.043712513 0.159974161 13.02002579 0.041367532 0.010466503 9.120899374 -0.960037664 0.153418674 THILLFLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 THILLFLPK 9 0 P07237;H7BZ94;I3L398;I3L312;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ; 104.17 0.0033041 295680000 793370 1715860 634760 674220 1635640 404350 854400 1441270 1516810 FALSE TRUE 743714.3879 1842904.06 649816.807 691521.6267 1507183.432 521079.2809 726290.6519 1621215.732 1263644.612 0.588547113 1.458403765 0.51424016 0.547243758 1.192727305 0.412362207 0.574758635 1.282968104 1 20.26915935 3.957604032 22.70246197 0.745316769 1.073197178 0.054143117 0.360548445 245.1078632 285110.5919 0.084728012 0.153162192 9069.932021 -3.957604032 0.327880409 THINIVVIGHVDSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 230.82 1.60E-13 2105136000 3427449 2658762 3396767 3194172 3142815 2516915.5 4124741 2677374 3598546 FALSE TRUE 3212931.085 2855619.505 3477339.917 3276139.861 2895990.987 3243508.146 3506274.379 3011650.038 2997925.425 1.071718148 0.952531868 1.159915416 1.092802321 0.965998341 1.081917555 1.169566911 1.004578037 1 21.51553307 3.988739386 24.35818051 1.080216752 1.010188172 0.074059288 0.072117645 540.1332489 1132412.092 0.017259966 0.036782685 9744.047348 -3.988739386 -0.07002858 THKHS(ph)PEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 THKHSPEKR 9 2 Q86X95 Q86X95 CIR1 Corepressor interacting with RBPJ 1 1 THKHS(1)PEKR;THKHS(1)PEKR;T(0.002)HKHS(0.998)PEKR;THKHS(1)PEKR;THKHS(1)PEKR 125.61 0.00023587 470618000 777385 382779 504665 494153 526216 363114 659738 414039 570124 TRUE FALSE 728729.8605 411120.3554 516635.8921 506833.8026 484889.118 467939.1171 560816.4116 465732.6806 474966.6213 1.534275943 0.865577363 1.087730946 1.067093518 1.020890935 0.985204215 1.180749102 0.980558759 1 18.8574666 4.75048861 24.99384663 1.031630166 1.534276247 0.793836149 0.081713876 873.2303221 1829728.09 0.01973604 0.330756817 56297.43528 -4.75048861 0.502646081 SRTS(ph)PVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 SRTSPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.161)RT(0.115)S(0.723)PVSR;S(0.221)RT(0.117)S(0.662)PVSR 87.184 0.0093893 3598100000 1408100 522200 514680 407860 544840 468470 561730 488860 642110 TRUE FALSE 1319969.535 560864.2313 526888.4526 418326.3781 502050.4642 603709.684 477503.8013 549895.2471 534937.6928 2.467520147 1.048466464 0.984952939 0.782009538 0.938521385 1.12856075 0.892634428 1.027961302 1 19.02901134 4.740429263 4.638746883 0.968031184 2.561548757 0.965032385 0.089396905 0.031112241 1.806496595 0.021014744 0.161707436 55008.43161 -4.740429263 1.593517573 up THLENNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 THLENNR 7 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;; 183.9 0.00063596 400407000 550912 688153 537702 547985 697395 464993 638133 575213 748727 FALSE TRUE 516431.4013 739104.5641 550456.5454 562047.2228 642624.4099 599228.9306 542450.8808 647029.6092 623759.6267 0.827933356 1.184918889 0.882481844 0.901063805 1.030243675 0.960672838 0.869647309 1.037306009 1 19.25063065 3.760372438 23.50419219 0.945795443 1.032457806 0.023625777 0.103036058 339.9592588 240302.8362 0.023941021 0.043155077 5759.336291 -3.760372438 0.086662363 THLMSEEEWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 THLMSEEEWR 10 0 P33552 P33552 CKS2 Cyclin-dependent kinases regulatory subunit 2 0 ;;; 229.53 1.58E-09 1240480000 582591 675706 600202 617022 694948 505200 627677 554327 653590 FALSE TRUE 546127.6693 725735.9753 614439.0749 632855.8291 640369.5874 651043.0388 533562.6609 623535.9462 544501.6066 1.002986332 1.332844507 1.128443089 1.162266229 1.176065561 1.195667801 0.979910168 1.145149874 1 19.05457678 1.751883328 25 1.044283234 1.181423758 0.285281709 0.090953409 4.433987049 8332.706617 0.038532972 0.021368471 56.47852259 -1.751883328 0.137140523 THLMSESEWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 THLMSESEWR 10 0 P61024;Q5T179;Q9BZU3 P61024 CKS1B Cyclin-dependent kinases regulatory subunit 1;Cyclin-dependent kinases regulatory subunit 0 ; 164.97 6.00E-06 750290000 485010 755530 622780 584850 807300 489010 676190 720940 909590 FALSE TRUE 454654.0899 811470.2273 637552.6357 599858.2411 743897.9145 630179.2486 574801.5869 810950.946 757773.5528 0.599986748 1.070861109 0.841349811 0.791606198 0.981688938 0.831619481 0.758540048 1.070175837 1 19.53140726 1.224677304 24.99987011 1.035088037 0.860066377 0.280028109 0.127141294 372.7370323 671173.1608 0.112329998 0.028665638 16.77557072 -1.224677304 -0.17502166 THLPGFVEQAEALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 THLPGFVEQAEALK 14 0 P30044-2;P30044 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 ; 165.64 3.93E-06 3875200000 1328800 1053740 1034690 1029590 1293680 812720 1236080 982230 1362090 FALSE TRUE 1245632.78 1131760.006 1059233.335 1056011.022 1192079.591 1047339.071 1050741.279 1104863.578 1134748.38 1.09771717 0.997366488 0.933452168 0.930612497 1.050523281 0.922970316 0.925968521 0.97366394 1 20.113941 4.748497035 1.940065204 0.957161611 1.143001166 0.529499999 0.039821687 0.605096016 2.370556183 0.009765904 0.203811838 56039.85914 -4.748497035 0.185839554 THLTELQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THLTELQR 8 0 Q02218;E9PDF2;E9PCR7;Q02218-2;E9PFG7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 96.311 0.009031 81203000 71904 108030 61090 61247 124720 47843 71641 96845 160600 FALSE TRUE 67403.65699 116028.6536 62539.08365 62818.70171 114924.9943 61654.49743 60899.09713 108936.3114 133794.8225 0.503783747 0.86721333 0.46742529 0.469515192 0.858964436 0.460813777 0.455167816 0.814204238 1 17.02966276 1.015422716 5.544443361 0.999420533 0.593356924 0.44716871 0.156965052 0.130881129 13.43368437 0.148128852 0.03733585 10.36150201 -1.015422716 -0.40606361 THMQDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 105.57 0.0078976 157060000 280540 290660 237260 243040 369820 161160 318450 279070 429130 FALSE TRUE 262981.5022 312180.7688 242887.9192 249276.8179 340775.829 207684.2758 270701.3788 313912.5038 357505.4307 0.735601419 0.873219655 0.679396447 0.69726722 0.953204622 0.580926212 0.757195152 0.878063595 1 18.44760563 1.021118055 3.292174141 0.998204532 0.754908908 0.394349359 0.101725325 0.209379381 5.300086892 0.089885739 0.023470571 10.49827767 -1.021118055 -0.243295624 THNDIIHNENMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 THNDIIHNENMR 12 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;;;;;;;;;; 237.32 2.44E-16 20423520000 3745485 4286094 4070979 3959023 4980128 3263591 4298641 3566077 4738054 FALSE TRUE 3511061.78 4603440.859 4167544.544 4060618.233 4589008.836 4205736.742 3654099.689 4011309.563 3947242.178 0.889497432 1.166242316 1.055811718 1.028722852 1.162586086 1.065487384 0.925734861 1.016230923 1 21.91241361 1.824217702 8.217449332 0.975044312 1.075794626 0.168750036 0.080170822 0.400868511 34.81293976 0.031561044 0.019535906 66.71411075 -1.824217702 0.100750314 THPQYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 THPQYSR 7 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;; 91.318 0.016492 782440000 1366100 2503360 1058380 1036090 2441680 556871 1118450 2124480 2748580 FALSE TRUE 1280598.24 2688711.379 1083485.273 1062677.823 2249920.302 717630.6177 950748.8057 2389726.005 2289824.241 0.559256128 1.174199893 0.47317399 0.46408707 0.982573361 0.313399869 0.415206018 1.043628573 1 21.12680544 1.217020688 24.95446215 1.021814924 0.644605622 0.277825691 0.263991971 396.4871755 459326.5329 0.259257695 0.065057356 16.48240904 -1.217020688 -0.377209303 THPVEIFYTPEPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 THPVEIFYTPEPER 14 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ;; 162.48 4.43E-06 264300000 319522 271389 314045 309840 290805 278280 364230 286673 247710 FALSE TRUE 299523.6884 291482.9239 321494.2957 317791.019 267966.3484 358614.9185 309617.0928 322464.7551 206365.6007 1.451422559 1.412458874 1.557887044 1.539941821 1.298502984 1.737765002 1.500332864 1.562589666 1 17.65484298 -1.461640033 6.292770948 0.999791969 1.508046241 0.664657184 0.113312835 0.000302315 2.59E-05 0.10029386 0.02363003 0.034542993 1.461640033 0.508254271 THPVEIFYTPEPERDYLEAAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 THPVEIFYTPEPERDYLEAAIR 22 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ;;; 190.71 1.01E-17 664613000 80534 86181 99411 105819 97353 68440.5 88913 91659 102855 FALSE TRUE 75493.5207 92561.93091 101769.0759 108534.4947 89707.28808 88198.16131 75581.32108 103102.8279 85687.83603 0.881029609 1.080222529 1.187672377 1.266626627 1.046908082 1.029296168 0.882054263 1.20323762 1 16.3868028 2.4887777 23.25497349 1.008734441 1.118193634 0.062430655 0.124242888 431.9716551 861801.175 0.040603657 0.036334645 308.1610176 -2.4887777 0.109459193 THPYS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 THPYSPK 7 0 M0QZ39;M0R1C6;H0YD59;E9PME6;M0QXT0;B1AQP1;B4DLJ1;Q15853-4;P22415-2;Q15853-3;P22415;Q15853-2;Q15853 M0QZ39 USF2;USF1 Upstream stimulatory factor 2;Upstream stimulatory factor 1 1 THPYS(1)PK;THPYS(1)PK;THPYS(1)PK;THPYS(1)PK 113.71 0.0063664 1759670000 7237810 4678440 5208250 4763780 6260420 4174880 7079980 5941250 9033750 TRUE FALSE 6784808.392 5024836.566 5331792.15 4886026.66 5768751.867 5380100.082 6018402.726 6683028.141 7525958.765 0.901520803 0.6676673 0.708453543 0.649223151 0.766513882 0.714872384 0.799685849 0.887996912 1 22.84344395 1.156893785 1.353462258 0.999005284 0.71953362 0.61866442 0.069451554 0.231827392 0.842992446 0.059169266 0.018224896 14.351384 -1.156893785 -0.279471664 THS(ph)EGSLLQEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 THSEGSLLQEPR 12 0 P49796-1;P49796-4;P49796-6;P49796;C9J582 P49796-1 RGS3 Regulator of G-protein signaling 3 1 T(0.026)HS(0.974)EGSLLQEPR;T(0.039)HS(0.961)EGSLLQEPR;T(0.197)HS(0.803)EGSLLQEPR 212.7 1.11E-08 1047660000 532500 536720 558080 552910 679690 462820 684080 498100 833520 TRUE FALSE 499171.7755 576459.3073 571317.9211 567098.6067 626309.8891 596428.6207 581508.5547 560288.8815 694400.1273 0.718853232 0.83015438 0.822750312 0.816674111 0.901943799 0.858912027 0.837425761 0.806867481 1 19.40540769 -5 0.137611758 1.554639063 0.766710543 0.647115963 0.042648313 92.49986121 0.786083348 14.26765541 0.264709865 1.00E-05 5 -0.787928519 THS(ph)FENVSCHLPDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 THSFENVSCHLPDSR 15 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 T(0.003)HS(0.997)FENVSCHLPDSR;T(0.008)HS(0.992)FENVSCHLPDSR;T(0.012)HS(0.988)FENVSCHLPDSR;T(0.01)HS(0.99)FENVSCHLPDSR 231.42 1.27E-13 4136020000 1043532 1414390 1207960 1395920 1266870 1060769 1934890 1176360 1487180 TRUE FALSE 978219.1949 1519112.907 1236613.382 1431741.67 1167375.141 1366995.79 1644771.207 1323231.135 1238960.05 0.789548617 1.226119363 0.998105937 1.155599545 0.942221777 1.103341298 1.327541761 1.068017597 1 20.24069824 1.993555344 24.9338984 1.180045373 1.050359339 0.063753891 0.145730045 507.5533554 1963688.443 0.050949467 0.036310813 98.52701914 -1.993555344 -0.129686034 THS(ph)LHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THSLHQR 7 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 T(0.473)HS(0.527)LHQR 58.433 0.070586 16657000 15093 17576 15569 15503 21212 11572 20809 13818 31057 TRUE FALSE 14148.35607 18877.34533 15938.30403 15900.83323 19546.09509 14912.64854 17688.88363 15543.20772 25873.38606 0.546830478 0.729604748 0.616011526 0.614563289 0.755451762 0.576370194 0.683670996 0.600741151 1 14.65918125 -1.321915285 4.800801036 1.000195176 0.648620252 0.744323571 0.066078117 0.000119495 1.69E-05 0.055385093 0.013047207 0.047652393 1.321915285 -0.351574924 THS(ph)TSS(ph)SLGSGESPFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 2 T(0.001)HS(0.74)T(0.259)S(0.002)S(0.921)S(0.077)LGSGESPFSR 179.92 1.30E-09 177900000 291330 328650 295190 366020 501720 199780 530890 325380 470630 TRUE FALSE 273096.1753 352983.588 302192.0462 375412.6929 462316.935 257453.2428 451287.973 366004.4092 392078.8126 0.696533877 0.900287332 0.770743117 0.957492935 1.179142867 0.656636458 1.151013415 0.933497035 1 18.58078416 5.09932629 0.338591846 1.014460881 0.46469198 0.225270656 0.152548939 12.35186315 0.948322262 0.135000135 2.92710446 125697.3988 -5.09932629 -0.549768901 THS(ph)TSSS(ph)LGSGESPFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 2 THS(0.977)T(0.023)SS(0.136)S(0.864)LGSGESPFSR 407.87 3.40E-140 246670000 392710 420630 347640 485160 596690 260970 628490 378750 626010 TRUE FALSE 368130.9821 451773.8829 355886.185 497610.027 549828.3743 336307.8025 534253.7591 426037.7712 521524.8868 0.705874238 0.866255656 0.682395402 0.954144355 1.054270636 0.644854754 1.024407028 0.816907845 1 18.99237657 7.999999998 0.114676946 1.043566286 0.112363635 0.188159015 0.133205897 159.0370914 1.263122625 0.965555475 23.54831942 99999999.62 -7.999999998 -0.931202651 THS(ph)TSSSLGSGESPFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 1 THS(0.929)T(0.053)S(0.009)S(0.009)SLGSGESPFSR;T(0.148)HS(0.701)T(0.148)S(0.004)SSLGSGESPFSR;T(0.005)HS(0.848)T(0.148)SSSLGSGESPFSR 410.83 1.85E-140 3644100000 772810 1115610 1045440 1397200 1526010 931650 1498060 1049420 1085940 TRUE FALSE 724441.2016 1198210.925 1070238.33 1433054.517 1406163.33 1200602.231 1273439.81 1180442.397 904689.5986 0.800762165 1.324444237 1.182989538 1.584028953 1.554304739 1.32708747 1.407598598 1.304803768 1 19.78706336 3.388018194 10.29837922 1.390730294 1.158112926 0.241511587 0.206527976 0.50524114 54.2934853 0.052777537 0.071488562 2443.532918 -3.388018194 -0.232617368 THSDQFLVAFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THSDQFLVAFK 11 0 P36542-2;P36542 P36542-2 ATP5C1 "ATP synthase subunit gamma, mitochondrial" 0 87.001 0.01405 103910000 485590 466180 403430 380640 622540 316220 387970 505410 662480 FALSE TRUE 455197.7887 500696.4523 412999.5501 390407.8668 573648.2196 407507.5806 329797.5002 568511.551 551907.8082 0.824771424 0.907210307 0.74831257 0.707378771 1.039391382 0.738361687 0.59755904 1.030084269 1 19.07406777 1.198343123 24.99508926 1.015043177 0.79394289 0.375265167 0.118184809 195.772167 121667.6953 0.115184851 0.028797657 15.78858185 -1.198343123 -0.221100287 THSDSKPYGPMSVGLDFSLPGMEHVYGIPEHADNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THSDSKPYGPMSVGLDFSLPGMEHVYGIPEHADNLR 36 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 85.239 0.00034105 321070000 105150 123800 122650 111070 139790 107820 157930 111380 158320 FALSE TRUE 98568.8492 132966.2808 125559.3159 113920.2442 128811.4573 138945.8837 134249.8627 125286.0382 131895.3692 0.74732608 1.008119403 0.951961518 0.863716785 0.976618497 1.05345536 1.017851221 0.94988959 1 17.00903439 2.486283365 23.15265382 1.010313647 0.921697458 0.320430145 0.07289815 229.6708827 580383.2648 0.023668789 0.020847634 306.3961931 -2.486283365 -0.08861619 THSLCNGDS(ph)PGPVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THSLCNGDSPGPVQK 15 0 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-2;Q674X7 A0A1B0GWK2 KAZN Kazrin 1 THSLCNGDS(1)PGPVQK 100.02 0.0014924 447140000 254730 179380 226880 210160 219740 180910 250450 217880 333100 TRUE FALSE 238786.904 192661.4818 232261.7007 215553.0614 202482.5068 233135.7802 212897.3476 245082.7976 277503.4581 0.860482625 0.694266959 0.836968672 0.776758109 0.729657598 0.840118468 0.767188088 0.883170247 1 18.08214622 0.981839074 2.730075107 0.999875052 0.781508491 0.649721851 0.051195572 0.148268209 2.59849183 0.04382921 0.011688471 9.590451957 -0.981839074 -0.218366561 THSQGGYGSQGYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THSQGGYGSQGYK 13 0 K7ER00;Q9Y285;Q9Y285-2;K7EPH2;K7ERS0 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 129.93 0.00014797 126760000 207520 190410 198910 188590 211460 157280 263390 183870 231590 FALSE TRUE 194531.6936 204508.1545 203628.2391 193429.5387 194852.7846 202684.1828 223897.1147 206826.5742 192936.1329 1.008269891 1.059978509 1.055417853 1.002557353 1.009934125 1.05052475 1.160472698 1.071995023 1 17.55776383 1.981164491 24.364585 1.097864345 1.034069934 0.157349004 0.044139511 633.9241256 820007.6891 0.016780238 0.011042866 95.75566816 -1.981164491 -0.063794412 THST(ph)S(ph)SSLGSGESPFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 2 T(0.078)HS(0.385)T(0.545)S(0.531)S(0.441)S(0.021)LGSGESPFSR 80.382 0.020476 137150000 52811 51233 44485 55826 64585 47698 66788 43210 78618 TRUE FALSE 49505.65378 55026.34463 45540.20521 57258.58967 59512.75462 61467.63829 56773.75943 48604.86362 65496.14791 0.75585596 0.840146274 0.6953112 0.874228355 0.908645112 0.938492419 0.866825932 0.74210263 1 15.99912244 3.122591898 8.108782227 0.88619475 0.770621516 0.392059659 0.073088044 0.249790424 16.7191393 0.020011283 0.02396623 1326.147704 -3.122591898 -0.115573234 THST(ph)SS(ph)SLGSGESPFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 2 T(0.047)HS(0.354)T(0.468)S(0.276)S(0.843)S(0.013)LGSGESPFSR 132.6 4.10E-05 273780000 79897 93042 83442 101280 118870 64467 122120 78490 110760 TRUE FALSE 74896.38939 99930.92649 85421.28364 103879.0163 109534.4297 83077.57637 103809.2397 88289.64928 92273.44046 0.811678735 1.082986892 0.925740746 1.125773741 1.187063462 0.900341159 1.125017548 0.956826242 1 16.49362783 4.74547934 24.51479695 1.039127595 0.811678596 0.365155811 0.093758577 662.0991093 2345905.424 0.020552304 0.202697696 55651.81596 -4.74547934 -0.227448999 THST(ph)SSSLGSGESPFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 1 THST(0.76)S(0.187)S(0.048)S(0.004)LGSGESPFSR 326.09 1.07E-58 2635700000 178410 213810 209380 268790 256540 211600 291480 208470 239810 TRUE FALSE 167243.6366 229640.7149 214346.5925 275687.6065 236392.3832 272685.485 247775.28 234497.9384 199784.1618 0.837121597 1.149444044 1.072890817 1.379927238 1.183238857 1.364900413 1.240214829 1.1737564 1 17.60808269 5.462590242 0.819125789 1.230152771 1.69E-15 0.457003218 0.119047377 5.734561549 1.257525131 0.036348364 8.457447932 290128.3995 -5.462590242 -1.230152771 THSTSS(ph)SLGSGESPFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 1 T(0.003)HS(0.016)T(0.094)S(0.094)S(0.42)S(0.373)LGSGESPFSR;THST(0.008)S(0.07)S(0.461)S(0.461)LGSGESPFSR;THST(0.001)S(0.03)S(0.962)S(0.008)LGSGESPFSR 358.65 4.77E-88 9272410000 446480 545670 524350 572360 641330 527590 710800 524100 690750 TRUE FALSE 418535.6138 586071.9746 536787.8296 587047.7266 590962.5288 679896.6683 604222.1387 589535.0387 575459.3626 0.727306985 1.018441983 0.932798846 1.020137589 1.026940506 1.18148511 1.049982289 1.024459896 1 19.13435453 5.569303599 0.782687981 1.050897004 1.70E-54 0.639519102 0.068264153 5.533548814 0.998889942 0.023427977 6.877952771 370939.9418 -5.569303599 -1.050897004 THSTSSSLGSGES(ph)PFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 1 THSTSSSLGSGES(0.999)PFS(0.001)R;THSTSSSLGSGES(1)PFSR 293.35 2.46E-33 136610000 214840 219168 262310 238980 259840 196144 267990 226010 319600 TRUE FALSE 201393.5479 235395.4268 268532.1171 245112.6314 239433.2145 252767.5887 227807.3874 254227.846 266256.6953 0.756388671 0.884092047 1.00854597 0.920587672 0.899257066 0.949337963 0.855593085 0.954822359 1 18.02245828 4.685410104 2.65910098 0.932806191 0.732269813 0.624088552 0.045081228 0.280047997 2.854276174 0.011094635 0.11774054 48462.97873 -4.685410104 -0.200536378 THSTSSSLGSGESPFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 0 ; 281.92 5.29E-36 970910000 247340 421910 406600 347010 376340 346650 471420 377540 486050 FALSE TRUE 231859.4309 453148.6554 416244.744 355914.8641 346783.7745 446722.2276 400734.9474 424676.7001 404925.115 0.572598296 1.11909249 1.02795487 0.878964655 0.856414585 1.103221833 0.989651994 1.048778365 1 18.6272956 2.233694865 24.99293876 1.032192661 0.940235522 0.149939967 0.146737874 329.121862 1690516 0.053068359 0.040433128 171.2753504 -2.233694865 -0.09195714 THT(ph)GEKPYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 THTGEKPYK 9 1 O75362;P15621-3;C9J2N8;B9EG95;H9KV89;A0A087X254;E7EX64;B4DI05;F8W7T7;A0A0C4DFQ3;F8WEL6;R4GMT1;E9PJ50;F8W6Y9;Q7Z7L9;Q32M78;Q96RE9-3;Q9H7R0;Q8N184-1;P17025-2;Q6ZMW2;A0A0A0MS50;Q8N7K0-2;Q6ZT77;P17025;Q96RE9-2;Q8N972;Q9Y2A4;Q8N184;P51814-8;P51814;P51814-5;P51814-3;Q9NPC7;P51814-2;Q9HBT7;Q99676;P51814-7;Q8N8J6-2;O95125;Q9P2J8-2;Q8N8J6-3;Q8N8J6;P51814-6;P51814-4;I3L4C4;Q8N7K0;P16415-2;P15621;P16415;Q9NPC7-2;Q96RE9;P15621-2;O75346-2;O95780-2;Q96BR6-2;Q13887-4;Q9UJN7;Q15973;Q9H4T2;Q13360-2;Q8IZC7-2;Q13887-2;O75840;Q15973-1;Q15973-4;O75840-4;O75840-2;Q15973-2;A0A3F2YPB8;C9JN71;Q8IZC7;P0CG31;Q8NDW4;P36508;Q96RE9-4;Q9UC07;Q9H7R0-2;Q14584;P36508-2;O95125-2;Q8N8L2;Q9NPC7-3;O95780;Q13360;O95780-3;Q96BR6;Q13887;Q9UC06;O14978;A6NHJ4;A0A087WXA8;Q2M218;Q2M218-2;Q9P0L1;Q6ZMS4;P57682;Q86YE8;Q86YE8-3;Q86YE8-2;Q86YE8-4;Q86WZ6-2;P17040-3;P17040-2;Q9P2J8;Q86WZ6;Q86XU0;O75346;A6NP11;Q96H40;Q6U7Q0;P17040;P52743;Q8N859;A0A0M3HEQ9;A0A087WT67;O14628-4;O14628-7;O14628-5;O14628-6;O14628;Q9Y4X4;A0A087WUV0;A0A087WVT1;Q96MX3;Q96N95;Q9UEG4 O75362;A6NHJ4;Q9P0L1;P57682;Q86YE8;P52743;Q8N859;A0A087WT67;Q9Y4X4;A0A087WUV0;A0A087WVT1;Q96N95;Q9UEG4 ZNF217;ZNF44;ZNF823;ZNF682;ZNF615;ZNF76;ZNF263;ZSCAN2;ZNF567;MYNN;ZNF48;ZNF699;ZNF300;ZNF442;ZNF182;ZNF782;ZNF433;ZNF826P;ZNF709;ZNF443;ZNF41;ZNF287;ZNF184;ZNF202;ZNF624;ZNF253;ZNF669;KLF5;ZNF391;ZNF124;ZSCAN16;ZNF177;ZNF101;KLF7;ZNF878;ZNF286B;ZNF248;ZNF69;ZNF266;ZNF491;ZNF70;ZNF860;ZNF630;ZKSCAN7;ZNF852;KLF3;ZNF573;ZNF227;ZSCAN20;ZNF677;ZNF716;ZNF486;ZNF322;ZNF137P;ZNF713;ZNF195;KLF12;ZNF396;ZNF629 Zinc finger protein 217;Zinc finger protein 44;Zinc finger and SCAN domain-containing protein 2;Zinc finger protein 699;Zinc finger protein 300;Zinc finger protein 442;Zinc finger protein 567;Zinc finger protein 182;Zinc finger protein 782;Zinc finger protein 433;Putative zinc finger protein 826;Zinc finger protein 709;Zinc finger protein 443;Zinc finger protein 41;Myoneurin;Zinc finger protein 287;Zinc finger protein 184;Zinc finger protein 615;Zinc finger protein 202;Zinc finger protein 624;Zinc finger protein 823;Zinc finger protein 253;Zinc finger protein 682;Zinc finger protein 669;Krueppel-like factor 5;Zinc finger protein 391;Zinc finger protein 124;Zinc finger and SCAN domain-containing protein 16;Zinc finger protein 177;Zinc finger protein 101;Krueppel-like factor 7;Zinc finger protein 878;Putative zinc finger protein 286B;Zinc finger protein 248;Zinc finger protein 76;Zinc finger protein 69;Zinc finger protein 266;Zinc finger protein 491;Zinc finger protein 70;Zinc finger protein 263;Zinc finger protein 860;Zinc finger protein 630;Zinc finger protein with KRAB and SCAN domains 7;Zinc finger protein 852;Krueppel-like factor 3;Zinc finger protein 573;Zinc finger protein 227;Zinc finger and SCAN domain-containing protein 20;Zinc finger protein 677;Zinc finger protein 716;Zinc finger protein 486;Zinc finger protein 322;Putative zinc finger protein 137;Zinc finger protein 713;Zinc finger protein 195;Krueppel-like factor 12;Zinc finger protein 48;Zinc finger protein 396;Zinc finger protein 629 1 T(0.002)HT(0.998)GEKPYK;T(0.012)HT(0.988)GEKPYK;T(0.025)HT(0.975)GEKPYK 115.14 0.0022354 337082000 949660 483661 615176 581975 697030 391426 947850 515564 1051470 TRUE FALSE 890222.4758 519471.7637 629768.2652 596909.4638 642288.0755 504424.3319 805728.6919 579933.3003 875972.8642 1.016267184 0.593022666 0.718935815 0.681424606 0.733228279 0.575844701 0.919810105 0.662044823 1 19.74052665 -0.006354057 0.619529743 1.01519703 0.714986579 0.241166325 0.13876272 5.638055998 2.442003457 0.345725226 0.049825472 0.985475753 0.006354057 -0.300210451 ELPPAAAIGATSLVAAPHSSS(ph)SSPSKDSSR ddPTM_SK-BR-3_Pertuzumab_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(0.091)S(0.071)S(0.277)S(0.277)S(0.277)PS(0.005)KDSSR 196.64 1.71E-25 286640000 113650 266830 262420 287300 302300 243860 376080 283180 337030 TRUE FALSE 106536.8494 286586.3708 268644.7263 294672.6044 278558.5774 314258.4233 319690.2954 318535.6464 280777.5157 0.379435116 1.020688463 0.956788601 1.049487897 0.992097165 1.119243549 1.138589372 1.134477045 1 18.09906789 4.742134176 4.611575803 1.052908939 0.335609207 0.921630265 0.061655601 0.058169719 3.291902985 0.017202952 0.135587087 55224.80307 -4.742134176 -0.717299733 down THTGEKPYR ddPTM_SK-BR-3_Pertuzumab_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 53.751 0.083844 37698000 44382 60837 52423 44660 71607 36748 59534 60477 94085 FALSE TRUE 41604.20984 65341.43478 53666.49832 45806.05121 65983.27507 47356.55105 50607.42939 68027.68658 78381.60569 0.530790477 0.833632256 0.684682303 0.584397969 0.841820916 0.604179394 0.64565441 0.867903713 1 16.25822751 1.044000449 4.008533038 0.998064366 0.689174447 0.552493057 0.099967871 0.138194196 4.806874905 0.089421927 0.022936373 11.06624929 -1.044000449 -0.308889919 THTGEKPYVCDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THTGEKPYVCDK 12 1 Q49AA0 Q49AA0 ZFP69 Zinc finger protein ZFP69 0 52.344 0.089716 342020000 282770 97520 105380 98987 127470 83381 109550 79137 141540 FALSE TRUE 265071.9305 104740.4823 107879.6634 101527.174 117459.0204 107451.7411 93123.99451 89017.42865 117916.0596 2.247971407 0.88826308 0.914885247 0.861012269 0.996124029 0.911256206 0.789748189 0.754922009 1 16.84740069 4.738566473 9.590347665 0.884108576 2.252213163 0.968245535 0.077308171 0.011948642 29.55025686 0.018191156 0.105771338 54772.99298 -4.738566473 1.368104587 THTGERPNACADCGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THTGERPNACADCGK 15 1 Q6DD87 Q6DD87 ZNF787 Zinc finger protein 787 0 54.859 0.086081 60163000 76406 91811 96754 93486 105180 92338 109600 66294 90332 FALSE TRUE 71623.88485 98608.78197 99049.05057 95885.00903 96919.58708 118994.4816 93166.49748 74570.95183 75255.00563 0.951749113 1.310328544 1.3161789 1.274134634 1.287882265 1.581216832 1.238010637 0.990910189 1 16.19949993 1.285044986 5.027102613 0.99192939 1.301133441 0.381816876 0.15021066 0.171772822 8.9307548 0.106574237 0.035255065 19.27724585 -1.285044986 0.309204051 THTRVS(ph)VQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 THTRVSVQR 9 1 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 1 THTRVS(1)VQR;THTRVS(1)VQR;THT(0.01)RVS(0.99)VQR;THTRVS(1)VQR;THTRVS(1)VQR;THT(0.004)RVS(0.996)VQR;T(0.002)HT(0.008)RVS(0.991)VQR;THT(0.001)RVS(0.999)VQR 130.56 0.00021663 12538760000 2411900 2474980 2352690 2147228 2676250 1769334 2836720 2117005 3545660 TRUE FALSE 2260943.484 2658230.094 2408496.918 2202329.506 2466068.12 2280112.003 2411380.171 2381317.734 2953866.44 0.765418319 0.899915466 0.815370961 0.745575181 0.834861078 0.771907616 0.816347056 0.806169738 1 21.49417317 -1.212972775 4.112958882 1.000107839 0.813658912 0.66292362 0.043026723 4670880.253 1377514.323 4506.50499 0.010395277 0.061238878 1.212972775 -0.186448926 THTTALAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THTTALAGR 9 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 82.287 0.01888 33434000 18514 44022 29719 34889 43238 26371 25408 36998 29468 FALSE TRUE 17355.24179 47281.43468 30423.94871 35784.31081 39842.26189 33983.8796 21598.30628 41617.28174 24549.60043 0.706945999 1.925955366 1.239284884 1.457633126 1.622929139 1.384294612 0.879782396 1.69523255 1 14.58341192 1.978418713 23.84935252 1.16674517 1.450784318 0.044807149 0.371624994 898.1494417 992537.3749 0.137274933 0.089654681 95.15217346 -1.978418713 0.284039148 THTTALAGRS(ph)PS(ph)PASGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 THTTALAGRSPSPASGR 17 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 THTTALAGRS(1)PS(1)PASGR;T(0.002)HT(0.002)T(0.002)ALAGRS(0.99)PS(0.735)PAS(0.269)GR;T(0.001)HT(0.001)T(0.001)ALAGRS(0.984)PS(0.992)PAS(0.022)GR;THTTALAGRS(1)PS(0.98)PAS(0.021)GR;THTTALAGRS(1)PS(0.999)PAS(0.001)GR;THTTALAGRS(1)PS(1)PASGR;T(0.002)HT(0.002)T(0.002)ALAGRS(0.995)PS(0.999)PASGR 161.62 1.67E-09 24702310000 4808821 8596492 7333590 8305265 9199057 5603961 8078020 6871303 9864659 TRUE FALSE 4507845.478 9232985.212 7507546.218 8518392.161 8476600.17 7221733.568 6866795.894 7729200.305 8218183.685 0.548520896 1.123482459 0.913528646 1.036529784 1.031444477 0.878750566 0.835561257 0.940499824 1 22.97038815 0.965314539 22.05114111 1.000000011 0.930293866 0.020376586 0.155099252 6178.060223 3927688.134 0.13706355 0.034265887 9.232398433 -0.965314539 -0.069706144 THTTALAGRS(ph)PS(ph)PASGRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 THTTALAGRSPSPASGRR 18 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 THTTALAGRS(0.999)PS(0.903)PAS(0.098)GRR;THTTALAGRS(1)PS(0.991)PAS(0.009)GRR;THTTALAGRS(1)PS(0.991)PAS(0.009)GRR 119.83 3.36E-05 2850870000 409539 728441 613909 774039 924862 411501 751976 559824 1026120 TRUE FALSE 383906.685 782375.5296 628471.2114 793902.1512 852227.0692 530294.6585 639224.1798 629719.2587 854853.943 0.449090383 0.915215442 0.735179637 0.928699174 0.996927108 0.62033364 0.747758357 0.736639591 1 19.70531842 4.74817716 24.45778032 0.817757391 0.449090114 0.473843351 0.126664697 914.0266868 2324580.851 0.02914769 0.376190973 55998.59875 -4.74817716 -0.368667277 THTTALAGRS(ph)PSPASGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THTTALAGRSPSPASGR 17 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 THTTALAGRS(0.805)PS(0.187)PAS(0.008)GR 62.648 0.036424 38065000 13284 20143 18997 18936 20538 13424 17023 13793 21580 TRUE FALSE 12452.57815 21634.40868 19447.61781 19421.92982 18925.02833 17299.29088 14470.55918 15515.08641 17978.15859 0.692650367 1.203371779 1.081735803 1.080306958 1.052667782 0.962239308 0.804896626 0.862996415 1 14.13395764 2.043517853 3.662157343 0.86958045 1.05711163 0.125716936 0.140264245 0.293232705 8.156585153 0.056684817 0.037131925 110.5395909 -2.043517853 0.18753118 THVADFAPEVAWVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 THVADFAPEVAWVTR 15 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;;; 183.01 5.23E-07 2248480000 1292308 1354418 1365959 1343947 1478606 1076163 1593006 1310863 1610170 FALSE TRUE 1211424.749 1454700.518 1398360.193 1378434.955 1362482.249 1386833.788 1354149.539 1474527.131 1341422.225 0.903089815 1.084446411 1.04244597 1.027592155 1.015699773 1.033853296 1.009487926 1.099226704 1 20.35533198 4.750506219 24.67013336 1.039772915 0.903089716 0.651332364 0.031268756 955.1230336 1972482.613 0.00718888 0.117191745 56299.71794 -4.750506219 -0.136683199 THVEKEDGEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 THVEKEDGEAR 11 1 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 0 ;; 144.28 2.21E-05 572280000 861890 741440 773330 782140 863400 617490 835120 635000 933280 FALSE TRUE 807945.8434 796336.9891 791673.7528 802211.0366 795592.0468 795749.3389 709901.5089 714281.1478 777509.5388 1.039145892 1.024215073 1.018217415 1.031770025 1.02325696 1.023459262 0.913045401 0.918678308 1 19.56850085 1.763432429 10.69019209 0.93725014 1.025502201 0.724307292 0.023945364 0.095533344 37.98273569 0.009887721 0.005442727 58.00059235 -1.763432429 0.08825206 THYDPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 THYDPPR 7 0 P31943;G8JLB6;E9PCY7;H0YB39;D6RBM0;H0YBD7;E7EN40;E5RGV0;P55795 P31943;P55795 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 ;;;;; 104.45 0.0081492 4102680000 1683070 1695020 1814630 1821220 1790720 1652550 2035790 1500190 1813130 FALSE TRUE 1577729.653 1820521.044 1857673.881 1867955.589 1650084.075 2129614.358 1730542.189 1687492.024 1510506.89 1.044503447 1.205238491 1.229834762 1.236641555 1.092404203 1.409867358 1.145669841 1.117169366 1 20.52660133 -0.439871631 7.814516258 0.999990967 1.196034117 0.244896332 0.100585914 0 0 0.087216016 0.020557012 0.363185389 0.439871631 0.19604315 THYDPPRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 115.49 0.0015924 1689260000 2308550 2493640 2491970 2510170 2558580 2095670 2649900 2338390 2776400 FALSE TRUE 2164061.976 2678271.7 2551080.705 2574585.212 2357639.448 2700655.909 2252572.095 2630343.139 2313000.904 0.935607925 1.157920732 1.102931132 1.113093042 1.019298974 1.167598294 0.973874282 1.137199356 1 21.1413344 1.731402424 25 1.037780976 1.092474462 0.06074572 0.078753145 1.572715609 5457.862933 0.032692935 0.018130007 53.8768783 -1.731402424 0.054693486 THYSNIEANESEEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THYSNIEANESEEVR 15 0 A0A0C4DGQ5;K7ELJ7;P04632;U3KQE2;K7EIV0;A0A075B7C0;K7EM73 A0A0C4DGQ5 CAPNS1 Calpain small subunit 1 0 208.66 2.78E-09 973380000 232040 701510 538500 533980 592800 470050 712020 581740 642190 FALSE TRUE 217517.0306 753450.5303 551273.4743 547682.8308 546243.8792 605745.8044 605259.2111 654371.5196 535004.3403 0.406570591 1.408307323 1.03040935 1.023697921 1.021008314 1.132225963 1.13131645 1.223114413 1 19.02919107 2.227083116 22.59866025 1.132455419 1.045901303 0.037904671 0.251042136 322.1038997 634192.6376 0.087466946 0.065301164 168.6875832 -2.227083116 -0.086554116 TIADHCPDSACK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TIADHCPDSACK 12 0 P35221-2;P35221;G3XAM7;P35221-3 P35221-2 CTNNA1 Catenin alpha-1 0 ;; 159.99 6.93E-05 896620000 2100630 1676760 1884220 1790280 2051020 1639460 2481260 1824610 1963270 FALSE TRUE 1969155.318 1800909.055 1928914.588 1836221.616 1889941.163 2112745.488 2109218.098 2052416.575 1635587.554 1.203943692 1.101077745 1.179340466 1.122667883 1.155512072 1.291734877 1.289578227 1.254849715 1 20.64137756 2.327571264 7.895567854 1.241111251 1.147233919 0.039470451 0.088346947 0.349006403 26.99005086 0.027224637 0.022713732 212.6039181 -2.327571264 -0.093877331 TIADLELHYQEFIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TIADLELHYQEFIR 14 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;; 226.88 2.24E-12 320049000 305217 379531 353306 347886 412549 289614 399374 353148 319046 FALSE TRUE 286114.0128 407631.8701 361686.5852 356813.3437 380149.0657 373220.8603 339491.5763 397239.3052 265795.1615 1.076445527 1.533631643 1.360771893 1.342437318 1.430233205 1.404167248 1.277267706 1.49453174 1 18.01995532 -1.03469581 4.129256519 0.999963963 1.375382225 0.450440193 0.12621196 6180227.714 3097243.587 2011.238489 0.026247427 0.092321784 1.03469581 0.375418262 TIAECLADELINAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TIAECLADELINAAK 15 0 M0R0F0;M0R0R2;P46782;M0QZN2 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ; 237.13 2.32E-17 97071000 221890 217660 244340 211250 255110 207148 290860 190233 243400 FALSE TRUE 208002.301 233775.7729 250135.8602 216671.0326 235074.6897 266948.2648 247248.2432 213984.0088 202774.9676 1.025778988 1.152882802 1.233563803 1.06852949 1.159288508 1.316475441 1.219323303 1.05527823 1 17.62952004 1.087402468 4.861967227 1.002285934 1.178197005 0.340895135 0.081889232 0.202461944 7.608482676 0.077759182 0.019733083 12.22932447 -1.087402468 0.175911071 TIAPTGHLHTVEFHQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TIAPTGHLHTVEFHQQR 17 0 Q96FX7;H0Y2Q1 Q96FX7 TRMT61A tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 0 ; 105.39 0.00027946 131795000 67902 111293 99421 93200 109465 87149 89814 98388 108162 FALSE TRUE 63652.13503 119533.2495 101779.3131 95591.66979 100868.0605 112307.5016 76347.22449 110671.9584 90109.06345 0.70638993 1.326539695 1.129512495 1.060844116 1.119399721 1.24635078 0.847275752 1.228200074 1 16.4593846 1.75324795 25 1.012059319 1.127520128 0.01582925 0.185475862 12.76141071 21750.51259 0.078282662 0.043412256 56.65626615 -1.75324795 0.115460809 TIAQMIEDEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TIAQMIEDEQR 11 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;O95359-2;Q4VXL4;H0Y9C3;O75410-3;E7ET87;E7EVI4;O75410-2;O75410;O75410-9;O75410-7;O75410-6;O75410-4;O75410-5;O75410-10 O95359-3;O75410-3 TACC2;TACC1 Transforming acidic coiled-coil-containing protein 2;Transforming acidic coiled-coil-containing protein 1 0 134.3 0.00033416 45842000 45563 55685 55861 58211 64634 48094 53809 55334 53658 FALSE TRUE 42711.29316 59807.97534 57186.0493 59704.79281 59557.90636 61977.95706 45740.83999 62242.57171 44702.13316 0.955464318 1.337922178 1.279268913 1.335613954 1.33232806 1.386465313 1.02323618 1.392384822 1 15.44805606 -1.034709027 5.373035178 0.999998321 1.257926526 0.22485856 0.148918294 2.76E-06 4.95E-07 0.13283071 0.031308295 0.092318975 1.034709027 0.257928204 TIAS(ph)DS(ph)EEEAGKELSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TIASDSEEEAGKELSDK 17 1 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 2 T(0.001)IAS(0.999)DS(1)EEEAGKELSDK 134.62 9.32E-06 584880000 3822300 1395100 2109100 2097000 2189000 1377700 2610500 1769600 2642000 TRUE FALSE 3583069.066 1498394.656 2159128.848 2150812.57 2017084.77 1775419.625 2219079.76 1990538.455 2201033.132 1.627903285 0.680768787 0.980961539 0.977183187 0.916426355 0.806630122 1.008199162 0.904365512 1 21.06974943 4.749668787 24.99786377 0.904472908 1.627903702 0.834818372 0.100433254 644.8199417 1451077.632 0.023544196 0.361209737 56191.26219 -4.749668787 0.723430795 TICTFDSSGFESMS(ph)PIKETVSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TICTFDSSGFESMSPIKETVSSR 23 1 E9PEI0;Q69YH5 E9PEI0 CDCA2 Cell division cycle-associated protein 2 1 TICTFDSSGFES(0.141)MS(0.858)PIKETVSSR;TICTFDSSGFESMS(1)PIKETVSSR;TICTFDSSGFES(0.004)MS(0.996)PIKETVSSR;TICTFDSSGFES(0.134)MS(0.866)PIKETVSSR 270.18 7.98E-46 586788000 488060 352315 400222 403486 381496 287073 505439 329425 436696 TRUE FALSE 457513.1958 378400.7692 409715.4548 413840.1339 351534.843 369946.3149 429653.1142 370554.4364 363808.6164 1.257565586 1.04010942 1.126184033 1.13752153 0.966263104 1.016870679 1.180986636 1.018542222 1 18.47282019 4.745036196 24.62306921 1.073522383 1.257565689 0.436948901 0.068860941 605.7788378 2303368.43 0.01583972 0.148551872 55595.05913 -4.745036196 0.184043305 TIDDLEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TIDDLEDK 8 0 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 122.19 0.0075452 0 255960 146420 174980 190980 180460 150640 227480 176150 144350 FALSE TRUE 239939.9205 157261.0891 179130.6082 195880.8701 166287.3995 194127.3226 193371.4858 198142.7153 120257.0525 1.995225358 1.30770783 1.489564267 1.628851415 1.3827663 1.614269755 1.607984579 1.647659835 1 16.87576198 -1.248345037 4.642880518 0.999821358 1.551858003 0.486977216 0.185833805 0.000316968 5.13E-05 0.165970077 0.039107009 0.056448832 1.248345037 0.552036645 TIDDLEDKLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TIDDLEDKLK 10 1 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ; 159.94 6.87E-06 978070000 2433780 1430570 1641320 1735320 2135710 1046130 2260800 1527730 2411000 FALSE TRUE 2281454.054 1536490.891 1680252.885 1779851.249 1967979.952 1348130.748 1921814.028 1718470.453 2008588.524 1.135849392 0.764960505 0.836534146 0.886120391 0.979782533 0.671183138 0.956798271 0.855561223 1 20.93775062 0.16203094 1.233158073 1.000207707 0.868872935 0.060188335 0.125979408 17.06584716 22.6050566 0.117537745 0.03247413 1.452215072 -0.16203094 -0.131334772 TIDDLEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TIDDLEEK 8 0 P67936;A0A2R8YE05;K7ENT6;A0A5F9UN72;K7EPB9;P67936-2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 145.65 0.0013167 78885000 333470 266000 267340 287900 300960 190020 322110 246870 355150 FALSE TRUE 312598.708 285694.9168 273681.431 295288.0014 277323.8156 244875.6893 273812.5958 277692.2629 295873.1706 1.056529415 0.965599267 0.924995769 0.998022229 0.937306397 0.827637358 0.925439083 0.938551685 1 18.17461936 2.481635238 24.99902377 0.910452786 0.972127694 0.209504347 0.053696112 280.8237958 1555253.031 0.017363372 0.014867615 303.1344103 -2.481635238 0.061674907 TIDEELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TIDEELER 8 0 Q9Y320-2;Q9Y320 Q9Y320-2 TMX2 Thioredoxin-related transmembrane protein 2 0 93.267 0.026033 45684000 159140 148150 146120 147930 169640 155450 198800 179250 196540 FALSE TRUE 149179.7115 159119.1801 149586.0354 151726.1342 156317.1587 200325.8915 168991.7856 201629.7571 163736.2043 0.911097897 0.971802057 0.913579474 0.926649881 0.954689034 1.223467298 1.032097857 1.231430507 1 17.32101383 2.34489011 7.636580727 1.117610837 0.935558979 0.617315956 0.072936602 0.139855658 9.066177941 0.022041279 0.018389631 221.25348 -2.34489011 -0.182051858 TIDLGAAAHYTGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TIDLGAAAHYTGDK 14 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 138.21 1.67E-05 347300000 471240 429520 521530 492000 530500 402240 624710 454770 640530 FALSE TRUE 441745.9296 461322.1077 533900.9379 504625.553 488836.6699 518360.1582 531040.535 511549.0356 533621.405 0.82782648 0.864511999 1.000523841 0.945662127 0.916073953 0.97140061 0.995163481 0.958636649 1 19.02545701 4.226567057 2.371697642 0.968224566 0.832856721 0.79280238 0.026490562 0.136881486 1.475435257 0.006980127 0.024251592 16848.72558 -4.226567057 -0.135367845 TIDLGAAAHYTGDKAS(ph)PDQNASTHTPQSSVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TIDLGAAAHYTGDKASPDQNASTHTPQSSVK 31 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 1 TIDLGAAAHYTGDKAS(1)PDQNASTHTPQSSVK;TIDLGAAAHYTGDKAS(1)PDQNASTHTPQSSVK;TIDLGAAAHYTGDKAS(1)PDQNASTHTPQSSVK 333.35 5.65E-106 1963170000 1235380 1051440 1380270 1332750 1383440 930650 1680300 1160440 1676360 TRUE FALSE 1158059.771 1129289.712 1413010.656 1366950.621 1274790.203 1199313.547 1428354.614 1305323.488 1396564.686 0.829220288 0.808619696 1.011776017 0.978795064 0.912804266 0.858759755 1.022762947 0.934667403 1 20.41345097 4.083808988 3.892872128 0.957802434 0.819532387 0.581677679 0.049557276 0.157483995 4.292491851 0.01234132 0.028873248 12128.55294 -4.083808988 -0.138270047 TIDQIHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 113.5 0.0061158 2193510000 4877960 4599690 4790470 4719810 5057660 3859500 5894900 4562800 5988740 FALSE TRUE 4572657.191 4940255.834 4904102.211 4840928.315 4660451.785 4973674.996 5011014.471 5132475.624 4989180.605 0.916514665 0.990193826 0.982947421 0.970285243 0.934111662 0.996892153 1.004376243 1.028721153 1 22.25037146 2.016989068 23.71522707 1.008797592 0.966786284 0.508724139 0.023357366 123.6399504 172589.0048 0.008661467 0.006394805 103.989399 -2.016989068 -0.042011308 TIEAEAAHGTVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TIEAEAAHGTVTR 13 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 269.14 6.11E-25 1314790000 941760 1146470 1045730 1038210 1396630 958720 1010060 1071650 1368940 FALSE TRUE 882816.9227 1231355.832 1070535.209 1064852.226 1286944.314 1235486.9 858610.8799 1205447.861 1140455.07 0.774091804 1.079705693 0.938691262 0.933708178 1.128448062 1.083327991 0.752866906 1.056988471 1 20.12117818 TIEDAIAVLSVAEEAADRHPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TIEDAIAVLSVAEEAADRHPER 22 1 Q96CT7 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 ;;;; 220.63 6.01E-26 658783000 345309 391498 397930 387089 412573 329206 430623 344066 419651 FALSE TRUE 323696.7261 420484.9193 407369.0875 397022.3591 380171.1808 424242.428 366055.0789 387023.3975 349608.5371 0.925883357 1.202730697 1.165214931 1.135619749 1.087419615 1.213478457 1.047042735 1.107019299 1 18.41538089 0.925088228 1.014997573 1.002760434 1.133234641 0.124292996 0.083847487 1.012055774 2.153796816 0.072568173 0.023813317 8.415660909 -0.925088228 0.130474207 TIEDAIAVLSVAEEAADRHPERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TIEDAIAVLSVAEEAADRHPERR 23 2 Q96CT7 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 80.303 0.0067907 11938000 3528.8 5779.9 4308.3 3802.1 6891.8 2346.8 3865.9 4419.5 14210 FALSE TRUE 3307.938707 6207.84981 4410.494911 3899.668323 6350.545828 3024.283063 3286.244184 4971.284304 11838.2592 0.279427799 0.524388739 0.372562793 0.329412311 0.536442539 0.255466873 0.277595221 0.419933727 1 13.53116933 0.950555884 22.64035024 1.000000001 0.375874125 0.807358327 0.096302195 2030.160395 929607.3648 0.093303948 0.023325987 8.923924424 -0.950555884 -0.624125876 TIEELSNAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TIEELSNAR 9 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 ;;;; 73.573 0.043539 17496690000 4737210 19200710 12766140 14343060 14980760 14007290 10281630 12751450 6982040 FALSE TRUE 4440716.482 20622350.55 13068958.87 14711127.2 13804231.54 18050967.23 8739995.031 14343496.6 5816692.418 0.76344358 3.545374083 2.246802466 2.529122419 2.373209815 3.10330441 1.50257129 2.465919731 1 22.47176759 0.584222937 0.687064987 0.992047992 2.51523403 0.197223658 0.77990705 1.907883636 1.602472773 0.767523237 0.265663626 3.83904265 -0.584222937 1.523186038 TIEGQS(ph)PEPVFGDADVDVSAVQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TIEGQSPEPVFGDADVDVSAVQAK 24 0 Q9Y2I9;F8VZ81;Q9Y2I9-2 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 T(0.234)IEGQS(0.766)PEPVFGDADVDVSAVQAK;T(0.031)IEGQS(0.969)PEPVFGDADVDVSAVQAK 164.66 9.81E-12 87796000 96630 79277 87790 83307 90670 76558 110327 69056 90547 TRUE FALSE 90582.10079 85146.75157 89872.42026 85444.79866 83549.14395 98659.05178 93784.49058 77677.79361 75434.12074 1.200810719 1.128756466 1.191402768 1.132707557 1.10757762 1.307883632 1.243263521 1.029743475 1 16.20292962 1.164036812 6.668841775 1.007367665 1.186199364 0.600262992 0.058642074 0.167964839 11.74152826 0.059070369 0.014919813 14.58937918 -1.164036812 0.178831698 TIEKFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TIEKFEK 7 1 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5;P68104;A0A087WVQ9;Q5VTE0;A0A087WV01;A6PW80;Q5JR01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;; 117.04 0.0048531 16285820000 14345700 12983280 12871640 14247230 18277050 9350500 16812640 11747060 27752080 FALSE TRUE 13447828.24 13944575.56 13176961.38 14612838.04 16841644.22 12049837.56 14291740.71 13213706.3 23120078.56 0.581651494 0.603137032 0.569935839 0.63204102 0.728442344 0.521184975 0.618152775 0.571525147 1 24.46264296 -1.565597208 4.079510631 1.006719482 0.602363146 0.843042434 0.053798009 0.003079406 0.000327908 0.048787365 0.011353676 0.027189598 1.565597208 -0.404356336 TIFTGHTAVVEDVSWHLLHESLFGSVADDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TIFTGHTAVVEDVSWHLLHESLFGSVADDQK 31 0 Q09028-3;Q09028;Q09028-2;Q09028-4 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 ;; 188.22 4.97E-19 418120000 344865 343451 407430 371395 452850 321991 389821 344210 429299 FALSE TRUE 323280.5153 368880.4694 417094.432 380925.6245 417284.9877 414944.5746 331370.96 387185.3762 357646.2235 0.903911447 1.031411616 1.166220708 1.065090582 1.166753513 1.16020958 0.926532809 1.082593218 1 18.44817368 1.739231616 24.99999982 0.999723654 1.088674928 0.154000902 0.086553786 0.174281599 6305.078618 0.03915951 0.021715869 54.85694474 -1.739231616 0.088951274 TIGDMFQNQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TIGDMFQNQDR 11 0 Q96AY3;H0Y827;Q96AY3-2 Q96AY3 FKBP10 Peptidyl-prolyl cis-trans isomerase FKBP10 0 147.74 8.18E-05 79371000 38637 53665 40055 41714 48658 25925 42795 39444 42581 FALSE TRUE 36218.77914 57638.41244 41005.12352 42784.45186 44836.59696 33409.12664 36378.28704 44368.67023 35473.95602 1.020996337 1.624809266 1.155921925 1.206080648 1.263929992 0.94179309 1.025492816 1.250739281 1 15.11447261 3.009639103 1.039288385 1.059626047 1.355313387 0.182820852 0.177648817 0.601631682 1.399132658 0.077772388 0.097078022 1022.442993 -3.009639103 0.29568734 TIGGGDDS(ph)FNTFFSETGAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TIGGGDDSFNTFFSETGAGK 20 0 P68363;P68363-2;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;F8VWV9;F8VX09;F8VRK0;F8W0F6;F8VXZ7;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 1 TIGGGDDS(1)FNTFFSETGAGK;TIGGGDDS(0.994)FNT(0.006)FFSETGAGK;TIGGGDDS(0.998)FNT(0.002)FFSETGAGK;TIGGGDDS(1)FNTFFSETGAGK;TIGGGDDS(1)FNTFFSETGAGK 379.39 1.11E-112 2322337000 2330628 1701988 2028569 1945187 2093807 1647452.6 2767095 1934974.8 2948299 TRUE FALSE 2184758.154 1828004.962 2076687.615 1995103.792 1929367.844 2123045.421 2352194.793 2176560.663 2456208.85 0.88948387 0.744238407 0.845484949 0.812269605 0.78550643 0.864358673 0.957652601 0.886146413 1 21.22800181 1.943238262 3.466025918 0.941130455 0.809909551 0.624772858 0.04652594 0.145866449 3.276149623 0.020552151 0.011730699 87.74820923 -1.943238262 -0.131220903 TIGGGDDSFNTFFSETGAGK ddPTM_SK-BR-3_Pertuzumab_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 ;;; 389.57 1.56E-130 475634000 784120 685986 752620 744294 821720 587712 992230 773341 1067470 FALSE TRUE 735043.3289 736777.1172 770472.5018 763393.8441 757185.4259 757374.9137 843454.3229 869894.3262 889302.3609 0.826539275 0.82848888 0.866378563 0.858418776 0.851437553 0.851650628 0.948444938 0.978176112 1 19.76231449 1.621275571 2.224905461 0.990302256 0.846185652 0.955571997 0.01325935 0.055543046 0.602507099 0.010367606 0.003928406 41.80955747 -1.621275571 -0.144116604 TIGNNGDQSHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TIGNNGDQSHK 11 0 H0YJR8;H0YJ66;Q9Y394-2;Q9Y394 H0YJR8 DHRS7 Dehydrogenase/reductase SDR family member 7 0 83.573 0.016607 58244000 124740 100970 106080 116890 130780 84663 131410 117860 124930 FALSE TRUE 116932.7461 108445.9239 108596.2677 119889.5953 120509.0663 109103.8337 111706.2905 132575.0804 104078.3759 1.123506637 1.041964029 1.043408554 1.151916469 1.157868436 1.048285321 1.0732901 1.273800434 1 16.66731083 3.252186653 24.84867426 1.114954728 1.059953341 0.075229039 0.076355477 488.1517295 890196.3603 0.019783185 0.026638751 1787.255545 -3.252186653 -0.055001388 TIGTKPVAHIDQFTADMLGSAELAEEVNLNGSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TIGTKPVAHIDQFTADMLGSAELAEEVNLNGSGK 34 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ; 114.23 4.14E-06 266807000 164747 114241 133436 128242 153871 94374 156390 131864 173716 FALSE TRUE 154435.7794 122699.5225 136601.1649 131532.9068 141786.5923 121618.2418 132940.7714 148327.5107 144721.6774 1.067122647 0.847830987 0.943888762 0.908868037 0.979719106 0.840359537 0.91859612 1.024915641 1 17.14292151 1.24297739 24.72410451 1.012457843 0.919416724 0.208992723 0.064849569 110.9572654 621146.8173 0.041714524 0.014051355 17.4975559 -1.24297739 -0.09304112 TIHLSSIRPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TIHLSSIRPPR 11 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 172.92 7.68E-06 797360000 267180 823090 626270 660750 720280 633080 746460 715900 646020 FALSE TRUE 250457.6807 884032.44 641125.4201 677705.9636 663712.1143 815839.9188 634535.2528 805281.6909 538195.0886 0.465365972 1.642587342 1.191250968 1.259219896 1.233218453 1.51588139 1.179006026 1.496263545 1 19.0377697 4.751962246 24.87032242 1.327205465 0.465365367 0.663455018 0.189915407 1193.64666 2215090.473 0.040724148 0.796026922 56488.78653 -4.751962246 -0.861840098 TIHWIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TIHWIK 6 0 P78406;E9PQ57;E9PPG9;B0QZ36 P78406 RAE1 mRNA export factor 0 ; 105.42 0.032993 1149630000 3259900 3259600 3386600 3231400 3499100 2714300 3975900 2973300 3484300 FALSE TRUE 3055868.678 3500944.176 3466931.751 3314323.195 3224294.801 3497874.347 3379750.705 3344523.05 2902747.821 1.052750313 1.20607934 1.19436202 1.141788195 1.110773309 1.20502178 1.164328049 1.15219208 1 21.46898781 0.681970597 3.52021215 1.000001344 1.16337503 0.503220398 0.047129795 4.110599829 44.70545928 0.042625712 0.010985473 4.808067958 -0.681970597 0.163373687 TIISYIDEQFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TIISYIDEQFER 12 0 Q15019-2;Q15019-3;Q15019;B5MCX3;C9J2Q4;C9J938;C9JB25;C9IY94;H7C310;C9IZU3;C9JQJ4 Q15019-2 2-Sep Septin-2 0 ;;; 218.11 8.16E-11 169850000 189862 249842 251587 231132 251377 223776 252688 217812 231567 FALSE TRUE 177978.8763 268340.5616 257554.7624 237063.2384 231634.8644 288376.4985 214799.7802 245006.3077 192916.9717 0.922567231 1.390963995 1.335054973 1.228835578 1.200697183 1.494821819 1.113431225 1.27000909 1 17.55762054 0.466044245 0.989842521 1.000174244 1.273881127 0.174712122 0.157088091 2.833770859 3.825988437 0.139919642 0.043973903 2.924450297 -0.466044245 0.273706883 TILHYMGTSTFSEYTVVADISVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TILHYMGTSTFSEYTVVADISVAK 24 0 P11766;H0YAG8 P11766 ADH5 Alcohol dehydrogenase class-3 0 ; 176.67 9.50E-14 67410000 68765 63181 65588 69148 67252 56882 77321 55853 54525 FALSE TRUE 64461.1214 67858.98698 67143.77833 70922.45475 61970.2992 73302.91 65727.43386 62826.37 45424.42526 1.41908502 1.49388763 1.478142606 1.56132861 1.364250595 1.613733351 1.446962366 1.383096641 1 15.47118064 0.735836776 1.933109919 1.000318246 1.487641419 0.828840231 0.068662455 0.351129432 2.002018885 0.056682455 0.015750556 5.442980464 -0.735836776 0.487323172 TILTYAEEDLELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TILTYAEEDLELR 13 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 0 ; 170.52 6.20E-05 13655800 15637.8 17388.7 17024.1 18774.6 18979.5 14532.8 18325.8 15537.6 15321.5 FALSE TRUE 14659.05801 18676.17744 17427.91969 19256.38802 17488.92663 18728.18344 15578.01642 17477.50356 12764.24267 1.148447142 1.463163771 1.365370445 1.508619706 1.370149964 1.467238122 1.220441888 1.369255037 1 13.63982032 0.383033777 0.743486542 0.995425247 1.391845624 0.514480727 0.110508725 1.550851284 1.240942912 0.116871683 0.035130235 2.415648701 -0.383033777 0.396420377 TIPIDGDFFSYTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TIPIDGDFFSYTR 13 0 P05091;P05091-2;F8VP50 P05091 ALDH2 "Aldehyde dehydrogenase, mitochondrial" 0 90.108 0.016615 330910000 460210 430120 463380 400710 505820 378760 518990 393800 586510 FALSE TRUE 431406.2776 461966.5323 474371.5924 410992.897 466094.9376 488101.8633 441172.2676 442966.7969 488617.692 0.882911701 0.945456008 0.970844077 0.841133884 0.95390516 0.99894431 0.902898677 0.906571342 1 18.89834658 TIPLTDNTVIEEHLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TIPLTDNTVIEEHLGK 16 0 Q6DKI1 Q6DKI1 RPL7L1 60S ribosomal protein L7-like 1 0 61.821 0.070442 0 74341 165730 95790 98964 152790 94561 110450 129130 117350 FALSE TRUE 69688.12951 178000.8216 98062.18404 101503.5838 140790.4897 121859.2256 93889.04787 145252.1648 97763.52689 0.712823399 1.820728316 1.003054893 1.038256158 1.440112629 1.246469205 0.96036887 1.485750048 1 16.57700871 -4.999999951 0.158755754 0.153420265 1.296412268 0.010693445 0.318962943 463.8585951 4.251915396 124.0835885 1.290036664 1.00E-05 4.999999951 1.142992003 TIPWLEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TIPWLEDR 8 0 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ;; 171.38 0.00067396 293361000 530183 429948 481394 432121 351346 381394 512787 420149 351477 FALSE TRUE 496999.7924 461781.7973 492812.893 443209.9564 323752.7024 491496.2564 435899.3498 472605.5275 292813.2181 1.697327039 1.577052431 1.683028165 1.513626876 1.105662868 1.678531658 1.488660084 1.614017054 1 18.15962116 -2.978813628 0.245720544 1.06E-17 1.614298963 0.497192545 0.171557974 49.53435812 1.198350121 26.42578935 0.260187334 0.001049993 2.978813628 1.614298963 TIPWLEDRVPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TIPWLEDRVPQK 12 1 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ; 193.28 2.74E-06 1343860000 1445150 1235940 1249470 1131780 1167310 911310 1413040 1221020 1380280 FALSE TRUE 1354700.641 1327450.284 1279108.018 1160823.391 1075634.181 1174390.403 1201167.77 1373467.035 1149902.351 1.178100593 1.154402617 1.112362295 1.009497363 0.935413499 1.021295767 1.044582411 1.194420581 1 20.13307992 3.436150026 3.202990137 1.031844573 1.153703368 0.41468472 0.065382616 0.24234615 5.063355597 0.018693362 0.027632411 2729.920663 -3.436150026 0.121858795 TIQAPTQVPVVVS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TIQAPTQVPVVVSPR 15 0 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 TIQAPT(0.002)QVPVVVS(0.998)PR 95.666 0.0041931 63033000 63784 71750 58351 64748 70546 62018 69618 63519 88990 TRUE FALSE 59791.8733 77062.44466 59735.11328 66409.5433 65005.60173 79921.58982 59179.4272 71449.48697 74136.9941 0.806505228 1.039460064 0.805739618 0.895767951 0.876830825 1.078025766 0.798244222 0.963749446 1 16.177906 TIQEVLEEQS(ph)EDEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TIQEVLEEQSEDEDR 15 0 P18858;P18858-3;P18858-2;M0R0Q7 P18858 LIG1 DNA ligase 1;DNA ligase 1 TIQEVLEEQS(1)EDEDR;TIQEVLEEQS(1)EDEDR;TIQEVLEEQS(1)EDEDR;TIQEVLEEQS(1)EDEDR;TIQEVLEEQS(1)EDEDR;TIQEVLEEQS(1)EDEDR 396.06 8.61E-115 2585190000 2211880 1738660 2158400 1938650 1708120 2190350 2569740 1888820 1477120 TRUE FALSE 2073442.379 1867392.195 2209598.267 1988399.041 1573971.145 2822668.488 2184431.343 2124643.335 1230579.129 1.684932183 1.517490546 1.795575932 1.615823797 1.279049114 2.293772436 1.775124647 1.726539386 1 20.230906 TIQEVLEEQS(ph)EDEDREAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TIQEVLEEQSEDEDREAK 18 1 P18858;P18858-3;P18858-2;M0R0Q7 P18858 LIG1 DNA ligase 1;DNA ligase 1 TIQEVLEEQS(1)EDEDREAK;TIQEVLEEQS(1)EDEDREAK;TIQEVLEEQS(1)EDEDREAK;TIQEVLEEQS(1)EDEDREAK;TIQEVLEEQS(1)EDEDREAK;TIQEVLEEQS(1)EDEDREAK 337.79 2.11E-75 3056550000 3028830 1993485 2319310 2198150 2404469 1718704 2939910 2120767 3140210 TRUE FALSE 2839260.937 2141084.704 2374325.128 2254558.25 2215631.704 2214865.944 2499097.788 2385549.428 2616088.664 1.08530761 0.818429716 0.907585878 0.861804984 0.84692531 0.846632599 0.955280233 0.911876367 1 21.31898001 1.019112263 1.208877484 0.995473764 0.886994223 0.123805044 0.076032843 0.818796963 2.476025524 0.064637347 0.020208446 10.44990309 -1.019112263 -0.108479541 TIQEVLEEQS(ph)EDEDREAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TIQEVLEEQSEDEDREAKR 19 2 P18858;P18858-3;P18858-2;M0R0Q7 P18858 LIG1 DNA ligase 1;DNA ligase 1 TIQEVLEEQS(1)EDEDREAKR;TIQEVLEEQS(1)EDEDREAKR 205.02 2.25E-16 2097630000 986640 826700 839270 830300 1046970 607250 1051100 765510 1501460 TRUE FALSE 924887.9636 887909.7282 859177.8807 851606.9037 964745.1995 782553.2171 893497.3129 861085.6086 1250856.626 0.739403657 0.709841328 0.686871591 0.680818957 0.771267609 0.62561384 0.714308334 0.688396728 1 20.25448501 -1.795899015 2.484361153 1.093195432 0.70044397 0.857314919 0.038193094 9380126.349 6233375.702 5273914.027 0.008467591 0.0159993 1.795899015 -0.392751461 TIQFVDWCPTGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TIQFVDWCPTGFK 13 0 Q9BQE3;F5H5D3;A0A1W2PQM2 Q9BQE3 TUBA1C Tubulin alpha-1C chain 0 ; 213.73 8.25E-09 234310000 1184470 1085970 1181690 1083670 1291610 918550 1402630 1148470 1401260 FALSE TRUE 1110336.137 1166376.349 1209720.245 1111478.807 1190172.161 1183720.474 1192318.653 1291859.008 1167380.654 0.951134605 0.999139694 1.036268882 0.952113437 1.019523629 1.013996994 1.021362355 1.106630475 1 20.15484363 1.527883246 3.700663309 1.056088173 1.000076557 0.27828297 0.037231112 0.235038097 7.035108248 0.022306105 0.008885738 33.71966461 -1.527883246 -0.056011616 TIQGDEEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TIQGDEEDLR 10 0 P54920;M0R0Y2;M0R213 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;; 192.21 1.65E-06 1483150000 2162120 1954310 2040780 1949430 2143480 1719320 2275540 1727350 2214380 FALSE TRUE 2026796.769 2099009.146 2089188.265 1999455.674 1975139.727 2215659.773 1934343.902 1943013.45 1844785.673 1.098662462 1.137806509 1.13248292 1.083841719 1.070660813 1.201039127 1.048546685 1.053246173 1 20.81502178 1.580144109 8.461874792 1.0353288 1.121157716 0.543003918 0.037737714 0.085729497 12.77905739 0.018869831 0.008914821 38.03155732 -1.580144109 0.085828917 TIQQTLILANILEACEHMTSDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TIQQTLILANILEACEHMTSDQR 23 0 Q9NQT5 Q9NQT5 EXOSC3 Exosome complex component RRP40 0 144.22 1.53E-07 11269000 7998.3 8645.7 8950.2 10727 9663.6 9302.7 11811 9134 8176.6 FALSE TRUE 7497.70068 9285.836624 9162.502971 11002.27298 8904.659837 11988.23847 10040.0502 10274.40001 6811.872637 1.100681278 1.363184123 1.345078433 1.615161288 1.307226414 1.759903497 1.473904568 1.508307708 1 12.73383575 5.662856814 0.742978347 1.475062803 3.44E-08 0.178600626 0.203512988 12.81679787 1.939791454 0.063793299 21.69586873 460104.853 -5.662856814 -1.475062768 TIS(ph)AQDTLAYATALLNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TISAQDTLAYATALLNEK 18 0 Q9UPU5;A0A0U1RQI9 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 TIS(1)AQDTLAYATALLNEK;T(0.012)IS(0.988)AQDTLAYATALLNEK;T(0.023)IS(0.977)AQDTLAYATALLNEK;T(0.043)IS(0.957)AQDTLAYATALLNEK;T(0.061)IS(0.939)AQDTLAYATALLNEK 367.43 1.71E-107 1582983000 1028631 907446 980111 1100110 1238042 929475 1487756 1029914 1473560 TRUE FALSE 964250.8219 974634.246 1003359.696 1128340.685 1140811.175 1197799.344 1264680.799 1158501.03 1227613.316 0.785467874 0.793926095 0.817325523 0.919133631 0.929291952 0.975713873 1.030194755 0.943701909 1 20.22742477 3.012970873 1.065935757 0.996177212 0.785551957 0.913329379 0.025215378 0.117745193 0.286968801 0.010897635 0.013611741 1030.317016 -3.012970873 -0.210625256 TIS(ph)DGTISASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 TISDGTISASK 11 0 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 TIS(0.788)DGT(0.211)ISASK;TIS(0.998)DGT(0.002)ISASK;TIS(0.995)DGT(0.005)ISASK;TIS(0.999)DGT(0.001)ISASK;TIS(1)DGTISASK;TIS(1)DGTISASK;T(0.004)IS(0.992)DGT(0.004)ISASK;TIS(1)DGTISASK;T(0.004)IS(0.996)DGTISASK;TIS(1)DGTISASK 322.06 3.86E-46 30331330000 34622910 26906920 29294160 28511760 30317880 21659650 35498450 23866940 33860750 TRUE FALSE 32455923.87 28899136.35 29989031.31 29243420.03 27936836 27912439.34 30175786.97 26846780 28209172.08 1.15054507 1.024458863 1.063095054 1.036663535 0.990345832 0.989480984 1.069715442 0.951703932 1 24.74966099 7.999999999 1.007177238 1.018880469 133.1731488 0.559446071 0.03670263 1468.666672 1.905274738 0.010323263 448036.7702 99999999.82 -7.999999999 132.1542684 TIS(ph)DGTISASKQESGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TISDGTISASKQESGK 16 1 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 T(0.005)IS(0.991)DGT(0.004)ISASKQESGK 86.575 0.0040956 217420000 61942 96122 71083 92062 170800 37516 90755 68099 515770 TRUE FALSE 58065.16079 103238.9729 72769.12233 94424.46678 157386.057 48346.26018 77147.13028 76601.31005 429684.655 0.13513436 0.240266837 0.169354715 0.219752941 0.366282703 0.112515678 0.179543601 0.17827332 1 18.71291873 -1.597971296 2.983863763 1.050456505 0.200997368 0.92915843 0.069408577 28842583.27 30951170.09 11444886.36 0.015762315 0.025236476 1.597971296 -0.849459137 TIS(ph)EPDEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TISEPDEQR 9 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 TIS(1)EPDEQR;TIS(1)EPDEQR;T(0.001)IS(0.999)EPDEQR 211.68 4.99E-06 1727240000 2417300 2308820 2285230 2316020 2523510 2019620 2694580 2202760 2202810 TRUE FALSE 2266005.508 2479767.435 2339436.735 2375452.994 2325323.704 2602651.508 2290552.744 2477779.435 1835146.78 1.234781617 1.351263813 1.274795433 1.294421253 1.267105023 1.418225254 1.248157787 1.35018052 1 20.80746403 -1.263867384 4.079099693 0.999696262 1.305673013 0.749377631 0.055406131 0.000132183 2.39E-05 0.046333855 0.010910245 0.054466895 1.263867384 0.305976751 TIS(ph)EPDEQRSELPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TISEPDEQRSELPR 14 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 T(0.034)IS(0.966)EPDEQRSELPR 140.46 1.16E-05 0 88595 112880 96086 122320 159880 63360 107220 94240 222890 TRUE FALSE 83049.9971 121237.7527 98365.2053 125458.9383 147323.6697 81651.00344 91143.35638 106006.0714 185688.2191 0.447255068 0.65291031 0.52973315 0.675642962 0.793392658 0.439720968 0.490840813 0.570882052 1 17.50252276 -2.184738199 2.255716 2.109199699 0.575132866 0.598547512 0.109373172 3306406.764 734804.4354 18708824.64 0.027665501 0.006535244 2.184738199 -1.534066833 TIS(ph)NPEVVMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.002)IS(0.998)NPEVVMK;T(0.004)IS(0.996)NPEVVMK;T(0.004)IS(0.996)NPEVVMK;TIS(1)NPEVVMK 167.73 5.41E-06 1131590000 2607850 1926530 2137780 1809440 1891120 1456120 2167170 1501130 2673010 TRUE FALSE 2444629.324 2069172.286 2188489.151 1855873.294 1742599.064 1876478.206 1842222.978 1688549.385 2226867.363 1.097788474 0.92918524 0.98276583 0.833400913 0.782533838 0.842653782 0.827271084 0.758262218 1 21.0865842 3.23667134 7.053210852 0.829105354 0.984889971 0.493360406 0.076325821 0.101811525 27.41686538 0.01938269 0.024644725 1724.532329 -3.23667134 0.155784617 TIS(ph)QSSSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TISQSSSLK 9 0 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 TIS(0.999)QSSSLK;T(0.001)IS(0.995)QS(0.004)S(0.001)SLK;TIS(1)QSSSLK 173.72 5.79E-05 1094890000 919920 1089770 924750 1244460 2004180 745090 1706910 1133730 1847560 TRUE FALSE 862343.8493 1170457.705 946685.5067 1276394.95 1846779.787 960185.3875 1450974.692 1275278.686 1539190.3 0.56025811 0.760437293 0.615054231 0.829263899 1.199838504 0.623824999 0.942687003 0.828538671 1 20.55374018 3.094687916 5.44682325 0.904199625 0.667538212 0.400186135 0.151269669 0.213593417 9.931355268 0.040437007 0.048630628 1243.620625 -3.094687916 -0.236661413 TIS(ph)VSGSTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TISVSGSTAK 10 0 Q8TDJ6-3;Q8TDJ6 Q8TDJ6-3 DMXL2 DmX-like protein 2 1 T(0.001)IS(0.999)VS(0.001)GSTAK 103.91 0.003999 0 105220 130660 106760 115120 113790 65726 175160 116970 154440 TRUE FALSE 98634.46802 140334.2024 109292.3976 118074.1741 104853.3924 84700.02923 148896.3841 131573.962 128662.9663 0.766611177 1.090711697 0.849447209 0.917701321 0.814946176 0.658309315 1.157259065 1.02262497 1 16.97323733 1.671516715 12.16660519 1.066236824 0.878927926 0.39477684 0.118947208 0.135323562 24.41736943 0.056084461 0.030644211 46.93714989 -1.671516715 -0.187308897 TISAQDT(ph)LAYATALLNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TISAQDTLAYATALLNEK 18 0 Q9UPU5;A0A0U1RQI9 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 T(0.24)IS(0.181)AQDT(0.579)LAYATALLNEK 182.7 3.48E-14 0 211670 186950 183690 210510 240110 162710 282290 211540 277200 TRUE FALSE 198421.9525 200791.9725 188047.2135 215912.043 221252.7292 209681.7356 239963.2352 237951.2347 230933.5292 0.859216733 0.869479513 0.814291516 0.934953204 0.958079712 0.907974413 1.039100887 1.030388422 1 17.81711813 2.455521238 0.868521602 1.025330854 0.847131326 0.754979319 0.036905983 0.268589495 0.405490119 0.025726418 0.018173215 285.4442101 -2.455521238 -0.178199528 TISIDENMEPS(ph)PTGDFYPSPSS(ph)PAAGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TISIDENMEPSPTGDFYPSPSSPAAGSR 28 0 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A1B0GWJ4;Q5VW27;O00712-5;Q5VW26;A0A2R8Y7V8;Q5VW30;A0A1B0GWI9;Q5VW31;A0A1B0GVN4;A0A1B0GWB8;O00712-6 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 2 TISIDENMEPS(0.761)PT(0.239)GDFYPS(0.003)PS(0.076)S(0.903)PAAGS(0.018)R 96.241 0.0010923 60584000 50527 56383 52869 48247 55438 45612 60098 48553 51685 TRUE FALSE 47364.60526 60557.65599 54123.07765 49485.0997 51084.12311 58779.44395 51086.86282 54614.94893 43058.4396 1.100007471 1.40640619 1.256967929 1.149254366 1.186390486 1.365108548 1.186454114 1.268391271 1 15.39400842 -3.724209226 0.337308983 3.81E-10 1.263430904 0.371235952 0.09499061 147.9442464 2.86494931 103.9640011 0.074322833 0.000188708 3.724209226 1.263430904 TISIDENMEPSPT(ph)GDFYPSPS(ph)SPAAGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TISIDENMEPSPTGDFYPSPSSPAAGSR 28 0 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A1B0GWJ4;Q5VW27;O00712-5;Q5VW26;A0A2R8Y7V8;Q5VW30;A0A1B0GWI9;Q5VW31;A0A1B0GVN4;A0A1B0GWB8;O00712-6 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 2 TISIDENMEPS(0.391)PT(0.609)GDFYPS(0.011)PS(0.623)S(0.366)PAAGSR 189.55 2.46E-18 124520000 82152 67818 70381 73275 75528 57462 96766 69979 70545 TRUE FALSE 77010.25297 72839.31528 72050.47056 75155.36055 69596.33555 74050.34658 82256.83663 78716.03219 58770.58376 1.310353718 1.2393839 1.225961458 1.27879214 1.184203578 1.259989979 1.399625993 1.339378089 1 15.84280661 1.984475748 24.52526383 1.300505181 1.243129419 0 0.111161225 1672.839256 2642756.235 0.039606369 0.026444858 96.48854294 -1.984475748 -0.057375762 TISINS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TISINSPK 8 0 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 TIS(0.023)INS(0.977)PK;TISINS(1)PK;TISINS(1)PK;TIS(0.076)INS(0.924)PK;TIS(0.018)INS(0.982)PK 142.71 0.00064321 1608040000 5460410 3340270 4200850 3856020 4511790 3198070 5567230 4050640 5877380 TRUE FALSE 5118652.685 3587587.066 4300496.146 3954972.001 4157452.213 4121300.893 4732475.545 4556371.321 4896407.309 1.045389479 0.732697842 0.878296243 0.807729372 0.849082184 0.84169895 0.96651999 0.930553982 1 22.22329214 1.733503662 5.577996581 0.961390091 0.844185993 0.267799412 0.080274013 0.176620231 13.86954621 0.03691513 0.018992651 54.13818131 -1.733503662 -0.117204098 TITDVINIGIGGSDLGPLMVTEALKPYSSGGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TITDVINIGIGGSDLGPLMVTEALKPYSSGGPR 33 1 P06744;A0A2U3TZU2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;K7ENA0;A0A0J9YXM3 P06744 GPI Glucose-6-phosphate isomerase 0 118.74 1.34E-06 87061000 266100 278330 270520 298810 390030 251800 405510 323940 318490 FALSE TRUE 249445.276 298937.8428 276936.8621 306477.9705 359398.6171 324490.5724 344707.5401 364384.6221 265331.9615 0.940125248 1.126655986 1.043737289 1.1550737 1.354524404 1.222960742 1.299155737 1.373315978 1 18.01743895 3.001379664 4.153545183 1.268450359 1.058897873 0.420417208 0.111956081 0.17651309 7.213595158 0.030079667 0.034546116 1003.181844 -3.001379664 -0.209552486 TITEYAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TITEYAR 7 0 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 119.57 0.011058 174000000 106350 182760 119630 115440 194870 104670 123770 132710 185790 FALSE TRUE 99693.74334 196291.7406 122467.6801 118402.3858 179565.6963 134886.5298 105211.8375 149279.1356 154780.4488 0.644097779 1.268194673 0.791234817 0.764969909 1.160131643 0.871470079 0.679748885 0.964457313 1 17.23986372 2.01093529 24.99048498 0.828266287 0.9525311 0 0.202530152 571.8790415 1306913.003 0.07176378 0.052955793 102.5499115 -2.01093529 0.124264813 TITGFQTHTTPVLLAHGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TITGFQTHTTPVLLAHGER 19 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 200.1 3.83E-16 1281840000 782900 1054710 948130 889260 953500 814310 1076360 843840 1093840 FALSE TRUE 733899.6865 1132801.826 970620.0913 912079.9171 878615.9562 1049388.078 914969.8104 949195.2815 911271.0375 0.805358292 1.243100877 1.065127774 1.000887639 0.964165347 1.151565269 1.004058916 1.041616865 1 19.79752069 3.470748676 22.95660119 1.031439895 1.089171939 0 0.118310078 189.3258788 682024.0172 0.030283033 0.04141481 2956.301172 -3.470748676 0.057732044 TITLVKS(ph)PISVPGGSALISNLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TITLVKSPISVPGGSALISNLGK 23 1 P51610-2;P51610;A6NEM2;P51610-4 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 1 TITLVKS(0.992)PIS(0.007)VPGGSALISNLGK;TITLVKS(0.717)PIS(0.283)VPGGSALISNLGK 223.34 8.96E-33 613230000 1602740 1165640 1273730 1329630 1636540 934590 1720210 1224290 2612100 TRUE FALSE 1502427.364 1251945.198 1303943.477 1363750.557 1508012.75 1204390.961 1462280.48 1377145.301 2176123.635 0.690414524 0.575309775 0.599204685 0.626687995 0.692981192 0.553457047 0.671965718 0.632843318 1 21.05332909 -4.13010242 0.369088874 3.362828235 0.613400267 0.860165321 0.046746815 82.40304901 1.209204049 151.6981842 0.029960793 7.41E-05 4.13010242 -2.749427968 TITVALADGGRPDNTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TITVALADGGRPDNTGR 17 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 92.264 0.0030568 502230000 113360 112440 118430 96042 113470 77324 121500 100460 129040 FALSE TRUE 106265 120765.1746 121239.2155 98506.60032 104558.5239 99646.18355 103282.203 113002.6521 107502.3904 0.988489647 1.123371994 1.127781579 0.916320093 0.972615805 0.926920631 0.960743316 1.051164088 1 16.71400921 3.24333069 24.99995643 0.965824853 1.096043499 0.467066795 0.053550527 81.34059004 426302.7132 0.014331887 0.018795697 1751.179601 -3.24333069 0.130218645 TIVEELLADSEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TIVEELLADSEFR 13 0 Q5QJE6 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 0 ;;; 194.5 2.24E-06 22434900 58280.7 53270.8 65031 59106.9 61516.1 56028.7 63444 50110.6 55371.8 FALSE TRUE 54633.01502 57215.02546 66573.56603 60623.68312 56684.87365 72203.27614 53931.16119 56367.01872 46129.88886 1.184330081 1.240302695 1.44317638 1.3141953 1.228810107 1.565216781 1.16911535 1.221919673 1 15.4934142 0.980743419 1.529925088 1.006675866 1.324140473 0.409960626 0.11843745 0.394510861 1.887738318 0.104005193 0.030577187 9.56628729 -0.980743419 0.317464607 TIVEELLADSEFRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TIVEELLADSEFRR 14 1 Q5QJE6 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 0 ; 226.19 4.00E-12 70719000 84349 111798 108249 105636 111892 81765 117951 92058 134330 FALSE TRUE 79069.74666 120075.6402 110816.7174 108346.7986 103104.4537 105369.2282 100265.3426 103551.6439 111909.4552 0.706551082 1.072971359 0.990235519 0.968164829 0.921320307 0.941557869 0.895950591 0.925316308 1 16.77197241 2.744156925 21.72932918 0.928036028 0.966854954 0 0.097758655 310.3200334 1204903.915 0.028493887 0.029366776 554.826154 -2.744156925 0.038818927 TIVMGAS(ph)FR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TIVMGASFR 9 0 P37837;F2Z393 P37837 TALDO1 Transaldolase 1 TIVMGAS(1)FR;TIVMGAS(1)FR;TIVMGAS(1)FR;TIVMGAS(1)FR 129.16 0.00041663 381136000 385076 574234 381374 412469 540978 333611 474739 476011 776250 TRUE FALSE 360974.7805 616750.8828 390420.3714 423053.6528 498491.7701 429919.08 403556.2942 535442.0212 646688.8602 0.558189266 0.953705748 0.603722123 0.654184228 0.770837107 0.664800504 0.624034708 0.827974709 1 19.30271223 0.974539843 5.42371393 0.999867249 0.704327922 0.456622923 0.109901338 0.160573846 19.03183878 0.102585116 0.025868613 9.430611266 -0.974539843 -0.295539327 TIYENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TIYENR 6 0 I3L0A0;Q13404;Q13404-7;Q13404-2;Q13404-1;G3V2F7;Q13404-6 I3L0A0 TMEM189-UBE2V1;UBE2V1 Ubiquitin-conjugating enzyme E2 variant 1 0 ;;; 143.37 0.02654 3030980000 3943050 4193420 4357230 4522200 4421370 3745850 4924500 3889820 4026370 FALSE TRUE 3696261.539 4503905.18 4460585.553 4638247.308 4074133.435 4827216.086 4186116.942 4375472.59 3354342.836 1.101933142 1.342708662 1.329794172 1.38275887 1.214584685 1.439094429 1.247969318 1.304420211 1 21.67759872 -1.012283664 4.958330525 0.999996137 1.305089096 0.493821568 0.093536744 3.49E-06 6.96E-07 0.079189028 0.018664796 0.097211207 1.012283664 0.305092959 TIYFFGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TIYFFGDK 8 0 O15305;H3BRM0;H3BV55 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 83.005 0.043746 101840000 133200 161420 134050 130600 201430 97847 146480 155770 185990 FALSE TRUE 124863.2498 173371.7048 137229.7293 133951.4171 185610.5003 126093.8405 124516.6839 175218.2274 154947.0675 0.805844549 1.118909235 0.885655544 0.864497917 1.197896181 0.813786557 0.803607877 1.130826354 1 17.24141593 TKADVTPPPDGSTTHNLEVS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TKADVTPPPDGSTTHNLEVSPK 22 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 TKADVTPPPDGSTTHNLEVS(1)PK;TKADVTPPPDGSTTHNLEVS(1)PK 221.8 5.47E-26 923330000 684000 352560 531250 502090 533290 343580 682860 390110 584200 TRUE FALSE 641189.661 378663.9092 543851.5009 514974.4794 491407.5546 442765.9684 580471.4824 438816.0922 486693.2459 1.31744105 0.778034034 1.117442055 1.05810895 1.009686407 0.9097434 1.192684483 0.90162766 1 18.89265323 3.763422604 24.98336128 1.037769376 0.990767387 0 0.15630159 1717.419305 1181955.484 0.036323999 0.065482417 5799.928021 -3.763422604 -0.047001989 TKDGVVEITGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TKDGVVEITGK 11 1 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;; 168.61 1.63E-05 10791360000 16948950 11716530 12921270 12548870 15841460 8907860 16182680 13624380 22268760 FALSE TRUE 15888145.47 12584034.07 13227768.63 12870895.25 14597335.63 11479414.57 13756237.37 15325413.83 18551960.09 0.856413306 0.678312912 0.713011917 0.693775492 0.786835222 0.618770983 0.741497788 0.826080573 1 24.14506829 0.938915505 2.338939127 0.999042418 0.716603696 0.653027394 0.063598739 0.187815596 2.273379976 0.053893782 0.014659192 8.687913828 -0.938915505 -0.282438722 TKDIEDVFYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TKDIEDVFYK 10 1 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ; 113.65 0.0013317 2724090000 9980000 7432200 8371200 7935300 9639100 5493900 9530200 7274700 12241900 FALSE TRUE 9355369.615 7982487.821 8569768.817 8138933.232 8882083.968 7079899.744 8101234.984 8182962.309 10198647.8 0.917314706 0.782700606 0.840284808 0.798040425 0.870908001 0.694199847 0.794344029 0.802357574 1 23.28187455 -1.168089779 3.047306364 1.000559359 0.8073754 0.501020031 0.058600114 3999990.323 5550890.181 21739.90134 0.013136627 0.067906324 1.168089779 -0.193183959 TKDIVNGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKDIVNGLR 9 1 P47756-2;B1AK88;B1AK87;P47756 P47756-2 CAPZB F-actin-capping protein subunit beta 0 65.5 0.060541 353650000 556730 781680 545850 614440 829420 438400 618130 682550 852100 FALSE TRUE 521885.2631 839556.4005 558797.8198 630207.5706 764280.6989 564958.9632 525447.1449 767767.87 709879.0052 0.735174951 1.182675349 0.787173329 0.887767586 1.076635164 0.795852475 0.740192541 1.081547509 1 19.43721362 2.203351672 24.99777748 0.86437045 0.945709147 0 0.160480629 576.1087223 409024.4793 0.057034467 0.042124441 159.717194 -2.203351672 0.081338697 TKDQILLLIDIEQSYINTNHEDFIGFANAQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TKDQILLLIDIEQSYINTNHEDFIGFANAQQR 32 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 ;; 229.2 1.17E-36 267462000 174458 167958 165692 177918 197152 141788 180088 178628 198937 FALSE TRUE 163538.9852 180393.7851 169622.2925 182483.6771 181668.4772 182719.8939 153085.4763 200930.099 165733.1295 0.986760979 1.088459414 1.023466418 1.101069398 1.096150647 1.102494682 0.923686632 1.212371356 1 17.3385025 4.754065992 22.58423906 1.060311538 0.986760769 0.093616524 0.076231348 1943.247595 2830234.565 0.016660503 0.35662166 56763.08521 -4.754065992 -0.073550769 TKDQPDGSSLS(ph)PAQS(ph)PSQSQPPAASSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKDQPDGSSLSPAQSPSQSQPPAASSLR 28 1 A0A494BZV2;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 2 TKDQPDGS(0.001)S(0.002)LS(0.998)PAQS(0.986)PS(0.013)QS(0.001)QPPAASSLR 107.32 8.84E-10 0 100330 88358 89181 94771 88085 63623 104770 72132 83620 TRUE FALSE 94050.52439 94900.11826 91296.41543 97202.98431 81167.15942 81989.92727 89060.71114 81137.83898 69663.28179 1.350073123 1.362268843 1.310538537 1.395325942 1.165135453 1.176946092 1.278445529 1.164714565 1 16.08811082 0.149128632 0.156934459 0.786091027 1.472791166 0.767610011 0.058000734 5.89666957 0.35818214 1.033438891 0.412029254 1.409706272 -0.149128632 0.686700139 TKDQPDGSSLS(ph)PAQSPSQSQPPAASSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKDQPDGSSLSPAQSPSQSQPPAASSLR 28 1 A0A494BZV2;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 TKDQPDGSSLS(1)PAQSPSQSQPPAASSLR 194.9 3.33E-19 278760000 51291 31131 43377 37158 39829 31608 49430 34983 34862 TRUE FALSE 48080.78787 33435.97163 44405.92292 38111.53719 36700.991 40732.71649 42018.43039 39350.70456 29043.30698 1.655485992 1.151245333 1.528955465 1.312231324 1.263664328 1.402482042 1.446750895 1.354897518 1 14.82591811 0.946423928 20.96981341 0.999999999 1.381601238 0.43812502 0.138721045 2010.217312 786806.7319 0.119570509 0.029892627 8.839423232 -0.946423928 0.381601239 TKECS(ph)VEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TKECSVEK 8 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 T(0.001)KECS(0.999)VEK;TKECS(1)VEK;TKECS(1)VEK 89.663 0.0083246 2412510000 6897300 3048440 4215220 3984240 4510060 3166360 5634900 3679130 6081100 TRUE FALSE 6465610.305 3274149.669 4315207.009 4086482.344 4155858.08 4080436.73 4789999.057 4138477.479 5066125.125 1.276243706 0.646282827 0.851776635 0.806628783 0.820322826 0.805435442 0.945495608 0.816892078 1 22.27245128 -1.023631342 4.682437674 1.00000344 0.850007108 0.044879144 0.162668196 18915679.22 4135171.561 782.6654099 0.034002179 0.094704073 1.023631342 -0.149996332 TKECS(ph)VEKGTGDSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TKECSVEKGTGDSLR 15 2 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 T(0.001)KECS(0.997)VEKGT(0.002)GDSLR;T(0.003)KECS(0.997)VEKGTGDSLR 91.589 0.0029062 382890000 937470 743430 864200 864340 1172740 654410 1128130 804340 2197270 TRUE FALSE 878795.4261 798474.3307 884699.2321 886520.4277 1080637.731 843327.5435 958977.3795 904763.6196 1830531.442 0.480076663 0.436198097 0.48330185 0.48429675 0.590340983 0.460700933 0.523879218 0.494262813 1 20.80383112 -5 0.327610416 6.073560683 0.470590751 0.940386921 0.040077553 72.82846081 0.633626593 257.0098091 0.032542977 1.00E-05 5 -5.602969932 TKEELEAEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TKEELEAEKR 10 2 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ; 93.959 0.0047414 710900000 949680 666020 776420 780900 864510 561850 974090 694630 1094770 FALSE TRUE 890241.224 715332.8138 794837.0491 800939.2161 796614.8719 724046.9741 828034.2475 781356.0846 912045.8145 0.976092659 0.784316755 0.871488073 0.878178709 0.873437342 0.793871276 0.907886681 0.856707056 1 19.79874677 -0.102649947 0.817311377 1.003913213 0.858403727 0.357592749 0.054486909 7.087963394 4.301546064 0.136971789 0.016242737 0.789496217 0.102649947 -0.145509486 TKENILEEFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TKENILEEFSK 11 1 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ; 166.7 1.83E-05 1325190000 4242100 2857100 3566800 3310800 3860400 2556610 4324300 3001800 4877500 FALSE TRUE 3976594.533 3068642.657 3651406.18 3395760.733 3557219.756 3294661.804 3675911.36 3376581.338 4063413.74 0.978633924 0.755188335 0.89860556 0.835691601 0.875426423 0.810811307 0.904636248 0.83097158 1 21.95426084 -4.999996316 0.432068428 3.887677583 0.853939887 0.332993966 0.060711712 1115.250084 6.92485444 3067.181741 0.029976043 1.00E-05 4.999996316 -3.033737696 TKEPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TKEPSR 6 1 Q9NYU2-2;Q9NYU2;H7BZG0 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ; 65.252 0.095336 184990000 310110 385320 366760 374150 374990 251130 415490 342720 296010 FALSE TRUE 290700.7687 413849.4937 375459.7204 383751.3224 345539.798 323627.1542 353191.1317 385509.3464 246604.0187 1.178816023 1.678194443 1.522520689 1.556143831 1.401192892 1.312335281 1.432219692 1.563272766 1 17.91183678 2.62630583 4.746236465 1.367542429 1.522356666 0.101213416 0.189836994 0.449147512 15.8171408 0.057076909 0.053584006 422.9663622 -2.62630583 0.154814237 TKEPSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKEPSTR 7 1 Q641Q2;F8W7U3;A0A0A0MR88;A0A096LPC5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A 0 80.165 0.027954 34400000 54705 49855 51095 52396 57170 44753 61259 50170 67509 FALSE TRUE 51281.1117 53546.31607 52306.99753 53740.57007 52680.09881 57672.4646 52073.78165 56433.83494 56241.31178 0.911805043 0.952081564 0.930045831 0.955535502 0.936679767 1.025446647 0.92589913 1.003423163 1 15.77934262 2.96587693 0.199224554 1.011460319 0.893340795 0.39308358 0.029354592 6.665986598 0.561304893 0.081688497 0.226148682 924.4361702 -2.96587693 -0.118119524 TKEQILEEFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TKEQILEEFSK 11 1 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ; 186.13 3.80E-06 704510000 2866800 2060700 2488900 2539400 2730900 1742490 3179700 2341700 3504300 FALSE TRUE 2687372.105 2213276.372 2547937.883 2604565.303 2516426.13 2245518.576 2702933.504 2634066.4 2919409.691 0.920519005 0.758124623 0.872757904 0.892154777 0.861964026 0.769168706 0.925849329 0.902259935 1 21.47724525 1.091672726 1.27364645 0.99571666 0.842427748 0.42471243 0.054383536 0.379692991 1.25982044 0.048106941 0.014933657 12.35016402 -1.091672726 -0.153288912 TKEVYELLDS(ph)PGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TKEVYELLDSPGK 13 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 1 TKEVYELLDS(1)PGK;TKEVYELLDS(1)PGK 193.42 1.14E-06 1065320000 4549100 2081240 3256400 3070400 3023900 2413410 4488200 2596000 3900400 TRUE FALSE 4264379.951 2235337.175 3333643.346 3149191.662 2786415.092 3110122.289 3815236.076 2920116.315 3249398.042 1.31235998 0.687923469 1.025926434 0.969161556 0.857517317 0.957137983 1.174136264 0.898663776 1 21.63174105 1.97255024 23.90154838 1.049120676 0.936834687 0 0.16961678 1028.238727 895324.0399 0.063834184 0.041341742 93.8750627 -1.97255024 -0.112285989 TKEVYELLDS(ph)PGKVLLQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKEVYELLDSPGKVLLQSK 19 2 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 1 TKEVYELLDS(1)PGKVLLQSK 96.44 0.00066583 222510000 301670 194670 231340 248430 287510 152450 300420 232430 468060 TRUE FALSE 282789.0132 209083.5694 236827.494 254805.1344 264930.1244 196459.8402 255374.81 261449.3971 389937.7622 0.725215767 0.536197285 0.607346908 0.653450779 0.679416435 0.503823582 0.654911719 0.670490069 1 18.57288435 0.597367778 1.635031305 0.999852416 0.610664866 0.764997293 0.065035276 0.788484901 2.674612781 0.057318371 0.016343429 3.957015742 -0.597367778 -0.38918755 TKEVYELLDSPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TKEVYELLDSPGK 13 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 165.49 3.21E-05 1181380000 5816100 4431600 5016800 5170200 5986300 3672700 6740000 4706500 7489700 FALSE TRUE 5452080.683 4759720.275 5135800.865 5302876.085 5516160.146 4732948.869 5729399.571 5294116.885 6239620.685 0.873783994 0.762822055 0.823095044 0.849871547 0.884053763 0.758531505 0.918228825 0.848467744 1 22.5730269 -0.423525425 0.282003302 1.070614257 0.801846628 0.528103991 0.048599548 6.207297775 0.592968954 0.466723305 0.060852849 0.377115666 0.423525425 -0.268767629 TKEYVSNDAAQS(ph)DDEEKLQSQPTDTDGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TKEYVSNDAAQSDDEEKLQSQPTDTDGGR 29 2 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 TKEYVSNDAAQS(1)DDEEKLQSQPTDTDGGR;TKEYVSNDAAQS(1)DDEEKLQSQPTDTDGGR;TKEYVSNDAAQS(1)DDEEKLQSQPTDTDGGR;TKEYVSNDAAQS(1)DDEEKLQSQPTDTDGGR;TKEYVSNDAAQS(1)DDEEKLQSQPTDTDGGR 383.48 7.13E-155 3735620000 3309430 1657320 2090320 2156520 2517050 1527145 3036480 1857790 3759310 TRUE FALSE 3102298.684 1780029.697 2139903.378 2211859.954 2319371.046 1968006.97 2581188.013 2089739.171 3131856.875 0.990562088 0.568362402 0.68326985 0.706245541 0.740573768 0.628383432 0.824171767 0.667252449 1 21.57858685 -1.119650173 0.489559727 1.109796381 0.702948087 0.331838869 0.117691233 22.9766418 3.19693011 3.576940808 0.052584777 0.075918886 1.119650173 -0.406848294 TKFAS(ph)DDEHDEHDENGATGPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TKFASDDEHDEHDENGATGPVK 22 1 P05455 P05455 SSB Lupus La protein 1 T(0.161)KFAS(0.839)DDEHDEHDENGATGPVK;T(0.294)KFAS(0.706)DDEHDEHDENGATGPVK;T(0.154)KFAS(0.846)DDEHDEHDENGATGPVK 305.1 2.08E-56 4917300000 6749370 3905000 4840730 4746610 5008410 3189960 5986570 4003080 5840830 TRUE FALSE 6326938.98 4194130.263 4955554.402 4868416.049 4615069.682 4110849.667 5088939.405 4502873.35 4865957.74 1.300245361 0.861933146 1.018412955 1.000505206 0.948440149 0.844818202 1.045824826 0.925382749 1 22.21429236 4.748515465 24.89465781 0.957229164 1.300245559 0.734703369 0.065067329 668.0346413 1670557.137 0.014599105 0.198004147 56042.23728 -4.748515465 0.343016395 TKFAS(ph)DDEHDEHDENGATGPVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TKFASDDEHDEHDENGATGPVKR 23 2 P05455 P05455 SSB Lupus La protein 1 T(0.25)KFAS(0.75)DDEHDEHDENGATGPVKR;T(0.016)KFAS(0.984)DDEHDEHDENGATGPVKR;T(0.014)KFAS(0.986)DDEHDEHDENGATGPVKR 204.86 7.84E-25 7368770000 1683820 1496990 1464340 1730620 2278500 820650 1856690 1285710 4313910 TRUE FALSE 1578432.712 1607828.697 1499074.836 1775030.639 2099555.801 1057558.333 1578296.571 1446233.724 3593890.552 0.439198882 0.447378314 0.417117554 0.493902253 0.584201375 0.294265593 0.439161001 0.402414515 1 21.77711504 -1.324790557 3.275795211 1.00343749 0.437883626 0.855954082 0.072231041 21859964.03 30488397.34 732582.6211 0.016462441 0.04733795 1.324790557 -0.565553863 TKFEECR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TKFEECR 7 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JGV6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;;;;; 107.57 0.0067915 4323300000 5031520 5197840 4177500 4194500 5919510 3067660 5273580 5082440 6437870 FALSE TRUE 4716606.145 5582693.482 4276592.273 4302137.971 5454615.563 3953243.643 4482855.637 5716993.822 5363347.907 0.879414542 1.040897137 0.797373646 0.802136659 1.017016919 0.737085065 0.835831595 1.06593753 1 22.35470241 1.23703384 24.99929907 1.032968819 0.875706483 0.327510438 0.095334908 49.63116179 812522.6399 0.075973361 0.022880946 17.25972372 -1.23703384 -0.157262336 TKFENLCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TKFENLCK 8 1 P07900;P07900-2;Q58FG0 P07900 HSP90AA1;HSP90AA5P Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5 0 ; 96.342 0.0082163 3234500000 2747400 3816000 1941600 2040120 4555300 1319480 2666500 3821900 4036900 FALSE TRUE 2575445.138 4098540.611 1987655.669 2092472.933 4197545.113 1700392.456 2266683.08 4299072.628 3363115.311 0.765791506 1.218673828 0.591016211 0.622182929 1.24811216 0.505600403 0.673983159 1.278300692 1 21.68136681 1.238810098 24.99999356 1.139150373 0.810775657 0.227301899 0.25692608 10.03481905 1006501.556 0.193902641 0.060644757 17.33046033 -1.238810098 -0.328374716 TKGDFILVGDLMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKGDFILVGDLMR 13 1 Q16531;F5GY55;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 129.93 0.00013495 99344000 230110 299060 214160 210200 361280 147760 239470 269580 383110 FALSE TRUE 215707.8259 321202.7136 219239.9763 215594.0879 332906.5261 190415.9133 203563.6966 303237.6564 319166.466 0.675847399 1.006379892 0.686914196 0.675491039 1.043049824 0.596603759 0.637797884 0.950092471 1 18.28394955 3.946618217 22.78681713 0.768262435 0.86246358 0 0.176232751 390.3779378 291625.3281 0.042114853 0.075943993 8843.378582 -3.946618217 0.094201145 TKGGQQVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TKGGQQVDR 9 1 Q8TE77;Q8TE77-3;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ; 96.89 0.0064407 119201000 158792 143390 139375 157692 167511 106478 171758 146953 196534 FALSE TRUE 148853.4922 154006.7448 142681.0408 161738.6437 154355.3618 137216.4701 146004.4824 165300.4055 163731.2057 0.909133305 0.940607162 0.871434619 0.987830285 0.942736365 0.838059364 0.891732775 1.009583999 1 17.32096979 1.233772751 24.99290766 1.004792064 0.90956193 0.471047627 0.040988599 110.7688628 578184.8123 0.035062094 0.009879119 17.13060698 -1.233772751 -0.095230134 TKGTSSFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TKGTSSFGK 9 1 P61927;D6RG19;D6R9X9 P61927 RPL37 60S ribosomal protein L37;Ribosomal protein L37 0 ; 103.91 0.0030515 823040000 530360 638970 546640 643320 874490 505230 884360 672390 1384670 FALSE TRUE 497165.7143 686280.0036 559606.5589 659828.6803 805811.0829 651081.6993 751758.428 756339.3716 1153559.632 0.430983974 0.594923734 0.485112814 0.57199356 0.698543067 0.56441096 0.651685797 0.655656934 1 20.13766115 -5 0.149205441 2.543045483 0.442510688 0.856341597 0.058198155 45.1526277 0.401404225 20.51705466 0.276847796 1.00E-05 5 -2.100534795 TKIDWNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TKIDWNK 7 1 P47755;P52907 P47755;P52907 CAPZA2;CAPZA1 F-actin-capping protein subunit alpha-2;F-actin-capping protein subunit alpha-1 0 ; 73.665 0.04403 2211900000 6749000 7076100 5295600 5067600 9673500 3276400 6407300 7295600 10392700 FALSE TRUE 6326592.137 7600021.807 5421214.133 5197643.195 8913782.331 4222243.492 5446584.847 8206471.72 8658091.231 0.730714423 0.877794147 0.626144261 0.600322064 1.02953204 0.487664472 0.62907455 0.947838444 1 23.04561757 1.152493398 6.136836402 0.99002374 0.711674327 0.342711296 0.151458624 0.241596629 13.2313209 0.138162228 0.034916234 14.20670615 -1.152493398 -0.278349413 TKKDDSHS(ph)AEDS(ph)EDEKEDHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKKDDSHSAEDSEDEKEDHK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 TKKDDS(0.163)HS(0.837)AEDS(1)EDEKEDHK 82.639 0.001744 146410000 163140 23293 44348 67849 91857 31583 66346 32617 85352 TRUE FALSE 152929.3586 25017.63796 45399.9555 69590.12021 84642.92175 40700.49939 56398.03323 36689.30425 71106.19981 2.150717645 0.351834833 0.638480971 0.978678658 1.190373301 0.572390305 0.793152121 0.515978977 1 16.11768773 4.748049522 24.79209475 0.728008759 2.150718496 0.750524388 0.252440366 592.4259917 1547822.277 0.06161451 0.790471837 55982.14332 -4.748049522 1.422709737 TKMIMVEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TKMIMVEER 9 1 Q5JYW6;H0Y5P0;H0YE38;B1AJZ9-4;B1AJZ9;B1AJZ9-3 Q5JYW6 FHAD1 Forkhead-associated domain-containing protein 1 0 ;;; 84.213 0.021041 1268696000 226086 958380 642125 699402 858133 666004 541295 713197 593195 FALSE TRUE 211935.6808 1029339.452 657356.5082 717349.8394 790738.6957 858268.5431 460132.8399 802241.2154 494186.9223 0.428857324 2.082894965 1.330177871 1.451575926 1.600080172 1.736728562 0.931090685 1.623355818 1 18.91469731 -1.092689399 4.423207377 0.999960276 1.43827717 0.064589947 0.453758199 0.000171987 3.53E-05 0.397216133 0.093615676 0.080781256 1.092689399 0.438316894 TKNETDEDGWTTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TKNETDEDGWTTVR 14 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 97.417 0.0034038 469010000 532669 502003 534497 554997 567520 377311 611365 483313 621480 FALSE TRUE 499330.1981 539171.8245 547175.5212 569239.1626 522949.2685 486234.5606 519696.4939 543655.692 517750.9731 0.964421554 1.041372885 1.056831469 1.099445858 1.010040146 0.939128241 1.003757638 1.050033163 1 18.98189883 2.490629886 24.9624836 0.994180233 1.04451572 0.181728272 0.041991823 888.9389664 1642665.181 0.013525923 0.012243795 309.4780741 -2.490629886 0.050335487 TKPFPWGDGNHTLFHNPHVNPLPTGYEDE ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKPFPWGDGNHTLFHNPHVNPLPTGYEDE 29 1 P12074 P12074 COX6A1 "Cytochrome c oxidase subunit 6A1, mitochondrial" 0 208.37 9.36E-26 281660000 342280 300990 243480 218780 424140 245960 277420 340470 507250 FALSE TRUE 320857.3058 323275.6128 249255.4606 224394.2652 390829.7553 316964.6592 235823.4464 382978.429 422586.698 0.759269772 0.764992401 0.589832718 0.531001724 0.924851059 0.750058297 0.558047491 0.906271851 1 18.68888783 1.064746483 5.929644072 0.998727367 0.691855386 0.464965275 0.116456551 0.151461096 9.20609056 0.109620445 0.027588348 11.60770822 -1.064746483 -0.306871981 TKPFQHHTHDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKPFQHHTHDVR 12 1 A0A0J9YWM9;H3BSH7;Q969X6;A0A0J9YXV4;A0A0J9YWK2;Q969X6-2;Q969X6-3 A0A0J9YWM9 CIRH1A Cirhin 0 159.08 4.63E-05 179330000 221010 273990 240570 243250 301110 163320 300620 265480 335670 FALSE TRUE 207177.3786 294276.5047 246276.434 249492.2068 277462.0352 210467.8327 255544.8218 298625.7624 279644.5085 0.740859814 1.05232356 0.880676811 0.892176314 0.992195544 0.752626375 0.913820276 1.067876369 1 18.09323447 1.273148299 9.535591287 1.033820781 0.901667696 0.27768977 0.095414631 0.402229221 107.0688194 0.060800693 0.021872599 18.75634874 -1.273148299 -0.132153085 TKPHLFYIPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKPHLFYIPGR 11 1 Q9H307 Q9H307 PNN Pinin 0 100.56 0.0023666 175430000 202920 438990 171840 169890 538150 125820 229430 383820 554570 FALSE TRUE 190219.5994 471493.2764 175916.1259 174249.665 495885.8698 162142.1915 195029.1014 431740.7719 462008.6843 0.411722995 1.020529034 0.380763678 0.377156688 1.073325863 0.350950528 0.422132977 0.934486269 1 18.81756044 1.137468904 6.632341434 0.990540201 0.592023108 0.274279533 0.263851692 0.299956815 16.32643917 0.242541738 0.060992225 13.72362695 -1.137468904 -0.398517093 TKPIVKPQTS(ph)PEYGQGINPISR ddPTM_SK-BR-3_Pertuzumab_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(0.201)S(0.799)PEYGQGINPISR 206 7.72E-23 295800000 375510 278370 336160 347090 327480 232730 442510 287840 487800 TRUE FALSE 352007.4994 298980.8044 344133.8739 355996.917 301761.0418 299915.3729 376159.7336 323777.4576 406383.0287 0.866196358 0.735711837 0.846821471 0.876013248 0.742553258 0.73801156 0.92562855 0.796729772 1 18.63248063 0.159557738 0.595152737 1.009375462 0.803826378 0.435792647 0.065046387 2.965919892 1.376218786 0.129517802 0.025972206 1.443968562 -0.159557738 -0.205549084 TKPIWTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TKPIWTR 7 1 P08238;P07900;P07900-2;Q58FG0;Q14568;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AA1;HSP90AA5P;HSP90AA2P;HSP90AB2P Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5;Heat shock protein HSP 90-alpha A2;Putative heat shock protein HSP 90-beta 2 0 ;; 78.334 0.032482 22398959400 662585 668587 638824 676790 710749 465896 704449 655106 671584 FALSE TRUE 621114.9876 718089.8771 653977.207 694157.5772 654929.6406 600392.612 598823.4122 736897.4262 559492.2918 1.110140384 1.283466971 1.16887617 1.24069194 1.170578487 1.073102562 1.070297877 1.317082357 1 19.09375873 2.449589192 6.169874832 1.114232882 1.209045528 0.160909743 0.091754802 0.269379959 32.628154 0.029121129 0.024668602 281.5718227 -2.449589192 0.094812646 TKPPRPDS(ph)PATTPNISVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKPPRPDSPATTPNISVK 18 2 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 TKPPRPDS(1)PATTPNISVK 161.04 3.08E-11 357000000 594000 382490 478720 424340 493360 354510 612230 425160 640260 TRUE FALSE 556822.6003 410809.9576 490075.4645 435229.2828 454613.4957 456851.282 520431.7952 478242.1619 533396.4698 1.043918796 0.770177496 0.91878273 0.815958311 0.852299409 0.856494761 0.975694112 0.896597914 1 19.02484875 1.752077974 10.99098547 0.951361872 0.865687866 0.191133224 0.076309401 0.180959463 109.5900612 0.032032705 0.017511528 56.50384143 -1.752077974 -0.085674006 TKPSDEEMLFIYGHYK ddPTM_SK-BR-3_Pertuzumab_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 ; 197.49 2.59E-11 3246200000 7146200 4874300 5234400 4681700 5277500 3299240 6770600 5108600 7975700 FALSE TRUE 6698932.098 5235198.244 5358562.44 4801840.348 4863026.438 4251677.029 5755411.385 5746419.955 6644504.145 1.008191424 0.787899011 0.806465362 0.722678509 0.731887035 0.639878753 0.866191255 0.864838042 1 22.66373011 1.011107862 1.82565441 0.995475149 0.783554283 0.323235772 0.096014412 0.3994999 2.765062367 0.08641974 0.024626331 10.2590669 -1.011107862 -0.211920866 TKPTQAAGPSS(ph)PQKPPT(ph)PEETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TKPTQAAGPSSPQKPPTPEETK 22 2 F5H8D7;P18887 F5H8D7 XRCC1 DNA repair protein XRCC1 2 TKPTQAAGPS(0.067)S(0.938)PQKPPT(0.844)PEET(0.151)K;T(0.003)KPT(0.003)QAAGPS(0.168)S(0.825)PQKPPT(0.956)PEET(0.043)K 67.353 0.039457 1335820000 1967650 550870 918720 860450 821270 582950 1267260 683060 1131920 TRUE FALSE 1844498.299 591656.988 940512.4723 882530.6037 756770.767 751238.2016 1077246.128 768341.5446 942995.2395 1.955999587 0.627423091 0.997367148 0.935880232 0.80251812 0.796651107 1.142366454 0.81478836 1 19.84689096 4.747463338 24.99316215 0.893741832 1.956000133 0.848449307 0.141628092 439.3136168 1233285.938 0.033634724 0.40798416 55906.63305 -4.747463338 1.062258301 TKPTQAAGPSS(ph)PQKPPTPEETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TKPTQAAGPSSPQKPPTPEETK 22 2 F5H8D7;P18887 F5H8D7 XRCC1 DNA repair protein XRCC1 1 TKPTQAAGPS(0.014)S(0.976)PQKPPT(0.011)PEETK;TKPTQAAGPS(0.041)S(0.956)PQKPPT(0.003)PEETK;T(0.001)KPT(0.003)QAAGPS(0.015)S(0.977)PQKPPT(0.004)PEETK 205.26 5.58E-23 1300350000 3099840 1182540 1868710 1797990 1948200 1315600 2579130 1581590 2549100 TRUE FALSE 2905826.548 1270096.492 1913036.684 1844129.467 1795196.231 1695392.363 2192413.4 1779054.993 2123638.742 1.368324325 0.598075589 0.900829621 0.86838191 0.845339744 0.798343112 1.032385291 0.837738998 1 21.01810694 1.744174716 24.99999999 0.955814966 0.859550384 0 0.19852442 3.704773827 16558.493 0.083751761 0.046444576 55.48488826 -1.744174716 -0.096264582 TKPVTGNLRPEEALQALTIYEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKPVTGNLRPEEALQALTIYEGK 23 2 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 90.35 0.0031199 184910000 243640 205300 242660 226630 275060 172240 310100 228720 328910 FALSE TRUE 228391.0073 220500.6256 248416.0098 232445.7095 253457.8971 221962.8919 263603.3838 257276.1955 274012.7962 0.833504897 0.804709228 0.906585434 0.848302389 0.924985624 0.810045717 0.962011218 0.938920368 1 18.06388374 2.174346361 0.138777428 1.077884836 0.71855892 0.604678783 0.041777354 4.891129819 0.466090537 0.438835626 0.634036372 149.3985428 -2.174346361 -0.359325916 TKQDFIDLIEVIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKQDFIDLIEVIYR 14 1 Q9NX01 Q9NX01 TXNL4B Thioredoxin-like protein 4B 0 80.632 0.011066 0 66444 78660 81657 82711 102190 68321 91545 74219 86459 FALSE TRUE 62285.38865 84484.06825 83593.9426 84833.50429 94164.40961 88044.1636 77818.67711 83485.40553 72028.43435 0.86473334 1.172926623 1.160568647 1.177777985 1.307322732 1.222352872 1.080388291 1.159061783 1 16.13627893 0.396459404 1.217602384 1.000176207 1.154656268 0.125382521 0.114766452 5.733956897 9.674201151 0.104244546 0.031246935 2.491491468 -0.396459404 0.154480062 TKS(ph)DES(ph)GEEKNGDEDCQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TKSDESGEEKNGDEDCQR 18 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 2 T(0.168)KS(0.835)DES(0.997)GEEKNGDEDCQR;T(0.436)KS(0.564)DES(1)GEEKNGDEDCQR;T(0.446)KS(0.554)DES(1)GEEKNGDEDCQR 101.33 0.0016717 832700000 2866210 742865 1196550 1163436 1190666 826136 1871530 754881 1442970 TRUE FALSE 2686819.032 797867.4976 1224932.731 1193291.737 1097155.895 1064628.052 1590911.451 849129.5545 1202128.985 2.235050536 0.663712054 1.018969467 0.992648669 0.912677349 0.885618819 1.323411606 0.70635478 1 20.19716027 4.746591132 24.9449703 0.954023351 2.235051183 0.834461178 0.181438888 391.8639004 1217207.444 0.043289922 0.479479883 55794.46691 -4.746591132 1.281027833 TKS(ph)PTDDEVTPSAVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TKSPTDDEVTPSAVVR 16 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 T(0.246)KS(0.707)PT(0.047)DDEVTPSAVVR;T(0.014)KS(0.694)PT(0.292)DDEVTPSAVVR;T(0.349)KS(0.649)PT(0.002)DDEVTPSAVVR;T(0.195)KS(0.804)PT(0.001)DDEVTPSAVVR 204.5 1.52E-11 2334180000 1011650 712680 784190 827230 908840 565302 1026000 748080 859890 TRUE FALSE 948332.6323 765447.5687 802791.3571 848458.1223 837463.3725 728495.5105 872160.8249 841479.4347 716368.8039 1.323805039 1.068510472 1.12063975 1.184387312 1.169039422 1.016928022 1.217474603 1.17464556 1 19.45034299 -1.551241407 2.734182565 0.991269105 1.147673514 0.255788909 0.083345599 11629483.69 11748749.61 747081.7025 0.018359758 0.028103382 1.551241407 0.156404409 TKSPPASSAASADQHSQS(ph)GSSSDNTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKSPPASSAASADQHSQSGSSSDNTER 27 1 Q8IY57;Q8IY57-5;Q8IY57-3 Q8IY57 YAF2 YY1-associated factor 2 1 TKSPPASSAASADQHS(0.014)QS(0.259)GS(0.224)S(0.224)S(0.224)DNT(0.055)ER 46.149 0.080921 37107000 18776 20840 20456 20287 23581 19719 26825 22641 31472 TRUE FALSE 17600.84368 22383.01528 20941.22598 20807.59877 21729.04338 25411.55519 22802.84028 25467.77869 26219.11988 0.671298036 0.853690566 0.798700569 0.793604013 0.828748008 0.969199397 0.869702735 0.971343768 1 14.67833164 2.292840582 0.326890306 1.017339215 0.729302062 0.692953066 0.055034217 1.019346497 0.272555784 0.070641587 0.104999917 196.2639713 -2.292840582 -0.288037153 TKSVS(ph)SMSEFESLLDCSPYLAGGDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKSVSSMSEFESLLDCSPYLAGGDAR 26 1 O94964-2;H0YDM2;O94964;O94964-3;X6R3R3;O94964-4 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 T(0.175)KS(0.175)VS(0.216)S(0.216)MS(0.216)EFES(0.002)LLDCSPYLAGGDAR 91.873 0.0058731 101780000 44939 41014 38913 41608 48814 35886 56237 38805 56776 TRUE FALSE 42126.34821 44050.71924 39836.03474 42675.73172 44980.34535 46245.70564 47804.78393 43649.88967 47299.71881 0.890625764 0.931310383 0.842204473 0.902240707 0.950964329 0.977716291 1.010677973 0.922836134 1 15.52954399 2.61886299 2.578875252 0.981452661 0.889087104 0.63466451 0.031099303 0.172958701 2.251841684 0.010945052 0.010132459 415.7794209 -2.61886299 -0.092365557 TKVEAFQTTISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKVEAFQTTISK 12 1 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 156.6 6.69E-05 278270000 942750 753770 794360 866840 993000 563860 1018600 796940 1027400 FALSE TRUE 883744.9604 809579.9151 813202.5943 889084.582 915013.7856 726637.2285 865870.3862 896439.7133 855920.3027 1.032508468 0.945858992 0.950091488 1.038746924 1.069040871 0.848954308 1.011625012 1.047340168 1 19.70711694 1.493734058 24.99999498 1.025612758 0.975120773 0.077148271 0.062085432 1.793790247 2693.312823 0.03196613 0.01479856 31.16980307 -1.493734058 -0.050491985 TKVFPGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TKVFPGER 8 1 Q7L0J3-2;Q7L0J3 Q7L0J3-2 SV2A Synaptic vesicle glycoprotein 2A 0 58.676 0.094339 645960000 336610 390270 400870 436590 456170 341350 489470 384400 473670 FALSE TRUE 315542.181 419165.9969 410378.8257 447793.6385 420344.2483 439892.2036 416078.5175 432393.1862 394611.417 0.799627602 1.062224707 1.039956798 1.134771117 1.06521056 1.114747787 1.054400607 1.095744237 1 18.59007317 4.740399171 5.050059453 1.072955748 0.78622109 0.835340626 0.037869894 0.058865003 4.799026344 0.008165162 0.059019169 55004.6203 -4.740399171 -0.286734658 TKYWELIYEDSMDLIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TKYWELIYEDSMDLIAK 17 1 O75390;B4DJV2;A0A0C4DGI3;F8VPA1;F8VRI6;F8VR34 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ; 195.77 1.51E-11 508090000 781780 629350 667640 656150 1056670 593170 696570 707110 1402110 FALSE TRUE 732849.7853 675947.7288 683476.7361 672987.9199 973683.4006 764408.5497 592125.7951 795394.24 1168088.783 0.627392195 0.578678384 0.585123961 0.576144493 0.833569686 0.654409631 0.506918484 0.680936459 1 20.1557185 TLAGDVHIVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TLAGDVHIVR 10 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ;;; 150.15 2.21E-05 1442270000 2476600 2865040 2634520 2616220 3205360 2213970 2759280 2698560 3239100 FALSE TRUE 2321594.027 3077170.543 2697012.059 2683356.634 2953623.955 2853107.198 2345551.58 3035481.156 2698473.285 0.860336117 1.140337598 0.999458499 0.994398073 1.094553714 1.057304223 0.869214305 1.124888348 1 21.36371197 TLALLAFDSPEESPFGDLLHTMQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLALLAFDSPEESPFGDLLHTMQR 24 0 Q9NWU2 Q9NWU2 GID8 Glucose-induced degradation protein 8 homolog 0 140.73 2.90E-07 75547000 92730 99800 95915 98528 110390 99851 94359 82564 95980 FALSE TRUE 86926.19483 107189.2958 98190.14909 101056.3953 101720.4147 128676.3628 80210.74394 92872.29715 79960.31795 1.087116673 1.340531136 1.227985976 1.263831834 1.272136196 1.609252765 1.003131878 1.161479838 1 16.28699659 1.615001082 25 1.061723431 1.294886618 0.417770371 0.136316373 0.560047346 1955.882262 0.059137999 0.031925371 41.20985462 -1.615001082 0.233163186 TLAPTWEELSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLAPTWEELSKK 12 1 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 141.32 9.69E-05 395210000 838170 746270 803320 905400 951020 560860 1085200 784190 1379800 FALSE TRUE 785710.4359 801524.6073 822375.1298 928634.0968 876330.7254 722771.1772 922484.3345 882097.8477 1149502.466 0.683522184 0.697279589 0.715418326 0.80785742 0.762356542 0.628768705 0.802507486 0.767373602 1 20.13257813 -5 0.211799122 2.320940505 0.692634122 0.739302663 0.051250804 73.3992485 0.73261809 41.10655022 0.102834968 1.00E-05 5 -1.628306383 TLAQLNPESSLFIIASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLAQLNPESSLFIIASK 17 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90 P06744 GPI Glucose-6-phosphate isomerase 0 171.15 3.19E-13 0 63976 64252 71989 62448 76645 49683 69851 67094 66915 FALSE TRUE 59971.85636 69009.28493 73696.61308 64050.5214 70625.61087 64025.67556 59377.49101 75470.83359 55746.45421 1.075796788 1.237913441 1.321996423 1.148961352 1.266907678 1.148515658 1.065134848 1.353823031 1 15.76659242 2.145212697 7.112733689 1.137357147 1.226353849 0.076223041 0.110839216 0.454389577 29.63519885 0.038833988 0.028643536 139.7052405 -2.145212697 0.088996703 TLAYIITELDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TLAYIITELDER 12 0 G3V2V6;H0YJH8;G3V2S6;Q9Y5K8 G3V2V6 ATP6V1D V-type proton ATPase subunit D 0 ;; 175.86 6.18E-05 36851000 183856 179183 169434 170601 206089 169234 184990 167722 217761 FALSE TRUE 172348.7812 192449.8958 173453.0545 174978.9105 189903.6013 218089.1085 157252.4669 188662.4609 181415.2823 0.950023498 1.060825159 0.95611049 0.964521336 1.046789437 1.202154007 0.866809372 1.039948005 1 17.46893647 TLAYLLPAIVHINHQPYLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLAYLLPAIVHINHQPYLER 20 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ; 124.94 1.50E-05 793610000 287170 408970 330270 287290 436560 230878 304300 346150 350830 FALSE TRUE 269196.5423 439250.5643 338104.1604 294662.3478 402274.3386 297528.7306 258673.04 389367.5895 292274.2066 0.921041051 1.502871463 1.156804647 1.008170893 1.376359356 1.017978063 0.885035471 1.332199629 1 18.15696299 2.695093046 0.901555471 1.042925511 1.252170649 0.00589326 0.207336351 1.178025023 2.021004474 0.122018191 0.109142526 495.5563505 -2.695093046 0.209245139 TLCGCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLCGCR 6 0 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 106.84 0.073922 155750000 108590 152720 87048 100580 180130 81083 111430 153590 158400 FALSE TRUE 101793.5457 164027.5477 89112.81967 103161.0531 165983.3164 104490.3458 94722.10597 172766.0496 131962.0167 0.771385193 1.242990611 0.675291435 0.781748079 1.257811305 0.791821377 0.71779826 1.309210437 1 17.00976321 1.234897384 24.99999757 1.154605163 0.899230432 0.203955966 0.215846282 161.9318357 1105032.956 0.174691461 0.050263627 17.17502524 -1.234897384 -0.255374731 TLDELGIHLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLDELGIHLTK 11 0 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 138.63 5.36E-05 191650000 791810 873730 864280 828950 946640 606250 1074200 852820 999750 FALSE TRUE 742252.0255 938421.8783 884781.1297 850222.2604 872294.713 781264.5334 913133.6824 959296.4543 832885.2664 0.891181601 1.126712065 1.062308538 1.020815585 1.047316777 0.938021796 1.096349905 1.151775032 1 19.66775825 1.600353294 25 1.093058347 1.033165148 0.118558967 0.075486126 1.404223148 4658.130075 0.037595936 0.017934763 39.84311583 -1.600353294 -0.059893199 TLDFDPLLSPAS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TLDFDPLLSPASPK 14 0 Q53H80 Q53H80 AKIRIN2 Akirin-2 1 TLDFDPLLSPAS(1)PK;TLDFDPLLSPAS(1)PK;TLDFDPLLSPAS(1)PK;TLDFDPLLSPAS(1)PK 216 6.60E-12 163490000 628623 400659 479858 448942 480699 340585 585787 406462 547612 TRUE FALSE 589278.6086 430324.2092 491240.4584 460462.6118 442946.8396 438906.3606 497953.6775 457209.6754 456212.0195 1.291677079 0.94325487 1.076781052 1.009317142 0.970923213 0.962066631 1.091496182 1.002186825 1 18.79934493 4.747443146 24.93573777 1.012853276 1.291677227 0.784227828 0.046838149 527.6114787 1481119.713 0.01100498 0.132174247 55904.03377 -4.747443146 0.27882395 TLDFDPLLSPAS(ph)PKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLDFDPLLSPASPKR 15 1 Q53H80 Q53H80 AKIRIN2 Akirin-2 1 TLDFDPLLS(0.003)PAS(0.997)PKR 127.32 4.83E-05 47307000 106090 92920 89640 90472 101910 69432 109750 85556 129820 TRUE FALSE 99450.01628 99799.89348 91766.30313 92793.66469 93906.39969 89475.89127 93294.00637 96237.85493 108152.2033 0.919537589 0.922772633 0.84849222 0.85799144 0.868280042 0.827314548 0.862617714 0.889837211 1 16.72270353 -1.89277312 7.161193358 1.02167308 0.873003121 0.636519285 0.029757524 0.011236388 0.000168246 0.03144162 0.007134981 0.012800498 1.89277312 -0.148669959 TLDGFKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLDGFKK 7 1 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ; 100.19 0.015998 8391700000 6251000 6510700 6344700 7482400 7602800 5054900 9855600 6402300 8615500 FALSE TRUE 5859761.068 6992759.002 6495199.28 7674411.052 7005706.756 6514167.571 8377844.275 7201641.248 7177517.392 0.816404998 0.974258733 0.904936753 1.069229182 0.976062665 0.90757949 1.16723427 1.003361031 1 22.77505349 7.029334927 0.317461381 1.048895866 1.23E-12 0.35430554 0.076539236 31.69024856 0.796653715 0.070525992 17.14773086 10698796.49 -7.029334927 -1.048895866 TLDGIFSEQVAMGYSHSLVIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLDGIFSEQVAMGYSHSLVIAR 22 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 227.38 4.50E-26 81511000 56504 72226 62038 70084 87308 65376 72318 58081 61434 FALSE TRUE 52967.5155 77573.68819 63509.57066 71882.47409 80451.18186 84248.98991 61474.58727 65332.5407 51180.26852 1.034920625 1.515695217 1.24089952 1.404495837 1.571917932 1.646122468 1.201138428 1.276518131 1 15.6433001 0.994835804 1.578001922 1.010687135 1.395808864 0.306388715 0.180166248 0.475118796 2.423847872 0.160104658 0.046823985 9.881794178 -0.994835804 0.385121729 TLDS(ph)DEERPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLDSDEERPR 10 1 Q9BW71;Q9BW71-2 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 T(0.003)LDS(0.997)DEERPR;TLDS(1)DEERPR 134.18 0.00010745 344000000 559230 443030 594580 538700 548570 388290 701280 530280 849800 TRUE FALSE 524228.7926 475832.4022 608683.7184 552523.954 505487.525 500383.0196 596129.5744 596486.6253 707962.8901 0.74047496 0.672114893 0.859767831 0.780441972 0.714002855 0.706792724 0.84203506 0.842539395 1 19.43331421 0.96520373 1.187051479 0.997146972 0.751793107 0.68244125 0.054220013 0.323571641 0.935532816 0.052401253 0.016388724 9.230043115 -0.96520373 -0.245353865 TLDS(ph)DEERPRPAPPDWSHMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 TLDSDEERPRPAPPDWSHMR 20 2 Q9BW71;Q9BW71-2 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 TLDS(1)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;T(0.002)LDS(0.998)DEERPRPAPPDWSHMR;T(0.011)LDS(0.989)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;T(0.038)LDS(0.962)DEERPRPAPPDWSHMR;T(0.003)LDS(0.997)DEERPRPAPPDWSHMR;T(0.013)LDS(0.987)DEERPRPAPPDWSHMR;T(0.011)LDS(0.989)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;T(0.007)LDS(0.993)DEERPRPAPPDWSHMR;T(0.025)LDS(0.975)DEERPRPAPPDWSHMR;T(0.001)LDS(0.999)DEERPRPAPPDWSHMR 250.06 7.58E-31 15607020000 4906628 4981552 4866906 4891593 5528768 4107435 5655119 4782211 7329510 TRUE FALSE 4599530.912 5350391.293 4982351.309 5017119.558 5094560.863 5293184.806 4807186.406 5379280.57 6106167.431 0.753259874 0.876227413 0.815953929 0.821647886 0.834330359 0.866858773 0.787267375 0.880958577 1 22.54183572 0.941649446 5.95970082 0.999987688 0.827714632 0.717055374 0.035423037 0.210261479 20.25022772 0.030514895 0.007674883 8.742777911 -0.941649446 -0.172273055 TLDSGTSEIVKS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TLDSGTSEIVKSPR 14 1 Q9H501 Q9H501 ESF1 ESF1 homolog 1 TLDSGTSEIVKS(1)PR;TLDSGTSEIVKS(1)PR;TLDSGTSEIVKS(1)PR;TLDSGTSEIVKS(1)PR;TLDSGTSEIVKS(0.999)PR 258.8 1.30E-24 4366770000 6021780 4673970 5383230 5238810 5832140 3997720 6244650 4469870 5864250 TRUE FALSE 5644887.539 5020035.602 5510922.758 5373246.734 5374107.25 5151796.866 5308322.705 5027943.109 4885468.79 1.155444397 1.027544299 1.128023327 1.099842608 1.100018746 1.054514334 1.086553396 1.029162876 1 22.22006557 1.104627376 1.060650467 0.998634459 1.093688603 0.480875741 0.034847446 0.44344584 1.058906046 0.030219677 0.009965169 12.72410887 -1.104627376 0.095054144 TLEAEFNSPSPPT(ph)PEPGEGPR ddPTM_SK-BR-3_Pertuzumab_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(0.005)PS(0.034)PPT(0.961)PEPGEGPR 172.3 6.46E-11 66032000 45242 48736 45118 51736 57876 41770 55141 41651 50498 TRUE FALSE 42410.38398 52344.46415 46188.22027 53063.63335 53330.65242 53828.32092 46873.11895 46851.21904 42069.55757 1.008101497 1.244236145 1.09790126 1.26133091 1.267677996 1.279507654 1.11418141 1.113660845 1 15.36048903 1.064280333 1.702749081 1.005539517 1.191194934 0.323290638 0.08658175 0.40079711 2.333389465 0.076902868 0.022304201 11.59525578 -1.064280333 0.185655417 TLEDEEEQERER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLEDEEEQERER 12 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 0 ; 221.56 2.45E-11 1276250000 739710 826230 834840 812860 1044220 671030 901450 888570 1087780 FALSE TRUE 693412.8715 887404.9289 854642.799 833719.3638 962211.1734 864745.4677 766285.9412 999509.9205 906222.4907 0.765168464 0.979235164 0.94308275 0.919994121 1.061782491 0.954230861 0.845582568 1.102940978 1 19.78950577 4.741513094 24.5102155 0.962804259 0.76516837 0.447017441 0.072360643 204.8634244 1700574.374 0.016240856 0.113500378 55145.88282 -4.741513094 -0.197635889 TLEDPDLNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLEDPDLNVR 10 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 103.7 0.0064666 137540000 131060 142630 138150 145510 155580 113640 158420 128430 154610 FALSE TRUE 122857.1885 153190.4736 141426.9832 149244.0329 143361.3744 146446.0232 134666.3917 144464.7682 128804.5922 0.953826152 1.189324627 1.097996437 1.158685653 1.113014466 1.136962749 1.045509243 1.121580883 1 16.9748245 0.43733865 0.672375077 0.998680035 1.116261083 0.166951395 0.065955202 2.80639796 2.004417155 0.072706453 0.022557067 2.737402441 -0.43733865 0.117581048 TLEEDEEELFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TLEEDEEELFK 11 0 P43487;F6WQW2;P43487-2;C9JJ34;C9JDM3 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;; 234.2 4.00E-15 539680000 1772310 1222120 1416660 1337910 1396900 1061290 1718610 1215750 1775850 FALSE TRUE 1661384.281 1312607.036 1450263.844 1372243.036 1287193.109 1367667.194 1460920.385 1367539.064 1479449.163 1.122974904 0.887226861 0.980272848 0.927536458 0.870048895 0.924443522 0.987475895 0.924356915 1 20.49662869 -1.648863101 6.873886652 1.000200551 0.948012455 0.037983024 0.070330573 0.000193286 9.87E-06 0.060891547 0.01429726 0.022445894 1.648863101 -0.052188095 TLEGELHDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 TLEGELHDLR 10 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;;; 242.49 2.30E-12 26347850000 12880642 15263251 13551907 13231486 14599100 10937399 14810727 13263700 16595003 FALSE TRUE 12074465.61 16393357.99 13873364.63 13571028.33 13452545.58 14094848.54 12589995.98 14919702.14 13825189.79 0.873367078 1.185760068 1.00348457 0.98161606 0.973045996 1.019504886 0.910656286 1.07916798 1 23.72079595 3.581089153 5.351228126 0.985589275 1.064147425 0 0.086339915 0.390816943 16.66607088 0.021083766 0.032990786 3811.440576 -3.581089153 0.07855815 TLEKEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLEKEPR 7 1 Q9BRX8-2;Q9BRX8 Q9BRX8-2 FAM213A Redox-regulatory protein FAM213A 0 81.297 0.025157 188820000 443040 393680 392360 330560 551070 321760 436220 423700 922920 FALSE TRUE 415310.9172 422828.4768 401666.9645 339042.7292 507791.1851 414646.8887 370812.8607 476599.8777 768878.6897 0.540151422 0.549928724 0.522406161 0.440957376 0.660430822 0.539287789 0.482277459 0.619863555 1 19.55239647 0.865428098 4.759862572 0.999983541 0.533567236 0.872794751 0.055606877 0.360129682 12.40473202 0.049969802 0.012656189 7.335472572 -0.865428098 -0.466416304 TLEPVKPPTVPNDYMT(ph)SPAR ddPTM_SK-BR-3_Pertuzumab_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 TLEPVKPPTVPNDYMT(0.885)S(0.115)PAR;TLEPVKPPTVPNDYMT(0.865)S(0.135)PAR 153.27 8.87E-08 511670000 599550 511170 616880 565990 587710 459620 649690 493510 759720 TRUE FALSE 562025.2357 549017.5587 631512.6849 580514.2616 541553.6273 592304.8327 552275.0159 555125.8098 632917.824 0.887990849 0.867438928 0.997779903 0.917203213 0.855646036 0.935832126 0.872585658 0.877089867 1 19.27165867 2.980861983 24.79601233 0.899076133 0.923280543 0 0.052198071 2421.103619 3136883.949 0.01506791 0.016234142 956.8899278 -2.980861983 0.02420441 TLEPVKPPTVPNDYMTS(ph)PAR ddPTM_SK-BR-3_Pertuzumab_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 TLEPVKPPTVPNDYMT(0.041)S(0.959)PAR;TLEPVKPPTVPNDY(0.036)MT(0.185)S(0.78)PAR;TLEPVKPPTVPNDY(0.001)MT(0.239)S(0.761)PAR 157.9 9.36E-10 692210000 726640 603760 719490 714670 773400 562330 830990 632000 994170 TRUE FALSE 681160.8995 648463.0186 736556.6426 733009.6421 712660.2837 724665.5423 706390.764 710906.5912 828236.6044 0.82242308 0.782944167 0.889307039 0.885024446 0.860454947 0.87494991 0.852885227 0.858337566 1 19.65968344 -5 0.151898411 1.517342402 0.807653401 0.733862555 0.028714935 75.87600353 0.680767726 11.91384434 0.149343516 1.00E-05 5 -0.709689002 TLEPVRPPVVPNDYVPS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLEPVRPPVVPNDYVPSPTR 20 1 H7C3Q7;B7Z836;E7EW77;E7EP65;A0A0C4DG21;F8WAL6;Q9NYB9-3;Q9NYB9-2;Q9NYB9-4;Q9NYB9;H0Y6B5 H7C3Q7 ABI2 Abl interactor 2 1 TLEPVRPPVVPNDYVPS(0.991)PT(0.009)R;TLEPVRPPVVPNDYVPS(0.961)PT(0.039)R 144.48 9.45E-08 249970000 188135 171848 198081 200862 218008 148591 208626 167356 276490 TRUE FALSE 176359.9662 184571.8047 202779.5749 206016.459 200886.5311 191486.8095 177344.4681 188250.765 230342.0328 0.765643873 0.801294503 0.880341171 0.894393683 0.872122767 0.831315098 0.76991796 0.817266231 1 17.81341817 4.384558675 2.404119772 0.851754523 0.767687953 0.226429235 0.060912903 0.560568568 5.895201144 0.015263276 0.07066503 24241.45456 -4.384558675 -0.084066569 TLEQHDNIVTHYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLEQHDNIVTHYK 13 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ; 190.27 2.63E-06 439000000 765400 790570 808660 826140 818100 605790 978240 744120 897060 FALSE TRUE 717494.9803 849104.6254 827841.7971 847340.1511 753849.7261 780671.7388 831561.9935 837025.02 747334.8908 0.960071568 1.136176881 1.107725341 1.133815859 1.008717424 1.044607643 1.112703292 1.120013304 1 19.51139535 2.769952901 24.97379684 1.067044105 1.096948635 0.015176321 0.062396872 2243.837077 1785055.069 0.018255759 0.019360613 588.7797995 -2.769952901 0.02990453 TLESTWEKPQELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLESTWEKPQELK 13 1 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 140.08 3.57E-05 179620000 432090 316950 361580 340760 394150 254770 474800 307810 476710 FALSE TRUE 405046.2582 340417.3078 370156.8484 349504.4785 363195.0489 328317.9632 403608.1478 346240.7561 397144.0213 1.01989766 0.85716337 0.932046886 0.880044668 0.914517227 0.826697484 1.01627653 0.871826686 1 18.59930276 0.281564388 0.656457519 1.001668788 0.908580528 0.127647854 0.06397894 4.715136808 2.832978223 0.086494913 0.022055571 1.912336826 -0.281564388 -0.09308826 TLETVPLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TLETVPLER 9 0 P22626;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;; 136.27 0.0004595 822560000 941760 1035570 1068290 1017350 1116770 923220 1135990 949800 1194460 FALSE TRUE 882816.9227 1112244.68 1093630.343 1043456.923 1029063.389 1189738.627 965658.8455 1068384.621 995096.9095 0.887166782 1.117724987 1.099018933 1.048598296 1.034133841 1.195600766 0.970416887 1.073648818 1 19.92447751 1.633868739 25 1.016504866 1.073067124 0.06641222 0.081662141 1.8284548 1752.040473 0.034585491 0.019170405 43.03965075 -1.633868739 0.056562258 TLFATEDALEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLFATEDALEVR 12 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 96.113 0.0040214 0 33490 97476 87257 91600 93064 188080 67944 71465 50639 FALSE TRUE 31393.92068 104693.2245 89326.77725 93950.61108 85755.12884 242375.6428 57756.42796 80387.56256 42187.02376 0.744160595 2.481645187 2.117399363 2.227002588 2.032737112 5.745265278 1.36905671 1.905504475 1 15.36451169 4.739258288 24.154361 2.448576513 0.744159737 0.132651485 1.28060794 69.99282173 2422439.052 0.281239804 1.68256591 54860.31392 -4.739258288 -1.704416775 TLFDILDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TLFDILDDR 9 0 Q86UD0 Q86UD0 SAPCD2 Suppressor APC domain-containing protein 2 0 ;; 97.431 0.015578 34165100 101205 128082 121198 117954 136799 117282 137678 113661 100016 FALSE TRUE 94870.75971 137565.3245 124072.8738 120980.8993 126055.3584 151139.4095 117034.462 127851.826 83322.68347 1.138594627 1.650994889 1.489064786 1.45195635 1.512857641 1.813904728 1.404593049 1.534418009 1 16.34642168 -0.165934349 1.564753376 0.999304304 1.517628883 0.45017601 0.172424252 48.96141112 63.25861289 0.34324776 0.04235162 0.682441849 0.165934349 0.518324579 TLGECGFTSQTARPQAPATVGLAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLGECGFTSQTARPQAPATVGLAFR 25 1 B8ZZU8;Q15370;Q15370-2;I3L0M9 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 ; 244.71 8.02E-39 680760000 47041 52861 55295 50608 61862 38233 60314 52321 58706 FALSE TRUE 44096.78778 56774.88344 56606.62351 51906.68696 57003.60806 49270.24644 51270.47563 58853.39202 48907.58934 0.901634866 1.160860394 1.15742003 1.061321722 1.165537063 1.00741515 1.048313285 1.203359086 1 15.57777074 2.237398141 24.99995778 1.064410966 1.107112958 0 0.094348096 111.2719939 2392941.673 0.032241969 0.025134025 172.7420784 -2.237398141 0.042701992 TLGEDDPWLDDTAAWIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TLGEDDPWLDDTAAWIER 18 0 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 ;;;; 212.95 3.15E-16 133500000 225321 252951 241219 245185 251060 217155 272415 218035 249191 FALSE TRUE 211218.5608 271679.7552 246940.8286 251476.8622 231342.7603 279844.1233 231568.8997 245257.1497 207599.4123 1.017433328 1.308673046 1.189506396 1.21135633 1.114370979 1.348000557 1.115460286 1.181396166 1 17.66344283 0.565464722 1.114371396 1.000375552 1.204264093 0.264201488 0.095333932 1.753784432 3.174110853 0.080724336 0.025017265 3.676755258 -0.565464722 0.203888541 TLGT(ph)PTQPGSTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TLGTPTQPGSTPR 13 0 Q8NFH5-2;Q8NFH5;Q8NFH5-3 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 TLGT(0.995)PT(0.005)QPGSTPR;TLGT(0.999)PTQPGSTPR;TLGT(0.975)PT(0.025)QPGSTPR;T(0.001)LGT(0.997)PT(0.002)QPGSTPR 186.62 8.55E-05 911430000 958474 977954 994603 990551 1024587 855206 1117976 899193 1094453 TRUE FALSE 898484.8233 1050362.732 1018195.453 1015970.216 944120.07 1102090.089 950345.8776 1011459.225 911781.7239 0.985416575 1.151989236 1.116709653 1.114269116 1.035467202 1.208721408 1.042295379 1.109321671 1 19.79832897 0.217493708 0.925730565 0.999251999 1.104581282 0.17019454 0.063451919 5.594245213 5.337505367 0.065574011 0.017677975 1.650037096 -0.217493708 0.105329283 TLGTMIAGDTSGDYRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TLGTMIAGDTSGDYRR 16 1 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;; 253.79 2.33E-26 947230000 570393 731522 681747 558387 677785 255010 846748 647700 1170844 FALSE TRUE 534693.1203 785684.65 697918.3608 572716.1558 624554.5002 328627.2473 719785.9982 728566.7708 975422.5725 0.548165621 0.805481309 0.715503599 0.587146712 0.640291211 0.336907569 0.737922228 0.746924247 1 19.89566783 0.891794527 2.071872524 0.997639716 0.639898063 0.471863348 0.126461907 0.447383666 3.925080729 0.123233406 0.034073716 7.794612454 -0.891794527 -0.357741653 TLHCEGTEINS(ph)DDEQESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TLHCEGTEINSDDEQESK 18 0 Q9BPX3;H0Y9Z8 Q9BPX3 NCAPG Condensin complex subunit 3 1 TLHCEGTEINS(1)DDEQESK;TLHCEGTEINS(1)DDEQESK;TLHCEGTEINS(1)DDEQESK;TLHCEGTEINS(1)DDEQESK 357.1 7.35E-91 4519130000 3143190 1662120 2293500 2212270 2020440 1809700 3026960 1944950 1926700 TRUE FALSE 2946463.349 1785185.094 2347902.903 2269040.594 1861762.792 2332131.012 2573095.449 2187781.289 1605121.323 1.83566395 1.112180786 1.462757282 1.4136256 1.159889141 1.452931301 1.603053559 1.363000577 1 20.61425092 -2.160808846 2.163770743 0.090238099 1.408185188 0.295942235 0.204676677 2559141.651 551390.8758 11419086.16 0.048033626 0.006905437 2.160808846 1.317947088 TLHCEGTEINS(ph)DDEQESKEVEETATAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TLHCEGTEINSDDEQESKEVEETATAK 27 1 Q9BPX3;H0Y9Z8 Q9BPX3 NCAPG Condensin complex subunit 3 1 TLHCEGTEINS(1)DDEQESKEVEETATAK;TLHCEGT(0.002)EINS(0.998)DDEQESKEVEETATAK;T(0.004)LHCEGT(0.014)EINS(0.957)DDEQES(0.025)KEVEETATAK 274.22 4.69E-61 1968100000 1138400 703391 802500 858605 1040200 532506 1226970 703517 1516240 TRUE FALSE 1067149.576 755470.8015 821535.679 880638.2579 958506.888 686231.8377 1042997.239 791352.6461 1263169.749 0.84481882 0.598075439 0.650376309 0.697165412 0.758810832 0.543261773 0.825698399 0.626481632 1 20.2686171 -3.559436821 0.369151229 2.217208483 0.676474156 0.486407492 0.097449025 126.7276371 2.754276072 119.361939 0.061838395 0.00027578 3.559436821 -1.540734326 TLHEWCDGCEAVLLGIEQQVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLHEWCDGCEAVLLGIEQQVLR 22 0 J3QT73;A0A087X1P5;J3KQ34;Q9H9Q2-2;Q9H9Q2;J3QT95;J3KQ41;Q9H9Q2-3 J3QT73 COPS7B COP9 signalosome complex subunit 7b 0 149.36 6.40E-08 23406000 24688 28953 28569 29177 29755 27313 36385 23012 35488 FALSE TRUE 23142.82215 31096.71025 29246.67017 29925.73122 27418.16233 35197.81971 30929.40703 25885.09886 29564.82354 0.782782353 1.051814505 0.989238787 1.012207334 0.927391374 1.19053035 1.046155645 0.875537066 1 14.85159405 4.743238873 24.76554853 1.020316293 0.782782243 0.426885865 0.082780179 396.6054195 2099449.959 0.01866073 0.151495726 55365.45497 -4.743238873 -0.23753405 TLHEWLQQHGIPGLQGVDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLHEWLQQHGIPGLQGVDTR 20 0 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 181.85 2.86E-17 211980000 80936 117600 116190 114860 128590 97225 125600 113450 149970 FALSE TRUE 75870.36023 126307.2264 118946.0817 117807.5021 118491.0601 125292.2792 106767.446 127614.4822 124939.0382 0.607259039 1.010950846 0.952032955 0.942919874 0.948391006 1.002827307 0.854556331 1.021413996 1 16.9308648 4.743736088 24.91735408 0.959094713 0.607258886 0.84165381 0.048890898 199.0026184 958068.2399 0.011173305 0.094783858 55428.87809 -4.743736088 -0.351835828 TLHGQETYTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TLHGQETYTPR 11 0 Q9BUK6-2;Q9BUK6;A0A3B3IUD2;Q9BUK6-7;Q9BUK6-3;Q9BUK6-4 Q9BUK6-2 MSTO1 Protein misato homolog 1 0 ;; 164.81 2.23E-05 571920000 274084 338650 307195 312225 365760 245579 328273 298987 323506 FALSE TRUE 256929.5717 363723.9984 314481.8105 320237.2221 337034.685 316473.6707 279051.5112 336316.1851 269510.7587 0.953318424 1.34957135 1.166861806 1.18821684 1.2505426 1.174252457 1.035400266 1.247876659 1 18.03998334 0.5515637 0.465578934 0.992880985 1.204660204 0.133822279 0.11446503 2.97849935 1.254391537 0.183964147 0.062424903 3.560932157 -0.5515637 0.211779219 TLHLPVSTTLSDVLDRVSDT(ph)PS(ph)IT(ph)AKLISEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLHLPVSTTLSDVLDRVSDTPSITAKLISEQK 32 2 Q9NR09 Q9NR09 BIRC6 Baculoviral IAP repeat-containing protein 6 3 T(0.25)LHLPVS(0.25)T(0.252)T(0.252)LS(0.252)DVLDRVS(0.249)DT(0.374)PS(0.374)IT(0.374)AKLIS(0.374)EQK 44.05 0.091433 72817000 20284 63458 44824 50981 79563 39429 43089 48252 80594 TRUE FALSE 19014.46065 68156.49635 45887.24645 52289.25877 73314.44292 50811.51222 36628.20447 54276.36842 67142.34074 0.283196273 1.015104561 0.683432331 0.778782184 1.091925633 0.756773024 0.545530645 0.808377662 1 16.03493521 4.753279348 24.52641211 0.808528767 0.28319579 0.516581578 0.166008461 1860.852002 3100743.64 0.040234238 0.886120271 56660.36238 -4.753279348 -0.525332977 TLHPDLGTDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TLHPDLGTDK 10 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;;;; 175.49 2.79E-06 6751940000 17980200 14226100 14098300 13736900 14832500 10132600 16774100 14205800 10851900 FALSE TRUE 16854851.38 15279415.25 14432718.33 14089412.11 13667615.28 13057717.13 14258979.43 15979425.4 9040647.784 1.864341116 1.690079695 1.596425243 1.558451612 1.511796014 1.444334238 1.577207714 1.767508898 1 23.10799472 -2.834481382 0.237879765 2.71E-29 1.695110952 0.707360983 0.125375548 30.13661688 0.754729014 15.96742795 0.209308729 0.001463924 2.834481382 1.695110952 TLHPDLGTDKDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TLHPDLGTDKDK 12 1 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;;;; 196.57 1.23E-07 4806620000 17754100 9005800 12246650 11128770 10605780 7878340 15316100 9528230 9975810 FALSE TRUE 16642902.57 9672598.803 12537146.32 11414353.08 9772844.82 10152688.86 13019592.99 10717850.49 8310782.865 2.002567369 1.16386133 1.508539752 1.373438973 1.175923494 1.221628459 1.566590441 1.289631875 1 22.98655295 7.9999999 0.033345319 4.72E-12 3.442937642 0.332343246 0.22843835 1675.003021 4.272474207 133.6041801 357.8622943 99999977.07 -7.9999999 3.442937642 TLHPDLGTDKDKEQWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TLHPDLGTDKDKEQWK 16 2 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;; 212.7 2.29E-12 35775970000 42977580 19680180 27367530 25252470 26714650 16309090 36084910 19227120 30761310 FALSE TRUE 40287689.98 21137321 28016700.74 25900491.13 24616589.15 21017259.53 30674312.74 21627668.26 25627048.64 1.572076854 0.824805123 1.093247261 1.010670074 0.960570587 0.820120172 1.196950659 0.843939096 1 24.611164 4.748118875 24.72070902 0.981589956 1.572077222 0.712401489 0.120220055 599.5311631 1550541.561 0.026678501 0.343905438 55991.08388 -4.748118875 0.590487266 TLHS(ph)PPLQLQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TLHSPPLQLQQR 12 0 B7WPL9;Q6PFW1-7;Q6PFW1-4;Q6PFW1-3;Q6PFW1-2;A0A2R8YGT1;F8W9A8;Q6PFW1 B7WPL9 PPIP5K1 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 1 1 T(0.168)LHS(0.832)PPLQLQQR;T(0.004)LHS(0.996)PPLQLQQR;T(0.001)LHS(0.999)PPLQLQQR 158.93 4.65E-05 946400000 362488 815270 385995 402223 794950 232901 381727 627511 589973 TRUE FALSE 339800.5231 875633.4391 395150.9837 412544.7231 732517.8337 300135.7379 324490.5801 705857.1297 491502.6949 0.691350275 1.781543516 0.80396504 0.839353939 1.490363819 0.610649221 0.660201019 1.436120569 1 18.9068398 3.743956351 22.32656827 0.939159852 1.307849293 0.057767109 0.390573763 210.7717737 279517.5406 0.093422958 0.167589114 5545.699728 -3.743956351 0.368689441 TLHSCSVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLHSCSVR 8 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 79.474 0.027943 95880000 35512 99140 30618 33983 111910 21795 42807 78569 89753 FALSE TRUE 33289.36731 106480.4288 31344.27342 34855.06131 103121.04 28086.86269 36388.48775 88378.5126 74772.64447 0.445207837 1.424055943 0.419194394 0.466147233 1.379127898 0.37563019 0.486655086 1.18196318 1 16.19022294 4.997940027 24.67611967 0.799962193 0.129643167 0.080060113 0.400763346 42236.28047 275778.7567 0.089365801 756891.5759 99526.79684 -4.997940027 -0.670319026 TLHSDDEGTVLDDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TLHSDDEGTVLDDSR 15 0 O00170;E9PMH2 O00170 AIP AH receptor-interacting protein 0 ;; 254.18 1.09E-24 1298680000 746260 799550 791990 772590 871010 673610 867030 741320 930950 FALSE TRUE 699552.9187 858749.5139 810776.3768 792415.9674 802604.3881 868070.2719 737026.9006 833875.4338 775568.4308 0.901987357 1.107251765 1.045396311 1.021722824 1.034859538 1.119269735 0.950305442 1.075179701 1 19.56489455 1.723046448 25 1.006152924 1.046387576 0.034878513 0.065431397 2.399142209 3850.447185 0.027425709 0.015208963 52.85017722 -1.723046448 0.040234651 TLIPS(ph)PPPRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLIPSPPPRPK 11 1 J3KSG3;J3KSS7;Q9NZ52-3;Q9NZ52-4;Q9NZ52-2;Q9NZ52 J3KSG3 GGA3 ADP-ribosylation factor-binding protein GGA3 1 T(0.007)LIPS(0.993)PPPRPK;T(0.001)LIPS(0.999)PPPRPK 66.004 0.038695 697250000 1358520 1212340 1259080 1358150 1403880 944170 1468010 1138410 1652140 TRUE FALSE 1273492.658 1302102.915 1288945.972 1393002.428 1293624.928 1216736.552 1247895.529 1280542.994 1376387.161 0.925243053 0.946029542 0.9364705 1.012071653 0.939869947 0.884007484 0.90664572 0.930365402 1 20.39245491 2.468556332 24.9798542 0.918471952 0.952944299 0.049068565 0.037562598 342.0548133 997604.4131 0.012058956 0.010101758 294.1415195 -2.468556332 0.034472347 TLKPEEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLKPEEQR 8 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 84.213 0.016062 386330000 1509210 1377290 1462240 1565390 1633230 1056060 1808020 1434440 1246750 FALSE TRUE 1414751.24 1479265.985 1496925.023 1605560.558 1504962.704 1360927.378 1536924.186 1613532.992 1038659.371 1.36209356 1.424207037 1.441208798 1.545800869 1.448947313 1.310273047 1.479719174 1.553476565 1 19.98629117 -1.186600581 5.234846037 0.999975537 1.443135619 0.783887528 0.073537362 2.00E-05 3.10E-06 0.067724935 0.01596204 0.065072789 1.186600581 0.443160082 TLKPTYRT(ph)PER ddPTM_SK-BR-3_Pertuzumab_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(0.075)YRT(0.925)PER 68.168 0.064292 0 159200 157750 159840 175570 172820 114090 183080 155380 191910 TRUE FALSE 149235.9562 169429.9741 163631.4803 180075.4234 159247.4143 147025.9309 155628.8536 174779.535 159878.9812 0.933430743 1.05973889 1.023470872 1.126323311 0.996049719 0.919607629 0.973416596 1.093198954 1 17.28662076 2.501937891 24.95555174 0.985479502 1.040044689 0.074156449 0.063044984 1375.055916 1382752.479 0.019351005 0.018168365 317.6419771 -2.501937891 0.054565187 TLLEEEYFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLLEEEYFR 9 0 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;P52701-4 P52701 MSH6 DNA mismatch repair protein Msh6 0 ; 197.3 6.57E-05 150010000 131017 187577 152551 153212 196479 106256 162553 165908 202070 FALSE TRUE 122816.8798 201465.3963 156169.5818 157143.6793 181048.3319 136930.3823 138179.6867 186621.979 168343.2116 0.729562414 1.196753907 0.927685651 0.933472029 1.075471533 0.813400083 0.820821258 1.108580365 1 17.36104602 2.243514735 24.99977688 0.906225597 0.995255774 0 0.145931332 324.1138767 1635569.486 0.0485613 0.039449255 175.1921875 -2.243514735 0.089030177 TLLEGSGLESIISIIHSSLAEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLLEGSGLESIISIIHSSLAEPR 23 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 283.01 4.41E-52 2560300000 235440 710070 699870 688150 713010 614550 843720 695140 735230 FALSE TRUE 220704.2307 762644.3216 716471.2469 705809.094 657013.0707 791960.6086 717212.0187 781929.7592 612515.3632 0.3603244 1.245102356 1.169719635 1.152312475 1.072647496 1.292964481 1.170929028 1.276587995 1 19.2243865 4.741176294 24.98858553 1.183290694 0.360324107 0.890910941 0.089248382 64.81389848 619157.554 0.018706959 0.128542908 55103.13324 -4.741176294 -0.822966587 TLLEQLDDDQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLLEQLDDDQ 10 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ; 206.48 3.48E-07 44817000 175839 196576 195195 180057 195041 161436 214148 167979 212473 FALSE TRUE 164833.5509 211130.6916 199825.1176 184677.5675 179723.2666 208039.9525 182038.4955 188951.5479 177009.8837 0.931211 1.192762162 1.128892429 1.043317829 1.015328991 1.175301335 1.02840865 1.067463262 1 17.43347039 0.833292525 0.539541135 0.9972726 1.100133127 0.037339803 0.07942557 2.496494879 1.658337106 0.089675128 0.037962942 6.812280545 -0.833292525 0.102860527 TLLISSLS(ph)PALPAEHLEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLLISSLSPALPAEHLEDR 19 0 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 T(0.016)LLIS(0.246)S(0.246)LS(0.492)PALPAEHLEDR 65.197 0.018643 18804000 12117 19917 16767 15644 19131 14906 20797 17868 23674 TRUE FALSE 11358.6186 21391.6754 17164.72116 16045.45153 17628.52843 19209.12022 17678.68292 20098.85913 19722.65646 0.575917277 1.084624449 0.870304728 0.813554277 0.893821198 0.973962116 0.896364187 1.019074645 1 14.26756626 1.499312837 0.999702315 1.008123948 0.883596763 0.160143115 0.128550513 1.153316321 2.271303525 0.109932017 0.04060016 31.57278095 -1.499312837 -0.124527185 TLLIVSHDQGFLDDVCTDIIHLDAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TLLIVSHDQGFLDDVCTDIIHLDAQR 26 0 Q8NE71;Q8NE71-2;H0YGW7 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ;;;; 319.88 2.33E-82 1093723000 484270 478835 521684 477336 519355 466057 593670 431847 448681 FALSE TRUE 453960.4051 514288.4416 534058.5908 489585.2499 478566.9533 600600.0901 504654.6949 485764.0486 373793.2425 1.214469267 1.3758634 1.428754001 1.30977555 1.280298568 1.606770861 1.350090471 1.299552783 1 18.51188096 0.799085878 2.624418919 1.000270194 1.378603498 0.547977056 0.103601219 0.631961833 6.935586056 0.092891909 0.024708148 6.296306743 -0.799085878 0.378333304 TLLPWDS(ph)DESPEASPGPPGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TLLPWDSDESPEASPGPPGPR 21 0 A0A669KBI7;Q9UMN6 A0A669KBI7 KMT2B Histone-lysine N-methyltransferase 2B 1 TLLPWDS(1)DESPEASPGPPGPR;TLLPWDS(1)DESPEASPGPPGPR;TLLPWDS(0.973)DES(0.027)PEASPGPPGPR 252.33 2.58E-36 59675000 48487.4 50997.1 48067.3 54994 52638.1 41387.6 52127.5 46062.4 51317 TRUE FALSE 45452.66019 54772.97835 49207.47906 56405.23914 48504.11596 53335.52825 44311.4653 51813.39204 42751.86118 1.063173835 1.281183481 1.151002031 1.319363358 1.13454981 1.247560382 1.03648038 1.211956406 1 15.38369961 0.887836049 0.59938715 1.003389712 1.207805212 0.271059255 0.090626986 1.103945677 0.908344202 0.0858257 0.035727425 7.723889448 -0.887836049 0.2044155 TLLSESSSQSSKS(ph)PSLSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TLLSESSSQSSKSPSLSSK 19 1 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 TLLSESSSQS(0.003)S(0.282)KS(0.711)PS(0.004)LSSK;TLLSESSSQSS(0.008)KS(0.95)PS(0.042)LSSK;TLLSESSSQSS(0.002)KS(0.985)PS(0.013)LSSK;TLLSESSSQSS(0.004)KS(0.995)PS(0.001)LSSK 292.29 8.58E-50 1799870000 1946810 1528880 1734670 1875870 1958230 1247430 2431210 1792230 2777590 TRUE FALSE 1824962.637 1642079.866 1775817.192 1924008 1804438.515 1607542.791 2066672.631 2015993.861 2313992.285 0.788664098 0.709630657 0.767425718 0.831466904 0.779794525 0.694705337 0.893119931 0.871218921 1 21.14195262 1.216771763 1.170659957 0.992798512 0.759369141 0.711107225 0.048582166 0.222643028 0.619815678 0.043420782 0.014075716 16.47296454 -1.216771763 -0.233429371 TLLTGDGGGEATGS(ph)PLAQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLLTGDGGGEATGSPLAQGK 20 0 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 TLLTGDGGGEATGS(1)PLAQGK;TLLTGDGGGEAT(0.001)GS(0.999)PLAQGK 376.5 2.11E-112 148850000 269637 216804 247872 260751 276054 190604 268263 217797 409147 TRUE FALSE 252760.9015 232856.3937 253751.6409 267442.3121 254373.8324 245628.2806 228039.4536 244989.4349 340857.7225 0.741543714 0.683148359 0.744450321 0.784615675 0.746275691 0.720618206 0.669016538 0.718743976 1 18.37881014 -0.893171382 4.381166523 1.000003777 0.722010931 0.872554079 0.03287097 3207275.974 2196298.65 105.2540705 0.008273223 0.127887653 0.893171382 -0.277992846 TLMELLNQMDGFDTLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLMELLNQMDGFDTLHR 17 0 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ; 223.15 3.13E-15 1003390000 928580 1098850 1020560 1013110 1100720 891220 1149980 935500 1026700 FALSE TRUE 870461.8354 1180209.997 1044768.165 1039108.118 1014273.891 1148500.746 977551.1749 1052299.234 855337.1373 1.017682733 1.37981849 1.22146943 1.2148521 1.18581767 1.342746265 1.142884054 1.230274226 1 19.70613366 -0.006985951 0.663090771 0.9888531 1.239646307 0.297609543 0.100938642 5.067959502 2.437599537 0.236605539 0.034441716 0.984042938 0.006985951 0.250793207 TLMLPLTEGS(ph)LR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TLMLPLTEGSLR 12 0 Q7L4E1;Q7L4E1-3 Q7L4E1 FAM73B Protein FAM73B 1 TLMLPLT(0.003)EGS(0.997)LR;TLMLPLTEGS(1)LR;TLMLPLTEGS(1)LR;TLMLPLTEGS(1)LR;TLMLPLTEGS(1)LR 196.75 2.13E-07 293988000 362033 407458 350706 364251 494978 369055 464373 455881 617606 TRUE FALSE 339374.0008 437626.6143 359024.9119 373598.2973 456104.4245 475595.1874 394744.5797 512798.7464 514523.5687 0.659588834 0.850547265 0.697781275 0.726105314 0.886459731 0.924340917 0.767204077 0.996647729 1 18.97287764 1.601942991 0.458134736 1.007986356 0.735297627 0.556465503 0.080125777 0.759816029 0.418042483 0.08522121 0.059762468 39.98922529 -1.601942991 -0.272688729 TLMNLGGLAVARDDGLFSGDPNWFPKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLMNLGGLAVARDDGLFSGDPNWFPKK 27 2 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 100.95 0.0016074 169290000 119360 118730 197590 233200 231670 351010 283400 83435 117640 FALSE TRUE 111889.4707 127520.8927 202276.9281 239184.3068 213475.5727 452340.8888 240906.801 93852.04341 98005.12402 1.141669599 1.301165567 2.063942372 2.440528587 2.178208281 4.615482031 2.458104139 0.957623842 1 16.58056956 3.771084172 1.394675782 2.517946041 1.171006383 0.124429696 1.014987518 0.707479363 2.64975989 0.303971247 0.802846031 5903.1548 -3.771084172 -1.346939658 TLNAETPKSS(ph)PLPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TLNAETPKSSPLPAK 15 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 TLNAETPKS(0.253)S(0.747)PLPAK;TLNAETPKS(0.044)S(0.956)PLPAK;TLNAETPKS(0.251)S(0.749)PLPAK;TLNAETPKS(0.242)S(0.758)PLPAK;TLNAETPKS(0.07)S(0.93)PLPAK 197.6 3.06E-11 2625790000 3306950 1976870 2482440 2332510 2477470 1780870 3903510 2269130 4682860 TRUE FALSE 3099973.903 2123239.512 2541324.649 2392366.156 2282899.5 2294978.259 3318214.914 2552435.875 3901260.414 0.794608299 0.544244497 0.65141118 0.613229034 0.585169729 0.588265846 0.850549454 0.654259292 1 21.89550887 0.708609149 0.652977523 1.000368342 0.620034368 0.565182971 0.094154235 0.781299811 0.664801738 0.093583509 0.034854235 5.112215454 -0.708609149 -0.380333974 TLNDELEIIEGMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLNDELEIIEGMK 13 0 P10809;E7EXB4;E7ESH4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 220.66 4.75E-11 85308000 235980 165411 185339 154498 235100 158177 186731 183798 248030 FALSE TRUE 221210.433 177658.2025 189735.3286 158462.6802 216636.1943 203840.1321 158732.4201 206745.5849 206632.1907 1.070551652 0.859779892 0.918227349 0.766882835 1.048414546 0.986487785 0.768188246 1.000548773 1 17.6567055 4.748350245 24.11952664 0.903980288 1.070551801 0.180309719 0.097528257 1259.793557 3103752.793 0.021511487 0.280399112 56020.92112 -4.748350245 0.166571513 TLNDELEIIEGMKFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TLNDELEIIEGMKFDR 16 1 P10809;E7EXB4;E7ESH4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;;;;; 262.74 6.08E-27 656283000 721617 872609 746350 765193 1409830 600606 890985 763730 2718630 FALSE TRUE 676452.2801 937217.8783 764053.7745 784829.1478 1299107.639 773991.2022 757390.0707 859083.3717 2264873.09 0.298671163 0.413805914 0.337349487 0.346522351 0.573589595 0.341737118 0.334407289 0.37930751 1 21.11099878 -2.034223563 2.419627765 1.752986022 0.377732588 0.869264813 0.075786301 6321228.484 2312140.478 26381818.35 0.017479419 0.009242223 2.034223563 -1.375253434 TLNMT(ph)TSPEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLNMTTSPEEK 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 1 TLNMT(0.528)T(0.236)S(0.236)PEEK 145.6 0.0003771 133810000 372680 265350 308710 302310 331280 206690 407820 276120 365040 TRUE FALSE 349354.6241 284996.7901 316032.747 310067.7864 305262.6051 266358.0477 346671.177 310594.1898 304112.4658 1.148767852 0.937142742 1.03919695 1.019582626 1.003781954 0.875853764 1.139943988 1.021313576 1 18.21424543 1.703682933 24.99999997 1.063192615 1.000950305 0.077373517 0.07819244 1.370061744 974.7782491 0.032584042 0.018069484 50.54555079 -1.703682933 -0.06224231 TLNMTT(ph)SPEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLNMTTSPEEK 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 1 TLNMT(0.141)T(0.615)S(0.245)PEEK 168.89 0.00018288 93178000 388100 258640 306760 295810 305490 223230 376320 262590 346920 TRUE FALSE 363809.5138 277789.9747 314036.4921 303400.9854 281498.0477 287672.8772 319894.3096 295374.9395 289016.8108 1.258783227 0.961155076 1.086568256 1.049769335 0.973985032 0.995349981 1.106836342 1.021999166 1 18.14079388 4.749680521 24.73079834 1.030966903 1.258783381 0.711743341 0.046702104 826.7343111 1838625.996 0.011080603 0.169034159 56192.78031 -4.749680521 0.227816478 TLNMTTS(ph)PEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 TLNMTTSPEEK 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 1 TLNMT(0.114)T(0.266)S(0.62)PEEK;TLNMTT(0.177)S(0.823)PEEK;TLNMT(0.039)T(0.203)S(0.758)PEEK;TLNMT(0.003)T(0.062)S(0.935)PEEK;TLNMT(0.001)T(0.204)S(0.795)PEEK;TLNMT(0.076)T(0.323)S(0.601)PEEK;TLNMT(0.101)T(0.392)S(0.506)PEEK 267.93 3.07E-21 2887930000 9242500 5906570 7242290 6966270 7315110 5221140 9223640 5988150 8192850 TRUE FALSE 8664028.423 6343898.589 7414080.539 7145036.282 6740610.768 6728398.36 7840640.81 6735783.709 6825410.407 1.269378383 0.92945306 1.086246848 1.046828814 0.987575892 0.985786635 1.148742763 0.986868673 1 22.70248437 4.75443159 24.46984559 1.029914599 1.269378624 0.612828141 0.061607857 1656.381333 2553749.247 0.014576522 0.365585349 56810.88959 -4.75443159 0.239464025 TLNPS(ph)PAGWFVQQHPELELMSSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TLNPSPAGWFVQQHPELELMSSFR 24 0 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 TLNPS(1)PAGWFVQQHPELELMSSFR;TLNPS(1)PAGWFVQQHPELELMSSFR;T(0.011)LNPS(0.989)PAGWFVQQHPELELMSSFR 238.18 1.18E-37 1035333000 331847 390016 367238 386061 420766 366929 461669 365507 432933 TRUE FALSE 311077.2886 418893.1905 375949.0588 395967.9789 387720.7356 472855.4457 392446.0194 411141.3535 360673.6854 0.862489561 1.161418776 1.042352337 1.09785658 1.074990362 1.311033948 1.088091633 1.139926116 1 18.46033464 2.444343455 24.99985378 1.148682831 1.063825391 0.125181125 0.107441065 373.3703436 284770.3104 0.033669254 0.028169857 278.191243 -2.444343455 -0.084857441 TLPAHSDPVSAVHFNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLPAHSDPVSAVHFNR 16 0 P61964 P61964 WDR5 WD repeat-containing protein 5 0 150.76 4.10E-07 126420000 97369 249710 164470 174440 281230 141430 192650 182280 211390 FALSE TRUE 91274.8481 268198.7882 168371.3061 178916.4257 259143.3302 182258.5451 163763.921 205038.0592 176107.6434 0.5182901 1.522925315 0.956070406 1.015949236 1.471505298 1.034926943 0.929908083 1.16427689 1 17.426098 2.027829077 24.99928838 1.013309128 1.142232851 0 0.283466595 728.4151041 654343.6084 0.097691732 0.072148599 106.617643 -2.027829077 0.128923723 TLPLTGSTFHDQIAMLSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLPLTGSTFHDQIAMLSHR 19 0 P55265-5;P55265;P55265-4 P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 314.72 6.99E-62 1061840000 598430 835070 771410 784030 952790 662100 920900 802680 901030 FALSE TRUE 560975.3345 896899.4517 789708.2095 804149.5372 877961.7168 853237.5217 782819.5942 902896.3649 750642.2721 0.74732713 1.194842717 1.052043348 1.071281977 1.169614008 1.136676621 1.042866387 1.202831759 1 19.51776601 4.747007378 24.84455487 1.109098907 0.747326932 0.736550787 0.067933991 477.197399 1403552.22 0.014636326 0.168805995 55847.96821 -4.747007378 -0.361771975 TLPLTTAPEAGEVTPSDSGGQEDS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLPLTTAPEAGEVTPSDSGGQEDSPAK 27 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;H0Y8P9 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 TLPLTTAPEAGEVTPSDSGGQEDS(1)PAK;TLPLTTAPEAGEVTPSDSGGQEDS(1)PAK 223.15 1.40E-34 222310000 667670 434030 550840 602890 541440 267880 432410 319100 315650 TRUE FALSE 625881.7265 466166.0328 563906.1849 618361.1781 498917.4865 345212.6073 367574.1348 358940.3374 262965.9758 2.380086338 1.772723758 2.144407402 2.351487397 1.897270112 1.312765297 1.397801117 1.364968743 1 18.00451662 2.31578152 3.704988247 1.306517814 2.096998927 0.815053447 0.200727292 0.101501183 2.746856379 0.072595533 0.057977849 206.9100187 -2.31578152 0.790481113 TLPQQES(ph)LEIELAEEKPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLPQQESLEIELAEEKPVK 19 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 TLPQQES(1)LEIELAEEKPVK;TLPQQES(1)LEIELAEEKPVK 197.44 4.77E-16 329350000 799540 383150 489340 464050 362110 339320 661010 376050 509830 TRUE FALSE 749498.2186 411518.8247 500947.3759 475958.3086 333671.3413 437276.1756 561897.687 423000.6703 424736.0794 1.764621032 0.968881253 1.179432123 1.120597782 0.785596886 1.029524443 1.322933733 0.995914147 1 18.69620714 4.743776829 24.93094168 1.071838691 1.764621332 0.711645847 0.142303659 317.1645203 1515842.031 0.03447039 0.293280873 55434.07808 -4.743776829 0.692782641 TLPQQES(ph)LEIELAEEKPVKR ddPTM_SK-BR-3_Pertuzumab_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 225.7 2.57E-25 2883990000 2519470 1537340 1796550 1821200 1501670 1211730 2497560 1465340 2882150 TRUE FALSE 2361780.87 1651166.253 1839165.014 1867935.075 1383734.896 1561536.78 2123074.064 1648290.925 2401100.546 0.983624311 0.6876706 0.765967513 0.777949544 0.576291942 0.650342104 0.88420873 0.686473096 1 21.19526439 -1.238995381 4.426065484 1.000107801 0.748299287 0.310352345 0.116295123 0.000114604 1.97E-05 0.104312493 0.024576195 0.05767726 1.238995381 -0.251808514 TLPSGS(ph)PRPGQLERPTSLALDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TLPSGSPRPGQLERPTSLALDSR 23 2 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 T(0.002)LPS(0.041)GS(0.957)PRPGQLERPTSLALDSR;T(0.003)LPS(0.066)GS(0.931)PRPGQLERPTSLALDSR;T(0.014)LPS(0.416)GS(0.569)PRPGQLERPTSLALDSR;TLPS(0.032)GS(0.968)PRPGQLERPTSLALDSR 190.93 7.16E-18 2234680000 1740470 2030400 2063620 2293760 2335290 1611060 2300460 1947470 1968270 TRUE FALSE 1631537.09 2180732.929 2112570.041 2352621.765 2151885.744 2076146.869 1955527.379 2190615.916 1639753.021 0.994989531 1.329915481 1.288346485 1.434741534 1.312323085 1.266133888 1.192574341 1.335942601 1 20.6450471 -1.401811779 3.211538791 0.996696891 1.276316335 0.349688627 0.115098552 19625530.58 22724859.83 583476.4675 0.026204748 0.039644982 1.401811779 0.279619443 TLPSTSSS(ph)GSKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLPSTSSSGSKR 12 1 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5;P08651-4 P08651-3 NFIC Nuclear factor 1 C-type 1 TLPSTS(0.001)S(0.058)S(0.471)GS(0.471)KR 80.379 0.012555 153170000 207620 154480 184530 167900 195110 140770 211820 153900 240760 TRUE FALSE 194625.4348 165917.8599 188907.1387 172208.5983 179786.8476 181408.0138 180059.5574 173114.7538 200575.6006 0.970334548 0.827208591 0.941825118 0.858572018 0.896354527 0.904437096 0.897714163 0.863089794 1 17.61378659 -1.629882627 3.112620822 1.007546403 0.892821564 0.395457094 0.040747219 15278231.64 17415594.87 931472.1871 0.008524645 0.023448625 1.629882627 -0.11472484 TLPSTSSSGS(ph)KR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLPSTSSSGSKR 12 1 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5;P08651-4 P08651-3 NFIC Nuclear factor 1 C-type 1 TLPSTS(0.004)S(0.033)S(0.314)GS(0.649)KR 87.727 0.0063613 88217000 86216 66503 94108 79894 87780 55534 98145 69427 116820 TRUE FALSE 80819.89446 71426.95132 96340.2862 81944.2153 80886.11289 71565.76428 83429.06838 78095.11378 97321.98731 0.830438185 0.733924093 0.989912854 0.841990773 0.83111859 0.73535042 0.857247891 0.802440599 1 16.57047816 -1.037499074 5.168745567 1.000001778 0.832167661 0.365340482 0.071119792 1.44E-06 2.69E-07 0.06812904 0.016057999 0.091727789 1.037499074 -0.167834118 TLQALEFHTVPFQLLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLQALEFHTVPFQLLAR 17 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ; 170.91 1.79E-09 936950000 458100 2662200 438220 372710 2760700 389790 554400 2425580 479170 FALSE TRUE 429428.3387 2859312.058 448614.7853 382274.3696 2543885.758 502316.0453 471272.8668 2728419.002 399193.4314 1.075739992 7.162723213 1.123803024 0.957616883 6.37256417 1.258327432 1.180562679 6.834829402 1 18.60672846 0.463187807 0.108674533 1.21E-11 4.889333664 0.014367158 2.671043755 76.33814825 3.721676974 99.10864835 59.00214405 2.905278745 -0.463187807 4.889333664 TLQEVTEMDSVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TLQEVTEMDSVKR 13 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 124.62 0.00022003 1095680000 370560 329873 326441 351849 380100 229411 393960 306811 415420 FALSE TRUE 347367.3111 354297.1402 334184.3347 360878.041 350248.4792 295638.2315 334889.3553 345117.0287 346083.7183 1.003708908 1.023732471 0.965617037 1.042747815 1.01203397 0.854239064 0.967654176 0.997206775 1 18.40076155 TLQRLS(ph)SGFDDIDLPSAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TLQRLSSGFDDIDLPSAVK 19 1 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 TLQRLS(0.957)S(0.043)GFDDIDLPSAVK;TLQRLS(0.626)S(0.374)GFDDIDLPSAVK;T(0.015)LQRLS(0.795)S(0.19)GFDDIDLPSAVK;TLQRLS(0.969)S(0.031)GFDDIDLPSAVK;T(0.003)LQRLS(0.85)S(0.147)GFDDIDLPSAVK 237.41 1.95E-24 2985130000 4191110 4350160 4035230 4503720 6194770 2806750 4761030 3698980 8472190 TRUE FALSE 3928795.906 4672250.373 4130947.561 4619293.08 5708257.753 3617013.161 4047157.751 4160805.795 7058126.757 0.556634365 0.661967479 0.585275343 0.654464455 0.80874968 0.512460783 0.573403948 0.589505677 1 22.75085391 -1.371154755 3.775350082 1.001614879 0.617625801 0.689670366 0.080570266 19546046.33 39226463.16 344039.9545 0.018775332 0.042544678 1.371154755 -0.383989078 TLQRLSS(ph)GFDDIDLPSAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLQRLSSGFDDIDLPSAVK 19 1 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 TLQRLS(0.252)S(0.748)GFDDIDLPSAVK 230.8 2.95E-20 959000000 603090 661060 606870 656600 860940 434820 666900 499950 1178700 TRUE FALSE 565343.6734 710005.5702 621265.243 673449.4676 793325.2453 560345.4753 566904.5362 562369.858 981967.3553 0.575725527 0.723043965 0.632674029 0.685816554 0.807893705 0.570635543 0.577315053 0.572697101 1 19.90531554 -1.364690183 3.243358019 1.003063092 0.647153045 0.673947472 0.077945389 24976286.13 32571387.96 718559.4719 0.019450588 0.043182702 1.364690183 -0.355910047 TLQTDSIDSFETQRT(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TLQTDSIDSFETQRTPR 17 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFET(0.022)QRT(0.978)PR 254.36 7.92E-27 8687680000 4961550 5900690 5501110 5708020 6505450 4286220 6945540 5750140 7889710 TRUE FALSE 4651015.442 6337583.227 5631598.927 5854497.457 5994538.199 5523582.133 5904120.756 6468057.637 6572866.432 0.707608391 0.964203866 0.856794975 0.890706896 0.912012782 0.840361232 0.898256616 0.984054325 1 22.64809124 -4.999999399 0.038810403 1.571397537 0.549484949 0.379382611 0.066237001 1137.096259 3.300450127 76.88006316 23.9720149 1.00E-05 4.999999399 -1.021912588 TLQVVPPSDPDPLLAS(ph)WHGGTGTSPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLQVVPPSDPDPLLASWHGGTGTSPPR 27 0 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 TLQVVPPSDPDPLLAS(0.28)WHGGT(0.24)GT(0.24)S(0.24)PPR 74.806 0.010951 85210000 21470 44772 38782 38657 45360 35615 44794 37891 30093 TRUE FALSE 20126.23103 48086.96547 39701.92735 39649.00407 41797.60857 45896.47234 38077.55555 42621.77476 25070.28389 0.802792306 1.918086196 1.583624961 1.581513964 1.667217202 1.830712111 1.518832244 1.700091429 1 14.61369071 -1.489893191 5.914635466 0.999409657 1.614045129 0.256368994 0.301624691 0.00205324 0.000177082 0.255382747 0.06014039 0.032367325 1.489893191 0.614635472 TLQVVPPSDPDPLLASWHGGT(ph)GTSPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLQVVPPSDPDPLLASWHGGTGTSPPR 27 0 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 TLQVVPPSDPDPLLAS(0.047)WHGGT(0.318)GT(0.318)S(0.318)PPR;TLQVVPPSDPDPLLAS(0.006)WHGGT(0.432)GT(0.281)S(0.281)PPR 96.963 0.015871 163025000 93876 166372 151659 157316 171822 120476 166446 131143 132907 TRUE FALSE 88000.46873 178690.356 155256.4231 161352.9949 158327.7932 155255.4654 141488.9675 147516.4922 110723.9631 0.794773473 1.613836346 1.402193516 1.457254513 1.429932499 1.402184867 1.277853173 1.332290573 1 16.75660796 0.502683535 0.875692467 0.999113612 1.390064887 0.174905771 0.215755539 2.361571502 2.736602012 0.195246828 0.063199091 3.181878083 -0.502683535 0.390951275 TLQVVPPSDPDPLLASWHGGTGT(ph)SPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLQVVPPSDPDPLLASWHGGTGTSPPR 27 0 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 TLQVVPPSDPDPLLASWHGGT(0.132)GT(0.488)S(0.38)PPR 126.66 0.0002487 91013000 75854 119570 108100 123290 129810 100440 125830 103450 90987 TRUE FALSE 71106.43354 128423.0872 110664.183 126453.8301 119615.2462 129435.3975 106962.9596 116365.9602 75800.6819 0.938071159 1.694220738 1.459936511 1.668241327 1.578023353 1.707575634 1.411108145 1.535157169 1 16.20992321 -1.4874903 10.02929904 0.999996223 1.521524232 0.327758166 0.222547216 1.65E-05 8.43E-07 0.189030258 0.044554537 0.032546905 1.4874903 0.521528009 TLRDS(ph)PNVEAAHLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TLRDSPNVEAAHLAR 15 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 T(0.002)LRDS(0.998)PNVEAAHLAR;T(0.005)LRDS(0.995)PNVEAAHLAR;T(0.007)LRDS(0.993)PNVEAAHLAR;T(0.077)LRDS(0.923)PNVEAAHLAR 213.5 2.06E-10 3323410000 2210600 3341670 2207300 2101920 3637580 1675320 2582760 3192830 3973130 TRUE FALSE 2072242.492 3589090.724 2259658.198 2155858.826 3351899.14 2158957.687 2195499.115 3591461.854 3309988.936 0.626057226 1.084321064 0.682678475 0.651319043 1.012661736 0.652255258 0.663295001 1.08503742 1 21.65839496 1.227904479 24.99924085 1.04251888 0.783002129 0.334598342 0.160074258 292.1006344 685243.759 0.144232539 0.037548196 16.90069169 -1.227904479 -0.259516751 TLS(ph)ADASVNTLPVVVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLSADASVNTLPVVVSR 17 0 Q92615;H0Y4V9;H0Y641 Q92615 LARP4B La-related protein 4B 1 T(0.001)LS(0.999)ADASVNTLPVVVSR;T(0.001)LS(0.999)ADASVNTLPVVVSR 178.1 1.04E-09 228300000 347880 263180 267720 319900 347500 217583 275350 210583 362170 TRUE FALSE 326106.8118 282666.121 274070.4448 328109.1756 320208.7517 280395.6799 234063.8237 236874.7511 301721.4873 1.080820643 0.936844517 0.90835574 1.087457107 1.061272615 0.92931956 0.775761202 0.785077501 1 18.20285792 1.96829739 6.201652989 0.833362469 0.993447409 0.413415822 0.084963693 0.184462304 22.41924862 0.035889174 0.022838573 92.96027294 -1.96829739 0.160084939 TLS(ph)ASAAEVAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLSASAAEVAPR 12 0 Q16825 Q16825 PTPN21 Tyrosine-protein phosphatase non-receptor type 21 1 T(0.002)LS(0.998)ASAAEVAPR 145.71 6.73E-05 85751000 49235 59733 56815 81719 87880 46376 48257 37434 51467 TRUE FALSE 46153.46924 64155.69347 58162.67863 83816.04789 80978.25929 59763.99835 41021.31085 42107.7173 42876.82521 1.076419931 1.496279008 1.356506186 1.954810028 1.888625356 1.393853161 0.956724539 0.982062387 1 15.38791047 1.822872793 3.992165395 0.977239329 1.543852441 0.528285089 0.24725797 0.189370811 5.082982026 0.128221886 0.069279821 66.50783229 -1.822872793 0.566613113 TLS(ph)DDLDEAAKEFQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TLSDDLDEAAKEFQEK 16 1 Q9H0A0;Q9H0A0-2;A0A087WV29 Q9H0A0 NAT10 N-acetyltransferase 10 1 T(0.003)LS(0.997)DDLDEAAKEFQEK;T(0.012)LS(0.988)DDLDEAAKEFQEK;T(0.168)LS(0.832)DDLDEAAKEFQEK;T(0.141)LS(0.859)DDLDEAAKEFQEK 149.94 4.77E-07 35029000 175525 76497 101253 110605 121641 64558 136256 87316 163357 TRUE FALSE 164539.2036 82160.91748 103654.769 113443.3116 112087.8065 83194.84659 115825.6777 98217.59481 136091.6614 1.209032221 0.603717499 0.761654079 0.83358018 0.823619944 0.611314799 0.85108578 0.721701784 1 17.05421915 -1.236280914 4.986449599 1.000034362 0.779031121 0.106376896 0.169151092 5.71E-05 8.74E-06 0.144653455 0.03408985 0.058038888 1.236280914 -0.221003241 TLS(ph)DESIYNSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TLSDESIYNSQR 12 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 TLS(1)DESIYNSQR;TLS(1)DESIYNSQR;TLS(0.997)DES(0.003)IYNSQR;TLS(1)DESIYNSQR 311.32 2.81E-46 2510730000 1599990 1506000 1426890 1432910 1541860 1158210 1722530 1238950 1528140 TRUE FALSE 1499849.482 1617505.807 1460736.505 1469680.897 1420768.535 1492566.425 1464252.618 1393635.635 1273083.562 1.178123359 1.270541742 1.147400334 1.154426104 1.116005719 1.172402558 1.150162222 1.094692977 1 20.27989569 -5 0.068991871 0.384186187 1.391670746 0.747197533 0.034378624 152.1566336 0.75733967 14.84045179 1.908201746 1.00E-05 5 1.007484559 TLS(ph)DESLCSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLSDESLCSGR 11 0 O60292;M0R2Q7 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 TLS(1)DESLCSGR;T(0.274)LS(0.726)DESLCSGR 264.32 7.72E-21 894830000 703620 621300 629000 655190 686830 542370 761650 523820 664460 TRUE FALSE 659581.6802 667301.6985 643920.177 672003.2846 632889.1423 698943.4144 647447.6533 589220.0801 553557.3334 1.191532729 1.205478924 1.163240261 1.213972328 1.143312723 1.262639608 1.169612639 1.064424667 1 19.07837322 1.146835234 2.881413284 1.003346963 1.194269551 0.826175396 0.031554404 0.085624351 1.289188277 0.026415735 0.007189987 14.02281596 -1.146835234 0.190922588 TLS(ph)INEEEPEGGFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLSINEEEPEGGFSK 15 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2 E9PP16 PPFIBP2 Liprin-beta-2 1 T(0.031)LS(0.969)INEEEPEGGFSK;TLS(1)INEEEPEGGFSK 338.97 3.30E-69 99157000 381694 291620 308553 390647 293450 189434 398658 226295 239566 TRUE FALSE 357804.4539 313211.8482 315872.0229 400671.6634 270403.6207 244120.5206 338882.9339 254548.4289 199580.8869 1.792779155 1.569347912 1.582676717 2.007565301 1.354857296 1.223165827 1.697972882 1.27541486 1 17.60661404 2.657712259 24.99997992 1.374105386 1.684072478 0.472882485 0.215418454 113.5441106 35109.06364 0.066741176 0.062924188 454.6867084 -2.657712259 0.309967092 TLS(ph)MDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLSMDK 6 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 1 TLS(1)MDK 114.5 0.026469 102980000 574040 289060 386990 395750 232590 264640 458860 210090 208300 TRUE FALSE 538111.8611 310462.3032 396169.5855 405905.615 214323.3196 341037.2719 390058.2028 236320.199 173533.3843 3.100912618 1.789063841 2.282958908 2.339063556 1.235055263 1.965254543 2.247741576 1.361814039 1 17.40485371 3.182307922 0.080647382 1.18E-13 4.161958277 0.500571655 0.437892067 47.71187754 1.177740802 21.55024326 38.85533574 1521.626006 -3.182307922 4.161958277 TLS(ph)MDKGF ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TLSMDKGF 8 1 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 1 T(0.001)LS(0.999)MDKGF;T(0.001)LS(0.999)MDKGF;TLS(1)MDKGF;T(0.002)LS(0.998)MDKGF;TLS(1)MDKGF;TLS(1)MDKGF 136.02 0.0021275 1489800000 5761780 4219400 4417440 4784910 3161530 2448820 4838060 2499620 3744440 TRUE FALSE 5401160.475 4531808.766 4522223.763 4907698.891 2913236.187 3155754.581 4112637.817 2811703.059 3119468.774 1.73143598 1.452750162 1.449677522 1.573248283 0.933888555 1.011632047 1.31837762 0.901340344 1 21.57286894 2.745217618 24.85198925 1.072728209 1.518256623 0.769430261 0.139634354 262.6399429 980490.4407 0.042883661 0.044546611 556.1828819 -2.745217618 0.445528414 TLS(ph)MIEEEIR ddPTM_SK-BR-3_Pertuzumab_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(0.002)LS(0.998)MIEEEIR;T(0.001)LS(0.999)MIEEEIR;T(0.002)LS(0.998)MIEEEIR;T(0.025)LS(0.975)MIEEEIR 167.71 5.41E-06 78025000 165132 204408 186544 200225 233242 148062 179859 164368 178687 TRUE FALSE 154796.6829 219542.581 190968.9118 205363.1125 214924.1142 190805.0958 152890.8127 184889.7066 148862.9853 1.039860127 1.474796307 1.282850208 1.379544499 1.443771356 1.281749761 1.027057279 1.242012621 1 17.18362555 1.888523725 5.176701022 1.100052079 1.343091885 0.389793408 0.133457149 0.205240866 7.80622406 0.054673368 0.032334931 77.36129386 -1.888523725 0.243039807 TLS(ph)NAEDYLDDEDS(ph)D ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TLSNAEDYLDDEDSD 15 0 Q92882 Q92882 OSTF1 Osteoclast-stimulating factor 1 2 T(0.012)LS(0.988)NAEDYLDDEDS(1)D;T(0.017)LS(0.983)NAEDYLDDEDS(1)D;T(0.001)LS(0.999)NAEDYLDDEDS(1)D;T(0.003)LS(0.997)NAEDYLDDEDS(1)D 327.02 1.35E-68 235482000 631151 646782 647819 827977 821955 435457 526641 326765 473602 TRUE FALSE 591648.3855 694670.4123 663185.5726 849224.2916 757401.9699 561166.3668 447676.0711 367562.3295 394554.7666 1.499534249 1.760643822 1.680845421 2.152360999 1.919637105 1.422277499 1.134636073 0.931587604 1 18.58986604 1.868871822 2.242568525 0.995519986 1.793351286 0.806456601 0.174435999 0.131045608 1.220531941 0.106849471 0.051347853 73.938702 -1.868871822 0.797831301 TLS(ph)PGKNGVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TLSPGKNGVVK 11 1 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 T(0.001)LS(0.999)PGKNGVVK;T(0.001)LS(0.999)PGKNGVVK;T(0.135)LS(0.865)PGKNGVVK 115.06 0.00071057 1078040000 2918860 2432930 2410960 3313040 4549010 1405610 2290440 1731950 2461640 TRUE FALSE 2736173.763 2613066.669 2468149.11 3398058.215 4191749.104 1811386.789 1947009.785 1948187.77 2050776.381 1.334213612 1.274184105 1.203519376 1.656961845 2.043981559 0.883268798 0.949401311 0.94997572 1 20.96773876 TLS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLSPGR 6 0 Q13523 Q13523;REV__F5H6U2 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 T(0.001)LS(0.999)PGR;T(0.012)LS(0.988)PGR 93.195 0.048142 1356680000 1729480 1954660 1978750 1943450 1979070 1715780 2165850 1727570 1786470 TRUE FALSE 1621234.934 2099385.06 2025686.884 1993322.217 1823641.825 2211097.833 1841100.899 1943260.917 1488296.616 1.089322462 1.41059587 1.361077397 1.339331284 1.225321489 1.485656696 1.237052399 1.305694642 1 20.50523065 0.315267042 1.108096208 0.999335866 1.328020887 0.429906557 0.109478055 2.863214778 3.871512768 0.097233248 0.029001423 2.066650522 -0.315267042 0.328685021 TLS(ph)PGRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TLSPGRR 7 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 T(0.002)LS(0.998)PGRR;T(0.004)LS(0.996)PGRR;T(0.001)LS(0.999)PGRR;TLS(1)PGRR;T(0.005)LS(0.995)PGRR;T(0.001)LS(0.999)PGRR 89.029 0.011131 4305320000 3496610 3792350 3920520 3793230 4049400 3399750 4267510 3720640 4515850 TRUE FALSE 3277763.422 4073139.54 4013516.586 3890570.704 3731376.458 4381202.635 3627636.493 4185170.094 3762125.461 0.871253087 1.082669778 1.066821569 1.034141669 0.991826694 1.164555164 0.964251865 1.112448305 1 21.84311653 4.744322895 24.90593018 1.052922947 0.871253004 0.477261695 0.059471707 496.0257698 2143875.526 0.012477538 0.112641603 55503.82262 -4.744322895 -0.181669943 TLS(ph)PSLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLSPSLSR 8 0 A0A1B0GV45 A0A1B0GV45 1 T(0.028)LS(0.899)PS(0.073)LSR 92.445 0.012349 243460000 182340 176880 187850 177960 206320 151270 191150 180390 272190 TRUE FALSE 170927.6649 189976.3792 192305.8907 182526.7549 190116.4595 194939.1933 162488.832 202912.0886 226759.7306 0.753783154 0.83778711 0.848060148 0.804934608 0.838404857 0.859672892 0.716568289 0.894832994 1 17.79080493 0.995491973 24.59404552 1.000000007 0.813361092 0.668393908 0.044173913 73.49410514 400958.1119 0.041983527 0.010495882 9.896735721 -0.995491973 -0.186638915 TLS(ph)PTPSAEGYQDVR ddPTM_SK-BR-3_Pertuzumab_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(1)PTPSAEGYQDVR;TLS(1)PTPSAEGYQDVR;TLS(1)PTPSAEGYQDVR 397.75 5.83E-115 5376450000 1734839 1824580 1679310 1751310 1942470 1424885 2038360 1587100 1551580 TRUE FALSE 1626258.524 1959673.802 1719144.026 1796251.58 1789916.242 1836226.168 1732726.841 1785252.929 1292611.274 1.258118783 1.516058107 1.329977589 1.389630135 1.384728941 1.420555588 1.340485632 1.381121273 1 20.30185705 -2.968499074 0.407519116 0.021084423 1.394543699 0.757580858 0.066842265 54.66318384 1.829839758 46.31685245 0.036588693 0.001075229 2.968499074 1.373459275 TLS(ph)SSAQEDIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TLSSSAQEDIIR 12 0 Q9H788-2;Q9H788 Q9H788-2 SH2D4A SH2 domain-containing protein 4A 1 TLS(0.567)S(0.398)S(0.035)AQEDIIR;TLS(0.876)S(0.12)S(0.003)AQEDIIR;T(0.002)LS(0.497)S(0.497)S(0.004)AQEDIIR 239.39 7.35E-07 94474000 407165 454257 340541 383903 577620 253258 380435 293357 968050 TRUE FALSE 381681.2695 487890.6609 348618.7933 393754.6009 532256.0552 326369.4733 323392.3035 329983.2672 806476.2012 0.473270344 0.604965974 0.432274124 0.488240819 0.659977386 0.404685808 0.40099423 0.409166776 1 19.62127243 -1.269752024 3.592382301 1.001215308 0.48583831 0.778677696 0.086417229 36496267.39 56940596.83 486380.5426 0.020880703 0.053733852 1.269752024 -0.515376998 TLSAS(ph)AAEVAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLSASAAEVAPR 12 0 Q16825 Q16825 PTPN21 Tyrosine-protein phosphatase non-receptor type 21 1 T(0.001)LS(0.014)AS(0.985)AAEVAPR;TLS(0.016)AS(0.984)AAEVAPR 141.88 6.39E-05 396970000 588540 519190 511030 513660 561790 422970 701620 549200 610130 TRUE FALSE 551704.332 557631.3678 523151.8729 526841.3852 517669.2796 545074.5727 596418.5945 617768.8289 508295.3614 1.085401076 1.097061689 1.029228108 1.036486707 1.018441872 1.072357952 1.17337013 1.215373729 1 18.95530754 1.856809297 5.475380273 1.146130208 1.054645935 0.239722865 0.059619098 0.246403844 9.731233201 0.024766878 0.014634467 71.91331308 -1.856809297 -0.091484273 TLSAS(ph)TQDLSPH ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLSASTQDLSPH 12 0 Q6P597;Q6P597-3;Q6P597-2 Q6P597 KLC3 Kinesin light chain 3 1 TLSAS(0.931)T(0.069)QDLSPH 241.22 3.22E-16 1226000000 555120 649490 662030 641540 599950 502900 822370 623810 779600 TRUE FALSE 520376.0301 697578.9154 677733.6642 658003.0025 552832.3471 648079.0661 699063.253 701694.0517 649479.7236 0.801219824 1.074058035 1.043502421 1.013123241 0.851192619 0.997843416 1.07634346 1.080394085 1 19.30892496 1.827323951 5.868722168 1.058698265 0.982436876 0.167897348 0.08657653 0.464167487 23.2361572 0.039286978 0.023158208 67.19298751 -1.827323951 -0.076261389 TLSASTQDLS(ph)PH ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLSASTQDLSPH 12 0 Q6P597;Q6P597-3;Q6P597-2 Q6P597 KLC3 Kinesin light chain 3 1 TLSASTQDLS(1)PH;TLSASTQDLS(1)PH 258.62 3.19E-21 888680000 943780 1129130 1063720 1082930 1116970 668440 834080 726620 901340 TRUE FALSE 884710.4945 1212731.96 1088951.941 1110719.817 1029247.682 861407.7768 709017.4472 817340.1065 750900.5311 1.178199319 1.615036759 1.45019466 1.479183688 1.37068445 1.14716629 0.94422286 1.088479862 1 19.51826229 2.197132088 2.330796315 1.006488059 1.463435206 0.732123905 0.114201358 0.130499248 1.433073411 0.04911249 0.032475291 157.4461654 -2.197132088 0.456947147 TLSDDLDEAAKEFQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLSDDLDEAAKEFQEK 16 1 Q9H0A0;Q9H0A0-2;A0A087WV29 Q9H0A0 NAT10 N-acetyltransferase 10 0 151.62 5.71E-07 25160000 103840 64992 76165 85462 97033 51954 99317 64801 140460 FALSE TRUE 97340.83976 69804.0753 77971.66977 87655.09961 89412.41959 66952.2764 84425.33786 72891.54749 117016.3186 0.831856966 0.596532827 0.666331591 0.749084407 0.764102141 0.572161876 0.721483455 0.622917798 1 16.83635021 -1.047721189 4.149332927 1.00003474 0.681587345 0.591154627 0.080567613 15963150.49 27925710.39 7429.668293 0.017728462 0.089593976 1.047721189 -0.318447395 TLSDPPS(ph)PLPHGPPNK ddPTM_SK-BR-3_Pertuzumab_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(0.002)LS(0.002)DPPS(0.997)PLPHGPPNK;TLSDPPS(1)PLPHGPPNK 111.01 0.00054769 351160000 1215560 979300 1189350 1244050 1551830 881710 1230930 1000380 1490540 TRUE FALSE 1139480.269 1051808.391 1217561.944 1275974.429 1429955.532 1136245.364 1046363.474 1125279.645 1241759.245 0.917633812 0.847030852 0.980513694 1.027553799 1.151556179 0.915028713 0.842646011 0.90619792 1 20.24395406 -3.106000208 9.12320633 0.999680029 0.944878543 0 0.092504788 0 0 0 0.021740775 0.000783429 3.106000208 -0.054801486 TLSDVEDQKELASPVS(ph)PELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLSDVEDQKELASPVSPELR 20 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 TLSDVEDQKELAS(0.001)PVS(0.999)PELR;TLSDVEDQKELASPVS(1)PELR 211.49 1.62E-22 172232000 243360 226330 245230 261590 303750 188444 320170 233400 340670 TRUE FALSE 228128.532 243087.7087 251046.9714 268302.8423 279894.7003 242844.7237 272163.4808 262540.5038 283809.9762 0.803807305 0.856515729 0.884560066 0.945360857 0.986204587 0.855659575 0.958963756 0.925057348 1 18.11456578 7.728999203 0.264864299 0.96519499 9.21E-21 0.618771558 0.038747073 29.02117457 0.460043665 0.043420891 12.37572279 53579567.45 -7.728999203 -0.96519499 TLSGGRPGAGPELELGTAGS(ph)PGGAPPEAAPGDCTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLSGGRPGAGPELELGTAGSPGGAPPEAAPGDCTR 35 1 Q8WYP3-2;Q8WYP3 Q8WYP3-2 RIN2 Ras and Rab interactor 2 1 TLSGGRPGAGPELELGTAGS(1)PGGAPPEAAPGDCTR 149.97 4.05E-11 149730000 45283 58192 53140 64077 67611 50221 68351 48349 42304 TRUE FALSE 42448.81786 62500.59623 54400.50589 65721.3243 62301.10479 64718.98743 58102.40209 54385.47908 35243.18911 1.204454504 1.773409212 1.543575008 1.864795042 1.767748787 1.836354458 1.648613635 1.543148633 1 15.10505686 0.757284057 2.310972576 1.000301634 1.679124343 0.545136606 0.188647837 0.752909787 5.997874705 0.16435847 0.044443369 5.718525436 -0.757284057 0.678822709 TLSKEEETKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLSKEEETKK 10 2 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 117.79 0.00051217 1636800000 1725500 956080 1104500 1030500 1217500 621850 1255200 832440 1837800 FALSE TRUE 1617504.035 1026869.158 1130699.262 1056944.375 1121882.461 801368.0001 1066994.413 936371.9664 1531059.307 1.056460731 0.670691954 0.738507814 0.690335358 0.732749186 0.523407549 0.696899465 0.611584386 1 20.54609874 4.740572424 24.23129387 0.691172905 1.056460927 0.440340816 0.122145575 94.02626316 1132371.753 0.024972754 0.163249943 55026.56761 -4.740572424 0.365288022 TLSNAEDYLDDEDS(ph)D ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TLSNAEDYLDDEDSD 15 0 Q92882 Q92882 OSTF1 Osteoclast-stimulating factor 1 1 TLSNAEDYLDDEDS(1)D;TLSNAEDYLDDEDS(1)D;TLSNAEDYLDDEDS(1)D;TLSNAEDYLDDEDS(1)D;TLSNAEDYLDDEDS(1)D;TLSNAEDYLDDEDS(1)D 516.36 4.93E-278 1503730000 2978640 2946520 2817080 2071640 2502350 3148580 4244700 3796550 4633430 TRUE FALSE 2792212.239 3164683.407 2883902.468 2124801.79 2305825.525 4057523.933 3608246.641 4270557.625 3860080.6 0.723355942 0.819849048 0.747109391 0.550455291 0.597351652 1.051150055 0.934759404 1.106338978 1 21.88019954 2.230494469 24.99999933 1.009944258 0.707531568 0.784415471 0.086913879 97.8454259 303256.9186 0.035210242 0.026458421 170.01783 -2.230494469 -0.30241269 TLSS(ph)PSNRPSGETSVPPPPAVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TLSSPSNRPSGETSVPPPPAVGR 23 1 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3 Q8WWM7 ATXN2L Ataxin-2-like protein 1 TLS(0.03)S(0.946)PS(0.024)NRPSGETSVPPPPAVGR;TLS(0.004)S(0.987)PS(0.009)NRPSGETSVPPPPAVGR;TLS(0.027)S(0.964)PS(0.009)NRPSGETSVPPPPAVGR;TLS(0.028)S(0.956)PS(0.016)NRPSGETSVPPPPAVGR 199.03 1.63E-24 5004800000 1081090 1077530 1131080 1179410 1178390 1026570 1196440 960210 1241340 TRUE FALSE 1013426.507 1157311.442 1157909.752 1209675.657 1085844.003 1322924.094 1017044.929 1080094.332 1034152.335 0.979958632 1.119091843 1.119670394 1.169726758 1.049984578 1.279235225 0.983457558 1.044424787 1 19.98001729 1.612763251 25 1.010451138 1.119707853 0.30930733 0.077700937 0.497955148 2529.58148 0.033286166 0.017721058 40.99805471 -1.612763251 0.109256715 TLSS(ph)SDTELLVLNGSDPVAEVAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLSSSDTELLVLNGSDPVAEVAIR 24 0 Q9Y426-2;Q9Y426-3;Q9Y426 Q9Y426-2 C2CD2 C2 domain-containing protein 2 1 T(0.01)LS(0.061)S(0.379)S(0.275)DT(0.275)ELLVLNGSDPVAEVAIR 205.43 6.28E-25 29801000 36188 39285 35445 31242 43435 39362 46138 38346 44391 TRUE FALSE 33923.05768 42193.70228 36285.77214 32043.72261 40023.79031 50725.17041 39220.03522 43133.58251 36981.85532 0.917289232 1.14092984 0.981177711 0.866471472 1.082254797 1.371623191 1.060521028 1.166344472 1 15.17452998 2.477386965 24.99999986 1.161653635 1.001632675 0.312713877 0.118168144 11.80896234 1111259.186 0.038470022 0.032518969 300.1836023 -2.477386965 -0.16002096 TLSSS(ph)SMDLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 TLSSSSMDLSR 11 0 Q9H0B6;Q9H0B6-2 Q9H0B6 KLC2 Kinesin light chain 2 1 TLSS(0.093)S(0.697)S(0.21)MDLSR;TLSS(0.057)S(0.898)S(0.044)MDLSR;TLSS(0.198)S(0.771)S(0.03)MDLSR;TLSS(0.014)S(0.973)S(0.013)MDLSR;TLSS(0.107)S(0.888)S(0.005)MDLSR;TLSS(0.028)S(0.822)S(0.15)MDLSR;TLSS(0.029)S(0.819)S(0.152)MDLSR 265.75 5.88E-21 1880141000 2383840 3247970 2441250 2451360 3123530 1638071 3563580 2846240 5780490 TRUE FALSE 2234639.71 3488453.078 2499157.603 2514266.048 2878220.554 2110955.506 3029254.262 3201599.329 4815688.876 0.46403324 0.724393367 0.5189616 0.522098938 0.597675769 0.438349644 0.629038615 0.664826863 1 22.19931076 0.739384732 1.66042782 0.999360694 0.563958833 0.74805719 0.081100417 0.458887016 2.03870662 0.073862049 0.021086582 5.487628871 -0.739384732 -0.435401861 TLSVAAAFNEDEDS(ph)EPEEMPPEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK 215.05 4.84E-32 1819364000 2353163 1721570 1949441 1961797 2144436 1484296 2513502 1834416 2409992 TRUE FALSE 2205882.728 1849036.834 1995682.661 2012140.032 1976020.647 1912788.16 2136625.709 2063446.876 2007748.766 1.098684639 0.920950303 0.993990232 1.002187159 0.984197167 0.952702944 1.064189776 1.027741573 1 20.93714732 1.737081912 24.99999999 1.034848451 0.984205436 0.109542664 0.047893434 0.311590171 5077.794106 0.020319125 0.011268006 54.58608061 -1.737081912 -0.050643014 TLTAEEAEEEWERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLTAEEAEEEWERR 14 1 P35269;M0R0R9 P35269 GTF2F1 General transcription factor IIF subunit 1 0 140.1 1.61E-05 70746000 35053 45481 46904 42572 45731 45441 45877 40938 45330 FALSE TRUE 32859.0953 48848.46056 48016.58503 43664.46959 42139.47173 58559.07903 38998.16975 46049.19942 37764.13016 0.870113919 1.293514781 1.271486589 1.1562419 1.115859721 1.550653458 1.032677559 1.219389914 1 15.20472894 -0.28024541 7.546475479 1.000000007 1.205683148 0.093635784 0.177728634 0 0 0.153669553 0.036220261 0.524510987 0.28024541 0.205683141 TLTAVHDAILEDLVFPSEIVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLTAVHDAILEDLVFPSEIVGK 22 0 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ; 192.18 1.16E-17 4241800000 2378990 2190610 2444580 2188530 2483040 1970220 2948800 2147210 2631440 FALSE TRUE 2230093.263 2352805.044 2502566.592 2244691.385 2288032.055 2538990.53 2506654.815 2415293.895 2192235.664 1.017268946 1.07324458 1.141559109 1.023927957 1.043698035 1.158174083 1.143423974 1.101749203 1 21.06397146 2.248497481 24.99991026 1.117692058 1.071247044 0.066461347 0.055041382 396.0359296 996378.238 0.018647725 0.015420108 177.2137767 -2.248497481 -0.046445014 TLTDEELADWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLTDEELADWK 11 0 P40763;P40763-2;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 141.95 8.81E-05 57277000 141290 114760 130170 121150 143110 101020 152260 125600 175340 FALSE TRUE 132446.9111 123256.9498 133257.6939 124258.9141 131870.7179 130182.8341 129430.0265 141281.4365 146074.6213 0.906707202 0.843794416 0.912257672 0.85065368 0.902762689 0.891207747 0.886054165 0.967186738 1 17.15634602 1.148448808 3.031637738 0.999474319 0.882421932 0.77597033 0.022409525 0.097048226 1.608989884 0.018951103 0.005127985 14.07501311 -1.148448808 -0.117052387 TLTDEELADWKR ddPTM_SK-BR-3_Pertuzumab_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 ; 126.65 0.00045495 334480000 379910 378100 389360 363770 479550 316590 488030 385290 578540 FALSE TRUE 356132.1113 406094.9174 398595.8031 373104.9541 441888.0774 407984.3936 414854.4321 433394.3046 481977.9365 0.738897124 0.842559144 0.827000103 0.774112103 0.916822211 0.846479398 0.860733243 0.899199469 1 18.87860758 -5 0.083782013 1.558260306 0.681233523 0.71919696 0.038640382 126.2468722 0.744262191 12.70318531 1.066973816 1.00E-05 5 -0.877026783 TLTDEVNS(ph)PDSDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TLTDEVNSPDSDRR 14 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 TLTDEVNS(1)PDSDRR;TLTDEVNS(1)PDSDRR;TLTDEVNS(1)PDSDRR;TLTDEVNS(1)PDSDRR 220.1 2.92E-12 4661540000 2475150 2424390 2612630 2535290 2806690 2434670 2988790 2476460 2965000 TRUE FALSE 2320234.78 2603894.358 2674602.817 2600349.834 2586263.889 3137519.705 2540648.686 2785651.482 2470122.345 0.939319781 1.054156027 1.082781516 1.052721068 1.047018539 1.270187977 1.02855176 1.127738263 1 21.23615107 5.941744433 0.845305853 1.094922501 1.26E-12 0.275859403 0.074110023 18.74979017 2.140325004 0.021899523 30.47778961 874469.0298 -5.941744433 -1.094922501 TLTDEVNSPDS(ph)DRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLTDEVNSPDSDRR 14 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 TLTDEVNS(0.042)PDS(0.958)DRR;TLTDEVNSPDS(1)DRR 287.54 5.27E-34 2627500000 1764570 1754110 1753770 1624750 1829710 1660410 1936540 1576080 1959560 TRUE FALSE 1654128.714 1883986.13 1795370.253 1666443.836 1686011.957 2139743.412 1646173.805 1772857.057 1632496.777 1.01325083 1.154051975 1.099769554 1.020794564 1.032781186 1.310718308 1.008377982 1.085978902 1 20.63864871 1.036744687 1.771173459 1.006291018 1.102487832 0.084805205 0.090676771 0.792416163 5.080554458 0.078870788 0.022649715 10.88290121 -1.036744687 0.096196813 TLTELILDAQEHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLTELILDAQEHVK 14 0 E9PKP7;P17480-2;P17480 E9PKP7 UBTF Nucleolar transcription factor 1 0 145.29 8.62E-06 46289000 147050 123930 156440 131830 135180 99965 156490 114870 123080 FALSE TRUE 137846.403 133105.9061 160150.8307 135212.981 124563.5081 128823.2727 133025.7773 129211.7724 102537.1529 1.344355671 1.298123679 1.561880998 1.318673058 1.214813408 1.256357029 1.297342217 1.260145896 1 16.64578722 3.001436038 24.99971142 1.237367649 1.406985518 0.402565098 0.105984535 49.82228443 867314.1558 0.029130665 0.034573107 1003.312074 -3.001436038 0.169617869 TLTEPSVDFNHS(ph)DDFTPISTVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLTEPSVDFNHSDDFTPISTVQK 23 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 T(0.031)LT(0.17)EPS(0.031)VDFNHS(0.768)DDFTPISTVQK 145.34 3.18E-10 0 57771 57822 53661 55750 67927 42408 66379 50740 94369 TRUE FALSE 54155.21623 62103.20104 54933.86426 57180.63938 62592.28742 54650.50116 56426.08518 57075.00069 78618.20425 0.688838123 0.789934108 0.698742292 0.727320599 0.79615514 0.695137999 0.717722895 0.725976906 1 16.26257579 -0.988579748 5.475887878 1.000000776 0.731833427 0.843090016 0.036601332 3.21E-07 5.95E-08 0.032859864 0.007745122 0.10266449 0.988579748 -0.268167349 TLTGDVKT(ph)SPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLTGDVKTSPPR 12 1 Q9H8T0;Q9H8T0-2;H3BSX7;H3BNB8;H3BVH0;H3BRV2;H3BM79 Q9H8T0 AKTIP AKT-interacting protein 1 TLT(0.033)GDVKT(0.497)S(0.47)PPR 102.5 0.014947 49153000 194180 168200 185650 189030 211600 124980 225270 157980 310940 TRUE FALSE 182026.6204 180653.703 190053.7057 193880.8298 194981.7896 161059.6971 191492.8548 177704.1508 259042.1053 0.702691249 0.697391271 0.733678818 0.748452958 0.752703076 0.621751035 0.739234475 0.686004889 1 17.98282709 -1.089205446 4.748169431 1.000013654 0.711688954 0.848622962 0.038456242 5.11E-06 9.81E-07 0.034261157 0.00807505 0.081431897 1.089205446 -0.288324699 TLTGDVKTS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLTGDVKTSPPR 12 1 Q9H8T0;Q9H8T0-2;H3BSX7;H3BNB8;H3BVH0;H3BRV2;H3BM79 Q9H8T0 AKTIP AKT-interacting protein 1 TLT(0.001)GDVKT(0.193)S(0.807)PPR 51.03 0.096067 632250000 554880 492360 533260 576560 632970 379580 664150 441040 912540 TRUE FALSE 520151.0513 528814.8467 545909.179 591355.5057 583259.0895 489158.584 564566.8732 496104.8148 760231.1788 0.684201156 0.69559742 0.718083123 0.777862737 0.767212798 0.643433994 0.742625255 0.652570992 1 19.53607867 -0.992571217 4.689193032 1.000001843 0.712572048 0.808642706 0.044291077 2.34E-06 5.02E-07 0.039889354 0.009401833 0.101725254 0.992571217 -0.287429795 TLTPDQWAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TLTPDQWAR 9 0 Q9H3K6;A0A087WZT3 Q9H3K6 BOLA2 BolA-like protein 2 0 ;;; 173.73 0.00012845 1314400000 1541890 1898790 1654030 1638570 1961980 1319140 1819670 1639470 1938370 FALSE TRUE 1445385.857 2039378.387 1693264.373 1680618.48 1807894.005 1699954.304 1546827.376 1844161.438 1614843.525 0.895062484 1.262895356 1.048562506 1.040731473 1.119547484 1.052705279 0.957880657 1.142006275 1 20.62296295 2.578583295 0.951473962 1.026884448 1.105501913 0 0.10319374 1.466958101 2.731004897 0.06117403 0.04818231 378.9512071 -2.578583295 0.078617465 TLTPGGHAEHDGKPFCHKPCYATLFGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLTPGGHAEHDGKPFCHKPCYATLFGPK 28 2 P52943;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 114.83 0.00012595 616000000 1430000 1526000 1588500 1533500 1895400 1293600 2330400 1693100 2102500 FALSE TRUE 1340498.853 1638986.628 1626179.97 1572852.206 1746542.93 1667041.32 1980978.154 1904487.262 1751579.167 0.765308744 0.935719412 0.928407919 0.897962385 0.997124744 0.951736211 1.130966953 1.087297279 1 20.74022477 2.29067885 1.201597213 1.081488369 0.894104998 0.595838251 0.064098323 0.313139314 0.883061177 0.038333033 0.022950024 195.2894806 -2.29067885 -0.187383371 TLTPGGHAEHDGQPYCHKPCYGILFGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TLTPGGHAEHDGQPYCHKPCYGILFGPK 28 1 P52943;H0YFA4;H0YHD8;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 ; 101.86 0.00038953 3414500000 2707100 3426000 3428200 3759700 4071700 3400700 5601200 3715000 4398100 FALSE TRUE 2537667.443 3679664.605 3509518.523 3856180.267 3751925.106 4382426.884 4761352.059 4178825.928 3664028.697 0.692589402 1.004267409 0.957830523 1.052442703 1.023989007 1.196067839 1.299485471 1.140500327 1 21.80499937 5.687463992 0.391085661 1.182378503 1.13E-13 0.595026846 0.102287024 8.024622604 0.547593926 0.080163085 5.15745105 486927.1521 -5.687463992 -1.182378503 TLTTGSSAYLWKPPS(ph)R ddPTM_SK-BR-3_Pertuzumab_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 206.11 1.26E-11 1769950000 1867270 1395740 1527020 1694440 1864120 1090030 2148190 1406830 1740890 TRUE FALSE 1750400.904 1499082.042 1563241.636 1737922.199 1717719.535 1404703.966 1826088.852 1582475.822 1450324.212 1.20690318 1.033618572 1.077856677 1.1982991 1.184369343 0.968544794 1.259090096 1.091118668 1 20.46794401 TLTVHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLTVHEK 7 0 Q2TAY7;Q2TAY7-2 Q2TAY7 SMU1 "WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed" 0 87.323 0.019427 128130000 225490 188960 222860 224120 217820 168650 253310 192460 272280 FALSE TRUE 211376.9834 202950.795 228146.3444 229871.2986 200713.2958 217336.5172 215328.5171 216489.0547 226834.709 0.931854672 0.894707851 1.00578234 1.013386794 0.884843844 0.958127256 0.949274994 0.95439122 1 17.79128188 -4.649483443 0.006210396 2.009373997 4.35E-08 0.141623681 0.040440942 75412.88322 37.59940878 6645.046171 5564.415091 2.24E-05 4.649483443 -2.009373953 TLVGICSEHQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLVGICSEHQSR 12 0 Q9H3U1;A0A1W2PNX8;Q9H3U1-2 Q9H3U1;Q9H3U1-2 UNC45A Protein unc-45 homolog A 0 122.97 0.00023254 0 227220 375450 317150 369600 444060 250170 421120 325230 543820 FALSE TRUE 212998.7058 403248.7087 324672.9478 379084.5617 409185.3189 322390.0178 357976.9655 365835.6814 453052.9288 0.470140887 0.890069754 0.716633592 0.836733498 0.903173322 0.7115946 0.790143806 0.807489938 1 18.78932008 -4.999998501 0.029611457 2.116351093 5.89E-07 0.362687404 0.113905768 1984.99935 4.426618275 245.2616184 100.603459 1.00E-05 4.999998501 -2.116350504 TLVLSNLSYSATEETLQEVFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TLVLSNLSYSATEETLQEVFEK 22 0 P19338;H7BY16 P19338 NCL Nucleolin 0 160.57 1.84E-11 88750000 133750 119470 117470 122950 133930 92216 135700 100390 124910 FALSE TRUE 125378.8263 128315.6831 120256.4439 126105.1052 123411.678 118837.2622 115353.0448 112923.9125 104061.7141 1.204850673 1.233072934 1.155626207 1.211829983 1.185947004 1.141988322 1.1085061 1.08516291 1 16.66707985 1.345113614 0.586177226 0.997958398 1.209279421 0.923102344 0.019276008 0.185379549 0.156192441 0.019292369 0.009616585 22.13673744 -1.345113614 0.211321023 TLVS(ph)PNKAETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TLVSPNKAETK 11 1 O75363;G3XAF7;O75363-2;H0Y542;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 TLVS(1)PNKAETK;T(0.001)LVS(0.999)PNKAETK;TLVS(1)PNKAETK;TLVS(1)PNKAETK 202.25 2.46E-08 2488000000 2783160 1349990 1907440 1847220 1982090 1409570 2572890 1486420 2935900 TRUE FALSE 2608966.984 1449944.664 1952685.378 1894622.793 1826424.647 1816489.977 2187109.03 1672002.809 2445879.323 1.066678539 0.592811203 0.798357204 0.774618263 0.746735389 0.742673589 0.894201529 0.683599879 1 21.22192179 -4.99995301 0.403712887 4.705045898 0.771814861 0.203749892 0.126940155 1114.294873 7.685303992 3643.511111 0.070637196 1.00E-05 4.99995301 -3.933231037 TLVVHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 TLVVHEK 7 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;;;;; 100.45 0.0097841 10184790000 21403260 20886340 20421900 20520720 21812360 15026620 22244470 18294530 24045790 FALSE TRUE 20063668.16 22432786.35 20906317.11 21047316.42 20099305.23 19364561.26 18909118.23 20578642.34 20032392.31 1.001561264 1.11982563 1.043625584 1.050664149 1.003340236 0.966662442 0.943927113 1.027268338 1 24.25583139 2.721120473 1.932686645 0.975440117 1.067244607 0.431630194 0.036509236 0.238586078 1.764031417 0.012981525 0.012647495 526.1632032 -2.721120473 0.09180449 TMCPLLSMKPGEYSYFS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TMCPLLSMKPGEYSYFSPR 19 1 C9J470;E9PHA2;Q15003;Q15003-2 C9J470 NCAPH Condensin complex subunit 2 1 TMCPLLSMKPGEYSYFS(1)PR;TMCPLLSMKPGEYSYFS(1)PR 158.94 2.08E-11 568310000 984170 860650 925000 855040 1007880 717510 1140340 927580 1406470 TRUE FALSE 922572.5565 924373.4215 946941.4368 876981.774 928725.1704 924643.4892 969356.6034 1043390.405 1171721.071 0.787365338 0.788902278 0.808162847 0.748456092 0.792616258 0.789132766 0.827292969 0.890476779 1 20.16019775 1.003851917 1.344394475 0.999583068 0.786575488 0.95605329 0.015004862 0.083718401 0.309628746 0.013857378 0.004203753 10.08908815 -1.003851917 -0.213007579 TMFAQVES(ph)DDEEAKNEPEWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TMFAQVESDDEEAKNEPEWK 20 1 Q9NW82 Q9NW82 WDR70 WD repeat-containing protein 70 1 TMFAQVES(1)DDEEAKNEPEWK;T(0.013)MFAQVES(0.987)DDEEAKNEPEWK;TMFAQVES(1)DDEEAKNEPEWK;TMFAQVES(1)DDEEAKNEPEWK;TMFAQVES(1)DDEEAKNEPEWK 276.11 9.42E-45 1279590000 2607120 1054640 1542380 1441590 1537980 1016330 1960080 1117100 1795930 TRUE FALSE 2443945.013 1132726.643 1578965.982 1478583.64 1417193.255 1309727.972 1666184.2 1256572.394 1496177.681 1.633459077 0.757080297 1.055333202 0.988240674 0.947209194 0.875382643 1.113627226 0.839855059 1 20.51285008 4.74895058 24.97867906 0.954204029 1.633459458 0.811631204 0.103866295 611.1391921 1469220.582 0.02361323 0.335748491 56098.41355 -4.74895058 0.679255428 TMGYSVTAPEDTRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TMGYSVTAPEDTRR 14 1 O15305;H3BRM0;H3BV55 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 ;;;; 230.96 1.15E-12 1328410000 644748 747947 695307 701573 772567 584392 770375 563569 818830 FALSE TRUE 604394.3736 803325.7741 711800.0104 719576.5509 711892.7042 753096.4836 654864.4206 633931.8302 682161.9832 0.885998324 1.177617331 1.043447199 1.054847043 1.043583081 1.103984834 0.959983753 0.929298093 1 19.37975483 1.662709756 6.371390114 0.957453427 1.064784565 0.224465383 0.074472798 0.156002014 12.92061645 0.035289543 0.017684698 45.99490816 -1.662709756 0.107331138 TMHHLLLEVEVIEGTLQCPESGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 TMHHLLLEVEVIEGTLQCPESGR 23 0 F5GYQ2;Q9UI30;Q9UI30-2 F5GYQ2 TRMT112 Multifunctional methyltransferase subunit TRM112-like protein 0 ;;;;;;;;; 278.02 4.67E-52 1197207500 385339.3 464001.8 426304.9 417592 470236 384399 470285 390316 379025 FALSE TRUE 361221.6011 498356.9761 436417.0535 428308.1177 433305.5614 495368.7511 399770.1302 439047.8118 315763.2789 1.143963295 1.578261341 1.382101982 1.356421555 1.372248106 1.568797844 1.266043764 1.390433407 1 18.26848388 0.139793191 0.80234125 0.992571487 1.410317388 0.45980305 0.128298614 3.132581916 2.266544569 0.176323297 0.038916411 1.379727088 -0.139793191 0.417745901 TMIIS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TMIISPER 8 0 O75533;B4DGZ4;A0A494C1M2;O75533-2 O75533 SF3B1 Splicing factor 3B subunit 1 1 T(0.001)MIIS(0.999)PER;TMIIS(1)PER;TMIIS(1)PER;TMIIS(1)PER;T(0.001)MIIS(0.999)PER 146.17 0.00058492 1352310000 1585028 1525914 1543517 1569179 1498662 1497623 1799290 1426353 1142528 TRUE FALSE 1485823.927 1638894.26 1580129.952 1609446.79 1380963.132 1929962.448 1529503.168 1604436.312 951832.6958 1.561013751 1.721830178 1.660092114 1.690892524 1.450846496 2.027627814 1.606903372 1.685628492 1 19.86034849 0.091289272 2.139924046 0.999977964 1.682879081 0.674646045 0.147365057 36.8609673 85.01699294 0.125577752 0.033950978 1.233926444 -0.091289272 0.682901116 TMIIS(ph)PERLDPFADGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 TMIISPERLDPFADGGK 17 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 TMIIS(1)PERLDPFADGGK;TMIIS(1)PERLDPFADGGK;TMIIS(1)PERLDPFADGGK;T(0.003)MIIS(0.997)PERLDPFADGGK;T(0.166)MIIS(0.834)PERLDPFADGGK;T(0.011)MIIS(0.989)PERLDPFADGGK;T(0.29)MIIS(0.71)PERLDPFADGGK;T(0.002)MIIS(0.998)PERLDPFADGGK;T(0.004)MIIS(0.996)PERLDPFADGGK 222.72 1.98E-15 1827017000 5452460 4017450 4748800 4851240 4884960 3803700 5332670 4046050 3763910 TRUE FALSE 5111200.262 4314906.178 4861443.779 4975731.032 4501314.947 4901766.442 4533085.64 4551208.249 3135689.105 1.630008617 1.376063134 1.550358985 1.586806238 1.435510599 1.563218252 1.445642565 1.451422031 1 21.5803511 0.137169454 0.908208081 0.99428724 1.508523272 0.820046243 0.075116056 1.724500026 1.487300892 0.092801694 0.021892208 1.371416763 -0.137169454 0.514236033 TMIIS(ph)PERLDPFADGGKT(ph)PDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TMIISPERLDPFADGGKTPDPK 22 2 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 T(0.148)MIIS(0.852)PERLDPFADGGKT(1)PDPK;T(0.126)MIIS(0.874)PERLDPFADGGKT(1)PDPK 109.48 0.00073424 157555000 611610 321040 363900 378680 494100 183297 639220 378180 832060 TRUE FALSE 573330.4219 344810.1356 372531.8798 388397.5699 455295.3791 236211.8683 543374.8952 425396.6055 693183.8107 0.827097248 0.497429586 0.537421495 0.560309638 0.656817675 0.340763683 0.783882842 0.613685142 1 19.40287844 0.581131293 0.935422211 0.999192833 0.568811724 0.447412667 0.138552461 1.120593329 1.559776027 0.120274054 0.039076853 3.811810419 -0.581131293 -0.430381109 TMIIS(ph)PERLDPFADGGKTPDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TMIISPERLDPFADGGKTPDPK 22 2 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 T(0.056)MIIS(0.944)PERLDPFADGGKTPDPK;T(0.002)MIIS(0.998)PERLDPFADGGKTPDPK 114.74 0.00011396 186467000 525140 371230 443430 470050 556360 304070 569150 332890 650200 TRUE FALSE 492272.4248 398716.2555 453948.369 482112.2788 512665.7298 391850.0728 483811.2412 374452.0493 541677.4195 0.90879259 0.736076936 0.838041891 0.890035769 0.946441021 0.723401159 0.893172253 0.691282368 1 19.04707443 -2.363142322 2.343934438 2.230904964 0.826627713 0.281138618 0.086190273 4436066.475 739409.4406 29015366.09 0.018901505 0.004333688 2.363142322 -1.404277251 TMKDDETFEISIPFDEAPHLDPQIFYS(ph)LSPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TMKDDETFEISIPFDEAPHLDPQIFYSLSPSR 32 1 K7EMP7;Q9BWC9;K7ES29 K7EMP7 CCDC106 Coiled-coil domain-containing protein 106 1 TMKDDETFEISIPFDEAPHLDPQIFY(0.001)S(0.756)LS(0.186)PS(0.056)R;TMKDDETFEISIPFDEAPHLDPQIFY(0.008)S(0.475)LS(0.475)PS(0.041)R 67.279 0.0025515 82530000 136374 99042.2 115008 108096 127370 115022 145213 110353 142792 TRUE FALSE 127838.5948 106375.3875 117736.0441 110869.9264 117366.874 148226.9842 123439.6587 124130.815 118959.0927 1.074643324 0.894218215 0.989718746 0.932000437 0.986615409 1.246033244 1.037664763 1.043474796 1 16.86010602 2.452205929 24.99947438 1.089459138 0.962108392 0.304349503 0.079062291 219.9178302 220659.2882 0.024876215 0.020813597 283.2734871 -2.452205929 -0.127350745 TMKDDETFEISIPFDEAPHLDPQIFYS(ph)LSPSRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TMKDDETFEISIPFDEAPHLDPQIFYSLSPSRR 33 2 K7EMP7;Q9BWC9;K7ES29 K7EMP7 CCDC106 Coiled-coil domain-containing protein 106 1 TMKDDETFEISIPFDEAPHLDPQIFYS(0.946)LS(0.053)PS(0.001)RR 231.53 2.73E-37 75152000 94373 78636 83497 80637 95143 72717 115840 86705 147650 TRUE FALSE 88466.36239 84458.29126 85477.58827 82706.28194 87670.85257 93709.21744 98470.86741 97530.31011 123006.2611 0.719202109 0.686617823 0.694904369 0.67237457 0.712734878 0.761824777 0.800535408 0.79288899 1 16.90837223 0.764513014 0.520827438 1.00893272 0.685313829 0.952486851 0.020746104 0.247138092 0.147749277 0.0262412 0.010726272 5.814508552 -0.764513014 -0.323618891 TMLELINQLDGFDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TMLELINQLDGFDPR 15 0 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 78.096 0.055672 83447000 85913 100670 93344 87422 100070 82114 104030 84854 91100 FALSE TRUE 80535.85869 108123.7115 95558.16376 89665.39653 92210.90586 105818.9788 88431.66727 95448.20869 75894.82147 1.061150908 1.424652031 1.259086745 1.181442881 1.214982842 1.394284574 1.165187104 1.257637963 1 16.21171383 -0.549719749 0.504042934 0.949710552 1.271221283 0.324063502 0.107300595 10.55476347 2.234539781 1.005395998 0.048221755 0.282020222 0.549719749 0.321510731 TMLELLNQLDGFDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TMLELLNQLDGFDSR 15 0 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 178.58 1.64E-06 175773000 302170 358170 337740 379850 331860 315670 387360 316420 342570 FALSE TRUE 283257.7191 384689.2795 345751.3523 389597.5941 305797.0543 406798.8045 329278.9641 355925.7335 285392.8539 0.992518611 1.347928913 1.211492676 1.365127363 1.071495134 1.425399406 1.153774383 1.247143117 1 18.12258969 -1.133941791 4.075603293 0.999930667 1.238390587 0.219053838 0.133041464 7.21E-05 1.53E-05 0.109189965 0.025728735 0.073461232 1.133941791 0.238459921 TMLITHMQDLQEVTQDLHYENFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TMLITHMQDLQEVTQDLHYENFR 23 0 Q15019-2;Q15019-3;Q15019;B5MCX3 Q15019-2 2-Sep Septin-2 0 ; 321.13 7.12E-74 536240000 364080 423040 410510 376150 433220 327150 451610 362780 434250 FALSE TRUE 341292.8827 454362.3218 420247.4911 385802.6458 399196.6487 421592.8942 383895.273 408073.8816 361770.8696 0.943395147 1.255939491 1.161639939 1.066428168 1.10345161 1.165358876 1.061155845 1.127989885 1 18.46471672 0.219532296 0.39768349 0.982948368 1.142974746 0.096059471 0.084040958 5.715686538 1.429432531 0.259738471 0.058479399 1.657800615 -0.219532296 0.160026378 TMLTHSSKLQSGLMMSEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TMLTHSSKLQSGLMMSEQK 19 1 F5GX61 F5GX61 RAB6A 0 50.053 0.088164 739560000 44260 161150 122630 149370 130890 244510 59015 96489 33721 FALSE TRUE 41489.84561 173081.7137 125538.8415 153203.0871 120610.4274 315096.0677 50166.24862 108535.864 28092.74725 1.476888153 6.161081795 4.468727831 5.453474724 4.293294148 11.21627817 1.785736659 3.863483449 1 14.7779101 4.750851644 23.75900324 5.014414819 1.47688379 0.118863523 2.761904569 1887.033991 3647569.528 0.593640704 9.64689271 56344.51489 -4.750851644 -3.537531029 TMPGGNDHEIFTDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TMPGGNDHEIFTDPR 15 0 O15305;H3BRM0;H3BV55 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 ;; 75.961 0.030275 2047180000 2361980 2620910 2522290 2490680 2585210 2178610 2826830 2186750 2566830 FALSE TRUE 2214147.888 2814964.903 2582119.91 2554595.066 2382178.035 2807539.34 2402973.085 2459770.551 2138409.491 1.035418098 1.316382534 1.207495534 1.194623891 1.113995259 1.312910064 1.1237198 1.150280413 1 21.02810671 0.808761303 1.071986524 1.000866097 1.208030249 0.308931392 0.085818836 0.80000824 1.744719543 0.074185126 0.023646252 6.438153142 -0.808761303 0.207164152 TMPPTKPQPPARPPPPVLPANR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TMPPTKPQPPARPPPPVLPANR 22 2 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 119.87 2.95E-05 245280000 106680 104010 90539 98614 110630 81911 108070 88793 109130 FALSE TRUE 100003.0892 111711.0086 92686.62784 101144.6022 101941.5661 105557.376 91865.90677 99879.00151 90915.49799 1.099956459 1.228734496 1.019481055 1.112512217 1.121278201 1.161049307 1.01045376 1.09859159 1 16.47223863 2.351448067 0.016747716 2.01E-07 2.187456848 0.296955163 0.05939288 736.4164381 6.613236076 417.9280023 444.3204713 224.619816 -2.351448067 2.187456647 TMS(ph)EVGGSVEDLIAK ddPTM_SK-BR-3_Pertuzumab_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(0.114)MS(0.885)EVGGS(0.001)VEDLIAK 68.809 0.040779 0 24560 19993 20007 21978 20445 11407 27490 15911 18315 TRUE FALSE 23022.83344 21473.30252 20481.57549 22541.99269 18839.33217 14700.01572 23368.1297 17897.52337 15258.10818 1.508891743 1.407337153 1.342340429 1.477377957 1.234709569 0.963423221 1.531522088 1.172984433 1 13.89728848 -1.698077759 0.052566208 6.03E-10 2.102773881 0.419011023 0.153558248 247.9626512 1.996992757 57.69102018 26.46255296 0.020041132 1.698077759 2.102773881 TNEGVIEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TNEGVIEFR 9 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;; 162.64 0.00014802 1553530000 2312450 2696350 2772050 2620580 2863550 2298550 3042710 2399170 3025850 FALSE TRUE 2167717.882 2895990.56 2837804.335 2687828.519 2638658.334 2962104.071 2586483.883 2698711.656 2520816.087 0.859927027 1.148830561 1.125748264 1.066253319 1.046747657 1.175057588 1.026050213 1.070570626 1 21.26545944 0.86478787 1.338915813 1.001575379 1.082719857 0.023206083 0.087480635 1.632598028 5.65169138 0.076034611 0.022857163 7.324666745 -0.86478787 0.081144479 TNEQMHQLVAAYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TNEQMHQLVAAYK 13 0 P08133;P08133-2;E5RJF5;E5RK63 P08133 ANXA6 Annexin A6;Annexin 0 112.42 0.00038864 0 948480 682190 733140 605380 1007100 406290 938120 875550 1479500 FALSE TRUE 889116.3299 732700.0574 750530.427 620915.0757 928006.4284 523579.3274 797457.6151 984864.3448 1232561.892 0.721356336 0.594452954 0.608919059 0.503759754 0.752908584 0.424789482 0.646991944 0.799038451 1 20.23322866 1.032664386 2.494812771 0.996575918 0.598895815 0.658877825 0.093922212 0.141144472 1.904634533 0.078233917 0.021244159 10.78113255 -1.032664386 -0.397680103 TNHRLS(ph)LPMPASGTSLSAAIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 TNHRLSLPMPASGTSLSAAIHR 22 1 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 1 T(0.197)NHRLS(0.803)LPMPASGTSLSAAIHR;T(0.249)NHRLS(0.751)LPMPASGTSLSAAIHR;T(0.147)NHRLS(0.853)LPMPASGTSLSAAIHR;T(0.356)NHRLS(0.644)LPMPASGTSLSAAIHR;T(0.37)NHRLS(0.63)LPMPASGTSLSAAIHR;T(0.297)NHRLS(0.703)LPMPASGTSLSAAIHR;T(0.026)NHRLS(0.974)LPMPASGTSLSAAIHR;T(0.352)NHRLS(0.648)LPMPASGTSLSAAIHR 272.12 1.47E-45 17864740000 1534236 1978133 1652996 1914736 2275270 1263090 2086570 1647124 1540380 TRUE FALSE 1438210.907 2124596.026 1692205.846 1963871.367 2096579.472 1627723.578 1773708.199 1852771.057 1283280.627 1.120729852 1.655597366 1.318656115 1.530352229 1.633765389 1.268408129 1.382167051 1.443777003 1 20.29140526 -0.599376344 0.520693196 0.917111775 1.44816478 0.384153977 0.164273952 10.56795135 2.273164916 1.685802279 0.069157734 0.251549614 0.599376344 0.531053004 TNIIPVLEDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TNIIPVLEDAR 11 0 A6NHQ2 A6NHQ2 FBLL1 rRNA/tRNA 2-O-methyltransferase fibrillarin-like protein 1 0 ; 111.63 0.0038024 144729000 211860 222370 221960 211710 261010 170525 248200 201750 374060 FALSE TRUE 198600.0608 238834.5062 227224.996 217142.837 240511.3275 219752.7993 210984.7142 226938.9316 311626.9695 0.63730062 0.766411542 0.729157032 0.696803737 0.771792403 0.705179015 0.677042538 0.728239061 1 18.24946057 0.934579235 21.26883545 1 0.717205192 0.837629503 0.039584653 2173.414707 706596.8532 0.036578907 0.009144727 8.601599841 -0.934579235 -0.282794808 TNILQYASTRPPTLS(ph)PIPHIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TNILQYASTRPPTLSPIPHIPR 22 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 TNILQYASTRPPT(0.001)LS(0.999)PIPHIPR;TNILQYASTRPPT(0.003)LS(0.997)PIPHIPR 267.38 5.26E-38 1943330000 1080510 882290 921580 861170 902810 959420 1313000 984030 748230 TRUE FALSE 1012882.808 947615.6696 943440.3128 883269.0802 831906.9444 1236388.979 1116127.839 1106888.312 623345.5792 1.624913758 1.520209176 1.513510875 1.416981382 1.334583852 1.983472764 1.790544245 1.775721764 1 19.24967268 2.255675453 24.99989136 1.722665351 1.488579062 0.036341974 0.268066838 414.5621433 605555.8522 0.082563672 0.068917292 180.1670853 -2.255675453 -0.23408629 TNIVTASVDAINFHDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TNIVTASVDAINFHDK 16 0 O00154-6;O00154-4;O00154-7;O00154;O00154-5;K7EKP8;O00154-2;O00154-3 O00154-6 ACOT7 Cytosolic acyl coenzyme A thioester hydrolase 0 ; 309.45 1.28E-57 1556120000 3198600 2364300 2919200 2796500 2806900 2314200 3455100 2638300 2693400 FALSE TRUE 2998405.336 2539355.232 2988444.803 2868262.924 2586457.396 2982271.972 2937039.831 2967697.563 2243854.14 1.336274619 1.131693539 1.33183559 1.278275122 1.152685173 1.329084596 1.308926359 1.322589338 1 21.09754747 -1.183593468 6.961394183 0.999999444 1.268377319 0.575220836 0.07383964 6.14E-07 7.20E-08 0.0688322 0.016223872 0.065524925 1.183593468 0.268377875 TNKPS(ph)TPTTATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TNKPSTPTTATR 12 1 A0A2R8Y7K2;A0A2R8Y481;A0A2R8YGN6;A0A2R8Y4I8;A0A2U3TZR0;Q9UBP0-4;Q9UBP0-3;Q9UBP0-2;Q9UBP0;A0A2R8Y5N9;A0A2R8YFW8;A0A2R8YCL5;A0A2R8YEA0 A0A2R8Y7K2 SPAST Spastin 1 T(0.002)NKPS(0.593)T(0.401)PT(0.003)T(0.001)ATR 65.374 0.036895 84094000 224420 143050 183680 184880 196740 138950 242490 171460 242440 TRUE FALSE 210373.9528 153641.5708 188036.9763 189624.3338 181288.834 179062.6093 206130.8757 192867.1584 201975.1978 1.041583101 0.760695237 0.930990431 0.938849601 0.897579683 0.886557415 1.020575189 0.954905159 1 17.62381862 1.753638505 13.11385827 0.990306777 0.895391928 0.216141682 0.070725975 0.244766649 203.0223492 0.031402521 0.017279311 56.70723934 -1.753638505 -0.094914849 TNKPST(ph)PTTATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TNKPSTPTTATR 12 1 A0A2R8Y7K2;A0A2R8Y481;A0A2R8YGN6;A0A2R8Y4I8;A0A2U3TZR0;Q9UBP0-4;Q9UBP0-3;Q9UBP0-2;Q9UBP0;A0A2R8Y5N9;A0A2R8YFW8;A0A2R8YCL5;A0A2R8YEA0 A0A2R8Y7K2 SPAST Spastin 1 TNKPS(0.146)T(0.768)PT(0.085)T(0.001)ATR 123.02 0.00056281 203220000 542170 354390 431920 428910 457300 331150 586430 409680 576960 TRUE FALSE 508236.5475 380629.4043 442165.3464 439916.5567 421385.5027 426747.6292 498500.2656 460829.4498 480661.6487 1.057368627 0.791886362 0.919909769 0.91523124 0.87667802 0.88783374 1.037112628 0.958739794 1 18.87466217 1.749316232 24.99999927 0.998720075 0.895154634 0.270247356 0.067874586 3.053047498 7109.87683 0.028781115 0.015960638 56.14566528 -1.749316232 -0.103565441 TNKS(ph)PEAKPLPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TNKSPEAKPLPGK 13 2 P46087-2;P46087;P46087-4;P46087-3;F5H359;F5GWB7;F5H709;F5H5X6 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 T(0.047)NKS(0.953)PEAKPLPGK;T(0.023)NKS(0.977)PEAKPLPGK 89.866 0.0037847 1060860000 5181700 1886060 3082560 2760160 2609160 2075490 3735900 2218660 2615340 TRUE FALSE 4857386.647 2025705.845 3155679.779 2830990.379 2404247.098 2674650.27 3175736.477 2495664.585 2178822.858 2.229362809 0.929724891 1.448341597 1.299321038 1.103461481 1.227566647 1.457546888 1.145418764 1 21.05511748 4.749499621 24.97535271 1.233135831 2.229363386 0.773934076 0.17384721 761.8209285 1739315.511 0.039861324 0.599916335 56169.3788 -4.749499621 0.996227554 TNKS(ph)PEAKPLPGKLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TNKSPEAKPLPGKLPK 16 3 P46087-2;P46087;P46087-4;P46087-3;F5H359;F5GWB7;F5H709;F5H5X6 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 T(0.057)NKS(0.943)PEAKPLPGKLPK 97.618 0.0021497 1225000000 2368600 909430 1415500 1409300 1483900 1031900 1910400 1044100 2082200 TRUE FALSE 2220353.554 976765.1435 1449076.328 1445465.024 1367360.48 1329792.779 1623953.255 1174458.183 1734667.368 1.27998808 0.563084982 0.835362649 0.833280807 0.788255146 0.76659814 0.936175595 0.677050946 1 20.72622761 -1.029602014 4.51710606 1.000006459 0.815183447 0.062310116 0.187716409 21724218.99 4951688.921 1642.700204 0.038978522 0.093410992 1.029602014 -0.184823012 TNLDESDVQPVKEQLAQAMFDHIPVGVGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TNLDESDVQPVKEQLAQAMFDHIPVGVGSK 30 1 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ; 204.14 9.77E-26 387970000 1066420 817430 914580 876420 1049970 669670 1191670 813450 1480550 FALSE TRUE 999674.6758 877953.3677 936274.2695 898910.421 967509.5916 862992.8578 1012990.146 915011.0231 1233436.64 0.810479147 0.71179446 0.759077717 0.728785242 0.784401533 0.699665333 0.82127457 0.741838691 1 20.23425218 -1.642841212 0.423981208 1.178648222 0.746601786 0.781509267 0.040185639 13.74875674 1.133491543 2.5777075 0.020539194 0.022759294 1.642841212 -0.432046436 TNLEFLQEQFNSIAAHVLHCTDSGFGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TNLEFLQEQFNSIAAHVLHCTDSGFGAR 28 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 0 ; 184.25 6.42E-18 369640000 201741 252010 245330 265650 301330 245060 316590 245340 238790 FALSE TRUE 189114.3909 270669.0826 251149.3435 272467.0287 277664.7573 315804.8438 269120.2686 275971.2391 198934.4064 0.950636918 1.360594618 1.262473134 1.369632502 1.395760353 1.587482274 1.352809067 1.387247405 1 17.60193329 4.738757273 23.81763324 1.358389584 0.950636797 0.405948142 0.146256349 7.433338893 898974.1369 0.031350521 0.182267216 54797.06183 -4.738757273 -0.407752786 TNLQPLESTQS(ph)QDF ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TNLQPLESTQSQDF 14 0 Q9Y248 Q9Y248 GINS2 DNA replication complex GINS protein PSF2 1 TNLQPLESTQS(1)QDF 154.51 6.40E-06 33695000 105900 126010 113050 107830 117320 80979 142400 105070 116800 TRUE FALSE 99271.90804 135339.9115 115731.5994 110597.1004 108106.1604 104356.3227 121048.442 118188.2208 97305.32544 1.020210431 1.390878772 1.189365524 1.136598638 1.110999423 1.072462604 1.244006342 1.21461205 1 16.57023114 -5 0.18414417 0.232491226 1.227325751 0.161697328 0.105523711 208.3169247 2.021328796 58.92777582 0.308309679 1.00E-05 5 0.994834525 TNLSGRQS(ph)PSFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TNLSGRQSPSFK 12 1 Q6IN85-2;Q6IN85;Q6IN85-4 Q6IN85-2 SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3A 1 TNLS(0.001)GRQS(0.986)PS(0.013)FK 66.436 0.035162 288890000 269190 382030 297000 358650 511650 172050 475480 278110 1645800 TRUE FALSE 252341.8784 410315.8987 304044.9803 367853.5662 471467.0729 221718.042 404186.1881 312832.6457 1371105.348 0.184042662 0.299259207 0.221751728 0.26828979 0.343859116 0.161707517 0.294788572 0.228160911 1 20.38690799 -1.664473922 2.699938035 1.092587841 0.254452578 0.94847144 0.054913494 7197764.134 6366640.789 4598577.607 0.012382772 0.021653399 1.664473922 -0.838135264 TNNVSEHEDTDKYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TNNVSEHEDTDKYR 14 1 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ;;;; 203.04 9.37E-09 4150820000 3011600 2871370 3057080 3345830 3145640 2172912 3815360 2789560 3366010 FALSE TRUE 2823109.332 3083969.222 3129595.381 3431689.662 2898594.123 2800196.42 3243282.188 3137842.707 2804201.186 1.006742792 1.099767463 1.116038106 1.223767282 1.033661257 0.998571869 1.156579708 1.118979167 1 21.41915843 TNPPTQKPPS(ph)PPMSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 TNPPTQKPPSPPMSGR 16 1 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 1 TNPPTQKPPS(0.999)PPMS(0.001)GR;TNPPTQKPPS(0.992)PPMS(0.008)GR;TNPPTQKPPS(0.973)PPMS(0.027)GR;TNPPT(0.003)QKPPS(0.913)PPMS(0.083)GR;TNPPTQKPPS(0.997)PPMS(0.003)GR;TNPPT(0.011)QKPPS(0.919)PPMS(0.07)GR;TNPPTQKPPS(0.906)PPMS(0.093)GR;TNPPT(0.001)QKPPS(0.907)PPMS(0.092)GR;TNPPT(0.007)QKPPS(0.969)PPMS(0.024)GR;TNPPTQKPPS(0.946)PPMS(0.054)GR;TNPPTQKPPS(0.98)PPMS(0.02)GR;TNPPT(0.002)QKPPS(0.968)PPMS(0.03)GR 157.14 5.78E-08 19683900000 7254190 4274850 5057330 4869140 5311630 3507240 6047230 4254990 6789370 TRUE FALSE 6800163.197 4591364.342 5177292.256 4994090.376 4894476.006 4519723.253 5140504.001 4786234.868 5656180.286 1.202253615 0.811742927 0.915333669 0.882943988 0.86533239 0.799076943 0.908829588 0.846195599 1 22.43139667 4.745081709 24.99748261 0.872847585 1.202253763 0.759943702 0.057069302 322.3623369 1235688.406 0.011851514 0.113847544 55600.88556 -4.745081709 0.329406178 TNPS(ph)PTNPFSSDLQK ddPTM_SK-BR-3_Pertuzumab_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(1)PTNPFSSDLQK;TNPS(1)PTNPFSSDLQK;TNPS(0.993)PT(0.007)NPFSSDLQK;TNPS(0.986)PT(0.014)NPFSSDLQK 340.32 2.58E-69 1089030000 1484920 997740 1121720 1001920 1264900 966380 1588850 1176170 2608140 TRUE FALSE 1391981.508 1071613.708 1148327.728 1027630.963 1165559.856 1245358.218 1350616.693 1323017.414 2172824.585 0.640632252 0.493189241 0.528495368 0.472947044 0.536426118 0.573151752 0.621594906 0.608892877 1 21.05114028 0.130596034 0.58807563 1.025712288 0.52415364 0.89796926 0.047496583 0.915037435 0.406893093 0.098614115 0.018679929 1.350815495 -0.130596034 -0.501558648 TNRGS(ph)QLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TNRGSQLHK 9 1 P42356;P42356-2 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 T(0.006)NRGS(0.994)QLHK;T(0.078)NRGS(0.922)QLHK 85.973 0.01485 55076000 97320 77174 91328 90214 102666 66215 104039 88812 139115 TRUE FALSE 91228.91492 82888.04326 93494.34329 92529.04397 94603.02649 85330.19559 88439.3178 99900.3737 115895.8078 0.7871632 0.715194491 0.806710312 0.798381285 0.816276519 0.736266455 0.763093329 0.86198436 1 16.82246886 0.948637725 3.051358652 0.99959046 0.771991754 0.842825967 0.031309197 0.105521712 2.406817153 0.030469103 0.007993523 8.88459684 -0.948637725 -0.227598706 TNS(ph)DSALHQSTMTPTQPESFSSGSQDVHQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TNSDSALHQSTMTPTQPESFSSGSQDVHQK 30 0 M0QXN6;M0QX46;Q6UUV9;Q6UUV9-2;Q6UUV9-3 M0QXN6 CRTC1 CREB-regulated transcription coactivator 1 1 T(0.236)NS(0.615)DS(0.15)ALHQSTMTPTQPESFSSGSQDVHQK 245.99 1.16E-45 294500000 100590 188470 176830 166640 209930 120180 235180 170050 251620 TRUE FALSE 94294.25146 202424.5149 181024.4911 170916.2645 193442.9446 154874.015 199916.9423 191281.1168 209622.9965 0.449827801 0.965659867 0.863571718 0.815350736 0.922813565 0.738821683 0.95369757 0.912500632 1 17.67743747 4.744575487 24.95507692 0.890291854 0.449827603 0.771112844 0.076420441 294.2922511 1220953.338 0.016592466 0.152001933 55536.11389 -4.744575487 -0.44046425 TNS(ph)MGSATGPLPGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TNSMGSATGPLPGTK 15 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 T(0.001)NS(0.999)MGSATGPLPGTK;TNS(0.965)MGS(0.035)ATGPLPGTK 281.36 2.02E-27 157820000 829690 556590 613650 778720 931120 611210 1092850 653230 883620 TRUE FALSE 777761.1839 597800.5027 628206.0678 798703.2736 857993.5912 787656.4048 928987.288 734787.2034 736138.1136 1.056542474 0.812076554 0.853380712 1.084991062 1.165533444 1.069984545 1.261974174 0.998164869 1 19.48961694 3.176995111 5.052385266 1.124219511 0.879013099 0.416661181 0.10119339 0.136129597 6.867964263 0.027574884 0.033767797 1503.125046 -3.176995111 -0.245206412 TNS(ph)PGFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TNSPGFQK 8 0 A0A087X0H9;Q5T8P6-3;Q5T8P6-2;Q5T8P6;Q5T8P6-5;Q5T8P6-4 A0A087X0H9 RBM26 RNA-binding protein 26 1 TNS(1)PGFQK;TNS(1)PGFQK;TNS(1)PGFQK;TNS(1)PGFQK 151.07 0.00050243 732780000 2771540 1756350 2036900 1982790 2214920 1602900 2722570 1828930 2777860 TRUE FALSE 2598074.259 1886391.981 2085216.23 2033671.748 2040969.118 2065631.209 2314345.904 2057275.936 2314217.22 1.122657906 0.815131771 0.901046026 0.87877306 0.881926338 0.892583112 1.000055606 0.888972702 1 21.14209286 1.758340293 25 0.961346032 0.899445617 0.043729293 0.085600458 19.7854825 25030.33237 0.036030922 0.019981118 57.32450237 -1.758340293 -0.061900415 TNS(ph)SSSSPVVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TNSSSSSPVVLK 12 0 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 1 TNS(0.684)S(0.265)S(0.042)S(0.005)S(0.005)PVVLK;TNS(0.851)S(0.072)S(0.072)S(0.002)S(0.002)PVVLK 215.96 4.22E-11 408610000 850780 581250 678280 706240 751390 518070 945320 613530 900920 TRUE FALSE 797531.1985 624286.3548 694369.1219 724363.3141 692378.8604 667628.3988 803578.0419 690130.571 750550.6318 1.0625948 0.83177114 0.925146276 0.965109192 0.922494541 0.889518136 1.070651343 0.919499021 1 19.51758987 1.755696812 25 1.002117604 0.92108672 0.146140996 0.068703888 9.155670322 13371.87351 0.029338671 0.016269676 56.97663705 -1.755696812 -0.081030883 TNS(ph)TGGSSGSSVGGGSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.993)T(0.007)GGSSGSSVGGGSGK;TNS(0.536)T(0.404)GGS(0.052)S(0.006)GS(0.002)SVGGGSGK;TNS(0.97)T(0.03)GGSSGSSVGGGSGK;TNS(0.5)T(0.5)GGSSGSSVGGGSGK 289.21 4.17E-49 966430000 2033060 1291720 1481960 1619010 1455080 974600 1718870 1134960 1536060 TRUE FALSE 1905814.404 1387360.293 1517112.791 1660556.538 1340803.886 1255951.199 1461141.401 1276662.254 1279681.663 1.48928789 1.084144857 1.185539213 1.297632518 1.047763616 0.981455963 1.141800686 0.9976405 1 20.28735354 2.720571827 23.20741107 1.046259286 1.221048082 0.48694305 0.113360169 343.5582033 443224.3623 0.035175528 0.033247698 525.4989186 -2.720571827 0.174788797 TNSGISSASGGSTEPT(ph)TPDSERPAQALLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TNSGISSASGGSTEPTTPDSERPAQALLR 29 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 TNS(0.001)GIS(0.022)S(0.022)AS(0.031)GGS(0.164)T(0.031)EPT(0.623)T(0.105)PDSERPAQALLR;TNSGISSASGGST(0.001)EPT(0.615)T(0.384)PDSERPAQALLR 202.68 4.64E-25 1088400000 150393 169669 172128 201170 229275 121181 190988 160004 211798 TRUE FALSE 140980.1706 182231.4693 176210.9574 206332.3628 211268.6664 156163.9875 162351.1224 179980.8516 176447.5455 0.798991962 1.032779848 0.998659159 1.169369413 1.197345453 0.885044827 0.920109837 1.020024683 1 17.42887984 4.740400018 24.26381557 1.021355696 0.798991855 0.35829198 0.095925501 138.763097 1830219.181 0.024363726 0.157227516 55004.72762 -4.740400018 -0.222363841 TNSGISSASGGSTEPTT(ph)PDSERPAQALLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TNSGISSASGGSTEPTTPDSERPAQALLR 29 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 TNSGISSAS(0.002)GGS(0.007)T(0.017)EPT(0.248)T(0.724)PDS(0.001)ERPAQALLR;TNSGISSASGGSTEPT(0.045)T(0.955)PDSERPAQALLR 173.2 2.40E-12 1027000000 155614 176141 185168 225500 205585 170019 216568 168701 240197 TRUE FALSE 145874.3975 189182.6629 189560.2724 231286.7118 189439.1834 219100.7253 184095.6389 189763.6912 200106.569 0.728983552 0.945409558 0.9472966 1.155817687 0.946691477 1.094920204 0.919987984 0.948313152 1 17.610409 5.380741336 1.136846231 1.000212789 4.92E-11 0.569801561 0.073674571 4.376891946 1.668097306 0.019829929 7.443604687 240293.1197 -5.380741336 -1.000212788 TNSMSSSGLGS(ph)PNR ddPTM_SK-BR-3_Pertuzumab_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 324.25 1.51E-56 4066390000 3435630 3589290 3331320 3441470 3813900 2485010 3659530 3056600 3240220 TRUE FALSE 3220600.051 3855044.766 3410340.484 3529783.947 3514371.679 3202392.046 3110817.45 3438223.238 2699406.349 1.193077156 1.428108357 1.263366845 1.307614894 1.301905391 1.186331968 1.152407992 1.273696063 1 21.36421074 0.73567151 0.310257974 0.958200004 1.349339495 0.574623421 0.07388718 1.556518709 0.381558232 0.205083222 0.092125289 5.4409096 -0.73567151 0.391139491 TNSS(ph)DSERS(ph)PDLGHSTQIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TNSSDSERSPDLGHSTQIPR 20 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 2 T(0.079)NS(0.416)S(0.506)DSERS(1)PDLGHSTQIPR 111.4 9.59E-05 378740000 485120 252390 274410 302950 344560 203040 317000 192580 272050 TRUE FALSE 454757.2052 271077.2182 280919.1348 310724.2099 317499.6475 261654.3519 269468.7929 216624.0369 226643.0975 2.006490426 1.196053271 1.239478007 1.37098466 1.400879405 1.154477479 1.188956539 0.955793666 1 17.7900627 4.739126001 24.96550362 1.209011201 2.006490674 0.771388659 0.139573106 21.46152379 947437.8222 0.031750885 0.188590344 54843.60588 -4.739126001 0.797479473 TNSTFNQVVLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TNSTFNQVVLKR 12 1 J3QQ67;Q07020;F8VYV2;G3V203;H0YHA7;Q07020-2;A0A075B7A0 J3QQ67 RPL18 60S ribosomal protein L18 0 ; 180.61 3.08E-05 1076780000 859110 947370 825300 938240 1156050 641420 1154660 826970 1477860 FALSE TRUE 805339.8387 1017514.261 844876.5057 962316.8268 1065258.496 826587.5414 981529.4523 930219.0249 1231195.619 0.654112008 0.826444023 0.686224425 0.78161164 0.86522278 0.671369788 0.797216492 0.755541208 1 20.23162857 -5 0.336245866 3.55114064 0.749187914 0.567689917 0.067596216 265.2593894 2.257521917 484.9702604 0.04947702 1.00E-05 5 -2.801952727 TNT(ph)PVKEDWNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TNTPVKEDWNVR 12 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 1 T(0.085)NT(0.915)PVKEDWNVR;TNT(1)PVKEDWNVR;T(0.001)NT(0.999)PVKEDWNVR;TNT(1)PVKEDWNVR 210.37 7.16E-08 2834670000 6327960 2710200 3945260 3340920 3826700 2899880 5100890 3312210 5446780 TRUE FALSE 5931904.279 2910866.028 4038843.43 3426653.663 3526166.418 3737028.28 4336058.899 3725746.71 4537677.23 1.307255668 0.641488118 0.89006847 0.755155885 0.777086214 0.823555333 0.955567943 0.821069133 1 22.11352256 -1.14109788 6.433912933 1.000000441 0.851802917 0.039785113 0.176561819 9.90E-07 1.32E-07 0.151465477 0.035700649 0.072260693 1.14109788 -0.148197524 TNTMNGSKS(ph)PVISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 TNTMNGSKSPVISR 14 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 TNTMNGS(0.058)KS(0.942)PVISR;TNTMNGS(0.346)KS(0.654)PVISR;TNTMNGS(0.013)KS(0.987)PVISR;TNTMNGS(0.005)KS(0.995)PVISR;TNTMNGS(0.195)KS(0.805)PVIS(0.001)R;TNTMNGS(0.009)KS(0.991)PVISR;TNTMNGS(0.031)KS(0.968)PVISR;TNTMNGSKS(1)PVISR;TNTMNGS(0.01)KS(0.99)PVISR;TNTMNGS(0.005)KS(0.994)PVISR;TNTMNGS(0.183)KS(0.817)PVISR 223.65 2.08E-12 15005768000 15433750 10964820 13151500 12764210 13449750 9203160 15886700 10799120 15697960 TRUE FALSE 14467779.14 11776666.68 13463459.79 13091761.24 12393460.89 11859962.89 13504636.82 12147413.9 13077869.06 1.106279553 0.900503486 1.029484217 1.001062266 0.94766669 0.906872735 1.032632821 0.928852693 1 23.64062415 4.759359463 24.27165878 0.971214839 1.106279751 0.452466904 0.047581526 3324.140455 3879085.415 0.010693739 0.45735687 57459.18513 -4.759359463 0.135064912 TNTMNGSKS(ph)PVISRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TNTMNGSKSPVISRPK 16 2 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2 A0A0U1RRM6 ENAH Protein enabled homolog 1 TNT(0.001)MNGS(0.054)KS(0.94)PVIS(0.005)RPK 132.01 3.26E-05 592940000 354460 221600 268910 298040 338520 196860 344190 280620 423470 TRUE FALSE 332274.9813 238007.4946 275288.6722 305688.211 311934.0047 253690.2862 292581.9048 315656.0247 352790.1213 0.941848882 0.674643308 0.78031854 0.866487445 0.884191438 0.71909691 0.829337011 0.894741677 1 18.42845064 1.027419881 2.139086732 0.998415941 0.79560265 0.363415379 0.07851542 0.296492247 2.870547699 0.072520713 0.020158562 10.65172341 -1.027419881 -0.202813291 TNTMNGSKSPVIS(ph)RPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TNTMNGSKSPVISRPK 16 2 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2 A0A0U1RRM6 ENAH Protein enabled homolog 1 TNTMNGS(0.002)KS(0.035)PVIS(0.963)RPK 78.088 0.017415 525870000 299900 146490 202580 239150 280960 143940 300780 233740 326110 TRUE FALSE 281129.7943 157336.272 207385.2933 245286.9939 258894.5349 185493.1413 255680.8313 262922.9535 271680.1342 1.034782301 0.579123212 0.763343606 0.902852152 0.952938777 0.682762992 0.94110978 0.967766577 1 18.05154955 1.728213468 0.512604232 1.010161395 0.755040865 0.136793099 0.137689813 1.215911811 0.749166108 0.135056639 0.08945222 53.48271779 -1.728213468 -0.255120531 TNTNVNCPIECFMPLDVQADREDS(ph)RE ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TNTNVNCPIECFMPLDVQADREDSRE 26 2 H0Y7Z1;P02751-12;P02751-10;P02751-6;P02751-5;P02751-9;P02751-14;P02751-13;P02751-8;P02751-17;P02751-3;P02751-11;P02751-1;P02751-7;P02751 H0Y7Z1 FN1 Fibronectin;Anastellin;Ugl-Y1;Ugl-Y2;Ugl-Y3 1 TNTNVNCPIECFMPLDVQADREDS(1)RE;TNTNVNCPIECFMPLDVQADREDS(1)RE;TNTNVNCPIECFMPLDVQADREDS(1)RE;TNTNVNCPIECFMPLDVQADREDS(1)RE;TNTNVNCPIECFMPLDVQADREDS(1)RE 247.09 1.42E-45 529643000 165262 165002 149981 160488.8 181463 172702 197885 134918 235530 TRUE FALSE 154918.5464 177218.9198 153538.6201 164607.2143 167211.628 222558.2638 168213.9813 151762.8093 196218.5214 0.789520507 0.903171212 0.782487907 0.838897435 0.852170462 1.13423678 0.857278814 0.773437738 1 17.5821017 2.449853747 24.99087337 0.936973901 0.834513677 0.234300911 0.097436279 338.070706 309842.4698 0.032339879 0.027058025 281.7433974 -2.449853747 -0.102460224 TNTPADVFIVFTDNETFAGGVHPAIALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TNTPADVFIVFTDNETFAGGVHPAIALR 28 0 P10155-3;P10155-5;P10155-4;P10155;G5E9R9 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 107.19 0.00084153 7285100 21400 16966 19188 15185 20248 11960 17877 16675 26936 FALSE TRUE 20060.6122 18222.18029 19643.14842 15574.67281 18657.80376 15412.65785 15196.50981 18756.91046 22440.20759 0.893958406 0.812032608 0.875355023 0.694052083 0.831445239 0.686832231 0.677200055 0.835861718 1 14.4537984 3.256420993 24.93255276 0.760493976 0.852203301 0.063551489 0.099302659 400.0197037 558412.1803 0.024907985 0.033655457 1804.766384 -3.256420993 0.091709325 TNTPVKEDWNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TNTPVKEDWNVR 12 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 ;;; 158.58 5.47E-05 1638870000 2113600 2027240 2092650 2157060 2663460 1678990 2718700 2039400 3205770 FALSE TRUE 1981313.549 2177338.959 2142288.646 2212413.811 2454282.595 2163687.157 2311056.174 2294023.579 2670706.277 0.741868758 0.815267099 0.802143113 0.828400274 0.918963877 0.810155417 0.865335209 0.858957647 1 21.34878989 -5 0.080201653 1.562502407 0.658811957 0.752890988 0.035074379 121.0176061 0.687390542 12.05363859 1.121803096 1.00E-05 5 -0.90369045 TNVLGHLQQGGAPTPFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TNVLGHLQQGGAPTPFDR 18 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ; 236.96 7.78E-24 1854990000 1285280 1348910 1236180 1300810 1337850 875550 1452850 1091360 1130310 FALSE TRUE 1204836.619 1448784.7 1265502.773 1334190.987 1232780.658 1128307.072 1235008.63 1227618.698 941653.9589 1.279489783 1.538553187 1.343914887 1.416859107 1.309165268 1.19821837 1.311531289 1.303683468 1 19.84483747 -1.81372465 0.154410852 0.53073691 1.510826561 0.654701999 0.081588485 21.4425718 0.512645421 4.140304106 0.444308168 0.015355903 1.81372465 0.980089651 TNYNDRYDEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TNYNDRYDEIR 11 1 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 ;;;; 193.28 9.31E-07 13864200000 7488890 8182640 8104340 8272510 8240740 6452840 8432970 7076420 7578380 FALSE TRUE 7020173.743 8788491.18 8296578.772 8484796.612 7593545.522 8315670.155 7168524.436 7959926.614 6313499.42 1.111930686 1.392015837 1.314101455 1.343913422 1.202747481 1.317125353 1.135428066 1.260778862 1 22.59000845 0.680005435 0.49661283 0.99042179 1.310623243 0.452186195 0.089417138 1.166944736 0.605238048 0.115407713 0.044424832 4.786360817 -0.680005435 0.320201453 TNYNDRYDEIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 TNYNDRYDEIRR 12 2 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 ;;;;;; 161.76 3.63E-05 14718760000 2802960 3835870 3367950 3511300 4321920 2412950 3784340 3045260 5591510 FALSE TRUE 2627527.737 4119881.806 3447839.364 3601405.903 3982493.837 3109529.494 3216913.349 3425467.414 4658250.858 0.564058875 0.88442678 0.740157512 0.773124079 0.854933313 0.667531567 0.690583965 0.735354861 1 22.1513569 -0.772893431 4.239491927 1.000001486 0.748891122 0.444956381 0.091069976 103945272.8 244689733.4 2688.900779 0.020880568 0.168696693 0.772893431 -0.251110364 TPAAAAAMNLAS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 TPAAAAAMNLASPR 14 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR 148.44 1.85E-06 2696773000 915686 939852 1007913 1024111 1105448 900744 1169253 920483 1246254 TRUE FALSE 858374.8478 1009439.62 1031821.172 1050391.422 1018630.573 1160774.17 993934.3675 1035407.329 1038246.156 0.82675466 0.972254618 0.993811695 1.011697867 0.981107002 1.118014416 0.957320537 0.997265747 1 19.9857171 5.604804805 1.087850808 1.009344 1.46E-10 0.641980328 0.042233775 5.829357318 1.391999636 0.011308529 10.62382923 402536.0727 -5.604804805 -1.009344 TPAAPAS(ph)PAAVPSEGSGGSTTGWR ddPTM_SK-BR-3_Pertuzumab_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 375.45 6.09E-119 7933320000 2091890 2224920 2204980 2195510 2346010 1936580 2542480 2093040 2354450 TRUE FALSE 1960962.339 2389655.392 2257283.167 2251850.504 2161763.838 2495639.208 2161258.727 2354360.651 1961477.085 0.999737572 1.218293811 1.15080782 1.14803814 1.102110167 1.272326466 1.101852652 1.20029985 1 20.90350905 -0.629635702 7.469408733 0.999998134 1.15558261 0.281428145 0.074293007 0 0 0.062201976 0.014661146 0.234619604 0.629635702 0.155584476 TPADTGFAFPDWAYKPES(ph)SPGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TPADTGFAFPDWAYKPESSPGSR 23 1 P50548 P50548 ERF ETS domain-containing transcription factor ERF 1 TPADTGFAFPDWAYKPES(0.5)S(0.5)PGSR;TPADTGFAFPDWAYKPES(0.63)S(0.37)PGSR;TPADTGFAFPDWAYKPES(0.638)S(0.286)PGS(0.076)R 221.29 1.09E-32 457580000 849030 696360 846950 963020 1003810 566040 505760 330330 478000 TRUE FALSE 795890.7279 747919.219 867040.054 987732.7236 924974.8118 729446.5591 429925.9832 371572.4276 398218.712 1.998627146 1.878161916 2.177296113 2.480377476 2.322780884 1.831773689 1.079622756 0.933086308 1 18.60320149 1.799569789 2.782319016 0.968619438 2.1444502 0.910807385 0.166818555 0.078962259 1.160583308 0.108207375 0.052340607 63.03326294 -1.799569789 1.175830762 TPAEGRDS(ph)PTREPGALPCACGQLPDLEDELSLLDPLPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TPAEGRDSPTREPGALPCACGQLPDLEDELSLLDPLPR 38 2 Q96RY5 Q96RY5 CRAMP1L Protein cramped-like 1 T(0.007)PAEGRDS(0.989)PT(0.004)REPGALPCACGQLPDLEDELSLLDPLPR;TPAEGRDS(0.995)PT(0.005)REPGALPCACGQLPDLEDELSLLDPLPR;T(0.003)PAEGRDS(0.992)PT(0.005)REPGALPCACGQLPDLEDELSLLDPLPR;T(0.055)PAEGRDS(0.778)PT(0.167)REPGALPCACGQLPDLEDELSLLDPLPR 295.66 1.37E-92 247436000 48508.4 51977.9 50694 51336.1 58986 42673.4 57940 45295.8 60701 TRUE FALSE 45472.34583 55826.3978 51896.48562 52653.47124 54353.4775 54992.51784 49252.43489 50951.08034 50569.61096 0.899202999 1.103951499 1.026238578 1.041207758 1.074824909 1.087461754 0.973953209 1.007543451 1 15.62598306 1.697511162 10.20257271 0.993618161 1.046314316 0.114613945 0.056308165 0.200459954 36.96954082 0.02439182 0.013188774 49.83232633 -1.697511162 0.052696155 TPAGNFVTLEEGKGDLEEYGQDLLHTVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPAGNFVTLEEGKGDLEEYGQDLLHTVFK 29 1 P43490 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 119.42 4.02E-05 209220000 311600 191940 222570 207370 270440 174140 305810 199160 293960 FALSE TRUE 292097.5122 206151.4373 227849.4655 212691.4653 249200.7333 224411.3911 259956.6295 224025.5644 244896.1769 1.192740188 0.841791162 0.930392088 0.86849647 1.017577066 0.916353182 1.061497295 0.914777712 1 17.90181073 2.710548937 24.85120855 0.986604928 0.934267166 0 0.103571202 2086.436689 1851029.087 0.030882572 0.0291229 513.5100369 -2.710548937 -0.052337762 TPALAALAALGAPGPAPTAAS(ph)SP ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPALAALAALGAPGPAPTAASSP 23 0 Q86V15 Q86V15 CASZ1 Zinc finger protein castor homolog 1 1 TPALAALAALGAPGPAPT(0.057)AAS(0.472)S(0.472)P;TPALAALAALGAPGPAPTAAS(0.5)S(0.5)P 222.29 1.52E-34 76693000 615470 614610 560230 504810 504500 506230 672060 468920 720740 TRUE FALSE 576948.8313 660116.3639 573518.9202 517764.2792 464878.6051 652370.383 571290.8421 527465.6942 600443.8378 0.960870601 1.099380695 0.955158308 0.862302595 0.774224958 1.08648027 0.951447589 0.878459668 1 19.19566979 3.677086528 3.990892035 0.928056531 1.037407866 0.184579373 0.088913781 0.321689157 10.61799048 0.023566044 0.039253277 4754.299407 -3.677086528 0.109351335 TPALVFEHVNNTDFK ddPTM_SK-BR-3_Pertuzumab_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 ; 210.37 1.92E-09 1659390000 1782620 1452290 1519880 1483880 1693940 1100110 1960920 1546270 2113490 FALSE TRUE 1671048.996 1559819.063 1555932.271 1521958.873 1560904.785 1417693.898 1666898.25 1739325.213 1760734.865 0.949063388 0.885890939 0.883683456 0.864388445 0.886507569 0.805171708 0.946705994 0.987840502 1 20.74774625 1.51568968 5.362490028 0.98677811 0.87971554 0.657582669 0.034830432 0.087865641 5.556742644 0.019214028 0.008428779 32.78609404 -1.51568968 -0.107062571 TPAPPEPGS(ph)PAPGEGPSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TPAPPEPGSPAPGEGPSGR 19 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 TPAPPEPGS(1)PAPGEGPSGR;TPAPPEPGS(1)PAPGEGPSGR;TPAPPEPGS(1)PAPGEGPSGR;TPAPPEPGS(1)PAPGEGPSGR 272.23 2.52E-39 1540490000 1436980 1208040 1385790 1303990 1403660 1308460 1576830 1265440 1324290 TRUE FALSE 1347041.987 1297484.539 1418661.593 1337452.591 1293422.206 1686191.161 1340398.98 1423432.97 1103257.444 1.220967957 1.176048751 1.285884452 1.212276064 1.172366625 1.528375059 1.214946691 1.29020926 1 20.07333805 -0.832113067 5.186097381 0.999999771 1.261211005 0.394384371 0.10226695 2.52E-07 5.72E-08 0.092540742 0.021812043 0.147192924 0.832113067 0.261211234 TPARPFGS(ph)VGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPARPFGSVGR 11 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 TPARPFGS(1)VGR;TPARPFGS(1)VGR 108.71 0.001227 816460000 258450 251502 297750 268710 283820 200185 318830 237850 217706 TRUE FALSE 242274.0758 270123.4698 304812.7706 275605.5535 261529.9221 257975.1598 271024.4014 267546.0961 181369.4622 1.335804126 1.489354749 1.680617933 1.519580806 1.441973301 1.422373737 1.494322132 1.475144122 1 17.46857204 -1.633500021 0.424089216 0.63957286 1.516063649 0.741922581 0.08871968 17.66835524 1.465548932 6.699853263 0.054294218 0.023254124 1.633500021 0.876490789 TPASTPVSGT(ph)PQAS(ph)PMIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TPASTPVSGTPQASPMIER 19 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 2 TPASTPVS(0.001)GT(0.999)PQAS(1)PMIER;TPASTPVS(0.001)GT(0.999)PQAS(1)PMIER;TPASTPVS(0.016)GT(0.984)PQAS(1)PMIER;TPASTPVSGT(1)PQAS(1)PMIER;TPASTPVS(0.047)GT(0.953)PQAS(1)PMIER 336.94 1.41E-74 2944900000 2498590 2842070 2733880 2861900 3065680 2547860 3231130 2682050 2772890 TRUE FALSE 2342207.712 3052499.82 2798728.925 2935341.199 2824913.859 3283385.821 2746652.053 3016909.846 2310076.745 1.013909047 1.321384593 1.211530712 1.27066826 1.222865805 1.421331922 1.188987361 1.30597819 1 21.13950935 -1.131645101 4.953995274 0.999987431 1.251853165 0.345617026 0.105344342 1.27E-05 2.22E-06 0.088350482 0.02082337 0.073850748 1.131645101 0.251865734 TPASTPVSGT(ph)PQASPMIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TPASTPVSGTPQASPMIER 19 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 TPASTPVS(0.015)GT(0.985)PQASPMIER;TPASTPVS(0.001)GT(0.903)PQAS(0.096)PMIER;TPASTPVS(0.02)GT(0.98)PQASPMIER 254.02 7.13E-30 2613130000 412570 471600 472450 505010 535170 489170 493590 425910 458580 TRUE FALSE 386747.9802 506517.7547 483656.7371 517969.4116 493139.907 630385.438 419580.7618 479085.801 382040.0355 1.012323171 1.325823756 1.265984432 1.355798774 1.290806882 1.650050726 1.098263854 1.254019884 1 18.54336431 0.904513115 1.491879911 1.00728544 1.304360846 0.225522406 0.166184481 0.709471866 3.137451981 0.143524965 0.04219765 8.02625799 -0.904513115 0.297075406 TPASTPVSGTPQAS(ph)PMIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 TPASTPVSGTPQASPMIER 19 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 TPASTPVSGT(0.003)PQAS(0.997)PMIER;TPASTPVSGT(0.001)PQAS(0.999)PMIER;TPASTPVSGTPQAS(1)PMIER;TPASTPVSGTPQAS(1)PMIER;TPASTPVSGTPQAS(1)PMIER;TPASTPVSGT(0.001)PQAS(0.999)PMIER;TPASTPVSGT(0.001)PQAS(0.999)PMIER 363.37 3.85E-92 3485830000 1324904 1349740 1395821 1512797 1688226 1357404 1440394 1246715 1300068 TRUE FALSE 1241980.624 1449676.154 1428930.533 1551617.932 1555639.54 1749264.499 1224420.292 1402370.112 1083078.252 1.146713657 1.338477761 1.319323447 1.432600026 1.436313154 1.615085979 1.130500303 1.294800361 1 20.04670605 0.950583151 1.318923493 1.011081709 1.362724632 0.391821147 0.137438525 0.506784232 1.786833909 0.124070062 0.037655268 8.924484726 -0.950583151 0.351642924 TPAVEGLTEAEEEELRAELTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPAVEGLTEAEEEELRAELTK 21 1 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;O43399-6;A0A087WZ51;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 0 ; 195.39 2.26E-19 72598000 88428 71038 68891 62912 61592 61771 90646 60904 85695 FALSE TRUE 82893.44933 76297.72743 70525.12705 64526.42843 56754.81277 79603.28493 77054.47382 68507.99847 71391.95089 1.161103574 1.068716102 0.987858241 0.903833382 0.794974953 1.115017645 1.079315985 0.959603956 1 16.12347381 4.519604181 1.530860483 0.985705987 1.185747376 0.320449375 0.08806259 1.036734403 3.115596827 0.025753171 0.276199448 33082.9464 -4.519604181 0.200041389 TPDS(ph)PPTPAPLLLDLGIPVGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPDSPPTPAPLLLDLGIPVGQR 22 0 Q16584;Q16584-2;E9PID4 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 T(0.331)PDS(0.625)PPT(0.044)PAPLLLDLGIPVGQR;T(0.001)PDS(0.999)PPTPAPLLLDLGIPVGQR 149.74 6.41E-08 55604000 16319.8 18577.2 17965.1 21481.2 20167.3 16053.5 21363.1 13758.8 17566.3 TRUE FALSE 15298.37285 19952.67522 18391.24066 22032.44396 18583.44161 20687.88484 18159.90148 15476.61647 14634.37105 1.04537276 1.363411871 1.256715481 1.50552722 1.269849012 1.413650424 1.240907547 1.057552553 1 13.83707312 1.263434087 2.949955673 1.005477077 1.316020285 0.481977322 0.118949797 0.195043523 2.856049343 0.095338541 0.0276955 18.34146778 -1.263434087 0.310543207 TPDTIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPDTIRR 7 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 80.229 0.048871 248149000 253245 430390 321080 378060 492680 254967 415310 405150 677620 FALSE TRUE 237394.8475 462256.5234 328696.1692 387761.6597 453986.9002 328571.8339 353038.121 455733.8693 564520.8444 0.420524503 0.818847573 0.582256922 0.686886345 0.804198649 0.582036673 0.625376591 0.807293254 1 19.10666733 0.975836834 3.626373867 0.999261445 0.659038636 0.505811774 0.114326416 0.171017987 6.104586785 0.098785867 0.025483457 9.458817229 -0.975836834 -0.340222809 TPDVLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPDVLKK 7 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 77.923 0.058899 653380000 1616700 1282800 1327800 1371700 1576700 1097400 1788500 1301600 1774300 FALSE TRUE 1515513.633 1377779.847 1359296.043 1406900.144 1452872.342 1414201.565 1520331.029 1464107.625 1478157.868 1.025271837 0.93209249 0.919587869 0.951792887 0.982893894 0.956732428 1.028530891 0.990494762 1 20.49536893 2.136623906 1.483632502 1.007577621 0.948184129 0.232514253 0.032104999 0.430376356 1.814155643 0.019356068 0.010442533 136.9695112 -2.136623906 -0.059393492 TPEAVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPEAVQK 7 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 82.671 0.055501 288040000 416780 416800 423490 471520 494060 347870 556090 444230 565670 FALSE TRUE 390694.4838 447660.3057 433535.3828 483620.0015 455258.5205 448294.4218 472709.467 499693.0934 471256.0226 0.829049317 0.949930153 0.919957225 1.026236225 0.96605348 0.95127574 1.003084193 1.060343145 1 18.84615153 7.138530295 0.352799925 1.009644406 1.85E-12 0.649616856 0.037641835 21.75045435 0.541884077 0.029807237 13.19277204 13757207.73 -7.138530295 -1.009644406 TPEEIRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TPEEIRK 7 1 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ;; 113.7 0.013067 840900000 1407420 1380820 1366460 1298430 1639410 992150 1573200 1376480 2043870 FALSE TRUE 1319332.095 1483057.35 1398873.076 1331749.912 1510657.352 1278567.599 1337313.265 1548336.558 1702734.893 0.774831185 0.870985469 0.821544847 0.782124051 0.887194688 0.750890584 0.785391355 0.909323327 1 20.6994224 1.010805223 4.144573095 0.999382951 0.815212788 0.690345325 0.042459409 0.100369163 4.597344924 0.039989969 0.010218931 10.25192035 -1.010805223 -0.184170163 TPEEIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPEEIRR 7 1 P09525;Q6P452;P09525-2;B4E1S2 P09525 ANXA4 Annexin A4;Annexin 0 76.035 0.067107 832500000 260310 517900 477630 518740 443040 490390 407030 475870 753910 FALSE TRUE 244017.6618 556245.8549 488959.6092 532051.7466 408245.4255 631957.6322 345999.6302 535283.417 628077.5506 0.388515179 0.885632442 0.778501968 0.847111549 0.649992067 1.006177711 0.550886797 0.852256885 1 19.26058318 -3.330311841 1.105776528 8.188040841 0.757017522 0.165420959 0.178262433 221504.201 2575.889304 3997319.078 0.046548573 0.000467399 3.330311841 -7.431023319 TPEELDDS(ph)DFETEDFDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 TPEELDDSDFETEDFDVR 18 0 P35221-2;P35221;G3XAM7;P35221-3 P35221-2 CTNNA1 Catenin alpha-1 1 TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR 404.74 3.84E-147 17934875000 5390373 5747831 6038296 5910179 6344918 5177098 6906786 5586269 6180309 TRUE FALSE 5052999.176 6173406.388 6181527.233 6061844.199 5846613.734 6671642.149 5871177.559 6283726.982 5148775.502 0.981398232 1.19900477 1.200582008 1.177337058 1.135534795 1.295772587 1.140305604 1.220431339 1 22.29579794 -0.981845285 4.738016987 0.999998464 1.176587618 0.298753417 0.080489313 1.99E-06 4.28E-07 0.06890177 0.01624006 0.104268882 0.981845285 0.176589154 TPEEREWR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 79.906 0.024464 5347000000 3657300 4385930 4104710 4525080 4530770 3571660 4904310 3826990 4030290 FALSE TRUE 3428396.121 4710668.821 4202075.66 4641201.214 4174941.6 4602740.261 4168954.245 4304798.126 3357608.562 1.021082731 1.402983324 1.251508501 1.382293715 1.243427137 1.37083885 1.241643916 1.282102439 1 21.67900262 0.06873519 1.158411927 0.998874202 1.290085211 0.380946255 0.108526113 7.780942905 8.702595442 0.116037483 0.027514068 1.17148084 -0.06873519 0.291211009 TPEERLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPEERLK 7 1 Q99767;Q99767-2 Q99767 APBA2 Amyloid beta A4 precursor protein-binding family A member 2 0 105.12 0.0072951 329170000 311330 262270 262300 263110 369780 234120 359710 281650 425740 FALSE TRUE 291844.411 281688.7437 268521.8799 269861.848 340738.9704 301706.6434 305774.8249 316814.6225 354681.2436 0.822835761 0.794202538 0.757079447 0.760857398 0.960690695 0.850641664 0.862111629 0.893237599 1 18.43616351 2.752666662 24.99060991 0.896182575 0.78104285 0.629477642 0.048401514 534.7556256 947385.2712 0.0139019 0.014679584 565.804845 -2.752666662 -0.115139726 TPEEVIEYSAVFWER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPEEVIEYSAVFWER 15 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 116.54 0.0028983 0 8270 9387.4 9235.5 10095 9657.3 8060.8 11469 9710.6 8370.8 FALSE TRUE 7752.395462 10082.45286 9454.570421 10354.05479 8898.854614 10387.8221 9749.329923 10922.98979 6973.659403 1.11166821 1.445790837 1.355754544 1.484737667 1.27606671 1.489579789 1.398022094 1.566321088 1 12.76770019 -1.567276494 6.006123009 0.999001393 1.396630229 0.483269593 0.126940917 0.001478556 0.000106526 0.107061345 0.025176048 0.027084667 1.567276494 0.397628836 TPEFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TPEFLR 6 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;; 114.6 0.058509 1610700000 2295370 2927990 2478570 2427030 2830140 2091200 2729510 2407070 2830530 FALSE TRUE 2151706.889 3144781.426 2537362.851 2489311.699 2607872.221 2694895.492 2320245.315 2707597.988 2358096.257 0.912476275 1.333610287 1.076021746 1.05564465 1.105922717 1.142826754 0.983948517 1.148213513 1 21.16919118 3.709464727 21.76117493 1.072054253 1.168631746 0 0.11451785 163.050456 200955.4236 0.02754549 0.042846925 5122.296653 -3.709464727 0.096577493 TPEKLDNTPAS(ph)PPRS(ph)PAEPNDIPIAK ddPTM_SK-BR-3_Pertuzumab_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 TPEKLDNT(0.002)PAS(0.998)PPRS(1)PAEPNDIPIAK;TPEKLDNT(0.001)PAS(0.999)PPRS(1)PAEPNDIPIAK;TPEKLDNTPAS(1)PPRS(1)PAEPNDIPIAK;TPEKLDNTPAS(1)PPRS(1)PAEPNDIPIAK 180.23 1.17E-17 2395784000 3699590 2614520 3168580 3201190 4117530 1981320 3039910 2065360 3240510 TRUE FALSE 3468039.266 2808101.781 3243740.214 3283337.955 3794155.803 2553294.92 2584103.717 2323224.742 2699647.947 1.28462649 1.040173325 1.201541934 1.216209676 1.405426144 0.945788107 0.95720026 0.860565818 1 21.36433985 2.150058826 11.50649094 0.939057505 1.19926138 0.678431177 0.0975357 0.310407408 38.4654578 0.036908061 0.027258599 141.272889 -2.150058826 0.260203875 TPEKLDNTPAS(ph)PPRSPAEPNDIPIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TPEKLDNTPASPPRSPAEPNDIPIAK 26 2 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911;H0Y8P9 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 TPEKLDNT(0.179)PAS(0.82)PPRS(0.002)PAEPNDIPIAK;T(0.005)PEKLDNT(0.048)PAS(0.9)PPRS(0.048)PAEPNDIPIAK;TPEKLDNT(0.063)PAS(0.874)PPRS(0.063)PAEPNDIPIAK 105.98 0.0016164 826210000 849020 614370 602390 429840 543540 602270 1526740 1060330 1659040 TRUE FALSE 795881.3537 659858.5941 616678.9753 440870.4221 500852.5609 776135.572 1297819.511 1192714.535 1382135.506 0.575834533 0.47741961 0.446178376 0.318977712 0.362375873 0.561548103 0.938995854 0.862950506 1 20.39846764 1.827596227 3.280744051 0.931607905 0.438584772 0.899082002 0.076208131 0.071793129 1.363728188 0.041080974 0.021232637 67.23512654 -1.827596227 -0.493023133 TPELNLDQFHDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TPELNLDQFHDK 12 0 P27824;P27824-2;P27824-3;H0Y9Q7;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ;;; 198.37 1.84E-07 3336950000 4326630 3295690 3080140 3105060 3733780 2581190 4615940 3663650 2295610 FALSE TRUE 4055833.952 3539706.317 3153202.375 3184741.096 3440543.98 3326337.651 3923822.649 4121064.767 1912457.861 2.120744219 1.850867614 1.648769596 1.665260794 1.799016883 1.73929984 2.05171718 2.154852586 1 20.86699653 -0.479015347 10.16869036 1.000020707 1.855361615 0.698686461 0.180789049 0 0 0.180502723 0.0425449 0.33188273 0.479015347 0.855340908 TPELRDDDFLGGAECSLGQIVSSQVLTLPLMLKPGKPAGR ddPTM_SK-BR-3_Pertuzumab_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 0 151.65 6.54E-14 135410000 141430 142590 124650 106200 172220 89104 153740 156010 105890 FALSE TRUE 132578.1488 153147.512 127606.7569 108925.2718 158694.5359 114826.8783 130688.1143 175488.1919 88216.27492 1.502876299 1.736046008 1.44652171 1.234752566 1.798925834 1.30165186 1.48145129 1.989294969 1 16.42875722 -1.161723646 3.957629656 0.999763133 1.547556921 0.37283142 0.228214631 11989786.57 7039018.541 25212.3309 0.048742397 0.068909064 1.161723646 0.547793788 TPELTWER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 139.88 0.001532 456206000 339498 540391 374999 366693 591598 276900 356447 493330 509140 FALSE TRUE 318249.4262 580402.1119 383894.1534 376102.9632 545136.2795 356836.5349 303001.0814 554923.3365 424161.2448 0.750302933 1.368352529 0.905066547 0.886698084 1.285210014 0.841275669 0.714353527 1.308283921 1 18.69425328 TPEPLEEFPKREDQEGS(ph)PPETSLPYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPEPLEEFPKREDQEGSPPETSLPYK 26 2 P10244-2;P10244 P10244-2 MYBL2 Myb-related protein B 1 TPEPLEEFPKREDQEGS(0.997)PPET(0.001)S(0.001)LPYK 80.93 0.0091466 125380000 78340 54313 66134 66528 71441 41003 67171 47037 99251 TRUE FALSE 73436.83924 58334.39103 67702.72971 68235.22111 65830.31204 52839.90047 57099.33213 52909.67299 82685.36691 0.888147951 0.705498363 0.818799411 0.825239382 0.79615432 0.639047784 0.690561514 0.639891615 1 16.33534441 2.283061388 24.12523645 0.711030738 0.795438838 0.039705591 0.111695577 181.9607272 98645.43309 0.034295869 0.028693796 191.8939966 -2.283061388 0.0844081 TPEPVVPTAPELRPSTSTDRPVT(ph)PKPTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TPEPVVPTAPELRPSTSTDRPVTPKPTSR 29 3 Q14676;Q14676-2 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 TPEPVVPTAPELRPS(0.004)T(0.004)S(0.004)T(0.004)DRPVT(0.861)PKPT(0.055)S(0.068)R;TPEPVVPTAPELRPS(0.019)T(0.019)S(0.019)T(0.019)DRPVT(0.843)PKPT(0.034)S(0.047)R;TPEPVVPTAPELRPS(0.115)T(0.115)S(0.115)T(0.115)DRPVT(0.54)PKPTSR;TPEPVVPTAPELRPS(0.101)T(0.101)S(0.101)T(0.101)DRPVT(0.553)PKPT(0.019)S(0.022)R 148.66 4.69E-08 6100180000 2132840 1872130 1907410 1847420 2143250 1326946 2764400 1873470 2441070 TRUE FALSE 1999349.352 2010744.453 1952654.666 1894827.925 1974927.79 1710013.769 2349903.883 2107376.854 2033639.647 0.98313846 0.988741765 0.96017732 0.931742223 0.971129666 0.840863705 1.15551636 1.036258738 1 20.95563263 1.729846231 24.9999999 1.072922648 0.952961411 0.484205412 0.056835907 0.584648514 1668.130529 0.023968108 0.013291545 53.68416856 -1.729846231 -0.119961237 TPEQCPSVVSLLSESYNPHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPEQCPSVVSLLSESYNPHVR 21 0 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 172 6.18E-12 92381000 56571 69315 51126 73417 77697 47667 63576 52189 90779 FALSE TRUE 53030.32209 74447.15472 52338.73286 75301.00451 71594.99103 61427.68909 54043.36901 58704.91153 75627.39845 0.701205161 0.984393966 0.692060469 0.995684184 0.946680601 0.812241203 0.714600398 0.776238675 1 16.20662137 -0.40324318 7.416434701 1.000000004 0.829052913 0.183625463 0.114025548 0 0 0.106618124 0.025130133 0.3951453 0.40324318 -0.170947091 TPES(ph)FLGPNAALVDLDSLVSRPGPTPPGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPESFLGPNAALVDLDSLVSRPGPTPPGAK 30 1 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 T(0.46)PES(0.54)FLGPNAALVDLDSLVSRPGPTPPGAK 113.76 9.51E-05 225770000 121640 99976 122480 107970 112710 113120 198880 127480 164270 TRUE FALSE 114026.7695 107378.3271 125385.2834 110740.693 103858.2113 145775.9077 169059.7903 143396.1586 136852.2758 0.83321062 0.784629459 0.916208976 0.809198768 0.758907447 1.06520631 1.235345115 1.047817128 1 17.0622599 2.137888259 5.317056795 1.126679671 0.828718123 0.755757962 0.074429648 0.087589002 3.84792938 0.026956753 0.019746617 137.3688489 -2.137888259 -0.297961547 TPESQPDT(ph)PPGTPLVSQDEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TPESQPDTPPGTPLVSQDEKR 21 1 A0A0D9SFD6;M0R3C8;A0A0D9SFL2;M0QYH2;Q96T60-2;Q96T60;A0A0D9SEV0;M0R000;M0QYI1 A0A0D9SFD6 PNKP Bifunctional polynucleotide phosphatase/kinase;Polynucleotide 3-phosphatase;Polynucleotide 5-hydroxyl-kinase 1 TPESQPDT(0.999)PPGT(0.001)PLVSQDEKR;TPESQPDT(0.995)PPGT(0.004)PLVSQDEKR;TPESQPDT(0.875)PPGT(0.125)PLVSQDEKR;TPESQPDT(0.995)PPGT(0.005)PLVSQDEKR;TPESQPDT(0.972)PPGT(0.027)PLVS(0.001)QDEKR;TPESQPDT(0.986)PPGT(0.012)PLVS(0.002)QDEKR 184.29 2.35E-17 15152310000 5169620 4218950 4681080 4538930 4827800 3500610 5712410 3943110 5984040 TRUE FALSE 4846062.712 4531325.448 4792117.428 4655406.628 4448644.062 4511179.279 4855887.152 4435415.963 4985265.066 0.972077241 0.908943735 0.961256295 0.93383332 0.892358582 0.904902592 0.974047937 0.889705142 1 22.24923878 -1.214026265 4.233290033 1.000032156 0.931684452 0.330442904 0.031355575 8.75E-06 1.62E-06 0.027921029 0.006577954 0.061090508 1.214026265 -0.068347704 NNRQPYAVSELAGHQTSAESWGTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 NNRQPYAVSELAGHQTSAESWGTGR 25 1 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 58.812 0.050485 48822000 9847.3 18834 18038 19487 23420 19890 21339 18285 29196 FALSE TRUE 9230.975071 20228.48896 18465.86988 19987.06941 21580.68767 25631.92011 18139.41505 20567.9225 24322.99899 0.37951632 0.831660971 0.759193794 0.821735405 0.887254392 1.053814134 0.745772142 0.845616222 1 14.5700335 4.742586146 4.652207347 0.852607994 0.349294053 0.71350435 0.096951383 0.107451863 6.284497719 0.022491614 0.176980266 55282.30543 -4.742586146 -0.503313941 down TPGHPPPPEIPSELGACDFEKPES(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 141.17 1.83E-07 160940000 330660 222180 261010 368510 348110 236090 337860 231020 242150 TRUE FALSE 309964.5808 238630.4384 267201.2805 377966.5905 320770.8448 304245.3504 287201.0295 259863.3555 201733.6007 1.536504478 1.182898821 1.324525412 1.873592645 1.590071479 1.508154068 1.423664816 1.28815108 1 17.62209187 0.916522873 2.019979233 1.0011789 1.462692613 0.435674984 0.179671546 0.482322246 4.116442986 0.188654508 0.052458562 8.251309421 -0.916522873 0.461513713 TPGNERPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPGNERPPR 9 1 P82673;H0YG82;P82673-2 P82673 MRPS35 "28S ribosomal protein S35, mitochondrial" 0 81.338 0.019668 23407000 14468 23269 24113 26023 22032 26555 18247 20342 20216 FALSE TRUE 13562.47371 24991.86097 24684.97175 26690.79424 20301.69559 34220.99742 15511.03175 22881.74348 16841.819 0.805285564 1.483916967 1.46569511 1.584792844 1.205433664 2.031906258 0.920983164 1.358626611 1 14.03976034 1.624235887 25 1.104847528 1.44013424 0.19302177 0.323356793 1.295215288 1973.385818 0.13435583 0.074225918 42.09552082 -1.624235887 0.335286712 TPGRQS(ph)PGPGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TPGRQSPGPGHR 12 1 O15169-2;O15169 O15169-2 AXIN1 Axin-1 1 TPGRQS(1)PGPGHR;T(0.002)PGRQS(0.998)PGPGHR;TPGRQS(1)PGPGHR 106.33 0.0011707 352776000 318283 332283 338091 334694 304774 289771 328231 276448 250389 TRUE FALSE 298362.2352 356885.5791 346110.6782 343282.8147 280838.2794 373423.1837 279015.8087 310963.1413 208597.4583 1.430325362 1.710881724 1.659227686 1.645671129 1.346316881 1.790161715 1.337580098 1.490733127 1 17.67036205 0.360951355 0.487204803 0.957187348 1.632486248 0.596871377 0.146521794 1.474909279 0.577958554 0.263282617 0.070376329 2.295891473 -0.360951355 0.675298899 TPHDILEDINAS(ph)PEMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TPHDILEDINASPEMR 16 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 TPHDILEDINAS(1)PEMR;TPHDILEDINAS(1)PEMR;TPHDILEDINAS(1)PEMR;TPHDILEDINAS(1)PEMR;TPHDILEDINAS(1)PEMR 256.4 1.01E-26 674194000 436793 506121 493417 527472 517183 435423 569961 457408 516528 TRUE FALSE 409454.9058 543594.7255 505121.0842 541007.8245 476565.5334 561122.5516 484500.6393 514516.3957 430316.1399 0.951521144 1.263245031 1.17383718 1.257233402 1.10747771 1.30397747 1.125917888 1.195670689 1 18.71503743 -0.495263827 6.067764501 1.000000224 1.182871117 0.22218123 0.099639657 0 34742642.98 0.118973985 0.020110274 0.319695242 0.495263827 0.182870893 TPHS(ph)PPLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPHSPPLAK 9 0 Q8IZW8 Q8IZW8 TNS4 Tensin-4 1 T(0.106)PHS(0.894)PPLAK 80.245 0.015883 176640000 310540 296420 327290 368500 403750 197830 288300 240690 318540 TRUE FALSE 291103.8557 318367.2452 335053.4734 377956.3339 372041.1036 254940.3095 245072.0914 270740.6763 265373.6162 1.096958545 1.199694415 1.262572663 1.424242317 1.40195212 0.960684461 0.92349833 1.020224543 1 18.01766542 2.223265189 24.99612871 0.964450603 1.27124107 0.709511185 0.09552721 136.6571804 223326.7321 0.037841932 0.028051915 167.2111327 -2.223265189 0.306790466 TPHYGSQTPLHDGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TPHYGSQTPLHDGSR 15 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 0 ;;; 174.87 5.14E-07 735282000 232782 341616 293333 300118 346470 277124 333674 295936 362635 FALSE TRUE 218212.5901 366909.6041 300290.9973 307819.536 319259.6438 357125.2001 283642.6814 332884.261 302108.8758 0.722297846 1.214494619 0.993982704 1.018902656 1.056770156 1.182107607 0.938875697 1.101868524 1 18.20470904 4.755331477 24.8705563 1.062587254 0.722297559 0.614844155 0.084836099 2211.70668 3279820.2 0.019235111 0.557591512 56928.72756 -4.755331477 -0.340289695 TPILEDFELEGVCQLPDQS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPILEDFELEGVCQLPDQSPPR 22 0 Q7Z2Z1;Q7Z2Z1-2;H0YN97 Q7Z2Z1 TICRR Treslin 1 TPILEDFELEGVCQLPDQS(1)PPR 82.342 0.0028391 17931000 20816 24220 24182 22340 24461 21363 27960 19812 19890 TRUE FALSE 19513.16372 26013.274 24755.60846 22913.28222 22539.93173 27530.1513 23767.65757 22285.57181 16570.23051 1.177603637 1.569880032 1.493980935 1.382798037 1.360266637 1.66142235 1.434358898 1.344916222 1 14.01630605 0.832535304 2.501510414 1.00048067 1.462859801 0.526170101 0.129429259 0.465440186 5.228923186 0.11396875 0.030538934 6.800413242 -0.832535304 0.462379132 TPIS(ph)PLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TPISPLK 7 0 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 T(0.002)PIS(0.998)PLK;TPIS(1)PLK;TPIS(1)PLK;T(0.006)PIS(0.994)PLK;TPIS(1)PLK;T(0.004)PIS(0.996)PLK 113.74 0.0063586 13435767000 23038220 15138470 19003420 17173780 17698180 14798680 23831640 16290260 20375800 TRUE FALSE 21596298.93 16259338.07 19454190.1 17614488.27 16308236.33 19070818.68 20258306.82 18324134.82 16974947.35 1.272245415 0.957843211 1.146053045 1.037675576 0.960723824 1.123468503 1.193423839 1.079481099 1 24.01690376 2.077132119 24.99999982 1.12398453 1.064882384 0 0.102637047 93.09621051 30170.01855 0.035254449 0.026037135 119.4351389 -2.077132119 -0.059102146 TPIS(ph)PLKTGVSKPIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPISPLKTGVSKPIVK 16 2 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 T(0.024)PIS(0.976)PLKTGVSKPIVK;T(0.003)PIS(0.997)PLKT(0.001)GVSKPIVK 106.73 0.00061708 1775290000 1428620 1287630 1400390 1547540 2194500 983097 2243100 1303290 5103880 TRUE FALSE 1339205.224 1382967.465 1433607.912 1587252.496 2022152.822 1266901.145 1906767.979 1466008.625 4252009.456 0.314958195 0.325250327 0.337160095 0.373294677 0.475575806 0.297953511 0.448439261 0.344780189 1 22.01971337 -5 0.313716332 6.782253654 0.335450832 0.927114546 0.056041213 67.79685534 0.609465363 259.4431464 0.046587818 1.00E-05 5 -6.446802822 TPKDS(ph)PGIPPSAGAHQLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPKDSPGIPPSAGAHQLFR 19 1 E9PGT3;Q15418-4;Q15418;Q15418-2;Q15418-3;Q5SVM6 E9PGT3 RPS6KA1 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1 1 T(0.001)PKDS(0.999)PGIPPSAGAHQLFR;TPKDS(1)PGIPPSAGAHQLFR 142.41 9.38E-08 883630000 670870 654400 704740 724580 785050 463500 549060 358690 579310 TRUE FALSE 628881.4442 702852.4569 721456.7656 743173.9495 723395.3397 597304.9257 466733.5502 403473.2361 482619.4185 1.303058725 1.456328589 1.494877201 1.539875772 1.498893977 1.237631357 0.967084067 0.836007049 1 18.88052644 1.894150826 2.32147634 0.913636124 1.46684981 0.908931684 0.075586714 0.076547827 0.755397217 0.042691028 0.021154817 78.37017664 -1.894150826 0.553213686 TPKDS(ph)PGIPPSANAHQLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPKDSPGIPPSANAHQLFR 19 1 B4DG22;B1AXG1;B7ZB17;P51812 B4DG22 RPS6KA3 Ribosomal protein S6 kinase alpha-3 1 T(0.017)PKDS(0.983)PGIPPSANAHQLFR 110.06 0.00014683 217110000 186620 163000 169870 163770 169720 147740 253950 178980 297880 TRUE FALSE 174939.7873 175068.6896 173899.3966 167972.6155 156390.8758 190390.1396 215872.5551 201326.047 248161.9036 0.704942156 0.705461584 0.700749769 0.676867049 0.630196954 0.767201318 0.869885957 0.81126895 1 17.92092213 1.387758502 0.902034369 0.978703051 0.686674249 0.83428995 0.044084787 0.199594164 0.338848309 0.041079046 0.015391826 24.42072214 -1.387758502 -0.292028803 TPKHS(ph)PIKEEPCGSLSETVCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPKHSPIKEEPCGSLSETVCK 21 2 J3QQY0;Q68DK7;J3KSZ8;Q68DK7-2;Q68DK7-3;J3KTC2 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 T(0.183)PKHS(0.805)PIKEEPCGS(0.011)LSETVCK 122.78 1.44E-05 69421000 124940 57756 87650 90160 92786 65775 115020 78987 121530 TRUE FALSE 117120.2284 62032.31434 89729.09939 92473.65824 85498.96184 84763.17473 97773.81879 88848.70082 101245.8579 1.156790321 0.612689898 0.886249584 0.913357447 0.844468738 0.837201408 0.965706853 0.877553933 1 16.62750336 1.325480345 0.573906962 0.995287153 0.835813469 0.01858307 0.136434089 1.667535799 1.36444464 0.128419939 0.064717594 21.15827924 -1.325480345 -0.159473684 TPLAVELEVLDGHDPDPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TPLAVELEVLDGHDPDPGR 19 0 Q86TX2;G3V4F2;A0A087X0W7;A0A087WT95;P49753 Q86TX2 ACOT1;ACOT2 "Acyl-coenzyme A thioesterase 1;Acyl-coenzyme A thioesterase 2, mitochondrial" 0 ;;;; 185.33 2.29E-14 437452000 412019 456677 432378 418506 526402 379452 442043 418051 577138 FALSE TRUE 386231.4663 490489.8403 442634.2103 429245.5725 485060.5103 488993.6325 375762.7559 470245.5876 480809.9393 0.803293432 1.020132489 0.920601207 0.892755198 1.008840439 1.017020641 0.781520358 0.978028009 1 18.87510719 -1.734780781 9.181073511 1.00025815 0.929713997 0.067359182 0.084186104 0.000423331 1.22E-05 0.077570992 0.018217287 0.018417014 1.734780781 -0.070544152 TPLDLFAHFGPEPGDHSDPLPPS(ph)APSPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPLDLFAHFGPEPGDHSDPLPPSAPSPTR 29 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 TPLDLFAHFGPEPGDHSDPLPPS(0.595)APS(0.389)PT(0.017)R;TPLDLFAHFGPEPGDHSDPLPPS(0.613)APS(0.37)PT(0.018)R 138.84 1.42E-06 95320000 60906 63786 67177 59338 62220 64421 75463 57522 57278 TRUE FALSE 57094.00218 68508.78181 68770.47016 60860.71354 57333.49218 83018.29691 64148.02371 64703.74832 47717.93177 1.196489455 1.435703084 1.441187152 1.275426476 1.201508323 1.739771483 1.344316934 1.355962967 1 15.54224389 0.660123291 2.611757056 1.000067418 1.393687278 0.362171221 0.154884088 2.882079193 20.89454872 0.137836875 0.036603499 4.572179699 -0.660123291 0.39361986 TPLDLFAHFGPEPGDHSDPLPPSAPS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TPLDLFAHFGPEPGDHSDPLPPSAPSPTR 29 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 TPLDLFAHFGPEPGDHSDPLPPS(0.471)APS(0.517)PT(0.012)R;TPLDLFAHFGPEPGDHSDPLPPS(0.144)APS(0.835)PT(0.021)R;TPLDLFAHFGPEPGDHSDPLPPS(0.339)APS(0.646)PT(0.015)R;TPLDLFAHFGPEPGDHSDPLPPS(0.018)APS(0.797)PT(0.185)R;TPLDLFAHFGPEPGDHSDPLPPS(0.007)APS(0.988)PT(0.005)R;TPLDLFAHFGPEPGDHSDPLPPS(0.013)APS(0.969)PT(0.018)R 265.68 3.21E-58 4069680000 1421357 1546642 1483397 1463810 1445232 1328639 1628729 1280448 1153420 TRUE FALSE 1332396.803 1661156.983 1518583.877 1501373.843 1331729.309 1712195.511 1384516.207 1440314.751 960906.7506 1.386603645 1.728739008 1.5803655 1.562455297 1.385908994 1.781853972 1.44084346 1.498912096 1 19.87403691 0.202964848 0.781727467 0.989047315 1.584215446 0.63510942 0.130413627 1.88749581 1.388747926 0.164902802 0.040237803 1.595749983 -0.202964848 0.595168132 TPLEQEIFNLLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPLEQEIFNLLHK 13 0 Q9BVJ6-3;Q9BVJ6;Q9BVJ6-2;Q5TAP6;X6RJY0 Q9BVJ6-3 UTP14A;UTP14C U3 small nucleolar RNA-associated protein 14 homolog A;U3 small nucleolar RNA-associated protein 14 homolog C 0 165.73 3.48E-05 103760000 162770 168800 168140 161570 186160 136940 195100 147330 177080 FALSE TRUE 152582.5163 181298.1276 172128.3602 165716.1597 171539.7445 176472.355 165846.5662 165724.4748 147524.204 1.034288016 1.228938186 1.166780471 1.123315058 1.162790511 1.196226451 1.124199024 1.123371422 1 17.17059215 0.677190807 1.173904256 1.00024599 1.161188866 0.434051476 0.05186323 0.892106265 2.002091331 0.045455237 0.013990087 4.755441099 -0.677190807 0.160942876 TPLGAS(ph)LDEQSSSTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TPLGASLDEQSSSTLK 16 0 E9PHV5;P28290-3;P28290 E9PHV5 SSFA2 Sperm-specific antigen 2 1 TPLGAS(1)LDEQSSSTLK;TPLGAS(1)LDEQSSSTLK;TPLGAS(1)LDEQSSSTLK 298.33 9.31E-46 777350000 625360 581970 556860 636060 461180 380853 876290 578490 662410 TRUE FALSE 586219.8339 625059.6643 570068.9822 652382.3764 424960.7831 490799.0785 744898.4496 650715.7499 551849.4917 1.062282095 1.132663296 1.033015325 1.182174463 0.770066457 0.889371261 1.349821755 1.179154389 1 19.07391532 1.740171991 25 1.205643506 1.025306517 0.214687864 0.143358081 0.349152797 5446.367859 0.064966112 0.036027128 54.97585487 -1.740171991 -0.180336989 TPLRPLDPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TPLRPLDPTR 10 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;; 122.69 0.00043945 798500000 756350 1939190 622984 632443 2074580 434798 751270 1716690 1989190 FALSE TRUE 709011.4036 2082769.645 637761.4747 648672.5581 1911650.855 560317.1242 638624.0379 1931022.525 1657181.338 0.427841774 1.256814566 0.384847126 0.391431247 1.153555625 0.338114551 0.385367626 1.165245155 1 20.66030005 1.223940019 24.98493465 1.082622899 0.642784763 0.250428576 0.33108763 408.0431158 697279.2355 0.307200638 0.078163388 16.74711562 -1.223940019 -0.439838136 TPLSEAEFEEIMNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TPLSEAEFEEIMNR 14 0 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 0 ;; 265 4.58E-17 0 64397.4 82518 72833.8 70221.2 78146 63509 69758 66424.4 80646 FALSE TRUE 60366.88169 88627.71858 74561.45213 72023.19488 72008.72839 81843.01732 59298.4355 74717.63256 67185.66161 0.898508406 1.319146325 1.109782212 1.072002465 1.071787144 1.218161961 0.882605516 1.112106821 1 16.03586575 1.744851199 25 0.991708416 1.134567458 0.158286661 0.120977186 1.814546146 7235.30586 0.052235424 0.028967328 55.57138216 -1.744851199 0.142859042 TPLSFTNPLHS(ph)DDS(ph)DSDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TPLSFTNPLHSDDSDSDER 19 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 2 TPLSFTNPLHS(1)DDS(1)DSDER;TPLSFTNPLHS(1)DDS(0.996)DS(0.004)DER;TPLSFTNPLHS(1)DDS(1)DSDER;TPLSFTNPLHS(1)DDS(0.999)DS(0.001)DER 191.09 5.50E-15 254084000 283938 266239 290464 291531 285396 265075 308838 239788 219999 TRUE FALSE 266166.8274 285951.6126 297353.9432 299012.179 262982.1494 341597.8494 262530.609 269726.0596 183279.7457 1.452243544 1.560192107 1.622404823 1.63145239 1.434867494 1.86380578 1.432403827 1.471663214 1 17.48368784 0.690285118 1.426718644 1.001358849 1.585330277 0.673902322 0.124824969 0.567755592 1.802384007 0.105088504 0.030878209 4.901004688 -0.690285118 0.583971428 TPLSFTNPLHS(ph)DDS(ph)DSDERNSDGAVTQNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TPLSFTNPLHSDDSDSDERNSDGAVTQNK 29 1 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 2 TPLSFTNPLHS(1)DDS(0.954)DS(0.046)DERNSDGAVTQNK;TPLSFTNPLHS(1)DDS(0.943)DS(0.057)DERNSDGAVTQNK;TPLSFTNPLHS(1)DDS(0.993)DS(0.007)DERNSDGAVTQNK 143.22 9.58E-08 336146000 378572 313974 335806 343970 388900 246053 399583 325425 420944 TRUE FALSE 354877.8543 337220.9616 343771.4769 352796.8525 358357.3627 317084.5068 339669.2387 366055.0276 350685.727 1.011954086 0.961604467 0.980283628 1.006019993 1.021876099 0.904184238 0.968585866 1.043826422 1 18.41981919 -1.327370554 5.471431495 1.000003908 0.981286272 0 0.038880842 1.75E-06 2.15E-07 0.035604834 0.008390388 0.047057565 1.327370554 -0.018717635 TPLSFTNPLHSDDS(ph)DSDERNSDGAVTQNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPLSFTNPLHSDDSDSDERNSDGAVTQNK 29 1 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 TPLSFTNPLHS(0.001)DDS(0.952)DS(0.047)DERNS(0.001)DGAVTQNK 109.71 0.00022418 56300000 59738 46238 55581 53921 60159 41287 66377 50191 77393 TRUE FALSE 55999.10522 49661.50963 56899.40757 55304.70415 55434.35481 53205.88666 56424.38506 56457.45683 64475.60832 0.86853163 0.770237163 0.882495087 0.85776165 0.859772498 0.825209533 0.875127611 0.875640545 1 15.97646586 -5 0.183619998 1.646534018 0.816811267 0.70576407 0.030952003 70.07698158 0.679387998 16.47005595 0.087393348 1.00E-05 5 -0.829722751 TPPRDLPT(ph)IPGVTSPSSDEPPMEASQSHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPPRDLPTIPGVTSPSSDEPPMEASQSHLR 30 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 T(0.181)PPRDLPT(0.697)IPGVT(0.088)S(0.032)PS(0.001)S(0.001)DEPPMEASQSHLR 96.027 0.002035 234300000 11699 15617 14207 17034 18058 15589 17695 16465 19221 TRUE FALSE 10966.78047 16773.29893 14543.99675 17471.12128 16639.79752 20089.29123 15041.79902 18520.69149 16012.89093 0.68487199 1.04748724 0.908268021 1.091066027 1.03915012 1.254569916 0.939355616 1.156611356 1 13.96694617 5.168406045 1.663303141 1.049586636 9.23E-25 0.554884486 0.102196554 2.899940825 2.970855745 0.025120403 6.954051921 147368.9689 -5.168406045 -1.049586636 TPPSTTVGSHS(ph)PPETPVLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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;TPPSTTVGS(0.005)HS(0.995)PPETPVLTR;TPPSTTVGSHS(1)PPETPVLTR;TPPSTTVGSHS(1)PPETPVLTR 259.35 1.76E-36 7876210000 1680620 2085950 1976640 2051400 2014490 1725620 2240490 1827260 2063360 TRUE FALSE 1575432.994 2240395.908 2023526.834 2104042.397 1856280.081 2223778.481 1904549.324 2055397.433 1718971.886 0.916497243 1.303334817 1.177172734 1.224012105 1.079878092 1.293667743 1.10795839 1.195713234 1 20.71311452 -1.253443406 2.948455433 0.998893145 1.176403156 0.160542613 0.112573715 7962149.241 10129432.13 79312.44437 0.024634612 0.05579003 1.253443406 0.177510011 TPQEAIMDGTEIAVS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPQEAIMDGTEIAVSPR 17 0 Q06587 Q06587 RING1 E3 ubiquitin-protein ligase RING1 1 TPQEAIMDGTEIAVS(1)PR 135.91 1.26E-05 55117000 46080 50235 54387 49469 52719 42688 49233 40604 57186 TRUE FALSE 43195.93506 53954.45167 55677.08532 50738.45829 48578.6624 55011.33262 41850.96871 45673.49878 47641.28716 0.906691184 1.132514566 1.168672986 1.065010232 1.019675691 1.154698706 0.878460075 0.958695734 1 15.53992477 1.736711582 13.24515187 0.940021025 1.089610471 0.34951756 0.080988791 0.06786651 95.15605725 0.0365606 0.020095436 54.53955402 -1.736711582 0.149589446 TPQMHGTEMANS(ph)PQPPPLS(ph)PHPCDVVDEGVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPQMHGTEMANSPQPPPLSPHPCDVVDEGVTK 32 0 Q9UHV7;J3QRB7 Q9UHV7 MED13 Mediator of RNA polymerase II transcription subunit 13 2 T(0.001)PQMHGT(0.007)EMANS(0.992)PQPPPLS(1)PHPCDVVDEGVTK 121.08 8.37E-08 130290000 37226 32606 36424 38703 38402 30856 52005 35248 43673 TRUE FALSE 34896.09111 35020.18217 37287.99448 39696.1845 35386.06183 39763.62629 44207.33304 39648.79039 36383.69416 0.959113469 0.962524091 1.024854549 1.091043266 0.972580235 1.092896893 1.21503146 1.089740646 1 15.15100441 3.14920687 0.732213011 1.118663014 0.956199039 0.313264293 0.066053406 0.700150836 0.828993848 0.039650162 0.063836348 1409.960252 -3.14920687 -0.162463974 TPRPAS(ph)PGPSLPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPRPASPGPSLPAR 14 1 Q8IY33;Q8IY33-5;Q8IY33-3 Q8IY33 MICALL2 MICAL-like protein 2 1 TPRPAS(0.996)PGPS(0.004)LPAR 97.271 0.0018416 674430000 393480 394740 395390 392440 379870 388970 440490 405620 464960 TRUE FALSE 368852.7892 423966.9603 404768.8375 402510.6748 350036.5425 501259.3246 374442.6138 456262.5499 387355.1722 0.952234062 1.09451736 1.044955293 1.039125597 0.903657851 1.294056103 0.96666481 1.177891978 1 18.56329748 TPRPAS(ph)PGPSLPARS(ph)PS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPRPASPGPSLPARSPSPPR 20 2 Q8IY33;Q8IY33-5;Q8IY33-3 Q8IY33 MICALL2 MICAL-like protein 2 3 T(0.361)PRPAS(0.639)PGPS(0.458)LPARS(0.543)PS(0.999)PPR 74.274 0.010281 213840000 54660 63983 62207 55399 71874 52345 63625 56195 76021 TRUE FALSE 51238.92817 68720.36789 63682.57942 56820.63213 66229.30597 67456.15175 54085.02192 63211.06945 63332.60399 0.809045025 1.085070936 1.005525991 0.897178208 1.045737926 1.065109399 0.853983865 0.998081012 1 15.95066078 1.747687084 25 0.936975761 0.997604641 0.009589749 0.09117783 5.487139952 15065.03481 0.039208873 0.021743287 55.93544325 -1.747687084 0.06062888 TPRT(ph)PRT(ph)PQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPRTPRTPQLK 11 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 2 T(0.471)PRT(0.536)PRT(0.993)PQLK;T(0.318)PRT(0.682)PRT(0.999)PQLK 82.663 0.029395 1684570000 1234650 1459120 1177980 1595240 2313600 666250 1255890 1213410 3447500 TRUE FALSE 1157375.46 1567154.763 1205922.242 1636176.559 2131899.189 858585.5593 1067580.954 1364906.91 2872089.978 0.40297326 0.545649605 0.419876205 0.569681511 0.742281476 0.298941038 0.371708742 0.47523125 1 21.45366952 -1.359952791 2.865277657 1.007692682 0.474034802 0.641122624 0.122631348 9618301.057 11411049.85 618858.2444 0.030751959 0.043656329 1.359952791 -0.533657879 TPS(ph)EADRWLEEVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPSEADRWLEEVSK 14 1 P49757-3;P49757;G3V3Z8;P49757-8;P49757-7;P49757-6;P49757-5;P49757-4;P49757-2;P49757-9 P49757-3 NUMB Protein numb homolog 1 T(0.203)PS(0.797)EADRWLEEVSK;T(0.17)PS(0.83)EADRWLEEVSK 74.519 0.019875 41222000 34564 39492 34810 41477 42722 25031 31745 23409 45152 TRUE FALSE 32400.70094 42416.02877 35635.70964 42541.37004 39366.78645 32257.04336 26985.13196 26331.66518 37615.83951 0.861357911 1.12761085 0.947359147 1.130942991 1.046548129 0.857538839 0.717387471 0.700015353 1 15.19905267 2.11315522 3.939882632 0.776899867 1.031573425 0.441116981 0.113166663 0.162628869 4.694603265 0.040996606 0.028932765 129.7642976 -2.11315522 0.254673558 TPS(ph)FHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPSFHIK 7 0 O60890 O60890 OPHN1 Oligophrenin-1 1 T(0.038)PS(0.962)FHIK 74.92 0.028905 47275000 92725 95551 94563 93867 118940 57962 118360 97849 149320 TRUE FALSE 86921.50777 102625.6955 96806.07902 96275.78614 109598.9322 74694.68847 100613.0168 110065.663 124397.5274 0.698739835 0.824981795 0.778199383 0.773936494 0.881037867 0.600451553 0.808802385 0.884789798 1 16.92459828 1.044284443 2.613903043 0.996929731 0.770201307 0.523241343 0.074721084 0.194626825 2.851756887 0.06496673 0.017542975 11.0734881 -1.044284443 -0.226728424 TPS(ph)FLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPSFLK 6 0 P35611;P35611-3;P35612;Q9UEY8-2;Q9UEY8 P35611;Q9UEY8-2 ADD1;ADD2;ADD3 Alpha-adducin;Beta-adducin;Gamma-adducin 1 T(0.001)PS(0.999)FLK;T(0.003)PS(0.997)FLK 107.66 0.032595 109978000 768510 590200 655940 632160 736780 502740 849030 662120 778400 TRUE FALSE 720410.3309 633899.0221 671499.2066 648382.2958 678916.2708 647872.8767 721725.8335 744787.1395 648480.0113 1.110921414 0.977515129 1.035497155 0.999849316 1.046934769 0.999063757 1.112950008 1.1485121 1 19.30670258 1.72243235 8.532395372 1.097078828 1.022925576 0.211198974 0.051637333 0.122114051 25.130739 0.022063708 0.011768632 52.77549915 -1.72243235 -0.074153252 TPS(ph)FLKK ddPTM_SK-BR-3_Pertuzumab_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(0.379)PS(0.621)FLKK 66.568 0.071524 148510000 265310 184950 221740 217350 249490 134740 281130 202930 321770 TRUE FALSE 248704.7207 198643.8904 226999.7775 222927.569 229896.0618 173637.2507 238977.1664 228266.2572 268064.5083 0.92777937 0.741030179 0.846810266 0.831619114 0.857614696 0.647744275 0.89149126 0.851534799 1 18.03222069 0.826609784 1.561509229 0.998392629 0.810122272 0.342217688 0.077948191 0.653462332 2.94785631 0.066315049 0.019230461 6.708258409 -0.826609784 -0.188270357 TPS(ph)GEFLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPSGEFLER 9 0 Q9UNN5;B3KT28;B1ANM7;Q9UNN5-2 Q9UNN5 FAF1 FAS-associated factor 1 1 T(0.004)PS(0.996)GEFLER 106.62 0.0030488 335100000 282510 265750 267270 265460 288070 195630 274860 194780 199710 TRUE FALSE 264828.2034 285426.4065 273609.7706 272272.153 265446.1442 252105.2052 233647.2947 219098.7118 166377.1108 1.591734597 1.715538905 1.644515698 1.636476025 1.595448694 1.515263752 1.404323549 1.316880133 1 17.34409744 1.146284377 0.61860491 0.99497826 1.674649947 0.976765443 0.031961842 0.089956849 0.084354809 0.029263756 0.013094535 14.00504076 -1.146284377 0.679671687 TPS(ph)IQPSLLPHAAPFAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPSIQPSLLPHAAPFAK 17 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;H0YF36 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 T(0.052)PS(0.917)IQPS(0.03)LLPHAAPFAK;T(0.02)PS(0.975)IQPS(0.004)LLPHAAPFAK 148.91 2.22E-07 558190000 607140 817630 613370 666280 760480 356480 984090 656010 1205570 TRUE FALSE 569140.1912 878168.1759 627919.4261 683377.8728 700754.9684 459389.989 836534.8403 737914.2926 1004352.579 0.566673699 0.874362445 0.625198202 0.680416307 0.697718095 0.457399123 0.832909536 0.734716382 1 19.93783439 0.762078943 1.33631662 0.99736476 0.682617182 0.432085177 0.117474621 0.799410156 2.487465797 0.105079227 0.031430271 5.782011391 -0.762078943 -0.314747578 TPS(ph)LGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPSLGR 6 0 Q9P2Q2;A0A0J9YYA7 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 T(0.024)PS(0.976)LGR 75.109 0.082403 438240000 322440 246200 272910 252120 305850 200690 309150 248870 355760 TRUE FALSE 302259.056 264428.9042 279383.5541 258589.826 281829.7747 258625.9451 262795.8275 279941.9673 296381.3577 1.019831538 0.892191419 0.942648877 0.872490186 0.950902503 0.872612053 0.886681367 0.944532981 1 18.17709518 0.970816443 9.371706108 0.99999971 0.91498852 0.240777483 0.04468399 0.865329366 276.8187587 0.038580731 0.009652779 9.35010404 -0.970816443 -0.08501119 TPS(ph)PAAEDAREPEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPSPAAEDAREPEAK 15 1 Q92797 Q92797 SYMPK Symplekin 1 T(0.231)PS(0.769)PAAEDAREPEAK;T(0.17)PS(0.83)PAAEDAREPEAK 167.99 7.75E-07 1477790000 1675760 1195080 1308660 1456450 1387820 1010650 1865500 1232920 1139070 TRUE FALSE 1570877.173 1283564.967 1339702.033 1493824.973 1278826.215 1302408.248 1585785.593 1386852.776 948951.8583 1.655381313 1.352613365 1.411770283 1.574184148 1.347619697 1.372470307 1.67109172 1.461457464 1 19.85597537 -1.209296473 5.910212316 0.999989984 1.471976512 0.617180132 0.118827462 1.54E-05 2.07E-06 0.113340113 0.026713955 0.061759465 1.209296473 0.471986528 TPS(ph)PAPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.299)PS(0.701)PAPK;T(0.391)PS(0.609)PAPK;T(0.025)PS(0.975)PAPK 122.19 0.0045789 4650390000 8574900 6234700 7130600 6691300 6911300 5607400 8837700 5926500 7953000 TRUE FALSE 8038212.316 6696323.675 7299741.199 6863010.086 6368514.377 7226165.351 7512568.93 6666436.571 6625592.922 1.213206487 1.010675385 1.101749124 1.035833346 0.961199164 1.09064433 1.13387119 1.006164527 1 22.65961814 4.748186893 24.70226805 1.053373127 1.213206589 0.490577446 0.053658844 1042.316588 2674653.44 0.012841393 0.16247392 55999.85372 -4.748186893 0.159833461 TPS(ph)PARPALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPSPARPALR 10 1 Q9H211 Q9H211 CDT1 DNA replication factor Cdt1 1 T(0.442)PS(0.558)PARPALR 75.479 0.027451 0 86476 86582 77418 95101 83681 75474 104010 82097 65882 TRUE FALSE 81063.62152 92992.62137 79254.39152 97541.45267 77109.03181 97262.11858 88414.66608 92346.99117 54885.86859 1.476948869 1.694290785 1.443985375 1.77716879 1.404897723 1.772079428 1.610882152 1.682527644 1 15.74414713 -1.110652208 5.416774782 0.999990752 1.607515606 0.680955109 0.130756492 1.26E-05 2.06E-06 0.108856483 0.025657329 0.077508225 1.110652208 0.607524854 TPS(ph)PNSNEQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPSPNSNEQQK 11 0 Q9H4E7 Q9H4E7 DEF6 Differentially expressed in FDCP 6 homolog 1 TPS(1)PNSNEQQK 177.1 8.53E-06 75125000 124730 102520 111030 116590 121710 88829 139480 109240 109440 TRUE FALSE 116923.3719 110110.6875 113663.684 119581.8968 112151.3876 114472.4903 118566.2689 122878.8545 91173.75699 1.282423537 1.207701548 1.246671057 1.311582419 1.230084086 1.2555421 1.300442943 1.347743677 1 16.47633101 -0.993151094 4.969627401 0.99999736 1.266271637 0.810758169 0.041309969 1.24E-06 2.51E-07 0.041089643 0.009684826 0.101589519 0.993151094 0.266274277 TPS(ph)PSQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TPSPSQPK 8 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 T(0.123)PS(0.873)PS(0.004)QPK;T(0.07)PS(0.929)PSQPK;T(0.153)PS(0.845)PS(0.002)QPK 114.39 0.0027951 4015100000 3775510 2929270 3202000 2975880 3298410 2493650 4195170 2981140 3726260 TRUE FALSE 3539207.569 3146156.199 3277952.952 3052246.119 3039366.184 3213526.274 3566143.205 3353341.891 3104323.133 1.140089938 1.013475744 1.055931619 0.983224358 0.979075326 1.035177762 1.148766752 1.080216765 1 21.56584731 1.939240087 17.27174588 1.09263981 1.030045713 0.080676701 0.057475884 14.78652114 4201.852456 0.022090509 0.014236254 86.94409413 -1.939240087 -0.062594098 TPS(ph)PSQPKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPSPSQPKK 9 1 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 T(0.253)PS(0.746)PS(0.001)QPKK;T(0.116)PS(0.88)PS(0.005)QPKK 78.324 0.018433 619200000 1986580 953970 1326040 1309640 1280070 912180 1700800 1122260 1707220 TRUE FALSE 1862243.504 1024602.931 1357494.295 1343247.58 1179538.466 1175511.558 1445780.829 1262376.631 1422273.953 1.309342339 0.720397733 0.95445346 0.944436602 0.829332818 0.826501502 1.016527671 0.887576285 1 20.43976795 -1.387392385 5.656150805 1.000028134 0.917919435 0.004488573 0.156742438 4.92E-05 5.33E-06 0.134370369 0.031660552 0.040983365 1.387392385 -0.082108699 TPS(ph)SEEISPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPSSEEISPTK 11 0 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 T(0.07)PS(0.929)S(0.001)EEISPTK;T(0.029)PS(0.969)S(0.003)EEISPTK 227.48 4.16E-12 579410000 1228900 913350 1063770 1033650 1063310 840460 1281360 1008770 1003340 TRUE FALSE 1151985.343 980975.3843 1089003.127 1060175.209 979801.9218 1083087.158 1089231.964 1134717.155 835876.0722 1.378177198 1.173589503 1.302828449 1.268340181 1.172185632 1.295750883 1.303102218 1.357518408 1 19.67292954 -1.169081018 4.539300671 0.99995384 1.272934415 0.632362807 0.067161225 2.94E-05 5.38E-06 0.060870149 0.014344809 0.067751511 1.169081018 0.272980576 TPS(ph)SEEISPTKFPGLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TPSSEEISPTKFPGLYR 17 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 T(0.001)PS(0.998)S(0.002)EEISPTKFPGLYR;T(0.004)PS(0.874)S(0.122)EEISPTKFPGLYR;T(0.005)PS(0.983)S(0.012)EEISPTKFPGLYR;T(0.002)PS(0.995)S(0.002)EEISPTKFPGLYR;T(0.003)PS(0.984)S(0.013)EEISPTKFPGLYR 336.39 1.97E-72 4109100000 2807480 2554390 2771620 2800900 2995890 2083809 3673740 2745080 3961190 TRUE FALSE 2631764.838 2743519.693 2837364.135 2872775.836 2760604.884 2685370.83 3122896.792 3087809.281 3300041.799 0.797494395 0.831359074 0.859796423 0.870527106 0.836536339 0.813738429 0.946320375 0.93568793 1 21.65405287 1.658782669 4.936172467 0.959292182 0.838915199 0.836123298 0.026221162 0.061410724 3.353583928 0.01396806 0.006682853 45.58087614 -1.658782669 -0.120376983 TPS(ph)SPSKS(ph)PASFEIPASAMEANGVDGDGLNKPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPSSPSKSPASFEIPASAMEANGVDGDGLNKPAK 34 2 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911;H0YA73 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 2 T(0.273)PS(0.36)S(0.366)PS(0.033)KS(0.967)PAS(0.001)FEIPASAMEANGVDGDGLNKPAK 176.96 5.42E-20 79156000 103650 47527 81125 86181 88276 31543 62791 36108 49174 TRUE FALSE 97162.73152 51045.94853 83049.32331 88392.55036 81343.15905 40648.95204 53376.07247 40616.16328 40966.54172 2.371758206 1.246039973 2.027247598 2.157676646 1.985599849 0.992247584 1.30291868 0.991447205 1 15.32215849 2.239315236 24.99992782 1.115232845 1.879204884 0.671867077 0.304273791 13.98213969 463237.2239 0.110199841 0.087176241 173.5062951 -2.239315236 0.763972038 TPS(ph)TPVACSTPAQLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPSTPVACSTPAQLKR 16 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 T(0.264)PS(0.368)T(0.368)PVACSTPAQLKR;T(0.066)PS(0.467)T(0.467)PVACSTPAQLKR 80.238 0.0098758 326400000 600370 577640 584600 578380 717790 436820 847490 533680 765880 TRUE FALSE 562793.9134 620409.0666 598466.9881 593222.21 661417.6688 562922.8428 720416.7422 600311.1228 638049.6802 0.882053437 0.972352288 0.937962994 0.929742978 1.03662409 0.882255505 1.129091926 0.940853262 1 19.28330923 2.356201796 1.146638834 1.021544713 0.938713079 0.150304698 0.06839236 0.752797156 1.953269828 0.038863461 0.024652813 227.0919793 -2.356201796 -0.082831634 YTDHGSDHHYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YTDHGSDHHYR 11 0 J3KPD3;Q9Y580;G3V1T9 J3KPD3 RBM7 RNA-binding protein 7 0 54.784 0.074874 19544000 15157 27474 27035 28905 33934 25051 35873 30424 34835 FALSE TRUE 14208.35043 29508.20355 27676.28297 29646.75124 31268.96052 32282.81703 30494.17668 34222.50337 29020.81346 0.489591735 1.016794501 0.953670131 1.021568581 1.077466714 1.11240221 1.050769191 1.179239976 1 14.82480034 4.745017781 4.242238036 1.047446816 0.442971789 0.891262144 0.061757155 0.074426921 3.063311312 0.015747517 0.137485448 55592.70174 -4.745017781 -0.604475027 down TPSNELYKPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPSNELYKPLR 11 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 142.19 3.44E-05 1977910000 1901870 2153440 2133420 2256990 2657000 1768670 2737500 2339530 2802900 FALSE TRUE 1782835.352 2312882.938 2184025.73 2314908.184 2448329.938 2279256.317 2327037.289 2631625.47 2335077.883 0.763501451 0.990494988 0.935311728 0.991362302 1.048500333 0.976094345 0.996556606 1.126996872 1 21.15503924 5.406021281 1.269348799 1.005976611 1.33E-33 0.678854211 0.052106375 4.046339289 1.669762497 0.013853691 8.029272853 254695.5053 -5.406021281 -1.005976611 TPSNTPSAEADWS(ph)PGLELHPDYK ddPTM_SK-BR-3_Pertuzumab_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 260.7 6.28E-44 4409310000 3917120 3021720 3432790 3187180 3627240 2717940 3974640 3104440 4511180 TRUE FALSE 3671954.451 3245451.293 3514217.4 3268968.435 3342371.202 3502565.156 3378679.631 3492036.168 3758234.915 0.977042291 0.863557326 0.935071245 0.869814822 0.889346004 0.931970788 0.899007036 0.92916921 1 21.84162382 0.827775384 2.816327897 0.999997126 0.906178145 0.416674256 0.033357659 0.642634832 8.70212108 0.028072989 0.007406461 6.726286841 -0.827775384 -0.093818982 TPSPKEEDEEPES(ph)PPEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 151.06 2.63E-08 18363420000 5219820 1703190 2491880 2854070 2874430 1662570 3299500 2024500 4011750 TRUE FALSE 4893120.784 1829295.96 2550988.57 2927310.268 2648683.863 2142526.969 2804770.606 2277263.281 3342163.008 1.464058088 0.54733894 0.763274731 0.875872978 0.792505888 0.641059985 0.839208201 0.681374091 1 21.67235067 4.748785194 24.95954385 0.751011644 1.464058489 0.74652632 0.127217101 675.8917047 1649907.364 0.028391195 0.396902214 56077.05448 -4.748785194 0.713046846 TPSS(ph)PCPASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TPSSPCPASK 10 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 TPS(0.039)S(0.961)PCPASK;TPS(0.011)S(0.963)PCPAS(0.025)K;TPS(0.041)S(0.959)PCPAS(0.001)K;T(0.001)PS(0.048)S(0.951)PCPASK 150.59 2.23E-05 1699660000 3071540 2314480 2704080 2363630 2444050 2079560 3049240 2231810 2819300 TRUE FALSE 2879297.794 2485846.507 2768222.055 2424284.747 2252104.172 2679895.213 2592034.77 2510456.391 2348740.617 1.225890068 1.058374215 1.178598452 1.032163675 0.958856059 1.140992409 1.103584939 1.068852122 1 21.16345597 6.670944668 1.721966683 1.079423717 111.7984639 0.340576095 0.065742723 1458.268501 7.200368866 0.01695658 636362.6798 4687536.562 -6.670944668 110.7190402 TPSS(ph)PLQSCTPSLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TPSSPLQSCTPSLSPR 16 0 R4GNJ5;A0A590TQL1;Q96AP0-2;Q96AP0 R4GNJ5 ACD Adrenocortical dysplasia protein homolog 2 T(0.004)PS(0.118)S(0.877)PLQSCTPS(0.004)LS(0.996)PR;TPSS(1)PLQSCTPS(0.023)LS(0.977)PR;T(0.001)PS(0.026)S(0.973)PLQS(0.003)CT(0.001)PS(0.113)LS(0.882)PR 322.22 4.67E-58 343784000 407645 446579 421801 431839 460033 382777 527790 398503 450750 TRUE FALSE 382131.2271 479644.1738 431806.3189 442920.7198 423903.8639 493278.506 448652.7893 448256.9768 375516.913 1.017613891 1.277290469 1.149898457 1.179496061 1.128854252 1.313598639 1.194760539 1.193706491 1 18.51851836 -0.500042941 7.039317348 1.000000064 1.192023962 0.328669787 0.080554944 0 0 0.069169359 0.016303374 0.3161965 0.500042941 0.192023898 TPSS(ph)PLQSCTPSLSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPSSPLQSCTPSLSPR 16 0 R4GNJ5;A0A590TQL1;Q96AP0-2;Q96AP0 R4GNJ5 ACD Adrenocortical dysplasia protein homolog 1 TPS(0.028)S(0.972)PLQSCTPSLSPR;TPS(0.058)S(0.942)PLQSCTPSLSPR 185.74 1.69E-09 422380000 314150 315060 291550 314680 332800 260310 331910 275760 364760 TRUE FALSE 294487.9123 338387.3702 298465.7037 322755.2216 306663.2305 335457.2712 282143.1768 310189.243 303879.1996 0.969095327 1.113558844 0.982185369 1.062116861 1.009161637 1.103916529 0.928471502 1.020764973 1 18.2131384 1.731995161 25 0.979230637 1.041485799 0.210779674 0.051696223 0.851980163 3222.016346 0.021233219 0.011774898 53.9504611 -1.731995161 0.062255161 TPSS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.193)S(0.807)PSK;TPS(0.033)S(0.967)PSK;TPS(0.001)S(0.999)PSK 148.5 0.0021816 1434158000 6442970 3380690 4885380 4247350 4281760 3314030 4721730 4421610 2754780 TRUE FALSE 6039716.009 3630999.805 5001263.521 4356344.192 3945487.841 4270736.662 4013750.421 4973657.742 2294989.421 2.631696666 1.582142284 2.179209836 1.89819794 1.71917474 1.860896012 1.74891892 2.167181119 1 21.13005607 -2.094155885 0.315676302 1.07E-18 1.998050171 0.504984981 0.300516813 30.6172994 1.40265236 22.95014802 0.256504215 0.008050894 2.094155885 1.998050171 TPSSPLQSCTPSLS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPSSPLQSCTPSLSPR 16 0 R4GNJ5;A0A590TQL1;Q96AP0-2;Q96AP0 R4GNJ5 ACD Adrenocortical dysplasia protein homolog 1 TPSSPLQSCTPS(0.053)LS(0.947)PR 113.13 0.0016944 0 20110 21508 17229 20391 27523 15269 24700 16875 23443 TRUE FALSE 18851.351 23100.4747 17637.68002 20914.26758 25361.4546 19676.91243 20996.4643 18981.8809 19530.21185 0.965240477 1.182807175 0.903097219 1.07086742 1.298575499 1.007511469 1.075076116 0.971923963 1 14.25341998 1.242555791 24.75951389 0.985961963 1.07064262 0.095936358 0.109602687 207.9124278 1288579.477 0.076208527 0.025507142 17.48057811 -1.242555791 0.084680657 TPSSS(ph)PPIT(ph)PPASETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPSSSPPITPPASETK 16 0 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 2 TPS(0.004)S(0.031)S(0.965)PPIT(1)PPASETK 140.89 8.79E-06 89534000 365730 245140 309170 282230 299360 261990 324870 248610 337330 TRUE FALSE 342839.6121 263290.4207 316503.6584 289472.4996 275849.4732 337622.2599 276158.7594 279649.5058 281027.4438 1.219950648 0.936885085 1.126237545 1.030050645 0.981574858 1.201385372 0.982675413 0.995096785 1 18.1003515 2.425289642 0.009672659 1.37E-07 2.093740064 0.095463842 0.092683546 6370.8851 30.89848674 3277.624125 3406.918192 266.2500159 -2.425289642 2.093739927 TPST(ph)PVACSTPAQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TPSTPVACSTPAQLK 15 0 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 T(0.001)PS(0.022)T(0.978)PVACSTPAQLK;TPS(0.001)T(0.999)PVACSTPAQLK;TPST(1)PVACSTPAQLK;TPS(0.009)T(0.991)PVACSTPAQLK 299.56 3.57E-43 1484760000 2455260 1826530 2051720 1942970 2062090 1552160 2687830 1804450 1617940 TRUE FALSE 2301589.659 1961768.182 2100387.767 1992829.9 1900141.769 2000243.395 2284814.844 2029739.555 1347895.362 1.707543274 1.45543062 1.558272123 1.478475226 1.409710148 1.483975279 1.695098083 1.505858401 1 20.36227707 0.947708283 23.10251059 1 1.537187475 0.754599545 0.096387378 3796.085685 1677114.876 0.091156025 0.022789006 8.865603069 -0.947708283 0.537187475 TPT(ph)PEPAEVETR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPTPEPAEVETR 12 0 F8W6G1;Q9UHY1 F8W6G1 NRBP1 Nuclear receptor-binding protein 1 T(0.018)PT(0.982)PEPAEVETR;T(0.151)PT(0.849)PEPAEVETR 199.51 1.91E-06 1578830000 483100 509610 562650 520610 534580 503890 563110 490280 509640 TRUE FALSE 452863.6334 547342.0546 575996.3237 533969.734 492596.2432 649354.863 478676.8832 551492.5372 424577.7916 1.066621105 1.289144335 1.35663319 1.257648762 1.160202566 1.529413163 1.127418562 1.298919887 1 18.69566938 -1.15640447 4.297439473 0.999935979 1.270162632 0.284883496 0.129068507 7.06E-05 1.39E-05 0.111521909 0.026279749 0.069758242 1.15640447 0.270226653 TPTHQPPKPGS(ph)PGRPACPLSNLLLQSYEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPTHQPPKPGSPGRPACPLSNLLLQSYEER 30 2 Q96F63 Q96F63 CCDC97 Coiled-coil domain-containing protein 97 1 T(0.178)PT(0.038)HQPPKPGS(0.783)PGRPACPLSNLLLQSYEER;T(0.093)PT(0.093)HQPPKPGS(0.813)PGRPACPLS(0.001)NLLLQSYEER 107.78 0.00013182 1541350000 564700 534140 540630 547850 574390 482090 676190 468090 586900 TRUE FALSE 529356.435 573688.2814 553453.9989 561908.7585 529279.7264 621261.5569 574801.5869 526532.0669 488942.5985 1.082655585 1.173324401 1.131940642 1.149232569 1.082498698 1.270622684 1.175601367 1.076879103 1 18.89930558 1.012453773 4.048092904 1.000675671 1.156201735 0.474833481 0.053056719 0.14709747 6.280172441 0.048477693 0.012409172 10.29090982 -1.012453773 0.155526064 TPTQTNGSNVPFKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TPTQTNGSNVPFKPR 15 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 68.179 0.048701 182140000 108960 155360 155700 149880 153020 145330 167800 140770 194560 FALSE TRUE 102140.3881 166863.0161 159393.2775 153726.1745 141002.4265 187284.4118 142639.9478 158345.4444 162086.6791 0.630159052 1.029467795 0.983382955 0.948419546 0.869919892 1.155458381 0.880022643 0.976918309 1 17.306406 4.743673141 24.66167659 0.979159904 0.630158876 0.657630119 0.079425549 261.4963874 1261351.137 0.017132418 0.14404645 55420.84468 -4.743673141 -0.349001028 TPTS(ph)PLK ddPTM_SK-BR-3_Pertuzumab_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(0.006)PT(0.011)S(0.983)PLK;T(0.051)PT(0.038)S(0.911)PLK;TPT(0.001)S(0.999)PLK;T(0.051)PT(0.216)S(0.733)PLK;TPT(0.001)S(0.999)PLK;T(0.02)PT(0.171)S(0.809)PLK 149.57 0.0021055 20017600000 54630000 36875000 43747400 39476100 47313100 30373500 53994500 39091000 56348100 TRUE FALSE 51210805.82 39605263.37 44785108.99 40489123.56 43597319.98 39141836.38 45898525.99 43971597.4 46943238.09 1.090909104 0.843684096 0.954026838 0.86251237 0.928724173 0.833812024 0.977745206 0.936697152 1 25.48441402 1.174321292 1.611955071 0.992030267 0.914343676 0.074111219 0.074931283 0.748740086 3.676113797 0.061710872 0.018337015 14.93899191 -1.174321292 -0.077686591 TPTSS(ph)PASSPLVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TPTSSPASSPLVAK 14 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 TPTS(0.002)S(0.953)PAS(0.034)S(0.011)PLVAK;TPT(0.001)S(0.003)S(0.995)PAS(0.001)SPLVAK;TPTSS(1)PASSPLVAK;TPTSS(1)PASSPLVAK;TPTS(0.001)S(0.997)PAS(0.001)SPLVAK;TPTS(0.004)S(0.991)PAS(0.004)S(0.001)PLVAK 237.59 2.80E-17 999368000 2901200 2177980 2746670 2746260 2768200 2370610 3296680 2533480 2651750 TRUE FALSE 2719619.071 2339239.905 2811822.309 2816733.681 2550796.738 3054966.623 2802373.439 2849790.555 2209155.794 1.231067124 1.058884082 1.27280399 1.275027179 1.154647737 1.382866085 1.268526849 1.289990757 1 21.07506373 3.830426578 4.877955963 1.2539313 1.138138429 0.083116715 0.109693 0.334848024 12.72209282 0.025055549 0.046296672 6767.473724 -3.830426578 -0.115792871 TPTVPDS(ph)PGYMGPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TPTVPDSPGYMGPTR 15 0 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 TPTVPDS(1)PGYMGPTR;TPTVPDS(1)PGYMGPTR;TPTVPDS(1)PGYMGPTR 293.38 5.88E-44 1020800000 630260 717560 805990 1108560 1239680 502960 430990 363788 441423 TRUE FALSE 590813.1516 770688.889 825108.4634 1137007.526 1142320.533 648156.3871 366367.0506 409207.7326 367746.6496 1.606576572 2.095706079 2.243687235 3.091822937 3.106270403 1.762507933 0.996248507 1.112743605 1 18.48835267 1.95137905 4.11701937 1.076328499 2.393969429 0.671210172 0.443443245 0.147811566 5.053815701 0.2192285 0.130215529 89.40854969 -1.95137905 1.31764093 TPVEPEVAIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TPVEPEVAIHR 11 0 P60866;P60866-2;E5RJX2;E5RIP1 P60866 RPS20 40S ribosomal protein S20 0 ;;;;; 193.96 7.21E-07 18657900000 7418420 7686220 7915330 7760090 7603590 7013560 8308660 6827500 6611980 FALSE TRUE 6954114.334 8255315.726 8103085.365 7959227.047 7006434.713 9038260.916 7062853.567 7679928.404 5508397.823 1.262456808 1.498678199 1.471042148 1.444925966 1.271955102 1.640814844 1.282197436 1.394221814 1 22.39320133 0.28330051 0.845026721 0.995402764 1.43481762 0.544267547 0.117282985 1.935191198 1.719996215 0.121191522 0.034133481 1.919996823 -0.28330051 0.439414856 TPVLLHDHDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPVLLHDHDER 11 0 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-3;Q03154-4;C9JMV9 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 ; 101.72 0.0017775 709570000 183959 228020 175797 202422 208341 171989 204250 164102 238180 FALSE TRUE 172445.3346 244902.8381 179966.9879 207616.4912 191978.7383 221639.4323 173624.6087 184590.4959 198426.2193 0.869065264 1.234226197 0.906971813 1.046315814 0.96750691 1.116986621 0.8750084 0.930272706 1 17.59824315 1.717104997 12.73802193 0.927797337 1.033084782 0.126681718 0.106874779 0.190582432 86.26888521 0.046225001 0.025358204 52.13207333 -1.717104997 0.105287445 TPVPSDIDISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPVPSDIDISR 11 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 ; 102.06 0.0067909 197557000 131576 137398 142090 144203 158500 121385 154883 133708 174211 FALSE TRUE 123340.893 147571.0909 145460.4419 147903.4931 146052.0494 156426.879 131659.732 150401.7381 145134.0587 0.849841134 1.016791594 1.00224884 1.019081906 1.006325123 1.077809581 0.907159444 1.036295267 1 17.14702659 4.741420806 24.53245703 1.004337796 0.849841061 0.576907177 0.042508342 153.5126318 1316619.566 0.009591467 0.067378212 55134.16555 -4.741420806 -0.154496735 TPVQYSQQQNS(ph)PQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TPVQYSQQQNSPQK 14 0 P46013 P46013 MKI67 Antigen KI-67 1 TPVQYSQQQNS(1)PQK;TPVQYSQQQNS(1)PQK;TPVQYSQQQNS(1)PQK;TPVQYSQQQNS(1)PQK;TPVQYSQQQNS(1)PQK;TPVQYSQQQNS(1)PQK 365.02 6.22E-97 1564980000 1777880 1056768 1264670 935966 1042852 987153 1173161 684792 756175 TRUE FALSE 1666605.664 1135012.202 1294668.57 959984.4721 960950.6106 1272128.046 997256.3991 770289.7886 629964.5074 2.64555486 1.801708174 2.055145257 1.523870727 1.525404367 2.019364632 1.583035849 1.222751091 1 19.26491102 8 0.092627044 0.524110787 5.497760146 0.679950803 0.261627911 91.50617049 0.606649357 4.105724403 57.81802101 99999999.99 -8 4.97364936 TPVS(ph)PVKFSPGDFWGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPVSPVKFSPGDFWGR 16 1 P23443-5;P23443;P23443-3;P23443-2 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 1 T(0.011)PVS(0.989)PVKFSPGDFWGR;T(0.02)PVS(0.98)PVKFSPGDFWGR 171.47 2.97E-09 874460000 1314470 1213810 1233400 1278160 1434200 852910 1460850 1004470 1543080 TRUE FALSE 1232199.669 1303681.755 1262656.83 1310959.75 1321563.717 1099131.271 1241809.104 1129880.291 1285529.979 0.958514923 1.014120072 0.982207223 1.019781546 1.028030259 0.855002442 0.96599 0.878921775 1 20.29393182 2.260174202 24.99999849 0.924444167 1.000760255 0.416867161 0.044399738 203.7549256 235678.5225 0.013467182 0.011258086 182.0430915 -2.260174202 0.076316088 TPYHVNLLLAGYDEHEGPALYYMDYLAALAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TPYHVNLLLAGYDEHEGPALYYMDYLAALAK 31 0 P49721 P49721 PSMB2 Proteasome subunit beta type-2 0 ; 142.45 1.30E-08 325847000 346951 464456 229473.1 169815.4 559925 193807.7 336186 443233 171394.6 FALSE TRUE 325235.9562 498844.8055 234916.3103 174173.1507 515950.7491 249756.8368 285778.0303 498571.6157 142787.734 2.27775837 3.493611051 1.645213519 1.219804711 3.613410863 1.749147702 2.001418625 3.491697793 1 17.12351253 -1.839743928 2.83924229 0.509526135 2.39869848 0.221117257 0.844650576 62031549.95 13042545.94 200925898.6 0.191410903 0.014462923 1.839743928 1.889172346 TQADLDSLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TQADLDSLVR 10 0 Q7Z4W1;J3KS22;J3QS36 Q7Z4W1 DCXR L-xylulose reductase 0 77.64 0.075359 94649000 132980 177120 154730 146810 191710 146860 172040 157800 182950 FALSE TRUE 124657.0192 190234.1491 158400.2687 150577.3931 176653.8699 189256.0979 146244.1991 177501.6774 152414.4631 0.817881825 1.24813712 1.039273212 0.987946879 1.159036133 1.241720071 0.959516546 1.164598646 1 17.21764029 -1.041823369 3.930820898 0.999985777 1.086803244 0.027509681 0.1341019 7808557.794 2070134.372 982.5851304 0.028170768 0.090818982 1.041823369 0.086817466 TQAPTKAS(ph)E ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TQAPTKASE 9 1 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 1 TQAPT(0.04)KAS(0.96)E;TQAPT(0.214)KAS(0.786)E;TQAPT(0.463)KAS(0.537)E;TQAPT(0.053)KAS(0.947)E 108.53 0.0068323 686760000 2338170 1804590 2176340 2445140 2014610 1259290 2018360 1326840 1923330 TRUE FALSE 2191828.113 1938203.721 2227963.813 2507886.432 1856390.657 1622826.58 1715725.656 1492498.895 1602313.798 1.367914398 1.209628054 1.390466596 1.565165597 1.158568727 1.012801976 1.070780054 0.931464796 1 20.61172528 2.494701551 5.377747955 1.022227569 1.357287779 0.785224104 0.093010995 0.090319079 8.146111127 0.032588968 0.029108126 312.3931854 -2.494701551 0.335060209 TQAVFNHTEDYVLLPDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TQAVFNHTEDYVLLPDER 18 0 Q05048 Q05048 CSTF1 Cleavage stimulation factor subunit 1 0 ;; 189.48 3.25E-14 734620000 368410 387449 299894 377118 404990 326524 389994 386450 380150 FALSE TRUE 345351.8757 416136.1271 307007.6273 386795.4863 373183.7191 420786.1781 331518.0202 434699.1332 316700.5091 1.090468331 1.31397366 0.96939417 1.221328906 1.178348971 1.328656462 1.04678714 1.372587415 1 18.27275966 TQDECILHFLR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 203.51 3.64E-08 759030000 1269190 1629030 1259720 1245760 1699910 966600 1315880 1451460 1566990 FALSE TRUE 1189753.663 1749645.076 1289601.153 1277728.311 1566405.926 1245641.729 1118576.01 1632677.976 1305449.246 0.91137489 1.340262811 0.987860047 0.978765214 1.19989799 0.954186256 0.856851397 1.250663694 1 20.31611494 3.733218721 23.91682732 1.016797878 1.15873606 0.04285426 0.154354401 277.2905921 1087633.711 0.037318503 0.065071344 5410.26728 -3.733218721 0.141938182 TQDPSS(ph)PGTTPPQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TQDPSSPGTTPPQAR 15 0 Q13112 Q13112 CHAF1B Chromatin assembly factor 1 subunit B 1 TQDPS(0.007)S(0.989)PGT(0.004)TPPQAR;TQDPS(0.073)S(0.925)PGT(0.002)TPPQAR 255.53 1.05E-24 1805330000 2138480 2006890 2127850 1960090 2100520 1812390 2416140 1709340 2167310 TRUE FALSE 2004636.354 2155482.224 2178323.607 2010389.228 1935553.632 2335597.571 2053862.237 1922754.862 1805571.96 1.110250048 1.193794693 1.206445191 1.113436226 1.071989195 1.293549979 1.137513366 1.06490071 1 20.78402449 1.137348397 2.852700515 1.004648892 1.170545526 0.447416905 0.061615215 0.206313066 3.07909401 0.055053053 0.014957105 13.71981947 -1.137348397 0.165896634 TQEDEEEISTS(ph)PGVSEFVSDAFDACNLNQEDLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TQEDEEEISTSPGVSEFVSDAFDACNLNQEDLRK 34 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 1 TQEDEEEIS(0.001)T(0.037)S(0.962)PGVSEFVSDAFDACNLNQEDLRK;TQEDEEEIS(0.008)T(0.04)S(0.945)PGVS(0.007)EFVSDAFDACNLNQEDLRK;TQEDEEEISTS(1)PGVSEFVSDAFDACNLNQEDLRK;TQEDEEEIS(0.002)T(0.054)S(0.915)PGVS(0.029)EFVSDAFDACNLNQEDLRK;TQEDEEEIS(0.001)T(0.005)S(0.994)PGVSEFVSDAFDACNLNQEDLRK 209.61 5.81E-28 455472000 346485 277649 288248 353609 361791 236305 398024 259520 425888 TRUE FALSE 324799.1223 298206.4209 295085.3787 362683.2056 333377.3943 304522.4174 338343.9963 291921.6433 354804.5415 0.91543113 0.840480845 0.831684334 1.022205646 0.939608588 0.858282186 0.953606724 0.822767494 1 18.43666495 -5 0.111845982 1.303159633 0.840023136 0.139788752 0.065395924 283.1095349 2.09734198 20.18378793 0.766082015 1.00E-05 5 -0.463136497 TQEELRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TQEELRR 7 1 P15924 P15924 DSP Desmoplakin 0 69.628 0.094963 136850000 222210 207500 234340 243130 209360 192860 257700 183100 199440 FALSE TRUE 208302.2728 222863.5159 239898.6555 249369.1274 192917.7101 248535.5512 219060.2774 205960.4381 166152.1756 1.253683691 1.341321684 1.443849018 1.500847802 1.161090485 1.495830857 1.318431592 1.239589174 1 17.34214566 0.895871495 1.867450838 1.001035613 1.371229601 0.547225167 0.104288334 0.325150681 2.292346166 0.090262864 0.025405846 7.868129425 -0.895871495 0.370193988 TQES(ph)GDQDPQEAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TQESGDQDPQEAQK 14 0 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 TQES(1)GDQDPQEAQK 228.84 1.58E-12 203790000 837640 429300 546380 516290 329700 294990 669320 303130 750660 TRUE FALSE 785213.6076 461085.8187 559340.3916 529538.8755 303806.6919 380148.8242 568961.6797 340976.4478 625369.9966 1.255598465 0.737300832 0.894415138 0.846760923 0.485803114 0.607878258 0.909800091 0.545239538 1 19.25435048 4.740000141 24.59643307 0.75759771 1.255598663 0.472230079 0.166796517 87.89861421 1501690.147 0.037415152 0.2349617 54954.10526 -4.740000141 0.498000953 TQHEILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TQHEILR 7 0 P49257 P49257 LMAN1 Protein ERGIC-53 0 69.825 0.05869 107460000 62579 88953 62812 77907 94459 70081 80552 83440 58943 FALSE TRUE 58662.2921 95539.17268 64301.9303 79906.22552 87040.57117 90312.24703 68473.97541 93857.66767 49105.03251 1.194628923 1.945608582 1.3094774 1.62725125 1.772538714 1.839164794 1.394439061 1.911365554 1 15.58358327 -1.112889694 5.958779579 0.999996781 1.622036544 0.369777166 0.256125842 9.69E-06 1.44E-06 0.219359474 0.051703256 0.07710993 1.112889694 0.622039763 TQHLSNDHICYFLYQILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TQHLSNDHICYFLYQILR 18 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 ; 255.24 8.56E-31 150161000 69294 183272 113228 130538 194268 106621 137924 173397 97433 FALSE TRUE 64957.01223 196841.6496 115913.8216 133887.8261 179010.9749 137400.7519 117243.5766 195045.9971 81170.80286 0.800250952 2.425030216 1.428023594 1.64945795 2.20536164 1.692736144 1.444405778 2.402908315 1 16.30867326 -0.785592382 9.49050483 0.999998587 1.769683985 0.186956661 0.49474799 0 0 0.42186133 0.099433669 0.163835352 0.785592382 0.769685397 TQIAICPNNHEVHIYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TQIAICPNNHEVHIYEK 17 0 A0A1W2PNV4;C9JEY1;C9K057;O15143;F8VXW2;C9JBJ7;C9JTT6 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 ; 194.27 4.84E-11 1296620000 1533050 1376090 1393100 1410170 1535270 972890 1707910 1289740 1796320 FALSE TRUE 1437099.137 1477977.135 1426144.99 1446357.35 1414696.087 1253747.549 1451824.751 1450766.878 1496502.587 0.960305147 0.987620835 0.952985315 0.966491713 0.945334876 0.837785086 0.970145166 0.969438269 1 20.51316334 2.684202019 5.042149765 0.935728707 0.968066144 0.043145254 0.04316036 0.471717682 26.39257273 0.013464561 0.012822358 483.2835571 -2.684202019 0.032337437 TQIDHYVGIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TQIDHYVGIAR 11 0 O95197-3;O95197-4;O95197-7;O95197-2;O95197 O95197-3;O95197-7 RTN3 Reticulon-3 0 ;;; 105.65 0.0024374 697220000 981510 1338550 1116370 1142900 1339690 1071290 1197270 1309570 1325320 FALSE TRUE 920079.0411 1437657.635 1142850.824 1172228.749 1234476.151 1380554.032 1017750.478 1473072.697 1104115.53 0.833317725 1.302089859 1.035082645 1.0616903 1.118067918 1.250370993 0.921778972 1.334165363 1 20.07445971 -1.009372144 4.313226862 0.999994162 1.109471416 0.04280859 0.15875273 8860886.108 2073605.596 486.3607395 0.032521094 0.097865103 1.009372144 0.109477255 TQLAS(ph)WSDPTEETGPVAGILDTETLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.028)QLAS(0.445)WS(0.445)DPT(0.08)EET(0.003)GPVAGILDTETLEK;T(0.022)QLAS(0.946)WS(0.026)DPT(0.005)EET(0.001)GPVAGILDTETLEK;T(0.094)QLAS(0.567)WS(0.134)DPT(0.197)EET(0.007)GPVAGILDTETLEK 251.06 1.14E-46 155135000 126697.9 120214.3 145387.4 231249 192792 62990.7 69482.5 44208.8 54482.3 TRUE FALSE 118768.1046 129115.0919 148836.0578 237183.2408 177650.894 81175.09252 59064.24417 49728.366 45388.85216 2.616680065 2.844643248 3.279132446 5.225583586 3.913976352 1.788436778 1.30129407 1.095607481 1 15.47005038 2.11962695 4.394707403 1.248948622 3.506843289 0.7212154 0.71051776 0.133537471 4.501680163 0.304822421 0.219210479 131.712487 -2.11962695 2.257894667 TQLEELEDELQATEDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 276.64 2.15E-35 126331000 304740 208342 246578 235201 227118 168162 297962 201259 231461 FALSE TRUE 285666.8674 223767.8585 252426.9466 241236.6559 209281.0684 216707.6395 253285.3642 226386.6292 192828.6638 1.481454374 1.160449147 1.309073774 1.251041474 1.085321364 1.123835198 1.313525486 1.174029964 1 17.55696 0.16260432 0.029627135 2.35E-14 2.252381318 0.444458118 0.101443505 360.6170407 3.634929122 150.844893 124.8085514 1.454133634 -0.16260432 2.252381318 TQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYR 36 1 P11388;P11388-2;P11388-3;P11388-4;J3KTB7 P11388 TOP2A DNA topoisomerase 2-alpha 0 ; 237.42 7.72E-50 291060000 160974 191822 131322 95252 213053 91608 148770 176144 93496 FALSE TRUE 150898.9247 206024.7005 134437.0199 97696.32758 196320.6768 118053.7425 126463.3196 198135.9661 77890.91359 1.937311013 2.64504152 1.725965375 1.254271173 2.520456723 1.515629192 1.623595279 2.543762257 1 16.24916742 -1.990789668 0.151082586 2.10E-24 2.327318089 0.235724237 0.489782828 62.75578168 1.377692303 28.24796745 2.810051076 0.010214341 1.990789668 2.327318089 TQLEWTEAILEDEQTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TQLEWTEAILEDEQTQR 17 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 186.95 1.15E-09 11877000 19569 16483 14088 19139 18420 12409 20514 14902 15915 FALSE TRUE 18344.21122 17703.41847 14422.17401 19630.13914 16973.3675 15991.27686 17438.11614 16762.5475 13258.68369 1.383562023 1.33523198 1.08775308 1.480549624 1.28016988 1.206098376 1.315222277 1.264269357 1 13.69464993 -3.218480583 0.444600108 1.29E-09 1.28759971 0.444294069 0.103413056 208.7913716 5.965087665 197.3063828 0.05439541 0.000604671 3.218480583 1.287599709 TQLGEDHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TQLGEDHEK 9 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ; 110.84 0.0022221 910960000 1392940 1126720 1258890 1302800 1318760 932540 1511700 1197580 1439810 FALSE TRUE 1305758.372 1210143.521 1288751.465 1336232.054 1215189.909 1201749.159 1285034.619 1347100.499 1199496.409 1.088588812 1.008876318 1.07441044 1.113994209 1.013083407 1.00187808 1.071311768 1.123055049 1 20.19399741 -0.963940452 4.239329268 0.999997699 1.056767463 0.162898726 0.04271229 3766983.517 11639144.02 136.5917214 0.009922904 0.10865746 0.963940452 0.056769764 TQLS(ph)PSIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TQLSPSIK 8 0 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 TQLS(0.911)PS(0.089)IK 91.123 0.013333 127270000 184830 171070 185580 173150 187960 164520 194580 163120 175250 TRUE FALSE 173261.8202 183736.2008 189982.0452 177593.3221 173198.3798 212014.2532 165404.5354 183485.8911 145999.6428 1.186727699 1.258470207 1.301250068 1.216395593 1.186293175 1.452155972 1.132910548 1.256755753 1 17.15560531 0.313906707 0.995403115 0.99917417 1.258680432 0.44937611 0.086237281 2.54739585 2.96029082 0.079647157 0.023727273 2.060187307 -0.313906707 0.259506262 TQLS(ph)PSIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TQLSPSIKR 9 1 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 T(0.03)QLS(0.961)PS(0.01)IKR;TQLS(0.548)PS(0.452)IKR 96.334 0.0045561 652970000 926300 686510 746860 751470 776500 586150 926990 679100 1018680 TRUE FALSE 868324.5365 737339.9147 764575.8719 770753.9924 715516.8223 755361.9896 787996.4553 763887.1299 848655.7271 1.023176429 0.86883278 0.900925838 0.908205728 0.843117886 0.890068806 0.92852311 0.90011427 1 19.69481989 0.091781354 1.018096564 1.000666091 0.901391122 0.262323967 0.04739777 7.499989064 7.25391858 0.056744962 0.013091974 1.23532535 -0.091781354 -0.099274969 TQLS(ph)QGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TQLSQGR 7 0 Q8ND56-2;Q8ND56 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 TQLS(1)QGR 86.898 0.020705 173100000 155890 141530 153970 144700 121650 118990 182400 134550 150520 TRUE FALSE 146133.1232 152009.0285 157622.2411 148413.247 112096.0997 153340.4814 155050.8133 151348.8637 125397.2396 1.165361563 1.212219894 1.25698334 1.183544769 0.893927969 1.222837774 1.236477085 1.206955306 1 16.93614606 -2.106607448 2.531450812 0.661533087 1.181818192 0.21260069 0.102756844 5433691.481 2102278.275 10648490.86 0.024780853 0.007823346 2.106607448 0.520285106 TQLWASEPGT(ph)PPLPTSLPSQNPILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TQLWASEPGTPPLPTSLPSQNPILK 25 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 TQLWASEPGT(1)PPLPTSLPSQNPILK;TQLWASEPGT(1)PPLPTSLPSQNPILK 224.07 3.21E-33 2519900000 3455700 2767400 3023300 2819200 3290300 2486900 3814100 2956700 4111900 TRUE FALSE 3239413.906 2972301.175 3095014.104 2891545.445 3031893.11 3204827.659 3242211.113 3325850.503 3425597.326 0.945649356 0.867673837 0.903496182 0.844099633 0.885069908 0.935552943 0.946465917 0.970881918 1 21.70792414 1.673455859 1.234210996 0.990679393 0.886402426 0.669028256 0.027484274 0.241814249 0.698327275 0.02188135 0.008210862 47.14719491 -1.673455859 -0.104276968 TQMAEVLPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 TQMAEVLPSPR 11 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR 206.55 2.73E-08 10785560000 5292690 5518600 5830130 5537940 5963920 4400980 6714260 5162230 7305940 TRUE FALSE 4961429.981 5927202.886 5968423.437 5680052.916 5495537.78 5671471.482 5707519.045 5806745.779 6086531.416 0.815148997 0.973822771 0.980595191 0.933216725 0.902901407 0.93180682 0.937729333 0.954032006 1 22.53718887 -5 0.264401163 1.419452065 0.931909793 0.195661712 0.045892607 400.9793248 3.922302513 91.5404274 0.057858713 1.00E-05 5 -0.487542272 TQNKEESYDFSK ddPTM_SK-BR-3_Pertuzumab_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 0 115.68 0.00084209 158490000 242380 135960 186750 156130 188810 123800 225750 150590 292570 FALSE TRUE 227209.8685 146026.6199 191179.7982 160136.5601 173981.6242 159539.0503 191900.8833 169391.493 243738.1769 0.932188266 0.599112629 0.784365423 0.657002371 0.713805389 0.65455093 0.787323864 0.694973168 1 17.89497271 -1.350999385 2.922733368 1.003541005 0.720592889 0.458668797 0.092590948 16320081.77 19711480.94 493490.3268 0.020470717 0.044565688 1.350999385 -0.282948117 TQPDGTSVPGEPAS(ph)PISQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 449.84 2.84E-191 14612184000 5541681 5141242 5387307 5653234 6211930 4775443 6523481 5042970 6691190 TRUE FALSE 5194837.078 5521904.907 5515096.466 5798305.555 5724070.076 6154035.871 5545345.585 5672595.905 5574387.162 0.931911783 0.990585108 0.989363728 1.04016915 1.026851905 1.103984293 0.994790176 1.017617855 1 22.41038178 4.700227682 0.715953095 1.031647798 0.886008707 0.461617369 0.032182788 2.480720559 0.995511307 0.012323207 0.29062706 50145.0054 -4.700227682 -0.145639091 TQPHHS(ph)TPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TQPHHSTPTK 10 0 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 1 T(0.015)QPHHS(0.493)T(0.493)PTK 89.959 0.018649 72452000 25870 51290 43916 43920 44628 47427 57388 56549 59439 TRUE FALSE 24250.84288 55087.56497 44957.70826 45047.06156 41123.0969 61118.40499 48783.20216 63609.26713 49518.24691 0.489735489 1.112470017 0.907901856 0.909706308 0.830463505 1.234260274 0.985156083 1.284562179 1 15.59567262 2.247479276 24.99685416 1.113711147 0.896438781 0.352520173 0.179479529 248.1467119 695495.8238 0.058153183 0.047979204 176.7987848 -2.247479276 -0.217272365 TQPSSGVDSAVGTLPATS(ph)PQSTSVQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TQPSSGVDSAVGTLPATSPQSTSVQAK 27 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0 Q13428-4;Q13428-3 TCOF1 Treacle protein 1 TQPSSGVDSAVGTLPAT(0.024)S(0.966)PQS(0.006)T(0.004)SVQAK;TQPSSGVDSAVGTLPAT(0.071)S(0.917)PQS(0.009)T(0.002)SVQAK;TQPSSGVDSAVGTLPAT(0.04)S(0.952)PQS(0.008)TSVQAK 223.12 1.40E-34 1017970000 1038460 815660 910130 852690 974680 648940 1096810 833420 954740 TRUE FALSE 973464.6423 876052.3151 931718.7134 874571.469 898132.5645 836278.4433 932353.5228 937474.3216 795387.7261 1.22388693 1.101415431 1.171401925 1.099553639 1.129175791 1.051409792 1.172200038 1.178638154 1 19.60129877 -1.437087587 3.679995486 0.998846381 1.13716226 0.446506861 0.049160658 162.7679245 10952526.94 16512.65985 0.01045324 0.036552107 1.437087587 0.138315879 TQQHYYDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TQQHYYDK 8 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 72.006 0.047273 184610000 699520 828530 681170 743190 913910 457740 785700 723030 537920 FALSE TRUE 655738.2919 889875.2233 697327.6741 762261.5136 842135.1951 589882.1072 667891.5791 813301.8871 448137.6769 1.463251866 1.985718383 1.556056788 1.700953865 1.879188559 1.316296615 1.490371405 1.814848269 1 18.7735825 -2.582878149 0.219379811 6.31E-11 1.773448222 0.472423553 0.209965548 36.7245748 0.947673774 18.12949719 0.411484485 0.002612894 2.582878149 1.773448222 TQQHYYER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TQQHYYER 8 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;; 125.97 0.0012392 711540000 520580 919260 461973 484270 931960 327248 500970 866260 844620 FALSE TRUE 487997.8271 987322.9669 472931.2177 496697.1881 858767.6209 421719.1852 425854.1993 974414.4679 703647.4655 0.693526021 1.403150036 0.672113865 0.705889259 1.220451523 0.599333055 0.605209597 1.384804914 1 19.42449328 5.015799463 21.03361914 0.917514981 0.212084624 0.055248544 0.308501244 9917.557533 212820.4962 0.069788393 234975.7393 103704.9445 -5.015799463 -0.705430357 TQQHYYERDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TQQHYYERDPK 11 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 73.881 0.025444 110220000 173340 162420 159050 154390 221620 112040 211530 145950 283390 FALSE TRUE 162490.9588 174445.7458 162822.7411 158351.9088 204214.8592 144384.1292 179813.0402 164172.1788 236090.3782 0.688257438 0.738893923 0.689662757 0.670725804 0.864985946 0.611562954 0.76162799 0.695378524 1 17.84897972 -1.588686379 2.775511028 1.020418122 0.716835616 0.645125383 0.06638723 13310736.83 13124192.93 1992342.189 0.014585653 0.025781823 1.588686379 -0.303582507 TQQLHPVLQKPSVFGNDS(ph)DDDDETSVSESLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TQQLHPVLQKPSVFGNDSDDDDETSVSESLQR 32 1 Q9H0G5 Q9H0G5 NSRP1 Nuclear speckle splicing regulatory protein 1 1 TQQLHPVLQKPSVFGNDS(1)DDDDETSVSESLQR;TQQLHPVLQKPSVFGNDS(1)DDDDETSVSESLQR;TQQLHPVLQKPS(0.001)VFGNDS(0.999)DDDDETSVSESLQR;TQQLHPVLQKPS(0.005)VFGNDS(0.995)DDDDETSVSESLQR;TQQLHPVLQKPSVFGNDS(1)DDDDETSVSESLQR;TQQLHPVLQKPS(0.012)VFGNDS(0.986)DDDDET(0.002)SVSESLQR 398.56 4.53E-167 10378890000 2697793 2047937 2190741 2054734 2052428 1816214 2766240 1932915 2070145 TRUE FALSE 2528942.952 2199568.386 2242706.411 2107461.953 1891238.584 2340525.498 2351467.993 2174243.693 1724624.426 1.46637315 1.275389791 1.300402788 1.221983129 1.096608952 1.357121854 1.36346671 1.260705612 1 20.71785079 0.957996868 21.28631998 0.999999997 1.29397248 0.481967953 0.096067555 1067.45915 540968.0876 0.090265731 0.022566433 9.078139824 -0.957996868 0.293972483 TQS(ph)GNFYTDTLGMAEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TQSGNFYTDTLGMAEFR 17 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2 E9PP16 PPFIBP2 Liprin-beta-2 1 T(0.004)QS(0.996)GNFYTDTLGMAEFR;T(0.049)QS(0.951)GNFYTDTLGMAEFR;TQS(1)GNFYTDTLGMAEFR;TQS(1)GNFYTDTLGMAEFR;T(0.045)QS(0.955)GNFYTDTLGMAEFR;TQS(1)GNFYTDTLGMAEFR 338.94 2.42E-72 980173000 800395 850521 697411 817468 880324 485842 914512 674531 536975 TRUE FALSE 750299.7057 913494.4598 713953.9183 838445.6129 811186.9041 626096.6984 777389.4155 758747.6802 447350.4035 1.677208067 2.042011034 1.59596127 1.874248031 1.813314345 1.399566634 1.737763975 1.696092536 1 18.77104579 -2.335516961 0.224064084 1.92E-11 1.873314559 0.677151798 0.161746674 21.54104125 0.625798846 11.18772034 0.303140892 0.00461831 2.335516961 1.873314559 TQS(ph)LPVTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TQSLPVTEK 9 0 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 TQS(1)LPVTEK;TQS(1)LPVTEK 192.95 3.58E-05 217340000 922750 669190 712750 712840 796110 445210 824330 562190 909570 TRUE FALSE 864996.7247 718737.5239 729656.7666 731132.6812 733586.732 573734.8996 700729.3692 632380.659 757756.891 1.141522743 0.948506747 0.962916702 0.964864444 0.968103017 0.757149036 0.924741665 0.834542934 1 19.53137554 2.44795453 24.87227399 0.872811283 0.986033522 0.336128742 0.081842416 220.1652607 187747.3433 0.025576149 0.021398829 280.5139927 -2.44795453 0.113222239 TQS(ph)LSALPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TQSLSALPK 9 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 TQS(1)LSALPK 101.71 0.0039837 229810000 500870 391980 432820 498490 569450 235780 432040 259190 467710 TRUE FALSE 469521.4408 421002.6071 443086.6948 511282.0973 524727.6941 303845.8584 367259.6129 291550.442 389646.1795 1.20499434 1.080474105 1.13715139 1.31217018 1.346677375 0.779799404 0.942546423 0.748244067 1 18.57180515 2.231278192 24.99913898 0.868431072 1.191338589 0.729016577 0.105012275 96.15558597 330080.4483 0.039569472 0.029818267 170.3249194 -2.231278192 0.322907517 TQS(ph)PEFEAQSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TQSPEFEAQSSK 12 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 TQS(1)PEFEAQSSK;TQS(1)PEFEAQSSK;TQS(1)PEFEAQSSK;TQS(1)PEFEAQSSK;TQS(1)PEFEAQSSK 288.06 5.94E-29 1050608000 3921630 2757150 3184830 3104600 3033730 2346280 3759590 2555050 3122040 TRUE FALSE 3676182.179 2961292.255 3260375.672 3184269.292 2795473.083 3023612.947 3195874.382 2874053.617 2600951.355 1.413399052 1.138541961 1.253531968 1.224270991 1.074788684 1.16250269 1.228732854 1.105000911 1 21.31060799 7.999994761 0.022747143 2.31E-07 2.756127386 0.525906021 0.077932067 2183.268111 3.822157463 164.6626602 322.9651045 99998793.64 -7.999994761 2.756127155 TQS(ph)PGGCSAEAVLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TQSPGGCSAEAVLAR 15 0 Q96MH2;K7ESM2;K7ELS4;K7EJA3;K7ERG7 Q96MH2 HEXIM2 Protein HEXIM2 1 TQS(1)PGGCSAEAVLAR;TQS(1)PGGCSAEAVLAR;TQS(1)PGGCSAEAVLAR 264.64 4.02E-25 812840000 572090 563100 555120 541800 614600 504454 708590 578470 768080 TRUE FALSE 536283.9081 604792.5099 568287.7085 555703.5053 566331.7952 650081.6807 602343.5077 650693.2529 639882.486 0.838097494 0.945161843 0.888112616 0.868446187 0.88505594 1.015939168 0.941334575 1.016894925 1 19.28744745 2.247699298 24.99985192 0.984558003 0.892858705 0.707813308 0.034239302 118.9212619 325322.1489 0.011559513 0.009545775 176.8883773 -2.247699298 -0.091699298 TQS(ph)SLTVSEVLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TQSSLTVSEVLTR 13 0 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 T(0.001)QS(0.99)S(0.01)LTVSEVLTR 134.49 9.96E-05 100500000 117130 99318 104050 94376 117990 78690 127080 96613 142170 TRUE FALSE 109799.0424 106671.6081 106518.1151 96797.84794 108723.5413 101406.5256 108025.5338 108675.3457 118440.9085 0.927036475 0.900631457 0.899335512 0.817267016 0.917955989 0.856178214 0.912062691 0.917549072 1 16.85380794 0.765037636 1.419426162 0.999695647 0.888491525 0.54656275 0.031756512 0.591049458 2.060470263 0.027834065 0.008212367 5.821536648 -0.765037636 -0.111204122 TQS(ph)VEITK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TQSVEITK 8 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 TQS(1)VEITK;TQS(1)VEITK;TQS(1)VEITK 156.01 0.00041933 538130000 1872440 953010 1292600 1036910 1015640 931950 1189550 791410 1562730 TRUE FALSE 1755247.323 1023571.852 1323261.082 1063518.866 935875.7313 1200988.836 1011188.021 890219.2806 1301900.267 1.348219496 0.78621372 1.016407413 0.816897341 0.718853629 0.922489123 0.7767016 0.683784544 1 20.3121875 4.742464214 24.8964437 0.842556773 1.348219704 0.675725414 0.110595634 215.6347896 1375222.551 0.025177486 0.190841559 55266.78661 -4.742464214 0.505662931 TQSAS(ph)PPPKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TQSASPPPKER 11 1 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 T(0.005)QS(0.106)AS(0.89)PPPKER 58.079 0.065768 259020000 370360 331260 371520 359950 385480 307400 463980 312430 400500 TRUE FALSE 347179.8287 355786.8351 380332.6298 369186.9264 355205.9558 396141.3898 394410.5064 351437.5732 333653.9627 1.040538605 1.066334811 1.139901432 1.106496454 1.064593847 1.187282137 1.182094477 1.053299564 1 18.34799311 4.2921628 2.246772598 1.119745787 1.042615413 0.083429834 0.058586029 0.566407211 5.31235562 0.014581621 0.059350561 19595.79104 -4.2921628 -0.077130373 TQSPCFGDDDPAKKEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TQSPCFGDDDPAKKEPR 17 2 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 ; 163.18 1.55E-09 971000000 1488740 835690 1048170 1045840 1149720 710450 1342460 866700 1985780 FALSE TRUE 1395562.421 897565.3571 1073033.087 1072678.025 1059425.629 915545.3818 1141170.586 974909.4028 1654340.489 0.843576295 0.542551768 0.648616832 0.648402207 0.640391525 0.553420162 0.689803939 0.589303961 1 20.65782476 -1.349854188 2.98381457 1.004176215 0.635698323 0.635443936 0.084386273 12761433.98 15638998.72 464717.3285 0.01823435 0.044683359 1.349854188 -0.368477893 TQSSSCERDS(ph)PSTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TQSSSCERDSPSTSR 15 1 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;Q5JS79 A0A2U3TZM1 CASK Peripheral plasma membrane protein CASK 1 TQSSSCERDS(0.991)PS(0.008)T(0.001)SR;TQSSSCERDS(0.993)PS(0.004)T(0.003)S(0.001)R 130.36 3.65E-05 960310000 394650 357140 364980 332450 368030 276150 363080 280550 353770 TRUE FALSE 369949.561 383583.0172 373637.498 340981.2298 339126.4084 355870.0221 308639.5247 315577.2851 294723.5016 1.255242826 1.301501289 1.267756036 1.156952968 1.150659539 1.2074708 1.047217216 1.070757111 1 18.16900258 2.24546904 0.470674202 0.995683224 1.306544624 0.847428547 0.038909325 0.342293774 0.163991209 0.037513748 0.036305882 175.9823207 -2.24546904 0.310861399 TQT(ph)PPLGQTPQLGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TQTPPLGQTPQLGLK 15 0 D3DQV9;P78344;H0Y3P2;P78344-2;E9PKF8 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 T(0.154)QT(0.846)PPLGQTPQLGLK;T(0.007)QT(0.993)PPLGQTPQLGLK;T(0.009)QT(0.991)PPLGQTPQLGLK;T(0.004)QT(0.996)PPLGQTPQLGLK;T(0.015)QT(0.985)PPLGQTPQLGLK 204.07 5.69E-08 1968860000 3777570 2696580 3147670 3009490 3203030 2593440 4692770 3297390 4235750 TRUE FALSE 3541138.637 2896237.589 3222334.219 3086718.608 2951476.944 3342124.027 3989132.704 3709076.4 3528775.961 1.003503389 0.820748503 0.913159196 0.87472785 0.836402474 0.947105757 1.130457912 1.051094329 1 21.75073641 1.939835479 5.109142478 1.069610476 0.883168065 0.63921931 0.058272152 0.111104033 5.852740652 0.023568042 0.014258154 87.06337104 -1.939835479 -0.18644241 TQT(ph)PPVS(ph)PAPQPTEER ddPTM_SK-BR-3_Pertuzumab_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;T(0.003)QT(0.997)PPVS(1)PAPQPTEER;TQT(1)PPVS(1)PAPQPTEER;TQT(1)PPVS(1)PAPQPTEER 306.4 6.71E-46 3519430000 2563470 1837860 2288620 2810430 2417150 1545820 1541100 1177120 959415 TRUE FALSE 2403026.989 1973937.067 2342907.147 2882550.392 2227316.789 1992073.14 1310026.362 1324086.023 799282.4384 3.006480404 2.469636479 2.931263136 3.606422778 2.786645474 2.492326922 1.639003059 1.656593414 1 19.60834587 1.730004566 1.567567978 1.264171781 2.926948524 0.839359343 0.309310355 0.152041135 0.729549288 0.249939315 0.097516199 53.70374427 -1.730004566 1.662776743 TQT(ph)PPVS(ph)PAPQPTEERLPSSPVYEDAASFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 TQT(1)PPVS(0.795)PAPQPT(0.204)EERLPSS(0.001)PVYEDAASFK;TQT(1)PPVS(0.361)PAPQPT(0.333)EERLPS(0.305)S(0.001)PVYEDAASFK 246.6 1.41E-45 3527200000 1776630 1303640 1471320 1992980 1892710 964940 1259420 920300 1318010 TRUE FALSE 1665433.9 1400162.862 1506220.405 2044123.241 1744064.191 1243502.514 1070581.663 1035201.481 1098025.616 1.51675323 1.275164114 1.37175343 1.861635294 1.588363846 1.132489529 0.97500609 0.942784454 1 20.06648028 2.088220354 4.252939659 0.986383119 1.482534274 0.730763405 0.154939245 0.137129256 4.611005202 0.069740968 0.049263246 122.5237706 -2.088220354 0.496151155 TQT(ph)PPVSPAPQPTEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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;TQT(1)PPVSPAPQPTEER;TQT(1)PPVSPAPQPTEER;TQT(0.996)PPVS(0.004)PAPQPTEER;TQT(1)PPVSPAPQPTEER;T(0.202)QT(0.798)PPVSPAPQPTEER 273.32 3.75E-34 6562402000 2013133 1452108 1690347 1576524 1324176 1125406 1458558 1103638 981670 TRUE FALSE 1887134.599 1559623.587 1730442.829 1616980.275 1220180.558 1450292.443 1239860.768 1241429.634 817822.9352 2.307509997 1.907043102 2.115913793 1.977176483 1.491986231 1.773357509 1.516050376 1.51796872 1 19.641429 1.742990712 0.208996254 0.764375087 2.462139203 0.850396968 0.144543614 0.935756876 0.195567379 0.564931375 0.653605558 55.33382748 -1.742990712 1.697764116 TQT(ph)PPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 T(0.132)QT(0.868)PPVS(0.025)PAPQPT(0.01)EERLPS(0.591)S(0.374)PVYEDAASFK 157.86 1.24E-09 166750000 111910 77222 93720 122040 120040 58852 83112 56362 92077 TRUE FALSE 104905.7529 82939.59723 95943.08266 125171.753 110612.5426 75841.61702 70650.12717 63398.91977 76708.75386 1.367585153 1.081227279 1.2507449 1.631779252 1.4419807 0.988695725 0.921017793 0.82648872 1 16.2271036 2.133617828 5.624210654 0.919494701 1.314883251 0.666060664 0.146998278 0.153931743 7.13621471 0.062746858 0.046036789 136.024716 -2.133617828 0.39538855 TQT(ph)PPVSPAPQPTEERLPSS(ph)PVYEDAASFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 T(0.083)QT(0.896)PPVS(0.022)PAPQPT(0.338)EERLPS(0.196)S(0.465)PVY(0.001)EDAASFK;TQT(0.999)PPVS(0.084)PAPQPT(0.011)EERLPS(0.411)S(0.495)PVYEDAASFK 167.58 5.67E-12 1065740000 785360 617380 693410 889920 856500 430581 582050 395491 600110 TRUE FALSE 736205.7195 663091.4576 709858.0127 912756.8538 789233.945 554882.7448 494777.006 444868.9219 499947.7641 1.47256528 1.326321478 1.419864361 1.825704442 1.578632812 1.109881441 0.989657403 0.889830806 1 18.93141784 2.113353692 4.132693301 0.977332327 1.49624797 0.79482238 0.134089761 0.115370893 3.57618523 0.059908659 0.042621675 129.8236131 -2.113353692 0.518915643 TQTGDSSS(ph)ISSFSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TQTGDSSSISSFSYR 15 0 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6;Q4V328-2;Q4V328-3 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 TQTGDS(0.061)S(0.211)S(0.722)IS(0.006)SFSYR;TQTGDSS(0.102)S(0.895)IS(0.002)SFSYR;TQTGDS(0.001)S(0.17)S(0.64)IS(0.187)S(0.002)FSYR 326.38 1.80E-58 576340000 1074050 1164100 1111250 1197860 1312620 868440 1306040 1074770 1095440 TRUE FALSE 1006827.128 1250291.175 1137609.375 1228599.116 1209532.12 1119144.53 1110211.427 1208957.4 912603.9872 1.10324647 1.370025984 1.24655315 1.346256572 1.325363616 1.226320009 1.216531422 1.324733858 1 19.79962943 -3.317474958 0.419826317 3.59E-11 1.280040883 0.528336567 0.079218361 141.548621 3.712797761 125.7784886 0.042364574 0.000481421 3.317474958 1.280040883 TQTPPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_SK-BR-3_Pertuzumab_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;TQT(0.009)PPVS(0.007)PAPQPT(0.002)EERLPS(0.491)S(0.491)PVYEDAASFK;TQTPPVSPAPQPTEERLPS(0.5)S(0.5)PVYEDAASFK 197.66 1.62E-25 3631440000 320559 288287 288014 286667 346401 211371 362544 270681 489301 TRUE FALSE 300495.7844 309632.0694 294845.8281 294023.3605 319196.0628 272390.3764 308183.8929 304476.1187 407633.5021 0.737171461 0.75958445 0.723311079 0.721293414 0.783046686 0.668223723 0.756031806 0.746935954 1 18.6369131 0.317304634 1.767491361 1.000013549 0.735533303 0.883863611 0.030003654 2.580578619 6.312161164 0.025556096 0.007155392 2.076369467 -0.317304634 -0.264480246 TQTPPVSPAPQPTEERLPSS(ph)PVYEDAASFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 TQTPPVSPAPQPTEERLPS(0.131)S(0.869)PVYEDAASFK;TQTPPVSPAPQPTEERLPS(0.075)S(0.925)PVYEDAASFK;TQTPPVSPAPQPTEERLPS(0.031)S(0.969)PVYEDAASFK 364.62 9.60E-137 8986340000 2762660 2276740 2384660 2437160 3099610 2001150 3093330 2246130 4077520 TRUE FALSE 2589750.042 2445312.199 2441225.261 2499701.652 2856179.134 2578849.519 2629513.884 2526564.275 3396955.57 0.762373834 0.719854042 0.718650925 0.735865277 0.840805561 0.759164925 0.774079563 0.743773129 1 21.69581092 -5 0.249234755 2.492253981 0.730466558 0.826151962 0.034991288 71.19116226 0.706403282 54.08047143 0.05063896 1.00E-05 5 -1.761787424 TQVLS(ph)PDSLFTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TQVLSPDSLFTAK 13 0 P55196-5;P55196;J3KN01;A8MQ02;H0Y8L4;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 TQVLS(1)PDSLFTAK;TQVLS(1)PDSLFTAK 245.39 4.41E-17 162283000 517060 428240 477520 483100 531580 367300 558970 415150 579720 TRUE FALSE 484698.1376 459947.3352 488846.9999 495497.1639 489831.8511 473333.5474 475157.6377 466982.3914 482960.9869 1.003596876 0.952348839 1.012187347 1.025956914 1.014226541 0.980065803 0.983842693 0.966915349 1 18.88154713 3.963627859 23.96412635 0.996926013 0.975306761 0.125125954 0.021260124 431.4156737 766193.042 0.005562376 0.010112839 9196.611895 -3.963627859 -0.021619252 TQVYRPPPPYPPPRPANS(ph)TPDLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TQVYRPPPPYPPPRPANSTPDLSR 24 2 Q16825 Q16825 PTPN21 Tyrosine-protein phosphatase non-receptor type 21 1 TQVYRPPPPYPPPRPANS(0.984)T(0.015)PDLSR 173.25 2.30E-12 155470000 38022 45535 47510 41383 52979 27618 49975 40834 61142 TRUE FALSE 35642.27089 48906.45878 48636.95964 42444.95784 48818.24305 35590.86826 42481.7127 45932.21479 50937.00521 0.699732361 0.960136125 0.954845292 0.83328334 0.958404265 0.698723219 0.834004915 0.901745491 1 15.63642652 TRAS(ph)LPVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TRASLPVVR 9 1 Q5T5P2;Q5T5P2-7;Q5T5P2-9;Q5T5P2-2;Q5T5P2-10;Q5T5P1;Q5T5P0 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 T(0.108)RAS(0.892)LPVVR;T(0.176)RAS(0.824)LPVVR;TRAS(1)LPVVR;T(0.006)RAS(0.994)LPVVR;T(0.068)RAS(0.932)LPVVR 159.44 4.00E-05 1945230000 631513 771490 574789 552757 986620 384793 862218 683802 1265520 TRUE FALSE 591987.7286 828611.9223 588423.2665 566941.6804 909134.845 495876.4925 732936.4153 769176.1849 1054296.536 0.561500212 0.7859382 0.55811932 0.537744041 0.862314172 0.470338729 0.695190006 0.729563418 1 20.00784927 0.787147556 1.928267494 0.9994342 0.642473697 0.4825407 0.117936887 0.636593661 4.021888023 0.101052124 0.028140656 6.1255848 -0.787147556 -0.356960503 TRDDEPVCGRPLGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TRDDEPVCGRPLGIR 15 2 Q9HDC9;H0Y512;Q9HDC9-2 Q9HDC9 APMAP Adipocyte plasma membrane-associated protein 0 109.84 0.00054472 247970000 45450 50279 40126 42824 65615 29471 45319 51088 78015 FALSE TRUE 42605.36563 54001.70948 41077.80767 43922.93634 60461.86258 37978.79928 38523.83667 57466.44926 64993.7925 0.655529767 0.830874879 0.63202663 0.675802021 0.930271342 0.584345025 0.592731016 0.884183659 1 15.98801431 1.037607883 5.615632829 0.999233891 0.702815069 0.487336777 0.106715561 0.132544149 10.22705698 0.100945825 0.025437715 10.90455339 -1.037607883 -0.296418822 TRDDGDEEGLLT(ph)HS(ph)EEELEHS(ph)QDTDADDGALQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 3 TRDDGDEEGLLT(1)HS(1)EEELEHS(0.57)QDT(0.43)DADDGALQ;T(0.002)RDDGDEEGLLT(0.998)HS(0.999)EEELEHS(0.593)QDT(0.409)DADDGALQ 96.886 6.20E-05 630650000 192343 162907 164145 157945 185678 124932 208572 158634 241019 TRUE FALSE 180304.595 174968.8038 168038.5969 161998.1361 171095.5989 160997.8403 177298.5649 178439.8041 200791.3719 0.897969835 0.871396027 0.836881562 0.806798293 0.85210633 0.801816526 0.882998922 0.888682628 1 17.61533775 0.80355268 1.439645566 0.99937309 0.846526399 0.723735942 0.029449919 0.366889716 1.376740067 0.027319025 0.008049661 6.361399647 -0.80355268 -0.152846692 TRDDGDEEGLLT(ph)HS(ph)EEELEHSQDTDADDGALQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 2 TRDDGDEEGLLT(1)HS(1)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(1)HS(1)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(1)HS(1)EEELEHSQDTDADDGALQ 265.45 1.88E-58 2923310000 1910710 1513220 1808790 1611440 1930760 1482670 2039600 1567620 2369620 TRUE FALSE 1791122.072 1625260.383 1851695.353 1652792.279 1779125.898 1910692.76 1733780.915 1763340.808 1974115.114 0.907303763 0.823285518 0.937987527 0.837231966 0.901227029 0.967873022 0.878257252 0.893230995 1 20.91277469 -4.999999999 0.152409364 1.39036242 0.858539977 0.406617612 0.041569138 128.9555224 1.15896533 15.23802518 0.188364343 1.00E-05 4.999999999 -0.531822442 TRDDGDEEGLLT(ph)HSEEELEHSQDTDADDGALQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 T(0.001)RDDGDEEGLLT(0.5)HS(0.5)EEELEHSQDTDADDGALQ 129.66 1.38E-07 3485300000 1090300 910490 931310 919020 941810 766600 1127500 846150 1175300 TRUE FALSE 1022060.069 977903.627 953401.113 942603.6091 867844.0417 987904.9753 958441.8422 951793.6901 979134.8373 1.04383996 0.998742553 0.973717895 0.962690299 0.88633762 1.008957028 0.978866041 0.972076219 1 19.90114802 4.753852481 1.195635072 0.967898405 1.080150529 0.352627413 0.032669693 1.811037299 2.131132183 0.009134675 0.255540054 56735.18571 -4.753852481 0.112252124 TRDDGDEEGLLTHS(ph)EEELEHS(ph)QDT(ph)DADDGALQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 3 TRDDGDEEGLLT(0.072)HS(0.93)EEELEHS(0.999)QDT(0.999)DADDGALQ 55.765 0.047749 328920000 59909 69802 70564 70792 76226 66660 107980 74113 75023 TRUE FALSE 56159.40263 74970.21271 72237.8114 72608.64257 70239.51744 85903.65987 91789.40144 83366.17119 62501.17663 0.898533526 1.199500821 1.155783224 1.161716411 1.123811122 1.374432683 1.468602775 1.333833628 1 15.93159573 2.241680494 24.95771768 1.349237914 1.129345603 0.241530396 0.14797169 83.60803102 668836.0203 0.047900839 0.038500833 174.4538243 -2.241680494 -0.219892311 TRDDGDEEGLLTHS(ph)EEELEHSQDTDADDGALQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 TRDDGDEEGLLT(0.032)HS(0.967)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(0.195)HS(0.805)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(0.17)HS(0.83)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(0.011)HS(0.989)EEELEHSQDTDADDGALQ;T(0.006)RDDGDEEGLLT(0.15)HS(0.545)EEELEHS(0.15)QDT(0.15)DADDGALQ;TRDDGDEEGLLT(0.186)HS(0.803)EEELEHS(0.011)QDT(0.001)DADDGALQ;TRDDGDEEGLLT(0.003)HS(0.997)EEELEHSQDTDADDGALQ;TRDDGDEEGLLTHS(1)EEELEHSQDTDADDGALQ 418.62 2.89E-187 11396120000 3423735 2956849 3244682 3068788 3578507 2859919 3771157 2942588 4321404 TRUE FALSE 3209449.538 3175777.177 3321647.389 3147538.296 3297465.495 3685531.188 3205707.018 3309976.589 3600133.755 0.891480638 0.882127552 0.92264555 0.87428371 0.915928607 1.023720628 0.890441088 0.919403782 1 21.77961908 2.468677363 24.99937066 0.948644297 0.895807192 0.374037673 0.039307752 238.1035449 704934.5476 0.012855297 0.010771886 294.2235041 -2.468677363 -0.052837105 TRDDGDEEGLLTHSEEELEHSQDT(ph)DADDGALQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 TRDDGDEEGLLTHSEEELEHS(0.114)QDT(0.886)DADDGALQ;TRDDGDEEGLLTHS(0.001)EEELEHS(0.422)QDT(0.578)DADDGALQ 133.36 8.55E-08 594700000 142326 142905 137501 142289 162279 106006 179729 148466 200748 TRUE FALSE 133418.0697 153485.8349 140762.5887 145940.3766 149534.2619 136608.2113 152780.305 167002.3069 167241.8619 0.797755228 0.917747705 0.841670782 0.872630662 0.894119811 0.816830247 0.913529084 0.998567613 1 17.35157648 1.370970794 3.258537047 1.001187327 0.864107254 0.730697352 0.035249042 0.120034879 2.099946044 0.025639451 0.008260529 23.49474817 -1.370970794 -0.137080073 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 0 111.52 2.03E-06 83351000 101100 81216 85881 89272 99280 74852 93267 78977 124350 FALSE TRUE 94772.33147 87229.31715 87918.13788 91562.87066 91482.94928 96460.55728 79282.4792 88837.4523 103595.1817 0.914833392 0.842020987 0.848670145 0.8838526 0.883081122 0.931129766 0.76531049 0.857544249 1 16.66059738 -1.137298763 3.486166617 1.000136352 0.859119618 0.45587077 0.045557716 23379852898 35780960924 35826717.78 0.010743639 0.072895587 1.137298763 -0.141016734 EHSDYVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 EHSDYVR 7 0 H0Y8P4;Q8TED0-3;Q8TED0 H0Y8P4 UTP15 U3 small nucleolar RNA-associated protein 15 homolog 0 71.342 0.054575 110340000 115350 46305 43318 37517 50932 30992 52070 45002 49778 FALSE TRUE 108130.4494 49733.47038 44345.52342 38479.74974 46932.00617 39938.88729 44262.58689 50620.59876 41469.73022 2.607454855 1.199271616 1.069346803 0.927899688 1.131717181 0.963085293 1.067346873 1.220663807 1 15.33977104 4.748050942 3.604950039 1.063027805 2.799858679 0.971152971 0.083479938 0.044088533 1.026852768 0.019805121 0.209468135 55982.32646 -4.748050942 1.736830873 up TRDELDQFLDKMDDPDYWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TRDELDQFLDKMDDPDYWR 19 2 Q14137;Q14137-2;A0A075B729 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 ; 177 2.31E-14 94427000 50233 53750 56656 56762 69140 34462 66831 46491 114681 FALSE TRUE 47089.0062 57729.70593 57999.90707 58218.60902 63710.0233 44410.61996 56810.31198 52295.50369 95540.00023 0.492872159 0.60424645 0.607074596 0.60936371 0.666841356 0.464837972 0.594623318 0.547367632 1 16.54381726 -1.792324138 2.749117617 1.112958395 0.579324028 0.835521916 0.059431707 9244670.136 7154945.844 6996183.062 0.013503171 0.016131541 1.792324138 -0.533634367 TRDELEVIHLIEEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 TRDELEVIHLIEEHR 15 1 P10155-3;P10155-5;P10155-4;P10155 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 ;;;;;; 220.59 1.06E-12 1521039000 633587 724336 695138 728296 719440 602274 782373 636766 762251 FALSE TRUE 593931.9207 777966.5911 711627.0016 746985.3084 662938.0845 776140.7267 665063.4318 716267.6368 635026.3838 0.935286999 1.225093336 1.120625882 1.176305942 1.043953608 1.222218079 1.047300473 1.127933666 1 19.27645701 0.40049946 0.732521113 0.998461554 1.129633859 0.115311791 0.089045058 3.568541704 2.833053473 0.092274839 0.028099707 2.514776888 -0.40049946 0.131172305 TREEECHFYAGGQVYPGEASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TREEECHFYAGGQVYPGEASR 21 1 Q13162;A6NG45 Q13162 PRDX4 Peroxiredoxin-4 0 ;; 146.25 6.65E-08 1693500000 382625 404301 401887 400728 422729 310040 470257 359808 390456 FALSE TRUE 358677.1843 434235.8667 411419.9494 411011.3589 389529.5695 399543.5149 399746.3285 404730.8208 325286.3712 1.102650514 1.334934093 1.264793074 1.26353698 1.197497356 1.22828237 1.228905862 1.24422926 1 18.31135085 -3.812083474 0.327954134 2.45E-11 1.254926391 0.58575379 0.060319734 94.92236254 1.738185678 64.66251861 0.048437099 0.00015414 3.812083474 1.254926391 TREEIQEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TREEIQEVR 9 1 P08559-3;P08559;P08559-2;P08559-4;Q5JPU3;P29803 P08559-3 PDHA1;PDHA2 "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial;Pyruvate dehydrogenase E1 component subunit alpha, testis-specific form, mitochondrial" 0 ; 153.12 7.19E-05 1758780000 1196730 1199200 1154620 1104380 1642110 1117910 1187580 1197730 2230100 FALSE TRUE 1121828.806 1287990.016 1182008.132 1132720.261 1513145.305 1440632.469 1009513.404 1347269.227 1857881.903 0.603821375 0.693257205 0.636212738 0.609683672 0.814446441 0.7754166 0.543367909 0.725164083 1 20.82522737 -2.272755158 1.326590017 1.75804179 0.670499675 0.60660305 0.08213396 31474.52935 4039.245595 70958.80364 0.022500424 0.005336357 2.272755158 -1.087542115 TREFEDRDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TREFEDRDR 9 2 Q13951-2;A0A494C0A9;Q13951;J3KS23 Q13951-2 CBFB Core-binding factor subunit beta 0 113.69 0.00098991 54732000 65427 66397 61164 65094 81403 48864 66895 62401 95891 FALSE TRUE 61332.04086 71313.10297 62614.83896 66764.42224 75009.93674 62970.24356 56864.71577 70191.90221 79886.17262 0.767742888 0.892683935 0.783800712 0.835744411 0.938960202 0.788249599 0.711821757 0.878648956 1 16.28565819 0.987655614 24.22662309 1.00000001 0.817698431 0.457178441 0.063573768 393.5772488 772421.9355 0.062670064 0.015667516 9.719761627 -0.987655614 -0.182301579 TRHGS(ph)ASQVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TRHGSASQVQK 11 1 H0Y465;P21359-2;P21359-6;P21359;J3QSG6 H0Y465 NF1 Neurofibromin;Neurofibromin truncated 1 T(0.015)RHGS(0.981)AS(0.004)QVQK;T(0.152)RHGS(0.848)ASQVQK 128.71 0.00015758 47389000 93410 119075 101375 121108 141677 70500 149099 133948 182165 TRUE FALSE 87563.63484 127891.4369 103779.6629 124215.8363 130550.2599 90852.20553 126742.9891 150671.7027 151760.4847 0.576985735 0.842718954 0.683838504 0.818499207 0.860238818 0.598655215 0.835151452 0.992825655 1 17.21143667 1.356687135 3.673829369 0.998527795 0.744670144 0.561367138 0.09571434 0.164120756 3.55001173 0.06794629 0.022243063 22.73459045 -1.356687135 -0.253857651 TRHS(ph)PT(ph)PQQSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TRHSPTPQQSNR 12 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 TRHS(1)PT(1)PQQSNR 139.66 0.00013524 717250000 202410 243340 237250 234310 254160 179120 226150 204620 286810 TRUE FALSE 189741.5194 261357.1468 242877.682 240322.7913 234199.2988 230829.0362 192240.907 230167.2574 238939.5581 0.794098394 1.093821169 1.016481674 1.00578905 0.980161262 0.966056178 0.804558728 0.963286528 1 17.8662862 1.980476928 17.08168828 0.897000631 0.99808293 0.024235555 0.091313125 19.56047785 17112.23095 0.0345325 0.022858552 95.60419034 -1.980476928 0.101082299 TRHS(ph)PTPQQSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TRHSPTPQQSNR 12 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 TRHS(0.911)PT(0.087)PQQS(0.001)NR;TRHS(1)PTPQQSNR;TRHS(0.894)PT(0.106)PQQSNR;TRHS(0.999)PT(0.001)PQQSNR 160.03 4.19E-05 48384490000 9889254 10858313 8988792 10281057 9839653 8161613 11136973 8438974 10854073 TRUE FALSE 9270303.245 11662273.79 9202010.391 10544886.33 9066886.345 10517738.18 9467087.289 9492598.48 9042458.096 1.025197258 1.289723842 1.017644792 1.166152634 1.002701505 1.163150337 1.046959487 1.049780754 1 23.10828358 2.240575262 0.255670999 0.987997324 1.185368399 0.153274309 0.086430358 3.788487276 0.733659433 0.163294549 0.269518655 174.0104228 -2.240575262 0.197371075 TRLQQELDDLLVDLDHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TRLQQELDDLLVDLDHQR 18 1 P35579 P35579 MYH9 Myosin-9 0 ;;; 193.9 6.02E-15 116513000 88561 161623 112732 155857 236205 92057 179729 135829 442215 FALSE TRUE 83018.1251 173589.7351 115406.0563 159856.5545 217654.4121 118632.3615 152780.305 152787.5496 368406.4597 0.225343837 0.471190802 0.313257418 0.433913549 0.590799663 0.322014879 0.414705825 0.41472549 1 18.49093883 -5 0.374549174 9.141797901 0.386086108 0.792238603 0.097170018 235.4239565 1.791663335 1553.873822 0.061401606 1.00E-05 5 -8.755711793 TRLS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 TRLSPPR 7 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 1 T(0.006)RLS(0.994)PPR;T(0.006)RLS(0.994)PPR;T(0.02)RLS(0.98)PPR;T(0.128)RLS(0.872)PPR;T(0.002)RLS(0.998)PPR;T(0.02)RLS(0.98)PPR;T(0.006)RLS(0.994)PPR;T(0.027)RLS(0.973)PPR;T(0.003)RLS(0.997)PPR;T(0.032)RLS(0.968)PPR;T(0.009)RLS(0.991)PPR;T(0.002)RLS(0.998)PPR 81.338 0.016638 32844884800 1279216.6 1095860.5 1159794.7 1191506.2 1180605.9 950360.5 1422979.2 1073438 1346584.1 TRUE FALSE 1199152.716 1176999.152 1187305.578 1222082.266 1087885.875 1224714.149 1209616.679 1207459.097 1121830.514 1.06892503 1.049177337 1.058364488 1.089364437 0.96974174 1.091710497 1.078252609 1.07632934 1 20.0974233 TRNEELAQTWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TRNEELAQTWK 11 1 Q8TAT6;Q8TAT6-2;I3L283;I3L281;I3L3I1 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 113.93 0.0012088 170560000 115800 100600 93892 113660 127640 84929 136410 95371 139420 FALSE TRUE 108552.2847 108048.5287 96119.16258 116576.708 117615.6693 109446.6236 115956.5869 107278.2793 116149.9013 0.934587834 0.930250714 0.827544074 1.00367462 1.012619623 0.942287702 0.998335647 0.923619203 1 16.8256284 3.219144853 24.99999077 0.980159132 0.894499133 0.487456682 0.03990265 185.2096728 238477.8276 0.011275789 0.013495302 1656.322317 -3.219144853 -0.085659999 TRNEMTAEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TRNEMTAEEK 10 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;;;; 116.03 0.0012015 667561000 1093994 905101 914658 951934 1057124 712369 1271720 887368 1364644 FALSE TRUE 1025522.868 972115.6198 936354.1197 976362.2381 974101.7453 918018.366 1081037.392 998157.8481 1136876.1 0.902053327 0.855076133 0.823620199 0.858811473 0.856823136 0.807492009 0.950884086 0.877982964 1 20.1166436 0.996758304 0.84456237 0.996043638 0.849441541 0.57256125 0.037708916 0.426972451 0.671299437 0.03337464 0.011953079 9.925635088 -0.996758304 -0.146602097 TRNS(ph)GIWESPELDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TRNSGIWESPELDR 14 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 T(0.012)RNS(0.945)GIWES(0.043)PELDR;T(0.432)RNS(0.568)GIWESPELDR;TRNS(1)GIWESPELDR;TRNS(1)GIWESPELDR;T(0.363)RNS(0.637)GIWESPELDR;T(0.112)RNS(0.888)GIWESPELDR 267.69 2.96E-25 1723590000 931498 952520 910883 922126 1087860 791758 1025829 911633 1140260 TRUE FALSE 873197.203 1023045.572 932489.5749 945789.3143 1002423.864 1020325.681 872015.4648 1025452.387 949943.2396 0.919209871 1.076954421 0.981626624 0.995627186 1.055246063 1.074091208 0.917965862 1.079488062 1 19.85748179 4.764518598 23.35636456 1.017609165 0.919209557 0.27960449 0.05161227 4902.892521 4411328.435 0.011749402 0.827795831 58145.83323 -4.764518598 -0.098399608 TRPASQPTPFALHHAAS(ph)CEVDPSSGDSISLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TRPASQPTPFALHHAASCEVDPSSGDSISLAR 32 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 TRPASQPTPFALHHAAS(1)CEVDPSSGDSISLAR;T(0.037)RPAS(0.088)QPT(0.052)PFALHHAAS(0.823)CEVDPSSGDSISLAR 174.49 6.33E-15 449610000 87929 97479 82786 87101 88635 71801 139813 81416 121336 TRUE FALSE 82425.68085 104696.4466 84749.72301 89336.15912 81673.96464 92528.78311 118849.3386 91580.96682 101084.2377 0.815415763 1.03573464 0.838406906 0.883779322 0.807979231 0.915363119 1.17574551 0.905986619 1 16.62519853 1.966769645 21.76083106 1.046467355 0.890562257 0.353053709 0.091235382 130.7609195 85627.51432 0.035632153 0.023027589 92.63383516 -1.966769645 -0.155905097 TRPDGNCFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TRPDGNCFYR 10 1 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ;;; 204.56 1.69E-07 2218690000 579450 703150 517630 553514 742810 428407 576760 558780 601990 FALSE TRUE 543183.2588 755211.9576 529908.428 567718.1063 684472.699 552081.1463 490280.1924 628544.913 501513.98 1.083086974 1.505864219 1.056617461 1.132008536 1.364812799 1.100829026 0.97760025 1.253294899 1 18.93593039 2.609598547 0.340367125 1.01190098 1.328692843 0.132843449 0.155171934 2.821204324 0.698380898 0.182357351 0.325012514 407.0038781 -2.609598547 0.316791862 TRPVVAAGAVGLAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TRPVVAAGAVGLAQR 15 1 B7Z9I1;Q5T4U5;P11310;P11310-2;H0YDT5 B7Z9I1 ACADM "Medium-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 97.579 0.0029726 198020000 142820 152450 127900 125220 175010 118860 150990 148910 226080 FALSE TRUE 133881.1511 163737.5566 130933.8484 128433.3572 161265.4206 153172.9525 128350.4512 167501.7413 188345.7875 0.710826363 0.869345467 0.695178003 0.681901936 0.856219949 0.813253933 0.681461757 0.889330967 1 17.52302424 1.011946105 5.541369368 0.999729915 0.762975937 0.581092019 0.069260955 0.096688284 10.39398599 0.064424331 0.016238066 10.2788873 -1.011946105 -0.236753978 TRPWLQELSMGS(ph)PGPVTNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TRPWLQELSMGSPGPVTNK 19 1 A0A1B0GV70;Q96N21-2;Q96N21 A0A1B0GV70 ENTHD2 AP-4 complex accessory subunit tepsin 1 TRPWLQELS(0.002)MGS(0.998)PGPVTNK 104.38 0.00021451 344460000 408430 359290 417560 395120 456920 344330 529290 406780 629660 TRUE FALSE 382867.0954 385892.2054 427464.7204 405259.4481 421035.3463 443732.4813 449927.8782 457567.3784 524565.6782 0.729874468 0.735641353 0.814892659 0.772561883 0.802636093 0.845904526 0.857715052 0.872278529 1 19.00076389 -5 0.052283264 1.878331081 0.387105084 0.958332313 0.01592082 92.29412712 0.356017188 10.85401173 2.272688204 1.00E-05 5 -1.491225997 TRS(ph)LSSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TRSLSSLR 8 1 O94915;H0Y9X0;A0A286YEZ9;A0A2C9F2R7 O94915 FRYL Protein furry homolog-like 1 T(0.165)RS(0.835)LSSLR;T(0.029)RS(0.971)LSSLR 114.89 0.0015555 613440000 108763 132093 110978 146943 179795 84027 149378 141743 202210 TRUE FALSE 101955.718 141873.3032 113610.4506 150713.8062 165674.626 108284.2308 126980.1557 159439.9256 168459.8447 0.605222676 0.84217876 0.674406716 0.89465716 0.983466572 0.642789568 0.75377106 0.946456563 1 17.36204522 -5 0.106272698 1.685966734 0.652799358 0.30888257 0.118913532 243.2327712 1.73514509 36.59290436 1.624082348 1.00E-05 5 -1.033167376 TRS(ph)NPEGAEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TRSNPEGAEDR 11 1 M0R3H9;M0QXG9;M0R3F4;M0R2A4;M0R2K3;M0R193;M0R0I0;J3KQS6;Q9NWV8-3;Q9NWV8;M0R2I2 M0R3H9 BABAM1 BRISC and BRCA1-A complex member 1 1 T(0.007)RS(0.993)NPEGAEDR;T(0.028)RS(0.972)NPEGAEDR;T(0.297)RS(0.703)NPEGAEDR;T(0.013)RS(0.987)NPEGAEDR;TRS(1)NPEGAEDR 135.81 0.00011658 908960000 1217565 1212244 1100953 1303804 1301907 951595 1387501 964931 1324848 TRUE FALSE 1141359.78 1301999.807 1127068.125 1337261.818 1199660.476 1226305.029 1179458.106 1085404.759 1103722.31 1.034100489 1.179644368 1.021151892 1.211592632 1.086922376 1.111063007 1.068618524 0.983403841 1 20.07394581 1.403814811 2.771877979 0.990235601 1.108838545 0.401503547 0.057447329 0.246106666 3.294335566 0.042540484 0.013624933 25.34047848 -1.403814811 0.118602944 TRS(ph)PDVISS(ph)ASTALSQDIPEIASEALSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TRSPDVISSASTALSQDIPEIASEALSR 28 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 2 T(0.298)RS(0.699)PDVIS(0.255)S(0.284)AS(0.229)T(0.134)ALS(0.101)QDIPEIASEALSR 91.485 0.0016146 30439000 23953 21639 25123 21596 22883 16124 25469 21609 25181 TRUE FALSE 22453.82449 23241.17408 25718.92942 22150.18992 21085.86149 20778.73705 21650.15989 24306.93122 20978.12842 1.070344505 1.107876432 1.225987796 1.055870642 1.005135494 0.990495273 1.032034863 1.158679684 1 14.35659835 3.050708232 11.85821102 1.034292559 1.141960407 0.353214908 0.060344278 0.730660994 168.8781551 0.017314821 0.020696301 1123.849695 -3.050708232 0.107667848 TRS(ph)PDVISSASTALSQDIPEIASEALSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TRSPDVISSASTALSQDIPEIASEALSR 28 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 T(0.11)RS(0.89)PDVISSASTALSQDIPEIASEALSR 217.37 1.94E-34 191390000 147110 155520 132800 147180 187140 130750 207540 145690 175840 TRUE FALSE 137902.6477 167034.8626 135950.0787 150956.888 172442.7793 168495.4025 176421.3037 163879.7172 146491.168 0.941371753 1.140238452 0.928042834 1.030484568 1.177154784 1.150208608 1.204313585 1.118700324 1 17.16045416 2.782081897 7.055327548 1.149253806 1.017573517 0.348611704 0.078900458 0.234364672 31.86316118 0.022532983 0.023743817 605.4550372 -2.782081897 -0.131680289 TRS(ph)PEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TRSPEKK 7 2 Q5TCQ9;Q5TCQ9-1 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 T(0.095)RS(0.905)PEKK 57.598 0.090265 209140000 226750 86118 149140 126360 131650 88970 135910 101940 166560 TRUE FALSE 212558.1223 92494.26633 152677.6712 129602.6115 121310.7401 114654.1947 115531.5572 114667.4334 138760.06 1.531839366 0.666577013 1.100299836 0.934005156 0.874248253 0.82627663 0.832599505 0.826372037 1 17.08223284 2.900843105 3.263072386 0.855272776 1.007890944 0.142218392 0.217013112 0.603468168 12.19559227 0.06408989 0.069911329 795.8717779 -2.900843105 0.152618169 TRS(ph)PPPRPPPPAINSLHT(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TRSPPPRPPPPAINSLHTSPR 21 2 Q8WYP3-2;Q8WYP3 Q8WYP3-2 RIN2 Ras and Rab interactor 2 2 T(0.452)RS(0.548)PPPRPPPPAINS(0.002)LHT(0.616)S(0.382)PR 73.975 0.026333 207570000 54361 68698 58797 67255 58135 55408 79346 54508 52001 TRUE FALSE 50958.64205 73784.4714 60191.69261 68980.87716 53569.31161 71403.39013 67448.80391 61313.44379 43321.69716 1.176284527 1.70317592 1.389412155 1.59229397 1.23654693 1.648213131 1.556928937 1.415305674 1 15.40280214 0.886286538 6.338631636 1.000002842 1.494156014 0.424478392 0.169765068 1.703882571 94.68165617 0.143982356 0.036165874 7.696380636 -0.886286538 0.494153173 TRS(ph)WDSSSPVDRPEPEAAS(ph)PTTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TRSWDSSSPVDRPEPEAASPTTR 23 2 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 2 T(0.159)RS(0.839)WDS(0.001)S(0.001)SPVDRPEPEAAS(0.884)PT(0.108)T(0.008)R 169.15 4.34E-11 388280000 200400 200540 235120 247930 242030 115120 165560 143070 224530 TRUE FALSE 187857.3217 215388.1903 240697.1574 254292.3035 223021.9401 148353.2752 140735.815 160932.6044 187054.4925 1.004291954 1.151472961 1.286775603 1.35945574 1.19228326 0.79310191 0.752378695 0.860351453 1 17.51309909 2.248989072 10.4222345 0.820977606 1.211856367 0.69888246 0.112342683 0.112296104 103.3172389 0.039473789 0.031930009 177.4144839 -2.248989072 0.390878762 TRS(ph)WDSSSPVDRPEPEAASPTTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TRSWDSSSPVDRPEPEAASPTTR 23 2 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 T(0.249)RS(0.749)WDSS(0.001)SPVDRPEPEAASPTTR;T(0.037)RS(0.963)WDSSSPVDRPEPEAASPTTR 245.19 8.87E-38 1778170000 109857 113933 102312 131058 158741 74425 107056 101336 168174 TRUE FALSE 102981.2465 122368.7179 104738.889 134421.1702 146274.1222 95910.28931 91003.94666 113988.0227 140104.673 0.735030776 0.873409254 0.747575985 0.959433881 1.044034571 0.684561673 0.649542551 0.813591869 1 17.09614555 0.937031618 22.25709912 1.000000001 0.806220061 0.187698555 0.121289485 17316.24092 6120688.663 0.122500308 0.030625077 8.65030894 -0.937031618 -0.193779939 TRSDIVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TRSDIVSR 8 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ; 145.9 0.00051245 383930000 123702 140794 122875 137185 142379 104270 162874 155972 162930 FALSE TRUE 115959.7126 151218.5343 125789.653 140705.3994 131197.1277 134371.0563 138452.5557 175445.4475 135735.9304 0.854303737 1.114064152 0.926723327 1.0366113 0.966561523 0.989944637 1.020014047 1.292549784 1 17.05044314 1.419101231 11.64586009 1.14996643 0.994034049 0.321857493 0.096533673 0.648606033 127.017626 0.053332327 0.020388846 26.24830304 -1.419101231 -0.155932381 TRT(ph)SQEELLAEVVQGQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TRTSQEELLAEVVQGQSR 18 1 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;A0A087WTC9;Q6PJT7-9;Q6PJT7-2;H0YJA2;Q6PJT7-3;Q6PJT7-11;G3V5I6 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 1 T(0.11)RT(0.445)S(0.445)QEELLAEVVQGQSR;T(0.128)RT(0.436)S(0.436)QEELLAEVVQGQSR;T(0.134)RT(0.433)S(0.433)QEELLAEVVQGQSR 250.82 6.66E-25 786120000 891640 1158340 868560 905810 679590 428190 556820 428080 682600 TRUE FALSE 835833.844 1244104.699 889162.6534 929054.6181 626217.7427 551801.5019 473330.0103 481526.7303 568669.6502 1.469805613 2.187745905 1.563583801 1.63373343 1.101197756 0.970337527 0.832346179 0.84676003 1 19.11723128 2.776982567 1.267989177 0.863964469 1.851676703 0.79972114 0.192147436 0.15680961 0.518587434 0.079775209 0.078259861 598.3875741 -2.776982567 0.987712234 TRTDS(ph)TSDGRPAWMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TRTDSTSDGRPAWMR 15 2 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 1 TRT(0.001)DS(0.828)T(0.151)S(0.02)DGRPAWMR;T(0.003)RT(0.002)DS(0.828)T(0.141)S(0.027)DGRPAWMR;T(0.005)RT(0.003)DS(0.903)T(0.077)S(0.013)DGRPAWMR 100.67 0.0016276 1723870000 341000 483950 408050 508300 485800 196340 358330 246438 385840 TRUE FALSE 319657.4187 519782.1615 417729.1387 521343.8385 447647.2276 253020.1707 304601.7431 277206.3268 321440.8114 0.994451879 1.617038482 1.299552278 1.621896847 1.392627233 0.78714389 0.947613782 0.862386844 1 18.29419359 2.247745844 24.7371549 0.89671714 1.415835083 0.63325876 0.182881588 92.23436122 248400.6918 0.057611314 0.047561698 176.9073365 -2.247745844 0.519117944 TRTFS(ph)ATVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TRTFSATVR 9 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 TRT(0.001)FS(0.994)AT(0.005)VR;TRTFS(0.999)ATVR;TRTFS(1)ATVR;TRTFS(1)ATVR;TRTFS(0.515)AT(0.485)VR 152.96 4.80E-05 4216760000 801077 927972 577222 977936 1400889 516918 1479093 1565153 4429440 TRUE FALSE 750939.0205 996680.0124 590913.9784 1003031.493 1290868.829 666143.8351 1257316.736 1760565.797 3690137.849 0.203498907 0.270092894 0.160133307 0.271814099 0.349815883 0.180520041 0.340723514 0.477100279 1 21.81524328 0.723465843 1.1407125 1.000539948 0.234698685 0.949086774 0.055079447 0.178230728 0.400751697 0.049690335 0.015455114 5.290123895 -0.723465843 -0.765841262 TRYDSGQDLDEEGMNMGDFDPNNIFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TRYDSGQDLDEEGMNMGDFDPNNIFK 26 1 Q99615;A0A6I8PUD4;A0A6I8PU73;A0A6I8PS32;A0A6I8PIK4;A0A6I8PRZ0;Q99615-2;K7ER44 Q99615 DNAJC7 DnaJ homolog subfamily C member 7 0 142.87 2.48E-07 66898000 74814 58906 62832 66933 89369 47824 85117 64054 101870 FALSE TRUE 70131.52529 63267.46153 64322.40471 68650.6141 82350.31924 61630.01244 72354.49604 72051.2829 84867.23889 0.826367468 0.74548745 0.757917962 0.808917728 0.970342859 0.726193208 0.852560976 0.848988182 1 16.37292012 -5 0.13661679 1.677959469 0.732328276 0.449412004 0.06661724 119.3882105 1.010229125 21.90714079 0.417748411 1.00E-05 5 -0.945631193 FNWYVDGVEVHNAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 FNWYVDGVEVHNAK 14 0 A0A0A0MS08;P01857 A0A0A0MS08 IGHG1 Ig gamma-1 chain C region 0 ; 198.78 2.16E-08 3054800000 11151100 3301000 529920 278246 273960 57760 72573 49085 100387 FALSE TRUE 10453172.56 3545409.475 542489.9526 285386.2634 252444.2867 74434.37434 61691.35238 55213.3703 83631.76118 124.9904631 42.39309833 6.486649869 3.412414846 3.018521709 0.890025193 0.737654589 0.660196192 1 16.35176332 4.858570584 1.223796703 2.178436168 200 0.990502858 3.807807271 0.180883526 0.192239692 1.176053844 48.45135794 72205.55054 -4.858570584 197.8215638 up TS(ph)FSVGSDDELGPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSFSVGSDDELGPIR 15 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 T(0.154)S(0.846)FSVGSDDELGPIR 118.52 0.00029848 35535000 43513 37971 42651 38991 41904 29008 46159 30754 55659 TRUE FALSE 40789.599 40782.41235 43662.70186 39991.57507 38613.02887 37382.13869 39237.88647 34593.7046 46369.15333 0.87967099 0.879516002 0.941632502 0.862460757 0.832730945 0.806185492 0.846206662 0.746049952 1 15.50087776 3.020783402 6.564384591 0.835513561 0.902023368 0.112566851 0.06550957 0.248782633 41.04942026 0.016965422 0.019948961 1049.019115 -3.020783402 0.066509807 TS(ph)LASLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TSLASLR 7 0 Q9HDC5 Q9HDC5 JPH1 Junctophilin-1 1 T(0.187)S(0.813)LASLR;T(0.117)S(0.883)LASLR;T(0.244)S(0.756)LASLR 182.98 0.00068108 551045000 763240 628670 656290 609830 717600 553819 850520 662840 714250 TRUE FALSE 715470.1708 675217.3809 671857.5087 625479.2702 661242.5907 713697.5548 722992.4218 745597.0331 595037.0608 1.202395982 1.134748448 1.129101955 1.051160191 1.111262868 1.199416981 1.215037633 1.25302621 1 19.18262 2.237533914 24.99984123 1.188553224 1.124032711 0.034448675 0.076218496 50.98123913 1241315.767 0.025040781 0.019559036 172.7960911 -2.237533914 -0.064520513 TS(ph)LMAFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSLMAFLR 8 0 O75363;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 T(0.247)S(0.753)LMAFLR 137.69 0.0007733 29003000 154630 104610 79829 81280 139040 59570 77395 94128 137020 TRUE FALSE 144951.9843 112355.4332 81722.58158 83365.78241 128120.3593 76766.89196 65790.33825 105880.088 114150.4768 1.269832491 0.984274761 0.715919757 0.730314798 1.122381289 0.6725061 0.576347468 0.927548364 1 16.80057736 4.666137416 1.62302944 0.789676336 1.401166256 0.423517957 0.164437726 0.791351355 2.257320675 0.043150458 0.72999135 46359.35829 -4.666137416 0.61148992 TS(ph)PADGKPR ddPTM_SK-BR-3_Pertuzumab_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(0.015)S(0.985)PADGKPR 147.37 5.61E-05 524360000 945070 592180 740040 679510 730540 498280 907670 604990 737810 TRUE FALSE 885919.7557 636025.6234 757594.0983 696947.377 673166.3353 642125.3471 771573.3099 680524.3332 614664.7446 1.441305628 1.034752081 1.232532214 1.133865873 1.095176421 1.04467574 1.255275037 1.107147171 1 19.22944021 7.99999977 0.017796685 2.43E-05 2.585548183 0.268640665 0.112131703 6771.156627 9.293501431 517.2925652 876.5975265 99999946.95 -7.99999977 2.585523931 TS(ph)PAPWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSPAPWK 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.002)S(0.998)PAPWK;T(0.004)S(0.996)PAPWK 118.32 0.0052783 1117280000 5391200 3090600 3946200 3505300 3189000 3266700 5017700 3223700 2725500 TRUE FALSE 5053774.416 3319431.24 4039805.728 3595251.932 2938548.804 4209743.26 4265342.467 3626186.041 2270596.443 2.225747526 1.461920391 1.77918262 1.583395387 1.294174847 1.854025304 1.878511913 1.597019168 1 21.11463989 0.964624243 21.20740616 0.99999999 1.703120336 0.444622727 0.252147897 650.4136024 389918.0135 0.226349008 0.056587252 9.217735528 -0.964624243 0.703120346 TS(ph)PAPWKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSPAPWKR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.124)S(0.876)PAPWKR 97.565 0.0049867 271800000 401840 327150 343910 326530 382750 273040 436090 295250 399430 TRUE FALSE 376689.5517 351372.5264 352067.7076 334909.3126 352690.3589 351862.2156 370702.353 332112.6124 332762.5526 1.132007039 1.055925685 1.058014806 1.006451327 1.059885964 1.057397273 1.114014633 0.998046835 1 18.34413356 1.298819839 0.007330922 1.53E-07 2.09318606 0.279350359 0.038026076 3671.896026 24.27870067 3479.745624 3449.608575 19.89847708 -1.298819839 2.093185906 TS(ph)PCQS(ph)PTISEGPVPSLPIRPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSPCQSPTISEGPVPSLPIRPSR 23 1 A0A0D9SGJ6;J3KQV8;O43426;J3KPK1;C9JFZ1;O43426-4;O43426-2 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 2 T(0.138)S(0.862)PCQS(0.993)PT(0.007)ISEGPVPSLPIRPSR;T(0.419)S(0.581)PCQS(0.498)PT(0.498)IS(0.003)EGPVPSLPIRPSR 154.14 2.45E-08 553230000 401600 314390 387320 333540 299060 344590 524450 327960 378680 TRUE FALSE 376464.5729 337667.7627 396507.4133 342099.2011 275573.034 444067.539 445813.5913 368906.5279 315475.8616 1.193322909 1.070344213 1.256854998 1.084391051 0.873515433 1.40761178 1.413146442 1.169365307 1 18.2671701 2.207576769 24.9999055 1.300503 1.113693948 0.149203384 0.15596285 274.2031903 221244.4857 0.055474441 0.040974938 161.2786089 -2.207576769 -0.186809052 TS(ph)PDPSPVSAAPSK ddPTM_SK-BR-3_Pertuzumab_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(0.012)S(0.988)PDPSPVSAAPSK;T(0.404)S(0.595)PDPSPVSAAPSK 202.58 1.70E-08 400380000 856830 665260 687550 761860 800260 438740 797370 545890 528010 TRUE FALSE 803202.5398 714516.5426 703859.0107 781410.6174 737410.8077 565397.1157 677811.7709 614045.5682 439881.7199 1.825951167 1.624337885 1.600109709 1.776410753 1.676384297 1.285338967 1.540895519 1.395933362 1 18.74675612 0.394718693 0.283395951 0.842580025 1.759740398 0.780172633 0.115077638 1.886491034 0.310363455 0.529585067 0.172916442 2.481525216 -0.394718693 0.917160374 TS(ph)PDSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSPDSLR 7 0 Q9BRL6-2;Q9BRL6 Q9BRL6-2 SRSF8 Serine/arginine-rich splicing factor 8 1 T(0.166)S(0.834)PDSLR 190.26 0.00056959 144970000 314280 303190 347630 342210 339620 348860 353940 328920 336320 TRUE FALSE 294609.7758 325638.5031 355875.9478 350991.688 312947.6152 449570.2187 300869.9828 369986.386 280186.0193 1.051479216 1.162222526 1.270141703 1.252709499 1.116928018 1.604541939 1.073822254 1.320502668 1 18.09602544 4.659854767 1.506516314 1.24538544 0.994752651 0.111050142 0.163871293 1.918287118 4.565788141 0.039039487 0.685428032 45693.53594 -4.659854767 -0.25063279 TS(ph)PDTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TSPDTLR 7 0 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.004)S(0.996)PDTLR;T(0.245)S(0.755)PDTLR;T(0.03)S(0.97)PDTLR;T(0.036)S(0.964)PDTLR;T(0.115)S(0.885)PDTLR;T(0.477)S(0.523)PDTLR 211.79 0.00010134 15660300000 33785410 26466520 28330790 27476680 27814160 22124270 32455240 26230930 26621510 TRUE FALSE 31670841.5 28426128.68 29002809.72 28181778.13 25629748.07 28511187.59 27588878.06 29505919.35 22178208 1.428016254 1.281714405 1.307716553 1.270696809 1.155627545 1.285549653 1.243963356 1.330401417 1 24.40263946 -4.764619871 0.179349155 1.22E-18 1.341144185 0.656912958 0.066298887 75.86582763 0.788301103 27.38750395 0.197579866 1.72E-05 4.764619871 1.341144185 TS(ph)PDTLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSPDTLRR 8 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.416)S(0.584)PDTLRR 91.584 0.0075851 88427000 154510 139880 124940 127760 164470 118560 154170 133090 177220 TRUE FALSE 144839.4949 150236.8607 127903.6358 131038.5379 151553.1896 152786.3473 131053.6397 149706.5795 147640.8371 0.981025966 1.017583371 0.866316111 0.88754941 1.026499122 1.034851538 0.887651698 1.013991673 1 17.1717323 2.733114599 24.96108114 0.981132699 0.939395724 0.160645401 0.058683017 1130.615003 5182001.335 0.019842064 0.019164513 540.897033 -2.733114599 -0.041736975 TS(ph)PENVQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSPENVQDR 9 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 T(0.002)S(0.998)PENVQDR;T(0.103)S(0.897)PENVQDR 169.33 6.14E-05 583880000 630440 539450 574490 553910 576540 482470 690660 491290 538480 TRUE FALSE 590981.8858 579391.4393 588117.1741 568124.2684 531260.8741 621751.2568 587101.9448 552628.638 448604.2093 1.31737927 1.291542583 1.310993437 1.266426522 1.184252985 1.385968397 1.308730352 1.231884647 1 18.77508363 0.843191286 3.449693474 1.000070418 1.2961975 0.774124003 0.049870277 0.363461793 7.187508754 0.045941952 0.011871874 6.969334131 -0.843191286 0.296127082 TS(ph)PHWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSPHWK 6 0 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 T(0.491)S(0.509)PHWK;T(0.498)S(0.502)PHWK 124.37 0.011841 686320000 1997190 1534150 1735760 1569720 1623290 1337660 2120190 1425940 1451800 TRUE FALSE 1872189.443 1647740.062 1776933.047 1610001.673 1495803.351 1723820.727 1802287.192 1603971.748 1209485.201 1.547922572 1.362348263 1.46916477 1.331146236 1.236727287 1.425251607 1.490127528 1.326160706 1 20.20596169 0.967612575 18.69243153 0.999999997 1.407054151 0.684959253 0.086734488 75.60157424 43634.34059 0.081525881 0.02038147 9.281380447 -0.967612575 0.407054154 TS(ph)PINLGLNVNDLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSPINLGLNVNDLLK 15 0 P50616 P50616 TOB1 Protein Tob1 1 T(0.245)S(0.755)PINLGLNVNDLLK 250.19 1.02E-18 189940000 581980 358320 451820 439840 437150 331720 576910 351560 515900 TRUE FALSE 545554.9107 384850.3856 462537.3838 451127.039 402818.0024 427482.179 490407.7013 395453.0399 429792.9572 1.269343533 0.895432043 1.076186513 1.049638044 0.937237327 0.994623508 1.141032428 0.920101256 1 18.71328232 4.755512658 24.87204038 1.011575552 1.269343752 0.556083039 0.074674715 2735.409038 4013323.03 0.017494934 0.52153019 56952.48233 -4.755512658 0.257768201 TS(ph)PITR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSPITR 6 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.281)S(0.719)PITR 139.68 0.012457 913950000 1545900 1245700 1505500 1497900 1297600 1318000 1678500 1185400 1268900 TRUE FALSE 1449144.879 1337932.924 1541211.171 1536338.65 1195691.73 1698485.204 1426824.507 1333399.799 1057112.393 1.370852228 1.265648699 1.457944474 1.453335199 1.13109234 1.606721495 1.349737755 1.261360484 1 20.01169734 0.887526694 2.649195879 1.000753847 1.377624398 0.48064896 0.124111322 0.361686264 5.296610748 0.10778075 0.028712184 7.718389557 -0.887526694 0.376870551 TS(ph)PLKDNPS(ph)PEPQLDDIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSPLKDNPSPEPQLDDIKR 19 2 Q96JC9-2;Q96JC9 Q96JC9-2 EAF1 ELL-associated factor 1 2 T(0.452)S(0.548)PLKDNPS(1)PEPQLDDIKR 113.31 9.63E-05 128700000 343740 114420 182420 173300 185040 123740 244890 131590 275620 TRUE FALSE 322225.927 122891.7759 186747.0885 177747.1714 170507.7048 159461.7292 208171.0179 148019.3012 229617.2414 1.403317647 0.535202736 0.813297326 0.774102024 0.742573614 0.694467577 0.906600117 0.64463496 1 17.80887145 -0.404268598 7.913176149 1.000011851 0.789249041 0.04991214 0.232922056 0 0 0.196714235 0.04636599 0.394213418 0.404268598 -0.21076281 TS(ph)PLKDNPSPEPQLDDIKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSPLKDNPSPEPQLDDIKR 19 2 Q96JC9-2;Q96JC9 Q96JC9-2 EAF1 ELL-associated factor 1 1 T(0.019)S(0.981)PLKDNPSPEPQLDDIKR;T(0.115)S(0.885)PLKDNPSPEPQLDDIKR 209.75 1.09E-16 582940000 538240 225270 341740 338870 329930 235170 433440 249330 476570 TRUE FALSE 504552.5192 241949.2252 349846.2342 347565.9779 304018.6287 303059.7613 368449.6959 280459.3993 397027.3882 1.270825475 0.609401851 0.881163981 0.875420659 0.76573717 0.763322054 0.928020854 0.706398117 1 18.59887901 -1.961717952 6.870282849 1.091279839 0.832743362 0.059071176 0.176482088 0.108367862 0.000603839 0.07504734 0.035183798 0.010921494 1.961717952 -0.258536477 TS(ph)PPCS(ph)PANLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TSPPCSPANLSR 12 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 T(0.043)S(0.957)PPCS(1)PANLSR;T(0.048)S(0.952)PPCS(1)PANLSR;T(0.385)S(0.615)PPCS(1)PANLSR;T(0.011)S(0.989)PPCS(1)PANLSR;T(0.016)S(0.984)PPCS(1)PANLSR 201.37 2.18E-07 3607000000 3416340 2647553 3049000 2748742 3125613 3323350 4381190 2845498 3665040 TRUE FALSE 3202517.378 2843580.579 3121323.72 2819279.373 2880139.963 4282747.195 3724271.232 3200764.689 3053321.147 1.048863589 0.9313074 1.022271674 0.923348458 0.943281045 1.402652059 1.219744355 1.048289562 1 21.54194791 2.275178853 24.99999762 1.197339188 0.972331784 0.405844275 0.1140621 135.0632547 92209.87681 0.036728581 0.030728486 188.4424981 -2.275178853 -0.225007403 TS(ph)PPCSPANLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TSPPCSPANLSR 12 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 T(0.347)S(0.653)PPCSPANLSR;T(0.023)S(0.977)PPCSPANLSR;T(0.192)S(0.808)PPCSPANLSR 163.51 6.27E-05 4509210000 2655020 2241490 2288400 2216780 2273690 1644970 2338990 1687440 2311790 TRUE FALSE 2488847.038 2407452.252 2342681.929 2273666.328 2095123.559 2119846.135 1988280.164 1898120.599 1925937.314 1.29227832 1.250015893 1.216385347 1.180550536 1.087846185 1.100682831 1.032370134 0.985556791 1 20.87712932 2.670623699 0.582860327 0.984450434 1.286305192 0.967045831 0.019194662 0.131277489 0.093629521 0.015184928 0.016286571 468.4073475 -2.670623699 0.301854758 TS(ph)PPLLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TSPPLLDR 8 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.223)S(0.777)PPLLDR;T(0.161)S(0.839)PPLLDR;T(0.152)S(0.848)PPLLDR 167.93 0.00032493 23171950000 4283780 3700540 3725020 3688040 3588780 2995560 4392780 3089640 3408190 TRUE FALSE 4015665.857 3974531.832 3813379.233 3782681.35 3306931.695 3860329.543 3734123.42 3475388.355 2839341.071 1.414294992 1.399807819 1.343050778 1.332239155 1.164682795 1.359586413 1.315137324 1.224012286 1 21.43712473 -4.661069978 0.12784983 3.09E-18 1.474747391 0.785067222 0.0581054 61.38835223 0.541680692 15.98304685 0.472812811 2.18E-05 4.661069978 1.474747391 TS(ph)PQVLGSILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSPQVLGSILK 11 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 T(0.142)S(0.858)PQVLGSILK;T(0.13)S(0.87)PQVLGSILK 195.87 6.55E-08 359580000 1017140 730460 824180 798390 935580 617880 952110 820590 938200 TRUE FALSE 953479.023 784544.0184 843729.9388 818878.0391 862103.3207 796251.9256 809349.9445 923042.4678 781608.359 1.219893585 1.003755921 1.079479165 1.047683318 1.102986311 1.018735171 1.035492949 1.180952656 1 19.57608637 7.999995235 0.006753309 2.28E-10 2.228614169 0.08533669 0.070693951 87225.26047 45.55645264 6797.877563 8305.915888 99998902.71 -7.999995235 2.228614168 TS(ph)PSGGTWSSVVSGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSPSGGTWSSVVSGAK 16 0 F8WB06;F8VRK6 F8WB06 ATXN2 1 T(0.327)S(0.671)PS(0.002)GGTWSSVVSGAK;T(0.028)S(0.972)PSGGTWSSVVSGAK 107.34 0.0011912 150920000 274298 214744 250728 244224 227280 202438 309249 179101 264672 TRUE FALSE 257130.1778 230643.8692 256675.3866 250491.2013 209430.3456 260878.5643 262879.9834 201462.1541 220496.5334 1.166141589 1.046020387 1.164079011 1.136032379 0.949812418 1.183141342 1.192218215 0.913674927 1 17.75039645 1.231909889 24.99999748 0.956837409 1.11848495 0.443581471 0.075793956 157.2935008 591237.239 0.064759786 0.017663396 17.05728434 -1.231909889 0.161647542 TS(ph)PSGGTWSSVVSGVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.064)S(0.93)PS(0.005)GGTWSSVVSGVPR;T(0.118)S(0.882)PSGGTWSSVVSGVPR;T(0.2)S(0.8)PSGGTWSSVVSGVPR 246.34 1.26E-20 2308850000 2728800 2332420 2430070 2432490 2473010 2262360 3017910 2251310 2124040 TRUE FALSE 2558009.279 2505114.804 2487712.408 2494911.812 2278789.77 2915466.606 2565402.412 2532391.009 1769524.002 1.445591739 1.415699816 1.405865309 1.409933863 1.287798169 1.647599356 1.449769774 1.431114247 1 20.7549299 0.892992323 17.07393417 1 1.437533522 0.710715827 0.087562244 1717.510719 274045.7441 0.08042796 0.02010699 7.816139882 -0.892992323 0.437533522 TS(ph)PSKSPFLHSGMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSPSKSPFLHSGMK 14 1 O14497;H0Y488;A0A1B0GTU5;O14497-3;O14497-2;H0YEW5 O14497 ARID1A AT-rich interactive domain-containing protein 1A 1 T(0.386)S(0.613)PS(0.001)KSPFLHSGMK 139.46 1.29E-05 438700000 800620 535530 696630 655280 724710 447810 930080 613110 882440 TRUE FALSE 750510.6233 575181.1984 713154.3926 672095.5942 667794.1999 577085.4774 790623.1384 689658.1331 735155.0632 1.020887512 0.782394392 0.970073428 0.9142229 0.908371898 0.784984701 1.075450851 0.938112471 1 19.48768906 1.721398896 17.76707981 1.004852309 0.893185881 0.290948468 0.07911856 0.238909971 234.8294495 0.033388537 0.018476337 52.65006306 -1.721398896 -0.111666428 TS(ph)PSSDKVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSPSSDKVQK 10 1 F8WDU9;P38435 F8WDU9 GGCX Vitamin K-dependent gamma-carboxylase 1 T(0.187)S(0.798)PS(0.014)S(0.001)DKVQK 116.03 0.0031744 0 150530 88580 89786 98373 121520 67154 141210 104090 133180 TRUE FALSE 141108.596 95138.55537 91915.76632 100897.4177 111976.3094 86540.26965 120036.8714 117085.8656 110951.3976 1.271805484 0.857479558 0.828432704 0.909383927 1.009237484 0.779983592 1.08188697 1.055289687 1 16.75956832 1.623021902 18.64259876 1.051415743 0.921608021 0.099450028 0.136186304 0.369374411 442.4484217 0.060069672 0.032855897 41.97801534 -1.623021902 -0.129807721 TS(ph)PTFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSPTFR 6 0 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3 P62750 RPL23A 60S ribosomal protein L23a 1 T(0.158)S(0.842)PTFR;T(0.101)S(0.899)PTFR 128.57 0.017382 995130000 2102900 1689350 1855150 1976610 1950850 1486840 2112600 1583040 2028800 TRUE FALSE 1971283.243 1814431.232 1899155.034 2027333.159 1797638.11 1916066.571 1795835.242 1780686.029 1690180.173 1.166315446 1.073513499 1.123640582 1.199477541 1.0635778 1.133646342 1.062511128 1.053548052 1 20.68874562 1.281811167 1.047161943 1.002274128 1.123313115 0.543170877 0.039994526 0.369622721 0.836689154 0.034932946 0.011935523 19.1342378 -1.281811167 0.121038987 TS(ph)PTPPESATTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TSPTPPESATTVK 13 0 Q5M775-4;Q5M775;J3KSG2 Q5M775-4 SPECC1 Cytospin-B 1 T(0.014)S(0.986)PT(0.001)PPESATTVK;T(0.17)S(0.822)PT(0.008)PPESATTVK;T(0.087)S(0.912)PT(0.001)PPESATTVK 209.11 4.25E-08 673930000 2027860 1396080 1555080 1516690 1701850 1061870 1976140 1409500 1681800 TRUE FALSE 1900939.862 1499447.216 1591967.232 1555610.833 1568193.566 1368414.631 1679836.153 1585479.178 1401096.715 1.356751352 1.070195369 1.136229366 1.110280837 1.119261468 0.976673927 1.198943752 1.131598669 1 20.41812512 4.742947032 24.91709832 1.10207475 1.356751458 0.611148093 0.065782002 284.2281074 1614501.948 0.014279195 0.112757218 55328.26255 -4.742947032 0.254676708 TS(ph)PTVATQTGASATSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSPTVATQTGASATSTR 17 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 T(0.144)S(0.722)PT(0.134)VATQTGASATSTR 289.02 6.46E-46 483330000 269680 242890 247600 245070 236490 196530 268190 214900 252070 TRUE FALSE 252801.2102 260873.8283 253473.1889 251358.9111 217917.0294 253265.0206 227977.3993 241730.7381 209997.8886 1.20382739 1.242268816 1.207027321 1.19695923 1.037710573 1.206036034 1.085617578 1.151110326 1 17.6800153 1.763786517 0.07615399 0.735635792 1.524531958 0.58946417 0.051974932 10.75452036 0.775446789 3.703656646 3.982864701 58.0479005 -1.763786517 0.788896167 TS(ph)PYILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSPYILR 7 0 P49454 P49454 CENPF Centromere protein F 1 T(0.377)S(0.617)PY(0.006)ILR;T(0.241)S(0.759)PYILR 167.23 0.0011476 277317000 601190 531190 573250 550980 550730 478120 684340 516140 563320 TRUE FALSE 563562.5911 570519.8603 586847.7607 565119.0796 507477.8873 616145.4824 581729.5701 580581.2152 469298.2528 1.200862325 1.21568716 1.250479321 1.204178955 1.081354734 1.312908111 1.239573271 1.237126309 1 18.84014556 -1.116410419 4.219055015 0.999958531 1.221634418 0.582127697 0.057902839 3828594.513 1013907.001 1456.841088 0.012883724 0.076487344 1.116410419 0.221675886 TS(ph)QETADVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSQETADVK 9 0 H3BVG0;Q8N1F7;H3BM93;H3BNN5;H3BV11;H3BRI8 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 T(0.445)S(0.555)QETADVK;T(0.155)S(0.842)QET(0.003)ADVK 85.274 0.014928 0 1303950 772680 938050 939410 910200 623960 1121070 746980 822100 TRUE FALSE 1222338.097 829890.0312 960300.989 963516.851 838716.5636 804087.1229 952975.961 840242.0973 684886.199 1.784731681 1.2117196 1.402132194 1.406827663 1.22460719 1.174044862 1.391436946 1.226834616 1 19.38550476 8 0.034213455 5.44E-08 3.329358858 0.495800798 0.147471547 1029.119152 2.691755057 78.29455695 215.1124948 100000000 -8 3.329358804 TS(ph)SESIYSRPGSSIPGSPGHTIYAK ddPTM_SK-BR-3_Pertuzumab_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(0.131)S(0.843)S(0.022)ES(0.003)IYSRPGSSIPGSPGHTIYAK 122.68 0.00010293 164620000 27188 39558 47710 46259 42801 31424 51248 39308 44544 TRUE FALSE 25486.35161 42486.91548 48841.70373 47446.08426 39439.58211 40495.59867 43563.83816 44215.69033 37109.31863 0.68679115 1.144912304 1.316157384 1.278549055 1.062794564 1.091251474 1.17393258 1.191498307 1 15.17949389 4.736936924 4.754598603 1.176179992 0.659414157 0.705421083 0.095119596 0.0959622 6.158398498 0.022667086 0.164544306 54567.86023 -4.736936924 -0.516765836 TS(ph)SKESS(ph)PIPSPTSDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSSKESSPIPSPTSDRK 17 2 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 2 T(0.312)S(0.342)S(0.342)KES(0.082)S(0.773)PIPS(0.109)PT(0.021)S(0.019)DRK 52.061 0.078508 251150000 379540 119920 201800 182720 229170 127370 268030 165910 276320 TRUE FALSE 355785.2689 128799.0016 206586.7913 187408.9045 211171.9126 164139.6513 227841.3898 186624.2287 230200.4069 1.545545786 0.55950814 0.897421486 0.81411196 0.917339441 0.713029371 0.989752333 0.810703296 1 17.81253086 -1.060860413 7.065914506 1.000000027 0.871900017 0 0.258267076 1.06E-07 1.41E-08 0.218486399 0.051497726 0.086923977 1.060860413 -0.12810001 TS(ph)SPHKEESPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSSPHKEESPK 11 1 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.01)S(0.495)S(0.495)PHKEESPK 183.81 3.14E-06 301640000 568210 299810 362750 381080 380930 228660 471040 277320 437860 TRUE FALSE 532646.7504 322008.2444 371354.6013 390859.158 351013.2944 294670.43 400411.9249 311944.0125 364778.3373 1.460192933 0.882750458 1.01802811 1.071497723 0.962264637 0.807806824 1.097685591 0.855160465 1 18.47666053 4.744604472 24.96743602 0.967495681 1.460193154 0.741875856 0.092318748 325.8290231 1345975.954 0.020280103 0.186337144 55539.82057 -4.744604472 0.492697472 TS(ph)SPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSSPPR 6 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(0.083)S(0.458)S(0.458)PPR 94.262 0.04687 146950000 510940 449540 489570 502290 476290 385970 504810 420890 498580 TRUE FALSE 478961.1775 482824.4093 501182.8316 515179.6118 438884.1047 497393.2733 429118.4269 473439.043 415363.7771 1.153112534 1.162413374 1.206611793 1.240309435 1.056625852 1.197488324 1.033114707 1.13981784 1 18.66401588 1.470833072 0.602459189 1.010444132 1.185958124 0.453004492 0.058288545 0.577306939 0.490212496 0.051478993 0.026192542 29.56875729 -1.470833072 0.175513993 TS(ph)SPPRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSSPPRK 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(0.036)S(0.482)S(0.482)PPRK 84.498 0.01317 2977800000 311370 223710 280380 240330 252040 180220 261930 215070 282160 TRUE FALSE 291881.9075 240273.7212 287030.746 246497.2747 232245.7951 232246.5884 222656.0281 241921.9629 235065.6732 1.241703663 1.022155715 1.22106619 1.048631522 0.988003871 0.988007246 0.947207753 1.02916755 1 17.84270435 3.019177892 5.224663266 0.986298087 1.140636922 0.608171396 0.061838535 0.119354586 9.40958464 0.017314396 0.020222331 1045.148237 -3.019177892 0.154338835 TS(ph)STLDSEGTFNSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSSTLDSEGTFNSYR 15 0 Q92609;Q92609-2;C9J397;C9JWX0;C9JW04;C9JDR8;C9JNM0;C9JED7;F2Z3C3;C9K0P2 Q92609 TBC1D5 TBC1 domain family member 5 1 T(0.028)S(0.867)S(0.105)T(0.001)LDSEGTFNSYR 377.58 6.35E-98 244440000 354190 300010 309680 265540 302780 234130 363010 336360 241480 TRUE FALSE 332021.8801 322223.0526 317025.7558 272354.206 279000.8802 301719.5302 308580.0205 378355.2864 201175.428 1.650409712 1.601701837 1.575867187 1.353814473 1.386853668 1.499783215 1.533885244 1.880723159 1 17.61809458 3.455515938 23.62823408 1.473587543 1.607420209 0.10842086 0.215539568 313.9906702 343388.0314 0.054512091 0.073837326 2854.407267 -3.455515938 0.133832666 TS(ph)VQTEDDQLIAGQSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.05)S(0.95)VQTEDDQLIAGQSAR 233.59 6.80E-19 0 191080 140080 160250 150110 156360 130040 173000 130950 137720 TRUE FALSE 179120.6439 150451.669 164051.2057 153962.0767 144080.1163 167580.437 147060.2561 147299.3958 114733.6423 1.561186765 1.311312584 1.429843962 1.341908734 1.255779155 1.460604175 1.281753574 1.283837877 1 16.80792896 -4.03638329 0.169514604 7.37E-11 1.460213409 0.703468012 0.081099016 49.36061398 0.626796338 17.05494366 0.278078036 9.20E-05 4.03638329 1.460213409 TSAAACAVTDLS(ph)DDS(ph)DFDEKAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSAAACAVTDLSDDSDFDEKAK 22 1 Q9NQZ2 Q9NQZ2 UTP3 Something about silencing protein 10 2 TSAAACAVTDLS(1)DDS(1)DFDEKAK;TSAAACAVTDLS(1)DDS(1)DFDEKAK 178.2 3.48E-17 310880000 1311560 603710 758410 801360 906050 446860 1125080 590210 1386630 TRUE FALSE 1229471.801 648409.3166 776399.8433 821924.2543 834892.4878 575861.2278 956384.6987 663899.0177 1155192.495 1.064300371 0.5612998 0.672095644 0.71150415 0.722730187 0.498498069 0.82790072 0.574708562 1 20.13970184 -1.178693381 4.863149989 1.00003139 0.690306447 0.251168901 0.158966088 4.73E-05 7.98E-06 0.134476833 0.031693285 0.066268421 1.178693381 -0.309724943 TSADAQEPAS(ph)PVVSPQQS(ph)PPT(ph)SPHTWR ddPTM_SK-BR-3_Pertuzumab_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 TSADAQEPAS(1)PVVS(0.023)PQQS(0.875)PPT(0.627)S(0.379)PHT(0.097)WR 112.34 0.0034423 385540000 86352 94381 93770 108730 123030 82541 121010 97577 119720 TRUE FALSE 80947.38246 101369.0674 95994.26868 111520.1959 113367.7201 106369.2468 102865.6739 109759.7032 99737.95858 0.811600554 1.016353943 0.962464743 1.118131928 1.13665571 1.066487106 1.031359328 1.100480748 1 16.60585505 5.734437192 0.749708686 1.067020432 1.63E-11 0.660234795 0.054511251 6.627327488 0.925773048 0.019230699 8.407389566 542546.7822 -5.734437192 -1.067020432 TSADAQEPAS(ph)PVVSPQQS(ph)PPTS(ph)PHTWR ddPTM_SK-BR-3_Pertuzumab_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 TSADAQEPAS(1)PVVSPQQS(0.879)PPT(0.408)S(0.705)PHT(0.008)WR 135.77 9.03E-06 215980000 144020 141790 132360 145400 167060 123730 180410 150210 175730 TRUE FALSE 135006.0453 152288.2791 135499.6417 149131.2102 153939.7815 159448.8424 153359.1953 168964.0492 146399.5277 0.922175415 1.040223841 0.925546986 1.018659093 1.051504632 1.089134951 1.047538866 1.154129742 1 17.15955137 2.843185882 2.684746115 1.072632301 0.973979622 0.471277703 0.050432904 0.237211361 3.333697289 0.015178463 0.01614376 696.9247407 -2.843185882 -0.098652679 TSADAQEPASPVVSPQQS(ph)PPTS(ph)PHTWR ddPTM_SK-BR-3_Pertuzumab_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(0.998)PPT(0.296)S(0.704)PHT(0.002)WR;TSADAQEPASPVVSPQQS(0.998)PPT(0.334)S(0.663)PHT(0.004)WR;TSADAQEPASPVVSPQQS(0.998)PPT(0.337)S(0.663)PHT(0.002)WR 217.93 1.76E-34 1519640000 687220 717420 687060 725630 774900 591679 851090 699040 789650 TRUE FALSE 644208.1269 770538.5233 703357.3877 744250.8943 714042.4798 762487.1222 723476.9556 786316.6828 657852.3137 0.979259499 1.171294084 1.069172173 1.131334311 1.08541456 1.159055165 1.099755888 1.195278433 1 19.32740421 TSAEAPSHHLQQQQQQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSAEAPSHHLQQQQQQQR 18 0 Q92609;Q92609-2;C9J3F6 Q92609 TBC1D5 TBC1 domain family member 5 0 188.04 2.31E-14 78050000 41132 55715 51859 58992 57141 40186 65011 49376 48940 FALSE TRUE 38557.62154 59840.19657 53089.11997 60505.83459 52653.37636 51787.04583 55263.20408 55540.70229 40771.59784 0.945698074 1.467693192 1.302110361 1.484019214 1.29142293 1.270174548 1.355433856 1.362240021 1 15.31527688 -0.49251743 8.999000302 0.999999999 1.328196552 0.295173449 0.148078534 0 0 0.125536142 0.029589152 0.321723341 0.49251743 0.328196553 TSAQT(ph)TPSKIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSAQTTPSKIPR 12 1 O95684 O95684 FGFR1OP FGFR1 oncogene partner 1 T(0.008)S(0.009)AQT(0.75)T(0.232)PSKIPR 81.48 0.028345 166070000 517700 267200 345130 344260 353510 244660 393170 282230 540330 TRUE FALSE 485298.0811 286983.766 353316.6466 353094.2944 325746.7506 315289.3703 334217.8085 317467.0368 450145.4323 1.078091759 0.637535662 0.784894439 0.784400483 0.723647797 0.700416682 0.742466289 0.705254378 1 18.78003166 -1.165060384 4.123003169 1.000082074 0.754229216 0.263351631 0.118660537 8.206878069 57116138.29 9742.914179 0.024327581 0.068381656 1.165060384 -0.245852858 TSAVSS(ph)PLLDQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TSAVSSPLLDQQR 13 0 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 TSAVS(0.009)S(0.991)PLLDQQR;TSAVS(0.001)S(0.999)PLLDQQR;TSAVSS(1)PLLDQQR;TSAVSS(1)PLLDQQR;TSAVS(0.043)S(0.957)PLLDQQR 361.92 9.33E-77 2201370000 3421350 3398860 3181630 3055520 3722510 2883760 4083670 3608790 4086040 TRUE FALSE 3207213.811 3650515.131 3257099.766 3133929.816 3430159.08 3716254.698 3471361.594 4059355.375 3404053.527 0.942174906 1.072402388 0.956829774 0.920646456 1.007668961 1.09171453 1.019772917 1.192506329 1 21.69882229 2.361455123 5.168012453 1.071553359 0.984881888 0.357239607 0.064390905 0.262065441 10.82708369 0.021719924 0.017990694 229.8556179 -2.361455123 -0.086671471 TSCDSLDLSSAALPDS(ph)SPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSCDSLDLSSAALPDSSPSK 20 0 Q8NEV8-2;Q8NEV8;E9PPH6;F5GXG5 Q8NEV8-2 EXPH5 Exophilin-5 1 TSCDS(0.003)LDLS(0.114)S(0.325)AALPDS(0.33)S(0.227)PS(0.001)K 157.54 9.36E-11 0 138550 72257 100080 95455 97064 70962 120690 76328 71380 TRUE FALSE 129878.4028 77606.98346 102453.9449 97904.5369 89440.98498 91447.57743 102593.6549 85857.71882 59466.21687 2.184070379 1.305060042 1.72289327 1.646389195 1.504063815 1.537807216 1.725242673 1.443806641 1 15.85978268 -2.61560238 0.303578192 8.71E-15 1.65915319 0.459478697 0.225460119 49.72570724 1.684455739 32.86546255 0.207565158 0.002423247 2.61560238 1.65915319 TSCSGSGERES(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSCSGSGERESPER 14 1 Q9H8Y5;C9JQZ3;C9K022 Q9H8Y5 ANKZF1 Ankyrin repeat and zinc finger domain-containing protein 1 1 TSCSGSGERES(1)PER;TSCSGSGERES(1)PER 161.91 2.74E-06 295160000 281500 277450 280330 284280 274740 223935 319010 244031 261330 TRUE FALSE 263881.4175 297992.6867 286979.56 291575.1061 253163.0286 288581.3992 271177.412 274498.8075 217712.3347 1.212064616 1.368745078 1.318159397 1.339267738 1.16283273 1.325516993 1.245576703 1.260832593 1 17.73206362 -4.006032885 0.2307825 0.056248373 1.325579529 0.670149461 0.061755911 52.22004056 0.792846381 23.04432397 0.09953374 9.86E-05 4.006032885 1.269331156 TSCSGSGERES(ph)PERK ddPTM_SK-BR-3_Pertuzumab_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 200.99 3.46E-09 3442400000 2646700 1768770 1966070 1957670 2168800 1232630 2736700 1950840 2587600 TRUE FALSE 2481047.771 1899731.571 2012706.109 2007907.127 1998471.197 1588470.271 2326357.241 2194406.668 2155712.843 1.150917563 0.881254466 0.93366151 0.931435341 0.927058167 0.73686543 1.079159151 1.017949434 1 21.03973358 1.616882171 25 1.036417493 0.921524385 0.193061645 0.101168334 0.979609506 2708.804557 0.043588159 0.023730222 41.38873668 -1.616882171 -0.114893108 TSDANETEDHLESLICK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSDANETEDHLESLICK 17 0 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 132.13 2.46E-05 169960000 37247 28937 32525 32488 35192 33825 56469 37791 45150 FALSE TRUE 34915.77676 31079.52559 33296.50836 33321.69708 32428.16228 43589.7284 48001.99768 42509.28954 37614.17332 0.928261176 0.826271664 0.885211755 0.885881415 0.862126146 1.158864453 1.276167823 1.130140205 1 15.19898876 2.225907393 7.138378767 1.177277595 0.871627136 0.751371803 0.074095081 0.057110115 14.14376488 0.024982015 0.019146923 168.2315293 -2.225907393 -0.305650459 TSDIFGS(ph)PVTATSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 TSDIFGSPVTATSR 14 0 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BTV5;Q9H910-2;H3BU16;H3BMT0 A6NGP5;Q9H910-2 HN1L Hematological and neurological expressed 1-like protein 1 TSDIFGS(1)PVTATSR;TSDIFGS(0.998)PVT(0.002)ATSR;TSDIFGS(1)PVTATSR;TSDIFGS(1)PVTATSR;TSDIFGS(1)PVTATSR;TSDIFGS(1)PVTATSR;TSDIFGS(1)PVTATSR;TSDIFGS(1)PVTATSR;TSDIFGS(1)PVTATSR 366.96 5.53E-97 11951360000 5323650 5023750 5126500 5408840 5911170 4610160 6543690 4839130 6033400 TRUE FALSE 4990452.249 5395713.677 5248103.001 5547639.992 5446930.553 5941038.352 5562524.433 5443306.033 5026386.563 0.992850866 1.073477658 1.044110503 1.10370341 1.08366726 1.181970045 1.106664671 1.082946161 1 22.2610902 3.236952268 22.4682247 1.104551781 1.045712196 0.199493645 0.048763169 15.5330927 217003.648 0.012723768 0.016009137 1725.64822 -3.236952268 -0.058839585 TSEEFVHINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSEEFVHINR 10 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6;A0A3B3IS13;A0A3B3ISK3;A0A3B3IU76 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 185.08 1.49E-06 571620000 623880 734350 702080 749510 752740 560730 799590 634600 695670 FALSE TRUE 584832.4645 788722.0381 718733.6691 768743.6955 693622.8368 722603.6483 679698.9025 713831.2069 579558.1828 1.009100521 1.360902255 1.240140663 1.326430578 1.19681312 1.246818128 1.172788035 1.231681698 1 19.14459398 0.036397914 0.554089996 0.982285961 1.251214453 0.331358858 0.095922474 3.977825299 1.492417389 0.245831325 0.038519727 1.087421496 -0.036397914 0.268928491 TSELLSGMGVSALEKEEPDSENIPQELLSNLGHPES(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSELLSGMGVSALEKEEPDSENIPQELLSNLGHPESPPR 39 1 D6RF40;D6RAG5;D6R9R7;A0A0A0MTL5;Q13309-2;Q13309 D6RF40 SKP2 S-phase kinase-associated protein 2 1 TSELLSGMGVSALEKEEPDSENIPQELLS(0.002)NLGHPES(0.998)PPR 225.7 5.24E-40 93216000 83141 64985 73264 74379 96012 44359 79891 70547 137310 TRUE FALSE 77937.35322 69796.55702 75001.85668 76287.69106 88471.60481 57164.72319 67912.08622 79354.94824 114392.0739 0.681317774 0.610152038 0.655656062 0.666896651 0.773406773 0.499726259 0.59367825 0.693710198 1 16.80362757 0.874422934 5.719861284 0.999995841 0.635326155 0.723088325 0.069408634 0.913363042 41.309116 0.065188296 0.016410725 7.488984545 -0.874422934 -0.364669686 TSES(ph)PSKPGEK ddPTM_SK-BR-3_Pertuzumab_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 T(0.029)S(0.161)ES(0.799)PS(0.011)KPGEK;T(0.002)SES(0.996)PS(0.002)KPGEK;TSES(0.5)PS(0.5)KPGEK;TSES(0.997)PS(0.003)KPGEK;TSES(1)PSKPGEK;TSES(1)PSKPGEK;TSES(1)PSKPGEK 216.15 7.45E-12 5344490000 10954620 4225180 6396990 5667460 6200880 4528340 8808360 5506950 9791560 TRUE FALSE 10268989.89 4538016.723 6548729.624 5812896.619 5713887.898 5835598.247 7487628.191 6194504.83 8157285.38 1.258873438 0.556314572 0.802807468 0.712601846 0.700464386 0.715384834 0.917906858 0.759383121 1 22.95965769 0.604953429 0.819568254 0.998054933 0.76696938 0.070750317 0.188640287 2.74357833 3.146835319 0.169593389 0.057289609 4.026738517 -0.604953429 -0.231085553 TSESPSKPGEK ddPTM_SK-BR-3_Pertuzumab_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 85.258 0.013999 102780000 231540 120830 156200 164300 169420 110680 209920 139990 206420 FALSE TRUE 217048.3247 129776.3789 159905.1378 168516.2162 156114.4366 142631.5193 178444.4448 157468.0597 171967.1685 1.262149785 0.754657881 0.929858526 0.979932493 0.907815358 0.829411338 1.037665773 0.915686762 1 17.39177363 1.715414461 24.99997992 0.98314937 0.92048973 0 0.135037492 3.11163268 3346.675297 0.057535477 0.031906334 51.92953829 -1.715414461 -0.06265964 TSETNHTSRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSETNHTSRPR 11 1 Q8N488 Q8N488 RYBP RING1 and YY1-binding protein 0 ; 103.44 0.0016427 23538100 6862.4 18507.4 15205.7 13511.6 16430.5 13870.1 16710.5 14969.6 17579.7 FALSE TRUE 6432.894634 19877.70715 15566.38638 13858.33053 15140.11481 17874.17271 14204.91566 16838.58751 14645.5345 0.439239321 1.357253786 1.062875949 0.946249557 1.033770041 1.220452057 0.969914458 1.149742095 1 13.83817323 TSEVNCYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TSEVNCYR 8 0 P62633-2;P62633;P62633-7;P62633-3;P62633-5;P62633-6;P62633-8;P62633-4 P62633-2;P62633-8 CNBP Cellular nucleic acid-binding protein 0 ;;; 183.89 0.00051389 1654460000 1007090 1056990 1099850 976820 1155730 891210 1173800 911870 1038300 FALSE TRUE 944058.0346 1135250.639 1125938.961 1001886.855 1064963.628 1148487.859 997799.587 1025718.977 865001.0223 1.091395282 1.312426934 1.301662001 1.15824933 1.231170369 1.32773006 1.153524171 1.185800884 1 19.72234231 0.753986085 0.977784985 1.000794825 1.248831148 0.456663774 0.076128935 0.732517387 1.295516832 0.069107072 0.022606052 5.675264207 -0.753986085 0.248036323 TSFGS(ph)LTDSSEEALEGMVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TSFGSLTDSSEEALEGMVR 19 0 G3V160;Q969H4-2;Q969H4 G3V160 CNKSR1 Connector enhancer of kinase suppressor of ras 1 1 T(0.001)S(0.001)FGS(0.996)LT(0.001)DSSEEALEGMVR;TSFGS(0.999)LTDSSEEALEGMVR;T(0.006)S(0.024)FGS(0.967)LT(0.003)DSSEEALEGMVR;TSFGS(0.997)LT(0.003)DSSEEALEGMVR 155.79 2.34E-08 62797000 93673 105047 99409 128506 130084 81983 116226 88132 105098 TRUE FALSE 87810.17414 112824.7892 101767.0284 131803.6815 119867.7274 105650.1612 98798.99029 99135.4742 87556.46484 1.002897665 1.288594616 1.162301706 1.505356364 1.36903343 1.206651746 1.128403145 1.132246195 1 16.41792609 1.5807419 1.776654371 1.05708369 1.265032544 0.284569369 0.132151043 0.446116625 2.852079386 0.106164638 0.037201792 38.08394241 -1.5807419 0.207948854 TSFLDDAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSFLDDAFR 9 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542;H0YJ21 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 182.53 0.00010752 76653000 81076 140580 82448 95694 151280 71227 88855 120220 113030 FALSE TRUE 76001.59788 150988.6895 84403.70549 98149.67005 139399.079 91789.07863 75532.01764 135229.7316 94164.5628 0.807114647 1.603455536 0.896342562 1.042320669 1.480377277 0.974773056 0.802127843 1.436100032 1 16.52289661 TSFSVGS(ph)DDELGPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 388.11 2.17E-114 2959290000 1909200 1924160 2048700 2014060 1983550 1768180 2415790 1835770 2232550 TRUE FALSE 1789706.58 2066626.808 2097296.131 2065744.189 1827769.984 2278624.862 2053564.717 2064969.926 1859922.982 0.962247683 1.111135691 1.127625257 1.110661145 0.982712726 1.225117859 1.10411277 1.110244857 1 20.82681145 2.246176649 24.99999669 1.120804811 1.077731459 0.062405915 0.076681036 494.9963797 1624850.908 0.025125782 0.020656515 176.2692875 -2.246176649 -0.043073351 TSGFRPIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSGFRPIAK 9 1 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 0 90.15 0.010147 0 307280 274120 263410 250780 316300 176720 316280 284750 277840 FALSE TRUE 288047.8933 294416.13 269658.2096 257215.4394 291459.0739 227736.1952 268856.7502 320301.6643 231466.7091 1.244446316 1.271958854 1.164997812 1.111241614 1.259183556 0.983883151 1.161535286 1.383791499 1 17.82044519 3.845558325 2.658856545 1.15085506 1.257388041 0.128873092 0.114900758 0.54339135 7.546612106 0.02884989 0.060054517 7007.422844 -3.845558325 0.106532981 TSGGDHAPDS(ph)PSGENSPAPQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSGGDHAPDSPSGENSPAPQGR 22 0 H0YDE3;E9PRI1;Q96NY9;E9PL60;E9PII7;H0YDU2 H0YDE3 MUS81 Crossover junction endonuclease MUS81 1 TSGGDHAPDS(0.973)PS(0.027)GENSPAPQGR 178.95 3.77E-17 174990000 91504 101880 93152 94491 110570 91101 119230 87442 132520 TRUE FALSE 85776.92798 109423.3012 95361.60943 96915.79903 101886.2782 117400.3798 101352.5684 98359.32618 110401.5559 0.776953978 0.991139122 0.863770521 0.877848127 0.922869949 1.063394251 0.918035689 0.89092337 1 16.75240098 2.47036179 24.97619168 0.964381902 0.894729103 0.260880781 0.069141959 276.4721305 1021553.082 0.022692018 0.019027001 295.3668763 -2.47036179 -0.069652799 TSGHDHPDVATMLNILALVYR ddPTM_SK-BR-3_Pertuzumab_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 ; 156.73 7.08E-09 150999000 181107 266810 231477 231133 277130 182019 256780 241500 237450 FALSE TRUE 169771.8362 286564.89 236967.7438 237064.2641 255365.3277 234564.9305 218278.2228 271651.8066 197818.061 0.858222122 1.448628546 1.197907524 1.198395449 1.290910074 1.185760942 1.10342919 1.37324067 1 17.59381463 2.014910537 22.60920615 1.163935314 1.233202781 0 0.172288744 298.0426691 451923.6806 0.059149944 0.043656913 103.4928952 -2.014910537 0.069267467 TSGHVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TSGHVDK 7 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;;; 66.799 0.066894 884570000 1934350 1526880 1975600 1665840 1804650 1330460 1993620 1794370 1681220 FALSE TRUE 1813282.486 1639931.784 2022462.165 1708588.275 1662920.069 1714542.204 1694695.189 2018401.044 1400613.521 1.294634429 1.170866738 1.443983037 1.219885607 1.187279748 1.22413655 1.209966321 1.441083507 1 20.41762749 TSGNVEDDLIIFPDDCEFKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSGNVEDDLIIFPDDCEFKR 20 1 Q16186 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 0 ; 173.43 7.84E-12 102251000 115582.1 83113.3 94730.7 84172 91903.8 77963.3 133491.7 77676.8 109907 FALSE TRUE 108348.0227 89267.09521 96977.75694 86331.99602 84686.04627 100470.0391 113475.8589 87374.91947 91562.81167 1.183319087 0.974927414 1.059139133 0.942871832 0.924895651 1.097279968 1.239322568 0.954262084 1 16.48247414 2.033158961 24.27479614 1.110415051 1.013446024 0.013174996 0.104585248 234.4688627 171647.199 0.036883024 0.027239748 107.9341713 -2.033158961 -0.096969027 TSGQTSANAHSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TSGQTSANAHSSR 13 0 O00139-1;O00139-5;O00139;O00139-4;O00139-2 O00139-1 KIF2A Kinesin-like protein KIF2A 0 ;;; 171.26 2.54E-05 58511200 10579.7 31612.2 26092.9 27723.2 30759 23884.2 29037.1 25596.1 27434.2 FALSE TRUE 9917.535462 33952.80018 26711.83591 28434.62425 28343.31222 30779.18081 24683.25642 28791.82943 22855.25479 0.43392802 1.485557719 1.168739362 1.244117579 1.240122347 1.346700402 1.079981678 1.259746596 1 14.48023828 4.749501198 24.99299556 1.239896331 0.43392756 0.777255553 0.133481106 713.5546273 1630034.63 0.029863006 0.450243912 56169.5828 -4.749501198 -0.805968772 TSIDAYDNFDNISLAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSIDAYDNFDNISLAQR 17 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 264.29 4.30E-27 119487000 99148 120095 114885 126726 125980 103879 145830 110701 129946 FALSE TRUE 92942.50366 128986.9588 117610.1265 129978.0037 116086.039 133867.181 123964.1453 124522.2635 108257.1731 0.858534368 1.191486486 1.086395692 1.200641029 1.072317294 1.236566383 1.145089436 1.150244921 1 16.7241031 4.744492991 24.8573025 1.143556332 0.858534233 0.609974999 0.069285789 358.4716905 1501990.097 0.014092648 0.12780707 55525.56556 -4.744492991 -0.2850221 TSIFWNDVKDPVSIEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TSIFWNDVKDPVSIEER 17 1 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;; 303.14 1.38E-46 1962770000 2369960 1715710 2111300 2115600 2059230 1638430 2481870 1743840 2488720 FALSE TRUE 2221628.434 1842742.954 2161381.033 2169889.878 1897506.382 2111418.143 2109736.634 1961562.263 2073336.554 1.071523304 0.888781394 1.042465117 1.046569055 0.915194583 1.018367297 1.017556281 0.946089654 1 20.98352289 TSISDPPES(ph)PPLLPPREPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSISDPPESPPLLPPREPVR 20 1 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 TSISDPPES(0.999)PPLLPPREPVR 57.802 0.048315 153890000 341030 368920 365290 352070 404000 273300 329860 285480 381520 TRUE FALSE 319685.5411 396235.2207 373954.8513 361104.7123 372271.4697 352197.2733 280400.5553 321122.8064 317841.8473 1.005800664 1.246642706 1.176543789 1.13611444 1.171247502 1.108089688 0.882201503 1.010322615 1 18.27794956 1.912900155 5.108411017 0.956877277 1.162707021 0.590179507 0.069214701 0.129667343 5.505255029 0.029436251 0.017529116 81.82766431 -1.912900155 0.205829744 TSKEPPSS(ph)PLQPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TSKEPPSSPLQPQK 14 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 TSKEPPS(0.202)S(0.798)PLQPQK;TSKEPPS(0.041)S(0.959)PLQPQK;TSKEPPS(0.032)S(0.968)PLQPQK 151.41 3.28E-07 1120260000 2164490 1660480 1985770 2565260 2272350 923930 1604390 917420 1478040 TRUE FALSE 2029018.435 1783423.667 2032873.402 2631088.915 2093888.797 1190653.592 1363826.614 1031961.906 1231345.575 1.647805843 1.448353494 1.650936539 2.136759141 1.700488343 0.966953239 1.107590461 0.838076594 1 20.23180428 2.23967793 24.9995728 0.999308031 1.690348223 0.800934386 0.182597964 14.57422547 326103.7587 0.070373262 0.055810672 173.6512565 -2.23967793 0.691040193 TSKEPVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSKEPVSR 8 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 ; 90.15 0.012221 352590000 339880 322320 358100 352750 354350 229540 369430 318190 426040 FALSE TRUE 318607.5175 346184.9082 366594.3011 361802.1622 326520.7804 295804.4717 314037.4011 357916.7219 354931.1717 0.897660005 0.97535786 1.032860257 1.019358656 0.919955209 0.833413617 0.884783942 1.008411632 1 18.43717976 2.656289927 6.751793058 0.910632678 0.988776383 0.102882478 0.062880217 0.345198825 23.99207669 0.020005232 0.018849934 453.2000266 -2.656289927 0.078143705 TSLAEDSCLGRHS(ph)PVPR ddPTM_SK-BR-3_Pertuzumab_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 224.1 1.71E-15 418230000 316010 389370 336580 365450 406980 244040 379990 323520 284860 TRUE FALSE 296231.4982 418199.3599 344563.8365 374828.0657 375017.4325 314490.3863 323014.0272 363912.1842 237315.0257 1.248262714 1.76221189 1.451925918 1.579453575 1.58025153 1.325202167 1.361119154 1.533456143 1 17.85644392 -0.892481457 0.287637982 0.731630793 1.570744105 0.490989889 0.150413672 10.00330099 0.757104236 2.423137172 0.173456134 0.128090978 0.892481457 0.839113311 TSLDIEEYS(ph)DTEVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TSLDIEEYSDTEVQK 15 0 P51580 P51580 TPMT Thiopurine S-methyltransferase 1 TSLDIEEYS(1)DTEVQK;TSLDIEEYS(1)DTEVQK;TSLDIEEYS(1)DTEVQK;TSLDIEEYS(1)DTEVQK;TSLDIEEYS(1)DTEVQK 373.42 1.16E-97 756973000 2224410 1603130 1817980 1811190 1925780 1322920 2391110 1580040 2311780 TRUE FALSE 2085188.149 1721827.413 1861103.344 1857668.202 1774537.007 1704825.528 2032585.253 1777311.472 1925928.983 1.082692128 0.894024353 0.966340587 0.964556958 0.921392752 0.885196465 1.055379129 0.922833338 1 20.87712308 1.737226035 25 0.99603046 0.946524352 0.078852836 0.062631481 0.375696504 6746.981351 0.026173159 0.014514376 54.6041983 -1.737226035 -0.049506108 TSLPTVGPSGLYS(ph)PSTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSLPTVGPSGLYSPSTNR 18 0 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 TSLPTVGPS(0.003)GLYS(0.996)PSTNR;TSLPTVGPSGLYS(0.998)PS(0.001)T(0.001)NR 185.99 5.28E-14 122212000 116512 106900 119452 125592 124936 99528 152350 99212 145729 TRUE FALSE 109219.7219 114814.9872 122285.4578 128814.9033 115124.0305 128260.1179 129506.5318 111598.8366 121405.8885 0.899624584 0.945711849 1.007244866 1.061026817 0.948257387 1.056457142 1.066723645 0.919220954 1 16.88947887 4.3249902 1.314781595 1.017292384 0.890122747 0.362757845 0.048060932 0.692307314 1.71940437 0.013195928 0.096944647 21134.4135 -4.3249902 -0.127169637 TSNEHLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSNEHLQK 8 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 90.709 0.013004 145610000 313880 338320 317860 347100 387010 241040 381170 355440 421620 FALSE TRUE 294234.8111 363369.5648 325399.7893 356007.1736 356615.7957 310624.335 324017.0971 399817.4664 351248.8982 0.837681805 1.034507344 0.926408 1.013546734 1.015279471 0.884342518 0.922471497 1.138273937 1 18.42213417 4.753342071 23.8273256 0.979830761 0.83768161 0.302015568 0.071613182 1837.512906 2961925.661 0.016160866 0.342840072 56668.54618 -4.753342071 -0.142149151 TSNRYS(ph)PESQAQSVHHQRPGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TSNRYSPESQAQSVHHQRPGSR 22 2 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 T(0.063)S(0.063)NRYS(0.865)PES(0.009)QAQSVHHQRPGSR;TSNRYS(0.999)PES(0.001)QAQSVHHQRPGSR;T(0.005)S(0.005)NRYS(0.989)PES(0.001)QAQSVHHQRPGSR;T(0.033)S(0.033)NRYS(0.924)PES(0.01)QAQSVHHQRPGSR;T(0.001)S(0.001)NRYS(0.999)PESQAQSVHHQRPGSR;T(0.002)S(0.002)NRYS(0.994)PES(0.001)QAQSVHHQRPGSR 220.96 4.63E-26 2428410000 265240 507904 442294 513989 515507 388238 553227 429598 549365 TRUE FALSE 248639.1019 545509.7406 452785.4225 527178.8279 475021.1597 500316.0081 470275.7473 483234.256 457672.4325 0.543268688 1.191921781 0.989322036 1.151869308 1.037906428 1.093174884 1.02753785 1.055851788 1 18.80395587 4.746718647 24.99948448 1.070380724 0.543268428 0.87022356 0.063733258 322.6421169 988682.9076 0.013717914 0.15596531 55810.85135 -4.746718647 -0.527112295 TSPDTLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TSPDTLRR 8 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;;; 172.21 0.00045678 1057200000 1343860 1931990 1522050 1539060 2107340 1194140 1791780 1628100 2539240 FALSE TRUE 1259750.201 2075036.55 1558153.745 1578554.885 1941838.017 1538868.833 1523119.223 1831371.869 2115424.44 0.595507066 0.980907902 0.736567904 0.746211897 0.917942509 0.727451571 0.720006441 0.865723131 1 21.01251572 0.969483894 8.057212924 0.999996346 0.789539931 0.307843762 0.107565628 0.499693962 128.6439284 0.096645256 0.02420218 9.321459 -0.969483894 -0.210456415 TSPENVQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSPENVQDR 9 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 0 66.435 0.063739 647840000 226920 231650 207930 198940 224120 372240 408730 205660 255150 FALSE TRUE 212717.4823 248801.607 212862.1978 204045.1372 206518.5193 479699.6452 347444.731 231337.1037 212563.8167 1.000722915 1.170479581 1.001403725 0.959924132 0.971560082 2.256732367 1.634543152 1.088318357 1 17.69753651 TSPGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSPGSPR 7 0 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 T(0.001)S(0.001)PGS(0.999)PR;TSPGS(1)PR 110.55 0.0071096 191930000 2082080 1641150 1963480 1755630 1733240 1344650 1849390 1547010 2174470 TRUE FALSE 1951766.329 1762662.454 2010054.673 1800682.438 1597118.322 1732828.626 1572091.138 1740157.604 1811536.909 1.077409088 0.973020447 1.109585271 0.994008142 0.881637196 0.956551654 0.867821754 0.960597377 1 20.78878277 2.972352414 6.209014502 0.923468451 1.045299055 0.529253559 0.051196458 0.124115943 16.29340964 0.014299285 0.015725954 938.3231128 -2.972352414 0.121830604 HHHHDSDSNS(ph)PCCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 HHHHDSDSNSPCCK 14 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 HHHHDSDSNS(1)PCCK;HHHHDSDSNS(1)PCCK 171.56 5.01E-06 150764000 33809.7 65669 66388 67051 78554 71852 96068 60819 83710 TRUE FALSE 31693.61123 70531.20109 67962.75471 68771.64218 72384.68571 92594.50598 81663.49525 68412.38603 69738.26021 0.454465184 1.011370242 0.974540439 0.986139344 1.037947971 1.327743275 1.170999893 0.980987851 1 16.08966275 4.930091683 1.811088897 1.081695398 2.31E-19 0.742440399 0.11179032 0.892152453 1.967917721 0.031299139 1.928991871 85131.77398 -4.930091683 -1.081695398 down TSQLGDS(ph)PFYPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSQLGDSPFYPGK 13 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 TSQLGDS(1)PFYPGK;TSQLGDS(1)PFYPGK 283.68 1.39E-32 563100000 1294430 899980 1104790 1006270 1157070 789610 1396880 945590 1666280 TRUE FALSE 1213413.937 966615.4556 1130996.141 1032092.592 1066198.39 1017557.589 1187430.812 1063648.993 1388167.103 0.874112298 0.696324998 0.81474063 0.743493049 0.768061991 0.733022405 0.855394721 0.766225471 1 20.40474982 -0.362884399 0.545089927 1.029271026 0.768820483 0.604321757 0.055106854 4.791481177 1.303096669 0.329464535 0.021907023 0.433626286 0.362884399 -0.260450542 TSQSWVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSQSWVER 8 0 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EIJ4 Q9H6Z4 RANBP3 Ran-binding protein 3 0 76.345 0.083848 54279000 60788 67130 60968 65838 72474 50554 68438 57839 59252 FALSE TRUE 56983.38759 72100.37505 62414.18975 67527.51454 66782.18439 65148.11912 58176.35725 65060.32647 49362.45842 1.154387148 1.460631771 1.264406023 1.367993344 1.352894214 1.319790813 1.178554697 1.318012282 1 15.59112663 0.181969098 0.483885086 0.972557793 1.338541934 0.522891101 0.089836026 2.274128702 0.765614827 0.213592739 0.043591567 1.520439341 -0.181969098 0.365984141 TSQTWHGGIATIFQSPGDEVWGVVWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TSQTWHGGIATIFQSPGDEVWGVVWK 26 0 O75223;B8ZZK2;H7BZK5;O75223-2;O75223-4 O75223 GGCT Gamma-glutamylcyclotransferase 0 ;; 234.89 6.69E-45 570536000 765465 822140 672909 628911 792783 475571 846041 829427 615806 FALSE TRUE 717555.912 883012.101 688870.7193 645049.921 730521.0211 612860.6274 719185.0063 932982.7867 513024.0003 1.398679032 1.721190627 1.342765092 1.257348429 1.423950966 1.194604204 1.401854506 1.818594815 1 18.96866679 3.790090672 4.931614509 1.35741465 1.573361205 0.135574047 0.220146529 0.358361701 17.32726918 0.052225963 0.095241135 6167.237476 -3.790090672 0.215946555 TSQVGAASAPAKES(ph)PR ddPTM_SK-BR-3_Pertuzumab_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;TSQVGAASAPAKES(1)PR 298 2.42E-45 89094260000 39907590 25570640 30545570 29580680 32962160 23165371 40096510 27821970 36757800 TRUE FALSE 37409845.18 27463916.79 31270125.35 30339770.33 30373444.92 29852837.55 34084410.56 31295604.2 30622685.72 1.221638282 0.89684873 1.021142484 0.990761248 0.99186091 0.974860201 1.113044456 1.021974509 1 24.86809748 1.760359308 25 1.056203294 1.001074208 0 0.08714863 27.88448088 32005.57662 0.036532779 0.020259865 57.59162174 -1.760359308 -0.055129086 TSQVGAASAPAKES(ph)PRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TSQVGAASAPAKESPRK 17 2 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 TSQVGAASAPAKES(1)PRK;TSQVGAASAPAKES(1)PRK;TSQVGAASAPAKES(1)PRK;TSQVGAASAPAKES(1)PRK 198.64 7.31E-12 4868090000 6041570 2961570 3995350 3996230 4272350 2749770 5279850 3570370 5252600 TRUE FALSE 5663438.918 3180847.724 4090121.589 4098780.027 3936816.865 3543583.96 4488185.508 4016138.554 4375907.127 1.294231974 0.726900191 0.934691133 0.936669794 0.899657317 0.809794143 1.02565831 0.91778423 1 22.06115069 1.680414696 14.77740763 0.978496994 0.9087573 0.003810809 0.14883634 0.467274936 107.4928731 0.063269994 0.034874346 47.90873419 -1.680414696 -0.069739694 TSRPENAIIYNNNEDFQVGQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TSRPENAIIYNNNEDFQVGQAK 22 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;;; 323.08 6.76E-68 4438900000 2205701 2122378 1625386 1523001 2888991 1319795 2133724 2604307 3231008 FALSE TRUE 2067650.112 2279521.075 1663940.923 1562083.784 2662101.3 1700798.391 1813791.895 2929460.462 2691731.892 0.76814861 0.846860374 0.618167407 0.580326662 0.988991998 0.631860252 0.673838245 1.088318072 1 21.36010329 1.237632064 24.99999381 1.044159169 0.726485311 0.534511553 0.121954722 18.31746589 493042.3614 0.092361754 0.028169705 17.28351473 -1.237632064 -0.317673858 TSS(ph)DDES(ph)EEDEDDLLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSSDDESEEDEDDLLQR 17 0 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 2 T(0.008)S(0.016)S(0.975)DDES(1)EEDEDDLLQR;T(0.028)S(0.057)S(0.915)DDES(1)EEDEDDLLQR 376.05 7.22E-105 264332000 418030 275180 334310 312780 301860 275120 376960 261930 289440 TRUE FALSE 391866.2485 295554.6135 342239.9911 320806.4643 278153.1332 354542.6778 320438.3475 294632.5371 241130.5941 1.625120404 1.225703501 1.419313846 1.330426218 1.153537295 1.470334692 1.328899589 1.22187953 1 17.87945518 -4.106960619 0.187186678 1.35E-10 1.413991986 0.472462747 0.126535799 86.71348047 1.143768616 32.93692397 0.339772704 7.82E-05 4.106960619 1.413991986 TSS(ph)DPVLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 TSSDPVLLK 9 0 Q9BRG2;Q9BRG2-2 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 TS(0.002)S(0.998)DPVLLK;TS(0.001)S(0.999)DPVLLK;TS(0.001)S(0.999)DPVLLK;TS(0.006)S(0.994)DPVLLK;TS(0.001)S(0.998)DPVLLK;TSS(1)DPVLLK;TSS(0.999)DPVLLK;TSS(1)DPVLLK 210.64 6.77E-06 1600291000 8181200 5714940 6899970 6351240 6392200 5471350 8917790 5586630 9073350 TRUE FALSE 7669153.296 6138080.104 7063640.547 6514223.571 5890182.397 7050839.925 7580650.178 6284133.053 7558949.269 1.014579279 0.812028218 0.934473866 0.861789561 0.779232958 0.932780427 1.00287089 0.831350077 1 22.84975428 2.020095268 24.93199755 0.950750936 0.875817527 0.12904999 0.078661267 378.0283871 469013.9323 0.026991014 0.01993214 104.7358274 -2.020095268 -0.074933409 TSS(ph)EDNLYLAVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 TSSEDNLYLAVLR 13 0 Q15149-4 Q15149-4 PLEC Plectin 1 TS(0.019)S(0.98)EDNLYLAVLR;TS(0.008)S(0.992)EDNLYLAVLR;TSS(1)EDNLYLAVLR;TSS(1)EDNLYLAVLR;T(0.007)S(0.019)S(0.975)EDNLYLAVLR;TS(0.002)S(0.998)EDNLYLAVLR;TS(0.001)S(0.999)EDNLYLAVLR;TSS(1)EDNLYLAVLR;TS(0.011)S(0.989)EDNLYLAVLR 368.19 3.72E-91 3055548000 3584892 3501733 3258334 3569890 3590397 2563843 4255791 3151105 3034022 TRUE FALSE 3360520.009 3761004.955 3335623.221 3661499.421 3308421.703 3303982.854 3617674.648 3544527.396 2527624.128 1.329517301 1.487960537 1.319667424 1.448593318 1.308905729 1.307149595 1.431254991 1.402315857 1 21.26935051 -1.458626174 3.073073985 0.991677552 1.384037197 0.779243437 0.063424067 29107969.84 36671436.45 2096587.421 0.014272277 0.034783544 1.458626174 0.392359645 TSS(ph)EEEDSRREEPSLLLVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSSEEEDSRREEPSLLLVLK 20 2 A0A087WZV0;O43314-2;O43314;D6RBU4 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 T(0.302)S(0.302)S(0.397)EEEDSRREEPSLLLVLK 193.77 3.21E-18 65577000 134380 170610 159060 178360 177730 147570 173880 143520 204690 TRUE FALSE 125969.3957 183242.1419 162832.9783 182937.0196 163771.8027 190171.0634 147808.3082 161438.7879 170525.9167 0.738711148 1.074570631 0.954886984 1.072781329 0.960392449 1.115203291 0.866779145 0.946711157 1 17.37963149 -0.196401405 6.49830894 0.999999999 0.976427995 0.001698063 0.109702091 12726755.68 1958471.285 0.094332349 0.022878955 0.636207222 0.196401405 -0.023572004 TSS(ph)FTEQLDEGTPNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TSSFTEQLDEGTPNR 15 0 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71;C9JHJ5;C9J0Y3 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 TS(0.001)S(0.816)FT(0.183)EQLDEGTPNR;TSS(0.998)FT(0.002)EQLDEGTPNR;TSS(0.94)FT(0.06)EQLDEGTPNR;TS(0.001)S(0.905)FT(0.094)EQLDEGTPNR;TS(0.001)S(0.983)FT(0.015)EQLDEGTPNR;T(0.004)S(0.089)S(0.704)FT(0.203)EQLDEGTPNR 360.74 5.91E-83 3941790000 3939080 3704820 3751000 4468840 4290660 3225250 4653320 3404610 3192350 TRUE FALSE 3692540.014 3979128.728 3839975.491 4583518 3953688.871 4156327.317 3955597.865 3829683.053 2659526.162 1.388420264 1.496179577 1.44385701 1.723434071 1.486614017 1.562807457 1.487331812 1.439986983 1 21.3427378 0.57280258 1.724852634 1.00006465 1.512918222 0.771009082 0.087183238 1.007550347 3.534006765 0.078939359 0.022279553 3.739405651 -0.57280258 0.512853572 TSS(ph)GTSLSAMHSSGSSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TSSGTSLSAMHSSGSSGK 18 0 Q12888;Q12888-2;A6NNK5;Q12888-3;M0R142 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 T(0.129)S(0.129)S(0.7)GT(0.02)S(0.02)LS(0.001)AMHSSGSSGK;T(0.124)S(0.124)S(0.709)GT(0.019)S(0.019)LS(0.005)AMHSSGSSGK;T(0.021)S(0.021)S(0.894)GT(0.029)S(0.029)LS(0.005)AMHSSGSSGK;T(0.003)S(0.171)S(0.792)GT(0.016)S(0.016)LS(0.002)AMHSSGSSGK;T(0.002)S(0.085)S(0.903)GT(0.004)S(0.005)LS(0.001)AMHSSGSSGK 214.55 6.43E-19 1721550000 715237 1799140 1597180 1756380 1866010 1468210 2179930 1746920 1849120 TRUE FALSE 670471.5929 1932350.198 1635065.864 1801451.684 1719461.102 1892058.393 1853069.734 1965026.807 1540489.926 0.435232702 1.254373797 1.061393415 1.169401795 1.116178089 1.228218608 1.202909349 1.275585626 1 20.55495782 4.74261197 24.99730664 1.169185037 0.435232416 0.87672676 0.085798812 122.0728873 753174.5179 0.018658558 0.143401089 55285.59275 -4.74261197 -0.73395262 TSS(ph)IADEGTYTLDSILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TSSIADEGTYTLDSILR 17 0 A0A087WY00;G3V394;F8WE88;F8W6H6;Q9Y4I1-2;Q9Y4I1;Q9Y4I1-3;E7ERV5 A0A087WY00 MYO5A Unconventional myosin-Va 1 TSS(1)IADEGTYTLDSILR;TS(0.004)S(0.996)IADEGTYTLDSILR;T(0.002)S(0.002)S(0.996)IADEGTYTLDSILR;T(0.032)S(0.191)S(0.778)IADEGTYTLDSILR 359.66 3.85E-88 547130000 542800 564760 593780 841310 679320 342278 463663 288683 347965 TRUE FALSE 508827.1169 606575.418 607864.742 862899.4389 625968.9474 441088.1022 394141.0376 324725.708 289887.3936 1.755257828 2.092451868 2.096899539 2.976671142 2.159352084 1.521584284 1.35963497 1.120178784 1 18.14513307 2.064830321 2.360836771 1.197397685 2.220732933 0.705801258 0.316344498 0.180139522 1.935648384 0.164957565 0.096064277 116.0994925 -2.064830321 1.023335248 TSS(ph)KSEAGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TSSKSEAGAR 10 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 T(0.038)S(0.14)S(0.506)KS(0.316)EAGAR;T(0.003)S(0.056)S(0.772)KS(0.169)EAGAR;T(0.017)S(0.388)S(0.576)KS(0.018)EAGAR 112.95 0.00094034 774760000 1292030 725830 952400 1073540 1086910 779180 1286720 895700 1301610 TRUE FALSE 1211164.149 779571.2084 974991.3778 1101088.854 1001548.473 1004116.617 1093788.281 1007530.117 1084362.882 1.116936192 0.718920964 0.899137543 1.0154247 0.92362851 0.925996854 1.008692108 0.929144785 1 20.04841621 3.438872147 7.414695051 0.965200568 0.863441996 0.004441458 0.102925129 0.332802253 51.91137672 0.026259193 0.035954527 2747.085314 -3.438872147 -0.101758572 TSS(ph)LDTITGPYLTGQWPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TSSLDTITGPYLTGQWPR 18 0 Q86VQ1;H7C2L5;H7C0Q2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 TSS(1)LDTITGPYLTGQWPR;T(0.034)S(0.034)S(0.932)LDTITGPYLTGQWPR;T(0.002)S(0.049)S(0.949)LDTITGPYLTGQWPR 254.68 1.61E-30 445451000 790325 620117 712630 638283 689968 557227 784248 587856 901061 TRUE FALSE 740859.969 666031.1079 729533.9201 654662.4224 635780.6965 718089.3891 666657.293 661251.1156 750668.098 0.986934134 0.887251116 0.971846175 0.87210636 0.846953132 0.956600382 0.888085287 0.880883466 1 19.51781565 4.75038856 23.81849942 0.911040936 0.986934223 0.184875968 0.048662323 1543.394746 3107895.141 0.010598759 0.1663812 56284.46724 -4.75038856 0.075893288 TSS(ph)LDTLAAPYLAGHWPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TSSLDTLAAPYLAGHWPR 18 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 T(0.128)S(0.128)S(0.743)LDTLAAPYLAGHWPR;T(0.14)S(0.14)S(0.721)LDTLAAPYLAGHWPR;T(0.069)S(0.172)S(0.758)LDTLAAPYLAGHWPR 316.66 1.52E-61 889680000 406720 361791 347103 354284 333877 288131 394120 292805 336224 TRUE FALSE 381264.1212 388578.3821 355336.4471 363375.5272 307655.6472 371309.7423 335025.3648 329362.3488 280106.0423 1.361142081 1.387254551 1.2685783 1.297278432 1.098354197 1.325604186 1.196066183 1.175848782 1 18.09561358 1.832810417 0.037214098 1.18E-09 2.424223101 0.725283609 0.063287384 37.7680808 1.251919375 39.39050451 41.29706911 68.04722466 -1.832810417 2.424223099 TSS(ph)LTQFPPSQSEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TSSLTQFPPSQSEER 15 0 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3 Q9H6Z4 RANBP3 Ran-binding protein 3 1 T(0.074)S(0.074)S(0.845)LT(0.007)QFPPSQSEER;T(0.001)S(0.027)S(0.945)LT(0.027)QFPPSQSEER;T(0.038)S(0.038)S(0.923)LT(0.002)QFPPSQSEER;TS(0.001)S(0.999)LTQFPPSQSEER 294.29 5.51E-44 360640000 369228 380521 390776 416122 518480 404678 553070 386078 524550 TRUE FALSE 346118.6786 408695.1708 400045.3913 426800.395 477760.6722 521501.9692 470142.288 434280.6882 436999.2163 0.79203501 0.935230901 0.91543732 0.976661694 1.09327581 1.193370491 1.075842405 0.993779101 1 18.73727117 2.994058764 2.395538446 1.085865664 0.89529382 0.621689583 0.067051445 0.18634249 2.147900572 0.021338822 0.024870083 986.4129468 -2.994058764 -0.190571845 TSS(ph)PHKEES(ph)PKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSSPHKEESPKK 12 2 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 2 T(0.275)S(0.329)S(0.396)PHKEES(1)PKK;T(0.24)S(0.323)S(0.437)PHKEES(1)PKK 140.22 3.19E-05 723330000 1610090 334552 639410 626050 613870 430824 924080 454910 711540 TRUE FALSE 1509317.341 359322.5782 654577.1072 642115.5029 565659.1264 555195.895 785522.7827 511706.5149 592779.3773 2.546170462 0.606165788 1.104250809 1.083228478 0.954248997 0.936597858 1.325152009 0.863232654 1 19.17713573 4.747552474 24.91033768 0.997028472 2.546171303 0.877442847 0.183411523 391.7805127 1085333.739 0.045060389 0.551977597 55918.10871 -4.747552474 1.549142831 TSS(ph)PHKEESPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSSPHKEESPK 11 1 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.149)S(0.01)S(0.84)PHKEESPK;T(0.006)S(0.131)S(0.862)PHKEES(0.001)PK 176.43 5.24E-06 408370000 869280 443170 570930 593570 566050 336640 702460 453740 723220 TRUE FALSE 814873.3165 475982.7679 584472.7292 608802.0111 521594.7163 433822.5031 597132.6443 510390.4378 602509.9098 1.352464587 0.789999899 0.970063263 1.01044315 0.865703133 0.720025507 0.991075225 0.847107126 1 19.20062544 4.746928487 24.93116527 0.897273943 1.352464824 0.685079765 0.096548808 585.7904315 1745259.069 0.021693486 0.249446315 55837.82422 -4.746928487 0.45519088 TSS(ph)TLDSEGTFNSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSSTLDSEGTFNSYR 15 0 Q92609;Q92609-2;C9J397;C9JWX0;C9JW04;C9JDR8;C9JNM0;C9JED7;F2Z3C3;C9K0P2 Q92609 TBC1D5 TBC1 domain family member 5 1 TS(0.003)S(0.995)T(0.002)LDSEGTFNSYR 244.05 5.45E-18 73331000 119460 110300 97791 117700 158030 81577 146350 116720 109300 TRUE FALSE 111983.2118 118466.7268 100110.6487 120720.3813 145618.9613 105126.9556 124406.1761 131292.7489 91057.1239 1.229812749 1.301015469 1.09942687 1.325765367 1.599204489 1.15451654 1.366243198 1.441872347 1 16.47448427 3.041062987 23.52449119 1.337893131 1.213615759 0.069953267 0.166212022 166.8191973 95566.90771 0.04358688 0.0520962 1099.165243 -3.041062987 -0.124277372 TSS(ph)VLGMSVESAPAVEEEKGEELEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSSVLGMSVESAPAVEEEKGEELEQK 26 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 T(0.035)S(0.035)S(0.93)VLGMSVESAPAVEEEKGEELEQK 190.23 4.54E-18 54018000 56282 24774 26184 28976 37704 21664 44738 25558 41665 TRUE FALSE 52759.41009 26608.29274 26805.09684 29719.57322 34742.87993 27918.04511 38029.95223 28748.97256 34710.84233 1.519969166 0.766570067 0.772239884 0.856204322 1.000922985 0.804303302 1.095621704 0.828241858 1 15.08309876 -0.83028368 8.330517673 0.999998277 0.926424178 0 0.227372373 0 0 0.201748571 0.047552594 0.147814256 0.83028368 -0.073574099 TSS(ph)VVTLEVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TSSVVTLEVAK 11 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 TSS(1)VVTLEVAK;TSS(1)VVTLEVAK;TSS(1)VVTLEVAK;TSS(1)VVTLEVAK 293.71 1.68E-35 2245040000 5321870 4366210 4095410 4233050 4947220 2607680 5385400 4185810 4710510 TRUE FALSE 4988783.657 4689488.731 4192555.059 4341677.23 4558685.297 3360474.884 4577909.266 4708417.593 3924295.45 1.271255878 1.194988703 1.068358668 1.106358399 1.161657005 0.856325658 1.16655571 1.199812209 1 21.90400223 4.473236168 1.227755222 1.080668343 1.311286677 0.312708763 0.097787765 1.183659556 2.124563212 0.02692274 0.307666969 29732.82453 -4.473236168 0.230618334 TSSAVST(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSSAVSTPSK 10 0 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 TSSAVS(0.05)T(0.949)PS(0.001)K;TSSAVS(0.156)T(0.843)PS(0.001)K 181.49 2.10E-05 214720000 1282590 739000 1013610 804660 902710 702050 1164910 834080 1061200 TRUE FALSE 1202314.981 793716.3289 1037653.308 825308.9379 831814.798 904720.4382 990242.56 938216.724 884078.8644 1.359963494 0.897789056 1.173711249 0.933524113 0.940883027 1.023348114 1.120083965 1.06123646 1 19.75381555 4.753205039 24.80826881 1.028767032 1.359963752 0.611538352 0.085120068 1712.9533 2901760.49 0.020024127 0.443075787 56650.66848 -4.753205039 0.33119672 TSSGDPPS(ph)PLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TSSGDPPSPLVK 12 0 Q99618;F5GX58;F8WDL1 Q99618 CDCA3 Cell division cycle-associated protein 3 1 TSSGDPPS(1)PLVK;TSSGDPPS(1)PLVK;TSSGDPPS(1)PLVK;TSS(0.001)GDPPS(0.998)PLVK 131.06 0.00021549 496152000 2529580 1780480 2047510 2296860 2425490 1296470 2056160 1370040 2042820 TRUE FALSE 2371258.103 1912308.592 2096077.904 2355801.316 2235001.799 1670739.843 1747857.896 1541092.51 1701860.145 1.393333119 1.123657897 1.231639339 1.384250829 1.313269957 0.981713948 1.027027927 0.905534168 1 20.69868105 2.232735626 24.99968305 0.985803861 1.263118006 0.770099914 0.083629682 77.49693179 332597.6922 0.032368863 0.024545225 170.8974673 -2.232735626 0.277314145 TSSIS(ph)GPLSPAYTGQVPYNYNQLEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSSISGPLSPAYTGQVPYNYNQLEGR 26 0 Q01082-3 Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 T(0.238)S(0.238)S(0.238)IS(0.285)GPLS(0.001)PAYTGQVPYNYNQLEGR 103.75 0.0022858 134420000 43689 38375 32876 34354 44004 29876 55558 35546 53584 TRUE FALSE 40954.58348 41216.32493 33655.83425 35235.5818 40548.10334 38500.7162 47227.59368 39983.99635 44640.48423 0.917431434 0.923294754 0.753930761 0.789318987 0.908325795 0.862461886 1.057954332 0.895689127 1 15.44606506 1.761986478 25 0.987909559 0.853600396 0.440844941 0.066356187 11.36555957 12138.31773 0.03074012 0.017047746 57.80780486 -1.761986478 -0.134309163 TSSKDDKGS(ph)TSSTSGSSGSSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSSKDDKGSTSSTSGSSGSSTK 22 2 Q9NWH9;H7BXE3 Q9NWH9 SLTM SAFB-like transcription modulator 1 T(0.002)S(0.002)S(0.002)KDDKGS(0.888)T(0.063)S(0.018)S(0.018)T(0.005)S(0.002)GSS(0.001)GSSTK 60.993 0.026563 44850000 46140 18266 24843 24503 28536 18835 34414 19951 57342 TRUE FALSE 43252.17976 19618.43365 25432.28769 25131.78846 26294.89767 24272.35874 29253.94018 22441.92627 47771.24976 0.905401889 0.41067449 0.532376436 0.526086058 0.550433531 0.508095536 0.612375442 0.469778923 1 15.543855 -1.45297815 3.26865109 1.00734212 0.548456144 0.511615509 0.132941799 151138659.6 179022847.8 10026349.22 0.028368407 0.03523886 1.45297815 -0.458885976 TSSPHKEES(ph)PKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSSPHKEESPKK 12 2 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 TSSPHKEES(1)PKK 68.944 0.02677 42499000 105290 28372 51274 50782 48108 34953 72333 36666 63182 TRUE FALSE 98700.08685 30472.6924 52490.24349 52085.15209 44329.79174 45043.36369 61487.33816 41243.83081 52636.51603 1.875125755 0.57892685 0.997221083 0.989525068 0.842187042 0.855743637 1.168149847 0.783559284 1 15.68377638 4.750810978 24.99388129 0.906798755 1.875126351 0.791683888 0.156872223 916.7273597 1870325.074 0.03796737 0.662260152 56339.23914 -4.750810978 0.968327596 TSSPRS(ph)PPSSSEIFTPAHEENVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSSPRSPPSSSEIFTPAHEENVR 23 1 I3L3A7;I3L2L5;I3L317;I3L4Q0;C9JLW8 I3L3A7 FAM195B Protein FAM195B 1 T(0.128)S(0.128)S(0.128)PRS(0.608)PPS(0.003)S(0.003)S(0.003)EIFTPAHEENVR;T(0.135)S(0.135)S(0.135)PRS(0.591)PPS(0.002)S(0.002)S(0.002)EIFTPAHEENVR 124.57 3.46E-05 204356000 50985 80909 67500 79241 101038 53878 57402 59430 96194 TRUE FALSE 47793.93986 86899.58655 69101.13188 81274.45821 93102.88305 69431.70396 48795.10299 66849.96632 80138.59996 0.596391001 1.084366168 0.862270266 1.014173672 1.161773266 0.86639527 0.608883896 0.834179364 1 16.29020969 -0.785156587 4.916476805 1.00000011 0.886748822 0.04071664 0.181420858 23760801.49 4832891.544 30.76413493 0.04345305 0.163999836 0.785156587 -0.113251288 TSSVSNPQDSVGS(ph)PCSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSSVSNPQDSVGSPCSR 17 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 TSSVSNPQDSVGS(1)PCSR 287 1.58E-36 221060000 120160 123140 140220 161460 168000 105500 137960 98983 136450 TRUE FALSE 112639.4001 132257.4137 143546.0846 165603.337 154805.9577 135956.1374 117274.1788 111341.2454 113675.6135 0.990884471 1.163463382 1.262769386 1.456806186 1.361822056 1.196000911 1.03165644 0.979464654 1 16.79456326 1.741968364 3.186385071 0.994738571 1.249099334 0.462910153 0.120659475 0.214671276 4.572430427 0.072707101 0.034596424 55.20372255 -1.741968364 0.254360764 TSSVSSISQVS(ph)PER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TSSVSSISQVSPER 14 0 P42356 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 TSSVSSISQVS(1)PER 168.69 3.62E-06 150040000 85152 70691 76829 76682 79562 55616 97990 74493 92568 TRUE FALSE 79822.48832 75925.03519 78651.42016 78649.78994 73313.52146 71671.43635 83297.30919 83793.61503 77117.80279 1.035072129 0.984533175 1.019886684 1.019865545 0.95066922 0.929376016 1.080130737 1.086566422 1 16.23477633 1.658150171 10.12170465 1.062165067 0.992542876 0.376421297 0.039346871 0.111814153 17.76259184 0.018246193 0.00979475 45.51454137 -1.658150171 -0.069622192 TSTDRHS(ph)LSLDDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSTDRHSLSLDDIR 14 1 Q96NE9-3;Q96NE9-2;Q96NE9 Q96NE9-3 FRMD6 FERM domain-containing protein 6 1 T(0.004)S(0.003)T(0.003)DRHS(0.983)LS(0.008)LDDIR;T(0.009)S(0.009)T(0.009)DRHS(0.973)LSLDDIR 104.89 0.00062456 202225000 390900 445760 425910 399510 523480 313240 499720 432460 472230 TRUE FALSE 366434.2668 478764.5342 436012.7863 409762.103 482367.9924 403667.303 424791.6252 486453.583 393411.7623 0.93142682 1.216955313 1.108286096 1.041560376 1.226114821 1.026068211 1.079763408 1.236499845 1 18.58568057 TSTS(ph)PPPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TSTSPPPEK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 TST(0.001)S(0.999)PPPEK;TST(0.001)S(0.999)PPPEK;TST(0.002)S(0.997)PPPEK;TST(0.036)S(0.964)PPPEK 155 7.80E-05 13540200000 14977300 9376600 12137900 11020800 9280860 11002900 15461000 8964750 8425150 TRUE FALSE 14039897.53 10070853.22 12425816.72 11303612.39 8551978.693 14179258.61 13142766.58 10084018.77 7018938.036 2.000288 1.43481153 1.770327171 1.610444818 1.218414901 2.02014301 1.872472234 1.436687248 1 22.74282134 0.960346873 5.968838102 1.000114163 1.688395288 0.460343374 0.244813575 0.230649676 29.62227347 0.226867439 0.057059743 9.127395574 -0.960346873 0.688281125 TSVDTGQVSRPENPSQPAS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TSVDTGQVSRPENPSQPASPR 21 1 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 TSVDTGQVSRPENPSQPAS(1)PR;TSVDTGQVSRPENPSQPAS(1)PR;TSVDTGQVSRPENPSQPAS(1)PR 217.02 3.61E-25 1197830000 1266900 1312740 1426180 1353690 1545930 1217164 1537150 1237340 1718390 TRUE FALSE 1187606.99 1409936.636 1460009.663 1388427.977 1424518.894 1568539.488 1306668.628 1391824.623 1431579.608 0.82957803 0.984881754 1.019859221 0.969857331 0.995067886 1.09567046 0.912746047 0.972229986 1 20.44917647 4.738274606 4.876298867 0.993802387 0.820890676 0.562494003 0.045588712 0.128918892 9.143611709 0.010469124 0.075638947 54736.1952 -4.738274606 -0.172911711 TSVLGGGEDGIEPVS(ph)PPEGMTEPGHSR ddPTM_SK-BR-3_Pertuzumab_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(0.999)PPEGMT(0.001)EPGHSR;TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR;TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR;TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR;TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR 213.9 6.24E-27 2014380000 1048910 972607 1024810 1008640 921430 773638 1122680 888956 744515 TRUE FALSE 983260.5955 1044619.834 1049118.977 1034523.41 849064.6047 996974.7316 954344.5565 999944.1134 620250.6367 1.585263339 1.684189862 1.691443612 1.667911887 1.368905656 1.607373975 1.538643413 1.612161365 1 19.24249179 -2.692882718 0.271375396 1.12E-21 1.664247778 0.804425814 0.092242286 21.11430588 0.627659668 12.48731006 0.114303564 0.00202823 2.692882718 1.664247778 TSVPENHAQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TSVPENHAQSR 11 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ;;; 168.05 1.85E-05 916770000 872378 1040100 958070 1024510 1073470 807529 1098890 882907 1008770 FALSE TRUE 817777.4182 1117110.086 980795.8728 1050800.661 989163.9964 1040649.513 934121.6461 993139.8825 840399.7701 0.97308144 1.329260342 1.167058711 1.250358102 1.177016024 1.23827915 1.111520587 1.181746971 1 19.68071624 0.486129702 0.693276595 0.997556747 1.203954599 0.243258796 0.094686156 2.045279814 1.602539004 0.096893147 0.031447306 3.062878028 -0.486129702 0.206397852 TSVS(ph)PAPDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSVSPAPDK 9 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 TSVS(1)PAPDK;TSVS(1)PAPDK 147.28 9.73E-05 835070000 2468400 1613550 1981090 1919860 1899600 1383790 2244300 1583240 1684780 TRUE FALSE 2313907.25 1733018.921 2028082.39 1969126.858 1750413.079 1783267.709 1907788.05 1780910.999 1403579.334 1.648576033 1.234713905 1.444936058 1.402932353 1.24710662 1.270514367 1.35923065 1.268835296 1 20.42067918 -4.433257044 0.127848624 5.60E-13 1.513189401 0.590529922 0.107084156 92.16259983 0.860492057 24.38653069 0.823283355 3.69E-05 4.433257044 1.513189401 TSVS(ph)PAPDKTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TSVSPAPDKTK 11 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 TS(0.007)VS(0.993)PAPDKTK;TS(0.001)VS(0.999)PAPDKTK 120.49 0.00026947 934620000 1340450 772820 1004550 983610 1079210 641880 1198410 775190 1177750 TRUE FALSE 1256553.627 830040.3969 1028378.4 1008851.098 994453.1999 827180.3359 1018719.546 871974.1779 981175.9164 1.280660895 0.845964911 1.048108074 1.028206136 1.013532011 0.843049979 1.038263913 0.888703201 1 19.9041523 2.424487266 24.99987203 0.948988557 1.016639825 0.130768275 0.118035138 269.4179962 127965.1104 0.037801164 0.031626726 265.7585627 -2.424487266 0.067651268 TSYAQLLEECPRDETSGLHLLPLPESAPALPTEEQVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TSYAQLLEECPRDETSGLHLLPLPESAPALPTEEQVQR 38 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 156.52 2.56E-14 232113000 83176.8 107810 86522 111537 118221 72312.6 122922 93314.6 157803 FALSE TRUE 77970.91256 115792.3646 88574.3427 114399.2283 108936.3995 93188.07372 104490.9873 104965.1332 131464.6599 0.593094088 0.880787009 0.673750214 0.870189969 0.828636378 0.708845053 0.794821874 0.798428516 1 17.0043155 -5 0.253590562 2.406451232 0.753614297 0.423120025 0.087360806 180.2128199 1.78199413 131.5776469 0.110020966 1.00E-05 5 -1.652836935 TSYGWIEIVGCADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TSYGWIEIVGCADR 14 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;; 161.99 1.05E-05 113699000 181514 192706 174490 153577 196603 161500 212211 163406 184408 FALSE TRUE 170153.3628 206974.1528 178628.9852 157518.0458 181162.5934 208122.4283 180391.9306 183807.5988 153629.1135 1.107559361 1.347232618 1.162728738 1.025313772 1.179220457 1.354706953 1.174204072 1.196437281 1 17.22909211 0.486607812 2.259814761 1.000012074 1.205086581 0.26873762 0.098776589 9.273920108 39.08682882 0.093381656 0.025235224 3.066251773 -0.486607812 0.205074507 TT(ph)PDQELAPASEPVWERPWSVEEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTPDQELAPASEPVWERPWSVEEIR 25 1 Q641Q2;Q641Q2-2;E7ESD2;A0A087WYF6;Q5T1D7 Q641Q2 FAM21A WASH complex subunit FAM21A 1 T(0.157)T(0.843)PDQELAPASEPVWERPWSVEEIR 156.37 6.01E-08 63600000 3926.6 5952.4 4512.3 5459.7 5688.6 5584.8 6094.9 4857.1 6046.9 TRUE FALSE 3680.841115 6393.121889 4619.333887 5599.805145 5241.840303 7197.041098 5181.026327 5463.519627 5037.633326 0.730668724 1.269072494 0.916965088 1.11159443 1.040536292 1.42865521 1.028464359 1.084540949 1 12.2985304 2.401843867 24.99957882 1.148728151 1.039701043 0.091118023 0.178701471 97.43953942 32356.21162 0.056707346 0.047444774 252.2573718 -2.401843867 -0.109027108 TT(ph)PDQELAPASEPVWERPWSVEEIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TTPDQELAPASEPVWERPWSVEEIRR 26 2 Q641Q2;Q641Q2-2;E7ESD2;A0A087WYF6;Q5T1D7 Q641Q2 FAM21A WASH complex subunit FAM21A 1 T(0.458)T(0.542)PDQELAPASEPVWERPWSVEEIRR;T(0.446)T(0.554)PDQELAPASEPVWERPWSVEEIRR;T(0.445)T(0.555)PDQELAPASEPVWERPWSVEEIRR 186.23 6.30E-16 592555000 240447 206499 202410 214268 237013 166870 243814 179585 273947 TRUE FALSE 225397.8515 221788.4008 207211.2608 219766.4796 218398.955 215042.6601 207256.3542 202006.5826 228223.4759 0.987619046 0.971803623 0.907931403 0.962944231 0.95695219 0.942246012 0.908128988 0.88512622 1 17.80008767 1.950277827 5.786654461 0.921595595 0.952698847 0.076622452 0.035546533 0.413463551 32.37811612 0.014549856 0.008998227 89.18212716 -1.950277827 0.031103252 TT(ph)PPESAPQNGPSPMAALMSVADTLGTAHS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTPPESAPQNGPSPMAALMSVADTLGTAHSPK 32 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 2 T(0.474)T(0.516)PPES(0.009)APQNGPSPMAALMS(0.001)VADT(0.018)LGT(0.15)AHS(0.831)PK 60.807 0.041293 59126000 70959 34501 45580 45515 46035 30352 66159 38927 52825 TRUE FALSE 66517.80286 37055.48994 46661.17912 46682.99196 42419.5968 39114.12968 56239.07214 43787.12164 44008.16624 1.51148772 0.842013951 1.060284559 1.060780213 0.963902849 0.888792536 1.277923553 0.994977191 1 15.42548364 TT(ph)PTLGLEEVLSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTPTLGLEEVLSSR 14 0 O43474-4;O43474-1;O43474 O43474-4 KLF4 Krueppel-like factor 4 1 T(0.342)T(0.658)PTLGLEEVLSSR 114.7 0.0051647 31615000 32765 27220 29071 28769 37535 21493 35488 28399 33874 TRUE FALSE 30714.29714 29235.39712 29760.57785 29507.26125 34587.15251 27697.68019 30166.90385 31944.67766 28220.21057 1.088379446 1.035973741 1.054583834 1.045607409 1.225616387 0.981483824 1.068982238 1.131978714 1 14.78444113 TT(ph)SPEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTSPEPR 7 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 T(0.123)T(0.673)S(0.204)PEPR 109.01 0.079633 378420000 559930 503740 538680 520050 547170 483540 621580 456990 584440 TRUE FALSE 524884.9808 541037.4337 551457.744 533395.3634 504197.4754 623130.1484 528379.8495 514046.2075 486893.1884 1.078029008 1.111203538 1.132605173 1.09550796 1.035540212 1.27980872 1.085206904 1.055767917 1 18.89324579 1.114985732 2.797478219 1.004592276 1.121477378 0.279178621 0.06345606 0.296212817 4.38940448 0.05512315 0.014923266 13.03123967 -1.114985732 0.116885103 TT(ph)SPLEEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTSPLEEEER 10 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 T(0.005)T(0.497)S(0.497)PLEEEER 145.41 0.00034082 367700000 211250 303160 253260 251570 264420 239890 280810 191380 238930 TRUE FALSE 198028.2396 325606.2818 259267.4468 258025.7121 243653.5198 309142.3487 238705.1474 215274.2143 199051.0395 0.99486162 1.635792924 1.302517422 1.296279149 1.224075596 1.553080806 1.199215779 1.081502588 1 17.60277888 1.398630186 3.114151713 1.035194086 1.36060569 0.312373511 0.175836671 0.262246263 4.342544755 0.130011624 0.042470891 25.03976138 -1.398630186 0.325411604 TTAAHGLELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TTAAHGLELR 10 0 P08243-2;P08243;P08243-3 P08243-2 ASNS Asparagine synthetase [glutamine-hydrolyzing] 0 ; 157.97 8.23E-06 348470000 378710 641610 374980 386830 598620 228120 373270 527610 401480 FALSE TRUE 355007.2171 689115.472 383874.7027 396756.7127 551606.7999 293974.5408 317301.6288 593483.2699 334470.3943 1.061401018 2.060318293 1.147709062 1.186223712 1.649194695 0.878925447 0.948668803 1.774397017 1 18.35151899 3.734210198 22.11939481 1.203109014 1.623752149 0.115155167 0.372175832 98.84347136 308406.4735 0.089311046 0.15614739 5422.632814 -3.734210198 0.420643135 TTAGS(ph)VDWTDQLGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TTAGSVDWTDQLGLR 15 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 T(0.002)T(0.008)AGS(0.99)VDWTDQLGLR;TTAGS(1)VDWTDQLGLR;TTAGS(1)VDWTDQLGLR;TTAGS(0.999)VDWT(0.001)DQLGLR;TTAGS(1)VDWTDQLGLR;TTAGS(1)VDWTDQLGLR 342.28 1.53E-69 1635212000 1496490 1382315 1323650 1366647 1150169 1049488 1749751 1127922 1430025 TRUE FALSE 1402827.362 1484663.041 1355047.603 1401717.476 1059839.366 1352458.149 1487392.081 1268745.545 1191344.589 1.177516039 1.246207902 1.137410297 1.176584414 0.889616133 1.135236741 1.248498625 1.06496941 1 20.18415933 7.999999972 0.05089029 0.797506265 1.773480916 0.213377717 0.098047425 830.8379252 3.187444909 14.19369102 63.27827546 99999993.61 -7.999999972 0.975974651 TTAPTEGKS(ph)PLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TTAPTEGKSPLKK 13 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 TTAPT(0.368)EGKS(0.632)PLKK;TT(0.002)APT(0.004)EGKS(0.994)PLKK 152.94 2.37E-05 2139090000 8622900 2618030 4768600 4202400 4483000 3374300 6699100 4109300 5577500 TRUE FALSE 8083208.081 2811871.665 4881713.444 4310240.699 4130923.264 4348405.633 5694632.146 4622355.151 4646579.218 1.739604062 0.605148763 1.050603727 0.927615886 0.889024607 0.935829441 1.225553656 0.994786688 1 22.14773757 1.772132882 25 1.096720837 0.97028369 0 0.293935507 124.5299214 92776.76585 0.123484045 0.068508121 59.17426638 -1.772132882 -0.126437148 TTAPTEGKS(ph)PLKKEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTAPTEGKSPLKKEDR 16 3 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 TTAPT(0.001)EGKS(0.999)PLKKEDR 96.391 0.018947 770190000 1081100 401400 627640 591180 673040 372860 889620 533140 1270800 TRUE FALSE 1013435.881 431120.0737 642527.9172 606350.6797 620182.1533 480498.6291 756229.7398 599703.7026 1058695.27 0.957249843 0.407218286 0.606905438 0.572733908 0.585798549 0.453859238 0.714303503 0.566455447 1 20.01385596 -0.295468004 0.786856334 1.018814041 0.583756379 0.389460639 0.151279589 9.891032572 4.899514575 0.717018565 0.04533614 0.506444659 0.295468004 -0.435057662 TTDEELS(ph)ELEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TTDEELSELEDR 12 0 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;H7C2D8;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 1 TTDEELS(1)ELEDR;TTDEELS(1)ELEDR 222.74 2.53E-11 665900000 720790 632370 591920 614390 717540 485880 716230 605090 716230 TRUE FALSE 675677.0405 679191.3328 605960.6219 630156.2876 661187.3028 626145.6684 608837.9607 680636.8185 596686.586 1.132381817 1.138271496 1.015542558 1.056092599 1.108098151 1.049371116 1.020364753 1.140694017 1 19.18661382 4.136214788 4.040663157 1.055619964 1.135760716 0.37968486 0.04220535 0.211466516 6.264990741 0.009862461 0.023565671 13684.05429 -4.136214788 0.080140752 TTDGVYEGVAIGGDRYPGSTFMDHVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TTDGVYEGVAIGGDRYPGSTFMDHVLR 27 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;; 284.13 1.54E-61 2974550000 1404950 1720130 1632860 1627920 1892340 1333770 1892830 1529760 2038740 FALSE TRUE 1317016.687 1847490.215 1671592.21 1669695.183 1743723.25 1718807.747 1609017.714 1720753.903 1698461.123 0.775417623 1.087743599 0.984180437 0.983063528 1.026648903 1.011979446 0.947338559 1.013125281 1 20.69579677 4.75162645 24.86964372 1.005479286 0.775417464 0.802797041 0.036028943 951.8333957 1811695.151 0.009024742 0.171219692 56445.12638 -4.75162645 -0.230061822 TTDGYLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TTDGYLLR 8 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;H0Y9Y4;D6RB09;D6RAS7;D6R9B6;D6RED7 P61247 RPS3A 40S ribosomal protein S3a 0 ;;; 109.01 0.0086081 1588570000 826820 1157260 846860 846780 1290190 695660 797720 1007380 918460 FALSE TRUE 775070.8121 1242944.735 866947.9191 868509.8084 1188863.682 896485.7489 678109.2917 1133153.611 765163.0925 1.012948507 1.624418045 1.133023701 1.135064951 1.553738926 1.171627013 0.886228437 1.480930826 1 19.54540776 2.009504329 24.81793961 1.089540753 1.312930787 0.091035097 0.238407841 318.9654922 832886.6779 0.083080894 0.061284034 102.2125748 -2.009504329 0.223390034 TTEATLQTIQDMVTIEDYDVSECFQHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTEATLQTIQDMVTIEDYDVSECFQHSR 28 0 G5EA48;Q7Z6B7-2;Q7Z6B7 G5EA48 SRGAP1 SLIT-ROBO Rho GTPase-activating protein 1 0 75.695 0.0085754 13002000 2629.1 2469.1 2081.9 3006.8 2928.2 3126.8 2951.3 2596.7 2207.4 FALSE TRUE 2464.549324 2651.914733 2131.283651 3083.959579 2698.230984 4029.456401 2508.779964 2920.903711 1838.97068 1.340178694 1.442064717 1.158954667 1.677003126 1.467250682 2.191147714 1.36423054 1.588336205 1 10.84468276 3.228716233 24.99840653 1.592202442 1.319121254 0.106070741 0.302846018 344.6468766 875180.2797 0.079113711 0.095651511 1693.231084 -3.228716233 -0.273081187 TTEYHDRDEQFYWIIEALGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TTEYHDRDEQFYWIIEALGIR 21 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;; 193.27 4.73E-18 2596087000 2951272 3123537 2909147 2979020 3494640 2618602 3237790 2931667 2926660 FALSE TRUE 2766557.154 3354806.93 2978153.341 3055466.697 3220185.071 3374549.888 2752313.448 3297692.078 2438181.539 1.134680543 1.375946325 1.22146497 1.253174404 1.320732283 1.384043737 1.128838605 1.352521141 1 21.21737412 -1.194979606 3.547836715 0.999623225 1.271625242 0.467886599 0.090966914 16780683.35 30635603.57 73228.41444 0.019925412 0.063829346 1.194979606 0.272002017 TTFDEAMADLHTLSEDSYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TTFDEAMADLHTLSEDSYK 19 0 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ;;; 273.33 2.25E-39 1058750000 2875150 2019650 2457100 2208070 2537230 1924160 2987710 2289940 3427930 FALSE TRUE 2695199.494 2169186.987 2515383.572 2264732.814 2337966.19 2479633.756 2539730.622 2575844.05 2855786.338 0.943767907 0.759576079 0.880802439 0.793033003 0.81867686 0.86828406 0.889327954 0.901973658 1 21.44545661 1.021840233 0.832228467 0.998211479 0.832138592 0.487569292 0.050356494 0.477844091 0.736815635 0.043066526 0.015601189 10.51574953 -1.021840233 -0.166072887 TTFFHHEYPWILSASDDQTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TTFFHHEYPWILSASDDQTIR 21 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 253.89 1.30E-36 764050000 479420 599240 499420 457300 596080 377660 584270 552170 353210 FALSE TRUE 449413.958 643608.3531 511266.4782 469035.0922 549266.2813 486684.3112 496664.1376 621109.64 294256.9692 1.52728399 2.187232319 1.737482989 1.59396426 1.866621147 1.653943193 1.687858537 2.110772913 1 18.16671706 -1.416412346 3.294878839 0.990392787 1.806410292 0.580255036 0.212494154 40960973.04 52121989.23 3665997.782 0.049191232 0.03833431 1.416412346 0.816017506 TTGFGMIYDSLDYAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TTGFGMIYDSLDYAK 15 0 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4;A0A2R8Y8A0 E7ETK0 RPS24 40S ribosomal protein S24 0 ; 211.67 2.94E-09 120524000 539010 478910 523120 524900 622700 420760 629840 602470 653860 FALSE TRUE 505274.3263 514368.9947 535528.6534 538369.8227 573795.6539 542226.5815 535401.3391 677689.7057 544726.5419 0.927574273 0.944270116 0.983114668 0.98833044 1.053364596 0.995410614 0.982880947 1.244091583 1 19.05517264 2.989603537 0.526765253 1.069400615 0.92450402 0.327405676 0.072297048 1.327695669 0.765363554 0.056442737 0.090196928 976.3455173 -2.989603537 -0.144896596 TTGIVMDSGDGVTHTVPIYEGYALPHAILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 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 ;;;;;;;;;;; 373.27 5.75E-137 48885520000 7701393 8938630 7927359 7959529 9668871 6419291 8675634 7668734 7727652 FALSE TRUE 7219376.56 9600455.466 8115399.699 8163783.99 8909516.874 8272436.103 7374803.222 8626192.321 6437856.959 1.121394372 1.491250198 1.260574715 1.268090304 1.383925883 1.284967367 1.145536981 1.339916742 1 22.61814909 -0.426003936 0.322658544 0.897813012 1.339037506 0.383471567 0.109679045 7.493004703 0.870990614 0.95585385 0.10375771 0.374969604 0.426003936 0.441224494 TTGT(ph)PPDSSLVTYELHSRPEQDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TTGTPPDSSLVTYELHSRPEQDK 23 1 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18 Q13561 DCTN2 Dynactin subunit 2 1 T(0.001)T(0.003)GT(0.996)PPDSSLVTYELHSRPEQDK;T(0.007)T(0.007)GT(0.985)PPDSSLVTYELHSRPEQDK;T(0.028)T(0.152)GT(0.82)PPDSSLVTYELHSRPEQDK 309.96 5.59E-73 407750000 709000 430100 535600 533010 526230 421780 686720 476960 547680 TRUE FALSE 664624.9556 461945.0515 548304.6849 546687.939 484902.0185 543541.039 583752.7112 536509.5059 456268.6699 1.456652625 1.012440875 1.201714519 1.198171111 1.062755456 1.191274078 1.279405644 1.175863129 1 18.79952407 4.756689068 24.34536516 1.154154461 1.456652994 0.541885082 0.090637584 2307.330789 3098527.455 0.021515698 0.678004081 57106.96348 -4.756689068 0.302498533 TTGT(ph)PPDSSLVTYELHSRPEQDKFSQAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TTGTPPDSSLVTYELHSRPEQDKFSQAAK 29 2 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18 Q13561 DCTN2 Dynactin subunit 2 1 T(0.028)T(0.028)GT(0.945)PPDSSLVTYELHSRPEQDKFSQAAK;T(0.001)T(0.001)GT(0.998)PPDSSLVTYELHSRPEQDKFSQAAK 273.73 4.32E-71 621890000 671560 474040 569530 541610 631130 396350 752380 488970 1009760 TRUE FALSE 629528.2584 509138.4148 583039.5206 555508.6295 581563.5957 510769.8108 639567.6038 550018.9809 841224.5327 0.748347479 0.605234863 0.693084305 0.660357144 0.691329809 0.607174174 0.760281683 0.653831361 1 19.6821314 -2.714122171 0.380298966 1.62745711 0.664139819 0.791390373 0.051809316 32.93452787 1.253247863 16.8631964 0.031094803 0.001931425 2.714122171 -0.96331729 TTHFVEGGDAGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TTHFVEGGDAGNR 13 0 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 164.53 3.69E-05 1378480000 1235390 1143650 1146250 1246370 1067520 1103910 1365560 1187550 846090 FALSE TRUE 1158069.145 1228327.036 1173439.591 1278353.964 983681.2854 1422590.897 1160806.955 1335818.232 704872.113 1.642949301 1.742623964 1.664755307 1.813597021 1.395545755 2.018225534 1.646833424 1.895121408 1 19.427002 -0.560063361 7.071102739 0.999991922 1.723184933 0.654540179 0.166062937 0 0 0.136654634 0.032209806 0.275382691 0.560063361 0.723193011 TTHFVEGGDAGNREDQINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 TTHFVEGGDAGNREDQINR 19 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ;;;;;;; 188.96 9.04E-15 45120410000 3479600 3137960 3256370 3228470 3361870 2621610 3806850 2729660 3506150 FALSE TRUE 3261818.047 3370297.823 3333612.634 3311318.006 3097842.291 3378426.249 3236048.184 3070464.06 2920950.914 1.116697316 1.15383583 1.141276499 1.133643838 1.060559517 1.156618631 1.107874894 1.051186463 1 21.47800668 1.115680335 2.099309398 1.00076523 1.130050439 0.718920311 0.026898208 0.148424229 1.251922555 0.024587092 0.006934748 13.05209826 -1.115680335 0.129285209 TTHLAGALS(ph)PGEAWPFESV ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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;TTHLAGALS(1)PGEAWPFESV;TTHLAGALS(1)PGEAWPFESV 220.96 2.91E-19 747727000 567344 592851 629080 629343 677929 526818 730883 573503 637699 TRUE FALSE 531834.9518 636746.3049 644002.0747 645493.0069 624687.191 678901.8044 621293.8793 645106.112 531262.9172 1.001076745 1.198552137 1.212209725 1.215016117 1.175853181 1.277901736 1.169465926 1.214287862 1 19.01906649 -1.026162935 4.569623051 0.999995038 1.190465627 0.390094474 0.071395733 4.41E-06 9.41E-07 0.062084719 0.014632989 0.094153629 1.026162935 0.190470588 TTHLAGALS(ph)PGGGQSAPAFPESGPSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TTHLAGALSPGGGQSAPAFPESGPSLR 27 0 A0A2R8Y4Z8 A0A2R8Y4Z8 1 TTHLAGALS(1)PGGGQSAPAFPESGPSLR;TTHLAGALS(1)PGGGQSAPAFPESGPSLR 225.71 1.03E-34 476820000 282250 300440 271330 366110 331380 207360 296420 192693 234680 TRUE FALSE 264584.4763 322684.8902 277766.0757 375505.0024 305354.7515 267221.4658 251974.5728 216751.1452 195510.3919 1.353301345 1.650474366 1.420722822 1.920639608 1.561833867 1.366789065 1.288803988 1.10864258 1 17.57688577 1.600138136 1.30159662 1.025135097 1.580725277 0.657708917 0.153607094 0.248294863 0.806152393 0.126866385 0.045391737 39.82338169 -1.600138136 0.55559018 TTHLIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTHLIAK 7 0 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 66.682 0.067212 232170000 338320 430200 427210 466530 554950 348270 505270 537660 596050 FALSE TRUE 317145.1551 462052.4556 437343.6229 478501.9496 511366.4656 448809.8953 429509.4542 604788.0345 496565.4044 0.638677508 0.930496671 0.880737198 0.963623211 1.029806871 0.90382836 0.864960487 1.217942348 1 18.92162423 5.236826854 1.327552525 0.961596158 1.02E-26 0.509886459 0.101910028 3.799002565 2.374411744 0.026135111 6.81520753 172514.9967 -5.236826854 -0.961596158 TTHS(ph)PYEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TTHSPYEER 9 0 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 TTHS(1)PYEER;T(0.011)T(0.011)HS(0.979)PYEER 154.15 4.92E-05 410820000 203620 201832 203769 214520 214241 171187 230939 177058 227102 TRUE FALSE 190875.7877 216775.8513 208602.4969 220024.9464 197415.3761 220605.9079 196311.8409 199164.0811 189197.2091 1.008872111 1.145766644 1.102566459 1.162939704 1.043437041 1.166010371 1.037604317 1.052679805 1 17.52953128 1.611632097 8.343448287 1.032517739 1.109161476 0.322112325 0.050940016 0.115229371 19.67631131 0.023214669 0.011491896 40.89141104 -1.611632097 0.076643737 TTIENIQLPHTLLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTIENIQLPHTLLSR 15 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 149.3 3.38E-06 203990000 270040 280240 274500 280990 325400 233580 328430 279990 268270 FALSE TRUE 253138.6784 300989.2612 281011.2696 288200.6791 299844.3966 301010.7541 279184.9705 314947.3678 223494.0039 1.132641923 1.346744234 1.257354849 1.289523093 1.34162166 1.346840402 1.249183269 1.409198289 1 17.7698766 -0.159010883 8.646301011 0.99999782 1.297388443 0.607798767 0.074884516 0 0 0.063001694 0.014849642 0.693408429 0.159010883 0.297390623 TTIPEEEEEEEEAAGVVVEEELFHQQGT(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR 30 0 P20700 P20700 LMNB1 Lamin-B1 1 TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR 249.29 1.05E-45 581891000 245484 238553 230864.7 242897.4 244959.4 189358.5 279190.2 212221.3 252736 TRUE FALSE 230119.5946 256215.7123 236340.9197 249130.5585 225721.2768 244023.225 237328.2214 238717.5965 210552.7289 1.092930953 1.216871962 1.12247854 1.183221703 1.072041564 1.158964912 1.127167635 1.133766338 1 17.68382205 -5 0.217257025 0.276054789 1.162719937 0.520640798 0.041602651 107.0887694 1.071068976 33.82448942 0.073239394 1.00E-05 5 0.886665147 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR 30 0 P20700 P20700 LMNB1 Lamin-B1 0 ;;;;; 318.74 1.53E-92 543067000 108714.7 110558.1 109059.2 109231.2 123446 77898.8 127801 94518.5 118980 FALSE TRUE 101910.441 118743.9368 111646.1357 112034.2575 113751.0491 100386.919 108638.4265 106319.3428 99121.46936 1.028136908 1.197963847 1.126356746 1.130272364 1.147592442 1.012766655 1.096013076 1.072616694 1 16.59690995 2.253473105 24.99110352 1.056471804 1.136100061 0.372903738 0.05018579 232.4791097 389599.6354 0.01609994 0.013416272 179.2557539 -2.253473105 0.079628257 TTIPHALLTWRPNSGETAPPPPS(ph)PVSEKPLDTISQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTIPHALLTWRPNSGETAPPPPSPVSEKPLDTISQK 36 2 Q9Y6D6;E5RIF2;E5RHL7 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 TTIPHALLTWRPNSGETAPPPPS(0.748)PVS(0.216)EKPLDT(0.027)IS(0.009)QK 56.637 0.019039 362610000 460430 340740 395980 461540 446020 238470 367680 232710 374080 TRUE FALSE 431612.5082 365968.7441 405372.8326 473383.8978 410991.3884 307312.4178 312549.7974 261764.3558 311643.6314 1.38495533 1.174318059 1.300757634 1.518991085 1.318786418 0.986102031 1.002907699 0.839947714 1 18.24953771 2.226158195 5.882588396 0.96075816 1.320819544 0.795138036 0.096230705 0.080644928 9.492773875 0.037585526 0.028837254 168.32871 -2.226158195 0.360061384 TTLIPGGSESLVYTTLSGGIGILVPFTSHEDHDFFQHVEMHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TTLIPGGSESLVYTTLSGGIGILVPFTSHEDHDFFQHVEMHLR 43 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 172.51 7.19E-21 380880000 324140 695660 177436 141354 734840 202389 299170 654260 67725 FALSE TRUE 303852.656 747167.3902 181644.8657 144981.383 677128.6306 260815.4188 254312.2359 735945.8012 56421.25998 5.385428403 13.24265694 3.219440079 2.569623277 12.00130289 4.622644352 4.507383138 13.04376757 1 15.78395126 3.968698496 24.15359262 5.932725466 9.669745261 0.09991432 4.285216037 391.3981763 1122403.281 0.996568396 1.836521742 9304.616886 -3.968698496 3.737019794 TTLLHMLKDDR ddPTM_SK-BR-3_Pertuzumab_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 0 146.16 2.16E-05 238300000 118500 656950 75398 89732 773000 37499 90772 500090 850320 FALSE TRUE 111083.2965 705591.2616 77186.47617 92034.67504 712291.6981 48324.35255 77161.58129 562527.3373 708396.0987 0.156809583 0.996040581 0.108959488 0.129919794 1.005499182 0.068216571 0.108924345 0.794085877 1 19.43419674 1.048696398 6.290416221 0.998602666 0.390070736 0.285992003 0.354401214 0.220108836 18.63114797 0.331207773 0.083229933 11.18655592 -1.048696398 -0.60853193 TTMRPQSFYDGSHSCAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 133.16 1.27E-05 285610000 207891 236630 219509 250920 269820 184702 279920 233200 284790 FALSE TRUE 194879.4734 254150.3314 224715.8571 257359.032 248629.4256 238022.469 237948.5946 262315.5333 237256.7092 0.821386565 1.071203981 0.947142266 1.084728153 1.047934225 1.003227558 1.002916189 1.105619033 1 17.85608936 4.746264941 24.64349502 1.026968917 0.821386443 0.661917539 0.047328711 471.5226831 1508195.549 0.010527382 0.112479867 55752.57638 -4.746264941 -0.205582474 TTNSS(ph)LEEIMDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTNSSLEEIMDK 12 0 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 1 TTNS(0.012)S(0.988)LEEIMDK 201.4 1.56E-07 54829000 144220 138030 115590 127050 160330 102700 160290 136100 146390 TRUE FALSE 135193.5276 148249.8848 118331.8494 130310.3181 147738.3285 132347.8228 136256.0026 153092.3846 121956.5633 1.108538352 1.215595789 0.970278648 1.068497788 1.211401212 1.085204594 1.117250264 1.255302548 1 16.89600788 TTPATGEQS(ph)PGAR ddPTM_SK-BR-3_Pertuzumab_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 245.82 4.11E-17 1009280000 514290 478320 469200 461330 471250 425260 575760 454750 499640 TRUE FALSE 482101.5069 513735.3105 480329.6456 473168.5088 434239.9259 548025.6585 489430.1331 511526.5385 416246.8562 1.158210566 1.234208266 1.15395381 1.136749748 1.04322692 1.316588102 1.175817008 1.228901867 1 18.66707985 -1.70001419 6.935226015 0.998476319 1.183384901 0.388324343 0.071316359 0.001580656 6.84E-05 0.064963097 0.015194754 0.019951971 1.70001419 0.184908582 TTPDQELVPASEPVWERPWS(ph)VEEIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTPDQELVPASEPVWERPWSVEEIRR 26 2 A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;A0A0A0MT65 A0A0A0MR88 FAM21C WASH complex subunit FAM21C 1 T(0.078)T(0.029)PDQELVPAS(0.078)EPVWERPWS(0.816)VEEIRR 80.36 0.014368 105880000 22577 20071 18974 25869 27495 13339 27325 18421 27519 TRUE FALSE 21163.94587 21557.07772 19424.07224 26532.84234 25335.65361 17189.75276 23227.86992 20720.9024 22925.90112 0.923145649 0.940293584 0.847254472 1.157330401 1.105110481 0.749796166 1.013171513 0.90382063 1 14.48469082 TTPDVIFVFGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TTPDVIFVFGFR 12 0 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4;A0A2R8Y8A0 E7ETK0 RPS24 40S ribosomal protein S24 0 ; 168.83 0.0001058 321910000 465630 462430 438150 419000 508170 349060 435680 402800 419490 FALSE TRUE 436487.0495 496668.7984 448543.1249 429752.2494 468260.3781 449827.9555 370353.8287 453090.4667 349474.409 1.248981437 1.421187891 1.283479171 1.229710211 1.339898905 1.287155637 1.059745203 1.296491116 1 18.41482729 1.119902447 0.328082875 0.972559358 1.36630214 0.524032408 0.086165184 1.119693675 0.383306063 0.165996638 0.105457678 13.17960661 -1.119902447 0.393742781 TTPPESAPQNGPSPMAALMSVADTLGT(ph)AHSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTPPESAPQNGPSPMAALMSVADTLGTAHSPK 32 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 TTPPESAPQNGPSPMAALMSVADT(0.193)LGT(0.786)AHS(0.021)PK 246.49 1.61E-46 160580000 277090 164870 202720 188250 214960 167810 272330 180470 270940 TRUE FALSE 259747.4315 177077.1463 207528.6141 193080.8137 198077.9087 216254.0228 231496.6447 203002.0768 225718.3637 1.150758969 0.784504829 0.919413958 0.855405872 0.877544501 0.958070134 1.025599517 0.899360041 1 17.78416427 2.108827214 5.188211238 0.980983213 0.897122519 0.045742434 0.09928566 0.402635241 16.84916489 0.035012529 0.025498178 128.4775406 -2.108827214 -0.083860694 TTPPESAPQNGPSPMAALMSVADTLGTAHS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTPPESAPQNGPSPMAALMSVADTLGTAHSPK 32 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 TTPPESAPQNGPSPMAALMSVADTLGT(0.023)AHS(0.977)PK 279.11 8.78E-74 155810000 275170 162610 203510 181530 224360 173480 249080 186370 257020 TRUE FALSE 257947.6009 174649.8136 208337.3533 186188.3671 206739.6706 223560.8598 211732.7663 209638.7048 214121.7016 1.204677522 0.815656761 0.972985698 0.86954459 0.965524135 1.044083146 0.988843096 0.979063323 1 17.7080715 2.470754232 23.85553031 1.00248285 0.939479492 0.003604046 0.102277882 240.8968328 902559.0805 0.032277713 0.027079739 295.6338999 -2.470754232 -0.063003358 TTPPPGAQCEVPAS(ph)PQRPSRPGALPEQTRPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TTPPPGAQCEVPASPQRPSRPGALPEQTRPLR 32 3 Q9H074;D6R9H8 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 1 TTPPPGAQCEVPAS(0.999)PQRPS(0.001)RPGALPEQTRPLR;T(0.001)T(0.002)PPPGAQCEVPAS(0.98)PQRPS(0.001)RPGALPEQT(0.017)RPLR;TTPPPGAQCEVPAS(1)PQRPSRPGALPEQTRPLR 215.31 6.60E-36 2928240000 105646 95106 102726 95425 105054 77507 108066 83667.2 93955 TRUE FALSE 99033.80544 102147.7472 105162.7092 97873.76705 96803.48261 99882.01268 91862.50654 94113.23409 78273.30353 1.265230941 1.305013876 1.343532271 1.250410582 1.236736898 1.276067422 1.173612233 1.202366961 1 16.25623271 0.670303894 0.409504123 0.976505748 1.314692217 0.879558253 0.032546251 0.564112197 0.208415505 0.060703864 0.023779437 4.680625501 -0.670303894 0.338186469 TTPQQGASGPGRS(ph)PVGQAR ddPTM_SK-BR-3_Pertuzumab_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;TTPQQGAS(0.003)GPGRS(0.997)PVGQAR;TTPQQGASGPGRS(1)PVGQAR 212.63 4.42E-17 696420000 176987 129714 173341 162354 166697 121611.8 195752 168422 186241 TRUE FALSE 165909.6996 139318.1595 177452.7304 166520.2785 153605.29 156719.1525 166400.8049 189449.8574 155156.1739 1.069307752 0.897922113 1.143703959 1.073243006 0.990004369 1.010073583 1.072472984 1.22102687 1 17.24336158 1.503355255 5.701527275 1.121795518 1.029334713 0.136207476 0.082073636 0.232802256 17.04119197 0.045222614 0.019867069 31.86803274 -1.503355255 -0.092460805 TTPS(ph)YVAFTDTER ddPTM_SK-BR-3_Pertuzumab_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(0.001)T(0.006)PS(0.992)YVAFTDTER 130.27 0.00015108 66734000 48670 74000 51385 49270 91737 48277 62958 63675 90335 TRUE FALSE 45623.83158 79479.037 52603.87647 50534.35161 84532.34607 62213.78619 53518.03237 71624.96392 75257.50491 0.606236303 1.0560945 0.698985125 0.671485876 1.123241412 0.826678831 0.711132165 0.951731844 1 16.19954784 TTPSVVAFTADGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTPSVVAFTADGER 14 0 P38646;D6RJI2;A0A3B3ITI4;D6RA73 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 171.85 6.86E-06 132170000 177820 154770 154150 141560 184020 126950 195760 165890 266560 FALSE TRUE 166690.5636 166229.3318 157806.5108 145192.6693 169567.8115 163598.4041 166407.6053 186601.7317 222069.414 0.750623693 0.748546722 0.710617946 0.6538166 0.763580218 0.736699401 0.749349505 0.840285604 1 17.76065118 0.89566239 1.435145383 1.000223962 0.724869386 0.895872416 0.029889207 0.155024122 0.629951666 0.027709387 0.008211683 7.864341964 -0.89566239 -0.275354576 TTPSYVAFTDTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 TTPSYVAFTDTER 13 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;Q53FA3;P34931;P11142;E9PKE3;E9PNE6;P11142-2;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25;E9PI65;P54652;P17066;P48741 A0A0G2JIW1;Q53FA3;P11142;P54652;P17066 HSPA1B;HSPA1A;HSPA1L;HSPA8;HSPA2;HSPA6;HSPA7 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like;Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2;Heat shock 70 kDa protein 6;Putative heat shock 70 kDa protein 7 0 ;;;;;;; 258.72 1.41E-23 6499590000 2320599 2647261 2141011 2075685 2768040 1698186 2734513 2416967 3109020 FALSE TRUE 2175356.851 2843266.959 2191796.792 2128950.591 2550649.304 2188424.73 2324498.162 2718730.65 2590104.477 0.839872241 1.097742189 0.846219452 0.821955489 0.984766957 0.844917551 0.897453436 1.049660612 1 21.30457886 1.241135443 24.99985972 1.024830333 0.91409205 0.255467832 0.084077864 96.48277425 936864.565 0.062010714 0.020273086 17.42350173 -1.241135443 -0.110738283 TTQIPQWCVEYMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTQIPQWCVEYMR 13 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 128.41 0.00013025 0 61209 65376 66093 60579 67595 46274 74318 66466 74857 FALSE TRUE 57378.03795 70216.50706 67660.75717 62133.5597 62286.36137 59632.5526 63174.70583 74764.42641 62362.88311 0.920067115 1.125934267 1.08495236 0.996322758 0.99877296 0.956218661 1.013017723 1.198860968 1 15.92840001 -1.982139265 7.906324067 0.970359514 1.041029676 0.017177975 0.081950233 0.055569848 0.000125535 0.102982533 0.018107664 0.010419832 1.982139265 0.070670162 TTQSMQDFPVVDS(ph)EEEAEEEFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TTQSMQDFPVVDSEEEAEEEFQK 23 0 Q9UBB9 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 TTQSMQDFPVVDS(1)EEEAEEEFQK;TTQSMQDFPVVDS(1)EEEAEEEFQK 235.44 2.76E-37 219001000 572510 419270 487820 487410 488890 344300 633500 436840 540840 TRUE FALSE 536677.6211 450313.1871 499391.3208 499917.7658 450494.5515 443693.8208 538512.5561 491380.4356 450570.31 1.191107379 0.999429339 1.108353812 1.109522209 0.999831861 0.984738255 1.195179851 1.090574378 1 18.78139273 1.741093082 24.99999985 1.114236685 1.061985745 0.011066477 0.078164655 1.022929807 10160.9002 0.033304849 0.018469006 55.09257629 -1.741093082 -0.05225094 TTQVPQFILDDFIQNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TTQVPQFILDDFIQNDR 17 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;; 255.91 1.03E-26 237843000 242873.6 257360.7 268527 266519.1 279571 212464.9 301525 240904.4 302481 FALSE TRUE 227672.5749 276415.954 274896.5872 273358.4313 257614.6214 273800.0676 256314.1255 270981.8446 251994.967 0.903480643 1.096910614 1.090881261 1.084777345 1.022300661 1.086529905 1.01713986 1.075346257 1 17.94303539 -0.180833421 7.657155812 0.999999983 1.054866605 0.046583868 0.058483563 0 0 0.051596929 0.012161513 0.659426778 0.180833421 0.054866622 TTS(ph)FAESCKPVQQPSAFGSMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TTSFAESCKPVQQPSAFGSMK 21 1 A0A3B3ITW1;P49841;P49841-2 A0A3B3ITW1 GSK3B Glycogen synthase kinase-3 beta 1 T(0.036)T(0.036)S(0.929)FAESCKPVQQPSAFGSMK;T(0.104)T(0.104)S(0.792)FAESCKPVQQPSAFGSMK 210.19 1.32E-22 981830000 550770 455170 451580 552330 752350 337203 842000 488480 845590 TRUE FALSE 516298.2889 488871.2604 462291.6909 566503.7229 693263.4658 434548.0321 715749.9167 549467.8033 704455.5663 0.732903981 0.693970328 0.656239674 0.804172399 0.984112411 0.616856553 1.016032736 0.779989299 1 19.42614919 2.256441104 0.349683421 0.992880666 0.645584624 0.328701829 0.119092217 1.503212994 0.452344965 0.136270377 0.185658564 180.4849958 -2.256441104 -0.347296042 TTS(ph)FFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TTSFFSR 7 0 Q9BZ67-2;Q9BZ67-3;Q9BZ67 Q9BZ67-2 FRMD8 FERM domain-containing protein 8 1 T(0.063)T(0.359)S(0.578)FFSR;T(0.001)T(0.073)S(0.927)FFSR;T(0.015)T(0.112)S(0.874)FFSR;T(0.098)T(0.058)S(0.844)FFSR;T(0.011)T(0.03)S(0.96)FFSR 133.58 0.0034172 330794000 1035030 1275680 956260 968310 1151080 537436 1542520 898460 1554310 TRUE FALSE 970249.3199 1370132.675 978942.9388 993158.4739 1060678.82 692585.0487 1311233.446 1010634.709 1294885.62 0.749293455 1.058110966 0.756007267 0.766985484 0.819129353 0.534861951 1.012624919 0.780481838 1 20.30439324 -1.688792038 5.753927096 1.002791159 0.827633624 0.13467881 0.145410593 0.005003319 0.00027061 0.135298643 0.03142484 0.020474248 1.688792038 -0.175157535 TTS(ph)GDDACNLTSFRPATLTVTNFFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TTSGDDACNLTSFRPATLTVTNFFK 25 1 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GUE9;Q96N67-7;A0A0U1RQT6 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 TT(0.001)S(0.999)GDDACNLTSFRPATLTVTNFFK;T(0.028)T(0.028)S(0.945)GDDACNLTSFRPATLTVTNFFK 223.34 5.72E-34 762100000 832820 778900 702900 831130 760470 520050 1133580 669010 1011090 TRUE FALSE 780695.2828 836570.5664 719573.1199 852458.2029 700745.7538 670179.9927 963610.2026 752537.3712 842332.5471 0.926825498 0.993159494 0.854262515 1.012020972 0.83191105 0.795624003 1.143978356 0.893397001 1 19.68403039 1.741124892 24.99999998 1.022591049 0.908753123 0.248457723 0.089270983 0.549132338 5386.834944 0.038398432 0.021293911 55.09661171 -1.741124892 -0.113837927 TTS(ph)PEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TTSPEPR 7 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 T(0.074)T(0.147)S(0.779)PEPR;T(0.012)T(0.025)S(0.963)PEPR;T(0.01)T(0.118)S(0.872)PEPR;T(0.017)T(0.122)S(0.86)PEPR 119.86 0.0049155 4872200000 4960920 4791270 5056150 4901030 5099880 4164220 5310530 4388390 5256870 TRUE FALSE 4650424.873 5146020.616 5176084.266 5026798.727 4699355.997 5366362.714 4514265.327 4936290.152 4379464.436 1.061870679 1.175034229 1.181898915 1.147811291 1.073043534 1.225346796 1.030780223 1.127144705 1 22.06232302 0.965175072 0.654576999 1.001437141 1.151819367 0.317905417 0.059278307 0.837577305 0.832601898 0.054330094 0.022182435 9.229434078 -0.965175072 0.150382227 TTS(ph)PLEEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TTSPLEEEER 10 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 T(0.006)T(0.002)S(0.992)PLEEEER;T(0.038)T(0.012)S(0.951)PLEEEER 344.95 6.54E-55 1939920000 1188200 1161740 1167930 1097620 1152540 1045410 1324770 995120 1092230 TRUE FALSE 1113832.683 1247756.438 1195633.851 1125786.787 1062024.158 1347202.896 1126133.037 1119362.923 909929.7569 1.224086447 1.37126677 1.31398478 1.237223839 1.167149606 1.480557028 1.237604363 1.230164102 1 19.79539565 0.786922518 1.796061586 1.000767265 1.302424762 0.519746916 0.087257902 0.564758477 3.135395996 0.077361405 0.021809759 6.122411528 -0.786922518 0.301657497 TTS(ph)PSSDTDLLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TTSPSSDTDLLDR 13 0 K7ENU0;K7ERZ4;K7EJ43;Q96QT6;C9J9G2;Q96QT6-2;Q96QT6-5;Q96QT6-3 K7ENU0;Q96QT6 PHF12 PHD finger protein 12 1 T(0.003)T(0.037)S(0.958)PS(0.002)SDTDLLDR;TTS(0.999)PS(0.001)SDTDLLDR;TT(0.032)S(0.94)PS(0.02)S(0.007)DTDLLDR;T(0.027)T(0.027)S(0.821)PS(0.098)S(0.027)DTDLLDR 261.32 4.92E-24 1004900000 1285380 1333410 1348680 1310690 1348720 1097960 1491990 1126340 1344190 TRUE FALSE 1204930.36 1432137.064 1380671.326 1344324.524 1242796.972 1414923.228 1268279.95 1266966.028 1119836.005 1.075988229 1.278881066 1.232922785 1.200465531 1.109802655 1.263509319 1.132558647 1.13138533 1 20.09485604 0.750559952 0.676922571 0.996968079 1.211229971 0.442406111 0.065158766 0.879662719 0.821427969 0.06330296 0.023718959 5.630668402 -0.750559952 0.214261892 TTSIS(ph)PALAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.001)IS(0.999)PALAR;TT(0.001)S(0.011)IS(0.989)PALAR;TTS(0.003)IS(0.997)PALAR;TTS(0.004)IS(0.996)PALAR 162.21 7.17E-06 814040000 1129720 1228690 1202420 1178490 1350870 935200 1266150 1116320 1708140 TRUE FALSE 1059012.842 1319663.486 1230941.97 1208732.049 1244778.119 1205177.058 1076302.562 1255695.009 1423040.399 0.744190286 0.927354899 0.86500845 0.849401078 0.874731399 0.846902912 0.756340131 0.882402924 1 20.44054519 0.979621639 24.52393658 1.000000004 0.845194635 0.470106716 0.05388561 1192.238278 1434777.556 0.052996417 0.013249104 9.541609517 -0.979621639 -0.154805368 TTSQAHSLPLS(ph)PASTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TTSQAHSLPLSPASTR 16 0 P19838;P19838-2;P19838-3 P19838 NFKB1 Nuclear factor NF-kappa-B p105 subunit;Nuclear factor NF-kappa-B p50 subunit 1 TTSQAHSLPLS(1)PASTR;TTSQAHSLPLS(1)PASTR;TTSQAHSLPLS(1)PASTR;TTSQAHSLPLS(1)PASTR 144.18 8.64E-07 2167200000 2158760 2970100 3058060 3654990 3516760 2444650 2831500 2148270 2633440 TRUE FALSE 2023647.065 3190009.294 3130598.627 3748783.231 3240567.856 3150380.769 2406942.861 2416486.238 2193901.851 0.922396352 1.454034643 1.426954732 1.708728779 1.477079685 1.435971608 1.097105989 1.101455946 1 21.06506755 1.69881822 4.310994929 1.065332092 1.428008425 0.396143435 0.19543657 0.169391612 7.370005102 0.102600277 0.049499533 49.98252828 -1.69881822 0.362676333 TTSSANNPNLMYQDECDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 TTSSANNPNLMYQDECDRR 19 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;;;;; 260.53 6.58E-31 4019090000 918328 955101 956673 985843 1099107 852976 1154840 966819 1204925 FALSE TRUE 860851.4897 1025817.672 979365.7353 1011141.4 1012787.57 1099216.324 981682.463 1087528.48 1003815.233 0.857579623 1.021918813 0.975643428 1.007298322 1.008938235 1.095038497 0.97795135 1.083395075 1 19.93706231 4.739602177 24.62167128 1.017205642 0.857579562 0.625321202 0.039710151 45.67612161 1079565.221 0.008680901 0.053227762 54903.77131 -4.739602177 -0.15962608 TTSSYQNLVWSDHSQELHS(ph)PTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TTSSYQNLVWSDHSQELHSPTLK 23 0 Q8WVV4-1;Q8WVV4;Q8WVV4-3 Q8WVV4-1 POF1B Protein POF1B 1 TTSSYQNLVWSDHSQELHS(0.999)PT(0.001)LK;TTSSYQNLVWSDHSQELHS(0.999)PT(0.001)LK;TTSSYQNLVWSDHSQELHS(0.996)PT(0.004)LK;TTSSYQNLVWSDHSQELHS(0.999)PTLK 246.36 2.32E-37 1283850000 727320 935950 987990 1288050 1260650 574450 757890 524876 644490 TRUE FALSE 681798.3395 1005248.712 1011425.589 1321103.544 1161643.634 740284.3896 644251.4304 590407.924 536920.4554 1.269831187 1.872248862 1.883753132 2.460520046 2.163530226 1.378759893 1.199901073 1.099618981 1 19.03434884 2.080377337 4.412715542 1.155737014 1.937988009 0.61995337 0.30064851 0.149109312 5.44799932 0.121554846 0.086063159 120.3309477 -2.080377337 0.782250994 TTTELFHSNEESGFFNELEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTTELFHSNEESGFFNELEALR 22 0 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;A0A0A0MRE9;H7BYL6 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 0 131.82 1.15E-05 38066000 13553 15062 14407 14127 15302 12278 16613 15986 17910 FALSE TRUE 12704.74192 16177.20615 14748.74084 14489.52274 14100.24265 15822.45928 14122.03488 17981.88729 14920.7053 0.851484006 1.084211894 0.988474777 0.971101731 0.945011805 1.060436418 0.946472341 1.205163357 1 13.86502811 1.2587642 24.99775026 1.102581852 0.99019111 0.283203153 0.080539753 261.1175125 323080.5568 0.047770919 0.017398876 18.14530197 -1.2587642 -0.112390742 TTTPGPSLS(ph)QGVSVDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TTTPGPSLSQGVSVDEK 17 0 O60934;A0A0C4DG07 O60934 NBN Nibrin 1 TTTPGPS(0.001)LS(0.998)QGVS(0.001)VDEK 142.94 5.96E-07 123800000 140570 110990 116250 124850 151610 81175 203370 145530 208680 TRUE FALSE 131771.9746 119207.8151 119007.5049 128053.8624 139703.1622 104608.9047 172876.5565 163699.7409 173849.9599 0.757963791 0.685693659 0.684541457 0.736576888 0.803584667 0.601719464 0.9944009 0.941615063 1 17.40748321 1.680306573 7.075040435 0.975665786 0.710493446 0.837174261 0.055353018 0.044814462 4.415098433 0.025672093 0.013214475 47.89680811 -1.680306573 -0.265172341 TTYLVLDEADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TTYLVLDEADR 11 0 P17844;P17844-2;J3KTA4;J3QSF1;J3KRZ1 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;; 217.66 2.60E-11 572290000 781260 857500 818320 786050 895200 646080 861160 766030 937730 FALSE TRUE 732362.3312 920990.1922 837730.9368 806221.3738 824894.6031 832592.8078 732037.0526 861670.5317 781216.805 0.937463616 1.178917538 1.072341162 1.032007208 1.055909957 1.065764078 0.937047242 1.102985146 1 19.57536346 2.686182597 1.098162636 1.012422674 1.087167641 0 0.073299763 0.9375755 2.345726751 0.036657765 0.032397027 485.4925805 -2.686182597 0.074744966 TVAISDAAQLPHDYCT(ph)TPGGTLFS(ph)TTPGGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDYCT(0.878)T(0.122)PGGT(0.21)LFS(0.383)T(0.251)T(0.155)PGGT(0.001)R 173.08 8.16E-13 260670000 87858 97347 102030 114950 138410 128100 162440 112070 146000 TRUE FALSE 82359.12461 104554.6732 104450.1998 117899.8116 127539.8369 165080.3905 138083.63 126062.1862 121631.6568 0.677119154 0.85960083 0.858741898 0.969318471 1.048574362 1.357215669 1.135260619 1.036425792 1 16.89215924 2.979147456 1.632001218 1.150645333 0.808145853 0.642472433 0.108084008 0.216271233 1.169055034 0.03786203 0.044488585 953.1197211 -2.979147456 -0.34249948 TVAISDAAQLPHDYCT(ph)TPGGTLFSTTPGGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 TVAISDAAQLPHDY(0.014)CT(0.755)T(0.231)PGGTLFSTTPGGTR 105.14 0.00056355 76868000 42619 60539 55208 58739 54746 42733 59353 47789 53286 TRUE FALSE 39951.55287 65021.37055 56517.55983 60246.34218 50446.46999 55069.32339 50453.56866 53755.56185 44392.22236 0.899967398 1.464701858 1.273141033 1.357137331 1.136380819 1.24051738 1.136540727 1.210922972 1 15.43801931 1.015957 0.550118421 1.003398118 1.280717313 0.13432886 0.151695421 1.345016238 1.00795805 0.152114369 0.070125875 10.37425693 -1.015957 0.277319195 TVAISDAAQLPHDYCTT(ph)PGGT(ph)LFSTTPGGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDYCT(0.017)T(0.983)PGGT(0.722)LFS(0.034)T(0.141)T(0.096)PGGT(0.008)R;TVAISDAAQLPHDY(0.001)CT(0.438)T(0.56)PGGT(0.467)LFS(0.22)T(0.173)T(0.137)PGGT(0.003)R;TVAISDAAQLPHDY(0.004)CT(0.474)T(0.501)PGGT(0.336)LFS(0.231)T(0.219)T(0.208)PGGT(0.027)R;TVAISDAAQLPHDYCT(0.222)T(0.778)PGGT(0.38)LFS(0.087)T(0.261)T(0.266)PGGT(0.006)R 161.62 3.22E-12 5196591000 688541.9 699200.1 692955.2 747833.2 952781.1 839541.4 1023967.6 737260.2 882100.7 TRUE FALSE 645447.2916 750969.6029 709392.4246 767023.866 877953.5157 1081903.373 870433.1644 829308.7589 734872.3946 0.878312067 1.021904767 0.965327355 1.043751094 1.194701995 1.472232977 1.184468448 1.12850716 1 19.48713423 2.819931676 3.133472757 1.229966414 0.97395417 0.436801308 0.123061507 0.211188223 4.038100645 0.03768153 0.039613471 660.5895149 -2.819931676 -0.256012244 TVAISDAAQLPHDYCTT(ph)PGGT(ph)LFSTTPGGTRIIYDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.001)CT(0.472)T(0.527)PGGT(0.34)LFS(0.243)T(0.218)T(0.195)PGGT(0.004)RIIYDRK 131.6 1.20E-08 133900000 21777 24115 28326 38404 46868 24294 40199 31301 97127 TRUE FALSE 20414.01644 25900.49969 28997.9061 39389.51166 43187.17634 31307.28342 34171.53314 35208.99875 80915.87624 0.252286911 0.320091691 0.358371032 0.486795836 0.533729329 0.386911505 0.422309375 0.435130909 1 16.30413518 -5 0.209948105 3.892958139 0.307724126 0.887197052 0.068816439 48.23812767 0.481025477 58.76850325 0.154412681 1.00E-05 5 -3.585234014 TVAISDAAQLPHDYCTT(ph)PGGTLFS(ph)TTPGGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDYCT(0.096)T(0.904)PGGT(0.025)LFS(0.472)T(0.304)T(0.198)PGGT(0.001)R;TVAISDAAQLPHDY(0.004)CT(0.461)T(0.535)PGGT(0.003)LFS(0.412)T(0.355)T(0.228)PGGT(0.002)R 140.61 4.47E-08 279323000 54564 55085 61252 68345 82980 67996 90178 65663 74922 TRUE FALSE 51148.93664 59163.55072 62704.92637 70098.84841 76463.08553 87625.34138 76656.64607 73861.17009 62417.03419 0.819470795 0.947875071 1.004612398 1.1230724 1.225035546 1.403869032 1.228136631 1.183349562 1 15.92965219 3.289626975 1.397498642 1.23892236 0.903413482 0.609400341 0.104717374 0.241015255 0.977264534 0.034260049 0.053821204 1948.170557 -3.289626975 -0.335508878 TVAISDAAQLPHDYCTT(ph)PGGTLFS(ph)TTPGGTRIIYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDR 36 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.074)CT(0.428)T(0.488)PGGT(0.011)LFS(0.377)T(0.335)T(0.285)PGGTRIIYDR 125.73 3.10E-07 332230000 21069 38300 25996 33708 64618 27443 43146 32887 94024 TRUE FALSE 19750.3289 41135.77185 26612.6374 34573.00435 59543.16294 35365.3486 36676.65785 36993.01434 78330.78698 0.252140055 0.525154584 0.339746841 0.44137185 0.760150194 0.451487212 0.468227874 0.472266599 1 16.25729183 -5 0.224676985 3.772038951 0.400255544 0.652098768 0.125595555 98.14690949 0.982711831 123.4979325 0.219879284 1.00E-05 5 -3.371783408 TVAISDAAQLPHDYCTT(ph)PGGTLFS(ph)TTPGGTRIIYDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDYCT(0.028)T(0.9)PGGT(0.099)LFS(0.502)T(0.415)T(0.055)PGGTRIIYDRK 210.52 1.59E-30 609780000 130220 201460 146600 212720 352910 146930 303270 175220 798520 TRUE FALSE 122069.7626 216376.308 150077.4212 218178.7553 325193.8722 189346.3058 257797.4789 197096.6027 665241.8534 0.183496817 0.325259613 0.225598285 0.327969075 0.488835557 0.284627771 0.387524443 0.296278116 1 19.34351941 -5 0.271454067 5.740960686 0.267138621 0.879131705 0.080243912 65.11125986 0.631396845 173.1308101 0.091238938 1.00E-05 5 -5.473822066 TVAISDAAQLPHDYCTT(ph)PGGTLFSTT(ph)PGGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDYCT(0.049)T(0.932)PGGT(0.02)LFS(0.009)T(0.071)T(0.914)PGGT(0.006)R;TVAISDAAQLPHDYCT(0.132)T(0.867)PGGT(0.001)LFS(0.014)T(0.102)T(0.884)PGGTR;TVAISDAAQLPHDYCT(0.185)T(0.815)PGGT(0.009)LFS(0.087)T(0.211)T(0.69)PGGT(0.003)R;TVAISDAAQLPHDYCT(0.166)T(0.834)PGGTLFS(0.1)T(0.041)T(0.857)PGGT(0.001)R;TVAISDAAQLPHDYCT(0.159)T(0.841)PGGTLFS(0.264)T(0.156)T(0.573)PGGT(0.007)R;TVAISDAAQLPHDYCT(0.113)T(0.887)PGGTLFS(0.35)T(0.189)T(0.461)PGGTR 214.42 1.59E-34 28261500000 7040200 7392370 7297300 7908660 10259460 9046510 11464510 8398530 10079030 TRUE FALSE 6599566.449 7939708.767 7470395.402 8111609.605 9453723.396 11658090.58 9745513.157 9447104.958 8396774.78 0.785964447 0.945566479 0.889674381 0.966038725 1.125875547 1.388401009 1.160625766 1.125087335 1 23.00140386 2.770321548 2.891406415 1.192966744 0.89490148 0.615539732 0.1040799 0.157988278 2.649869927 0.032357032 0.032992541 589.2797916 -2.770321548 -0.298065264 TVAISDAAQLPHDYCTT(ph)PGGTLFSTT(ph)PGGTRIIYDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.008)CT(0.472)T(0.517)PGGT(0.018)LFS(0.184)T(0.168)T(0.54)PGGT(0.091)RIIY(0.003)DRK;TVAISDAAQLPHDY(0.001)CT(0.412)T(0.584)PGGT(0.011)LFS(0.154)T(0.135)T(0.7)PGGT(0.002)RIIY(0.001)DRK 159.77 1.71E-17 1384540000 114619 184798 130841 204396 327290 128597 276489 165240 714350 TRUE FALSE 107445.2014 198480.6362 133944.6103 209641.1474 301585.9636 165720.8663 235032.0412 185870.5777 595120.3701 0.180543646 0.333513431 0.22507146 0.352266798 0.506764646 0.27846613 0.394931938 0.312324342 1 19.18282197 -5 0.261921113 5.418715318 0.26969216 0.862221108 0.085660322 65.58240971 0.643284718 156.0551312 0.105162165 1.00E-05 5 -5.149023157 TVAISDAAQLPHDYCTT(ph)PGGTLFSTTPGGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 TVAISDAAQLPHDYCT(0.439)T(0.559)PGGT(0.002)LFSTTPGGTR;TVAISDAAQLPHDY(0.001)CT(0.199)T(0.791)PGGT(0.008)LFSTTPGGTR 128.54 1.87E-05 1149820000 113594 115947 122757 117489 128699 101460 138212 109943 130757 TRUE FALSE 106484.3543 124531.8365 125668.854 120503.9666 118591.4997 130749.8549 117488.3937 123669.6256 108932.812 0.977523231 1.143198585 1.153636372 1.106222858 1.088666468 1.200279811 1.078539988 1.135283514 1 16.73307905 -0.998939932 7.389498216 0.999999995 1.117561566 0.250459194 0.058889667 3.81E-09 5.16E-10 0.051186017 0.012064659 0.100244388 0.998939932 0.11756157 TVAISDAAQLPHDYCTTPGGTLFST(ph)TPGGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 TVAISDAAQLPHDYCTTPGGTLFS(0.215)T(0.458)T(0.305)PGGT(0.021)R 157.38 3.51E-09 251450000 176270 167450 175830 173580 191040 153500 171970 149920 175420 TRUE FALSE 165237.5754 179848.1722 180000.7706 178034.3567 176036.489 197812.9581 146184.695 168637.842 146141.2687 1.130670185 1.23064603 1.231690214 1.218234645 1.204563848 1.353573565 1.000297153 1.15393717 1 17.15700411 1.697271206 9.975711506 1.059636272 1.227469783 0.596481813 0.068352033 0.074662769 13.27495393 0.028979437 0.015639032 49.80480061 -1.697271206 0.167833511 TVAISDAAQLPHDYCTTPGGTLFSTT(ph)PGGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 TVAISDAAQLPHDYCTTPGGTLFS(0.014)T(0.204)T(0.775)PGGT(0.006)R;TVAISDAAQLPHDYCTTPGGTLFS(0.007)T(0.034)T(0.958)PGGT(0.001)R;TVAISDAAQLPHDYCTTPGGTLFST(0.003)T(0.997)PGGTR;TVAISDAAQLPHDYCTTPGGTLFS(0.011)T(0.095)T(0.888)PGGT(0.006)R;TVAISDAAQLPHDYCTTPGGTLFS(0.002)T(0.017)T(0.981)PGGTR 323.92 8.39E-93 12037290000 4277320 4460340 4648200 4279250 4531460 4096910 4843840 3671860 4375690 TRUE FALSE 4009610.176 4790588.215 4758457.499 4389062.8 4175577.411 5279621.409 4117551.16 4130299.804 3645359.071 1.099921873 1.314160861 1.305346718 1.204013847 1.145450237 1.448313131 1.129532394 1.13302962 1 21.7976295 1.196334046 1.887187619 1.015089933 1.258962335 0.375697371 0.101392162 0.295693907 1.895762516 0.086712124 0.025198895 15.71571145 -1.196334046 0.243872402 TVALWDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVALWDLR 8 0 Q09028-3;Q09028;Q09028-2;Q09028-4;H0YF10;H0YCT5;H0YDK2;H0YEU5;Q16576;E9PC52;Q16576-2;Q5JP02 Q09028-3;Q16576 RBBP4;RBBP7 Histone-binding protein RBBP4;Histone-binding protein RBBP7 0 103.74 0.010969 84818000 85474 529270 106140 106520 575080 77817 94806 383690 362260 FALSE TRUE 80124.33492 568457.7015 108657.6909 109253.4835 529915.5366 100281.5046 80590.72044 431594.5411 301796.4657 0.265491296 1.883579717 0.360036327 0.36201048 1.755870584 0.332281905 0.267036661 1.430084809 1 18.20321639 3.895224973 10.34368135 0.723951483 1.181101311 0.021351416 0.632203361 1.024758974 123.4891609 0.151093873 0.272701944 7856.425072 -3.895224973 0.457149828 TVANLLSGKS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TVANLLSGKSPR 12 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 TVANLLSGKS(1)PR;TVANLLSGKS(1)PR;TVANLLS(0.026)GKS(0.974)PR;TVANLLSGKS(1)PR 195.58 5.70E-07 14930310000 19901140 15023030 18366730 15437310 22770320 13902230 22347880 18491080 24297270 TRUE FALSE 18655563.17 16135350.77 18802397.51 15833457.51 20982030.92 17915578.12 18997022.86 20799732.04 20241898.67 0.921631092 0.797126348 0.928885072 0.782212072 1.036564369 0.885073995 0.938500047 1.027558352 1 24.27084128 2.104552613 0.581948817 1.007560726 0.853769164 0.350433962 0.069604515 0.846203244 0.580203936 0.057995944 0.040792544 127.2191862 -2.104552613 -0.153791562 TVAQQHDEDGIEEEDDDDDEIDDDDTISDWNLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVAQQHDEDGIEEEDDDDDEIDDDDTISDWNLRK 34 1 Q92973-2;Q92973;Q92973-3 Q92973-2 TNPO1 Transportin-1 0 262.48 6.07E-60 104610000 15041 15432 12683 14863 19729 9451.6 19520 12789 37157 FALSE TRUE 14099.61066 16574.60134 12983.84675 15244.40974 18179.56392 12180.12349 16593.15721 14385.7348 30955.25666 0.455483565 0.535437374 0.419439157 0.492465946 0.587285194 0.393475125 0.536036816 0.464726717 1 14.9178968 -1.65024266 2.706926977 1.05798243 0.486881529 0.888115593 0.057383596 10942711.01 9899558.765 4418279.454 0.012615188 0.022374706 1.65024266 -0.571100901 TVART(ph)PLGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVARTPLGQR 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.005)VART(0.995)PLGQR;T(0.071)VART(0.929)PLGQR 110.92 0.0029451 5456900000 2946800 3324000 3350900 3203900 4075100 2553800 3550900 3245300 6850700 TRUE FALSE 2762365.048 3570112.419 3430384.93 3286117.498 3755058.084 3291040.603 3018475.51 3650482.849 5707273.913 0.484007793 0.625537248 0.601054896 0.575777078 0.657942503 0.57663968 0.528882187 0.639619353 1 22.44437037 0.955549883 18.43011977 1.000000001 0.584994106 0.882189111 0.047986916 79.07274367 32786.00178 0.044103622 0.011025897 9.027133874 -0.955549883 -0.415005895 TVAS(ph)DLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TVASDLQK 8 0 Q7L8J4;Q7L8J4-2 Q7L8J4 SH3BP5L SH3 domain-binding protein 5-like 1 TVAS(1)DLQK;TVAS(1)DLQK;TVAS(1)DLQK;T(0.002)VAS(0.998)DLQK;T(0.001)VAS(0.999)DLQK;TVAS(1)DLQK 153.23 0.0004661 1360908000 3228370 2343080 2610080 2597710 2776900 1943430 3589230 2319250 3843580 TRUE FALSE 3026312.085 2516564.081 2671992.33 2664371.637 2558813.475 2504466.692 3051058.282 2608813.468 3202061.668 0.945113617 0.78591993 0.834459985 0.832080051 0.799114365 0.78214193 0.952841825 0.814729302 1 21.61056966 0.47962175 0.655446853 1.001797031 0.828678488 0.373547276 0.061420343 1.699549545 1.207215875 0.069107381 0.022205595 3.017322632 -0.47962175 -0.173118543 TVATPLNQVANPNSAIFGGARPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVATPLNQVANPNSAIFGGARPR 23 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ; 238.87 3.08E-37 1347560000 278080 321630 283730 338320 366030 251540 355890 256250 388070 FALSE TRUE 260675.4692 345443.8199 290460.2096 347001.864 337283.4803 324155.5146 302527.5984 288243.3766 323298.61 0.806299381 1.068497696 0.898427029 1.073316907 1.043256822 1.002650505 0.935752858 0.891570108 1 18.30250778 -0.488861633 7.274345861 1.000008991 0.972778326 0.009009088 0.085854388 0 0 0.075484615 0.017791894 0.324442969 0.488861633 -0.027230665 TVCERPGPAACAQVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVCERPGPAACAQVAR 16 1 Q9P2H5 Q9P2H5 USP35 Ubiquitin carboxyl-terminal hydrolase 35 0 60.55 0.084389 539030000 108710 691030 518700 696340 628080 631140 332270 472990 367160 FALSE TRUE 101906.0352 742194.5802 531003.8089 714209.2633 578753.1304 813339.8723 282449.1981 532043.8427 305878.6241 0.333158407 2.426434938 1.735995154 2.334943364 1.892100607 2.659028151 0.923402866 1.739395305 1 18.22259976 1.690306027 11.42798367 1.254603425 1.955635457 0.183287188 0.663033761 0.178875766 34.49217045 0.279930937 0.152553279 49.01240647 -1.690306027 0.701032032 TVCIYGHLDVQPAALEDGWDSEPFTLVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVCIYGHLDVQPAALEDGWDSEPFTLVER 29 0 Q96KP4;J3QKT2;J3QRH4;A0A087WYZ1;J3KSV5;J3QRD0;J3QKQ0;J3QLU1;J3QR27;A0A087WVS2;J3KRD5 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 296.96 7.46E-81 165590000 72619 92764 86238 83785 99165 77514 98067 76523 100080 FALSE TRUE 68073.90642 99632.34308 88283.60608 85935.06495 91376.98091 99891.03347 83362.76376 86077.065 83376.00146 0.816468831 1.194976268 1.058861118 1.030693046 1.095962619 1.198078964 0.999841229 1.032396175 1 16.34734456 1.60501284 25 1.012081888 1.081115718 0.044289056 0.105751435 0.707985446 6140.121693 0.04930855 0.024391693 40.27289408 -1.60501284 0.06903383 TVDGPSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 TVDGPSGK 8 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;; 166.68 0.00073762 8432010000 18487720 16283520 17529560 17115030 16919600 13017770 20151000 14452110 17625690 FALSE TRUE 17330606.61 17489168.76 17945369.44 17554230.65 15590802.87 16775788.87 17129544.62 16256487.75 14683848.47 1.180249622 1.191048028 1.222116223 1.195478875 1.061765442 1.142465404 1.166556891 1.107099939 1 23.8077268 -2.543791795 0.14183667 0.709385288 1.245610276 0.670906506 0.038981304 35.39765568 0.608417968 3.488270227 0.277840011 0.002858961 2.543791795 0.536224988 TVDLKPDWGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVDLKPDWGK 10 1 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 161.19 6.52E-06 8112900000 16810000 12345700 13570700 13647000 15964800 9542600 16857800 12689200 17375800 FALSE TRUE 15757892.11 13259788.47 13892603.41 13997205.12 14710989.01 12297393.71 14330129.39 14273474.55 14475666.73 1.088577984 0.916005371 0.959721143 0.96694718 1.016256403 0.849521748 0.98994607 0.986032272 1 23.78712646 1.524095345 25 0.991495919 0.958340567 0.027550501 0.061579456 1.327615989 688.9804662 0.030130413 0.01394874 33.42684172 -1.524095345 -0.033155352 TVDS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TVDSPK 6 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 TVDS(1)PK;TVDS(1)PK;TVDS(1)PK;TVDS(1)PK 129.72 0.016858 3161070000 15506400 8771200 13024400 11308300 10913700 8652400 13335200 9620500 13124100 TRUE FALSE 14535882.1 9420628.774 13333344.92 11598490.12 10056582.03 11150207.42 11335710.56 10821640.6 10933602.93 1.32946863 0.86162163 1.219483185 1.060811354 0.919786652 1.019810898 1.03677723 0.989759796 1 23.38226555 2.990420669 24.78697457 1.000033052 1.095990376 0.201737856 0.121553647 855.5329675 2213741.257 0.033787067 0.038315759 978.1842564 -2.990420669 0.095957324 TVDSQGPT(ph)PVCTPTFLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVDSQGPTPVCTPTFLER 18 0 Q9BYG3;H7BZL0;C9J808 Q9BYG3 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 1 TVDSQGPT(0.837)PVCT(0.162)PT(0.001)FLER 135.09 0.00010229 90768000 88157 85872 104290 103250 96585 131340 121440 81805 66735 TRUE FALSE 82639.41073 92230.05223 106763.808 105899.5698 88999.60371 169255.7259 103231.1994 92018.53433 55596.49738 1.486413976 1.658918396 1.92033335 1.904788517 1.600813143 3.044359517 1.85679322 1.655113877 1 15.76270637 TVDVPASLPT(ph)PPHNNQEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVDVPASLPTPPHNNQEELR 20 0 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37;H0Y765;H7C2V8 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 TVDVPASLPT(1)PPHNNQEELR;TVDVPASLPT(1)PPHNNQEELR 178.11 2.32E-16 302800000 153313 163927 181101 178095 209450 172050 241140 185782 248470 TRUE FALSE 143717.413 176064.3256 185396.8012 182665.2192 193000.6419 221718.042 204983.2956 208977.2917 206998.7518 0.694291206 0.850557427 0.895642122 0.882445994 0.932375873 1.071108111 0.990263438 1.009558221 1 17.65926254 6.228164634 0.311994437 1.031624744 3.56E-13 0.835863468 0.04267903 7.20384395 0.273760616 0.04271581 3.374638995 1691081.873 -6.228164634 -1.031624744 TVEAEAAHGTVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TVEAEAAHGTVTR 13 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;;;;; 262.64 4.00E-24 4599000000 2235670 3008810 2876720 2767370 3096890 2525680 3114550 2758300 3338690 FALSE TRUE 2095743.405 3231585.423 2944957.157 2838385.399 2853672.752 3254802.815 2647552.142 3102679.827 2781441.07 0.753473956 1.161838537 1.058788262 1.020472959 1.025969158 1.17018579 0.951863467 1.115493641 1 21.40740111 4.749840874 24.91079756 1.064566375 0.753473764 0.661714442 0.069561367 981.7885197 2168093.228 0.015672943 0.24663409 56213.53207 -4.749840874 -0.311092611 TVEDEDQDS(ph)EEEKDNDSYIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TVEDEDQDSEEEKDNDSYIK 20 1 Q9Y5T5-4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5 Q9Y5T5-4 USP16 Ubiquitin carboxyl-terminal hydrolase 16 1 TVEDEDQDS(1)EEEKDNDSYIK;TVEDEDQDS(1)EEEKDNDSYIK;TVEDEDQDS(1)EEEKDNDSYIK 314.05 1.39E-66 958280000 3170820 1198000 1726750 1719560 1695070 1204870 2368820 1387130 1956520 TRUE FALSE 2972364.036 1286701.167 1767709.325 1763686.821 1561946.04 1552696.41 2013637.432 1560316.234 1629964.172 1.823576301 0.78940457 1.084508086 1.082040238 0.958270167 0.952595423 1.235387542 0.957270264 1 20.63640882 4.748678476 24.85777573 1.016718667 1.823576781 0.831676008 0.115321675 548.3720968 1347223.521 0.028289081 0.386606475 56063.2765 -4.748678476 0.806858114 TVEGVLIVHEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TVEGVLIVHEHR 12 0 O43809;H3BND3;H3BV41 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 ;; 103.75 0.0012793 482447000 378026 406541 413282 426641 465269 357914 416096 439653 324123 FALSE TRUE 354366.0275 436641.7186 423085.2442 437589.3304 428728.6495 461237.9616 353706.2676 494544.6448 270024.7774 1.312346337 1.617043158 1.5668386 1.620552509 1.587738183 1.708131994 1.309903006 1.831478761 1 18.04273227 -1.188322446 3.818591994 0.999561824 1.562749698 0.559064314 0.158785216 4567915.817 2132304.429 16191.86088 0.032885814 0.064815303 1.188322446 0.563187873 TVEIVHIDIADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TVEIVHIDIADR 12 0 A0A0A0MSW4;P48739;P48739-3;P48739-2;B3KYB7;B3KYB6 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 ;;;;; 172.99 3.43E-05 1334470000 1900800 2157690 2035800 2162700 2218860 1805460 2325960 1943430 2237370 FALSE TRUE 1781832.321 2317447.613 2084090.137 2218198.543 2044599.686 2326666.993 1977203.891 2186071.514 1863938.493 0.955950171 1.243306912 1.118111003 1.190059947 1.096924439 1.248253095 1.060766704 1.172823847 1 20.82992282 -1.253729738 4.78353567 0.99996145 1.14317008 0.188287311 0.087404588 3.10E-05 4.84E-06 0.073008277 0.017203587 0.055753259 1.253729738 0.14320863 TVEMHNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 TVEMHNK 7 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;;;;;; 114.02 0.0059982 1865496000 3717520 3979590 3564470 3327220 4176790 2354123 3448130 3762880 4982230 FALSE TRUE 3484847.059 4274242.984 3649020.912 3412602.098 3848761.762 3033720.094 2931114.917 4232683.851 4150663.627 0.839587924 1.029773397 0.879141564 0.822182283 0.927264194 0.730900012 0.706179826 1.01976075 1 21.98491059 3.558404481 3.329414847 0.83701689 0.949880905 0.004916562 0.113193944 0.438496196 9.413355505 0.030281629 0.048470118 3617.466193 -3.558404481 0.112864015 TVENIKDPLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVENIKDPLFR 11 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 102.87 0.0025629 1377880000 3976700 4254400 4292300 4394000 4843100 3553600 5719600 4551000 5231300 FALSE TRUE 3727805.446 4569400.203 4394115.383 4506757.479 4462742.462 4579466.632 4861999.078 5119202.368 4358162.235 0.855361789 1.048469505 1.008249612 1.03409585 1.023996405 1.050779293 1.115607638 1.174624094 1 22.05528847 5.524962694 1.208188904 1.062209297 6.04E-146 0.573222229 0.053674227 6.722153372 2.053918689 0.015315212 14.16209619 334936.6668 -5.524962694 -1.062209297 TVEVAEGEAVRT(ph)PQSVTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVEVAEGEAVRTPQSVTAK 19 1 E5RJU9;Q86UE4;H0YB56 E5RJU9 MTDH Protein LYRIC 1 TVEVAEGEAVRT(0.998)PQS(0.002)VTAK;TVEVAEGEAVRT(1)PQSVTAK 280.21 2.04E-39 587890000 651440 492580 497430 540160 616460 414810 685060 499860 789170 TRUE FALSE 610667.5333 529051.1357 509229.2745 554021.4201 568045.7183 534558.9131 582341.6128 562268.6213 657452.4288 0.928839117 0.804698732 0.774549233 0.842679099 0.864010373 0.813076186 0.885754752 0.855223278 1 19.32652698 0.30267744 0.555274318 1.008493253 0.824268186 0.543790977 0.043779162 1.783459215 0.830219302 0.077416069 0.019352837 2.007601171 -0.30267744 -0.184225067 TVFAEHISDECK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TVFAEHISDECK 12 0 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ;;;;; 209.19 5.81E-08 8120210000 9473270 11642780 11980750 12278980 12872840 10559550 17499900 11216630 14049920 FALSE TRUE 8880354.941 12504823.55 12264939.05 12594079.42 11861859.07 13607920.67 14875952.46 12617050.95 11704897.59 0.758687112 1.068341133 1.047846763 1.075966648 1.013409898 1.162583488 1.270916926 1.077929205 1 23.48060898 5.279561691 1.252522735 1.112172801 6.23E-29 0.611268 0.081000495 3.514364819 1.85121181 0.02434836 7.014956614 190353.8613 -5.279561691 -1.112172801 TVFAEHISDECKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVFAEHISDECKR 13 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ; 210.41 1.96E-08 1299030000 772020 1073650 1108400 1111770 1130680 881010 1485370 1038360 1247730 FALSE TRUE 723700.6463 1153144.163 1134691.771 1140299.9 1041880.954 1135343.285 1262652.558 1168001.532 1039475.802 0.696216925 1.109351618 1.091599986 1.096995137 1.002313812 1.092226757 1.214701251 1.123644754 1 19.98742474 4.739212816 24.87378195 1.101776635 0.696216793 0.803367028 0.061243167 21.79439239 831011.864 0.01493496 0.089116746 54854.57018 -4.739212816 -0.405559842 TVFDEAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVFDEAIR 8 0 P63000;J3KSC4;J3QLK0;P60763;P63000-2;B1AH77;B1AH80;P15153 P63000 RAC1;RAC3;RAC2 Ras-related C3 botulinum toxin substrate 1;Ras-related C3 botulinum toxin substrate 3;Ras-related C3 botulinum toxin substrate 2 0 94.114 0.022202 0 94173 106710 82092 80979 119430 71639 96769 96429 125430 FALSE TRUE 88278.88003 114610.9194 84039.26101 83057.05824 110050.4496 92320.01634 82259.38681 108468.3729 104494.9227 0.844815018 1.0968085 0.80424253 0.794843004 1.05316552 0.883488058 0.787209414 1.038025295 1 16.67307332 3.967344492 24.69816681 0.892105483 0.984025572 0.030254271 0.1150995 632.9877391 1599066.229 0.027354769 0.050120569 9275.652972 -3.967344492 0.091920089 TVFPGAVPVLPAS(ph)PPPK ddPTM_SK-BR-3_Pertuzumab_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 134.85 1.63E-05 154379000 613810 382810 506460 512000 462900 433480 551940 411670 391560 TRUE FALSE 575392.7278 411153.6507 518473.4704 525138.7868 426545.7012 558618.639 469181.721 463067.9057 326206.1064 1.763893184 1.26041065 1.589404552 1.60983739 1.307595697 1.712471435 1.4382984 1.419556215 1 18.31542426 0.670958051 1.76609346 1.000372122 1.5088226 0.514255832 0.159589725 1.07651324 4.67223473 0.136930453 0.038572162 4.687681013 -0.670958051 0.508450478 TVFPGAVPVLPAS(ph)PPPKDSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TVFPGAVPVLPASPPPKDSLR 21 1 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4;M0R2S2 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 TVFPGAVPVLPAS(1)PPPKDSLR;TVFPGAVPVLPAS(1)PPPKDSLR;TVFPGAVPVLPAS(1)PPPKDSLR 192.18 7.12E-18 4230055000 2203596 2045112 2076383 2251879 2436283 1601932 2343136 1742682 2583618 TRUE FALSE 2065676.86 2196534.22 2125635.785 2309666.028 2244947.161 2064383.763 1991804.509 1960259.684 2152395.465 0.959710654 1.020506806 0.987567489 1.073067689 1.042999392 0.959109883 0.925389661 0.910733978 1 21.03751174 2.087239831 5.364440715 0.938256617 1.015592518 0.44449595 0.03765231 0.169763929 8.035186266 0.013877164 0.010088821 122.2474563 -2.087239831 0.077335901 TVFRPPLDIYDVLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVFRPPLDIYDVLIR 15 1 Q9H6R4-4;Q9H6R4;A0A0C4DFX0 Q9H6R4-4 NOL6 Nucleolar protein 6 0 ; 121.45 0.00010487 131939000 195313 247910 240080 228510 276120 197821 288290 234240 269070 FALSE TRUE 183088.708 266265.5144 245774.811 234373.9535 254434.649 254928.7113 245063.5909 263485.3796 224160.4787 0.816775147 1.18783434 1.096423475 1.045563227 1.135055789 1.137259845 1.093250658 1.17543191 1 17.77417242 4.747283055 24.99081397 1.114618596 0.816774995 0.72485742 0.056453358 551.1678667 1579126.537 0.012153986 0.145681321 55883.43011 -4.747283055 -0.297843601 TVFS(ph)PTLPAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 TVFSPTLPAAR 11 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 T(0.001)VFS(0.991)PT(0.008)LPAAR;TVFS(0.996)PT(0.004)LPAAR;T(0.001)VFS(0.998)PT(0.001)LPAAR;TVFS(1)PTLPAAR;TVFS(1)PTLPAAR;TVFS(0.968)PT(0.032)LPAAR;TVFS(0.735)PT(0.265)LPAAR 183.08 5.77E-06 2846676000 2990544 3037483 3139719 3263297 3360814 2625945 3672485 2692646 3381640 TRUE FALSE 2803371.189 3262381.402 3214194.617 3347038.726 3096869.225 3384012.693 3121829.968 3028828.78 2817222.438 0.995083367 1.158013424 1.140909065 1.18806335 1.099263297 1.201187612 1.108123351 1.075111691 1 21.42584205 1.011559114 2.0862336 1.001351874 1.136373373 0.341300439 0.056906335 0.311039015 2.884195292 0.048219527 0.013436201 10.26973208 -1.011559114 0.135021499 TVHRDS(ph)EEEDDYLFDDPLPIPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVHRDSEEEDDYLFDDPLPIPLR 23 1 B3KSJ7;Q96SD1-2;Q96SD1-3;Q96SD1 B3KSJ7 DCLRE1C Protein artemis 1 T(0.011)VHRDS(0.989)EEEDDYLFDDPLPIPLR;T(0.125)VHRDS(0.875)EEEDDYLFDDPLPIPLR 143.8 9.53E-08 132141000 69066 67659 70305 72519 72041 63371 84066 63149 70254 TRUE FALSE 64743.28235 72668.54276 71972.6678 74379.96031 66383.19046 81665.17896 71461.08373 71033.29166 58528.15354 1.106190413 1.241599783 1.229710207 1.270840712 1.134209546 1.39531446 1.220969387 1.213660219 1 15.83684314 -0.612163234 7.16736744 1.000000011 1.233382513 0.454743844 0.077647525 0 0 0.066770895 0.015738051 0.244251233 0.612163234 0.233382502 TVHTEWTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TVHTEWTQR 9 0 C9JIF9;P13798;H7C393 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 ;;; 145.72 9.65E-05 1493350000 161352 502191 232729 258573 465672 254091 273216 401145 343844 FALSE TRUE 151253.2663 539373.7442 238249.4418 265208.4209 429099.9996 327442.9469 232249.7972 451228.8363 286454.2151 0.528018994 1.882931777 0.831719099 0.925831798 1.497970625 1.143089994 0.810774585 1.575221493 1 18.12794504 -4.999999958 0.146423355 0.47684378 1.214025741 0 0.411434048 918.1079397 8.080793584 143.0056563 2.082481404 1.00E-05 4.999999958 0.737181961 TVIDKCS(ph)PPLEFLDDSDSHLEIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TVIDKCSPPLEFLDDSDSHLEIQK 24 1 Q93075;H7C1W4 Q93075 TATDN2 Putative deoxyribonuclease TATDN2 1 TVIDKCS(1)PPLEFLDDSDSHLEIQK;T(0.002)VIDKCS(0.998)PPLEFLDDSDSHLEIQK;TVIDKCS(1)PPLEFLDDSDSHLEIQK 192.42 4.33E-18 237474000 667904 395530 491936 482111 560882 421105 782433 462490 782801 TRUE FALSE 626101.0809 424815.4527 503604.9542 494482.7845 516832.5902 542671.1774 665114.4354 520232.8946 652146.456 0.960062077 0.651411119 0.772226775 0.758238859 0.792510004 0.832130839 1.019885072 0.797724023 1 19.31483647 1.990744426 4.080975961 0.939872989 0.76674415 0.333941308 0.09550818 0.200061618 7.562168674 0.039160467 0.024503741 97.89137439 -1.990744426 -0.173128839 TVIDYNGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TVIDYNGER 9 0 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ;;;;; 186.54 9.67E-05 5023020000 5653630 8483440 6101410 6670200 8098660 4438540 6153780 6703410 5972180 FALSE TRUE 5299779.39 9111562.725 6246138.326 6841368.625 7462623.912 5719874.444 5231077.818 7540345.495 4975384.576 1.065199948 1.831328329 1.255408146 1.375043179 1.499908961 1.149634638 1.051391654 1.515530182 1 22.24637661 2.233460527 24.98001256 1.16806894 1.441632658 0.176130961 0.235467406 175.109741 857670.3904 0.081128666 0.061742694 171.1829581 -2.233460527 0.273563718 TVIIEQSWGS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TVIIEQSWGSPK 12 0 P10809;E7EXB4;E7ESH4;P10809-2;C9JCQ4;C9JL25;C9JL19 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 1 TVIIEQSWGS(1)PK;TVIIEQSWGS(1)PK;TVIIEQSWGS(1)PK 236.4 4.71E-16 417981000 1592220 927830 1067890 996880 1384040 862220 1144920 1080780 1714650 TRUE FALSE 1492565.792 996527.4986 1093220.855 1022461.629 1275343.081 1111128.917 973249.8749 1215717.762 1428463.838 1.044874748 0.697621789 0.765312237 0.715777048 0.892807397 0.777848824 0.681326225 0.85106653 1 20.44603308 0.986732875 23.22204634 1.000000009 0.777801358 0.248765034 0.107648499 320.2352956 560524.782 0.094209561 0.02355239 9.699132117 -0.986732875 -0.222198651 TVIIHDRPDITHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TVIIHDRPDITHPR 14 1 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 0 ;;; 142.45 6.06E-06 692541000 416925 465602 481661 432429 516279 404933 516976 391241 592818 FALSE TRUE 390830.4085 500075.6565 493086.2264 443525.8602 475732.5299 521830.5836 439460.2482 440088.3001 493872.846 0.791358366 1.012559529 0.998407243 0.898056785 0.963269258 1.056609181 0.889824682 0.891096369 1 18.91378012 -0.93602897 3.850971478 1.000003878 0.95020128 0.039918178 0.076590269 19582022.41 37091217.09 1045.366462 0.017406559 0.115870006 0.93602897 -0.049802597 TVIQAEIDAAAELIDFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVIQAEIDAAAELIDFFR 18 0 P30038-2;P30038;P30038-3;Q5TF55 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 102.28 0.001324 48967000 66798 44738 63801 73069 64274 62039 55160 37309 58787 FALSE TRUE 62617.23242 48050.44807 65314.38985 74944.07425 59226.17931 79948.65218 46889.27008 41967.11078 48975.06992 1.278553201 0.981120561 1.33362525 1.530249459 1.209312808 1.632435692 0.957410988 0.856907624 1 15.57975993 1.597278648 10.11599703 0.92451249 1.292525306 0.506908858 0.178966843 0.086874753 26.0754446 0.095037928 0.046042532 39.56203727 -1.597278648 0.368012816 TVIQIHMCEEEEGDLLLFLTGQEEIDEACKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVIQIHMCEEEEGDLLLFLTGQEEIDEACKR 31 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 236.61 5.94E-46 30068000 84390 68150 72851 74213 85649 82902 109280 77375 111600 FALSE TRUE 79108.18054 73195.89691 74579.06012 76117.43122 78922.47303 106834.4616 92894.47851 87035.43907 92973.23904 0.850870437 0.787279196 0.8021562 0.818702586 0.848873007 1.149088304 0.999152869 0.936134311 1 16.5045279 2.382972515 7.085647513 1.022616721 0.810611363 0.768042204 0.054713904 0.095556872 6.168302896 0.018166308 0.015157353 241.5307971 -2.382972515 -0.212005359 TVIVHGFTLGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVIVHGFTLGEK 12 0 Q9NSE4 Q9NSE4 IARS2 "Isoleucine--tRNA ligase, mitochondrial" 0 ; 156.69 5.92E-05 206920000 682120 583800 555630 511930 804000 483320 590170 702890 1111740 FALSE TRUE 639427.3268 627025.1594 568809.806 525066.9905 740857.0832 622846.638 501679.4874 790647.3638 926183.4119 0.690389526 0.676998909 0.614143806 0.566914699 0.799903209 0.67248736 0.541663218 0.853661762 1 19.82093839 1.032402905 5.068529316 0.999010145 0.649328214 0.736706723 0.071269705 0.076832069 4.924011714 0.067054778 0.01695737 10.7746434 -1.032402905 -0.349681931 TVKEEAEKPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TVKEEAEKPER 11 2 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;; 109.84 0.0010541 3779010000 9118780 5903020 7159480 7283010 7928550 4751640 9351890 5948820 10293250 FALSE TRUE 8548051.837 6340085.743 7329306.247 7469904.367 7305873.665 6123361.332 7949660.913 6691543.272 8575240.078 0.996829448 0.7393479 0.854705662 0.871101485 0.851973076 0.714074624 0.927048204 0.780333053 1 23.03174563 -1.524038281 3.295379665 1.00441201 0.83611689 0.257433121 0.083857221 31050569.89 40875228.56 1229725.501 0.017878261 0.029920009 1.524038281 -0.16829512 TVKPVENKDDDDSIADFLNS(ph)DEEEDRVSLQNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TVKPVENKDDDDSIADFLNSDEEEDRVSLQNLK 33 3 Q15649-2;Q15649 Q15649-2 ZNHIT3 Zinc finger HIT domain-containing protein 3 1 TVKPVENKDDDDS(0.001)IADFLNS(0.99)DEEEDRVS(0.009)LQNLK;TVKPVENKDDDDSIADFLNS(1)DEEEDRVSLQNLK;TVKPVENKDDDDSIADFLNS(1)DEEEDRVSLQNLK 252.4 2.37E-59 897620000 716487 271027 426124 383466 408976 271824 565774 340060 586166 TRUE FALSE 671643.3576 291094.1211 436231.8625 393306.3868 376856.6747 350295.1761 480941.4411 382517.2396 488331.1078 1.375385157 0.596099893 0.893311639 0.805409241 0.77172367 0.717331275 0.984867508 0.783315323 1 18.89750016 -1.713032623 6.486014831 1.002154022 0.843496231 0.029532913 0.208891106 0.005787479 0.000256062 0.179905971 0.041871699 0.019362765 1.713032623 -0.158657791 TVLELQYVLDKLGDDEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVLELQYVLDKLGDDEVR 18 1 Q14444-2;Q14444;G3V153;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ; 285.5 1.08E-39 1205740000 1172390 1219160 1195830 1216870 1562250 958070 1508890 1128830 2129100 FALSE TRUE 1099012.203 1309427.875 1224195.652 1248096.944 1439557.187 1234649.256 1282645.952 1269766.91 1773739.455 0.619601824 0.738230111 0.690177832 0.703652918 0.8115945 0.696071372 0.723130981 0.715870026 1 20.75836268 -5 0.311418447 3.550077057 0.70148646 0.796014465 0.046074273 124.384182 1.123842209 208.2080507 0.039619845 1.00E-05 5 -2.848590597 TVLPTVPES(ph)PEEEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TVLPTVPESPEEEVK 15 0 O75152;E9PBY7;E9PQ61;A0A1W2PPR9 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 TVLPTVPES(1)PEEEVK;TVLPT(0.001)VPES(0.999)PEEEVK;TVLPTVPES(1)PEEEVK;TVLPTVPES(1)PEEEVK 293.52 5.83E-44 490663000 1544990 960490 1186160 1057080 1115180 807680 1299620 937790 1490820 TRUE FALSE 1448291.834 1031605.679 1214296.275 1084206.462 1027598.261 1040844.104 1104754.046 1054875.146 1241992.511 1.166103516 0.830605394 0.977700159 0.872957327 0.82737879 0.838043785 0.889501375 0.849340988 1 20.24422504 4.745175631 24.75286118 0.883295585 1.166103664 0.68728477 0.059424206 369.8323719 1383841.861 0.013202237 0.127667576 55612.9113 -4.745175631 0.282808078 TVLS(ph)LFDEEEDKMEDQNIIQAPQK ddPTM_SK-BR-3_Pertuzumab_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(0.121)VLS(0.879)LFDEEEDKMEDQNIIQAPQK;TVLS(1)LFDEEEDKMEDQNIIQAPQK;T(0.025)VLS(0.975)LFDEEEDKMEDQNIIQAPQK 234.95 1.38E-37 134694000 245024 159777 175837 238427 307678 114772 317246 210845 285882 TRUE FALSE 229688.3852 171607.0553 180007.9367 244545.4405 283514.211 147904.8132 269677.9075 237169.4624 238166.4473 0.964402786 0.720534136 0.755807288 1.026783761 1.190403662 0.621014483 1.132308562 0.995813915 1 17.86161066 3.239219937 24.99973191 0.993257738 0.785389234 0.211332178 0.161613335 22.03882387 835630.1463 0.042530956 0.054309381 1734.68226 -3.239219937 -0.207868504 TVLSANADHMAQIEGLMDDVDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVLSANADHMAQIEGLMDDVDFK 23 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 206.94 1.28E-24 221100000 464970 423650 451450 473760 497670 356710 592450 415660 462520 FALSE TRUE 435868.3577 455017.4868 462158.6072 485917.4837 458585.0057 459686.3863 503617.6225 467556.066 385322.424 1.131178282 1.180874661 1.199407505 1.261067235 1.19013319 1.192991525 1.307003152 1.213415148 1 18.55570662 4.786409865 1.059337338 1.215051702 1.085087924 0.0113476 0.080438377 4.577466169 3.903874527 0.02162765 0.68724009 61151.8873 -4.786409865 -0.129963778 TVLSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TVLSSAR 7 0 Q6GYQ0-2;A0A1B0GUI1;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5;Q6GYQ0-6 Q6GYQ0-2 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 0 ;;; 148.28 0.0048727 2245650000 1265370 2508860 1038430 988630 2785020 906570 1092130 1901020 2225400 FALSE TRUE 1186172.75 2694618.605 1063062.05 1013999.92 2566295.763 1168282.042 928375.2453 2138366.532 1853966.363 0.639802735 1.453434463 0.573398779 0.546935446 1.384219161 0.630152771 0.500750857 1.153400932 1 20.82218364 3.957423999 22.8036986 0.788630234 1.093320231 0.052925859 0.346498674 272.0876843 314999.2527 0.083174511 0.150331892 9066.172934 -3.957423999 0.304689998 TVMDGGLES(ph)DGPNMTENGLEDESRPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVMDGGLESDGPNMTENGLEDESRPQR 27 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 TVMDGGLES(1)DGPNMTENGLEDESRPQR;TVMDGGLES(1)DGPNMTENGLEDESRPQR 217.83 2.04E-34 754180000 399380 389790 409930 391100 376700 328710 452540 338760 369600 TRUE FALSE 374383.5187 418650.4572 419653.7332 401136.2881 347115.5015 423603.2408 384685.8282 381054.9317 307911.3723 1.215880777 1.359645972 1.3629043 1.30276542 1.127322771 1.375731067 1.249339462 1.237547444 1 18.23215563 -1.911492302 0.274472818 0.690674173 1.327607684 0.574942385 0.075966805 20.14006699 0.868847416 4.085341753 0.093489643 0.012260486 1.911492302 0.636933511 TVNESHGSVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVNESHGSVER 11 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 91.093 0.010998 446420000 79866 175530 152570 145750 153770 123040 143960 170110 162790 FALSE TRUE 74867.32962 188526.4238 156189.0324 149490.1918 141693.5245 158559.6506 122374.5345 191348.608 135619.2973 0.552040389 1.390115032 1.151672627 1.102278176 1.044788811 1.169152574 0.902338656 1.410924638 1 17.04920295 3.009134762 19.73388772 1.08691284 1.125570434 0 0.248270642 163.645097 353475.5954 0.066990633 0.079799735 1021.256332 -3.009134762 0.038657594 TVPAHVETVVLFFPDVWHCLPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVPAHVETVVLFFPDVWHCLPTR 23 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 176.54 1.42E-13 65211000 78071 87399 71651 90436 106940 67275 94846 76687 97255 FALSE TRUE 73184.67547 93870.1129 73350.59556 92756.74087 98541.36378 86696.20038 80624.72281 86261.54076 81022.51221 0.903263469 1.158568284 0.905311296 1.144826769 1.216222024 1.070026071 0.995090384 1.064661394 1 16.3060352 4.763926383 23.50153439 1.063264788 0.903263015 0.249704669 0.089924776 5495.539898 5091463.067 0.021391942 1.391499596 58066.59812 -4.763926383 -0.160001773 TVPLFPHPPVPSLSTSESKPPPQPS(ph)PPT(ph)SPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVPLFPHPPVPSLSTSESKPPPQPSPPTSPVR 32 1 E9PKC0;Q6IQ23;Q6IQ23-2;H0YDE2;Q6IQ23-3;A0A1B0GUN0;A0A1B0GUM1 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 2 TVPLFPHPPVPSLSTSESKPPPQPS(0.998)PPT(0.533)S(0.469)PVR 112.34 4.71E-05 273390000 453610 309490 400240 423290 465020 285520 360510 249440 318410 TRUE FALSE 425219.3598 332404.9616 409733.8818 434152.338 428499.205 367944.989 306454.8723 280583.1331 265265.314 1.602996462 1.253103757 1.544619142 1.636672098 1.615360857 1.38708293 1.155276835 1.057745277 1 18.01707652 1.704537182 2.281735885 1.037724254 1.499779374 0.78376812 0.110682999 0.142780261 1.585596257 0.080960976 0.033761208 50.64507073 -1.704537182 0.46205512 TVPLFPHPPVPSLSTSESKPPPQPS(ph)PPTSPVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVPLFPHPPVPSLSTSESKPPPQPSPPTSPVR 32 1 E9PKC0;Q6IQ23;Q6IQ23-2;H0YDE2;Q6IQ23-3;A0A1B0GUN0;A0A1B0GUM1 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 TVPLFPHPPVPSLSTSESKPPPQPS(0.984)PPT(0.013)S(0.003)PVR;TVPLFPHPPVPSLSTSESKPPPQPS(0.958)PPT(0.021)S(0.021)PVR 178.5 1.19E-19 1805540000 1442530 1279840 1314180 1116260 1335160 1095160 1687250 1414690 2002900 TRUE FALSE 1352244.622 1374600.685 1345352.97 1144905.121 1230301.919 1411314.914 1434262.526 1591317.161 1668603.051 0.81040522 0.823803291 0.806275027 0.686145888 0.737324506 0.845806265 0.859558854 0.953682279 1 20.67020936 1.385348205 1.431661728 0.997639853 0.782935688 0.776470345 0.043239103 0.196851402 0.758486145 0.042475501 0.013578501 24.2855646 -1.385348205 -0.214704165 TVPST(ph)PTLVVPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TVPSTPTLVVPHR 13 0 P12270 P12270 TPR Nucleoprotein TPR 1 T(0.015)VPS(0.481)T(0.502)PT(0.001)LVVPHR;T(0.001)VPS(0.028)T(0.971)PTLVVPHR;T(0.001)VPS(0.069)T(0.93)PTLVVPHR;T(0.001)VPS(0.013)T(0.986)PTLVVPHR;T(0.001)VPS(0.037)T(0.962)PTLVVPHR 181.26 4.49E-05 2493500000 1424453 1756170 2090180 3662920 3091760 1296510 1308338 881158 1079228 TRUE FALSE 1335299.029 1886198.654 2139760.057 3756916.729 2848945.641 1670791.39 1112164.863 991172.516 899097.8747 1.48515425 2.097879115 2.379896691 4.178540328 3.168671311 1.858297563 1.236978636 1.102407807 1 19.77811865 1.931732417 3.151445298 1.146357563 2.612578649 0.500617457 0.703131653 0.246929879 4.454757876 0.381419645 0.211061758 85.45400403 -1.931732417 1.466221086 TVQGSGHQEHINIHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TVQGSGHQEHINIHK 15 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;; 134.88 1.13E-05 1447040000 1076840 1138040 1142340 1204790 1221870 926110 1372230 1115030 1409050 FALSE TRUE 1009442.507 1222301.666 1169436.844 1235706.951 1125909.259 1193462.923 1166476.851 1254243.95 1173870.452 0.859926668 1.041257716 0.996223086 1.052677447 0.959142686 1.016690488 0.993701518 1.068468797 1 20.16284177 4.74477996 24.94521495 1.014022929 0.859926598 0.702790024 0.031877636 349.1423261 1400339.088 0.006740259 0.061883405 55562.26731 -4.74477996 -0.154096331 TVQS(ph)LEIDLDSMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 TVQSLEIDLDSMR 13 0 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;T(0.001)VQS(0.999)LEIDLDSMR;TVQS(1)LEIDLDSMR;T(0.034)VQS(0.966)LEIDLDSMR 279.44 2.48E-32 1870554000 1479844 1545177 1554642 1555005 1772870 1262672 1634575 1427632 1841909 TRUE FALSE 1387223.206 1659583.513 1591518.842 1594909.061 1633635.942 1627184.909 1389485.653 1605874.998 1534482.489 0.904033259 1.081526524 1.037169765 1.039379121 1.064616868 1.060412824 0.905507664 1.046525464 1 20.54932075 -0.902715709 4.801783973 0.999999891 1.020332992 0.005625749 0.062676297 7.19E-08 1.64E-08 0.059544216 0.014034631 0.125107772 0.902715709 0.020333102 TVQSLEIDLDSMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 20 TVQSLEIDLDSMR 13 0 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;;;;;;;; 322.77 7.60E-51 12552772000 7489937 9079793 8376966 8066969 9290827 7390430 8972775 8157565 11164465 FALSE TRUE 7021155.213 9752070.321 8575671.589 8273981.082 8561162.925 9523927.167 7627390.688 9176054.947 9301043.666 0.754878212 1.048492048 0.922011754 0.889575555 0.920451858 1.023963279 0.820057508 0.986561861 1 23.14896118 1.02668453 24.90368759 1.00000053 0.924484698 0.123489152 0.085755619 381.5560217 356090.8425 0.075763282 0.01894082 10.63370309 -1.02668453 -0.075515832 TVQTDHNAVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVQTDHNAVQR 11 0 O43747;O43747-2 O43747 AP1G1 AP-1 complex subunit gamma-1 0 ; 184.03 5.09E-06 441930000 313060 435200 355210 412590 426890 315700 459400 362310 422730 FALSE TRUE 293466.1334 467422.6608 363635.7489 423177.7579 393363.7814 406837.465 390517.2349 407545.201 352173.6321 0.833299562 1.32725059 1.032546778 1.201616815 1.116959777 1.155218415 1.108876984 1.157228037 1 18.42592737 -1.289485114 5.244288345 0.999975462 1.130610546 0.068249068 0.126355869 3.11E-05 4.22E-06 0.105064678 0.024759333 0.051346978 1.289485114 0.130635083 TVQVVPHITDAIQEWVMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVQVVPHITDAIQEWVMR 18 0 P17812;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6;A0A3B3ITB8 P17812 CTPS1 CTP synthase 1 0 ; 217.36 8.46E-19 622290000 303294 426280 374770 391190 447650 293977 409790 376310 490600 FALSE TRUE 284311.3699 457842.2147 383659.7214 401228.5977 412493.3747 378843.3876 348345.7938 423293.1319 408715.6906 0.695621373 1.120197304 0.938695847 0.981681415 1.009242817 0.926911778 0.852293665 1.035666459 1 18.6407381 2.200856694 24.41563816 0.931343217 0.972485368 0 0.116864339 585.8910562 379396.5574 0.040436704 0.029865243 158.8022657 -2.200856694 0.041142152 TVS(ph)ASS(ph)TGDLPK ddPTM_SK-BR-3_Pertuzumab_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 TVS(1)ASS(0.866)T(0.134)GDLPK;TVS(1)ASS(0.855)T(0.145)GDLPK 276.31 1.09E-27 1139760000 4037400 2707400 3226900 3600000 3623400 2039040 3454500 2152980 3135600 TRUE FALSE 3784706.341 2907858.713 3303443.592 3692382.095 3338832.78 2627677.747 2936529.795 2421784.292 2612248.103 1.448831118 1.113163298 1.264597948 1.413488286 1.278145355 1.005906653 1.124138933 0.927088162 1 21.3168605 2.242578419 24.96707341 1.034621547 1.277338671 0.651809932 0.10363553 73.87083398 459044.5321 0.036810264 0.029749466 174.814889 -2.242578419 0.242717124 TVS(ph)DNS(ph)LSNSRGEGKPDLK ddPTM_SK-BR-3_Pertuzumab_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(0.125)VS(0.875)DNS(0.995)LS(0.005)NSRGEGKPDLK 135.62 3.98E-06 134200000 159130 132110 119330 158540 206590 86470 151380 119330 384980 TRUE FALSE 149170.3374 141891.5619 122160.564 162608.4048 190365.2547 111432.4853 128681.9743 134228.6132 320724.3509 0.465104495 0.442409694 0.380889582 0.507003613 0.593547868 0.347440052 0.401222963 0.418517062 1 18.29097437 -1.57340198 2.968705775 1.030433033 0.437863132 0.864538451 0.069057141 17021635.38 18634855.62 4098087.367 0.017627292 0.026705334 1.57340198 -0.592569901 TVS(ph)DNSLSNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TVSDNSLSNSR 11 0 Q96RU3-5;Q96RU3-2;Q96RU3;H0Y7W6;Q96RU3-3;B7ZL14;Q96RU3-4 Q96RU3-5 FNBP1 Formin-binding protein 1 1 T(0.003)VS(0.997)DNSLSNSR;TVS(0.998)DNS(0.002)LSNSR;TVS(1)DNSLSNSR;TVS(1)DNSLSNSR;T(0.007)VS(0.989)DNS(0.004)LSNSR 251.85 2.38E-20 2937700000 2147740 2142575 2207759 2145931 2328810 1871884 2379050 1916858 2222660 TRUE FALSE 2013316.787 2301213.482 2260128.086 2200999.223 2145914.657 2412266.523 2022333.539 2156181.941 1851683.687 1.087289801 1.242768135 1.220580006 1.18864752 1.158899153 1.302742223 1.092159289 1.16444399 1 20.82040624 0.791429793 0.943482069 1.001758417 1.202846914 0.451638493 0.063984171 0.672578567 1.152349332 0.055112866 0.018327767 6.186283138 -0.791429793 0.201088497 TVS(ph)FEALPIMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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;T(0.002)VS(0.998)FEALPIMR;T(0.001)VS(0.999)FEALPIMR;T(0.001)VS(0.999)FEALPIMR;TVS(1)FEALPIMR;T(0.001)VS(0.999)FEALPIMR 210.95 1.15E-08 614225000 756370 778699 673057 755507 616841 475602 815125 571258 710626 TRUE FALSE 709030.1519 836354.6842 689022.2299 774894.5887 568396.7961 612900.5766 692904.5735 642580.8188 592017.9298 1.197649794 1.412718504 1.163853652 1.308903919 0.960100645 1.035273673 1.170411467 1.085407699 1 19.17528134 2.751895244 24.96526775 1.068473311 1.276616348 0.614314347 0.086107844 542.2215182 1015153.74 0.026131266 0.027574677 564.8007228 -2.751895244 0.208143037 TVS(ph)LCDITITQMLEEDSNQGHLIGDFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVSLCDITITQMLEEDSNQGHLIGDFSK 28 0 P30307-4;P30307-3;P30307-2;P30307;H0Y999 P30307-4 CDC25C M-phase inducer phosphatase 3 1 T(0.002)VS(0.997)LCDIT(0.001)ITQMLEEDSNQGHLIGDFSK;T(0.331)VS(0.66)LCDIT(0.008)IT(0.001)QMLEEDSNQGHLIGDFSK 359.84 1.48E-111 141030000 123302 118166 108756 111317 107992 80243 175752 99941 148214 TRUE FALSE 115584.7479 126915.1336 111335.7437 114173.5827 99510.74394 103407.8515 149399.6192 112418.8538 123476.1259 0.936089848 1.0278516 0.901678303 0.924661199 0.805910804 0.837472432 1.209947414 0.910450122 1 16.9138726 1.757719753 25 1.059479855 0.91615952 0.301001098 0.094215465 9.411484389 12292.42511 0.042459204 0.023546153 57.24265288 -1.757719753 -0.143320335 TVS(ph)PGS(ph)VSPIHGQGQVVENLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 2 T(0.009)VS(0.991)PGS(0.714)VS(0.287)PIHGQGQVVENLK;T(0.011)VS(0.987)PGS(0.619)VS(0.383)PIHGQGQVVENLK;T(0.038)VS(0.962)PGS(0.562)VS(0.438)PIHGQGQVVENLK 261.78 6.17E-37 1788790000 2697880 2115930 2339490 2143480 2428460 2035820 3136460 2364400 3647630 TRUE FALSE 2529024.507 2272595.659 2394983.808 2198485.326 2237738.548 2623528.185 2666176.94 2659600.545 3038816.988 0.832239821 0.747855388 0.788130321 0.723467499 0.736384769 0.863338659 0.877373317 0.875209187 1 21.53507836 1.391256774 0.839270012 0.987018033 0.764369397 0.76680575 0.040352181 0.246185678 0.368839552 0.03642238 0.014200768 24.61822709 -1.391256774 -0.222648636 TVS(ph)PGSVS(ph)PIHGQGQVVENLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 2 T(0.025)VS(0.973)PGS(0.088)VS(0.913)PIHGQGQVVENLK;T(0.003)VS(0.996)PGS(0.005)VS(0.995)PIHGQGQVVENLK;TVS(1)PGS(0.007)VS(0.993)PIHGQGQVVENLK 296.86 3.46E-55 568390000 1093300 853310 974380 897940 1043200 844510 1304730 989020 1583180 TRUE FALSE 1024872.305 916489.9603 997492.7537 920982.6606 961271.2801 1088306.328 1109097.849 1112501.324 1318937.03 0.777044151 0.694870141 0.75628535 0.698276445 0.728822725 0.825138959 0.840902805 0.843483274 1 20.33094426 1.173362208 0.611138696 0.997728513 0.721435721 0.865267071 0.033049529 0.237520809 0.218409332 0.031577869 0.014378286 14.90603746 -1.173362208 -0.276292792 TVS(ph)PGSVSPIHGQGQVVENLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 1 T(0.084)VS(0.908)PGS(0.006)VS(0.001)PIHGQGQVVENLK 168.26 7.10E-12 128820000 168240 158350 152820 154480 199180 138310 218540 160040 236990 TRUE FALSE 157710.1587 170074.3988 156444.9626 158444.2183 183537.2063 178237.8517 185771.9558 180021.3463 197434.838 0.798795999 0.861420408 0.792387829 0.802513984 0.92960902 0.902767989 0.940927942 0.911801322 1 17.59101705 2.733136051 24.61136937 0.931210599 0.818154408 0.785131214 0.031919883 163.03911 739709.9076 0.009411685 0.00911326 540.9237513 -2.733136051 -0.113056191 TVS(ph)PPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVSPPIR 7 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 TVS(1)PPIR;T(0.001)VS(0.999)PPIR 117.81 0.0053992 1966280000 283555 569550 401410 383090 652020 420899 448840 495650 666380 TRUE FALSE 265807.7987 611720.0746 410931.6348 392920.738 600812.9793 542405.7086 381540.6088 557532.9936 555156.873 0.478797637 1.10188688 0.740208137 0.707765241 1.082240009 0.977031421 0.687266298 1.004280088 1 19.08253597 2.76506505 24.97822802 0.91312042 0.811792173 0.170825198 0.185753867 2273.807461 2142870.945 0.055723172 0.059088792 582.1904132 -2.76506505 -0.101328247 TVS(ph)PPIRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 TVSPPIRK 8 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 T(0.009)VS(0.991)PPIRK;T(0.035)VS(0.965)PPIRK;T(0.034)VS(0.966)PPIRK;T(0.024)VS(0.976)PPIRK;T(0.023)VS(0.977)PPIRK;T(0.042)VS(0.958)PPIRK;T(0.022)VS(0.978)PPIRK 86.18 0.0099325 8754780000 9137760 7751020 8984100 8175900 8810970 7162390 9892640 7930470 12329900 TRUE FALSE 8565843.913 8324913.586 9197207.095 8385707.436 8118991.958 9230055.721 8409330.471 8920606.637 10271960.04 0.833905494 0.810450348 0.895370218 0.816368775 0.790403383 0.898568111 0.818668535 0.868442498 1 23.29220816 0.885245501 5.849000062 0.999998574 0.840454713 0.679411428 0.034798369 0.86014607 43.50036859 0.031159148 0.007839882 7.677953911 -0.885245501 -0.159543861 TVS(ph)PSTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVSPSTIR 8 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 1 T(0.02)VS(0.923)PS(0.048)T(0.009)IR 93.098 0.011863 417220000 643250 946450 934950 950310 973900 956880 975010 885550 886550 TRUE FALSE 602990.1307 1016526.143 957127.4555 974696.5635 897413.8225 1233115.722 828816.302 996112.8668 738579.0777 0.816419188 1.376326752 1.29590383 1.319691544 1.215054487 1.669578464 1.122176795 1.348688173 1 19.49439287 -1.126930498 3.644097591 0.999818387 1.287576809 0.131724023 0.214280001 28538804.4 45917047.6 62635.77456 0.045538594 0.074656822 1.126930498 0.287758421 TVS(ph)SDGCSTPSREEGGCSLASTPATTLHLLQLSGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVSSDGCSTPSREEGGCSLASTPATTLHLLQLSGQR 36 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 T(0.078)VS(0.46)S(0.46)DGCS(0.001)T(0.001)PSREEGGCSLASTPATTLHLLQLSGQR 145.77 2.47E-13 636820000 13001 12735 10939 12599 15265 10768 11661 9860.6 15536 TRUE FALSE 12187.29062 13677.91265 11198.47825 12922.31167 14066.14848 13876.5468 9912.541305 11091.71762 12942.94123 0.941616778 1.056785502 0.865218967 0.998406115 1.086781453 1.072132411 0.765864661 0.856970407 1 13.65987788 1.742030301 25 0.85532804 0.996693615 0.324545399 0.086072464 0.637701409 4619.461269 0.0388163 0.021525609 55.21159596 -1.742030301 0.141365576 TVS(ph)SPIPYTPS(ph)PSSS(ph)RPISPGLSYASHTVGFTPPTSLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.077)VS(0.461)S(0.461)PIPY(0.012)T(0.052)PS(0.9)PS(0.177)S(0.179)S(0.59)RPIS(0.09)PGLSYASHTVGFTPPTSLTR 134.41 2.34E-08 304600000 17857 23840 20372 24487 22013 16336 22444 20578 25547 TRUE FALSE 16739.36225 25605.13841 20855.23346 25115.37788 20284.18778 21051.93801 19078.73056 23147.2086 21283.04066 0.786511782 1.20307708 0.97989915 1.180065305 0.953068131 0.989141464 0.896428798 1.087589361 1 14.37741666 THKPDPGT(ph)PQHTSSRPPEPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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;THKPDPGT(1)PQHTSSRPPEPQK 154.71 3.14E-08 509493000 337131 591380 678930 686200 701780 548720 908420 681970 881460 TRUE FALSE 316030.5725 635166.3905 695034.5402 703809.0537 646665.0296 707126.5563 772210.8544 767115.4557 734338.6316 0.430360816 0.86495026 0.946476885 0.95842575 0.880608757 0.962943424 1.05157324 1.044634482 1 19.48608597 4.942963554 1.516091748 0.975429458 1.29E-15 0.917118085 0.051268261 0.560911554 0.819659406 0.015063116 0.944035999 87692.72261 -4.942963554 -0.975429458 down TVS(ph)SPIPYTPS(ph)PSSSRPISPGLSY(ph)ASHTVGFTPPTSLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.447)VS(0.52)S(0.018)PIPY(0.046)T(0.067)PS(0.615)PS(0.065)S(0.063)S(0.061)RPIS(0.178)PGLS(0.149)Y(0.326)AS(0.121)HT(0.318)VGFT(0.005)PPTSLTR 69.784 0.023675 145340000 11030 19544 17412 15313 27858 16532 27509 22145 27171 TRUE FALSE 10339.65199 20991.0581 17825.02086 15705.9575 25670.14505 21304.52003 23384.28083 24909.852 22635.98457 0.456779424 0.927331349 0.787463908 0.693849099 1.134041463 0.941179296 1.033057818 1.100453657 1 14.46633044 2.742427848 24.99123044 1.034478346 0.763369835 0.600528431 0.129295434 260.167166 1681282.765 0.038082532 0.039030731 552.6215902 -2.742427848 -0.271108511 TVS(ph)SPPTS(ph)PRPGSAATVSASTSNIIPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 2 T(0.021)VS(0.537)S(0.441)PPT(0.111)S(0.89)PRPGSAATVSASTSNIIPPR 135.9 5.38E-06 968470000 355410 346440 372790 417800 390920 284410 377600 269740 335870 TRUE FALSE 333165.5225 372090.7781 381632.7548 428521.4553 360218.7201 366514.55 320982.3855 303417.6328 279811.1272 1.190680034 1.329792642 1.363894133 1.531466813 1.287363815 1.309864099 1.14713946 1.084365857 1 18.09409381 1.559574132 1.447849356 1.017034772 1.352244502 0.692799879 0.08417332 0.211200291 0.856845455 0.070857543 0.024484551 36.27221959 -1.559574132 0.33520973 TVS(ph)SSGCEGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TVSSSGCEGKR 11 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 T(0.002)VS(0.956)S(0.011)S(0.032)GCEGKR;T(0.001)VS(0.933)S(0.032)S(0.034)GCEGKR;TVS(0.987)S(0.013)SGCEGKR 94.767 0.0059084 399200000 550240 544497 532230 573061 740012 413016 678351 462501 879200 TRUE FALSE 515801.4606 584812.1244 544854.7469 587766.7154 681894.4426 532247.0144 576638.5651 520245.2679 732455.8402 0.704208271 0.798426461 0.743873852 0.802460276 0.93097004 0.726660892 0.787267346 0.710275268 1 19.48238226 -2.21640535 2.457673389 1.753332998 0.778636615 0.53823763 0.065287353 3838550.802 1035396.027 16082303.36 0.015365854 0.006075677 2.21640535 -0.974696383 TVSASS(ph)TGDLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.998)T(0.002)GDLPK;TVSAS(0.009)S(0.973)T(0.017)GDLPK;TVSAS(0.001)S(0.999)TGDLPK;TVSASS(0.997)T(0.003)GDLPK;TVSAS(0.001)S(0.996)T(0.004)GDLPK;TVSAS(0.107)S(0.89)T(0.002)GDLPK 324.41 4.55E-58 1681990000 6078620 4410030 5047070 4707910 4466420 3194520 5454930 3655570 5152510 TRUE FALSE 5698170.025 4736553.21 5166788.884 4828722.941 4115645.39 4116726.065 4637013.888 4111975.961 4292522.795 1.327464127 1.103442762 1.203671857 1.124914921 0.958794067 0.959045825 1.08025376 0.957939226 1 22.03339436 2.920282598 3.94962947 1.001052939 1.185868638 0.698012534 0.065973976 0.141389352 4.136265915 0.019651586 0.021422958 832.3051817 -2.920282598 0.184815699 TVSGPGTPEPRPAT(ph)PGASSVEQLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVSGPGTPEPRPATPGASSVEQLRK 25 2 Q9H3U1 Q9H3U1 UNC45A Protein unc-45 homolog A 1 TVSGPGTPEPRPAT(0.998)PGAS(0.001)SVEQLRK 186.35 7.42E-16 561690000 276530 371610 316410 315800 483940 238970 444150 323250 865180 TRUE FALSE 259222.4809 399124.3911 323915.3946 323903.9626 445933.3045 307956.7596 377553.8308 363608.4741 720775.8687 0.359643673 0.553742721 0.449398223 0.449382362 0.61868512 0.427257311 0.523815859 0.504468157 1 19.45919119 -5 0.362032013 7.3750905 0.476420325 0.843657082 0.069877616 167.637484 1.326384071 833.3767885 0.044820643 1.00E-05 5 -6.898670175 TVSLGAGAKDELHIVEAEAMNY(ph)EGS(ph)PIKVTLATLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLK 35 2 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 2 T(0.003)VS(0.003)LGAGAKDELHIVEAEAMNY(0.993)EGS(0.98)PIKVT(0.019)LAT(0.002)LK 57.229 0.029851 38941000 13765 11240 12065 13616 18664 5856 14895 12194 24477 TRUE FALSE 12903.47322 12072.2213 12351.1875 13965.40961 17198.20473 7546.532136 12661.63303 13716.44774 20391.63057 0.632782806 0.592018439 0.605698865 0.684859877 0.843395268 0.370079877 0.620923029 0.672650855 1 14.31568952 0.778571622 3.296824508 0.999945137 0.615188934 0.514751346 0.114497773 1.216924504 17.10801404 0.103312932 0.026787273 6.005810465 -0.778571622 -0.384756203 TVSLGAGAKDELHIVEAEAMNYEGS(ph)PIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TVSLGAGAKDELHIVEAEAMNYEGSPIK 28 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNY(0.006)EGS(0.994)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK 184.78 6.39E-18 903697000 1252080 727215 905035 862299 953049 621846 1075614 760407 1042657 TRUE FALSE 1173714.548 781058.7553 926502.8576 884427.0522 878200.376 801362.8454 914335.6662 855345.4878 868630.8109 1.351223711 0.899183802 1.066624446 1.018185219 1.011016838 0.922558624 1.052617124 0.984705443 1 19.7283836 4.748496745 24.87831922 0.99727936 1.351223917 0.825780265 0.051497817 509.7189174 1276219.308 0.011606537 0.157204621 56039.82172 -4.748496745 0.353944557 TVSLGAGAKDELHIVEAEAMNYEGS(ph)PIKVTLATLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 TVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLK 35 2 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 TVSLGAGAKDELHIVEAEAMNY(0.001)EGS(0.999)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNYEGS(0.999)PIKVT(0.001)LATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNY(0.023)EGS(0.976)PIKVT(0.001)LATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK 496.9 0 6081733000 4344755 2873897 3376001 3616383 4453560 2073135 4567586 2900475 6754796 TRUE FALSE 4072824.54 3086683.324 3456081.338 3709185.51 4103795.362 2671615.42 3882718.883 3262605.688 5627376.91 0.723751866 0.548511922 0.614154942 0.659132233 0.729255465 0.47475324 0.68996958 0.579773799 1 22.42403116 -1.129653433 3.791859272 1.000186081 0.621426423 0.684153847 0.079466872 14545934.86 28253789.71 34698.64055 0.016905108 0.074190204 1.129653433 -0.378759657 TVSLGAGAKDELHIVEAEAMNYEGSPIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 TVSLGAGAKDELHIVEAEAMNYEGSPIK 28 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;; 193.08 1.42E-18 1038931000 2065878 1847708 1908345 1997709 2406827 1281015 2391044 1721896 3275600 FALSE TRUE 1936578.384 1984514.223 1953611.845 2048973.595 2217804.516 1650823.235 2032529.15 1936878.506 2728881.199 0.709660202 0.727226317 0.715902123 0.750847489 0.812715672 0.604945073 0.744821413 0.709770182 1 21.37987816 -1.49927703 2.989291436 1.008843969 0.721946806 0.743915197 0.051262432 22186982.13 26065648.38 1618722.201 0.011246925 0.031675463 1.49927703 -0.286897163 TVSLPLSS(ph)PNIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.34)S(0.66)PNIK;TVSLPLS(0.111)S(0.889)PNIK;TVSLPLS(0.233)S(0.767)PNIK 234.82 5.20E-16 653762000 2580000 2143340 2445090 2355730 2594760 1921100 2925840 2180860 2570440 TRUE FALSE 2418522.405 2302035.124 2503088.689 2416182.02 2390978.016 2475690.384 2487137.454 2453145.172 2141416.958 1.129402845 1.075005554 1.168893652 1.128309931 1.116540152 1.156099177 1.161444736 1.145571002 1 21.0301343 -0.956135762 4.619510016 1.000000121 1.134947485 0.716609168 0.02671114 5.85E-07 1.32E-07 0.027071292 0.006380668 0.11062779 0.956135762 0.134947364 TVSLT(ph)PS(ph)PTTQVETPDLVDHDNTS(ph)PLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 3 T(0.003)VS(0.039)LT(0.958)PS(0.682)PT(0.159)T(0.159)QVET(0.001)PDLVDHDNT(0.284)S(0.715)PLFR 131.71 6.16E-05 57244000 46748 56438 60110 61155 60131 40144 44112 40498 40942 TRUE FALSE 43822.12613 60616.72824 61535.83759 62724.34084 55408.55382 51732.92112 37497.81512 45554.26445 34108.5157 1.284785492 1.777172855 1.804119479 1.838964245 1.624478599 1.516715695 1.09936813 1.335568655 1 15.05784435 1.948239336 2.275465095 1.149642557 1.711211341 0.638571161 0.176817961 0.175627218 1.672050318 0.094737027 0.048839276 88.76450506 -1.948239336 0.561568784 TVSLTPS(ph)PTTQVETPDLVDHDNT(ph)SPLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 2 TVSLT(0.001)PS(0.998)PTTQVETPDLVDHDNT(0.55)S(0.45)PLFR 116.84 0.00048496 97736000 58870 62323 72384 76352 68992 48266 46276 40404 36493 TRUE FALSE 55185.43179 66937.45977 74100.98266 78311.32158 63573.64662 62199.61067 39337.34341 45448.52834 30402.08255 1.815185907 2.201739294 2.437365353 2.575853857 2.091095126 2.045899671 1.293902921 1.494914971 1 14.89188253 1.815430811 1.855060181 1.217854789 2.274826907 0.782510609 0.232697749 0.144321478 0.955581153 0.153910628 0.066882038 65.37787664 -1.815430811 1.056972118 TVSLTPS(ph)PTTQVETPDLVDHDNTS(ph)PLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 2 TVSLT(0.005)PS(0.968)PT(0.021)T(0.006)QVETPDLVDHDNT(0.331)S(0.669)PLFR 119.23 6.98E-05 95017000 59899 67815 70256 75860 64604 53323 55120 38614 44975 TRUE FALSE 56150.02851 72836.09316 71922.5055 77806.69603 59530.26244 68716.48447 46855.26771 43435.0429 37468.38195 1.498597633 1.943934842 1.919551946 2.076596105 1.58881327 1.833985907 1.250528186 1.159245226 1 15.19338606 1.63708424 1.507334161 1.023009171 1.864349067 0.764701522 0.1761818 0.158335085 0.705393564 0.134227316 0.048687559 43.35949744 -1.63708424 0.841339896 TVSLTPSPTTQVETPDLVDHDNT(ph)SPLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 TVSLTPSPTTQVETPDLVDHDNT(0.873)S(0.127)PLFR 149.37 2.41E-07 176760000 86567 88254 90561 118720 87739 65370 74976 56302 63549 TRUE FALSE 81148.926 94788.41799 92709.14969 121766.5562 80848.33286 84241.25781 63734.04484 63331.42864 52942.26136 1.532781636 1.790411206 1.751136943 2.299987818 1.527103882 1.591191151 1.203840622 1.196235805 1 15.6921322 1.847845797 1.440353391 1.077933125 1.811748406 0.674745913 0.209145241 0.229814431 0.895593003 0.148688094 0.062736186 70.44429019 -1.847845797 0.733815281 TVSLTPSPTTQVETPDLVDHDNTS(ph)PLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 TVSLTPSPTTQVETPDLVDHDNT(0.419)S(0.581)PLFR;TVS(0.001)LT(0.006)PS(0.064)PT(0.207)T(0.207)QVET(0.084)PDLVDHDNT(0.185)S(0.245)PLFR 195.67 3.86E-25 422610000 154204 148204 170829 184447 161135 131466 146165 114461 114447 TRUE FALSE 144552.6469 159177.1784 174881.1446 189180.2223 148480.1071 169418.1 124248.9152 128751.7078 95345.05634 1.516100073 1.669485388 1.834192052 1.984163936 1.557292143 1.776894435 1.303150052 1.350376336 1 16.54087052 1.400689535 1.121379659 1.040015276 1.747631654 0.718979907 0.151936565 0.222472867 0.551784017 0.132066695 0.045304684 25.15877754 -1.400689535 0.707616378 TVSPDRLELEAAQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVSPDRLELEAAQK 14 1 Q14974;J3QR48 Q14974 KPNB1 Importin subunit beta-1 0 ; 226.24 2.26E-12 760180000 1361900 1339840 1455380 1498610 1747890 1239340 1987340 1422850 2026930 FALSE TRUE 1276661.11 1439043.148 1489902.301 1537066.87 1610617.77 1597117.339 1689356.817 1600495.955 1688622.289 0.756037107 0.852199546 0.882318273 0.910249071 0.953805822 0.945810884 1.000434987 0.947811696 1 20.68741523 7.027377207 0.259026882 1.005600865 2.78E-17 0.926168503 0.019913528 6.944461467 0.149523178 0.023303318 2.781407825 10650676.83 -7.027377207 -1.005600865 TVSPGS(ph)VSPIHGQGQVVENLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 1 TVSPGS(0.546)VS(0.454)PIHGQGQVVENLK 169.36 6.18E-12 211210000 112310 77110 84709 84333 91242 68928 107410 88978 115300 TRUE FALSE 105280.7176 82819.30463 86718.33748 86497.12756 84076.22137 88826.39465 91304.86765 100087.0992 96055.68513 1.096038381 0.862200967 0.902792348 0.900489413 0.87528626 0.924738546 0.950541007 1.041969552 1 16.55158338 1.443909525 2.999699704 1.020286504 0.914048471 0.235248299 0.065760864 0.294017326 4.87928981 0.046982121 0.015880275 27.79134242 -1.443909525 -0.106238033 TVSPGSVS(ph)PIHGQGQVVENLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 1 TVSPGS(0.012)VS(0.988)PIHGQGQVVENLK;TVSPGS(0.001)VS(0.999)PIHGQGQVVENLK;TVSPGS(0.366)VS(0.634)PIHGQGQVVENLK;TVSPGS(0.136)VS(0.864)PIHGQGQVVENLK 393.35 1.61E-131 5110170000 4408330 3684070 4105050 3936070 4546500 3160590 5038110 3685700 5031430 TRUE FALSE 4132420.494 3956842.376 4202423.725 4037076.22 4189436.23 4073001.025 4282692.177 4145867.758 4191651.829 0.985869214 0.943981642 1.002569845 0.963122985 0.999471426 0.971693545 1.021719444 0.98907732 1 21.99908746 2.888066383 0.567474873 1.004107524 0.964718303 0.246256376 0.019260765 1.071594894 0.735002797 0.014298721 0.019395511 772.7987006 -2.888066383 -0.03938922 TVSS(ph)DGCSTPSREEGGCSLASTPATTLHLLQLSGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVSSDGCSTPSREEGGCSLASTPATTLHLLQLSGQR 36 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 T(0.051)VS(0.192)S(0.742)DGCS(0.005)T(0.005)PS(0.005)REEGGCSLASTPATTLHLLQLSGQR 97.669 0.00016958 637870000 14898 14929 13594 15622 16149 14452 15938 12976 21202 TRUE FALSE 13965.56077 16034.35869 13916.4561 16022.88697 14880.72268 18624.05779 13548.24486 14596.08216 17663.24923 0.790656384 0.90778081 0.787876337 0.907131341 0.842468024 1.054395913 0.767030159 0.82635318 1 14.10846314 3.20958863 24.95309107 0.887898782 0.839859616 0.110897563 0.088728943 598.985648 515894.865 0.024221159 0.028954369 1620.274624 -3.20958863 -0.048039166 TVSS(ph)PIPYTPS(ph)PSSSRPIS(ph)PGLSY(ph)ASHTVGFTPPTSLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 4 T(0.083)VS(0.436)S(0.481)PIPY(0.096)T(0.096)PS(0.706)PS(0.084)S(0.083)S(0.082)RPIS(0.768)PGLS(0.235)Y(0.303)AS(0.192)HT(0.147)VGFT(0.182)PPT(0.01)S(0.009)LT(0.008)R 86.959 0.00033642 85191000 61269 75856 70663 87189 94354 70891 97732 78467 85704 TRUE FALSE 57434.28266 81472.45717 72339.15973 89426.41735 86943.81745 91356.08088 83077.9939 88263.77768 71399.44873 0.804407929 1.141079639 1.01316132 1.252480501 1.217709926 1.27950681 1.163566321 1.236196907 1 16.12362531 5.529572368 0.767928652 1.188946703 1.02E-14 0.533491355 0.100203871 5.926755386 1.098804494 0.032614188 8.029339123 338510.6744 -5.529572368 -1.188946703 TVSS(ph)PIPYTPS(ph)PSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.015)VS(0.119)S(0.866)PIPY(0.038)T(0.03)PS(0.858)PS(0.166)S(0.123)S(0.087)RPIS(0.683)PGLS(0.012)Y(0.002)ASHTVGFTPPTSLTR;T(0.004)VS(0.141)S(0.855)PIPYT(0.003)PS(0.979)PS(0.014)S(0.004)S(0.012)RPIS(0.464)PGLS(0.249)Y(0.095)AS(0.157)HT(0.023)VGFTPPTSLTR 168.4 1.79E-17 689520000 157486 200008 194726 222880 221249 156079 226123 171418 185609 TRUE FALSE 147629.2324 214816.8004 199344.9927 228599.4781 203872.996 201136.4736 192217.9554 192819.9146 154629.6588 0.95472779 1.389234136 1.289176955 1.478367603 1.318459845 1.300762578 1.243085944 1.246978853 1 17.23845754 0.57383414 1.003913145 1.000166918 1.306546491 0.293321122 0.134381277 1.597176262 2.472265702 0.117726949 0.037510066 3.748298248 -0.57383414 0.306379572 TVSS(ph)PIPYTPSPSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TVSSPIPYTPSPSSSR 16 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 TVS(0.001)S(0.999)PIPYTPSPSSSR;TVSS(1)PIPYTPSPSSSR;TVSS(1)PIPYTPSPSSSR;TVSS(1)PIPYTPSPSSSR;TVSS(1)PIPYTPSPSSSR;TVS(0.001)S(0.999)PIPYTPSPSSSR 367.33 3.47E-104 2429310000 2310920 1896680 2220180 2257190 1814740 2091620 2438220 1691440 1323674 TRUE FALSE 2166283.642 2037112.161 2272843.718 2315113.317 1672217.641 2695436.739 2072631.546 1902620.007 1102744.258 1.9644479 1.84731151 2.061079621 2.099410901 1.516414734 2.444299047 1.879521504 1.725350183 1 20.07266682 0.825011244 2.271182169 1.001371371 1.977592027 0.639557834 0.230084437 0.381694946 3.529949222 0.195675206 0.053159528 6.683612212 -0.825011244 0.976220656 TVSS(ph)PIPYTPSPSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 T(0.017)VS(0.157)S(0.826)PIPYTPS(0.004)PS(0.009)S(0.01)S(0.009)RPIS(0.968)PGLSYASHTVGFTPPTSLTR;T(0.02)VS(0.13)S(0.85)PIPYTPS(0.004)PS(0.002)S(0.001)S(0.004)RPIS(0.988)PGLSYASHTVGFTPPTSLTR;T(0.003)VS(0.13)S(0.867)PIPYT(0.013)PS(0.008)PS(0.027)S(0.023)S(0.02)RPIS(0.909)PGLSYASHTVGFTPPTSLTR;T(0.015)VS(0.111)S(0.874)PIPYT(0.001)PS(0.004)PS(0.015)S(0.013)S(0.011)RPIS(0.956)PGLSYASHTVGFTPPTSLTR 208.86 6.60E-31 4745930000 1425980 1622340 1601900 1573370 1642220 1315617 1817910 1362390 1349592 TRUE FALSE 1336730.457 1742459.742 1639897.824 1613745.338 1513246.666 1695414.271 1545331.272 1532487.39 1124336.377 1.188906172 1.549767292 1.458547334 1.435286958 1.345902078 1.507924413 1.374438562 1.363015039 1 20.10064229 0.397566066 1.051607935 0.998814951 1.433764252 0.616531619 0.099537328 1.453386798 1.994901851 0.089222708 0.027367602 2.497848339 -0.397566066 0.434949302 TVSS(ph)PIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 T(0.011)VS(0.195)S(0.792)PIPYT(0.001)PSPSSSRPISPGLSYASHTVGFTPPTSLTR;T(0.194)VS(0.173)S(0.621)PIPY(0.008)T(0.001)PS(0.001)PS(0.001)S(0.001)S(0.001)RPISPGLSYASHTVGFTPPTSLTR 131.51 5.00E-09 1778890000 176418 199491 171070 154650 194890 146464 221874 175360 177269 TRUE FALSE 165376.3123 214261.5212 175127.8612 158618.5808 179584.1255 188745.7792 188606.0535 197254.082 147681.6587 1.119816189 1.450833659 1.185847063 1.074057417 1.216021862 1.278058364 1.277112237 1.335670819 1 17.17213114 3.733986612 24.45504211 1.211548103 1.311780448 0.060784786 0.126776987 471.4659037 1679386.835 0.030682906 0.053830208 5419.84182 -3.733986612 0.100232345 TVSS(ph)PPT(ph)SPRPGSAATVSASTSNIIPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 2 T(0.002)VS(0.123)S(0.874)PPT(0.545)S(0.455)PRPGSAATVSASTSNIIPPR 140.38 3.06E-07 1107800000 330180 312370 321050 342480 384240 269970 341230 295000 317050 TRUE FALSE 309514.6232 335498.1998 328665.4576 351268.6166 354063.3403 347905.9564 290065.7293 331831.3994 264132.3068 1.171816606 1.270189943 1.244321309 1.329896448 1.34047722 1.317165479 1.098183455 1.256307505 1 18.01090125 0.782326524 0.829115246 1.004801167 1.271873747 0.550306096 0.072694927 0.68357699 0.928045023 0.069196507 0.024158241 6.057961707 -0.782326524 0.26707258 TVSS(ph)PPTS(ph)PRPGSAATVSASTSNIIPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 2 T(0.006)VS(0.189)S(0.791)PPT(0.108)S(0.861)PRPGS(0.022)AAT(0.007)VS(0.008)AS(0.002)T(0.003)S(0.002)NIIPPR;T(0.041)VS(0.324)S(0.634)PPT(0.082)S(0.918)PRPGSAATVSASTSNIIPPR;TVS(0.03)S(0.969)PPT(0.011)S(0.988)PRPGS(0.001)AATVSASTSNIIPPR 161.61 5.16E-12 2256770000 755452 794611 805865 878508 833937 641527 856884 650059 734360 TRUE FALSE 708169.6078 853444.8252 824980.4984 901052.0026 768442.952 826725.4306 728402.1991 731220.2971 611790.5719 1.157535994 1.39499506 1.3484688 1.472811194 1.256055564 1.351320973 1.190607101 1.195213412 1 19.22267835 1.137493583 0.894737985 1.006297889 1.349619535 0.593723107 0.086754022 0.337148579 0.596462195 0.073972219 0.026362144 13.72440682 -1.137493583 0.343321646 TVSS(ph)PPTSPRPGSAATVSASTSNIIPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 1 TVS(0.044)S(0.948)PPT(0.007)S(0.001)PRPGSAATVSASTSNIIPPR;T(0.009)VS(0.181)S(0.8)PPT(0.007)S(0.002)PRPGSAATVSASTSNIIPPR;T(0.028)VS(0.16)S(0.81)PPT(0.002)S(0.001)PRPGSAATVSASTSNIIPPR;T(0.001)VS(0.142)S(0.857)PPTSPRPGSAATVSASTSNIIPPR 180.83 8.78E-18 1406850000 193411 207884 218528 212188 203197 159342 225318 176586 211500 TRUE FALSE 181305.7508 223275.9477 223711.5874 217633.1033 187238.7273 205341.4487 191533.6576 198633.1508 176199.2837 1.028981202 1.267178521 1.269650947 1.235153167 1.06265317 1.16539321 1.087028583 1.12732099 1 17.42684853 2.745694088 24.77458746 1.099602729 1.222965556 0.300178287 0.080590567 522.1809617 1813538.821 0.023352504 0.024296608 556.7934118 -2.745694088 0.123362828 TVSSHEVFLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVSSHEVFLQR 11 0 Q9Y5X3;Q5QPE5;Q5QPE4 Q9Y5X3 SNX5 Sorting nexin-5 0 114.86 0.0012005 124510000 110340 207830 153000 154030 214830 134820 169370 175630 173860 FALSE TRUE 103434.0164 223217.9494 156629.2323 157982.6706 197958.1184 173740.3454 143974.5409 197557.7921 144841.6428 0.714117945 1.541117217 1.0813826 1.090726862 1.366721024 1.199519296 0.994013448 1.363957135 1 17.14411692 -1.357101982 3.616210189 0.999124383 1.185109069 0.047201356 0.228506344 0.001461084 0.000259755 0.200278114 0.046986176 0.043943841 1.357101982 0.185984686 TVSSPIPYT(ph)PSPSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 TVSSPIPY(0.001)T(0.608)PS(0.39)PS(0.001)SSRPIS(0.999)PGLSYASHTVGFTPPTSLTR;TVSSPIPY(0.005)T(0.584)PS(0.405)PS(0.055)S(0.013)S(0.011)RPIS(0.925)PGLS(0.002)YASHTVGFTPPTSLTR 290.21 3.38E-91 1552380000 923500 1110350 1014550 939110 1151450 904470 1230510 1006680 1276380 TRUE FALSE 865699.7835 1192561.469 1038615.605 963209.1525 1061019.762 1165575.806 1046006.449 1132366.214 1063343.932 0.814129612 1.121519983 0.976744752 0.905830299 0.997814281 1.09614187 0.983695319 1.06491059 1 20.02017687 2.462184865 24.86687191 1.0334693 0.982655628 0.140351454 0.083089942 616.6676574 1026653.715 0.027884107 0.023338228 289.8577155 -2.462184865 -0.050813672 TVSSPIPYTPSPSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 TVSSPIPYTPSPS(0.001)S(0.001)S(0.001)RPIS(0.993)PGLS(0.003)YASHTVGFTPPTSLTR;TVSSPIPYTPSPS(0.01)S(0.005)S(0.004)RPIS(0.982)PGLSYASHTVGFTPPTSLTR 321.91 8.33E-111 9221800000 1399070 1826080 1671660 1502960 1878180 1385880 1906960 1632320 1712060 TRUE FALSE 1311504.706 1961284.863 1711312.565 1541528.498 1730675.319 1785961.058 1621029.051 1836118.745 1426306.126 0.919511375 1.375079885 1.199821366 1.08078376 1.213396821 1.252158303 1.136522533 1.287324447 1 20.44385223 -1.461113915 6.036215276 0.999889315 1.198117322 0.16897936 0.123654003 0.000166922 1.49E-05 0.108503029 0.02556019 0.034584865 1.461113915 0.198228008 TVSTLHHVLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVSTLHHVLQR 11 0 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ; 179.57 4.07E-06 1374250000 914860 1274220 963360 1094570 1264230 1002370 1507580 1108940 1264490 FALSE TRUE 857600.5457 1368564.575 986211.3541 1122658.519 1164942.475 1291737.947 1281532.375 1247393.6 1053438.45 0.814096491 1.299140519 0.936183176 1.065708698 1.105847689 1.226211125 1.216523257 1.184116262 1 20.00667459 2.446486797 4.391998889 1.180802031 1.060130137 0.135331015 0.137127807 0.38312956 17.22297063 0.044922063 0.038199652 279.5675734 -2.446486797 -0.120671894 TVTAMDVVYALKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVTAMDVVYALKR 13 1 P62805 P62805 HIST1H4A Histone H4 0 ; 238.13 1.46E-16 420970000 837320 1049370 739220 908160 1619780 874550 1199390 1097620 1646710 FALSE TRUE 784913.6359 1127066.447 756754.6475 931464.9231 1492569.013 1127018.388 1019552.604 1234660.273 1371863.463 0.572151425 0.821558761 0.551625339 0.678977864 1.087986562 0.821523729 0.743188103 0.899987722 1 20.38770547 2.954303274 24.90409473 0.875764013 0.664658493 0.519266594 0.119037765 384.7223716 209668.278 0.035722679 0.037891119 900.1259325 -2.954303274 -0.211105521 TVTCVTVVEPEAPPS(ph)PDVLQAATHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 TVTCVTVVEPEAPPSPDVLQAATHR 25 0 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 TVTCVTVVEPEAPPS(1)PDVLQAATHR;TVTCVTVVEPEAPPS(1)PDVLQAATHR;TVTCVTVVEPEAPPS(1)PDVLQAATHR;TVTCVTVVEPEAPPS(1)PDVLQAATHR;TVTCVTVVEPEAPPS(1)PDVLQAATHR;TVTCVTVVEPEAPPS(1)PDVLQAATHR;TVTCVTVVEPEAPPS(1)PDVLQAATHR 229.7 2.03E-34 6137568000 2151580 2155826 2326687 2120150 2507651 2157533 2857290 2369191 2772176 TRUE FALSE 2016916.448 2315445.6 2381877.114 2174556.638 2310710.206 2780377.752 2428865.89 2664989.712 2309481.917 0.873319871 1.00258226 1.031346943 0.941577686 1.000531846 1.203896741 1.051692967 1.153934002 1 21.13913782 2.415039337 11.18250058 1.104176819 0.979519487 0.481581879 0.068283472 0.48678862 85.6498771 0.021590819 0.018059718 260.0395088 -2.415039337 -0.124657333 TVTLPENEDELESTNRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVTLPENEDELESTNRR 17 1 P30876;C9J2Y9;C9J4M6 P30876 POLR2B DNA-directed RNA polymerase II subunit RPB2;DNA-directed RNA polymerase 0 127.88 6.22E-05 178930000 64977 76980 74084 81118 92702 59298 74305 65628 84540 FALSE TRUE 60910.20556 82679.6793 75841.30746 83199.62521 85421.55886 76416.36998 63163.65506 73821.80027 70429.72785 0.864836588 1.173931546 1.076836583 1.181314024 1.21286226 1.085001637 0.896832304 1.048162509 1 16.10389689 1.917056546 7.448577748 0.974097176 1.114921129 0.222574563 0.101992286 0.343775623 27.21952917 0.040440275 0.025202879 82.61455074 -1.917056546 0.140823953 TVTLPHEAERPDGSEDAEDDDDDDALSDWNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVTLPHEAERPDGSEDAEDDDDDDALSDWNLR 32 1 O14787-2;O14787;A0A075B780 O14787-2 TNPO2 Transportin-2 0 ; 385.63 2.58E-166 368710000 161839 179674 184753 192170 180087 145088 225980 179226 189852 FALSE TRUE 151709.7859 192977.2499 189135.4284 197101.4075 165943.6935 186972.5503 192096.3969 201602.7606 158164.4747 0.959190021 1.220104896 1.195814855 1.246180015 1.049184362 1.182139988 1.214535674 1.274639966 1 17.27106607 -1.302787171 4.088485719 0.999750061 1.177167837 0.229036065 0.095318166 0.000196927 3.36E-05 0.083692415 0.019698812 0.049798106 1.302787171 0.177417776 TVTNAVVTVPAYFNDSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVTNAVVTVPAYFNDSQR 18 0 P11142;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 240.2 1.41E-23 131580000 297520 328090 252410 239320 319580 197970 333570 290380 345450 FALSE TRUE 278898.7543 352382.125 258397.2844 245461.3564 294481.4759 255120.7252 283554.2752 326634.5822 287792.1633 0.969097807 1.224432663 0.897860739 0.852911885 1.023243554 0.886475581 0.985274484 1.13496691 1 18.13466778 3.924005619 6.911778306 0.962706068 1.108025203 0.21703634 0.100100783 0.250738378 26.60411951 0.023827067 0.043681068 8394.708476 -3.924005619 0.145319135 TVVLHIDGLDDTSRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVVLHIDGLDDTSRR 15 1 Q9NVT9;E5RJ86 Q9NVT9 ARMC1 Armadillo repeat-containing protein 1 0 ; 136.81 1.33E-05 199742000 58407 88220 78934 81265 95405 77183 88117 78556 95327 FALSE TRUE 54751.41013 94751.90059 80806.35176 83350.39748 87912.27615 99464.47914 74904.67389 88363.88952 79416.30786 0.68942276 1.193103824 1.017503255 1.049537554 1.106980147 1.252444011 0.943190082 1.112666805 1 16.27714767 4.748469587 24.86616878 1.084063334 0.689422529 0.651712531 0.09074961 789.7714078 1981857.001 0.020253025 0.273960654 56036.31746 -4.748469587 -0.394640805 TVVNKDVFRDPALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVVNKDVFRDPALK 14 2 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ; 89.541 0.0034355 453780000 429900 548140 523840 585330 787980 396560 847040 463740 1643350 FALSE TRUE 402993.3264 588724.8559 536265.7322 600350.5588 726095.2294 511040.4344 720034.2155 521638.9598 1369064.269 0.294356763 0.430019883 0.39170238 0.438511597 0.530358761 0.373277169 0.52593164 0.381018607 1 20.38475874 -5 0.283075747 5.273488045 0.390787008 0.874900848 0.068996465 69.47391723 0.66238444 174.6871068 0.068321131 1.00E-05 5 -4.882701038 TVVSGLVNHVPLEQMQNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVVSGLVNHVPLEQMQNR 18 0 Q12904;Q12904-2;A0A5F9ZHC5 Q12904 AIMP1 Aminoacyl tRNA synthase complex-interacting multifunctional protein 1;Endothelial monocyte-activating polypeptide 2 0 ; 151.95 4.40E-08 1124680000 1150710 1362760 1373590 1350410 1444690 1176140 1511440 1275300 1613530 FALSE TRUE 1078689.115 1463660.168 1406172.203 1385063.807 1331229.875 1515672.525 1284813.604 1434524.012 1344221.419 0.802463865 1.088853479 1.046086741 1.030383676 0.990335265 1.127546774 0.955805037 1.067178362 1 20.35833937 4.745987535 24.83872549 1.039296673 0.802463742 0.691387415 0.049507798 450.1975597 1505609.34 0.010862209 0.114104795 55716.97569 -4.745987535 -0.236832932 TVVTGIEMFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVVTGIEMFHK 11 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 ; 193.28 1.02E-06 1246820000 2844600 2639600 2337300 2384800 3733900 2255600 2536800 2943800 4660800 FALSE TRUE 2666561.564 2835038.731 2392741.86 2445998.005 3440654.556 2906755.103 2156430.39 3311339.91 3882882.37 0.686747964 0.730137681 0.616228263 0.629943885 0.886108367 0.748607562 0.555368457 0.852804591 1 21.88869657 1.006517039 6.986107834 0.999916165 0.690100172 0.573838504 0.08864924 0.07901353 22.55572744 0.08478004 0.021263849 10.15119193 -1.006517039 -0.309815993 TVWDWELMNDIKPIWQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVWDWELMNDIKPIWQR 17 1 P14625 P14625 HSP90B1 Endoplasmin 0 ; 204.13 8.27E-12 290330000 652490 640990 603280 593150 635690 398650 648720 581510 322230 FALSE TRUE 611651.8156 688449.5665 617590.0865 608371.2332 585765.4717 513733.7835 551450.4584 654112.8036 268447.7313 2.278476382 2.564557216 2.300597153 2.266255819 2.182046646 1.913719967 2.054219105 2.436648655 1 18.03428169 -1.558125122 0.25898122 8.01E-17 2.441989734 0.812140362 0.187338675 9.430087452 0.448673413 6.671215271 0.273741551 0.027661446 1.558125122 2.441989734 TVWDWELMNDIKPIWQRPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVWDWELMNDIKPIWQRPSK 20 2 P14625 P14625 HSP90B1 Endoplasmin 0 ; 298.87 5.47E-55 3332900000 6626000 6996100 6006900 5981200 7221400 3850600 8230300 5986200 5296200 FALSE TRUE 6211290.488 7514098.523 6149386.505 6134687.718 6654260.374 4962205.711 6996242.921 6733590.247 4412230.005 1.407744039 1.703016052 1.393713949 1.390382575 1.508139958 1.124648014 1.585647827 1.526119499 1 22.07307657 -3.100349196 0.292657002 1.84E-26 1.499139646 0.452070116 0.154034812 65.88721331 1.703363411 41.04490457 0.159404675 0.00079369 3.100349196 1.499139646 TVWIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TVWIAR 6 0 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ;;; 122.51 0.044642 1888909000 1637208 2249660 1745099 1678005 2360240 1484188 1918690 1946171 2459080 FALSE TRUE 1534738.074 2416227.167 1786493.572 1721065.449 2174876.271 1912648.982 1631000.247 2189154.733 2048643.662 0.749148377 1.179427742 0.872037244 0.840099956 1.061617651 0.933617211 0.796136623 1.068587366 1 20.96623764 3.740686078 24.84966483 0.923414349 1.004235366 0 0.136498708 1112.823795 2038589.813 0.032278465 0.05779 5504.096993 -3.740686078 0.080821017 TVYCNVHKHEPLVLFCESCDTLTCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVYCNVHKHEPLVLFCESCDTLTCR 25 1 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 132.84 4.29E-05 405920000 115103 116863 130708 128566 163407 136499 212375 116034 254470 FALSE TRUE 107898.9087 125515.6581 133808.4555 131865.2212 150573.6734 175904.0454 180531.3403 130521.1003 211997.3131 0.508963567 0.592062495 0.63117996 0.622013644 0.710262178 0.82974658 0.851573719 0.615673371 1 17.69368645 3.855105462 0.101961035 1.228063646 9.09E-12 0.717943543 0.078288212 20.37739492 0.467266024 1.559556731 4.380991167 7163.173357 -3.855105462 -1.228063646 TVYFAEEVQCEGNSFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TVYFAEEVQCEGNSFHK 17 0 P21291;E9PS42 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ; 305.32 7.94E-47 835350000 603990 657380 757070 682200 754540 768960 1122630 743500 1015890 FALSE TRUE 566187.3441 706053.0992 775028.0579 699706.407 695281.4721 990946.269 954302.0535 836327.6116 846331.3961 0.668990122 0.834251338 0.915750097 0.826752275 0.821523903 1.170872632 1.127574917 0.988179826 1 19.69086316 2.248352943 24.99934457 1.090303981 0.830843583 0.707723963 0.081639781 106.0778925 270811.8553 0.028060717 0.023207618 177.1548078 -2.248352943 -0.259460398 TVYGGGCSEMLMAHAVTQLANR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TVYGGGCSEMLMAHAVTQLANR 22 0 P78371;P78371-2;F5GWF6 P78371 CCT2 T-complex protein 1 subunit beta 0 ;; 291.7 2.10E-55 1376803000 241518 294399 272447 267198 312176 231616 281810 254290 287953 FALSE TRUE 226401.8195 316196.6083 278909.5715 274054.753 287658.9562 298479.7792 239555.2067 286038.6663 239891.7841 0.943766459 1.31808019 1.162647452 1.142409917 1.199119667 1.244226768 0.998596962 1.192365413 1 17.87202422 1.138426222 0.736189821 1.010952892 1.183532713 0.109968301 0.112090586 1.053007423 1.32827505 0.099083762 0.039351765 13.75391139 -1.138426222 0.172579821 TVYGNHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TVYGNHER 8 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ;; 120.31 0.0015271 529100000 526470 560370 567850 572170 596270 463160 613160 577870 713370 FALSE TRUE 493519.1825 601860.3779 581319.6702 586852.8509 549441.3594 596866.7732 521222.3503 650018.3415 594303.9385 0.830415467 1.012714773 0.978152142 0.987462497 0.924512398 1.00431233 0.877029945 1.093747323 1 19.18084142 4.747408606 24.7568903 0.976608778 0.830415381 0.415055169 0.05685252 1028.939658 2878926.729 0.012395312 0.150103121 55899.58782 -4.747408606 -0.146193397 TWDHFWLNEGHTVYLER ddPTM_SK-BR-3_Pertuzumab_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 879842000 896412 1036296 1042092 951031 1177520 840613 1104576 981798 1066561 FALSE TRUE 840307.1731 1113024.434 1066810.914 975436.0656 1085042.329 1083284.327 938955.0832 1104377.642 888545.0789 0.945711358 1.252636991 1.200626665 1.097790184 1.221144942 1.219166425 1.056733198 1.242905586 1 19.76108545 -1.216490263 4.198682505 0.999916469 1.162762633 0.195716439 0.097238982 6.93E-05 1.29E-05 0.085783818 0.020209082 0.060744888 1.216490263 0.162846163 TWEQQQEVVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TWEQQQEVVSR 11 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ;;; 310.21 3.17E-45 957210000 479934 485256 442886 490480 533300 352611 532220 398781 537650 FALSE TRUE 449895.7876 521184.8591 453391.4651 503066.5472 491416.7692 454404.0715 452418.5519 448569.6857 447912.7416 1.004427304 1.163585696 1.012231676 1.123135156 1.097126122 1.014492398 1.010059571 1.001466679 1 18.77285818 2.201576731 7.137149905 1.007430964 1.084185235 0.37813949 0.046745521 0.195949773 28.5815615 0.016177153 0.012069762 159.0657694 -2.201576731 0.076754271 TWESVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TWESVKR 7 1 A6NFX8;Q9UKK9;A6NCQ0;A6NJU6;C9JYY9 A6NFX8 NUDT5 ADP-sugar pyrophosphatase 0 ; 107.59 0.011934 845410000 969160 1211130 971330 1049280 1511670 853600 1219340 1151440 1683010 FALSE TRUE 908502.0056 1300803.325 994370.4063 1076206.301 1392949.536 1100020.463 1036511.287 1295199.819 1402104.758 0.647955868 0.927750453 0.709198368 0.767564831 0.993470372 0.784549411 0.739253812 0.923753957 1 20.41916271 -5 0.208417678 1.916490795 0.781482636 0.283468672 0.103993706 204.9218867 2.041673938 78.2449625 0.214105471 1.00E-05 5 -1.135008158 TWNHFSDNEAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TWNHFSDNEAER 12 0 Q99543 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 0 143.98 6.27E-05 294680000 85929 235690 207430 181060 217730 170830 210290 197850 234900 FALSE TRUE 80550.85728 253140.7328 212350.3376 185706.3061 200630.3641 220145.8478 178758.9667 222552.008 195693.6725 0.411617076 1.293556044 1.085116012 0.948964286 1.025226629 1.124951282 0.913463192 1.137246827 1 17.57823758 4.750872123 24.97797724 1.069803197 0.411616663 0.785725435 0.107390054 949.2497953 1925833.192 0.027155607 0.469682903 56347.1718 -4.750872123 -0.658186533 TWNLVEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TWNLVEGR 8 0 Q9NWT1 Q9NWT1 PAK1IP1 p21-activated protein kinase-interacting protein 1 0 91.265 0.029335 43811000 86857 115790 99982 100530 113610 68338 102780 88592 106450 FALSE TRUE 81420.77541 124363.2121 102353.6203 103109.77 104687.5289 88066.07123 87369.09316 99652.90622 88682.80731 0.918112291 1.40233734 1.154154039 1.162680492 1.180471526 0.993045596 0.985186372 1.123700402 1 16.43636682 2.270078306 7.309228122 1.018904679 1.195359289 0.214833428 0.122840851 0.216945976 37.83948782 0.040980392 0.033652228 186.2422913 -2.270078306 0.17645461 TWS(ph)PTACGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TWSPTACGGK 10 0 Q15464;Q15464-2 Q15464 SHB SH2 domain-containing adapter protein B 1 TWS(0.957)PT(0.043)ACGGK 134.38 0.00018057 81838000 294410 217100 273930 246960 271030 212540 303840 259540 309550 TRUE FALSE 275983.4036 233174.3099 280427.749 253297.4117 249744.3971 273896.8477 258282.0127 291944.1403 257884.1052 1.070183846 0.904182558 1.087417733 0.982214129 0.968436565 1.062092786 1.00154297 1.132074969 1 17.97636333 1.809761856 1.694099091 1.055016493 1.001564293 0.083614328 0.063457935 0.800072494 4.410146233 0.041725778 0.017624964 64.5300284 -1.809761856 -0.0534522 TWS(ph)TDDFFAGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TWSTDDFFAGLR 12 0 Q9H6Y2;G3V1J0;Q9H6Y2-2 Q9H6Y2 WDR55 WD repeat-containing protein 55 1 T(0.004)WS(0.974)T(0.022)DDFFAGLR;TWS(0.998)T(0.002)DDFFAGLR 122.34 0.00037781 18374400 68423 47407 53011 51952 45490 45055 58508 41303 53601 TRUE FALSE 64140.52657 50917.06361 54268.44595 53285.17627 41917.3989 58061.64709 49735.26856 46459.77047 44654.64682 1.436368466 1.1402411 1.215292244 1.193272818 0.938701835 1.300237517 1.11377588 1.040424094 1 15.44652269 7.477793121 1.137078416 1.127302446 199.9827121 0.452865768 0.107808671 944.8964812 2.489646471 0.028018693 488528.032 30046446.83 -7.477793121 198.8554097 TWSTDDFFAGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TWSTDDFFAGLR 12 0 Q9H6Y2;G3V1J0;Q9H6Y2-2 Q9H6Y2 WDR55 WD repeat-containing protein 55 0 ; 251.98 1.11E-20 192094000 283500 300560 297850 284570 305710 257370 348550 280650 229150 FALSE TRUE 265756.2411 322813.7751 304915.1427 291872.548 281700.7698 331668.5409 296288.1633 315689.7703 190903.3846 1.392098111 1.690979842 1.597222298 1.528901903 1.475619567 1.737363335 1.552032007 1.65366251 1 17.54248316 -1.270029912 4.712634115 0.999785836 1.589969212 0.760326192 0.101890399 0.000205836 3.19E-05 0.088572128 0.020869191 0.053699481 1.270029912 0.590183376 TWTDFEHMETIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TWTDFEHMETIEK 13 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-4;H7C5K1;Q7Z2W4-5 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 0 186.91 7.41E-06 80053000 225390 210260 230540 222450 244510 165410 234670 224990 232020 FALSE TRUE 211283.2422 225827.8692 236008.5177 228158.4436 225307.1709 213161.1818 199483.4121 253080.4968 193294.3631 1.093064686 1.168310682 1.220979825 1.180367808 1.165616872 1.102780124 1.032018776 1.309300968 1 17.56044004 2.272829228 5.366975344 1.104356707 1.174814762 0.08332626 0.086309802 0.36682186 26.6601924 0.028696964 0.023168194 187.4257372 -2.272829228 0.070458055 TWYVQATCATQGTGLYDGLDWLSHELSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TWYVQATCATQGTGLYDGLDWLSHELSK 28 0 P84085 P84085 ARF5 ADP-ribosylation factor 5 0 ;; 399.28 1.23E-146 693820000 1275810 1383680 985110 764489 1491200 854798 1326070 1275530 634957 FALSE TRUE 1195959.329 1486129.107 1008477.274 784107.082 1374087.167 1101564.306 1127238.114 1434782.728 528978.5747 2.260884252 2.809431569 1.906461476 1.482304047 2.597623482 2.082436527 2.130971211 2.71236454 1 19.01284976 -1.957050167 2.79611504 0.059867258 2.239614467 0.49742264 0.394098871 101530585.8 89930847.89 622904841.4 0.092234164 0.011039511 1.957050167 2.179747209 TYDATTHFETTCDDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 TYDATTHFETTCDDIK 16 0 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;;; 297.28 9.86E-46 14661870000 17124000 12792900 12680310 13440900 14807950 9852020 17630700 12163060 17049400 FALSE TRUE 16052239.41 13740099.63 12981092.94 13785816.25 13644993.34 12696138.24 14987140.21 13681644.82 14203745 1.13014134 0.967357526 0.913920445 0.970576158 0.960661667 0.893858503 1.055154131 0.963242076 1 23.75976803 1.716965535 24.99999935 1.008495736 0.96478983 0.044504969 0.066092753 2.292706606 2643.357377 0.028998823 0.016081391 52.11533515 -1.716965535 -0.043705906 TYEDIDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TYEDIDKR 8 1 G5E9W7;G5E9V5;P82650;H7C5L9 G5E9W7 MRPS22 "28S ribosomal protein S22, mitochondrial" 0 ;; 106.6 0.0066774 699580000 1078230 786810 912460 801940 1162780 763700 852850 882380 1469840 FALSE TRUE 1010745.509 845066.2311 934103.9821 822519.1381 1071459.949 984167.7924 724973.06 992547.0854 1224514.208 0.825425709 0.690123663 0.762836377 0.671710571 0.87500818 0.803721007 0.592049529 0.81056396 1 20.22377808 0.983164438 24.46766463 1.000000008 0.737190975 0.48940178 0.081262221 653.7832659 950166.0691 0.074985695 0.018746424 9.619764457 -0.983164438 -0.262809033 TYEDLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TYEDLKR 7 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ;; 92.47 0.025087 972060000 1618820 1487180 1689240 1478440 1669830 1322100 2044520 1569080 1978260 FALSE TRUE 1517500.946 1597292.355 1729309.571 1516379.273 1538688.288 1703768.807 1737963.206 1764983.092 1648075.626 0.920771427 0.969186322 1.04929018 0.920090832 0.933627234 1.033792856 1.054540932 1.070935741 1 20.65235101 2.11251512 6.492220514 1.046883143 0.97084656 0.472222772 0.041481005 0.214097353 11.4100923 0.016419957 0.012077829 129.5731808 -2.11251512 -0.076036583 TYEDMTLEELEDHEDEFNEEDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TYEDMTLEELEDHEDEFNEEDER 23 0 Q9H2J4 Q9H2J4 PDCL3 Phosducin-like protein 3 0 ; 186.55 2.70E-17 114569000 45010 55814 46431 55054 47552 42366 56773 44526 55984 FALSE TRUE 42192.90445 59946.52663 47532.36525 56466.77885 43817.45774 54596.37645 48260.4157 50085.16911 46639.90873 0.90465238 1.285305402 1.01913504 1.210696598 0.939484208 1.170593552 1.034745072 1.073869364 1 15.50927734 2.75323621 24.99680698 1.055490523 1.120704966 0.051335045 0.116781136 2208.131791 3761089.11 0.032005087 0.033804681 566.5473466 -2.75323621 0.065214442 TYEEGLKHEANNPQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TYEEGLKHEANNPQLK 16 1 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 217.48 8.54E-15 4037800000 4074600 2931200 3335200 3237100 3476800 2307400 4156100 2906900 4273400 FALSE TRUE 3819578.059 3148229.098 3414312.519 3320169.466 3203746.153 2973508.922 3532931.388 3269832.864 3560141.933 1.072872411 0.88429876 0.959038315 0.932594691 0.899892817 0.835222016 0.992356893 0.91845576 1 21.76350333 0.188318903 1.194206654 1.000077137 0.931940981 0.080672744 0.06426638 14.37671864 18.78280901 0.060031128 0.016841416 1.542832942 -0.188318903 -0.068136156 TYEIWHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TYEIWHR 7 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y4X2;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 110.14 0.0068713 133530000 189680 207990 213700 205990 222970 170300 234660 192190 208240 FALSE TRUE 177808.2674 223389.796 218769.0649 211276.0521 205458.8356 219462.8454 199474.9115 216185.3446 173483.3987 1.024929582 1.287672467 1.261037463 1.217845936 1.184314102 1.26503658 1.149821326 1.246144278 1 17.40443809 -1.974547853 0.491790891 0.787868238 1.218436359 0.400156503 0.076820469 65.1005871 5.110923917 15.73113979 0.034283274 0.010603571 1.974547853 0.430568121 TYEQGPDT(ph)PVSADAPVHPPALEQHPYEHCEPSTMPGDLGLGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TYEQGPDTPVSADAPVHPPALEQHPYEHCEPSTMPGDLGLGLR 43 0 A0A5F9UK94;H0Y360;Q01433-2;Q01433;A0A590UK85;Q01433-5;A0A590UJY6;Q01433-3;Q01433-4 A0A5F9UK94 AMPD2 AMP deaminase 2 1 TYEQGPDT(0.997)PVS(0.002)ADAPVHPPALEQHPYEHCEPSTMPGDLGLGLR;TYEQGPDT(0.999)PVS(0.001)ADAPVHPPALEQHPYEHCEPSTMPGDLGLGLR;TYEQGPDT(0.999)PVS(0.001)ADAPVHPPALEQHPYEHCEPSTMPGDLGLGLR 172.27 4.61E-20 387093000 79046 83719 93167 102734 113027 59050 58019 58551 103556 TRUE FALSE 74098.65196 89917.64187 95376.96524 105370.3284 104150.3153 76096.7764 49319.58957 65861.22124 86271.8346 0.858897371 1.042259531 1.105540014 1.221375769 1.207234271 0.882058168 0.571676606 0.7634151 1 16.39660202 2.025957434 6.055683528 0.729007663 1.087601571 0.488603862 0.143956649 0.114761002 13.53982927 0.053613613 0.038166773 106.1591505 -2.025957434 0.358593907 TYEVSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TYEVSLR 7 0 Q16531;F5GY55;F5H2L3 Q16531 DDB1 DNA damage-binding protein 1 0 143 0.005702 164200000 192560 231830 180950 172630 228740 150170 266780 213100 267740 FALSE TRUE 180508.0133 248994.9344 185242.2195 177059.9781 210775.6831 193521.6412 226778.8157 239706.0041 223052.4643 0.809262583 1.116306584 0.830487213 0.793804178 0.944960118 0.867605932 1.016706165 1.074661985 1 17.76702356 1.621344314 5.308304836 1.039517493 0.910529722 0.313206714 0.09344273 0.199338602 12.10406588 0.051766353 0.024443438 41.81617586 -1.621344314 -0.128987771 TYFKFNLDSVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TYFKFNLDSVGK 12 1 Q9UL58 Q9UL58 ZNF215 Zinc finger protein 215 0 52.344 0.089716 40080000 54429 134990 102230 108830 184540 73426 164950 90560 470890 FALSE TRUE 51022.38605 144984.8001 104654.9439 111622.762 170046.9728 94622.89423 140217.2788 101866.6153 392295.4169 0.130061132 0.369580662 0.266775851 0.284537512 0.433466631 0.24120316 0.357427777 0.259668125 1 18.58158096 -1.733097414 2.696356029 1.13287231 0.303072509 0.877936167 0.082788987 14023775.99 11428775.88 12503993.81 0.017205545 0.018488539 1.733097414 -0.8297998 TYFTDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TYFTDKK 7 1 P27824;P27824-2;P27824-3;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ; 95.741 0.021235 1818470000 2899100 2302480 1844920 1921940 3113600 1418970 3085200 2605400 2701800 FALSE TRUE 2717650.506 2472958.015 1888682.374 1971260.234 2869070.416 1828603.604 2622602.902 2930689.925 2250852.126 1.207387405 1.098676358 0.839096603 0.875783981 1.274659665 0.812405037 1.165160017 1.302035745 1 21.10203985 1.600030098 21.21748396 1.175321455 1.009472196 0.126937911 0.166692432 0.458724257 1212.831953 0.081635073 0.039148772 39.81347614 -1.600030098 -0.16584926 TYGEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TYGEHK 6 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 72.021 0.086696 373520000 307570 257440 290930 287310 268450 212390 331660 243900 231890 FALSE TRUE 288319.7427 276501.1255 297830.997 294682.861 247367.0199 273703.5451 281930.662 274351.4519 193186.0609 1.49244589 1.431268509 1.541679537 1.525383662 1.280459981 1.416787235 1.459373728 1.420141032 1 17.55963148 -3.074576489 0.299192066 1.65E-10 1.481972038 0.805576783 0.069516719 31.40667776 0.833979363 19.79314013 0.071423705 0.000842216 3.074576489 1.481972037 TYGLPCHCPFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TYGLPCHCPFK 11 0 P17900;H0YBY3 P17900 GM2A Ganglioside GM2 activator;Ganglioside GM2 activator isoform short 0 62.466 0.080795 393190000 1620300 1448200 1247500 1199200 1874700 1147300 1694100 1218100 2770400 FALSE TRUE 1518888.315 1555426.235 1277091.289 1229973.502 1727468.624 1478506.885 1440085.432 1370182.466 2308002.343 0.658096522 0.673927494 0.553331886 0.532916921 0.748469181 0.640600253 0.623953194 0.593665977 1 21.13821326 -1.320314053 3.51364559 1.001526705 0.626634219 0.785742166 0.061024217 21221531.01 27931866.65 328281.394 0.014365069 0.04782841 1.320314053 -0.374892486 TYGNVLVLDGVIQCTERDEFSYQEMIANLPLCSHPNPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TYGNVLVLDGVIQCTERDEFSYQEMIANLPLCSHPNPR 38 1 P19623;K7ESL0 P19623 SRM Spermidine synthase 0 ;;; 300.25 9.77E-93 557241000 394749 464854 394556 413865 515345 320000.7 430792 388024 356451 FALSE TRUE 370042.3647 499272.2738 403915.0546 424485.4766 474871.8825 412379.7073 366198.7389 436469.6505 296957.0253 1.246114196 1.681294703 1.360180161 1.429450864 1.599126614 1.3886848 1.233170821 1.469807458 1 18.17989464 -0.01610864 0.375148108 0.915241098 1.493104125 0.470227489 0.140140496 3.805089146 0.729848276 0.626352028 0.10368488 0.96358795 0.01610864 0.577863027 TYHTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TYHTEK 6 0 Q99805 Q99805 TM9SF2 Transmembrane 9 superfamily member 2 0 80.999 0.063035 147600000 172500 196240 161160 166130 231390 126030 185890 211940 156610 FALSE TRUE 161703.5329 210769.8138 164982.7913 170393.1771 213217.5628 162412.8151 158017.5202 238401.1755 130470.7793 1.239385047 1.615456081 1.264519092 1.305987272 1.634216979 1.244821377 1.211133413 1.827238075 1 16.99336721 -1.341923034 3.183639069 0.996774505 1.402874094 0.279318612 0.209708373 18784925.96 25799827.6 571791.8124 0.047678943 0.04550687 1.341923034 0.406099588 TYIPPKGETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TYIPPKGETK 10 1 P09429;Q5T7C4;B2RPK0 P09429 HMGB1;HMGB1P1 High mobility group protein B1;Putative high mobility group protein B1-like 1 0 ; 136.48 0.00010642 1171750000 1264070 1034230 1050810 1008670 1324360 687020 1282530 1076600 1552120 FALSE TRUE 1184954.115 1110805.465 1075735.709 1034554.18 1220350.108 885351.5212 1090226.533 1211015.88 1293061.145 0.916394495 0.859050997 0.831929498 0.800081407 0.943768292 0.684694243 0.843136102 0.936549586 1 20.30235907 1.093232192 3.51783467 0.996813485 0.835814664 0.390281819 0.069069208 0.201353166 4.63853965 0.060388551 0.015774086 12.39459076 -1.093232192 -0.160998821 TYLGEEGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TYLGEEGKR 9 1 Q9BV86;S4R338;Q9BV86-2 Q9BV86 NTMT1 "N-terminal Xaa-Pro-Lys N-methyltransferase 1;N-terminal Xaa-Pro-Lys N-methyltransferase 1, N-terminally processed" 0 ; 125.48 0.00080236 611900000 388170 359130 355220 355290 386670 243030 406040 312880 399480 FALSE TRUE 363875.1326 385720.3589 363645.9861 364407.3429 356302.498 313188.8157 345158.0715 351943.7567 332804.2073 1.093360975 1.159000849 1.092672443 1.094960145 1.070606952 0.941060266 1.037120517 1.057509938 1 18.34431415 2.569771638 3.01223472 1.011735728 1.115930347 0.625517621 0.036254115 0.16071384 2.824029406 0.01240453 0.011267021 371.3399183 -2.569771638 0.104194619 TYQEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 TYQEHK 6 0 P09960-4;P09960 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ;;; 134.12 0.014168 1639990000 2717120 2325110 2317440 2372990 2835900 1686410 2690620 2320650 3225270 FALSE TRUE 2547060.309 2497263.564 2372410.771 2433884.941 2613179.853 2173249.19 2287186.509 2610388.261 2686951.601 0.947936803 0.929403999 0.882937664 0.905816443 0.972544445 0.808815905 0.851219839 0.971505501 1 21.3575389 TYS(ph)APAINAIQGGSFESPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TYSAPAINAIQGGSFESPK 19 0 Q9H4L5-5;Q9H4L5;Q9H4L5-7;Q9H4L5-3 Q9H4L5-5 OSBPL3 Oxysterol-binding protein-related protein 3 1 T(0.026)YS(0.974)APAINAIQGGSFESPK 168.79 1.61E-11 63550000 43361 34485 35987 32355 38222 29464 45366 31521 49680 TRUE FALSE 40647.11241 37038.30528 36840.62863 33185.28408 35220.1983 37969.77849 38563.78946 35456.46624 41388.08705 0.98209691 0.894902565 0.890126393 0.801807632 0.850974297 0.917408394 0.931760615 0.856682895 1 15.33692795 2.085396286 9.781750123 0.922565049 0.882604278 0.123858643 0.055833814 0.770784765 81.5370154 0.02025077 0.01495116 121.7296255 -2.085396286 -0.039960771 TYS(ph)APAINAIQVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TYSAPAINAIQVPK 14 0 Q9H4L5-6;Q9H4L5-2;Q9H4L5-8;Q9H4L5-4 Q9H4L5-6 OSBPL3 Oxysterol-binding protein-related protein 3 1 TYS(1)APAINAIQVPK;T(0.003)YS(0.997)APAINAIQVPK 213.83 5.10E-10 62585000 134489 93442 106503 105830 120212 67572 141882 111139 140325 TRUE FALSE 126071.5736 100360.5429 109029.3015 108545.777 110771.0344 87078.93946 120608.1113 125014.9488 116903.851 1.078421049 0.858487912 0.932640803 0.928504716 0.947539653 0.744876569 1.031686384 1.06938264 1 16.83496293 1.599873438 24.99999779 1.037932673 0.91062107 0.307498821 0.083652239 0.725709344 2263.080884 0.039614914 0.018847821 39.79911714 -1.599873438 -0.127311603 TYS(ph)APAINAIQVPKPFSGPVR ddPTM_SK-BR-3_Pertuzumab_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(0.254)YS(0.746)APAINAIQVPKPFSGPVR;T(0.001)YS(0.999)APAINAIQVPKPFSGPVR 232 2.01E-26 1179430000 468340 479660 417860 444460 577080 325680 654370 476280 1033200 TRUE FALSE 439027.4354 515174.5255 427771.8365 455865.5961 531758.4646 419698.529 556253.2934 535744.6064 860752.2453 0.510050874 0.598516621 0.496974407 0.52961302 0.617783419 0.487595044 0.646240886 0.622414416 1 19.71523851 0.18405122 0.66167582 1.016171649 0.540507506 0.898236561 0.047307394 0.834503018 0.467596608 0.074202368 0.016154314 1.527746226 -0.18405122 -0.475664143 TYS(ph)DEANQMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TYSDEANQMR 10 0 A0A1B0GTL5;Q9BXF6 A0A1B0GTL5 RAB11FIP5 Rab11 family-interacting protein 5 1 T(0.014)YS(0.986)DEANQMR;T(0.002)YS(0.998)DEANQMR;T(0.199)YS(0.801)DEANQMR 103.2 0.0029847 401310000 617210 588720 593710 571930 582190 412703 617770 480220 618890 TRUE FALSE 578579.9279 632309.4414 607793.0816 586606.6921 536467.1458 531843.6564 525141.1236 540176.5241 515593.2608 1.12216348 1.226372587 1.178822781 1.137731496 1.040485178 1.031517859 1.018518207 1.047679567 1 18.97587388 2.848149536 2.091348205 1.024609801 1.187957174 0.860442544 0.028029744 0.095454271 0.824104749 0.009116701 0.009721322 704.9357501 -2.848149536 0.163347373 TYS(ph)FEQPWPNAR ddPTM_SK-BR-3_Pertuzumab_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 T(0.003)YS(0.997)FEQPWPNAR;TYS(1)FEQPWPNAR;T(0.035)YS(0.965)FEQPWPNAR;TYS(1)FEQPWPNAR;T(0.001)YS(0.999)FEQPWPNAR;TYS(1)FEQPWPNAR 257.76 3.43E-21 1039720000 1324496 1348276 1240398 1439170 1514290 1024260 1641370 1224823 1135944 TRUE FALSE 1241598.16 1448103.758 1269820.826 1476101.539 1395363.772 1319947.235 1395261.806 1377744.848 946347.6079 1.311989537 1.530202798 1.341812264 1.55978789 1.474472763 1.394780547 1.474365016 1.455854948 1 19.85201068 -1.66943332 2.505253989 0.933744901 1.446060744 0.766177231 0.076876918 6335007.728 5059411.127 2676435.263 0.017514756 0.021407536 1.66943332 0.512315842 TYSHLNIAGLVGSIDNDFCGTDMTIGTDSALHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TYSHLNIAGLVGSIDNDFCGTDMTIGTDSALHR 33 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 267.78 2.71E-60 235500000 244490 285320 300560 291560 364980 253490 351510 224250 332860 FALSE TRUE 229187.8073 306445.3897 307689.4251 299041.9232 336315.9431 326668.4479 298804.3388 252248.1061 277303.5156 0.826487204 1.105090172 1.109576359 1.07839211 1.212808075 1.178017694 1.077535343 0.909646261 1 18.08110638 1.317185719 6.612135837 0.956029382 1.09722963 0.202798325 0.1043581 0.274532172 17.92822786 0.067987549 0.024348231 20.75801008 -1.317185719 0.141200247 TYSS(ph)PGSFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TYSSPGSFK 9 0 Q8N3Z6 Q8N3Z6 ZCCHC7 Zinc finger CCHC domain-containing protein 7 1 TYSS(1)PGSFK;TYS(0.069)S(0.931)PGSFK 213.81 6.34E-05 245630000 1223730 979670 1178510 1039800 1117460 880500 1365250 963740 1168790 TRUE FALSE 1147138.924 1052205.786 1206464.814 1066483.028 1029699.199 1134686.056 1160543.437 1084065.06 973711.3983 1.178109783 1.080613607 1.239037374 1.095276311 1.057499379 1.165320708 1.191876195 1.113333029 1 19.8931347 0.976571962 22.85118718 0.999999998 1.146350985 0.404418162 0.054626425 661.2231462 644944.1548 0.051618311 0.012904578 9.474841677 -0.976571962 0.146350987 TYSS(ph)SLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TYSSSLKR 8 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 T(0.001)YS(0.046)S(0.476)S(0.476)LKR;T(0.001)YS(0.037)S(0.481)S(0.481)LKR 98.048 0.0047768 1891850000 856850 581550 615530 452970 697760 301090 647180 453450 1085470 TRUE FALSE 803221.288 624608.5671 630130.6623 464593.9771 642960.7442 388009.7952 550141.3671 510064.2307 904298.0446 0.88822628 0.690710956 0.696817455 0.513762006 0.711005346 0.429072912 0.608362885 0.564044381 1 19.78643882 -1.302292623 3.480412257 1.001355603 0.634940995 0.454936526 0.124577931 46638895.48 69588658.85 660669.1617 0.028905191 0.049854846 1.302292623 -0.366414608 TYSYLTPDLWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TYSYLTPDLWK 11 0 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 0 ; 182.71 1.32E-05 303390000 640090 1183900 478690 475140 1324950 318520 555180 1065570 1071840 FALSE TRUE 600027.9095 1271557.188 490044.7529 487332.8968 1220893.772 410471.5533 471935.913 1198608.76 892942.9796 0.671966658 1.42400715 0.548797363 0.545760377 1.367269579 0.459683947 0.528517412 1.342312765 1 19.76820853 3.964222458 24.12335504 0.779859723 1.087291344 0.042732912 0.375590711 519.66305 971878.1074 0.089483669 0.162751496 9209.211733 -3.964222458 0.307431621 TYT(ph)HEVVTLWYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TYTHEVVTLWYR 12 0 G3V5T9;P24941;Q00526;K7EJ83 G3V5T9 CDK2;CDK3 Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 1 T(0.06)YT(0.94)HEVVTLWYR;T(0.049)YT(0.951)HEVVTLWYR 164.92 0.00020604 484540000 566890 666520 499240 524520 662870 332020 569620 580290 636690 TRUE FALSE 531409.3668 715869.8343 511082.2086 537980.0712 610810.8641 427868.7841 484210.7691 652740.4839 530422.3258 1.001860859 1.349622366 0.963538267 1.014248543 1.151555721 0.806656815 0.912877806 1.230605222 1 19.01678198 3.802586874 5.339130326 0.99614593 1.192295766 0.176635873 0.143233791 0.269223704 13.6280641 0.035014485 0.063927875 6347.268556 -3.802586874 0.196149836 TYTAYVDLEKDFAAEVVHPGDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TYTAYVDLEKDFAAEVVHPGDLK 23 1 P54577;A0A0C4DGZ5 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed;Tyrosine--tRNA ligase" 0 103.02 0.0010658 52599000 193550 131260 155160 163620 185030 101620 197350 128830 230940 FALSE TRUE 181436.051 140978.627 158840.4685 167818.7662 170498.4902 130956.0443 167759.1996 144914.7091 192394.6221 0.943041178 0.732757628 0.825597237 0.872263291 0.88619156 0.680663747 0.871953685 0.753216007 1 17.55370895 -1.329823223 3.919429259 1.000436856 0.814762563 0.332677788 0.079405662 11253986.92 3818449.759 41860.57315 0.016572501 0.046792557 1.329823223 -0.185674293 TYTETVNHHYLLFQDTDLGSFHDLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TYTETVNHHYLLFQDTDLGSFHDLLR 26 0 Q8WUA4;H0Y4Q6;H7C318 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 0 69.152 0.011224 15231000 5263.1 8413.1 5068.7 7538.1 7323 4843.4 5795 6705.8 5727.4 FALSE TRUE 4933.691966 9036.014678 5188.931958 7731.540408 6747.88112 6241.610954 4926.093548 7543.033891 4771.45994 1.034000501 1.893763081 1.08749356 1.620372068 1.414217285 1.308113456 1.032408028 1.580864974 1 12.22021504 0.79494481 0.279143996 0.937864615 1.503328357 0.113353775 0.283623003 4.71330778 1.025178346 0.920102142 0.453589641 6.236555766 -0.79494481 0.565463741 TYYVDHNTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TYYVDHNTR 9 0 Q9H0M0-3;Q9H0M0;Q9H0M0-6 Q9H0M0-3 WWP1 NEDD4-like E3 ubiquitin-protein ligase WWP1 0 ; 85.355 0.016526 56576000 127658 147663 169935 157978 179984 143959 191048 153488 171487 FALSE TRUE 119668.1137 158596.1222 173965.9384 162031.9829 165848.7827 185517.6263 162402.126 172651.3147 142864.7119 0.837632415 1.110114038 1.217697052 1.134163789 1.160879972 1.298554583 1.136754653 1.208495173 1 17.12429008 4.778990443 2.28857909 1.175501634 0.731338916 0.640261025 0.076280645 0.383642448 2.176227397 0.016586489 0.356059572 60116.05076 -4.778990443 -0.444162718 TYYYNNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 TYYYNNR 7 0 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 ; 132.53 0.0078173 289350000 255300 386100 257020 246540 411030 203729 272360 313050 398170 FALSE TRUE 239321.2287 414687.2457 263116.6358 252866.6338 378749.3618 262542.255 231522.1465 352134.9816 331712.8547 0.721471071 1.250139209 0.793206028 0.762305802 1.141798867 0.791474467 0.697959525 1.061565678 1 18.3395754 3.747742291 22.90989949 0.868505642 1.022998968 0.020196373 0.189658209 330.0556034 366684.6118 0.04530858 0.081511113 5594.255416 -3.747742291 0.154493326 VAAAPDEDLDGDDEDDAEDENNIDNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VAAAPDEDLDGDDEDDAEDENNIDNR 26 0 Q9BXV9 Q9BXV9 C14orf142 Uncharacterized protein C14orf142 0 ; 295.73 2.21E-70 537100000 253496 284600 284370 293100 290061 244193 327460 266960 357020 FALSE TRUE 237630.1379 305672.0801 291115.3907 300621.4422 267280.7791 314687.555 278360.413 300290.5437 297431.0556 0.798941918 1.027707344 0.978765953 1.010726475 0.898631041 1.058018486 0.935882141 1.009613953 1 18.18219577 4.746020576 24.96515009 0.987818804 0.798941826 0.637669085 0.045216877 527.7931707 1766244.827 0.009446913 0.099179302 55721.21479 -4.746020576 -0.188876978 VAAASGHCGAFSGSDSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VAAASGHCGAFSGSDSSR 18 0 Q9NZB2;Q9NZB2-6;A0A494C0Y9 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 ; 225.01 4.29E-19 560850000 207427 338310 291960 342200 357850 285130 355400 347320 346000 FALSE TRUE 194444.5143 363358.8244 298885.4291 350981.4313 329745.9045 367442.4023 302111.0694 390683.6665 288250.3648 0.674568147 1.260566746 1.036895233 1.217627015 1.143956591 1.274733521 1.048085645 1.355362263 1 18.13696291 4.745681024 24.74166613 1.162864656 0.674567883 0.646135349 0.114522941 418.731282 1454946.171 0.023587745 0.237944377 55677.66637 -4.745681024 -0.488296773 VAAETQS(ph)PSLFGSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAAETQSPSLFGSTK 15 0 Q9UKX7-2;Q9UKX7 Q9UKX7-2 NUP50 Nuclear pore complex protein Nup50 1 VAAETQS(0.993)PS(0.007)LFGSTK 161.14 1.75E-06 126880000 877930 569310 773030 794500 793520 685900 951700 702210 861840 TRUE FALSE 822981.9284 611462.3048 791366.6367 814888.2151 731200.1401 883908.1953 809001.4201 789882.4643 717993.3363 1.146225023 0.851626713 1.102192175 1.134952337 1.018394048 1.231081336 1.126753382 1.100125063 1 19.45361093 3.710255641 5.829322278 1.114269662 0.976987315 0.152413444 0.094913164 0.184474048 22.11857593 0.022651129 0.037234554 5131.633617 -3.710255641 -0.137282347 VAAQSPPS(ph)PASAEALLPALPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAAQSPPSPASAEALLPALPLR 22 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 VAAQSPPS(0.996)PAS(0.004)AEALLPALPLR 114.55 0.00023528 26279000 31283 34017 32749 42659 39453 24048 29625 25307 40955 TRUE FALSE 29325.05287 36535.65407 33525.82175 43753.70216 36354.52053 30990.26721 25183.00628 28466.63466 34119.34592 0.859484614 1.070819299 0.982604468 1.282372243 1.065510476 0.908290191 0.738085845 0.834325333 1 15.05830237 2.100559886 4.170370742 0.827266579 1.055111002 0.349990984 0.122011142 0.202041833 6.429657675 0.046503984 0.032940611 126.0549448 -2.100559886 0.227844423 VAAYDKLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VAAYDKLEK 9 1 P35579 P35579 MYH9 Myosin-9 0 ; 116.23 0.0012285 1468920000 3708700 4268900 3052000 3072300 5559000 1789030 3620000 4385800 5835100 FALSE TRUE 3476579.087 4584973.798 3124394.881 3151140.419 5122418.564 2305493.919 3077214.606 4933376.784 4861184.114 0.715171243 0.943180445 0.642723009 0.648224866 1.053738851 0.474265912 0.633017498 1.014850841 1 22.21287635 1.226233842 24.68004617 1.00742577 0.732861399 0.332876448 0.163213699 258.0634503 516663.03 0.147788012 0.038059457 16.83580328 -1.226233842 -0.27456437 VADAKGDS(ph)ES(ph)EEDEDLEVPVPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VADAKGDSESEEDEDLEVPVPSR 23 1 P13861-2;P13861 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 2 VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR 242.19 1.42E-37 11116350000 15619080 8744660 10454540 10458750 11657600 7274130 14381230 9175690 15541070 TRUE FALSE 14641509.66 9392123.725 10702526.63 10727139.23 10742059.12 9374053.245 12224898.07 10321295.09 12947165.02 1.130866073 0.725419326 0.826630896 0.8285319 0.829684267 0.724023617 0.944214278 0.797185722 1 23.6261329 -0.501826263 0.764727321 1.011618996 0.83623153 0.123201018 0.118088224 30.16090517 12.32965326 1.123406148 0.036150222 0.31490078 0.501826263 -0.175387467 VADEDDVDNEEAALLHEEATMTIEELLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VADEDDVDNEEAALLHEEATMTIEELLTR 29 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ;;;; 262.48 3.25E-58 532289000 550787.3 404611.9 480306.3 479997.2 445160.3 443108.8 477021.3 398130.5 360228.9 FALSE TRUE 516314.5061 434569.7861 491699.3923 492314.7408 410199.2057 571027.1173 405496.3845 447837.9693 300104.3694 1.720449812 1.448062176 1.638427968 1.640478417 1.366855159 1.902761757 1.351184541 1.492274072 1 18.1951048 0.617412882 1.042803064 1.001100924 1.586787031 0.565210827 0.16180504 0.860577363 1.484125977 0.135686118 0.042975581 4.143934495 -0.617412882 0.585686108 VADEISFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VADEISFR 8 0 Q9H814 Q9H814 PHAX Phosphorylated adapter RNA export protein 0 ; 94.114 0.024634 101647000 180700 341030 209923 220144 353950 194427 231050 286430 342560 FALSE TRUE 169390.3096 366280.216 214902.4727 225793.2677 326152.1948 250554.9186 196406.1975 322191.416 285384.523 0.593551142 1.283462089 0.753027776 0.791189604 1.142851726 0.877955525 0.688216009 1.128972982 1 18.12254757 VADKIQLINNMLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VADKIQLINNMLDK 14 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 203.2 1.40E-08 662780000 1007820 935020 807450 786310 1039170 575200 1242630 868600 913080 FALSE TRUE 944742.3452 1004249.854 826603.0953 806488.0458 957557.78 741250.9024 1056309.168 977046.622 760681.0493 1.241969083 1.320198334 1.086661875 1.060218401 1.2588164 0.974456907 1.388636102 1.284436654 1 19.53693214 1.709249079 25 1.258959496 1.167913466 0.026176278 0.140273112 2.001911729 1698.403373 0.060409341 0.033499978 51.19753825 -1.709249079 -0.09104603 VADMALHYANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VADMALHYANK 11 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;; 138.71 5.18E-05 2138130000 6553580 7693150 5919250 5665670 8409840 4258820 5998660 7368670 6047390 FALSE TRUE 6143403.126 8262758.831 6059657.405 5811060.684 7749365.09 5488272.198 5099216.622 8288664.67 5038041.541 1.219403031 1.640073581 1.202780357 1.153436437 1.538170145 1.089366206 1.012142631 1.645215626 1 22.26443159 7.999999761 0.043946777 0.398118004 2.80704114 0.102935531 0.23238336 1090.233627 3.63514586 51.38997908 187.49272 99999944.88 -7.999999761 2.408923136 VADNS(ph)FDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VADNSFDAK 9 0 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 VADNS(1)FDAK;VADNS(1)FDAK;VADNS(1)FDAK;VADNS(1)FDAK;VADNS(1)FDAK 208.63 1.02E-05 994000000 4116110 2457900 3130020 2888950 2899700 2419940 4135450 2579610 4066330 TRUE FALSE 3858490.023 2639885.473 3204265.553 2963085.348 2671969.259 3118537.394 3515377.664 2901679.987 3387633.254 1.138992841 0.779271331 0.945871443 0.874677135 0.788742186 0.920565232 1.037709044 0.856550804 1 21.69184627 1.991527222 24.93097024 0.971491674 0.889253239 0.046326834 0.108727648 829.4021248 2440497.816 0.038400612 0.026985526 98.06797817 -1.991527222 -0.082238436 VADNS(ph)FDAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VADNSFDAKR 10 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 VADNS(1)FDAKR 134.88 9.73E-05 559320000 504620 350210 424190 409730 413580 293460 504310 350680 626870 TRUE FALSE 473036.735 376139.9128 434251.9871 420244.3655 381099.0951 378177.1381 428693.3973 394463.1699 522241.3473 0.905781852 0.720241541 0.831515906 0.804693783 0.7297375 0.724142468 0.820872188 0.755327344 1 18.99435716 -1.318241486 5.008832795 1.000083309 0.78347321 0.571477438 0.05803696 4.83E-05 6.57E-06 0.050274567 0.011845283 0.048057206 1.318241486 -0.2166101 VADPDHDHTGFLT(ph)EYVATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VADPDHDHTGFLTEYVATR 19 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 1 VADPDHDHTGFLT(0.637)EY(0.363)VATR 240.31 9.43E-24 988550000 436230 537000 589450 858640 990110 484820 311070 260920 371560 TRUE FALSE 408927.143 576760.0387 603432.0324 880674.1561 912350.7545 624779.6636 264427.9413 293496.4364 309544.2356 1.321062052 1.863255627 1.949420997 2.845067214 2.94740024 2.018385716 0.854249283 0.948156685 1 18.23978607 1.769006548 5.03091624 0.926697673 2.163313115 0.60638115 0.46525587 0.140276947 7.692742161 0.24817735 0.132513449 58.74982102 -1.769006548 1.236615443 VADPDHDHTGFLTEY(ph)VATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VADPDHDHTGFLTEYVATR 19 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 1 VADPDHDHTGFLTEY(1)VATR;VADPDHDHTGFLTEY(1)VATR;VADPDHDHTGFLTEY(1)VATR;VADPDHDHTGFLTEY(1)VATR 254.59 5.01E-31 5418620000 2145117 2288504 3041090 3988770 4798640 2278426 1633321 1329605 1770817 TRUE FALSE 2010857.956 2457947.217 3113226.091 4091128.591 4421774.171 2936170.599 1388419.679 1495609.111 1475256.203 1.363056771 1.666115494 2.110295205 2.773164813 2.997292377 1.99027843 0.941138005 1.013796186 1 20.49253409 1.770386689 4.731003257 0.981438184 2.154100993 0.580102586 0.468494207 0.157165537 7.368081391 0.258202124 0.136883558 58.93681857 -1.770386689 1.17266281 VADPDHDHTGFLTEYVATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VADPDHDHTGFLTEYVATR 19 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 ;;; 212.32 5.07E-17 3800630000 3619480 4569290 4128670 4088550 4313320 3669980 5078130 4303790 4975870 FALSE TRUE 3392943.208 4907604.986 4226604.002 4193469.115 3974569.246 4729443.649 4316711.55 4841127.655 4145365.152 0.818490792 1.183877609 1.019597514 1.011604276 0.958798345 1.140899167 1.041334452 1.167841065 1 21.98306776 2.229735917 24.99204669 1.08742925 1.027233417 0.127602291 0.101209648 521.9708126 1478240.795 0.035515511 0.02662627 169.7211309 -2.229735917 -0.060195833 VADPTPFHIQAEVTMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VADPTPFHIQAEVTMK 16 0 P16152;E9PQ63;A8MTM1;P16152-2 P16152 CBR1 Carbonyl reductase [NADPH] 1 0 134.85 2.60E-05 185810000 245400 209050 223740 202990 245360 183060 252170 215030 303040 FALSE TRUE 230040.8521 224528.2795 229047.2185 208199.0671 226090.4153 235906.4503 214359.4495 241876.9688 252460.6663 0.911194823 0.889359451 0.907259027 0.824679227 0.895547091 0.934428534 0.849080582 0.958077836 1 17.94569911 1.045263964 5.316200802 0.999648409 0.888394852 0.615099564 0.031086815 0.10151108 6.261843166 0.027752607 0.007006675 11.09849175 -1.045263964 -0.111253557 VADWTGATYQDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VADWTGATYQDKR 13 1 O15371-2;O15371;O15371-3;B0QYA5;B0QYA6;B0QYA8 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 142.1 6.44E-05 390900000 362240 393550 312170 313830 416060 257110 381200 301570 480090 FALSE TRUE 339568.045 422688.8515 319574.8198 321883.4091 383384.3259 331333.4832 324042.5989 339221.6783 399959.8775 0.849005273 1.056828135 0.799017196 0.804789248 0.958556964 0.828416803 0.810187764 0.84813927 1 18.60949576 3.933235135 8.07479768 0.853578416 0.962676365 0.153583264 0.083100677 0.325428837 54.34664327 0.019163824 0.034960003 8575.019869 -3.933235135 0.109097949 VAEAHVPNFIFDEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAEAHVPNFIFDEFR 15 0 Q12768;E7EQI7 Q12768 KIAA0196 WASH complex subunit strumpellin 0 134.44 3.51E-05 55020000 50060 66117 52194 55128 68851 45553 64949 66961 64832 FALSE TRUE 46926.83396 71012.37147 53432.06633 56542.67781 63443.72019 58703.41161 55210.50041 75321.22825 54011.12037 0.868836522 1.314773161 0.989278985 1.046871041 1.17464181 1.086876392 1.022206168 1.394550377 1 15.72096885 VAEEHAPSIVFIDEIDAIGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VAEEHAPSIVFIDEIDAIGTK 21 0 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ;;; 223.36 3.58E-25 324738000 451858 371771 411565 389792 384028 326056 508501 349856 404112 FALSE TRUE 423577.0144 399297.3117 421327.5162 399794.7226 353867.99 420183.0741 432255.9957 393536.2917 336663.0965 1.25816289 1.186044196 1.251481141 1.18752167 1.051104186 1.248081772 1.283942316 1.168932074 1 18.36094606 -2.29773317 1.453531446 0.432762099 1.209417781 0.486941173 0.065761897 122059.2022 15326.13089 225774.5171 0.018257014 0.005038101 2.29773317 0.776655681 VAEEHAPSIVFIDEIDAIGTKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAEEHAPSIVFIDEIDAIGTKR 22 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 157.79 1.18E-09 44896000 56017 56678 59548 57375 60078 43738 73940 53688 89163 FALSE TRUE 52510.99596 60874.49809 60960.50668 58847.33964 55359.71622 56364.45057 62853.38343 60391.06498 74281.11929 0.706922519 0.819515089 0.820672969 0.79222473 0.745273049 0.758799155 0.846155578 0.813006933 1 16.18070793 0.390726128 0.88547354 1.001205859 0.786612332 0.751305946 0.039110253 1.152667107 1.217546153 0.040617477 0.012547569 2.458816554 -0.390726128 -0.214593527 VAEFHTELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VAEFHTELER 10 0 K7EJR3;R4GMR5;P48556;K7EJC1;K7ERW6 K7EJR3 PSMD8 26S proteasome non-ATPase regulatory subunit 8 0 ;;;; 171.85 3.89E-06 1747760000 1935490 2221040 2163110 2105860 2265100 1815380 2337450 1979790 2138570 FALSE TRUE 1814351.136 2385488.113 2214419.991 2159899.933 2087208.183 2339450.736 1986971.072 2226971.14 1781628.851 1.018366499 1.33893662 1.242918798 1.212317555 1.171516829 1.313096571 1.11525533 1.249963559 1 20.7647654 -0.785786745 0.453587304 0.935755561 1.230077784 0.301500145 0.094663825 13.96728874 2.15779592 1.346580986 0.047200796 0.163762046 0.785786745 0.294322223 VAEIEHAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VAEIEHAEK 9 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;;;; 189.18 3.85E-05 9112860000 20268000 15476700 17607100 16168700 17365300 13773700 21242000 15354200 18431100 FALSE TRUE 18999462.06 16622610.97 18024748.73 16583616.22 16001499.39 17749943.59 18056959.3 17271205.67 15354830.34 1.237360598 1.08256559 1.173881334 1.080026014 1.042115024 1.155984351 1.175979083 1.124806024 1 23.87218924 -1.884535355 2.161422648 0.92521568 1.132876679 0.358181307 0.056388793 3187848.487 1522366.124 1216858.143 0.013921566 0.013045618 1.884535355 0.207660999 VAEKLDEIYVAGLVAHSDLDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VAEKLDEIYVAGLVAHSDLDER 22 1 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;; 185.14 2.20E-17 900100000 2921590 2491980 2838400 2704940 3149440 2180000 3493200 2476380 4224260 FALSE TRUE 2738732.897 2676488.792 2905728.188 2774353.34 2902095.687 2809330.611 2969427.089 2785561.494 3519203.716 0.778225166 0.760538181 0.825677745 0.7883469 0.824645551 0.798285873 0.843778118 0.791531755 1 21.7468176 -5 0.218868003 1.998217135 0.776845519 0.883800641 0.022860434 44.59931863 0.446247362 19.60377468 0.04067942 1.00E-05 5 -1.221371615 VAELALSLSST(ph)SDDEPPSSVSHGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VAELALSLSSTSDDEPPSSVSHGAK 25 0 Q8N1G2;Q5T7F5 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 1 VAELALSLSS(0.003)T(0.955)S(0.042)DDEPPSSVSHGAK;VAELALSLS(0.001)S(0.058)T(0.537)S(0.404)DDEPPSSVSHGAK;VAELALSLSS(0.005)T(0.735)S(0.26)DDEPPSSVSHGAK 293.77 2.38E-62 700580000 503250 613780 606830 631040 647130 503790 838890 604520 819250 TRUE FALSE 471752.4808 659224.9098 621224.2942 647233.5547 596307.0202 649225.9947 713106.2324 679995.6527 682511.8824 0.691200392 0.965880488 0.910202899 0.948311042 0.873694709 0.951230318 1.044826106 0.996313281 1 19.38049464 4.739500924 24.91938575 0.958666554 0.691200304 0.761152041 0.047530943 41.0761837 1088406.346 0.012347092 0.075043781 54890.97235 -4.739500924 -0.267466249 VAELSSDDFHLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAELSSDDFHLDR 13 0 Q92896;Q92896-3;Q92896-2;H3BM42 Q92896 GLG1 Golgi apparatus protein 1 0 103.85 0.0015778 75005000 26550 33938 22835 22790 31794 23385 33571 30712 28516 FALSE TRUE 24888.28289 36450.80483 23376.65698 23374.82998 29297.02749 30135.86988 28537.34021 34546.46081 23756.49538 1.047641182 1.534351101 0.984011177 0.983934272 1.233221779 1.268531801 1.201243692 1.454190117 1 14.5360344 2.507536298 24.43641826 1.244439207 1.171102822 0.042557601 0.189566674 2247.689776 1805864.682 0.060987256 0.057420869 321.763145 -2.507536298 -0.073336384 VAEPGAEATSSTGEES(ph)GSEHPPAVPMHNKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAEPGAEATSSTGEESGSEHPPAVPMHNKR 30 1 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 VAEPGAEATSSTGEES(0.876)GS(0.124)EHPPAVPMHNKR 210.36 2.90E-26 108280000 103580 128720 115590 128090 119270 90755 190720 111860 222640 TRUE FALSE 97097.1127 138250.5627 118331.8494 131377.0063 109903.0153 116954.4952 162123.3066 125825.9672 185479.9457 0.523491164 0.745366634 0.637976515 0.708308415 0.592533144 0.630550622 0.874074585 0.67838044 1 17.50090368 0.556438479 0.504689638 1.014859063 0.646138179 0.60038406 0.087734706 1.223626905 0.594277094 0.128034574 0.043612763 3.601127343 -0.556438479 -0.368720885 VAEYAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAEYAR 6 0 P20839-3;P20839-7;P20839-5;P20839-6;P20839;A0A3B3IRL5;C9J381;P20839-2;P20839-4 P20839-3 IMPDH1 Inosine-5-monophosphate dehydrogenase 1;Inosine-5-monophosphate dehydrogenase 0 104.25 0.079083 135170000 129360 194440 131200 130910 196080 121930 135200 174730 211300 FALSE TRUE 121263.5885 208836.5399 134312.126 134269.3722 180680.6677 157129.2116 114928.0151 196545.4251 176032.6649 0.68886981 1.186351067 0.76299547 0.762752596 1.026404206 0.892613946 0.652878914 1.116528147 1 17.42548364 5.027378828 15.74554205 0.902744249 0.11178532 0.152954147 0.167514358 4217448.163 66811815.66 0.039149461 85809419.77 106507.1657 -5.027378828 -0.790958929 VAGHPLAQNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAGHPLAQNER 11 0 O60493-4;O60493;O60493-2 O60493-4 SNX3 Sorting nexin-3 0 72.652 0.045709 123780000 31322 132880 17517 25126 138510 14841 22914 121180 122750 FALSE TRUE 29361.61193 142718.5735 17932.51151 25770.7757 127631.9833 19125.35578 19478.25842 136309.5898 102262.232 0.287120781 1.395613715 0.175358108 0.252006779 1.248085249 0.187022671 0.190473629 1.332941665 1 16.64191389 1.226281978 24.99948564 1.166471086 0.562071694 0.253168891 0.449798128 381.7915897 777309.3846 0.413048987 0.106296191 16.83766939 -1.226281978 -0.604399392 VAGHPNIVINNAAGNFISPTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VAGHPNIVINNAAGNFISPTER 22 0 Q16698-2;Q16698;E5RJD2;E5RJG7;E5RFV2 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 ; 321.17 1.16E-67 2475200000 868140 876980 743010 725640 1079730 784480 768970 826150 1214210 FALSE TRUE 813804.6671 941912.5117 760634.5481 744261.1509 994932.3612 1010946.641 653670.0873 929296.6461 1011550.507 0.804512144 0.931157174 0.751949154 0.735762719 0.983571611 0.999403029 0.646206079 0.918685364 1 19.94813693 1.000683475 24.99997807 1.000000061 0.83410718 0.194181649 0.111397835 28.51579534 1042994.827 0.104335332 0.026083833 10.01574998 -1.000683475 -0.165892881 VAGTGEGGLEEMVEELNSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAGTGEGGLEEMVEELNSGK 20 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;F8WBG8;Q9UJU6 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 92.063 0.0039684 11652000 19334 19867 16586 20121 20493 14602 28149 18920 26385 FALSE TRUE 18123.91945 21337.97335 16979.42775 20637.33892 18883.56244 18817.36036 23928.31877 21282.20365 21981.17305 0.824520121 0.970738609 0.772453213 0.938864313 0.859078922 0.856067159 1.08858243 0.968201451 1 14.42398076 1.750246141 24.99999153 1.023132559 0.87279552 0.55990576 0.062058434 2.203346331 4721.981552 0.026303053 0.014586514 56.26601284 -1.750246141 -0.150337039 VAHALAEGLGVIACIGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VAHALAEGLGVIACIGEK 18 0 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3 P60174 TPI1 Triosephosphate isomerase 0 ; 300.89 1.47E-49 1328180000 1855850 1836190 1582820 1554420 1966780 1153540 2442200 1648050 3106500 FALSE TRUE 1739695.661 1972143.418 1620365.238 1594309.049 1812317.032 1486548.272 2076014.782 1853812.67 2588005.081 0.672214933 0.762032282 0.626105895 0.616037836 0.700275686 0.574399286 0.80216797 0.716309517 1 21.30340902 0.569217659 0.911313983 0.999837749 0.671043972 0.716101937 0.06413948 0.746048903 0.983780757 0.05974859 0.019500275 3.708665457 -0.569217659 -0.328793777 VAHFLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VAHFLEK 7 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ; 124.37 0.0041527 1127290000 2536800 3719900 2287300 2471000 4319800 1556710 2957500 3780300 4463500 FALSE TRUE 2378026.216 3995325.267 2341555.836 2534410.043 3980540.333 2006106.906 2514050.331 4252278.776 3718513.015 0.639509989 1.074441652 0.629702203 0.681565463 1.070465618 0.5394917 0.676090233 1.143542798 1 21.82629439 1.236078356 24.999986 1.071771495 0.769426122 0.335970788 0.182471771 78.81910175 793740.4623 0.144284194 0.042572737 17.22179265 -1.236078356 -0.302345373 VAHPIRPKPPSATSIPAILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VAHPIRPKPPSATSIPAILK 20 2 Q9UMS4;F5GY56 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ; 69.737 0.0117 823390000 1890450 1544380 1588210 1571390 1791460 1272660 2045710 1670710 2238800 FALSE TRUE 1772130.109 1658727.502 1625883.091 1611714.528 1650765.958 1640056.282 1738974.777 1879301.821 1865129.817 0.950137676 0.889336221 0.871726502 0.864129946 0.885067593 0.879325539 0.932361255 1.007598401 1 20.83084462 1.415437166 2.685418145 1.005623748 0.886740983 0.794084411 0.023628154 0.110536083 1.414505498 0.018894674 0.006074447 26.0277823 -1.415437166 -0.118882764 VAHSFNCTPIEGMLSHQLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VAHSFNCTPIEGMLSHQLK 19 0 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 321.49 2.96E-62 2138300000 2164880 2228190 2359010 2009830 2390410 1737330 2660400 2081410 2693200 FALSE TRUE 2029384.025 2393167.506 2414966.831 2061405.64 2202676.841 2238868.968 2261497.718 2341278.62 2243687.521 0.904486033 1.066622461 1.076338308 0.918757902 0.981721751 0.997852395 1.007937913 1.043495851 1 21.09744033 -0.625752877 17.89115632 1 1.009378422 0 0.056802595 0 0 0.055096274 0.012986316 0.236726634 0.625752877 0.009378422 VAIEHLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 VAIEHLDK 8 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;;;;;; 175.38 0.00026649 8492532000 24474430 21193950 22466780 21194240 23187580 16936340 26469350 19714940 26324570 FALSE TRUE 22942619.11 22763172.11 22999702.63 21738120.08 21366521 21825586.42 22500516.7 22176393.66 21930829.2 1.046135506 1.037953098 1.048738396 0.991212867 0.974268725 0.995201149 1.02597656 1.011197226 1 24.38645703 3.242486253 24.99986083 1.00116279 1.04355837 0.707539425 0.013500999 62.69755293 399278.6941 0.004295077 0.005598971 1747.777937 -3.242486253 0.042395579 VAILVDDMADTCGTICHAADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VAILVDDMADTCGTICHAADK 21 0 B1ALA9;P60891;A0A2R8Y7H4;P60891-2;B7ZB02;P11908;P11908-2 B1ALA9;P11908 PRPS1;PRPS2 Ribose-phosphate pyrophosphokinase 1;Ribose-phosphate pyrophosphokinase 2 0 ;;; 326.07 3.82E-68 314501000 345317 265599 307280 277989 312647 266628 374580 257763 368470 FALSE TRUE 323704.2254 285264.2263 314568.8267 285122.6684 288092.9658 343599.1753 318415.2064 289945.278 306969.9766 1.054514285 0.929290315 1.024754376 0.928829169 0.938505351 1.11932502 1.037284525 0.944539532 1 18.22773803 2.285598101 24.99998607 1.032595572 0.973574735 0.148379807 0.058427631 188.7714463 100329.4418 0.019098687 0.015979059 193.0181289 -2.285598101 -0.059020836 VAIQLNDTHPALSIPELMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAIQLNDTHPALSIPELMR 19 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 110.41 0.00023621 247430000 125180 139150 138820 127610 154680 102740 146050 147210 158830 FALSE TRUE 117345.2073 149452.8108 142112.876 130884.6886 142532.0567 132399.3702 124151.1584 165589.4925 132320.2469 0.8868273 1.129478022 1.074007034 0.98915088 1.077174961 1.000597968 0.938262747 1.251429743 1 17.01367431 VAKPVVEMDGDEMTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VAKPVVEMDGDEMTR 15 1 P48735;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;;;;; 150.59 2.88E-06 2410200000 2391210 1652470 1670542 1616909 2349080 1415906 1809491 1706080 2653700 FALSE TRUE 2241548.435 1774820.598 1710168.045 1658401.622 2164592.733 1824655.077 1538174.623 1919087.844 2210780.326 1.013917307 0.802802783 0.77355856 0.750143107 0.979108013 0.825344361 0.695760951 0.868059038 1 21.07612425 1.998596716 24.99706639 0.805739903 0.843427854 0 0.113737489 267.5849389 4766620.362 0.041100706 0.029936492 99.67740339 -1.998596716 0.037687951 VALAAGS(ph)PARPPPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VALAAGSPARPPPAR 15 1 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 VALAAGS(1)PARPPPAR 83.758 0.0052025 110180000 114910 121470 105040 94463 117090 80441 118090 97910 116990 TRUE FALSE 107717.9882 130463.7652 107531.5984 96887.08051 107894.2237 103663.0108 100383.5008 110134.279 97463.61322 1.105212342 1.338589458 1.103299938 0.994084636 1.10702056 1.063607304 1.029958745 1.130004064 1 16.57257609 3.660058778 3.675278872 1.056602255 1.235183602 0.487029585 0.069715421 0.147924215 3.931890386 0.016799107 0.028022677 4571.500562 -3.660058778 0.178581347 VALENDDRS(ph)EEEKYTAVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VALENDDRSEEEKYTAVQR 19 2 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;A0A5F9ZH85;F8WB06;F8VRK6 Q99700;F8WB06 ATXN2 Ataxin-2 1 VALENDDRS(0.999)EEEKYT(0.001)AVQR;VALENDDRS(1)EEEKYTAVQR 262.15 1.79E-31 372960000 450950 313210 349870 348940 372820 276904 458740 334416 459430 TRUE FALSE 422725.8445 336400.3943 358169.0816 357894.3912 343540.2211 356841.6896 389956.1957 376168.5737 382748.165 1.104449043 0.878907922 0.935782623 0.935064943 0.897562033 0.932314567 1.018832307 0.982809607 1 18.54603594 1.756347301 11.56699603 1.000200698 0.935723072 0.125374018 0.061297502 0.273725616 160.4524113 0.026338716 0.014450405 57.06204091 -1.756347301 -0.064477626 VALNVSCANLLDKDIGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VALNVSCANLLDKDIGSK 18 1 O75131;A0A087WYQ3;E5RHZ0;A0A087WXR6;A0A087WUS8;E5RFT7 O75131 CPNE3 Copine-3 0 140.32 1.17E-07 62546000 238740 162800 160320 124240 305140 97947 197110 210540 457340 FALSE TRUE 223797.6896 174853.8814 164122.8661 127428.2087 281175.5353 126222.7089 167555.1854 236826.3825 381006.9995 0.58738472 0.458925641 0.430760764 0.334451096 0.737979973 0.331287113 0.43976931 0.621580136 1 18.53945798 0.889145052 3.280692225 0.999655963 0.465327025 0.660776222 0.118619815 0.25204148 5.678295297 0.102769294 0.026700217 7.747205065 -0.889145052 -0.534328939 VALS(ph)DDETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VALSDDETK 9 0 Q15054;H0YD46;Q15054-3;Q15054-2 Q15054 POLD3 DNA polymerase delta subunit 3 1 VALS(1)DDETK 117.86 0.0017966 0 126990 75212 91907 93905 87407 84616 119190 83643 75660 TRUE FALSE 119041.9226 80780.77474 94087.07744 96314.76128 80542.4068 109043.2656 101318.566 94086.01267 63031.85722 1.888599318 1.28158646 1.492690865 1.528033054 1.277804754 1.729970691 1.607418383 1.492673972 1 15.94379355 0.939406119 20.93294531 0.999999999 1.519210472 0.45577108 0.183839195 3188.271667 1101433.219 0.16686705 0.041716762 8.697733954 -0.939406119 0.519210473 VALS(ph)DDETKETENMR ddPTM_SK-BR-3_Pertuzumab_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(0.999)DDET(0.001)KETENMR;VALS(1)DDETKETENMR;VALS(1)DDETKETENMR 294.65 3.10E-44 6713280000 9285510 5727180 6772510 6767820 6989190 5077090 8835020 5998830 7090410 TRUE FALSE 8704346.504 6151226.366 6933157.135 6941493.719 6440287.21 6542763.463 7510290.771 6747797.131 5906974.765 1.473570965 1.041349694 1.173723845 1.175135157 1.090285208 1.107633556 1.271427604 1.142343991 1 22.49398802 -4.999999999 0.019031216 7.02E-07 1.994253767 0.228212294 0.116626273 7980.991 11.50414289 800.7328236 451.1029363 1.00E-05 4.999999999 1.994253065 VALSEPQPERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VALSEPQPERR 11 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1;H7C1K0 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;; 100.93 0.0058708 860800000 581740 722540 663560 691310 787870 567000 778130 636730 953470 FALSE TRUE 545329.9318 776037.6134 679299.9566 709050.185 725993.8683 730683.6955 661456.6303 716227.1421 794329.6973 0.686528445 0.976971673 0.855186403 0.892639652 0.913970447 0.919874578 0.832723027 0.90167489 1 19.59937842 VALVTFNSAAHNKPSLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VALVTFNSAAHNKPSLIR 18 1 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 249.16 7.78E-25 1269660000 771320 1087110 909100 949160 1125040 745190 1254460 1099610 1173830 FALSE TRUE 723044.458 1167600.756 930664.2813 973517.0525 1036683.897 960314.2559 1066365.369 1236898.729 977910.1898 0.739377159 1.193975447 0.951686864 0.995507627 1.060101334 0.982006595 1.090453275 1.264838778 1 19.89934245 1.553926289 4.918357525 1.145726131 1.010694265 0.174171165 0.12907913 0.253208853 13.26791699 0.067375212 0.029946072 35.80356643 -1.553926289 -0.135031866 VAMHILNNGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VAMHILNNGR 10 0 P49748;P49748-3;P49748-2;J3KSR4 P49748 ACADVL "Very long-chain specific acyl-CoA dehydrogenase, mitochondrial" 0 ; 140.35 3.94E-05 774890000 489020 595900 407540 424730 767490 376380 418690 598640 784570 FALSE TRUE 458413.1111 640021.056 417207.0413 435629.2909 707214.4313 485034.796 355911.3214 673381.5218 653620.1985 0.701344775 0.979194121 0.638301941 0.666486886 1.081995986 0.742074368 0.544523138 1.030233648 1 19.31809304 1.195284975 24.99921792 1.015118232 0.768519581 0.301170716 0.158416427 207.9111445 120100.2379 0.150953267 0.03773925 15.67779477 -1.195284975 -0.24659865 VAMSHFEPNEYIHYDLLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAMSHFEPNEYIHYDLLEK 19 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 200.39 3.75E-16 327230000 254480 221020 202180 187570 261600 163920 192510 217150 325160 FALSE TRUE 238552.5511 237384.5508 206975.8051 192383.3638 241054.9912 211241.043 163644.9127 244261.6555 270888.6954 0.880629407 0.876317671 0.764062172 0.710193401 0.889867297 0.779807525 0.604103883 0.901704869 1 18.04734066 4.06249333 2.915383108 0.778335513 0.879823054 0.018060281 0.111593171 0.555894637 9.231780317 0.027482198 0.068864597 11547.6425 -4.06249333 0.101487541 VANILHDDCAFLSAFGDVSKPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VANILHDDCAFLSAFGDVSKPER 23 1 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 ; 201.15 1.39E-24 407180000 459530 478640 449370 424800 558540 327260 552390 457280 513850 FALSE TRUE 430768.8376 514079.0036 460029.2686 435701.0872 514674.5214 421734.6494 469564.2476 514372.4146 428085.1154 1.006269132 1.200880351 1.074621032 1.017790789 1.202271471 0.985165413 1.096894591 1.201565754 1 18.70753815 -2.397759526 2.367464441 0.12007745 1.100636849 0.123702719 0.081893031 3880310.433 1687734.673 19557271.58 0.01805851 0.004001663 2.397759526 0.9805594 VANS(ph)PTMVNLLLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VANSPTMVNLLLGK 14 0 Q6UB99;A0A087WTN8;A0A2R8Y438 Q6UB99 ANKRD11 Ankyrin repeat domain-containing protein 11 1 VANS(0.999)PT(0.001)MVNLLLGK;VANS(0.964)PT(0.036)MVNLLLGK 114.01 0.0011479 56458000 246800 240880 233790 237520 265590 182879 283550 224860 236610 TRUE FALSE 231353.2286 258715.0058 239335.6092 243615.1653 244731.6327 235673.1985 241034.3098 252934.266 197118.2624 1.173677292 1.312486234 1.214172681 1.235883283 1.24154723 1.195592918 1.222790354 1.283159981 1 17.58870192 -1.690853 2.671522406 0.964560456 1.237380624 0.773959595 0.039877615 8752188.372 7567320.012 2099017.146 0.00904278 0.020377317 1.690853 0.272820168 VAPEEHPVLLTEAPLNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 312.66 3.33E-61 34627600000 22105940 18897750 19578270 19417390 21380030 16108070 24652600 18741860 22970800 FALSE TRUE 20722368.68 20296959.07 20042675.81 19915673.1 19700928.69 20758208.32 20956171.49 21081822.48 19136825.08 1.082853012 1.060623117 1.047335476 1.040698915 1.029477387 1.084725822 1.095070442 1.101636368 1 24.18984816 2.211684593 24.99749112 1.080309793 1.05216083 0.036757866 0.031313263 381.0090512 354376.1518 0.010624907 0.007849304 162.8113184 -2.211684593 -0.028148963 VAPGPSSGSTPGQVPGSSALS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VAPGPSSGSTPGQVPGSSALSSPR 24 0 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4 Q8NEY1-5 NAV1 Neuron navigator 1 1 VAPGPSSGSTPGQVPGSS(0.002)ALS(0.499)S(0.499)PR;VAPGPSSGSTPGQVPGSSALS(0.5)S(0.5)PR 211.06 1.16E-28 163990000 145215 137590 163343 152219 175121 160834 169234 135757 175041 TRUE FALSE 136126.2524 147777.3068 167217.5731 156125.1972 161367.7031 207264.1649 143858.9328 152706.5603 145825.5263 0.933487132 1.013384354 1.146696174 1.070630096 1.106580632 1.421316076 0.986514065 1.047186759 1 17.15388376 4.448921804 1.521860243 1.120484481 0.911351213 0.194326054 0.121112534 1.040323113 3.339058694 0.031719835 0.277710424 28113.94583 -4.448921804 -0.209133268 VAPGPSSGSTPGQVPGSSALS(ph)SPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VAPGPSSGSTPGQVPGSSALSSPRR 25 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4 Q8NEY1-5 NAV1 Neuron navigator 1 1 VAPGPSSGSTPGQVPGS(0.004)S(0.021)ALS(0.572)S(0.403)PRR;VAPGPSSGSTPGQVPGS(0.031)S(0.148)ALS(0.533)S(0.289)PRR;VAPGPSSGSTPGQVPGSS(0.001)ALS(0.636)S(0.363)PRR 185.22 1.07E-17 814540000 129238 154065 168005 175302 196116 128676 152386 129815 231767 TRUE FALSE 121149.2243 165472.1329 171990.1579 179800.5461 180713.8405 165822.6723 129537.134 146022.6885 193083.5904 0.627444435 0.856997389 0.890754919 0.931205732 0.935935778 0.858812869 0.670886292 0.756266694 1 17.55886603 -0.291080646 7.41822274 0.999999971 0.823909605 0.232924661 0.104048022 0 0 0.104450829 0.024619297 0.511586828 0.291080646 -0.176090365 VAPGPSSGSTPGQVPGSSALSS(ph)PRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAPGPSSGSTPGQVPGSSALSSPRR 25 1 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4 Q8NEY1-5 NAV1 Neuron navigator 1 1 VAPGPSSGSTPGQVPGSSALS(0.197)S(0.803)PRR 194.26 1.26E-18 496190000 87018 97973 99491 102880 135130 84556 92776 84958 156930 TRUE FALSE 81571.69871 105227.0229 101850.9735 105520.075 124517.4349 108965.9445 78865.10009 95565.19332 130737.3692 0.623935599 0.804873339 0.779050199 0.807114872 0.952424205 0.833472061 0.603233036 0.730970754 1 16.99631205 -2.355127823 2.189925254 2.38613459 0.76874507 0.347619234 0.100334009 4176529.954 549357.7451 28610748.22 0.02497831 0.004414405 2.355127823 -1.61738952 VAPLWHSS(ph)SEVISMADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VAPLWHSSSEVISMADR 17 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 VAPLWHS(0.006)S(0.992)S(0.002)EVISMADR;VAPLWHS(0.003)S(0.994)S(0.002)EVISMADR;VAPLWHS(0.001)S(0.997)S(0.001)EVISMADR 268.65 3.28E-28 401300000 327480 395534 362420 394491 420481 293733 469492 370381 392290 TRUE FALSE 306983.6114 424819.7489 371016.7735 404614.3069 387458.1184 378528.9487 399096.0332 416623.8832 326814.2647 0.939321335 1.299881293 1.135252691 1.238055834 1.185560608 1.15823876 1.221170788 1.274803239 1 18.31811143 4.752982025 24.78080433 1.198773876 0.939321132 0.463215855 0.083938838 1816.32113 3120987.646 0.017253805 0.374874859 56621.58535 -4.752982025 -0.259452744 VAPPYPHLFSSCSPPGMVLDGS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAPPYPHLFSSCSPPGMVLDGSPK 24 0 Q9BUK6-2;Q9BUK6;Q9BUK6-5;V9GYF2;Q9BUK6-6 Q9BUK6-2 MSTO1 Protein misato homolog 1 1 VAPPYPHLFSSCSPPGMVLDGS(1)PK 182.91 1.90E-17 141890000 145180 125310 120980 118910 131420 100810 158890 128260 202650 TRUE FALSE 136093.443 134588.0828 123849.7027 121961.4319 121098.8033 129912.2105 135065.9196 144273.5433 168826.4058 0.806114673 0.797198058 0.733592012 0.722407323 0.717297764 0.769501725 0.800028401 0.854567404 1 17.36518105 0.912485503 1.27701618 0.999128422 0.756502258 0.874665333 0.029199303 0.194760295 0.634109511 0.029665448 0.009053202 8.174957492 -0.912485503 -0.242626163 VAPVINNGS(ph)PTILGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VAPVINNGSPTILGK 15 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 VAPVINNGS(0.748)PT(0.252)ILGK;VAPVINNGS(0.974)PT(0.026)ILGK 213.02 6.14E-10 245570000 322070 248520 303500 276500 274460 257760 357680 272080 270310 TRUE FALSE 301912.2136 266920.6794 310699.1633 283595.4581 252905.0187 332171.1276 304049.2045 306049.7869 225193.5147 1.340678989 1.1852947 1.379698539 1.259341142 1.123056403 1.475047485 1.350168565 1.359052401 1 17.78080575 2.238741111 25 1.333267861 1.264478666 0 0.14043516 15.26630216 2114887.607 0.045396179 0.035785364 173.2770761 -2.238741111 -0.068789195 VAPVINNGSPT(ph)ILGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAPVINNGSPTILGK 15 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 VAPVINNGS(0.457)PT(0.543)ILGK 150.12 3.62E-05 374270000 141620 112180 144620 121260 138360 118530 159510 130330 141170 TRUE FALSE 132756.257 120485.9239 148050.4547 124371.7369 127493.7637 152747.6868 135592.9563 146601.9874 117607.815 1.128804723 1.024472089 1.258848782 1.057512521 1.084058604 1.298788578 1.152924713 1.246532702 1 16.8436244 VAPYRPDQQVEEDDDFMDENQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VAPYRPDQQVEEDDDFMDENQGK 23 1 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;; 201.15 2.11E-24 474160000 397492 330802 373094 367334 407421 318717 465830 333280 485560 FALSE TRUE 372613.6853 355294.9243 381943.9659 376760.4123 375423.7981 410725.424 395983.1161 374890.7416 404516.8992 0.921132556 0.878319114 0.944197799 0.931383616 0.928079393 1.015347999 0.978903766 0.926761632 1 18.62584045 3.027017402 0.840944593 0.979296964 0.899330457 0.486007782 0.029174496 0.480221088 0.751855592 0.015574907 0.020606105 1064.18566 -3.027017402 -0.079966507 VAQEQGGHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VAQEQGGHPK 10 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 ; 105.46 0.0025462 304390000 191319 207184 188608 190628 216266 132355 235370 196351 231415 FALSE TRUE 179344.6853 222524.1189 193081.8708 195519.8372 199281.3407 170563.7399 200078.4536 220865.8546 192790.3415 0.930257625 1.154228564 1.001512157 1.014157845 1.033668695 0.884711021 1.037803305 1.145627176 1 17.55667325 6.751763794 9.823965099 1.027434807 0.437799911 0 0.082735773 0 0 0.017443315 0 5646297.979 -6.751763794 -0.589634896 VAQGATEKS(ph)PEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAQGATEKSPEDK 13 1 P49321;P49321-3;P49321-4 P49321 NASP Nuclear autoantigenic sperm protein 1 VAQGAT(0.003)EKS(0.997)PEDK 99.569 0.0016959 348240000 575840 188500 305660 284410 309710 205850 398730 238600 326840 TRUE FALSE 539799.2023 202456.7361 312910.3995 291708.4421 285386.6259 265275.5533 338944.1381 268389.7352 272288.2925 1.982454689 0.74353816 1.149187858 1.071322015 1.048104651 0.974245168 1.244798794 0.985682244 1 18.05477543 4.749744969 24.99807597 1.037590236 1.982455235 0.842739815 0.129625346 662.8779251 1481566.492 0.031219097 0.483288201 56201.11987 -4.749744969 0.944864999 VAQGATEKS(ph)PEDKVQIAANEETQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VAQGATEKSPEDKVQIAANEETQER 25 2 P49321;P49321-3;P49321-4 P49321 NASP Nuclear autoantigenic sperm protein 1 VAQGATEKS(1)PEDKVQIAANEETQER;VAQGAT(0.055)EKS(0.945)PEDKVQIAANEETQER;VAQGATEKS(1)PEDKVQIAANEETQER 257.88 3.17E-45 1132140000 1315570 503892 738950 718820 748380 509027 1028030 642130 845970 TRUE FALSE 1233230.822 541200.688 756478.243 737266.1382 689605.2536 655974.8315 873886.4453 722301.344 704772.1418 1.749829128 0.767908741 1.073365699 1.046105676 0.978479728 0.930761579 1.239955999 1.024872155 1 19.42679737 4.750614178 24.99889617 1.013555328 1.749829577 0.796995201 0.117678134 911.9188219 1891270.865 0.029532446 0.50330493 56313.71497 -4.750614178 0.736274249 VAQWMIQQPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAQWMIQQPHK 11 0 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZGZ8 P55263-3 ADK Adenosine kinase 0 94.616 0.0083709 338560000 168110 281500 93535 74621 346140 101960 112340 235450 315040 FALSE TRUE 157588.2952 302342.5529 95753.69437 76535.90119 318955.5607 131394.1968 95495.65991 264846.4508 262457.7888 0.600432915 1.151966396 0.364834646 0.29161223 1.215264223 0.500629825 0.363851499 1.009101128 1 18.00172589 1.199959186 24.55642059 1.004552674 0.65061802 0.187346146 0.314116813 275.9317448 175527.5318 0.296646584 0.074167982 15.84744254 -1.199959186 -0.353934654 VARPLPAEEPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VARPLPAEEPER 12 1 P26358;P26358-2;K7ENQ6 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 135.02 0.00024768 0 87551 102980 93771 93863 109090 63210 96469 97374 121220 FALSE TRUE 82071.33919 110604.7464 95995.2924 96271.68349 100522.5114 81457.70087 82004.36902 109531.3582 100987.5989 0.812687301 1.095230975 0.950565153 0.953302035 0.995394608 0.806610928 0.812024149 1.084602065 1 16.62381862 2.285766323 24.99933661 0.895933473 0.977828733 0 0.10757603 250.6592727 132743.7586 0.035406719 0.029623308 193.092908 -2.285766323 0.08189526 VARPTSSEVDRFS(ph)PSGSVVPLTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VARPTSSEVDRFSPSGSVVPLTER 24 2 Q5TC79;Q5TC79-2 Q5TC79 ZBTB37 Zinc finger and BTB domain-containing protein 37 1 VARPTSSEVDRFS(0.999)PS(0.001)GSVVPLTER;VARPTSSEVDRFS(0.997)PS(0.003)GSVVPLTER 147.25 9.45E-08 183022000 211180 187406 175488 181605 216501 154818 237120 173971 236220 TRUE FALSE 197962.6208 201281.7352 179650.6582 186265.2918 199497.8848 199511.4433 201566.0573 195691.6623 196793.356 1.005941587 1.022807575 0.912889855 0.946501933 1.013742988 1.013811886 1.02425235 0.994401774 1 17.58632199 2.716555115 24.06429702 1.01222088 0.970639731 0.262374188 0.03073518 676.5844155 739882.9452 0.010708025 0.010104306 520.6610804 -2.716555115 -0.041581149 VAS(ph)DTEEADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VASDTEEADR 10 0 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 VAS(0.997)DT(0.003)EEADR;VAS(0.997)DT(0.003)EEADR 200.27 2.76E-07 1038200000 802320 677800 698400 665590 666800 603420 849070 627650 721700 TRUE FALSE 752104.2234 727985.0173 714966.3778 682670.1662 614432.2177 777617.5583 721759.8359 706013.4841 601243.6076 1.250914295 1.210798764 1.189145911 1.135430228 1.021935551 1.293348567 1.200444922 1.174255285 1 19.19759012 0.880370267 9.323714735 1.000000003 1.187612312 0.397352083 0.071541525 18.71613227 1459.537893 0.0666687 0.016680586 7.592245917 -0.880370267 0.187612309 VAS(ph)DTEEADRTSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VASDTEEADRTSSK 14 1 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 VAS(0.627)DT(0.373)EEADRTSSK 113.47 0.0012383 0 113460 85858 104190 115110 131580 79797 117070 91001 201390 TRUE FALSE 106358.7411 92215.01566 106661.436 118063.9175 121246.2376 102833.0985 99516.44032 102362.6752 167776.708 0.633930314 0.549629426 0.635734467 0.70369671 0.722664302 0.612916416 0.593148128 0.61011255 1 17.35618292 -2.17357522 2.353052747 1.955470273 0.626949846 0.840050766 0.050308683 3359645.811 685953.0773 17138295.92 0.013174294 0.006705401 2.17357522 -1.328520427 VAS(ph)EEEEVPLVVYLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VASEEEEVPLVVYLK 15 0 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 VAS(1)EEEEVPLVVYLK;VAS(1)EEEEVPLVVYLK;VAS(1)EEEEVPLVVYLK;VAS(1)EEEEVPLVVYLK 270.97 2.30E-33 38642800 169252 118547 123630 130540 109186 97784 159064 101189 227182 TRUE FALSE 158658.8194 127324.3432 126562.562 133889.8774 100610.972 126012.6534 135213.8299 113822.6694 189263.8565 0.838294339 0.672734592 0.668709622 0.707424438 0.531591049 0.665804109 0.714419712 0.601396756 1 17.5300394 -1.2031704 4.644985562 1.000064938 0.673589651 0.628797492 0.078457418 3.683680631 44514144.08 5303.712787 0.016829356 0.062636805 1.2031704 -0.326475288 VAS(ph)FSIPGSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 VASFSIPGSSSR 12 0 Q14573 Q14573 ITPR3 "Inositol 1,4,5-trisphosphate receptor type 3" 1 VAS(0.993)FS(0.007)IPGSSSR;VAS(0.997)FS(0.003)IPGSSSR;VAS(0.997)FS(0.003)IPGSSSR;VAS(0.994)FS(0.006)IPGSSSR;VAS(0.587)FS(0.413)IPGSSSR;VAS(0.995)FS(0.005)IPGSSSR;VAS(0.985)FS(0.015)IPGSSSR;VAS(0.994)FS(0.006)IPGSSSR 243.4 2.54E-16 1521749000 1537652 1555634 1217320 1074027 1708637 1184845 1866147 1831699 2198086 TRUE FALSE 1441413.106 1670814.76 1246195.405 1101588.351 1574447.542 1526890.517 1586335.582 2060390.652 1831211.246 0.787136443 0.912409621 0.680530664 0.601562683 0.859784771 0.833814515 0.866276671 1.125151812 1 20.8043668 1.45034902 2.524287579 1.061919061 0.77840022 0.594885134 0.094188519 0.196258236 2.341936483 0.078003646 0.025545332 28.2064883 -1.45034902 -0.283518841 VASASAGSCDVPS(ph)PFNHRPGSHLDSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VASASAGSCDVPSPFNHRPGSHLDSHR 27 1 Q16643;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 VASASAGSCDVPS(0.818)PFNHRPGS(0.153)HLDS(0.029)HR 117.43 0.00025548 348760000 22368 24259 25142 22726 27203 20022 24307 20233 26456 TRUE FALSE 20968.02681 26055.1616 25738.38011 23309.18764 25066.58611 25802.02637 20662.39101 22759.13459 22040.32269 0.951348449 1.182158808 1.167785993 1.057570162 1.137305768 1.170673712 0.937481329 1.032613493 1 14.42785773 1.74137988 13.39822889 0.989712142 1.124813701 0.376594116 0.072025377 0.065957634 109.8867641 0.031747256 0.0174597 55.12897015 -1.74137988 0.135101559 VASEAPLEHKPQVEAS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VASEAPLEHKPQVEASSPR 19 1 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 VASEAPLEHKPQVEAS(0.811)S(0.189)PR 185.96 1.30E-14 435200000 302260 286260 332150 402190 346850 192510 296070 222740 256620 TRUE FALSE 283342.0861 307454.9883 340028.7549 412510.8763 319609.8001 248084.5119 251677.0521 250549.5793 213788.4642 1.325338517 1.43812712 1.590491593 1.929528227 1.494981506 1.160420478 1.17722466 1.171950883 1 17.70582448 2.268701278 4.625977988 1.14337021 1.565831706 0.640274337 0.160058766 0.135661104 6.784006101 0.060187197 0.047820403 185.6527034 -2.268701278 0.422461496 VASEAPLEHKPQVEASS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VASEAPLEHKPQVEASSPR 19 1 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 VASEAPLEHKPQVEAS(0.122)S(0.878)PR 174.53 2.61E-12 855060000 727410 694710 795750 968920 930680 493990 757030 581950 621010 TRUE FALSE 681882.7066 746147.0512 814625.5658 993784.1276 857588.147 636596.8937 643520.3794 654607.7385 517359.4191 1.318005784 1.442221836 1.574583424 1.920877616 1.657625464 1.230473188 1.24385554 1.26528621 1 18.98080737 2.228287232 23.61095773 1.210265477 1.577783434 0.574186574 0.169553497 87.50024945 201095.8151 0.065483725 0.048967535 169.1559319 -2.228287232 0.367517957 VASGPSPGEGIS(ph)PQSAQAPQAPGDNHVVPVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VASGPSPGEGISPQSAQAPQAPGDNHVVPVLR 32 0 Q14764 Q14764 MVP Major vault protein 1 VASGPSPGEGIS(1)PQSAQAPQAPGDNHVVPVLR 193.84 1.21E-20 263140000 46754 47766 39916 46429 43587 28124 52251 39661 34730 TRUE FALSE 43827.7506 51302.64434 40862.82637 47620.44674 40163.85284 36242.94225 44416.44762 44612.76315 28933.33864 1.514783729 1.773132544 1.412309408 1.645867673 1.388151342 1.252636023 1.535130397 1.541915495 1 14.82044519 -3.280347161 0.14930396 4.06E-14 1.704495263 0.585324775 0.137334366 51.79818524 0.748427846 17.35623463 0.746930047 0.000524388 3.280347161 1.704495263 VASGSDLHLTDIDS(ph)DSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VASGSDLHLTDIDSDSNR 18 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VASGSDLHLTDIDS(1)DSNR;VASGSDLHLTDIDS(1)DSNR;VASGSDLHLTDIDS(1)DSNR 303.17 6.31E-50 921450000 1298980 1615770 1677320 1617350 1740670 1705730 1936430 1728730 1612710 TRUE FALSE 1217679.161 1735403.292 1717106.822 1658853.939 1603964.8 2198146.561 1646080.298 1944565.746 1343538.282 0.906322638 1.291666426 1.278048303 1.234690489 1.193836321 1.636087776 1.225183026 1.447346735 1 20.357606 4.739165049 5.68980165 1.303242206 0.8932825 0.341583079 0.165632334 0.145310304 19.84346202 0.034844551 0.231378095 54848.53712 -4.739165049 -0.409959706 VASGSDLHLTDIDSDSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VASGSDLHLTDIDSDSNR 18 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 0 149.57 6.12E-08 249230000 200780 290290 277600 311250 292490 217960 270130 212600 255680 FALSE TRUE 188213.5382 311783.3736 284184.8031 319237.2019 269519.0152 280881.5137 229626.5143 239143.578 213005.3562 0.883609415 1.463734899 1.334167404 1.498728518 1.265315671 1.318659393 1.078031643 1.12271157 1 17.70053018 1.732599321 3.993554517 1.070077399 1.326641091 0.273582825 0.168811858 0.221525179 7.848592167 0.084473403 0.041674942 54.02556545 -1.732599321 0.256563692 VASLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VASLEK 6 0 Q92805;H0YE54 Q92805 GOLGA1 Golgin subfamily A member 1 0 94.669 0.044219 336610000 938060 1842600 1666400 1949200 1741100 1811400 1595300 1808500 1640600 FALSE TRUE 879348.4991 1979028.021 1705927.795 1999219.772 1604361.029 2334321.774 1356099.575 2034295.206 1366773.261 0.64337555 1.447956349 1.2481425 1.462729648 1.17383115 1.707907113 0.992190595 1.488392599 1 20.3823425 4.745292332 24.67951263 1.320079062 0.643375177 0.470084264 0.224094883 524.5870108 1923157.382 0.045853075 0.444815053 55627.85728 -4.745292332 -0.676703885 VASPLS(ph)PTSLTHTSRPPAALTPVPLSQGDLSHPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VASPLSPTSLTHTSRPPAALTPVPLSQGDLSHPPR 35 1 I3L4Q4;Q9BUL5-4;Q9BUL5;I3L0Y2;I3L410;I3L1N0;Q9BUL5-3;I3L2W6 I3L4Q4 PHF23 PHD finger protein 23 1 VAS(0.018)PLS(0.975)PT(0.003)S(0.003)LT(0.001)HTSRPPAALTPVPLSQGDLSHPPR;VAS(0.003)PLS(0.249)PT(0.249)S(0.249)LT(0.249)HTSRPPAALTPVPLSQGDLSHPPR 255.35 5.04E-60 434690000 62311 156697 139089 148711 164880 130159 145349 135781 128530 TRUE FALSE 58411.06574 168299.0089 142388.2568 152527.176 151930.9899 167733.7903 123555.2668 152733.5567 107077.5127 0.545502639 1.571749331 1.329768064 1.424455726 1.418887926 1.566470739 1.153886224 1.426383121 1 16.70829601 -1.661588214 6.156865991 0.997228607 1.335934134 0.086381407 0.296201089 0.009984695 0.000548808 0.254133061 0.059501493 0.021797756 1.661588214 0.338705527 VASPSQGQVGSS(ph)SPKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VASPSQGQVGSSSPKR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 VASPSQGQVGS(0.073)S(0.463)S(0.463)PKR 145.05 7.70E-07 465170000 121670 72742 85414 82224 90864 58829 96375 79576 115040 TRUE FALSE 114054.8919 78127.89337 87440.06042 84334.00704 83727.90797 75811.97729 81924.46345 89511.23877 95839.08081 1.19006663 0.815198692 0.912363304 0.879954256 0.873630123 0.791034061 0.8548127 0.933974304 1 16.54832645 4.744753873 24.99541704 0.871398729 1.19006677 0.721128764 0.059723706 333.6633978 1346598.163 0.012839022 0.119331441 55558.92996 -4.744753873 0.318668041 VASPSQGQVGSSS(ph)PKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VASPSQGQVGSSSPKR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 VASPSQGQVGS(0.018)S(0.22)S(0.762)PKR;VASPSQGQVGSS(0.032)S(0.968)PKR 248.23 1.35E-20 756680000 460320 319430 358400 332470 379360 277550 405910 330240 493380 TRUE FALSE 431509.3929 343080.9296 366901.4172 341001.7431 349566.5959 357674.1794 345047.5638 371471.1909 411031.6906 1.049820252 0.834682428 0.892635351 0.82962397 0.850461421 0.870186381 0.839467057 0.903753164 1 18.6488901 0.975047903 19.65470875 1.000000003 0.872657887 0.24596279 0.063840147 153.9641499 121279.0521 0.05447001 0.013617503 9.44165012 -0.975047903 -0.127342116 VASS(ph)PVMVSNPATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VASSPVMVSNPATR 14 0 P51610-2;P51610;A6NEM2;P51610-4 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 1 VAS(0.002)S(0.998)PVMVSNPATR;VAS(0.002)S(0.998)PVMVSNPATR;VAS(0.003)S(0.997)PVMVSNPATR;VAS(0.022)S(0.978)PVMVSNPATR 282.15 2.41E-33 852160000 978230 1018880 1043520 1021410 1153740 923920 1182390 946750 1434010 TRUE FALSE 917004.3305 1094318.935 1068272.787 1047621.11 1063129.914 1190640.705 1005101.596 1064953.822 1194664.467 0.767583163 0.91600526 0.894203198 0.876916606 0.88989833 0.99663189 0.84132543 0.891425041 1 20.18817405 -4.464802591 0.014112712 2.023143828 6.69E-07 0.362198443 0.054059065 7974.53812 9.298740849 809.1651145 547.2723518 3.43E-05 4.464802591 -2.023143159 VASSTLLDDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VASSTLLDDRR 11 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;; 159.94 4.50E-05 803530000 482165 775560 570800 553290 736370 389244 631880 637040 831700 FALSE TRUE 451987.1533 832983.2694 584339.6456 567488.3581 678538.4706 501612.424 537135.4601 716575.8463 692883.897 0.652327403 1.202197472 0.843344243 0.819023736 0.97929606 0.72394874 0.775217121 1.034193246 1 19.4022541 3.720450182 24.66167389 0.859513653 0.983408469 0 0.166488284 510.8429905 1888495.569 0.040358322 0.064150878 5253.517481 -3.720450182 0.123894816 VASWELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VASWELR 7 0 J3KMX2;B9EGA3;Q92925-3;Q92925-2;Q92925 J3KMX2 SMARCD2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 0 79.116 0.077928 61586000 101910 114260 104460 113730 137130 94838 126070 118140 153220 FALSE TRUE 95531.63501 122719.9293 106937.8405 116648.5043 126360.363 122216.191 107166.9739 132890.0391 127646.5922 0.74840725 0.961403882 0.837764947 0.91383955 0.989923513 0.957457531 0.839560008 1.041077845 1 16.9617955 8 0.262426843 0.96396478 3.60E-13 0.361675647 0.071347117 71.69492949 0.99523225 0.082767534 31.00716445 100000000 -8 -0.96396478 VATLNS(ph)EEESDPPTYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VATLNSEEESDPPTYK 16 0 Q00341;A0A024R4E5;Q00341-2;C9JIZ1;C9JZI8;C9J5E5;C9JHZ8;C9JES8;C9JK79;C9JHS7;C9JT62;C9JQ82;C9JHN6;C9JEJ8;C9JBS3;C9JMQ6 Q00341 HDLBP Vigilin 1 VATLNS(1)EEESDPPTYK;VATLNS(1)EEESDPPTYK;VATLNS(1)EEESDPPTYK;VATLNS(1)EEESDPPTYK;VATLNS(0.998)EEES(0.002)DPPTYK;VATLNS(0.997)EEES(0.003)DPPTYK 315.94 8.32E-58 2410266000 7863740 6187850 6875960 6790940 6490930 5378010 8607730 5713130 5806820 TRUE FALSE 7371562.551 6646004.852 7039061.018 6965207.017 5981158.541 6930554.182 7317080.797 6426426.857 4837624.229 1.523798088 1.373815852 1.455065686 1.439799101 1.236383452 1.432635909 1.512535999 1.328426218 1 22.20586728 0.944264139 9.79080492 1.000000159 1.42190495 0.737251274 0.079486155 1.422884527 250.1298843 0.073690534 0.018434022 8.795573031 -0.944264139 0.42190479 VATTAGLYGSNLMEHTEIDHWLEFSATK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VATTAGLYGSNLMEHTEIDHWLEFSATK 28 0 P07814;V9GYZ6;V9GZ76 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 211.94 4.18E-26 505450000 411949 380931 422060 408169 436477 342780 493090 408648 429971 FALSE TRUE 386165.8474 409135.5276 432071.4625 418643.3076 402197.8571 441735.0214 419155.7321 459668.6023 358206.0624 1.07805503 1.142179239 1.206209241 1.168722005 1.122811419 1.233186894 1.170152535 1.283251878 1 18.45043023 4.657128565 2.04148346 1.178384153 1.059348571 0.12102479 0.074439506 1.022864102 5.389188913 0.016378293 0.212624995 45407.60178 -4.657128565 -0.119035582 VATTPGS(ph)PSLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VATTPGSPSLGR 12 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 VAT(0.002)T(0.028)PGS(0.949)PS(0.02)LGR;VATT(0.029)PGS(0.944)PS(0.027)LGR;VATTPGS(0.999)PSLGR;VAT(0.002)T(0.074)PGS(0.889)PS(0.035)LGR 208.82 6.55E-08 2845660000 1724120 1545490 1868310 1705580 1972750 1906570 2149620 1803710 2912990 TRUE FALSE 1616210.407 1659919.688 1912627.195 1749348.07 1817818.173 2456965.808 1827304.437 2028907.164 2426793.15 0.665986059 0.683997187 0.788129468 0.720847622 0.749061852 1.01243314 0.752970824 0.83604454 1 21.21061971 5.895395302 0.072218301 1.251069935 2.24E-11 0.587798008 0.076878681 106.5059302 0.880396575 3.621630437 14.87078315 785950.6952 -5.895395302 -1.251069935 VAVAT(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VAVATPAK 8 0 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 VAVAT(1)PAK;VAVAT(1)PAK;VAVAT(1)PAK 128.81 0.0075751 349260000 2330530 1985190 2119310 1803660 2488990 1120660 2859850 1704090 3850720 TRUE FALSE 2184666.287 2132175.533 2169581.034 1849944.969 2293514.766 1444176.35 2431042.042 1916849.388 3208009.955 0.681003587 0.664641183 0.676301216 0.576664348 0.714933806 0.450178263 0.757803771 0.597519775 1 21.61324719 -1.488748916 3.476283526 1.005913406 0.645592778 0.638181391 0.085119677 155710364 364793409.1 9916885.61 0.017814764 0.032452719 1.488748916 -0.360320628 VAVAT(ph)PAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VAVATPAKK 9 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 VAVAT(1)PAKK;VAVAT(1)PAKK;VAVAT(1)PAKK;VAVAT(1)PAKK;VAVAT(1)PAKK 109.24 0.0014544 10476770000 23384900 16264400 18858000 15600800 20287700 8187750 27643200 14093300 43239100 TRUE FALSE 21921280.85 17468633.1 19305320.67 16001142.94 18694385.88 10551420.51 23498358.79 15852879.53 36022214.87 0.608548945 0.484940561 0.535928197 0.444202085 0.518968252 0.292914263 0.652329649 0.440086196 1 25.10238355 -1.317217703 3.238137749 1.003063413 0.500825737 0.721949843 0.098032937 12763474.61 17642478.81 377345.3075 0.022154676 0.048170627 1.317217703 -0.502237676 VAVEEVDEEGKFVR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;; 249.32 3.96E-18 8476100000 8224310 6149640 7000350 6797480 7734090 5049652 8339150 6146320 10754610 FALSE TRUE 7709565.118 6604965.744 7166401.608 6971914.845 7126685.769 6507404.558 7088771.874 6913701.582 8959596.114 0.860481323 0.737194586 0.799857663 0.778150572 0.795424892 0.72630557 0.79119324 0.771653264 1 23.09500227 -1.145585008 5.193303639 1.000008086 0.77869325 0.776151979 0.036651335 2.98E-06 4.90E-07 0.030774892 0.007253447 0.071517939 1.145585008 -0.221314837 VAVPTGPTPLDS(ph)TPPGGAPHPLTGQEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAVPTGPTPLDSTPPGGAPHPLTGQEEAR 29 0 O94966-3;O94966;O94966-7;O94966-6;O94966-5;A0A0A0MR08;E7ESU0;O94966-2;O94966-4 O94966-3 USP19 Ubiquitin carboxyl-terminal hydrolase 19;Ubiquitin carboxyl-terminal hydrolase 1 VAVPTGPT(0.002)PLDS(0.538)T(0.46)PPGGAPHPLTGQEEAR 91.079 0.00099182 130260000 22808 28378 28306 25205 23755 23156 27832 21443 29614 TRUE FALSE 21380.48799 30479.13665 28977.43169 25851.80297 21889.37812 29840.76129 23658.84998 24120.20575 24671.23209 0.866616143 1.235412019 1.174543354 1.047852125 0.887243006 1.209536726 0.958965077 0.977665228 1 14.59054215 3.08436042 5.95430818 1.01267935 1.13364957 0.055501003 0.125691598 0.356028533 19.84148294 0.034483913 0.041378661 1214.396257 -3.08436042 0.12097022 VAVPTGPTPLDST(ph)PPGGAPHPLTGQEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAVPTGPTPLDSTPPGGAPHPLTGQEEAR 29 0 O94966-3;O94966;O94966-7;O94966-6;O94966-5;A0A0A0MR08;E7ESU0;O94966-2;O94966-4 O94966-3 USP19 Ubiquitin carboxyl-terminal hydrolase 19;Ubiquitin carboxyl-terminal hydrolase 1 VAVPTGPTPLDS(0.047)T(0.953)PPGGAPHPLTGQEEAR 197.89 1.50E-24 114230000 42259 38267 39675 37493 41565 38166 49372 42309 48986 TRUE FALSE 39614.08462 41100.3285 40616.10974 38455.13386 38300.65257 49183.90463 41969.12695 47591.37178 40809.92014 0.970697431 1.007116122 0.9952509 0.942298679 0.938513294 1.205194827 1.028405025 1.166171647 1 15.31663227 2.260759902 24.99999448 1.098066091 0.977774035 0.515515098 0.062004465 183.4759656 206623.1402 0.019248049 0.01609213 182.2887647 -2.260759902 -0.120292057 VAVVTGS(ph)TSGIGFAIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAVVTGSTSGIGFAIAR 17 0 Q13268;C9JZP6;Q13268-2 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 1 VAVVTGS(0.859)T(0.1)S(0.04)GIGFAIAR 185.74 1.43E-14 0 54323 62112 54246 52223 75416 56562 59891 50957 74419 TRUE FALSE 50923.0204 66710.83711 55532.74074 53563.13059 69493.13157 72890.53119 50910.90055 57319.09362 61997.98813 0.821365692 1.07601616 0.895718432 0.863949496 1.120893333 1.175691879 0.821170204 0.924531511 1 15.91993378 VAVVTGST(ph)SGIGFAIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAVVTGSTSGIGFAIAR 17 0 Q13268;C9JZP6;Q13268-2 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 1 VAVVT(0.001)GS(0.223)T(0.388)S(0.388)GIGFAIAR 111.78 0.005512 33938000 55054 57716 53611 54019 68056 49255 56754 51891 74709 TRUE FALSE 51608.26841 61989.35269 54882.67824 55405.21899 62711.15628 63474.11891 48244.26458 58369.70558 62239.58526 0.829187216 0.995979527 0.881796979 0.890192612 1.007576706 1.019835184 0.775137951 0.937822856 1 15.92554483 -2.656686147 1.965418845 2.621650683 0.916980097 0.099365538 0.078347126 3542586.652 137520.9914 25753684.72 0.01847534 0.002204519 2.656686147 -1.704670586 VAWVSHDSTVCLADADKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAWVSHDSTVCLADADKK 18 1 A0A1W2PNV4;C9JEY1;C9K057;O15143 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 249.86 6.01E-25 199560000 363030 445930 525490 540210 594210 378960 732100 488190 700990 FALSE TRUE 340308.6003 478947.1212 537954.871 554072.7032 547543.1435 488359.6001 622328.4015 549141.5961 583990.2404 0.582729944 0.820128639 0.921170995 0.948770484 0.937589545 0.836246167 1.065648633 0.940326667 1 19.15558473 5.270591143 0.817815495 0.95892599 4.41E-13 0.804885756 0.057810852 2.200653855 0.61401173 0.018771408 2.340256171 186462.3457 -5.270591143 -0.95892599 VAYEGS(ph)DSEKGEGAEPLKVPVWEPQDWQQQLVNIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VAYEGSDSEKGEGAEPLKVPVWEPQDWQQQLVNIR 35 2 P78549-3;P78549-2;P78549;H3BRL9;A0A494C106;H3BPD5 P78549-3 NTHL1 Endonuclease III-like protein 1 1 VAYEGS(0.919)DS(0.081)EKGEGAEPLKVPVWEPQDWQQQLVNIR 76.31 0.0015179 115920000 412520 193720 206880 240680 216690 152280 209920 166040 145680 TRUE FALSE 386701.1096 208063.2304 211787.2913 246856.2563 199672.0415 196240.7639 178444.4448 186770.4595 121365.0669 3.186263721 1.71435847 1.745043255 2.033997613 1.645218403 1.616946037 1.470311428 1.538914486 1 16.8889937 4.741387941 4.580197695 1.633343088 3.288286092 0.78619609 0.260396188 0.084968167 4.690282335 0.057815756 0.454328211 55129.99343 -4.741387941 1.654943005 VAYTEADYYHTELWMEQALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VAYTEADYYHTELWMEQALR 20 0 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ;;; 352.84 3.53E-95 517320000 542219 721490 598680 663290 753520 467012 708500 573950 398943 FALSE TRUE 508282.4807 774909.8703 612880.9723 680311.1443 694341.5788 601830.7831 602267.0024 645608.9209 332356.836 1.529327595 2.331559897 1.844045032 2.046929898 2.089144869 1.810797065 1.812109567 1.942517352 1 18.3423735 -1.309485976 0.382013982 0.453166303 2.006760067 0.646364371 0.213326313 11.75602875 1.035799393 6.636662216 0.134136921 0.049035886 1.309485976 1.553593764 VAYVSFGPHAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VAYVSFGPHAGK 12 0 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ; 210.35 4.45E-08 1598570000 2960050 6169900 3045630 3211240 7411800 2439880 3887200 5974400 6766800 FALSE TRUE 2774785.754 6626725.816 3117873.782 3293645.855 6829707.126 3144233.748 3304350.447 6720316.991 5637377.365 0.492212172 1.175498 0.553071682 0.584251442 1.211504337 0.557747609 0.586150302 1.1920999 1 22.42659271 1.230952558 24.99839466 1.096050058 0.755581819 0.244930754 0.260388546 280.0917237 920281.1974 0.221222764 0.059535022 17.01972575 -1.230952558 -0.340468239 VCCSPGTYGPDCLACQGGSQRPCSGNGHCSGDGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VCCSPGTYGPDCLACQGGSQRPCSGNGHCSGDGSR 35 1 A6PWM2;Q6UXH1-3;Q6UXH1-2;Q6UXH1-4;Q6UXH1;Q6UXH1-6;Q6UXH1-5 A6PWM2 CRELD2 Cysteine-rich with EGF-like domain protein 2 0 ; 166.28 6.41E-15 349838000 17086.3 38115 34019 35638 37821 40405 48453 39080 40428 FALSE TRUE 16016.89898 40937.07426 34825.94674 36552.53141 34850.69122 52069.26758 41187.92247 43959.22403 33680.30563 0.475556818 1.215460296 1.034015164 1.085279089 1.034749851 1.545985602 1.222908216 1.30519077 1 15.03961761 2.427984327 22.58830019 1.289580069 1.014969401 0.276339774 0.233513733 57.28798527 26334.37693 0.073912017 0.061839261 267.9071641 -2.427984327 -0.274610668 VCDGAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VCDGAIR 7 0 P42345 P42345 MTOR Serine/threonine-protein kinase mTOR 0 91.26 0.038468 13842000 3205.2 1698.7 2379.6 1855.6 3271.8 2551.8 2426.8 1980.1 2576.2 FALSE TRUE 3004.592253 1824.473515 2436.045236 1903.217838 3014.846026 3288.463235 2062.923869 2227.319844 2146.215577 1.399948955 0.850088656 1.135042193 0.886778503 1.404726561 1.532214783 0.96119136 1.037789432 1 11.06757928 1.595782967 25 0.999598561 1.155955628 0.137637687 0.219186825 2.212399772 4565.322268 0.119166421 0.055821139 39.42602262 -1.595782967 0.156357067 VCEEIAIIPSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VCEEIAIIPSKK 12 1 H3BNC9;P08708;H0YN88;A0A075B716;H0YN73 H3BNC9 RPS17 40S ribosomal protein S17 0 ; 150.21 0.00010892 2431800000 3639000 2926000 3121200 2882400 3254900 2399900 3939900 2780900 4246000 FALSE TRUE 3411241.486 3142644.085 3195236.338 2956367.264 2999273.284 3092712.171 3349148.571 3128101.487 3537315.17 0.964358934 0.888426372 0.903294217 0.835765863 0.847895406 0.874310606 0.946805249 0.884315176 1 21.75422334 -1.169879982 3.074132976 1.000296972 0.893689375 0.422818153 0.039230187 5589855.113 8073196.609 16403.93213 0.009752629 0.067626984 1.169879982 -0.106607597 VCENIPIVLCGNKVDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VCENIPIVLCGNKVDIK 17 1 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 153.21 1.68E-07 621970000 955990 660470 747150 721970 929760 560770 1011230 665350 1446970 FALSE TRUE 896156.2924 709371.886 764872.7508 740496.9725 856740.4001 722655.1957 859605.4493 748420.4121 1205461.359 0.743413537 0.588465056 0.634506237 0.614285117 0.710715772 0.59948433 0.713092496 0.620858069 1 20.20115398 -5 0.378025783 5.901276771 0.639796898 0.801135639 0.054003477 223.0963718 1.678968602 895.6982484 0.032498428 1.00E-05 5 -5.261479873 VCEVCSAYLGLHDNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 240.2 7.45E-20 4453410000 1309765 1402350 1385370 1392830 1573160 1420340 1602960 1301510 1418860 FALSE TRUE 1227789.147 1506181.453 1418231.631 1428572.376 1449610.359 1830369.101 1362611.029 1464006.388 1182043.1 1.038700828 1.274218726 1.199813806 1.208562003 1.226359986 1.548479155 1.152759176 1.238538924 1 20.17285121 0.484675769 1.87889792 1.000095229 1.244523048 0.249195852 0.128065774 5.823432074 19.64054264 0.113202743 0.031448392 3.052641257 -0.484675769 0.244427818 VCEVCSAYLGLHDNDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VCEVCSAYLGLHDNDRR 17 1 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2;Q9NQ29-3;Q9NQ29;Q9NQ29-2;A8MYV2;B8ZZ10 Q9Y383;Q9NQ29-3 LUC7L2;LUC7L Putative RNA-binding protein Luc7-like 2;Putative RNA-binding protein Luc7-like 1 0 ;;;;; 182.15 4.96E-10 3968870000 1944650 2410660 2201950 2186680 2588420 1994360 2565900 2216220 3059880 FALSE TRUE 1822937.828 2589147.775 2254181.294 2242793.911 2385135.934 2570099.356 2181167.116 2492919.946 2549166.26 0.71511139 1.015684153 0.884281786 0.879814685 0.935653343 1.008211742 0.85563941 0.977935407 1 21.28159404 4.751901158 24.6112036 0.935963511 0.71511121 0.608748103 0.057458443 1262.579289 2329209.616 0.012848802 0.247643261 56480.84139 -4.751901158 -0.220852301 VCGEEGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VCGEEGVR 8 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 133.81 0.0021016 399930000 276090 332830 294900 282560 316510 249310 337020 260610 281530 FALSE TRUE 258810.0197 357473.0795 301895.1673 289810.968 291652.5813 321281.7498 286486.9797 293147.7322 234540.8242 1.103475357 1.524140118 1.287175349 1.235652552 1.243504547 1.369832953 1.221480229 1.249879347 1 17.83947953 -1.208666099 0.265363137 0.785512837 1.349339298 0.373901413 0.110620191 16.35737102 0.947302584 2.621174707 0.15168731 0.061849174 1.208666099 0.56382646 VCGTLLEYLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VCGTLLEYLGK 11 0 F8VWW7;Q8NCJ5 F8VWW7 SPRYD3 SPRY domain-containing protein 3 0 ; 81.338 0.021948 939770000 795520 4098300 1945370 2112700 4200500 1831990 1635280 3352500 2618100 FALSE TRUE 745729.8232 4401742.396 1991515.095 2166915.459 3870609.674 2360855.773 1390084.945 3771067.005 2181122.196 0.3419019 2.018109028 0.913069015 0.993486501 1.774595518 1.082404176 0.637325569 1.728957236 1 21.05663917 2.022053986 24.99235438 1.026313711 1.281979397 0 0.530548805 764.9569711 866872.6552 0.184606856 0.136331726 105.2092649 -2.022053986 0.255665686 VCHAHPTLSEAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VCHAHPTLSEAFR 13 0 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 ; 232.14 7.19E-13 398280000 60538 188567 65503 59887 226621 46365 63072 198528 260715 FALSE TRUE 56749.03464 202528.6969 67056.76209 61423.80181 208823.1008 59749.82283 53614.93913 223314.6578 217199.9822 0.261275503 0.93245264 0.308732816 0.282798374 0.961432403 0.275091288 0.246845965 1.028152284 1 17.72866446 1.222681331 24.92908308 1.014076858 0.486143134 0.415777605 0.268883179 270.5033488 424654.3673 0.247747795 0.062768031 16.69864882 -1.222681331 -0.527933724 VCHANPSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VCHANPSER 9 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ;;;; 154.56 7.54E-05 1389675000 454744 513397 424087 502611 494310 363434 495850 462885 354159 FALSE TRUE 426282.3848 551409.4481 434146.5439 515508.8492 455488.8866 468351.4959 421501.8957 520677.2112 295047.5749 1.44479203 1.868883173 1.471445898 1.747205851 1.543781157 1.587376192 1.428589596 1.764722897 1 18.17058808 -2.62546108 0.320017443 1.38E-11 1.64480705 0.602635001 0.15175956 36.35223762 1.279240813 25.35793851 0.125086911 0.002368857 2.62546108 1.644807049 VCIESEHSMDTLLATLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VCIESEHSMDTLLATLK 17 0 O00244;E5RGN3;E5RIM7 O00244 ATOX1 Copper transport protein ATOX1 0 ;; 309.17 4.55E-58 574525000 1384930 1418919 1448740 1428029 1650335 1174965 1680764 1443396 1785548 FALSE TRUE 1298249.703 1523977.239 1483104.797 1464674.642 1520724.346 1514158.322 1428749.042 1623607.168 1487528.504 0.872756186 1.024502882 0.997026136 0.984636354 1.022316105 1.017902055 0.960485152 1.091479702 1 20.50448588 4.742847548 24.93930361 1.007945523 0.872756131 0.619531196 0.034214878 267.6891994 1557226.923 0.007328011 0.05725713 55315.58991 -4.742847548 -0.135189392 VCIESEHSMDTLLATLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VCIESEHSMDTLLATLKK 18 1 O00244;E5RGN3;E5RIM7 O00244 ATOX1 Copper transport protein ATOX1 0 ; 205.95 5.89E-16 477933000 425313 442315 508809 509194 588980 353953 604363 457160 804575 FALSE TRUE 398693.4185 475064.4628 520878.1898 522260.7801 542723.8866 456133.4852 513744.3788 514237.4323 670286.2347 0.594810691 0.708748648 0.777098145 0.779160832 0.809689739 0.680505524 0.766455213 0.7671908 1 19.35441778 -5 0.181266717 2.058686983 0.68578986 0.710329258 0.055829892 79.2245779 0.765022907 30.28286653 0.171184238 1.00E-05 5 -1.372897123 VCSTLLGLEEHLNALDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 287.15 1.40E-36 482267000 611298 773797 719952 748493 846202 693258 776494 691057 852508 FALSE TRUE 573037.9494 831089.735 737029.6014 767700.5976 779744.7083 893390.3305 660065.9333 777336.9877 710218.9074 0.806846936 1.17018813 1.037749902 1.080935173 1.097893481 1.257908401 0.929383781 1.09450337 1 19.43790424 1.655952946 24.9999339 1.008619068 1.083764896 0.061945685 0.120430954 1.09370644 553.4810346 0.050451957 0.027977616 45.28485127 -1.655952946 0.075145828 VCTFSPQRVS(ph)PTTSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VCTFSPQRVSPTTSPR 16 1 A0A5E8;Q99501;Q99501-4;Q99501-2 A0A5E8 GAS2L1 GAS2-like protein 1 1 VCTFSPQRVS(0.941)PT(0.042)T(0.014)S(0.003)PR 74.698 0.019111 316680000 40698 42316 50624 40893 45531 34645 43965 32889 54973 TRUE FALSE 38150.78483 45449.12067 51824.82519 41942.38361 41955.17892 44646.44909 37372.8564 36995.26405 45797.65116 0.83302929 0.992389774 1.131604435 0.915819535 0.916098923 0.974863294 0.816043082 0.807798285 1 15.48298599 2.440931424 1.378669743 0.869881294 1.000794343 0.077556847 0.095579653 0.608609318 2.335935112 0.049915582 0.035781696 276.0141988 -2.440931424 0.130913049 VCTLAIIDPGDSDIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VCTLAIIDPGDSDIIR 16 0 E5RI99;P62888;A0A0C4DH44;A0A0B4J213 E5RI99 RPL30 60S ribosomal protein L30 0 ;;; 162.6 1.87E-08 312215000 591288 641300 686904 643690 681771 559903 715239 573476 569313 FALSE TRUE 554280.3396 688782.5193 703197.6873 660208.1752 628227.4558 721537.9068 607995.5519 645075.741 474290.9824 1.168650386 1.452236169 1.482629258 1.391989727 1.324561248 1.521297966 1.281904094 1.360084347 1 18.85541291 0.282476669 0.826268726 0.995320239 1.402845835 0.560299986 0.102925608 1.890387718 1.62356143 0.113150501 0.031604501 1.91635811 -0.282476669 0.407525597 VCYYYDGDIGNYYYGQGHPMKPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VCYYYDGDIGNYYYGQGHPMKPHR 24 1 Q92769;H3BM24 Q92769 HDAC2 Histone deacetylase 2 0 199.16 1.08E-24 339560000 179860 163320 196690 175970 200850 146770 246230 206510 177660 FALSE TRUE 168602.8837 175412.3827 201355.5797 180485.6881 185076.0512 189140.1164 209310.0974 232293.2281 148007.3983 1.139151729 1.185159558 1.360442667 1.219436935 1.250451351 1.277909879 1.414186722 1.569470383 1 17.17530977 1.917471285 4.897032032 1.370282377 1.243251092 0.052532932 0.151787373 0.441351592 17.96508708 0.062462607 0.037043316 82.69348317 -1.917471285 -0.127031285 VDAFEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VDAFEER 7 0 P51580 P51580 TPMT Thiopurine S-methyltransferase 0 77.282 0.089494 195620000 385660 424360 452610 427960 462600 348580 422070 408350 504240 FALSE TRUE 361522.229 455780.0559 463346.1229 438942.1781 426269.262 449209.3873 358784.5218 459333.3964 420079.0865 0.860605159 1.084986305 1.102997359 1.044903668 1.014735738 1.069344801 0.854088036 1.093445047 1 18.68030144 VDATEESDLAQQYGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VDATEESDLAQQYGVR 16 0 P07237;H7BZ94;I3L3U6;I3NI03 P07237 P4HB Protein disulfide-isomerase 0 ;; 388.54 5.20E-121 401570000 402186 420415 397812 447747 440174 302847 502314 347089 423732 FALSE TRUE 377013.8962 451542.964 407248.2885 459236.9461 405604.5096 390274.0126 426996.679 390423.8257 353008.3918 1.068002645 1.27912813 1.153650446 1.300923595 1.148993959 1.105565821 1.209593565 1.105990211 1 18.42934295 0.534789694 0.594615841 0.993766208 1.200407945 0.38313516 0.072221203 1.55550016 0.982824515 0.08389875 0.028109715 3.426018426 -0.534789694 0.206641737 VDCDQHSDIAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VDCDQHSDIAQR 12 0 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 ;;; 194.06 2.01E-06 3749820000 3307400 3598020 3228300 3251580 3702670 2559710 3703060 3169420 3288000 FALSE TRUE 3100395.738 3864421.145 3304876.801 3335021.048 3411877.234 3298656.724 3147820.531 3565129.064 2739211.559 1.131856986 1.410778635 1.206506591 1.217511308 1.245569085 1.204235837 1.149170286 1.301516508 1 21.38532926 -4.999999999 0.161705012 0.095106095 1.304249453 0.419505139 0.08186377 112.9728376 1.044253427 32.73572004 0.31409329 1.00E-05 4.999999999 1.209143358 VDCTAHSDVCSAQGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VDCTAHSDVCSAQGVR 16 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;; 263.99 5.56E-27 3713900000 2340960 1837480 1980470 1867110 2020070 1689490 2518370 1732560 1975280 FALSE TRUE 2194443.492 1973528.931 2027447.684 1915023.204 1861421.851 2177218.336 2140763.798 1948873.93 1645593.007 1.333527478 1.199281306 1.232046852 1.163728331 1.131155664 1.323060032 1.300907204 1.184298864 1 20.65017614 0.975838935 22.46302917 0.999999998 1.237092543 0.56849979 0.065678083 434.2597635 403741.4405 0.063935499 0.015983875 9.45886299 -0.975838935 0.237092546 VDCTANTNTCNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDCTANTNTCNK 12 0 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 186.81 2.62E-05 83483000 91114 82857 90612 90652 94497 70577 111596 85390 95078 FALSE TRUE 85411.33738 88991.81849 92761.35943 92978.28379 87075.5868 90951.43418 94863.21581 96051.12947 79208.86757 1.078305245 1.123508279 1.171098165 1.173836802 1.099316143 1.148248131 1.197633784 1.212631015 1 16.27337433 4.621421968 1.906237195 1.153949906 1.065373752 0.083481087 0.06035362 1.17767331 5.473068652 0.013997222 0.169914708 41823.65348 -4.621421968 -0.088576154 VDCTQHYELCSGNQVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VDCTQHYELCSGNQVR 16 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;;; 258.2 1.07E-26 3308180000 2044040 2215990 2142960 2203310 2194130 1815710 2563520 2001460 2169760 FALSE TRUE 1916107.185 2380064.205 2193792.023 2259850.665 2021811.88 2339876.001 2179143.975 2251346.687 1807613.039 1.06002067 1.316689 1.213640296 1.250184977 1.118498172 1.294456253 1.205536765 1.245480442 1 20.78565444 -1.33438193 3.186205996 0.998319866 1.223019919 0.427360995 0.076743911 12684624.8 16752761.15 200351.0317 0.016305834 0.046303953 1.33438193 0.224700053 VDDDALLVFWDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDDDALLVFWDAR 13 0 G3V4B8;Q96FK6 G3V4B8 WDR89 WD repeat-containing protein 89 0 ; 84.658 0.022434 15038100 32165 32825 29418 28674 31763 28956 38398 29647 31570 FALSE TRUE 30151.85007 35255.39715 30115.80885 29409.82338 29268.46211 37315.12714 32640.57637 33348.49321 26300.76305 1.146424916 1.340470506 1.145054567 1.118211792 1.112836995 1.418784963 1.241050547 1.267966756 1 14.68281704 VDDDS(ph)LGEFPVTNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDDDSLGEFPVTNSR 15 0 Q92785;J3KMZ8;Q92785-2 Q92785 DPF2 Zinc finger protein ubi-d4 1 VDDDS(1)LGEFPVTNSR;VDDDS(1)LGEFPVTNSR 344.18 5.23E-70 795560000 537000 486810 556050 502300 588830 419800 644150 569590 1175000 TRUE FALSE 503390.1286 522853.9189 569239.7686 515189.8684 542585.667 540989.4451 547565.6875 640704.5653 978884.9092 0.514248533 0.534132168 0.581518586 0.5263028 0.554289541 0.552658888 0.559376983 0.654524918 1 19.90077972 0.6984827 1.63286752 0.999983289 0.545990876 0.984018926 0.0181617 0.122325379 0.492598399 0.017043374 0.004874316 4.994392844 -0.6984827 -0.453992414 VDDHDSEEICLDHLCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VDDHDSEEICLDHLCK 16 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;H7C5K1 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 0 242.19 3.56E-20 178910000 292530 316780 330430 332660 360890 285900 512580 287210 409220 FALSE TRUE 274221.0695 340234.7208 338267.9556 341196.6188 332547.1552 368434.6888 435723.3876 323068.8007 340918.5383 0.804359513 0.997994191 0.992225173 1.00081568 0.975444623 1.080711805 1.278086518 0.947642221 1 18.37906753 2.182634021 4.383048981 1.122084108 0.96683669 0.204891 0.105030859 0.239331022 9.414157076 0.038199057 0.028139321 152.2768979 -2.182634021 -0.155247418 VDDKPS(ph)SPGDSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VDDKPSSPGDSSK 13 1 Q9HC52;C9JM54;C9J6K3 Q9HC52 CBX8 Chromobox protein homolog 8 1 VDDKPS(0.401)S(0.32)PGDS(0.122)S(0.158)K;VDDKPS(0.746)S(0.254)PGDSSK;VDDKPS(0.508)S(0.492)PGDSSK;VDDKPS(0.5)S(0.5)PGDSSK 183.77 6.10E-06 6014170000 13410370 5053316 7857172 6951747 7200556 5308380 9999050 5600045 9848950 TRUE FALSE 12571038.88 5427468.775 8043547.83 7130140.597 6635053.377 6840823.132 8499785.279 6299222.945 8205096.618 1.532101262 0.661475303 0.980311166 0.868989231 0.808650243 0.833728529 1.035915319 0.767720752 1 22.96808889 4.750141572 24.80553465 0.872125775 1.532101698 0.771294489 0.113367797 742.5153091 1590378.899 0.025848169 0.413970315 56252.46679 -4.750141572 0.659975923 VDDKPSS(ph)PGDSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VDDKPSSPGDSSK 13 1 Q9HC52;C9JM54;C9J6K3 Q9HC52 CBX8 Chromobox protein homolog 8 1 VDDKPS(0.151)S(0.849)PGDSSK;VDDKPS(0.03)S(0.97)PGDSSK;VDDKPS(0.255)S(0.745)PGDSSK 180.88 7.59E-06 2890490000 9961800 3650000 5413900 5009000 5294900 3758300 7243400 3973800 6829200 TRUE FALSE 9338308.72 3920249.798 5542320.265 5137539.42 4879059.913 4843260.199 6157319.414 4469937.677 5689362.402 1.641362961 0.689049057 0.974154901 0.90300794 0.85757587 0.851283476 1.082251222 0.785665838 1 22.43983555 4.748484403 24.99829383 0.896254848 1.641363365 0.818840088 0.11063174 574.1133172 1446178.55 0.025778994 0.349791785 56038.22912 -4.748484403 0.745108518 VDDKWEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VDDKWEK 7 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;; 126.41 0.0036066 1269060000 2619850 1674120 2050900 1995860 2066620 1376660 2541910 1743940 2274400 FALSE TRUE 2455878.265 1798073.587 2099548.317 2047077.147 1904316.002 1774079.394 2160774.193 1961674.748 1894787.947 1.296123014 0.948957687 1.108065058 1.080372688 1.00502856 0.936294426 1.140377844 1.035300415 1 20.85360497 4.751307362 24.91809846 1.039002591 1.296123184 0.61816734 0.065067702 1390.263123 2717718.465 0.015035081 0.274851212 56403.66988 -4.751307362 0.257120593 VDDNEETIKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDDNEETIKK 10 1 P00568;Q5T9B7 P00568 AK1 Adenylate kinase isoenzyme 1 0 ; 143.17 5.52E-05 855410000 1808990 956830 1264010 1198790 1294600 865740 1614640 979990 2056520 FALSE TRUE 1695768.545 1027674.689 1293992.914 1229552.981 1192927.338 1115665.084 1372539.722 1102343.909 1713273.526 0.989782728 0.599831068 0.755275147 0.717662978 0.696285397 0.651189122 0.801121187 0.643413846 1 20.70832407 -1.297894531 3.679536766 1.000722337 0.72284828 0.374407134 0.108393687 1624226108 2280576445 12619355.83 0.022786873 0.05036229 1.297894531 -0.277874056 VDDQIYSEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDDQIYSEFR 10 0 Q9BVG4;A6NDF3 Q9BVG4;A6NDF3 PBDC1 Protein PBDC1 0 ; 171.85 9.06E-06 133784000 208778 250420 232325 230663 246854 185665 241140 214604 197886 FALSE TRUE 195710.9577 268961.3574 237835.8587 236582.2031 227467.0826 239263.4715 204983.2956 241397.7818 164857.5482 1.187151937 1.631477359 1.442674972 1.435070494 1.379779604 1.451334647 1.243396483 1.464281038 1 17.33086042 -0.94803103 0.301383031 0.774434028 1.475835521 0.485314837 0.126279801 10.25152536 0.802613127 2.136037648 0.130025614 0.112711692 0.94803103 0.701401493 VDDQIYSEFRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDDQIYSEFRK 11 1 Q9BVG4;A6NDF3 Q9BVG4;A6NDF3 PBDC1 Protein PBDC1 0 ; 146.36 5.74E-05 255180000 415160 463560 453090 498310 571110 341240 572530 426070 729050 FALSE TRUE 389175.8767 497882.4647 463837.5088 511097.4782 526257.3243 439750.4484 486684.4416 479265.7774 607366.8452 0.640759172 0.819739287 0.763685921 0.841497165 0.866457115 0.724027747 0.801302286 0.789087816 1 19.21220863 -5 0.278614401 2.546186795 0.771321694 0.556757872 0.062318558 169.9069143 1.631123726 151.8997735 0.066601378 1.00E-05 5 -1.774865102 VDDSTGTVIS(ph)DVEEDAGELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VDDSTGTVISDVEEDAGELSR 21 0 S4R403;Q9Y2D8-2;Q9Y2D8-3;Q9Y2D8 S4R403 SSX2IP Afadin- and alpha-actinin-binding protein 1 VDDSTGTVIS(1)DVEEDAGELSR;VDDSTGTVIS(1)DVEEDAGELSR;VDDSTGTVIS(1)DVEEDAGELSR 288.78 1.72E-46 98885000 282020 251049 275150 274222 261580 256106 332202 227346 298820 TRUE FALSE 264368.8716 269636.9292 281676.6879 281259.0008 241036.562 330039.6447 282391.3941 255730.6486 248945.0115 1.061956896 1.083118426 1.131481552 1.129803723 0.968232143 1.325753196 1.134352492 1.027257574 1 17.92546758 4.343783174 2.087093952 1.118300036 1.062315057 0 0.099128036 1.5227345 11.77350474 0.024373372 0.117846786 22069.02637 -4.343783174 -0.055984979 VDEFPLCGHMVSDEYEQLSSEALEAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 VDEFPLCGHMVSDEYEQLSSEALEAAR 27 0 P27635;X1WI28;A6QRI9;B8A6G2 P27635 RPL10 60S ribosomal protein L10 0 ;;;;;;;;;; 391.36 2.79E-145 3405232000 1413231 1409973 1504407 1454331 1555268 1224314 1702090 1350512 1710311 FALSE TRUE 1324779.394 1514368.868 1540092.244 1491651.596 1433123.525 1577753.577 1446877.406 1519126.396 1424849.045 0.929768244 1.062827584 1.080880989 1.046883949 1.005807268 1.107312794 1.015460137 1.066166554 1 20.44237765 4.741636588 24.43797813 1.052253728 0.929768181 0.54176114 0.03403711 150.0388808 1191946.935 0.007317383 0.051732452 55161.56609 -4.741636588 -0.122485547 VDEFVTHNLSFDEINK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VDEFVTHNLSFDEINK 16 0 P11766 P11766 ADH5 Alcohol dehydrogenase class-3 0 ;; 207.79 1.65E-11 731040000 852420 789330 894610 801410 876640 710540 1052720 824970 875210 FALSE TRUE 799068.5538 847772.8145 915830.5717 821975.5374 807792.2306 915661.3633 894874.409 927969.3205 729131.7969 1.095917854 1.162715463 1.256056279 1.127334648 1.107882325 1.255824211 1.227315024 1.272704502 1 19.47582009 2.228476532 24.99923689 1.211695046 1.165153158 0.002303739 0.087242548 618.6245647 1533608.304 0.030091636 0.022475765 169.2296794 -2.228476532 -0.046541888 VDFGS(ph)SER ddPTM_SK-BR-3_Pertuzumab_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(0.736)S(0.264)ER 80.102 0.024474 0 318340 302080 295310 317680 340380 297790 374550 298000 334360 TRUE FALSE 298415.6677 324446.3175 302314.8927 325832.2066 313647.9278 383757.1388 318389.7047 335205.956 278553.156 1.071306001 1.16475549 1.085304137 1.169730802 1.125989497 1.377680097 1.143012376 1.203382366 1 18.08759314 VDGAEWGVDLPSVEAQLGSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VDGAEWGVDLPSVEAQLGSHR 21 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 191.78 1.32E-17 803620000 1041900 1147310 1100610 1146290 1174180 911880 1311030 1065730 1043360 FALSE TRUE 976689.3388 1232258.026 1126716.989 1175705.742 1081964.639 1175124.953 1114453.223 1198788.736 869216.4756 1.12364338 1.417665289 1.2962444 1.352604069 1.244758549 1.351935894 1.28213541 1.379160163 1 19.72935599 -1.424399487 4.298589798 0.99894525 1.314354875 0.578164407 0.081873009 0.000718646 9.62E-05 0.068837315 0.016172642 0.037635745 1.424399487 0.315409626 VDGETAS(ph)DSESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDGETASDSESR 12 0 O95674 O95674 CDS2 Phosphatidate cytidylyltransferase 2 1 VDGET(0.012)AS(0.987)DS(0.001)ESR;VDGET(0.015)AS(0.985)DSESR 267.86 6.69E-22 521840000 970700 581500 645630 612610 604680 651020 875200 727830 351330 TRUE FALSE 909945.6197 624554.8651 660944.6485 628330.6097 557190.872 838958.9056 743971.885 818701.1777 292690.7533 3.108897734 2.133838729 2.258167164 2.146738845 1.903684574 2.866366279 2.54183597 2.797154226 1 18.15901764 -1.12283418 13.34923501 0.999999962 2.420850863 0.59765489 0.377060918 0 0 0.352306802 0.08303951 0.075364326 1.12283418 1.420850902 VDGETAS(ph)DSESRAESAPLPVSADDTPEVLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VDGETASDSESRAESAPLPVSADDTPEVLNR 31 1 O95674 O95674 CDS2 Phosphatidate cytidylyltransferase 2 1 VDGET(0.066)AS(0.932)DS(0.001)ESRAESAPLPVSADDTPEVLNR 191.05 5.97E-19 74172000 44811 37388 38141 41966 49044 35570 63088 37834 46615 TRUE FALSE 42006.3595 40156.24642 39045.72253 43042.91861 45192.28207 45838.48157 53628.54008 42557.65818 38834.65536 1.081672004 1.034031229 1.005435021 1.108363605 1.163710136 1.1803499 1.380945436 1.095868054 1 15.24505704 2.796006407 1.967032721 1.211845665 1.034725947 0.167583173 0.101163855 0.338923938 2.592140968 0.034846068 0.035826282 625.1819153 -2.796006407 -0.177119718 VDGPRS(ph)PS(ph)YGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDGPRSPSYGR 11 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 2 VDGPRS(0.988)PS(0.939)Y(0.073)GR;VDGPRS(1)PS(0.951)Y(0.049)GR 102.83 0.033664 1748468000 1617910 1748700 1620300 1608430 1836510 1216020 1785550 1568070 1809340 TRUE FALSE 1516647.901 1878175.568 1658734.281 1649705.037 1692277.913 1567065.234 1517823.354 1763846.991 1507349.465 1.006168733 1.24601203 1.100431134 1.094440987 1.122684521 1.039616406 1.006948547 1.170164605 1 20.5235825 2.783381842 1.124822268 1.050902855 1.144888858 0.079749225 0.075983971 0.743799584 1.966583518 0.034999641 0.034254944 607.2700214 -2.783381842 0.093986003 VDGPRS(ph)PSYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VDGPRSPSYGR 11 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 1 VDGPRS(0.997)PS(0.002)Y(0.002)GR;VDGPRS(0.5)PS(0.5)YGR;VDGPRS(0.987)PS(0.013)YGR;VDGPRS(0.921)PS(0.078)Y(0.001)GR;VDGPRS(0.95)PS(0.049)Y(0.001)GR 168.89 1.06E-05 3983070000 2490730 4840380 3303290 3922770 6498290 1678480 2926280 3305810 12535940 TRUE FALSE 2334839.655 5198766.772 3381645.599 4023434.919 5987940.516 2163029.928 2487511.48 3718547.655 10443610.63 0.223566326 0.497794006 0.323800429 0.385253248 0.573359227 0.207115145 0.238185008 0.356059584 1 23.31611724 -1.368677493 3.937083758 1.002111761 0.354025831 0.753342497 0.116757497 1535602092 4333712095 42699586.5 0.028060319 0.042788051 1.368677493 -0.64808593 VDHQTGPIVWGEPGTNGQHAFYQLIHQGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDHQTGPIVWGEPGTNGQHAFYQLIHQGTK 30 0 P06744;A0A2U3TZU2;P06744-2;K7EQ48;K7ESF4 P06744;K7ESF4 GPI Glucose-6-phosphate isomerase 0 ; 332.07 7.92E-106 13319700000 5179500 5905200 5109500 5316100 5939900 4306400 7228400 5487200 5832900 FALSE TRUE 4855324.341 6342427.152 5230699.753 5452520.126 5473404.214 5549587.771 6144568.525 6172288.999 4859351.308 0.999171295 1.305200376 1.076419345 1.12206749 1.126365201 1.142042923 1.264483289 1.270187852 1 22.21233231 1.786272984 25 1.207173182 1.142580425 0.01197999 0.106587858 275.785215 144548.9384 0.044864775 0.02513865 61.13261651 -1.786272984 -0.064592757 VDHSQNQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VDHSQNQK 8 0 E7EQ69;Q9GZZ1 E7EQ69 NAA50 N-alpha-acetyltransferase 50 0 ;;; 131.06 0.0010211 349382000 579700 431934 577200 515530 522340 412299 515660 486560 479640 FALSE TRUE 543417.6118 463914.8428 590891.4566 528759.3726 481317.5234 531323.0282 438341.5702 547308.0871 399584.9854 1.359955032 1.160991678 1.478762912 1.323271374 1.204543566 1.329687169 1.096992095 1.369691322 1 18.60814285 -0.324724892 0.326453042 0.912179565 1.32619145 0.397252569 0.111538156 7.327533066 0.922642855 0.873927064 0.1071062 0.473451076 0.324724892 0.414011885 VDIDAPDVDVHGPDWHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VDIDAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;;; 264.38 3.37E-31 11005560000 20267760 15752800 17591560 16090840 21084000 13498620 20831020 16457900 24804950 FALSE TRUE 18999237.08 16919153.7 18008840.11 16503758.2 19428147.69 17395452.46 17707601.94 18512705.04 20664843.6 0.919399026 0.818740951 0.871472364 0.798639395 0.940154596 0.841789698 0.856895038 0.895855077 1 24.30067511 0.841281688 2.738347718 0.999939208 0.85939121 0.504635445 0.042100408 0.46960951 6.358213709 0.035496041 0.009400535 6.938757151 -0.841281688 -0.140547998 VDIDAPDVEVHDPDWHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VDIDAPDVEVHDPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;; 280.15 1.72E-39 3524395000 5570330 4075570 4619790 4386140 5336210 3438536 5553700 4283970 6617320 FALSE TRUE 5221692.989 4377329.443 4729373.6 4498695.778 4917125.592 4431185.523 4720974.243 4818833.085 5512846.542 0.947186349 0.794023452 0.857882323 0.816038637 0.891939501 0.803792649 0.856358726 0.874109781 1 22.39436601 0.707596025 2.016252597 0.99993339 0.845279738 0.509898485 0.044730621 0.897610385 5.141040663 0.037222631 0.010264085 5.100303562 -0.707596025 -0.154653652 VDIDDHTDLAIEYEVSAVPTVLAMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDIDDHTDLAIEYEVSAVPTVLAMK 25 0 M0QXH0;Q99757 M0QXH0 TXN2 "Thioredoxin, mitochondrial" 0 ; 205.02 4.44E-25 40482000 101509 88176 90547 79655 120164 76392 100592 91277 161867 FALSE TRUE 95155.73289 94704.64279 92694.8176 81699.08216 110726.8042 98445.13028 85509.16345 102673.1344 134850.352 0.705639485 0.702294368 0.687390253 0.605849973 0.821108751 0.730032431 0.634104118 0.761385735 1 17.04099976 0.943941861 10.14224511 0.999999935 0.696951119 0.735091624 0.05671983 1.717065184 310.8794142 0.051487354 0.012878353 8.789048503 -0.943941861 -0.303048817 VDIDT(ph)PDINIEGSEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VDIDTPDINIEGSEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VDIDT(1)PDINIEGSEGK;VDIDT(1)PDINIEGSEGK;VDIDT(1)PDINIEGSEGK 300.97 7.13E-45 228569000 587330 402216 452414 490364 804870 402696 652760 571620 1215590 TRUE FALSE 550570.0637 431996.4911 463145.4737 502947.5704 741658.7569 518947.798 554884.6979 642988.0153 1012700.176 0.543665417 0.426578864 0.457337211 0.496640153 0.732357685 0.512439723 0.547925942 0.634924364 1 19.94977568 -5 0.176829139 2.944990114 0.422366907 0.790150275 0.076827479 57.56920913 0.551360998 39.12227579 0.24923422 1.00E-05 5 -2.522623207 VDIDTPDIDIHGPEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VDIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;; 285.43 7.69E-36 2196590000 2676270 1865390 2206610 1978320 2439500 1720660 2568800 1999620 2548140 FALSE TRUE 2508767.038 2003505.417 2258951.831 2029087.04 2247911.51 2217386.609 2183632.288 2249276.959 2122838.972 1.181798088 0.943785865 1.064118315 0.955836532 1.058917581 1.044538299 1.028637742 1.059560799 1 21.01756351 VDIDVPDVDVQGPDWHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VDIDVPDVDVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 263.09 7.10E-31 1881920000 4968967 3930141 4283958 4217745 5026978 3396327 5211339 4064789 6254054 FALSE TRUE 4657968.225 4221132.729 4385575.507 4325979.477 4632179.426 4376791.47 4429947.097 4572286.854 5210211.985 0.89400743 0.810165256 0.841726886 0.830288574 0.889057766 0.840040959 0.850243159 0.877562538 1 22.31291064 -0.512417479 0.492486939 1.029468525 0.841066124 0.762132568 0.025776856 4.011922909 0.840672285 0.221885844 0.011887747 0.307314124 0.512417479 -0.188402401 VDIDVPDVNVQGPDWHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDIDVPDVNVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 229.6 1.79E-19 466850000 992710 815790 877120 824760 1032280 620170 1005910 805060 1209600 FALSE TRUE 930578.0531 876191.9404 897925.7006 845924.7379 951208.8928 799203.0114 855083.1339 905573.5132 1007709.946 0.92345824 0.869488233 0.891055709 0.839452604 0.943931234 0.793088343 0.848540929 0.898645009 1 19.94264901 0.912118998 6.33218539 0.999997728 0.870568075 0.469840073 0.04224061 0.909613809 64.95053785 0.037697477 0.009469254 8.168061489 -0.912118998 -0.129429653 VDIIENQVMDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 VDIIENQVMDFR 12 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;;;;;;;;;; 199.82 3.89E-07 1558936900 1303730 1253886 1427123 1359967 1449556 1304206 1416873 1310750 1424302 FALSE TRUE 1222131.867 1346725.024 1460975.031 1394866.056 1335713.719 1680709.1 1204426.047 1474400.023 1186576.795 1.029964408 1.134966595 1.231251983 1.175537952 1.125686702 1.416435167 1.015042644 1.242566035 1 20.17837404 -1.222002325 3.700111391 0.999804975 1.171569283 0.183065755 0.113810326 7464153.969 2465132.652 13422.49763 0.023793181 0.059978787 1.222002325 0.171764308 VDIIPGFEFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDIIPGFEFDR 11 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ; 153.24 7.58E-05 366610000 450370 499880 501170 484120 524530 379320 577690 452120 515310 FALSE TRUE 422182.1456 536891.6353 513057.9891 496543.3388 483335.5297 488823.5263 491070.7475 508568.1772 429301.432 0.983416579 1.250616922 1.195099645 1.156630987 1.12586517 1.138648721 1.143883321 1.184641232 1 18.71163146 -3.923358471 0.411364883 3.19E-08 1.162163337 0.285802493 0.069657018 365.8887226 6.017612934 320.3922027 0.039511471 0.0001193 3.923358471 1.162163306 VDIKDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VDIKDR 6 1 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ;;; 91.065 0.044065 2058640000 6866000 6076400 6663400 6949600 7620100 4910410 7784700 5908700 9765900 FALSE TRUE 6436269.316 6526302.978 6821458.995 7127938.502 7021648.084 6327965.653 6617456.505 6646414.202 8135908.2 0.791094142 0.802160351 0.83843854 0.876108521 0.863044163 0.777782332 0.813364205 0.816923451 1 22.95587197 -1.169067955 4.010472725 1.00008221 0.822160569 0.771945258 0.030342828 3202033306 10985584399 4184476.624 0.007793659 0.067753548 1.169067955 -0.177921641 VDINAPDVDVHGPDWHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VDINAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 265.64 2.65E-31 1956300000 3540760 2873100 3059270 2957870 3681130 2419850 3666650 2842700 4441360 FALSE TRUE 3319150.152 3085827.313 3131837.329 3033773.952 3392028.899 3118421.412 3116869.872 3197617.353 3700068.324 0.897051044 0.833991982 0.846426891 0.819923765 0.916747639 0.842801035 0.842381707 0.864204948 1 21.81912048 0.904883069 11.48747343 1 0.853241707 0.698834581 0.029261823 18.56923312 2243.241991 0.025754616 0.006440183 8.033098079 -0.904883069 -0.146758293 VDINAPDVDVQGPDWHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDINAPDVDVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 305.98 3.77E-50 1773770000 3182900 2481000 2864000 2677900 3336700 2151100 3472300 2533600 3753700 FALSE TRUE 2983687.971 2664695.821 2931935.432 2746619.448 3074649.042 2772087.65 2951660.85 2849925.537 3127183.22 0.954113578 0.852107355 0.937564327 0.878304613 0.983200799 0.886448748 0.943872054 0.911339482 1 21.57643232 -4.999999999 0.164220363 1.326212438 0.893013613 0.294206127 0.039092224 143.0451363 1.331176003 15.14965864 0.135756658 1.00E-05 4.999999999 -0.433198825 VDINAPDVDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDINAPDVDVR 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 137.89 0.00016018 204670000 400490 401360 399900 384930 466930 372840 472090 387570 530040 FALSE TRUE 375424.0458 431077.112 409385.8168 394807.9555 430259.2013 480472.8554 401304.4872 435958.9676 441572.8998 0.850197206 0.976230906 0.927108111 0.894094623 0.974378639 1.088094074 0.908806875 0.987286511 1 18.75229211 2.569707423 6.962162303 0.989177715 0.92560446 0.346310401 0.053358072 0.361536086 23.39976616 0.016751388 0.015736744 371.2850161 -2.569707423 -0.063573255 VDINAPDVEVHGPDWHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VDINAPDVEVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 269 7.43E-32 1807100000 2613260 2216780 2285630 2251880 2802560 1800030 2716720 2193170 3420600 FALSE TRUE 2449700.721 2380912.698 2339846.223 2309667.053 2582458.243 2319669.44 2309373.057 2466992.102 2849679.762 0.859640706 0.835501845 0.821090936 0.810500564 0.906227527 0.814010567 0.810397395 0.865708539 1 21.44236837 0.894726068 5.99089308 0.999997787 0.834359289 0.75575782 0.028947485 0.619955945 34.986787 0.026413322 0.006642192 7.847405028 -0.894726068 -0.165638498 VDINT(ph)PDVDVHGPDWHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDINTPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VDINT(1)PDVDVHGPDWHLK;VDINT(1)PDVDVHGPDWHLK 268.25 3.79E-31 958370000 1055340 897460 912910 983520 1452170 787980 1320270 1117240 2163250 TRUE FALSE 989288.1532 963908.8722 934564.6563 1008758.788 1338122.426 1015457.034 1122307.77 1256729.873 1802189.6 0.548936779 0.534854308 0.518571773 0.559740656 0.74249814 0.563457382 0.62274678 0.697334994 1 20.78131937 -5 0.165159127 2.623381394 0.479354102 0.853457147 0.055620315 45.92465267 0.428413478 24.25114521 0.211848025 1.00E-05 5 -2.144027292 VDINTPDVDVHGPDWHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDINTPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 287.65 2.67E-40 1059590000 1926160 1589450 1725510 1648960 1996970 1267310 1991950 1535940 2425200 FALSE TRUE 1805605.084 1707134.532 1766439.912 1691275.105 1840136.032 1633161.824 1693275.59 1727705.49 2020418.453 0.893678773 0.844941071 0.87429409 0.837091496 0.910769761 0.808328503 0.83808163 0.855122605 1 20.94622269 -0.512334477 8.11974725 1 0.855560819 0.695790393 0.029519187 0 0 0.026191549 0.006173407 0.307372863 0.512334477 -0.144439181 VDISAPDVDVHGPDWHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VDISAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 281.67 1.42E-39 1619320000 2724980 2266470 2365210 2377350 2938740 1845260 2695450 2250760 3299430 FALSE TRUE 2554428.366 2434281.797 2421313.898 2438356.826 2707943.215 2377956.607 2291292.296 2531772.341 2748733.818 0.929310925 0.885601138 0.880883366 0.887083649 0.985160221 0.865109816 0.833581004 0.921068575 1 21.39033578 0.98310751 24.32809303 1.000000003 0.890428632 0.398175933 0.040116784 757.8010428 1091365.892 0.03874959 0.009687398 9.618503556 -0.98310751 -0.109571371 VDIVAINDPFIDLNYMVYMFQYDSTHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 VDIVAINDPFIDLNYMVYMFQYDSTHGK 28 0 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;; 297.14 1.76E-71 8801400000 4960656 5351558 4935837 4519762 5957519 4509227 6120169 4924314 3511156 FALSE TRUE 4650177.396 5747792.923 5052917.385 4635746.745 5489639.489 5810967.634 5202506.475 5539125.443 2925121.381 1.589738268 1.964975868 1.727421439 1.584804916 1.876721946 1.986573163 1.778560886 1.893639518 1 21.48006506 -1.057449208 4.807596702 0.999977734 1.810341354 0.765937525 0.138937463 3.32E-05 6.50E-06 0.125663275 0.029618248 0.087609417 1.057449208 0.810363621 VDKDAELVAQWNYCTLSQEILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VDKDAELVAQWNYCTLSQEILR 22 1 Q9BY42;A2A2L6 Q9BY42 RTFDC1 Protein RTF2 homolog 0 ;; 200.9 1.45E-22 316570000 641902 520640 603202 560318 627599 457599 707352 521978 690889 FALSE TRUE 601726.4996 559188.7273 617510.2363 574696.7085 578309.9062 589700.4028 601291.1343 587148.1023 575575.1626 1.045435138 0.971530329 1.072857685 0.99847378 1.004751323 1.024541087 1.044678738 1.020106739 1 19.13464481 2.007572385 24.72259571 1.028572077 1.018336459 0 0.029105647 768.2779622 2508275.727 0.010455231 0.007709784 101.7588955 -2.007572385 -0.010235618 VDKGGDPALIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VDKGGDPALIR 11 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 68.355 0.052407 231460000 133130 193420 146060 162160 209860 117450 170950 165950 185940 FALSE TRUE 124797.6309 207741.0181 149524.6122 166321.3001 193378.4421 151355.9084 145317.6345 186669.2228 154905.4128 0.805637638 1.341083015 0.96526396 1.073695858 1.248364655 0.977085988 0.938105596 1.205052938 1 17.24102803 VDKGVVPLAGTDGETTTQGLDGLSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VDKGVVPLAGTDGETTTQGLDGLSER 26 1 P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5 P09972 ALDOC Fructose-bisphosphate aldolase C;Fructose-bisphosphate aldolase 0 160.41 1.67E-11 338360000 201050 210570 173870 179570 233280 121610 196180 168780 261410 FALSE TRUE 188466.6394 226160.8219 177994.2785 184178.0702 214959.1298 156716.8328 166764.6302 189852.5545 217778.9822 0.865403252 1.038487826 0.817316146 0.845710951 0.98705177 0.71961413 0.76575172 0.871767113 1 17.7325052 2.24413219 24.9994798 0.810398948 0.912501477 0.084221521 0.098386809 212.1856762 952073.2873 0.032905911 0.026809368 175.4414429 -2.24413219 0.102102529 VDKGVVPLAGTNGETTTQGLDGLSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VDKGVVPLAGTNGETTTQGLDGLSER 26 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;; 311.26 8.50E-82 4198730000 1926280 1838060 2004730 2243240 2080410 1623260 2588830 1629210 2418360 FALSE TRUE 1805717.573 1974151.875 2052283.142 2300805.336 1917022.991 2091868.811 2200658.975 1832620.455 2014720.093 0.896262255 0.979864092 1.018644302 1.141997513 0.95150835 1.038292524 1.092290181 0.909615416 1 20.94214799 4.745094282 1.316064832 1.030797414 0.837663611 0.261838562 0.065364447 1.69409552 2.535095127 0.016836532 0.441998422 55602.49535 -4.745094282 -0.193133803 VDKITEYLCEPLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDKITEYLCEPLRK 14 2 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;K7ERB2;K7EN71;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ; 91.355 0.0030306 465540000 550820 487840 459840 510200 624200 396550 618320 500310 773530 FALSE TRUE 516345.1594 523960.1812 470747.622 523292.5958 575177.8499 511027.5475 525608.6562 562774.8048 644422.8458 0.801252101 0.813068911 0.73049493 0.812032967 0.892547267 0.793000358 0.815626975 0.873300518 1 19.29764812 -0.449989905 0.330527957 1.066941589 0.782386726 0.712549783 0.03881934 4.557086383 0.541136522 0.377289763 0.038373081 0.354821637 0.449989905 -0.284554863 VDKLDASESLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDKLDASESLR 11 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 95.417 0.0070895 1443390000 653580 707750 655160 737850 833790 494550 791540 783530 925080 FALSE TRUE 612673.5945 760152.5464 670700.7046 756784.4802 768307.4967 637318.5567 672855.9253 881355.4453 770678.1718 0.79497982 0.986342386 0.870273389 0.981972123 0.996923911 0.8269581 0.873069914 1.143610235 1 19.555769 8 0.030080799 1.342807651 0.336328938 0.165760427 0.094005017 3177.808516 7.327625648 78.02050928 189.8978764 99999999.99 -8 -1.006478713 VDKWWGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDKWWGNR 8 1 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9R4 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 124.23 0.0011981 1259230000 2598100 2910100 2730200 2497400 3143400 1892040 2661800 2583700 2340120 FALSE TRUE 2435489.559 3125566.832 2794961.633 2561487.512 2896530.044 2438241.233 2262687.801 2906280.632 1949538.854 1.249264437 1.603233926 1.433652695 1.313894056 1.48575138 1.250675886 1.160627189 1.490752865 1 20.89470148 0.193120675 0.228848683 0.851338266 1.520286803 0.398161155 0.138323103 5.700213356 0.590978575 1.085917537 0.334530786 1.559985908 -0.193120675 0.668948537 VDKWWGNRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDKWWGNRK 9 2 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9R4 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 96.89 0.003972 1387030000 2036010 2948600 1802200 1849950 3471200 1216760 2256400 2853900 3397100 FALSE TRUE 1908579.768 3166917.412 1844949.035 1897422.849 3198585.954 1568018.86 1918073.767 3210215.697 2830102.064 0.67438549 1.119011732 0.651901943 0.670443258 1.130201626 0.554050287 0.677740139 1.134310928 1 21.43242265 1.23231254 24.99952617 1.067155565 0.79357109 0.264257768 0.196772398 228.5608558 914463.8276 0.167231865 0.045930851 17.07310613 -1.23231254 -0.273584475 VDLENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VDLENR 6 0 P20700;E9PBF6;A0A0D9SFE5;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 0 ;; 107.66 0.072303 992030000 1883950 2061090 2041190 2100540 2011300 1602210 2238510 1727910 2270820 FALSE TRUE 1766036.932 2213695.248 2089607.991 2154443.413 1853340.611 2064742.017 1902866.207 1943643.367 1891805.472 0.933519307 1.170149511 1.104557536 1.138829253 0.979667645 1.091413493 1.005846655 1.027401282 1 20.85133232 2.743483008 24.99410408 1.025818006 1.103627109 0.166163802 0.06839632 579.5054956 2942517.308 0.019472547 0.020102917 553.9658689 -2.743483008 0.077809103 VDLFYLHMPDHSTPVEETLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VDLFYLHMPDHSTPVEETLR 20 0 O95154 O95154 AKR7A3 Aflatoxin B1 aldehyde reductase member 3 0 ;; 249 1.43E-30 243648000 117002 163182 155926 148223.9 174323 134491 177388 156984 179052 FALSE TRUE 109679.0537 175264.1651 159624.6384 152027.5762 160632.3748 173316.3684 150790.3162 176583.798 149167.0645 0.735276611 1.174952163 1.070106454 1.019176564 1.07686221 1.161894343 1.010882105 1.18379884 1 17.1865695 4.747269977 24.80161928 1.088803744 0.735276409 0.728196343 0.067565512 502.6659802 1431405.48 0.014735572 0.174811812 55881.74725 -4.747269977 -0.353527335 VDLHFIALVHVDGHLYELDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDLHFIALVHVDGHLYELDGR 21 0 A0A087WTB8;P15374;Q5TBK7 A0A087WTB8;Q5TBK7 UCHL3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L3 0 ; 203.48 2.02E-22 17333700 37486 33562 34861 32345 40945 28861 38382 31974 36918 FALSE TRUE 35139.81817 36046.9654 35687.91938 33175.02746 37729.34486 37192.70218 32626.97542 35966.02428 30756.1473 1.142529909 1.172024735 1.160350776 1.078647047 1.226725327 1.209277021 1.060827779 1.16939303 1 14.90858717 0.148572631 0.616888259 0.993135285 1.159766032 0.460097495 0.051424915 2.935818665 1.42987152 0.099479142 0.019749192 1.407902666 -0.148572631 0.166630747 VDLHLLNHDGNIIDAASIAAIVALCHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VDLHLLNHDGNIIDAASIAAIVALCHFR 28 0 D6RIY6;Q06265-3;Q06265-4;Q06265;Q06265-2;D6RA17 D6RIY6 EXOSC9 Exosome complex component RRP45 0 221.26 8.37E-35 135400000 103770 110870 91699 86231 114900 79080 101730 97653 62012 FALSE TRUE 97275.22093 119078.9302 93874.14358 88443.83345 105876.2175 101909.1122 86476.53092 109845.192 51661.79659 1.882923695 2.304970753 1.817090186 1.711977502 2.049410289 1.972620369 1.673897089 2.126236393 1 15.65681019 -2.043641504 0.318260879 1.33E-14 2.012732189 0.686321455 0.196820249 20.30330508 0.962818722 15.29491843 0.178277703 0.009043957 2.043641504 2.012732189 VDLNSNGFICDYELHELFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VDLNSNGFICDYELHELFK 19 0 P13797;U3KQI3 P13797 PLS3 Plastin-3 0 246.31 1.20E-24 496720000 674150 595540 622130 603370 640030 507720 789940 581750 803950 FALSE TRUE 631956.1549 639634.4013 636887.2174 618853.4957 589764.6256 654290.5219 671495.8304 654382.7681 669765.5513 0.943548311 0.955012392 0.950910682 0.923985258 0.880553836 0.976894856 1.00258341 0.977032585 1 19.35329665 2.016727408 24.99589605 0.992554077 0.935884766 0.642196836 0.021731775 163.9670186 245016.1525 0.008512291 0.006285161 103.9267648 -2.016727408 -0.05666931 VDLPDKYPFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VDLPDKYPFK 10 1 C9JZY6;P62256-2;P62256;H7C4M9;C9JZG9;C9J8Q9 C9JZY6 UBE2H Ubiquitin-conjugating enzyme E2 H 0 91.313 0.0093335 232400000 1227100 1028500 1078600 994970 1272400 789150 1318500 1088500 1591700 FALSE TRUE 1150298.001 1104651.21 1104184.901 1020502.615 1172470.837 1016964.794 1120803.165 1224401.621 1326034.987 0.867471833 0.833048314 0.832696657 0.769589509 0.884192987 0.76692154 0.845228954 0.923355442 1 20.33868741 1.073090306 2.569002002 0.998265231 0.825853985 0.718600203 0.036559672 0.1197857 1.611507351 0.030591871 0.008316084 11.8328758 -1.073090306 -0.172411246 VDLTLDPDTAHPALMLS(ph)PDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VDLTLDPDTAHPALMLSPDRR 21 1 H0YAD6;D6REK2;Q8WV44-3;Q8WV44-2;Q8WV44 H0YAD6 TRIM41 E3 ubiquitin-protein ligase TRIM41 1 VDLTLDPDTAHPALMLS(1)PDRR 122.73 1.69E-05 59252000 77329 102180 95465 103830 84768 82532 119900 91248 108300 TRUE FALSE 72489.11593 109745.5135 97729.47488 106494.4536 78110.66322 106357.6486 101922.1081 102640.5137 90224.03036 0.803434691 1.216366783 1.083186757 1.180333589 0.865741232 1.178817308 1.129655899 1.137618362 1 16.46122411 VDLTLLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDLTLLSPK 9 0 E7EVA0;P27816-4;B5MEG9 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 VDLTLLS(1)PK;VDLTLLS(1)PK 102.62 0.0037289 81896000 388640 248520 306440 284920 322520 181064 274770 222002 467130 TRUE FALSE 364315.7161 266920.6794 313708.9015 292231.5296 297190.5802 233334.2375 233570.7893 249719.4384 389162.9852 0.936152024 0.685884037 0.806111869 0.75092324 0.763666103 0.59957973 0.600187577 0.641683428 1 18.57001497 4.742953823 24.33875177 0.713195277 0.936152154 0.216230601 0.118509367 439.3074542 2433671.251 0.02683283 0.210514422 55329.1276 -4.742953823 0.222956877 VDLVDENFTELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDLVDENFTELR 12 0 D6RDM7;P61086;P61086-3 D6RDM7 UBE2K Ubiquitin-conjugating enzyme E2 K 0 ; 161.93 0.000149 97596000 158476 146968 145688 149892 148883 141177 187258 138984 175788 FALSE TRUE 148557.27 157849.6636 149143.7882 153738.4825 137190.3297 181932.5081 159180.4013 156336.4583 146447.8472 1.014403919 1.077855815 1.018408881 1.049783151 0.936786251 1.242302373 1.086942583 1.06752309 1 17.16002746 2.258201771 24.99999322 1.109200949 1.028649644 0.234303483 0.069512542 320.1816885 407537.9903 0.022062113 0.018434866 181.2181826 -2.258201771 -0.080551305 VDLVDENFTELRGEIAGPPDTPYEGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDLVDENFTELRGEIAGPPDTPYEGGR 27 1 D6RDM7;P61086;P61086-3 D6RDM7 UBE2K Ubiquitin-conjugating enzyme E2 K 0 ; 108.75 0.001485 123964000 73592 82958 89255 96516 116935 68857 99625 85322 137487 FALSE TRUE 68986.00809 89100.29664 91372.17075 98992.76396 107751.3968 88734.8981 84687.15612 95974.63952 114539.5315 0.602289945 0.777899957 0.797734804 0.864267233 0.940735442 0.774709805 0.739370548 0.837917165 1 16.80548608 -4.999959296 0.027320656 2.103253056 5.68E-07 0.480496091 0.078681365 1954.931126 4.028109134 232.5422738 102.1536809 1.00E-05 4.999959296 -2.103252488 VDNDENEHQLSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 VDNDENEHQLSLR 13 0 P06748;P06748-3;P06748-2;E5RGW4 P06748 NPM1 Nucleophosmin 0 ;;;;;;;;;;; 271.73 4.27E-32 1.31157E+11 46987752 45557625 48358418 45556805 45852609 38652013 53647441 39784930 45340865 FALSE TRUE 44046872.48 48930758.96 49505502.51 46725869.74 42251530.05 49810221.69 45603505.26 44752166.09 37773181.72 1.166088491 1.295383569 1.31059922 1.237011753 1.118558939 1.318666298 1.20729849 1.1847603 1 25.17085897 -0.285074931 0.42493125 0.950712574 1.263180087 0.566907384 0.063837502 4.426113529 0.860088725 0.39395459 0.0384515 0.518710536 0.285074931 0.312467513 VDNEFDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDNEFDQR 8 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 108.98 0.0086237 1057790000 1538510 1911900 1806770 1865880 2057700 1494540 2267400 1824570 2081040 FALSE TRUE 1442217.405 2053459.065 1849627.438 1913761.64 1896096.542 1925989.436 1927424.42 2052371.581 1733700.98 0.83187206 1.184436699 1.066866466 1.103859121 1.09366988 1.110912123 1.111739822 1.183809437 1 20.72542366 4.74794218 24.88420118 1.111135299 0.831871903 0.726000032 0.053044862 566.5362011 1502680.327 0.011165786 0.142071772 55968.30831 -4.74794218 -0.279263396 VDNIQAGELTEGIWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDNIQAGELTEGIWR 15 0 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 194.59 1.05E-07 198682000 121572 112820 119022 119751 112221 96961 126783 108074 132629 FALSE TRUE 113963.0255 121173.3102 121845.258 122824.0134 103407.6153 124952.0667 107773.0661 121567.2768 110492.3631 1.031410881 1.096666836 1.102748232 1.111606359 0.935880204 1.13086609 0.975389277 1.100232391 1 16.75358713 VDNLTYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 135.77 0.0070847 1547930000 1506150 1821680 1652510 1604890 1747050 1402160 1752670 1608040 1736020 FALSE TRUE 1411882.76 1956559.083 1691708.318 1646074.194 1609843.74 1806940.83 1489873.404 1808807.334 1446267.047 0.976225492 1.352833895 1.169706743 1.138153703 1.11310269 1.249382563 1.030150972 1.25067313 1 20.46390253 -2.878926649 0.196840156 0.695055826 1.208622022 0.120837727 0.11250082 86.47338358 1.81102002 11.34597206 0.280613067 0.001321519 2.878926649 0.513566196 VDNLTYRT(ph)SPDTLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDNLTYRTSPDTLRR 15 2 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLT(0.002)YRT(0.499)S(0.499)PDTLRR;VDNLTYRT(0.5)S(0.5)PDTLRR 153.25 0.00012805 582340000 210177 500830 315358 409050 828140 190537 385054 321102 1497620 TRUE FALSE 197022.3967 537911.9743 322838.4407 419546.9155 763101.225 245541.9388 327318.7274 361192.2915 1247657.547 0.157913842 0.431137515 0.258755651 0.336267685 0.611627146 0.196802351 0.26234661 0.289496338 1 20.25079057 -1.581036646 2.704097617 1.049891111 0.322269045 0.737314016 0.127901718 12859778.24 12328521.07 4589200.463 0.030304317 0.026239971 1.581036646 -0.727622066 VDNLTYRTS(ph)PDTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VDNLTYRTSPDTLR 14 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLTYRT(0.07)S(0.86)PDT(0.07)LR;VDNLTYRT(0.287)S(0.702)PDT(0.011)LR;VDNLTYRT(0.011)S(0.989)PDTLR;VDNLTYRT(0.04)S(0.95)PDT(0.009)LR;VDNLTYRT(0.337)S(0.662)PDT(0.001)LR;VDNLTYRT(0.14)S(0.86)PDTLR 211.09 2.62E-09 9500840000 2238800 3771860 2770420 3533570 5473390 1745520 3082750 2982060 8395680 TRUE FALSE 2098677.504 4051132.439 2836135.671 3624247.389 5043532.028 2249423.288 2620520.256 3354376.755 6994386.77 0.300051681 0.579197658 0.405487395 0.518165138 0.721082805 0.321604075 0.374660473 0.479581251 1 22.73776614 -1.286241263 2.807798909 1.005300482 0.464218092 0.645381097 0.125213292 3678031.458 4446067.309 164982.0335 0.030837832 0.051731937 1.286241263 -0.54108239 VDNLTYRTS(ph)PDTLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VDNLTYRTSPDTLRR 15 2 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLTYRT(0.183)S(0.817)PDTLRR 159.75 9.12E-07 530970000 215440 465480 332890 364070 860400 210560 346570 358230 1540200 TRUE FALSE 201955.995 499944.6235 340786.308 373412.6526 792827.6547 271345.2538 294605.0459 402955.8041 1283130.67 0.157393163 0.389628769 0.265589714 0.291016855 0.617885359 0.211471256 0.229598632 0.314041129 1 20.29123667 -1.635996827 2.683931277 1.072652091 0.310989878 0.747717086 0.126032959 13860370.64 12530397.46 6986235.496 0.029850465 0.023120817 1.635996827 -0.761662214 VDPSLMEDS(ph)DDGPSLPTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 VDPSLMEDSDDGPSLPTK 18 0 O15258;Q5T092;A0A0A0MR06;Q5T091 O15258 RER1 Protein RER1 1 VDPSLMEDS(1)DDGPSLPTK;VDPSLMEDS(1)DDGPSLPTK;VDPSLMEDS(1)DDGPSLPTK;VDPSLMEDS(1)DDGPSLPTK;VDPSLMEDS(1)DDGPSLPTK;VDPSLMEDS(1)DDGPSLPTK;VDPSLMEDS(1)DDGPSLPTK;VDPSLMEDS(1)DDGPSLPTK;VDPS(0.018)LMEDS(0.982)DDGPSLPTK;VDPSLMEDS(1)DDGPSLPTK 282.5 2.29E-39 1582269000 2516205 2105395 2023130 2010939 2013753 1511323 2973845 2339400 1654534 TRUE FALSE 2358720.221 2261280.636 2071119.599 2062543.099 1855600.962 1947617.416 2527944.55 2631479.24 1378381.587 1.711224412 1.640533114 1.502573467 1.496351315 1.346217173 1.412974052 1.833994718 1.909107946 1 20.3945439 1.752457838 25 1.668673465 1.523134457 0 0.263733766 12.94361337 23317.41744 0.110714262 0.061396303 56.55328516 -1.752457838 -0.145539008 VDQDSALHNDLQILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VDQDSALHNDLQILK 15 0 Q7Z7E8;Q7Z7E8-2 Q7Z7E8 UBE2Q1 Ubiquitin-conjugating enzyme E2 Q1 0 90.367 0.0060415 52931000 149680 122820 141580 130930 151020 118390 181200 149060 162400 FALSE TRUE 140311.796 131913.7206 144938.3445 134289.8855 139159.4984 152567.2711 154030.7422 167670.4691 135294.3909 1.037085093 0.975012488 1.071281252 0.99257541 1.028568128 1.127668857 1.138485795 1.239300965 1 17.0457425 2.231761315 4.363140009 1.139349685 1.019335723 0.408501529 0.062456447 0.167391999 7.579946001 0.021152902 0.016169186 170.5144995 -2.231761315 -0.120013962 VDQICHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 96.253 0.012868 898440000 1264450 1252340 1213000 1154520 1407890 1018840 1381640 1215850 1341850 FALSE TRUE 1185310.332 1345064.557 1241772.933 1184146.938 1297319.999 1312962.569 1174475.909 1367651.549 1117886.566 1.060313602 1.203220968 1.110821948 1.059272894 1.160511306 1.174504291 1.050621721 1.223426052 1 20.09234237 -1.441084662 3.183056783 0.997846161 1.129952834 0.310500438 0.061036244 16171298.19 24802574.25 324503.3904 0.013434699 0.036217239 1.441084662 0.132106673 VDQICHKNS(ph)IK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VDQICHKNSIK 11 1 Q9UBE0;M0QX65;B3KNJ4;Q9UBE0-2;Q9UBE0-3;A0A590UK93;A0A590UKC5;M0QYM8;M0R054;M0R286;M0QYP2 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 1 VDQICHKNS(1)IK 66.299 0.081356 0 124040 121030 114710 108390 167050 80207 141100 133520 203760 TRUE FALSE 116276.5578 129991.1871 117430.9754 111171.4709 153930.5668 103361.4588 119943.3649 150190.2659 169751.1397 0.684982487 0.765775048 0.691783134 0.654908539 0.906801375 0.608899941 0.706583562 0.88476735 1 17.37306173 1.065629746 3.521041663 0.997245683 0.717835852 0.602641831 0.078983916 0.129993653 3.237278665 0.068540448 0.017832073 11.63133987 -1.065629746 -0.279409831 VDS(ph)EGDFS(ph)ENDDAAGDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDSEGDFSENDDAAGDFR 18 0 O43823;M0QYL4 O43823 AKAP8 A-kinase anchor protein 8 2 VDS(1)EGDFS(1)ENDDAAGDFR;VDS(1)EGDFS(1)ENDDAAGDFR 368.06 2.28E-107 829390000 909210 576470 718230 667730 616890 593590 897610 548580 612940 TRUE FALSE 852304.1691 619152.4386 735266.7548 684865.0823 568441.9478 764949.7969 763021.7135 617071.4206 510636.3543 1.669102017 1.212511474 1.439902875 1.341199224 1.113203052 1.498032387 1.494256543 1.208436132 1 18.96193673 0.986136674 5.578204448 1.000218421 1.380575416 0.414177694 0.154535289 0.140279097 19.06217165 0.139016476 0.035027647 9.685826238 -0.986136674 0.380356995 VDS(ph)PGRTEPCTAALDLGVQLTPETLVEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VDSPGRTEPCTAALDLGVQLTPETLVEAK 29 1 H9KVB4;O15417;O15417-2;O15417-3 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 VDS(0.978)PGRT(0.008)EPCT(0.013)AALDLGVQLTPETLVEAK 111.56 0.00018962 66649000 56532 40763 41344 42112 48996 30181 58014 42775 76110 TRUE FALSE 52993.76303 43781.13493 42324.6992 43192.66522 45148.0518 38893.76475 49315.33928 48115.55291 63406.74931 0.835774797 0.690480673 0.667510946 0.681199804 0.712038581 0.613401021 0.777761671 0.75883961 1 15.9523488 0.658351651 1.184894274 0.999328397 0.697472222 0.696803696 0.059720509 0.5806105 1.294697028 0.052175907 0.016003187 4.553566158 -0.658351651 -0.301856174 VDS(ph)PSHGLVTSSLCIPSPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VDSPSHGLVTSSLCIPSPAR 20 0 Q9UER7-3;Q9UER7 Q9UER7-3 DAXX Death domain-associated protein 6 1 VDS(0.968)PS(0.032)HGLVTSSLCIPSPAR;VDS(0.993)PS(0.007)HGLVTSSLCIPSPAR;VDS(0.926)PS(0.074)HGLVTSSLCIPSPAR;VDS(0.668)PS(0.332)HGLVTSSLCIPSPAR;VDS(0.639)PS(0.361)HGLVTSSLCIPSPAR;VDS(0.897)PS(0.103)HGLVTSSLCIPSPAR 220.91 5.28E-25 1729088000 638188 483019 558947 481624 623982 571270 837118 625135 745162 TRUE FALSE 598244.9523 518782.2293 572205.4868 493983.2872 574976.9707 736186.3752 711599.9273 703184.4808 620789.6483 0.96368384 0.835681186 0.921738126 0.79573377 0.926202575 1.185887003 1.146281884 1.132725848 1 19.24374498 2.329949036 5.264349509 1.131771381 0.877870311 0.747241395 0.065816223 0.084120498 3.781812931 0.02076002 0.017129262 213.7711217 -2.329949036 -0.253901069 VDS(ph)PTVTTTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDSPTVTTTLK 11 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;H0YG16;G5E9S8;H0YJU9;H0YJT3;H0YJL0 Q07866-6 KLC1 Kinesin light chain 1 1 VDS(0.976)PT(0.024)VTTTLK;VDS(1)PTVTTTLK 210.15 1.44E-08 160196000 774260 436600 570700 528500 518280 418660 714730 459800 551780 TRUE FALSE 725800.4487 468926.3183 584237.2735 542062.2047 477576.3794 539520.3456 607562.8717 517207.0421 459684.3534 1.578910492 1.020105024 1.270953143 1.179205254 1.038922417 1.173675679 1.321695784 1.12513519 1 18.81028404 7.99993416 0.01848414 4.16E-06 2.68742931 0.218598799 0.152405285 8070.778787 11.50229259 634.120736 1096.62788 99984841.03 -7.99993416 2.68742515 VDS(ph)TTCLFPVEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VDSTTCLFPVEEK 13 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 1 VDS(0.991)T(0.008)T(0.001)CLFPVEEK;VDS(0.928)T(0.072)TCLFPVEEK;VDS(0.333)T(0.333)T(0.333)CLFPVEEK 302.85 4.73E-41 272253000 1117761 754668 786783 795507 786255 522981 1299719 646185 1003521 TRUE FALSE 1047802.334 810544.404 805445.8643 815921.0564 724505.7039 673957.1248 1104838.202 726862.6197 836026.8621 1.253311803 0.96951957 0.963421034 0.975950766 0.866605772 0.806142907 1.321534333 0.869424958 1 19.67318977 -0.594019358 7.735545835 0.9999108 1.006448944 0 0.164255761 0 0 0.1510127 0.035594035 0.254671673 0.594019358 0.006538144 VDSDKEDDITELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VDSDKEDDITELK 13 1 P52306-4;P52306;P52306-5;P52306-6;P52306-2;P52306-3;H0Y8M2 P52306-4 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 0 103.21 0.001485 262070000 330570 152610 198300 209010 203540 155970 293570 164290 251650 FALSE TRUE 309880.2138 163909.4032 203003.7696 214373.5505 187554.7894 200996.007 249551.9039 184801.9681 209647.9893 1.478097714 0.781831506 0.968307735 1.022540456 0.89461764 0.958730908 1.190337693 0.881486957 1 17.67760947 VDSEGDFS(ph)ENDDAAGDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VDSEGDFSENDDAAGDFR 18 0 O43823;M0QYL4 O43823 AKAP8 A-kinase anchor protein 8 1 VDSEGDFS(1)ENDDAAGDFR 360.92 5.23E-91 244690000 107590 101450 99631 98122 100810 102540 114850 80231 94171 TRUE FALSE 100856.134 108961.4636 101994.2944 100639.9766 92892.78925 132141.6334 97629.30872 90248.01696 78453.25173 1.285557089 1.388871221 1.300064588 1.282801852 1.18405276 1.684335964 1.244426541 1.150341318 1 16.25954562 1.141164169 2.639812523 1.013523554 1.348639437 0.434647031 0.132969005 0.224917321 2.876359848 0.114986937 0.03159578 13.84089484 -1.141164169 0.335115883 VDSLVS(ph)LSEEDLESDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDSLVSLSEEDLESDQR 17 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36;H0YLH1 Q12802-2 AKAP13 A-kinase anchor protein 13 1 VDSLVS(1)LSEEDLESDQR;VDSLVS(0.999)LS(0.001)EEDLESDQR 206.74 7.03E-12 29641000 24314 25359 24366 27525 27732 22789 25752 23450 30272 TRUE FALSE 22792.23014 27236.60675 24943.97303 28231.3381 25554.04059 29367.81435 21890.72667 26377.78412 25219.40764 0.903757553 1.079985983 0.989078466 1.119429073 1.013268866 1.164492631 0.868011136 1.045931947 1 14.62224677 -1.20333963 3.834245124 0.999980194 1.022459029 0.006402697 0.089802236 29827700146 6197399446 5440701.778 0.019109484 0.062612403 1.20333963 0.022478835 VDSSTNSS(ph)PSPQQSESLS(ph)PAHTSDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VDSSTNSSPSPQQSESLSPAHTSDFR 26 0 F2Z3H6;Q9BQE9-2;Q9BQE9-3;Q9BQE9 F2Z3H6 BCL7B B-cell CLL/lymphoma 7 protein family member B 2 VDS(0.006)S(0.006)T(0.006)NS(0.054)S(0.464)PS(0.464)PQQS(0.011)ES(0.145)LS(0.844)PAHT(0.001)S(0.001)DFR 70.534 0.00067633 0 59864 82246 77076 89008 86124 83436 99964 72896 94020 TRUE FALSE 56117.2191 88335.57942 78904.27912 91292.09597 79360.16845 107522.6187 84975.32622 81997.22606 78327.45461 0.716443798 1.127772884 1.00736427 1.165518482 1.01318457 1.372732195 1.084872816 1.046851662 1 16.25723046 4.740322291 24.50455317 1.108309201 0.716443626 0.548101404 0.109983339 85.9858616 1195914.852 0.024353059 0.156331409 54994.88411 -4.740322291 -0.391865575 VDSSTNSSPSPQQSESLS(ph)PAHTSDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VDSSTNSSPSPQQSESLSPAHTSDFR 26 0 F2Z3H6;Q9BQE9-2;Q9BQE9-3;Q9BQE9 F2Z3H6 BCL7B B-cell CLL/lymphoma 7 protein family member B 1 VDSSTNSSPSPQQSESLS(0.997)PAHT(0.003)SDFR;VDSSTNSSPSPQQSES(0.1)LS(0.899)PAHTSDFR 288.02 6.13E-62 732570000 182480 326400 344130 367360 384650 298448 364510 313962 341800 TRUE FALSE 171058.9025 350566.9956 352292.9261 376787.0795 354441.1406 384605.0927 309855.1094 353160.8468 284751.3719 0.600730741 1.231133649 1.237194833 1.323214273 1.24473901 1.35066985 1.088160199 1.240242828 1 18.11934327 4.738931152 24.78051503 1.22453749 0.600730537 0.777584189 0.10302147 11.14600568 745108.4555 0.022028474 0.129497782 54819.00545 -4.738931152 -0.623806953 VDST(ph)TCLFPVEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 VDSTTCLFPVEEK 13 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 1 VDS(0.412)T(0.588)TCLFPVEEK;VDS(0.235)T(0.668)T(0.097)CLFPVEEK;VDS(0.02)T(0.976)T(0.004)CLFPVEEK;VDS(0.021)T(0.977)T(0.002)CLFPVEEK;VDS(0.335)T(0.656)T(0.009)CLFPVEEK;VDS(0.383)T(0.559)T(0.058)CLFPVEEK;VDS(0.33)T(0.563)T(0.107)CLFPVEEK;VDS(0.383)T(0.606)T(0.012)CLFPVEEK 364.02 5.12E-90 24312510000 20294151 12333679 13793626 14110365 12656939 9082920 23599669 11340614 17217297 TRUE FALSE 19023976.32 13246877.43 14120817.32 14472460.85 11662914.07 11705011.56 20061117.72 12756514.62 14343618.9 1.32630241 0.923538022 0.98446685 1.008982528 0.813108194 0.816043122 1.398609225 0.889351196 1 23.77390573 -0.421534793 7.821428029 0.999989014 1.020774937 0.001009884 0.197014081 0 0 0.183618842 0.043279376 0.378848182 0.421534793 0.020785923 VDTPHYPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VDTPHYPR 8 0 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 0 ;; 123.72 0.0013355 1026090000 1469350 2185610 1615930 1755690 2143440 1388910 1963950 1928520 1981820 FALSE TRUE 1377386.006 2347434.839 1654260.623 1800743.978 1975102.869 1789865.77 1669473.93 2169299.967 1651041.439 0.834252838 1.421790382 1.00194979 1.090671582 1.196276981 1.084082887 1.01116416 1.313897953 1 20.6549449 -2.326033521 2.255077443 0.309305291 1.127068428 0.047349012 0.164842708 5625079.329 1042866.615 19826822.75 0.036088712 0.004720266 2.326033521 0.817763137 VDVADQAQDKDRDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 VDVADQAQDKDRDDR 15 2 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;;;; 213.94 6.77E-11 12464530000 14665730 8762290 10948540 9967880 10087690 8109040 13268240 9245880 10693040 FALSE TRUE 13747828.14 9411059.069 11208244.54 10223672.68 9295443.519 10449988.21 11278790.59 10400248.47 8908302.544 1.54326013 1.056436849 1.258179601 1.147656652 1.043458445 1.173061664 1.266098736 1.167478138 1 23.08671913 7.999999881 0.019506664 2.78E-09 2.691061612 0.264512867 0.131904189 5923.275234 8.905077993 458.7053798 817.6084751 99999972.68 -7.999999881 2.691061609 VDVFREDLCTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VDVFREDLCTK 11 1 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;;;;; 179.67 6.39E-06 1703170000 3757650 4139530 3897700 4204470 5238240 2858800 5109710 3540120 7328310 FALSE TRUE 3522465.394 4446025.108 3990155.285 4312363.818 4826849.76 3684089.151 4343556.422 3982111.775 6105167.718 0.576964558 0.728239635 0.653570134 0.706346495 0.790617061 0.603437829 0.711455708 0.652252642 1 22.5415995 -1.819950681 2.404332077 1.116892849 0.683190024 0.727975475 0.061809684 8428172.838 5135968.118 5704124.608 0.013113948 0.015137331 1.819950681 -0.433702825 VDVKS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VDVKSPK 7 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VDVKS(1)PK;VDVKS(1)PK;VDVKS(1)PK 85.958 0.012372 1525020000 4296780 2145990 2999380 4039000 4329380 1506850 2642170 1854630 2655520 TRUE FALSE 4027852.21 2304881.333 3070526.71 4142647.578 3989367.959 1941853.133 2246001.137 2086184.638 2212296.557 1.820665587 1.041850075 1.387936306 1.872555271 1.803269976 0.877754444 1.01523511 0.942995021 1 21.07711336 2.223303907 24.99606166 0.963208351 1.497306654 0.593605069 0.251696553 214.0625683 350710.4412 0.103229564 0.076525084 167.2260404 -2.223303907 0.534098303 VDVNAPDVQAPDWHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VDVNAPDVQAPDWHLK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 237.01 9.54E-20 1273550000 1072860 891160 927100 878620 1107050 754020 1121200 846990 1238140 FALSE TRUE 1005711.608 957142.4137 949091.2498 901166.8767 1020106.759 971693.3335 953086.4687 952738.566 1031486.435 0.975011957 0.927925352 0.920119952 0.873658485 0.988967691 0.942032101 0.923993216 0.923655933 1 19.97629342 2.724206566 24.97802611 0.947720995 0.924126837 0.149316312 0.034602052 1917.446445 3336616.148 0.010684312 0.010109975 529.9154303 -2.724206566 -0.023594158 VDVSAPDVEAHGPEWNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VDVSAPDVEAHGPEWNLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 274.08 5.00E-39 1386880000 3029060 2671850 2825620 2675770 3464870 2149510 3411870 2602060 4196500 FALSE TRUE 2839476.542 2869676.554 2892645.041 2744434.788 3192753.087 2770038.643 2900291.768 2926932.919 3496077.04 0.812189351 0.820827608 0.827397397 0.785004094 0.913238768 0.792327689 0.829584627 0.837204926 1 21.73730555 -5 0.378847589 3.430203404 0.822318258 0.71645003 0.034283492 289.4773258 2.172732744 577.703688 0.020542346 1.00E-05 5 -2.607885145 VEADIPGHGQEVLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEADIPGHGQEVLIR 15 0 B0QYF8;P02144;F2Z2F1;F2Z337 B0QYF8 MB Myoglobin 0 176.23 8.11E-07 71622000 139030 194710 161630 162120 196030 96820 222760 285320 377230 FALSE TRUE 130328.3605 209126.531 165463.9399 166280.2737 180634.5945 124770.3623 189359.206 320942.8301 314267.876 0.414704685 0.665440368 0.526506056 0.529103629 0.574779061 0.397019141 0.602540764 1.021239696 1 18.26163528 1.272716199 4.771080784 1.019129321 0.536796751 0.870175423 0.077477099 0.058492447 2.873775951 0.057485162 0.018374163 18.73769643 -1.272716199 -0.482332571 VEADRPGK ddPTM_SK-BR-3_Pertuzumab_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 ; 89.698 0.012514 404680000 596280 457350 491170 479570 469400 416000 596510 376940 657810 FALSE TRUE 558959.8992 491212.6699 502820.7843 491876.5781 432535.2175 536092.4468 507068.8632 424001.7887 548017.2614 1.019967688 0.896345251 0.917527275 0.897556725 0.789272981 0.978240075 0.925278999 0.773701521 1 19.06386181 4.739203628 23.05928097 0.898424353 1.019967771 0.228177677 0.070906149 26.39706659 945963.8214 0.015233419 0.090413695 54853.40959 -4.739203628 0.121543418 VEAEAGGSGART(ph)PPLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VEAEAGGSGARTPPLSR 17 1 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 VEAEAGGSGART(1)PPLSR;VEAEAGGSGART(1)PPLSR;VEAEAGGSGART(1)PPLSR;VEAEAGGS(0.006)GART(0.994)PPLSR 160.45 4.99E-09 5176600000 982790 1172330 1108230 1143570 1306370 839670 1147840 1006480 1760700 TRUE FALSE 921278.9282 1259130.533 1134517.739 1172915.942 1203772.97 1082069.098 975732.048 1132141.244 1466827.795 0.628075723 0.858403786 0.77344985 0.799627568 0.820664139 0.737693342 0.665198772 0.771829691 1 20.48426808 0.941123967 23.16389657 1 0.761957619 0.554225205 0.068455019 10260.06279 4036673.915 0.066893305 0.016723326 8.732205885 -0.941123967 -0.238042382 VEAFEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VEAFEHR 7 0 P42285 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 ; 152.47 0.0018115 507140000 760440 1061000 933770 1061300 1061030 950230 915970 841420 811210 FALSE TRUE 712845.4178 1139557.544 955919.4654 1088534.755 977700.9838 1224545.975 778628.8019 946473.1392 675813.8104 1.054795577 1.686200439 1.414471635 1.610702146 1.446701693 1.811957608 1.152135085 1.40049393 1 19.36626631 1.039657227 1.165220061 1.020764225 1.505403485 0.289353682 0.224615538 0.531950523 1.50477683 0.186886048 0.059208977 10.95613126 -1.039657227 0.48463926 VEAKEES(ph)EES(ph)DEDMGFGLFD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 76.768 0.0071159 126040000 168880 112990 116220 132160 147750 75566 144290 111430 197280 TRUE FALSE 158310.1023 121355.8972 118976.7933 135551.4493 136146.311 97380.67749 122655.054 125342.2808 164352.6935 0.963233999 0.73838703 0.723911429 0.824759524 0.828378946 0.592510384 0.746291718 0.762642085 1 17.32643557 -1.109940815 4.041314336 1.000060866 0.759302057 0.357003996 0.09447772 28597541.82 47661874.49 21660.54566 0.021311504 0.077635291 1.109940815 -0.240758808 VEAKPEVQSQPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEAKPEVQSQPPR 13 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 103.14 0.0014905 273290000 161510 149360 153060 157530 182900 139240 206730 148650 227370 FALSE TRUE 151401.3774 160418.7698 156690.6555 161572.4865 168535.7718 179436.3276 175732.7557 167209.2797 189420.4781 0.799287273 0.846892434 0.827210748 0.852983205 0.8897442 0.947291071 0.927738951 0.882741303 1 17.53123278 2.638350488 1.833520906 0.934117314 0.829703247 0.727575431 0.031178135 0.177565101 1.189909558 0.011190139 0.010198188 434.8610277 -2.638350488 -0.104414066 VEALTKEELEFEVPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEALTKEELEFEVPFR 16 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 61.444 0.077638 25588000 26443 28200 27871 29507 36255 23385 30719 23131 40824 FALSE TRUE 24787.97983 30287.95734 28532.11328 30264.19958 33407.67855 30135.86988 26112.97113 26018.95627 34010.21067 0.72883935 0.890554829 0.838927861 0.889856281 0.982283787 0.886083011 0.767797982 0.76503367 1 15.05368032 -2.478990236 2.297035682 2.904777939 0.848814945 0.297877008 0.075058794 7685412.491 655475.457 76529752.37 0.019604089 0.003319019 2.478990236 -2.055962995 VEAPSLDVHMDS(ph)PDINIEGPDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VEAPSLDVHMDSPDINIEGPDVK 23 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VEAPS(0.001)LDVHMDS(0.999)PDINIEGPDVK;VEAPSLDVHMDS(1)PDINIEGPDVK;VEAPSLDVHMDS(1)PDINIEGPDVK 176.21 3.99E-13 289496000 463411 319355 381493 386697 424090 307182 477520 354352 588563 TRUE FALSE 434406.9327 343000.3765 390542.1941 396620.2997 390783.6821 395860.4567 405920.3091 398593.6272 490328.033 0.885951656 0.699532463 0.79649167 0.808887669 0.796984173 0.807338006 0.827854582 0.812912174 1 18.90338772 -2.056724645 0.272423301 1.235706793 0.771829683 0.635743145 0.046048594 18.77832007 0.751032264 2.815830156 0.055283236 0.00877557 2.056724645 -0.463877111 VEAPSLDVHMDSPDINIEGPDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEAPSLDVHMDSPDINIEGPDVK 23 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 277.71 8.30E-52 108960000 158900 127510 139600 133110 164880 109190 167970 118760 191200 FALSE TRUE 148954.7326 136950.9731 142911.3779 136525.828 151930.9899 140711.3804 142784.4579 133587.4474 159287.4848 0.935131425 0.859772337 0.897191503 0.857103294 0.95381624 0.883380013 0.896394704 0.838656267 1 17.28127339 -1.455922413 6.116303244 1.000052082 0.889227922 0.49602051 0.034776872 2.18E-05 1.94E-06 0.029715496 0.007000722 0.035000769 1.455922413 -0.11082416 VEAVNMAEGIIHDTETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VEAVNMAEGIIHDTETK 17 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;;; 264.88 1.67E-27 790369000 1701078 1251926 1389065 1242790 1760628 1276220 1516970 1518981 2230460 FALSE TRUE 1594610.564 1344619.904 1422014.278 1274682.095 1622355.379 1644643.996 1289514.431 1708629.122 1858181.817 0.858156371 0.723621279 0.765271872 0.685983516 0.873087533 0.885082386 0.693965693 0.919516651 1 20.82546024 0.44304433 0.601564852 1.00968331 0.766662566 0.429536721 0.078360669 1.764053022 1.053464 0.102595928 0.031389065 2.773603201 -0.44304433 -0.243020744 VECQSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VECQSHR 7 0 O14818;H0Y586;O14818-2;O14818-4 O14818 PSMA7 Proteasome subunit alpha type-7 0 78.728 0.034549 109590000 110100 151530 97554 93391 159540 72793 102740 148470 118850 FALSE TRUE 103209.0375 162749.4389 99868.02695 95787.57117 147010.372 93807.1574 87335.09079 167006.8063 99013.1672 1.042376892 1.643715109 1.008633799 0.967422555 1.484755777 0.947421036 0.882055319 1.686713101 1 16.59533277 3.850603521 6.227133943 1.116452767 1.376121173 0.069838686 0.293452314 0.422694933 20.3723397 0.069925026 0.127541494 7089.302707 -3.850603521 0.259668406 VECYDYDNDGSHDLIGTFQTTMTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VECYDYDNDGSHDLIGTFQTTMTK 24 0 O75131;H0YB26 O75131 CPNE3 Copine-3 0 ;; 240.96 1.45E-37 607188000 640760 601520 532440 380144 937340 453040 752480 777960 1148240 FALSE TRUE 600655.9754 646057.1667 545069.7282 389899.1386 863725.0974 583825.2935 639652.6097 875090.0185 956591.3261 0.627912839 0.675374268 0.569804172 0.407592174 0.902919642 0.610318406 0.668679082 0.914800286 1 19.86754318 1.189858746 2.902024509 0.998881574 0.631296689 0.557243338 0.120249484 0.176372666 2.60263174 0.104032386 0.028824033 15.4831295 -1.189858746 -0.367584885 VEDLAWHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEDLAWHR 8 0 Q9NZU5;B4DEY6;Q9NZU5-2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 117.04 0.0021563 117940000 253670 271050 285050 285780 303790 263050 296740 226620 263400 FALSE TRUE 237793.2475 291118.824 291811.5206 293113.5986 279931.5588 338988.2647 252246.5918 254914.0059 219436.8384 1.083652359 1.326663409 1.32982011 1.335753836 1.275681699 1.544810193 1.149517983 1.161673709 1 17.74344622 1.253951641 2.052280376 1.02951044 1.316385331 0.413113939 0.118418585 0.270824004 1.959131449 0.099009717 0.028888708 17.94533793 -1.253951641 0.286874891 VEDMAELTCLNEASVLHNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 319.33 1.31E-66 1103204000 2207376 2105431 2224729 2250693 2304713 1745866 2904511 2005873 2178722 FALSE TRUE 2069220.276 2261319.302 2277500.622 2308449.593 2123710.138 2249869.172 2469006.54 2256310.66 1815079.223 1.140016507 1.245851571 1.25476651 1.27181754 1.170037159 1.239543235 1.360274807 1.243092109 1 20.79160109 0.928741847 21.86581415 0.999999999 1.249815419 0.619425835 0.058926965 8330.828458 2556348.34 0.057262573 0.014315643 8.486758556 -0.928741847 0.24981542 VEDVEALDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VEDVEALDR 9 0 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ; 146.79 0.00021858 912790000 977340 1187770 1218700 1230620 1338450 1009310 1330780 1050470 1303430 FALSE TRUE 916170.034 1275713.727 1247608.14 1262199.793 1233333.536 1300681.412 1131241.893 1181623.492 1085879.113 0.843712733 1.174821131 1.148938335 1.162375975 1.13579267 1.197814192 1.041775167 1.088172227 1 20.05043207 -0.795345469 5.137689122 0.999999931 1.112522598 0.072680172 0.101852621 7.76E-08 1.82E-08 0.089771725 0.021159385 0.160197056 0.795345469 0.112522667 VEDVEALDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VEDVEALDRK 10 1 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ; 113.69 0.0023332 420480000 667580 588690 652090 611380 692620 516680 760110 600420 861000 FALSE TRUE 625797.3595 632277.2201 667557.8827 627069.0459 638224.4191 665837.1284 646138.562 675383.7587 717293.5377 0.872442489 0.881476253 0.930662062 0.874215384 0.889767418 0.928263108 0.900800757 0.941572345 1 19.45220411 -5 0.153953127 1.370769613 0.872109924 0.766262456 0.01890478 66.30817086 0.598933411 7.44109836 0.088184995 1.00E-05 5 -0.498659689 VEEAEPEEFVVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEEAEPEEFVVEK 13 0 Q13185;S4R2Y4;C9JMM0;B8ZZ43 Q13185 CBX3 Chromobox protein homolog 3 0 133.07 1.36E-05 0 47323 37306 37345 38907 44088 34287 49501 33061 48515 FALSE TRUE 44361.1379 40068.17506 38230.84104 39905.41949 40625.50632 44185.1003 42078.78459 37188.73863 40417.53308 1.097571636 0.991356275 0.945897439 0.98732942 1.005145619 1.09321616 1.041102249 0.920114015 1 15.30269365 2.467187763 24.94516716 1.025688914 0.993535015 0 0.057484001 629.425051 1580613.112 0.019580324 0.016398252 293.2160666 -2.467187763 -0.032153899 VEEAS(ph)PGRPSSVDTLLSPTALIDSILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEEASPGRPSSVDTLLSPTALIDSILR 27 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 1 VEEAS(0.706)PGRPS(0.142)S(0.142)VDT(0.01)LLSPTALIDSILR 103.1 0.0014269 764760000 50541 51488 52913 43093 39699 37291 48268 42284 46864 TRUE FALSE 47377.72903 55300.22509 54168.12135 44198.83934 36581.20068 48056.30633 41030.6615 47563.25048 39042.09565 1.213503739 1.416425634 1.387428632 1.132081631 0.936968164 1.230884396 1.050933891 1.21825557 1 15.25274287 3.191895917 5.602911067 1.094015456 1.362884182 0.552297817 0.103271016 0.116317725 8.325443817 0.027288278 0.033410013 1555.592773 -3.191895917 0.268868726 VEECQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEECQR 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 0 107.22 0.07317 196470000 368460 342100 369300 393970 400390 295430 435110 330090 375500 FALSE TRUE 345398.7463 367429.44 378059.9704 404079.9372 368944.9845 380715.8451 369869.2949 371302.4631 312826.6242 1.104121963 1.174546575 1.208528754 1.291705712 1.179391254 1.21701868 1.182345959 1.186927309 1 18.25500378 0.147238586 1.29160044 0.99967935 1.197174147 0.63420403 0.046092589 5.259187701 7.267158404 0.045934034 0.012641249 1.403584574 -0.147238586 0.197494798 VEEEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VEEEEER 7 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ;;; 183.9 0.0014795 6298820000 4725190 4779740 4782680 4579630 4883110 3889690 5372200 4109410 4840190 FALSE TRUE 4429448.793 5133636.923 4896127.428 4697151.059 4499610.238 5012580.359 4566688.483 4622478.884 4032331.02 1.098483426 1.273118922 1.214217633 1.164872387 1.115883149 1.243097438 1.132518253 1.146354022 1 21.94318265 -0.155892706 0.353255999 0.953319703 1.210667646 0.494583692 0.055394621 4.361389817 0.691366873 0.322534375 0.045877299 0.698404926 0.155892706 0.257347943 VEEEERDPQS(ph)PEFEIEEEEEMLSSVIPDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VEEEERDPQSPEFEIEEEEEMLSSVIPDSR 30 1 A0A087WZP0;E9PLV2;Q8NCY6 A0A087WZP0 MSANTD4 Myb/SANT-like DNA-binding domain-containing protein 4 1 VEEEERDPQS(1)PEFEIEEEEEMLSSVIPDSR;VEEEERDPQS(1)PEFEIEEEEEMLSSVIPDSR 94.059 0.00051523 28621200 27973.7 18827.2 26329.7 22676 24419.9 23131.4 28454.1 20893.2 19876 TRUE FALSE 26222.87605 20221.18548 26954.25292 23257.90455 22502.05956 29809.05967 24187.67186 23501.76201 16558.5672 1.583644028 1.221191739 1.627813119 1.404584363 1.3589376 1.800219748 1.46073459 1.419311329 1 14.01529022 0.741062982 2.942050321 1.000085502 1.485500438 0.489925718 0.157023668 1.541234204 16.39833115 0.143066459 0.037504213 5.508875816 -0.741062982 0.485414936 VEEEHTNAIGTLHGGLTATLVDNISTMALLCTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEEEHTNAIGTLHGGLTATLVDNISTMALLCTER 34 0 Q9NPJ3-2;Q9NPJ3 Q9NPJ3-2 ACOT13 "Acyl-coenzyme A thioesterase 13;Acyl-coenzyme A thioesterase 13, N-terminally processed" 0 71.288 0.0022997 21946000 44660 36559 41431 38777 51771 40099 35031 40109 68268 FALSE TRUE 41864.81032 39265.8664 42413.76289 39772.08347 47705.11449 51674.93035 29778.42676 45116.69694 56873.62977 0.736102311 0.690405493 0.745754457 0.699306227 0.838791452 0.908592094 0.523589349 0.793279717 1 15.79547226 0.979864726 24.73947068 1.000000009 0.727627735 0.409093275 0.099624369 1306.739349 1605544.844 0.09302457 0.023256142 9.546951711 -0.979864726 -0.272372274 VEEESTGDPFGFDS(ph)DDESLPVSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VEEESTGDPFGFDSDDESLPVSSK 24 0 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 1 VEEESTGDPFGFDS(0.987)DDES(0.013)LPVSSK;VEEESTGDPFGFDS(0.969)DDES(0.03)LPVSSK 155.44 2.80E-08 218040000 674100 551900 613170 597810 620320 475570 775680 538030 731750 TRUE FALSE 631909.2843 592763.2503 627714.682 613150.8167 571602.5695 612859.3388 659373.9851 605204.2299 609616.1977 1.036569052 0.972354823 1.029688326 1.005798105 0.937643343 1.005319972 1.081621498 0.992762712 1 19.21754171 1.979076816 24.63754677 1.036265533 0.99587716 0.084476768 0.036676932 970.4437611 1142718.058 0.014063889 0.009189374 95.29647045 -1.979076816 -0.040388373 VEEGGRHPS(ph)PCQFTIATPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEEGGRHPSPCQFTIATPK 19 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 VEEGGRHPS(0.994)PCQFT(0.006)IATPK 139.26 1.91E-07 452840000 553020 457790 494350 501770 602310 463580 745070 497260 753070 TRUE FALSE 518407.4654 491685.2479 506076.2154 514646.2677 555007.0022 597408.0204 633353.6704 559344.0056 627377.752 0.826308335 0.78371483 0.806653111 0.820313226 0.884645655 0.952230165 1.009525232 0.891558561 1 19.25897484 2.489521295 1.874195723 0.971787098 0.801757946 0.830097608 0.032892138 0.115972764 0.825119188 0.012927872 0.010487801 308.6891006 -2.489521295 -0.170029152 VEELDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VEELDRK 7 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ; 96.492 0.028822 259200000 463970 445720 430700 438830 475550 382710 481600 379970 570360 FALSE TRUE 434930.9459 478721.5726 440916.4074 450091.1207 438202.2213 493192.1642 409388.551 427410.0909 475163.2313 0.915329548 1.007488671 0.927926191 0.947234742 0.922214078 1.037942609 0.861574558 0.899501609 1 18.85806368 1.714218037 24.99999808 0.909438046 0.959621924 0.104141556 0.05113783 1.404576089 1436.229961 0.02117987 0.011745321 51.78667616 -1.714218037 0.050183879 VEENPDADS(ph)DFDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEENPDADSDFDAK 14 0 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 1 VEENPDADS(1)DFDAK 298.6 1.03E-43 191680000 510910 266030 378640 348900 327500 256740 405110 261520 267100 TRUE FALSE 478933.0551 285727.138 387621.5196 357853.3647 301779.4711 330856.6702 344367.5164 294171.3477 222519.2845 2.152321567 1.284055621 1.74196821 1.608190344 1.356194686 1.486867401 1.547585043 1.322003836 1 17.76357085 -2.422712912 0.10735748 3.07E-15 1.96771235 0.502523962 0.216401357 76.11758023 1.026404127 22.14413975 3.329716741 0.003778219 2.422712912 1.96771235 VEEPSQCLASGTAISELIIEDNNAS(ph)PQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VEEPSQCLASGTAISELIIEDNNASPQK 28 0 Q5UIP0-2;Q5UIP0;H7C2B5 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 VEEPSQCLASGTAISELIIEDNNAS(1)PQK;VEEPSQCLASGTAISELIIEDNNAS(1)PQK;VEEPSQCLASGTAISELIIEDNNAS(1)PQK 252.75 1.21E-53 123542000 164426 102401 122554 115854 101575 103167 196790 114236 87498 TRUE FALSE 154134.8702 109982.8766 125461.0388 118827.0098 93597.70923 132949.6381 167283.1664 128498.6161 72894.01854 2.11450642 1.508805232 1.721143123 1.630133887 1.284024548 1.823875824 2.294881936 1.76281427 1 16.15351282 2.019153844 24.96696788 1.887175729 1.633488274 0 0.386654416 556.1446068 724929.5772 0.131539645 0.097135371 104.5090365 -2.019153844 -0.253687456 VEEPSQCLASGTAISELIIEDNNAS(ph)PQKLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEEPSQCLASGTAISELIIEDNNASPQKLR 30 1 Q5UIP0-2;Q5UIP0;H7C2B5 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 VEEPSQCLASGTAISELIIEDNNAS(1)PQKLR 124.17 9.38E-06 76485000 21391 18521 20601 20185 21767 12255 30158 19607 32076 TRUE FALSE 20052.17549 19892.31411 21089.66545 20702.98127 20057.50762 15792.81956 25636.08787 22054.97711 26722.30838 0.750390842 0.744408523 0.789215705 0.774745242 0.750590381 0.590997579 0.959351547 0.825339518 1 14.70575702 1.657245265 9.859146799 0.918482859 0.743758321 0.630946232 0.069690088 0.075427133 11.67567325 0.030976491 0.016573562 45.41980492 -1.657245265 -0.174724538 VEERDPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VEERDPPR 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 117.89 0.0018168 1346770000 2286400 2257300 2485500 2409400 2449100 2320400 2640200 2136400 2387400 FALSE TRUE 2143298.305 2424432.841 2544457.234 2471229.283 2256757.565 2990261.811 2244326.52 2403134.243 1988927.517 1.07761509 1.218964905 1.279311193 1.242493385 1.134660537 1.503454392 1.128410413 1.20825632 1 20.92355927 -0.520011122 7.317938495 1.000008775 1.231324682 0.268201366 0.115820206 0 0 0.100213171 0.023620471 0.301987438 0.520011122 0.231315906 VEESGEHVILGTGELYLDCVMHDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 15 VEESGEHVILGTGELYLDCVMHDLR 25 0 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;;;;;;;;;;;;; 247.54 2.99E-39 611011000 456166.2 490514.8 496299.7 458600.5 475414.6 420123.8 591379.4 439444.8 451025.1 FALSE TRUE 427615.5718 526833.0262 508072.1633 470368.9652 438077.455 541406.7209 502707.5491 494310.4506 375746.0971 1.138043948 1.402098466 1.352168837 1.251826616 1.165886907 1.440884483 1.337891605 1.315543806 1 18.51939859 0.860115635 17.34590524 1 1.316721053 0.484207473 0.096204835 15623.18436 1937316.559 0.088070547 0.022017637 7.246288739 -0.860115635 0.316721053 VEESGEHVILGTGELYLDCVMHDLRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEESGEHVILGTGELYLDCVMHDLRK 26 1 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 106.43 0.0012231 12998000 11075 17150 14806 17279 18380 9151.1 18161 14195 34306 FALSE TRUE 10381.83552 18419.80384 15157.20531 17722.40839 16936.50894 11792.87401 15437.92665 15967.277 28580.10697 0.363253907 0.644497372 0.530341098 0.620095943 0.592597815 0.412625258 0.540163361 0.558684998 1 14.8027237 0.63993395 3.791734772 0.999999187 0.540264695 0.74123338 0.086731181 5.615249979 58.6127816 0.077239291 0.019797183 4.364494497 -0.63993395 -0.459734491 VEESSWLIEDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEESSWLIEDGK 12 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 138.99 0.00015031 30554000 63145 42915 50492 45681 51785 37751 66889 50829 56174 FALSE TRUE 59192.86717 46092.47125 51689.69408 46853.2518 47718.01499 48649.10086 56859.61542 57175.11254 46798.1965 1.264853597 0.98491982 1.104523207 1.001176441 1.019654999 1.039550763 1.214995869 1.22173752 1 15.51416531 1.748762455 25 1.165251961 1.058969037 0.101072995 0.098985329 3.897758337 9570.843115 0.041047251 0.02276284 56.07411844 -1.748762455 -0.106282925 VEESSWLIEDGKVVTVHLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEESSWLIEDGKVVTVHLEK 20 1 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 117.65 4.63E-05 11380000 31021 24006 27474 30061 32284 24967 39360 22262 34687 FALSE TRUE 29079.45098 25783.42922 28125.69625 30832.41615 29748.54487 32174.56759 33458.3334 25041.4597 28897.51561 1.006295883 0.892236882 0.973291152 1.066957332 1.029449911 1.113402551 1.157827332 0.866560989 1 14.81865785 3.354876847 3.451607825 1.059283504 0.939779518 0.152259756 0.082377061 0.285810683 6.587316826 0.022694664 0.031759315 2264.002213 -3.354876847 -0.119503985 VEETVKHDWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VEETVKHDWDR 11 1 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881;E9PKD3;A0A0B4J225 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 ;;;;; 245.69 3.51E-16 7810290000 4259320 3959800 4143240 4020000 5268320 2898910 5005910 3852410 8359930 FALSE TRUE 3992736.764 4252987.712 4241519.609 4123160.006 4854567.399 3735778.257 4255320.268 4333391.869 6964603.676 0.573289874 0.610657535 0.609010908 0.592016459 0.697034264 0.536394952 0.610992451 0.62220222 1 22.73160983 0.524030229 2.762661441 0.999998231 0.605197198 0.905283608 0.040046542 2.595643239 14.71374247 0.034259871 0.009030507 3.342183027 -0.524030229 -0.394801033 VEFATLQEALAHALTEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VEFATLQEALAHALTEK 17 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 272.31 1.25E-35 874490000 2025060 1762150 1865500 1914570 2066500 1467760 2326100 1692030 2434000 FALSE TRUE 1898315.109 1892621.42 1909750.541 1963701.108 1904205.426 1891478.485 1977322.899 1903283.67 2027749.676 0.93616837 0.933360484 0.941807839 0.968413967 0.939073224 0.932796838 0.975131656 0.938618653 1 20.95144813 -5 0.147598687 1.19388259 0.928241559 0.599160807 0.014195605 87.87424447 0.776750101 4.981642547 0.070244075 1.00E-05 5 -0.26564103 VEFEELCADLFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VEFEELCADLFER 13 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;;;;; 253.53 2.03E-23 525331000 511807 536643 535481 546002 556594 470524 706679 501363 424852 FALSE TRUE 479773.9135 576376.6061 548182.8622 560013.3357 512881.3524 606356.6405 600719.0444 563959.2742 353941.4566 1.355517712 1.628451812 1.548795294 1.582220238 1.44905702 1.713155182 1.697227135 1.593368801 1 18.43315123 VEFMDDTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 VEFMDDTSR 9 0 P62857 P62857 RPS28 40S ribosomal protein S28 0 ;;;;;;; 217.66 1.30E-06 6244130000 5765610 6013420 5859930 5478020 6601670 4410820 6401290 5281630 7087570 FALSE TRUE 5404750.762 6458659.874 5998930.307 5618595.267 6083201.468 5684152.13 5441475.991 5941053.132 5904608.78 0.915344431 1.093833667 1.015974221 0.951560972 1.03024632 0.962663632 0.921564187 1.006172187 1 22.49341004 3.375815032 5.72075196 0.972677333 1.029640935 0.013721122 0.053277051 0.326727152 15.61201841 0.014154078 0.019318244 2375.828192 -3.375815032 0.056963602 VEGDLKGPEVDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VEGDLKGPEVDLK 13 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 113.72 0.00072903 708200000 1874560 1148430 1476410 1412350 1785570 942570 1902530 1206290 2698220 FALSE TRUE 1757234.636 1233460.952 1511431.142 1448593.292 1645338.535 1214674.658 1617263.289 1356897.962 2247869.651 0.781733334 0.548724412 0.672383802 0.644429401 0.731954602 0.540367035 0.719464889 0.603637298 1 21.10012695 -1.486977602 3.307735821 1.007045316 0.64936127 0.661402716 0.077395881 40326627.27 60538111.48 2666476.653 0.016269158 0.032585351 1.486977602 -0.357684045 VEGGFDQYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEGGFDQYR 9 0 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 95.815 0.018122 116930000 99741 164250 105400 99367 180140 77772 103090 139820 175570 FALSE TRUE 93498.38885 176411.2409 107900.1378 101916.9254 165992.531 100223.5139 87632.61154 157276.8348 146266.2328 0.639234272 1.206096838 0.73769684 0.696790527 1.134865703 0.68521293 0.599130844 1.075277812 1 17.15823722 3.745507275 23.20109257 0.813239494 0.965778187 0 0.224319056 458.0380597 577984.3148 0.053924605 0.096909243 5565.539576 -3.745507275 0.152538693 VEGQKEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VEGQKEEK 8 1 A0A1W2PNT1 A0A1W2PNT1 0 ;;; 81.548 0.013565 1414880000 436645 1807470 1400380 1375620 1605130 1518500 1228730 1345080 993110 FALSE TRUE 409316.1689 1941296.959 1433597.675 1410920.738 1479069.565 1956866.299 1044493.343 1513016.199 827353.5253 0.494729467 2.346393531 1.732751032 1.705342027 1.787711685 2.365211774 1.26245107 1.828742071 1 19.65814439 -0.383518742 13.22591156 1 1.750123075 0.133836309 0.533084383 0 0 0.459197516 0.108233892 0.413505469 0.383518742 0.750123075 VEHES(ph)FEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 VEHESFEK 8 0 K7EMC6;A0A0A0MSA9;A0A0C4DG49;P15151-3;P15151-2;P15151-4;P15151 K7EMC6 PVR Poliovirus receptor 1 VEHES(1)FEK;VEHES(1)FEK;VEHES(1)FEK;VEHES(1)FEK;VEHES(1)FEK;VEHES(1)FEK;VEHES(1)FEK;VEHES(1)FEK 95.62 0.0099869 13236630000 4553111 3717614 3623021 3738147 4329549 3988622 4527481 2783447 5177229 TRUE FALSE 4268139.91 3992870.009 3708960.769 3834074.181 3989523.686 5140072.422 3848627.255 3130966.485 4313116.034 0.989572244 0.925750659 0.859926035 0.888933697 0.924974811 1.191730615 0.892307841 0.725917518 1 22.0402991 -2.427433122 2.339624915 1.726468715 0.927406796 0.039220598 0.11623921 11821304.21 2625097.567 45081147.21 0.027184616 0.003737377 2.427433122 -0.799061919 VEHHDHAVVSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VEHHDHAVVSGR 12 0 O95831-3;O95831;E9PMA0;O95831-5;O95831-2 O95831-3 AIFM1 "Apoptosis-inducing factor 1, mitochondrial" 0 ; 141.58 3.51E-05 168021000 96560 107010 99458 97435 138969 96095 91496 123708 135159 FALSE TRUE 90516.48196 114933.1317 101817.1907 99935.34706 128054.9353 123836.0665 77777.02421 139153.2161 112600.0897 0.803875753 1.020719717 0.904237208 0.887524577 1.137254292 1.09978657 0.690736787 1.235817986 1 16.78084845 4.749535005 22.92118426 0.973049504 0.803875431 0.121347772 0.15159217 1154.020037 2410138.279 0.03391668 0.4658647 56173.95539 -4.749535005 -0.169174073 VEHTNTGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VEHTNTGTK 9 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ; 106.2 0.0029745 111284000 151321 151272 133853 157797 162142 90532 158979 146042 123200 FALSE TRUE 141850.0887 162472.3363 137028.0564 161846.3382 149408.0214 116667.1187 135141.5748 164275.6652 102637.1241 1.382054398 1.582978262 1.335073031 1.576879122 1.455691814 1.136695126 1.316692922 1.600548209 1 16.64719313 2.373388947 10.24553846 1.287465713 1.470839859 0.260151741 0.168122506 0.475837996 43.48556549 0.053344421 0.044604646 236.2593186 -2.373388947 0.183374146 VEHTPDGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VEHTPDGVK 9 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;; 119.75 0.00077709 2034130000 2447350 2902080 2524440 2696500 3242650 1999010 3149440 2816860 3722940 FALSE TRUE 2294174.732 3116953.023 2584320.909 2765696.755 2987985.349 2576091.736 2677210.71 3168551.172 3101557.263 0.73968479 1.004963881 0.833233337 0.891712298 0.963382293 0.830580098 0.863182744 1.021600088 1 21.56456133 1.235786302 24.99897424 1.010800113 0.884079647 0.36907329 0.072974546 79.43508292 715710.7285 0.054886724 0.01609612 17.21021523 -1.235786302 -0.126720466 VEIFYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VEIFYR 6 0 Q08380;K7ESM3;K7EKQ5;K7EP36;K7EQT9;K7ES75;K7EN99;K7ERZ6;K7EJD3 Q08380 LGALS3BP Galectin-3-binding protein 0 ;;; 154.29 0.023318 1202630000 2966270 3603740 2803830 2637970 3494210 2326480 3536020 3049810 4614880 FALSE TRUE 2780616.456 3870564.659 2870338.172 2705664.776 3219788.842 2998097.009 3005826.628 3430585.492 3844626.715 0.723247447 1.006746544 0.746584359 0.70375227 0.837477623 0.779814851 0.78182535 0.892306522 1 21.8744121 0.976578272 3.973383457 0.999677937 0.809281728 0.37995929 0.08432336 0.232071574 10.64443182 0.081454887 0.020859164 9.474979344 -0.976578272 -0.19039621 VEILANDQGNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VEILANDQGNR 11 0 P17066;P48741 P17066 HSPA6;HSPA7 Heat shock 70 kDa protein 6;Putative heat shock 70 kDa protein 7 0 ; 172.56 3.07E-05 1109760000 1107180 1248200 1160690 1008970 1274830 796730 1360310 1184100 1426660 FALSE TRUE 1037883.58 1340618.027 1188222.115 1034861.878 1174709.994 1026733.017 1156344.144 1331937.492 1188541.229 0.873241546 1.12795248 0.999731507 0.870699184 0.988362848 0.863859824 0.972910418 1.120648959 1 20.18076052 -0.943365029 5.277229231 1.000000043 0.983955557 0.001200598 0.093878221 4.65E-08 9.19E-09 0.08914172 0.021010849 0.11392918 0.943365029 -0.016044485 VEKIPGGIIEDSCVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VEKIPGGIIEDSCVLR 16 1 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;E9PQ35 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 150.68 6.54E-07 1025660000 798710 837010 832530 915100 998200 727350 1104940 815300 1345270 FALSE TRUE 748720.1668 898983.0913 852278.0047 938583.0153 919805.3985 937324.1375 939264.5048 917091.9997 1120735.746 0.668061289 0.802136538 0.760462944 0.837470401 0.820715679 0.836347141 0.838078475 0.818294592 1 20.09601472 -5 0.067589051 1.686909705 0.541137935 0.796285691 0.036929519 138.5255828 0.676905388 15.11142388 2.023691158 1.00E-05 5 -1.14577177 VEKPDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VEKPDTK 7 1 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 0 ;;;; 87.476 0.017614 8938870000 13822600 8599050 10927900 10815600 11192700 8204840 14789300 9839250 13864000 FALSE TRUE 12957468.14 9235732.609 11187114.95 11093146.61 10313670.49 10573444.11 12571781.76 11067702.02 11550008.84 1.121857855 0.799629917 0.96858064 0.960444859 0.892957801 0.915449007 1.088465121 0.958241866 1 23.46139062 1.760310895 25 1.023053484 0.928261249 0.118129151 0.08635089 16.12832499 18553.21374 0.036515821 0.020250881 57.58520201 -1.760310895 -0.094792235 VELELS(ph)MTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VELELSMTK 9 0 Q5TZA2-2;Q5TZA2;B1AKD8;A0A087WW81 Q5TZA2-2 CROCC Rootletin 1 VELELS(0.5)MT(0.5)K 61.999 0.08968 61159000 54898 54855 53224 49789 68251 45663 43051 58948 45171 TRUE FALSE 51462.03218 58916.52128 54486.49841 51066.67003 62890.84177 58845.16682 36595.90222 66307.78756 37631.66828 1.367519287 1.565610135 1.447889528 1.357013185 1.671221198 1.563714008 0.972476212 1.762020941 1 15.19965963 -3.312192867 0.22754418 7.24E-08 1.509568731 0.27162114 0.221374906 86.25429785 1.720025414 40.97106772 0.388661346 0.000487312 3.312192867 1.509568659 VELFFKDDANNDPQWSEEQLIAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VELFFKDDANNDPQWSEEQLIAAK 24 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 318.17 8.97E-74 113570000 357800 232810 282790 302540 330200 196500 375260 254060 283890 FALSE TRUE 335405.9367 250047.4946 289497.9123 310303.6886 304267.424 253226.3601 318993.2467 285779.9503 236506.925 1.418165395 1.057252318 1.224056811 1.312027919 1.286505348 1.070693216 1.348769161 1.208336501 1 17.8515229 -0.88937828 4.811894351 0.999998969 1.227717872 0.302605852 0.113329467 0.00102138 33954804.93 89.48228777 0.024783867 0.129009508 0.88937828 0.227718903 VELS(ph)PGPPKPAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VELSPGPPKPAGR 13 1 A0A087WXE2;Q8IZ73-2;Q8IZ73 A0A087WXE2 RPUSD2 RNA pseudouridylate synthase domain-containing protein 2 1 VELS(1)PGPPKPAGR;VELS(1)PGPPKPAGR;VELS(1)PGPPKPAGR;VELS(1)PGPPKPAGR 138.28 3.08E-05 2069090000 4442410 3127090 3671530 3468690 3690200 2950660 4614330 3258860 4696530 TRUE FALSE 4164367.488 3358622.997 3758620.425 3557702.458 3400386.578 3802467.642 3922454.054 3665735.845 3912648.802 1.064334597 0.858401346 0.960633222 0.90928234 0.869075337 0.971839752 1.002506039 0.936893657 1 21.89971419 2.027124744 24.81009146 0.981852004 0.924686713 0.121668509 0.058967547 315.4331946 288514.7052 0.020101588 0.014845725 106.4448719 -2.027124744 -0.057165291 VEMYS(ph)GS(ph)DDDDDFNKLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VEMYSGSDDDDDFNKLPK 18 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 2 VEMY(0.306)S(0.977)GS(0.717)DDDDDFNKLPK;VEMY(0.038)S(0.963)GS(0.999)DDDDDFNKLPK;VEMY(0.252)S(0.793)GS(0.954)DDDDDFNKLPK;VEMY(0.005)S(0.998)GS(0.998)DDDDDFNKLPK 152.81 2.48E-08 765070000 4890430 1924560 2772590 2701070 2776450 1906980 3805720 2221310 3865000 TRUE FALSE 4584346.716 2067056.425 2838357.144 2770384.029 2558398.817 2457494.169 3235087.617 2498645.443 3219906.531 1.423751488 0.641961624 0.881502962 0.860392686 0.794556858 0.763219101 1.00471476 0.775999371 1 21.61858738 -0.915779211 7.465047714 0.999999999 0.870007094 0.014191288 0.211592429 2.69E-09 5.40E-10 0.180379608 0.042515881 0.121400588 0.915779211 -0.129992905 VEMYSGS(ph)DDDDDFNKLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VEMYSGSDDDDDFNKLPK 18 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 VEMYS(0.017)GS(0.983)DDDDDFNKLPK;VEMYS(0.002)GS(0.998)DDDDDFNKLPK 217.82 4.97E-19 218772000 455330 182968 285120 261500 289710 201464 353910 225750 563170 TRUE FALSE 426831.7081 196515.1411 291883.181 268210.5327 266957.3452 259623.3863 300844.481 253935.3844 469173.2888 0.909752789 0.418854069 0.622122333 0.571666246 0.568995191 0.553363528 0.641222525 0.541240072 1 18.83976135 -1.440397383 3.137080171 1.007197514 0.588287292 0.496240755 0.124755845 28196820.32 35642061.18 1803783.081 0.026096291 0.036274599 1.440397383 -0.418910223 VENDWHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VENDWHR 7 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 117.39 0.015032 0 211590 250120 241790 246730 304400 194310 280610 258040 201270 FALSE TRUE 198346.9596 268639.145 247525.373 253061.5095 280493.6519 250404.1426 238535.1356 290256.862 167676.7367 1.182912809 1.602125317 1.47620581 1.509222534 1.672823895 1.493374379 1.422589324 1.73105028 1 17.35532302 -1.551988477 7.636549443 0.999805355 1.513457993 0.537476655 0.149045868 0.000435127 2.55E-05 0.127133515 0.029954654 0.028055081 1.551988477 0.513652637 VENFEAAVHFYGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VENFEAAVHFYGK 13 0 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 0 126.48 0.00018801 219670000 1083800 953640 1048300 1007700 1124500 854420 1292000 1008400 1223400 FALSE TRUE 1015966.893 1024248.498 1073166.171 1033559.288 1036186.306 1101077.184 1098276.594 1134300.96 1019206.637 0.996821308 1.004946849 1.052942684 1.01408218 1.016659693 1.080327722 1.077579909 1.112925406 1 19.95901515 2.239861771 24.99828901 1.074758059 1.020186764 0.377413345 0.031597037 31.46469066 604527.985 0.010347599 0.008220389 173.7247804 -2.239861771 -0.054571295 VENMSSNQDGNDS(ph)DEFM ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VENMSSNQDGNDSDEFM 17 0 Q86WR0;Q86WR0-2 Q86WR0 CCDC25 Coiled-coil domain-containing protein 25 1 VENMSSNQDGNDS(1)DEFM 122.63 5.90E-05 60648000 53156 32774 90613 119220 41474 96109 90743 31337 209560 TRUE FALSE 49829.06085 35200.62106 92762.38315 122279.387 38216.79934 123854.1081 77136.92957 35249.49343 174583.0822 0.285417466 0.201626759 0.531336611 0.700407998 0.218903223 0.709427893 0.441835077 0.201906697 1 17.41355424 -5 0.306534081 5.944787905 0.392600866 0.464025059 0.194689257 260.9610407 2.382584093 833.0937723 0.179363635 1.00E-05 5 -5.552187039 VENS(ph)PQVDGSPPGLEGLLGGIGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VENSPQVDGSPPGLEGLLGGIGEK 24 0 E7EXA6;A0A0D9SF58;Q8WVB6;Q8WVB6-2;Q8WVB6-3 E7EXA6 CHTF18 Chromosome transmission fidelity protein 18 homolog 1 VENS(0.773)PQVDGS(0.227)PPGLEGLLGGIGEK 107.2 0.0016439 16277000 27715 24431 31003 29033 28759 18951 36540 23778 35485 TRUE FALSE 25980.36762 26239.89666 31738.4058 29778.03593 26500.38415 24421.84606 31061.16622 26746.73564 29562.32426 0.878833728 0.887612775 1.073609961 1.007296844 0.896424243 0.826113869 1.050701087 0.904757536 1 14.85147208 VENSPQVDGS(ph)PPGLEGLLGGIGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VENSPQVDGSPPGLEGLLGGIGEK 24 0 E7EXA6;A0A0D9SF58;Q8WVB6;Q8WVB6-2;Q8WVB6-3 E7EXA6 CHTF18 Chromosome transmission fidelity protein 18 homolog 1 VENSPQVDGS(1)PPGLEGLLGGIGEK;VENSPQVDGS(1)PPGLEGLLGGIGEK;VENSPQVDGS(1)PPGLEGLLGGIGEK;VENSPQVDGS(1)PPGLEGLLGGIGEK 292.97 4.70E-62 387973000 615470 486826 551270 546750 549255 426974 731050 516410 639310 TRUE FALSE 576948.8313 522871.1036 564346.3847 560780.5306 506118.7279 550234.4625 621435.8392 580884.9253 532605.0309 1.083258321 0.981723929 1.059596421 1.052901302 0.950270273 1.033100385 1.166785522 1.090648589 1 19.02270653 1.925630505 11.26318649 1.103355957 1.02265759 0.178949709 0.055512237 0.925168819 137.9079482 0.021100125 0.013481673 84.26175596 -1.925630505 -0.080698367 VENSWGEDHGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VENSWGEDHGHK 12 0 Q13867;K7ESE8 Q13867 BLMH Bleomycin hydrolase 0 ; 102.62 0.0013499 522390000 485632 541050 471059 452091 642440 339334 583640 604520 474465 FALSE TRUE 455237.16 581109.905 482232.7419 463692.4204 591985.3539 437294.2172 496128.6002 679995.6527 395273.7263 1.151701036 1.470145538 1.219996953 1.173091935 1.497659253 1.106307321 1.25515198 1.72031584 1 18.59249254 5.055244833 12.53649989 1.306067105 0.391363608 0.050245593 0.209892877 593516.6716 4634965.794 0.044639991 12578903.94 113565.0858 -5.055244833 -0.914703497 VEPSSQS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEPSSQSPGR 10 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 VEPSSQS(1)PGR 105.2 0.0027066 99103000 134420 130540 127750 137700 134040 125500 143430 129320 137750 TRUE FALSE 126006.8921 140205.3174 130780.2903 141233.6151 123513.0391 161729.8127 121924.003 145465.8867 114758.6351 1.098016651 1.221740894 1.139611762 1.23070142 1.076285362 1.40930408 1.062438595 1.267581185 1 16.80824319 -0.470359021 7.838541276 1.000000006 1.185503806 0.244691297 0.103823037 0 0 0.084525292 0.019922802 0.338564157 0.470359021 0.185503799 VEPSSQS(ph)PGRSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEPSSQSPGRSPR 13 1 G8JLD3;X6RLX0;Q8IUD2-3;Q8IUD2;Q8IUD2-2;X6RM00;Q8IUD2-4;Q8IUD2-5;K7EKH8;K7EIZ7 G8JLD3 ERC1 ELKS/Rab6-interacting/CAST family member 1 1 VEPS(0.002)S(0.041)QS(0.659)PGRS(0.298)PR 110.9 0.0026879 184520000 220020 277210 277960 262840 292210 241560 321900 245860 298270 TRUE FALSE 206249.3409 297734.9168 284553.3425 269584.9194 269261.0053 311294.4506 273634.0834 276556.1622 248486.8101 0.830021283 1.198192036 1.145144655 1.084906355 1.083602809 1.25276046 1.101201642 1.112961135 1 17.92280975 4.745967656 24.95799495 1.134375862 0.830021135 0.635817534 0.068996391 509.7038369 1717403.176 0.014997263 0.155557207 55714.42546 -4.745967656 -0.304354727 VEPSSQSPGRS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 VEPS(0.007)S(0.242)QS(0.105)PGRS(0.645)PR;VEPSSQS(0.019)PGRS(0.981)PR;VEPSSQS(0.004)PGRS(0.996)PR 152.94 2.47E-05 1460930000 935740 1027480 1064850 1088860 1175650 929720 1177920 983700 1094450 TRUE FALSE 877173.7037 1103555.688 1090108.745 1116801.991 1083319.191 1198115.071 1001301.831 1106517.11 911779.2246 0.962046162 1.210332127 1.195584101 1.224860099 1.188137613 1.314040767 1.098184521 1.213580087 1 19.79832501 -1.498191288 2.916451694 0.993728617 1.182432369 0.261248123 0.092341611 13214188.09 15914002.72 671800.2414 0.020177807 0.031754751 1.498191288 0.188703753 VEQATKPS(ph)FESGR ddPTM_SK-BR-3_Pertuzumab_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" 1 VEQAT(0.002)KPS(0.997)FES(0.001)GR;VEQATKPS(1)FESGR;VEQATKPS(0.999)FES(0.001)GR;VEQAT(0.106)KPS(0.893)FES(0.001)GR;VEQAT(0.006)KPS(0.993)FES(0.001)GR 123.08 0.00013783 1781910000 1983970 1473200 1593920 1539670 1705550 1290580 2044160 1529320 1989110 TRUE FALSE 1859796.859 1582277.261 1631728.535 1579180.539 1571602.983 1663149.495 1737657.185 1720258.968 1657114.691 1.122310284 0.954838714 0.984680508 0.952969971 0.94839723 1.003641754 1.048604055 1.038104953 1 20.66024203 1.993126947 23.39738846 1.032258331 0.983881529 0.080196306 0.051167773 236.525324 805184.9707 0.018411054 0.013061101 98.42987795 -1.993126947 -0.048376801 VEQATKPSFESGR ddPTM_SK-BR-3_Pertuzumab_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 ;;;; 188.19 5.76E-06 4872430000 5314900 4645730 4989650 4805670 5255190 4234970 6464810 4806700 5588780 FALSE TRUE 4982249.896 4989704.683 5108006.854 4928991.628 4842468.576 5457537.09 5495471.757 5406827.076 4655976.513 1.070076252 1.071677374 1.097086044 1.058637563 1.040054339 1.17215735 1.180304871 1.161265969 1 22.15065235 2.234959421 24.99996695 1.148430392 1.071705568 0.204034908 0.053327802 99.69226298 692067.9331 0.017506293 0.013428263 171.7747879 -2.234959421 -0.076724824 VEQHVVDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VEQHVVDGK 9 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;;;; 80.706 0.023353 2637880000 10030770 10062550 10115330 9850060 10926790 8017390 11700380 9695120 12863790 FALSE TRUE 9402962.011 10807591.67 10355270.4 10102829.22 10068643.99 10331880.34 9946016.64 10905577.07 10716740.35 0.877408774 1.008477515 0.966270533 0.942714752 0.939524862 0.96408796 0.928082264 1.017620724 1 23.35336282 1.227444392 24.99983489 1.0088104 0.95388872 0.355331958 0.033729071 295.0287689 663483.6293 0.03005971 0.007793285 16.88279673 -1.227444392 -0.054921679 VEQIAAIAQELNELDYYDSHNVNTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VEQIAAIAQELNELDYYDSHNVNTR 25 0 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 ;;;;; 336.14 4.71E-88 1214099000 1295003 902451 1021268 805567 694512 812774 1236827 958862 873241 FALSE TRUE 1213951.074 969269.411 1045492.959 826239.213 639967.829 1047408.66 1051376.273 1078578.031 727491.4357 1.668680914 1.332344772 1.437120642 1.135737374 0.879691221 1.439753938 1.445207767 1.48259894 1 19.47257074 7.999993202 0.024426858 7.98E-10 3.126835641 0.192573158 0.216351072 4630.949125 8.698704389 385.9948353 795.5235319 99998434.79 -7.999993202 3.12683564 VEQMPQAS(ph)PGLAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VEQMPQASPGLAPR 14 0 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 VEQMPQAS(1)PGLAPR;VEQMPQAS(1)PGLAPR;VEQMPQAS(1)PGLAPR 204.18 1.47E-08 283660000 563870 622210 655880 630830 728280 497760 716120 600110 817400 TRUE FALSE 528578.3832 668279.0758 671437.7833 647018.1658 671083.8265 641455.2315 608744.4541 675035.0545 680970.6594 0.776213154 0.98136251 0.986001047 0.950141033 0.985481265 0.941971908 0.893936392 0.991283611 1 19.37723311 4.742278084 24.99096431 0.961608314 0.776213083 0.780018752 0.031633797 190.9680048 1283743.424 0.008144631 0.061382355 55243.10546 -4.742278084 -0.185395231 VEQVLSLEPQHELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VEQVLSLEPQHELK 14 0 O95292;E5RK64;O95292-2 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 0 ;; 211.57 3.65E-09 464190000 928158 711309 695793 642912 867358 599871 959195 741603 1052791 FALSE TRUE 870066.2476 763975.0585 712297.5385 659410.2104 799239.2014 773044.0196 815372.6145 834193.767 877073.3808 0.992010779 0.871050331 0.812129924 0.751830149 0.911256936 0.881390356 0.929651535 0.951110574 1 19.74233803 1.502383855 1.138265344 0.992116 0.855211664 0.348596945 0.061903071 0.47616074 1.192770538 0.055151414 0.019468567 31.79683223 -1.502383855 -0.136904336 VERLS(ph)SGPEQITLEASSTEGHPGAPS(ph)PQHTDQTEAFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VERLSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 38 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 2 VERLS(0.931)S(0.069)GPEQIT(0.001)LEASSTEGHPGAPS(1)PQHTDQTEAFQK 220.28 3.47E-39 79051000 30045 36807 29613 36939 32940 25799 48531 28968 38213 TRUE FALSE 28164.53708 39532.22858 30315.43434 37886.91728 30353.02527 33246.75249 41254.22709 32584.71857 31835.00343 0.884703441 1.241784963 0.95226735 1.190102503 0.953448155 1.044345811 1.29587632 1.023550025 1 14.9583263 VERLS(ph)SGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VERLSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 38 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 VERLS(0.947)S(0.053)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK;VERLS(0.745)S(0.255)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK;VERLS(0.956)S(0.043)GPEQIT(0.001)LEASSTEGHPGAPSPQHTDQTEAFQK;VERLS(0.944)S(0.056)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK;VERLS(0.964)S(0.036)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 390.02 1.05E-179 5469480000 758400 1047783 1014894 1154621 1039061 777215 1390017 972159 962497 TRUE FALSE 710933.0978 1125361.944 1038967.765 1184250.53 957457.3404 1001584.353 1181596.855 1093535.191 801850.0327 0.886616036 1.403456878 1.295713316 1.476897776 1.194060362 1.249091866 1.473588336 1.363765226 1 19.61297291 4.744198217 24.88148748 1.332127701 0.886615832 0.451698819 0.14323665 466.1464052 2057267.749 0.030125471 0.266765917 55487.89081 -4.744198217 -0.445511869 VERPPS(ph)PFSMAPQASLPPVPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VERPPSPFSMAPQASLPPVPPR 22 1 P22681;A0A1B0GW38;A0A0U1RQX8 P22681 CBL E3 ubiquitin-protein ligase CBL 1 VERPPS(0.998)PFS(0.002)MAPQASLPPVPPR;VERPPS(1)PFSMAPQASLPPVPPR;VERPPS(0.992)PFS(0.008)MAPQASLPPVPPR;VERPPS(0.994)PFS(0.006)MAPQASLPPVPPR;VERPPS(0.988)PFS(0.012)MAPQASLPPVPPR 223 4.89E-26 1018150000 607569 551724 527334 591236 657068 451207 697757 484865 790793 TRUE FALSE 569542.3408 592574.219 539842.6115 606408.1167 605464.5298 581463.1362 593134.8155 545401.4626 658804.5396 0.864508829 0.899468937 0.819427583 0.920467423 0.919035151 0.882603415 0.900319867 0.827865368 1 19.32949097 -1.291337333 3.439241453 1.000431594 0.879777407 0.550559134 0.034293948 11706533.95 15250648.02 51386.21953 0.008012929 0.051128455 1.291337333 -0.120654187 VES(ph)LESLYFTPIPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VESLESLYFTPIPAR 15 0 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 VES(1)LESLYFTPIPAR;VES(1)LESLYFTPIPAR;VES(1)LESLYFTPIPAR 175.15 9.15E-07 97832000 92701 69925 89994 79010 76837 80620 110367 80603 76913 TRUE FALSE 86899.00989 75102.31976 92128.70018 81037.53036 70802.53197 103893.6852 93818.49295 90666.46198 64075.72342 1.356192412 1.172086958 1.437809755 1.264715028 1.104982171 1.621420402 1.464181564 1.414989284 1 15.96749024 2.243816136 24.9991542 1.426638409 1.277352949 0.047832963 0.180868291 243.2458684 1157060.482 0.057861017 0.047089867 175.3138133 -2.243816136 -0.14928546 VES(ph)MEALPILSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VESMEALPILSR 12 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 VES(1)MEALPILSR;VES(1)MEALPILSR 152.4 6.17E-05 51388000 82574 68459 80533 62181 79000 62594 74832 68798 115458 TRUE FALSE 77405.84074 73527.77559 82443.28079 63776.66973 72795.65867 80663.87167 63611.63631 77387.58174 96187.31391 0.804740642 0.764422798 0.85711179 0.663046582 0.756811431 0.838612374 0.661330832 0.804550814 1 16.55355901 0.970775904 24.06155126 1.000000002 0.76583787 0.571331806 0.063867686 1610.563712 1326053.38 0.059623395 0.014905849 9.349231302 -0.970775904 -0.234162132 VES(ph)PPLEEWPSPAPSFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VESPPLEEWPSPAPSFK 17 0 A0A0D9SFF0;Q08050-2;Q08050;Q08050-3 A0A0D9SFF0 FOXM1 Forkhead box protein M1 1 VES(1)PPLEEWPSPAPSFK 109.35 0.00064103 19516000 45849 28088 40260 28693 28959 31359 45510 30080 33026 TRUE FALSE 42979.39293 30167.66475 41214.98621 29429.31096 26684.67695 40411.83423 38686.19799 33835.55421 27513.74724 1.562106119 1.096457872 1.497977933 1.069622058 0.969867053 1.468786998 1.406067943 1.229769028 1 14.74786502 -2.347714445 1.54569385 5.72E-05 1.290087298 0.171510415 0.198570952 547281.2034 61052.19895 1898903.115 0.051326316 0.004490405 2.347714445 1.290030078 VESEIKVPDVELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VESEIKVPDVELK 13 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 129.93 0.00013495 94294000 303800 153930 189400 193920 242550 143480 252070 173130 304790 FALSE TRUE 284785.7003 165327.1374 193892.6574 198896.3155 223501.1014 184900.3468 214274.4436 194745.6616 253918.58 1.121563063 0.651102953 0.763601693 0.78330745 0.880207748 0.728187543 0.843870675 0.766961054 1 17.95400644 -1.710170773 2.660142358 1.034227491 0.797944268 0.157614398 0.125780948 31371998.72 26517612.67 7183851.826 0.027247041 0.01949078 1.710170773 -0.236283223 VESGDPSLHPPPSPGTPSAT(ph)PASPPASATPSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VESGDPSLHPPPSPGTPSATPASPPASATPSQR 33 0 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 1 VESGDPSLHPPPS(0.011)PGT(0.156)PS(0.1)AT(0.699)PAS(0.034)PPASATPSQR 203.21 1.69E-26 694440000 89791 137370 132850 153610 119280 83195 93625 67301 64907 TRUE FALSE 84171.14159 147541.0177 136001.2647 157551.8927 109912.23 107212.0459 79586.80042 75703.678 54073.60238 1.556603183 2.728522074 2.515113822 2.913656308 2.032641161 1.982705816 1.471823531 1.400011737 1 15.72263685 1.834063755 1.153394945 1.131140178 2.483646081 0.635511862 0.373797082 0.268592388 0.661519373 0.28454047 0.118369774 68.24388696 -1.834063755 1.352505903 VESGDPSLHPPPSPGTPSATPAS(ph)PPASATPSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VESGDPSLHPPPSPGTPSATPASPPASATPSQR 33 0 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 1 VESGDPSLHPPPSPGTPSAT(0.084)PAS(0.915)PPASATPSQR 220.94 2.97E-36 500060000 113090 176740 175560 203560 167820 114040 128610 91258 89207 TRUE FALSE 106011.8988 189826.0135 179724.3661 208783.6942 154640.0942 146961.4967 109326.1245 102651.7622 74317.7754 1.426467601 2.554247789 2.418322738 2.809337243 2.080795521 1.977474378 1.47106293 1.381254506 1 16.1814197 1.735690819 1.261727666 1.116618101 2.360625136 0.606334777 0.365225248 0.264671896 0.794495308 0.283797312 0.110229648 54.41151503 -1.735690819 1.244007036 VESLESLYFT(ph)PIPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VESLESLYFTPIPAR 15 0 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 VESLESLYFT(1)PIPAR 127.75 0.00085211 8411800 15418 19227 16498 13350 15691 8402.5 22502 15922 27024 TRUE FALSE 14453.0149 20650.58709 16889.34035 13692.5836 14458.69215 10828.16535 19128.034 17909.89675 22513.51982 0.64197047 0.917252711 0.750186576 0.608193819 0.642222641 0.480962792 0.849624321 0.7955174 1 14.45850401 0.9660541 1.67481342 0.993639201 0.711138814 0.390404077 0.121456101 0.498354769 2.880617809 0.12188489 0.035155266 9.248133711 -0.9660541 -0.282500387 VESTDVSDLLHQYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VESTDVSDLLHQYR 14 0 Q5JNW7;A0A140T998;X5D2R7;P28062-2;P28062 Q5JNW7 PSMB8;PSM8 Proteasome subunit beta type;Proteasome subunit beta type-8 0 218.5 5.36E-12 109160000 171210 192030 185900 166980 193960 147100 194580 180370 199930 FALSE TRUE 160494.2717 206248.101 190309.6358 171264.9895 178727.164 189565.382 165404.5354 202889.5915 166560.3914 0.963580059 1.238278196 1.142586387 1.028245599 1.073047214 1.138118015 0.993060439 1.218114282 1 17.34568584 3.304721777 10.79253478 1.073415448 1.14538693 0.004136165 0.094692819 1.024170648 161.7473569 0.023947741 0.03242325 2017.073749 -3.304721777 0.071971482 VETGILRPGMVVTFAPVNITTEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VETGILRPGMVVTFAPVNITTEVK 24 1 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 148.87 1.40E-07 127530000 157730 135490 142370 130760 165450 114270 171680 151020 154130 FALSE TRUE 147857.9609 145521.8206 145747.0836 134115.523 152456.2244 147257.894 145938.1778 169875.1794 128404.7073 1.151499536 1.133305964 1.135060285 1.044475127 1.187310244 1.146826289 1.136548503 1.322966915 1 16.97033857 VETGVLKPGMVVTFAPVNVTTEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VETGVLKPGMVVTFAPVNVTTEVK 24 1 P68104;A0A087WVQ9;Q5VTE0 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3 0 ; 253.08 8.19E-44 628370000 1937790 1293280 1491320 1432430 1616870 1113360 1951380 1454910 2079130 FALSE TRUE 1816507.183 1389035.797 1526694.815 1469188.579 1489887.552 1434768.958 1658788.685 1636558.716 1732109.771 1.04872521 0.801932891 0.881407657 0.848207546 0.860157697 0.828336045 0.957669492 0.944835451 1 20.72409893 1.64061335 6.007562301 0.965638067 0.86807484 0.27315079 0.067405857 0.157373436 11.91677601 0.032295418 0.015778742 43.71327552 -1.64061335 -0.097563227 VETISLGEHPCDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VETISLGEHPCDR 13 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C103 Q9H8V3-2 ECT2 Protein ECT2 0 ; 170.79 2.62E-05 305460000 182177 282170 237370 227060 266090 184186 227860 204060 198635 FALSE TRUE 170774.8668 303062.1604 243000.5285 232886.744 245192.3648 237357.5082 193694.5083 229537.3402 165481.5353 1.031987445 1.831395629 1.468444972 1.407327673 1.481690174 1.434344368 1.170490158 1.387087326 1 17.33631072 1.255084742 0.54076698 1.01028635 1.52966066 0.257746705 0.209131074 0.862405089 0.648189948 0.203753721 0.105056137 17.99221954 -1.255084742 0.51937431 VEVGKDQEFTVDTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VEVGKDQEFTVDTR 14 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ;;;; 169.94 2.97E-06 6599710000 13652190 11678860 12215400 12414960 14317690 8988970 15175640 11609220 14943750 FALSE TRUE 12797723.8 12543574.95 12505155.06 12733548.89 13193236.38 11583939.72 12900193.67 13058656.67 12449541.58 1.027967473 1.007553159 1.00446711 1.022812672 1.059736721 0.930471185 1.036198287 1.048926708 1 23.56958928 1.562321404 25 1.031947704 1.008693878 0.06367455 0.034387714 1.22438497 660.1187335 0.016848505 0.00780003 36.50239867 -1.562321404 -0.023253826 VEVNNLNNLNNHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEVNNLNNLNNHDR 14 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 0 143.97 8.98E-06 372650000 179730 158640 152190 163290 159240 162920 214080 175680 134030 FALSE TRUE 168481.0201 170385.8707 155800.0187 167480.2978 146733.9327 209952.3592 181980.6914 197614.0347 111659.5271 1.508881727 1.525941181 1.395313259 1.499919462 1.314119238 1.8802906 1.629782036 1.769791076 1 16.76874683 2.262871221 24.99999698 1.632442559 1.454373116 0.031744929 0.238888873 450.662224 463440.5249 0.072085134 0.060283052 183.1771176 -2.262871221 -0.178069443 VEVRPMMYVALTYDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEVRPMMYVALTYDHR 16 1 P36957-2;P36957 P36957-2 DLST "Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial" 0 105.6 0.00076363 142120000 72906 90235 73338 74944 126270 66946 75808 90859 129310 FALSE TRUE 68342.9436 96916.09329 75077.61199 76867.18992 116353.2635 86272.22342 64441.29417 102202.9462 107727.3256 0.63440676 0.899642618 0.696922638 0.713534746 1.080071958 0.800838812 0.598188935 0.948718866 1 16.71702472 1.021461232 24.17117907 1.000000115 0.779399087 0.270370955 0.137567242 170.8243492 192393.6349 0.127897452 0.031974363 10.50657663 -1.021461232 -0.220601028 VEVTEFEDIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VEVTEFEDIK 10 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ; 180.8 4.55E-06 811680000 1979640 1446560 1687270 1698210 1754160 1241150 2033120 1519680 1988340 FALSE TRUE 1855737.866 1553664.808 1727292.841 1741788.944 1616395.35 1599449.857 1728272.531 1709415.393 1656473.209 1.120294525 0.937935367 1.042753262 1.051504446 0.975805308 0.965575446 1.043344692 1.031960785 1 20.65968344 2.74031062 24.98614597 1.005932424 1.022196035 0.067531715 0.050170191 873.1836085 12467337.71 0.015339561 0.015551506 549.9340617 -2.74031062 0.016263611 VEWSAFLEAADNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VEWSAFLEAADNLR 14 0 F5GYQ2;Q9UI30;F5GX77 F5GYQ2 TRMT112 Multifunctional methyltransferase subunit TRM112-like protein 0 ; 160.52 1.10E-05 97987000 116598 130286 110079 114740 142228 108104 118339 109980 125814 FALSE TRUE 109300.3393 139932.511 112690.1259 117684.4227 131057.9866 139311.8699 100595.1656 123711.2451 104814.8306 1.0427946 1.335044957 1.075135314 1.122784075 1.250376362 1.329123647 0.959741718 1.180283786 1 16.67748334 1.728151454 24.99999734 1.05239734 1.194979992 0.276316531 0.111106741 1.067982596 2552.638708 0.048053219 0.026647963 53.47508141 -1.728151454 0.142582651 VEYFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VEYFLK 6 0 Q13185;S4R2Y4;C9JMM0;B8ZZ43 Q13185 CBX3 Chromobox protein homolog 3 0 118.06 0.05163 485120000 1539100 1587800 1322700 1307600 1795500 871240 1559400 1575800 1991800 FALSE TRUE 1442770.478 1705362.364 1354075.069 1341155.23 1654488.673 1122752.845 1325582.447 1772542.099 1659355.712 0.869476308 1.027725611 0.816024592 0.808238535 0.99706691 0.676619748 0.798853698 1.068211044 1 20.66219176 1.233033231 24.99979598 1.0341056 0.860368198 0.34948424 0.100739373 174.4830425 789127.1875 0.089195182 0.024797422 17.10146165 -1.233033231 -0.173737401 VEYHAGGSTQNSIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VEYHAGGSTQNSIK 14 0 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZH83 P55263-3 ADK Adenosine kinase 0 ; 209.53 6.51E-09 551860000 479180 437200 432350 423580 519180 345360 546760 445230 511780 FALSE TRUE 449188.9792 469570.7429 442605.5462 434449.7799 478405.6971 445059.8255 464778.4139 500817.9456 426360.6118 1.053542393 1.101346442 1.038101396 1.018972597 1.12206823 1.043857742 1.090106358 1.174634644 1 18.70171464 2.732008409 24.99632252 1.087947411 1.058568444 0.093864318 0.049670206 1356.879044 5176413.727 0.014826469 0.01424788 539.5210687 -2.732008409 -0.029378966 VEYSEEELKTHISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VEYSEEELKTHISK 14 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;; 273.61 3.10E-33 1298850000 3602050 4468060 4422270 4774000 5666510 3160320 6121110 4125400 8024900 FALSE TRUE 3376604.12 4798879.811 4527168.333 4896508.922 5221485.162 4072653.08 5203306.381 4640465.271 6685492.347 0.505064391 0.717804997 0.677163042 0.732408126 0.781017297 0.609177734 0.778298158 0.694109727 1 22.67260238 -5 0.17188695 2.191812958 0.623701773 0.651837488 0.075317417 80.91964471 0.7670637 32.92729466 0.239718382 1.00E-05 5 -1.568111184 VFDDES(ph)DEKEDEEYADEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VFDDESDEKEDEEYADEK 18 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 VFDDES(1)DEKEDEEYADEK;VFDDES(1)DEKEDEEYADEK;VFDDES(1)DEKEDEEYADEK;VFDDES(1)DEKEDEEYADEK;VFDDES(1)DEKEDEEYADEK 290.56 2.23E-49 2753440000 7722540 2224580 3571580 3279820 3284980 2637670 4481180 2654620 2885700 TRUE FALSE 7239200.007 2389290.218 3656299.564 3363985.734 3026990.922 3399122.51 3809268.66 2986055.151 2404058.028 3.011241793 0.993857133 1.520886569 1.399294732 1.259117245 1.413910343 1.584516104 1.242089465 1 21.19704029 4.745847225 24.97742984 1.339175186 3.011242588 0.880054187 0.197914234 279.0618456 956559.7764 0.04538001 0.468636262 55698.97779 -4.745847225 1.672067402 VFDDES(ph)DEKEDEEYADEKGLEAADKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFDDESDEKEDEEYADEKGLEAADKK 26 3 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 VFDDES(0.999)DEKEDEEY(0.001)ADEKGLEAADKK;VFDDES(1)DEKEDEEYADEKGLEAADKK 195.2 2.68E-19 176434000 531170 103488 190623 205749 222195 117518 272147 118345 305590 TRUE FALSE 497925.0179 111150.3592 195144.6676 211028.8677 204744.701 151443.5389 231341.0838 133120.6338 254585.0548 1.955829725 0.436594203 0.766520516 0.828913024 0.804229067 0.594864215 0.908698604 0.522892571 1 17.9577882 4.74676459 24.97507969 0.722296218 1.955830341 0.831350736 0.173053513 379.6674518 1155782.502 0.038434183 0.434609453 55816.75572 -4.74676459 1.233534124 VFDEHKEEDLFELSHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VFDEHKEEDLFELSHR 16 1 Q9NSV4-1;Q9NSV4-7;Q9NSV4-6;Q9NSV4-5;Q9NSV4-4;Q9NSV4;Q9NSV4-2 Q9NSV4-1 DIAPH3 Protein diaphanous homolog 3 0 ;; 177.67 1.88E-09 121894000 299235 220447 266922 270290 280994 199965 348138 247687 277041 FALSE TRUE 280506.4155 236769.1253 273253.5159 277226.099 258925.8647 257691.6493 295937.9389 278611.2672 230801.0673 1.215360131 1.025858017 1.183935235 1.201147387 1.121857311 1.116509782 1.282220842 1.207148955 1 17.81629037 3.731252823 23.88099434 1.174683848 1.106420217 0.002323263 0.087210844 227.4356561 1314581.952 0.020998468 0.036179293 5385.83225 -3.731252823 -0.06826363 VFDFTFSPEEMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFDFTFSPEEMK 12 0 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 164.65 0.00013195 53442000 138970 124700 122300 118530 160100 104830 127530 118710 169490 FALSE TRUE 130272.1158 133932.9178 125201.0138 121571.6805 147526.3918 135092.7192 108408.0604 133531.2048 141201.0241 0.922600361 0.948526533 0.886686301 0.860982994 1.044796897 0.956740365 0.767756899 0.945681561 1 17.10739103 VFDGIPPPYDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFDGIPPPYDKK 12 1 P40429;M0QYS1;Q8J015;Q6NVV1 P40429 RPL13A;RPL13a;RPL13AP3 60S ribosomal protein L13a;Putative 60S ribosomal protein L13a protein RPL13AP3 0 ; 134.98 0.0002179 849070000 1538270 1194970 1395630 1319230 1436210 971620 1773690 1269800 1968800 FALSE TRUE 1441992.427 1283446.822 1428735.003 1353083.675 1323415.86 1252110.921 1507741.651 1428337.325 1640194.561 0.879159376 0.782496694 0.87107654 0.824953153 0.806865168 0.763391704 0.919245611 0.870834082 1 20.64543553 0.97037074 1.105259451 0.996031154 0.824829583 0.59817969 0.043843648 0.355912275 0.901780858 0.038403562 0.012288292 9.340513232 -0.97037074 -0.171201571 VFDKDGNGYIS(ph)AAELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFDKDGNGYISAAELR 16 1 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2 P0DP25 CALM2;CALM1 1 VFDKDGNGYIS(1)AAELR 116.35 0.00026333 139450000 106920 95758 91877 100420 108000 71203 136730 94460 116750 TRUE FALSE 100228.0681 102848.022 94056.36583 102996.9472 99518.11565 91758.15022 116228.6058 106253.5389 97263.67077 1.03047795 1.057414563 0.967024636 1.058945713 1.023178694 0.943395921 1.194984776 1.092427811 1 16.56961342 1.742337717 25 1.112644252 1.015259265 0.288441054 0.059018098 0.649926012 4323.579742 0.024589285 0.013635907 55.25069141 -1.742337717 -0.097384987 VFDKDGNGYISAAELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VFDKDGNGYISAAELR 16 1 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2 P0DP25 CALM2;CALM1 0 ;;;;; 259.22 8.91E-27 22332140000 23250000 20569600 20238700 18233140 21094490 11590000 24353800 24588800 27922900 FALSE TRUE 21794824 22092594.59 20718771.52 18701033.24 19437813.85 14935844.85 20702173.78 27658765.81 23262387.6 0.936912598 0.949713115 0.890655417 0.803917189 0.835589802 0.64205984 0.889941915 1.188990841 1 24.47149584 1.334703537 6.870831138 1.09161084 0.851498927 0.530645906 0.096155722 0.167673475 9.832381982 0.067265012 0.024276816 21.61242688 -1.334703537 -0.240111913 VFDKEGNGTVMGAELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VFDKEGNGTVMGAELR 16 1 P08590;P05976-2;P05976 P08590 MYL3;MYL1 "Myosin light chain 3;Myosin light chain 1/3, skeletal muscle isoform" 0 ;;; 237.3 8.53E-20 1717620000 1566590 1932640 1673690 1760900 2225420 1265870 1914520 1660680 2558080 FALSE TRUE 1468539.928 2075734.677 1713390.717 1806087.675 2050644.49 1631306.119 1627455.5 1868019.554 2131119.922 0.689093051 0.974011202 0.803986064 0.847482892 0.962237962 0.765468945 0.763662093 0.876543612 1 21.02318035 VFDLQFSTDS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VFDLQFSTDSPR 12 0 C9J470;E9PHA2;Q15003;C9JZP1 C9J470 NCAPH Condensin complex subunit 2 1 VFDLQFS(0.001)T(0.001)DS(0.998)PR;VFDLQFST(0.004)DS(0.996)PR;VFDLQFST(0.021)DS(0.979)PR;VFDLQFSTDS(1)PR;VFDLQFST(0.004)DS(0.996)PR 229.31 8.91E-12 238781000 283380 282316 323591 313533 302157 297820 337850 265004 394465 TRUE FALSE 265643.7516 303218.9704 331266.7313 321578.7876 278426.8081 383795.7993 287192.5289 298090.3327 328626.2432 0.808346129 0.922686416 1.008034928 0.9785548 0.847244594 1.167879338 0.873918425 0.907080122 1 18.32608817 4.713886197 2.236666741 0.96705873 0.772808054 0.248667841 0.088116891 0.809528521 4.940613383 0.020118179 0.305219281 51747.12156 -4.713886197 -0.194250677 VFDMLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VFDMLNR 7 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;J3QR64;J3QLN6;J3KS25;J3QKZ9;Q14240;Q14240-2;E7EQG2 P60842;Q14240 EIF4A1;EIF4A2 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ;;; 153.15 0.0041078 908602000 2066600 3028040 2066210 1890050 3157380 1440526 2004250 2790090 2427430 FALSE TRUE 1937255.195 3252239.232 2115221.477 1938551.883 2909412.111 1856382.471 1703731.319 3138438.878 2022276.251 0.957957744 1.608207202 1.045960697 0.958598946 1.438681837 0.917966806 0.842481989 1.551933805 1 20.94754866 3.732868518 23.71316862 1.082588774 1.328795471 0.05497566 0.273041763 241.1858165 995112.8606 0.065692737 0.114271446 5405.906354 -3.732868518 0.246206698 VFDMLNRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFDMLNRR 8 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;J3QR64;J3QLN6;J3KS25;J3QKZ9;Q14240;Q14240-2;E7EQG2 P60842;Q14240 EIF4A1;EIF4A2 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ; 138.54 0.0011236 1545090000 954370 3447900 946640 1032490 3720100 675530 931700 2686100 3353900 FALSE TRUE 894637.6853 3703186.104 969094.7478 1058985.441 3427938.352 870544.5447 792000.2345 3021465.498 2794112.423 0.320186718 1.325353294 0.346834558 0.379006024 1.226843388 0.311563893 0.283453245 1.081368621 1 21.41395864 1.205824511 24.99307549 1.040685479 0.627958094 0.185927873 0.380475441 408.8734578 312153.928 0.359014723 0.089779404 16.06292053 -1.205824511 -0.412727385 VFDPQNDKPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFDPQNDKPSK 11 1 O15145 O15145 ARPC3 Actin-related protein 2/3 complex subunit 3 0 71.076 0.045618 470870000 1629000 1110500 1313900 1268100 1369600 999390 1607200 1212900 1612700 FALSE TRUE 1527043.798 1192722.575 1345066.328 1300641.593 1262037.141 1287897.669 1366215.281 1364333.235 1343529.952 1.136590811 0.887752874 1.001143538 0.968077854 0.939344254 0.958592451 1.01688487 1.015484049 1 20.35759705 1.706758298 7.404230101 1.011783155 0.971138179 0.025340177 0.063770278 0.317140531 39.62357538 0.028533173 0.014917551 50.90474867 -1.706758298 -0.040644976 VFEEDALSWEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFEEDALSWEDK 12 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 135.66 0.00028781 21901000 66973 57242 72733 62546 63298 56735 70398 54108 50424 FALSE TRUE 62781.27948 61480.25724 74458.26111 64151.03625 58326.83041 73113.47348 59842.47344 60863.50291 42007.90865 1.49451095 1.463540062 1.77248198 1.527118067 1.388472606 1.740469255 1.424552551 1.4488582 1 15.35837334 0.558755261 0.986833201 0.999025215 1.568732335 0.662156249 0.12230888 0.855114185 1.267504341 0.11310219 0.036126924 3.620389203 -0.558755261 0.56970712 VFEEDALSWEDKLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VFEEDALSWEDKLNR 15 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 266.15 2.56E-25 619658000 799254 857320 867904 976875 1027111 728452 1145780 886483 1047935 FALSE TRUE 749230.1188 920796.8648 888491.0927 1001943.266 946445.8452 938744.267 973980.9259 997162.3539 873027.8786 0.858197243 1.05471645 1.017712165 1.147664686 1.084095787 1.075274101 1.115635537 1.142188444 1 19.7356682 5.660859571 0.906974602 1.091748774 1.50E-11 0.659417537 0.049316551 5.623839271 1.042781827 0.01427428 9.020464467 457993.771 -5.660859571 -1.091748774 VFEHIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFEHIGK 7 0 P04040 P04040 CAT Catalase 0 68.915 0.061157 308770000 280470 300070 275790 308560 401600 229110 340580 319120 262470 FALSE TRUE 262915.8834 322287.495 282331.869 316478.172 370059.956 295250.3377 289513.1908 358962.8345 218662.0614 1.202384546 1.473906781 1.291179033 1.447339195 1.692383003 1.35025864 1.324021135 1.641632902 1 17.7383434 -1.105732958 4.395748965 0.999956299 1.417770449 0.440925635 0.151039106 6.70E-05 1.36E-05 0.13519356 0.031861701 0.078391151 1.105732958 0.417814149 VFELMTSLHTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFELMTSLHTK 11 0 Q06323;Q06323-3;Q06323-2;H0YLU2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ; 204.69 3.24E-08 1175740000 1068570 1707910 1379140 1352130 1918010 1024880 1675730 1671070 1713740 FALSE TRUE 1001690.111 1834365.433 1411853.852 1386827.945 1767377.231 1320746.218 1424469.843 1879706.768 1427705.723 0.701608248 1.284834405 0.988896962 0.971368205 1.237914231 0.925082948 0.997733511 1.316592585 1 20.44526721 4.759704265 24.38142041 1.08220202 0.701607714 0.426587424 0.141348115 3858.217879 4448934.699 0.031714282 1.416800697 57504.82226 -4.759704265 -0.380594306 VFELQTSACQILHGHTDIVLALDVFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VFELQTSACQILHGHTDIVLALDVFR 26 0 Q12788;J3KNP2;A0A087WYP7 Q12788 TBL3 Transducin beta-like protein 3 0 ;; 210.22 8.90E-26 40706000 20334.4 26041.5 21497.5 20860.7 27498 19603 23573.2 26577.2 14737.3 FALSE TRUE 19061.7062 27969.63976 22007.43085 21396.02088 25338.418 25262.06787 20038.6175 29895.42192 12277.54942 1.552566033 2.278112577 1.79249377 1.742694746 2.063800937 2.057582259 1.632134949 2.434966531 1 13.58373501 -0.985193755 5.827954331 0.999998855 1.940224469 0.533117691 0.277693404 3.67E-06 6.39E-07 0.238805553 0.05628694 0.103468045 0.985193755 0.940225615 VFEVSLADLQNDEVAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFEVSLADLQNDEVAFR 17 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;D6RB09;D6RAS7;D6RI02;D6RED7;D6RGE0 P61247 RPS3A 40S ribosomal protein S3a 0 95.401 0.0059962 88765000 10362 10941 12238 14694 16028 12381 15785 12347 16542 FALSE TRUE 9713.460917 11751.08302 12528.29114 15071.07292 14769.22553 15955.19371 13418.18579 13888.55013 13781.03333 0.704842713 0.852699702 0.909096643 1.093609786 1.071706684 1.157764685 0.973670513 1.007801795 1 13.75039645 3.976403379 1.041197886 1.051680137 0.724598475 0.751380061 0.064544897 0.353048671 0.633039176 0.021650832 0.097485172 9471.164489 -3.976403379 -0.327081663 VFEVSLADLQNDEVAFRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFEVSLADLQNDEVAFRK 18 1 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;D6RB09;D6RAS7;D6RI02;D6RED7;D6RGE0 P61247 RPS3A 40S ribosomal protein S3a 0 310.49 6.17E-61 37567000 44446 52592 46529 50320 62086 39074 62834 41354 80249 FALSE TRUE 41664.2042 56485.9664 47632.68985 51611.29639 57210.016 50354.02949 53412.62502 46517.13793 66854.92347 0.623203229 0.844903613 0.712478414 0.771989462 0.855733774 0.753183563 0.798933306 0.695792255 1 16.02874619 -1.565918753 3.114954945 1.010351032 0.766545299 0.54145011 0.069783744 16536629.5 21134643.96 1446079.257 0.014815949 0.027169475 1.565918753 -0.243805733 VFFRPGK ddPTM_SK-BR-3_Pertuzumab_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 83.843 0.020048 368110000 765640 806520 730530 729100 949640 622410 881770 823390 1007200 FALSE TRUE 717719.9591 866235.58 747858.5166 747809.9404 875059.1051 802089.663 749556.7745 926192.054 839091.8132 0.855353309 1.032348983 0.891271378 0.891213486 1.042864549 0.955902144 0.893295302 1.103802992 1 19.67846915 1.239364056 24.99992969 1.0519015 0.942671335 0.341036128 0.065824401 23.48117012 730852.7292 0.046935881 0.01483668 17.35258004 -1.239364056 -0.109230165 VFGGTVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFGGTVHK 8 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ; 77.282 0.033615 586430000 1488330 1638560 1443960 1446050 1610750 1138520 1448380 1452350 1392100 FALSE TRUE 1395178.082 1759880.687 1478211.413 1483158.091 1484248.192 1467192.242 1231208.865 1633679.095 1159749.517 1.202999494 1.517466196 1.274595412 1.278860711 1.279800656 1.265094075 1.061616192 1.408648222 1 20.14538181 0.316557369 0.146685354 0.787372486 1.502281041 0.33943234 0.120942538 11.69333076 0.730750033 2.221807247 1.03495716 2.07279985 -0.316557369 0.714908555 VFGPGVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFGPGVER 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 98.503 0.017393 191310000 221880 291150 270090 255350 351420 193640 316200 276730 495600 FALSE TRUE 207992.9269 312707.0489 276496.6623 261902.7133 323820.8908 249540.7245 268788.7455 311280.3497 412881.1583 0.503759793 0.757377862 0.669676145 0.634329535 0.784295636 0.604388744 0.651007536 0.75392239 1 18.65536706 0.86783943 3.382494661 0.999879142 0.669244782 0.656958715 0.077653957 0.347503349 7.500129018 0.067382297 0.017448749 7.376314584 -0.86783943 -0.33063436 VFGS(ph)LER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VFGSLER 7 0 Q14680-3;Q14680-4;Q14680-5;Q14680-2;Q14680-8;Q14680-6;Q14680;Q14680-7 Q14680-3 MELK Maternal embryonic leucine zipper kinase 1 VFGS(1)LER;VFGS(1)LER;VFGS(1)LER;VFGS(1)LER 146.27 0.0023392 2044250000 1022450 1107780 1094570 1125560 1186280 967950 1361330 1062840 1169030 TRUE FALSE 958456.6796 1189801.184 1120533.717 1154443.775 1093114.354 1247381.452 1157211.204 1195537.914 973911.3408 0.984131347 1.221672994 1.150550025 1.185368449 1.122396165 1.280795694 1.188210011 1.227563397 1 19.89343092 4.745452332 24.77435802 1.18306322 0.984131243 0.37229969 0.07550141 658.2935036 2366366.626 0.015471777 0.15336941 55648.35519 -4.745452332 -0.198931977 VFGWVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFGWVHR 7 0 O43776;K7EIU7;O43776-2;K7EPK2;K7EMQ6;K7EQ35 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 133.99 0.0032182 1178230000 1055600 1607400 1181360 1094680 1567680 871130 1171200 1527020 1173250 FALSE TRUE 989531.8803 1726413.568 1209382.417 1122771.342 1444560.737 1122611.089 995589.4329 1717671.808 977426.9955 1.012384439 1.766283903 1.237312273 1.148700974 1.477921874 1.148537021 1.018581886 1.757340258 1 19.89862943 3.720874178 23.9577184 1.240810204 1.46076833 0.021314801 0.287092472 324.311469 1243751.249 0.069193384 0.110316787 5258.648929 -3.720874178 0.219958126 VFHGADSDIEWLQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFHGADSDIEWLQK 14 0 Q01780;Q01780-2 Q01780 EXOSC10 Exosome component 10 0 133.71 4.30E-05 122040000 213010 194900 188890 209770 217250 149880 239860 175550 235530 FALSE TRUE 199678.0843 209330.5988 193370.56 215153.0533 200188.0613 193147.9229 203895.2198 197467.8039 196218.5214 1.017631174 1.066823852 0.985485767 1.09649717 1.0202302 0.984351128 1.03912321 1.006366792 1 17.5821017 2.49011624 24.97007094 1.011505516 1.038648504 0.198690764 0.031740623 1175.557134 2258859.747 0.009906215 0.008925088 309.112267 -2.49011624 0.027142988 VFHGNESLWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VFHGNESLWK 10 0 Q13268;H0YJG9 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;;; 141.1 3.81E-05 14317680000 7314900 9592730 5568792 5083972 12257650 4080046 5047712 9664440 11489780 FALSE TRUE 6857073.466 10302985.71 5700886.376 5214435.329 11294983.61 5257889.046 4290854.446 10871066.61 9572061.491 0.71636329 1.076360168 0.595575612 0.544755728 1.179994887 0.549295369 0.448268584 1.135707979 1 23.19039823 3.971108223 24.09570466 0.730775097 0.911312309 0.006843071 0.272666656 409.6225352 1641475.232 0.065853333 0.12290738 9356.388002 -3.971108223 0.180537212 VFHHNAWDNVEWSEEQAAAAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFHHNAWDNVEWSEEQAAAAER 22 0 Q6P1Q9;F8WAS9;Q96IZ6 Q6P1Q9 METTL2B;METTL2A Methyltransferase-like protein 2B;Methyltransferase-like protein 2A 0 93.572 0.0010992 128430000 52293 57411 57753 53579 60762 51769 68307 49549 61399 FALSE TRUE 49020.07448 61661.77018 59122.92843 54953.92785 55989.99762 66713.8699 58064.99948 55735.30172 51151.11025 0.958338426 1.205482537 1.15584839 1.074344771 1.09459985 1.304250672 1.135165966 1.089620566 1 15.64247793 0.956711513 3.083686333 1.000664189 1.146340182 0.169720049 0.089343627 0.405843615 9.564861578 0.079264182 0.020776738 9.051311529 -0.956711513 0.145675993 VFHTEDDQYCWQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFHTEDDQYCWQHR 14 0 Q8IWR0;Q8IWR0-2 Q8IWR0 ZC3H7A Zinc finger CCCH domain-containing protein 7A 0 ; 230.96 4.16E-13 460770000 211760 549440 275940 266860 620000 331500 257580 425560 559850 FALSE TRUE 198506.3196 590121.1093 282485.4271 273708.0794 571307.701 427198.6685 218958.2703 478692.1028 466407.4182 0.425607123 1.26524812 0.60566238 0.586843323 1.224911266 0.91593455 0.469457092 1.026338956 1 18.83123121 VFIDQNLS(ph)PGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VFIDQNLSPGK 11 0 F5H452;Q5JSB6;Q5JSB5;Q14186 F5H452 TFDP1 Transcription factor Dp-1 1 VFIDQNLS(1)PGK;VFIDQNLS(1)PGK;VFIDQNLS(1)PGK 175.29 1.05E-05 233520000 1299990 783420 1012850 891250 956250 784290 1254640 897810 969870 TRUE FALSE 1218625.946 841425.2319 1036875.28 914120.9839 881149.9823 1010701.791 1066518.38 1009903.555 807992.4314 1.508214556 1.041377616 1.283273506 1.131348449 1.090542372 1.25088027 1.319960854 1.249892345 1 19.62398225 4.756629103 24.11024088 1.189191632 1.508214998 0.485927299 0.10758048 2241.545791 2990996 0.025144676 0.786773517 57099.07903 -4.756629103 0.319023366 VFIDQNLS(ph)PGKGVVSLVAVHPSTVNPLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFIDQNLSPGKGVVSLVAVHPSTVNPLGK 29 1 F5H452;Q5JSB6;Q5JSB5;Q14186 F5H452 TFDP1 Transcription factor Dp-1 1 VFIDQNLS(1)PGKGVVSLVAVHPSTVNPLGK;VFIDQNLS(1)PGKGVVSLVAVHPSTVNPLGK 247.6 4.54E-46 430240000 589700 738900 818060 849460 1055060 656820 1166660 847860 1273440 TRUE FALSE 552791.7296 793608.9248 837464.7695 871258.5817 972199.8435 846433.2714 991730.1637 953717.1874 1060894.637 0.521061857 0.748056307 0.789394856 0.821248926 0.916396228 0.797848572 0.934805521 0.898974464 1 20.01684995 5.70115503 0.341775252 0.939213621 2.69E-32 0.830765849 0.054303753 5.015955353 0.282917038 0.045410219 2.210476401 502521.9426 -5.70115503 -0.939213621 VFIEDVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFIEDVSR 8 0 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ; 117.18 0.0049536 228210000 319810 481240 301630 315200 517730 220619 306000 439390 412430 FALSE TRUE 299793.663 516871.5103 308784.806 323288.5656 477069.5742 284308.1238 260118.1408 494248.8087 343592.7686 0.872526113 1.504314286 0.898694135 0.940906198 1.38847385 0.827456658 0.757053595 1.438472674 1 18.39034015 3.82614241 7.243130964 1.008655754 1.227501501 0.041368551 0.267638959 0.510162543 32.43772665 0.064793418 0.117442734 6701.043088 -3.82614241 0.218845748 VFIEY(ph)TMDVFFRQT(ph)WTDERLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFIEYTMDVFFRQTWTDERLK 21 2 H0YBS7 H0YBS7 GABRA6 2 VFIEY(0.568)T(0.421)MDVFFRQT(0.512)WT(0.499)DERLK 40.669 0.090796 8493200 5146.4 13518 9360.8 9662.3 12028 7814.7 6554.5 11113 13358 TRUE FALSE 4824.296011 14518.88679 9582.842596 9910.250976 11083.3694 10070.67703 5571.713574 12500.48251 11128.4635 0.433509622 1.3046623 0.861111023 0.890531831 0.995947859 0.904947662 0.500672314 1.123289168 1 13.44196679 1.982604632 24.64139271 0.790082241 0.947751496 0 0.267453839 1721.286448 2438284.664 0.100262839 0.066322553 96.07372548 -1.982604632 0.157669254 VFIGEFAYTYAAMYDKGPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFIGEFAYTYAAMYDKGPFR 20 1 P15559-2;P15559;H3BNV2 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 168.09 1.16E-11 13484000 25039 35513 22088 22481 33295 20555 26335 35363 20212 FALSE TRUE 23471.85369 38142.41947 22611.93779 23057.90052 30680.14501 26488.89482 22386.31123 39778.14839 16838.48663 1.39394081 2.265192848 1.342872331 1.369357059 1.822025084 1.573116124 1.329472875 2.362335124 1 14.03947486 -1.41707461 3.47893613 0.993751074 1.668718634 0.247160274 0.373558227 67143929.36 81088971.22 4037414.608 0.084238571 0.038275898 1.41707461 0.67496756 VFITDDFHDMMPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VFITDDFHDMMPK 13 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;; 198.32 1.27E-07 2079655000 6251500 5761080 5827080 6047950 6063630 4173422 7204380 5263500 3718643 FALSE TRUE 5860229.774 6187636.358 5965301.089 6203150.636 5587416.959 5378221.182 6124150.101 5920659.561 3097977.46 1.891630862 1.997314841 1.925546963 2.002322714 1.803569274 1.736042709 1.976822033 1.911137069 1 21.56289522 -2.071477988 0.496908761 5.97E-17 1.926690345 0.919281327 0.084255608 21.28722011 1.574703838 24.19776405 0.040337215 0.008482464 2.071477988 1.926690345 VFKEENQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFKEENQK 8 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 80.755 0.022461 405170000 240090 181030 204480 219070 226440 150740 252600 203180 264290 FALSE TRUE 225063.1955 194433.6496 209330.3622 224691.7071 208656.3158 194256.1909 214724.975 228547.4703 220178.2916 1.022186128 0.883073659 0.950731158 1.020498912 0.947669792 0.882267682 0.975232269 1.038010916 1 17.74831271 1.453994192 6.730029911 1.015930105 0.944594972 0.248406859 0.047429626 0.200671554 22.24167945 0.027744416 0.011595427 28.44423069 -1.453994192 -0.071335133 VFLENVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFLENVIR 8 0 P62805 P62805 HIST1H4A Histone H4 0 ; 129.65 0.0025163 161726000 248970 400930 222200 237160 502750 219110 249610 372520 390360 FALSE TRUE 233387.4121 430615.2744 227470.6889 243245.9271 463266.043 282363.5 212183.2978 419029.942 325206.3942 0.717659358 1.324129175 0.69946561 0.747973999 1.424529318 0.868259373 0.652457337 1.288504622 1 18.3109961 VFLKNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFLKNEK 7 1 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 87.616 0.017521 2265100000 3371200 4885800 4114300 4131800 5884000 3533300 4984800 4194100 7284100 FALSE TRUE 3160202.61 5247549.716 4211893.139 4237828.983 5421894.375 4553306.352 4237375.517 4717742.617 6068336.653 0.520769165 0.864742683 0.69407704 0.698351002 0.893472905 0.750338456 0.698276276 0.777435875 1 22.53286969 -5 0.322349163 3.444666869 0.734393525 0.407366616 0.101223743 337.976134 2.978352818 564.3335724 0.081542309 1.00E-05 5 -2.710273344 VFLLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFLLDR 6 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ; 126.68 0.040453 328290000 526300 782170 574100 557190 826660 456220 635700 697430 913220 FALSE TRUE 493359.8225 840082.6806 587717.9231 571488.4387 761737.4582 587923.3079 540382.6865 784505.6707 760797.6824 0.648477031 1.104212986 0.772502252 0.751170057 1.001235251 0.772772212 0.710284349 1.031162014 1 19.53715333 1.211427461 24.96970152 1.015581379 0.840284307 0.250023648 0.136150565 386.2030628 355399.601 0.127214706 0.031837116 16.27149513 -1.211427461 -0.175297072 VFLQGPAPVGT(ph)PSFNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFLQGPAPVGTPSFNR 16 0 Q8IWZ3-6;Q8IWZ3;Q8IWZ3-4;H0Y785;H0Y472;H0Y4P6;H7C0V5 Q8IWZ3-6 ANKHD1;ANKHD1-EIF4EBP3 Ankyrin repeat and KH domain-containing protein 1 1 VFLQGPAPVGT(0.961)PS(0.039)FNR 125.73 0.0015269 0 73295 70867 64319 79392 83661 54205 76104 58845 70965 TRUE FALSE 68707.59679 76114.06642 65844.67705 81429.33313 77090.60253 69853.10356 64692.91171 66191.92778 59120.48305 1.162162304 1.28743986 1.113737129 1.377345531 1.303957589 1.181538106 1.094255466 1.11961074 1 15.85137044 1.800468514 2.562023668 1.071982108 1.24156149 0.515260322 0.078330786 0.237357645 2.986181257 0.045850566 0.021672576 63.1638384 -1.800468514 0.169579382 VFNGSGKPIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFNGSGKPIDR 11 1 P21281;H0YC04 P21281 ATP6V1B2 "V-type proton ATPase subunit B, brain isoform" 0 ; 114.24 0.0011711 679660000 1446790 1457380 1543350 1433730 1589690 1316460 1910320 1442460 1984970 FALSE TRUE 1356237.996 1565285.932 1579958.991 1470521.939 1464842.16 1696500.631 1623885.251 1622554.306 1653665.684 0.820140377 0.946555248 0.955428299 0.889249837 0.885815177 1.025903027 0.981991261 0.981186417 1 20.65723617 2.239959785 24.99999729 0.995369416 0.913034874 0.588926403 0.039708286 31.30108349 559292.7344 0.014404934 0.011448122 173.7639918 -2.239959785 -0.082334542 VFNPYTEFPEFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFNPYTEFPEFSR 13 0 Q9BUP0;H7C0I0 Q9BUP0 EFHD1 EF-hand domain-containing protein D1 0 164.48 8.60E-05 28865000 24885 25143 22949 25928 23344 17953 26789 26028 19225 FALSE TRUE 23327.49227 27004.61388 23493.36112 26593.35638 21510.65641 23135.73966 22772.23815 29277.65309 16016.2233 1.456491448 1.686078757 1.46684775 1.660401199 1.343054227 1.444519049 1.421823217 1.827999806 1 13.96724637 -1.301662681 3.618401256 0.998426053 1.530700498 0.570752529 0.146601629 35774047.77 69208312.59 644275.6489 0.032728262 0.049927212 1.301662681 0.532274446 VFNTTPDDLDLHVIYDVSHNIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VFNTTPDDLDLHVIYDVSHNIAK 23 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;; 296.62 6.18E-62 875140000 1249618 1171644 1332102 1291367 1360561 1089748 1402228 1164139 1560528 FALSE TRUE 1171406.64 1258393.741 1363700.089 1324505.663 1253708.027 1404340.557 1191976.929 1309484.317 1300065.795 0.901036428 0.967946196 1.048946979 1.018798947 0.964341983 1.080207296 0.916858926 1.00724465 1 20.31015321 4.640687564 2.540673792 1.002414783 0.890378715 0.364683139 0.043855085 0.445573741 4.255086908 0.01042779 0.097251969 43720.74606 -4.640687564 -0.112036068 VFPEHIGEDVLRPAMLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFPEHIGEDVLRPAMLAK 18 1 A0A1B0GUA3;Q96EK5 A0A1B0GUA3 KIAA1279 KIF1-binding protein 0 88.427 0.0018499 62142000 160740 152600 153160 134820 162460 125880 170010 153570 101060 FALSE TRUE 150679.5703 163898.6628 156793.0275 138279.7094 149701.0469 162219.5125 144518.5788 172743.5525 84192.43313 1.789704427 1.946714885 1.862317333 1.642424435 1.778081965 1.92677069 1.71652693 2.051770523 1 16.36140296 -1.635624964 3.01301333 0.933135236 1.838111389 0.833678641 0.117810714 34896812.27 35666705.91 18196417.02 0.026692547 0.023140622 1.635624964 0.904976153 VFPEPT(ph)ESGDEGEELGLPLLSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFPEPTESGDEGEELGLPLLSTR 23 0 Q9BUR4;E9PMG4 Q9BUR4 WRAP53 Telomerase Cajal body protein 1 1 VFPEPT(0.565)ES(0.435)GDEGEELGLPLLSTR;VFPEPT(0.535)ES(0.465)GDEGEELGLPLLSTR 114.07 0.0025938 89776000 70175 67944 74222 72019 79291 63401 76840 69700 68691 TRUE FALSE 65782.87202 72974.64446 75982.58089 73867.12947 73063.8047 81703.83947 65318.55535 78402.19843 57226.02834 1.149527128 1.275200229 1.327762612 1.290796017 1.276758266 1.427739122 1.141413396 1.370044378 1 15.80438386 -0.876886634 5.125768466 0.999999689 1.281925233 0.508384313 0.087274273 4.40E-07 9.69E-08 0.075729662 0.017849621 0.1327741 0.876886634 0.281925544 VFPEPTES(ph)GDEGEELGLPLLSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFPEPTESGDEGEELGLPLLSTR 23 0 Q9BUR4;E9PMG4 Q9BUR4 WRAP53 Telomerase Cajal body protein 1 1 VFPEPT(0.149)ES(0.851)GDEGEELGLPLLSTR;VFPEPT(0.159)ES(0.841)GDEGEELGLPLLSTR 120.85 4.62E-05 46652000 42051 43577 45668 39939 44502 37127 50046 41730 43737 TRUE FALSE 39419.10297 46803.48642 46751.26653 40963.90236 41006.99243 47844.96219 42542.0669 46940.08236 36437.01215 1.081842353 1.284503961 1.283070805 1.124238787 1.125421378 1.313086869 1.167550916 1.288252785 1 15.15311704 -1.258713579 4.836934335 0.999943414 1.217910989 0.383153552 0.082372097 4.74E-05 7.27E-06 0.075278573 0.017738731 0.055117108 1.258713579 0.217967576 VFPLS(ph)PASNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VFPLSPASNLR 11 0 A0A2R8YH03;Q5VWN6;J3KPH3 A0A2R8YH03 FAM208B Protein FAM208B 1 VFPLS(0.999)PAS(0.001)NLR;VFPLS(0.998)PAS(0.002)NLR;VFPLS(0.997)PAS(0.003)NLR;VFPLS(0.991)PAS(0.009)NLR 152.23 3.47E-05 180842000 402248 358121 356595 348417 367001 295306 411599 304291 384052 TRUE FALSE 377072.0157 384636.6515 365053.6018 357357.9701 338178.2219 380556.0483 349883.551 342282.4012 319951.2401 1.178529627 1.202172716 1.14096636 1.116913846 1.056967998 1.189418888 1.093552727 1.069795513 1 18.28749253 5.157125533 0.019578834 1.65E-07 2.390786052 0.671285978 0.036725145 1024.198598 2.761471491 142.9392168 197.6676464 143590.4422 -5.157125533 2.390785887 VFQGTDEQLNDLYHNHQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFQGTDEQLNDLYHNHQR 18 0 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7;E7EN38;A0A494BZX5;A0A494C122;A0A494C0Y7;E7ESD9 Q92878-2 RAD50 DNA repair protein RAD50 0 ; 214.54 5.78E-19 850930000 156391 192389 176626 171292 172884 168976 190148 185531 195843 FALSE TRUE 146602.7665 206633.6817 180815.6521 175687.6427 159306.388 217756.6281 161637.0726 208694.9538 163155.5381 0.898546063 1.266482794 1.108240972 1.076810783 0.976408094 1.334656676 0.990693142 1.279116579 1 17.31588843 VFQSLPHENKPLTLSNYQTNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFQSLPHENKPLTLSNYQTNK 21 1 P04080;A0A1W2PQG6 P04080 CSTB Cystatin-B 0 156.05 1.12E-08 268580000 365920 287810 285790 274010 280330 218400 479480 296540 515930 FALSE TRUE 343017.7204 309119.7519 292569.0738 281041.5605 258314.0126 281448.5346 407586.4253 333563.6718 429817.95 0.798053502 0.719187628 0.680681376 0.653861851 0.600984702 0.654808704 0.948276882 0.776058031 1 18.71336621 1.747712625 9.883853608 0.894272009 0.683724317 0.660266191 0.075328093 0.065021131 30.14266073 0.033795993 0.018352096 55.938733 -1.747712625 -0.210547692 VFQSWWDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFQSWWDR 8 0 Q92934 Q92934 BAD Bcl2-associated agonist of cell death 0 ; 93.162 0.026205 504220000 380010 550620 462290 424630 561390 319230 506190 497500 527330 FALSE TRUE 356225.8524 591388.4777 473255.7371 435526.7247 517300.6939 411386.5187 430291.5087 559613.9701 439315.2163 0.810866183 1.346159786 1.077257786 0.991376371 1.177515995 0.936426747 0.979459606 1.273832431 1 18.74489694 3.494636462 21.68519361 1.048969696 1.145111032 0 0.164127394 234.5492224 290384.1292 0.040402522 0.061891714 3123.463696 -3.494636462 0.096141336 VFS(ph)LSEADSHGGHWV ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VFSLSEADSHGGHWV 15 0 H7BXG1 H7BXG1 CLEC16A 1 VFS(0.952)LS(0.048)EADSHGGHWV;VFS(0.976)LS(0.024)EADSHGGHWV;VFS(0.834)LS(0.166)EADSHGGHWV 201.3 4.17E-09 175383000 169853 202297 208713 251820 279008 171358 262783 193483 256960 TRUE FALSE 159222.2039 217275.2804 213663.7709 258282.1275 257095.8371 220826.2728 223381.1287 217639.7785 214071.716 0.743779734 1.014964912 0.998094353 1.206521498 1.200979943 1.031552776 1.043487355 1.016667604 1 17.70773467 5.314727526 1.15125243 1.075184122 2.00E-10 0.636612202 0.076462577 3.562923055 1.559149013 0.022443978 6.368979882 206408.4753 -5.314727526 -1.075184122 VFS(ph)QENVCDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFSQENVCDR 10 0 Q6NV74;C9JFM2;C9JXD6;C9JK00 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 VFS(1)QENVCDR;VFS(1)QENVCDR 120.21 0.00061935 169260000 649410 370560 495510 439080 519810 311170 597370 378350 702560 TRUE FALSE 608764.5873 397996.648 507263.7312 450347.5362 478986.2194 400999.7276 507799.9142 425587.8304 585298.1973 1.04009305 0.679989533 0.866675711 0.769432638 0.818362711 0.685120387 0.867591796 0.727129918 1 19.15881231 -1.203613465 4.985422866 1.000021451 0.799656622 0.245200115 0.105871365 2.15E-05 3.44E-06 0.087444698 0.020608708 0.062572936 1.203613465 -0.200364829 VFSGLVS(ph)TGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFSGLVSTGLK 11 0 P13639 P13639 EEF2 Elongation factor 2 1 VFSGLVS(0.804)T(0.196)GLK 116.51 0.0010271 40821000 137550 119210 132860 126130 129050 91238 149800 108140 140220 TRUE FALSE 128940.991 128036.4324 136011.5019 129366.7093 118914.9336 117576.9295 127338.8807 121641.517 116816.3761 1.103792082 1.096048659 1.164318792 1.10743642 1.017964582 1.006510674 1.090077307 1.041305347 1 16.83388301 2.840109822 5.218605375 1.0392453 1.12340455 0.658290222 0.03079808 0.149144366 6.176066174 0.00972549 0.010339687 692.0059398 -2.840109822 0.08415925 VFSWGFGGYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFSWGFGGYGR 11 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 230.7 3.74E-12 627930000 170717 327310 170284 171841 338350 126618 172147 287810 276970 FALSE TRUE 160032.1277 351544.373 174323.2169 176250.731 311777.3558 163170.5611 146335.1555 323743.712 230741.9177 0.69355464 1.52353927 0.755490024 0.763843574 1.351195132 0.707156128 0.634194068 1.40305548 1 17.81592059 3.827311598 8.04955335 0.908214074 1.162508292 0.026579785 0.326527769 0.582997175 41.72532915 0.078069179 0.141218224 6719.107632 -3.827311598 0.254294219 VFSWLQQEGHLSEEEMAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFSWLQQEGHLSEEEMAR 18 0 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ; 176.69 2.52E-13 105151000 40930 74422 69564 70029 72854 60138 75619 70300 70379 FALSE TRUE 38368.26436 79932.28232 71214.09093 71826.0627 67132.34072 77498.86434 64280.63296 79077.10975 58632.29023 0.654387953 1.363280916 1.214588252 1.225025705 1.144972172 1.321777881 1.096335018 1.348695564 1 15.83940779 4.747283333 24.90764867 1.223760452 0.654387646 0.703289857 0.114154618 541.9687464 1547552.221 0.024123524 0.285915723 55883.4659 -4.747283333 -0.569372806 VFTTQELVQAFTHAPATLEADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFTTQELVQAFTHAPATLEADR 22 0 O95433;O95433-2;G3V438;H0YJ63;H0YJG7 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ; 286.92 3.02E-46 2119580000 2204780 2358300 2357600 2259010 2540600 2036130 2543800 2381700 2415600 FALSE TRUE 2066786.755 2532910.986 2413523.385 2316980.021 2341071.524 2623927.677 2162380.805 2679060.488 2012420.755 1.027015226 1.258638871 1.199313503 1.151339756 1.163311161 1.303866337 1.074517245 1.331262601 1 20.94050054 -1.368301971 3.558711313 0.998924338 1.190510965 0.283625989 0.09418597 0.000701141 0.000124458 0.079507604 0.018636333 0.042825065 1.368301971 0.191586627 VFTTVGSAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFTTVGSAEK 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 96.89 0.012401 0 170720 179700 149650 148530 208170 108480 164300 177560 264070 FALSE TRUE 160034.9399 193005.175 153199.7687 152341.5313 191821.1679 139796.415 139664.7403 199728.7569 219995.011 0.727448042 0.877316145 0.696378377 0.692477209 0.871934173 0.63545266 0.634854125 0.907878574 1 17.74711128 1.049839655 5.732567008 0.999125544 0.738131552 0.558950478 0.083415908 0.129113071 8.835946741 0.083070627 0.020922903 11.21604271 -1.049839655 -0.260993992 VFTTVGSAEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFTTVGSAEKR 11 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 181.4 1.00E-05 3670800000 4468400 4287200 3681800 3615100 5346500 2290600 5509000 3816800 9017600 FALSE TRUE 4188730.82 4604628.749 3769134.035 3707869.586 4926607.457 2951859.035 4682976.593 4293335.882 7512504.304 0.557567843 0.6129286 0.501714725 0.493559729 0.655787638 0.392926102 0.623357592 0.57149197 1 22.84086248 0.230901954 1.23895566 1.000693514 0.546192481 0.782168563 0.074659273 2.266374372 3.244810637 0.066081859 0.019051467 1.701774275 -0.230901954 -0.454501033 VFVHYTGWLLDGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VFVHYTGWLLDGTK 14 0 Q02790;F5H1U3 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ; 277.11 3.99E-33 990240000 1552820 3163700 1681190 1477540 3380200 1208390 2111710 3212500 2228460 FALSE TRUE 1455631.768 3397943.64 1721068.621 1515456.178 3114732.727 1557232.576 1795078.69 3613587.697 1856515.63 0.78406653 1.830280115 0.927042355 0.816290557 1.677730409 0.838793141 0.966907394 1.946435375 1 20.82416603 3.824778308 13.59958367 1.141902298 1.381335019 0.008145167 0.445656937 2.745005912 372.3048046 0.104752599 0.18887107 6680.028389 -3.824778308 0.239432721 VFVHYTGWLLDGTKFDSSLDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFVHYTGWLLDGTKFDSSLDRK 22 2 Q02790;F5H1U3 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 248.76 1.93E-31 26535000 31128 53793 47492 56667 86528 37022 80222 49818 97046 FALSE TRUE 29179.75405 57775.88969 48618.53267 58121.17116 79732.43992 47709.6504 68193.45584 56037.88696 80848.39566 0.360919395 0.714620114 0.601354328 0.718890841 0.986196934 0.590112519 0.84347321 0.693123055 1 16.30293152 5.576275808 0.177297116 0.955701765 3.97E-36 0.472396105 0.138041755 23.46501603 0.558332167 0.342907629 5.210538143 376943.1089 -5.576275808 -0.955701765 VFVLDEADVMIATQGHQDQSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFVLDEADVMIATQGHQDQSIR 22 0 Q9NUU7;I3L0H8;F6QDS0;H3BQK0;Q9UMR2;Q9UMR2-2;Q9UMR2-4;I3L352;Q9UMR2-3;Q9NUU7-2;H3BN59 Q9NUU7 DDX19A;DDX19B ATP-dependent RNA helicase DDX19A;ATP-dependent RNA helicase DDX19B 0 252.4 5.32E-37 18647000 25729 36072 28275 31388 31631 26386 30541 27333 34525 FALSE TRUE 24118.66782 38742.80841 28945.69635 32193.46922 29146.82885 34003.20986 25961.66058 30745.58522 28762.55446 0.838544012 1.346987746 1.006367372 1.119284077 1.013360232 1.182204102 0.902620128 1.068944876 1 14.81190419 2.09386601 0.929934346 0.989807011 1.114456554 0.008330824 0.141972826 1.330006015 2.138648045 0.104135501 0.053558043 124.1269289 -2.09386601 0.124649543 VFYELQHSDKPVGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VFYELQHSDKPVGTK 15 1 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 136.48 1.36E-05 557720000 987420 747060 753260 612770 813790 492980 963370 762630 1004500 FALSE TRUE 925619.1448 802373.0997 771127.6829 628494.7156 749878.2161 635295.3231 818921.612 857846.0343 836842.4607 1.106085301 0.958810215 0.92147294 0.751031102 0.896080507 0.759157611 0.978585158 1.025098599 1 19.67459653 1.527563922 9.005244762 1.00876646 0.900389703 0.196491413 0.099325822 0.192676117 26.21707071 0.05369691 0.024926756 33.69488061 -1.527563922 -0.108376757 VGATAAVYSAAILEYLTAEVLELAGNASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGATAAVYSAAILEYLTAEVLELAGNASK 29 0 Q71UI9;P0C0S5;C9J0D1;A0A494C189;Q71UI9-4;Q71UI9-2 Q71UI9 H2AFV;H2AFZ Histone H2A.V;Histone H2A.Z;Histone H2A 0 256.57 5.69E-58 115560000 218820 180290 202050 202020 251300 158830 257290 164450 232350 FALSE TRUE 205124.4468 193638.8592 206842.7214 207204.1752 231563.9117 204681.6426 218711.7531 184981.9445 193569.284 1.05969523 1.000359433 1.068572023 1.070439333 1.196284384 1.057407655 1.129888733 0.955636869 1 17.56249051 3.644542369 2.766167434 1.082853083 1.027245802 0.023753694 0.067251644 0.569899248 8.569585473 0.017254922 0.030079438 4411.053944 -3.644542369 -0.055607281 VGCYDANDAS(ph)DEEEFDREGDCISLPGALPGPIRPLSEDDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGCYDANDASDEEEFDREGDCISLPGALPGPIRPLSEDDPR 41 2 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 VGCYDANDAS(1)DEEEFDREGDCISLPGALPGPIRPLSEDDPR 91.041 0.00011671 79787000 101100 88607 98149 91443 110260 99225 115750 88130 119660 TRUE FALSE 94772.33147 95167.55448 100477.1406 93789.58219 101600.6244 127869.6467 98394.36207 99133.2245 99687.97297 0.950689724 0.954654324 1.007916378 0.94083147 1.019186381 1.282698834 0.987023401 0.994435151 1 16.60513184 2.474684307 24.99554974 1.075204061 0.970500268 0.237228988 0.085591362 105.1227355 1078209.911 0.028148512 0.023683741 298.32133 -2.474684307 -0.104703794 VGDAIPAVEVFEGEPGNKVNLAELFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGDAIPAVEVFEGEPGNKVNLAELFK 26 1 P30044-2;P30044;P30044-3 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 ; 268.68 1.33E-53 611720000 722510 551380 576130 502520 700170 375150 704570 495830 894850 FALSE TRUE 677289.3888 592204.7489 589796.0757 515415.514 645181.4725 483449.7149 598926.2694 557735.467 745493.754 0.908511151 0.794379223 0.791148246 0.691374691 0.865441822 0.648495997 0.803395422 0.748142374 1 19.50783674 -1.096615836 7.713902325 1.000000024 0.779091618 0.45482562 0.075190759 2.70E-08 3.16E-09 0.064106415 0.015110025 0.080054208 1.096615836 -0.220908406 VGDDVEFEVSSDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGDDVEFEVSSDRR 14 1 O75534-2;O75534;O75534-3;O75534-4;E9PLD4 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ; 115.34 0.0010927 560370000 566440 607210 580580 621270 687160 405320 581780 615780 694270 FALSE TRUE 530987.5315 652168.4602 594351.6318 637212.84 633193.2255 522329.3042 494547.49 692661.4885 578391.8518 0.918041169 1.127554716 1.027593369 1.10169747 1.094747831 0.903071685 0.855038826 1.197564396 1 19.1416877 2.247632636 24.99211627 0.961154113 1.062547522 0.055546472 0.105899459 320.4192912 882709.588 0.03487985 0.028793928 176.8612279 -2.247632636 0.10139341 VGDGDLS(ph)AEEIPENEVSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VGDGDLSAEEIPENEVSLR 19 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 VGDGDLS(1)AEEIPENEVSLR;VGDGDLS(1)AEEIPENEVSLR;VGDGDLS(1)AEEIPENEVSLR;VGDGDLS(1)AEEIPENEVSLR 304.49 3.13E-50 205234000 360969 300736 306723 301732 297248 262914 366600 257738 308634 TRUE FALSE 338376.5946 323002.8064 313998.6144 309474.954 273903.3411 338813.0037 311631.7333 289917.1567 257120.9915 1.316020884 1.256228845 1.221209566 1.203616057 1.065270243 1.317718175 1.212004245 1.127551488 1 17.97208787 -5 0.130679227 0.263169447 1.31138886 0.555485767 0.068054026 115.0503156 0.947382625 22.18682788 0.498491184 1.00E-05 5 1.048219413 VGDGDLS(ph)AEEIPENEVSLRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VGDGDLSAEEIPENEVSLRR 20 1 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 VGDGDLS(1)AEEIPENEVSLRR;VGDGDLS(1)AEEIPENEVSLRR;VGDGDLS(1)AEEIPENEVSLRR 88.504 0.0011446 404690000 246496 220444 265893 215457 256130 213383 313829 225922 345737 TRUE FALSE 231068.2554 236765.9031 272200.1075 220985.9914 236014.583 274983.2081 266773.2549 254128.859 288031.2612 0.802233252 0.822014604 0.945036683 0.767229191 0.819406137 0.954699177 0.926195489 0.882296102 1 18.13586588 -4.999997889 0.044441837 1.6334356 0.532158826 0.463940746 0.055731803 672.4098936 2.223330751 52.78318663 13.9275499 1.00E-05 4.999997889 -1.101276774 VGDPPQPLPEEPMEVQGAERAS(ph)PEPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 153.69 3.33E-08 1525620000 173052 166016 169981 189581 165816 145410 191321 143371 198348 TRUE FALSE 162220.9842 178307.9974 174013.0296 194445.9694 152793.4802 187387.5065 162634.1922 161271.1849 165242.4374 0.981715029 1.079069034 1.053077117 1.176731428 0.924662469 1.134015628 0.984215645 0.975967115 1 17.33422472 1.608382904 25 0.985059206 1.059427153 0.187343267 0.070124672 0.094001053 3655.541972 0.03062924 0.015679119 40.58662172 -1.608382904 0.074367947 VGDPPQPLPEEPMEVQGAERAS(ph)PEPQRENASPAPGTTAEEAMSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGDPPQPLPEEPMEVQGAERASPEPQRENASPAPGTTAEEAMSR 44 2 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 VGDPPQPLPEEPMEVQGAERAS(0.999)PEPQRENASPAPGTTAEEAMSR 86.044 8.95E-05 116430000 9279.8 6809.1 7419.1 5441.1 6748.3 2674 7178.7 5609.4 8751.4 TRUE FALSE 8698.993883 7313.252849 7595.084556 5580.727838 6218.315739 3445.940391 6102.320579 6309.745938 7290.734804 1.193157359 1.003088584 1.041744729 0.765454784 0.852906587 0.472646514 0.836996646 0.865447188 1 12.83184851 3.253316954 6.379514213 0.773807101 1.059281187 0.455892793 0.142153716 0.128005241 19.91445024 0.037581313 0.049133501 1791.913138 -3.253316954 0.285474086 VGDPQELNGITR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 215.71 9.49E-11 2125990000 1331720 1533820 1430550 1488110 1570450 1315730 1901910 1361250 1772580 FALSE TRUE 1248370.022 1647385.629 1464483.322 1526297.422 1447113.192 1695559.892 1616736.252 1531205.059 1476724.947 0.845363942 1.115567007 0.991710288 1.0335692 0.979947684 1.148189374 1.09481204 1.036892525 1 20.49396971 2.257039364 24.99839716 1.0822005 1.011539793 0.167781303 0.07719814 413.0700226 558807.5746 0.024781691 0.020699479 180.7337935 -2.257039364 -0.070660706 VGDQVWLFIDEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VGDQVWLFIDEPR 13 0 P49588;P49588-2;H3BPK7 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;; 165.7 8.12E-05 161873000 178287 204272 201727 199369 220612 172403 208161 181568 176531 FALSE TRUE 167128.3349 219396.5114 206512.0597 204485.1461 203286.0234 222172.9474 176949.1905 204237.1645 147066.8357 1.136410763 1.491815 1.404205501 1.39042324 1.38226965 1.510693736 1.203188943 1.388737057 1 17.16611242 0.221835905 0.681224624 0.989438345 1.393750813 0.478519443 0.116987311 2.277487646 1.37907817 0.167842964 0.0395422 1.666617375 -0.221835905 0.404312468 VGDST(ph)PVSEKPVSAAVDANASESP ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGDSTPVSEKPVSAAVDANASESP 24 1 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 1 VGDS(0.355)T(0.506)PVS(0.139)EKPVSAAVDANASESP 97.352 0.009627 107260000 256440 187260 210730 208260 273590 178970 246020 181360 367670 TRUE FALSE 240389.8782 201124.9252 215728.6151 213604.3042 252103.345 230635.7337 209131.5849 204003.1952 306303.5018 0.784809435 0.656619739 0.704296927 0.697361613 0.823050809 0.752964731 0.682759367 0.66601653 1 18.22460233 -2.115621206 2.550408732 1.561867637 0.715087372 0.731839477 0.052971809 4378460.799 1093680.42 14334425.84 0.01335881 0.007662647 2.115621206 -0.846780265 VGDSTPVSEKPVSAAVDANASES(ph)P ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGDSTPVSEKPVSAAVDANASESP 24 1 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 1 VGDSTPVSEKPVSAAVDANAS(0.013)ES(0.987)P 125.42 3.35E-07 0 765070 704330 778560 785350 693980 511940 835900 548280 721710 TRUE FALSE 717185.6344 756479.3261 797027.8109 805503.4106 639477.6102 659728.7673 710564.5551 616733.9649 601251.9386 1.192820494 1.258173617 1.325613707 1.339710293 1.063576796 1.097258445 1.181808339 1.025749649 1 19.19761011 2.733887965 24.96872732 1.094754895 1.283350907 0.717058543 0.063323722 221.7579102 1184978.934 0.01998074 0.019407871 541.8610884 -2.733887965 0.188596013 VGDTEKPEPERS(ph)PPNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 VGDTEKPEPERSPPNR 16 2 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 1 VGDTEKPEPERS(1)PPNR;VGDTEKPEPERS(1)PPNR;VGDTEKPEPERS(1)PPNR;VGDTEKPEPERS(1)PPNR;VGDT(0.001)EKPEPERS(0.999)PPNR;VGDTEKPEPERS(1)PPNR;VGDTEKPEPERS(1)PPNR;VGDT(0.001)EKPEPERS(0.999)PPNR 146.97 5.60E-07 6649500000 8164494 5267276 6277820 6090732 6558644 4874913 7834373 5431196 8460124 TRUE FALSE 7653492.895 5657270.596 6426732.855 6247030.495 6043554.557 6282221.245 6659681.499 6109292.776 7048074.65 1.085898387 0.802668938 0.911842336 0.886345677 0.857475957 0.891338636 0.944893723 0.866803075 1 22.74879777 -1.144851992 4.324538455 1.000020438 0.898011053 0.129424055 0.074220911 1.30E-05 2.57E-06 0.06379351 0.015033263 0.071638751 1.144851992 -0.102009385 VGDTEKPEPERS(ph)PPNRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGDTEKPEPERSPPNRK 17 3 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 1 VGDTEKPEPERS(1)PPNRK;VGDTEKPEPERS(1)PPNRK 114.88 0.0018884 163747000 205792 126297 149846 151319 167117 102701 198308 134045 378840 TRUE FALSE 192911.8461 135648.1613 153400.4179 155202.1017 153992.3049 132349.1115 168573.5564 150780.8133 315609.1566 0.611236531 0.429797927 0.486045524 0.491754116 0.487920904 0.419344967 0.534121247 0.47774537 1 18.26777954 -0.919187718 0.880995262 1.057552592 0.484436479 0.898086483 0.053689812 17.55899214 6.52135837 2.981483464 0.015259678 0.120451519 0.919187718 -0.573116113 VGDVT(ph)PQVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VGDVTPQVK 9 0 Q13428-4;Q13428;Q13428-3;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 VGDVT(1)PQVK;VGDVT(1)PQVK;VGDVT(1)PQVK;VGDVT(1)PQVK 150.09 0.00096223 1339860000 3812500 2573950 3159740 2794340 3572560 2337610 4041180 3095790 5027010 TRUE FALSE 3573882.431 2764527.936 3234690.525 2866047.495 3291985.549 3012440.059 3435242.575 3482306.196 4187969.555 0.853368771 0.660111756 0.7723768 0.684352514 0.78605766 0.719308013 0.820264458 0.831502271 1 21.99781952 0.848099225 0.839761064 0.999988048 0.734490222 0.664985236 0.055943255 0.41354516 0.600600515 0.047004166 0.016495835 7.048540918 -0.848099225 -0.265497826 VGDVVLPPWASSPEDFIQQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGDVVLPPWASSPEDFIQQHR 21 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7;H7C408 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 0 116.39 0.00013111 79268000 135290 153720 143820 148130 160540 121700 185250 125990 149930 FALSE TRUE 126822.4404 165101.5887 147231.4783 151931.2666 147931.836 156832.8144 157473.4823 141720.1288 124905.7144 1.015345383 1.321809731 1.178740933 1.21636762 1.184348023 1.255609602 1.260738814 1.134616855 1 16.93047996 0.957089554 4.709954257 1.000124744 1.217483476 0.391948948 0.080095033 0.194246475 13.78084829 0.068384487 0.017335268 9.05919388 -0.957089554 0.217358732 VGDVYIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 VGDVYIPR 8 0 Q01130;Q01130-2;J3KP15;J3QL05;Q9BRL6-2;Q9BRL6 Q01130;Q9BRL6-2 SRSF2;SRSF8 Serine/arginine-rich splicing factor 2;Serine/arginine-rich splicing factor 8 0 ;;;;;;; 153.73 0.0010153 3342126000 3226880 3607280 3596370 3409230 3630200 2949130 3956340 3146570 4130560 FALSE TRUE 3024915.341 3874366.765 3681677.595 3496716.614 3345098.736 3800495.956 3363123.546 3539426.191 3441142.852 0.879043815 1.125895359 1.069899668 1.016149798 0.972089471 1.104428418 0.977327502 1.028561249 1 21.71445635 3.220630925 23.48697957 1.016714532 1.053000132 0 0.072661016 377.3081227 494252.2315 0.019699998 0.023604307 1661.99964 -3.220630925 0.0362856 VGDYGSLSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGDYGSLSGR 10 0 Q9UBR2 Q9UBR2 CTSZ Cathepsin Z 0 140.83 8.98E-05 120810000 174090 214470 214990 189510 205880 151220 190420 184170 183010 FALSE TRUE 163194.0177 230349.582 220089.6643 194373.1474 189711.0153 194874.7591 161868.2888 207164.0299 152464.4487 1.070374235 1.510841274 1.443547438 1.274875219 1.244296732 1.278165243 1.061678904 1.358769416 1 17.21811335 2.51343196 1.166202381 1.15185018 1.386550937 0.171170268 0.151429169 0.588332712 1.622060987 0.079945454 0.059575598 326.1609476 -2.51343196 0.234700757 VGEDEDGS(ph)DEEVVHNEDIHFEPIVSLPEVEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 VGEDEDGSDEEVVHNEDIHFEPIVSLPEVEVK 32 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK 347.59 2.61E-131 3067714000 1774179 893008 1146496 1141971 1219642 813946 1552865 975297 1426791 TRUE FALSE 1663136.303 959127.2415 1173691.427 1171275.909 1123856.237 1048918.997 1320027.309 1097064.977 1188650.365 1.399180409 0.806904427 0.987415191 0.985383039 0.94548933 0.882445358 1.110526147 0.922950104 1 20.18089299 -0.210719752 6.992826134 0.999999883 0.987074917 0 0.161356825 18730449.72 2678523.633 0.138394326 0.033565554 0.615573971 0.210719752 -0.012924966 VGEEEHVY(ph)SFPNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGEEEHVYSFPNK 13 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 VGEEEHVY(0.985)S(0.015)FPNK;VGEEEHVY(0.98)S(0.02)FPNK 173.19 0.00012832 782390000 1489450 1180730 1205550 1287730 1548530 836940 1501410 1295110 1739660 TRUE FALSE 1396227.983 1268152.478 1234146.215 1320775.332 1426914.7 1078550.991 1276287.509 1456807.334 1449299.507 0.963381258 0.875010632 0.851546702 0.911319796 0.98455474 0.744187786 0.88062371 1.005180314 1 20.46692434 1.239649077 23.95104021 1.002590254 0.879519911 0.346781407 0.065156673 16.56790623 364701.1861 0.047011864 0.014939039 17.36397202 -1.239649077 -0.123070343 VGEEFEEQTVDGRPCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VGEEFEEQTVDGRPCK 16 1 P29373 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 ;;;; 279.44 1.87E-35 2667760000 2359960 1503956 1716630 1678325 1976560 1293647 2178550 1549722 3484480 FALSE TRUE 2212254.316 1615310.467 1757349.274 1721393.661 1821328.951 1667101.888 1851896.652 1743208.203 2902897.777 0.762084815 0.556447588 0.605377595 0.592991484 0.627417529 0.574288871 0.637947594 0.600506231 1 21.46906234 -1.362032498 2.793025119 1.006407784 0.612038103 0.818175581 0.056250705 3994943.846 4611140.078 208132.2433 0.012225645 0.043447771 1.362032498 -0.394369681 VGEFCHNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VGEFCHNR 8 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;;; 183.26 0.00022424 12125100000 9245420 11344400 9002160 8543500 12292000 6723450 9623300 10131500 10506000 FALSE TRUE 8666765.666 12184351.18 9215695.486 8762740.674 11326635.9 8664400.869 8180375.503 11396440.08 8752480.729 0.990206769 1.3921026 1.052923825 1.001172233 1.29410578 0.989936583 0.934635077 1.302081139 1 23.06126055 3.731014009 23.96241549 1.070820554 1.220657071 0.066918289 0.15674257 183.3069224 1128348.535 0.037812349 0.065013809 5382.87146 -3.731014009 0.149836517 VGEFSGANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGEFSGANK 9 0 P10599;P10599-2 P10599 TXN Thioredoxin 0 ; 85.862 0.033798 174876000 182616 165965 182603 167259 196983 193022 202002 149347 185769 FALSE TRUE 171186.3905 178253.2213 186934.4294 171551.1491 181512.7498 248744.3179 171713.6754 167993.3017 154762.9538 1.106119949 1.151782238 1.207875818 1.108476834 1.172843664 1.607260083 1.109526997 1.085487822 1 17.23970064 1.491409334 25 1.060985401 1.220279519 0.223675142 0.144029969 1.328828029 2319.803403 0.076006717 0.035186943 31.00340073 -1.491409334 0.159294118 VGEGDKEDATRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGEGDKEDATRR 12 2 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 ; 146.79 3.50E-05 637280000 1493760 949810 1149000 1023120 1196040 781720 1354170 879700 1597250 FALSE TRUE 1400268.228 1020134.921 1176254.823 1049374.991 1102107.843 1007389.874 1151124.78 989532.4815 1330658.656 1.052312117 0.766639074 0.883964356 0.788613208 0.828242343 0.757061076 0.86507894 0.743641111 1 20.3437091 4.74744076 24.84389891 0.823530472 1.052312246 0.45936913 0.075864329 850.0485433 2378117.308 0.015221598 0.184557482 55903.72667 -4.74744076 0.228781774 VGESTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGESTER 7 0 A0A087WX83;A0A075B749;Q5VU43-3;Q5VU43;Q5VU43-4 A0A087WX83 PDE4DIP Myomegalin 0 84.359 0.050259 288060000 234410 296730 295930 298360 318120 238160 284680 239190 312760 FALSE TRUE 219738.6965 318700.1979 302949.5993 306016.4227 293136.1384 306912.9258 241994.8768 269053.398 260558.3355 0.843337812 1.22314336 1.162693946 1.174464145 1.125030746 1.177904845 0.928755077 1.032603304 1 17.99124688 1.745315911 14.44277899 0.986284108 1.137565735 0.235207779 0.107144224 0.123752536 221.3117517 0.045970206 0.025342252 55.63087758 -1.745315911 0.151281627 VGEVCHITCKPEYAYGSAGSPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGEVCHITCKPEYAYGSAGSPPK 23 1 Q02790;F5H1U3 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ; 240.87 1.71E-37 2356800000 3314180 2125000 2695010 2532510 2577590 2002640 3663900 2503040 2645870 FALSE TRUE 3106751.39 2282337.211 2758936.91 2597498.494 2375156.479 2580769.658 3114532.209 2815550.054 2204257.204 1.40943234 1.035422367 1.251640192 1.178400819 1.077531458 1.170811488 1.412962246 1.277323739 1 21.07186114 VGFQYEGTYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGFQYEGTYK 10 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 133.99 0.00042442 352390000 294870 336810 301170 308120 406440 235850 373450 334860 464600 FALSE TRUE 276414.6131 361747.7629 308313.8946 316026.8808 374519.8419 303936.0663 317454.6394 376668.0081 387055.2586 0.714147675 0.93461529 0.796562991 0.816490343 0.967613367 0.785252389 0.820179115 0.973163391 1 18.56218002 1.191383622 6.111874366 0.992245944 0.840314181 0.434080689 0.072418067 0.187693025 15.81800122 0.061291487 0.015922371 15.53758875 -1.191383622 -0.151931763 VGGDVPETNYLFMGDFVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGGDVPETNYLFMGDFVDR 19 0 P60510;I3L4X0 P60510 PPP4C Serine/threonine-protein phosphatase 4 catalytic subunit 0 ; 154.65 7.84E-08 61466000 13159.4 12721.4 16823 14417.2 11843.6 14341 12949.3 12466.1 15820.1 FALSE TRUE 12335.77664 13663.30569 17222.0495 14787.16976 10913.45143 18481.01389 11007.67268 14022.52003 13179.62311 0.935973399 1.036699273 1.306717906 1.121972126 0.828054895 1.402241456 0.835203905 1.063954554 1 13.68602149 1.645658156 25 0.962117808 1.111212532 0.125326415 0.172366025 1.115125181 731.0622114 0.074466908 0.041293273 44.22401366 -1.645658156 0.149094724 VGGS(ph)DEEASGIPSR ddPTM_SK-BR-3_Pertuzumab_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(0.999)DEEAS(0.001)GIPSR;VGGS(1)DEEASGIPSR;VGGS(1)DEEASGIPSR;VGGS(1)DEEASGIPSR 282.39 2.33E-33 8602530000 4035120 3201510 3483980 3451530 3347130 2852530 3828760 2806050 3355800 TRUE FALSE 3782569.042 3438553.132 3566621.651 3540102.103 3084259.911 3676009.104 3254672.982 3156391.519 2795695.301 1.352997604 1.229945599 1.275754783 1.266268932 1.103217475 1.314881884 1.164172999 1.12901843 1 21.4147757 -5 0.09403783 0.194049861 1.421347738 0.661619923 0.062283124 116.9129131 0.75818767 18.40563043 1.154169929 1.00E-05 5 1.227297877 VGGS(ph)SVDLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.647)S(0.353)VDLHR 130.01 0.00018555 210550000 106960 108580 108130 114030 121510 84496 137430 95292 148690 TRUE FALSE 100265.5645 116619.3762 110694.8947 116956.2029 111967.0947 108888.6235 116823.6473 107189.416 123872.6784 0.809424369 0.941445504 0.893618319 0.94416464 0.903888542 0.879036644 0.943094545 0.865319272 1 16.91849849 -2.676333061 2.245763127 4.147458343 0.904708652 0.361024627 0.041890316 1454873.262 287196.4493 23465848.19 0.008934229 0.002107012 2.676333061 -3.24274969 VGGSS(ph)VDLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.025)S(0.975)VDLHR 116.03 0.00073748 158020000 68877 67954 60757 60742 73500 53474 83639 67804 83858 TRUE FALSE 64566.11152 72985.38487 62198.18473 62300.74256 67727.60648 68911.07572 71098.10842 76269.47866 69861.55806 0.924200853 1.044714531 0.890306292 0.891774307 0.969454567 0.986394773 1.017700011 1.091723128 1 16.0922112 1.85108542 1.876369822 1.045264174 0.948227017 0.432366527 0.048687235 0.343430149 2.287706429 0.032770209 0.014718486 70.97173466 -1.85108542 -0.097037157 VGGSSVDLHR ddPTM_SK-BR-3_Pertuzumab_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 0 ;;;; 177.78 2.29E-06 1782070000 1361060 1913960 1708710 1663750 2075140 1549140 2012710 1687630 2275990 FALSE TRUE 1275873.684 2055671.59 1749241.408 1706444.642 1912166.875 1996351.57 1710922.821 1898334.32 1896112.566 0.672889209 1.084150608 0.922540908 0.899970114 1.00846696 1.052865535 0.902331882 1.001171742 1 20.85461318 4.751020254 24.87994371 0.979234771 0.672889006 0.71860758 0.061107294 1040.506811 2077689.248 0.014260656 0.25153902 56366.39429 -4.751020254 -0.306345766 VGGTKPAGGDFGEVLNSAANASATTTEPLPEKTQES(ph)L ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGGTKPAGGDFGEVLNSAANASATTTEPLPEKTQESL 37 2 P55327-2;P55327-4;P55327-3 P55327-2 1 VGGTKPAGGDFGEVLNSAANASATTTEPLPEKTQES(1)L 200.11 1.69E-30 80591000 313430 208850 227320 258480 295860 158570 325910 197210 341710 TRUE FALSE 293812.9758 224313.4713 232712.1377 265113.0344 272624.349 204346.5848 277042.8211 221832.1026 284676.3935 1.032094626 0.787959509 0.817462013 0.931278604 0.957664054 0.717820618 0.973185088 0.779243055 1 18.11896334 -1.135040442 4.273150691 1.000026815 0.866806211 0.130952472 0.099757611 12717693.7 3378092.534 3175.028058 0.021064918 0.073275629 1.135040442 -0.133220605 VGGTNPNGGS(ph)FEEVLSSTAHASAQSLAGGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VGGTNPNGGSFEEVLSSTAHASAQSLAGGSR 31 0 Q16890-5;E9PPQ1;J3KNE7;Q16890 Q16890-5 TPD52L1 Tumor protein D53 1 VGGTNPNGGS(1)FEEVLSSTAHASAQSLAGGSR;VGGT(0.001)NPNGGS(0.999)FEEVLSSTAHASAQSLAGGSR;VGGTNPNGGS(1)FEEVLSSTAHASAQSLAGGSR;VGGTNPNGGS(1)FEEVLSSTAHASAQSLAGGSR 320.42 3.50E-93 1590090000 207185 540990 497660 540670 423944 405718 622330 510740 649370 TRUE FALSE 194217.6607 581045.4625 509464.7302 554544.5076 390649.1483 522842.2003 529017.3939 574507.0133 540985.9519 0.359006847 1.074049077 0.941733752 1.025062676 0.722105901 0.966461695 0.977876398 1.061962905 1 19.04523161 4.744673557 24.91001728 0.968312025 0.359006564 0.795532317 0.097521715 286.5063753 1167469.431 0.022341065 0.207251491 55548.65616 -4.744673557 -0.609305461 VGGTSDVEVNEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGGTSDVEVNEK 12 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 145.55 0.00014888 67639000 103420 83377 88685 85061 115580 69726 93293 87988 136530 FALSE TRUE 96947.12681 89550.31983 90788.65008 87243.80927 106502.813 89854.76429 79304.58074 98973.49549 113742.261 0.852340423 0.787309124 0.798196284 0.767030728 0.936352171 0.789985741 0.697230564 0.870155865 1 16.79540886 0.98945454 24.38749756 1.000000007 0.798336614 0.511297653 0.060881086 278.010864 642931.8564 0.058026765 0.014506691 9.760106118 -0.98945454 -0.201663393 VGGTSDVEVNEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGGTSDVEVNEKK 13 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 123.76 0.00035225 230640000 343670 220140 238710 242800 388640 193580 290620 251120 714140 FALSE TRUE 322160.3082 236439.3947 244372.3139 249030.6591 358117.7821 249463.4035 247044.229 282472.8848 594945.4205 0.541495568 0.397413589 0.410747449 0.418577319 0.601933841 0.419304687 0.415238475 0.474787897 1 19.1823978 0.926963792 17.49550348 1 0.447087194 0.868189241 0.066061832 245.4359518 58793.91621 0.061248443 0.015312287 8.452083761 -0.926963792 -0.552912806 VGGVS(ph)PEEHPAPEVSTPFPPLPPEPEGGGEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGGVSPEEHPAPEVSTPFPPLPPEPEGGGEEK 32 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 VGGVS(0.995)PEEHPAPEVS(0.004)T(0.001)PFPPLPPEPEGGGEEK;VGGVS(0.956)PEEHPAPEVS(0.022)T(0.022)PFPPLPPEPEGGGEEK 73.665 0.0016848 77650000 96815 63899 71966 79668 82664 56708 82042 59716 75945 TRUE FALSE 90755.52197 68630.14845 73673.0675 81712.41576 76171.90289 73078.67902 69740.56374 67171.67405 63269.28888 1.434432464 1.084730833 1.164436472 1.291502042 1.203931706 1.15504189 1.102281454 1.06167898 1 15.94921776 1.506907879 1.188470976 1.008714002 1.208277676 0.449647646 0.092018855 0.460570871 1.252174548 0.080303202 0.028046653 32.12978944 -1.506907879 0.199563674 VGHFDPVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGHFDPVTR 9 0 Q9UNE7;Q9UNE7-2;H3BTA3 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ; 114.86 0.00157 796060000 372490 399220 383500 349140 434090 312820 455280 382420 411200 FALSE TRUE 349176.5158 428778.6642 392596.8011 358099.5235 399998.3224 403126.0558 387014.9906 430165.9788 342568.0635 1.019290918 1.251659772 1.146040285 1.045338318 1.167646272 1.176776526 1.129746266 1.25570952 1 18.38603113 -1.694405471 2.787077199 0.978239697 1.154784412 0.275331499 0.075468976 8825802.639 7513946.224 1345391.912 0.016730325 0.020211313 1.694405471 0.176544716 VGHSELVGEIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VGHSELVGEIIR 12 0 P38606;P38606-2;C9JVW8;C9JA17 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ;;; 210.91 3.80E-08 1029600000 926800 1059130 1007890 960780 1152730 822070 992230 967760 1150550 FALSE TRUE 868793.2424 1137549.087 1031797.627 985435.2414 1062199.236 1059388.264 843454.3229 1088586.966 958515.7722 0.90639431 1.186781814 1.076453468 1.028084534 1.108170848 1.105238218 0.879958731 1.13570063 1 19.87044265 VGIDTPDIDIHGPEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VGIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 228.73 3.83E-15 1181850000 2663410 2024360 2324810 2277980 2637230 1765280 2737650 2114770 3259520 FALSE TRUE 2496711.922 2174245.721 2379955.591 2336436.823 2430112.594 2274887.679 2327164.798 2378803.69 2715485.055 0.919434971 0.800684105 0.876438479 0.86041233 0.894909213 0.837746345 0.856997829 0.876014282 1 21.37277849 0.718627424 2.963408235 0.999993165 0.858529624 0.637144526 0.031871113 1.304903576 13.036411 0.028012631 0.007336053 5.231514386 -0.718627424 -0.141463541 VGLSPDSPAGDRNS(ph)VGSEGSVGSIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGLSPDSPAGDRNSVGSEGSVGSIR 25 1 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 VGLSPDSPAGDRNS(1)VGSEGSVGSIR 165.4 9.31E-12 434620000 426510 404340 472220 368910 496870 438360 459140 458520 949780 TRUE FALSE 399815.5004 434277.7543 483421.2814 378376.8552 457847.8345 564907.4158 390296.2194 515767.2313 791255.5822 0.505292486 0.54884637 0.610954655 0.478198023 0.578634571 0.713937985 0.493261884 0.651833924 1 19.59378425 -4.999999997 0.286376138 4.284088701 0.544698603 0.802088242 0.068023608 98.77469781 0.936693065 193.2952675 0.069481111 1.00E-05 4.999999997 -3.739390097 VGMVETNSQDRPVDDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGMVETNSQDRPVDDVK 17 1 Q9Y3C6 Q9Y3C6 PPIL1 Peptidyl-prolyl cis-trans isomerase-like 1 0 157.11 3.45E-08 173530000 203940 142630 154460 145170 172520 115090 200460 135430 229610 FALSE TRUE 191175.7594 153190.4736 158123.8641 148895.308 158970.9751 148314.6147 170402.884 152338.7336 191286.6077 0.999420512 0.800842649 0.826633218 0.778388565 0.831061709 0.775352841 0.890824957 0.796389959 1 17.54537635 -1.209443786 3.898808453 1.000137899 0.832742021 0.369763275 0.066485041 6349721.2 1969742.643 7393.467025 0.014293525 0.06173852 1.209443786 -0.167395878 VGNES(ph)PVQELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 301.95 6.92E-36 2452470000 8115080 4857190 6064620 5630050 6086150 4422830 7163970 4945160 6634380 TRUE FALSE 7607171.629 5216821.402 6208475.65 5774526.615 5608168.329 5699629.222 6089799.206 5562574.112 5527059.118 1.37635069 0.943869296 1.123287361 1.04477381 1.014674931 1.031222772 1.101815464 1.006425658 1 22.39808061 4.749048369 24.92659538 1.041665592 1.376350884 0.814702513 0.0512828 608.1526498 1445387.833 0.011682665 0.168622601 56111.04652 -4.749048369 0.334685292 VGNHTAEGTGTNKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGNHTAEGTGTNKK 14 1 O95793-2;O95793-3;O95793;Q5JW30;A0A087X1A5 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 105.14 0.00066031 233460000 321990 202630 247700 248040 271830 209240 329050 241840 414770 FALSE TRUE 301837.2207 217632.936 253575.561 254405.1263 250481.5683 269644.1913 279712.0073 272034.2564 345542.2075 0.87351766 0.629830253 0.733848298 0.736249063 0.724894276 0.780350954 0.809487238 0.787267808 1 18.39850242 0.405628729 0.467080583 1.01948494 0.716280115 0.604465246 0.061961617 1.387485377 0.524348469 0.115498998 0.032772284 2.54465394 -0.405628729 -0.303204825 VGNLGLATSFFNER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGNLGLATSFFNER 14 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8Y7T2;A0A087WVZ1;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 0 ; 211.22 9.65E-09 130160000 106396 160839 111220 100644 170315 105575 109392 126395 163119 FALSE TRUE 99736.86428 172747.6869 113858.1909 103226.6954 156939.1469 136052.7886 92989.68515 142175.694 135893.3851 0.733934652 1.271200116 0.837849398 0.759615307 1.154869656 1.001173004 0.684284118 1.046229689 1 17.05211571 3.743767366 24.0507 0.906885321 1.045017922 0.008644381 0.189270676 649.2758081 938080.5162 0.045801184 0.082244837 5543.287014 -3.743767366 0.138132602 VGPAT(ph)PSAQVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.963)PS(0.037)AQVGK;VGPAT(0.989)PS(0.011)AQVGK 171.93 0.00041508 247860000 1090760 723290 856920 736970 1019160 682560 1268450 919720 1420170 TRUE FALSE 1022491.279 776843.1442 877246.5471 755881.8979 939119.2847 879603.9916 1078257.698 1034549.067 1183134.452 0.864222385 0.656597517 0.741459726 0.638880811 0.793755336 0.743452268 0.911356859 0.874413778 1 20.1741826 1.595869808 1.058558302 0.978251029 0.717192835 0.625574952 0.069224334 0.266335567 0.571097748 0.054937832 0.020588539 39.43390704 -1.595869808 -0.261058194 VGPCS(ph)SPPAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGPCSSPPAAR 11 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1 Q8TDM6-4 DLG5 Disks large homolog 5 1 VGPCS(0.751)S(0.249)PPAAR 114.86 0.0012592 427680000 331920 304650 328730 349550 363370 252830 337410 262110 320880 TRUE FALSE 311145.7197 327206.603 336527.6308 358520.0448 334832.386 325817.9166 286818.5029 294835.0105 267323.055 1.163931482 1.224011909 1.258879938 1.341148988 1.252538379 1.218817122 1.072928419 1.102916508 1 18.02822474 1.761503346 2.647762568 1.056233646 1.250607984 0.759424909 0.049302706 0.126088652 1.782695201 0.029703118 0.013697537 57.74353213 -1.761503346 0.194374338 VGPCSS(ph)PPAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGPCSSPPAAR 11 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1 Q8TDM6-4 DLG5 Disks large homolog 5 1 VGPCS(0.405)S(0.595)PPAAR;VGPCS(0.202)S(0.798)PPAAR 81.525 0.016122 187810000 382710 372730 401510 429370 415680 317010 440200 344630 390600 TRUE FALSE 358756.8643 400327.317 411034.0068 440388.3611 383034.1696 408525.6408 374196.0966 387657.8141 325406.3366 1.10248887 1.230238234 1.263140758 1.353349064 1.177094993 1.255432347 1.14993488 1.191303827 1 18.31188282 0.641367665 0.787013359 0.999933378 1.237119047 0.515098378 0.06705144 0.929929622 1.029822818 0.063390276 0.021861103 4.37892659 -0.641367665 0.237185669 VGPDTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGPDTER 7 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 99.139 0.025003 1590590000 1964490 2160900 2050500 2137100 2261200 1709380 2364600 1843530 2427700 FALSE TRUE 1841536.078 2320895.284 2099138.828 2191941.604 2083614.473 2202850.257 2010050.182 2073698.779 2022501.186 0.910524103 1.147537168 1.037892508 1.08377766 1.030216688 1.089171305 0.993843759 1.025313999 1 20.94770912 1.704362575 8.995260995 1.007793956 1.060247451 0.0850234 0.060928648 0.21594258 36.45145796 0.026510243 0.014176733 50.62471307 -1.704362575 0.052453495 VGPGNHGTEGSGGERHS(ph)DTDSDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VGPGNHGTEGSGGERHSDTDSDRR 24 2 Q99442 Q99442 SEC62 Translocation protein SEC62 1 VGPGNHGTEGS(0.013)GGERHS(0.985)DT(0.001)DSDRR;VGPGNHGTEGS(0.001)GGERHS(0.999)DTDSDRR;VGPGNHGTEGS(0.007)GGERHS(0.992)DTDSDRR 207.48 3.54E-25 1531273000 203054 210175 188765 192348 217799 189955 253123 196382 134258 TRUE FALSE 190345.2126 225736.5757 193242.5949 197283.9753 200693.9451 244791.9248 215169.556 220900.725 111849.4725 1.701798036 2.018217616 1.727702337 1.763834652 1.794321785 2.188583633 1.923742252 1.97498227 1 16.77119893 VGQEIEVRPGIVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VGQEIEVRPGIVSK 14 1 P41091 P41091 EIF2S3 Eukaryotic translation initiation factor 2 subunit 3 0 ;; 129.93 5.93E-05 1073370000 1934010 1707690 1923930 1884440 2154740 1598320 2487810 1789750 2512070 FALSE TRUE 1812963.766 1834129.144 1969566.528 1932797.921 1985515.412 2059729.037 2114785.986 2013204.227 2092789.288 0.866290637 0.876404115 0.941120322 0.923551134 0.948741196 0.984202781 1.010510708 0.961971775 1 20.99699563 3.614995698 0.442577158 1.003500294 0.832816086 0.876051102 0.016812644 0.650707595 0.198620235 0.014730456 0.053580915 4120.934371 -3.614995698 -0.170684208 VGQGYPHDPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGQGYPHDPPK 11 0 P61081;M0QYI6 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ; 89.403 0.012258 551300000 1621750 1315060 1500730 1452150 1597240 1156640 1825100 1377320 1974680 FALSE TRUE 1520247.562 1412428.411 1536328.024 1489414.627 1471799.213 1490543.192 1551443.198 1549281.434 1645093.151 0.924110323 0.858570477 0.933885126 0.905367958 0.894660106 0.906053977 0.943073161 0.941759093 1 20.64973785 1.002761997 0.673365514 1.000655493 0.898195314 0.686928608 0.020731828 0.422282581 0.446784557 0.019731861 0.008009402 10.0638 -1.002761997 -0.102460179 VGQQAIVLCIS(ph)PSKPNPVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGQQAIVLCISPSKPNPVFK 20 1 Q16656-2;Q16656;Q16656-4;C9JP85 Q16656-2 NRF1 Nuclear respiratory factor 1 1 VGQQAIVLCIS(0.999)PS(0.001)KPNPVFK 160.57 1.44E-11 218450000 277240 174470 200840 196730 219550 156270 304570 170410 257570 TRUE FALSE 259888.0433 187387.9403 205604.0196 201778.4249 202307.4286 201382.6122 258902.556 191686.0636 214579.903 1.211148107 0.873278148 0.958169972 0.940341672 0.942806972 0.938497079 1.206555471 0.893308557 1 17.71115544 VGQTIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGQTIER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 130 0.0083885 765630000 567710 649030 594920 616280 721810 557760 736080 584170 876400 FALSE TRUE 532178.0445 697084.8565 609031.7833 632094.7882 665121.9542 718776.2575 625711.6374 657104.9104 730123.1782 0.728888029 0.95474966 0.834149362 0.865737189 0.91097225 0.984458895 0.856994622 0.899991851 1 19.47778035 2.71230435 4.696420387 0.921513294 0.861790433 0.258232638 0.068199968 0.377957368 21.88343443 0.020807076 0.020249942 515.5898388 -2.71230435 -0.059722861 VGRPSNIGQAQPIIDQLAEEAR ddPTM_SK-BR-3_Pertuzumab_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 ; 148.4 6.47E-08 251960000 207220 213310 215897 206680 223820 186525 245080 203451 262840 FALSE TRUE 194250.4701 229103.6943 221018.1788 211983.7587 206242.08 240371.7395 208332.5292 228852.3052 218970.306 0.88710873 1.046277454 1.009352285 0.968093631 0.941872365 1.097736693 0.95141909 1.045129403 1 17.74037572 VGRPTASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGRPTASK 8 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ; 80.231 0.023697 2443700000 2472800 2674900 1407400 1483180 2702400 1036200 1906070 2398400 2920800 FALSE TRUE 2318031.862 2872952.379 1440784.193 1521240.91 2490164.405 1335334.119 1620272.499 2697845.52 2433299.611 0.952629036 1.180681724 0.592111299 0.625176161 1.023369417 0.548775051 0.665874638 1.108719003 1 21.21448254 3.999938678 7.032965661 0.760826606 1.060592515 0.221867209 0.20388993 0.210705901 42.71549039 0.047295005 0.0993566 9998.588102 -3.999938678 0.29976591 VGS(ph)LDNVGHLPAGGAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 191.61 2.44E-10 2598074000 9774990 4721620 6167180 5182720 6631120 4351690 7677410 5458390 9174320 TRUE FALSE 9163190.825 5071213.658 6313468.422 5315717.37 6110338.584 5607952.259 6526253.644 6139882.007 7643066.724 1.198889288 0.663505088 0.826038637 0.69549535 0.79946163 0.733730643 0.853878931 0.803327019 1 22.86572019 0.192311821 1.141524771 1.000523907 0.800516223 0.111614462 0.14772499 9.951781166 12.31720259 0.137084895 0.038278913 1.557083208 -0.192311821 -0.200007684 VGS(ph)PLTLTDAQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VGSPLTLTDAQTR 13 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 VGS(0.99)PLT(0.01)LTDAQTR;VGS(0.992)PLT(0.008)LTDAQTR;VGS(0.999)PLT(0.001)LTDAQTR 193.45 1.95E-06 301115000 500970 316610 356526 332048 405068 254247 398840 290566 389071 TRUE FALSE 469615.182 340052.1338 364982.9651 340568.9138 373255.5932 327643.9815 339037.6446 326843.8047 324132.5366 1.448836908 1.049114468 1.126030015 1.050708816 1.151552378 1.010833361 1.045984609 1.00836469 1 18.30622432 4.739800356 24.97926569 1.062869311 1.448837033 0.861221763 0.049561605 35.82995396 721848.969 0.011226459 0.069303361 54928.83095 -4.739800356 0.385967722 VGS(ph)PQPSSSGGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGSPQPSSSGGEK 13 0 V9GYB6;O94761 V9GYB6 RECQL4 ATP-dependent DNA helicase Q4 1 VGS(1)PQPSSSGGEK 128.71 0.00017011 157230000 304080 160870 211500 195100 220670 184430 287030 212450 331670 TRUE FALSE 285048.1756 172780.9822 216516.8799 200106.5963 203339.4683 237671.947 243992.5162 238974.8502 276312.1343 1.031616568 0.625310874 0.783595264 0.724204881 0.735904953 0.860157472 0.883032216 0.864872803 1 18.07593939 1.472630927 0.857995766 0.980446363 0.756348643 0.255840985 0.106981462 0.594485801 0.899988126 0.090360904 0.035615796 29.69141718 -1.472630927 -0.22409772 VGS(ph)PSGDAASSTPPSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGSPSGDAASSTPPSTR 17 0 Q9NP87 Q9NP87 POLM DNA-directed DNA/RNA polymerase mu 1 VGS(0.914)PS(0.086)GDAASSTPPSTR 195.38 2.23E-11 226310000 157870 127810 135670 139990 139500 114930 163010 120520 149080 TRUE FALSE 147989.1985 137273.1854 138888.1565 143582.3804 128544.2327 148108.4253 138568.1638 135567.1873 124197.5849 1.191562611 1.105280634 1.118283875 1.156080293 1.034997845 1.192522587 1.115707394 1.091544472 1 16.92227759 0.85221139 2.391855675 1.000202989 1.127128326 0.454634813 0.045220891 0.483509129 5.275746934 0.038153424 0.010296493 7.11559777 -0.85221139 0.126925337 VGS(ph)TENIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.751)T(0.249)ENIK;VGS(0.979)T(0.021)ENIK 168.46 0.0003217 986070000 2220570 943930 1309670 1139730 1338800 936990 1581520 1131040 1599530 TRUE FALSE 2081588.488 1013819.559 1340735.991 1168977.401 1233656.048 1207483.802 1344385.758 1272252.834 1332558.11 1.562099598 0.760807016 1.006136979 0.877243096 0.925780301 0.906139697 1.008875897 0.954744731 1 20.34576702 4.747925105 24.99916706 0.927753847 1.562099932 0.877529439 0.074211709 408.1382717 1089531.614 0.017184674 0.218557373 55966.10783 -4.747925105 0.634346085 VGSEIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VGSEIER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;; 117.18 0.012306 2399700000 3035630 3205550 3270230 3265280 3333000 2802690 3555880 2956800 3476280 FALSE TRUE 2845635.337 3442892.257 3347801.4 3349072.613 3071239.625 3611781.105 3022708.805 3325962.989 2896066.41 0.982586355 1.18881675 1.155982262 1.156421207 1.060486601 1.247133385 1.043729106 1.148441547 1 21.46566325 0.098247256 0.712754173 0.996083063 1.135320039 0.183240943 0.077355803 5.696324419 3.333039923 0.130411985 0.024772157 1.253854827 -0.098247256 0.139236976 VGSGQGGS(ph)PCWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGSGQGGSPCWK 12 0 A0A669KBI7;Q9UMN6;Q9UMN6-2 A0A669KBI7 KMT2B Histone-lysine N-methyltransferase 2B 1 VGSGQGGS(1)PCWK;VGS(0.071)GQGGS(0.929)PCWK 105.46 0.0021269 472640000 928650 595450 748200 749490 822750 632990 1019290 648710 1012400 TRUE FALSE 870527.4542 639537.7376 765947.6573 768723.1823 758134.5338 815723.9373 866456.9271 729702.8715 843423.8996 1.032135151 0.758263713 0.908140803 0.911431586 0.898877224 0.967157722 1.027308958 0.865167411 1 19.68589838 2.548260426 1.402129568 0.974220943 0.872932318 0.085717619 0.079150212 0.600248677 2.393450306 0.035988289 0.028822427 353.3950203 -2.548260426 -0.101288625 VGSGS(ph)LDNLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGSGSLDNLGR 11 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 VGS(0.073)GS(0.927)LDNLGR;VGS(0.067)GS(0.933)LDNLGR 119.52 0.00087703 0 531140 479500 512330 462330 551090 457410 609330 504740 862810 TRUE FALSE 497896.8955 515002.6789 524482.7095 474194.1705 507809.6144 589456.8416 517966.6232 567757.9001 718801.437 0.692676544 0.716474192 0.729662856 0.6597012 0.706467166 0.82005518 0.720597646 0.789867508 1 19.45523377 -0.499906438 0.375847804 1.081484165 0.70062159 0.85276269 0.037053165 2.955068409 0.41274982 0.335501893 0.026542054 0.3162959 0.499906438 -0.380862575 VGSLT(ph)PPS(ph)SPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VGSLTPPSSPK 11 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 2 VGSLT(1)PPS(0.92)S(0.08)PK;VGSLT(1)PPS(0.837)S(0.163)PK;VGSLT(1)PPS(0.749)S(0.251)PK;VGSLT(1)PPS(0.805)S(0.195)PK 177.64 4.19E-05 1989410000 3363700 1822160 2268140 2237250 2278640 1639300 2873280 1902470 2990360 TRUE FALSE 3153172.021 1957074.622 2321941.352 2294661.623 2099684.806 2112539.298 2442458.338 2139997.567 2491249.598 1.265698959 0.785579504 0.932038827 0.921088607 0.842823942 0.847983799 0.980414945 0.859005685 1 21.24843814 4.748922021 24.85689228 0.892970795 1.265699184 0.758444501 0.065526688 648.1178199 1554794.218 0.014784081 0.20939882 56094.72466 -4.748922021 0.372728388 VGSLT(ph)PPSS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGSLTPPSSPK 11 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 2 VGSLT(1)PPS(0.372)S(0.628)PK 168.31 9.67E-05 124800000 866400 486840 581150 592200 646530 461640 813780 545130 847620 TRUE FALSE 812173.5706 522886.1402 594935.1524 607396.8546 595754.1418 594907.9739 691761.2438 613190.6805 706146.7462 1.150148429 0.740478014 0.842509232 0.8601567 0.843669032 0.842470743 0.979628169 0.868361546 1 19.4296085 1.747329383 24.99941591 0.94346983 0.85734935 0.055581566 0.110640151 4.363783639 12470.52066 0.04707193 0.026103712 55.88939171 -1.747329383 -0.08612048 VGTEGLVDS(ph)FSQGLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(1)FSQGLER;VGTEGLVDS(0.592)FS(0.408)QGLER;VGTEGLVDS(0.999)FS(0.001)QGLER 342.02 3.51E-72 211171000 237533 243470 241841 230840 214238 188815 284746 215557 180237 TRUE FALSE 222666.2335 261496.7721 247577.5827 236763.7452 197412.6117 243322.8253 242050.9808 242469.7659 150154.2803 1.482916325 1.741520598 1.648821347 1.57680317 1.314731829 1.620485442 1.61201519 1.614804223 1 17.19608608 -1.868500838 2.449583082 0.71746526 1.593322821 0.715337757 0.113855059 4594398.067 2654340.468 7549233.658 0.028778381 0.013536275 1.868500838 0.875857561 VGTLWR ddPTM_SK-BR-3_Pertuzumab_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 ; 150.72 0.024372 400770000 540020 710210 539650 545680 595700 437160 669980 547940 731610 FALSE TRUE 506221.1122 762794.6874 552450.7528 559683.0726 548916.1249 563360.9953 569522.7188 616351.5152 609499.5646 0.830552049 1.251509815 0.90640057 0.918266567 0.900601341 0.924300899 0.934410378 1.011241929 1 19.21726566 3.733216434 24.81255805 0.935654239 1.073456122 0.110473168 0.107018506 302.7420663 1232406.405 0.024594686 0.042930544 5410.238797 -3.733216434 0.137801883 VGVAAPPFLGS(ph)PVPFGGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGVAAPPFLGSPVPFGGFR 19 0 Q9BRQ0;Q5T171 Q9BRQ0 PYGO2 Pygopus homolog 2 1 VGVAAPPFLGS(1)PVPFGGFR 142.01 1.67E-07 92160000 119940 96283 121470 125150 113050 103790 137090 105170 145120 TRUE FALSE 112433.1695 103411.8935 124351.3258 128361.5609 104171.509 133752.4881 116534.6272 118300.706 120898.5345 0.92997959 0.855361018 1.028559414 1.061729668 0.861644101 1.106320177 0.963904382 0.978512324 1 16.88343723 3.958242358 4.974108243 0.999357012 0.893061566 0.310928102 0.066392427 0.190302892 13.05042029 0.015318655 0.030330037 9083.272799 -3.958242358 -0.106295446 VGVEASEETPQTSSSSARPGT(ph)PSDHQSQEASQFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VGVEASEETPQTSSSSARPGTPSDHQSQEASQFER 35 1 Q6Y7W6;I1E4Y6;Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 VGVEASEETPQTSSSSARPGT(0.892)PS(0.108)DHQSQEASQFER;VGVEASEETPQTSSSSARPGT(0.787)PS(0.213)DHQSQEASQFER;VGVEASEETPQTSSSSARPGT(0.607)PS(0.393)DHQSQEASQFER;VGVEASEETPQTSSSSARPGT(0.98)PS(0.02)DHQSQEASQFER;VGVEASEETPQTSSSS(0.002)ARPGT(0.867)PS(0.131)DHQSQEASQFER 319.64 7.24E-105 7013300000 993057 2174077 1978316 2023606 2348595 1860525 2430125 1975396 2214176 TRUE FALSE 930903.335 2335047.923 2025242.59 2075535.156 2164145.822 2397628.364 2065750.316 2222028.539 1844615.721 0.504659764 1.265872288 1.097921137 1.125185659 1.173223126 1.299798292 1.119881118 1.204602407 1 20.81488887 4.74369046 24.98349677 1.16861086 0.504659488 0.853368987 0.08542288 175.8496306 856400.1961 0.018226138 0.153606218 55423.05489 -4.74369046 -0.663951372 VGVEASEETPQTSSSSARPGTPS(ph)DHQSQEASQFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VGVEASEETPQTSSSSARPGTPSDHQSQEASQFER 35 1 Q6Y7W6;I1E4Y6;Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 VGVEASEETPQTSSSSARPGT(0.382)PS(0.618)DHQSQEASQFER 311.11 6.72E-105 1957600000 505930 1232200 1045700 1219100 1202800 934960 1296500 1104300 1168700 TRUE FALSE 474264.7444 1323433.37 1070504.498 1250384.17 1108336.94 1204867.774 1102101.861 1242174.286 973636.4199 0.487106619 1.359268556 1.099491017 1.28424137 1.138347865 1.237492507 1.131943956 1.275809183 1 19.89302361 4.746631691 24.99866399 1.197220043 0.487106273 0.818096629 0.104245547 367.390896 1137899.707 0.021541501 0.241436063 55799.67772 -4.746631691 -0.71011377 VGVNGFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGVNGFGR 8 0 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 163.84 0.00077597 12967400000 3242000 3564600 3661200 3516900 3443600 2971900 3801200 3208700 2892600 FALSE TRUE 3039089.007 3828526.693 3748045.393 3607149.608 3173153.547 3829839.285 3231245.349 3609313.258 2409806.373 1.261134106 1.588727931 1.555330517 1.496862839 1.316767016 1.589272619 1.340873435 1.497760691 1 21.2004858 -2.517890316 0.332320707 0.261164724 1.497799196 0.586324725 0.118202578 35.67312754 1.372075056 19.10672863 0.09324155 0.003034658 2.517890316 1.236634472 VGVSSKPDSS(ph)PVLSPGNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VGVSSKPDSSPVLSPGNK 18 1 Q8N4C8;Q8N4C8-4;Q8N4C8-2;Q8N4C8-3;Q8N4C8-5 Q8N4C8 MINK1 Misshapen-like kinase 1 1 VGVSSKPDS(0.132)S(0.868)PVLSPGNK;VGVSSKPDS(0.183)S(0.817)PVLSPGNK;VGVSSKPDS(0.13)S(0.869)PVLS(0.002)PGNK;VGVSSKPDS(0.148)S(0.852)PVLSPGNK;VGVSSKPDS(0.253)S(0.747)PVLSPGNK 253.83 9.80E-31 4024580000 9715480 5941330 7086940 6696640 8042540 5334620 9772730 6616740 11219630 TRUE FALSE 9107405.449 6381232.255 7255045.563 6868487.12 7410911.35 6874638.194 8307399.862 7442854.554 9347001.271 0.974366557 0.68270369 0.776189641 0.734833228 0.792865127 0.735491308 0.888777012 0.796282609 1 23.15607216 0.622771004 0.68751051 1.001036224 0.769236141 0.355287594 0.08353945 1.25037526 1.085752458 0.080968447 0.028600478 4.195377105 -0.622771004 -0.231800083 VGWEQLLTTIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 217.14 8.70E-11 96805000 144080 155990 131130 120140 128100 111380 137420 142400 106250 FALSE TRUE 135062.29 167539.6619 134240.4655 123222.9958 118039.5427 143533.5979 116815.1467 160178.9535 88516.1886 1.525848459 1.892757297 1.516564005 1.39209559 1.333536211 1.621551946 1.319703758 1.809600662 1 16.43365371 -3.25441961 0.130762063 4.52E-16 1.803785504 0.397351639 0.198227409 79.9411746 1.034269208 24.87419383 1.566389698 0.000556648 3.25441961 1.803785504 VGWSVDFSRPQLGEDEFSYGFDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VGWSVDFSRPQLGEDEFSYGFDGR 24 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;; 203.7 1.07E-24 1154368000 862407 971317 948640 907157 1082067 829523 1108048 961424 1085810 FALSE TRUE 808430.4853 1043234.321 971142.1888 930436.1844 997085.8227 1068992.824 941906.489 1081459.903 904581.2964 0.893706833 1.153278678 1.073581991 1.028582161 1.102262258 1.181754286 1.041262397 1.19553644 1 19.78689064 2.572070445 9.125195794 1.108297545 1.062802345 0.097675605 0.086471474 1.135885614 101.4266479 0.025825686 0.024324885 373.3107062 -2.572070445 -0.045495199 VGYTPDWIFLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VGYTPDWIFLLR 12 0 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ; 126.31 0.00067398 485270000 524540 1145650 637190 571090 1167750 563840 572850 1079270 389510 FALSE TRUE 491709.9777 1230475.118 652304.4477 585745.1363 1076039.625 726611.4548 486956.4606 1214019.235 324498.2647 1.515293089 3.791931274 2.010193948 1.80507941 3.316010416 2.239184408 1.500644267 3.741219499 1 18.30785124 -1.937748665 2.750165432 0.000579152 2.483236714 0.229215225 0.858574105 258942.3541 5798693.406 808392.4246 0.190942878 0.01154121 1.937748665 2.482657562 VHACGVNPVETYIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VHACGVNPVETYIR 14 0 A6NP24;Q08257;C9JH92;Q08257-3 A6NP24 CRYZ Quinone oxidoreductase 0 85.287 0.0077964 110730000 140240 193700 201110 131890 186120 115060 168630 154990 208890 FALSE TRUE 131462.6287 208041.7495 205880.4242 135274.5207 171502.886 148275.9542 143345.497 174340.8427 174024.9095 0.755424204 1.195471097 1.183051465 0.777328493 0.985507686 0.85203868 0.823706775 1.001815448 1 17.4089343 3.243584492 24.9999924 0.892910175 1.096739755 0.134261471 0.143533034 144.4251359 718688.6394 0.038118752 0.050062885 1752.203291 -3.243584492 0.203829579 VHAEEKLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 156.12 4.31E-05 327283000 465378 501829 473847 489330 672950 326993 562160 473291 747250 FALSE TRUE 436250.8217 538984.9413 485086.8746 501887.0362 620099.2215 421390.5708 477869.3268 532382.4232 622529.1476 0.70077172 0.865798723 0.779219538 0.806206486 0.996096687 0.676900949 0.767625626 0.855192765 1 19.24778186 0.921068935 5.565505749 0.999984396 0.802863554 0.342213588 0.087820789 0.669844106 45.32782028 0.078599488 0.019802352 8.338135245 -0.921068935 -0.197120842 VHAELADVLTEAVVDSILAIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VHAELADVLTEAVVDSILAIK 21 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 68.82 0.01992 1302100000 52512 48015 50010 54874 53835 45018 56469 40938 45755 FALSE TRUE 49225.36766 51570.08056 51196.26082 56282.15974 49607.01626 58013.96579 48001.99768 46049.19942 38118.19491 1.29138769 1.352899335 1.343092477 1.47651692 1.301399932 1.52194945 1.259293568 1.208063486 1 15.21819218 1.034738361 1.686774812 1.005293833 1.373012819 0.714664 0.076570215 0.178071608 1.032714739 0.064727216 0.018750979 10.83274103 -1.034738361 0.367718986 VHAIQCDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VHAIQCDVR 9 0 Q16698-2;Q16698;E5RJD2;E5RJG7;E5RFV2 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 61.765 0.087032 397760000 457350 421000 448700 492080 482390 384350 605570 412020 585050 FALSE TRUE 428725.2799 452171.2781 459343.3759 504707.6059 444505.0353 495305.6056 514770.4003 463461.604 487401.3754 0.879614424 0.927718511 0.942433483 1.035507143 0.911989702 1.016217086 1.05615295 0.95088284 1 18.8947508 4.418053195 0.484376836 1.011195408 0.823353936 0.436126189 0.04276292 3.002495468 0.683122218 0.027667695 0.311880366 26185.0372 -4.418053195 -0.187841472 VHAYFAPVT(ph)PPPSVGGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VHAYFAPVTPPPSVGGSR 18 0 J3KTA1;Q96IG2-2;Q96IG2 J3KTA1 FBXL20 F-box/LRR-repeat protein 20 1 VHAYFAPVT(1)PPPSVGGSR;VHAYFAPVT(1)PPPSVGGSR;VHAYFAPVT(1)PPPSVGGSR;VHAYFAPVT(1)PPPSVGGSR 170.91 5.36E-11 1596210000 542510 596240 529885 488003 659020 468670 653170 617150 626890 TRUE FALSE 508555.2675 640386.23 542454.1224 500525.9832 607263.2276 603967.4208 555233.2222 694202.536 522258.0091 0.973762506 1.226187476 1.038670758 0.958388334 1.162764796 1.156454109 1.063139698 1.329232915 1 18.99440319 VHCEELEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VHCEELEK 8 0 Q9UJC3;Q9UJC3-2 Q9UJC3 HOOK1 Protein Hook homolog 1 0 116.25 0.0023075 262320000 258530 305780 271540 318190 330570 217720 368910 251280 356970 FALSE TRUE 242349.0688 328420.2694 277981.057 326355.2941 304608.3657 280572.2296 313595.3703 282652.8611 297389.4009 0.814921675 1.104344231 0.934737607 1.097400557 1.024274452 0.94345067 1.054494106 0.950446991 1 18.1819937 4.75554857 24.51494159 1.015100981 0.814921467 0.520099542 0.059975709 2078.118012 2998821.859 0.01285371 0.371056423 56957.19195 -4.75554857 -0.200179513 VHDAES(ph)S(ph)DEDGYDWGPATDL ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(1)S(1)DEDGYDWGPATDL;VHDAES(1)S(1)DEDGYDWGPATDL 245.96 7.80E-30 197711000 265572 249216 249816 251606 268699 198978 281510 221895 293877 TRUE FALSE 248950.3226 267668.2119 255741.7535 258062.6359 247596.4644 256419.7185 239300.1889 249599.0792 244827.0302 1.016841655 1.09329518 1.044581365 1.054061048 1.011311799 1.047350524 0.977425527 1.019491512 1 17.90140332 2.490967601 0.952809314 0.999101918 1.061589439 0.392896695 0.025170647 0.437215803 0.800987482 0.015050762 0.010848534 309.7188235 -2.490967601 0.062487521 VHDRS(ph)EEEEEEEEEEEEEQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VHDRSEEEEEEEEEEEEEQPR 21 1 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2;V9GYQ9 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR 366.49 1.77E-112 11428300000 1066194 986428 928740 1027796 1117311 920427 1157852 907363 1073441 TRUE FALSE 999462.8208 1059464.155 950770.1514 1054170.985 1029561.901 1186139.333 984242.8416 1020649.268 894276.7624 1.11762137 1.184716186 1.063172154 1.178797247 1.151278826 1.326367164 1.100602054 1.141312523 1 19.77036186 0.661471789 1.808741445 1.000307451 1.15877731 0.343906905 0.069321984 1.731294309 7.65036919 0.063514491 0.017812712 4.586398529 -0.661471789 0.15846986 VHDRS(ph)EEEEEEEEEEEEEQPRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VHDRSEEEEEEEEEEEEEQPRR 22 2 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2;V9GYQ9 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 VHDRS(1)EEEEEEEEEEEEEQPRR;VHDRS(1)EEEEEEEEEEEEEQPRR 403.13 2.00E-152 1458200000 153748 183108 168177 172777 174721 127678 177037 121751 150440 TRUE FALSE 144125.1871 196665.5068 172166.2379 177210.7503 160999.1175 164536.5659 150491.9454 136951.8804 125330.5921 1.149960155 1.569174002 1.373696836 1.413946486 1.284595522 1.312820463 1.200759869 1.092725072 1 16.93537908 1.532619096 0.783829671 0.995980086 1.410485659 0.594875381 0.105324194 0.344740186 0.437893641 0.08978102 0.038065323 34.08937948 -1.532619096 0.414505573 VHEDS(ph)TSPAVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VHEDSTSPAVAK 12 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 VHEDS(0.598)T(0.098)S(0.304)PAVAK 169.98 0.00015 0 155930 119280 153270 144330 160760 112170 154470 127690 175910 TRUE FALSE 146170.6196 128111.6153 156905.6368 148033.7522 148134.5581 144551.6581 131308.6575 143632.3776 146549.4846 0.997414764 0.874186734 1.070666589 1.010128098 1.010815961 0.986367564 0.896002179 0.98009473 1 17.16102837 -0.304962427 7.524209219 0.999999999 0.973668633 0.008844247 0.056581291 0 0 0.055894401 0.013174437 0.495493057 0.304962427 -0.026331366 VHEDSTS(ph)PAVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VHEDSTSPAVAK 12 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 VHEDS(0.01)T(0.221)S(0.769)PAVAK 103.76 0.0014242 523010000 555950 518000 620280 589090 624290 428780 631880 536910 687840 TRUE FALSE 521154.0819 556353.259 634993.3345 604207.0467 575260.7817 552561.8253 537135.4601 603944.3954 573035.0604 0.90946282 0.97088869 1.108123008 1.054398044 1.003884093 0.964272282 0.937351826 1.053939693 1 19.12826389 2.446040399 6.683710824 0.978505376 1.021188296 0.002983418 0.059371236 0.456179164 64.93379101 0.021346137 0.01800937 279.2803623 -2.446040399 0.04268292 VHEDSTSPAVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VHEDSTSPAVAK 12 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 0 98.353 0.0017268 0 206510 213890 223340 221310 280140 175710 258510 226930 230280 FALSE TRUE 193584.9077 229726.6382 228637.7303 226989.1893 258138.9344 226434.6246 219748.8254 255262.71 191844.7803 1.009070496 1.197460977 1.191784993 1.183191895 1.345561417 1.180301201 1.145451156 1.330568961 1 17.54957999 4.738895686 6.10700637 1.201943249 1.004159996 0.275013229 0.095490843 0.156142324 29.58659906 0.019990969 0.128103074 54814.52892 -4.738895686 -0.197783253 VHELNEEIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VHELNEEIGK 10 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2;B8ZZ09;Q9NQ29-3;Q9NQ29;Q9NQ29-2;A8MYV2;B8ZZ10 Q9Y383;Q9NQ29-3 LUC7L2;LUC7L Putative RNA-binding protein Luc7-like 2;Putative RNA-binding protein Luc7-like 1 0 ;;;;; 164.31 6.20E-06 4711130000 11801760 7937650 8759690 8534470 9694060 6602320 10922890 8090240 12828240 FALSE TRUE 11063108.91 8525361.865 8967473.983 8753478.949 8932727.632 8508302.604 9285104.048 9100324.273 10687123.87 1.035181125 0.797722752 0.839091424 0.819067792 0.835840189 0.796126508 0.868812242 0.851522298 1 23.34937031 0.297654194 1.483527212 1.000037858 0.844751241 0.296361295 0.068436318 6.921389699 13.39689371 0.058794417 0.016911851 1.984514123 -0.297654194 -0.155286617 VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_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 104.03 6.49E-06 387160000 264264 219967 243232 256485 272925 217467 298498 234802 233344 TRUE FALSE 247724.188 236253.5856 249001.5779 263066.8393 251490.5714 280246.1926 253740.996 264117.5466 194397.3789 1.27431856 1.215312608 1.280889584 1.353242728 1.293693222 1.441615078 1.305269636 1.358647673 1 17.56864924 -1.045404513 4.527258709 0.99998526 1.309169625 0.727437869 0.060562676 9.57E-06 2.02E-06 0.062253213 0.014672524 0.090073178 1.045404513 0.309184365 VHFALLGTWDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VHFALLGTWDEK 12 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 62.338 0.078474 241320000 168150 175470 149940 115040 211740 97416 147110 151830 251090 FALSE TRUE 157625.7917 188461.9814 153496.6476 117992.1212 195110.7945 125538.4178 125052.2212 170786.3097 209181.4569 0.753536159 0.90094975 0.733796628 0.564065873 0.932734657 0.600141235 0.597816953 0.816450522 1 17.67439544 3.725843013 4.689079241 0.715749211 0.833422871 0.00845315 0.14883792 0.403060894 23.8019221 0.036188025 0.06209588 5319.1595 -3.725843013 0.11767366 VHFEESSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VHFEESSK 8 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;; 126.41 0.0012203 2262770000 3337850 2882990 2866350 2591680 2939050 2171160 3507050 3122490 2579410 FALSE TRUE 3128939.927 3096449.579 2934341.176 2658186.897 2708228.869 2797938.646 2981200.41 3512339.75 2148889.807 1.456072767 1.44095317 1.365514958 1.237004749 1.26029211 1.302039144 1.387321211 1.634490395 1 21.03516007 3.79260008 2.394003785 1.324274718 1.445063613 0.116135562 0.15581628 0.697918152 7.896271905 0.040092225 0.082346604 6202.975697 -3.79260008 0.120788895 VHFEESSKLEDLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VHFEESSKLEDLLR 14 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;;; 256.57 1.54E-24 1602621000 3298605 3116202 3068785 3249103 3633593 2114823 3428315 3020376 3952706 FALSE TRUE 3092151.201 3346928.838 3141578.029 3332480.484 3348225.263 2725338.069 2914270.993 3397476.592 3292973.833 0.939014811 1.016384887 0.954024596 1.011997256 1.016778582 0.827622145 0.884996705 1.031735071 1 21.65095962 2.288642966 24.99991859 0.918524632 0.988083023 0.118916475 0.062009218 152.9055914 76326.07501 0.02039901 0.017067013 194.3761456 -2.288642966 0.069558391 VHFTAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VHFTAER 7 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;; 143.37 0.0024264 5390240000 1230217 3641350 1126158 1129367 3774460 667183 1312761 3110540 3179500 FALSE TRUE 1153219.914 3910959.343 1152871 1158348.469 3478029.137 859787.9013 1115924.675 3498897.766 2648820.91 0.43537104 1.476490664 0.435239315 0.437307205 1.313048053 0.324592689 0.4212911 1.320926512 1 21.33691887 4.999189861 24.98409496 0.795769992 0.091437961 0.072196885 0.430655434 54939.03167 438339.8382 0.09674515 1086818.922 99813.63241 -4.999189861 -0.704332031 VHGEPTS(ph)DLS(ph)DID ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VHGEPTSDLSDID 13 0 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 2 VHGEPT(0.119)S(0.881)DLS(1)DID;VHGEPT(0.076)S(0.924)DLS(1)DID 173.76 3.09E-05 1014890000 1125980 1079350 1050180 1037050 1123440 814590 1235590 861700 1027630 TRUE FALSE 1055506.922 1159266.197 1075090.766 1063662.459 1035209.554 1049748.909 1050324.75 969285.1418 856111.9143 1.232907642 1.354105903 1.255782974 1.242433893 1.209198864 1.226181871 1.226854495 1.132194431 1 19.70743988 0.062603455 0.248867168 0.900247358 1.323655918 0.839283532 0.036627645 2.328602049 0.24995723 0.278283171 0.070569612 1.155057102 -0.062603455 0.42340856 VHGLPT(ph)TSPSGMNMAELAQQVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VHGLPTTSPSGMNMAELAQQVVK 23 0 B1AKB5;B0QYS6;B0QYS7;P19484-2;P19484 B1AKB5 TFEB Transcription factor EB 1 VHGLPT(0.333)T(0.333)S(0.333)PS(0.001)GMNMAELAQQVVK;VHGLPT(0.325)T(0.325)S(0.325)PS(0.026)GMNMAELAQQVVK 224.21 4.95E-32 363860000 295190 246340 250220 245710 291710 260790 336950 265930 400990 TRUE FALSE 276714.5848 264579.2699 256155.3366 252015.3346 268800.2733 336075.8394 286427.4756 299131.9459 334062.1785 0.828332576 0.79200606 0.766789397 0.754396489 0.804641443 1.006027803 0.857407674 0.895437931 1 18.34975713 2.37126646 7.309964259 0.922637025 0.783075681 0.699686378 0.048530251 0.127033498 7.880100409 0.015702771 0.013101922 235.107487 -2.37126646 -0.139561344 VHHEPQLSDK ddPTM_SK-BR-3_Pertuzumab_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 ; 131.43 0.00025026 215120000 630180 530090 547750 565680 580320 416920 709840 522520 568020 FALSE TRUE 590738.1587 569338.4152 560742.8887 580196.3065 534744.0081 537278.0359 603406.0818 587757.7722 473213.7925 1.248353637 1.20313149 1.18496734 1.226076492 1.130026252 1.135381184 1.275123615 1.242055455 1 18.8521326 -1.196400635 3.820129214 0.999826772 1.204072957 0.658273569 0.046551269 5.832130623 11869093.1 3815.947116 0.010912477 0.063620835 1.196400635 0.204246184 VHIAEDQLIGVELLSVLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VHIAEDQLIGVELLSVLHR 19 0 Q9P2D3;Q9P2D3-3 Q9P2D3 HEATR5B HEAT repeat-containing protein 5B 0 55.437 0.05964 6360300 2197.4 6423.7 5323.5 7100 7341.2 5208.1 4807.8 6505.6 4746.7 FALSE TRUE 2059.868656 6899.317432 5449.775934 7282.19802 6764.651765 6711.593924 4086.915023 7317.838481 3954.445105 0.520899545 1.744699256 1.37813923 1.841522091 1.710645005 1.697227739 1.03349899 1.85053485 1 11.94925955 -1.269959228 4.507299774 0.999752669 1.482826993 0.111705312 0.417462792 0.000931452 0.000150867 0.362869335 0.08548591 0.053708222 1.269959228 0.483074324 VHIDIGADGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VHIDIGADGR 10 0 P31942;P31942-3;P31942-2;P31942-4;P31942-5;P31942-6 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;; 160.53 7.35E-06 1613349000 782993 1116950 849840 832440 1104330 680087 892790 922560 1146180 FALSE TRUE 733986.8658 1199650.14 869998.6061 853801.8197 1017600.376 876417.0766 758924.4278 1037743.647 954875.1534 0.768673123 1.256342398 0.911112414 0.894150211 1.065689449 0.917834204 0.794789167 1.086784637 1 19.86495259 3.726940923 24.99933356 0.935947848 1.058257125 0 0.145067682 17.05981247 2365392.125 0.035068803 0.058342634 5332.623506 -3.726940923 0.122309277 VHIEIGPDGR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;;; 194.12 4.99E-07 15059860000 6794400 7678220 6995540 6358710 7750990 5450430 6832950 7099750 8063220 FALSE TRUE 6369150.632 8246723.398 7161477.512 6521885.264 7142258.511 7023880.661 5808412.581 7986169.416 6717416.492 0.948154791 1.227662958 1.066105924 0.9708919 1.063244853 1.045622327 0.864679537 1.188875132 1 22.67947505 3.472231181 5.104012669 1.009020778 1.118428736 0.040342078 0.105385878 0.285643488 21.56093065 0.027122958 0.039398853 2966.410029 -3.472231181 0.109407959 VHIPNDDAQFDASHCDSDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VHIPNDDAQFDASHCDSDK 19 0 Q16576;E9PC52;Q16576-2;Q5JP01;C9J7L0 Q16576 RBBP7 Histone-binding protein RBBP7 0 ; 189.44 8.10E-15 364950000 489670 291120 403110 374130 375170 301660 472500 326850 295740 FALSE TRUE 459022.4288 312674.8277 412671.9596 383730.8092 345705.6616 388744.345 401653.0115 367657.942 246379.0834 1.863073855 1.269080246 1.674947215 1.557481276 1.403145335 1.577830145 1.630223661 1.492244946 1 17.91052026 0.954731139 20.77286933 0.999999998 1.548664836 0.557790591 0.156958568 802.7615197 368370.8408 0.136814599 0.03420365 9.010131697 -0.954731139 0.548664838 VHIPNDDAQFDASHCDSDKGEFGGFGSVTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VHIPNDDAQFDASHCDSDKGEFGGFGSVTGK 31 1 Q16576;Q16576-2;Q5JP01 Q16576 RBBP7 Histone-binding protein RBBP7 0 77.522 0.0016203 128390000 328380 225790 278610 274980 302680 226090 363600 240900 380540 FALSE TRUE 307827.282 242507.7265 285218.7608 282036.4523 278908.7338 291358.5127 309081.5555 270976.8953 317025.4156 0.970986132 0.764947271 0.899671593 0.88963357 0.879767741 0.919038343 0.974942513 0.854748175 1 18.27423898 1.693320249 0.354749075 0.995555852 0.843787685 0.192975824 0.061002956 1.475036897 0.571457962 0.079134605 0.07401817 49.35376043 -1.693320249 -0.151768167 VHLVGIDIFTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VHLVGIDIFTGK 12 0 P63241;P63241-2;I3L397;I3L504;Q6IS14;F8WCJ1;C9J7B5;C9J4W5;Q9GZV4 P63241 EIF5A;EIF5AL1;EIF5A2 Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A;Eukaryotic translation initiation factor 5A-1-like;Eukaryotic translation initiation factor 5A-2 0 ;; 199.7 1.69E-07 8906829000 23236919 22718400 24157040 22403102 26156355 19925837 29131544 21982323 28343536 FALSE TRUE 21782561.72 24400493.97 24730056.4 22978003.53 24102140.39 25678102.67 24763539.42 24726864.42 23612816.74 0.922488916 1.033358038 1.047314968 0.973115736 1.020722799 1.087464616 1.04873297 1.047179788 1 24.49306681 2.461005241 24.29956564 1.051492785 1.008234524 0.231445946 0.040436244 271.4569016 409296.1453 0.013529306 0.011322782 289.0714765 -2.461005241 -0.043258261 VHMFEAHSDYIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VHMFEAHSDYIR 12 0 P35606;P35606-2;D6R997;D6RBT6;D6RBZ7;D6RCL6;D6RBG7 P35606 COPB2 Coatomer subunit beta 0 ;;; 199.82 9.67E-08 697080000 205404 406260 199891 243430 404454 131462 217890 343966 320169 FALSE TRUE 192548.1303 436339.9131 204632.5089 249676.8259 372689.8143 169412.9453 185219.4173 386910.9123 266730.7255 0.721882078 1.635881701 0.767187614 0.936063235 1.397251155 0.63514597 0.694406004 1.450567465 1 18.0250245 2.233591956 24.99988012 0.88528195 1.11454856 0.027541293 0.348029765 312.509765 1572379.531 0.122848121 0.093572684 171.2347705 -2.233591956 0.22926661 VHNDAQS(ph)FDYDHDAFLGAEEAK ddPTM_SK-BR-3_Pertuzumab_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 1 VHNDAQS(0.797)FDY(0.203)DHDAFLGAEEAK;VHNDAQS(0.544)FDY(0.456)DHDAFLGAEEAK;VHNDAQS(1)FDYDHDAFLGAEEAK 147.85 1.25E-07 682550000 308424 371443 269290 436180 116272 141118 756540 346875 99238 TRUE FALSE 289120.2924 398945.0262 275677.686 447373.1173 107140.4661 181856.4757 643103.8504 390183.1073 82674.5367 3.497089962 4.825488502 3.334493267 5.411256417 1.295930651 2.19966731 7.778741509 4.719507637 1 16.33515544 -2.838176504 11.07961307 4.024189859 4.082090198 0 2.057438083 0 0 0 0.440348224 0.001451522 2.838176504 0.057900339 VHNDAQSFDYDHDAFLGAEEAK ddPTM_SK-BR-3_Pertuzumab_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 ;; 180.45 3.07E-17 2914470000 1661760 1191040 1369160 1344520 1418000 1030880 1625340 1095490 1373440 FALSE TRUE 1557753.408 1279225.841 1401637.122 1379022.659 1306636 1328478.321 1381635.356 1232264.338 1144203.991 1.361429797 1.11800505 1.224988842 1.205224479 1.141960708 1.161050242 1.207507898 1.076962104 1 20.12591285 -4.999999998 0.112880307 0.377776694 1.291100938 0.558195283 0.063955089 132.0256486 0.984608744 18.75159472 0.69140314 1.00E-05 4.999999998 0.913324244 VHNGMDDLILDGHNILDGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 90.316 0.00113 7689500 6392.3 6606.7 5981.4 5339.3 6345.3 4597.2 8294.8 7207 9129.4 FALSE TRUE 5992.217354 7095.866942 6123.281633 5476.315477 5846.965734 5924.337011 7051.071745 8106.809815 7605.644162 0.787864542 0.932973827 0.805097044 0.720033091 0.76876667 0.778939546 0.927084096 1.065893913 1 12.89285473 1.512790359 3.450087161 1.029062745 0.811446916 0.742100847 0.057225107 0.123322178 3.118232888 0.043723667 0.016689986 32.56794519 -1.512790359 -0.217615829 VHNNS(ph)PDTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VHNNSPDTSR 10 0 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 1 VHNNS(1)PDTSR;VHNNS(0.999)PDT(0.001)SR;VHNNS(0.974)PDT(0.013)S(0.013)R;VHNNS(1)PDTSR;VHNNS(1)PDTSR 233 4.93E-12 1076823000 806786 771712 803393 788553 765777 742841 883890 674701 653599 TRUE FALSE 756290.7044 828850.3594 822449.8613 808788.605 705635.9634 957287.1377 751358.9001 758938.9051 544509.1045 1.38894042 1.52219743 1.510442809 1.485353685 1.295912148 1.758073703 1.37988308 1.393803885 1 19.05459665 0.71229531 1.630111844 1.000910679 1.490391018 0.605753092 0.120599055 0.63387301 2.606148114 0.101789221 0.029133678 5.155791067 -0.71229531 0.489480339 VHPAVVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VHPAVVIR 8 0 J3KTJ3;P62829;J3KT29;J3QQT9;C9JD32 J3KTJ3 RPL23 60S ribosomal protein L23 0 ; 121.29 0.0014395 1068850000 1199100 1645810 1303570 1211310 1837600 891860 1223800 1340070 1607960 FALSE TRUE 1124050.471 1767667.485 1334491.296 1242394.265 1693282.309 1149325.504 1040302.551 1507380.689 1339581.088 0.839105957 1.319567364 0.99620046 0.92744984 1.264038679 0.85797382 0.776587965 1.125262743 1 20.35335048 2.207267559 24.99983013 0.903566378 1.086992882 0.105362464 0.169060252 298.7468035 238665.28 0.059833545 0.044194152 161.1638224 -2.207267559 0.183426505 VHPEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VHPEGK 6 0 P62195-2;P62195;J3QSA9;J3KRP2;J3QLH6;J3QRW1 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ;; 91.584 0.047726 438140000 2339790 1939420 2201380 2023290 2049650 1726200 2315570 1962220 2272280 FALSE TRUE 2193346.721 2083016.675 2253597.773 2075211.047 1888678.757 2224525.917 1968371.775 2207207.486 1893021.789 1.158648429 1.100365927 1.190476405 1.096242557 0.997705768 1.175119025 1.039804078 1.16597046 1 20.85225959 3.025132141 18.51025964 1.079596866 1.144828583 0.223294945 0.062771012 18.46138295 13594.82333 0.01616389 0.01931453 1059.576069 -3.025132141 0.065231716 VHPEPGTWDSFLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VHPEPGTWDSFLEK 14 0 P50225;H3BRY5;P50225-2;H3BQX5 P50225 SULT1A1 Sulfotransferase 1A1;Sulfotransferase 0 109.99 0.00073554 78167000 101130 187680 151710 170650 160180 146510 144110 153850 88345 FALSE TRUE 94800.45382 201576.0225 155308.6328 175029.1679 147600.1089 188805.0586 122502.0434 173058.5112 73599.64877 1.288055791 2.738817723 2.110181712 2.378125043 2.005445833 2.565298364 1.66443788 2.351349688 1 16.16741126 -0.897363056 0.474168545 0.635211075 2.22222791 0.394443195 0.431115494 14.09821022 2.163932727 7.703090564 0.196664255 0.126659259 0.897363056 1.587016834 VHPETYEWAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VHPETYEWAR 10 0 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 136.96 0.00010389 195890000 31686 26312 31533 33027 17645 30150 27447 19404 36130 FALSE TRUE 29702.82982 28260.16786 32280.97765 33874.52873 16259.23288 38853.81556 23331.57716 21826.63211 30099.66959 0.98681581 0.938886315 1.072469502 1.125411979 0.540179779 1.290838607 0.775143962 0.725145239 1 14.87746003 VHQFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VHQFEK 6 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ;;;; 155.73 0.0098399 1361180000 3312420 3078620 3116910 3263270 3518420 2318190 3604790 3134990 3317860 FALSE TRUE 3105101.545 3306564.228 3190844.577 3347011.033 3242097.486 2987413.82 3064285.205 3526400.402 2764087.732 1.123373006 1.196258784 1.154393379 1.210891751 1.172935811 1.080795586 1.108606348 1.275791778 1 21.39837198 2.328487528 11.24331224 1.12199003 1.174483642 0.127647494 0.070890646 0.911986061 107.833085 0.022295131 0.018645644 213.0529381 -2.328487528 0.052493612 VHQLYETIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VHQLYETIQR 10 0 Q13561;Q13561-3;Q13561-2;H0YI98 Q13561 DCTN2 Dynactin subunit 2 0 128.03 0.00034028 333620000 129450 198760 165280 229170 234350 163940 164190 214270 217200 FALSE TRUE 121347.9556 213476.3972 169200.5197 235050.8902 215945.0963 211266.8167 139571.2338 241022.0812 180947.9168 0.670623667 1.17976709 0.935078572 1.298997492 1.193410237 1.167555948 0.771333742 1.331996993 1 17.46521497 4.746531201 24.5620573 1.087390181 0.670623404 0.390285887 0.170469288 864.8877989 2665148.332 0.039198215 0.426785197 55786.768 -4.746531201 -0.416766777 VHRPRS(ph)PILEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VHRPRSPILEEK 12 2 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2;A0A0A0MR81 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 VHRPRS(1)PILEEK;VHRPRS(1)PILEEK 98.508 0.0022539 285720000 152809 252960 184453 210470 403560 95841 179940 180238 899260 TRUE FALSE 143244.9575 271689.4216 188828.3123 215871.0165 371866.0255 123508.7409 152959.6675 202741.1111 749167.6966 0.191205465 0.362655014 0.252050793 0.288147791 0.49637221 0.164861274 0.204172802 0.270621801 1 19.51492917 -1.36195886 3.029375884 1.008377306 0.279906185 0.850191108 0.0951453 10539109.24 13314264.4 782199.7338 0.023275203 0.043455139 1.36195886 -0.728471121 VHS(ph)PCPTSGSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VHSPCPTSGSEK 12 0 Q96LT9-2;Q96LT9;X6RLP6 Q96LT9-2 RNPC3 RNA-binding protein 40 1 VHS(1)PCPTSGSEK;VHS(1)PCPTSGSEK 89.466 0.0060593 238510000 365050 212364 276550 271633 265910 208032 343310 247690 240615 TRUE FALSE 342202.1721 228087.6515 283109.8966 278603.5627 245026.5012 268087.4613 291833.8526 278614.6417 200454.8021 1.707128832 1.137850773 1.412337812 1.389857263 1.222352863 1.337396054 1.455858626 1.389912533 1 17.61291745 -1.060177885 3.858563255 0.999918105 1.362961133 0.385292849 0.149839959 16184170.55 35039964.74 18758.75742 0.032819632 0.087060692 1.060177885 0.363043029 VHSDFTAAATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VHSDFTAAATR 11 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ;;; 168.3 1.82E-05 1104610000 398022 581332 457186 443495 605601 362292 482715 509565 537636 FALSE TRUE 373110.5135 624374.4262 468030.6678 454875.8325 558039.5403 466879.8191 410336.3671 573185.3119 447901.0783 0.833019905 1.394000721 1.044942043 1.015572086 1.245899078 1.042372617 0.916131679 1.27971407 1 18.77282061 2.04864525 24.98641814 1.036784935 1.134207345 0 0.172449361 314.0407941 161304.1786 0.060646463 0.04479037 111.8523853 -2.04864525 0.097422411 VHSFPTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VHSFPTLK 8 0 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ; 186.13 0.00020911 4108400000 4611500 5136100 4527200 4621700 5380700 3621100 5821000 4643200 5171700 FALSE TRUE 4322874.447 5516382.188 4634587.322 4740300.647 4958121.527 4666452.786 4948195.09 5222913.741 4308509.86 1.003334004 1.280345727 1.07568219 1.100218127 1.150774093 1.083078126 1.148470179 1.21223205 1 22.03875755 VHSPSGAVEECHVSELEPDKYAVR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 427.52 6.09E-180 3314450000 1757430 2863400 2603560 2801380 3157450 2335600 3693810 2661030 3117660 FALSE TRUE 1647435.593 3075409.115 2665317.673 2873268.154 2909476.614 3009849.805 3139957.482 2993265.453 2597302.405 0.63428717 1.184078184 1.026186888 1.106250912 1.120191707 1.158836876 1.208930264 1.152451654 1 21.30858257 4.742641751 24.96047707 1.126603536 0.634286975 0.844926448 0.065281826 149.7284415 915713.0413 0.015535673 0.119596648 55289.38401 -4.742641751 -0.492316561 VHTGERPHQCPECGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VHTGERPHQCPECGK 15 1 Q9BWE0;Q9BWE0-4;C9JZE3;C9JYJ8 Q9BWE0 REPIN1 Replication initiator 1 0 58.21 0.074692 36412000 24959 17948 23891 23220 20663 19822 27337 20482 25356 FALSE TRUE 23396.86074 19276.88859 24457.7058 23815.86451 19040.21133 25544.28962 23238.07063 23039.22279 21123.91979 1.10760034 0.912562099 1.157820425 1.127435852 0.901357869 1.209258976 1.100083264 1.090669867 1 14.36658995 3.968481346 24.59738001 1.090920749 1.001030085 0.087001547 0.096195023 467.4774723 1330891.332 0.022490847 0.041357946 9299.965675 -3.968481346 -0.089890664 VHTGFDQHEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VHTGFDQHEQK 11 0 O96013;O96013-4;O96013-2;O96013-3;M0R2X4;M0R0L9;M0R3G6 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ; 158.04 1.75E-05 266250000 359350 366050 339460 333290 384770 277570 399870 323750 428290 FALSE TRUE 336858.925 393152.7229 347512.1515 341842.7857 354551.7163 357699.953 339913.2057 364170.9002 356805.6321 0.944096434 1.101868041 0.97395366 0.958064433 0.993683071 1.002506465 0.952656503 1.020642241 1 18.44477886 3.73100724 24.80643995 0.982371829 1.035349409 0.094903558 0.042953818 215.6909184 1376856.045 0.009961791 0.017156222 5382.787555 -3.73100724 0.05297758 VHTVEDYQAIVDAEWNILYDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VHTVEDYQAIVDAEWNILYDK 21 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 204.31 5.37E-22 122775000 203427 130346 165510 148801 124108 137576 187801 145896 92125 FALSE TRUE 190694.8672 139996.9535 169435.9754 152619.4856 114361.0583 177291.9578 159641.9835 164111.4368 76748.74235 2.484664391 1.82409443 2.207671034 1.988560085 1.490070779 2.310030789 2.080059928 2.138294801 1 16.22785549 -1.203177524 4.493321532 0.999723994 2.050262833 0.604710775 0.270467384 9198874.648 2463216.143 25021.19182 0.057556292 0.062635778 1.203177524 1.050538839 VHTVEDYQAIVDAEWNILYDKLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VHTVEDYQAIVDAEWNILYDKLEK 24 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 278.67 2.35E-52 2900800000 4969600 3662400 4258600 4224900 5012500 3001400 5344600 3793700 5063900 FALSE TRUE 4658561.607 3933567.907 4359616.003 4333318.087 4618838.469 3867855.456 4543226.847 4267351.796 4218702.376 1.104264106 0.932411807 1.033402126 1.027168475 1.094848145 0.916835347 1.076925187 1.011531845 1 22.00836788 3.714972123 23.98344534 1.025835231 0.999116043 0 0.06297318 890.1780511 1757297.526 0.01505819 0.023548687 5187.66739 -3.714972123 -0.026719188 VHTVMTLEQQDMVCYTAQTLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VHTVMTLEQQDMVCYTAQTLVR 22 0 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 166.21 1.19E-11 42762000 26294 23515 24040 24476 27363 22012 28108 20753 23993 FALSE TRUE 24648.30548 25256.07507 24610.24015 25104.0956 25214.02036 28366.50707 23893.46634 23344.05773 19988.4133 1.233129669 1.263535764 1.2312253 1.255932386 1.261431809 1.419147515 1.195365834 1.16787948 1 14.28687633 0.962586449 1.881584167 1.00276796 1.268704219 0.697365867 0.056914614 0.206267591 1.536932315 0.051593677 0.014566987 9.174585431 -0.962586449 0.265936259 VHVGDEDFVHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VHVGDEDFVHLR 12 0 P04080 P04080 CSTB Cystatin-B 0 ;;;;; 231.7 1.63E-12 2572421000 1539218 1617422 1427387 1357742 1381160 1208069 2138995 1437005 2176046 FALSE TRUE 1442881.093 1737177.608 1461245.294 1392583.958 1272689.265 1556818.909 1818272.557 1616418.237 1812849.865 0.795918692 0.958257847 0.806048709 0.768173904 0.702037874 0.858768803 1.002991253 0.891644845 1 20.78982802 1.891752103 5.559232812 0.960589283 0.821811376 0.504631481 0.070730216 0.228151345 9.679765719 0.033952474 0.020335366 77.93851073 -1.891752103 -0.138777907 VHVQFFDDS(ph)PTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VHVQFFDDSPTR 12 0 P52701;P52701-2;A0A087WWJ1;A0A494C0M1;F8WAX8;C9J7Y7;C9J8Y8;C9JH55 P52701 MSH6 DNA mismatch repair protein Msh6 1 VHVQFFDDS(1)PTR;VHVQFFDDS(0.995)PT(0.005)R;VHVQFFDDS(0.999)PT(0.001)R;VHVQFFDDS(0.998)PT(0.002)R;VHVQFFDDS(0.738)PT(0.262)R;VHVQFFDDS(0.999)PT(0.001)R 226.39 9.94E-12 1435278000 1292231 1380405 1435702 1396424 1576633 1338055 1683821 1446246 1834310 TRUE FALSE 1211352.568 1482611.623 1469757.529 1432258.604 1452810.604 1724329.757 1431347.673 1626812.997 1528151.811 0.792691249 0.970199173 0.961787644 0.9372489 0.950697826 1.128375954 0.9366528 1.064562424 1 20.54335644 5.554589543 1.103868024 0.995295975 2.72E-32 0.517752212 0.060792333 7.094870513 1.888144389 0.016237563 12.68111238 358582.8735 -5.554589543 -0.995295975 VHVTQEDFEMAVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VHVTQEDFEMAVAK 14 0 P62195-2;P62195 P62195-2 PSMC5 26S protease regulatory subunit 8 0 82.102 0.011652 70981000 118320 138980 132900 101100 126610 99844 139810 111540 111300 FALSE TRUE 110914.5624 149270.2238 136052.4508 103694.3972 116666.5613 128667.342 118846.7884 125466.0145 92723.31097 1.196188545 1.609845704 1.467295002 1.118320691 1.258222556 1.387648269 1.281735814 1.353122674 1 16.50064446 -4.330456703 0.126553901 2.50E-16 1.530660474 0.324861618 0.142389426 126.5267834 1.202773 33.35597555 1.234008038 4.67E-05 4.330456703 1.530660474 VIADNVKDWSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIADNVKDWSK 11 1 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3 P60174 TPI1 Triosephosphate isomerase 0 131.69 0.00018063 467500000 332670 234970 412770 392090 382830 456470 378720 207330 343200 FALSE TRUE 311848.7785 252367.4233 422561.0993 402151.6932 352764.0761 588245.4788 321934.4519 233215.6069 285917.7028 1.090694194 0.882657565 1.477911634 1.406529534 1.233795853 2.057394393 1.125968937 0.815673897 1 18.12524042 1.478185635 24.99999999 0.928826817 1.335679461 0.271552278 0.305435621 0.190305864 4264.747431 0.166909901 0.077269947 30.07361495 -1.478185635 0.406852644 VIAIDSDAES(ph)PAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIAIDSDAESPAKR 14 1 P28749 P28749 RBL1 Retinoblastoma-like protein 1 1 VIAIDSDAES(1)PAKR 138.91 7.77E-06 337110000 249740 207010 221560 221940 233770 201350 300410 218330 236130 TRUE FALSE 234109.2192 222337.2358 226815.5078 227635.3561 215410.6472 259476.4764 255366.3094 245588.9811 196718.3775 1.190072947 1.130231138 1.152996027 1.157163652 1.095020454 1.319025094 1.298131433 1.248429273 1 17.58577222 2.24497221 24.99950459 1.250114183 1.144695356 0.082984767 0.091027856 197.9254434 771734.241 0.028379892 0.0232136 175.7811131 -2.24497221 -0.105418827 VIAINVDDPDAANYNDINDVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VIAINVDDPDAANYNDINDVKR 22 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;;;; 280.39 1.99E-45 16031760000 8285370 7136350 7791450 7602980 8211980 6180550 9670220 6918710 9386560 FALSE TRUE 7766803.482 7664732.779 7976266.873 7798085.339 7567044.216 7964774.452 8220260.285 7782526.173 7819882.497 0.9932123 0.980159585 1.019998303 0.997212598 0.967667253 1.018528661 1.051199975 0.995222905 1 22.8987155 2.024591828 24.61141201 1.024588468 0.994109666 0.222176105 0.020411223 207.8378972 208002.6836 0.007382601 0.005452178 105.8258652 -2.024591828 -0.030478801 VIAPWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VIAPWR 6 0 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ; 141.66 0.027043 194890000 178213 204526 189364 201900 212426 173408 225708 188332 201638 FALSE TRUE 167058.9664 219669.3178 193855.8035 207081.0958 195742.9188 223468.0746 191865.1808 211845.6648 167983.3152 0.994497378 1.307685335 1.154018203 1.232748 1.165252148 1.330299228 1.142168081 1.261111346 1 17.35795842 -0.219637947 8.350527056 1.000000004 1.205481054 0.295218039 0.095831415 0 0 0.079034432 0.018628594 0.603062124 0.219637947 0.205481051 VICILSHPIKNTNDANSCQIIIPQNQVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VICILSHPIKNTNDANSCQIIIPQNQVNR 29 1 P50395;P50395-2;Q5SX91 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 43.895 0.079895 218500000 23499 32077 30622 29010 47317 29131 37646 27292 74888 FALSE TRUE 22028.23954 34452.01446 31348.3683 29754.44571 43600.91369 37540.6468 32001.33179 30699.46628 62388.70901 0.353080548 0.552215537 0.502468617 0.476920362 0.698859046 0.601721808 0.512934669 0.492067664 1 15.92899734 -5 0.290102916 4.643451271 0.502473675 0.745969967 0.087625636 124.5954339 1.174055973 274.8996912 0.089847427 1.00E-05 5 -4.140977595 VIDFDENTALDDAEEESFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIDFDENTALDDAEEESFR 19 0 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 133.14 2.86E-05 19291000 17167 15724 17475 20055 16844 15600 22089 13299 21116 FALSE TRUE 16092.54811 16888.22132 17889.51525 20569.64525 15521.14019 20103.46676 18776.95951 14959.40942 17591.60319 0.914785761 0.960016045 1.016934901 1.169287701 0.882303905 1.142787644 1.067381939 0.85037215 1 14.10259935 4.21370431 1.768196233 1.030706613 0.92060758 0.099803157 0.099496122 0.83018136 4.634768603 0.025055332 0.10829662 16357.02473 -4.21370431 -0.110099033 VIDFDENTALDDAEEESFRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VIDFDENTALDDAEEESFRK 20 1 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 ; 298.76 1.58E-54 96952000 109633 98032 100414 106693 115797 86353 142122 98896 156622 FALSE TRUE 102771.2662 105290.3913 102795.8675 109430.923 106702.7707 111281.7093 120812.1255 111243.3833 130480.7764 0.787635306 0.80694179 0.787823849 0.838674677 0.817766216 0.852859037 0.925899806 0.852565308 1 16.99347775 1.210904537 0.35728544 1.012037234 0.778447496 0.842944117 0.026090139 0.458830588 0.183887908 0.041016058 0.027185183 16.25191481 -1.210904537 -0.233589738 VIDGPHSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VIDGPHSGR 9 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 0 ; 103.88 0.0033509 505980000 331780 395220 380300 394290 429390 333190 435420 380090 468100 FALSE TRUE 311014.482 424482.5 389320.8956 404408.1489 395667.4415 429376.5441 370132.8132 427545.0732 389971.086 0.797532159 1.088497366 0.998332722 1.037020855 1.014607123 1.101047128 0.949128863 1.0963507 1 18.57300764 4.747021795 24.97887203 1.032440235 0.79753204 0.701279118 0.048795877 570.9761658 1685583.033 0.010391578 0.121632079 55849.82219 -4.747021795 -0.234908196 VIDPATATSVDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIDPATATSVDLR 13 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 129.82 0.00034724 112340000 102280 119920 112230 98338 124570 91181 122520 97689 122250 FALSE TRUE 95878.47738 128799.0016 114892.1486 100861.5196 114786.7747 117503.4745 104149.2634 109885.6867 101845.6852 0.941409321 1.264648584 1.128100305 0.990336697 1.127065662 1.15374033 1.022618319 1.078942976 1 16.63602534 1.364287469 0.464290337 0.998041525 1.133616328 0.043929889 0.092751434 1.783339866 1.053360022 0.10185609 0.062688283 23.135957 -1.364287469 0.135574803 VIDTLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VIDTLHR 7 0 Q9H993 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 ; 132.29 0.0033837 469170000 1037560 1121360 1115070 1108640 1239960 897120 1289020 1083140 1288530 FALSE TRUE 972620.9717 1204386.661 1141519.987 1137089.579 1142578.543 1156103.98 1095743.418 1218372.413 1073466.019 0.9060566 1.121960677 1.063396481 1.059269282 1.064382592 1.076982373 1.020752775 1.13498927 1 20.03384509 4.750280312 24.90981545 1.069127015 0.906056498 0.616149921 0.040086125 1140.737443 2424550.782 0.008740673 0.146977701 56270.44013 -4.750280312 -0.163070517 VIEEEWQQVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VIEEEWQQVDR 11 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 0 ;; 200.71 1.07E-07 809620000 276042 302394 328580 324522 321013 292852 357000 283348 400862 FALSE TRUE 258765.024 324783.5664 336374.0728 332849.7839 295801.9339 377393.6183 303471.1642 318724.6215 333955.5425 0.774848718 0.972535338 1.007242072 0.996688905 0.885752432 1.130071433 0.908717256 0.954392369 1 18.34929653 4.73854807 5.053480657 0.982451745 0.764941535 0.498178336 0.065397618 0.129292451 10.60397807 0.013924702 0.098379711 54770.67206 -4.73854807 -0.21751021 VIEETEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VIEETEER 8 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 195.81 0.00036559 5619580000 3262900 3755660 3665300 3627760 3445020 3140750 4235550 3086430 3260780 FALSE TRUE 3058680.913 4033732.974 3752242.647 3720854.463 3174462.026 4047433.539 3600468.598 3471777.58 2716534.753 1.125949488 1.484881786 1.381260683 1.369706189 1.168570372 1.489925183 1.325390222 1.278016994 1 21.37333607 0.766526304 2.114743846 1.00027613 1.356550743 0.434694754 0.117489225 0.773635236 5.476339122 0.102686723 0.028149248 5.841525871 -0.766526304 0.356274613 VIEHIMEDLDTNADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 VIEHIMEDLDTNADK 15 0 P06702 P06702 S100A9 Protein S100-A9 0 ;;;;;;;;; 326.21 5.75E-58 1472753000 2962772 1897474 2315344 1859199 1910224 1345139 2849021 1973348 2860685 FALSE TRUE 2777337.389 2037964.949 2370265.053 1906909.194 1760202.713 1733458.793 2421836.75 2219724.842 2383218.193 1.165372687 0.855131501 0.994564854 0.800140415 0.738582274 0.727360507 1.016204373 0.931398077 1 21.18447961 1.617330063 25 0.980352049 0.881238632 0.123189815 0.128639442 1.603035233 4223.243068 0.059801935 0.032610282 41.43144332 -1.617330063 -0.099113417 VIENPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIENPR 6 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 0 104.11 0.079355 73549000 47957 75088 51800 63381 67897 51918 65468 55165 55745 FALSE TRUE 44955.45698 80647.59365 53028.72046 65007.46376 62564.6435 66905.88378 55651.68118 62052.47168 46440.79937 0.968016433 1.736567732 1.141856324 1.399792093 1.347191356 1.440670374 1.198335987 1.336162868 1 15.50310518 0.039856432 0.509765263 0.967452712 1.367254505 0.182502368 0.203855929 5.762496992 1.89453884 0.569311833 0.090380588 1.096115784 -0.039856432 0.399801793 VIEPLKDFHKDEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VIEPLKDFHKDEVR 14 2 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ; 206.63 6.35E-09 1939350000 4781600 3614900 4133100 4020100 4435500 2941300 5280500 3592700 5387900 FALSE TRUE 4482328.191 3882550.957 4231139.084 4123262.572 4087153.722 3790405.562 4488738.047 4041256.504 4488624.683 0.998597234 0.864975629 0.94263597 0.91860266 0.910558135 0.844446981 1.000025256 0.900332906 1 22.09784204 0.557687073 0.777129827 0.999510755 0.915840163 0.170268561 0.050436546 2.284340932 2.299806477 0.04704709 0.015815729 3.611495461 -0.557687073 -0.083670592 VIEPPAASCPS(ph)SPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIEPPAASCPSSPR 14 0 A0A0A0MRX4;Q3MIN7;Q3MIN7-2 A0A0A0MRX4 RGL3 Ral guanine nucleotide dissociation stimulator-like 3 1 VIEPPAAS(0.022)CPS(0.489)S(0.489)PR 103.83 0.0011463 108810000 159420 185210 215540 195020 195220 188530 197580 159200 154540 TRUE FALSE 149442.1868 198923.1411 220652.7106 200024.5434 179888.2087 242955.5505 167954.7132 179076.4704 128746.2756 1.160749591 1.5450788 1.713857038 1.553633628 1.397230388 1.88708799 1.304540364 1.390925443 1 16.97417117 0.925576395 1.373862675 1.007905408 1.551535146 0.392196222 0.20011907 0.471771431 1.785786243 0.174365811 0.052298155 8.425125815 -0.925576395 0.543629737 VIEPPAASCPSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIEPPAASCPSSPR 14 0 A0A0A0MRX4;Q3MIN7;Q3MIN7-2 A0A0A0MRX4 RGL3 Ral guanine nucleotide dissociation stimulator-like 3 1 VIEPPAASCPS(0.022)S(0.978)PR 174.02 2.74E-06 152960000 196690 230300 229930 246470 234730 216510 241820 184800 151510 TRUE FALSE 184379.524 247351.6516 235384.0482 252794.8375 216295.2527 279012.9223 205561.3359 207872.6868 126222.0022 1.460755817 1.959655585 1.86484166 2.002779492 1.713609742 2.210493554 1.628569761 1.646881551 1 16.94560389 0.787376793 1.372074953 1.003752399 1.872361911 0.625163702 0.203907052 0.428988227 1.443300018 0.170142564 0.050639043 6.128818958 -0.787376793 0.868609512 VIET(ph)PENDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VIETPENDFK 10 0 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 1 VIET(1)PENDFK;VIET(1)PENDFK;VIET(1)PENDFK;VIET(1)PENDFK 184.98 1.68E-05 609526000 3299100 2164580 2726630 2516060 2623020 2078160 3317870 2329250 2994100 TRUE FALSE 3092615.22 2324847.755 2791306.951 2580626.359 2417018.59 2678091.056 2820386.195 2620061.99 2494365.367 1.239840506 0.932039783 1.119044943 1.03458234 0.9689914 1.073656286 1.130702916 1.050392226 1 21.25024137 2.021187505 24.97374246 1.08171065 1.046415888 0 0.089419272 914.8267185 1078303.554 0.030635154 0.022622799 104.9995663 -2.021187505 -0.035294762 VIFGLFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIFGLFGK 8 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 146.21 0.0012957 21491000 110840 159020 109160 97860 121920 67705 128170 120480 175900 FALSE TRUE 103902.7223 170794.0063 111749.3267 100371.2533 112344.895 87250.3344 108952.0984 135522.1932 146541.1536 0.709034423 1.16550199 0.762579821 0.684935602 0.766643992 0.595398168 0.743491474 0.924806376 1 17.16094635 3.725186583 7.013676144 0.754954298 0.968838773 0.117161433 0.158365195 0.158407236 47.64597823 0.037469693 0.062639321 5311.125729 -3.725186583 0.213884475 VIFLEDDDVAAVVDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VIFLEDDDVAAVVDGR 16 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ;;;; 236.61 2.28E-19 204602000 124050 144219 147729 147248 144092 121489 156503 122979 121326 FALSE TRUE 116285.9319 154897.1248 151233.2016 151026.633 132775.5956 156560.9021 133036.8281 138333.1989 101075.9068 1.150481214 1.532483158 1.496233934 1.494190235 1.313622601 1.548943829 1.316207119 1.368607052 1 16.62507962 0.401509515 0.804689408 0.99558581 1.442565097 0.510346122 0.123340272 1.501960071 1.383828147 0.122434877 0.037837073 2.520632403 -0.401509515 0.446979287 VIFWSALAGAIPLNGDS(ph)EEEANRDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VIFWSALAGAIPLNGDSEEEANRDDR 26 1 Q9H089 Q9H089 LSG1 Large subunit GTPase 1 homolog 1 VIFWSALAGAIPLNGDS(1)EEEANRDDR;VIFWSALAGAIPLNGDS(1)EEEANRDDR 251.18 1.02E-46 793750000 561390 527840 591170 562050 539020 503300 602310 490570 459990 TRUE FALSE 526253.602 566921.8228 605192.8316 576473.1545 496687.5435 648594.5396 511999.2071 551818.7444 383214.6974 1.373260487 1.479384342 1.579252664 1.504308573 1.296107761 1.692509562 1.336063597 1.439972809 1 18.54779337 0.205678681 0.804231077 0.992188959 1.488206153 0.61645028 0.115113837 2.008013269 1.545057382 0.139806175 0.034761583 1.605752775 -0.205678681 0.496017194 VIGELVGHTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIGELVGHTER 11 0 Q8TEQ6 Q8TEQ6 GEMIN5 Gem-associated protein 5 0 171.62 1.43E-05 177710000 123040 162140 140190 134890 161560 125310 153750 127980 152930 FALSE TRUE 115339.146 174145.0143 143515.373 138351.5058 148871.7293 161484.9628 130696.6148 143958.5847 127404.995 0.905295322 1.366861749 1.126450128 1.085919008 1.168492093 1.267493184 1.025835877 1.129928891 1 16.95906232 1.675319961 9.699965477 1.059309132 1.17273812 0.116197918 0.123656435 0.212877377 30.20231715 0.055305203 0.029679808 47.34999753 -1.675319961 0.113428988 VIGIDHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIGIDHIK 8 0 F6S8N6;A0A0A0MRJ6;P22061;P22061-2;A0A3F2YNX8;C9J0F2 F6S8N6 PCMT1 Protein-L-isoaspartate O-methyltransferase;Protein-L-isoaspartate(D-aspartate) O-methyltransferase 0 134.81 0.00086063 490870000 725150 773290 698890 637370 755470 495170 966920 651960 1359900 FALSE TRUE 679764.1559 830545.1962 715468.0008 653725.9933 696138.4336 638117.5406 821939.3224 733358.6411 1132923.905 0.600008662 0.733098836 0.631523439 0.577025509 0.614461775 0.563248368 0.725502674 0.647315003 1 20.11161953 0.067072704 0.94014752 1.003923718 0.638263835 0.810229049 0.055398882 2.511848492 2.134566118 0.084447593 0.01753837 1.167004966 -0.067072704 -0.365659883 VIGQDSSEIHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIGQDSSEIHFK 12 0 B8ZZN6;P63165;B8ZZJ0;B9A032;G2XKQ0 B8ZZN6;G2XKQ0 SUMO1 Small ubiquitin-related modifier 1;Small ubiquitin-related modifier 0 134.21 0.00014956 157160000 435480 462030 497140 505470 536010 399470 562660 466900 603610 FALSE TRUE 408224.0842 496239.1819 508932.3956 518441.216 493913.9368 514790.5041 478294.3565 525193.4928 502863.5915 0.811798848 0.986826627 1.01206849 1.030977833 0.982202619 1.023717988 0.951141352 1.044405484 1 18.93980758 4.742214716 3.972844475 1.002001182 0.793728772 0.84193563 0.026239446 0.087389614 2.860605432 0.005855093 0.052903732 55235.04548 -4.742214716 -0.20827241 VIGSGCNLDSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VIGSGCNLDSAR 12 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5;Q6ZMR3;A0A087WUM2;F5H5G7;F5H155;P07864;G3XAP5;F5H245;A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50 P00338;A0A5F9ZHM4 LDHA;LDHAL6A;LDHC;LDHB L-lactate dehydrogenase A chain;L-lactate dehydrogenase A-like 6A;L-lactate dehydrogenase;L-lactate dehydrogenase C chain;L-lactate dehydrogenase B chain 0 ;;;; 262.23 4.89E-21 2195400000 356201 1116623 270069 326897 1150480 217053 306935 891596 852434 FALSE TRUE 333907.0152 1199298.929 276475.1642 335285.7305 1060125.942 279712.6775 260912.9462 1002913.723 710157.2585 0.470187429 1.688779372 0.38931541 0.472128851 1.492804487 0.393874278 0.367401647 1.412241741 1 19.43777901 3.958497832 23.63937378 0.731639583 1.150590861 0.040472706 0.505359131 430.6288464 546613.5676 0.120276557 0.217440451 9088.617625 -3.958497832 0.418951278 VIGTLEEVHMPQNGINHPGITALAQAFAVNPLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIGTLEEVHMPQNGINHPGITALAQAFAVNPLLR 34 0 P46060;H0Y4Q3 P46060 RANGAP1 Ran GTPase-activating protein 1 0 247.11 1.05E-47 233630000 93542 104010 80390 72112 117460 79739 94646 101460 67015 FALSE TRUE 87687.3732 111711.0086 82296.88876 73962.51601 108235.1654 102758.3548 80454.71095 114127.5043 55829.76357 1.570620536 2.000922115 1.474068373 1.324786481 1.938664227 1.840565825 1.441072034 2.044205403 1 15.76874683 -1.700342668 2.880787716 0.905026871 1.693240722 0.439040561 0.249933601 17305951.32 15942488.23 11933703.62 0.056992705 0.019936886 1.700342668 0.788213851 VIHDNFGIVEGLMTTVHAIT(ph)ATQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VIHDNFGIVEGLMTTVHAITATQK 24 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 VIHDNFGIVEGLMT(0.131)T(0.106)VHAIT(0.382)AT(0.382)QK;VIHDNFGIVEGLMT(0.137)T(0.181)VHAIT(0.682)ATQK;VIHDNFGIVEGLMT(0.05)T(0.064)VHAIT(0.882)AT(0.004)QK 136 4.45E-05 186425000 286621 285485 283845 296575 359758 253928 385120 273046 488161 TRUE FALSE 268681.9032 306622.6064 290577.9374 304185.6166 331504.0579 327232.8914 327374.8313 307136.3941 406683.7755 0.66066541 0.753958296 0.714505852 0.74796595 0.815139619 0.804637193 0.80498621 0.755221655 1 18.63354791 -5 0.124320312 1.798976857 0.647230976 0.838445495 0.035840917 54.86658019 0.43746967 10.96413132 0.29384081 1.00E-05 5 -1.151745881 VIHDNFGIVEGLMTTVHAIT(ph)ATQKTVDGPSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIHDNFGIVEGLMTTVHAITATQKTVDGPSGK 32 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 VIHDNFGIVEGLMTTVHAIT(0.487)AT(0.487)QKT(0.025)VDGPSGK 146.78 2.35E-10 46692000 117810 80665 107600 119530 109950 60312 99878 78549 26554 TRUE FALSE 110436.4824 86637.52053 110152.3228 122597.3422 101314.9705 77723.09532 84902.22112 88356.01556 22121.96585 4.992164038 3.916357213 4.979318906 5.541882804 4.57983577 3.513390077 3.837914844 3.994039957 1 14.43319198 0.179153086 0.471356594 0.668876984 4.739957207 0.817233594 0.531544819 1.413225555 0.45455007 1.501714874 0.305826296 1.510612541 -0.179153086 4.071080224 VIHDNFGIVEGLMTTVHAITAT(ph)QK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 VIHDNFGIVEGLMTTVHAITATQK 24 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 VIHDNFGIVEGLMTTVHAITAT(1)QK;VIHDNFGIVEGLMTTVHAITAT(1)QK;VIHDNFGIVEGLMTTVHAIT(0.002)AT(0.998)QK;VIHDNFGIVEGLMTTVHAIT(0.001)AT(0.999)QK;VIHDNFGIVEGLMT(0.002)T(0.002)VHAIT(0.126)AT(0.87)QK;VIHDNFGIVEGLMTTVHAITAT(1)QK;VIHDNFGIVEGLMTTVHAIT(0.004)AT(0.996)QK;VIHDNFGIVEGLMTTVHAITAT(1)QK;VIHDNFGIVEGLMTTVHAIT(0.001)AT(0.999)QK 333.89 1.17E-86 12370421600 7542891 4917502.4 6410821 6179430 5052930.7 6308610 7410271 5121228 2986135.2 TRUE FALSE 7070794.917 5281599.394 6562888.702 6338004.636 4656093.905 8129803.295 6299169.657 5760624.589 2487729.944 2.842267881 2.123059783 2.638103351 2.547706053 1.871623532 3.267960542 2.532095444 2.315614926 1 21.24639845 VIHDNFGIVEGLMTTVHAITAT(ph)QKTVDGPSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIHDNFGIVEGLMTTVHAITATQKTVDGPSGK 32 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 VIHDNFGIVEGLMTTVHAIT(0.028)AT(0.969)QKT(0.002)VDGPSGK 267.87 3.43E-60 39817000 220350 142390 191310 209490 184340 101560 190270 158350 53718 TRUE FALSE 206558.6868 152932.7038 195847.9635 214865.8681 169862.68 130878.7233 161740.7799 178120.3461 44752.11877 4.615618043 3.417328787 4.376283602 4.801244589 3.795634367 2.924525741 3.614147985 3.980154481 1 15.44966837 -0.769755657 0.371734369 9.09E-14 4.142518246 0.752468204 0.53759319 5.924699376 0.689917771 7.691624791 0.403212382 0.169919939 0.769755657 4.142518246 VIHDNFGIVEGLMTTVHAITATQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 29 VIHDNFGIVEGLMTTVHAITATQK 24 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;; 387 2.17E-137 78678612000 20135876.4 21567473.4 21715150.2 21846844 22458888.7 16447406.5 25031664.5 19279922.8 21467611.6 FALSE TRUE 18875607.84 23164351.57 22230243.82 22407471 20695058.18 21195505.76 21278398.79 21687063.6 17884528.54 1.055415456 1.295217345 1.242987411 1.252896936 1.157148657 1.185130808 1.18976571 1.212615896 1 24.09220875 -1.968114672 0.345731937 0.783391398 1.222839146 0.455539006 0.06604029 29.82075122 1.608061576 5.222321659 0.050229489 0.01076181 1.968114672 0.439447748 TEHSHS(ph)PGDSSAPIQNTDCCHSSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TEHSHSPGDSSAPIQNTDCCHSSER 25 0 Q13129 Q13129 RLF Zinc finger protein Rlf 1 TEHS(0.015)HS(0.984)PGDSSAPIQNTDCCHSSER 200.06 1.14E-24 505840000 10406 19530 19919 20314 19881 18286 30588 20978 25017 TRUE FALSE 9754.707035 20976.02152 20391.48809 20835.29163 18319.62646 23564.87135 26001.61337 23597.14948 20841.50108 0.468042441 1.00645445 0.978407841 0.999702063 0.878997457 1.130670543 1.247588322 1.132219286 1 14.34717157 4.945459572 1.938257593 1.061225212 1.01E-11 0.755206451 0.103153998 0.926760703 2.273719316 0.030083772 2.11690224 88198.16956 -4.945459572 -1.061225212 down VIHEQVNHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIHEQVNHR 9 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 0 105.2 0.0031373 43829000 27788 50753 41402 35678 45649 33745 46798 45728 42112 FALSE TRUE 26048.79868 54510.80493 42384.07499 36593.55788 42063.91168 43486.6337 39781.07435 51437.24146 35083.23515 0.742485651 1.553756508 1.20810053 1.0430497 1.19897471 1.23952747 1.13390553 1.466148753 1 15.09849417 3.491309779 24.63688312 1.182874936 1.2645248 0 0.234588283 1593.598139 2767104.419 0.057445548 0.087518125 3099.629456 -3.491309779 0.081649864 VIHLVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 97.033 0.012295 99045000 67719 105970 71273 69888 122620 52671 91498 100280 123960 FALSE TRUE 63480.58867 113816.1291 72963.62922 71681.4444 112989.9198 67876.26266 77778.72433 112800.1787 103270.2752 0.614703394 1.102118967 0.706530791 0.694114974 1.094118512 0.657268149 0.753156939 1.092281187 1 16.65606553 1.235602701 24.99938878 1.04614068 0.818620481 0.257148319 0.170129516 113.2791543 957314.9299 0.13241072 0.038662791 17.20294105 -1.235602701 -0.227520198 VIISAPSADAPMFVMGVNHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 VIISAPSADAPMFVMGVNHEK 21 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;; 341.21 1.21E-80 28834703900 18739299 17020441 18344240 17298032 17789904 14702510 21488348 15178796 17607445 FALSE TRUE 17566439.73 18280652.16 18779374.04 17741928.79 16392756.7 18946885.96 18266369.71 17073902.09 14668648.68 1.197549966 1.246239688 1.280238858 1.209513512 1.117536936 1.291658582 1.245266016 1.163972392 1 23.80623264 0.893224555 3.319002853 1.00015444 1.233190616 0.682871944 0.048575838 0.250346579 5.868797156 0.046239775 0.012000856 7.820320557 -0.893224555 0.233036176 VIISAPSADAPMFVMGVNHEKYDNSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VIISAPSADAPMFVMGVNHEKYDNSLK 27 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;; 240.24 4.99E-45 1256765000 1235859 1161373 1379599 1629898 1603939 971042 1340502 1080537 1857080 FALSE TRUE 1158508.791 1247362.265 1412323.74 1671723.942 1477972.101 1251366.062 1139506.17 1215444.423 1547121.351 0.748815722 0.806247205 0.912871986 1.080538344 0.955304573 0.808835106 0.736533155 0.785616734 1 20.56115493 -0.326013015 7.349710216 0.999999998 0.854224292 0.160133195 0.104831066 0 0 0.109366684 0.025777975 0.472048895 0.326013015 -0.145775706 VIKDFMIQGGDFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VIKDFMIQGGDFTR 14 1 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ; 186.43 9.70E-07 1297390000 3395300 4331300 3142200 3161100 3624500 2469800 4836500 3628100 7203100 FALSE TRUE 3182794.234 4651993.959 3216734.468 3242219.178 3339846.391 3182791.166 4111311.725 4081076.271 6000856.076 0.53039003 0.775221718 0.536045929 0.540292774 0.556561655 0.530389519 0.685120868 0.680082345 1 22.5167369 0.651729298 1.22257432 0.999217959 0.597223293 0.732483813 0.077612823 0.650001566 1.514638547 0.075548989 0.022979105 4.484657681 -0.651729298 -0.401994666 VIKDFMIQGGDFVNGDGTGVASIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIKDFMIQGGDFVNGDGTGVASIYR 25 1 C9JQD4;O43447;O43447-2 C9JQD4 PPIH Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase H 0 176.09 8.17E-13 86261000 165550 196980 167910 162400 200040 148860 226280 166100 294830 FALSE TRUE 155188.521 211564.6042 171892.9045 166567.4589 184329.6653 191833.4655 192351.4147 186837.9506 245620.9683 0.631821143 0.86134586 0.699829928 0.678148369 0.750463882 0.781014206 0.783122939 0.760675898 1 17.9060742 -0.676582127 0.4717404 1.061532778 0.739709402 0.638660428 0.061573228 7.496054134 1.318364286 0.759595325 0.030893774 0.210580365 0.676582127 -0.321823375 VILGSEAAQQHPEEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VILGSEAAQQHPEEVR 16 0 G3V1D3;G3V180;Q9NY33-4;Q9NY33;Q9NY33-2;E9PKK8;E9PPK9;E9PQ14;E9PNX5 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ;; 266.71 3.18E-27 1215340000 635430 761120 702670 752680 756210 652770 815240 719930 887970 FALSE TRUE 595659.5706 817474.1167 719337.6642 771995.0431 696820.317 841214.1022 693002.3303 809814.8453 739762.0705 0.80520426 1.105050055 0.972390574 1.043572081 0.941951939 1.137141435 0.936790839 1.094696359 1 19.49670181 4.752015555 24.57082475 1.02515485 0.805204076 0.512333637 0.068513761 1388.213092 2535038.113 0.014177977 0.27656064 56495.7209 -4.752015555 -0.219950774 VILHGEHAVVHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VILHGEHAVVHGK 13 0 F5H8H2;Q03426;F5H092;F5H163;F5H368;A0A1W2PS16;F5GXC0 F5H8H2 MVK Mevalonate kinase 0 152.14 1.57E-05 473790000 339360 339240 344290 351940 397440 337230 435280 347690 395530 FALSE TRUE 318120.0634 364357.6826 352456.7214 360971.3762 366226.6656 434582.8265 370013.8049 391099.8619 329513.4878 0.965423496 1.105744366 1.069627601 1.095467681 1.111416313 1.318862027 1.122909437 1.18690092 1 18.32997799 2.469045834 24.93143015 1.173937504 1.07208945 0.206447993 0.08634052 242.1274633 747518.3357 0.026646074 0.022329465 294.4732395 -2.469045834 -0.101848054 VILHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VILHLK 6 0 P08238;Q58FF7;Q58FF6;P07900;P07900-2;G3V2J8;Q14568 P08238;P07900 HSP90AB1;HSP90AB3P;HSP90AB4P;HSP90AA1;HSP90AA2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 4;Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2 0 ; 100.78 0.037275 17904300000 35601000 34590000 35274000 31629000 35647000 28658000 40450000 33764000 27660000 FALSE TRUE 33372796.96 37151079.59 36110715.94 32440653.69 32847428.41 36931099.38 34384898.02 37979509.72 23043367.31 1.448260426 1.612224424 1.56707635 1.407808731 1.425461304 1.602678067 1.492182004 1.648175339 1 24.45784822 -1.447139926 3.143801536 0.990302894 1.531034567 0.79964581 0.082621599 12688551.25 16507636.14 1094961.927 0.019429604 0.035715775 1.447139926 0.540731673 VILHLKEDQTEYLEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 17 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 ;;;;;;;;;;;;;;;; 347.45 2.46E-87 8869828200 7995939.3 8982409 8878918.5 9492482.2 11050973 7318202.2 10607772 8003963.3 13093387 FALSE TRUE 7495487.732 9647475.909 9089530.64 9736075.364 10183074.16 9430848.374 9017235.066 9003275.737 10908016.12 0.687154075 0.884439095 0.833289073 0.892561512 0.933540439 0.864579614 0.826661325 0.825381594 1 23.3788854 -4.267472116 0.018001257 1.999506851 1.83E-06 0.39802089 0.063127318 4546.506497 6.98513548 492.4393956 304.0394117 5.40E-05 4.267472116 -1.999505025 VILSNMVSISSEPFGHLVDDDDIS(ph)DQEDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VILSNMVSISSEPFGHLVDDDDISDQEDHR 30 0 A8MUM1;Q53HC9;C9JVR6 A8MUM1 TSSC1 Protein TSSC1 1 VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHR;VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHR;VILSNMVSIS(0.003)S(0.076)EPFGHLVDDDDIS(0.921)DQEDHR 189.91 4.42E-18 201889000 119651.8 152266 147045.4 155076.4 141351.3 151464.5 173097 128115.8 108842 TRUE FALSE 112163.0074 163539.9331 150533.3863 159055.923 130250.1391 195189.8423 147142.7118 144111.3396 90675.56705 1.236970565 1.803572212 1.660131734 1.754121073 1.436441407 2.152617829 1.622738259 1.589307289 1 16.46842624 0.725469853 2.495866623 1.00027973 1.693698316 0.431384232 0.237269791 1.282452218 10.46461294 0.201548684 0.053882669 5.314591059 -0.725469853 0.693418585 VILSNMVSISSEPFGHLVDDDDIS(ph)DQEDHRSEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 VILSNMVSISSEPFGHLVDDDDISDQEDHRSEEK 34 1 A8MUM1;Q53HC9 A8MUM1 TSSC1 Protein TSSC1 1 VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHRSEEK;VILSNMVSIS(0.012)S(0.033)EPFGHLVDDDDIS(0.929)DQEDHRS(0.025)EEK;VILSNMVSISSEPFGHLVDDDDIS(0.993)DQEDHRS(0.007)EEK;VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHRSEEK;VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHRSEEK;VILSNMVSISSEPFGHLVDDDDIS(0.986)DQEDHRS(0.014)EEK;VILSNMVSISSEPFGHLVDDDDIS(0.948)DQEDHRS(0.052)EEK 335.18 1.12E-117 1011300000 387572 508135 522056 532609 562554 422831 629360 461035 544634 TRUE FALSE 363314.5604 545757.8441 534439.4149 546276.6486 518373.2781 544895.4456 534993.3107 518596.2346 453731.0669 0.800726657 1.202822297 1.177877059 1.203965716 1.142468118 1.200921615 1.179097817 1.142959503 1 18.79147792 4.741643651 24.98033903 1.170152149 0.80072652 0.766521516 0.061241562 113.9647702 923357.0204 0.012278787 0.087305445 55162.46329 -4.741643651 -0.369425629 VINAAHSFYNGTTTLPIS(ph)DEDRTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VINAAHSFYNGTTTLPISDEDRTPR 25 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 1 VINAAHSFYNGT(0.002)T(0.008)T(0.015)LPIS(0.573)DEDRT(0.402)PR 154.02 5.40E-08 712700000 81090 116150 78703 83312 113860 99137 112940 77315 82204 TRUE FALSE 76014.72165 124749.8669 80569.87233 85449.92697 104917.8949 127756.2425 96005.69548 86967.94794 68483.62134 1.109969364 1.821601493 1.176483818 1.24774253 1.532014412 1.865500685 1.401878195 1.26990872 1 16.06347137 0.991618384 2.652928066 1.004136412 1.473643069 0.254794703 0.24797626 0.354155407 5.762952275 0.225986049 0.060559577 9.808856566 -0.991618384 0.469506658 VINAAHSFYNGTTTLPISDEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VINAAHSFYNGTTTLPISDEDR 22 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ; 282.05 1.00E-45 1802960000 925320 875160 976670 913340 953130 817970 1054810 875410 706070 FALSE TRUE 867405.8729 939957.757 999837.0736 936777.8507 878275.0145 1054104.66 896651.0329 984706.8655 588222.3556 1.474622419 1.597963335 1.699760412 1.592557375 1.493100366 1.792017339 1.524340284 1.674038493 1 19.16600209 -1.085625557 4.969804383 0.99998253 1.611747383 0.79291092 0.097298144 1.68E-05 3.09E-06 0.084042117 0.019808352 0.082105915 1.085625557 0.611764853 VINAAHSFYNGTTTLPISDEDRT(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VINAAHSFYNGTTTLPISDEDRTPR 25 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 1 VINAAHSFYNGT(0.002)T(0.001)TLPIS(0.002)DEDRT(0.995)PR;VINAAHSFYNGTT(0.001)T(0.005)LPIS(0.02)DEDRT(0.973)PR;VINAAHSFYNGTTTLPIS(0.001)DEDRT(0.999)PR;VINAAHSFYNGTTTLPISDEDRT(1)PR;VINAAHSFYNGTTTLPIS(0.003)DEDRT(0.997)PR 253.79 1.18E-44 4990130000 1057530 1192920 1225350 1161240 1240880 1074010 1290420 1010980 1054530 TRUE FALSE 991341.085 1281245.038 1254415.881 1191039.384 1143426.29 1384059.252 1096933.501 1137203.078 878522.1305 1.128419024 1.458409519 1.427870553 1.355730656 1.301533849 1.575440395 1.248612258 1.294450121 1 19.7447191 0.774589163 1.298358989 1.002059855 1.383244837 0.459614512 0.120447862 0.626308575 1.875585609 0.103493455 0.031191344 5.950989206 -0.774589163 0.381184982 VINAAHSFYNGTTTLPISDEDRTPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VINAAHSFYNGTTTLPISDEDRTPR 25 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ; 225.84 4.20E-34 735670000 174735 313916 248440 265474 309385 245077 266849 247527 316740 FALSE TRUE 163798.6483 337158.6673 254333.1141 272286.5123 285087.1501 315826.7514 226837.4698 278431.2908 263874.0478 0.620745578 1.277725756 0.963842849 1.031880606 1.080391014 1.196884476 0.859642969 1.055167392 1 18.00948994 1.721180723 24.99999994 0.963221238 1.051982418 0.010312192 0.178710454 2.984167686 4275.526467 0.074783726 0.041471384 52.62362035 -1.721180723 0.088761179 VINIDFRDPEESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VINIDFRDPEESK 13 1 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ; 82.55 0.010985 123754000 220490 191792 219400 212413 207500 164217 268570 192728 233580 FALSE TRUE 206689.9245 205992.4792 224604.2716 217863.8772 191203.787 211623.7821 228300.4218 216790.515 194593.989 1.062159862 1.058575757 1.154219988 1.119581742 0.982578074 1.087514487 1.173214152 1.114065836 1 17.57010762 1.970708232 24.82183218 1.118845592 1.081641988 0 0.061945599 1843.751201 1562390.296 0.024728076 0.015988938 93.47774601 -1.970708232 -0.037203604 VINIDFRDPEESKWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VINIDFRDPEESKWK 15 2 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 78.285 0.013143 188370000 284630 230690 305730 326130 334950 218250 360780 243620 611540 FALSE TRUE 266815.5164 247770.5276 312982.06 334499.0479 308644.3781 281255.232 306684.3883 274036.4933 509470.0233 0.523711905 0.486329943 0.614328706 0.656562766 0.6058146 0.552054526 0.601967484 0.537885412 1 18.95863774 -1.632212664 2.775732701 1.040673516 0.573147772 0.879751135 0.049689289 11758696.61 11057626.79 3438100.901 0.013446021 0.023323157 1.632212664 -0.467525744 VIPAKS(ph)PPPPTHSTQLGAPSR ddPTM_SK-BR-3_Pertuzumab_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(0.981)PPPPT(0.019)HSTQLGAPSR;VIPAKS(0.998)PPPPT(0.002)HSTQLGAPSR;VIPAKS(1)PPPPTHSTQLGAPSR;VIPAKS(1)PPPPTHSTQLGAPSR;VIPAKS(1)PPPPTHSTQLGAPSR;VIPAKS(0.99)PPPPT(0.01)HSTQLGAPSR 284.56 1.78E-45 5443040000 2194725 3074520 3021670 3155820 3164530 2244957 3588530 2760120 3054780 TRUE FALSE 2057361.08 3302160.66 3093345.439 3236803.684 2916000.579 2893039.642 3050463.241 3104727.058 2544917.483 0.808419563 1.297551171 1.215499308 1.271869797 1.14581341 1.136791138 1.198649175 1.219971601 1 21.27918745 -0.570178354 7.828544019 0.999979428 1.18173166 0.10739491 0.136259347 0 0 0.117888524 0.027786592 0.269042969 0.570178354 0.181752232 VIPELNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VIPELNGK 8 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 122.18 0.0032608 3091800000 7288900 7661800 7228600 7204900 8306600 5646200 8403300 6977100 8056700 FALSE TRUE 6832700.76 8229087.644 7400065.806 7389789.932 7654233.143 7276166.282 7143303.177 7848206.293 6711984.722 1.017985148 1.226028959 1.102515294 1.10098432 1.140382981 1.084055847 1.064260941 1.169282503 1 22.678308 -5 0.180891168 0.513557529 1.14251549 0.222971589 0.059187762 170.1019329 1.641487265 29.70491613 0.169622682 1.00E-05 5 0.628957961 VIPEYCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VIPEYCR 7 0 B0YIW6;P48444;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 ; 119.89 0.01089 492470000 420610 620290 386390 384620 669910 320940 463480 543010 635290 FALSE TRUE 394284.7709 666216.917 395555.3533 394490.0004 617297.9709 413590.168 393985.4767 610805.9938 529255.9949 0.74497932 1.258780105 0.747380015 0.745367089 1.166350456 0.781455802 0.74441382 1.154084223 1 19.01360618 3.952462699 23.87117591 0.882591035 1.034142304 0.022921335 0.2023539 506.4202301 490249.9981 0.047851964 0.086329615 8963.191995 -3.952462699 0.151551269 VIPSQEHLNGPLPVPFT(ph)NGEIQKENSREALAEAALESPRPALVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VIPSQEHLNGPLPVPFTNGEIQKENSREALAEAALESPRPALVR 44 3 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 VIPSQEHLNGPLPVPFT(0.357)NGEIQKENS(0.357)REALAEAALES(0.287)PRPALVR;VIPSQEHLNGPLPVPFT(0.457)NGEIQKENS(0.457)REALAEAALES(0.086)PRPALVR 109.19 1.21E-06 306590000 47438 51189 49376 51981 60150 40780 72752 42565 109523 TRUE FALSE 44468.94026 54979.08682 50547.22204 53314.92046 55426.06163 52552.52399 61843.513 47879.33395 91242.90375 0.487368753 0.6025574 0.553985241 0.584318542 0.607456135 0.575962862 0.677789838 0.524745838 1 16.47742474 -5 0.283184122 4.103002169 0.558161985 0.870168777 0.051282483 71.7048665 0.683536846 130.9650309 0.051079347 1.00E-05 5 -3.544840184 VIQENEHALQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIQENEHALQK 11 0 Q9NTJ3;E9PD53 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 0 159.99 2.80E-05 172360000 424040 438040 450170 485270 518900 400270 559680 440120 572170 FALSE TRUE 397500.0933 470472.9374 460848.245 497722.8498 478147.6871 515821.4512 475761.1798 495069.9508 476671.1306 0.83390847 0.986996919 0.966805446 1.044164032 1.003097642 1.08213277 0.99809103 1.038598562 1 18.86263473 5.866816129 0.786876245 1.023945002 7.30E-18 0.752158187 0.032695721 6.047967825 0.738348918 0.010244537 8.179184389 735895.4698 -5.866816129 -1.023945002 VIQLMPS(ph)PIMHPLILNPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VIQLMPSPIMHPLILNPR 18 0 P41212 P41212 ETV6 Transcription factor ETV6 1 VIQLMPS(1)PIMHPLILNPR;VIQLMPS(1)PIMHPLILNPR 167.73 1.45E-11 284490000 299250 327170 320370 293620 386780 264600 322700 300470 395570 TRUE FALSE 280520.4767 351394.0072 327969.3277 301154.7863 356403.859 340985.7246 274314.1308 337984.3409 329546.8115 0.851231045 1.066294666 0.995213172 0.913845244 1.081496912 1.034711042 0.832398073 1.025603432 1 18.33012389 VIQPMGMS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 118.87 0.00080587 584836000 505530 613450 549212 587609 689660 489422 672350 582440 723120 TRUE FALSE 473889.7797 658870.4763 562239.568 602688.0418 635496.8856 630710.1863 571537.3593 655158.9161 602426.6005 0.786634885 1.093694196 0.933291404 1.00043398 1.054895128 1.046949431 0.948725303 1.087533179 1 19.20042595 4.751351505 24.78290424 1.014158734 0.786634722 0.653358185 0.053389851 1173.26692 2273210.07 0.012006204 0.219458721 56409.40325 -4.751351505 -0.227524011 VIQQSLEQEEAEHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VIQQSLEQEEAEHK 14 0 O75116;E9PF63;Q14DU5 O75116 ROCK2 Rho-associated protein kinase 2 0 151.56 6.91E-06 83381000 105150 88674 95111 96866 112880 80465 111080 88210 132160 FALSE TRUE 98568.8492 95239.51523 97367.07783 99351.74555 104014.8601 103693.9393 94424.58522 99223.21267 110101.6422 0.895253215 0.865014484 0.884338107 0.902363884 0.9447167 0.941801931 0.857612869 0.901196482 1 16.74847646 -5 0.254078725 1.642869782 0.886131245 0.555500701 0.028195029 151.7199123 1.499616904 50.85352481 0.041986835 1.00E-05 5 -0.756738537 VIQYLAYVASSHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VIQYLAYVASSHK 13 0 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 ; 198.23 1.28E-07 458280000 606470 1986980 696420 669710 2066460 523120 1043670 1833810 1640260 FALSE TRUE 568512.1253 2134098.067 712939.4113 686895.8924 1904168.567 674136.2519 887181.3725 2062765.215 1366490.01 0.41603826 1.561737043 0.521730423 0.502671727 1.393474196 0.493334197 0.649241024 1.509535526 1 20.38204348 1.244860723 24.99827271 1.254767791 0.827346615 0.178063664 0.408373313 246.8433852 979482.227 0.274826469 0.094897494 17.57359945 -1.244860723 -0.427421176 VIREPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VIREPK 6 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;; 114.19 0.023257 2983120000 6631590 5661630 6544000 6503660 6732200 5475720 8147970 6485370 6279830 FALSE TRUE 6216530.62 6080822.976 6699226.77 6670554.926 6203480.168 7056471.473 6926257.541 7295082.721 5231685.804 1.18824617 1.162306607 1.280510149 1.275029728 1.185751668 1.348794965 1.323905487 1.39440383 1 22.31884447 3.930214503 2.876764134 1.277832718 1.175623875 0.069234781 0.108980909 0.49796923 8.2139048 0.026048339 0.057079941 8515.585287 -3.930214503 -0.102208843 VIREPKPR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 158.87 0.00020385 23515480000 6289910 8124860 7559780 7349980 9262540 5882420 9837460 7595260 11221560 FALSE TRUE 5896235.761 8726433.088 7739101.552 7538592.93 8535097.472 7580579.161 8362424.2 8543544.93 9348609.142 0.630707271 0.933447207 0.82783454 0.806386577 0.91298046 0.810877752 0.894509982 0.913884066 1 23.15632031 -2.533652145 0.024129763 2.004547973 2.80E-06 0.432920065 0.075631684 1513.173633 4.432616888 229.9048156 146.084362 0.002926495 2.533652145 -2.004545173 VIS(ph)DSESDIGGS(ph)DVEFKPDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VISDSESDIGGSDVEFKPDTK 21 1 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1 P52701 MSH6 DNA mismatch repair protein Msh6 2 VIS(0.842)DS(0.155)ES(0.089)DIGGS(0.914)DVEFKPDTK 147.23 5.77E-08 53905000 300010 123470 192900 164320 158290 165930 225910 141870 151900 TRUE FALSE 281232.9096 132611.8473 197475.6791 168536.7294 145858.5419 213831.2974 192036.8927 159582.7818 126546.9087 2.222360961 1.047926406 1.5604939 1.331812299 1.152604543 1.689739398 1.517515479 1.261056342 1 16.94931274 4.751863964 24.86614043 1.36098807 2.222361565 0.609530875 0.224836282 1481.204679 2768562.462 0.050907024 0.989668952 56476.00444 -4.751863964 0.861373495 VIS(ph)PSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VISPSQK 7 0 E7EWD6;Q76L83;A0A5F9ZHC8 E7EWD6 ASXL2 Putative Polycomb group protein ASXL2 1 VIS(0.724)PS(0.276)QK 83.309 0.037598 0 280790 214020 255410 223790 240160 207470 301470 210090 276590 TRUE FALSE 263215.8551 229866.2635 261468.4458 229532.8303 221298.8024 267363.221 256267.3722 236320.199 230425.3422 1.142304282 0.99757371 1.134720875 0.996126677 0.960392639 1.160303023 1.112149253 1.025582502 1 17.81393987 2.221510996 24.99998561 1.089616304 1.04938019 0.017049212 0.072259046 722.488618 1059384.127 0.025717771 0.019047192 166.5370994 -2.221510996 -0.040236114 VISFIENTST(ph)PVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VISFIENTSTPVDR 14 0 Q9NUY8-2;Q9NUY8;E9PGE5 Q9NUY8-2 TBC1D23 TBC1 domain family member 23 1 VISFIENTS(0.022)T(0.978)PVDR;VISFIENTS(0.014)T(0.986)PVDR;VIS(0.01)FIENT(0.088)S(0.241)T(0.661)PVDR 209.89 6.71E-08 60325000 158087 157826 176829 186391 178472 159518 201221 143961 207903 TRUE FALSE 148192.6169 169511.6013 181023.4674 191174.1086 164455.529 205568.257 171049.7791 161934.8477 173202.6462 0.855602499 0.978689443 1.045154167 1.103759745 0.949497786 1.186865568 0.987570241 0.934944421 1 17.40210145 4.808168871 1.555675551 1.034818962 0.766209588 0.355617761 0.073653955 1.337079135 2.691288395 0.017984803 0.575474198 64293.76687 -4.808168871 -0.268609374 VISGTTLGYLS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VISGTTLGYLSPK 13 0 E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3;H0YBY0;E5RJN7;E5RJ67 E7EPX0 STAU2 Double-stranded RNA-binding protein Staufen homolog 2 1 VISGTTLGYLS(1)PK;VISGTTLGYLS(1)PK 216 2.96E-11 177084000 679510 455100 554370 680890 729630 324680 478520 377710 503190 TRUE FALSE 636980.6821 488796.0775 567519.9182 698362.7901 672327.803 418409.8453 406770.3684 424867.9249 419204.3383 1.519499261 1.16600911 1.353802588 1.66592453 1.60381881 0.99810476 0.970339119 1.013510325 1 18.67729412 2.221229886 24.85197235 0.990768565 1.416023727 0.728811772 0.13979231 145.7608806 209017.236 0.059142746 0.043784756 166.4293382 -2.221229886 0.425255161 VISHDRDS(ph)PPPPPPPPPPPQPQPSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VISHDRDSPPPPPPPPPPPQPQPSLK 26 1 Q69YN4-3;Q69YN4;Q69YN4-4;Q69YN4-2 Q69YN4-3 KIAA1429 Protein virilizer homolog 1 VIS(0.166)HDRDS(0.834)PPPPPPPPPPPQPQPSLK 109.26 0.0014716 427750000 135360 111660 122030 120820 107870 99139 146630 112820 110390 TRUE FALSE 126888.0592 119927.4226 124924.6092 123920.4457 99398.32533 127758.8199 124644.1927 126905.8253 91965.19585 1.379739999 1.304052272 1.358390074 1.347471123 1.080825462 1.389208371 1.355340916 1.379933182 1 16.48880036 -1.5432022 3.23924131 0.989259351 1.324240908 0.562525712 0.089897614 38390853.22 51762073.56 3658473.426 0.020435017 0.028628448 1.5432022 0.334981556 VISRPPPSVS(ph)PPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VISRPPPSVSPPK 13 1 Q8NHM5-4;Q8NHM5-2;Q8NHM5-3;Q8NHM5;A0A0C4DGG3 Q8NHM5-4 KDM2B Lysine-specific demethylase 2B 1 VIS(0.001)RPPPS(0.207)VS(0.792)PPK 63.918 0.039618 170660000 191640 126970 146150 137840 147190 97961 186370 119610 156010 TRUE FALSE 179645.5945 136370.9909 149616.747 141377.2078 135630.2911 126240.7504 158425.5487 134543.5718 129970.9231 1.382198342 1.049242305 1.151155531 1.08776028 1.043543339 0.971299945 1.218930703 1.03518209 1 16.98782938 4.74267893 24.76283516 1.084084529 1.382198476 0.640830548 0.07282789 237.345889 1427064.748 0.016402356 0.127270575 55294.11741 -4.74267893 0.298113947 VITEEEKNFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VITEEEKNFK 10 1 P26373;P26373-2;J3KS98;H3BUK8 P26373 RPL13 60S ribosomal protein L13 0 122.51 0.0004438 159110000 174660 229260 185190 197980 270730 114760 207800 140370 508360 FALSE TRUE 163728.3424 246234.6489 189582.7943 203060.502 249467.9579 147889.349 176642.3191 157895.5035 423511.4319 0.38659722 0.581412048 0.447645046 0.479468762 0.589046574 0.34919801 0.417089849 0.372824655 1 18.69204139 -1.564126531 4.646890817 1.005084177 0.46089041 0.81785521 0.081061567 0.004242865 0.000397976 0.077993846 0.018265903 0.027281828 1.564126531 -0.544193767 VITLWYRPPELLLGEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VITLWYRPPELLLGEER 17 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2;A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61;A0A2R8YD28;Q9BVE2;A0A087X209;A0A2R8Y644;A0A2R8YEB7 Q9NYV4-3;Q9NYV4;Q9NYV4-2;A0A2R8Y4Z0 CDK12;CDK13 Cyclin-dependent kinase 12;Cyclin-dependent kinase 13 0 ; 143.83 4.88E-07 200807000 197303 264000 247120 233830 281860 191446 225680 222230 202355 FALSE TRUE 184954.1574 283546.8347 252981.8031 239830.4737 259723.8526 246713.3523 191841.3791 249975.9047 168580.6432 1.097125707 1.681965552 1.500657479 1.422645382 1.540650502 1.463473787 1.137979874 1.482826853 1 17.36307937 0.861422512 0.547447768 1.001576257 1.498497048 0.314363676 0.181611403 1.093037027 0.757031282 0.195101016 0.083486775 7.268127082 -0.861422512 0.496920791 VIY(ph)DFIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VIYDFIEK 8 0 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 1 VIY(1)DFIEK;VIY(1)DFIEK;VIY(1)DFIEK;VIY(1)DFIEK 152.59 0.0046851 251610000 418177 344699 405610 470680 609292 338976 577901 544938 513753 TRUE FALSE 392004.048 370220.8726 415231.2607 482758.4457 561440.6641 436832.8684 491250.11 612974.7089 428004.3053 0.915888095 0.864993338 0.970156738 1.127928948 1.311764057 1.020627276 1.147769085 1.432169493 1 18.70726578 3.293568427 2.686987225 1.178226114 0.899453796 0.491778054 0.12556662 0.210090478 3.072479006 0.034962243 0.048498407 1965.931705 -3.293568427 -0.278772318 VKADRDESSPYAAMLAAQDVAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VKADRDESSPYAAMLAAQDVAQR 23 2 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ;; 151.3 4.19E-08 1079590000 1165658 1222465 1197360 1269755 1494980 944047 1510110 1079080 2136620 FALSE TRUE 1092701.547 1312977.581 1225761.945 1302339.063 1377570.301 1216578.044 1283683.025 1213805.513 1780004.319 0.613875784 0.737626065 0.688628635 0.731649384 0.773914022 0.683469153 0.721168489 0.681911555 1 20.76344931 -1.646754389 2.590746284 1.035425477 0.708588378 0.824731579 0.04283326 4990643.959 4197229.853 1175597.89 0.009521638 0.022555144 1.646754389 -0.3268371 VKAEAEAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 90.05 0.010664 171870000 114860 325950 74021 75485 327510 45818 84265 286020 271010 FALSE TRUE 107671.1176 350083.6772 75776.81308 77422.0729 301788.6857 59044.91281 71630.24553 321730.2266 225776.6802 0.476892111 1.550575005 0.33562728 0.342914391 1.336668984 0.261519094 0.317261488 1.424993167 1 17.78453696 3.962117569 23.7698728 0.650024832 1.072009645 0.042370557 0.498058364 435.8839102 690559.3838 0.117993754 0.213975071 9164.685564 -3.962117569 0.421984813 VKAEPAKIEAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKAEPAKIEAFR 12 2 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 54.276 0.07628 432030000 125210 151570 133870 138450 198240 100870 158310 132290 260050 FALSE TRUE 117373.3296 162792.4005 137045.4596 142002.8614 182671.0301 129989.5315 134572.8852 148806.6977 216645.975 0.541774799 0.751421301 0.632577917 0.655460418 0.843177585 0.600008985 0.621164945 0.686865739 1 17.72497991 0.942034113 21.2267873 1 0.668446619 0.615871889 0.082889438 2246.248414 822565.8656 0.073947856 0.018486964 8.75052506 -0.942034113 -0.331553381 VKAQT(ph)PPGPSLSGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKAQTPPGPSLSGSK 15 1 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VKAQT(0.996)PPGPS(0.004)LSGSK;VKAQT(0.992)PPGPS(0.007)LSGSK 90.972 0.0093894 1191800000 2256300 1269130 1596380 1469340 1508750 1248030 2112140 1243830 1907020 TRUE FALSE 2115082.211 1363097.706 1634246.887 1507045.752 1390258.861 1608316.001 1795444.215 1399124.914 1588726.042 1.331307069 0.857981596 1.02865242 0.948587555 0.875077782 1.012330608 1.130115682 0.880658387 1 20.59943894 -2.901404461 12.20727574 0.054058374 1.000565416 0 0.141522522 0 0 0 0.028338037 0.001254861 2.901404461 0.946507042 VKAQT(ph)PPGPSLSGSKS(ph)PCPQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKAQTPPGPSLSGSKSPCPQEK 22 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 VKAQT(1)PPGPSLS(0.052)GS(0.244)KS(0.704)PCPQEK 109.62 0.00072523 1039000000 1120900 468050 657620 718600 724730 465150 997600 516620 932340 TRUE FALSE 1050744.87 502704.909 673219.057 737040.4926 667812.6292 599431.2539 848019.1413 581121.1442 776726.4309 1.352786294 0.647209737 0.866738958 0.948906157 0.859778427 0.771740513 1.091786126 0.748167078 1 19.56704703 1.755314316 25 0.954333359 0.872769313 0 0.200273548 25.20583149 37654.75918 0.085011276 0.047143107 56.92647812 -1.755314316 -0.081564045 VKDDIESLHDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VKDDIESLHDK 11 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 168.61 1.07E-05 707970000 2226690 1654920 2057470 2041130 2074280 1564950 2926520 2062110 2171690 FALSE TRUE 2087325.448 1777451.999 2106274.16 2093508.851 1911374.416 2016725.66 2487715.494 2319568.973 1809220.909 1.153715081 0.982440557 1.164188491 1.157132797 1.056462705 1.114692877 1.375020309 1.282081674 1 20.78693714 1.897183189 8.962828649 1.257832172 1.096311952 0.167339978 0.109017073 0.388351341 31.16440182 0.041905125 0.026456606 78.91929351 -1.897183189 -0.16152022 VKDEPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 VKDEPQR 7 1 P05204;O00479 P05204 HMGN2;HMGN4 Non-histone chromosomal protein HMG-17;High mobility group nucleosome-binding domain-containing protein 4 0 ;;;;;;; 107.29 0.0068488 3513500000 4677930 3944110 4183610 4141880 3993650 3437760 4825590 3102890 3122300 FALSE TRUE 4385146.712 4236136.008 4282847.205 4248167.653 3680004.839 4430185.505 4102037.578 3490292.647 2601167.959 1.685837585 1.62855151 1.646509288 1.633176988 1.414750949 1.70315242 1.576998349 1.341817484 1 21.31072813 0.975390695 2.187458434 1.001520765 1.61872326 0.868449154 0.078151235 0.102520455 1.074253955 0.069573564 0.019176518 9.44910543 -0.975390695 0.617202495 VKDEPQRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 VKDEPQRR 8 2 P05204;O00479 P05204 HMGN2;HMGN4 Non-histone chromosomal protein HMG-17;High mobility group nucleosome-binding domain-containing protein 4 0 ;;;;;;;;; 131.44 0.00056525 9081697000 11407210 11581210 10735480 11221780 12277560 8632220 13138910 8464390 12282520 FALSE TRUE 10693253.09 12438694.84 10990130.66 11509749.87 11313329.96 11124201.78 11168852.42 9521187.724 10232488.06 1.045029618 1.215608048 1.074042851 1.124824168 1.105628454 1.087145346 1.091508962 0.930486082 1 23.28665365 1.345862157 4.342924319 0.966203792 1.115284808 0.598380559 0.047714959 0.133297409 3.871942045 0.034098705 0.011520118 22.17492488 -1.345862157 0.149081016 VKDGPGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKDGPGGK 8 1 H0YF61;P22307-6;P22307-2;P22307-4;P22307-7;P22307-8;P22307 H0YF61 SCP2 Non-specific lipid-transfer protein 0 ; 71.349 0.044663 1146040000 3252500 2501000 3031200 3008900 3125300 2164630 3575900 2608200 3838300 FALSE TRUE 3048931.831 2686176.642 3103101.495 3086113.468 2879851.545 2789523.541 3039726.992 2933839.511 3197662.934 0.953487561 0.840043713 0.970427953 0.965115315 0.900611354 0.872363222 0.950608946 0.917494924 1 21.60858644 0.092737442 0.896399567 1.001041996 0.917401939 0.25536758 0.041859418 6.981194005 5.681923184 0.060969943 0.013032672 1.238047884 -0.092737442 -0.083640056 VKDLESLFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKDLESLFHR 10 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 183 1.03E-06 482020000 759610 1029190 828030 791470 1257260 578910 1047520 1045600 1431590 FALSE TRUE 712067.366 1105392.298 847671.2626 811780.4602 1158519.871 746031.9192 890454.1007 1176145.462 1192648.381 0.597047191 0.926838385 0.710747003 0.680653639 0.971384265 0.625525454 0.746619134 0.986162796 1 20.18573734 1.234944971 23.80672762 0.993081729 0.762482989 0.415932816 0.118555596 50.43858092 332059.3672 0.090550423 0.026180741 17.17690728 -1.234944971 -0.23059874 VKDSS(ph)PGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VKDSSPGEK 9 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 VKDS(0.197)S(0.803)PGEK;VKDS(0.054)S(0.946)PGEK;VKDS(0.017)S(0.983)PGEK;VKDS(0.026)S(0.974)PGEK;VKDS(0.182)S(0.818)PGEK;VKDS(0.032)S(0.968)PGEK 121.01 0.00037899 5777140000 24056800 10755000 15070600 14994200 14981800 10535400 19165000 11759100 15230100 TRUE FALSE 22551127.83 11551311.39 15428081.75 15378976.56 13805189.86 13576798.95 16291386.17 13227249.52 12688097.92 1.777345034 0.910405284 1.21594914 1.212078962 1.088042506 1.070042101 1.283989631 1.042492705 1 23.59697247 4.750025299 24.89436424 1.119200521 1.777345446 0.781868221 0.11166312 776.3716668 1685776.938 0.026023095 0.413287807 56237.40837 -4.750025299 0.658144925 VKEDPDGEHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VKEDPDGEHAR 11 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;; 164.48 1.37E-05 9208532000 22789220 19795670 20970110 19720560 21198830 16790680 25225060 18881620 23611840 FALSE TRUE 21362883.4 21261362 21467530.91 20226622.96 19533959.4 21637876.74 21442796.43 21239031.82 19670871.37 1.08601612 1.080855119 1.091336043 1.028252515 0.993039863 1.099995844 1.090078626 1.079719928 1 24.22955753 VKEDPDGEHARR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKEDPDGEHARR 12 2 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 88.021 0.0061383 347340000 332610 379990 383260 378750 509210 284914 458150 344200 861810 FALSE TRUE 311792.5338 408124.855 392351.1082 388469.3662 469218.7007 367164.0466 389454.6608 387174.1277 717968.3435 0.434270587 0.568444081 0.546474105 0.541067541 0.653536754 0.511393086 0.542439878 0.539263508 1 19.45356071 -1.921214753 2.430219701 1.291826955 0.54647824 0.87804812 0.053606785 7611703.031 3743430.121 12628134.81 0.012174271 0.011989063 1.921214753 -0.745348715 VKEDQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKEDQIR 7 1 Q8N5G2;Q8N5G2-2;Q8N5G2-3 Q8N5G2 TMEM57 Macoilin 0 65.038 0.065363 138380000 797560 789150 805320 786940 893430 674640 986010 751360 1031200 FALSE TRUE 747642.1433 847579.4871 824422.5707 807134.2127 823263.6117 869397.6161 838166.9542 845168.9499 859086.0582 0.870276192 0.986606032 0.959650739 0.939526611 0.958301679 1.012002939 0.975649583 0.9838001 1 19.71244313 2.387641971 6.91928153 0.989809454 0.950249321 0.37724355 0.031194256 0.287583245 18.74174513 0.010327392 0.00861634 244.1417039 -2.387641971 -0.039560133 VKEEIIEAFVQELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKEEIIEAFVQELR 14 1 P50552 P50552 VASP Vasodilator-stimulated phosphoprotein 0 ; 186.85 9.26E-07 623640000 1181610 1039490 1168660 1190940 1221090 902220 1346500 1011420 1384350 FALSE TRUE 1107655.139 1116454.921 1196381.167 1221501.537 1125190.517 1162676.268 1144604.825 1137698.013 1153293.042 0.960428182 0.968058317 1.037360951 1.05914238 0.975632798 1.008136029 0.992466601 0.986477827 1 20.13732771 4.227702261 4.116669097 1.008666196 0.962678636 0.365987883 0.024271612 0.223388938 8.879098365 0.006190981 0.016566443 16892.82415 -4.227702261 -0.04598756 VKEEPPS(ph)PPQS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VKEEPPSPPQSPR 13 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 2 VKEEPPS(1)PPQS(1)PR;VKEEPPS(1)PPQS(1)PR;VKEEPPS(1)PPQS(1)PR;VKEEPPS(1)PPQS(1)PR 81.639 0.0082637 3373030000 4050750 3142590 3484460 3508460 3928940 2948550 4386430 3110570 3718110 TRUE FALSE 3797220.788 3375270.633 3567113.037 3598493.023 3620376.901 3799748.519 3728725.543 3498931.512 3097533.421 1.225885333 1.089663992 1.151597917 1.161728554 1.168793491 1.226701379 1.203772498 1.129586363 1 21.56268842 0.935312143 8.125383843 1.000000489 1.168205625 0.651223391 0.040140144 1.10172867 138.2980496 0.042278868 0.010586837 8.616128022 -0.935312143 0.168205136 VKEEPPS(ph)PPQSPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VKEEPPSPPQSPR 13 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 1 VKEEPPS(1)PPQSPR;VKEEPPS(0.999)PPQS(0.001)PR;VKEEPPS(1)PPQSPR;VKEEPPS(1)PPQSPR 149.86 2.66E-05 3908240000 6728100 5517300 5832600 5171900 5264200 4326190 7045500 5258200 7350400 TRUE FALSE 6307000.231 5925806.633 5970952.026 5304619.71 4850770.967 5575090.823 5989092.682 5914697.845 6123570.755 1.029954659 0.967704444 0.975076841 0.8662625 0.792147451 0.910431356 0.978039272 0.965890341 1 22.54594173 1.665579442 6.184780945 0.979540018 0.927471157 0.149086708 0.064429779 0.336962958 26.72831153 0.036454419 0.018205318 46.2998349 -1.665579442 -0.052068861 VKEFCENLSADCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKEFCENLSADCR 13 1 P30153;B3KQV6;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 118.08 0.00041567 187470000 216920 292080 216160 220270 296860 172910 305590 224580 474310 FALSE TRUE 203343.3644 313705.9071 221287.4173 225922.5011 273545.8131 222826.31 259769.6165 252619.3074 395144.5968 0.514604947 0.793901548 0.560016306 0.571746401 0.692267629 0.563910811 0.657403944 0.63930852 1 18.59202116 0.039206863 1.487971772 1.000336567 0.631773165 0.684749447 0.080030245 11.10658808 16.2923414 0.081277155 0.020555123 1.094477563 -0.039206863 -0.368563403 VKEFLHNQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKEFLHNQGK 10 1 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ; 175.15 1.74E-06 1496960000 2137110 2039010 2036420 2256250 2633600 1639200 2800500 2430700 3420600 FALSE TRUE 2003352.1 2189980.422 2084724.844 2314149.195 2426767.679 2112410.43 2380591.024 2734178.246 2849679.762 0.703009554 0.768500535 0.731564603 0.812073422 0.85159312 0.741279935 0.835388964 0.959468598 1 21.44236837 1.291783758 2.185569164 1.000814362 0.76824351 0.814400533 0.041483403 0.122300531 0.984958913 0.037519513 0.011042227 19.57869579 -1.291783758 -0.232570852 VKEGMNIVEAMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 19 VKEGMNIVEAMER 13 1 P62937;P62937-2 P62937;P62937-2 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed" 0 ;;;;;;;;;;;;;;;;;; 223.7 1.40E-11 72313210000 37347310 41049940 36443650 36645100 50265650 31575770 46211230 42922420 66959320 FALSE TRUE 35009808.53 44089320.27 37308110.59 37585475.31 46317988.61 40691182.21 39282285.07 48281378.62 55783376.92 0.627602889 0.790366642 0.668803372 0.673775547 0.830318836 0.729449963 0.704193386 0.865515523 1 25.73333194 1.019475291 3.178766829 0.999044939 0.721917927 0.71982133 0.058955807 0.110407205 2.597323892 0.052162449 0.013675411 10.45864185 -1.019475291 -0.277127012 VKELEEQLENETLHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VKELEEQLENETLHK 15 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 ;;; 195.38 7.59E-09 331488000 813402 539668 644732 635247 687225 462741 800036 584127 796559 FALSE TRUE 762492.6208 579625.5802 660025.3475 651548.5135 633253.1206 596326.8147 680078.029 657056.5418 663608.1569 1.14901032 0.873445533 0.994601017 0.981827162 0.95425759 0.898612846 1.02481867 0.990127284 1 19.33997209 1.622273189 25 1.005604603 0.964958381 0.022552831 0.073461783 2.419887328 4189.29329 0.03110535 0.0171493 41.90570859 -1.622273189 -0.040646222 VKELQAEQEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VKELQAEQEDR 11 1 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 ;;; 212.59 4.95E-09 3205150000 3654930 3429920 3644610 3662010 3937460 3077170 4592380 3302050 4676400 FALSE TRUE 3426174.456 3683874.846 3731061.87 3755983.376 3628227.775 3965499.025 3903795.253 3714318.211 3895878.629 0.879435625 0.945582549 0.957694586 0.964091476 0.931298975 1.017870268 1.002032051 0.953396798 1 21.8935173 7.988554341 0.322876439 0.99327658 1.73E-13 0.606232212 0.02500353 39.0611134 0.562519705 0.022594477 22.94732967 97398964.7 -7.988554341 -0.99327658 VKELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGS(ph)SPQRDDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGSSPQRDDLK 44 3 O00139-1;O00139-5;O00139;O00139-4;O00139-2;H0Y8H2 O00139-1 KIF2A Kinesin-like protein KIF2A 1 VKELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGS(0.5)S(0.5)PQRDDLK 181.69 2.48E-28 98158000 173670 121140 133660 136340 165930 107060 191200 133020 282100 TRUE FALSE 162800.3047 130109.3316 136830.4783 139838.7152 152898.5271 137966.484 162531.335 149627.8398 235015.6876 0.692721011 0.553619773 0.582218488 0.595018642 0.6505886 0.587052232 0.691576536 0.636671711 1 17.84239754 -0.878136058 0.403567135 1.143564645 0.59145804 0.874380065 0.044978101 3.945873801 0.484784157 0.717947368 0.026734727 0.13239267 0.878136058 -0.552106605 VKELVEFAQDDDRLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKELVEFAQDDDRLR 15 2 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 196.66 4.96E-09 98114000 194425 222170 222940 213390 261200 163453 264220 179346 382790 FALSE TRUE 182256.2863 238619.698 228228.2421 218865.9487 240686.4056 210639.2277 224602.6639 201737.7429 318899.8761 0.571515701 0.748258986 0.715673662 0.686315565 0.754739728 0.660518374 0.704304645 0.632605272 1 18.28274401 -2.286704044 2.484248606 2.574350543 0.694616339 0.763004055 0.05503569 1806492.963 756930.1128 15723108.7 0.011959937 0.005167684 2.286704044 -1.879734204 VKENDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VKENDQK 7 1 P46778;M0R181 P46778 RPL21 60S ribosomal protein L21 0 ;;; 74.92 0.040926 1045410000 1256700 696273 1211910 1187790 1093670 607019 1049700 995560 1074600 FALSE TRUE 1178045.39 747825.7774 1240657.078 1218270.702 1007777.57 782255.5312 892307.2299 1119857.857 895242.3178 1.315895559 0.835333365 1.385833816 1.360827877 1.125703678 0.873791951 0.99672146 1.250899153 1 19.77191871 2.468728178 24.82995188 1.018277029 1.192185253 0.198918974 0.177756167 324.3229884 959463.4197 0.062615312 0.052469486 294.2579319 -2.468728178 0.173908224 VKENFDK ddPTM_SK-BR-3_Pertuzumab_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 76.679 0.036576 402210000 1251900 939140 1011600 1042300 1244000 959260 1174800 883450 1587000 FALSE TRUE 1173545.814 1008674.903 1035595.63 1069047.183 1146301.258 1236182.79 998649.6463 993750.6772 1322119.448 0.887624651 0.762922673 0.783284469 0.80858593 0.867017923 0.935000837 0.755339957 0.751634566 1 20.33442109 2.905017357 5.666276507 0.845220297 0.796786177 0.060822971 0.080911116 0.639641319 30.6443857 0.023767276 0.02540228 803.5582371 -2.905017357 -0.04843412 VKESSIIAPAPAEDVDT(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VKESSIIAPAPAEDVDTPPR 20 1 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 VKESSIIAPAPAEDVDT(1)PPR;VKESSIIAPAPAEDVDT(1)PPR;VKESSIIAPAPAEDVDT(1)PPR;VKESSIIAPAPAEDVDT(1)PPR;VKESSIIAPAPAEDVDT(1)PPR 157.09 1.76E-08 1486068000 2374900 2120920 2396520 2294610 2551600 2120430 2793980 2252890 2982390 TRUE FALSE 2226259.248 2277955.124 2453366.586 2353493.577 2351207.629 2732563.719 2375048.637 2534168.276 2484609.842 0.896019653 0.916826089 0.987425287 0.94722863 0.946308587 1.099795901 0.955904061 1.019946163 1 21.24458789 4.741059042 0.432738415 1.010519304 0.806658907 0.450319406 0.042770282 4.811397907 0.705757764 0.029700805 0.511298056 55088.25834 -4.741059042 -0.203860397 VKETTYYDVLGVKPNATQEELKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKETTYYDVLGVKPNATQEELKK 23 3 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 99.387 0.0011736 129800000 273280 116870 184280 141840 152330 109280 224790 149720 281140 FALSE TRUE 256175.8926 125523.1764 188651.2086 145479.8545 140366.6163 140827.362 191084.8263 168412.8716 234215.9178 1.093759532 0.535929315 0.805458529 0.621135642 0.599304341 0.601271525 0.815849017 0.719049641 1 17.8374796 0.480223046 1.111065143 0.999578567 0.701100807 0.218597828 0.160339764 2.67958458 4.373108365 0.138036061 0.042494747 3.021503112 -0.480223046 -0.29847776 VKEVHDELEDLPS(ph)PPPPLS(ph)PPPTTSPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKEVHDELEDLPSPPPPLSPPPTTSPHK 28 1 F5H039;Q9NQX3;Q9NQX3-2;H0YJ30;G3V582 F5H039 GPHN Gephyrin;Molybdopterin adenylyltransferase;Molybdopterin molybdenumtransferase 2 VKEVHDELEDLPS(1)PPPPLS(0.999)PPPTTSPHK;VKEVHDELEDLPS(1)PPPPLS(0.998)PPPT(0.001)T(0.001)SPHK 107.14 0.0011206 433870000 536640 468370 562880 632380 629020 299570 457170 362020 545910 TRUE FALSE 503052.6603 503048.6021 576231.7794 648607.9414 579619.3065 386050.9959 388621.6027 407218.9939 454794.0943 1.106110802 1.106101879 1.267016847 1.426157352 1.274465332 0.848847865 0.854500108 0.895392001 1 18.79485399 2.237609472 24.99998493 0.882635248 1.231139577 0.738937101 0.099069731 13.3976353 352129.8881 0.03847111 0.030066116 172.8261568 -2.237609472 0.348504329 VKEVHDELEDLPSPPPPLS(ph)PPPTTSPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VKEVHDELEDLPSPPPPLSPPPTTSPHK 28 1 F5H039;Q9NQX3;Q9NQX3-2;H0YJ30;G3V582 F5H039 GPHN Gephyrin;Molybdopterin adenylyltransferase;Molybdopterin molybdenumtransferase 1 VKEVHDELEDLPSPPPPLS(1)PPPTTSPHK;VKEVHDELEDLPSPPPPLS(1)PPPTTSPHK;VKEVHDELEDLPS(0.001)PPPPLS(0.537)PPPT(0.154)T(0.154)S(0.154)PHK 164.11 4.58E-12 425220000 694940 568538 533448 463387 656976 507294 950580 724700 1002670 TRUE FALSE 651444.9459 610633.1451 546101.6385 475278.2949 605379.7551 653741.5426 808049.3538 815180.3903 835317.8995 0.779876675 0.731018868 0.653765038 0.568978942 0.724729777 0.782626043 0.967355487 0.975892401 1 19.67196583 1.866772735 2.061173006 0.991931932 0.685359721 0.853854696 0.0547807 0.116210125 0.923116002 0.035624689 0.016664973 73.5821944 -1.866772735 -0.306572211 VKEYQVETIVDTLCTNMLSDKEQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKEYQVETIVDTLCTNMLSDKEQLR 25 2 Q86VP6;Q86VP6-2 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 248.58 2.17E-39 403240000 659920 595630 638970 707030 805880 509250 887760 655350 1159680 FALSE TRUE 618616.7852 639731.065 654126.6701 725173.5868 742589.4356 656262.208 754648.6296 737171.8901 966121.9162 0.640309235 0.662163909 0.677064312 0.750602563 0.768629117 0.679274734 0.78111118 0.7630216 1 19.88184573 -5 0.131011758 1.997336316 0.588685759 0.90059684 0.032215756 39.55945491 0.326272713 10.28301834 0.228921305 1.00E-05 5 -1.408650557 VKFEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VKFEER 6 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;;; 94.262 0.040751 4913630000 7756820 7892670 7379480 7288890 7845200 5518990 9131650 7031920 8725240 FALSE TRUE 7271334.483 8477051.499 7554524.75 7475935.257 7229069.638 7112232.82 7762443.857 7909870.691 7268941.077 1.000329265 1.166201708 1.039288209 1.028476525 0.994514822 0.978441391 1.067891977 1.088173725 1 22.79331378 3.664961107 4.742052632 1.028124806 1.097482663 0.15751157 0.051369614 0.264287798 11.87409189 0.013130444 0.021165438 4623.396145 -3.664961107 0.069357857 VKGDMDVSLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKGDMDVSLPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 137.59 6.86E-05 650810000 3253200 2552100 2605200 2420500 3581700 1819580 3243500 2712600 4392600 FALSE TRUE 3049588.019 2741060.139 2666996.574 2482614.128 3300407.73 2344863.208 2757167.286 3051274.081 3659446.683 0.833346755 0.749036774 0.728797768 0.678412433 0.901887093 0.640769879 0.7534383 0.833807498 1 21.8031941 0.911356337 2.864302366 0.999564627 0.749094549 0.532315315 0.072764264 0.260457252 4.78468042 0.062119516 0.016396893 8.153730196 -0.911356337 -0.250470078 VKGEEIYSMDEGIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKGEEIYSMDEGIR 14 1 Q96P70 Q96P70 IPO9 Importin-9 0 ; 115.31 0.00038926 426670000 435240 443890 429170 444150 490380 362200 547730 432840 604500 FALSE TRUE 407999.1053 476756.0775 439350.1151 455547.6409 451867.5329 466761.2602 465602.9714 486881.0268 503605.0448 0.810156907 0.946686461 0.872410075 0.904573228 0.8972657 0.926839922 0.924539927 0.966791401 1 18.94193321 1.249088428 0.649622708 1.002289592 0.889046831 0.573052513 0.033986625 0.511806731 0.518153886 0.030201569 0.013448144 17.74550765 -1.249088428 -0.113242761 VKGNVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKGNVFK 7 1 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ; 105.95 0.0071249 3636900000 4172800 4271600 4305000 4035100 5299600 3400900 5675000 4441600 6064000 FALSE TRUE 3911631.897 4587873.709 4407116.633 4138647.497 4883390.794 4382684.621 4824086.434 4996143.537 5051879.225 0.774292441 0.908151898 0.872371733 0.819229303 0.966648365 0.86753551 0.954909296 0.988967336 1 22.26838872 1.745171205 0.653530061 1.008152347 0.856575813 0.576137221 0.048175833 0.520218926 0.457833384 0.041582491 0.021888095 55.61234464 -1.745171205 -0.151576534 VKHYLILPSEEEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKHYLILPSEEEGR 14 1 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 0 54.09 0.086178 283190000 283530 280380 284320 274600 327970 215380 338980 253590 255670 FALSE TRUE 265784.3634 301139.6269 291064.2047 281646.7009 302212.5592 277556.7096 288153.0959 285251.2697 212997.0253 1.24783134 1.41382081 1.366517698 1.322303448 1.418858121 1.303101342 1.35285033 1.339226542 1 17.70047376 -1.424624697 0.539220932 0.824216917 1.359169428 0.81974242 0.05075218 14.99032051 1.941183737 3.72924308 0.02003761 0.037616233 1.424624697 0.534952511 VKKPAPPQHFS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKKPAPPQHFSPR 13 2 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 VKKPAPPQHFS(1)PR;VKKPAPPQHFS(1)PR 80.07 0.0098037 422180000 508640 393300 473160 413480 527740 383040 571970 499030 639050 TRUE FALSE 476805.1303 422420.3412 484383.5786 424090.5968 486293.4292 493617.4299 486208.4084 561334.994 532388.4266 0.895596348 0.793443884 0.909831158 0.796581172 0.913418483 0.927175358 0.913258787 1.054371143 1 19.02211968 1.713915608 0.946856383 1.021441959 0.850521679 0.63499701 0.047612181 0.316356322 0.535037498 0.038317276 0.015741063 51.75062603 -1.713915608 -0.17092028 VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK 39 3 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 221.64 5.94E-40 138920000 368830 112640 191040 182350 222950 107260 272750 124990 438970 FALSE TRUE 345745.5887 120979.9828 195571.559 187029.4097 205440.4063 138224.2208 231853.6696 140595.2766 365703.0711 0.945427085 0.330814785 0.534782381 0.511424225 0.561768338 0.377968444 0.633994319 0.384451999 1 18.48031322 -1.372297694 3.603606654 1.002627152 0.518439368 0.412266207 0.173446387 10454932.5 6093789.51 205320.2121 0.035307492 0.04243286 1.372297694 -0.484187784 VKLDGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VKLDGSR 7 1 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ;;;;; 117.04 0.0048531 4752660000 8114790 9237280 7167470 6812640 10285510 5215370 8770570 8320980 11563740 FALSE TRUE 7606899.779 9921217.823 7337485.773 6987463.876 9477727.534 6720962.655 7455504.45 9359872.67 9633677.089 0.789615399 1.029847454 0.761649545 0.725316389 0.983812043 0.697652889 0.773900182 0.97157841 1 23.19965514 1.150691213 6.438232824 0.994521469 0.830751934 0.286724112 0.106367459 0.30437064 17.60016383 0.100730229 0.025395893 14.14787498 -1.150691213 -0.163769536 VKLEAEIATYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VKLEAEIATYR 11 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 187.44 3.27E-06 23519270000 27002240 24757330 24694820 24006540 27635090 21403300 30880560 24591080 37374440 FALSE TRUE 25312218 26590388.47 25280592.79 24622588.46 25464741.51 27582085.26 26250306.71 27661330.47 31136404.52 0.81294608 0.853996757 0.811930381 0.790797423 0.817844639 0.885846831 0.843074437 0.888391929 1 24.89209902 0.620893104 0.659518813 1.002889706 0.822066608 0.846001391 0.023527439 0.514155239 0.415461958 0.026016269 0.00924293 4.17727536 -0.620893104 -0.180823098 VKLEAEIATYRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKLEAEIATYRR 12 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 154.23 4.01E-05 1340030000 703330 1147840 949030 1065160 1739580 786040 1359600 965450 3695400 FALSE TRUE 659309.8308 1232827.268 971541.4398 1092493.809 1602960.404 1012956.988 1155740.602 1085988.558 3078613.867 0.214158014 0.400448813 0.315577556 0.354865487 0.520676016 0.329030217 0.375409406 0.352752441 1 21.5538495 -4.813928552 0.405930818 10 0.349995933 0.877704725 0.075406584 204.4816459 1.638421159 1625.878276 0.042272326 1.53E-05 4.813928552 -9.650004067 VKLEGSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKLEGSK 7 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 87.308 0.03343 0 1068400 934700 811580 531470 562570 321550 503440 475180 644420 FALSE TRUE 1001530.751 1003906.161 830831.0609 545108.42 518388.0215 414376.2651 427953.8457 534507.269 536862.1389 1.86552688 1.869951497 1.547568734 1.015360146 0.965588713 0.771848553 0.797139181 0.995613641 1 19.03419214 3.340869042 1.570915551 0.864854292 1.854166747 0.957568949 0.084900459 0.062361452 0.315959804 0.027160408 0.043249444 2192.143813 -3.340869042 0.989312455 VKPAPDETSFSEALLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKPAPDETSFSEALLK 16 1 Q12905;B4DY09;A0A0A0MRL0;X6R6Z1 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 148.56 8.39E-07 174830000 346100 262620 304550 288520 331120 220580 381520 286240 374540 FALSE TRUE 324438.2188 282064.6581 311774.0698 295923.9117 305115.1709 284257.8652 324314.6179 321977.6941 312026.8544 1.039776591 0.903975584 0.999189863 0.948392446 0.977849075 0.911004489 1.039380468 1.031890972 1 18.25131067 1.664256495 9.040067498 1.026408237 0.960766048 0.326962861 0.040555552 0.115751684 15.35377832 0.01754001 0.0093074 46.159011 -1.664256495 -0.06564219 VKPAPDETSFSEALLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKPAPDETSFSEALLKR 17 2 Q12905;B4DY09;A0A0A0MRL0;X6R6Z1 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 118.24 0.00010036 768630000 601090 615460 545430 575490 672450 432070 768920 553420 1128080 FALSE TRUE 563468.8499 661029.2988 558367.8572 590258.0477 619638.4895 556801.5949 653627.5843 622515.7052 939796.1603 0.599564963 0.703375186 0.594137198 0.628070291 0.659332859 0.5924706 0.695499313 0.662394391 1 19.84198835 -0.120703091 0.76953073 1.012919107 0.636319047 0.900686178 0.037597362 1.870978708 1.026792556 0.106880275 0.011839161 0.757350487 0.120703091 -0.37660006 VKPAS(ph)PVAQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VKPASPVAQPK 11 1 Q96EV2;H0Y3K4 Q96EV2 RBM33 RNA-binding protein 33 1 VKPAS(1)PVAQPK;VKPAS(1)PVAQPK;VKPAS(1)PVAQPK;VKPAS(1)PVAQPK 155.56 1.91E-05 4641900000 15487500 8429100 10974700 10259000 11686400 7766200 14457000 9708000 16564000 TRUE FALSE 14518165.02 9053199.334 11235025.07 10522263.31 10768597.28 10008175.87 12289307.06 10920065.17 13799361.39 1.05208963 0.656059297 0.814169928 0.762518135 0.780369249 0.725263697 0.890570709 0.791345691 1 23.71809817 0.365825609 0.765126623 1.002213721 0.786258959 0.220972809 0.106842134 2.853194566 2.351401247 0.111338858 0.033142789 2.321804287 -0.365825609 -0.215954762 VKPET(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 83.862 0.028875 10569360000 7469000 4832720 6310000 6118600 5583500 5144220 7565300 5185470 5675900 TRUE FALSE 7001528.623 5190539.617 6459676.18 6275613.635 5144994.433 6629272.805 6430953.498 5832887.344 4728555.622 1.480690761 1.097700869 1.366099227 1.327173483 1.088068925 1.401965702 1.360024923 1.233545254 1 22.17296814 0.97042254 20.48300395 0.999999995 1.29142271 0.367098648 0.124044806 320.5580933 221994.9059 0.110951662 0.027737916 9.34162737 -0.97042254 0.291422714 VKPET(ph)PPRQSHSGSIS(ph)PYPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKPETPPRQSHSGSISPYPK 20 2 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 VKPET(0.994)PPRQS(0.004)HS(0.004)GS(0.004)IS(0.995)PYPK;VKPET(1)PPRQSHS(0.002)GS(0.027)IS(0.97)PYPK 124.03 5.22E-05 1081180000 968320 737140 736210 926890 1207640 466520 1147610 723040 2160800 TRUE FALSE 907714.5797 791718.6126 753673.2489 950675.5666 1112796.826 601196.7507 975536.5344 813313.1356 1800148.521 0.504244272 0.439807384 0.418672815 0.528109517 0.618169453 0.333970638 0.541920027 0.451803352 1 20.77968451 -4.381729322 0.516766227 9.9997172 0.470819829 0.816146603 0.077505408 560.2445016 4.86170264 5761.362259 0.032895681 4.15E-05 4.381729322 -9.528897371 VKPETPPRQS(ph)HSGSISPYPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKPETPPRQSHSGSISPYPK 20 2 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VKPET(0.379)PPRQS(0.538)HS(0.07)GS(0.013)ISPYPK 105.38 0.000122 461010000 906420 863130 876240 1043400 1259500 582790 1190100 877110 2029800 TRUE FALSE 849688.7902 927037.0433 897024.8266 1070175.41 1160583.951 751032.0122 1011655.553 986619.1143 1691013.267 0.502473166 0.548213939 0.530465872 0.632860446 0.686324568 0.444131354 0.598254061 0.583448476 1 20.68945655 0.274610353 1.555405081 1.000110441 0.560581163 0.806727967 0.066891941 3.174672537 6.326849286 0.060968707 0.017385123 1.881959844 -0.274610353 -0.439529277 VKPFVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKPFVVR 7 1 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 117.93 0.0046691 1041400000 1670660 2129840 1698820 1738240 2174120 1232720 2030540 1894940 1778840 FALSE TRUE 1566096.373 2287535.57 1739116.813 1782846.181 2003373.385 1588586.252 1726079.378 2131527.43 1481940.112 1.056787896 1.543608646 1.173540549 1.203048738 1.351858532 1.071963866 1.164743004 1.438335742 1 20.49905572 3.730471468 24.75672557 1.203276223 1.342052222 0.043740328 0.170053469 275.2042157 2033615.456 0.03983197 0.068277914 5376.151122 -3.730471468 0.138775999 VKPLQDQNELFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKPLQDQNELFGK 13 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 104.7 0.00098177 0 471190 356550 351590 383560 454280 243160 440580 346060 510160 FALSE TRUE 441699.059 382949.333 359929.8808 393402.799 418602.6813 313356.3446 374519.1191 389266.3528 425011.0002 1.039265004 0.901033933 0.846871918 0.925629687 0.984921993 0.737289963 0.881198649 0.915897124 1 18.69714066 4.736711279 3.895082188 0.885491996 1.053719347 0.248669945 0.073792668 0.301495513 9.273183208 0.016458913 0.144349373 54539.51594 -4.736711279 0.168227351 VKPPGGHS(ph)PQVNHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKPPGGHSPQVNHLK 15 1 Q92610 Q92610 ZNF592 Zinc finger protein 592 1 VKPPGGHS(1)PQVNHLK 158.45 1.10E-06 424860000 853780 569290 621160 597780 788650 508740 909610 746480 1239900 TRUE FALSE 800343.4338 611440.8239 635894.2085 613120.0468 726712.6103 655604.9793 773222.4249 839679.6712 1032952.68 0.774811324 0.59193498 0.615608266 0.593560633 0.70352943 0.634690235 0.748555515 0.812892679 1 19.97834273 1.032166846 0.961665596 0.999306244 0.634335762 0.796766281 0.056562963 0.218177469 0.435717857 0.048945743 0.016612829 10.76878845 -1.032166846 -0.364970482 VKPPPS(ph)PTTEGPSLQPDLAPEEAAGTQRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKPPPSPTTEGPSLQPDLAPEEAAGTQRPK 30 2 Q9Y2D5;Q9Y2D5-5;Q9Y2D5-7;Q9Y2D5-6;Q9Y2D5-4 Q9Y2D5 AKAP2 A-kinase anchor protein 2 1 VKPPPS(0.857)PT(0.071)T(0.071)EGPSLQPDLAPEEAAGTQRPK 94.629 0.00042664 149970000 147040 93738 98605 113860 114130 73618 121050 86422 121350 TRUE FALSE 137837.0289 100678.4591 100943.9572 116781.8404 105166.6902 94870.32151 102899.6763 97211.97694 101095.901 1.363428462 0.995870832 0.998497032 1.155159004 1.040266609 0.938419071 1.017842219 0.961581785 1 16.62536498 4.740310312 24.97794115 1.013464765 1.36342858 0.784803534 0.057593731 70.528492 1006752.946 0.013600884 0.088286279 54993.36722 -4.740310312 0.349963815 VKPTLIAVRPPVPLPAPSHPASTNEPIVLED ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKPTLIAVRPPVPLPAPSHPASTNEPIVLED 31 2 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 0 41.432 0.085666 123740000 267600 268770 278530 276360 325090 248170 309870 281820 339600 FALSE TRUE 250851.3937 288670.0105 285136.8631 283451.8655 299558.7427 319812.6503 263407.8702 317005.8474 282918.5661 0.886655822 1.020328975 1.007840762 1.001884993 1.058816135 1.130405313 0.931037768 1.120484427 1 18.11002733 5.590322684 1.333850173 1.031423315 9.94E-12 0.376751024 0.059023759 12.09179642 3.401074824 0.014760646 29.09225473 389334.3158 -5.590322684 -1.031423315 VKQEEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKQEEQR 7 1 O75410-3;E7ET87;E7EVI4;O75410-2;O75410;O75410-9;O75410-7;H0YAY0;O75410-6;O75410-4;O75410-5;O75410-10;B4E3H6;H0YBT8;O75410-8 O75410-3 TACC1 Transforming acidic coiled-coil-containing protein 1 0 ; 123.72 0.0038452 332350000 481970 486500 449950 436940 575670 335040 488280 549260 691040 FALSE TRUE 451804.358 522520.9662 460623.0265 448152.6201 530459.2003 431760.6091 415066.947 617836.3201 575700.9597 0.784790003 0.907625665 0.800108144 0.778446887 0.92141448 0.749973753 0.720976646 1.073189665 1 19.13496009 1.229741976 24.999998 1.036594966 0.81310922 0.679192605 0.064969043 128.8383412 365230.7186 0.060635091 0.016070532 16.97234987 -1.229741976 -0.223485746 VKQIESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKQIESK 7 1 P10599;P10599-2 P10599 TXN Thioredoxin 0 ; 101.64 0.0081244 4649200000 8725300 6569700 7546800 7605700 8796800 6495800 11916800 7052500 12624800 FALSE TRUE 8179199.048 7056127.424 7725813.66 7800875.138 8105934.813 8371032.009 10129986.47 7933020.149 10517639.32 0.777664911 0.670885092 0.734557768 0.741694491 0.770699067 0.795904076 0.963142599 0.754258623 1 23.32630759 1.732431641 0.488061808 0.982386646 0.697578222 0.590289471 0.065563723 0.528620208 0.303930477 0.063087432 0.044124908 54.00471029 -1.732431641 -0.284808424 VKS(ph)PGGPGSHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VKSPGGPGSHVR 12 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 VKS(0.846)PGGPGS(0.154)HVR;VKS(0.987)PGGPGS(0.013)HVR;VKS(0.77)PGGPGS(0.23)HVR;VKS(1)PGGPGSHVR;VKS(0.991)PGGPGS(0.009)HVR;VKS(1)PGGPGSHVR 130.01 0.00013536 5949480000 2863390 2325310 2483670 2365790 2819050 1991780 3054540 2475530 4026900 TRUE FALSE 2684175.531 2497478.372 2542583.825 2426500.177 2597653.185 2566774.552 2596540.084 2784605.37 3354784.375 0.800103742 0.744452726 0.757897838 0.723295421 0.774313009 0.765108652 0.773981214 0.830040044 1 21.67778861 0.708047438 1.255931042 1.000133339 0.75651342 0.935520451 0.019686099 0.199911671 0.522296513 0.01694223 0.005131892 5.105607654 -0.708047438 -0.243619919 VKS(ph)PQRPSDWSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKSPQRPSDWSK 12 2 Q5UIP0-2;Q5UIP0;H7BZN3 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 VKS(1)PQRPSDWSK;VKS(0.948)PQRPS(0.049)DWS(0.003)K 92.439 0.0040356 1119860000 897370 683820 720750 763620 806060 545490 1087700 719660 766810 TRUE FALSE 841205.2136 734450.7443 737846.5304 783215.782 742755.2991 702964.1077 924609.4827 809511.1352 638824.4572 1.316801829 1.149691024 1.155006703 1.226026607 1.162690768 1.100402622 1.447360808 1.267188703 1 19.28506002 VKS(ph)S(ph)TPPRQSPS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKSSTPPRQSPSR 13 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 VKS(0.948)S(0.55)T(0.501)PPRQS(0.285)PS(0.716)R 77.871 0.016358 620080000 794220 492840 551750 554120 614910 433280 673010 493980 618990 TRUE FALSE 744511.1879 529330.3864 564837.7706 568339.6573 566617.449 558360.9023 572098.3984 555654.4904 515676.5702 1.443756089 1.02647748 1.095333399 1.102124258 1.098784552 1.082773456 1.109413209 1.077525182 1 18.97610697 4.74369695 24.98171092 1.07984858 1.443756241 0.915376064 0.035287479 138.5496245 673845.7699 0.007839696 0.066484098 55423.88306 -4.74369695 0.363907662 VKS(ph)ST(ph)PPRQS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKSSTPPRQSPSR 13 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 VKS(0.996)S(0.154)T(0.848)PPRQS(0.501)PS(0.501)R 83.666 0.016163 384460000 826430 579650 659670 617630 657970 471910 751010 527160 654610 TRUE FALSE 774705.2215 622567.8891 675317.6839 633479.4314 606295.6903 608142.7562 638403.0225 592977.0864 545351.3621 1.420561633 1.141590418 1.238316672 1.161598697 1.111752409 1.115139337 1.170626988 1.087330348 1 19.05682651 8 0.181612481 1.034890781 2.227339534 0.652871165 0.065045875 39.31257346 0.445142107 0.136347999 12.98488826 100000000 -8 1.192448754 VKSGT(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VKSGTPPR 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VKS(0.007)GT(0.993)PPR;VKS(0.161)GT(0.839)PPR;VKS(0.08)GT(0.92)PPR;VKS(0.044)GT(0.956)PPR 113.44 0.0046031 4396570000 3095900 2903590 2958080 2895060 3318160 2306610 3680910 2587210 3751020 TRUE FALSE 2902133.145 3118574.825 3028247.055 2969352.141 3057565.098 2972490.862 3128991.717 2910228.864 3124950.529 0.928697308 0.997959742 0.969054398 0.950207727 0.978436321 0.951212134 1.001293201 0.931287979 1 21.57540192 -1.298047881 4.516516543 1.000020937 0.969005114 0.142127287 0.025137565 4.72E-06 7.33E-07 0.021667346 0.005103595 0.05034451 1.298047881 -0.031015823 VKSST(ph)PPRQSPS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKSSTPPRQSPSR 13 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 VKS(0.072)S(0.082)T(0.845)PPRQS(0.054)PS(0.947)R 73.11 0.041629 105140000 132080 136090 136510 146200 193410 111800 181420 137930 236870 TRUE FALSE 123813.3486 146166.2452 139748.0817 149951.7395 178220.3588 144074.8451 154217.7552 155150.8641 197334.8668 0.627427634 0.740701568 0.708177343 0.759884667 0.903136692 0.730103339 0.781502822 0.786231377 1 17.59028636 -5 0.099913667 1.769487635 0.586730528 0.685559995 0.058048479 110.691198 0.753174057 17.86307968 0.948452471 1.00E-05 5 -1.182757107 VKT(ph)PEMIIQKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKTPEMIIQKPK 12 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VKT(1)PEMIIQKPK;VKT(1)PEMIIQKPK 148.7 0.0031764 5854100000 11084000 4628100 6997800 6488100 7078600 4252700 8548500 5080900 8810900 TRUE FALSE 10390272.23 4970769.34 7163791.121 6654595.63 6522675.31 5480385.453 7266731.785 5715261.549 7340303.869 1.415509822 0.677188496 0.975952937 0.906583126 0.888611075 0.74661561 0.98997697 0.778613754 1 22.80740836 4.751424689 24.84500393 0.869497701 1.415510201 0.715582084 0.107992918 1009.056593 1948802.181 0.023634164 0.438094528 56418.90968 -4.751424689 0.5460125 VKT(ph)PSFGISAPQVSIPDVNVNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKTPSFGISAPQVSIPDVNVNLK 23 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VKT(0.476)PS(0.365)FGIS(0.159)APQVSIPDVNVNLK 64.583 0.011658 0 70312 78039 69848 53719 67579 49049 67506 48070 103480 TRUE FALSE 65911.29743 83817.08876 71504.82754 55097.52049 62271.61794 63208.65006 57384.10199 54071.64532 86208.51949 0.764556657 0.972259926 0.829440384 0.639119205 0.722337169 0.733206537 0.665643052 0.627219278 1 16.39554283 3.419465343 5.370314217 0.711733627 0.885495127 0.193071146 0.115714004 0.203037911 11.97917457 0.028379131 0.039231561 2627.031882 -3.419465343 0.1737615 VKTSEDADELHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKTSEDADELHK 12 1 Q9UKX7-2;Q9UKX7 Q9UKX7-2 NUP50 Nuclear pore complex protein Nup50 0 ; 112.42 0.00076632 328090000 996950 633110 837580 730650 808180 588220 1004950 689890 1082000 FALSE TRUE 934552.6791 679986.1232 857447.7931 749399.716 744708.8028 758029.565 854267.077 776024.2851 901407.21 1.036770805 0.754360644 0.951232455 0.831366454 0.826162465 0.840940206 0.947703843 0.860903126 1 19.78181946 0.346291519 0.745741279 1.001362734 0.869969377 0.163739505 0.080483207 3.704341886 2.881432396 0.088015522 0.025525759 2.219685876 -0.346291519 -0.131393357 VKVDGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VKVDGPR 7 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;; 81.548 0.024536 589830000 1122770 2504950 849700 837340 2899060 612400 1141780 2631530 2792620 FALSE TRUE 1052497.83 2690419.104 869855.2853 858827.562 2671379.522 789189.9385 970580.6888 2960082.313 2326513.681 0.45239271 1.156416627 0.373887887 0.369147867 1.148232888 0.339215688 0.417182455 1.272325341 1 21.14973824 1.233627479 24.99969673 1.136162829 0.625384989 0.3300003 0.312075702 157.2553618 796878.3197 0.260475254 0.073150616 17.12487774 -1.233627479 -0.51077784 VKVDGPRS(ph)PSYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VKVDGPRSPSYGR 13 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 1 VKVDGPRS(0.951)PS(0.049)YGR;VKVDGPRS(0.849)PS(0.151)YGR;VKVDGPRS(0.993)PS(0.007)YGR;VKVDGPRS(0.992)PS(0.008)YGR;VKVDGPRS(0.996)PS(0.004)YGR 131.18 6.96E-05 10783100000 3570360 6436660 4491090 6102980 10586300 2256690 4345420 4671460 24260000 TRUE FALSE 3346897.541 6913237.004 4597620.776 6259592.799 9754894.701 2908159.769 3693864.612 5254702.064 20210849.27 0.165599055 0.34205574 0.22748281 0.309714486 0.482656348 0.143891023 0.182766422 0.259994125 1 24.26862661 -1.403986896 2.8371443 1.014977108 0.264339412 0.845310482 0.098910693 5864353.924 6737832.311 712683.275 0.024286192 0.03944692 1.403986896 -0.750637697 VKVDGPRSPS(ph)YGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKVDGPRSPSYGR 13 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 1 VKVDGPRS(0.357)PS(0.642)Y(0.001)GR 119.54 0.00017757 3205300000 417170 555630 418080 459880 1003800 158510 350970 542760 2034500 TRUE FALSE 391060.0744 596769.4233 427997.055 471681.2994 924965.5971 204269.2638 298345.3067 610524.7808 1694928.807 0.230723599 0.352091144 0.252516243 0.278289741 0.545725339 0.120517902 0.176022324 0.36020674 1 20.69279325 0.956343723 20.5356143 1.000000002 0.279015694 0.797705185 0.1131558 367.7447185 172985.4458 0.106436017 0.02660948 9.043649516 -0.956343723 -0.720984308 VKVDPSHDASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VKVDPSHDASK 11 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ;;;;; 115.14 0.00069919 2508710000 3816630 2718740 3036160 2884220 3048010 2177281 4161780 2625070 3763280 FALSE TRUE 3577753.941 2920038.338 3108179.149 2958233.968 2808631.59 2805826.679 3537759.725 2952815.768 3135164.256 1.141169536 0.931382888 0.991392761 0.943565863 0.895848307 0.894953645 1.128412879 0.94183766 1 21.5801096 VKVEPAVDTSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VKVEPAVDTSR 11 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ;; 155.86 2.86E-05 2018980000 3481930 3294510 2888360 2875970 3508680 1982570 3970090 3091540 5319700 FALSE TRUE 3264002.217 3538438.948 2956873.263 2949772.259 3233122.426 2554905.775 3374811.861 3477525.574 4431807.703 0.736494549 0.798418881 0.667193493 0.665591212 0.729526785 0.576492922 0.76149781 0.784674293 1 22.07946385 0.821893638 1.798876677 0.999085115 0.704552853 0.710623924 0.059677914 0.353773353 2.090605365 0.056064524 0.015824732 6.635805351 -0.821893638 -0.294532261 VKVETYNDESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 182.1 5.41E-06 2256070000 2492120 2089870 2328910 2518660 2499570 1957230 2922910 2188270 2541800 FALSE TRUE 2336142.658 2244606.149 2384152.845 2583293.08 2303263.855 2522250.528 2484646.78 2461480.326 2117557.159 1.103225312 1.059997903 1.125897752 1.219940188 1.087698552 1.191113315 1.173355236 1.162415057 1 21.01396948 3.654908339 3.61411632 1.151742255 1.081836905 0.097477137 0.062408339 0.338565324 8.623529692 0.014899739 0.024841154 4517.605875 -3.654908339 -0.06990535 VKVFGPGVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 88.596 0.011023 263160000 136420 191590 193070 193900 224870 140020 187940 168050 195320 FALSE TRUE 127881.7157 205775.5229 197649.7116 198875.8023 207209.6173 180441.501 159760.1417 189031.4124 162719.8302 0.785901236 1.264600158 1.21466272 1.2221977 1.273413431 1.108909103 0.981811139 1.161698683 1 17.31203055 2.002108784 24.76419447 1.045701737 1.18019312 0.078328529 0.146764797 105.7054574 1241318.74 0.051514486 0.037797387 100.4867461 -2.002108784 0.134491383 VKVGVNGFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKVGVNGFGR 10 1 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 144.65 2.90E-05 3402700000 1873270 2375200 2301820 2568500 2633800 1962030 2558250 2102340 2516400 FALSE TRUE 1756025.375 2551062.279 2356420.257 2634412.058 2426951.972 2528436.21 2174664.162 2364821.777 2096396.583 0.837639876 1.216879621 1.124033628 1.256638214 1.157677889 1.206086782 1.037334338 1.128041228 1 20.99948023 -0.833506774 5.800683933 0.999999977 1.131458794 0.087673237 0.11760535 3.06E-08 6.33E-09 0.102595371 0.024181957 0.14672132 0.833506774 0.131458817 VKVPEVDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKVPEVDVR 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 93.058 0.0088067 496900000 2502100 2822700 2192900 2068800 3623500 1491230 2536300 2814300 3984600 FALSE TRUE 2345498.027 3031695.645 2244916.624 2121888.91 3338924.926 1921723.893 2156005.361 3165671.55 3319544.519 0.706572246 0.913286636 0.676272486 0.639210861 1.005838273 0.578911921 0.64948831 0.953646361 1 21.66255387 1.13533178 6.222929203 0.993805239 0.743114862 0.370670753 0.129432302 0.229819264 11.4002917 0.119732177 0.030162126 13.65626012 -1.13533178 -0.250690377 VKWGDIEFPPPFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VKWGDIEFPPPFGR 14 1 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ; 96.962 0.0028851 246820000 732020 964080 887910 920760 1150130 646200 1090840 793900 1800450 FALSE TRUE 686204.1749 1035461.486 908971.6445 944388.2604 1059803.429 832747.4498 927278.6689 893020.1626 1499943.264 0.457486754 0.690333769 0.606004018 0.629615988 0.706562345 0.555185966 0.618209163 0.595369294 1 20.5164765 -1.851391932 2.678255837 1.153529412 0.616105428 0.75916109 0.069348037 7688417.451 5651555.043 7573999.512 0.014980117 0.014080176 1.851391932 -0.537423984 VKYEETVFYGLQYILNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VKYEETVFYGLQYILNK 17 1 P43490;A0A0C4DFS8;C9JG65 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 143.14 5.11E-07 169160000 435230 421470 407200 418260 503740 312460 520240 460520 462110 FALSE TRUE 407989.7312 452676.0773 416858.9763 428993.2597 464178.2924 402662.1296 442234.8417 518016.9357 384980.8557 1.059766285 1.175840488 1.082804431 1.114323617 1.205717857 1.045927671 1.148719047 1.345565443 1 18.55442718 1.464632755 17.94088961 1.197566225 1.119643719 0.047795728 0.095398473 0.882044195 1261.580635 0.044343484 0.020523286 29.14961042 -1.464632755 -0.077922505 VLADPSDDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLADPSDDTK 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 Q15149-3;Q15149-4;Q15149-5;Q15149-8;A0A075B730;P58107 PLEC;EPPK1 Plectin;Epiplakin 0 ; 131.44 0.00058181 311550000 1669790 1263770 1433810 1452950 1521690 1071480 1798860 1189150 1576930 FALSE TRUE 1565280.825 1357340.846 1467820.65 1490235.157 1402182.606 1380798.882 1529137.643 1337617.995 1313730.196 1.191478151 1.033196048 1.117292314 1.134354041 1.067329205 1.051052101 1.163966275 1.018183185 1 20.32523759 1.093135449 7.436159218 1.000456317 1.10147252 0.410809501 0.049132347 0.207276676 13.21056125 0.043505059 0.010905093 12.39183006 -1.093135449 0.101016202 VLAEDEELYGDFEDLETGDVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VLAEDEELYGDFEDLETGDVHK 22 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 0 ;;; 261.78 2.54E-37 164013000 326734 260013 304173 281309 281557 234070 365936 252764 338022 FALSE TRUE 306284.3022 279264.6331 311388.1272 288527.8652 259444.649 301642.2092 311067.294 284322.1418 281603.9445 1.087642088 0.991692902 1.105766213 1.024587442 0.921310422 1.071157614 1.104626906 1.009652554 1 18.10330802 1.022721087 24.91345429 0.999999811 1.045193599 0.078131767 0.056086583 479.76844 526059.8121 0.05328869 0.013322172 10.53709965 -1.022721087 0.045193788 VLAELYVSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLAELYVSDR 10 0 O43776;K7EIU7;O43776-2;K7EJ19;K7EQ35 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 101.9 0.010058 40493000 68225 92665 74330 77670 94564 63981 80807 82921 101614 FALSE TRUE 63954.91904 99526.01302 76093.1427 79663.14369 87137.32489 82451.27606 68690.74053 93273.86938 84653.96695 0.75548638 1.175680439 0.898872734 0.941044426 1.0293354 0.973980063 0.811429671 1.101825145 1 16.36929006 1.972738572 24.75808711 0.935775744 0.982053261 0 0.127723427 2936.893278 2667202.931 0.048801475 0.031602659 93.91578052 -1.972738572 0.046277516 VLAGDKNFITAEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VLAGDKNFITAEELR 15 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;;; 209.66 2.07E-09 2935680000 6491580 4405910 3032200 3054090 3717920 2249370 3667200 3513340 3979550 FALSE TRUE 6085283.596 4732128.161 3104125.216 3132463.12 3425929.561 2898726.604 3117337.405 3951988.233 3315337.396 1.835494512 1.427344368 0.936292403 0.94483992 1.03335774 0.874338342 0.940277574 1.19203199 1 21.66072427 4.539544457 1.312958811 0.974795851 2.02768547 0.909839931 0.088925275 0.247549611 0.488199698 0.024189011 0.316851678 34637.33396 -4.539544457 1.052889619 VLAGDKNFITAEELRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLAGDKNFITAEELRR 16 2 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ; 232.74 7.68E-17 1409530000 2100840 2769100 2283400 2370700 3242600 1696120 2811000 2243000 4604300 FALSE TRUE 1969352.175 2974127.045 2337563.326 2431536.176 2987939.276 2185762.31 2389516.646 2523043.487 3835812.585 0.513411991 0.775357758 0.609404989 0.6339038 0.77895862 0.569830319 0.622949269 0.657759844 1 21.8711008 -1.515780773 2.472078644 1.022121013 0.651777735 0.649156153 0.081846231 2611083.747 2376507.221 387398.8986 0.019629029 0.030494339 1.515780773 -0.370343277 VLAMSGDPNYLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLAMSGDPNYLHR 13 0 P30153;B3KQV6;E9PH38 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 117.93 0.00046742 289710000 448280 1075200 736670 857330 1197800 930830 863620 828680 1344000 FALSE TRUE 420222.955 1154808.927 754144.1603 879330.5393 1103729.62 1199545.51 734128.1985 932142.5221 1119677.717 0.375307062 1.03137618 0.673536812 0.785342537 0.985756528 1.071331055 0.655660274 0.832509666 1 20.0946521 4.751676432 24.67661367 0.859033771 0.375306688 0.53609624 0.14628968 1526.30297 2871585.98 0.034040288 0.637701935 56451.62291 -4.751676432 -0.483727082 VLAPILPDNFST(ph)PTGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VLAPILPDNFSTPTGSR 17 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 VLAPILPDNFS(0.099)T(0.779)PT(0.09)GS(0.032)R;VLAPILPDNFS(0.05)T(0.948)PT(0.002)GSR;VLAPILPDNFS(0.005)T(0.975)PT(0.02)GSR;VLAPILPDNFS(0.007)T(0.981)PT(0.011)GSR 269.59 2.49E-27 636250000 283650 318899 323773 322353 327150 313272 396555 284111 450792 TRUE FALSE 265896.8528 342510.6138 331453.0485 330625.1237 301456.9587 403708.5409 337095.2592 319582.8838 375551.903 0.708016257 0.91201938 0.882575873 0.880371318 0.802703851 1.074974025 0.897599657 0.850968618 1 18.51865278 2.279820493 24.99996899 0.946580431 0.85550989 0.328244102 0.081626688 209.5195589 126950.1936 0.026740005 0.02237208 190.4673297 -2.279820493 -0.091070541 VLATVTKPVGGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLATVTKPVGGDK 13 1 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 0 155.43 1.26E-06 0 2546800 1821800 2262200 2098200 2102000 1570500 2847800 1839600 2515900 FALSE TRUE 2387400.334 1956687.968 2315860.452 2152043.364 1936917.399 2023877.855 2420798.828 2069278.109 2095980.037 1.139037726 0.933543227 1.104905778 1.026748026 0.924110614 0.965599777 1.154972273 0.98726041 1 20.99919355 VLAVNQENEHLMEDYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 VLAVNQENEHLMEDYEK 17 0 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ;;;;;; 347.2 1.45E-87 2643170000 6493530 4295840 4780980 4244090 4224470 3303380 5612250 4512150 4787740 FALSE TRUE 6087111.549 4613908.463 4894387.103 4353000.535 3892697.167 4257012.18 4770745.214 5075501.86 3988635.264 1.526113857 1.156763694 1.227083145 1.091350862 0.975947137 1.067285399 1.1960846 1.272490846 1 21.92746377 7.396972963 1.125582423 1.124142078 199.9986766 0.629707815 0.096149947 550.4666608 1.859509094 0.027565409 281223.3757 24944394.29 -7.396972963 198.8745345 VLDEEGS(ph)ER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VLDEEGSER 9 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 VLDEEGS(1)ER;VLDEEGS(1)ER;VLDEEGS(1)ER;VLDEEGS(1)ER;VLDEEGS(1)ER 205.32 1.59E-05 4991460000 3353630 2300758 3142970 2603230 1933149 3645470 3617420 2474700 1094105 TRUE FALSE 3143732.285 2471108.516 3217522.733 2670033.289 1781327.275 4697858.01 3075021.453 2783671.742 911491.8073 3.448996754 2.711059492 3.529952444 2.929300371 1.954298723 5.154032074 3.373613925 3.053973409 1 19.79787016 5.061255944 18.35296834 3.148316641 7.455665728 0 1.080550528 40690989.12 188585528.6 0.232447915 6782677986 115147.8794 -5.061255944 4.307349087 VLDEEGS(ph)EREFDEDS(ph)DEKEEEEDTYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLDEEGSEREFDEDSDEKEEEEDTYEK 27 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 2 VLDEEGS(1)EREFDEDS(0.999)DEKEEEEDT(0.001)YEK 90.843 0.0035121 86932000 148920 42509 66986 74817 64087 54650 86401 54220 54711 TRUE FALSE 139599.363 45656.41059 68574.93955 76736.93088 59053.86553 70426.56783 73445.97216 60989.48635 45579.38065 3.062774461 1.001690017 1.504516704 1.683588715 1.295626766 1.545140957 1.611385918 1.338093793 1 15.4760937 4.747210101 24.96010106 1.405366188 3.062775318 0.836949023 0.234061832 428.9784091 1237889.741 0.054304165 0.643125096 55874.04342 -4.747210101 1.657409129 VLDFEHFLPMLQTVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLDFEHFLPMLQTVAK 16 0 F8VPF3;P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;G3V1Y7;P60660-2;G8JLA2;F8VZU9;F8W180 F8VPF3;P60660;P60660-2 MYL6 Myosin light polypeptide 6 0 146.16 8.73E-07 127170000 255190 306710 221540 227220 338480 162180 225000 286040 308900 FALSE TRUE 239218.1134 329419.1275 226795.0334 233050.8499 311897.1462 208998.7332 191263.3388 321752.7237 257342.5944 0.929570614 1.280080075 0.881296133 0.905605426 1.211991924 0.812142015 0.743224569 1.250289422 1 17.97333074 3.867209495 5.86608792 0.947039753 1.122324465 0.070677181 0.180405816 0.390722467 18.09857859 0.044572166 0.081682036 7365.623152 -3.867209495 0.175284712 VLDHAMIGPEGTDNCHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLDHAMIGPEGTDNCHK 17 0 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 ; 203.9 5.36E-12 368940000 689360 617060 691410 689430 765350 572660 920400 721250 912260 FALSE TRUE 646214.1881 662747.7645 707810.5717 707121.941 705242.4983 737977.6456 782394.5646 811299.6502 759997.9126 0.850284162 0.872038927 0.931332258 0.930426162 0.927953204 0.971025885 1.02946936 1.067502472 1 19.53563593 2.505007526 0.64905166 1.043860153 0.870623806 0.83845435 0.026863048 0.291096575 0.25047342 0.022352078 0.019007314 319.8950547 -2.505007526 -0.173236347 VLDLDLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLDLDLFR 8 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 132.08 0.0022738 123088000 386030 953610 323260 316190 1048020 187774 270730 803480 634940 FALSE TRUE 361869.0714 1024216.277 330927.8799 324303.9707 965712.7367 241981.3055 230136.5498 903796.2467 528964.4121 0.684108539 1.936266889 0.625614639 0.613092229 1.825666745 0.457462355 0.435070006 1.708614466 1 19.01281114 3.88379961 7.106539488 0.894231794 1.382417379 0.054015824 0.566620009 0.462589541 29.99626149 0.136778776 0.248583567 7652.434298 -3.88379961 0.488185584 VLDNYLTSPLPEEVDETSAEDEGVSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLDNYLTSPLPEEVDETSAEDEGVSQR 27 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 95.823 0.0047298 23291000 28182 40704 35131 39468 38994 30048 40090 31893 36951 FALSE TRUE 26418.13893 43717.76651 35964.32391 40480.8157 35931.56853 38722.36981 34078.87668 35874.91126 30783.63939 0.858187643 1.420162378 1.168293439 1.315010717 1.167229387 1.257887975 1.107045085 1.165388887 1 14.90987618 0.953723184 0.83019722 1.0038328 1.224692902 0.113931834 0.147471825 1.142286052 1.716595476 0.125801542 0.0451203 8.989244309 -0.953723184 0.220860102 VLDPFTIKPLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VLDPFTIKPLDR 12 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;; 190.78 5.66E-06 12097814000 22102070 27570690 19955060 16707756 37591950 17187685 24348740 31105580 33901690 FALSE TRUE 20718740.89 29612052.57 20428403.45 17136505.31 34639629.89 22149490.64 20697872.48 34989180.13 28243278.93 0.733581287 1.048463695 0.723301409 0.606746311 1.226473384 0.784239348 0.732842406 1.238849789 1 24.75140425 1.239668464 24.99955238 1.119424916 0.843471283 0.282374368 0.18724308 36.53373811 824585.9684 0.134024007 0.04263597 17.36474717 -1.239668464 -0.275953633 VLDPFTIKPLDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLDPFTIKPLDRK 13 2 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 180.84 7.06E-06 1627000000 1435820 1621330 1252900 1112990 2296080 1023210 1733700 1699520 3541400 FALSE TRUE 1345954.589 1741374.96 1282619.38 1141551.208 2115755.139 1318594.117 1473747.78 1911708.813 2950317.462 0.456206699 0.590233079 0.434739446 0.386924872 0.717127959 0.44693296 0.499521763 0.647967155 1 21.49243877 0.86124452 2.676405562 0.999697693 0.506060701 0.7403858 0.092658352 0.256923293 3.560955274 0.081665807 0.021704718 7.265148903 -0.86124452 -0.493636992 VLDQDTDAIAVHVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLDQDTDAIAVHVVR 15 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 0 185.26 1.30E-11 0 61500 79470 71399 76722 85642 64402 78499 63420 74225 FALSE TRUE 57650.82478 85354.04149 73092.618 78690.81641 78916.02278 82993.81192 66728.8037 71338.1266 61836.36799 0.932312596 1.380321068 1.182032845 1.272565304 1.276207277 1.342152112 1.079119066 1.153659714 1 15.91616796 1.649313754 7.740830679 1.086545501 1.2454959 0.239841917 0.126302463 0.155852197 17.88867147 0.056950634 0.029262458 44.5978327 -1.649313754 0.158950399 VLDSGAPIKIPVGPETLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLDSGAPIKIPVGPETLGR 19 1 P06576;H0YH81;F8W079 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ; 145.77 1.11E-07 1125600000 1329240 1216300 1164270 1133550 1720990 1150960 1244310 1246170 2415500 FALSE TRUE 1246045.241 1306356.118 1191887.034 1162638.812 1585830.388 1483223.468 1057737.267 1401757.068 2012337.445 0.619202929 0.649173488 0.592289845 0.577755393 0.788053908 0.737064984 0.525626191 0.696581516 1 20.94044082 0.970101091 23.75774177 1.000000002 0.637468937 0.687444142 0.075411101 1116.380162 887079.5014 0.071699105 0.017924776 9.334715606 -0.970101091 -0.362531065 VLDTSSLTQS(ph)APAS(ph)PTNK ddPTM_SK-BR-3_Pertuzumab_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(1)PTNK;VLDTSSLT(0.001)QS(0.999)APAS(1)PTNK;VLDTSSLT(0.006)QS(0.994)APAS(1)PTNK;VLDTSSLT(0.001)QS(0.999)APAS(1)PTNK 372.52 1.58E-107 857940000 1924710 1691310 1655330 1798290 1929850 1244630 2634330 1749290 2601150 TRUE FALSE 1804245.837 1816536.352 1694595.209 1844437.166 1778287.366 1603934.476 2239336.672 1967692.707 2167001.261 0.832600271 0.838271941 0.782000103 0.851147251 0.820621288 0.740163149 1.03338042 0.90802564 1 21.04726856 1.729678944 10.86282315 0.976147639 0.812607954 0.768119625 0.043892922 0.039716941 19.20996896 0.018608919 0.010128003 53.66349372 -1.729678944 -0.163539686 VLDTSSLTQSAPAS(ph)PTNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VLDTSSLTQSAPASPTNK 18 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 1 VLDTSSLTQSAPAS(1)PTNK;VLDTSSLTQS(0.002)APAS(0.997)PTNK;VLDTSSLTQSAPAS(1)PTNK;VLDTSSLTQSAPAS(1)PTNK;VLDTSSLTQS(0.017)APAS(0.929)PT(0.053)NK 501.25 8.59E-267 1596600000 2126390 1810551 1966950 2118940 2239790 1719670 2411150 1751540 2226040 TRUE FALSE 1993303.046 1944606.08 2013606.983 2173315.588 2063885.928 2216110.812 2049620.442 1970223.625 1854499.543 1.074846879 1.048588061 1.085795351 1.171914868 1.112907218 1.194991296 1.105214854 1.062401785 1 20.82259848 3.469084063 24.72304456 1.119517987 1.064454576 0.08513356 0.054361436 249.0917892 766224.1658 0.013654339 0.018600559 2944.991617 -3.469084063 -0.055063411 VLDWICR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLDWICR 7 0 Q16822;Q16822-3;H0YML5 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 79.116 0.077928 60679000 91043 109640 93186 102920 120340 85337 104230 91099 106010 FALSE TRUE 85344.78115 117757.8597 95396.41593 105561.1014 110888.9818 109972.4066 88601.67912 102472.9107 88316.24615 0.966354265 1.333365771 1.080168373 1.195262548 1.255589845 1.245211514 1.003231942 1.160295134 1 16.43039123 1.739497007 17.16731848 1.061659544 1.189203794 0.221582544 0.108964624 0.077841738 490.0176372 0.045857989 0.025365615 54.89047723 -1.739497007 0.127544249 VLEALLPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLEALLPLK 9 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 95.099 0.012822 0 100440 231780 93232 93833 237600 73781 112950 223210 170190 FALSE TRUE 94153.63969 248941.2324 95443.50707 96240.91364 218939.8544 95080.37697 96014.19608 251078.2598 141784.1895 0.664063038 1.755775684 0.673160438 0.678784524 1.544176788 0.670599291 0.677185492 1.77084808 1 17.11333714 5.006394835 18.49649776 1.060674879 0.143306586 0.078902228 0.449715639 71216473.4 2155727356 0.102820741 1562992459 101483.3594 -5.006394835 -0.917368293 VLEALLPLKGLEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLEALLPLKGLEER 14 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 146.78 7.49E-06 1436260000 1159320 2072270 1708130 2073610 3039000 1428720 2800500 1696840 5965500 FALSE TRUE 1086760.231 2225703.027 1748647.65 2126822.343 2800329.199 1841168.271 2380591.024 1908694.209 4969819.511 0.218671972 0.447843835 0.351853351 0.427947602 0.563466982 0.370469846 0.479009553 0.384057048 1 22.24476203 -5 0.272684005 5.098594439 0.370713885 0.824152155 0.086886247 80.39766016 0.778353658 185.8123048 0.094872369 1.00E-05 5 -4.727880554 VLEDEEGSKDIELSDDPYDCIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLEDEEGSKDIELSDDPYDCIR 22 1 Q15024 Q15024 EXOSC7 Exosome complex component RRP42 0 112.58 0.00026272 77138000 99042 64377 80776 84155 93406 75412 124310 63877 118780 FALSE TRUE 92843.13802 69143.54006 82692.04487 86314.55977 86070.26954 97182.22019 105670.8695 71852.18406 98954.85065 0.938237362 0.698738259 0.835654284 0.872262039 0.869793335 0.982086472 1.067869527 0.726110783 1 16.59448281 2.80578686 1.437014083 0.959396394 0.797331701 0.160535433 0.106508179 0.49099977 2.056970817 0.041668263 0.04240948 639.4209484 -2.80578686 -0.162064693 VLEDSDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLEDSDLK 8 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 103.83 0.010927 212570000 735020 591190 582810 595830 615860 364860 767860 529350 552450 FALSE TRUE 689016.4102 634962.3227 596634.5284 611120.0065 567492.8399 470189.159 652726.5215 595440.5127 460242.526 1.497072459 1.379625495 1.296348109 1.327821685 1.233029996 1.021611721 1.418222968 1.293753791 1 18.81203477 7.999998176 0.029667637 3.45E-08 3.149898163 0.500697027 0.111963262 1303.321805 2.964757533 100.7976176 242.3776655 99999580.05 -7.999998176 3.149898129 VLEEMESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLEEMESR 8 0 Q9NUP9;G3V1D4 Q9NUP9 LIN7C Protein lin-7 homolog C 0 100.02 0.018709 0 262160 294730 263330 242720 316280 222550 285210 239110 378180 FALSE TRUE 245751.8736 316552.1159 269576.312 248948.6061 291440.6446 286796.5722 242445.4083 268963.4098 315059.3149 0.7800178 1.004738159 0.855636698 0.790164246 0.925034211 0.910293899 0.769523061 0.853691344 1 18.26526394 3.719030736 24.11584464 0.858364507 0.914956833 0 0.085663885 497.2198514 1482095.685 0.020943831 0.033109249 5236.374944 -3.719030736 0.056592326 VLEFNCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VLEFNCR 7 0 P22102;P22102-2;F8WD69 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ;;;; 189.88 0.0012762 752580000 441877 638885 527323 511038 675567 479607 560924 568064 638571 FALSE TRUE 414220.7073 686188.7102 539831.3506 524152.1003 622510.6929 618061.7551 476818.6536 638988.0409 531989.3748 0.778625903 1.289854164 1.01474085 0.985267987 1.170156252 1.16179342 0.896293566 1.201129329 1 19.02103791 -4.999717863 0.373423173 0.048821888 1.072555092 0.00884831 0.152889134 3098.230578 23.66852086 2381.426783 0.096788389 1.00E-05 4.999717863 1.023733205 VLEGHTDFINGLVFDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLEGHTDFINGLVFDPK 17 0 Q8NFH4;F8VTY2 Q8NFH4 NUP37 Nucleoporin Nup37 0 126.88 4.21E-05 79727000 197530 153880 183960 175510 183320 138320 211490 147470 184700 FALSE TRUE 185166.9499 165273.4353 188323.6181 180013.8837 168922.7867 178250.7386 179779.0379 165881.9541 153872.3768 1.203380059 1.074094251 1.223894906 1.169890837 1.097810992 1.158432347 1.168364599 1.078048949 1 17.23137474 1.006001569 3.438159683 1.000487024 1.154203895 0.582624191 0.044044586 0.144536089 4.230670047 0.039878412 0.010353466 10.13915049 -1.006001569 0.153716871 VLEGMEVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLEGMEVVR 9 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ; 85.212 0.034822 79339000 63856 95804 68072 63898 85635 54969 88299 80664 106373 FALSE TRUE 59859.36695 102897.4278 69686.69999 65537.73086 78909.57253 70837.65795 75059.38468 90735.07796 88618.6591 0.675471369 1.161125985 0.786365994 0.73954776 0.890439703 0.799353755 0.846993008 1.023882316 1 16.43532288 1.237432029 24.99907045 1.011941232 0.863746127 0.215659222 0.129408855 52.61745338 1165260.323 0.102322367 0.031070568 17.2755558 -1.237432029 -0.148195105 VLELEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLELEER 7 0 A0A1B0GUE0;Q96N16-5;Q96N16-2 A0A1B0GUE0 0 ; 94.401 0.033099 360010000 245220 898660 654970 736030 719590 805110 549230 664060 500140 FALSE TRUE 229872.1179 965197.7215 670506.1977 754917.7759 663076.3041 1037532.187 466878.0603 746969.3528 416663.403 0.551697404 2.316492676 1.609227479 1.811816854 1.591395595 2.490096754 1.120516122 1.792740489 1 18.66852286 -1.281959949 7.051634397 0.999993862 1.710243291 0.119664704 0.548449166 4.66E-05 4.75E-06 0.46771032 0.110239428 0.052244437 1.281959949 0.710249429 VLEMET(ph)TVEDLQWDIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLEMETTVEDLQWDIEK 17 0 H3BP71;O75150-4;O75150;O75150-3;H3BS50 H3BP71 RNF40 E3 ubiquitin-protein ligase BRE1B 1 VLEMET(0.5)T(0.5)VEDLQWDIEK 72.09 0.082588 470110000 705930 512740 644930 590980 518420 569290 939060 563130 423220 TRUE FALSE 661747.1014 550703.8031 660228.0442 606145.5473 477705.3844 733634.7813 798256.6708 633438.0201 352581.8479 1.876860948 1.561917627 1.872552566 1.71916266 1.354877987 2.080750287 2.26403224 1.796570141 1 18.42759868 2.202706876 24.99918325 1.937465194 1.689939542 0 0.368731559 408.9255875 285122.9481 0.125432858 0.092641385 159.4802384 -2.202706876 -0.247525652 VLENAEGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLENAEGAR 9 0 P38646;D6RJI2;A0A3B3ITI4;D6RA73 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ; 234.93 8.07E-10 574800000 435000 649090 542740 512810 751630 477800 545410 613290 764260 FALSE TRUE 407774.1265 697149.299 555614.0491 525969.5728 692600.0117 615733.1036 463630.8338 689860.6065 636700.0687 0.640449321 1.094941454 0.872646441 0.826086879 1.087796352 0.967069322 0.728177766 1.083493847 1 19.28025439 4.759061418 24.14392341 0.94039382 0.640448855 0.39542352 0.121584916 3512.598695 4136703.669 0.028435888 1.142949959 57419.76603 -4.759061418 -0.299944965 VLEQLEDLDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLEQLEDLDSR 11 0 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ; 110.66 0.0041048 72051000 81012 95068 94221 84526 93876 80343 91621 82604 97656 FALSE TRUE 75941.60353 102106.9336 96455.96661 86695.08026 86503.35764 103536.7198 77883.28162 92917.29123 81356.58272 0.933441413 1.255054357 1.18559511 1.065618508 1.063261936 1.272628672 0.957307682 1.142099239 1 16.31197146 1.405589293 0.719760624 1.008716235 1.147276133 0.042525846 0.114627118 1.253359852 1.444202912 0.10174603 0.043956053 25.44422882 -1.405589293 0.138559899 VLFDPFELDTSVT(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLFDPFELDTSVTPGR 16 0 A0A0B4J2E5;Q15269 A0A0B4J2E5 PWP2 Periodic tryptophan protein 2 homolog 1 VLFDPFELDT(0.042)S(0.147)VT(0.811)PGR;VLFDPFELDT(0.032)S(0.032)VT(0.937)PGR 102.65 0.016773 15173200 18041.1 20646 21603 22143.3 19114.2 19423.4 23797 16654.3 19917.2 TRUE FALSE 16911.93976 22174.65132 22115.43336 22711.53457 17613.04783 25030.62027 20228.86077 18733.62602 16592.89065 1.019228061 1.336394712 1.332825837 1.368750933 1.061481583 1.508514749 1.219128192 1.129015216 1 14.01827762 1.099436599 2.541431599 1.006473207 1.285851918 0.269720937 0.143494062 0.292488116 3.687497726 0.121097064 0.033124027 12.57293294 -1.099436599 0.279378711 VLFSNIEDILEVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLFSNIEDILEVHK 14 0 Q8TCU6;Q8TCU6-3 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 0 ; 176.75 2.18E-06 77764000 233770 195128 215180 211370 197344 211314 288390 216114 101055 FALSE TRUE 219138.753 209575.4802 220284.1712 216794.112 181845.3983 272316.9214 245148.5968 243096.3086 84188.26766 2.60296071 2.48936682 2.616566148 2.575110738 2.159985035 3.234618421 2.911909267 2.887531902 1 16.36133158 VLGAHILGPGAGEMVNEAALALEYGASCEDIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLGAHILGPGAGEMVNEAALALEYGASCEDIAR 33 0 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 ; 290.67 1.74E-89 309790000 105928 120002 116540 104745 160723 113925 115290 129616 199648 FALSE TRUE 99298.15557 128887.0729 119304.3838 107432.934 148100.4639 146813.2981 98003.3348 145798.8429 166325.459 0.597011162 0.774908867 0.717294782 0.645919961 0.890425704 0.882686866 0.5892263 0.876587648 1 17.34364949 -5 0.178206131 2.045964408 0.686158815 0.407892103 0.106390765 145.2224427 1.394539835 53.74805655 0.329931265 1.00E-05 5 -1.359805592 VLGEKPELPDGGDDDDIIADISNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VLGEKPELPDGGDDDDIIADISNR 24 1 Q9Y6U3;Q9Y6U3-2;E5RHN8;E5RHX6 Q9Y6U3 SCIN Adseverin 0 ;; 273.59 5.31E-52 1612915000 1146231 792695 1041336 808009 1101090 796456 1140046 1134890 2174540 FALSE TRUE 1074490.448 851386.9626 1066036.982 828743.8789 1014614.833 1026379.918 969106.686 1276583.515 1811595.226 0.593118392 0.469965338 0.588452082 0.457466363 0.560067072 0.566561395 0.534946589 0.704673702 1 20.78882921 0.891232264 2.091408857 0.999907388 0.533569639 0.913096437 0.045529301 0.107334745 0.960130166 0.038568295 0.010647358 7.784527625 -0.891232264 -0.466337749 RYIGIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 RYIGIVK 7 1 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 124.34 0.0066634 2715100000 3601700 4928500 4864300 5899800 7397400 5190900 7927500 6749200 9246100 FALSE TRUE 3376276.026 5293411.268 4979683.493 6051198.856 6816438.044 6689428.563 6738844.97 7591852.477 7702866.178 0.438314252 0.687200212 0.646471505 0.785577565 0.884922299 0.868433698 0.874849026 0.985588001 1 22.87696393 5.000146775 0.254360448 1.024400859 1.83E-17 0.892861067 0.05554481 3.296431447 0.162995115 0.074306447 1.088893789 100033.8019 -5.000146775 -1.024400859 down VLGEMGEAPAPEQYLVLEELIDMNQHHLNALGVGHASLDQLCQVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLGEMGEAPAPEQYLVLEELIDMNQHHLNALGVGHASLDQLCQVTR 46 0 F5H8H2;Q03426;A0A1B0GWC2 F5H8H2 MVK Mevalonate kinase 0 50.007 0.0070101 44510000 4054.2 5518.4 5558.7 3789.1 6622.1 6324.4 7795.5 5275 5697 FALSE TRUE 3800.454859 5926.988078 5690.554989 3886.334721 6102.026978 8150.151612 6626.637145 5933.595362 4746.133896 0.800747501 1.248803386 1.198987452 0.8188422 1.285683698 1.717219065 1.396217909 1.250195526 1 12.21253709 2.486773824 24.83236564 1.402684659 1.082501984 0.283407757 0.2296153 504.9508579 1299049.439 0.072808361 0.064244898 306.7424089 -2.486773824 -0.320182675 VLGFSHEEIISMLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLGFSHEEIISMLR 14 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 117.7 0.000288 167570000 136380 197300 149630 170430 241610 119100 186980 180570 227390 FALSE TRUE 127844.2192 211908.2973 153179.2943 174803.5223 222634.9252 153482.2366 158944.0848 203114.562 189437.14 0.674863542 1.118620653 0.808602232 0.922752119 1.175244333 0.810201403 0.839033385 1.072200319 1 17.53135968 4.764445391 23.81361886 0.950408621 0.67486286 0.331679701 0.128700929 5618.32257 5168614.187 0.029595509 2.110467462 58136.03269 -4.764445391 -0.275545761 VLGQPHHELDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLGQPHHELDSK 12 0 B4DHE8;Q96DH6-2;Q96DH6;J3QKT5;J3KTC1 B4DHE8 MSI2 RNA-binding protein Musashi homolog 2 0 60.301 0.05373 40784000 64358 61747 75334 65148 76504 50205 82517 67316 86174 FALSE TRUE 60329.94766 66318.81213 77120.95806 66819.80798 70495.68444 64698.36849 70144.3419 75720.55078 71791.00269 0.840355273 0.923776095 1.074242665 0.930754628 0.981957095 0.901204414 0.977063131 1.054735941 1 16.13151543 4.56275157 2.77739546 0.984263164 0.836703634 0.473765243 0.050792558 0.29358235 3.812467844 0.012425812 0.080770114 36538.57199 -4.56275157 -0.14755953 VLGS(ph)EGEEEDEALS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_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 411.11 2.50E-140 788040000 1908800 1070250 1378160 1258540 1281670 1016960 1779980 1096400 1458840 TRUE FALSE 1789331.615 1149492.424 1410850.606 1290836.267 1181012.808 1310539.843 1513088.524 1233287.953 1215350.18 1.472276588 0.945811703 1.160859339 1.062110566 0.971746932 1.078322828 1.244981528 1.014759346 1 20.21294063 4.750436389 24.87112183 1.075699228 1.472276845 0.670797962 0.090198044 1136.725151 2380567.447 0.021833883 0.363288055 56290.6662 -4.750436389 0.396577617 VLGS(ph)EGEEEDEALSPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VLGSEGEEEDEALSPAK 17 0 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 1 VLGS(1)EGEEEDEALSPAK;VLGS(1)EGEEEDEALSPAK;VLGS(1)EGEEEDEALSPAK 386.69 9.36E-122 957030000 1279150 980010 1118480 1092310 1155520 882140 1349440 952300 1413320 TRUE FALSE 1199090.285 1052570.96 1145010.874 1120340.524 1064770.12 1136799.498 1147104 1071196.751 1177427.762 1.018398176 0.893957994 0.972468045 0.951515295 0.904318851 0.96549405 0.974245756 0.909777046 1 20.16720712 -1.420981861 3.187595241 1.000735707 0.947485927 0.152805954 0.03780045 690839903 753565825.9 4550421.833 0.008216776 0.037933083 1.420981861 -0.05324978 VLGSEGEEEDEALS(ph)PAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VLGSEGEEEDEALSPAK 17 0 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 1 VLGSEGEEEDEALS(1)PAK;VLGSEGEEEDEALS(1)PAK;VLGSEGEEEDEALS(1)PAK 202.05 1.15E-11 493490000 473706 291013 371833 345098 375104 309567 486166 349981 458950 TRUE FALSE 444057.587 312559.9053 380653.0544 353953.7989 345644.8449 398933.9675 413269.9216 393676.8983 382348.2801 1.16139554 0.817474333 0.995566279 0.925736606 0.90400523 1.043378481 1.080872972 1.029629055 1 18.54452786 2.219165796 21.13533149 1.048965623 0.944427026 0.139473597 0.089201166 54.62380788 59523.18205 0.030456925 0.022558877 165.6402189 -2.219165796 -0.104538597 VLGTEDLYDYIDKYNIELDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLGTEDLYDYIDKYNIELDPR 21 1 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2 P68400 CSNK2A1 Casein kinase II subunit alpha 0 ; 184.7 3.52E-17 425617000 1275325 1289642 1267370 1218548 1433422 959255 1538465 1257667 1767850 FALSE TRUE 1195504.685 1385128.436 1297432.615 1249818.005 1320846.818 1236176.346 1307786.456 1414689.493 1472784.414 0.811730945 0.940482818 0.880938583 0.848608929 0.896836499 0.839346434 0.887968696 0.960554362 1 20.49011483 1.139511199 3.11187796 0.997981813 0.877941149 0.628956364 0.035056897 0.155624974 2.730932999 0.031753158 0.008534365 13.78831508 -1.139511199 -0.120040664 VLGTPVETIELTEDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLGTPVETIELTEDRR 16 1 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 ; 234.93 1.75E-19 362500000 126483 195939 187226 194998 222680 197078 204772 197979 250960 FALSE TRUE 118566.6548 210446.5274 191667.0891 200001.9788 205191.611 253971.2193 174068.3396 222697.114 209073.1547 0.567106068 1.006568862 0.91674653 0.956612431 0.981434519 1.214748109 0.83257145 1.065163599 1 17.6736483 4.740274354 24.8115973 0.986073875 0.567105913 0.648541848 0.099118252 82.73289583 1197701.289 0.0216652 0.138945415 54988.81411 -4.740274354 -0.418967962 VLHEAEGHIVTCETNTGEVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VLHEAEGHIVTCETNTGEVYR 21 0 P62318;P62318-2;H3BT13 P62318 SNRPD3 Small nuclear ribonucleoprotein Sm D3 0 ;;;; 309.59 9.88E-67 1547076000 626329 847084 622146 607676 912673 551858 760690 833139 916598 FALSE TRUE 587128.1859 909802.9808 636903.5969 623269.995 840995.3441 711170.4459 646631.5964 937158.2381 763611.8724 0.768882998 1.191446877 0.834067175 0.816213076 1.101338749 0.931324501 0.84680663 1.227270387 1 19.54248001 1.242379246 24.9999926 1.113635188 0.941610337 0.226268429 0.141411824 141.2141959 924558.4178 0.097316973 0.032489537 17.47347353 -1.242379246 -0.17202485 VLHEEHVELLMEEFAFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VLHEEHVELLMEEFAFLK 18 0 P53004 P53004 BLVRA Biliverdin reductase A 0 ;;; 130.98 1.04E-05 280112300 353256 302505 358278 345120 346617 292131.5 386608 331155.6 300084 FALSE TRUE 331146.3375 324902.785 366776.5234 353976.3635 319395.099 376465.1217 328639.7195 372501.1056 249998.0418 1.324595726 1.29962132 1.467117585 1.415916545 1.277590403 1.505872282 1.314569175 1.490016094 1 17.93155727 -0.897408396 6.782465352 0.999999996 1.384023678 0.686238424 0.082199376 1.48E-08 2.19E-09 0.071055094 0.016747846 0.126646037 0.897408396 0.384023682 VLHEEHVELLMEEFAFLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLHEEHVELLMEEFAFLKK 19 1 P53004 P53004 BLVRA Biliverdin reductase A 0 ; 202.33 2.27E-16 413179000 686600 644110 689600 683060 853730 529576 908510 688300 1133660 FALSE TRUE 643626.9316 691800.5746 705957.6377 700588.476 786681.4896 682455.9943 772287.3597 774235.7701 944444.8223 0.681487067 0.732494433 0.747484258 0.741799266 0.832956538 0.722600175 0.817715701 0.819778723 1 19.84910699 -5 0.129604581 1.833531648 0.655436216 0.868405264 0.032296039 44.55175057 0.364952654 9.561992689 0.221324781 1.00E-05 5 -1.178095431 VLHNDSDILFPVSGVGSYS(ph)PADAPLGSLENGTGPEDHVLPDPGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLHNDSDILFPVSGVGSYSPADAPLGSLENGTGPEDHVLPDPGLR 45 0 Q8TEQ0;Q8TEQ0-2;H3BQF0 Q8TEQ0 SNX29 Sorting nexin-29 1 VLHNDSDILFPVS(0.027)GVGS(0.13)Y(0.125)S(0.682)PADAPLGS(0.029)LENGT(0.006)GPEDHVLPDPGLR 46.446 0.0467 78370000 17609 20080 19292 22323 24009 20624 21940 19019 24852 TRUE FALSE 16506.88412 21566.74409 19749.61535 22895.84597 22123.42999 26577.814 18650.30068 21393.56402 20704.04065 0.797278386 1.041668361 0.953901496 1.10586365 1.068556151 1.283701788 0.900804872 1.033303807 1 14.33762473 4.738766274 8.123067893 1.043062781 0.795420938 0.376150472 0.101454906 0.102479386 87.8538667 0.023295655 0.13836373 54798.19755 -4.738766274 -0.247641843 VLHNDSDILFPVSGVGSYSPADAPLGS(ph)LENGTGPEDHVLPDPGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLHNDSDILFPVSGVGSYSPADAPLGSLENGTGPEDHVLPDPGLR 45 0 Q8TEQ0;Q8TEQ0-2;H3BQF0 Q8TEQ0 SNX29 Sorting nexin-29 1 VLHNDSDILFPVSGVGSYSPADAPLGS(0.952)LENGT(0.048)GPEDHVLPDPGLR;VLHNDSDILFPVSGVGSYSPADAPLGS(0.5)LENGT(0.5)GPEDHVLPDPGLR 291.61 5.85E-97 238656000 39079 57481 51525 60619 64697 50787 59011 52637 59975 TRUE FALSE 36633.11515 61736.95305 52747.19733 62174.58617 59615.9586 65448.38244 50162.84838 59208.84532 49964.78505 0.73317868 1.235609299 1.055687466 1.244368131 1.193159513 1.309890203 1.003964059 1.185011509 1 15.60862403 4.74540516 24.95179078 1.153930138 0.733178482 0.616873512 0.104091307 502.9230383 1833358.805 0.022771781 0.225522176 55642.31114 -4.74540516 -0.420751656 VLHNDSDILFPVSGVGSYSPADAPLGSLENGT(ph)GPEDHVLPDPGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLHNDSDILFPVSGVGSYSPADAPLGSLENGTGPEDHVLPDPGLR 45 0 Q8TEQ0;Q8TEQ0-2;H3BQF0 Q8TEQ0 SNX29 Sorting nexin-29 1 VLHNDSDILFPVSGVGSYS(0.005)PADAPLGS(0.436)LENGT(0.56)GPEDHVLPDPGLR 154.63 1.76E-14 186080000 8414.6 13669 10831 10840 13602 11590 12048 10924 13485 TRUE FALSE 7887.945206 14681.06698 11087.91643 11118.17275 12533.75379 14935.84485 10241.51425 12287.88545 11234.26638 0.702132648 1.306811365 0.986972897 0.989666114 1.115671764 1.329490003 0.911631779 1.093786192 1 13.4556183 1.635798756 25 1.001943207 1.090005734 0.025963688 0.180352204 2.508209764 2236.326732 0.076724014 0.042533871 43.23134587 -1.635798756 0.088062527 VLHVSENPVPLTVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLHVSENPVPLTVR 14 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 73.887 0.022185 0 379840 394140 328840 309900 461360 286770 358150 346650 540630 FALSE TRUE 356066.4924 423322.5357 336640.2401 317852.5587 425126.6466 369555.8437 304448.7324 389930.0156 450395.3604 0.790564299 0.939890978 0.747432744 0.70571899 0.943896594 0.820514322 0.675958856 0.865750516 1 18.78083244 5.105688844 13.52246065 0.820008274 4.24E-05 0 0.107128839 949656.1503 1756061.751 0.024450329 23037651.92 127552.4614 -5.105688844 -0.819965882 VLIAAHGNSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLIAAHGNSLR 11 0 P18669;P15259 P18669 PGAM1;PGAM2 Phosphoglycerate mutase 1;Phosphoglycerate mutase 2 0 ; 186.87 3.84E-06 3525300000 1474240 3497400 1587900 1837230 3329500 1266790 1915030 2798100 2555400 FALSE TRUE 1381969.95 3756351.135 1625565.738 1884376.432 3068014.501 1632491.708 1627889.03 3147448.944 2128887.231 0.649151317 1.764466938 0.763575315 0.885146195 1.441135282 0.766828644 0.764666632 1.478447941 1 21.0216681 3.841712887 9.446923358 0.988191866 1.28275553 0.032278536 0.37106939 0.66080924 50.81123736 0.087373859 0.157762619 6945.649872 -3.841712887 0.294563664 VLIEILCTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLIEILCTR 9 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ; 140.5 0.00025346 74925000 161982 204980 181059 160559 197430 94609 207807 179070 226840 FALSE TRUE 151843.8358 220156.9325 185353.805 164679.2158 181924.6442 121921.0825 176648.2695 201427.2837 188978.9386 0.803496077 1.164981316 0.980817261 0.871415709 0.962671531 0.645156986 0.934751094 1.0658716 1 17.52786593 3.405549354 4.404974886 0.896187349 1.029038782 0.021054799 0.140866623 0.379106829 14.13515129 0.037457391 0.052348148 2544.188904 -3.405549354 0.132851433 VLISVGS(ph)YK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLISVGSYK 9 0 Q8TEV9;Q8TEV9-2 Q8TEV9 SMCR8 Smith-Magenis syndrome chromosomal region candidate gene 8 protein 1 VLISVGS(1)YK 131.12 0.00035892 90871000 395620 358290 330290 366080 577070 287180 474060 377390 554140 TRUE FALSE 370858.8504 384818.1644 338124.6348 375474.2326 531749.25 370084.204 402979.104 424507.9722 461650.4541 0.80333258 0.833570423 0.732425652 0.813330149 1.151843879 0.801654587 0.87290958 0.919544145 1 18.81644138 2.973063411 24.99632322 0.929389325 0.788706477 0.390103886 0.093967593 796.706497 739319.4739 0.027477361 0.02922435 939.8605286 -2.973063411 -0.140682848 VLKGDVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLKGDVEK 8 1 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ; 72.006 0.043113 1124030000 2670900 2327800 2359500 2529400 2976100 1852550 3067100 2458800 3868800 FALSE TRUE 2503733.137 2500152.734 2415468.454 2594308.686 2742369.111 2387351.111 2607216.829 2765786.592 3223072.287 0.776815694 0.775704828 0.749430431 0.804917934 0.850855602 0.740706661 0.808922853 0.85812118 1 21.62000511 0.860105083 1.599459748 0.999735576 0.781008112 0.833054772 0.030523341 0.21225784 1.043293177 0.028498427 0.008238643 7.246112669 -0.860105083 -0.218727464 VLKPNFAAAWEEVGDTFEKEETFALSSTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLKPNFAAAWEEVGDTFEKEETFALSSTK 29 2 Q9UBF2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 224.91 7.22E-35 178450000 87428 63643 73781 71389 81697 59189 95548 55370 104810 FALSE TRUE 81956.03754 68355.19394 75531.12016 73220.9626 75280.84717 76275.90345 81221.46442 62283.06638 87316.5339 0.938608461 0.782843648 0.865026551 0.838569276 0.862160278 0.873556245 0.930195701 0.713302093 1 16.41396724 2.429456811 3.061280891 0.879425384 0.845615272 0.010802061 0.080113433 0.988548237 19.04262779 0.026938042 0.022446565 268.8170504 -2.429456811 -0.033810112 VLLGFSSDES(ph)DVEASPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLLGFSSDESDVEASPR 17 0 Q9Y2U8 Q9Y2U8 LEMD3 Inner nuclear membrane protein Man1 1 VLLGFSS(0.012)DES(0.987)DVEASPR;VLLGFSSDES(1)DVEASPR 146.76 4.46E-07 74930000 42674 41057 32566 33918 42119 32488 58048 47705 43888 TRUE FALSE 40003.11052 44096.903 33338.4809 34788.3933 38811.14364 41866.7582 49344.24129 53661.07426 36562.80927 1.094092913 1.20605894 0.911813987 0.951469375 1.061492386 1.145064043 1.349574671 1.467640899 1 15.1580893 1.960670098 3.30801838 1.305844605 1.045767309 0.344257474 0.140401797 0.238733786 4.993810526 0.065330523 0.037581845 91.34191201 -1.960670098 -0.260077296 VLLLEANRHS(ph)PGPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLLLEANRHSPGPER 15 1 Q9UDT6;Q9UDT6-2;H7C4L6 Q9UDT6 CLIP2 CAP-Gly domain-containing linker protein 2 1 VLLLEANRHS(1)PGPER 94.057 0.0027888 70337000 69992 99426 90871 98918 99960 88708 94745 81185 84406 TRUE FALSE 65611.32566 106787.6045 93026.50303 101456.4033 92109.54482 114316.5595 80538.86682 91321.12596 70318.09332 0.933064629 1.518636235 1.32293836 1.442820739 1.309898214 1.62570619 1.145350549 1.298686037 1 16.10160833 0.886358411 1.224367439 1.007219253 1.365803229 0.217406476 0.191625387 0.776382194 2.29541923 0.160325784 0.049393382 7.697654447 -0.886358411 0.358583976 VLLMELEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLLMELEEAR 10 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 136.57 0.00026585 12561000 15044 29126 15291 14298 29870 9465.2 16153 23391 27118 FALSE TRUE 14102.42289 31282.51935 15653.70974 14664.91089 27524.13069 12197.64959 13731.00761 26311.41784 22591.83061 0.624226657 1.384682803 0.692892489 0.649124506 1.218322285 0.539914175 0.607786409 1.16464302 1 14.46351356 3.76599345 11.86457637 0.800586703 1.052956135 0.034133827 0.294455904 2.041744821 618.2659207 0.069916967 0.125794324 5834.363048 -3.76599345 0.252369432 VLLRPGDFQSQWDEDDNEDESSSASDVMSHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLLRPGDFQSQWDEDDNEDESSSASDVMSHK 31 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 0 ; 275.19 6.89E-72 173991000 79583 61709 70428 75805 77834 53620 89040 59151 84188 FALSE TRUE 74602.04209 66277.99857 72098.58542 77750.28464 71721.23161 69099.22355 75689.27861 66536.13256 70136.47892 1.063669623 0.944986113 1.027975549 1.108557 1.02259527 0.9852109 1.079171349 0.948666565 1 16.09787738 3.696254081 8.211262555 1.031727085 0.993042283 0.001270612 0.053348051 0.553642463 132.0521049 0.013040789 0.020540923 4968.829338 -3.696254081 -0.038684803 VLLS(ph)DSNLHDA ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLLSDSNLHDA 11 0 Q6FI81-3;Q6FI81;H3BV90;Q6FI81-2 Q6FI81-3 CIAPIN1 Anamorsin 1 VLLS(0.999)DS(0.001)NLHDA;VLLS(0.995)DS(0.005)NLHDA 102.45 0.0030069 119092000 327197 341767 338490 355841 419989 325022 389421 292683 378238 TRUE FALSE 306718.3238 367071.7843 346519.1426 364972.4825 387004.7581 418850.5751 331030.9363 329225.1168 315107.6343 0.973376366 1.164909207 1.099685012 1.158247033 1.228166874 1.329230173 1.050532898 1.044802096 1 18.26548518 1.564349246 10.52900758 1.032015902 1.157751241 0.309030337 0.090058657 0.147987523 26.85193321 0.047542499 0.022173521 36.67323707 -1.564349246 0.125735339 VLLS(ph)LLSIKMPITDADQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLLSLLSIKMPITDADQIR 19 1 Q9Y4B6-3;Q9Y4B6-2;Q9Y4B6 Q9Y4B6-3 VPRBP Protein VPRBP 1 VLLS(0.498)LLS(0.498)IKMPIT(0.004)DADQIR 46.415 0.088566 1069300000 591650 814150 815150 826000 893760 602510 1031500 752230 898880 TRUE FALSE 554619.6826 874430.5131 834485.7429 847196.5584 823567.6949 776444.8561 876836.151 846147.5714 748851.121 0.740627432 1.167696073 1.114354669 1.131328424 1.099774938 1.036848092 1.170908511 1.129927629 1 19.5143194 4.743379957 24.96991801 1.116018177 0.740627276 0.819026103 0.053858012 181.4991085 940349.8815 0.011627597 0.095301689 55383.44374 -4.743379957 -0.375390901 VLLSLEHGLWAPNLHFHS(ph)PNPEIPALLDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLLSLEHGLWAPNLHFHSPNPEIPALLDGR 30 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 VLLS(0.032)LEHGLWAPNLHFHS(0.968)PNPEIPALLDGR 77.522 0.0016335 166170000 27659 46631 42820 40727 53055 37354 48595 44078 38905 TRUE FALSE 25927.87256 50083.60776 43835.71062 41772.12377 48888.27431 48137.49341 41308.63088 49581.23533 32411.50416 0.799958941 1.545241699 1.352473813 1.288805467 1.508361786 1.485197761 1.274505209 1.52974188 1 14.98421835 -1.135982356 4.57016694 0.99995969 1.368256476 0.195717296 0.218331809 8.07E-05 1.53E-05 0.185153028 0.043636085 0.073116879 1.135982356 0.368296786 VLLSLEHGLWAPNLHFHSPNPEIPALLDGR ddPTM_SK-BR-3_Pertuzumab_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 0 ; 237.97 9.73E-46 5479460000 1107460 2341640 1077160 752058 2463790 967034 1581550 2251710 732192 FALSE TRUE 1038146.055 2515017.462 1102710.744 771357.0815 2270293.872 1246201.017 1344411.26 2532840.95 609984.4251 1.701922234 4.123084719 1.807768688 1.264552093 3.721888262 2.043004651 2.204009159 4.152304298 1 19.21841288 3.895107767 9.720347711 2.35287164 3.069399138 0.04144274 1.131493488 0.978628598 109.1118229 0.263364594 0.475591373 7854.305095 -3.895107767 0.716527498 VLMATNRPDTLDPALMRPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLMATNRPDTLDPALMRPGR 20 2 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ; 144.01 9.08E-08 942390000 1282030 1449810 1372610 1282450 1462830 1189640 1523070 1253240 1338480 FALSE TRUE 1201790.031 1557155.441 1405168.957 1315359.838 1347945.233 1533069.756 1294699.793 1409709.773 1115079.041 1.077762191 1.396452972 1.260151887 1.179611301 1.208833798 1.374852992 1.161083426 1.264224078 1 20.08871455 -2.037424472 0.368410615 0.726566034 1.265059439 0.364271121 0.096626939 41.52072626 2.304538328 9.641970067 0.064942653 0.009174355 2.037424472 0.538493405 VLMSVQYFLEDVDCKQS(ph)MR ddPTM_SK-BR-3_Pertuzumab_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 97.5 0.00067009 109040000 57112 35850 41559 36318 41042 36585 38530 27056 64001 TRUE FALSE 53537.46187 38504.3713 42544.79911 37249.98137 37818.72688 47146.49559 32752.78419 30434.00116 53318.81964 1.004100658 0.722153483 0.797932126 0.698627269 0.70929415 0.884237421 0.614281869 0.570792853 1 15.70235722 4.740707188 24.50756778 0.738236557 1.00410078 0.288312088 0.124484403 172.7369839 1971968.971 0.026681076 0.176222589 55043.64532 -4.740707188 0.265864223 VLNEAVGALMYHTITLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLNEAVGALMYHTITLTR 18 0 Q13363-2;Q13363;E9PGB1;E7ESU7;D6RAX2;E7EPF8 Q13363-2 CTBP1 C-terminal-binding protein 1 0 ; 164.2 3.12E-11 95372000 104845 139215 135427 141657 158006 122588 138770 127066 117164 FALSE TRUE 98282.9386 149522.6235 138639.3924 145292.1584 145596.8461 157977.1656 117962.7268 142930.4698 97608.57149 1.006908892 1.531859561 1.420360838 1.488518439 1.491639965 1.618476361 1.208528359 1.464322934 1 16.57472022 -0.941468731 5.93140852 0.999999782 1.416047252 0.340728017 0.175804122 4.61E-07 8.20E-08 0.153992943 0.036296466 0.114427726 0.941468731 0.41604747 VLNNMEIGTSLFDEEGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLNNMEIGTSLFDEEGAK 18 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 125.53 0.00013291 0 37152 35734 29929 31570 42623 23453 42256 34708 37475 FALSE TRUE 34826.72264 38379.78254 30638.93001 32380.13965 39275.56151 30223.50037 35920.10509 39041.3702 31220.1804 1.115519583 1.229326098 0.981382222 1.037154149 1.258018404 0.968075776 1.15054124 1.250517124 1 14.93019125 1.567280763 25 1.150465115 1.100512533 0.014655848 0.110565383 2.191523183 1334.663128 0.055347027 0.025623253 36.92162127 -1.567280763 -0.049952582 VLNSYWVGEDSTYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLNSYWVGEDSTYK 14 0 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 334.19 3.62E-68 296340000 664990 573800 626200 595070 669880 495450 754960 552660 626080 FALSE TRUE 623369.4629 616284.749 641053.7597 610340.5037 617270.327 638478.372 641760.7567 621660.8176 521583.2034 1.195148653 1.181565559 1.229053688 1.170169016 1.183455148 1.224116053 1.230409171 1.19187277 1 18.99253789 0.947138448 22.78070472 1 1.20386187 0.902539576 0.020747978 1919.534745 827225.4614 0.020618648 0.005154662 8.853978192 -0.947138448 0.20386187 VLNT(ph)GSDVEEAVADALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLNTGSDVEEAVADALK 17 0 E3W994;J3KR49;O75122 E3W994 CLASP2 CLIP-associating protein 2 1 VLNT(0.5)GS(0.5)DVEEAVADALK;VLNT(0.5)GS(0.5)DVEEAVADALK 84.874 0.019044 18186000 48359 35429 39740 40490 42661 35200 52026 37951 47185 TRUE FALSE 45332.29651 38052.20002 40682.65157 41529.04195 39310.57715 45361.66858 44225.18429 42689.26589 39309.51867 1.153214235 0.968014906 1.034931308 1.056462744 1.000026927 1.153961435 1.125050262 1.085977833 1 15.26259108 2.246176178 24.99916459 1.106041071 1.031965988 0.099590329 0.062115334 224.795439 737924.5368 0.019961892 0.016410571 176.2690962 -2.246176178 -0.074075083 VLNTGS(ph)DVEEAVADALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VLNTGSDVEEAVADALK 17 0 E3W994;J3KR49;O75122 E3W994 CLASP2 CLIP-associating protein 2 1 VLNT(0.02)GS(0.98)DVEEAVADALK;VLNT(0.001)GS(0.999)DVEEAVADALK;VLNT(0.203)GS(0.797)DVEEAVADALK 228.29 1.55E-15 122104000 134121 99242 111560 112180 113408 89093.6 143161 96718 124063 TRUE FALSE 125726.606 106589.9809 114206.2559 115058.7287 104501.3931 114813.476 121695.3371 108793.4552 103356.0838 1.216441272 1.03128889 1.104978552 1.113226474 1.011081199 1.110853583 1.177437579 1.052608141 1 16.65726379 4.754586159 24.06194508 1.085768198 1.216441439 0.382753787 0.054931741 2102.358088 3156548.49 0.012970902 0.312583029 56831.11267 -4.754586159 0.130673241 VLNTNIDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VLNTNIDGR 9 0 P62269;A0A0G2JQH2;Q5GGW2 P62269 RPS18 40S ribosomal protein S18 0 ;;; 182.4 0.00010788 1139540000 1177510 1455810 1245520 1195070 1515960 1046150 1313810 1328510 1373840 FALSE TRUE 1103811.751 1563599.687 1275064.323 1225737.519 1396902.617 1348156.522 1116816.387 1494377.398 1144537.229 0.964417516 1.366141396 1.114043555 1.070945959 1.220495569 1.177905348 0.975779869 1.305660804 1 20.12633296 -4.999999929 0.149415506 0.450164 1.203039939 0.063511492 0.132560289 289.2311007 2.573136804 47.18860417 0.633091502 1.00E-05 4.999999929 0.752875939 VLPAQATEYAFAFIQVPQDDDARTDAVDSVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLPAQATEYAFAFIQVPQDDDARTDAVDSVVR 32 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 316.89 2.88E-104 421503000 87910.7 133006.4 115357.1 98046.4 122469.6 99255.9 137968.5 121686.7 171027.3 FALSE TRUE 82408.52621 142854.3322 118093.4249 100562.4366 112851.3316 127909.467 117281.4043 136879.5524 142481.7388 0.578379566 1.002615026 0.828832003 0.705791756 0.792040669 0.897725338 0.823132882 0.960681373 1 17.1204175 1.162191237 2.795717658 1.002247711 0.824764924 0.28740365 0.11220569 0.356916543 4.989549038 0.100035314 0.027482323 14.52751181 -1.162191237 -0.177482787 VLPFFERPDFQLFTGNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLPFFERPDFQLFTGNK 17 1 Q96HE7 Q96HE7 ERO1L ERO1-like protein alpha 0 145.1 4.44E-07 41012000 91955 112040 108020 103100 117610 67702 123130 99706 60245 FALSE TRUE 86199.70069 120335.5582 110582.2854 105745.7205 108373.385 87246.46835 104667.7996 112154.5136 50189.7203 1.717477208 2.397613644 2.203285548 2.106919901 2.159274536 1.738333424 2.085442974 2.234611249 1 15.61510429 -1.885645982 0.42571224 7.33E-14 2.140502726 0.702764229 0.217523034 24.32425309 1.730683343 24.64177872 0.121409063 0.013012299 1.885645982 2.140502726 VLPPPAGYVPIRT(ph)PAR ddPTM_SK-BR-3_Pertuzumab_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 188.96 1.77E-09 897220000 805006 893820 794873 868160 1022250 601429 1101170 902590 1045060 TRUE FALSE 754622.1114 959999.3628 813727.7629 890438.4554 941966.6086 775051.7889 936059.7813 1015280.348 870632.7347 0.866751365 1.10264561 0.934639522 1.022748652 1.08193337 0.890216687 1.075148848 1.166140794 1 19.73170474 1.5626981 8.76206779 1.094650242 0.995701766 0.213838693 0.085102482 0.164655854 22.18725286 0.041042323 0.019179083 36.5340737 -1.5626981 -0.098948476 VLPSISLS(ph)PGPQPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLPSISLSPGPQPPK 15 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 1 VLPSIS(0.017)LS(0.983)PGPQPPK;VLPSIS(0.002)LS(0.998)PGPQPPK 218.98 6.70E-12 70430000 479560 331008 395840 386470 351860 403810 517740 394020 291420 TRUE FALSE 449545.1956 355516.1767 405229.5117 396387.4745 324226.3349 520383.3917 440109.6935 443214.2643 242780.1194 1.851655716 1.464354568 1.669121478 1.632701539 1.335473167 2.143434945 1.812791322 1.825578905 1 17.88929076 2.260804845 24.99994931 1.782079803 1.586047816 0 0.316628842 564.8601587 634835.824 0.096708223 0.080852946 182.3076297 -2.260804845 -0.196031987 VLPYIFEDPDWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLPYIFEDPDWR 12 0 Q8IV36-2;Q8IV36;J3KSF1;E9PIM7 Q8IV36-2 HID1 Protein HID1 0 142.43 0.00014273 107300000 155540 215960 193600 192400 219820 178750 243090 174300 170820 FALSE TRUE 145805.029 231949.9031 198192.2834 197337.3097 202556.2239 230352.2232 206640.9112 196061.7387 142309.0385 1.024566188 1.62990282 1.392689358 1.386681492 1.423354596 1.618675987 1.452057532 1.377718104 1 17.11866777 0.786108814 3.420407524 1.000042834 1.445067113 0.374099348 0.165946625 1.442707015 21.89185039 0.142200445 0.036752792 6.110951183 -0.786108814 0.445024279 VLQGDLVMNVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 129.82 0.00052918 148820000 110740 182620 116610 126580 223220 83244 122710 179790 197650 FALSE TRUE 103808.9811 196141.3748 119376.0443 129828.2571 205689.2016 107275.1914 104310.7747 202237.1773 164660.9381 0.630440846 1.191183392 0.724980956 0.788458141 1.249168163 0.651491438 0.633488281 1.228203723 1 17.32913883 VLQIVTNRDDVQGYAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLQIVTNRDDVQGYAAK 17 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 ; 221.47 3.35E-15 1341480000 800880 687100 701940 727580 704200 535150 849770 716650 616800 FALSE TRUE 750754.3504 737973.5989 718590.3483 746250.9346 648894.9726 689639.1176 722354.8774 806125.33 513852.0953 1.461031992 1.43615956 1.398438101 1.452267961 1.262804956 1.342096537 1.405764195 1.568788641 1 18.97099364 -1.81463438 2.898882764 0.881325875 1.409124362 0.729754889 0.079447357 18723999.84 16059406.74 15629788.04 0.018344524 0.01532377 1.81463438 0.527798487 VLRPPGGGSNFSLGFDEPTEQPVRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLRPPGGGSNFSLGFDEPTEQPVRK 25 2 Q9UK76;J3KT51;Q9UK76-2 Q9UK76 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 0 ; 199.46 4.01E-25 786670000 424820 463120 423990 401480 505240 391080 548110 381510 509900 FALSE TRUE 398231.2745 497409.8867 434047.243 411782.6565 465560.4884 503978.4473 465925.9939 429142.3633 424794.3959 0.937468287 1.170942676 1.021781942 0.969369324 1.095966644 1.186405593 1.096827073 1.010235463 1 18.69640521 VLS(ph)PLIIK ddPTM_SK-BR-3_Pertuzumab_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 1063697000 2651086 2335351 2501397 2478700 2682465 2032681 2983030 2181929 2744269 TRUE FALSE 2485159.26 2508262.818 2560731.318 2542307.638 2471795.019 2619483.007 2535752.345 2454347.639 2286232.775 1.087010599 1.097116114 1.120065877 1.112007345 1.08116507 1.145763911 1.109140054 1.073533572 1 21.12454087 0.902153221 2.940116594 1.00014038 1.108736012 0.78332327 0.017924558 0.169138084 3.205162658 0.016301329 0.00428768 7.982762722 -0.902153221 0.108595632 VLS(ph)PPKLNEVSSDANR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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(0.998)PPKLNEVSS(0.001)DANR 162.85 4.81E-09 5525262000 3543290 2256860 2670260 2635210 2876420 2024250 3319270 2242290 3519210 TRUE FALSE 3321521.804 2423960.263 2733599.828 2702833.95 2650517.576 2608618.114 2821576.278 2522244.842 2931831.116 1.132917168 0.826773496 0.932386526 0.921892784 0.904048518 0.889757292 0.962393865 0.860296771 1 21.48337057 -1.010670029 4.672064637 1.000000607 0.920428923 0.061046154 0.082093252 1.41E-06 2.99E-07 0.069244914 0.016320793 0.09757307 1.010670029 -0.079571684 VLS(ph)PTAAKPSPFEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLSPTAAKPSPFEGK 15 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 1 VLS(0.576)PT(0.424)AAKPSPFEGK;VLS(0.903)PT(0.096)AAKPS(0.001)PFEGK 115.63 0.00031011 4680600000 2942560 2198410 2469420 2430820 2504420 1294300 2579780 1693030 3306000 TRUE FALSE 2758390.422 2361182.564 2527995.809 2493198.957 2307732.956 1667943.399 2192965.939 1904408.522 2754207.242 1.001518833 0.857300252 0.917866953 0.905232881 0.837893721 0.605598364 0.796224011 0.69145433 1 21.39320569 2.47281861 24.95596118 0.751042577 0.905719261 0.287588629 0.105617602 126.5837136 734193.2541 0.031863185 0.026759952 297.0425129 -2.47281861 0.154676684 VLS(ph)TSTDLEAAVADALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VLSTSTDLEAAVADALK 17 0 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 1 VLS(0.331)T(0.331)S(0.331)T(0.007)DLEAAVADALK;VLS(0.25)T(0.25)S(0.25)T(0.25)DLEAAVADALK;VLS(0.25)T(0.25)S(0.25)T(0.25)DLEAAVADALK;VLS(0.25)T(0.25)S(0.25)T(0.25)DLEAAVADALK 132.13 1.59E-05 62137800 155774 126852 136610 133740 140320 117912 188994 135123 159526 TRUE FALSE 146024.3834 136244.2541 139850.4537 137171.9948 129299.8332 151951.2803 160656.1042 151993.404 132900.08 1.098753164 1.02516307 1.052297739 1.032143809 0.972910123 1.143349803 1.208848815 1.143666761 1 17.01998245 2.172654831 9.880284671 1.149003949 1.036795458 0.299358525 0.061604175 0.333734788 47.53209142 0.020956875 0.015482546 148.8177833 -2.172654831 -0.11220849 VLSAPPHFHFGQT(ph)NRTPEFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLSAPPHFHFGQTNRTPEFLR 21 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 1 VLSAPPHFHFGQT(0.681)NRT(0.319)PEFLR 228.95 2.17E-25 505720000 344390 467180 413360 348200 440260 360380 414790 401670 328210 TRUE FALSE 322835.2447 501770.4933 423165.0944 357135.4015 405683.7555 464415.8557 352596.0902 451819.3837 273429.6307 1.180688588 1.835099188 1.547619742 1.306132772 1.483686148 1.698484011 1.289531385 1.652415587 1 18.06081007 -2.823348951 0.323364377 8.15E-12 1.549484875 0.346459185 0.205720282 71.00858739 2.265479883 49.14461345 0.173000345 0.001501935 2.823348951 1.549484875 VLSAPPHFHFGQTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLSAPPHFHFGQTNR 15 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 94.007 0.0046373 599920000 458890 386520 398050 391510 501380 366430 404240 355800 563350 FALSE TRUE 430168.894 415138.343 407491.934 401556.8094 462003.6373 472212.3925 343627.9648 400222.4132 469323.2456 0.916572742 0.884546732 0.868254317 0.855608183 0.984403908 1.006155985 0.732177594 0.852764948 1 18.84022239 -0.853605631 4.154823286 1.000001989 0.881654068 0.175958837 0.075514294 20445891.49 42300789.16 625.5932359 0.018397614 0.140085882 0.853605631 -0.118347921 VLSAPPHFHFGQTNRT(ph)PEFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLSAPPHFHFGQTNRTPEFLR 21 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 1 VLSAPPHFHFGQT(0.026)NRT(0.974)PEFLR 231.07 1.00E-25 500650000 167240 206650 204550 185660 230350 190240 216400 208750 178870 TRUE FALSE 156772.7469 221950.581 209402.0226 190424.3499 212259.2402 245159.1997 183952.829 234812.897 149015.4415 1.052057058 1.489446858 1.405237072 1.277883339 1.424411042 1.645193259 1.234454813 1.575762181 1 17.18510231 -0.830950818 8.177807108 1 1.39593361 0.336992678 0.170741287 0 2.65E-10 0.145275064 0.034241661 0.147587366 0.830950818 0.39593361 VLSEDEEDVDFDIIHNANDTFTVK ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 356.44 3.69E-102 1493336000 1331343 1166517 1217954.8 1201793.5 1327514 966264.1 1536046 1106178.7 1431314 FALSE TRUE 1248016.618 1252887.132 1246845.263 1232633.556 1223256.405 1245208.86 1305730.162 1244287.546 1192418.447 1.046626393 1.050710961 1.045644058 1.033725668 1.025861692 1.044271718 1.095026805 1.043499075 1 20.18545917 1.968547251 24.93215862 1.059962684 1.041692926 0 0.024791233 1412.151179 1119389.893 0.009358076 0.006049413 93.01377081 -1.968547251 -0.018269758 VLSEDEEDVDFDIIHNANDTFTVKYVPPAAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 88.413 9.50E-05 69907000 29519 25702 25861 27306 29115 15802 26769 21345 22221 FALSE TRUE 27671.45848 27605.00282 26474.43513 28006.71819 26828.42534 20363.78088 22755.23696 24009.97024 18512.17155 1.494771071 1.491181235 1.430109648 1.512881302 1.449231673 1.100021185 1.229204089 1.296982916 1 14.17618652 2.281436555 8.061844399 1.17885301 1.47405097 0.790631958 0.081241891 0.103850943 17.10795396 0.025748133 0.021364738 191.1774016 -2.281436555 0.295197961 VLSFTHPISFHSAETFESLLACLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLSFTHPISFHSAETFESLLACLK 24 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 0 73.21 0.015835 62791000 39005 83118 50471 38567 93277 40225 65086 87854 35185 FALSE TRUE 36563.74668 89272.1432 51668.19595 39556.69451 85951.40068 51837.3045 55326.95853 98822.76529 29312.3962 1.247381703 3.045542323 1.762673908 1.349486895 2.93225433 1.76844309 1.887493542 3.371364273 1 14.83922329 -1.928140286 2.682221128 0.248647133 2.171436349 0.205039421 0.724363634 22395156.35 5261208.138 104447343.6 0.165956461 0.011799394 1.928140286 1.922789216 VLSIGDGIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLSIGDGIAR 10 0 P25705;P25705-2;P25705-3;K7EK77;K7ERX7;K7EJP1;K7EQH4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ; 104.2 0.0063123 89935000 179826 216473 182283 170887 275300 167890 205692 211138 321370 FALSE TRUE 168571.0117 232500.8862 186606.8388 175272.2497 253679.0485 216357.1175 174850.3942 237499.0441 267731.2709 0.629627653 0.868411394 0.696993064 0.65465737 0.947513705 0.808112989 0.653081702 0.887079956 1 18.03042613 -4.999999986 0.266752695 2.590874865 0.747776963 0.341744699 0.10685258 246.5642787 2.405202429 215.438521 0.128152313 1.00E-05 4.999999986 -1.843097902 VLSQSTPGT(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLSQSTPGTPSK 12 0 Q6MZP7-3;Q6MZP7 Q6MZP7-3 LIN54 Protein lin-54 homolog 1 VLSQSTPGT(1)PSK;VLSQSTPGT(0.922)PS(0.078)K 242.92 2.87E-15 618890000 1050070 780210 911740 821970 923400 767330 1254860 900620 1167790 TRUE FALSE 984347.9931 837977.5602 933366.9034 843063.1418 850879.8888 988845.7144 1066705.393 1013064.39 972878.3048 1.011789438 0.861338521 0.959387108 0.866565877 0.874600538 1.016412546 1.096442779 1.041306384 1 19.89189983 2.099050406 4.982611122 1.056586379 0.911834378 0.593018062 0.05103255 0.120300511 4.908458457 0.018129571 0.013133519 125.6175751 -2.099050406 -0.144752001 VLSSAAS(ph)LPGSELPSSRPEGSQGGELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLSSAASLPGSELPSSRPEGSQGGELSR 28 1 O15027;O15027-5;A0A0C4DH09;Q8N9G1 O15027 SEC16A Protein transport protein Sec16A 1 VLSSAAS(1)LPGSELPSSRPEGSQGGELSR;VLSSAAS(0.5)LPGS(0.5)ELPSSRPEGSQGGELSR 275.58 9.24E-62 681160000 138777 169972 160546 184415 191064 136116 175282 140002 133440 TRUE FALSE 130091.1953 182556.9037 164354.2269 189147.4011 176058.6042 175410.4795 149000.0913 157481.5579 111168.0019 1.170221584 1.642171313 1.47843106 1.701455435 1.583716547 1.57788641 1.340314558 1.416608692 1 16.76238206 0.760042498 0.945363968 1.003854971 1.538199698 0.523586791 0.150338557 0.642953787 1.077719605 0.130979443 0.043379161 5.7549625 -0.760042498 0.534344727 VLSSTS(ph)EEDEPGVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLSSTSEEDEPGVVK 15 0 Q8NI08-4;Q8NI08-3;Q8NI08-2;Q8NI08;Q8NI08-7 Q8NI08-4 NCOA7 Nuclear receptor coactivator 7 1 VLS(0.027)S(0.023)T(0.147)S(0.802)EEDEPGVVK 62.69 0.069816 0 202890 139130 148530 147710 160430 119050 208580 156670 169800 TRUE FALSE 190191.4771 149431.33 152053.2017 151500.4887 147830.4749 153417.8024 177305.3654 176230.5944 141459.2831 1.34449626 1.056355771 1.074890233 1.070983009 1.045039051 1.08453683 1.253402121 1.24580438 1 17.11002733 1.758217847 25 1.191998989 1.097640818 0.021591256 0.110723847 16.61182561 21146.42686 0.046731635 0.025916001 57.30834245 -1.758217847 -0.094358171 VLSTNTDDNIGGAHFTETLAQYLASEFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLSTNTDDNIGGAHFTETLAQYLASEFQR 29 0 Q0VDF9 Q0VDF9 HSPA14 Heat shock 70 kDa protein 14 0 ; 366.11 2.27E-136 280740000 109351 134193 133476 144689 159597 130700 135082 126063 126265 FALSE TRUE 102506.9161 144128.7893 136642.1138 148401.9647 147062.8954 168430.9683 114827.7081 141802.243 105190.5558 0.974487827 1.370168531 1.298996024 1.410791716 1.398061777 1.601198577 1.091616137 1.348051087 1 16.68264566 -0.537705218 7.678138322 0.999917784 1.317425011 0.242835343 0.172691792 0 0 0.153447637 0.036167955 0.289931086 0.537705218 0.317507227 VLSTS(ph)TDLEAAVADALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLSTSTDLEAAVADALK 17 0 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 1 VLS(0.087)T(0.087)S(0.813)T(0.013)DLEAAVADALK;VLS(0.001)T(0.027)S(0.968)T(0.004)DLEAAVADALK 220.42 4.21E-15 86585000 332206 242973 262574 260162 277064 202168 385910 291104 317017 TRUE FALSE 311413.8195 260962.9737 268802.3793 266838.1974 255304.5111 260530.6197 328046.3781 327448.9752 264104.8147 1.179129657 0.98810381 1.017786743 1.010349613 0.966678746 0.986466756 1.242106769 1.239844777 1 18.01075108 1.74840628 17.06936056 1.180358972 1.01693245 0.334240641 0.08851765 0.244204297 424.2474937 0.037025844 0.020480305 56.02814969 -1.74840628 -0.163426522 DRKPGSHAS(ph)SSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 DRKPGSHASSSAR 13 2 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 DRKPGSHAS(0.697)S(0.152)S(0.152)AR;DRKPGSHAS(0.798)S(0.124)S(0.078)AR 112.5 0.00046743 53733000 23410.2 35772 37289 38383 53380 31074 48096 41798 55423 TRUE FALSE 21944.99737 38420.5961 38173.51269 39367.97276 49187.75012 40044.55936 40884.4513 47016.57231 46172.54325 0.475282404 0.832109158 0.826757852 0.852627341 1.065303028 0.867280781 0.88547107 1.018279891 1 15.49474758 5.118028592 0.937250966 0.927256285 1.84E-36 0.75099919 0.080920933 1.982777624 0.847311268 0.024090512 2.206641663 131228.629 -5.118028592 -0.927256285 down VLT(ph)PEEQLADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLTPEEQLADK 11 0 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 VLT(1)PEEQLADK;VLT(1)PEEQLADK 223.06 8.07E-11 336800000 1452210 629860 964190 788270 763070 689670 1163870 765540 666190 TRUE FALSE 1361318.768 676495.4898 987061.0421 808498.3427 703141.5603 888766.5331 989358.4983 861119.3542 554998.5852 2.452832862 1.2189139 1.778492898 1.456757484 1.26692496 1.601385223 1.782632469 1.551570359 1 19.08212457 4.749672374 24.89680378 1.50957882 2.452833441 0.60420821 0.250087214 1107.185606 2480690.064 0.055958989 0.854770084 56191.72628 -4.749672374 0.943254621 VLT(ph)PEEQLADKLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VLTPEEQLADKLR 13 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 VLT(1)PEEQLADKLR;VLT(1)PEEQLADKLR;VLT(1)PEEQLADKLR;VLT(1)PEEQLADKLR 195.46 2.49E-07 1110050000 2468020 1774810 2020700 2034730 2184860 1511690 2520450 1834770 2788710 TRUE FALSE 2313551.034 1906218.779 2068631.958 2086944.617 2013269.909 1948090.363 2142531.921 2063845.073 2323256.285 0.995822565 0.820494403 0.890401964 0.898284287 0.866572458 0.838517203 0.92221075 0.888341543 1 21.14771688 0.370065556 0.97939355 1.000336299 0.880279944 0.328603202 0.048149524 2.578073418 3.099411454 0.04377462 0.013388799 2.344582699 -0.370065556 -0.120056355 VLT(ph)PPHDVDSLPHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLTPPHDVDSLPHLR 15 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 VLT(1)PPHDVDSLPHLR 70.335 0.087712 75316000 59979 47978 52571 56095 55205 41782 57553 48699 67790 TRUE FALSE 56225.02146 51530.34104 53818.00895 57534.49267 50869.42199 53843.78513 48923.46195 54779.17735 56475.41106 0.995566396 0.91243853 0.952945856 1.018752969 0.900735754 0.95340227 0.866278988 0.969965093 1 15.78533525 VLTANSNPS(ph)SPSAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLTANSNPSSPSAAK 15 0 Q9NV56 Q9NV56 MRGBP MRG/MORF4L-binding protein 1 VLTANSNPS(0.769)S(0.224)PS(0.007)AAK 255.96 1.02E-24 476720000 1371500 1007500 1178300 997700 1201600 1145400 1681000 1219800 1421600 TRUE FALSE 1285660.263 1082096.348 1206249.832 1023302.671 1107231.183 1476058.386 1428949.656 1372094.715 1184325.776 1.085563017 0.913681328 1.018511846 0.864038166 0.934904234 1.246328009 1.206551174 1.158545007 1 20.17563455 2.245859496 24.99994949 1.176701042 0.959577859 0.530793857 0.087229245 104.1737794 356813.9127 0.027881426 0.022881442 176.1406101 -2.245859496 -0.217123183 VLTANSNPSS(ph)PSAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLTANSNPSSPSAAK 15 0 Q9NV56 Q9NV56 MRGBP MRG/MORF4L-binding protein 1 VLTANSNPS(0.031)S(0.968)PS(0.001)AAK;VLTANSNPS(0.026)S(0.973)PSAAK 368.65 1.77E-97 708640000 2297860 1555110 1927040 1738100 1982980 1761870 2632100 1768910 2285450 TRUE FALSE 2154041.044 1670251.962 1972750.299 1782702.589 1827244.75 2270493.267 2237441.04 1989762.307 1903993.63 1.131327863 0.877236108 1.036111816 0.936296509 0.959690579 1.192489949 1.175130528 1.045046725 1 20.86059722 2.250260687 24.95657904 1.126576637 0.977196746 0.279624389 0.087286024 196.0525746 418185.4048 0.027914434 0.023174122 177.934715 -2.250260687 -0.149379891 VLTANSNPSS(ph)PSAAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLTANSNPSSPSAAKR 16 1 Q9NV56 Q9NV56 MRGBP MRG/MORF4L-binding protein 1 VLTANSNPS(0.092)S(0.881)PS(0.027)AAKR;VLTANSNPS(0.039)S(0.954)PS(0.006)AAKR 125.51 4.69E-05 383250000 200941 178507 172493 169234 210058 171010 255898 176313 293543 TRUE FALSE 188364.4615 191723.844 176584.6154 173576.831 193560.892 220377.8109 217528.4705 198326.0662 244548.7769 0.770253133 0.783990198 0.722083413 0.709784089 0.791502188 0.901160961 0.889509542 0.810987765 1 17.89976272 2.356752166 3.884921839 0.891527406 0.748737702 0.679556753 0.050001205 0.131164768 3.705540267 0.016859292 0.013758534 227.3799496 -2.356752166 -0.142789704 VLTEDEMGHPEIGDAIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VLTEDEMGHPEIGDAIAR 18 0 P14324-2;P14324;A0A087WVN4;A0A087X1D8;A0A087WTP2 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 ;; 204.05 8.46E-16 999170000 614770 756350 699730 703380 760410 655460 818250 652880 755130 FALSE TRUE 576292.6431 812350.941 716327.926 721429.9216 700690.4659 844680.6615 695561.0088 734393.5052 629093.9247 0.916067729 1.291303109 1.1386661 1.14677617 1.113808985 1.342694037 1.105655263 1.167382924 1 19.2629159 -0.56320802 7.095491429 0.99999894 1.166548193 0.141223682 0.114012682 0 0 0.096887216 0.022836536 0.273395889 0.56320802 0.166549253 VLTELLEQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VLTELLEQER 10 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 0 ;;; 166.34 1.30E-05 163608000 165685 272064 191254 197268 304115 134435 174262 235931 286739 FALSE TRUE 155315.0716 292207.9016 195790.6352 202330.2309 280231.0346 173244.2021 148133.0309 265387.5047 238880.4085 0.650179195 1.223239292 0.819617801 0.846993825 1.173101789 0.725234033 0.620113771 1.110963877 1 17.86592901 2.193359474 24.99999548 0.805845491 0.959772373 0 0.21471494 291.3055801 161114.4569 0.075458921 0.055730351 156.084391 -2.193359474 0.153926881 VLTLSDDLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VLTLSDDLER 10 0 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ;;;;; 221.94 1.20E-08 478731000 491817 581650 548235 548628 632140 480358 576283 508446 551135 FALSE TRUE 461035.0519 624715.9712 561239.3931 562706.7233 582494.2743 619029.5566 489874.7141 571926.6023 459147.008 1.004112068 1.360601202 1.222352282 1.225548056 1.268644387 1.348216466 1.066923459 1.245628507 1 18.80859662 0.652090295 0.768045696 1.001535328 1.244399094 0.251741104 0.11219912 1.446863595 1.552141587 0.102884466 0.035834357 4.488386992 -0.652090295 0.242863766 VLTLSERPLDFLDLERPPT(ph)TPQNEEIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VLTLSERPLDFLDLERPPTTPQNEEIR 27 2 Q9GZY8-5;Q9GZY8-2;Q9GZY8;C9JHF5;A0A0A0MS29;Q9GZY8-4;Q9GZY8-3 Q9GZY8-5 MFF Mitochondrial fission factor 1 VLTLSERPLDFLDLERPPT(0.5)T(0.5)PQNEEIR;VLTLSERPLDFLDLERPPT(0.582)T(0.418)PQNEEIR;VLTLSERPLDFLDLERPPT(0.5)T(0.5)PQNEEIR 142.37 9.45E-06 217050000 104201 120106 109845 119738 172726 88064 105883 115469 140596 TRUE FALSE 97679.24541 128998.7732 112450.5753 122810.6798 159160.7967 113486.6472 90006.82712 129885.5588 117129.6193 0.833941457 1.101333497 0.960052427 1.048502339 1.358843285 0.968897943 0.768437801 1.108904473 1 16.83774642 2.010068284 24.9992511 0.917205628 1.061184162 0.070645295 0.155626279 371.5997678 922667.3449 0.055684296 0.041081645 102.3453898 -2.010068284 0.143978534 VLTLSERPLDFLDLERPPTT(ph)PQNEEIR ddPTM_SK-BR-3_Pertuzumab_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(0.042)T(0.958)PQNEEIR 167.02 3.96E-10 282640000 90361 78591 79856 83492 79931 64072 104880 86814 68953 TRUE FALSE 84705.46631 84409.95941 81750.22203 85634.54607 73653.54169 82568.54628 89154.21766 97652.919 57444.29885 1.474566981 1.469422747 1.423121592 1.490740557 1.282173221 1.437367118 1.552011591 1.699958411 1 15.8098761 -1.871809639 2.844173426 0.796342788 1.471519809 0.673786598 0.104566389 38690286.35 39674084.78 53980577.47 0.024799775 0.013433537 1.871809639 0.67517702 VLTPEEQLADKLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLTPEEQLADKLR 13 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 134.13 9.04E-05 249320000 247400 424450 349670 372600 440440 280590 409660 349010 458290 FALSE TRUE 231915.6756 455876.7196 357964.3375 382161.5468 405849.619 361591.778 348235.2861 392584.6668 381798.4383 0.607429608 1.194024579 0.937574127 1.000951048 1.062994445 0.947075058 0.91209196 1.028251107 1 18.54245168 4.756309712 24.99999998 1.006307247 0.607429278 0.719867083 0.078958828 2275.674492 3205286.718 0.019523411 0.627920664 57057.10227 -4.756309712 -0.398877969 VLVDVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLVDVER 7 0 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ; 108.92 0.016619 186358000 193834 234210 235830 221564 242420 207003 250650 222851 265900 FALSE TRUE 181702.2759 251551.1521 241423.999 227249.7073 223381.3111 266761.4057 213067.3594 250674.4379 221519.5722 0.820253823 1.135570774 1.089854032 1.025867399 1.008404399 1.204234023 0.961844397 1.131613046 1 17.75707465 4.747513066 24.88881921 1.072297108 0.820253685 0.530441467 0.073712812 838.4108926 2330824.224 0.016037327 0.195068826 55913.03491 -4.747513066 -0.252043424 VLVEWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLVEWLR 7 0 P49354;P49354-2;E9PQP6;H0YCW1;B3KVN2;E9PPM9 P49354 FNTA Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha 0 119.89 0.01089 27591000 79700 100110 90138 90638 103480 68099 95933 90584 100310 FALSE TRUE 74711.71927 107522.2486 92276.11593 92963.92453 95353.09822 87758.07581 81548.73725 101893.6118 83567.61297 0.894027203 1.286649753 1.104209067 1.112439631 1.141029339 1.05014458 0.97584141 1.219295468 1 16.35065631 2.234400449 23.85559064 1.050037128 1.13182187 0.011262192 0.114696707 134.454751 770983.6278 0.039107315 0.029946785 171.5538422 -2.234400449 0.081784743 VLVPEHEKDVLEWIACVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLVPEHEKDVLEWIACVR 18 1 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ; 199.76 9.54E-16 358090000 641430 610180 604210 652370 684250 507530 782370 559820 648100 FALSE TRUE 601284.0413 655358.3621 618542.1465 669110.9187 630511.7651 654045.6719 665060.8817 629714.7593 539927.9231 1.113637609 1.213788608 1.145601329 1.239259705 1.167770249 1.211357376 1.231758635 1.166294115 1 19.0424073 -0.334994253 8.175631548 0.999999999 1.190278753 0.685598121 0.039536999 0 0 0.034881001 0.008221531 0.46238714 0.334994253 0.190278755 VLVTVEEDDTIMEELVDNHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 VLVTVEEDDTIMEELVDNHGK 21 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;;;;;;;;;; 356.18 1.35E-95 752865700 630974.7 510455.4 595573.9 557799.7 556784.2 481934.4 696916.8 509743.5 560722.6 FALSE TRUE 591483.1198 548250.0489 609701.1942 572113.7847 513056.6149 621061.0377 592420.5957 573386.0981 467134.3757 1.266194805 1.173645267 1.305194449 1.224730644 1.098306273 1.329512599 1.268201671 1.2274543 1 18.83347809 0.938146782 20.52458299 1 1.239680607 0.564602292 0.065361536 2069.18048 686612.975 0.059948099 0.014987025 8.672549399 -0.938146782 0.239680607 VLVTVEEDDTIMEELVDNHGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VLVTVEEDDTIMEELVDNHGKK 22 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;; 366.78 4.04E-113 457513000 968890 773860 841900 868100 963710 601490 1117200 756420 1509570 FALSE TRUE 908248.9044 831157.3996 861870.2656 890376.9157 888024.104 775130.3986 949686.2316 850860.7021 1257613.015 0.722200624 0.660900762 0.685322317 0.707989584 0.706118729 0.616350491 0.755149812 0.676567984 1 20.26225662 -2.7650308 0.442496148 1.687698368 0.684564791 0.870033285 0.037430027 39.38517996 1.591120696 25.71280078 0.018362002 0.001717787 2.7650308 -1.003133577 VLVVHDGFEGLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VLVVHDGFEGLAK 13 0 A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0;F8VP00 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 188.29 6.24E-06 352150000 440150 394280 448620 412990 455790 339650 510550 401990 477360 FALSE TRUE 412601.7972 423472.9014 459261.4783 423588.0226 419994.092 437701.4412 433997.7672 452179.3364 397685.5321 1.037507688 1.064843619 1.154835771 1.065133097 1.05609598 1.100621989 1.091308917 1.137027374 1 18.60126855 VLVWDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLVWDLR 7 0 O43684;O43684-2;J3QT28 O43684 BUB3 Mitotic checkpoint protein BUB3 0 ; 110.36 0.015867 144399000 346550 901350 338950 339510 948200 238240 357820 793810 785050 FALSE TRUE 324860.0541 968086.8919 346990.0541 348222.4014 873732.1969 307016.0205 304168.2128 892918.9259 654020.0834 0.496712658 1.480209731 0.53054954 0.532433805 1.335940928 0.469429041 0.465074729 1.365277533 1 19.31897541 5.00260977 24.99948165 0.855581714 0.079682282 0.083478454 0.396264738 55716.7806 713651.864 0.089231334 1339324.545 100602.731 -5.00260977 -0.775899432 VLWLADCDVSDSSCSSLAATLLANHSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VLWLADCDVSDSSCSSLAATLLANHSLR 28 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 ;; 324.02 1.77E-83 714650000 545983 634282 567853 555762 754996 626720 795355 628603 628539 FALSE TRUE 511810.8986 681244.8992 581322.7413 570023.7938 695701.6597 807643.8901 676098.9015 707085.4683 523631.7804 0.977425202 1.30099991 1.110174674 1.088596634 1.328608548 1.542388985 1.291172398 1.350348651 1 18.99819313 2.723028877 21.17383952 1.337726275 1.148061869 0.231656333 0.154859815 138.058662 188208.4737 0.045446217 0.043081437 528.4803902 -2.723028877 -0.189664406 VLYIDIDIHHGDGVEEAFYTTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VLYIDIDIHHGDGVEEAFYTTDR 23 0 Q92769;Q92769-3;Q13547;Q5TEE2 Q92769;Q13547 HDAC2;HDAC1 Histone deacetylase 2;Histone deacetylase 1 0 ;;;; 87.156 0.003794 70799700 49355.6 55145.3 53354.2 54698.1 58753.3 49319.5 55637.8 50588.7 55410.9 FALSE TRUE 46266.5211 59228.31539 54619.78682 56101.74585 54139.05282 63557.23901 47295.42841 56904.81055 46162.46282 1.002254175 1.28304063 1.183207816 1.215310935 1.172793857 1.376816468 1.024543006 1.232707422 1 15.49443258 0.389626925 0.788406969 0.999089746 1.200916838 0.200460161 0.111420315 3.018169274 2.66401466 0.110882416 0.033878649 2.452601137 -0.389626925 0.201827092 VLYSNMLGEENTYLWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VLYSNMLGEENTYLWR 16 0 F8VVM2;Q00325-2;Q00325 F8VVM2 SLC25A3 "Phosphate carrier protein, mitochondrial" 0 ; 224.05 1.90E-14 49603000 56385 62367 62649 61059 86468 61645 53815 84896 51111 FALSE TRUE 52855.9635 66984.71757 64135.06386 62625.87731 79677.15208 79440.91078 45745.94034 95495.45248 42580.24391 1.241325992 1.573140767 1.506216451 1.470773099 1.871223477 1.865675334 1.074346602 2.242717366 1 15.37789659 -1.236872032 4.908981907 0.99989735 1.572241806 0.24131268 0.332848267 0.00033376 5.19E-05 0.287627357 0.067782352 0.057959945 1.236872032 0.572344456 VMDQHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VMDQHK 6 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;; 79.454 0.067107 426566000 314554 966860 195933 161869 1229700 143167 206119 945220 965580 FALSE TRUE 294866.6266 1038447.32 200580.6233 166022.8326 1133124.322 184496.9888 175213.3695 1063232.798 804418.4601 0.366558752 1.290929251 0.249348608 0.206388641 1.408625459 0.229354494 0.21781371 1.321740923 1 19.61758666 1.225244292 24.97401503 1.160870707 0.587926752 0.233156132 0.446503223 402.6729414 755167.8012 0.406806504 0.104088537 16.79748616 -1.225244292 -0.572943955 VMDS(ph)DEDDDY ddPTM_SK-BR-3_Pertuzumab_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 276.13 7.49E-24 1679460000 1213690 1294070 1240650 1232650 1269780 1026850 1318390 1100110 1040390 TRUE FALSE 1137727.309 1389884.289 1270078.804 1264281.886 1170056.601 1323284.925 1120709.659 1237461.155 866742.1878 1.312647896 1.603572906 1.465347853 1.458659684 1.349947675 1.526734182 1.293013856 1.427715384 1 19.7252434 -1.233930281 0.284540328 0.69698594 1.503708766 0.67284107 0.094301359 9.185159265 0.574288809 2.20723234 0.105741421 0.058353877 1.233930281 0.806722826 VMEGLDAFDDLMQHTHIQPWYLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VMEGLDAFDDLMQHTHIQPWYLR 23 0 Q9H7Z7;A6NHH0 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 175.77 6.58E-13 354470000 66680 75837 48987 54023 91375 48317 57103 68072 55913 FALSE TRUE 62506.61783 81452.05039 50148.99477 55409.32164 84198.77609 62265.33354 48540.93527 76570.93904 46580.75909 1.341897793 1.748620074 1.07660321 1.189532389 1.807587032 1.33671788 1.042081242 1.643831929 1 15.50744653 -4.317423547 0.134862066 2.38E-12 1.531919052 0.151380884 0.269892297 216.4756938 2.165088205 61.23392658 1.861000208 4.81E-05 4.317423547 1.531919052 VMEHFIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VMEHFIK 7 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 107.22 0.007526 3015530000 7941910 9089560 7239860 7289210 8452150 4700240 9365810 7103100 6967180 FALSE TRUE 7444840.03 9762560.48 7411592.898 7476263.469 7788352.233 6057122.986 7961493.738 7989937.671 5804312.648 1.282639389 1.681949452 1.276911384 1.288053198 1.341821626 1.043555603 1.371651429 1.376551911 1 22.4686938 3.729600018 4.517721758 1.256961973 1.505177783 0.276674493 0.159166427 0.207422608 10.87161151 0.038006434 0.065762199 5365.374219 -3.729600018 0.24821581 VMEIVDADEKVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VMEIVDADEKVR 12 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 108.32 0.001567 292440000 330320 371210 338240 367010 475780 246408 468150 356120 667990 FALSE TRUE 309645.8608 398694.7746 346263.2125 376428.0979 438414.158 317541.9895 397955.2536 400582.3659 556498.1536 0.556418487 0.716435036 0.62221808 0.676422905 0.787808828 0.570607445 0.715106153 0.719826945 1 19.08601738 -5 0.254526731 3.063092965 0.643444135 0.714914217 0.067090562 95.87948241 0.947311423 103.0099042 0.084066263 1.00E-05 5 -2.41964883 VMES(ph)MLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VMESMLK 7 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 VMES(1)MLK;VMES(1)MLK 69.432 0.03979 498210000 388710 859860 751350 786780 840800 798470 747180 732170 826210 TRUE FALSE 364381.335 923524.9291 769172.3768 806970.1068 774766.9596 1028975.327 635147.2955 823583.0362 688310.2135 0.529385338 1.341727772 1.117479244 1.172393045 1.12560724 1.494929622 0.922763142 1.196528862 1 19.39269939 4.747671293 24.91376931 1.176396548 0.529384984 0.613500003 0.160109531 746.0781784 2040156.518 0.034884969 0.433942835 55933.4095 -4.747671293 -0.647011564 VMEYINR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VMEYINR 7 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 164.89 0.0027471 630140000 632330 774730 651180 687540 874190 501700 720760 723560 812960 FALSE TRUE 592753.594 832091.8153 666626.2971 705183.4404 805534.6437 646532.6456 612688.7292 813898.0588 677271.7241 0.875207945 1.228593762 0.984281897 1.041211991 1.189381773 0.954613374 0.904642417 1.201730457 1 19.36937524 2.178275909 24.9998948 0.994419398 1.074361848 0.020675064 0.124072703 180.1330551 74698.88913 0.043294197 0.031974893 150.7564525 -2.178275909 0.07994245 VMHETVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VMHETVK 7 0 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 76.035 0.041852 60416000 99072 130800 105130 113760 167250 83389 131350 133500 145550 FALSE TRUE 92871.26037 140484.5681 107623.7332 116679.2742 154114.8597 107462.0506 111655.2869 150167.7689 121256.7647 0.765905808 1.158570975 0.8875689 0.962249607 1.270979479 0.886235509 0.920816972 1.238427969 1 16.88770571 4.759615567 23.82513063 1.024088867 0.765905318 0.267506515 0.140511912 3967.910654 4489827.554 0.031516559 1.314661481 57493.0789 -4.759615567 -0.258183549 VMLGETNPADSKPGTIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 216.19 4.90E-15 7280500000 2782530 2682453 2591226 2660644 3075532 2082049 3529086 2470278 3380453 FALSE TRUE 2608376.414 2881064.611 2652691.104 2728920.629 2833992.123 2683102.747 2999932.317 2778697.646 2816233.556 0.926193216 1.023020483 0.941928662 0.968996561 1.006305786 0.952727355 1.065228525 0.986671592 1 21.42533555 1.754408058 25 1.022990055 0.974140904 0.283026819 0.034764398 6.461436277 10205.49243 0.014538878 0.008062648 56.80781143 -1.754408058 -0.048849151 VMPNS(ph)PQNGVLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VMPNSPQNGVLVK 13 0 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 VMPNS(1)PQNGVLVK;VMPNS(1)PQNGVLVK;VMPNS(1)PQNGVLVK 208.47 4.79E-08 308611000 506430 423220 502590 486920 541370 414500 566640 460720 679730 TRUE FALSE 474733.4503 454555.6492 514511.6721 499415.1916 498852.984 534159.4212 481677.5924 518241.9062 566278.6718 0.83833892 0.802706639 0.908583879 0.881924777 0.880931967 0.943280134 0.850601685 0.915171155 1 19.11115267 -4.756939105 0.018482771 2.089672474 1.33E-06 0.66144163 0.032391581 2264.379709 3.293480546 242.8234892 141.975072 1.75E-05 4.756939105 -2.089671146 VMQEQGTHPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 VMQEQGTHPK 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;; 156.01 1.17E-05 3944220000 8478280 8099770 7984980 7950960 8827990 5989130 9419090 7485460 9033430 FALSE TRUE 7947639.589 8699485.399 8174387.496 8154995.095 8134675.276 7718094.606 8006784.897 8420036.159 7525692.175 1.056067589 1.155971464 1.08619743 1.083620603 1.080920543 1.025566078 1.063926707 1.118838768 1 22.84339285 3.111176072 1.364909839 1.058252949 1.11373184 0.195758623 0.039274038 0.538474573 2.090327211 0.013571869 0.018134706 1291.742868 -3.111176072 0.055478891 VMS(ph)KSAADLISQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VMSKSAADLISQAR 14 1 Q14195-2;Q14195 Q14195-2 DPYSL3 Dihydropyrimidinase-related protein 3 1 VMS(0.5)KS(0.5)AADLISQAR 63.181 0.043077 336530000 55234 200640 142650 177230 185770 199300 118830 156250 106950 TRUE FALSE 51777.00254 215495.5944 146033.7254 181778.0218 171180.3736 256834.6746 101012.5447 175758.1564 89099.35408 0.581115352 2.418598839 1.638998698 2.040172162 1.921230242 2.882564944 1.133706812 1.972608649 1 16.44312735 0.579299477 1.076730044 1.007733832 1.897388269 0.129183916 0.638303078 2.563731046 4.464484883 0.544950985 0.170564709 3.795766398 -0.579299477 0.889654437 VMS(ph)PENFPTASVEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VMSPENFPTASVEGK 15 0 H3BRU9;H3BSP3;H3BTW3;Q3L8U1-2;Q3L8U1-3;Q3L8U1 H3BRU9 CHD9 Chromodomain-helicase-DNA-binding protein 9 1 VMS(1)PENFPTASVEGK;VMS(0.999)PENFPT(0.001)ASVEGK 107.03 0.0012483 93294000 99829 85987 96017 97957 101324 75730 117482 83981 105436 TRUE FALSE 93580.88109 92353.56695 98294.56858 100470.7425 93366.42176 97592.02163 99866.66475 94466.21271 87838.05046 1.06537976 1.051407294 1.119043149 1.143817992 1.062938229 1.111044941 1.136940816 1.075458895 1 16.42255841 4.037215133 4.362300938 1.102488701 1.059104279 0.066868315 0.042365079 0.361267697 13.8508405 0.009617956 0.02147234 10894.69643 -4.037215133 -0.043384423 VMTIPYQPMPASS(ph)PVICAGGQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 VMTIPYQPMPASSPVICAGGQDR 23 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 VMTIPYQPMPAS(0.357)S(0.643)PVICAGGQDR;VMTIPYQPMPAS(0.359)S(0.641)PVICAGGQDR;VMTIPYQPMPAS(0.064)S(0.936)PVICAGGQDR;VMTIPYQPMPAS(0.019)S(0.981)PVICAGGQDR;VMTIPYQPMPAS(0.044)S(0.956)PVICAGGQDR;VMTIPYQPMPAS(0.031)S(0.969)PVICAGGQDR;VMTIPYQPMPAS(0.279)S(0.721)PVICAGGQDR;VMTIPYQPMPAS(0.063)S(0.937)PVICAGGQDR;VMTIPYQPMPAS(0.386)S(0.614)PVICAGGQDR;VMTIPYQPMPAS(0.037)S(0.963)PVICAGGQDR;VMTIPYQPMPAS(0.225)S(0.775)PVICAGGQDR 230.85 6.59E-33 3176240000 2946030 3043240 3269040 3048980 3687960 3182540 3877370 3334490 4230060 TRUE FALSE 2761643.241 3268564.656 3346583.173 3127221.989 3398322.498 4101287.634 3295994.364 3750808.417 3524035.659 0.783659278 0.927506124 0.949645093 0.887397941 0.964326933 1.163804238 0.935289731 1.064350302 1 21.74879709 2.47400125 24.99859684 1.033661908 0.906390183 0.495555744 0.07182499 88.67401263 710475.2957 0.023183732 0.019491857 297.8525001 -2.47400125 -0.127271725 VNCLDKFWHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VNCLDKFWHK 10 1 Q14847;Q14847-2;F6S2S5;K7ESD6 Q14847 LASP1 LIM and SH3 domain protein 1 0 ; 105.46 0.0015299 681710000 1381510 1628780 1399170 1375720 2051540 1267470 2098140 1549120 3686740 FALSE TRUE 1295043.755 1749376.566 1432358.973 1411023.304 1890420.324 1633368.013 1783543.385 1742531.042 3071399.277 0.421646174 0.569569896 0.466353881 0.459407318 0.615491557 0.531799309 0.580694083 0.567341099 1 21.55046464 -5 0.23569965 3.65455963 0.47750708 0.897780336 0.051418413 46.14050721 0.461180203 58.47191446 0.077945464 1.00E-05 5 -3.17705255 VNDAEPGS(ph)PEAPQGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VNDAEPGSPEAPQGK 15 0 Q8N8A6 Q8N8A6 DDX51 ATP-dependent RNA helicase DDX51 1 VNDAEPGS(1)PEAPQGK;VNDAEPGS(1)PEAPQGK;VNDAEPGS(1)PEAPQGK;VNDAEPGS(1)PEAPQGK 377.12 6.93E-98 2941750000 5857860 4126390 4857430 4510110 4407690 3721450 6154000 4177340 5773880 TRUE FALSE 5491226.999 4431912.209 4972650.533 4625847.058 4061527.807 4795772.202 5231264.831 4698890.094 4810182.127 1.141584009 0.921360583 1.033775937 0.961678152 0.844360504 0.997004287 1.087539867 0.976863239 1 22.19766009 3.235437454 24.99791687 0.984593401 1.008699655 0.065000865 0.079690154 477.2892315 3820241.843 0.023463737 0.029158202 1719.639666 -3.235437454 0.024106254 VNFDDYTVNLGGLKDHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VNFDDYTVNLGGLKDHIK 18 1 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 286.7 4.67E-40 754810000 1862970 1559320 1606870 1566200 1765110 1120160 1993470 1382030 1794780 FALSE TRUE 1746370.033 1674773.675 1644985.715 1606391.344 1626485.381 1443532.008 1694567.68 1554579.488 1495219.623 1.16796891 1.120085404 1.100163273 1.074351432 1.087790285 0.965431422 1.133323596 1.039699763 1 20.51192598 8 0.191221173 1.017676288 1.665547735 0.494776228 0.043513936 47.70395428 0.559607919 0.081120814 9.147528562 100000000 -8 0.647871446 VNFEDDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 199.68 0.00029305 1527427000 2138780 2462010 2462530 2473450 2686550 2114500 2808010 2256870 2651990 FALSE TRUE 2004917.578 2644299.782 2520942.374 2536922.915 2475559.2 2724921.824 2386974.969 2538645.187 2209355.736 0.90746707 1.196864651 1.141030542 1.148263665 1.120489181 1.233355851 1.08039413 1.149043201 1 21.0751943 -1.307525182 7.641885067 0.999999324 1.1323384 0.1536929 0.087166575 8.82E-07 7.99E-08 0.074146099 0.017476314 0.049257778 1.307525182 0.132339076 VNFHMFDVGGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VNFHMFDVGGQR 12 0 P63092-4;P63092;P63092-3;A0A590UJ58;B0AZR9;A0A590UJF0;A0A590UJY2;A0A590UJR6;A0A590UJI6;A0A590UJQ9;A0A590UKB4;A0A590UJQ2;A0A590UJG5;P38405-2;P38405;K7EPE2;K7EQ80;P63092-2;A0A590UJB0;A0A590UJS2;A0A590UJJ0;Q5JWF2 P63092-4;P63092-2;Q5JWF2 GNAS;GNAL Guanine nucleotide-binding protein G(s) subunit alpha isoforms short;Guanine nucleotide-binding protein G(olf) subunit alpha;Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas 0 119.69 0.00049041 169260000 274070 351830 249870 220630 379520 181420 256670 319000 327660 FALSE TRUE 256916.4479 377879.8593 255797.0344 226291.7393 349714.0301 233793.0089 218184.7163 358827.8522 272971.4292 0.941184389 1.384320184 0.937083544 0.828994228 1.281137851 0.856474282 0.799295065 1.314525308 1 18.05839043 3.779720167 6.526687927 0.978767514 1.186743128 0.084517363 0.204252736 0.362263609 34.51655986 0.049099438 0.088555361 6021.714584 -3.779720167 0.207975614 VNFNDCS(ph)FDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VNFNDCSFDLK 11 0 A0A087WVX1;P0C875 A0A087WVX1 FAM228B Protein FAM228B 1 VNFNDCS(1)FDLK;VNFNDCS(1)FDLK 68.551 0.036668 67892000 12406.7 61605 47472 60886 85320 120748 45454 37786 68283 TRUE FALSE 11630.18679 66166.2983 48598.05826 62448.43784 78619.31136 155605.9874 38638.59467 42503.66528 56886.12617 0.204446806 1.163135948 0.854304231 1.097779758 1.382047199 2.735394337 0.679227033 0.747171026 1 15.79578922 3.019298606 3.126291299 1.352646211 0.847628354 0.142221521 0.612158099 0.544648911 11.00476991 0.188085279 0.220168118 1045.43878 -3.019298606 -0.505017858 VNFPENGFLS(ph)PDKLSLLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VNFPENGFLSPDKLSLLEK 19 1 P31689 P31689 DNAJA1 DnaJ homolog subfamily A member 1 1 VNFPENGFLS(1)PDKLSLLEK 243.27 1.15E-24 361250000 1126000 506740 768210 752190 899100 677760 1085200 751940 1359000 TRUE FALSE 1055525.67 544259.5569 786432.304 771492.4689 828488.3128 873418.3095 922484.3345 845821.3642 1132174.121 0.932299768 0.480720719 0.694621339 0.681425635 0.731767577 0.771452283 0.814790161 0.747077105 1 20.11066442 0.915123816 0.403576089 1.01485286 0.645615921 0.346492717 0.114263543 1.308163739 0.555494562 0.171274046 0.085042271 8.224771014 -0.915123816 -0.369236938 VNFSEEGET(ph)EEDDQDSSHSSVTTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VNFSEEGETEEDDQDSSHSSVTTVK 25 0 A0A0A0MSK5;J3KN66;Q5JTV8;Q5JTV8-3;H0YD16;Q5JTV8-2 A0A0A0MSK5 TOR1AIP1 Torsin-1A-interacting protein 1 1 VNFSEEGET(1)EEDDQDSSHSSVTTVK;VNFSEEGET(1)EEDDQDSSHSSVTTVK 253.12 3.09E-44 494150000 292750 482110 381600 379720 485260 301530 661920 521400 546960 TRUE FALSE 274427.3001 517805.926 390651.7322 389464.2581 447149.637 388576.8161 562671.241 586497.9377 455668.8425 0.602251623 1.136364565 0.857314997 0.854708994 0.981303954 0.852761435 1.234824918 1.28711442 1 18.7976262 1.725594956 7.621530578 1.1925064 0.910502903 0.441554796 0.152279704 0.106137295 17.34252143 0.068278647 0.036034007 53.16122211 -1.725594956 -0.282003497 VNGDAS(ph)PAAAESGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VNGDASPAAAESGAK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 VNGDAS(1)PAAAESGAK;VNGDAS(1)PAAAESGAK;VNGDAS(1)PAAAESGAK 348.67 2.86E-82 1679580000 4808160 2731830 3766100 3510280 3451240 2688940 4743850 2875070 3028950 TRUE FALSE 4507225.848 2934097.536 3855433.67 3600359.728 3180193.532 3465193.327 4032553.732 3234028.818 2523398.677 1.786172708 1.162756231 1.527873382 1.426789893 1.260281842 1.373224674 1.598064455 1.281616277 1 21.26693673 0.987472679 23.0396562 0.999999988 1.426501934 0.404950884 0.172916935 221.3784436 407151.0025 0.151950533 0.037987633 9.71566829 -0.987472679 0.426501947 VNGDDHHEEDMDMS(ph)D ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 VNGDDHHEEDMDMSD 15 0 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D 286.88 1.02E-33 10129452000 5462808 5331294 5391164 5401315 5589420 4478095 6062580 4531310 5886754 TRUE FALSE 5120900.599 5726028.555 5519044.956 5539921.887 5150449.5 5770848.331 5153552.411 5097054.028 4904216.728 1.044183176 1.167572494 1.125367263 1.129624198 1.050208379 1.176711522 1.050841082 1.039320713 1 22.22559131 1.567305231 5.543501191 1.02750224 1.120795561 0.465192833 0.043719273 0.115846326 7.458648319 0.022614566 0.010354326 36.9237015 -1.567305231 0.093293321 VNGRPLEMIEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VNGRPLEMIEPR 12 1 P62249;M0R3H0;M0R1M5;Q6IPX4 P62249 RPS16 40S ribosomal protein S16 0 ;;;; 182.02 1.59E-05 4421500000 4896740 6634100 5020450 4869820 6868300 3677180 5637900 5659000 7082400 FALSE TRUE 4590261.784 7125295.667 5139537.445 4994787.826 6328891.423 4738722.172 4792549.235 6365538.607 5900301.686 0.777970692 1.207615482 0.871063501 0.846530922 1.072638614 0.803132183 0.812254947 1.078849684 1 22.49235729 3.734853225 24.50895729 0.90799672 1.028239269 0.010676795 0.14332467 491.6389938 1558392.472 0.034005537 0.059849284 5430.667642 -3.734853225 0.120242549 VNHEPEPAGGATPGATLPKS(ph)PSQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VNHEPEPAGGATPGATLPKSPSQLR 25 1 O00499-6;O00499-11;O00499-2;O00499 O00499-6 BIN1 Myc box-dependent-interacting protein 1 1 VNHEPEPAGGATPGAT(0.05)LPKS(0.942)PS(0.008)QLR 150.82 9.71E-08 281280000 84483 83816 84786 90089 145530 58979 89153 104390 382700 TRUE FALSE 79195.35984 90021.82385 86797.16396 92400.83626 134100.6608 76005.27986 75785.33531 117423.3213 318824.8977 0.248397664 0.282355062 0.272240859 0.289816877 0.420609124 0.238391921 0.237702061 0.36830035 1 18.28240477 0.807744502 4.520590102 0.999992247 0.283642682 0.94839163 0.0520609 0.503198165 11.67300406 0.049271421 0.012506388 6.423097312 -0.807744502 -0.716349565 VNIAFNYDMPEDSDTYLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 VNIAFNYDMPEDSDTYLHR 19 0 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;H0Y400 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ;;;;;;;; 206.98 2.57E-16 3445549000 1724261 2076420 1938050 1885520 2073385 1611910 2161391 1856780 1951682 FALSE TRUE 1616342.582 2230160.297 1984021.461 1933905.635 1910549.706 2077242.25 1837310.485 2088603.07 1625933.666 0.994101184 1.371618255 1.220235181 1.189412383 1.175047756 1.277568878 1.130003347 1.284556138 1 20.63283697 -3.545761198 0.425224071 3.02E-11 1.220917697 0.271535517 0.101906287 300.3079749 6.606687592 271.0226038 0.053558919 0.000284603 3.545761198 1.220917697 VNIKPQVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VNIKPQVDR 9 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;; 142 9.61E-05 11946700000 15001890 15576340 15384520 15168050 17701630 12410310 18955000 15606020 18949240 FALSE TRUE 14062948.48 16729628.42 15749448.08 15557287.84 16311415.38 15992965.03 16112873.72 17554465.95 15786489.43 0.890821772 1.059743428 0.997653605 0.985481156 1.033251595 1.01307926 1.020674913 1.111993013 1 23.91218705 1.437776404 7.330984679 1.05970559 1.006346108 0.166322413 0.051417549 0.320435734 38.42076601 0.02843684 0.011457001 27.40163041 -1.437776404 -0.053359481 VNIVDLQQVINVDLIHIENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VNIVDLQQVINVDLIHIENR 20 0 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 0 126.02 2.41E-05 35225000 33869 38819 36372 38987 42663 35424 38765 31547 30331 FALSE TRUE 31749.19975 41693.19915 37234.76102 39987.47242 39312.42007 45650.33374 32952.54813 35485.71239 25268.56015 1.256470474 1.650002964 1.473560851 1.582499049 1.55578394 1.806606054 1.30409283 1.404342478 1 14.62505584 0.894633628 1.283257784 1.007669898 1.548644725 0.53588186 0.153979121 0.40032425 1.302505319 0.1309024 0.039848195 7.845734875 -0.894633628 0.540974827 VNIVFNYDMPEDSDTYLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VNIVFNYDMPEDSDTYLHR 19 0 O00148 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ; 135.49 7.67E-06 561670000 366755 415842 371178 382885 438098 342745 423825 362744 398102 FALSE TRUE 343800.4592 446631.3744 379982.5174 392710.4773 403691.5503 441689.9175 360276.3758 408033.3869 331656.2044 1.036616999 1.34666974 1.145712073 1.184089042 1.217198849 1.331770405 1.086294696 1.230290227 1 18.33932899 -0.041380287 0.692546236 0.991133397 1.210780906 0.278987377 0.097008381 6.143209779 3.071761117 0.237342118 0.032062173 0.909116862 0.041380287 0.219647509 VNKDDIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VNKDDIQK 8 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ;;;; 109.66 0.0032602 6220110000 15875760 10942870 12977900 13097280 13875040 8862030 16324200 11333890 15434320 FALSE TRUE 14882124.52 11753091.48 13285741.92 13433378.38 12785350.33 11420354.2 13876537.76 12748951.12 12858232.28 1.157400504 0.914051887 1.033247932 1.044729795 0.994331884 0.888174513 1.079194826 0.991501074 1 23.61618898 VNKPPYPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VNKPPYPK 8 1 P13797;A0A0A0MSQ0;P13797-3;P13797-2;H7C4N2;P13796 P13797;P13796 PLS3;LCP1 Plastin-3;Plastin-2 0 ; 94.302 0.0095355 1026090000 2671200 2751400 2581300 2559900 3351300 1659520 3209000 3139800 4095500 FALSE TRUE 2504014.36 2955116.519 2642529.655 2625591.368 3088102.416 2138596.484 2727840.241 3531810.942 3411934.592 0.7338987 0.866111714 0.774495989 0.769531565 0.905088399 0.626798793 0.79949957 1.035134422 1 21.70215856 1.249466216 10.82259253 1.017714339 0.786257876 0.633109451 0.074440603 0.146806721 143.4179414 0.049824367 0.016853058 17.76095101 -1.249466216 -0.231456463 VNLAELFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VNLAELFK 8 0 P30044-2;P30044;P30044-3 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 148.05 0.0012269 89657000 299960 324340 262350 259090 367510 197610 288900 347370 319750 FALSE TRUE 281186.039 348354.4711 268573.0659 265738.688 338647.2471 254656.7991 245582.127 390739.9092 266381.6593 1.055575822 1.307726936 1.008226567 0.997586278 1.271285898 0.955984731 0.921918302 1.466842387 1 18.02313523 3.929669105 8.313898188 1.072627788 1.194314014 0.038806263 0.175865147 0.692412524 112.0078796 0.04198775 0.076383389 8504.897922 -3.929669105 0.121686226 VNLEESSGVENS(ph)PAGARPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VNLEESSGVENSPAGARPK 19 1 Q8WVM8;Q8WVM8-2;Q8WVM8-3 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 1 VNLEESSGVENS(1)PAGARPK 115.11 8.74E-05 1018200000 254160 162500 229780 196220 196100 177310 261620 179250 283380 TRUE FALSE 238252.5793 174531.6691 235230.4901 201255.3374 180699.097 228496.5186 222392.5098 201629.7571 236082.0473 1.009193973 0.739283953 0.996392961 0.852480482 0.76540804 0.9678691 0.942013644 0.854066454 1 17.84892881 -0.159141762 0.364532404 1.025048399 0.874120726 0.105441733 0.092358415 11.91879694 1.980565494 0.516147621 0.070997768 0.693199495 0.159141762 -0.150927673 VNLEVIKPWITK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VNLEVIKPWITK 12 1 A9Z1X7;Q8IYB3-2;E9PCT1;M0R1E7;M0QXG5;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 0 ; 147.68 6.00E-05 263160000 1133690 1047740 1112430 1136590 1283970 862690 1502490 1097360 1438480 FALSE TRUE 1062734.367 1125315.76 1138817.365 1165756.824 1183132.175 1111734.598 1277205.573 1234367.812 1198388.395 0.886802952 0.939024247 0.950290715 0.972770454 0.987269386 0.927691392 1.06576931 1.030023168 1 20.19266413 3.243081889 0.43648171 1.030775744 0.890342985 0.57517162 0.033617905 1.137968332 0.392067863 0.030004893 0.072445423 1750.176665 -3.243081889 -0.140432759 VNLFPGLS(ph)PSALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VNLFPGLSPSALK 13 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 VNLFPGLS(0.963)PS(0.037)ALK;VNLFPGLS(0.924)PS(0.076)ALK 208.39 4.86E-08 1234460000 1870530 1594430 1714180 1692620 1610630 1294160 2119640 1397180 1783140 TRUE FALSE 1753456.866 1712483.256 1754841.159 1736055.495 1484137.617 1667762.983 1801819.66 1571620.999 1485522.414 1.180363789 1.152781836 1.181295645 1.168649815 0.999067804 1.122677764 1.212919874 1.057958455 1 20.50253894 -5 0.149658374 0.489030106 1.187905677 0.380800337 0.060017065 153.377851 1.365674646 23.27645388 0.310211784 1.00E-05 5 0.698875571 VNMSKYDAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VNMSKYDAAR 10 1 Q86UK0-2;Q86UK0 Q86UK0-2 ABCA12 ATP-binding cassette sub-family A member 12 0 64.711 0.074661 170550000 16864 34867 15610 17264 31421 13761 18604 25324 27485 FALSE TRUE 15808.51234 37448.58896 15980.27657 17707.02347 28953.32141 17733.57731 15814.50291 28485.75714 22897.57594 0.690401132 1.635482684 0.697902547 0.773314324 1.264471029 0.774474004 0.690662756 1.244051214 1 14.48290725 3.871988172 7.50243803 0.89544181 1.220871797 0.087621954 0.304155903 0.376260792 23.62637411 0.071433504 0.129526431 7447.116921 -3.871988172 0.325429987 VNNGNTAPEDSS(ph)PAKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VNNGNTAPEDSSPAKK 16 1 G3V167;Q9UGN5-2;Q9UGN5;E9PJ27 G3V167 PARP2 Poly [ADP-ribose] polymerase 2 1 VNNGNTAPEDS(0.042)S(0.958)PAKK;VNNGNTAPEDS(0.126)S(0.874)PAKK 178.1 1.74E-09 704450000 585060 259880 373410 327350 362070 247500 524140 313730 484420 TRUE FALSE 548442.139 279121.7856 382267.4615 335750.3552 333634.4827 318949.2322 445550.0729 352899.8811 403567.1725 1.358986004 0.691636497 0.947221398 0.831956557 0.826713631 0.790325016 1.104029523 0.874451405 1 18.6224493 -1.22926895 6.580797065 1.000000754 0.911021258 0.007011257 0.18756589 1.87E-06 2.19E-07 0.163548925 0.038548525 0.058983569 1.22926895 -0.088979495 VNNVVWDLDRPLEEDCTLELLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VNNVVWDLDRPLEEDCTLELLK 22 1 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ;;; 263.32 1.89E-37 370546000 713610 486149 569881 507189 521701 530711 814290 526539 477045 FALSE TRUE 668946.4239 522143.9778 583398.8464 520204.3284 480728.7079 683918.6503 692194.774 592278.5532 397423.1077 1.683209685 1.313823901 1.467954015 1.308943336 1.209614385 1.720882951 1.741707416 1.490297222 1 18.60031623 2.231478685 24.99998399 1.57666945 1.391132409 0 0.241507799 336.3314182 1187275.207 0.081154775 0.061219311 170.4035683 -2.231478685 -0.185537042 VNPCIGGVILFHETLYQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 VNPCIGGVILFHETLYQK 18 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;; 278.34 3.58E-39 6235834000 6134615 8228540 7555552 7639922 8294172 6508490 9105577 7741255 5703402 FALSE TRUE 5750660.398 8837789.663 7734773.261 7835975.333 7642781.188 8387385.406 7740280.261 8707767.727 4751467.361 1.210291466 1.860012706 1.62787044 1.649169559 1.608509668 1.76522004 1.62902945 1.83264812 1 22.17994169 -1.543121225 6.387988607 0.999196121 1.666388519 0.561284041 0.179335368 0.0017799 0.000127301 0.150530597 0.035442631 0.028633786 1.543121225 0.667192398 VNPFRPGDSEPPPAPGAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VNPFRPGDSEPPPAPGAQR 19 1 Q15942;H0Y2Y8;C9IZ41 Q15942 ZYX Zyxin 0 ;; 146.88 1.01E-07 595300000 286467 269848 292864 271691 295812 243394 294067 256294 332654 FALSE TRUE 268537.5418 289827.8267 299810.8724 278663.051 272580.1188 313657.8966 249974.3833 288292.8701 277131.8984 0.968988209 1.045811862 1.081834585 1.005524996 0.983575404 1.131800051 0.902005091 1.04027314 1 18.08021325 1.727667271 25 0.97456892 1.03941163 0.167103511 0.057572213 1.208570371 2760.630507 0.024300909 0.01347605 53.41549665 -1.727667271 0.06484271 VNPLGGAVALGHPLGCTGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VNPLGGAVALGHPLGCTGAR 20 0 P09110;C9JDE9;H7C131;H0Y4D4;P09110-2 P09110 ACAA1 "3-ketoacyl-CoA thiolase, peroxisomal" 0 ; 183.45 4.36E-17 1779470000 1144300 1313670 1289160 1198680 1556170 1132080 1464770 1323350 1393530 FALSE TRUE 1072680.306 1410935.494 1319739.484 1229440.158 1433954.685 1458893.118 1245141.337 1488573.161 1160940.84 0.923974994 1.215337978 1.136784441 1.05900328 1.235166027 1.256647253 1.07252781 1.282212761 1 20.14686303 4.746893414 24.31872505 1.161015519 0.923974819 0.385070643 0.092516154 705.6440121 2059306.56 0.01957373 0.220302676 55833.31504 -4.746893414 -0.2370407 VNPTVFFDIAVDGEPLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 240.46 1.38E-23 1479203000 592736 654168 652421 643068 726431 633059 738026 633730 941919 FALSE TRUE 555637.7118 702603.2794 667896.7342 659570.2136 669380.0395 815812.8564 627365.8528 712852.5855 784706.6339 0.708083362 0.895370638 0.85114195 0.840530951 0.853032217 1.039640576 0.799490951 0.90843196 1 19.58179387 7.999999915 0.053280205 1.191871844 0.262764809 0.37197546 0.074724672 533.9543609 2.139568543 8.35634051 39.89798822 99999980.44 -7.999999915 -0.929107035 VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFR 36 3 P62937;F8WE65;C9J5S7 P62937 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 162.81 6.91E-18 114770000 382680 248470 219750 349570 342870 164690 246640 191450 101170 FALSE TRUE 358728.7419 266866.9773 224962.5738 358540.558 315942.3733 212233.3295 209658.6217 215352.9539 84284.07342 4.256186577 3.166280016 2.669099447 4.253953843 3.748541812 2.518071575 2.4875236 2.555084789 1 16.36297242 1.027578889 0.645759576 1.014509132 3.461444398 0.677125803 0.553101904 0.521142111 0.516329438 0.578303038 0.24249558 10.65562404 -1.027578889 2.446935265 VNQAIWLLCTGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VNQAIWLLCTGAR 13 0 M0R0F0;M0R0R2;P46782;M0QZN2 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 171.67 1.47E-06 0 94997 151580 98001 88122 143700 89827 110320 110090 120120 FALSE TRUE 89051.30734 162803.1409 100325.63 90383.35971 132414.3817 115758.5967 93778.54016 123834.9788 100071.196 0.889879515 1.626873141 1.00254253 0.903190562 1.32320175 1.156762398 0.937118211 1.23746876 1 16.61066725 3.738301038 24.22150669 1.076353237 1.312125539 0.091794577 0.218928032 408.3129486 884620.0623 0.051372577 0.091467838 5473.952672 -3.738301038 0.235772301 VNQSALEAVTPS(ph)PSFQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VNQSALEAVTPSPSFQQR 18 0 Q9UKG1 Q9UKG1 APPL1 DCC-interacting protein 13-alpha 1 VNQSALEAVT(0.011)PS(0.989)PSFQQR;VNQSALEAVTPS(1)PSFQQR;VNQSALEAVTPS(1)PSFQQR;VNQSALEAVTPS(1)PSFQQR;VNQSALEAVTPS(1)PSFQQR;VNQSALEAVTPS(1)PSFQQR 418.58 3.61E-148 4019320000 2793990 3128290 3287290 3309900 3521750 2567160 3353220 2818710 3524740 TRUE FALSE 2619119.153 3359911.847 3365266.071 3394837.638 3245165.961 3308257.418 2850435.791 3170632.148 2936438.123 0.891937457 1.144213399 1.146036773 1.15610733 1.105136844 1.126622554 0.970712023 1.079754456 1 21.48563581 1.749896983 25 1.017074325 1.109313846 0.157810382 0.080757189 4.536448473 10022.09573 0.034945219 0.019378845 56.22079511 -1.749896983 0.09223952 VNS(ph)GDTEVGSSLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VNSGDTEVGSSLLR 14 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 VNS(0.955)GDT(0.045)EVGSSLLR;VNS(0.993)GDT(0.007)EVGSSLLR;VNS(0.5)GDT(0.5)EVGSSLLR;VNS(0.975)GDT(0.025)EVGSSLLR;VNS(0.894)GDT(0.106)EVGSSLLR;VNS(0.979)GDT(0.021)EVGSSLLR 326.09 2.48E-57 1280640000 2185250 1595440 1843360 2029000 1952420 1259650 1747750 1349250 1466710 TRUE FALSE 2048479.103 1713568.038 1887085.37 2081067.575 1799084.809 1623290.506 1485691.113 1517706.833 1221906.626 1.676461245 1.402372327 1.544377721 1.703131427 1.472358666 1.328489814 1.215879415 1.24208086 1 20.22070261 1.749052126 1.013625079 1.06855778 1.551110849 0.792242394 0.098269495 0.241340082 0.462714044 0.085985865 0.035048539 56.11153198 -1.749052126 0.48255307 VNSNGKES(ph)PGSSEFFQEAVSHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VNSNGKESPGSSEFFQEAVSHGK 23 1 Q8N108-17;Q8N108;Q8N108-13;Q8N108-12 Q8N108-17 MIER1 Mesoderm induction early response protein 1 1 VNS(0.028)NGKES(0.95)PGS(0.018)S(0.004)EFFQEAVSHGK 200.76 1.44E-24 161600000 315910 167540 234380 168040 154300 153920 345010 205690 243630 TRUE FALSE 296137.757 179944.8359 239939.6043 172352.1909 142181.9004 198354.2053 293278.9534 231370.8493 202966.5791 1.459046895 0.886573724 1.182163119 0.849165373 0.70051878 0.977275206 1.4449618 1.139945553 1 17.63088266 -0.69053174 8.499582757 1.000000692 1.07647676 0.010308908 0.244098798 0 0 0.236778869 0.055809315 0.203923962 0.69053174 0.076476067 VNSNS(ph)LDLPSSSDTTHASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VNSNSLDLPSSSDTTHASK 19 0 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6 Q8NEY1-5 NAV1 Neuron navigator 1 1 VNS(0.064)NS(0.936)LDLPSSSDTTHASK;VNS(0.286)NS(0.714)LDLPSSSDTTHASK;VNS(0.071)NS(0.929)LDLPSSSDTTHASK;VNS(0.006)NS(0.994)LDLPSSSDTTHASK;VNSNS(1)LDLPSSSDTTHASK 303.7 2.38E-50 2596300000 2497590 3396520 3363170 3607690 2781370 2720280 5152450 3574410 2865380 TRUE FALSE 2341270.3 3648001.875 3442945.981 3700269.433 2562932.42 3505580.676 4379887.956 4020682.957 2387129.567 0.980788949 1.528196008 1.442295395 1.550091576 1.073646129 1.468533893 1.834792722 1.684317019 1 21.18684544 1.994500465 24.91598812 1.612259342 1.363700004 0.038437402 0.284469297 428.9148515 1943229.139 0.099558337 0.071313234 98.74166921 -1.994500465 -0.248559338 VNSSLSDELRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VNSSLSDELRR 11 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 0 98.407 0.0088889 247230000 95523 122140 116830 110020 146420 107350 129660 140730 141850 FALSE TRUE 89544.38594 131183.3727 119601.2628 112843.2995 134920.7638 138340.2023 110218.6867 158300.4503 118174.3186 0.75773135 1.110083597 1.012074909 0.954888514 1.141709683 1.170645229 0.932678843 1.339550354 1 16.85055702 4.742927829 24.69741025 1.071339663 0.757731201 0.417293749 0.120018962 361.702186 2045406.526 0.025613766 0.200697794 55325.81608 -4.742927829 -0.313608463 VNTLIRPDGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VNTLIRPDGEK 11 1 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3;K7EMA7 P62750 RPL23A 60S ribosomal protein L23a 0 ; 149.57 3.13E-05 578360000 488390 508880 551600 639030 706970 503420 807200 603980 724380 FALSE TRUE 457822.5417 546558.0047 564684.2125 655428.5917 651447.428 648749.1817 686167.8537 679388.2325 603476.2983 0.758642126 0.905682636 0.935718957 1.086088374 1.079491323 1.075020152 1.137025357 1.125791078 1 19.20293758 4.001198499 0.686863387 1.10653148 0.735144824 0.814853367 0.050516617 0.516373735 0.344405119 0.022130145 0.130335844 10027.63457 -4.001198499 -0.371386656 VNTLIRPDGEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VNTLIRPDGEKK 12 2 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3;K7EMA7 P62750 RPL23A 60S ribosomal protein L23a 0 ; 154.47 4.02E-05 4545100000 5345000 3578180 4302900 4526000 5136100 3384800 5811900 4033200 7339700 FALSE TRUE 5010465.991 3843112.17 4404966.82 4642144.822 4732731.424 4361936.812 4940459.55 4536753.898 6114656.654 0.819419025 0.628508253 0.720394794 0.759183236 0.773997902 0.713357603 0.807970068 0.741947448 1 22.54384006 -5 0.193276974 2.176288743 0.689292111 0.681666052 0.054266824 71.62642014 0.703991441 32.32604856 0.132403936 1.00E-05 5 -1.486996632 VNVPVIGGHAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VNVPVIGGHAGK 12 0 P40926;G3XAL0;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 ; 109.72 0.0015673 7152700000 5174000 4059700 4364000 3839500 5432200 3575700 4547600 4197600 7281300 FALSE TRUE 4850168.576 4360284.412 4467516.141 3938028.07 5005576.924 4607946.543 3865729.598 4721679.6 6066003.991 0.799565675 0.718806717 0.736484207 0.649196419 0.825185234 0.759634605 0.637277787 0.77838386 1 22.53231502 0.973299374 23.88330315 1.000000002 0.72734519 0.674768141 0.057933749 878.8776125 786143.848 0.052620682 0.013155171 9.403713169 -0.973299374 -0.272654812 VNVTVDYIRPAS(ph)PATETVPAFSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VNVTVDYIRPASPATETVPAFSER 24 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 1 VNVTVDYIRPAS(0.968)PAT(0.031)ETVPAFSER;VNVTVDYIRPAS(0.962)PAT(0.035)ET(0.003)VPAFSER;VNVTVDYIRPAS(0.951)PAT(0.049)ETVPAFSER;VNVTVDYIRPAS(1)PATETVPAFSER;VNVTVDYIRPAS(0.999)PAT(0.001)ETVPAFSER;VNVTVDYIRPAS(0.986)PAT(0.014)ETVPAFSER 267.55 8.71E-45 5298250000 3686440 3676170 4042840 3858320 3880570 3360980 4216260 3379730 3935330 TRUE FALSE 3455712.301 3948357.452 4138738.074 3957331.023 3575805.686 4331240.365 3584070.955 3801696.73 3278498 1.054053503 1.204319006 1.26238847 1.207056104 1.090684114 1.321105081 1.093205167 1.159584886 1 21.64460358 0.738411573 1.00117294 1.001173994 1.19456257 0.310191524 0.081403023 0.997609799 1.813229619 0.071225632 0.023081447 5.475346057 -0.738411573 0.193388576 VNVTVDYIRPASPATETVPAFSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VNVTVDYIRPASPATETVPAFSER 24 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 258.9 5.42E-44 1590600000 621761 648553 749777 664049 651323 644214 796160 627547 729340 FALSE TRUE 582846.0889 696572.5389 767562.0645 681089.6216 600170.7189 830188.1239 676783.1992 705897.6244 607608.4423 0.959246199 1.146416821 1.263251152 1.120935086 0.987759019 1.366320917 1.11384759 1.161764016 1 19.21278239 -1.084414548 4.558539013 0.999989703 1.153622799 0.112657327 0.118002204 1.13E-05 2.28E-06 0.10495409 0.024736258 0.082335182 1.084414548 0.153633097 VPADTEVVCAPPTAYIDFAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VPADTEVVCAPPTAYIDFAR 20 0 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 0 ;;; 207.31 1.58E-21 165203000 61972 94495 78353 76645 81318 48246 98011 79848 119302 FALSE TRUE 58093.28314 101491.5081 80211.57016 78611.84046 74931.6123 62173.83699 83315.16044 89817.19857 99389.72548 0.584499885 1.02114688 0.807040866 0.790945342 0.753917087 0.625555979 0.838267336 0.903686957 1 16.6008091 1.078617421 2.665346463 0.995723567 0.795406135 0.286364183 0.118972894 0.368808361 5.291139 0.112997324 0.030578023 11.98443106 -1.078617421 -0.200317432 VPAHPDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VPAHPDSR 8 0 O76071 O76071 CIAO1 Probable cytosolic iron-sulfur protein assembly protein CIAO1 0 ;;; 70.919 0.050085 347317000 396536 618854 426668 460773 684703 331749 460527 586035 686830 FALSE TRUE 371717.5196 664674.5941 436788.7664 472597.2153 630929.1883 427519.5508 391475.2517 659202.7598 572193.6359 0.649635886 1.161625283 0.763358309 0.825939307 1.102649783 0.747158871 0.684165686 1.152062376 1 19.12614393 VPAS(ph)PLPGLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 VPASPLPGLER 11 0 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 VPAS(1)PLPGLER;VPAS(1)PLPGLER;VPAS(1)PLPGLER;VPAS(1)PLPGLER;VPAS(1)PLPGLER;VPAS(1)PLPGLER;VPAS(1)PLPGLER;VPAS(1)PLPGLER 159.44 3.01E-05 14323630000 2928090 3425530 3557770 3444620 3750720 3110490 3912650 3280280 4308160 TRUE FALSE 2744826.074 3679159.805 3642161.985 3533014.781 3456153.581 4008437.968 3325984.456 3689830.179 3589100.264 0.764767176 1.025092512 1.014784129 0.984373386 0.962958214 1.116836442 0.926690315 1.028065506 1 21.7751908 4.741290362 24.97356709 1.006183855 0.764767088 0.705259109 0.049279161 130.01413 1189392.735 0.010560967 0.073283993 55117.60799 -4.741290362 -0.241416766 VPASETS(ph)PGPPPMGPPPPSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VPASETSPGPPPMGPPPPSSK 21 0 Q9HD15 Q9HD15 SRA1 Steroid receptor RNA activator 1 1 VPASET(0.038)S(0.962)PGPPPMGPPPPSSK;VPAS(0.005)ET(0.262)S(0.733)PGPPPMGPPPPSSK;VPAS(0.021)ET(0.131)S(0.848)PGPPPMGPPPPSSK 229.6 1.30E-25 159655000 254569 198337 231978 221628 230914 185564 288350 204504 232554 TRUE FALSE 238635.9807 213022.0778 237480.6277 227315.3497 212778.9459 239133.3144 245114.5944 230036.7746 193739.235 1.231738015 1.09952988 1.225774571 1.173305705 1.098274936 1.234305041 1.265177879 1.187352549 1 17.56375662 -1.387234605 7.617777608 0.999995937 1.189118666 0.536841108 0.055295951 3.92E-06 3.15E-07 0.054993964 0.012961923 0.040998257 1.387234605 0.189122729 VPCNVEGIS(ph)PELEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VPCNVEGISPELEK 14 0 Q86VQ1;H7C2L5;H7C0B2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 VPCNVEGIS(1)PELEK;VPCNVEGIS(1)PELEK;VPCNVEGIS(1)PELEK;VPCNVEGIS(1)PELEK 216.29 6.49E-12 1286120000 1695050 1235120 1393540 1317000 1502740 1097400 1728090 1261140 2160360 TRUE FALSE 1588959.846 1326569.57 1426595.427 1350796.45 1384720.862 1414201.565 1468978.947 1418596.105 1799781.96 0.882862414 0.737072379 0.792649031 0.750533387 0.769382566 0.785762718 0.816198284 0.788204425 1 20.77939071 -0.438456033 0.638469755 1.0220076 0.780401778 0.727044311 0.040166844 4.93594166 1.619723833 0.291944007 0.013857093 0.364371136 0.438456033 -0.241605822 VPDEEENEES(ph)DNEKETEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VPDEEENEESDNEKETEK 18 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 VPDEEENEES(1)DNEKETEK;VPDEEENEES(1)DNEKETEK;VPDEEENEES(1)DNEKETEK;VPDEEENEES(1)DNEKETEK;VPDEEENEES(1)DNEKETEK;VPDEEENEES(1)DNEKETEK 296.45 1.47E-49 13565300000 24869600 6484360 13350010 11984890 8626280 7896220 17048980 8421480 9905560 TRUE FALSE 23313056.13 6964468.761 13666678.54 12292442.57 7948806.766 10175730.53 14492643.72 9472920.316 8252258.044 2.825051762 0.843947041 1.656113814 1.489585336 0.963228091 1.233084384 1.756203411 1.147918578 1 22.9763575 4.749803967 24.73213364 1.312336063 2.825052788 0.724475454 0.301616263 799.8599368 1759422.917 0.070260122 1.076376787 56208.75511 -4.749803967 1.512716725 VPDGKPENEFAFNAEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VPDGKPENEFAFNAEFK 17 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 191.95 1.95E-10 834000000 1756690 1007880 1286230 1239810 1252230 926030 1642960 1162940 1392790 FALSE TRUE 1646741.909 1082504.484 1316739.983 1271625.624 1153884.907 1193359.828 1396613.4 1308135.619 1160324.351 1.419208264 0.93293266 1.134803369 1.095922552 0.994450307 1.028470899 1.203640516 1.127387887 1 20.14609671 4.753655266 24.55508451 1.072508252 1.419208584 0.659567991 0.079866204 1461.688159 2377736.813 0.019521914 0.450855852 56709.42788 -4.753655266 0.346700332 VPDHHPC ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VPDHHPC 7 0 P78371;P78371-2 P78371 CCT2 T-complex protein 1 subunit beta 0 ;; 118.06 0.0050921 593521000 724345 905942 760543 745764 950710 756474 1000637 855063 857224 FALSE TRUE 679009.5394 973018.8883 778583.4391 764901.5668 876045.0716 974855.7635 850600.7713 961819.4978 714147.7765 0.950796966 1.362489558 1.090227352 1.071069031 1.226699992 1.36506168 1.191071091 1.346807383 1 19.44586311 2.499887251 23.82459025 1.247549407 1.153983407 0.092237085 0.142918377 1015.709579 1062938.895 0.04282259 0.040070281 316.1456798 -2.499887251 -0.093566 VPDS(ph)PENELK ddPTM_SK-BR-3_Pertuzumab_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 81.92 0.020524 109980000 85023 61304 76563 68337 74519 53868 83562 62972 89319 TRUE FALSE 79701.5622 65843.01195 78379.11052 70090.64311 68666.57834 69418.81713 71032.65385 70834.19282 74411.08188 1.071098016 0.884854921 1.053325775 0.941938235 0.92280043 0.93290966 0.954597784 0.951930694 1 16.18322987 4.764858463 23.92007785 0.956098746 1.071098291 0.394047602 0.045120527 5176.85854 4708644.05 0.010342282 0.774134807 58191.35404 -4.764858463 0.114999545 VPDVDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VPDVDIR 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 79.116 0.077928 288430000 539180 624790 583910 602410 712340 542600 622360 567900 745530 FALSE TRUE 505433.6863 671050.1017 597760.6209 617868.8605 656395.6898 699239.8116 529042.8957 638803.5651 621096.2267 0.813776778 1.08042856 0.962428357 0.994803758 1.056834129 1.125815585 0.851788939 1.028509815 1 19.24445728 -1.408751759 7.886418934 1.000000156 0.99282117 3.01E-05 0.096383808 2.42E-07 1.80E-08 0.08522251 0.020086702 0.039016494 1.408751759 -0.007178986 VPEASSEPFDTSS(ph)PQAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VPEASSEPFDTSSPQAGR 18 0 H0Y6F5;Q9H4I2 H0Y6F5 ZHX3 Zinc fingers and homeoboxes protein 3 1 VPEASSEPFDTS(0.004)S(0.996)PQAGR 199.99 1.64E-15 386180000 377620 363800 385720 336400 384780 316360 451590 347240 483030 TRUE FALSE 353985.4383 390736.1305 394869.4606 345032.5935 354560.9309 407687.9963 383878.2719 390593.6784 402409.1725 0.879665431 0.970992108 0.981263568 0.857417318 0.881095549 1.01311805 0.953950104 0.970638109 1 18.61830366 2.229320286 24.9999789 0.978896641 0.928431192 0.37265427 0.042910014 314.6121896 851184.9135 0.017311452 0.012958226 169.5587813 -2.229320286 -0.050465449 VPEEDLKR ddPTM_SK-BR-3_Pertuzumab_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 5530600000 5016500 4437500 4502300 4518700 5157100 3438650 5197300 4165670 6185000 FALSE TRUE 4702526.22 4766057.117 4609096.682 4634657.492 4752082.169 4431332.433 4418013.114 4685763.069 5152683.543 0.912636334 0.924966006 0.894504125 0.899464804 0.922253837 0.860004771 0.857419843 0.909383049 1 22.29689256 2.281813814 24.99983396 0.889569368 0.909970471 0 0.041133389 423.3092268 244665.9917 0.012937199 0.010823971 191.343544 -2.281813814 0.020401104 VPEWCLDDWHPSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VPEWCLDDWHPSEK 14 0 E9PH64;Q9Y6M9;A0A3B3IT57;E7EWZ0;E9PF49 E9PH64 NDUFB9 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 0 ; 214.65 6.79E-12 230770000 585520 587600 588330 509230 838480 726520 707850 751160 1141940 FALSE TRUE 548873.3484 631106.5154 602285.4654 522297.7039 772629.1631 936254.5299 601714.4639 844943.9795 951342.8368 0.576945899 0.663384945 0.63308982 0.549011023 0.812145878 0.98413999 0.632489614 0.888159291 1 19.85960582 2.671712348 6.812924804 0.835043511 0.620055375 0.582231694 0.106768943 0.207071919 17.82646932 0.03301391 0.031155127 469.58298 -2.671712348 -0.214988137 VPGGGEQPAQPNGWQYHS(ph)PSRPGSTAFPSQDGETGGHRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VPGGGEQPAQPNGWQYHSPSRPGSTAFPSQDGETGGHRR 39 2 A0A1B0GUN5;A0A5F9ZH45;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 VPGGGEQPAQPNGWQY(0.002)HS(0.806)PS(0.161)RPGS(0.013)T(0.013)AFPS(0.003)QDGET(0.001)GGHRR 105.18 7.12E-06 91183000 1675.5 2206.8 1409.1 1916.7 3481 2129.2 1307.9 2341.6 2688.1 TRUE FALSE 1570.633446 2370.193768 1442.524517 1965.885767 3207.616302 2743.865475 1111.792537 2633.953914 2239.438744 0.701351377 1.058387408 0.644145557 0.877847529 1.432330449 1.225246943 0.496460347 1.176166984 1 11.12892149 4.757671795 22.5028911 0.946181354 0.701350499 0.079646962 0.275023782 3212.751162 3782681.241 0.065969184 1.982260326 57236.3321 -4.757671795 -0.244830856 VPGGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VPGGSPR 7 0 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 VPGGS(1)PR 75.738 0.044744 623320000 392430 386490 350760 344270 363210 302570 471320 375470 357830 TRUE FALSE 367868.5068 415106.1217 359080.1928 353104.551 334684.9517 389917.0472 400649.9415 422348.256 298105.8613 1.234019704 1.3924789 1.20453919 1.184493822 1.122705036 1.30798182 1.343985454 1.416772733 1 18.18546522 3.932693293 8.71488299 1.24538509 1.321244038 0.062454729 0.123079842 0.894790868 165.5693593 0.030532013 0.055504862 8564.328016 -3.932693293 0.075858948 VPHDPVALEEHFRDDDEGPVSNQGYMPYLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VPHDPVALEEHFRDDDEGPVSNQGYMPYLNR 31 1 Q9UH65;E7EMB1;E9PJK8 Q9UH65 SWAP70 Switch-associated protein 70 0 ;; 170.82 1.07E-12 701802000 184071 197064 195121 183694 212527 183068 227349 169367 212868 FALSE TRUE 172550.3247 211654.8236 199749.3623 188407.899 195835.9867 235916.7597 193260.1281 190512.8428 177338.9556 0.972997298 1.193504399 1.126370467 1.062416875 1.104303259 1.330315491 1.089778201 1.074286482 1 17.43614996 1.066641955 2.553795514 1.004113443 1.138069314 0.158338451 0.091989685 0.411322652 5.527060511 0.080930797 0.021997772 11.65848061 -1.066641955 0.13395587 VPKPEPIPEPKEPS(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VPKPEPIPEPKEPSPEK 17 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 VPKPEPIPEPKEPS(1)PEK;VPKPEPIPEPKEPS(1)PEK;VPKPEPIPEPKEPS(1)PEK;VPKPEPIPEPKEPS(1)PEK 170.91 9.34E-10 2495620000 2609580 995240 1466620 1612870 1838540 834039 1961290 1218300 2513270 TRUE FALSE 2446251.046 1068928.605 1501408.919 1654258.975 1694148.485 1074812.52 1667212.772 1370407.437 2093789.001 1.168336946 0.510523556 0.71707747 0.790079122 0.809130473 0.513333731 0.796265895 0.654510763 1 20.99768463 -1.351341538 5.722015841 1.000054388 0.720012552 0.145507573 0.185760161 0.000113962 1.29E-05 0.159033315 0.037477251 0.044530591 1.351341538 -0.280041836 VPLAPITDPQQLQLS(ph)PLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VPLAPITDPQQLQLSPLK 18 0 P31350;P31350-2;A0A286YFD6 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 VPLAPITDPQQLQLS(1)PLK;VPLAPITDPQQLQLS(1)PLK;VPLAPITDPQQLQLS(1)PLK;VPLAPITDPQQLQLS(1)PLK 293.83 3.13E-49 4575090000 3406050 2217884 3118303 2485675 2626715 2394706 3183840 2538172 3000950 TRUE FALSE 3192871.41 2382098.439 3192270.62 2549461.629 2420423.4 3086018.747 2706452.749 2855068.361 2500072.058 1.277111754 0.952811912 1.276871444 1.019755259 0.968141455 1.23437192 1.082549897 1.141994429 1 21.25353825 -1.313519969 3.611127668 0.99962285 1.113769545 0.089846995 0.118111405 47.72765384 25465821.71 15200.35539 0.024768442 0.048582519 1.313519969 0.114146695 VPLAPITDPQQLQLS(ph)PLKGLSLVDKENTPPALSGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VPLAPITDPQQLQLSPLKGLSLVDKENTPPALSGTR 36 2 P31350;P31350-2;A0A286YFD6 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 VPLAPITDPQQLQLS(0.999)PLKGLS(0.001)LVDKENTPPALSGTR;VPLAPITDPQQLQLS(1)PLKGLSLVDKENTPPALSGTR 280.8 1.19E-76 831140000 299007 320730 349690 347001 577160 243877 521972 325988 1647800 TRUE FALSE 280292.6856 344477.1829 357984.8119 355905.6331 531832.1818 314280.3309 443707.1444 366688.3194 1372771.535 0.204180141 0.250935552 0.260775229 0.259260645 0.387414925 0.228938555 0.323219948 0.267115328 1 20.38866011 -4.950881973 0.366832904 10 0.254125682 0.95530397 0.049495951 85.92364636 0.695181017 611.3572392 0.031730381 1.12E-05 4.950881973 -9.745874318 VPLS(ph)PLSLLAGPADAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VPLSPLSLLAGPADAR 16 0 Q53ET0;H0YDQ8;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 VPLS(0.997)PLS(0.003)LLAGPADAR;VPLS(0.999)PLS(0.001)LLAGPADAR;VPLS(0.916)PLS(0.084)LLAGPADAR;VPLS(0.998)PLS(0.002)LLAGPADAR;VPLS(0.995)PLS(0.005)LLAGPADAR 177.04 3.16E-09 835458000 305885.9 320306.6 372878.8 404676.3 423935.9 269507.6 303381 250810.8 291927.4 TRUE FALSE 286741.0475 344022.4339 381723.6612 415060.979 390641.6845 347310.069 257891.8355 282125.0805 243202.831 1.179020188 1.414549463 1.569569152 1.706645343 1.606238229 1.428067542 1.060398164 1.160040281 1 17.8918005 1.798935497 3.989832345 1.080202009 1.504597532 0.647314155 0.143152644 0.141040259 4.068243923 0.074909307 0.039656949 62.94126931 -1.798935497 0.424395523 VPLVAEKPLKEPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VPLVAEKPLKEPK 13 2 P41250 P41250 GARS Glycine--tRNA ligase 0 120.53 0.00014784 525000000 1693400 1090700 1316200 1277100 1699400 1041300 2005100 1488700 1968400 FALSE TRUE 1587413.117 1171456.563 1347420.886 1309872.548 1565935.979 1341906.406 1704453.869 1674567.472 1639861.324 0.968016682 0.714363188 0.82166758 0.798770316 0.954919758 0.818304808 1.039389029 1.021164075 1 20.64514239 2.014678789 1.059136794 1.032443948 0.808317334 0.463441888 0.080657311 0.372038585 0.770284617 0.057976926 0.027456143 103.4376842 -2.014678789 -0.224126613 VPMDIPVFTGTHADLLIVVFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VPMDIPVFTGTHADLLIVVFHK 22 0 Q8IV36-2;Q8IV36;Q8IV36-3;X6R4D2 Q8IV36-2 HID1 Protein HID1 0 99.508 0.00057659 36763000 33126 33040 34208 31937 37199 28439 39293 28977 28308 FALSE TRUE 31052.70279 35486.31598 35019.42991 32756.55749 34277.54059 36648.87763 33401.37943 32594.84224 23583.21192 1.316729159 1.504727859 1.484930468 1.388977786 1.453472101 1.554024013 1.4163202 1.382120567 1 14.5254726 0.633080605 1.724626567 1.000184165 1.458424506 0.819693661 0.06506652 0.599132472 2.338886073 0.057663659 0.016296477 4.29616156 -0.633080605 0.458240341 VPMYEEQWSYYDDKQPYPSRPPFDNQHS(ph)QDLDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VPMYEEQWSYYDDKQPYPSRPPFDNQHSQDLDSR 34 2 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 VPMYEEQWSYYDDKQPYPS(0.01)RPPFDNQHS(0.954)QDLDS(0.035)R 65.177 0.0029502 54906000 29944 26750 26268 28711 19136 13538 33716 22987 22961 TRUE FALSE 28069.85849 28730.59783 26891.08936 29447.77287 17633.13575 17446.20083 28660.5988 25856.97755 19128.66077 1.467424136 1.501965986 1.405800944 1.539458158 0.921817579 0.912045074 1.498306607 1.351740086 1 14.22344825 2.764248598 24.96148775 1.17586453 1.470402713 0.448295839 0.185567363 837.7764694 814081.5169 0.059203178 0.06277467 581.0969524 -2.764248598 0.294538182 VPPELLGGS(ph)PPWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VPPELLGGSPPWK 13 0 E7EVA0 E7EVA0 MAP4 Microtubule-associated protein 1 VPPELLGGS(1)PPWK;VPPELLGGS(1)PPWK;VPPELLGGS(1)PPWK 152.11 4.73E-05 724011000 2077995 1561151 1900394 1864864 2074073 1530355 2143605 1586247 2516777 TRUE FALSE 1947937.002 1676740.244 1945472.243 1912719.567 1911183.673 1972143.645 1822191.331 1784293.43 2096710.66 0.92904426 0.799700348 0.927868723 0.912247743 0.911515217 0.940589316 0.86907143 0.850996498 1 20.99969636 VPQALNFS(ph)PEESDSTFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VPQALNFSPEESDSTFSK 18 0 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 1 VPQALNFS(1)PEESDSTFSK;VPQALNFS(1)PEESDSTFSK;VPQALNFS(1)PEESDSTFSK 210.12 4.69E-16 148805000 389110 294704 346390 343635 350490 294817 427970 325355 401840 TRUE FALSE 364756.2997 316524.1908 354606.5344 352453.2559 322963.9292 379925.8819 363799.8716 365976.2879 334770.308 1.089571838 0.945496608 1.059253243 1.052821136 0.964732897 1.134885242 1.086714869 1.093216092 1 18.35281205 2.235325491 24.99991194 1.087762737 1.01830445 0.202981888 0.053822568 103.3700263 798797.9313 0.017989332 0.013854216 171.9196393 -2.235325491 -0.069458287 VPQIEVETHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VPQIEVETHK 10 0 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 167.6 5.19E-06 495230000 289830 328836 314916 317247 372498 248729 385235 333108 410162 FALSE TRUE 271690.0577 353183.3596 322385.9562 325388.0951 343243.5097 320533.0245 327472.5881 374697.2671 341703.3125 0.795105133 1.033596535 0.94346746 0.952253266 1.004507411 0.938044827 0.958353566 1.096557316 1 18.38238471 4.748100814 24.83243774 0.983460248 0.795105023 0.612313226 0.048633949 808.4513366 2104292.416 0.010784155 0.13922318 55988.75546 -4.748100814 -0.188355225 VPS(ph)GAAGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VPSGAAGGK 9 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 VPS(1)GAAGGK 81.771 0.021336 164860000 386280 336580 343600 311470 409070 249090 343090 323330 442540 TRUE FALSE 362103.4243 361500.7334 351750.3543 319462.8475 376943.2923 320998.2394 291646.8396 363698.4622 368677.2151 0.982169251 0.980534513 0.954087586 0.86651096 1.022420906 0.870675556 0.791062826 0.986495632 1 18.49199873 2.209468902 24.98458327 0.882692593 0.958524886 0.038521291 0.072025434 321.1566628 275814.2679 0.025366018 0.018736993 161.9828001 -2.209468902 0.075832293 VPS(ph)GIFDVNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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;VPS(1)GIFDVNSR 167.05 2.07E-05 343227000 196380 248403 232561 259297 275957 190957 226813 198149 266884 TRUE FALSE 184088.9263 266795.0166 238077.4567 265951 254284.4504 246083.186 192804.4963 222888.3388 222339.3363 0.827963821 1.199945188 1.070784238 1.196149114 1.143677294 1.106791043 0.867163227 1.00246921 1 17.76240369 1.757401508 25 0.946301385 1.107228824 0.237959238 0.110277524 8.807426746 11697.99711 0.046209878 0.025626156 57.20072167 -1.757401508 0.160927439 VPS(ph)PDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VPSPDHR 7 0 Q8NAV1;Q8NAV1-2 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 1 VPS(1)PDHR 67.993 0.066775 314740000 283020 312470 299420 307620 286470 231810 328210 277900 307440 TRUE FALSE 265306.2834 335605.6039 306522.3838 315514.05 263971.8018 298729.7839 278997.9575 312596.4267 256126.2779 1.035841717 1.310313048 1.196762731 1.23186911 1.030631468 1.166337895 1.08929845 1.220477763 1 17.96649575 2.762836587 24.86118278 1.110721643 1.21364374 0.182394983 0.091801657 997.3693068 1021410.711 0.025285116 0.026809291 579.2107143 -2.762836587 0.102922097 VPS(ph)PDHRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VPSPDHRR 8 1 Q8NAV1;Q8NAV1-2 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 1 VPS(1)PDHRR;VPS(1)PDHRR 84.658 0.010594 509150000 177395 233911 190420 193874 238011 172709 258922 183101 345204 TRUE FALSE 166292.1636 251230.0138 194936.8523 198849.1351 219318.5762 222567.2846 220099.0498 205961.5629 287587.2223 0.5782321 0.873578498 0.677835582 0.691439395 0.762615858 0.773912286 0.765329725 0.716170772 1 18.13364005 -5 0.360181279 4.194135704 0.733987674 0.550381081 0.076498924 367.4195553 2.923328364 909.9044736 0.051225639 1.00E-05 5 -3.46014803 VPS(ph)PGMEEAGCSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VPSPGMEEAGCSR 13 0 Q96RL1-2;Q96RL1-3;Q96RL1;Q96RL1-4 Q96RL1-2 UIMC1 BRCA1-A complex subunit RAP80 1 VPS(1)PGMEEAGCSR;VPS(1)PGMEEAGCSR;VPS(1)PGMEEAGCSR;VPS(1)PGMEEAGCSR 196.74 1.46E-07 1923990000 297549 325395 322734 303409 325614 273952 350873 272838 307949 TRUE FALSE 278925.9392 349487.5844 330389.4029 311194.9886 300041.5899 353037.4952 298262.851 306902.4249 256550.3225 1.087217262 1.362257436 1.287815192 1.212997846 1.16952334 1.376094529 1.162590045 1.196265988 1 17.96888231 0.708076954 0.95442464 1.000097648 1.262144 0.401850666 0.089284661 0.895910499 1.458483094 0.079732865 0.026173657 5.105954661 -0.708076954 0.262046352 VPS(ph)S(ph)DEEVVEEPQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VPSSDEEVVEEPQSR 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 VPS(1)S(1)DEEVVEEPQSR;VPS(1)S(1)DEEVVEEPQSR;VPS(1)S(1)DEEVVEEPQSR;VPS(1)S(1)DEEVVEEPQSR;VPS(1)S(1)DEEVVEEPQSR;VPS(1)S(1)DEEVVEEPQSR 222.57 2.02E-12 7608870000 1698240 1574910 1555700 1652950 1577310 1300730 1855080 1345610 1449990 TRUE FALSE 1591950.19 1691517.975 1592601.939 1695367.495 1453434.435 1676229.635 1576927.976 1513612.371 1207977.302 1.317864324 1.400289536 1.318403861 1.403476285 1.203196809 1.387633388 1.305428482 1.253013917 1 20.20416192 -2.501783015 0.265637981 0.498733484 1.368467025 0.767345715 0.057825101 18.69257942 0.595023685 5.479655655 0.068742202 0.003149321 2.501783015 0.869733542 VPS(ph)VESLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 181.87 4.93E-05 2958075000 297189 328136 279093 296165 305172 242976 319693 233819 264864 TRUE FALSE 278588.471 352431.5309 285713.2178 303765.0953 281205.0221 313119.2268 271758.0025 263011.8168 220656.4873 1.262543759 1.59719542 1.294832621 1.376642486 1.274401789 1.419034766 1.231588547 1.191951436 1 17.75144264 0.905273731 0.372025832 0.96077098 1.44156309 0.598849847 0.098236071 0.992231914 0.366533797 0.168424049 0.084951151 8.040327359 -0.905273731 0.48079211 VPS(ph)WGLEDNVVCSQPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VPSWGLEDNVVCSQPAR 17 0 B8ZZD4;Q86VP1-2;Q86VP1;Q86VP1-4;Q86VP1-3;H7C3L5 B8ZZD4 TAX1BP1 Tax1-binding protein 1 1 VPS(1)WGLEDNVVCSQPAR;VPS(1)WGLEDNVVCSQPAR;VPS(1)WGLEDNVVCSQPAR;VPS(1)WGLEDNVVCSQPAR;VPS(1)WGLEDNVVCSQPAR 278.07 8.57E-36 816536000 156448.9 122774.2 143953.4 140995.8 167137.8 100451.3 150985.6 92702.5 198758.4 TRUE FALSE 146657.0426 131864.5295 147368.0426 144613.9909 154011.4714 129449.9596 128346.711 104276.6112 165584.339 0.885693922 0.796358703 0.889987806 0.873355486 0.930108924 0.781776588 0.775113829 0.629749237 1 17.3372067 2.143045277 9.65375332 0.777234606 0.86625421 0.12655113 0.09506899 0.516945709 47.82820719 0.031968563 0.023607491 139.0097548 -2.143045277 0.089019604 VPSS(ph)DEEVVEEPQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VPSSDEEVVEEPQSR 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 VPS(0.001)S(0.999)DEEVVEEPQSR;VPS(0.023)S(0.977)DEEVVEEPQSR 330.99 7.55E-69 509420000 219018 239140 235450 230520 240900 193031 242840 174079 244020 TRUE FALSE 205310.0543 256846.1744 241034.9852 236435.5335 221980.6857 248755.9161 206428.3964 195813.1463 203291.4856 1.009929431 1.263437933 1.185661979 1.163037069 1.09193302 1.223641587 1.015430606 0.963213712 1 17.63319027 1.628683892 5.044853442 0.984430338 1.169484893 0.542572241 0.070330661 0.10183888 5.664753211 0.036838647 0.017336726 42.52887475 -1.628683892 0.185054555 VPT(ph)ANVSVVDLTCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VPTANVSVVDLTCR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 VPT(1)ANVSVVDLTCR 86.497 0.081785 76878000 13171 17721 14984 15709 22132 10751 19932 19369 23511 TRUE FALSE 12346.65062 19033.08128 15339.42756 16112.11954 20393.842 13854.63917 16943.38164 21787.26229 19586.86221 0.630353677 0.971726919 0.783148796 0.822598299 1.041200054 0.707343474 0.865038078 1.112340611 1 14.25759868 1.290074682 7.442762069 1.055469213 0.841559064 0.374841128 0.120140482 0.19972052 23.94343457 0.073986946 0.026489189 19.50179927 -1.290074682 -0.213910148 VPTANVSVVDLTCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VPTANVSVVDLTCR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 234.49 7.60E-17 3286140000 751020 728740 673630 666810 774170 614850 878250 620330 810160 FALSE TRUE 704014.9988 782696.6679 689608.8217 683921.4735 713369.8111 792347.2137 746564.5658 697779.566 674939.0622 1.043079351 1.159655311 1.021734939 1.013308478 1.056939583 1.173953707 1.106121438 1.033840839 1 19.36439773 VPVAS(ph)PSAHNISSSGGAPDR ddPTM_SK-BR-3_Pertuzumab_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(0.986)PS(0.014)AHNISSSGGAPDR;VPVAS(0.994)PS(0.006)AHNISSSGGAPDR 237.41 8.66E-30 714580000 267760 392600 428960 396430 397120 372960 466300 373880 459770 TRUE FALSE 251001.3796 421668.5125 439135.1338 406603.065 365931.7971 480627.4975 396382.6439 420559.741 383031.4168 0.655302329 1.100871871 1.146472886 1.061539725 0.955357135 1.254799153 1.034856742 1.097977144 1 18.5471032 4.739382577 24.74597416 1.090677178 0.655302174 0.72590995 0.082128074 28.59039135 860577.0478 0.017665804 0.106781686 54876.01632 -4.739382577 -0.435375005 VPVASPS(ph)AHNISSSGGAPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 186.82 2.02E-17 464590000 58408 66859 50684 54618 79994 38295 79429 56958 119280 TRUE FALSE 54752.34754 71809.30993 51886.24841 56019.59035 73711.59392 49350.14483 67519.35883 64069.33168 99371.39742 0.550986994 0.722635605 0.522144699 0.563739585 0.74177878 0.496623235 0.679464721 0.644746208 1 16.60054303 0.154673459 0.96070321 1.003224144 0.60984683 0.690002775 0.081667132 2.457911116 2.328967064 0.091223894 0.022868964 1.427819993 -0.154673459 -0.393377314 VPVDVAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 ;;;;;; 137.18 0.0017663 3300850000 1587933 2015050 1733777 1856160 1980160 1409697 1926280 1783378 1656534 FALSE TRUE 1488547.108 2164246.399 1774903.009 1903792.208 1824646.221 1816653.639 1637452.197 2006036.669 1380047.774 1.078619984 1.568240201 1.286117077 1.379511814 1.322161635 1.31637011 1.186518487 1.453599438 1 20.39628678 -3.727033861 0.25595579 6.80E-18 1.366197679 0.326080212 0.137745549 96.16058742 1.71991807 50.51971278 0.175949166 0.000187485 3.727033861 1.366197679 VPVPDERFDFLCQYHKPASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VPVPDERFDFLCQYHKPASK 20 2 J3KQ32;Q9NTK5;Q9NTK5-3;C9JTK6 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 170.91 5.17E-12 560060000 897080 1081970 948460 1072090 1403330 688110 1359990 958230 2004040 FALSE TRUE 840933.3641 1162080.185 970957.9191 1099601.644 1293118.123 886756.1865 1156072.125 1077867.125 1669552.777 0.503687799 0.696042797 0.58156767 0.658620476 0.774529647 0.531133965 0.692444193 0.645602307 1 20.67103027 -5 0.304380235 4.086118473 0.621407771 0.682132859 0.078881772 153.0683685 1.403757632 301.984885 0.068661207 1.00E-05 5 -3.464710702 VPVPGPGS(ph)GGNGPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VPVPGPGSGGNGPER 15 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 VPVPGPGS(1)GGNGPER;VPVPGPGS(1)GGNGPER;VPVPGPGS(1)GGNGPER;VPVPGPGS(1)GGNGPER;VPVPGPGS(1)GGNGPER;VPVPGPGS(1)GGNGPER 174.21 9.71E-07 3914680000 893460 940870 920300 874980 934680 815950 1002700 832160 983280 TRUE FALSE 837539.9335 1010532.994 942129.9506 897433.4681 861274.0031 1051501.519 852354.4436 936057.0078 819164.2158 1.022432276 1.23361467 1.150111214 1.095547695 1.051405795 1.283627262 1.040517185 1.14269763 1 19.64379317 -0.306103221 0.427500398 0.972295255 1.147627082 0.167440142 0.083982315 10.12021994 1.957155407 0.506864122 0.047411218 0.494193216 0.306103221 0.175331826 VQAAEHTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VQAAEHTLR 9 0 Q9GZZ9-2;Q9GZZ9;E7EWE1;E7EQ61;C9JRV9;C9J5W5 Q9GZZ9-2 UBA5 Ubiquitin-like modifier-activating enzyme 5 0 ; 138.25 0.00014188 472090000 206744 362620 214906 224100 375600 153395 184709 324990 352530 FALSE TRUE 193804.2621 389468.7621 220003.6718 229850.7854 346101.8911 197677.6463 157013.6002 365565.7169 293690.4656 0.659892931 1.32611987 0.74910049 0.782629375 1.178458042 0.673081593 0.534622736 1.244731306 1 18.1639369 2.213808376 24.99117538 0.787886094 0.958949833 0 0.274586726 603.0261101 608843.2713 0.098278019 0.072614078 163.6094467 -2.213808376 0.171063739 VQAERPDTMLGVVCGALHVADVSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VQAERPDTMLGVVCGALHVADVSLR 25 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 101.47 0.0032367 37536000 42788 54710 50159 49978 53385 44216 55222 46288 53803 FALSE TRUE 40109.97546 58760.78533 51348.79517 51260.52009 49192.35744 56980.44141 46941.97376 52067.15869 44822.93172 0.894853904 1.310953636 1.145592071 1.143622653 1.097481926 1.271234148 1.047275846 1.161618767 1 15.45194939 0.360922708 0.680974759 0.99702469 1.158277985 0.089140145 0.116089427 4.231560937 2.88685076 0.137415971 0.039446201 2.295740037 -0.360922708 0.161253295 VQAGPGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VQAGPGSPR 9 0 Q6PK04;I3L0U5;I3L4F6 Q6PK04 CCDC137 Coiled-coil domain-containing protein 137 1 VQAGPGS(1)PR;VQAGPGS(1)PR;VQAGPGS(1)PR;VQAGPGS(1)PR 142.89 0.00010829 3680720000 3144880 3177610 3403360 3186880 3506220 3632260 3751520 2871260 3325210 TRUE FALSE 2948047.575 3412883.551 3484089.306 3268660.736 3230855.625 4680834.497 3189014.403 3229743.131 2770210.969 1.064196051 1.231994093 1.257698184 1.17993206 1.166285045 1.689703257 1.151181061 1.165883453 1 21.40156442 0.995655942 2.376324775 1.005319409 1.259967115 0.186415855 0.166433263 0.468082451 5.887749203 0.148423064 0.040450908 9.900472963 -0.995655942 0.254647706 VQAGPGS(ph)PRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VQAGPGSPRR 10 1 Q6PK04;I3L0U5;I3L4F6 Q6PK04 CCDC137 Coiled-coil domain-containing protein 137 1 VQAGPGS(1)PRR 66.004 0.033802 0 29367 61978 52177 46894 71822 51921 43598 50380 65558 TRUE FALSE 27528.97189 66566.91561 53414.66308 48097.37943 66181.38984 66909.74983 37060.88464 56670.0539 54615.94628 0.504046414 1.218818315 0.9780049 0.880647187 1.211759465 1.225095497 0.6785726 1.037610034 1 15.73703462 1.739225342 25 0.877899642 1.028386696 0.025872776 0.23286366 0.258305859 9424.30161 0.0990587 0.054933135 54.85615227 -1.739225342 0.150487054 VQAMQISSEKEEDDNEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VQAMQISSEKEEDDNEKR 18 2 Q9UKY7;Q9UKY7-2;H0Y8K3 Q9UKY7 CDV3 Protein CDV3 homolog 0 ; 166.6 1.42E-11 737710000 624230 264340 384420 370810 352470 255190 472200 319410 337260 FALSE TRUE 585160.5586 283912.0086 393538.6239 380325.6124 324788.428 328859.2103 401397.9937 359289.0416 280969.1272 2.082650732 1.010474038 1.400647209 1.353620649 1.155957707 1.170446069 1.42861957 1.278749182 1 18.10005209 4.748835357 24.83733847 1.248683218 2.082651239 0.76396186 0.149328895 642.2663386 1552529.999 0.033915982 0.469897175 56083.53199 -4.748835357 0.833968021 VQAYEEPSVASS(ph)PNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VQAYEEPSVASSPNGK 16 0 Q99575 Q99575 POP1 Ribonucleases P/MRP protein subunit POP1 1 VQAYEEPSVAS(0.022)S(0.978)PNGK;VQAYEEPSVAS(0.098)S(0.902)PNGK;VQAYEEPSVAS(0.004)S(0.996)PNGK;VQAYEEPSVAS(0.001)S(0.999)PNGK;VQAYEEPSVAS(0.017)S(0.983)PNGK;VQAYEEPSVAS(0.011)S(0.989)PNGK 336.47 9.70E-72 3753320000 6411890 4622810 5553080 5253900 4938720 4403270 6684600 4518480 6347870 TRUE FALSE 6010581.25 4965087.662 5684801.68 5388723.969 4550852.853 5674422.568 5682306.287 5082622.174 5288369.488 1.136566056 0.938869282 1.074963028 1.01897645 0.860539882 1.073000398 1.074491164 0.961094376 1 22.33439155 1.196393692 24.99918144 0.980547191 1.021077336 0.051555499 0.078231884 611.6870831 362632.6767 0.070280067 0.017570861 15.71787 -1.196393692 0.040530144 VQCCLYFIAPSGHGLKPLDIEFMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VQCCLYFIAPSGHGLKPLDIEFMK 24 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1 E7EPK1 7-Sep Septin-7 0 89.663 0.0060648 75718000 161290 203080 114100 89325 244930 113200 191130 207200 117750 FALSE TRUE 151195.1468 218116.2545 116806.5059 91617.23073 225694.1858 145879.0024 162471.8309 233069.3761 98096.76431 1.541285769 2.223480622 1.190727408 0.93394753 2.300730176 1.487092907 1.656240468 2.375912985 1 16.58191793 2.724323137 24.91923312 1.76839825 1.550608164 0.066790412 0.505220338 2937.487216 5141347.394 0.157587802 0.149214352 530.0576872 -2.724323137 -0.217790086 VQDAVQQHQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VQDAVQQHQQK 11 0 Q9NVI7-3;Q9NVI7-2;Q9NVI7;Q5SV16 Q9NVI7-3 ATAD3A ATPase family AAA domain-containing protein 3A 0 119.05 0.00096643 0 128680 133790 113900 105770 185000 90592 108650 159310 212730 FALSE TRUE 120626.1485 143695.9508 116601.7618 108484.2373 170470.8463 116744.4398 92358.94116 179200.2042 177223.9887 0.680642329 0.810815465 0.657934418 0.612130661 0.961894874 0.658739489 0.521142436 1.011150948 1 17.43521437 1.215684635 24.9676027 1.005576081 0.701874917 0.537671705 0.117615738 211.3358433 230652.7957 0.112254262 0.028140822 16.43178087 -1.215684635 -0.303701164 VQDT(ph)SNTGLGEDIIHQLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VQDTSNTGLGEDIIHQLSK 19 0 Q8IWA0 Q8IWA0 WDR75 WD repeat-containing protein 75 1 VQDT(0.459)S(0.459)NT(0.082)GLGEDIIHQLSK;VQDT(0.619)S(0.376)NT(0.006)GLGEDIIHQLSK 195.71 3.20E-15 80916000 87078 92882 95076 96732 95959 72833 128338 91409 96429 TRUE FALSE 81627.94342 99759.07992 97331.24762 99214.30689 88422.76722 93858.70476 109094.9083 102821.6149 80334.37694 1.016102278 1.241798141 1.211576554 1.235016822 1.100684048 1.168350441 1.358010263 1.279920487 1 16.29372986 VQDTS(ph)NTGLGEDIIHQLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VQDTSNTGLGEDIIHQLSK 19 0 Q8IWA0 Q8IWA0 WDR75 WD repeat-containing protein 75 1 VQDT(0.265)S(0.732)NT(0.003)GLGEDIIHQLSK;VQDT(0.299)S(0.697)NT(0.003)GLGEDIIHQLSK;VQDT(0.068)S(0.913)NT(0.019)GLGEDIIHQLSK;VQDT(0.262)S(0.735)NT(0.003)GLGEDIIHQLSK;VQDT(0.203)S(0.793)NT(0.003)GLGEDIIHQLSK;VQDT(0.086)S(0.902)NT(0.012)GLGEDIIHQLSK 310.16 1.08E-61 2854700000 2605540 2490910 2558270 2592620 2528170 2008970 3680660 2604670 2683960 TRUE FALSE 2442463.902 2675339.568 2618953.373 2659151.018 2329617.726 2588927.026 3128779.203 2929868.783 2235989.737 1.092341285 1.196490093 1.171272537 1.1892501 1.041873175 1.157843877 1.399281558 1.310323001 1 21.09248214 1.924599813 14.90062599 1.280353293 1.148583447 0.096877091 0.111879883 3.882497578 765.3449852 0.041766028 0.026868697 84.06201825 -1.924599813 -0.131769846 VQEAEENFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VQEAEENFR 9 0 F6WE04;Q5SRH9-5;Q5SRH9-6;Q5SRH9-4;Q5SRH9;Q5SRH9-2 F6WE04 TTC39A Tetratricopeptide repeat protein 39A 0 102.06 0.009568 0 109040 110130 99930 107620 112350 91106 118890 83933 123610 FALSE TRUE 102215.381 118284.1398 102300.3868 110381.7114 103526.4842 117406.8232 101063.5482 94412.21981 102978.6924 0.992587676 1.148627323 0.993413146 1.071888842 1.005319467 1.140107924 0.981402519 0.916813154 1 16.65198633 1.563004178 6.941620969 0.955903398 1.060248022 0.368351625 0.057633277 0.116908572 10.93571382 0.028376168 0.013215836 36.55983088 -1.563004178 0.104344624 VQEFEHVNGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VQEFEHVNGR 10 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ; 136.5 0.00011603 946200000 838880 1018210 1047280 1035260 944420 927460 1070450 913200 806050 FALSE TRUE 786375.9982 1093599.328 1072121.976 1061826.524 870249.0628 1195202.646 909945.9601 1027215.03 671515.0477 1.171047471 1.628555207 1.596571782 1.581240105 1.295948714 1.779859811 1.355064139 1.529697709 1 19.3570602 -0.307634433 0.768242152 0.974049533 1.520817613 0.420459262 0.178969686 9.25681428 4.39091057 0.887892985 0.054494717 0.492453884 0.307634433 0.54676808 VQEHEDS(ph)GDS(ph)EVENEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VQEHEDSGDSEVENEAK 17 0 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 2 VQEHEDS(1)GDS(1)EVENEAK;VQEHEDS(1)GDS(1)EVENEAK 220.28 5.93E-15 1129420000 3478900 2020400 2615800 2325700 2683000 1918960 3125600 2080910 3304100 TRUE FALSE 3261161.859 2169992.518 2677848.011 2385381.399 2472288.003 2472932.6 2656945.297 2340716.194 2752624.365 1.184746419 0.788335868 0.972834523 0.866584424 0.898156695 0.898390871 0.965240783 0.850358016 1 21.39237632 -0.222870971 8.287800025 1.000035582 0.918965399 0.037460844 0.105963292 0 0 0.088402941 0.020836773 0.59858941 0.222870971 -0.081070184 VQEKPDS(ph)PGGSTQIQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VQEKPDSPGGSTQIQR 16 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 VQEKPDS(1)PGGSTQIQR;VQEKPDS(0.999)PGGS(0.001)TQIQR;VQEKPDS(0.992)PGGS(0.007)T(0.001)QIQR 219.97 3.14E-14 595010000 969650 694837 803861 787221 955340 577686 1035640 799084 1122460 TRUE FALSE 908961.3374 746283.4545 822928.9625 807422.4236 880311.4501 744454.5703 880355.3964 898851.3964 935114.1746 0.972032466 0.798066669 0.880030466 0.863447957 0.941394617 0.796110882 0.941441612 0.961221015 1 19.834783 1.545116852 5.736072267 0.971748502 0.868648411 0.39231171 0.055100522 0.129050213 8.842783769 0.02834466 0.012866807 35.08462607 -1.545116852 -0.103100091 VQENSPGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VQENSPGHR 9 0 Q9H8Y8;F8WEG2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 0 ;; 179.1 0.00042176 324230000 729260 541724 599476 593980 608360 498143 691630 563404 650090 FALSE TRUE 683616.9184 581833.8086 613695.8538 609222.5324 560581.8596 641948.7974 587926.5023 633746.2296 541585.7793 1.262250496 1.074315152 1.133146174 1.124886501 1.035074925 1.185313245 1.085564881 1.170167781 1 19.04683033 VQESTKGPDEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VQESTKGPDEAK 12 1 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;; 184.21 1.33E-05 1787110000 2157830 1164670 1610280 1484550 1700870 1180130 2017150 1255060 2579470 FALSE TRUE 2022775.272 1250903.379 1648476.602 1522646.066 1567290.531 1520814.373 1714697.084 1411757.004 2148939.793 0.941289876 0.582102571 0.767111581 0.708556876 0.729331988 0.707704505 0.797927001 0.656955122 1 21.03519363 -1.827583378 2.383989502 1.105471958 0.728190111 0.436649318 0.093696943 9174381.376 5457197.119 5540910.033 0.020319726 0.014873618 1.827583378 -0.377281847 VQFHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VQFHLK 6 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 74.743 0.079523 207010000 629220 980500 618020 638340 1100900 436380 749340 897130 901900 FALSE TRUE 589838.2434 1053097.24 632679.7263 654720.8851 1014439.755 562355.822 636983.4235 1009138.655 751367.0635 0.785020095 1.401574931 0.842038142 0.871372884 1.350125397 0.748443536 0.847765965 1.343070124 1 19.51915835 3.899002567 13.13458602 0.979790411 1.135360387 0.012087971 0.250514823 2.742410014 455.8691696 0.059518234 0.107321354 7925.060143 -3.899002567 0.155569975 VQGGVPAGS(ph)DEYEDECPHLIALSSLNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VQGGVPAGSDEYEDECPHLIALSSLNR 27 0 Q9BVS4-2;Q9BVS4;H0Y919;H0Y8R4 Q9BVS4-2 RIOK2 Serine/threonine-protein kinase RIO2 1 VQGGVPAGS(0.999)DEY(0.001)EDECPHLIALSSLNR;VQGGVPAGS(1)DEYEDECPHLIALSSLNR;VQGGVPAGS(1)DEYEDECPHLIALSSLNR;VQGGVPAGS(1)DEYEDECPHLIALSSLNR 262.47 2.50E-53 2122550000 486387 497394 483359 459725 474199 398627 589748 416493.4 386100 TRUE FALSE 455944.9059 534221.5693 494824.5037 471522.3218 436957.3234 513704.1437 501320.7624 468493.5178 321657.4157 1.417486069 1.660840208 1.538358762 1.465914662 1.358455618 1.597053631 1.558554965 1.45649842 1 18.29516542 0.802502517 4.014016161 1.000015179 1.528932366 0.769975328 0.087257442 0.875117896 17.3073356 0.084286624 0.021532105 6.346035792 -0.802502517 0.528917187 VQGLLENGDSVTS(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VQGLLENGDSVTSPEK 16 0 P41229-4;P41229-3;P41229-2;P41229-5;P41229 P41229-4 KDM5C Lysine-specific demethylase 5C 1 VQGLLENGDSVT(0.002)S(0.998)PEK;VQGLLENGDSVTS(1)PEK;VQGLLENGDSVT(0.011)S(0.989)PEK;VQGLLENGDS(0.007)VT(0.149)S(0.844)PEK 309.33 1.36E-57 504002000 1420520 872030 1092173 1036339 946422 803395 1487190 932416 685109 TRUE FALSE 1331612.189 936596.0085 1118079.859 1062933.213 872093.8338 1035322.094 1264199.666 1048830.19 570759.8819 2.333051483 1.640963281 1.958932109 1.862312414 1.527952229 1.813936346 2.214941354 1.837603208 1 19.12252441 -1.195271056 3.210953018 0.99768608 1.889369061 0.584853391 0.237842114 13674966.04 19747737.08 319172.1518 0.058552755 0.063786525 1.195271056 0.89168298 VQHQDALQISDVVMASLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VQHQDALQISDVVMASLLR 19 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;; 216.49 3.82E-19 435054000 412319 502209 499428 511532 536358 433158 544691 498066 406740 FALSE TRUE 386512.6898 539393.0769 511274.668 524658.7771 494234.6062 558203.6829 463019.6412 560250.6365 338852.4664 1.140651842 1.591822786 1.508841513 1.548339851 1.458553959 1.647335458 1.366434325 1.653376298 1 18.37029775 -1.343344766 3.571431265 0.997750699 1.498390106 0.509306698 0.150744532 5148416.61 5811352.88 75522.95083 0.030605877 0.04535814 1.343344766 0.500639406 VQHQTS(ph)STSPLSSPNQTSSEPRPLPAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VQHQTSSTSPLSSPNQTSSEPRPLPAPR 28 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 VQHQT(0.028)S(0.799)S(0.17)T(0.003)SPLSSPNQTSSEPRPLPAPR;VQHQT(0.122)S(0.754)S(0.122)TSPLSSPNQTSSEPRPLPAPR;VQHQT(0.174)S(0.694)S(0.102)T(0.025)S(0.005)PLSSPNQTSSEPRPLPAPR 128.33 1.82E-05 773190000 72107 84119 78186 78215 73493 49476 111494 81432 127839 TRUE FALSE 67593.95158 90347.25829 80040.60884 80222.12932 67721.15624 63758.91802 94776.50976 91598.96445 106501.845 0.634673996 0.848316367 0.751541993 0.753246381 0.635868385 0.598664915 0.889904863 0.860069273 1 16.7005189 1.60449956 7.284275749 0.911471809 0.725322969 0.597573609 0.081240742 0.099506482 11.73005516 0.04475189 0.021642969 40.22532485 -1.60449956 -0.18614884 VQIPVSRPDPEPVS(ph)DNEEDS(ph)YDEEIHDPR ddPTM_SK-BR-3_Pertuzumab_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(0.578)Y(0.423)DEEIHDPR;VQIPVS(0.001)RPDPEPVS(0.999)DNEEDS(0.63)Y(0.37)DEEIHDPR;VQIPVSRPDPEPVS(0.999)DNEEDS(0.889)Y(0.111)DEEIHDPR 146.48 7.47E-08 2309560000 854650 900330 922270 857750 975810 821810 973650 814550 980020 TRUE FALSE 801158.9821 966991.37 944146.6799 879761.3172 899173.8188 1059053.206 827660.2214 916248.3605 816448.3308 0.981273342 1.184387711 1.156407141 1.077546838 1.101323605 1.297146636 1.013732517 1.122236798 1 19.63900206 0.962901889 1.268808394 1.00549929 1.133338265 0.131936058 0.08870437 0.862841487 2.831676007 0.076326496 0.023422712 9.181251606 -0.962901889 0.127838975 VQIPVSRPDPEPVS(ph)DNEEDSY(ph)DEEIHDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VQIPVSRPDPEPVSDNEEDSYDEEIHDPR 29 1 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 2 VQIPVSRPDPEPVS(1)DNEEDS(0.215)Y(0.785)DEEIHDPR;VQIPVS(0.002)RPDPEPVS(0.998)DNEEDS(0.337)Y(0.664)DEEIHDPR;VQIPVSRPDPEPVS(1)DNEEDS(0.236)Y(0.764)DEEIHDPR 176.51 2.27E-13 1399990000 586618 618427 618770 659954 711129 569487 744151 582936 731473 TRUE FALSE 549902.6265 664215.9786 633447.5166 676889.5369 655279.7969 733888.6521 632572.4659 655716.8428 609385.4308 0.902388864 1.089976795 1.039485824 1.110774073 1.075312542 1.204309481 1.038049868 1.076029734 1 19.21699548 4.740153027 24.24899001 1.081997107 0.902388771 0.512438089 0.054154609 70.55649532 1074270.42 0.011776199 0.074809145 54973.45427 -4.740153027 -0.179608336 VQIPVSRPDPEPVSDNEEDS(ph)Y(ph)DEEIHDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VQIPVSRPDPEPVSDNEEDSYDEEIHDPR 29 1 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 2 VQIPVSRPDPEPVS(0.581)DNEEDS(0.698)Y(0.721)DEEIHDPR 86.131 0.0045405 1090000000 432700 483880 414420 433670 466980 415990 475650 357490 442890 TRUE FALSE 405618.0794 519706.9787 424250.2381 444798.7064 430305.2745 536079.56 404330.6982 402123.4134 368968.7978 1.099328945 1.408539101 1.14982687 1.205518486 1.166237571 1.452912992 1.095839812 1.089857505 1 18.49313929 1.567262877 8.73251038 1.062262441 1.25153733 0.381273049 0.111956235 0.116315732 16.21976055 0.055713424 0.026086245 36.92010067 -1.567262877 0.189274889 VQIS(ph)PDSGGLPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VQISPDSGGLPER 13 0 A0A087WTP3;Q92945;M0QYH3;M0QXW7 A0A087WTP3 KHSRP Far upstream element-binding protein 2 1 VQIS(0.977)PDS(0.023)GGLPER;VQIS(0.755)PDS(0.245)GGLPER;VQIS(0.999)PDS(0.001)GGLPER;VQIS(0.96)PDS(0.04)GGLPER 245.23 4.53E-17 2478290000 2098230 2221670 2109690 2144840 2341660 1893630 2406120 1997630 2688070 TRUE FALSE 1966905.53 2386164.758 2159732.843 2199880.226 2157755.469 2440290.24 2045344.643 2247038.503 2239413.751 0.878312696 1.065530993 0.964418854 0.982346484 0.963535866 1.08970048 0.913339325 1.003404798 1 21.09468967 3.726964752 24.85093933 0.985154572 0.994198677 0 0.063301587 81.06982634 12878484.05 0.015183908 0.025123705 5332.916107 -3.726964752 0.009044105 VQLAEPDLEQAAHLIQALSNHEDVIHVYDNIE ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VQLAEPDLEQAAHLIQALSNHEDVIHVYDNIE 32 0 Q9BSH4 Q9BSH4 TACO1 Translational activator of cytochrome c oxidase 1 0 ;; 184.44 7.38E-20 228932000 109930 135885 140728 151643 198860 164737 146891 135471 180912 FALSE TRUE 103049.6775 145946.0668 144066.1346 155534.4161 183242.3378 212293.8976 124866.0582 152384.8526 150716.6185 0.683731353 0.96834754 0.95587425 1.031965935 1.21580712 1.408563301 0.82848235 1.01106868 1 17.20147898 5.368839744 0.791901313 1.073615121 1.64E-11 0.369006673 0.155713497 7.310647876 1.721739448 0.054614644 8.727150783 233797.4362 -5.368839744 -1.073615121 VQLTTCIHHIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VQLTTCIHHIIK 12 0 O95373;E9PLB2 O95373 IPO7 Importin-7 0 173.19 1.95E-05 245980000 323770 294940 326700 313280 309380 247370 378850 313900 246740 FALSE TRUE 303505.8136 316777.6645 334449.4783 321319.2952 285082.5428 318781.7033 322044.9596 353091.106 205557.5 1.476500802 1.541065952 1.627036125 1.563160163 1.386874927 1.550815238 1.566690389 1.717724267 1 17.64918249 -1.106495161 7.248980463 0.999999815 1.555191493 0.803817828 0.085968762 2.46E-07 3.05E-08 0.0796698 0.018778346 0.078253692 1.106495161 0.555191678 VQMTS(ph)PSSTGSPMFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VQMTSPSSTGSPMFK 15 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 VQMTS(0.518)PS(0.361)S(0.095)T(0.026)GSPMFK;VQMTS(0.997)PS(0.002)S(0.001)TGSPMFK;VQMTS(0.903)PS(0.076)S(0.017)T(0.004)GSPMFK;VQMT(0.141)S(0.795)PS(0.046)S(0.006)T(0.006)GS(0.006)PMFK 246.03 4.02E-18 264291000 1503930 1425850 1529530 2151130 2153940 1065186 1349540 1036493 1380440 TRUE FALSE 1409801.706 1531421.418 1565811.174 2206331.638 1984778.241 1372687.906 1147189.006 1165901.433 1150035.646 1.225876529 1.331629522 1.361532731 1.918489784 1.725840628 1.19360466 0.997524737 1.013795909 1 20.13324715 2.034808745 5.943762264 1.024100867 1.485775969 0.583195869 0.198213845 0.148400582 14.60240006 0.084242 0.060395351 108.3449678 -2.034808745 0.461675103 VQNS(ph)PPVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 VQNSPPVGR 9 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;H0Y8P9;H0YA73 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 VQNS(1)PPVGR;VQNS(1)PPVGR;VQNS(1)PPVGR;VQNS(1)PPVGR;VQNS(1)PPVGR;VQNS(1)PPVGR;VQNS(1)PPVGR;VQNS(1)PPVGR 215.71 6.60E-07 28877310000 13688640 14762120 14434220 14464880 16601370 12112210 15921820 13421870 12833250 TRUE FALSE 12831892.46 15855122.72 14776606.51 14836073.31 15297565.37 15608808.4 13534490.9 15097620.01 10691297.67 1.200218426 1.482993292 1.38211534 1.387677508 1.430842713 1.459954524 1.265935279 1.412141022 1 23.34993364 -0.497809307 0.612416985 0.952815882 1.394916347 0.644552692 0.087261557 6.396697131 1.889507093 0.744157455 0.031480769 0.31782693 0.497809307 0.442100465 VQNS(ph)PPVGRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VQNSPPVGRK 10 1 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;H0Y8P9;H0YA73 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 VQNS(1)PPVGRK 66.989 0.039397 390630000 250330 385560 323420 330840 554010 220130 440620 310480 1022000 TRUE FALSE 234662.2922 414107.2636 331091.6751 339329.9145 510500.2894 283677.9575 374553.1215 349244.1115 851421.5976 0.275612332 0.486371575 0.388869247 0.39854511 0.599585788 0.333181538 0.439914988 0.410189397 1 19.69951416 -1.928155684 2.429630634 1.386169117 0.422783968 0.818173776 0.086397132 15061874.56 7528829.181 33020756.19 0.018588138 0.011798976 1.928155684 -0.963385149 VQPGCY(ph)LPSNPEAIVLDIDY(ph)KSGT(ph)PMQS(ph)AAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VQPGCYLPSNPEAIVLDIDYKSGTPMQSAAK 31 1 P42356;P42356-2;A8MTF1 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 4 VQPGCY(0.715)LPS(0.285)NPEAIVLDIDY(0.552)KS(0.464)GT(0.993)PMQS(0.991)AAK 57.832 0.019813 318470000 17794 72345 47303 54423 54971 64283 53708 50817 42104 TRUE FALSE 16680.3053 77701.49907 48425.0495 55819.58632 50653.7994 82840.45855 45654.984 57161.61431 35076.5704 0.475539801 2.215196588 1.380552573 1.591363856 1.444092134 2.361703485 1.301580613 1.629623811 1 15.09822008 0.353017915 1.476461432 1.000196183 1.612759546 0.089684882 0.516192327 10.09412814 20.81511437 0.436181528 0.125969299 2.254332204 -0.353017915 0.612563363 VQPQWS(ph)PPAGTQPCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.999)PPAGT(0.001)QPCR 214.54 2.58E-12 416830000 403307 428202 430077 413620 399042 353556 479432 370654 354369 TRUE FALSE 378064.7348 459906.5216 440278.6295 424234.1895 367702.851 455621.8777 407545.6224 416930.9678 295222.5246 1.280609382 1.557830055 1.491344978 1.436998041 1.245510828 1.543316786 1.380469268 1.412260018 1 18.17144327 -3.052442447 0.322878092 7.83E-10 1.458939636 0.616642068 0.102526158 49.99786303 1.406434657 33.99535268 0.086126987 0.000886253 3.052442447 1.458939635 VQQLLHICSEHFDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VQQLLHICSEHFDSK 15 0 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 210.9 9.53E-10 1358860000 1938560 1931470 2069300 2138010 2115500 1645510 2696400 1951200 2460500 FALSE TRUE 1817228.99 2074478.048 2118384.773 2192874.956 1949357.164 2120542.024 2292099.852 2194811.615 2049826.655 0.88652813 1.012026087 1.033445813 1.06978556 0.950986348 1.034498219 1.118192042 1.070730352 1 20.96707048 5.744000052 1.006246879 1.046867417 8.30E-14 0.525208207 0.04484686 9.931782705 1.732827877 0.013803238 18.03530805 554625.7795 -5.744000052 -1.046867417 VQRPHS(ph)SPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.799)S(0.201)PPR;VQRPHS(0.593)S(0.407)PPR;VQRPHS(0.613)S(0.387)PPR 96.866 0.0039055 622410000 72095.4 171939 138742 142255 166667 130283 172392 162437 153487 TRUE FALSE 67583.07761 184669.5425 142033.0258 145905.5041 153577.6461 167893.5871 146543.42 182717.617 127869.0281 0.528533599 1.44420854 1.110769573 1.141054298 1.2010543 1.313012147 1.14604312 1.428943503 1 16.96430734 4.749763926 24.77174305 1.228021083 0.528533136 0.710010699 0.139476289 757.8584225 1675671.897 0.029999512 0.462360121 56203.57304 -4.749763926 -0.699487947 VQRPHSS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VQRPHSSPPR 10 1 R4GNF5;E9PP52;E9PMB0;E9PJ55;Q9NUJ3 R4GNF5 TCP11L1 T-complex protein 11-like protein 1 1 VQRPHS(0.008)S(0.992)PPR;VQRPHS(0.043)S(0.957)PPR;VQRPHS(0.194)S(0.806)PPR;VQRPHS(0.072)S(0.928)PPR;VQRPHS(0.088)S(0.912)PPR;VQRPHS(0.08)S(0.92)PPR 115.34 0.00074829 5578310000 2581642 2447008 2449581 2436524 2642977 2189370 2975348 2349839 2593178 TRUE FALSE 2420061.636 2628187.018 2507686.218 2499049.331 2435408.248 2821405.578 2529222.189 2643221.572 2160359.839 1.120212287 1.216550581 1.160772466 1.156774573 1.127316016 1.305988718 1.170741162 1.223509863 1 21.0428402 -1.131161939 5.107271881 0.999993154 1.187430353 0.536962885 0.054023406 3.82E-06 6.50E-07 0.047428534 0.011178604 0.073932954 1.131161939 0.187437199 VQS(ph)LPSVPLSCAAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VQSLPSVPLSCAAYR 15 0 Q96AD5-2;Q96AD5 Q96AD5-2 PNPLA2 Patatin-like phospholipase domain-containing protein 2 1 VQS(1)LPSVPLSCAAYR 217.58 2.15E-12 125500000 106770 119430 110120 100710 117180 76882 113090 106170 129330 TRUE FALSE 100087.4563 128272.7215 112732.0984 103294.3891 107977.1555 99076.58533 96133.20438 119425.5582 107743.9875 0.92893774 1.190532525 1.046295956 0.958702119 1.002164093 0.919555584 0.892237299 1.108419699 1 16.71724784 3.380319899 3.595733452 0.966036848 1.089919075 0.110220631 0.085995144 0.276187286 6.887591727 0.023108014 0.032590549 2400.600535 -3.380319899 0.123882227 VQS(ph)PSQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VQSPSQTR 8 0 Q12830-4;Q12830;F5GXF5;E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-2;J3KSK9 Q12830-4 BPTF Nucleosome-remodeling factor subunit BPTF 1 VQS(0.91)PS(0.09)QTR 108.31 0.0040225 694130000 765040 663360 613450 632100 648950 552700 807660 633410 623750 TRUE FALSE 717157.512 712475.8646 628001.3237 648320.7561 597984.0847 712255.5177 686558.8809 712492.6328 519642.0954 1.380098953 1.371089584 1.208526656 1.247629401 1.150761438 1.370665548 1.321214903 1.371121853 1 18.98715878 -2.258870554 2.026111255 3.15E-05 1.298877801 0.594684559 0.078465336 1714896.94 242549.7671 7857097.941 0.019617101 0.005509719 2.258870554 1.298846313 VQSCPDPAVYGVVQSGDHIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VQSCPDPAVYGVVQSGDHIGR 21 0 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 0 151.2 6.41E-08 270090000 191510 169780 176020 201680 205470 166710 200210 159800 224950 FALSE TRUE 179523.731 182350.6879 180195.2775 206855.4502 189333.215 214836.4707 170190.3692 179751.3818 187404.3918 0.957948366 0.973033162 0.961531775 1.103791903 1.010292306 1.146379061 0.908145042 0.959163123 1 17.51579524 VQSGMGLILQGYES(ph)GS(ph)EEEGEIHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VQSGMGLILQGYESGSEEEGEIHEK 25 0 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 VQSGMGLILQGY(0.022)ES(0.981)GS(0.997)EEEGEIHEK 91.603 0.0067557 49784000 111800 78015 96152 89633 101520 80292 110880 85373 116400 TRUE FALSE 104802.6376 83791.31177 98432.77085 91933.13453 93547.02871 103470.997 94254.57336 96032.00698 96972.08803 1.080750551 0.864076596 1.01506292 0.948037073 0.964679947 1.067018346 0.971976321 0.990305653 1 16.56528193 2.412925773 24.99985125 1.005190685 0.963693969 0.053413907 0.059333458 138.1133582 53784.23137 0.01895218 0.015856532 258.7770589 -2.412925773 -0.041496716 VQSGSESVIQEYVDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VQSGSESVIQEYVDLR 16 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 190.87 1.83E-09 85209000 53052 71008 63429 70871 87234 63842 77902 63618 57129 FALSE TRUE 49731.57002 76265.5062 64933.56583 72689.66984 80382.99353 82272.14901 66221.31831 71560.84734 47593.80083 1.044916967 1.602425208 1.364328225 1.527292811 1.68893831 1.72863162 1.391385373 1.503574963 1 15.53848605 0.046781559 1.611246365 0.999761727 1.494250544 0.378968223 0.192996659 25.62539091 41.43939936 0.185949071 0.048683671 1.113734207 -0.046781559 0.494488816 VQSLPS(ph)VPLSCAAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VQSLPSVPLSCAAYR 15 0 Q96AD5-2;Q96AD5 Q96AD5-2 PNPLA2 Patatin-like phospholipase domain-containing protein 2 1 VQS(0.097)LPS(0.903)VPLSCAAYR 133.47 4.31E-05 112050000 87826 91349 98096 90001 98075 71575 121370 94091 106650 TRUE FALSE 82329.12743 98112.57501 100422.8834 92310.57803 90372.58512 92237.54058 103171.6952 105838.4685 88849.42601 0.926614061 1.104256712 1.130259226 1.038955255 1.017143151 1.038133218 1.161197093 1.191211617 1 16.43907484 1.745020116 16.03583691 1.13190499 1.058682142 0.155845189 0.073751751 0.231241189 538.5591469 0.033231984 0.018362119 55.59300072 -1.745020116 -0.073222848 VQSPDGVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VQSPDGVKR 9 1 Q8TAT6;Q8TAT6-2;A0A0D9SFI9;I3L4U9 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 72.848 0.073102 98534000 163060 223980 195010 199090 252100 167390 251040 226250 275240 FALSE TRUE 152854.3657 240563.7123 199635.7293 204198.9865 232301.0829 215712.7757 213398.8825 254497.8105 229300.6659 0.666611085 1.049119118 0.87062865 0.890529409 1.013085078 0.940742038 0.93065095 1.109886923 1 17.80688102 4.748922474 24.80538564 0.9636884 0.6666109 0.635305065 0.073076332 870.7749347 2084513.873 0.016358821 0.229873861 56094.78319 -4.748922474 -0.2970775 VQT(ph)TPSKPGGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VQTTPSKPGGDR 12 1 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 VQT(0.493)T(0.493)PS(0.013)KPGGDR;VQT(0.497)T(0.497)PS(0.006)KPGGDR 89.541 0.01514 805040000 1255970 1011860 1096080 1035470 1096500 904530 1383180 950740 1188100 TRUE FALSE 1177361.08 1086779.167 1122079.535 1062041.913 1010385.313 1165653.127 1175785 1069441.982 989798.4346 1.189495799 1.097980285 1.133644484 1.072988071 1.020799061 1.177667176 1.187903475 1.08046441 1 19.91677523 4.744160714 23.69350447 1.110037691 1.189495864 0.155922131 0.06115424 614.9224072 2601508.455 0.014377798 0.121499348 55483.09948 -4.744160714 0.079458174 VQTEKEEKEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VQTEKEEKEEAR 12 2 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;; 121.18 0.00021418 468659000 1217530 863400 994090 1010840 1231880 651880 1230480 872370 1890880 FALSE TRUE 1141326.971 927327.0344 1017670.284 1036779.866 1135133.114 840067.1736 1045980.947 981287.3148 1575279.912 0.724523281 0.588674449 0.64602505 0.658155962 0.720591372 0.533281207 0.66399688 0.622928857 1 20.58717677 -1.77748498 2.750384245 1.088113207 0.639369194 0.794526987 0.056712658 13101519.7 11155870.51 7813771.139 0.012910337 0.016692255 1.77748498 -0.448744012 VQTT(ph)PPPAVQGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VQTTPPPAVQGQK 13 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 VQT(0.014)T(0.986)PPPAVQGQK;VQT(0.027)T(0.973)PPPAVQGQK;VQT(0.028)T(0.972)PPPAVQGQK;VQT(0.036)T(0.964)PPPAVQGQK 176.98 0.00017699 2689650000 2630910 2248760 2466730 2337630 2517640 2000900 2985250 2260100 3551010 TRUE FALSE 2466246.039 2415260.53 2525242 2397617.543 2319914.71 2578527.348 2537639.476 2542278.46 2958323.491 0.833663407 0.816428811 0.85360577 0.810464965 0.784199131 0.871617778 0.85779648 0.859364592 1 21.49634839 0.226122328 0.593231922 1.007953319 0.824969752 0.84201113 0.023048485 1.075810309 0.524278691 0.042493414 0.009571027 1.683148086 -0.226122328 -0.182983567 VQTT(ph)PSKPGGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VQTTPSKPGGDR 12 1 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 VQT(0.096)T(0.901)PS(0.003)KPGGDR;VQT(0.105)T(0.709)PS(0.186)KPGGDR;VQT(0.112)T(0.851)PS(0.037)KPGGDR;VQT(0.12)T(0.88)PSKPGGDR 154.19 0.00011524 8801300000 9655200 7113000 8234800 7580300 7784500 6073300 10176100 6878800 8991000 TRUE FALSE 9050898.267 7639653.921 8430133.345 7774823.331 7173136.771 7826563.118 8650288.275 7737633.322 7490344.016 1.208342133 1.019933651 1.125466778 1.037979473 0.957651178 1.044887004 1.15485861 1.033014412 1 22.83660055 4.747893952 24.47274735 1.058463195 1.20834224 0.423556045 0.057829855 1014.263827 2659404.46 0.014040104 0.172277778 55962.09341 -4.747893952 0.149879045 VQVAALQAS(ph)PPLDQDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VQVAALQASPPLDQDDR 17 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IU26;B1AN86;U3KQJ2 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 VQVAALQAS(1)PPLDQDDR;VQVAALQAS(1)PPLDQDDR;VQVAALQAS(1)PPLDQDDR;VQVAALQAS(1)PPLDQDDR 245.82 1.38E-20 424132000 607730 606250 642980 630730 634810 531492 670980 539643 632040 TRUE FALSE 569693.2641 651137.3808 658231.7892 646915.5996 584954.5833 684925.1123 570372.7781 607018.6165 526548.4409 1.081938944 1.236614393 1.250087814 1.228596553 1.110922639 1.300782719 1.08322945 1.152825779 1 19.00620674 0.95125616 0.842386561 1.002450041 1.209512473 0.398453645 0.072460483 0.604501638 0.931282369 0.06284666 0.022375547 8.938325368 -0.95125616 0.207062432 VQVEYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 135.35 0.031729 1361140000 2656330 2505810 2044420 1766250 2667700 1419780 2857370 2673280 2762380 FALSE TRUE 2490075.047 2691342.78 2092914.608 1811574.965 2458189.603 1829647.438 2428933.895 3007044.893 2301320.932 1.082019901 1.169477382 0.909440565 0.787189192 1.068164622 0.795042279 1.05545205 1.306660384 1 21.13403076 -0.250531385 6.836731135 0.999998743 1.012323342 0 0.159739003 0 0 0.148389363 0.034975708 0.561653688 0.250531385 0.012324599 GFSNLKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 GFSNLKK 7 1 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 70.919 0.089348 594420000 637930 1016800 913590 1129900 1430500 925220 1503400 1177800 1822700 FALSE TRUE 598003.1 1092084.93 935260.7862 1158895.147 1318154.3 1192315.994 1277979.127 1324850.923 1518479.595 0.393817014 0.719196316 0.615919232 0.763194416 0.868075083 0.78520383 0.841617583 0.872485167 1 20.53419609 5.231436032 0.213283738 0.995157341 4.22E-12 0.79271502 0.075227349 7.190635854 0.2474052 0.130791973 1.966707666 170386.8336 -5.231436032 -0.995157341 down VQVNHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VQVNHEK 7 0 P19367-4;P19367-2;P19367;P19367-3;B1AR62 P19367-4 HK1 Hexokinase-1 0 ; 106.36 0.0077204 1703390000 2207000 2004810 1994440 1836720 2139500 1350090 2155200 1941240 2718900 FALSE TRUE 2068867.81 2153248.218 2041749.059 1883853.345 1971472.3 1739839.066 1832047.768 2183608.087 2265098.025 0.913367892 0.950620324 0.901395452 0.831687337 0.870369529 0.768107626 0.808816108 0.964023659 1 21.11114206 3.451336463 3.5505601 0.853438056 0.931001872 0.055443818 0.07035567 0.35714018 9.455490403 0.018581252 0.027400041 2827.069359 -3.451336463 0.077563817 VRAS(ph)LDSAGGSGSSPILLPTPVVGGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VRASLDSAGGSGSSPILLPTPVVGGPR 27 1 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 1 VRAS(0.604)LDS(0.125)AGGS(0.191)GS(0.06)S(0.02)PILLPTPVVGGPR 76.909 0.0091324 98257000 56631 74601 68389 64214 82247 60119 73648 76611 70634 TRUE FALSE 53086.5668 80124.53566 70011.21938 65861.83995 75787.65239 77474.37935 62605.16611 86176.05199 58844.72909 0.902146507 1.361626384 1.189761946 1.119247908 1.287925929 1.316589957 1.063904399 1.464465099 1 15.84462557 -0.975986174 4.152549131 0.999988261 1.217027476 0.149077217 0.159852173 7570900.413 3647026.969 774.4908675 0.03275741 0.105685115 0.975986174 0.217039215 VRDVFEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VRDVFEAK 8 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 110.88 0.0030464 862300000 484380 584210 410670 414450 653440 327690 506570 540210 775390 FALSE TRUE 454063.5204 627465.5163 420411.2863 425085.4887 602121.4583 422288.7834 430614.5313 607656.4076 645972.3998 0.702914738 0.971350349 0.650819271 0.658055187 0.932116385 0.653725737 0.666614443 0.940684784 1 19.301113 1.101501648 5.670950201 0.996885581 0.755090777 0.394733697 0.115266662 0.206153958 8.918615974 0.109329205 0.027573076 12.63285897 -1.101501648 -0.241794804 VRDVLDFYNVPIQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VRDVLDFYNVPIQDR 15 1 Q8N5N7 Q8N5N7 MRPL50 "39S ribosomal protein L50, mitochondrial" 0 172.09 9.54E-07 388410000 134780 139690 149720 130780 206570 134220 123470 134510 229940 FALSE TRUE 126344.3604 150032.7929 153271.4291 134136.0362 190346.8255 172967.1351 104956.8197 151303.8696 191561.5285 0.659549761 0.783209416 0.800115922 0.700224295 0.99365894 0.902932527 0.547901348 0.78984476 1 17.54744833 -2.461492076 2.159898174 3.288430668 0.769453394 0.25363376 0.122740385 4484958.866 324147.4785 50427566.83 0.029498249 0.003455476 2.461492076 -2.518977274 VRDVVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VRDVVTK 7 1 Q12931-2;Q12931;I3L0K7;I3L239;I3L2D5 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 78.334 0.032482 221100000 713720 744940 688730 687780 979760 571320 765870 786640 1087000 FALSE TRUE 669049.5392 800096.1327 705067.0008 705429.5992 902813.6018 736250.8094 651034.9035 884853.7356 905572.6777 0.738813743 0.883525036 0.778586875 0.778987282 0.996953225 0.813022331 0.718920656 0.977120619 1 19.78847091 1.132179623 7.489045438 0.997209851 0.818558659 0.456059061 0.07862674 0.212901985 13.03021922 0.073008508 0.018308226 13.55750031 -1.132179623 -0.178651191 VREAAEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VREAAEK 7 1 P38646;H0YBG6;A0A3B3ITN1 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;;;; 101.43 0.008267 3969530000 4323620 3523240 3222090 3025540 4630260 2362770 4090470 4051960 6794970 FALSE TRUE 4053012.342 3784104.356 3298519.496 3103180.479 4266618.057 3044863.343 3477141.998 4557856.125 5660845.61 0.715972952 0.668469804 0.582690242 0.548183203 0.75370684 0.537881361 0.614244273 0.805154643 1 22.43258615 1.001059079 3.160058194 0.998534522 0.626626751 0.757102765 0.068730807 0.10135149 2.455336028 0.061735577 0.016175164 10.02441595 -1.001059079 -0.371907771 VREEAER ddPTM_SK-BR-3_Pertuzumab_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 72.038 0.048052 51049000 44086 71317 62819 56775 65782 57067 57985 54565 68437 FALSE TRUE 41326.73596 76597.38489 64309.09635 58231.94262 60615.74707 73541.31649 49290.68756 61377.56036 57014.42258 0.724847049 1.343473834 1.127944359 1.021354597 1.063165149 1.289872162 0.864530154 1.076526913 1 15.79903929 1.725069008 24.99999999 0.976459134 1.123491356 0.073082135 0.173902591 1.749479057 3228.110122 0.074809711 0.041485775 53.09688073 -1.725069008 0.147032223 VREEEIEVDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VREEEIEVDSR 11 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 ;;;; 186.17 3.78E-06 2786880000 4575890 4759860 4950710 4754450 5004050 4219090 5473570 4188100 5501190 FALSE TRUE 4289493.213 5112284.987 5068143.179 4876457.236 4611052.098 5437072.792 4652858.993 4710993.504 4583005.85 0.935956303 1.115487336 1.105855708 1.064030332 1.006119619 1.186355193 1.015241775 1.027926574 1 22.1278627 1.594755764 24.99999917 1.016170525 1.077756334 0.121016124 0.066529088 1.581880116 3008.479434 0.032621044 0.015244904 39.3328815 -1.594755764 0.061585809 VREEFK ddPTM_SK-BR-3_Pertuzumab_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 ;;; 86.866 0.048418 20417170000 27945920 26293630 25426450 24737640 27495580 19193650 31215200 24680240 33563400 FALSE TRUE 26196834.75 28240437.72 26029577.4 25372449.72 25336188.06 24734545.17 26534770.55 27761622.29 27961451.71 0.936891082 1.009977522 0.93090937 0.90740817 0.906111325 0.884594456 0.948976856 0.992853396 1 24.73693593 1.267843099 4.330352308 0.998479022 0.935639556 0.396910691 0.033123775 0.249908431 9.500246483 0.030626259 0.009473595 18.52862103 -1.267843099 -0.062839466 VREEILAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VREEILAK 8 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 120.12 0.0014256 174320000 140370 119240 132860 129890 134240 101530 157200 103880 193200 FALSE TRUE 131584.4923 128068.6537 136011.5019 133223.1973 123697.3319 130840.0628 133629.3194 116849.6467 160953.6719 0.817530229 0.795686437 0.845035098 0.827711451 0.768527555 0.812905113 0.830234674 0.725983106 1 17.29628596 -0.986857349 4.707571819 1.000003267 0.807894138 0.760673325 0.034636868 1.09E-06 2.34E-07 0.030735834 0.007244382 0.103072462 0.986857349 -0.192109129 VREELIDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VREELIDK 8 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;; 94.909 0.0091433 1620880000 964690 910540 909720 890460 949370 768380 1031100 876480 1062250 FALSE TRUE 904311.7749 977957.329 931298.988 913310.7111 874810.3098 990198.8324 876496.1273 985910.4574 884953.6126 1.021874776 1.105094454 1.052370401 1.032043599 0.98853804 1.118927386 0.990443018 1.11408151 1 19.75524231 3.530766888 4.441749638 1.03986528 1.071881067 0.029204348 0.049545835 0.528724541 21.55755021 0.011996569 0.018558225 3394.430243 -3.530766888 0.032015787 VREEVPLELVEAHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VREEVPLELVEAHVK 15 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 0 125.89 5.27E-05 33849000 74721 73168 66983 66695 83415 63172 84313 62317 94477 FALSE TRUE 70044.34599 78585.43485 68571.86839 68406.50661 76863.92238 81408.73089 71671.04837 70097.41463 78708.17836 0.889924624 0.998440524 0.87121656 0.869115612 0.976568433 1.034310952 0.910592138 0.890598869 1 16.26422593 2.708455909 24.91597993 0.959119887 0.916392384 0.194870542 0.054147735 1463.827941 1211527.111 0.017887163 0.016865981 511.041194 -2.708455909 -0.042727503 VREYELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VREYELR 7 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ; 125.31 0.0037039 4403700000 5605400 4480600 6415100 7454000 5219000 8523700 6718200 3706300 7495200 FALSE TRUE 5254568.02 4812348.286 6567269.201 7645282.26 4809120.792 10984353.82 5710868.279 4169039.714 6244202.699 0.841511442 0.770690594 1.051738631 1.224380858 0.770173715 1.759128322 0.914587267 0.66766566 1 22.57408594 3.861191757 2.831947195 1.081381043 0.808943262 0.104910878 0.295427489 0.532774352 8.35919613 0.074808631 0.154800661 7264.266305 -3.861191757 -0.272437781 VRGEVAPDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VRGEVAPDAK 10 1 P09382;F8WEI7 P09382 LGALS1 Galectin-1 0 ; 93.839 0.0077631 2416300000 3986600 3535600 3438000 3627600 4042500 2254000 4212200 3331700 3916200 FALSE TRUE 3737085.822 3797379.503 3519550.984 3720690.358 3725018.357 2904693.209 3580619.714 3747670.079 3262560.92 1.14544553 1.163926006 1.07876943 1.140420194 1.141746759 0.890310796 1.097487465 1.148689686 1 21.63757341 TVS(ph)SPIPYTPS(ph)PSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.179)VS(0.735)S(0.08)PIPY(0.011)T(0.026)PS(0.394)PS(0.241)S(0.237)S(0.231)RPIS(0.416)PGLS(0.111)Y(0.088)AS(0.095)HT(0.085)VGFT(0.055)PPT(0.005)S(0.005)LT(0.004)R 65.722 0.048934 135150000 12721 17497 19816 19882 25582 18085 29836 21138 31979 TRUE FALSE 11924.81532 18792.49609 20286.04488 20392.20578 23572.89291 23305.84591 25362.36878 23777.12583 26641.49831 0.447603028 0.705384354 0.761445345 0.76543014 0.884818588 0.874794865 0.951987328 0.892484558 1 14.7013876 5.268534534 0.319436391 0.975843559 2.37E-15 0.900663973 0.049218221 2.925648366 0.186918652 0.047660457 1.182540376 185581.4372 -5.268534534 -0.975843559 down KIDTHPS(ph)PSHSSTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 KIDTHPSPSHSSTVK 15 1 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477;H0Y594 Q8NI27 THOC2 THO complex subunit 2 1 KIDT(0.001)HPS(0.961)PS(0.038)HSSTVK;KIDT(0.001)HPS(0.959)PS(0.04)HSSTVK;KIDTHPS(0.979)PS(0.021)HSSTVK;KIDT(0.001)HPS(0.97)PS(0.03)HSSTVK 183.56 2.35E-07 2876720000 1807310 2683250 2849830 2867370 3307690 2468070 4323320 3484970 4585640 TRUE FALSE 1694193.693 2881920.622 2917429.313 2940951.569 3047917.37 3180561.743 3675078.302 3920076.176 3820267.06 0.443475199 0.754376743 0.763671562 0.76982879 0.797828351 0.832549582 0.961995129 1.026126214 1 21.86524206 5.385085502 0.22396339 1.046817555 4.34E-14 0.81337439 0.071620022 7.16479297 0.249949884 0.120979656 2.183326074 242708.7881 -5.385085502 -1.046817555 down VRGQTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VRGQTPK 7 1 P62861;E9PR30;E9PM49 P62861 FAU 40S ribosomal protein S30 0 91.9 0.014651 604080000 981890 928200 915460 1169100 1366500 816200 1425900 1391400 1651500 FALSE TRUE 920435.2576 996924.8938 937175.1435 1199101.085 1259180.602 1051823.69 1212099.532 1565119.353 1375853.981 0.668991965 0.724586263 0.68115887 0.871532228 0.915199301 0.764487878 0.880979776 1.137562107 1 20.39189593 2.327788829 0.459009387 1.041569077 0.66226392 0.66006273 0.085859892 0.668168893 0.303125789 0.084688451 0.089048339 212.7104513 -2.327788829 -0.379305157 VRGSEYDDFLDEFMEAVSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VRGSEYDDFLDEFMEAVSSK 20 1 P48163;P48163-2 P48163 ME1 NADP-dependent malic enzyme 0 130.09 3.17E-06 0 60118 84524 89730 84163 120970 86807 104110 90049 157760 FALSE TRUE 56355.32169 90782.24491 91858.43797 86322.76507 111469.5042 111866.7717 88499.67201 101291.8159 131428.8368 0.428789625 0.690733077 0.698921486 0.656802321 0.848135819 0.851158501 0.67336571 0.770697043 1 17.00392233 5.254596895 0.097982766 1.133936115 3.80E-24 0.651811061 0.088997334 50.77691135 0.681806105 1.660506664 8.21574187 179720.2006 -5.254596895 -1.133936115 VRLDDDDEGVPSSALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VRLDDDDEGVPSSALR 16 1 Q00535;Q00535-2 Q00535 CDK5 Cyclin-dependent-like kinase 5 0 ; 208.85 1.26E-11 367880000 116982 136000 148064 159890 150376 140067 155041 119298 217787 FALSE TRUE 109660.3054 146069.5815 151576.148 163993.0481 138566.0755 180502.0691 131794.0414 134192.6179 181436.9427 0.604398993 0.805070783 0.835420536 0.903856985 0.763714784 0.994847391 0.726390334 0.739610224 1 17.46910871 -4.999995387 0.023073338 2.041047415 7.10E-11 0.28216584 0.103895834 3911.17087 6.822124555 425.3648685 212.2302186 1.00E-05 4.999995387 -2.041047414 VRPAS(ph)TGGLSLLPPPPGGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VRPASTGGLSLLPPPPGGK 19 1 Q9NVZ3;Q9NVZ3-2;D6RB24;Q9NVZ3-4 Q9NVZ3 NECAP2 Adaptin ear-binding coat-associated protein 2 1 VRPAS(0.485)T(0.485)GGLS(0.03)LLPPPPGGK 116.45 7.15E-05 376940000 543410 475670 492020 517620 569640 338330 551030 422740 605580 TRUE FALSE 509398.9381 510889.1017 503690.9467 530903.0055 524902.7722 436000.3787 468408.167 475520.0196 504504.7858 1.009700904 1.012654619 0.998386856 1.052325013 1.040431701 0.864214554 0.928451385 0.942548085 1 18.94450843 2.254560236 24.99972394 0.92563412 1.019361226 0.595581888 0.03606396 145.5686768 227453.6075 0.011680288 0.009743193 179.705031 -2.254560236 0.093727106 VRPCVVYGGADIGQQIR ddPTM_SK-BR-3_Pertuzumab_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 ; 193.3 1.26E-10 2586400000 994180 989740 1074170 1034710 1181580 877230 1202450 941950 1297000 FALSE TRUE 931956.0485 1063021.379 1099649.82 1061262.41 1088783.473 1130472.06 1022153.785 1059554.531 1080522.321 0.862505133 0.983803258 1.017702086 0.98217537 1.007645517 1.046227402 0.945981185 0.980594765 1 20.04329744 4.739383977 3.919559406 0.996041836 0.849788419 0.723210495 0.025981169 0.13201861 4.138575524 0.006208118 0.055395796 54876.19333 -4.739383977 -0.146253417 VRPEEK ddPTM_SK-BR-3_Pertuzumab_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 ;; 85.265 0.050079 448696000 461555 406398 438249 399932 471726 351080 484850 399398 574435 FALSE TRUE 432667.0964 436488.1308 448644.4732 410194.9322 434678.5428 452431.0967 412151.2436 449263.7195 478558.0875 0.904105704 0.912090177 0.937492198 0.857147634 0.908308843 0.945404766 0.861235562 0.938786181 1 18.86833452 -1.474971094 3.29519544 1.001716695 0.907753135 0.48354333 0.029855822 3034408.786 2716945.253 33899.9001 0.006508697 0.033498773 1.474971094 -0.09396356 VRPGETLLIHSGSGGVGQAAIAIALSLGCR ddPTM_SK-BR-3_Pertuzumab_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 ;; 151.41 1.25E-08 413185000 273422 391056 325079 280061 466101 305356 425406 423767 282074 FALSE TRUE 256309.0051 420010.1931 332790.0274 287247.8394 429495.3076 393507.3202 361620.3196 476675.2428 234994.0271 1.090704339 1.787322845 1.41616377 1.2223623 1.82768606 1.674541796 1.538848983 2.028456845 1 17.84226456 2.729925935 24.9034078 1.642640884 1.453339975 0.096137881 0.317219758 1580.521333 4558393.433 0.092682847 0.088646572 536.9402184 -2.729925935 -0.189300909 VRPS(ph)SDLNNSTGQSPHHK ddPTM_SK-BR-3_Pertuzumab_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 VRPS(0.649)S(0.351)DLNNSTGQSPHHK;VRPS(0.5)S(0.5)DLNNSTGQSPHHK 200.17 9.31E-16 532170000 168610 364310 318420 350450 392570 260540 401200 303270 353750 TRUE FALSE 158057.0011 391283.8915 325973.0728 359443.1403 361739.1358 335753.6685 341043.7846 341133.9271 294706.8397 0.536319419 1.327705498 1.106092662 1.21966338 1.227454158 1.139280204 1.15723064 1.157536511 1 18.16892102 4.746897679 24.91407894 1.177285077 0.536319082 0.842968935 0.085423203 346.5819254 1035684.69 0.018342558 0.210885579 55833.86325 -4.746897679 -0.640965995 VRPSSDLNNSTGQS(ph)PHHK ddPTM_SK-BR-3_Pertuzumab_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 VRPSSDLNNSTGQS(1)PHHK 183.25 3.88E-14 150050000 125930 110670 127690 132680 135050 106720 152200 122740 162730 TRUE FALSE 118048.2661 118864.122 130718.8671 136084.7934 124443.7178 137528.3315 129379.023 138064.3592 135569.3117 0.8707595 0.876777498 0.964221662 1.003802348 0.917934274 1.014450319 0.954338569 1.01840422 1 17.04867111 3.932605952 1.835119484 0.980309666 0.869744097 0.690877251 0.030204905 0.18696839 1.217011528 0.007556394 0.020472692 8562.605822 -3.932605952 -0.110565569 VRS(ph)PHYVHSTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VRSPHYVHSTR 11 1 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 VRS(1)PHYVHSTR;VRS(0.997)PHY(0.002)VHS(0.001)TR;VRS(0.977)PHY(0.023)VHSTR 68.413 0.034608 141083000 139257 257964 220683 223392 251333 178275 201027 213221 221362 TRUE FALSE 130541.153 277063.923 225917.705 229124.6169 231594.32 229740.0984 170884.8676 239842.1112 184415.2521 0.707865274 1.502391585 1.225048917 1.242438542 1.255830618 1.245776018 0.926630881 1.300554636 1 17.49259845 1.77702451 25 1.069445356 1.23917866 0.040502789 0.218768316 104.9253005 68224.68389 0.092226899 0.051212802 59.84453686 -1.77702451 0.169733305 VRSPSSCMVTVTVT(ph)ATSEQPHIYIPAPASELDSSSTTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VRSPSSCMVTVTVTATSEQPHIYIPAPASELDSSSTTK 38 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 1 VRS(0.117)PS(0.117)S(0.117)CMVT(0.117)VT(0.117)VT(0.133)AT(0.133)S(0.133)EQPHIY(0.018)IPAPASELDSSSTTK 68.049 0.0064859 33029000 10173 9377.7 9929.3 11372 12875 6856 15488 12000 9585.9 TRUE FALSE 9536.290089 10072.03467 10164.82768 11663.82477 11863.84944 8835.215902 13165.71818 13498.22642 7985.951363 1.194133254 1.261219134 1.272838667 1.460542926 1.485589994 1.106344817 1.648609863 1.690246509 1 12.96324857 3.303678993 5.469977811 1.429042322 1.247944723 0.094902993 0.214012668 0.392504257 22.31706957 0.05598293 0.075691979 2012.236362 -3.303678993 -0.181097599 VRTDITYPAGFMDVISIDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VRTDITYPAGFMDVISIDK 19 1 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ; 180.52 3.05E-14 466060000 1302150 1108350 988380 1088440 1355420 805050 1484870 1337890 1829080 FALSE TRUE 1220650.756 1190413.387 1011824.84 1116371.213 1248970.781 1037454.866 1262227.528 1504928.512 1523794.732 0.801059835 0.781216369 0.664016497 0.73262572 0.819645031 0.680836365 0.828344856 0.987618923 1 20.53923714 1.349345763 2.943629229 1.002121341 0.7434919 0.810486557 0.048771903 0.1030433 1.473202286 0.04027289 0.012488607 22.35351186 -1.349345763 -0.258629441 VRTELADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VRTELADK 8 1 P35579 P35579 MYH9 Myosin-9 0 ;; 145.9 0.00051245 678060000 1579430 1279250 1171910 1257960 1485980 861440 1572280 1492270 1547970 FALSE TRUE 1480576.296 1373967.001 1199708.259 1290241.383 1369277.125 1110123.744 1336531.21 1678583.194 1289603.807 1.14808617 1.065417917 0.930292119 1.000494397 1.061781237 0.860825424 1.036389008 1.301627047 1 20.29849648 1.454071216 24.99996264 1.15687868 1.004409464 0.225930758 0.105063284 12.96773568 14067.91067 0.051606525 0.02387778 28.44927583 -1.454071216 -0.152469216 VRVDLPDKYPFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VRVDLPDKYPFK 12 2 C9JZY6;P62256-2;P62256;H7C4M9;C9JZG9;C9J8Q9 C9JZY6 UBE2H Ubiquitin-conjugating enzyme E2 H 0 ; 128.54 0.00014069 980610000 1734260 1557010 1622280 1531310 2015450 1254850 2079940 1688530 2982020 FALSE TRUE 1625715.762 1672292.64 1660761.248 1570606.007 1857164.687 1617104.824 1768072.306 1899346.687 2484301.597 0.65439549 0.67314397 0.668502266 0.632212292 0.747560074 0.65092935 0.711697931 0.764539494 1 21.2444089 0.537082461 0.880434096 1.002133752 0.668266686 0.920837199 0.030067604 0.347453365 0.41999691 0.026458028 0.008639882 3.444153199 -0.537082461 -0.333867066 VRVDSTAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VRVDSTAK 8 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 82.749 0.017753 798930000 611130 937300 475410 505580 1102770 369010 618480 939670 1090540 FALSE TRUE 572880.4642 1006698.667 486686.9497 518554.0387 1016162.893 475537.1966 525744.6657 1056989.868 908521.8288 0.630563236 1.108062168 0.535690981 0.570766736 1.118479337 0.52341857 0.57868138 1.16341714 1 19.79316165 1.231160997 24.99964712 1.081708714 0.733457579 0.308173141 0.222651283 235.079272 794182.9297 0.193517927 0.052206679 17.02789632 -1.231160997 -0.348251135 VRVELSNGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VRVELSNGEK 10 1 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;;;; 199.82 2.48E-07 5282280000 4257360 3354810 3466840 3611060 3977010 2804780 4501070 3461390 5019840 FALSE TRUE 3990899.437 3603203.623 3549075.082 3703725.913 3664671.677 3614474.454 3826176.339 3893552.161 4181996.275 0.954304876 0.861598956 0.848655725 0.885635871 0.876297212 0.86429404 0.914916248 0.931027171 1 21.99576035 1.02716827 1.191161806 0.998877561 0.875278169 0.611809933 0.029472143 0.292676227 0.86160629 0.026287721 0.008261511 10.64555408 -1.02716827 -0.123599392 VRVELSTGMPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VRVELSTGMPR 11 1 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ; 136.7 8.55E-05 983900000 301200 474070 323840 367260 502560 290220 393030 422730 528600 FALSE TRUE 282348.4297 509170.6361 331521.6377 376684.5134 463090.9648 374001.8027 334098.8002 475508.771 440373.2451 0.641157093 1.156225183 0.752819662 0.855375565 1.05158742 0.849283663 0.758671886 1.079785787 1 18.7483673 1.217875801 24.99788421 1.039893016 0.882543489 0.184411826 0.148677359 500.9960775 605444.861 0.132968024 0.033390548 16.51489439 -1.217875801 -0.157349527 VRYDS(ph)SNQVK ddPTM_SK-BR-3_Pertuzumab_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(0.963)S(0.037)NQVK;VRYDS(0.778)S(0.222)NQVK;VRYDS(0.824)S(0.176)NQVK;VRYDS(0.817)S(0.183)NQVK;VRYDS(0.721)S(0.279)NQVK 171.32 1.07E-05 1255200000 1870110 1589380 1510620 1635380 2253060 1088512 2089340 1639260 2693030 TRUE FALSE 1753063.153 1707059.349 1546452.62 1677346.619 2076113.756 1402747.744 1776062.863 1843925.219 2243545.895 0.781380562 0.760875609 0.689289496 0.747631962 0.925371645 0.625236928 0.791632062 0.821879875 1 21.09734927 0.832805645 1.95807307 0.999436672 0.752582921 0.496179635 0.076054743 0.476589564 3.384061785 0.066746846 0.018574337 6.804647699 -0.832805645 -0.246853751 VS(ph)EGGPAEIAGLQIGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSEGGPAEIAGLQIGDK 17 0 O14907 O14907 TAX1BP3 Tax1-binding protein 3 1 VS(1)EGGPAEIAGLQIGDK 119.37 0.00012962 13454000 18643 12057 13515 14960 16442 9749.2 16306 12705 17386 TRUE FALSE 17476.16791 12949.71283 13835.58218 15343.89893 15150.71164 12563.63577 13861.06668 14291.24722 14484.16428 1.206570677 0.894060063 0.955221296 1.059356869 1.046019042 0.867404949 0.956980769 0.986680829 1 13.82218882 2.266277174 24.99967811 0.947096574 1.00413111 0.122825043 0.08888709 558.4218263 503681.6729 0.030401376 0.025430293 184.6193316 -2.266277174 0.057034536 VS(ph)LDVNHFAPDELTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSLDVNHFAPDELTVK 16 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 VS(1)LDVNHFAPDELTVK 187.76 8.29E-10 54866000 134860 87885 86940 92805 100150 67710 100080 84250 137930 TRUE FALSE 126419.3533 94392.09684 89002.25786 95186.53342 92284.62299 87256.77782 85073.9331 94768.79796 114908.5919 1.1001732 0.821453777 0.774548329 0.828367416 0.803113339 0.759358168 0.74036181 0.824732044 1 16.81012715 4.740232109 4.236358772 0.799797085 1.124061774 0.588850354 0.072524185 0.128192364 5.292270304 0.015195692 0.126358283 54983.46546 -4.740232109 0.324264689 VS(ph)LERLDLDLTADSQPPVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VSLERLDLDLTADSQPPVFK 20 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 VS(1)LERLDLDLTADSQPPVFK;VS(1)LERLDLDLTADSQPPVFK;VS(1)LERLDLDLTADSQPPVFK;VS(1)LERLDLDLTADSQPPVFK 248.95 1.52E-30 387441000 845870 700512 777940 795750 1004030 551578 969350 718232 1768470 TRUE FALSE 792928.5066 752378.6374 796393.1042 816170.2922 925177.5339 710809.6145 824004.9665 807904.8462 1473300.932 0.538198605 0.510675464 0.540550194 0.55397392 0.627962362 0.482460575 0.559291689 0.548363765 1 20.49062071 -4.537273869 0.508782719 10 0.539280917 0.937046333 0.037046437 339.8329769 2.55112675 3449.92855 0.01613041 2.90E-05 4.537273869 -9.460719083 VS(ph)PAAAQLADTLFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSPAAAQLADTLFSK 15 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 VS(1)PAAAQLADTLFSK;VS(1)PAAAQLADTLFSK 209.23 2.61E-09 217149000 756050 467440 621960 528230 516180 503430 751980 543670 465920 TRUE FALSE 708730.1801 502049.744 636713.1849 541785.2761 475641.305 648762.0685 639227.58 611548.3963 388154.942 1.825895031 1.293426129 1.64035831 1.395796414 1.225390311 1.671399738 1.646836123 1.575526497 1 18.56627313 -1.035748393 4.647119027 0.999985618 1.524183767 0.455088815 0.18345098 3.11E-05 6.46E-06 0.167895337 0.039572005 0.092098299 1.035748393 0.524198149 VS(ph)PAHS(ph)PPENGLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VSPAHSPPENGLDK 14 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 2 VS(1)PAHS(1)PPENGLDK;VS(1)PAHS(1)PPENGLDK;VS(1)PAHS(1)PPENGLDK 230.06 5.56E-13 1172168000 1856200 892610 1267970 1059750 992160 1031220 1565270 1108210 1081200 TRUE FALSE 1740023.755 958699.7732 1298046.847 1086944.979 914239.7558 1328916.474 1330572.295 1246572.458 900740.7352 1.931769806 1.064345972 1.441088203 1.206723463 1.014986577 1.475359581 1.477197869 1.383941471 1 19.78075238 4.751271787 24.66852805 1.287371475 1.931770298 0.555537062 0.18777901 1399.674065 2716284.211 0.044017904 0.790758687 56399.04984 -4.751271787 0.644398823 VS(ph)PENLVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VSPENLVDK 9 0 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 VS(1)PENLVDK;VS(1)PENLVDK;VS(1)PENLVDK;VS(1)PENLVDK;VS(1)PENLVDK 182.23 4.88E-05 1030090000 2939870 1802304 2126760 2095597 2152670 1549167 2725200 1828811 2550450 TRUE FALSE 2755868.785 1935748.463 2177207.752 2149373.567 1983607.982 1996386.364 2316581.56 2057142.079 2124763.418 1.297023829 0.911041882 1.024682434 1.011582536 0.933566516 0.939580542 1.090277411 0.96817465 1 21.01887078 4.747510718 24.94737063 0.988619481 1.297023993 0.781656333 0.051815506 550.7649792 1535160.085 0.01247376 0.151796023 55912.73261 -4.747510718 0.308404511 VS(ph)PGLPSPNLENGAPAVGPVQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSPGLPSPNLENGAPAVGPVQPR 23 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 VS(1)PGLPSPNLENGAPAVGPVQPR 269.85 4.87E-45 225990000 16702 10403 12445 12210 14588 10575 14889 12305 13024 TRUE FALSE 15656.65163 11173.24894 12740.20128 12523.32927 13442.31733 13627.83083 12656.53267 13841.30634 10850.21026 1.442981404 1.029772574 1.174189345 1.154201529 1.238899247 1.255996935 1.166478102 1.275671715 1 13.40543538 -1.016382273 4.376100472 0.999990877 1.194993048 0.267816104 0.107426538 9.38E-06 2.11E-06 0.096206569 0.022674981 0.096298102 1.016382273 0.195002172 VS(ph)PPAADVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VSPPAADVLK 10 0 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 VS(1)PPAADVLK;VS(1)PPAADVLK;VS(1)PPAADVLK;VS(1)PPAADVLK;VS(1)PPAADVLK;VS(1)PPAADVLK 151.26 2.11E-05 1688360000 4085800 2253020 3013620 2720840 2697330 2158040 3238190 2425690 1974940 TRUE FALSE 3830077.071 2419835.945 3085104.49 2790661.361 2485492.582 2781031.115 2752653.471 2728542.736 1645309.755 2.327875987 1.470747947 1.875090377 1.696131292 1.510653282 1.690278141 1.673030542 1.658376319 1 20.64992779 -2.483439563 0.204456154 6.95E-20 1.865548336 0.556045881 0.220794129 33.8106661 0.848038495 16.20420894 0.50663308 0.00328519 2.483439563 1.865548336 VS(ph)PPAS(ph)PTLEVELGSAELPLQGAVGPELPPGGGHGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSPPASPTLEVELGSAELPLQGAVGPELPPGGGHGR 36 0 Q7Z6J0 Q7Z6J0 SH3RF1 E3 ubiquitin-protein ligase SH3RF1 2 VS(0.984)PPAS(0.846)PT(0.17)LEVELGSAELPLQGAVGPELPPGGGHGR;VS(0.962)PPAS(0.754)PT(0.27)LEVELGS(0.014)AELPLQGAVGPELPPGGGHGR 96.794 0.0001756 63284000 23713.1 23300.9 23612.8 22441.6 26549.1 21435.3 25784.6 17921.2 21937.7 TRUE FALSE 22228.9394 25026.12288 24172.90677 23017.48945 24464.04078 27623.32314 21918.4386 20158.70127 18276.15615 1.216280886 1.369331859 1.322647201 1.25942727 1.338576919 1.51144053 1.199291494 1.103005528 1 14.15767505 1.317984647 2.612053491 1.026410643 1.335846425 0.679445468 0.08075028 0.148146475 1.670435693 0.066253312 0.019798967 20.79623169 -1.317984647 0.309435782 VS(ph)PQPMISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSPQPMISR 9 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 VS(1)PQPMISR;VS(1)PQPMISR 94.402 0.0091744 244840000 106322 94594 111820 111389 122750 87680 129109 109842 132824 TRUE FALSE 99667.49581 101597.8382 114472.4232 114247.4303 113109.7101 112991.7926 109750.304 123556.0155 110654.8163 0.900706351 0.918151072 1.034500142 1.032466856 1.022185151 1.021119517 0.991825821 1.116589585 1 16.75570672 4.079538551 2.163008678 1.027982819 0.902742775 0.69277919 0.033687063 0.17375075 1.570365483 0.008365071 0.024826242 12009.87678 -4.079538551 -0.125240043 VS(ph)PSDTTPLVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VSPSDTTPLVSR 12 0 Q9HCK8-2;Q9HCK8;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 VS(0.967)PS(0.033)DTTPLVSR;VS(0.997)PS(0.003)DTTPLVSR;VS(0.917)PS(0.018)DT(0.055)T(0.01)PLVSR;VS(0.997)PS(0.002)DTTPLVSR 210.61 4.36E-08 2016060000 1680870 1396870 1528510 1442830 1405220 1268040 1704400 1314280 1439980 TRUE FALSE 1575667.347 1500295.708 1564766.979 1479855.461 1294859.69 1634102.563 1448841.043 1478370.751 1199638.035 1.313452309 1.250623658 1.304365928 1.233584979 1.079375321 1.362163015 1.207731833 1.232347348 1 20.19416774 -4.444495586 0.229108937 6.68E-12 1.2806973 0.537889863 0.073655919 91.9076522 1.161709764 42.58317794 0.120669803 3.59E-05 4.444495586 1.2806973 VS(ph)PSFSAELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSPSFSAELK 10 0 Q13416 Q13416 ORC2 Origin recognition complex subunit 2 1 VS(0.974)PS(0.026)FSAELK 122.33 0.00051558 52174000 136060 93529 110000 112490 127300 79960 131590 97754 156940 TRUE FALSE 127544.2475 100453.9845 112609.2519 115376.6838 117302.3715 103043.154 111859.3011 109958.8021 130745.7001 0.975513897 0.768315779 0.861284553 0.882451077 0.897179574 0.788118874 0.855548603 0.84101276 1 16.99640398 -1.029376786 4.99172149 1.000002144 0.849937689 0.365309677 0.057524768 1.24E-06 2.41E-07 0.050394212 0.01187786 0.093459448 1.029376786 -0.150064454 VS(ph)PSPSQESLSSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSPSPSQESLSSSK 14 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 VS(0.658)PS(0.342)PSQESLSSSK;VS(0.683)PS(0.317)PSQESLSSSK 313.32 8.99E-56 533980000 922990 556510 700260 675380 624890 537530 886700 590640 415080 TRUE FALSE 865221.7035 597714.5794 716870.4979 692711.3942 575813.6601 692706.1849 753747.5667 664382.7042 345800.4665 2.502083679 1.728495585 2.073075566 2.003211277 1.665161606 2.003196213 2.179718189 1.921289207 1 18.39958029 0.950996114 22.09293269 0.999999998 1.997449761 0.656503952 0.230075934 1912.854823 862393.966 0.203121799 0.05078045 8.932974901 -0.950996114 0.997449763 VS(ph)PSTSYTPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSPSTSYTPSR 11 0 Q9BTE3;Q9BTE3-2 Q9BTE3 MCMBP Mini-chromosome maintenance complex-binding protein 1 VS(0.858)PS(0.123)T(0.014)S(0.005)YTPSR;VS(0.857)PS(0.136)T(0.005)S(0.001)YTPSR 181.49 6.51E-06 204240000 278050 260260 259530 294350 303720 205540 284720 236950 305560 TRUE FALSE 260647.3468 279529.9212 265686.1742 301903.5193 279867.0563 264876.0613 242028.8792 266533.7291 254560.062 1.023912961 1.098090246 1.043707218 1.185981481 1.09941463 1.040524815 0.950773178 1.047036707 1 17.95764657 2.018993858 4.904859533 0.993776002 1.088549308 0.429729371 0.047917799 0.162643956 10.51939331 0.018869372 0.012862503 104.4705445 -2.018993858 0.094773306 VS(ph)SGYVPPPVATPFSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSSGYVPPPVATPFSSK 17 0 Q15942;Q15942-2;H7C3R3 Q15942 ZYX Zyxin 1 VS(0.968)S(0.031)GYVPPPVATPFSSK 107.5 0.00073582 33239000 430830 338310 396790 363000 453260 304570 520500 383640 512940 TRUE FALSE 403865.1194 363358.8244 406202.0462 372315.1946 417662.788 392494.4147 442455.8571 431538.2985 427327.0003 0.945096189 0.850306262 0.950564897 0.871265317 0.977384503 0.918487281 1.035403466 1.009854978 1 18.70498095 2.07606284 1.215795201 1.019761174 0.90372411 0.544176013 0.039798664 0.302596082 0.836143716 0.025479278 0.01259918 119.1414386 -2.07606284 -0.116037064 VS(ph)SLLHKPEFPDGEMMEVLI ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSSLLHKPEFPDGEMMEVLI 20 1 Q8IY63-2;Q8IY63 Q8IY63-2 AMOTL1 Angiomotin-like protein 1 1 VS(0.5)S(0.5)LLHKPEFPDGEMMEVLI 95.71 0.00071906 14675000 43180 35095 40572 34839 50111 24704 53307 38427 73473 TRUE FALSE 40477.44088 37693.47032 41534.387 35733.02772 46175.4842 31835.64376 45314.11023 43224.69554 61209.88165 0.661289318 0.615806947 0.678556891 0.583778742 0.75437957 0.520106279 0.740307104 0.706171853 1 15.90147696 0.522011032 0.995771235 1.000569455 0.642076918 0.7320315 0.066686822 0.732584286 1.05938577 0.054992249 0.017435808 3.326680038 -0.522011032 -0.358492537 VS(ph)SPTKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VSSPTKPK 8 1 Q8WUA4;A0A087WZD8;Q8WUA4-2 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 VS(0.59)S(0.41)PTKPK;VS(0.59)S(0.41)PTKPK;VS(0.678)S(0.321)PTKPK;VS(0.921)S(0.078)PT(0.001)KPK 112.11 0.0018802 4681730000 11753200 6134080 8361400 8087600 8526500 5484220 10772600 6756100 10372900 TRUE FALSE 11017588.19 6588253.666 8559736.357 8295141.508 7856863.084 7067425.285 9157348.638 7599613.957 8641595.979 1.27494831 0.762388531 0.990527257 0.959908509 0.909191208 0.817837967 1.05968257 0.879422502 1 23.04286635 -1.269093298 4.247333041 1.000044437 0.943486973 0.001438119 0.141309457 5.23E-05 8.99E-06 0.120272818 0.028326307 0.053815416 1.269093298 -0.056557464 VSADGSQEPTHDILQMLSDLQESVASSRPQEVSAYLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSADGSQEPTHDILQMLSDLQESVASSRPQEVSAYLTR 38 1 F5GWV0;F5H4P3;Q6NXE6-2;Q6NXE6;F5H052;F5H2X2;F5H2K4 F5GWV0 ARMC6 Armadillo repeat-containing protein 6 0 82.384 0.00059749 63583000 30104 38039 38074 35509 47982 35841 40659 30193 38629 FALSE TRUE 28219.84438 40855.44714 38977.13326 36420.22106 44213.68727 46187.71487 34562.56041 33962.66251 32181.57035 0.876894573 1.269529321 1.211163186 1.1317105 1.373882219 1.435222532 1.073986137 1.055345098 1 14.97394711 1.565356948 9.045923257 1.041447711 1.226797063 0.231431576 0.149290618 0.162568119 23.57789335 0.076630244 0.035837174 36.75842946 -1.565356948 0.185349352 VSALEEDMDDVES(ph)S(ph)EEEEEEDEKLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VSALEEDMDDVESSEEEEEEDEKLER 26 1 Q8NAV1 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 2 VSALEEDMDDVES(1)S(1)EEEEEEDEKLER;VSALEEDMDDVES(1)S(1)EEEEEEDEKLER;VSALEEDMDDVES(1)S(1)EEEEEEDEKLER;VSALEEDMDDVES(1)S(1)EEEEEEDEKLER 193.05 2.27E-18 790176000 1625340 966210 1167470 1164860 1234970 854940 1502030 1001450 1444310 TRUE FALSE 1523612.871 1037749.194 1195162.94 1194752.28 1137980.438 1101747.299 1276814.546 1126483.237 1203245.33 1.266252885 0.862458526 0.993282841 0.992941547 0.94575928 0.915646437 1.061142324 0.936204121 1 20.19849939 4.75084879 24.87292915 0.964473445 1.266253084 0.756826036 0.053942281 934.8026116 1892130.834 0.012862788 0.224804265 56344.14462 -4.75084879 0.301779639 VSAPEVSVGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSAPEVSVGHK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 76.332 0.035643 107750000 158530 156620 163390 173850 203790 130890 210490 164940 201320 FALSE TRUE 148607.8903 168216.3078 167265.688 178311.2853 187785.1554 168675.8182 178928.9786 185533.1221 167718.3914 0.886056019 1.002968764 0.997300812 1.063158809 1.119645579 1.005708538 1.066841728 1.106218111 1 17.35568137 6.272333309 0.578962435 1.061234637 4.17E-14 0.611206732 0.041702674 12.46715794 0.777496841 0.017574805 13.10510292 1872118.389 -6.272333309 -1.061234637 VSAQEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSAQEVR 7 0 P15311;E7EQR4 P15311 EZR Ezrin 0 83.206 0.052228 115760000 160670 314900 131550 140580 347870 125090 159810 249550 302890 FALSE TRUE 150613.9515 338215.5237 134670.4281 144187.5208 320549.6934 161201.4523 135847.9741 280706.8668 252335.7023 0.596879277 1.340339558 0.533695497 0.571411495 1.27033032 0.638837275 0.538362082 1.112434207 1 17.94498482 3.962931531 24.5257848 0.771851004 1.011126705 0.029216075 0.310128346 695.5936758 1202279.835 0.073943389 0.134149023 9181.878274 -3.962931531 0.239275702 VSAWELINSEYFSEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSAWELINSEYFSEGR 16 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 267.23 6.31E-27 164640000 164510 166726 143570 168490 182241 133019 185155 146052 156644 FALSE TRUE 154213.6128 179070.5665 146975.5482 172813.7387 167928.527 171419.4259 157392.7266 164286.9137 130499.1044 1.181721617 1.372197666 1.12625714 1.324252296 1.286817467 1.313567834 1.20608281 1.258912193 1 16.99368038 -0.074807334 0.923817401 0.995706342 1.262262216 0.557804033 0.072410666 5.946647776 4.372869384 0.154378812 0.020992324 0.841768493 0.074807334 0.266555874 VSCHDS(ph)DDDIMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSCHDSDDDIMR 12 0 Q76FK4-2;Q76FK4-4;Q76FK4;F8WE42;F5H101;F5GWN9 Q76FK4-2 NOL8 Nucleolar protein 8 1 VSCHDS(1)DDDIMR;VSCHDS(1)DDDIMR 155.57 4.05E-05 596300000 489410 677630 596360 603880 590380 588350 741950 577410 483180 TRUE FALSE 458778.7017 727802.4303 610505.9408 619376.5832 544013.9363 758197.0939 630701.4854 649500.9095 402534.1365 1.1397262 1.808051453 1.516656317 1.538693311 1.351472799 1.883559741 1.566827328 1.61353001 1 18.61875161 -1.391239014 6.450055168 0.99993137 1.579506912 0.400507716 0.21003218 0.000183747 1.73E-05 0.180269842 0.042485023 0.04062197 1.391239014 0.579575542 VSDFGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSDFGGR 7 0 P27694;I3L4R8 P27694 RPA1 "Replication protein A 70 kDa DNA-binding subunit;Replication protein A 70 kDa DNA-binding subunit, N-terminally processed" 0 82.913 0.053976 127940000 211430 248160 233580 250000 251910 187920 249200 201660 285400 FALSE TRUE 198196.9737 266534.0246 239120.6279 256415.4232 232126.0048 242169.4534 211834.7735 226837.6949 237764.8962 0.833583834 1.120998216 1.005701984 1.078441045 0.976283751 1.018524842 0.890942174 0.954041991 1 17.8591762 1.762444869 24.9995835 0.938063048 1.020593372 0.079147927 0.079513324 21.11888748 22121.14501 0.033534248 0.018597466 57.86885229 -1.762444869 0.082530324 VSDILHSIFSSYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSDILHSIFSSYK 13 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ; 194.7 7.98E-07 155416000 404710 1234890 428690 443570 1432700 248706 513450 1212860 1164540 FALSE TRUE 379379.9235 1326322.541 438858.7292 454952.7572 1320181.521 320503.3848 436462.9391 1364288.241 970170.7508 0.391044487 1.367102172 0.452352051 0.468940913 1.360772338 0.330357707 0.449882599 1.40623518 1 19.88787916 1.234021935 24.99993759 1.20311762 0.716243534 0.227759938 0.391287915 189.8449795 1045638.264 0.321688082 0.09102277 17.14043876 -1.234021935 -0.486874086 VSDQNS(ph)PVLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 VSDQNSPVLPK 11 0 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 VSDQNS(1)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK 276.78 3.55E-27 7827010000 8476270 6951840 7550400 7775140 8035580 6023960 9966250 7207350 9722390 TRUE FALSE 7945755.391 7466561.467 7729499.054 7974663.256 7404497.961 7762979.461 8471903.335 8107203.513 8099660.3 0.980998597 0.921836372 0.954299164 0.984567619 0.91417389 0.958432721 1.045957858 1.0009313 1 22.94942997 1.844308755 6.404854821 1.018654922 0.948284257 0.581152832 0.025220801 0.141399501 7.165659059 0.010275677 0.006208968 69.8728978 -1.844308755 -0.070370666 VSDS(ph)LTDLALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSDSLTDLALK 11 0 Q8N3C0 Q8N3C0 ASCC3 Activating signal cointegrator 1 complex subunit 3 1 VSDS(0.999)LTDLALK;VSDS(0.998)LT(0.002)DLALK 185.57 4.62E-06 69696000 256160 222540 250920 229030 254260 180545 297400 229070 289580 TRUE FALSE 240127.4029 239017.0932 256871.9409 234907.2975 234291.4452 232665.4106 252807.6309 257669.8937 241247.2272 0.995358188 0.990755815 1.064766397 0.973720197 0.971167412 0.964427294 1.047919323 1.068074011 1 17.88015284 1.636838123 9.649331316 1.043574895 0.99982148 0.281764558 0.032670033 0.15017765 29.44762009 0.01667622 0.00877689 43.33493236 -1.636838123 -0.043753416 VSDSISAQYPVVDHEFDAVVVGAGGAGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSDSISAQYPVVDHEFDAVVVGAGGAGLR 29 0 P31040;D6RFM5;P31040-2;A0A087X1I3;P31040-3;A0A494C1T6 P31040 SDHA "Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial" 0 106.1 0.00048422 18315000 19687 22894 23045 21339 22872 15380 22812 23228 30454 FALSE TRUE 18454.82581 24589.09558 23591.63828 21886.59487 21075.72538 19819.95633 19391.55238 26128.06693 25371.03066 0.727397561 0.969180003 0.929865191 0.86266085 0.830700403 0.781204224 0.764318669 1.029838609 1 14.63089451 1.221369115 24.99915965 1.014919496 0.853273808 0.488554168 0.07400843 293.1946392 426339.8753 0.078932048 0.019928715 16.64827018 -1.221369115 -0.161645688 VSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 174.16 5.37E-19 76826000 37436.6 51916 52821 48276 57665 58694 70110 47024 59881 FALSE TRUE 35093.51003 55759.91466 54073.93906 49514.84389 53136.22351 75638.00498 59597.65637 52895.04991 49886.47425 0.703467434 1.11773613 1.083939883 0.992550478 1.065142893 1.51620266 1.194665634 1.060308444 1 15.60636109 2.455718728 24.99935919 1.227477604 1.017790076 0.230685943 0.175730584 322.7593256 376998.9923 0.057187526 0.047850369 285.5740417 -2.455718728 -0.209687528 VSDYEMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSDYEMK 7 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ; 125.25 0.0094623 409530000 915290 767790 833210 836850 921990 649280 1010740 766840 1055980 FALSE TRUE 858003.6327 824637.9705 852974.1347 858324.9878 849580.6245 836716.5958 859188.9203 862581.662 879730.1161 0.97530324 0.937376083 0.969586148 0.975668528 0.965728704 0.951106005 0.976650571 0.980507142 1 19.74670148 0.463930099 0.321201792 1.007628965 0.955517597 0.47661361 0.01218756 2.588483077 0.546771125 0.04183573 0.013879222 2.910248664 -0.463930099 -0.052111368 VSEHVGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VSEHVGSR 8 0 Q92922;F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 Q92922;F8VXC8 SMARCC1;SMARCC2 SWI/SNF complex subunit SMARCC1;SWI/SNF complex subunit SMARCC2 0 ;;; 133.86 0.00090124 1533180000 974570 1304950 1456280 1374630 1239790 1271290 1548080 1261840 1227030 FALSE TRUE 913573.4034 1401569.856 1490823.649 1409905.333 1142421.894 1638290.785 1315959.776 1419383.502 1022230.766 0.893705642 1.371089486 1.45840225 1.379243689 1.117577295 1.602662373 1.287341195 1.388515733 1 19.96328949 -1.0734763 5.20391635 0.99999493 1.336201548 0.19563381 0.193714416 1.02E-05 1.82E-06 0.168637935 0.039747743 0.084435232 1.0734763 0.336206618 VSELKEELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSELKEELK 9 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 108.43 0.0023825 458990000 993980 779810 666600 627860 987310 382840 806530 788290 1244900 FALSE TRUE 931768.5661 837547.9438 682412.0668 643971.9506 909770.6552 493359.6931 685598.314 886709.7417 1037118.148 0.898420848 0.807572354 0.657988743 0.620924387 0.877210236 0.475702498 0.661060956 0.854974666 1 19.98414882 1.009050893 4.273847471 0.998958072 0.707132712 0.363238924 0.125361348 0.179392122 9.015566129 0.116416926 0.029687353 10.21059129 -1.009050893 -0.29182536 VSELKEELKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSELKEELKK 10 2 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 90.614 0.0060244 1117100000 6622000 3115500 4438600 4180700 4911900 2999000 6049300 3724600 6949300 FALSE TRUE 6207540.841 3346174.862 4543885.688 4287983.84 4526139.188 3864762.615 5142263.624 4189624.509 5789416.936 1.07222211 0.577981323 0.784860676 0.740659014 0.781795341 0.66755645 0.888217878 0.723669509 1 22.46498663 -0.389439173 0.552896739 1.0309238 0.755211406 0.190869526 0.133580638 11.6341617 3.1740972 0.849851208 0.052460877 0.407906688 0.389439173 -0.275712394 VSFELFADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSFELFADK 9 0 P62937;F8WE65;C9J5S7 P62937 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 116.52 0.0030249 384150000 817770 762730 622960 569870 859480 412150 717860 877530 1134600 FALSE TRUE 766587.2355 819203.3228 637736.9054 584493.829 791979.9078 531131.0143 610223.5573 987091.5522 945227.9302 0.811007812 0.866672785 0.674691135 0.618362842 0.837871885 0.561907871 0.645583502 1.044289447 1 19.85030273 1.232918541 24.99984754 1.022144928 0.716870527 0.624030176 0.098602927 100.4916198 445251.9549 0.088770983 0.024627965 17.09694603 -1.232918541 -0.305274401 VSFELFADKVPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VSFELFADKVPK 12 1 P62937;F8WE65;C9J5S7 P62937 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ;;; 162.31 5.75E-05 26949955000 16630286 11566789 13483247 12313721 14070787 10105947 17174345 12896448 22493122 FALSE TRUE 15589426.09 12423206.09 13803075.99 12629711.93 12965724.15 13023369.84 14599211.41 14506597.92 18738874.63 0.831929686 0.662964364 0.736601117 0.673984547 0.691915838 0.694992101 0.779086882 0.774144564 1 24.15953098 0.599638719 0.953384579 1.00013112 0.710314357 0.75527167 0.049348484 0.567522307 0.830046063 0.042822756 0.01388036 3.977761311 -0.599638719 -0.289816762 VSFELFADKVPKTAENFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSFELFADKVPKTAENFR 18 2 P62937;F8WE65;C9J5S7 P62937 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 169.19 1.06E-11 321100000 172980 225980 549660 509060 647190 612690 453890 107900 107360 FALSE TRUE 162153.4906 242711.7943 562698.1948 522123.3414 596362.308 789563.6568 385833.4082 121371.5525 89440.92243 1.812967556 2.713654866 6.291283447 5.837633683 6.667667236 8.827767373 4.313835297 1.357002468 1 16.44864745 4.226800842 2.648897306 5.32836158 1.984310854 0.161460622 2.377883868 0.417108582 5.718159733 0.583100784 1.884004451 16857.79786 -4.226800842 -3.344050726 VSGAGFS(ph)PSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VSGAGFSPSSK 11 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 VSGAGFS(1)PSSK;VSGAGFS(0.965)PS(0.035)SK;VSGAGFS(0.999)PS(0.001)SK;VSGAGFS(1)PSSK;VSGAGFS(0.997)PS(0.003)SK;VSGAGFS(0.998)PS(0.002)SK 244.14 7.72E-16 7424550000 5508070 4415910 5079630 5675120 5182760 3131870 4583510 3081030 3797440 TRUE FALSE 5163329.731 4742868.571 5200121.222 5820753.187 4775726.936 4035990.027 3896255.227 3465703.378 3163622.732 1.632094017 1.499189054 1.643723561 1.839901177 1.509575364 1.275749471 1.231580235 1.095485673 1 21.59314614 2.010792 1.454678131 1.085513927 1.629556525 0.85800116 0.099172265 0.160404837 0.633509979 0.07036432 0.033811891 102.516082 -2.010792 0.544042598 VSGEEELHTGPPAPQGPLSVPQGLPTQSLAS(ph)PPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSGEEELHTGPPAPQGPLSVPQGLPTQSLASPPAR 35 0 Q9UPN7 Q9UPN7 PPP6R1 Serine/threonine-protein phosphatase 6 regulatory subunit 1 1 VSGEEELHTGPPAPQGPLSVPQGLPT(0.213)QS(0.172)LAS(0.614)PPAR;VSGEEELHTGPPAPQGPLSVPQGLPT(0.006)QS(0.015)LAS(0.979)PPAR 143.33 7.85E-11 205134000 80369 83328 84912 113898 99716 58157 83798 59756 82499 TRUE FALSE 75338.84775 89497.69182 86926.15274 116820.8155 91884.70759 74945.9818 71233.26784 67216.66814 68729.38394 1.096166493 1.302175092 1.264759667 1.699721557 1.336905736 1.090450365 1.036431054 0.977990261 1 16.06863941 2.164122779 3.895065266 1.021221438 1.341644343 0.52863946 0.148652177 0.190069568 5.652407525 0.059659049 0.043110187 145.9226738 -2.164122779 0.320422904 VSGRT(ph)SPPLLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VSGRTSPPLLDR 12 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VS(0.051)GRT(0.594)S(0.355)PPLLDR;VS(0.141)GRT(0.64)S(0.219)PPLLDR;VS(0.004)GRT(0.498)S(0.498)PPLLDR 100.4 0.0080902 3701470000 1176540 1954460 1316690 1552890 2268130 795480 1425180 1265600 4066390 TRUE FALSE 1102902.462 2099170.252 1347922.509 1592739.786 2090000.219 1025122.162 1211487.49 1423612.946 3387683.239 0.325562452 0.619647737 0.397889181 0.470156055 0.616940862 0.30260272 0.357615339 0.420232013 1 21.69186755 -1.790431318 4.679290884 1.058032208 0.444988588 0.725664773 0.108376129 0.051495129 0.002306282 0.082357143 0.024452664 0.016202002 1.790431318 -0.613043619 VSGRTS(ph)PPLLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSGRTSPPLLDR 12 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VS(0.039)GRT(0.45)S(0.511)PPLLDR;VS(0.016)GRT(0.475)S(0.51)PPLLDR 87.974 0.0062055 3154140000 770330 1287100 949330 1039530 1487410 506620 964560 851260 2570820 TRUE FALSE 722116.4204 1382398.223 971848.5559 1066206.1 1370594.819 652872.9697 819933.1825 957541.6849 2141733.534 0.337164455 0.645457617 0.453767259 0.497823881 0.639946472 0.304833892 0.382836226 0.447087217 1 21.03034757 -1.27433189 3.76067567 1.000983032 0.471570484 0.691379774 0.112513048 102449891.8 190424473.7 1188100.149 0.027226796 0.053170177 1.27433189 -0.529412547 VSGS(ph)PEQAVEENLSSYSLDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSGSPEQAVEENLSSYSLDRR 21 1 Q9Y6A5;A0A494BZT8;E7EMT0;C9JA91 Q9Y6A5 TACC3 Transforming acidic coiled-coil-containing protein 3 1 VS(0.044)GS(0.956)PEQAVEENLSSYSLDRR 65.836 0.014324 76931000 18219 25854 24086 24834 24983 17289 25462 20146 24559 TRUE FALSE 17078.70531 27768.25706 24657.33129 25471.28248 23020.93596 22280.05364 21644.20948 22661.27245 20459.94424 0.834738605 1.357201013 1.205151441 1.24493411 1.125171002 1.088959646 1.057882134 1.107592092 1 14.32051459 2.434909618 2.758901578 1.066719384 1.200495447 0.067661788 0.136371704 0.469420574 7.309907467 0.048305432 0.040026601 272.2134737 -2.434909618 0.133776064 VSGTLDT(ph)PEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSGTLDTPEK 10 0 Q9BYG3;H7BZL0;C9J808 Q9BYG3 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 1 VSGTLDT(1)PEK 247.67 1.11E-11 192790000 912060 455860 680550 601750 525450 610540 807810 512000 357590 TRUE FALSE 854975.7927 489612.3487 696692.9674 617191.9238 484183.2766 786792.9867 686686.3898 575924.3271 297905.9189 2.869952352 1.64351333 2.33863419 2.071767913 1.625289213 2.641078733 2.305044466 1.933242311 1 18.18449726 3.022969627 24.01545557 2.046762404 2.160906854 0.047120251 0.527908673 1101.684364 1151832.743 0.1418302 0.169506951 1054.313159 -3.022969627 0.114144449 VSGTLDT(ph)PEKTVDSQGPTPVCTPTFLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VSGTLDTPEKTVDSQGPTPVCTPTFLER 28 1 Q9BYG3;H7BZL0;C9J808 Q9BYG3 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 1 VSGT(0.003)LDT(0.993)PEKT(0.004)VDSQGPTPVCTPTFLER;VSGTLDT(0.996)PEKT(0.004)VDSQGPTPVCTPTFLER;VSGTLDT(1)PEKTVDSQGPTPVCTPTFLER;VSGT(0.004)LDT(0.979)PEKT(0.017)VDSQGPTPVCTPTFLER 386.87 1.42E-145 2298750000 2944910 1772100 2330290 2216590 2309730 1932690 2931550 1883900 1937130 TRUE FALSE 2760593.34 1903308.128 2385565.579 2273471.452 2128333.123 2490626.228 2491991.293 2119109.062 1613810.489 1.71060565 1.17938763 1.478219156 1.408759869 1.318824693 1.543320139 1.544166003 1.313108991 1 20.62203974 0.94855627 8.05765471 1.000002616 1.433613245 0.503839889 0.141971062 0.792537536 123.6922726 0.130369131 0.032647271 8.882930612 -0.94855627 0.433610629 VSHEQFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VSHEQFR 7 0 O96013;O96013-4;O96013-2;O96013-3 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ;; 101.33 0.0091406 271063000 1193720 1326200 1224640 1185760 1439350 850121 1329980 1185090 1523010 FALSE TRUE 1119007.196 1424393.228 1253689.039 1216188.609 1326309.257 1095537.132 1130561.846 1333051.095 1268809.792 0.881934552 1.12262156 0.988082727 0.958527131 1.04531764 0.863436852 0.891041237 1.050631153 1 20.27504438 2.256755498 24.99953185 0.93390349 1.012731402 0.048931136 0.080683209 399.6589105 549125.1487 0.026781412 0.022365843 180.6156996 -2.256755498 0.078827912 VSHLLGINVTDFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSHLLGINVTDFTR 14 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 246.63 9.49E-18 4504400000 1568980 2189790 1711050 1639570 1966240 1229340 1884230 1753540 1790170 FALSE TRUE 1470780.343 2351924.33 1751636.914 1681644.142 1811819.442 1584230.501 1601707.204 1972473.329 1491379.062 0.98618814 1.577013108 1.174508184 1.127576607 1.214861793 1.062258779 1.073977263 1.322583493 1 20.50821556 3.625444821 4.699587563 1.133315942 1.338565936 0.095358617 0.166644906 0.289322471 10.50349053 0.040657253 0.064622637 4221.286427 -3.625444821 0.205249994 VSHS(ph)PPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSHSPPPK 8 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 VS(0.025)HS(0.975)PPPK 58.592 0.066972 1011400000 1010500 807730 905960 854610 1012000 714130 1040500 909880 1211000 TRUE FALSE 947254.6088 867535.1696 927449.799 876540.7395 932521.6022 920287.7381 884486.6845 1023480.521 1008876.277 0.938920491 0.859902438 0.919289927 0.868828775 0.924317108 0.912190879 0.87670481 1.014475753 1 19.94431783 1.234307809 24.99957805 1.007237946 0.897329053 0.751234015 0.02561361 47.87738345 281422.3977 0.019400208 0.00552338 17.15172515 -1.234307809 -0.109908893 VSHYIINSSGPRPPVPPSPAQPPPGVS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSHYIINSSGPRPPVPPSPAQPPPGVSPSR 30 1 P46108-2;P46108;I3L297 P46108-2 CRK Adapter molecule crk 1 VSHYIINSSGPRPPVPPSPAQPPPGVS(0.822)PS(0.178)R;VSHYIINSSGPRPPVPPSPAQPPPGVS(0.79)PS(0.21)R 141.03 3.21E-08 793930000 111204 124456 114087 115320 125942 106402 128816 106442 137738 TRUE FALSE 104243.9401 133670.8517 116793.1975 118279.3064 116051.0233 137118.5301 109501.2367 119731.518 114748.638 0.908454706 1.164901424 1.017817724 1.030768718 1.011349898 1.194946908 0.95427047 1.043424307 1 16.8081175 1.62726441 25 0.999126286 1.061582928 0.087427915 0.082511475 1.802412478 2317.076129 0.034752207 0.019234517 42.39009699 -1.62726441 0.062456642 VSIGNITLS(ph)PAISR ddPTM_SK-BR-3_Pertuzumab_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 267.92 4.69E-25 864540000 962290 1070500 1112800 1061730 1108590 909810 1165060 949220 917770 TRUE FALSE 902061.9866 1149760.934 1139196.142 1088975.789 1021525.813 1172457.377 990370.0689 1067732.206 764588.258 1.179800994 1.503764833 1.48994721 1.424264338 1.336046954 1.533449363 1.295298559 1.396479995 1 19.54432352 -0.009039442 0.657768732 0.979557587 1.427270925 0.564172163 0.107626721 3.08099427 1.461275277 0.259947937 0.037591629 0.979401035 0.009039442 0.447713338 VSILESLDKWER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSILESLDKWER 12 1 P10644;P10644-2;K7EPB2;K7EM13 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 0 ; 126.51 0.00026109 223077000 544220 590140 522220 470270 694550 419440 551970 574940 721980 FALSE TRUE 510158.2417 633834.5796 534607.305 482337.9244 640002.8447 540525.519 469207.2227 646722.5246 601476.8738 0.848175988 1.05379709 0.888824373 0.801922643 1.064052289 0.898663843 0.780091876 1.075224257 1 19.19814974 3.739539445 23.76919472 0.911174549 0.967364871 0 0.110365597 739.9075717 1416213.123 0.026620915 0.04752138 5489.584125 -3.739539445 0.056190322 VSISEGDDKIEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VSISEGDDKIEYR 13 1 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ;;;; 210.14 2.95E-08 5666630000 8541360 5927770 7086820 6678610 7221240 5270810 8977580 6262390 8902490 FALSE TRUE 8006771.524 6366668.259 7254922.717 6849994.439 6654112.939 6792407.283 7631475.223 7044263.177 7416606.907 1.079573399 0.858434098 0.978199709 0.923602198 0.897190996 0.915837575 1.028971242 0.949795946 1 22.82232787 1.748668183 25 0.99376973 0.934200238 0.12370916 0.061319442 4.272832388 10589.90897 0.025593936 0.01419303 56.06194787 -1.748668183 -0.059569492 VSIVNHLEFLRDEELEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSIVNHLEFLRDEELEER 18 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 148.85 3.99E-08 40128000 35453 46370 44879 46713 49587 36873 48466 44730 48111 FALSE TRUE 33234.06002 49803.28305 45943.55107 47911.73466 45692.63704 47517.63652 41198.97324 50314.63896 40080.96329 0.829173186 1.242567018 1.146268635 1.195373832 1.140008455 1.18554128 1.027893789 1.255325093 1 15.29062956 -0.890691007 7.669704873 1.000000568 1.136566374 0.091698576 0.123649555 1.57E-09 0 0.105667611 0.024906095 0.128620144 0.890691007 0.136565806 VSKEEEEKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSKEEEEKER 10 2 P23921;E9PL69 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 79.82 0.014544 560190000 1045100 555640 776250 713480 669600 441810 903150 591010 989920 FALSE TRUE 979689.0566 596780.1637 794663.0166 731789.1047 617012.317 569353.3748 767731.0419 664798.8995 824695.9569 1.187939687 0.723636582 0.963583015 0.887344116 0.748169446 0.690379733 0.930926162 0.806113931 1 19.65350281 4.751043372 24.44009732 0.840790582 1.187939985 0.520720719 0.103734125 1157.786199 2266783.326 0.023194009 0.40126496 56369.39481 -4.751043372 0.347149402 VSLDVNHFAPDELTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VSLDVNHFAPDELTVK 16 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;; 219.97 1.19E-14 8954490000 10828110 9747190 9801090 9594610 12492740 7065550 11558220 11118760 16751880 FALSE TRUE 10150397.92 10468882.09 10033576.48 9840823.936 11511610.59 9105259.585 9825172.212 12506961.66 13955883.01 0.727320365 0.750141147 0.718949598 0.705138036 0.824857201 0.652431636 0.704016522 0.896178454 1 23.73437007 1.075823825 3.752261997 0.997196087 0.725856798 0.825311805 0.043784426 0.074977437 2.009180309 0.039830766 0.010303758 11.90758868 -1.075823825 -0.27133929 VSLEPHQGPGT(ph)PESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VSLEPHQGPGTPESK 15 0 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 VSLEPHQGPGT(1)PESK;VSLEPHQGPGT(1)PESK;VSLEPHQGPGT(1)PESK;VSLEPHQGPGT(1)PESK;VSLEPHQGPGT(0.999)PES(0.001)K;VSLEPHQGPGT(1)PESK 193.71 3.01E-07 8564960000 2691460 2127840 2544490 2288220 2628080 2095920 3388630 2292060 3150130 TRUE FALSE 2523006.323 2285387.488 2604846.504 2346939.599 2421681.198 2700978.08 2880536.39 2578228.736 2624352.952 0.961382241 0.870838462 0.99256714 0.894292666 0.922772677 1.029197722 1.097617753 0.982424538 1 21.32353033 2.207441184 5.726359411 1.043081101 0.927547205 0.532467381 0.045111222 0.116974802 10.5050304 0.015980364 0.012015389 161.2282663 -2.207441184 -0.115533896 VSLEPHQGPGTPESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSLEPHQGPGTPESK 15 0 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 107.34 0.0011653 227160000 94580 116890 123860 126310 147070 91259 131230 124110 159680 FALSE TRUE 88660.40663 125544.6572 126798.0177 129551.3284 135519.7155 117603.9918 111553.2798 139605.4067 133028.3764 0.666477401 0.943743437 0.95316519 0.973862359 1.018727877 0.884051922 0.838567551 1.049440807 1 17.0213745 4.7385571 8.333440336 0.945602287 0.664627823 0.678362782 0.062529649 0.056183204 56.49630026 0.015072144 0.08884071 54771.81088 -4.7385571 -0.280974463 VSLQVHPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 VSLQVHPDR 9 0 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 ;;;;;; 149.33 8.79E-05 5389800000 3213047 4333180 3719730 3655990 4506530 3211549 4233540 3958480 4253660 FALSE TRUE 3011948.124 4654013.156 3807963.752 3749808.893 4152605.312 4138671.061 3598759.979 4452704.942 3543696.666 0.849945243 1.313321538 1.074573845 1.058163056 1.171828659 1.167896536 1.015538382 1.256514132 1 21.75682369 -1.000247919 4.635326761 0.999997158 1.122436467 0.066755406 0.129537942 3.38E-06 7.30E-07 0.111496505 0.026279368 0.099942931 1.000247919 0.122439309 VSMPDVELNLKS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSMPDVELNLKSPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VSMPDVELNLKS(1)PK;VSMPDVELNLKS(1)PK 194.19 1.05E-07 1963380000 4625400 2304900 3687000 4696800 4883900 1799930 3251300 2020550 4107000 TRUE FALSE 4335904.471 2475557.194 3774457.381 4817327.84 4500338.195 2319540.572 2763797.749 2272820.115 3421515.168 1.267246894 0.723526588 1.103153777 1.407951625 1.315305639 0.677927894 0.807770129 0.664272991 1 21.70620391 2.226117022 24.9997604 0.772021555 1.106343027 0.438034214 0.20569597 258.3005775 518934.3624 0.082157395 0.061098651 168.3127525 -2.226117022 0.334321473 VSNAS(ph)EMY(ph)T(ph)QK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSNASEMYTQK 11 0 P53804-3;P53804-2;P53804 P53804-3 TTC3 E3 ubiquitin-protein ligase TTC3 3 VS(0.4)NAS(0.602)EMY(1)T(0.999)QK 43.991 0.078712 344290000 67207 69009 106160 94008 56035 103110 106860 59289 34009 TRUE FALSE 63000.63384 74118.49816 108678.1653 96420.40444 51634.23713 132876.1831 90837.33504 66691.36216 28332.67819 2.223603198 2.616007483 3.835788646 3.403151787 1.822426979 4.689856082 3.206097723 2.35386721 1 14.79017936 0.9462651 3.326408611 1.005148575 3.175932011 0.412120646 0.805520649 0.25527654 7.163487635 0.727344585 0.188997638 8.836191097 -0.9462651 2.170783436 VSNEEVTEELLHVNDDLNNVFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VSNEEVTEELLHVNDDLNNVFLR 23 0 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-4;Q6ZVM7-3;Q6ZVM7-5;F5H3S6;B7Z2U2 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 0 ;;; 283.64 3.95E-52 233560000 173832 184165 177141 183105 203696 162555 207434 181309 225406 FALSE TRUE 162952.1654 197800.7682 181342.8682 187803.7843 187698.5378 209481.9896 176331.1974 203945.8278 187784.2824 0.867762538 1.053340384 0.965697799 1.000103853 0.999543388 1.115545918 0.939009352 1.08606442 1 17.51871679 2.464603157 24.99459311 1.027640285 0.98587376 0.153216215 0.065719757 569.869796 1137838.507 0.020799818 0.017413219 291.4762392 -2.464603157 -0.041766525 VSNGS(ph)PSLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSNGSPSLER 10 0 P46527;E7ES52 P46527 CDKN1B Cyclin-dependent kinase inhibitor 1B 1 VS(0.066)NGS(0.896)PS(0.037)LER 115.35 0.0024346 0 84743 83677 75093 84292 89197 78154 98921 79684 101010 TRUE FALSE 79439.0869 89872.53215 76874.24142 86455.07543 82191.82742 100715.7911 84088.71439 89632.72281 84150.77845 0.944008937 1.067994067 0.913529772 1.027382955 0.97672094 1.196849191 0.999262466 1.065144309 1 16.360689 VSNLQVS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSNLQVSPK 9 0 O00443;A0A0C4DGF9;O00443-2 O00443 PIK3C2A Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha 1 VSNLQVS(1)PK 128.68 0.00043079 117310000 219820 189140 221990 334580 263300 132040 153240 88328 145060 TRUE FALSE 206061.8586 203144.1224 227255.7076 343165.8892 242621.4801 170157.8045 130263.0846 99355.94523 120848.5489 1.705124807 1.680981065 1.880500095 2.839635994 2.007649098 1.408025219 1.077903589 0.822152572 1 16.88284062 1.987014289 2.43962563 0.965907026 1.991988511 0.688979841 0.325909071 0.191843142 2.129732125 0.187156833 0.101993722 97.05418996 -1.987014289 1.026081484 VSNQDSKS(ph)PLGFYCDQNPVESSMCQSNSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSNQDSKSPLGFYCDQNPVESSMCQSNSR 29 1 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 VSNQDS(0.205)KS(0.795)PLGFYCDQNPVESSMCQSNSR 272.54 2.80E-71 285560000 183640 152660 163600 167580 206280 106070 201160 146830 261500 TRUE FALSE 172146.3002 163963.1052 167480.6693 171880.3865 190079.6009 136690.6871 170997.9255 165162.0487 217853.9606 0.790191281 0.752628526 0.768774957 0.788970676 0.872509273 0.627441827 0.784919976 0.758131953 1 17.73300182 -2.044382059 2.424717299 1.300389958 0.765551623 0.597022812 0.059886375 4978415.856 1839055.108 8293692.094 0.013576394 0.009028549 2.044382059 -0.534838335 VSNS(ph)PEPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSNSPEPQK 9 0 O60271;O60271-3;D6RHI8 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 VS(0.005)NS(0.995)PEPQK 134.75 0.00025178 210980000 814600 611920 652350 659450 622140 559580 778660 570200 651430 TRUE FALSE 763615.6401 657227.1935 667824.0501 676372.6034 573279.634 721121.662 661907.1617 641390.7252 542702.1246 1.40706219 1.211027493 1.230553594 1.246305428 1.05634308 1.32876145 1.21965095 1.181846719 1 19.04980103 -5 0.164455972 0.136467354 1.290506281 0.469899417 0.085208405 125.0816045 1.164722872 35.35607631 0.314807147 1.00E-05 5 1.154038927 VSPAHS(ph)PPENGLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSPAHSPPENGLDK 14 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 VSPAHS(1)PPENGLDK 96.153 0.0022445 124160000 71995 74283 72976 77897 102190 71593 92313 72901 107710 TRUE FALSE 67488.96146 79782.99061 74707.02518 79895.9689 94164.40961 92260.73688 78471.52264 82002.85032 89732.50517 0.752112753 0.889120285 0.832552541 0.890379342 1.049390179 1.028175205 0.87450498 0.913858921 1 16.45334307 2.978518764 7.004932696 0.963482867 0.841921017 0.54707129 0.0611647 0.159796883 34.4556893 0.018879105 0.020844578 951.7409669 -2.978518764 -0.12156185 VSPAS(ph)PAGS(ph)PSADFAVHGESLGDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSPASPAGSPSADFAVHGESLGDR 24 0 A0A0A0MRP9;Q96C92-3;Q96C92;Q96C92-2;Q96C92-4 A0A0A0MRP9;Q96C92-4 SDCCAG3 Serologically defined colon cancer antigen 3 2 VSPAS(1)PAGS(0.982)PS(0.018)ADFAVHGESLGDR;VS(0.004)PAS(0.996)PAGS(0.969)PS(0.031)ADFAVHGESLGDR 287.17 3.68E-53 507270000 372430 366980 382240 408910 482740 374840 473510 363260 520580 TRUE FALSE 349120.2711 394151.581 391306.9133 419403.3229 444827.5477 483050.223 402511.5714 408613.8106 433691.8349 0.804996182 0.908828687 0.902269496 0.967053767 1.025676556 1.113809816 0.928105025 0.942175475 1 18.72631076 3.262866854 2.047809177 1.001093449 0.876272135 0.529672972 0.056315223 0.276757688 2.36968926 0.018026637 0.025455157 1831.752759 -3.262866854 -0.124821314 VSPGLPS(ph)PNLENGAPAVGPVQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSPGLPSPNLENGAPAVGPVQPR 23 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 VSPGLPS(1)PNLENGAPAVGPVQPR;VS(0.01)PGLPS(0.99)PNLENGAPAVGPVQPR 271.34 1.36E-51 1201230000 217200 224265 177858 234580 299840 168931 221425 192375 232300 TRUE FALSE 203605.8397 240869.8139 182076.8758 240599.7199 276291.7759 217698.6373 188224.3769 216393.4422 193527.6293 1.052076339 1.244627523 0.940831428 1.243231888 1.427660624 1.124896937 0.972596924 1.118152705 1 17.56218002 1.987422648 24.8093304 1.032590524 1.169893719 0.213542488 0.131546416 951.9032074 1877666.065 0.053650769 0.036516969 97.14549097 -1.987422648 0.137303195 VSPNELILGWYATGHDITEHSVLIHEYYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VSPNELILGWYATGHDITEHSVLIHEYYSR 30 0 O00303 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 ;; 214.29 6.79E-35 978310000 321127 456335 349729 265911 487770 283683 421999 423717 212132 FALSE TRUE 301028.2343 490122.5182 358024.737 272734.7264 449462.5118 365577.6769 358724.1676 476619.0002 176725.7988 1.703363269 2.773350137 2.025877034 1.543264924 2.543276165 2.068615219 2.02983475 2.696940704 1 17.43115314 -1.398561575 5.286835062 0.999213696 2.189313859 0.458122141 0.400598614 0.003426834 0.000389842 0.358006462 0.084335006 0.039942793 1.398561575 1.190100163 VSPPAPGS(ph)APET(ph)PEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSPPAPGSAPETPEDK 16 0 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 2 VSPPAPGS(1)APET(1)PEDK;VSPPAPGS(1)APET(1)PEDK 291.38 8.18E-45 471250000 877790 577100 697020 647830 818710 508020 862290 668340 946150 TRUE FALSE 822850.6908 619829.0845 713553.6436 664454.4146 754411.8191 654677.127 732997.6196 751783.7202 788231.4526 1.043920143 0.786354163 0.905259034 0.842968664 0.957094286 0.830564582 0.929926885 0.953760114 1 19.58825979 1.222471889 1.870301449 0.996145051 0.883465188 0.176759853 0.07174984 0.439806545 2.733931651 0.059347031 0.017363166 16.69059769 -1.222471889 -0.112679863 VSPS(ph)PSQESLSSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSPSPSQESLSSSK 14 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 VS(0.105)PS(0.895)PSQESLSSSK;VS(0.01)PS(0.987)PS(0.003)QESLSSSK 325.77 4.64E-57 776370000 1000210 598840 762420 671190 658050 559200 904090 624860 430540 TRUE FALSE 937608.6415 643178.7367 780504.9624 688413.8717 606369.4074 720631.9621 768530.0977 702875.1465 358680.0926 2.614052636 1.793182142 2.176047622 1.919297686 1.690557742 2.009121713 2.142661702 1.959615716 1 18.45233815 -1.970652062 1.167666507 0.055211983 2.022348403 0.628310411 0.250664878 3654.336202 727.6669778 9329.12385 0.066146313 0.010699117 1.970652062 1.96713642 VSPSTSYT(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSPSTSYTPSR 11 0 Q9BTE3;Q9BTE3-2 Q9BTE3 MCMBP Mini-chromosome maintenance complex-binding protein 1 VSPSTSYT(0.956)PS(0.044)R;VSPSTSYT(0.999)PS(0.001)R 184.87 5.27E-05 458560000 323530 360800 382220 350100 396140 309500 417960 350990 442890 TRUE FALSE 303280.8348 387514.0074 391286.4389 359084.1587 365028.7624 398847.6257 355290.7782 394811.8741 368968.7978 0.821968786 1.050262271 1.060486527 0.973210095 0.989321494 1.080979281 0.962929061 1.07004136 1 18.49313929 4.74299711 24.97461465 1.024558753 0.821968704 0.699590455 0.041477065 246.1052444 1385365.059 0.009463613 0.074638786 55334.64267 -4.74299711 -0.202590049 VSPTTSPRPAS(ph)PVPGSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSPTTSPRPASPVPGSER 18 1 A0A5E8;Q99501;Q99501-4;Q99501-2 A0A5E8 GAS2L1 GAS2-like protein 1 1 VSPTTSPRPAS(0.997)PVPGS(0.003)ER;VSPTTS(0.001)PRPAS(0.998)PVPGS(0.001)ER 119.5 4.37E-05 638420000 262370 324180 306870 317760 329540 253640 351790 279800 407670 TRUE FALSE 245948.73 348182.6245 314149.1013 325914.2596 303659.2577 326861.7505 299042.3554 314733.6459 339627.2434 0.724172559 1.025190503 0.924982043 0.959623428 0.894095699 0.962413225 0.880501671 0.926703178 1 18.37359266 -0.438059221 0.007661356 1.906790072 1.59E-06 0.115208528 0.077723942 24966.79093 46.61089828 6005.080176 5597.365469 0.364704212 0.438059221 -1.906788478 VSQGSAESLS(ph)PSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSQGSAESLSPSFR 14 0 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 VSQGSAES(0.003)LS(0.996)PS(0.001)FR 156.17 5.92E-06 99297000 157630 152900 181490 195490 223870 106500 109120 76147 114380 TRUE FALSE 147764.2197 164220.8751 185795.0285 200506.6044 206288.1532 137244.8211 92758.46902 85654.12057 95289.23908 1.550691569 1.723393708 1.949800736 2.104189374 2.164863055 1.440297167 0.973441177 0.898885555 1 16.54002568 1.937312439 3.120260547 0.960586985 1.889727223 0.849552057 0.180253529 0.099186659 1.766121694 0.096546303 0.053570863 86.55904148 -1.937312439 0.929140238 VSQGSKDPAEGDGAQPEETPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VSQGSKDPAEGDGAQPEETPR 21 1 Q14697;F5H6X6 Q14697 GANAB Neutral alpha-glucosidase AB 0 ;; 180.03 5.05E-17 1800110000 2096750 1678910 1836330 1812250 1947140 1371070 2327650 1552840 1838520 FALSE TRUE 1965518.16 1803218.243 1879888.615 1858755.403 1794219.479 1766875.652 1978640.491 1746715.492 1531659.135 1.283260822 1.177297352 1.227354424 1.213556829 1.171422178 1.153569754 1.291828219 1.140407453 1 20.54666384 0.987564976 22.86747985 0.999999997 1.213356954 0.707553552 0.044564047 104.7778896 192683.2489 0.039944619 0.009986155 9.717733307 -0.987564976 0.213356957 VSQGVEDGPDTKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSQGVEDGPDTKR 13 1 Q9UBE0;M0QX65;B3KNJ4;Q9UBE0-2;Q9UBE0-3;A0A590UK93;A0A590UKC5;M0QYM8;M0R054 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 ; 125.73 0.00031557 1396410000 1061120 927530 942040 1022990 1146540 798710 1199850 877870 1421290 FALSE TRUE 994706.3934 996205.2863 964385.6337 1049241.655 1056495.373 1029284.611 1019943.631 987474.0019 1184067.517 0.840075738 0.841341623 0.814468449 0.886133299 0.892259401 0.869278649 0.861389757 0.833967648 1 20.17531992 -5 0.250691158 1.887731579 0.83995394 0.770365325 0.024653146 90.45550979 0.896568976 41.20004401 0.037144677 1.00E-05 5 -1.047777639 VSQPIEGHAASFAQFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSQPIEGHAASFAQFK 16 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 189.81 9.58E-10 1000860000 1042850 1202920 1097820 1111740 1339020 862630 1411080 1208480 1328300 FALSE TRUE 977579.88 1291985.448 1123860.809 1140269.131 1233858.771 1111657.277 1199501.654 1359361.388 1106598.149 0.883410008 1.167529017 1.015599755 1.03042747 1.115001658 1.004571785 1.083954148 1.228414659 1 20.07769998 1.468183927 9.56139104 1.128095553 1.051707566 0.095145046 0.092015113 0.216764815 79.64291092 0.04488678 0.020470402 29.38894031 -1.468183927 -0.076387987 VSRPENEQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VSRPENEQLR 10 1 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;;; 140.14 3.63E-05 1310290000 469616 772850 403649 422798 822000 288529 403721 693200 750250 FALSE TRUE 440223.5728 830072.6181 413223.7449 433647.7125 757443.4358 371822.6384 343186.784 779747.5459 625028.4282 0.70432568 1.328055782 0.66112792 0.693804782 1.211854376 0.594889163 0.54907388 1.247539329 1 19.25356228 3.916196385 8.729405198 0.810334952 1.05209757 0.036754052 0.285961364 0.646871605 86.74345103 0.068856957 0.124699625 8245.108689 -3.916196385 0.241762618 VSS(ph)PLASFLQQQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSSPLASFLQQQR 13 0 Q8NEV8-2;Q8NEV8;E9PPH6 Q8NEV8-2 EXPH5 Exophilin-5 1 VS(0.001)S(0.999)PLASFLQQQR;VS(0.001)S(0.999)PLASFLQQQR 283.82 1.35E-32 423050000 419790 451870 389270 404810 480100 295590 407120 369340 386140 TRUE FALSE 393516.0932 485326.925 398503.6682 415198.1099 442394.8826 380922.0345 346076.1355 415452.912 321690.7394 1.223274546 1.508675462 1.2387788 1.290674735 1.375217961 1.184124962 1.075803849 1.291466807 1 18.29531488 1.729378677 0.386353384 1.003190598 1.394328877 0.453881445 0.105539604 0.88098376 0.374262464 0.124390453 0.110596908 53.62640413 -1.729378677 0.391138279 VSS(ph)PPNAMMSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VSSPPNAMMSSR 12 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 VS(0.016)S(0.984)PPNAMMSSR;VS(0.278)S(0.722)PPNAMMSSR;VS(0.027)S(0.973)PPNAMMSSR 97.716 0.018627 65579000 520127 492233 492512 500057 528429 361281 511808 414304 515315 TRUE FALSE 487573.1795 528678.4435 504194.6172 512889.3092 486928.3179 465576.9598 435067.1418 466030.7664 429305.5974 1.135725186 1.231473446 1.174442216 1.194695136 1.134223082 1.084488445 1.013420613 1.085545516 1 18.71164546 2.280334561 1.672042327 1.03314192 1.191492283 0.804002276 0.032849808 0.135094486 0.757973421 0.015421911 0.009932718 190.6929165 -2.280334561 0.158350363 VSS(ph)PSPELGTTPASIFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VSSPSPELGTTPASIFR 17 0 A0A5E8;Q99501 A0A5E8 GAS2L1 GAS2-like protein 1 1 VS(0.008)S(0.835)PS(0.157)PELGTTPASIFR;VS(0.011)S(0.988)PSPELGTTPASIFR;VS(0.02)S(0.69)PS(0.289)PELGTTPASIFR;VSS(0.996)PS(0.003)PELGTTPASIFR 279.29 7.62E-36 577179000 533939 505053 539034 556966 610376 503299 645064 533335 738990 TRUE FALSE 500520.7111 542447.6496 551820.141 571258.6905 562439.5311 648593.2509 548342.6417 599923.0488 615647.7949 0.812998463 0.881100613 0.896324401 0.927898541 0.913573533 1.05351348 0.89067588 0.974458211 1 19.23174571 8 0.231464523 0.989363757 0.024838911 0.584245593 0.043586438 35.14424432 0.462331092 0.057666661 12.8758431 99999999.97 -8 -0.964524846 VSS(ph)PTKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VSSPTKPK 8 1 Q8WUA4;A0A087WZD8;Q8WUA4-2 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 VS(0.493)S(0.506)PT(0.001)KPK;VS(0.031)S(0.949)PT(0.02)KPK;VS(0.089)S(0.909)PT(0.001)KPK 120.45 0.00090779 1842960000 5493420 2678778 3869905 3647030 3871830 2573144 4902160 2930014 4767340 TRUE FALSE 5149596.648 2877117.51 3961700.974 3740618.964 3567752.09 3315968.901 4167126.617 3295832.698 3971640.156 1.296591948 0.724415455 0.997497462 0.941832295 0.898306984 0.834911717 1.049220587 0.82984172 1 21.92130349 -1.101070863 4.606014351 1.000004826 0.933309766 0.005225772 0.154507029 6.68E-06 1.30E-06 0.130593834 0.030779035 0.079237203 1.101070863 -0.06669506 VSS(ph)PVFGATSSIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VSSPVFGATSSIK 13 0 F6Q6H0;I6L8A6;Q99708-3;Q99708;Q99708-2 F6Q6H0 RBBP8 DNA endonuclease RBBP8 1 VSS(1)PVFGATSSIK;VS(0.093)S(0.907)PVFGATSSIK;VS(0.002)S(0.998)PVFGATSSIK;VSS(1)PVFGATSSIK 256.13 7.75E-24 536601000 2498670 1967510 2124520 1967610 2684900 1581170 2572260 2261260 3154400 TRUE FALSE 2342282.705 2113186.488 2174914.618 2018102.204 2474038.784 2037628.111 2186573.493 2543583.289 2627910.262 0.891310004 0.804131906 0.827621342 0.767949436 0.94144721 0.775379639 0.8320579 0.967911015 1 21.32548458 1.19738759 4.48841806 0.994786543 0.828693853 0.594593116 0.051522921 0.121656006 4.998823038 0.041731825 0.011257179 15.75388207 -1.19738759 -0.16609269 VSS(ph)QAEDTSSSFDNLFIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSSQAEDTSSSFDNLFIDR 19 0 H8Y6P7;P0CAP2-3;P0CAP2;Q9BZD3 H8Y6P7 GCOM1;POLR2M;GCOM2 DNA-directed RNA polymerase II subunit GRINL1A;Putative GRINL1B complex locus protein 2 1 VS(0.028)S(0.972)QAEDTSSSFDNLFIDR;VS(0.024)S(0.976)QAEDTSSSFDNLFIDR 181.4 3.31E-14 59302000 85467 89893 106705 160180 161305 62312 56305 35257 58844 TRUE FALSE 80117.77303 96548.77125 109236.093 164290.49 148636.756 80300.46285 47862.58796 39658.91406 49022.55625 1.63430427 1.969476474 2.228282271 3.351324422 3.032007454 1.638030919 0.97633807 0.808993188 1 15.58115809 1.95848937 3.613438356 0.958304486 2.391275281 0.662353869 0.492653976 0.164869366 4.214637582 0.255726065 0.149539253 90.88440535 -1.95848937 1.432970796 VSS(ph)SGLTDSLFILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSSSGLTDSLFILK 14 0 Q6P3S1 Q6P3S1 DENND1B DENN domain-containing protein 1B 1 VS(0.27)S(0.728)S(0.002)GLTDSLFILK 183.81 8.63E-08 0 129080 123310 117440 146230 180010 100900 126970 93573 122180 TRUE FALSE 121001.1132 132440.0007 120225.7323 149982.5094 165872.7407 130028.192 107932.0272 105255.795 101787.3687 1.188763545 1.301143771 1.181145891 1.473488423 1.629600439 1.277449193 1.060367594 1.034075214 1 16.63519902 1.744434229 3.779323502 1.028533305 1.337454476 0.560381834 0.130712785 0.175695211 5.356115282 0.076525839 0.03787204 55.5180533 -1.744434229 0.308921172 VSS(ph)SPGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSSSPGVK 8 0 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 VS(0.014)S(0.623)S(0.362)PGVK 85.716 0.01848 0 758900 532380 601320 573480 636470 488260 801740 568930 798690 TRUE FALSE 711401.8037 571797.9691 615583.5944 588196.4677 586484.2136 629212.7358 681526.53 639962.1629 665383.4793 1.069160606 0.859351016 0.925156115 0.883996201 0.881422866 0.945639252 1.024261274 0.961794488 1 19.34382652 1.963383211 5.825112564 0.995640407 0.913282168 0.224714893 0.058894912 0.234666926 22.22144118 0.023218984 0.014594408 91.91432679 -1.963383211 -0.082358239 VSS(ph)SPQKEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSSSPQKEGR 10 1 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 VSS(0.5)S(0.5)PQKEGR 113.22 0.0039893 24070000 114620 99707 103640 102080 124040 79170 128170 88872 178580 TRUE FALSE 107446.1388 107089.41 106098.3897 104699.5456 114298.3988 102025.0938 108952.0984 99967.86483 148773.8443 0.722211215 0.719813422 0.713152169 0.703749682 0.768269445 0.685773055 0.73233369 0.671945161 1 17.18276139 -1.35529829 3.256981846 1.002254743 0.716170923 0.922618798 0.025967058 4681309.839 6308974.476 100217.4735 0.005310201 0.044126726 1.35529829 -0.286083821 VSSDNVADLHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSSDNVADLHEK 12 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 151.99 6.94E-05 338690000 497350 416380 434590 413190 500300 326800 526640 411710 516790 FALSE TRUE 466221.7513 447209.2084 444898.68 423793.1549 461008.4561 421141.8548 447675.2211 463112.8998 430534.4104 1.082890798 1.038730465 1.033363813 0.984342122 1.070781905 0.978183961 1.03981287 1.075669885 1 18.71576902 5.183610868 1.266447974 1.026325388 1.179915975 0.230415489 0.03239526 5.56701562 3.598017982 0.008058987 1.460725123 152619.7957 -5.183610868 0.153590587 VSSFEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSSFEEK 7 0 P40926;G3XAL0;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 ; 101.33 0.021265 944450000 1455140 1158610 1264560 1124820 1513740 1036930 1285430 1251630 2000320 FALSE TRUE 1364065.385 1244394.69 1294555.96 1153684.786 1394856.967 1336274.858 1092691.705 1407898.761 1666453.669 0.818543839 0.746732245 0.776832854 0.692299346 0.83702115 0.801867392 0.65569882 0.844847226 1 20.66834978 0.989542217 24.12381337 1.000000004 0.758055814 0.658960598 0.054868983 171.1676699 394847.7216 0.049978425 0.012494606 9.76207673 -0.989542217 -0.24194419 VSSPSCDSQGLHAEEAPSSEPQS(ph)PVAQTSGWPACSTPLPLVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSSPSCDSQGLHAEEAPSSEPQSPVAQTSGWPACSTPLPLVSR 43 0 Q96RE7;K7ENW4 Q96RE7 NACC1 Nucleus accumbens-associated protein 1 1 VSSPSCDSQGLHAEEAPS(0.001)S(0.003)EPQS(0.996)PVAQTSGWPACSTPLPLVSR;VSSPSCDSQGLHAEEAPSSEPQS(1)PVAQTSGWPACSTPLPLVSR 155.74 4.25E-14 133369000 53661 60834 57881 64578 68705 62808 77926 56736 74024 TRUE FALSE 50302.4538 65338.21266 59253.96465 66235.18081 63309.18644 80939.65 66241.71973 63819.61449 61668.91619 0.815685712 1.059499934 0.960840052 1.074044833 1.026598007 1.312486987 1.074150866 1.034874917 1 15.91225587 3.049138206 1.735362865 1.112561731 0.968048566 0.265988952 0.105062725 0.463302818 2.841767729 0.034339698 0.042401503 1119.79418 -3.049138206 -0.144513166 VSSQS(ph)FSEIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VSSQSFSEIER 11 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;E9PIY6 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 VSSQS(0.991)FS(0.009)EIER;VSS(0.011)QS(0.964)FS(0.024)EIER;VSS(0.015)QS(0.98)FS(0.004)EIER 170.26 1.67E-05 761730000 446177 411796 404575 363489 383938 312425 453826 326037 441656 TRUE FALSE 418251.578 442285.8043 414171.7101 372816.7431 353785.0582 402617.0257 385779.0044 366743.4371 367940.7604 1.13673619 1.202057102 1.125647807 1.013252086 0.961527225 1.094244153 1.048481294 0.99674588 1 18.48911398 3.378760428 3.499841154 1.025760104 1.168693603 0.738288316 0.038510407 0.115994962 2.756801916 0.011056837 0.015626939 2391.995883 -3.378760428 0.142933499 VSSS(ph)PGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VSSSPGVK 8 0 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 VSS(0.027)S(0.972)PGVK;VSS(0.036)S(0.964)PGVK 123.29 0.0014203 483420000 1255640 880460 1053650 970600 1096410 839430 1297660 979550 1249810 TRUE FALSE 1177051.734 945650.1745 1078643.076 995507.2392 1010302.381 1081759.814 1103087.93 1101848.974 1041208.637 1.13046674 0.908223521 1.03595287 0.956107358 0.970316943 1.038946255 1.059430253 1.058240332 1 19.98982775 2.151657293 6.48563284 1.046400156 0.990640062 0.077633636 0.060081683 0.367061478 22.44092168 0.020567739 0.015162489 141.7938167 -2.151657293 -0.055760094 VSSSS(ph)ELDLPSGDHCEAGLLQLDVPLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VSSSSELDLPSGDHCEAGLLQLDVPLLR 28 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VS(0.014)S(0.091)S(0.091)S(0.804)ELDLPSGDHCEAGLLQLDVPLLR;VS(0.018)S(0.1)S(0.1)S(0.781)ELDLPSGDHCEAGLLQLDVPLLR;VS(0.002)S(0.014)S(0.109)S(0.875)ELDLPSGDHCEAGLLQLDVPLLR;VS(0.014)S(0.104)S(0.104)S(0.777)ELDLPSGDHCEAGLLQLDVPLLR 277.28 8.58E-62 710970000 258029 259492 288856 269012 273248 237026 354275 270159 331208 TRUE FALSE 241879.4255 278705.0577 295707.8007 275915.3034 251788.2043 305451.5584 301154.7527 303888.9458 275927.2451 0.876605807 1.010067192 1.071687577 0.999956721 0.912516646 1.107000355 1.091428114 1.101337223 1 18.07392839 2.21205421 24.99998818 1.084383425 0.99353282 0.369990665 0.062028251 259.4375374 244691.5145 0.023092345 0.017059738 162.9499421 -2.21205421 -0.090850606 VSTEVDAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VSTEVDAR 8 0 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ;;; 142.19 0.0014458 2797070000 5136560 6195230 6018660 5649670 6439300 5030360 6595300 5614540 6881000 FALSE TRUE 4815071.879 6653931.275 6161425.457 5794650.097 5933583.353 6482543.271 5606395.993 6315527.678 5732516.647 0.839957766 1.16073475 1.074820334 1.010838774 1.035074771 1.130837234 0.977999078 1.101702458 1 22.45073721 -1.521218642 2.841543541 0.9977143 1.05249244 0.007599999 0.090389968 32828593.58 44732649.91 604145.4442 0.019720464 0.030114895 1.521218642 0.05477814 VSTS(ph)PLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSTSPLTK 8 0 Q9Y320-2;Q9Y320 Q9Y320-2 TMX2 Thioredoxin-related transmembrane protein 2 1 VS(0.009)T(0.061)S(0.93)PLTK 63.734 0.086801 0 260920 201190 230630 198490 233630 204210 257870 232600 248630 TRUE FALSE 244589.483 216086.3169 236100.6525 203583.5894 215281.6422 263162.1119 219204.7874 261640.622 207132.0468 1.18083844 1.043229767 1.13985574 0.982868622 1.039344928 1.270504087 1.058285238 1.26315858 1 17.66019125 VSTTTDSPVS(ph)PAQAASPFIPLDELSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSTTTDSPVSPAQAASPFIPLDELSSK 27 0 Q96E09 Q96E09 FAM122A Protein FAM122A 1 VSTTTDS(0.063)PVS(0.936)PAQAASPFIPLDELSSK 152.82 4.25E-08 24608000 63881 45628 53794 49690 53819 49309 85068 56517 73942 TRUE FALSE 59882.80224 49006.3446 55070.01908 50965.12952 49592.27284 63543.70784 72312.84313 63573.27186 61600.60252 0.972113905 0.795549761 0.893985072 0.827347906 0.80506149 1.031543609 1.173898309 1.03202354 1 15.91065684 2.121148951 4.941160056 1.091019825 0.854135789 0.681247592 0.067724181 0.097866532 3.829188574 0.023841398 0.017342451 132.1748879 -2.121148951 -0.236884036 VSVADHSLHLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSVADHSLHLSK 12 0 Q13162;A6NG45 Q13162 PRDX4 Peroxiredoxin-4 0 84.169 0.0071638 147490000 155620 247950 167740 164370 278340 132570 161440 226340 180010 FALSE TRUE 145880.022 266308.476 171718.872 168588.0125 256480.2992 170840.8069 137233.5707 254599.0472 149965.1681 0.972759367 1.775802204 1.145058377 1.124181132 1.710265807 1.13920325 0.91510297 1.697721214 1 17.19426792 -4.999996961 0.10391237 0.00518249 1.507836416 0.038365854 0.322519888 448.5978558 3.146196168 95.83466641 4.545560468 1.00E-05 4.999996961 1.502653925 VSVGAPDLSLEASEGS(ph)IKLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VSVGAPDLSLEASEGSIKLPK 21 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VSVGAPDLS(0.002)LEAS(0.063)EGS(0.935)IKLPK;VSVGAPDLSLEAS(0.023)EGS(0.977)IKLPK;VSVGAPDLSLEASEGS(1)IKLPK 266.74 2.96E-37 300661000 540360 315594 350693 294368 396656 205436 432339 255852 824330 TRUE FALSE 506539.8322 338960.9081 359011.6036 301921.9812 365504.2378 264742.0382 367513.7806 287795.6854 686743.9976 0.737596301 0.493576805 0.522773559 0.439642694 0.532227787 0.385503243 0.535153976 0.419072735 1 19.38941287 -0.972780366 4.445202986 1.000012013 0.503713964 0.723239993 0.095575177 7761357.496 5238022.335 903.5124025 0.019837853 0.106468132 0.972780366 -0.49629805 VSVHVIEGDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 17 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 ;;;;;;;;;;;;;;;; 199.82 2.83E-08 69819070000 7188222 15122025 14310773 14794111 15393670 13684598 17119166 14059979 14875561 FALSE TRUE 6738324.016 16241675.47 14650231.29 15173752.93 14184713.25 17635119.29 14552305.98 15815398.33 12392733.77 0.543731847 1.31058052 1.182162997 1.224407239 1.144599208 1.42302091 1.174261164 1.276183175 1 23.56299114 4.74267308 24.99201176 1.229779017 0.543731577 0.782708319 0.111283948 162.7209435 988840.5016 0.022805594 0.176630291 55293.3726 -4.74267308 -0.68604744 VSVS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VSVSPGR 7 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 VS(0.001)VS(0.999)PGR;VS(0.016)VS(0.984)PGR;VS(0.002)VS(0.998)PGR;VS(0.004)VS(0.996)PGR 107.29 0.0078773 4553760000 3001820 3100720 3143230 2898720 3146690 2883290 3245930 2710420 3814270 TRUE FALSE 2813941.445 3330300.535 3217788.9 2973106.063 2899561.661 3715649.017 2759232.93 3048821.903 3177643.696 0.885543413 1.048040893 1.012633639 0.935632295 0.912487975 1.169309517 0.868326721 0.959459963 1 21.59952594 VSVT(ph)PPEESQNSDTPPRPDRLPLDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSVTPPEESQNSDTPPRPDRLPLDEK 26 2 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 VS(0.021)VT(0.977)PPEES(0.001)QNS(0.001)DTPPRPDRLPLDEK 136.73 0.0010059 255560000 300880 261320 254220 280100 334560 207100 334560 252330 478310 TRUE FALSE 282048.4579 280668.4047 260250.2185 287287.8402 308285.0072 266886.408 284395.8339 283833.9559 398476.971 0.707816206 0.704352886 0.653112319 0.720964726 0.773658278 0.669766203 0.713707076 0.712297012 1 18.60413682 -5 0.398169773 5.733932581 0.697270291 0.893766324 0.03173861 216.5787878 1.523101709 890.7736486 0.019758558 1.00E-05 5 -5.03666229 VSVTPPEESQNSDT(ph)PPRPDRLPLDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VSVTPPEESQNSDTPPRPDRLPLDEK 26 2 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 VSVTPPEESQNS(0.009)DT(0.991)PPRPDRLPLDEK 159.42 9.24E-10 258340000 169430 125060 139810 151720 170500 126370 173170 130230 188620 TRUE FALSE 158825.6787 134319.5725 143126.3592 155613.3921 157109.6178 162850.9676 147204.7661 146489.5022 157138.1035 1.01073944 0.854786774 0.910831657 0.990296998 0.999818722 1.036355689 0.936785941 0.932234124 1 17.26167353 3.244566283 23.7852821 0.981035982 0.908221197 0.206762325 0.048955981 89.44456333 354237.6518 0.013319946 0.017555686 1756.168902 -3.244566283 -0.072814785 VSYDEWNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VSYDEWNR 8 0 P35573-2;P35573-3;P35573 P35573-2 AGL "Glycogen debranching enzyme;4-alpha-glucanotransferase;Amylo-alpha-1,6-glucosidase" 0 ;;; 189.78 0.00044184 782860000 914080 1060270 1062440 1054890 1231070 907440 1198860 1028400 1296370 FALSE TRUE 856869.3645 1138773.494 1087641.579 1081960.263 1134386.728 1169403.197 1019102.073 1156798.004 1079997.472 0.793399417 1.05442237 1.007077893 1.001817404 1.05036054 1.082783272 0.943615239 1.07111177 1 20.0425965 4.74326625 24.95585047 1.023501026 0.793399321 0.761020474 0.041004972 229.4862527 1217014.725 0.009173179 0.075394633 55368.94515 -4.74326625 -0.230101705 VSYLVFDEADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 VSYLVFDEADR 11 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ;;;;;;; 223.87 1.54E-11 690089000 808110 911998 868283 867565 943861 742096 910518 819177 765235 FALSE TRUE 757531.8376 979523.2809 888879.0828 889828.1867 869733.9644 956327.0683 773994.2787 921453.0517 637512.3349 1.188262244 1.536477378 1.394293152 1.395781914 1.364262175 1.500091866 1.214085181 1.445388585 1 19.28209373 -1.199057732 0.388710863 0.799922747 1.411800526 0.517167103 0.112619961 13.63666433 1.311726398 2.967970633 0.069088659 0.063232779 1.199057732 0.611877779 VT(ph)KSPAPVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTKSPAPVHR 10 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B0QYZ7 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 VT(0.802)KS(0.198)PAPVHR 78.763 0.02703 0 341740 301750 313600 336380 419980 242660 390110 338250 424910 TRUE FALSE 320351.1034 324091.884 321038.7401 345012.0803 386996.4649 312712.0027 331616.6271 380481.2571 353989.776 0.904972757 0.915540239 0.906915289 0.974638545 1.093241927 0.883392753 0.936797189 1.074836854 1 18.43334817 3.207288017 5.961243769 0.984490401 0.91003458 0.296854793 0.060405349 0.248308596 25.02178274 0.017335949 0.021361154 1611.714144 -3.207288017 -0.074455821 VT(ph)PTKESYTEEIVSEAESHVSGISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTPTKESYTEEIVSEAESHVSGISR 25 1 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 VT(0.692)PT(0.149)KES(0.055)Y(0.048)T(0.055)EEIVSEAESHVSGISR;VT(0.982)PT(0.018)KESYTEEIVSEAESHVSGISR 224.99 1.15E-33 262450000 118552 163898 181588 166574 176447 133129 214127 152118 161030 TRUE FALSE 111132.0419 176033.1785 185895.3531 170848.5708 162589.5644 171561.1811 182020.6442 171110.2672 134153.0527 0.828397414 1.312181683 1.385696034 1.273534723 1.211970664 1.278846643 1.356813286 1.275485453 1 17.03352036 4.740238009 24.87336223 1.290024874 0.828397249 0.604871373 0.107971062 80.31816087 1190895.779 0.022866746 0.146570891 54984.21249 -4.740238009 -0.461627625 VTAAMVLTSLST(ph)SPLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTAAMVLTSLSTSPLVR 17 0 Q6ZNC4;E5RGL7 Q6ZNC4 ZNF704 Zinc finger protein 704 1 VTAAMVLTSLST(0.621)S(0.379)PLVR 288.82 1.18E-32 0 272560 252840 259870 249740 292830 312490 374070 313860 194690 TRUE FALSE 255500.9561 271560.5367 266034.2391 256148.7512 269832.313 402700.7901 317981.6762 353046.1119 162194.9813 1.575270419 1.67428446 1.640212521 1.579264347 1.663629238 2.482819055 1.960490231 2.176677164 1 17.30736965 2.436815258 24.99983942 2.00931551 1.629673265 0.092068025 0.377259003 223.6146114 138696.1014 0.113103523 0.094629301 273.4105433 -2.436815258 -0.379642245 VTAEADSSS(ph)PTGILATSESK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VTAEADSSSPTGILATSESK 20 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-7 A0MZ66 KIAA1598 Shootin-1 1 VTAEADSS(0.018)S(0.972)PT(0.011)GILATSESK;VTAEADSS(0.019)S(0.98)PTGILATSESK;VTAEADSSS(0.998)PT(0.002)GILATSESK 511.37 5.71E-277 608710000 1976470 1426420 1668310 1719080 1675350 1231000 1988170 1347980 1634380 TRUE FALSE 1852766.271 1532033.621 1707883.101 1763194.503 1543774.769 1586369.716 1690062.366 1516278.27 1361591.42 1.36073586 1.125178669 1.254328631 1.294951245 1.133801776 1.165084983 1.241240464 1.113607392 1 20.37686242 -4.99999992 0.168331241 0.162895549 1.261688396 0.521048369 0.071771914 112.9449812 1.061928607 31.33326579 0.251157271 1.00E-05 4.99999992 1.098792847 VTAEDKGTGNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTAEDKGTGNK 11 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 102.62 0.0023156 0 320310 212180 256230 280990 267790 215220 370050 237080 409880 FALSE TRUE 300262.3689 227890.028 262307.8966 288200.6791 246758.8536 277350.5202 314564.4379 266679.9599 341468.3801 0.879327008 0.66738252 0.768176241 0.844004001 0.72264042 0.812228998 0.921211029 0.780979954 1 18.38139247 0.908392044 0.38897824 1.012979522 0.742762966 0.424262221 0.07319576 1.244883983 0.495519332 0.118858744 0.059338403 8.09826612 -0.908392044 -0.270216556 VTAIHIDPATHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 12 VTAIHIDPATHR 12 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;;;;;;; 200.82 9.00E-08 72010119200 30268894.8 35268094 34011346.9 34216417.4 37559816.6 31343144.3 42369825 33746224 39915813.9 FALSE TRUE 28374418.71 37879380.38 34818112.11 35094468.6 34610020.11 40391401.25 36016863.08 37959514.35 33253606.69 0.85327342 1.139105924 1.047047691 1.055358263 1.040789964 1.21464723 1.083096442 1.141515707 1 24.98700749 VTAPDVDLHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTAPDVDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 139.32 3.91E-05 335430000 938680 829520 841120 857480 1001290 655990 1001290 803180 1082100 FALSE TRUE 879929.6944 890938.5239 861071.7636 879484.3885 922652.7224 845363.6639 851155.86 903458.791 901490.5194 0.976083137 0.988294946 0.955164525 0.975589171 1.023474682 0.937739938 0.944165071 1.002183353 1 19.78195279 4.200069995 21.46870685 0.971713002 0.982189025 0 0.027252659 331.7636278 263299.6036 0.006705347 0.014499595 15851.48648 -4.200069995 0.010476023 VTDALNATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTDALNATR 9 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 102.62 0.0082699 469850000 245240 408210 341800 314220 441930 347670 296870 340230 419370 FALSE TRUE 229890.8662 438434.2931 349907.6574 322283.4172 407222.6005 448036.685 252357.0995 382708.4644 349374.4378 0.658007116 1.25491234 1.001526213 0.922458492 1.165576403 1.282396869 0.722311286 1.095410606 1 18.41441453 1.733659234 24.99999985 0.917783827 1.065849539 0.052675842 0.200038103 1.177801804 5953.62432 0.084800714 0.047026204 54.157578 -1.733659234 0.148065712 VTDALPEPEPPGAMAAS(ph)EDEEEEEEALEAMQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 245.58 2.44E-47 200073000 255345 280808 264729 259680 261516 227423 301137 244281 305070 TRUE FALSE 239363.4123 301599.3165 271008.4969 266343.8284 240977.5883 293076.3282 255984.3025 274780.0206 254151.8462 0.941812605 1.186689458 1.066325116 1.047971252 0.948163832 1.153154434 1.007210085 1.081164763 1 17.95533119 3.44675337 4.073746763 1.041739402 1.095556543 0 0.080048384 0.520070467 18.97726726 0.020479797 0.029614562 2797.392265 -3.44675337 0.053817141 VTDHLEALIDPFDLDVFTPHLNSNLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTDHLEALIDPFDLDVFTPHLNSNLHR 27 0 A0A087WVI0;E9PBL8;Q8WTW3;J3QKY9;J3QLT5 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 0 126.27 2.42E-05 32475000 22950 36720 30478 35412 38611 24766 32346 29591 29383 FALSE TRUE 21513.60047 39438.78701 31200.95255 36320.73187 35578.64781 31915.54216 27496.01759 33285.50149 24478.78748 0.87886708 1.611141362 1.274611848 1.48376352 1.453448127 1.303804046 1.123258969 1.359769209 1 14.57924448 0.946707676 0.697526837 1.013215977 1.370096519 0.155592493 0.205928317 1.184678872 1.30645871 0.18599086 0.07291352 8.845200378 -0.946707676 0.356880541 VTDKLTPIHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VTDKLTPIHDR 11 1 P28072;A0A087X2I4;I3L3X7 P28072 PSMB6 Proteasome subunit beta type-6;Proteasome subunit beta type 0 ;;; 190.3 1.40E-06 1765540000 2202290 2852820 2361780 2348340 3388820 1825986 3124250 2356090 4648540 FALSE TRUE 2064452.6 3064045.761 2417802.537 2408602.38 3122675.747 2353118.516 2655797.717 2650253.023 3872668.643 0.533082685 0.791197503 0.624324661 0.621948997 0.806336931 0.607621961 0.685779746 0.684347995 1 21.88489663 0.386724419 2.464604011 0.999999604 0.676050916 0.61351722 0.082358583 12.02897479 47.22239915 0.070218489 0.018752399 2.436264401 -0.386724419 -0.323948688 VTEGGEPYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTEGGEPYR 9 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 125.5 0.001163 180400000 214830 233590 209000 219580 243480 175860 252790 197410 189490 FALSE TRUE 201384.1738 250885.2467 213957.5787 225214.7945 224358.063 226627.9272 214886.4863 222057.0731 157862.8948 1.275690364 1.589260395 1.355337991 1.426648072 1.421221011 1.435599717 1.361222259 1.406645135 1 17.26831258 -3.103447404 0.322233104 1.31E-14 1.441640447 0.716568613 0.080400098 40.40199389 1.103797069 27.33722693 0.064936742 0.000788048 3.103447404 1.441640447 VTEGLTDVILYHQPDDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VTEGLTDVILYHQPDDK 17 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;;; 272.16 1.26E-35 2323558000 5471919 3831105 4499370 4292921 4664329 3508979 5705340 3836189 5456313 FALSE TRUE 5129441.357 4114764 4606097.181 4403084.621 4298011.415 4521964.274 4849877.233 4315145.641 4545619.111 1.128436244 0.905215307 1.013304694 0.968643547 0.945528279 0.994796124 1.066934363 0.949297672 1 22.11604537 1.991172487 24.76635518 1.017352184 0.981163007 0 0.064384285 1077.848242 3023997.877 0.022789961 0.015993245 97.98790829 -1.991172487 -0.036189177 VTEGLVDVILYHQPDDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VTEGLVDVILYHQPDDK 17 0 O43390;O43390-3;B4DT28 O43390 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;;;; 248.54 6.98E-21 1855235000 5364420 3838060 4371430 4197110 4725280 3514570 5578130 3841880 5698800 FALSE TRUE 5028670.528 4122233.956 4475122.384 4304814.948 4354175.57 4529169.305 4741741.191 4321547.175 4747633.464 1.05919519 0.868271316 0.942600649 0.90672858 0.917125469 0.95398462 0.998758903 0.91025291 1 22.17877713 2.039419516 5.990600128 0.97122445 0.928563645 0.045050698 0.054583185 0.375801446 35.33371572 0.0192003 0.013828914 109.5013608 -2.039419516 -0.042660805 VTEGQQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VTEGQQER 8 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;; 163.2 0.00078465 1285250000 599617 673316 579965 654024 701380 529751 648539 618177 754996 FALSE TRUE 562088.0423 723169.0172 593722.0437 670807.3631 646296.444 682681.5139 551296.5977 695357.7592 628982.2901 0.89364685 1.149744641 0.943940796 1.066496424 1.027527252 1.085374779 0.876489857 1.105528359 1 19.26265987 VTEHGT(ph)PKPFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VTEHGTPKPFR 11 1 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 VT(0.005)EHGT(0.995)PKPFR;VTEHGT(1)PKPFR;VTEHGT(1)PKPFR;VTEHGT(1)PKPFR 167.32 2.84E-05 2174700000 2083030 1691360 1854080 1811070 2044450 1308540 2381840 1921250 2513400 TRUE FALSE 1952656.871 1816590.054 1898059.653 1857545.122 1883887.144 1686294.256 2024705.204 2161122.292 2093897.303 0.932546629 0.867564064 0.90647218 0.887123318 0.899703697 0.805337613 0.966955352 1.032105199 1 20.99775925 1.532417905 5.563675695 1.011440447 0.884616189 0.737422365 0.033674425 0.065708675 4.340713429 0.017470787 0.007828961 34.07359094 -1.532417905 -0.126824258 VTEKLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTEKLR 6 1 G3V2K4;G3V3A2;G3V536;G3V3S3;A0A1B0GTT1;A0A1B0GVM0;Q9BUH8 G3V2K4 BEGAIN Brain-enriched guanylate kinase-associated protein 0 67.055 0.091002 280490000 1009700 1043300 1067400 1055300 1276000 827410 1351700 1045700 1802000 FALSE TRUE 946504.6794 1120547.018 1092719.232 1082380.785 1175788.107 1066269.835 1149025.134 1176257.947 1501234.559 0.630484206 0.746417015 0.727880414 0.720993784 0.783214122 0.710261983 0.765386812 0.783527091 1 20.51771798 -5 0.199618027 2.215555644 0.691506401 0.86681017 0.03454088 45.756831 0.452804176 22.11462773 0.076471506 1.00E-05 5 -1.524049243 VTEQEWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VTEQEWR 7 0 P09497-2;P09497 P09497-2 CLTB Clathrin light chain B 0 ;; 125.58 0.0093872 1224120000 1917440 2070660 1916580 1840950 2222210 1745660 2140610 1872280 2365770 FALSE TRUE 1797430.853 2223973.821 1962042.183 1888191.894 2047686.591 2249603.704 1819645.403 2106038.279 1970907.704 0.911981241 1.128400796 0.995501808 0.958031617 1.038956105 1.141404897 0.923252469 1.06856261 1 20.91042879 VTFEDATDFFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTFEDATDFFGR 12 0 Q86WQ0;Q86WQ0-2 Q86WQ0 NR2C2AP Nuclear receptor 2C2-associated protein 0 117.02 0.0018112 43767000 40024 51952 58403 55447 51794 51147 54860 48577 44940 FALSE TRUE 37518.96928 55798.58014 59788.34674 56869.86389 47726.30817 65912.3086 46634.2523 54641.94538 37439.22368 1.002130002 1.490377595 1.596944083 1.518991536 1.274767569 1.760514832 1.245598806 1.459483932 1 15.1922629 0.185395668 0.969748418 0.997115489 1.450274953 0.270772145 0.210223982 5.118803492 5.056663264 0.22427217 0.059093265 1.532483009 -0.185395668 0.453159464 VTFFEPGS(ph)GDENGTSNKEDEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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;VTFFEPGS(1)GDENGTSNKEDEFR;VTFFEPGS(1)GDENGTSNKEDEFR 281.4 6.63E-46 1187156000 1813361 1279562 1455854 1399378 1348875 1040793 1788315 1155891 1410818 TRUE FALSE 1699865.972 1374302.102 1490387.544 1435288.409 1242939.799 1341253.043 1520173.768 1300206.536 1175343.362 1.446271811 1.169277121 1.26804438 1.221165198 1.057512076 1.141158479 1.293386952 1.106235487 1 20.16465085 8 0.024148366 6.58E-05 2.817254645 0.481865053 0.09196426 2173.693348 4.037058293 163.9500779 335.1330246 100000000 -8 2.81718882 VTFFEPGSGDENGTSNKEDEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTFFEPGSGDENGTSNKEDEFR 22 1 O95793-2;O95793-3;O95793;Q5JW30 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 ; 183.06 4.01E-17 278780000 250629 184773 222800 198665 231663 166159 271720 182106 291960 FALSE TRUE 234942.5783 198453.7852 228084.9212 203763.0802 213469.1225 214126.4059 230978.1085 204842.335 243229.9899 0.965927674 0.815910017 0.937733547 0.837738308 0.877643101 0.880345413 0.94962841 0.842175486 1 17.8919616 -4.999999662 0.323620284 2.082882699 0.883905745 0.314343453 0.050447364 382.5747844 3.361112401 284.1179473 0.039763283 1.00E-05 4.999999662 -1.198976954 VTGGLLDRLDDS(ph)PDQCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VTGGLLDRLDDSPDQCR 17 1 Q12955;A0A087WY90;A0A087WVC2;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;H0Y3A4;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 VTGGLLDRLDDS(1)PDQCR;VTGGLLDRLDDS(1)PDQCR;VTGGLLDRLDDS(1)PDQCR 174.55 8.11E-10 493292000 421687 438834 424483 440530 470198 366925 511871 410724 407258 TRUE FALSE 395294.3634 471325.726 434551.9372 451834.7456 433270.5458 472850.291 435120.6955 462003.7955 339284.0088 1.16508398 1.389177544 1.280791095 1.331730155 1.277014343 1.393671021 1.282467444 1.361702242 1 18.37213391 -1.68191014 6.453758419 0.997206106 1.315562195 0.678913906 0.066953082 0.002305485 0.000113632 0.055529533 0.012995962 0.02080127 1.68191014 0.318356089 VTGPPPGT(ph)PQPR ddPTM_SK-BR-3_Pertuzumab_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 151.66 0.00087432 0 257280 239392 304785 383882 356623 192536 213158 157435 206530 TRUE FALSE 241177.3041 257116.8328 312014.6441 393733.062 328615.2681 248118.0176 181196.9368 177091.1063 172058.8088 1.401714366 1.49435437 1.8134186 2.288363292 1.909900868 1.44205356 1.053110492 1.029247544 1 17.39254223 1.911192092 2.86640761 1.028927544 1.767512449 0.673758598 0.238683551 0.179569405 2.641062113 0.13852746 0.073674156 81.50647137 -1.911192092 0.738584905 VTGTEGSSSTLVDYTSTSSTGGS(ph)PVRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTGTEGSSSTLVDYTSTSSTGGSPVRK 27 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 VTGTEGSSSTLVDYTSTS(0.002)S(0.004)T(0.01)GGS(0.985)PVRK;VTGTEGSSSTLVDYTST(0.002)S(0.044)S(0.022)T(0.022)GGS(0.91)PVRK 261.83 2.57E-53 1652320000 716080 571290 632840 601800 621600 492860 688610 536740 605380 TRUE FALSE 671261.831 613588.906 647851.2636 617243.2068 572782.0434 635140.6811 585359.3232 603753.1705 504338.1671 1.330975672 1.216621993 1.284557279 1.223867728 1.135710285 1.259354779 1.160648472 1.19711973 1 18.94403188 -5 0.117030875 0.245963939 1.345158382 0.747712677 0.045654224 73.36860686 0.561380632 13.05759606 0.428711989 1.00E-05 5 1.099194443 VTHAVVTVPAYFNDAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTHAVVTVPAYFNDAQR 17 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 218.43 4.65E-15 4331300000 3683400 4480800 3563800 3650400 3886000 2523200 4615300 3539600 2931100 FALSE TRUE 3452862.569 4812563.094 3648335.019 3744075.444 3580809.235 3251606.879 3923278.611 3981526.852 2441880.474 1.414017846 1.970843022 1.494067813 1.533275475 1.466414623 1.331599525 1.606662837 1.630516683 1 21.21956115 -3.008257586 0.181631165 4.62E-14 1.721616482 0.478734998 0.176492494 48.83418801 0.911461284 19.93225585 0.574921595 0.000981166 3.008257586 1.721616482 VTHETSAHEGQTEAPSIDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTHETSAHEGQTEAPSIDEK 20 0 A0A087WTB8;P15374 A0A087WTB8 UCHL3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L3 0 128.32 1.15E-05 373320000 92690 113890 118260 123240 118600 96746 153370 113520 142430 FALSE TRUE 86888.69836 122322.5341 121065.183 126402.547 109285.6344 124674.9997 130373.5923 127693.2219 118657.5129 0.732264618 1.030887393 1.020290921 1.065272177 0.921017404 1.05071307 1.098738623 1.076149489 1 16.85644392 4.738750876 6.585412873 1.036259356 0.726474279 0.789541146 0.048758043 0.052859973 14.48085268 0.011731326 0.072997325 54796.25469 -4.738750876 -0.309785077 VTHTGQVYDDKDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VTHTGQVYDDKDYR 14 1 D6RBT3;O75380 D6RBT3 NDUFS6 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial" 0 ;; 245.4 7.11E-18 1301230000 1734620 1155410 1281570 1179990 1771360 1104520 1352170 1405980 2137480 FALSE TRUE 1626053.231 1240957.759 1311969.446 1210270.541 1632244.531 1423376.994 1149424.661 1581519.698 1780720.779 0.91314329 0.696885089 0.736763147 0.679652057 0.91662014 0.799326323 0.645482815 0.888134578 1 20.76402989 1.009410933 7.357756713 0.999948096 0.757394442 0.414761391 0.090703192 0.099181778 32.35417736 0.082576992 0.020697744 10.21905962 -1.009410933 -0.242553654 VTIAQGGVLPNIQAVLLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTIAQGGVLPNIQAVLLPK 19 0 A0A0U1RR32;A0A0U1RRH7;P20671;Q7L7L0;P04908;Q99878;Q96KK5;Q6FI13;P0C0S8;Q16777;Q9BTM1;H0YFX9 A0A0U1RR32;Q7L7L0;Q99878 HIST1H2AD;HIST3H2A;HIST1H2AB;HIST1H2AJ;HIST1H2AH;HIST2H2AA3;HIST1H2AG;HIST2H2AC;H2AFJ Histone H2A type 1-D;Histone H2A type 3;Histone H2A type 1-B/E;Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-A;Histone H2A type 1;Histone H2A type 2-C;Histone H2A.J;Histone H2A 0 ; 189.69 3.13E-14 171597000 655900 575640 579030 549370 645300 435790 722000 514570 667970 FALSE TRUE 614848.3898 618260.9846 592764.865 563467.7643 594620.741 561595.4985 613742.8027 578815.1972 556481.4917 1.104885605 1.111018055 1.065201402 1.012554366 1.06853642 1.009189896 1.10289886 1.040133779 1 19.08597418 7.999999791 0.30609102 1.037651598 1.778541932 0.400501857 0.031937123 58.20815438 0.833012282 0.030524703 23.77219001 99999951.8 -7.999999791 0.740890334 VTKNEEPS(ph)EEEIDAPKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 VTKNEEPSEEEIDAPKPK 18 2 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 VTKNEEPS(1)EEEIDAPKPK;VTKNEEPS(1)EEEIDAPKPK;VTKNEEPS(1)EEEIDAPKPK;VTKNEEPS(1)EEEIDAPKPK;VT(0.001)KNEEPS(0.999)EEEIDAPKPK;VT(0.002)KNEEPS(0.998)EEEIDAPKPK;VTKNEEPS(1)EEEIDAPKPK 170.28 1.27E-11 7019970000 8577860 3810554 5617520 5531440 6025380 3588987 7212740 3833496 9253100 TRUE FALSE 8040987.055 4092691.383 5750770.227 5673386.115 5552170.96 4625069.285 6131256.597 4312116.414 7708697.833 1.043105753 0.530918642 0.746010591 0.735972046 0.72024758 0.599980617 0.795368651 0.559383246 1 22.87805575 -1.830825999 6.519707705 1.023298753 0.704676702 0.272527363 0.144511789 0.040728242 0.00105682 0.116444532 0.028549261 0.014762979 1.830825999 -0.318622051 VTKS(ph)PAPVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VTKSPAPVHR 10 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B0QYZ7 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 VT(0.047)KS(0.953)PAPVHR;VT(0.009)KS(0.991)PAPVHR;VT(0.01)KS(0.99)PAPVHR 106.55 0.0014545 1458670000 1980610 1651150 1792600 1823810 2198780 1390800 2208990 1902360 2334250 TRUE FALSE 1856647.156 1773402.864 1835121.319 1870612.052 2026096.688 1792301.382 1877772.457 2139873.834 1944648.595 0.954746868 0.911940012 0.9436776 0.961928061 1.041883193 0.92165823 0.965610168 1.100391011 1 20.89107805 2.540811636 0.492511762 1.020830951 0.922291163 0.303333625 0.047553541 1.310978037 0.661970517 0.04332097 0.049008581 347.3854596 -2.540811636 -0.098539788 VTKS(ph)PGETSKPRPFAGGGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VTKSPGETSKPRPFAGGGYR 20 3 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 VT(0.102)KS(0.888)PGET(0.009)SKPRPFAGGGYR;VT(0.021)KS(0.979)PGETSKPRPFAGGGYR;VT(0.125)KS(0.872)PGET(0.002)S(0.001)KPRPFAGGGYR 104.77 0.00020038 3173840000 1591750 1288440 1513170 1620170 1873630 1062350 1963740 1246270 3581460 TRUE FALSE 1492125.209 1383837.438 1549063.107 1661746.305 1726482.658 1369033.199 1669295.417 1401869.553 2983691.189 0.500093714 0.463800491 0.519176754 0.556943128 0.578639862 0.458838771 0.559473254 0.46984405 1 21.50866679 -1.603095866 2.881098213 1.034941409 0.513663502 0.930101323 0.041926309 40962323.67 40660558.37 10795225.22 0.009589487 0.024940441 1.603095866 -0.521277908 VTKS(ph)PQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VTKSPQK 7 1 Q9NVP1 Q9NVP1 DDX18 ATP-dependent RNA helicase DDX18 1 VT(0.002)KS(0.998)PQK;VT(0.009)KS(0.991)PQK;VTKS(1)PQK;VTKS(1)PQK 98.943 0.0065963 2382960000 8856400 7229200 5234300 4717530 9591300 2549340 5882300 8103000 9050200 TRUE FALSE 8302093.733 7764457.49 5358460.068 4838589.807 8838037.987 3285293.073 5000303.724 9114677.387 7539663.153 1.101122632 1.029814904 0.710702847 0.641751456 1.172205947 0.435734728 0.663199883 1.208897162 1 22.84606864 4.20588732 2.753285799 0.793051503 1.08569018 0.121886691 0.243737239 0.459372596 6.853687324 0.05899042 0.180472079 16065.2438 -4.20588732 0.292638678 VTLDWAKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTLDWAKPK 9 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 76.943 0.03101 652940000 2249000 2008110 1876660 1735110 2237500 1322090 2045310 2009950 1823090 FALSE TRUE 2108239.105 2156792.554 1921175.261 1779635.86 2061775.776 1703755.921 1738634.753 2260896.682 1518804.501 1.388091162 1.420059364 1.264925973 1.17173465 1.357499121 1.121774342 1.144739005 1.488602832 1 20.53450475 7.803626462 0.028469899 2.81E-06 3.044705995 0.346227747 0.123969054 1525.544385 3.439703909 121.5001864 274.9078188 63624804.68 -7.803626462 3.044703184 VTLEYRPVIDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTLEYRPVIDK 11 1 P31040;D6RFM5;P31040-2;A0A087X1I3;P31040-3 P31040 SDHA "Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial" 0 90.861 0.010189 639920000 827630 737300 733490 658270 1153000 639860 772380 919210 1377200 FALSE TRUE 775830.1157 791890.4592 750888.7292 675162.3226 1062448.031 824577.1947 656568.7894 1033975.392 1147336.423 0.676201069 0.690199006 0.654462557 0.588460637 0.926012641 0.71868824 0.572254812 0.901196346 1 20.12985705 1.067687533 5.457010673 0.998250266 0.687154592 0.572124411 0.09581467 0.123107815 6.294034072 0.089130553 0.022489519 11.68658259 -1.067687533 -0.311095674 VTLLEGDHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTLLEGDHVR 10 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ; 116.77 0.0010468 360480000 421740 372650 417830 464200 372710 354670 467500 316160 432680 FALSE TRUE 395344.0462 400241.3937 427741.1249 476112.1579 343438.86 457057.4714 397402.7151 355633.272 360462.9128 1.096767607 1.11035388 1.186643923 1.320835351 0.952771694 1.267973639 1.102478788 0.98660156 1 18.45949131 1.352673156 4.239144732 0.993886686 1.154668228 0.309109269 0.098905049 0.24616207 6.824956504 0.067115606 0.022661436 22.52543342 -1.352673156 0.160781542 VTLTSEEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTLTSEEEAR 10 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 249.46 1.25E-12 2464600000 738600 899250 793360 835800 863620 667110 801320 677680 755800 FALSE TRUE 692372.3444 965831.4057 812178.8739 857248.043 795794.7689 859693.8274 681169.5051 762289.8398 629652.0973 1.099610956 1.53391279 1.289885124 1.361463015 1.263864239 1.365347358 1.081818846 1.210652427 1 19.26419539 1.481664522 0.764172843 1.015249819 1.357857156 0.395640926 0.122332308 0.488055972 0.604824903 0.103149051 0.043747797 30.31548512 -1.481664522 0.342607337 VTLVFEHVDQDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VTLVFEHVDQDLR 13 0 F8W1L8;F8VYH9;F8VTV8;F8VWX7;P11802;F8VXD2;F8VZZ0;F8VZ51 F8W1L8 CDK4 Cyclin-dependent kinase 4 0 ;;; 185.87 8.29E-06 222149000 302452 317311 336373 324050 344125 293343 366168 308199 374683 FALSE TRUE 283522.0692 340805.0366 344351.9264 332365.6716 317098.8106 378026.3621 311264.5077 346678.3236 312145.9868 0.908299582 1.091812969 1.103175889 1.064776373 1.015867011 1.211056295 0.997176068 1.110628803 1 18.25186139 4.741381527 24.26080869 1.078435351 0.908299487 0.401783145 0.06348432 160.8249136 1383035.918 0.013247959 0.09194793 55129.17929 -4.741381527 -0.170135864 VTLYNTDQDGSDS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VTLYNTDQDGSDSPR 15 0 Q9UPW0-2;Q9UPW0;C9JXI1;C9JVP0 Q9UPW0-2 FOXJ3 Forkhead box protein J3 1 VTLYNTDQDGSDS(1)PR;VTLYNTDQDGSDS(1)PR;VTLYNTDQDGS(0.101)DS(0.899)PR 305.64 2.68E-44 347950000 617440 595870 629120 514350 648390 715620 894400 640670 753360 TRUE FALSE 578795.5326 639988.8348 644043.0235 527549.0918 597468.0649 922207.8769 760293.0232 720659.0598 627619.3491 0.922207917 1.019708579 1.026168209 0.840555812 0.951959282 1.469374515 1.211391944 1.14824226 1 19.2595303 2.280786688 24.99991813 1.232156913 0.966362716 0.498420879 0.12563127 105.8324227 62657.58743 0.040713625 0.034063215 190.8915427 -2.280786688 -0.265794196 VTNDIS(ph)PESS(ph)PGVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTNDISPESSPGVGR 15 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;E7EV93;E9PGW9;E5RGQ4;Q15154-3 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 2 VTNDIS(1)PES(0.001)S(1)PGVGR 215.51 3.41E-12 107240000 186790 198360 203310 194430 194710 179050 232520 158390 180660 TRUE FALSE 175099.1473 213046.7808 208132.6092 199419.403 179418.262 230738.8284 197655.7846 178165.3402 150506.6789 1.163397855 1.415530409 1.382879556 1.324987067 1.192095018 1.533080326 1.313269192 1.183770325 1 17.19946798 1.013556856 2.620417935 1.002686994 1.349710979 0.512282121 0.105426355 0.187774436 2.900410686 0.092095667 0.024773719 10.31708138 -1.013556856 0.347023985 VTNDIS(ph)PESSPGVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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(0.637)PES(0.363)S(0.001)PGVGR;VTNDIS(0.917)PES(0.083)S(0.001)PGVGR 280.4 1.10E-33 1228020000 1680530 1754690 1742440 1819280 1687780 1658490 1890220 1465040 1592820 TRUE FALSE 1575348.627 1884609.073 1783771.5 1865965.805 1555228.567 2137269.14 1606799.059 1647953.469 1326968.052 1.187179017 1.420236961 1.344246003 1.406187438 1.172016587 1.610640992 1.210879988 1.241893855 1 20.33970221 0.939550793 1.551716589 1.004614874 1.355320668 0.410677666 0.128799891 0.394067847 1.924512012 0.105940118 0.030962168 8.700631864 -0.939550793 0.350705794 VTNDISPES(ph)SPGVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTNDISPESSPGVGR 15 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;E7EV93;E9PGW9;E5RGQ4;Q15154-3 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 VTNDIS(0.028)PES(0.842)S(0.13)PGVGR 201.3 6.80E-09 1201900000 1184300 1104200 1144400 1167800 1053900 1122200 1237800 878080 987080 TRUE FALSE 1110176.777 1185956.117 1171545.708 1197767.725 971130.9452 1446160.923 1052203.381 987710.2209 822329.9712 1.350038082 1.442190068 1.424666192 1.456553655 1.180950445 1.758613906 1.279539136 1.201111787 1 19.64935789 1.133514381 2.21766469 1.014553234 1.428367648 0.485095164 0.145542594 0.215994823 1.985571104 0.120134339 0.033724992 13.59923193 -1.133514381 0.413814414 VTNEFVHINNLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTNEFVHINNLK 12 0 O00743;O00743-2;O00743-3 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed" 0 101.6 0.0025824 369620000 362030 350010 335850 341670 376960 270310 402560 330830 375160 FALSE TRUE 339371.1885 375925.1046 343816.5206 350437.8306 347355.0822 348344.1089 342199.8652 372134.8537 312543.3724 1.085837098 1.202793397 1.100060187 1.121245439 1.111382013 1.114546459 1.094887607 1.190666278 1 18.25369688 -1.44262662 2.967146544 0.997156737 1.128180065 0.514348473 0.038986975 9087653.781 11454277.42 218318.2886 0.008927745 0.036088878 1.44262662 0.131023328 VTPDTDWAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VTPDTDWAR 9 0 P53396;P53396-2;P53396-3;K7ESG8 P53396 ACLY ATP-citrate synthase 0 ;;;;; 205.77 3.35E-05 6503430000 3870010 5854530 4232620 4329170 5696760 3348360 4154110 5023860 5303640 FALSE TRUE 3627792.982 6288005.493 4333019.745 4440263.831 5249359.449 4314977.176 3531239.77 5651099.98 4418428.221 0.821059617 1.423131751 0.980669942 1.004941941 1.188060366 0.97658646 0.799207228 1.278984222 1 22.07510182 3.728549753 24.98643735 1.013125017 1.176140853 0.011572566 0.193436505 136.2078501 2382398.278 0.047071758 0.079386243 5352.414683 -3.728549753 0.163015836 LGSQHSPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 82.749 0.017571 113577000 267990 363940 319960 375880 503330 319680 463800 433950 628580 FALSE TRUE 251216.9843 390886.4963 327549.6023 385525.7172 463800.4921 411966.4264 394257.4957 488129.6127 523665.9372 0.479727564 0.746442471 0.625493428 0.73620545 0.885680086 0.786697009 0.75287978 0.932139324 1 18.99828724 5.431613986 0.119235385 1.117882056 3.71E-13 0.716041859 0.079427573 28.25455947 0.444354745 0.707461783 5.148663022 270155.6069 -5.431613986 -1.117882056 down VTPTEEHVEGPLPSPVTNGT(ph)SPAQLNGGSACSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTPTEEHVEGPLPSPVTNGTSPAQLNGGSACSSR 34 0 H3BN50;Q15599-3;H3BQS0;H3BUQ9;Q15599;Q15599-2 H3BN50;Q15599 SLC9A3R2 Na(+)/H(+) exchange regulatory cofactor NHE-RF2 1 VTPTEEHVEGPLPSPVT(0.001)NGT(0.5)S(0.5)PAQLNGGSACSSR 184.43 2.22E-19 268670000 53949 59428 70540 56719 65123 56216 80940 62488 57160 TRUE FALSE 50572.42839 63828.11095 72213.24211 58174.50557 60008.50227 72444.64661 68803.79841 70289.76435 47619.62673 1.062008081 1.340374029 1.516459642 1.22164976 1.260163222 1.521319077 1.444862195 1.4760671 1 15.53926869 2.264488799 24.99889864 1.407111595 1.317914334 0 0.183478116 728.028259 701932.8416 0.059972748 0.050161644 183.8606533 -2.264488799 -0.089197261 VTPTEEHVEGPLPSPVTNGTS(ph)PAQLNGGSACSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTPTEEHVEGPLPSPVTNGTSPAQLNGGSACSSR 34 0 H3BN50;Q15599-3;H3BQS0;H3BUQ9;Q15599;Q15599-2 H3BN50;Q15599 SLC9A3R2 Na(+)/H(+) exchange regulatory cofactor NHE-RF2 1 VTPTEEHVEGPLPSPVTNGT(0.25)S(0.75)PAQLNGGSACSSR;VTPTEEHVEGPLPSPVT(0.001)NGT(0.116)S(0.44)PAQLNGGS(0.28)ACS(0.082)S(0.082)R 344.09 1.28E-118 722460000 154840 132046 157894 151654 148081 163985 181241 128937 143544 TRUE FALSE 145148.8408 141822.8232 161639.3202 155545.6984 136451.3156 211324.8074 154065.5946 145035.0683 119585.5791 1.213765422 1.185952557 1.351662312 1.300706152 1.141034869 1.767142904 1.28832921 1.212814032 1 16.8676839 0.929607766 3.08531245 1.001182539 1.323227754 0.264078814 0.171098643 0.436470434 9.898471236 0.157080045 0.041124913 8.503696777 -0.929607766 0.322045215 VTPTEEHVEGPLPSPVTNGTSPAQLNGGS(ph)ACSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTPTEEHVEGPLPSPVTNGTSPAQLNGGSACSSR 34 0 H3BN50;Q15599-3;H3BQS0;H3BUQ9;Q15599;Q15599-2 H3BN50;Q15599 SLC9A3R2 Na(+)/H(+) exchange regulatory cofactor NHE-RF2 1 VTPTEEHVEGPLPSPVT(0.125)NGT(0.026)S(0.026)PAQLNGGS(0.817)ACS(0.002)S(0.002)R 143.98 1.61E-10 115160000 92284 89581 101320 91634 81175 100140 100600 78209 66929 TRUE FALSE 86508.10917 96213.67045 103723.3582 93985.48358 74799.84294 129048.7924 85515.96392 87973.56581 55758.11752 1.551489057 1.725554497 1.860237807 1.685592838 1.341505888 2.314439549 1.533695321 1.577771448 1 15.76689423 0.78323333 1.782439002 1.002493016 1.740475446 0.440048303 0.25330384 0.657957469 3.578768149 0.216881798 0.06121751 6.070623941 -0.78323333 0.73798243 VTQDELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTQDELK 7 0 P19338;H7BY16 P19338 NCL Nucleolin 0 117.72 0.0305 0 175530 170200 161050 155100 199980 115860 182700 157960 251600 FALSE TRUE 164543.8906 182801.7851 164870.1821 159080.1286 184274.3775 149306.9012 155305.8311 177681.6537 209606.3346 0.785013921 0.872119564 0.786570608 0.758947142 0.879145078 0.712320558 0.740940542 0.847692194 1 17.67732279 0.957451447 10.59302117 0.999999931 0.793747744 0.617776673 0.051846756 1.780131653 443.4913843 0.051190018 0.012802523 9.066745948 -0.957451447 -0.206252187 VTQDFTHPPDQS(ph)PLRPDAANR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTQDFTHPPDQSPLRPDAANR 21 1 Q9BYX2-4;Q9BYX2-2;Q9BYX2;Q9BYX2-3 Q9BYX2-4 TBC1D2 TBC1 domain family member 2A 1 VTQDFTHPPDQS(1)PLRPDAANR 139.73 1.04E-07 131560000 60131 59927 55631 69222 72124 60824 70107 54026 72463 TRUE FALSE 56367.50805 64364.05743 56950.59359 70998.35371 66459.67197 78382.9014 59595.10619 60771.26503 60368.45717 0.933724509 1.066186887 0.943383288 1.176083621 1.100900621 1.298408226 0.987189486 1.006672489 1 15.88150731 3.246620045 24.99953706 1.101102275 0.993943666 0.222226072 0.098921108 278.4262078 863644.0332 0.026629243 0.035430588 1764.493429 -3.246620045 -0.107158609 VTQHES(ph)DNENEIQIQNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VTQHESDNENEIQIQNK 17 0 Q5VZL5-2;Q5VZL5-4;Q5VZL5 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 VT(0.027)QHES(0.973)DNENEIQIQNK;VT(0.033)QHES(0.967)DNENEIQIQNK;VT(0.002)QHES(0.998)DNENEIQIQNK;VT(0.111)QHES(0.889)DNENEIQIQNK 336.94 1.97E-72 1695220000 1736700 1415870 1500630 1461800 1624620 1170128 1984140 1511500 1701190 TRUE FALSE 1628003.047 1520702.488 1536225.652 1499312.263 1497028.899 1507924.958 1686636.627 1700214.102 1417250.399 1.148705302 1.072994927 1.083947941 1.057902163 1.056291041 1.063979209 1.190076664 1.199656817 1 20.43466324 1.752694046 25 1.148631846 1.078326208 0.103905966 0.060124332 6.170949358 10930.6237 0.024732024 0.013715087 56.58405223 -1.752694046 -0.070305638 VTQVDGHSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTQVDGHSSK 10 0 O43324;H0YAL7;D6RBD7;C9J1V9;O43324-2 O43324 EEF1E1;EEF1E1-BLOC1S5 Eukaryotic translation elongation factor 1 epsilon-1 0 ; 98.407 0.0053979 247330000 261670 499740 427020 489450 539810 411370 531710 508290 455010 FALSE TRUE 245292.5418 536741.2696 437149.1161 502010.1156 497415.5001 530125.841 451985.0217 571751.1254 379065.8915 0.647097371 1.415957704 1.153227251 1.324334705 1.312213816 1.398505782 1.192365316 1.508315937 1 18.53208912 4.745371208 24.86876649 1.291811155 0.647097051 0.658462699 0.145064444 404.1805636 1475817.935 0.029683271 0.29173847 55637.96132 -4.745371208 -0.644714104 VTQVDGNS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTQVDGNSPVR 11 0 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 1 VTQVDGNS(1)PVR 93.716 0.0036558 0 177720 201590 179270 204000 227080 164310 224200 192760 158620 TRUE FALSE 166596.8224 216515.9334 183522.3691 209234.9854 209246.0528 211743.6297 190583.2914 216826.5103 132145.2973 1.26070943 1.638468699 1.388792283 1.583370651 1.583454403 1.602354636 1.442225303 1.640818968 1 17.01176556 -1.495170543 6.940403251 0.999837327 1.518841287 0.639983552 0.121982446 0.000267883 1.95E-05 0.103046083 0.024280747 0.031976392 1.495170543 0.51900396 VTRS(ph)PPTQVAISSDSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VTRSPPTQVAISSDSAR 17 1 Q6ZUT6;Q6ZUT6-4;H0YM82;Q6ZUT6-3 Q6ZUT6 C15orf52 Uncharacterized protein C15orf52 1 VT(0.034)RS(0.966)PPTQVAISSDSAR;VT(0.017)RS(0.982)PPT(0.001)QVAISSDSAR;VT(0.001)RS(0.999)PPTQVAISSDSAR 181.83 4.73E-10 2846750000 320696 315988 326482 340117 389618 281325 353851 301058 463724 TRUE FALSE 300624.2098 339384.0803 334226.3072 348844.978 359018.9739 362538.9606 300794.3275 338645.754 386325.4686 0.778163063 0.878492639 0.865141789 0.902982087 0.929317384 0.938428838 0.778603411 0.876581488 1 18.55945727 VTRSPPTQVAISS(ph)DSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTRSPPTQVAISSDSAR 17 1 Q6ZUT6;Q6ZUT6-4;H0YM82;Q6ZUT6-3 Q6ZUT6 C15orf52 Uncharacterized protein C15orf52 1 VTRS(0.008)PPT(0.323)QVAIS(0.027)S(0.642)DS(0.001)AR 138.77 6.66E-06 105220000 29405 33216 30394 26949 36285 20543 32157 26097 39089 TRUE FALSE 27564.59354 35675.3472 31114.96003 27640.55696 33435.32247 26473.43061 27335.35638 29355.2679 32564.79338 0.846453814 1.095518918 0.955478503 0.848786499 1.026732216 0.812946371 0.839414397 0.90144186 1 14.99102545 3.449123665 5.605267798 0.89262477 0.998794371 0.065161791 0.090237565 0.247642256 22.02729008 0.023421752 0.032882813 2812.701629 -3.449123665 0.106169602 VTRVEFEELCADLFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTRVEFEELCADLFER 16 1 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 93.765 0.0039407 69984000 41334.5 54523 43919 56643 66173 38719.1 54419 43609 76734 FALSE TRUE 38747.44743 58559.93965 44960.77942 58096.55528 60976.03951 49896.67562 46259.37615 49053.67965 63926.59968 0.606124018 0.916049656 0.703318801 0.908800962 0.953844563 0.780530732 0.723632672 0.767343796 1 15.96412874 4.754497266 24.19524287 0.824857131 0.606123759 0.337632331 0.101634423 2464.029061 3740825.397 0.023448372 0.573244849 56819.48151 -4.754497266 -0.218733372 VTS(ph)GGVSESPSGFSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTSGGVSESPSGFSK 15 0 E7EPP6;O14757-2;O14757-3;O14757 E7EPP6 CHEK1 Serine/threonine-protein kinase Chk1 1 VT(0.039)S(0.961)GGVSESPSGFSK;VTS(0.967)GGVS(0.033)ESPSGFSK 237.89 2.49E-13 0 792410 667540 721820 906070 1084650 491830 775000 598890 818490 TRUE FALSE 742814.4726 716965.3562 738941.9113 929321.2902 999465.9643 633813.3368 658795.9447 673662.7348 681878.7314 1.089364484 1.051455813 1.083685232 1.362883527 1.465753247 0.929510348 0.966148253 0.987950942 1 19.37915566 VTSAHKGPDETLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VTSAHKGPDETLR 13 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;;;; 204.35 4.72E-08 4484820000 2412300 3463520 3057870 3137180 3862930 2444690 4044510 2958490 4778810 FALSE TRUE 2261318.449 3719962.625 3130404.12 3217685.35 3559551.06 3150432.317 3438073.273 3327863.989 3981195.739 0.567999817 0.934383253 0.786297466 0.808220836 0.894090945 0.791328165 0.863578055 0.835895597 1 21.92477037 -5 0.083892909 1.531434292 0.668901603 0.363126026 0.091213983 298.4843975 1.76161972 29.5741259 2.476138403 1.00E-05 5 -0.86253269 VTSSMS(ph)SPSMQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTSSMSSPSMQPK 13 0 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 1 VTS(0.001)S(0.01)MS(0.548)S(0.389)PS(0.052)MQPK 98.943 0.0020562 102500000 202590 159270 190210 176400 192430 128340 220050 164320 234090 TRUE FALSE 189910.2535 171062.5165 194721.871 180926.7226 177317.324 165389.6746 187055.5453 184835.7137 195018.8667 0.973804518 0.877158807 0.998477092 0.927739586 0.90923164 0.848070124 0.959166405 0.947783755 1 17.57325418 0.944664743 1.892617965 0.998749748 0.926049469 0.219266858 0.043734606 0.611946738 4.598534133 0.039916391 0.01124397 8.803690039 -0.944664743 -0.072700278 VTSSMSS(ph)PSMQPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 VTSSMSSPSMQPK 13 0 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 1 VTSSMS(0.006)S(0.994)PS(0.001)MQPK;VTSSMS(0.357)S(0.641)PS(0.001)MQPK;VTSSMS(0.048)S(0.936)PS(0.016)MQPK;VTSSMS(0.003)S(0.996)PS(0.001)MQPK;VTSSMS(0.002)S(0.993)PS(0.005)MQPK;VTSSMS(0.015)S(0.985)PSMQPK;VTSSMS(0.002)S(0.994)PS(0.004)MQPK;VTSSMSS(0.998)PS(0.002)MQPK;VTSS(0.003)MS(0.086)S(0.9)PS(0.011)MQPK;VT(0.001)S(0.005)S(0.05)MS(0.374)S(0.482)PS(0.089)MQPK 326.89 2.68E-62 2586167000 5577530 4539470 5191010 4935410 5842300 4080570 6593570 5269990 7818290 TRUE FALSE 5228442.353 4875577.082 5314143.209 5062060.976 5383469.325 5258564.316 5604925.39 5927959.852 6513366.891 0.802724987 0.748549431 0.815882676 0.777180383 0.826526344 0.807349625 0.860526588 0.910122207 1 22.63497206 1.119369611 0.703974213 1.002755084 0.78243169 0.92421781 0.019777368 0.153526426 0.17919546 0.017570201 0.007146297 13.16344645 -1.119369611 -0.220323395 VTSSVPLPSGSTSS(ph)PGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VTSSVPLPSGSTSSPGR 17 0 Q15036-2;Q15036 Q15036-2 SNX17 Sorting nexin-17 1 VTSSVPLPSGSTS(0.051)S(0.949)PGR;VTSSVPLPSGSTS(0.001)S(0.999)PGR;VTSSVPLPSGSTS(0.001)S(0.999)PGR;VTSSVPLPSGSTS(0.001)S(0.999)PGR;VTSSVPLPSGSTS(0.006)S(0.994)PGR 325.33 3.10E-59 2322840000 2244600 2236790 2379160 2247520 2443290 2223450 2733320 2202380 2391330 TRUE FALSE 2104114.493 2402404.259 2435594.799 2305195.168 2251403.859 2865323.92 2323484.041 2477351.991 1992201.574 1.056175499 1.205904207 1.222564438 1.1571094 1.130108463 1.438270081 1.166289632 1.243524763 1 20.9259322 4.738529191 6.040365699 1.209986444 1.052124497 0.12547664 0.109836564 0.228921404 41.25514715 0.023199035 0.148551966 54768.29117 -4.738529191 -0.157861947 VTTHPLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VTTHPLAK 8 0 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ;;;; 95.531 0.0095844 6579560000 10193740 11570760 9675203 9449899 13636130 6549359 11738420 11362780 15188940 FALSE TRUE 9555732.01 12427471.11 9904703.384 9692399.407 12565203.36 8440052.623 9978352.895 12781448.1 12653807.79 0.755166521 0.982113156 0.78274489 0.765967017 0.992997805 0.666997062 0.788565234 1.010087106 1 23.59306825 1.232122739 24.92592903 1.005043698 0.826266793 0.373505588 0.099728481 173.8243357 672973.8787 0.084385141 0.023105023 17.06564623 -1.232122739 -0.178776906 VTTVTEIGKDVIGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTTVTEIGKDVIGLR 15 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITI7 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 242.01 6.02E-18 285660000 706770 786720 823480 828800 993750 710800 1220000 795370 1330400 FALSE TRUE 662534.5273 844969.5674 843013.3345 850068.4112 915704.8836 915996.4211 1037072.326 894673.6953 1108347.645 0.597767794 0.762368713 0.760603713 0.766969114 0.826189226 0.826452264 0.935692272 0.807213963 1 20.07997904 6.815524966 0.119039833 1.074906828 6.16E-18 0.795268321 0.048648003 29.87742284 0.323838925 0.351876831 5.171200967 6539205.197 -6.815524966 -1.074906828 VTVAGGVHISGLHTESAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTVAGGVHISGLHTESAPR 19 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 264.23 1.48E-31 2765300000 357770 1035330 811910 951700 955500 829880 1016220 998210 795740 FALSE TRUE 335377.8143 1111986.91 831168.8886 976122.2332 880458.8843 1069452.884 863847.2451 1122838.716 662925.8533 0.505905468 1.677392585 1.253788617 1.472445566 1.328140817 1.613231523 1.303082752 1.693762146 1 19.33848799 4.748110089 24.95921761 1.429994811 0.505904967 0.643602871 0.213068004 714.2981332 1866904.051 0.043288611 0.563464588 55989.95121 -4.748110089 -0.924089844 VTVAGLAGKDPVQCSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTVAGLAGKDPVQCSR 16 1 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ; 214.63 1.54E-14 6085000000 3099400 3161000 2867700 3040900 4246100 3304200 5110100 3760500 5657000 FALSE TRUE 2905414.087 3395043.729 2935723.198 3118934.642 3912628.434 4258068.901 4343887.945 4230006.703 4712810.154 0.616492919 0.72038627 0.622924137 0.661799338 0.83021134 0.903509533 0.921719272 0.897555082 1 22.16815614 2.55688386 2.299953526 0.92513461 0.658653108 0.916038457 0.039394771 0.078272853 0.823777681 0.014072892 0.012417885 360.4822292 -2.55688386 -0.266481502 VTVDTGVIPASEEKAET(ph)PTAAEDDNEGDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTVDTGVIPASEEKAETPTAAEDDNEGDKK 30 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 VTVDTGVIPAS(0.001)EEKAET(0.993)PT(0.006)AAEDDNEGDKK 110.09 0.011008 81636000 173440 60431 96716 77808 92266 64292 124890 76200 137980 TRUE FALSE 162584.7 64905.37412 99010.14919 79804.68501 85019.80054 82852.05671 106163.9039 85713.73774 114950.2466 1.41439192 0.564638842 0.861330463 0.694254143 0.739622602 0.720764497 0.923563951 0.745659451 1 16.81065004 -0.87742122 7.470955491 1.000000001 0.80818108 0.04032961 0.229049411 2.89E-09 3.87E-10 0.19384769 0.045690339 0.132610765 0.87742122 -0.19181892 VTVDTGVIPASEEKAETPTAAEDDNEGDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTVDTGVIPASEEKAETPTAAEDDNEGDKK 30 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 104.51 0.00019313 103840000 59846 29018 34505 33396 41165 25407 39020 25890 66513 FALSE TRUE 56100.34569 31166.52291 35323.47489 34252.9979 37932.06695 32741.58845 33169.31324 29122.42349 55411.55061 1.012430532 0.562455347 0.63747494 0.618156278 0.684551624 0.590880206 0.598599261 0.525565937 1 15.75789912 -1.570133996 8.095899693 1.000119757 0.638212767 0.388286718 0.135329692 0.000259075 1.38E-05 0.116049745 0.027344273 0.026907045 1.570133996 -0.36190699 VTVHST(ph)PVRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTVHSTPVRR 10 1 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 1 VTVHS(0.022)T(0.978)PVRR 125.53 0.00030999 42897000 60283 58711 54311 59810 61948 40350 65142 55287 84627 TRUE FALSE 56509.99464 63058.02353 55599.28257 61344.82586 57082.85397 51998.38997 55374.56185 62189.70365 70502.20699 0.801535116 0.894412051 0.788617618 0.870112135 0.809660526 0.737542727 0.78543019 0.882095842 1 16.1053808 0.947161711 4.465692738 0.999880581 0.815331133 0.654529599 0.043697809 0.169818782 9.909059313 0.043982443 0.011177533 8.854452465 -0.947161711 -0.184549448 VTVLFAGQHISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTVLFAGQHISK 12 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 109.83 0.001555 341230000 451780 1029500 735770 717640 1115700 569740 859720 949350 1003500 FALSE TRUE 423503.8963 1105725.251 753222.8119 736055.8574 1028077.423 734214.689 730812.9672 1067878.437 836009.3671 0.506577932 1.322623041 0.90097413 0.880439725 1.229743904 0.878237395 0.874168396 1.277352239 1 19.67315958 4.761200558 24.0715881 1.030933686 0.506576983 0.483693361 0.174393124 3416.379459 3632318.972 0.040132323 2.053216742 57703.28773 -4.761200558 -0.524356703 VTWAHPEFGQVLASCSFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTWAHPEFGQVLASCSFDR 19 0 K7ELV2;Q96EE3;Q96EE3-1;K7EP88;K7EPZ5 K7ELV2 SEH1L Nucleoporin SEH1 0 104.06 0.00036061 228710000 112410 152660 146290 146580 162470 128280 144080 121550 143640 FALSE TRUE 105374.4588 163963.1052 149760.0679 150341.491 149710.2616 165312.3535 122476.5416 136725.7851 119665.5561 0.88057468 1.370177941 1.251488505 1.256347239 1.251072293 1.381453102 1.023490348 1.142565911 1 16.86864843 1.676021834 8.781050208 1.063573239 1.251432033 0.247469282 0.141735067 0.146286967 18.58932744 0.062494139 0.033156038 47.42658287 -1.676021834 0.187858795 VTYLVHNFEEGGGVAMGMYNQDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTYLVHNFEEGGGVAMGMYNQDK 23 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 279.74 6.81E-52 527840000 1294880 1119590 1241170 1138450 1371220 957610 1457490 1154210 1718290 FALSE TRUE 1213835.772 1202485.609 1270611.139 1167664.554 1263529.912 1234056.462 1238952.905 1298315.659 1431496.298 0.847948942 0.840020061 0.887610495 0.815695127 0.882663765 0.862074504 0.865495011 0.906964035 1 20.44909251 0.781869208 1.306962705 1.000166468 0.856215141 0.836454996 0.020206778 0.273260562 0.834966044 0.017475843 0.005260356 6.051585974 -0.781869208 -0.143951327 VTYMEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTYMEEER 8 0 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 107.01 0.014572 348870000 630620 767280 673840 685340 821610 495210 689530 719220 817200 FALSE TRUE 591150.6199 824090.2096 689823.803 702926.9847 757084.0648 638169.0879 586141.3778 809016.2002 680804.0407 0.868312443 1.210466096 1.013248691 1.032495318 1.112044024 0.937375588 0.860954611 1.188324616 1 19.37688007 2.232939131 24.99610649 0.970074193 1.064242701 0.011195297 0.118868881 281.2912994 1250758.503 0.041132306 0.031225397 170.9775663 -2.232939131 0.094168508 VTYRPLDPDNYDKDLSFIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VTYRPLDPDNYDKDLSFIK 19 2 O60825;O60825-2 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 0 ; 77.023 0.0068317 271930000 761460 579920 613030 652060 659750 472640 792930 544420 745760 FALSE TRUE 713801.5778 622857.8802 627571.3611 668792.9635 607935.8963 609083.4953 674037.5077 612392.0354 621287.8382 1.148906407 1.002527077 1.010113707 1.076462345 0.97850925 0.980356379 1.084903754 0.985681672 1 19.24490229 4.742868745 24.81065496 1.018494804 1.148906465 0.558116782 0.037368644 302.9615378 1744694.713 0.008501172 0.066824513 55318.28979 -4.742868745 0.130411661 VTYS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VTYSPR 6 0 Q96K76-2;Q96K76-4;Q96K76;Q96K76-3 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 VTYS(1)PR 85.813 0.056946 294170000 474270 725250 433350 440270 725770 292580 480620 619480 536440 TRUE FALSE 444586.2873 778948.2646 443629.2666 451568.0736 668770.9518 377043.0964 408555.4929 696823.4416 446904.6985 0.994812292 1.742985176 0.992670849 1.010434831 1.49645093 0.843676734 0.914189299 1.559221561 1 18.76960769 3.807353279 6.489537443 1.096866178 1.411292283 0.105344029 0.29487941 0.360100064 23.67530998 0.070254916 0.127534316 6417.31384 -3.807353279 0.314426104 VVACTSAFLLWDPTKVPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVACTSAFLLWDPTKVPPR 19 1 P30043 P30043 BLVRB Flavin reductase (NADPH) 0 127.78 2.07E-05 65265000 86723 82682 84170 78626 87634 64451 102150 77936 80257 FALSE TRUE 81295.16223 88803.86131 86166.55215 80643.67627 80751.57914 83056.95743 86833.55581 87666.48116 66861.58822 1.215872437 1.328174572 1.288730263 1.206128637 1.207742462 1.242222323 1.29870615 1.311163607 1 16.02889 -1.388908265 5.389242199 0.999863276 1.268636273 0.774118761 0.044420127 7.65E-05 8.67E-06 0.04508419 0.010621071 0.040840564 1.388908265 0.268772996 VVAEPVELAQEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVAEPVELAQEFR 13 0 O75489 O75489 NDUFS3 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial" 0 ; 151.98 0.00010468 59520000 65231 76539 72066 65046 86658 73756 71951 78393 106717 FALSE TRUE 61148.30815 82206.0272 73775.43955 66715.19048 79852.23024 95048.15987 61162.61551 88180.53861 88905.24328 0.687791922 0.924647683 0.829821019 0.750407828 0.898172338 1.069095099 0.68795285 0.991848572 1 16.43998089 2.524854323 22.65279847 0.904274115 0.824499474 0.205719611 0.117865312 333.0355424 158048.3737 0.036717156 0.034615504 334.8530995 -2.524854323 -0.079774642 VVAPVESHVPES(ph)NQAQGESPAANEGTTVQHPEAPQEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVAPVESHVPESNQAQGESPAANEGTTVQHPEAPQEEK 38 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 VVAPVESHVPES(0.493)NQAQGES(0.493)PAANEGT(0.007)T(0.007)VQHPEAPQEEK 60.181 0.03197 129090000 24571 23062 24973 26615 19589 18854 25771 17184 35446 TRUE FALSE 23033.14497 24769.53448 25565.37135 27297.98596 18050.55896 24296.84373 21906.8778 19329.46023 29529.83361 0.779995759 0.838796954 0.86574722 0.924420582 0.611265177 0.822789727 0.741855782 0.654573963 1 14.84988561 2.770574202 24.98251498 0.754459797 0.852250768 0.12939852 0.10872604 1092.980965 852930.0654 0.029257969 0.031030096 589.6227089 -2.770574202 0.097790971 VVASGPGLEHGK ddPTM_SK-BR-3_Pertuzumab_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 ; 186.17 1.21E-05 869990000 1962750 2088630 1694020 1725330 2007580 1106470 2264060 1922730 2608050 FALSE TRUE 1839904.981 2243274.338 1734202.954 1769604.889 1849912.765 1425889.927 1924585.222 2162787.073 2172749.606 0.846809488 1.032458748 0.798160519 0.814454129 0.851415533 0.656260585 0.885783256 0.995414781 1 21.05109049 1.292748356 4.889264603 0.999498526 0.846121551 0.344175558 0.091062779 0.242164585 11.08241577 0.072195468 0.023960669 19.62222975 -1.292748356 -0.153376975 VVDLMAHMASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 VVDLMAHMASK 11 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;; 166.97 2.95E-05 28487590000 29293650 35513540 27451780 26664880 36065910 21093760 34771310 31532090 30835120 FALSE TRUE 27460212.74 38142999.45 28102949.19 27349145.96 33233438.91 27183186.08 29557674.87 35468940.85 25688539.27 1.068967466 1.48482555 1.093987824 1.064643874 1.293706838 1.05818341 1.15061719 1.380730157 1 24.61462152 3.786146973 8.079156754 1.151921236 1.302402638 0.106007018 0.150231195 0.478406486 59.07845703 0.034689732 0.062596992 6111.488139 -3.786146973 0.150481403 VVDLMAHMASKE ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 VVDLMAHMASKE 12 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;; 184.31 2.32E-05 38604412000 19971240 29672450 21473930 23203200 32227960 14725030 21647760 24123930 32134620 FALSE TRUE 18721275.74 31869429.07 21983301.76 23798633.39 29696906.02 18975907.12 18401879.36 27135855.76 26771144.32 0.699308013 1.190439553 0.821156597 0.888965862 1.109287883 0.708819425 0.687377392 1.013623304 1 24.67417547 2.225443906 24.99808917 0.807308137 0.956874023 0.030304349 0.173504221 434.4679678 828012.1207 0.060736858 0.045128199 168.0520854 -2.225443906 0.149565886 VVDRDSEEAEIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VVDRDSEEAEIIR 13 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;; 255.85 6.87E-24 2984650000 2011900 2422370 2251180 2274700 2426260 1910030 2524380 2172230 2556240 FALSE TRUE 1885978.77 2601724.795 2304579.053 2333072.653 2235711.327 2461424.654 2145872.654 2443437.697 2129587.03 0.885607746 1.221703907 1.082171811 1.095551682 1.049833275 1.155822523 1.007647316 1.147376305 1 21.02214226 -4.942978178 0.350382467 0.001368701 1.093158893 0.052776409 0.09195139 1072.347367 9.143080596 803.2134899 0.063178851 1.14E-05 4.942978178 1.091790193 VVDRDSEEAEIIRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VVDRDSEEAEIIRK 14 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;; 204.82 7.37E-09 1936190000 1170040 1443690 1347760 1428310 1854420 1007820 1715500 1277630 2552300 FALSE TRUE 1096809.285 1550582.31 1379729.504 1464962.853 1708781.334 1298761.273 1458276.701 1437144.918 2126304.642 0.515828853 0.729238078 0.648886089 0.68897129 0.803638999 0.610806772 0.685826797 0.67588853 1 21.01991688 -5 0.418023441 6.903593171 0.670428748 0.662931943 0.074097403 526.760749 3.449028158 2854.325397 0.039126464 1.00E-05 5 -6.233164423 VVDYSQFQES(ph)DDADEDYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 30 VVDYSQFQESDDADEDYGR 19 0 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYS(0.001)QFQES(0.999)DDADEDYGR;VVDYS(0.002)QFQES(0.998)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYS(0.005)QFQES(0.995)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYS(0.004)QFQES(0.996)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR 343.12 4.33E-76 23734440500 4173316.2 4328707.9 4310004.2 4228831 4087385.8 4029034.2 4734100 3844165.2 3591929.1 TRUE FALSE 3912115.789 4649209.937 4412239.535 4337349.963 3766379.007 5192150.968 4024265.654 4324117.687 2992412.928 1.307344903 1.553665904 1.474475495 1.449449012 1.258642807 1.735105111 1.344822974 1.44502707 1 21.51287784 0.263560783 1.26661216 0.999509162 1.463295817 0.520261726 0.134113426 3.680338032 5.616361772 0.116683811 0.034004242 1.834681928 -0.263560783 0.463786656 VVDYSQFQES(ph)DDADEDYGRDSGPPTK ddPTM_SK-BR-3_Pertuzumab_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 305.42 2.58E-71 11666087000 2303278 2622070 2254163 2445224 2985886 1657822 2896408 2311980 4406807 TRUE FALSE 2159119.941 2816210.791 2307632.811 2507972.588 2751386.558 2136408.299 2462118.509 2600635.792 3671282.443 0.588110551 0.767091836 0.628563138 0.683132564 0.749434728 0.581924255 0.670642629 0.708372574 1 21.80785268 0.724657698 3.239029943 0.999987218 0.672467417 0.750133558 0.05985945 1.246794933 14.13084774 0.052721832 0.01368655 5.304661774 -0.724657698 -0.327519802 VVDYSQFQES(ph)DDADEDYGRDSGPPTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVDYSQFQESDDADEDYGRDSGPPTKK 27 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 VVDYSQFQES(1)DDADEDYGRDSGPPTKK;VVDYSQFQES(1)DDADEDYGRDSGPPTKK 199.22 2.78E-25 4042600000 237307 250822 217289 277242 352690 152797 328694 219808 742290 TRUE FALSE 222454.3785 269393.1219 222443.1977 284356.4991 324991.1501 196907.0134 279409.3861 247251.5127 618397.0036 0.359727452 0.435631351 0.359709372 0.459828391 0.525538041 0.318415213 0.451828493 0.399826505 1 19.2381738 -1.775755881 2.477648375 1.162970974 0.414169357 0.906050357 0.059321109 4896665.058 3348894.001 4834949.761 0.013644706 0.016758846 1.775755881 -0.748801617 VVDYSQFQESDDADEDYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVDYSQFQESDDADEDYGR 19 0 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 170.42 2.85E-11 57076000 27888 27407 28113 29201 29332 27751 31616 21978 30411 FALSE TRUE 26142.53986 29436.2428 28779.85364 29950.3471 27028.38304 35762.2632 26875.47431 24722.00168 25335.20764 1.03186602 1.161870991 1.135962809 1.18216308 1.066830927 1.411563849 1.060795502 0.975796292 1 14.62885603 1.497101009 10.87790632 0.997967283 1.163448031 0.357836388 0.099896866 0.099540239 32.51845072 0.049182889 0.022807315 31.41239206 -1.497101009 0.165480748 VVEAVNS(ph)DS(ph)DSEFGIPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVEAVNSDSDSEFGIPK 17 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 VVEAVNS(1)DS(0.997)DS(0.003)EFGIPK 198.77 2.03E-11 79650000 307270 233580 244560 246070 252850 196640 328500 210020 275780 TRUE FALSE 288038.5192 250874.5062 250361.0787 252384.5728 232992.1809 253406.7758 279244.4746 236241.4593 229750.5364 1.253701183 1.091943071 1.089708353 1.098515706 1.01410941 1.102964893 1.215424691 1.028252047 1 17.8097087 -4.999854999 0.013245017 4.17E-07 1.982236055 0.267760464 0.069664627 14912.55606 14.99196494 1368.050988 917.3704251 1.00E-05 4.999854999 1.982235638 VVEELTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVEELTR 7 0 Q16531;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ; 100.45 0.022762 151607000 287267 353650 333460 306786 393105 275112 352757 322493 413728 FALSE TRUE 269287.4713 379834.614 341369.8287 314658.6481 362232.119 354532.3683 299864.3627 362756.9609 344674.124 0.781281368 1.10201082 0.990413277 0.912916364 1.050940856 1.028601637 0.869993834 1.052463576 1 18.39487347 -1.666398553 9.255063879 1.000015331 0.981246715 0.001785936 0.096535531 2.81E-05 1.01E-06 0.085902264 0.020230821 0.021557651 1.666398553 -0.018768616 VVEHPEFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVEHPEFLK 9 0 P06396-2;Q5T0I0 P06396-2 GSN Gelsolin 0 91.867 0.010463 168660000 352080 498380 276070 294700 497130 164460 409480 447250 577460 FALSE TRUE 330043.9413 535280.5738 282618.5108 302262.5009 458087.4151 211936.9322 348082.2754 503090.147 481078.1955 0.68605051 1.112668541 0.587468967 0.628302226 0.952209889 0.440545704 0.723546148 1.045755455 1 18.87591189 1.238818373 24.99878719 1.022877845 0.744357433 0.292444687 0.186821275 9.042963288 877828.1114 0.143627923 0.044934477 17.33079054 -1.238818373 -0.278520411 VVENLQDDFDFNYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVENLQDDFDFNYK 14 0 P40763;P40763-2;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 ; 203.88 3.35E-08 85710000 141805 126578 131957 127056 158035 111230 160473 132860 191172 FALSE TRUE 132929.6782 135949.9668 135087.0824 130316.4721 145623.5686 143340.2953 136411.5634 149447.8635 159264.1582 0.834649049 0.853613069 0.848195124 0.81824105 0.914352421 0.90001603 0.856511377 0.938364697 1 17.2810621 0.407964386 0.318100253 1.028790082 0.834001007 0.76015525 0.026974243 1.650811008 0.329260908 0.098479303 0.030791774 2.558376081 -0.407964386 -0.194789075 VVESLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VVESLR 6 0 Q12905;B4DY09;X6R6Z1 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ;; 132.94 0.034151 881140000 776740 865350 844520 827350 866580 687480 879020 763850 939000 FALSE TRUE 728125.2299 929421.4144 864552.4132 848581.2017 798522.3024 885944.3157 747219.1114 859218.3539 782274.8338 0.93077931 1.188100875 1.105177331 1.084760963 1.020769515 1.132523095 0.95518746 1.09835868 1 19.57731603 2.289931608 1.015864557 1.02103108 1.100819204 0.011686444 0.08018555 1.068218689 2.129322492 0.052251959 0.031004153 194.9537567 -2.289931608 0.079788124 VVEVLAGHGHLYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 203.85 8.36E-09 11466444300 2465200.4 3864170.8 3174915.7 3188688.7 3912013.1 2809481 3995547.3 3413869.6 3764790 FALSE TRUE 2310907.907 4150278.027 3250226.2 3270515.85 3604779.371 3620532.557 3396452.075 3840098.734 3136422.228 0.736797453 1.323252332 1.036284647 1.04275369 1.149328474 1.154351134 1.082906519 1.224356434 1 21.58068836 2.72316604 23.86184247 1.126201143 1.083104177 0.034706279 0.15281893 2497.362022 3870942.861 0.046043818 0.043579803 528.6473261 -2.72316604 -0.043096966 VVFQEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVFQEFR 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 78.149 0.084026 46852000 27184 217620 28048 27263 194080 29172 25929 156420 111240 FALSE TRUE 25482.60196 233732.8112 28713.31181 27962.61474 178837.7397 37593.48283 22041.18716 175949.3813 92673.32536 0.274972349 2.522115294 0.309833619 0.301733154 1.929765 0.405655918 0.237837448 1.898597904 1 16.49986652 3.881802331 8.038429135 0.797316709 1.538550131 0.056223479 0.819922401 0.48301635 35.90259118 0.193856759 0.351012185 7617.322288 -3.881802331 0.741233422 VVFVFGPDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVFVFGPDKK 10 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 107.83 0.0054606 0 1144000 1586200 818750 831710 2070100 516770 1009700 1781000 2053800 FALSE TRUE 1072399.082 1703643.898 838171.1366 853053.0867 1907522.696 665953.1099 858304.8586 2003361.77 1711007.512 0.626764684 0.995696329 0.489869934 0.498567704 1.11485349 0.389216941 0.501637107 1.17086673 1 20.70641466 1.232120622 24.99995544 1.085433557 0.664256858 0.365855131 0.233059096 181.1541778 703204.8155 0.199566037 0.054622412 17.06556308 -1.232120622 -0.4211767 VVGFHVLGPNAGEVTQGFAAALK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVGFHVLGPNAGEVTQGFAAALK 23 0 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 128.09 4.37E-05 169830000 598030 510290 430540 426700 525010 383310 418730 377620 484960 FALSE TRUE 560600.3698 548072.4026 440752.6121 437649.8444 483777.8324 493965.3745 355945.3238 424766.6882 404017.043 1.387566142 1.35655763 1.090925791 1.083245997 1.197419368 1.222634993 0.881015615 1.051358341 1 18.62405663 7.999999992 0.2490744 0.974184359 3.830608759 0.656969542 0.091249304 30.06993176 0.409279125 0.119952712 35.95064338 99999998.08 -7.999999992 2.8564244 VVGS(ph)SPGHPAVQVESHSGGQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVGSSPGHPAVQVESHSGGQK 21 0 Q6AI39 Q6AI39 GLTSCR1L GLTSCR1-like protein 1 VVGS(0.5)S(0.5)PGHPAVQVESHSGGQK;VVGS(0.5)S(0.5)PGHPAVQVESHSGGQK 167.72 1.96E-11 248310000 328780 284260 308450 305700 354160 233441 386020 310970 368390 TRUE FALSE 308202.2467 305306.9062 315766.5797 313544.7795 326345.7022 300831.6271 328139.8846 349795.289 306903.3291 1.004232335 0.994798287 1.028879617 1.021640203 1.063350154 0.980216239 1.069196237 1.139757232 1 18.22742477 2.728641907 0.668015026 1.06259348 1.001542494 0.188133092 0.042404754 1.178163038 1.123754451 0.030249141 0.031142428 535.3550546 -2.728641907 -0.061050987 VVGSVGQHTGEPVEELALSHCGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VVGSVGQHTGEPVEELALSHCGR 23 0 Q9H6Y2;G3V1J0;Q9H6Y2-2 Q9H6Y2 WDR55 WD repeat-containing protein 55 0 ;;; 296.62 6.18E-62 1599550000 922380 1067260 1049340 1007390 1187070 886980 1199730 975740 1113590 FALSE TRUE 864649.8823 1146281.041 1074230.84 1033241.333 1093842.311 1143036.727 1019841.624 1097563.287 927724.6349 0.932011342 1.235583273 1.157919926 1.113737087 1.179059248 1.232086208 1.09929346 1.183070111 1 19.82333713 -0.554832272 7.96342234 0.99999998 1.151887524 0.200342398 0.086763395 0 0 0.074400271 0.017536312 0.27871974 0.554832272 0.151887544 VVHVNGYGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVHVNGYGK 9 0 E9PEX6;P09622-2;P09622 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 ; 163.99 6.26E-05 1599050000 2413500 2316700 2214700 1898470 3074400 2094100 2318200 2562800 4133400 FALSE TRUE 2262443.343 2488230.879 2267233.73 1947187.954 2832949.026 2698632.675 1970607.431 2882771.221 3443508.837 0.657016854 0.722585884 0.658407989 0.565466228 0.822692538 0.783686874 0.572267279 0.837160977 1 21.71544795 0.995643712 6.099679027 0.99986956 0.685264381 0.628663684 0.080752089 0.076752568 14.37162115 0.074131557 0.018637311 9.900194166 -0.995643712 -0.314605179 VVIEACDELGIILAHTNLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVIEACDELGIILAHTNLR 19 0 P31939-2;P31939 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 202.03 5.72E-16 53642000 50031 48845 51246 53954 50639 44142 51789 47180 36695.6 FALSE TRUE 46899.64902 52461.53462 52461.57932 55338.55098 46662.01721 56885.07881 44023.72024 53070.52686 30570.8673 1.534128835 1.716063012 1.716064474 1.810172752 1.526355689 1.86076104 1.440054671 1.735983685 1 14.89986986 -1.293453082 0.446368965 0.665336113 1.693188922 0.708669187 0.133737871 11.94638166 1.308651658 4.853120792 0.064531575 0.050879978 1.293453082 1.027852809 VVIVDPETGKEMSVYEAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVIVDPETGKEMSVYEAYR 19 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 166.6 1.79E-11 410680000 1295730 1337290 1356590 1391610 1392530 1167340 1618060 1363000 1101180 FALSE TRUE 1214632.572 1436304.343 1388768.955 1427321.069 1283166.311 1504332.108 1375446.924 1533173.55 917385.9441 1.324014805 1.565648953 1.513832825 1.555856701 1.398720265 1.639802874 1.499311095 1.671241597 1 19.80716928 -1.144889293 5.321537085 0.999985216 1.525174769 0.718904745 0.102365523 1.55E-05 2.49E-06 0.085569026 0.020168246 0.071632599 1.144889293 0.525189554 VVKPKS(ph)PEPEATLTFPFLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVKPKSPEPEATLTFPFLDK 20 2 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 VVKPKS(1)PEPEATLTFPFLDK 155.56 1.49E-08 229560000 1232800 757220 904730 1003900 1297700 521290 1056700 708110 1822400 TRUE FALSE 1155641.249 813285.3567 926190.6228 1029661.774 1195783.877 671777.9606 898257.6449 796519.0922 1518229.667 0.761176832 0.535680058 0.610046453 0.678198955 0.787617251 0.442474532 0.591648065 0.524636759 1 20.53395862 -1.123556892 4.739678349 1.000027586 0.606674012 0.563536296 0.105775585 2.88E-05 5.32E-06 0.095606942 0.022533194 0.075239016 1.123556892 -0.393353575 VVLAYEPVWAIGTGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVLAYEPVWAIGTGK 15 0 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3 P60174 TPI1 Triosephosphate isomerase 0 ; 158.04 4.29E-06 96922000 586150 626620 566700 543890 668850 480360 746860 561060 755780 FALSE TRUE 549463.9178 673015.5968 580142.3916 557847.1382 616321.219 619032.134 634875.2765 631109.576 629635.4355 0.87266994 1.068897268 0.921394126 0.885984344 0.978854086 0.983159618 1.008322024 1.00234126 1 19.26415721 2.217680312 2.729248983 1.002150542 0.955382757 0.191685552 0.053888214 0.58274427 8.897228843 0.023241868 0.016390097 165.0746223 -2.217680312 -0.046767785 VVLDDKDYFLFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VVLDDKDYFLFR 12 1 P61604;B8ZZ54 P61604 HSPE1 "10 kDa heat shock protein, mitochondrial" 0 ;; 172.76 3.18E-05 9000044000 10063960 8742750 7953810 7251980 12225480 6780220 8125310 9318660 14436240 FALSE TRUE 9434074.708 9390072.307 8142478.129 7438078.084 11265340.12 8737559.446 6906995.197 10482115.21 12026738.28 0.784425044 0.78076633 0.67703129 0.61846179 0.936691217 0.726511149 0.574303276 0.871567583 1 23.51974209 1.002656454 22.56145154 1.000000008 0.72412371 0.460780318 0.098805973 15.70902554 133411.3384 0.093404456 0.023351114 10.06135456 -1.002656454 -0.275876298 VVLEHEEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVLEHEEVR 9 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ; 166.33 6.08E-05 1085830000 815200 966350 856740 900920 1004250 783810 1009710 866200 880120 FALSE TRUE 764178.0872 1037899.559 877062.2774 924039.1325 925380.2559 1010083.223 858313.3592 974346.9767 733222.2862 1.042218849 1.415531932 1.196175149 1.260244199 1.26207328 1.377594819 1.17060457 1.328856194 1 19.48389111 -1.711807888 2.803171477 0.958886482 1.264173316 0.361516596 0.106781312 19011078.1 17292905.28 5514740.712 0.022987365 0.019417446 1.711807888 0.305286834 VVLGDGVQLPPGDYS(ph)TTPGGTLFS(ph)TTPGGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 31 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 VVLGDGVQLPPGDY(0.045)S(0.302)T(0.302)T(0.303)PGGT(0.099)LFS(0.313)T(0.313)T(0.278)PGGT(0.045)R 51.025 0.040093 28672000 16252 18124 17935 19243 20221 19163 21082 20503 31244 TRUE FALSE 15234.81633 19465.91982 18360.42667 19736.80796 18632.92423 24695.04701 17920.94982 23062.84468 26029.17456 0.585297713 0.747850062 0.705378752 0.758257159 0.71584768 0.948744915 0.688494742 0.886038266 1 14.66784194 -4.999999753 0.046648068 2.124695806 0.164511245 0.609158855 0.079506888 416.6306008 1.442767813 59.91049216 14.81014091 1.00E-05 4.999999753 -1.960184561 VVLGDGVQLPPGDYST(ph)TPGGTLFSTT(ph)PGGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 31 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 VVLGDGVQLPPGDY(0.005)S(0.09)T(0.395)T(0.395)PGGT(0.115)LFS(0.186)T(0.144)T(0.642)PGGT(0.028)R 88.595 0.0010228 32290000 39842 43057 45137 46771 52209 43885 45774 44335 74213 TRUE FALSE 37348.36034 46244.98508 46207.67096 47971.22304 48108.71574 56553.88709 38910.61364 49870.32234 61826.37087 0.60408463 0.747981556 0.747378025 0.775902295 0.778126147 0.914721118 0.629353027 0.80661895 1 15.9159347 -5 0.196248846 2.087008907 0.707472716 0.500903023 0.082582883 122.916411 1.21222092 52.54171346 0.198775271 1.00E-05 5 -1.379536191 VVLGDGVQLPPGDYSTT(ph)PGGTLFS(ph)TTPGGTRIIYDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 VVLGDGVQLPPGDY(0.075)S(0.104)T(0.115)T(0.699)PGGT(0.01)LFS(0.386)T(0.349)T(0.255)PGGT(0.005)RIIYDRK 129.18 2.58E-08 68188000 33360 42872 37158 38343 74733 32400 44271 34803 208980 TRUE FALSE 31272.05715 46046.28749 38039.40531 39326.94629 68863.77164 41753.35403 37632.97454 39148.23116 174099.8879 0.179621351 0.264482005 0.218491843 0.225887258 0.395541734 0.239824129 0.216157374 0.224860749 1 17.40955575 -1.921224387 2.603285389 1.470053109 0.246252206 0.944634351 0.057396616 11772159.87 6487490.086 33722499.93 0.013753999 0.011988797 1.921224387 -1.223800903 VVLGDGVQLPPGDYSTT(ph)PGGTLFSTT(ph)PGGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 31 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 VVLGDGVQLPPGDYS(0.004)T(0.013)T(0.974)PGGT(0.016)LFS(0.02)T(0.012)T(0.862)PGGT(0.1)R;VVLGDGVQLPPGDYS(0.01)T(0.031)T(0.909)PGGT(0.05)LFS(0.054)T(0.043)T(0.867)PGGT(0.035)R;VVLGDGVQLPPGDY(0.001)S(0.03)T(0.155)T(0.806)PGGT(0.008)LFS(0.047)T(0.034)T(0.895)PGGT(0.024)R;VVLGDGVQLPPGDYS(0.002)T(0.006)T(0.982)PGGT(0.01)LFS(0.001)T(0.006)T(0.979)PGGT(0.015)R;VVLGDGVQLPPGDYS(0.001)T(0.002)T(0.943)PGGT(0.055)LFS(0.024)T(0.078)T(0.887)PGGT(0.011)R;VVLGDGVQLPPGDY(0.003)S(0.195)T(0.195)T(0.554)PGGT(0.054)LFS(0.055)T(0.19)T(0.712)PGGT(0.042)R 155.61 5.95E-09 1091351000 1367319 1430938 1464329 1469283 1870380 1481585 1752750 1623793 2559040 TRUE FALSE 1281740.945 1536886.138 1499063.575 1506987.289 1723487.9 1909294.538 1489941.409 1826527.13 2131919.692 0.601214459 0.720893073 0.703151991 0.706868694 0.808420648 0.895575263 0.69887314 0.856752315 1 21.02372166 -4.999999995 0.045870881 2.149562147 0.136382555 0.724947733 0.060976409 351.1575886 1.196729539 51.33948887 12.98610061 1.00E-05 4.999999995 -2.013179592 VVLIGGKPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVLIGGKPDR 10 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ; 148.73 2.24E-05 11973000000 13753100 12988200 13186300 12953100 14207400 10822900 15479100 11782300 14799700 FALSE TRUE 12892318.02 13949859.84 13499085.26 13285498.48 13091608.11 13947295.53 13158152.66 13253346.09 12329534.46 1.045645159 1.131418213 1.094857661 1.077534478 1.061808794 1.131210232 1.06720596 1.074926724 1 23.55561499 0.525882682 0.941910258 0.999684239 1.0941219 0.485429063 0.027735515 1.23879505 1.648402455 0.025355165 0.008143887 3.356469323 -0.525882682 0.094437661 VVLLGEFLHPCEDDIVCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVLLGEFLHPCEDDIVCK 18 0 Q9NY12-2;Q9NY12 Q9NY12-2 GAR1 H/ACA ribonucleoprotein complex subunit 1 0 ; 228.21 2.55E-19 394310000 493410 430160 400400 383080 495520 437480 630390 411920 576970 FALSE TRUE 462528.3489 462009.494 409897.6771 392910.4814 456603.858 563773.3741 535868.8718 463349.1187 480669.9796 0.962257616 0.961178175 0.852763215 0.817422552 0.949932131 1.172890752 1.114837403 0.96396517 1 18.87468718 2.413371933 6.81437599 1.079702568 0.899515909 0.536910064 0.071792967 0.148819237 12.72356305 0.024968837 0.020866267 259.043043 -2.413371933 -0.180186659 VVNANQNAS(ph)PNVPGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVNANQNASPNVPGKR 16 1 Q8IWI9-3;Q8IWI9;H3BP52;H3BTF4 Q8IWI9-3 MGA MAX gene-associated protein 1 VVNANQNAS(1)PNVPGKR 170.89 1.45E-12 0 32255 26042 26456 26839 30714 25683 35058 29799 41039 TRUE FALSE 30236.21713 27970.17678 27083.54881 27527.73418 28301.84633 33097.26517 29801.37836 33519.47075 34189.32578 0.88437594 0.818096764 0.792163876 0.805155807 0.827797732 0.968058434 0.871657387 0.98040748 1 15.06125835 1.777294769 0.852996861 0.99041805 0.815848966 0.665096891 0.044036477 0.330594019 0.454848446 0.0372761 0.016539947 59.8817893 -1.777294769 -0.174569084 VVNAPIFHVNSDDPEAVMYVCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVNAPIFHVNSDDPEAVMYVCK 22 0 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;E9PFG7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 139.44 9.27E-09 0 71708 81093 67152 67333 96440 79730 70061 79327 105920 FALSE TRUE 67219.92428 87097.2101 68744.87715 69060.87877 88865.99142 102746.7567 59556.00346 89231.15057 88241.26773 0.761774236 0.987034891 0.779055865 0.782636974 1.007079723 1.164384413 0.674922346 1.011217913 1 16.4291659 2.738138823 24.99930372 0.944816424 0.846098789 0.196601972 0.136577123 91.57671562 5427558.403 0.043101782 0.042919363 547.190845 -2.738138823 -0.098717636 VVNGGVPWPS(ph)PCPS(ph)PSSRPPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(1)PCPS(0.874)PS(0.06)S(0.067)RPPSR;VVNGGVPWPS(1)PCPS(0.971)PS(0.02)S(0.008)RPPSR;VVNGGVPWPS(1)PCPS(0.964)PS(0.017)S(0.019)RPPSR 149.04 3.77E-08 546370000 608140 640430 666170 643090 717680 610030 826040 598930 747230 TRUE FALSE 570077.603 687848.1036 681971.867 659592.7781 661316.3078 786135.758 702182.9706 673707.7289 622512.4857 0.915768946 1.104954711 1.095515163 1.05956554 1.062334207 1.262843358 1.127982148 1.082239705 1 19.24774325 4.73900702 5.991445393 1.109695822 0.910466692 0.41250629 0.067932213 0.124543342 21.55990969 0.015623284 0.101076322 54828.58269 -4.73900702 -0.19922913 VVNGGVPWPSPCPS(ph)PSSRPPSR ddPTM_SK-BR-3_Pertuzumab_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 1 VVNGGVPWPS(0.004)PCPS(0.924)PS(0.055)S(0.017)RPPSR 118.9 5.07E-05 60955000 69080 65584 71344 71088 77867 65090 84169 55734 69599 TRUE FALSE 64756.40611 70439.9076 73036.31337 72912.23843 71751.63992 83880.42635 71548.63984 62692.51259 57982.47727 1.116827172 1.214848191 1.259627336 1.257487466 1.2374711 1.446651304 1.233970041 1.081232047 1 15.82332935 1.150236709 3.52396618 1.007718159 1.258431265 0.555749307 0.080487624 0.162400124 3.570298134 0.074172525 0.019705447 14.13307647 -1.150236709 0.250713106 VVNSCHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VVNSCHR 7 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;;;; 153.73 0.0017267 706271000 234596 1037320 298735 312692 998040 252661 344083 873680 725529 FALSE TRUE 219913.0551 1114124.252 305821.1353 320716.2061 919657.9643 325600.1291 292490.9485 982760.8712 604433.5228 0.36383332 1.843253576 0.505963226 0.530606252 1.521520448 0.538686418 0.48390921 1.625920526 1 19.20522415 3.892752748 12.57297678 0.834433886 1.204772233 0.012508682 0.542763264 1.903119445 277.7688674 0.128027553 0.230871684 7811.829357 -3.892752748 0.370338347 VVNTDHGS(ph)PEQLQIPVTDSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VVNTDHGSPEQLQIPVTDSGR 21 0 Q6IQ49-3;Q6IQ49-2;Q6IQ49 Q6IQ49-3 SDE2 Protein SDE2 homolog 1 VVNT(0.156)DHGS(0.844)PEQLQIPVTDSGR;VVNT(0.001)DHGS(0.999)PEQLQIPVTDSGR;VVNTDHGS(1)PEQLQIPVTDSGR;VVNT(0.007)DHGS(0.993)PEQLQIPVTDSGR;VVNT(0.058)DHGS(0.942)PEQLQIPVTDSGR 265.89 3.90E-37 1865031000 1212748 1203274 1261961 1202081 1402665 1159408 1377988 1285181 1413353 TRUE FALSE 1136844.267 1292365.659 1291895.311 1232928.434 1292505.349 1494110.268 1171371.492 1445638.677 1177455.254 0.965509529 1.097592163 1.097192702 1.047112771 1.0977108 1.268931676 0.994833127 1.227765278 1 20.1672408 4.740135226 4.90588209 1.103838139 0.958141111 0.199212302 0.087291638 0.271255525 19.6638476 0.018352428 0.134894745 54971.20103 -4.740135226 -0.145697027 VVPEDGS(ph)PEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VVPEDGSPEKR 11 1 Q02040 Q02040 AKAP17A A-kinase anchor protein 17A 1 VVPEDGS(1)PEKR;VVPEDGS(1)PEKR;VVPEDGS(1)PEKR;VVPEDGS(1)PEKR 130.24 0.00013988 5251400000 11251300 7730000 8782600 8715300 8815200 6402300 11140200 7541600 9733300 TRUE FALSE 10547101.22 8302337.243 8990927.419 8938949.353 8122889.751 8250540.077 9469830.431 8483185.361 8108749.35 1.300706282 1.023873952 1.108793358 1.102383237 1.001743845 1.01748614 1.167853392 1.046176789 1 22.95104799 4.745354251 24.88165713 1.068501466 1.300706395 0.656299472 0.054654288 480.744976 1760678.353 0.012713888 0.12452391 55635.78891 -4.745354251 0.232204929 VVPGQFDDADS(ph)SDSENRDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VVPGQFDDADSSDSENRDLK 20 1 E9PFQ8;Q9BRS2 E9PFQ8 RIOK1 Serine/threonine-protein kinase RIO1 1 VVPGQFDDADS(0.639)S(0.361)DSENRDLK;VVPGQFDDADS(0.5)S(0.5)DSENRDLK;VVPGQFDDADS(0.5)S(0.5)DS(0.001)ENRDLK 209.3 2.92E-22 665930000 571472 458079 514137 464876 593952 357836 637465 426263 994375 TRUE FALSE 535704.5876 491995.6458 526332.5724 476805.5052 547305.4058 461137.4442 541883.0412 479482.8739 828407.3886 0.646668046 0.593905429 0.635354754 0.575568871 0.660671806 0.556655398 0.654126277 0.578800818 1 19.6599809 -1.66196924 2.842526073 1.042249602 0.613877061 0.919206433 0.036082211 4706285.819 4468618.123 1447949.017 0.007266237 0.02177864 1.66196924 -0.428372542 VVPGQFDDADSS(ph)DSENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VVPGQFDDADSSDSENR 17 0 E9PFQ8;Q9BRS2 E9PFQ8 RIOK1 Serine/threonine-protein kinase RIO1 1 VVPGQFDDADS(0.001)S(0.999)DSENR;VVPGQFDDADS(0.006)S(0.994)DSENR;VVPGQFDDADS(0.201)S(0.799)DSENR;VVPGQFDDADS(0.029)S(0.971)DSENR 335.14 3.90E-72 1446110000 1217790 1101720 1244020 1132860 1128710 1182710 1441300 1120890 1058820 TRUE FALSE 1141570.698 1183292.495 1273528.742 1161931.106 1040065.67 1524139.177 1225190.445 1260835.584 882096.1018 1.294156833 1.341455305 1.443752828 1.317238681 1.179084306 1.727860688 1.388953474 1.429363061 1 19.75057632 VVPGQFDDADSS(ph)DSENRDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVPGQFDDADSSDSENRDLK 20 1 E9PFQ8;Q9BRS2 E9PFQ8 RIOK1 Serine/threonine-protein kinase RIO1 1 VVPGQFDDADS(0.022)S(0.978)DSENRDLK 243.94 4.40E-30 138660000 130450 109290 121140 105080 123730 85155 156060 104740 247000 TRUE FALSE 122285.3674 117381.9453 124013.498 107776.5307 114012.7449 109737.8661 132660.2518 117817.0196 205774.1043 0.594269953 0.570440803 0.602668146 0.523761389 0.554067507 0.533292887 0.644688758 0.572555132 1 17.65070191 -0.585176572 0.693920031 1.044687479 0.57075716 0.937994206 0.034401664 3.575954425 1.196029521 0.431356343 0.012064422 0.259910262 0.585176572 -0.473930319 VVPGYGHAVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVPGYGHAVLR 11 0 O75390;B4DJV2;A0A0C4DGI3;H0YIC4 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 ; 180.8 6.51E-06 1527710000 1112460 1611420 1248130 1225610 1944290 1353170 1142120 1610770 2056460 FALSE TRUE 1042833.114 1730731.213 1277736.233 1257061.228 1791593.306 1743808.212 970869.7089 1811878.18 1713223.541 0.608696466 1.010219141 0.74580824 0.733740342 1.04574404 1.017852119 0.566691786 1.057584219 1 20.70828198 VVPSFLPVDQGGS(ph)LVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VVPSFLPVDQGGSLVGR 17 0 Q14126 Q14126 DSG2 Desmoglein-2 1 VVPSFLPVDQGGS(1)LVGR;VVPSFLPVDQGGS(1)LVGR;VVPSFLPVDQGGS(1)LVGR;VVPSFLPVDQGGS(1)LVGR;VVPSFLPVDQGGS(1)LVGR 237 3.49E-20 383733000 317507 362410 286091 275398 413710 216039 386454 306720 269744 TRUE FALSE 297634.8036 389243.2135 292877.2136 282465.1789 381218.8854 278405.9522 328508.8104 345014.6672 224721.9838 1.324457886 1.732110081 1.303286882 1.256953922 1.696402279 1.238890595 1.461845454 1.535295574 1 17.77778174 -1.985077025 2.720805657 0.589655281 1.450561796 0.395445038 0.172206245 27585123.96 6032847.268 70984049.92 0.038394221 0.010349586 1.985077025 0.860906514 VVQVSAGDSHTAALTDDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VVQVSAGDSHTAALTDDGR 19 0 P18754-2;C9JW69;P18754;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4 P18754-2 RCC1 Regulator of chromosome condensation 0 ;;; 264.96 2.25E-31 2473050000 606442 753656 693971 642788 783514 642038 781528 667718 846057 FALSE TRUE 568485.8777 809457.4744 710432.3198 659283.0283 721979.971 827383.948 664345.1318 751084.0621 704844.621 0.806540705 1.148419737 1.007927561 0.935359381 1.024310819 1.173852965 0.942541252 1.065602318 1 19.42694573 VVS(ph)ETNDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVSETNDTK 9 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 VVS(0.948)ET(0.052)NDTK 123.26 0.0005904 249620000 357480 250790 281140 271570 321690 232060 328490 232430 381160 TRUE FALSE 335105.9649 269358.7525 287808.7736 278538.946 296425.765 299051.9548 279235.9741 261449.3971 317541.9336 1.055312478 0.84826199 0.906364619 0.877172167 0.933501165 0.941771537 0.879367241 0.823353924 1 18.2765876 1.655080406 11.87668341 0.88864364 0.913854439 0 0.069628021 0.521721347 106.3376838 0.030008214 0.016333316 45.19396095 -1.655080406 0.025210799 VVSETNDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VVSETNDTK 9 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 253.26 1.58E-14 1727190000 1612110 1200010 1397820 1272640 1385500 1141060 1650410 1193870 1983690 FALSE TRUE 1511210.913 1288859.989 1430976.95 1305298.097 1276688.419 1470465.498 1402946.342 1342927.298 1652599.324 0.914444833 0.779898654 0.865894673 0.789845474 0.772533548 0.889789483 0.848933145 0.81261518 1 20.65630555 -4.991885296 0.421669364 4.10496568 0.829950516 0.544277185 0.047392992 688.2100801 4.477698228 1979.926491 0.025248869 1.02E-05 4.991885296 -3.275015164 VVSHLIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVSHLIEK 8 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ; 99.139 0.0070255 452080000 1680500 1963650 1502300 1586080 2234630 1165100 1877120 1850950 2277660 FALSE TRUE 1575320.505 2109040.689 1537935.265 1626781.498 2059131.174 1501445.456 1595663.282 2082045.182 1897503.832 0.830206758 1.11148165 0.810504432 0.857327121 1.085178928 0.791274005 0.840927568 1.097254797 1 20.85567137 1.233237728 24.99992743 1.048627422 0.910545875 0.220793969 0.112530766 225.3818584 1058490.422 0.0943654 0.026331004 17.10951616 -1.233237728 -0.138081547 VVSHPTLPVTITAHEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVSHPTLPVTITAHEDR 17 0 Q13033-2;Q13033 Q13033-2 STRN3 Striatin-3 0 ; 242.48 1.20E-20 347040000 166319 216767 225808 215236 241290 186650 209694 184726 208294 FALSE TRUE 155909.3907 232816.6542 231164.2724 220759.3202 222340.0567 240532.825 178252.3314 207789.4477 173528.3858 0.898466208 1.341663228 1.332140971 1.272179875 1.281289258 1.38612956 1.027222899 1.197437796 1 17.40481215 1.707701011 9.613751249 1.0864728 1.273349917 0.243033725 0.143351169 0.142116662 28.49555396 0.063276376 0.034068601 51.01536645 -1.707701011 0.186877117 VVSISSEHLEPIT(ph)PTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVSISSEHLEPITPTK 16 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 1 VVSISSEHLEPIT(0.981)PT(0.019)K 111.02 0.0031253 252950000 302350 298380 306970 292360 337300 261030 398290 331190 341580 TRUE FALSE 283426.4532 320472.3657 314251.4734 299862.4526 310809.8186 336385.1235 338570.112 372539.8005 284568.0913 0.995988172 1.126171118 1.104310297 1.053745876 1.092215987 1.1820901 1.189768363 1.309141158 1 18.11841438 2.244937801 5.102889743 1.187132525 1.084033269 0.236946241 0.082173438 0.225937151 16.52069288 0.027178915 0.02125808 175.7671863 -2.244937801 -0.103099256 VVSQS(ph)QPGS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVSQSQPGSR 10 0 Q7Z460-4 Q7Z460-4 CLASP1 CLIP-associating protein 1 2 VVS(0.044)QS(0.956)QPGS(1)R;VVS(0.014)QS(0.986)QPGS(1)R 94.717 0.01157 420690000 540830 717460 615510 566100 704510 434510 789690 655380 840960 TRUE FALSE 506980.4157 770581.4849 630110.1879 580627.0844 649180.6265 559945.9833 671283.3156 737205.6357 700598.3432 0.723639187 1.099890533 0.899388635 0.82875886 0.926608852 0.799239662 0.958157155 1.052251469 1 19.41822805 1.463115061 6.949050409 1.020522676 0.905266105 0.248610929 0.099939849 0.237987347 30.30873465 0.057772252 0.024897539 29.04792143 -1.463115061 -0.115256571 VVSQSQPGS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VVSQSQPGSR 10 0 Q7Z460-4 Q7Z460-4 CLASP1 CLIP-associating protein 1 1 VVSQSQPGS(1)R;VVSQSQPGS(1)R;VVSQSQPGS(1)R;VVSQSQPGS(1)R 143.31 3.59E-05 637430000 878840 896520 1017240 1036810 962470 1087530 917650 848410 738940 TRUE FALSE 823834.9732 962899.2736 1041369.413 1063416.3 886881.4886 1401482.256 780056.9015 954335.8561 615606.1403 1.338250091 1.564148261 1.691616352 1.727429651 1.440663812 2.276589145 1.267136324 1.550237715 1 19.2316481 0.790802374 1.365387522 1.007317502 1.641355422 0.332849505 0.274702706 0.799332673 2.675298139 0.233873566 0.069697705 6.177352347 -0.790802374 0.63403792 VVSSVSSS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVSSVSSSPR 10 0 P29375;P29375-2 P29375 KDM5A Lysine-specific demethylase 5A 1 VVS(0.002)S(0.006)VS(0.01)S(0.235)S(0.747)PR 63.164 0.084304 156240000 290660 301220 297500 300640 357920 264420 363930 298750 310060 TRUE FALSE 272468.1094 323522.6422 304556.8405 308354.9314 329810.407 340753.7615 309362.0751 336049.5951 258308.9829 1.054814689 1.252463769 1.179040841 1.193744514 1.276805798 1.319171163 1.197643503 1.30095977 1 17.97873829 4.744467052 24.09400895 1.224851588 1.054814563 0.232949008 0.089762096 498.4606175 2033259.714 0.018496393 0.16311708 55522.24934 -4.744467052 -0.170037025 VVSVLTVLHQDWLNGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVSVLTVLHQDWLNGK 16 0 A0A0A0MS08;P01857;A0A4W9A917;A0A286YFJ8;A0A286YES1;P01861;P01860 A0A0A0MS08 IGHG1;IGHG4;IGHG3 Ig gamma-1 chain C region;Ig gamma-4 chain C region;Ig gamma-3 chain C region 0 ; 299.89 7.41E-46 542590000 10008600 3383000 502020 285640 288200 77398 59921 61201 60446 FALSE TRUE 9382179.592 3633480.84 513928.1515 292970.006 265565.9345 99741.54615 50936.40233 68842.07957 50357.1721 186.312678 72.15418754 10.20565949 5.817840712 5.273646701 1.980682036 1.011502438 1.367075963 1 15.61990965 4.544836794 1.482438152 4.107477821 200 0.974185057 9.438680475 0.117412204 0.314503128 2.540521363 30.41967423 35062.00877 -4.544836794 195.8925222 VVTDTDETELAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVTDTDETELAR 12 0 P05198 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ; 204.64 2.58E-07 524350000 362970 371730 373600 394390 436430 372400 458700 342890 469590 FALSE TRUE 340252.3556 399253.276 382461.9684 404510.7151 402154.5483 479905.8346 389922.1934 385700.5713 391212.3953 0.869738177 1.020553747 0.977632542 1.033992583 1.027969852 1.226714287 0.996702042 0.985910917 1 18.57759256 6.089984598 0.686997815 1.048020526 1.51E-13 0.319677141 0.072369061 20.14861175 1.688181503 0.026596581 24.99354934 1230225.142 -6.089984598 -1.048020526 VVTS(ph)ENEAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVTSENEAGK 10 0 P49321;P49321-3;P49321-4;E9PPR5 P49321 NASP Nuclear autoantigenic sperm protein 1 VVT(0.099)S(0.901)ENEAGK 103.2 0.0041438 0 297050 267560 254900 276320 255710 208080 289920 229060 216400 TRUE FALSE 278458.1707 287370.4208 260946.3484 283410.839 235627.5681 268149.3181 246449.1875 257658.6452 180281.442 1.544574792 1.594009997 1.447438768 1.572046661 1.306998466 1.487392796 1.367024718 1.429202265 1 17.45989137 -3.357715218 0.159832172 3.05E-14 1.627213034 0.825822659 0.071770862 25.45648761 0.380898211 8.77164738 0.290933968 0.000438818 3.357715218 1.627213034 VVTTPAFMCETALHYIHDGIGAMVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVTTPAFMCETALHYIHDGIGAMVR 25 0 P0DPI2-2;A0A0B4J2D5-2;P0DPI2;A0A0B4J2D5;A0A096LNH5;A0A096LPI6 P0DPI2-2 0 259.2 3.14E-45 102040000 109940 124070 72450 70060 164810 83872 76924 125200 99445 FALSE TRUE 103059.0516 133256.2719 74168.54821 71857.85821 151866.4874 108084.4849 65389.96033 140831.4956 82846.98706 1.243968614 1.6084625 0.895247381 0.867356325 1.833096082 1.304627829 0.789285919 1.699898821 1 16.33816161 7.999931962 0.021273463 1.16E-06 2.835408192 0.018978491 0.364808954 12221.6777 20.02339448 970.2732331 1822.075332 99984334.86 -7.999931962 2.835407034 VVTTSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVTTSAR 7 0 F8VTQ9;F8VXU8;Q8IUR5 F8VTQ9 TMTC1 Transmembrane and TPR repeat-containing protein 1 0 ; 132.94 0.0077236 679100000 384640 835500 318880 306780 887020 254590 314010 650320 722160 FALSE TRUE 360566.069 897361.2893 326443.9842 314652.4942 817357.0273 328086.0001 266927.1156 731513.8835 601626.8307 0.599318466 1.491557962 0.542602104 0.523002762 1.358578085 0.545331397 0.443675551 1.215893052 1 19.19850938 3.922422623 9.569809398 0.758770616 1.097340441 0.052471738 0.376758206 0.77708054 131.3639965 0.090209444 0.16317702 8364.165613 -3.922422623 0.338569825 VVTVFSVADGYSENNVFYGHHAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVTVFSVADGYSENNVFYGHHAK 23 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 286.6 1.03E-52 508840000 358300 332690 368120 354220 409430 336690 440840 379490 372530 FALSE TRUE 335874.6426 357322.7138 376851.9802 363309.8849 377275.0194 433886.9373 374740.1346 426870.1619 310352.3364 1.082236553 1.151345332 1.214271446 1.170636861 1.215634539 1.398046306 1.207466775 1.375437243 1 18.24354748 4.340870647 0.689672034 1.253305905 1.040919466 0.149736124 0.109784644 3.070555789 1.568415026 0.042825925 0.469559299 21921.51916 -4.340870647 -0.21238644 VVVHPLVLLSVVDHFNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVVHPLVLLSVVDHFNR 17 0 P51665;H3BNT7;H3BTM8;H3BQV2 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ; 291.46 3.10E-46 446530000 455020 719040 527140 500300 676690 381760 579480 648070 485990 FALSE TRUE 426541.1104 772278.4698 539644.0097 513138.545 623545.497 491967.9146 492592.3536 728982.9661 404875.1294 1.053512749 1.907448528 1.332865297 1.267399521 1.540093357 1.215110238 1.216652538 1.80051308 1 18.6271175 3.719000039 23.87457536 1.338065037 1.565080305 0.021061244 0.294912134 368.113793 1082178.399 0.070309801 0.111181778 5236.00483 -3.719000039 0.227015269 VVVLMGSTSDLGHCEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVVLMGSTSDLGHCEK 16 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 280.62 1.80E-35 1198820000 2194490 2178000 2364600 2472600 2541000 2064110 2908400 2268300 2169000 FALSE TRUE 2057140.788 2339261.386 2420689.429 2536051.102 2341440.11 2659985.049 2472312.42 2551502.248 1806979.888 1.138441442 1.294569686 1.339632746 1.403475002 1.295775413 1.472061237 1.368201404 1.412025815 1 20.78514902 5.260742848 1.120959842 1.353267638 0.715864082 0.150042678 0.128618738 6.65660236 3.084439848 0.031620134 6.635082252 182281.6066 -5.260742848 -0.637403556 VVVQVLAEEPEAVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVVQVLAEEPEAVLK 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 ; 218.95 4.35E-12 81780000 439330 413620 420220 444200 477000 376020 560040 437130 535950 FALSE TRUE 411833.1195 444244.8552 430187.8168 455598.924 439538.3441 484570.8698 476067.2012 491706.6427 446496.4826 0.922365876 0.994957122 0.963474145 1.020386368 0.98441614 1.085273655 1.066228335 1.101255356 1 18.76828928 2.24722903 23.98898103 1.069034266 0.979658112 0.585485893 0.035800886 69.84481033 193288.6888 0.011254148 0.009269737 176.6969405 -2.24722903 -0.089376153 VVVS(ph)PTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 VVVSPTK 7 0 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 VVVS(0.994)PT(0.006)K;VVVS(0.986)PT(0.014)K;VVVS(0.874)PT(0.126)K;VVVS(1)PTK;VVVS(0.999)PT(0.001)K;VVVS(0.994)PT(0.006)K;VVVS(0.999)PT(0.001)K 179.28 0.00073777 7062630000 15209160 10146530 12254060 10787980 11187740 9757480 14876770 9966580 11892960 TRUE FALSE 14257245.82 10897789.64 12544732.09 11064817.83 10309100.03 12574306.08 12646136.45 11210929.45 9907948.145 1.438970574 1.099903782 1.266128154 1.116761782 1.040487887 1.269113029 1.276362801 1.131508693 1 23.24015489 VVVS(ph)PTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVVSPTKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 VVVS(0.986)PT(0.014)KK;VVVS(0.873)PT(0.127)KK 94.692 0.0062348 14084400000 8017100 4161500 5658100 5200300 5826700 3809600 7360600 4851100 7212900 TRUE FALSE 7515324.022 4469621.79 5792312.804 5333748.502 5369094.486 4909369.676 6256946.362 5456770.514 6009020.393 1.250673742 0.743818709 0.963936287 0.887623631 0.893505785 0.817000003 1.041258966 0.908096521 1 22.51869839 1.723737601 24.99999958 0.981862396 0.906694171 0.024911564 0.135813607 2.633763423 4423.867771 0.056578828 0.031375885 52.93435202 -1.723737601 -0.075168225 VVVSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VVVSNR 6 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;; 143.18 0.026596 1464260000 626980 700810 658650 675190 752520 594140 784420 602030 734760 FALSE TRUE 587738.441 752698.7016 674273.489 692516.5185 693420.1147 765658.5729 666803.5032 677194.7707 612123.8093 0.960162686 1.229651077 1.101531224 1.131334067 1.132810233 1.250823055 1.089327834 1.106303595 1 19.22346396 0.842869755 1.702259243 1.001050498 1.140419074 0.195245226 0.079211735 0.820270136 4.481155996 0.066992347 0.019119614 6.964176263 -0.842869755 0.139368576 VVWVEESDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 187.97 1.88E-06 1371490000 1253190 1569740 945810 917480 1914740 614760 1005660 1510420 1856450 FALSE TRUE 1174755.075 1685965.183 968245.0598 941024.0901 1764364.044 792231.2322 854870.6191 1698999.262 1546596.502 0.759574377 1.090113149 0.626048914 0.60844835 1.140804367 0.512241707 0.552743148 1.098540738 1 20.56066542 5.088251202 14.80866265 0.797064608 3.97E-05 0 0.245344343 11237042.18 29398017.53 0.056676625 286495709 122532.4739 -5.088251202 -0.797024912 VVYAFS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VVYAFSPK 8 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 VVYAFS(1)PK;VVYAFS(1)PK;VVYAFS(1)PK 121.61 0.0014958 855580000 1155760 1544610 864560 948060 1857440 525534 1068660 1449270 1960460 TRUE FALSE 1083423.045 1658974.532 885067.7715 972388.8247 1711564.155 677247.1345 908424.354 1630214.55 1633246.561 0.663355473 1.015752656 0.541907017 0.595371726 1.047952095 0.414663132 0.556207725 0.998143568 1 20.63931117 1.220777621 24.61690098 0.999072357 0.696194969 0.291020279 0.199932513 311.199665 430777.9828 0.18772949 0.047365348 16.62561123 -1.220777621 -0.302877388 VVYENAYGQFIGPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VVYENAYGQFIGPHR 15 0 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881;E9PKD3 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 ; 198.81 7.74E-09 1596110000 1445630 1478860 1528490 1397720 1619630 1305000 1621910 1461170 1465210 FALSE TRUE 1355150.599 1588356.333 1564746.505 1433587.862 1492430.793 1681732.315 1378719.653 1643600.291 1220656.985 1.110181333 1.301230691 1.281888789 1.174439567 1.222645519 1.377727187 1.129489831 1.346488252 1 20.21922642 -1.115617325 4.112928846 0.99994545 1.246362011 0.429894867 0.08787263 5432362.7 1473509.776 2750.610958 0.018360717 0.07662715 1.115617325 0.246416561 VVYVENDIQHLQDMSHFPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VVYVENDIQHLQDMSHFPDR 20 0 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 0 165.06 9.96E-12 18482000 22697 32706 27277 27964 29935 23347 30358 25497 32445 FALSE TRUE 21276.43529 35127.58627 27924.02332 28681.60358 27584.02585 30086.89989 25806.09973 28680.35658 27029.7199 0.787149677 1.299591206 1.03308593 1.061113607 1.020507277 1.113104391 0.954730564 1.061067473 1 14.72225894 2.492102536 0.907916581 1.010909574 1.091968034 0 0.130307726 1.885216837 3.13713484 0.082596987 0.059923452 310.5292654 -2.492102536 0.08105846 VWAHYEEQPVEEVMPVLEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VWAHYEEQPVEEVMPVLEEK 20 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 221.41 7.86E-25 989380000 1467560 1182160 1294150 1189990 1257580 1013760 1577860 1131220 1422770 FALSE TRUE 1375708.039 1269688.356 1324847.849 1220527.158 1158814.74 1306416.055 1341274.541 1272455.307 1185300.496 1.160640736 1.071195331 1.117731625 1.029719605 0.977654817 1.102181312 1.131590298 1.073529718 1 20.17682142 1.259984758 0.008693024 4.40E-06 2.130808884 0.214655774 0.05138309 3146.370797 23.85173798 2938.858547 2904.182351 18.19636997 -1.259984758 2.130804485 VWDAVSGDELMTLAHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VWDAVSGDELMTLAHK 16 0 Q9Y3F4;Q9Y3F4-2 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 ; 183 2.05E-09 1102730000 1015340 992360 958570 966160 1121290 824120 1196030 902040 1142510 FALSE TRUE 951791.6818 1065835.367 981307.7331 990953.3013 1033228.406 1062030.066 1016696.405 1014661.68 951817.7001 0.999972665 1.119789395 1.030982858 1.041116698 1.085531826 1.115791464 1.068162953 1.066025227 1 19.86032576 0.667349376 3.639056884 1.000000607 1.069851905 0.237198212 0.036624845 9.74654739 105.2155752 0.032643126 0.008391324 4.648891132 -0.667349376 0.069851298 VWDDGIIDPADTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VWDDGIIDPADTR 13 0 Q9HCC0-2;Q9HCC0 Q9HCC0-2 MCCC2 "Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial" 0 93.561 0.012929 72700000 40575 44361 45663 38269 55114 42650 38726 44809 76029 FALSE TRUE 38035.48318 47645.5346 46746.14792 39251.04733 50785.56876 54962.36264 32919.39581 50403.50229 63339.26873 0.600503983 0.752227418 0.738027907 0.619695303 0.801802259 0.867745456 0.519731226 0.795770196 1 15.95081259 0.985592089 24.6213399 1.000000013 0.705534722 0.470676179 0.100961256 580.4305184 991885.9176 0.091993739 0.022998435 9.673688275 -0.985592089 -0.294465291 VWDLSDIDKDGHLDRDEFAVAMHLVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VWDLSDIDKDGHLDRDEFAVAMHLVYR 27 2 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4;M0R2S2 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 0 133.95 9.27E-06 122200000 108070 100250 96919 90837 108430 79531 120060 92444 110530 FALSE TRUE 101306.0916 107672.6143 99217.96445 93168.03121 99914.34519 102490.3086 102058.1176 103985.8369 92081.82895 1.100174625 1.169314462 1.07749776 1.011796054 1.08506039 1.11303511 1.108341556 1.129276406 1 16.49062887 3.815794551 4.630123101 1.081288728 1.13691583 0.2264797 0.044628623 0.313767452 11.70674892 0.011269911 0.020830826 6543.265628 -3.815794551 0.055627102 VWDPDNPLTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VWDPDNPLTDR 11 0 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 0 ;;;; 248.45 7.22E-16 596877000 855469 935560 941300 902363 978430 885159 1012510 809586 924420 FALSE TRUE 801926.7223 1004829.836 963628.0805 925519.1623 901588.0546 1140690.034 860693.5252 910664.5942 770128.33 1.041289732 1.304756359 1.251256502 1.201772648 1.170698466 1.481168773 1.117597537 1.182484216 1 19.55473934 0.91307498 1.584663558 1.004021229 1.242802032 0.265978221 0.116193608 0.572834755 2.885815452 0.099095558 0.028788757 8.18606106 -0.91307498 0.238780803 VWDVGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VWDVGTR 7 0 H3BQA8;H0YL19;H0YN81;Q9GZS3 H3BQA8 WDR61 "WD repeat-containing protein 61;WD repeat-containing protein 61, N-terminally processed" 0 ;; 105.04 0.018649 287330000 527500 614520 621920 596840 627790 561880 647280 532500 708030 FALSE TRUE 494484.7166 660019.7002 636672.2361 612155.9248 578485.9058 724085.6346 550226.3731 598983.7972 589855.219 0.838315405 1.118952039 1.079370353 1.037807084 0.980725248 1.227565022 0.932815978 1.015475964 1 19.17000136 1.619710398 24.99999999 0.980605384 1.057933743 0.076431366 0.100793479 1.64295057 3459.406152 0.042807608 0.023498917 41.65914939 -1.619710398 0.077328359 VWDVIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VWDVIGR 7 0 J3KNF4;O14618;E9PP76 J3KNF4 CCS Copper chaperone for superoxide dismutase;Superoxide dismutase [Cu-Zn] 0 ; 107.43 0.0174 128732000 391420 452960 422910 402680 448460 343880 454990 376730 492470 FALSE TRUE 366921.7209 486497.6297 432941.6249 413013.4505 413239.7606 443152.5736 386768.4734 423765.5698 410273.5755 0.894334275 1.185788359 1.055251059 1.006678166 1.007229774 1.080139205 0.942708711 1.03288536 1 18.64622671 3.36242421 4.086061857 1.008816451 1.079977216 0 0.078768656 0.409794908 12.38766579 0.02075866 0.028745526 2303.690915 -3.36242421 0.071160765 VWDYETGDFER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VWDYETGDFER 11 0 P43034 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ;; 275.28 8.84E-27 1371010000 1704030 2136900 1809370 1681580 1961560 1604450 2095650 2006660 1854480 FALSE TRUE 1597377.804 2295118.299 1852289.111 1724732.19 1807506.99 2067628.669 1781426.738 2257195.918 1544955.308 1.0339314 1.485556435 1.19892731 1.116363808 1.16994128 1.338309697 1.153060369 1.461010495 1 20.55913367 -1.558351075 2.864683115 0.986281426 1.252810394 0.216065849 0.145706923 17824082.14 17467393.09 1856680.802 0.033452593 0.027647058 1.558351075 0.266528967 VWEDRPS(ph)SAGSTPFPYNPLIMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VWEDRPSSAGSTPFPYNPLIMR 22 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 VWEDRPS(0.5)S(0.5)AGSTPFPYNPLIMR 112.86 0.00016893 56842000 26783 25414 31197 25000 29488 27244 36185 33279 23094 TRUE FALSE 25106.69984 27295.679 31937.00757 25641.54232 27172.13143 35108.90053 30759.39518 37433.95641 19239.46221 1.304958505 1.418733991 1.659974028 1.332757748 1.41231242 1.824837937 1.598765851 1.945686215 1 14.23178085 2.271121713 24.98427257 1.644086215 1.45250411 0.07071143 0.262983589 390.6946989 299780.4014 0.081068865 0.06782239 186.6902825 -2.271121713 -0.191582105 VWEDRPSS(ph)AGSTPFPYNPLIMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VWEDRPSSAGSTPFPYNPLIMR 22 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 VWEDRPS(0.14)S(0.857)AGS(0.003)TPFPYNPLIMR 167.74 6.19E-12 50981000 25283 27286 30667 27351 29405 26453 37108 28067 27228 TRUE FALSE 23700.58216 29306.28383 31394.43572 28052.87297 27095.64991 34089.55167 31543.99989 31571.22673 22683.4709 1.044839313 1.29196647 1.384022571 1.236709897 1.194510753 1.502836661 1.390616102 1.391816397 1 14.46935379 4.740433873 3.341397804 1.328370784 1.006333605 0.228132506 0.139676688 0.401583765 7.424152695 0.030808231 0.333421182 55009.01555 -4.740433873 -0.322037179 VWLDPNETNEIANANSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VWLDPNETNEIANANSR 17 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ; 161.21 6.97E-09 775960000 597040 705140 711240 715360 646260 577410 797760 608200 646230 FALSE TRUE 559672.3321 757349.2993 728110.9487 733717.3487 595505.3465 744098.8935 678143.294 684135.1088 538370.0382 1.039568127 1.406744888 1.352435866 1.362849521 1.106126464 1.38213281 1.259623021 1.270752568 1 19.0382386 -0.762834023 0.549790768 0.937290781 1.300462369 0.320312413 0.120641453 16.20325275 3.385815276 1.90067502 0.048527122 0.172649759 0.762834023 0.363171588 VWNVAENSYVETLFGHQDAVAALDALSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VWNVAENSYVETLFGHQDAVAALDALSR 28 0 O43818 O43818 RRP9 U3 small nucleolar RNA-interacting protein 2 0 262.76 8.07E-54 51753000 24382 32475 26504 24941 36667 20123 26750 25128 29220 FALSE TRUE 22855.97414 34879.48279 27132.6874 25581.02829 33787.32173 25932.18343 22739.08583 28265.28611 24342.99323 0.938913877 1.432834593 1.114599472 1.050857963 1.387969072 1.06528327 0.934112154 1.161126154 1 14.57121895 2.018929955 24.98833287 1.018243315 1.205080763 0.172274094 0.154905944 313.6945721 414088.3288 0.054022516 0.039892556 104.4551734 -2.018929955 0.186837448 VWQLGSSSPNFTLEGHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VWQLGSSSPNFTLEGHEK 18 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 223.18 5.29E-19 772450000 645580 601640 607760 571550 665530 427180 808900 568950 862850 FALSE TRUE 605174.3002 646186.0516 622176.3542 586216.9406 613261.9584 550499.9313 687612.9545 639984.6599 718834.7608 0.841882354 0.898935453 0.865534596 0.815510007 0.853133421 0.765822636 0.956566087 0.890308448 1 19.45530065 1.154994363 1.331261576 0.989654691 0.852540641 0.505582354 0.046988142 0.341882913 1.208325328 0.042182715 0.01304464 14.28875411 -1.154994363 -0.13711405 VWQVTIGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VWQVTIGTR 9 0 P63244;J3KPE3;D6RHH4;H0YAF8;D6RAC2;H0Y8R5;D6RF23;D6RHJ5 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 ; 152.38 0.00018752 523290000 465530 661710 515400 465790 627170 431160 550310 584420 589800 FALSE TRUE 436393.3083 710703.6969 527625.5314 477742.96 577914.5981 555628.8927 467796.1243 657386.1235 491358.5697 0.88813615 1.446405417 1.073809564 0.97228987 1.176156546 1.130801266 0.952046333 1.337894898 1 18.90641669 3.71978584 24.00838137 1.082836892 1.223035262 0.007444371 0.174606105 355.3554736 1163063.54 0.041757158 0.066246472 5245.487305 -3.71978584 0.14019837 VWQWDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VWQWDEK 7 0 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 101.99 0.020244 656750000 539740 499890 498520 467570 577690 400580 559070 462290 572570 FALSE TRUE 505958.6369 536902.3757 510345.1298 479568.6378 532320.5577 516220.9431 475242.6437 520007.9241 477004.3681 1.060700217 1.125571193 1.069896135 1.005375778 1.115965793 1.082214289 0.996306691 1.09015338 1 18.86364295 1.118101044 0.085325602 0.901838286 1.185881566 0.217279837 0.04125431 22.18539847 1.481581024 2.531870584 2.146514148 13.12505233 -1.118101044 0.28404328 VWS(ph)PLVTEEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VWSPLVTEEGK 11 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 VWS(0.996)PLVT(0.004)EEGK;VWS(1)PLVTEEGK;VWS(1)PLVTEEGK;VWS(1)PLVTEEGK;VWS(1)PLVTEEGK 188.68 3.19E-06 216450000 1033174 617175 832268 803335 780549 640001 1004598 635713 919492 TRUE FALSE 968509.4836 662871.2792 852009.79 823949.9361 719247.8301 824758.8992 853967.8561 715083.1674 766022.8451 1.264334987 0.865341397 1.11225115 1.075620579 0.938937833 1.076676635 1.114807295 0.933501099 1 19.54702789 4.572357263 0.005337309 0.040729775 2.061740481 0.045245228 0.111582682 147751.5454 129.0138887 23531.76222 25342.74848 37355.73304 -4.572357263 2.021010707 VWS(ph)PLVTEEGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VWSPLVTEEGKR 12 1 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 VWS(1)PLVTEEGKR;VWS(1)PLVTEEGKR;VWS(1)PLVTEEGKR;VWS(0.997)PLVT(0.003)EEGKR 235.22 2.96E-16 734840000 1079970 716857 908250 913690 923350 662699 1063240 768111 1095870 TRUE FALSE 1012376.606 769933.8382 929794.1189 937136.8323 850833.8156 854009.4433 903817.0326 864011.3492 912962.2174 1.108892116 0.843335927 1.018436581 1.026479316 0.931948551 0.935426929 0.989982954 0.946382372 1 19.80019563 -1.189363683 4.728058526 1.000004799 0.96734715 0.001528195 0.070509548 3.22E-06 5.53E-07 0.06168354 0.014536813 0.064660092 1.189363683 -0.032657649 VWSEVNQAVLDYENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VWSEVNQAVLDYENR 15 0 Q9NWU2 Q9NWU2 GID8 Glucose-induced degradation protein 8 homolog 0 ; 148.52 8.19E-06 44191000 32856 34433 31105 33929 40028 34717 40405 26813 41211 FALSE TRUE 30799.60161 36982.45515 31842.82529 34799.67558 36884.36235 44739.23432 34346.64535 30160.66207 34332.61787 0.897094469 1.077181335 0.927480258 1.013603906 1.074324204 1.30311165 1.000408576 0.878484192 1 15.06729225 6.373383681 0.666229257 1.047544193 1.63E-15 0.078866256 0.115739302 66.53017596 3.872573953 0.044992163 84.9614412 2362564.539 -6.373383681 -1.047544193 VWTESSSDDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VWTESSSDDLR 11 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 105.98 0.0055686 119330000 58395 73577 69206 76213 78688 64302 73683 65906 74743 FALSE TRUE 54740.16119 79024.71764 70847.599 78168.75461 72508.16189 82864.94354 62634.91819 74134.50918 62267.91044 0.879107084 1.26910823 1.137786679 1.255361775 1.164454715 1.330780862 1.005894011 1.190573261 1 15.92620125 0.776055275 0.984959144 1.004700844 1.173274372 0.099296649 0.132378613 1.664870199 3.03899403 0.112540713 0.03679849 5.971112791 -0.776055275 0.168573528 VWYVSNIDGTHIAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VWYVSNIDGTHIAK 14 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7EPY4;K7ENA0 P06744 GPI Glucose-6-phosphate isomerase 0 ; 212.39 2.50E-09 9551700000 4530800 5708800 4984500 5130300 5683100 3864900 6409000 5001600 5172100 FALSE TRUE 4247225.316 6131485.492 5102734.694 5261952.184 5236772.251 4980633.889 5448029.948 5626060.77 4308843.097 0.985699693 1.42300041 1.184247042 1.221198374 1.215354593 1.155909783 1.264383461 1.305701007 1 22.03886913 -1.101032397 4.715478346 0.999986513 1.233877826 0.267748346 0.111800919 1.42E-05 2.71E-06 0.097240679 0.022918527 0.079244221 1.101032397 0.233891313 VYADGIFDLFHSGHAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VYADGIFDLFHSGHAR 16 0 P49585;C9JEJ2;C9J050;H7C1T3;C9J2E1;C9JPY0;Q9Y5K3-2;Q9Y5K3-4;Q9Y5K3-3;Q9Y5K3;C9JVS0;F8WAZ5;F2Z2B1 P49585 PCYT1A;PCYT1B Choline-phosphate cytidylyltransferase A;Choline-phosphate cytidylyltransferase B 0 ; 131.24 2.64E-05 415730000 242500 383120 297970 304470 401490 271790 327950 338850 443450 FALSE TRUE 227322.3579 411486.6034 305037.9891 312283.2157 369958.5949 350251.3609 278776.942 381156.1684 369435.3302 0.615323818 1.113825803 0.825687107 0.845298731 1.001416391 0.948072185 0.75460282 1.03172636 1 18.49496232 VYAEADSQESADHLAHEVSLAVFQLAGGIGERPQPGF ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VYAEADSQESADHLAHEVSLAVFQLAGGIGERPQPGF 37 1 O95394-4;O95394;A0A494C0G1;A0A087WT27;A0A494C1E2;A0A494C1Q4;H0Y8I3 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 ; 143.23 2.73E-13 254990000 159511 209810 204121 195996 226909 187202 235102 189151 201845 FALSE TRUE 149527.4912 225344.5507 208962.8465 201025.5892 209088.4824 241244.1784 199850.6377 212766.9187 168155.7655 0.889220127 1.340094109 1.24267429 1.195472475 1.24342143 1.434647083 1.188485194 1.265296602 1 17.35943872 -0.984187509 4.541430809 0.999994435 1.241897684 0.194436449 0.140132856 0.032050329 37725265.42 520.1473119 0.029175845 0.103708055 0.984187509 0.241903249 VYAILTHGIFSGPAISR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VYAILTHGIFSGPAISR 17 0 B1ALA9;P60891;A0A2R8Y7H4;P60891-2;B7ZB02;P11908;P11908-2;H7C540;A0A0B4J207;P21108 B1ALA9;P11908;A0A0B4J207 PRPS1;PRPS2;PRPS1L1 Ribose-phosphate pyrophosphokinase 1;Ribose-phosphate pyrophosphokinase 2;Ribose-phosphate pyrophosphokinase 3 0 126.16 4.45E-05 127370000 59891 113410 85397 82438 120620 46668 72021 89016 99612 FALSE TRUE 56142.52922 121806.9944 87422.65717 84553.49865 111146.9918 60140.29401 61222.11966 100129.8435 82986.11368 0.676529201 1.46779972 1.053461275 1.018887316 1.339344462 0.724703102 0.737739327 1.206585525 1 16.34058233 2.23297711 24.99999886 0.872413135 1.147760739 0.110455285 0.248236954 199.6781489 894044.7081 0.085643558 0.06503483 170.9925189 -2.23297711 0.275347604 VYATILNAGTNTDGFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VYATILNAGTNTDGFK 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 0 175.29 5.61E-12 0 137810 110670 110290 117380 125930 102830 130790 103970 113490 FALSE TRUE 129184.7181 118864.122 112906.1309 120392.1695 116039.9658 132515.3517 111179.2537 116950.8834 94547.78583 1.366343135 1.257185675 1.194170016 1.273347318 1.227315529 1.401570122 1.175905419 1.236949997 1 16.52875605 0.511529037 1.157970285 1.000208111 1.266103711 0.605889434 0.068569644 1.249442084 2.250692154 0.061473859 0.018802382 3.247349533 -0.511529037 0.265895599 VYEDSGIPLPAES(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 164.82 1.53E-06 157726000 1034830 610760 705330 776430 693440 488440 1002360 669580 694600 TRUE FALSE 970061.8375 655981.3059 722060.7607 796354.5083 638980.0196 629444.6988 852065.4235 753178.5369 578666.7727 1.676373836 1.13360804 1.247800625 1.376188414 1.104227942 1.087749856 1.47246302 1.301575574 1 19.14237328 4.746727725 24.73364974 1.234548736 1.67637409 0.501155506 0.14339874 787.2906579 2384204.531 0.033110066 0.369976807 55812.0179 -4.746727725 0.441825354 VYEFLDKLDVVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VYEFLDKLDVVR 12 1 O43242;O43242-2;H0YGV8 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 158.11 6.44E-05 346590000 1377250 1672950 1417740 1406730 1787390 981620 1716340 1524080 1875060 FALSE TRUE 1291050.381 1796816.959 1451369.462 1442829.073 1647015.599 1264997.759 1458990.751 1714364.743 1562100.373 0.826483627 1.150257045 0.929114087 0.92364684 1.054359648 0.809805683 0.93399296 1.097474127 1 20.57505573 5.032137183 15.66653904 0.980229885 0.33639032 0.208946871 0.097489746 929330.1077 12912538.2 0.022966138 15961735.6 107680.5297 -5.032137183 -0.643839565 VYEGERPLTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VYEGERPLTK 10 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;;; 147.91 2.38E-05 7871890000 11069600 10394990 9855700 10547390 8905010 8133920 12590800 8469760 10948150 FALSE TRUE 10376773.5 11164645.88 10089481.86 10818053.88 8205646.436 10482050.66 10702926.43 9527228.18 9120833.037 1.137700192 1.224081817 1.106201793 1.18608178 0.899659757 1.149242686 1.173459308 1.044556801 1 23.12073417 7.999999836 0.055681181 0.828952122 1.688602882 0.2247519 0.085692425 611.0188562 2.55234485 8.512132055 43.52938716 99999962.27 -7.999999836 0.85965076 VYEHTS(ph)RFSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VYEHTSRFSPK 11 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;A0A096LNN3;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 VYEHT(0.011)S(0.973)RFS(0.016)PK;VYEHT(0.006)S(0.531)RFS(0.463)PK;VYEHT(0.016)S(0.631)RFS(0.352)PK 100.22 0.0025303 568673000 634905 732970 629280 671770 859920 472463 819550 792720 1108090 TRUE FALSE 595167.4294 787239.8615 644206.8188 689008.7555 792385.352 608855.3983 696666.0858 891692.837 923142.6205 0.644718829 0.852782489 0.697841053 0.746373031 0.858356374 0.659546407 0.754667882 0.965931826 1 19.81619403 1.218567525 5.35815227 0.991644866 0.750040231 0.665023396 0.070328124 0.099246982 7.79914966 0.056112849 0.015709368 16.54121951 -1.218567525 -0.241604635 VYEHTSRFS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VYEHTSRFSPK 11 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;A0A096LNN3;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 VYEHT(0.001)S(0.099)RFS(0.9)PK 102.52 0.0017257 106320000 62324 108640 85644 114230 148640 66865 121970 114860 198170 TRUE FALSE 58423.25209 116683.8186 87675.51612 117161.3352 136966.414 86167.84004 103681.7308 129200.5238 165094.1468 0.353878397 0.706771384 0.531063747 0.709663774 0.829626105 0.521931526 0.628015789 0.782586944 1 17.33292945 -5 0.135687804 2.254923688 0.488594462 0.530313823 0.123609878 119.1824316 1.004378102 40.5138058 0.792611721 1.00E-05 5 -1.766329226 VYENYPTYDLTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VYENYPTYDLTER 13 0 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;A0A494C198 H0Y993 DEK Protein DEK 0 ;;; 237.53 2.22E-16 415080000 513483 553600 506470 467999 572010 437427 551730 513351 623720 FALSE TRUE 481345.0156 594589.12 518483.7076 480008.6467 527086.642 563705.0739 469003.2085 577444.0024 519617.1026 0.926345598 1.144283198 0.997818788 0.923773764 1.014375084 1.084847036 0.902593864 1.111287522 1 18.98708939 3.717722825 23.33929582 0.997153536 1.056932256 0.001209902 0.081670767 325.5274216 808392.3177 0.019730188 0.031091209 5220.628922 -3.717722825 0.059778721 VYFQS(ph)PPGAAGEGPGGADDEGPVRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VYFQSPPGAAGEGPGGADDEGPVRR 25 1 Q96C90 Q96C90 PPP1R14B Protein phosphatase 1 regulatory subunit 14B 1 VY(0.002)FQS(0.998)PPGAAGEGPGGADDEGPVRR;VYFQS(1)PPGAAGEGPGGADDEGPVRR;VY(0.001)FQS(0.999)PPGAAGEGPGGADDEGPVRR;VY(0.005)FQS(0.995)PPGAAGEGPGGADDEGPVRR 125.79 8.47E-05 1330600000 574780 692530 661670 671540 732060 575620 749110 568480 880440 TRUE FALSE 538805.5458 743805.6418 677365.1249 688772.8533 674566.9606 741792.1496 636787.9099 639455.9794 733488.8761 0.734579028 1.014065333 0.923483841 0.939036536 0.919668972 1.011320245 0.868163009 0.871800514 1 19.48441556 4.751536149 24.86506489 0.940802674 0.734578886 0.611194711 0.052315269 1404.859894 2692087.654 0.012112566 0.227569853 56433.39124 -4.751536149 -0.206223788 VYFQSPPGAAGEGPGGADDEGPVRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 VYFQSPPGAAGEGPGGADDEGPVRR 25 1 Q96C90 Q96C90 PPP1R14B Protein phosphatase 1 regulatory subunit 14B 0 ;;;; 254.32 1.25E-44 2456340000 548830 615395 599055 623156 670185 501264 686710 553838 716664 FALSE TRUE 514479.71 660959.4861 613264.8675 639147.238 617551.3735 645970.7795 583744.2106 622985.8934 597048.1486 0.861705561 1.107045533 1.027161493 1.070512051 1.034340991 1.081940847 0.977717144 1.043443305 1 19.18748776 -0.737854795 7.33447659 1.000000707 1.03295156 0.003123825 0.068168274 0 0 0.058370273 0.013758005 0.182871154 0.737854795 0.032950853 VYIVHGVQEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VYIVHGVQEDLR 12 0 Q15024 Q15024 EXOSC7 Exosome complex component RRP42 0 110.66 0.00042222 0 90226 120830 103870 104490 124070 88367 89162 120300 143500 FALSE TRUE 84578.91572 129776.3789 106333.8455 107171.3903 114326.0427 113877.1184 75792.98584 135319.7198 119548.923 0.707483712 1.085550382 0.889458833 0.896464708 0.956311775 0.952556623 0.633991373 1.131919188 1 16.86724161 VYLLYRPGHYDILYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VYLLYRPGHYDILYK 15 1 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5H3F0;Q96FW1-2 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 130.88 3.43E-05 846960000 1300010 3419500 1226010 1069110 3615100 748110 2013450 3113600 3171700 FALSE TRUE 1218644.695 3672683.338 1255091.536 1096545.173 3331184.629 964077.2124 1711551.864 3502339.814 2642322.78 0.461202054 1.389945001 0.47499554 0.414992892 1.260703141 0.364859744 0.647745187 1.325477659 1 21.33337528 1.244068635 24.99937281 1.162738875 0.744773597 0.209089594 0.357630302 201.2369824 913391.3277 0.244109301 0.083522577 17.54157702 -1.244068635 -0.417965278 VYMFQYDSTHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VYMFQYDSTHGK 12 0 P04406-2 P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 152.4 6.98E-05 1039700000 532510 234330 1290500 1950000 262770 981840 1066600 244890 1926500 FALSE TRUE 499181.1497 251680.037 1321111.269 2000040.301 242133.1042 1265281.269 906673.2318 275465.0556 1604954.704 0.31102507 0.156814417 0.823145517 1.246166198 0.150866005 0.788359488 0.564921383 0.171634162 1 20.61410115 4.027196397 4.523627091 0.662947147 0.241602651 0.229230453 0.336895828 0.300660123 13.15514514 0.080229956 0.177019139 10646.24354 -4.027196397 -0.421344496 VYMGHGGKPWVSDFSHPHYLAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 VYMGHGGKPWVSDFSHPHYLAGR 23 1 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ;; 232.29 3.11E-34 6600210000 3964740 8194500 4358380 3305680 8298050 2842860 5339560 7485080 5089740 FALSE TRUE 3716594.001 8801229.306 4461762.832 3390509.345 7646354.626 3663547.532 4538942.548 8419608.715 4240229.513 0.876507743 2.075649273 1.052245596 0.799605148 1.803287912 0.863997461 1.070447374 1.985649288 1 22.01571093 3.744195215 22.68648748 1.203873334 1.56239664 0.03728518 0.47907893 311.3563709 413697.2637 0.111968798 0.200952982 5548.750724 -3.744195215 0.358523305 VYNLLT(ph)PDSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 VYNLLTPDSK 10 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 VYNLLT(0.999)PDS(0.001)K;VYNLLT(1)PDSK;VYNLLT(0.993)PDS(0.007)K;VYNLLT(1)PDSK;VYNLLT(0.999)PDS(0.001)K;VYNLLT(0.984)PDS(0.016)K 193.81 5.95E-06 1131706000 3017610 2248230 2685590 2500530 2776930 2178520 3340730 2433780 3754880 TRUE FALSE 2828743.177 2414691.288 2749293.463 2564697.833 2558841.119 2807423.359 2839818.55 2737642.79 3128166.271 0.904281592 0.771919099 0.878883418 0.819872606 0.818000355 0.897466156 0.907822125 0.875158976 1 21.57688577 0.869194155 0.469032849 1.004842579 0.828535635 0.5683195 0.040968497 0.828547258 0.441330619 0.051183415 0.023314932 7.399359965 -0.869194155 -0.176306944 VYNVTQHAVGIVVNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VYNVTQHAVGIVVNK 15 0 P46778;M0R181;G3V1B3 P46778 RPL21 60S ribosomal protein L21 0 138.73 8.80E-06 761710000 966510 946680 982650 903170 1006100 772320 1119100 858220 1032500 FALSE TRUE 906017.8644 1016773.172 1005958.922 926346.8713 927084.9644 995276.2464 951301.3442 965370.6562 860169.0798 1.053302061 1.182061988 1.16948975 1.076935794 1.077793874 1.157070476 1.10594692 1.122303369 1 19.71426075 -5 0.23853579 0.278081937 1.139736826 0.397076283 0.043568058 161.1775263 1.609261605 56.32691081 0.069715584 1.00E-05 5 0.861654889 VYNYNHLMPTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VYNYNHLMPTR 11 0 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ; 110.66 0.0017644 479970000 260440 1096450 321170 315800 1028070 311240 298400 854490 871360 FALSE TRUE 244139.5253 1177632.299 328788.3041 323903.9626 947329.5292 401089.9354 253657.6902 961174.9575 725924.3868 0.336315365 1.622252014 0.452923624 0.44619518 1.304997527 0.552523021 0.349427151 1.324070351 1 19.46945976 3.857837774 9.349170619 0.721232998 1.066082674 0.014510695 0.464061733 0.682616618 50.60994316 0.10975774 0.198213755 7208.381683 -3.857837774 0.344849677 VYQSLCPTSWVTDWDEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VYQSLCPTSWVTDWDEQR 18 0 P14854 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 ; 328.14 1.87E-74 232329000 141877 149077 129437 119319 163341 117622 158361 135004 142323 FALSE TRUE 132997.1718 160114.8162 132507.3068 122380.9275 150512.8567 151577.562 134616.2382 151859.5466 118568.3719 1.121691812 1.350400732 1.117560313 1.032154913 1.269418264 1.278397937 1.13534694 1.280776182 1 16.8553597 -1.026087976 4.078922384 0.999979174 1.200518385 0.289986782 0.097415317 21836325287 86786720197 8538680.305 0.022492414 0.094169881 1.026087976 0.20053921 VYQWDDPDPR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;; 150.35 5.05E-05 63040420000 36728160 46012460 46107430 44176460 49128250 41731500 53784830 43569140 49209640 FALSE TRUE 34429410.03 49419270.41 47201120.01 45310102.75 45269915.42 53778706.6 45720294.06 49008843.04 40996233.18 0.839818865 1.205458809 1.151352609 1.105225999 1.10424573 1.31179629 1.115231584 1.195447465 1 25.28898802 4.743707076 24.91458515 1.158720473 0.839818726 0.583400719 0.081603697 332.4593874 1609420.128 0.017172843 0.144525418 55425.17537 -4.743707076 -0.318901748 VYRDDIGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VYRDDIGR 8 1 A0A087WY71;Q96CW1-2;Q96CW1;C9JJ47;C9JJD3;C9JGT8 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 138.06 0.00065792 400220000 196110 180020 184300 175490 188920 169990 222530 177100 202040 FALSE TRUE 183835.8252 193348.8681 188671.683 179993.3705 174082.9853 219063.3534 189163.6924 199211.3248 168318.2188 1.092192078 1.148710279 1.120922526 1.069363565 1.034249213 1.301483316 1.123845617 1.183539882 1 17.36083182 VYSGHQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 VYSGHQGR 8 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;;;;; 169.57 0.00030026 2626452000 1343255 1856945 1731858 1663197 1734240 1479920 1760592 1425520 1643791 FALSE TRUE 1259183.067 1994435.14 1772938.49 1705877.451 1598039.786 1907148.88 1496607.574 1603499.31 1369431.663 0.919493175 1.456396251 1.294652766 1.245682787 1.166936496 1.392657211 1.092867658 1.170923204 1 20.38514584 1.176294497 1.000335027 1.007360727 1.274024521 0.168130783 0.150666806 0.677789121 1.450134574 0.129977953 0.044345768 15.00702123 -1.176294497 0.266663794 VYSLDDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VYSLDDIR 8 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 77.282 0.078204 51881000 94457 149510 93818 94600 149700 64452 97335 153250 110620 FALSE TRUE 88545.10498 160579.876 96043.40726 97027.59616 137943.1659 83058.24611 82740.52036 172383.5998 92156.80737 0.960809163 1.742463531 1.042173769 1.052853272 1.496830997 0.901270872 0.897823207 1.870546569 1 16.49180312 3.748797999 20.70272438 1.151178749 1.40292482 0.029955748 0.35257252 128.4193754 122642.6477 0.083522316 0.150183908 5607.870796 -3.748797999 0.251746071 VYSLFLDESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VYSLFLDESR 10 0 Q9Y230;Q9Y230-2 Q9Y230 RUVBL2 RuvB-like 2 0 117.7 0.0021476 12547000 10382 32145 6564.8 8572 32527 8384.5 9604.4 22836 24837 FALSE TRUE 9732.209152 34525.04925 6720.520156 8791.972032 29972.46063 10804.96904 8164.309383 25687.12487 20691.54425 0.470347164 1.668558365 0.324795485 0.424906519 1.448536671 0.522192491 0.39457226 1.241431019 1 14.3367537 3.964689773 24.71938279 0.71549777 1.135243988 0.055760927 0.471269799 635.4015699 1263467.681 0.111749676 0.203312138 9219.126465 -3.964689773 0.419746218 VYSS(ph)SEFLAVQPTPTFAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VYSSSEFLAVQPTPTFAER 19 0 O60307;V9GYV0 O60307 MAST3 Microtubule-associated serine/threonine-protein kinase 3 1 VYS(0.05)S(0.901)S(0.05)EFLAVQPTPTFAER 107.51 0.00030738 15306000 15157 18095 20130 18982 21911 14999 23162 18134 22812 TRUE FALSE 14208.35043 19434.77263 20607.49311 19469.11026 20190.19844 19328.96781 19689.07313 20398.06982 19004.52983 0.747629673 1.02263896 1.084346379 1.024445773 1.062388737 1.017071613 1.036020007 1.073326728 1 14.21405571 4.739131286 4.290312815 1.04442611 0.725059221 0.927745799 0.025698545 0.046583453 2.016868442 0.00561216 0.045601482 54844.27331 -4.739131286 -0.319366889 VYSTSVTGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VYSTSVTGSR 10 0 Q5T123;Q9H299 Q5T123 SH3BGRL3 SH3 domain-binding glutamic acid-rich-like protein 3 0 107.69 0.0073444 0 149800 101230 125920 122480 122740 100680 147650 96149 177450 FALSE TRUE 140424.2854 108725.1745 128906.8819 125623.0442 113100.4955 129744.6816 125511.2532 108153.4143 147832.4486 0.949888111 0.735462177 0.871979617 0.849766376 0.765058663 0.877646841 0.849010176 0.731594554 1 17.17360344 -1.868991053 2.711151143 1.076388097 0.826871269 0.382478692 0.068324761 11640583.57 6490421.327 5693868.43 0.014619005 0.013521004 1.868991053 -0.249516828 VYT(ph)HEVVTLWYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VYTHEVVTLWYR 12 0 P06493;A0A087WZZ9;E5RIU6 P06493 CDK1 Cyclin-dependent kinase 1 1 VYT(1)HEVVTLWYR;VYT(1)HEVVTLWYR;VYT(1)HEVVTLWYR;VYT(1)HEVVTLWYR 173.06 0.00012542 839970000 677063 789820 568166 609065 872640 346790 654070 697960 739787 TRUE FALSE 634686.8354 848299.0946 581643.1658 624694.639 804106.3745 446902.6433 555998.2756 785101.8424 616311.7705 1.029814561 1.376412289 0.943748268 1.013601669 1.304707151 0.725124304 0.902138012 1.273871245 1 19.23330082 3.871993821 5.348685439 1.006551288 1.217885595 0.131282788 0.187155097 0.332465351 14.05343178 0.046186297 0.085300933 7447.213786 -3.871993821 0.211334308 VYTDVNTHRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VYTDVNTHRPR 11 1 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;A0A2R8Y4H0;A0A2R8Y4D6;V9GYA2;A0A2R8YEW1;A0A2R8YDY7;A0A2R8YCK2;V9GY80;A0A2R8Y7T1;A0A2R8YF47;A0A2R8YEL7;A0A2R8Y797;A0A2R8Y3W6;A0A2R8YCC9 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 ;;; 165.66 1.28E-05 1802600000 962180 1011520 1079760 1057450 1135050 883890 1129470 1015940 1127680 FALSE TRUE 901958.8713 1086413.993 1105372.417 1084585.957 1045907.752 1139054.694 960116.459 1142782.345 939462.9229 0.960079264 1.156420298 1.176600364 1.154474467 1.113303917 1.212453059 1.021984408 1.216420912 1 19.8414767 -0.919527736 5.874658827 0.999999942 1.129880307 0.194347862 0.080655811 5.55E-08 1.02E-08 0.070256507 0.01655961 0.120357252 0.919527736 0.129880365 VYTDVQQVASSLTHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 VYTDVQQVASSLTHPR 16 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 259.68 9.37E-27 648990000 646960 1181650 1031910 1104350 1136770 949410 1235030 1077310 1157270 FALSE TRUE 606467.9285 1269140.596 1056387.393 1132689.491 1047492.67 1223489.255 1049848.717 1211814.525 964114.1608 0.629041615 1.316379996 1.095707786 1.174849968 1.086481988 1.269029441 1.088925731 1.25692016 1 19.87884446 4.748485172 24.99762343 1.166822323 0.629041321 0.744143442 0.097982592 628.0601554 1581904.224 0.02049335 0.276592946 56038.32846 -4.748485172 -0.537781002 VYTLNEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 VYTLNEDR 8 0 Q5MIZ7-3;Q5MIZ7-2;Q5MIZ7;Q5MIZ7-4;Q6IN85-2;Q6IN85;G3V5Z3;G3V231;H0YIY8;Q6IN85-5;Q6IN85-4;G3V4R3;G3V5A2 Q5MIZ7-3;Q6IN85-2 SMEK2;SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3B;Serine/threonine-protein phosphatase 4 regulatory subunit 3A 0 117.89 0.0046364 183860000 108660 136140 131070 121480 158190 98401 123920 126370 133700 FALSE TRUE 101859.1646 146219.9473 134179.0423 124597.3825 145766.3955 126807.7713 105339.3464 142147.5727 111384.6063 0.914481525 1.312748253 1.204646197 1.118623 1.30867631 1.138467653 0.945726254 1.276186876 1 16.76519034 1.994768331 24.69436768 1.061479699 1.195644844 0.077387557 0.13937691 326.5761994 1541498.118 0.048677673 0.034901835 98.80259036 -1.994768331 0.134165144 VYVGNLGNNGNKTELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VYVGNLGNNGNKTELER 17 1 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;; 337.35 2.64E-72 2525410000 1426860 1497800 1513370 1634260 2009190 1234680 1997570 1488740 3082300 FALSE TRUE 1337555.38 1608698.67 1549267.851 1676197.878 1851396.322 1591112.073 1698052.923 1674612.466 2567844.218 0.520886497 0.626478296 0.60333405 0.652764629 0.720992461 0.619629517 0.661275677 0.652147219 1 21.29212625 -5 0.221907061 2.885176217 0.586845419 0.879073961 0.043867037 48.56695633 0.486193189 40.9456514 0.078419241 1.00E-05 5 -2.298330798 VYWNDGLDQYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VYWNDGLDQYR 11 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ;;; 136.02 0.0002509 198704000 280720 396504 300627 296382 419821 205486 289897 353574 395655 FALSE TRUE 263150.2363 425861.5687 307758.0144 303987.6639 386849.9521 264806.4724 246429.6361 397718.4922 329617.6245 0.798350018 1.291986645 0.933681914 0.922243355 1.173632486 0.803374737 0.747622754 1.206605663 1 18.33043386 2.229547259 24.99335667 0.895968142 1.043587837 0.020744287 0.183623173 395.5296397 1096765.159 0.064969703 0.048681257 169.6474199 -2.229547259 0.147619695 VYYS(ph)PPVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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;VYY(0.003)S(0.997)PPVAR 132.32 0.00032349 2989260000 2242510 2698310 2571240 2640170 2644550 2141560 2879520 2225460 2032210 TRUE FALSE 2102155.302 2898095.68 2632231.027 2707921.232 2436857.711 2759793.607 2447762.708 2503313.58 1693021.022 1.241659303 1.711789542 1.554753894 1.599461079 1.439354667 1.630100022 1.445795815 1.478607499 1 20.69116846 0.057019192 0.690049095 0.979156076 1.555483867 0.606157971 0.129095835 2.48930667 1.340076025 0.248593388 0.042503013 1.140300178 -0.057019192 0.576327791 VYYTAGYNS(ph)PVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 VYYTAGYNSPVK 12 0 Q9Y5Z4-2;Q9Y5Z4 Q9Y5Z4-2 HEBP2 Heme-binding protein 2 1 VYYTAGYNS(1)PVK;VYYTAGYNS(1)PVK;VYYTAGYNS(1)PVK;VYYTAGYNS(1)PVK 199.37 1.81E-07 492240000 771210 690360 625790 612340 839700 477147 771690 711210 1098690 TRUE FALSE 722941.3427 741474.9727 640634.0343 628053.6811 773753.3492 614891.5931 655982.2485 800006.1341 915311.5412 0.789830905 0.810079344 0.699908179 0.686163839 0.845344251 0.67178394 0.716676475 0.874026053 1 19.80390335 1.012882068 3.746723827 0.998969023 0.744413533 0.695370159 0.056059556 0.104318278 3.666466564 0.052330766 0.013479341 10.30106359 -1.012882068 -0.25455549 WAAS(ph)LENLLEDPEGVKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WAASLENLLEDPEGVKR 17 1 O43665;O43665-2;O43665-1 O43665 RGS10 Regulator of G-protein signaling 10 1 WAAS(1)LENLLEDPEGVKR;WAAS(1)LENLLEDPEGVKR 123.53 3.26E-05 43035000 56265 41838 48832 44918 54209 45056 60259 41927 72363 TRUE FALSE 52743.47409 44935.72905 49990.3181 46070.67193 49951.64381 58062.93578 51223.72237 47161.67824 60285.14782 0.874899971 0.745386396 0.829231078 0.764212639 0.828589555 0.963138316 0.849690583 0.782310071 1 15.879515 2.466110371 24.98962315 0.886433791 0.797892238 0.299974411 0.068130735 267.2773255 606591.7615 0.021518796 0.018018862 292.4895609 -2.466110371 -0.088541553 WAEKLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WAEKLDR 7 1 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 61.999 0.080348 861660000 1545180 2042520 1376080 1766160 2324600 1006710 1858290 1617380 1921540 FALSE TRUE 1448469.942 2193750.306 1408721.267 1811482.656 2142035.293 1297330.834 1579656.666 1819313.453 1600822.56 0.904828541 1.370389424 0.879998385 1.131594907 1.338084149 0.810415137 0.986778113 1.13648664 1 20.61038197 2.227316449 24.99774711 0.976656683 1.125338414 0.141982791 0.172560966 413.7579763 919849.4759 0.061043012 0.045491983 168.7782381 -2.227316449 0.148681731 WAEYHADIYDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 WAEYHADIYDK 11 0 Q9NRX4;Q9NRX4-2 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 ;; 156.71 3.09E-05 1624190000 5211800 4271400 4175500 3960700 4315700 3476890 5400800 4217900 4855100 FALSE TRUE 4885602.741 4587658.9 4274544.832 4062338.267 3976762.331 4480611.7 4591000.179 4744514.1 4044752.445 1.207886714 1.134224891 1.056812472 1.004347812 0.983190538 1.107759192 1.135050968 1.173004817 1 21.94761998 4.55053253 1.747574493 1.072461754 1.225688303 0.367913297 0.061026236 0.784800538 3.204546892 0.017106546 0.177011202 35524.87265 -4.55053253 0.153226548 WAHDKFS(ph)GEEGEIEDDES(ph)GTENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 WAHDKFSGEEGEIEDDESGTENR 23 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 WAHDKFS(1)GEEGEIEDDES(0.985)GT(0.015)ENR;WAHDKFS(1)GEEGEIEDDES(0.994)GT(0.006)ENR;WAHDKFS(1)GEEGEIEDDES(0.872)GT(0.128)ENR;WAHDKFS(1)GEEGEIEDDES(0.978)GT(0.022)ENR;WAHDKFS(1)GEEGEIEDDES(0.856)GT(0.144)ENR;WAHDKFS(1)GEEGEIEDDES(0.969)GT(0.031)ENR;WAHDKFS(1)GEEGEIEDDES(0.987)GT(0.013)ENR 200.8 1.35E-24 2780960000 6604930 3578950 4879260 4453020 3813170 4386250 6676430 4324720 3720180 TRUE FALSE 6191539.221 3843939.182 4994998.351 4567292.032 3513699.01 5652489.17 5675361.302 4864670.812 3099257.925 1.997748936 1.240277278 1.611675592 1.473672777 1.133722683 1.823820188 1.831200062 1.569624384 1 21.56349139 2.180414495 24.99994019 1.654559574 1.472751191 0 0.326500479 220.7111309 94892.78118 0.110587182 0.08167408 151.5006495 -2.180414495 -0.181808383 WAHDKFS(ph)GEEGEIEDDES(ph)GTENREEKDNIQPTTE ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WAHDKFSGEEGEIEDDESGTENREEKDNIQPTTE 34 3 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 WAHDKFS(1)GEEGEIEDDES(0.843)GT(0.157)ENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDES(0.572)GT(0.428)ENREEKDNIQPTTE 163.31 4.22E-14 2111540000 903180 469740 614710 656910 725880 386340 771780 529700 1150040 TRUE FALSE 846651.576 504520.0384 629291.2115 673767.4227 668872.3129 497870.0863 656058.7539 595834.211 958090.8945 0.883686069 0.526588909 0.656817861 0.703239564 0.698130331 0.519648072 0.684756277 0.621897374 1 19.86980301 -1.525182232 2.795356582 1.016560866 0.647979064 0.514553786 0.102438069 15689963.46 16280417.5 1968003.235 0.023481531 0.029841302 1.525182232 -0.368581802 WAHDKFS(ph)GEEGEIEDDESGTENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 WAHDKFSGEEGEIEDDESGTENR 23 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR 306.46 7.42E-63 4784490000 4076200 2232672 3034747 2632722 2509750 2520091 3655163 2509862 2363997 TRUE FALSE 3821077.918 2397981.358 3106732.632 2700282.104 2312644.359 3247600.361 3107105.241 2823223.796 1969430.629 1.940194218 1.217601333 1.577477565 1.371097852 1.174270535 1.649004699 1.577666761 1.433522844 1 20.90934717 -2.049217452 1.900121529 0.408426814 1.476966445 0.328755355 0.220204614 1471712.45 410063.0665 3781677.907 0.053466786 0.008928583 2.049217452 1.06853963 WAHDKFS(ph)GEEGEIEDDESGTENREEKDNIQPTTE ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 WAHDKFSGEEGEIEDDESGTENREEKDNIQPTTE 34 3 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 WAHDKFS(1)GEEGEIEDDESGTENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDESGTENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDESGTENREEKDNIQPTTE 196.19 2.69E-26 1008840000 708786 458668 491487 571047 708904 318441 619504 412467 1077390 TRUE FALSE 664424.3495 492628.256 503145.3037 585701.0328 653229.5394 410369.7472 526615.1264 463964.4129 897566.6488 0.74025071 0.548848664 0.560565953 0.652543222 0.727778311 0.457202535 0.586714231 0.516913606 1 19.77565954 -1.930338215 2.543080414 1.272759766 0.5898224 0.667138605 0.088846049 7541816.937 3861101.997 12213845.93 0.020367514 0.011739829 1.930338215 -0.682937365 WAHDKFSGEEGEIEDDES(ph)GTENREEKDNIQPTTE ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WAHDKFSGEEGEIEDDESGTENREEKDNIQPTTE 34 3 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 WAHDKFSGEEGEIEDDES(0.968)GT(0.032)ENREEKDNIQPTTE 241.23 2.32E-46 88289000 46762 43701 39338 45916 69581 22442 50732 43262 141840 TRUE FALSE 43835.24989 46936.66751 40271.11594 47094.2823 64116.38894 28920.64108 43125.20757 48663.35593 118165.9877 0.370963344 0.397209624 0.340801247 0.398543466 0.542595972 0.244745901 0.364954488 0.411822022 1 16.85045531 0.70911834 4.195575959 0.999998627 0.376954751 0.877312702 0.072487154 2.304088846 32.98374649 0.065352403 0.016648765 5.118212814 -0.70911834 -0.623043875 WAPNENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WAPNENK 7 0 A0A1W2PNV4;C9JEY1;C9K057;O15143;F8VXW2 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 111.01 0.0363 0 211100 183770 184910 185680 203910 139020 230880 173050 212570 FALSE TRUE 197887.6278 197376.522 189296.1525 190444.8632 187895.7311 179152.8172 196261.6874 194655.6734 177090.6937 1.117436629 1.114550504 1.068922079 1.075408646 1.061014146 1.011644448 1.108255229 1.099186351 1 17.43412887 3.974309564 1.514705525 1.06408332 1.120102074 0.317077894 0.033612519 0.569360199 2.427067244 0.009368017 0.030826518 9425.61213 -3.974309564 0.056018754 WASLADSYS(ph)DPGLTEDGLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WASLADSYSDPGLTEDGLGR 20 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 WASLADS(0.338)Y(0.196)S(0.465)DPGLTEDGLGR 117.4 8.47E-05 31146000 56685 71354 61794 63552 70043 59419 78461 58528 60853 TRUE FALSE 53137.18704 76637.1244 63259.78286 65182.85191 64542.10532 76572.30071 66696.50145 65835.34964 50696.24117 1.048148458 1.511692438 1.247819984 1.285753153 1.273114216 1.510413769 1.315610387 1.298623884 1 15.62959116 0.682877266 2.854253891 1.000027145 1.332270249 0.347179984 0.132371088 2.876185533 24.68833843 0.11385849 0.029929813 4.818116154 -0.682877266 0.332243103 WATHGEPSPVNSHPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 WATHGEPSPVNSHPQR 16 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ;;; 207.55 9.92E-12 1626500000 515660 717830 613200 724070 705560 502690 738590 638230 644180 FALSE TRUE 483385.7611 770978.8801 627745.3936 742650.862 650148.1637 647808.4425 627845.2862 717914.4204 536662.1964 0.900726312 1.436618575 1.169721657 1.383833009 1.211466297 1.207106531 1.169907794 1.337739877 1 19.03365474 -1.230196656 5.391687266 0.999983107 1.238919707 0.186231934 0.14740032 2.62E-05 3.74E-06 0.124869974 0.029430055 0.058857708 1.230196656 0.2389366 WAYNNSDGGTAWISQES(ph)FDVDETDSGAGLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WAYNNSDGGTAWISQESFDVDETDSGAGLK 30 0 O00273;O00273-2;K7ERT1 O00273 DFFA DNA fragmentation factor subunit alpha 1 WAYNNSDGGTAWIS(0.124)QES(0.86)FDVDET(0.012)DS(0.004)GAGLK 70.701 0.0039679 18907000 15137 14835 13996 14305 11983 10296 17602 11683 15534 TRUE FALSE 14189.60219 15933.39884 14327.99173 14672.09052 11041.90352 13268.28806 14962.74351 13141.64827 12941.27505 1.096460908 1.231207804 1.107154564 1.133743813 0.8532315 1.025268995 1.156203191 1.015483267 1 13.65969215 2.970745451 24.98885817 1.028297375 1.153331344 0.383744897 0.081249518 793.3185814 677642.9088 0.025614898 0.027211361 934.8575747 -2.970745451 0.125033969 WCDKSDEDDWSKPLPPSER ddPTM_SK-BR-3_Pertuzumab_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 ; 193.22 3.25E-15 455880000 984220 631330 748110 693130 803670 544400 943930 636120 1151180 FALSE TRUE 922619.4271 678074.3301 765855.5225 710916.8893 740553 701559.4424 802396.4595 715540.9823 959040.6211 0.962023304 0.707034004 0.798564217 0.741279226 0.772181057 0.731522135 0.83666577 0.746100808 1 19.8712324 -1.303355541 4.70862601 1.000115025 0.78070317 0.460081873 0.072263359 7.61E-05 1.13E-05 0.061028006 0.014376921 0.049732977 1.303355541 -0.219411855 WCIYPTYDYTHCLCDSIEHITHSLCTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WCIYPTYDYTHCLCDSIEHITHSLCTK 27 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A1B0GTT3 P47897 QARS Glutamine--tRNA ligase 0 212.38 2.22E-26 200840000 237860 338990 219800 177220 331830 239480 376050 347460 198000 FALSE TRUE 222972.7672 364089.1723 225013.7598 181767.7652 305769.4103 308613.9884 319664.7936 390841.1459 164952.5209 1.35173907 2.207236182 1.364112283 1.101939905 1.853681343 1.870926172 1.937920026 2.369416022 1 17.3316913 2.519111929 24.98105374 1.877479102 1.587237429 0.078961043 0.439800965 1178.729963 701247.3755 0.135448991 0.127692062 330.454697 -2.519111929 -0.290241673 WDAADDIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WDAADDIHR 9 0 Q9HD15;R4GMW4 Q9HD15 SRA1 Steroid receptor RNA activator 1 0 156.83 7.00E-05 287940000 616780 738420 649470 660740 737520 595320 731280 611570 631880 FALSE TRUE 578176.8408 793093.3851 664875.7351 677695.707 679598.1542 767179.2198 621631.3529 687925.8607 526415.1459 1.098328658 1.506593021 1.263025466 1.287378816 1.290992783 1.4573654 1.180876648 1.306812439 1 19.00584147 0.167500848 0.663115763 0.988657467 1.327465348 0.375615354 0.11878335 3.078062048 1.706869727 0.193528051 0.040901198 1.470621288 -0.167500848 0.33880788 WDAWNELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WDAWNELK 8 0 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ; 130.96 0.0023855 764980000 1629630 1459810 1175470 1123140 1310150 815920 1382480 1339690 1653920 FALSE TRUE 1527634.367 1567895.851 1203352.703 1151961.674 1207256.104 1051462.859 1175189.958 1506953.246 1377870.067 1.108692614 1.137912702 0.873342656 0.836045213 0.876175579 0.76310741 0.852903322 1.093683128 1 20.39400842 3.963020702 2.784924937 0.879717474 1.12313449 0.490744335 0.092831985 0.194478841 3.017690199 0.023433108 0.053716526 9183.763717 -3.963020702 0.243417016 WDDPYYDIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 WDDPYYDIAR 10 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ;;;;; 187.22 2.92E-06 2105610000 2152533 2889964 2363408 2483990 2830289 1765485 2561546 2431071 2676715 FALSE TRUE 2017809.802 3103939.942 2419469.154 2547733.389 2608009.519 2275151.859 2177465.958 2734595.566 2229953.974 0.904866121 1.391930048 1.08498614 1.142504921 1.169535133 1.020268528 0.976462287 1.226301349 1 21.0885825 2.244548293 24.80748567 1.044313315 1.166123681 0.062151253 0.136080877 234.7375682 972541.95 0.044995755 0.036720147 175.6096158 -2.244548293 0.121810365 WDDQQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WDDQQK 6 0 P09874;Q5VX84;Q5VX85 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 118.69 0.050377 528930000 1207400 1009870 1092720 1088890 1136920 789160 1350750 1014700 1366120 FALSE TRUE 1131830.989 1084641.826 1118639.834 1116832.761 1047630.889 1016977.681 1148217.577 1141387.529 1138105.747 0.994486666 0.953023767 0.982896218 0.981308428 0.920503998 0.893570465 1.00888479 1.002883548 1 20.11820318 1.607059463 24.99999999 1.004418659 0.956762832 0.377132958 0.029949133 0.101147104 2834.974363 0.015280657 0.007716157 40.46312893 -1.607059463 -0.047655827 WDEAFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 WDEAFR 6 0 P27695;G3V3M6;G3V5Q1;H7C4A8 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ;;;;; 177.54 0.0084904 710016000 1160030 1517510 1163910 1141820 1525120 906830 1274940 1396970 1281080 FALSE TRUE 1087425.793 1629868.019 1191518.495 1171121.034 1405343.227 1168617.1 1083774.583 1571384.78 1067259.472 1.018895425 1.527152546 1.116428128 1.097316131 1.31677747 1.094969996 1.015474317 1.472354962 1 20.02547954 3.732931817 24.42462289 1.151353745 1.313066777 0.050562478 0.186030601 358.1725212 1505555.911 0.043681569 0.076113622 5406.69433 -3.732931817 0.161713032 WDEMNILATYHPADKDYGLMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WDEMNILATYHPADKDYGLMK 21 1 P41236;E7EMN6;E7EUI7 P41236 PPP1R2 Protein phosphatase inhibitor 2 0 ; 220.73 2.75E-25 379610000 634640 498440 562220 514610 571390 359220 668650 475920 643330 FALSE TRUE 594919.0153 535345.0162 575556.1239 527815.7638 526515.3343 462920.9826 568392.1399 535339.6596 535954.0669 1.11001866 0.998863614 1.073890767 0.984815297 0.982388915 0.863732568 1.06052398 0.998853619 1 19.03174984 8 0.457215389 0.985466993 3.55297649 0.270203253 0.056770782 130.2564655 1.540044539 0.032609619 313.6422123 100000000 -8 2.567509497 WDEQTSNTKGDDDEES(ph)DEEAVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WDEQTSNTKGDDDEESDEEAVKK 23 2 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 WDEQTSNTKGDDDEES(1)DEEAVKK;WDEQTSNTKGDDDEES(1)DEEAVKK 188.15 1.16E-17 370690000 708720 201413 327754 281039 280855 186822 393860 207283 369150 TRUE FALSE 664362.4803 216325.8281 335528.4797 288250.9365 258797.7812 240754.4786 334804.3494 233162.7388 307536.4802 2.160272108 0.703415178 1.091020094 0.937290224 0.841518967 0.782848521 1.088665479 0.758162865 1 18.23039803 4.744377903 24.99799324 0.910688237 2.160272649 0.897964745 0.13343052 181.5967822 780333.8309 0.029686995 0.26671981 55510.85321 -4.744377903 1.249584411 WDET(ph)PGR ddPTM_SK-BR-3_Pertuzumab_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 149.82 0.022254 3164880000 4607400 5120840 4756940 4924830 4939790 3708940 6215650 4378520 5349500 TRUE FALSE 4319031.058 5499992.322 4869776.863 5051209.476 4551838.82 4779650.768 5283670.986 4925187.86 4456633.891 0.969124044 1.234113561 1.092702919 1.133413603 1.02136252 1.072480012 1.185574385 1.105136294 1 22.08752302 3.696421935 24.20500818 1.098440043 1.133405139 0 0.083219305 964.0695605 760123.6929 0.020872295 0.032340308 4970.750153 -3.696421935 0.034965096 WDET(ph)PKTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 WDETPKTER 9 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 WDET(1)PKTER;WDET(1)PKTER;WDET(1)PKTER;WDET(1)PKTER 150.06 0.00013928 654410000 1715690 1071900 1226330 1301460 1291980 947640 1533930 1041700 1235840 TRUE FALSE 1608308.025 1151264.591 1255419.127 1334857.667 1190513.102 1221208.284 1303931.437 1171758.538 1029570.32 1.562115762 1.118199086 1.219362196 1.29651918 1.15632034 1.186133924 1.266481183 1.138104426 1 19.97361094 -4.999999999 0.038399606 4.50E-08 1.837442913 0.416236364 0.112631813 1131.637621 3.250992095 136.8161137 43.18487523 1.00E-05 4.999999999 1.837442868 WDETPGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WDETPGR 7 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 153.15 0.0041078 543130000 841140 923120 928650 915390 922780 771880 1052380 826630 871030 FALSE TRUE 788494.5489 991468.7653 950678.0165 938880.4572 850308.5811 994709.2256 894585.3888 929836.5751 725649.4659 1.086605291 1.366319155 1.31010641 1.293848478 1.171789715 1.370784755 1.232806514 1.281385323 1 19.46891328 -1.212493511 0.650355731 0.914005554 1.279695928 0.469679152 0.086909075 37.82599204 7.379606123 6.022817163 0.029677809 0.061306495 1.212493511 0.365690373 WDGS(ph)EEDEDNSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 WDGSEEDEDNSK 12 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK 361.96 2.44E-72 6996080000 9320640 5359200 6588320 6293540 6434490 4520050 8170910 5164980 8340110 TRUE FALSE 8737277.78 5756000.744 6744598.062 6455042.891 5929151.111 5824915.058 6945757.901 5809839.123 6948091.762 1.25750754 0.828429005 0.970712289 0.929038233 0.853349569 0.838347457 0.9996641 0.836177662 1 22.72818538 4.746626011 24.99329777 0.908094678 1.257507712 0.729140605 0.067141256 501.8568986 1555134.541 0.014729094 0.163123367 55798.94798 -4.746626011 0.349413034 WDGVPFILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WDGVPFILR 9 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 139.88 0.00025692 623240000 750410 1217040 767460 827990 1348970 840610 1139860 1193800 1314580 FALSE TRUE 703443.1776 1307150.908 785664.5136 849237.6252 1243027.338 1083280.461 968948.5749 1342848.558 1095168.105 0.642315252 1.193561885 0.717391704 0.775440429 1.135010535 0.98914537 0.884748716 1.226157474 1 20.06272091 2.742052075 24.97580415 1.022265339 0.873277147 0.259551693 0.171459423 583.732788 4175684.798 0.052171948 0.05333897 552.1436418 -2.742052075 -0.148988192 WDHS(ph)LAWDVPAAEDFPNGSGSPSAAIYNIDTSSESPDHYLVDHTLDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WDHSLAWDVPAAEDFPNGSGSPSAAIYNIDTSSESPDHYLVDHTLDGR 48 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 WDHS(0.99)LAWDVPAAEDFPNGS(0.006)GS(0.002)PS(0.001)AAIYNIDTSSESPDHYLVDHTLDGR 58.768 0.0027352 29746000 1547.3 7242.9 1645.9 2190.7 1014.3 1721.7 1941 1888.3 3337.1 TRUE FALSE 1450.457255 7779.171852 1684.941525 2246.917071 934.6409695 2218.726841 1649.965069 2124.058412 2780.116452 0.521725359 2.798146045 0.606068686 0.808209696 0.336187705 0.79806975 0.593487754 0.764017784 1 11.4409296 3.747328696 6.915048124 0.673986745 1.793015447 0.323575751 0.567816618 0.13719965 28.15173296 0.129170221 0.226212308 5588.930326 -3.747328696 1.119028702 WDHSLAWDVPAAEDFPNGSGS(ph)PSAAIYNIDTSSESPDHYLVDHTLDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 WDHSLAWDVPAAEDFPNGSGSPSAAIYNIDTSSESPDHYLVDHTLDGR 48 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 WDHSLAWDVPAAEDFPNGS(0.032)GS(0.934)PS(0.032)AAIY(0.001)NIDTSSESPDHYLVDHTLDGR;WDHSLAWDVPAAEDFPNGS(0.023)GS(0.838)PS(0.139)AAIYNIDTSSESPDHYLVDHTLDGR;WDHSLAWDVPAAEDFPNGS(0.155)GS(0.814)PS(0.03)AAIYNIDTSSESPDHYLVDHTLDGR 155.74 3.23E-16 1016170000 70585 121495 110310 110200 130623 106877 140186 111856 131303 TRUE FALSE 66167.21085 130490.6162 112926.6053 113027.9186 120364.3965 137730.6549 119166.4107 125821.4678 109387.6811 0.604887225 1.192918754 1.032352128 1.033278313 1.100346907 1.25910572 1.089395164 1.150234346 1 16.73909075 4.744189698 24.90287969 1.111810579 0.604886996 0.801894601 0.078434143 243.8405091 1078709.123 0.017775557 0.157183768 55486.80239 -4.744189698 -0.506923584 WDHSLAWDVPAAEDFPNGSGSPS(ph)AAIYNIDTSSESPDHYLVDHTLDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WDHSLAWDVPAAEDFPNGSGSPSAAIYNIDTSSESPDHYLVDHTLDGR 48 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 WDHSLAWDVPAAEDFPNGS(0.116)GS(0.127)PS(0.719)AAIY(0.035)NIDT(0.002)S(0.001)SESPDHYLVDHTLDGR;WDHSLAWDVPAAEDFPNGS(0.022)GS(0.022)PS(0.573)AAIY(0.109)NIDT(0.119)S(0.119)S(0.025)ES(0.006)PDHY(0.005)LVDHT(0.001)LDGR 162.7 1.64E-21 855300000 21547 31810.1 28203.4 32867.6 34042.3 25969.8 37437 29253 34367 TRUE FALSE 20198.41173 34165.3529 28872.39797 33711.03826 31368.75508 33466.85968 31823.6694 32905.30144 28630.92568 0.70547533 1.19330242 1.008433967 1.177434451 1.0956249 1.16890596 1.111513814 1.149292266 1 14.8052867 4.745247849 24.90694837 1.115606852 0.705475133 0.790585411 0.065913893 295.7746185 1101598.127 0.013872067 0.13471987 55622.15981 -4.745247849 -0.410131719 WDHSLAWDVPAAEDFPNGSGSPSAAIYNIDTSSESPDHYLVDHTLDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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 ;;;;;; 347.24 9.92E-160 22067514000 1055575 1717449.1 1581216 1603742 1677339 1387554.5 1872095 1580105.9 1737749 FALSE TRUE 989508.445 1844610.818 1618723.19 1644896.735 1545607.561 1788118.959 1591391.734 1777385.6 1447707.466 0.683500271 1.274159913 1.118128647 1.136207952 1.067624225 1.235138315 1.099249518 1.227724276 1 20.46533868 4.747819014 24.92866055 1.152413758 0.683500016 0.752599864 0.083013335 531.6411249 1431436.953 0.017642165 0.220499437 55952.43787 -4.747819014 -0.468913742 WDKDDFES(ph)EEEDVK ddPTM_SK-BR-3_Pertuzumab_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 176.44 1.35E-06 957412000 2866220 937649 1506018 1401858 1369478 1060619 2049608 1131373 1563942 TRUE FALSE 2686828.407 1007073.508 1541741.458 1437832.05 1261924.722 1366802.488 1742288.308 1272627.41 1302909.977 2.062175019 0.772941742 1.183306204 1.103554409 0.968543295 1.049038316 1.337228465 0.976757744 1 20.31330598 4.749115141 24.99755496 1.066430559 2.062175578 0.822182228 0.147890357 663.3488141 1571058.601 0.03624105 0.524039424 56119.67419 -4.749115141 0.995745018 WDKDNLQILR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WDKDNLQILR 10 1 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 101.71 0.0028684 636360000 1540230 1739260 1555790 1568570 2014180 1268910 1685220 1715600 1490380 FALSE TRUE 1443829.754 1868036.62 1592694.073 1608822.162 1855994.428 1635223.718 1432536.906 1929796.437 1241625.95 1.162854041 1.504508359 1.2827487 1.295738191 1.494809631 1.317001886 1.153758832 1.554249439 1 20.24379918 -1.745651426 2.919880884 0.938164984 1.341922949 0.386259875 0.136877068 18490778.75 23339335.8 8507173.806 0.030847351 0.017961747 1.745651426 0.403757965 WDLLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WDLLSR 6 0 F8VNY0 F8VNY0 AVIL 0 130.05 0.037058 101690000 353850 459630 396380 414390 431990 353470 473870 440370 327570 FALSE TRUE 331703.1601 493661.4834 405782.3208 425023.949 398063.248 455511.0509 402817.5927 495351.1639 272896.4508 1.215490928 1.808969966 1.486946128 1.557455026 1.458660407 1.669171767 1.476082197 1.81516162 1 18.05799411 -1.082634711 5.145390618 0.999989123 1.571156694 0.497987262 0.176752299 1.91E-05 3.41E-06 0.148207795 0.034932248 0.082673303 1.082634711 0.571167571 WDLPDSDWDNDSSSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WDLPDSDWDNDSSSAR 16 0 O15020;O15020-2;A4QPE4;E9PJZ2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 73.435 0.081601 37950000 19442 20937 19530 17102 26492 17914 22089 21300 26228 FALSE TRUE 18225.15992 22487.19726 19993.26082 17540.86627 24411.42518 23085.48099 18776.95951 23959.35189 21850.37736 0.834089024 1.029144572 0.915007576 0.802771778 1.117208402 1.056525506 0.859342574 1.096518906 1 14.41537058 2.735456678 24.9982499 1.00677393 0.920860853 0.301057027 0.09294028 511.6220143 4120443.354 0.029780013 0.02918615 543.821881 -2.735456678 -0.085913077 WDLSAQQIEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WDLSAQQIEER 11 0 P52888;K7EKB6 P52888 THOP1 Thimet oligopeptidase 0 92.866 0.010097 0 32074 43387 37416 32084 49163 28186 38369 39226 44228 FALSE TRUE 30066.54559 46599.41862 38303.52519 32907.32976 45301.93629 36322.84064 32615.92465 44123.45245 36846.06108 0.816004336 1.264705569 1.039555493 0.893103056 1.229491972 0.985799827 0.885194338 1.197507988 1 15.16922278 WDQSTFLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WDQSTFLGR 9 0 S4R3N9;A0A1P0AYU5;Q9BWM7 S4R3N9 SFXN3 Sideroflexin-3 0 ; 107.79 0.0063205 104901000 148858 143673 124757 120660 221360 149871 148747 166402 296110 FALSE TRUE 139541.2435 154310.6984 127716.295 123756.3399 203975.2785 193136.3247 126443.7682 187177.656 246687.3281 0.565660363 0.625531516 0.517725397 0.50167287 0.826857545 0.782919521 0.512566937 0.758764779 1 17.91232408 -5 0.168996108 2.494524789 0.529781593 0.559332027 0.109051689 102.4433914 0.964711993 51.08007648 0.402133752 1.00E-05 5 -1.964743196 WDQTADQT(ph)PGATPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WDQTADQTPGATPK 14 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 WDQTADQT(0.665)PGAT(0.335)PK 143.97 0.00010039 504670000 175950 122710 138430 133320 134740 102040 166650 115810 138930 TRUE FALSE 164937.6036 131795.5761 141713.625 136741.2169 124158.0639 131497.2915 141662.3796 130269.1334 115741.6855 1.425049263 1.138704483 1.224395726 1.181434471 1.072716916 1.136127325 1.223952969 1.125516126 1 16.82054903 WDQTADQTPGAT(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 WDQTADQTPGATPK 14 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 WDQTADQTPGAT(1)PK;WDQTADQTPGAT(1)PK;WDQTADQTPGAT(1)PK 325.49 7.01E-56 1158320000 3142270 1988430 2394270 2209490 2343490 1757210 2993860 1904000 2697640 TRUE FALSE 2945600.93 2135655.426 2451063.215 2266189.254 2159441.749 2264488.001 2544958.487 2141718.591 2247386.457 1.31067842 0.950284015 1.090628275 1.008366517 0.960868008 1.007609525 1.132408037 0.952981889 1 21.0998168 4.747638948 24.87157862 1.023340017 1.31067858 0.711351456 0.059282898 657.7795619 1802054.085 0.013911299 0.173594352 55929.24393 -4.747638948 0.287338563 WDS(ph)CDSLNGLDPSEKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WDSCDSLNGLDPSEKEK 17 1 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 WDS(0.994)CDS(0.006)LNGLDPSEKEK 83.063 0.0035424 256850000 156310 89360 98905 129710 117710 87808 165180 82329 138590 TRUE FALSE 146526.8361 95976.30738 101251.0733 133038.5782 108465.5314 113156.7442 140412.7925 92607.95688 115458.4337 1.269087337 0.831262856 0.876948267 1.15226384 0.939433595 0.980064778 1.216132837 0.80208915 1 16.81701403 3.262822098 24.99925069 1.032718974 0.941398639 0 0.16238862 668.5436124 688868.6117 0.042512464 0.057534354 1831.563995 -3.262822098 -0.091320334 WDS(ph)YDNFSGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WDSYDNFSGHR 11 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;E7ERH1;E7EMG1;H7C3Z4;Q9HBL0-2 E9PGF5 TNS1 Tensin-1 1 WDS(1)YDNFSGHR 148.52 2.24E-05 124950000 158910 127900 153190 121600 154760 153960 164680 153460 226200 TRUE FALSE 148964.1068 137369.8491 156823.7391 124720.4619 142605.7739 198405.7527 139987.7628 172619.8188 188445.7587 0.790487978 0.728962276 0.832195642 0.661837458 0.75674706 1.052853373 0.74285441 0.916018593 1 17.5237898 2.37914529 24.85980755 0.895526188 0.757045566 0.452973872 0.091902764 13.63282533 3445.34493 0.029521271 0.024699223 239.4116555 -2.37914529 -0.138480622 WDS(ph)YDNFSGHRDDGMEEVVGHTQGPLDGSLYAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WDSYDNFSGHRDDGMEEVVGHTQGPLDGSLYAK 33 1 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;E7ERH1;E7EMG1 E9PGF5 TNS1 Tensin-1 1 WDS(0.997)YDNFS(0.003)GHRDDGMEEVVGHTQGPLDGSLYAK;WDS(0.998)YDNFS(0.002)GHRDDGMEEVVGHTQGPLDGSLYAK 226.41 1.51E-36 284751000 158640 135705 147372 114559 164514 105432 182227 142255 329809 TRUE FALSE 148711.0056 145752.7394 150867.7334 117498.7779 151593.7341 135868.5069 154903.7531 160015.8499 274761.7473 0.541236206 0.530469546 0.549085653 0.427638778 0.551727945 0.494495716 0.563774814 0.582380377 1 18.06782164 0.279517981 1.040823662 1.001938952 0.519574312 0.94165701 0.037146396 0.710366521 0.848687095 0.035412239 0.010378623 1.903347041 -0.279517981 -0.48236464 WDS(ph)YENLSADGEVLHTQGPVDGSLYAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WDSYENLSADGEVLHTQGPVDGSLYAK 27 0 Q68CZ2;E9PCX8;C9JHU5;Q68CZ2-3 Q68CZ2 TNS3 Tensin-3 1 WDS(1)YENLSADGEVLHTQGPVDGSLYAK;WDS(1)YENLSADGEVLHTQGPVDGSLYAK 310.63 3.45E-82 843950000 661600 485350 549340 573740 618350 465310 665330 556450 476030 TRUE FALSE 620191.637 521285.819 562370.6042 588463.1397 569787.2853 599637.4433 565569.9431 625924.0074 396577.5177 1.563859799 1.314461349 1.418059721 1.483854009 1.43676144 1.512030855 1.426127095 1.578314401 1 18.59724337 -1.009270518 6.054477697 0.99999955 1.448665241 0.776643584 0.078123259 4.61E-07 7.53E-08 0.073403813 0.017301427 0.097888006 1.009270518 0.448665692 WDSNVIETFDIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 WDSNVIETFDIAR 13 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;F5GWK5;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 ;; 198.57 2.90E-07 161039000 271305 320983 283567 274539 334038 231431 287634 297123 279956 FALSE TRUE 254324.5043 344748.9153 290293.3432 281584.1355 307804.0029 298241.3727 244505.952 334219.4606 233229.535 1.090447247 1.478152908 1.244668018 1.207326231 1.319747102 1.278746162 1.048349009 1.43300659 1 17.83139097 -4.962103668 0.163665212 3.16E-09 1.335957934 0.218030822 0.138011172 169.3192303 1.591311824 54.90545133 0.513784273 1.09E-05 4.962103668 1.335957931 WDSYDNFS(ph)GHRDDGMEEVVGHTQGPLDGSLYAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WDSYDNFSGHRDDGMEEVVGHTQGPLDGSLYAK 33 1 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;E7ERH1;E7EMG1 E9PGF5 TNS1 Tensin-1 1 WDS(0.432)YDNFS(0.568)GHRDDGMEEVVGHTQGPLDGSLYAK 173.7 6.25E-15 198430000 16743 21505 25265 23943 25680 15047 22245 19811 44054 TRUE FALSE 15695.08552 23097.25258 25864.29773 24557.41792 23663.19639 19390.82463 18909.56876 22284.44696 36701.1028 0.427646156 0.62933402 0.704728081 0.669119346 0.644754369 0.528344468 0.515231623 0.607187394 1 15.16353579 -1.101364219 3.082429432 1.000676895 0.599324774 0.709888101 0.082050643 4273809.993 6263568.655 29458.81675 0.021600107 0.079183698 1.101364219 -0.40135212 WDYLTQVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 WDYLTQVEK 9 0 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;; 182.65 0.00010721 521364000 1155189 1064174 1053401 1070244 1201356 869614 1171064 1104436 1043338 FALSE TRUE 1082887.783 1142966.55 1078388.169 1097708.273 1107006.346 1120657.445 995473.8248 1242327.266 869198.1476 1.24584686 1.31496662 1.240670119 1.262897621 1.273594921 1.289300314 1.145278355 1.429279698 1 19.72932557 -1.628386027 3.211825988 0.982913032 1.266834796 0.596472038 0.070845663 5495589.002 2837632.186 652996.5095 0.014956383 0.023529569 1.628386027 0.283921763 WEAERDDWLHNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 WEAERDDWLHNR 12 1 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 0 ;;; 176.91 1.44E-05 1204570000 1061140 1474640 1325390 1332710 1474770 960940 1311350 1137890 1673180 FALSE TRUE 994725.1416 1583823.88 1356828.877 1366909.595 1358947.513 1238347.778 1114725.241 1279958.071 1393915.449 0.713619425 1.136240997 0.973393959 0.980625902 0.974913876 0.888395189 0.799707932 0.918246564 1 20.41071162 2.232150408 4.633332875 0.874530458 0.984676001 0 0.115411242 0.335221451 18.06884215 0.040444349 0.03103745 170.6673353 -2.232150408 0.110145543 WEEEGFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WEEEGFR 7 0 Q3KQV9 Q3KQV9 UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 ; 116.3 0.012765 381530000 912320 1050190 917350 1004580 1122270 729290 946760 1042550 731840 FALSE TRUE 855219.5197 1127947.16 939109.9752 1030359.224 1034131.441 939824.184 804802.1273 1172714.662 609691.1761 1.40270936 1.850030318 1.540304357 1.68996906 1.696156155 1.541475784 1.320016032 1.923456839 1 19.21771914 -2.589686577 0.342281364 1.13E-13 1.64397534 0.491427967 0.191307865 50.62598324 1.917559887 37.88342433 0.144699861 0.002572251 2.589686577 1.64397534 WENFIHSENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WENFIHSENR 10 0 P19784;H3BSA1;H3BV19 P19784 CSNK2A2 Casein kinase II subunit alpha 0 ; 195.68 3.47E-07 191690000 187077 229500 191112 182415 231770 137167 200940 206670 215290 FALSE TRUE 175368.1845 246492.4188 195645.2669 187096.0777 213567.7191 176764.8862 170810.9124 232473.2044 179356.7082 0.97776206 1.374313909 1.090816557 1.043150711 1.190742857 0.985549345 0.952353074 1.29615004 1 17.45247218 3.655780122 5.09021821 1.066555691 1.212625766 0.059454962 0.139082652 0.330775495 15.91213653 0.034643494 0.055174508 4526.683417 -3.655780122 0.146070075 WENPGLGAESHTDSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WENPGLGAESHTDSLR 16 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 153.36 4.58E-07 356250000 381730 942310 770830 847650 924020 812200 790570 844750 746240 FALSE TRUE 357838.2007 1012079.613 789114.4516 869402.1341 851451.1965 1046668.955 672031.3678 950218.897 621687.7231 0.575591551 1.627954961 1.269310013 1.398454725 1.369580201 1.683592769 1.080978991 1.528450477 1 19.24583056 -1.128464249 4.325715016 0.999953045 1.34137243 0.085864675 0.315826017 0.000153297 3.09E-05 0.265494838 0.06256713 0.07439363 1.128464249 0.341419385 WES(ph)QQDVSQTTVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WESQQDVSQTTVSR 14 0 Q9NQT8;H0YBA8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 WES(1)QQDVSQTTVSR;WES(1)QQDVSQTTVSR 259.29 3.11E-13 235790000 347110 300270 304490 317060 344990 235140 418730 286920 504800 TRUE FALSE 325385.0047 322502.3032 311712.6466 325196.2964 317895.877 303021.1008 355945.3238 322742.5936 420545.6189 0.773721066 0.766866396 0.741210068 0.773272344 0.755912944 0.72054276 0.846389328 0.767437774 1 18.68190278 -0.15174619 0.548239416 1.023211057 0.756229318 0.84573404 0.031283763 1.887733293 0.603765348 0.122050255 0.012955116 0.705105026 0.15174619 -0.266981738 WESGSLLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WESGSLLER 9 0 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 ; 124.08 0.0012556 276790000 497560 586300 529390 545480 604320 481340 604880 527870 642540 FALSE TRUE 466418.6078 629710.262 541947.3808 559477.9403 556859.1449 620295.0441 514183.8594 593775.7315 535295.923 0.871328526 1.176377841 1.012425758 1.045175045 1.040282806 1.158789031 0.960560014 1.109247625 1 19.02997714 -1.521936946 3.676799358 0.999071247 1.053167005 0.021675148 0.090069707 0.000610704 7.94E-05 0.077668518 0.017993328 0.030065128 1.521936946 0.054095758 WEWLVNQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WEWLVNQHR 9 0 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 ; 168.8 5.90E-05 1048010000 847750 1153180 805290 693950 1243280 576940 858300 1089450 877220 FALSE TRUE 794690.8408 1238562.647 824391.8591 711757.9319 1145637.804 743493.2122 729605.8831 1225470.231 730806.3149 1.087416494 1.694789196 1.12805793 0.973935114 1.567635337 1.017360136 0.998357387 1.676874167 1 19.47912957 3.740321874 18.1595973 1.178852553 1.427570747 0.071627209 0.283138444 25.59675356 35204.03784 0.066794868 0.118497554 5499.48313 -3.740321874 0.248718194 WFDFPFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WFDFPFTR 8 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5;A0A0A0MSW0 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 0 ; 107.66 0.0092114 95352000 421700 543130 525620 548700 595990 412270 581670 556730 506370 FALSE TRUE 395306.5498 583343.9103 538087.9546 562780.5709 549183.3495 531285.6564 494453.9835 626238.966 421853.5757 0.93707052 1.382811345 1.27553252 1.334066139 1.301834051 1.259407735 1.172098595 1.484493678 1 18.6863828 1.987886252 23.24446902 1.232427912 1.273511808 0 0.166937014 1493.029558 2864900.735 0.059691578 0.040821257 97.24924811 -1.987886252 0.041083896 WFHPNITGVEAENLLLTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WFHPNITGVEAENLLLTR 18 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ; 238.94 6.73E-24 339010000 439020 598420 537160 536770 645900 456680 596150 529400 608150 FALSE TRUE 411542.5219 642727.6395 549901.6889 550544.4269 595173.6194 588516.1024 506762.8419 595496.7554 506645.8362 0.812288373 1.268593549 1.085376903 1.086645518 1.174733072 1.161592695 1.000230942 1.175370866 1 18.95061808 -2.562448365 0.525553733 0.786232318 1.108273992 0.045341192 0.123837671 532.0422676 27.95028194 130.0243488 0.050196572 0.002738745 2.562448365 0.322041674 WFLTCINQPQFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WFLTCINQPQFR 12 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 238.32 9.13E-16 1385650000 337660 508390 372730 344720 464060 222450 340190 414190 372710 FALSE TRUE 316526.4633 546031.7246 381571.3316 353566.0988 427614.5995 286667.7038 289181.6677 465902.5332 310502.2932 1.019401371 1.758543291 1.228884102 1.138690781 1.377170504 0.923238604 0.931335046 1.500480169 1 18.2442444 3.562913541 3.410295387 1.124726504 1.456055637 0.118440259 0.254059411 0.324687191 7.254354124 0.066426616 0.10631573 3655.220163 -3.562913541 0.331329134 WFNGQPIHAELSPVTDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 WFNGQPIHAELSPVTDFR 18 0 P0DN76;Q01081;Q01081-2;Q01081-4 P0DN76;Q01081-2;Q01081-4 U2AF1 Splicing factor U2AF 35 kDa subunit 0 ;;; 204.23 1.10E-15 1766006000 1937571.8 2486039 2014142 1760923 2718705 1606299 2138847 2419174 2492024 FALSE TRUE 1816302.64 2670107.914 2061918.399 1806111.265 2505188.876 2070011.445 1818146.748 2721213.199 2076089.095 0.874867386 1.286123953 0.993174332 0.869958457 1.206686592 0.997072549 0.875755647 1.310740086 1 20.98543693 3.729254748 24.97965885 1.020069459 1.118804547 0 0.167275977 281.8958451 3300470.566 0.040086433 0.068000577 5361.11037 -3.729254748 0.098735088 WFSNPS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 110.88 0.0070319 535880000 512135 642434 572158 600854 657113 461591 716456 545399 742388 TRUE FALSE 480081.3845 690000.4818 585729.858 616272.9309 605505.9956 594844.8284 609030.0741 613493.2657 618478.6468 0.776229522 1.115641559 0.947049443 0.996433643 0.979024901 0.961787172 0.98472288 0.991939283 1 19.23836426 4.759656948 24.91217112 0.996534544 0.776229293 0.70291903 0.045119446 3085.509339 3643545.276 0.010763016 0.499660184 57498.55729 -4.759656948 -0.220305252 WFVTCVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WFVTCVR 7 0 P26640;A0A140T936;A0A140T954 P26640 VARS Valine--tRNA ligase 0 81.381 0.063639 204570000 122900 89517 99046 99474 140380 95280 157230 128540 146410 FALSE TRUE 115207.9084 96144.93182 101395.4179 102026.6712 129355.1211 122785.7893 133654.8212 144588.502 121973.2252 0.944534411 0.788246205 0.831292423 0.836467767 1.060520626 1.006661824 1.095771806 1.185411813 1 16.89620497 2.72704721 5.136432099 1.073399128 0.835741152 0.741475537 0.064174554 0.082294817 6.946298132 0.019689351 0.019412106 533.3928744 -2.72704721 -0.237657976 WGDIEFPPPFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 WGDIEFPPPFGR 12 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ;;; 150.35 0.00014734 722458000 493544 531812 556810 524693 553731 507687 582795 488892 526830 FALSE TRUE 462653.962 571187.9138 570017.7961 538157.5107 510243.2009 654247.9953 495410.3002 549931.2424 438898.6695 1.054124777 1.301411814 1.298745783 1.226154345 1.162553538 1.490658415 1.128757808 1.252979971 1 18.74352837 0.400112211 1.192233292 1.000089794 1.255272685 0.282018524 0.117914425 3.26179317 5.367701843 0.102081689 0.030725057 2.512535522 -0.400112211 0.255182891 WGDKPGVSPSIGLSVGSGWPSS(ph)PGSDPPLPKPCGDHPLNHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WGDKPGVSPSIGLSVGSGWPSSPGSDPPLPKPCGDHPLNHR 41 2 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 WGDKPGVSPSIGLSVGSGWPS(0.144)S(0.812)PGS(0.043)DPPLPKPCGDHPLNHR 147.15 1.02E-13 193410000 250830 197420 207120 241020 317080 159900 255760 197740 246530 TRUE FALSE 235130.998 212037.1822 212032.9842 247204.9812 292177.8158 206060.5342 217411.1624 222428.2743 205382.5504 1.144844086 1.032401155 1.032380715 1.203631861 1.42260292 1.003301078 1.058566865 1.082994996 1 17.64795409 WGDYDSHDIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WGDYDSHDIER 11 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 127.17 0.00029214 267850000 517430 676030 636580 657320 703690 477640 689740 628510 638670 FALSE TRUE 485044.9799 726083.9646 651679.9782 674187.944 648425.0259 615526.9142 586319.8902 706980.857 532071.851 0.911615563 1.364635177 1.224796946 1.267099439 1.218679441 1.156849236 1.101956228 1.328731929 1 19.02126155 2.242618008 4.849258998 1.148945077 1.227640499 0.006630614 0.14021611 0.537944837 33.43922121 0.047686548 0.037091445 174.8308253 -2.242618008 0.078695422 WGEEHIPGSPFHVTVP ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 WGEEHIPGSPFHVTVP 16 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;;; 106.13 0.0012297 488397000 369427 669538 588725 600436 728551 471091 680533 612156 675435 FALSE TRUE 346305.2235 719111.2902 602689.835 615844.2043 671333.5433 607087.3242 578493.3944 688585.0241 562700.535 0.615434324 1.277964469 1.071066753 1.094443964 1.193056522 1.078881726 1.028066189 1.223714891 1 19.10200781 4.749704083 24.81165025 1.121961801 0.615433996 0.767903542 0.087330475 697.8829362 1553848.765 0.019977305 0.302676384 56195.82906 -4.749704083 -0.506527805 WGEEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WGEEKR 6 1 Q15126 Q15126 PMVK Phosphomevalonate kinase 0 100.82 0.059688 121350000 170400 153500 151540 164000 184070 137970 215470 143130 215920 FALSE TRUE 159734.9682 164865.2997 155134.6004 168208.5177 169613.8847 177799.6992 183162.2738 161000.0956 179881.5571 0.888000809 0.916521418 0.862426381 0.93510708 0.942919816 0.988426507 1.018238205 0.895033922 1 17.45668775 2.750779557 1.910675866 0.980318283 0.89207519 0.500281395 0.036025221 0.246223729 1.779186927 0.012683023 0.012613209 563.3516325 -2.750779557 -0.088243094 WGLLSMPVDEEVESLHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WGLLSMPVDEEVESLHLR 18 0 O75165;A0A3B3IRM0 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 61.692 0.057526 7597500 5889.5 8349.3 8264.4 8929.3 9553.2 7775.1 11586 8573.2 7916.2 FALSE TRUE 5520.886708 8967.490859 8460.435471 9158.440955 8802.930208 10019.64515 9848.786859 9643.582892 6594.935079 0.837140418 1.359754228 1.282868651 1.388708281 1.334801647 1.519293978 1.493386476 1.462271088 1 12.68714274 4.740519748 5.170245132 1.378720678 0.812372196 0.546435719 0.147028622 0.114819444 10.31629323 0.03252539 0.231919763 55019.89388 -4.740519748 -0.566348482 WGQPPS(ph)PTPVPRPPDADPNT(ph)PSPKPLEGRPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WGQPPSPTPVPRPPDADPNTPSPKPLEGRPER 32 3 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 2 WGQPPS(0.987)PT(0.013)PVPRPPDADPNT(0.894)PS(0.106)PKPLEGRPER;WGQPPS(0.997)PT(0.003)PVPRPPDADPNT(0.573)PS(0.427)PKPLEGRPER 161.02 4.52E-14 2271400000 733040 495200 579220 592430 621740 396230 769340 526870 728690 TRUE FALSE 687160.3349 531865.1233 592959.3719 607632.7568 572911.0484 510615.1687 653984.6092 592650.8793 607066.9315 1.131935046 0.876122707 0.976761113 1.000932064 0.943736215 0.841118404 1.07728584 0.976252944 1 19.21149606 1.685366099 20.85620393 1.020021642 0.954431013 0.091849455 0.080864137 0.474799453 175.1981889 0.034267962 0.01899019 48.45806839 -1.685366099 -0.065590629 WGQPPS(ph)PTPVPRPPDADPNTPS(ph)PKPLEGRPER ddPTM_SK-BR-3_Pertuzumab_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(0.992)PT(0.008)PVPRPPDADPNT(0.079)PS(0.921)PKPLEGRPER;WGQPPS(0.997)PT(0.003)PVPRPPDADPNT(0.046)PS(0.954)PKPLEGRPER;WGQPPS(0.999)PT(0.001)PVPRPPDADPNT(0.325)PS(0.675)PKPLEGRPER 173.83 6.50E-15 1656280000 713840 472840 519520 542830 580390 409053 696020 500160 650620 TRUE FALSE 669162.0286 507849.5656 531843.2597 556759.9368 534808.5106 527139.9607 591658.2625 562606.077 542027.3188 1.234554063 0.936944593 0.98121117 1.027180582 0.986681837 0.972533934 1.091565392 1.037966275 1 19.04800604 1.743137158 25 1.051221758 1.007140059 0 0.08417018 2.676848824 14686.89083 0.036106336 0.020022874 55.35248953 -1.743137158 -0.044081699 WGQPPS(ph)PTPVPRPPDADPNTPSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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;WGQPPS(0.5)PT(0.5)PVPRPPDADPNTPSPK;WGQPPS(0.851)PT(0.149)PVPRPPDADPNTPSPK;WGQPPS(0.5)PT(0.5)PVPRPPDADPNTPSPK 219.67 6.48E-33 1733230000 3307460 2338310 2799640 2764770 2660490 2135500 3298760 2599220 2195880 TRUE FALSE 3100451.983 2511440.905 2866048.783 2835718.679 2451545.847 2751984.183 2804141.562 2923738.339 1829373.442 1.69481633 1.372842115 1.566683279 1.550103775 1.340101365 1.504331549 1.53284261 1.598218424 1 20.80291818 -1.395204659 6.040778413 0.999887235 1.507700098 0.714826444 0.102957727 0.00014188 1.42E-05 0.09045697 0.021316231 0.04025273 1.395204659 0.507812862 WGQPPSPT(ph)PVPRPPDADPNTPSPKPLEGRPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WGQPPSPTPVPRPPDADPNTPSPKPLEGRPER 32 3 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 WGQPPS(0.216)PT(0.732)PVPRPPDADPNT(0.038)PS(0.013)PKPLEGRPER;WGQPPS(0.491)PT(0.498)PVPRPPDADPNT(0.01)PS(0.001)PKPLEGRPER 90.999 6.84E-05 4348200000 920880 894810 910910 826730 899480 663210 1155340 767760 981340 TRUE FALSE 863243.7646 961062.6634 932517.2154 847945.2915 828838.4691 854667.9607 982107.4927 863616.526 817548.0143 1.055893659 1.175542777 1.140626849 1.03718103 1.013810143 1.045403996 1.201284176 1.05634961 1 19.64094394 -5 0.226834646 0.465227754 1.1162897 0.139358716 0.063721846 292.9462936 2.933072306 72.12649912 0.121328407 1.00E-05 5 0.651061946 WGQPPSPTPVPRPPDADPNT(ph)PSPKPLEGRPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WGQPPSPTPVPRPPDADPNTPSPKPLEGRPER 32 3 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 WGQPPS(0.15)PT(0.15)PVPRPPDADPNT(0.658)PS(0.042)PKPLEGRPER 101.59 1.05E-05 1075700000 647460 506990 493480 575710 555640 424450 739610 540030 672260 TRUE FALSE 606936.6343 544528.0671 505185.5786 590483.6933 512002.2757 546981.8246 628712.3467 607453.9343 560055.463 1.083708087 0.972275253 0.902027767 1.054330744 0.914199235 0.976656529 1.122589437 1.084631745 1 19.09521018 1.75496441 24.99999478 1.079390759 0.973116562 0.275286234 0.062858592 5.956251081 9088.05144 0.027276887 0.01512651 56.88063157 -1.75496441 -0.106274197 WGRDDIENIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 WGRDDIENIAR 11 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 ;;; 241.31 9.26E-16 1169900000 938560 1053740 1016430 1007480 1252130 840740 1209840 980810 1445060 FALSE TRUE 879817.205 1131760.006 1040540.2 1033333.642 1153792.761 1083447.99 1028435.724 1103266.288 1203870.151 0.730824005 0.940101393 0.864329263 0.858343105 0.958402997 0.899970806 0.854274627 0.916432962 1 20.19924836 WGTDEEKFITIFGTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WGTDEEKFITIFGTR 15 1 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ; 179.14 6.23E-07 699930000 957090 978120 936580 1015350 1268030 751750 1245460 1052810 1932720 FALSE TRUE 897187.4454 1050541.023 958796.1199 1041405.6 1168444.039 968768.0214 1058714.835 1184255.646 1610136.546 0.557212025 0.652454616 0.595475037 0.646780922 0.725680093 0.60166824 0.657531088 0.735500134 1 20.61875161 -5 0.216435441 2.808188601 0.594122911 0.879111297 0.043051788 46.6805764 0.466773303 36.6252813 0.081044673 1.00E-05 5 -2.21406569 WGTLTDCVVMRDPQTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WGTLTDCVVMRDPQTK 16 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 170.78 4.70E-09 596840000 693160 605760 615970 653040 794050 434400 797630 556600 1126760 FALSE TRUE 649776.3529 650611.1007 630581.0993 669798.112 731688.516 559804.2281 678032.7863 626092.7352 938696.4769 0.692211347 0.69310061 0.671762508 0.713540669 0.779472954 0.596363406 0.722313126 0.666981022 1 19.84029922 -1.105778617 3.776375028 1.000128834 0.691532439 0.814413708 0.046210911 12142201.62 20744025.82 19175.27341 0.010066615 0.07838291 1.105778617 -0.308596394 WHLVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WHLVYR 6 0 Q99829;B0QZ18;F2Z2V0;A6PVH9;E7ENH5;Q5JX45;Q5JX60;Q5JX52;Q5JX44;Q5JX61;Q5JX59;Q5JX58 Q99829 CPNE1 Copine-1 0 110.63 0.028535 467530000 142470 361740 126480 118940 365430 66161 117590 300480 267620 FALSE TRUE 133553.057 388523.606 129480.1653 121992.2018 336730.6019 85260.60667 99958.47115 337995.5894 222952.4931 0.599020245 1.742629565 0.580752265 0.547166798 1.510324452 0.382416027 0.448339777 1.51599825 1 17.76637681 3.853885022 6.708064422 0.797533491 1.237655778 0.054326275 0.486785578 0.426170103 22.21403471 0.11654669 0.211951544 7143.071902 -3.853885022 0.440122287 WHPHS(ph)PNVRPSFQDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 WHPHSPNVRPSFQDDR 16 1 Q9H329-2 Q9H329-2 EPB41L4B Band 4.1-like protein 4B 1 WHPHS(0.999)PNVRPS(0.001)FQDDR;WHPHS(1)PNVRPSFQDDR;WHPHS(0.986)PNVRPS(0.014)FQDDR 123.43 5.31E-05 946010000 417485 390980 391013 420329 618014 303552 376357 411459 505379 TRUE FALSE 391355.3591 419928.566 400288.013 431115.3538 569477.6734 391182.5346 319925.7618 462830.5619 421027.98 0.929523399 0.997388739 0.950739694 1.023958915 1.352588665 0.929112917 0.759868173 1.099286945 1 18.68355659 3.240453582 24.32502206 1.006380693 0.966185798 0.031776044 0.148375017 245.3475617 3152700.155 0.045166022 0.058211742 1739.616757 -3.240453582 -0.040194895 WHQPPPS(ph)PLPLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 WHQPPPSPLPLR 12 0 J3QQY0;Q68DK7;J3KSZ8;Q68DK7-2;Q68DK7-3;J3KTC2 J3QQY0;Q68DK7 MSL1 Male-specific lethal 1 homolog 1 WHQPPPS(1)PLPLR;WHQPPPS(1)PLPLR;WHQPPPS(1)PLPLR;WHQPPPS(1)PLPLR 150.76 4.41E-05 1662330000 1349860 1261330 1311830 1285770 1496350 1240040 1488740 1268440 1461400 TRUE FALSE 1265374.672 1354720.186 1342947.227 1318765.035 1378832.707 1598019.418 1265517.258 1426807.526 1217482.899 1.039336711 1.112722147 1.10305223 1.083189781 1.132527371 1.312560052 1.039453826 1.171932294 1 20.21547008 6.567975132 0.700694411 1.129558611 2.74E-09 0.075196562 0.083723143 83.19760854 3.731295713 0.028379078 127.491919 3698070.036 -6.567975132 -1.129558609 WIAQDLSSLAGLLDQHGVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WIAQDLSSLAGLLDQHGVR 19 0 A0A2P0CU24;A0A0A0MRV4;J3KPF5;A0A2P0CTB1;A0A0A0MT35;J3KPF6;A0A0G2JRR6;A0A0G2JSF1;J3QKK8;J3KRV9;A0A2P0CTH9;Q8TBF2-2;Q8TBF2;Q8TBF2-7;Q8TBF2-3;Q8TBF2-4;Q8TBF2-6 A0A2P0CU24 FAM213B Prostamide/prostaglandin F synthase 0 ; 188.04 1.70E-14 272040000 343560 415950 381040 385240 462040 328130 389880 374860 388300 FALSE TRUE 322057.1929 446747.3708 390078.4487 395125.9106 425753.2422 422855.8043 331421.1135 421662.0962 323490.2215 0.995570102 1.381022798 1.205843091 1.221446227 1.316123994 1.307167191 1.024516636 1.303477101 1 18.30336258 0.401096804 0.562195134 0.993306552 1.245618051 0.194495936 0.127384101 3.003107528 1.546832864 0.184870122 0.053112528 2.518238176 -0.401096804 0.252311499 WIDDVR ddPTM_SK-BR-3_Pertuzumab_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 316490000 766690 1004900 928620 941580 1095300 827690 1135700 1052000 1074000 FALSE TRUE 718704.2415 1079303.842 950647.3049 965742.5369 1009279.556 1066630.667 965412.3283 1183344.516 894742.4617 0.803252637 1.206273188 1.062481491 1.079352527 1.128011243 1.19210914 1.078983473 1.322553211 1 19.77111296 4.746557761 24.78992886 1.132419701 0.803252455 0.569786912 0.090237495 610.0617147 1891049.666 0.018992078 0.209497098 55790.17984 -4.746557761 -0.329167247 WIDFDNDYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 WIDFDNDYK 9 0 A0A0A0MSX9;P41252;J3KR24;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;; 205.12 3.60E-05 728328000 2616010 2028190 2386330 2345180 2334680 1746230 2738720 2076130 1965440 FALSE TRUE 2452278.604 2178359.298 2442934.875 2405361.289 2151323.65 2250338.253 2328074.361 2335339.401 1637395.367 1.497670418 1.330380763 1.491963959 1.469016792 1.313869389 1.374340186 1.421815652 1.426252601 1 20.64297129 -1.836808626 2.576933287 0.843450791 1.412274975 0.814405433 0.06234146 7107606.75 4835613.416 6886202.352 0.014213578 0.014561006 1.836808626 0.568824185 WIDFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WIDFVR 6 0 P05455 P05455 SSB Lupus La protein 0 ; 158.08 0.022184 1487720000 2634300 3706100 3039700 2984500 3788300 2624100 3317800 3271000 3593700 FALSE TRUE 2469423.865 3980503.5 3111803.119 3061087.323 3490782.199 3381635.071 2820326.691 3679391.55 2993888.254 0.824821655 1.32954311 1.039385193 1.022445417 1.165969436 1.129512789 0.942028042 1.228967563 1 21.51358894 -4.999961752 0.207055556 0.554568093 1.108646649 0.007592871 0.14461627 564.220291 5.616717334 104.2263455 0.295712283 1.00E-05 4.999961752 0.554078556 WIDLTMEDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WIDLTMEDIR 10 0 A0A0A0MSW4;P48739;P48739-3;P48739-2 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 81.594 0.047787 35915000 27623 35974 28323 28411 38466 25687 28146 37264 32735 FALSE TRUE 25894.12574 38637.55239 28994.83494 29140.07436 35445.03552 33102.41991 23925.76859 41916.49243 27271.31702 0.949500375 1.416783515 1.063198925 1.068524646 1.29971851 1.213818162 0.877323547 1.537017534 1 14.73509675 -1.979593646 2.895089992 0.852201487 1.169441173 0.069390361 0.202871153 9270881.248 12501269.41 9050359.237 0.04471003 0.010481088 1.979593646 0.317239685 WIDLTMEDIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WIDLTMEDIRR 11 1 A0A0A0MSW4;P48739;P48739-3;P48739-2 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 224.42 9.97E-12 21687000 42117 61497 45042 49618 69735 36414 43090 50055 54784 FALSE TRUE 39480.97215 66050.30187 46110.41751 50891.28188 64258.2944 46926.13067 36629.05453 56304.47693 45640.19648 0.865048251 1.447195826 1.010302783 1.115053961 1.407932028 1.028175474 0.80256128 1.233659828 1 15.47801738 2.017788219 24.95511706 0.971444097 1.185844028 0.114573379 0.198454492 343.3884853 481738.1432 0.068697448 0.050726821 104.1809275 -2.017788219 0.214399931 WIDNPTVDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 WIDNPTVDDR 10 0 P18206;P18206-2 P18206 VCL Vinculin 0 ;;;; 199.11 6.62E-07 1860520000 1893570 2012690 2013680 1887910 1859370 1734090 2163840 1798820 1553470 FALSE TRUE 1775054.834 2161711.662 2061445.441 1936356.967 1713342.581 2234693.632 1839392.28 2023406.637 1294185.821 1.371561027 1.670325564 1.592851202 1.496197018 1.323876798 1.726717752 1.421273707 1.563459129 1 20.30361335 -2.653851951 0.399247928 8.48E-14 1.550527042 0.613926615 0.128414054 54.85961092 2.243940531 47.26102455 0.074890273 0.002218953 2.653851951 1.550527042 WIGLDLSNGKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WIGLDLSNGKPR 12 1 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 186.58 1.06E-05 3143000000 5289900 5916500 5648600 5380800 7268800 4607500 7306500 6176700 7326700 FALSE TRUE 4958814.602 6354563.816 5782587.459 5518880.438 6697937.769 5937610.453 6210958.155 6947874.592 6103826.438 0.812410814 1.04107872 0.947370886 0.904167327 1.097334244 0.97276856 1.017551567 1.138281808 1 22.54128251 2.744385419 24.99321958 1.037824461 0.948912893 0.373431932 0.07366512 651.0071568 2793359.413 0.021627304 0.022384883 555.118139 -2.744385419 -0.088911568 WINEAQEAASSDNIMVQYHALGVLYHLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WINEAQEAASSDNIMVQYHALGVLYHLR 28 0 Q9UBF2;Q9UBF2-2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 103.29 0.00061954 78256000 32857 47843 32410 37065 52690 32189 44403 34336 33173 FALSE TRUE 30800.53902 51385.3455 33178.78051 38016.15065 48551.93994 41481.44176 37745.18237 38622.92518 27636.21199 1.114499304 1.859348362 1.200554566 1.375591946 1.756823256 1.500981457 1.365787119 1.397547724 1 14.75427226 0.594179722 1.09395579 1.000785731 1.482690693 0.282278675 0.224408785 1.664397305 3.023263807 0.199341475 0.062204295 3.928074551 -0.594179722 0.481904962 WIPLSSDAQAPLAQPES(ph)PTASAGDEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WIPLSSDAQAPLAQPESPTASAGDEPR 27 0 Q6GQQ9;Q6GQQ9-2 Q6GQQ9 OTUD7B OTU domain-containing protein 7B 1 WIPLSSDAQAPLAQPES(0.498)PT(0.498)AS(0.003)AGDEPR 102.27 0.0015872 31566000 22797 24147 26280 29320 24058 25903 22636 17675 25438 TRUE FALSE 21370.17646 25934.869 26903.37401 30072.40084 22168.58173 33380.7756 19241.94194 19881.76266 21192.23346 1.008396614 1.223791209 1.269492149 1.419029329 1.046071041 1.575141934 0.907971403 0.938162685 1 14.37124802 1.612910916 25 0.942283129 1.251940666 0.441877943 0.16320002 0.376197996 1855.455322 0.069488352 0.037033667 41.01199691 -1.612910916 0.309657536 WIQEHPECAYNLVNSPHLKPAWVLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WIQEHPECAYNLVNSPHLKPAWVLDR 26 1 P35573-2;P35573-3;P35573 P35573-2 AGL "Glycogen debranching enzyme;4-alpha-glucanotransferase;Amylo-alpha-1,6-glucosidase" 0 ; 236.03 4.02E-45 420020000 219459 337060 264870 257160 403070 220461 347920 319850 332200 FALSE TRUE 205723.4529 362016.2731 271152.8415 263759.161 371414.5081 284104.5118 295752.6259 359783.9766 276753.6739 0.743344975 1.308081183 0.979762392 0.953046647 1.342040027 1.026560941 1.068649322 1.300015178 1 18.07824294 WISIMTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WISIMTER 8 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;A6NMY6;H0YL33;H0YNP5;H0YN28 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 ; 183.74 0.00051576 455610000 370430 624870 384050 326820 743500 238440 407280 608030 1144350 FALSE TRUE 347245.4475 671136.025 393159.8474 335206.7545 685108.5091 307273.7573 346212.145 683943.8839 953350.5922 0.364236882 0.703976093 0.412397968 0.351609111 0.718632279 0.322309295 0.363153018 0.717410667 1 19.86264733 0.988712258 4.602651839 0.999224456 0.475098602 0.611164321 0.141315284 0.111708803 7.785089484 0.132282331 0.033580422 9.743438729 -0.988712258 -0.524125854 WISLNTVALVTDNAVYHWSMEGESQPVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WISLNTVALVTDNAVYHWSMEGESQPVK 28 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 202.88 3.66E-25 232430000 132620 225770 151450 138280 236220 137630 197470 231270 107370 FALSE TRUE 124319.5509 242486.2457 155042.4655 141828.4989 217668.2341 177361.5468 167861.2067 260144.5686 89449.25336 1.389833299 2.710880601 1.733300835 1.585574989 2.433427065 1.98281752 1.876608249 2.908292231 1 16.44878182 -1.914424259 2.691721087 0.364582798 2.079986045 0.329448096 0.483136473 17798723.99 5081254.33 70651570.27 0.107263224 0.012177994 1.914424259 1.715403247 WIVEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 WIVEER 6 0 O95433;O95433-2;G3V3W9 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ;;;;;;; 129.16 0.037954 3302720000 4710950 5710130 5522710 5495960 6037580 5193940 6117160 5287860 5757070 FALSE TRUE 4416100.049 6132913.967 5653711.289 5636995.638 5563412.821 6693346.161 5199948.647 5948060.961 4796177.825 0.920754027 1.278708628 1.178795177 1.175309975 1.159968005 1.395558381 1.084185957 1.240166895 1 22.19345372 -0.998780085 4.18751498 0.999988447 1.189220361 0.167895041 0.123577848 0.099075936 30224724.79 846.1806911 0.025350697 0.100281291 0.998780085 0.189231914 WIVNLIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WIVNLIR 7 0 P60228;E5RGA2;H0YAW4 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 ; 119.06 0.011322 54049000 104990 176059 122405 118423 186067 89646 134142 156903 136839 FALSE TRUE 98418.86331 189094.5915 125308.5044 121461.9347 171454.0484 115525.3449 114028.6524 176492.6849 113999.6869 0.863325734 1.658729043 1.099200426 1.065458494 1.503987011 1.013383002 1.000254084 1.548185699 1 16.79867034 3.7317587 24.921385 1.164675436 1.336178768 0 0.275078556 538.9198872 2896097.002 0.065399754 0.113176729 5392.109468 -3.7317587 0.171503331 WIYEDVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 WIYEDVER 8 0 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-13;O43852-14;O43852-11 O43852 CALU Calumenin 0 ;;;;;; 181.33 0.00054531 3597130000 5539650 9036500 6494910 6939660 8884950 5142480 6335930 7155420 6786280 FALSE TRUE 5192933.195 9705571.862 6648972.332 7117743.424 8187161.867 6627030.495 5385916.116 8048789.938 5653606.027 0.918516991 1.716704669 1.176058661 1.258974076 1.44813095 1.172177627 0.952651474 1.423655964 1 22.43073992 2.067609531 6.714227129 1.106065387 1.339503815 0.100043871 0.235769687 0.345784824 27.39012328 0.082949417 0.060852934 116.8448379 -2.067609531 0.233438428 WKDSDEADLVLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 WKDSDEADLVLAK 13 1 Q13185 Q13185 CBX3 Chromobox protein homolog 3 0 ;;;;; 185.27 8.02E-06 8402590000 27110000 18996280 22110460 20686620 24243000 15195600 28273360 20496720 33119480 FALSE TRUE 25413233.49 20402784.34 22634930.55 21217473.69 22339052.57 19582323.04 24034032.15 23055780.61 27591624.83 0.92104882 0.739455703 0.820355115 0.768982393 0.809631644 0.709719821 0.871062589 0.835607934 1 24.71772708 0.732594983 1.165515527 0.998872301 0.793704935 0.508462555 0.059947481 0.651836345 1.536731139 0.050128991 0.015506231 5.402502578 -0.732594983 -0.205167366 WKEPGSGGPQNLS(ph)GPGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 WKEPGSGGPQNLSGPGGR 18 1 Q9H0W8-2;Q9H0W8;M0R2N0;M0QZC7;M0QZH1;M0QX70;M0QYR7 Q9H0W8-2 SMG9 Protein SMG9 1 WKEPGSGGPQNLS(1)GPGGR;WKEPGSGGPQNLS(1)GPGGR;WKEPGSGGPQNLS(1)GPGGR;WKEPGSGGPQNLS(1)GPGGR;WKEPGSGGPQNLS(1)GPGGR 262.05 4.92E-31 2510360000 1444489 1364344 1366891 1447880 1635422 1176708 1743737 1413496 2019235 TRUE FALSE 1354081.012 1465361.449 1399314.3 1485035.052 1506982.553 1516404.497 1482279.825 1589974.087 1682211.634 0.804940939 0.87109221 0.831830117 0.882787292 0.895834105 0.901435032 0.881149432 0.945168881 1 20.68192779 -4.999996999 0.058116617 1.529134774 0.645979134 0.844405415 0.02136905 150.4596203 0.640562336 11.27498026 1.989680312 1.00E-05 4.999996999 -0.883155641 WKGYDS(ph)EDDTWEPEQHLVNCEEYIHDFNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WKGYDSEDDTWEPEQHLVNCEEYIHDFNR 29 1 Q9Y232;Q9Y232-2 Q9Y232 CDYL Chromodomain Y-like protein 1 WKGYDS(1)EDDTWEPEQHLVNCEEYIHDFNR;WKGYDS(1)EDDTWEPEQHLVNCEEYIHDFNR 403.25 8.63E-175 334162000 123462 92864 97204 96918 112003 87354 140201 87208 120418 TRUE FALSE 115734.7338 99739.74718 99509.72478 99405.07996 103206.7362 112571.6817 119179.1616 98096.11077 100319.4579 1.153661874 0.994221353 0.991928454 0.990885338 1.02878084 1.122132078 1.187996468 0.977837329 1 16.61424193 2.305436383 6.588776486 1.099489547 1.018862107 0 0.077017206 0.331365557 25.5978833 0.025731664 0.021339864 202.0395457 -2.305436383 -0.080627439 WKGYDS(ph)EDDTWEPEQHLVNCEEYIHDFNRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WKGYDSEDDTWEPEQHLVNCEEYIHDFNRR 30 2 Q9Y232;Q9Y232-2 Q9Y232 CDYL Chromodomain Y-like protein 1 WKGYDS(0.999)EDDT(0.001)WEPEQHLVNCEEYIHDFNRR 179.85 3.53E-18 173230000 62472 87360 63920 76563 115170 53034 105960 66616 256840 TRUE FALSE 58561.98904 93828.2253 65436.21259 78527.7362 106125.0128 68344.05486 90072.28168 74933.15424 213971.7448 0.273690291 0.438507549 0.305817073 0.367000495 0.49597676 0.319406915 0.420954093 0.350201165 1 17.70706077 -4.4170431 0.477878056 10 0.369750897 0.898320755 0.06643656 263.6059945 2.46318402 2488.280589 0.02939293 3.83E-05 4.4170431 -9.630249103 WKGYT(ph)SDDDTWEPEIHLEDCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 WKGYTSDDDTWEPEIHLEDCK 21 1 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 WKGYT(0.767)S(0.233)DDDTWEPEIHLEDCK;WKGYT(0.73)S(0.27)DDDTWEPEIHLEDCK;WKGYT(0.756)S(0.244)DDDTWEPEIHLEDCK;WKGYT(0.707)S(0.293)DDDTWEPEIHLEDCK 273.59 1.50E-44 686180000 1507180 884670 999580 959940 1213050 792620 2033620 876070 2082170 TRUE FALSE 1412848.294 950171.8873 1023290.51 984573.6856 1117781.946 1021436.527 1728697.56 985449.268 1734642.376 0.814489669 0.547762409 0.589914396 0.567594623 0.644387547 0.588845598 0.996572887 0.568099386 1 20.72620683 1.759151093 25 0.848329671 0.610922703 0.375268661 0.138589589 8.811319475 10707.65283 0.056423948 0.031290624 57.43162341 -1.759151093 -0.237406968 WKPDYDSAASEYGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WKPDYDSAASEYGK 14 1 Q99747;J3KTJ6 Q99747 NAPG Gamma-soluble NSF attachment protein 0 163.8 3.85E-06 116790000 228360 187030 206600 208210 214630 183110 257700 182900 256690 FALSE TRUE 214067.3552 200877.8958 211500.6496 213553.0211 197773.8256 235970.8845 219060.2774 205735.4676 213846.7807 1.001031461 0.939354313 0.989028915 0.998626308 0.924838919 1.103457736 1.024379589 0.96206951 1 17.70621796 2.259534572 24.99997545 1.02731423 0.970109821 0.269952592 0.042074053 278.9509463 332495.8334 0.013728475 0.011474501 181.7751751 -2.259534572 -0.057204409 WKPPMIDNPSYQGIWKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WKPPMIDNPSYQGIWKPR 18 2 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 ; 207.56 4.10E-16 1276990000 618080 648240 502770 504650 790930 353220 782200 744570 701880 FALSE TRUE 579395.4761 696236.3641 514695.9418 517600.1734 728813.5483 455188.88 664916.3716 837531.2035 584731.6937 0.990874075 1.190693735 0.880225832 0.885192609 1.246406781 0.778457684 1.13713072 1.432334201 1 19.15741526 1.495120211 8.463143642 1.238705003 1.007111086 0.224648567 0.172881902 0.133880404 24.83104659 0.085031673 0.0391606 31.2694477 -1.495120211 -0.231593916 WLAVDYENVRPDIVLLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WLAVDYENVRPDIVLLGK 18 1 P04181;P04181-2 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ; 241.74 4.78E-24 505960000 1129970 981130 980690 858550 1308710 919130 946290 1011690 1424710 FALSE TRUE 1059247.195 1053773.886 1003952.43 880581.8465 1205929.196 1184467.91 804402.5994 1138001.724 1186916.697 0.892436004 0.887824637 0.845849108 0.741907034 1.016018393 0.99793685 0.677724563 0.9587882 1 20.17878725 4.297333513 5.340963137 0.870351285 0.890932413 0 0.113692405 2.262700397 118.6428018 0.026762647 0.075573286 19830.4931 -4.297333513 0.020581128 WLDAIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WLDAIIR 7 0 Q8TCU6;Q8TCU6-3 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 0 ; 80.462 0.069435 29399000 155664 281120 166844 171669 295480 120418 158470 246120 204270 FALSE TRUE 145921.2681 301934.4173 170801.6185 176074.3172 272274.1927 155180.7218 134708.8947 276848.6238 170176.0174 0.857472577 1.774247758 1.0036762 1.034659994 1.599956309 0.911883614 0.791585658 1.626836895 1 17.37666821 2.200306415 24.99994718 1.030416033 1.280840487 0.044558677 0.347959827 370.5357945 242151.0174 0.123713352 0.091370123 158.6011802 -2.200306415 0.250424454 WLDDLLAS(ph)PPPSGGGAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 WLDDLLASPPPSGGGAR 17 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(0.997)PPPS(0.003)GGGAR;WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(1)PPPSGGGAR;WLDDLLAS(1)PPPSGGGAR 340.55 1.80E-72 3056378000 1391612 1584711 1597448 1799796 1731935 1230350 1518086 1108088 1092784 TRUE FALSE 1304513.489 1702044.651 1635340.221 1845981.812 1595915.811 1585532.072 1290463.098 1246435.226 910391.2907 1.432915168 1.86957484 1.796304773 2.027679561 1.752999867 1.741594068 1.417481813 1.369120332 1 19.79612723 1.313461276 1.083750114 1.028885288 1.808446055 0.732430854 0.155382569 0.211979472 0.505101182 0.133630952 0.045375746 20.58075375 -1.313461276 0.779560766 WLDES(ph)DAEMELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 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 261.38 2.44E-21 2413308000 3536980 3675582 2704513 2442783 3202278 2325706 3465599 3310387 4326891 TRUE FALSE 3315606.735 3947725.916 2768665.326 2505468.947 2950784.003 2997099.568 2945964.603 3723696.104 3604704.939 0.919799759 1.095159238 0.76806989 0.69505521 0.818592382 0.831441024 0.817255407 1.03300996 1 21.78144974 1.233552537 24.99434263 1.016505074 0.85664057 0.303258821 0.104888063 193.2411357 964373.1729 0.099163944 0.027796556 17.1219229 -1.233552537 -0.159864504 WLEASEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 WLEASEEER 9 0 Q14137;Q14137-2 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 ;; 169.12 0.00013657 260148000 267223 340141 326519 332550 334944 283071 366553 291017 368543 FALSE TRUE 250497.9894 365325.3936 334264.1849 341083.796 308638.8493 364789.0024 311591.7806 327351.1131 307030.7924 0.81587253 1.189865651 1.088699222 1.110910711 1.005237445 1.188118623 1.014855149 1.066183331 1 18.22802383 1.606548971 24.99999996 1.030386228 1.083962433 0.01181675 0.10714964 0.44030595 8022.530078 0.048834897 0.024530603 40.41559448 -1.606548971 0.053576205 WLETCQHESDEQPLDPIPQIS(ph)STPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WLETCQHESDEQPLDPIPQISSTPK 25 0 Q96R06;F5GZT2 Q96R06 SPAG5 Sperm-associated antigen 5 1 WLETCQHESDEQPLDPIPQIS(0.333)S(0.333)T(0.333)PK 98.121 0.0050888 52046000 32310 30862 31097 36152 39722 27094 48660 33951 49927 TRUE FALSE 30287.77477 33147.05459 31834.63553 37079.72153 36602.39435 34915.59797 41363.88474 38189.85709 41593.86116 0.728178965 0.796921797 0.765368606 0.891471013 0.879995108 0.839441134 0.994470905 0.918160902 1 15.344083 2.662071607 0.416505807 1.002720187 0.723515834 0.785365769 0.041604206 0.550517206 0.1968345 0.039598694 0.059228562 459.2737319 -2.662071607 -0.279204353 WLETCQHESDEQPLDPIPQISST(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WLETCQHESDEQPLDPIPQISSTPK 25 0 Q96R06;F5GZT2 Q96R06 SPAG5 Sperm-associated antigen 5 1 WLETCQHESDEQPLDPIPQIS(0.069)S(0.198)T(0.733)PK 131.97 0.00027731 44777000 42907 42360 43067 48105 49746 37752 66051 41845 63188 TRUE FALSE 40221.52746 45496.37848 44088.56958 49339.45574 45839.14983 48650.38955 56147.26574 47069.44036 52641.51459 0.764064784 0.864268037 0.837524716 0.937272723 0.870779463 0.924182937 1.0665967 0.894150572 1 15.68391338 2.941532341 0.510939323 1.004745165 0.793015786 0.568942647 0.055317618 0.739254551 0.398434387 0.045572916 0.071045494 874.042079 -2.941532341 -0.211729379 WLEVEIAPDIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WLEVEIAPDIR 11 0 A0A3B3IUD7;Q14690 A0A3B3IUD7 PDCD11 Protein RRP5 homolog 0 90.15 0.027223 7905600 25851 35494 31101 33962 34354 21594 33315 31153 40951 FALSE TRUE 24233.03206 38122.01269 31838.73041 34833.52242 31655.97542 27827.83725 28319.72503 35042.52063 34116.01355 0.710312535 1.117422838 0.93324885 1.021031439 0.927891982 0.81568256 0.83010065 1.027157542 1 15.05816146 2.480076785 24.81061876 0.890343106 0.972349278 0 0.12181706 263.6272244 2213094.903 0.038677561 0.032943475 302.0485709 -2.480076785 0.082006173 WLHNEDQMAVEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 WLHNEDQMAVEK 12 0 P37837 P37837 TALDO1 Transaldolase 0 ;;;;;;;;;;;; 247.88 1.10E-16 10357303000 14948440 15076860 14020140 13671930 17052550 10534200 15889520 14623300 18972170 FALSE TRUE 14012843.82 16193166.4 14352704.34 14022774.87 15713311.51 13575252.53 13507033.99 16449051.19 15805592.26 0.886575055 1.02452133 0.908077603 0.88720338 0.994161513 0.858889202 0.854573101 1.04071084 1 23.91393176 1.220718698 24.99840568 1.020355501 0.921604954 0.375370816 0.055482754 334.1056059 468104.5416 0.055003905 0.013867972 16.62335569 -1.220718698 -0.098750547 WLHSMTDDPPTTKPLTAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WLHSMTDDPPTTKPLTAR 18 1 Q9UI09 Q9UI09 NDUFA12 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 0 85.734 0.0021501 260560000 88600 101610 84457 77613 116810 76537 88791 82557 134670 FALSE TRUE 83054.68416 109133.3101 86460.35992 79604.68098 107636.2138 98631.98943 75477.61385 92864.42318 112192.707 0.740285945 0.972730876 0.770641535 0.709535255 0.959386904 0.879130133 0.672749734 0.827722458 1 16.77561937 3.769118936 18.52142621 0.812576725 0.872685704 0 0.115857147 52.79878751 23280.25762 0.028071498 0.050600069 5876.502644 -3.769118936 0.060108979 WLIS(ph)PVK ddPTM_SK-BR-3_Pertuzumab_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 104.2 0.0086071 396100000 1884980 1395040 1634660 1497850 1730710 1175200 1862490 1372760 2035130 TRUE FALSE 1767002.467 1498330.213 1673434.907 1536287.367 1594787.018 1514461.162 1583226.915 1544152.108 1695453.656 1.042200393 0.883734102 0.987013064 0.906121711 0.940625545 0.893248339 0.93380725 0.910760434 1 20.69323992 4.753999108 24.55647492 0.929869901 1.042200498 0.458808861 0.037584806 1880.321513 2990775.995 0.007902821 0.187772769 56754.34402 -4.753999108 0.112330597 WLKEDKLECSEELGDLVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WLKEDKLECSEELGDLVK 18 2 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ; 148.26 3.97E-08 807490000 1047930 612190 811830 822910 926420 540160 1257390 713270 1462860 FALSE TRUE 982341.9319 657517.1846 831086.991 844027.2638 853662.7102 696095.4232 1068856.043 802323.3296 1218699.216 0.806057737 0.539523761 0.681945947 0.692564049 0.700470386 0.57117902 0.877046632 0.658344011 1 20.21691067 0.070506543 0.393688839 1.052238218 0.642595627 0.482055353 0.099296019 3.132404719 0.690751615 0.361823196 0.066028419 1.176268706 -0.070506543 -0.409642591 WLPLGLGLNHLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WLPLGLGLNHLGK 13 0 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 193.21 4.21E-07 0 235440 347090 248370 205230 359090 167860 249290 297260 211900 FALSE TRUE 220704.2307 372788.9047 254261.4537 210496.5493 330888.5199 216318.457 211911.2788 334373.5653 176532.5211 1.25021854 2.111729343 1.440309424 1.192395305 1.874377128 1.225374541 1.200409293 1.894118791 1 17.42957446 -2.167457258 0.090281994 4.56E-19 2.068790556 0.136139996 0.344255336 154.9947434 1.886234765 42.97783319 9.546804451 0.00680053 2.167457258 2.068790556 WLPSS(ph)PSGVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WLPSSPSGVAK 11 0 Q8IWI9-3;Q8IWI9;H3BP52;H3BTF4 Q8IWI9-3 MGA MAX gene-associated protein 1 WLPS(0.001)S(0.964)PS(0.035)GVAK 159.44 3.01E-05 240620000 1225600 1039200 1140600 1119000 1303000 870450 1353700 968940 1253200 TRUE FALSE 1148891.884 1116143.449 1167655.571 1147715.434 1200667.636 1121734.784 1150725.252 1089914.292 1044032.824 1.100436555 1.069069309 1.11840887 1.099309723 1.150028628 1.074424825 1.102192599 1.043946384 1 19.99373564 1.047030383 2.307493031 0.999832921 1.101570019 0.706746118 0.022367045 0.149491123 1.670831827 0.020133529 0.005542652 11.14372493 -1.047030383 0.101737098 WLPSSPS(ph)GVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WLPSSPSGVAK 11 0 Q8IWI9-3;Q8IWI9;H3BP52;H3BTF4 Q8IWI9-3 MGA MAX gene-associated protein 1 WLPS(0.006)S(0.275)PS(0.719)GVAK 145.09 3.82E-05 315830000 2257600 1998700 2079200 2151700 2366800 1632900 2473500 1790000 2414300 TRUE FALSE 2116300.846 2146685.828 2128519.606 2206916.265 2180921.075 2104291.722 2102621.638 2013485.44 2011337.733 1.052185723 1.067292575 1.058260664 1.097238036 1.084313708 1.046215008 1.045384673 1.0010678 1 20.93972392 1.436537245 1.614133157 0.997188857 1.069471745 0.785031526 0.014424043 0.163027731 0.795466051 0.012855508 0.004114152 27.32355758 -1.436537245 0.072282888 WLSTSIPEAQWHSS(ph)LAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.299)S(0.701)LAR;WLSTSIPEAQWHS(0.005)S(0.995)LAR;WLSTSIPEAQWHS(0.249)S(0.751)LAR 249.32 3.34E-21 463480000 376676 499000 376053 390291 477820 265486 638810 409189 760600 TRUE FALSE 353100.5215 535946.4792 384973.1547 400306.5278 440293.9446 342127.4984 543026.3709 460277.1474 633650.9463 0.557247683 0.845807116 0.607547668 0.631746122 0.694852501 0.539930541 0.856980289 0.726389111 1 19.27332881 0.819236281 0.963377004 0.995476992 0.67188827 0.510551243 0.102441708 0.649662893 1.1795448 0.091629018 0.030326631 6.595326204 -0.819236281 -0.323588723 WLSTSIPEAQWHSSLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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 ;; 331.34 5.13E-72 11043459000 1290338 7362270 4166150 3978520 7034690 4194450 5645600 6629420 5115100 FALSE TRUE 1209578.048 7907380.131 4264973.045 4080615.559 6482213.824 5405319.624 4799094.691 7457117.68 4261356.765 0.283848106 1.85560153 1.000848622 0.957585995 1.521161963 1.268450384 1.12618937 1.749939771 1 22.02288141 2.739036624 24.99719062 1.317520736 1.159055747 0.075728565 0.432701464 194.4966727 10214121.76 0.12817686 0.128532841 548.3232031 -2.739036624 -0.158464989 WLVFDEADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 WLVFDEADR 9 0 F8WAJ0;Q9H8H2-4;Q9H8H2-2;Q9H8H2 F8WAJ0 DDX31 Probable ATP-dependent RNA helicase DDX31 0 ;;; 107.47 0.0064422 59230000 196290 246491 216346 207629 271966 164197 231530 205569 276958 FALSE TRUE 184004.5593 264741.4501 221477.8293 212957.1117 250606.8874 211598.0084 196814.2259 231234.7422 230731.9206 0.797482025 1.147398459 0.959892453 0.922963373 1.086138783 0.917072973 0.852999556 1.002179246 1 17.81585808 WLVLFCDEINLPDMDKYGTQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WLVLFCDEINLPDMDKYGTQR 21 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 138.3 1.71E-06 110990000 82451 119290 94882 95346 134120 104300 116770 108290 93106 FALSE TRUE 77290.53909 128122.3557 97132.64585 97792.73978 123586.7562 134409.7168 99261.42254 121810.2449 77566.00711 0.996448599 1.651784854 1.252257909 1.260768002 1.593310792 1.732843056 1.27970262 1.570407572 1 16.24313692 -0.952248019 5.08482804 0.999997997 1.427147178 0.251714276 0.225476137 4.63E-06 9.55E-07 0.197010331 0.046435562 0.111622561 0.952248019 0.427149181 WLYDAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WLYDAK 6 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 101.52 0.084748 192570000 734870 838610 740020 710960 918350 503030 854430 828350 817360 FALSE TRUE 688875.7985 900701.557 757573.6239 729204.4373 846226.4954 648246.595 726316.1536 931771.3209 680937.3357 1.01165814 1.322737805 1.112545287 1.070883324 1.242737696 0.951991558 1.066641695 1.36836574 1 19.37716251 3.716840808 22.27907722 1.109527214 1.197885025 0.010501618 0.139509618 233.4097215 505833.545 0.034132087 0.053700177 5210.037011 -3.716840808 0.088357811 WMDEAQALDTADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 WMDEAQALDTADR 13 0 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ;;;; 158.42 2.90E-06 427028000 421002 443132 461330 446611 455879 404991 507373 406512 432911 FALSE TRUE 394652.2363 475941.9544 472272.9655 458071.7944 420076.1023 521905.3272 431297.1289 457265.918 360655.3574 1.094264173 1.319658629 1.309485512 1.270109496 1.164757694 1.447102661 1.195870573 1.267875019 1 18.46026133 0.223756847 1.312773273 0.999739839 1.272007421 0.411698159 0.096098723 5.686502729 8.69074871 0.084683069 0.024337052 1.67400537 -0.223756847 0.272267581 WMGGAELSDDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WMGGAELSDDGR 12 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ; 198.72 4.19E-07 253130000 269470 364250 319190 337550 376150 282380 369260 327240 355070 FALSE TRUE 252604.3537 391219.449 326761.3375 346212.1045 346608.6963 363898.5219 313892.891 368096.6343 295806.5232 0.853951262 1.322551798 1.104645476 1.170400506 1.17174122 1.230190998 1.061142559 1.244383087 1 18.17429434 -1.313015853 5.03351492 0.999945822 1.155524921 0.109534757 0.12662124 6.69E-05 9.14E-06 0.106597611 0.025116558 0.048638945 1.313015853 0.155579099 WMHPQVTPTDDSNPWWAAFSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WMHPQVTPTDDSNPWWAAFSR 21 0 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-3;Q03154-4;C9JMV9 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 ; 138.22 2.00E-06 144467000 196614 262450 207814 196307 267120 138770 204113 222160 233050 FALSE TRUE 184308.2807 281882.0711 212743.4462 201344.57 246141.4727 178830.6463 173508.1505 249897.165 194152.4494 0.949296706 1.451859463 1.095754634 1.037043676 1.267774233 0.921083647 0.893669645 1.287118271 1 17.56683038 3.619804442 4.366508386 1.051402373 1.247008014 0.068688236 0.175675108 0.343835134 11.13406853 0.045116368 0.072090084 4166.81714 -3.619804442 0.195605641 WMIDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WMIDSR 6 0 P21912 P21912 SDHB "Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial" 0 ; 98.133 0.093712 126917000 431260 565830 400360 381300 708560 372860 384160 537660 724790 FALSE TRUE 404268.2064 607724.6419 409856.7283 391084.8035 652912.5558 480498.6291 326558.7744 604788.0345 603817.8667 0.669520113 1.006470122 0.678775424 0.647686703 1.081307116 0.795767492 0.540823305 1.001606723 1 19.20375392 2.855588233 20.06200477 0.826647192 0.781314307 0.0605045 0.182495521 32.27579282 5427.40898 0.056636375 0.060072082 717.1140527 -2.855588233 -0.045332886 WNDFAEDSLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WNDFAEDSLR 10 0 O60313-10;O60313-9;O60313-2;E5KLJ9;O60313-13;O60313;O60313-11;A0A2R8YDM2;A0A2R8Y3X5;C9JMB8;A0A2R8YE78;A0A2R8YFD1 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 131.52 0.008332 0 105050 106050 92578 88402 139540 67564 94939 106130 103670 FALSE TRUE 98475.10802 113902.0523 94773.99388 90670.54498 128581.0913 87068.62999 80703.77832 119380.5641 86366.80727 1.14019623 1.318817448 1.097342797 1.049830923 1.488779027 1.00812607 0.934430493 1.382250518 1 16.39818934 1.19906463 0.023710757 1.24E-06 2.222291091 0.056575332 0.176941196 495.1734989 9.686180156 460.7761389 443.1838308 15.81483373 -1.19906463 2.222289856 WNDNCPSWNTIDPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 WNDNCPSWNTIDPEER 16 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;; 220.4 2.68E-14 2074840000 1303910 1454110 1467340 1429200 1497540 1308040 1806560 1339830 1863540 FALSE TRUE 1222300.601 1561773.817 1502145.998 1465875.692 1379929.249 1685649.914 1535683.099 1507110.725 1552503.135 0.787309586 1.005971442 0.967563906 0.944201437 0.888841522 1.085762647 0.98916586 0.970761792 1 20.56616475 2.251177378 24.99998469 1.010919078 0.938475971 0.307647254 0.065452273 333.232284 660296.1438 0.021898139 0.01820565 178.3106888 -2.251177378 -0.072443107 WNENVQYLSEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WNENVQYLSEDR 12 0 O43929-2;O43929-3;O43929 O43929-2 ORC4 Origin recognition complex subunit 4 0 ; 142.91 0.00014368 96267000 128786 142549 124928 143463 150449 113264 123607 116228 152343 FALSE TRUE 120725.5141 153103.4763 127891.3512 147144.5035 138633.3424 145961.4781 105073.2779 130739.3216 126915.9691 0.951223987 1.206337369 1.007685258 1.159385257 1.092323869 1.150063929 0.827896431 1.030125071 1 16.95351408 1.752443411 25 0.939092597 1.099801645 0.353034555 0.089693463 3.869042395 6977.185928 0.036611183 0.020302817 56.55140652 -1.752443411 0.160709048 WNGHTDMIDQDGLYEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WNGHTDMIDQDGLYEK 16 0 Q9UHG3;Q9UHG3-2 Q9UHG3 PCYOX1 Prenylcysteine oxidase 1 0 ; 170.16 5.37E-09 115160000 303680 257419 259460 238287 332950 204340 315350 250880 361770 FALSE TRUE 284673.2109 276478.5706 265614.5137 244401.8478 306801.4501 263329.6408 268066.1951 282202.9203 301388.2499 0.944539845 0.917350198 0.881303481 0.810920293 1.017960887 0.87372232 0.889438109 0.936343472 1 18.20126365 0.936811712 4.159901522 0.999935738 0.902593891 0.245085151 0.052879346 0.38566586 17.93395214 0.046283512 0.011808574 8.645929939 -0.936811712 -0.097341847 WNQQQLDDLYLIAICHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WNQQQLDDLYLIAICHR 17 0 Q96C86;A0A3B3ITF0 Q96C86 DCPS m7GpppX diphosphatase 0 192.24 1.97E-10 182790000 168120 186090 166280 150760 201530 142680 202840 149980 167220 FALSE TRUE 157597.6693 199868.2972 170224.2401 154628.7568 185702.6467 183869.3998 172426.0251 168705.3331 139309.9017 1.131273997 1.434702737 1.221910561 1.109962429 1.333018288 1.319858801 1.237715503 1.211007481 1 17.08793828 0.706967744 1.607040379 1.000275765 1.270984106 0.407166579 0.095196564 0.999917227 3.978311973 0.087286722 0.025046732 5.092930437 -0.706967744 0.270708341 WNS(ph)NDFIDAFASPVEAEGTPEPGAEAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WNSNDFIDAFASPVEAEGTPEPGAEAAK 28 0 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 WNS(1)NDFIDAFASPVEAEGTPEPGAEAAK 128.58 1.89E-05 39611000 94404 72454 66769 74736 83256 55280 120880 70822 92989 TRUE FALSE 88495.42216 77818.56955 68352.79221 76653.85229 76717.4096 71238.4386 102755.1662 79664.2826 77468.53517 1.142340203 1.004518407 0.882329736 0.989483693 0.990304121 0.919579006 1.326411632 1.028343732 1 16.24132284 1.766953889 25 1.15136003 0.977922869 0.215284132 0.110179323 21.6910921 19109.969 0.046967352 0.026049219 58.47279982 -1.766953889 -0.173437161 WNSVS(ph)PASAGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WNSVSPASAGK 11 0 E5RJU9;Q86UE4;H0YB56;H0YBE0 E5RJU9 MTDH Protein LYRIC 1 WNSVS(0.96)PAS(0.04)AGK 159.75 0.001208 0 396960 250230 289440 282360 314290 260270 353950 270150 251690 TRUE FALSE 372114.9822 268757.2896 296305.6535 289605.8356 289606.9312 335405.7239 300878.4834 303878.8222 209681.313 1.774669268 1.281741733 1.413123798 1.381171414 1.381176639 1.599597594 1.434932274 1.449241317 1 17.67783877 -1.021218443 4.488112582 0.999985302 1.443906495 0.527298422 0.136978683 8133919.396 1850780.037 1435.057462 0.029423031 0.095231704 1.021218443 0.443921193 WNSVSPAS(ph)AGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WNSVSPASAGK 11 0 E5RJU9;Q86UE4;H0YB56;H0YBE0 E5RJU9 MTDH Protein LYRIC 1 WNSVS(0.34)PAS(0.66)AGK 127.27 0.00030439 297090000 422020 287480 330590 343520 338020 271070 417130 321360 295640 TRUE FALSE 395606.5215 308765.3183 338431.7509 352335.3048 311473.2727 349323.5085 354585.2289 361482.5034 246295.7741 1.606225373 1.253636281 1.374086714 1.430537353 1.264631007 1.418308982 1.439672403 1.467676434 1 17.91003235 -1.108946652 4.491597332 0.999961121 1.390814041 0.61180871 0.101132818 3.67E-05 7.28E-06 0.091258859 0.021507783 0.077813213 1.108946652 0.39085292 WNTEDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 WNTEDK 6 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ;;; 158.38 0.021967 6774690000 6705460 5422500 4937950 4704970 4899810 3038130 6950560 4550940 4673750 FALSE TRUE 6285777.228 5823987.542 5055080.506 4825707.496 4514998.687 3915188.811 5908388.054 5119134.877 3893670.931 1.614357592 1.495757511 1.298281389 1.239372197 1.159573772 1.005526373 1.517433845 1.314732284 1 21.89269953 4.151112646 1.221230564 1.235379103 1.628168774 0.475284572 0.149706258 0.643351061 1.517898641 0.045662845 0.247015402 14161.61052 -4.151112646 0.392789671 WNTEDKVSHVSTGGGASLELLEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WNTEDKVSHVSTGGGASLELLEGK 24 1 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ; 166.91 7.45E-12 1093990000 983310 1907200 1514530 1703920 2213800 880520 2195400 1511590 3197700 FALSE TRUE 921766.3824 2048411.072 1550455.367 1747645.472 2039937.078 1134711.83 1866220.151 1700315.339 2663983.212 0.346010582 0.768927921 0.582006433 0.656027209 0.765746972 0.425945563 0.700537504 0.638260531 1 21.34515356 0.282018159 1.361698518 1.000218581 0.621215749 0.448999757 0.135496159 4.883923033 8.34286473 0.115849413 0.03366266 1.914335968 -0.282018159 -0.379002832 WNTTLYEGTWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WNTTLYEGTWR 11 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 234.9 3.83E-15 720250000 636270 786760 671190 739010 825180 577200 745930 722600 770080 FALSE TRUE 596446.9965 845012.529 687110.9438 757974.2477 760373.6914 743828.2699 634084.7214 812818.2006 641548.6731 0.929698745 1.317144847 1.071019196 1.181475825 1.185215905 1.159426091 0.988365728 1.26696264 1 19.2911992 WNYRDEADVLEVDQGFDDHNLPCDVIWLDIEHADGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WNYRDEADVLEVDQGFDDHNLPCDVIWLDIEHADGK 36 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 127.77 1.11E-08 38092000 30543 22456.3 24871.8 30305 28254 20686.9 29194 28485 21626.3 FALSE TRUE 28631.36815 24118.98782 25461.77084 31082.67761 26035.04481 26658.87221 24816.63072 32041.41495 18016.73082 1.589154461 1.33869946 1.413229242 1.725211856 1.445048221 1.479673115 1.377421408 1.77842558 1 14.13704963 -1.301488697 3.60981599 0.998537991 1.486936094 0.544237776 0.146590005 4641195.217 2510468.399 50615.85258 0.032377564 0.049947218 1.301488697 0.488398103 WNYRDEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 WNYRDEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR 37 2 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 216.87 1.53E-39 571259000 103936 121704 99301 114778 148592 84288.6 140523 101507 156005 FALSE TRUE 97430.83129 130715.0908 101656.4666 117723.3978 136922.1837 108621.3505 119452.8807 114180.3724 129966.7577 0.749659629 1.005757881 0.78217283 0.90579622 1.053516962 0.835762563 0.919103337 0.878535207 1 16.98778314 -5 0.123327467 1.313775996 0.850593101 0.141920447 0.090614542 339.8942784 2.695668101 27.06266549 0.745576047 1.00E-05 5 -0.463182895 WPAS(ph)PGSHSNDDFDNWSTFRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WPASPGSHSNDDFDNWSTFRPR 22 1 Q12778 Q12778 FOXO1 Forkhead box protein O1 1 WPAS(0.999)PGS(0.001)HSNDDFDNWSTFRPR 161.39 1.05E-11 68210000 77595 65392 75483 66309 76712 51661 69666 56116 68689 TRUE FALSE 72738.46746 70233.69172 77273.49241 68010.6012 70687.34896 66574.69205 59220.23005 63122.20613 57224.36215 1.271110148 1.227339005 1.350360048 1.188490332 1.235266699 1.163397713 1.03487794 1.103065264 1 15.80434186 2.038203563 1.138844114 1.028757867 1.273894233 0.803971687 0.047159841 0.191731085 0.461101073 0.033635406 0.016117745 109.1952038 -2.038203563 0.245136367 WPFSGKTS(ph)PPCS(ph)PANLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WPFSGKTSPPCSPANLSR 18 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 WPFSGKT(0.209)S(0.791)PPCS(1)PANLSR;WPFS(0.004)GKT(0.208)S(0.789)PPCS(0.999)PANLSR 144.27 5.66E-08 996490000 1115950 1160940 1164830 1134490 1712090 971020 1656220 1214990 3420700 TRUE FALSE 1046104.682 1246897.206 1192460.318 1163602.934 1577629.358 1251337.711 1407885.187 1366684.176 2849763.071 0.367084791 0.437544166 0.418441915 0.408315676 0.553600183 0.439102367 0.494035873 0.479578176 1 21.44241055 -5 0.261165088 4.597808187 0.404938745 0.944311113 0.042549942 38.47475308 0.377696285 74.25069293 0.051023602 1.00E-05 5 -4.192869442 WPFSGKTS(ph)PPCSPANLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WPFSGKTSPPCSPANLSR 18 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 WPFS(0.001)GKT(0.015)S(0.985)PPCSPANLSR;WPFS(0.001)GKT(0.04)S(0.959)PPCSPANLSR 125.31 1.82E-05 2611100000 1918470 2303460 1940330 2259490 2706100 1271530 2201080 1780930 4504400 TRUE FALSE 1798396.387 2474010.575 1986355.544 2317472.339 2493573.822 1638600.069 1871048.488 2003283.031 3752586.54 0.479241816 0.659281418 0.52932971 0.617566661 0.664494688 0.436658836 0.498602355 0.533840595 1 21.83945391 -1.438257081 3.267581904 1.006484667 0.555734364 0.777832804 0.07516259 95609441.07 124898511.5 5714952.602 0.018236236 0.036453809 1.438257081 -0.450750303 WPS(ph)DSWIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 WPSDSWIR 8 0 Q5VT97-2;Q5VT97 Q5VT97-2 SYDE2 Rho GTPase-activating protein SYDE2 1 WPS(0.992)DS(0.008)WIR;WPS(0.997)DS(0.003)WIR;WPS(1)DSWIR;WPS(0.999)DS(0.001)WIR 139.78 0.0006924 207618000 343618 377206 366923 360121 395574 287418 414547 323289 375040 TRUE FALSE 322111.5628 405134.7247 375626.5868 369362.3145 364507.2137 370390.9108 352389.5258 363652.3433 312443.4011 1.030943722 1.296665966 1.20222282 1.182173517 1.16663438 1.185465622 1.127850755 1.1638983 1 18.25323534 0.247756064 0.446766164 0.981277127 1.203291704 0.36707673 0.067172826 2.743974462 0.850937314 0.165206621 0.037644974 1.769114997 -0.247756064 0.222014577 WPS(ph)VSSLDSALESSPSLHSPADPSHLSPPAS(ph)SPRPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WPSVSSLDSALESSPSLHSPADPSHLSPPASSPRPSR 37 1 O15211 O15211 RGL2 Ral guanine nucleotide dissociation stimulator-like 2 2 WPS(0.556)VS(0.175)S(0.184)LDS(0.072)ALES(0.003)S(0.004)PS(0.004)LHS(0.003)PADPS(0.02)HLS(0.139)PPAS(0.377)S(0.358)PRPS(0.105)R 46.539 0.036711 26468000 5271.8 6616.7 8263.9 6810.3 8810.8 6753.5 12050 11735 10511 TRUE FALSE 4941.847448 7106.607353 8459.92361 6985.063828 8118.835309 8703.125816 10243.21437 13200.14058 8756.646196 0.564353902 0.811567259 0.966114586 0.797687113 0.927162652 0.993888028 1.169764558 1.507442494 1 13.09616271 1.934522591 1.635274875 1.265121208 0.824658092 0.586168822 0.159230357 0.257400855 1.282434621 0.099891066 0.046291793 86.00478043 -1.934522591 -0.440463115 WQDEDGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 WQDEDGKK 8 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ;;;;; 127.3 0.0018956 6989240000 12830430 7356190 9633700 9602520 10387720 7338520 14300800 8344460 14231100 FALSE TRUE 12027396.29 7900849.962 9862215.913 9848936.92 9571910.373 9457031.593 12156527.8 9386284.199 11855837.47 1.014470409 0.666410111 0.831844729 0.830724691 0.807358434 0.797668795 1.025362217 0.791701491 1 23.49909424 1.761931739 25 0.93880573 0.806856797 0.199678364 0.103807436 16.32588952 17476.78043 0.043616797 0.024188727 57.80051913 -1.761931739 -0.131948933 WQDIQNDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WQDIQNDPR 9 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y4X2;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 76.064 0.08489 648950000 484660 551470 538320 524840 562300 480000 591650 488860 570080 FALSE TRUE 454325.9957 592301.4126 551089.2046 538308.283 518139.2262 618568.2079 502937.5751 549895.2471 474929.9651 0.956616826 1.247134222 1.160358885 1.133447713 1.09098028 1.302440893 1.058972084 1.157844919 1 18.85735526 0.360775175 0.990936137 0.999726278 1.153726434 0.154509567 0.096079639 4.136578762 5.010574288 0.086832362 0.026449381 2.29496029 -0.360775175 0.154000155 WQFDIECDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WQFDIECDK 9 0 Q13257 Q13257 MAD2L1 Mitotic spindle assembly checkpoint protein MAD2A 0 ; 132.78 0.00068739 120663000 242040 196306 213868 211457 227867 188267 274750 200379 229590 FALSE TRUE 226891.1485 210840.7005 218941.05 216883.3446 209971.245 242616.6266 233553.7882 225396.7592 191269.9458 1.186235232 1.102320072 1.144670424 1.133912302 1.097774374 1.26845138 1.221068931 1.178422247 1 17.54525068 2.269097141 24.99765374 1.192194851 1.130437324 0 0.073758506 360.0803419 294766.0332 0.02274084 0.019024316 185.8220046 -2.269097141 -0.061757527 WQGGER ddPTM_SK-BR-3_Pertuzumab_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 ; 124.12 0.043019 803510000 601790 539080 568540 538430 622300 466140 594980 511190 670690 FALSE TRUE 564125.0381 578994.0441 582026.0373 552247.0254 573427.0682 600707.0508 505768.2725 575013.1968 558747.5062 1.009624261 1.036235576 1.041661987 0.988365978 1.026272264 1.075095717 0.905182156 1.029110986 1 19.09183696 1.750304686 25 0.969821571 1.030004016 0.281613481 0.037969607 3.330194225 7101.285003 0.015781332 0.008751546 56.27359825 -1.750304686 0.060182445 WQLSVATEQPELEGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WQLSVATEQPELEGPR 16 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 186.56 3.44E-09 81350000 20307 21051 21598 21406 18792 17130 21546 18148 19473 FALSE TRUE 19036.02112 22609.63794 22110.31476 21955.3142 17316.15212 22075.15292 18315.37732 20413.81775 16222.8305 1.173409358 1.393692546 1.362913504 1.353359033 1.067394011 1.360746074 1.128987776 1.258338842 1 13.98573794 0.82661841 0.348667583 0.972027015 1.347764871 0.381249188 0.108182105 1.703910702 0.537936214 0.220448415 0.104986623 6.708391659 -0.82661841 0.375737856 WQRPS(ph)SPPPFLPAASEEAEPAEGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 WQRPSSPPPFLPAASEEAEPAEGLR 25 1 H3BLU1;Q4KMQ1;Q4KMQ1-2;Q4KMQ1-4;Q4KMQ1-3 H3BLU1 TPRN Taperin 1 WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLR;WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLR;WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLR;WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLR;WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLR;WQRPS(0.598)S(0.402)PPPFLPAASEEAEPAEGLR;WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLR 201.01 3.87E-25 8336784000 1647182 1665735 1796926 1710250 1775935 1618746 1938243 1534763 1211458 TRUE FALSE 1544087.819 1789067.753 1839549.933 1754137.91 1636460.229 2086051.692 1647621.456 1726381.539 1009257.833 1.529924037 1.772656791 1.822675903 1.738047357 1.621449123 2.066916523 1.632507969 1.710545593 1 19.94486335 0.377694293 1.510909867 0.99996699 1.758758056 0.722409948 0.143529676 2.17223796 4.762348211 0.123590789 0.035582363 2.386131053 -0.377694293 0.758791065 WQRPSS(ph)PPPFLPAASEEAEPAEGLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WQRPSSPPPFLPAASEEAEPAEGLR 25 1 H3BLU1;Q4KMQ1;Q4KMQ1-2;Q4KMQ1-4;Q4KMQ1-3 H3BLU1 TPRN Taperin 1 WQRPS(0.412)S(0.588)PPPFLPAASEEAEPAEGLR;WQRPS(0.181)S(0.819)PPPFLPAASEEAEPAEGLR 175.95 6.53E-13 2107820000 366351 374561 396290 390395 385202 348295 432055 334865 268057 TRUE FALSE 343421.7449 402293.8862 405690.1859 400413.1966 354949.7888 448842.1124 367272.3638 376673.6324 223316.555 1.537824837 1.801451246 1.816659701 1.793029615 1.589446823 2.009891799 1.644626677 1.686725072 1 17.76873068 0.421083946 1.38121351 0.999904895 1.762297827 0.752717032 0.132681626 1.38246055 2.855696743 0.112862773 0.033093019 2.636841017 -0.421083946 0.762392932 WQRPSS(ph)PPPFLPAASEEAEPAEGLRVPGLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WQRPSSPPPFLPAASEEAEPAEGLRVPGLAK 31 2 H3BLU1;Q4KMQ1;Q4KMQ1-2;Q4KMQ1-4;Q4KMQ1-3 H3BLU1 TPRN Taperin 1 WQRPS(0.385)S(0.615)PPPFLPAASEEAEPAEGLRVPGLAK;WQRPS(0.399)S(0.601)PPPFLPAASEEAEPAEGLRVPGLAK 213.51 2.65E-27 851630000 267220 366410 310260 349080 476990 236900 440890 274500 614760 TRUE FALSE 250495.1772 393539.3776 317619.5137 358037.9838 439529.1295 305289.1842 374782.6375 308771.9292 512152.5845 0.489102632 0.7684026 0.620165793 0.699084598 0.858199573 0.596090293 0.731779257 0.602890503 1 18.96621417 -2.140266197 2.462801949 1.705061847 0.681769963 0.498670861 0.103232262 11753123.44 1768749.862 46618851.17 0.022990632 0.007239921 2.140266197 -1.023291884 WQS(ph)PVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 WQSPVTK 7 0 A9Z1X7 A9Z1X7 SRRM1 1 WQS(1)PVTK;WQS(1)PVTK;WQS(0.997)PVT(0.003)K;WQS(0.999)PVT(0.001)K;WQS(0.985)PVT(0.015)K;WQS(0.998)PVT(0.002)K;WQS(0.988)PVT(0.012)K;WQS(1)PVTK 157.24 0.0015619 33311800000 22025100 18090580 20022300 18651400 18884700 15533060 23773900 15966130 22615400 TRUE FALSE 20646588.31 19430025.37 20497238.41 19130026.5 17401571.84 20017202.26 20209224.4 17959536.48 18840743.64 1.095847845 1.031276989 1.087920881 1.015354111 0.923613854 1.062442261 1.072634116 0.953228642 1 24.16735257 3.216516116 20.53821911 1.012758054 1.065343468 0.294731771 0.047509522 47.91697377 44641.81975 0.013983012 0.016743836 1646.327058 -3.216516116 0.052585414 WQTKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WQTKPK 6 1 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ; 77.674 0.065479 931210000 734560 644570 678000 675530 719450 502690 756780 598420 913480 FALSE TRUE 688585.2008 692294.6335 694082.4802 692865.2435 662947.2991 647808.4425 643307.8646 673134.0543 761014.2867 0.90482559 0.909699917 0.912049212 0.910449719 0.87113647 0.851243471 0.84532955 0.88452223 1 19.53756401 2.741761886 23.5983663 0.874826901 0.909795597 0 0.043757428 247.8124713 1826767.997 0.012110505 0.01235727 551.7748303 -2.741761886 0.034968696 WQTMIEAHVDVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WQTMIEAHVDVK 12 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;D6RB09;D6RAS7;D6RED7 P61247 RPS3A 40S ribosomal protein S3a 0 ; 97.631 0.0048131 565670000 865160 775770 882480 873930 912940 701310 968920 755530 808170 FALSE TRUE 811011.18 833208.818 903412.8423 896356.5234 841241.375 903766.8122 823639.441 849859.5836 673281.206 1.204565303 1.237534645 1.341806119 1.331325626 1.249465108 1.342331858 1.223321598 1.262265419 1 19.36084967 0.189725951 0.940805311 0.997716075 1.283632094 0.756381816 0.049023029 1.92088749 1.826673353 0.056825125 0.014868344 1.547839591 -0.189725951 0.285916018 WQVVDTPGILDHPLEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 WQVVDTPGILDHPLEDR 17 0 Q9BZE4-2;Q9BZE4;Q9BZE4-3 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 ;; 242.45 2.08E-20 341953000 355695 390752 436292 391021 371107 327822 429851 354788 327082 FALSE TRUE 333432.6849 419683.6847 446641.0523 401055.2609 341961.7532 422458.8897 365398.8331 399084.0628 272489.9012 1.223651531 1.540180692 1.639110478 1.471816971 1.254952025 1.550365308 1.340962845 1.464582948 1 18.05584324 -1.342559586 0.352171783 0.713500192 1.490847979 0.494515398 0.13467546 16.21186358 1.260264648 4.388294767 0.105298291 0.045440219 1.342559586 0.777347788 WRCPVPT(ph)LPGCQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 WRCPVPTLPGCQK 13 1 E5RJ64 E5RJ64 C8orf58 1 WRCPVPT(1)LPGCQK;WRCPVPT(1)LPGCQK;WRCPVPT(1)LPGCQK 75.045 0.052475 698260000 355120 1153600 907900 1091280 1136180 2458960 458850 598650 415080 TRUE FALSE 332893.6731 1239013.744 929435.8167 1119284.092 1046949.006 3168821.834 390049.7023 673392.7703 345800.4665 0.962675605 3.583030864 2.687780691 3.236791736 3.027610161 9.163729206 1.127961758 1.947344887 1 18.39958029 4.742030452 22.87441934 3.364178075 0.962672446 0.085366117 2.281985663 251.0160752 1654520.641 0.505646795 3.622237876 55211.61515 -4.742030452 -2.401505629 WREEQMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 WREEQMER 8 1 P09496-2;F8WF69;P09496-4;P09496-3;P09496 P09496-2 CLTA Clathrin light chain A 0 ;; 154.85 0.0003816 1230220000 1001800 1243790 1008030 1047400 1336360 874770 1176990 1124140 1327000 FALSE TRUE 939099.1263 1335881.506 1031940.948 1074278.057 1231407.676 1127301.898 1000511.276 1264491.354 1105515.127 0.849467459 1.208379219 0.933448057 0.971744331 1.113876822 1.019707348 0.905018169 1.14380285 1 20.07628734 WREEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 164.89 0.0067867 2085800000 1658240 2540730 1547440 1587960 2662740 1085368 1686590 2238530 3042200 FALSE TRUE 1554453.718 2728848.293 1584146.008 1628709.742 2453619.141 1398696.122 1433701.487 2518015.398 2534437.167 0.613332908 1.076707811 0.625048444 0.64263173 0.968112042 0.551876425 0.565688314 0.993520546 1 21.27323397 1.209530203 23.70540749 0.996761732 0.735079809 0.303726718 0.172809317 187.3034893 152938.7079 0.167860043 0.042004102 16.20056657 -1.209530203 -0.261681923 WRLS(ph)PGETPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WRLSPGETPER 11 1 A0A0G2JHC2;Q6NYC8-2;Q6NYC8 A0A0G2JHC2 PPP1R18 Phostensin 1 WRLS(0.999)PGET(0.001)PER;WRLS(0.997)PGET(0.003)PER 102.65 0.00172 180100000 101732 130375 121507 124339 139063 107909 120578 107846 143027 TRUE FALSE 95364.77572 140028.1007 124389.2034 127529.7492 128141.5529 139060.5765 102498.4483 121310.8105 119154.8697 0.800343082 1.175177322 1.043928827 1.070285667 1.075420193 1.167057434 0.860211996 1.018093602 1 16.86247839 1.736469229 25 0.950866879 1.069218502 0.135243995 0.110012476 0.404956661 4728.361027 0.045800609 0.025398744 54.50912733 -1.736469229 0.118351624 WRPHS(ph)PDGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 135.26 8.99E-05 18166170000 11221630 12816220 11628730 11474100 14130830 10354230 12413260 11349080 13590730 TRUE FALSE 10519288.21 13765146.26 11904568.97 11768544.83 13021051.61 13343328.11 10552006.9 12766037.62 11322349.36 0.929072922 1.215750002 1.051422155 1.039408382 1.150030899 1.178494647 0.931962666 1.127507835 1 23.43267001 1.742342224 25 1.016559237 1.103211875 0.119285185 0.092701534 1.167002724 7754.113068 0.039227284 0.021753462 55.25126473 -1.742342224 0.086652638 WRPHS(ph)PGWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WRPHSPGWR 9 1 Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 WRPHS(1)PGWR;WRPHS(1)PGWR 115.92 0.00084649 636490000 784730 896420 882030 899940 1081180 781560 842610 762500 983990 TRUE FALSE 735615.1501 962791.8695 902952.1681 923033.984 996268.4841 1007183.684 716268.4529 857699.8035 819755.7122 0.89735898 1.17448632 1.101489327 1.125986645 1.215323625 1.228638812 0.873758416 1.046287072 1 19.64483452 1.737887646 25 0.96849319 1.13073444 0.333132053 0.100008894 0.105295364 3501.882778 0.042857562 0.023766683 54.68744656 -1.737887646 0.162241249 WRS(ph)LQQLAEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WRSLQQLAEER 11 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 WRS(1)LQQLAEER 119.99 0.00030988 273030000 125310 224270 209650 244270 280990 203430 214660 268000 306950 TRUE FALSE 117467.0708 240875.1842 214622.997 250538.3817 258922.1789 262156.9386 182473.7258 301460.3899 255718.062 0.45936165 0.941956083 0.839295415 0.979744566 1.012529881 1.025179592 0.713573865 1.17887797 1 17.96419454 4.739079391 24.55815423 0.934977922 0.459361471 0.612688675 0.123869735 22.69030654 1073760.58 0.02751962 0.163049584 54837.7202 -4.739079391 -0.475616451 WRVS(ph)LDVNHFAPDELTVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WRVSLDVNHFAPDELTVK 18 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 WRVS(1)LDVNHFAPDELTVK;WRVS(1)LDVNHFAPDELTVK 161.16 2.34E-11 324220000 548140 541050 476470 525310 622570 380830 537320 538740 795290 TRUE FALSE 513832.8959 581109.905 487772.0934 538790.3439 573675.8635 490769.4387 456753.8542 606002.8749 662550.9612 0.775537168 0.877079559 0.736203133 0.81320589 0.865859228 0.74072708 0.689386751 0.914650963 1 19.3376719 1.02786221 6.537441892 0.999802064 0.786577407 0.627280018 0.057194942 0.098000642 13.31711179 0.05786044 0.014527902 10.66257772 -1.02786221 -0.213224657 WRYPSLSLHGIEGAFSGSGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WRYPSLSLHGIEGAFSGSGAK 21 1 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 198.24 5.21E-22 272140000 81679 175710 113940 106970 209110 64852 118860 187080 203640 FALSE TRUE 76566.85719 188719.7512 116642.7106 109715.0313 192687.3441 83573.71962 101038.0464 210437.3498 169651.1684 0.451319363 1.112398771 0.687544399 0.646709553 1.135785541 0.492620949 0.595563516 1.240412028 1 17.37221184 1.234745846 24.99989919 1.120206085 0.755638358 0.313817035 0.23678483 128.773811 843852.2342 0.190836586 0.054762955 17.16903342 -1.234745846 -0.364567727 WS(ph)GNEPTDEFSDLPLR ddPTM_SK-BR-3_Pertuzumab_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 316.25 8.08E-58 872690000 843149 739872 744522 694130 771663 607550 858574 714623 570879 TRUE FALSE 790377.8092 794652.8927 762182.4134 711942.551 711059.7007 782939.8222 729838.7993 803845.2546 475595.6069 1.661869449 1.670858354 1.602585058 1.496949384 1.49509308 1.646230139 1.534578513 1.690186459 1 18.85937586 -1.279244104 3.526515486 0.998285466 1.59758932 0.87645751 0.070765373 7779077.948 12153252.56 142545.0245 0.017613974 0.052572169 1.279244104 0.599303854 WS(ph)GSHQFEQLSGSILWMAPEVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WSGSHQFEQLSGSILWMAPEVIR 23 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8Y492;H7C4S5 P15056 BRAF Serine/threonine-protein kinase B-raf 1 WS(0.813)GS(0.185)HQFEQLS(0.002)GSILWMAPEVIR 81.534 0.0063237 108040000 80532 121240 91302 100460 102680 90065 109730 112040 79282 TRUE FALSE 75491.64587 130216.7358 93467.72656 103037.9737 94615.92699 116065.3034 93277.00518 126028.4406 66049.32202 1.142958679 1.971507531 1.415120151 1.560015615 1.432504136 1.757252003 1.412232591 1.908095901 1 16.01125613 -1.337438051 5.170420112 0.999779897 1.586608947 0.342621799 0.249825809 0.000552624 7.08E-05 0.210893945 0.049689881 0.045979257 1.337438051 0.58682905 WS(ph)PPQNYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 WSPPQNYK 8 0 H3BRF9;Q96K21-2;Q96K21;H3BRM1;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 WS(1)PPQNYK;WS(1)PPQNYK;WS(1)PPQNYK;WS(1)PPQNYK;WS(1)PPQNYK;WS(1)PPQNYK;WS(1)PPQNYK 115.57 0.002557 8807650000 3863130 3161130 3251420 3360620 3387040 2522420 4257910 2792430 3025210 TRUE FALSE 3621343.589 3395183.354 3328545.218 3446859.199 3121035.541 3250601.706 3619475.924 3141071.032 2520282.907 1.436879796 1.347143745 1.320703008 1.367647731 1.238367142 1.289776515 1.436138742 1.246316841 1 21.26515426 0.954173448 8.771653187 1.000001001 1.343914458 0.771092846 0.059938056 0.499787643 95.54464152 0.055702776 0.013941177 8.998568927 -0.954173448 0.343913457 WS(ph)TTAGFLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WSTTAGFLK 9 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 WS(0.862)T(0.113)T(0.025)AGFLK;WS(0.899)T(0.1)T(0.001)AGFLK 155 7.80E-05 632010000 687120 812520 547040 538930 1019360 296000 740600 879940 977130 TRUE FALSE 644114.3857 872679.8262 560016.0471 552759.8562 939303.5775 381450.3948 629553.9054 989802.446 814040.6905 0.791255761 1.072034649 0.687946013 0.679032219 1.153877918 0.468588855 0.773369087 1.215912739 1 19.63474139 1.247236088 24.99643697 1.107956389 0.807940678 0.285286743 0.200104636 210.5505626 606666.801 0.131252194 0.046294476 17.66998124 -1.247236088 -0.30001571 WS(ph)WGGSLHGSPSIHSADPDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WSWGGSLHGSPSIHSADPDRR 21 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5 Q14244-6 MAP7 Ensconsin 1 WS(0.874)WGGS(0.122)LHGS(0.001)PS(0.001)IHS(0.001)ADPDRR 57.432 0.037873 133250000 49172 62425 49624 47764 74216 33766 60284 43144 113760 TRUE FALSE 46094.41229 67047.01195 50801.10471 48989.7051 68387.37473 43513.69605 51244.97385 48530.62337 94772.72108 0.486367931 0.707450532 0.536030876 0.516917785 0.72159345 0.45913735 0.540714388 0.512073757 1 16.53218424 -1.543101231 2.899704149 1.02043145 0.568064045 0.712961644 0.087600186 25951219.1 27895366.84 4141885.47 0.019857681 0.028635104 1.543101231 -0.452367405 WSAEASGKPSPSDPGSGTATMMNS(ph)SSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WSAEASGKPSPSDPGSGTATMMNSSSR 27 1 Q5JRA6-2;Q5JRA6;Q5JRA6-4 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 1 WSAEASGKPSPSDPGSGTATMMNS(0.333)S(0.333)S(0.333)R;WSAEASGKPSPSDPGS(0.016)GT(0.054)AT(0.113)MMNS(0.272)S(0.272)S(0.272)R 148.13 7.60E-08 895140000 1216860 1046870 1014240 924400 1302450 918310 1450790 1181300 1114600 TRUE FALSE 1140698.905 1124381.344 1038298.252 948121.669 1200160.831 1183411.189 1233257.508 1328787.905 928566.0594 1.228452077 1.210879218 1.118173814 1.021060009 1.292488368 1.274450189 1.32813115 1.431010634 1 19.82464502 2.681800183 24.34769323 1.289458161 1.151269608 0.179864168 0.121615729 290.7429602 124715.0924 0.035939069 0.033883695 480.6181674 -2.681800183 -0.138188553 WSAEASGKPSPSDPGSGTATMMNSSS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WSAEASGKPSPSDPGSGTATMMNSSSR 27 1 Q5JRA6-2;Q5JRA6;Q5JRA6-4 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 1 WSAEASGKPSPSDPGSGTATMMNS(0.029)S(0.219)S(0.752)R 96.211 0.0027785 514400000 479900 462150 425390 405320 534640 365890 542470 468630 441990 TRUE FALSE 449863.9156 496368.0669 435480.4517 415721.1974 492651.531 471516.5033 461131.6595 527139.4871 368219.0136 1.221729186 1.348023998 1.182666933 1.129005244 1.337930723 1.280532742 1.252329843 1.431592252 1 18.4902046 -1.06551349 4.481588332 0.999982591 1.268390701 0.495859846 0.086391596 1.41E-05 2.93E-06 0.078296323 0.018453424 0.085997635 1.06551349 0.268408111 WSALESEDMHFILQTLEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WSALESEDMHFILQTLEDR 19 0 P78345;Q5VUC9;Q5VUC3 P78345 RPP38 Ribonuclease P protein subunit p38 0 127.97 2.24E-05 7460200 11569 14297 12050 13001 17201 13541 13972 12312 10778 FALSE TRUE 10844.91694 15355.56476 12335.83169 13334.62767 15850.10285 17450.06688 11877.02831 13849.1803 8979.082171 1.207797939 1.710148595 1.373841051 1.485076917 1.765225281 1.943413207 1.322744138 1.542382622 1 13.13235227 0.471845494 1.331495535 1.000747979 1.560589323 0.378062336 0.218895979 2.54574038 5.345888669 0.197851999 0.058564816 2.963776799 -0.471845494 0.559841345 WSDSSKQDDS(ph)PSGASYGQDYDLS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 WSDSSKQDDSPSGASYGQDYDLSPSR 26 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 WSDSSKQDDS(0.993)PS(0.007)GASYGQDYDLS(0.905)PS(0.095)R;WSDSSKQDDS(0.995)PS(0.004)GASYGQDYDLS(0.828)PS(0.172)R;WSDS(0.001)S(0.001)KQDDS(0.998)PSGASYGQDYDLS(0.989)PS(0.011)R;WSDSSKQDDS(0.992)PS(0.008)GAS(0.001)YGQDYDLS(0.816)PS(0.183)R 211.25 6.48E-26 856670000 887890 821573 793260 805159 1166910 671613 1310000 862815 2242800 TRUE FALSE 832318.5498 882403.1198 812076.5018 825820.7431 1075265.596 865496.7704 1113577.661 970539.352 1868462.191 0.445456458 0.472261694 0.434622925 0.441978835 0.575481592 0.463213425 0.59598619 0.51943216 1 20.83341994 -5 0.216073725 3.563149613 0.422603269 0.930378125 0.044473634 31.90037857 0.31894565 35.42028075 0.079131365 1.00E-05 5 -3.140546344 WSEPWVPVEALPPS(ph)PLELSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 WSEPWVPVEALPPSPLELSR 20 0 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 WSEPWVPVEALPPS(0.977)PLELS(0.023)R;WSEPWVPVEALPPS(0.972)PLELS(0.028)R;WSEPWVPVEALPPS(0.999)PLELS(0.001)R;WSEPWVPVEALPPS(0.983)PLELS(0.017)R;WSEPWVPVEALPPS(0.996)PLELS(0.004)R;WSEPWVPVEALPPS(0.967)PLELS(0.033)R 218.88 5.92E-26 0 129785.7 148317 138904.9 147517.9 173512 108108.3 130752 114237 148104 TRUE FALSE 121662.6447 159298.545 142199.7898 151303.4591 159885.0674 139317.4112 111146.9514 128499.7409 123384.4856 0.986044916 1.291074354 1.152493274 1.226276207 1.295827969 1.129132326 0.900817886 1.041457848 1 16.91280148 1.93145343 5.504498889 0.97692603 1.201630301 0.51483748 0.092525458 0.150864049 8.560634381 0.03728374 0.022624811 85.39912686 -1.93145343 0.224704271 WSGPLSLQEVDEQPQHPLHVTYAGAAVDELGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WSGPLSLQEVDEQPQHPLHVTYAGAAVDELGK 32 0 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 254.75 2.27E-59 368769000 353448 331217 333347 284263 354675 260731 430352 349935 677083 FALSE TRUE 331326.3206 355740.6513 341254.1483 291557.6698 326820.2562 335999.8071 365824.7128 393625.1551 564073.4732 0.587381496 0.630663678 0.604981735 0.516878888 0.579393061 0.59566674 0.648540891 0.697826035 1 19.10552357 0.637906003 1.065856091 1.000130634 0.58983914 0.94917043 0.029754203 0.262865945 0.480436157 0.030675674 0.009672277 4.344161906 -0.637906003 -0.410291494 WSHDGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 WSHDGK 6 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;;;; 144.29 0.011291 3650420000 10799970 8870980 10248260 9689930 10016330 8250350 12206200 8993210 11159860 FALSE TRUE 10124019.16 9527796.589 10491353.57 9938590.009 9229687.846 10632092.11 10375993.63 10116032.06 9297207.271 1.088931209 1.024801998 1.128441398 1.068986602 0.992737666 1.14357912 1.116033377 1.088072124 1 23.14836599 2.195466454 24.99999808 1.100351817 1.065472735 0.028043109 0.051432834 330.6609214 191822.6806 0.018037037 0.013321297 156.8434744 -2.195466454 -0.034879082 WSLELEDQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 WSLELEDQER 10 0 P37198 P37198 NUP62 Nuclear pore glycoprotein p62 0 ;;; 251.53 4.26E-14 501789000 447534 536990 493276 486821 544070 452303 565690 482773 529776 FALSE TRUE 419523.6458 576749.2983 504976.7397 499313.651 501340.9369 582875.5336 480870.0361 543048.2718 441352.9631 0.950540001 1.306775634 1.144156224 1.131325023 1.135918366 1.320656215 1.089536213 1.230417188 1 18.75157336 -1.621792503 2.857445028 0.985622653 1.173689956 0.181858172 0.107238228 236551905 217063914.7 25168666.25 0.022787493 0.023889524 1.621792503 0.188067303 WT(ph)SQDSLLGMEFSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WTSQDSLLGMEFSGR 15 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 WT(0.924)S(0.076)QDSLLGMEFSGR 158.98 2.00E-05 37778000 92851 100610 98651 107750 93183 85517 121580 95470 95133 TRUE FALSE 87039.62165 108059.2691 100991.0483 110515.0474 85864.78306 110204.3696 103350.2077 107389.6397 79254.68772 1.098226795 1.363443251 1.274259621 1.394429157 1.08340321 1.390509165 1.304026433 1.354994168 1 16.27420865 -1.359306264 3.538468058 0.998422667 1.292406839 0.388498866 0.110979832 19582293.44 22867241.43 300687.5053 0.023355767 0.043721367 1.359306264 0.293984172 WTDGSLS(ph)PPAKEPLASDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WTDGSLSPPAKEPLASDSR 19 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 WTDGS(0.053)LS(0.947)PPAKEPLASDSR 114.74 9.19E-05 197360000 543030 449970 502040 544850 656900 430860 573050 503320 698370 TRUE FALSE 509042.7216 483286.247 513948.6259 558831.7734 605309.7238 555242.2876 487126.4724 566160.6099 581807.5354 0.874933188 0.830663437 0.883365365 0.960509687 1.040395126 0.954340145 0.837263945 0.973106355 1 19.15018246 3.39275604 3.761678852 0.94807443 0.853652766 0.424422167 0.053117008 0.252611945 6.909155615 0.016466176 0.023248718 2470.336074 -3.39275604 -0.094421663 WTELAGCTADFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WTELAGCTADFR 12 0 Q12907;D6RBV2;D6RDX1;D6RIU4 Q12907 LMAN2 Vesicular integral-membrane protein VIP36 0 ; 150.15 0.00015791 233260000 202503 274010 172310 187969 285090 125613 230466 263444 233281 FALSE TRUE 189828.6987 294297.9855 176397.2746 192792.6028 262700.1814 161875.4339 195909.7628 296335.5633 194344.894 0.976761955 1.514307782 0.907650677 0.992012698 1.35172155 0.832928669 1.008052019 1.524792122 1 17.56825968 3.963681133 24.57725899 1.07440571 1.274812026 0.062884276 0.242393181 648.2197237 1185369.121 0.05701734 0.10355718 9197.740082 -3.963681133 0.200406316 WTETYVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 WTETYVR 7 0 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;; 160.03 0.0031676 440265000 364622 857340 420024 434408 900860 368580 388465 753320 643090 FALSE TRUE 341800.9599 920818.3457 429987.1676 445555.6447 830110.0895 474983.0626 330218.2796 847373.6603 535754.1245 0.637981015 1.718733097 0.802583028 0.831642025 1.54942361 0.88656912 0.616361619 1.581646546 1 19.03121153 3.764944217 23.37121 1.002173125 1.257085501 0.006090839 0.403156713 389.8114348 240864.5569 0.096423612 0.173838881 5820.284537 -3.764944217 0.254912376 WTGPEISPNTSGSS(ph)PVIHFTPSDLEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WTGPEISPNTSGSSPVIHFTPSDLEVR 27 0 A0AVK6 A0AVK6 E2F8 Transcription factor E2F8 1 WTGPEISPNTS(0.027)GS(0.157)S(0.816)PVIHFTPSDLEVR 175.42 7.32E-13 164260000 42464 53460 51998 56809 62299 62366 68249 55898 68001 TRUE FALSE 39806.25404 57418.23403 53231.41712 58266.81512 57406.28784 80370.05177 58015.69604 62876.98835 56651.1938 0.702655167 1.013539701 0.939634517 1.028518752 1.013328828 1.418682403 1.024086028 1.10989697 1 15.78981874 5.708284957 0.485829336 1.122216342 4.15E-17 0.425871973 0.132261557 10.66372102 0.94443489 0.072477287 8.364367973 510840.072 -5.708284957 -1.122216342 WTKPSSFS(ph)DSER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 WTKPSSFSDSER 12 1 Q8NC56;H0Y9B7;Q8NC56-2 Q8NC56 LEMD2 LEM domain-containing protein 2 1 WTKPS(0.011)S(0.058)FS(0.925)DS(0.007)ER;WTKPS(0.005)S(0.115)FS(0.88)DSER;WTKPSSFS(1)DSER;WTKPSS(0.009)FS(0.99)DSER;WTKPS(0.003)S(0.021)FS(0.976)DSER;WTKPSS(0.002)FS(0.941)DS(0.057)ER 161.14 3.57E-05 4512710000 6154370 5637200 4564489 4649057 5962460 4000688 7234250 5514230 5321870 TRUE FALSE 5769178.968 6054584.154 4672760.835 4768359.673 5494192.443 5155621.68 6149541.372 6202693.754 4433615.516 1.30123574 1.365608752 1.05393912 1.075501395 1.239212652 1.162848168 1.387026311 1.399014807 1 22.08005223 1.756553414 25 1.302007305 1.198784276 0.015704683 0.143479949 17.26355262 24011.54603 0.063881472 0.035426392 57.08912864 -1.756553414 -0.10322303 THTCPPCPAPELLGGPSVFLFPPKPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 THTCPPCPAPELLGGPSVFLFPPKPK 26 1 A0A0A0MS08;P01857;A0A0A0MS07 A0A0A0MS08 IGHG1 Ig gamma-1 chain C region 0 121.38 8.66E-05 98006000 905160 241210 44686 35820 35876 19065 15263 14328 25441 FALSE TRUE 848507.6514 259069.4394 45745.97302 36739.20184 33058.44368 24568.75601 12974.45484 16116.88234 21194.73274 40.03389246 12.22329352 2.158365174 1.733411895 1.559748079 1.159191593 0.61215468 0.760419229 1 14.37141815 5.626276854 0.976917686 1.051246324 200 0.993792075 0.964553532 0.683346637 0.14331852 0.305710022 216.225056 422938.1427 -5.626276854 198.9487537 up WTPKS(ph)PLDPDSGLLSCTLPNGFGGQSGPEGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WTPKSPLDPDSGLLSCTLPNGFGGQSGPEGER 32 1 A0A087X0R7;Q9H4L4 A0A087X0R7 SENP3-EIF4A1;SENP3 Sentrin-specific protease 3 1 WT(0.001)PKS(0.999)PLDPDSGLLSCTLPNGFGGQSGPEGER;WT(0.003)PKS(0.996)PLDPDS(0.001)GLLSCTLPNGFGGQSGPEGER 220.48 3.96E-36 362060000 678480 599960 637330 727520 777190 458700 750520 561130 791470 TRUE FALSE 636015.1479 644381.6627 652447.7686 746189.3949 716152.6324 591119.2436 637986.4935 631188.3157 659368.5439 0.964582181 0.977270858 0.989503935 1.131672722 1.086118892 0.896492939 0.967571928 0.957261795 1 19.33072554 -0.4753895 8.109319364 1 0.99425586 0 0.066793206 0 0 0.066071652 0.015573238 0.334665158 0.4753895 -0.00574414 WTS(ph)QDSLLGMEFSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WTSQDSLLGMEFSGR 15 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 WT(0.037)S(0.951)QDS(0.012)LLGMEFSGR 98.507 0.0030434 47403000 90300 97066 96672 92460 90429 82500 112670 92776 92762 TRUE FALSE 84648.28419 104252.8676 98965.10549 94832.68013 83327.07111 106316.4107 95776.17948 104359.2878 77279.42293 1.095353472 1.349037864 1.28061393 1.227140117 1.078256901 1.375740225 1.239349051 1.350414947 1 16.2377967 -1.78415798 2.714957281 0.932707757 1.259557081 0.373373085 0.100827511 18663643.65 13919430.61 8318398.184 0.022221586 0.016437737 1.78415798 0.326849324 WTSQDSLLGMEFSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 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 ;;;;;;;;;; 305.6 1.94E-44 5028254000 2494119 3520318 3194397 3460077 3748597 3203290 3852990 3328964 3363816 FALSE TRUE 2338016.544 3780966.008 3270169.605 3548868.434 3454197.313 4128027.822 3275269.919 3744592.483 2802373.379 0.834298728 1.349201372 1.166928586 1.266379584 1.232597105 1.473047044 1.168748584 1.33622183 1 21.41821776 4.746096205 24.82883962 1.259087634 0.834298504 0.51314388 0.1266599 608.1994684 2003889.647 0.026083767 0.275034642 55730.91899 -4.746096205 -0.42478913 WTVHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WTVHGK 6 0 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 76.592 0.07465 222760000 598850 556340 631210 603270 623240 540860 701070 606090 501850 FALSE TRUE 561369.0475 597531.9925 646182.5993 618750.9295 574293.2444 696997.5019 595951.0619 681761.6707 418087.9929 1.3427055 1.429201514 1.54556603 1.479953837 1.373618124 1.667107197 1.425420179 1.630665511 1 18.67344709 -1.758932881 12.8243736 0.999605711 1.486799986 0.683867056 0.104012134 0.001041527 1.96E-05 0.089454615 0.021070448 0.017420761 1.758932881 0.487194276 WVAIQSVSAWPEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WVAIQSVSAWPEKR 14 1 Q96KP4;Q96KP4-2;J3QKT2;A0A087WYZ1;J3KSV5;J3QRA8;J3QRD0;J3QKQ0;J3QLU1;J3QR27;J3QL02;J3QQN6;J3KSS4 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 194.77 1.68E-07 1434340000 352340 548120 375690 372520 610670 275360 400970 532330 530710 FALSE TRUE 330287.6683 588703.3751 384601.5442 382079.4939 562710.4415 354851.9619 340848.2709 598792.5723 442131.0725 0.747035639 1.331513236 0.869881282 0.864176977 1.272723128 0.802594488 0.770921322 1.354332707 1 18.7541146 3.755924496 23.78798012 0.96430709 1.086925263 0 0.237195173 716.3390788 591602.3218 0.05669943 0.102185547 5700.651548 -3.755924496 0.122618173 WVDEVVPAAPYVTTLETLDKYNCDFCVHGNDITLTVDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 WVDEVVPAAPYVTTLETLDKYNCDFCVHGNDITLTVDGR 39 1 Q99447-3;Q99447;Q99447-4;I3L1R7;Q99447-2;I3L2Q1;I3L1C4 Q99447-3 PCYT2 Ethanolamine-phosphate cytidylyltransferase 0 ;; 205.11 5.09E-31 203578000 234126 218682 226637 215254 256015 205718 309039 204530 277512 FALSE TRUE 219472.4716 234873.4428 232012.9367 220777.7821 235908.6146 265105.447 262701.4709 230066.0207 231193.4544 0.949302272 1.015917356 1.003544574 0.954948239 1.020394869 1.146682322 1.136284207 0.995123419 1 17.81874103 2.430693546 7.78101492 1.088863989 0.990218492 0.347582349 0.053786916 0.213517839 30.69915484 0.017833927 0.014935588 269.5836481 -2.430693546 -0.098645497 WVEENVPSSVTDVALPALLDS(ph)DEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WVEENVPSSVTDVALPALLDSDEER 25 0 Q8NBN3-3;Q8NBN3 Q8NBN3-3 TMEM87A Transmembrane protein 87A 1 WVEENVPSSVTDVALPALLDS(1)DEER 93.388 0.007376 19918000 16386 16595 18272 15180 18150 18280 20643 17323 17583 TRUE FALSE 15360.42951 17823.71107 18705.42047 15569.5445 16724.57221 23557.13925 17547.77379 19485.81468 14648.28371 1.04861633 1.216778117 1.276970111 1.062892064 1.141742783 1.608184257 1.197940601 1.330245582 1 13.83844402 WVEQHLGPQFVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WVEQHLGPQFVER 13 0 Q8TCD5;J3KSY6;J3KRC4 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 0 129.93 0.00014797 66962000 115450 178770 113870 121600 178600 85351 113590 140280 142540 FALSE TRUE 108224.1906 192006.3168 116571.0502 124720.4619 164573.4764 109990.4481 96558.23402 157794.2668 118749.1532 0.911368104 1.61690683 0.981657949 1.050285064 1.38589179 0.926241958 0.813127769 1.328803302 1 16.8575577 3.739181489 22.84728754 1.05063012 1.309958097 0.091055519 0.240848666 217.543126 412112.7255 0.058535514 0.104276277 5485.06134 -3.739181489 0.259327977 WVESLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 149.06 0.024861 7582450000 11561560 11784760 12267480 12210770 13547200 10100290 15704170 11898620 14690730 FALSE TRUE 10837942.6 12657315.89 12558470.42 12524119.03 12483257.56 13016079.76 13349475.5 13384188.9 12238752.26 0.885543099 1.034199862 1.026123428 1.023316656 1.01997796 1.063513623 1.090754614 1.093590966 1 23.54495315 5.579211495 1.267226852 1.050259009 1.28E-11 0.709829402 0.031452347 5.944979761 1.669215713 0.009110303 13.54681497 379499.7511 -5.579211495 -1.050259009 WVGESER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WVGESER 7 0 Q6PL18;Q6PL18-2;Q9ULI0-2;Q9ULI0 Q6PL18;Q9ULI0-2 ATAD2;ATAD2B ATPase family AAA domain-containing protein 2;ATPase family AAA domain-containing protein 2B 0 ; 106.42 0.025003 130200000 286470 493900 297890 302440 539720 208479 279600 462470 544600 FALSE TRUE 268540.3541 530468.8699 304956.0915 310201.1224 497332.5683 268663.5029 237676.5757 520210.3975 453702.7417 0.591886117 1.169199172 0.672149545 0.683710046 1.096163903 0.592157548 0.523859686 1.146588613 1 18.79138785 3.761227682 21.83385247 0.773909565 0.921448382 0 0.25339823 234.1117433 149866.0448 0.061065466 0.110068427 5770.689162 -3.761227682 0.147538817 WVGGQHPCFIIAEIGQNHQGDLDVAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WVGGQHPCFIIAEIGQNHQGDLDVAK 26 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ; 281.4 4.19E-61 626550000 931040 712680 732650 716320 761600 586480 958870 688670 878160 FALSE TRUE 872767.8684 765447.5687 750028.804 734701.9839 701787.0081 755787.2553 815096.3452 774651.9654 731589.4229 1.192974968 1.046280256 1.025204549 1.004254519 0.95926347 1.0330757 1.114144518 1.058861625 1 19.48067469 4.741583123 4.064779267 1.034125954 1.207172997 0.615139288 0.040494785 0.18569106 6.594651856 0.010813294 0.09488428 55154.77576 -4.741583123 0.173047042 WVGGQHPCFIIAEIGQNHQGDLDVAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WVGGQHPCFIIAEIGQNHQGDLDVAKR 27 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ; 219.38 1.23E-34 311827000 122996 140861 130628 153554 162114 120254 179358 124275 226622 FALSE TRUE 115297.8999 151290.495 133726.5578 157494.4556 149382.2204 154969.3776 152464.933 139791.0073 188797.3242 0.610696685 0.801338132 0.708307485 0.834198558 0.791230602 0.820824015 0.80755876 0.740428965 1 17.52647879 -5 0.117678216 1.713755856 0.656540471 0.623531262 0.060919275 101.7014038 0.78117354 17.51757167 0.564845724 1.00E-05 5 -1.057215385 WVGTIHGAAGTVYEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WVGTIHGAAGTVYEDLR 17 0 O00762;O00762-2 O00762 UBE2C Ubiquitin-conjugating enzyme E2 C 0 132.15 2.46E-05 230300000 250470 212700 179140 163210 229090 140420 170460 167350 191680 FALSE TRUE 234793.5298 228448.5293 183389.2854 167398.2449 211098.1955 180956.9745 144901.1055 188244.0159 159687.3697 1.470332502 1.430598611 1.14842699 1.048287321 1.321946726 1.133195285 0.907404923 1.178828459 1 17.28489068 7.99999763 0.272054006 1.002016808 4.783612531 0.639496448 0.108601726 30.36372116 0.426177525 0.122821959 54.05216949 99999454.36 -7.99999763 3.781595723 WVIYNDQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WVIYNDQK 8 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 131.06 0.0040948 0 305050 263710 276030 272990 301470 208790 322990 248500 315960 FALSE TRUE 285957.465 283235.3628 282577.562 279995.3856 277793.7623 269064.2836 274560.648 279525.772 263224.2348 1.086364503 1.076023121 1.073524108 1.063714311 1.055350251 1.022186592 1.043067513 1.061930229 1 18.0059328 8 0.041880006 0.852532123 1.397583582 0.768723848 0.012539337 310.8837294 0.989559998 3.42714776 11.77565417 100000000 -8 0.54505146 WVKDENVEFDS(ph)DEEEPPDLPLD ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WVKDENVEFDSDEEEPPDLPLD 22 1 Q9BWG6-2;Q9BWG6 Q9BWG6-2 SCNM1 Sodium channel modifier 1 1 WVKDENVEFDS(1)DEEEPPDLPLD 91.725 0.0013214 28346000 147310 123120 133930 131740 150130 110660 162870 119640 163090 TRUE FALSE 138090.1301 132235.9329 137106.8828 135120.6714 138339.3954 142605.7456 138449.1555 134577.3174 135869.2254 1.016345899 0.9732589 1.009109182 0.994490629 1.018180497 1.049580913 1.018988333 0.990491533 1 17.05185919 2.724150302 7.890325214 1.019676608 0.995916274 0.143099791 0.018980934 0.238519461 96.8904824 0.0058447 0.005683233 529.8467837 -2.724150302 -0.023760334 WVNDPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WVNDPHR 7 0 Q9H4A6 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 0 ; 107.29 0.0091406 135150000 431520 592210 396530 366580 556760 357640 444610 574130 537620 FALSE TRUE 404511.9335 636057.8446 405935.8789 375987.0634 513034.3155 460884.8622 377944.8581 645811.3943 447887.7488 0.903154718 1.420127803 0.906333964 0.839467175 1.145452888 1.029018685 0.843838348 1.441904575 1 18.77277768 3.862804565 7.205285712 1.010291466 1.193030111 0.052415729 0.213014683 0.454226152 25.98037207 0.049846436 0.090462632 7291.293238 -3.862804565 0.182738646 WVNEAQEAASSDNIMVQYHALGLLYHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WVNEAQEAASSDNIMVQYHALGLLYHVR 28 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ; 204.53 1.81E-25 272390000 139668 174933 145582 145889 203590 133326 185567 176930 132523 FALSE TRUE 130926.4292 187885.2213 149035.2738 149632.7587 187600.8626 171815.0518 157742.9511 199020.1 110404.0552 1.185884241 1.701796379 1.349907606 1.355319408 1.699220761 1.556238596 1.428778597 1.802652083 1 16.75243364 -0.433283087 9.734887879 1.000000001 1.50987082 0.41822741 0.189025947 0 0 0.162282234 0.038250289 0.368737166 0.433283087 0.509870819 WVNPHKL ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WVNPHKL 7 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 83.614 0.035516 512780000 337810 2246000 359220 377080 2598300 352890 348270 1999880 1569670 FALSE TRUE 316667.0751 2412296.177 367740.868 386756.5112 2394239.999 454763.6143 296050.1467 2249569.42 1307681.937 0.242159096 1.844711707 0.281215835 0.295757325 1.830903932 0.347763169 0.226393084 1.720272612 1 20.31858025 3.953022681 24.57844238 0.738049455 1.146036105 0.004428856 0.695324663 924.0203554 942420.7427 0.166122099 0.299684514 8974.756649 -3.953022681 0.40798665 WVPEITHHCPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WVPEITHHCPK 11 0 A0A590UJK8;P60953-1;P60953;A0A494C1M1;Q5JYX0;A0A494BZX6 A0A590UJK8 CDC42 Cell division control protein 42 homolog 0 128.01 0.00015881 954040000 556710 522590 443910 491870 637170 481520 526710 569420 635990 FALSE TRUE 521866.5149 561283.1074 454439.7548 504492.2169 587129.2384 620527.0072 447734.7252 640513.3404 529839.1603 0.984952706 1.059346212 0.857693785 0.952161061 1.1081273 1.171161087 0.845038945 1.208882598 1 19.01519495 2.762410535 24.14380437 1.048276048 0.961865614 0.167342797 0.110098289 1081.723545 1095050.399 0.032931882 0.034908743 578.6427748 -2.762410535 -0.086410434 WVPFDGDDIQLEFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WVPFDGDDIQLEFVR 15 0 A0A0C4DGS1;P39656-2;P39656-3;P39656 A0A0C4DGS1 DDOST Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit 0 ; 216.68 5.06E-12 111790000 87857 123836 79736 91189 120547 72080 109003 120329 82237 FALSE TRUE 82358.1872 133004.9463 81627.37557 93529.06412 111079.7249 92888.32588 92659.01208 135352.3405 68511.11343 1.202114271 1.941363082 1.191447219 1.365166313 1.621338777 1.355813987 1.352466884 1.975626052 1 16.06405041 -2.039296759 2.697011987 0.368319989 1.494884276 0.246390483 0.275012133 70849825.25 62266365.66 274379327.3 0.060224294 0.009134888 2.039296759 1.126564287 WVTYFNKPDIDAWELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WVTYFNKPDIDAWELR 16 1 H3BRI0;H3BNX8;P20674 H3BRI0 COX5A "Cytochrome c oxidase subunit 5A, mitochondrial" 0 ; 199.49 3.46E-11 377370000 589980 645070 472320 354330 846050 525490 548710 789790 584630 FALSE TRUE 553054.2049 692831.654 483523.6534 363422.7077 779604.6458 677190.4324 466436.0295 888397.02 487051.4761 1.135514893 1.422501908 0.992756776 0.746168989 1.600661704 1.390387804 0.957672961 1.824031059 1 18.89371473 2.721156639 24.94733097 1.322112442 1.118700157 0.16483879 0.301471508 1966.440084 2818743.928 0.094554416 0.089334108 526.2070216 -2.721156639 -0.203412284 WVTYFNKPDIDAWELRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WVTYFNKPDIDAWELRK 17 2 H3BRI0;H3BNX8;P20674 H3BRI0 COX5A "Cytochrome c oxidase subunit 5A, mitochondrial" 0 162.15 1.62E-09 272330000 378910 342320 308140 224410 563240 256230 333150 439800 675370 FALSE TRUE 355194.6995 367665.729 315449.2263 230168.7405 519005.4024 330199.4415 283197.2503 494709.9981 562646.3839 0.631292957 0.653457908 0.560652721 0.409082413 0.922436218 0.586868504 0.503330792 0.879255625 1 19.10186897 1.084388908 4.890493318 0.996126211 0.607514974 0.529957889 0.131560503 0.138486634 5.323396022 0.118237626 0.029991332 12.14475919 -1.084388908 -0.388611237 WVVIGDENYGEGSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 WVVIGDENYGEGSSR 15 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ;;;; 370.72 1.11E-71 406876000 353381 377798 328632 342262 446537 374002 333880 350932 515084 FALSE TRUE 331263.514 405770.557 336427.3062 351045.0224 411467.7853 481970.306 283817.7936 394746.6327 429113.1528 0.771972408 0.945602703 0.784006046 0.818070991 0.958879453 1.123177658 0.661405486 0.919912685 1 18.7109986 2.755190785 24.08762982 0.907133674 0.841543482 0.124678674 0.123851346 1635.622979 2369080.64 0.037926721 0.040105412 569.1028818 -2.755190785 -0.065590193 WWAAS(ph)PAPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WWAASPAPAR 10 0 Q8NC56;H7C2Z0 Q8NC56 LEMD2 LEM domain-containing protein 2 1 WWAAS(1)PAPAR;WWAAS(1)PAPAR 95.618 0.0076567 123430000 274513 306380 267297 272732 321980 221659 350020 282838 302791 TRUE FALSE 257331.7213 329064.694 273637.4111 279730.7649 296692.9896 285648.355 297537.7504 318150.9469 252253.226 1.020132529 1.30450143 1.084772692 1.108928394 1.17617124 1.132387322 1.1795201 1.261236385 1 17.94451319 WWDNLNHLNQFVDHEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WWDNLNHLNQFVDHEK 16 0 Q13907;Q13907-2 Q13907 IDI1 Isopentenyl-diphosphate Delta-isomerase 1 0 ; 312.66 6.02E-58 463450000 820430 641220 814270 730310 717140 554810 726330 680180 581830 FALSE TRUE 769080.7508 688696.596 833584.8689 749050.991 660818.7172 714974.6404 617423.5594 765101.9703 484718.8142 1.586653392 1.42081672 1.719728726 1.545330961 1.363303214 1.475029686 1.273776757 1.578444962 1 18.88678856 -3.056440882 0.181765566 0.044050798 1.621430788 0.629441582 0.121530994 37.5414296 0.689810714 14.09894077 0.390020797 0.000878131 3.056440882 1.57737999 WWGNRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WWGNRK 6 1 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9R4 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 119.22 0.033985 1124800000 799650 1386580 822420 897780 1501700 592150 1097140 1156660 1610830 FALSE TRUE 749601.3339 1489243.826 841928.1908 920818.5547 1383762.54 763094.0922 932634.0423 1301071.547 1341972.067 0.55858192 1.10974279 0.627381308 0.686168198 1.03114109 0.568636346 0.694972768 0.969522078 1 20.35592321 1.187604592 8.491345625 0.987897808 0.770525447 0.211371176 0.183306616 0.527727558 77.97171596 0.16533582 0.041801232 15.40297434 -1.187604592 -0.217372361 WYNHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 WYNHIK 6 0 P24534;C9JZW3;F2Z2G2 P24534 EEF1B2 Elongation factor 1-beta 0 ; 95.445 0.043338 1825920000 3028100 5524200 2445200 2405000 6360700 1807370 2972600 5138900 6479800 FALSE TRUE 2838576.626 5933217.516 2503201.299 2466716.372 5861156.28 2329128.379 2526886.226 5780502.977 5398279.519 0.525829872 1.099094164 0.463703536 0.456944914 1.085745238 0.431457536 0.468091031 1.070804681 1 22.36406825 1.222795835 24.87961198 1.035402769 0.661656405 0.292358406 0.25026874 349.3158842 551266.0433 0.232100259 0.058826434 16.70305209 -1.222795835 -0.373746364 WYPEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 WYPEVR 6 0 P63000;J3KSC4;J3QLK0;P60763;P63000-2 P63000 RAC1;RAC3 Ras-related C3 botulinum toxin substrate 1;Ras-related C3 botulinum toxin substrate 3 0 98.513 0.092707 117210000 193750 327400 166500 175970 378910 175160 216060 324690 306850 FALSE TRUE 181623.5334 351641.0367 170449.4586 180485.6881 349151.937 225725.8485 183663.8088 365228.2612 255634.7527 0.710480603 1.375560377 0.666769509 0.706029545 1.365823439 0.883001416 0.718461817 1.428711306 1 17.96372445 Y(ph)ATPQVIQAPGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YATPQVIQAPGPR 13 0 A0A5F9ZHP4;C9J1X3;A0A5F9ZI29;A0A5F9ZGX5;A0A5F9ZHJ2;A0A499FJ16;Q07912;Q07912-3;A0A5F9ZHD0 A0A5F9ZHP4 TNK2 Activated CDC42 kinase 1 1 Y(1)ATPQVIQAPGPR 194.12 1.33E-05 112190000 41425 52158 48125 61025 71096 47447 53313 46360 46487 TRUE FALSE 38832.2832 56019.83259 49266.54773 62591.00482 65512.40695 61144.17866 45319.21058 52148.14805 38728.01938 1.002692206 1.446493611 1.272116378 1.616168495 1.691602307 1.578809855 1.170191797 1.346522463 1 15.2410901 0.944756596 1.262087038 1.013755221 1.419751979 0.268716483 0.207649517 0.714199212 2.306001105 0.193108893 0.059259089 8.805552206 -0.944756596 0.405996758 Y(ph)FQRITLY(ph)LMEKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YFQRITLYLMEKK 13 2 P01570;P01567 P01570 IFNA14;IFNA7 Interferon alpha-14;Interferon alpha-7 2 Y(0.897)FQRIT(0.103)LY(1)LMEKK 49.12 0.059193 109130000 22884 88084 65010 68431 70947 153340 26946 50066 19798 TRUE FALSE 21451.73129 94605.83101 66552.0679 70187.05531 65375.10881 197606.7687 22905.69745 56316.85031 16493.5859 1.300610517 5.73591647 4.03502721 4.25541515 3.963668617 11.98082515 1.388763947 3.414469761 1 14.00961747 4.750438162 23.23050286 4.692982455 1.300604918 0.094870616 3.010116436 1513.226855 2959466.912 0.655306188 9.985437985 56290.89604 -4.750438162 -3.392377537 Y(ph)QQCKTEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YQQCKTEIK 9 1 C9J524;F8W927;F8VWP7;B9A061;Q9BXY5 C9J524 CAPS2 Calcyphosin-2 1 Y(0.851)QQCKT(0.149)EIK 101.11 0.06572 90728000 192520 306150 304620 300660 303390 281020 362120 314230 286260 TRUE FALSE 180470.5169 328817.6645 311845.7303 308375.4446 279562.9732 362145.912 307823.4678 353462.3072 238481.3567 0.756748952 1.378798197 1.307631484 1.293079882 1.17226343 1.518550201 1.290765333 1.48213811 1 17.86351696 4.742016164 24.87510144 1.322948614 0.756748723 0.575084288 0.14752959 197.4048858 1420971.122 0.03015495 0.22123468 55209.79874 -4.742016164 -0.566199891 Y(ph)RY(ph)QRRS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YRYQRRSR 8 3 Q9Y698 Q9Y698 CACNG2 Voltage-dependent calcium channel gamma-2 subunit 3 Y(1)RY(1)QRRS(1)R 43.651 0.053694 372410000 20464 29259 34566 28070 31747 25180 37540 35819 38951 TRUE FALSE 19183.19477 31425.3668 35385.92184 28790.32372 29253.71868 32449.05724 31911.2255 40291.081 32449.82647 0.591164788 0.968429426 1.090481081 0.887225815 0.901506167 0.999976295 0.983402039 1.241642418 1 14.98592314 4.738279547 3.932709226 1.007697784 0.552259792 0.640268522 0.098929445 0.152614951 4.845803065 0.022677905 0.199604439 54736.81797 -4.738279547 -0.455437992 Y(ph)Y(ph)S(ph)QPRSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YYSQPRSYR 9 1 A0A1W2PNU3 A0A1W2PNU3 3 Y(1)Y(1)S(1)QPRSYR 68.893 0.075975 449510000 0 25330 20590 17194 18332 11348 12230 15145 16733 TRUE FALSE 0 27205.45956 21078.40452 17635.22715 16892.27867 14623.98338 10396.22504 17035.88659 13940.1542 0 1.951589571 1.512063943 1.265066863 1.211771292 1.049054635 0.745775469 1.222073038 1 13.7669589 2.39475742 2.073084156 0.951157376 1.36585387 0 0.511946951 0.707885352 6.223867017 0.208988375 0.15997418 248.1746509 -2.39475742 0.414696494 YAALSVDGEDENEGEDYAE ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YAALSVDGEDENEGEDYAE 19 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 318.7 1.86E-61 133940000 234170 259920 261230 256530 283330 236890 274640 231691 255090 FALSE TRUE 219513.7177 279164.7472 267426.499 263112.9941 261078.4047 305276.2974 233460.2816 260618.1314 212513.8311 1.032938499 1.313630957 1.258395737 1.238098211 1.228524296 1.436500843 1.098565117 1.226358445 1 17.69719721 0.724344693 1.114796363 1.002569832 1.250803191 0.296491315 0.109464507 1.03608012 2.240132961 0.093589493 0.029303085 5.300839968 -0.724344693 0.248233358 YADEEIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 161.9 0.00080229 481510000 481590 548980 539190 492530 542980 388250 523180 482220 529470 FALSE TRUE 451448.1416 589627.0504 551979.8414 505169.1537 500336.5411 500331.4723 444734.016 542426.2285 441098.0365 1.02346441 1.336725629 1.251376782 1.145253689 1.13429782 1.134286328 1.008243019 1.229718075 1 18.75073981 2.891469821 1.695173029 1.089926351 1.238269407 0.142591998 0.102269953 0.44695882 2.576444529 0.035357444 0.03881591 778.8786887 -2.891469821 0.148343057 YADEEIPRS(ph)PFK ddPTM_SK-BR-3_Pertuzumab_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 206.43 5.46E-08 1487050000 2838460 2025170 2526180 2657340 2749690 1828520 2906610 2076630 3345160 TRUE FALSE 2660805.855 2175115.694 2586102.183 2725531.843 2533740.439 2356384.04 2470790.814 2335901.827 2786831.185 0.954778269 0.78049783 0.927972314 0.978003927 0.909183323 0.84554244 0.886595079 0.838192797 1 21.41019418 3.745281012 22.99856059 0.904940699 0.854903089 0.058230443 0.065620249 371.691686 470724.4015 0.015872443 0.0285167 5562.640737 -3.745281012 -0.05003761 YADLSHNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YADLSHNR 8 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;;;; 140.5 0.00064854 1860950000 1967147 3780040 2011151 2093406 3853350 1540809 2115185 3443910 3413630 FALSE TRUE 1844026.781 4059918.095 2058856.451 2147126.342 3550723.435 1985615.545 1798032.646 3873889.744 2843873.1 0.648420909 1.427601708 0.723962139 0.755000757 1.248551996 0.69820821 0.632247847 1.362187977 1 21.43942566 3.843222959 9.179184056 0.88063314 1.090708984 0.009345199 0.302940324 0.731085207 54.07335509 0.072089347 0.130201011 6969.842415 -3.843222959 0.210075845 YADLTEDQLPSCESLKDTIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YADLTEDQLPSCESLKDTIAR 21 1 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;; 254.71 1.95E-36 5524840000 5300010 4509580 4446300 4500510 5173020 3591480 6045770 4086470 5728090 FALSE TRUE 4968291.835 4843473.995 4551768.336 4616000.706 4766751.876 4628281.973 5139262.915 4596674.775 4772034.774 1.041126494 1.01497039 0.953842239 0.967302403 0.998892946 0.969875995 1.076954205 0.963252573 1 22.18617313 YADVIVHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YADVIVHR 8 0 Q9Y2L1;G3V1J5;Q9Y2L1-2 Q9Y2L1 DIS3 Exosome complex exonuclease RRP44 0 87.616 0.018317 0 48708 48351 53235 49158 53278 57138 72350 52643 51943 FALSE TRUE 45659.45323 51930.95835 54497.75934 50419.4775 49093.76079 73632.81304 61501.78916 59215.59443 43273.37774 1.055139571 1.200067133 1.259383071 1.165138479 1.134502629 1.701573043 1.42123847 1.368407033 1 15.40119212 2.318294865 24.99999885 1.419899355 1.181188703 0.235902873 0.177359494 34.90636762 10942.31999 0.055307806 0.046273814 208.1109178 -2.318294865 -0.238710652 YAEAVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YAEAVTR 7 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;;; 154.01 0.0039719 4306820000 2815010 3767400 2883170 2955910 3416220 2040570 3525390 2949230 3341270 FALSE TRUE 2638823.549 4046342.216 2951560.154 3031763.655 3147923.862 2629649.433 2996790.498 3317447.858 2783590.452 0.947992744 1.453641362 1.060342822 1.089155789 1.13088614 0.944696958 1.076591744 1.191787339 1 21.40851553 3.726155931 24.95556656 1.069574958 1.24295201 0.117909724 0.137856192 58.5196362 1512896.912 0.032527081 0.053758551 5322.993444 -3.726155931 0.173377052 YAEEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YAEEDR 6 0 P38646;H0Y8S0 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 97.071 0.096521 306320000 354890 346030 322820 300480 420420 322920 291850 356880 438980 FALSE TRUE 332678.0684 371650.4212 330477.4428 308190.8255 387401.9091 416141.7618 248089.8019 401437.2536 365711.4021 0.909673766 1.016239634 0.903656383 0.842715933 1.059310448 1.137896602 0.678375901 1.097688645 1 18.48034608 YAEEDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YAEEDRR 7 1 P38646;H0Y8S0 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;;; 156.16 0.0025054 7847250000 6493050 6483740 5574490 5683960 8619010 5705800 5180740 6585260 9060580 FALSE TRUE 6086661.591 6963802.856 5706719.535 5829820.037 7942107.722 7352971.834 4403936.133 7407444.207 7548310.664 0.806360769 0.922564421 0.756026055 0.772334406 1.052170224 0.974121517 0.583433344 0.981338015 1 22.84772237 5.087045362 12.66965579 0.8531223 0.214086836 0 0.143674757 3539219.616 12227380.59 0.033359579 59702457.17 122192.7285 -5.087045362 -0.639035464 YAELLEEHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YAELLEEHR 9 0 P40222 P40222 TXLNA Alpha-taxilin 0 ;;; 131.44 0.00033308 563386000 522358 722249 569948 571624 759950 454912 616305 617772 843130 FALSE TRUE 489664.5452 775725.0675 583467.4357 586292.8396 700266.5925 586237.7095 523895.7867 694902.1941 702406.1562 0.697124507 1.104382501 0.830669593 0.834692057 0.996953951 0.83461357 0.745858763 0.989316776 1 19.42194596 3.734149324 24.78639658 0.870943361 0.941148167 0 0.130231286 827.4549601 2918221.271 0.031163925 0.054739217 5421.872787 -3.734149324 0.070204805 YAEYFLRPMLQYVCDNSPEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YAEYFLRPMLQYVCDNSPEVR 21 1 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ; 240.59 5.22E-30 225720000 268020 303630 247240 236450 309920 209104 313790 281180 268110 FALSE TRUE 251245.1066 326111.0811 253104.6496 242517.7073 285580.1334 269468.9303 266740.1026 316285.942 223360.7089 1.124840209 1.460019905 1.133165501 1.085767092 1.278560292 1.206429419 1.194212285 1.416032137 1 17.7690159 -1.520630519 2.877618336 0.990007243 1.239892749 0.274021659 0.121365034 33832649.16 38220075.48 2666688.136 0.028768824 0.030155705 1.520630519 0.249885506 YAGKDGYNYTLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YAGKDGYNYTLSK 13 1 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ; 151.72 4.09E-05 1199450000 431370 797220 511520 635060 1301070 385170 664100 524180 2548680 FALSE TRUE 404371.3217 856246.9983 523653.496 651356.7148 1198889.21 496362.3263 564524.3702 589625.0269 2123288.843 0.190445743 0.403264493 0.246623768 0.306767832 0.564637833 0.233770515 0.265872621 0.277694214 1 21.01786921 -1.745892509 2.746686276 1.137475162 0.313989966 0.807227917 0.105785767 24456699.25 19930171.95 22873145.12 0.024598125 0.017951779 1.745892509 -0.823485196 YAGLLFSSRPDAHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YAGLLFSSRPDAHDR 15 1 A0A087WYJ2;M0R2B7;P28340;M0QZR8;M0QXE6;M0QXQ2 A0A087WYJ2 POLD1 DNA polymerase;DNA polymerase delta catalytic subunit 0 65.092 0.037596 155090000 172870 186650 198690 167730 213350 125220 221670 184850 188140 FALSE TRUE 162050.3753 200469.7602 203403.0206 172034.2358 196594.3516 161368.9812 188432.6414 207928.9294 156738.2186 1.033891904 1.279010072 1.297724464 1.097589582 1.254284714 1.029544566 1.202212473 1.326600055 1 17.25799748 3.23785523 24.99909343 1.160673957 1.233168453 0.016948189 0.120642108 50.55022007 1791548.068 0.031929352 0.040393174 1729.239831 -3.23785523 0.072494496 YAHDLK ddPTM_SK-BR-3_Pertuzumab_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 157810000 243270 214040 221220 215470 262000 186410 265000 222200 270010 FALSE TRUE 228044.1649 229887.7443 226467.4429 220999.325 241423.5769 240223.5409 225265.7101 249942.1591 224943.5867 1.013783804 1.021979545 1.006774393 0.982465552 1.07326277 1.067927939 1.001432019 1.11113263 1 17.77920371 2.737333823 24.99997238 1.048152112 1.008959539 0.294534821 0.033975594 153.2342026 3122622.924 0.00997509 0.009820556 546.1775218 -2.737333823 -0.039192573 YAHQSGFHVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YAHQSGFHVDR 11 0 A0A0A0MSX9;P41252;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;;;; 184.87 2.73E-06 2536740000 320989 1028535 769782 850183 932642 728946 914777 942204 740795 FALSE TRUE 300898.8715 1104688.802 788041.5926 872000.1351 859396.0594 939380.8768 777614.6812 1059840.243 617151.5288 0.487560765 1.789979851 1.276901305 1.412943328 1.392520344 1.522123551 1.260006084 1.717309597 1 19.23526523 4.752288102 24.99995449 1.43425529 0.487560137 0.627079928 0.226145811 1426.145338 2597194.979 0.047821193 0.968737017 56531.18661 -4.752288102 -0.946695153 YAHVVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YAHVVLR 7 0 P62269 P62269 RPS18 40S ribosomal protein S18 0 ;;; 154.29 0.0016884 2576920000 3681230 4076820 4100900 3887420 4069630 3156820 4360830 3832730 3536040 FALSE TRUE 3450828.385 4378671.995 4198175.285 3987177.779 3750017.676 4068142.687 3706964.025 4311254.777 2945852.08 1.171419437 1.48638556 1.425114082 1.353488794 1.27298234 1.380973171 1.258367333 1.463500088 1 21.49025356 -3.221078492 0.351643253 1.52E-12 1.375991903 0.532958782 0.100372235 80.83767159 2.152480502 59.78203864 0.073133326 0.000601065 3.221078492 1.375991903 YALPLVGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YALPLVGHR 9 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 143.85 0.00010096 1246950000 1384830 1923340 1599420 1643930 1816280 1278900 1799630 1547970 1399980 FALSE TRUE 1298155.962 2065746.095 1637358.998 1686116.027 1673636.695 1648097.669 1529792.188 1741237.462 1166314.294 1.113041287 1.771174465 1.403874587 1.445678953 1.434979151 1.413081943 1.311646609 1.492940172 1 20.15352518 -3.293982816 0.228503574 1.70E-11 1.509404843 0.362134265 0.167315094 62.2573983 1.254206987 29.65476654 0.281626312 0.00050818 3.293982816 1.509404843 YALQMEQLNGILLHLESELAQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YALQMEQLNGILLHLESELAQTR 23 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;; 342.25 3.16E-87 10645491000 3258283 4184588 3863685 3671951 4653326 3578730 4414947 3829665 4777434 FALSE TRUE 3054352.883 4494419.25 3955333.433 3766179.479 4287872.547 4611851.255 3752966.684 4307807.105 3980049.402 0.767415822 1.129237051 0.993790035 0.946264506 1.077341539 1.158742214 0.942944749 1.08235016 1 21.92435491 4.750616076 24.59342463 1.039733417 0.767415613 0.585513223 0.07241745 1086.836762 2217121.886 0.01650486 0.275594286 56313.96099 -4.750616076 -0.272317804 YALTGDEVKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YALTGDEVKK 10 1 P62701;C9JEH7;P22090;Q8TD47 P62701 RPS4X;RPS4Y1;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1;40S ribosomal protein S4, Y isoform 2" 0 ;;; 190.86 1.37E-06 2551970000 5025400 3382100 4052310 3798420 3968340 2787600 4862340 3270150 4485610 FALSE TRUE 4710869.185 3632514.203 4148432.707 3895893.888 3656682.584 3592334.867 4133277.257 3678435.426 3736932.713 1.260624567 0.972057696 1.110117047 1.042537875 0.978525134 0.96130574 1.106061461 0.984346176 1 21.83342316 4.747186034 24.96119843 1.028455741 1.260624688 0.664156661 0.053570139 693.3424269 2006428.311 0.012374737 0.144993913 55870.94715 -4.747186034 0.232168947 YALYDASFETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YALYDASFETK 11 0 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;;;;; 221.68 1.92E-11 3958620000 3256830 2699930 2873930 2750410 3278780 2667430 3213490 2441140 3842590 FALSE TRUE 3052990.824 2899835.626 2942100.977 2820990.177 3021277.845 3437473.739 2731657.007 2745921.703 3201236.905 0.953691 0.905848493 0.919051312 0.88121881 0.943784523 1.073795486 0.853312981 0.857768976 1 21.61019802 5.641848 4.463416008 0.924924512 22.10070179 0.009021373 0.066755268 21140.53729 439.6492292 0.016270186 4580924.247 438377.2418 -5.641848 21.17577728 YALYDATYETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YALYDATYETK 11 0 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;Q9Y281;Q9Y281-3 G3V1A4;P23528;Q9Y281 CFL1;CFL2 Cofilin-1;Cofilin-2 0 ;;;; 290.04 4.70E-35 2661740000 5134910 4289520 4470070 4295640 5034290 3475780 5327680 4206180 5753060 FALSE TRUE 4813525.149 4607120.524 4576102.171 4405873.395 4638917.171 4479181.261 4528843.844 4731330.832 4792837.12 1.004316447 0.961251219 0.954779405 0.919262075 0.96788542 0.934557372 0.944919206 0.98716704 1 22.19244848 1.111520016 4.744116514 0.999163397 0.95369343 0.342491808 0.022285113 0.210366104 7.174650659 0.020146259 0.005130205 12.9276628 -1.111520016 -0.045469967 YASFQVENDQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YASFQVENDQER 12 0 P53992;G5EA31 P53992 SEC24C Protein transport protein Sec24C 0 183.99 3.47E-05 127040000 42803 54399 58655 52913 65472 45798 60185 55603 66429 FALSE TRUE 40124.03664 58426.75856 60046.3243 54270.83716 60330.09322 59019.13913 51160.81798 62545.15695 55341.57075 0.725025258 1.055748107 1.085013011 0.980652273 1.090140601 1.066452186 0.924455473 1.130165915 1 15.75607597 4.740349254 24.96778153 1.039589057 0.725025151 0.73500404 0.059723703 79.39224648 1108154.864 0.013701504 0.088316665 54998.2985 -4.740349254 -0.314563906 YASICQQNGIVPIVEPEILPDGDHDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 289.14 1.89E-70 7320747000 7080171 5421193 5174952 4535394 5931703 3893255 6402034 5142863 3825295 FALSE TRUE 6637035.736 5822583.77 5297704.305 4651779.888 5465850.974 5017174.517 5442108.435 5784960.766 3186828.552 2.082646 1.827077822 1.66237506 1.45968941 1.71513807 1.574347171 1.707687862 1.81527204 1 21.60368998 -2.562787636 0.24282021 1.53E-32 1.812517442 0.664477538 0.16360875 29.1751244 0.833253313 16.33223315 0.266119401 0.002736607 2.562787636 1.812517442 YASICQQNGIVPIVEPEILPDGDHDLKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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 ;;;;;;; 234.55 6.98E-45 35251144000 9596468 7652248 8326649 8561416 8488661 5962814 10454650 6600287 8593705 FALSE TRUE 8995842.198 8218828.404 8524161.046 8781116.429 7821995.807 7684181.604 8887072.289 7424347.361 7159360.118 1.256514835 1.147983656 1.190631691 1.226522522 1.092555155 1.073305641 1.241322149 1.037012699 1 22.77139922 -4.999999948 0.108985355 0.443271954 1.264619503 0.487106142 0.063545397 154.5636369 1.123520863 18.99581547 0.781211108 1.00E-05 4.999999948 0.821347549 YASS(ph)PKPNNSYMFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YASSPKPNNSYMFK 14 1 Q86VQ1;H7C0B2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 YAS(0.086)S(0.914)PKPNNSYMFK 157.91 3.13E-06 420020000 692880 521480 488240 466770 730350 331630 603990 557670 991120 TRUE FALSE 649513.8776 560090.9218 499821.2834 478748.1084 672991.2571 427366.1974 513427.3067 627296.3271 825695.6691 0.786626238 0.678326099 0.605333541 0.57981182 0.815059691 0.517583189 0.621811796 0.759718563 1 19.65525061 0.913094139 3.709596778 0.999756403 0.64987124 0.592578146 0.08954266 0.241587798 7.738663626 0.079826499 0.020524106 8.186422198 -0.913094139 -0.349885163 YATDTFAGLCHQLTNALVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YATDTFAGLCHQLTNALVER 20 0 Q9UNS2-2;Q9UNS2;H7C3P9;J3QKR0;K7ES36;C9JLV5 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 0 ; 287.37 2.00E-45 314240000 433610 478800 455680 458800 518970 453060 526800 414620 463240 FALSE TRUE 406471.1241 514250.8502 466488.9448 470573.5847 478212.1896 583851.0672 447811.2306 466386.2197 385922.2514 1.053246147 1.332524487 1.208764053 1.219348154 1.239141272 1.512872256 1.160366444 1.208497872 1 18.5579507 -0.633562573 6.943455531 0.999997347 1.251579489 0.286859389 0.118960634 0 0 0.104228512 0.024566896 0.232507747 0.633562573 0.251582142 YAVTTGDHGIIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YAVTTGDHGIIR 12 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;;;;; 268.98 3.47E-22 1292436000 1029308 1525220 1183516 1213561 1559730 908688 1216768 1315766 1377140 FALSE TRUE 964885.4496 1638148.876 1211589.558 1244703.03 1437235.097 1171011.474 1034324.934 1480042.281 1147286.437 0.841015302 1.427846458 1.056048009 1.084910437 1.252725606 1.020679262 0.901540279 1.290037286 1 20.1297942 2.211805201 24.77133772 1.028639966 1.160192338 0.026760022 0.177624776 434.086335 401893.3078 0.06222716 0.045970384 162.8565389 -2.211805201 0.131552372 YAWQGVALLPFVDER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YAWQGVALLPFVDER 15 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 162.32 3.73E-06 139251000 306700 469510 340440 319630 456290 249420 335610 402780 432240 FALSE TRUE 287504.1945 504273.0089 348515.3976 327832.2469 420454.824 321423.505 285288.3962 453067.9696 360096.3516 0.798409074 1.400383555 0.967839291 0.910401467 1.167617561 0.89260417 0.792255725 1.258185393 1 18.45802346 3.722872605 24.60881343 0.975549043 1.154909579 0.016985589 0.197062172 283.2582854 1640688.05 0.048173766 0.077651361 5282.902619 -3.722872605 0.179360536 YAYDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YAYDKR 6 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 110.24 0.046296 525570000 506370 1434410 430720 432220 1620650 259760 520310 1388710 1590780 FALSE TRUE 474677.2056 1540615.209 440936.8818 443311.4969 1493370.686 334748.4951 442294.3458 1562093.5 1325268.541 0.358174355 1.162492854 0.33271512 0.334506919 1.126843836 0.252589181 0.333739414 1.178699601 1 20.33785329 1.227589961 24.99652186 1.089350125 0.579051639 0.305724997 0.332076539 313.0651897 713292.4206 0.30000191 0.077916003 16.88845655 -1.227589961 -0.510298487 YAYLNVVGMVGSIDNDFCGTDMTIGTDSALHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YAYLNVVGMVGSIDNDFCGTDMTIGTDSALHR 32 0 Q01813;Q01813-2;Q5VSR5 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 112.33 3.09E-06 16303000 16167 20886 15713 17563 20475 16121 21111 17251 9311.6 FALSE TRUE 15155.13633 22432.42117 16085.71978 18013.69631 18866.97609 20774.871 17945.60153 19404.82532 7757.433805 1.953627541 2.891732206 2.073587759 2.322120532 2.432115641 2.678059719 2.313342529 2.501449037 1 12.92136377 -1.279915787 6.642523495 0.999976689 2.415242969 0.725908773 0.269300201 8.36E-05 9.07E-06 0.234522048 0.055276473 0.052490923 1.279915787 1.415266279 YCDPDSYHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YCDPDSYHR 9 0 P26368-2;P26368;K7ENG2 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ;;; 169.09 5.87E-05 3077350000 4047570 4951970 4283780 4476130 5103170 4368130 5157950 4698830 4823930 FALSE TRUE 3794239.819 5318619.011 4385393.285 4590995.074 4702387.613 5629138.22 4384563.282 5285489.269 4018784.919 0.944126121 1.323439576 1.091223684 1.142383871 1.170101836 1.400706515 1.091017153 1.315195855 1 21.93832794 2.460859111 24.99955597 1.213716403 1.152999711 0.042366698 0.142439104 882.7564006 1357039.988 0.044526496 0.037261581 288.974227 -2.460859111 -0.060716692 YCDPDSYHRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YCDPDSYHRR 10 1 P26368-2;P26368;K7ENG2 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 70.1 0.035699 703520000 344670 520920 430120 424270 538690 376230 473720 426320 720300 FALSE TRUE 323097.72 559489.4588 440322.6495 435157.4865 496383.4604 484841.4934 402690.0838 479546.9904 600077.2767 0.538426854 0.932362348 0.733776576 0.72516908 0.827199229 0.807965094 0.67106371 0.799142059 1 19.19478877 0.967159646 22.73989395 1.000000004 0.763159492 0.361209326 0.103296367 1548.712943 1072389.398 0.09141678 0.022854195 9.271705875 -0.967159646 -0.236840512 YCFPNYVGRPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YCFPNYVGRPK 11 1 P61163;R4GMT0;A0A1B0GVS3;P42025 P61163;P42025 ACTR1A;ACTR1B Alpha-centractin;Beta-centractin 0 ; 215.93 1.14E-11 724830000 1033720 1062170 982310 1003250 1294640 658300 1101520 984670 1617080 FALSE TRUE 969021.3104 1140814.172 1005610.857 1028995.093 1192964.197 848340.5234 936357.302 1107608.217 1347178.901 0.71929668 0.846817131 0.746456804 0.763814734 0.885527672 0.629716308 0.69505045 0.822168619 1 20.36151002 0.970026002 14.91010178 1.000000002 0.758633096 0.536324028 0.071696439 10.96190674 5453.734989 0.069511024 0.017378336 9.333101789 -0.970026002 -0.241366906 YCLS(ph)ILTSHVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YCLSILTSHVK 11 0 O95163;F5H2T0 O95163 IKBKAP Elongator complex protein 1 1 Y(0.258)CLS(0.305)ILT(0.219)S(0.219)HVK;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;Y(0.22)CLS(0.26)ILT(0.26)S(0.26)HVK 58.223 0.069361 11430900000 9417200 3736540 5254900 5859100 5502500 12922900 12082800 3433460 8314000 TRUE FALSE 8827794.262 4013197.309 5379548.71 6009454.425 5070355.846 16653531.44 10271096.31 3862135.039 6926339.69 1.274525169 0.579410986 0.776679884 0.867623405 0.732039731 2.404376942 1.482903925 0.557601159 1 22.72366171 YCPDNLEVYFEDEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YCPDNLEVYFEDEDR 15 0 O95801 O95801 TTC4 Tetratricopeptide repeat protein 4 0 187.57 2.10E-11 0 17761 17551 19932 20485 17796 15526 19658 15412 14830 FALSE TRUE 16649.37071 18850.4943 20404.79645 21010.67978 16398.37395 20008.10416 16710.4654 17336.22213 12354.77719 1.347605906 1.525765621 1.651571383 1.700611792 1.327290139 1.619462969 1.352550931 1.4031999 1 13.59278137 0.668132874 0.706869274 0.99586251 1.550796558 0.619309277 0.126108012 0.739609798 0.698594784 0.122798978 0.043989488 4.657285632 -0.668132874 0.554934048 YCPEGVHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YCPEGVHK 8 0 Q99986;H0YJ50 Q99986 VRK1 Serine/threonine-protein kinase VRK1 0 72.547 0.045871 145260000 662760 511730 572680 537820 567500 571280 935250 546600 781340 FALSE TRUE 621279.0347 549619.0217 586264.24 551621.3717 522930.8392 736199.262 795017.9449 614844.2132 650929.3064 0.954449321 0.844360542 0.900657313 0.847436682 0.803360417 1.13099726 1.221358352 0.944563729 1 19.31214134 2.232191944 24.99998786 1.107832368 0.86969468 0.574048078 0.08523743 89.03841165 349513.6091 0.029800691 0.022542143 170.6836588 -2.232191944 -0.238137689 YCQVIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YCQVIR 6 0 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ;; 113.07 0.061539 1331840000 764480 926820 809040 810610 980540 684460 936890 867570 953790 FALSE TRUE 716632.5614 995442.7172 828230.8109 831411.625 903532.3437 882052.4907 796412.0422 975888.0243 794596.2873 0.901882595 1.252765377 1.042329072 1.046332129 1.137096105 1.110063695 1.002285129 1.228155782 1 19.59986253 -2.044185858 3.602920114 0.86364791 1.094506933 0.068794558 0.103072756 0.109189419 0.001339088 0.096526918 0.021030549 0.009032628 2.044185858 0.230859023 YCRPESQEHPEADPGSAAPYLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YCRPESQEHPEADPGSAAPYLK 22 1 P40763;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 ;;; 220.63 6.01E-26 2025420000 1966770 2399470 1787030 1681260 2830180 1470960 2287580 2487800 3153280 FALSE TRUE 1843673.376 2577129.255 1829419.195 1724403.978 2607909.079 1895602.273 1944578.616 2798407.306 2626977.197 0.701823137 0.981024601 0.69639706 0.656421373 0.992741422 0.721590684 0.740234296 1.065257555 1 21.32497225 1.235787135 24.99735257 1.032628891 0.79202696 0.440183368 0.116165664 69.36730896 625147.3648 0.091238784 0.026743477 17.21024826 -1.235787135 -0.240601931 YDAVQHCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YDAVQHCR 8 0 P49585;C9JEJ2;C9J050;H7C1T3;C9J2E1;H7BZN1 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 0 ; 107.66 0.0039594 317360000 617450 920300 659020 608870 1030180 487010 640830 799930 1200530 FALSE TRUE 578804.9067 988439.9696 674652.2656 624494.635 949273.8183 627601.8811 544743.4907 899803.0214 1000153.787 0.578715908 0.988287983 0.674548529 0.62439861 0.949127855 0.627505379 0.544659729 0.899664664 1 19.93179042 1.010173358 23.11166876 1.00000005 0.727245215 0.31734658 0.147601584 81.78075192 185786.0003 0.142262081 0.03556552 10.23701542 -1.010173358 -0.272754834 YDCGEEILITVLSAMTEEAAVAIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YDCGEEILITVLSAMTEEAAVAIK 24 0 P63241;P63241-2;Q6IS14 P63241 EIF5A;EIF5AL1 Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A-1-like 0 ;; 221.82 8.95E-33 895097000 468503 398388 464516 435528 487976 427740 551624 409544 520081 FALSE TRUE 439180.2335 427885.062 475534.5389 446704.3858 449652.3334 551221.5942 468913.1022 460676.4699 433276.1212 1.013626674 0.987557451 1.097532302 1.030992395 1.037796249 1.272217801 1.082250046 1.063239923 1 18.7249272 3.730523098 0.898604953 1.104106137 0.991887036 0.146035295 0.074856931 1.164546854 1.719113506 0.028572864 0.095756596 5376.790291 -3.730523098 -0.112219102 YDDAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 109.63 0.068384 758740000 2167600 2149490 2265120 2200550 2184490 2013340 2466000 1950370 1761010 FALSE TRUE 2031933.785 2308640.476 2318849.716 2257019.839 2012928.967 2594558.574 2096246.193 2193877.988 1467086.054 1.38501336 1.57362308 1.580581936 1.538437252 1.372059233 1.76851151 1.428850194 1.495398297 1 20.48452207 0.364766212 1.311417893 0.999772534 1.536843788 0.669981864 0.114248099 1.949591704 3.500830491 0.097593889 0.028789894 2.316147492 -0.364766212 0.537071254 YDDAERR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 130.27 0.0057394 5079220000 6568380 7588170 7106840 7104470 7502940 5576800 7687610 6248830 8811140 FALSE TRUE 6157276.821 8150006.002 7275417.601 7286782.728 6913689.358 7186731.628 6534924.249 7029010.181 7340503.812 0.838808477 1.110278833 0.991133277 0.992681554 0.941854883 0.979051549 0.890255549 0.957565088 1 22.80744765 2.860365678 1.919865078 0.942715859 1.010062746 0 0.072457213 0.638339112 4.668116287 0.024231616 0.026033904 725.0461955 -2.860365678 0.067346888 YDDMAACMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YDDMAACMK 9 0 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;E5RGE1 P63104 YWHAZ 14-3-3 protein zeta/delta 0 105.78 0.0078283 0 185210 216590 171350 169360 213300 121310 199040 195560 223390 FALSE TRUE 173618.0367 232626.549 175414.5029 173706.0643 196548.2784 156330.2277 169195.7998 219976.0965 186104.7658 0.932904839 1.249976313 0.942557823 0.93337784 1.056116309 0.840011952 0.909142756 1.182001415 1 17.50575548 3.759609963 7.592858961 0.965843098 1.109498863 0.117300792 0.119095254 0.313809917 60.47354166 0.028339482 0.050498259 5749.23371 -3.759609963 0.143655766 YDDMATCMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YDDMATCMK 9 0 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 137.13 0.0029895 0 116090 122360 115050 124300 143490 106830 153950 125780 163190 FALSE TRUE 108824.1341 131419.6617 117779.0403 127489.7484 132220.8742 137670.0868 130866.6267 141483.9099 135952.5348 0.800456824 0.966658415 0.866324711 0.937751905 0.97255174 1.012633468 0.962590561 1.040686076 1 17.05274352 2.821564531 2.189013258 0.996750532 0.895206207 0.583215896 0.045698594 0.241897688 2.282724985 0.014736964 0.015452464 663.0778659 -2.821564531 -0.101544325 YDDPPDWQEILTYFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YDDPPDWQEILTYFR 15 0 P61221;D6R9I9;D6RGF4;H0Y990 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 ; 153.39 6.19E-06 412650000 206035 189822 214226 189747 201824 172792 221319 180121 158631 FALSE TRUE 193139.6371 203876.6184 219307.5419 194616.2293 185973.5572 222674.2454 188134.2706 202609.5033 132154.4613 1.461468915 1.542714611 1.659478914 1.472642144 1.407243882 1.684954433 1.423593791 1.533126474 1 17.0118656 -2.684817653 0.379016773 1.79E-11 1.550300818 0.759630624 0.092190912 36.86586576 1.425467539 30.03738323 0.059306819 0.002066248 2.684817653 1.550300818 YDDYRDYDS(ph)PERER ddPTM_SK-BR-3_Pertuzumab_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 175.21 1.91E-06 1830320000 1315660 1635770 1371700 1568540 1845060 1097768 1581490 1329970 1810330 TRUE FALSE 1233315.189 1756884.113 1404237.372 1608791.392 1700156.43 1414675.801 1344360.256 1496019.682 1508174.228 0.817753789 1.164907927 0.931084318 1.066714549 1.127294446 0.938005553 0.891382595 0.991940888 1 20.52437167 2.12078169 18.95433973 0.940040548 1.031011023 0.082799015 0.101434294 2.990467622 475.5398249 0.034845767 0.025735352 132.0631616 -2.12078169 0.090970475 YDDYSSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YDDYSSSR 8 0 P38159;P38159-2;H3BUY5;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;;; 226.54 7.10E-06 5238400000 6101000 7021000 6314800 6287200 6999900 5315200 6922900 5999400 7736100 FALSE TRUE 5719149.301 7540842.145 6464590.038 6448540.196 6450156.09 6849611.955 5884875.414 6748438.296 6444894.933 0.88739217 1.170048887 1.003055923 1.000565605 1.000816329 1.062796528 0.913106494 1.047098264 1 22.61972541 3.660786936 7.858604423 0.998301507 1.06009223 0 0.078694788 0.55340449 58.45533418 0.019179312 0.029853382 4579.171784 -3.660786936 0.061790723 YDECLAVYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YDECLAVYR 9 0 O76094-2;O76094;R4GNC1;D6RDY6 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 ; 90.37 0.021758 0 107141 198887 193066 177790 228086 218674 186531 183761 187279 FALSE TRUE 100435.2361 213612.8004 197645.6167 182352.3924 210173.0456 281801.6339 158562.4082 206703.9654 156020.925 0.643729269 1.369129175 1.266789161 1.16876882 1.347082422 1.806178459 1.016289374 1.324847711 1 17.25138001 4.742275788 24.69800118 1.3000507 0.643728969 0.447733636 0.22426577 271.8167433 1806914.689 0.049012762 0.365093481 55242.81343 -4.742275788 -0.65632173 YDEEFQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YDEEFQR 7 0 P55060-3;P55060 P55060-3 CSE1L Exportin-2 0 ;;; 203.41 0.00066703 3037330000 4853400 5295490 5273010 5251950 5029760 4259450 5824920 5294010 3219290 FALSE TRUE 4549634.358 5687573.59 5398088.287 5386723.929 4634742.939 5489084.069 4951527.322 5954978.802 2681969.702 1.696377985 2.120670336 2.012732763 2.008495445 1.728111595 2.046661476 1.846227912 2.220375122 1 21.35486151 -1.402759878 5.097688164 0.999126028 1.968370451 0.771068157 0.164327634 0.001464749 0.000171608 0.142783095 0.033627539 0.039558528 1.402759878 0.969244423 YDEELEGERPHSFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YDEELEGERPHSFR 14 1 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 ; 151.44 4.17E-06 287660000 365720 390150 409400 382010 368030 334240 432620 337630 402680 FALSE TRUE 342830.238 419037.112 419111.1613 391813.0233 339126.4084 430729.6621 367752.6472 379783.8487 335470.1066 1.021939753 1.249104179 1.249324912 1.167952123 1.010899039 1.283958402 1.096230752 1.132094459 1 18.35582469 0.438419291 0.475170041 0.987517834 1.187930442 0.189459862 0.093601959 3.065892073 1.224128186 0.169161683 0.050090784 2.744222312 -0.438419291 0.200412608 YDEGS(ph)GGS(ph)GDEGRDEAHKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YDEGSGGSGDEGRDEAHKR 19 2 O94762-4;O94762 O94762-4 RECQL5 ATP-dependent DNA helicase Q5 2 Y(0.023)DEGS(0.977)GGS(1)GDEGRDEAHKR;Y(0.013)DEGS(0.987)GGS(1)GDEGRDEAHKR 82.177 0.0025889 475390000 326850 252566 265120 276200 259556 195742 285460 223411 296100 TRUE FALSE 306393.0419 271266.2494 271408.7716 283287.7596 239171.5188 252249.5378 242657.9231 251304.3551 246678.9971 1.242071865 1.099673067 1.100250831 1.148406483 0.969565798 1.022582144 0.983699163 1.018750514 1 17.91227536 7.999999995 0.252095094 0.975395459 2.523316118 0.709065813 0.045710484 26.77725167 0.366255675 0.055924802 17.62862206 99999998.78 -7.999999995 1.547920658 YDEIRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YDEIRR 6 1 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 ;;; 89.427 0.080459 2267260000 4247170 4788760 4793210 4818790 4911340 3894380 5077970 4487080 4444940 FALSE TRUE 3981347.211 5143324.773 4906907.205 4942448.31 4525623.168 5018624.286 4316575.54 5047301.815 3703050.799 1.07515328 1.388942538 1.325098539 1.33469633 1.222133698 1.35526747 1.165680887 1.363011768 1 21.82028291 -3.446709438 0.365003065 3.55E-10 1.296871769 0.417278549 0.100785715 127.919474 2.989340548 97.835904 0.065917537 0.000357512 3.446709438 1.296871768 YDEIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YDEIVK 6 0 A0A2U3TZH3;Q05639;A0A2R8Y488 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 99.171 0.090968 105690000 287570 236150 249100 267800 277840 209660 299910 234640 227530 FALSE TRUE 269571.507 253634.7917 255008.7696 274672.2014 256019.5672 270185.4385 254941.2797 263935.3205 189553.7731 1.422137384 1.33806248 1.345310966 1.449046341 1.350643477 1.425376209 1.34495492 1.392403412 1 17.53224765 -1.276761355 3.212779881 0.998217867 1.376501872 0.902370468 0.039582806 6388048.231 9137388.55 111630.4714 0.009215065 0.052873571 1.276761355 0.378284005 YDEMVESMKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YDEMVESMKK 10 1 P62258;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 120.96 0.00084614 482880000 3941300 1626700 2277000 1954200 2075000 1562200 2588700 1674300 2944300 FALSE TRUE 3694621.068 1747142.561 2331011.515 2004348.08 1912037.87 2013181.78 2200548.467 1883340.041 2452877.309 1.506239654 0.712282899 0.950317208 0.817141597 0.779508157 0.820742959 0.897129448 0.767808497 1 21.22604364 4.745350017 24.97810106 0.840614631 1.506239961 0.853502548 0.086333941 259.3051319 953955.0177 0.018429324 0.182627861 55635.24654 -4.745350017 0.66562533 YDERPGPS(ph)PLPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YDERPGPSPLPHR 13 1 P08621;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 1 YDERPGPS(1)PLPHR;YDERPGPS(1)PLPHR;YDERPGPS(1)PLPHR;YDERPGPS(1)PLPHR;YDERPGPS(1)PLPHR;YDERPGPS(1)PLPHR 147.17 2.56E-05 14850500000 6680140 6666090 6908580 6602900 7843480 6484320 8273940 7219870 9871270 TRUE FALSE 6262041.962 7159654.24 7072454.78 6772341.593 7227484.72 8356237.92 7033339.508 8121286.662 8223691.266 0.761463649 0.870613209 0.860009763 0.823516031 0.878861388 1.016117659 0.85525335 0.987547611 1 22.97135467 7.999999984 0.099671346 1.077695363 0.260644409 0.578727573 0.053373767 95.55527771 0.674696371 0.633026041 10.68176826 99999996.35 -7.999999984 -0.817050954 YDERPGPSPLPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YDERPGPSPLPHR 13 1 P08621;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;;;; 118.37 0.00026027 2894760000 1814670 2835120 2370390 2403370 2928970 1980460 2782540 2544100 3163640 FALSE TRUE 1701093.044 3045035.235 2426616.77 2465044.543 2698940.511 2552186.652 2365323.959 2861736.485 2635608.046 0.645427171 1.15534449 0.920704721 0.935284951 1.024029546 0.968348331 0.897449058 1.085797446 1 21.32970441 4.756708404 24.79398537 0.990857009 0.645426842 0.669267775 0.07781397 2243.028797 3064429.873 0.018398897 0.596311415 57109.50603 -4.756708404 -0.345430166 YDEYVNVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YDEYVNVK 8 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 131.06 0.0023756 176040000 238950 202790 240180 213310 242210 165340 271890 204130 240770 FALSE TRUE 223994.546 217804.7826 245877.183 218783.8957 223187.8036 213070.9739 231122.6186 229616.0798 200583.9316 1.116712312 1.085853592 1.225806978 1.090734906 1.112690343 1.062253453 1.15224892 1.144738156 1 17.61384651 YDGHLPIEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YDGHLPIEIK 10 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ; 118.4 0.0008296 1072430000 3111400 2804900 2892500 2879500 3128400 2097850 3619800 2684800 3527600 FALSE TRUE 2916663.028 3012577.714 2961111.466 2953392.845 2882708.083 2703465.239 3077044.595 3020003.19 2938820.771 0.992460329 1.025097462 1.007584911 1.004958477 0.980906393 0.919914976 1.047033771 1.027624148 1 21.48680595 1.616353316 25 1.027997713 0.994414714 0.229062067 0.030017341 1.069070638 3140.039078 0.014436543 0.007843001 41.33836692 -1.616353316 -0.033583 YDGQVAVFGSDLQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YDGQVAVFGSDLQEK 15 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 132.44 0.00011036 69949000 63767 66278 67768 65651 71341 58472 80654 59136 71984 FALSE TRUE 59775.9373 71185.29208 69375.48896 67335.71581 65738.16564 75351.91719 68560.68146 66519.25977 59969.40537 0.996773887 1.187026812 1.156848038 1.122834475 1.096195055 1.256505992 1.143260985 1.109219933 1 15.87193905 -0.348015433 7.345416124 0.999910351 1.144432252 0.269868172 0.066971422 0 0 0.058828018 0.013865897 0.448729444 0.348015433 0.144521901 YDGSTIVPGEQGAEYQHFIQQCTDDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YDGSTIVPGEQGAEYQHFIQQCTDDVR 27 0 Q14019 Q14019 COTL1 Coactosin-like protein 0 ;; 208.96 1.85E-25 923280000 541460 606370 565010 564210 604340 493430 661460 517220 506590 FALSE TRUE 507570.9851 651266.2657 578412.304 578688.5838 556877.5742 635875.2308 562280.2137 581796.0555 422036.8563 1.202669808 1.543150215 1.370525572 1.371180207 1.319499863 1.506681754 1.332301209 1.378543241 1 18.68700947 -0.191774899 0.853615219 0.988657019 1.397597067 0.602998288 0.09561229 5.983323728 3.596724601 0.315721546 0.028059813 0.643020919 0.191774899 0.408940048 YDHLDPTEMEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YDHLDPTEMEK 11 0 O95757;E9PDE8 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 ; 223.71 6.74E-12 456240000 898880 641540 777090 698220 765170 574740 929800 701670 776080 FALSE TRUE 842620.7053 689040.2891 795522.9418 716137.5073 705076.6347 740658.1079 790385.1218 789275.0441 646547.2343 1.303262408 1.065723048 1.230417361 1.107633703 1.090526101 1.145559162 1.222470811 1.220753879 1 19.30239625 3.216852439 24.99812097 1.146630604 1.175443799 0.082742906 0.087441723 1163.591834 1339936.072 0.024191915 0.028938519 1647.602487 -3.216852439 0.028813195 YDHQAEEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YDHQAEEDLR 10 0 Q15417;Q15417-3 Q15417 CNN3 Calponin-3 0 121.02 0.00052607 137810000 401730 408530 424230 383300 385410 326000 478470 393200 383190 FALSE TRUE 376586.4364 438777.9863 434292.9359 393136.1269 355141.4533 420110.9078 406727.8654 442291.8855 319233.1135 1.179659692 1.374475165 1.360425713 1.231501716 1.11248313 1.316000409 1.274077933 1.385482479 1 18.28425078 -1.267856015 3.85903664 0.999574837 1.289172268 0.497901638 0.087632332 10246221.29 22731189.9 52134.47743 0.021288198 0.053968952 1.267856015 0.28959743 YDIDLPNKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YDIDLPNKK 9 1 O00244;E5RGN3;E5RIM7 O00244 ATOX1 Copper transport protein ATOX1 0 ;; 111.06 0.003506 5955460000 32800600 21142040 25993000 24347800 25052400 20712730 35337700 21770830 29580700 FALSE TRUE 30747669 22707418.64 26609566.23 24972605.77 23084885.56 26692158.91 30039139.94 24488966.05 24643490.07 1.24769945 0.9214368 1.079780752 1.013355077 0.936753905 1.083132252 1.218948284 0.993729621 1 24.55470325 2.013552058 24.94206354 1.109175246 1.026415485 0 0.109717713 471.4860867 867749.1558 0.037678113 0.02781365 103.1696739 -2.013552058 -0.082759762 YDLANQDHMMDAPPLS(ph)PFPHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YDLANQDHMMDAPPLSPFPHIK 22 0 P28749;P28749-2 P28749 RBL1 Retinoblastoma-like protein 1 1 YDLANQDHMMDAPPLS(1)PFPHIK 125.74 2.36E-05 44322000 61471 59764 61677 56270 62564 57208 84691 60449 68750 TRUE FALSE 57623.63984 64188.98874 63140.00757 57713.98346 57650.47581 73723.02091 71992.37078 67996.19071 57275.18086 1.006083944 1.120712109 1.102397349 1.007661305 1.006552488 1.287172206 1.2569558 1.187184217 1 15.80562249 2.242523681 24.99990432 1.212850879 1.063964145 0.341364729 0.086888747 95.11241369 599993.8262 0.028989166 0.023414848 174.7928568 -2.242523681 -0.148886734 YDLDFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YDLDFK 6 0 P06733;A0A2R8Y6G6;P06733-2;P13929-3;P13929-2;P13929;E5RGZ4;P09104-2;F5H0C8;P09104;U3KQP4 P06733 ENO1;ENO3;ENO2 Alpha-enolase;Beta-enolase;Enolase;Gamma-enolase 0 ; 112.75 0.062188 1440470000 3173360 2496140 2520300 2313220 3000960 1533040 3043250 2835540 2652490 FALSE TRUE 2974745.062 2680956.803 2580082.706 2372581.141 2765276.707 1975603.761 2586942.915 3189563.411 2209772.283 1.346177199 1.213227636 1.167578545 1.073676758 1.25138537 0.894030474 1.170683031 1.443390088 1 21.07546628 5.224021653 0.919021794 1.137876088 1.67552192 0.16436955 0.145661119 8.313623981 2.97390791 0.042704137 5.51491319 167502.6388 -5.224021653 0.537645832 YDLDFKSPDDPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YDLDFKSPDDPSR 13 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;; 95.264 0.0043555 2308760000 4577710 5090140 4176010 4490550 7084950 2925490 6047270 4316700 14036500 FALSE TRUE 4291199.303 5467019.262 4275066.929 4605785.115 6528526.606 3770031.472 5140538.004 4855649.497 11693717.47 0.36696622 0.467517646 0.365586644 0.393868342 0.558293513 0.32239803 0.439598273 0.415235746 1 23.4792303 -0.395781928 1.852617332 1.00062164 0.417153583 0.889422302 0.064692175 118.0986926 153.5996503 0.66776647 0.015350505 0.401992612 0.395781928 -0.583468056 YDLEQGLGDLLTER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YDLEQGLGDLLTER 14 0 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 0 107.18 0.0044828 0 19335 21200 23381 21417 23613 17748 23049 18782 21306 FALSE TRUE 18124.85686 22769.67006 23935.60836 21966.59648 21758.53023 22871.55949 19593.01643 21126.97404 17749.89096 1.02112497 1.282806194 1.348493262 1.237562334 1.22584022 1.288546478 1.103838692 1.190259371 1 14.11552254 1.031385646 0.823138851 1.006544226 1.254315073 0.33368202 0.093870204 0.637360896 0.965980727 0.085861047 0.031329256 10.7494352 -1.031385646 0.247770847 YDLLDCHISICSPQVAQLFTDNFDYQTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YDLLDCHISICSPQVAQLFTDNFDYQTR 28 0 Q13144;A0A3B3IUB1;A0A3B3ITG6;A0A3B3IRP4;A0A3B3ISX3;A0A3B3ISM8;A0A3B3IUF2;A0A3B3ITQ2;A0A3B3ISV1;A0A3B3ISI2;A0A3B3IST9 Q13144 EIF2B5 Translation initiation factor eIF-2B subunit epsilon 0 164.7 7.22E-12 53400000 22259 47046 37923 39413 44439 36537 56162 41376 30625 FALSE TRUE 20865.84892 50529.33479 38822.55147 40424.40431 40948.9402 47084.63877 47741.02948 46541.88468 25513.48965 0.817835945 1.980494847 1.521648038 1.584432583 1.604991742 1.845480152 1.871207355 1.824206932 1 14.63897262 2.414380018 8.838125573 1.730162384 1.570409932 0 0.381851194 1.13560626 147.1177756 0.120377861 0.100651498 259.6450325 -2.414380018 -0.159752452 YDNGSGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YDNGSGYR 8 0 Q08211;Q08211-2 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 102.62 0.011469 195100000 285100 376581 304806 309910 345988 281982 357212 321384 356763 FALSE TRUE 267256.0999 404463.4491 312036.1423 317862.8153 318815.4981 363385.6258 303651.3768 361509.4999 297216.9505 0.89919535 1.360835741 1.049859847 1.069463955 1.0726693 1.222627529 1.021648921 1.216315218 1 18.18115687 -2.504816796 1.788899656 7.48E-05 1.125003674 0.067491899 0.127639605 2880999.233 193848.904 11643044.14 0.028910123 0.003127398 2.504816796 1.124928858 YDNQIHIIDFDDENNIINK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YDNQIHIIDFDDENNIINK 19 0 A8MUM1;Q53HC9;F8WDS8;C9J0U9;D3YTH5 A8MUM1 TSSC1 Protein TSSC1 0 263.92 2.68E-31 121550000 156990 118690 129460 133520 129240 107380 168820 120990 133940 FALSE TRUE 147164.2761 127477.9311 132530.8523 136946.3492 119090.0117 138378.8628 143507.0082 136095.8678 111584.5487 1.318858909 1.142433541 1.187716883 1.227287746 1.067262565 1.240125666 1.286083153 1.219665889 1 16.76777774 YDNSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YDNSLK 6 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;; 146.94 0.025485 26202300000 14001800 11483140 12343730 11926920 11648960 9796910 15363000 10073910 12514540 FALSE TRUE 13125452.33 12333363.63 12636529.1 12232984.96 10734097.67 12625118.88 13059460.77 11331659.84 10425782.43 1.258941708 1.182967678 1.212046117 1.173339751 1.029572384 1.210951693 1.252612057 1.086888195 1 23.31365232 -5 0.208234707 0.133740082 1.209606831 0.436848991 0.067220905 148.3309683 1.477685283 53.62106497 0.147440429 1.00E-05 5 1.075866748 YDPSIGIYGLDFYVVLGRPGFSIADKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YDPSIGIYGLDFYVVLGRPGFSIADKK 27 2 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ; 162.82 6.69E-12 124158000 163113 220560 139940 118425 254232 102596 200219 195857 149162 FALSE TRUE 152904.0485 236890.4919 143259.4429 121463.986 234265.6442 132213.7997 170198.0197 220310.1776 124265.8986 1.230458639 1.906319389 1.15284599 0.977452281 1.885196558 1.063958827 1.369627723 1.772893289 1 16.92307092 -1.797084025 2.817173458 0.887279712 1.42045585 0.13430766 0.334979141 1543915086 1238687299 1194283928 0.074949354 0.015955704 1.797084025 0.533176138 YDQDLCYTDILFTEQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YDQDLCYTDILFTEQER 17 0 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 98.531 0.0048247 0 8017 9549.8 9452.7 8054.4 10296 6560.4 9629 7718.6 7632.2 FALSE TRUE 7515.230281 10256.87713 9676.922508 8261.08954 9487.393692 8454.280981 8185.220841 8682.284201 6358.336514 1.181949125 1.613138453 1.521926763 1.299253275 1.492118838 1.329637235 1.287321113 1.365496177 1 12.63443366 0.458445873 0.395149215 0.954381023 1.480842658 0.467491593 0.127907747 1.923828847 0.570271704 0.301945927 0.09331857 2.873729413 -0.458445873 0.526461635 YDS(ph)DGDKSDDLVVDVSNEDPATPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YDSDGDKSDDLVVDVSNEDPATPR 24 1 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 Y(0.003)DS(0.947)DGDKS(0.05)DDLVVDVSNEDPATPR;YDS(1)DGDKSDDLVVDVSNEDPATPR 247.36 3.51E-38 126894000 385880 162113 239090 229410 249620 168664 279500 191397 328700 TRUE FALSE 361728.4596 174116.0152 244761.3277 235297.049 230015.8521 217354.5588 237591.5698 215293.3368 273837.8465 1.320958605 0.635836198 0.89381848 0.859256863 0.839971009 0.793734546 0.867635985 0.786207383 1 18.06296233 4.752495625 24.98801606 0.824747911 1.320958939 0.731570193 0.092424682 1192.558055 2138437.418 0.0204094 0.425479399 56558.20598 -4.752495625 0.496211029 YDS(ph)SNQVK ddPTM_SK-BR-3_Pertuzumab_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(0.5)S(0.5)NQVK;YDS(0.925)S(0.075)NQVK;YDS(0.915)S(0.085)NQVK;YDS(0.5)S(0.5)NQVK 146.71 0.00057583 1358440000 2719080 2037320 1989770 2187210 2782650 1406720 2658210 2013860 3236330 TRUE FALSE 2548897.636 2188165.293 2036968.284 2243337.512 2564111.894 1812817.228 2259636.088 2265294.854 2696165.616 0.945378734 0.811584155 0.755505623 0.832047371 0.951021658 0.672368647 0.838092466 0.840191285 1 21.36247769 0.697063338 2.61208084 0.999955404 0.81825082 0.293102175 0.081380406 2.403574497 19.2394716 0.072095599 0.019153354 4.978096805 -0.697063338 -0.181704584 YDSDGVWDPEKWHASLYPAS(ph)GR ddPTM_SK-BR-3_Pertuzumab_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 149.66 3.73E-08 143611000 98320 218562 193007 183760 219943 147836 342850 223901 231600 TRUE FALSE 92166.32671 234744.5579 197585.2172 188475.5927 202669.564 190513.8533 291442.8254 251855.5327 192944.4638 0.477683189 1.216643138 1.024052275 0.976838563 1.050403624 0.987402538 1.510501103 1.305326557 1 17.55782612 1.760328744 25 1.320693515 0.9980151 0.283096266 0.226478965 12.39971394 14252.29529 0.09539178 0.052901279 57.58756881 -1.760328744 -0.322678415 YDVDTLDMVFLDHWK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YDVDTLDMVFLDHWK 15 0 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ;;; 252.43 1.21E-24 938088000 2388970 2048658 2167188 1833495 2221657 1744486 2501910 2032041 2138331 FALSE TRUE 2239448.632 2200342.77 2218594.723 1880545.586 2047177.021 2248090.789 2126771.822 2285745.792 1781429.742 1.257107468 1.235155515 1.245401191 1.055638368 1.149176402 1.261958715 1.193856694 1.283096233 1 20.76460416 -1.391376301 3.051937646 0.997090582 1.210228791 0.495767411 0.066612761 42868611.23 53626105.4 1098579.648 0.015846874 0.040609131 1.391376301 0.213138209 YDWDLLAAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YDWDLLAAR 9 0 Q15029;Q15029-3;Q15029-2;K7EP67;K7EJ74 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ; 176.09 0.00012428 168711000 295870 521780 281580 271940 512840 175599 250490 421700 399760 FALSE TRUE 277352.0248 560413.1341 288259.2106 278918.4408 472563.6151 226291.5807 212931.3499 474350.1733 333037.4735 0.832795247 1.682732962 0.865545873 0.837498669 1.418950277 0.679477833 0.639361534 1.424314713 1 18.34532499 3.762777867 7.993202536 0.941174612 1.306842848 0.093009667 0.334581726 0.404189701 79.38381721 0.081084197 0.144983295 5791.324065 -3.762777867 0.365668236 YEAQKLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 79.986 0.024277 1391050000 825200 1141260 928070 875560 1363470 713470 932170 1068070 1694060 FALSE TRUE 773552.205 1225760.078 950084.2587 898028.3519 1256388.566 919437.2068 792399.7623 1201420.891 1411310.442 0.548109177 0.868526188 0.673192963 0.636308161 0.89022835 0.651477648 0.561463827 0.851280381 1 20.42860394 1.000212062 8.970725096 0.999991877 0.70198181 0.457743108 0.112690723 0.077223537 92.69522333 0.105552477 0.026414383 10.00488409 -1.000212062 -0.298010067 YEAVS(ph)PERLELER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YEAVSPERLELER 13 1 Q92585 Q92585 MAML1 Mastermind-like protein 1 1 YEAVS(1)PERLELER 149.09 1.74E-06 0 67473 89176 73486 83009 88580 61118 69041 73645 78872 TRUE FALSE 63249.98537 95778.68383 75229.12262 85139.15147 81623.28411 78761.77443 58688.943 82839.74036 65707.75367 0.96259546 1.457646602 1.144904801 1.295724579 1.242216931 1.19866789 0.893181394 1.260730062 1 16.003776 1.945243315 9.863937921 1.040737739 1.24393417 0.199827245 0.152441986 0.719076164 126.5386469 0.057494331 0.03661807 88.15426223 -1.945243315 0.20319643 YEDFKEEGSENAVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YEDFKEEGSENAVK 14 1 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 ;; 219.52 4.54E-12 1423850000 2315670 1259620 1649760 1825800 2037530 1313770 2540000 1607900 2558860 FALSE TRUE 2170736.348 1352883.575 1688893.086 1872653.119 1877510.613 1693034.072 2159150.58 1808649.854 2131769.735 1.018278997 0.634629319 0.792249303 0.878449998 0.880728618 0.794191813 1.012844185 0.848426462 1 21.02362018 2.196500715 0.684012132 0.969711628 0.776854513 0.13156984 0.110715709 0.938025969 0.850166171 0.090086538 0.058196821 157.217438 -2.196500715 -0.192857115 YEDHTIFHDISLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YEDHTIFHDISLR 13 0 P82675 P82675 MRPS5 "28S ribosomal protein S5, mitochondrial" 0 ;;; 198.74 7.14E-08 486585000 270816 298387 258667 270450 368372 280207 246720 308180 402465 FALSE TRUE 253866.11 320479.884 264802.7034 277390.2049 339441.5491 361098.2121 209726.6264 346656.9514 335290.9915 0.757151598 0.95582611 0.789769812 0.827311833 1.012378971 1.076969621 0.625506297 1.033898793 1 18.3550542 4.759481604 22.46796744 0.890142845 0.757151065 0.091320054 0.137820159 3315.783286 3560732.919 0.031286379 1.131302889 57475.34731 -4.759481604 -0.13299178 YEDICPSTHNMDVPNIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YEDICPSTHNMDVPNIK 17 0 P63241;P63241-2;I3L397;I3L504;Q6IS14;F8WCJ1;C9J7B5;C9J4W5;Q9GZV4 P63241 EIF5A;EIF5AL1;EIF5A2 Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A;Eukaryotic translation initiation factor 5A-1-like;Eukaryotic translation initiation factor 5A-2 0 ;;; 215.79 5.50E-15 825620000 1487330 1483140 1631490 1637530 1553080 1438130 2072000 1502770 1568550 FALSE TRUE 1394240.67 1592953.229 1670189.713 1679551.792 1431107.362 1853294.785 1761322.836 1690394.143 1306748.872 1.066953797 1.219020168 1.278126004 1.285290409 1.095166327 1.418248621 1.347866353 1.293587604 1 20.31755048 5.192212394 1.243936333 1.270924588 0.709061363 0.148452809 0.121511252 6.025774485 3.721367534 0.031071666 5.703226929 155672.677 -5.192212394 -0.561863225 YEDRYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YEDRYDR 7 1 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 182.09 0.00060413 3304600000 4328000 4668700 4639600 4658300 4803900 4102500 5019900 4131000 3760000 FALSE TRUE 4057118.206 5014375.406 4749653.503 4777839.864 4426621.072 5286825.151 4267212.597 4646764.443 3132431.709 1.295197655 1.600793208 1.516283177 1.525281413 1.413158045 1.687770283 1.362268357 1.483436791 1 21.57885163 0.087699095 0.833311359 0.991062556 1.510207918 0.643790541 0.113051338 2.555164549 1.867079605 0.16234784 0.032804107 1.223768008 -0.087699095 0.519145361 YEDYDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YEDYDYR 7 0 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 0 ;;; 127.84 0.0088763 2218830000 5740800 6010700 6108600 5734800 6243700 5571800 7095900 5886800 6865100 FALSE TRUE 5381493.576 6455738.482 6253498.877 5881964.677 5753344.988 7180288.209 6031935.67 6621779.938 5719270.46 0.940940565 1.128769574 1.09340849 1.028446673 1.005957845 1.255455265 1.054668723 1.157801504 1 22.4473997 YEECKEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YEECKEK 7 1 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ; 72.485 0.046948 384470000 411330 255680 285550 311570 338670 217390 393660 267540 498360 FALSE TRUE 385585.5895 274610.8132 292323.3808 319565.4137 312072.2243 280146.964 334634.3376 300942.9579 415180.4965 0.928717974 0.661425129 0.704087459 0.769702374 0.751654345 0.674759451 0.805997248 0.724848495 1 18.66337915 -0.941840053 0.62434722 1.05719089 0.737949077 0.495414013 0.077105571 20.03655134 4.467112556 2.273378152 0.027527609 0.114329932 0.941840053 -0.319241813 YEEDCEDRHDGSSNGNPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YEEDCEDRHDGSSNGNPR 18 1 Q92754 Q92754 TFAP2C Transcription factor AP-2 gamma 0 160.45 2.44E-11 108260000 92853 123060 110100 120610 116630 93412 130440 92870 136270 FALSE TRUE 87041.49648 132171.4904 112711.624 123705.0568 107470.3503 120378.528 110881.7329 104465.0239 113525.6567 0.766712116 1.164243347 0.992829527 1.089666076 0.94666134 1.060364076 0.976710782 0.920188678 1 16.79265886 1.554313306 6.071534461 0.956576939 1.021869351 0.00925632 0.106033381 0.372896829 27.89453634 0.053291956 0.024480373 35.83548661 -1.554313306 0.065292413 YEEEEEQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YEEEEEQSR 9 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 291.42 1.98E-28 1562570000 828570 884340 907170 894990 888110 738370 1033200 782110 922630 FALSE TRUE 776711.2827 949817.4538 928688.5008 917956.9586 818361.4231 951525.4326 878281.2518 879758.1551 768637.0926 1.010504554 1.235716391 1.208227536 1.194265756 1.064691557 1.237938478 1.142647499 1.144568957 1 19.55194307 0.48369285 1.226908812 0.999901985 1.17148272 0.293300864 0.073270757 2.363320566 4.482429226 0.064690754 0.019496174 3.045740164 -0.48369285 0.171580735 YEEIDNAPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YEEIDNAPEER 11 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 208.6 4.42E-08 366540000 237180 233780 226750 207280 286020 219230 205600 245780 382670 FALSE TRUE 222335.3272 251089.3144 232128.6171 212599.1557 263557.1429 282518.1421 174772.1887 276466.174 318799.9049 0.697413405 0.787607871 0.728132642 0.666873335 0.826716504 0.88619268 0.548219074 0.867209086 1 18.28229167 0.999763244 24.99992987 1.00000003 0.736215392 0.484351255 0.091315501 5.261847742 555683.796 0.083622117 0.020905529 9.994549978 -0.999763244 -0.263784638 YEEIVK ddPTM_SK-BR-3_Pertuzumab_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 ;;;;; 132.22 0.034881 7335070000 9892540 8359680 9131990 9010150 9219730 7569180 11188400 8200810 10252100 FALSE TRUE 9273383.58 8978639.405 9348605.115 9241365.703 8495649.596 9754279.391 9510803.288 9224699.181 8540958.279 1.085754464 1.051244967 1.094561618 1.082005719 0.994695129 1.142059131 1.113552248 1.080054354 1 23.02596652 2.19762512 24.99999787 1.097278997 1.065645478 0.016112478 0.045679441 339.2142828 207162.0893 0.015605208 0.011525375 157.6250075 -2.19762512 -0.031633519 YEELFPAFSDSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YEELFPAFSDSR 12 0 P54920;M0R0Y2;M0R2M1;M0R213;M0R0I4 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;;;;; 289.67 1.01E-35 712697000 685834 807416 782246 754381 849476 654713 806642 721800 846543 FALSE TRUE 642908.8742 867197.9208 800801.2445 773739.6936 782761.5816 843718.0147 685693.5206 811918.3189 705249.5044 0.911604858 1.229632797 1.135486434 1.097114835 1.109907312 1.196339748 0.972270829 1.151249755 1 19.42777422 1.739662179 24.99999999 1.042709586 1.128563518 0.099302787 0.095353949 0.303238666 6877.489502 0.040218117 0.022302931 54.91135729 -1.739662179 0.085853932 YEEVAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 126.16 0.040975 740910000 1470670 1480390 1490110 1593600 1618390 1285440 1723330 1437580 1540290 FALSE TRUE 1378623.39 1589999.616 1525456.113 1634494.474 1491288.178 1656525.661 1464932.665 1617065.028 1283205.648 1.074358885 1.239084022 1.188785379 1.27375879 1.162158365 1.290927657 1.141619558 1.260176052 1 20.29132097 -1.338447164 5.317298788 0.999937568 1.205626996 0.482998666 0.066260888 4.17E-05 5.18E-06 0.05449854 0.012841538 0.045872545 1.338447164 0.205689428 YEEVSVSGFEEFHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YEEVSVSGFEEFHR 14 0 Q9BRA2;I3L2R6;I3L0K2;I3L3M7 Q9BRA2 TXNDC17 Thioredoxin domain-containing protein 17 0 ;;; 233.59 3.44E-17 1946190000 1530620 1828280 1761270 1842200 1792510 1516990 2106860 1555840 1818600 FALSE TRUE 1434821.226 1963647.754 1803048.156 1889473.971 1651733.495 1954920.387 1790955.902 1750090.049 1515063.911 0.947036766 1.296082455 1.190080592 1.247124928 1.090207141 1.29032206 1.182099243 1.15512622 1 20.53094722 0.784061941 2.537423728 1.000112501 1.194544465 0.213094534 0.102490179 1.247663868 12.39462019 0.086346295 0.02306105 6.082217428 -0.784061941 0.194431963 YEFTDALLCHDDELEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YEFTDALLCHDDELEGR 17 0 A0A0A0MTR2;Q8N543;H3BR79;H3BUA6;Q8N543-2 A0A0A0MTR2 OGFOD1 Prolyl 3-hydroxylase OGFOD1 0 ;;; 236.81 3.37E-20 372515000 491023 574952 484696 474686 601830 506364 644210 545141 576358 FALSE TRUE 460290.7469 617522.0443 496193.218 486867.2464 554564.6995 652543.0667 547616.6911 613203.0539 480160.1264 0.958619264 1.286075229 1.033391135 1.013968507 1.154957834 1.359011361 1.140487644 1.277080332 1 18.87315608 2.476757156 24.99999847 1.210901996 1.100174385 0.152916797 0.12571671 23.71861826 1628338.051 0.040204019 0.033939584 299.7485947 -2.476757156 -0.110727612 YEFTDALLCHDDELEGRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YEFTDALLCHDDELEGRR 18 1 A0A0A0MTR2;Q8N543;H3BR79;H3BUA6;Q8N543-2 A0A0A0MTR2 OGFOD1 Prolyl 3-hydroxylase OGFOD1 0 ; 149.97 3.79E-08 70607000 57462 58833 56320 54281 60723 47306 72622 52205 79954 FALSE TRUE 53865.55599 63189.05654 57655.937 55673.94236 55954.06052 60962.47425 61733.00529 58722.90917 66609.16088 0.808680897 0.948654145 0.865585698 0.835830111 0.840035511 0.915226576 0.92679452 0.881604098 1 16.02343299 0.432493858 0.579664697 1.003426157 0.874795664 0.465881078 0.042351685 1.98192753 1.10270289 0.062077626 0.018640784 2.70703492 -0.432493858 -0.128630493 YEHANDDK ddPTM_SK-BR-3_Pertuzumab_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 ;;; 108.43 0.0041983 1312780000 3252500 2238610 2602590 2658040 2443850 2009560 3321500 2248330 2402630 FALSE TRUE 3048931.831 2404359.014 2664324.664 2726249.806 2251919.879 2589687.35 2823471.91 2529038.95 2001615.531 1.523235498 1.201209211 1.331087125 1.362024706 1.125051162 1.293798589 1.410596524 1.263498864 1 20.93273346 0.966860628 22.60183286 0.999999997 1.310460633 0.460635083 0.10799939 1180.477388 805115.3496 0.096306448 0.024076612 9.265324368 -0.966860628 0.310460636 YEIDLDTSDHAHLEHITR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YEIDLDTSDHAHLEHITR 18 0 A0A2R8Y891;P08237;P08237-3;P08237-2;F8VZI0 A0A2R8Y891 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 ;; 132.47 5.12E-06 624200000 291025 410539 397569 421002 403871 339300 432910 385042 446610 FALSE TRUE 272810.2647 440935.7347 406999.5244 431805.6241 372152.6008 437250.4019 367999.1644 433115.3413 372067.9058 0.733227082 1.185094785 1.093885063 1.160555956 1.000227633 1.175189784 0.989064519 1.164076059 1 18.50520642 4.746972614 24.91697526 1.098598698 0.73322689 0.688553409 0.07666108 548.8419788 1625674.051 0.016449884 0.188660116 55843.49796 -4.746972614 -0.365371808 YEIMDGAPVKGESIPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YEIMDGAPVKGESIPIR 17 1 O75436 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ; 110.37 0.00051232 240180000 276450 257670 249670 262170 281600 176466 311280 230580 335090 FALSE TRUE 259147.488 276748.1549 255592.2903 268897.7261 259484.2719 227408.8695 264606.4538 259368.4206 279161.3142 0.928307308 0.991355681 0.915572027 0.963234203 0.929513721 0.814614554 0.947862187 0.929098723 1 18.0907395 3.824912911 4.850717909 0.92249408 0.962540991 0.052975567 0.049558687 0.466315848 17.92859389 0.01208462 0.022311488 6682.099085 -3.824912911 0.040046911 YEKDIAAYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YEKDIAAYR 9 1 P26583;P09429 P26583;P09429 HMGB2;HMGB1 High mobility group protein B2;High mobility group protein B1 0 ;;; 127.42 0.00040659 1302410000 1366750 2518720 1514740 1642990 2955930 1061530 1727520 1909710 3688670 FALSE TRUE 1281207.557 2705208.65 1550670.348 1685151.905 2723783.181 1367976.479 1468494.414 2148141.497 3073007.147 0.416923065 0.880313166 0.504610069 0.54837227 0.886357581 0.445158899 0.477868857 0.699035633 1 21.55121969 0.976964661 22.28792181 1.000000009 0.606757545 0.37212571 0.165198652 509.4235869 492896.5116 0.152626572 0.038156643 9.483412917 -0.976964661 -0.393242464 YELGRPAANTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YELGRPAANTK 11 1 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 143.42 3.39E-05 943850000 1146270 1274080 1158880 1119280 1490620 763080 1325210 1288620 1626100 FALSE TRUE 1074527.007 1368414.209 1186369.181 1148002.62 1373552.718 983368.8084 1126507.063 1449507.044 1354693.405 0.793188335 1.010128346 0.875747366 0.847426152 1.013921462 0.725897686 0.831558683 1.069989001 1 20.36953495 1.235624759 24.9999809 1.034994555 0.879648853 0.364364256 0.08943298 90.75796449 772771.0638 0.072922669 0.021307547 17.20381483 -1.235624759 -0.155345702 YELHLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YELHLK 6 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;; 102.98 0.035077 5361510000 13564030 13515250 12755230 12224860 15435600 9692490 13580810 13756890 11446590 FALSE TRUE 12715081.57 14515933.17 13057790.08 12538570.6 14223350.24 12490554.52 11544493.62 15474468 9536080.181 1.333365632 1.522211737 1.369303721 1.314855828 1.49153006 1.309820627 1.210612054 1.622728386 1 23.18496494 -3.226020701 0.327182013 2.71E-15 1.408187541 0.479160047 0.124868765 81.36299199 2.092315628 56.10112184 0.102415964 0.000594264 3.226020701 1.408187541 YELISETGGSHDKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YELISETGGSHDKR 14 1 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6;Q96SI9;Q96SI9-2 Q12906;Q12906-7;Q96SI9 ILF3;STRBP Interleukin enhancer-binding factor 3;Spermatid perinuclear RNA-binding protein 0 ;;;;; 197.19 1.54E-08 3149780000 5434410 4600370 5242680 4967460 5143770 4212070 6563980 4835440 5598910 FALSE TRUE 5094279.979 4940986.181 5367038.845 5094933.433 4739799.053 5428026.232 5579772.136 5439155.328 4664415.751 1.092158215 1.059293692 1.150634749 1.092298308 1.01616136 1.163709781 1.196242452 1.166095738 1 22.15326495 2.169088407 24.99999838 1.153615015 1.088802614 0.083402651 0.062952048 75.81282491 27280.23692 0.021748648 0.016062445 147.6006966 -2.169088407 -0.064812401 YELYSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YELYSR 6 0 A0A0G2JQD6;Q8IXL6 A0A0G2JQD6 FAM20C Extracellular serine/threonine protein kinase FAM20C 0 ;;; 105.42 0.076756 4544900000 1713300 1780030 1401440 1391960 2077500 2276520 2130700 1442120 1864320 FALSE TRUE 1606067.611 1911825.273 1434682.819 1427680.05 1914341.53 2933714.368 1811221.315 1622171.856 1553152.948 1.03406919 1.230931748 0.923722818 0.919214075 1.232551844 1.88887667 1.16615773 1.044437934 1 20.56676848 2.488356169 24.90802902 1.329979834 1.046977127 0.162017744 0.257152173 797.0681793 1767119.711 0.083069368 0.074068726 307.8620584 -2.488356169 -0.283002707 YEMACAIADAFNLPSSHLRPITDS(ph)PVLGAQRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YEMACAIADAFNLPSSHLRPITDSPVLGAQRPR 33 2 Q9NZL9;Q9NZL9-2 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 1 YEMACAIADAFNLPSS(0.002)HLRPIT(0.121)DS(0.877)PVLGAQRPR;YEMACAIADAFNLPSSHLRPIT(0.028)DS(0.971)PVLGAQRPR;YEMACAIADAFNLPSSHLRPIT(0.12)DS(0.88)PVLGAQRPR 286.79 1.18E-74 1179140000 199939 285957 266473 270136 315035 245098 293688 260325 287048 TRUE FALSE 187425.1749 307129.5538 272793.8654 277068.1471 290293.4219 315853.8138 249652.2109 292827.1493 239137.8344 0.783753752 1.284320211 1.140739047 1.158612763 1.213916746 1.32080235 1.04396785 1.224512006 1 17.86748287 -1.597738266 2.903686396 0.989166832 1.159741795 0.079494149 0.150452423 66008931.99 64181549.83 5430731.096 0.032027297 0.02525002 1.597738266 0.170574963 YENNDKYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YENNDKYR 8 1 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 0 64.841 0.060026 122850000 372760 407250 399630 404880 521090 311640 462870 456370 542890 FALSE TRUE 349429.617 437403.2137 409109.4123 415269.9063 480165.6934 401605.4089 393466.9406 513348.7991 452278.1518 0.772598932 0.967111084 0.904552676 0.918173705 1.061660156 0.887961108 0.869966721 1.135028957 1 18.78685078 4.741599401 24.13434031 0.951998113 0.772598823 0.338670777 0.083188999 212.6959077 1689110.558 0.018378193 0.129031315 55156.84301 -4.741599401 -0.17939929 YEPFSFADDIGSNNCGYYDLQAVLTHQGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YEPFSFADDIGSNNCGYYDLQAVLTHQGR 29 0 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 ;; 362.29 7.22E-121 196170000 183641 236977 232194 229953 249371 223826 267182 215540 243004 FALSE TRUE 172147.2376 254523.0237 237701.7513 235853.9833 229786.4076 288440.9327 227120.5395 242450.6435 202445.0625 0.850340509 1.257244906 1.174154353 1.165027096 1.135055628 1.424786207 1.121887275 1.197612036 1 17.62717093 4.744678433 24.80657934 1.197242225 0.850340338 0.481645359 0.108216672 480.833449 1949627.447 0.022758438 0.209665513 55549.2798 -4.744678433 -0.346901887 YEPPHIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YEPPHIK 7 0 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 79.116 0.048147 0 126330 129990 143200 123520 137560 107310 147440 119500 140420 FALSE TRUE 118423.2308 139614.5949 146596.7716 126689.7323 126756.5925 138288.655 125332.7408 134419.8381 116982.9949 1.012311498 1.193460597 1.253145996 1.082975628 1.083547166 1.18212613 1.071375724 1.149054512 1 16.8359393 0.197848887 0.387437438 0.979697021 1.161502359 0.191237034 0.072559656 4.847152852 1.142557877 0.251687218 0.055518571 1.577062434 -0.197848887 0.181805338 YEPQS(ph)PGYEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YEPQSPGYEPR 11 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 YEPQS(1)PGYEPR;YEPQS(1)PGYEPR;YEPQS(1)PGYEPR 190.27 2.46E-06 1967210000 994050 1049010 962900 994330 1108650 927400 1190920 934160 1019950 TRUE FALSE 931834.1849 1126679.792 985740.4427 1019846.191 1021581.101 1195125.325 1012352.602 1050791.932 849713.7559 1.096644815 1.325952162 1.160085306 1.200223233 1.202264991 1.406503445 1.191404276 1.236642252 1 19.6966174 0.117484241 2.065444139 0.999990957 1.233850602 0.40704071 0.085963343 46.73393397 106.767211 0.075360646 0.020498717 1.310642482 -0.117484241 0.233859645 YEPSDKDRQS(ph)PPPAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 YEPSDKDRQSPPPAK 15 2 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 YEPS(0.001)DKDRQS(0.999)PPPAK;YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK 150.7 1.64E-06 5504480000 8743220 4855170 6371420 5802300 6012420 4651930 7808530 5556200 7519720 TRUE FALSE 8195997.467 5214651.839 6522553.091 5951196.841 5540228.786 5994866.673 6637713.417 6249903.801 6264630.153 1.308297101 0.832395802 1.041171295 0.949967787 0.884366459 0.956938642 1.059553917 0.997649286 1 22.57879791 1.751121057 25 1.023941362 0.975940163 0 0.127921548 15.94221634 31781.47959 0.053752121 0.029807401 56.37947888 -1.751121057 -0.048001199 YEQGTGCWQGPNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YEQGTGCWQGPNR 13 0 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 279.49 5.48E-32 651120000 173831 291140 161945 167079 287300 120109 181594 225240 255870 FALSE TRUE 162951.228 312696.3085 165786.4119 171366.53 264736.6169 154782.5185 154365.6655 253361.7098 213163.644 0.764441933 1.46693077 0.777742437 0.803920062 1.241940755 0.726120625 0.724165072 1.188578432 1 17.70160188 3.828862217 6.866609695 0.897874825 1.157823662 0.082765069 0.246485445 0.373636568 21.80346576 0.058637217 0.10644343 6743.140625 -3.828862217 0.259948838 YESHPVCADLQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YESHPVCADLQAK 13 0 C9JRZ6;Q9NX63 C9JRZ6 CHCHD3 MICOS complex subunit MIC19 0 89.46 0.0074395 120240000 217460 168010 160310 137790 206940 148770 200460 167110 239290 FALSE TRUE 203849.5668 180449.6352 164112.6289 141325.9247 190687.7672 191717.4839 170402.884 187974.0514 199350.9531 1.022566301 0.905185716 0.823234734 0.708930268 0.956543042 0.961708389 0.854788409 0.942930287 1 17.60495098 YESLTDPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YESLTDPSK 9 0 P08238;Q58FF7;Q58FF6;P07900;P07900-2;G3V2J8;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AB3P;HSP90AB4P;HSP90AA1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 4;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-beta 2 0 ; 135.71 0.00049586 372670000 1642920 1246020 1392860 1333000 1337070 1031610 1684620 1259740 1268740 FALSE TRUE 1540092.57 1338276.617 1425899.297 1367207.037 1232061.916 1329419.06 1432026.87 1417021.312 1056979.098 1.457070034 1.266133474 1.349032635 1.293504327 1.165644542 1.257753406 1.354829886 1.34063324 1 20.01151542 -1.909151879 2.629878431 0.823255716 1.306448796 0.622104727 0.076011265 11570454.7 7434166.574 12657935.94 0.017268431 0.012326737 1.909151879 0.483193081 YESLTDPSKLDSGK ddPTM_SK-BR-3_Pertuzumab_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 ;;; 190.87 5.05E-07 12810560000 37724700 24840600 29880200 29353900 34591700 22178600 40819300 26396500 42604300 FALSE TRUE 35363578.37 26679823.87 30588972.45 30107170.77 31875007.42 28581201.78 34698824.91 29692161.13 35493367.1 0.996343296 0.751684781 0.861822221 0.848247806 0.898055328 0.805254731 0.977614347 0.836555209 1 25.08104611 0.686437141 0.443834881 1.006290619 0.842094751 0.185864684 0.075326334 2.174362963 0.933016005 0.112802768 0.044361354 4.857772156 -0.686437141 -0.164195868 YESQEPLAGQES(ph)PLPLATR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 YESQEPLAGQESPLPLATR 19 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR 407.95 1.30E-147 9162340000 4790732 5398139 5396724 5717510 5387778 4190373 5279105 3920846 4055496 TRUE FALSE 4490888.636 5797822.828 5524736.842 5864230.986 4964643.649 5400065.66 4487552.214 4410372.254 3378607.518 1.329212882 1.716039166 1.635211196 1.735694648 1.469434855 1.598311029 1.328225368 1.305381649 1 21.68799734 1.227191648 0.866155087 1.009405216 1.62364358 0.700705178 0.123870552 0.26235791 0.4339396 0.105530521 0.038891835 16.8729744 -1.227191648 0.614238364 YETPSDAIEVIS(ph)PASS(ph)PAPPQEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YETPSDAIEVISPASSPAPPQEK 23 0 O75376;O75376-2;A0A088AWL3;E7EVK1 O75376 NCOR1 Nuclear receptor corepressor 1 2 YETPSDAIEVIS(1)PAS(0.001)S(0.999)PAPPQEK 251.19 5.71E-39 81602000 116690 92200 113500 99422 106050 87042 135530 105260 114700 TRUE FALSE 109386.5812 99026.58393 116192.2736 101973.3368 97721.26079 112169.6124 115208.5347 118401.9427 95555.82901 1.144740016 1.03632175 1.215962174 1.067159773 1.02266143 1.173864677 1.205667262 1.239086552 1 16.54405626 2.062653419 24.99773943 1.175770171 1.103377839 0.078599652 0.083338281 117.0088096 46683.5968 0.029061853 0.021463598 115.5189995 -2.062653419 -0.072392332 YETSSTSAGDRYDSLLGR ddPTM_SK-BR-3_Pertuzumab_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 0 265.22 4.56E-31 495110000 76003 88910 82861 92574 87413 67086 95297 70230 92024 FALSE TRUE 71246.1079 95492.98891 84826.50205 94949.60557 80547.93559 86452.63915 81008.09954 78998.3701 76664.5999 0.929322112 1.245594303 1.106462463 1.238506504 1.05065357 1.127673519 1.05665587 1.030441301 1 16.22627294 1.583174034 1.045208172 1.001523898 1.139884936 0.165832515 0.090317871 0.669210943 1.404032631 0.072617783 0.027190395 38.29781823 -1.583174034 0.138361038 YEVCIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YEVCIR 6 0 F5H283;Q92563 F5H283 SPOCK2 Testican-2 0 ;; 109.88 0.067884 558180000 854870 643110 1060790 1114860 625630 1087520 1105510 673680 585570 FALSE TRUE 801365.2127 690726.5336 1085952.44 1143469.195 576495.5435 1401469.37 939749.0386 757790.431 487834.5841 1.64269865 1.415903169 2.22606694 2.343969108 1.181743899 2.872837259 1.926368218 1.553375787 1 18.89603251 4.052232054 5.225052707 1.964376869 1.537502006 0.042107046 0.555525537 0.471542958 23.00973736 0.125164572 0.27678407 11277.99906 -4.052232054 -0.426874863 YEWDVAEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 YEWDVAEAR 9 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;; 285.4 2.12E-21 11470300000 11120380 11830480 12038420 10676620 11608850 10310910 13046130 10907230 9982970 FALSE TRUE 10424375.27 12706421.05 12323977.01 10950600.14 10697137.75 13287502.33 11089983.92 12269021.68 8316747.815 1.253419666 1.527811271 1.481826464 1.316692581 1.286216438 1.597680082 1.33345199 1.475218673 1 22.98758806 -1.319581504 3.0161129 0.996297772 1.421636775 0.563580319 0.112636878 10268064.69 13269136.25 344267.2772 0.025081952 0.047909153 1.319581504 0.425339002 YEYDPDIS(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YEYDPDISPPR 11 0 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 YEYDPDIS(1)PPR;YEYDPDIS(1)PPR;YEYDPDIS(1)PPR;YEYDPDIS(1)PPR 201.04 4.70E-08 1703330000 955750 946910 996730 991510 969190 903170 1134120 871400 885230 TRUE FALSE 895931.3136 1017020.202 1020372.906 1016953.825 893073.7269 1163900.517 964069.2347 980196.2082 737479.3942 1.214856063 1.379048974 1.383595141 1.378958969 1.210981261 1.578214288 1.307249046 1.32911674 1 19.49224321 0.566171614 2.030984972 1.000080567 1.360908935 0.530927542 0.102657493 2.220856953 9.550181102 0.087215868 0.023957807 3.682744711 -0.566171614 0.360828368 YEYHWADGTNIK ddPTM_SK-BR-3_Pertuzumab_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 ;; 224.24 2.05E-11 437620000 665750 673840 625840 686140 731800 494854 787480 597610 746220 FALSE TRUE 624081.8959 723731.8147 640685.2203 703747.514 674327.3799 637710.3165 669404.6846 672222.924 621671.0612 1.003877991 1.164171633 1.030585563 1.132025532 1.084701254 1.025800228 1.076782766 1.081316095 1 19.2457919 2.401157323 10.56443453 1.054105231 1.089641335 0.100946884 0.050747195 0.952310059 126.3758723 0.015980656 0.01336459 251.8589121 -2.401157323 0.035536103 YFAEALGPLQSFQARPDDLLISTYPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YFAEALGPLQSFQARPDDLLISTYPK 26 1 P50225;H3BRY5;H3BQX5;E9PKW4;E9PM76;P50226;E9PKR8 P50225;P50226 SULT1A1;SULT1A2 Sulfotransferase 1A1;Sulfotransferase;Sulfotransferase 1A2 0 132.33 5.14E-05 87893000 129260 149050 121620 121870 156690 126280 168620 140710 122620 FALSE TRUE 121169.8473 160085.8171 124504.8838 124997.3905 144384.1995 162734.986 143336.9964 158277.9532 102153.9298 1.186149642 1.567103853 1.21879681 1.223618031 1.413398385 1.593036962 1.403147159 1.549406405 1 16.64038518 2.502547738 23.87661855 1.434224571 1.329086153 0.020765834 0.191013539 1196.890781 1123934.152 0.05647328 0.053001104 318.0883313 -2.502547738 -0.105138417 YFAES(ph)DEEEDDVDFAMFN ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YFAESDEEEDDVDFAMFN 18 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 Y(0.094)FAES(0.906)DEEEDDVDFAMFN 96.64 0.0060796 10416000 23102 23106 22186 21685 21858 12788 25535 21246 21888 TRUE FALSE 21656.08706 24816.79228 22712.2624 22241.47381 20141.36085 16479.688 21706.26381 23898.60987 18234.7514 1.187627217 1.360961372 1.245548234 1.219730027 1.104559114 0.903751724 1.190378927 1.310607935 1 14.15440291 2.955562541 2.557098185 1.103942499 1.283016932 0.304603096 0.114342257 0.327531616 4.263687046 0.036543575 0.041477187 902.7396983 -2.955562541 0.179074433 YFDDEFTAQSIT(ph)ITPPDRYDSLGLLELDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YFDDEFTAQSITITPPDRYDSLGLLELDQR 30 1 P31751;P31751-2 P31751 AKT2 RAC-beta serine/threonine-protein kinase 1 YFDDEFT(0.027)AQS(0.021)IT(0.476)IT(0.476)PPDRYDSLGLLELDQR 102.86 0.00060876 33852000 19452 25143 24271 21184 27463 19194 29089 25759 30884 TRUE FALSE 18234.53404 27004.61388 24846.71958 21727.6173 25306.16676 24734.99621 24727.3745 28975.06785 25729.26088 0.70870804 1.049568194 0.965698925 0.844471103 0.983555916 0.961356656 0.961060429 1.12615236 1 14.65112239 1.377969245 5.862393116 1.062026792 0.94121807 0.246212853 0.097774227 0.310155981 14.28942378 0.062394762 0.022512297 23.87642192 -1.377969245 -0.120808722 YFDDEFTAQSITIT(ph)PPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YFDDEFTAQSITITPPDR 18 0 P31751;P31751-2;M0R0P9;M0R283 P31751 AKT2 RAC-beta serine/threonine-protein kinase 1 YFDDEFTAQSITIT(1)PPDR;YFDDEFTAQSITIT(1)PPDR;YFDDEFTAQS(0.001)IT(0.02)IT(0.979)PPDR;YFDDEFTAQSITIT(1)PPDR;YFDDEFTAQSITIT(1)PPDR 222.6 6.27E-18 283747000 269397 242723 286645 261597 275909 275829 340937 275453 206030 TRUE FALSE 252535.9227 260694.4635 293444.3548 268310.0219 254240.2201 355456.3546 289816.662 309843.9134 171642.262 1.471292208 1.518824446 1.709627637 1.56319323 1.481221566 2.070913949 1.688492441 1.805172629 1 17.38904529 YFDDEFTAQSITIT(ph)PPDRYDSLGLLELDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YFDDEFTAQSITITPPDRYDSLGLLELDQR 30 1 P31751;P31751-2 P31751 AKT2 RAC-beta serine/threonine-protein kinase 1 YFDDEFTAQSIT(0.002)IT(0.998)PPDRYDSLGLLELDQR;YFDDEFTAQSITIT(0.999)PPDRYDSLGLLELDQR;YFDDEFTAQSITIT(0.999)PPDRYDSLGLLELDQR;YFDDEFTAQS(0.003)IT(0.003)IT(0.991)PPDRYDS(0.003)LGLLELDQR;YFDDEFTAQSIT(0.006)IT(0.994)PPDRYDSLGLLELDQR;YFDDEFTAQSITIT(1)PPDRYDSLGLLELDQR 342.14 8.50E-106 3729328000 296498 375893 357377 354429 431175 319547 428191 373288 423689 TRUE FALSE 277940.7194 403724.5088 365854.1512 363524.2482 397312.2548 411795.0315 363987.7347 419893.8285 352972.5688 0.787428667 1.143784375 1.036494571 1.029893766 1.125617937 1.166648822 1.031206861 1.189593373 1 18.42919654 4.744870086 24.89218047 1.089713933 0.787428524 0.682308367 0.064970093 373.7746339 1474576.639 0.014004516 0.132293974 55573.79903 -4.744870086 -0.302285408 YFDEHYEYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YFDEHYEYR 9 0 P33552 P33552 CKS2 Cyclin-dependent kinases regulatory subunit 2 0 ;; 112.36 0.0019756 735680000 1969320 2104500 2150100 2029690 2188230 1984020 2182700 2068910 1722050 FALSE TRUE 1846063.777 2260319.37 2201101.387 2081775.282 2016375.243 2556774.366 1855424.398 2327217.968 1434628.73 1.286788517 1.575543081 1.534265515 1.451089915 1.40550318 1.782185392 1.293313287 1.622174378 1 20.452246 -1.603190249 4.904922125 0.994359415 1.498476944 0.518949391 0.149371021 0.008103228 0.000655553 0.127199663 0.029766782 0.024935022 1.603190249 0.504117529 YFDGSGGNNHAVEHYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YFDGSGGNNHAVEHYR 16 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;;;; 195.23 4.93E-11 4535920000 1780090 2262660 1861520 1985940 2325397 1631347 2218510 2078846 2205740 FALSE TRUE 1668677.344 2430189.701 1905676.133 2036902.583 2142769.7 2102290.396 1885865.021 2338394.499 1837587.744 0.908080362 1.322489067 1.037053136 1.108465481 1.166077487 1.144048986 1.026272093 1.27253488 1 20.80938171 -1.376670995 3.065022409 0.998470865 1.12749966 0.094438621 0.11914181 12684348.02 15869200.77 175342.8525 0.026462572 0.04200771 1.376670995 0.129028794 YFDLGLPNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YFDLGLPNR 9 0 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 133.6 0.00063377 514590000 554190 673600 542630 524760 763120 516860 518410 616620 738570 FALSE TRUE 519504.2372 723474.0449 555501.4398 538226.23 703187.6335 666069.0915 440679.2332 693606.3643 615297.8957 0.844313366 1.175811018 0.902817064 0.874740892 1.142840953 1.082514821 0.716204681 1.127269196 1 19.23092553 YFDNKDDDS(ph)DTETSNDLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YFDNKDDDSDTETSNDLPK 19 1 C9J3R1;C9IZP0;J3KR59;J3KR68;Q9UID6 C9J3R1 ZNF639 Zinc finger protein 639 1 YFDNKDDDS(0.987)DT(0.01)ET(0.003)SNDLPK;YFDNKDDDS(0.856)DT(0.142)ET(0.002)SNDLPK 189.62 8.24E-15 207790000 701100 270650 391160 381640 427500 276370 514920 327130 571860 TRUE FALSE 657219.4025 290689.2076 400438.4999 391433.5285 393925.8745 356153.5325 437712.5263 367972.9006 476412.8716 1.379516469 0.610162372 0.840528298 0.821626685 0.826858168 0.747573279 0.918767213 0.772382365 1 18.86185287 -0.780741939 5.748916361 1.000000016 0.838085538 0.028311795 0.201251155 3.57E-08 7.53E-09 0.170918812 0.040285946 0.165675413 0.780741939 -0.161914478 YFDPANGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YFDPANGK 8 0 P13639 P13639 EEF2 Elongation factor 2 0 ; 144.38 0.0013642 505410000 1310120 1263070 1363230 1226950 1427690 1134750 1605260 1224770 1557350 FALSE TRUE 1228121.928 1356589.017 1395566.459 1258435.614 1315564.986 1462333.904 1364566.166 1377685.231 1297418.224 0.946589084 1.045606568 1.07564888 0.969953706 1.013986825 1.127110655 1.051755047 1.061866717 1 20.30721218 YFDS(ph)GDYNMAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 15 YFDSGDYNMAK 11 0 A6NMQ3;Q5T5H1;O43768-2;O43768;O43768-9;O43768-3;O43768-4;O43768-6;O43768-5;O43768-7;P56211;H3BMD8;P56211-2;H3BQ52;H3BTD3 A6NMQ3;P56211 ENSA;ARPP19 Alpha-endosulfine;cAMP-regulated phosphoprotein 19 1 YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK 252.44 2.30E-20 18326350000 31192590 25493170 25239280 24101360 27096980 20911020 42887510 29355450 42097750 TRUE FALSE 29240301.47 27380710.83 25837967.64 24719841.7 24968892.49 26947692.01 36456926.02 33020542.55 35071363.56 0.833737229 0.78071418 0.736725494 0.704844043 0.711945301 0.768367388 1.039506946 0.941524343 1 25.06379019 1.773049568 7.134698901 0.99187666 0.752513347 0.870963545 0.043093377 0.05986049 8.003521172 0.020071205 0.011157767 59.29930016 -1.773049568 -0.239363313 YFEADPPGQVAAS(ph)PDPTT ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YFEADPPGQVAASPDPTT 18 0 O43598;H0Y8X4 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 1 YFEADPPGQVAAS(1)PDPTT;YFEADPPGQVAAS(1)PDPTT 200.94 1.53E-15 136147000 350330 397430 394420 412000 430910 315610 380860 338010 423980 TRUE FALSE 328403.4707 426856.1307 403775.8287 422572.6175 397068.0668 406721.4835 323753.5787 380211.2926 353214.999 0.929755168 1.208488122 1.143144628 1.19636091 1.124154036 1.15148418 0.916590687 1.076430202 1 18.43018708 1.755008146 25 0.992966319 1.139829899 0.324946337 0.085168184 5.667273946 8624.108079 0.03568001 0.019786475 56.88636011 -1.755008146 0.14686358 YFEITEEPPYIHFLNTFTSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YFEITEEPPYIHFLNTFTSK 20 0 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ; 223.44 6.47E-25 219954000 383620 427480 394550 394700 448800 333290 476910 398630 367510 FALSE TRUE 359609.909 459131.064 403908.9123 404828.6702 413553.0584 429505.4125 405401.7729 448399.833 306170.2068 1.174542464 1.499594192 1.319229969 1.322234043 1.350729265 1.40283216 1.324105886 1.464544306 1 18.22397438 -1.141093837 4.759874033 0.999970266 1.364371822 0.612665157 0.089103462 2.48E-05 4.47E-06 0.075949418 0.017899991 0.072261365 1.141093837 0.364401556 YFHVVIAGPQDSPFEGGTFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YFHVVIAGPQDSPFEGGTFK 20 0 P61088;F8VSD4;F8VV71;F8VZ29 P61088 UBE2N Ubiquitin-conjugating enzyme E2 N 0 ; 286.7 2.80E-45 1192350000 1683980 1612490 1564190 1453720 1830990 1113990 1901290 1634970 1529740 FALSE TRUE 1578582.698 1731880.437 1601293.325 1491024.916 1687191.431 1435580.829 1616209.215 1839099.604 1274416.512 1.23867094 1.35895951 1.256491352 1.169966728 1.323893261 1.12646126 1.268195445 1.443091475 1 20.28140543 -2.269860598 2.100910852 3.93E-05 1.271043977 0.477684071 0.089759721 1272679.237 139979.3794 6080310.613 0.020398395 0.005372042 2.269860598 1.271004639 YFIRDEFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YFIRDEFLR 9 1 P63092-4;P63092;P63092-3;A0A590UJ58;B0AZR9;A0A590UJF0;A0A590UJY2;A0A0A0MR13;P63092-2;Q5JWF2 P63092-4;P63092-2;Q5JWF2 GNAS Guanine nucleotide-binding protein G(s) subunit alpha isoforms short;Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas 0 ; 170.68 5.25E-05 440750000 228830 637280 197251 233530 768090 128215 193487 569580 697840 FALSE TRUE 214507.9388 684464.8743 201929.8869 239522.7752 707767.3097 165228.5891 164475.4206 640693.3168 581365.9958 0.368972283 1.177339024 0.347336942 0.411999974 1.217421237 0.284207522 0.282912007 1.102048144 1 19.14908716 1.214207341 24.93220938 1.051024832 0.603896697 0.238456727 0.345370131 399.2653342 408745.7086 0.324536402 0.08129354 16.37598159 -1.214207341 -0.447128135 YFLNHIDQTTTWQDPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YFLNHIDQTTTWQDPR 16 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8;P46937-4 P46937-6 YAP1 Transcriptional coactivator YAP1 0 64.275 0.061676 346300000 173640 183340 209150 170510 216620 160640 209580 186120 222510 FALSE TRUE 162772.1824 196914.6844 214111.1368 174885.5753 199607.539 207014.1602 178155.4246 209357.4917 185371.6435 0.878085662 1.062269723 1.15503716 0.943432188 1.076796511 1.116752035 0.961071614 1.129393297 1 17.50006104 4.73911553 24.14694761 1.059468954 0.878085584 0.38635072 0.070154797 29.14886717 1267876.509 0.015906425 0.094145298 54842.2836 -4.73911553 -0.18138337 YFLNLVLVDEEDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YFLNLVLVDEEDRR 14 1 O75436 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ; 262.37 2.37E-24 768170000 587830 748700 703590 683660 781850 586540 774060 735250 596900 FALSE TRUE 551038.7696 804134.527 720279.4871 701203.873 720446.6548 755864.5763 657996.889 827047.581 497273.5339 1.108120043 1.617086919 1.448457314 1.410096909 1.448793482 1.520017706 1.323209148 1.663164284 1 18.92368012 -1.158465033 4.234772372 0.999878244 1.451678054 0.448500462 0.153854505 10.96505122 38145805.99 9116.962034 0.031637385 0.06942805 1.158465033 0.45179981 YFNEMSAQGLRPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YFNEMSAQGLRPR 13 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 129.29 4.31E-05 0 362660 381100 373820 376500 459220 298650 465290 375700 525180 FALSE TRUE 339961.758 409317.0405 382687.1869 386161.6274 423154.7136 384865.4068 395524.084 422606.972 437524.0652 0.777012706 0.935530347 0.874665458 0.8826066 0.967157574 0.879643973 0.904005323 0.965905662 1 18.73900285 7.999990913 0.021052115 1.604990811 1.44E-10 0.496636331 0.044737258 2643.211164 4.285836743 119.1905385 222.37075 99997907.71 -7.999990913 -1.604990811 YFQFQEEGKEGENR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YFQFQEEGKEGENR 14 1 O15144 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;; 212.39 2.28E-09 690920000 3642930 2173320 3047310 3721660 3653940 1414430 2427670 1587620 3315970 FALSE TRUE 3414925.514 2334234.874 3119593.632 3817164.096 3366974.292 1822752.98 2063663.421 1785837.852 2762513.185 1.236166232 0.844967867 1.129259273 1.381772263 1.218808406 0.659816934 0.747023917 0.646454055 1 21.39754992 2.237260198 24.99840042 0.73981089 1.124426191 0.580633494 0.166201428 26.8286212 515718.9701 0.062391355 0.048632153 172.6872198 -2.237260198 0.384615301 YFQHLLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YFQHLLGK 8 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2;J3QL06;J3KTF1;Q9BST8;J3QQH7;J3QLE9 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 86.794 0.015781 834990000 3080100 4145600 2952300 3094900 4183800 1881840 3554900 3491100 3321800 FALSE TRUE 2887322.039 4452544.537 3022329.95 3174320.374 3855221.225 2425096.659 3021875.747 3926971.52 2767370.12 1.043345094 1.608944357 1.09213073 1.147053063 1.393099245 0.876318148 1.091966602 1.419026494 1 21.40008418 3.73797088 21.9143752 1.140128044 1.361742836 0.107433828 0.210334992 127.0172378 256544.5112 0.049791453 0.088311868 5469.792858 -3.73797088 0.221614792 YFQINQDEEEEEDED ddPTM_SK-BR-3_Pertuzumab_2h_R1 22 YFQINQDEEEEEDED 15 0 P35268;K7ERI7 P35268 RPL22 60S ribosomal protein L22 0 ;;;;;;;;;;;;;;;;;;;;; 351.94 4.99E-82 9112203000 9368949 10524745 10512323 10567537 10670197 9658652 11374822 9004961 10246763 FALSE TRUE 8782563.206 11304008.07 10761680.27 10838717.89 9832202.769 12446948.04 9669273.04 10129250.2 8536512.059 1.028823382 1.324195174 1.2606648 1.269689285 1.151782215 1.458083577 1.132695997 1.186579499 1 23.02521529 0.905297522 1.478653982 1.003593396 1.25302582 0.283286252 0.115282471 0.570804933 2.479857171 0.096624859 0.028464434 8.040767821 -0.905297522 0.249432424 YFQS(ph)PS(ph)RS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YFQSPSRSR 9 1 Q16629;Q16629-4;H7BZZ6 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 3 Y(0.007)FQS(0.994)PS(0.999)RS(1)R;Y(0.004)FQS(0.998)PS(0.997)RS(1)R 69.92 0.043927 1043060000 1424920 1335430 1497740 1324150 1120200 1478420 1670330 1058220 990030 TRUE FALSE 1335736.801 1434306.627 1533267.1 1358129.931 1032224.011 1905215.854 1419879.523 1190341.096 824787.5972 1.619491861 1.739001207 1.858984186 1.646642039 1.251502828 2.309947264 1.721509305 1.443209258 1 19.65366311 0.968200097 3.026669302 1.003275333 1.754421586 0.45590025 0.259018326 0.219466433 4.955676539 0.231156088 0.060761303 9.29394497 -0.968200097 0.751146253 YFQS(ph)PSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YFQSPSR 7 0 Q16629;Q16629-4;H7BZZ6 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 1 YFQS(0.918)PS(0.082)R 121.8 0.0046187 351810000 471150 795670 439490 405580 814150 328040 372170 805640 752910 TRUE FALSE 441661.5625 854582.2347 449914.9103 415987.8694 750209.9431 422739.8227 316366.5636 906225.9274 627244.457 0.704129877 1.362438879 0.717287981 0.663198957 1.19604077 0.673963425 0.504375224 1.444773114 1 19.25866829 5.026038541 16.34330409 0.910018765 0.155660318 0.044382649 0.316031883 2174534.69 36123881.01 0.073741079 43695296.26 106178.9779 -5.026038541 -0.754358448 YFSDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YFSDLR 6 0 E7ESC6;Q9UIA9 E7ESC6 XPO7 Exportin-7 0 ;;; 113.25 0.061181 812482000 1683950 2288410 1951720 2012190 2183640 1555850 2117050 1962640 1849440 FALSE TRUE 1578554.575 2457846.257 1998015.72 2063826.202 2012145.723 2004998.638 1799618.006 2207679.924 1540756.516 1.024532143 1.59522042 1.296775772 1.339488868 1.305946593 1.301307907 1.168009343 1.432854511 1 20.55520746 -4.04760217 0.210404311 2.54E-13 1.374736414 0.245311033 0.154193504 112.1059075 1.606273375 47.73595818 0.308823171 8.96E-05 4.04760217 1.374736414 YFSIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YFSIDR 6 0 K7ER00;Q9Y285;Q9Y285-2;K7EPH2;K7ERS0 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ; 102.81 0.08195 464510000 702430 928340 805680 807830 917090 673830 893390 840610 848510 FALSE TRUE 658466.1602 997075.2595 824791.1101 828560.2855 845065.4508 868353.7823 759434.4633 945562.0089 706888.1994 0.93149972 1.410513374 1.166791454 1.172123521 1.195472568 1.228417426 1.074334617 1.33764011 1 19.43112253 -1.928057913 2.561278966 0.869579763 1.199398656 0.168623296 0.130705626 16681540.44 9609928.444 13037435.8 0.029523632 0.011801633 1.928057913 0.329818893 YFTWDPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YFTWDPSR 8 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 82.241 0.048351 126790000 351710 1062700 360330 377700 1138100 335870 420800 876420 743180 FALSE TRUE 329697.0989 1141383.414 368877.1978 387392.4214 1048718.217 432830.2166 357704.9465 985842.9662 619138.4569 0.532509482 1.843502695 0.595791125 0.625695944 1.693834723 0.699084691 0.57774629 1.592281913 1 19.23990255 3.946961541 24.22055098 0.927902242 1.273898341 0.020488785 0.503758172 591.2010901 474779.5503 0.119725785 0.21588194 8850.372311 -3.946961541 0.345996099 YFTWDPSRFPQPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YFTWDPSRFPQPR 13 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 91.62 0.0058807 646660000 461260 885870 560100 616210 939930 389340 734150 633950 1206630 FALSE TRUE 432390.56 951460.7365 573385.8365 632022.9918 866111.6893 501736.1376 624071.023 713100.053 1005235.658 0.430138502 0.946505159 0.57039942 0.628731171 0.861600643 0.499122901 0.620820619 0.709385951 1 19.93910232 0.95236612 17.83826795 1.000000004 0.668327001 0.328916639 0.154025999 265.1407894 99293.64979 0.13773579 0.034434576 8.961198959 -0.95236612 -0.331673003 YFVAFDGDLVQEFDMTSATHVLGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YFVAFDGDLVQEFDMTSATHVLGSR 25 0 P49916-3;P49916 P49916-3 LIG3 DNA ligase 3 0 ;; 146.25 2.63E-07 21777400 18118.6 28203.4 25113.7 26141.1 26622.5 21042.3 27487 24201.7 23279.7 FALSE TRUE 16984.58917 30291.60908 25709.40882 26811.92488 24531.67624 27116.87042 23365.57953 27223.33552 19394.16768 0.875757571 1.561892708 1.325625789 1.382473604 1.264899667 1.398197173 1.204773513 1.403686715 1 14.24333524 -3.002837888 0.482904435 7.02E-10 1.328153462 0.203406884 0.180437924 313.7434693 10.89414231 324.0878689 0.079479707 0.000993487 3.002837888 1.328153461 YGAFGLPITVAHVDGQTHMLFGSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YGAFGLPITVAHVDGQTHMLFGSDR 25 0 Q9Y2Q3-3;Q9Y2Q3;Q9Y2Q3-2;Q9Y2Q3-4 Q9Y2Q3-3 GSTK1 Glutathione S-transferase kappa 1 0 ;; 234.74 1.25E-38 551059000 437552 592587 428136 407289 679505 346606 494916 554936 441908 FALSE TRUE 410166.4014 636462.7581 438291.5881 417740.7253 626139.4183 446665.5255 420707.9404 624220.9812 368150.7 1.114126366 1.728810398 1.190522219 1.134700342 1.700769327 1.213268169 1.142760126 1.695558317 1 18.48993692 -2.155525625 2.370100223 0.153856831 1.361994883 0.171165178 0.252382941 6691196.275 2000666.11 30343040.15 0.056665555 0.006989955 2.155525625 1.208138051 YGAHNYHPLPVALER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YGAHNYHPLPVALER 15 0 P04181 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ; 108.71 0.00061131 261590000 360170 443300 291460 254200 565690 248360 277300 420270 570430 FALSE TRUE 337627.6026 476122.3933 298373.5688 260723.2024 521262.9893 320057.5002 235721.4393 472741.6346 475221.5479 0.710463581 1.001895632 0.627862036 0.54863506 1.096884162 0.673491136 0.496024308 0.994781564 1 18.85824073 1.11113499 15.20979706 0.999966837 0.742345915 0.254151271 0.185629866 1.129837676 144.9240295 0.177499446 0.044376199 12.91620681 -1.11113499 -0.257620922 YGASLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YGASLR 6 0 Q6P4E4;E9PEL3;P61513;G5E9R3;E9PPK6;G3V1E1;P17405-3;P17405-4;P17405;P17405-2;E9PQT3 Q6P4E4;P17405-2 RPL37A;SMPD1 60S ribosomal protein L37a;Sphingomyelin phosphodiesterase 0 107.73 0.072163 578370000 436700 563640 543700 565000 591910 477150 589070 496460 507130 FALSE TRUE 409367.7265 605372.4921 556596.8208 579498.8565 545423.7763 614895.4591 500744.4222 558444.1238 422486.7268 0.968948136 1.432879316 1.317430313 1.371638018 1.290984406 1.455419591 1.185231134 1.321802765 1 18.68854649 -1.019416061 4.773720077 0.999993578 1.30813221 0.302252287 0.138245473 8.37E-06 1.72E-06 0.118587534 0.027950767 0.09562775 1.019416061 0.308138633 YGDFFIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YGDFFIR 7 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90;H0Y7E6 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ; 118.01 0.01187 111639000 233760 384480 293690 317130 403180 290020 270170 330660 326080 FALSE TRUE 219129.3789 412947.2993 300656.4655 325268.0927 371515.8691 373744.0659 229660.5166 371943.6289 271655.1414 0.806645432 1.520115898 1.106757869 1.19735666 1.367601096 1.375803395 0.845412001 1.369175738 1 18.05141683 1.756519329 24.99999999 1.059986 1.252631967 0.08922055 0.228135929 13.72533723 19126.58602 0.09515374 0.052768564 57.08464824 -1.756519329 0.192645967 YGDGGSSFQSTTGHCVHMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YGDGGSSFQSTTGHCVHMR 19 0 P55795 P55795 HNRNPH2 Heterogeneous nuclear ribonucleoprotein H2 0 ; 189.9 7.52E-15 814770000 123059 223780 177036 193006 269290 145354 233910 200961 308330 FALSE TRUE 115356.9569 240348.904 181235.3775 197958.8607 248141.0497 187315.3402 198837.367 226051.4232 256867.7311 0.449090886 0.935691311 0.705559148 0.770664575 0.966026556 0.729228772 0.774084647 0.880030443 1 17.97066614 -4.999999999 0.030598981 2.163715781 3.63E-08 0.32157157 0.131948852 2046.988455 4.713966085 262.1276476 104.3937185 1.00E-05 4.999999999 -2.163715745 YGDGGSTFQSTTGHCVHMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YGDGGSTFQSTTGHCVHMR 19 0 P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7;D6RIT2;H0YBG7 P31943 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 114.03 9.57E-05 646640000 459050 645100 603550 455180 621110 389200 631700 453800 670450 FALSE TRUE 430318.8799 692863.8752 617866.491 466860.6894 572330.526 501555.7219 536982.4494 510457.9289 558547.5637 0.770424773 1.240474259 1.106202105 0.835847687 1.024676434 0.89796421 0.961390729 0.913902346 1 19.09132061 3.262295433 24.77305536 0.939838343 1.09179511 0.072145732 0.129148314 284.9068376 297367.3266 0.033079267 0.044763946 1829.344224 -3.262295433 0.151956767 YGDGYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YGDGYR 6 0 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 0 112.27 0.06314 424960000 759800 822260 797850 830370 725340 644920 906590 702760 1018900 FALSE TRUE 712245.4743 883140.986 816775.3788 851678.7 668374.7223 831097.9346 770655.2459 790501.133 848839.0077 0.839081932 1.040410464 0.96222649 1.003345384 0.78739869 0.979099602 0.907893298 0.931273334 1 19.69513143 4.780268983 22.88084708 0.950928491 0.839080884 0.206727798 0.069173032 15319.8705 8403791.816 0.016047082 5.310733262 60293.29004 -4.780268983 -0.111847607 YGDSEFTVQSTTGHCVHMR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YGDSEFTVQSTTGHCVHMR 19 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 206.74 2.02E-16 717940000 462990 634040 623500 601690 667540 506770 688500 587020 782620 FALSE TRUE 434012.2824 680984.9813 638289.7144 617130.3841 615114.1011 653066.2723 585265.8167 660310.7392 651995.6661 0.665667435 1.044462435 0.978978462 0.946525286 0.943432807 1.001642045 0.897652925 1.012753264 1 19.31450285 4.74654768 24.99394773 0.974669277 0.665667284 0.849117643 0.041377057 391.673199 1225636.51 0.010144576 0.113055355 55788.88473 -4.74654768 -0.309001994 YGDSLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YGDSLYR 7 0 Q9BZE4-2;Q9BZE4;Q9BZE4-3;Q5T3R7 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 ;;; 114.02 0.013954 836030000 1130090 1336370 1231160 1161850 1242950 930200 1309680 1121930 1242260 FALSE TRUE 1059359.684 1435316.225 1260363.697 1191665.038 1145333.721 1198733.639 1113305.642 1262005.43 1034918.781 1.023616253 1.386887795 1.217838269 1.151457545 1.106689474 1.158287647 1.075742042 1.21942461 1 19.98108612 3.22827723 2.749078877 1.117907212 1.253120631 0.115828144 0.104642188 0.346223022 5.342909094 0.028805519 0.038295739 1691.520361 -3.22827723 0.135213419 YGEAGEGPGWGGAHPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YGEAGEGPGWGGAHPR 16 0 P26640;A0A140T954;A2ABF4;A0A0G2JJT9 P26640 VARS Valine--tRNA ligase 0 ; 248.68 1.91E-20 1395310000 1245700 1150880 1373100 1279240 1340650 836210 1177940 1200610 1205990 FALSE TRUE 1167733.861 1236092.353 1405670.58 1312067.464 1235360.757 1077610.252 1001318.832 1350508.801 1004702.478 1.162268319 1.230306862 1.399091384 1.305926374 1.22957869 1.072566532 0.996632191 1.344187788 1 19.93833691 2.364742623 3.964482942 1.090844391 1.286366494 0.339607659 0.112365378 0.223101459 6.51402888 0.03944747 0.032322816 231.6021695 -2.364742623 0.195522103 YGEIPAELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YGEIPAELR 9 0 F8WAU4;C9IZ01;Q96RP9;Q96RP9-2 F8WAU4 GFM1 "Elongation factor G, mitochondrial" 0 ; 85.731 0.034005 173471000 492770 420810 404360 367010 564670 406360 432200 473860 774220 FALSE TRUE 461928.4053 451967.2103 413951.6102 376428.0979 520323.096 523669.5353 367395.6223 533022.4641 644997.6803 0.716170646 0.700726877 0.64178775 0.583611553 0.806705376 0.811893672 0.569607665 0.826394389 1 19.29893445 0.98647819 7.023559359 0.999964433 0.687254035 0.61650026 0.079928679 0.085397277 27.24275091 0.074371274 0.018651456 9.693445882 -0.98647819 -0.312710398 YGEPGEVFINK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YGEPGEVFINK 11 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 129.85 0.0022796 0 192154 170124 191839 177302 198658 139786 220380 163147 249100 FALSE TRUE 180127.4241 182720.158 196389.5117 181851.8695 183056.202 180139.949 187336.0649 183516.2621 207523.6008 0.867985248 0.88047893 0.946347842 0.876294883 0.882098235 0.868045602 0.902721735 0.88431514 1 17.66291589 -1.920273903 2.485981635 1.068225552 0.892294694 0.696073761 0.023028198 6229314.282 3004478.512 2470471.366 0.005717876 0.012015064 1.920273903 -0.175930857 YGEPTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YGEPTLR 7 0 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 110.36 0.036942 0 172990 181340 196730 188300 184990 154020 208350 171190 181460 FALSE TRUE 162162.8647 194766.6023 201396.5285 193132.0968 170461.6316 198483.0737 177109.8517 192563.4483 151173.1537 1.072696181 1.28836766 1.332224165 1.277555519 1.127591953 1.312951862 1.171569471 1.273793948 1 17.20584243 -2.344511907 0.401545751 0.65587931 1.250492051 0.40697558 0.085679629 61.49197652 3.083954321 18.79628475 0.05082796 0.004523641 2.344511907 0.594612741 YGEYFPGTGDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YGEYFPGTGDLR 12 0 Q92769;Q92769-3;Q13547;Q5TEE2 Q92769;Q13547 HDAC2;HDAC1 Histone deacetylase 2;Histone deacetylase 1 0 ;;;;; 208.63 1.50E-07 2383270000 2103550 2220910 2226970 2237080 2276370 1838200 2460800 2004670 2258610 FALSE TRUE 1971892.56 2385348.487 2279794.78 2294487.26 2097593.083 2368858.499 2091825.885 2254957.462 1881633.4 1.047968515 1.267700971 1.21160412 1.219412485 1.114772454 1.258937315 1.111707459 1.198404249 1 20.84355414 -0.456990536 0.459838539 0.961661519 1.199123781 0.370048027 0.070780198 7.673201602 1.501583999 0.532896584 0.034821456 0.349147924 0.456990536 0.237462262 YGGELVPHFPAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 122.42 0.00035881 336440000 527350 1060300 455070 450170 938180 310170 562950 843170 1116350 FALSE TRUE 494344.1048 1138805.715 465864.4753 461722.1243 864499.1272 399711.0438 478540.8737 948441.6305 930023.9731 0.531539099 1.22449071 0.500916631 0.496462605 0.929544993 0.429785742 0.514546815 1.019803422 1 19.82690838 -1.582417326 2.919643999 1.017641137 0.707626258 0.106240774 0.268048924 74382581.53 79687083.84 10175928.38 0.062707059 0.026156683 1.582417326 -0.310014879 YGGGGYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YGGGGYGR 8 0 Q01130;J3KP15 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;;;;; 140.01 0.001527 4540930000 4286530 4626350 4154820 4363780 4804850 3204790 4474950 4188360 4594640 FALSE TRUE 4018243.739 4968889.768 4253374.292 4475761.983 4427496.463 4129960.848 3803972.791 4711285.966 3827764.901 1.049762418 1.298117804 1.111190055 1.169288631 1.156679309 1.078948408 0.993784333 1.230819052 1 21.86807079 2.249429283 4.129539088 1.065373396 1.171787478 0.158664037 0.089035087 0.290348261 11.28133275 0.031175754 0.024106294 177.5944065 -2.249429283 0.106414082 YGGPPPGWEGPHPQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YGGPPPGWEGPHPQR 15 0 B7Z8Z7;A0AV96;A0AV96-2;D6R9D6;D6RBS9;D6REZ6;D6R9M7;D6RBP6;D6RFL5;D6RA49 B7Z8Z7 RBM47 RNA-binding protein 47 0 ; 138.21 1.19E-05 216800000 183823 202704 198495 181385 193986 185449 227180 184066 214570 FALSE TRUE 172317.8466 217712.4151 203203.3951 186039.6462 178751.1221 238985.1158 193116.468 207047.0453 178756.8808 0.963978817 1.21792467 1.136758452 1.040741175 0.999967784 1.336928205 1.080330263 1.158260562 1 17.44763925 YGGSVGSQPPPVAPEPGPVPSS(ph)PSQEPPTKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YGGSVGSQPPPVAPEPGPVPSSPSQEPPTKR 31 1 A0A087WTZ5;Q04323;E9PJ81;E9PRQ7;Q04323-2;E9PS08 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 1 YGGSVGSQPPPVAPEPGPVPS(0.105)S(0.713)PS(0.143)QEPPT(0.04)KR;YGGSVGSQPPPVAPEPGPVPS(0.154)S(0.739)PS(0.097)QEPPT(0.011)KR;YGGSVGSQPPPVAPEPGPVPS(0.151)S(0.755)PS(0.092)QEPPT(0.002)KR;YGGSVGSQPPPVAPEPGPVPS(0.151)S(0.697)PS(0.151)QEPPT(0.002)KR 268.23 1.78E-59 3421570000 1874385 1691861 1853885 2073861 2078166 1356114 1953941 1373942 2102890 TRUE FALSE 1757070.589 1817128.149 1897860.028 2127079.784 1914955.225 1747602.097 1660965.687 1545481.683 1751904.074 1.002949086 1.037230392 1.083312754 1.214153113 1.093070822 0.997544399 0.948091686 0.882172549 1 20.74049235 2.029091 2.912537224 0.940147555 1.084631392 0.541410893 0.060577152 0.214761309 3.564968345 0.030068472 0.018054953 106.9278907 -2.029091 0.144483837 YGIDKDKVDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YGIDKDKVDK 10 2 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 78.116 0.017418 942530000 3148400 1630000 2116600 1964300 2320800 1328100 2765600 1716900 3210700 FALSE TRUE 2951347.264 1750686.896 2166806.752 2014707.264 2138533.73 1711500.91 2350923.955 1931258.744 2674813.428 1.103384346 0.654508041 0.810077716 0.753214128 0.799507624 0.639858052 0.878911377 0.722016244 1 21.35100683 -1.094293427 4.485534873 1.000016308 0.782999365 0.189446442 0.131003379 2.13E-05 4.30E-06 0.109744242 0.025864727 0.080483448 1.094293427 -0.217016943 YGIICMEDLIHEIYTVGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YGIICMEDLIHEIYTVGK 18 0 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 249.06 1.35E-24 848310000 1344980 1258350 1383710 1384110 1437010 1101140 1548450 1329280 1187860 FALSE TRUE 1260800.103 1351519.543 1416532.255 1419628.606 1324153.031 1419021.242 1316274.298 1495243.534 989598.4921 1.274052166 1.365725144 1.431421193 1.43455009 1.338070987 1.433936343 1.330109441 1.510959794 1 19.91648378 -0.937522759 6.524134336 0.999999955 1.388797602 0.768964874 0.067154474 3.97E-08 6.48E-09 0.057881029 0.013642688 0.115472147 0.937522759 0.388797647 YGIICMEDLIHEIYTVGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YGIICMEDLIHEIYTVGKR 19 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 254.59 4.28E-31 1348640000 638630 1109620 826170 869930 1301120 616600 1123560 860150 1714940 FALSE TRUE 598659.2883 1191777.419 845767.1425 892253.8766 1198935.284 794602.4103 955092.6086 967541.6209 1428705.435 0.419022196 0.834165945 0.591981469 0.624519131 0.83917598 0.556169516 0.668502117 0.677215609 1 20.44627707 0.584860507 3.137958367 0.999998293 0.662228553 0.43810168 0.123676926 8.702236323 64.62388327 0.10522305 0.0273803 3.844682734 -0.584860507 -0.337769741 YGINTTDIFQTVDLWEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YGINTTDIFQTVDLWEGK 18 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 328.14 1.87E-74 78328000 358240 360070 293270 311930 334780 187420 393670 306260 533320 FALSE TRUE 335818.3979 386729.9575 300226.5029 319934.6519 308487.7292 241525.1115 334642.8382 344497.2352 444305.4466 0.755827777 0.870414622 0.67572096 0.720078168 0.694314534 0.54360151 0.75318194 0.77536127 1 18.7611923 0.775752389 2.40351491 0.999746711 0.72031658 0.547992054 0.080689098 0.816564727 7.275864293 0.080704828 0.021711011 5.966949866 -0.775752389 -0.279430131 YGISSMIQSQEKPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YGISSMIQSQEKPDR 15 1 P14868;H7C278 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ; 233.02 1.17E-17 953380000 404300 371490 404080 379500 394960 272997 459230 321350 405160 FALSE TRUE 378995.5847 398995.5061 413664.9684 389238.6125 363941.4348 351806.8022 390372.7248 361471.2549 337536.1786 1.122829518 1.182082193 1.225542608 1.153175977 1.07822941 1.042278797 1.15653595 1.070911143 1 18.36468262 2.866275017 3.868487112 1.083377555 1.185297587 0.524608626 0.046972644 0.190924801 5.003134878 0.014369426 0.015395252 734.9791462 -2.866275017 0.101920032 YGLFQHICTAYELVLADGSFVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YGLFQHICTAYELVLADGSFVR 22 0 A0A0A0MTI1;Q15392-2;Q15392;A0A3B3IT58;A0A3B3ITT9 A0A0A0MTI1 DHCR24 Delta(24)-sterol reductase 0 194.37 3.88E-18 41257000 37957 60641 30599 31201 71226 27482 40961 71493 28843 FALSE TRUE 35581.33913 65130.92274 31324.82273 32001.67048 65632.19727 35415.60727 34819.27831 80419.05843 24028.91697 1.480771654 2.71052261 1.303630237 1.331798288 2.731383914 1.47387447 1.449057332 3.346761676 1 14.552484 3.971118574 24.69531369 1.789887919 2.161435222 0.022055207 0.771817193 742.9536908 3056570.646 0.179920968 0.335653977 9356.610991 -3.971118574 0.371547302 YGLLVGGAASHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YGLLVGGAASHR 12 0 Q15274 Q15274 QPRT Nicotinate-nucleotide pyrophosphorylase [carboxylating] 0 ; 148.28 6.43E-05 1268140000 810790 1544050 961250 879440 1678120 819200 977380 1571700 1615370 FALSE TRUE 760044.1012 1658373.069 984051.3039 902007.9193 1546327.224 1055689.741 830830.9426 1767930.205 1345754.311 0.564771812 1.232300023 0.731226566 0.670261958 1.149041256 0.784459491 0.617371935 1.313709486 1 20.35998362 1.230441704 24.99997906 1.156854704 0.845654033 0.266999937 0.228364804 285.2362718 878272.7859 0.196819749 0.052615398 16.99971749 -1.230441704 -0.31120067 YGLQDS(ph)DEEEEEHPSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YGLQDSDEEEEEHPSK 16 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 YGLQDS(1)DEEEEEHPSK;YGLQDS(1)DEEEEEHPSK;YGLQDS(1)DEEEEEHPSK;YGLQDS(1)DEEEEEHPSK;YGLQDS(1)DEEEEEHPSK;YGLQDS(1)DEEEEEHPSK 315.98 5.09E-58 3366770000 2728160 2298490 2414610 2540420 2558500 1976330 3138620 2353090 2538870 TRUE FALSE 2557409.336 2468672.591 2471885.689 2605611.478 2357565.73 2546864.388 2668013.069 2646878.466 2115116.195 1.209110564 1.167156961 1.168676073 1.231899923 1.114627053 1.204125047 1.2614026 1.251410429 1 21.01230549 2.033429388 24.99716818 1.208177911 1.176356789 0 0.078988045 688.0226525 514473.0469 0.026208609 0.019356166 108.0014006 -2.033429388 -0.031821122 YGMGTS(ph)VER ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 YGMGTSVER 9 0 P08559-3;P08559;P08559-2;P08559-4 P08559-3 PDHA1 "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial" 1 YGMGT(0.141)S(0.859)VER;YGMGT(0.036)S(0.964)VER;YGMGT(0.045)S(0.955)VER;YGMGT(0.178)S(0.822)VER;YGMGT(0.02)S(0.98)VER;YGMGT(0.023)S(0.977)VER;YGMGT(0.022)S(0.978)VER 119.53 0.003086 12681550000 13012780 16306680 11596190 12657920 18498670 9902880 13411040 12757160 9271870 TRUE FALSE 12198333.33 17514043.55 11871257.1 12982743.66 17045859.08 12761680.7 11400179.05 14349919.51 7724334.998 1.579208221 2.26738529 1.536864611 1.680758753 2.206773668 1.652139724 1.475878384 1.857754682 1 22.8809793 -2.154760205 0.225001688 5.06E-10 1.936288525 0.454205004 0.268357607 30.35962226 0.953053602 16.07273272 0.515451292 0.007002285 2.154760205 1.936288525 YGNPWEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YGNPWEK 7 0 P11216;P11217;P11217-2;E9PK47;P06737-2;P06737 P11216;E9PK47 PYGB;PYGM;PYGL "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form;Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ; 120.49 0.010575 692270000 766000 778670 851470 882450 930260 628110 960070 755480 1008510 FALSE TRUE 718057.4273 836323.537 871667.2705 905095.161 857201.1321 809435.1605 816116.4164 849803.341 840183.1658 0.854643912 0.995406206 1.037472906 1.077259338 1.020255067 0.963403212 0.971355354 1.011450093 1 19.68034435 4.738934287 3.911775949 1.009916946 0.839857259 0.701857976 0.031889692 0.158247552 4.929260592 0.008652692 0.077056203 54819.40115 -4.738934287 -0.170059687 YGPADVEDTTGSGATDSKDDDDIDLFGS(ph)DDEEESEEAKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 14 YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR 39 2 P24534;C9JZW3 P24534 EEF1B2 Elongation factor 1-beta 1 YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(0.999)DDEEES(0.001)EEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR 442.81 2.71E-244 39887184000 8248750 3042387 4527242 4278406 4336041 2769734 5788515 3398824 6023380 TRUE FALSE 7732475.462 3267648.499 4634630.318 4388197.141 3995505.831 3569311.243 4920580.914 3823174.658 5018038.965 1.540935715 0.651180376 0.923593928 0.874484469 0.796228538 0.71129604 0.980578459 0.761886204 1 22.25869224 4.747772023 24.97323467 0.834117346 1.540936089 0.794452709 0.112451189 510.0807569 1382861.073 0.024840195 0.312147917 55946.38408 -4.747772023 0.706818743 YGPIVDVYVPLDFYTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YGPIVDVYVPLDFYTR 16 0 O75494-2;O75494;O75494-5;Q6IQ42;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10;FUSIP1 Serine/arginine-rich splicing factor 10 0 ; 152.31 1.30E-06 97351000 147351 184028 155166 130175 189008 124134 166188 167434 142741 FALSE TRUE 138128.5639 197653.6246 158846.6108 133515.5109 174164.0741 159969.4707 141269.6522 188338.5035 118916.605 1.161558253 1.66211964 1.335781583 1.122765916 1.464590031 1.345223997 1.187972464 1.583786415 1 16.85959065 -3.660124036 0.251138103 2.74E-14 1.402978608 0.24197895 0.181755938 117.0782512 2.138901591 61.0791237 0.252907251 0.000218714 3.660124036 1.402978608 YGPLS(ph)EPGSAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YGPLSEPGSAR 11 0 Q9H1Z4 Q9H1Z4 WDR13 WD repeat-containing protein 13 1 YGPLS(0.999)EPGS(0.001)AR 112.73 0.0015599 211130000 261060 262090 236430 250160 244790 202090 311770 208130 296130 TRUE FALSE 244720.7206 281495.4163 242038.2313 256579.5291 225565.1808 260430.1023 265022.9828 234115.4887 246703.9899 0.991960935 1.141024985 0.981087624 1.040029913 0.91431509 1.055637983 1.074254952 0.948973256 1 17.91242152 3.868256338 6.37671389 1.010444935 1.074666631 0.152940582 0.059848811 0.356759124 18.23586188 0.014613221 0.026655472 7383.398987 -3.868256338 0.064221696 YGQFSGLNPGGRPIT(ph)PPR ddPTM_SK-BR-3_Pertuzumab_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 179.17 1.37E-13 3157470000 3279010 3451810 3366280 3305410 3452010 2615630 4452100 3034760 3909210 TRUE FALSE 3073782.617 3707385.604 3446129.751 3390232.417 3180903.059 3370719.92 3784548.936 3413656.466 3256737.597 0.943822622 1.138374061 1.05815395 1.040990352 0.976714569 1.034998928 1.162067506 1.048182841 1 21.63499605 YGQFSGLNPGGRPITPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YGQFSGLNPGGRPITPPR 18 1 P62136;P62136-2;P62136-3 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 ; 229.4 1.73E-19 721610000 354560 381330 353810 376630 406660 316860 433350 317150 376700 FALSE TRUE 332368.7225 409564.07 362202.5403 386294.9634 374722.564 408332.3382 368373.1905 356746.8756 313826.3364 1.059084863 1.305065963 1.154149599 1.23091952 1.19404435 1.30114108 1.173812226 1.136765256 1 18.2596069 0.919912189 1.93355469 1.001105451 1.213242374 0.45224793 0.070744794 0.332939693 2.586987801 0.0591322 0.016568111 8.315956109 -0.919912189 0.212136923 YGQNCHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YGQNCHK 7 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ;; 128.82 0.0037209 1090390000 987430 937150 943750 876240 1056800 808900 1120130 929220 1230190 FALSE TRUE 925628.5189 1006537.561 966136.1957 898725.8019 973803.1909 1042416.299 952176.9053 1045235.162 1024863.342 0.903172629 0.982118806 0.942697584 0.876922576 0.950178576 1.01712712 0.929076948 1.019877597 1 19.96700012 2.463435198 24.27696732 0.98105043 0.935814254 0.382071216 0.037408559 235.566333 417854.6755 0.0127727 0.010692327 290.6934179 -2.463435198 -0.045236176 YGQNGDFTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YGQNGDFTR 9 0 O76094-2;O76094;R4GNC1 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 80.787 0.053794 194860000 80292 105530 96763 97936 105730 72932 99009 87418 105250 FALSE TRUE 75266.66705 113343.551 99058.26405 100449.2036 97426.39229 93986.28445 84163.5196 98332.32973 87683.09506 0.858394278 1.292649979 1.129730468 1.145593726 1.111119449 1.071886028 0.959860273 1.1214514 1 16.4200111 2.18040937 2.740473458 1.02178663 1.139760197 0.055229816 0.114364883 0.453726486 6.914675196 0.046553691 0.031809234 151.4988619 -2.18040937 0.117973567 YGREDLDVLGLTFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YGREDLDVLGLTFR 14 1 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 ;; 141.85 8.72E-06 188755000 221729 247941 246773 216618 313769 197250 240233 264045 334449 FALSE TRUE 207851.3777 266298.8096 252626.5721 222176.7846 289126.8484 254192.8729 204212.2919 297011.5995 278627.3013 0.74598353 0.955752751 0.906682766 0.797397755 1.037683124 0.912304256 0.732922764 1.065981683 1 18.0879771 1.205197119 24.99999922 1.032991148 0.879887682 0.334649962 0.094829784 264.7894159 198406.5966 0.087513647 0.021883719 16.03973241 -1.205197119 -0.153103466 YGRPPDSHHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YGRPPDSHHSR 11 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;; 86.772 0.0085445 338496000 50241 185163 113585 111357 163194 86451.4 123138 152376 139118 FALSE TRUE 47096.50549 198872.6612 116279.2898 114214.6091 150377.4015 111408.5158 104674.6001 171400.479 115898.3071 0.406360599 1.71592378 1.003287216 0.985472627 1.297494375 0.961260941 0.903159008 1.478886822 1 16.82249997 3.707114168 24.93041648 1.071978421 1.2161594 0 0.362109781 1663.402361 2072732.108 0.088155667 0.136767827 5094.647821 -3.707114168 0.144180978 YGS(ph)FEEAEASYPILNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YGSFEEAEASYPILNR 16 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 YGS(1)FEEAEASYPILNR;YGS(1)FEEAEASYPILNR 209.56 1.25E-11 54524000 96623 62584 66626 81730 68805 47983 99033 63022 114272 TRUE FALSE 90575.53891 67217.78448 68206.40018 83827.33017 63401.33285 61834.91316 84183.92103 70890.43543 95199.26497 0.951431074 0.706074616 0.716459315 0.880545981 0.665985529 0.649531414 0.884291712 0.74465318 1 16.53866281 0.160242633 0.868800959 1.002681039 0.760048479 0.314820628 0.101749603 4.48328662 3.70727307 0.127407515 0.03057114 1.446247539 -0.160242633 -0.24263256 YGS(ph)PPQRDPNWNGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YGSPPQRDPNWNGER 15 1 O15234;J3KSY7 O15234 CASC3 Protein CASC3 1 YGS(1)PPQRDPNWNGER;YGS(1)PPQRDPNWNGER;YGS(1)PPQRDPNWNGER;YGS(1)PPQRDPNWNGER 177.76 1.67E-06 2470130000 2790660 1958310 2205220 2309790 2425430 1818980 2727820 1811410 2899760 TRUE FALSE 2615997.572 2103305.31 2257528.86 2369063.122 2234946.512 2344089.997 2318808.715 2037568.526 2415771.323 1.082882948 0.870655798 0.934496092 0.980665305 0.925148209 0.970327769 0.959862671 0.843444289 1 21.20405246 4.754637436 24.61332419 0.934104769 1.082883088 0.480791438 0.048086855 2226.962346 3409369.103 0.010842018 0.282639103 56837.82309 -4.754637436 0.148778319 YGSIIDRDDRDER ddPTM_SK-BR-3_Pertuzumab_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 0 105 0.00083648 252170000 217270 247210 219930 258080 278980 193200 279910 208070 216440 FALSE TRUE 203671.4585 265513.6856 225146.8435 264702.7697 257070.0362 248973.7037 237940.0941 234047.9975 180314.7657 1.12953289 1.472501071 1.248632315 1.468003847 1.425673794 1.380772687 1.319581861 1.297996848 1 17.46015802 0.564563967 1.343124786 1.000143143 1.360722162 0.527376217 0.103040618 1.223991232 2.951215481 0.0877696 0.0260199 3.669137331 -0.564563967 0.360579019 YGTCPHGGYGLGLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YGTCPHGGYGLGLER 15 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;; 236.17 1.06E-17 2122090000 1856680 2532080 2191980 2207760 2805390 1735510 2368550 2474270 2696190 FALSE TRUE 1740473.713 2719557.838 2243974.801 2264414.859 2585065.986 2236523.563 2013407.916 2783188.056 2246178.471 0.774859939 1.210748778 0.999018925 1.008118851 1.150872924 0.995701629 0.89637041 1.239076989 1 21.09904113 YGVIILDEAHER ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 YGVIILDEAHER 12 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ;;;;;;; 208.03 7.16E-08 2646211000 2251841 2610910 2561438 2501310 2718001 2252537 2771613 2398927 2882850 FALSE TRUE 2110902.291 2804224.493 2622196.519 2565497.849 2504540.165 2902807.865 2356035.361 2698438.317 2401683.711 0.878926014 1.167607741 1.091815923 1.06820804 1.042826811 1.208655349 0.980993188 1.123561069 1 21.19561474 -2.597021233 0.654031645 0.805438762 1.079204 0.045459885 0.093066899 1458.823373 83.34278098 405.3330739 0.03104624 0.002529174 2.597021233 0.273765238 YGVYEDENYEVGS(ph)DDEEIPFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YGVYEDENYEVGSDDEEIPFK 21 0 O15541 O15541 RNF113A RING finger protein 113A 1 YGVYEDENYEVGS(1)DDEEIPFK;YGVYEDENY(0.001)EVGS(0.999)DDEEIPFK;YGVYEDENYEVGS(1)DDEEIPFK 139.22 2.24E-07 640666000 657746 502703 577640 575441 590399 441224 700448 515462 756010 TRUE FALSE 616578.852 539923.6532 591341.8936 590207.7903 544031.4441 568598.2061 595422.325 579818.5654 629827.047 0.978965344 0.857257013 0.93889568 0.937095022 0.863779107 0.902784675 0.945374334 0.92059966 1 19.26459619 0.531584339 0.867259838 1.000077823 0.910432199 0.322568885 0.036908927 1.679647988 1.971364589 0.034088934 0.011147454 3.400825429 -0.531584339 -0.089645624 YGYIHLYDLETGTCIYMNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YGYIHLYDLETGTCIYMNR 19 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 308 1.90E-61 554996000 805566 1068224 838820 800380 1125280 742198 1039781 1104809 721490 FALSE TRUE 755147.062 1147316.416 858717.2065 820919.1058 1036905.048 956458.514 883875.4919 1242746.836 601068.658 1.256340772 1.90879428 1.428650779 1.365765949 1.725102506 1.59126333 1.470506705 2.067562198 1 19.19717027 -1.039401257 4.939240669 0.999989194 1.600231248 0.369671872 0.246933542 2.62E-05 5.10E-06 0.213354578 0.050287252 0.091326906 1.039401257 0.600242055 YGYTHLSAGELLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YGYTHLSAGELLR 13 0 P30085;P30085-3;Q5T0D2 P30085 CMPK1 UMP-CMP kinase 0 ; 154.36 4.62E-05 927020000 542540 1600720 950290 937880 1620060 753820 919570 1427940 1436020 FALSE TRUE 508583.3899 1719238.974 972831.3276 961947.5886 1492827.023 971435.5968 781689.0154 1606221.452 1196338.985 0.425116456 1.437083465 0.81317364 0.804076103 1.247829454 0.812006972 0.653400938 1.342613985 1 20.19019481 YHCAIPGS(ph)KK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YHCAIPGSKK 10 1 Q709C8-3;Q709C8 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 1 YHCAIPGS(1)KK 80.469 0.014649 158190000 135180 79407 93614 86714 98315 60008 134360 78319 120090 TRUE FALSE 126719.3251 85286.3769 95834.56829 88939.22805 90593.73648 77331.33545 114213.9653 88097.29955 100046.2032 1.266608038 0.852469901 0.957903101 0.888981543 0.905518986 0.772956224 1.141612192 0.880566146 1 16.61030689 -1.594609515 7.840711779 1.000032428 0.951081465 0.005933327 0.144630987 7.37E-05 3.81E-06 0.125839935 0.029641118 0.025432584 1.594609515 -0.048950963 YHDGNRNPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YHDGNRNPK 9 1 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 100.02 0.0029712 77276000 51655 83860 52491 71050 95384 26373 63405 54549 104310 FALSE TRUE 48422.00576 90069.08166 53736.11131 72873.26329 87892.9254 33986.45697 53898.00887 61359.56273 86899.98713 0.557215339 1.036468297 0.61836731 0.838587734 1.011426219 0.391098527 0.620230344 0.706094037 1 16.40706834 2.248510422 24.99997728 0.635599531 0.817694918 0.074621204 0.208482758 361.2793043 907753.8121 0.066387775 0.054926739 177.2190574 -2.248510422 0.182095388 YHEAWQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YHEAWQK 7 0 P17812;B4E1E0;P17812-2;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ; 116.54 0.0054322 460150000 947050 1038300 983100 944670 1194580 747760 1177200 918640 1344140 FALSE TRUE 887775.831 1115176.812 1006419.596 968911.8315 1100762.506 963626.1731 1000689.789 1033334.226 1119794.351 0.792802563 0.995876441 0.89875395 0.865258725 0.983004161 0.86053852 0.893637111 0.922789283 1 20.09480238 0.906032758 7.426891334 0.999999802 0.907317818 0.217426116 0.058597225 3.910383074 308.9903502 0.051366753 0.012873087 8.054391923 -0.906032758 -0.092681985 YHEDFEK ddPTM_SK-BR-3_Pertuzumab_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 ; 170.06 0.00098884 545050000 1842810 1681110 1532910 1664500 1935680 1113900 1867530 1574670 1949740 FALSE TRUE 1727471.812 1805581.134 1569271.349 1707213.888 1783659.501 1435464.847 1587511.214 1771271.016 1624315.798 1.063507363 1.111594885 0.966112225 1.051035698 1.098098968 0.883735077 0.977341485 1.090472073 1 20.63140072 2.271030442 24.99998426 0.981418803 1.052509276 0.233092534 0.062319757 280.1909627 215730.6968 0.021360152 0.017869942 186.651052 -2.271030442 0.071090473 YHEEFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YHEEFEK 7 0 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;;;; 155.51 0.0016062 5341430000 12322600 9850680 10904900 10039680 11634800 8829900 13068900 9725510 17707500 FALSE TRUE 11551350.46 10580034.6 11163569.38 10297315.19 10721049.74 11378948.79 11109339.77 10939761.33 14752003.86 0.783036025 0.717193047 0.756749353 0.698028233 0.726752097 0.771349364 0.753073269 0.741577988 1 23.8144076 -2.655633028 0.45568389 1.521249618 0.737981036 0.911176171 0.025160926 31.95625548 1.425148072 16.38236656 0.012294815 0.002209871 2.655633028 -0.783268583 YHEEKER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YHEEKER 7 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 130.27 0.0021507 47915000 37578 42767 32502 41561 55129 26483 39461 41397 55357 FALSE TRUE 35226.06006 45933.51318 33272.96279 42627.52562 50799.39072 34128.21218 33544.18939 46565.50658 46117.55908 0.763831841 0.996009201 0.721481437 0.92432311 1.101519502 0.740026421 0.727362637 1.009713166 1 15.49302854 1.20026635 24.79087882 1.004857346 0.853220623 0.201566269 0.125229743 287.176293 185904.8453 0.118789071 0.02969978 15.85865497 -1.20026635 -0.151636724 YHGHS(ph)MSDPGVS(ph)YR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YHGHSMSDPGVSYR 14 0 P08559-3;P08559;P08559-2;P08559-4;Q5JPU3;P29803 P08559-3 PDHA1;PDHA2 "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial;Pyruvate dehydrogenase E1 component subunit alpha, testis-specific form, mitochondrial" 2 YHGHS(0.997)MS(0.003)DPGVS(1)YR;YHGHS(0.999)MS(0.001)DPGVS(0.995)Y(0.005)R 92.679 0.0025685 234910000 274930 422710 218848 261347 456480 174105 375370 297580 535510 TRUE FALSE 257722.6221 454007.8882 224039.1779 268053.6065 420629.9022 224366.2871 319086.7533 334733.5181 446129.9215 0.577685131 1.017658459 0.502183707 0.600842027 0.942841719 0.502916922 0.715232801 0.750305016 1 18.76710439 0.772306395 3.070166671 0.999936559 0.70413019 0.236204485 0.171049339 2.17330591 27.22266091 0.153645461 0.040110946 5.91979129 -0.772306395 -0.295806368 YHGHS(ph)MSDPGVSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 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(0.998)MS(0.002)DPGVSYR;YHGHS(0.759)MS(0.241)DPGVSYR;YHGHS(1)MSDPGVSYR;YHGHS(1)MSDPGVSYR;Y(0.002)HGHS(0.991)MS(0.007)DPGVSYR;YHGHS(0.999)MS(0.001)DPGVSYR;Y(0.276)HGHS(0.362)MS(0.362)DPGVSYR;YHGHS(0.998)MS(0.002)DPGVSYR;YHGHS(0.987)MS(0.013)DPGVSYR;YHGHS(0.978)MS(0.022)DPGVSYR;YHGHS(0.999)MS(0.001)DPGVSYR 211.17 1.41E-08 25348047000 8169400 8900158 7443732 7668455 10736943 6248106 7789116 7541858 7830275 TRUE FALSE 7658091.837 9559134.959 7620300.838 7865240.538 9893706.808 8051832.773 6621210.366 8483475.573 6523351.517 1.173950509 1.465371739 1.168157322 1.205705459 1.516660076 1.234309197 1.015001315 1.300478067 1 22.63718194 1.991572509 24.83762609 1.111283743 1.310283213 0.302589505 0.138970665 421.4268085 1242035.857 0.05014429 0.03523835 98.07820505 -1.991572509 0.19899947 YHGHSMS(ph)DPGVSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YHGHSMSDPGVSYR 14 0 P08559-3;P08559;P08559-2;P08559-4;Q5JPU3;P29803 P08559-3 PDHA1;PDHA2 "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial;Pyruvate dehydrogenase E1 component subunit alpha, testis-specific form, mitochondrial" 1 YHGHS(0.374)MS(0.626)DPGVSYR;YHGHS(0.227)MS(0.773)DPGVSYR 213.99 2.75E-10 247803000 341680 418360 302970 312540 464290 273390 341830 318720 349640 TRUE FALSE 320294.8587 449335.8097 310156.5915 320560.3055 427826.5363 352313.2549 290575.7649 358512.8936 291282.8252 1.099600907 1.542610037 1.064795328 1.100512209 1.468766776 1.209522925 0.997572599 1.23080684 1 18.15206111 1.579120452 0.292883786 0.971339243 1.331625984 0.146976594 0.171155264 2.550698725 0.813819777 0.334772762 0.321848753 37.94202028 -1.579120452 0.36028674 YHGNVMLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YHGNVMLLR 9 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 164.77 6.20E-05 1774620000 310420 1239580 369290 284945 1187570 263465 218599 985190 745810 FALSE TRUE 290991.3663 1331359.793 378049.7332 292257.1711 1094303.043 339523.0685 185822.1093 1108193.14 621329.4929 0.468336639 2.142759692 0.608452902 0.470373891 1.761228229 0.546446084 0.299071767 1.783583675 1 19.24499901 3.780284072 9.422923879 0.854263941 1.412027442 0.043198645 0.644907133 0.830140166 140.8224836 0.153765262 0.27712899 6029.538493 -3.780284072 0.557763501 YHIDLDPHFNDILGQHSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YHIDLDPHFNDILGQHSR 18 0 P19784;H3BSA1;H3BV19 P19784 CSNK2A2 Casein kinase II subunit alpha 0 ;; 135.27 3.05E-06 191099000 319370 401109 368499 361367 415568 292969 396824 343545 384923 FALSE TRUE 299381.2018 430807.5277 377239.9703 370640.289 382930.9656 377544.3943 337323.9251 386437.3495 320676.8646 0.933591521 1.343431894 1.176386612 1.15580614 1.194133434 1.177335929 1.051912259 1.205067756 1 18.29076075 0.641248396 0.4596886 0.993570248 1.193930058 0.115555111 0.109236628 2.68285429 1.183120515 0.164690314 0.061602903 4.377724184 -0.641248396 0.20035981 YHIEVNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YHIEVNR 7 0 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;;; 164.89 0.0011808 1211420000 1524890 1758070 1785190 1630390 1755000 1567050 1845520 1685350 1426400 FALSE TRUE 1429449.857 1888239.332 1827535.55 1672228.568 1617169.379 2019431.896 1568801.409 1895769.657 1188324.625 1.20291192 1.588992849 1.537909348 1.407215278 1.360881821 1.699394133 1.320179163 1.595329776 1 20.18049757 -1.291414564 3.881021754 0.99915357 1.476021824 0.490631726 0.148170176 356.9341142 34171208.36 47188.3503 0.030924176 0.051119363 1.291414564 0.476868254 YHNEMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YHNEMK 6 0 Q00059;Q00059-2 Q00059 TFAM "Transcription factor A, mitochondrial" 0 ;;;;; 129.96 0.015968 510740000 1319720 1166160 1082770 1105621 1486970 933598 1237490 1079160 1879420 FALSE TRUE 1237121.081 1252503.7 1108453.816 1133993.107 1370189.374 1203112.587 1051939.863 1213895.502 1565732.66 0.790122805 0.799947355 0.707945771 0.724257171 0.875110681 0.768402306 0.671851517 0.775289123 1 20.57840647 0.952842856 23.18309257 1.000000001 0.757161222 0.640412582 0.055515902 3595.053875 1767379.603 0.054264873 0.013566218 8.971041301 -0.952842856 -0.242838779 YHNTICGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YHNTICGR 8 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 ;;; 168.27 0.00030783 581329000 226364 398798 310412 367615 347105 316417 356388 319193 298905 FALSE TRUE 212196.2813 428325.4189 317775.1192 377048.6233 319844.7735 407761.4513 302950.9279 359044.9487 249015.8245 0.852139745 1.720073091 1.276124198 1.514155271 1.284435534 1.637492124 1.216593076 1.441855952 1 17.9258779 -1.156507742 5.592622402 0.999992486 1.392041959 0.17836489 0.243250233 1.96E-05 2.96E-06 0.202826264 0.047805693 0.069741656 1.156507742 0.392049473 YHNVGLSK ddPTM_SK-BR-3_Pertuzumab_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 ; 117.89 0.001992 1670240000 4174700 4423900 4240700 3908000 4602100 3058600 5115000 4053400 5170600 FALSE TRUE 3913412.979 4751450.159 4341291.407 4008285.896 4240669.63 3941568.168 4348053.235 4559475.913 4307593.457 0.908491718 1.103040528 1.007822918 0.930516293 0.984463755 0.915027894 1.009392664 1.058474055 1 22.03845067 5.093338149 10.57066524 1.002184434 3.18E-05 0.223317837 0.054237815 68866.72578 251551.862 0.013655905 1473665.475 123976.1509 -5.093338149 -1.002152599 YHPDEVGKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YHPDEVGKR 9 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 101.64 0.0024952 34724000 117550 117620 101200 94452 108810 79961 128560 92041 146090 FALSE TRUE 110192.7553 126328.7072 103600.5118 96875.79823 100264.5015 103044.4426 109283.6215 103532.5215 121706.6352 0.905396449 1.037977157 0.851231419 0.795977952 0.823821161 0.846662488 0.89792657 0.850672778 1 16.8930483 3.826573988 4.356183702 0.859043719 0.975440118 0.317579105 0.063060232 0.202622683 6.66191291 0.014915227 0.027818218 6707.705527 -3.826573988 0.1163964 YHPDKNKEPGAEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YHPDKNKEPGAEEK 14 2 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 164.65 2.46E-06 80559000 103130 62469 87735 89251 98245 49236 102900 65793 179770 FALSE TRUE 96675.27739 67094.26976 89816.11563 91541.33176 90529.234 63449.63392 87471.10028 74007.40088 149765.2256 0.645512181 0.447996319 0.599712752 0.611232223 0.604474327 0.423660657 0.584054809 0.494156107 1 17.19234315 -1.530221925 3.150087138 1.014990839 0.546857219 0.784509015 0.073863478 22165980.95 27402638.9 2856970.6 0.016685986 0.029497015 1.530221925 -0.46813362 YHPDKNPEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YHPDKNPEGR 10 1 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 ; 99.215 0.0029123 132100000 76565 123554 98065 132858 124339 111124 95866 101442 111616 FALSE TRUE 71772.93332 132702.0667 100391.1481 136267.3612 114573.9165 143203.6949 81491.78328 114107.257 92986.56853 0.771863447 1.427110053 1.079630636 1.46545209 1.23215555 1.540047096 0.876382305 1.227136981 1 16.50473472 1.712086305 19.34941727 1.039090509 1.260252421 0.163945322 0.23178936 0.478546435 339.9493034 0.095764362 0.053041441 51.53310429 -1.712086305 0.221161911 YHPDTNKDDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YHPDTNKDDPK 11 1 Q96EY1-2;Q96EY1;I3L1T6 Q96EY1-2 DNAJA3 "DnaJ homolog subfamily A member 3, mitochondrial" 0 87.363 0.0082798 56425000 132820 62486 74205 71548 95368 64997 93642 74563 131980 FALSE TRUE 124507.0333 67112.52846 75965.17764 73384.04281 87878.18198 83760.57876 79601.25143 83872.35468 109951.6854 1.132379489 0.610381989 0.690895982 0.667420809 0.79924361 0.761794405 0.723965723 0.762810996 1 16.74651019 0.860156391 7.624774392 0.999999967 0.742454977 0.189668428 0.142093028 12.74090732 695.1722888 0.123843243 0.031027989 7.246968793 -0.860156391 -0.257544991 YHPGYFGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YHPGYFGK 8 0 P46776;E9PLL6 P46776 RPL27A 60S ribosomal protein L27a 0 ; 135.35 0.00083753 6275100000 11966600 12155600 11613100 10548600 12191000 8552700 12822900 11178900 11364000 FALSE TRUE 11217631.87 13055613.27 11888568.22 10819294.93 11233568.04 11021725.65 10900225.19 12574610.27 9467274.986 1.184884973 1.379025463 1.255753977 1.142809832 1.186568263 1.164191984 1.151358253 1.328218552 1 23.1745178 -5 0.088179915 0.298302642 1.417815969 0.385067842 0.082212138 201.0166138 1.236883517 27.10092773 2.007573019 1.00E-05 5 1.119513327 YHQIGSGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YHQIGSGK 8 0 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 ;;; 141.2 0.0006374 2341670000 5043010 4552110 4940190 4853280 5423720 4124700 6120800 4584920 6994050 FALSE TRUE 4727377.006 4889152.961 5057373.64 4977823.381 4997762.909 5315433.931 5203042.863 5157357.355 5826697.872 0.811330381 0.839094985 0.867965656 0.854312939 0.857735036 0.912254942 0.892965961 0.88512524 1 22.47424707 -5 0.086060551 1.454531816 0.741875209 0.906652259 0.015553582 62.15307414 0.374770004 5.211643293 0.410135401 1.00E-05 5 -0.712656606 YHSDDYIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YHSDDYIK 8 0 Q13547;Q5TEE2 Q13547 HDAC1 Histone deacetylase 1 0 ;; 138.54 0.00070074 1415970000 1649170 2655580 1342630 1321850 2987350 688545 1400080 2432490 2931060 FALSE TRUE 1545951.394 2852201.906 1374477.818 1355770.909 2752735.581 887316.7639 1190151.002 2736191.731 2441847.151 0.633107356 1.168050959 0.562884461 0.555223495 1.127316909 0.363379323 0.48739783 1.120541771 1 21.21954147 5.032688806 16.34619162 0.761844334 0.192565776 0.016808432 0.298203594 65274926.2 898830968 0.069328631 1052568952 107817.3879 -5.032688806 -0.569278559 YHSDEYIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YHSDEYIK 8 0 Q92769;Q92769-3;H3BM24;E5RFI6;E5RJ04;E5RGV4;E5RHE7;E5RH52;E5RG37;E5RFP9;E5RK19 Q92769 HDAC2 Histone deacetylase 2 0 ; 150.4 0.0004898 347090000 553670 840430 510000 514070 828880 370890 552930 727190 998180 FALSE TRUE 519016.783 902656.3117 522097.4408 527261.9065 763783.1083 477959.9221 470023.2797 817981.2722 831577.3095 0.624135335 1.085474918 0.627839931 0.634050377 0.918475167 0.574763064 0.565218981 0.983650303 1 19.66549087 5.031093523 16.55743764 0.77111725 0.14322165 0.058444363 0.193895015 39110544.39 564083023.2 0.045444439 697670710.5 107422.0716 -5.031093523 -0.627895601 YHSDFNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YHSDFNR 7 0 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 ; 114.6 0.005868 311810000 209022 297140 212310 197446 325480 193850 231948 276144 303270 FALSE TRUE 195939.6861 319140.5548 217346.0935 202512.7986 299918.1137 249811.3481 197169.5507 310621.1863 252652.2778 0.775531049 1.263161201 0.860257803 0.801547488 1.187078606 0.988755575 0.780398864 1.229441464 1 17.94679366 3.809614391 24.99984631 0.96019684 1.056437758 0 0.187230042 164.6790208 49900.60103 0.044511963 0.080245077 6450.812093 -3.809614391 0.096240919 YHSDFNRQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YHSDFNRQDR 10 1 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 52.79 0.088821 29567000 11040 16159 13472 14075 20070 15093 11448 16693 23551 FALSE TRUE 10349.02611 17355.42917 13791.5622 14436.18833 18493.78316 19450.10409 9731.478678 18777.1578 19620.18595 0.527468299 0.884570065 0.702927191 0.735782442 0.942589596 0.991331281 0.495993193 0.957032611 1 14.26005109 -5 0.196243253 1.978359313 0.736244071 0.180038579 0.167740422 277.1908165 2.733682958 106.6805334 0.403653172 1.00E-05 5 -1.242115242 YHTINGHNAEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 YHTINGHNAEVR 12 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;; 273.27 5.32E-28 38223990000 4040140 5010360 3684150 3925630 5299730 2930040 4497450 4676380 5603400 FALSE TRUE 3787274.849 5381332.268 3771539.778 4026368.312 4883510.584 3775894.983 3823099.125 5260236.337 4668156.341 0.811299916 1.152774645 0.807929191 0.86251788 1.046132612 0.808862152 0.818974097 1.126833798 1 22.15442145 1.231907025 24.99466138 1.063416903 0.911187119 0.241145221 0.118603103 265.1103898 995859.3804 0.10329796 0.028194699 17.05717184 -1.231907025 -0.152229784 YHTINGHNCEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YHTINGHNCEVK 12 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 196.11 1.22E-07 1558820000 1582890 1475370 1338900 1400680 1537800 1100740 1884830 1447020 1783460 FALSE TRUE 1483819.74 1584607.93 1370659.34 1436623.82 1417027.391 1418505.769 1602217.239 1627683.632 1485789.004 0.998674601 1.066509393 0.922512777 0.966909713 0.953720472 0.954715484 1.078361217 1.095501197 1 20.50279782 1.716752388 7.898253902 1.064216306 0.979930409 0.416254014 0.044715031 0.114420841 18.13993123 0.022284245 0.011774525 52.08976378 -1.716752388 -0.084285897 YHTLS(ph)LGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YHTLSLGR 8 0 V9GZ20;V9GXZ5;Q70EL4-2;Q70EL4-3;Q70EL4-4;Q70EL4 V9GZ20 USP43 Ubiquitin carboxyl-terminal hydrolase 43 1 YHTLS(1)LGR;YHTLS(1)LGR 74.255 0.0267 363220000 195771 239540 249420 303080 222023 271020 281410 192143 230400 TRUE FALSE 183518.0426 257275.7908 255336.3602 310857.5459 204586.2092 349259.0744 239215.183 216132.4765 191944.7516 0.956098258 1.34036377 1.330259661 1.619515738 1.065859876 1.819581268 1.246271029 1.126013995 1 17.55033159 1.222413862 3.321106249 1.028129821 1.361248908 0.191855108 0.244652006 0.345195625 6.792332859 0.197841152 0.055712806 16.68836776 -1.222413862 0.333119088 YHTSQSGDEMTSLSEYVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 16 YHTSQSGDEMTSLSEYVSR 19 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;;;;;;;;; 348.88 1.08E-90 18964380000 2105838 5930948 5225212 5671186 5727212 5158147 5903870 5166101 4340076 FALSE TRUE 1974037.359 6370081.561 5349156.496 5816718.234 5277419.872 6647220.303 5018639.502 5811100.082 3615689.278 0.545964326 1.76178899 1.479429256 1.608743945 1.459588882 1.838437928 1.388017365 1.607190119 1 21.78583927 -1.597242259 6.651476354 0.998947716 1.502421397 0.134083195 0.354764601 0.004830514 0.000292496 0.299726614 0.070516955 0.025278875 1.597242259 0.503473682 YHTVNGHNCEVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 YHTVNGHNCEVR 12 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;F8VTQ5;A0A2R8Y4L2;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 ;;;;;;;;; 254.18 2.43E-21 29218581000 3975771 4888583 4313029 3953276 5312302 3438371 4930017.6 4667494 5442095 FALSE TRUE 3726934.59 5250538.772 4415336.085 4054723.755 4895095.23 4430972.89 4190807.229 5250240.9 4533774.187 0.822037983 1.158094461 0.973876488 0.894337386 1.079695421 0.977325448 0.92435288 1.15802876 1 22.11228111 1.243479245 24.99907811 1.079014372 0.990988236 0.141155951 0.100601169 242.0995068 1230528.254 0.068126932 0.023113676 17.51778716 -1.243479245 -0.088026136 YHVLVNLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YHVLVNLGK 9 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 98.458 0.0060003 377020000 903830 1006370 866560 884180 1071880 661640 1037270 950160 1034190 FALSE TRUE 847260.8937 1080882.682 887115.2124 906869.5557 987698.8686 852644.7272 881740.993 1068789.568 861577.0079 0.983383825 1.25453984 1.029641233 1.052569355 1.146384896 0.989632638 1.023403579 1.240503818 1 19.71662022 3.744180212 23.93272788 1.064935337 1.139458281 0.032444154 0.098923033 576.4855867 808767.2769 0.023134604 0.041549348 5548.559049 -3.744180212 0.074522944 YHYLGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YHYLGGR 7 0 Q8NCW5-2;Q8NCW5 Q8NCW5-2 APOA1BP NAD(P)H-hydrate epimerase 0 ;;;; 126.68 0.0039289 1551840000 1305140 2068070 1406170 1406660 2001330 1005280 1562730 1754580 2262330 FALSE TRUE 1223453.617 2221192.055 1439525.016 1442757.277 1844153.615 1295488.017 1328413.144 1973643.175 1884732.508 0.649139128 1.178518461 0.763782134 0.765497104 0.978469681 0.687359087 0.704828478 1.047174157 1 20.84592835 5.019275433 18.98342759 0.871944725 0.131839518 0.171206239 0.162435789 1652.906025 39643.2724 0.037762594 38287.6884 104538.3 -5.019275433 -0.740105208 YIAIVSTTVETKEPEKEIRPALELLEPIEQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YIAIVSTTVETKEPEKEIRPALELLEPIEQK 31 3 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 40.094 0.073395 184420000 147360 94563 115270 109110 135820 84756 154870 88946 210590 FALSE TRUE 138137.0006 101564.5429 118004.2588 111909.9473 125153.2451 109223.6813 131648.6812 100051.1039 175441.1685 0.78736936 0.578909407 0.672614414 0.637877348 0.713363039 0.622565856 0.750386482 0.570282931 1 17.4206278 -1.299827557 3.310025691 1.001613107 0.664325926 0.693631198 0.069604392 16228260.38 22517464.84 258390.2557 0.014884726 0.050138628 1.299827557 -0.337287181 YIDENQDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YIDENQDR 8 0 Q96KP4;Q96KP4-2;J3QKT2;A0A087WYZ1;J3KSV5;J3QRA8;J3QRD0;J3QKQ0;J3QLU1;J3QR27;J3QL02;J3QQN6;J3KSS4;J3QRP4 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ;;;;; 231.73 1.33E-06 8638440000 3459890 4096620 3729430 3965060 4222730 3284400 4166640 3545670 3636900 FALSE TRUE 3243341.661 4399938.007 3817893.841 4066810.152 3891093.819 4232552.962 3541891.013 3988354.704 3029877.895 1.070452927 1.452183276 1.26008175 1.342235659 1.284241133 1.396938461 1.168988037 1.316341728 1 21.53082822 -0.074679233 0.601519699 0.979182349 1.31028074 0.390410751 0.109727476 4.518771856 1.772345765 0.322556743 0.039796591 0.842016819 0.074679233 0.33109839 YIDQEELNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 YIDQEELNK 9 0 P08238;P07900;P07900-2;Q14568;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AA1;HSP90AA2P;HSP90AB2P Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2;Putative heat shock protein HSP 90-beta 2 0 ;;;;;; 214.93 1.53E-06 9601630000 11957650 9200410 10300800 9875130 10525710 7887930 11945540 8910300 11135180 FALSE TRUE 11209242.03 9881617.929 10545139.84 10128542.55 9699063.195 10165047.34 10154417.17 10022770.57 9276646.522 1.20832911 1.065214451 1.136740504 1.091832327 1.045535493 1.095767454 1.094621548 1.080430363 1 23.14517194 -4.999999375 0.015589044 1.18E-06 1.92575771 0.515245171 0.038148555 4703.006119 5.560250709 433.6309479 270.948913 1.00E-05 4.999999375 1.925756529 YIDTEHGGSQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YIDTEHGGSQAR 12 0 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ;; 176.87 2.40E-05 885440000 879310 1083320 1009480 1073810 1198820 899560 1254890 1005730 1224290 FALSE TRUE 824275.5567 1163530.14 1033425.342 1101365.783 1104669.513 1159248.369 1066730.894 1131297.604 1019948.09 0.80815442 1.14077388 1.013213665 1.07982533 1.083064446 1.136575852 1.045867829 1.109171747 1 19.9600643 4.746924614 24.94782077 1.077326181 0.808154282 0.764319128 0.046748541 459.261186 1369836.106 0.009999006 0.114950767 55837.32625 -4.746924614 -0.269171899 YIEIDS(ph)DEEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YIEIDSDEEPR 11 0 E7EW05;Q9NVU7-2;Q9NVU7 E7EW05 SDAD1 Protein SDA1 homolog 1 YIEIDS(1)DEEPR;YIEIDS(1)DEEPR;YIEIDS(1)DEEPR 241.35 1.06E-15 1282360000 1905690 1728510 1870950 1681750 1375380 2126020 2212840 1481690 1087690 TRUE FALSE 1786416.265 1856490.679 1915329.818 1724906.552 1267363.203 2739767.461 1881045.185 1666682.258 906147.5123 1.971440897 2.048773134 2.113706424 1.903560435 1.398627912 3.023533612 2.075870826 1.839305671 1 19.7893864 3.258197121 24.21888217 1.993013581 2.055392292 0 0.521784052 2279.880891 2811885.439 0.13566492 0.183394554 1812.162424 -3.258197121 0.062378711 YIEIDS(ph)DEEPRGELLSLR ddPTM_SK-BR-3_Pertuzumab_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(1)DEEPRGELLSLR;YIEIDS(1)DEEPRGELLSLR;YIEIDS(1)DEEPRGELLSLR 352.68 1.14E-90 5377520000 1822037 2048630 1993020 1940418 2018868 1634328 2076590 1748605 1893481 TRUE FALSE 1707998.957 2200312.697 2040295.376 1990212.411 1860314.251 2106131.963 1765224.608 1966922.183 1577446.789 1.082761694 1.394857001 1.293416292 1.261666907 1.179319812 1.335152461 1.119039083 1.246902398 1 20.58915991 0.444542465 0.434694161 0.977932921 1.289490305 0.367204943 0.095704589 2.122229161 0.731612744 0.189947712 0.056886059 2.783187498 -0.444542465 0.311557383 YIEIFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 106.84 0.073935 495220000 1791180 1829070 1796990 1870480 1960330 1524600 2163860 1700530 2076180 FALSE TRUE 1679073.241 1964496.246 1839615.451 1918479.684 1806373.589 1964727.27 1839409.281 1912844.914 1729652.145 0.970757759 1.135775336 1.063575388 1.109170817 1.044356574 1.135908903 1.06345619 1.10591307 1 20.72205049 -0.24683034 7.603845619 0.999996273 1.083356264 0.196909701 0.049070736 0 2.11E-18 0.040329772 0.009505818 0.566460537 0.24683034 0.083359991 YIELFR ddPTM_SK-BR-3_Pertuzumab_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 ;;;;;; 168.62 0.01465 3525165000 3634110 4767000 4226430 4315080 4952670 3682870 4606870 4115580 5009620 FALSE TRUE 3406657.542 5119953.64 4326682.915 4425812.258 4563707.276 4746054.783 3916112.612 4629419.223 4173482.059 0.816262654 1.226782233 1.036708162 1.060460353 1.093501113 1.137193048 0.938332202 1.109246226 1 21.99282014 1.746742997 25 1.011884268 1.079121743 0.0208743 0.111382834 5.0022839 15322.72826 0.04669461 0.025894969 55.81398063 -1.746742997 0.067237475 YIEVFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YIEVFK 6 0 P52597;A0A1B0GW42 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ;;; 118.03 0.051687 980768000 3661310 3411440 3615890 3349960 3834390 2777680 4121630 3310630 4490440 FALSE TRUE 3432155.143 3664026.567 3701660.618 3435925.645 3533252.477 3579551.124 3503629.845 3723969.443 3740956.555 0.91745389 0.979435744 0.989495752 0.918461788 0.944478351 0.956854503 0.936559886 0.995459153 1 21.83497578 1.218012563 21.08931111 0.99773021 0.954314895 0.414532924 0.023432376 53.45324653 54850.68739 0.023562492 0.005947337 16.52009586 -1.218012563 -0.043415314 YIGENLQLLVDRPDGTYCFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YIGENLQLLVDRPDGTYCFR 20 1 Q9Y221;J3QLW7;Q9Y221-2 Q9Y221 NIP7 60S ribosome subunit biogenesis protein NIP7 homolog 0 186.15 3.08E-17 263010000 231520 251300 262740 244230 262650 228460 291540 217670 256680 FALSE TRUE 217029.5765 269906.5135 268972.3169 250497.3553 242022.5285 294412.6933 247826.2835 244846.5787 213838.4498 1.014923073 1.262198233 1.25782953 1.171432713 1.1318008 1.376799605 1.158941639 1.145007266 1 17.70616176 0.90571166 2.028060448 1.001397279 1.213188766 0.289410757 0.094924121 0.481388303 4.100779805 0.082804239 0.022994579 8.048439058 -0.90571166 0.211791487 YIHILGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YIHILGR 7 0 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 149.11 0.0020382 223640000 356280 458920 397180 438310 469880 322080 488690 381550 287980 FALSE TRUE 333981.0708 492898.9143 406601.2972 449557.7767 432977.5202 415059.2675 415415.4713 429187.3574 239914.2776 1.392085015 2.054479289 1.694777407 1.87382669 1.804717604 1.730031542 1.731516254 1.788919616 1 17.87215949 -2.21123605 0.478334426 1.53E-11 1.792797409 0.667381649 0.167110227 46.48222061 2.991209136 49.83237323 0.07377452 0.006148426 2.21123605 1.792797409 YIHLENLLAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YIHLENLLAR 10 0 Q2TAY7 Q2TAY7 SMU1 "WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed" 0 ; 210.27 8.02E-08 616890000 513450 768320 539380 563720 813210 438980 619690 720030 678700 FALSE TRUE 481314.081 825207.2122 552174.3483 578186.0096 749343.7669 565706.3998 526773.2374 809927.3305 565420.5854 0.85124966 1.45945732 0.976572772 1.022576865 1.325285613 1.00050549 0.931648495 1.432433398 1 19.10896488 3.767248846 24.68994882 1.086338773 1.204562453 0 0.216421241 744.91625 458332.059 0.050926631 0.091807637 5851.252582 -3.767248846 0.11822368 YIHPDDELVLEDELQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YIHPDDELVLEDELQR 16 0 C9IZD2;C9J8Z7;C9JLE1;F8W8R3;A0A087WWF6;P49005 C9IZD2 POLD2 DNA polymerase delta subunit 2 0 ; 272.96 3.43E-35 337290000 342360 392270 414550 383930 413400 354860 413190 365330 340720 FALSE TRUE 320932.2987 421314.079 424383.3218 393782.2938 380933.2316 457302.3213 351235.9954 410942.2547 283851.6309 1.130633979 1.484275703 1.495088545 1.387282125 1.3420153 1.611061102 1.237392909 1.447736106 1 18.11477751 -0.40943315 0.692179486 0.967459742 1.413662787 0.437118749 0.137323153 9.633098621 3.641524988 0.949148842 0.045412363 0.389553267 0.40943315 0.446203044 YIHSADIIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YIHSADIIHR 10 0 Q16539-2;Q16539;B4E0K5;Q16539-5;Q16539-3;Q16539-4;E7EX54;B5TY33 Q16539-2 MAPK14 Mitogen-activated protein kinase 14 0 ; 180.67 1.14E-06 249890000 255000 346370 291090 287620 343450 246690 307910 292060 316300 FALSE TRUE 239040.0052 372015.5952 297994.7923 295000.8161 316476.8224 317905.3983 261741.754 328524.3339 263507.4866 0.907146921 1.411783779 1.130877897 1.119515881 1.201016436 1.206437822 0.993299118 1.246736243 1 18.00748443 0.785061081 0.369757097 0.989659677 1.202429118 0.047996736 0.141405778 3.754261875 1.267923454 0.269653625 0.121399742 6.096226312 -0.785061081 0.212769441 YIHSANVLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YIHSANVLHR 10 0 P28482;P28482-2;K7EN18;P27361;E9PBK7;E9PQW4;P27361-3;P27361-2;E9PJF0;B3KR49;H0YDH9;K7ELV1;P31152;Q16659 P28482;P27361;K7ELV1;Q16659 MAPK1;MAPK4;MAPK3;MAPK6 Mitogen-activated protein kinase 1;Mitogen-activated protein kinase 3;Mitogen-activated protein kinase;Mitogen-activated protein kinase 4;Mitogen-activated protein kinase 6 0 ; 148.32 1.46E-05 407120000 331150 519300 431020 390010 557930 307640 378570 461210 324650 FALSE TRUE 310423.9126 557749.5123 441243.9979 400018.3169 514112.4284 396450.6739 321806.943 518793.0837 270463.8177 1.147746546 2.062196404 1.631434481 1.479008617 1.900854735 1.465817784 1.189833619 1.918160766 1 18.04507608 -1.206037652 0.245209547 0.546139762 1.736003986 0.222269485 0.312640112 23.38844551 1.227340892 7.520134573 0.518086259 0.062224634 1.206037652 1.189864224 YIIEELNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YIIEELNVR 9 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;; 126.41 0.0011033 115822000 149020 181710 179482 181711 207227 137962 164088 167856 213744 FALSE TRUE 139693.1042 195163.9975 183739.3978 186374.0119 190952.2273 177789.3898 139484.5277 188813.1911 178068.7456 0.784489742 1.096003663 1.031845298 1.046640786 1.072351168 0.998431191 0.783318416 1.06033875 1 17.44207479 1.979594205 24.37443512 0.915576183 1.024790095 0.015223883 0.111145858 924.2144677 1103959.513 0.04156001 0.027190496 95.41006782 -1.979594205 0.109213912 YIKNPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YIKNPR 6 1 P49368;P49368-2;B4DUR8;Q5SZX6 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 106.84 0.028984 3282300000 4168200 5640800 4617200 4849100 6432100 3654900 5664100 5407600 6734300 FALSE TRUE 3907319.802 6058450.701 4726722.164 4973536.116 5926948.812 4710010.298 4814820.788 6082750.764 5610301.825 0.696454473 1.079879638 0.842507643 0.886500632 1.056440277 0.83952886 0.858210652 1.084210966 1 22.41964696 YILEQFLQQELLINITEHELVPEHVVMTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YILEQFLQQELLINITEHELVPEHVVMTK 29 0 P19388;A0A0A0MQR7;A0A087WWX0 P19388 POLR2E "DNA-directed RNA polymerases I, II, and III subunit RPABC1" 0 187.92 3.89E-18 73633000 155310 142100 161250 136130 173480 136350 169960 161320 133560 FALSE TRUE 145589.4243 152621.2319 165074.9261 139623.3263 159855.5806 175712.0315 144476.0758 181461.1571 111267.9732 1.308457593 1.371654642 1.483579879 1.254838408 1.436671991 1.579178865 1.298451582 1.63084805 1 16.76367887 -0.836920878 5.421223777 0.999999794 1.415643173 0.544825927 0.120706462 2.64E-07 5.70E-08 0.103132612 0.024308577 0.145572427 0.836920878 0.415643379 YIMIFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YIMIFR 6 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ; 142.14 0.026902 133163000 153247 542970 140858 151414 540890 101202 182311 462180 384160 FALSE TRUE 143655.5438 583172.0638 144199.2183 155299.5396 498410.6812 130417.3745 154975.158 519884.1904 320041.2142 0.448865763 1.822178013 0.450564527 0.485248564 1.557332803 0.407501811 0.484235002 1.624428877 1 18.28789818 4.996023387 24.75790921 0.934055109 0.062110585 0.083246021 0.534684643 37225.75268 345241.7827 0.119992473 819548.1259 99088.53024 -4.996023387 -0.871944524 YINENLIVNTDELGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YINENLIVNTDELGR 15 0 P17987;E7ERF2;F5H136;F5H7Y1 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;; 314.39 6.72E-56 941670000 470467 551604 525399 548723 570659 465524 574169 512705 566874 FALSE TRUE 441021.3103 592445.3341 537861.7124 562804.1612 525841.7441 599913.2216 488077.6888 576717.3479 472259.0673 0.933854617 1.254492238 1.13891241 1.191727592 1.113460345 1.270305354 1.033495644 1.221188512 1 18.84921897 -1.112640538 3.664946986 0.999918319 1.151303032 0.162514423 0.102239197 13476632.91 21813172.46 13319.30063 0.021510318 0.07715418 1.112640538 0.151384713 YINTEHGGSQAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YINTEHGGSQAR 12 0 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;;; 208.51 6.60E-08 3422510000 1344480 1668600 1486410 1573010 1570460 1304850 1714830 1325470 1542790 FALSE TRUE 1260331.397 1792144.88 1521668.347 1613376.1 1447122.407 1681539.013 1457707.161 1490957.847 1285288.382 0.980582579 1.394352353 1.183912006 1.255263894 1.125912617 1.308297061 1.134147932 1.160018147 1 20.29366066 0.758754764 0.828341732 0.999513201 1.227305426 0.22101276 0.112033703 1.180636559 1.572014244 0.097552071 0.033933281 5.737923637 -0.758754764 0.227792225 YIQELWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YIQELWR 7 0 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;;;;; 180.7 0.001588 5372495000 3202024 7291140 3198071 3241888 7214820 1965725 3388581 6059050 6174520 FALSE TRUE 3001615.034 7830983.592 3273930.754 3325080.335 6648197.14 2533197.897 2880494.737 6815535.73 5143952.723 0.58352306 1.522366945 0.636462061 0.646405695 1.292429674 0.492461349 0.559976907 1.324960803 1 22.29444595 3.828506044 7.578215566 0.805642574 1.112428405 0.034077107 0.365886986 0.506071291 33.33386751 0.08707026 0.157676462 6737.612721 -3.828506044 0.306785832 YIQHTYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YIQHTYR 7 0 P52565;J3KTF8;J3QQX2;J3KRY1;P52565-2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;;;; 175.24 0.00079652 4830670000 1489770 3790310 1502480 1488370 3842870 1233630 1731340 3167510 2413070 FALSE TRUE 1396527.955 4070948.496 1538119.535 1526564.094 3541066.492 1589758.955 1471741.64 3562980.596 2010313.028 0.694681841 2.025032142 0.765114444 0.759366364 1.761450303 0.790801697 0.732095758 1.772351145 1 20.93898873 3.873628296 8.612001527 1.049924521 1.446198724 0.040893232 0.501583906 0.590656186 44.09267233 0.118586319 0.214407539 7475.294311 -3.873628296 0.396274203 YIQPWESEFIDSQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YIQPWESEFIDSQR 14 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 166.24 8.93E-06 33361000 16604 20484 19591 18559 19627 15990 22149 18678 16954 FALSE TRUE 15564.78528 22000.65667 20055.70777 19035.25536 18085.57459 20606.05342 18827.96307 21009.98942 14124.26787 1.101988819 1.55764935 1.419946715 1.347698552 1.28046103 1.458911259 1.333022231 1.48750998 1 13.78588847 -1.531483707 2.910337915 0.983141339 1.390095391 0.459305059 0.126170338 19039567.99 20587702.42 2529468.156 0.028653 0.02941144 1.531483707 0.406954052 YIQQTKPLTLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YIQQTKPLTLER 12 1 O43809 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 ; 115.24 0.00088559 1479330000 483760 657960 475130 444740 701210 342300 529440 629370 837700 FALSE TRUE 453482.3251 706676.043 486400.308 456152.7813 646139.7951 441116.4532 450055.3871 707948.2299 697882.4583 0.649797569 1.012600381 0.696965946 0.653624082 0.925857625 0.632078437 0.644887089 1.014423305 1 19.41262454 1.222615565 24.89484251 1.007211994 0.758470704 0.416152318 0.128307819 279.1150359 435766.7721 0.122412496 0.031011102 16.69612028 -1.222615565 -0.248741291 YIS(ph)PDQLADLYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YISPDQLADLYK 12 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 1 YIS(1)PDQLADLYK;YIS(1)PDQLADLYK;YIS(1)PDQLADLYK 171.08 4.13E-05 55254000 236916 232490 205667 191378 272023 136975 231581 218480 336479 TRUE FALSE 222087.8505 249703.8015 210545.5184 196289.0835 250659.4109 176517.4589 196857.5789 245757.7089 280318.4812 0.792269741 0.890786082 0.751093961 0.70023597 0.894195095 0.629703251 0.702264004 0.876708906 1 18.09670734 0.990384199 5.447024199 0.999817698 0.769302488 0.472437931 0.081675458 0.130585307 16.13624179 0.080203411 0.020223415 9.781021165 -0.990384199 -0.23051521 YISKPENLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YISKPENLK 9 1 Q9H9S4;Q5TAW7;B7ZBJ4;Q9Y376;A0A087X0K1 Q9H9S4;Q9Y376 CAB39L;CAB39 Calcium-binding protein 39-like;Calcium-binding protein 39 0 74.162 0.031577 0 285280 262670 287440 285060 378520 192080 331780 335270 500480 FALSE TRUE 267424.834 282118.3601 294258.2125 292375.1222 348792.5661 247530.3778 282032.6691 377129.1975 416946.6548 0.641388607 0.676629389 0.705745469 0.701229087 0.836540028 0.593673975 0.676423868 0.904502274 1 18.66950329 1.120752671 3.859934264 0.994503557 0.68995538 0.76209891 0.061954151 0.095538155 2.442867544 0.05619512 0.014605269 13.20543375 -1.120752671 -0.304548177 YISPDQLADLYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YISPDQLADLYK 12 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;; 195.51 5.06E-07 2254777000 2807230 3284790 2383790 2258782 3733800 1545231 2674700 3053690 3651400 FALSE TRUE 2631530.485 3527999.269 2440334.625 2316746.17 3440562.409 1991314.105 2273653.566 3434949.919 3041957.751 0.86507792 1.159779181 0.802225022 0.76159709 1.131035567 0.654615964 0.747431014 1.129190541 1 21.53656869 3.88724925 5.848308064 0.863040508 1.025999486 0.061797872 0.175150233 0.391705379 20.20666387 0.042266697 0.077685716 7713.460316 -3.88724925 0.162958978 YISSQIERPIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YISSQIERPIR 11 1 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 83.775 0.013181 0 197730 205900 203230 175180 181320 128260 201480 163170 255810 FALSE TRUE 185354.4323 221145.0502 208050.7116 179675.4154 167079.8586 165286.5799 171269.9444 183542.1337 213113.6584 0.8697445 1.037685955 0.976242973 0.843096668 0.783994137 0.775579478 0.80365541 0.861240594 1 17.70126353 3.215962047 4.793364636 0.824021335 0.980852395 0.312959875 0.076262533 0.148450531 8.447090157 0.020034237 0.025263817 1644.228028 -3.215962047 0.15683106 YITDWQNVFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YITDWQNVFR 10 0 O75340-2;O75340;A0A024QZ42 O75340-2 PDCD6 Programmed cell death protein 6 0 ; 179.51 4.88E-06 1550620000 551620 839900 620680 615180 831760 433850 697550 704080 843200 FALSE TRUE 517095.0889 902087.0699 635402.8227 630966.5603 766436.9248 559095.452 592958.8532 791985.9379 702464.4727 0.736115646 1.284174652 0.904533749 0.898218465 1.091068594 0.795905663 0.844112231 1.127439136 1 19.42206574 3.726492141 24.99236188 0.933740753 1.062810821 0 0.16717913 64.77003845 2573208.251 0.040286166 0.066795271 5327.115843 -3.726492141 0.129070068 YITEPEMVFEEHEVNEDIQPMTAFESEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YITEPEMVFEEHEVNEDIQPMTAFESEK 28 0 H0Y8R1;F5H5I6;H0YAK1;Q12849;Q12849-5 H0Y8R1 GRSF1 G-rich sequence factor 1 0 140.8 1.30E-07 16447000 23307 17053 20260 16730 21885 23176 23162 21119 25201 FALSE TRUE 21848.25647 18315.62186 20740.57677 17159.32012 20166.24038 29866.53497 19689.07313 23755.75364 20994.7903 1.040651331 0.872388893 0.98789159 0.817313242 0.960535452 1.422568863 0.937807563 1.131507069 1 14.35774376 2.450748382 24.99988051 1.119659905 0.925671103 0.314824795 0.137822439 243.3483985 230678.1207 0.043122169 0.036079432 282.3243791 -2.450748382 -0.193988802 YIVNGSHEANK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YIVNGSHEANK 11 0 P55010;H0YLZ1;H0YN40;H0YMJ8;H0YM54 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 118.77 0.00096041 193480000 1618110 1197590 1367820 1235220 1362700 1032840 1644590 1254640 1434300 FALSE TRUE 1516835.384 1286260.81 1400265.336 1266917.836 1255679.039 1331004.141 1397998.997 1411284.566 1194906.064 1.269418098 1.076453496 1.171862273 1.060265635 1.050860044 1.113898558 1.169965606 1.18108411 1 20.18846578 YIYFYEKENDAVTIQVLNQLIQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YIYFYEKENDAVTIQVLNQLIQK 23 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;;;; 329.24 1.57E-86 468884000 1082531 1111737 1061521 1194587 1625880 801893 1274517 1157756 1230233 FALSE TRUE 1014777.317 1194051.164 1086700.779 1225242.125 1498189.943 1033386.491 1083415.008 1302304.385 1024899.165 0.990124055 1.165042577 1.06030019 1.195475777 1.46179253 1.008281133 1.057094244 1.270665866 1 19.96705055 -1.704496241 2.656852055 0.976737189 1.142077306 0.099874119 0.140250756 69646378.98 58891134.06 10859387.78 0.033350171 0.01974712 1.704496241 0.165340118 YKAEDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 YKAEDEK 7 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;; 121.96 0.0040016 32024000000 42714700 18633900 25525600 23572400 23545300 18946000 33368800 22655200 28885900 FALSE TRUE 40041263.17 20013573.34 26131079.29 24177307.69 21696147.12 24415402.64 28365458.22 25483751.59 24064656.68 1.663903363 0.831658378 1.085869607 1.004681181 0.901577255 1.014575149 1.178718591 1.058970088 1 24.52041251 4.748743189 24.85062515 1.015411588 1.663903752 0.825139254 0.094638347 586.3132477 1430869.929 0.024032837 0.332893098 56071.63098 -4.748743189 0.648492164 YKAEDEKQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YKAEDEKQR 9 2 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;; 141.95 5.93E-05 2280570000 3197710 2847720 2973050 3064590 4221130 2098800 3819790 2614280 7304670 FALSE TRUE 2997571.039 3058568.152 3043572.15 3143232.568 3889619.477 2704689.489 3247047.951 2940678.613 6085473.387 0.49257812 0.502601516 0.500137287 0.51651406 0.639164652 0.444450138 0.533573601 0.483229229 1 22.53693806 -1.7212556 2.794415781 1.080847873 0.513923614 0.902725644 0.050133979 7545893.77 6431519.505 4259137.405 0.011378088 0.018999597 1.7212556 -0.566924259 YKAEDEVQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 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 ;;;;;;;; 187.99 3.64E-05 14382460000 18468920 15178060 15227410 15153370 17877880 11585730 18655870 15459220 20452420 FALSE TRUE 17312983.27 16301859.36 15588611.36 15542231.13 16473823.42 14930342.17 15858595.49 17389337.65 17038778.97 1.016092954 0.956750444 0.914890168 0.912168128 0.966842955 0.876256579 0.930735442 1.020574166 1 24.02231862 1.24127058 24.99934392 1.010287106 0.935175962 0.380443517 0.037504892 64.33762771 593561.2595 0.026699883 0.008760117 17.42892416 -1.24127058 -0.075111144 YKDAIHFYNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YKDAIHFYNK 10 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 139.86 2.42E-05 2786400000 4697800 7992300 4254100 4293500 9958100 2885300 4451900 8125400 7260700 FALSE TRUE 4403773.084 8584058.208 4355009.261 4403678.479 9176030.995 3718239.271 3784378.924 9139874.076 6048842.264 0.728035695 1.419124162 0.719974017 0.728020055 1.516989631 0.614702634 0.6256369 1.511012137 1 22.52822761 YKDDDDDQLFYTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YKDDDDDQLFYTR 13 1 O60568;H7C2V1 O60568 PLOD3 "Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3" 0 ;;; 246.63 3.07E-17 1627830000 2576100 1904443 2124000 2207190 2150090 1427731 2598200 1961155 1759820 FALSE TRUE 2414866.499 2045449.941 2174382.283 2263830.232 1981230.604 1839893.762 2208624.031 2206009.519 1466094.673 1.647142264 1.39516907 1.483111782 1.544122814 1.351366075 1.25496245 1.506467537 1.504684219 1 20.48354684 -2.961151847 0.350769746 5.95E-27 1.470133973 0.641583189 0.108137694 56.93572049 1.770537483 42.53565305 0.080009755 0.001093574 2.961151847 1.470133973 YKDDPVDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YKDDPVDLR 9 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;;; 95.573 0.0072536 3226900000 10870700 9706600 10595800 10178200 10991200 8297550 12489900 9437000 13107200 FALSE TRUE 10190322.29 10425286.76 10847137.38 10439389.84 10127995.49 10692917.99 10617155.45 10615230.22 10919523.64 0.933220406 0.954738238 0.993370932 0.956029785 0.927512575 0.979247661 0.972309397 0.972133087 1 23.38040659 0.874268014 0.75846816 0.999754275 0.959680126 0.333206061 0.019124862 1.140411839 1.406467976 0.019256632 0.007112344 7.486313572 -0.874268014 -0.040074149 YKDEDGDLITIFDSSDLSFAIQCSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YKDEDGDLITIFDSSDLSFAIQCSR 25 1 Q92734-2;Q92734;Q92734-4;Q92734-3;C9JTY3;C9JUE0;C9JJP5 Q92734-2 TFG Protein TFG 0 ;;; 197.33 7.45E-25 50661900 131570 95926 107076 90988 93780 90369.4 141334 102301 160240 FALSE TRUE 123335.2686 103028.4609 109615.8933 93322.90612 86414.89709 116457.5788 120142.2788 115073.505 133494.9088 0.923894923 0.771778203 0.821124148 0.699074646 0.647327287 0.872374683 0.899976485 0.862006694 1 17.0264252 2.019939655 24.81872324 0.903704431 0.774461691 0.422250519 0.079851721 224.3945065 279300.7082 0.029087413 0.021480111 104.6983061 -2.019939655 -0.12924274 YKDIIRQPS(ph)EEEIIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YKDIIRQPSEEEIIK 15 2 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 1 YKDIIRQPS(1)EEEIIK;YKDIIRQPS(1)EEEIIK 218.76 9.89E-13 663990000 576550 746630 486540 901700 1109400 388460 897540 715000 3269700 TRUE FALSE 540464.7647 801911.2621 498080.9586 924839.1486 1022272.199 500602.0959 762962.2094 804269.3239 2723965.947 0.198410984 0.294391075 0.18285139 0.33951935 0.375288171 0.183776929 0.280092418 0.295256747 1 21.37727724 -4.358091179 0.459404284 10 0.256868111 0.928888439 0.063651943 177.4622339 1.842864431 1600.286913 0.031588649 4.38E-05 4.358091179 -9.743131889 YKDLDEDELLGNLS(ph)ETELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YKDLDEDELLGNLSETELK 19 1 Q9NYL9;H0YNU8 Q9NYL9 TMOD3 Tropomodulin-3 1 YKDLDEDELLGNLS(0.882)ET(0.118)ELK;YKDLDEDELLGNLS(0.824)ET(0.176)ELK;YKDLDEDELLGNLS(0.991)ET(0.009)ELK 174.4 2.76E-12 563469000 793637 393044 501419 508241 506877 371600 739316 429078 558351 TRUE FALSE 743964.6769 422145.3867 513312.8955 521283.3245 467068.9251 478874.8876 628462.4293 482649.3328 465158.611 1.59937849 0.907529984 1.10352229 1.120657153 1.004106801 1.029487311 1.351071257 1.03760163 1 18.82736321 YKDLDEDELLGNLSETELK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YKDLDEDELLGNLSETELK 19 1 Q9NYL9;H0YNU8 Q9NYL9 TMOD3 Tropomodulin-3 0 248.94 5.52E-25 173740000 699100 369340 481100 468960 521050 351530 652470 407100 700300 FALSE TRUE 655344.5789 396686.3179 492511.9192 480994.3075 480128.8348 453011.0044 554638.1807 457927.3311 583415.4059 1.123289807 0.679938023 0.844187374 0.824445674 0.822962215 0.776481046 0.950674554 0.784907849 1 19.15416396 -0.385603967 0.530542893 1.02280584 0.830760472 0.107838468 0.119712033 14.73590444 3.781647318 0.766229331 0.049629452 0.411524819 0.385603967 -0.192045368 YKDNPFSLGES(ph)FGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YKDNPFSLGESFGSR 15 1 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;Q8N6H7-3;H0YDN9;E9PMU9 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 YKDNPFSLGES(1)FGSR;YKDNPFSLGES(0.998)FGS(0.002)R 168.81 7.47E-07 509630000 755570 754050 677030 786110 670820 452060 1125560 686080 1104700 TRUE FALSE 708280.2224 809880.6466 693089.4713 806282.9135 618136.5032 582562.3834 956792.7272 771738.5982 920318.4334 0.769603429 0.880000462 0.753097456 0.876091236 0.671655028 0.633000886 1.039632254 0.838556059 1 19.8117736 1.713900609 12.32502004 0.952849983 0.776860166 0.498374286 0.091733306 0.103296447 39.08110547 0.041753383 0.022869315 51.74883878 -1.713900609 -0.175989817 YKDNPFSLGESFGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YKDNPFSLGESFGSR 15 1 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;Q8N6H7-3;H0YDN9;E9PMU9 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 0 139.08 6.02E-06 368620000 180700 151290 156260 151950 179460 132670 200850 171170 204050 FALSE TRUE 169390.3096 162491.669 159966.561 155849.2943 165365.9355 170969.6753 170734.4071 192540.9513 169992.7368 0.996456159 0.955874187 0.941019975 0.916799724 0.972782359 1.005746943 1.004362953 1.132642223 1 17.37511358 1.815351691 1.583664991 1.059345527 0.952591589 0.518215634 0.040163515 0.267582928 1.279681787 0.026910759 0.011251762 65.36596709 -1.815351691 -0.106753938 YKDPQDENK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YKDPQDENK 9 1 C9JVE2;Q96GG9;C9J8R4;C9JRU6;C9J0B2;C9JRE2;C9JAV2;H7C216;Q6PH85-2;Q6PH85 C9JVE2 DCUN1D1;DCUN1D2 DCN1-like protein;DCN1-like protein 1;DCN1-like protein 2 0 ;; 118.4 0.00090745 919340000 3315740 1920600 2406310 2254440 2585760 1542240 3200830 2203420 3791210 FALSE TRUE 3108213.752 2062803.222 2463388.81 2312292.747 2382684.84 1987459.652 2720895.257 2478521.837 3158432.559 0.984100086 0.653109789 0.779940291 0.732101352 0.754388386 0.629255054 0.861470114 0.784731601 1 21.59077734 0.663621844 1.106856818 0.998692644 0.750592008 0.333228194 0.100259292 1.12049178 2.242867452 0.084886437 0.026529412 4.60916063 -0.663621844 -0.248100636 YKDQTGGYTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YKDQTGGYTR 10 1 E9PKV2;Q9NRX2 E9PKV2 MRPL17 "39S ribosomal protein L17, mitochondrial" 0 ; 103.91 0.0025097 121196000 198603 204460 193286 159493 263490 166918 192080 207980 326810 FALSE TRUE 186172.7927 219598.4311 197870.8352 163585.8604 242796.5583 215104.5169 163279.3872 233946.7608 272263.2997 0.683796872 0.806566406 0.72676279 0.600836986 0.891771159 0.79006064 0.599711336 0.859266604 1 18.054643 0.998015003 24.37886954 1.000000006 0.733374986 0.503715123 0.089189934 34.48347569 423519.724 0.082191732 0.020547933 9.954398047 -0.998015003 -0.26662502 YKDSAQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YKDSAQR 7 1 P05026-2;P05026;V9GYR2 P05026-2;V9GYR2 ATP1B1 Sodium/potassium-transporting ATPase subunit beta-1 0 60.973 0.085988 85332000 86798 88900 72313 79020 104710 58317 97131 118020 161880 FALSE TRUE 81365.46812 95482.2485 74028.29851 81047.78698 96486.49898 75152.1712 82567.10827 132755.0568 134861.1822 0.603327561 0.708003941 0.548922212 0.600971945 0.715450491 0.557255765 0.612237761 0.984383012 1 17.04111562 1.23613127 16.26160136 0.992220265 0.621245908 0.889427465 0.054428423 0.237327843 1566.539934 0.041929176 0.012612093 17.22389108 -1.23613127 -0.370974358 YKEALLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YKEALLGR 8 1 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ; 147.51 0.00048898 1701600000 2476200 3143400 2567800 2646700 3551500 1907420 3181400 3053700 3785200 FALSE TRUE 2321219.062 3376140.607 2628709.429 2714618.803 3272579.516 2458061.19 2704378.605 3434961.167 3153425.667 0.736094428 1.070626348 0.833604374 0.860847564 1.037785527 0.779489181 0.857600239 1.089279257 1 21.5884885 1.24055088 24.99999341 1.044639658 0.893596943 0.286431023 0.105361913 65.90023815 827873.8832 0.074098815 0.023983505 17.40006538 -1.24055088 -0.151042715 YKEEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YKEEAR 6 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 79.454 0.061202 1491460000 2757600 2575500 2702000 2446800 2866300 2064030 2989800 2508500 3404600 FALSE TRUE 2585006.738 2766192.7 2766092.716 2509589.03 2641192.36 2659881.954 2541507.246 2821691.747 2836350.265 0.911384877 0.975264844 0.975229593 0.884795175 0.931194004 0.937783315 0.896048445 0.994831908 1 21.43560427 1.147323886 8.849913895 0.998965316 0.936083555 0.460590514 0.029713811 0.326146788 28.14926803 0.031268038 0.007829034 14.03860277 -1.147323886 -0.062881761 YKEEFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YKEEFEK 7 1 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;; 92.062 0.014542 3430110000 4034080 2466860 3125850 2872110 3304030 2523490 4125260 2824240 5287070 FALSE TRUE 3781594.134 2649508.881 3199996.638 2945813.205 3044544.812 3251980.598 3506715.56 3176852.581 4404623.861 0.85855098 0.601528976 0.726508492 0.668800174 0.69121562 0.738310625 0.796144159 0.721254001 1 22.07058739 -0.086452025 0.456126913 1.039777611 0.692619102 0.600696767 0.069769428 2.93619326 0.734144459 0.274093526 0.035954671 0.819498145 0.086452025 -0.347158509 AGTFIAPPVYSNITPYQSHLRS(ph)PVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 AGTFIAPPVYSNITPYQSHLRSPVR 25 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 AGTFIAPPVYSNIT(0.103)PY(0.16)QS(0.303)HLRS(0.434)PVR 125.59 8.48E-05 1005200000 593530 749760 726250 848470 1060900 731620 988160 788420 1366900 TRUE FALSE 556382.0168 805273.0105 743476.993 870243.1767 977581.1935 942826.8171 839994.5816 886855.9725 1138755.559 0.48858775 0.707151771 0.6528855 0.764205425 0.858464475 0.827944864 0.737642574 0.778793978 1 20.11902667 5.912918346 0.118332551 1.061202114 2.33E-18 0.727619723 0.069727487 33.28776536 0.453063561 0.616657186 5.65493466 818310.9193 -5.912918346 -1.061202114 down YKEETIEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YKEETIEK 8 1 P61254 P61254 RPL26 60S ribosomal protein L26 0 ;;; 123.63 0.0012217 3642510000 6526960 5820790 5878680 5742980 6544300 4409290 6652100 5460460 6728400 FALSE TRUE 6118449.225 6251767.348 6018125.066 5890354.59 6030337.076 5682180.444 5654679.36 6142210.451 5605386.573 1.091530289 1.115314219 1.073632476 1.050838245 1.075811097 1.013700013 1.008793825 1.095769287 1 22.41838244 3.188104488 0.814002123 1.028385013 1.10778457 0.460516985 0.029170008 0.516456436 0.753216305 0.014619424 0.023889929 1542.071421 -3.188104488 0.079399557 YKELGEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YKELGEK 7 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 98.033 0.010543 2975910000 4620800 3655290 4286540 4147030 4536550 3065970 5504600 3750160 4375140 FALSE TRUE 4331592.376 3925931.475 4388218.753 4253449.811 4180267.663 3951065.767 4679236.332 4218375.731 3644900.87 1.188397855 1.0771024 1.203933635 1.166958983 1.14688103 1.083998141 1.28377602 1.157336203 1 21.79744815 3.966777891 24.35179406 1.165085036 1.126765148 0 0.078940792 892.2353783 2100635.429 0.018569772 0.033972118 9263.559407 -3.966777891 -0.038319888 YKETDLLILFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YKETDLLILFK 11 1 P05455 P05455 SSB Lupus La protein 0 146.5 3.26E-05 107820000 934540 802840 722260 694930 948320 544100 980870 859270 1058500 FALSE TRUE 876048.8096 862283.109 739392.3483 712763.0803 873842.7725 701172.8373 833797.6495 966551.751 881829.5118 0.993444649 0.977834261 0.838475395 0.808277644 0.990942989 0.795134238 0.945531578 1.096075532 1 19.75014023 1.407953701 5.960412508 1.044004506 0.900114559 0.389242304 0.075273536 0.204549663 11.59252307 0.048553874 0.017975376 25.58313138 -1.407953701 -0.143889946 YKHDYVS(ph)H ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YKHDYVSH 8 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 YKHDYVS(1)H;YKHDYVS(1)H;YKHDYVS(1)H 82.417 0.01231 555010000 1023490 912640 980440 921000 1111750 759660 1128510 903940 1369570 TRUE FALSE 959431.5879 980212.8152 1003696.5 944634.4192 1024437.64 978961.51 959300.4021 1016798.899 1140979.919 0.840883851 0.859097341 0.879679373 0.827915026 0.897857729 0.858000648 0.840768874 0.891162834 1 20.12184197 0.889733537 4.848966824 0.999990839 0.859655691 0.83297465 0.019965386 0.288042782 12.15022818 0.017755197 0.004493836 7.757709934 -0.889733537 -0.140335149 YKLDEDEDEDDADLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YKLDEDEDEDDADLSK 16 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 0 ;;; 201.12 3.08E-11 997090000 2495250 862610 1326780 1241350 1177420 911560 1707000 1006840 1030150 FALSE TRUE 2339076.757 926478.5419 1358251.848 1273205.143 1084950.183 1174712.574 1451051.197 1132546.19 858211.31 2.725525438 1.079545948 1.582654333 1.483556704 1.264199353 1.368791765 1.690785451 1.319658897 1 19.71097339 4.74683545 24.98330413 1.391251162 2.725526105 0.804147404 0.212625409 445.6172334 1345373.281 0.048112363 0.547064599 55825.86358 -4.74683545 1.334274943 YKLDEDEDEDDADLSKYNLDAS(ph)EEEDSNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YKLDEDEDEDDADLSKYNLDASEEEDSNK 29 2 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YKLDEDEDEDDADLSKYNLDAS(0.997)EEEDS(0.003)NK;YKLDEDEDEDDADLSKYNLDAS(1)EEEDSNK 327.29 2.54E-105 704340000 1542750 398526 681440 701480 668010 416732 938610 439806 751750 TRUE FALSE 1446192.031 428033.2797 697604.0786 719481.1644 615547.1892 537035.7633 797874.1441 494716.7472 626278.0685 2.309185175 0.683455643 1.113888724 1.148820629 0.982865631 0.857503704 1.273993429 0.789931457 1 19.25644383 4.746998805 24.97484424 0.995967071 2.309185842 0.851036666 0.174496932 390.6731731 1156265.071 0.040361064 0.467868635 55846.86586 -4.746998805 1.31321877 YKLDEDEDEDDADLSKYNLDAS(ph)EEEDSNKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YKLDEDEDEDDADLSKYNLDASEEEDSNKK 30 3 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YKLDEDEDEDDADLSKYNLDAS(1)EEEDSNKK 187.06 2.21E-17 196750000 174200 33335 66117 72698 70584 41807 96119 39868 102070 TRUE FALSE 163297.133 35803.15809 67685.32646 74563.55376 65040.61736 53876.00222 81706.84828 44845.60756 85033.8576 1.920377807 0.421045912 0.7959809 0.876869001 0.764879063 0.633582948 0.960874299 0.527385312 1 16.37574977 4.748260095 24.83283252 0.740182208 1.920378503 0.80444289 0.181692973 502.4713599 1286410.228 0.041165239 0.538078208 56009.29351 -4.748260095 1.180196295 YKPESEELTAER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YKPESEELTAER 12 1 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 ;;;;; 206.46 8.19E-08 15127670000 15645220 14413680 14874300 15234947 14573680 10999210 19148000 13543511 15773960 FALSE TRUE 14666013.61 15480883.86 15227125.42 15625901.53 13429121.96 14174503.37 16276935.16 15234448.16 13141184.17 1.116034401 1.178043292 1.158733126 1.18907865 1.021911099 1.078632122 1.238620123 1.159290362 1 23.64759195 YKQDVYLLPK ddPTM_SK-BR-3_Pertuzumab_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 87.363 0.013675 0 1180000 1179100 1017100 946260 1520000 753170 1341500 1311400 1935300 FALSE TRUE 1106145.906 1266401.791 1041226.092 970542.6336 1400625.331 970597.9523 1140354.529 1475131.177 1612285.927 0.686073039 0.785469729 0.645807344 0.601966821 0.868720186 0.602001131 0.707290506 0.914931497 1 20.62067619 1.148662591 3.634946891 0.993827886 0.699644665 0.646111456 0.080598761 0.12795832 2.974125161 0.069760832 0.018447746 14.08194328 -1.148662591 -0.294183221 YKQENTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YKQENTR 7 1 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 87.639 0.017505 48554000 64799 76863 58211 64351 85449 47026 75732 76083 92298 FALSE TRUE 60743.34626 82554.0165 59591.79241 66002.35561 78738.18022 60601.6428 64376.68966 85582.13003 76892.86753 0.789973742 1.07362385 0.77499766 0.858367723 1.02399849 0.788130873 0.837225763 1.113004792 1 16.23056216 1.240419176 24.99944952 1.056502425 0.884538119 0.341995937 0.102603297 53.78969078 723610.6445 0.073778086 0.023830383 17.39478944 -1.240419176 -0.171964305 TPEVTCVVVDVSHEDPEVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 TPEVTCVVVDVSHEDPEVK 19 0 A0A0A0MS08;P01857;A0A0A0MS07 A0A0A0MS08 IGHG1 Ig gamma-1 chain C region 0 ;; 111.63 0.00021249 251939000 2978040 853150 391117 326259 343785 254717 366166 239797 334754 FALSE TRUE 2791649.792 916318.1137 400394.4799 334631.3583 316785.5129 328249.6629 311262.8076 269736.1833 278881.3948 10.01016864 3.285691089 1.435715998 1.199905639 1.135914832 1.177022451 1.116111772 0.967207524 1 18.08929216 6.372059069 0.96647523 1.111519553 200 0.992074498 0.247952787 3.309464803 0.173196464 0.078297959 1301.441022 2355369.622 -6.372059069 198.8884804 up YKVEGFPTIYFAPSGDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YKVEGFPTIYFAPSGDK 17 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 115.34 0.00029146 121540000 337450 320460 289910 299230 362230 198630 377860 301470 326960 FALSE TRUE 316329.6069 344187.1918 296786.8021 306908.7484 333781.917 255971.2565 321203.4009 339109.1931 272388.2638 1.161318783 1.263590388 1.089572649 1.126732643 1.225390229 0.939729388 1.179211602 1.244947886 1 18.05530502 3.940880873 5.765220368 1.120712811 1.214594543 0.148081672 0.096266471 0.313642451 28.70413998 0.022740059 0.042996305 8727.319458 -3.940880873 0.093881732 YKVPDGKPENEFAFNAEFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YKVPDGKPENEFAFNAEFK 19 2 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 250.94 8.36E-26 3852800000 8840800 4422300 6498100 5739800 6312100 4107300 8338700 4988900 7916500 FALSE TRUE 8287470.109 4749731.693 6652238.001 5887092.985 5816373.128 5293010.834 7088389.348 5611775.147 6595185.007 1.25659403 0.720181722 1.008650704 0.892635002 0.88191205 0.802556839 1.074782487 0.850889723 1 22.6529817 -1.143984297 4.810319679 1.00000281 0.925456764 0.013233193 0.150793155 8.09E-06 1.44E-06 0.128431467 0.030269279 0.071782024 1.143984297 -0.074546046 YLADPSNLFVVSSDFCHWGQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YLADPSNLFVVSSDFCHWGQR 21 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 ; 189.15 2.26E-17 405650000 634690 906840 689740 627870 893730 644170 823730 811090 582940 FALSE TRUE 594965.8859 973983.3772 706100.9585 643982.2072 823540.0509 830131.4218 700219.3336 912356.3719 485643.5481 1.225108185 2.005551975 1.453949015 1.32603884 1.6957706 1.709343046 1.441838024 1.878654366 1 18.88953827 -1.196419399 4.386799822 0.99981947 1.604935672 0.370974886 0.241756858 0.000390845 7.16E-05 0.2143287 0.050502861 0.063618086 1.196419399 0.605116202 YLAEFATGNDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 YLAEFATGNDR 11 0 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;;;;; 216.12 2.86E-11 3037950000 1700628 1688616 1583518 1614419 1640932 1561685 1738188 1524633 1450996 FALSE TRUE 1594188.729 1813642.886 1621079.795 1655847.725 1512059.82 2012518.108 1477562.846 1714986.786 1208815.394 1.318802472 1.500347278 1.341048272 1.369810257 1.250860824 1.664868034 1.22232299 1.41873341 1 20.20516251 -3.020540941 0.391092147 1.70E-09 1.398954612 0.47540129 0.126860807 95.60668877 3.030742316 79.173608 0.072781044 0.000953804 3.020540941 1.398954611 YLAEFATGNDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YLAEFATGNDRK 12 1 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ; 210.79 6.33E-08 1697310000 1568750 1597510 1589530 1673510 1741110 1234980 2250850 1565170 2066730 FALSE TRUE 1470564.738 1715791.303 1627234.402 1716455.1 1604370.244 1591498.678 1913355.938 1760584.92 1721779.411 0.854095901 0.996522139 0.945088779 0.996907669 0.931809402 0.924333667 1.111266592 1.022538026 1 20.71546889 1.749935404 25 1.053051304 0.949993042 0.487192425 0.049114183 2.404619918 5294.396823 0.020581497 0.011413399 56.22576906 -1.749935404 -0.103058261 YLAEKYEWDVAEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 YLAEKYEWDVAEAR 14 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;; 228.73 1.41E-12 5168479000 7665660 8402190 8872760 9485210 10395160 6374440 10079830 7366260 14363570 FALSE TRUE 7185880.024 9024296.89 9083226.057 9728616.547 9578766.066 8214637.348 8568453.068 8285953.776 11966197.37 0.600514917 0.754149092 0.759073728 0.813008197 0.800485381 0.686486867 0.7160548 0.692446691 1 23.51246143 -1.98749008 2.48541791 1.247187949 0.734435787 0.659231546 0.061342988 12860239.26 5959670.777 18235864.89 0.014308758 0.01029224 1.98749008 -0.512752162 YLAEVAAGDDKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YLAEVAAGDDKK 12 1 B7Z2E6;H0YB80;P63104-2;P63104;E7EX29;B0AZS6 B7Z2E6;P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;; 185.59 2.06E-05 7294220000 9118900 4777460 6780400 6375800 6406800 4742730 9145300 5481660 7251100 FALSE TRUE 8548164.327 5131188.109 6941234.29 6539413.822 5903635.772 6111879.159 7774047.166 6166057.318 6040844.566 1.415061128 0.849415682 1.149050305 1.082533038 0.977286488 1.01175905 1.286913954 1.02072769 1 22.52631884 YLAEVACGDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 YLAEVACGDDR 11 0 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;;;;; 235.66 3.66E-15 7367090000 3644300 4358970 4136410 4340800 4660910 3985760 4836010 3905810 3916980 FALSE TRUE 3416209.768 4681712.674 4234527.599 4452192.277 4294860.93 5136384.209 4110895.196 4393458.976 3263210.733 1.046886042 1.434695169 1.2976568 1.364359412 1.316145747 1.574027738 1.259770064 1.346360789 1 21.63786073 -0.604983554 7.184390139 1.000000179 1.341881475 0.375030644 0.13308908 0 0 0.11304008 0.026643802 0.248322714 0.604983554 0.341881297 YLAEVACGDDRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 YLAEVACGDDRK 12 1 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;;;;;; 232.42 1.79E-12 10309890000 5881900 5016460 5720410 6671470 7221240 5991770 9577230 6487800 7445380 FALSE TRUE 5513762.378 5387883.918 5856100.827 6842671.215 6654112.939 7721496.731 8141213.272 7297816.111 6202697.979 0.888929688 0.868635542 0.944121549 1.103176592 1.072777195 1.244860987 1.312527758 1.176555127 1 22.56446445 3.06162865 1.190845673 1.214393073 0.876801627 0.643924376 0.088037438 0.229173115 0.68714274 0.034250002 0.044442402 1152.467402 -3.06162865 -0.337591446 YLAEVATGEKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YLAEVATGEKR 11 1 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;;;; 194.43 8.25E-07 4229930000 3334230 3445450 3589100 3496350 3992710 2764820 4264390 3490560 4947360 FALSE TRUE 3125546.496 3700554.703 3674235.147 3586072.26 3679138.662 3562978.651 3624984.308 3926364.1 4121613.655 0.75833078 0.897841237 0.891455496 0.870065115 0.892645204 0.864462065 0.87950609 0.952627885 1 21.97477785 -5 0.097948968 1.39976292 0.789550839 0.611245243 0.038652822 149.2715615 0.999986017 12.17634965 0.683442452 1.00E-05 5 -0.610212081 YLAFLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YLAFLR 6 0 P40429;M0QYS1 P40429 RPL13A 60S ribosomal protein L13a 0 118.11 0.051516 83994000 37810 278850 22436 21162 260500 18282 19653 215160 95346 FALSE TRUE 35443.53959 299496.3441 22968.19252 21705.05275 240041.3808 23559.71662 16706.2151 242023.1996 79432.13664 0.446211585 3.770468186 0.289154912 0.273252787 3.021968072 0.296601824 0.210320606 3.046917908 1 16.27743519 3.909911409 8.566744093 1.068821561 2.303983435 0.072998576 1.329530466 0.55063082 64.83156817 0.314851516 0.570081006 8126.647247 -3.909911409 1.235161873 YLANIEQQHGNSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YLANIEQQHGNSGR 14 0 Q9UKX7-2;Q9UKX7 Q9UKX7-2 NUP50 Nuclear pore complex protein Nup50 0 ;; 225.85 2.62E-12 1265620000 429220 582450 566190 584260 593370 571340 621540 547930 560070 FALSE TRUE 402355.8864 625575.204 579620.2942 599253.1007 546769.1137 736276.5831 528345.8471 616340.2666 466590.6988 0.862331563 1.340736551 1.242245711 1.28432286 1.171838862 1.577992414 1.132354006 1.320944177 1 18.83179802 4.744425052 24.76180443 1.272751453 0.862331358 0.402076634 0.151095708 508.5438773 2147188.753 0.030958102 0.277651361 55516.88007 -4.744425052 -0.410420095 YLDEDTIYHLQPSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YLDEDTIYHLQPSGR 15 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ;;;;; 230.16 3.65E-13 3209260000 2338779 3894436 3578290 3744795 4401237 3999204 3737595 3479792 3749807 FALSE TRUE 2192398.997 4182784.094 3663168.729 3840892.78 4055581.6 5153709.273 3177177.328 3914251.691 3123939.987 0.701805735 1.338945086 1.172611748 1.229502742 1.298226476 1.649746568 1.01704173 1.252985559 1 21.57493531 4.744029387 24.80946404 1.253466431 0.701805474 0.471153871 0.180616805 452.4033718 2052290.55 0.039533875 0.343259338 55466.32441 -4.744029387 -0.551660957 YLDESSGGWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YLDESSGGWR 10 0 K7ENE5;O00115-2;O00115 K7ENE5 DNASE2 Deoxyribonuclease-2-alpha 0 ;; 195.06 9.19E-07 513970000 467650 681710 489650 434980 693540 397610 538360 569200 624110 FALSE TRUE 438380.6213 732184.5177 501264.7292 446142.3232 639072.166 512393.5523 457637.9159 640265.873 519942.0091 0.843133683 1.408204194 0.964078148 0.858061698 1.229122008 0.985482118 0.880171073 1.231417854 1 18.9879912 3.733749409 24.21230449 1.00810897 1.172064169 0.036372284 0.183808396 349.938537 1278292.617 0.043388428 0.075923859 5416.882422 -3.733749409 0.163955199 YLDESSGGWRDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YLDESSGGWRDGR 13 1 K7ENE5;O00115-2;O00115 K7ENE5 DNASE2 Deoxyribonuclease-2-alpha 0 70.622 0.039268 0 97838 91442 197020 194680 148290 206170 229200 79163 140630 FALSE TRUE 91714.49423 98212.46083 201693.4074 199675.8184 136643.9016 265687.9321 194833.5878 89046.67481 117157.9445 0.782827785 0.838291089 1.721551264 1.704330161 1.166322115 2.267775636 1.662999369 0.76005665 1 16.83809526 4.106934508 2.985831841 1.548315294 0.793330372 0.274869537 0.429068597 0.283531757 4.873641744 0.104202353 0.270408425 12791.88386 -4.106934508 -0.754984922 YLDLHDCYLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YLDLHDCYLK 10 0 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ;; 131.28 0.0002542 416210000 994560 1471860 1123160 1229290 1653460 965860 1256110 1371220 1418100 FALSE TRUE 932312.2649 1580838.046 1149801.886 1260835.663 1523603.921 1244688.103 1067767.967 1542419.835 1181409.949 0.789152204 1.338094408 0.973245474 1.067229596 1.289648799 1.053561555 0.903808172 1.305575458 1 20.17207824 -1.042857167 4.553300697 0.999995992 1.091436328 0.024313931 0.179057259 6.63E-06 1.39E-06 0.157668086 0.037161095 0.090603053 1.042857167 0.091440336 YLDPEYIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YLDPEYIDR 9 0 X6RA56;X6RLR1;O75935-2;O75935;X6RCK5;A0A0A0MRV8;O75935-3 X6RA56 DCTN3 Dynactin subunit 3 0 ;; 170.22 0.00013465 392720000 1061890 1256200 1276310 1255870 1320400 1112320 1332690 1149600 1293730 FALSE TRUE 995428.2004 1349210.355 1306584.676 1288097.75 1216701.11 1433428.727 1132865.507 1293130.091 1077798.105 0.923575757 1.251821049 1.212272196 1.195119702 1.128876646 1.329960333 1.051092502 1.199788796 1 20.03965552 -1.280029193 2.759685001 0.998239523 1.172679693 0.164821218 0.111833957 6490815.474 7770423.915 96313.43464 0.026628788 0.052477218 1.280029193 0.17444017 YLDQMEDLYEDFHIVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YLDQMEDLYEDFHIVK 16 0 O43681 O43681 ASNA1 ATPase ASNA1 0 173.03 4.36E-09 39691000 246190 218710 241610 247530 291790 191220 284620 222020 282380 FALSE TRUE 230781.4074 234903.516 247341.1033 253882.0389 268873.9904 246422.1098 241943.8733 249739.6857 235248.9538 0.981009283 0.998531608 1.051401502 1.079205815 1.142933841 1.04749503 1.028458871 1.061597434 1 17.84382878 4.02086792 1.853291172 1.061898203 0.985190297 0.381525008 0.036712838 0.387110924 2.540955244 0.010313063 0.031248578 10492.23286 -4.02086792 -0.076707906 YLEEDNS(ph)DES(ph)DAEGEHGDGAEEEAPPAGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YLEEDNSDESDAEGEHGDGAEEEAPPAGPR 30 0 Q9H1C4 Q9H1C4 UNC93B1 Protein unc-93 homolog B1 2 YLEEDNS(1)DES(1)DAEGEHGDGAEEEAPPAGPR 192.75 6.81E-19 273550000 205590 153620 162030 168180 176580 150610 198150 198190 76580 TRUE FALSE 192722.4889 164994.1846 165873.4281 172495.7835 162712.1191 194088.6621 168439.247 222934.4578 63798.30327 3.020809003 2.586184525 2.599966137 2.703767572 2.550414521 3.042222945 2.640183804 3.494363429 1 15.96123044 -1.8827304 2.814913013 0.170218961 2.774726773 0.788967373 0.296185018 111690682.1 103112946.7 623867386.6 0.065124576 0.013099949 1.8827304 2.604507813 YLEEDNS(ph)DES(ph)DAEGEHGDGAEEEAPPAGPRPGPEPAGLGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YLEEDNSDESDAEGEHGDGAEEEAPPAGPRPGPEPAGLGR 40 1 Q9H1C4 Q9H1C4 UNC93B1 Protein unc-93 homolog B1 2 YLEEDNS(1)DES(1)DAEGEHGDGAEEEAPPAGPRPGPEPAGLGR;YLEEDNS(1)DES(1)DAEGEHGDGAEEEAPPAGPRPGPEPAGLGR;YLEEDNS(1)DES(1)DAEGEHGDGAEEEAPPAGPRPGPEPAGLGR;YLEEDNS(1)DES(1)DAEGEHGDGAEEEAPPAGPRPGPEPAGLGR;YLEEDNS(1)DES(1)DAEGEHGDGAEEEAPPAGPRPGPEPAGLGR;YLEEDNS(1)DES(1)DAEGEHGDGAEEEAPPAGPRPGPEPAGLGR 225.48 3.55E-40 2951800000 558264 648928 516252 556391 736783 453369.2 736418 581471 500469 TRUE FALSE 523323.2528 696975.3043 528497.7412 570668.935 678919.0352 584249.5282 625998.9575 654068.9343 416937.4907 1.255159981 1.671654192 1.267570686 1.368715809 1.628347295 1.401288062 1.501421607 1.568745792 1 18.66947158 -1.171090946 5.181705804 0.999976548 1.46274817 0.511754982 0.140476358 3.45E-05 5.53E-06 0.123458057 0.029097871 0.067438679 1.171090946 0.462771622 YLEEERPFAIEQVTGMLLAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YLEEERPFAIEQVTGMLLAK 20 1 O95757;E9PDE8 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 197.86 1.47E-21 115720000 200880 194890 219630 195000 246950 167810 263420 208550 252960 FALSE TRUE 188307.2794 209319.8584 224839.7273 200004.0301 227555.5431 216254.0228 223922.6165 234587.9266 210739.3418 0.893555412 0.993264269 1.066909128 0.949058816 1.079796213 1.026168256 1.062557255 1.113166268 1 17.68510014 5.901708725 0.851068218 1.046810939 7.96E-12 0.52636515 0.044976384 10.70443931 1.30432418 0.013409689 16.56614846 797459.6641 -5.901708725 -1.046810939 YLEES(ph)DEDDLF ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YLEESDEDDLF 11 0 P11388;P11388-2;P11388-3;P11388-4;J3QR57 P11388 TOP2A DNA topoisomerase 2-alpha 1 YLEES(1)DEDDLF;YLEES(1)DEDDLF;YLEES(1)DEDDLF;YLEES(1)DEDDLF;YLEES(1)DEDDLF;YLEES(1)DEDDLF 207.34 2.45E-08 3431740000 2918090 3211360 3271700 3128080 3265000 2634100 3889410 2918990 3750170 TRUE FALSE 2735451.956 3449132.436 3349306.269 3208351.829 3008580.07 3394521.909 3306229.078 3283432.327 3124242.4 0.875556889 1.103990022 1.072037902 1.026921544 0.962979079 1.086510416 1.058249859 1.050953129 1 21.57507496 YLELLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YLELLER 7 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 ;;;;; 164.24 0.0028038 556655000 872668 1403870 996350 1047200 1387070 826093 1122360 1257430 1341740 FALSE TRUE 818049.2676 1507813.996 1019983.893 1074072.925 1278135.117 1064572.639 954072.5375 1414422.903 1117794.926 0.731841994 1.348918268 0.912496442 0.96088549 1.143443299 0.952386358 0.853530925 1.265368871 1 20.0922241 3.7474095 24.65036113 0.997348825 1.098332117 0 0.189011615 1156.090869 1404648.57 0.044289542 0.079716241 5589.970298 -3.7474095 0.100983293 YLELLGYR ddPTM_SK-BR-3_Pertuzumab_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 0 126.67 0.0028134 74346000 92250 165780 100930 91594 177880 77174 72220 142450 124560 FALSE TRUE 86476.23717 178054.5237 103324.1073 93944.45711 163910.0223 99452.88098 61391.28146 160235.1961 103770.1313 0.833344201 1.715855241 0.995701807 0.905313079 1.579549146 0.958396021 0.591608401 1.544136006 1 16.66303172 2.050999603 24.99182009 0.94365188 1.236134542 0.036453531 0.359822062 202.1778568 99074.1138 0.127752099 0.094351162 112.4603947 -2.050999603 0.292482662 YLEMMFTPT(ph)GVVMGARIS(ph)EYLLEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YLEMMFTPTGVVMGARISEYLLEK 24 1 F5H2J1;Q8WXR4-6;Q8WXR4-3;Q8WXR4-5;Q8WXR4-2;Q8WXR4-4;Q8WXR4;Q8WXR4-7 F5H2J1 MYO3B Myosin-IIIb 2 Y(0.131)LEMMFT(0.137)PT(0.584)GVVMGARIS(0.584)EY(0.563)LLEK 43.198 0.059398 16326000 26060 15080 19644 18676 20337 12832 19584 13847 17672 TRUE FALSE 24428.95112 16196.53889 20109.96496 19155.25778 18739.81406 16536.39009 16647.56101 15575.82843 14722.42903 1.659301672 1.10012681 1.365940696 1.301093572 1.272875149 1.123210718 1.130761844 1.057965937 1 13.8457281 1.934118962 0.599101815 0.991702611 1.343596932 0.495752354 0.135954806 0.713901856 0.524245755 0.119024148 0.074100171 85.92488544 -1.934118962 0.351894321 YLEPLYNDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YLEPLYNDYR 10 0 Q8NAV1 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 0 ; 77.789 0.074322 148679000 176796 231428 207874 199426 239904 145387 199527 211187 226815 FALSE TRUE 165730.6539 248563.1699 212804.8694 204543.6088 221062.9076 187357.8667 169609.7787 237554.1618 188958.1112 0.877076157 1.315440593 1.126201294 1.082481231 1.169904304 0.991531221 0.897605176 1.25717896 1 17.52770692 2.236723176 24.99236774 1.01276603 1.141850807 0.039364681 0.140795078 86.33666778 1174295.455 0.0482428 0.037475206 172.4738175 -2.236723176 0.129084777 YLEQLHQLYSDSFPMELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YLEQLHQLYSDSFPMELR 18 0 P40763;P40763-2;P40763-3;K7EP08 P40763 STAT3 Signal transducer and activator of transcription 3 0 ; 279.53 3.18E-39 1025350000 850790 1115090 1055290 987510 1231490 898760 1119870 1069050 1294630 FALSE TRUE 797540.5726 1197652.424 1080321.977 1012851.178 1134773.743 1158217.422 951955.8899 1202523.246 1078547.889 0.739457729 1.110430455 1.001644885 0.939087813 1.052131068 1.073867404 0.882627373 1.114946548 1 20.04065881 4.750973936 24.72852659 1.016429135 0.739457528 0.598012954 0.072639752 1206.173818 2402763.68 0.016778246 0.286163705 56360.38304 -4.750973936 -0.276971607 YLETADYAIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YLETADYAIR 10 0 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 79.474 0.062573 42695000 59320 65464 67061 65194 59791 54177 73714 57581 52191 FALSE TRUE 55607.26709 70311.02268 68651.71859 66866.98841 55095.25605 69817.02041 62661.27003 64770.1146 43479.98493 1.27891643 1.617089398 1.578926918 1.537879751 1.267140643 1.605727797 1.441152064 1.489653566 1 15.40806382 -2.761456585 0.38235672 7.32E-08 1.512635992 0.583327385 0.124966464 58.29124722 2.160608054 47.72360734 0.078755059 0.001731982 2.761456585 1.512635918 YLFLGDYVDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 99.442 0.010917 160807000 343900 429480 359120 393890 469080 298434 375550 410820 379890 FALSE TRUE 322375.9129 461279.1461 367638.496 403997.8843 432240.349 384587.0511 319239.7639 462111.7813 316483.9048 1.018617086 1.45751218 1.1616341 1.276519526 1.36575776 1.215186761 1.008707739 1.460143073 1 18.27177261 -4.459993684 0.233098735 6.24E-10 1.271410419 0.155129594 0.160824278 212.9501773 2.684296915 100.4430071 0.254748967 3.47E-05 4.459993684 1.271410418 YLGDAFGS(ph)PQTDHGFETDPDPFLLDEPAPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YLGDAFGSPQTDHGFETDPDPFLLDEPAPR 30 0 Q9H8N7 Q9H8N7 ZNF395 Zinc finger protein 395 1 Y(0.001)LGDAFGS(0.958)PQT(0.04)DHGFET(0.002)DPDPFLLDEPAPR;YLGDAFGS(0.958)PQT(0.042)DHGFETDPDPFLLDEPAPR 118.14 4.44E-05 51087000 36543 43343 40215 44505 57371 40475 55767 45793 40712 TRUE FALSE 34255.83886 46552.16082 41168.91879 45647.07365 52865.31308 52159.47544 47405.25607 51510.35685 33916.90419 1.00999309 1.37253567 1.213817115 1.34585024 1.558671534 1.537860742 1.397688179 1.518722244 1 15.04971687 5.742139365 0.673913281 1.41173925 1.74E-09 0.25127024 0.1736662 13.40278527 1.666696479 0.061784624 19.75949799 552254.6293 -5.742139365 -1.411739248 YLGEGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YLGEGPR 7 0 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 97.596 0.02764 144860000 131230 172600 162320 173780 170380 144140 158390 144550 198190 FALSE TRUE 123016.5486 185379.4836 166170.3071 178239.489 156999.0421 185750.8781 134640.8899 162597.3857 165110.8086 0.745054485 1.122758014 1.006416893 1.079514361 0.950870772 1.125007379 0.815457759 0.984777357 1 17.33307504 1.737795997 24.99999959 0.918636819 1.019492535 0.061277247 0.118900702 0.21507156 6413.341444 0.049049799 0.027200572 54.67590717 -1.737795997 0.100855716 YLGGS(ph)MDLSTFDFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 YLGGSMDLSTFDFR 14 0 O95983-2;O95983 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 1 YLGGS(1)MDLSTFDFR;YLGGS(1)MDLSTFDFR;YLGGS(1)MDLSTFDFR;YLGGS(1)MDLSTFDFR;YLGGS(1)MDLSTFDFR;YLGGS(1)MDLSTFDFR;YLGGS(1)MDLSTFDFR;YLGGS(1)MDLSTFDFR;YLGGS(0.999)MDLS(0.001)TFDFR;YLGGS(1)MDLSTFDFR 280.97 2.83E-33 615400000 694774 941381 609062 663296 517018 365151.3 1055634 580990.5 1217693 TRUE FALSE 651289.3355 1011081.829 623509.2383 680317.2983 476413.4918 470564.5526 897351.4817 653528.4428 1014452.172 0.642010884 0.996677672 0.61462655 0.670625306 0.469626371 0.463860757 0.884567559 0.644218092 1 19.95226942 -0.462439163 7.370676984 1.00000002 0.695555938 0.27162177 0.164587116 0 0 0.162653904 0.038337893 0.344794903 0.462439163 -0.304444082 YLGHVEVDESR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 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 ; 139.31 3.95E-05 250050000 421460 505260 499090 508170 563480 470440 543770 458640 612970 FALSE TRUE 395081.5709 542669.9761 510928.6505 521210.5025 519226.5538 606248.391 462236.7366 515902.2136 510661.3471 0.773666488 1.062680736 1.000523446 1.02065783 1.016772773 1.187182845 0.905172752 1.0102629 1 18.96200734 4.744009975 24.7861625 1.024053778 0.773666368 0.563509095 0.069620265 385.2627731 1752290.292 0.015517332 0.134588414 55463.84525 -4.744009975 -0.25038741 YLGIPGDKEYCISSDDLFSLPYCPGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YLGIPGDKEYCISSDDLFSLPYCPGK 26 1 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 ; 273.54 1.34E-60 424030000 1526800 1191500 1302850 1148800 1686840 1099750 1785930 1347710 1710850 FALSE TRUE 1431240.313 1279719.9 1333754.217 1178280.153 1554362.391 1417229.972 1518146.376 1515974.56 1425298.082 1.004169115 0.897861237 0.935772126 0.826690338 1.090552503 0.994339352 1.065143071 1.063619308 1 20.44283224 2.726309017 24.99963058 1.044184969 0.916354361 0.59865139 0.051503942 476.4489771 972202.1228 0.01498518 0.014224031 532.4870098 -2.726309017 -0.127830608 YLGQDYEQLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YLGQDYEQLR 10 0 P07384;E9PRM1;E9PJJ3;E9PLC9;E9PMC6;E9PJA6;E9PSA6;E9PQB3;E9PLX0;E9PIA9 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 149.27 5.50E-05 440180000 273590 701960 252080 250410 723710 129060 214649 593750 671660 FALSE TRUE 256466.4903 753933.8488 258059.4566 256835.9445 666872.7359 166317.5269 182464.3752 667880.9945 559555.6069 0.458339595 1.34737967 0.461186437 0.458999859 1.191789927 0.297231454 0.326088011 1.193591819 1 19.09392198 5.009543292 18.82617167 0.739574959 0.033015731 0.05410749 0.390261912 127259818 3596863693 0.09180994 2312739778 102221.7453 -5.009543292 -0.706559228 YLIATSEQPIAALHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YLIATSEQPIAALHR 15 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 204.35 4.95E-09 1125770000 684080 922210 803520 758340 977490 665500 842300 837620 792470 FALSE TRUE 641264.6539 990491.388 822579.8738 777800.2883 900721.8784 857619.0465 716004.9345 942198.7008 660201.6374 0.971316364 1.500286173 1.24595249 1.178125355 1.364313306 1.299025931 1.084524627 1.427137782 1 19.33254719 -3.670817069 0.333334817 2.31E-08 1.280030029 0.187641006 0.158591872 211.0668642 4.214690661 146.5822833 0.122618094 0.000213394 3.670817069 1.280030005 YLKDVTLQK ddPTM_SK-BR-3_Pertuzumab_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 0 118.4 0.0018379 0 598700 1035600 900180 1006700 1488600 913320 1291700 1077400 1909700 FALSE TRUE 561228.4357 1112276.902 921532.6947 1032533.626 1371691.361 1176980.657 1098021.577 1211915.762 1590958.733 0.352761152 0.699123666 0.579231048 0.649000885 0.862179095 0.739793329 0.690163455 0.761751852 1 20.60146498 3.73896929 0.095385037 1.237333035 2.86E-15 0.663016333 0.098558082 29.25403408 0.655597871 2.508638295 6.31801415 5482.381958 -3.73896929 -1.237333035 YLLGDAPVS(ph)PSSQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YLLGDAPVSPSSQK 14 0 Q9NYB0;A0A590UJT3;H3BMI8 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 YLLGDAPVS(0.974)PS(0.009)S(0.017)QK;YLLGDAPVS(0.986)PS(0.014)SQK;YLLGDAPVS(0.992)PS(0.007)S(0.001)QK;YLLGDAPVS(0.95)PS(0.049)S(0.001)QK 227.47 2.12E-12 1046867000 2349120 1797230 2088370 1924740 2210680 1718840 2551910 1889710 2633570 TRUE FALSE 2202092.772 1930298.779 2137907.123 1974132.087 2037062.11 2215041.205 2169274.786 2125644.453 2194010.153 1.003683948 0.879803941 0.974429001 0.899782567 0.928465216 1.009585667 0.988725956 0.968839843 1 21.06513877 2.247030302 24.99949166 0.991290153 0.932771601 0.359638755 0.035897192 175.8107198 518931.2515 0.011445112 0.009429841 176.6161047 -2.247030302 -0.058518551 YLLGDAPVSPS(ph)SQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YLLGDAPVSPSSQK 14 0 Q9NYB0;A0A590UJT3;H3BMI8 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 YLLGDAPVS(0.466)PS(0.473)S(0.061)QK;YLLGDAPVS(0.164)PS(0.782)S(0.054)QK;YLLGDAPVS(0.324)PS(0.338)S(0.338)QK 305.58 2.42E-44 2004980000 3356010 2539070 2981600 2748430 3147810 2633360 3771100 2816560 4003700 TRUE FALSE 3145963.325 2727065.385 3052324.96 2818959.367 2900593.7 3393568.283 3205658.564 3168213.716 3335456.605 0.943188204 0.81759882 0.915114577 0.845149465 0.869624176 1.017422406 0.961085376 0.949859072 1 21.66945284 2.250727923 24.99647065 0.978323227 0.873423406 0.636122037 0.038932279 128.3356762 263652.2588 0.01239329 0.010296683 178.1262492 -2.250727923 -0.10489982 YLLGDMEGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YLLGDMEGR 9 0 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 ;;;;; 134.48 0.00057639 464492000 754940 1090095 835707 780880 1136605 629621 914717 983453 1099874 FALSE TRUE 707689.653 1170806.768 855530.3647 800918.7028 1047340.628 811382.3617 777563.6777 1106239.272 916297.9239 0.772335759 1.277757744 0.93368144 0.874081106 1.143013206 0.8855006 0.848592644 1.20729213 1 19.80545723 3.72782275 24.98416665 0.967050392 1.074519705 0 0.167605656 87.01782555 3099037.616 0.040260697 0.067519807 5343.46231 -3.72782275 0.107469313 YLLHGLECVVAMHQAQLISK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YLLHGLECVVAMHQAQLISK 20 0 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 277.6 7.96E-45 266050000 361490 375340 358310 330890 436920 289780 375570 373170 263870 FALSE TRUE 338864.9862 403130.5641 366809.2824 339381.1976 402606.0657 373434.7818 319256.7651 419761.0959 219828.3923 1.541497814 1.833842116 1.668616499 1.543846061 1.831456171 1.698755915 1.452299959 1.909494454 1 17.74601821 -1.719123295 2.890604414 0.895120918 1.680583023 0.687752516 0.145020998 17923855.62 18711235.69 13782431.11 0.034041976 0.019093111 1.719123295 0.785462105 YLLSQSS(ph)PAPLTAAEEELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YLLSQSSPAPLTAAEEELR 19 0 Q12792;Q12792-3;Q12792-4;F8VS81 Q12792 TWF1 Twinfilin-1 1 YLLSQS(0.068)S(0.932)PAPLTAAEEELR;YLLSQS(0.028)S(0.971)PAPLT(0.001)AAEEELR;YLLSQSS(1)PAPLTAAEEELR;YLLSQS(0.018)S(0.982)PAPLTAAEEELR;YLLSQSS(1)PAPLTAAEEELR;YLLSQSS(1)PAPLTAAEEELR 290.29 1.68E-49 383474000 439553 498111 503454 566719 558855 410750 522895 420151 523518 TRUE FALSE 412042.1624 534991.6567 515396.1666 581261.969 514964.7826 529326.857 444491.7491 472607.7772 436139.4637 0.944748633 1.226652714 1.181723301 1.332743348 1.180734204 1.213664208 1.019150492 1.083616174 1 18.73443001 1.731245041 7.369133909 1.040138585 1.191521192 0.323022989 0.098250846 0.133913824 21.2779756 0.044850945 0.023648703 53.85735747 -1.731245041 0.151382607 YLMAS(ph)DPNLQVLGAAYIQHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YLMASDPNLQVLGAAYIQHK 20 0 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 YLMAS(1)DPNLQVLGAAYIQHK;YLMAS(1)DPNLQVLGAAYIQHK;YLMAS(1)DPNLQVLGAAYIQHK;YLMAS(1)DPNLQVLGAAYIQHK 293.04 1.04E-54 3837850000 4144410 4085380 4046670 3884130 4260270 3311000 5012050 3728760 4817220 TRUE FALSE 3885018.776 4387865.786 4142658.923 3983803.352 3925685.579 4266831.95 4260539.632 4194303.894 4013194.862 0.968061335 1.093359764 1.0322596 0.992676281 0.978194609 1.063200791 1.061632883 1.045128392 1 21.93631978 YLMDEGAHLHIYDPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YLMDEGAHLHIYDPK 15 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 132.05 2.88E-05 138250000 151030 122850 132420 145670 138240 91853 163500 125220 145530 FALSE TRUE 141577.3019 131945.9418 135561.0649 149408.1388 127383.188 118369.47 138984.6929 140853.9926 121240.1028 1.167743169 1.088302787 1.118120669 1.232332663 1.050668756 0.976322745 1.146359081 1.161777245 1 16.88750746 YLMEEDEDAYKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 16 YLMEEDEDAYKK 12 1 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;;;;;;;;;;;; 229.54 1.27E-11 16768320000 14923490 9110940 11675240 11263770 11704100 8212484 14741120 9715919 14313720 FALSE TRUE 13989455.4 9785523.478 11952182.21 11552817.41 10784907.2 10583294.81 12530825.91 10928972.87 11924667.66 1.173152644 0.820611841 1.002307364 0.96881672 0.904419939 0.887512769 1.050832297 0.916501255 1 23.50744572 1.738249051 24.99999959 0.992199712 0.94663224 0.008597844 0.097348389 0.209307962 12143.50313 0.040882052 0.022671224 54.73297455 -1.738249051 -0.045567471 YLMGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YLMGER 6 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 109.7 0.068236 3003800000 1073700 4449300 863600 884100 3941500 561330 858430 3291900 2964670 FALSE TRUE 1006499.034 4778730.801 884084.9998 906787.5028 3631950.489 723376.8586 729716.3908 3702900.961 2469847.424 0.40751466 1.934828344 0.357951261 0.367143125 1.470516135 0.292883217 0.295449988 1.499242797 1 21.23599049 3.885215935 7.351135939 0.688874933 1.261014398 0.067631004 0.584234775 0.409996455 28.16732286 0.138286127 0.251043334 7677.431224 -3.885215935 0.572139465 YLNQDYEALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YLNQDYEALR 10 0 P17655 P17655 CAPN2 Calpain-2 catalytic subunit 0 165.58 1.35E-05 375320000 252490 437140 182380 193080 433320 142370 225590 403350 438780 FALSE TRUE 236687.1016 469506.3004 186706.1397 198034.7597 399288.7951 183469.9078 191764.8738 453709.1354 365544.7834 0.647491395 1.284401589 0.51076133 0.541752389 1.092311567 0.501908155 0.52460022 1.241186186 1 18.47968864 6.815943501 17.28114547 0.792556684 0.329665286 0 0.315471102 0 0 0.066655615 0 6545510.149 -6.815943501 -0.462891398 YLPDTLLLEECGLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YLPDTLLLEECGLLR 15 0 P21964-2;P21964;E7EMS6 P21964-2 COMT Catechol O-methyltransferase 0 ;;;; 197.31 1.97E-08 171267000 87654.5 88417.5 85134.1 81483.4 106152.1 88780.8 98442.8 90624.8 108633.3 FALSE TRUE 82168.36131 94964.0237 87153.52106 83574.402 97815.34226 114410.3757 83682.21604 101939.5058 90501.70043 0.907920635 1.049306513 0.963004238 0.923456704 1.080812203 1.264179294 0.924647997 1.126382215 1 16.46565728 2.719478696 24.12026734 1.077553019 0.975999808 0.274938342 0.094019506 783.0067202 989747.9327 0.028979088 0.02736654 524.1778868 -2.719478696 -0.10155321 YLPEFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YLPEFR 6 0 A0A1B0GVZ4;A0A494C085;P06132;A0A1B0GVN9;H0Y5R6;Q5T446;A0A494BZY8;A0A494C0Q8;A0A494C007;A0A494C0P4;A0A494C1D8;A0A494C0S8;A0A494C1T3 A0A1B0GVZ4 UROD Uroporphyrinogen decarboxylase 0 ;; 118.06 0.05163 226284000 434880 587530 546150 542440 596440 483080 555200 504020 621890 FALSE TRUE 407661.6371 631031.3325 559104.9359 556359.9287 549598.0083 622537.3539 471952.9142 566948.0065 518092.5414 0.786851005 1.21798961 1.079160365 1.07386207 1.060810501 1.201594897 0.910943271 1.094298723 1 18.98285029 1.728119521 25 0.998283607 1.087960799 0.050557631 0.123985153 1.837534938 4378.591839 0.051937417 0.028801947 53.47114955 -1.728119521 0.089677192 YLPHSAGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 YLPHSAGR 8 0 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;;;;;;;; 178.87 0.00024735 8881460000 6393730 10312530 7046120 7114640 10245870 4816190 7486930 8795550 10347540 FALSE TRUE 5993557.852 11076080.45 7213257.294 7297213.707 9441200.7 6206545.869 6364334.352 9893693.779 8620468.726 0.695270529 1.28485826 0.83675929 0.846498484 1.095207349 0.719977772 0.738281705 1.147697891 1 23.03933489 3.733701823 24.57899674 0.885409393 1.040767117 0 0.199383745 488.3775255 1824114.072 0.047835086 0.083723036 5416.288919 -3.733701823 0.155357724 YLQDLLAWVEENQHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YLQDLLAWVEENQHR 15 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 203.2 5.53E-09 3785900000 817440 1074420 974070 1027490 1161070 869710 1212650 932180 929620 FALSE TRUE 766277.8896 1153971.175 997175.4004 1053857.133 1069884.246 1120781.158 1030824.39 1048564.725 774460.4164 0.989434545 1.49003248 1.287574393 1.360763069 1.381457623 1.447176815 1.331022694 1.353929397 1 19.56283198 -1.448353817 9.754495624 0.999998556 1.347153786 0.366371917 0.134824896 3.68E-06 2.08E-07 0.113439951 0.026737942 0.035616085 1.448353817 0.34715523 YLQEAFHVEPEEHQQTLQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YLQEAFHVEPEEHQQTLQR 19 0 Q70J99;Q70J99-3;K7EQ37;Q70J99-2;K7EN81;K7EIH3 Q70J99 UNC13D Protein unc-13 homolog D 0 ;;; 256 3.48E-31 772980000 570194 602290 613396 660340 708540 499616 589180 476246 475299 FALSE TRUE 534506.5754 646884.1783 627946.0428 677285.4424 652894.1265 643847.0286 500837.9287 535706.3614 395968.5264 1.349871366 1.633675748 1.585848372 1.710452719 1.648853591 1.626005568 1.264842772 1.352901369 1 18.59502624 1.274414392 1.121504338 1.034695805 1.605544099 0.713936894 0.118945415 0.220712859 0.563133352 0.103741945 0.034498533 18.81110866 -1.274414392 0.570848294 YLQEVIDVLETDGHFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YLQEVIDVLETDGHFR 16 0 Q02818;H7BZI1;C9JKZ2;C9JBD3;C9J3C1 Q02818 NUCB1 Nucleobindin-1 0 110.37 0.0021667 0 22844 40762 35376 34566 46314 29498 33182 32763 25173 FALSE TRUE 21414.23482 43780.06089 36215.13543 35453.02208 42676.68526 38013.59374 28206.66715 36853.53267 20971.46368 1.02111303 2.087601589 1.726876864 1.69053637 2.034988398 1.812634269 1.345002313 1.757318099 1 14.35613994 0.494596011 0.703005931 0.994729423 1.764957632 0.297167905 0.316250563 1.854867384 1.498010136 0.329352557 0.107629866 3.123172783 -0.494596011 0.770228209 YLQLAEELIRPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YLQLAEELIRPER 13 1 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ;; 204.28 7.22E-08 84689000 104295 125308 110270 121175 131271 111954 133399 118371 113420 FALSE TRUE 97767.36212 134585.9347 112885.6565 124284.5556 120961.5052 144273.3024 113397.0584 133149.8799 94489.46928 1.034690563 1.424348509 1.194690343 1.315327058 1.280158584 1.526871761 1.200102606 1.409150469 1 16.52786593 -0.954064844 4.861798309 0.999997511 1.302755168 0.315513305 0.137871113 3.21E-06 6.92E-07 0.115401185 0.027200096 0.111156575 0.954064844 0.302757656 YLQSLLAEVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YLQSLLAEVER 11 0 O95232;J3KPP4;D6RDI2;D6RHH0;U3KQT3 O95232 LUC7L3 Luc7-like protein 3 0 ; 120.77 0.00098992 16088300 26119 38975 24112 24642 37521 21387 25010 34209 38512 FALSE TRUE 24484.25841 41860.74955 24683.94803 25274.35544 34574.25201 27561.07971 21259.98268 38480.06895 32084.0984 0.763127519 1.304719523 0.769351462 0.787753333 1.077613327 0.859026156 0.662633009 1.199350172 1 14.96957082 3.866535024 7.394243464 0.880352568 1.067137261 0.043828363 0.203487367 0.43702069 26.12672804 0.048198781 0.087416524 7354.193015 -3.866535024 0.186784693 YLS(ph)FTPPEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YLSFTPPEK 9 0 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 YLS(0.991)FT(0.009)PPEK;YLS(0.995)FT(0.005)PPEK;YLS(0.986)FT(0.014)PPEK;YLS(0.999)FT(0.001)PPEK;YLS(0.953)FT(0.047)PPEK;YLS(0.988)FT(0.012)PPEK 205.32 1.59E-05 3018050000 5119840 4177570 4281450 4049960 4910830 3035530 6080450 4474900 5006680 TRUE FALSE 4799398.354 4486881.63 4383008.016 4153888.83 4525153.221 3911838.233 5168742.971 5033601.115 4171032.764 1.150649881 1.075724379 1.050820807 0.995889763 1.084899946 0.937858429 1.239199801 1.206799707 1 21.99197321 1.718573569 16.55942729 1.166914131 1.05184704 0.231111221 0.083152434 0.204374338 156.9015076 0.03480705 0.019240837 52.3086569 -1.718573569 -0.115067091 YLS(ph)FTPPEKDGFPSGTPALNAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YLSFTPPEKDGFPSGTPALNAK 22 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 YLS(0.989)FT(0.011)PPEKDGFPSGTPALNAK;YLS(0.98)FT(0.02)PPEKDGFPSGTPALNAK 212.9 9.36E-24 4543200000 3907170 3325660 3129700 3496660 4641050 2126790 4998010 3647270 6505260 TRUE FALSE 3662627.204 3571895.327 3203937.962 3586390.215 4276560.654 2740759.747 4248604.8 4102639.688 5419490.08 0.675825059 0.659083285 0.591188085 0.661757871 0.789107571 0.505722809 0.783949179 0.757015813 1 22.36972568 0.835452543 1.026439992 0.998778766 0.647753846 0.653761172 0.078417911 0.410263401 0.844418745 0.067045379 0.021728323 6.846246681 -0.835452543 -0.351024919 YLS(ph)PLGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YLSPLGK 7 0 A0A075B754;Q96QE3-2;Q96QE3 A0A075B754 ATAD5 ATPase family AAA domain-containing protein 5 1 YLS(1)PLGK;YLS(1)PLGK 100.25 0.010421 124187000 237882 223940 250110 231520 234350 218300 305710 202440 212793 TRUE FALSE 222993.3903 240520.7506 256042.7273 237461.1952 215945.0963 281319.6662 259871.6236 227715.0796 177276.4736 1.257884849 1.356755049 1.444313067 1.339496383 1.218126083 1.586897914 1.465911513 1.284519457 1 17.43564156 0.925398902 5.657772158 1.0000301 1.391564081 0.566589749 0.104553694 0.402213461 29.2236627 0.099581055 0.025077414 8.421683231 -0.925398902 0.391533981 YLSEVASGDNK ddPTM_SK-BR-3_Pertuzumab_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 ; 230.06 4.83E-12 896170000 1072060 794280 930720 931780 953000 699020 1045550 869560 875290 FALSE TRUE 1004961.678 853089.3176 952797.1179 955691.0523 878155.2242 900815.7264 888779.4839 978126.4801 729198.4444 1.378173097 1.169900079 1.306636246 1.310604897 1.204274681 1.235350587 1.21884446 1.341372143 1 19.47595196 -1.819168045 2.77702822 0.918367556 1.25944706 0.622092461 0.065780274 14548044.72 11448782.77 7978546.405 0.014381096 0.015164635 1.819168045 0.341079504 YLSVPPSPNISTSES(ph)RSPPEGDTTLFLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YLSVPPSPNISTSESRSPPEGDTTLFLSR 29 1 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 YLS(0.002)VPPS(0.055)PNIS(0.051)T(0.051)S(0.051)ES(0.453)RS(0.331)PPEGDT(0.001)T(0.002)LFLS(0.002)R 47.044 0.064206 138030000 49489 61916 66131 51624 62690 50163 67668 49157 83459 TRUE FALSE 46391.57183 66500.32506 67699.65855 52948.75924 57766.58028 64644.24377 57521.8116 55294.35966 69529.15373 0.667224744 0.956438005 0.973687366 0.761533204 0.830825304 0.929742997 0.827304929 0.795268699 1 16.08533041 -1.051647038 4.717621489 1.000004596 0.863102422 0.187306754 0.094862816 4.52E-06 9.08E-07 0.090433452 0.021314653 0.088787732 1.051647038 -0.136902175 YLSVPPSPNISTSESRS(ph)PPEGDTTLFLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YLSVPPSPNISTSESRSPPEGDTTLFLSR 29 1 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 YLSVPPS(0.008)PNIS(0.01)T(0.01)S(0.008)ES(0.187)RS(0.774)PPEGDT(0.001)T(0.001)LFLSR;YLSVPPS(0.003)PNIS(0.01)T(0.01)S(0.01)ES(0.175)RS(0.791)PPEGDT(0.001)T(0.001)LFLS(0.001)R 75.654 0.0033695 235428000 66648 78875 73058 79465 79766 59236 88263 68028 126679 TRUE FALSE 62476.62065 84714.98707 74790.97026 81504.20643 73501.50012 76336.47158 75028.78254 76521.44555 105535.4565 0.591996498 0.802715882 0.708680975 0.772292167 0.696462616 0.723325355 0.710934363 0.725078074 1 16.68736825 0.863364329 17.08904599 1 0.723810941 0.723907888 0.054867877 6548.120836 818981.8211 0.046695704 0.011673926 7.300697087 -0.863364329 -0.276189059 YLTESYGTGQDIDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 305.11 2.38E-44 148930000 109400 112760 126200 110610 121400 100030 130820 117920 128530 FALSE TRUE 102552.8493 121108.8677 129193.5236 113448.4399 111865.7337 128907.0371 111204.7555 132642.5716 107077.5127 0.957744037 1.131039232 1.206542068 1.059498274 1.044717335 1.203866563 1.03854444 1.238752827 1 16.70829601 -1.955099587 2.642866684 0.912055198 1.115589855 0.129969334 0.088501953 29573119.21 12208605.15 15931016.61 0.019473745 0.011089205 1.955099587 0.203534657 YLTLDSFDAMFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YLTLDSFDAMFR 12 0 A0A0G2JR96;A0A0G2JQT1 A0A0G2JR96 0 82.417 0.025 0 59176 67177 69837 75491 83840 61119 73051 58456 70381 FALSE TRUE 55472.27979 72150.85498 71493.56662 77428.22687 77255.54459 78763.06312 62097.68072 65754.36028 58633.95642 0.94607772 1.230530215 1.219320185 1.320535601 1.317590511 1.343301185 1.059073692 1.121438229 1 15.83944879 1.644936315 7.99963366 1.06686588 1.234964265 0.326396509 0.114181113 0.139931558 17.42948413 0.055199118 0.028421678 44.15057003 -1.644936315 0.168098385 YLVIDEAHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YLVIDEAHR 9 0 O60264;A0A0A0MRP6;B7ZLQ5;P28370-2;P28370 O60264 SMARCA5;SMARCA1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5;Probable global transcription activator SNF2L1 0 ; 114.84 0.0015728 656600000 267520 406010 310980 324300 458780 278530 328090 345180 377120 FALSE TRUE 250776.4007 436071.4029 318356.5925 332622.087 422749.2694 358937.0894 278895.9503 388276.4828 314176.2357 0.798202958 1.38798341 1.01330577 1.058711797 1.345580032 1.142470527 0.88770543 1.235855672 1 18.26121453 1.94805699 24.92035468 1.02530429 1.148416011 0.030277482 0.185329326 804.2866912 385865.8225 0.070188875 0.045306262 88.72724364 -1.94805699 0.123111721 YLVLDEADR ddPTM_SK-BR-3_Pertuzumab_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 ;;; 190.26 8.67E-05 1778160000 2073600 2709740 2495860 2234620 2849100 1999560 2500970 2455690 3002400 FALSE TRUE 1943817.077 2910371.969 2555062.978 2291964.132 2625343.179 2576800.512 2125972.766 2762288.302 2501280.044 0.777128927 1.163553028 1.021502164 0.916316483 1.049599858 1.030192728 0.849953915 1.104349874 1 21.25423516 3.451942054 24.85543224 0.979534612 1.031434324 0 0.118503324 761.6542864 751858.8547 0.030778076 0.041678793 2831.01424 -3.451942054 0.051899711 YLYPNIDKDHAFGK ddPTM_SK-BR-3_Pertuzumab_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 0 139.58 6.12E-06 368650000 558530 508780 549780 599100 638920 424740 764210 573080 765500 FALSE TRUE 523572.6043 546450.6006 562821.0412 614473.9203 588741.8005 547355.5429 649623.8051 644630.2995 637733.1047 0.820990161 0.856864097 0.882533833 0.963528341 0.923178985 0.858283095 1.018645261 1.010815175 1 19.28259325 3.445478517 0.300531099 1.022062563 0.765676422 0.658254381 0.041314134 2.176842124 0.291202368 0.052123223 0.195660777 2789.192682 -3.445478517 -0.256386141 YLYRPES(ph)D ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YLYRPESD 8 1 A0A1B0GV45 A0A1B0GV45 1 YLYRPES(1)D;YLYRPES(1)D;YLYRPES(1)D;YLYRPES(1)D 123.75 0.0035101 1507130000 1411030 1643210 1602520 1600340 1779230 1470420 1736330 1563690 1955680 TRUE FALSE 1322716.151 1764874.978 1640532.531 1641407.434 1639496.453 1894906.384 1475983.436 1758920.139 1629264.374 0.811848692 1.083234254 1.006916101 1.007453094 1.006280183 1.163044141 0.905920156 1.079579328 1 20.63578929 4.747541868 24.99833338 1.028458778 0.81184858 0.511222699 0.067453456 938.917416 2613318.546 0.014618637 0.176893024 55916.74308 -4.747541868 -0.216610198 YLYVDKNFINNPLAQADWAAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YLYVDKNFINNPLAQADWAAK 21 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ; 224.56 2.86E-25 155844000 261854 320730 269790 294310 399850 219179 400570 278340 501210 FALSE TRUE 245465.0256 344477.1829 276189.5462 301862.4929 368447.3939 282452.4192 340508.2472 313091.3617 417554.8131 0.587863001 0.824986737 0.661445007 0.722929023 0.88239288 0.676443931 0.815481553 0.749820986 1 18.67160607 -5 0.17588758 2.026533892 0.689036081 0.523304873 0.082000194 104.113498 0.995273146 37.24860324 0.243402285 1.00E-05 5 -1.337497811 YLYYTGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YLYYTGR 7 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 146.01 0.0052301 920710000 608490 818280 698140 685300 807240 564180 746480 684100 738760 FALSE TRUE 570405.6971 878866.3026 714700.2105 702885.9582 743842.6266 727049.6073 634552.254 769511.3909 615456.1834 0.926801473 1.427991669 1.161252791 1.142056863 1.20860371 1.181318227 1.031027506 1.250310601 1 19.23129662 0.843404301 0.349850154 0.987257583 1.226628706 0.069719651 0.135783841 3.30834801 1.062385858 0.274227982 0.13264677 6.972753319 -0.843404301 0.239371123 YMACCLLYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 90.986 0.025729 84745000 145290 197630 176240 186820 208350 146540 218960 188620 229810 FALSE TRUE 136196.5583 212262.7308 180420.496 191614.1175 191987.0314 188843.7191 186128.9807 212169.6222 191453.2264 0.711382936 1.108692368 0.942373756 1.000840368 1.002788175 0.986370001 0.972190358 1.108206042 1 17.54663245 4.750622405 24.91332414 1.009486724 0.711382746 0.757176493 0.053981944 880.6720471 1818971.535 0.012104993 0.205408584 56314.78169 -4.750622405 -0.298103978 YMAENPTAGVVQEEEEDNLEYDS(ph)DGNPIAPTKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YMAENPTAGVVQEEEEDNLEYDSDGNPIAPTKK 33 1 A0A0A0MSJ0;Q86XP3-2;Q86XP3;J3KRE3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 1 YMAENPTAGVVQEEEEDNLEYDS(1)DGNPIAPTKK;YMAENPTAGVVQEEEEDNLEY(0.005)DS(0.995)DGNPIAPTKK;YMAENPTAGVVQEEEEDNLEYDS(1)DGNPIAPTKK;YMAENPTAGVVQEEEEDNLEYDS(1)DGNPIAPTKK;YMAENPTAGVVQEEEEDNLEYDS(1)DGNPIAPTKK 339.21 8.05E-118 1060793000 548846 344927 420266 420742 451217 320633 552451 375796 618525 TRUE FALSE 514494.7086 370465.754 430234.908 431538.952 415780.2369 413194.5421 469616.1013 422714.9578 515289.1817 0.9984582 0.718947277 0.834938755 0.837469459 0.806887184 0.801869235 0.911364178 0.820345105 1 18.97502278 0.151059735 0.543115547 1.011143998 0.819715666 0.284139188 0.074725683 3.614884398 1.436484274 0.161518069 0.03135105 1.415988529 -0.151059735 -0.191428332 YMEHEERPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YMEHEERPK 9 1 O95757;E9PDE8 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 ; 83.883 0.021341 128037000 168166 176653 198385 191364 192358 157955 212038 167191 180818 FALSE TRUE 157640.7902 189732.5719 203090.7859 196274.7242 177250.9786 203554.0443 180244.8704 188065.1644 150638.3077 1.046485404 1.259524054 1.348201457 1.302953593 1.176666024 1.35127676 1.196540728 1.248455106 1 17.20072917 0.087291272 0.995573217 0.997942556 1.257368813 0.404771312 0.09040592 5.506341712 5.148154751 0.114948696 0.025918298 1.22261937 -0.087291272 0.259426257 YMHSGPVVAMVWEGLNVVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 216.29 3.86E-19 1143790000 1465610 1680590 1275080 1212910 1781290 1034140 1618670 1449100 1459290 FALSE TRUE 1373880.086 1805022.632 1305325.5 1244035.324 1641394.669 1332679.43 1375965.46 1630023.325 1215725.072 1.130091102 1.484729298 1.073701226 1.023286723 1.350136398 1.096201322 1.131806436 1.340782849 1 20.21338558 7.999999889 0.020814625 4.45E-08 2.738812514 0.109625902 0.150101001 5442.115117 8.725513341 420.3114455 778.6829241 99999974.33 -7.999999889 2.738812469 YMIGVTYGGDDIPLSPYR ddPTM_SK-BR-3_Pertuzumab_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 0 272.59 1.28E-38 47824000 51462 60182 56252 54043 62656 43629 62129 55125 56786 FALSE TRUE 48241.08528 64637.9379 57586.324 55429.83487 57735.2505 56223.98404 52813.33323 62007.4776 47308.04975 1.019722553 1.366320071 1.217262692 1.171678714 1.220410708 1.18846548 1.116370967 1.310717265 1 15.52979807 -4.43981654 0.267194381 8.73E-09 1.226540789 0.261620223 0.098013106 181.404487 2.342097574 99.31044846 0.115883215 3.63E-05 4.43981654 1.22654078 YMLTHQELAS(ph)DGEIETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YMLTHQELASDGEIETK 17 0 Q02241;H7BYN4;A0A2U3TZL8;Q02241-2;Q02241-3 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 YMLTHQELAS(1)DGEIETK;YMLTHQELAS(1)DGEIETK;YMLTHQELAS(1)DGEIETK;YMLTHQELAS(1)DGEIETK;YMLTHQELAS(1)DGEIETK 296.41 2.40E-46 1226000000 2582210 1938520 2207710 2114820 2266830 1623362 2591350 1863034 2203940 TRUE FALSE 2420594.085 2082050.038 2260077.924 2169089.862 2088802.316 2092000.256 2202801.124 2095637.896 1836088.176 1.31834305 1.133959722 1.230920145 1.181364757 1.137637257 1.139378971 1.199725129 1.141360161 1 20.80820391 -5 0.147467007 0.351675172 1.243046743 0.625743849 0.049735595 91.46970777 0.808147077 17.38071853 0.245963864 1.00E-05 5 0.891371571 YMNSDTTS(ph)PELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YMNSDTTSPELR 12 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 YMNSDTT(0.001)S(0.999)PELR;YMNSDTTS(1)PELR 258.09 3.33E-21 1173140000 1180610 1467570 1417640 1454460 1474710 1122520 1565220 1245220 1456430 TRUE FALSE 1106717.728 1576230.41 1451267.09 1491783.906 1358892.225 1446573.301 1330529.792 1400688.458 1213342.424 0.912123161 1.299081264 1.196090289 1.229483018 1.119957729 1.19222181 1.096582272 1.154404915 1 20.21055533 0.667762213 0.627793439 0.998795499 1.183479874 0.138609541 0.103908261 1.936989733 1.493182246 0.106707967 0.039274658 4.65331243 -0.667762213 0.184684375 YMTISGFQIEETIDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YMTISGFQIEETIDR 15 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 138.94 4.31E-05 0 10917 11924 7038.3 7936.6 11550 9689.1 10024 13983 14265 FALSE TRUE 10233.72446 12806.86537 7205.2518 8140.266593 10642.90959 12486.18588 8520.994258 15728.80833 11884.07934 0.861128924 1.077648928 0.606294488 0.68497242 0.895560294 1.050664971 0.717009203 1.323519296 1 13.53674252 1.242513344 24.9999917 1.161759666 0.842615993 0.388519167 0.166826479 95.49014971 603982.4141 0.118247646 0.039577345 17.47886965 -1.242513344 -0.319143673 YMVADKFTELQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YMVADKFTELQK 12 1 P30153;B3KQV6;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ; 155.98 6.64E-05 794570000 602270 685960 699980 747200 937210 576900 954990 781470 1339420 FALSE TRUE 564574.9958 736749.1921 716583.8562 766374.417 863605.3071 743441.6648 811798.1152 879038.2497 1115862.149 0.50595407 0.660251083 0.642179553 0.686800263 0.773935479 0.666248663 0.727507529 0.787765989 1 20.08972738 -5 0.089379799 2.069307618 0.404152488 0.862968686 0.04703421 74.37651734 0.462786891 15.11073919 1.081739287 1.00E-05 5 -1.665155131 YMWDSQSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YMWDSQSGR 9 0 Q9UKD2 Q9UKD2 MRTO4 mRNA turnover protein 4 homolog 0 ; 175.51 0.00012529 307570000 345830 431490 394470 365410 448950 289900 383250 395300 385330 FALSE TRUE 324185.1176 463437.9686 403827.0147 374787.0392 413691.278 373589.4239 325785.2204 444654.0752 321015.9337 1.009872357 1.443660329 1.257965641 1.167502918 1.288693908 1.163772214 1.014856854 1.385146432 1 18.29228538 2.115081587 5.155207609 1.12458625 1.262071167 0.070021801 0.149794007 0.379018205 15.61616642 0.053862835 0.039251615 130.3411617 -2.115081587 0.137484916 YNADEAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YNADEAR 7 0 P47813;O14602;X6RAC9;A6NJH9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 ;; 129.47 0.0085095 2681620000 4945080 6630590 4880910 5113660 6459750 4099840 5509710 5468030 5919750 FALSE TRUE 4635576.27 7121525.783 4996687.49 5244885.173 5952427.292 5283397.253 4683580.135 6150725.582 4931705.482 0.939953995 1.44402901 1.013176376 1.063503324 1.206971364 1.071312403 0.94968772 1.247180231 1 22.23365521 3.74197964 23.7926524 1.073352191 1.228178691 0.077955033 0.149863216 378.9690818 606834.8706 0.034982029 0.0626885 5520.515577 -3.74197964 0.1548265 YNEDLELEDAIHTAILTLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YNEDLELEDAIHTAILTLK 19 0 A0A024RA52;P25787;C9JCK5 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 0 ; 215.06 4.15E-19 1755440000 1251940 1132100 1130250 1034990 1269460 946340 1411690 1163400 1306800 FALSE TRUE 1173583.31 1215921.862 1157060.064 1061549.596 1169761.732 1219532.995 1200020.19 1308653.051 1088686.638 1.077980816 1.116870383 1.062803587 0.975073597 1.074470552 1.120187346 1.102264094 1.2020475 1 20.05415732 2.306749035 5.722723841 1.113465815 1.064746276 0.117012319 0.059504825 0.410189889 24.58744066 0.02004713 0.016529287 202.6511325 -2.306749035 -0.04871954 YNEEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YNEEER 6 0 K7EP07;Q99426-2;Q99426;A0A494C0X0;K7EK42 K7EP07 TBCB Tubulin-folding cofactor B 0 158.12 0.022155 424850000 553220 554370 506630 570620 583470 474840 601330 482630 535070 FALSE TRUE 518594.9477 595416.1316 518647.5028 585263.0753 537646.6198 611918.5996 511166.149 542887.4179 445763.3603 1.163386213 1.335722459 1.163504112 1.312945673 1.206125643 1.37274315 1.146720871 1.21788255 1 18.76591851 0.606732446 1.025682849 1.000631356 1.253005384 0.502434187 0.076303141 0.969096045 1.608256794 0.064095712 0.020374939 4.043267231 -0.606732446 0.252374028 YNFLPEALDFVGVHQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YNFLPEALDFVGVHQER 17 0 Q5SRE5;Q5SRE5-2 Q5SRE5 NUP188 Nucleoporin NUP188 homolog 0 122.29 5.74E-05 53434000 100450 153140 119120 128850 151310 119270 144670 133730 121520 FALSE TRUE 94163.01381 164478.6449 121945.5827 132156.5091 139426.723 153701.3128 122978.0766 150426.4849 101237.527 0.930119657 1.624680589 1.204549205 1.305410287 1.377223715 1.518224688 1.214747932 1.485876724 1 16.62738465 -1.275895703 3.386664372 0.99878134 1.346306352 0.221784837 0.194299444 16505546.37 22477605.66 202305.8108 0.04101099 0.052979066 1.275895703 0.347525011 YNGGVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YNGGVGR 7 0 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2;J3KRB3;A0A087WWH0;J3QS96;A0A087WY81 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 0 ;; 153.88 0.0039921 1905440000 1173410 1387180 1340410 1300580 1507730 1291640 1395830 1191910 1363420 FALSE TRUE 1099968.363 1489888.251 1372205.158 1333955.085 1389318.968 1664515.5 1186538.25 1340722.587 1135856.394 0.968404429 1.311687163 1.208079794 1.174404697 1.223146672 1.465427768 1.04461995 1.180362759 1 20.11534902 1.109504509 1.51542904 1.016852901 1.224899418 0.170933478 0.134636397 0.565762886 2.568474804 0.114553256 0.034164576 12.86780613 -1.109504509 0.208046516 YNGLIHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 YNGLIHR 7 0 P46779;H0YKD8;P46779-2;P46779-3;H0YLP6;H0YMF4;P46779-4;P46779-5 P46779 RPL28 60S ribosomal protein L28 0 ;;;;;;; 135.35 0.0030858 4259910000 4551100 6886040 5229550 5319150 7388740 4392170 6093470 6132820 6995050 FALSE TRUE 4266254.775 7395889.567 5353597.396 5455648.394 6808458.165 5660118.178 5179810.743 6898516.077 5827530.965 0.732086161 1.269129175 0.91867335 0.936185226 1.168326381 0.97127209 0.888851689 1.183780252 1 22.47445333 YNHIDESEMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YNHIDESEMK 10 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;Q5TBM3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;; 176.95 2.38E-06 924300000 2989910 2451620 2422360 2320120 3083540 1629990 2769530 2562470 3343960 FALSE TRUE 2802776.87 2633140.496 2479819.523 2379658.207 2841371.207 2100541.652 2354264.688 2882400.02 2785831.473 1.006082707 0.94519016 0.890154177 0.854200346 1.019936502 0.754008874 0.845085107 1.034664174 1 21.40967656 4.642432254 1.430796344 0.896887818 1.037465724 0.074441353 0.088075997 2.035481398 4.359912009 0.022707434 0.389309641 43896.73852 -4.642432254 0.140577905 YNILGTNTIMDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YNILGTNTIMDK 12 0 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 99.318 0.0033259 0 114440 107690 107410 112000 120360 92238 131920 97567 125640 FALSE TRUE 107277.4047 115663.4797 109957.8159 114874.1096 110907.4111 118865.6132 112139.8207 109748.4547 104669.8723 1.024911966 1.105031248 1.050520207 1.097489727 1.059592494 1.135623944 1.071366748 1.048520002 1 16.67548672 0.959045136 2.639959448 1.000423582 1.080275595 0.400314265 0.030566158 0.268928965 4.365349157 0.02592823 0.006936301 9.100078437 -0.959045136 0.079852013 YNLDAS(ph)EEEDSNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YNLDASEEEDSNK 13 0 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YNLDAS(1)EEEDSNK;YNLDAS(1)EEEDSNK;YNLDAS(1)EEEDSNK;YNLDAS(1)EEEDSNK 339.38 8.49E-63 1306110000 4186250 2021980 2715270 2522170 2096520 2102400 3223490 2158020 1328030 TRUE FALSE 3924240.085 2171689.503 2779677.487 2586893.152 1931867.776 2709328.75 2740157.6 2427453.547 1106373.214 3.546940614 1.96289053 2.51242298 2.338174063 1.746126671 2.448837984 2.476702767 2.194063918 1 20.0774067 -1.616009153 0.344021558 2.90E-24 2.457738359 0.493525843 0.459473597 23.11223199 1.501310456 20.73694852 0.349376323 0.02420978 1.616009153 2.457738359 YNLDAS(ph)EEEDSNKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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(0.734)EEEDS(0.266)NKK;YNLDAS(1)EEEDSNKK;YNLDAS(1)EEEDSNKK 273.46 3.19E-33 3087150000 5844230 2279330 3441690 3144960 2854360 2431340 4336950 2542060 2555250 TRUE FALSE 5478450.077 2448093.965 3523328.512 3225664.998 2630190.08 3133228.388 3686664.61 2859441.787 2128762.267 2.57353776 1.150008154 1.655106616 1.515277233 1.235548995 1.471854531 1.731834816 1.343241484 1 21.02158341 8 0.041891255 6.18E-06 4.055984819 0.302558668 0.362409265 1169.903938 3.724823461 95.95403722 329.8061416 100000000 -8 4.055978641 YNLDAS(ph)EEEDSNKKK ddPTM_SK-BR-3_Pertuzumab_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 217.36 1.09E-12 1744100000 3381560 1110560 1710850 1762660 1584240 958480 2313760 1268490 1701060 TRUE FALSE 3169914.196 1192787.018 1751432.17 1807892.84 1459820.181 1235177.616 1966833.168 1426863.769 1417142.097 2.236835814 0.841684839 1.235890299 1.275731519 1.0301156 0.871597576 1.387887053 1.006860055 1 20.43455299 4.746648998 24.91815709 1.100685366 2.236836398 0.811580186 0.174766436 411.7199729 1268369.718 0.04032409 0.452369821 55801.90148 -4.746648998 1.136151032 YNMGLPVDFDQYNELHLPAVILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YNMGLPVDFDQYNELHLPAVILK 23 0 Q07960;H0YE29 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 165.66 1.29E-11 399560000 875180 936320 851260 843470 984260 687080 1103690 842180 909070 FALSE TRUE 820404.046 1005646.107 871452.2892 865114.8682 906960.1899 885428.8422 938201.9307 947328.0269 757340.3442 1.083269962 1.32786549 1.150674589 1.142306593 1.197559587 1.169129374 1.238811504 1.250861695 1 19.53058226 -1.325283185 3.58649543 0.99923138 1.202990156 0.447729079 0.067574719 4908434.565 1813870.157 29116.17402 0.014784543 0.047284284 1.325283185 0.203758776 YNNNGEYEESSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YNNNGEYEESSR 12 0 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 0 ; 252.51 1.08E-20 118060000 109142 133876 119951 127149 126179 114057 138327 113704 101912 FALSE TRUE 102310.997 143788.3183 122796.2944 130411.8586 116269.4103 146983.4043 117586.1505 127900.1947 84902.22882 1.205044891 1.693575308 1.446325922 1.53602397 1.369450625 1.731207842 1.384959525 1.506440955 1 16.37351481 -0.098892634 1.042659477 0.994798437 1.50492823 0.489519872 0.154114794 8.612382328 7.278586264 0.305366364 0.040498175 0.796356201 0.098892634 0.510129792 YNPTWHCIVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YNPTWHCIVGR 11 0 P63167;Q96FJ2 P63167;Q96FJ2 DYNLL1;DYNLL2 "Dynein light chain 1, cytoplasmic;Dynein light chain 2, cytoplasmic" 0 ; 170.04 1.62E-05 925700000 266110 629910 366490 360640 726560 206340 317030 417640 1085080 FALSE TRUE 249454.6501 676549.1918 375183.3159 369894.633 669498.9084 265907.0083 269494.2947 469783.2733 903973.1381 0.275953609 0.748417363 0.415038125 0.409187638 0.740618145 0.294153661 0.298122016 0.519687205 1 19.78592038 0.958362706 23.12702494 1.000000002 0.467378434 0.504040061 0.168347034 3086.799625 1714534.915 0.161046129 0.040261532 9.085790226 -0.958362706 -0.532621568 YNQLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YNQLLR 6 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;; 160.1 0.020734 15220700000 7404000 11372200 7141820 6641330 11635200 4868700 8142670 10021200 10540500 FALSE TRUE 6940596.857 12214209.52 7311227.343 6811757.772 10721418.33 6274214.653 6921752.226 11272368.88 8781222.456 0.790390733 1.390946372 0.832597896 0.775718621 1.220948265 0.714503554 0.788244719 1.283690162 1 23.06599036 3.785078285 8.498223681 0.918798239 1.128114077 0.047946433 0.235924309 0.613018316 82.96897885 0.055748228 0.10055898 6096.467815 -3.785078285 0.209315838 YNRFEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YNRFEK 6 1 P62280;M0QZC5;M0R1H5 P62280 RPS11 40S ribosomal protein S11 0 ; 107.43 0.028522 1452230000 2199000 2413200 2195700 2111400 2519500 1770750 2598900 2087300 2829600 FALSE TRUE 2061368.515 2591875.839 2247783.041 2165582.099 2321628.633 2281936.779 2209219.072 2347904 2357321.48 0.874453711 1.09950037 0.953532668 0.918662184 0.984858727 0.968021035 0.937173436 0.996005008 1 21.16871709 3.720358679 24.7771793 0.96050943 1.010091218 0 0.059818912 483.3410074 1770903.294 0.014267568 0.022657144 5252.410721 -3.720358679 0.049581788 YNSCRPNMALGHPQLQQVT(ph)SPSRPSHAVIPADQDCSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YNSCRPNMALGHPQLQQVTSPSRPSHAVIPADQDCSSR 38 2 F5GX32;P43351 F5GX32 RAD52 DNA repair protein RAD52 homolog 1 YNSCRPNMALGHPQLQQVT(0.447)S(0.447)PS(0.089)RPS(0.018)HAVIPADQDCSSR 146.36 3.31E-13 87892000 51874 65776 66558 67266 72917 60556 79855 68445 93175 TRUE FALSE 48627.29894 70646.12348 68136.78719 68992.15944 67190.39295 78037.53416 67881.48409 76990.50892 77623.49057 0.626450815 0.910112686 0.877785664 0.888805166 0.865593552 1.005333999 0.874496671 0.991845488 1 16.24420569 4.739114182 6.11046185 0.916443336 0.619055563 0.744903229 0.054947596 0.06110148 11.59573656 0.011723971 0.075350591 54842.11331 -4.739114182 -0.297387773 YNTEGRVS(ph)PSPSQESLSSSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YNTEGRVSPSPSQESLSSSK 20 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 YNTEGRVS(0.629)PS(0.216)PS(0.154)QESLSSSK;YNTEGRVS(0.993)PS(0.007)PSQESLSSSK;YNTEGRVS(0.951)PS(0.049)PSQESLSSSK;YNTEGRVS(0.993)PS(0.007)PSQESLSSSK;YNTEGRVS(0.854)PS(0.146)PSQESLSSSK 301.86 3.91E-55 4611550000 3430020 2732384 2933910 3030420 3170990 2045081 3342890 2643041 2508480 TRUE FALSE 3215341.171 2934692.554 3003503.731 3108185.708 2921953.237 2635462.686 2841654.678 2973030.487 2089798.483 1.538589102 1.404294519 1.437221701 1.487313602 1.398198564 1.261108527 1.359774496 1.422639796 1 20.9949324 -3.686085594 0.187651289 6.21E-16 1.497415007 0.814878154 0.064180625 32.3595131 0.492803553 12.58045565 0.183693332 0.000206022 3.686085594 1.497415007 YNVYPTYDFACPIVDSIEGVTHALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YNVYPTYDFACPIVDSIEGVTHALR 25 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 191.2 7.29E-18 841760000 445070 571900 474960 413400 625690 415280 568460 601370 380120 FALSE TRUE 417213.8632 614244.0711 486226.2755 424008.5439 576550.8313 535164.5945 483224.7003 676452.3683 316675.5163 1.317480644 1.939663913 1.535408487 1.338936931 1.820635956 1.689946229 1.525930094 2.136105677 1 18.2726458 -1.135405912 6.133909899 0.999996706 1.662412735 0.400284088 0.255042095 1.03E-05 1.45E-06 0.220699946 0.052019217 0.073213992 1.135405912 0.662416029 YNYHLDSSGSYVFENTVATVMALR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YNYHLDSSGSYVFENTVATVMALR 24 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;; 270.82 6.86E-52 273387000 285452 342104 274189 250663 364599 256557 310589 323524 187238 FALSE TRUE 267586.0689 367433.7361 280692.8926 257095.437 335964.8653 330620.841 264019.0628 363916.6836 155986.7682 1.715440816 2.355544258 1.799466043 1.648187471 2.153803615 2.119544144 1.692573453 2.332997137 1 17.25106413 -1.537602841 4.638590585 0.993009471 1.975845629 0.581619047 0.260463257 0.017442836 0.001738787 0.233617499 0.054980258 0.028999944 1.537602841 0.982836158 YNYIEGTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YNYIEGTK 8 0 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 94.309 0.024312 369840000 346640 330960 349890 333440 359360 264520 389570 317420 376170 FALSE TRUE 324944.4212 355464.6228 358189.556 341996.6349 331137.3152 340882.6299 331157.5951 357050.5857 313384.7968 1.03688636 1.134275263 1.14297043 1.091299381 1.056647669 1.08774463 1.056712382 1.139336015 1 18.25757567 3.006225661 19.32545463 1.072133315 1.116589699 0.105042953 0.044474819 15.87878036 49279.41761 0.011854781 0.014084597 1014.438355 -3.006225661 0.044456383 YPDSHQLFVGNLPHDIDENELKEFFMSFGNVVELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YPDSHQLFVGNLPHDIDENELKEFFMSFGNVVELR 35 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ; 309.52 7.93E-105 369780000 504700 514620 363970 271120 580360 351040 459740 495290 256751 FALSE TRUE 473111.7279 552723.0003 372603.5403 278077.3982 534780.8667 452379.5493 390806.255 557128.0468 213897.5994 2.211860859 2.584054247 1.741971585 1.300049178 2.500172363 2.11493514 1.827071721 2.604648431 1 17.70656077 -1.538391099 2.821036641 0.945763994 2.088129769 0.420141943 0.409279518 23352738.54 24027238.52 9615292.641 0.094867613 0.028947356 1.538391099 1.142365775 YPDVAS(ph)PTLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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(0.964)PT(0.036)LR 100.07 0.0044756 105510000 103510 152840 135560 140000 145720 122240 128110 121740 111770 TRUE FALSE 97031.49387 164156.4326 138775.5472 143592.637 134275.739 157528.7036 108901.0948 136939.507 93114.86494 1.042062338 1.762945505 1.49036942 1.542102189 1.442044072 1.691767514 1.169535013 1.470651405 1 16.50672388 0.773607501 0.703645623 1.003108439 1.522954002 0.284637822 0.217140421 1.08742755 1.103749588 0.198507633 0.073886762 5.937553018 -0.773607501 0.519845563 YPEPERPSS(ph)R ddPTM_SK-BR-3_Pertuzumab_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(0.322)S(0.678)R;YPEPERPS(0.327)S(0.673)R;YPEPERPS(0.231)S(0.769)R 93.839 0.022392 2388160000 1526150 1606250 1696020 1533060 1478890 1591460 1778030 1313900 1272710 TRUE FALSE 1430630.996 1725178.421 1736250.395 1572400.915 1362743.945 2050888.667 1511430.908 1477943.307 1060286.479 1.34928722 1.627087071 1.637529507 1.48299629 1.285260137 1.934277865 1.425492957 1.393909417 1 20.01602269 0.870207313 1.895912498 1.002713716 1.560349508 0.467684455 0.179515642 0.413120609 2.917068092 0.156031816 0.043739883 7.41664195 -0.870207313 0.557635792 YPES(ph)NRTPVKPSSVEEEDSFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YPESNRTPVKPSSVEEEDSFFR 22 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 YPES(0.608)NRT(0.392)PVKPSSVEEEDSFFR 169.13 4.51E-12 446310000 635000 551820 579610 604540 632880 478850 737460 529460 687230 TRUE FALSE 595256.4835 592677.327 593358.6229 620053.5199 583176.1577 617086.2215 626884.7192 595564.2465 572526.8733 1.039700512 1.035195647 1.036385628 1.08301208 1.018600497 1.077829269 1.094943746 1.040238064 1 19.12698389 3.32593413 24.99562809 1.059844786 1.036585426 0.017800877 0.029383843 45.25347053 12937.176 0.007669229 0.010384185 2118.039863 -3.32593413 -0.02325936 YPESNRT(ph)PVKPSSVEEEDSFFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YPESNRTPVKPSSVEEEDSFFR 22 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 YPES(0.025)NRT(0.974)PVKPS(0.001)SVEEEDSFFR;YPES(0.113)NRT(0.887)PVKPSSVEEEDSFFR 164.13 6.82E-10 675290000 567600 486430 561920 552960 605150 434170 704200 541980 616050 TRUE FALSE 532074.9292 522445.7833 575249.0078 567149.8898 557623.9601 559507.8308 598611.7475 609647.396 513227.2752 1.036723797 1.017961844 1.120846525 1.105065762 1.086504921 1.090175558 1.16636776 1.18787022 1 18.96923832 3.952652214 2.887340426 1.115981582 1.027542847 0.293833628 0.050675523 0.281613776 4.712265297 0.012687261 0.028410243 8967.104141 -3.952652214 -0.088438735 YPGSTFMDHVLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YPGSTFMDHVLR 12 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 180.24 1.97E-05 660720000 825600 921740 906110 834680 911110 767910 959650 891130 750770 FALSE TRUE 773927.1697 989986.5887 927603.3571 856099.3019 839555.0958 989593.151 815759.3915 1002389.542 625461.6368 1.237369527 1.582809449 1.483069948 1.3687479 1.342296708 1.582180413 1.304251681 1.602639527 1 19.25456187 -1.114331608 4.296219256 0.999930143 1.445907724 0.542197342 0.126272066 7960580.109 2064776.663 5207.142983 0.026778771 0.076854339 1.114331608 0.445977582 YPHYFPLLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YPHYFPLLK 9 0 P52888;K7EP46 P52888 THOP1 Thimet oligopeptidase 0 ; 68.227 0.058667 161472000 141882 844310 564950 574280 833430 683690 534050 804020 609260 FALSE TRUE 133001.8589 906823.5909 578350.8808 589016.9971 767975.7697 881060.2042 453974.1604 904403.6669 507570.57 0.262036191 1.78659608 1.139449202 1.160463257 1.513042353 1.735837845 0.894405994 1.78182842 1 18.9532489 4.75244957 24.83475975 1.368814305 0.262035371 0.535350701 0.326213318 1690.05002 3021911.953 0.071429767 1.461025427 56552.20848 -4.75244957 -1.106778935 YPIEHGIITNWDDMEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 19 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 ;;;;;;;;;;;;;;;;;; 209.13 1.31E-11 1.18876E+11 65047151 51824566 53985153 50997261 59974353 40802540 63572011 48807809 58738729 FALSE TRUE 60975965.93 55661710.79 55265706.32 52305937.06 55264209.24 52581570.92 54039978.12 54901571.39 48934855.66 1.246064081 1.137465515 1.129373032 1.068889166 1.129342439 1.074521835 1.10432487 1.121931814 1 25.54435911 8 0.561528104 1.088255405 8.332043755 0.637095865 0.037667553 86.44008549 0.758636737 0.014879339 758.6212418 100000000 -8 7.24378835 YPIEHGIITNWDDMEKIWHHTFYNELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YPIEHGIITNWDDMEKIWHHTFYNELR 27 1 P68133;P68032;A6NL76 P68133 ACTA1;ACTC1 "Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1" 0 ; 234.39 3.63E-45 432836000 308023 603290 610850 803270 731180 317378 407400 239235 600160 FALSE TRUE 288744.3903 647958.2193 625339.6505 823883.2681 673756.0722 408999.8764 346314.1521 269104.0164 499989.4188 0.577501002 1.295943864 1.250705769 1.647801408 1.347540662 0.818017064 0.692642962 0.538219423 1 18.93153804 2.15533424 5.070362443 0.72225169 1.256091075 0.38806324 0.286480255 0.189966505 8.438391909 0.105343896 0.077276543 142.9994081 -2.15533424 0.533839385 YPIEHGIVTNWDDMEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 13 YPIEHGIVTNWDDMEK 16 0 P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65 P60709;P63261 ACTB;ACTG1 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 ;;;;;;;;;;;; 300.03 5.52E-46 22833410000 32308324 25196910 26672106 24411687 30635002 18890150 31644016 25688980 32158089 FALSE TRUE 30286203.67 27062515.43 27304780.95 25038132.22 28229052.52 24343429.65 26899289.57 28896305.7 26790696.2 1.130474679 1.010146031 1.019188928 0.934583112 1.05368865 0.908652372 1.004053399 1.078594804 1 24.67522874 6.751122867 1.198115168 0.995607323 18.16412187 0.393168031 0.049971808 189.5699863 2.800815694 0.012707358 8724.690534 5637971.385 -6.751122867 17.16851455 YPLFEGQETGKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YPLFEGQETGKK 12 1 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 141.73 9.48E-05 1274790000 2742100 1988790 2373200 2413300 2420000 1797640 3112700 2181900 3309000 FALSE TRUE 2570476.856 2136042.081 2429493.425 2475229.364 2229942.962 2316589.486 2645979.532 2454315.018 2756706.523 0.93244487 0.774852913 0.88130289 0.89789368 0.808915618 0.840346793 0.959833595 0.890306965 1 21.39451426 1.28269374 0.878900755 0.991720241 0.848050875 0.396880931 0.052513289 0.476913544 0.798691886 0.046350414 0.017155855 19.17316193 -1.28269374 -0.143669366 YPPYTT(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YPPYTTPPR 9 0 O43896 O43896 KIF1C Kinesin-like protein KIF1C 1 YPPYT(0.195)T(0.804)PPR;YPPYT(0.035)T(0.965)PPR;YPPYT(0.001)T(0.999)PPR 110.31 0.025798 977940000 932790 1042900 1013060 996070 925560 855660 1158810 810860 1019600 TRUE FALSE 874408.339 1120117.401 1037090.262 1021630.843 852870.2511 1102675.152 985057.1984 912097.6559 849422.1731 1.029415486 1.318681613 1.220936178 1.202736254 1.004059322 1.29814736 1.159679167 1.073786022 1 19.69612224 1.136676745 2.619137744 1.003829495 1.196310361 0.252717166 0.100751998 0.306286719 3.879653834 0.089486944 0.024583759 13.69861768 -1.136676745 0.192480865 YPSLSLHGIEGAFSGSGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YPSLSLHGIEGAFSGSGAK 19 0 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 235.73 3.60E-24 215670000 163110 247420 238160 242830 281180 184080 293970 257030 224140 FALSE TRUE 152901.2363 265739.2342 243809.2677 249061.4289 259097.257 237220.9077 249891.9276 289120.7613 186729.586 0.818837762 1.423123351 1.305680974 1.333808071 1.38755332 1.270398081 1.338255672 1.548339326 1 17.51059101 4.744184522 24.87266629 1.339922465 0.818837522 0.565733586 0.139133133 367.5660222 1625570.647 0.028210708 0.248104992 55486.14112 -4.744184522 -0.521084942 YPSS(ph)ISSS(ph)PQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YPSSISSSPQK 11 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 2 YPS(0.001)S(0.999)ISS(0.007)S(0.993)PQK;YPS(0.039)S(0.953)IS(0.01)S(0.083)S(0.914)PQK 203.74 5.20E-08 163703000 1153060 603480 861320 733090 726770 701170 1022520 808830 604720 TRUE FALSE 1080892.033 648162.2871 881750.9171 751902.3305 669692.4158 903586.3965 869202.6186 909814.206 503788.3254 2.145528148 1.286576632 1.750240871 1.492496536 1.329313091 1.793583438 1.725332992 1.805945394 1 18.94245816 -0.959393612 5.934818434 0.999999575 1.636750585 0.404393019 0.25182749 1.29E-06 2.27E-07 0.222961078 0.052552395 0.109801023 0.959393612 0.63675101 YPSSISSS(ph)PQK ddPTM_SK-BR-3_Pertuzumab_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 YPSSISS(0.005)S(0.995)PQK;YPSSIS(0.002)S(0.071)S(0.927)PQK 218.94 1.07E-11 880050000 2769500 2052480 1793450 1541550 2122990 1466670 2280640 2294800 1844410 TRUE FALSE 2596161.939 2204447.755 1835991.481 1581108.783 1956258.929 1890073.82 1938679.204 2581310.831 1536566.056 1.689586939 1.434658632 1.194866615 1.028988488 1.27313689 1.230063499 1.261695973 1.679921811 1 20.55127836 4.604300027 1.68494248 1.244450939 1.774457794 0.391881589 0.182860304 0.742978274 2.562878814 0.045278617 0.586182803 40206.84794 -4.604300027 0.530006855 YPSSISSS(ph)PQKDLTQAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YPSSISSSPQKDLTQAK 17 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 YPSS(0.002)IS(0.102)S(0.404)S(0.492)PQKDLTQAK;YPSSIS(0.002)S(0.193)S(0.805)PQKDLTQAK 162.32 1.73E-09 1526390000 4169900 2104800 2995700 2727400 2637800 2583300 3886100 2601800 3170700 TRUE FALSE 3908913.402 2260641.582 3066759.419 2797389.701 2430637.828 3329056.774 3303415.382 2926640.457 2641489.686 1.479813994 0.855820711 1.160996174 1.059019733 0.920176914 1.2602952 1.250588029 1.107950742 1 21.33292035 2.21156066 24.99975463 1.186651366 1.069861353 0.002013262 0.181122126 535.6236822 495940.3429 0.061910165 0.045734932 162.7648642 -2.21156066 -0.116790012 YPSVLLLVCQDSEQSKPDVHFFHCDEVEAELVHEDIESALADCR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YPSVLLLVCQDSEQSKPDVHFFHCDEVEAELVHEDIESALADCR 44 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 ;; 141.25 3.89E-14 416792000 148282 145960.2 137372 141150.4 172976 141139.4 208055 143322 170332 FALSE TRUE 139001.2943 156767.2451 140630.5287 144772.5582 159391.1627 181884.0536 176859.0842 161216.0672 141902.4888 0.979555013 1.104753316 0.991036379 1.020225645 1.123244307 1.281753795 1.24634237 1.136104578 1 17.11454037 2.530205538 4.255405318 1.197468177 1.033243906 0.368182248 0.083378809 0.183060009 6.886244567 0.026174 0.023795495 339.0045587 -2.530205538 -0.164224271 YQAEIPDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YQAEIPDR 8 0 O94776 O94776 MTA2 Metastasis-associated protein MTA2 0 100.25 0.014518 121320000 188040 225800 205630 210130 231910 194150 235600 211240 202270 FALSE TRUE 176270.9121 242518.4669 210507.6407 215522.2915 213696.7241 250197.9532 200273.9672 237613.779 168509.8303 1.046057146 1.439194773 1.249230626 1.278989429 1.268155832 1.484767701 1.188500201 1.410088531 1 17.36247323 -1.667395213 2.808620695 0.96475368 1.302938229 0.344708843 0.127741411 26340871.68 26357401.32 6715454.425 0.026577646 0.021508236 1.667395213 0.338184549 YQDEDT(ph)PPQEHISPQITNEVIGPELVHVSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YQDEDTPPQEHISPQITNEVIGPELVHVSEK 31 0 A0A590UJD9;A0A0C4DFT3;A0A590UJ18;A0A590UK02;E7EQD7;B4E2H8;C9JCP6;A8MUT6;A0A590UJ95;A0A590UJZ4;A0A590UJ86;C9JN61;A0A590UK13;A0A590UK52;C9IYP1;A0A590UJ08;Q12959-4;Q12959-2;A0A590UJC5;A0A590UJL2;Q12959;Q12959-3;Q12959-5;Q12959-7;Q12959-6;A0A590UKA8;A0A590UJR5;A0A590UJ68;A0A590UJS9;A0A590UJ81;C9JUA9;A0A590UJ64;A0A590UK81;A0A590UJ29 A0A590UJD9;A0A590UJ08;Q12959 DLG1 Disks large homolog 1 1 YQDEDT(0.998)PPQEHIS(0.001)PQITNEVIGPELVHVSEK;YQDEDT(1)PPQEHISPQITNEVIGPELVHVSEK;YQDEDT(1)PPQEHISPQITNEVIGPELVHVSEK 183.3 5.07E-18 261955000 91629 324060 305361 303355 365508 273495 382713 343570 424580 TRUE FALSE 85894.10445 348053.7396 312604.3071 311139.6029 336802.4761 352448.5667 325328.7386 386465.4708 353714.8551 0.242834315 0.983995257 0.88377489 0.879633972 0.952186404 0.99642003 0.919748588 1.092590445 1 18.43222728 4.740125935 24.9998283 0.952064299 0.242834081 0.927540412 0.063233583 32.22096726 514557.4175 0.0141601 0.090017091 54970.02509 -4.740125935 -0.709230218 YQDEVFGGFVTEPQEES(ph)EEEVEEPEER ddPTM_SK-BR-3_Pertuzumab_2h_R1 10 YQDEVFGGFVTEPQEESEEEVEEPEER 27 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 1 YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER 259.07 3.58E-53 10710677000 7051750 7759945 7692547 8002859 8570660 7409094 8786680 7312826 9229042 TRUE FALSE 6610393.555 8334499.402 7875017.848 8208225.911 7897554.936 9547979.161 7469198.906 8225848.424 7688655.268 0.859759389 1.083999622 1.024238644 1.06757627 1.027169857 1.241826929 0.97145712 1.069868285 1 22.87429986 4.742523868 24.75132197 1.061331022 0.859759299 0.430094659 0.072714182 315.1691044 1968206.023 0.015569503 0.119220016 55274.37843 -4.742523868 -0.201571723 YQDILVFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YQDILVFR 8 0 P19623;K7EKM4 P19623 SRM Spermidine synthase 0 ;;; 149.65 0.0011673 370398000 671321 742571 746404 764614 777697 654793 800303 650782 576811 FALSE TRUE 629304.217 797551.7295 764109.0554 784235.2897 716619.8147 843821.1094 680304.9948 732033.5652 480537.5178 1.309583942 1.659707515 1.590113211 1.631995964 1.49128796 1.755994232 1.415716712 1.523364021 1 18.87428955 0.316036287 0.933357272 0.996714723 1.578341106 0.650774661 0.125963166 1.533413278 1.627700448 0.117813751 0.034928433 2.070314325 -0.316036287 0.581626383 YQDTHPER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YQDTHPER 8 0 C9JAH0;F8WD54;A0A087WUI8;Q96IJ6;Q96IJ6-2 C9JAH0 GMPPA Mannose-1-phosphate guanyltransferase alpha 0 89.029 0.014196 574500000 538220 619450 584750 650770 560220 529270 692970 516980 550650 FALSE TRUE 504533.771 665314.7225 598620.5461 667469.86 516222.581 682061.657 589065.5817 581526.091 458742.9577 1.099818019 1.450299588 1.304914955 1.454997507 1.125298105 1.486805728 1.284086375 1.267651266 1 18.80732649 0.710541893 1.816275856 1.000314457 1.332795828 0.359143382 0.130111649 1.069449124 5.235258699 0.107401831 0.030139538 5.135017085 -0.710541893 0.332481371 YQDTPGVK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YQDTPGVK 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 95.815 0.021828 96711000 170350 148660 152230 146500 171480 117910 177250 145720 204770 FALSE TRUE 159688.0976 159666.9411 155840.9675 150259.438 158012.6525 151948.7029 150673.008 163913.4628 170592.5641 0.936078887 0.935954869 0.913527317 0.880808837 0.926257562 0.890711173 0.883233151 0.960847641 1 17.38019524 1.025576678 5.094156858 0.999772507 0.910128651 0.704148437 0.0199919 0.090244552 6.336652808 0.020622075 0.00521357 10.60661189 -1.025576678 -0.089643855 YQEALHLGSQLLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YQEALHLGSQLLR 13 0 O00231;O00231-2 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 ; 201.06 1.05E-07 751580000 679500 1012970 892500 854900 1040430 713330 932290 944550 857370 FALSE TRUE 636971.3079 1087971.353 913670.5215 876838.1813 958718.8247 919256.7911 792501.7695 1062479.147 714269.4082 0.891780189 1.523194666 1.279167932 1.227601478 1.342236996 1.286988888 1.109527806 1.487504763 1 19.44610881 -1.549830758 2.857700081 0.985507416 1.281256591 0.178520673 0.179161533 20480585.99 22751887.63 2301559.749 0.040546022 0.028194815 1.549830758 0.295749175 YQEEFEHFQQELDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YQEEFEHFQQELDK 14 0 P49257 P49257 LMAN1 Protein ERGIC-53 0 ; 162.87 2.34E-07 94728000 158538 168056 118634 127349 188153 85453 162558 167856 126535 FALSE TRUE 148615.3896 180499.0411 121448.0545 130616.9909 173376.2224 110121.8939 138183.937 188813.1911 105415.4911 1.409805979 1.712262963 1.152089255 1.239068278 1.644693969 1.044646216 1.310850385 1.79113325 1 16.68572736 -2.18603313 2.166025469 4.81E-05 1.395404583 0.218614214 0.243396653 5267527.567 887419.4581 25898629.25 0.055904976 0.006515787 2.18603313 1.395356499 YQEGGVESAFHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YQEGGVESAFHK 12 0 P40121-2;P40121;E7ENU9;B8ZZL6 P40121-2 CAPG Macrophage-capping protein 0 ;; 198.14 1.87E-07 2418310000 1882930 2367750 2381040 2343670 2546160 1955910 2839200 2433030 3737910 FALSE TRUE 1765080.772 2543060.674 2437519.393 2403812.54 2346194.864 2520549.465 2413488.318 2736799.151 3114028.673 0.566815838 0.816646518 0.782754319 0.771930124 0.753427508 0.809417552 0.775037282 0.878861256 1 21.5703508 -5 0.108508609 1.74129414 0.638103427 0.650158244 0.063768101 116.7917665 0.846207198 19.18753736 0.799728721 1.00E-05 5 -1.103190713 YQELLER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YQELLER 7 0 Q9H074;Q9H074-3;Q9H074-2;H0YA44 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 0 ;; 118.07 0.01184 300521000 601460 625630 645070 629080 698050 574400 702100 588080 691770 FALSE TRUE 563815.6922 671952.2962 660371.365 645223.2578 643227.9688 740219.9554 596826.623 661503.0825 576309.118 0.978321659 1.165958121 1.145863122 1.119578431 1.116116245 1.284414791 1.035601562 1.147826855 1 19.13648332 -0.586136446 6.92127802 1.000001747 1.129661857 0.188818552 0.080204386 0 0 0.069200455 0.016310704 0.259336445 0.586136446 0.12966011 YQELPNSGPPHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YQELPNSGPPHDR 13 0 P19525-2;P19525;C9JZT2;F8WBH4 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 0 128.95 0.00015935 412440000 458130 495580 455250 482500 417760 394840 491860 445350 424470 FALSE TRUE 429456.4611 532273.2589 466048.745 494881.7669 384950.8148 508823.8983 418110.1592 500952.9278 353623.2148 1.214446459 1.505198857 1.317924631 1.39946063 1.088590337 1.438887146 1.182360608 1.416629075 1 18.43185346 -4.234158621 0.188348228 1.97E-10 1.393850089 0.350130165 0.13136686 96.67679802 1.225624335 36.89752302 0.332510745 5.83E-05 4.234158621 1.393850089 YQEQGGEAS(ph)PQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 YQEQGGEASPQR 12 0 Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6 DBNL Drebrin-like protein 1 YQEQGGEAS(1)PQR;YQEQGGEAS(1)PQR;YQEQGGEAS(1)PQR;YQEQGGEAS(1)PQR;YQEQGGEAS(1)PQR;YQEQGGEAS(1)PQR;YQEQGGEAS(1)PQR;YQEQGGEAS(1)PQR 194.13 2.01E-06 1110728000 1238017 1210080 1323510 1248820 1308710 1204714 1488212 1161974 1203509 TRUE FALSE 1160531.726 1299675.582 1354904.282 1280866.835 1205929.196 1552495.375 1265068.426 1307049.012 1002635.573 1.1574811 1.296259197 1.35134272 1.277499891 1.202759236 1.548414416 1.261743011 1.303613244 1 19.9353659 -0.142475264 8.102641002 0.999999997 1.308260624 0.45089358 0.103639687 0 0 0.091020953 0.021453844 0.720318778 0.142475264 0.308260627 YQEQGGEAS(ph)PQRTWEQQQEVVSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YQEQGGEASPQRTWEQQQEVVSR 23 1 Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6 DBNL Drebrin-like protein 1 YQEQGGEAS(0.855)PQRT(0.145)WEQQQEVVSR;YQEQGGEAS(1)PQRTWEQQQEVVSR 252.77 1.08E-43 532200000 102823 179675 129466 176725 225060 106858 161849 135397 443570 TRUE FALSE 96387.49197 192978.324 132536.9947 181260.0627 207384.6954 137706.1699 137581.245 152301.6135 369535.3014 0.260834328 0.522218914 0.358658548 0.490508111 0.561204017 0.37264686 0.372308801 0.412143611 1 18.49535266 -1.400263508 2.919054675 1.010230644 0.423212673 0.812663871 0.08767181 9417779.458 11183629.85 806392.5707 0.020274534 0.039786569 1.400263508 -0.587017971 YQEQGGEAS(ph)PQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YQEQGGEASPQSR 13 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4 Q9UJU6-2 DBNL Drebrin-like protein 1 YQEQGGEAS(0.998)PQS(0.002)R;YQEQGGEAS(0.994)PQS(0.006)R;YQEQGGEAS(0.994)PQS(0.006)R;YQEQGGEAS(0.972)PQS(0.028)R 202.52 9.78E-08 1018430000 756710 976180 933320 982990 934680 800519 976740 769972 951200 TRUE FALSE 709348.8719 1048457.383 955458.7911 1008215.188 861274.0031 1031615.84 830286.9046 866104.6991 792438.575 0.895146822 1.323077165 1.205719688 1.272294433 1.086865317 1.301824359 1.047761847 1.092961305 1 19.59593959 1.635467215 8.312088592 1.051726016 1.199653203 0.192213974 0.125145 0.156952053 22.70410807 0.056787811 0.029153257 43.19835561 -1.635467215 0.147927187 YQES(ph)PGIQMK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YQESPGIQMK 10 0 Q9UHI6;E9PJ60 Q9UHI6 DDX20 Probable ATP-dependent RNA helicase DDX20 1 YQES(1)PGIQMK 92.906 0.0063532 0 332450 254150 294590 264390 268870 211630 309620 222770 330630 TRUE FALSE 311642.5479 272967.5304 301577.8139 271174.695 247754.0348 272724.1455 263195.3554 250583.3249 275445.717 1.131411849 0.991002995 1.094872039 0.984494143 0.899465918 0.99011939 0.955525314 0.909737598 1 18.0714085 3.071030574 5.581288928 0.951147435 1.057475075 0.579320566 0.046727167 0.143134923 8.085853766 0.012484717 0.014961032 1177.688879 -3.071030574 0.10632764 YQETFNVIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YQETFNVIER 10 0 Q13011;M0R248;M0QZW4 Q13011 ECH1 "Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial" 0 ;; 160.53 1.71E-05 369703000 263904 286952 258487 267191 362660 233420 260318 300305 347300 FALSE TRUE 247386.7197 308198.2247 264618.4337 274047.5734 334178.1465 300804.5647 221285.7326 337798.7403 289333.3864 0.855023068 1.065201042 0.914579672 0.947168859 1.154993382 1.039646923 0.7648123 1.167506953 1 18.14237328 4.763263741 23.00011427 0.988515638 0.855022584 0.124150439 0.118133142 5854.966326 5451068.593 0.027346868 1.57562562 57978.06822 -4.763263741 -0.133493054 YQEVDRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YQEVDRR 7 1 Q96MU7-2;Q96MU7 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 117.39 0.0084057 185140000 97183 121420 111920 116910 132710 109860 112470 102980 141860 FALSE TRUE 91100.48951 130410.0631 114574.7953 119910.1085 122287.4919 141574.7986 95606.16762 115837.2797 118182.6495 0.770844873 1.103462003 0.969472217 1.014616858 1.034733037 1.197932176 0.808969574 0.980154702 1 16.85065872 1.71114755 25 0.917939495 1.020832292 0.099990611 0.118337842 1.511399257 1371.665168 0.049454998 0.027425291 51.42183261 -1.71114755 0.102892797 YQILPLHSQIPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YQILPLHSQIPR 12 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 196.57 2.05E-07 1508180000 1829120 2327500 2059010 1976170 2477300 1521870 2514200 2253200 2606800 FALSE TRUE 1714638.644 2499830.522 2107850.69 2026881.868 2282742.851 1961209.164 2137219.051 2534516.98 2171708.239 0.78953453 1.151089486 0.970595705 0.933312234 1.051127776 0.90307212 0.984118866 1.167061456 1 21.05039887 1.281593998 24.53544619 1.083530775 0.985275974 0.16516901 0.102075472 187.1767609 106718.3402 0.062882793 0.022962383 19.12467212 -1.281593998 -0.0982548 YQLDKDGVVLFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YQLDKDGVVLFK 12 1 P07237;H7BZ94;I3L398;I3L312;I3L3U6 P07237 P4HB Protein disulfide-isomerase 0 ; 192.86 3.23E-06 5852800000 14210900 11093300 11689200 11798200 11208200 7681000 15720000 11022000 13050800 FALSE TRUE 13321465.14 11914659.47 11966473.34 12100961.79 10327953.18 9898380.009 13362931.94 12398120.96 10872537.17 1.225239788 1.095849045 1.100614618 1.112984173 0.949911968 0.910402039 1.229053691 1.140315344 1 23.3741853 7.999996583 0.949607654 1.070352432 109.0791561 0.223226101 0.093171825 2171.049175 3.729319699 0.028942348 509377.9731 99999213.27 -7.999996583 108.0088037 YQPLASTAS(ph)DNDFVTPEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YQPLASTASDNDFVTPEPR 19 0 Q15021 Q15021 NCAPD2 Condensin complex subunit 1 1 YQPLAST(0.005)AS(0.995)DNDFVTPEPR;YQPLASTAS(1)DNDFVTPEPR;YQPLASTAS(1)DNDFVTPEPR 359.19 3.53E-91 573200000 398290 391490 391960 509570 476670 319478 385250 306977 354024 TRUE FALSE 373361.7399 420476.3269 401257.4763 522646.4289 439234.261 411706.1123 327485.339 345303.7542 294935.1073 1.265911486 1.42565709 1.36049411 1.772072622 1.489257298 1.395921008 1.110364046 1.170778743 1 18.17003804 1.775993049 3.220480431 1.095994844 1.457394267 0.615058149 0.134311642 0.165239261 3.34287118 0.074921547 0.036924491 59.70257315 -1.775993049 0.361399423 YQPLASTASDNDFVT(ph)PEPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YQPLASTASDNDFVTPEPR 19 0 Q15021 Q15021 NCAPD2 Condensin complex subunit 1 1 YQPLASTASDNDFVT(1)PEPR;YQPLASTASDNDFVT(1)PEPR 204.63 5.03E-15 145445000 154603 187114 186290 191371 198042 156927 232570 195651 256860 TRUE FALSE 144926.6742 200968.1153 190708.8868 196281.9039 182488.5802 202229.2774 197698.2876 220078.458 213988.4066 0.67726414 0.939154221 0.891211303 0.91725485 0.852796575 0.945047821 0.923873824 1.028459726 1 17.70717311 4.740150068 24.95423413 0.927724857 0.677264055 0.721805533 0.050413695 70.77999225 1111138.658 0.011036274 0.070323645 54973.07968 -4.740150068 -0.250460802 YQQETSVSQLPGRPKS(ph)PLSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YQQETSVSQLPGRPKSPLSK 20 2 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 YQQETSVSQLPGRPKS(1)PLSK 171.52 4.02E-12 580000000 342700 248490 300910 295860 393090 190880 320990 254560 700300 TRUE FALSE 321251.0187 266888.4582 308047.7273 303452.2685 362218.297 245983.9573 272860.5294 286342.3764 583415.4059 0.55063856 0.457458709 0.52800753 0.520130709 0.6208583 0.421627463 0.467695105 0.490803591 1 19.15416396 -1.31109464 3.486632764 1.001973185 0.501964627 0.887845836 0.055022119 108893193.7 156993794.7 2217028.765 0.012842258 0.048854589 1.31109464 -0.500008558 YQQGDFGYCPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YQQGDFGYCPR 11 0 P67870;Q5SRQ3;Q5SRQ6;N0E472;A0A0G2JM12 P67870 CSNK2B;CSNK2B-LY6G5B-1181;CSNK2B-LY6G5B--991 Casein kinase II subunit beta 0 ;;; 215.06 3.05E-11 1865630000 1196430 1446450 962280 962410 1373330 936490 1430690 1286080 1782670 FALSE TRUE 1121547.582 1553546.663 985105.736 987107.07 1265474.202 1206839.46 1216171.316 1446649.919 1485130.861 0.755184349 1.046067188 0.663312414 0.664659995 0.852096091 0.812614896 0.818898421 0.974089191 1 20.50215863 1.216591349 4.000667762 0.998831206 0.80900737 0.34126547 0.107013086 0.265917302 8.436994163 0.09777353 0.027324854 16.46612275 -1.216591349 -0.189823836 YQVAGAEYWDNNDHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YQVAGAEYWDNNDHR 15 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 0 ;; 174.62 9.03E-07 721350000 605660 633720 599640 610080 659380 549910 690510 590280 606080 FALSE TRUE 567752.8217 680641.2882 613863.744 625735.6857 607594.9546 708660.09 586974.4359 663977.7574 504921.3326 1.124438175 1.348014521 1.215761158 1.239273616 1.20334578 1.403505941 1.162506708 1.315012289 1 18.94569911 -1.360097304 3.15119526 0.997552476 1.255029075 0.465763326 0.084567789 84006370.9 104926692.3 1876233.143 0.017724107 0.043641804 1.360097304 0.257476599 YQVFFFGTHETAFLGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YQVFFFGTHETAFLGPK 17 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ; 260.25 3.09E-27 847250000 1203640 1846470 1378310 1203740 1950400 690070 1230480 1708220 1658150 FALSE TRUE 1128306.321 1983184.56 1411004.164 1234630.006 1797223.452 889282.0066 1045980.947 1921495.027 1381394.053 0.81678817 1.435640001 1.021434949 0.893756567 1.301021564 0.643756939 0.757192305 1.390982554 1 20.39769349 3.594763897 4.569266508 0.959844781 1.186325996 0.01333613 0.268356565 0.452358376 15.34671767 0.069172029 0.109378954 3933.361811 -3.594763897 0.226481215 YQYGGLNSGRPVT(ph)PPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 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;YQYGGLNSGRPVT(1)PPR;YQYGGLNSGRPVT(1)PPR 153.25 7.59E-07 15117240000 2138970 2312030 2190920 2109490 2432500 1747370 2716540 2102520 2697520 TRUE FALSE 2005095.686 2483215.107 2242889.657 2163623.085 2241461.262 2251807.353 2309220.046 2365024.25 2247286.485 0.892229673 1.104983776 0.998043495 0.962771368 0.997407886 1.002011701 1.027559264 1.052391079 1 21.09975262 1.670475763 5.257887138 1.030452292 1.005473597 0.047123612 0.053846522 0.581276575 35.80364388 0.027970107 0.013628483 46.82478185 -1.670475763 -0.024978695 YQYGGLNSGRPVTPPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YQYGGLNSGRPVTPPR 16 1 P62140 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit 0 ; 207.92 1.48E-11 1101720000 779730 794320 828180 816080 904260 680610 947050 754650 1068360 FALSE TRUE 730928.0912 853132.2793 847824.8207 837021.9944 833243.0672 877091.0582 805048.6445 848869.7137 890043.8141 0.82122709 0.958528407 0.952565264 0.940427854 0.936182078 0.985447058 0.904504511 0.953739243 1 19.76351683 YQYPLFGLPFVHNDFQSEADWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YQYPLFGLPFVHNDFQSEADWLR 23 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 ; 167.24 1.10E-11 214551000 238285 405317 217453 222418 452080 229028 235644 377230 193273 FALSE TRUE 223371.1672 435327.0924 222611.0878 228125.6224 416575.4604 295144.6656 200311.3698 424327.9959 161014.4877 1.387273719 2.703651694 1.382553154 1.41680184 2.587192409 1.833031734 1.244058051 2.635340471 1 17.29683098 -1.878444653 2.696941371 0.586449524 1.880333632 0.20003984 0.563754935 51202322.59 34687233.11 135549839.7 0.13135105 0.013229863 1.878444653 1.293884108 YRDELKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YRDELKR 7 2 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 67.464 0.03661 77850000 69083 156350 129100 224070 168860 229280 81434 124440 82698 FALSE TRUE 64759.21835 167926.3167 132162.313 229820.0155 155598.4167 295469.414 69223.7277 139976.6079 68895.16955 0.939967472 2.437417859 1.918310294 3.335792873 2.258480787 4.288681135 1.004768958 2.031733267 1 16.07211521 1.614898514 25 1.388660685 2.481860634 0.272051176 0.910004386 0.799950713 2834.335048 0.400262986 0.215963377 41.2001231 -1.614898514 1.093199949 YRDYYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YRDYYR 6 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 107.49 0.028472 350910000 153681 385200 148360 143037 417380 106740 194082 355510 450840 FALSE TRUE 144062.3805 413720.6088 151879.1693 146707.5716 384600.6584 137554.1052 164981.2059 399896.2061 375591.8915 0.383560944 1.101516348 0.404372865 0.390603671 1.02398552 0.366232894 0.43925657 1.06470937 1 18.51880639 1.226904707 24.93655282 1.032355085 0.608408671 0.321277668 0.267673259 302.1629328 646423.7041 0.241186636 0.062333409 16.86183 -1.226904707 -0.423946414 YREDIINVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YREDIINVR 9 1 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 158.85 6.06E-05 199640000 61516 89295 79171 84161 77564 62930 75058 67929 83620 FALSE TRUE 57665.82337 95906.49471 81048.97351 86320.71374 71472.43632 81096.86942 63803.7497 76410.08518 69663.28179 0.82777931 1.376715139 1.163438922 1.239113512 1.025969987 1.164126457 0.915887797 1.096848773 1 16.08811082 2.35443641 1.436101372 1.009211583 1.189365169 0.073428311 0.152755212 0.635958267 2.630271678 0.076153098 0.050537016 226.1707351 -2.35443641 0.180153586 YREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVR 33 1 P28072;A0A087X2I4 P28072 PSMB6 Proteasome subunit beta type-6;Proteasome subunit beta type 0 ; 77.995 0.0016733 120173000 95247 101979 80283 65505 117384 62505 98401 98392 67556 FALSE TRUE 89285.66029 109529.6313 82187.35067 67185.9692 108165.1341 80549.17882 83646.68356 110676.4578 56280.46717 1.58644135 1.946139341 1.460317492 1.193770638 1.921894746 1.431210202 1.486247143 1.966516331 1 15.78034668 -1.964483977 2.660747645 0.504488757 1.615974466 0.373502456 0.253815343 6904105.281 3491167.848 21066134.64 0.058615597 0.010852156 1.964483977 1.111485709 YREEEMTVVEEADDDKKR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YREEEMTVVEEADDDKKR 18 3 A0A087WUB9;Q8WYA6;Q8WYA6-4;A2A2P1 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 162.33 1.57E-11 125900000 105480 59029 70789 63973 83011 54268 94418 68566 96429 FALSE TRUE 98878.19509 63399.56858 72468.14851 65614.65549 76491.65091 69934.29063 80260.89743 77126.61603 80334.37694 1.230832912 0.789195995 0.902081416 0.816769333 0.952165857 0.870540026 0.999085329 0.960069885 1 16.29372986 1.704163151 8.167092716 0.983851591 0.904983294 0.030182327 0.121060548 0.298714135 42.85455054 0.053887523 0.028505837 50.60147205 -1.704163151 -0.078868297 YREYS(ph)PPYAPSHQQYPPSHATPLPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YREYSPPYAPSHQQYPPSHATPLPK 25 1 Q9UPT8 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 YREYS(0.997)PPYAPS(0.002)HQQYPPSHATPLPK;YREYS(0.999)PPYAPS(0.001)HQQYPPSHATPLPK 115.92 0.00085402 475060000 674530 614750 641060 665130 784740 513320 832340 622040 951910 TRUE FALSE 632312.3714 660266.7296 656266.2459 682198.3619 723109.6859 661507.1509 707538.3441 699703.0633 793030.0714 0.797337193 0.832587254 0.827542699 0.86024274 0.911831357 0.834151408 0.892196109 0.882315928 1 19.59701605 -4.999999999 0.092578553 1.487703722 0.734381826 0.828503558 0.023567862 75.67610821 0.484602445 7.199676809 0.470575331 1.00E-05 4.999999999 -0.753321896 YRGDYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YRGDYDR 7 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;;; 137.88 0.0025897 3399830000 2267810 2992080 2374190 2404040 3073900 1986113 2692950 2697320 3466490 FALSE TRUE 2125871.82 3213616.716 2430506.908 2465731.736 2832488.294 2559471.581 2289167.148 3034086.34 2887910.425 0.736128033 1.112782685 0.841614368 0.853811709 0.980808916 0.886271111 0.79267249 1.050616499 1 21.46159456 1.210615612 24.99565012 1.025308438 0.900890438 0.226849234 0.104012767 409.5832058 366345.2464 0.096440281 0.02412989 16.2411064 -1.210615612 -0.124418 YRLEVGIQAMEHLIHVLQTDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YRLEVGIQAMEHLIHVLQTDR 21 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ; 211.06 1.10E-22 113998000 108459 167526 128579 137907 177087 94693 143143 156768 108603 FALSE TRUE 101670.7448 179929.7994 131628.9546 141445.9271 163179.3014 122029.3319 121680.036 176340.8299 90476.4577 1.123725966 1.988691909 1.454842043 1.563345103 1.803555372 1.348741264 1.344880637 1.949024469 1 16.46525483 -1.990994416 2.741851185 0.453857957 1.578145447 0.297632349 0.276057136 46858538.01 42778111.1 162056011.5 0.063479606 0.010209526 1.990994416 1.12428749 YRPAS(ph)ASVSALIGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YRPASASVSALIGGR 15 1 P46108-2 P46108-2 CRK Adapter molecule crk 1 YRPAS(1)ASVSALIGGR;YRPAS(0.996)AS(0.004)VSALIGGR;YRPAS(0.999)AS(0.001)VSALIGGR;YRPAS(0.886)AS(0.114)VSALIGGR 206.72 2.27E-09 546335000 286241 328014 318617 354068 401413 257198 338499 322781 374725 TRUE FALSE 268325.6868 352300.4979 326174.7457 363153.9843 369887.6422 331446.8873 287744.2174 363080.9184 312180.9767 0.859519659 1.128513664 1.044825822 1.163280313 1.184850038 1.061713916 0.921722459 1.163046263 1 18.2520231 -0.609437042 7.001179435 1.000000001 1.065206729 0.036869004 0.105848833 0 0 0.097496634 0.022980177 0.245789292 0.609437042 0.065206727 YRPCS(ph)LGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YRPCSLGR 8 1 P40938;P40938-2 P40938 RFC3 Replication factor C subunit 3 1 YRPCS(1)LGR;YRPCS(1)LGR 77.744 0.019634 423820000 128269 161822 134455 150019 149986 121887 170892 139625 151963 TRUE FALSE 120240.8723 173803.4693 137644.3361 153868.7415 138206.7046 157073.7982 145268.3311 157057.4886 126599.3936 0.949774472 1.372861783 1.08724325 1.215398725 1.09168536 1.24071525 1.147464668 1.240586421 1 16.94991097 -1.052531307 4.304997304 0.999986172 1.179286764 0.172272991 0.11359823 1.41E-05 3.11E-06 0.095407999 0.022486006 0.088607135 1.052531307 0.179300592 YRPETK ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 YRPETK 6 1 P62424;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 ;;;;;;;; 128.38 0.015185 8335300000 6571300 7014880 7037200 7274420 7355090 5767290 8203010 6545730 7692100 FALSE TRUE 6160014.063 7534269.014 7204125.707 7461093.933 6777450.9 7432212.999 6973044.804 7362978.799 6408238.817 0.961264747 1.175716016 1.124197445 1.16429711 1.057615219 1.159790265 1.088137475 1.14898633 1 22.61149648 -1.585831668 2.932331587 0.992857713 1.117269323 0.217228759 0.064320665 1339124.422 1587748.98 53865.1195 0.013160291 0.025951851 1.585831668 0.12441161 YRQDDDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 YRQDDDQR 8 1 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;;; 148.38 0.00073033 3653532000 4297630 5091800 4700150 4854660 5020750 4196238 5211430 4295150 5195120 FALSE TRUE 4028649.01 5468802.17 4811639.778 4979238.795 4626440.548 5407623.79 4430024.452 4831408.932 4328020.91 0.930829378 1.263580348 1.111741343 1.150465512 1.0689506 1.249444932 1.023568172 1.116309055 1 22.04527604 1.028740057 0.982436409 1.004624818 1.138714778 0.098550317 0.098792633 0.99709543 2.067619549 0.083257959 0.02799904 10.68415197 -1.028740057 0.13408996 YRS(ph)PEPDPYLSYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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;Y(0.005)RS(0.995)PEPDPYLSYR 197.1 8.27E-08 7462750000 2411850 2879740 2795020 2765080 3008320 2333060 3070180 2535860 3148110 TRUE FALSE 2260896.614 3092958.946 2861319.194 2836036.634 2772058.682 3006576.548 2609835.011 2852467.703 2622670.103 0.862059094 1.179316812 1.090994704 1.081354697 1.056960492 1.146379998 0.995106097 1.087619712 1 21.32260492 1.710630991 16.34846427 1.031178772 1.084630575 0.0297872 0.087300916 0.472850747 256.1533695 0.037095368 0.020500655 51.36070668 -1.710630991 0.053451803 YRS(ph)PYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YRSPYR 6 1 Q14498-3 Q14498-3 RBM39 RNA-binding protein 39 1 Y(0.002)RS(0.991)PY(0.006)R;YRS(1)PYR;YRS(1)PYR;Y(0.004)RS(0.985)PY(0.012)R 71.491 0.05335 3860370000 595810 859580 796460 741160 979480 695690 783420 778490 849600 TRUE FALSE 558519.3157 923224.1976 815352.4073 760179.4204 902555.5918 896524.4094 665953.4439 875686.1902 707796.2714 0.789096154 1.304364313 1.151959173 1.074008795 1.275162965 1.266641894 0.94088295 1.237200909 1 19.43297464 0.346365963 0.691160248 0.999438651 1.149750209 0.033711966 0.16456513 6.762901155 4.665188586 0.198959907 0.056392229 2.220066394 -0.346365963 0.150311557 YRS(ph)PYSGPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YRSPYSGPK 9 1 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23 Q14498-2 RBM39 RNA-binding protein 39 1 YRS(0.744)PYS(0.255)GPK;YRS(0.966)PY(0.002)S(0.031)GPK;YRS(0.985)PYS(0.014)GPK;YRS(0.99)PYS(0.01)GPK;Y(0.071)RS(0.875)PY(0.003)S(0.051)GPK;Y(0.167)RS(0.82)PY(0.012)S(0.001)GPK 155.24 0.00019409 11037810000 13224600 10330610 12178650 10680030 12502170 9856760 14729150 11095540 15738470 TRUE FALSE 12396895.89 11095499.11 12467533.33 10954097.65 11520300 12702246.6 12520650.7 12480842.59 13111617.68 0.945489427 0.846234186 0.95087682 0.835449745 0.878633002 0.968777988 0.954927988 0.951891894 1 23.64434236 2.234982595 24.99688611 0.964178768 0.890765101 0.498855765 0.03849821 77.8557697 543910.6257 0.013112331 0.01006993 171.783954 -2.234982595 -0.073413667 YRSPYS(ph)GPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YRSPYSGPK 9 1 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23 Q14498-2 RBM39 RNA-binding protein 39 1 YRS(0.266)PYS(0.733)GPK;YRS(0.189)PYS(0.811)GPK 182.93 0.00012037 6212200000 3647400 2976400 3254300 2988800 3370200 2642100 4004000 2910300 4223200 TRUE FALSE 3419115.745 3196775.753 3331493.533 3065497.668 3105518.087 3404831.379 3403637.371 3273657.361 3518320.637 0.97180334 0.908608419 0.946898784 0.871295707 0.882670571 0.967743344 0.967403975 0.930460211 1 21.74645554 2.21070345 24.98162466 0.964228902 0.917347622 0.364951006 0.032796811 249.5008178 223744.6779 0.011860959 0.008761698 162.443916 -2.21070345 -0.04688128 YRTEAHQDVVGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YRTEAHQDVVGR 12 1 Q9H0A0;Q9H0A0-2;A0A087WV29;E9PMU0 Q9H0A0 NAT10 N-acetyltransferase 10 0 ; 153.63 4.25E-05 257825000 141152 177278 141978 171623 179354 119939 183551 161218 206320 FALSE TRUE 132317.5483 190403.8476 145345.7852 176027.1367 165268.2603 154563.4423 156029.2316 181346.4222 171883.8591 0.769807875 1.107747106 0.845604619 1.0241051 0.961511227 0.899231859 0.907759649 1.055052075 1 17.39107455 1.236377095 24.99980144 1.027526056 0.940733157 0.151093661 0.09301502 115.135132 1318059.977 0.06857824 0.020328204 17.23364313 -1.236377095 -0.086792899 YRVPDVLVADPPIAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YRVPDVLVADPPIAR 15 1 Q14697;F5H6X6;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;; 102.78 0.0013905 3064090000 3783320 4857690 4260580 4676070 4904380 3647020 5149330 4135840 4336390 FALSE TRUE 3546528.755 5217358.422 4361642.97 4796065.873 4519209.778 4699855.47 4377235.771 4652208.728 3612618.495 0.981705862 1.444204094 1.207335614 1.327587145 1.250951293 1.300955381 1.211651819 1.287766404 1 21.78461348 -1.562413907 0.581803754 0.850793983 1.268216344 0.3002757 0.118050192 68.60523861 8.891704661 15.06210894 0.042522979 0.027389625 1.562413907 0.417422361 YS(ph)DDGNRETDEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSDDGNRETDEK 12 1 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 YS(1)DDGNRETDEK 131.56 0.00011908 153460000 426290 230430 318570 278610 271630 264630 445640 266670 203540 TRUE FALSE 399609.2698 247491.277 326126.6308 285759.6043 250297.2755 341024.3851 378820.4191 299964.3365 169567.8591 2.356633339 1.459541203 1.923280937 1.685222694 1.476089141 2.011138119 2.234034334 1.768992887 1 17.37150321 0.959627618 23.38682372 0.999999995 1.856423026 0.471406255 0.289191593 3507.757063 2031968.303 0.276998766 0.069249691 9.112291784 -0.959627618 0.856423031 YS(ph)PESQAQSVHHQRPGSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSPESQAQSVHHQRPGSR 18 1 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 Y(0.034)S(0.966)PESQAQSVHHQRPGSR 76.733 0.0089042 138420000 42261 49444 47796 46942 47847 43050 51101 42070 47361 TRUE FALSE 39615.95945 53104.88521 48929.74369 48146.61119 44089.28963 55477.83614 43438.87945 47322.53211 39456.14314 1.00405048 1.345921851 1.240104577 1.2202564 1.117425225 1.406063333 1.100940842 1.199370449 1 15.26796232 0.68396067 0.997466115 1.001138535 1.230765359 0.220757695 0.116867259 1.356277345 2.326298106 0.100377343 0.03240636 4.830150581 -0.68396067 0.229626824 YS(ph)PPAISPLVSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSPPAISPLVSEK 13 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 YS(1)PPAISPLVSEK 98.654 0.0033782 42784000 135480 82700 111120 104810 101000 97278 122630 95519 100010 TRUE FALSE 127000.5486 88823.19405 113755.8189 107499.602 93067.86741 125360.5794 104242.7699 107444.7574 83317.68491 1.524292817 1.066078518 1.365326209 1.290237507 1.117024165 1.50460949 1.251148181 1.289579248 1 16.34633513 -1.193346168 2.267934264 0.995760048 1.286421051 0.294444932 0.144886951 232898.1904 234542.9182 7006.279491 0.033751353 0.064069868 1.193346168 0.290661003 YS(ph)PPRDDDKVDNQAK ddPTM_SK-BR-3_Pertuzumab_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;Y(0.002)S(0.998)PPRDDDKVDNQAK 165.74 7.34E-07 1847590000 8957100 3972120 5568600 5256700 5002900 3616950 7851300 4238260 6484600 TRUE FALSE 8396491.1 4266219.898 5700689.822 5391595.822 4609992.415 4661104.749 6674070.453 4767416.091 5402278.368 1.55424999 0.789707528 1.055238074 0.998022585 0.853342257 0.862803512 1.235417725 0.882482495 1 22.36513655 4.749773929 24.87994647 0.970890773 1.554250353 0.683870364 0.126849164 978.8178516 2171744.174 0.030398931 0.469898076 56204.86754 -4.749773929 0.58335958 YS(ph)PQSLTDPQIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSPQSLTDPQIR 12 0 Q9ULL0 Q9ULL0 KIAA1210 Uncharacterized protein KIAA1210 1 Y(0.02)S(0.962)PQS(0.015)LT(0.003)DPQIR 75.088 0.036456 106700000 287970 247600 280740 296270 258300 223660 323500 261890 342120 TRUE FALSE 269946.4717 265932.5616 287399.2854 303872.7898 238014.1599 288227.0112 274994.1782 294587.543 285017.9618 0.947120911 0.933037904 1.008354995 1.066153122 0.835084773 1.011259113 0.964831046 1.033575362 1 18.12069332 4.083311651 4.573988219 0.984474845 0.940612348 0.095157184 0.060944671 0.543617847 18.70414716 0.014276354 0.032379832 12114.67173 -4.083311651 -0.043862497 YS(ph)PRHS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YSPRHSR 7 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 2 Y(0.055)S(0.945)PRHS(1)R;Y(0.058)S(0.942)PRHS(1)R;Y(0.02)S(0.98)PRHS(1)R;Y(0.202)S(0.798)PRHS(1)R;Y(0.019)S(0.981)PRHS(1)R 96.229 0.0073316 45418520000 8458910 8503220 8524410 8306870 8564950 7425240 9463990 7464600 8454370 TRUE FALSE 7929481.923 9132807.256 8726613.031 8520038.348 7892293.376 9568786.249 8044952.559 8396571.742 7043281.03 1.125822169 1.296669438 1.238998273 1.209668947 1.120542165 1.358569424 1.142216607 1.192139247 1 22.74781622 0.526435751 0.949351747 0.999508899 1.229111312 0.441157163 0.074689809 1.330497139 1.793542613 0.066090478 0.02119397 3.360746468 -0.526435751 0.229602412 YS(ph)PRHS(ph)RS(ph)R ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSPRHSRSR 9 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 3 Y(0.078)S(0.925)PRHS(0.997)RS(1)R 56.514 0.080192 457100000 494450 707210 512560 616260 912160 294600 387420 523270 1210700 TRUE FALSE 463503.2571 759572.5643 524718.1652 632074.2749 840522.6331 379646.2376 329329.9676 588601.4114 1008626.349 0.459539113 0.753076266 0.520230476 0.626668415 0.833334003 0.376399286 0.32651335 0.583567356 1 19.94396039 0.948137955 22.98701324 1.000000002 0.556813401 0.444148827 0.155009119 7175.239303 3180313.12 0.15856839 0.039642097 8.874378649 -0.948137955 -0.443186601 YS(ph)PS(ph)PPPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSPSPPPK 8 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 Y(0.116)S(0.884)PS(1)PPPK 74.162 0.060951 106830000 508880 316130 453420 407730 360360 289700 471390 307170 420240 TRUE FALSE 477030.1092 339536.5941 464175.3365 418193.0421 332058.7792 373331.6871 400709.4457 345520.8507 350099.2291 1.362556868 0.969829596 1.325839356 1.194498609 0.948470467 1.066359638 1.144559634 0.986922626 1 18.41740436 2.770001594 23.74610526 1.049993092 1.191398949 0.367388624 0.116650751 492.4333416 371913.6122 0.034442753 0.036528109 588.8458168 -2.770001594 0.141405857 YS(ph)PSQNS(ph)PIHHIPSR ddPTM_SK-BR-3_Pertuzumab_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(0.333)S(0.418)PS(0.249)QNS(1)PIHHIPSR;Y(0.345)S(0.535)PS(0.12)QNS(1)PIHHIPSR;YS(0.99)PS(0.01)QNS(1)PIHHIPSR;Y(0.142)S(0.844)PS(0.014)QNS(1)PIHHIPSR;YS(0.978)PS(0.022)QNS(1)PIHHIPSR;Y(0.042)S(0.934)PS(0.026)QNS(0.998)PIHHIPSR;Y(0.052)S(0.674)PS(0.274)QNS(1)PIHHIPSR;Y(0.171)S(0.743)PS(0.086)QNS(1)PIHHIPSR 218.38 9.20E-13 17832970000 5787765 4670952 5666016 4763919 4937394 5337130 6153785 5035522 4470187 TRUE FALSE 5425519.12 5016794.146 5800416.575 4886169.227 4549630.992 6877872.79 5231082.068 5664218.006 3724083.911 1.456873489 1.347121672 1.557541858 1.312045954 1.221677895 1.846863001 1.404662782 1.52096949 1 21.82845415 YS(ph)PSQNS(ph)PIHHIPSRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 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(0.005)S(0.905)PS(0.09)QNS(1)PIHHIPSRR;Y(0.003)S(0.996)PS(0.001)QNS(1)PIHHIPSRR;Y(0.001)S(0.999)PSQNS(1)PIHHIPSRR;Y(0.001)S(0.995)PS(0.004)QNS(1)PIHHIPSRR;Y(0.002)S(0.967)PS(0.031)QNS(1)PIHHIPSRR;YS(0.979)PS(0.021)QNS(1)PIHHIPSRR;YS(0.867)PS(0.132)QNS(1)PIHHIPSRR 212.65 4.04E-12 13564380000 2887560 3593070 3342450 3512490 4094570 3136860 4365770 3369720 6343420 TRUE FALSE 2706832.774 3859104.641 3421734.492 3602626.44 3772998.989 4042420.559 3711163.318 3790436.96 5284662.222 0.512205447 0.730246226 0.647484049 0.681713663 0.713952724 0.76493452 0.702251755 0.717252456 1 22.33337983 -5 0.16224525 2.174567645 0.605866674 0.774341175 0.057262139 60.45786125 0.559663666 22.8261804 0.215820547 1.00E-05 5 -1.568700971 YS(ph)PSQNSPIHHIPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YSPSQNSPIHHIPSR 15 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 YS(0.995)PS(0.005)QNSPIHHIPSR;YS(0.978)PS(0.022)QNSPIHHIPSR;YS(0.995)PS(0.005)QNSPIHHIPSR;YS(0.993)PS(0.007)QNSPIHHIPSR;YS(0.999)PS(0.001)QNSPIHHIPSR 212.85 1.12E-09 3887290000 492119 666661 627876 664398 558738 495723 548114 483771 456048 TRUE FALSE 461318.1502 716021.2741 642769.5152 681447.5775 514856.9713 638830.1827 465929.3941 544170.8743 379930.6426 1.21421675 1.884610489 1.691807512 1.793610467 1.355134105 1.681438955 1.226353818 1.432290037 1 18.53537655 1.352004865 0.644036901 1.022348059 1.688857984 0.418188536 0.217319587 0.540703347 0.528353337 0.191450702 0.088523509 22.49079802 -1.352004865 0.666509925 YS(ph)PSQNSPIHHIPSRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 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(0.972)PS(0.028)QNSPIHHIPSRR;YS(0.878)PS(0.121)QNSPIHHIPSRR;Y(0.172)S(0.624)PS(0.203)QNSPIHHIPSRR 157.85 1.27E-08 1712150000 171687 278500 255210 283122 264681 187406 235109 194608 351185 TRUE FALSE 160941.4171 299120.4298 261263.7017 290387.3898 243894.0219 241507.0699 199856.5881 218905.2372 292569.9548 0.550095505 1.022389432 0.892995666 0.992540024 0.833626345 0.825467776 0.683107014 0.748215029 1 18.1584221 2.299951268 2.877752813 0.774502211 0.895847836 0 0.151868993 0.550991915 9.341527752 0.055628982 0.042391409 199.5038438 -2.299951268 0.121345624 YS(ph)PVSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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(0.844)PVS(0.156)K;YS(0.973)PVS(0.027)K;YS(0.968)PVS(0.032)K;YS(0.994)PVS(0.005)K 89.752 0.052248 3530050000 18896000 11540700 14638800 12387500 13895100 12099400 16833000 12776300 14206700 TRUE FALSE 17713333.09 12395185.44 14986039.25 12705384.22 12803834.9 15592300.36 14309047.92 14371449.18 11835509.99 1.496626094 1.047287818 1.266192945 1.073496979 1.081815224 1.317416856 1.208992931 1.214265308 1 23.49661854 4.751984314 24.60022745 1.166925839 1.496626365 0.523714542 0.102557542 1491.188226 2732687.293 0.022918589 0.438940298 56491.65706 -4.751984314 0.329700526 YSAQGER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSAQGER 7 0 O43324;H0YAL7;D6RBD7;C9J1V9;O43324-2 O43324 EEF1E1;EEF1E1-BLOC1S5 Eukaryotic translation elongation factor 1 epsilon-1 0 105.25 0.042029 0 117420 206440 147550 142690 207080 116820 171850 190110 193100 FALSE TRUE 110070.8918 221725.0324 151049.9557 146351.667 190816.7721 150544.0376 146082.6879 213845.652 160870.3625 0.684221071 1.378283911 0.93895453 0.909749097 1.186152434 0.93580965 0.908077073 1.329304221 1 17.29553903 7.060715849 7.386312826 1.04034288 0.114659281 0 0.211652043 0 0 0.042679915 0 11500476.87 -7.060715849 -0.925683599 YSASKPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YSASKPLK 8 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 89.886 0.012392 1869310000 3060400 2886000 2754000 2642300 3271300 2058520 3483200 2931300 3661700 FALSE TRUE 2868855.027 3099682.443 2819326.181 2710105.891 3014385.294 2652781.307 2960926.496 3297279.258 3050538.615 0.940442128 1.016109886 0.924206029 0.888402421 0.988148545 0.869610794 0.970624165 1.080884288 1 21.54063256 1.409359132 6.766100497 1.037920276 0.943462402 0.445366983 0.04648402 0.200709529 14.63757528 0.029606343 0.011058966 25.66605569 -1.409359132 -0.094457875 YSCPESPSQELGGPLPS(ph)PGPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YSCPESPSQELGGPLPSPGPR 21 0 A0A494BZV2;A0A1W2PPU9 A0A494BZV2 1 YSCPESPSQELGGPLPS(1)PGPR;YSCPESPSQELGGPLPS(1)PGPR;YSCPESPSQELGGPLPS(1)PGPR 248.52 1.68E-30 313693000 173272 210513 205147 243520 289537 166769 146822 108153 168092 TRUE FALSE 162427.2148 226099.6016 210013.1837 249769.1355 266797.932 214912.503 124807.4041 121656.1401 140036.3593 1.159893157 1.614577833 1.499704682 1.783602036 1.905204715 1.534690734 0.891249992 0.868746808 1 17.09544193 1.756595422 4.82358121 0.908192869 1.600773242 0.71877315 0.195423795 0.094905527 4.93853139 0.098070083 0.051170151 57.09465087 -1.756595422 0.692580373 YSCQFIEMCLMVTADHGPAVSGAHNTIICAR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSCQFIEMCLMVTADHGPAVSGAHNTIICAR 31 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 73.126 0.0022329 17181000 3740.4 3596.2 3598 3008.1 4338.2 3291.7 5147.2 4832.2 4096 FALSE TRUE 3506.295041 3862.46639 3683.346259 3085.292939 3997.495271 4241.960354 4375.425144 5435.510807 3412.351139 1.02753055 1.131907659 1.079415954 0.904154588 1.171478288 1.243119533 1.2822318 1.592893165 1 11.7365504 2.281256976 2.398541144 1.31054862 1.058446877 0.348398508 0.153456399 0.301803964 3.561398617 0.060253813 0.043409282 191.0983669 -2.281256976 -0.252101743 YSDESGNMDFDNFISCLVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YSDESGNMDFDNFISCLVR 19 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;K7EMQ1 A0A0C4DGQ5 CAPNS1 Calpain small subunit 1 0 ;;;;; 256.52 1.35E-30 298635000 233164 295677 248038 233222 325877 209554 288616 281731 311979 FALSE TRUE 218570.6814 317569.2327 253921.5785 239206.8714 300283.9349 270048.838 245340.7102 316905.7355 259907.6894 0.84095504 1.221853934 0.976968319 0.920353191 1.155348407 1.039018271 0.943953258 1.219301115 1 17.98763979 2.731323307 24.96611434 1.055070749 1.026492123 0.05498946 0.124263661 3898.274214 13447649.21 0.03866475 0.037150461 538.6706419 -2.731323307 -0.028578627 YSDFEWLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YSDFEWLR 8 0 O60493-4;O60493;O60493-3 O60493-4 SNX3 Sorting nexin-3 0 ;; 165.52 0.00075332 269225000 376180 775920 382620 368177 843110 222739 279106 693670 622000 FALSE TRUE 352635.5653 833369.9241 391695.9271 377625.0451 776895.5415 287040.1334 237256.6464 780276.2265 518184.1817 0.680521671 1.608250413 0.755900973 0.728746763 1.499265259 0.553934573 0.457861615 1.505789358 1 18.98310545 2.210376592 24.99834516 0.783884315 1.074512186 0.018569207 0.417480323 507.7626873 450366.4423 0.149744585 0.110615893 162.3217034 -2.210376592 0.290627871 YSDFVVHEIGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSDFVVHEIGK 11 0 Q96PZ0;Q96PZ0-2;E7EUH7;H0Y863 Q96PZ0 PUS7 Pseudouridylate synthase 7 homolog 0 112.15 0.001565 220720000 488410 435760 473180 442260 512990 373730 506580 428000 538850 FALSE TRUE 457841.2899 468024.1238 484404.0531 453609.1403 472701.8347 481619.784 430623.0319 481436.7421 448912.4539 1.019889927 1.042573267 1.079061293 1.010462366 1.052993363 1.072859039 0.959258377 1.072451294 1 18.7760746 1.760871308 25 1.007046606 1.048533798 0.192102258 0.034091562 15.33469061 17196.70252 0.014342717 0.007953819 57.65955789 -1.760871308 0.041487192 YSDPGPVYDCLVWHDGEVWR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YSDPGPVYDCLVWHDGEVWR 20 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ;;; 275.49 1.63E-44 598024000 287957 328963 301174 274903 348815 296879 373302 302561 266369 FALSE TRUE 269934.2854 353319.7628 308317.9895 281957.4764 321420.477 382583.1479 317328.8307 340336.4069 221910.2931 1.216411738 1.592173837 1.389381201 1.27059215 1.448425273 1.724044174 1.429986984 1.53366661 1 17.75961706 -0.892177923 5.898269216 0.999999865 1.462187838 0.480160097 0.146899899 2.43E-07 4.59E-08 0.132626446 0.031260344 0.128180534 0.892177923 0.462187973 YSDVEVPASVTGYSFASDGDSGTCSPLRHS(ph)FQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YSDVEVPASVTGYSFASDGDSGTCSPLRHSFQK 33 1 P35611;P35611-3;E7EV99;E7ENY0;P35611-2;P35611-6;P35611-4;H0Y9H2;P35611-5 P35611 ADD1 Alpha-adducin 1 YSDVEVPASVTGYSFASDGDS(0.001)GT(0.001)CS(0.142)PLRHS(0.856)FQK;YSDVEVPASVTGYSFASDGDSGTCS(0.004)PLRHS(0.996)FQK 312.33 2.06E-104 361680000 327360 374130 351800 333500 482520 253350 431220 378820 705980 TRUE FALSE 306871.122 401830.9745 360144.8621 342058.1746 444624.8256 326488.0322 366562.5643 426116.5109 588147.3772 0.521758889 0.683214769 0.612337785 0.58158582 0.755975191 0.555112621 0.623249509 0.724506352 1 19.16581818 0.846494094 2.711149135 0.999783154 0.624911049 0.772083231 0.065197757 0.263265926 3.563987614 0.055869286 0.01481701 7.022537943 -0.846494094 -0.374872105 YSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPSPR 42 1 P04626-5;P04626-4;P04626;B4DTR1;P04626-3;P04626-2 P04626-5 ERBB2 Receptor tyrosine-protein kinase erbB-2;Receptor protein-tyrosine kinase 1 YSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPS(1)PR;YSEDPTVPLPSETDGYVAPLTCS(0.002)PQPEY(0.009)VNQPDVRPQPPS(0.988)PR;YSEDPTVPLPSETDGYVAPLTCSPQPEY(0.007)VNQPDVRPQPPS(0.993)PR;YSEDPTVPLPSETDGYVAPLTCS(0.016)PQPEY(0.013)VNQPDVRPQPPS(0.97)PR 217.37 2.80E-44 607531000 225691 293511 236015 291164 367163 192585 198099 181723 179793 TRUE FALSE 211565.4032 315242.8598 241613.3873 298635.7612 338327.499 248181.1631 168395.894 204411.5166 149784.3868 1.412466331 2.104644326 1.613074583 1.993770964 2.258763455 1.656922784 1.124255322 1.3647051 1 17.19252772 1.869984658 3.993359186 1.187439049 1.88218902 0.621603429 0.252975342 0.146738068 3.723872098 0.115184194 0.064175706 74.12840539 -1.869984658 0.694749971 YSEEGLS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YSEEGLSPSK 10 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9;A0A0C4DGI9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 YSEEGLS(0.985)PS(0.015)K;YSEEGLS(0.991)PS(0.009)K;YSEEGLS(0.999)PS(0.001)K 273.23 9.17E-24 744160000 2160070 1474040 1754510 1539990 1523600 1297500 2262630 1427860 1804430 TRUE FALSE 2024875.075 1583179.455 1796127.806 1579508.751 1403942.602 1672067.187 1923369.637 1606131.464 1503258.976 1.346990177 1.053164811 1.194822605 1.05072298 0.933932625 1.11229483 1.279466591 1.068432978 1 20.51966214 4.746599125 24.36959801 1.106502177 1.346990348 0.398244391 0.097911053 825.2737285 2501822.321 0.02412668 0.260063626 55795.49372 -4.746599125 0.240488171 YSEKEDKYEEEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YSEKEDKYEEEIK 13 2 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YE05;K7ENT6;A0A5F9UN72;K7EPB9;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;; 210.36 1.72E-08 3109610000 8270900 2900320 4482040 4398180 4865740 2857360 5915610 3343300 6566490 FALSE TRUE 7753239.133 3115062.711 4588356.105 4511044.745 4483604.408 3682233.447 5028619.198 3760718.365 5470500.398 1.417281523 0.569429208 0.838745228 0.824612817 0.819596761 0.673107244 0.91922472 0.68745418 1 22.38324137 4.750792135 24.78976869 0.782456968 1.417281962 0.714645774 0.124149999 880.5828471 1784651.521 0.027217795 0.465350414 56336.79482 -4.750792135 0.634824994 YSESNFS(ph)VDDQDLSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YSESNFSVDDQDLSR 15 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 YSESNFS(1)VDDQDLSR;YSESNFS(1)VDDQDLSR;YSESNFS(1)VDDQDLSR 450.52 2.17E-175 749510000 690780 802570 718650 735000 660900 632580 965330 694070 725290 TRUE FALSE 647545.3129 861993.1179 735696.7174 753861.3444 608995.5799 815195.5769 820587.7282 780726.1673 604234.4134 1.071678968 1.426587263 1.217568382 1.247630601 1.007879668 1.349137948 1.358061888 1.292091529 1 19.20474883 3.715870162 24.28554118 1.234287767 1.288761945 0 0.150769016 1240.47686 2677582.748 0.038368454 0.060063076 5198.405603 -3.715870162 0.054474178 YSFHPVEDFPAPEEYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YSFHPVEDFPAPEEYK 16 0 Q8TF74;Q8TF74-2;A8MWR2 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 0 ; 109.35 0.00097902 96811000 252567 390820 460710 363308 369950 314306 448320 364745 425510 FALSE TRUE 236759.2823 419756.7194 471638.2588 372631.0984 340895.6193 405041.0399 381098.578 410284.2162 354489.6321 0.667887749 1.184115645 1.330471235 1.051176296 0.961651875 1.142603346 1.075062692 1.157394121 1 18.43538391 YSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDK 37 1 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 101.11 4.00E-05 22660000 58591 58823 43990 33590 72663 29136 59787 54146 31740 FALSE TRUE 54923.8939 63178.31613 45033.46357 34451.97627 66956.34109 37547.09022 50822.49439 60906.24729 26442.38895 2.077115422 2.389281704 1.70307848 1.302907099 2.5321593 1.419958321 1.922008427 2.303356455 1 14.6905649 -1.936378035 2.646124189 0.35912224 1.94435281 0.361249649 0.399324776 26838446.44 15739455.78 106266151.1 0.090906513 0.011577691 1.936378035 1.58523057 YSGGNYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YSGGNYR 7 0 P98179 P98179 RBM3 RNA-binding protein 3 0 ;;; 125.08 0.0095001 1743240000 1590740 1977540 1893340 1770490 1763070 1551720 1989880 1449440 1925240 FALSE TRUE 1491178.423 2123959.119 1938250.919 1815923.771 1624605.594 1999676.374 1691515.967 1630405.775 1603905.006 0.929717419 1.324242465 1.208457428 1.132189103 1.012906368 1.246754868 1.054623535 1.016522654 1 20.61315727 1.578363921 0.689714188 0.988974759 1.183914534 0.125986342 0.116666675 0.95499636 0.966359979 0.104977039 0.049529327 37.87598372 -1.578363921 0.194939775 YSGGNYRDNYDN ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSGGNYRDNYDN 12 1 P98179 P98179 RBM3 RNA-binding protein 3 0 98.754 0.034097 207650000 87814 191560 161530 148860 192890 149360 179490 131320 374490 FALSE TRUE 82317.87849 205743.3017 165361.5679 152679.9996 177741.1975 192477.8073 152577.1408 147715.5911 311985.1997 0.26385187 0.659464942 0.530030168 0.489382188 0.569710351 0.616945315 0.489052497 0.473469867 1 18.25111806 -1.861554593 2.700628371 1.198983859 0.529204129 0.67047193 0.106991123 17767289.36 11475733.26 22713514.32 0.02326139 0.013754519 1.861554593 -0.669779729 YSGTLNLDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 ;;;;; 197.66 6.43E-05 5644500000 2539213 7654690 2108814 2109467 8429520 1249394 1926646 7188570 5736980 FALSE TRUE 2380288.191 8221451.212 2158836.064 2163599.495 7767499.502 1610073.766 1637763.318 8086078.788 4779440.976 0.498026485 1.720170048 0.45169217 0.45268882 1.625189963 0.336874914 0.342668385 1.691846145 1 22.18841045 3.955262859 23.25255724 0.774298669 1.182586245 0.021915945 0.573451631 412.4087155 438713.3042 0.137069038 0.247475158 9021.169824 -3.955262859 0.408287576 YSHDFNFHINYGDLGFLGPEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YSHDFNFHINYGDLGFLGPEDLR 23 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 113.73 0.00042657 744930000 485350 675630 542560 536520 696020 436590 623920 591550 381170 FALSE TRUE 454972.8099 725654.3482 555429.7794 550288.0115 641357.3968 562626.4456 530368.9882 665406.3197 317550.2645 1.432758403 2.285163734 1.749108225 1.732916243 2.019703551 1.771771302 1.670189093 2.0954362 1 18.27662545 -1.903991652 2.606519508 0.516767396 1.859991824 0.550383042 0.239558105 8982234.421 4792536.237 26557271.48 0.053193872 0.012474075 1.903991652 1.343224428 YSHLQPGDHLTDITLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSHLQPGDHLTDITLK 16 0 Q15046;Q15046-2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 136.01 1.14E-05 164560000 400200 376790 426740 409840 455540 341700 532680 393540 466360 FALSE TRUE 375152.1964 404687.9236 436862.4743 420357.1883 419763.726 440343.243 452809.5792 442674.3353 388521.5032 0.965589274 1.041610105 1.124422897 1.0819406 1.080413111 1.133381909 1.165468514 1.139381815 1 18.56763492 5.485365736 0.742195239 1.117663754 0.611666017 0.468346853 0.046501132 5.716410853 1.069817912 0.015755793 3.116466021 305749.4866 -5.485365736 -0.505997737 YSHSGS(ph)SS(ph)PDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 YSHSGS(0.926)S(0.315)S(0.75)PDT(0.009)K 179.21 3.07E-05 226910000 621260 416330 487420 467940 481170 364130 606530 408720 518300 TRUE FALSE 582376.4456 447155.5064 498981.8326 479948.1326 443380.8491 469248.4198 515586.4572 459749.5917 431792.3817 1.348741827 1.035579888 1.15560592 1.111525245 1.026838055 1.086745482 1.194061033 1.064746881 1 18.71997826 YSHSGSS(ph)SPDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 YSHS(0.002)GS(0.037)S(0.728)S(0.233)PDTK;YSHSGS(0.065)S(0.468)S(0.468)PDTK 265.77 1.24E-21 654110000 1874200 1380570 1766210 1841670 1882840 1609920 2302150 1506520 1773440 TRUE FALSE 1756897.168 1482788.839 1808105.335 1888930.37 1734969.341 2074677.769 1956963.98 1694612.338 1477441.407 1.189148456 1.003619387 1.223808488 1.278514573 1.174306699 1.404236919 1.324562836 1.146991231 1 20.49466949 3.71261105 3.527662251 1.253202076 1.088358755 0.12438057 0.119092516 0.288896767 7.615721132 0.029647744 0.051998781 5159.540792 -3.71261105 -0.164843322 YSHSGSSS(ph)PDTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 YSHS(0.002)GS(0.012)S(0.432)S(0.554)PDTK;YSHSGS(0.003)S(0.13)S(0.868)PDTK;YSHSGSS(0.065)S(0.935)PDTK;YSHSGS(0.117)S(0.016)S(0.867)PDTK;YSHSGS(0.005)S(0.402)S(0.593)PDTK;YSHS(0.001)GS(0.018)S(0.066)S(0.915)PDTK 173.19 2.96E-05 4097486000 6443900 4856990 5784840 5966580 6441750 5024360 7582480 5016840 5841000 TRUE FALSE 6040587.802 5216606.593 5922059.137 6119692.544 5935840.94 6474811.168 6445557.516 5643203.517 4866099.366 1.241361375 1.07203043 1.217003331 1.25761767 1.219835538 1.330595757 1.324584032 1.159697551 1 22.21433435 3.620643029 3.578175517 1.245194569 1.144254115 0 0.103557449 0.410990749 9.815764574 0.02585505 0.042345634 4174.870695 -3.620643029 -0.100940454 YSHSYLS(ph)DS(ph)DTEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YSHSYLSDSDTEAK 14 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 2 YSHSYLS(1)DS(0.93)DT(0.07)EAK;YSHS(0.004)Y(0.002)LS(0.995)DS(0.993)DT(0.007)EAK;YSHSYLS(1)DS(1)DTEAK;YSHSYLS(1)DS(1)DTEAK 322.68 3.60E-56 1185210000 3861450 2046990 2713240 2605880 2591750 2253880 3407870 2280080 2474690 TRUE FALSE 3619768.737 2198551.269 2777599.334 2672751.293 2388204.41 2904538.567 2896891.531 2564753.007 2061648.252 1.755764464 1.066404644 1.34727121 1.296414793 1.158395671 1.408842932 1.405133746 1.244030355 1 20.97536678 0.973106421 18.83921333 0.999999984 1.320019275 0.259206973 0.18158267 133.1822494 93297.50603 0.158792817 0.039698174 9.39953611 -0.973106421 0.320019291 YSHSYLS(ph)DS(ph)DTEAKLTETNA ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSHSYLSDSDTEAKLTETNA 20 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 2 YS(0.001)HS(0.004)Y(0.002)LS(0.994)DS(0.996)DT(0.004)EAKLTETNA 142.32 1.03E-07 106150000 257330 218660 230180 251250 256860 172230 322230 215720 342460 TRUE FALSE 241224.1746 234849.8139 235639.9783 257697.5004 236687.2517 221950.0051 273914.6029 242653.1169 285301.2136 0.845507005 0.823164441 0.82593402 0.903247123 0.829604784 0.77794974 0.960089161 0.850515544 1 18.12212636 0.660287456 0.511671085 1.006031585 0.831411317 0.501592371 0.047835395 1.176054173 0.633125211 0.06223365 0.023452925 4.57390833 -0.660287456 -0.174620268 YSHSYLS(ph)DSDTEAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSHSYLSDSDTEAK 14 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 YSHSYLS(1)DSDTEAK 263.56 1.32E-24 156040000 353750 244690 285340 278960 303470 253670 346070 243600 287550 TRUE FALSE 331609.419 262807.1022 292108.3995 286118.5859 279636.6903 326900.411 294180.0163 274013.9962 239556.0474 1.384266532 1.097058935 1.219373933 1.194370124 1.167312174 1.364609304 1.228021666 1.143840864 1 17.87000371 0.932910255 3.340276623 1.000404557 1.223314627 0.437078813 0.085567718 0.298311006 8.20504181 0.078314293 0.02033268 8.568607605 -0.932910255 0.22291007 YSHVQEVQER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 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 0 125.97 0.00039497 145730000 133350 175140 155900 167110 184470 132180 180540 161660 163340 FALSE TRUE 125003.8615 188107.5478 159598.0216 171398.3255 169982.4703 170338.2202 153469.7031 181843.6069 136077.4988 0.918622569 1.382356007 1.172846525 1.25956405 1.249159279 1.251773598 1.127811023 1.336323848 1 17.054069 -1.192385457 4.156291402 0.999905079 1.221302488 0.213698998 0.126947213 9.98E-05 1.94E-05 0.107140382 0.02524215 0.064211755 1.192385457 0.221397409 YSHVSQHS(ph)PSKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YSHVSQHSPSKK 12 1 A0A3B3IUD7;Q14690 A0A3B3IUD7 PDCD11 Protein RRP5 homolog 1 YSHVS(0.089)QHS(0.896)PS(0.016)KK;YSHVS(0.002)QHS(0.842)PS(0.156)KK 116.58 0.00038877 131922000 233830 274610 316320 317950 328680 232310 432080 303830 404330 TRUE FALSE 219194.9977 294942.4101 323823.2598 326109.1353 302866.7986 299374.1258 367293.6152 341763.8443 336844.7109 0.650730116 0.875603507 0.961342866 0.968129006 0.899128853 0.888760061 1.090394485 1.014603564 1 18.36172412 5.359007598 0.886587298 0.981396254 1.03E-18 0.762267771 0.057179195 3.049568435 0.857142462 0.01934487 3.76741046 228563.879 -5.359007598 -0.981396254 YSLS(ph)PSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YSLSPSK 7 0 P49792;J3KNE0;A6NKT7;Q7Z3J3;O14715;Q99666;J3KQ37;F8W705;Q99666-2;F8VYC4;A0A286YES2;P0DJD0;A0A1W2PNU4;P0DJD1 P49792;F8VYC4 RANBP2;RGPD3;RGPD4;RGPD8;RGPD5;RGPD1;RGPD2 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6;RANBP2-like and GRIP domain-containing protein 1;RANBP2-like and GRIP domain-containing protein 2 1 YSLS(0.999)PSK;YSLS(1)PSK;YSLS(1)PSK;YSLS(0.999)PS(0.001)K 158.57 0.0014852 1437110000 1820710 4319970 1010730 1075200 5088000 640020 1237530 4221980 5172300 TRUE FALSE 1706755.011 4639825.074 1034704.993 1102791.452 4688409.004 824783.3841 1051973.865 4749103.497 4309009.716 0.39608985 1.076772943 0.240125936 0.255926889 1.088047907 0.191409033 0.244133556 1.102133393 1 22.03892492 1.22357197 24.93477704 1.051067272 0.513296989 0.324597551 0.33060883 327.9664827 545581.8692 0.307838089 0.078218201 16.73292906 -1.22357197 -0.537770283 YSLT(ph)PPNHWGHPHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YSLTPPNHWGHPHR 14 0 Q99990;Q5H916 Q99990 VGLL1 Transcription cofactor vestigial-like protein 1 1 YS(0.025)LT(0.975)PPNHWGHPHR;YS(0.004)LT(0.996)PPNHWGHPHR 111.22 0.0012397 328440000 81365 86359 88194 96041 112437 94278 125111 103658 128797 TRUE FALSE 76272.50989 92753.11022 90286.00333 98505.57466 103606.6516 121494.5281 106351.767 116599.9295 107299.9486 0.710834542 0.864428282 0.841435662 0.918039346 0.965579694 1.132288782 0.991163261 1.086672743 1 16.71128986 2.933072008 1.24165718 1.050461729 0.809617115 0.772854667 0.058046353 0.199652244 0.641829216 0.022907254 0.026085492 857.1799587 -2.933072008 -0.240844614 YSNEDTLSVALPYFWEHFDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YSNEDTLSVALPYFWEHFDK 20 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 147.08 1.26E-07 706990000 667910 502170 368710 274210 383320 216160 562390 490610 253770 FALSE TRUE 626106.7054 539351.1893 377455.9753 281246.6928 353215.5934 278561.8829 478064.8405 551863.7385 211414.1476 2.961517536 2.551159397 1.785386549 1.3303116 1.670728272 1.317612308 2.261271755 2.610344411 1 17.6897124 4.223555737 1.68829414 1.753245407 2.945532957 0.472690245 0.466140346 0.415470489 2.069306101 0.126286903 0.580889067 16732.30365 -4.223555737 1.19228755 YSNSNVIMHETSQYHVQHLATFIMDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSNSNVIMHETSQYHVQHLATFIMDK 26 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;E9PN68;E9PLN2;E9PNT0;E9PLH1 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 54.259 0.034883 119550000 186120 239820 211490 201380 274870 185880 273620 211700 214580 FALSE TRUE 174471.0814 257576.5223 216506.6427 206547.7517 253282.819 239540.5385 232593.2212 238131.211 178765.2118 0.975978937 1.440864919 1.211122906 1.155413571 1.416846245 1.339972896 1.301110092 1.332089217 1 17.44770649 -1.082155464 6.122022951 0.999999311 1.28642095 0.278764633 0.135499012 1.13E-06 1.70E-07 0.11673144 0.027513798 0.082764584 1.082155464 0.286421639 YSPNCK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YSPNCK 6 0 P00338;P00338-3;P00338-2;P00338-5;F5GXY2;F5GYU2 P00338 LDHA L-lactate dehydrogenase A chain 0 ;; 122.15 0.045 1002960000 2185280 2199910 2069070 2176000 2344080 1585470 2618270 2063990 2287410 FALSE TRUE 2048507.226 2362793.625 2118149.317 2231839.844 2159985.412 2043169.451 2225684.72 2321683.695 1905626.494 1.074978351 1.23990385 1.111523861 1.171184307 1.133477845 1.072177291 1.167954333 1.218330928 1 20.86183395 -1.712709453 2.819896867 0.976551452 1.151546926 0.42033026 0.054784936 34060529.15 30790219.34 5665998.955 0.012267114 0.019377179 1.712709453 0.174995475 YSPPAIS(ph)PLVSEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YSPPAISPLVSEK 13 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 YSPPAIS(1)PLVSEK;YSPPAIS(1)PLVSEK 158.91 4.87E-05 121182000 291900 251216 286410 290850 283870 195769 266476 211970 231425 TRUE FALSE 273630.5001 269816.294 293203.7805 298313.7034 261575.9953 252284.3323 226520.3976 238434.9211 192798.6724 1.419255105 1.399471742 1.520776968 1.5472809 1.356731309 1.308537704 1.174906418 1.236704164 1 17.55673559 1.678431139 0.837553922 1.044758769 1.469996998 0.838466707 0.065526388 0.216864831 0.295189182 0.059930565 0.025737779 47.69041915 -1.678431139 0.42523823 YSPS(ph)QNS(ph)PIHHIPSRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSPSQNSPIHHIPSRR 16 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 2 YS(0.117)PS(0.883)QNS(1)PIHHIPSRR 124.2 8.54E-05 313550000 83805 85204 87619 85515 91338 74403 94735 78941 143280 TRUE FALSE 78559.79465 91512.59281 89697.36406 87709.45968 84164.68192 95881.93827 80530.36623 88796.95762 119365.6424 0.658144112 0.766657733 0.751450436 0.734796529 0.705099728 0.803262449 0.674652812 0.743907173 1 16.86502811 0.941516646 23.23653252 1 0.732701327 0.800653495 0.042397701 5184.63929 2059956.916 0.037142481 0.00928562 8.740104926 -0.941516646 -0.267298673 YSPSQNS(ph)PIHHIPSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 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 YSPS(0.003)QNS(0.997)PIHHIPSR;YSPSQNS(1)PIHHIPSR;YSPSQNS(1)PIHHIPSR;YS(0.233)PS(0.2)QNS(0.567)PIHHIPSR;YSPSQNS(1)PIHHIPSR;YSPSQNS(1)PIHHIPSR 213.5 5.69E-10 5521000000 964836 1163288 1107632 1021049 1265048 1116147 1198945 1016262 1319896 TRUE FALSE 904448.637 1249419.054 1133905.554 1047250.846 1165696.233 1438360.52 1019174.328 1143144.548 1099596.831 0.822527504 1.13625196 1.031201184 0.952395293 1.060112398 1.308079907 0.926861827 1.039603349 1 20.06854322 4.75065406 24.15084499 1.059453156 0.82252727 0.324430426 0.106187713 1399.802919 2795350.657 0.023991205 0.390834922 56318.88649 -4.75065406 -0.236925886 YSPSQNS(ph)PIHHIPSRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YSPSQNSPIHHIPSRR 16 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 YSPSQNS(1)PIHHIPSRR;YSPSQNS(1)PIHHIPSRR 189.47 4.76E-10 1742890000 998720 1384740 1175490 1165460 1432190 1069790 1413210 1143720 2393220 TRUE FALSE 936211.898 1487267.59 1203373.178 1195367.677 1319711.575 1378621.006 1201312.28 1286515.96 1993776.121 0.469567214 0.745955162 0.603564846 0.5995496 0.661915629 0.691462292 0.602531181 0.645266009 1 20.92707199 -1.596346345 1.868410872 1.06401697 0.636471192 0.722242408 0.072411141 74309.73543 44047.60779 23087.37486 0.017265977 0.025331077 1.596346345 -0.427545778 YSPT(ph)SPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSPTSPK 7 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPT(0.68)S(0.32)PK 118.41 0.056037 1566200000 5260600 3247000 3950400 3562700 3938700 2894600 4688700 3158800 5171900 TRUE FALSE 4931348.436 3487411.259 4044105.354 3654124.914 3629370.39 3730224.03 3985672.963 3553183.133 4308676.478 1.14451583 0.809392693 0.938595732 0.848085237 0.842339964 0.865747068 0.925034168 0.824657677 1 22.03881335 4.747949339 24.99684986 0.879345924 1.144515969 0.667372937 0.058282099 701.100745 1866595.484 0.012243262 0.157800794 55969.23093 -4.747949339 0.265170045 YSPTS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YSPTSPK 7 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPT(0.331)S(0.669)PK;YSPT(0.055)S(0.945)PK;YS(0.003)PT(0.275)S(0.722)PK 115.86 0.0058588 2686380000 8552300 5081220 6326400 5604700 6334900 4402790 7307800 5021820 8160400 TRUE FALSE 8017026.809 5457438.816 6476465.196 5748526.091 5837382.508 5673804 6212063.232 5648805.281 6798376.522 1.179256074 0.802756187 0.952648794 0.845573362 0.858643602 0.834582195 0.913756867 0.830905035 1 22.69675884 4.747318332 24.90274551 0.877074685 1.179256237 0.707221812 0.060516477 539.6235746 1534395.644 0.012603381 0.151144974 55887.96961 -4.747318332 0.302181552 YSPTS(ph)PTYS(ph)PTSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 2 YSPT(0.003)S(0.933)PT(0.058)Y(0.007)S(0.999)PT(0.001)SPK;YSPT(0.003)S(0.995)PT(0.001)YS(0.999)PT(0.001)SPK;YSPT(0.036)S(0.909)PT(0.015)Y(0.04)S(0.976)PT(0.019)S(0.004)PK 219.41 7.34E-12 1054390000 1189910 825580 968600 941520 1002000 718380 1214030 885840 1219780 TRUE FALSE 1115435.657 886706.8022 991575.6494 965680.9972 923306.9619 925764.6441 1031997.472 996439.074 1016190.838 1.097663564 0.872579017 0.975777002 0.950294926 0.908596031 0.911014555 1.015554789 0.980562938 1 19.95473993 1.707803921 9.768265071 0.997909146 0.944333356 0.104313955 0.060279519 0.204647963 42.3141855 0.026149127 0.014098887 51.0274565 -1.707803921 -0.05357579 YSPTS(ph)PTYSPT(ph)SPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 2 YSPT(0.008)S(0.992)PTYS(0.443)PT(0.528)S(0.029)PK 226.14 1.33E-11 558110000 588510 400960 438590 428830 457690 367300 608070 427290 557570 TRUE FALSE 551676.2096 430647.4956 448993.5619 439834.5038 421744.8736 473333.5474 516895.5485 480638.0971 464507.965 1.187657158 0.927104653 0.966600351 0.946882588 0.907938949 1.018999852 1.112780808 1.0347252 1 18.82534381 2.000691372 24.9603658 1.062747491 0.97347864 0.08715218 0.081852798 34.51659824 1246097.077 0.028661088 0.020978086 100.1593211 -2.000691372 -0.089268851 YSPTS(ph)PTYSPTS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 2 YSPT(0.001)S(0.998)PTYSPT(0.437)S(0.563)PK 269.55 2.09E-25 123980000 474190 287030 348400 306020 391310 259050 394250 302420 483620 TRUE FALSE 444511.2944 308281.9999 356664.2125 313872.9913 360578.0911 333833.5297 335135.8725 340177.8027 402900.6977 1.103277549 0.765156282 0.88524099 0.779033129 0.894955241 0.828575209 0.831807625 0.844321702 1 18.62006478 -0.915044918 3.958118385 1.000006794 0.854018482 0.154877666 0.094006353 98940769.94 216831859.6 10697.70521 0.019625834 0.121606022 0.915044918 -0.145988312 YSPTS(ph)PTYSPTSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPT(0.103)S(0.548)PT(0.233)Y(0.001)S(0.112)PT(0.002)SPK;YSPT(0.002)S(0.983)PT(0.013)YS(0.001)PTSPK 227.92 1.94E-12 214780000 498310 298790 387780 415430 402790 247950 378550 260640 363870 TRUE FALSE 467121.6666 320912.7225 396978.3247 426090.6371 371156.4982 319529.1399 321789.9418 293181.4777 303137.7463 1.540955134 1.058636631 1.309564149 1.405600729 1.224382324 1.054072427 1.061530429 0.967155959 1 18.20961398 2.268398995 3.296164277 1.025117378 1.283410381 0.57111911 0.123923498 0.206034379 4.656138247 0.047460695 0.036199272 185.5235283 -2.268398995 0.258293003 YSPTS(ph)PTYSPTTPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YSPTSPTYSPTTPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPT(0.011)S(0.774)PT(0.215)YSPTTPK;YSPT(0.058)S(0.938)PT(0.004)YSPTTPK;YSPT(0.001)S(0.999)PTYSPTTPK;YSPTS(0.998)PT(0.001)YSPTTPK 261.41 1.74E-24 4321690000 5939200 4563060 5277300 4765060 5478200 4064580 6093700 4683230 6749400 TRUE FALSE 5567476.074 4900913.71 5402480.048 4887339.507 5047964.27 5237958.263 5180006.256 5267941.575 5622881.537 0.990146429 0.871601807 0.960802751 0.869187706 0.897753978 0.931543414 0.921236953 0.936875789 1 22.42287822 0.611435511 1.197135095 1.00000494 0.916549088 0.312004308 0.036817011 1.474868149 3.159963902 0.031278899 0.009545727 4.087290553 -0.611435511 -0.083455852 YSPTSPTYS(ph)PTSPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPTSPTYS(1)PTSPK;YSPTSPT(0.001)YS(0.716)PT(0.141)S(0.141)PK 282.63 2.24E-33 853110000 783700 574570 661520 642330 662880 485090 850740 585870 844090 TRUE FALSE 734649.6159 617111.7606 677211.5668 658813.2753 610820.0787 625127.6082 723179.4349 659017.1592 703205.926 1.044714768 0.877569056 0.963034499 0.936871051 0.868621916 0.888968061 1.028403499 0.937160986 1 19.4235877 1.74042801 25 0.988382785 0.925639892 0.200079748 0.054742115 0.423260076 5701.206916 0.023314731 0.01292924 55.00827302 -1.74042801 -0.062742893 YSPTSPTYSPT(ph)SPK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPTSPTYS(0.019)PT(0.62)S(0.361)PK 147.31 9.02E-05 161640000 571480 355210 431400 449590 487740 309600 527220 356070 673830 TRUE FALSE 535712.0869 381510.118 441633.0117 461127.2406 449434.8678 398976.4941 448168.2555 400526.1233 561363.4199 0.9543053 0.679613428 0.78671498 0.821441555 0.800613029 0.710727632 0.798356714 0.713488106 1 19.09857553 -1.290366504 5.323485579 1.000037635 0.774411258 0.438488181 0.076549822 3.02E-05 4.03E-06 0.065534389 0.01544403 0.051242876 1.290366504 -0.225626378 YSPTSPTYSPTS(ph)PK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPTSPTYSPT(0.08)S(0.92)PK 167.56 3.81E-06 172780000 543390 344370 411530 401090 478400 273140 509570 379650 607620 TRUE FALSE 509380.1899 369867.5131 421291.6859 411382.6484 440828.3938 351991.0839 433164.7091 427050.1382 506204.2966 1.006273936 0.730668459 0.832256243 0.812681068 0.870850755 0.695353805 0.855711245 0.84363199 1 18.94936023 0.672326567 1.821027339 0.999785982 0.81572024 0.28116459 0.083498764 1.566828247 7.143953562 0.07037337 0.019718656 4.702475781 -0.672326567 -0.184065742 YSQKEDKYEEEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 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 ;;; 179.79 7.56E-06 7592400000 10114300 4148180 5990830 6070380 6282430 3555030 7943100 4245370 7464370 FALSE TRUE 9481264.018 4455315.563 6132935.317 6226156.228 5789033.29 4581309.45 6752105.895 4775413.79 6218518.425 1.524682146 0.716459333 0.98623738 1.001228235 0.930934492 0.736720411 1.085806205 0.767934331 1 22.56813947 4.749641031 24.89490329 0.906451496 1.524682525 0.708902708 0.12514879 832.1042432 1869491.252 0.027728894 0.42152775 56187.67097 -4.749641031 0.618231029 YSQKEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YSQKEDR 7 1 H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;H0YL42;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 ;; 84.568 0.019562 259460000 945780 710270 864950 804150 736480 762070 1016470 764650 496571 FALSE TRUE 886585.3181 762859.1298 885467.0225 824785.8504 678639.8316 982067.2378 864059.7599 860118.2357 413690.0921 2.143114701 1.844035292 2.14041148 1.993728799 1.640454641 2.373920131 2.08866438 2.079136658 1 18.65819088 -0.798189096 5.124160346 0.999999289 2.035568421 0.740075565 0.19330687 1.49E-06 3.48E-07 0.175183669 0.041291158 0.159151561 0.798189096 1.035569132 YSQKEDRYEEEIK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSQKEDRYEEEIK 13 2 H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;H0YL42;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 111.12 0.00056527 242090000 213420 147660 156940 191800 225490 138250 213240 140040 245560 FALSE TRUE 200062.4232 158592.9 160662.6909 196721.9127 207780.925 178160.5307 181266.6416 157524.3023 204574.4496 0.97794433 0.775233175 0.785350718 0.961615261 1.01567388 0.870883588 0.886066867 0.770009659 1 17.64226645 3.243795909 24.99994084 0.911359737 0.822284686 0.103207691 0.089025559 219.2481375 1046962.615 0.024341078 0.031995462 1753.056484 -3.243795909 -0.089075051 YSS(ph)PTAGSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YSSPTAGSAK 10 0 P28749;P28749-2 P28749 RBL1 Retinoblastoma-like protein 1 1 YS(0.072)S(0.916)PT(0.012)AGSAK;YS(0.003)S(0.98)PT(0.016)AGSAK;YSS(0.99)PT(0.01)AGSAK 237.8 3.65E-12 658260000 2159550 1914310 1813330 1726880 2046810 1555680 2575520 2029360 2062770 TRUE FALSE 2024387.62 2056047.504 1856343.044 1771194.664 1886061.799 2004779.562 2189344.686 2282730.063 1718480.361 1.178010332 1.196433518 1.080223601 1.030674952 1.097517226 1.166600217 1.274000411 1.328342246 1 20.71270193 1.981526114 5.583290728 1.229393774 1.11930396 0.11692951 0.096424628 0.262806422 26.69283411 0.038254272 0.024740833 95.83543403 -1.981526114 -0.110089814 YSS(ph)SGS(ph)PANSFHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YSSSGSPANSFHFK 14 0 O00418;H3BRH4 O00418 EEF2K Eukaryotic elongation factor 2 kinase 2 Y(0.072)S(0.14)S(0.675)S(0.301)GS(0.81)PANS(0.001)FHFK;Y(0.115)S(0.126)S(0.515)S(0.396)GS(0.847)PANS(0.001)FHFK;Y(0.096)S(0.392)S(0.475)S(0.067)GS(0.971)PANSFHFK;Y(0.322)S(0.229)S(0.455)S(0.432)GS(0.562)PANSFHFK 110.22 0.00038159 882864000 1109030 1478450 1358170 1592370 2079760 1433310 2212050 1728740 1527010 TRUE FALSE 1039617.792 1587915.976 1390386.434 1633232.91 1916424.039 1847083.329 1880373.638 1944576.994 1272142.166 0.817218248 1.248222108 1.092948941 1.283844647 1.506454302 1.451947257 1.478115959 1.528584655 1 20.27882847 3.055996421 3.14766884 1.430949649 1.099391464 0.397265428 0.184640388 0.225444717 4.563814707 0.050856272 0.060841155 1137.61791 -3.055996421 -0.331558185 YSS(ph)TETLKDDDLWSSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YSSTETLKDDDLWSSR 16 1 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 YS(0.031)S(0.965)T(0.003)ET(0.001)LKDDDLWSSR;YS(0.012)S(0.756)T(0.185)ET(0.047)LKDDDLWSSR;YS(0.028)S(0.931)T(0.021)ET(0.021)LKDDDLWSSR 103.9 0.0008497 423380000 648610 462960 486030 538800 551760 379980 640790 452690 515600 TRUE FALSE 608014.6579 497238.0401 497558.8611 552626.5202 508426.9953 489674.0575 544709.4883 509209.343 429543.0291 1.415491852 1.157597741 1.15834463 1.286545195 1.183646249 1.13998837 1.268113906 1.185467598 1 18.71244313 -4.0155007 0.325555225 8.00E-14 1.223156759 0.433657276 0.081739774 170.5467903 2.764063438 115.596086 0.067022613 9.65E-05 4.0155007 1.223156759 YSSDYFQAPSDYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YSSDYFQAPSDYR 13 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ;;; 238.98 1.99E-16 1262440000 728400 1023790 736210 813160 1001640 593400 855030 862100 695520 FALSE TRUE 682810.7442 1099592.477 753673.2489 834027.0623 922975.2348 764704.947 726826.1892 969735.0827 579433.2188 1.178411458 1.897703551 1.300707699 1.439384273 1.592893201 1.319746473 1.254374388 1.673592489 1 19.14428287 -3.427616457 0.185450183 2.36E-12 1.572808951 0.254972093 0.224265834 85.5092774 1.409035949 33.69400786 0.639632287 0.00037358 3.427616457 1.572808951 YSSS(ph)GS(ph)PANSFHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YSSSGSPANSFHFK 14 0 O00418;H3BRH4 O00418 EEF2K Eukaryotic elongation factor 2 kinase 2 YS(0.003)S(0.061)S(0.936)GS(1)PANSFHFK;Y(0.003)S(0.003)S(0.028)S(0.975)GS(0.982)PANS(0.01)FHFK 178.14 2.95E-06 388050000 455900 605430 567530 672580 873920 641520 976250 752940 608150 TRUE FALSE 427366.0328 650256.6671 580992.0796 689839.5415 805285.8484 826716.4098 829870.3756 846946.2164 506645.8362 0.843520271 1.283454083 1.14674204 1.361581389 1.58944531 1.63174421 1.637969398 1.671673102 1 18.95061808 3.037517246 2.416923545 1.563435969 1.134630089 0.399745594 0.223353242 0.250231188 2.956911454 0.064258027 0.076922203 1090.227784 -3.037517246 -0.428805881 YSSS(ph)GSPANSFHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSSSGSPANSFHFK 14 0 O00418;H3BRH4 O00418 EEF2K Eukaryotic elongation factor 2 kinase 1 YS(0.009)S(0.054)S(0.469)GS(0.469)PANSFHFK 157.54 3.39E-06 358280000 441330 612790 581740 587620 605510 516220 821690 569560 567420 TRUE FALSE 413707.9431 658161.6092 595539.1475 602699.324 557955.6871 665244.3339 698485.2127 640670.8198 472713.9363 0.875176108 1.392304222 1.259829892 1.274976847 1.180324175 1.407287331 1.477606559 1.355303431 1 18.85060787 2.234969832 24.98197888 1.365589437 1.235418768 0.027617555 0.184881942 207.0073712 1440180.421 0.062069241 0.04766785 171.7789057 -2.234969832 -0.130170669 YSSSFCTHDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YSSSFCTHDR 10 0 P04183;K7ERV3;K7ES52;K7ERJ1;K7ENW5 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 0 ;;; 179.57 2.09E-06 3770400000 1749920 2577750 2098230 1902010 3128600 1796720 2198480 2754910 3679570 FALSE TRUE 1640395.631 2768609.292 2148001.006 1950818.797 2882892.376 2315403.897 1868838.334 3098866.578 3065425.996 0.535128114 0.903172771 0.700718598 0.636394028 0.940454077 0.75532859 0.609650449 1.010908951 1 21.54765615 1.220826979 24.99838261 1.005454866 0.739954089 0.464989717 0.123977295 250.4945106 353102.3857 0.110685445 0.027914606 16.62750085 -1.220826979 -0.265500777 YSSSGS(ph)PANSFHFK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSSSGSPANSFHFK 14 0 O00418;H3BRH4 O00418 EEF2K Eukaryotic elongation factor 2 kinase 1 YS(0.001)S(0.013)S(0.11)GS(0.877)PANSFHFK 180.32 1.14E-06 319450000 462070 669940 584400 576720 721300 591090 826500 602240 585090 TRUE FALSE 433149.8635 719543.0547 598262.244 591519.6116 664652.0076 761728.0875 702573.9978 677430.9897 487434.6992 0.888631573 1.476183489 1.22736901 1.213536116 1.363571384 1.562728482 1.441370504 1.389788193 1 18.89484943 2.603324939 5.249474248 1.404697071 1.252310862 0.066902526 0.204165715 0.491846061 19.02418499 0.061399005 0.057547132 401.1667583 -2.603324939 -0.152386209 YSSSSIPEPFGSRGS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YSSSSIPEPFGSRGSPR 17 1 Q8WUF5;K7EN03 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 YSSSSIPEPFGS(0.317)RGS(0.683)PR;YSSSSIPEPFGS(0.076)RGS(0.924)PR;YSSSSIPEPFGS(0.119)RGS(0.88)PR;YSSS(0.002)S(0.009)IPEPFGS(0.279)RGS(0.71)PR 231.06 1.09E-18 701380000 731307 913610 809280 862560 1049950 689980 1008820 743644 1195140 TRUE FALSE 685535.8003 981254.635 828476.5038 884694.7499 967491.1623 889166.0251 857556.8064 836489.5904 995663.4131 0.688521634 0.985528465 0.832084912 0.888548016 0.971705046 0.893038765 0.861291873 0.8401329 1 19.92529859 4.753355481 24.67482343 0.901098307 0.688521454 0.570351057 0.059797771 1701.735813 2838091.318 0.013371982 0.302710467 56670.29605 -4.753355481 -0.212576854 YSTVVMADVSQYPVNHLVTFCLGEDDGVHTVEDASR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSTVVMADVSQYPVNHLVTFCLGEDDGVHTVEDASR 36 0 Q8TE68 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 0 135.17 3.59E-09 30619000 26215 31357 32404 31358 37428 32037 41343 31877 20346 FALSE TRUE 24574.24995 33678.70491 33172.63818 32162.69937 34488.55586 41285.56182 35144.00096 35856.91362 16950.12116 1.449797893 1.98693004 1.957073809 1.897490824 2.034708515 2.435708951 2.073377566 2.11543701 1 14.04900797 4.739449039 5.492058521 2.004656208 1.42918425 0.125358176 0.369202292 0.239783531 27.96801676 0.076447154 0.519022755 54884.41489 -4.739449039 -0.575471958 YSVDIPLDK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YSVDIPLDK 9 0 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ; 158.37 0.00015556 293010000 780740 805280 764500 769900 796430 666790 1038370 778490 950290 FALSE TRUE 731874.8771 864903.7691 782634.301 789656.9374 733881.6004 859281.4486 882676.0583 875686.1902 791680.4599 0.924457422 1.09249099 0.988573472 0.997444016 0.926992186 1.085389235 1.114939806 1.106110653 1 19.59455872 2.11988786 10.86207185 1.089844412 1.001424081 0.361625446 0.056672864 0.36984594 33.34879395 0.020382929 0.015052828 131.7916393 -2.11988786 -0.08842033 YSVEASS(ph)PGHGS(ph)PLSSLLPSASVPESMTISELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YSVEASSPGHGSPLSSLLPSASVPESMTISELR 33 0 Q8TEQ0;Q8TEQ0-2;H3BQF0 Q8TEQ0 SNX29 Sorting nexin-29 2 YS(0.001)VEAS(0.468)S(0.531)PGHGS(0.987)PLS(0.006)S(0.007)LLPSASVPESMTISELR;Y(0.001)S(0.002)VEAS(0.187)S(0.823)PGHGS(0.956)PLS(0.015)S(0.015)LLPSASVPESMTISELR;Y(0.002)S(0.016)VEAS(0.466)S(0.507)PGHGS(0.719)PLS(0.14)S(0.151)LLPSASVPESMTISELR;YSVEAS(0.133)S(0.867)PGHGS(0.989)PLS(0.005)S(0.006)LLPSASVPESMTISELR 152.31 8.34E-11 237959000 94987 118933 113541 121608 136787 104057 141739 108237 138988 TRUE FALSE 89041.93323 127738.9231 116234.2461 124728.6672 126044.3008 134096.5667 120486.5528 121750.6277 115790.0049 0.768994986 1.103194729 1.003836611 1.077197184 1.088559422 1.158101399 1.040560909 1.05147787 1 16.8211512 4.742751665 24.99470705 1.067382198 0.768994869 0.799204329 0.046676256 178.5289867 1064676.813 0.010605552 0.082946406 55303.37875 -4.742751665 -0.298387329 YSVGSLS(ph)PVSASVLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YSVGSLSPVSASVLK 15 0 Q9UBU7 Q9UBU7 DBF4 Protein DBF4 homolog A 1 YSVGSLS(1)PVSASVLK;YSVGSLS(0.994)PVS(0.006)ASVLK 270.75 2.33E-33 267870000 855290 650190 732160 705380 813970 615380 878000 713210 802010 TRUE FALSE 801758.9256 698330.7441 749527.181 723481.245 750044.0796 793030.2161 746352.051 802255.8385 668149.3498 1.199969626 1.045171629 1.12179587 1.082813663 1.122569497 1.186905617 1.117043744 1.200713342 1 19.3498111 2.481372604 24.7954728 1.138095332 1.102776898 0 0.066116055 463.2501194 2701875.276 0.019872323 0.017013274 302.9511489 -2.481372604 -0.035318434 YSVLNNDDYFADVS(ph)PLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YSVLNNDDYFADVSPLR 17 0 Q1ED39;H3BMC9 Q1ED39 KNOP1 Lysine-rich nucleolar protein 1 1 YSVLNNDDYFADVS(1)PLR;YSVLNNDDYFADVS(1)PLR;YSVLNNDDYFADVS(1)PLR;YSVLNNDDYFADVS(1)PLR;YSVLNNDDYFADVS(1)PLR;YSVLNNDDYFADVS(1)PLR 343.13 7.89E-73 940425000 890810 887668 909645 865239 1018621 1001484 1269740 1008363 989249 TRUE FALSE 835055.7922 953391.8623 931222.209 887442.4976 938622.6156 1290596.173 1079354.275 1134259.34 824136.9511 1.013248819 1.15683669 1.129936241 1.076814353 1.138915825 1.565997218 1.309678292 1.376299581 1 19.65252457 2.442760264 24.95826951 1.344877259 1.110327819 0.33998667 0.142655662 163.3932525 118680.6532 0.043288021 0.036217499 277.1789621 -2.442760264 -0.234549441 YSVLQQHAEANGVDGVDALDT(ph)ASHTNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YSVLQQHAEANGVDGVDALDTASHTNK 27 0 Q99523;Q99523-2 Q99523 SORT1 Sortilin 1 YSVLQQHAEANGVDGVDALDT(0.546)AS(0.369)HT(0.085)NK 160.27 2.63E-11 150360000 103210 48335 72624 68305 89259 49078 96013 61432 135990 TRUE FALSE 96750.27034 51913.77369 74346.67558 70057.82194 82248.95819 63246.02189 81616.74199 69101.92043 113292.3905 0.853987368 0.458228249 0.656237151 0.618380649 0.725988373 0.55825481 0.720407978 0.609943176 1 16.78969144 -5 0.321412736 4.485794409 0.621015591 0.49905855 0.107845116 244.0693127 2.15560851 578.8254866 0.085627945 1.00E-05 5 -3.864778818 YSYLTEPGMS(ph)PQSPCER ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YSYLTEPGMSPQSPCER 17 0 Q12955-4;Q12955-5;Q12955-6;H0Y3A4;H0YA66 Q12955-4 ANK3 Ankyrin-3 1 YSYLTEPGMS(0.636)PQS(0.364)PCER;YSYLTEPGMS(1)PQSPCER;YSYLTEPGMS(1)PQSPCER 371.87 8.50E-105 788980000 793130 943190 963630 1302450 1385150 700310 586170 453815 509360 TRUE FALSE 743489.4091 1013024.769 986487.7587 1335873.072 1276365.906 902478.1284 498279.2502 510474.8017 424344.5254 1.75208908 2.387269561 2.324733087 3.148086029 3.007852888 2.126758034 1.174232776 1.202972517 1 18.69487654 1.812325201 3.284305847 1.121453245 2.509855511 0.73421903 0.383578234 0.129006427 2.515120455 0.212471925 0.10855643 64.91203156 -1.812325201 1.388402265 YSYLTEPGMSPQS(ph)PCER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YSYLTEPGMSPQSPCER 17 0 Q12955-4;Q12955-5;Q12955-6;H0Y3A4;H0YA66 Q12955-4 ANK3 Ankyrin-3 1 YSYLTEPGMS(0.001)PQS(0.999)PCER;YSYLTEPGMS(0.227)PQS(0.773)PCER;YSYLTEPGMS(0.073)PQS(0.927)PCER;YSYLTEPGMS(0.007)PQS(0.993)PCER;YSYLTEPGMS(0.001)PQS(0.999)PCER 272.01 4.96E-35 780684000 570548 666704 718022 1022219 1105356 509581 441316 323220 394515 TRUE FALSE 534838.4191 716067.4579 735053.8209 1048450.87 1018545.799 656688.7623 375144.7628 363574.7285 328667.8978 1.627291326 2.178696072 2.236463694 3.19000084 3.099012119 1.998031346 1.14140981 1.106206998 1 18.32627102 1.825290655 3.318295671 1.079193775 2.434460062 0.662270502 0.448769763 0.159778026 3.105703486 0.25256639 0.130687676 66.87913614 -1.825290655 1.355266287 YSYYDESQGEIYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YSYYDESQGEIYR 13 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 ;;; 393.02 6.71E-108 1060520000 344666 377033 360736 376896 427402 320974 405902 340935 344826 FALSE TRUE 323093.9703 404948.9156 369292.8283 386567.7894 393835.571 413633.9832 345040.7633 383501.4852 287272.3129 1.124695823 1.409634334 1.285514864 1.345649309 1.370948585 1.439867208 1.201092997 1.33497545 1 18.13205943 -0.830354001 6.062849097 0.999999974 1.31949207 0.524362655 0.093870999 3.06E-08 5.66E-09 0.082192301 0.01937291 0.147790323 0.830354001 0.319492095 YT(ph)T(ph)T(ph)QQVVKLIGS(ph)HTISKVTVKIGDLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YTTTQQVVKLIGSHTISKVTVKIGDLK 27 3 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 4 Y(0.533)T(0.559)T(0.547)T(0.547)QQVVKLIGS(0.547)HT(0.547)IS(0.547)KVT(0.171)VKIGDLK 50.029 0.064317 237070000 64757 256560 161500 193650 258490 141660 174320 202500 237160 TRUE FALSE 60703.97496 275555.9694 165330.8563 198619.3868 238189.2381 182554.9423 148182.3343 227782.5708 197576.4639 0.307242947 1.394680135 0.836794287 1.005278579 1.205554717 0.923971098 0.749999931 1.152883123 1 17.59205157 4.759465227 24.63995764 1.017029948 0.307242096 0.60132919 0.185441031 3339.096521 3935667.234 0.044889747 1.998750359 57473.17992 -4.759465227 -0.709787851 YTCGEAPDYDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 YTCGEAPDYDR 11 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;;;;; 325.68 1.50E-46 17140340000 6378570 6975560 7133660 7018560 7421810 6501760 7854600 6651110 10060030 FALSE TRUE 5979346.69 7492037.72 7302873.784 7198668.132 6838930.981 8378712.565 6676875.649 7481515.724 8380946.003 0.713445318 0.893936999 0.871366285 0.858932647 0.816009431 0.99973351 0.796673269 0.892681533 1 22.99868167 -5 0.124860276 1.433641849 0.7996778 0.349811318 0.069947923 189.6665848 1.516616736 20.96779118 0.553574743 1.00E-05 5 -0.63396405 HS(ph)DENDGGQPHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HSDENDGGQPHK 12 0 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 HS(1)DENDGGQPHK 97.291 0.0032233 183130000 102160 76101 66139 72526 47873 50164 78727 39077 34466 TRUE FALSE 95765.98796 81735.59722 67707.84831 74387.13995 44113.24769 64645.53246 66922.61722 43955.84947 28713.40194 3.335236562 2.846600949 2.358057344 2.59067665 1.536329543 2.251406245 2.330710145 1.530847844 1 14.80943665 8 0.084935538 0.067618168 8.492934687 0.792109973 0.312670881 81.32061204 0.499762144 6.962446858 80.05905033 100000000 -8 8.425316519 up YTEFYHVPTHSDASK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YTEFYHVPTHSDASK 15 0 Q96HC4;Q96HC4-4;Q96HC4-7;H0YBI4;Q96HC4-3;Q96HC4-2;Q96HC4-6 Q96HC4;Q96HC4-6 PDLIM5 PDZ and LIM domain protein 5 0 ;;; 267.11 1.25E-25 2684340000 4167390 3939310 3965060 3974500 4727040 2832610 4868890 4088480 4911350 FALSE TRUE 3906560.499 4230980.611 4059113.096 4076492.399 4355797.346 3650338.523 4138845.145 4598935.728 4091613.956 0.954772503 1.034061536 0.992056714 0.996304256 1.064567037 0.892151254 1.011543413 1.123990625 1 21.9642386 1.458495594 25 1.063919531 0.993601567 0.231306687 0.053930926 8.970686388 12044.27821 0.026261354 0.012155128 28.74058433 -1.458495594 -0.070317964 YTELEYIHALTLLHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YTELEYIHALTLLHR 15 0 Q96A65 Q96A65 EXOC4 Exocyst complex component 4 0 102.63 0.00088835 127250000 43096 87210 73276 104870 88862 96453 95072 61011 58510 FALSE TRUE 40398.69829 93667.11914 75014.14132 107561.1417 81883.13697 124297.4153 80816.83621 68628.35765 48744.30301 0.8287881 1.921601364 1.538931458 2.206640266 1.679850401 2.549988566 1.657975009 1.407925715 1 15.57294599 4.742997166 24.60653016 1.800151376 0.828787612 0.305992138 0.426776637 400.8189828 2222970.713 0.090537144 0.71477961 55334.64978 -4.742997166 -0.971363764 YTGEDFDEDLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YTGEDFDEDLR 11 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 136.63 0.00022124 160812000 247310 315690 289150 330770 346910 268670 363150 317690 326950 FALSE TRUE 231831.3086 339064.0161 296008.7745 339258.1182 319665.088 346230.6675 308699.0288 357354.2958 272379.9328 0.851132116 1.244820103 1.086749569 1.245532718 1.173599996 1.271131335 1.133339838 1.311969983 1 18.05526089 4.744792716 24.93857721 1.185602909 0.851131962 0.558705666 0.092782863 464.4520462 1858515.223 0.018935293 0.178417999 55563.89931 -4.744792716 -0.334470947 YTGEEDGAGGHS(ph)PAPPQTEECLR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YTGEEDGAGGHSPAPPQTEECLR 23 0 O94762-4;O94762;J3KS37;J3KSV9 O94762-4 RECQL5 ATP-dependent DNA helicase Q5 1 YTGEEDGAGGHS(1)PAPPQTEECLR 141.15 6.05E-10 0 93029 102880 87473 83667 93196 75497 118220 70657 85983 TRUE FALSE 87206.48095 110497.3422 89547.90087 85814.03687 85876.76209 97291.75831 100494.0085 79478.68199 71631.88183 1.21742552 1.542572098 1.25011236 1.197986632 1.198862293 1.358218657 1.402922916 1.109543404 1 16.12831422 -4.390747629 0.17755776 6.43E-12 1.383315988 0.375860107 0.120453978 110.5485729 1.290273461 39.39037657 0.40253497 4.07E-05 4.390747629 1.383315988 YTIENPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YTIENPR 7 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;; 155.53 0.0037329 3366210000 3006590 3585230 3452920 3379240 3592520 2970320 3662460 3060210 3722330 FALSE TRUE 2818412.899 3850684.16 3534824.893 3465957.019 3310377.971 3827803.165 3113308.124 3442283.955 3101049.076 0.908857883 1.241735963 1.139880346 1.117672418 1.067502606 1.234357494 1.003953194 1.110038529 1 21.56432493 1.667648057 11.76296031 1.043319224 1.132947624 0.119385719 0.097079575 0.208041949 36.6658416 0.041900272 0.022836387 46.52089452 -1.667648057 0.0896284 YTIHSQLEHLQSK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YTIHSQLEHLQSK 13 0 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 ; 206.66 3.48E-08 748000000 1003880 1057670 1004290 934380 1013730 784700 1256340 1134540 1082570 FALSE TRUE 941048.9428 1135980.987 1028112.233 958357.7727 934115.735 1011230.151 1067963.48 1276189.816 901882.0733 1.043427928 1.2595671 1.139963043 1.062619827 1.035740439 1.121244319 1.184149804 1.415029586 1 19.78257928 1.551970898 5.244882903 1.234817886 1.127296295 0.091808606 0.118016243 0.288569651 16.92924461 0.063172404 0.028393022 35.64272482 -1.551970898 -0.107521591 YTLETRPNQEGIDVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YTLETRPNQEGIDVR 15 1 A0A3B3ISG5;P14735;Q5T5N3 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 68.413 0.048067 554650000 610880 717690 756420 735910 719140 623750 809490 624140 761420 FALSE TRUE 572646.1113 770828.5144 774362.6396 754794.6965 662661.6453 803816.4993 688114.4894 702065.2529 634334.083 0.902751604 1.215177514 1.220748909 1.1899009 1.044657166 1.267181633 1.084782464 1.106775234 1 19.27488334 0.942364162 1.389491592 1.002099196 1.155335934 0.113750227 0.10604027 0.845669389 3.297394332 0.092214487 0.027616972 8.757177696 -0.942364162 0.153236738 YTQLQYIGEGAYGMVSSAYDHVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YTQLQYIGEGAYGMVSSAYDHVR 23 0 P27361;E9PBK7;E9PQW4;P27361-3;P27361-2;E9PJF0 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 172.49 4.94E-12 71577000 108140 134330 135300 147210 161360 116300 168210 152240 156050 FALSE TRUE 101371.7104 144275.933 138509.3799 150987.6578 148687.4365 149873.922 142988.4721 171247.4991 130004.2469 0.779756915 1.109778614 1.065421963 1.161405581 1.143712148 1.152838662 1.099875393 1.317245423 1 16.98819923 5.219675114 1.553237421 1.134529803 7.06E-15 0.640207996 0.082188631 2.585618993 2.105118029 0.019403319 6.472050303 165834.5872 -5.219675114 -1.134529803 YTQSNGR ddPTM_SK-BR-3_Pertuzumab_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 ; 169.97 0.0023079 139080000 119915 148496 139718 144165 170776 110889 157957 142790 176837 FALSE TRUE 112409.7342 159490.7983 143032.1769 147864.518 157363.9418 142900.8542 134272.8143 160617.6458 147321.7623 0.763021922 1.082601755 0.970882881 1.003684151 1.068164943 0.96999148 0.911425523 1.090250641 1 17.16861103 4.750182887 24.78690937 1.005125187 0.763021759 0.658213441 0.056211765 1049.152268 2237488.345 0.013428762 0.216503451 56257.81838 -4.750182887 -0.242103429 YTQVGPDHNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YTQVGPDHNR 10 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;; 127.83 0.00034568 7946310000 6060250 6846300 7003120 7054160 7093210 5758660 7527220 6410140 6695190 FALSE TRUE 5680949.77 7353207.176 7169237.314 7235181.688 6536137.899 7421091.658 6398583.24 7210460.089 5577719.536 1.018507606 1.318317841 1.285334852 1.297157672 1.171829788 1.330488493 1.147168336 1.292725466 1 22.41124396 -2.323306131 0.508734996 0.64162678 1.245454815 0.350009137 0.097804241 123.1043848 7.68533535 49.68998973 0.041044437 0.004750003 2.323306131 0.603828035 YTRPTPVQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YTRPTPVQK 9 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8Y4D2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;O15523-2;O15523;O15523-3;C9J8G5;C9J081 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ; 86.898 0.01261 860760000 886190 901340 742160 770570 1237470 552140 1023000 990530 1510130 FALSE TRUE 830724.9498 968076.1514 759764.3857 790344.1308 1140284.098 711533.8548 869610.6471 1114199.851 1258079.547 0.660311943 0.769487234 0.603908066 0.628214752 0.906368838 0.565571435 0.691220717 0.885635454 1 20.26279171 1.098950724 3.377060965 0.995631742 0.687440018 0.566823139 0.094932549 0.149099675 3.175957785 0.083249642 0.02188047 12.55887459 -1.098950724 -0.308191725 YTVQDESHSEWVSCVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 7 YTVQDESHSEWVSCVR 16 0 P63244;J3KPE3;D6RHH4;H0YAF8;D6R9L0;H0Y8W2;D6R9Z1;D6RFX4;D6RFZ9;H0YAM7;D6RBD0 P63244 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 ;;;;;; 276.38 2.70E-35 11394220000 4602993 4645527 4847760 4861842 4750192 4428404 5459776 4055402 3864287 FALSE TRUE 4314899.885 4989486.653 4962751.156 4986605.097 4377131.082 5706812.346 4641133.275 4561727.867 3219312.535 1.340317176 1.549860909 1.541556187 1.548965825 1.359647761 1.772680435 1.441653528 1.416988197 1 21.61832121 0.734753661 1.901654948 1.000628144 1.521999672 0.636735605 0.119777505 0.583035303 3.229039065 0.101357077 0.028241082 5.42942278 -0.734753661 0.521371528 YVAQAHDKPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YVAQAHDKPR 10 1 Q12931-2;Q12931;I3L0K7;I3L239 Q12931-2 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 ;;; 112.13 0.00099874 808760000 2065300 1876130 1674840 1652490 2301640 1412400 1569100 1869590 2456140 FALSE TRUE 1936036.56 2015040.617 1714567.996 1694895.691 2120878.479 1820136.952 1333828.022 2103012.427 2046194.367 0.946164544 0.984774785 0.837930171 0.828316077 1.036499031 0.889523 0.651857929 1.027767675 1 20.96451176 1.990438109 24.97127411 0.833567183 0.921812784 0 0.121069333 1038.727357 2712679.934 0.044614099 0.031118507 97.82235398 -1.990438109 0.088245602 YVASYLLAALGGNSS(ph)PSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YVASYLLAALGGNSSPSAK 19 0 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 1 YVASYLLAALGGNSS(1)PSAK;YVASYLLAALGGNSS(0.991)PS(0.009)AK;YVASYLLAALGGNS(0.026)S(0.974)PSAK 440.07 6.49E-191 3496259000 3027840 2216152 2663340 2308100 2656030 2222854 3540020 2266210 2981230 TRUE FALSE 2838332.899 2380238.2 2726515.683 2367329.754 2447436.118 2864555.865 3009226.865 2549151.307 2483643.454 1.142810131 0.9583655 1.097788686 0.953168117 0.985421685 1.153368395 1.2116179 1.026375708 1 21.24402665 2.234273667 24.99972353 1.127129649 1.024286044 0.104263219 0.084659034 144.6035412 843257.3668 0.028982916 0.022142204 171.5037684 -2.234273667 -0.102843605 YVASYLLAALGGNSSPSAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YVASYLLAALGGNSSPSAK 19 0 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ; 227.42 3.20E-21 33036000 198496 196348 185080 185383 205260 166192 227630 167509 197610 FALSE TRUE 186072.4897 210885.8102 189470.185 190140.2416 189139.7076 214168.9325 193498.9947 188422.8674 164627.6144 1.130262929 1.280986856 1.150901601 1.154971736 1.148894177 1.300929575 1.175373861 1.144539864 1 17.32884683 0.841289042 2.274707556 1.000365434 1.198299395 0.528816264 0.056717992 0.441443149 4.260133826 0.051068568 0.013879425 6.938874647 -0.841289042 0.197933961 YVATLGVEVHPLVFHTNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YVATLGVEVHPLVFHTNR 18 0 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ;; 302.44 6.58E-50 8325076000 3511264 3822486 3805415 3362015 4253336 3445797 4123739 3673036 3359937 FALSE TRUE 3291500.254 4105506.841 3895681.241 3448289.997 3919296.148 4440542.656 3505422.62 4131622.63 2799141.809 1.175896214 1.466701983 1.391741293 1.231909718 1.400177774 1.586394316 1.252320482 1.47603191 1 21.41655315 -1.166073432 4.954277727 0.999971966 1.379481419 0.468313695 0.124595016 3.47E-05 5.84E-06 0.108484501 0.025568156 0.068222333 1.166073432 0.379509453 YVAVMPPHIGDQPLTGAYTVTLDGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YVAVMPPHIGDQPLTGAYTVTLDGR 25 0 P30043;A0A2R8YEP4 P30043 BLVRB Flavin reductase (NADPH) 0 ;; 229.71 3.15E-34 1291990000 1186020 1441120 1247080 1153550 1358380 1080720 1503980 1215480 1254450 FALSE TRUE 1111789.125 1547822.024 1276661.327 1183152.046 1251698.314 1392706.32 1278472.161 1367235.354 1045074.191 1.06383751 1.481064251 1.221598751 1.132122538 1.197712397 1.332638708 1.223331484 1.308266308 1 19.99517393 -2.003536875 3.054799328 0.732970052 1.260467405 0.303580263 0.114562046 4963261.063 14758509.03 9354423.621 0.025669198 0.009918891 2.003536875 0.527497352 YVDEASKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YVDEASKK 8 1 P62249;M0R210 P62249 RPS16 40S ribosomal protein S16 0 ;;;; 102.61 0.0079085 3532990000 5362890 3551760 4401110 4001950 4313990 3219110 5196160 3488360 4613460 FALSE TRUE 5027236.288 3814736.006 4505506.408 4104646.812 3975186.627 4148414.799 4417044.047 3923889.425 3843443.722 1.308003096 0.992530731 1.172257677 1.067960691 1.034277308 1.079348392 1.149241245 1.020930631 1 21.87396811 4.752362664 24.48218655 1.077818772 1.308003302 0.611445692 0.060167669 1235.81488 2192047.68 0.013527488 0.26887602 56540.89307 -4.752362664 0.23018453 YVDEENS(ph)DGETSNHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YVDEENSDGETSNHR 15 0 A0A494C108;Q8N9T8;H0YFD2;H0YH26;F8WFC1 A0A494C108 KRI1 Protein KRI1 homolog 1 YVDEENS(1)DGETSNHR;YVDEENS(1)DGETSNHR 279.5 7.46E-34 4212300000 1060650 1457590 1374310 1356570 1410530 1329110 1529370 1196280 1650950 TRUE FALSE 994265.8098 1565511.48 1406909.282 1391381.883 1299752.664 1712802.481 1300055.166 1345638.191 1375395.779 0.72289433 1.138226177 1.022912316 1.011622911 0.945002655 1.24531608 0.945222594 0.978364345 1 20.39141539 4.749713677 24.60049752 1.040966079 0.722894098 0.532044601 0.092122148 1009.464815 2226540.925 0.020393651 0.307575551 56197.07053 -4.749713677 -0.318071981 YVDIAIPCNNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YVDIAIPCNNK 11 0 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 105.78 0.0040056 0 65226 67926 73787 71501 74640 66232 84135 66420 79501 FALSE TRUE 61143.62109 72955.31172 75537.26248 73335.83671 68778.07548 85352.10321 71519.73782 74712.68321 66231.7695 0.92317662 1.101515364 1.140498934 1.107260719 1.038445387 1.288688251 1.07984036 1.128049028 1 16.01523578 4.742872287 3.675422272 1.120692064 0.900669018 0.37220795 0.075904195 0.264146041 6.623110067 0.016207147 0.160137265 55318.74089 -4.742872287 -0.220023046 YVGFGNT(ph)PPPQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YVGFGNTPPPQK 12 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;F8W1U7;E5RHT6;E5RHC5;Q8N6T3-3 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 YVGFGNT(1)PPPQK;YVGFGNT(1)PPPQK;YVGFGNT(1)PPPQK 148.52 0.00074333 297268000 1316520 1055780 1247840 1311160 1430990 1135500 1552240 1107770 1189900 TRUE FALSE 1234121.363 1133951.05 1277439.354 1344806.585 1318605.818 1463300.417 1319496.022 1246077.523 991298.003 1.244954958 1.14390531 1.288653211 1.356611817 1.330181049 1.476145833 1.331079068 1.257016073 1 19.9189593 3.689833699 3.025223477 1.323716875 1.192013325 0.056246411 0.124279615 0.407505641 7.488072728 0.030501044 0.053987185 4895.913085 -3.689833699 -0.13170355 YVGFGNT(ph)PPPQKK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YVGFGNTPPPQKK 13 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;F8W1U7;E5RHT6;E5RHC5;Q8N6T3-3 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 YVGFGNT(1)PPPQKK 71.692 0.024365 691320000 1581800 1194700 1366100 1496500 1858100 1174500 1791600 1242100 1844000 TRUE FALSE 1482797.962 1283156.831 1398504.537 1534902.724 1712172.321 1513559.084 1522966.212 1397178.919 1536224.487 0.965222188 0.835266487 0.910351676 0.999139602 1.114532632 0.985246034 0.991369572 0.90948877 1 20.55095762 3.292855845 4.165375989 1.003592307 0.886856571 0.373030782 0.058235046 0.186734162 6.618347195 0.016220404 0.021865004 1962.708688 -3.292855845 -0.116735736 YVHADAPTNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YVHADAPTNK 10 0 Q92922;F8WE13 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 0 80.102 0.023551 0 137440 136120 131360 148030 157310 126940 165440 138360 162810 FALSE TRUE 128837.8757 146198.4664 134475.9212 151828.7004 144955.5072 163585.5173 140633.8079 155634.5506 135635.9592 0.949879932 1.077873945 0.991447416 1.119383837 1.068710009 1.20606304 1.03684752 1.147443137 1 17.04938018 3.234672669 24.99847427 1.100239368 1.019580036 0.291493758 0.064894488 120.9473042 777659.454 0.01650643 0.020440627 1716.614074 -3.234672669 -0.080659333 YVHPLTEEAIEEMER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YVHPLTEEAIEEMER 15 0 P22830;P22830-2;K7ELX4;A0A499FJN5 P22830 FECH "Ferrochelatase, mitochondrial" 0 107.69 0.0011378 141680000 363680 192700 239760 232300 239220 172140 321860 209370 283800 FALSE TRUE 340917.918 206967.7085 245447.2204 238261.2113 220432.6262 221834.0235 273600.081 235510.3054 236431.9466 1.441928313 0.875379624 1.038130523 1.007736961 0.932330124 0.9382574 1.157204367 0.996101875 1 17.85106546 4.74848524 24.89120059 0.99826581 1.44192857 0.781495675 0.074533818 651.5724048 1634124.714 0.018629999 0.251271613 56038.33716 -4.74848524 0.443662759 YVIHTVGPIAYGEPSASQAAELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YVIHTVGPIAYGEPSASQAAELR 23 0 Q9BQ69 Q9BQ69 MACROD1 O-acetyl-ADP-ribose deacetylase MACROD1 0 150.64 6.79E-14 0 98173 108850 87662 100620 112380 83913 116120 94764 112890 FALSE TRUE 92028.52717 116909.3673 89741.38404 103202.0795 103554.1281 108137.3209 98708.88401 106595.494 94047.9297 0.978527943 1.243082837 0.954209033 1.097334943 1.101078232 1.149810753 1.04955935 1.133416699 1 16.52110857 -1.137096632 4.639142505 0.99999101 1.090554518 0.10080684 0.082724931 6.95E-06 1.29E-06 0.072328347 0.017046263 0.072929522 1.137096632 0.090563509 YVIS(ph)DEEEEDDD ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YVISDEEEEDDD 12 0 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 YVIS(1)DEEEEDDD;YVIS(1)DEEEEDDD 298.64 2.30E-36 676490000 1106340 1244520 1215890 1155870 1245330 1142800 1307770 1105590 1292010 TRUE FALSE 1037096.154 1336665.556 1244731.485 1185531.581 1147526.805 1472707.808 1111682.029 1243625.345 1076365.184 0.963517001 1.241832768 1.156421169 1.101421338 1.066112897 1.368223192 1.032811211 1.155393507 1 20.0377362 0.550057091 1.193029882 1.000710195 1.150514958 0.112905383 0.112660922 3.130052094 6.183106021 0.096807591 0.02947419 3.548600354 -0.550057091 0.149804763 YVIYIER ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 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 ;;;; 151.51 0.0043652 2067137000 1865480 2378440 2190210 2299980 2538900 1914810 2298990 2087570 2027010 FALSE TRUE 1748722.937 2554542.172 2242162.815 2359001.381 2339505.035 2467584.563 1954277.792 2348207.71 1688688.936 1.035550657 1.512736963 1.327753601 1.396942522 1.385397266 1.461242808 1.15727518 1.390550776 1 20.68747217 0.1149808 0.640460629 0.985708815 1.362316884 0.331074871 0.143511866 3.685161484 1.853025364 0.268157832 0.050479616 1.303109166 -0.1149808 0.376608069 YVLGQLVGLNS(ph)PNSILK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YVLGQLVGLNSPNSILK 17 0 P33981-2;P33981 P33981-2 TTK Dual specificity protein kinase TTK 1 YVLGQLVGLNS(1)PNSILK;YVLGQLVGLNS(1)PNSILK 272.24 1.31E-35 249690000 568650 483200 560320 582640 576180 449730 679310 504960 702870 TRUE FALSE 533059.2116 518976.6308 573611.055 597591.5288 530929.147 579559.7502 577453.7719 568005.3676 585556.4563 0.910346399 0.886296488 0.979599915 1.020553223 0.906708723 0.989758962 0.98616242 0.97002665 1 19.15944875 3.918886348 3.222894499 0.97821845 0.899117705 0.557209937 0.029799317 0.16784458 3.476145173 0.007333263 0.015343475 8296.336288 -3.918886348 -0.079100745 YVLHCQGTEEEK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YVLHCQGTEEEK 12 0 B7Z7P8;P62495-2;P62495 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 ; 216.83 3.81E-11 1383520000 1240360 787500 942820 876140 965000 747990 1232360 767010 972680 FALSE TRUE 1162728.082 845807.3194 965184.1356 898623.2357 889212.7926 963922.5704 1047579.059 862772.8869 810333.4242 1.434876122 1.043776912 1.191095056 1.108954918 1.097341867 1.189538209 1.292775328 1.064713439 1 19.62815612 4.750882868 24.80477245 1.142587313 1.434876324 0.556142558 0.085927038 1451.03287 2920879.621 0.020327169 0.3502151 56348.56595 -4.750882868 0.29228901 YVLHMIEDGEIFASINQK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YVLHMIEDGEIFASINQK 18 0 Q9UNS2-2;Q9UNS2;H7C3P9 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 0 136.48 6.20E-06 5868600 20321 16955 17396 16898 20096 13510 21892 17871 16323 FALSE TRUE 19049.14488 18210.36584 17808.64133 17331.63129 18517.74122 17410.11768 18609.49784 20102.23369 13598.58585 1.400818077 1.339136734 1.309595096 1.27451718 1.361740215 1.280288839 1.368487727 1.47825913 1 13.73116901 -0.971564582 5.145918088 0.999998248 1.343406513 0.771772401 0.059942131 1.13E-06 2.27E-07 0.054640365 0.012878792 0.106766601 0.971564582 0.343408265 YVLTS(ph)PR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YVLTSPR 7 0 Q9NQR7 Q9NQR7 CCDC177 Coiled-coil domain-containing protein 177 1 YVLT(0.198)S(0.802)PR;YVLT(0.093)S(0.907)PR 82.75 0.024799 397920000 658440 678190 735080 648330 910970 666170 695950 775290 1732150 TRUE FALSE 617229.4157 728403.8933 752516.4447 664967.2454 839426.0909 858482.4646 591598.7584 872086.6631 1443042.975 0.427727674 0.50476937 0.521478887 0.460809038 0.581705539 0.594911225 0.40996614 0.604338664 1 20.46068283 -5 0.356169397 6.910315043 0.494674896 0.855703515 0.063456759 159.3810156 1.283268778 720.9741958 0.044823222 1.00E-05 5 -6.415640147 YVQHTYR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YVQHTYR 7 0 P52566;F5H3P3;H0YGX7 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 91.041 0.016695 59879000 18672 67708 19533 19598 63544 21688 23211 47828 43997 FALSE TRUE 17503.35285 72721.17077 19996.33198 20100.91786 58553.51056 27948.97352 19730.72603 53799.43108 36653.61647 0.47753413 1.984010796 0.545548677 0.548402035 1.597482492 0.762516123 0.5383023 1.467779615 1 15.16166793 3.896982683 9.931010301 0.885968279 1.328639978 0.047578756 0.513984668 0.776834652 91.28166686 0.121282782 0.218976831 7888.286641 -3.896982683 0.442671698 YVSERPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YVSERPR 7 1 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 0 ; 173.11 0.00079841 156130000 98200 232752 185343 209943 216789 185981 178749 193414 189755 FALSE TRUE 92053.83729 249985.2003 189739.4235 215330.4928 199763.2664 239670.6956 151947.2469 217562.1637 158083.6646 0.582310876 1.581347452 1.200246869 1.362129941 1.263655336 1.516100326 0.961182468 1.376246965 1 17.27032877 -1.298558978 7.073395703 0.999997219 1.254925989 0.053974113 0.287273936 1.11E-05 1.10E-06 0.244982371 0.057742267 0.050285297 1.298558978 0.25492877 YVSGDVTHPQAGAEDALIVHCVDDSGHWGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YVSGDVTHPQAGAEDALIVHCVDDSGHWGR 30 0 A0A494C179;A0A0A0MRH8;A0A494C1P7;A0A0A0MSH9;A0A494C1F7;Q86WJ1-5;Q86WJ1-3;Q86WJ1-4;Q86WJ1-2;Q86WJ1 A0A494C179 CHD1L Chromodomain-helicase-DNA-binding protein 1-like 0 210.93 1.83E-26 113360000 42603 55439 56655 56675 62153 54931 67118 56536 64630 FALSE TRUE 39936.55428 59543.76124 57998.88335 58129.37645 57271.75409 70788.68797 57054.27899 63594.64405 53842.83547 0.741724575 1.105880861 1.077188503 1.079612096 1.063683842 1.314728085 1.05964477 1.181116178 1 15.71646677 4.738981767 6.18625344 1.113874133 0.732676913 0.647080034 0.08551258 0.073860637 14.87420288 0.018511068 0.118164514 54825.39472 -4.738981767 -0.38119722 YVSGS(ph)SPDLVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YVSGSSPDLVTR 12 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 YVS(0.001)GS(0.982)S(0.017)PDLVTR;YVS(0.002)GS(0.945)S(0.053)PDLVTR 189.61 8.08E-06 364320000 364520 418490 393770 401820 483520 305820 479820 409150 578570 TRUE FALSE 341705.3439 449475.435 403110.4104 412131.3815 445546.2896 394105.2694 407875.4454 460233.2782 482002.9293 0.70892794 0.932515982 0.83632357 0.855039164 0.924364278 0.817640818 0.846209474 0.954835023 1 18.87868239 -5 0.158169922 1.52597783 0.822167702 0.395906312 0.064163935 151.5869507 1.387117363 24.85106237 0.262519292 1.00E-05 5 -0.703810129 YVSGSS(ph)PDLVTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YVSGSSPDLVTR 12 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 YVSGS(0.069)S(0.931)PDLVTR;YVSGS(0.125)S(0.875)PDLVTR 256.25 3.84E-21 472730000 564930 594090 603140 610330 677370 495210 705750 593540 759590 TRUE FALSE 529572.0397 638077.0418 617446.7656 625992.1011 624172.0926 638169.0879 599929.3394 667644.7755 632809.5219 0.83685852 1.008324021 0.975722938 0.989226741 0.986350665 1.008469478 0.948040949 1.055048561 1 19.27141178 4.74235516 24.77063304 0.991639734 0.836858452 0.766417596 0.027568452 148.2157941 967501.2882 0.005843309 0.044188452 55252.91052 -4.74235516 -0.154781282 YVSHGATGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 YVSHGATGK 9 0 P00966;Q5T6L5;Q5T6L6 P00966 ASS1 Argininosuccinate synthase 0 ;;;;;;; 183.65 4.49E-05 5273790000 8522610 8709690 8222670 7960260 9378960 6489780 9823670 8409050 8750930 FALSE TRUE 7989195.053 9354564.51 8417715.615 8164533.748 8642374.315 8363274.133 8350701.882 9458938.403 7290343.25 1.095859931 1.283144591 1.154639134 1.119910746 1.185455063 1.147171518 1.145447011 1.297461324 1 22.79755531 -1.182307854 4.642790477 0.999971187 1.180287771 0.426722669 0.065045053 0.314033901 18792747.63 1019.500347 0.014216577 0.065719182 1.182307854 0.180316583 YVTAFNGELEDYMSDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YVTAFNGELEDYMSDR 16 0 F5H8D7 F5H8D7 XRCC1 0 ;; 212.11 1.25E-11 94931000 85613 94304 80117 85956 96994 70006 105350 85222 95888 FALSE TRUE 80254.63515 101286.3663 82017.41307 88161.77648 89376.48249 90215.59575 89553.74552 95862.1543 79883.67334 1.004643775 1.267923244 1.026710586 1.103626972 1.118832907 1.129337097 1.121051922 1.20002186 1 16.28561305 -1.591284418 2.861132426 0.991516401 1.125540053 0.203836517 0.075102461 9693982.821 10867569.16 628218.0014 0.016281753 0.025628051 1.591284418 0.134023652 YVVLCRGAK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YVVLCRGAK 9 1 O75426-2;O75426-4;O75426;O75426-3 O75426-2 FBXO24 F-box only protein 24 0 ; 70.919 0.030673 1507240000 1762690 2353700 1519930 1684820 2540800 1079260 1837510 2155300 2682400 FALSE TRUE 1652366.379 2527970.397 1555983.457 1728055.334 2341255.817 1390824.842 1561992.434 2424393.949 2234690.111 0.739416338 1.131239801 0.696286008 0.773286338 1.047687017 0.622379289 0.698974961 1.084890445 1 21.09164335 3.96280492 24.27334419 0.817233585 0.957121387 0.017823775 0.183901613 620.3117669 1051741.174 0.043748505 0.079370961 9179.201844 -3.96280492 0.139887802 YVVTSVSWWSHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YVVTSVSWWSHK 12 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 86.592 0.011024 339250000 123790 256520 177470 198790 253810 200100 173230 214230 213590 FALSE TRUE 116042.2049 275513.0077 181679.6722 203891.288 233876.7864 257865.6216 147255.7697 240977.0871 177940.4492 0.652140676 1.548343893 1.021013901 1.145840021 1.314354255 1.449168095 0.827556468 1.354256934 1 17.44103497 0.233371743 0.638511681 0.996991693 1.186882459 0.017084988 0.278019671 11.28695039 6.229135265 0.426380962 0.099686983 1.711479663 -0.233371743 0.189890766 YVWLVYEQDRPLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YVWLVYEQDRPLK 13 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 191.06 3.54E-06 1754720000 2074040 1735670 1707910 1532110 1910600 1314660 2049550 1856870 3186300 FALSE TRUE 1944229.539 1864180.813 1748422.432 1571426.536 1760549.183 1694181 1742239.005 2088704.307 2654485.946 0.732431657 0.702275639 0.658667052 0.591989021 0.663235451 0.638233178 0.656337626 0.786858303 1 21.34000107 0.923931359 2.728247736 0.999559165 0.662581312 0.894548426 0.037052272 0.106363606 1.799550431 0.036662461 0.009743899 8.393273198 -0.923931359 -0.336977853 YVWLVYEQDRPLKCDEPILSNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YVWLVYEQDRPLKCDEPILSNR 22 2 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 230.71 1.00E-26 521410000 334420 345300 277240 295270 446590 297250 509160 331590 858630 FALSE TRUE 313489.2492 370866.3713 283816.2637 302847.1281 411516.6229 383061.2495 432816.1848 372989.7414 715319.106 0.43825091 0.518462834 0.396768745 0.423373464 0.575290971 0.535511 0.605067279 0.521431258 1 19.44822745 -2.778642292 0.230536838 1.869171531 0.423127958 0.898181555 0.054207475 14.53210038 0.362615666 6.301162895 0.098574561 0.001664783 2.778642292 -1.446043573 YWDGWFR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YWDGWFR 7 0 Q9Y570;Q9Y570-4;Q9Y570-2;Q9Y570-3 Q9Y570 PPME1 Protein phosphatase methylesterase 1 0 ; 81.297 0.064172 284520000 1127310 1583240 1362230 1345350 1588650 1019000 1450990 1355850 1419460 FALSE TRUE 1056753.679 1700464.737 1394542.739 1379873.959 1463883.837 1313168.758 1233427.52 1525130.857 1182542.956 0.893628155 1.437972911 1.179274488 1.16687005 1.237911765 1.110461782 1.043029781 1.289704403 1 20.17346116 2.229840333 23.17156511 1.106599433 1.216617467 0.027992592 0.151507232 170.8503083 453975.5845 0.052346688 0.039329294 169.7619414 -2.229840333 0.110018034 YWDVPPPGFEHITPMQYK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YWDVPPPGFEHITPMQYK 18 0 P26368-2;P26368;K7ELP8 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 112.3 0.00027985 75930000 211430 228380 232440 220920 246380 196620 270190 232660 241460 FALSE TRUE 198196.9737 245289.4928 237953.5866 226589.1812 227030.3086 253381.0021 229677.5178 261708.1131 201158.7661 0.985276344 1.219382568 1.182914328 1.126419622 1.128612553 1.259607061 1.141772354 1.301002776 1 17.61797508 4.746289123 24.21953235 1.178397517 0.985276198 0.325408961 0.082781198 633.5961193 1985484.698 0.016979028 0.178918414 55755.68082 -4.746289123 -0.193121319 YWEAFLPEAK ddPTM_SK-BR-3_Pertuzumab_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 ; 138.11 0.00017046 84036000 562710 463630 522590 529790 603600 468800 610490 490120 559470 FALSE TRUE 527490.9856 497957.6476 534986.0816 543385.3083 556195.6908 604134.9497 518952.692 551312.5609 466090.8427 1.131734283 1.068370373 1.147815045 1.165835624 1.193320357 1.296174253 1.113415336 1.18284358 1 18.83025164 3.617198301 2.474130984 1.171397497 1.09752391 0.075107956 0.075269377 0.51004076 6.144020612 0.019395248 0.034012413 4141.887526 -3.617198301 -0.073873586 HGS(ph)GADS(ph)DYENTQSGDPLLGLEGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 HGSGADSDYENTQSGDPLLGLEGK 24 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 2 HGS(1)GADS(0.962)DY(0.038)ENTQSGDPLLGLEGK 177.44 2.24E-17 351710000 716490 417750 496870 485770 508020 250190 487220 318170 376600 TRUE FALSE 671646.1699 448680.6447 508655.991 498235.6806 468122.1585 322415.7915 414165.8841 357894.2249 313743.0271 2.140752501 1.430089615 1.621250346 1.588037463 1.492055976 1.027642891 1.320079965 1.140724077 1 18.25922387 8 0.15488402 0.8910157 4.692224408 0.703832833 0.18247109 37.77129792 0.38071012 0.561197367 32.53670902 100000000 -8 3.801208708 up YWGPAS(ph)PTHKLPPSFPGNK ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YWGPASPTHKLPPSFPGNK 19 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 Y(0.011)WGPAS(0.948)PT(0.041)HKLPPSFPGNK 77.576 0.0068612 156160000 224770 189610 234770 275640 263920 152030 175810 122640 144430 TRUE FALSE 210702.0469 203648.9217 240338.8553 282713.3891 243192.7878 195918.593 149448.9226 137951.874 120323.6999 1.751126727 1.692508806 1.997435712 2.349606845 2.021154502 1.628262704 1.24205724 1.14650625 1 16.87656131 1.818994116 2.116918974 1.094491693 1.945975972 0.814818968 0.181600101 0.142418384 1.222922231 0.127845587 0.057937621 65.91649649 -1.818994116 0.851484279 YWGPAS(ph)PTHKLPPSFPGNKDELMQHMDEVNDELIR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YWGPASPTHKLPPSFPGNKDELMQHMDEVNDELIR 35 2 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 YWGPAS(0.56)PT(0.44)HKLPPSFPGNKDELMQHMDEVNDELIR;Y(0.006)WGPAS(0.937)PT(0.056)HKLPPSFPGNKDELMQHMDEVNDELIR;YWGPAS(0.845)PT(0.155)HKLPPSFPGNKDELMQHMDEVNDELIR;YWGPAS(0.904)PT(0.096)HKLPPSFPGNKDELMQHMDEVNDELIR 312.16 4.92E-105 1996910000 1183930 1348630 1348920 1598020 2028600 935237 1244970 884262 1474340 TRUE FALSE 1109829.935 1448483.968 1380917.019 1639027.899 1869281.939 1205224.74 1058298.306 994664.0572 1228263.129 0.903576691 1.179294513 1.124284354 1.334427338 1.52189046 0.981243115 0.861621814 0.809813495 1 20.22818823 2.015025258 24.99694931 0.886685371 1.205779943 0.466734136 0.161425421 204.5280132 340264.0906 0.060254222 0.044485024 103.5202371 -2.015025258 0.319094573 YWGPASPT(ph)HKLPPSFPGNKDELMQHMDEVNDELIR ddPTM_SK-BR-3_Pertuzumab_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(0.163)PT(0.676)HKLPPS(0.161)FPGNKDELMQHMDEVNDELIR;YWGPAS(0.18)PT(0.82)HKLPPSFPGNKDELMQHMDEVNDELIR 202.8 2.01E-27 1440770000 522210 650205 685820 749540 921850 518620 625331 456836 819640 TRUE FALSE 489525.8083 698346.8547 702087.9743 768774.4654 849451.6196 668337.1749 531568.4218 513872.9802 682836.7889 0.716900167 1.022714163 1.028192953 1.125853905 1.244003887 0.978765623 0.778470684 0.752556084 1 19.38118126 1.873891634 5.167114802 0.825531019 1.037087548 0.242978076 0.146103404 0.277026801 10.13178884 0.0646267 0.038018114 74.79828392 -1.873891634 0.21155653 YWLEEAECR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YWLEEAECR 9 0 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;;;; 215.39 1.49E-06 1570080000 1220630 1675650 1252720 1274550 1898510 1171702 1444560 1529310 1606710 FALSE TRUE 1144232.947 1799716.87 1282435.11 1307257.111 1749408.683 1509953.346 1227961.639 1720247.72 1338539.721 0.854836752 1.344537514 0.95808521 0.9766293 1.306953133 1.128060171 0.917389017 1.28516748 1 20.35222852 -1.296410778 4.353599544 0.99991613 1.096999698 0.030099578 0.172051814 0.000128348 2.07E-05 0.152649763 0.035948836 0.050534645 1.296410778 0.097083568 YWQQVIDMNDYQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YWQQVIDMNDYQR 13 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 188.06 1.50E-05 72814000 83925 93385 84192 84570 90210 74378 99332 84677 98155 FALSE TRUE 78672.28406 100299.3226 86189.074 86740.20938 83125.27049 95849.72117 84438.08875 95249.10985 81772.29639 0.962089699 1.226568496 1.054013129 1.060753008 1.016545629 1.172153962 1.03260019 1.164809037 1 16.31932454 3.727757991 24.99733835 1.073832881 1.121341553 0 0.085228271 87.9542935 3452783.174 0.019840519 0.033273254 5342.665582 -3.727757991 0.047508671 YWSQQIEESTTVVTTQSAEVGAAETTLTELR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YWSQQIEESTTVVTTQSAEVGAAETTLTELR 31 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 88.688 0.00059974 9306700 11488 8281.3 9033.7 6807.7 7605.9 11553 9513.4 7458 5317 FALSE TRUE 10768.98659 8894.456069 9247.98363 6982.397107 7008.563295 14888.16355 8086.953988 8389.147717 4429.558351 2.431164855 2.007978079 2.087789097 1.576319026 1.582226204 3.361094351 1.825679525 1.893901616 1 12.11294715 6.192140895 14.58609595 2.035523323 2.11853492 0 0.620922948 0 0 0.123077343 0 1556470.503 -6.192140895 0.083011597 YWSQQIEESTTVVTTQSAEVGAAETTLTELRR ddPTM_SK-BR-3_Pertuzumab_2h_R1 11 YWSQQIEESTTVVTTQSAEVGAAETTLTELRR 32 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;; 338.44 4.23E-117 2427340700 632285.1 613054.7 675590.5 661959.8 668366.6 640279.4 757851.7 636324.6 702415.06 FALSE TRUE 592711.5043 658445.9079 691615.8257 678946.8092 615875.7833 825117.6687 644218.8731 715771.127 585177.4487 1.012874822 1.12520725 1.18189077 1.160240899 1.052459873 1.410029847 1.100894907 1.223169363 1 19.15851465 5.227103675 1.143238382 1.172635778 0.719061131 0.14567128 0.109868891 7.299742679 3.697400461 0.027752098 5.191647441 168695.569 -5.227103675 -0.453574647 YWVSGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YWVSGR 6 0 P26640;A0A140T936;H0Y426 P26640 VARS Valine--tRNA ligase 0 ; 149.11 0.024845 240060000 288260 508780 385610 494930 479040 225610 309420 321840 359740 FALSE TRUE 270218.3212 546450.6006 394756.8513 507630.7417 441418.1308 290739.9445 263025.3435 362022.4325 299697.07 0.901638181 1.823343153 1.317186222 1.693812828 1.472881035 0.970112736 0.877637354 1.207961201 1 18.19314545 2.243422527 12.3975439 0.988963024 1.488335735 0.400465983 0.255826707 0.211982988 519.2827232 0.082911578 0.066321855 175.1549951 -2.243422527 0.499372712 YYAGWADK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YYAGWADK 8 0 P05091;P05091-2;F8VP50;H0YKL3;H0YMG7;O94788-4;O94788-2;O94788-3;O94788 P05091 ALDH2;ALDH1A2 "Aldehyde dehydrogenase, mitochondrial;Retinal dehydrogenase 2" 0 ; 129.4 0.0025415 574610000 1207230 1045360 909800 883460 1350900 728490 877620 1171310 1375680 FALSE TRUE 1131671.629 1122759.542 931380.8856 906131.0793 1244805.763 938793.237 746029.0284 1317550.632 1146070.121 0.98743664 0.979660425 0.812673561 0.790641919 1.086151485 0.819141185 0.650945361 1.149624799 1 20.12826389 4.177382132 3.871755729 0.870666624 0.985964336 0.019190374 0.149706444 0.544879589 16.7581521 0.036411649 0.091800712 15044.6515 -4.177382132 0.115297711 YYAGWADKYHGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YYAGWADKYHGK 12 1 P05091;P05091-2;F8VP50 P05091 ALDH2 "Aldehyde dehydrogenase, mitochondrial" 0 ; 154.36 4.29E-05 1313750000 1676530 1906920 1355850 1368910 2954300 1062890 1532730 1936570 4382800 FALSE TRUE 1571598.98 2048110.341 1388011.402 1404038.548 2722281.195 1369729.088 1302911.366 2178355.027 3651282.366 0.430423841 0.560929048 0.380143539 0.384532996 0.745568521 0.375136446 0.356836649 0.596599991 1 21.79997181 0.922730925 6.133829961 0.999983341 0.461532065 0.677388709 0.116689252 0.427496583 33.28127481 0.107714951 0.027074139 8.37010537 -0.922730925 -0.538451276 YYDDIYFDS(ph)DS(ph)EDEDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YYDDIYFDSDSEDEDR 16 0 G3V2W9;A0A087X060;Q56P03 G3V2W9 EAPP E2F-associated phosphoprotein 2 YYDDIYFDS(1)DS(1)EDEDR;YYDDIYFDS(1)DS(1)EDEDR 150.28 1.10E-06 88151000 331520 315920 338870 316070 304760 312620 383840 280120 282670 TRUE FALSE 310770.755 339311.0455 346908.1564 324180.8913 280825.3789 402868.319 326286.7554 315093.5986 235490.5509 1.31967399 1.440869047 1.473129835 1.376619529 1.192512302 1.710762141 1.385561986 1.338030751 1 17.84530965 0.793391169 2.547808441 1.000343268 1.425885116 0.494677679 0.130445374 0.705111645 7.254726667 0.11473492 0.030633181 6.214285029 -0.793391169 0.425541848 YYDDIYFDS(ph)DS(ph)EDEDRAVQVTK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YYDDIYFDSDSEDEDRAVQVTK 22 1 G3V2W9;A0A087X060;Q56P03 G3V2W9 EAPP E2F-associated phosphoprotein 2 YYDDIYFDS(1)DS(1)EDEDRAVQVTK;YYDDIYFDS(1)DS(1)EDEDRAVQVTK 227.24 2.63E-26 538940000 1367800 1334070 1358560 1314160 1504620 924270 1561310 1255580 2233700 TRUE FALSE 1282191.84 1432845.931 1390785.685 1347883.57 1386453.215 1191091.745 1327206.06 1412341.927 1860881.04 0.689024076 0.769982551 0.747380222 0.72432549 0.74505204 0.64006872 0.713213812 0.758964113 1 20.8275544 0.787154946 3.862263667 0.999990311 0.723465193 0.857897438 0.035688186 0.790342512 13.9443084 0.036148687 0.009257045 6.125689033 -0.787154946 -0.276525119 YYDSRPGGYGYGYGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YYDSRPGGYGYGYGR 15 1 P98179 P98179 RBM3 RNA-binding protein 3 0 ;;;; 176.4 7.31E-07 5023740000 5240700 6747390 6436440 5825200 5650810 5736030 6903740 4875570 6970970 FALSE TRUE 4912693.942 7246973.776 6589115.396 5974684.494 5207018.177 7391928.744 5868588.278 5484295.647 5807470.073 0.845926691 1.24787105 1.134593087 1.028792989 0.896606975 1.272831138 1.010524067 0.944351943 1 22.46947838 3.236050837 24.89080272 1.035976591 1.121283707 0 0.140608115 167.4437967 1660631.206 0.03800401 0.047474291 1722.070141 -3.236050837 0.085307116 YYEAADTVTQFDNVR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YYEAADTVTQFDNVR 15 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2;F8VZW6 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 0 81.494 0.032184 57565000 38433 89580 81051 82493 83347 97212 65183 69791 60472 FALSE TRUE 36027.54713 96212.59641 82973.568 84609.91004 76801.26283 125275.5263 55409.41428 78504.55998 50378.83254 0.715132633 1.909782176 1.646992672 1.679473417 1.524474843 2.486669897 1.099855068 1.558284621 1 15.62053007 1.064077236 1.487923075 1.042882284 1.662931018 0.122700179 0.46558337 0.688770909 3.076409977 0.392348267 0.116894856 11.58983453 -1.064077236 0.620048735 YYEVLGAAATTDYNNNHEGREEDQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YYEVLGAAATTDYNNNHEGREEDQR 25 1 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4;A0A0G2JJM1;X6REW1;F6S6P2 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 0 133.38 3.66E-05 313250000 38560 46070 46018 45407 60068 36712 43426 41793 71632 FALSE TRUE 36146.59843 49481.07074 47109.56869 46572.22049 55350.50158 47310.15843 36914.67445 47010.94805 59676.15644 0.605712576 0.829159813 0.789420289 0.780415886 0.92751452 0.792781594 0.618583311 0.787767692 1 15.864867 4.744967044 24.30125052 0.795502086 0.605712448 0.280842115 0.10111137 723.4719962 2744206.669 0.023705439 0.219882195 55586.20749 -4.744967044 -0.189789638 YYFQVER ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YYFQVER 7 0 Q96PQ1-2;Q96PQ1 Q96PQ1-2 SIGLEC12 Sialic acid-binding Ig-like lectin 12 0 81.381 0.063639 434830000 264300 267830 325960 334600 260820 262090 337610 217270 275090 FALSE TRUE 247757.9348 287660.4119 333691.9251 343186.4025 240336.2493 337751.1283 286988.5147 244396.6378 229175.7019 1.081082911 1.255195946 1.456052812 1.497481625 1.048698651 1.473765 1.252264147 1.066416011 1 17.80609457 1.235646352 3.326022699 1.008965133 1.315483146 0.342661116 0.152278813 0.244452314 4.801772837 0.128202692 0.036568591 17.20467019 -1.235646352 0.306518013 YYFSHDTD ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YYFSHDTD 8 0 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ;;; 198.32 0.00031846 1030070000 1790610 2265730 2133790 2116720 2255410 1846380 2490620 1903260 2428320 FALSE TRUE 1678538.916 2433487.007 2184404.506 2171038.619 2078279.196 2379399.933 2117174.653 2140886.201 2023017.704 0.82972033 1.202899511 1.079775279 1.073168373 1.027316366 1.176163672 1.04654282 1.0582637 1 20.94807752 0.919258994 1.880940539 1.001035187 1.081533134 0.010622409 0.100633867 1.298326655 9.489461378 0.085864801 0.024172025 8.303458014 -0.919258994 0.080497946 YYGGAEVVDEIELLCQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YYGGAEVVDEIELLCQR 17 0 P34897-3;P34897-2;P34897;G3V540;G3V5L0;G3V4W5;G3V241;G3V3Y8;G3V4T0;G3V4X0;G3V2W0;G3V2E4 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial" 0 ;;; 207.66 3.18E-17 56912300 73804 80396 78645 66332 100286 79324 72387 79466 106558 FALSE TRUE 69184.73938 86348.60349 80510.49654 68034.19142 92409.94209 102223.5511 61533.24136 89387.50503 88772.78141 0.779346307 0.972692329 0.906927723 0.766385714 1.040971575 1.151519074 0.69315437 1.006924686 1 16.43782978 2.722738448 24.94343164 0.95210408 0.884162009 0.147854144 0.130482666 2623.075757 4135236.769 0.042588326 0.040280418 528.127094 -2.722738448 -0.067942071 YYGGGSEGGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YYGGGSEGGR 10 0 P14866 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 113.5 0.0034417 477850000 111430 151110 126670 124330 146950 117810 142970 116550 115450 FALSE TRUE 104455.7952 162298.3416 129674.6722 127520.5183 135409.1398 151819.8345 121532.9758 131101.5241 96180.64916 1.086037536 1.687432379 1.348240767 1.32584381 1.40786261 1.578486274 1.26359072 1.363075891 1 16.55345904 0.496499647 0.880793882 0.998448215 1.424284535 0.340491093 0.164421623 1.706699151 1.983880861 0.151169214 0.048795025 3.136892581 -0.496499647 0.425836321 YYGTKDPVPGYSVPAAEHSTITAWGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YYGTKDPVPGYSVPAAEHSTITAWGK 26 1 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ; 195.63 4.33E-25 357920000 551760 724650 721990 684470 805400 565570 984470 710930 943220 FALSE TRUE 517226.3265 778303.84 739115.9437 702034.659 742147.1328 728840.8777 836857.8629 799691.1754 785790.4886 0.658224214 0.990472462 0.940601795 0.893412009 0.944459298 0.927525706 1.064988537 1.017690068 1 19.58378518 4.740695093 24.64080268 0.97152445 0.658224081 0.801238516 0.049174139 74.34127582 858137.4316 0.012609519 0.083007643 55042.11239 -4.740695093 -0.313300369 YYHSPTNTVHMYPPEMAPSSAPPS(ph)TPPTHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YYHSPTNTVHMYPPEMAPSSAPPSTPPTHK 30 0 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 YYHSPTNTVHMYPPEMAPS(0.001)S(0.002)APPS(0.494)T(0.494)PPT(0.008)HK;YYHSPTNTVHMYPPEMAPSSAPPS(0.45)T(0.45)PPT(0.101)HK;YYHSPTNTVHMYPPEMAPSSAPPS(0.56)T(0.437)PPT(0.003)HK;YYHSPTNTVHMYPPEMAPSS(0.001)APPS(0.453)T(0.453)PPT(0.092)HK 125.56 2.35E-05 352070000 219659 235886 248961 261327 265261 186568 288161 224617 314318 TRUE FALSE 205910.9353 253351.2449 254866.4725 268033.0932 244428.4711 240427.1529 244953.9332 252660.9269 261856.2952 0.786350907 0.967520161 0.973306646 1.023588503 0.933445082 0.918164494 0.935451764 0.964883913 1 17.99841576 4.739845266 24.9031375 0.961086817 0.786350848 0.759868183 0.031427827 54.58870146 1058087.843 0.007716496 0.048109523 54934.51137 -4.739845266 -0.174735969 YYIADR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YYIADR 6 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 100.82 0.086601 1040520000 956510 1221280 1084360 1012570 1279790 916030 1087370 1064640 1279340 FALSE TRUE 896643.7465 1311704.842 1110081.531 1038554.26 1179280.456 1180472.99 924328.9631 1197562.648 1065809.889 0.841279252 1.230711833 1.041538029 0.974427307 1.106464171 1.107583071 0.867255007 1.123617504 1 20.02351869 YYIQNGIQSFMQNYSSIDVLLHQSR ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YYIQNGIQSFMQNYSSIDVLLHQSR 25 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;; 205.65 4.14E-25 106915000 86757 156327 92122 106865 160896 96720.9 121520 129779 73462.6 FALSE TRUE 81327.03424 167901.6137 94307.17734 109607.3368 148259.8772 124642.6537 103299.2041 145982.1938 61201.21747 1.328846673 2.743435844 1.540936296 1.790933928 2.422498821 2.036604153 1.687861915 2.385282513 1 15.90127273 -1.263012821 6.099898239 0.999967923 2.004175295 0.341582025 0.432560879 0.000171485 2.07E-05 0.380564824 0.089697142 0.054574175 1.263012821 1.004207372 YYITIIDAPGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YYITIIDAPGHR 12 0 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ;;;; 164.04 5.84E-05 2459500000 3870150 4608852 4116957 4396523 4581230 3672084 4415260 3892160 2945580 FALSE TRUE 3627924.22 4950096.198 4214613.164 4509345.223 4221438.676 4732155.039 3753232.752 4378104.744 2453943.669 1.478405664 2.017200419 1.717485702 1.837591172 1.720267148 1.928387803 1.529469808 1.784109717 1 21.2266707 -0.652883854 0.466155298 0.811360394 1.805150603 0.670096707 0.164533805 5.733364792 1.005914506 1.778907082 0.077421642 0.222390457 0.652883854 0.993790209 YYKVDENGK ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YYKVDENGK 9 1 P62979;A0A2R8Y422 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ;;;;; 158.79 6.07E-05 5581030000 9446260 9334320 9895520 10806570 13661380 8226260 15602510 10475130 21250620 FALSE TRUE 8855035.449 10025442.77 10130246.41 11083884.88 12588470.32 10601047.72 13263058.47 11782973.04 17703754.24 0.500178399 0.566289084 0.572208938 0.626075392 0.711062194 0.598802241 0.749166436 0.665563523 1 24.07755199 -5 0.105432868 2.261072807 0.377624749 0.893248101 0.045278987 45.9827661 0.326070826 12.50447361 0.568247027 1.00E-05 5 -1.883448058 YYLHDDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YYLHDDR 7 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;;; 116.88 0.0053555 2833400000 2791710 4881920 4005300 4077840 4612520 3477130 4202170 4323510 3670450 FALSE TRUE 2616981.854 5243382.436 4100307.607 4182484.278 4250271.285 4480920.985 3572093.62 4863309.741 3057828.183 0.855830249 1.714740699 1.340921518 1.367795712 1.389964063 1.465393317 1.168179965 1.590445718 1 21.54407591 -1.471396283 3.033204737 0.990508254 1.381197224 0.189124678 0.232233257 94237517.45 108263658.7 7505023.532 0.050118269 0.03377565 1.471396283 0.39068897 YYPTEDVPR ddPTM_SK-BR-3_Pertuzumab_2h_R1 6 YYPTEDVPR 9 0 Q02878;F8VZ45;U3KQR5;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ;;;;; 255.13 1.40E-14 5551650000 4580090 5536010 5235540 5083720 5503870 4353630 5755280 4890810 5209500 FALSE TRUE 4293430.343 5945901.941 5359729.481 5214176.862 5071618.252 5610452.306 4892329.193 5501438.395 4340000.795 0.989269483 1.370023238 1.234960484 1.20142302 1.16857542 1.292730709 1.127264585 1.267612301 1 22.04926388 -3.931729399 0.331674012 5.87E-08 1.229041184 0.258271697 0.104122766 200.0236881 3.409091236 138.0359663 0.080185243 0.000117023 3.931729399 1.229041125 YYPTEDVPRK ddPTM_SK-BR-3_Pertuzumab_2h_R1 4 YYPTEDVPRK 10 1 Q02878;F8VZ45;U3KQR5;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ;;; 164.97 9.61E-06 2002890000 1281860 1405630 1436250 1412210 1493440 1036270 1643990 1314350 1972910 FALSE TRUE 1201630.671 1509704.308 1470318.528 1448449.699 1376151.247 1335424.327 1397488.962 1478449.491 1643618.576 0.731088519 0.91852473 0.894561883 0.881256589 0.837269222 0.812490408 0.85025138 0.899508872 1 20.64844411 0.894524489 3.386890126 0.999901835 0.857429302 0.462421537 0.051797429 0.429627342 10.53034645 0.048692508 0.012613457 7.843763469 -0.894524489 -0.142472534 YYS(ph)DS(ph)DDELTVEQR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YYSDSDDELTVEQR 14 0 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 2 YYS(0.999)DS(1)DDELTVEQR 156.17 8.25E-06 70971000 96053 94647 82577 85793 92210 88320 119350 84620 124280 TRUE FALSE 90041.21419 101654.7624 84535.76544 87994.59363 84968.19856 113816.5502 101454.5755 95184.99327 103536.8651 0.869653665 0.981821907 0.816479863 0.849886594 0.820656473 1.099285265 0.979888423 0.919334318 1 16.65978502 2.251699602 24.99978052 0.999634854 0.87546761 0.521214225 0.062584806 198.2805549 377271.4685 0.022006756 0.018308872 178.5252302 -2.251699602 -0.124167244 YYTLFGR ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YYTLFGR 7 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 138.85 0.0063879 537880000 538230 1031970 506900 515870 1171530 325140 559240 908070 834980 FALSE TRUE 504543.1451 1108378.133 518923.9074 529108.0976 1079522.76 419002.6398 475387.1537 1021444.538 695616.4438 0.725318025 1.593375405 0.745991432 0.760631958 1.551893675 0.602347232 0.683404134 1.468401944 1 19.40793251 3.887055752 8.504350973 0.937628779 1.214147748 0.029297227 0.378716111 0.659444626 55.85529313 0.090821456 0.164285396 7710.02439 -3.887055752 0.27651897 YYTSASGDEMVS(ph)LKDYCTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YYTSASGDEMVSLKDYCTR 19 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 YYTSASGDEMVS(1)LKDYCTR 232.79 1.33E-21 194440000 260950 187750 206410 213150 246480 144470 307770 189290 375000 TRUE FALSE 244617.6053 201651.2054 211306.1427 218619.7899 227122.4551 186176.1437 261622.7457 212923.2732 312410.0774 0.783001648 0.645469592 0.676374285 0.699784692 0.727001052 0.595935142 0.83743376 0.681550592 1 18.25308147 -0.312500625 0.485030611 1.047202819 0.684264615 0.641935758 0.068477764 3.850652956 0.904200398 0.384430517 0.031557477 0.486966825 0.312500625 -0.362938204 YYTSASGDEMVSLK ddPTM_SK-BR-3_Pertuzumab_2h_R1 2 YYTSASGDEMVSLK 14 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 224.82 7.00E-12 140219000 169014 151437 157078 157588 173192 138052 188154 158132 157815 FALSE TRUE 158435.7154 162649.5531 160803.9643 161631.9749 159590.1989 177905.3713 159942.0544 177875.1283 131474.657 1.205066582 1.237117151 1.22307955 1.229377422 1.213847616 1.353153341 1.216523839 1.352923311 1 17.00442521 -0.829119664 4.923791758 0.999999571 1.249670033 0.679015462 0.054790345 3155377.048 640842.8652 14.58833659 0.011539559 0.148210965 0.829119664 0.249670462 YYTSASGDEMVSLKDYCTR ddPTM_SK-BR-3_Pertuzumab_2h_R1 1 YYTSASGDEMVSLKDYCTR 19 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 212.69 6.40E-17 415930000 66134 105010 75709 92915 135250 74076 116930 81532 221510 FALSE TRUE 61994.79099 112785.0497 77504.85323 95299.3562 124628.0106 95460.53868 99397.43202 91711.44967 184538.55 0.335944934 0.611173382 0.419992751 0.516419774 0.675349463 0.517293209 0.538626927 0.496977188 1 17.4935627 -5 0.316640687 5.436718357 0.498789581 0.737122503 0.091543068 154.2515838 1.377545162 457.9211348 0.076384981 1.00E-05 5 -4.937928776 YYTVFDR ddPTM_SK-BR-3_Pertuzumab_2h_R1 8 YYTVFDR 7 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;H7C469;H7C1V0 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ;;;;;;; 158.36 0.003312 5504501000 6296660 8401300 6904430 6658350 8457680 5822582 7406980 7647700 8776480 FALSE TRUE 5902563.29 9023340.994 7068206.34 6829214.534 7793447.929 7503466.902 6296372.112 8602532.18 7311628.79 0.807284322 1.234108193 0.966707493 0.934020959 1.065897648 1.026237398 0.861144937 1.176554832 1 22.8017614 3.722642478 24.88299676 0.991685647 1.065950927 0 0.132128839 548.1477171 3045402.092 0.031879803 0.05131589 5280.104018 -3.722642478 0.074265279 YYTVFDRDNNR ddPTM_SK-BR-3_Pertuzumab_2h_R1 5 YYTVFDRDNNR 11 1 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;H7C469;H7C1V0 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ;;;; 166.29 1.88E-05 5212230000 5900980 5446140 4168430 4303030 6444260 3073730 5399740 4605860 9059800 FALSE TRUE 5531648.195 5849377.872 4267307.128 4413453.035 5938153.814 3961065.953 4590099.116 5180911.76 7547660.851 0.732895702 0.774992145 0.565381409 0.584744482 0.786754192 0.524807093 0.608148565 0.686426147 1 22.84759817 0.950461808 19.00639041 1.000000002 0.650582245 0.599505985 0.088197964 350.7119954 134559.4482 0.083822416 0.020955604 8.92199156 -0.950461808 -0.349417757 YYVGHK ddPTM_SK-BR-3_Pertuzumab_2h_R1 3 YYVGHK 6 0 P61326;Q96A72;F5H6N1;P61326-2;F5H124 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ;; 105.82 0.032648 832010000 1651510 1583050 1592030 1561100 1790110 1333510 1841800 1585940 1735140 FALSE TRUE 1548144.937 1700260.669 1629793.703 1601160.469 1649521.982 1718472.689 1565639.188 1783948.1 1445533.925 1.070984853 1.176216373 1.127468319 1.10766025 1.141116063 1.188815191 1.083087129 1.234110158 1 20.46317104 -1.223422513 4.645997064 0.99996548 1.139976278 0.448662882 0.049168686 1.52E-05 2.54E-06 0.04116517 0.009700333 0.05978297 1.223422513 0.140010798 YYVTIIDAPGHR ddPTM_SK-BR-3_Pertuzumab_2h_R1 9 YYVTIIDAPGHR 12 0 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01;A6PW80;Q5JR01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;;;;;;; 215.5 4.13E-11 62091690000 21146980 22079430 22919600 22459100 23623170 21103300 23564680 19905650 18616710 FALSE TRUE 19823428.27 23714213.97 23463263.74 23035438.53 21767901.52 27195480.13 20031375 22390914.22 15509460.83 1.278150703 1.529016013 1.512835552 1.485250763 1.403524065 1.753476824 1.291558437 1.443693914 1 23.8866452 0.496447794 1.069899826 1.000307592 1.487551973 0.546210891 0.132665323 1.252755262 1.967588581 0.113955777 0.035434462 3.136518069 -0.496447794 0.487244381